diff --git a/data/covid/ack-preprints.csv b/data/covid/ack-preprints.csv
index 75179786..b790c58a 100644
--- a/data/covid/ack-preprints.csv
+++ b/data/covid/ack-preprints.csv
@@ -49,8 +49,8 @@ PPR625922,https://doi.org/10.1101/2023.03.01.23286627,Effectiveness of successiv
 PPR717811,https://doi.org/10.1101/2023.08.30.23294821,Symptom experience before vs. after confirmed SARS-CoV-2 infection: a population and case control study using prospectively recorded symptom data,"Sudre CH, Antonelli M, Cheetham NJ, Molteni E, Canas LS, Bowyer V, Murray B, Rjoob K, Modat M, Pujol JC, Hu C, Wolf J, Spector TD, Hammers A, Steves CJ, Ourselin S, Duncan EL.",,No Journal Info,2023,2023-09-01,Y,,,,"<h4>Background</h4> Some individuals experience prolonged illness after acute COVID-19. We assessed whether pre-infection symptoms affected post-COVID illness duration. <h4>Methods</h4> Survival analysis was performed in adults (n=23,452) with community-managed SARC-CoV-2 infection prospectively self-logging data through the ZOE COVID Symptom Study app, at least weekly, from 8 weeks before to 12 weeks after COVID-19 onset, conditioned on presence vs. absence of baseline symptoms (4-8 weeks before COVID-19). A case-control study was performed in 1350 individuals with long illness (≥8 weeks, 906 [67.1%] with illness ≥12 weeks), matched 1:1 (for age, sex, body mass index, testing week, prior infection, vaccination, smoking, index of multiple deprivation) with 1350 individuals with short illness (<4 weeks). Baseline symptoms were compared between the two groups; and against post-COVID symptoms. <h4>Findings</h4> Individuals reporting baseline symptoms had longer post-COVID symptom duration (from 10 to 15 days) with baseline fatigue nearly doubling duration. Two-thirds (910 of 1350 [67.4%]) of individuals with long illness were asymptomatic beforehand. However, 440 (32.6%) had baseline symptoms, vs. 255 (18.9%) of 1350 individuals with short illness (p<0.0001). Baseline symptoms increased the odds ratio for long illness (2.14 [CI: 1.78; 2.57]). Prior comorbidities were more common in individuals with long vs. short illness. In individuals with long illness, baseline symptomatic (vs. asymptomatic) individuals were more likely to be female, younger, and have prior comorbidities; and baseline and post-acute symptoms and symptom burden correlated strongly. <h4>Interpretation</h4> Individuals experiencing symptoms before COVID-19 have longer illness duration and increased odds of long illness. However, many individuals with long illness are well before SARS-CoV-2 infection.",,doi:https://doi.org/10.1101/2023.08.30.23294821; html:https://europepmc.org/article/PPR/PPR717811; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR717811&type=FILE&fileName=EMS187353-pdf.pdf&mimeType=application/pdf
 PPR704142,https://doi.org/10.2139/ssrn.4544777,Use of Sodium Valproate and Other Anti-Seizure Medications in England and Wales During the COVID-19 Pandemic: A Population-Level Analysis of 60 Million Individuals,"Dale C, Takhar R, Fan YY, Torabi F, Kim S, Lambarth A, Shankar R, Tomlinson C, Wilkinson T, Mueller T, Kurdi A, Ashworth M, Mamas M, Khunti K, Akbari A, Morris A, Pirmohamed M, Marson A, Williams D, Sudlow C, Sofat R, CVD-COVID-UK Consortium.",,No Journal Info,2023,2023-08-23,N,,,,"Background: Key policy statements in 2018 on the use of sodium valproate (SV), an evidence-based treatment for idiopathic generalised epilepsy (IGE), which also has teratogenic effects, were followed by the onset of the COVID-19 pandemic. We investigated the use of SV in England and Wales, the impact of policy implementation and the pandemic. <br><br>Methods: Prevalent (current) and incident (new) uses of SV and other anti-seizure medications (ASMs) before and during the COVID-19 pandemic (2019-2021) were identified in England and Wales (n=60 million), stratifying use by age-bands, sex, geography, ethnic group, deprivation and disease indication. We assessed pregnancy rates and examine the timing and dose of ASMs dispensed during pregnancy. Using multivariate logistic regression we investigated factors associated with SV use during pregnancy and trends in epilepsy-related deaths between 2015 to 2021 using time series analysis. <br><br>Findings: Use of SV in women of CBP  decreased whilst use of other ASMs increased between 2019 and 2021. New initiation of SV per 100,000 women fell from 13 to 8 in women aged 30-39, 10 to 6 in women aged 20-29 and 7 to 5 in women aged 15-19 between 2019 and 2021, while pregnancy rates fell from 5.9 to 5.1 per 1000 women of CBP dispensed SV. The number of pregnant women with evidence of a SV dispense during the pregnancy period fell from 112 in 2019 to 67 in 2021. Epilepsy was the most common indication, followed by bipolar disorder (678 and 190 per 1,000 women of CBP dispensed SV respectively). There was no clear evidence that epilepsy-related deaths increased in women and men aged 15-49 during the period 2018-2021.<br><br>Interpretation: Rates of use of SV by women, including during pregnancy, fell before and continued to decline during the COVID-19 pandemic. Further research using linked health data is needed to investigate how policy changes impact on seizure control and mortality in men and women of CBP and on harms to children exposed in utero. Our approach could be used to investigate medicines safety more broadly in pregnancy and demonstrate how linked routinely-collected electronic health record data can be used to inform policy.<br><br>Funding: This work was carried out with the support of the BHF Data Science Centre led by HDR UK (BHF Grant no. SP/19/3/34678).<br><br>Declaration of Interest: The views represented in this manuscript are entirely those of the authors, and do not represent the views of any organisations they represent. MP has received partnership funding for the following: MRC Clinical Pharmacology Training Scheme (co- funded by MRC and Roche, UCB, Eli Lilly and Novartis). He has developed an HLA genotyping panel with MC Diagnostics, but does not benefit financially from this. He is part of the IMI Consortium ARDAT (www.ardat.org) and Chair of the Commission on Human Medicines (CHM). RS is a member of the Pharmacovigilance Expert Advisory Group, a sub-committee of the CHM. CT has received funding paid to University College London from GlaxoSmithKline (GSK), outside of the scope of the submitted work. AGM has received funding paid to University of Liverpool from UCB Pharma, Sanofi, Eiasi and GSK. He is a member of the MHRA valproate implementation group, chief investigator of the SANAD trials and senior author of the Cochrane reviews assessing the teratogenic effects of anti-seizure medications.<br><br>Ethical Approval: The North East - Newcastle and North Tyneside 2 research ethics committee provided ethical approval for the CVD-COVID-UK/COVID-IMPACT research programme (REC No 20/NE/0161) to access, within secure trusted research environments, unconsented, whole-population, de-identified data from electronic health records collected as part of patients’ routine healthcare.",,doi:https://doi.org/10.2139/ssrn.4544777; html:https://europepmc.org/article/PPR/PPR704142; doi:https://doi.org/10.2139/ssrn.4544777
 PPR497639,https://doi.org/10.1101/2022.05.21.22275368,"Variant-specific symptoms of COVID-19 among 1,542,510 people in England","Whitaker M, Elliott J, Bodinier B, Barclay W, Ward H, Cooke G, Donnelly CA, Chadeau-Hyam M, Elliott P.",,No Journal Info,2022,2022-05-23,Y,,,,"Infection with SARS-CoV-2 virus is associated with a wide range of symptoms. The REal-time Assessment of Community Transmission -1 (REACT-1) study has been monitoring the spread and clinical manifestation of SARS-CoV-2 among random samples of the population in England from 1 May 2020 to 31 March 2022. We show changing symptom profiles associated with the different variants over that period, with lower reporting of loss of sense of smell and taste for Omicron compared to previous variants, and higher reporting of cold-like and influenza-like symptoms, controlling for vaccination status. Contrary to the perception that recent variants have become successively milder, Omicron BA.2 was associated with reporting more symptoms, with greater disruption to daily activities, than BA.1. With restrictions lifted and routine testing limited in many countries, monitoring the changing symptom profiles associated with SARS-CoV-2 infection and induced changes in daily activities will become increasingly important.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/05/23/2022.05.21.22275368.full.pdf; doi:https://doi.org/10.1101/2022.05.21.22275368; html:https://europepmc.org/article/PPR/PPR497639; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR497639&type=FILE&fileName=EMS145381-pdf.pdf&mimeType=application/pdf
-PPR802874,https://doi.org/10.1101/2024.02.08.24302486,Bidirectional relationship between sleep problems and long COVID: a longitudinal analysis of data from the COVIDENCE UK study,"Vivaldi G, Talaei M, Blaikley J, Jackson C, Pfeffer PE, Shaheen SO, Martineau AR.",,No Journal Info,2024,2024-02-08,Y,,,,"<h4>Summary</h4> <h4>Background</h4> Studies into the bidirectional relationship between sleep and long COVID have been limited by retrospective pre-infection sleep data and infrequent post-infection follow-up. We therefore used prospectively collected monthly data to evaluate how pre-infection sleep characteristics affect risk of long COVID, and to track changes in sleep duration during the year after SARS-CoV-2 infection. <h4>Methods</h4> COVIDENCE UK is a prospective, population-based UK study of COVID-19 in adults. We included non-hospitalised participants with evidence of SARS-CoV-2 infection, and estimated odds ratios (ORs) for the association between pre-infection sleep characteristics and long COVID using logistic regression, adjusting for potential confounders. We assessed changes in sleep duration after infection using multilevel mixed models. We defined long COVID as unresolved symptoms at least 12 weeks after infection. We defined sleep quality according to age-dependent combinations of sleep duration and efficiency. COVIDENCE UK is registered with ClinicalTrials.gov, NCT04330599 . <h4>Findings</h4> We included 3994 participants in our long COVID risk analysis, of whom 327 (8.2%) reported long COVID. We found an inverse relationship between pre-infection sleep quality and risk of long COVID (medium vs good quality: OR 1.37 [95% CI 1.04–1.81]; medium–low vs good: 1.55 [1.12–2.16]; low vs good: 1.94 [1.11–3.38]). Greater variability in pre-infection sleep efficiency was also associated with long COVID (OR per percentage-point increase 1.06 [1.01–1.11]). We assessed post-infection sleep duration in 6860 participants, observing a 0.11 h (95% CI 0.08–0.13) increase in the first month after infection compared with pre-infection, with larger increases for more severe infections. After 1 month, sleep duration largely returned to pre-infection levels, although fluctuations in duration lasted up to 6 months after infection among people reporting long COVID. <h4>Interpretation</h4> Our findings highlight the bidirectional relationship between sleep and long COVID. While poor-quality sleep before SARS-CoV-2 infection associates with increased risk of long COVID thereafter, changes in sleep duration after infection in these non-hospitalised cases were modest and generally quick to resolve. <h4>Funding</h4> Barts Charity.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2024/02/08/2024.02.08.24302486.full.pdf; doi:https://doi.org/10.1101/2024.02.08.24302486; html:https://europepmc.org/article/PPR/PPR802874; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR802874&type=FILE&fileName=EMS193995-pdf.pdf&mimeType=application/pdf
 PPR625199,https://doi.org/10.2139/ssrn.4322399,Baby and Maternal Outcomes Following SARS-CoV-2 Infection and COVID-19 Vaccination During Pregnancy: A National Population-Based Matched Cohort Study,"Lindsay L, Calvert C, Shi T, Carruthers J, Denny C, Donaghy J, Hopcroft LE, Hopkins L, Goulding A, McLaughlin T, Moore E, Taylor B, Bhaskaran K, Katikireddi SV, McCabe R, McCowan C, Simpson C, Robertson C, Sheikh A, Wood R, Stock SJ.",,No Journal Info,2023,2023-01-20,N,,,,"Background: Understanding the impact of SARS-CoV-2 infection and COVID-19 vaccination in pregnancy on maternal and perinatal outcomes informs clinical decision-making.<br><br>Methods: We undertook a national, population-based, matched cohort study to investigate associations between SARS-CoV-2 infection and, separately, COVID-19 vaccination just before or during pregnancy and the risk of adverse baby and maternal outcomes among women in Scotland with a singleton pregnancy ending at ≥20 weeks gestation. Baby outcomes examined were stillbirth, neonatal death, extended perinatal mortality, preterm birth (overall, spontaneous, and provider-initiated), small-for-gestational age, and low Apgar score. Maternal outcomes were admission to critical care or death, venous thromboembolism, hypertensive disorders of pregnancy, and pregnancy-related bleeding. Conditional logistic regression models were used to derive odds ratios adjusted for socio-demographic and clinical characteristics (aORs) and 95% confidence intervals (CIs).<br><br>Findings: Our infection analyses of 4,074 women with confirmed SARS-CoV-2 infection matched on maternal age, season of conception, and gestational age at infection/matching to 12,222 uninfected controls, found that infection was associated with an increased risk of preterm (aOR=1·36, 95% CI 1·16-1·59) and very preterm birth (aOR=1·90, 95% CI 1·20-3·02), maternal admission to critical care or death (aOR=1·72, 95% CI 1·39-2·12), and venous thromboembolism (aOR=2·53, 95% CI 1·47-4·35).  Our vaccination analyses found no evidence of increased risk for any baby or maternal outcomes following vaccination.InterpretationSARS-CoV-2 infection during pregnancy is associated with adverse baby and maternal outcomes, but COVID-19 vaccination is not. COVID-19 vaccination remains the safest way for pregnant women to protect themselves and their babies against SARS-CoV-2 infection.<br><br>Funding: Our thanks to the EAVE II Patient Advisory Group and Sands charity for their support. COPS is a sub-study of EAVE II, which is funded by the Medical Research Council (MC_PC_19075) with the support of BREATHE – The Health Data Research Hub for Respiratory Health [MC_PC_19004], which is funded through the UK Research and Innovation Industrial Strategy Challenge Fund and delivered through Health Data Research UK. Additional support has been provided through Public Health Scotland and Scottish Government DG Health and Social Care and the Data and Connectivity National Core Study, led by Health Data Research UK in partnership with the Office for National Statistics and funded by UK Research and Innovation. COPS has received additional funding from Tommy’s charity. SJS is funded by a Wellcome Trust Clinical Career Development Fellowship (209560/Z/17/Z). SVK acknowledges funding from a NRS Senior Clinical Fellowship (SCAF/15/02), the Medical Research Council (MC_UU_00022/2) and the Scottish Government Chief Scientist Office (SPHSU17).<br><br>Declaration of Interests: AS and CR were members of the Scottish Government’s COVID-19 Advisory Group. AS is a member of the New and Emerging Respiratory Virus Threats Advisory Group (NERVTAG) risk stratification subgroup and the Scottish Government’s Committee on Pandemic Preparedness. CR is a member of the Scientific Pandemic Influenza Group on Modelling and the MHRA Covid 19 Vaccine Benefit and Risk Working Group. AS is a member of AstraZeneca’s Thrombotic Thrombocytopenic Advisory Group. All roles are unremunerated. SVK was co-chair of Scottish Government’s Expert Reference Group on Ethnicity and COVID-19. All others have nothing to declare. <br><br>Ethics Approval: COPS has ethical approval from the National Research Ethics Service Committee, South East Scotland 02 (REC 12/SS/0201: SA 2) and information governance approval from the Public Benefit and Privacy Panel for Health and Social Care (2021-0116).",,doi:https://doi.org/10.2139/ssrn.4322399; html:https://europepmc.org/article/PPR/PPR625199; doi:https://doi.org/10.2139/ssrn.4322399
+PPR802874,https://doi.org/10.1101/2024.02.08.24302486,Bidirectional relationship between sleep problems and long COVID: a longitudinal analysis of data from the COVIDENCE UK study,"Vivaldi G, Talaei M, Blaikley J, Jackson C, Pfeffer PE, Shaheen SO, Martineau AR.",,No Journal Info,2024,2024-02-08,Y,,,,"<h4>Summary</h4> <h4>Background</h4> Studies into the bidirectional relationship between sleep and long COVID have been limited by retrospective pre-infection sleep data and infrequent post-infection follow-up. We therefore used prospectively collected monthly data to evaluate how pre-infection sleep characteristics affect risk of long COVID, and to track changes in sleep duration during the year after SARS-CoV-2 infection. <h4>Methods</h4> COVIDENCE UK is a prospective, population-based UK study of COVID-19 in adults. We included non-hospitalised participants with evidence of SARS-CoV-2 infection, and estimated odds ratios (ORs) for the association between pre-infection sleep characteristics and long COVID using logistic regression, adjusting for potential confounders. We assessed changes in sleep duration after infection using multilevel mixed models. We defined long COVID as unresolved symptoms at least 12 weeks after infection. We defined sleep quality according to age-dependent combinations of sleep duration and efficiency. COVIDENCE UK is registered with ClinicalTrials.gov, NCT04330599 . <h4>Findings</h4> We included 3994 participants in our long COVID risk analysis, of whom 327 (8.2%) reported long COVID. We found an inverse relationship between pre-infection sleep quality and risk of long COVID (medium vs good quality: OR 1.37 [95% CI 1.04–1.81]; medium–low vs good: 1.55 [1.12–2.16]; low vs good: 1.94 [1.11–3.38]). Greater variability in pre-infection sleep efficiency was also associated with long COVID (OR per percentage-point increase 1.06 [1.01–1.11]). We assessed post-infection sleep duration in 6860 participants, observing a 0.11 h (95% CI 0.08–0.13) increase in the first month after infection compared with pre-infection, with larger increases for more severe infections. After 1 month, sleep duration largely returned to pre-infection levels, although fluctuations in duration lasted up to 6 months after infection among people reporting long COVID. <h4>Interpretation</h4> Our findings highlight the bidirectional relationship between sleep and long COVID. While poor-quality sleep before SARS-CoV-2 infection associates with increased risk of long COVID thereafter, changes in sleep duration after infection in these non-hospitalised cases were modest and generally quick to resolve. <h4>Funding</h4> Barts Charity.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2024/02/08/2024.02.08.24302486.full.pdf; doi:https://doi.org/10.1101/2024.02.08.24302486; html:https://europepmc.org/article/PPR/PPR802874; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR802874&type=FILE&fileName=EMS193995-pdf.pdf&mimeType=application/pdf
 PPR660616,https://doi.org/10.1101/2023.05.12.23289914,Effectiveness of Sotrovimab and Molnupiravir in community settings in England across the Omicron BA.1 and BA.2 sublineages: emulated target trials using the OpenSAFELY platform,"The OpenSAFELY collaborative, Tazare J, Nab L, Zheng B, Hulme WJ, Green ACA, Curtis HJ, Mahalingasivam V, Higgins R, Schultze A, Bhaskaran K, Mehrkar A, Schaffer A, Smith RM, Bates C, Cockburn J, Parry J, Hester F, Harper S, Eggo RM, Walker AJ, Marks M, Brown M, Maringe C, Leyrat C, Evans SJW, Goldacre B, MacKenna B, Sterne JAC, Tomlinson LA, Douglas IJ.",,No Journal Info,2023,2023-05-16,Y,,,,"<h4>Background</h4> The effectiveness of COVID-19 monoclonal antibody and antiviral therapies against severe COVID-19 outcomes is unclear. Initial benefit was shown in unvaccinated patients and before the Omicron variant emerged. We used the OpenSAFELY platform to emulate target trials to estimate the effectiveness of sotrovimab or molnupiravir, versus no treatment. <h4>Methods</h4> With the approval of NHS England, we derived population-based cohorts of non-hospitalised high-risk individuals in England testing positive for SARS-CoV-2 during periods of dominance of the BA.1 (16/12/2021-10/02/2022) and BA.2 (11/02/2022-21/05/2022) Omicron sublineages. We used the clone-censor-weight approach to estimate the effect of treatment with sotrovimab or molnupiravir initiated within 5 days after positive test versus no treatment. Hazard ratios (HR) for COVID-19 hospitalisation or death within 28 days were estimated using weighted Cox models. <h4>Results</h4> Of the 35,856 [BA.1 period] and 39,192 [BA.2 period] patients, 1,830 [BA.1] and 1,242 [BA.2] were treated with molnupiravir and 2,244 [BA.1] and 4,164 [BA.2] with sotrovimab. The estimated HRs for molnupiravir versus untreated were 1.00 (95%CI: 0.81;1.22) [BA.1] and 1.22 (0.96;1.56) [BA.2]; corresponding HRs for sotrovimab versus untreated were 0.76 (0.66;0.89) [BA.1] and 0.92 (0.79;1.06) [BA.2]. <h4>Interpretation</h4> Compared with no treatment, sotrovimab was associated with reduced risk of adverse outcomes after COVID-19 in the BA.1 period, but there was weaker evidence of benefit in the BA2 period. Molnupiravir was not associated with reduced risk in either period. <h4>Funding</h4> UKRI, Wellcome Trust, MRC, NIHR and HDRUK.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2023/05/16/2023.05.12.23289914.full.pdf; doi:https://doi.org/10.1101/2023.05.12.23289914; html:https://europepmc.org/article/PPR/PPR660616; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR660616&type=FILE&fileName=EMS175947-pdf.pdf&mimeType=application/pdf
 PPR700442,https://doi.org/10.1101/2023.07.31.23293422,Associations between SARS-CoV-2 infection and subsequent economic inactivity and employment status: pooled analyses of five linked longitudinal surveys,"Shaw RJ, Rhead R, Silverwood RJ, Wels J, Zhu J, Hamilton OK, Gessa GD, Bowyer RC, Moltrecht B, Green MJ, Demou E, Pattaro S, Zaninotto P, Boyd A, Greaves F, Chaturvedi N, Ploubidis GB, Katikireddi SV.",,No Journal Info,2023,2023-07-31,Y,,,,"<h4>Introduction</h4> Following the acute phase of the COVID-19 pandemic, record numbers of people became economically inactive (i.e., neither working nor looking for work), or non-employed (including unemployed job seekers and economically inactive people). A possible explanation is people leaving the workforce after contracting COVID-19. We investigated whether testing positive for SARS-CoV-2 is related to subsequent economic inactivity and non-employment, among people employed pre-pandemic. <h4>Methods</h4> The data came from five UK longitudinal population studies held by both the UK Longitudinal Linkage Collaboration (UK LLC; primary analyses) and the UK Data Service (UKDS; secondary analyses). We pooled data from five long established studies (1970 British Cohort Study, English Longitudinal Study of Ageing, 1958 National Child Development Study, Next Steps, and Understanding Society). The study population were aged 25-65 years between March 2020 to March 2021 and employed pre-pandemic. Outcomes were economic inactivity and non-employment measured at the time of the last follow-up survey (November 2020 to March 2021, depending on study). For the UK LLC sample (n=8,174), COVID-19 infection was indicated by a positive SARS-CoV-2 test in NHS England records. For the UKDS sample we used self-reported measures of COVID-19 infection (n=13,881). Logistic regression models estimated odds ratios (ORs) with 95% confidence intervals (95%CIs) adjusting for potential confounders including sociodemographic variables, pre-pandemic health and occupational class. <h4>Rebsults</h4> Testing positive for SARS-CoV-2 was very weakly associated with economic inactivity (OR 1.08 95%CI 0.68-1.73) and non-employment status (OR 1.09. 95%CI 0.77-1.55) in the primary analyses. In secondary analyses, self-reported test-confirmed COVID-19 was not associated with either economic inactivity (OR 1.01 95%CI 0.70-1.44) or non-employment status (OR 1.03 95%CI 0.79-1.35). <h4>Conclusions</h4> Among people employed pre-pandemic, testing positive for SARS-CoV-2 was either weakly or not associated with increased economic inactivity or non-employment. Research on the recent increases in economic inactivity should focus on other potential causes. <h4>Key messages</h4> <h4>What is already known on this topic</h4> Economic inactivity has increased following the pandemic. Infection with SARS-CoV-2 has the potential to lead to post-COVID-19 condition, which is associated with reduced working capacity and absences from work. It is unclear if infection with SARS-CoV-2 leads to economic inactivity among those who were initially in employment just before the pandemic. <h4>What this study adds</h4> Infection is only very weakly or not associated with economic inactivity and non-employment in people who were in employment just prior to the pandemic. <h4>How this study might affect research, practice or policy</h4> Alternative explanations for the rise in economic inactivity need to be investigated such as long-term sickness. Possible biases introduced by linkage consent need considering when using linked healthcare data.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10473774; doi:https://doi.org/10.1101/2023.07.31.23293422; html:https://europepmc.org/article/PPR/PPR700442; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR700442&type=FILE&fileName=EMS183903-pdf.pdf&mimeType=application/pdf
 PPR517024,https://doi.org/,Brazilian COVID-19 data streaming,"Silva NBd, Valencia LIO, Filho FMHS, Ferreira ACS, Pereira FAC, Oliveira GLd, Oliveira PF, Rodrigues MS, Ramos PIP, Oliveira JF.",,No Journal Info,2022,2022-05-10,Y,,,,"We collected individualized (unidentifiable) and aggregated openly available data from various sources related to suspected/confirmed SARS-CoV-2 infections, vaccinations, non-pharmaceutical government interventions, human mobility, and levels of population inequality in Brazil. In addition, a data structure allowing real-time data collection, curation, integration, and extract-transform-load processes for different objectives was developed. The granularity of this dataset (state- and municipality-wide) enables its application to individualized and ecological epidemiological studies, statistical, mathematical, and computational modeling, data visualization as well as the scientific dissemination of information on the COVID-19 pandemic in Brazil.",,arxiv:https://arxiv.org/abs/2205.05032v1; html:https://europepmc.org/article/PPR/PPR517024; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR517024&type=FILE&fileName=EMS150464-pdf.pdf&mimeType=application/pdf
@@ -88,8 +88,8 @@ PPR605221,https://doi.org/10.2139/ssrn.4142082,Comparative Risk of Cerebral Veno
 PPR601911,https://doi.org/10.2139/ssrn.4099405,Sociodemographic and Health Factors Affecting Uptake of Second Dose Covid-19 Vaccine in England: Retrospective Cohort Study Using Data from the National Primary Care Sentinel Surveillance Network (Oxford-Royal College of General Practitioners Clinical Informatics Digital Hub),"Tsang RSM, Joy M, Byford R, Fan X, Jamie G, Kar D, Anand S, Victor W, Williams J, Bedston S, Bradley D, Owen RK, Torabi F, Lowthian E, Robertson C, Beggs J, Howsam G, Sheikh A, Hobbs R, Lusignan Sd.",,No Journal Info,2022,2022-05-03,Y,,,,"Background: Two doses of COVID-19 vaccine offer greater protection than one dose. There are known disparities in COVID-19 outcomes and vaccine uptake. However, it is not known whether non-uptake of the second dose in people who have already received their first dose is predicted by differences in demographic characteristics and disease risk.<br><br>Methods: We conducted a retrospective cohort study using computerised medical record data from the nationally representative Oxford-Royal College of General Practitioners primary care sentinel cohort (N=7,952,861). Among adults who received at least one dose of Oxford-AstraZeneca ChAdOx1, mRNA Pfizer-BioNTech BNT162b2 or Moderna mRNA-1273 vaccines, we used univariable and multivariable logistic regressions to estimate the odds ratios (ORs) and adjusted ORs (aORs), and their 95% confidence intervals (95% CI), of second dose uptake.<br><br>Findings: In adults vaccinated with one dose (n=2,802,314), younger age, ethnic minorities, rurality (aOR=0.93 (95% CI 0.91-0.94)), East of England and the South West, current (0.59 (0.58-0.60)) and ex-smokers (0.93 (0.91-0.94)), severe mental illness (0.58 (0.56-0.60)) among other comorbidities, COVID-19 (0.57 (0.55-0.58)) or adverse events after their first dose, were associated with lower second dose uptake. Male sex (1.02 (1.00-1.03)), increasing socioeconomic status, asthma (1.04 (1.02-1.07)), and first dose mRNA vaccine (1.28 (1.27-1.30)) were associated with higher likelihood of second dose uptake.<br><br>Interpretation: Several demographic and risk groups at higher risk of adverse COVID-19 outcomes are less likely to receive second COVID-19 vaccination. Initiatives to increase vaccine uptake targeting people in sociodemographic groups and with comorbidities where interventions might have the greatest impact are needed.<br><br>Funding Information: This study was funded by UK Research and Innovation 460 (grant ref MC_PC_20029, MC_PC_20058).<br><br>Declaration of Interests: The authors declare that they have no conflict of interests.<br><br>Ethics Approval Statement: Ethical permission was obtained from the UK’s Health Research Authority (REC reference: 21/HRA/2786). Participation in DaCVaP was approved by the RCGP Joint Research and Surveillance Centre Committee (JRSCC).<br>",,doi:https://doi.org/10.2139/ssrn.4099405; html:https://europepmc.org/article/PPR/PPR601911; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR601911&type=FILE&fileName=EMS164007-pdf.pdf&mimeType=application/pdf
 PPR501811,https://doi.org/10.1101/2022.06.02.22275900,"Trends in SARS-CoV-2 infection prevalence during England’s roadmap out of lockdown, January to July 2021","Eales O, Wang H, Haw D, Ainslie KEC, Walters CE, Atchison C, Cooke G, Barclay W, Ward H, Darzi A, Ashby D, Donnelly CA, Elliott P, Riley S.",,No Journal Info,2022,2022-06-02,Y,,,,"<h4>Background</h4> Following rapidly rising COVID-19 case numbers, England entered a national lockdown on 6 January 2021, with staged relaxations of restrictions from 8 March 2021 onwards. <h4>Aim</h4> We characterise how the lockdown and subsequent easing of restrictions affected trends in SARS-CoV-2 infection prevalence. <h4>Methods</h4> On average, risk of infection is proportional to infection prevalence. The REal-time Assessment of Community Transmission-1 (REACT-1) study is a repeat cross-sectional study of over 98,000 people every round (rounds approximately monthly) that estimates infection prevalence in England. We used Bayesian P-splines to estimate prevalence and the time-varying reproduction number ( R t ) nationally, regionally and by age group from round 8 (beginning 6 January 2021) to round 13 (ending 12 July 2021) of REACT-1. As a comparator, a separate segmented-exponential model was used to quantify the impact on R t of each relaxation of restrictions. <h4>Results</h4> Following an initial plateau of 1.54% until mid-January, infection prevalence decreased until 13 May when it reached a minimum of 0.09%, before increasing until the end of the study to 0.76%. Following the first easing of restrictions, which included schools reopening, the reproduction number R t increased by 82% (55%, 108%), but then decreased by 61% (82%, 53%) at the second easing of restrictions, which was timed to match the Easter school holidays. Following further relaxations of restrictions, the observed R t increased steadily, though the increase due to these restrictions being relaxed was masked by the effects of vaccination and the rapid rise of Delta. There was a high degree of synchrony in the temporal patterns of prevalence between regions and age groups. <h4>Conclusion</h4> High-resolution prevalence data fitted to P-splines allowed us to show that the lockdown was highly effective at reducing risk of infection with school holidays/closures playing a significant part.",,pdf:http://spiral.imperial.ac.uk/bitstream/10044/1/100816/10/journal.pcbi.1010724.pdf; doi:https://doi.org/10.1101/2022.06.02.22275900; html:https://europepmc.org/article/PPR/PPR501811; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR501811&type=FILE&fileName=EMS145736-pdf.pdf&mimeType=application/pdf
 PPR498079,https://doi.org/10.1101/2022.05.25.493397,Distinct antigenic properties of the SARS-CoV-2 Omicron lineages BA.4 and BA.5,"Willett BJ, Kurshan A, Thakur N, Newman J, Manali M, Tyson G, Logan N, Murcia PR, Snell LB, Edgeworth JD, Zhou J, Sukhova K, Amirthalingam G, Brown K, Charleston B, Malim MH, Thomson EC, Barclay WS, Bailey D, Doores KJ, Peacock TP.",,No Journal Info,2022,2022-05-25,Y,,,,"Over the course of the pandemic variants have arisen at a steady rate. The most recent variants to emerge, BA.4 and BA.5, form part of the Omicron lineage and were first found in Southern Africa where they are driving the current wave of infection. In this report, we perform an in-depth characterisation of the antigenicity of the BA.4/BA.5 Spike protein by comparing sera collected post-vaccination, post-BA.1 or BA.2 infection, or post breakthrough infection of vaccinated individuals with the Omicron variant. In addition, we assess sensitivity to neutralisation by commonly used therapeutic monoclonal antibodies. We find sera collected post-vaccination have a similar ability to neutralise BA.1, BA.2 and BA.4/BA.5. In contrast, in the absence of vaccination, prior infection with BA.2 or, in particular, BA.1 results in an antibody response that neutralises BA.4/BA.5 poorly. Breakthrough infection with Omicron in vaccinees leads to a broad neutralising response against the new variants. The sensitivity of BA.4/BA.5 to neutralisation by therapeutic monoclonal antibodies was similar to that of BA.2. These data suggest BA.4/BA.5 are antigenically distinct from BA.1 and, to a lesser extent, BA.2. The enhanced breadth of neutralisation observed following breakthrough infection with Omicron suggests that vaccination with heterologous or multivalent antigens may represent viable strategies for the development of cross-neutralising antibody responses.",,pdf:https://www.biorxiv.org/content/biorxiv/early/2022/05/25/2022.05.25.493397.full.pdf; doi:https://doi.org/10.1101/2022.05.25.493397; html:https://europepmc.org/article/PPR/PPR498079; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR498079&type=FILE&fileName=EMS145422-pdf.pdf&mimeType=application/pdf
-PPR906782,https://doi.org/10.1101/2024.09.04.24312992,"Higher dose corticosteroids in hospitalised COVID-19 patients requiring ventilatory support (RECOVERY): a randomised, controlled, open-label, platform trial","RECOVERY Collaborative Group, Horby PW, Emberson JR, Thwaites L, Campbell M, Peto L, Pessoa-Amorim G, Staplin N, Hamers RL, Amuasi J, Nel J, Kestelyn E, Phong NT, Shrestha A, Nasronudin N, Sarkar R, Thach PN, Patel D, Samardi U, Stewart R, Nelwan E, Rawal M, Baillie JK, Buch MH, Day JN, Faust SN, Jaki T, Jeffery K, Juszczak E, Knight M, Lim WS, Mafham M, Montgomery A, Mumford A, Rowan K, Basnyat B, Haynes R, Landray MJ.",,No Journal Info,2024,2024-09-06,Y,,,,"<h4>SUMMARY</h4> <h4>Background</h4> Low-dose corticosteroids (e.g. 6 mg dexamethasone) have been shown to reduce mortality for hypoxic COVID-19 patients. We have previously reported that higher dose corticosteroids cause harm in patients with hypoxia but not receiving ventilatory support (non-invasive mechanical ventilation, invasive mechanical ventilation or extra-corporeal membrane oxygenation), but the balance of efficacy and safety in patients receiving ventilatory support is uncertain. <h4>Methods</h4> This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]) assessed multiple possible treatments in patients hospitalised for COVID-19. Eligible and consenting adult patients receiving ventilatory support were randomly allocated (1:1) to either usual care with higher dose corticosteroids (dexamethasone 20 mg once daily for 5 days followed by 10 mg once daily for 5 days or until discharge if sooner) or usual standard of care alone (which includes dexamethasone 6 mg once daily for 10 days or until discharge if sooner). The primary outcome was 28-day mortality; secondary outcomes were duration of hospitalisation and (among participants not on invasive mechanical ventilation at baseline) the composite of invasive mechanical ventilation or death. Recruitment closed on 31 March 2024 when funding for the trial ended. The RECOVERY trial is registered with ISRCTN (50189673) and clinicaltrials.gov ( NCT04381936 ). <h4>Findings</h4> Between 25 May 2021 and 9 January 2024, 477 COVID-19 patients receiving ventilatory support were randomly allocated to receive usual care plus higher dose corticosteroids versus usual care alone (of whom 99% received corticosteroids during the follow-up period). Of those randomised, 221 (46%) were in Asia, 245 (51%) in the UK and 11 (2%) in Africa. 143 (30%) had diabetes mellitus. Overall, 86 (35%) of 246 patients allocated to higher dose corticosteroids versus 86 (37%) of 231 patients allocated to usual care died within 28 days (rate ratio [RR] 0.87; 95% CI 0.64-1.18; p=0.37). There was no significant difference in the proportion of patients discharged from hospital alive within 28 days (128 [52%] in the higher dose corticosteroids group vs 120 [52%] in the usual care group; RR 1.04, 0.81-1.33]; p=0.78). Among those not on invasive mechanical ventilation at baseline, there was no significant difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (76 [37%] of 206 vs 93 [45%] of 205; RR 0.79 [95% CI 0.63–1.00]; p=0.05). <h4>Interpretation</h4> In patients hospitalised for COVID-19 receiving ventilatory support, we found no evidence that higher dose corticosteroids reduced the risk of death compared to usual care, which included low dose corticosteroids. <h4>Funding</h4> UK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056), and Wellcome Trust (Grant Ref: 222406/Z/20/Z).",,doi:https://doi.org/10.1101/2024.09.04.24312992; doi:https://doi.org/10.1101/2024.09.04.24312992; html:https://europepmc.org/article/PPR/PPR906782; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR906782&type=FILE&fileName=EMS198596-pdf.pdf&mimeType=application/pdf
 PPR519618,https://doi.org/10.1101/2022.07.15.22277678,Influence of vitamin D supplementation on SARS-CoV-2 vaccine efficacy and immunogenicity,"Jolliffe DA, Vivaldi G, Chambers ES, Cai W, Li W, Faustini SE, Gibbons JM, Pade C, Richter AG, McKnight Á, Martineau AR.",,No Journal Info,2022,2022-07-17,Y,,,,"<h4>SUMMARY</h4> <h4>Background & Aims</h4> Vitamin D deficiency has been reported to associate with impaired development of antigen-specific responses following vaccination. We aimed to determine whether vitamin D supplements might boost immunogenicity and efficacy of SARS-CoV-2 vaccination. <h4>Methods</h4> We conducted three sub-studies nested within the CORONAVIT randomised controlled trial, which investigated effects of offering vitamin D supplements at a dose of 800 IU/day or 3200 IU/day vs. no offer on risk of acute respiratory infections, including COVID-19, in UK adults with circulating 25-hydroxyvitamin D concentrations <75 nmol/L. Sub-study 1 (n=2808) investigated effects of vitamin D supplementation on risk of breakthrough SARS-CoV-2 infection following two doses of SARS-CoV-2 vaccine. Sub-study 2 (n=1853) investigated effects of vitamin D supplementation on titres of combined IgG, IgA and IgM (IgGAM) anti-Spike antibodies in eluates of dried blood spots collected after SARS-CoV-2 vaccination. Sub-study 3 (n=100) investigated effects of vitamin D supplementation on neutralising antibody and cellular responses in venous blood samples collected after SARS-CoV-2 vaccination. <h4>Results</h4> 1945/2808 (69.3%) sub-study 1 participants received two doses of ChAdOx1 nCoV-19 (Oxford–AstraZeneca); the remainder received two doses of BNT162b2 (Pfizer). Vitamin D supplementation did not influence risk of breakthrough SARS-CoV-2 infection (800 IU/day vs. no offer: adjusted hazard ratio 1.28, 95% CI 0.89 to 1.84; 3200 IU/day vs. no offer: 1.17, 0.81 to 1.70). Neither did it influence IgGAM anti-Spike titres, neutralising antibody titres or IFN-γ concentrations in supernatants of S peptide-stimulated whole blood. <h4>Conclusions</h4> Among adults with sub-optimal baseline vitamin D status, vitamin D replacement at a dose of 800 or 3200 IU/day did not influence protective efficacy or immunogenicity of SARS-CoV-2 vaccination. <h4>Clinical Trial Registration</h4> ClinicalTrials.gov NCT04579640 .",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/07/18/2022.07.15.22277678.full.pdf; doi:https://doi.org/10.1101/2022.07.15.22277678; html:https://europepmc.org/article/PPR/PPR519618; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR519618&type=FILE&fileName=EMS151031-pdf.pdf&mimeType=application/pdf
+PPR906782,https://doi.org/10.1101/2024.09.04.24312992,"Higher dose corticosteroids in hospitalised COVID-19 patients requiring ventilatory support (RECOVERY): a randomised, controlled, open-label, platform trial","RECOVERY Collaborative Group, Horby PW, Emberson JR, Thwaites L, Campbell M, Peto L, Pessoa-Amorim G, Staplin N, Hamers RL, Amuasi J, Nel J, Kestelyn E, Phong NT, Shrestha A, Nasronudin N, Sarkar R, Thach PN, Patel D, Samardi U, Stewart R, Nelwan E, Rawal M, Baillie JK, Buch MH, Day JN, Faust SN, Jaki T, Jeffery K, Juszczak E, Knight M, Lim WS, Mafham M, Montgomery A, Mumford A, Rowan K, Basnyat B, Haynes R, Landray MJ.",,No Journal Info,2024,2024-09-06,Y,,,,"<h4>SUMMARY</h4> <h4>Background</h4> Low-dose corticosteroids (e.g. 6 mg dexamethasone) have been shown to reduce mortality for hypoxic COVID-19 patients. We have previously reported that higher dose corticosteroids cause harm in patients with hypoxia but not receiving ventilatory support (non-invasive mechanical ventilation, invasive mechanical ventilation or extra-corporeal membrane oxygenation), but the balance of efficacy and safety in patients receiving ventilatory support is uncertain. <h4>Methods</h4> This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]) assessed multiple possible treatments in patients hospitalised for COVID-19. Eligible and consenting adult patients receiving ventilatory support were randomly allocated (1:1) to either usual care with higher dose corticosteroids (dexamethasone 20 mg once daily for 5 days followed by 10 mg once daily for 5 days or until discharge if sooner) or usual standard of care alone (which includes dexamethasone 6 mg once daily for 10 days or until discharge if sooner). The primary outcome was 28-day mortality; secondary outcomes were duration of hospitalisation and (among participants not on invasive mechanical ventilation at baseline) the composite of invasive mechanical ventilation or death. Recruitment closed on 31 March 2024 when funding for the trial ended. The RECOVERY trial is registered with ISRCTN (50189673) and clinicaltrials.gov ( NCT04381936 ). <h4>Findings</h4> Between 25 May 2021 and 9 January 2024, 477 COVID-19 patients receiving ventilatory support were randomly allocated to receive usual care plus higher dose corticosteroids versus usual care alone (of whom 99% received corticosteroids during the follow-up period). Of those randomised, 221 (46%) were in Asia, 245 (51%) in the UK and 11 (2%) in Africa. 143 (30%) had diabetes mellitus. Overall, 86 (35%) of 246 patients allocated to higher dose corticosteroids versus 86 (37%) of 231 patients allocated to usual care died within 28 days (rate ratio [RR] 0.87; 95% CI 0.64-1.18; p=0.37). There was no significant difference in the proportion of patients discharged from hospital alive within 28 days (128 [52%] in the higher dose corticosteroids group vs 120 [52%] in the usual care group; RR 1.04, 0.81-1.33]; p=0.78). Among those not on invasive mechanical ventilation at baseline, there was no significant difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (76 [37%] of 206 vs 93 [45%] of 205; RR 0.79 [95% CI 0.63–1.00]; p=0.05). <h4>Interpretation</h4> In patients hospitalised for COVID-19 receiving ventilatory support, we found no evidence that higher dose corticosteroids reduced the risk of death compared to usual care, which included low dose corticosteroids. <h4>Funding</h4> UK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056), and Wellcome Trust (Grant Ref: 222406/Z/20/Z).",,doi:https://doi.org/10.1101/2024.09.04.24312992; doi:https://doi.org/10.1101/2024.09.04.24312992; html:https://europepmc.org/article/PPR/PPR906782; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR906782&type=FILE&fileName=EMS198596-pdf.pdf&mimeType=application/pdf
 PPR530735,https://doi.org/10.1101/2022.08.08.22278576,Outcome of COVID-19 in hospitalised immunocompromised patients: an analysis of the WHO ISARIC CCP-UK prospective cohort study,"Turtle L, Thorpe M, Drake TM, Swets M, Palmieri C, Russell CD, Ho A, Aston S, Wootton DG, Richter A, de Silva TI, Hardwick HE, Leeming G, Law A, Openshaw PJ, Harrison EM, ISARIC4C investigators, Baillie JK, Semple MG, Docherty AB.",,No Journal Info,2022,2022-08-11,Y,,,,"<h4>Background</h4> Immunocompromised patients may be at higher risk of mortality if hospitalised with COVID-19 compared with immunocompetent patients. However, previous studies have been contradictory. We aimed to determine whether immunocompromised patients were at greater risk of in-hospital death, and how this risk changed over the pandemic. <h4>Methods</h4> We included patients >=19yrs with symptomatic community-acquired COVID-19 recruited to the ISARIC WHO Clinical Characterisation Protocol UK. We defined immunocompromise as: immunosuppressant medication preadmission, cancer treatment, organ transplant, HIV, or congenital immunodeficiency. We used logistic regression to compare the risk of death in both groups, adjusting for age, sex, deprivation, ethnicity, vaccination and co-morbidities. We used Bayesian logistic regression to explore mortality over time. <h4>Findings</h4> Between 17/01/2020 and 28/02/2022 we recruited 156,552 eligible patients, of whom 21,954 (14%) were immunocompromised. 29% (n=6,499) of immunocompromised and 21% (n=28,608) of immunocompetent patients died in hospital. The odds of in-hospital mortality were elevated for immunocompromised patients (adjOR 1.44, 95% CI 1.39-1.50, p<0.001). As the pandemic progressed, in-hospital mortality reduced more slowly for immunocompromised patients than for immunocompetent patients. This was particularly evident with increasing age: the probability of the reduction in hospital mortality being less for immunocompromised patients aged 50-69yrs was 88% for men and 83% for women, and for those >80yrs was 99% for men, and 98% for women. <h4>Conclusions</h4> Immunocompromised patients remain at elevated risk of death from COVID-19. Targeted measures such as additional vaccine doses and monoclonal antibodies should be considered for this group. <h4>Funding</h4> National Institute for Health Research; Medical Research Council; Chief Scientist Office, Scotland.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004086&type=printable; doi:https://doi.org/10.1101/2022.08.08.22278576; html:https://europepmc.org/article/PPR/PPR530735; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR530735&type=FILE&fileName=EMS152614-pdf.pdf&mimeType=application/pdf
 PPR553749,https://doi.org/10.1101/2022.10.03.22280649,Impact of vaccination on COVID-19-associated admissions to critical care in England: a population cohort study of linked data,"Harrison DA, Watkinson PJ, Doidge JC, Shankar-Hari M, Mouncey PR, Patone M, Coupland CAC, Hippisley-Cox J, Rowan KM.",,No Journal Info,2022,2022-10-04,Y,,,,"<h4>Introduction</h4> This study aims to explore the impact of COVID-19 vaccination on critical care by examining associations between vaccination and admission to critical care with COVID-19 during England’s Delta wave, by age group, dose, and over time. <h4>Methods</h4> We used linked routinely-collected data to conduct a population cohort study of patients admitted to adult critical care in England for management of COVID-19 between 1 May and 15 December 2021. Included participants were the whole population of England aged 18 years or over (44.7 million), including 10,141 patients admitted to critical care with COVID-19. The intervention was vaccination with one, two, or a booster/three doses of any COVID-19 vaccine. <h4>Results</h4> Compared with unvaccinated patients, vaccinated patients were older (median 64 years for patients receiving two or more doses versus 50 years for unvaccinated), with higher levels of severe comorbidity (20.3% versus 3.9%) and immunocompromise (15.0% versus 2.3%). Compared with patients who were unvaccinated, those vaccinated with two doses had a relative risk reduction (RRR) of between 90.1% (patients aged 18–29, 95% CI, 86.8% to 92.7%) and 95.9% (patients aged 60–69, 95% CI, 95.5% to 96.2%). Waning was only observed for those aged 70+, for whom the RRR reduced from 97.3% (91.0% to 99.2%) to 86.7% (85.3% to 90.1%) between May and December but increased again to 98.3% (97.6% to 98.8%) with a booster/third dose. <h4>Conclusion</h4> Important demographic and clinical differences exist between vaccinated and unvaccinated patients admitted to critical care with COVID-19. While not a causal analysis, our findings are consistent with a substantial and sustained impact of vaccination on reducing admissions to critical care during England’s Delta wave, with evidence of waning predominantly restricted to those aged 70+.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/10/04/2022.10.03.22280649.full.pdf; doi:https://doi.org/10.1101/2022.10.03.22280649; html:https://europepmc.org/article/PPR/PPR553749; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR553749&type=FILE&fileName=EMS155352-pdf.pdf&mimeType=application/pdf
 PPR432994,https://doi.org/10.1101/2021.12.14.21267806,"REACT-1 round 15 final report: Increased breakthrough SARS-CoV-2 infections among adults who had received two doses of vaccine, but booster doses and first doses in children are providing important protection","Chadeau-Hyam M, Eales O, Bodinier B, Wang H, Haw D, Whitaker M, Walters CE, Jonnerby J, Atchison C, Diggle PJ, Page AJ, Ashby D, Barclay W, Taylor G, Cooke G, Ward H, Darzi A, Donnelly CA, Elliott P.",,No Journal Info,2021,2021-12-16,Y,,,,"<h4>Background</h4> It has been nearly a year since the first vaccinations against SARS-CoV-2 were delivered in England. The third wave of COVID-19 in England began in May 2021 as the Delta variant began to outcompete and largely replace other strains. The REal-time Assessment of Community Transmission-1 (REACT-1) series of community surveys for SARS-CoV-2 infection has provided insights into transmission dynamics since May 2020. Round 15 of the REACT-1 study was carried out from 19 October to 5 November 2021. <h4>Methods</h4> We estimated prevalence of SARS-CoV2 infection and used multiple logistic regression to analyse associations between SARS-CoV-2 infection in England and demographic and other risk factors, based on RT-PCR results from self-administered throat and nose swabs in over 100,000 participants. We estimated (single-dose) vaccine effectiveness among children aged 12 to 17 years, and among adults compared swab-positivity in people who had received a third (booster) dose with those who had received two vaccine doses. We used splines to analyse time trends in swab-positivity. <h4>Results</h4> During mid-October to early-November 2021, weighted prevalence was 1.57% (1.48%, 1.66%) compared to 0.83% (0.76%, 0.89%) in September 2021 (round 14). Weighted prevalence increased between rounds 14 and 15 across most age groups (including older ages, 65 years and over) and regions, with average reproduction number across rounds of R=1.09 (1.08, 1.11). During round 15, there was a fall in prevalence from a maximum around 20-21 October, with an R of 0.76 (0.70, 0.83), reflecting falls in prevalence at ages 17 years and below and 18 to 54 years. School-aged children had the highest weighted prevalence of infection: 4.95% (4.39%, 5.58%) in those aged 5 to 12 years and 5.21% (4.61%, 5.87%) in those aged 13 to 17 years. In multiple logistic regression, age, sex, key worker status and presence of one or more children in the home were associated with swab positivity. There was evidence of heterogeneity between rounds in swab positivity rates among vaccinated individuals at ages 18 to 64 years, and differences in key demographic and other variables between vaccinated and unvaccinated adults at these ages. Vaccine effectiveness against infection in children was estimated to be 56.2% (41.3%, 67.4%) in rounds 13, 14 and 15 combined, adjusted for demographic factors, with a similar estimate obtained for round 15 only. Among adults we found that those who received a third dose of vaccine were less likely to test positive compared to those who received only two vaccine doses, with adjusted odds ratio (OR) =0.38 (0.26, 0.55). <h4>Discussion</h4> Swab-positivity was very high at the start of round 15, reaching a maximum around 20 to 21 October 2021, and then falling through late October with an uncertain trend in the last few days of data collection. The observational nature of survey data and the relatively small proportion of unvaccinated adults call into question the comparability of vaccinated and unvaccinated groups at this relatively late stage in the vaccination programme. However, third vaccine doses for eligible adults and the vaccination of children aged 12 years and over are associated with lower infection risk and, thus, remain a high priority (with possible extension to children aged 5-12 years). These should help reduce SARS-CoV-2 transmission during the winter period when healthcare demands typically rise.",,pdf:http://www.thelancet.com/article/S2589537022001493/pdf; doi:https://doi.org/10.1101/2021.12.14.21267806; html:https://europepmc.org/article/PPR/PPR432994; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR432994&type=FILE&fileName=EMS141765-pdf.pdf&mimeType=application/pdf
@@ -109,11 +109,11 @@ PPR618591,https://doi.org/10.1101/2023.02.18.23286127,Antipsychotic prescribing
 PPR303184,https://doi.org/10.1101/2021.03.26.21254391,Vaccine effectiveness of the first dose of ChAdOx1 nCoV-19 and BNT162b2 against SARS-CoV-2 infection in residents of Long-Term Care Facilities (VIVALDI study),"Shrotri M, Krutikov M, Palmer T, Giddings R, Azmi B, Subbarao S, Fuller C, Irwin-Singer A, Davies D, Tut G, Bernal JL, Moss P, Hayward A, Copas A, Shallcross L.",,No Journal Info,2021,2021-03-26,Y,,,,"<h4>Background</h4> The effectiveness of SARS-CoV-2 vaccines in frail older adults living in Long-Term Care Facilities (LTCFs) is uncertain. We estimated protective effects of the first dose of ChAdOx1 and BNT162b2 vaccines against infection in this population. <h4>Methods</h4> Cohort study comparing vaccinated and unvaccinated LTCF residents in England, undergoing routine asymptomatic testing (8 December 2020 - 15 March 2021). We estimated the relative hazard of PCR-positive infection using Cox proportional hazards regression, adjusting for age, sex, prior infection, local SARS-CoV-2 incidence, LTCF bed capacity, and clustering by LTCF. <h4>Results</h4> Of 10,412 residents (median age 86 years) from 310 LTCFs, 9,160 were vaccinated with either ChAdOx1 (6,138; 67%) or BNT162b2 (3,022; 33%) vaccines. A total of 670,628 person days and 1,335 PCR-positive infections were included. Adjusted hazard ratios (aHRs) for PCR-positive infection relative to unvaccinated residents declined from 28 days following the first vaccine dose to 0·44 (0·24, 0·81) at 28-34 days and 0·38 (0·19, 0·77) at 35-48 days. Similar effect sizes were seen for ChAdOx1 (aHR 0·32 [0·15-0·66] and BNT162b2 (aHR 0·35 [0·17, 0·71]) vaccines at 35-48 days. Mean PCR cycle threshold values were higher, implying lower infectivity, for infections ≥28 days post-vaccination compared with those prior to vaccination (31·3 vs 26·6, p<0·001). <h4>Interpretation</h4> The first dose of BNT162b2 and ChAdOx1 vaccines was associated with substantially reduced SARS-CoV-2 infection risk in LTCF residents from 4 weeks to at least 7 weeks. <h4>Funding</h4> UK Government Department of Health and Social Care. <h4>Research in Context</h4> <h4>Evidence before this study</h4> We conducted a systematic search for studies which evaluated SARS-CoV-2 vaccine effectiveness in residents of long-term care facilities (LTCFs) published between 01/01/2020 and 11/03/2021. We used variations of search terms for “COVID-19” AND “vaccine effectiveness” OR “vaccine efficacy” AND “care homes” OR “long term care facilities” OR “older people” on Ovid MEDLINE and MedRxiv. We identified one pre-print article regarding LTCFs in Denmark, which reported that a single dose of BNT162b was ineffective against SARS-CoV-2 infection in residents, however, participants received the second vaccine dose 24 days following the first dose on average, which is likely to be too soon to capture the protective effects of a single vaccine dose. Additionally, we identified two pre-print reports of studies evaluating vaccine effectiveness against symptomatic infection and hospitalisation amongst older adults in the community. The first of these found 81% vaccine effectiveness against COVID-19-related hospitalisation at 28-34 days following a single dose of BNT162b or ChAdOx1 in ≥80-year-olds. The second of these found vaccine effectiveness against symptomatic infection of 60% at 28-34 days and 73% at 35+ days following a single dose of ChAdOx1 in ≥70-year-olds. No studies were identified that focused on the effectiveness of a single vaccine dose against infection amongst LTCF residents at more than 4 weeks post-vaccination, a particularly important question in the context of the UK policy decision to extend the dose interval beyond 3 weeks. <h4>Added value of this study</h4> We conducted a prospective cohort study of 10,412 residents aged ≥65 years, from 310 LTCFs across England, to investigate the protective effect of the first dose of the ChAdOx1 and BNT162b vaccines against SARS-CoV-2 infection in frail older adults. We retrieved results from routine monthly PCR testing, as well as outbreak and clinical testing for SARS-CoV-2, thereby capturing data on asymptomatic as well as symptomatic infections, which we linked to vaccination records. We estimated vaccine effectiveness to be 56% (19-76%) at 28-34 days, and 62% (23-81%) at 35-48 days following a single dose of ChAdOx1 or BNT162. Our findings suggest that the risk of SARS-CoV-2 infection is substantially reduced from 28 days following the first dose of either vaccine and that this effect is maintained for at least 7 weeks, with similar protection offered by both vaccine types. We also found that PCR cycle threshold (Ct) values, which are negatively associated with the ability to isolate virus, were significantly higher in infections occurring at ≥ 28days post vaccination compared to those occurring in the unvaccinated period, suggesting that vaccination may reduce onward transmission of SARS-CoV-2 in breakthrough infections. To the best of our knowledge, our findings constitute the first real-world evidence on vaccine effectiveness against infection for ChAdOx1, in any age group. We can also infer that both vaccines are effective against the B.1.1.7 variant, because our analysis period coincided with the rapid emergence of B.1.1.7 in England during the second wave of the pandemic. <h4>Implications of all the available evidence</h4> Our findings add to the growing body of evidence on the protective effect of the BNT162b vaccines in residents of LTCFs and demonstrate the effectiveness of ChAdOx1 in this vulnerable population. Evaluating single-dose vaccine efficacy has become increasingly important in light of extended dosing intervals that have been implemented in order to maximise vaccine coverage across high-risk groups. Further work is required to evaluate the effectiveness of the first vaccine dose after 8-12 weeks, as well as following the second dose, and to evaluate the long-term impact of vaccination on SARS-CoV-2 infection, transmission and mortality in LTCFs. This will inform policy decisions regarding the ongoing need for disease control measures in LTCF such as visitor restrictions, which continue to have a detrimental impact on the wellbeing of residents, their relatives, and staff. Supplementary material attached.",,doi:https://doi.org/10.1101/2021.03.26.21254391; doi:https://doi.org/10.1101/2021.03.26.21254391; html:https://europepmc.org/article/PPR/PPR303184; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR303184&type=FILE&fileName=EMS120994-pdf.pdf&mimeType=application/pdf
 PPR600925,https://doi.org/10.1101/2023.01.20.23284849,Comparative effectiveness of Paxlovid versus sotrovimab and molnupiravir for preventing severe COVID-19 outcomes in non-hospitalised patients: observational cohort study using the OpenSAFELY platform,"Zheng B, Tazare J, Nab L, Mehrkar A, MacKenna B, Goldacre B, Douglas IJ, Tomlinson LA.",,No Journal Info,2023,2023-01-22,Y,,,,"<h4>Objective</h4> To compare the effectiveness of Paxlovid vs. sotrovimab and molnupiravir in preventing severe COVID-19 outcomes in non-hospitalised high-risk COVID-19 adult patients. <h4>Design</h4> With the approval of NHS England, we conducted a real-world cohort study using the OpenSAFELY-TPP platform. <h4>Setting</h4> Patient-level electronic health record data were obtained from 24 million people registered with a general practice in England that uses TPP software. The primary care data were securely linked with data on COVID-19 infection and therapeutics, hospital admission, and death within the OpenSAFELY-TPP platform, covering a period where both Paxlovid and sotrovimab were first-line treatment options in community settings. <h4>Participants</h4> Non-hospitalised adult COVID-19 patients at high risk of severe outcomes treated with Paxlovid, sotrovimab or molnupiravir between February 11, 2022 and October 1, 2022. <h4>Interventions</h4> Paxlovid, sotrovimab or molnupiravir administered in the community by COVID-19 Medicine Delivery Units. <h4>Main outcome measure</h4> COVID-19 related hospitalisation or COVID-19 related death within 28 days after treatment initiation. <h4>Results</h4> A total of 7683 eligible patients treated with Paxlovid (n=4836) and sotrovimab (n=2847) were included in the main analysis. The mean age was 54.3 (SD=14.9) years; 64% were female, 93% White and 93% had three or more COVID-19 vaccinations. Within 28 days after treatment initiation, 52 (0.68%) COVID-19 related hospitalisations/deaths were observed (33 (0.68%) treated with Paxlovid and 19 (0.67%) with sotrovimab). Cox proportional hazards model stratified by region showed that after adjusting for demographics, high-risk cohort categories, vaccination status, calendar time, body mass index and other comorbidities, treatment with Paxlovid was associated with a similar risk of outcome event as treatment with sotrovimab (HR=1.14, 95% CI: 0.62 to 2.08; P=0.673). Results from propensity score weighted Cox model also showed comparable risks in these two treatment groups (HR=0.88, 95% CI: 0.45 to 1.71; P=0.700). An exploratory analysis comparing Paxlovid users with 802 molnupiravir users (11 (1.37%) COVID-19 related hospitalisations/deaths) showed some evidence in favour of Paxlovid but with variation in the effect estimates between models (HR ranging from 0.26 to 0.61). <h4>Conclusion</h4> In routine care of non-hospitalised high-risk adult patients with COVID-19 in England, no substantial difference in the risk of severe COVID-19 outcomes was observed between those who received Paxlovid and sotrovimab between February and October 2022, when different subvariants of Omicron were dominant.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2023/01/22/2023.01.20.23284849.full.pdf; doi:https://doi.org/10.1101/2023.01.20.23284849; html:https://europepmc.org/article/PPR/PPR600925; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR600925&type=FILE&fileName=EMS163205-pdf.pdf&mimeType=application/pdf
 PPR471516,https://doi.org/10.1101/2022.03.23.22272804,Waning effectiveness of BNT162b2 and ChAdOx1 COVID-19 vaccines over six months since second dose: a cohort study using linked electronic health records,"Horne EM, Hulme WJ, Keogh RH, Palmer TM, Williamson EJ, Parker EP, Green A, Walker V, Walker AJ, Curtis H, Fisher L, MacKenna B, Croker R, Hopcroft L, Park RY, Massey J, Morley J, Mehrkar A, Bacon S, Evans D, Inglesby P, Morton CE, Hickman G, Davy S, Ward T, Dillingham I, Goldacre B, Hernán MA, Sterne JA.",,No Journal Info,2022,2022-03-23,Y,,,,"<h4>Summary</h4> <h4>Background</h4> The rate at which COVID-19 vaccine effectiveness wanes over time is crucial for vaccination policies, but is incompletely understood with conflicting results from different studies. <h4>Methods</h4> This cohort study, using the OpenSAFELY-TPP database and approved by NHS England, included individuals without prior SARS-CoV-2 infection assigned to vaccines priority groups 2-12 defined by the UK Joint Committee on Vaccination and Immunisation. We compared individuals who had received two doses of BNT162b2 or ChAdOx1 with unvaccinated individuals during six 4-week comparison periods, separately for subgroups aged 65+ years; 16-64 years and clinically vulnerable; 40-64 years and 18-39 years. We used Cox regression, stratified by first dose eligibility and geographical region and controlled for calendar time, to estimate adjusted hazard ratios (aHRs) comparing vaccinated with unvaccinated individuals, and quantified waning vaccine effectiveness as ratios of aHRs per-4-week period. The outcomes were COVID-19 hospitalisation, COVID-19 death, positive SARS-CoV-2 test, and non-COVID-19 death. <h4>Findings</h4> The BNT162b2, ChAdOx1 and unvaccinated groups comprised 1,773,970, 2,961,011 and 2,433,988 individuals, respectively. Waning of vaccine effectiveness was similar across outcomes and vaccine brands: e.g. in the 65+ years subgroup ratios of aHRs versus unvaccinated for COVID-19 hospitalisation, COVID-19 death and positive SARS-CoV-2 test ranged from 1.23 (95% CI 1.15-1.32) to 1.27 (1.20-1.34) for BNT162b2 and 1.16 (0.98-1.37) to 1.20 (1.14-1.27) for ChAdOx1. Despite waning, rates of COVID-19 hospitalisation and COVID-19 death were substantially lower among vaccinated individuals compared to unvaccinated individuals up to 26 weeks after second dose, with estimated aHRs <0.20 (>80% vaccine effectiveness) for BNT162b2, and <0.26 (>74%) for ChAdOx1. By weeks 23-26, rates of SARS-CoV-2 infection in fully vaccinated individuals were similar to or higher than those in unvaccinated individuals: aHRs ranged from 0.85 (0.78-0.92) to 1.53 (1.07-2.18) for BNT162b2, and 1.21 (1.13-1.30) to 1.99 (1.94-2.05) for ChAdOx1. <h4>Interpretation</h4> The rate at which estimated vaccine effectiveness waned was strikingly consistent for COVID-19 hospitalisation, COVID-19 death and positive SARS-CoV-2 test, and similar across subgroups defined by age and clinical vulnerability. If sustained to outcomes of infection with the Omicron variant and to booster vaccination, these findings will facilitate scheduling of booster vaccination doses.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/03/23/2022.03.23.22272804.full.pdf; doi:https://doi.org/10.1101/2022.03.23.22272804; html:https://europepmc.org/article/PPR/PPR471516; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR471516&type=FILE&fileName=EMS149099-pdf.pdf&mimeType=application/pdf
-PPR699913,https://doi.org/10.2139/ssrn.4523754,Long-Term Air Pollution Exposure and Risk of SARS-CoV-2 Infection and COVID-19 Severity: A UK-Wide Cohort Study (COVIDENCE UK),"Hajmohammadi H, Talaei M, Fecht D, Wang W, Vivaldi G, Faustini S, Richter AG, Shaheen SO, Martineau AR, Sheikh A, Mudway I, Griffiths CJ.",,No Journal Info,2023,2023-08-01,N,,,,"Background: The association between air quality and risk of SARS-CoV-2 infection is poorly understood. We investigated this association using serological individual-level data adjusting for a wide range of confounders, in a large population-based cohort (COVIDENCE UK).<br><br>Methods: We assessed the associations between long-term (2015–19) nitrogen dioxide (NO2) and fine particulate matter (PM with an aerodynamic diameter of ≤2.5 µm [PM<sub>2.5</sub>]), exposures with SARS-CoV-2 infection, level of antibody response among those infected, and COVID-19 disease severity. We used serological data from 10,489 participants in the COVIDENCE UK cohort, and estimated annual average air pollution exposure at each participant’s home postcode.<br><br>Findings: After controlling for potential confounders, we found a positive association between 5-year NO<sub>2</sub> and PM<sub>2.5</sub> exposures and the risk of seropositivity: a per-unit increase in NO2 (μg/m<sup>3</sup>) was associated with an increasing risk of seropositivity of 0.8% (95% CI 0·2 to 1·5; <i>p</i>-for-trend 0.016). For PM<sub>2.5</sub>, a per-unit increase (μg/m<sup>3</sup>) was associated with an increasing risk of seropositivity of 4.9% (–0·1 to 10·2; <i>p</i>-for-trend 0·051). In addition, we found that NO2 was positively associated with higher antibody titres (<i>p</i>-for-trend 0·013) among seropositive participants, with no evidence of an association for PM<sub>2.5</sub>.<br><br>Interpretation: Our findings suggest that the long-term burden of air pollution increased the risks of SARS-CoV-2 infection and has important implications for future pandemic preparedness. This evidence strengthens the case for reducing long-term air pollution exposures to reduce the vulnerability of individuals to respiratory viruses.<br><br>Funding: NIHR, school of primary care research (SPCR). NIHR ARC North Thames. NIHR Health Protection Research Units in Chemical and Radiation Threats and Hazards and Environmental Exposures and Health, partnerships between Imperial College London and The UK Health Security Agency (UKHSA).Barts Charity (MGU0570, MGU0459, MGU0466).Pharma Nord, the Fischer Family Foundation, DSM Nutritional Products, the Exilarch’s Foundation, the Karl R Pfleger Foundation, the AIM Foundation, Synergy Biologics, Cytoplan, the UK National Institute for Health and Care Research Clinical Research Network (52255; 52257), the Health Data Research UK BREATHE Hub, the UK Research and Innovation Industrial Strategy Challenge Fund (MC_PC_19004), Thornton & Ross, Warburtons, Matthew Isaacs (personal donation), Barbara Boucher (personal donation), and Hyphens Pharma.<br><br>Declaration of Interest: AS is a member of the Scottish Government Chief Medical Officer’s COVID-19 Advisory Group and its Standing Committee on Pandemics. He is also a member of the UK Government’s NERVTAG’s Risk Stratification Subgroup. ARM declares receipt of funding in the last 36 months to support vitamin D research from the following companies who manufacture or sell vitamin D supplements: Pharma Nord, DSM Nutritional Products, Thornton & Ross and Hyphens Pharma. He also declares support for attending meetings from the following companies who manufacture or sell vitamin D supplements: Pharma Nord and Abiogen Pharma. He also declares participation on the Data and Safety Monitoring Board for the Chair, DSMB, VITALITY trial (Vitamin D for Adolescents with HIV to reduce musculoskeletal morbidity and immunopathology). He also declares unpaid work as a Programme Committee member for the Vitamin D Workshop. He also declares receipt of vitamin D capsules for clinical trial use from Pharma Nord, Synergy Biologics and Cytoplan. CJG is supported by the NIHR ARC North Thames. All other authors declare that they have no competing interests.",,doi:https://doi.org/10.2139/ssrn.4523754; html:https://europepmc.org/article/PPR/PPR699913; doi:https://doi.org/10.2139/ssrn.4523754
 PPR371282,https://doi.org/10.1101/2021.07.14.21260497,"Vaccine uptake and SARS-CoV-2 antibody prevalence among 207,337 adults during May 2021 in England: REACT-2 study","Ward H, Whitaker M, Tang SN, Atchison C, Darzi A, Donnelly CA, Diggle PJ, Ashby D, Riley S, Barclay WS, Elliott P, Cooke G.",,No Journal Info,2021,2021-07-18,Y,,,,"<h4>Background</h4> The programme to vaccinate adults in England has been rapidly implemented since it began in December 2020. The community prevalence of SARS-CoV-2 anti-spike protein antibodies provides an estimate of total cumulative response to natural infection and vaccination. We describe the distribution of SARS-CoV-2 IgG antibodies in adults in England in May 2021 at a time when approximately 7 in 10 adults had received at least one dose of vaccine. <h4>Methods</h4> Sixth round of REACT-2 (REal-time Assessment of Community Transmission-2), a cross-sectional random community survey of adults in England, from 12 to 25 May 2021; 207,337 participants completed questionnaires and self-administered a lateral flow immunoassay test producing a positive or negative result. <h4>Results</h4> Vaccine coverage with one or more doses, weighted to the adult population in England, was 72.9% (95% confidence interval 72.7-73.0), varying by age from 25.1% (24.5-25.6) of those aged 18 to 24 years, to 99.2% (99.1-99.3) of those 75 years and older. In adjusted models, odds of vaccination were lower in men (odds ratio [OR] 0.89 [0.85-0.94]) than women, and in people of Black (0.41 [0.34-0.49]) compared to white ethnicity. There was higher vaccine coverage in the least deprived and highest income households. People who reported a history of COVID-19 were less likely to be vaccinated (OR 0.61 [0.55-0.67]). There was high coverage among health workers (OR 9.84 [8.79-11.02] and care workers (OR 4.17 [3.20-5.43]) compared to non-key workers, but lower in hospitality and retail workers (OR 0.73 [0.64-0.82] and 0.77 [0.70-0.85] respectively) after adjusting for age and key covariates. The prevalence of antibodies (weighted to the adult population of England and adjusted for test characteristics) was 61.1% (95% CI 60.9-61.4), up from 6.6% (5.4-5.7) in round 4 (27 October to 10 November 2020) and 13.9% (13.7-14.1) in round 5 (26 January to 8 February 2021). Prevalence (adjusted and weighted) increased with age, from 35.8% (35.1-36.5) in those aged 18 to 24 years, to 95.3% (94.6-95.9) in people 75 and over. Antibodies were 30% less likely to be detected in men than women (adjusted OR 0.69, 0.68-0.70), and were higher in people of Asian (OR 1.67 [1.58-1.77]), Black (1.55 [1.41-1.69]), mixed 1.17 [1.06-1.29] and other (1.37 [1.23-1.51]) ethnicities compared with white ethnicity. Workers in hospitality (OR 0.69 [0.63-0.74]) and retail (0.71 [0.67-0.75]) were less likely to have antibodies. Following two doses of Pfizer-BioNTech vaccine, antibody positivity (adjusted for test performance) was 100% (100-100) at all ages except 80 years and older when it was 97.8% (95.9-99.6). For AstraZeneca positivity was over 90% up to age 69, and then 89.2% (88.5-89.9) in 70-79 year olds and 83.6% (78.5-88.3) in those aged 80 and over. Following a single dose of Pfizer-BioNTech positivity ranged from 100.0% (91.1-100.0) in those aged 18-29 to 32.2% (18.2-51.1) in those aged 70-79 years. For AstraZeneca this was 72.2% (68.5-75.9) in the youngest and 46.2% (40.0-52.7) in the oldest age group. <h4>Discussion</h4> The successful roll out of the vaccination programme in England has led to a high proportion of individuals having detectable antibodies, particularly in older age groups and those who have had two doses of vaccine. This is likely to be associated with high levels of protection from severe disease, and possibly from infection. Nonetheless, there remain some key groups with a lower prevalence of antibody, notably unvaccinated younger people, certain minority ethnic groups, those living in deprived areas and workers in some public facing employment. Obtaining improved rates of vaccination in these groups is essential to achieving high levels of protection against the virus through population immunity. <h4>Funding</h4> Department of Health and Social Care in England.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2021/07/18/2021.07.14.21260497.full.pdf; doi:https://doi.org/10.1101/2021.07.14.21260497; html:https://europepmc.org/article/PPR/PPR371282; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR371282&type=FILE&fileName=EMS130807-pdf.pdf&mimeType=application/pdf
+PPR699913,https://doi.org/10.2139/ssrn.4523754,Long-Term Air Pollution Exposure and Risk of SARS-CoV-2 Infection and COVID-19 Severity: A UK-Wide Cohort Study (COVIDENCE UK),"Hajmohammadi H, Talaei M, Fecht D, Wang W, Vivaldi G, Faustini S, Richter AG, Shaheen SO, Martineau AR, Sheikh A, Mudway I, Griffiths CJ.",,No Journal Info,2023,2023-08-01,N,,,,"Background: The association between air quality and risk of SARS-CoV-2 infection is poorly understood. We investigated this association using serological individual-level data adjusting for a wide range of confounders, in a large population-based cohort (COVIDENCE UK).<br><br>Methods: We assessed the associations between long-term (2015–19) nitrogen dioxide (NO2) and fine particulate matter (PM with an aerodynamic diameter of ≤2.5 µm [PM<sub>2.5</sub>]), exposures with SARS-CoV-2 infection, level of antibody response among those infected, and COVID-19 disease severity. We used serological data from 10,489 participants in the COVIDENCE UK cohort, and estimated annual average air pollution exposure at each participant’s home postcode.<br><br>Findings: After controlling for potential confounders, we found a positive association between 5-year NO<sub>2</sub> and PM<sub>2.5</sub> exposures and the risk of seropositivity: a per-unit increase in NO2 (μg/m<sup>3</sup>) was associated with an increasing risk of seropositivity of 0.8% (95% CI 0·2 to 1·5; <i>p</i>-for-trend 0.016). For PM<sub>2.5</sub>, a per-unit increase (μg/m<sup>3</sup>) was associated with an increasing risk of seropositivity of 4.9% (–0·1 to 10·2; <i>p</i>-for-trend 0·051). In addition, we found that NO2 was positively associated with higher antibody titres (<i>p</i>-for-trend 0·013) among seropositive participants, with no evidence of an association for PM<sub>2.5</sub>.<br><br>Interpretation: Our findings suggest that the long-term burden of air pollution increased the risks of SARS-CoV-2 infection and has important implications for future pandemic preparedness. This evidence strengthens the case for reducing long-term air pollution exposures to reduce the vulnerability of individuals to respiratory viruses.<br><br>Funding: NIHR, school of primary care research (SPCR). NIHR ARC North Thames. NIHR Health Protection Research Units in Chemical and Radiation Threats and Hazards and Environmental Exposures and Health, partnerships between Imperial College London and The UK Health Security Agency (UKHSA).Barts Charity (MGU0570, MGU0459, MGU0466).Pharma Nord, the Fischer Family Foundation, DSM Nutritional Products, the Exilarch’s Foundation, the Karl R Pfleger Foundation, the AIM Foundation, Synergy Biologics, Cytoplan, the UK National Institute for Health and Care Research Clinical Research Network (52255; 52257), the Health Data Research UK BREATHE Hub, the UK Research and Innovation Industrial Strategy Challenge Fund (MC_PC_19004), Thornton & Ross, Warburtons, Matthew Isaacs (personal donation), Barbara Boucher (personal donation), and Hyphens Pharma.<br><br>Declaration of Interest: AS is a member of the Scottish Government Chief Medical Officer’s COVID-19 Advisory Group and its Standing Committee on Pandemics. He is also a member of the UK Government’s NERVTAG’s Risk Stratification Subgroup. ARM declares receipt of funding in the last 36 months to support vitamin D research from the following companies who manufacture or sell vitamin D supplements: Pharma Nord, DSM Nutritional Products, Thornton & Ross and Hyphens Pharma. He also declares support for attending meetings from the following companies who manufacture or sell vitamin D supplements: Pharma Nord and Abiogen Pharma. He also declares participation on the Data and Safety Monitoring Board for the Chair, DSMB, VITALITY trial (Vitamin D for Adolescents with HIV to reduce musculoskeletal morbidity and immunopathology). He also declares unpaid work as a Programme Committee member for the Vitamin D Workshop. He also declares receipt of vitamin D capsules for clinical trial use from Pharma Nord, Synergy Biologics and Cytoplan. CJG is supported by the NIHR ARC North Thames. All other authors declare that they have no competing interests.",,doi:https://doi.org/10.2139/ssrn.4523754; html:https://europepmc.org/article/PPR/PPR699913; doi:https://doi.org/10.2139/ssrn.4523754
 PPR436211,https://doi.org/10.1101/2021.12.23.21268276,Risk of myocarditis following sequential COVID-19 vaccinations by age and sex,"Patone M, Mei XW, Handunnetthi L, Dixon S, Zaccardi F, Shankar-Hari M, Watkinson P, Khunti K, Harnden A, Coupland CA, Channon KM, Mills NL, Sheikh A, Hippisley-Cox J.",,No Journal Info,2021,2021-12-25,Y,,,,"<h4>ABSTRACT</h4> In an updated self-controlled case series analysis of 42,200,614 people aged 13 years or more, we evaluate the association between COVID-19 vaccination and myocarditis, stratified by age and sex, including 10,978,507 people receiving a third vaccine dose. Myocarditis risk was increased during 1-28 days following a third dose of BNT162b2 (IRR 2.02, 95%CI 1.40, 2.91). Associations were strongest in males younger than 40 years for all vaccine types with an additional 3 (95%CI 1, 5) and 12 (95% CI 1,17) events per million estimated in the 1-28 days following a first dose of BNT162b2 and mRNA-1273, respectively; 14 (95%CI 8, 17), 12 (95%CI 1, 7) and 101 (95%CI 95, 104) additional events following a second dose of ChAdOx1, BNT162b2 and mRNA-1273, respectively; and 13 (95%CI 7, 15) additional events following a third dose of BNT162b2, compared with 7 (95%CI 2, 11) additional events following COVID-19 infection. An association between COVID-19 infection and myocarditis was observed in all ages for both sexes but was substantially higher in those older than 40 years. These findings have important implications for public health and vaccination policy. <h4>Funding</h4> Health Data Research UK.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCULATIONAHA.122.059970; doi:https://doi.org/10.1101/2021.12.23.21268276; html:https://europepmc.org/article/PPR/PPR436211; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR436211&type=FILE&fileName=EMS141882-pdf.pdf&mimeType=application/pdf
-PPR558630,https://doi.org/10.1101/2022.10.17.22281085,COVID-19 among adults living with HIV: Correlates of mortality in a general population in a resource-limited setting,"Kassanjee R, Davies M, Ngwenya O, Osei-Yeboah R, Jacobs T, Morden E, Timmerman V, Britz S, Mendelson M, Taljaard J, Riou J, Boulle A, Tiffin N, Zinyakatira N.",,No Journal Info,2022,2022-10-17,Y,,,,"<h4>Introduction</h4> While a large proportion of people with HIV (PWH) have experienced SARS-CoV-2 infections, there is uncertainty about the role of HIV disease severity on COVID-19 outcomes, especially in lower income settings. We studied the association between mortality and characteristics of HIV severity and management, and vaccination, among adult PWH. <h4>Methods</h4> We analysed observational cohort data on all PWH aged ≥15 years experiencing a diagnosed SARS-CoV-2 infection (until March 2022), who accessed public sector healthcare in the Western Cape province of South Africa. Logistic regression was used to study the association of mortality with CD4 cell count, viral load, evidence of ART, time since first HIV evidence, and vaccination, adjusting for demographic characteristics, comorbidities, admission pressure, location and time period. <h4>Results</h4> Mortality occurred in 5.7% (95% CI: 5.3,6.0) of 17 831 first diagnosed infections. Higher mortality was associated with lower recent CD4, no evidence of ART collection, high or unknown recent viral load (among those with ART evidence), and recent first HIV evidence, differentially by age. Vaccination was protective. The burden of comorbidities was high, and tuberculosis, chronic kidney disease, diabetes and hypertension were associated with higher mortality, more strongly in younger adults. <h4>Conclusions</h4> Mortality was strongly associated with suboptimal HIV control, and prevalence of these risk factors increased in later COVID-19 waves. It remains a public health priority to ensure PWH are on suppressive ART and vaccinated, and manage any disruptions in care that occurred during the pandemic. The diagnosis and management of comorbidities, including for tuberculosis, should be optimised.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9603837; doi:https://doi.org/10.1101/2022.10.17.22281085; html:https://europepmc.org/article/PPR/PPR558630; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR558630&type=FILE&fileName=EMS155815-pdf.pdf&mimeType=application/pdf
 PPR599577,https://doi.org/10.21203/rs.3.rs-2349826/v1,"COVID-19 Vaccination in Pregnancy: The Impact of Multimorbidity and Smoking Status on Vaccine Hesitancy, a Cohort Study of 25,111 Women in Wales, UK","Mhereeg M, Jones H, Kennedy J, Seaborne M, Parker M, Kennedy N, Akbari A, Zuccolo L, Azcoaga-Lorenzo A, Davies A, Nirantharakumar K, Brophy S.",,No Journal Info,2023,2023-01-18,Y,,,,"<h4>Background: </h4> Multimorbidity and pregnancy are two risk factors for more severe outcomes after a SARS-CoV-2 infection, thus vaccination uptake is important for pregnant women living with multimorbidity. This study aimed to examine the impact of multimorbidity, smoking status, and demographics (age, ethnic group, area of deprivation) on vaccine hesitancy among pregnant women in Wales using electronic health records (EHR) linkage. Methods This cohort study utilised routinely collected, individual-level, anonymised population-scale linked data within the Secure Anonymised Information Linkage (SAIL) Databank. Pregnant women were identified from 13 th April 2021 to 31 st December 2021. Survival analysis was utilised to examine and compare the length of time to vaccination uptake in pregnancy by multimorbidity and smoking status, as well as depression, diabetes, asthma, and cardiovascular conditions independently. Variation in uptake by; multimorbidity, smoking status, and demographics was examined jointly and separately for the independent conditions using hazard ratios (HR) from the Cox regression model. Results Within the population cohort, 8,203 (32.7%) received at least one dose of the COVID-19 vaccine during pregnancy, with 8,572 (34.1%) remaining unvaccinated throughout the follow-up period, and 8,336 (33.2%) receiving the vaccine postpartum. Women aged 30 years or older were more likely to have the vaccine in pregnancy. Those who had depression were slightly but significantly more likely to have the vaccine compared to those without depression (HR = 1.08, 95% CI 1.03 to 1.14, p = 0.02). Women living with multimorbidity were 1.12 times more likely to have the vaccine compared to those living without multimorbidity (HR = 1.12, 95% CI 1.04 to 1.19, p = 0.001). Vaccine uptakes were significantly lower among both current smokers and former smokers compared to never smokers (HR = 0.87, 95% CI 0.81 to 0.94, p < 0.001 and HR = 0.92, 95% CI 0.85 to 0.98, p = 0.015 respectively). Uptake was also lower among those living in the most deprived areas compared to those living in the most affluent areas (HR = 0.89, 95% CI 0.83 to 0.96, p = 0.002). Conclusion Younger women, living without multimorbidity, current and former smokers, and those living in the more deprived areas are less likely to have the vaccine, thus, a targeted approach to vaccinations may be required for these groups. Women living with multimorbidity are slightly but significantly less likely to be hesitant about COVID-19 vaccination when pregnant.",,pdf:https://bmcinfectdis.biomedcentral.com/counter/pdf/10.1186/s12879-023-08555-8; doi:https://doi.org/10.21203/rs.3.rs-2349826/v1; html:https://europepmc.org/article/PPR/PPR599577; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR599577&type=FILE&fileName=EMS163297-pdf.pdf&mimeType=application/pdf
+PPR558630,https://doi.org/10.1101/2022.10.17.22281085,COVID-19 among adults living with HIV: Correlates of mortality in a general population in a resource-limited setting,"Kassanjee R, Davies M, Ngwenya O, Osei-Yeboah R, Jacobs T, Morden E, Timmerman V, Britz S, Mendelson M, Taljaard J, Riou J, Boulle A, Tiffin N, Zinyakatira N.",,No Journal Info,2022,2022-10-17,Y,,,,"<h4>Introduction</h4> While a large proportion of people with HIV (PWH) have experienced SARS-CoV-2 infections, there is uncertainty about the role of HIV disease severity on COVID-19 outcomes, especially in lower income settings. We studied the association between mortality and characteristics of HIV severity and management, and vaccination, among adult PWH. <h4>Methods</h4> We analysed observational cohort data on all PWH aged ≥15 years experiencing a diagnosed SARS-CoV-2 infection (until March 2022), who accessed public sector healthcare in the Western Cape province of South Africa. Logistic regression was used to study the association of mortality with CD4 cell count, viral load, evidence of ART, time since first HIV evidence, and vaccination, adjusting for demographic characteristics, comorbidities, admission pressure, location and time period. <h4>Results</h4> Mortality occurred in 5.7% (95% CI: 5.3,6.0) of 17 831 first diagnosed infections. Higher mortality was associated with lower recent CD4, no evidence of ART collection, high or unknown recent viral load (among those with ART evidence), and recent first HIV evidence, differentially by age. Vaccination was protective. The burden of comorbidities was high, and tuberculosis, chronic kidney disease, diabetes and hypertension were associated with higher mortality, more strongly in younger adults. <h4>Conclusions</h4> Mortality was strongly associated with suboptimal HIV control, and prevalence of these risk factors increased in later COVID-19 waves. It remains a public health priority to ensure PWH are on suppressive ART and vaccinated, and manage any disruptions in care that occurred during the pandemic. The diagnosis and management of comorbidities, including for tuberculosis, should be optimised.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9603837; doi:https://doi.org/10.1101/2022.10.17.22281085; html:https://europepmc.org/article/PPR/PPR558630; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR558630&type=FILE&fileName=EMS155815-pdf.pdf&mimeType=application/pdf
 PPR373622,https://doi.org/10.1101/2021.07.19.21260770,Uptake of infant and pre-school immunisations in Scotland and England during the COVID-19 pandemic: an observational study of routinely collected data,"McQuaid F, Mulholland R, Rai YS, Agrawal U, Bedford H, Claire Cameron J, Gibbons C, Roy P, Sheikh A, Shi T, Simpson CR, Tait J, Tessier E, Turner S, Ortega JV, White J, Wood R.",,No Journal Info,2021,2021-07-22,N,,,,"<h4>Background</h4> In 2020, the COVID-19 pandemic and control measures such as national lockdowns threatened to disrupt routine childhood immunisation programmes. Initial reports from the early weeks of lockdown in the UK and worldwide suggested that uptake could fall putting children at risk from multiple other infectious diseases. In Scotland and England, enhanced surveillance of national data for childhood immunisations was established to inform and rapidly assess the impact of the pandemic on infant and preschool immunisation uptake rates. <h4>Methods and findings</h4> We undertook an observational study using routinely collected data for the year prior to the pandemic (2019), and immediately before, during and after the first period of the UK ‘lockdown’ in 2020. Data were obtained for Scotland from the Public Health Scotland “COVID19 wider impacts on the health care system” dashboard ( https://scotland.shinyapps.io/phs-covid-wider-impact/ ) and for England from ImmForm. Five vaccinations delivered at different ages were evaluated; three doses of the ‘6-in-1’ DTaP/IPV/Hib/HepB vaccine and two doses of MMR. Uptake in the periods in 2020 compared to that in the baseline year of 2019 using binary logistic regression analysis. For Scotland, we analysed timely uptake of immunisations, defined as uptake within four weeks of the child becoming eligible by age for each immunisation and data were also analysed by geographical region and indices of deprivation. For both Scotland and England, we assessed whether immunisations were up to date at approximately 6 months (all doses 6-in-1) and 16-18 months (first MMR) of age. We found that uptake rates within four weeks of eligibility in Scotland for all the five vaccine visits were higher during the 2020 lockdown period than in 2019. The difference ranged from 1.3% for the first dose of the 6-in-1 vaccine (95.3 vs 94%, OR 1.28, CI 1.18-1.39) to 14.3% for the second MMR dose (66.1 vs 51.8 %, OR 1.8, CI 1.74-1.87). Significant increases in uptake were seen across all deprivation levels, though, for MMR, there was evidence of greater improvement for children living in the least deprived areas. In England, fewer children who had been due to receive their immunisations during the lockdown period were up to date at 6 months (6-in-1) or 18 months (first dose MMR). The fall in percentage uptake ranged from 0.5% for first 6-in1 (95.8 vs 96.3%, OR 0.89, CI 0.86-0.91) to 2.1% for third 6-in-1 (86.6 vs 88.7%, OR 0.82, CI 0.81-0.83). <h4>Conclusions</h4> This study suggests that the national lockdown in Scotland was associated with a positive effect on timely childhood immunisation uptake, however in England a lower percentage of children were up to date at 6 and 18 months. Reason for the improve uptake in Scotland may include active measures taken to promote immunisation at local and national level during this period. Promoting immunisation uptake and addressing potential vaccine hesitancy is particularly important given the ongoing pandemic and COVID-19 vaccination campaigns.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003916&type=printable; doi:https://doi.org/10.1101/2021.07.19.21260770; html:https://europepmc.org/article/PPR/PPR373622; doi:https://doi.org/10.1101/2021.07.19.21260770
 PPR506599,https://doi.org/10.1101/2022.06.15.22276423,How acceptable is rapid whole genome sequencing for infectious disease management in hospitals? Perspectives of those involved in managing nosocomial SARS-CoV-2,"Flowers P, McLeod J, Mapp F, Stirrup O, Blackstone J, Snell LB, Peters C, Thomson E, Holmes A, Price J, Partridge D, Shallcross L, de Silva TI, Breuer J.",,No Journal Info,2022,2022-06-16,Y,,,,"<h4>Structured summary</h4> <h4>Background</h4> Whole genome sequencing (WGS) for managing healthcare associated infections (HCAIs) has developed considerably through experiences with SARS-CoV-2. We interviewed various healthcare professionals (HCPs) with direct experience of using WGS in hospitals (within the COG-UK Hospital Onset COVID-19 Infection (HOCI) study) to explore its acceptability and future use. <h4>Method</h4> An exploratory, cross-sectional, qualitative design employed semi-structured interviews with 39 diverse HCPs between December 2020 and June 2021. Participants were recruited from five sites within the larger clinical study of a novel genome sequencing reporting tool for SARS-CoV-2 (the HOCI study). All had experience, in their diverse roles, of using sequencing data to manage nosocomial SARS-CoV-2 infection. Deductive and inductive thematic analysis identified themes exploring aspects of the acceptability of sequencing. <h4>Findings</h4> The analysis highlighted the overall acceptability of rapid WGS for infectious disease using SARS-CoV-2 as a case study. Diverse professionals were largely very positive about its future use and believed that it could become a valuable and routine tool for managing HCAIs. We identified three key themes ‘1) ‘Proof of concept achieved’; 2) ‘Novel insights and implications’; and 3) ‘Challenges and demands’. <h4>Conclusion</h4> Our qualitative analysis, drawn from five diverse hospitals, shows the broad acceptability of rapid sequencing and its potential. Participants believed it could and should become an everyday technology capable of being embedded within typical hospital processes and systems. However, its future integration into existing healthcare systems will not be without challenges (e.g., resource, multi-level change) warranting further mixed methods research.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/06/16/2022.06.15.22276423.full.pdf; doi:https://doi.org/10.1101/2022.06.15.22276423; html:https://europepmc.org/article/PPR/PPR506599; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR506599&type=FILE&fileName=EMS146081-pdf.pdf&mimeType=application/pdf
 PPR417646,https://doi.org/10.21203/rs.3.rs-1051010/v1,COVID-19 vaccination rates and SARS-CoV-2 infection in pregnant women in Scotland,"Stock S, Carruthers J, Calvert C, Denny C, Donaghy J, Goulding A, Hopcroft L, Hopkins L, McLaughlin T, Pan J, Shi T, Taylor J, Agrawal U, Auyeung B, Katikireddi S, McCowan C, Murray J, Simpson C, Robertson C, Vasileiou E, Sheikh A, Wood R.",,No Journal Info,2021,2021-11-09,Y,,,,"We describe SARS-CoV-2 infection and COVID-19 vaccine uptake in Scotland in a prospective cohort of all pregnant women in Scotland drawn from national databases. As of mid-October 2021, the Covid-19 in pregnancy in Scotland (COPS) cohort included linked data on a total of 139,136 pregnancies in 126,749 women. Up to September 30, 2021, a total of 22,779 COVID-19 vaccinations had been administered to 16,229 pregnant women. Vaccine coverage was substantially lower in pregnant women than in the general female population of reproductive age (23.7% of women giving birth in September 2021 were fully vaccinated compared to 74.9 % in women 18-44 years). Of the 4,274 cases of COVID-19 in pregnancy (confirmed by SARS-CoV-2 viral reverse transcriptase polymerase chain reaction) between December 2020 (the month the COVID-19 vaccination programme started in Scotland) and September 2021 inclusive, 629 women (14.7%) were admitted to hospital and 89 (2.1%) were admitted to critical care. Of the COVID-19 cases occurring in pregnant women, 81.7% (3,491/4,274; 95% CI 80.5-82.8) were in unvaccinated women. Of the COVID-19 associated hospital admissions, 93.0% (585/629; 95% CI 90.7-94.8) were in women who were unvaccinated at the time of COVID-19 diagnosis. Of the COVID-19 associated critical care admissions 98.9% (88/89; 95% CI 93.9-100) were in women who were unvaccinated at the time of COVID-19 diagnosis. The extended perinatal mortality rate for women who gave birth within 28 days of COVID-19 diagnosis was 15.9 per 1000 births (95% CI 7.8 to 31.0; background rate in 2020 6.3 per 1,000 total births [95% CI 5.7-7.1]; background rate 2019 5.7 per 1,000 total births [95% CI 5.0-6.4]). All baby deaths occurred after pregnancies in women who were unvaccinated at the time of COVID-19 diagnosis. Addressing low vaccine uptake rates in pregnant women is imperative to protect the health of women and babies.",,pdf:https://www.nature.com/articles/s41591-021-01666-2.pdf; doi:https://doi.org/10.21203/rs.3.rs-1051010/v1; html:https://europepmc.org/article/PPR/PPR417646; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR417646&type=FILE&fileName=EMS138218-pdf.pdf&mimeType=application/pdf
@@ -133,8 +133,8 @@ PPR601887,https://doi.org/10.2139/ssrn.4052647,Using National Electronic Health
 PPR538705,https://doi.org/10.1101/2022.08.30.22279427,A qualitative process evaluation using the behaviour change wheel approach: Did a whole genome sequence report form (SRF) used to reduce nosocomial SARS-CoV-2 within UK hospitals operate as anticipated?,"Flowers P, Leiser R, Mapp F, McLeod J, Stirrup O, Illingworth CJ, Blackstone J, Breuer J.",,No Journal Info,2022,2022-09-01,Y,,,,"<h4>Purpose</h4> To conduct a process evaluation of a whole genome sequence report form (SRF) used to reduce nosocomial SARS-CoV-2 through changing infection prevention and control (IPC) behaviours. Here using qualitative behavioural analyses we report how the SRF worked. <h4>Methods</h4> Prior to a multisite non-randomised trial of its effectiveness, the SRF was coded in relation to its putative behaviour change content (using the theoretical domains framework (TDF), the behaviour change wheel (BCW) and the behaviour change technique taxonomy (BCTTv1)). After the SRF had been used, through the peak of the Alpha variant, we conducted in-depth interviews from diverse professional staff (N=39) from a heterogeneous purposive sub-sample of hospital trial sites (n=5/14). Deductive thematic analysis explored participants’ accounts of using the SRF according to its putative content in addition to inductive exploration of their experiences. <h4>Results</h4> We found empirical support for the putative theoretical mechanisms of ‘Knowledge’ and ‘Behavioural regulation’, as well as for intervention functions of ‘Education’ and ‘Persuasion’ and ‘Enablement’, and for particular BCTs ‘1.2 Problem solving’, ‘2.6 Biofeedback’, ‘2.7 Feedback on outcomes of behaviour’, and ‘7.1 Prompts and cues’. Most participants found the SRF useful and believed it could shape IPC behaviour. <h4>Conclusions</h4> Our process evaluation of the SRF provided granular and general support for the SRF working to change IPC behaviours. Our analysis highlighted useful SRF content. However, we also note that, without complementary work on systematically embedding the SRF within routine practice and wider hospital systems, it may not reach its full potential to reduce nosocomial infection. <h4>What is already known on this subject?</h4> Health psychology remains under-exploited within infection prevention and control (IPC) interventions For genomic insights to be understood by a range of health care professionals and elicit changes in IPC behaviour, ways of translating complex genomic insights into a simple format are needed. These simple translation tools can be described as whole genome sequence report forms (SRFs) Nothing is currently known about the use of SRFs, for SARS-CoV-2 or other infections, to change hospital-based IPC behaviour. Health psychological tools such as the behaviour change wheel (BCW), the theoretical domains framework (TDF), and the behaviour change technique taxonomy (BCTTv1) are widely used to develop behaviour change interventions but are rarely used to evaluate them Contemporary guidance on conducting process evaluations highlights the value of explicitly theorising how an intervention is intended to work before systematically examining how it actually worked in practice <h4>What does this study add?</h4> The paper presents a novel worked example of using tools from health psychology within a qualitative process evaluation of using an SRF during the COVID-19 pandemic in UK hospitals This paper is the first to report how people experienced using whole genome sequence report forms (SRFs) in order to change hospital-based IPC behaviour We provide qualitative evidence detailing empirical support for much of the SRF’s putative content, including casual mechanisms ‘Knowledge’ and ‘Behavioural regulation’, intervention functions such as ‘Education’ and ‘Enablement’, and for particular BCTs: ‘1.2 Problem solving’, ‘2.6 Biofeedback’, ‘2.7 Feedback on outcomes of behaviour’, and ‘7.1 Prompts and cues’",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/09/01/2022.08.30.22279427.full.pdf; doi:https://doi.org/10.1101/2022.08.30.22279427; html:https://europepmc.org/article/PPR/PPR538705; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR538705&type=FILE&fileName=EMS153681-pdf.pdf&mimeType=application/pdf
 PPR453191,https://doi.org/10.1101/2022.02.10.22270799,Evaluating the effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control teams: the COG-UK hospital-onset COVID-19 infection study,"Stirrup O, Blackstone J, Mapp F, MacNeil A, Panca M, Holmes A, Machin N, Shin GY, Mahungu T, Saeed K, Saluja T, Taha Y, Mahida N, Pope C, Chawla A, Cutino-Moguel M, Tamuri A, Williams R, Darby A, Robertson D, Flaviani F, Nastouli E, Robson S, Smith D, Loose M, Laing K, Monahan I, Kele B, Haldenby S, George R, Bashton M, Witney A, Byott M, Coll F, Chapman M, Peacock S, COG-UK HOCI Investigators, The COVID-19 Genomics UK (COG-UK) consortium, Hughes J, Nebbia G, Partridge DG, Parker M, Price J, Peters C, Roy S, Snell LB, de Silva TI, Thomson E, Flowers P, Copas A, Breuer J.",,No Journal Info,2022,2022-02-13,Y,,,,"<h4>Introduction</h4> Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings. <h4>Methods</h4> We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data-collection period, followed by intervention periods comprising 8 weeks of ‘rapid’ (<48h) and 4 weeks of ‘longer-turnaround’ (5-10 day) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital onset COVID-19 infections (HOCIs; detected ≥48h from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on incidence of probable/definite hospital-acquired infections (HAIs) was evaluated. <h4>Results</h4> A total of 2170 HOCI cases were recorded from October 2020-April 2021, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (IRR 1.60, 95%CI 0.85-3.01; P= 0.14) or rapid (0.85, 0.48-1.50; P= 0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8% and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2% and 11.6% of cases where the report was returned. In a per-protocol sensitivity analysis there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. <h4>Conclusion</h4> While we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days.",,doi:https://doi.org/10.7554/elife.78427; doi:https://doi.org/10.1101/2022.02.10.22270799; html:https://europepmc.org/article/PPR/PPR453191; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR453191&type=FILE&fileName=EMS143624-pdf.pdf&mimeType=application/pdf
 PPR254798,https://doi.org/10.1101/2020.12.15.20248244,REACT-1 round 7 updated report: regional heterogeneity in changes in prevalence of SARS-CoV-2 infection during the second national COVID-19 lockdown in England,"Riley S, Walters CE, Wang H, Eales O, Ainslie KEC, Atchinson C, Fronterre C, Diggle PJ, Ashby D, Donnelly CA, Cooke G, Barclay W, Ward H, Darzi A, Elliott P.",,No Journal Info,2020,2020-12-16,Y,,,,"<h4>Background: </h4> England exited a four-week second national lockdown on 2nd December 2020 initiated in response to the COVID-19 pandemic. Prior results showed that prevalence dropped during the first half of lockdown, with greater reductions in higher-prevalence northern regions.  Methods REACT-1 is a series of community surveys of SARS-CoV-2 RT-PCR swab-positivity in England, designed to monitor the spread of the epidemic and thus increase situational awareness. Round 7 of REACT-1 commenced swab-collection on 13th November 2020. A prior interim report included data from 13th to 24th November 2020 for 105,122 participants. Here, we report data for the entire round with swab results obtained up to 3rd December 2020.  Results Between 13th November and 3rd December (round 7) there were 1,299 positive swabs out of 168,181 giving a weighted prevalence of 0.94% (95% CI 0.87%, 1.01%) or 94 per 10,000 people infected in the community in England. This compares with a prevalence of 1.30% (1.21%, 1.39%) from 16th October to 2nd November 2020 (round 6), a decline of 28%. Prevalence during the latter half of round 7 was 0.91% (95% CI, 0.81%, 1.03%) compared with 0.96% (0.87%, 1.05%) in the first half. The national R number in round 7 was estimated at 0.96 (0.88, 1.03) with a decline in prevalence observed during the first half of this period no longer apparent during the second half at the end of lockdown. During round 7 there was a marked fall in prevalence in West Midlands, a levelling off in some regions and a rise in London. R numbers at regional level ranged from 0.60 (0.41, 0.80) in West Midlands up to 1.27 (1.04, 1.54) in London, where prevalence was highest in the east and south-east of the city. Nationally, between 13th November and 3rd December, the highest prevalence was in school-aged children especially at ages 13-17 years at 2.04% (1.69%, 2.46%), or approximately 1 in 50.  Conclusion Between the previous round and round 7 (during lockdown), there was a fall in prevalence of SARS-CoV-2 swab-positivity nationally, but it did not fall uniformly over time or by geography. Continued vigilance is required to reduce rates of infection until effective immunity at the population level can be achieved through the vaccination programme.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2020/12/16/2020.12.15.20248244.full.pdf; doi:https://doi.org/10.1101/2020.12.15.20248244; html:https://europepmc.org/article/PPR/PPR254798; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR254798&type=FILE&fileName=EMS108699-pdf.pdf&mimeType=application/pdf
-PPR225520,https://doi.org/10.1101/2020.10.12.20211227,High and increasing prevalence of SARS-CoV-2 swab positivity in England during end September beginning October 2020: REACT-1 round 5 updated report,"Riley S, Ainslie KEC, Eales O, Walters CE, Wang H, Atchison C, Fronterre C, Diggle PJ, Ashby D, Donnelly CA, Cooke G, Barclay W, Ward H, Darzi A, Elliott P.",,No Journal Info,2020,2020-10-14,Y,,,,"<h4>Background</h4> REACT-1 is quantifying prevalence of SARS-CoV-2 infection among random samples of the population in England based on PCR testing of self-administered nose and throat swabs. Here we report results from the fifth round of observations for swabs collected from the 18th September to 5th October 2020. This report updates and should be read alongside our round 5 interim report. <h4>Methods</h4> Representative samples of the population aged 5 years and over in England with sample size ranging from 120,000 to 175,000 people at each round. Prevalence of PCR-confirmed SARS-CoV-2 infection, estimation of reproduction number (R) and time trends between and within rounds using exponential growth or decay models. <h4>Results</h4> 175,000 volunteers tested across England between 18th September and 5th October. Findings show a national prevalence of 0.60% (95% confidence interval 0.55%, 0.71%) and doubling of the virus every 29 (17, 84) days in England corresponding to an estimated national R of 1.16 (1.05, 1.27). These results correspond to 1 in 170 people currently swab-positive for the virus and approximately 45,000 new infections each day. At regional level, the highest prevalence is in the North West, Yorkshire and The Humber and the North East with strongest regional growth in North West, Yorkshire and The Humber and West Midlands. <h4>Conclusion</h4> Rapid growth has led to high prevalence of SARS-CoV-2 virus in England, with highest rates in the North of England. Prevalence has increased in all age groups, including those at highest risk. Improved compliance with existing policy and, as necessary, additional interventions are required to control the spread of SARS-CoV-2 in the community and limit the numbers of hospital admissions and deaths from COVID-19.",,doi:https://doi.org/10.1101/2020.10.12.20211227; doi:https://doi.org/10.1101/2020.10.12.20211227; html:https://europepmc.org/article/PPR/PPR225520; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR225520&type=FILE&fileName=EMS98335-pdf.pdf&mimeType=application/pdf
 PPR276226,https://doi.org/10.1101/2021.01.28.21250606,REACT-1 round 8 final report: high average prevalence with regional heterogeneity of trends in SARS-CoV-2 infection in the community in England during January 2021,"Riley S, Eales O, Walters CE, Wang H, Ainslie KEC, Atchison C, Fronterre C, Diggle PJ, Ashby D, Donnelly CA, Cooke G, Barclay W, Ward H, Darzi A, Elliott P.",,No Journal Info,2021,2021-01-31,Y,,,,"In early January 2021, England entered its third national lockdown of the COVID-19 pandemic to reduce numbers of deaths and pressure on healthcare services, while rapidly rolling out vaccination to healthcare workers and those most at risk of severe disease and death. REACT-1 is a survey of SARS-CoV-2 prevalence in the community in England, based on repeated cross-sectional samples of the population. Between 6th and 22nd January 2021, out of 167,642 results, 2,282 were positive giving a weighted national prevalence of infection of 1.57% (95% CI, 1.49%, 1.66%). The R number nationally over this period was estimated at 0.98 (0.92, 1.04). Prevalence remained high throughout, but with suggestion of a decline at the end of the study period. The average national trend masked regional heterogeneity, with robustly decreasing prevalence in one region (South West) and increasing prevalence in another (East Midlands). Overall prevalence at regional level was highest in London at 2.83% (2.53%, 3.16%). Although prevalence nationally was highest in the low-risk 18 to 24 year old group at 2.44% (1.96%, 3.03%), it was also high in those over 65 years who are most at risk, at 0.93% (0.82%, 1.05%). Large household size, living in a deprived neighbourhood, and Black and Asian ethnicity were all associated with higher levels of infections compared to smaller households, less deprived neighbourhoods and other ethnicities. Healthcare and care home workers, and other key workers, were more likely to test positive compared to other workers. If sustained lower prevalence is not achieved rapidly in England, pressure on healthcare services and numbers of COVID-19 deaths will remain unacceptably high.",,doi:https://doi.org/10.1101/2021.01.28.21250606; doi:https://doi.org/10.1101/2021.01.28.21250606; html:https://europepmc.org/article/PPR/PPR276226; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR276226&type=FILE&fileName=EMS115605-pdf.pdf&mimeType=application/pdf
+PPR225520,https://doi.org/10.1101/2020.10.12.20211227,High and increasing prevalence of SARS-CoV-2 swab positivity in England during end September beginning October 2020: REACT-1 round 5 updated report,"Riley S, Ainslie KEC, Eales O, Walters CE, Wang H, Atchison C, Fronterre C, Diggle PJ, Ashby D, Donnelly CA, Cooke G, Barclay W, Ward H, Darzi A, Elliott P.",,No Journal Info,2020,2020-10-14,Y,,,,"<h4>Background</h4> REACT-1 is quantifying prevalence of SARS-CoV-2 infection among random samples of the population in England based on PCR testing of self-administered nose and throat swabs. Here we report results from the fifth round of observations for swabs collected from the 18th September to 5th October 2020. This report updates and should be read alongside our round 5 interim report. <h4>Methods</h4> Representative samples of the population aged 5 years and over in England with sample size ranging from 120,000 to 175,000 people at each round. Prevalence of PCR-confirmed SARS-CoV-2 infection, estimation of reproduction number (R) and time trends between and within rounds using exponential growth or decay models. <h4>Results</h4> 175,000 volunteers tested across England between 18th September and 5th October. Findings show a national prevalence of 0.60% (95% confidence interval 0.55%, 0.71%) and doubling of the virus every 29 (17, 84) days in England corresponding to an estimated national R of 1.16 (1.05, 1.27). These results correspond to 1 in 170 people currently swab-positive for the virus and approximately 45,000 new infections each day. At regional level, the highest prevalence is in the North West, Yorkshire and The Humber and the North East with strongest regional growth in North West, Yorkshire and The Humber and West Midlands. <h4>Conclusion</h4> Rapid growth has led to high prevalence of SARS-CoV-2 virus in England, with highest rates in the North of England. Prevalence has increased in all age groups, including those at highest risk. Improved compliance with existing policy and, as necessary, additional interventions are required to control the spread of SARS-CoV-2 in the community and limit the numbers of hospital admissions and deaths from COVID-19.",,doi:https://doi.org/10.1101/2020.10.12.20211227; doi:https://doi.org/10.1101/2020.10.12.20211227; html:https://europepmc.org/article/PPR/PPR225520; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR225520&type=FILE&fileName=EMS98335-pdf.pdf&mimeType=application/pdf
 PPR160431,https://doi.org/10.1101/2020.05.05.20092296,Ethnicity and risk of death in patients hospitalised for COVID-19 infection in the UK: an observational cohort study in an urban catchment area,"Sapey E, Gallier S, Mainey C, Nightingale P, McNulty D, Crothers H, Evison F, Reeves K, Pagano D, Denniston A, Nirantharakumar K, Diggle P, Ball S.",,No Journal Info,2020,2020-05-09,N,,,,"<h4>Background</h4> Studies suggest that certain Black and Asian Minority Ethnic groups experience poorer outcomes from COVID-19 but these studies have not provided insight into potential reasons for this. We hypothesised that outcomes would be poorer for those of South Asian ethnicity hospitalised from a confirmed SARS-CoV-2 infection, once confounding factors, health seeking behaviours and community demographics were considered and that this might reflect a more aggressive disease course in these patients. <h4>Methods</h4> Patients with confirmed SARS-CoV-2 infection requiring admission to University Hospitals Birmingham NHS Foundation Trust(UHB) in Birmingham UK between 10 th March 2020-17 th April 2020 were included. Standardised Admission Ratio(SAR) and Standardised Mortality Ratio(SMR) were calculated using observed COVID-19 admissions/deaths and 2011 census data. Hazard Ratio (aHR) for mortality was estimated using Cox proportional hazard model adjusting and propensity score matching. <h4>Results</h4> All patients admitted to UHB with COVID-19 during the study period were included (2217 in total). Fifty-eight percent were male, 69.5% White and the majority (80.2%) had co-morbidities. Eighteen and a half percent were of South Asian ethnicity, and these patients were more likely to be younger, have no co-morbidities but twice the prevalence of diabetes than White patients. SAR and SMR suggested more admissions and deaths in South Asian patients than would be predicted and they were more likely to present with severe disease despite no delay in presentation since symptom onset. South Asian ethnicity was associated with an increased risk of death; both by Cox regression (Hazard Ratio 1.4 (95%CI 1.2–1.8) after adjusting for age, sex, deprivation and comorbidities and by propensity score matching, matching for the same factors but categorising ethnicity into South Asian or not (Hazard ratio 1.3 (1.0-1.6)). <h4>Conclusions</h4> Those of South Asian ethnicity appear at risk of worse COVID-19 outcomes, further studies need to establish the underlying mechanistic pathways.","The objective of this study was to determine if specific ethnic groups are at higher risk of dying from covid-19 infection. They found that those of South Asian ethnicity may be at risk of worse COVID-19 outcomes. However, further studies are required to understand this better.",pdf:https://bmjopenrespres.bmj.com/content/bmjresp/7/1/e000644.full.pdf; doi:https://doi.org/10.1101/2020.05.05.20092296; html:https://europepmc.org/article/PPR/PPR160431; doi:https://doi.org/10.1101/2020.05.05.20092296
 PPR602604,https://doi.org/10.2139/ssrn.4244745,The Effect of the COVID-19 Pandemic on the Treated Incidence of Psychotic Disorders in South London,"Spinazzola E, Meyer Z, Gray Z, Azlan A, Wratten C, Rayat M, Hiscott L, Kyriacou L, Cottrell D, Pritchard M, Quattrone A, Stewart R, Forti MD, Murray R, Quattrone D.",,No Journal Info,2022,2022-11-08,N,,,,"Background: The impact of the COVID-19 pandemic on the incidence of psychotic disorders has not yet been investigated. We, therefore, carried out an incidence study to ascertain rates of first-episode psychosis (FEP) before and during the COVID-19 pandemic in South London. <br><br>Methods: We screened the clinical records of all individuals living in the London boroughs of Southwark and Lambeth who were referred to the early intervention in psychosis services before (from 1 March 2019 to 28 February 2020) and during (from 1 March 2020 to 28 February 2021) the COVID-19 pandemic. We used Office for National Statistics (ONS) data to estimate the risk populations stratified by sex and age group. We computed crude and sex-age standardised FEP incidence per 100,000 persons-year. We used Poisson regression to calculate the incidence rate ratio (IRR) before and during the COVID-19 pandemic and to examine the incidence variation by sociodemographic factors. <br><br>Findings:  A total of 321 incident cases of FEP were identified during the COVID-19 pandemic accounting for a crude rate of 70·1 (95% CI 62·39 - 77·73) per 100,000 person-year. The crude rate for the year before was 47·5 (95% CI 41·25 - 53·81). The incidence variation between the two years accounted for an adjusted IRR of 1·46 (95% CI 1·23 – 1·76).  <br><br>Interpretation: The pandemic resulted in a 46% spike in the rates of first-episode psychosis. This finding should inform public health research and demonstrates the need for adequate resources for mental health secondary services. <br><br>Funding: DQ is supported by MRC/UKRI CARP (MRC CARP grant MR/W030608/1). ES and MDF are supported by MRC SRF Fellowship to MDF (MRC MR/T007818/1). RMM and RS are supported by NIHR BRC at SLaM and KCL. RS is further supported by NIHR ARC South London and DATAMIND HDR UK Mental Health Data Hub (MRC grant MR/W014386).<br><br>Declaration of Interest: None to declare. <br><br>Ethical Approval: CRIS is an anonymised system for analysing patient data, which was granted ethical approval by the Oxfordshire Research Ethics Committee (reference 08/H0606/71). All information accessed and analysed in CRIS is regularly monitored and audited. Ethical approval for this study was granted by the CRIS Oversight Committee (reference 20-061 to DQ).",,doi:https://doi.org/10.2139/ssrn.4244745; html:https://europepmc.org/article/PPR/PPR602604; doi:https://doi.org/10.2139/ssrn.4244745
 PPR525831,https://doi.org/10.1101/2022.07.29.22278186,Comparative effectiveness of BNT162b2 versus mRNA-1273 boosting in England: a cohort study in OpenSAFELY-TPP,"Hulme WJ, Horne EM, Parker EP, Keogh RH, Williamson EJ, Walker V, Palmer T, Curtis HJ, Walker A, Mehrkar A, Morley J, MacKenna B, Bacon SC, Goldacre B, Hernán MA, Sterne JA, the OpenSAFELY collaborative.",,No Journal Info,2022,2022-07-30,Y,,,,"<h4>Introduction</h4> The COVID-19 booster vaccination programme in England used both BNT162b2 and mRNA-1273 vaccines. Direct comparisons of the effectiveness against severe COVID-19 of these two vaccines for boosting have not been made in trials or observational data. <h4>Methods</h4> On behalf of NHS England, we used the OpenSAFELY-TPP database to match adult recipients of each vaccine type on date of vaccination, primary vaccine course, age, and other characteristics. Recipients were eligible if boosted between 29 October 2021 and 31 January 2022, and followed up for 12 weeks. Outcomes were positive SARS-CoV-2 test, COVID-19 hospitalisation, and COVID-19 death. We estimated the cumulative incidence of each outcome, and quantified comparative effectiveness using risk differences (RD) and hazard ratios (HRs). <h4>Results</h4> 1,528,431 people were matched in each group, contributing a total 23,150,504 person-weeks of follow-up. The 12-week risks per 1,000 people of positive SARS-CoV-2 test were 103.2 (95%CI 102.4 to 104.0) for BNT162b2 and 96.0 (95.2 to 96.8) for mRNA-1273: the HR comparing mRNA-1273 with BNT162b2 was 0.92 (95%CI 0.91 to 0.92). For COVID-19 hospitalisations the 12-week risks per 1,000 were 0.65 (95%CI 0.56 to 0.75) and 0.44 (0.36 to 0.54): HR 0.67 (95%CI 0.58 to 0.78). COVID-19 deaths were rare: the 12-week risks per 1,000 were 0.03 (95%CI 0.02 to 0.06) and 0.01 (0.01 to 0.02): HR 1.23 (95%CI 0.59 to 2.56). Comparative effectiveness was generally similar within subgroups defined by the primary course vaccine brand, age, prior SARS-CoV-2 infection and clinical vulnerability. <h4>Conclusion</h4> Booster vaccination with mRNA-1273 COVID-19 vaccine was more effective than BNT162b2 in preventing SARS-CoV-2 infection and COVID-19 hospitalisation during the first 12 weeks after vaccination, during a period of Delta followed by Omicron variant dominance.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/07/30/2022.07.29.22278186.full.pdf; doi:https://doi.org/10.1101/2022.07.29.22278186; html:https://europepmc.org/article/PPR/PPR525831; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR525831&type=FILE&fileName=EMS151978-pdf.pdf&mimeType=application/pdf
@@ -143,8 +143,8 @@ PPR526793,https://doi.org/10.1101/2022.07.30.22278161,Changes in COVID-19-relate
 PPR393002,https://doi.org/10.1101/2021.09.02.21262979,"REACT-1 round 13 final report: exponential growth, high prevalence of SARS-CoV-2 and vaccine effectiveness associated with Delta variant in England during May to July 2021","Elliott P, Haw D, Wang H, Eales O, Walters CE, Ainslie KEC, Atchison C, Fronterre C, Diggle PJ, Page AJ, Trotter AJ, Prosolek SJ, The COVID-19 Genomics UK (COG-UK) Consortium, Ashby D, Donnelly CA, Barclay W, Taylor G, Cooke G, Ward H, Darzi A, Riley S.",,No Journal Info,2021,2021-09-10,Y,,,,"<h4>Background</h4> The prevalence of SARS-CoV-2 infection continues to drive rates of illness and hospitalisations despite high levels of vaccination, with the proportion of cases caused by the Delta lineage increasing in many populations. As vaccination programs roll out globally and social distancing is relaxed, future SARS-CoV-2 trends are uncertain. <h4>Methods</h4> We analysed prevalence trends and their drivers using reverse transcription-polymerase chain reaction (RT-PCR) swab-positivity data from round 12 (between 20 May and 7 June 2021) and round 13 (between 24 June and 12 July 2021) of the REal-time Assessment of Community Transmission-1 (REACT-1) study, with swabs sent to non-overlapping random samples of the population ages 5 years and over in England. <h4>Results</h4> We observed sustained exponential growth with an average doubling time in round 13 of 25 days (lower Credible Interval of 15 days) and an increase in average prevalence from 0.15% (0.12%, 0.18%) in round 12 to 0.63% (0.57%, 0.18%) in round 13. The rapid growth across and within rounds appears to have been driven by complete replacement of Alpha variant by Delta, and by the high prevalence in younger less-vaccinated age groups, with a nine-fold increase between rounds 12 and 13 among those aged 13 to 17 years. Prevalence among those who reported being unvaccinated was three-fold higher than those who reported being fully vaccinated. However, in round 13, 44% of infections occurred in fully vaccinated individuals, reflecting imperfect vaccine effectiveness against infection despite high overall levels of vaccination. Using self-reported vaccination status, we estimated adjusted vaccine effectiveness against infection in round 13 of 49% (22%, 67%) among participants aged 18 to 64 years, which rose to 58% (33%, 73%) when considering only strong positives (Cycle threshold [Ct] values < 27); also, we estimated adjusted vaccine effectiveness against symptomatic infection of 59% (23%, 78%), with any one of three common COVID-19 symptoms reported in the month prior to swabbing. Sex (round 13 only), ethnicity, household size and local levels of deprivation jointly contributed to the risk of higher prevalence of swab-positivity. <h4>Discussion</h4> From end May to beginning July 2021 in England, where there has been a highly successful vaccination campaign with high vaccine uptake, infections were increasing exponentially driven by the Delta variant and high infection prevalence among younger, unvaccinated individuals despite double vaccination continuing to effectively reduce transmission. Although slower growth or declining prevalence may be observed during the summer in the northern hemisphere, increased mixing during the autumn in the presence of the Delta variant may lead to renewed growth, even at high levels of vaccination.",,pdf:https://www.science.org/history/7d0b03b2-b465-410e-a40d-7300157d8b54/science.abl9551.v1.pdf; doi:https://doi.org/10.1101/2021.09.02.21262979; html:https://europepmc.org/article/PPR/PPR393002; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR393002&type=FILE&fileName=EMS134814-pdf.pdf&mimeType=application/pdf
 PPR511151,https://doi.org/10.1101/2022.06.06.22276026,Effectiveness of BNT162b2 booster doses in England: an observational study in OpenSAFELY-TPP,"Hulme WJ, Williamson EJ, Horne E, Green A, Nab L, Keogh R, Parker EP, Walker V, Palmer T, Curtis H, Wiedemann M, Cunningham C, Walker AJ, Fisher L, MacKenna B, Rentsch CT, Schultze A, Bhaskaran K, Tazare J, Tomlinson L, McDonald HI, Morton CE, Croker R, Andrews C, Parks R, Hopcroft L, Massey J, Morley J, Mehrkar A, Bacon S, Evans D, Inglesby P, Hickman G, Davy S, Dillingham I, Ward T, Mahalingasivam V, Zheng B, Douglas IJ, Evans SJ, Bates C, Sterne JA, Hernán MA, Goldacre B.",,No Journal Info,2022,2022-06-06,Y,,,,"<h4>Background</h4> The UK COVID-19 vaccination programme delivered its first “booster” doses in September 2021, initially in groups at high risk of severe disease then across the adult population. The BNT162b2 Pfizer-BioNTech vaccine was used initially, with Moderna mRNA-1273 subsequently also used. <h4>Methods</h4> We used the OpenSAFELY-TPP database, covering 40% of English primary care practices and linked to national coronavirus surveillance, hospital episodes, and death registry data, to estimate the effectiveness of boosting with BNT162b2 compared with no boosting in eligible adults who had received two primary course vaccine doses between 16 September and 16 December 2021 when the Delta variant of SARS-CoV-2 was dominant. Follow up was for up to 10 weeks. Each booster recipient was matched with an unboosted control on factors relating to booster priority status and prior immunisation. Additional factors were adjusted for in Cox models estimating hazard ratios (HRs). Outcomes were positive SARS-CoV-2 test, COVID-19 hospitalisation, COVID-19 death and non-COVID-9 death. Booster vaccine effectiveness was defined as 1−HR. <h4>Results</h4> Among 4,352,417 BNT162b2 booster recipients matched with unboosted controls, estimated effectiveness of a booster dose compared with two doses only was 50.7% (95% CI 50.1-51.3) for positive SARS-CoV-2 test, 80.1% (78.3-81.8) for COVID-19 hospitalisation, 88.5% (85.0-91.1) for COVID-19 death, and 80.3% (79.0-81.5) for non-COVID-19 death. Estimated effectiveness was similar among those who had received a BNT162b2 or ChAdOx1-S two-dose primary vaccination course, but effectiveness against severe COVID-19 was slightly lower in those classified as clinically extremely vulnerable (76.3% (73.1-79.1) for COVID-19 hospitalisation, and 85.1% (79.6-89.1) for COVID-19 death). Estimated effectiveness against each outcome was lower in those aged 18-65 years than in those aged 65 and over. <h4>Conclusion</h4> Our findings are consistent with strong protection of BNT162b2 boosting against positive SARS-CoV-2 test, COVID-19 hospitalisation, and COVID-19 death.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/06/06/2022.06.06.22276026.full.pdf; doi:https://doi.org/10.1101/2022.06.06.22276026; html:https://europepmc.org/article/PPR/PPR511151; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR511151&type=FILE&fileName=EMS149933-pdf.pdf&mimeType=application/pdf
 PPR411044,https://doi.org/10.1101/2021.10.14.21264965,REACT-1 study round 14: High and increasing prevalence of SARS-CoV-2 infection among school-aged children during September 2021 and vaccine effectiveness against infection in England,"Chadeau-Hyam M, Wang H, Eales O, Haw D, Bodinier B, Whitaker M, Walters CE, Ainslie KEC, Atchison C, Fronterre C, Diggle PJ, Page AJ, Trotter AJ, The COVID-19 Genomics UK (COG-UK) Consortium, Ashby D, Barclay W, Taylor G, Cooke G, Ward H, Darzi A, Riley S, Donnelly CA, Elliott P.",,No Journal Info,2021,2021-10-22,Y,,,,"<h4>Background</h4> England experienced a third wave of the COVID-19 epidemic from end May 2021 coinciding with the rapid spread of Delta variant. Since then, the population eligible for vaccination against COVID-19 has been extended to include all 12-15-year-olds, and a booster programme has been initiated among adults aged 50 years and over, health care and care home workers, and immunocompromised people. Meanwhile, schoolchildren have returned to school often with few COVID-19-related precautions in place. <h4>Methods</h4> In the REal-time Assessment of Community Transmission-1 (REACT-1) study, throat and nose swabs were sent to non-overlapping random samples of the population aged 5 years and over in England. We analysed prevalence of SARS-CoV-2 using reverse transcription-polymerase chain reaction (RT-PCR) swab-positivity data from REACT-1 round 14 (between 9 and 27 September 2021). We combined results for round 14 with round 13 (between 24 June and 12 July 2021) and estimated vaccine effectiveness and prevalence of swab-positivity among double-vaccinated individuals. Unlike all previous rounds, in round 14, we switched from dry swabs transported by courier on a cold chain to wet swabs using saline. Also, at random, 50% of swabs (not chilled until they reached the depot) were transported by courier and 50% were sent through the priority COVID-19 postal service. <h4>Results</h4> We observed stable or rising prevalence (with an R of 1.03 (0.94, 1.14) overall) during round 14 with a weighted prevalence of 0.83% (0.76%, 0.89%). The highest weighted prevalence was found in children aged 5 to 12 years at 2.32% (1.96%, 2.73%) and 13 to 17 years at 2.55% (2.11%, 3.08%). All positive virus samples analysed correspond to the Delta variant or sub-lineages of Delta with one instance of the E484K escape mutation detected. The epidemic was growing in those aged 17 years and under with an R of 1.18 (1.03, 1.34), but decreasing in those aged 18 to 54 years with an R of 0.81 (0.68, 0.97). For all participants and all vaccines combined, at ages 18 to 64 years, vaccine effectiveness against infection (rounds 13 and 14 combined) was estimated to be 62.8% (49.3%, 72.7%) after two doses compared to unvaccinated people when adjusted for round, age, sex, index of multiple deprivation, region and ethnicity; the adjusted estimate was 44.8% (22.5%, 60.7%) for AstraZeneca and 71.3% (56.6%, 81.0%) for Pfizer-BioNTech, and for all vaccines combined it was 66.4% (49.6%, 77.6%) against symptomatic infection (one or more of 26 surveyed symptoms in month prior). Across rounds 13 and 14, at ages 18 years and over, weighted prevalence of swab-positivity was 0.55% (0.50%, 0.61%) for those who received their second dose 3-6 months before their swab compared to 0.35% (0.31%, 0.40%) for those whose second dose was within 3 months of their swab, while weighted prevalence among unvaccinated individuals was1.76% (1.60%, 1.95%). In round 14, age group, region, key worker status, and household size jointly contributed to the risk of higher prevalence of swab-positivity. <h4>Discussion</h4> In September 2021 infections were increasing exponentially in the 5-to-17-year age group coinciding with the start of the autumn school term in England. Relatively few schoolchildren aged 5 to 17 years have been vaccinated in the UK though single doses are now being offered to those aged 12 years and over. In adults, the higher prevalence of swab-positivity following two doses of vaccine from 3 to 6 months compared to within 3 months of second dose supports the use of a booster vaccine. It is important that the vaccination programme maintains high coverage and reaches children and unvaccinated or partially vaccinated adults to reduce transmission and associated disruptions to work and education.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2021/10/22/2021.10.14.21264965.full.pdf; doi:https://doi.org/10.1101/2021.10.14.21264965; html:https://europepmc.org/article/PPR/PPR411044; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR411044&type=FILE&fileName=EMS137524-pdf.pdf&mimeType=application/pdf
-PPR357531,https://doi.org/10.1101/2021.06.15.21258542,"Casirivimab and imdevimab in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial","RECOVERY Collaborative Group, Horby PW, Mafham M, Peto L, Campbell M, Pessoa-Amorim G, Spata E, Staplin N, Emberson JR, Prudon B, Hine P, Brown T, Green CA, Sarkar R, Desai P, Yates B, Bewick T, Tiberi S, Felton T, Baillie JK, Buch MH, Chappell LC, Day JN, Faust SN, Jaki T, Jeffery K, Juszczak E, Lim WS, Montgomery A, Mumford A, Rowan K, Thwaites G, Weinreich DM, Haynes R, Landray MJ.",,No Journal Info,2021,2021-06-16,Y,,,,"<h4>SUMMARY</h4> <h4>Background</h4> REGEN-COV is a combination of 2 monoclonal antibodies (casirivimab and imdevimab) that bind to two different sites on the receptor binding domain of the SARS-CoV-2 spike protein. We aimed to evaluate the efficacy and safety of REGEN-COV in patients admitted to hospital with COVID-19. <h4>Methods</h4> In this randomised, controlled, open-label platform trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19. Eligible and consenting patients were randomly allocated (1:1) to either usual standard of care alone (usual care group) or usual care plus a single dose of REGEN-COV 8g (casirivimab 4g and imdevimab 4g) by intravenous infusion (REGEN-COV group). The primary outcome was 28-day mortality assessed first among patients without detectable antibodies to SARS-CoV-2 at randomisation (seronegative) and then in the overall population. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov ( NCT04381936 ). <h4>Findings</h4> Between 18 September 2020 and 22 May 2021, 9785 patients were randomly allocated to receive usual care plus REGEN-COV or usual care alone, including 3153 (32%) seronegative patients, 5272 (54%) seropositive patients and 1360 (14%) patients with unknown baseline antibody status. In the primary efficacy population of seronegative patients, 396 (24%) of 1633 patients allocated to REGEN-COV and 451 (30%) of 1520 patients allocated to usual care died within 28 days (rate ratio 0·80; 95% CI 0·70-0·91; p=0·0010). In an analysis involving all randomised patients (regardless of baseline antibody status), 944 (20%) of 4839 patients allocated to REGEN-COV and 1026 (21%) of 4946 patients allocated to usual care died within 28 days (rate ratio 0·94; 95% CI 0·86-1·03; p=0·17). The proportional effect of REGEN-COV on mortality differed significantly between seropositive and seronegative patients (p value for heterogeneity = 0·001). <h4>Interpretation</h4> In patients hospitalised with COVID-19, the monoclonal antibody combination of casirivimab and imdevimab (REGEN-COV) reduced 28-day mortality among patients who were seronegative at baseline. <h4>Funding</h4> UK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056).",,pdf:https://nottingham-repository.worktribe.com/preview/7415985/1-s2.0-S0140673622001635-main.pdf; doi:https://doi.org/10.1101/2021.06.15.21258542; html:https://europepmc.org/article/PPR/PPR357531; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR357531&type=FILE&fileName=EMS127953-pdf.pdf&mimeType=application/pdf
 PPR241902,https://doi.org/10.1101/2020.11.19.20234120,Actionable druggable genome-wide Mendelian randomization identifies repurposing opportunities for COVID-19,"Gaziano L, Giambartolomei C, Pereira AC, Gaulton A, Posner DC, Swanson SA, Ho Y, Iyengar SK, Kosik NM, Vujkovic M, Gagnon DR, Bento AP, Beltrao P, Barrio-Hernandez I, Rönnblom L, Hagberg N, Lundtoft C, Langenberg C, Pietzner M, Valentine D, Allara E, Surendran P, Burgess S, Zhao JH, Peters JE, Prins BP, Danesh J, Devineni P, Shi Y, Lynch KE, DuVall SL, Garcon H, Thomann LO, Zhou JJ, Gorman BR, Huffman JE, O’Donnell CJ, Tsao PS, Beckham JC, Pyarajan S, Muralidhar S, Huang GD, Ramoni R, Hung AM, Chang K, Sun YV, Joseph J, Leach AR, Edwards TL, Cho K, Gaziano JM, Butterworth AS, Casas JP.",,No Journal Info,2020,2020-11-23,Y,,,,"Drug repurposing provides a rapid approach to meet the urgent need for therapeutics to address COVID-19. To identify therapeutic targets relevant to COVID-19, we conducted Mendelian randomization (MR) analyses, deriving genetic instruments based on transcriptomic and proteomic data for 1,263 actionable proteins that are targeted by approved drugs or in clinical phase of drug development. Using summary statistics from the Host Genetics Initiative and the Million Veteran Program, we studied 7,554 patients hospitalized with COVID-19 and >1 million controls. We found significant Mendelian randomization results for three proteins (ACE2: P= 1.6×10 −6 , IFNAR2: P= 9.8×10 −11 , and IL-10RB: P= 1.9×10 −14 ) using cis -eQTL genetic instruments that also had strong evidence for colocalization with COVID-19 hospitalization. To disentangle the shared eQTL signal for IL10RB and IFNAR2 , we conducted phenome-wide association scans and pathway enrichment analysis, which suggested that IFNAR2 is more likely to play a role in COVID-19 hospitalization. Our findings prioritize trials of drugs targeting IFNAR2 and ACE2 for early management of COVID-19.",,pdf:https://www.nature.com/articles/s41591-021-01310-z.pdf; doi:https://doi.org/10.1101/2020.11.19.20234120; html:https://europepmc.org/article/PPR/PPR241902; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR241902&type=FILE&fileName=EMS105387-pdf.pdf&mimeType=application/pdf
+PPR357531,https://doi.org/10.1101/2021.06.15.21258542,"Casirivimab and imdevimab in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial","RECOVERY Collaborative Group, Horby PW, Mafham M, Peto L, Campbell M, Pessoa-Amorim G, Spata E, Staplin N, Emberson JR, Prudon B, Hine P, Brown T, Green CA, Sarkar R, Desai P, Yates B, Bewick T, Tiberi S, Felton T, Baillie JK, Buch MH, Chappell LC, Day JN, Faust SN, Jaki T, Jeffery K, Juszczak E, Lim WS, Montgomery A, Mumford A, Rowan K, Thwaites G, Weinreich DM, Haynes R, Landray MJ.",,No Journal Info,2021,2021-06-16,Y,,,,"<h4>SUMMARY</h4> <h4>Background</h4> REGEN-COV is a combination of 2 monoclonal antibodies (casirivimab and imdevimab) that bind to two different sites on the receptor binding domain of the SARS-CoV-2 spike protein. We aimed to evaluate the efficacy and safety of REGEN-COV in patients admitted to hospital with COVID-19. <h4>Methods</h4> In this randomised, controlled, open-label platform trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19. Eligible and consenting patients were randomly allocated (1:1) to either usual standard of care alone (usual care group) or usual care plus a single dose of REGEN-COV 8g (casirivimab 4g and imdevimab 4g) by intravenous infusion (REGEN-COV group). The primary outcome was 28-day mortality assessed first among patients without detectable antibodies to SARS-CoV-2 at randomisation (seronegative) and then in the overall population. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov ( NCT04381936 ). <h4>Findings</h4> Between 18 September 2020 and 22 May 2021, 9785 patients were randomly allocated to receive usual care plus REGEN-COV or usual care alone, including 3153 (32%) seronegative patients, 5272 (54%) seropositive patients and 1360 (14%) patients with unknown baseline antibody status. In the primary efficacy population of seronegative patients, 396 (24%) of 1633 patients allocated to REGEN-COV and 451 (30%) of 1520 patients allocated to usual care died within 28 days (rate ratio 0·80; 95% CI 0·70-0·91; p=0·0010). In an analysis involving all randomised patients (regardless of baseline antibody status), 944 (20%) of 4839 patients allocated to REGEN-COV and 1026 (21%) of 4946 patients allocated to usual care died within 28 days (rate ratio 0·94; 95% CI 0·86-1·03; p=0·17). The proportional effect of REGEN-COV on mortality differed significantly between seropositive and seronegative patients (p value for heterogeneity = 0·001). <h4>Interpretation</h4> In patients hospitalised with COVID-19, the monoclonal antibody combination of casirivimab and imdevimab (REGEN-COV) reduced 28-day mortality among patients who were seronegative at baseline. <h4>Funding</h4> UK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056).",,pdf:https://nottingham-repository.worktribe.com/preview/7415985/1-s2.0-S0140673622001635-main.pdf; doi:https://doi.org/10.1101/2021.06.15.21258542; html:https://europepmc.org/article/PPR/PPR357531; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR357531&type=FILE&fileName=EMS127953-pdf.pdf&mimeType=application/pdf
 PPR303187,https://doi.org/10.1101/2021.03.26.21254390,Regional performance variation in external validation of four prediction models for severity of COVID-19 at hospital admission: An observational multi-centre cohort study,"Wickstrøm KE, Vitelli V, Carr E, Holten AR, Bendayan R, Reiner AH, Bean D, Searle T, Shek A, Kraljevic Z, Teo J, Dobson R, Tonby K, Köhn- Luque A, Amundsen EK.",,No Journal Info,2021,2021-03-26,N,,,,"<h4>Background</h4> Several prediction models for coronavirus disease-19 (COVID-19) have been published. Prediction models should be externally validated to assess their performance before implementation. This observational cohort study aimed to validate published models of severity for hospitalized patients with COVID-19 using clinical and laboratory predictors. <h4>Methods</h4> Prediction models fitting relevant inclusion criteria were chosen for validation. The outcome was either mortality or a composite outcome of mortality and ICU admission (severe disease). 1295 patients admitted with symptoms of COVID-19 at Kings Cross Hospital (KCH) in London, United Kingdom, and 307 patients at Oslo University Hospital (OUH) in Oslo, Norway were included. The performance of the models was assessed in terms of discrimination and calibration. <h4>Results</h4> We identified two models for prediction of mortality (referred to as Xie and Zhang1) and two models for prediction of severe disease (Allenbach and Zhang2). The performance of the models was variable. For prediction of mortality Xie had good discrimination at OUH with an area under the receiver-operating characteristic (AUROC) 0.87 [95 % confidence interval (CI) 0.79-0.95] and acceptable discrimination at KCH, AUROC 0.79 [0.76-0.82]. In prediction of severe disease, Allenbach had acceptable discrimination (OUH AUROC 0.81 [0.74-0.88] and KCH AUROC 0.72 [0.68-0.75]). The Zhang models had moderate to poor discrimination. Initial calibration was poor for all models but improved with recalibration. <h4>Conclusions</h4> The performance of the four prediction models was variable. The Xie model had the best discrimination for mortality, while the Allenbach model had acceptable results for prediction of severe disease.",,doi:https://doi.org/10.1371/journal.pone.0255748; doi:https://doi.org/10.1101/2021.03.26.21254390; html:https://europepmc.org/article/PPR/PPR303187; doi:https://doi.org/10.1101/2021.03.26.21254390
 PPR286480,https://doi.org/10.1101/2021.02.17.21251928,Mortality after surgery with SARS-CoV-2 infection in England: A population-wide epidemiological study,"Abbott TEF, Fowler AJ, Dobbs TD, Gibson J, Shahid T, Dias P, Akbari A, Whitaker IS, Pearse RM.",,No Journal Info,2021,2021-02-20,Y,,,,"<h4>Objectives</h4> To confirm the incidence of perioperative SARS-CoV-2 infection and associated mortality after surgery. <h4>Design and setting</h4> Analysis of routine electronic health record data from National Health Service (NHS) hospitals in England. <h4>Methods</h4> We extracted data from Hospital Episode Statistics in England describing adult patients undergoing surgery between 1 st January 2020 and 31 st October 2020. The exposure was SARS-CoV-2 infection defined by ICD-10 codes. The primary outcome measure was 90-day in-hospital mortality. Data were analysed using multivariable logistic regression adjusted for age, sex, Charlson co-morbidity index, index of multiple deprivation, presence of cancer, surgical procedure type and admission acuity. Results are presented as n (%) and odds ratios (OR) with 95% confidence intervals. <h4>Results</h4> We identified 1,972,153 patients undergoing surgery of whom 11,940 (0.6%) had SARS-CoV-2. In total, 19,100 (1.0%) patients died in hospital. SARS-CoV-2 infection was associated with a much greater risk of death (SARS-CoV-2: 2,618/11,940 [21.9%] vs No SARS-CoV-2: 16,482/1,960,213 [0.8%]; OR: 5.8 [5.5 – 6.1]; p<0.001). Amongst patients undergoing elective surgery 1,030/1,374,985 (0.1%) had SARS-CoV-2 of whom 83/1,030 (8.1%) died, compared with 1,092/1,373,955 (0.1%) patients without SARS-CoV-2 (OR: 29.0 [22.5 −37.3]; p<0.001). Amongst patients undergoing emergency surgery 9,742/437,891 (2.2%) patients had SARS-CoV-2, of whom 2,466/9,742 (25.3%) died compared with 14,817/428,149 (3.5%) patients without SARS-CoV-2 (OR: 5.7 [5.4 – 6.0]; p<0.001). <h4>Conclusions</h4> The low incidence of SARS-CoV-2 infection in NHS surgical pathways suggests current infection prevention and control policies are highly effective. However, the high mortality amongst patients with SARS-CoV-2 suggests these precautions cannot be safely relaxed. <h4>Summary boxes</h4> <h4>What is already known on this topic</h4> High mortality rates have been reported amongst surgical patients who develop COVID-19 but we don’t know how this compares to the concurrent surgical population unaffected by COVID-19. Strict infection prevention and control procedures have substantially reduced the capacity of surgical treatment pathways in many hospitals. The very large backlog in delayed and cancelled surgical procedures is a growing public health concern. <h4>What this study adds</h4> Fewer than 1 in 100 surgical patients are affected by COVID-19 in the English National Health Service. Elective surgical patients who do develop COVID-19 are 30 times more likely to die while in hospital. Infection prevention and control procedures in NHS surgical pathways are highly effective but cannot be safely relaxed.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2021/02/20/2021.02.17.21251928.full.pdf; doi:https://doi.org/10.1101/2021.02.17.21251928; html:https://europepmc.org/article/PPR/PPR286480; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR286480&type=FILE&fileName=EMS117258-pdf.pdf&mimeType=application/pdf
 PPR725114,https://doi.org/10.21203/rs.3.rs-3316645/v1,"Uptake, effectiveness and safety of COVID-19 vaccines in the immunocompromised population: A population-based cohort study in England","Chen D, Copland E, Hirst J, Mi E, Dixon S, Coupland C, Hippisley-Cox J.",,No Journal Info,2023,2023-09-14,Y,,,,"Immunocompromised individuals face increased risks of severe COVID-19 outcomes, underscoring the importance of receiving COVID-19 vaccination. However, there's a lack of comprehensive real-world data on their COVID-19 vaccine uptake, effectiveness, and safety profile. We analysed data in the QResearch UK database from 01/12/2020 to 11/04/2022. We included 12,274,948 people aged ≥ 12 years in our analysis, of whom 583,541 (4.8%) were immunocompromised, defined as on immune-modifying drugs, chemotherapy, organ transplants, or dialysis. Overall, 93.7% of immunocompromised patients received at least one COVID-19 vaccine dose. Uptake reduced with increasing deprivation (Hazard Ratio [HR] 0.78 [95% CI 0.77–0.79] in the most deprived quintile compared to the least for the first dose). Using a nested case-control design, estimated vaccine effectiveness against COVID-19 hospitalisation 2–6 weeks after the second and third doses compared to the unvaccinated was 78% (95%CI 72–83) and 91% (95%CI 88–93) for the immunocompromised, versus 85% (95%CI 83–86) and 86% (95%CI 85–89) respectively for the general population. COVID-19 vaccines were protective against intensive care unit admission and death in both groups. There were no differing risks of adverse events during the first 28 days after each dose between the two populations. These findings underscore the importance of ongoing vaccination prioritisation for immunocompromised individuals to maximise protection against severe COVID-19-related outcomes.",,pdf:https://www.researchsquare.com/article/rs-3316645/latest.pdf; doi:https://doi.org/10.21203/rs.3.rs-3316645/v1; html:https://europepmc.org/article/PPR/PPR725114; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR725114&type=FILE&fileName=EMS188044-pdf.pdf&mimeType=application/pdf
@@ -163,15 +163,15 @@ PPR241057,https://doi.org/10.1101/2020.11.18.20233932,REACT-1 round 6 updated re
 PPR602637,https://doi.org/10.2139/ssrn.4031570,Determinants of Antibody Responses to Two Doses of ChAdOx1 nCoV-19 or Bnt162b2 and a Subsequent Booster Dose of BNT162b2 or mRNA-1273: Population-Based Cohort Study (COVIDENCE UK),"Jolliffe D, Faustini S, Holt H, Perdek N, Maltby S, Talaei M, Greenig M, Vivaldi G, Tydeman F, Symons J, Davies GA, Lyons RA, Griffiths CJ, Kee F, Sheikh A, Shaheen SO, Richter AG, Martineau AR.",,No Journal Info,2022,2022-03-03,Y,,,,"Background:  Antibody responses to SARS-CoV-2 vaccination vary for reasons that remain poorly understood. <br><br>Methods:  We tested for presence of combined IgG, IgA and IgM (IgGAM) anti-spike antibodies before and after administration of two doses of ChAdOx1 nCoV-19 (ChAdOx1, Oxford-AstraZeneca) or BNT162b2 (Pfizer-BioNTech) in UK adults participating in a population-based longitudinal study who received their first dose of vaccine from December 15, 2020 to July 10, 2021. Information on sixty-six potential sociodemographic, behavioural, clinical, pharmacological and nutritional determinants of serological response to vaccination was captured using serial online questionnaires. We used logistic regression to estimate multivariable-adjusted odds ratios (aORs) for associations between independent variables and risk of seronegativity following two vaccine doses. Participants who were seronegative after receiving two vaccine doses were offered an additional antibody test following subsequent administration of a ‘booster’ dose of BNT162b2 or mRNA-1273 (Moderna) from September 23 to December 12, 2021. <br><br>Findings:  Serology results following two vaccine doses were available for 9,101 participants, of whom 5,770 (63.4%) received ChAdOx1 and 3,331 (36.6%) received BNT162b2. Anti-spike IgGAM was undetectable in 378 (4.2%) participants at a median of 8.6 weeks (IQR 6.4-10.7 weeks) after their second dose of vaccine. Seronegativity following two doses of SARS-CoV-2 vaccination was associated with administration of ChAdOx1  vs  BNT162b2 (aOR 7.03, 95% CI 4.39-11.24), shorter interval between first and second vaccine doses (aOR 2.37, 1.06-5.26, for <6 weeks  vs  >10 weeks; aOR 1.59, 1.18-2.13, for 6-10 weeks  vs  >10 weeks), poorer self-assessed general health (aOR 3.33, 1.49-7.46, for poor  vs  excellent), immunodeficiencies (aOR 6.75, 2.63-17.35) and prescription of systemic immunosuppressants (aOR 3.76, 2.44-5.78). By contrast, pre-vaccination SARS-CoV-2 seropositivity (aOR 0.16, 0.04-0.70, for symptomatic seropositives  vs  seronegatives) and supplemental vitamin D intake (aOR 0.73, 0.53-0.99) were associated with reduced risk of post-vaccination seronegativity. 247/378 (65.3%) of participants who were seronegative after two doses of ChAdOx1  vs  BNT162b2 provided a third sample at a median of 7.8 weeks (IQR 5.8-10.4) after receiving a booster dose of BNT162b2 or mRNA-1273: eight (3.2%) of them remained seronegative after three vaccine doses, all of whom either had a primary immunodeficiency or were taking systemic immunosuppressant drugs.<br><br>Interpretation:  We identify multiple determinants of antibody responses to two doses of ChAdOx1 or BNT162b2, many of which are potentially modifiable. Booster doses of BNT162b2 or mRNA-1273 were highly effective in achieving seroconversion in those who failed to mount antibody responses following two doses of ChAdOx1 or BNT162b2.<br><br>Trial Registration Details:  Registered with ClinicalTrials.gov (NCT04330599).<br>		<br>Funding Information: This study was supported by a grant from Barts Charity to ARM and CJG (MGU0466) and by donations to Queen Mary University of London from the Fischer Family Trust, the Exilarch’s Foundation and DSM Nutritional Products Ltd. DAJ is supported by a Barts Charity Lectureship (MGU0459). MT is supported by a grant from the Rosetrees Trust and The Bloom Foundation (M771). The work was carried out with the support 20 of BREATHE - The Health Data Research Hub for Respiratory Health (MC_PC_19004) in partnership with SAIL Databank. BREATHE is funded through the UK Research and Innovation Industrial Strategy Challenge Fund and delivered through Health Data Research UK.<br>	<br>Declaration of Interests: JS declares receipt of payments from Reach plc for news stories written about recruitment to, and findings of, the COVIDENCE UK study. AS is a member of the Scottish Government Chief Medical Officer’s COVID-19 Advisory Group and its Standing Committee on Pandemics. He is also a member of the UK Government’s NERVTAG’s Risk Stratification Subgroup. ARM declares receipt of funding in the last 36 months to support vitamin D research from the following companies who manufacture or sell vitamin D supplements: Pharma Nord Ltd, DSM Nutritional Products Ltd, Thornton & Ross Ltd and Hyphens Pharma Ltd. ARM also declares support for attending meetings from the following companies who manufacture or sell vitamin D supplements: Pharma Nord Ltd and Abiogen Pharma Ltd. ARM also declares participation on the Data and Safety Monitoring Board for the Chair, DSMB, VITALITY trial (Vitamin D for Adolescents with HIV to reduce musculoskeletal morbidity and immunopathology). ARM also declares unpaid work as a Programme Committee member for the Vitamin D Workshop. ARM also declares receipt of vitamin D capsules for clinical trial use from Pharma Nord Ltd, Synergy Biologics Ltd and Cytoplan Ltd. All other authors have nothing to declare. <br><br>Ethics Approval Statement: Approved by Leicester South Research Ethics Committee (ref 20/EM/0117). <br>",,doi:https://doi.org/10.1101/2022.02.14.22270930; doi:https://doi.org/10.2139/ssrn.4031570; html:https://europepmc.org/article/PPR/PPR602637; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR602637&type=FILE&fileName=EMS165240-pdf.pdf&mimeType=application/pdf
 PPR605135,https://doi.org/10.2139/ssrn.4066712,Using National Electronic Health Records for Pandemic Preparedness: Validation of a Parsimonious Model for Predicting Excess Deaths Among Those With COVID-19,"Mizani MA, Dashtban MH, Pasea L, Lai AG, Thygesen JH, Tomlinson C, Handy A, Mamza JB, Morris T, Khalid S, Zaccardi F, Macleod MJ, Torabi F, Canoy D, Akbari A, Berry C, Bolton T, Nolan J, Khunti K, Denaxas S, Hemingway H, Sudlow C, Banerjee A, CVD-COVID-UK Consortium.",,No Journal Info,2022,2022-03-25,N,,,,"Background:  Throughout the pandemic, research, public health, and policy emphasised prediction and surveillance of excess deaths, which have mostly occurred in older individuals with underlying conditions, highlighting importance of baseline mortality risk, infection rate (IR) and pandemic-related relative risk (RR). We now use national, pre- and post-pandemic electronic health records (EHR) to develop and validate a model incorporating these factors for prediction of excess deaths.<br><br>Methods: In development (Clinical Practice Research Datalink) and validation (NHS Digital Trusted Research Environment) cohorts in primary and secondary care EHR in England, we included 3·8 million and 35·1 million individuals aged ≥30 years, respectively. For model development, we predicted excess deaths using baseline one-year all-cause mortality risk and assumed RR=3 and IR=10%. For model validation, we observed number of excess deaths from March 2020 to March 2021. We used baseline mortality risk, IR and RR (assumed and observed) to predict excess deaths related to COVID-19.   <br><br>Findings: Among individuals with at least one high-risk condition, baseline (pre-pandemic) 1-year mortality risk at one year was 4·46% (95% CI 4·41–4·51) and 3.55% (3.54-3.57) in development and validation cohorts, respectively. In our original published model, we predicted 73,498 COVID-19 deaths over 1 year for the population of England. From 1st March 2020 to 1st March 2021, there were 127,020 observed excess deaths. Observed RR was 4·34 (4·31-4·38, 95% CI) and IR was 6·27% (6·26-6·28, 95%CI). In the validation cohort, predicted excess deaths over one year were 100,338 compared with the observed 127,020 deaths with a ratio of predicted to observed excess deaths of 0.79. We found that vaccination had a negligible effect on overall RR or IR between 1st December 2020 and 1st March 2021, compared to the likely effect of under-reported COVID-19 cases from the pre-vaccination period.<br><br>Interpretation: We show that a simple, parsimonious model incorporating baseline mortality risk, one-year infection rate and relative risk of the pandemic can be used to predict excess deaths. Our analyses show that EHR could inform pandemic planning and surveillance, despite limited use in emergency preparedness to-date. Although infection dynamics are important in prediction of morbidity and mortality, future models should take greater account of underlying conditions and their associated risks.<br><br>Funding Information: The British Heart Foundation Data Science Centre (grant No SP/19/3/34678, awarded to Health Data Research (HDR) UK) funded co-development (with NHS Digital) of the trusted research environment, provision of linked datasets, data access, user software licences, computational usage, and data management and wrangling support, with additional contributions from the HDR UK data and connectivity component of the UK Government Chief Scientific Adviser’s National Core Studies programme to coordinate national Covid-19 priority research. Consortium partner organisations funded the time of contributing data analysts, biostatisticians, epidemiologists, and clinicians. AB, MAM, MHD and LP were supported by research funding from AstraZeneca. AB has received funding from the National Institute for Health Research (NIHR), British Medical Association, and UK Research and Innovation. AB, SD and HH are part of the BigData@Heart Consortium, funded by the Innovative Medicines Initiative-2 Joint Undertaking under grant agreement No 116074. K.K. is supported by the National Institute for Health Research (NIHR) Applied Research Collaboration East Midlands (ARC EM) and NIHR Lifestyle BRC.<br>		<br>Declaration of Interests: JBM and TM are employees of AstraZeneca. KK is chair of the ethnicity subgroup of the Independent Scientific Advisory Group for Emergencies (SAGE) and director of the University of Leicester Centre for Black Minority Ethnic Health. KK and AB are trustees of the South Asian Health Foundation (SAHF). CS is Director of the BHF Data Science Centre. All other authors report no competing interests.<br><br>Ethics Approval Statement: Approval for the study in CPRD was granted by the Independent Scientific Advisory Committee (20_074R) of the Medicines and Healthcare products Regulatory Agency in the UK in accordance with the Declaration of Helsinki. The North East-Newcastle and North Tyneside 2 research ethics committee provided ethical approval for the CVD- COVID-UK research programme (REC No 20/NE/0161).<br>",,doi:https://doi.org/10.2139/ssrn.4066712; html:https://europepmc.org/article/PPR/PPR605135; doi:https://doi.org/10.2139/ssrn.4066712
 PPR230575,https://doi.org/10.1101/2020.10.26.20219725,"Declining prevalence of antibody positivity to SARS-CoV-2: a community study of 365,000 adults","Ward H, Cooke G, Atchison C, Whitaker M, Elliott J, Moshe M, Brown JC, Flower B, Daunt A, Ainslie K, Ashby D, Donnelly C, Riley S, Darzi A, Barclay W, Elliott P, for the REACT study team.",,No Journal Info,2020,2020-10-27,Y,,,,"<h4>Background</h4> The prevalence and persistence of antibodies following a peak SARS-CoV-2 infection provides insights into its spread in the community, the likelihood of reinfection and potential for some level of population immunity. <h4>Methods</h4> Prevalence of antibody positivity in England, UK (REACT2) with three cross-sectional surveys between late June and September 2020. 365104 adults used a self-administered lateral flow immunoassay (LFIA) test for IgG. A laboratory comparison of LFIA results to neutralization activity in panel of sera was performed. <h4>Results</h4> There were 17,576 positive tests over the three rounds. Antibody prevalence, adjusted for test characteristics and weighted to the adult population of England, declined from 6.0% [5.8, 6.1], to 4.8% [4.7, 5.0] and 4.4% [4.3, 4.5], a fall of 26.5% [-29.0, −23.8] over the three months of the study. There was a decline between rounds 1 and 3 in all age groups, with the highest prevalence of a positive result and smallest overall decline in positivity in the youngest age group (18-24 years: −14.9% [-21.6, −8.1]), and lowest prevalence and largest decline in the oldest group (75+ years: −39.0% [-50.8, −27.2]); there was no change in antibody positivity between rounds 1 and 3 in healthcare workers (+3.45% [-5.7, +12.7]). The decline from rounds 1 to 3 was largest in those who did not report a history of COVID-19, (−64.0% [-75.6, −52.3]), compared to −22.3% ([-27.0, −17.7]) in those with SARS-CoV-2 infection confirmed on PCR. <h4>Discussion</h4> These findings provide evidence of variable waning in antibody positivity over time such that, at the start of the second wave of infection in England, only 4.4% of adults had detectable IgG antibodies using an LFIA. Antibody positivity was greater in those who reported a positive PCR and lower in older people and those with asymptomatic infection. These data suggest the possibility of decreasing population immunity and increasing risk of reinfection as detectable antibodies decline in the population.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2020/10/27/2020.10.26.20219725.full.pdf; doi:https://doi.org/10.1101/2020.10.26.20219725; html:https://europepmc.org/article/PPR/PPR230575; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR230575&type=FILE&fileName=EMS101563-pdf.pdf&mimeType=application/pdf
-PPR233362,https://doi.org/10.1101/2020.10.30.20223123,High prevalence of SARS-CoV-2 swab positivity and increasing R number in England during October 2020: REACT-1 round 6 interim report,"Riley S, Ainslie KEC, Eales O, Walters CE, Wang H, Atchison C, Fronterre C, Diggle PJ, Ashby D, Donnelly CA, Cooke G, Barclay W, Ward H, Darzi A, Elliott P.",,No Journal Info,2020,2020-11-03,Y,,,,"<h4>Background</h4> REACT-1 measures prevalence of SARS-CoV-2 infection in representative samples of the population in England using PCR testing from self-administered nose and throat swabs. Here we report interim results for round 6 of observations for swabs collected from the 16th to 25th October 2020 inclusive. <h4>Methods</h4> REACT-1 round 6 aims to collect data and swab results from 160,000 people aged 5 and above. Here we report results from the first 86,000 individuals. We estimate prevalence of PCR-confirmed SARS-CoV-2 infection, reproduction numbers (R) and temporal trends using exponential growth or decay models. Prevalence estimates are presented both unweighted and weighted to be representative of the population of England, accounting for response rate, region, deprivation and ethnicity. We compare these interim results with data from round 5, based on swabs collected from 18th September to 5th October 2020 inclusive. <h4>Results</h4> Overall prevalence of infection in the community in England was 1.28% or 128 people per 10,000, up from 60 per 10,000 in the previous round. Infections were doubling every 9.0 (6.1, 18) days with a national reproduction number (R) estimated at 1.56 (1.27, 1.88) compared to 1.16 (1.05, 1.27) in the previous round. Prevalence of infection was highest in Yorkshire and The Humber at 2.72% (2.12%, 3.50%), up from 0.84% (0.60%, 1.17%), and the North West at 2.27% (1.90%, 2.72%), up from 1.21% (1.01%, 1.46%), and lowest in South East at 0.55% (0.45%, 0.68%), up from 0.29% (0.23%, 0.37%). Clustering of cases was more prevalent in Lancashire, Manchester, Liverpool and West Yorkshire, West Midlands and East Midlands. Interim estimates of R were above 2 in the South East, East of England, London and South West, but with wide confidence intervals. Nationally, prevalence increased across all age groups with the greatest increase in those aged 55-64 at 1.20% (0.99%, 1.46%), up 3-fold from 0.37% (0.30%, 0.46%). In those aged over 65, prevalence was 0.81% (0.58%, 0.96%) up 2-fold from 0.35% (0.28%, 0.43%). Prevalence remained highest in 18 to 24-year olds at 2.25% (1.47%, 3.42%). <h4>Conclusion</h4> The co-occurrence of high prevalence and rapid growth means that the second wave of the epidemic in England has now reached a critical stage. Whether via regional or national measures, it is now time-critical to control the virus and turn R below one if further hospital admissions and deaths from COVID-19 are to be avoided.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2020/11/03/2020.10.30.20223123.full.pdf; doi:https://doi.org/10.1101/2020.10.30.20223123; html:https://europepmc.org/article/PPR/PPR233362; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR233362&type=FILE&fileName=EMS103475-pdf.pdf&mimeType=application/pdf
 PPR579535,https://doi.org/10.1101/2022.12.02.22283049,Comparative effectiveness of sotrovimab and molnupiravir for preventing severe COVID-19 outcomes in non-hospitalised patients on kidney replacement therapy: observational cohort study using the OpenSAFELY-UKRR linked platform and SRR database,"The OpenSAFELY Collaborative, Zheng B, Campbell J, Carr EJ, Tazare J, Nab L, Mahalingasivam V, Mehrkar A, Santhakumaran S, Steenkamp R, Loud F, Lyon S, Scanlon M, Hulme WJ, Green AC, Curtis HJ, Fisher L, Parker E, Goldacre B, Douglas I, Evans S, MacKenna B, Bell S, Tomlinson LA, Nitsch D, The LH&W NCS (or CONVALESCENCE) Collaborative.",,No Journal Info,2022,2022-12-04,Y,,,,"<h4>Background</h4> Patients on kidney replacement therapy (KRT; dialysis and kidney transplantation) are at the highest risk of severe outcomes from COVID-19. Due to limited inclusion of patients on KRT in clinical trials, information is limited on the effectiveness of sotrovimab (a neutralising monoclonal antibody). We sought to address this by comparing its effectiveness against molnupiravir (an antiviral) in preventing severe COVID-19 outcomes in non-hospitalised adults with symptomatic COVID-19. <h4>Methods</h4> With the approval of NHS England we used routine clinical data from 24 million patients in England linked to the UK Renal Registry (UKRR) to identify patients on KRT, and data on antiviral treatments, COVID-19 test results, hospitalisation events and death from the OpenSAFELY-TPP data resource. Cox proportional hazards models (stratified for region) were used to estimate hazard ratios of sotrovimab vs. molnupiravir with regards to COVID-19 related hospitalisation or deaths in the subsequent 28 days (as the primary outcome). Further analyses were conducted using propensity score weighting (adjusted for region) and to investigate robustness of results with regards to different time periods, missing data, and adjustment variables. We also conducted a complementary analysis using data from patients in the Scottish Renal Registry (SRR) treated with sotrovimab or molnupiravir, following similar analytical approaches. <h4>Results</h4> Among the 2367 renal patients treated with sotrovimab (n=1852) or molnupiravir (n=515) between December 16, 2021 and August 1, 2022 in England, 38 cases (1.6%) of COVID-19 related hospitalisations/deaths were observed during the 28 days of follow-up after treatment initiation, with 21 (1.1%) in the sotrovimab group and 17 (3.3%) in the molnupiravir group. In multiple-adjusted analysis sotrovimab was associated with substantially lower risk of 28-day COVID-19 related hospitalisation/death than treatment with molnupiravir (hazard ratio, HR=0.35, 95% CI: 0.17 to 0.71; P=0.004), with results remaining robust in sensitivity analyses. In the SRR cohort, there were 19 cases (1.9%) of COVID-19 related hospitalisations/deaths during the 28 days of follow-up after treatment initiation of sotrovimab (n=723) or molnupiravir (n=270). In multiple-adjusted analysis, sotrovimab showed a trend toward lower risk of 28-day COVID-19 related hospitalisation/death than treatment with molnupiravir (HR=0.39, 95% CI: 0.13 to 1.21; P=0.106). In both datasets, sotrovimab had no evidence of association with other hospitalisation/death compared with molnupiravir (HRs ranging from 0.73-1.29; P>0.05). <h4>Conclusions</h4> In routine care of non-hospitalised patients with COVID-19 on kidney replacement therapy, those who received sotrovimab had substantially lower risk of severe COVID-19 outcomes than those receiving molnupiravir.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/12/05/2022.12.02.22283049.full.pdf; doi:https://doi.org/10.1101/2022.12.02.22283049; html:https://europepmc.org/article/PPR/PPR579535; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR579535&type=FILE&fileName=EMS158097-pdf.pdf&mimeType=application/pdf
+PPR233362,https://doi.org/10.1101/2020.10.30.20223123,High prevalence of SARS-CoV-2 swab positivity and increasing R number in England during October 2020: REACT-1 round 6 interim report,"Riley S, Ainslie KEC, Eales O, Walters CE, Wang H, Atchison C, Fronterre C, Diggle PJ, Ashby D, Donnelly CA, Cooke G, Barclay W, Ward H, Darzi A, Elliott P.",,No Journal Info,2020,2020-11-03,Y,,,,"<h4>Background</h4> REACT-1 measures prevalence of SARS-CoV-2 infection in representative samples of the population in England using PCR testing from self-administered nose and throat swabs. Here we report interim results for round 6 of observations for swabs collected from the 16th to 25th October 2020 inclusive. <h4>Methods</h4> REACT-1 round 6 aims to collect data and swab results from 160,000 people aged 5 and above. Here we report results from the first 86,000 individuals. We estimate prevalence of PCR-confirmed SARS-CoV-2 infection, reproduction numbers (R) and temporal trends using exponential growth or decay models. Prevalence estimates are presented both unweighted and weighted to be representative of the population of England, accounting for response rate, region, deprivation and ethnicity. We compare these interim results with data from round 5, based on swabs collected from 18th September to 5th October 2020 inclusive. <h4>Results</h4> Overall prevalence of infection in the community in England was 1.28% or 128 people per 10,000, up from 60 per 10,000 in the previous round. Infections were doubling every 9.0 (6.1, 18) days with a national reproduction number (R) estimated at 1.56 (1.27, 1.88) compared to 1.16 (1.05, 1.27) in the previous round. Prevalence of infection was highest in Yorkshire and The Humber at 2.72% (2.12%, 3.50%), up from 0.84% (0.60%, 1.17%), and the North West at 2.27% (1.90%, 2.72%), up from 1.21% (1.01%, 1.46%), and lowest in South East at 0.55% (0.45%, 0.68%), up from 0.29% (0.23%, 0.37%). Clustering of cases was more prevalent in Lancashire, Manchester, Liverpool and West Yorkshire, West Midlands and East Midlands. Interim estimates of R were above 2 in the South East, East of England, London and South West, but with wide confidence intervals. Nationally, prevalence increased across all age groups with the greatest increase in those aged 55-64 at 1.20% (0.99%, 1.46%), up 3-fold from 0.37% (0.30%, 0.46%). In those aged over 65, prevalence was 0.81% (0.58%, 0.96%) up 2-fold from 0.35% (0.28%, 0.43%). Prevalence remained highest in 18 to 24-year olds at 2.25% (1.47%, 3.42%). <h4>Conclusion</h4> The co-occurrence of high prevalence and rapid growth means that the second wave of the epidemic in England has now reached a critical stage. Whether via regional or national measures, it is now time-critical to control the virus and turn R below one if further hospital admissions and deaths from COVID-19 are to be avoided.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2020/11/03/2020.10.30.20223123.full.pdf; doi:https://doi.org/10.1101/2020.10.30.20223123; html:https://europepmc.org/article/PPR/PPR233362; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR233362&type=FILE&fileName=EMS103475-pdf.pdf&mimeType=application/pdf
 PPR339757,https://doi.org/10.1101/2021.05.08.21256867,SARS-CoV-2 lineage dynamics in England from January to March 2021 inferred from representative community samples,"Eales O, Page AJ, Tang SN, Walters CE, Wang H, Haw D, Trotter AJ, Viet TL, Foster-Nyarko E, Prosolek S, Atchison C, Ashby D, Cooke G, Barclay W, Donnelly CA, O’Grady J, Volz E, The COVID-19 Genomics UK (COG-UK) Consortium, Darzi A, Ward H, Elliott P, Riley S.",,No Journal Info,2021,2021-05-14,Y,,,,"Genomic surveillance for SARS-CoV-2 lineages informs our understanding of possible future changes in transmissibility and vaccine efficacy. However, small changes in the frequency of one lineage over another are often difficult to interpret because surveillance samples are obtained from a variety of sources. Here, we describe lineage dynamics and phylogenetic relationships using sequences obtained from a random community sample who provided a throat and nose swab for rt-PCR during the first three months of 2021 as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. Overall, diversity decreased during the first quarter of 2021, with the B.1.1.7 lineage (first identified in Kent) predominant, driven by a 0.3 unit higher reproduction number over the prior wild type. During January, positive samples were more likely B.1.1.7 in younger and middle-aged adults (aged 18 to 54) than in other age groups. Although individuals infected with the B.1.1.7 lineage were no more likely to report one or more classic COVID-19 symptoms compared to those infected with wild type, they were more likely to be antibody positive 6 weeks after infection. Viral load was higher in B.1.1.7 infection as measured by cycle threshold (Ct) values, but did not account for the increased rate of testing positive for antibodies. The presence of infections with non-imported B.1.351 lineage (first identified in South Africa) during January, but not during February or March, suggests initial establishment in the community followed by fade-out. However, this occurred during a period of stringent social distancing and targeted public health interventions and does not immediately imply similar lineages could not become established in the future. Sequence data from representative community surveys such as REACT-1 can augment routine genomic surveillance.",,doi:https://doi.org/10.1101/2021.05.08.21256867; doi:https://doi.org/10.1101/2021.05.08.21256867; html:https://europepmc.org/article/PPR/PPR339757; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR339757&type=FILE&fileName=EMS127680-pdf.pdf&mimeType=application/pdf
 PPR211672,https://doi.org/10.1101/2020.09.07.20189621,COVID-19 in patients with hepatobiliary and pancreatic diseases: A single-centre cross-sectional study in East London,"Ullah AZMD, Sivapalan L, Kocher HM, Chelala C.",,No Journal Info,2020,2020-09-09,N,,,,"<h4>ABSTRACT</h4> <h4>Objective</h4> To explore risk factors associated with COVID-19 susceptibility and survival in patients with pre-existing hepato-pancreato-biliary (HPB) conditions. <h4>Design</h4> Cross-sectional study. <h4>Setting</h4> East London Pancreatic Cancer Epidemiology (EL-PaC-Epidem) study at Barts Health NHS Trust, UK. Linked electronic health records were interrogated on a cohort of participants (age ≥ 18 years), reported with HPB conditions between 1 April 2008 and 6 March 2020. <h4>Participants</h4> EL-PaC-Epidem study participants, alive on 12 February 2020, and living in East London within the previous six months (n=15 440). The cohort represents a multi-ethnic population with 51.7% belonging to the non-White background. <h4>Main outcome measure</h4> COVID-19 incidence and mortality. <h4>Results</h4> Some 226 (1.5%) participants had confirmed COVID-19 diagnosis between 12 February and 12 June 2020, with an increased odds for men (OR 1.56; 95% CI 1.2 to 2.04) and Black ethnicity (2.04; 1.39 to 2.95) as well as patients with moderate to severe liver disease (2.2; 1.35 to 3.59). Each additional comorbidity increased the odds of infection by 62%. Substance mis-users were at more risk of infection, so were patients on Vitamin D treatment. The higher odds ratios in patients with chronic pancreatic or mild liver conditions, age>70, and history of smoking or obesity were due to co-existing comorbidities. Increased odds of death were observed for men (3.54; 1.68 to 7.85) and Black ethnicity (3.77; 1.38 to 10.7). Patients having respiratory complications from COVID-19 without a history of chronic respiratory disease also had higher odds of death (5.77; 1.75 to 19). <h4>Conclusions</h4> In this large population-based study of HPB patients, men, Black ethnicity, pre-existing moderate to severe liver conditions, six common medical multi-morbidities, substance mis-use, and a history of Vitamin D treatment independently posed higher odds of acquiring COVID-19 compared to their respective counterparts. The odds of death were significantly high for men and Black people. <h4>STRENGTHS AND LIMITATIONS OF THIS STUDY</h4> First multi-ethnic population-based study on COVID-19 in patients with hepato-pancreato-biliary group of diseases. Systematic identification of the effect, or the lack of it, of individual demographic and clinical factors on the infection and mortality of COVID-19 in a large cohort of over 15 000 patients, robustly controlling for potential confounders in their evaluation. Access to longitudinal data from linked primary and secondary care electronic health records, and use of rule-based phenotyping algorithms allowed for improved completeness and accuracy of the explored variables. Some observed increased odds of SARS-CoV-2 infection and related death could be plausibly explained by unmeasured confounding. The effects reported in the study could be influenced by the relatively smaller size of COVID-19 cases within this cohort.",,pdf:https://qmro.qmul.ac.uk/xmlui/bitstream/123456789/75991/2/Kocher%20COVID-19%20in%20patients%20with%20hepatobiliary%20and%20pancreatic%20diseases%3a%20A%20single-centre%20cross-sectional%20study%20in%20East%20London%202021%20Published.pdf; doi:https://doi.org/10.1101/2020.09.07.20189621; html:https://europepmc.org/article/PPR/PPR211672; doi:https://doi.org/10.1101/2020.09.07.20189621
 PPR850159,https://doi.org/10.1101/2024.05.08.24306990,The impact of the COVID-19 pandemic on Antidepressant Prescribing with a focus on people with learning disability and autism: An interrupted time-series analysis in England using OpenSAFELY-TPP,"Cunningham C, Macdonald O, Schaffer AL, Brown A, Wiedemann M, Higgins R, Bates C, Parry J, Fisher L, Curtis HJ, Mehrkar A, Hart LC, Bacon S, Hulme W, Speed V, Ward T, Croker R, Wood C, Walker A, Andrews C, Butler-Cole B, Evans D, Inglesby P, Dillingham I, Davy S, Bridges L, O’Dwyer T, Maude S, Smith R, Goldacre B, MacKenna B.",,No Journal Info,2024,2024-05-08,Y,,,,"<h4>Background</h4> COVID-19 lockdowns led to increased reports of depressive symptoms in the general population and impacted the health and social care services of people with learning disability and autism. We explored whether the COVID-19 pandemic had an impact on antidepressant prescribing trends within these and the general population. <h4>Methods</h4> With the approval of NHS England, we used >24 million patients’ primary care data from the OpenSAFELY-TPP platform. We identified patients with learning disability or autism and used an interrupted time series analysis to quantify trends in those prescribed and newly prescribed an antidepressant across key demographic and clinical subgroups, comparing pre-COVID-19 (January 2018-February 2020), COVID-19 lockdown (March 2020-February 2021) and the recovery period (March 2021-December 2022). <h4>Results</h4> Prior to COVID-19 lockdown, antidepressant prescribing was increasing at 0.3% (95% CI 0.2% to 0.3%) patients per month, in the general population and in those with learning disability, and 0.3% (95% CI 0.2% to 0.4%) in those with autism. We did not find evidence that the pandemic was associated with a change in trend of antidepressant prescribing in the general population (RR 1.00 (95% CI 0.97 to 1.02)), in those with autism (RR 0.99 (95% CI 0.97 to 1.01)), or in those with learning disability (RR 0.98 (95% CI 0.96 to 1.00)). New prescribing post lockdown was 13% and 12% below expected if COVID-19 had not happened in both the general population and those with autism (RR 0.87 (95% CI 0.83 to 0.93), RR 0.88 (95% CI 0.83 to 0.92))), but not learning disability (RR 0.96 (95% CI 0.87 to 1.05)). <h4>Conclusions and Implications</h4> Pre-COVID-19, antidepressant prescribing was increasing at 0.3% per month. While we did not see an impact of COVID-19 on overall prescribing in the general population, prescriptions to those aged 0-19, 20-29, and new prescriptions were lower than pre-COVID-19 trends would have predicted, but tricyclics and new prescriptions in care homes were higher than expected. <h4>What is already known on this topic</h4> ⇒ The prescribing of antidepressants in the UK has been increasing for more than a decade. ⇒ Studies globally have found differing impacts of COVID-19 on mental health outcomes in the general population, by age, sex, socio-economic status, and care home status. <h4>What this study adds</h4> ⇒ This study describes the impact of COVID-19 on antidepressant prescribing in England with additional follow-up through December 2022, with a focus on people with a learning disability or autism. <h4>How this study might affect research, practice, or policy</h4> ⇒ This study demonstrates how the pandemic did not lead to an increase in antidepressant prescriptions in the general population, but more is needed to ensure that antidepressants are used appropriately within vulnerable populations. ⇒ Improvements are needed in the documentation of diagnosis when prescribing medicines.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2024/05/08/2024.05.08.24306990.full.pdf; doi:https://doi.org/10.1101/2024.05.08.24306990; html:https://europepmc.org/article/PPR/PPR850159; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR850159&type=FILE&fileName=EMS196120-pdf.pdf&mimeType=application/pdf
 PPR924132,https://doi.org/10.1101/2024.10.13.24315407,Provision of medical Same Day Emergency Care services within the UK: analysis from the Society for Acute Medicine Benchmarking Audit,"Atkin C, Perrett M, Holland M, Cooksley T, Knight T, Varia R, Subbe C, Lasserson D, Sapey E.",,No Journal Info,2024,2024-10-14,Y,,,,"<h4>Aim</h4> To evaluate current provision of medical Same Day Emergency Care (SDEC) services within the UK, and current utilisation of these pathways in the assessment of unplanned medical attendances. <h4>Design</h4> Survey data was used from the Society for Acute Medicine Benchmarking Audit (SAMBA), including anonymised patient-level data collected annually using a day of care survey <h4>Setting</h4> Hospitals accepting unplanned medical attendances within the UK, 2019-2023. Participants: 34,948 unplanned and 4,342 planned attendances, across 188 hospital sites <h4>Results</h4> 29.8% of unplanned medical attendances received their initial medical assessment within SDEC services, with the proportion increasing over time. 82.4% of patients assessed in SDEC services were discharged without overnight admission. Assessment in SDEC services was less likely in male patients, patients with frailty, and older adults (all p<0.005). Selected operational standards for SDEC delivery were met in 64-91% of hospitals. Most hospitals (82%) accepted referrals from emergency department triage and 63% accepted referral directly from the paramedic team. 38% of hospitals did not use a recognised selection criteria to identify suitable patients for SDEC and only 8% used a criteria designed to identify patients suitable for discharge. Overall, 34.7% of medical attendances discharged without overnight admission received their medical assessment in locations other than SDEC. <h4>Conclusions</h4> Medical SDEC provides assessment for one third of patients seen through acute medicine services. Although the proportion of patients assessed within SDEC is increasing, further innovation and improvements are needed to ensure appropriate patients access this service. <h4>Strengths and limitations of this study</h4> -Medical same day emergency care (SDEC) has been widely adopted in the UK to deliver care to patients without overnight hospital admission, however there is limited evidence guiding development of this service. -This study compares hospital-level data describing SDEC service structure and processes, and patient level data for over 35,000 patient attendances at 188 hospitals in the UK. -This is the largest evaluation of medical SDEC to date and demonstrates an increase in the use of SDEC for medical patients nationally. -The participation rate was higher amongst hospitals in England compared to the other three UK nations, which may limit generalisability.",,doi:https://doi.org/10.1101/2024.10.13.24315407; doi:https://doi.org/10.1101/2024.10.13.24315407; html:https://europepmc.org/article/PPR/PPR924132; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR924132&type=FILE&fileName=EMS199443-pdf.pdf&mimeType=application/pdf
 PPR698319,https://doi.org/10.1101/2023.07.25.23293143,The Cost of Keeping Patients Waiting: Retrospective Treatment-Control Study of Additional Healthcare Utilisation for UK Patients Awaiting Elective Treatment Following COVID-19,"James C, Denholm R, Wood R.",,No Journal Info,2023,2023-07-27,Y,,,,"<h4>Objective</h4> The COVID-19 pandemic has led to increased waiting times for elective treatments in many countries. This study seeks to address a deficit in the literature concerning the effect of long waits on the wider consumption of healthcare resources. <h4>Methods</h4> We carried out a retrospective treatment-control study in a healthcare system in South West England from 15 June 2021 to 15 December 2021. We compared weekly contacts with health services of patients waiting over 18 weeks for treatment (‘Treatments’) and people not on a waiting list (‘Controls’). Controls were matched to Treatments based on age, sex, deprivation and multimorbidity. Treatments were stratified by the clinical specialty of the awaited treatment, with healthcare usage assessed over various healthcare settings. T-tests assessed whether there was an increase in healthcare utilisation and bootstrap resampling was used to estimate the magnitude of any differences. <h4>Results</h4> A total of 44,616 patients were waiting over 18 weeks (the constitutional target in England) for treatment during the study period. Evidence suggests increases (p < 0.05) in healthcare utilisation for all specialties. Patients in the Cardiothoracic Surgery specialty had the largest increase, requiring 17.9 [4.3, 33.8] additional contacts with secondary care and 17.3 [-1.1, 34.1] additional prescriptions per year. <h4>Conclusion</h4> People waiting for treatment consume higher levels of healthcare than comparable individuals not on a waiting list. These findings are relevant for clinicians and managers in better understanding patient need and reducing harm. Results also highlight the possible ‘false economy’ in failing to promptly resolve long elective waits. <h4>Highlights</h4> Long waits for elective care can result in additional healthcare needs to manage symptoms up to the point of definitive treatment. While previous studies indicate some association, these mainly consider only a single elective specialty and are limited in the range of healthcare settings covered. The large number of long-wait pathways produced as a consequence of COVID-19 disruption allows for a more holistic analysis, covering the full range of elective treatment specialties and wider healthcare impacts across primary, secondary, mental health, and community care, as well as emergency service calls and prescriptions. Analysis of 44,616 elective care pathways reveals evidence of increases in wider healthcare consumption additional to that expected for similar patients not awaiting elective treatment. This suggests a ‘false economy’ in failing to promptly resolve elective pathways, which should be reflected by healthcare providers in long-term resource allocation decisions.",,doi:https://doi.org/10.1101/2023.07.25.23293143; html:https://europepmc.org/article/PPR/PPR698319; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR698319&type=FILE&fileName=EMS182115-pdf.pdf&mimeType=application/pdf
-PPR573001,https://doi.org/10.1101/2022.11.16.22282338,Proteomic analysis of circulating immune cells identifies novel cellular phenotypes associated with COVID-19 severity,"Potts M, Fletcher-Etherington A, Nightingale K, Mescia F, Bergamaschi L, Calero-Nieto FJ, Antrobus R, Williamson J, Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID BioResource Collaboration, Kingston N, Göttgens B, Bradley JR, Lehner PJ, Matheson NJ, Smith KG, Wills MR, Lyons PA, Weekes MP.",,No Journal Info,2022,2022-11-18,Y,,,,"<h4>Summary</h4> Certain serum proteins, including CRP and D-dimer, have prognostic value in patients with SARS-CoV-2 infection. Nonetheless, these factors are non-specific, and provide limited mechanistic insight into the peripheral blood mononuclear cell (PBMC) populations which drive the pathogenesis of severe COVID-19. To identify novel cellular phenotypes associated with disease progression, we here describe a comprehensive, unbiased analysis of the total and plasma membrane proteomes of PBMCs from a cohort of 40 unvaccinated individuals with SARS-CoV-2 infection, spanning the whole spectrum of disease severity. Combined with RNA-seq and flow cytometry data from the same donors, we define a comprehensive multi-omic profile for each severity level, revealing cumulative immune cell dysregulation in progressive disease. In particular, the cell surface proteins CEACAMs1, 6 and 8, CD177, CD63 and CD89 are strongly associated with severe COVID-19, corresponding to the emergence of atypical CD3 + CD4 + CD177 + and CD16 + CEACAM1/6/8 + mononuclear cells. Utilisation of these markers may facilitate real-time patient assessment by flow cytometry, and identify immune cell populations that could be targeted to ameliorate immunopathology.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/11/18/2022.11.16.22282338.full.pdf; doi:https://doi.org/10.1101/2022.11.16.22282338; html:https://europepmc.org/article/PPR/PPR573001; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR573001&type=FILE&fileName=EMS157354-pdf.pdf&mimeType=application/pdf
 PPR265251,https://doi.org/10.1101/2021.01.15.21249724,Development and evaluation of rapid data-enabled access to routine clinical information to enhance early recruitment to the national clinical platform trial of COVID-19 community treatments,"Cake C, Ogburn E, Pinches H, Coleman G, Seymour D, Woodard F, Manohar S, Monsur M, Landray M, Dalton G, Morris AD, Chinnery PF, UK COVID-19 National Core Studies Consortium, Hobbs FR, Butler C.",,No Journal Info,2021,2021-01-15,Y,,,,"<h4>ABSTRACT</h4> <h4>Background</h4> The COVID-19 pandemic has presented unique challenges for rapidly designing, initiating, and delivering therapeutic clinical trials. PRINCIPLE is the UK national platform investigating repurposed therapies for COVID-19 treatment of older people in the community at high risk of complications. Standard methods of patient recruitment were failing to meet the required pace and scale of enrolment. This paper describes the development and appraisal of a near real-time, data-driven, ethical approach for enhancing recruitment in community care by contacting people with a recent COVID-19 positive test result from the central NHS Test and Trace service within 24-48 hours of their test result. <h4>Methods</h4> A multi-disciplinary team was formed to solve the technical, ethical, public perception, logistical and information governance issues required to provide a near-real time (within 24-48 hours of receiving a positive test) feed of potential trial participants from test result data to the research team. PRINCIPLE was also given unique access to the Summary Care Record (SCR) to ensure safe prescribing, and to enable the trial team to quickly and safely bring consented patients into the trial. A survey of the public was used to understand public perceptions of the use of test data for this proposed methodology. <h4>Results</h4> Prior to establishing the data service, PRINCIPLE registered on average 87 participants per week. This increased by up to 87 additional people registered per week from the test data, contributing to an increase from 1,013 recruits to PRINCIPLE at the start of October 2020 to 2,802 recruits by 20 th December 2020. While procedural caveats were identified by the public consultation, out of 2,639 people contacted by PRINCIPLE following a positive test result, no one raised a concern about being approached. <h4>Conclusions</h4> This paper describes a novel approach to using near-real time NHS operational data to recruit community-based patients within a few days of presentation with acute illness. This approach increased recruitment, and reduced time between positive test and randomisation, allowing more rapid evaluation of treatments and increased safety for participants. End-to-end public and patient involvement in the design of the approach provided evidence to inform information governance decisions. <h4>Trial registration</h4> PRINCIPLE is funded by UK Research and Innovation and the Department of Health and Social Care through the National Institute for Health Research. EudraCT number: 2020-001209-22 ISRCTN registry: ISRCTN86534580 REC number: 20/SC/058 IRAS number: 281958",,pdf:https://trialsjournal.biomedcentral.com/counter/pdf/10.1186/s13063-021-05965-4; doi:https://doi.org/10.1101/2021.01.15.21249724; html:https://europepmc.org/article/PPR/PPR265251; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR265251&type=FILE&fileName=EMS110588-pdf.pdf&mimeType=application/pdf
+PPR573001,https://doi.org/10.1101/2022.11.16.22282338,Proteomic analysis of circulating immune cells identifies novel cellular phenotypes associated with COVID-19 severity,"Potts M, Fletcher-Etherington A, Nightingale K, Mescia F, Bergamaschi L, Calero-Nieto FJ, Antrobus R, Williamson J, Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID BioResource Collaboration, Kingston N, Göttgens B, Bradley JR, Lehner PJ, Matheson NJ, Smith KG, Wills MR, Lyons PA, Weekes MP.",,No Journal Info,2022,2022-11-18,Y,,,,"<h4>Summary</h4> Certain serum proteins, including CRP and D-dimer, have prognostic value in patients with SARS-CoV-2 infection. Nonetheless, these factors are non-specific, and provide limited mechanistic insight into the peripheral blood mononuclear cell (PBMC) populations which drive the pathogenesis of severe COVID-19. To identify novel cellular phenotypes associated with disease progression, we here describe a comprehensive, unbiased analysis of the total and plasma membrane proteomes of PBMCs from a cohort of 40 unvaccinated individuals with SARS-CoV-2 infection, spanning the whole spectrum of disease severity. Combined with RNA-seq and flow cytometry data from the same donors, we define a comprehensive multi-omic profile for each severity level, revealing cumulative immune cell dysregulation in progressive disease. In particular, the cell surface proteins CEACAMs1, 6 and 8, CD177, CD63 and CD89 are strongly associated with severe COVID-19, corresponding to the emergence of atypical CD3 + CD4 + CD177 + and CD16 + CEACAM1/6/8 + mononuclear cells. Utilisation of these markers may facilitate real-time patient assessment by flow cytometry, and identify immune cell populations that could be targeted to ameliorate immunopathology.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/11/18/2022.11.16.22282338.full.pdf; doi:https://doi.org/10.1101/2022.11.16.22282338; html:https://europepmc.org/article/PPR/PPR573001; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR573001&type=FILE&fileName=EMS157354-pdf.pdf&mimeType=application/pdf
 PPR354056,https://doi.org/10.1101/2021.06.08.21258535,Altered neutrophil phenotype and function in non-ICU hospitalised COVID-19 patients correlated with disease severity,"Belchamber K, Thein O, Hazeldine J, Grudzinska F, Hughes M, Jasper A, Yip K, Sapey E, Parekh D, Thickett D, Scott A.",,No Journal Info,2021,2021-06-08,Y,,,,"<h4>Rational</h4> Infection with the SARS-CoV2 virus is associated with elevated neutrophil counts. Evidence of neutrophil dysfunction in COVID-19 is based predominantly on transcriptomics or single functional assays. Cell functions are interwoven pathways, and so understanding the effect of COVID-19 across the spectrum of neutrophil function may identify tractable therapeutic targets. <h4>Objectives</h4> Examine neutrophil phenotype and functional capacity in COVID-19 patients versus age-matched controls (AMC) <h4>Methods</h4> Isolated neutrophils from 41 hospitalised, non-ICU COVID-19 patients and 23 AMC underwent ex vivo analyses for migration, bacterial phagocytosis, ROS generation, NET formation (NETosis) and cell surface receptor expression. DNAse 1 activity was measured, alongside circulating levels of cfDNA, MPO, VEGF, IL-6 and sTNFRI. All measurements were correlated to clinical outcome. Serial sampling on day 3-5 post hospitalisation were also measured. <h4>Results</h4> Compared to AMC, COVID-19 neutrophils demonstrated elevated transmigration (p=0.0397) and NETosis (p=0.0366), but impaired phagocytosis (p=0.0236) associated with impaired ROS generation (p<0.0001). Surface expression of CD54 (p<0.0001) and CD11c (p=0.0008) was significantly increased and CD11b significantly decreased (p=0.0229) on COVID-19 patient neutrophils. COVID-19 patients showed increased systemic markers of NETosis including increased cfDNA (p=0.0153) and impaired DNAse activity (p<0.0.001). MPO (p<0.0001), VEGF (p<0.0001), TNFRI (p<0.0001) and IL-6 (p=0.009) were elevated in COVID-19, which positively correlated with disease severity by 4C score. <h4>Conclusion</h4> COVID-19 is associated with neutrophil dysfunction across all main effector functions, with altered phenotype, elevated migration, impaired antimicrobial responses and elevated NETosis. These changes represent a clear mechanism for tissue damage and highlight that targeting neutrophil function may help modulate COVID-19 severity.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2021/06/08/2021.06.08.21258535.full.pdf; doi:https://doi.org/10.1101/2021.06.08.21258535; html:https://europepmc.org/article/PPR/PPR354056; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR354056&type=FILE&fileName=EMS127476-pdf.pdf&mimeType=application/pdf
 PPR278785,https://doi.org/10.1101/2021.02.03.21251004,Ethnic differences in COVID-19 mortality during the first two waves of the Coronavirus Pandemic: a nationwide cohort study of 29 million adults in England,"Nafilyan V, Islam N, Mathur R, Ayoubkhani D, Banerjee A, Glickman M, Humberstone B, Diamond I, Khunti K.",,No Journal Info,2021,2021-02-05,Y,,,,"<h4>Background</h4> Ethnic minorities have experienced disproportionate COVID-19 mortality rates in the UK and many other countries. We compared the differences in the risk of COVID-19 related death between ethnic groups in the first and second waves the of COVID-19 pandemic in England. We also investigated whether the factors explaining differences in COVID-19 death between ethnic groups changed between the two waves. <h4>Methods</h4> Using data from the Office for National Statistics Public Health Data Asset on individuals aged 30-100 years living in private households, we conducted an observational cohort study to examine differences in the risk of death involving COVID-19 between ethnic groups in the first wave (from 24 th January 2020 until 31 st August 2020) and second wave (from 1 st September to 28 th December 2020). We estimated age-standardised mortality rates (ASMR) in the two waves stratified by ethnic groups and sex. We also estimated hazard ratios (HRs) for ethnic-minority groups compared with the White British population, adjusted for geographical factors, socio-demographic characteristics, and pre-pandemic health conditions. <h4>Results</h4> The study population included over 28.9 million individuals aged 30-100 years living in private households. In the first wave, all ethnic minority groups had a higher risk of COVID-19 related death compared to the White British population. In the second wave, the risk of COVID-19 death remained elevated for people from Pakistani (ASMR: 339.9 [95% CI: 303.7 – 376.2] and 166.8 [141.7 – 191.9] deaths per 100,000 population in men and women) and Bangladeshi (318.7 [247.4 – 390.1] and 127.1 [91.1 – 171.3] in men and women)background but not for people from Black ethnic groups. Adjustment for geographical factors explained a large proportion of the differences in COVID-19 mortality in the first wave but not in the second wave. Despite an attenuation of the elevated risk of COVID-19 mortality after adjusting for sociodemographic characteristics and health status, the risk was substantially higher in people from Bangladeshi and Pakistani background in both the first and the second waves. <h4>Conclusion</h4> Between the first and second waves of the pandemic, the reduction in the difference in COVID-19 mortality between people from Black ethnic background and people from the White British group shows that ethnic inequalities in COVID-19 mortality can be addressed. The continued higher rate of mortality in people from Bangladeshi and Pakistani background is alarming and requires focused public health campaign and policy changes. *VN and NI contributed equally to this paper <h4>Research in context</h4> <h4>Evidence before this study</h4> A recent systematic review by Pan and colleagues demonstrated that people of ethnic minority background in the UK and the USA have been disproportionately affected by the Coronavirus (COVID-19) pandemic, compared to White populations. While several studies have investigated whether adjusting for socio-demographic and economic factors and medical history reduces the estimated difference in risk of mortality and hospitalisation, the reasons for the differences in the risk of experiencing harms from COVID-19 are still being explored during the course of the pandemic. Studies so far have analysed the ethnic differences in COVID-19 mortality in the first wave of the pandemic. The evidence on the temporal trend of ethnic inequalities in COVID-19 mortality, especially those from the second wave of the pandemic, is scarce. <h4>Added value of this study</h4> Using data from the Office for National Statistics (ONS) Public Health Data Asset on 29 million adults aged 30-100 years living in private households in England, we conducted an observational cohort study to examine the differences in the risk of death involving COVID-19 between ethnic groups in the first wave (from 24 th January 2020 until 31 st August 2020) and second wave (from 1 st September to 28 th December 2020). We find that in the first wave all ethnic minority groups were at elevated risk of COVID-19 related death compared to the White British population. In the second wave, the differences in the risk of COVID-19 related death attenuated for Black African and Black Caribbean groups, remained substantially higher in people from Bangladeshi background, and worsened in people from Pakistani background. We also find that some of the factors explaining these differences in mortality have changed in the two waves. <h4>Implications of all the available evidence</h4> The risk of COVID-19 mortality during the first wave of the pandemic was elevated in people from ethnic minority background. An appreciable reduction in the difference in COVID-19 mortality in the second wave of the pandemic between people from Black ethnic background and people from the White British group is reassuring, but the continued higher rate of mortality in people from Bangladeshi and Pakistani background is alarming and requires focused public health campaign and policy response. Focusing on treating underlying conditions, although important, may not be enough in reducing the inequalities in COVID-19 mortality. Focused public health policy as well as community mobilisation and participatory public health campaign involving community leaders may help reduce the existing and widening inequalities in COVID-19 mortality.",,doi:https://doi.org/10.1007/s10654-021-00765-1; doi:https://doi.org/10.1101/2021.02.03.21251004; html:https://europepmc.org/article/PPR/PPR278785; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR278785&type=FILE&fileName=EMS116038-pdf.pdf&mimeType=application/pdf
 PPR365249,https://doi.org/10.1101/2021.06.28.21259452,"Persistent symptoms following SARS-CoV-2 infection in a random community sample of 508,707 people","Whitaker M, Elliott J, Chadeau-Hyam M, Riley S, Darzi A, Cooke G, Ward H, Elliott P.",,No Journal Info,2021,2021-07-03,Y,,,,"<h4>Summary</h4> <h4>Background</h4> Long COVID, describing the long-term sequelae after SARS-CoV-2 infection, remains a poorly defined syndrome. There is uncertainty about its predisposing factors and the extent of the resultant public health burden, with estimates of prevalence and duration varying widely. <h4>Methods</h4> Within rounds 3–5 of the REACT-2 study, 508,707 people in the community in England were asked about a prior history of COVID-19 and the presence and duration of 29 different symptoms. We used uni-and multivariable models to identify predictors of persistence of symptoms (12 weeks or more). We estimated the prevalence of symptom persistence at 12 weeks, and used unsupervised learning to cluster individuals by symptoms experienced. <h4>Findings</h4> Among the 508,707 participants, the weighted prevalence of self-reported COVID-19 was 19.2% (95% CI: 19.1,19.3). 37.7% of 76,155 symptomatic people post COVID-19 experienced at least one symptom, while 14.8% experienced three or more symptoms, lasting 12 weeks or more. This gives a weighted population prevalence of persistent symptoms of 5.75% (5.68, 5.81) for one and 2.22% (2.1, 2.26) for three or more symptoms. Almost a third of people (8,771/28,713 [30.5%]) with at least one symptom lasting 12 weeks or more reported having had severe COVID-19 symptoms (“significant effect on my daily life”) at the time of their illness, giving a weighted prevalence overall for this group of 1.72% (1.69,1.76). The prevalence of persistent symptoms was higher in women than men (OR: 1.51 [1.46,1.55]) and, conditional on reporting symptoms, risk of persistent symptoms increased linearly with age by 3.5 percentage points per decade of life. Obesity, smoking or vaping, hospitalisation, and deprivation were also associated with a higher probability of persistent symptoms, while Asian ethnicity was associated with a lower probability. Two stable clusters were identified based on symptoms that persisted for 12 weeks or more: in the largest cluster, tiredness predominated, while in the second there was a high prevalence of respiratory and related symptoms. <h4>Interpretation</h4> A substantial proportion of people with symptomatic COVID-19 go on to have persistent symptoms for 12 weeks or more, which is age-dependent. Clinicians need to be aware of the differing manifestations of Long COVID which may require tailored therapeutic approaches. Managing the long-term sequelae of SARS-CoV-2 infection in the population will remain a major challenge for health services in the next stage of the pandemic. <h4>Funding</h4> The study was funded by the Department of Health and Social Care in England. <h4>Research in context</h4> <h4>Evidence before this study</h4> Recent systematic reviews have documented the wide range of symptoms and reported prevalence of persistent symptoms following COVID-19. A dynamic review of Long COVID studies (NIHR Evidence) in March 2021 summarised the literature on the prevalence of persistent symptoms after acute COVID19, and reported that most studies (14) were of hospitalised patients, with higher prevalence of persistent symptoms compared with two community-based studies. There was limited evidence from community studies beyond 12 weeks. Another systematic review reported a median of over 70% of people with symptoms lasting at least 60 days. A review of risk factors for Long COVID found consistent evidence for an increased risk amongst women and those with high body mass index (BMI) but inconsistent findings on the role of age and little evidence concerning risks among different socioeconomic or ethnic groups which are often not well captured in routine healthcare records. Long COVID is increasingly recognised as heterogenous, likely underpinned by differing biological mechanisms, but there is not yet consensus on defining subtypes of the condition. <h4>Added value of this study</h4> This community-based study of over half a million people was designed to be representative of the adult population of England. A random sample of adults ages 18 years and above registered with a GP were invited irrespective of previous access to services for COVID-19, providing an estimate of population prevalence that was representative of the whole population. The findings show substantial declines in symptom prevalence over the first 12 weeks following Covid-19, reported by nearly one fifth of respondents, of whom over a third remained symptomatic at 12 weeks and beyond, with little evidence for decline thereafter. Risk factors identified for persistent symptoms (12 weeks or more) suggestive of Long COVID confirm some previous findings - an increased risk in women, obese and overweight individuals and those hospitalised for COVID-19, with strong evidence for an increasing risk with age. Additional evidence was found for an increased risk in those with lower income, smoking or vaping and healthcare or care home workers. A lower risk was found in those of Asian ethnicity. Clustering identified two distinct groups of individuals wit h different symptom profiles at 12 weeks, highlighting the heterogeneity of clinical presentation. The smaller cluster had higher prevalence of respiratory and related symptoms, while for those in the larger cluster tiredness was the dominant symptom, with lower prevalence of organ-specific symptoms. <h4>Implications of available evidence</h4> There is a high prevalence of persistent symptoms beyond 12 weeks after acute COVID-19, with little evidence of decline thereafter. This highlights the needs for greater support for patients, both through specialised services and, for those from low-income settings, financial support. The understanding that there are distinct clusters of persistent symptoms, the most common of which is dominated by fatigue, is important for the recognition and clinical management of the condition outside of specialised services.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2021/07/03/2021.06.28.21259452.full.pdf; doi:https://doi.org/10.1101/2021.06.28.21259452; html:https://europepmc.org/article/PPR/PPR365249; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR365249&type=FILE&fileName=EMS129876-pdf.pdf&mimeType=application/pdf
@@ -183,12 +183,12 @@ PPR449587,https://doi.org/10.1101/2022.02.01.22270235,Hospitalisation for COVID-
 PPR373640,https://doi.org/10.1101/2021.07.21.21260926,"Increasing SARS-CoV-2 antibody prevalence in England at the start of the second wave: REACT-2 Round 4 cross-sectional study in 160,000 adults","Ward H, Atchison C, Whitaker M, Donnelly CA, Riley S, Ashby D, Darzi A, Barclay WS, Cooke G, Elliott P, for the REACT study team.",,No Journal Info,2021,2021-07-22,Y,,,,"<h4>Background</h4> REACT-2 Study 5 is a population survey of the prevalence of SARS-CoV-2 antibodies in the community in England. <h4>Methods</h4> We contacted a random sample of the population by sending a letter to named individuals aged 18 or over from the NHS GP registrations list. We then sent respondents a lateral flow immunoassay (LFIA) kit for SARS-CoV-2 antibody self-testing and asked them to perform the test at home and complete a questionnaire, including reporting of their test result. Overall, 161,537 adults completed questionnaires and self-administered LFIA tests for IgG against SARS-CoV-2 between 27 October and 10 November 2020. <h4>Results</h4> The overall adjusted and weighted prevalence was 5.6% (95% CI 5.4-5.7). This was an increase from 4.4% (4.3-4.5) in round 3 (September), a relative increase of 26.9% (24.0-29.9).The largest increase by age was in the 18 to 24 year old age group, which increased (adjusted and weighted) from 6.7% (6.3-7.2) to 9.9% (9.3-10.4), and in students, (adjusted, unweighted) from 5.9% (4.8-7.1) to 12.1% (10.8-13.5). Prevalence increased most in Yorkshire and The Humber, from 3.4% (3.0-3.8) to 6.3% (5.9-6.8) and the North West from 4.5% (4.2-4.9) to 7.7% (7.2-8.1). In contrast, the prevalence in London was stable, at 9.5% (9.0-9.9) and 9.5% (9.1-10.0) in rounds 3 and 4 respectively. We found the highest prevalence in people of Bangladeshi 15.1% (10.9-20.5), Pakistani 13.9% (11.2-17.2) and African 13.5% (10.7-16.8) ethnicity, and lowest in those of white British ethnicity at 4.2% (4.0-4.3). <h4>Interpretation</h4> The second wave of infection in England is apparent in increasing antibody prevalence, particularly in younger people, students, and in the Northern Regions. By late October a large proportion of the population remained susceptible to SARS-CoV-2 infection in England based on naturally acquired immunity from the first and early second wave.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2021/07/22/2021.07.21.21260926.full.pdf; doi:https://doi.org/10.1101/2021.07.21.21260926; html:https://europepmc.org/article/PPR/PPR373640; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR373640&type=FILE&fileName=EMS132216-pdf.pdf&mimeType=application/pdf
 PPR247290,https://doi.org/10.1101/2020.11.30.20239806,REACT-1 round 7 interim report: fall in prevalence of swab-positivity in England during national lockdown,"Riley S, Eales O, Walters CE, Wang H, Ainslie KEC, Atchison C, Fronterre C, Diggle PJ, Ashby D, Donnelly CA, Cooke G, Barclay W, Ward H, Darzi A, Elliott P.",,No Journal Info,2020,2020-12-02,Y,,,,"<h4>Background</h4> The second wave of the 2020 COVID-19 pandemic in England has been characterized by high growth and prevalence in the North with lower prevalence in the South. High prevalence was first observed at younger adult ages before spreading out to school-aged children and older adults. Local tiered interventions were in place up to 5th November 2020 at which time a second national lockdown was implemented. <h4>Methods</h4> REACT-1 is a repeated cross-sectional survey of SARS-CoV-2 swab-positivity in random samples of the population of England. The current period of data collection (round 7) commenced on 13th November 2020 and we report interim results here for swabs collected up to and including 24th November 2020. Because there were two distinct periods of growth during the previous round 6, here we compare results from round 7 (mainly) with the second half of round 6, which obtained swabs between 26th October and 2nd November 2020. We report prevalence both unweighted and reweighted to be representative of the population of England. We describe trends in unweighted prevalence with daily growth rates, doubling times, reproduction numbers (R) and splines. We estimated odds ratios for swab-positivity using mutually-adjusted multivariable logistic regression models. <h4>Results</h4> We found 821 positives from 105,123 swabs giving an unweighted prevalence of 0.78% (95% CI, 0.73%, 0.84%) and a weighted prevalence of 0.96% (0.87%, 1.05%). The weighted prevalence estimate was ∼30% lower than that of 1.32% (1.20%, 1.45%) obtained in the second half of round 6. This decrease corresponds to a halving time of 37 (30, 47) days and an R number of 0.88 (0.86, 0.91). Using only data from the most recent period, we estimate an R number of 0.71 (0.54, 0.90). A spline fit to prevalence showed a rise shortly after the previous period of data collection followed by a fall coinciding with the start of lockdown. The national trends were driven mainly by reductions in higher-prevalence northern regions, with prevalence approximately unchanged in the Midlands and London, and smaller reductions in southern lower-prevalence regions. Sub-regional analyses showed variable changes in prevalence at the local level including marked declines in the North, but also local areas of growth in East and West Midlands. Mutually adjusted models in the most recent period indicated: people of Asian ethnicity, those living in the most deprived neighbourhoods, and those living in the largest households, had higher odds of swab-positivity. <h4>Conclusion</h4> Three weeks into the second national lockdown in England there has been a ∼30% proportionate reduction in prevalence overall, with greater reductions in the North. As a result, inter-regional heterogeneity has reduced, although average absolute prevalence remains high at ∼1%. Continued monitoring of the epidemic in the community remains essential until prevalence is reliably suppressed to much lower levels, for example, through widespread vaccination.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2020/12/02/2020.11.30.20239806.full.pdf; doi:https://doi.org/10.1101/2020.11.30.20239806; html:https://europepmc.org/article/PPR/PPR247290; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR247290&type=FILE&fileName=EMS107598-pdf.pdf&mimeType=application/pdf
 PPR380903,https://doi.org/10.1101/2021.08.10.21261834,Immuno-proteomic profiling reveals abundant airway CD8 T cells and ongoing epithelial injury in prolonged post-COVID19 respiratory disease,"Vijayakumar B, Boustani K, Ogger PP, Papadaki A, Tonkin J, Orton CM, Ghai P, Suveizdyte K, Hewitt RJ, Snelgrove RJ, Molyneaux PL, Garner JL, Peters JE, Shah PL, Lloyd CM, Harker JA.",,No Journal Info,2021,2021-08-10,Y,,,,"<h4>Summary</h4> Some patients hospitalized with acute COVID19 suffer respiratory symptoms that persist for many months. To characterize the local and systemic immune responses associated with this form of ‘Long COVID’, we delineated the immune and proteomic landscape in the airway and peripheral blood of normal volunteers and patients from 3 to 6 months after hospital discharge. The bronchoalveolar lavage (but not peripheral blood) proteome was abnormal in patients with post-COVID19 lung disease with significantly elevated concentration of proteins associated with apoptosis, tissue repair and epithelial injury. This correlated with an increase in cytotoxic lymphocytes (especially tissue resident CD8 + T cells), lactate dehydrogenase and albumin (biomarkers of cell death and barrier integrity). Follow-up of a subset of these patients greater than 1-year post-COVID19 indicated these abnormalities resolved over time. Collectively, these data indicate that COVID-19 results in a prolonged change to the airway immune landscape in those with persistent lung disease, with evidence of cell death and tissue repair linked to ongoing activation of cytotoxic T cells. <h4>Highlights</h4> The post-COVID19 airway is characterized by increased cytotoxic lymphocytes. Distinct airway proteomes are associated with the airway immune cell landscape. The peripheral blood does not predict immune-proteome alterations in the airway post-COVID19. Persistent abnormalities in the airway immune-proteome post-COVID19 airways correlate with ongoing epithelial damage.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2021/08/11/2021.08.10.21261834.full.pdf; doi:https://doi.org/10.1101/2021.08.10.21261834; html:https://europepmc.org/article/PPR/PPR380903; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR380903&type=FILE&fileName=EMS132662-pdf.pdf&mimeType=application/pdf
-PPR167068,https://doi.org/10.1101/2020.05.19.20106278,Benefit-risk analysis of health benefits of routine childhood immunisation against the excess risk of SARS-CoV-2 infections during the COVID-19 pandemic in Africa,"Abbas K, Procter SR, van Zandvoort K, Clark A, Funk S, LSHTM CMMID CMMID COVID-19 Working Group, Mengistu T, Hogan D, Dansereau E, Jit M, Flasche S.",,No Journal Info,2020,2020-05-26,Y,,,,"<h4>Summary</h4> <h4>Background</h4> National immunisation programmes globally are at risk of suspension due to the severe health system constraints and physical distancing measures in place to mitigate the ongoing COVID-19 pandemic. Our aim is to compare the health benefits of sustaining routine childhood immunisation in Africa against the risk of acquiring SARS-CoV-2 infections through visiting routine vaccination service delivery points. <h4>Methods</h4> We used two scenarios to approximate the child deaths that may be caused by immunisation coverage reductions during COVID-19 outbreaks. First, we used previously reported country-specific child mortality impact estimates of childhood immunisation for diphtheria, tetanus, pertussis, hepatitis B, Haemophilus influenzae type b, pneumococcal, rotavirus, measles, meningitis A, rubella, and yellow fever (DTP3, HepB3, Hib3, PCV3, RotaC, MCV1, MCV2, MenA, RCV, YFV) to approximate the future deaths averted before completing five years of age by routine childhood vaccination during a 6-month COVID-19 risk period without catch-up campaigns. Second, we analysed an alternative scenario that approximates the health benefits of sustaining routine childhood immunisation to only the child deaths averted from measles outbreaks during the COVID-19 risk period. The excess number of infections due to additional SARS-CoV-2 exposure during immunisation visits assumes that contact reducing interventions flatten the outbreak curve during the COVID-19 risk period, that 60% of the population will have been infected by the end of that period, that children can be infected by either vaccinators or during transport and that upon child infection the whole household would be infected. Country specific household age structure estimates and age dependent infection fatality rates are then applied to calculate the number of deaths attributable to the vaccination clinic visits. We present benefit-risk ratios for routine childhood immunisation alongside 95% uncertainty range estimates from probabilistic sensitivity analysis. <h4>Findings</h4> For every one excess COVID-19 death attributable to SARS-CoV-2 infections acquired during routine vaccination clinic visits, there could be 84 (14-267) deaths in children prevented by sustaining routine childhood immunisation in Africa. The benefit-risk ratio for the vaccinated children, siblings, parents or adult care-givers, and older adults in the households of vaccinated children are 85,000 (4,900 - 546,000), 75,000 (4,400 - 483,000), 769 (148 - 2,700), and 96 (14 - 307) respectively. In the alternative scenario that approximates the health benefits to only the child deaths averted from measles outbreaks, the benefit-risk ratio to the households of vaccinated children is 3 (0 - 10) under these highly conservative assumptions and if the risk to only the vaccinated children is considered, the benefit-risk ratio is 3,000 (182 - 21,000). <h4>Interpretation</h4> Our analysis suggests that the health benefits of deaths prevented by sustaining routine childhood immunisation in Africa far outweighs the excess risk of COVID-19 deaths associated with vaccination clinic visits, especially for the vaccinated children. However, there are other factors that must be considered for strategic decision making to sustain routine childhood immunisation in African countries during the COVID-19 pandemic. These include logistical constraints of vaccine supply chain problems caused by the COVID-19 pandemic, reallocation of immunisation providers to other prioritised health services, healthcare staff shortages caused by SARS-CoV-2 infections among the staff, decreased demand for vaccination arising from community reluctance to visit vaccination clinics for fear of contracting SARS-CoV-2 infections, and infection risk to healthcare staff providing immunisation services as well as to their households and onward SARS-CoV-2 transmission into the wider community. <h4>Funding</h4> Gavi, the Vaccine Alliance and Bill & Melinda Gates Foundation (OPP1157270) <h4>Research in context</h4> <h4>Evidence before the study</h4> National immunisation programmes globally are at risk of disruption due to the severe health system constraints caused by the ongoing COVID-19 pandemic and the physical distancing measures to mitigate the outbreak. The decrease in vaccination coverage increases the proportion of susceptible children at risk of increased morbidity and mortality from vaccine-preventable disease outbreaks. Outbreaks of vaccine preventable disease have been observed during previous interruptions to routine immunisation services during an ongoing infectious disease epidemic, such as during the 2013-2016 Ebola outbreak in West Africa, when most health resources were shifted towards the Ebola response which led to decreasing vaccination coverage and consequently outbreaks of measles and other vaccine-preventable diseases. <h4>Added value of this study</h4> We estimated the benefit-risk ratio by comparing the deaths prevented by sustaining routine childhood immunisation for diphtheria, tetanus, pertussis, hepatitis B, Haemophilus influenzae type b, pneumococcal, rotavirus, measles, meningitis A, rubella, and yellow fever vaccines with the excess COVID-19 deaths associated with vaccination clinic visits. The benefit of routine childhood immunization programmes in all the 54 countries of Africa is higher than the COVID-19 risk associated with these vaccination clinic visits. <h4>Implications of all the available evidence</h4> Routine childhood immunisation programmes should be safeguarded for continued service delivery and prioritised for the prevention of infectious diseases, as logistically possible, as part of delivering essential health services during the COVID-19 pandemic in Africa. The current immunisation service models will require adaptation, including physical distancing measures, personal protective equipment, and good hygiene practices for infection control at the vaccination clinics, and have to be complemented by new immunisation service models for sustaining routine childhood immunisation in the African countries during the COVID-19 risk period.",,pdf:http://www.thelancet.com/article/S2214109X20303089/pdf; doi:https://doi.org/10.1101/2020.05.19.20106278; html:https://europepmc.org/article/PPR/PPR167068; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR167068&type=FILE&fileName=EMS90726-pdf.pdf&mimeType=application/pdf
 PPR258079,https://doi.org/10.1101/2020.12.24.20248822,Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England,"Davies NG, Abbott S, Barnard RC, Jarvis CI, Kucharski AJ, Munday JD, Pearson CAB, Russell TW, Tully DC, Washburne AD, Wenseleers T, Gimma A, Waites W, Wong KLM, van Zandvoort K, Silverman JD, CMMID COVID-19 Working Group, The COVID-19 Genomics UK (COG-UK) Consortium, Diaz-Ordaz K, Keogh R, Eggo RM, Funk S, Jit M, Atkins KE, Edmunds WJ.",,No Journal Info,2020,2020-12-26,Y,,,,"A novel SARS-CoV-2 variant, VOC 202012/01 (lineage B.1.1.7), emerged in southeast England in November 2020 and is rapidly spreading towards fixation. Using a variety of statistical and dynamic modelling approaches, we estimate that this variant has a 43–90% (range of 95% credible intervals 38–130%) higher reproduction number than preexisting variants. A fitted two-strain dynamic transmission model shows that VOC 202012/01 will lead to large resurgences of COVID-19 cases. Without stringent control measures, including limited closure of educational institutions and a greatly accelerated vaccine roll-out, COVID-19 hospitalisations and deaths across England in 2021 will exceed those in 2020. Concerningly, VOC 202012/01 has spread globally and exhibits a similar transmission increase (59–74%) in Denmark, Switzerland, and the United States.",,pdf:https://www.science.org/cms/asset/9064b3e4-39f9-402c-8fa2-b689efda98b4/pap.pdf; doi:https://doi.org/10.1101/2020.12.24.20248822; html:https://europepmc.org/article/PPR/PPR258079; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR258079&type=FILE&fileName=EMS109285-pdf.pdf&mimeType=application/pdf
+PPR167068,https://doi.org/10.1101/2020.05.19.20106278,Benefit-risk analysis of health benefits of routine childhood immunisation against the excess risk of SARS-CoV-2 infections during the COVID-19 pandemic in Africa,"Abbas K, Procter SR, van Zandvoort K, Clark A, Funk S, LSHTM CMMID CMMID COVID-19 Working Group, Mengistu T, Hogan D, Dansereau E, Jit M, Flasche S.",,No Journal Info,2020,2020-05-26,Y,,,,"<h4>Summary</h4> <h4>Background</h4> National immunisation programmes globally are at risk of suspension due to the severe health system constraints and physical distancing measures in place to mitigate the ongoing COVID-19 pandemic. Our aim is to compare the health benefits of sustaining routine childhood immunisation in Africa against the risk of acquiring SARS-CoV-2 infections through visiting routine vaccination service delivery points. <h4>Methods</h4> We used two scenarios to approximate the child deaths that may be caused by immunisation coverage reductions during COVID-19 outbreaks. First, we used previously reported country-specific child mortality impact estimates of childhood immunisation for diphtheria, tetanus, pertussis, hepatitis B, Haemophilus influenzae type b, pneumococcal, rotavirus, measles, meningitis A, rubella, and yellow fever (DTP3, HepB3, Hib3, PCV3, RotaC, MCV1, MCV2, MenA, RCV, YFV) to approximate the future deaths averted before completing five years of age by routine childhood vaccination during a 6-month COVID-19 risk period without catch-up campaigns. Second, we analysed an alternative scenario that approximates the health benefits of sustaining routine childhood immunisation to only the child deaths averted from measles outbreaks during the COVID-19 risk period. The excess number of infections due to additional SARS-CoV-2 exposure during immunisation visits assumes that contact reducing interventions flatten the outbreak curve during the COVID-19 risk period, that 60% of the population will have been infected by the end of that period, that children can be infected by either vaccinators or during transport and that upon child infection the whole household would be infected. Country specific household age structure estimates and age dependent infection fatality rates are then applied to calculate the number of deaths attributable to the vaccination clinic visits. We present benefit-risk ratios for routine childhood immunisation alongside 95% uncertainty range estimates from probabilistic sensitivity analysis. <h4>Findings</h4> For every one excess COVID-19 death attributable to SARS-CoV-2 infections acquired during routine vaccination clinic visits, there could be 84 (14-267) deaths in children prevented by sustaining routine childhood immunisation in Africa. The benefit-risk ratio for the vaccinated children, siblings, parents or adult care-givers, and older adults in the households of vaccinated children are 85,000 (4,900 - 546,000), 75,000 (4,400 - 483,000), 769 (148 - 2,700), and 96 (14 - 307) respectively. In the alternative scenario that approximates the health benefits to only the child deaths averted from measles outbreaks, the benefit-risk ratio to the households of vaccinated children is 3 (0 - 10) under these highly conservative assumptions and if the risk to only the vaccinated children is considered, the benefit-risk ratio is 3,000 (182 - 21,000). <h4>Interpretation</h4> Our analysis suggests that the health benefits of deaths prevented by sustaining routine childhood immunisation in Africa far outweighs the excess risk of COVID-19 deaths associated with vaccination clinic visits, especially for the vaccinated children. However, there are other factors that must be considered for strategic decision making to sustain routine childhood immunisation in African countries during the COVID-19 pandemic. These include logistical constraints of vaccine supply chain problems caused by the COVID-19 pandemic, reallocation of immunisation providers to other prioritised health services, healthcare staff shortages caused by SARS-CoV-2 infections among the staff, decreased demand for vaccination arising from community reluctance to visit vaccination clinics for fear of contracting SARS-CoV-2 infections, and infection risk to healthcare staff providing immunisation services as well as to their households and onward SARS-CoV-2 transmission into the wider community. <h4>Funding</h4> Gavi, the Vaccine Alliance and Bill & Melinda Gates Foundation (OPP1157270) <h4>Research in context</h4> <h4>Evidence before the study</h4> National immunisation programmes globally are at risk of disruption due to the severe health system constraints caused by the ongoing COVID-19 pandemic and the physical distancing measures to mitigate the outbreak. The decrease in vaccination coverage increases the proportion of susceptible children at risk of increased morbidity and mortality from vaccine-preventable disease outbreaks. Outbreaks of vaccine preventable disease have been observed during previous interruptions to routine immunisation services during an ongoing infectious disease epidemic, such as during the 2013-2016 Ebola outbreak in West Africa, when most health resources were shifted towards the Ebola response which led to decreasing vaccination coverage and consequently outbreaks of measles and other vaccine-preventable diseases. <h4>Added value of this study</h4> We estimated the benefit-risk ratio by comparing the deaths prevented by sustaining routine childhood immunisation for diphtheria, tetanus, pertussis, hepatitis B, Haemophilus influenzae type b, pneumococcal, rotavirus, measles, meningitis A, rubella, and yellow fever vaccines with the excess COVID-19 deaths associated with vaccination clinic visits. The benefit of routine childhood immunization programmes in all the 54 countries of Africa is higher than the COVID-19 risk associated with these vaccination clinic visits. <h4>Implications of all the available evidence</h4> Routine childhood immunisation programmes should be safeguarded for continued service delivery and prioritised for the prevention of infectious diseases, as logistically possible, as part of delivering essential health services during the COVID-19 pandemic in Africa. The current immunisation service models will require adaptation, including physical distancing measures, personal protective equipment, and good hygiene practices for infection control at the vaccination clinics, and have to be complemented by new immunisation service models for sustaining routine childhood immunisation in the African countries during the COVID-19 risk period.",,pdf:http://www.thelancet.com/article/S2214109X20303089/pdf; doi:https://doi.org/10.1101/2020.05.19.20106278; html:https://europepmc.org/article/PPR/PPR167068; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR167068&type=FILE&fileName=EMS90726-pdf.pdf&mimeType=application/pdf
 PPR573047,https://doi.org/10.1101/2022.11.16.22282396,Comparative effectiveness of two- and three-dose schedules involving AZD1222 and BNT162b2 in people with kidney disease: a linked OpenSAFELY and UK Renal Registry cohort study,"The OpenSAFELY Collaborative, Parker EP, Horne EM, Hulme WJ, Tazare J, Zheng B, Carr EJ, Loud F, Lyon S, Mahalingasivam V, MacKenna B, Mehrkar A, Scanlon M, Santhakumaran S, Steenkamp R, Goldacre B, Sterne JA, Nitsch D, Tomlinson LA, The LH&W NCS (or CONVALESCENCE) Collaborative.",,No Journal Info,2022,2022-11-18,Y,,,,"<h4>Background</h4> Kidney disease is a key risk factor for COVID-19-related mortality and suboptimal vaccine response. Optimising vaccination strategies is essential to reduce the disease burden in this vulnerable population. <h4>Methods</h4> With the approval of NHS England, we performed a retrospective cohort study to estimate the comparative effectiveness of schedules involving AZD1222 (AZ; ChAdOx1-S) and BNT162b2 (BNT) among people with kidney disease. Using linked primary care and UK Renal Registry records in the OpenSAFELY-TPP platform, we identified adults with stage 3– 5 chronic kidney disease, dialysis recipients, and kidney transplant recipients. We used Cox proportional hazards models to compare COVID-19-related outcomes and non-COVID-19 death after two-dose (AZ–AZ vs BNT–BNT) and three-dose (AZ–AZ–BNT vs BNT–BNT– BNT) schedules. <h4>Findings</h4> After two doses, incidence during the Delta wave was higher in AZ–AZ (n=257,580) than BNT–BNT recipients (n=169,205; adjusted hazard ratios [95% CIs] 1·43 [1·37–1·50], 1·59 [1·43–1·77], 1·44 [1·12–1·85], and 1·09 [1·02–1·17] for SARS-CoV-2 infection, COVID-19-related hospitalisation, COVID-19-related death, and non-COVID-19 death, respectively). Findings were consistent across disease subgroups, including dialysis and transplant recipients. After three doses, there was little evidence of differences between AZ– AZ–BNT (n=220,330) and BNT–BNT–BNT recipients (n=157,065) for any outcome during a period of Omicron dominance. <h4>Interpretation</h4> Among individuals with moderate-to-severe kidney disease, two doses of BNT conferred stronger protection than AZ against SARS-CoV-2 infection and severe disease. A subsequent BNT dose levelled the playing field, emphasising the value of heterologous RNA doses in vulnerable populations. <h4>Funding</h4> National Core Studies, Wellcome Trust, MRC, and Health Data Research UK. <h4>Research in context</h4> <h4>Evidence before this study</h4> We searched Medline for studies published between 1 st December 2020 and 7 th September 2022 using the following term: “(coronavir* or covid* or sars*) and (vaccin* or immunis* or immuniz*) and (kidney or dialysis or h?emodialysis or transplant or renal) and (efficacy or effectiveness)” . We identified studies reporting on the effectiveness of various COVID-19 vaccines in individuals with chronic kidney disease (CKD) or end-stage renal disease. Several studies have reported no clear differences in effectiveness against outcomes of varying severity after two doses of BNT162b2 or AZD1222 compared to unvaccinated controls, which is contrary to the significantly higher antibody levels observed after BNT162b2 in immunogenicity studies. One study also showed that a third dose of RNA vaccine restored some protection against the Omicron variant among BNT162b2- and AZD1222-primed individuals, with no clear differences between these groups. This finding is consistent with immunogenicity data suggesting that a third dose of BNT162b2 may reduce the gap in antibody levels observed after two of AZD1222 versus BNT162b2. Notably, we found few studies directly comparing effectiveness in BNT162b2 versus AZD1222 recipients, which reduces biases associated with comparison to a small and potentially unrepresentative group of unvaccinated controls. We also found no studies exploring COVID-19 vaccine effectiveness in kidney disease groups of varying severity (CKD, dialysis, and kidney transplant). <h4>Added value of this study</h4> This is the largest study to compare the effectiveness of two- and three-dose regimens involving AZD1222 and BNT162b2 among people with moderate-to-severe kidney disease. We compared effectiveness after two and three doses in 426,780 and 377,395 individuals, respectively, and harnessed unique data linkages between primary care records and UK Renal Registry data to identify people with CKD and end-stage renal disease (including dialysis and kidney transplant recipients) with high accuracy. During the Delta wave of infection, we observed a higher risk of COVID-19-related outcomes of varying severity after two doses of AZD1222 versus BNT162b2, with consistent findings in CKD, dialysis, and transplant subgroups. After a third dose of BNT162b2, AZD1222- and BNT162b2-primed individuals had similar rates of COVID-19-related outcomes during a period of Omicron dominance. Implications of all the available evidence A growing body of immunogenicity and effectiveness data – including the present study – suggest that two doses of BNT162b2 confers stronger protection than AZD1222 among people with moderate-to-severe kidney disease. However, a third dose of BNT162b2 appears to compensate for this immunity deficit, providing equivalent protection in BNT162b2- and AZD1222-primed individuals. Achieving high coverage with additional RNA vaccine doses (whether homologous or heterologous) has the capacity to reduce the burden of disease in this vulnerable population.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/11/18/2022.11.16.22282396.full.pdf; doi:https://doi.org/10.1101/2022.11.16.22282396; html:https://europepmc.org/article/PPR/PPR573047; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR573047&type=FILE&fileName=EMS157362-pdf.pdf&mimeType=application/pdf
 PPR433539,https://doi.org/10.1101/2021.12.16.21267934,Predictors of SARS-CoV-2 infection in a multi-ethnic cohort of United Kingdom healthcare workers: a prospective nationwide cohort study (UK-REACH),"Martin CA, Pan D, Melbourne C, Teece L, Aujayeb A, Baggaley RF, Bryant L, Carr S, Gregary B, Gupta A, Guyatt AL, John C, McManus IC, Nazareth J, Nellums LB, Reza R, Simpson S, Tobin MD, Woolf K, Zingwe S, Khunti K, Abrams KR, Gray LJ, Pareek M.",,No Journal Info,2021,2021-12-17,Y,,,,"<h4>Introduction</h4> Healthcare workers (HCWs), particularly those from ethnic minority groups, have been shown to be at disproportionately higher risk of infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) compared to the general population. However, there is insufficient evidence on how demographic and occupational factors influence infection risk among ethnic minority HCWs. <h4>Methods</h4> We conducted a cross-sectional analysis using data from the United Kingdom Research study into Ethnicity And COVID-19 Outcomes in Healthcare workers (UK-REACH) cohort study. We used logistic regression to examine associations of demographic, household and occupational predictor variables with SARS-CoV-2 infection (defined by PCR, serology or suspected COVID-19) in a diverse group of HCWs. <h4>Results</h4> 2,496 of the 10,772 HCWs (23.2%) who worked during the first UK national lockdown in March 2020 reported previous SARS-CoV-2 infection. In an adjusted model, demographic and household factors associated with increased odds of infection included younger age, living with other key workers and higher religiosity. Important occupational risk factors associated with increased odds of infection included attending to a higher number of COVID-19 positive patients (aOR 2.49, 95%CI 2.03–3.05 for ≥21 patients per week vs none), working in a nursing or midwifery role (1.35, 1.15– 1.58, compared to doctors), reporting a lack of access to personal protective equipment (1.27, 1.15 – 1.41) and working in an ambulance (1.95, 1.52–2.50) or hospital inpatient setting (1.54, 1.37 – 1.74). Those who worked in Intensive Care Units were less likely to have been infected (0.76, 0.63–0.90) than those who did not. Black HCWs were more likely to have been infected than their White colleagues, an effect which attenuated after adjustment for other known predictors. <h4>Conclusions</h4> We identified key sociodemographic and occupational risk factors associated with SARS-CoV-2 infection amongst UK HCWs, and have determined factors that might contribute to a disproportionate odds of infection in HCWs from Black ethnic groups. These findings demonstrate the importance of social and occupational factors in driving ethnic disparities in COVID-19 outcomes, and should inform policies, including targeted vaccination strategies and risk assessments aimed at protecting HCWs in future waves of the COVID-19 pandemic. <h4>Trial registration</h4> ISRCTN 11811602",,pdf:https://www.medrxiv.org/content/medrxiv/early/2021/12/17/2021.12.16.21267934.full.pdf; doi:https://doi.org/10.1101/2021.12.16.21267934; html:https://europepmc.org/article/PPR/PPR433539; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR433539&type=FILE&fileName=EMS141796-pdf.pdf&mimeType=application/pdf
-PPR408448,https://doi.org/10.1101/2021.10.13.21264937,Comparative effectiveness of ChAdOx1 versus BNT162b2 COVID-19 vaccines in Health and Social Care workers in England: a cohort study using OpenSAFELY,"Hulme WJ, Williamson EJ, Green A, Bhaskaran K, McDonald HI, Rentsch CT, Schultze A, Tazare J, Curtis HJ, Walker AJ, Tomlinson L, Palmer T, Horne E, MacKenna B, Morton CE, Mehrkar A, Fisher L, Bacon S, Evans D, Inglesby P, Hickman G, Davy S, Ward T, Croker R, Eggo RM, Wong AY, Mathur R, Wing K, Forbes H, Grint D, Douglas IJ, Evans SJ, Smeeth L, Bates C, Cockburn J, Parry J, Hester F, Harper S, Sterne JA, Hernán M, Goldacre B.",,No Journal Info,2021,2021-10-18,Y,,,,"<h4>Objectives</h4> To compare the effectiveness of the BNT162b2 mRNA (Pfizer-BioNTech) and the ChAdOx1 (Oxford-AstraZeneca) COVID-19 vaccines against infection and COVID-19 disease in health and social care workers. <h4>Design</h4> Cohort study, emulating a comparative effectiveness trial. <h4>Setting</h4> Linked primary care, hospital, and COVID-19 surveillance records available within the OpenSAFELY-TPP research platform. <h4>Participants</h4> 317,341 health and social care workers vaccinated between 4 January and 28 February 2021, registered with a GP practice using the TPP SystmOne clinical information system in England, and not clinically extremely vulnerable. <h4>Interventions</h4> Vaccination with either BNT162b2 or ChAdOx1 administered as part of the national COVID-19 vaccine roll-out. <h4>Main outcome measures</h4> Recorded SARS-CoV-2 positive test, or COVID-19 related Accident and Emergency attendance or hospital admission occurring within 20 weeks of vaccination. <h4>Results</h4> The cumulative incidence of each outcome was similar for both vaccines during the first 20 weeks post-vaccination. The cumulative incidence of recorded SARS-CoV-2 infection 6 weeks after vaccination with BNT162b2 was 19.2 per 1000 people (95%CI 18.6 to 19.7) and with ChAdOx1 was 18.9 (95%CI 17.6 to 20.3), representing a difference of -0.24 per 1000 people (95%CI -1.71 to 1.22). The difference in the cumulative incidence per 1000 people of COVID-19 accident and emergency attendance at 6 weeks was 0.01 per 1000 people (95%CI -0.27 to 0.28). For COVID-19 hospital admission, this difference was 0.03 per 1000 people (95%CI -0.22 to 0.27). <h4>Conclusions</h4> In this cohort of healthcare workers where we would not anticipate vaccine type to be related to health status, we found no substantial differences in the incidence of SARS-CoV-2 infection or COVID-19 disease up to 20 weeks after vaccination. Incidence dropped sharply after 3-4 weeks and there were very few COVID-19 hospital attendance and admission events after this period. This is in line with expected onset of vaccine-induced immunity, and suggests strong protection against COVID-19 disease for both vaccines.",,pdf:https://www.bmj.com/content/bmj/378/bmj-2021-068946.full.pdf; doi:https://doi.org/10.1101/2021.10.13.21264937; html:https://europepmc.org/article/PPR/PPR408448; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR408448&type=FILE&fileName=EMS137186-pdf.pdf&mimeType=application/pdf
 PPR417361,https://doi.org/10.1101/2021.11.08.21265312,"Understanding COVID-19 trajectories from a nationwide linked electronic health record cohort of 56 million people: phenotypes, severity, waves & vaccination","Thygesen JH, Tomlinson C, Hollings S, Mizani M, Handy A, Akbari A, Banerjee A, Cooper J, Lai A, Li K, Mateen B, Sattar N, Sofat R, Torralbo A, Wu H, Wood A, Sterne JAC, Pagel C, Whiteley W, Sudlow C, Hemingway H, Denaxas S.",,No Journal Info,2021,2021-11-09,Y,,,,"<h4>Background</h4> Updatable understanding of the onset and progression of individuals COVID-19 trajectories underpins pandemic mitigation efforts. In order to identify and characterize individual trajectories, we defined and validated ten COVID-19 phenotypes from linked electronic health records (EHR) on a nationwide scale using an extensible framework. <h4>Methods</h4> Cohort study of 56.6 million people in England alive on 23/01/2020, followed until 31/05/2021, using eight linked national datasets spanning COVID-19 testing, vaccination, primary & secondary care and death registrations data. We defined ten COVID-19 phenotypes reflecting clinically relevant stages of disease severity using a combination of international clinical terminologies (e.g. SNOMED-CT, ICD-10) and bespoke data fields; positive test, primary care diagnosis, hospitalisation, critical care (four phenotypes), and death (three phenotypes). Using these phenotypes, we constructed patient trajectories illustrating the transition frequency and duration between phenotypes. Analyses were stratified by pandemic waves and vaccination status. <h4>Findings</h4> We identified 3,469,528 infected individuals (6.1%) with 8,825,738 recorded COVID-19 phenotypes. Of these, 364,260 (11%) were hospitalised and 140,908 (4%) died. Of those hospitalised, 38,072 (10%) were admitted to intensive care (ICU), 54,026 (15%) received non-invasive ventilation and 21,404 (6%) invasive ventilation. Amongst hospitalised patients, first wave mortality (30%) was higher than the second (23%) in non-ICU settings, but remained unchanged for ICU patients. The highest mortality was for patients receiving critical care outside of ICU in wave 1 (51%). 13,083 (9%) COVID-19 related deaths occurred without diagnoses on the death certificate, but within 30 days of a positive test while 10,403 (7%) of cases were identified from mortality data alone with no prior phenotypes recorded. We observed longer patient trajectories in the second pandemic wave compared to the first. <h4>Interpretation</h4> Our analyses illustrate the wide spectrum of severity that COVID-19 displays and significant differences in incidence, survival and pathways across pandemic waves. We provide an adaptable framework to answer questions of clinical and policy relevance; new variant impact, booster dose efficacy and a way of maximising existing data to understand individuals progression through disease states. <h4>Research in Context</h4> <h4>Evidence before the study</h4> We searched PubMed on October 14, 2021, for publications with the terms “COVID-19” or “SARS-CoV-2”, “severity”, and “electronic health records” or “EHR” without date or language restrictions. Multiple studies explore factors associated with severity of COVID-19 infection, and model predictions of outcome for hospitalised patients. However, most work to date focused on isolated facets of the healthcare system, such as primary or secondary care only, was conducted in subpopulations (e.g. hospitalised patients) of limited sample size, and often utilized dichotomised outcomes (e.g. mortality or hospitalisation) ignoring the full spectrum of disease. We identified no studies which comprehensively detailed severity of infections while describing disease severity across pandemic waves, vaccination status, and patient trajectories. <h4>Added value of this study</h4> To our knowledge, this is the first study providing a comprehensive view of COVID-19 across pandemic waves using national data and focusing on severity, vaccination, and patient trajectories. Drawing on linked electronic health record (EHR) data on a national scale (56.6 million people alive and registered with GP in England), we describe key demographic factors, frequency of comorbidities, impact of the two main waves in England, and effect of full vaccination on COVID-19 severities. Additionally, we identify and describe patient trajectory networks which illustrate the main transition pathways of COVID-19 patients in the healthcare system. Finally, we provide reproducible COVID-19 phenotyping algorithms reflecting clinically relevant stages of disease severity i.e. positive tests, primary care diagnoses, hospitalisation, critical care treatments (e.g. ventilatory support) and mortality. <h4>Implications of all the available evidence</h4> The COVID-19 phenotypes and trajectory analysis framework outlined produce a reproducible, extensible and repurposable means to generate national-scale data to support critical policy decision making. By modelling patient trajectories as a series of interactions with healthcare systems, and linking these to demographic and outcome data, we provide a means to identify and prioritise care pathways associated with adverse outcomes and highlight healthcare system ‘touch points’ which may act as tangible targets for intervention.",,pdf:http://www.thelancet.com/article/S2589750022000917/pdf; doi:https://doi.org/10.1101/2021.11.08.21265312; html:https://europepmc.org/article/PPR/PPR417361; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR417361&type=FILE&fileName=EMS138265-pdf.pdf&mimeType=application/pdf
+PPR408448,https://doi.org/10.1101/2021.10.13.21264937,Comparative effectiveness of ChAdOx1 versus BNT162b2 COVID-19 vaccines in Health and Social Care workers in England: a cohort study using OpenSAFELY,"Hulme WJ, Williamson EJ, Green A, Bhaskaran K, McDonald HI, Rentsch CT, Schultze A, Tazare J, Curtis HJ, Walker AJ, Tomlinson L, Palmer T, Horne E, MacKenna B, Morton CE, Mehrkar A, Fisher L, Bacon S, Evans D, Inglesby P, Hickman G, Davy S, Ward T, Croker R, Eggo RM, Wong AY, Mathur R, Wing K, Forbes H, Grint D, Douglas IJ, Evans SJ, Smeeth L, Bates C, Cockburn J, Parry J, Hester F, Harper S, Sterne JA, Hernán M, Goldacre B.",,No Journal Info,2021,2021-10-18,Y,,,,"<h4>Objectives</h4> To compare the effectiveness of the BNT162b2 mRNA (Pfizer-BioNTech) and the ChAdOx1 (Oxford-AstraZeneca) COVID-19 vaccines against infection and COVID-19 disease in health and social care workers. <h4>Design</h4> Cohort study, emulating a comparative effectiveness trial. <h4>Setting</h4> Linked primary care, hospital, and COVID-19 surveillance records available within the OpenSAFELY-TPP research platform. <h4>Participants</h4> 317,341 health and social care workers vaccinated between 4 January and 28 February 2021, registered with a GP practice using the TPP SystmOne clinical information system in England, and not clinically extremely vulnerable. <h4>Interventions</h4> Vaccination with either BNT162b2 or ChAdOx1 administered as part of the national COVID-19 vaccine roll-out. <h4>Main outcome measures</h4> Recorded SARS-CoV-2 positive test, or COVID-19 related Accident and Emergency attendance or hospital admission occurring within 20 weeks of vaccination. <h4>Results</h4> The cumulative incidence of each outcome was similar for both vaccines during the first 20 weeks post-vaccination. The cumulative incidence of recorded SARS-CoV-2 infection 6 weeks after vaccination with BNT162b2 was 19.2 per 1000 people (95%CI 18.6 to 19.7) and with ChAdOx1 was 18.9 (95%CI 17.6 to 20.3), representing a difference of -0.24 per 1000 people (95%CI -1.71 to 1.22). The difference in the cumulative incidence per 1000 people of COVID-19 accident and emergency attendance at 6 weeks was 0.01 per 1000 people (95%CI -0.27 to 0.28). For COVID-19 hospital admission, this difference was 0.03 per 1000 people (95%CI -0.22 to 0.27). <h4>Conclusions</h4> In this cohort of healthcare workers where we would not anticipate vaccine type to be related to health status, we found no substantial differences in the incidence of SARS-CoV-2 infection or COVID-19 disease up to 20 weeks after vaccination. Incidence dropped sharply after 3-4 weeks and there were very few COVID-19 hospital attendance and admission events after this period. This is in line with expected onset of vaccine-induced immunity, and suggests strong protection against COVID-19 disease for both vaccines.",,pdf:https://www.bmj.com/content/bmj/378/bmj-2021-068946.full.pdf; doi:https://doi.org/10.1101/2021.10.13.21264937; html:https://europepmc.org/article/PPR/PPR408448; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR408448&type=FILE&fileName=EMS137186-pdf.pdf&mimeType=application/pdf
 PPR486740,https://doi.org/10.1101/2022.04.26.22274332,"Community factors and excess mortality in the COVID-19 pandemic in England, Italy and Sweden","Parkes B, Stafoggia M, Fecht D, Davies B, Bonander C, de’ Donato F, Michelozzi P, Piel FB, Strömberg U, Blangiardo M.",,No Journal Info,2022,2022-04-27,Y,,,,"<h4>Background</h4> Analyses of COVID-19 suggest specific risk factors make communities more or less vulnerable to pandemic related deaths within countries. What is unclear is whether the characteristics affecting vulnerability of small communities within countries produce similar patterns of excess mortality across countries with different demographics and public health responses to the pandemic. Our aim is to quantify community-level variations in excess mortality within England, Italy and Sweden and identify how such spatial variability was driven by community-level characteristics. <h4>Methods</h4> We applied a two-stage Bayesian model to quantify inequalities in excess mortality in people aged 40 years and older at the community level in England, Italy and Sweden during the first year of the pandemic (March 2020–February 2021). We used community characteristics measuring deprivation, air pollution, living conditions, population density and movement of people as covariates to quantify their associations with excess mortality. <h4>Results</h4> We found just under half of communities in England (48.1%) and Italy (45.8%) had an excess mortality of over 300 per 100,000 males over the age of 40, while for Sweden that covered 23.1% of communities. We showed that deprivation is a strong predictor of excess mortality across the three countries, and communities with high levels of overcrowding were associated with higher excess mortality in England and Sweden. <h4>Conclusion</h4> These results highlight some international similarities in factors affecting mortality that will help policy makers target public health measures to increase resilience to the mortality impacts of this and future pandemics.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/05/09/2022.04.26.22274332.full.pdf; doi:https://doi.org/10.1101/2022.04.26.22274332; html:https://europepmc.org/article/PPR/PPR486740; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR486740&type=FILE&fileName=EMS144662-pdf.pdf&mimeType=application/pdf
 PPR340395,https://doi.org/10.1101/2021.05.13.21257144,REACT-1 round 11 report: low prevalence of SARS-CoV-2 infection in the community prior to the third step of the English roadmap out of lockdown,"Riley S, Haw D, Walters CE, Wang H, Eales O, Ainslie KEC, Atchison C, Fronterre C, Diggle PJ, Page AJ, Trotter AJ, Le Viet T, Alikhan N, O’Grady J, The COVID-19 Genomics UK (COG-UK) Consortium, Ashby D, Donnelly CA, Cooke G, Barclay W, Ward H, Darzi A, Elliott P.",,No Journal Info,2021,2021-05-17,Y,,,,"<h4>Background</h4> National epidemic dynamics of SARS-CoV-2 infections are being driven by: the degree of recent indoor mixing (both social and workplace), vaccine coverage, intrinsic properties of the circulating lineages, and prior history of infection (via natural immunity). In England, infections, hospitalisations and deaths fell during the first two steps of the “roadmap” for exiting the third national lockdown. The third step of the roadmap in England takes place on 17 May 2021. <h4>Methods</h4> We report the most recent findings on community infections from the REal-time Assessment of Community Transmission-1 (REACT-1) study in which a swab is obtained from a representative cross-sectional sample of the population in England and tested using PCR. Round 11 of REACT-1 commenced self-administered swab-collection on 15 April 2021 and completed collections on 3 May 2021. We compare the results of REACT-1 round 11 to round 10, in which swabs were collected from 11 to 30 March 2021. <h4>Results</h4> Between rounds 10 and 11, prevalence of swab-positivity dropped by 50% in England from 0.20% (0.17%, 0.23%) to 0.10% (0.08%, 0.13%), with a corresponding R estimate of 0.90 (0.87, 0.94). Rates of swab-positivity fell in the 55 to 64 year old group from 0.17% (0.12%, 0.25%) in round 10 to 0.06% (0.04%, 0.11%) in round 11. Prevalence in round 11 was higher in the 25 to 34 year old group at 0.21% (0.12%, 0.38%) than in the 55 to 64 year olds and also higher in participants of Asian ethnicity at 0.31% (0.16%, 0.60%) compared with white participants at 0.09% (0.07%, 0.11%). Based on sequence data for positive samples for which a lineage could be identified, we estimate that 92.3% (75.9%, 97.9%, n=24) of infections were from the B.1.1.7 lineage compared to 7.7% (2.1%, 24.1%, n=2) from the B.1.617.2 lineage. Both samples from the B.1.617.2 lineage were detected in London from participants not reporting travel in the previous two weeks. Also, allowing for suitable lag periods, the prior close alignment between prevalence of infections and hospitalisations and deaths nationally has diverged. <h4>Discussion</h4> We observed marked reductions in prevalence from March to April and early May 2021 in England reflecting the success of the vaccination programme and despite easing of restrictions during lockdown. However, there is potential upwards pressure on prevalence from the further easing of lockdown regulations and presence of the B.1.617.2 lineage. If prevalence rises in the coming weeks, policy-makers will need to assess the possible impact on hospitalisations and deaths. In addition, consideration should be given to other health and economic impacts if increased levels of community transmission occur.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2021/05/17/2021.05.13.21257144.full.pdf; doi:https://doi.org/10.1101/2021.05.13.21257144; html:https://europepmc.org/article/PPR/PPR340395; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR340395&type=FILE&fileName=EMS124703-pdf.pdf&mimeType=application/pdf
 PPR403344,https://doi.org/10.1101/2021.10.01.21264408,Reduced amplification efficiency of the RNA-dependent-RNA-polymerase (RdRp) target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests,"Valley-Omar Z, Marais G, Iranzadeh A, Naidoo M, Korsman S, Maponga T, Hussey H, Davies M, Boulle A, Doolabh D, Laubscher M, Deetlefs J, Maritz J, Scott L, Msomi N, Tegally H, de Oliveira T, Bhiman J, Williamson C, Preiser W, Hardie D, Hsiao N.",,No Journal Info,2021,2021-10-01,Y,,,,"Routine SARS-CoV-2 surveillance in the Western Cape region of South Africa (January-August 2021) found a reduced PCR amplification efficiency of the RdRp gene target of the Seegene, Allplex 2019-nCoV diagnostic assay when detecting the Delta variant. We propose that this can be used as a surrogate for variant detection.",,doi:https://doi.org/10.1016/j.jviromet.2022.114471; doi:https://doi.org/10.1101/2021.10.01.21264408; html:https://europepmc.org/article/PPR/PPR403344; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR403344&type=FILE&fileName=EMS136740-pdf.pdf&mimeType=application/pdf
@@ -201,13 +201,13 @@ PPR293368,https://doi.org/10.1101/2021.03.03.21252856,REACT-1 round 9 final repo
 PPR287082,https://doi.org/10.1101/2021.02.18.21251973,REACT-1 round 9 interim report: downward trend of SARS-CoV-2 in England in February 2021 but still at high prevalence,"Riley S, Walters CE, Wang H, Eales O, Haw D, Ainslie KEC, Atchison C, Fronterre C, Diggle PJ, Ashby D, Donnelly CA, Cooke G, Barclay W, Ward H, Darzi A, Elliott P.",,No Journal Info,2021,2021-02-23,Y,,,,"<h4>Background and Methods</h4> England entered its third national lockdown of the COVID-19 pandemic on 6th January 2021 with the aim of reducing the daily number of deaths and pressure on healthcare services. The real-time assessment of community transmission study (REACT-1) obtains throat and nose swabs from randomly selected people in England in order to describe patterns of SARS-CoV-2 prevalence. Here, we report data from round 9a of REACT-1 for swabs collected between 4th and 13th February 2021. <h4>Results</h4> Out of 85,473 tested-swabs, 378 were positive. Overall weighted prevalence of infection in the community in England was 0.51%, a fall of more than two thirds since our last report (round 8) in January 2021 when 1.57% of people tested positive. We estimate a halving time of 14.6 days and a reproduction number R of 0.72, based on the difference in prevalence between the end of round 8 and the beginning of round 9. Although prevalence fell in all nine regions of England over the same period, there was greater uncertainty in the trend for North West, North East, and Yorkshire and The Humber. Prevalence fell substantially across all age groups with highest prevalence among 18- to 24-year olds at 0.89% (0.47%, 1.67%) and those aged 5 to12 years at 0.86% (0.60%, 1.24%). Large household size, living in a deprived neighbourhood, and Asian ethnicity were all associated with increased prevalence. Healthcare and care home workers were more likely to test positive compared to other workers. <h4>Conclusions</h4> There is a strong decline in prevalence of SARS-CoV-2 in England among the general population five to six weeks into lockdown, but prevalence remains high: at levels similar to those observed in late September 2020. Also, the number of COVID-19 cases in hospitals is higher than at the peak of the first wave in April 2020. The effects of easing of social distancing when we transition out of lockdown need to be closely monitored to avoid a resurgence in infections and renewed pressure on health services.",,doi:https://doi.org/10.1101/2021.02.18.21251973; doi:https://doi.org/10.1101/2021.02.18.21251973; html:https://europepmc.org/article/PPR/PPR287082; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR287082&type=FILE&fileName=EMS117383-pdf.pdf&mimeType=application/pdf
 PPR397279,https://doi.org/10.1101/2021.09.16.21263629,Access to personal protective equipment in healthcare workers during the COVID-19 pandemic in the United Kingdom: results from a nationwide cohort study (UK-REACH),"Martin CA, Pan D, Nazareth J, Aujayeb A, Bryant L, Carr S, Gray LJ, Gregary B, Gupta A, Guyatt AL, Gopal A, Hine T, John C, McManus IC, Melbourne C, Nellums LB, Reza R, Simpson S, Tobin MD, Woolf K, Zingwe S, Khunti K, Pareek M.",,No Journal Info,2021,2021-09-21,Y,,,,"<h4>Objectives</h4> To determine the prevalence and predictors of self-reported access to appropriate personal protective equipment (aPPE) for healthcare workers (HCWs) in the United Kingdom (UK) during the first UK national COVID-19 lockdown (March 2020) and at the time of questionnaire response (December 2020 – February 2021). <h4>Design</h4> Two cross sectional analyses using data from a questionnaire-based cohort study. <h4>Setting</h4> Nationwide questionnaire from 4 th December 2020 to 28 th February 2021. <h4>Participants</h4> A representative sample of HCWs or ancillary workers in a UK healthcare setting aged 16 or over, registered with one of seven main UK healthcare regulatory bodies. <h4>Main outcome measure</h4> Binary measure of self-reported aPPE (access all of the time vs access most of the time or less frequently) at two timepoints: the first national lockdown in the UK (primary analysis) and at the time of questionnaire response (secondary analysis). <h4>Results</h4> 10,508 HCWs were included in the primary analysis, and 12,252 in the secondary analysis. 3702 (35.2%) of HCWs reported aPPE at all times in the primary analysis; 6806 (83.9%) reported aPPE at all times in the secondary analysis. After adjustment (for age, sex, ethnicity, migration status, occupation, aerosol generating procedure exposure, work sector, work region, working hours, night shift frequency and trust in employing organisation), older HCWs (per decade increase in age: aOR 1.2, 95% CI 1.16-1.26, p<0.001) and those working in Intensive Care Units (1.61, 1.38 – 1.89, p<0.001) were more likely to report aPPE at all times. Those from Asian ethnic groups compared to White (0.77, 0.67-0.89, p<0.001), those in allied health professional (AHPs) and dental roles (vs those in medical roles; AHPs: 0.77, 0.68 – 0.87, p<0.001; dental: 0.63, 0.49-0.81, p<0.001), and those who saw a higher number of COVID-19 patients compared to those who saw none (≥21 patients 0.74, 0.61-0.90, p=0.003) were less likely to report aPPE at all times in the primary analysis. aPPE at all times was also not uniform across UK regions (reported access being better in South West and North East England than London). Those who trusted their employing organisation to deal with concerns about unsafe clinical practice, compared to those who did not, were twice as likely to report aPPE at all times (2.18, 1.97-2.40, p<0.001). With the exception of occupation, these factors were also significantly associated with aPPE at all times in the secondary analysis. <h4>Conclusions</h4> We found that only a third of HCWs in the UK reported aPPE at all times during the period of the first lockdown and that aPPE had improved later in the pandemic. We also identified key sociodemographic and occupational determinants of aPPE during the first UK lockdown, the majority of which have persisted since lockdown was eased. These findings have important public health implications for HCWs, particularly as cases of infection and long-COVID continue to rise in the UK. <h4>Trial registration</h4> ISRCTN 11811602 <h4>What is already known on this topic</h4> Access to personal protective equipment (PPE) is crucial to protect healthcare workers (HCWs) from infection. Limited data exist concerning the prevalence of, and factors relating to, PPE access for HCWs in the United Kingdom (UK) during the COVID-19 pandemic. <h4>What this study adds</h4> Only a third of HCWs reported having access to appropriate PPE all of the time during the first UK national lockdown. Older HCWs, those working in Intensive Care Units and those who trusted their employing organisation to deal with concerns about unsafe clinical practice, were more likely to report access to adequate PPE. Those from Asian ethnic groups (compared to White ethnic groups) and those who saw a high number of COVID-19 were less likely to report access to adequate PPE. Our findings have important implications for the mental and physical health of HCWs working during the pandemic in the UK.",,pdf:https://bmchealthservres.biomedcentral.com/counter/pdf/10.1186/s12913-022-08202-z; doi:https://doi.org/10.1101/2021.09.16.21263629; html:https://europepmc.org/article/PPR/PPR397279; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR397279&type=FILE&fileName=EMS135495-pdf.pdf&mimeType=application/pdf
 PPR468085,https://doi.org/10.1101/2022.03.11.22272276,Risk factors for SARS-CoV-2 infection after primary vaccination with ChAdOx1 nCoV-19 or BNT1262b2 and after booster vaccination with BNT1262b2 or mRNA-1273: a population-based cohort study (COVIDENCE UK),"Vivaldi G, Jolliffe DA, Holt H, Tydeman F, Talaei M, Davies GA, Lyons RA, Griffiths CJ, Kee F, Sheikh A, Shaheen SO, Martineau AR.",,No Journal Info,2022,2022-03-13,Y,,,,"<h4>Background</h4> Little is known about the relative influence of demographic, behavioural, and vaccine-related factors on risk of post-vaccination SARS-CoV-2 infection. We aimed to identify risk factors for SARS-CoV-2 infection after primary and booster vaccinations. <h4>Methods</h4> We undertook a prospective population-based study in UK adults (≥16 years) vaccinated against SARS-CoV-2, including data from Jan 12, 2021, to Feb 21, 2022. We modelled risk of post-vaccination SARS-CoV-2 infection separately for participants who had completed a primary course of vaccination (two-dose or, in the immunosuppressed, three-dose course of either ChAdOx1 nCoV-19 [ChAdOx1] or BNT1262b2) and for those who had additionally received a booster dose (BNT1262b2 or mRNA-1273). Cox regression models were used to explore associations between sociodemographic, behavioural, clinical, pharmacological, and nutritional factors and breakthrough infection, defined as a self-reported positive result on a lateral flow or reverse transcription PCR (RT-PCR) test for SARS-CoV-2. Models were further adjusted for weekly SARS-CoV-2 incidence at the local (lower tier local authority) level. <h4>Findings</h4> 14,713 participants were included in the post-primary analysis and 10,665 in the post-booster analysis, with a median follow-up of 203 days (IQR 195–216) in the post-primary cohort and 85 days (66–103) in the post-booster cohort. 1051 (7.1%) participants in the post-primary cohort and 1009 (9.4%) participants in the post-booster cohort reported a breakthrough SARS-CoV-2 infection. A primary course of ChAdOx1 ( vs BNT182b2) was associated with higher risk of infection, both in the post-primary cohort (adjusted hazard ratio 1.63, 95% CI 1.41–1.88) and in the post-booster cohort after boosting with mRNA-1273 (1.29 [1.03–1.61] vs BNT162b2 primary plus BNT162b2 booster). A lower risk of breakthrough infection was associated with older age (post-primary: 0.96 [0.96–0.97] per year; post-booster: 0.97 [0.96–0.98]), whereas a higher risk of breakthrough infection was associated with lower levels of education (post-primary: 1.66 [1.35–2.06] for primary or secondary vs postgraduate; post-booster: 1.36 [1.08–1.71]) and at least three weekly visits to indoor public places (post-primary: 1.38 [1.15–1.66] vs none; post-booster: 1.33 [1.10–1.60]). <h4>Conclusions</h4> Vaccine type, socioeconomic status, age, and behaviours affect risk of breakthrough SARS-CoV-2 infection following a primary schedule and a booster dose. <h4>Research in context</h4> <h4>Evidence before this study</h4> We searched PubMed, medRxiv, and Google Scholar for papers published up to Feb 18, 2022, using the search terms (breakthrough OR post-vaccin*) AND (SARS-CoV-2 OR COVID) AND (disease OR infection) AND (determinant OR “risk factor” OR associat*), with no language restrictions. Existing studies on risk factors for breakthrough SARS-CoV-2 infection among vaccinated individuals have found associations with age, comorbidities, vaccine type, and previous infection; however, findings have been inconsistent across studies. Most studies have been limited to specific subgroups or have focused on severe outcomes, and very few have considered breakthrough infections after a booster dose or have adjusted for behaviours affecting exposure to other people. <h4>Added value of this study</h4> This study is among the first to provide a detailed analysis of a wide range of risk factors for breakthrough SARS-CoV-2 infection, both after the primary course of vaccination and after a booster dose. Our large study size and detailed data have allowed us to investigate associations with various sociodemographic, clinical, pharmacological, and nutritional factors. Monthly follow-up data have additionally given us the opportunity to consider the effects of behaviours that may have changed across the pandemic, while adjusting for local SARS-CoV-2 incidence. <h4>Implications of all the available evidence</h4> Our findings add to growing evidence that risk factors for SARS-CoV-2 infection after primary or booster vaccinations can differ to those in unvaccinated populations, with effects attenuated for previously observed risk factors such as body-mass index and Asian ethnicity. The clear difference we observed between the efficacies of ChAdOx1 and BNT162b2 as the primary course of vaccination appears to have been reduced by the use of BNT162b2 boosters, but not by mNRA-1273 boosters. As more countries introduce booster vaccinations, future population-based studies with longer follow-up will be needed to investigate our findings further.",,pdf:https://pure.qub.ac.uk/files/383171042/1_s2.0_S2666776222001971_main.pdf; doi:https://doi.org/10.1101/2022.03.11.22272276; html:https://europepmc.org/article/PPR/PPR468085; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR468085&type=FILE&fileName=EMS148998-pdf.pdf&mimeType=application/pdf
-PPR731647,https://doi.org/10.2139/ssrn.4580461,A Comprehensive Benchmark for COVID-19 Predictive Modeling Using Electronic Health Records in Intensive Care,"Gao J, Zhu Y, Wang W, Dong G, Tang W, Wang H, Wang Y, Harrison EM, Ma L.",,No Journal Info,2023,2023-09-27,N,,,,"The COVID-19 pandemic highlighted the need for predictive deep learning models in healthcare. However, practical prediction task design, fair comparison and model selection for clinical applications remain a challenge. To address this, we introduced and evaluated two new prediction tasks - Outcome-specific length-of-stay and Early mortality prediction for COVID-19 patients in intensive care - which better reflect clinical realities. We developed evaluation metrics, model adaptation designs, and open-source data preprocessing pipelines for these tasks, while also evaluating 18 predictive models, including clinical scoring methods, traditional machine learning, basic deep learning, and advanced deep learning models tailored for EHR data. Benchmarking results from two real-world COVID-19 EHR datasets are provided, and all results and trained models are released on an online platform for use by clinicians and researchers. Our efforts contribute to the advancement of deep learning and machine learning research in pandemic predictive modeling.",,doi:https://doi.org/10.2139/ssrn.4580461; html:https://europepmc.org/article/PPR/PPR731647; doi:https://doi.org/10.2139/ssrn.4580461
 PPR445654,https://doi.org/10.1101/2022.01.21.22269605,Outcomes of SARS-CoV-2 Omicron infection in residents of Long-Term Care,"Krutikov M, Stirrup O, Nacer-Laidi H, Azmi B, Fuller C, Tut G, Palmer T, Shrotri M, Irwin-Singer A, Baynton V, The COVID-19 Genomics UK (COG-UK) consortium, Hayward A, Moss P, Copas A, Shallcross L.",,No Journal Info,2022,2022-01-23,Y,,,,"<h4>Background</h4> Recently there has been a rapid, global increase in SARS-CoV-2 infections associated with the Omicron variant (B.1.1.529). Although severity of Omicron cases may be reduced, the scale of infection suggests hospital admissions and deaths may be substantial. Definitive conclusions about disease severity require evidence from populations with the greatest risk of severe outcomes, such as residents of Long-Term Care Facilities (LTCFs). <h4>Methods</h4> We used a cohort study to compare the risk of hospital admission or death in LTCF residents in England who had tested positive for SARS-CoV-2 in the period shortly before Omicron emerged (Delta dominant) and the Omicron-dominant period, adjusting for age, sex, vaccine type, and booster vaccination. Variants were confirmed by sequencing or spike-gene status in a subset. <h4>Results</h4> Risk of hospital admission was markedly lower in 1241 residents infected in the Omicron-period (4.01% hospitalised, 95% CI: 2.87-5.59) compared to 398 residents infected in the pre-Omicron period (10.8% hospitalised, 95% CI: 8.13-14.29, adjusted Hazard Ratio 0.50, 95% CI: 0.29-0.87, p=0.014); findings were similar in residents with confirmed variant. No residents with previous infection were hospitalised in either period. Mortality was lower in the Omicron versus the pre-Omicron period, (p<0.0001). <h4>Conclusions</h4> Risk of severe outcomes in LTCF residents with the SARS-CoV-2 Omicron variant was substantially lower than that seen for previous variants. This suggests the current wave of Omicron infections is unlikely to lead to a major surge in severe disease in LTCF populations with high levels of vaccine coverage and/or natural immunity. <h4>Trial Registration Number</h4> ISRCTN 14447421",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/01/27/2022.01.21.22269605.full.pdf; doi:https://doi.org/10.1101/2022.01.21.22269605; html:https://europepmc.org/article/PPR/PPR445654; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR445654&type=FILE&fileName=EMS142621-pdf.pdf&mimeType=application/pdf
+PPR731647,https://doi.org/10.2139/ssrn.4580461,A Comprehensive Benchmark for COVID-19 Predictive Modeling Using Electronic Health Records in Intensive Care,"Gao J, Zhu Y, Wang W, Dong G, Tang W, Wang H, Wang Y, Harrison EM, Ma L.",,No Journal Info,2023,2023-09-27,N,,,,"The COVID-19 pandemic highlighted the need for predictive deep learning models in healthcare. However, practical prediction task design, fair comparison and model selection for clinical applications remain a challenge. To address this, we introduced and evaluated two new prediction tasks - Outcome-specific length-of-stay and Early mortality prediction for COVID-19 patients in intensive care - which better reflect clinical realities. We developed evaluation metrics, model adaptation designs, and open-source data preprocessing pipelines for these tasks, while also evaluating 18 predictive models, including clinical scoring methods, traditional machine learning, basic deep learning, and advanced deep learning models tailored for EHR data. Benchmarking results from two real-world COVID-19 EHR datasets are provided, and all results and trained models are released on an online platform for use by clinicians and researchers. Our efforts contribute to the advancement of deep learning and machine learning research in pandemic predictive modeling.",,doi:https://doi.org/10.2139/ssrn.4580461; html:https://europepmc.org/article/PPR/PPR731647; doi:https://doi.org/10.2139/ssrn.4580461
 PPR241483,https://doi.org/10.1101/2020.11.19.20234849,Community factors and excess mortality in first wave of the COVID-19 pandemic,"Davies B, Parkes BL, Bennett J, Fecht D, Blangiardo M, Ezzati M, Elliott P.",,No Journal Info,2020,2020-11-22,Y,,,,"Risk factors for increased risk of death from Coronavirus Disease 19 (COVID-19) have been identified 1,2 but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality at the community level during the first wave of the pandemic in England. We used geocoded data on all deaths in people aged 40 years and older during March-May 2020 compared with 2015-2019 in 6,791 local communities. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or high percent of people with a non-White ethnicity (including Black, Asian and other minority ethnic groups). Conversely, after accounting for other community characteristics, we found no association between population density or air pollution and excess mortality. Overall, the social and environmental variables accounted for around 15% of the variation in mortality at community level. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed if England and other industrialised countries are to avoid further widening of inequalities in mortality patterns during the second wave.",,doi:https://doi.org/10.1038/s41467-021-23935-x; doi:https://doi.org/10.1101/2020.11.19.20234849; html:https://europepmc.org/article/PPR/PPR241483; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR241483&type=FILE&fileName=EMS105015-pdf.pdf&mimeType=application/pdf
 PPR558653,https://doi.org/10.1101/2022.10.13.22281031,Indirect effects of the first two years of the COVID-19 pandemic on secondary care for cardiovascular disease in the UK: an electronic health record analysis across three countries,"Wright FL, Cheema K, Goldacre R, Hall N, Herz N, Islam N, Karim Z, Moreno-Martos D, Morales DR, O’Connell D, Spata E, Akbari A, Ashworth M, Barber M, Briffa N, Canoy D, Denaxas S, Khunti K, Kurdi A, Mamas M, Priedon R, Sudlow C, Morris EJ, Lacey B, Banerjee A.",,No Journal Info,2022,2022-10-17,Y,,,,"<h4>Background</h4> Although morbidity and mortality from COVID-19 have been widely reported, the indirect effects of the pandemic beyond 2020 on other major diseases and health service activity have not been well described. <h4>Methods</h4> Analyses used national administrative electronic hospital records in England, Scotland and Wales for 2016-2021. Admissions and procedures during the pandemic (2020-2021) related to six major cardiovascular conditions (acute coronary syndrome, heart failure, stroke/transient ischaemic attack, peripheral arterial disease, aortic aneurysm, and venous thromboembolism) were compared to the annual average in the pre-pandemic period (2016-2019). Differences were assessed by time period and urgency of care. <h4>Results</h4> In 2020, there were 31,064 (−6%) fewer hospital admissions (14,506 [-4%] fewer emergencies, 16,560 [-23%] fewer elective admissions) compared to 2016-2019 for the six major cardiovascular diseases combined. The proportional reduction in admissions was similar in all three countries. Overall, hospital admissions returned to pre-pandemic levels in 2021. Elective admissions remained substantially below expected levels for almost all conditions in all three countries (−10,996 [-15%] fewer admissions). However, these reductions were offset by higher than expected total emergency admissions (+25,878 [+6%] higher admissions), notably for heart failure and stroke in England, and for venous thromboembolism in all three countries. Analyses for procedures showed similar temporal variations to admissions. <h4>Conclusion</h4> This study highlights increasing emergency cardiovascular admissions as a result of the pandemic, in the context of a substantial and sustained reduction in elective admissions and procedures. This is likely to increase further the demands on cardiovascular services over the coming years. <h4>Key Question</h4> What is the impact in 2020 and 2021 of the COVID-19 pandemic on hospital admissions and procedures for six major cardiovascular diseases in England, Scotland and Wales? <h4>Key Finding</h4> In 2020, there were 6% fewer hospital admissions (emergency: -4%, elective: -23%) compared to 2016-2019 for six major cardiovascular diseases, across three UK countries. Overall, admissions returned to pre-pandemic levels in 2021, but elective admissions remained below expected levels. <h4>Take-home Message</h4> There was increasing emergency cardiovascular admissions as a result of the pandemic, with substantial and sustained reduction in elective admissions and procedures. This is likely to increase further the demands on cardiovascular services over the coming years.",,pdf:https://eprints.keele.ac.uk/id/eprint/12374/1/2022.10.13.22281031v1.full.pdf; doi:https://doi.org/10.1101/2022.10.13.22281031; html:https://europepmc.org/article/PPR/PPR558653; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR558653&type=FILE&fileName=EMS155821-pdf.pdf&mimeType=application/pdf
 PPR447312,https://doi.org/10.1101/2022.01.26.22269885,SARS-CoV-2 anti-spike antibody levels following second dose of ChAdOx1 nCov-19 or BNT162b2 in residents of long-term care facilities in England (VIVALDI),"Stirrup O, Krutikov M, Tut G, Palmer T, Bone D, Bruton R, Fuller C, Azmi B, Lancaster T, Sylla P, Kaur N, Spalkova E, Bentley C, Amin U, Jadir A, Hulme S, Giddings R, Nacer-Laidi H, Baynton V, Irwin-Singer A, Hayward A, Moss P, Copas A, Shallcross L.",,No Journal Info,2022,2022-01-27,Y,,,,"<h4>Background</h4> General population studies have shown strong humoral response following SARS-CoV-2 vaccination with subsequent waning of anti-spike antibody levels. Vaccine-induced immune responses are often attenuated in frail and older populations such as Long-Term Care Facility (LTCF) residents but published data are scarce. <h4>Methods</h4> VIVALDI is a prospective cohort study in England which links serial blood sampling in LTCF staff and residents to routine healthcare records. We measured quantitative titres of SARS-CoV-2 anti-spike antibodies in residents and staff following second vaccination dose with ChAdOx1 nCov-19 (Oxford-AstraZeneca) or BNT162b2 (Pfizer-BioNTech). We investigated differences in peak antibody levels and rates of decline using linear mixed effects models. <h4>Results</h4> We report on 1317 samples from 402 residents (median age 86 years, IQR 78-91) and 632 staff (50 years, 37-58), ≤280 days from second vaccination dose. Peak antibody titres were 7.9-fold higher after Pfizer-BioNTech vaccine compared to Oxford-AstraZeneca (95%CI 3.6-17.0; P <0.01) but rate of decline was increased, and titres were similar at 6 months. Prior infection was associated with higher peak antibody levels in both Pfizer-BioNTech (2.8-fold, 1.9-4.1; P <0.01) and Oxford-AstraZeneca (4.8-fold, 3.2-7.1; P <0.01) recipients and slower rates of antibody decline. Increasing age was associated with a modest reduction in peak antibody levels for Oxford-AstraZeneca recipients. <h4>Conclusions</h4> Double-dose vaccination elicits robust and stable antibody responses in older LTCF residents, suggesting comparable levels of vaccine-induced immunity to that in the general population. Antibody levels are higher after Pfizer-BioNTech vaccination but fall more rapidly compared to Oxford-AstraZeneca recipients and are enhanced by prior infection in both groups.",,pdf:https://discovery.ucl.ac.uk/10147322/1/spike-waning-JID.pdf; doi:https://doi.org/10.1101/2022.01.26.22269885; html:https://europepmc.org/article/PPR/PPR447312; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR447312&type=FILE&fileName=EMS142768-pdf.pdf&mimeType=application/pdf
 PPR496296,https://doi.org/10.1101/2022.05.09.22274769,"COVID-19 vaccination in pregnancy: views and vaccination uptake rates in pregnancy, a mixed methods analysis from the Born In Wales study","Mhereeg M, Jones H, Kennedy J, Seaborne M, Parker M, Kennedy N, Beeson S, Zuccolo L, Davies A, Brophy S.",,No Journal Info,2022,2022-05-11,N,,,,"<h4>Background</h4> Vaccine hesitancy amongst pregnant women has been found to be a concern during past epidemics. <h4>Objectives</h4> The aims of this study were to 1) estimate COVID-19 vaccination rates among pregnant women in Wales and their association with age, ethnicity, and area of deprivation, using electronic health records (EHR) linkage, and 2) explore pregnant women’s views on receiving the COVID-19 vaccine during pregnancy using data from a survey recruiting via social media (Facebook, Twitter), through midwives, and posters in hospitals (Born in Wales Cohort). <h4>Design</h4> A mixed methods study utilising routinely collected linked data from the Secure Anonymised Information Linkage (SAIL) (Objective 1) and the Born In Wales Birth Cohort participants (Objective 2). SAIL combines data from general practice, hospital admissions, the national community child health dataset, maternal indicators dataset, and COVID-19 vaccination databases. <h4>Setting and participants</h4> <h4>Objective: </h4> 1) All women documented as being pregnant on or after 13 th April 2021, aged 18 years or older, and eligible for COVID-19 vaccination were identified in routine health care. They were linked to the vaccination data up to and including 31 st December 2021. Objective 2) Separately, a cross-section of pregnant women in Wales were invited to complete an online survey via social media advertising. The survey asked what their views were on having the COVID-19 vaccination during pregnancy, and if they had already received, or intended to receive, the COVID-19 vaccination during their pregnancies. They were also asked to give reasons for their decisions. <h4>Outcomes</h4> 1 (a). Rate of vaccination uptake per month during pregnancy among women eligible for vaccination. 1 (b). Survival analysis was utilised to examine and compare the length of time to vaccination uptake in pregnancy, and variation in uptake by; age, ethnicity, and deprivation area was examined using hazard ratios (HR) from Cox regression. 2.Expectant mothers’ views of the COVID-19 vaccination during pregnancy. <h4>Results</h4> <h4>Population-level data linkage (objective 1)</h4> Within the population cohort, 32.7% (n = 8,203) were vaccinated (at least one dose of the vaccine) during pregnancy, 34.1% (n = 8,572) remained unvaccinated throughout follow-up period, and 33.2% (n = 8,336) received the vaccine postpartum. Younger women (<30 years) were less likely to have the vaccine and those living in areas of high deprivation were also less likely to have the vaccine (HR=0.88, 95% CI 0.82 to 0.95). Asian and other ethnic groups were 1.12 and 1.18 times more likely to have the vaccine in pregnancy compared to women of White ethnicity (HR=1.12, 95% CI 1.00 to 1.25) and (HR=1.18, 95% CI 1.03 to 1.37) respectively. <h4>Survey responses (objective 2)</h4> 69% of participants stated that they would be happy to have the vaccine during pregnancy (n = 207). The remainder, 31%, indicated that they would not have the vaccine during pregnancy (n = 94). Reasons for having the vaccine related to protecting self and baby, perceived risk level, and receipt of sufficient evidence and advice. Reasons for vaccine refusal included lack of research about long-term outcomes for the baby, anxiety about vaccines, inconsistent advice/information, and preference to wait until after the pregnancy. <h4>Conclusion</h4> Potentially only 1 in 3 pregnant women would have the COVID-19 vaccine during pregnancy, even though 2 in 3 reported they would have the vaccination, thus it is critical to develop tailored strategies to increase its acceptance rate and to decrease vaccine hesitancy. A targeted approach to vaccinations may be required for groups such as younger people and those living in higher deprivation level areas.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/05/11/2022.05.09.22274769.full.pdf; doi:https://doi.org/10.1101/2022.05.09.22274769; html:https://europepmc.org/article/PPR/PPR496296; doi:https://doi.org/10.1101/2022.05.09.22274769
-PPR265323,https://doi.org/10.1101/2021.01.13.21249725,The cellular immune response to COVID-19 deciphered by single cell multi-omics across three UK centres,"Stephenson E, Reynolds G, Botting RA, Calero-Nieto FJ, Morgan M, Tuong ZK, Bach K, Sungnak W, Worlock KB, Yoshida M, Kumasaka N, Kania K, Engelbert J, Olabi B, Spegarova JS, Wilson NK, Mende N, Jardine L, Gardner LC, Goh I, Horsfall D, McGrath J, Webb S, Mather MW, Lindeboom RG, Dann E, Huang N, Polanski K, Prigmore E, Gothe F, Scott J, Payne RP, Baker KF, Hanrath AT, van der Loeff ICS, Barr AS, Sanchez-Gonzalez A, Bergamaschi L, Mescia F, Barnes JL, Kilich E, de Wilton A, Saigal A, Saleh A, Janes SM, Smith CM, Gopee N, Wilson C, Coupland P, Coxhead JM, Kiselev VY, van Dongen S, Bacardit J, King HW, Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID BioResource Collaboration, Rostron AJ, Simpson AJ, Hambleton S, Laurenti E, Lyons PA, Meyer KB, Nikolic MZ, Duncan CJ, Smith K, Teichmann SA, Clatworthy MR, Marioni JC, Gottgens B, Haniffa M.",,No Journal Info,2021,2021-01-15,Y,,,,"The COVID-19 pandemic, caused by SARS coronavirus 2 (SARS-CoV-2), has resulted in excess morbidity and mortality as well as economic decline. To characterise the systemic host immune response to SARS-CoV-2, we performed single-cell RNA-sequencing coupled with analysis of cell surface proteins, providing molecular profiling of over 800,000 peripheral blood mononuclear cells from a cohort of 130 patients with COVID-19. Our cohort, from three UK centres, spans the spectrum of clinical presentations and disease severities ranging from asymptomatic to critical. Three control groups were included: healthy volunteers, patients suffering from a non-COVID-19 severe respiratory illness and healthy individuals administered with intravenous lipopolysaccharide to model an acute inflammatory response. Full single cell transcriptomes coupled with quantification of 188 cell surface proteins, and T and B lymphocyte antigen receptor repertoires have provided several insights into COVID-19: 1. a new non-classical monocyte state that sequesters platelets and replenishes the alveolar macrophage pool; 2. platelet activation accompanied by early priming towards megakaryopoiesis in immature haematopoietic stem/progenitor cells and expansion of megakaryocyte-primed progenitors; 3. increased clonally expanded CD8 + effector:effector memory T cells, and proliferating CD4 + and CD8 + T cells in patients with more severe disease; and 4. relative increase of IgA plasmablasts in asymptomatic stages that switches to expansion of IgG plasmablasts and plasma cells, accompanied with higher incidence of BCR sharing, as disease severity increases. All data and analysis results are available for interrogation and data mining through an intuitive web portal. Together, these data detail the cellular processes present in peripheral blood during an acute immune response to COVID-19, and serve as a template for multi-omic single cell data integration across multiple centers to rapidly build powerful resources to help combat diseases such as COVID-19.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2021/01/15/2021.01.13.21249725.full.pdf; doi:https://doi.org/10.1101/2021.01.13.21249725; html:https://europepmc.org/article/PPR/PPR265323; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR265323&type=FILE&fileName=EMS110618-pdf.pdf&mimeType=application/pdf
+PPR265323,https://doi.org/10.1101/2021.01.13.21249725,The cellular immune response to COVID-19 deciphered by single cell multi-omics across three UK centres,"Stephenson E, Reynolds G, Botting RA, Calero-Nieto FJ, Morgan M, Tuong ZK, Bach K, Sungnak W, Worlock KB, Yoshida M, Kumasaka N, Kania K, Engelbert J, Olabi B, Spegarova JS, Wilson NK, Mende N, Jardine L, Gardner LC, Goh I, Horsfall D, McGrath J, Webb S, Mather MW, Lindeboom RG, Dann E, Huang N, Polanski K, Prigmore E, Gothe F, Scott J, Payne RP, Baker KF, Hanrath AT, van der Loeff ICS, Barr AS, Sanchez-Gonzalez A, Bergamaschi L, Mescia F, Barnes JL, Kilich E, de Wilton A, Saigal A, Saleh A, Janes SM, Smith CM, Gopee N, Wilson C, Coupland P, Coxhead JM, Kiselev VY, van Dongen S, Bacardit J, King HW, Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID BioResource Collaboration, Rostron AJ, Simpson AJ, Hambleton S, Laurenti E, Lyons PA, Meyer KB, Nikolic MZ, Duncan CJ, Smith K, Teichmann SA, Clatworthy MR, Marioni JC, Gottgens B, Haniffa M.",,No Journal Info,2021,2021-01-15,Y,,,,"The COVID-19 pandemic, caused by SARS coronavirus 2 (SARS-CoV-2), has resulted in excess morbidity and mortality as well as economic decline. To characterise the systemic host immune response to SARS-CoV-2, we performed single-cell RNA-sequencing coupled with analysis of cell surface proteins, providing molecular profiling of over 800,000 peripheral blood mononuclear cells from a cohort of 130 patients with COVID-19. Our cohort, from three UK centres, spans the spectrum of clinical presentations and disease severities ranging from asymptomatic to critical. Three control groups were included: healthy volunteers, patients suffering from a non-COVID-19 severe respiratory illness and healthy individuals administered with intravenous lipopolysaccharide to model an acute inflammatory response. Full single cell transcriptomes coupled with quantification of 188 cell surface proteins, and T and B lymphocyte antigen receptor repertoires have provided several insights into COVID-19: 1. a new non-classical monocyte state that sequesters platelets and replenishes the alveolar macrophage pool; 2. platelet activation accompanied by early priming towards megakaryopoiesis in immature haematopoietic stem/progenitor cells and expansion of megakaryocyte-primed progenitors; 3. increased clonally expanded CD8 + effector:effector memory T cells, and proliferating CD4 + and CD8 + T cells in patients with more severe disease; and 4. relative increase of IgA plasmablasts in asymptomatic stages that switches to expansion of IgG plasmablasts and plasma cells, accompanied with higher incidence of BCR sharing, as disease severity increases. All data and analysis results are available for interrogation and data mining through an intuitive web portal. Together, these data detail the cellular processes present in peripheral blood during an acute immune response to COVID-19, and serve as a template for multi-omic single cell data integration across multiple centers to rapidly build powerful resources to help combat diseases such as COVID-19.",,doi:https://doi.org/10.1038/s41591-021-01329-2; doi:https://doi.org/10.1101/2021.01.13.21249725; html:https://europepmc.org/article/PPR/PPR265323; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR265323&type=FILE&fileName=EMS110618-pdf.pdf&mimeType=application/pdf
 PPR520994,https://doi.org/10.21203/rs.3.rs-1831644/v1,"COVID-19 vaccination in pregnancy: views and vaccination uptake rates in pregnancy, a mixed methods analysis from the Born In Wales study","Mhereeg M, Jones H, Kennedy J, Seaborne M, Parker M, Kennedy N, Beeson S, Akbari A, Zuccolo L, Davies A, Brophy S.",,No Journal Info,2022,2022-07-20,Y,,,,"<h4>Background: </h4> Vaccine hesitancy amongst pregnant women has been found to be a concern during past epidemics. This study aimed to 1) estimate COVID-19 vaccination rates among pregnant women in Wales and their association with age, ethnicity, and area of deprivation, using electronic health records (EHR) linkage, and 2) explore pregnant women’s views on receiving the COVID-19 vaccine during pregnancy using data from a survey recruiting via social media (Facebook, Twitter), through midwives, and posters in hospitals (Born in Wales Cohort). Methods  This was a mixed-methods study utilising routinely collected linked data from the Secure Anonymised Information Linkage (SAIL) (Objective 1) and the Born-In-Wales Birth Cohort participants (Objective 2). Survival analysis was utilised to examine and compare the length of time to vaccination uptake in pregnancy, and variation in uptake by; age, ethnicity, and deprivation area was examined using hazard ratios (HR) from Cox regression. Codebook thematic analysis was used to generate themes from an open-ended question on the survey. Results  Population-level data linkage (objective 1) Within the population cohort, 32.7% (n = 8,203) were vaccinated (at least one dose of the vaccine) during pregnancy, 34.1% (n = 8,572) remained unvaccinated throughout follow-up period, and 33.2% (n = 8,336) received the vaccine postpartum. Younger women (< 30 years) were less likely to have the vaccine and those living in areas of high deprivation were also less likely to have the vaccine (HR = 0.88, 95% CI 0.82 to 0.95). Asian and other ethnic groups were 1.12 and 1.18 times more likely to have the vaccine in pregnancy compared to women of White ethnicity (HR = 1.12, 95% CI 1.00 to 1.25) and (HR = 1.18, 95% CI 1.03 to 1.37) respectively. Survey responses (objective 2) 69% of participants stated that they would be happy to have the vaccine during pregnancy (n = 207). The remainder, 31%, indicated that they would not have the vaccine during pregnancy (n = 94). Reasons for having the vaccine included protecting self and baby, perceived risk level, and receipt of sufficient evidence and advice. Reasons for vaccine refusal included lack of research about long-term outcomes for the baby, anxiety about vaccines, inconsistent advice/information, and preference to wait until after the pregnancy. Conclusion  Potentially only 1 in 3 pregnant women would have the COVID-19 vaccine during pregnancy, even though 2 in 3 reported they would have the vaccination, thus it is critical to develop tailored strategies to increase its acceptance rate and to decrease vaccine hesitancy. A targeted approach to vaccinations may be required for groups such as younger people and those living in higher deprivation level areas.",,pdf:https://www.researchsquare.com/article/rs-1831644/latest.pdf; doi:https://doi.org/10.21203/rs.3.rs-1831644/v1; html:https://europepmc.org/article/PPR/PPR520994; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR520994&type=FILE&fileName=EMS151343-pdf.pdf&mimeType=application/pdf
 PPR186543,https://doi.org/10.1101/2020.07.10.20150656,Diagnostic value of skin manifestation of SARS-CoV-2 infection,"Bataille V, Visconti A, Rossi N, Murray B, Bournot A, Wolf J, Wolf J, Ourselin S, Steves C, Spector T, Falchi M.",,No Journal Info,2020,2020-07-11,Y,,,,"SARS-CoV-2 causes multiple immune-related reactions at various stages of the disease. The wide variety of skin presentations has delayed linking these to the virus. Previous studies had attempted to look at the prevalence and timing of SARS-COV-2 rashes but were based on mostly hospitalized severe cases and had little follow up. Using data collected on a subset of 336,847 eligible UK users of the COVID Symptom Study app, we observed that 8.8% of the swab positive cases (total: 2,021 subjects) reported either a body rash or an acral rash, compared to 5.4% of those with a negative swab test (total: 25,136). Together, these two skin presentations showed an odds ratio (OR) of 1.67 (95% confidence interval [CI]: 1.41-1.96) for being swab positive. Skin rashes were also predictive in the larger untested group of symptomatic app users (N=54,652), as 8.2% of those who had reported at least one classical COVID-19 symptom, i . e ., fever, persistent cough, and/or anosmia, also reported a rash. Data from an independent online survey of 11,546 respondents with a rash showed that in 17% of swab positive cases, the rash was the initial presentation. Furthermore, in 21%, the rash was the only clinical sign. Skin rashes cluster with other COVID-19 symptoms, are predictive of a positive swab test and occur in a significant number of cases, either alone or before other classical symptoms. Recognising rashes is important in identifying new and earlier COVID-19 cases.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2020/10/26/2020.07.10.20150656.full.pdf; doi:https://doi.org/10.1101/2020.07.10.20150656; html:https://europepmc.org/article/PPR/PPR186543; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR186543&type=FILE&fileName=EMS87210-pdf.pdf&mimeType=application/pdf
 PPR585732,https://doi.org/10.1101/2022.12.16.22283578,"Higher dose corticosteroids in hospitalised COVID-19 patients with hypoxia but not requiring ventilatory support (RECOVERY): a randomised, controlled, open-label, platform trial","RECOVERY Collaborative Group, Horby PW, Emberson JR, Basnyat B, Basnyat B, Campbell M, Peto L, Pessoa-Amorim G, Staplin N, Hamers RL, Amuasi J, Nel J, Kestelyn E, Rawal M, Jha RK, Phong NT, Samardi U, Paudel D, Thach PN, Nasronudin N, Stratton E, Mew L, Sarkar R, Baillie JK, Buch MH, Day J, Faust SN, Jaki T, Jeffery K, Juszczak E, Knight M, Lim WS, Mafham M, Montgomery A, Mumford A, Rowan K, Thwaites G, Haynes R, Landray MJ.",,No Journal Info,2022,2022-12-17,Y,,,,"<h4>SUMMARY</h4> <h4>Background</h4> Low-dose corticosteroids have been shown to reduce mortality for hypoxic COVID-19 patients requiring oxygen or ventilatory support (non-invasive mechanical ventilation, invasive mechanical ventilation or extra-corporeal membrane oxygenation). We evaluated the use of a higher dose of corticosteroids in this patient group. <h4>Methods</h4> This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]) is assessing multiple possible treatments in patients hospitalised for COVID-19. Eligible and consenting adult patients with clinical evidence of hypoxia (i.e. receiving oxygen or with oxygen saturation <92% on room air) were randomly allocated (1:1) to either usual care with higher dose corticosteroids (dexamethasone 20 mg once daily for 5 days followed by 10 mg once daily for 5 days or until discharge if sooner) or usual standard of care alone (which includes dexamethasone 6 mg once daily for 10 days or until discharge if sooner). The primary outcome was 28-day mortality. On 11 May 2022, the independent Data Monitoring Committee recommended stopping recruitment of patients receiving no oxygen or simple oxygen only to this comparison due to safety concerns. We report the results for these participants only. Recruitment of patients receiving ventilatory support continues. The RECOVERY trial is registered with ISRCTN (50189673) and clinicaltrials.gov ( NCT04381936 ). <h4>Findings</h4> Between 25 May 2021 and 12 May 2022, 1272 COVID-19 patients with hypoxia and receiving no oxygen (1%) or simple oxygen only (99%) were randomly allocated to receive usual care plus higher dose corticosteroids versus usual care alone (of whom 87% received low dose corticosteroids during the follow-up period). Of those randomised, 745 (59%) were in Asia, 512 (40%) in the UK and 15 (1%) in Africa. 248 (19%) had diabetes mellitus. Overall, 121 (18%) of 659 patients allocated to higher dose corticosteroids versus 75 (12%) of 613 patients allocated to usual care died within 28 days (rate ratio [RR] 1·56; 95% CI 1·18-2·06; p=0·0020). There was also an excess of pneumonia reported to be due to non-COVID infection (10% vs. 6%; absolute difference 3.7%; 95% CI 0.7-6.6) and an increase in hyperglycaemia requiring increased insulin dose (22% vs. 14%; absolute difference 7.4%; 95% CI 3.2-11.5). <h4>Interpretation</h4> In patients hospitalised for COVID-19 with clinical hypoxia but requiring either no oxygen or simple oxygen only, higher dose corticosteroids significantly increased the risk of death compared to usual care, which included low dose corticosteroids. The RECOVERY trial continues to assess the effects of higher dose corticosteroids in patients hospitalised with COVID-19 who require non-invasive ventilation, invasive mechanical ventilation or extra-corporeal membrane oxygenation. <h4>Funding</h4> UK Research and Innovation (Medical Research Council) and National Institute of Health and Care Research (Grant ref: MC_PC_19056), and Wellcome Trust (Grant Ref: 222406/Z/20/Z).",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/12/17/2022.12.16.22283578.full.pdf; doi:https://doi.org/10.1101/2022.12.16.22283578; html:https://europepmc.org/article/PPR/PPR585732; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR585732&type=FILE&fileName=EMS158665-pdf.pdf&mimeType=application/pdf
@@ -261,15 +261,15 @@ PPR361566,https://doi.org/10.1101/2021.06.21.21259254,"Acceptability, usability
 PPR370874,https://doi.org/10.1101/2021.07.12.21260360,The impact of hypoxia on B cells in COVID-19,"Kotagiri P, Mescia F, Hanson A, Turner L, Bergamaschi L, Peñalver A, Richoz N, Moore SD, Ortmann BM, Dunmore BJ, Ruffieux H, Morgan MD, Tuong ZK, Bashford-Rogers RJM, Hosmillo M, Baker S, Elmer A, Goodfellow IG, Gupta RK, Kingston N, Lehner PJ, Matheson NJ, Richardson S, Saunders C, Weekes MP, Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID BioResource Collaboration, Göttgens B, Toshner M, Hess C, Maxwell PH, Clatworthy MR, Nathan JA, Bradley JR, Lyons PA, Burrows N, Smith KG.",,No Journal Info,2021,2021-07-15,N,,,,"Prominent early features of COVID-19 include severe, often clinically silent, hypoxia and a pronounced reduction in B cells, the latter important in defence against SARS-CoV-2. This brought to mind the phenotype of mice with VHL-deficient B cells, in which Hypoxia-Inducible Factors are constitutively active, suggesting hypoxia might drive B cell abnormalities in COVID-19. We demonstrated the breadth of early and persistent defects in B cell subsets in moderate/severe COVID-19, including reduced marginal zone-like, memory and transitional B cells, changes we also observed in B cell VHL-deficient mice. This was corroborated by hypoxia-related transcriptional changes in COVID-19 patients, and by similar B cell abnormalities in mice kept in hypoxic conditions, including reduced marginal zone and germinal center B cells. Thus hypoxia might contribute to B cell pathology in COVID-19, and in other hypoxic states. Through this mechanism it may impact on COVID-19 outcome, and be remediable through early oxygen therapy.",,pdf:http://www.thelancet.com/article/S2352396422000627/pdf; doi:https://doi.org/10.1101/2021.07.12.21260360; html:https://europepmc.org/article/PPR/PPR370874; doi:https://doi.org/10.1101/2021.07.12.21260360
 PPR182791,https://doi.org/10.1101/2020.07.01.182709,Genetic architecture of host proteins interacting with SARS-CoV-2,"Pietzner M, Wheeler E, Carrasco-Zanini J, Raffler J, Kerrison ND, Oerton E, Auyeung VP, Luan J, Finan C, Casas JP, Ostroff R, Williams SA, Kastenmüller G, Ralser M, Gamazon ER, Wareham NJ, Hingorani AD, Langenberg C.",,No Journal Info,2020,2020-07-01,Y,,,,"<h4>ABSTRACT</h4> Strategies to develop therapeutics for SARS-CoV-2 infection may be informed by experimental identification of viral-host protein interactions in cellular assays and measurement of host response proteins in COVID-19 patients. Identification of genetic variants that influence the level or activity of these proteins in the host could enable rapid ‘in silico’ assessment in human genetic studies of their causal relevance as molecular targets for new or repurposed drugs to treat COVID-19. We integrated large-scale genomic and aptamer-based plasma proteomic data from 10,708 individuals to characterize the genetic architecture of 179 host proteins reported to interact with SARS-CoV-2 proteins or to participate in the host response to COVID-19. We identified 220 host DNA sequence variants acting in cis (MAF 0.01-49.9%) and explaining 0.3-70.9% of the variance of 97 of these proteins, including 45 with no previously known protein quantitative trait loci (pQTL) and 38 encoding current drug targets. Systematic characterization of pQTLs across the phenome identified protein-drug-disease links, evidence that putative viral interaction partners such as MARK3 affect immune response, and establish the first link between a recently reported variant for respiratory failure of COVID-19 patients at the ABO locus and hypercoagulation, i.e. maladaptive host response. Our results accelerate the evaluation and prioritization of new drug development programmes and repurposing of trials to prevent, treat or reduce adverse outcomes. Rapid sharing and dynamic and detailed interrogation of results is facilitated through an interactive webserver ( https://omicscience.org/apps/covidpgwas/ ).",,doi:https://doi.org/10.1101/2020.07.01.182709; html:https://europepmc.org/article/PPR/PPR182791; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR182791&type=FILE&fileName=EMS93113-pdf.pdf&mimeType=application/pdf
 PPR416505,https://doi.org/10.1101/2021.11.08.21265380,Describing the population experiencing COVID-19 vaccine breakthrough following second vaccination in England: A cohort study from OpenSAFELY,"The OpenSAFELY Collaborative:, Green A, Curtis H, Hulme W, Williamson E, McDonald H, Bhaskaran K, Rentsch C, Schultze A, MacKenna B, Mahalingasivam V, Tomlinson L, Walker A, Fisher L, Massey J, Andrews C, Hopcroft L, Morton C, Croker R, Morley J, Mehrkar A, Bacon S, Evans D, Inglesby P, Hickman G, Ward T, Davy S, Mathur R, Tazare J, Eggo RM, Wing K, Wong A, Forbes H, Bates C, Cockburn J, Parry J, Hester F, Harper S, Douglas I, Evans S, Smeeth L, Goldacre B.",,No Journal Info,2021,2021-11-08,Y,,,,"<h4>Background</h4> While the vaccines against COVID-19 are considered to be highly effective, COVID-19 vaccine breakthrough is likely and a small number of people will still fall ill, be hospitalised, or die from COVID-19, despite being fully vaccinated. With the continued increase in numbers of positive SARS-CoV-2 tests, describing the characters of individuals who have experienced a COVID-19 vaccine breakthrough could be hugely important in helping to determine who may be at greatest risk. <h4>Method</h4> With the approval of NHS England we conducted a retrospective cohort study using routine clinical data from the OpenSAFELY TPP database of fully vaccinated individuals, linked to secondary care and death registry data, and described the characteristics of those experiencing a COVID-19 vaccine breakthrough. <h4>Results</h4> As of 01 st November 2021, a total of 15,436,455 individuals were identified as being fully vaccinated against COVID-19, with a median follow-up time of 149 days (IQR: 107-179). From within this population, a total of 577245 (<4%) individuals reported a positive SARS-CoV-2 test. For every 1000 years of patient follow-up time, the corresponding incidence rate was 98.02 (95% CI 97.9-98.15). There were 16,120 COVID-19-related hospital admissions, 1,100 COVID-19 critical care admission patients and 3,925 COVID-19-related deaths; corresponding incidence rates of 2.72 (95% C 2.7-2.74), 0.19 (95% C 0.18-0.19) and 0.66 (95% C 0.65-0.67), respectively. When broken down by the initial priority group, higher rates of hospitalisation and death were seen in those in care homes and those over 80 years of age. Comorbidities with the highest rates of breakthrough COVID-19 included chronic kidney disease, dialysis, transplant, haematological malignancy, and immunocompromised. <h4>Conclusion</h4> The majority of COVID-19 vaccine breakthrough cases in England were mild with relatively few fully vaccinated individuals being hospitalised or dying as a result. However, some concerning differences in rates of breakthrough cases were identified in several clinical and demographic groups. While it is important to note that these findings are simply descriptive and cannot be used to answer why certain groups have higher rates of COVID-19 breakthrough than others, the emergence of the Omicron variant of COVID-19 coupled with the continued increase in numbers of positive SARS-CoV-2 tests are concerning. As numbers of fully vaccinated individuals increases and follow-up time lengthens, so too will the number of COVID-19 breakthrough cases. Additional analyses, aimed at identifying individuals at higher risk, are therefore required.",,pdf:https://qmro.qmul.ac.uk/xmlui/bitstream/123456789/83135/2/Mathur%20Describing%20the%20population%20experiencing%20COVID-19%20vaccine%20breakthrough%20following%20second%20vaccination%20in%20England%3a%20a%20cohort%20study%20from%20OpenSAFELY%202022%20Published.pdf; doi:https://doi.org/10.1101/2021.11.08.21265380; html:https://europepmc.org/article/PPR/PPR416505; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR416505&type=FILE&fileName=EMS138253-pdf.pdf&mimeType=application/pdf
-PPR184537,https://doi.org/10.1101/2020.07.03.20145912,Ultraviolet A Radiation and COVID-19 Deaths in the USA with replication studies in England and Italy,"Cherrie M, Clemens T, Colandrea C, Feng Z, Webb DJ, Dibben C, Weller RB.",,No Journal Info,2020,2020-07-06,Y,,,,"<h4>Objectives</h4> To determine whether UVA exposure might be associated with COVID-19 deaths <h4>Design</h4> Ecological regression, with replication in two other countries and pooled estimation <h4>Setting</h4> 2,474 counties of the contiguous USA, 6,755 municipalities in Italy, 6,274 small areas in England. Only small areas in their ‘Vitamin D winter’ (monthly mean UV vitd of under 165 KJ/m 2 ) from Jan to April 2020. Participants The ‘at-risk’ population is the total small area population, with measures to incorporate spatial infection into the model. The model is adjusted for potential confounders including long-term winter temperature and humidity. <h4>Main outcome measures</h4> We derive UVA measures for each area from remote sensed data and estimate their relationship with COVID-19 mortality with a random effect for States, in a multilevel zero-inflated negative binomial model. In the USA and England death certificates had to record COVID-19. In Italy excess deaths in 2020 over expected from 2015-19. <h4>Data sources</h4> Satellite derived mean daily UVA dataset from Japan Aerospace Exploration Agency. Data on deaths compiled by Center for Disease Control (USA), Office for National Statistics (England) and Italian Institute of Statistics. <h4>Results</h4> Daily mean UVA (January-April 2020) varied between 450 to 1,000 KJ/m 2 across the three countries. Our fully adjusted model showed an inverse correlation between UVA and COVID-19 mortality with a Mortality Risk Ratio (MRR) of 0.71 (0.60 to 0.85) per 100KJ/m 2 increase UVA in the USA, 0.81 (0.71 to 0.93) in Italy and 0.49 (0.38 to 0.64) in England. Pooled MRR was 0.68 (0.52 to 0.88). <h4>Conclusions</h4> Our analysis, replicated in 3 independent national datasets, suggests ambient UVA exposure is associated with lower COVID-19 specific mortality. This effect is independent of vitamin D, as it occurred at irradiances below that likely to induce significant cutaneous vitamin D3 synthesis. Causal interpretations must be made cautiously in observational studies. Nonetheless this study suggests strategies for reduction of COVID-19 mortality.",,doi:https://doi.org/10.1111/bjd.20093; doi:https://doi.org/10.1101/2020.07.03.20145912; html:https://europepmc.org/article/PPR/PPR184537; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR184537&type=FILE&fileName=EMS87521-pdf.pdf&mimeType=application/pdf
 PPR625587,https://doi.org/10.2139/ssrn.4369346,"The Impact of the COVID-19 Pandemic on Anti-Psychotic Prescribing in Individuals with Autism, Dementia, Learning Disability, Serious Mental Illness or Living in a Care Home: A Federated Analysis of 59 Million Patients’ Primary Care Records in Situ Using OpenSAFELY","Macdonald O, Green A, Walker A, Curtis H, Croker R, Brown A, Butler-Cole B, Andrews C, Massey J, Inglesby P, Morton C, Fisher L, Morley J, Mehrkar A, Bacon S, Davy S, Evans D, Dillingham I, Ward T, Hulme W, Bates C, Cockburn J, Parry J, Hester F, Harper S, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Parkes N, Goldacre B, Mackenna B.",,No Journal Info,2023,2023-03-01,N,,,,"Background: The COVID-19 pandemic significantly affected health and social care services. We aimed to explore whether this affected antipsychotic prescribing in at-risk populations.<br><br>Methods: With the approval of NHS England, we completed a retrospective cohort study, using the OpenSAFELY platform to explore primary care data of 59 million patients.  We identified patients in five at-risk groups: autism, dementia, learning disability, serious mental illness and care home residents. We calculated the monthly prevalence of antipsychotic prescribing in these groups, as well as the incidence of new prescriptions in each month (Jan 2019-Dec 2021). <br><br>Findings: The average monthly rate of antipsychotic prescribing increased in dementia from 82.75 patients prescribed an antipsychotic per 1000 patients (95%CI 82.30-83.19) in Jan-Mar 2019 to 90.1 (95%CI 89.68-90.60) in Oct-Dec 2021 and from 154.61 (95%CI 153.79-155.43) to 166.95 (95%CI 166.23-167.67) in care homes. There were notable spikes in the rate of new prescriptions issued to patients with dementia and in care homes. In learning disability and autism groups, the rate of prescribing per 1000 decreased from 122.97 (95%CI 122.29-123.66) to 119.29 (95%CI 118.68-119.91), and from 54.91 (95%CI 54.52-55.29) to 51.04 (95%CI 50.74-51.35) respectively. <br><br>Interpretation: During the lockdowns in 2020, we observed a significant spike in antipsychotic prescribing in the dementia and care home groups.  We have shown that these peaks are likely due to prescribing of antipsychotics for palliative care. Over the study period, we observed gradual increases in antipsychotic use in dementia and care home patients and decreases in their use in patients with learning disability or autism.<br><br>Funding: This research used data assets made available as part of the Data and Connectivity National Core Study, led by Health Data Research UK in partnership with the Office for National Statistics and funded by UK Research and Innovation (grant ref MC_PC_20058). In addition, the OpenSAFELY Platform is supported by grants from the Wellcome Trust (222097/Z/20/Z); MRC (MR/V015757/1, MC_PC-20059, MR/W016729/1); NIHR (NIHR135559, COV-LT2- 0073), and Health Data Research UK (HDRUK2021.000, 2021.0157). BG has also received funding from: the Bennett Foundation, the Wellcome Trust, NIHR Oxford Biomedical Research Centre, NIHR Applied Research Collaboration Oxford and Thames Valley, the Mohn-Westlake Foundation; all Bennett Institute staff are supported by BG’s grants on this work. BMK is also employed by NHS England working on medicines policy and clinical lead for primary care medicines data. ID holds grants from NIHR and GSK. OM is employed by Oxford Health as Lead Learning Disabilities pharmacist and was funded by Buckinghamshire, Oxfordshire and Berkshire West Integrated Care System for this project.<br><br>Declaration of Interest: All authors have completed the ICMJE uniform disclosure form at www.icmje.org/coi_disclosure.pdf and declare the following: BG has received research funding from the Laura and John Arnold Foundation, the NHS National Institute for Health Research (NIHR), the NIHR School of Primary Care Research, the NIHR Oxford Biomedical Research Centre, the Mohn-Westlake Foundation, NIHR Applied Research Collaboration Oxford and Thames Valley, the Wellcome Trust, the Good Thinking Foundation, Health Data Research UK (HDRUK), the Health Foundation, and the World Health Organisation; he also receives personal income from speaking and writing for lay audiences on the misuse of science. OM is a member of the College of Mental Health Pharmacy Council and has received personal funding from CMHP and Aston university for teaching and supporting training in psychiatric pharmacy.<br><br>Ethical Approval: NHS England is the data controller; EMIS and TPP are the data processors; and the key researchers on OpenSAFELY are acting on behalf of NHS England. This implementation of OpenSAFELY is hosted within the EMIS and TPP environments which are accredited to the ISO 27001 information security standard and are NHS IG Toolkit compliant;[30,31] patient data has been pseudonymised for analysis and linkage using industry standard cryptographic hashing techniques; all pseudonymised datasets transmitted for linkage onto OpenSAFELY are encrypted; access to the platform is via a virtual private network (VPN) connection, restricted to a small group of researchers; the researchers hold contracts with NHS England and only access the platform to initiate database queries and statistical models; all database activity is logged; only aggregate statistical outputs leave the platform environment following best practice for anonymisation of results such as statistical disclosure control for low cell counts.[32] The OpenSAFELY research platform adheres to the obligations of the UK General Data Protection Regulation (GDPR) and the Data Protection Act 2018. In March 2020, the Secretary of State for Health and Social Care used powers under the UK Health Service (Control of Patient Information) Regulations 2002 (COPI) to require organisations to process confidential patient information for the purposes of protecting public health, providing healthcare services to the public and monitoring and managing the COVID-19 outbreak and incidents of exposure; this sets aside the requirement for patient consent.[33] Taken together, these provide the legal bases to link patient datasets on the OpenSAFELY platform. GP practices, from which the primary care data are obtained, are required to share relevant health information to support the public health response to the pandemic, and have been informed of the OpenSAFELY analytics platform. This study was approved by the Health Research Authority (REC reference 20/LO/0651) and by the LSHTM Ethics Board (reference 21863).",,doi:https://doi.org/10.1101/2023.01.05.23284214; doi:https://doi.org/10.2139/ssrn.4369346; html:https://europepmc.org/article/PPR/PPR625587; doi:https://doi.org/10.2139/ssrn.4369346
+PPR184537,https://doi.org/10.1101/2020.07.03.20145912,Ultraviolet A Radiation and COVID-19 Deaths in the USA with replication studies in England and Italy,"Cherrie M, Clemens T, Colandrea C, Feng Z, Webb DJ, Dibben C, Weller RB.",,No Journal Info,2020,2020-07-06,Y,,,,"<h4>Objectives</h4> To determine whether UVA exposure might be associated with COVID-19 deaths <h4>Design</h4> Ecological regression, with replication in two other countries and pooled estimation <h4>Setting</h4> 2,474 counties of the contiguous USA, 6,755 municipalities in Italy, 6,274 small areas in England. Only small areas in their ‘Vitamin D winter’ (monthly mean UV vitd of under 165 KJ/m 2 ) from Jan to April 2020. Participants The ‘at-risk’ population is the total small area population, with measures to incorporate spatial infection into the model. The model is adjusted for potential confounders including long-term winter temperature and humidity. <h4>Main outcome measures</h4> We derive UVA measures for each area from remote sensed data and estimate their relationship with COVID-19 mortality with a random effect for States, in a multilevel zero-inflated negative binomial model. In the USA and England death certificates had to record COVID-19. In Italy excess deaths in 2020 over expected from 2015-19. <h4>Data sources</h4> Satellite derived mean daily UVA dataset from Japan Aerospace Exploration Agency. Data on deaths compiled by Center for Disease Control (USA), Office for National Statistics (England) and Italian Institute of Statistics. <h4>Results</h4> Daily mean UVA (January-April 2020) varied between 450 to 1,000 KJ/m 2 across the three countries. Our fully adjusted model showed an inverse correlation between UVA and COVID-19 mortality with a Mortality Risk Ratio (MRR) of 0.71 (0.60 to 0.85) per 100KJ/m 2 increase UVA in the USA, 0.81 (0.71 to 0.93) in Italy and 0.49 (0.38 to 0.64) in England. Pooled MRR was 0.68 (0.52 to 0.88). <h4>Conclusions</h4> Our analysis, replicated in 3 independent national datasets, suggests ambient UVA exposure is associated with lower COVID-19 specific mortality. This effect is independent of vitamin D, as it occurred at irradiances below that likely to induce significant cutaneous vitamin D3 synthesis. Causal interpretations must be made cautiously in observational studies. Nonetheless this study suggests strategies for reduction of COVID-19 mortality.",,doi:https://doi.org/10.1111/bjd.20093; doi:https://doi.org/10.1101/2020.07.03.20145912; html:https://europepmc.org/article/PPR/PPR184537; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR184537&type=FILE&fileName=EMS87521-pdf.pdf&mimeType=application/pdf
 PPR373497,https://doi.org/10.1101/2021.07.22.21260416,"Obesity, Ethnicity, and Covid-19 Mortality: A population-based cohort study of 12.6 Million Adults in England","Yates T, Summerfield A, Razieh C, Banerjee A, Chudasama Y, Davies MJ, Gillies C, Islam N, Lawson C, Mirkes E, Zaccardi F, Khunti K, Nafilyan V.",,No Journal Info,2021,2021-07-23,Y,,,,"<h4>Importance</h4> Obesity and ethnicity are well characterised risk factors for severe COVID-19 outcomes, but the differential effects of obesity on COVID-19 outcomes by race/ethnicity has not been examined robustly in the general population. <h4>Objective</h4> To investigate the association between body mass index (BMI) and COVID-19 mortality across different ethnic groups. <h4>Design, Setting, and Participants</h4> This is a retrospective cohort study using linked national Census, electronic health records and mortality data for English adults aged 40 years or older who were alive at the start of pandemic (24 th January 2020). <h4>Exposures</h4> BMI obtained from electronic health records. Self-reported ethnicity (white, black, South Asian, other) was the effect-modifying variable. <h4>Main Outcomes and Measures</h4> COVID-19 related death identified by ICD-10 codes U07.1 or U07.2 mentioned on the death certificate from 24 th January 2020 until December 28 th 2020. <h4>Results</h4> The analysis included white (n = 11,074,708; mean age 61.9 [±13.4] years; 54% women), black (n = 416,542; 56.4 [±11.7] years; 57% women), South Asian (621,691; 55.7 [±12.4] years; 51% women) and other (n = 478,196; 55.3 [±11.6] years; 55% women) ethnicities with linked BMI data. The association between BMI and COVID-19 mortality was stronger in ethnic minority groups. Compared to a BMI of 22.5 kg/m 2 in white ethnicities, the adjusted HR for COVID-19 mortality at a BMI of 30 kg/m 2 in white, black, South Asian and other ethnicities was 0.95 (95% CI: 0.87-1.03), 1.72 (1.52-1.94), 2.00 (1.78-2.25) and 1.39 (1.21-1.61), respectively. The estimated risk of COVID-19 mortality at a BMI of 40 kg/m 2 in white ethnicities (HR = 1.73) was equivalent to the risk observed at a BMI of 30.1 kg/m 2 , 27.0 kg/m 2 , and 32.2 kg/m 2 in black, South Asian and other ethnic groups, respectively. <h4>Conclusions</h4> This population-based study using linked Census and electronic health care records demonstrates that the risk of COVID-19 mortality associated with obesity is greater in ethnic minority groups compared to white populations. <h4>Question</h4> Does the association between BMI and COVID-19 mortality vary by ethnicity? <h4>Findings</h4> In this study of 12.6 million adults, BMI was associated with COVID-19 in all ethnicities, but with stronger associations in ethnic minority populations such that the risk of COVID-19 mortality for a BMI of 40 kg/m 2 in white ethnicities was observed at a BMI of 30.1 kg/m 2 , 27.0 kg/m 2 , and 32.2 kg/m 2 in black, South Asian and other ethnicities, respectively. <h4>Meaning</h4> BMI is a stronger risk factor for COVID-19 mortality in ethnic minorities. Obesity management is therefore a priority in these populations.",,pdf:https://www.nature.com/articles/s41467-022-28248-1.pdf; doi:https://doi.org/10.1101/2021.07.22.21260416; html:https://europepmc.org/article/PPR/PPR373497; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR373497&type=FILE&fileName=EMS132179-pdf.pdf&mimeType=application/pdf
 PPR593389,https://doi.org/10.1101/2023.01.05.23284214,"The impact of the COVID-19 pandemic on Antipsychotic Prescribing in individuals with autism, dementia, learning disability, serious mental illness or living in a care home: A federated analysis of 59 million patients’ primary care records in situ using OpenSAFELY","The OpenSAFELY Collaborative:, Macdonald O, Green A, Walker A, Croker R, Curtis H, Brown A, Butler-Cole B, Andrews C, Morton C, Evans D, Inglesby P, Dillingham I, Massey J, Fisher L, Bacon S, Davy S, Ward T, Hulme W, Morley J, Mehrkar A, Bates C, Cockburn J, Parry J, Hester F, Harper S, O’Hanlon S, Eavis A, Jarvis R, Avramov D, Wood I, Parkes N, Goldacre B, MacKenna B.",,No Journal Info,2023,2023-01-07,Y,,,,"<h4>Background</h4> The COVID-19 pandemic significantly affected health and social care services. We aimed to explore whether this impacted the prescribing rates of antipsychotics within at-risk populations. <h4>Methods</h4> With the approval of NHS England, we completed a retrospective cohort study, using the OpenSAFELY platform to explore primary care data of 59 million patients. We identified patients in five at-risk groups: autism, dementia, learning disability, serious mental illness and care home residents. We then calculated the monthly prevalence of antipsychotic prescribing in the population, as well as the incidence of new prescriptions in each month over the study period (Jan 2019-Dec 2021). <h4>Results</h4> The average monthly rate of antipsychotic prescribing increased in dementia from 82.75 patients prescribed an antipsychotic per 1000 patients (95% CI 82.30-83.19) in Q1 2019 to 90.1 (95% CI 89.68-90.60) in Q4 2021 and from 154.61 (95% CI 153.79-155.43) in Q1 2019 to 166.95 (95% CI 166.23-167.67) in Q4 2021 in care homes. There were notable spikes in the rate of new prescriptions issued to patients with dementia and in care homes. In learning disability and autism groups, the average monthly rate of prescribing per 1000 decreased from 122.97 (95% CI 122.29-123.66) in Q1 2019 to 119.29 (95% CI 118.68-119.91) in Q4 2021, and from 54.91 (95% CI 54.52-55.29) in Q1 2019 to 51.04 (95% CI 50.74-51.35) in Q4 2021 respectively. <h4>Conclusions</h4> During each of the lockdowns in 2020, we observed a significant spike in antipsychotic prescribing in the dementia and care home groups. We have shown that these peaks are likely due to prescribing of antipsychotics for palliative care purposes and may have been linked to pre-emptive prescribing, when on-site medical visits would have been restricted. Over the study period, we observed gradual increases in antipsychotic use in patients with dementia and in care homes and a decrease in their use in patients with learning disability or autism.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2023/01/07/2023.01.05.23284214.full.pdf; doi:https://doi.org/10.1101/2023.01.05.23284214; html:https://europepmc.org/article/PPR/PPR593389; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR593389&type=FILE&fileName=EMS159469-pdf.pdf&mimeType=application/pdf
 PPR550426,https://doi.org/10.1101/2022.09.23.22280285,"Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial","RECOVERY Collaborative Group, Horby PW, Peto L, Staplin N, Campbell M, Pessoa-Amorim G, Mafham M, Emberson JR, Stewart R, Prudon B, Uriel A, Green CA, Dhasmana DJ, Malein F, Majumdar J, Collini P, Shurmer J, Yates B, Baillie JK, Buch MH, Day JN, Faust SN, Jaki T, Jeffery K, Juszczak E, Knight M, Lim WS, Montgomery A, Mumford A, Rowan K, Thwaites G, Haynes R, Landray M.",,No Journal Info,2022,2022-09-25,Y,,,,"<h4>SUMMARY</h4> <h4>Background</h4> Dimethyl fumarate (DMF) is an anti-inflammatory drug that has been proposed as a treatment for patients hospitalised with COVID-19 <h4>Methods</h4> This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple possible treatments in patients hospitalised for COVID-19. In this initial assessment of DMF, performed at 27 UK hospitals, eligible and consenting adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF 120mg twice daily for 2 days followed by 240mg twice daily for 8 days, or until discharge if sooner. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale, assessed using a proportional odds model. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov ( NCT04381936 ). <h4>Findings</h4> Between 2 March 2021 and 18 November 2021, 713 patients were enrolled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients were receiving corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.85-1.46; p=0.42). There was no significant effect of DMF on any secondary outcome. As expected, DMF caused flushing and gastrointestinal symptoms, each in around 6% of patients, but no new adverse effects were identified. <h4>Interpretation</h4> In adults hospitalised with COVID-19, DMF was not associated with an improvement in clinical outcomes. <h4>Funding</h4> UK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056).",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/09/25/2022.09.23.22280285.full.pdf; doi:https://doi.org/10.1101/2022.09.23.22280285; html:https://europepmc.org/article/PPR/PPR550426; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR550426&type=FILE&fileName=EMS154960-pdf.pdf&mimeType=application/pdf
-PPR393010,https://doi.org/10.1101/2021.09.03.21263023,Evaluation of antithrombotic use and COVID-19 outcomes in a nationwide atrial fibrillation cohort,"Handy A, Banerjee A, Wood A, Dale CE, Sudlow C, Tomlinson C, Bean D, Thygesen JH, Mizani MA, Katsoulis M, Sofat R, Dobson R, Takhar R, Hollings S, Denaxas S, Walker V.",,No Journal Info,2021,2021-09-10,N,,,,"<h4>ABSTRACT</h4> <h4>Objective</h4> Evaluate antithrombotic (AT) use in individuals with atrial fibrillation (AF) and high stroke risk (CHA 2 DS 2 -VASc score>=2) and investigate whether pre-existing AT use may improve COVID-19 outcomes. <h4>Methods</h4> Individuals with AF and a CHA 2 DS 2 -VASc score>=2 on January 1 st 2020 were identified using pseudonymised, linked electronic health records for 56 million people in England and followed-up until May 1 st 2021. Factors associated with pre-existing AT use were analysed using logistic regression. Differences in COVID-19 related hospitalisation and death were analysed using logistic and Cox regression for individuals exposed to pre-existing AT use vs no AT use, anticoagulants (AC) vs antiplatelets (AP) and direct oral anticoagulants (DOACs) vs warfarin. <h4>Results</h4> From 972,971 individuals with AF and a CHA 2 DS 2 -VASc score>=2, 88.0% (n=856,336) had pre-existing AT use, 3.8% (n=37,418) had a COVID-19 related hospitalisation and 2.2% (n=21,116) died. Factors associated with no AT use included comorbidities that may contraindicate AT use (liver disease and history of falls) and demographics (socioeconomic status and ethnicity). Pre-existing AT use was associated with lower odds of death (OR=0.92 [0 . 87-0 . 96 at 95% CI] ), but higher odds of hospitalisation OR=1.20 [1 . 15-1 . 26 at 95% CI] ). The same pattern was observed for AC vs AP (death (OR=0.93 [0.87-0.98]), hospitalisation (OR=1.17 [1.11-1.24])) but not for DOACs vs warfarin (death (OR=1.00 [0.95-1.05]), hospitalisation (OR=0.86 [0.82-0.89]). <h4>Conclusions</h4> Pre-existing AT use may offer marginal protection against COVID-19 death, with AC offering more protection than AP. Although this association may not be causal, it provides further incentive to improve AT coverage for eligible individuals with AF. <h4>KEY QUESTIONS</h4> <h4>What is already known about this subject?</h4> Anticoagulants (AC), a sub-class of antithrombotics (AT), reduce the risk of stroke and are recommended for individuals with atrial fibrillation (AF) and at high risk of stroke (CHA 2 DS 2 -VASc score>=2, National Institute for Health and Care Excellence threshold). However, previous evaluations suggest that up to one third of these individuals may not be taking AC. Over estimation of bleeding and fall risk in elderly patients have been identified as potential factors in this under medicating. In response to the COVID-19 pandemic, several observational studies have observed correlations between pre-existing AT use, particularly anticoagulants (AC), and lower risk of severe COVID-19 outcomes such as hospitalisation and death. However, these correlations are inconsistent across studies and have not compared all major sub-types of AT in one study. <h4>What does this study add?</h4> This study uses datasets covering primary care, secondary care, pharmacy dispensing, death registrations, multiple COVID-19 diagnoses routes and vaccination records for 56 million people in England and is the largest scale evaluation of AT use to date. This provides the statistical power to robustly analyse targeted sub-types of AT and control for a wide range of potential confounders. All code developed for the study is opensource and an updated nationwide evaluation can be rapidly created for future time points. In 972,971 individuals with AF and a CHA 2 DS 2 -VASc score>=2, we observed 88.0% (n=856,336) with pre-existing AT use which was associated with marginal protection against COVID-19 death (OR=0.92 [0 . 87-0 . 96 at 95% CI] ). <h4>How might this impact on clinical practice?</h4> These findings can help shape global AT medication policy and provide population-scale, observational analysis results alongside gold-standard randomised control trials to help assess whether a potential beneficial effect of pre-existing AT use on COVID-19 death alters risk to benefit assessments in AT prescribing decisions.",,pdf:https://heart.bmj.com/content/heartjnl/108/12/923.full.pdf; doi:https://doi.org/10.1101/2021.09.03.21263023; html:https://europepmc.org/article/PPR/PPR393010; doi:https://doi.org/10.1101/2021.09.03.21263023
 PPR289244,https://doi.org/10.2139/ssrn.3789264,Effectiveness of First Dose of COVID-19 Vaccines Against Hospital Admissions in Scotland: National Prospective Cohort Study of 5.4 Million People,"Vasileiou E, Simpson CR, Robertson C, Shi T, Kerr S, Agrawal U, Akbari A, Bedston S, Beggs J, Bradley D, Chuter A, Lusignan Sd, Docherty A, Ford D, Hobbs R, Joy M, Katikireddi SV, Marple J, McCowan C, McGagh D, McMenamin J, Moore E, Murray J, Pan J, Ritchie LD, Shah SA, Stock S, Torabi F, Tsang RSM, Wood R, Woolhouse M, Sheikh A.",,No Journal Info,2021,2021-02-19,N,,,,"Background: The BNT162b2 mRNA (Pfizer-BioNTech) and ChAdOx1 (Oxford-AstraZeneca) COVID-19 vaccines have demonstrated high efficacy against infection in phase 3 clinical trials and are now being used in national vaccination programmes in the UK and several other countries. There is an urgent need to study the ‘real-world’ effects of these vaccines. The aim of our study was to estimate the effectiveness of the first dose of these COVID-19 vaccines in preventing hospital admissions.<br><br>Methods: We conducted a prospective cohort study using the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) database comprising of linked vaccination, primary care, Real-Time Polymerase Chain Reaction (RT-PCR) testing, hospitalisation and mortality records for 5.4 million people in Scotland (covering ~99% of population). A time-dependent Cox model and Poisson regression models were fitted to estimate effectiveness against COVID-19 related hospitalisation (defined as 1- Adjusted Hazard Ratio) following the first dose of vaccine.<br><br>Findings: The first dose of the BNT162b2 vaccine was associated with a vaccine effect of 85% (95% confidence interval [CI] 76 to 91) for COVID-19 related hospitalisation at 28-34 days post-vaccination. Vaccine effect at the same time interval for the ChAdOx1 vaccine was 94% (95% CI 73 to 99). Results of combined vaccine effect for prevention of COVID-19 related hospitalisation were comparable when restricting the analysis to those aged ≥80 years (81%; 95% CI 65 to 90 at 28-34 days post-vaccination).<br><br>Interpretation: A single dose of the BNT162b2 mRNA and ChAdOx1 vaccines resulted in substantial reductions in the risk of COVID-19 related hospitalisation in Scotland.<br><br>Funding: UK Research and Innovation (Medical Research Council); Research and Innovation Industrial Strategy Challenge Fund; Health Data Research UK.<br><br>Conflict of Interest: AS is a member of the Scottish Government Chief Medical Officer’s COVID-19Advisory Group and the New and Emerging Respiratory Virus Threats (NERVTAG) Risk Stratification Subgroup. CRS declares funding from the MRC, NIHR, CSO and New Zealand Ministry for Business, Innovation and Employment and Health Research Council during the conduct of this study. SVK is co-chair of the Scottish Government’s Expert Reference Group on COVID-19 and ethnicity, is a member of the Scientific Advisory Group on Emergencies (SAGE) subgroup on ethnicity and acknowledges funding from a NRS Senior Clinical Fellowship, MRC and CSO. All other authors report no conflicts of interest.<br><br>Ethical Approval: Approvals were obtained from the National Research Ethics Service Committee, Southeast Scotland 02 (reference number: 12/SS/0201) and Public Benefit and Privacy Panel for Health and Social Care (reference number: 1920-0279).",,pdf:https://www.pure.ed.ac.uk/ws/files/197030199/SSRN_id3789264.pdf; doi:https://doi.org/10.2139/ssrn.3789264; html:https://europepmc.org/article/PPR/PPR289244; doi:https://doi.org/10.2139/ssrn.3789264
-PPR466607,https://doi.org/10.1101/2022.03.07.22272026,"Trends, variation and clinical characteristics of recipients of antivirals and neutralising monoclonal antibodies for non-hospitalised COVID-19: a descriptive cohort study of 23.4 million people in OpenSAFELY","The OpenSAFELY Collaborative, Green A, Curtis HJ, Higgins R, Smith R, Mehrkar A, Inglesby P, Mahalingasivam V, Drysdale H, DeVito NJ, Croker R, Rentsch CT, Bhaskaran K, Andrews C, Bacon S, Davy S, Dillingham I, Evans D, Fisher L, Hickman G, Hopcroft L, Hulme WJ, Nab L, Massey J, McDonald O, Morley J, Morton CE, Park R, Walker AJ, Ward T, Wiedemann M, Bates C, Cockburn J, Parry J, Hester F, Harper S, Douglas IJ, Evans SJ, Tomlinson L, MacKenna B, Goldacre B.",,No Journal Info,2022,2022-03-10,Y,,,,"<h4>ABSTRACT</h4> <h4>Objectives</h4> Ascertain patient eligibility status and describe coverage of antivirals and neutralising monoclonal antibodies (nMAB) as treatment for COVID-19 in community settings in England. <h4>Design</h4> Cohort study, approved by NHS England. <h4>Setting</h4> Routine clinical data from 23.4m people linked to data on COVID-19 infection and treatment, within the OpenSAFELY-TPP database. <h4>Participants</h4> Non-hospitalised COVID-19 patients at high-risk of severe outcomes. <h4>Interventions</h4> Nirmatrelvir/ritonavir (Paxlovid), sotrovimab, molnupiravir, casirivimab or remdesivir, administered in the community by COVID-19 Medicine Delivery Units. <h4>Results</h4> We identified 102,170 non-hospitalised patients with COVID-19 between 11 th December 2021 and 28 th April 2022 at high-risk of severe outcomes and therefore potentially eligible for antiviral and/or nMAB treatment. Of these patients, 18,210 (18%) received treatment; sotrovimab, 9,340 (51%); molnupiravir, 4,500 (25%); Paxlovid, 4,290 (24%); casirivimab, 50 (<1%); and remdesivir, 20 (<1%). The proportion of patients treated increased from 8% (180/2,380) in the first week of treatment availability to 22% (420/1870) in the latest week. The proportion treated varied by high risk group, lowest in those with Liver disease (12%; 95% CI 11 to 13); by treatment type, with sotrovimab favoured over molnupiravir/Paxlovid in all but three high risk groups: Down syndrome (36%; 95% CI 31 to 40), Rare neurological conditions (46%; 95% CI 44 to 48), and Primary immune deficiencies (49%; 95% CI 48 to 51); by ethnicity, from Black (10%; 95% CI 9 to 11) to White (18%; 95% CI 18 to 19); by NHS Region, from 11% (95% CI 10 to 12) in Yorkshire and the Humber to 23% (95% CI 22 to 24) in the East of England); and by deprivation level, from 12% (95% CI 12 to 13) in the most deprived areas to 21% (95% CI 21 to 22) in the least deprived areas. There was also lower coverage among unvaccinated patients (5%; 95% CI 4 to 7), those with dementia (5%; 95% CI 4 to 6) and care home residents (6%; 95% CI 5 to 6). <h4>Conclusions</h4> Using the OpenSAFELY platform we were able to identify patients who were potentially eligible to receive treatment and assess the coverage of these new treatments amongst these patients. Targeted activity may be needed to address apparent lower treatment coverage observed among certain groups, in particular (at present): different NHS regions, socioeconomically deprived areas, and care homes. <h4>What is already known about this topic</h4> Since the emergence of COVID-19, a number of approaches to treatment have been tried and evaluated. These have mainly consisted of treatments such as dexamethasone, which were used in UK hospitals,from early on in the pandemic to prevent progression to severe disease. Until recently (December 2021), no treatments have been widely used in community settings across England. <h4>What this study adds</h4> Following the rollout of antiviral medicines and neutralising monoclonal antibodies (nMABs) as treatment for patients with COVID-19, we were able to identify patients who were potentially eligible to receive antivirals or nMABs and assess the coverage of these new treatments amongst these patients, in as close to real-time as the available data flows would support. While the proportion of the potentially eligible patients receiving treatment increased over time, rising from 8% (180/2,380) in the first week of the roll out to 22% (420/1870) in the last week of April 2022, there were variations in coverage between key clinical, geographic, and demographic subgroup. <h4>How this study might affect research, practice, or policy</h4> Targeted activity may therefore be needed to address lower treatment rates observed among certain geographic areas and key groups including ethnic minorities, people living in areas of higher deprivation, and in care homes.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/06/01/2022.03.07.22272026.full.pdf; doi:https://doi.org/10.1101/2022.03.07.22272026; html:https://europepmc.org/article/PPR/PPR466607; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR466607&type=FILE&fileName=EMS145672-pdf.pdf&mimeType=application/pdf
+PPR393010,https://doi.org/10.1101/2021.09.03.21263023,Evaluation of antithrombotic use and COVID-19 outcomes in a nationwide atrial fibrillation cohort,"Handy A, Banerjee A, Wood A, Dale CE, Sudlow C, Tomlinson C, Bean D, Thygesen JH, Mizani MA, Katsoulis M, Sofat R, Dobson R, Takhar R, Hollings S, Denaxas S, Walker V.",,No Journal Info,2021,2021-09-10,N,,,,"<h4>ABSTRACT</h4> <h4>Objective</h4> Evaluate antithrombotic (AT) use in individuals with atrial fibrillation (AF) and high stroke risk (CHA 2 DS 2 -VASc score>=2) and investigate whether pre-existing AT use may improve COVID-19 outcomes. <h4>Methods</h4> Individuals with AF and a CHA 2 DS 2 -VASc score>=2 on January 1 st 2020 were identified using pseudonymised, linked electronic health records for 56 million people in England and followed-up until May 1 st 2021. Factors associated with pre-existing AT use were analysed using logistic regression. Differences in COVID-19 related hospitalisation and death were analysed using logistic and Cox regression for individuals exposed to pre-existing AT use vs no AT use, anticoagulants (AC) vs antiplatelets (AP) and direct oral anticoagulants (DOACs) vs warfarin. <h4>Results</h4> From 972,971 individuals with AF and a CHA 2 DS 2 -VASc score>=2, 88.0% (n=856,336) had pre-existing AT use, 3.8% (n=37,418) had a COVID-19 related hospitalisation and 2.2% (n=21,116) died. Factors associated with no AT use included comorbidities that may contraindicate AT use (liver disease and history of falls) and demographics (socioeconomic status and ethnicity). Pre-existing AT use was associated with lower odds of death (OR=0.92 [0 . 87-0 . 96 at 95% CI] ), but higher odds of hospitalisation OR=1.20 [1 . 15-1 . 26 at 95% CI] ). The same pattern was observed for AC vs AP (death (OR=0.93 [0.87-0.98]), hospitalisation (OR=1.17 [1.11-1.24])) but not for DOACs vs warfarin (death (OR=1.00 [0.95-1.05]), hospitalisation (OR=0.86 [0.82-0.89]). <h4>Conclusions</h4> Pre-existing AT use may offer marginal protection against COVID-19 death, with AC offering more protection than AP. Although this association may not be causal, it provides further incentive to improve AT coverage for eligible individuals with AF. <h4>KEY QUESTIONS</h4> <h4>What is already known about this subject?</h4> Anticoagulants (AC), a sub-class of antithrombotics (AT), reduce the risk of stroke and are recommended for individuals with atrial fibrillation (AF) and at high risk of stroke (CHA 2 DS 2 -VASc score>=2, National Institute for Health and Care Excellence threshold). However, previous evaluations suggest that up to one third of these individuals may not be taking AC. Over estimation of bleeding and fall risk in elderly patients have been identified as potential factors in this under medicating. In response to the COVID-19 pandemic, several observational studies have observed correlations between pre-existing AT use, particularly anticoagulants (AC), and lower risk of severe COVID-19 outcomes such as hospitalisation and death. However, these correlations are inconsistent across studies and have not compared all major sub-types of AT in one study. <h4>What does this study add?</h4> This study uses datasets covering primary care, secondary care, pharmacy dispensing, death registrations, multiple COVID-19 diagnoses routes and vaccination records for 56 million people in England and is the largest scale evaluation of AT use to date. This provides the statistical power to robustly analyse targeted sub-types of AT and control for a wide range of potential confounders. All code developed for the study is opensource and an updated nationwide evaluation can be rapidly created for future time points. In 972,971 individuals with AF and a CHA 2 DS 2 -VASc score>=2, we observed 88.0% (n=856,336) with pre-existing AT use which was associated with marginal protection against COVID-19 death (OR=0.92 [0 . 87-0 . 96 at 95% CI] ). <h4>How might this impact on clinical practice?</h4> These findings can help shape global AT medication policy and provide population-scale, observational analysis results alongside gold-standard randomised control trials to help assess whether a potential beneficial effect of pre-existing AT use on COVID-19 death alters risk to benefit assessments in AT prescribing decisions.",,pdf:https://heart.bmj.com/content/heartjnl/108/12/923.full.pdf; doi:https://doi.org/10.1101/2021.09.03.21263023; html:https://europepmc.org/article/PPR/PPR393010; doi:https://doi.org/10.1101/2021.09.03.21263023
 PPR729805,https://doi.org/10.1101/2023.09.22.23295850,Group A streptococcal cases and treatments during the COVID-19 pandemic and 2022 outbreak: a retrospective cohort study in England using OpenSAFELY-TPP,"Cunningham C, Fisher L, Wood C, The OpenSAFELY Collaborative, Speed V, Brown AD, Curtis HJ, Higgins R, Croker R, Butler-Cole BF, Evans D, Inglesby P, Dillingham I, Bacon SC, Beech E, Hand K, Davy S, Ward T, Hickman G, Bridges L, O’Dwyer T, Maude S, Smith RM, Mehrkar A, Hart LC, Bates C, Cockburn J, Parry J, Hester F, Harper S, Goldacre B, MacKenna B.",,No Journal Info,2023,2023-09-23,Y,,,,"<h4>Objective</h4> To investigate the impact of the COVID-19 pandemic on Group A streptococcal (GAS) cases and related antibiotic prescriptions. <h4>Design</h4> A retrospective cohort study with supporting dashboards with the approval of NHS England. <h4>Setting</h4> Primary care practices in England using TPP SystmOne software from January 2018 through March 2023. <h4>Participants</h4> Patients included were those registered at a TPP practice for each month of the study period. Patients with missing sex or age were excluded, resulting in a population of 23,816,470 in January 2018, increasing to 25,541,940 by March 2023. <h4>Main outcome measures</h4> We calculated monthly counts and crude rates of GAS cases (sore throat/tonsillitis, scarlet fever, invasive group A strep) and prescriptions linked with a GAS case, before (pre-April 2020), during and after (post-April 2021) COVID-19 restrictions. We calculated the maximum and minimum count and rate for each season (years running September-August), and the rate ratio (RR) of the 2022/23 season to the last comparably high season (2017/18). <h4>Results</h4> Recording of GAS cases and antibiotic prescription linked with a GAS case peaked in December 2022, higher than the 2017/2018 peak. The peak rate of monthly sore throat/tonsillitis (possible group A strep throat) recording was 5.33 per 1,000 (RR 2022/23 versus 2017/18 1.39 (CI: 1.38 to 1.40)). Scarlet fever recording peaked at 0.51 per 1,000 (RR 2.68 (CI: 2.59 to 2.77)), and invasive group A streptococcal infection (iGAS) at 0.01 per 1,000 (RR 4.37 (CI: 2.94 to 6.48)). First line antibiotics with a record of a GAS infection peaked at 2.80 per 1,000 (RR 1.37 (CI:1.35 to 1.38)), alternative antibiotics at 2.03 per 1,000 (RR 2.30 (CI:2.26 to 2.34)), and reserved antibiotics at 0.09 per 1,000 (RR 2.42 (CI:2.24 to 2.61)). For individual antibiotics, azithromycin with GAS indication showed the greatest relative increase (RR 7.37 (CI:6.22 to 8.74)).This followed a sharp drop in recording of cases and associated prescriptions during the period of COVID-19 restrictions where the maximum count and rates were lower than any pre COVID-19 minimum. More detailed demographic breakdowns can be found in our regularly updated dashboard report. <h4>Conclusions</h4> Rates of scarlet fever, sore throat/tonsillitis and iGAS recording and associated antibiotic prescribing peaked in December 2022. Primary care data can supplement existing infectious disease surveillance through linkages with relevant prescribing data and detailed clinical and demographic subgroups. <h4>What is known</h4> During the COVID-19 pandemic there has been a substantial change to the pattern of circulating viruses and bacteria that cause illnesses. A spike in group A streptococcal infections in England starting December 2022 was associated with 426 deaths, including 48 children as of 7th May 2023. Increased demand for antibiotics in this period led to medicines shortages and the introduction of Serious Shortage Protocols (SSPs). Existing surveillance systems such as notifiable disease reports and GP in-hours surveillance bulletins describe clinical events, but they do not link to relevant prescribing data. <h4>What this study adds</h4> - This study supports the findings of routine surveillance reports which indicated a drop in GAS infections during the COVID-19 restrictions, followed by a spike in December 2022, demonstrating that the OpenSAFELY platform and primary care data can be used to rapidly describe not only clinical events but also relevant prescribing in the case of future outbreaks. - Antibiotic prescribing with a GAS indication, particularly for phenoxymethylpenicillin alternatives and reserved antibiotics, was higher in the December 2022 peak than in the 2017/2018 peak.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2023/09/23/2023.09.22.23295850.full.pdf; doi:https://doi.org/10.1101/2023.09.22.23295850; html:https://europepmc.org/article/PPR/PPR729805; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR729805&type=FILE&fileName=EMS188482-pdf.pdf&mimeType=application/pdf
+PPR466607,https://doi.org/10.1101/2022.03.07.22272026,"Trends, variation and clinical characteristics of recipients of antivirals and neutralising monoclonal antibodies for non-hospitalised COVID-19: a descriptive cohort study of 23.4 million people in OpenSAFELY","The OpenSAFELY Collaborative, Green A, Curtis HJ, Higgins R, Smith R, Mehrkar A, Inglesby P, Mahalingasivam V, Drysdale H, DeVito NJ, Croker R, Rentsch CT, Bhaskaran K, Andrews C, Bacon S, Davy S, Dillingham I, Evans D, Fisher L, Hickman G, Hopcroft L, Hulme WJ, Nab L, Massey J, McDonald O, Morley J, Morton CE, Park R, Walker AJ, Ward T, Wiedemann M, Bates C, Cockburn J, Parry J, Hester F, Harper S, Douglas IJ, Evans SJ, Tomlinson L, MacKenna B, Goldacre B.",,No Journal Info,2022,2022-03-10,Y,,,,"<h4>ABSTRACT</h4> <h4>Objectives</h4> Ascertain patient eligibility status and describe coverage of antivirals and neutralising monoclonal antibodies (nMAB) as treatment for COVID-19 in community settings in England. <h4>Design</h4> Cohort study, approved by NHS England. <h4>Setting</h4> Routine clinical data from 23.4m people linked to data on COVID-19 infection and treatment, within the OpenSAFELY-TPP database. <h4>Participants</h4> Non-hospitalised COVID-19 patients at high-risk of severe outcomes. <h4>Interventions</h4> Nirmatrelvir/ritonavir (Paxlovid), sotrovimab, molnupiravir, casirivimab or remdesivir, administered in the community by COVID-19 Medicine Delivery Units. <h4>Results</h4> We identified 102,170 non-hospitalised patients with COVID-19 between 11 th December 2021 and 28 th April 2022 at high-risk of severe outcomes and therefore potentially eligible for antiviral and/or nMAB treatment. Of these patients, 18,210 (18%) received treatment; sotrovimab, 9,340 (51%); molnupiravir, 4,500 (25%); Paxlovid, 4,290 (24%); casirivimab, 50 (<1%); and remdesivir, 20 (<1%). The proportion of patients treated increased from 8% (180/2,380) in the first week of treatment availability to 22% (420/1870) in the latest week. The proportion treated varied by high risk group, lowest in those with Liver disease (12%; 95% CI 11 to 13); by treatment type, with sotrovimab favoured over molnupiravir/Paxlovid in all but three high risk groups: Down syndrome (36%; 95% CI 31 to 40), Rare neurological conditions (46%; 95% CI 44 to 48), and Primary immune deficiencies (49%; 95% CI 48 to 51); by ethnicity, from Black (10%; 95% CI 9 to 11) to White (18%; 95% CI 18 to 19); by NHS Region, from 11% (95% CI 10 to 12) in Yorkshire and the Humber to 23% (95% CI 22 to 24) in the East of England); and by deprivation level, from 12% (95% CI 12 to 13) in the most deprived areas to 21% (95% CI 21 to 22) in the least deprived areas. There was also lower coverage among unvaccinated patients (5%; 95% CI 4 to 7), those with dementia (5%; 95% CI 4 to 6) and care home residents (6%; 95% CI 5 to 6). <h4>Conclusions</h4> Using the OpenSAFELY platform we were able to identify patients who were potentially eligible to receive treatment and assess the coverage of these new treatments amongst these patients. Targeted activity may be needed to address apparent lower treatment coverage observed among certain groups, in particular (at present): different NHS regions, socioeconomically deprived areas, and care homes. <h4>What is already known about this topic</h4> Since the emergence of COVID-19, a number of approaches to treatment have been tried and evaluated. These have mainly consisted of treatments such as dexamethasone, which were used in UK hospitals,from early on in the pandemic to prevent progression to severe disease. Until recently (December 2021), no treatments have been widely used in community settings across England. <h4>What this study adds</h4> Following the rollout of antiviral medicines and neutralising monoclonal antibodies (nMABs) as treatment for patients with COVID-19, we were able to identify patients who were potentially eligible to receive antivirals or nMABs and assess the coverage of these new treatments amongst these patients, in as close to real-time as the available data flows would support. While the proportion of the potentially eligible patients receiving treatment increased over time, rising from 8% (180/2,380) in the first week of the roll out to 22% (420/1870) in the last week of April 2022, there were variations in coverage between key clinical, geographic, and demographic subgroup. <h4>How this study might affect research, practice, or policy</h4> Targeted activity may therefore be needed to address lower treatment rates observed among certain geographic areas and key groups including ethnic minorities, people living in areas of higher deprivation, and in care homes.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/06/01/2022.03.07.22272026.full.pdf; doi:https://doi.org/10.1101/2022.03.07.22272026; html:https://europepmc.org/article/PPR/PPR466607; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR466607&type=FILE&fileName=EMS145672-pdf.pdf&mimeType=application/pdf
 PPR648088,https://doi.org/10.1101/2023.04.13.23288469,"Empagliflozin in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial","Horby PW, Staplin N, Peto L, Emberson JR, Campbell M, Pessoa-Amorim G, Basnyat B, Thwaites L, Van Doorn R, Hamers RL, Nel J, Amuasi J, Rawal M, Ghosh D, Douse J, Hamilton F, Kerry A, Thu-Ta P, Widdrington J, Green C, Desai P, Stewart R, Phong NT, Baillie JK, Buch MH, Faust SN, Jaki T, Jeffery K, Juszczak E, Knight M, Lim WS, Montgomery A, Mukherjee A, Mumford A, Rowan K, Thwaites G, Mafham M, Haynes R, Landray MJ, RECOVERY Collaborative Group.",,No Journal Info,2023,2023-04-19,Y,,,,"<h4>SUMMARY</h4> <h4>Background</h4> Empagliflozin has been proposed as a treatment for COVID-19 on the basis of its anti-inflammatory, metabolic and haemodynamic effects. <h4>Methods</h4> In this randomised, controlled, open-label trial, several possible treatments are compared with usual care in patients hospitalised with COVID-19. Eligible and consenting adults were randomly allocated in a 1:1 ratio to either usual standard of care alone or usual standard of care plus empagliflozin 10mg once daily for 28 days or until discharge using web-based simple (unstratified) randomisation with allocation concealment. The primary outcome was 28-day mortality. On 3 March the independent data monitoring committee recommended that the investigators review the data and recruitment was consequently stopped on 7 March. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov ( NCT04381936 ). <h4>Findings</h4> Between 8 July 2021 and 6 March 2023, 4271 patients were randomly allocated to receive either empagliflozin (2113 patients) or usual care alone (2158 patients). Overall, 289 (14%) patients allocated to empagliflozin and 307 (14%) patients allocated to usual care died within 28 days (rate ratio 0.96; 95% confidence interval [CI] 0.82-1.13; p=0.64). There was no evidence of significant differences in duration of hospitalisation (median 8 days vs. 8 days) or the proportion of patients discharged from hospital alive within 28 days (79% vs. 78%; rate ratio 1.03; 95% CI 0.96-1.10; p=0.44). Among those not on invasive mechanical ventilation at baseline, there was no evidence of a significant difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (16% vs. 17%; risk ratio 0.95; 95% CI 0.84-1.08; p=0.44). <h4>Interpretation</h4> In adults hospitalised with COVID-19, empagliflozin was not associated with reductions in 28-day mortality, duration of hospital stay, or risk of progressing to invasive mechanical ventilation or death. <h4>Funding</h4> UK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056), and Wellcome Trust (Grant Ref: 222406/Z/20/Z). <h4>Trial registration</h4> ClinicalTrials.gov NCT04381936 https://clinicaltrials.gov/ct2/show/NCT04381936 ISRCTN50189673 http://www.isrctn.com/ISRCTN50189673",,pdf:https://nottingham-repository.worktribe.com/preview/26252707/PIIS221385872300253X.pdf; doi:https://doi.org/10.1101/2023.04.13.23288469; html:https://europepmc.org/article/PPR/PPR648088; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR648088&type=FILE&fileName=EMS174483-pdf.pdf&mimeType=application/pdf
 PPR860956,https://doi.org/10.1101/2024.06.02.24308329,The safety and efficacy of using age-adjusted D-dimers in hospitalised patients in a diverse urban centre: a real-world data study,"Gallier S, Evison F, Hodson J, Khosla R, Ranasinghe T, Rickard L, Atkin C, Reddy-Kolanu V, Nirantharakumar K, Lester W, Holloway B, Sapey E.",,No Journal Info,2024,2024-06-03,Y,,,,"<h4>Objective</h4> Despite recommendations, age adjusted thresholds (AAT) for D Dimers are not routinely used as part of venous thromboembolism (VTE) screening in many healthcare settings due to concerns about missing cases, especially in older and co-morbid adults. The National Institute for Health and Care Excellence in the UK has highlighted that evidence to support AAT is not plentiful. This study assessed the real-world use of AAT D-dimers for VTE in a large cohort of acutely hospitalised patients. <h4>Methods</h4> This retrospective data study included all adult patients attending a large hospital with a suspected VTE between January 2017 to December 2021. The predictive accuracy of D-dimer was assessed against gold standard imaging. Outcomes of false negative (with AAT) and false positives (with standard thresholds) cases were assessed. <h4>Results</h4> 27,526 suspected VTE attendances were included, with a 4.3% confirmed VTE diagnosis rate. The ST D-dimer exhibited high sensitivity (91.1%) but modest specificity (65.2%). The AAT demonstrated slightly lower sensitivity (87.0%) but higher specificity (71.7%, p<0.001). The performance of ST thresholds declined with age, with false positive rates increasing from 17.4% to 80.0% in people aged < 50 years and > 90 years respectively. The AAT accurately identified 1,700 true negatives misclassified as false positives by the ST. 14 patients in this group were admitted with a bleed within 30 days. AAT misdiagnosed 24 cases as false negatives, with most being small sub-segmental pulmonary emboli or non-occlusive DVTs. Using AAT thresholds could have avoided 64 scans per 1,000 attendances, saving approximately £235,310 of imaging costs in this cohort. <h4>Conclusion</h4> The age-adjusted D-dimer threshold enhances diagnostic precision and could decrease unnecessary imaging and anticoagulation, reducing investigations with time and cost savings with no significant safety signal.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2024/06/03/2024.06.02.24308329.full.pdf; doi:https://doi.org/10.1101/2024.06.02.24308329; html:https://europepmc.org/article/PPR/PPR860956; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR860956&type=FILE&fileName=EMS196708-pdf.pdf&mimeType=application/pdf
 PPR371921,https://doi.org/,Explainable Automated Coding of Clinical Notes using Hierarchical Label-wise Attention Networks and Label Embedding Initialisation,"Dong H, Suárez-Paniagua V, Whiteley W, Wu H.",,No Journal Info,2021,2021-07-16,Y,,,,"Diagnostic or procedural coding of clinical notes aims to derive a coded summary of disease-related information about patients. Such coding is usually done manually in hospitals but could potentially be automated to improve the efficiency and accuracy of medical coding. Recent studies on deep learning for automated medical coding achieved promising performances. However, the explainability of these models is usually poor, preventing them to be used confidently in supporting clinical practice. Another limitation is that these models mostly assume independence among labels, ignoring the complex correlation among medical codes which can potentially be exploited to improve the performance. We propose a Hierarchical Label-wise Attention Network (HLAN), which aimed to interpret the model by quantifying importance (as attention weights) of words and sentences related to each of the labels. Secondly, we propose to enhance the major deep learning models with a label embedding (LE) initialisation approach, which learns a dense, continuous vector representation and then injects the representation into the final layers and the label-wise attention layers in the models. We evaluated the methods using three settings on the MIMIC-III discharge summaries: full codes, top-50 codes, and the UK NHS COVID-19 shielding codes. Experiments were conducted to compare HLAN and LE initialisation to the state-of-the-art neural network based methods. HLAN achieved the best Micro-level AUC and $F_1$ on the top-50 code prediction and comparable results on the NHS COVID-19 shielding code prediction to other models. By highlighting the most salient words and sentences for each label, HLAN showed more meaningful and comprehensive model interpretation compared to its downgraded baselines and the CNN-based models. LE initialisation consistently boosted most deep learning models for automated medical coding.",,arxiv:https://arxiv.org/abs/2010.15728v4; html:https://europepmc.org/article/PPR/PPR371921; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR371921&type=FILE&fileName=EMS130963-pdf.pdf&mimeType=application/pdf
@@ -296,16 +296,16 @@ PPR150220,https://doi.org/10.1101/2020.04.07.20056788,ACE-inhibitors and Angiote
 PPR179288,https://doi.org/10.1101/2020.06.22.20137273,Effect of Dexamethasone in Hospitalized Patients with COVID-19 – Preliminary Report,"Horby P, Lim WS, Emberson J, Mafham M, Bell J, Linsell L, Staplin N, Brightling C, Ustianowski A, Elmahi E, Prudon B, Green C, Felton T, Chadwick D, Rege K, Fegan C, Chappell LC, Faust SN, Jaki T, Jeffery K, Montgomery A, Rowan K, Juszczak E, Baillie JK, Haynes R, Landray MJ, RECOVERY Collaborative Group.",,No Journal Info,2020,2020-06-22,Y,,,,"<h4>ABSTRACT</h4> <h4>Background</h4> Coronavirus disease 2019 (COVID-19) is associated with diffuse lung damage. Corticosteroids may modulate immune-mediated lung injury and reducing progression to respiratory failure and death. <h4>Methods</h4> The Randomised Evaluation of COVID-19 therapy (RECOVERY) trial is a randomized, controlled, open-label, adaptive, platform trial comparing a range of possible treatments with usual care in patients hospitalized with COVID-19. We report the preliminary results for the comparison of dexamethasone 6 mg given once daily for up to ten days vs. usual care alone. The primary outcome was 28-day mortality. <h4>Results</h4> 2104 patients randomly allocated to receive dexamethasone were compared with 4321 patients concurrently allocated to usual care. Overall, 454 (21.6%) patients allocated dexamethasone and 1065 (24.6%) patients allocated usual care died within 28 days (age-adjusted rate ratio [RR] 0.83; 95% confidence interval [CI] 0.74 to 0.92; P<0.001). The proportional and absolute mortality rate reductions varied significantly depending on level of respiratory support at randomization (test for trend p<0.001): Dexamethasone reduced deaths by one-third in patients receiving invasive mechanical ventilation (29.0% vs. 40.7%, RR 0.65 [95% CI 0.51 to 0.82]; p<0.001), by one-fifth in patients receiving oxygen without invasive mechanical ventilation (21.5% vs. 25.0%, RR 0.80 [95% CI 0.70 to 0.92]; p=0.002), but did not reduce mortality in patients not receiving respiratory support at randomization (17.0% vs. 13.2%, RR 1.22 [95% CI 0.93 to 1.61]; p=0.14). <h4>Conclusions</h4> In patients hospitalized with COVID-19, dexamethasone reduced 28-day mortality among those receiving invasive mechanical ventilation or oxygen at randomization, but not among patients not receiving respiratory support. <h4>Trial registrations</h4> The RECOVERY trial is registered with ISRCTN (50189673) and clinicaltrials.gov ( NCT04381936 ). <h4>Funding</h4> Medical Research Council and National Institute for Health Research (Grant ref: MC_PC_19056).",,pdf:https://www.nejm.org/doi/pdf/10.1056/NEJMoa2021436?articleTools=true; doi:https://doi.org/10.1101/2020.06.22.20137273; html:https://europepmc.org/article/PPR/PPR179288; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR179288&type=FILE&fileName=EMS88343-pdf.pdf&mimeType=application/pdf
 PPR465937,https://doi.org/10.1101/2022.03.06.21267462,Risk of myocarditis and pericarditis following BNT162b2 and ChAdOx1 COVID-19 vaccinations,"Ip S, Torabi F, Denaxas S, Akbari A, Abbasizanjani H, Knight R, Cooper J, Denholm R, Keene S, Bolton T, Hollings S, Omigie E, North T, Suseeladevi AK, Angelantonio ED, Khunti K, Sterne JAC, Sudlow C, Whiteley W, Wood A, Walker V.",,No Journal Info,2022,2022-03-08,Y,,,,"We describe our analyses of data from over 49.7 million people in England, representing near-complete coverage of the relevant population, to assess the risk of myocarditis and pericarditis following BNT162b2 and ChAdOx1 COVID-19 vaccination. A self-controlled case series (SCCS) design has previously reported increased risk of myocarditis after first ChAdOx1, BNT162b2, and mRNA-1273 dose and after second doses of mRNA COVID-19 vaccines in England. Here, we use a cohort design to estimate hazard ratios for hospitalised or fatal myocarditis/pericarditis after first and second doses of BNT162b2 and ChAdOx1 vaccinations. SCCS and cohort designs are subject to different assumptions and biases and therefore provide the opportunity for triangulation of evidence. In contrast to the findings from the SCCS approach previously reported for England, we found evidence for lower incidence of hospitalised or fatal myocarditis/pericarditis after first ChAdOx1 and BNT162b2 vaccination, as well as little evidence to suggest higher incidence of these events after second dose of either vaccination.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/03/08/2022.03.06.21267462.full.pdf; doi:https://doi.org/10.1101/2022.03.06.21267462; html:https://europepmc.org/article/PPR/PPR465937; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR465937&type=FILE&fileName=EMS148942-pdf.pdf&mimeType=application/pdf
 PPR180964,https://doi.org/10.1101/2020.06.26.20140921,Short Communication: Vitamin D and COVID-19 infection and mortality in UK Biobank,"Hastie CE, Pell JP, Sattar N.",,No Journal Info,2020,2020-06-28,N,,,,"<h4>Purpose</h4> Vitamin D has been proposed as a potential causal factor in COVID-19 risk. We aimed to establish whether blood 25-hydroxyvitamin D (25(OH)D) concentration was associated with COVID-19 mortality, and inpatient confirmed COVID-19 infection, in UK Biobank participants. <h4>Methods</h4> UK Biobank recruited 502,624 participants aged 37-73 years between 2006 and 2010. Baseline exposure data, including 25(OH)D concentration, were linked to COVID-19 mortality. Univariable and multivariable Cox proportional hazards regression analyses were performed for the association between 25(OH)D and COVID-19 death, and poisson regression analyses for the association between 25(OH)D and severe COVID-19 infection. <h4>Results</h4> Complete data were available for 341,484 UK Biobank participants, of which 656 had inpatient confirmed COVID-19 infection and 203 died of COVID-19 infection. Vitamin D was associated with severe COVID-19 infection and mortality univariably (mortality HR=0.99; 95% CI 0.98-0.998; p =0.016), but not after adjustment for confounders (mortality HR=0.998; 95% CI=0.99-1.01; p =0.696). <h4>Conclusions</h4> Our findings do not support a potential link between vitamin D concentrations and risk of severe COVID-19 infection and mortality. Recommendations for vitamin D supplementation to lessen COVID-19 risks may provide false reassurance.",,pdf:https://link.springer.com/content/pdf/10.1007/s00394-020-02372-4.pdf; doi:https://doi.org/10.1101/2020.06.26.20140921; html:https://europepmc.org/article/PPR/PPR180964; doi:https://doi.org/10.1101/2020.06.26.20140921
-PPR191930,https://doi.org/10.1101/2020.07.24.20161281,Strategies to reduce the risk of SARS-CoV-2 re-introduction from international travellers,"Clifford S, Quilty BJ, Russell TW, Liu Y, Chan YD, Pearson CAB, Eggo RM, Endo A, CMMID COVID-19 Working Group, Flasche S, Edmunds WJ.",,No Journal Info,2020,2020-07-24,Y,,,,"<h4>Summary</h4> To mitigate SARS-CoV-2 transmission risks from international travellers, many countries currently use a combination of up to 14 days of self-quarantine on arrival and testing for active infection. We used a simulation model of air travellers arriving to the UK from the EU or the USA and the timing of their stages of infection to evaluate the ability of these strategies to reduce the risk of seeding community transmission. We find that a quarantine period of 8 days on arrival with a PCR test on day 7 (with a 1-day delay for test results) can reduce the number of infectious arrivals released into the community by a median 94% compared to a no quarantine, no test scenario. This reduction is similar to that achieved by a 14-day quarantine period (median 99% reduction). Shorter quarantine periods still can prevent a substantial amount of transmission; all strategies in which travellers spend at least 5 days (the mean incubation period) in quarantine and have at least one negative test before release are highly effective (e.g. a test on day 5 with release on day 6 results in a median 88% reduction in transmission potential). Without intervention, the current high prevalence in the US (40 per 10,000) results in a higher expected number of infectious arrivals per week (up to 23) compared to the EU (up to 12), despite an estimated 8 times lower volume of travel in July 2020. Requiring a 14-day quarantine period likely results in less than 1 infectious traveller each entering the UK per week from the EU and the USA (97.5th percentile). We also find that on arrival the transmission risk is highest from pre-symptomatic travellers; quarantine policies will shift this risk increasingly towards asymptomatic infections if eventually-symptomatic individuals self-isolate after the onset of symptoms. As passenger numbers recover, strategies to reduce the risk of re-introduction should be evaluated in the context of domestic SARS-CoV-2 incidence, preparedness to manage new outbreaks, and the economic and psychological impacts of quarantine.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2020/07/25/2020.07.24.20161281.full.pdf; doi:https://doi.org/10.1101/2020.07.24.20161281; html:https://europepmc.org/article/PPR/PPR191930; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR191930&type=FILE&fileName=EMS87861-pdf.pdf&mimeType=application/pdf
 PPR776496,https://doi.org/10.1101/2023.12.19.23300228,Proteomic aging clock (PAC) predicts age-related outcomes in middle-aged and older adults,"Kuo C, Chen Z, Liu P, Pilling LC, Atkins JL, Fortinsky RH, Kuchel GA, Diniz BS.",,No Journal Info,2023,2023-12-20,Y,,,,"Beyond mere prognostication, optimal biomarkers of aging provide insights into qualitative and quantitative features of biological aging and might, therefore, offer useful information for the testing and, ultimately, clinical use of gerotherapeutics. We aimed to develop a proteomic aging clock (PAC) for all-cause mortality risk as a proxy of biological age. Data were from the UK Biobank Pharma Proteomics Project, including 53,021 participants aged between 39 and 70 years and 2,923 plasma proteins assessed using the Olink Explore 3072 assay®. The Spearman correlation between PAC proteomic age and chronological age was 0.77. A total of 10.9% of the participants died during a mean follow-up of 13.3 years, with the mean age at death 70.1 years. We developed a proteomic aging clock (PAC) for all-cause mortality risk as a surrogate of BA using a combination of least absolute shrinkage and selection operator (LASSO) penalized Cox regression and Gompertz proportional hazards models. PAC showed robust age-adjusted associations and predictions for all-cause mortality and the onset of various diseases in general and disease-free participants. The proteins associated with PAC were enriched in several processes related to the hallmarks of biological aging. Our results expand previous findings by showing that age acceleration, based on PAC, strongly predicts all-cause mortality and several incident disease outcomes. Particularly, it facilitates the evaluation of risk for multiple conditions in a disease-free population, thereby, contributing to the prevention of initial diseases, which vary among individuals and may subsequently lead to additional comorbidities.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2023/12/20/2023.12.19.23300228.full.pdf; doi:https://doi.org/10.1101/2023.12.19.23300228; html:https://europepmc.org/article/PPR/PPR776496; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR776496&type=FILE&fileName=EMS192958-pdf.pdf&mimeType=application/pdf
+PPR191930,https://doi.org/10.1101/2020.07.24.20161281,Strategies to reduce the risk of SARS-CoV-2 re-introduction from international travellers,"Clifford S, Quilty BJ, Russell TW, Liu Y, Chan YD, Pearson CAB, Eggo RM, Endo A, CMMID COVID-19 Working Group, Flasche S, Edmunds WJ.",,No Journal Info,2020,2020-07-24,Y,,,,"<h4>Summary</h4> To mitigate SARS-CoV-2 transmission risks from international travellers, many countries currently use a combination of up to 14 days of self-quarantine on arrival and testing for active infection. We used a simulation model of air travellers arriving to the UK from the EU or the USA and the timing of their stages of infection to evaluate the ability of these strategies to reduce the risk of seeding community transmission. We find that a quarantine period of 8 days on arrival with a PCR test on day 7 (with a 1-day delay for test results) can reduce the number of infectious arrivals released into the community by a median 94% compared to a no quarantine, no test scenario. This reduction is similar to that achieved by a 14-day quarantine period (median 99% reduction). Shorter quarantine periods still can prevent a substantial amount of transmission; all strategies in which travellers spend at least 5 days (the mean incubation period) in quarantine and have at least one negative test before release are highly effective (e.g. a test on day 5 with release on day 6 results in a median 88% reduction in transmission potential). Without intervention, the current high prevalence in the US (40 per 10,000) results in a higher expected number of infectious arrivals per week (up to 23) compared to the EU (up to 12), despite an estimated 8 times lower volume of travel in July 2020. Requiring a 14-day quarantine period likely results in less than 1 infectious traveller each entering the UK per week from the EU and the USA (97.5th percentile). We also find that on arrival the transmission risk is highest from pre-symptomatic travellers; quarantine policies will shift this risk increasingly towards asymptomatic infections if eventually-symptomatic individuals self-isolate after the onset of symptoms. As passenger numbers recover, strategies to reduce the risk of re-introduction should be evaluated in the context of domestic SARS-CoV-2 incidence, preparedness to manage new outbreaks, and the economic and psychological impacts of quarantine.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2020/07/25/2020.07.24.20161281.full.pdf; doi:https://doi.org/10.1101/2020.07.24.20161281; html:https://europepmc.org/article/PPR/PPR191930; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR191930&type=FILE&fileName=EMS87861-pdf.pdf&mimeType=application/pdf
 PPR191969,https://doi.org/10.1101/2020.07.22.20159772,Projecting contact matrices in 177 geographical regions: an update and comparison with empirical data for the COVID-19 era,"Prem K, van Zandvoort K, Klepac P, Eggo RM, Davies NG, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Cook AR, Jit M.",,No Journal Info,2020,2020-07-25,Y,,,,"Mathematical models have played a key role in understanding the spread of directly-transmissible infectious diseases such as Coronavirus Disease 2019 (COVID-19), as well as the effectiveness of public health responses. As the risk of contracting directly-transmitted infections depends on who interacts with whom, mathematical models often use contact matrices to characterise the spread of infectious pathogens. These contact matrices are usually generated from diary-based contact surveys. However, the majority of places in the world do not have representative empirical contact studies, so synthetic contact matrices have been constructed using more widely available setting-specific survey data on household, school, classroom, and workplace composition combined with empirical data on contact patterns in Europe. In 2017, the largest set of synthetic contact matrices to date were published for 152 geographical locations. In this study, we update these matrices with the most recent data and extend our analysis to 177 geographical locations. Due to the observed geographic differences within countries, we also quantify contact patterns in rural and urban settings where data is available. Further, we compare both the 2017 and 2020 synthetic matrices to out-of-sample empirically-constructed contact matrices, and explore the effects of using both the empirical and synthetic contact matrices when modelling physical distancing interventions for the COVID-19 pandemic. We found that the synthetic contact matrices reproduce the main traits of the contact patterns in the empirically-constructed contact matrices. Models parameterised with the empirical and synthetic matrices generated similar findings with few differences observed in age groups where the empirical matrices have missing or aggregated age groups. This finding means that synthetic contact matrices may be used in modelling outbreaks in settings for which empirical studies have yet to be conducted. <h4>Author summary</h4> The risk of contracting a directly transmitted infectious disease such as the Coronavirus Disease 2019 (COVID-19) depends on who interacts with whom. Such person-to-person interactions vary by age and locations—e.g., at home, at work, at school, or in the community—due to the different social structures. These social structures, and thus contact patterns, vary across and within countries. Although social contact patterns can be measured using contact surveys, the majority of countries around the world, particularly low- and middle-income countries, lack nationally representative contact surveys. A simple way to present contact data is to use matrices where the elements represent the rate of contact between subgroups such as age groups represented by the columns and rows. In 2017, we generated age- and location-specific synthetic contact matrices for 152 geographical regions by adapting contact pattern data from eight European countries using country-specific data on household size, school and workplace composition. We have now updated these matrices with the most recent data (Demographic Household Surveys, World Bank, UN Population Division) extending the coverage to 177 geographical locations, covering 97.2% of the world’s population. We also quantified contact patterns in rural and urban settings. When compared to out-of-sample empirically-measured contact patterns, we found that the synthetic matrices reproduce the main features of these contact patterns.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2020/07/28/2020.07.22.20159772.full.pdf; doi:https://doi.org/10.1101/2020.07.22.20159772; html:https://europepmc.org/article/PPR/PPR191969; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR191969&type=FILE&fileName=EMS87995-pdf.pdf&mimeType=application/pdf
 PPR435234,https://doi.org/10.1101/2021.12.20.21268113,A nationwide deep learning pipeline to predict stroke and COVID-19 death in atrial fibrillation,"Handy A, Wood A, Sudlow C, Tomlinson C, Kee F, Thygesen JH, Mamouei M, Sofat R, Dobson R, Ip S, Denaxas S.",,No Journal Info,2021,2021-12-21,N,,,,"<h4>ABSTRACT</h4> Deep learning (DL) and machine learning (ML) models trained on long-term patient trajectories held as medical codes in electronic health records (EHR) have the potential to improve disease prediction. Anticoagulant prescribing decisions in atrial fibrillation (AF) offer a use case where the benchmark stroke risk prediction tool (CHA 2 DS 2 -VASc) could be meaningfully improved by including more information from a patient’s medical history. In this study, we design and build the first DL and ML pipeline that uses the routinely updated, linked EHR data for 56 million people in England accessed via NHS Digital to predict first ischaemic stroke in people with AF, and as a secondary outcome, COVID-19 death. Our pipeline improves first stroke prediction in AF by 17% compared to CHA 2 DS 2 -VASc (0.61 (0.57-0.65) vs 0.52 (0.52-0.52) area under the receiver operating characteristics curves, 95% confidence interval) and provides a generalisable, opensource framework that other researchers and developers can build on.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2021/12/21/2021.12.20.21268113.full.pdf; doi:https://doi.org/10.1101/2021.12.20.21268113; html:https://europepmc.org/article/PPR/PPR435234; doi:https://doi.org/10.1101/2021.12.20.21268113
 PPR605310,https://doi.org/10.2139/ssrn.4237731,Insights into COVID-19 Epidemiology and Control from Temporal Changes in Serial Interval Distributions in Hong Kong,"Ali ST, Chen D, Lim WW, Yeung A, Adam DC, Lau YC, Lau EH, Wong JY, Xiao J, Ho F, Gao H, Wang L, Xu X, Du Z, Wu P, Leung G, Cowling BJ.",,No Journal Info,2022,2022-10-04,N,,,,"Background: The serial interval distribution is used to approximate the generation time distribution, an essential parameter to infer the transmissibility (<i>R<sub>t</sub></i>) of an epidemic. However, serial interval distributions may change as an epidemic progresses rather than remaining constant.<br><br>Method: We examined detailed contact tracing data on laboratory-confirmed cases of COVID-19 in Hong Kong during the five waves from January 2020 to July 2022. We reconstructed the transmission pairs and estimated time-varying effective serial interval distributions using Bayesian inferential framework with a sliding window of 7-14 days. We used regression models to identify the factors of temporal changes in serial intervals and quantify their respective impacts. Finally, we assessed the biases in estimating transmissibility using constant over time-varying serial interval distributions.<br><br>Findings: 2497 transmission pairs were identified for the ancestral strain of SARS-CoV-2 during the first two years of the COVID-19 pandemic in Hong Kong. We found clear temporal changes in mean serial interval estimates within each epidemic wave studied and across waves, with mean serial intervals ranged from 5.5 days (95% CrI: 4.4, 6.6) to 2.7 (95% CrI: 2.2, 3.2) days. The mean serial intervals shortened or lengthened over time, which were found to be closely associated with the temporal variation in COVID-19 case profiles and public health and social measures and could lead to the biases in predicting <i>R<sub>t</sub></i>.<br><br>Interpretation: Accounting for the impact of these factors, the time-varying quantification of serial interval distributions could lead to improved estimation of <i>R<sub>t</sub></i>, and provide additional insights into the impact of public health measures on transmission.<br><br>Funding Information: This study was supported by the Health and Medical Research Fund (project no. 20190712); the Collaborative Research Fund of the Research Grants Council of the Hong Kong Special Administrative Region, China (project No. C7123-20G); AIR@InnoHK administered by Innovation and Technology Commission, European Research Council (grant no. 804744); the Grand Challenges ICODA pilot initiative, delivered by Health Data Research UK and funded by the Bill & Melinda Gates Foundation and the Minderoo Foundation. <br><br>Declaration of Interests: BJC received honoraria from AstraZeneca, Fosun Pharma, GSK, Moderna, Pfizer, Roche, and Sanofi. The authors report no other potential conflicts of interest.",,doi:https://doi.org/10.1101/2022.08.29.22279351; doi:https://doi.org/10.2139/ssrn.4237731; html:https://europepmc.org/article/PPR/PPR605310; doi:https://doi.org/10.2139/ssrn.4237731
 PPR403434,https://doi.org/10.1101/2021.09.30.21264338,"COVID-19 risk factors amongst 14,786 care home residents: An observational longitudinal analysis including daily community positive test rates of COVID-19, hospital stays, and vaccination status in Wales (UK) between 1<sup>st</sup> September 2020 and 1<sup>st</sup> May 2021","Hollinghurst J, Hollinghurst R, North L, Mizen A, Akbari A, Long S, Lyons RA, Fry R.",,No Journal Info,2021,2021-10-03,Y,,,,"<h4>ABSTRACT</h4> <h4>Objectives</h4> Determine individual level risk factors for care home residents testing positive for SARS-CoV-2. <h4>Study Design</h4> Longitudinal observational cohort study using individual-level linked data. <h4>Setting</h4> Care home residents in Wales (United Kingdom) between 1st September 2020 and 1st May 2021. <h4>Participants</h4> 14,786 older care home residents (aged 65+). Our dataset consisted of 2,613,341 individual-level daily observations within 697 care homes. <h4>Methods</h4> We estimated odds ratios (ORs [95% confidence interval]) using multilevel logistic regression models. Our outcome of interest was a positive SARS-CoV-2 polymerase chain reaction (PCR) test. We included time dependent covariates for the estimated community positive test rate of COVID-19, hospital admissions, and vaccination status. Additional covariates were included for age, positive PCR tests prior to the study, sex, frailty (using the hospital frailty risk score), and specialist care home services. <h4>Results</h4> The multivariable logistic regression model indicated an increase in age (OR 1.01 [1.00,1.01] per year of age), community positive test rate (OR 1.13 [1.12,1.13] per percent increase in positive test rate), hospital inpatients (OR 7.40 [6.54,8.36]), and residents in care homes with non-specialist dementia care (OR 1.42 [1.01,1.99]) had an increased odds of a positive test. Having a positive test prior to the observation period (OR 0.58 [0.49,0.68]) and either one or two doses of a vaccine (0.21 [0.17,0.25] and 0.05 [0.02,0.09] respectively) were associated with a decreased odds of a positive test. <h4>Conclusions</h4> Our findings suggest care providers need to stay vigilant despite the vaccination rollout, and extra precautions should be taken when caring for the most vulnerable. Furthermore, minimising potential COVID-19 infection for care home residents admitted to hospital should be prioritised. <h4>SUMMARY BOXES</h4> <h4>Section 1: What is already known on this topic</h4> Care home residents are at a high risk of COVID-19 infection, but existing literature has mainly focussed on excess mortality rather than infection risk. In our study we were able to investigate associations between COVID-19 infections and the community positive test rate of COVID-19, the vaccination status of care home residents, hospital admissions, and frailty. <h4>Section 2: What this study adds</h4> Our study suggests an increased community positive test rate and hospital inpatients had an increased likelihood of a positive SARS-CoV-2 polymerase chain reaction test, whilst one or two doses of vaccination indicated a decreased chance of a positive test. Our findings suggest care providers need to stay vigilant despite the vaccination rollout, and extra precautions should be taken when caring for the most vulnerable, especially in a hospital setting.",,pdf:https://academic.oup.com/ageing/article-pdf/51/5/afac084/43520659/afac084.pdf; doi:https://doi.org/10.1101/2021.09.30.21264338; html:https://europepmc.org/article/PPR/PPR403434; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR403434&type=FILE&fileName=EMS136750-pdf.pdf&mimeType=application/pdf
-PPR467890,https://doi.org/10.1101/2022.03.09.22272098,"Duration of vaccine effectiveness against SARS-CoV2 infection, hospitalisation, and death in residents and staff of Long-Term Care Facilities (VIVALDI): a prospective cohort study, England, Dec 2020-Dec 2021","Shrotri M, Krutikov M, Nacer-Laidi H, Azmi B, Palmer T, Giddings R, Fuller C, Irwin-Singer A, Baynton V, Tut G, Moss P, Hayward A, Copas A, Shallcross L.",,No Journal Info,2022,2022-03-12,Y,,,,"<h4>Background</h4> Long-term care facilities (LTCF) have been prioritised for vaccination, but data on potential waning of vaccine effectiveness (VE) and the impact of booster doses in this vulnerable population remains scarce. <h4>Methods</h4> We included residents and staff from 331 LTCFs enrolled in VIVALDI ( ISRCTN 14447421 ), who underwent routine PCR testing between Dec 8, 2020 - Dec 11, 2021 in a Cox proportional hazards regression, estimating VE against SARS-CoV2 infection, COVID-19-related hospitalisation, and COVID-19-related death after 1-3 vaccine doses, stratifying by previous SARS-CoV2 exposure. <h4>Results</h4> For 15,518 older residents, VE declined from 50·7% (15·5, 71·3) to 17·2% (∼23·9, 44·6) against infection; from 85·4% (60·7, 94·.6) to 54·3% (26·2, 71·7) against hospitalisation; and from 94·4% (76·4, 98·7) to 62·8% (32·9, 79·4) against death, when comparing 2-12 weeks and ≥12 weeks after two doses. For 19,515 staff, VE against infection declined slightly from 50·3% (32·7, 63·3) to 42·1% 29·5, 52·4). High VE was restored following a third dose, with VE of 71·6% (53·5, 82·7) and 78·3% (70·1, 84·3) against infection and 89·9% (80·0, 94·6) and 95·8% (50·4, 99·6) against hospitalisation, for residents and staff respectively; and 97·5% (88·1, 99·5) against death for residents. <h4>Interpretation</h4> Substantial waning of VE is observed against all outcomes in residents from 12 weeks after a primary course of AstraZeneca or mRNA vaccines. Boosters restore protection, and maximise immunity across all outcomes. These findings demonstrate the importance of boosting and the need for ongoing surveillance of VE in this vulnerable cohort. <h4>Funding</h4> UK Government Department of Health and Social Care. <h4>Research in Context</h4> <h4>Evidence before this study</h4> We searched MEDLINE and medRxiv for studies reporting vaccine effectiveness (VE) over time after two or three doses against SARS-CoV2 infection, COVID-19-related hospitalisation, or COVID-19-related death amongst staff or residents of long-term care facilities (LTCFs), that were published between Jan 1, 2020, and December 21, 2021. We used variations of the search terms “COVID-19” OR “SARS-CoV-2” AND “vaccine effectiveness” OR “vaccine efficacy” AND “care homes” OR “long term care facilities”. We identified 8 articles reporting two-dose data from LTCFs, including 1 peer-reviewed paper from Israel, 1 preprint from Denmark, 1 preprint from Norway, 1 peer-reviewed paper from France, two peer-reviewed papers from Spain, 1 peer-reviewed paper from the USA, and 1 preprint from England; however none of these studies examined waning of protection over time after two doses. Five studies (mRNA vaccines 3-4 weeks interval) reported short-term two-dose VE of 49-71% in residents, and 82-90% in staff. Two-dose VE was reported to be 75-88% against hospitalisation, 87-97% against death, and 86% against either outcome. An English study of residents (Pfizer or AstraZeneca, 8-12 week interval) reported 73% VE against infection and noted VE waning from 7 weeks after the first dose, but did not examine waning after the second dose. All of these studies were set prior to emergence of the Delta variant and did not examine waning of immunity due to short lengths of follow-up after Dose 2. Only one study (USA) compared Pfizer/Moderna two-dose VE against infection in LTCF residents before (67·5% [60·1-73·5%]) and during (53·1% [49·1-56·7%]) Delta variant predominance; however, authors could not access vaccination dates therefore did not account for any waning of immunity over time; they also did not examine any severe clinical outcomes. We identified only one correspondence piece from Israel (Pfizer 3-4 week interval) describing the benefit of a third ‘booster’ dose in LTCFs; it reported relative rate reductions of 71% for infection and 80%, for hospitalisation in the period after booster roll-out. However, individual-level VE estimates by time since vaccination were not reported, and adjustment for prior infection was not undertaken. Overall, there was a paucity of data on non-mRNA vaccines, waning of immunity over time after two doses, and VE following a third (booster) dose in LTCF populations, which we address in this study. <h4>Added value of this study</h4> We report findings from a prospective cohort study that includes 15,518 residents and 19,515 staff from 331 LTCFs across England, who underwent routine PCR testing 2-3 times per month, looking at SARS-CoV2 vaccine effectiveness over 12 months (Dec 8, 2020-Dec 11, 2021), which is the longest duration of follow-up of any study within this vulnerable cohort. We evaluated the effectiveness of first, second, and booster vaccine doses of AstraZeneca, Pfizer, and Moderna against infection, hospitalisation, and death over the 12 months when the Alpha and Delta variants were dominant. Our findings affirm that complete vaccination with two doses of AstraZeneca or mRNA vaccines offers moderate protection against infection, and high protection against severe clinical outcomes, however this protection declines over time, particularly for residents. A third booster dose of an mRNA vaccine restores, and indeed maximises, VE to 71·6% (53·5, 82·7) and 78·3% (70·1, 84·3) against infection, and 89·9% (80·0, 94·6) and 95·8% (50·4, 99·6) against hospitalisation, for residents and staff respectively, and to 97·5% (88·1, 99·5) against death for residents, with similar protection offered after the third dose irrespective of primary course type. This is the first study to examine and describe waning of immunity over a one-year period, as well as vaccine effectiveness of a booster dose, in a large cohort of LTCF staff and residents. <h4>Implications of all the available evidence</h4> Taken together, our findings indicate high short-term immunity against SARS-CoV2 infection and very high immunity against severe clinical outcomes of COVID-19 for LTCF residents and staff following vaccination. However substantial waning in vaccine-derived immunity is seen beyond 3 months, irrespective of vaccine type, suggesting the need for regular boosting to maintain protection in this vulnerable cohort. Although this analysis took place in the pre-Omicron period, these trends of waning immunity over time are likely to be generalisable across variants, carrying important implications for long-term vaccination policy in LTCFs. Ongoing surveillance in this vulnerable cohort remains crucial, in order to describe further changes in vaccine-induced immunity, particularly in the context of new variants.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/03/18/2022.03.09.22272098.full.pdf; doi:https://doi.org/10.1101/2022.03.09.22272098; html:https://europepmc.org/article/PPR/PPR467890; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR467890&type=FILE&fileName=EMS148974-pdf.pdf&mimeType=application/pdf
+PPR672054,https://doi.org/10.1101/2023.06.06.23290826,"OpenSAFELY: The impact of COVID-19 on azathioprine, leflunomide, and methotrexate monitoring, and factors associated with change in monitoring rate","The OpenSAFELY Collaborative, Brown AD, Fisher L, Curtis HJ, Wiedemann M, Hulme WJ, Hopcroft LE, Cunningham C, Speed V, Costello RE, Galloway JB, Russell MD, Bechman K, Kurt Z, Croker R, Wood C, Walker AJ, Schaffer AL, Bacon SC, Mehrkar A, Hickman G, Bates C, Cockburn J, Parry J, Hester F, Harper S, Goldacre B, MacKenna B.",,No Journal Info,2023,2023-06-07,Y,,,,"<h4>Background</h4> The COVID-19 pandemic created unprecedented pressure on healthcare services. This study aimed to investigate if disease-modifying anti-rheumatic drug (DMARD) safety monitoring was affected during the COVID-19 pandemic. <h4>Methods</h4> A population-based cohort study was conducted with the approval of NHS England, using the OpenSAFELY platform to access electronic health record data from 24·2 million patients registered at general practices using TPP’s SystmOne software. Patients were included for further analysis if prescribed azathioprine, leflunomide, or methotrexate between November 2019 and July 2022. Outcomes were assessed as monthly trends and variation between various sociodemographic and clinical groups for adherence with standard safety monitoring recommendations. <h4>Findings</h4> An acute increase in the rate of missed monitoring occurred across the study population (+12·4 percentage points) when lockdown measures were implemented in March 2020. This increase was more pronounced for some patient groups (70-79 year-olds: +13·7 percentage points; females: +12·8 percentage points), regions (North West: +17·0 percentage points), medications (Leflunomide: +20·7 percentage points), and monitoring tests (Blood Pressure: +24·5 percentage points). Missed monitoring rates decreased substantially for all groups by July 2022. Substantial and consistent differences were observed in overall missed monitoring rates between several groups throughout the study. <h4>Interpretation</h4> DMARD monitoring rates temporarily deteriorated during the COVID-19 pandemic. Deterioration coincided with the onset of lockdown measures, with monitoring rates recovering rapidly as lockdown measures were eased. Differences observed in monitoring rates between medications, tests, regions, and patient groups, highlight opportunities to tackle potential inequalities in the provision or uptake of monitoring services. Further research should aim to evaluate the causes of the differences identified between groups. <h4>Funding</h4> None. <h4>Research in context</h4> <h4>Evidence before this study</h4> Disease-modifying anti-rheumatic drugs (DMARDs) are immunosuppressive and/or immunomodulatory drugs, which carry risks of serious adverse effects such as; gastrointestinal, renal, hepatic, and pulmonary toxicity; myelosuppression; and increased susceptibility to infection. To mitigate these safety risks, national safety guidance recommends that patients taking these drugs receive regular monitoring. We searched PubMed, Web of Science and Scopus for studies published between database inception and July 28th, 2022, using the terms ([covid-19] AND [monitoring OR shared care OR dmard OR outcome factors] AND [primary care]), with no language restrictions. Studies that investigated the effect of the COVID-19 pandemic on healthcare services were identified. One key study in England showed disruption to various monitoring services in primary care had occurred during the pandemic. Another English study highlighted a disproportionate impact of the COVID-19 pandemic on health outcomes in certain groups. <h4>Added value of this study</h4> Prior to this study knowledge of how high-risk drugs, such as DMARDs, were affected by the COVID-19 pandemic was limited. This study reports the impact of COVID-19 on the safety monitoring of DMARDs. Moreover, it reports variation in DMARD monitoring rates between demographic, clinical and regional subgroups, which has not yet been described. This is enabled through use of the OpenSAFELY platform, which provides secure access to pseudonymised primary care patient records in England for the purposes of analysing the COVID-19 pandemic impact. <h4>Implications of all the available evidence</h4> DMARD monitoring rates transiently deteriorated during the COVID-19 pandemic, consistent with previous research on other monitoring tests. Deterioration coincided with the onset of lockdown measures, with performance recovering rapidly as lockdown measures were eased. Differences observed in monitoring rates between demographic, clinical and regional subgroups highlight opportunities to identify and tackle potential inequalities in the provision or uptake of monitoring services. Further research should aim to evaluate the causes of the differences identified between groups, and establish the clinical relevance of missed monitoring. Several studies have demonstrated the capability of the OpenSAFELY platform as a secure and efficient approach for analysing NHS primary care data at scale, generating meaningful insights on service delivery.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2023/06/07/2023.06.06.23290826.full.pdf; doi:https://doi.org/10.1101/2023.06.06.23290826; html:https://europepmc.org/article/PPR/PPR672054; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR672054&type=FILE&fileName=EMS177037-pdf.pdf&mimeType=application/pdf
 PPR252028,https://doi.org/10.1101/2020.12.08.20246231,Artificial intelligence-enabled analysis of UK and US public attitudes on Facebook and Twitter towards COVID-19 vaccinations,"Hussain A, Tahir A, Hussain Z, Sheikh Z, Gogate M, Dashtipour K, Ali A, Sheikh A.",,No Journal Info,2020,2020-12-11,Y,,,,"<h4>Background</h4> Global efforts towards the development and deployment of a vaccine for SARS-CoV-2 are rapidly advancing. We developed and applied an artificial-intelligence (AI)-based approach to analyse social-media public sentiment in the UK and the US towards COVID-19 vaccinations, to understand public attitude and identify topics of concern. <h4>Methods</h4> Over 300,000 social-media posts related to COVID-19 vaccinations were extracted, including 23,571 Facebook-posts from the UK and 144,864 from the US, along with 40,268 tweets from the UK and 98,385 from the US respectively, from 1 st March - 22 nd November 2020. We used natural language processing and deep learning based techniques to predict average sentiments, sentiment trends and topics of discussion. These were analysed longitudinally and geo-spatially, and a manual reading of randomly selected posts around points of interest helped identify underlying themes and validated insights from the analysis. <h4>Results</h4> We found overall averaged positive, negative and neutral sentiment in the UK to be 58%, 22% and 17%, compared to 56%, 24% and 18% in the US, respectively. Public optimism over vaccine development, effectiveness and trials as well as concerns over safety, economic viability and corporation control were identified. We compared our findings to national surveys in both countries and found them to correlate broadly. <h4>Conclusions</h4> AI-enabled social-media analysis should be considered for adoption by institutions and governments, alongside surveys and other conventional methods of assessing public attitude. This could enable real-time assessment, at scale, of public confidence and trust in COVID-19 vaccinations, help address concerns of vaccine-sceptics and develop more effective policies and communication strategies to maximise uptake.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2020/12/11/2020.12.08.20246231.full.pdf; doi:https://doi.org/10.1101/2020.12.08.20246231; html:https://europepmc.org/article/PPR/PPR252028; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR252028&type=FILE&fileName=EMS108377-pdf.pdf&mimeType=application/pdf
+PPR467890,https://doi.org/10.1101/2022.03.09.22272098,"Duration of vaccine effectiveness against SARS-CoV2 infection, hospitalisation, and death in residents and staff of Long-Term Care Facilities (VIVALDI): a prospective cohort study, England, Dec 2020-Dec 2021","Shrotri M, Krutikov M, Nacer-Laidi H, Azmi B, Palmer T, Giddings R, Fuller C, Irwin-Singer A, Baynton V, Tut G, Moss P, Hayward A, Copas A, Shallcross L.",,No Journal Info,2022,2022-03-12,Y,,,,"<h4>Background</h4> Long-term care facilities (LTCF) have been prioritised for vaccination, but data on potential waning of vaccine effectiveness (VE) and the impact of booster doses in this vulnerable population remains scarce. <h4>Methods</h4> We included residents and staff from 331 LTCFs enrolled in VIVALDI ( ISRCTN 14447421 ), who underwent routine PCR testing between Dec 8, 2020 - Dec 11, 2021 in a Cox proportional hazards regression, estimating VE against SARS-CoV2 infection, COVID-19-related hospitalisation, and COVID-19-related death after 1-3 vaccine doses, stratifying by previous SARS-CoV2 exposure. <h4>Results</h4> For 15,518 older residents, VE declined from 50·7% (15·5, 71·3) to 17·2% (∼23·9, 44·6) against infection; from 85·4% (60·7, 94·.6) to 54·3% (26·2, 71·7) against hospitalisation; and from 94·4% (76·4, 98·7) to 62·8% (32·9, 79·4) against death, when comparing 2-12 weeks and ≥12 weeks after two doses. For 19,515 staff, VE against infection declined slightly from 50·3% (32·7, 63·3) to 42·1% 29·5, 52·4). High VE was restored following a third dose, with VE of 71·6% (53·5, 82·7) and 78·3% (70·1, 84·3) against infection and 89·9% (80·0, 94·6) and 95·8% (50·4, 99·6) against hospitalisation, for residents and staff respectively; and 97·5% (88·1, 99·5) against death for residents. <h4>Interpretation</h4> Substantial waning of VE is observed against all outcomes in residents from 12 weeks after a primary course of AstraZeneca or mRNA vaccines. Boosters restore protection, and maximise immunity across all outcomes. These findings demonstrate the importance of boosting and the need for ongoing surveillance of VE in this vulnerable cohort. <h4>Funding</h4> UK Government Department of Health and Social Care. <h4>Research in Context</h4> <h4>Evidence before this study</h4> We searched MEDLINE and medRxiv for studies reporting vaccine effectiveness (VE) over time after two or three doses against SARS-CoV2 infection, COVID-19-related hospitalisation, or COVID-19-related death amongst staff or residents of long-term care facilities (LTCFs), that were published between Jan 1, 2020, and December 21, 2021. We used variations of the search terms “COVID-19” OR “SARS-CoV-2” AND “vaccine effectiveness” OR “vaccine efficacy” AND “care homes” OR “long term care facilities”. We identified 8 articles reporting two-dose data from LTCFs, including 1 peer-reviewed paper from Israel, 1 preprint from Denmark, 1 preprint from Norway, 1 peer-reviewed paper from France, two peer-reviewed papers from Spain, 1 peer-reviewed paper from the USA, and 1 preprint from England; however none of these studies examined waning of protection over time after two doses. Five studies (mRNA vaccines 3-4 weeks interval) reported short-term two-dose VE of 49-71% in residents, and 82-90% in staff. Two-dose VE was reported to be 75-88% against hospitalisation, 87-97% against death, and 86% against either outcome. An English study of residents (Pfizer or AstraZeneca, 8-12 week interval) reported 73% VE against infection and noted VE waning from 7 weeks after the first dose, but did not examine waning after the second dose. All of these studies were set prior to emergence of the Delta variant and did not examine waning of immunity due to short lengths of follow-up after Dose 2. Only one study (USA) compared Pfizer/Moderna two-dose VE against infection in LTCF residents before (67·5% [60·1-73·5%]) and during (53·1% [49·1-56·7%]) Delta variant predominance; however, authors could not access vaccination dates therefore did not account for any waning of immunity over time; they also did not examine any severe clinical outcomes. We identified only one correspondence piece from Israel (Pfizer 3-4 week interval) describing the benefit of a third ‘booster’ dose in LTCFs; it reported relative rate reductions of 71% for infection and 80%, for hospitalisation in the period after booster roll-out. However, individual-level VE estimates by time since vaccination were not reported, and adjustment for prior infection was not undertaken. Overall, there was a paucity of data on non-mRNA vaccines, waning of immunity over time after two doses, and VE following a third (booster) dose in LTCF populations, which we address in this study. <h4>Added value of this study</h4> We report findings from a prospective cohort study that includes 15,518 residents and 19,515 staff from 331 LTCFs across England, who underwent routine PCR testing 2-3 times per month, looking at SARS-CoV2 vaccine effectiveness over 12 months (Dec 8, 2020-Dec 11, 2021), which is the longest duration of follow-up of any study within this vulnerable cohort. We evaluated the effectiveness of first, second, and booster vaccine doses of AstraZeneca, Pfizer, and Moderna against infection, hospitalisation, and death over the 12 months when the Alpha and Delta variants were dominant. Our findings affirm that complete vaccination with two doses of AstraZeneca or mRNA vaccines offers moderate protection against infection, and high protection against severe clinical outcomes, however this protection declines over time, particularly for residents. A third booster dose of an mRNA vaccine restores, and indeed maximises, VE to 71·6% (53·5, 82·7) and 78·3% (70·1, 84·3) against infection, and 89·9% (80·0, 94·6) and 95·8% (50·4, 99·6) against hospitalisation, for residents and staff respectively, and to 97·5% (88·1, 99·5) against death for residents, with similar protection offered after the third dose irrespective of primary course type. This is the first study to examine and describe waning of immunity over a one-year period, as well as vaccine effectiveness of a booster dose, in a large cohort of LTCF staff and residents. <h4>Implications of all the available evidence</h4> Taken together, our findings indicate high short-term immunity against SARS-CoV2 infection and very high immunity against severe clinical outcomes of COVID-19 for LTCF residents and staff following vaccination. However substantial waning in vaccine-derived immunity is seen beyond 3 months, irrespective of vaccine type, suggesting the need for regular boosting to maintain protection in this vulnerable cohort. Although this analysis took place in the pre-Omicron period, these trends of waning immunity over time are likely to be generalisable across variants, carrying important implications for long-term vaccination policy in LTCFs. Ongoing surveillance in this vulnerable cohort remains crucial, in order to describe further changes in vaccine-induced immunity, particularly in the context of new variants.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/03/18/2022.03.09.22272098.full.pdf; doi:https://doi.org/10.1101/2022.03.09.22272098; html:https://europepmc.org/article/PPR/PPR467890; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR467890&type=FILE&fileName=EMS148974-pdf.pdf&mimeType=application/pdf
 PPR415629,https://doi.org/10.1101/2021.11.02.21265767,Determinants of pre-vaccination antibody responses to SARS-CoV-2: a population-based longitudinal study (COVIDENCE UK),"Talaei M, Faustini S, Holt H, Jolliffe DA, Vivaldi G, Greenig M, Perdek N, Maltby S, Bigogno CM, Symons J, Davies GA, Lyons RA, Griffiths CJ, Kee F, Sheikh A, Richter AG, Shaheen SO, Martineau AR.",,No Journal Info,2021,2021-11-03,Y,,,,"<h4>Background</h4> Prospective population-based studies investigating multiple determinants of pre-vaccination antibody responses to SARS-CoV-2 are lacking. <h4>Methods</h4> We did a prospective population-based study in SARS-CoV-2 vaccine-naive UK adults recruited between May 1 and November 2, 2020, without a positive swab test result for SARS-CoV-2 prior to enrolment. Information on 88 potential sociodemographic, behavioural, nutritional, clinical and pharmacological risk factors was obtained through online questionnaires, and combined IgG/IgA/IgM responses to SARS-CoV-2 spike glycoprotein were determined in dried blood spots obtained between November 6, 2020 and April 18, 2021. We used logistic and linear regression to estimate adjusted odds ratios (aORs) and adjusted geometric mean ratios (aGMRs) for potential determinants of SARS-CoV-2 seropositivity (all participants) and antibody titres (seropositive participants only), respectively. <h4>Results</h4> 1696 (15.2%) of 11,130 participants were seropositive. Factors independently associated with increased risk of SARS-CoV-2 seropositivity included frontline health/care occupation (aOR 1.86, 95% CI 1.48–2.33), international travel (1.20, 1.07–1.35), number of visits to shops and other indoor public places (≥5 vs. 0/week: 1.29, 1.06-1.57, P-trend=0.01), body mass index (BMI) ≥25 vs <25 kg/m 2 (1.24, 1.11–1.39), Asian/Asian British vs White ethnicity (1.65, 1.10–2.49), and alcohol consumption ≥15 vs 0 units/week (1.23, 1.04–1.46). Light physical exercise associated with decreased risk (0.80, 0.70–0.93, for ≥10 vs 0–4 h/week). Among seropositive participants, higher titres of anti-Spike antibodies associated with factors including BMI ≥30 vs <25 kg/m 2 (aGMR 1.10, 1.02–1.19), Asian/Asian British vs White ethnicity (1.22, 1.04–1.44), frontline health/care occupation (1.24, 95% CI 1.11–1.39), international travel (1.11, 1.05–1.16), and number of visits to shops and other indoor public places (≥5 vs. 0/week: 1.12, 1.02-1.23, P-trend=0.01); these associations were not substantially attenuated by adjustment for COVID-19 disease severity. <h4>Conclusions</h4> Higher alcohol consumption and reduced light physical exercise represent new modifiable risk factors for SARS-CoV-2 infection. Recognised associations between Asian/Asian British ethnic origin and obesity and increased risk of SARS-CoV-2 seropositivity were independent of other sociodemographic, behavioural, nutritional, clinical and pharmacological factors investigated. Among seropositive participants, higher titres of anti-Spike antibodies in people of Asian ancestry and in obese people were not explained by greater COVID-19 disease severity in these groups. <h4>Funding</h4> Barts Charity, Health Data Research UK.",,pdf:https://bmcmedicine.biomedcentral.com/track/pdf/10.1186/s12916-022-02286-4; doi:https://doi.org/10.1101/2021.11.02.21265767; html:https://europepmc.org/article/PPR/PPR415629; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR415629&type=FILE&fileName=EMS138031-pdf.pdf&mimeType=application/pdf
-PPR672054,https://doi.org/10.1101/2023.06.06.23290826,"OpenSAFELY: The impact of COVID-19 on azathioprine, leflunomide, and methotrexate monitoring, and factors associated with change in monitoring rate","The OpenSAFELY Collaborative, Brown AD, Fisher L, Curtis HJ, Wiedemann M, Hulme WJ, Hopcroft LE, Cunningham C, Speed V, Costello RE, Galloway JB, Russell MD, Bechman K, Kurt Z, Croker R, Wood C, Walker AJ, Schaffer AL, Bacon SC, Mehrkar A, Hickman G, Bates C, Cockburn J, Parry J, Hester F, Harper S, Goldacre B, MacKenna B.",,No Journal Info,2023,2023-06-07,Y,,,,"<h4>Background</h4> The COVID-19 pandemic created unprecedented pressure on healthcare services. This study aimed to investigate if disease-modifying anti-rheumatic drug (DMARD) safety monitoring was affected during the COVID-19 pandemic. <h4>Methods</h4> A population-based cohort study was conducted with the approval of NHS England, using the OpenSAFELY platform to access electronic health record data from 24·2 million patients registered at general practices using TPP’s SystmOne software. Patients were included for further analysis if prescribed azathioprine, leflunomide, or methotrexate between November 2019 and July 2022. Outcomes were assessed as monthly trends and variation between various sociodemographic and clinical groups for adherence with standard safety monitoring recommendations. <h4>Findings</h4> An acute increase in the rate of missed monitoring occurred across the study population (+12·4 percentage points) when lockdown measures were implemented in March 2020. This increase was more pronounced for some patient groups (70-79 year-olds: +13·7 percentage points; females: +12·8 percentage points), regions (North West: +17·0 percentage points), medications (Leflunomide: +20·7 percentage points), and monitoring tests (Blood Pressure: +24·5 percentage points). Missed monitoring rates decreased substantially for all groups by July 2022. Substantial and consistent differences were observed in overall missed monitoring rates between several groups throughout the study. <h4>Interpretation</h4> DMARD monitoring rates temporarily deteriorated during the COVID-19 pandemic. Deterioration coincided with the onset of lockdown measures, with monitoring rates recovering rapidly as lockdown measures were eased. Differences observed in monitoring rates between medications, tests, regions, and patient groups, highlight opportunities to tackle potential inequalities in the provision or uptake of monitoring services. Further research should aim to evaluate the causes of the differences identified between groups. <h4>Funding</h4> None. <h4>Research in context</h4> <h4>Evidence before this study</h4> Disease-modifying anti-rheumatic drugs (DMARDs) are immunosuppressive and/or immunomodulatory drugs, which carry risks of serious adverse effects such as; gastrointestinal, renal, hepatic, and pulmonary toxicity; myelosuppression; and increased susceptibility to infection. To mitigate these safety risks, national safety guidance recommends that patients taking these drugs receive regular monitoring. We searched PubMed, Web of Science and Scopus for studies published between database inception and July 28th, 2022, using the terms ([covid-19] AND [monitoring OR shared care OR dmard OR outcome factors] AND [primary care]), with no language restrictions. Studies that investigated the effect of the COVID-19 pandemic on healthcare services were identified. One key study in England showed disruption to various monitoring services in primary care had occurred during the pandemic. Another English study highlighted a disproportionate impact of the COVID-19 pandemic on health outcomes in certain groups. <h4>Added value of this study</h4> Prior to this study knowledge of how high-risk drugs, such as DMARDs, were affected by the COVID-19 pandemic was limited. This study reports the impact of COVID-19 on the safety monitoring of DMARDs. Moreover, it reports variation in DMARD monitoring rates between demographic, clinical and regional subgroups, which has not yet been described. This is enabled through use of the OpenSAFELY platform, which provides secure access to pseudonymised primary care patient records in England for the purposes of analysing the COVID-19 pandemic impact. <h4>Implications of all the available evidence</h4> DMARD monitoring rates transiently deteriorated during the COVID-19 pandemic, consistent with previous research on other monitoring tests. Deterioration coincided with the onset of lockdown measures, with performance recovering rapidly as lockdown measures were eased. Differences observed in monitoring rates between demographic, clinical and regional subgroups highlight opportunities to identify and tackle potential inequalities in the provision or uptake of monitoring services. Further research should aim to evaluate the causes of the differences identified between groups, and establish the clinical relevance of missed monitoring. Several studies have demonstrated the capability of the OpenSAFELY platform as a secure and efficient approach for analysing NHS primary care data at scale, generating meaningful insights on service delivery.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2023/06/07/2023.06.06.23290826.full.pdf; doi:https://doi.org/10.1101/2023.06.06.23290826; html:https://europepmc.org/article/PPR/PPR672054; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR672054&type=FILE&fileName=EMS177037-pdf.pdf&mimeType=application/pdf
 PPR208611,https://doi.org/10.1101/2020.09.02.20185173,"Characteristics and outcomes of 627 044 COVID-19 patients with and without obesity in the United States, Spain, and the United Kingdom","Recalde M, Roel E, Pistillo A, Sena AG, Prats-Uribe A, Ahmed W, Alghoul H, Alshammari TM, Alser O, Areia C, Burn E, Casajust P, Dawoud D, DuVall SL, Falconer T, Fernández-Bertolín S, Golozar A, Gong M, Lai LYH, Lane JC, Lynch KE, Matheny ME, Mehta PP, Morales DR, Natarjan K, Nyberg F, Posada JD, Reich CG, Schilling LM, Shah K, Shah NH, Subbian V, Zhang L, Zhu H, Ryan P, Prieto-Alhambra D, Kostka K, Duarte-Salles T.",,No Journal Info,2020,2020-09-03,Y,,,,"<h4>Background</h4> COVID-19 may differentially impact people with obesity. We aimed to describe and compare the demographics, comorbidities, and outcomes of obese patients with COVID-19 to those of non-obese patients with COVID-19, or obese patients with seasonal influenza. <h4>Methods</h4> We conducted a cohort study based on outpatient/inpatient care, and claims data from January to June 2020 from the US, Spain, and the UK. We used six databases standardized to the OMOP common data model. We defined two cohorts of patients diagnosed and/or hospitalized with COVID-19. We created corresponding cohorts for patients with influenza in 2017-2018. We followed patients from index date to 30 days or death. We report the frequency of socio-demographics, prior comorbidities, and 30-days outcomes (hospitalization, events, and death) by obesity status. <h4>Findings</h4> We included 627 044 COVID-19 (US: 502 650, Spain: 122 058, UK: 2336) and 4 549 568 influenza (US: 4 431 801, Spain: 115 224, UK: 2543) patients. The prevalence of obesity was higher among hospitalized COVID-19 (range: 38% to 54%) than diagnosed COVID-19 (30% to 47%), or diagnosed (15% to 47%) or hospitalized (27% to 48%) influenza patients. Obese hospitalized COVID-19 patients were more often female and younger than non-obese COVID-19 patients or obese influenza patients. Obese COVID-19 patients were more likely to have prior comorbidities, present with cardiovascular and respiratory events during hospitalization, require intensive services, or die compared to non-obese COVID-19 patients. Obese COVID-19 patients were more likely to require intensive services or die compared to obese influenza patients, despite presenting with fewer comorbidities. <h4>Interpretation</h4> We show that obesity is more common amongst COVID-19 than influenza patients, and that obese patients present with more severe forms of COVID-19 with higher hospitalization, intensive services, and fatality than non-obese patients. These data are instrumental for guiding preventive strategies of COVID-19 infection and complications. <h4>Funding</h4> The European Health Data & Evidence Network has received funding from the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 806968. The JU receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA. This research received partial support from the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), US National Institutes of Health, US Department of Veterans Affairs, Janssen Research & Development, and IQVIA. The University of Oxford received funding related to this work from the Bill & Melinda Gates Foundation (Investment ID INV-016201 and INV-019257). APU has received funding from the Medical Research Council (MRC) [MR/K501256/1, MR/N013468/1] and Fundación Alfonso Martín Escudero (FAME) (APU). VINCI [VA HSR RES 13-457] (SLD, MEM, KEL). JCEL has received funding from the Medical Research Council (MR/K501256/1) and Versus Arthritis (21605). No funders had a direct role in this study. The views and opinions expressed are those of the authors and do not necessarily reflect those of the Clinician Scientist Award programme, NIHR, Department of Veterans Affairs or the United States Government, NHS, or the Department of Health, England. <h4>Research in context</h4> <h4>Evidence before this study</h4> Previous evidence suggests that obese individuals are a high risk population for COVID-19 infection and complications. We searched PubMed for articles published from December 2019 until June 2020, using terms referring to SARS-CoV-2 or COVID-19 combined with terms for obesity. Few studies reported obesity and most of them were limited by small sample sizes and restricted to hospitalized patients. Further, they used different definitions for obesity (i.e. some reported together overweight and obesity, others only reported obesity with BMI>40kg/m 2 ). To date, no study has provided detailed information on the characteristics of obese COVID-19 patients, such as the prevalence of comorbidities or COVID-19 related outcomes. In addition, despite the fact that COVID-19 has been often compared to seasonal influenza, there are no studies assessing whether obese patients with COVID-19 differ from obese patients with seasonal influenza. <h4>Added value of this study</h4> We report the largest cohort of obese patients with COVID-19 and provide information on more than 29 000 aggregate characteristics publicly available. Our findings were consistent across the participating databases and countries. We found that the prevalence of obesity is higher among COVID-19 compared to seasonal influenza patients. Obese patients with COVID-19 are more commonly female and have worse outcomes than non-obese patients. Further, they have worse outcomes than obese patients with influenza, despite presenting with fewer comorbidities. <h4>Implications of all the available evidence</h4> Our results show that individuals with obesity present more comorbidities and worse outcomes for COVID-19 than non-obese patients. These findings may be useful in guiding clinical practice and future preventative strategies for obese individuals, as well as provide useful data to support subsequent association studies focussed on obesity and COVID-19.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2020/09/03/2020.09.02.20185173.full.pdf; doi:https://doi.org/10.1101/2020.09.02.20185173; html:https://europepmc.org/article/PPR/PPR208611; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR208611&type=FILE&fileName=EMS94639-pdf.pdf&mimeType=application/pdf
 PPR291347,https://doi.org/10.21203/rs.3.rs-279400/v1,Unraveling COVID-19: a large-scale characterization of 4.5 million COVID-19 cases using CHARYBDIS,"Prieto-Alhambra D, Kostka K, Duarte-Salles T, Prats-Uribe A, Sena A, Pistillo A, Khalid S, Lai L, Golozar A, Alshammari TM, Dawoud D, Nyberg F, Wilcox A, Andryc A, Williams A, Ostropolets A, Areia C, Jung CY, Harle C, Reich C, Blacketer C, Morales D, Dorr DA, Burn E, Roel E, Tan EH, Minty E, DeFalco F, de Maeztu G, Lipori G, Alghoul H, Zhu H, Thomas J, Bian J, Park J, Roldán JM, Posada J, Banda JM, Horcajada JP, Kohler J, Shah K, Natarajan K, Lynch K, Liu L, Schilling L, Recalde M, Spotnitz M, Gong M, Matheny M, Valveny N, Weiskopf N, Shah N, Alser O, Casajust P, Park RW, Schuff R, Seager S, DuVall S, You SC, Song S, Fernández-Bertolín S, Fortin S, Magoc T, Falconer T, Subbian V, Huser V, Ahmed W, Carter W, Guan Y, Galvan Y, He X, Rijnbeek P, Hripcsak G, Ryan P, Suchard M.",,No Journal Info,2021,2021-03-01,Y,,,,"<h4>Background: </h4> Routinely collected real world data (RWD) have great utility in aiding the novel coronavirus disease (COVID-19) pandemic response [1,2]. Here we present the international Observational Health Data Sciences and Informatics (OHDSI) [3] Characterizing Health Associated Risks, and Your Baseline Disease In SARS-COV-2 (CHARYBDIS) framework for standardisation and analysis of COVID-19 RWD. <h4>Methods: </h4>: We conducted a descriptive cohort study using a federated network of data partners in the United States, Europe (the Netherlands, Spain, the UK, Germany, France and Italy) and Asia (South Korea and China). The study protocol and analytical package were released on 11 th June 2020 and are iteratively updated via GitHub [4]. <h4>Findings: </h4> We identified three non-mutually exclusive cohorts of 4,537,153 individuals with a clinical COVID-19 diagnosis or positive test, 886,193 hospitalized with COVID-19 , and 113,627 hospitalized with COVID-19 requiring intensive services . All comorbidities, symptoms, medications, and outcomes are described by cohort in aggregate counts, and are available in an interactive website: https://data.ohdsi.org/Covid19CharacterizationCharybdis/. Interpretation: CHARYBDIS findings provide benchmarks that contribute to our understanding of COVID-19 progression, management and evolution over time. This can enable timely assessment of real-world outcomes of preventative and therapeutic options as they are introduced in clinical practice.",,pdf:http://repositori.upf.edu/bitstream/10230/53956/1/Kostka_ce_unra.pdf; doi:https://doi.org/10.21203/rs.3.rs-279400/v1; html:https://europepmc.org/article/PPR/PPR291347; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR291347&type=FILE&fileName=EMS118164-pdf.pdf&mimeType=application/pdf
 PPR465564,https://doi.org/10.1101/2022.03.07.22271833,GWAS and meta-analysis identifies multiple new genetic mechanisms underlying severe Covid-19,"Pairo-Castineira E, Rawlik K, Klaric L, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Stuckey A, Odhams CA, Walker S, Griffiths F, Oosthuyzen W, Morrice K, Keating S, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJ, Walsh T, Tenesa A, GenOMICC Investigators, SCOURGE Consortium, ISARIC4C Investigators, 23andMe, Scott RH, Caulfield MJ, Moutsianas L, Ponting CP, Wilson JF, Vitart V, Pereira AC, Luchessi A, Parra E, Cruz-Guerrero R, Carracedo A, Fawkes A, Murphy L, Rowan K, Law A, Hendry SC, Baillie JK.",,No Journal Info,2022,2022-03-07,Y,,,,"Pulmonary inflammation drives critical illness in Covid-19, 1;2 creating a clinically homogeneous extreme phenotype, which we have previously shown to be highly efficient for discovery of genetic associations. 3;4 Despite the advanced stage of illness, we have found that immunomodulatory therapies have strong beneficial effects in this group. 1;5 Further genetic discoveries may identify additional therapeutic targets to modulate severe disease. 6 In this new data release from the GenOMICC (Genetics Of Mortality in Critical Care) study we include new microarray genotyping data from additional critically-ill cases in the UK and Brazil, together with cohorts of severe Covid-19 from the ISARIC4C 7 and SCOURGE 8 studies, and meta-analysis with previously-reported data. We find an additional 14 new genetic associations. Many are in potentially druggable targets, in inflammatory signalling (JAK1, PDE4A), monocyte-macrophage differentiation (CSF2), immunometabolism (SLC2A5, AK5), and host factors required for viral entry and replication (TMPRSS2, RAB2A). As with our previous work, these results provide tractable therapeutic targets for modulation of harmful host-mediated inflammation in Covid-19.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/03/07/2022.03.07.22271833.full.pdf; doi:https://doi.org/10.1101/2022.03.07.22271833; html:https://europepmc.org/article/PPR/PPR465564; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR465564&type=FILE&fileName=EMS161994-pdf.pdf&mimeType=application/pdf
@@ -328,8 +328,8 @@ PPR160456,https://doi.org/10.1101/2020.05.06.20092734,The impact of Coronavirus
 PPR217801,https://doi.org/10.1101/2020.09.22.20198754,"Ethnic differences in COVID-19 infection, hospitalisation, and mortality: an OpenSAFELY analysis of 17 million adults in England","The OpenSAFELY Collaborative, Mathur R, Mathur R, Rentsch CT, Morton CE, Hulme WJ, Hulme WJ, Schultze A, MacKenna B, Eggo R, Bhaskaran K, Wong AY, Williamson EJ, Forbes H, Wing K, McDonald HI, Bates C, Bacon S, Walker AJ, Evans D, Inglesby P, Mehrkar A, Curtis HJ, DeVito NJ, Croker R, Drysdale H, Cockburn J, Parry J, Hester F, Harper S, Douglas IJ, Tomlinson L, Evans SJ, Grieve R, Harrison D, Rowan K, Khunti K, Chaturvedi N, Smeeth L, Goldacre B.",,No Journal Info,2020,2020-09-23,Y,,,,"<h4>Background</h4> COVID-19 has had a disproportionate impact on ethnic minority populations, both in the UK and internationally. To date, much of the evidence has been derived from studies within single healthcare settings, mainly those hospitalised with COVID-19. Working on behalf of NHS England, the aim of this study was to identify ethnic differences in the risk of COVID-19 infection, hospitalisation and mortality using a large general population cohort in England. <h4>Methods</h4> We conducted an observational cohort study using linked primary care records of 17.5 million adults between 1 February 2020 and 3 August 2020. Exposure was self-reported ethnicity collapsed into the 5 and 16 ethnicity categories of the English Census. Multivariable Cox proportional hazards regression was used to identify ethnic differences in the risk of being tested and testing positive for SARS-CoV-2 infection, COVID-19 related intensive care unit (ICU) admission, and COVID-19 mortality, adjusted for socio-demographic factors, clinical co-morbidities, geographic region, care home residency, and household size. <h4>Results</h4> A total of 17,510,002 adults were included in the study; 63% white (n=11,030,673), 6% south Asian (n=1,034,337), 2% black (n=344,889), 2% other (n=324,730), 1% mixed (n=172,551), and 26% unknown (n=4,602,822). After adjusting for measured explanatory factors, south Asian, black, and mixed groups were marginally more likely to be tested (south Asian HR 1.08, 95%CI 1.07-1.09; black HR 1.08; 95%CI 1.06-1.09, mixed HR 1.03, 95%CI 1.01-1.05), and substantially more likely to test positive for SARS-CoV-2 compared with white adults (south Asian HR 2.02. 95% CI 1.97-2.07; black HR 1.68, 95%CI 1.61-1.76; mixed HR 1.46, 95%CI 1.36-1.56). The risk of being admitted to ICU for COVID-19 was substantially increased in all ethnic minority groups compared with white adults (south Asian HR 2.22, 95%CI 1.96-2.52; black HR 3.07, 95%CI 2.61-3.61; mixed HR 2.86, 95%CI 2.19-3.75, other HR 2.86, 95%CI 2.31-3.63). Risk of COVID-19 mortality was increased by 25-56% in ethnic minority groups compared with white adults (south Asian HR 1.27, 95%CI 1.17-1.38; black HR 1.55, 95%CI 1.38-1.75; mixed HR 1.40, 95%CI 1.12-1.76; other HR 1.25, 95%CI 1.05-1.49). We observed heterogeneity of associations after disaggregation into detailed ethnic groupings; Indian and African groups were at higher risk of all outcomes; Pakistani, Bangladeshi and Caribbean groups were less or equally likely to be tested for SARS-CoV-2, but at higher risk of all other outcomes, Chinese groups were less likely to be tested for and test positive for SARS-CoV-2, more likely to be admitted to ICU, and equally likely to die from COVID-19. <h4>Conclusions</h4> We found evidence of substantial ethnic inequalities in the risk of testing positive for SARS-CoV-2, ICU admission, and mortality, which persisted after accounting for explanatory factors, including household size. It is likely that some of this excess risk is related to factors not captured in clinical records such as occupation, experiences of structural discrimination, or inequitable access to health and social services. Prioritizing linkage between health, social care, and employment data and engaging with ethnic minority communities to better understand their lived experiences is essential for generating evidence to prevent further widening of inequalities in a timely and actionable manner.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2020/09/23/2020.09.22.20198754.full.pdf; doi:https://doi.org/10.1101/2020.09.22.20198754; html:https://europepmc.org/article/PPR/PPR217801; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR217801&type=FILE&fileName=EMS96320-pdf.pdf&mimeType=application/pdf
 PPR265407,https://doi.org/10.1101/2021.01.12.21249672,"Characteristics and outcomes of 118,155 COVID-19 individuals with a history of cancer in the United States and Spain","Roel E, Pistillo A, Recalde M, Sena AG, Fernández-Bertolín S, Aragón M, Puente D, Ahmed W, Alghoul H, Alser O, Alshammari TM, Areia C, Blacketer C, Carter W, Casajust P, Culhane AC, Dawoud D, DeFalco F, Duvall SL, Falconer T, Golozar A, Gong M, Hester L, Hripcsak G, Tan EH, Jeon H, Jonnagaddala J, Lai LY, Lynch KE, Matheny ME, Morales DR, Natarajan K, Nyberg F, Ostropolets A, Posada JD, Prats-Uribe A, Reich CG, Rivera D, Schilling LM, Soerjomataram I, Shah K, Shah N, Shen Y, Spotniz M, Subbian V, Suchard MA, Trama A, Zhang L, Zhang Y, Ryan P, Prieto-Alhambra D, Kostka K, Duarte-Salles T.",,No Journal Info,2021,2021-01-15,Y,,,,"<h4>Purpose</h4> We aimed to describe the demographics, cancer subtypes, comorbidities and outcomes of patients with a history of cancer with COVID-19 from March to June 2020. Secondly, we compared patients hospitalized with COVID-19 to patients diagnosed with COVID-19 and patients hospitalized with influenza. <h4>Methods</h4> We conducted a cohort study using eight routinely-collected healthcare databases from Spain and the US, standardized to the Observational Medical Outcome Partnership common data model. Three cohorts of patients with a history of cancer were included: i) diagnosed with COVID-19, ii) hospitalized with COVID-19, and iii) hospitalized with influenza in 2017-2018. Patients were followed from index date to 30 days or death. We reported demographics, cancer subtypes, comorbidities, and 30-day outcomes. <h4>Results</h4> We included 118,155 patients with a cancer history in the COVID-19 diagnosed and 41,939 in the COVID-19 hospitalized cohorts. The most frequent cancer subtypes were prostate and breast cancer (range: 5-19% and 1-14% in the diagnosed cohort, respectively). Hematological malignancies were also frequent, with non-Hodgkin’s lymphoma being among the 5 most common cancer subtypes in the diagnosed cohort. Overall, patients were more frequently aged above 65 years and had multiple comorbidities. Occurrence of death ranged from 8% to 14% and from 18% to 26% in the diagnosed and h ospitalized COVID-19 cohorts, respectively. Patients hospitalized with influenza (n=242,960) had a similar distribution of cancer subtypes, sex, age and comorbidities but lower occurrence of adverse events. <h4>Conclusion</h4> Patients with a history of cancer and COVID-19 have advanced age, multiple comorbidities, and a high occurence of COVID-19-related events. Additionaly, hematological malignancies were frequent in these patients.This observational study provides epidemiologic characteristics that can inform clinical care and future etiological studies.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2021/01/15/2021.01.12.21249672.full.pdf; doi:https://doi.org/10.1101/2021.01.12.21249672; html:https://europepmc.org/article/PPR/PPR265407; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR265407&type=FILE&fileName=EMS110647-pdf.pdf&mimeType=application/pdf
 PPR341253,https://doi.org/10.1101/2021.05.18.21257267,"Colchicine in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial","RECOVERY Collaborative Group, Horby PW, Campbell M, Spata E, Emberson JR, Emberson JR, Staplin N, Pessoa-Amorim G, Peto L, Wiselka M, Wiffen L, Tiberi S, Caplin B, Wroe C, Green C, Hine P, Prudon B, George T, Wight A, Baillie JK, Basnyat B, Buch MH, Chappell LC, Day JN, Faust SN, Hamers RL, Jaki T, Juszczak E, Jeffery K, Lim WS, Montgomery A, Mumford A, Rowan K, Thwaites G, Mafham M, Haynes R, Landray MJ.",,No Journal Info,2021,2021-05-18,Y,,,,"<h4>SUMMARY</h4> <h4>Background</h4> Colchicine has been proposed as a treatment for COVID-19 on the basis of its anti-inflammatory actions. <h4>Methods</h4> In this randomised, controlled, open-label trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19. Eligible and consenting adults were randomly allocated in a 1:1 ratio to either usual standard of care alone or usual standard of care plus colchicine twice daily for 10 days or until discharge (or one of the other treatment arms) using web-based simple (unstratified) randomisation with allocation concealment. The primary outcome was 28-day mortality. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov ( NCT04381936 ). <h4>Findings</h4> Between 27 November 2020 and 4 March 2021, 5610 patients were randomly allocated to receive colchicine and 5730 patients to receive usual care alone. Overall, 1173 (21%) patients allocated to colchicine and 1190 (21%) patients allocated to usual care died within 28 days (rate ratio 1.01; 95% confidence interval [CI] 0.93-1.10; p=0.77). Consistent results were seen in all pre-specified subgroups of patients. There was no significant difference in duration of hospitalisation (median 10 days vs. 10 days) or the proportion of patients discharged from hospital alive within 28 days (70% vs. 70%; rate ratio 0.98; 95% CI 0.94-1.03; p=0.44). Among those not on invasive mechanical ventilation at baseline, there was no significant difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (25% vs. 25%; risk ratio 1.02; 95% CI 0.96-1.09; p=0.47). <h4>Interpretation</h4> In adults hospitalised with COVID-19, colchicine was not associated with reductions in 28-day mortality, duration of hospital stay, or risk of progressing to invasive mechanical ventilation or death. <h4>Funding</h4> UK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056). Wellcome Trust (Grant Ref: 222406/Z/20/Z) through the COVID-19 Therapeutics Accelerator.",,pdf:https://discovery.ucl.ac.uk/10138014/1/1-s2.0-S2213260021004355-main.pdf; doi:https://doi.org/10.1101/2021.05.18.21257267; html:https://europepmc.org/article/PPR/PPR341253; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR341253&type=FILE&fileName=EMS129811-pdf.pdf&mimeType=application/pdf
-PPR369660,https://doi.org/10.1101/2021.07.09.21260272,Optimising health and economic impacts of COVID-19 vaccine prioritisation strategies in the WHO European Region,"Liu Y, Sandmann FG, Barnard RC, Pearson CA, CMMID COVID-19 Working Group, Pastore R, Pebody R, Flasche S, Jit M.",,No Journal Info,2021,2021-07-14,Y,,,,"<h4>Background</h4> Countries in the World Health Organization (WHO) European Region differ in terms of the COVID-19 vaccine roll-out speed. We evaluated the health and economic impact of different age-based vaccine prioritisation strategies across this demographically and socio-economically diverse region. <h4>Methods</h4> We fitted country-specific age-stratified compartmental transmission models to reported COVID-19 mortality in the WHO European Region to inform the immunity level before vaccine roll-out. Building upon broad recommendations from the WHO Strategic Advisory Group of Experts on Immunisation (SAGE), we examined four strategies that prioritise: all adults (V+), younger (20-59 year-olds) followed by older adults (60+) (V20), older followed by younger adults (V60), and the oldest adults (75+) (V75) followed by incremental expansion to successively younger five-year age groups. We explored four roll-out scenarios based on projections or recent observations (R1-4) - the slowest scenario (R1) covers 30% of the total population by December 2022 and the fastest (R4) 80% by December 2021. Five decision-making metrics were summarised over 2021-22: mortality, morbidity, and losses in comorbidity-adjusted life expectancy (cLE), comorbidity- and quality-adjusted life years (cQALY), and the value of human capital (HC). Six sets of infection-blocking and disease-reducing vaccine efficacies were considered. <h4>Findings</h4> The optimal age-based vaccine prioritisation strategies were sensitive to country characteristics, decision-making metrics and roll-out speeds. Overall, V60 consistently performed better than or comparably to V75. There were greater benefits in prioritising older adults when roll-out is slow and when VE is low. Under faster roll-out, V+ was the most desirable option. <h4>Interpretation</h4> A prioritisation strategy involving more age-based stages (V75) does not necessarily lead to better health and economic outcomes than targeting broad age groups (V60). Countries expecting a slow vaccine roll-out may particularly benefit from prioritising older adults. <h4>Funding</h4> World Health Organization, Bill and Melinda Gates Foundation, the Medical Research Council (United Kingdom), the National Institute of Health Research (United Kingdom), the European Commission, the Foreign, Commonwealth and Development Office (United Kingdom), Wellcome Trust <h4>Research in Context</h4> <h4>Evidence before this study</h4> We searched PubMed and medRxiv for articles published in English from inception to 9 Jun 2021, with the search terms: (“COVID-19” OR “SARS-CoV-2”) AND (“priorit*) AND (“model*”) AND (“vaccin*”) and identified 66 studies on vaccine prioritization strategies. Of the 25 studies that compared two or more age-based prioritisation strategies, 12 found that targeting younger adults minimised infections while targeting older adults minimised mortality; an additional handful of studies found similar outcomes between different age-based prioritisation strategies where large outbreaks had already occurred. However, only two studies have explored age-based vaccine prioritisation using models calibrated to observed outbreaks in more than one country, and no study has explored the effectiveness of vaccine prioritisation strategies across settings with different population structures, contact patterns, and outbreak history. <h4>Added-value of this study</h4> We evaluated various age-based vaccine prioritisation strategies for 38 countries in the WHO European Region using various health and economic outcomes for decision-making, by parameterising models using observed outbreak history, known epidemiologic and vaccine characteristics, and a range of realistic vaccine roll-out scenarios. We showed that while targeting older adults was generally advantageous, broadly targeting everyone above 60 years might perform better than or comparably to a more detailed strategy that targeted the oldest age group above 75 years followed by those in the next younger five-year age band. Rapid vaccine roll-out has only been observed in a small number of countries. If vaccine coverage can reach 80% by the end of 2021, prioritising older adults may not be optimal in terms of health and economic impact. Lower vaccine efficacy was associated with greater relative benefits only under relatively slow roll-out scenarios considered. <h4>Implication of all the available evidence</h4> COVID-19 vaccine prioritization strategies that require more precise targeting of individuals of a specific and narrow age range may not necessarily lead to better outcomes compared to strategies that prioritise populations across broader age ranges. In the WHO European Region, prioritising all adults equally or younger adults first will only optimise health and economic impact when roll-out is rapid, which may raise between-country equity issues given the global demand for COVID-19 vaccines.",,doi:https://doi.org/10.1101/2021.07.09.21260272; html:https://europepmc.org/article/PPR/PPR369660; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR369660&type=FILE&fileName=EMS130637-pdf.pdf&mimeType=application/pdf
 PPR408531,https://doi.org/10.1101/2021.10.18.21265046,Comparative assessment of methods for short-term forecasts of COVID-19 hospital admissions in England at the local level,"Meakin S, Abbott S, Bosse N, Munday J, Gruson H, Hellewell J, Sherratt K, CMMID COVID-19 Working Group, Funk S.",,No Journal Info,2021,2021-10-18,Y,,,,"<h4>Background</h4> Forecasting healthcare demand is essential in epidemic settings, both to inform situational awareness and facilitate resource planning. Ideally, forecasts should be robust across time and locations. During the COVID-19 pandemic in England, it is an ongoing concern that demand for hospital care for COVID-19 patients in England will exceed available resources. <h4>Methods</h4> We made weekly forecasts of daily COVID-19 hospital admissions for National Health Service (NHS) Trusts in England between August 2020 and April 2021 using three disease-agnostic forecasting models: a mean ensemble of autoregressive time series models, a linear regression model with 7-day-lagged local cases as a predictor, and a scaled convolution of local cases and a delay distribution. We compared their point and probabilistic accuracy to a mean-ensemble of them all, and to a simple baseline model of no change from the last day of admissions. We measured predictive performance using the Weighted Interval Score (WIS) and considered how this changed in different scenarios (the length of the predictive horizon, the date on which the forecast was made, and by location), as well as how much admissions forecasts improved when future cases were known. <h4>Results</h4> All models outperformed the baseline in the majority of scenarios. Forecasting accuracy varied by forecast date and location, depending on the trajectory of the outbreak, and all individual models had instances where they were the top- or bottom-ranked model. Forecasts produced by the mean-ensemble were both the most accurate and most consistently accurate forecasts amongst all the models considered. Forecasting accuracy was improved when using future observed, rather than forecast, cases, especially at longer forecast horizons. <h4>Conclusions</h4> Assuming no change in current admissions is rarely better than including at least a trend. Using confirmed COVID-19 cases as a predictor can improve admissions forecasts in some scenarios, but this is variable and depends on the ability to make consistently good case forecasts. However, ensemble forecasts can make forecasts that make consistently more accurate forecasts across time and locations. Given minimal requirements on data and computation, our admissions forecasting ensemble could be used to anticipate healthcare needs in future epidemic or pandemic settings.",,doi:https://doi.org/10.1101/2021.10.18.21265046; html:https://europepmc.org/article/PPR/PPR408531; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR408531&type=FILE&fileName=EMS137136-pdf.pdf&mimeType=application/pdf
+PPR369660,https://doi.org/10.1101/2021.07.09.21260272,Optimising health and economic impacts of COVID-19 vaccine prioritisation strategies in the WHO European Region,"Liu Y, Sandmann FG, Barnard RC, Pearson CA, CMMID COVID-19 Working Group, Pastore R, Pebody R, Flasche S, Jit M.",,No Journal Info,2021,2021-07-14,Y,,,,"<h4>Background</h4> Countries in the World Health Organization (WHO) European Region differ in terms of the COVID-19 vaccine roll-out speed. We evaluated the health and economic impact of different age-based vaccine prioritisation strategies across this demographically and socio-economically diverse region. <h4>Methods</h4> We fitted country-specific age-stratified compartmental transmission models to reported COVID-19 mortality in the WHO European Region to inform the immunity level before vaccine roll-out. Building upon broad recommendations from the WHO Strategic Advisory Group of Experts on Immunisation (SAGE), we examined four strategies that prioritise: all adults (V+), younger (20-59 year-olds) followed by older adults (60+) (V20), older followed by younger adults (V60), and the oldest adults (75+) (V75) followed by incremental expansion to successively younger five-year age groups. We explored four roll-out scenarios based on projections or recent observations (R1-4) - the slowest scenario (R1) covers 30% of the total population by December 2022 and the fastest (R4) 80% by December 2021. Five decision-making metrics were summarised over 2021-22: mortality, morbidity, and losses in comorbidity-adjusted life expectancy (cLE), comorbidity- and quality-adjusted life years (cQALY), and the value of human capital (HC). Six sets of infection-blocking and disease-reducing vaccine efficacies were considered. <h4>Findings</h4> The optimal age-based vaccine prioritisation strategies were sensitive to country characteristics, decision-making metrics and roll-out speeds. Overall, V60 consistently performed better than or comparably to V75. There were greater benefits in prioritising older adults when roll-out is slow and when VE is low. Under faster roll-out, V+ was the most desirable option. <h4>Interpretation</h4> A prioritisation strategy involving more age-based stages (V75) does not necessarily lead to better health and economic outcomes than targeting broad age groups (V60). Countries expecting a slow vaccine roll-out may particularly benefit from prioritising older adults. <h4>Funding</h4> World Health Organization, Bill and Melinda Gates Foundation, the Medical Research Council (United Kingdom), the National Institute of Health Research (United Kingdom), the European Commission, the Foreign, Commonwealth and Development Office (United Kingdom), Wellcome Trust <h4>Research in Context</h4> <h4>Evidence before this study</h4> We searched PubMed and medRxiv for articles published in English from inception to 9 Jun 2021, with the search terms: (“COVID-19” OR “SARS-CoV-2”) AND (“priorit*) AND (“model*”) AND (“vaccin*”) and identified 66 studies on vaccine prioritization strategies. Of the 25 studies that compared two or more age-based prioritisation strategies, 12 found that targeting younger adults minimised infections while targeting older adults minimised mortality; an additional handful of studies found similar outcomes between different age-based prioritisation strategies where large outbreaks had already occurred. However, only two studies have explored age-based vaccine prioritisation using models calibrated to observed outbreaks in more than one country, and no study has explored the effectiveness of vaccine prioritisation strategies across settings with different population structures, contact patterns, and outbreak history. <h4>Added-value of this study</h4> We evaluated various age-based vaccine prioritisation strategies for 38 countries in the WHO European Region using various health and economic outcomes for decision-making, by parameterising models using observed outbreak history, known epidemiologic and vaccine characteristics, and a range of realistic vaccine roll-out scenarios. We showed that while targeting older adults was generally advantageous, broadly targeting everyone above 60 years might perform better than or comparably to a more detailed strategy that targeted the oldest age group above 75 years followed by those in the next younger five-year age band. Rapid vaccine roll-out has only been observed in a small number of countries. If vaccine coverage can reach 80% by the end of 2021, prioritising older adults may not be optimal in terms of health and economic impact. Lower vaccine efficacy was associated with greater relative benefits only under relatively slow roll-out scenarios considered. <h4>Implication of all the available evidence</h4> COVID-19 vaccine prioritization strategies that require more precise targeting of individuals of a specific and narrow age range may not necessarily lead to better outcomes compared to strategies that prioritise populations across broader age ranges. In the WHO European Region, prioritising all adults equally or younger adults first will only optimise health and economic impact when roll-out is rapid, which may raise between-country equity issues given the global demand for COVID-19 vaccines.",,doi:https://doi.org/10.1101/2021.07.09.21260272; html:https://europepmc.org/article/PPR/PPR369660; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR369660&type=FILE&fileName=EMS130637-pdf.pdf&mimeType=application/pdf
 PPR213448,https://doi.org/10.1101/2020.09.11.20192492,Resurgence of SARS-CoV-2 in England: detection by community antigen surveillance,"REACT Study Investigators:, Riley S, Ainslie KEC, Eales O, Walters CE, Wang H, Atchison C, Fronterre C, Diggle PJ, Ashby D, Donnelly CA, Cooke G, Barclay W, Ward H, Darzi A, Elliott P.",,No Journal Info,2020,2020-09-11,Y,,,,"<h4>Summary</h4> <h4>Background</h4> Based on cases and deaths, transmission of SARS-CoV-2 in England peaked in late March and early April 2020 and then declined until the end of June. Since the start of July, cases have increased, while deaths have continued to decrease. <h4>Methods</h4> We report results from 594,000 swabs tested for SARS-CoV-2 virus obtained from a representative sample of people in England over four rounds collected regardless of symptoms, starting in May 2020 and finishing at the beginning of September 2020. Swabs for the most recent two rounds were taken between 24th July and 11th August and for round 4 between 22nd August and 7th September. We estimate weighted overall prevalence, doubling times between and within rounds and associated reproduction numbers. We obtained unweighted prevalence estimates by sub-groups: age, sex, region, ethnicity, key worker status, household size, for which we also estimated odds of infection. We identified clusters of swab-positive participants who were closer, on average, to other swab-positive participants than would be expected. <h4>Findings</h4> Over all four rounds of the study, we found that 72% (67%, 76%) of swab-positive individuals were asymptomatic at the time of swab and in the week prior. The epidemic declined between rounds 1 and 2, and rounds 2 and 3. However, the epidemic was increasing between rounds 3 and 4, with a doubling time of 17 (13, 23) days corresponding to an R value of 1.3 (1.2, 1.4). When analysing round 3 alone, we found that the epidemic had started to grow again with 93% probability. Using only the most recent round 4 data, we estimated a doubling time of 7.7 (5.5, 12.7) days, corresponding to an R value of 1.7 (1.4, 2.0). Cycle threshold values were lower (viral loads were higher) for rounds 1 and 4 than they were for rounds 2 and 3. In round 4, we observed the highest prevalence in participants aged 18 to 24 years at 0.25% (0.16%, 0.41%), increasing from 0.08% (0.04%, 0.18%) in round 3. We observed the lowest prevalence in those aged 65 and older at 0.04% (0.02%, 0.06%) which was stable compared with round 3. Participants of Asian ethnicity had elevated odds of infection. We identified clusters in and around London, transient clusters in the Midlands, and an expanding area of clustering in the North West and more recently in Yorkshire and the Humber. <h4>Interpretation</h4> Although low levels of transmission persisted in England through to mid-summer 2020, the prevalence of SARS-CoV-2 is now increasing. We found evidence of accelerating transmission at the end of August and beginning of September. Representative community antigen sampling can increase situational awareness and help improve public health decision making even at low prevalence.",,doi:https://doi.org/10.1126/science.abf0874; doi:https://doi.org/10.1101/2020.09.11.20192492; html:https://europepmc.org/article/PPR/PPR213448; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR213448&type=FILE&fileName=EMS95011-pdf.pdf&mimeType=application/pdf
 PPR672704,https://doi.org/,A Comprehensive Benchmark for COVID-19 Predictive Modeling Using Electronic Health Records in Intensive Care,"Gao J, Zhu Y, Wang W, Wang Y, Tang W, Harrison EM, Ma L.",,No Journal Info,2023,2023-06-07,Y,,,,"The COVID-19 pandemic has posed a heavy burden to the healthcare system worldwide and caused huge social disruption and economic loss. Many deep learning models have been proposed to conduct clinical predictive tasks such as mortality prediction for COVID-19 patients in intensive care units using Electronic Health Record (EHR) data. Despite their initial success in certain clinical applications, there is currently a lack of benchmarking results to achieve a fair comparison so that we can select the optimal model for clinical use. Furthermore, there is a discrepancy between the formulation of traditional prediction tasks and real-world clinical practice in intensive care. To fill these gaps, we propose two clinical prediction tasks, Outcome-specific length-of-stay prediction and Early mortality prediction for COVID-19 patients in intensive care units. The two tasks are adapted from the naive length-of-stay and mortality prediction tasks to accommodate the clinical practice for COVID-19 patients. We propose fair, detailed, open-source data-preprocessing pipelines and evaluate 17 state-of-the-art predictive models on two tasks, including 5 machine learning models, 6 basic deep learning models and 6 deep learning predictive models specifically designed for EHR data. We provide benchmarking results using data from two real-world COVID-19 EHR datasets. One dataset is publicly available without needing any inquiry and another dataset can be accessed on request. We provide fair, reproducible benchmarking results for two tasks. We deploy all experiment results and models on an online platform. We also allow clinicians and researchers to upload their data to the platform and get quick prediction results using our trained models. We hope our efforts can further facilitate deep learning and machine learning research for COVID-19 predictive modeling.",,arxiv:https://arxiv.org/abs/2209.07805v3; html:https://europepmc.org/article/PPR/PPR672704; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR672704&type=FILE&fileName=EMS177023-pdf.pdf&mimeType=application/pdf
 PPR203834,https://doi.org/10.1101/2020.08.17.20175117,Real-time spatial health surveillance: mapping the UK COVID-19 epidemic,"Fry R, Hollinghurst J, R Stagg H, A Thompson D, Fronterre C, Orton C, A Lyons R, V Ford D, Sheikh A, J Diggle P.",,No Journal Info,2020,2020-08-21,Y,,,,"The COVID-19 pandemic has highlighted the need for robust data linkage systems and methods for identifying outbreaks of disease in near real-time. Using self-reported app data and the Secure Anonymised Information Linkage (SAIL) Databank, we demonstrate the use of sophisticated spatial modelling for near-real-time prediction of COVID-19 prevalence at small-area resolution to inform strategic government policy areas. A pre-requisite to an effective control strategy is that predictions need to be accompanied by estimates of their precision, to guard against over-reaction to potentially spurious features of ‘best guess’ predictions. In the UK, important emerging risk-factors such as social deprivation or ethnicity vary over small distances, hence risk needs to be modelled at fine spatial resolution to avoid aggregation bias. We demonstrate that existing geospatial statistical methods originally developed for global health applications are well-suited to this task and can be used in an anonymised databank environment, thus preserving the privacy of the individuals who contribute their data.",,doi:https://doi.org/10.1016/j.ijmedinf.2021.104400; doi:https://doi.org/10.1101/2020.08.17.20175117; html:https://europepmc.org/article/PPR/PPR203834; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR203834&type=FILE&fileName=EMS95676-pdf.pdf&mimeType=application/pdf
@@ -345,8 +345,8 @@ PPR181164,https://doi.org/10.1101/2020.06.28.20141986,Protocol for the developme
 PPR296515,https://doi.org/10.1101/2021.03.11.21253189,"Risk, clinical course and outcome of ischemic stroke in patients hospitalized with COVID-19: a multicenter cohort study","Sluis WM, Linschoten M, Buijs JE, Biesbroek JM, Hertog HMd, Ribbers T, Nieuwkamp D, Houwelingen RCv, Dias A, Uden IWv, Kerklaan JP, Bienfait HP, Vermeer SE, de Jong SW, Ali M, Wermer MJ, de Graaf MT, Brouwers PJ, Asselbergs FW, Kappelle LJ, van der Worp HB, Algra AM.",,No Journal Info,2021,2021-03-12,N,,,,"<h4>Background and purpose</h4> The frequency of ischemic stroke in patients with COVID-19 varies in the current literature, and risk factors are unknown. We assessed the incidence, risk factors, and outcomes of acute ischemic stroke in hospitalized patients with COVID-19. <h4>Methods</h4> We included patients with a laboratory confirmed SARS-CoV-2 infection admitted in 16 hospitals participating in the international CAPACITY-COVID registry between March 1 st and August 1 st , 2020. Patients were screened for the occurrence of acute ischemic stroke. We calculated the cumulative incidence of ischemic stroke and compared risk factors, cardiovascular complications, and in-hospital mortality in patients with and without ischemic stroke. <h4>Results</h4> We included 2147 patients with COVID-19, of whom 586 (27.3%) needed treatment at an intensive care unit (ICU). Thirty-eight patients (1.8%) had an ischemic stroke. Patients with stroke were older, but did not differ in sex or cardiovascular risk factors. Median time between onset of COVID-19 symptoms and diagnosis of stroke was two weeks. The incidence of ischemic stroke was higher among patients who were treated at an ICU (16/586; 2.7% versus 22/1561; 1.4%; p=0.039). Pulmonary embolism was more common in patients with (8/38; 21.1%) than in those without stroke (160/2109; 7.6%; adjusted RR: 2.08; 95%CI:1.52-2.84). Twenty-seven patients with ischemic stroke (71.1%) died during admission or were functional dependent at discharge and in-hospital mortality. Patients with ischemic stroke were at a higher risk of in-hospital mortality (adjusted RR 1.56; 95%CI:1.13-2.15) than patients without stroke. <h4>Conclusions</h4> In this multicenter cohort study, the cumulative incidence of acute ischemic stroke in hospitalized patients with COVID-19 was approximately 2%, with a higher risk in patients treated at an ICU. The majority of stroke patients had a poor outcome. The association between ischemic stroke and pulmonary embolism warrants further investigation.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/STROKEAHA.121.034787; doi:https://doi.org/10.1101/2021.03.11.21253189; html:https://europepmc.org/article/PPR/PPR296515; doi:https://doi.org/10.1101/2021.03.11.21253189
 PPR611882,https://doi.org/10.1101/2023.02.01.23285333,Associations between reported healthcare disruption due to COVID-19 and avoidable hospitalisation: Evidence from seven linked longitudinal studies for England,"Green MA, McKee M, Hamilton O, Shaw RJ, Macleod J, Boyd A, The LH&W NCS Collaborative, and Srinivasa Vittal Katikireddi.",,No Journal Info,2023,2023-02-02,Y,,,,"<h4>Background</h4> Health services across the UK struggled to cope during the COVID-19 pandemic. Many treatments were postponed or cancelled, although the impact was mitigated by new models of delivery. While the scale of disruption has been studied, much less is known about if this disruption impacted health outcomes. The aim of our paper is to examine whether there is an association between individuals experiencing disrupted access to healthcare during the pandemic and risk of an avoidable hospitalisation. <h4>Methods</h4> We used individual-level data for England from seven longitudinal cohort studies linked to electronic health records from NHS Digital (n = 29 276) within the UK Longitudinal Linkage Collaboration trusted research environment. Avoidable hospitalisations were defined as emergency hospital admissions for ambulatory care sensitive and emergency urgent care sensitive conditions (1 st March 2020 to 25 th August 2022). Self-reported measures of whether people had experienced disruption during the pandemic to appointments (e.g., visiting their GP or an outpatient department), procedures (e.g., surgery, cancer treatment) or medications were used as our exposures. Logistic regression models examined associations. <h4>Results</h4> 35% of people experienced some form of disrupted access to healthcare. Those whose access was disrupted were at increased risk of any (Odds Ratio (OR) = 1.80, 95% Confidence Intervals (CIs) = 1.34-2.41), acute (OR = 1.68, CIs = 1.13-2.53) and chronic (OR = 1.93, CIs = 1.40-2.64) ambulatory care sensitive hospital admissions. There were positive associations between disrupted access to appointments and procedures to measures of avoidable hospitalisations as well. <h4>Conclusions</h4> Our study presents novel evidence from linked individual-level data showing that people whose access to healthcare was disrupted were more likely to have an avoidable or potentially preventable hospitalisation. Our findings highlight the need to increase healthcare investment to tackle the short- and long-term implications of the pandemic beyond directly dealing with SARS-CoV-2 infections.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2023/02/02/2023.02.01.23285333.full.pdf; doi:https://doi.org/10.1101/2023.02.01.23285333; html:https://europepmc.org/article/PPR/PPR611882; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR611882&type=FILE&fileName=EMS164989-pdf.pdf&mimeType=application/pdf
 PPR362014,https://doi.org/10.2139/ssrn.3864079,Indirect Effects of the COVID-19 Pandemic on Childhood Infection in England: A Population Based Observational Study,"Kadambari S, Goldacre R, Morris E, Goldacre M, Pollard A.",,No Journal Info,2021,2021-06-21,N,,,,"Background: Children are largely unaffected following Sars-CoV-2 infection with low rates of significant disease and the inflammatory syndrome MIS-C. However, the lives of children have been substantially disrupted by the pandemic through physical distancing measures and the impact on health systems and economies. In this study, the impact of the COVID-19 pandemic on hospital admissions for childhood respiratory infections, severe invasive infections, and vaccine preventable disease in England was assessed along with associated mortality outcomes.<br><br>Methods: In this population-based observational study, we examined hospital admission data from every National Health Service hospital from Mar 1 2017 to Feb 28 2021. We report monthly and annual numbers of individuals hospitalised with 19 common childhood respiratory, severe invasive, and vaccine preventable infections. We compare the frequency of admissions for these conditions before and after the onset of the pandemic in England and calculate percentage changes since Mar 1 2020 for each infection overall and by demographic characteristics including age, region, deprivation, and comorbidity, and quantify mortality outcomes.<br><br>Findings: In the 12 months from Mar 1 2020, there were significant reductions compared with the preceding 36 months in the numbers of children admitted for every infection studied except pyelonephritis. These reductions were seen in all geographic regions, Index of Multiple Deprivation categories, ethnic groups and in those with underlying comorbidities. Among the respiratory infections, the greatest percentage reductions were for influenza where the number of individuals admitted decreased by 94% (95% CI 88, 97) from 5,061 (annual mean from Mar 1 2017 - Feb 29 2020) to 290 in the 12 months after Mar 1 2020, and for bronchiolitis where the number of individuals admitted decreased by over 80% (95% CI 78, 83) from 41,777 (annual mean 2017–2020) to 7,883 in 2020-21. Among the severe invasive infections, percentage decreases ranged from 20% (95% CI 13, 26) for osteomyelitis to 54% (95% CI 51, 56) for meningitis. Among the vaccine preventable infections, the greatest reduction was for measles, where the number of individuals admitted in the 12 months after Mar 1 2020 (n=12) was 92% lower (95% CI 84, 96) than the average number admitted in the previous three years (n=143). Admissions for <i>Neisseria meningitidis</i> decreased by 70% (95% CI 55, 80), and admissions for <i>Streptococcus pneumoniae</i>, <i>Haemophilus influenzae</i> and mumps more than halved. Alongside the decreases in admissions, there were also decreases in the absolute numbers of 60-day fatalities after admission for sepsis, meningitis, bronchiolitis, pneumonia, viral wheeze and upper respiratory tract infection (RTI). For pneumonia, although the absolute number of 60-day fatalities decreased (from a 3-year average of 159 to 115 after Mar 1 2020), the proportion of individuals admitted who died within 60 days increased (age-sex adjusted odds ratio 1.73, 95% CI 1.42, 2.11).<br><br>Interpretation: During the COVID-19 pandemic, a range of behavioural changes (adoption of non-pharmacological interventions (NPIs)) and societal strategies (school closures, lockdowns and restricted travel) were used to reduce transmission of SARS CoV2 which have also significantly reduced transmission of common and severe childhood infections. NPIs could be used in the future to better protect healthcare systems and the most vulnerable children in society.<br><br>Funding Information: Public Health England, Health Data Research UK, and the National Institute for Health Research Oxford Biomedical Research Centre.<br><br>Declaration of Interests: None to declare. <br><br>Ethics Approval Statement: Ethical approval to study the record-linked datasets was obtained from the Central and South Bristol Multi-Centre Research Ethics Committee (04/Q2006/176). All patient records were pseudonymized by the data providers through encryption of personal identifiers.",,pdf:https://discovery.ucl.ac.uk/10158356/1/Indirect%20effects%20of%20the%20covid-19%20pandemic%20on%20childhood%20infection%20in%20England%20population%20based%20observational%20study.pdf; doi:https://doi.org/10.2139/ssrn.3864079; html:https://europepmc.org/article/PPR/PPR362014; doi:https://doi.org/10.2139/ssrn.3864079
-PPR302424,https://doi.org/10.1101/2021.03.19.21253940,"COVID-19 Infection Risk amongst 14,104 Vaccinated Care Home Residents: A national observational longitudinal cohort study in Wales, United Kingdom, December 2020 to March 2021","Hollinghurst J, North L, Perry M, Akbari A, Gravenor MB, Lyons RA, Fry R.",,No Journal Info,2021,2021-03-24,Y,,,,"<h4>ABSTRACT</h4> <h4>Background</h4> Vaccinations for COVID-19 have been prioritised for older people living in care homes. However, vaccination trials included limited numbers of older people. <h4>Aim</h4> We aimed to study infection rates of SARS-CoV-2 for older care home residents following vaccination and identify factors associated with increased risk of infection. <h4>Study Design and Setting</h4> We conducted an observational data-linkage study including 14,104 vaccinated older care home residents in Wales (UK) using anonymised electronic health records and administrative data. <h4>Methods</h4> We used Cox proportional hazards models to estimate hazard ratios (HRs) for the risk of testing positive for SARS-CoV-2 infection following vaccination, after landmark times of either 7 or 21-days post-vaccination. We adjusted hazard ratios for age, sex, frailty, prior SARS-CoV-2 infections and vaccination type. <h4>Results</h4> We observed a small proportion of care home residents with positive PCR tests following vaccination 1.05% (N=148), with 90% of infections occurring within 28-days. For the 7-day landmark analysis we found a reduced risk of SARS-CoV-2 infection for vaccinated individuals who had a previous infection; HR (95% confidence interval) 0.54 (0.30,0.95), and an increased HR for those receiving the Pfizer-BioNTECH vaccine compared to the Oxford-AstraZeneca; 3.83 (2.45,5.98). For the 21-day landmark analysis we observed high HRs for individuals with low and intermediate frailty compared to those without; 4.59 (1.23,17.12) and 4.85 (1.68,14.04) respectively. <h4>Conclusions</h4> Increased risk of infection after 21-days was associated with frailty. We found most infections occurred within 28-days of vaccination, suggesting extra precautions to reduce transmission risk should be taken in this time frame.",,pdf:https://academic.oup.com/ageing/article-pdf/51/1/afab223/42083726/afab223.pdf; doi:https://doi.org/10.1101/2021.03.19.21253940; html:https://europepmc.org/article/PPR/PPR302424; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR302424&type=FILE&fileName=EMS120789-pdf.pdf&mimeType=application/pdf
 PPR342175,https://doi.org/10.2139/ssrn.3590468,"Risk Prediction for Poor Outcome and Death in Hospital In-Patients with COVID-19: Derivation in Wuhan, China and External Validation in London, UK","Zhang H, Shi T, Wu X, Zhang X, Wang K, Bean D, Dobson R, Teo JT, Sun J, Zhao P, Li C, Dhaliwal K, Wu H, Li Q, Guthrie B.",,No Journal Info,2020,2020-06-04,N,,,,"Background: Accurate risk prediction of clinical outcome would usefully inform clinical decisions and intervention targeting in COVID-19. The aim of this study was to derive and validate risk prediction models for poor outcome and death in adult inpatients with COVID-19.     <br><br>Methods: Model derivation using data from Wuhan, China used logistic regression with death and poor outcome (death or severe disease) as outcomes. Predictors were demographic, comorbidity, symptom and laboratory test variables. The best performing models were externally validated in data from London, UK.     <br><br>Findings: 4.3% of the derivation cohort (n=775) died and 9.7% had a poor outcome, compared to 34.1% and 42.9% of the validation cohort (n=226). In derivation, prediction models based on age, sex, neutrophil count, lymphocyte count, platelet count, C-reactive protein and creatinine had excellent discrimination (death c-index=0.91, poor outcome c-index=0.88), with good-to-excellent calibration. Using two cut-offs to define low, high and very-high risk groups, derivation patients were stratified in groups with observed death rates of 0.34%, 15.0% and 28.3% and poor outcome rates 0.63%, 8.9% and 58.5%. External validation discrimination was good (c-index death=0.74, poor outcome=0.72) as was calibration. However, observed rates of death were 16.5%, 42.9% and 58.4% and poor outcome 26.3%, 28.4% and 64.8% in predicted low, high and very-high risk groups.     <br><br>Interpretation: Our prediction model using demography and routinely-available laboratory tests performed very well in internal validation in the lower-risk derivation population, but less well in the much higher-risk external validation population. Further external validation is needed. Collaboration to create larger derivation datasets, and to rapidly externally validate all proposed prediction models in a range of populations is needed, before routine implementation of any risk prediction tool in clinical care.     <br><br>Funding Statement:  HW and HZ are supported by Medical Research Council and Health Data Research UK Grant (MR/S004149/1), Industrial Strategy Challenge Grant (MC_PC_18029) and Wellcome Institutional Translation Partnership Award (PIII054). RD is supported by the National Institute for Health Research (NIHR) Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London. DMB is funded by a UKRI Innovation Fellowship as part of Health Data Research UK MR/S00310X/1 (https://www.hdruk.ac.uk). KD is supported by LifeArc STOPCOVID award. This work uses data provided by patients and collected by the NHS as part of their care and support. XW is supported by National Natural Science Foundation of China (grant number:81700006). QL is supported by National Key R&D Program (2018YFC1313700), National Natural Science Foundation of China (grant number: 81870064) and the “Gaoyuan” project of Pudong Health and Family Planning Commission (PWYgy2018-06).<br><br>Declaration of Interests: The authors declare no competing interests.<br><br>Ethics Approval Statement: The derivation study was approved by the Research Ethics Committee of Shanghai Dongfang Hospital and Taikang Tongji Hospital. The external validation study operated under London South East Research Ethics Committee (reference 18/LO/2048) approval granted to the King’s Electronic Records Research Interface (KERRI).",,doi:https://doi.org/10.1101/2020.04.28.20082222; doi:https://doi.org/10.2139/ssrn.3590468; html:https://europepmc.org/article/PPR/PPR342175; doi:https://doi.org/10.2139/ssrn.3590468
+PPR302424,https://doi.org/10.1101/2021.03.19.21253940,"COVID-19 Infection Risk amongst 14,104 Vaccinated Care Home Residents: A national observational longitudinal cohort study in Wales, United Kingdom, December 2020 to March 2021","Hollinghurst J, North L, Perry M, Akbari A, Gravenor MB, Lyons RA, Fry R.",,No Journal Info,2021,2021-03-24,Y,,,,"<h4>ABSTRACT</h4> <h4>Background</h4> Vaccinations for COVID-19 have been prioritised for older people living in care homes. However, vaccination trials included limited numbers of older people. <h4>Aim</h4> We aimed to study infection rates of SARS-CoV-2 for older care home residents following vaccination and identify factors associated with increased risk of infection. <h4>Study Design and Setting</h4> We conducted an observational data-linkage study including 14,104 vaccinated older care home residents in Wales (UK) using anonymised electronic health records and administrative data. <h4>Methods</h4> We used Cox proportional hazards models to estimate hazard ratios (HRs) for the risk of testing positive for SARS-CoV-2 infection following vaccination, after landmark times of either 7 or 21-days post-vaccination. We adjusted hazard ratios for age, sex, frailty, prior SARS-CoV-2 infections and vaccination type. <h4>Results</h4> We observed a small proportion of care home residents with positive PCR tests following vaccination 1.05% (N=148), with 90% of infections occurring within 28-days. For the 7-day landmark analysis we found a reduced risk of SARS-CoV-2 infection for vaccinated individuals who had a previous infection; HR (95% confidence interval) 0.54 (0.30,0.95), and an increased HR for those receiving the Pfizer-BioNTECH vaccine compared to the Oxford-AstraZeneca; 3.83 (2.45,5.98). For the 21-day landmark analysis we observed high HRs for individuals with low and intermediate frailty compared to those without; 4.59 (1.23,17.12) and 4.85 (1.68,14.04) respectively. <h4>Conclusions</h4> Increased risk of infection after 21-days was associated with frailty. We found most infections occurred within 28-days of vaccination, suggesting extra precautions to reduce transmission risk should be taken in this time frame.",,pdf:https://academic.oup.com/ageing/article-pdf/51/1/afab223/42083726/afab223.pdf; doi:https://doi.org/10.1101/2021.03.19.21253940; html:https://europepmc.org/article/PPR/PPR302424; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR302424&type=FILE&fileName=EMS120789-pdf.pdf&mimeType=application/pdf
 PPR197688,https://doi.org/10.1101/2020.08.07.20169490,HIV infection and COVID-19 death: population-based cohort analysis of UK primary care data and linked national death registrations within the OpenSAFELY platform,"Bhaskaran K, Rentsch C, MacKenna B, Schultz A, Mehrkar A, Bates C, Eggo R, Morton C, Bacon S, Inglesby P, Douglas I, Walker A, McDonald H, Cockburn J, Williamson E, Evans D, Forbes H, Curtis H, Hulme W, Parry J, Hester F, Harper S, Evans S, Smeeth L, Goldacre B.",,No Journal Info,2020,2020-08-07,Y,,,,"<h4>Background</h4> It is unclear whether HIV infection is associated with risk of COVID-19 death. We aimed to investigate this in a large-scale population-based study in England. <h4>Methods</h4> Working on behalf of NHS England, we used the OpenSAFELY platform to analyse routinely collected electronic primary care data linked to national death registrations. People with a primary care record for HIV infection were compared to people without HIV. COVID-19 death was defined by ICD-10 codes U07.1 or U07.2 anywhere on the death certificate. Cox regression models were used to estimate the association between HIV infection and COVID-19 death, initially adjusted for age and sex, then adding adjustment for index of multiple deprivation and ethnicity, and finally for a broad range of comorbidities. Interaction terms were added to assess effect modification by age, sex, ethnicity, comorbidities and calendar time. <h4>Results</h4> 17.3 million adults were included, of whom 27,480 (0.16%) had HIV recorded. People living with HIV were more likely to be male, of black ethnicity, and from a more deprived geographical area than the general population. There were 14,882 COVID-19 deaths during the study period, with 25 among people with HIV. People living with HIV had nearly three-fold higher risk of COVID-19 death than those without HIV after adjusting for age and sex (HR=2.90, 95% CI 1.96-4.30). The association was attenuated but risk remained substantially raised, after adjustment for deprivation and ethnicity (adjusted HR=2.52, 1.70-3.73) and further adjustment for comorbidities (HR=2.30, 1.55-3.41). There was some evidence that the association was larger among people of black ethnicity (HR = 3.80, 2.15-6.74, compared to 1.64, 0.92-2.90 in non-black individuals, p-interaction=0.045) <h4>Interpretation</h4> HIV infection was associated with a markedly raised risk of COVID-19 death in a country with high levels of antiretroviral therapy coverage and viral suppression; the association was larger in people of black ethnicity.",,pdf:https://europepmc.org/articles/pmc7773630?pdf=render; doi:https://doi.org/10.1101/2020.08.07.20169490; html:https://europepmc.org/article/PPR/PPR197688; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR197688&type=FILE&fileName=EMS91440-pdf.pdf&mimeType=application/pdf
 PPR272966,https://doi.org/10.1101/2021.01.22.21250304,Rates of serious clinical outcomes in survivors of hospitalisation with COVID-19: a descriptive cohort study within the OpenSAFELY platform,"The OpenSAFELY Collaborative, Tazare J, Tazare J, Walker AJ, Tomlinson L, Hickman G, Rentsch CT, Williamson EJ, Bhaskaran K, Evans D, Wing K, Mathur R, Wong AY, Schultze A, Bacon S, Bates C, Morton CE, Curtis HJ, Nightingale E, McDonald HI, Mehrkar A, Inglesby P, Davy S, MacKenna B, Cockburn J, Hulme WJ, Hulme WJ, Warren-Gash C, Bhate K, Nitsch D, Powell E, Mulick A, Forbes H, Minassian C, Croker R, Parry J, Hester F, Harper S, Eggo RM, Evans SJ, Smeeth L, Douglas IJ, Goldacre B.",,No Journal Info,2021,2021-01-25,Y,,,,"<h4>Background</h4> Patients with COVID-19 are thought to be at higher risk of cardiometabolic and pulmonary complications, but quantification of that risk is limited. We aimed to describe the overall burden of these complications in survivors of severe COVID-19. <h4>Methods</h4> Working on behalf of NHS England, we used linked primary care records, death certificate and hospital data from the OpenSAFELY platform. We constructed three cohorts: patients discharged following hospitalisation with COVID-19, patients discharged following hospitalisation with pneumonia in 2019, and a frequency-matched cohort from the general population in 2019. We studied eight cardiometabolic and pulmonary outcomes. Absolute rates were measured in each cohort and Cox regression models were fitted to estimate age/sex adjusted hazard ratios comparing outcome rates between discharged COVID-19 patients and the two comparator cohorts. <h4>Results</h4> Amongst the population of 31,716 patients discharged following hospitalisation with COVID-19, rates for majority of outcomes peaked in the first month post-discharge, then declined over the following four months. Patients in the COVID-19 population had markedly increased risk of all outcomes compared to matched controls from the 2019 general population, especially for pulmonary embolism (HR 12.86; 95% CI: 11.23 - 14.74). Outcome rates were more similar when comparing patients discharged with COVID-19 to those discharged with pneumonia in 2019, although COVID-19 patients had increased risk of type 2 diabetes (HR 1.23; 95% CI: 1.05 - 1.44). <h4>Interpretation</h4> Cardiometabolic and pulmonary adverse outcomes are markedly raised following hospitalisation for COVID-19 compared to the general population. However, the excess risks were more comparable to those seen following hospitalisation with pneumonia. Identifying patients at particularly high risk of outcomes would inform targeted preventive measures. <h4>Funding</h4> Wellcome, Royal Society, National Institute for Health Research, National Institute for Health Research Oxford Biomedical Research Centre, UK Medical Research Council, UK Research and Innovation, Health and Safety Executive.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2021/04/13/2021.01.22.21250304.full.pdf; doi:https://doi.org/10.1101/2021.01.22.21250304; html:https://europepmc.org/article/PPR/PPR272966; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR272966&type=FILE&fileName=EMS114490-pdf.pdf&mimeType=application/pdf
 PPR235017,https://doi.org/10.1101/2020.11.05.20223289,Longitudinal proteomic profiling of dialysis patients with COVID-19 reveals markers of severity and predictors of death,"Gisby J, Clarke CL, Medjeral-Thomas N, Malik TH, Papadaki A, Mortimer PM, Buang NB, Lewis S, Pereira M, Toulza F, Fagnano E, Mawhin M, Dutton EE, Tapeng L, Richard AC, Kirk PDW, Behmoaras J, Sandhu E, McAdoo SP, Prendecki MF, Pickering MC, Botto M, Willicombe M, Thomas DC, Peters JE.",,No Journal Info,2020,2020-11-06,Y,,,,"End-stage kidney disease (ESKD) patients are at high risk of severe COVID-19. We measured 436 circulating proteins in serial blood samples from hospitalised and non-hospitalised ESKD patients with COVID-19 (n=256 samples from 55 patients). Comparison to 51 non-infected patients revealed 221 differentially expressed proteins, with consistent results in a separate subcohort of 46 COVID-19 patients. 203 proteins were associated with clinical severity, including IL6, markers of monocyte recruitment (e.g. CCL2, CCL7), neutrophil activation (e.g. proteinase-3) and epithelial injury (e.g. KRT19). Machine learning identified predictors of severity including IL18BP, CTSD, GDF15, and KRT19. Survival analysis with joint models revealed 69 predictors of death. Longitudinal modelling with linear mixed models uncovered 32 proteins displaying different temporal profiles in severe versus non-severe disease, including integrins and adhesion molecules. These data implicate epithelial damage, innate immune activation, and leucocyte-endothelial interactions in the pathology of severe COVID-19 and provide a resource for identifying drug targets.",,doi:https://doi.org/10.7554/elife.64827; doi:https://doi.org/10.1101/2020.11.05.20223289; html:https://europepmc.org/article/PPR/PPR235017; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR235017&type=FILE&fileName=EMS103818-pdf.pdf&mimeType=application/pdf
@@ -354,18 +354,18 @@ PPR300650,https://doi.org/10.1101/2021.03.17.21253853,"Modelling the impact of r
 PPR256751,https://doi.org/10.1101/2020.12.10.20245944,"Azithromycin in Hospitalised Patients with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial","Horby PW, Roddick A, Spata E, Staplin N, Emberson JR, Pessoa-Amorim G, Peto L, Campbell M, Brightling C, Prudon B, Chadwick D, Ustianowski A, Ashish A, Todd S, Yates B, Buttery R, Scott S, Maseda D, Baillie JK, Buch MH, Chappell LC, Day JN, Faust SN, Jaki T, Jeffery K, Juszczak E, Lim WS, Montgomery A, Mumford A, Rowan K, Thwaites G, Mafham M, Haynes R, Landray MJ, RECOVERY Collaborative Group.",,No Journal Info,2020,2020-12-14,Y,,,,"<h4>SUMMARY</h4> <h4>Background</h4> Azithromycin has been proposed as a treatment for COVID-19 on the basis of its immunomodulatory actions. We evaluated the efficacy and safety of azithromycin in hospitalised patients with COVID-19. <h4>Methods</h4> In this randomised, controlled, open-label, adaptive platform trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19 in the UK. Eligible and consenting patients were randomly allocated to either usual standard of care alone or usual standard of care plus azithromycin 500 mg once daily by mouth or intravenously for 10 days or until discharge (or one of the other treatment arms). Patients were twice as likely to be randomised to usual care as to any of the active treatment groups. The primary outcome was 28-day mortality. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov ( NCT04381936 ). <h4>Findings</h4> Between 7 April and 27 November 2020, 2582 patients were randomly allocated to receive azithromycin and 5182 patients to receive usual care alone. Overall, 496 (19%) patients allocated to azithromycin and 997 (19%) patients allocated to usual care died within 28 days (rate ratio 1·00; 95% confidence interval [CI] 0·90-1·12; p=0·99). Consistent results were seen in all pre-specified subgroups of patients. There was no difference in duration of hospitalisation (median 12 days vs. 13 days) or the proportion of patients discharged from hospital alive within 28 days (60% vs. 59%; rate ratio 1·03; 95% CI 0·97-1·10; p=0·29). Among those not on invasive mechanical ventilation at baseline, there was no difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (21% vs. 22%; risk ratio 0·97; 95% CI 0·89-1·07; p=0·54). <h4>Interpretation</h4> In patients hospitalised with COVID-19, azithromycin did not provide any clinical benefit. Azithromycin use in patients hospitalised with COVID-19 should be restricted to patients where there is a clear antimicrobial indication. <h4>Funding</h4> UK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056).",,doi:https://doi.org/10.1101/2020.12.10.20245944; doi:https://doi.org/10.1101/2020.12.10.20245944; html:https://europepmc.org/article/PPR/PPR256751; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR256751&type=FILE&fileName=EMS109114-pdf.pdf&mimeType=application/pdf
 PPR158572,https://doi.org/10.1101/2020.04.30.20084780,COVID-19 length of hospital stay: a systematic review and data synthesis,"Rees EM, Nightingale ES, Jafari Y, Waterlow N, Clifford S, Pearson CAB, CMMID Working Group, Jombert T, Procter SR, Knight GM.",,No Journal Info,2020,2020-05-05,Y,,,,"<h4>Background: </h4> The COVID-19 pandemic has placed an unprecedented strain on health systems, with rapidly increasing demand for healthcare in hospitals and intensive care units (ICUs) worldwide. As the pandemic escalates, determining the resulting needs for healthcare resources (beds, staff, equipment) has become a key priority for many countries. Projecting future demand requires estimates of how long patients with COVID-19 need different levels of hospital care.  Methods We performed a systematic review to gather data on length of stay (LoS) of patients with COVID-19 in hospital and in ICU. We subsequently developed a method to generate LoS distributions which combines summary statistics reported in multiple studies, accounting for differences in sample sizes. Applying this approach we provide distributions for general hospital and ICU LoS from studies in China and elsewhere, for use by the community.  Results We identified 52 studies, the majority from China (46/52). Median hospital LoS ranged from 4 to 53 days within China, and 4 to 21 days outside of China, across 45 studies. ICU LoS was reported by eight studies - four each within and outside China - with median values ranging from 6 to 12 and 4 to 19 days, respectively. Our summary distributions have a median hospital LoS of 14 (IQR: 10-19) days for China, compared with 5 (IQR: 3-9) days outside of China. For ICU, the summary distributions are more similar (median (IQR) of 8 (5-13) days for China and 7 (4-11) days outside of China). There was a visible difference by discharge status, with patients who were discharged alive having longer LoS than those who died during their admission, but no trend associated with study date. Conclusion Patients with COVID-19 in China appeared to remain in hospital for longer than elsewhere. This may be explained by differences in criteria for admission and discharge between countries, and different timing within the pandemic. In the absence of local data, the combined summary LoS distributions provided here can be used to model bed demands for contingency planning and then updated, with the novel method presented here, as more studies with aggregated statistics emerge outside China.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-020-01726-3; doi:https://doi.org/10.1101/2020.04.30.20084780; html:https://europepmc.org/article/PPR/PPR158572; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR158572&type=FILE&fileName=EMS91902-pdf.pdf&mimeType=application/pdf
 PPR676615,https://doi.org/10.1101/2023.06.14.23291389,"Cohort Profile: Born in Wales - a birth cohort with maternity, parental, and child data linkage for life course research in Wales, UK","Jones H, Seaborne M, Kennedy N, James M, Dredge S, Bandyopadhyay A, Battaglia A, Davies S, Brophy S.",,No Journal Info,2023,2023-06-15,Y,,,,"<h4>Purpose</h4> Parental and neonatal child health and education records have been linked to provide an entire country birth cohort, to examine what will improve the health and wellbeing of families growing up in Wales. Established in 2020, Born in Wales utilised data linkage techniques to connect information from the 2011 census with health, social care, and education routine data in the Secure Anonymised Information Linkage (SAIL) Databank. We present the descriptive data available in the linked database, emphasise the robust data security and governance frameworks, and present the future expansion plans for the database beyond its initial development stage. <h4>Participants</h4> Descriptive information from 2011 to 2023 has been gathered from SAIL. This comprehensive dataset comprises over 400,000 child electronic records. To augment this data, the Born in Wales and primary school surveys have contributed quantitative and qualitative responses. <h4>Findings to date</h4> The cohort comprises all children born in Wales since 2011, with follow-up conducted until they finish primary school at age 11. 2,500 parents and 30,000 primary school children have been recruited for enhanced data collection and linkage to the data spine. The child cohort is 51%: 49% female: male, and 6% are from ethnic minority backgrounds. When considering age distribution, 26.8% of children are under the age of 5, while 63.2% fall within the age range of 5-11. <h4>Future plans</h4> Born in Wales will expand by 30,000 new births annually in Wales, while including follow-up data of children and parents already in the database. Supplementary datasets complement the existing linkage, including primary care, hospital data, educational attainment and social care. Future research includes exploring the long-term implications of COVID-19 on child health and development, the influence of environmental factors including climate change on health and examining the impact of parental work environment on child health and development. <h4>Strengths and limitations of this study</h4> Born in Wales has established a comprehensive, Wales-wide population-based database which consolidates clinical data from maternity, neonatal, child health, and education records. This national-scale database is supplemented by quantitative and qualitative results from surveys conducted by Born in Wales, providing rich insights into details that cannot be obtained through routinely collected data. The existence of this database enables further data linkage, facilitating life course research on the health and wellbeing of the Wales population. Missing data or errors in routine and administrative data may be constraint. A potential restriction of Born in Wales is the loss of data pertaining to individuals who relocate outside of Wales during pregnancy or after the child’s birth.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2023/06/15/2023.06.14.23291389.full.pdf; doi:https://doi.org/10.1101/2023.06.14.23291389; html:https://europepmc.org/article/PPR/PPR676615; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR676615&type=FILE&fileName=EMS177701-pdf.pdf&mimeType=application/pdf
-PPR447330,https://doi.org/10.1101/2022.01.19.22268871,Cohort Profile: The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers (UK-REACH),"Bryant L, Free RC, Woolf K, Melbourne C, Guyatt AL, John C, Gupta A, Gray LJ, Nellums L, Martin CA, McManus IC, Garwood C, Modhawdia V, Carr S, Wain LV, Tobin MD, Khunti K, Akubakar I, Pareek M.",,No Journal Info,2022,2022-01-27,Y,,,,"Key Features of the UK-REACH Cohort (Profile in a nutshell) The UK-REACH Cohort was established to understand why ethnic minority healthcare workers (HCWs) are at risk of poorer outcomes from COVID-19 when compared to their white ethnic counterparts in the United Kingdom (UK). Through study design, it contains a uniquely high percentage of participants from ethnic minority backgrounds about whom a wide range of qualitative and quantitative data has been collected. A total of 17891 HCWs aged 16-89 years (mean age: 44) have been recruited from across the UK via all major healthcare regulators, individual National Health Service (NHS) hospital trusts and UK HCW membership bodies who advertised the study to their registrants/staff to encourage participation in the study. Data available include linked healthcare records for 25 years from the date of consent and consent to obtain genomic sequencing data collected via saliva. Online questionnaires include information on demographics, COVID-19 exposures at work and home, redeployment in the workforce due to COVID-19, mental health measures, workforce attrition, and opinions on COVID-19 vaccines, with baseline (n=15 119), 6 (n=5632) and 12-month follow-up data captured. Request data access and collaborations by following documentation found at https://www.uk-reach.org/main/data_sharing .",,pdf:https://discovery.ucl.ac.uk/id/eprint/10154879/1/dyac171.pdf; doi:https://doi.org/10.1101/2022.01.19.22268871; html:https://europepmc.org/article/PPR/PPR447330; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR447330&type=FILE&fileName=EMS142772-pdf.pdf&mimeType=application/pdf
 PPR157903,https://doi.org/10.1101/2020.04.28.20082222,"Risk prediction for poor outcome and death in hospital in-patients with COVID-19: derivation in Wuhan, China and external validation in London, UK","Zhang H, Shi T, Wu X, Zhang X, Wang K, Bean D, Dobson R, Teo JT, Sun J, Zhao P, Li C, Dhaliwal K, Wu H, Li Q, Guthrie B.",,No Journal Info,2020,2020-05-03,Y,,,,"<h4>Background</h4> Accurate risk prediction of clinical outcome would usefully inform clinical decisions and intervention targeting in COVID-19. The aim of this study was to derive and validate risk prediction models for poor outcome and death in adult inpatients with COVID-19. <h4>Methods</h4> Model derivation using data from Wuhan, China used logistic regression with death and poor outcome (death or severe disease) as outcomes. Predictors were demographic, comorbidity, symptom and laboratory test variables. The best performing models were externally validated in data from London, UK. <h4>Findings</h4> 4.3% of the derivation cohort (n=775) died and 9.7% had a poor outcome, compared to 34.1% and 42.9% of the validation cohort (n=226). In derivation, prediction models based on age, sex, neutrophil count, lymphocyte count, platelet count, C-reactive protein and creatinine had excellent discrimination (death c-index=0.91, poor outcome c-index=0.88), with good-to-excellent calibration. Using two cut-offs to define low, high and very-high risk groups, derivation patients were stratified in groups with observed death rates of 0.34%, 15.0% and 28.3% and poor outcome rates 0.63%, 8.9% and 58.5%. External validation discrimination was good (c-index death=0.74, poor outcome=0.72) as was calibration. However, observed rates of death were 16.5%, 42.9% and 58.4% and poor outcome 26.3%, 28.4% and 64.8% in predicted low, high and very-high risk groups. <h4>Interpretation</h4> Our prediction model using demography and routinely-available laboratory tests performed very well in internal validation in the lower-risk derivation population, but less well in the much higher-risk external validation population. Further external validation is needed. Collaboration to create larger derivation datasets, and to rapidly externally validate all proposed prediction models in a range of populations is needed, before routine implementation of any risk prediction tool in clinical care. <h4>Funding</h4> MRC, Wellcome Trust, HDR-UK, LifeArc, participating hospitals, NNSFC, National Key R&D Program, Pudong Health and Family Planning Commission <h4>Research in context</h4> <h4>Evidence before this study</h4> Several prognostic models for predicting mortality risk, progression to severe disease, or length of hospital stay in COVID-19 have been published. 1 Commonly reported predictors of severe prognosis in patients with COVID-19 include age, sex, computed tomography scan features, C-reactive protein (CRP), lactic dehydrogenase, and lymphocyte count. Symptoms (notably dyspnoea) and comorbidities (e.g. chronic lung disease, cardiovascular disease and hypertension) are also reported to have associations with poor prognosis. 2 However, most studies have not described the study population or intended use of prediction models, and external validation is rare and to date done using datasets originating from different Wuhan hospitals. 3 Given different patterns of testing and organisation of healthcare pathways, external validation in datasets from other countries is required. <h4>Added value of this study</h4> This study used data from Wuhan, China to derive and internally validate multivariable models to predict poor outcome and death in COVID-19 patients after hospital admission, with external validation using data from King’s College Hospital, London, UK. Mortality and poor outcome occurred in 4.3% and 9.7% of patients in Wuhan, compared to 34.1% and 42.9% of patients in London. Models based on age, sex and simple routinely available laboratory tests (lymphocyte count, neutrophil count, platelet count, CRP and creatinine) had good discrimination and calibration in internal validation, but performed only moderately well in external validation. Models based on age, sex, symptoms and comorbidity were adequate in internal validation for poor outcome (ICU admission or death) but had poor performance for death alone. <h4>Implications of all the available evidence</h4> This study and others find that relatively simple risk prediction models using demographic, clinical and laboratory data perform well in internal validation but at best moderately in external validation, either because derivation and external validation populations are small (Xie et al 3 ) and/or because they vary greatly in casemix and severity (our study). There are three decision points where risk prediction may be most useful: (1) deciding who to test; (2) deciding which patients in the community are at high-risk of poor outcomes; and (3) identifying patients at high-risk at the point of hospital admission. Larger studies focusing on particular decision points, with rapid external validation in multiple datasets are needed. A key gap is risk prediction tools for use in community triage (decisions to admit, or to keep at home with varying intensities of follow-up including telemonitoring) or in low income settings where laboratory tests may not be routinely available at the point of decision-making. This requires systematic data collection in community and low-income settings to derive and evaluate appropriate models.","The paper utilises a model created on Wuhan data to identify outcomes. The model was validated on London data but this population was higher risk, so was not very comparable. The model obtained a good prediction on lower risk internal validation.",pdf:https://www.medrxiv.org/content/medrxiv/early/2020/05/03/2020.04.28.20082222.full.pdf; doi:https://doi.org/10.1101/2020.04.28.20082222; html:https://europepmc.org/article/PPR/PPR157903; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR157903&type=FILE&fileName=EMS92242-pdf.pdf&mimeType=application/pdf
+PPR447330,https://doi.org/10.1101/2022.01.19.22268871,Cohort Profile: The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers (UK-REACH),"Bryant L, Free RC, Woolf K, Melbourne C, Guyatt AL, John C, Gupta A, Gray LJ, Nellums L, Martin CA, McManus IC, Garwood C, Modhawdia V, Carr S, Wain LV, Tobin MD, Khunti K, Akubakar I, Pareek M.",,No Journal Info,2022,2022-01-27,Y,,,,"Key Features of the UK-REACH Cohort (Profile in a nutshell) The UK-REACH Cohort was established to understand why ethnic minority healthcare workers (HCWs) are at risk of poorer outcomes from COVID-19 when compared to their white ethnic counterparts in the United Kingdom (UK). Through study design, it contains a uniquely high percentage of participants from ethnic minority backgrounds about whom a wide range of qualitative and quantitative data has been collected. A total of 17891 HCWs aged 16-89 years (mean age: 44) have been recruited from across the UK via all major healthcare regulators, individual National Health Service (NHS) hospital trusts and UK HCW membership bodies who advertised the study to their registrants/staff to encourage participation in the study. Data available include linked healthcare records for 25 years from the date of consent and consent to obtain genomic sequencing data collected via saliva. Online questionnaires include information on demographics, COVID-19 exposures at work and home, redeployment in the workforce due to COVID-19, mental health measures, workforce attrition, and opinions on COVID-19 vaccines, with baseline (n=15 119), 6 (n=5632) and 12-month follow-up data captured. Request data access and collaborations by following documentation found at https://www.uk-reach.org/main/data_sharing .",,pdf:https://discovery.ucl.ac.uk/id/eprint/10154879/1/dyac171.pdf; doi:https://doi.org/10.1101/2022.01.19.22268871; html:https://europepmc.org/article/PPR/PPR447330; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR447330&type=FILE&fileName=EMS142772-pdf.pdf&mimeType=application/pdf
 PPR387586,https://doi.org/10.1101/2021.08.23.21262209,Population birth outcomes in 2020 and experiences of expectant mothers during the COVID-19 pandemic: a ‘Born in Wales’ mixed methods study using routine data,"Jones H, Seaborne M, Cowley L, Odd D, Paranjothy S, Akbari A, Brophy S.",,No Journal Info,2021,2021-08-23,Y,,,,"<h4>Background</h4> Pregnancy can be a stressful time and the COVID-19 pandemic has affected all aspects of life. This study aims to investigate the impact of the pandemic on population birth outcomes in Wales, rates of primary immunisations and examine expectant mothers’ experiences of pregnancy including self-reported levels of stress and anxiety. <h4>Methods</h4> Population-level birth outcomes in Wales: Stillbirths, prematurity, birth weight and Caesarean section births before (2016–2019) and during (2020) the pandemic were compared using national-level routine anonymised data held in the Secure Anonymised Information Linkage (SAIL) Databank. The first three scheduled primary immunisations were compared between 2019 and 2020. Self-reported pregnancy experience: 215 expectant mothers (aged 16+) in Wales completed an online survey about their experiences of pregnancy during the pandemic. The qualitative survey data was analysed using codebook thematic analysis. <h4>Findings</h4> There was no significant difference between annual outcomes including gestation and birth weight, stillbirths, and Caesarean sections for infants born in 2020 compared to 2016-2019. There was an increase in late term births (≥42 weeks gestation) during the first lockdown (OR: 1.28, p=0.019) and a decrease in moderate to late preterm births (32-36 weeks gestation) during the second lockdown (OR: 0.74, p=0.001). Fewer babies were born in 2020 (N=29,031) compared to 2016-2019 (average N=32,582). All babies received their immunisations in 2020, but there were minor delays in the timings of vaccines. Those due at 8-weeks were 8% less likely to be on time (within 28-days) and at 16-weeks, they were 19% less likely to be on time. The pandemic had a negative impact on the mental health of 71% of survey respondents, who reported anxiety, stress and loneliness; this was associated with attending scans without their partner, giving birth alone, and minimal contact with midwives. <h4>Interpretation</h4> The pandemic had a negative impact on mothers’ experiences of pregnancy; however, population-level data suggests that this did not translate to adverse birth outcomes for babies born during the pandemic.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0267176&type=printable; doi:https://doi.org/10.1101/2021.08.23.21262209; html:https://europepmc.org/article/PPR/PPR387586; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR387586&type=FILE&fileName=EMS134441-pdf.pdf&mimeType=application/pdf
 PPR494479,https://doi.org/10.1101/2022.04.22.22274176,Association between household composition and severe COVID-19 outcomes in older people by ethnicity: an observational cohort study using the OpenSAFELY platform,"Wing K, Grint DJ, Mathur R, Gibbs HP, Hickman G, Nightingale E, Schultze A, Forbes H, Nafilyan V, Bhaskaran K, Williamson E, House T, Pellis L, Herrett E, Gautam N, Curtis HJ, Rentsch CT, Wong AY, MacKenna B, Mehrkar A, Bacon S, Douglas IJ, Evans SJ, Tomlinson L, Goldacre B, Eggo RM.",,No Journal Info,2022,2022-04-22,Y,,,,"Ethnic differences in the risk of severe COVID-19 may be linked to household composition. We quantified the association between household composition and risk of severe COVID-19 by ethnicity for older individuals. With the approval of NHS England, we analysed ethnic differences in the association between household composition and severe COVID-19 in people aged 67 or over in England. We defined households by number of generations living together, and used multivariable Cox regression stratified by location and wave of the pandemic and accounted for age, sex, comorbidities, smoking, obesity, housing density and deprivation. We included 2 692 223 people over 67 years in wave 1 (01/02/2020-31/08/2020) and 2 731 427 in wave 2 (01/09/2020-31/01/2021). Multigenerational living was associated with increased risk of severe COVID-19 for White and South Asian older people in both waves (e.g. wave 2, 67+ living with 3 other generations vs 67+ year olds only: White HR 1·61 95% CI 1·38-1·87, South Asian HR 1·76 95% CI 1·48-2·10), with a trend for increased risks of severe COVID-19 with increasing generations in wave 2. Multigenerational living was associated with severe COVID-19 in older adults. Older South Asian people are over-represented within multigenerational households in England, especially in the most deprived settings. The number of generations in a household, number of occupants, ethnicity and deprivation status are important considerations in the continued roll-out of COVID-19 vaccination and targeting of interventions for future pandemics. <h4>Funding</h4> This research was funded in part, by the Wellcome Trust. For the purpose of open access, the author has applied a CC-BY public copyright licence to any Author Accepted Manuscript version arising from this submission.",,pdf:https://academic.oup.com/ije/article-pdf/51/6/1745/47882630/dyac158.pdf; doi:https://doi.org/10.1101/2022.04.22.22274176; html:https://europepmc.org/article/PPR/PPR494479; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR494479&type=FILE&fileName=EMS149524-pdf.pdf&mimeType=application/pdf
-PPR556407,https://doi.org/10.1101/2022.10.07.22280819,A Multi-Granular Stacked Regression for Forecasting Long-Term Demand in Emergency Departments,"James C, Wood R, Denholm R.",,No Journal Info,2022,2022-10-10,Y,,,,"<h4>Background</h4> In the United Kingdom, Emergency Departments (EDs) are under significant pressure due to an ever-increasing number of attendances. Understanding how the capacity of other urgent care services and the health of a population may influence ED attendances is imperative for commissioners and policy makers to develop long-term strategies for reducing this pressure and improving quality and safety. <h4>Methods</h4> We developed a novel Multi-Granular Stacked Regression (MGSR) model using publicly available data to predict future mean monthly ED attendances within Clinical Commissioning Group regions in England. The MGSR combines measures of population health and health service capacity in other related settings. We assessed model performance using the R-squared statistic, measuring variance explained, and the Mean Absolute Percentage Error (MAPE), measuring forecasting accuracy. We used the MGSR to forecast ED demand over a 4-year period under hypothetical scenarios where service capacity is increased, or population health is improved. <h4>Results</h4> Measures of service capacity explain 41 ± 4% of the variance in monthly ED attendances and measures of population health explain 61 ± 25%. The MGSR leads to an overall improvement in performance, with an R-squared of 0.75 ± 0.03 and MAPE of 4% when forecasting mean monthly ED attendances per CCG. Using the MGSR to forecast long-term demand under different scenarios, we found improving population health would reduce peak ED attendances per CCG by approximately 600 per month after 2 years. <h4>Conclusions</h4> Combining models of population health and wider urgent care service capacity for predicting monthly ED attendances leads to an improved performance compared to each model individually. Policies designed to improve population health will reduce ED attendances and enhance quality and safety in the long-term.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/10/10/2022.10.07.22280819.full.pdf; doi:https://doi.org/10.1101/2022.10.07.22280819; html:https://europepmc.org/article/PPR/PPR556407; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR556407&type=FILE&fileName=EMS155538-pdf.pdf&mimeType=application/pdf
 PPR721144,https://doi.org/10.1101/2023.09.04.23295015,Combinations of multiple long-term conditions and risk of hospitalisation and death during the winter season: population-based study of 48 million people in England,"Islam N, Shabnam S, Khan N, Gillies C, Zaccardi F, Banerjee A, Nafilyan V, Khunti K, Dambha-Miller H.",,No Journal Info,2023,2023-09-06,Y,,,,"<h4>Background</h4> The annual winter season poses substantial challenges to the National Health Service (NHS) in England. Hospitalisation and mortality increase during winter, especially in people with multiple long-term conditions (MLTC or multimorbidity). We aimed to describe which combinations of long-term conditions (LTC) are associated with a higher risk of hospitalisation and death during winter amongst adults in England. <h4>Methods</h4> In this population-based study, we used linked primary and secondary care data from the General Practice Extraction Service Data for Pandemic Planning (GDPPR) database, Hospital Episode Statistics, and Office for National Statistics death registry. We included individuals aged ≥18 years and alive on 1 st December 2021 and used overdispersed Poisson models to estimate the incidence rate ratios of all-cause hospitalisations and deaths associated with the combinations of MLTCs – compared to those with no LTC – during the winter season (1 December 2021 to 31 March 2022). <h4>Findings</h4> Complete data were available for 48,253,125 adults, of which 15 million (31.2%) had MLTC. Hospitalisation per 1000 person-years was higher in individuals with MLTCs, and varied by combination, e.g.: 96, 1643, and 1552 in individuals with no LTC, cancer+chronic kidney disease (CKD)+cardiovascular disease (CVD)+type 2 diabetes mellitus, and cancer+CKD+CVD+osteoarthritis, respectively. Incidence of death (per 1000 person-years) was 345 in individuals with cancer+CKD+CVD+dementia and 1 with no LTC. CVD+dementia appeared in all the top five MLTC combinations by death and was associated with a substantially higher rate of death than many 3-, 4- and 5-disease combinations. <h4>Interpretation</h4> Risks of hospitalisation and death vary by combinations of MLTCs and are substantially higher in those with vs. without any LTCs. We have highlighted high-risk combinations for prioritisation and preventive action by policymakers to help manage the challenges imposed by winter pressures on the NHS. <h4>Funding</h4> National Institute for Health and Care Research (NIHR) through Health Data Research UK rapid funding call for the research activity “Data Science to inform NHS compound winter pressure policy response” (grant number: HDRUK2022.0313) <h4>Research in context</h4> <h4>Evidence before this study</h4> We searched PubMed, from inception to April 2023, for published population-based studies examining MLTC combinations in cohorts of adults aged 18 years and over. The search terms were “multimorbidity” or ‘’multiple-long-term conditions’’ alongside “groups” or “combinations”. We found no previous studies examining MLTC in relation to death or hospitalisation during the winter season. <h4>Added value of this study</h4> We have identified distinct combinations of LTCs and estimated the associated risk of hospitalisation and deaths during the winter season using the whole-population primary and secondary care data in England. <h4>Implications of all the available evidence</h4> Understanding which combinations of MLTCs are associated with the highest risk of hospitalisation and death allows clinicians and policymakers to prioritise resources for preventative measures, such as vaccination to those that will benefit most during winter seasons.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2023/09/06/2023.09.04.23295015.full.pdf; doi:https://doi.org/10.1101/2023.09.04.23295015; html:https://europepmc.org/article/PPR/PPR721144; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR721144&type=FILE&fileName=EMS187607-pdf.pdf&mimeType=application/pdf
+PPR556407,https://doi.org/10.1101/2022.10.07.22280819,A Multi-Granular Stacked Regression for Forecasting Long-Term Demand in Emergency Departments,"James C, Wood R, Denholm R.",,No Journal Info,2022,2022-10-10,Y,,,,"<h4>Background</h4> In the United Kingdom, Emergency Departments (EDs) are under significant pressure due to an ever-increasing number of attendances. Understanding how the capacity of other urgent care services and the health of a population may influence ED attendances is imperative for commissioners and policy makers to develop long-term strategies for reducing this pressure and improving quality and safety. <h4>Methods</h4> We developed a novel Multi-Granular Stacked Regression (MGSR) model using publicly available data to predict future mean monthly ED attendances within Clinical Commissioning Group regions in England. The MGSR combines measures of population health and health service capacity in other related settings. We assessed model performance using the R-squared statistic, measuring variance explained, and the Mean Absolute Percentage Error (MAPE), measuring forecasting accuracy. We used the MGSR to forecast ED demand over a 4-year period under hypothetical scenarios where service capacity is increased, or population health is improved. <h4>Results</h4> Measures of service capacity explain 41 ± 4% of the variance in monthly ED attendances and measures of population health explain 61 ± 25%. The MGSR leads to an overall improvement in performance, with an R-squared of 0.75 ± 0.03 and MAPE of 4% when forecasting mean monthly ED attendances per CCG. Using the MGSR to forecast long-term demand under different scenarios, we found improving population health would reduce peak ED attendances per CCG by approximately 600 per month after 2 years. <h4>Conclusions</h4> Combining models of population health and wider urgent care service capacity for predicting monthly ED attendances leads to an improved performance compared to each model individually. Policies designed to improve population health will reduce ED attendances and enhance quality and safety in the long-term.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/10/10/2022.10.07.22280819.full.pdf; doi:https://doi.org/10.1101/2022.10.07.22280819; html:https://europepmc.org/article/PPR/PPR556407; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR556407&type=FILE&fileName=EMS155538-pdf.pdf&mimeType=application/pdf
 PPR320203,https://doi.org/10.21203/rs.3.rs-438237/v1,COVID-19-related acute kidney injury; temporal changes in incidence rate and outcomes in a large UK cohort,"Jewell PD, Bramham K, Galloway J, Post F, Norton S, Teo J, Fisher R, Saha R, Hutchings S, Hopkins P, Smith P, Joslin J, Jayawardene S, Mackie S, Mudhaffer A, Holloway A, Kibble H, Akter M, Zuckerman B, Palmer K, Murphy C, Iatropoulou D, Sharpe CC, Lioudaki E.",,No Journal Info,2021,2021-04-30,Y,,,,"<h4>Background: </h4> Acute kidney injury (AKI) is common among patients hospitalised with COVID-19, and associated with worse prognosis. The aim of this study was to investigate the epidemiology, risk factors and outcomes of AKI in patients with COVID-19 in a large UK tertiary centre. <h4>Methods: </h4>: We analysed data of consecutive adults admitted with a laboratory-confirmed diagnosis of COVID-19 across two sites of a hospital in London, UK, from 1st January to 13th May 2020. <h4>Results: </h4> Of the 1248 inpatients included, 487 (39%) experienced AKI (51% stage 1, 13% stage 2,and 36% stage 3). The weekly AKI incidence rate gradually increased to peak at week 5 (3.12 cases/100 patient-days), before reducing to its nadir (0.83 cases/100 patient-days) at the end the study period (week 10). Among AKI survivors, 84.0% had recovered renal function to pre-admission levels before discharge and none required on-going renal replacement therapy (RRT). Pre-existing renal impairment [odds ratio (OR) 3.05, 95%CI 2.24-4,18; p<0.0001], and inpatient diuretic use (OR 1.79, 95%CI 1.27-2.53; p<0.005) were independently associated with a higher risk for AKI. AKI was a strong predictor of 30-day mortality with an increasing risk across AKI stages [adjusted hazard ratio (HR) 1.59 (95%CI 1.19-2.13) for stage 1; p<0.005, 2.71(95%CI 1.82-4.05); p<0.001for stage 2 and 2.99 (95%CI 2.17-4.11); p<0.001for stage 3]. One third of AKI3 survivors (30.7%), had newly established renal impairment at 3 to 6 months. <h4>Conclusions: </h4>: This large UK cohort demonstrated a high AKI incidence with a changing pattern over time and was associated with increased mortality even at stage 1. Inpatient diuretic use was linked to a higher AKI risk. One third of survivors with AKI3 exhibited newly established renal impairment already at 3-6 months.",,pdf:https://www.researchsquare.com/article/rs-438237/latest.pdf; doi:https://doi.org/10.21203/rs.3.rs-438237/v1; html:https://europepmc.org/article/PPR/PPR320203; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR320203&type=FILE&fileName=EMS123857-pdf.pdf&mimeType=application/pdf
 PPR174275,https://doi.org/10.1101/2020.06.10.20127175,Excess deaths in people with cardiovascular diseases during the COVID-19 pandemic,"Banerjee A, Chen S, Pasea L, Lai AG, Katsoulis M, Denaxas S, Nafilyan V, Williams B, Wong WK, Bakhai A, Khunti K, Pillay D, Noursadeghi M, Wu H, Pareek N, Bromage D, McDonagh TA, Byrne J, Teo JT, Shah AM, Humberstone B, Tang LV, Shah ASV, Rubboli A, Guo Y, Hu Y, Sudlow CLM, Lip GYH, Hemingway H.",,No Journal Info,2020,2020-06-11,N,,,,"<h4>Background</h4> Cardiovascular diseases(CVD) increase mortality risk from coronavirus infection(COVID-19), but there are concerns that the pandemic has affected supply and demand of acute cardiovascular care. We estimated excess mortality in specific CVDs, both “direct”, through infection, and “indirect”, through changes in healthcare. <h4>Methods</h4> We used population-based electronic health records from 3,862,012 individuals in England to estimate pre- and post-COVID-19 mortality risk(“direct” effect) for people with incident and prevalent CVD. We incorporated: (i)pre-COVID-19 risk by age, sex and comorbidities, (ii)estimated population COVID-19 prevalence, and (iii)estimated relative impact of COVID-19 on mortality(relative risk, RR: 1.5, 2.0 and 3.0). For “indirect” effects, we analysed weekly mortality and emergency department data for England/Wales and monthly hospital data from England(n=2), China(n=5) and Italy(n=1) for CVD referral, diagnosis and treatment until 1 May 2020. <h4>Findings</h4> CVD service activity decreased by 60-100% compared with pre-pandemic levels in eight hospitals across China, Italy and England during the pandemic. In China, activity remained below pre-COVID-19 levels for 2-3 months even after easing lockdown, and is still reduced in Italy and England. Mortality data suggest indirect effects on CVD will be delayed rather than contemporaneous(peak RR 1.4). For total CVD(incident and prevalent), at 10% population COVID-19 rate, we estimated direct impact of 31,205 and 62,410 excess deaths in England at RR 1.5 and 2.0 respectively, and indirect effect of 49932 to 99865 excess deaths. <h4>Interpretation</h4> Supply and demand for CVD services have dramatically reduced across countries with potential for substantial, but avoidable, excess mortality during and after the COVID-19 pandemic. <h4>Funding</h4> NIHR, HDR UK, Astra Zeneca",,pdf:https://academic.oup.com/eurjpc/article-pdf/28/14/1599/41827245/zwaa155.pdf; doi:https://doi.org/10.1101/2020.06.10.20127175; html:https://europepmc.org/article/PPR/PPR174275; doi:https://doi.org/10.1101/2020.06.10.20127175
-PPR670288,https://doi.org/10.1101/2023.05.31.23290774,POST-COVID ORTHOPAEDIC ELECTIVE RESOURCE PLANNING USING SIMULATION MODELLING,"Harper A, Monks T, Wilson R, Redaniel MT, Eyles E, Jones T, Penfold C, Elliott A, Keen T, Pitt M, Blom A, Whitehouse M, Judge A.",,No Journal Info,2023,2023-06-05,Y,,,,"<h4>ABSTRACT</h4> <h4>Objectives</h4> To develop a simulation model to support orthopaedic elective capacity planning. <h4>Methods</h4> An open-source, generalisable discrete-event simulation was developed, including a web-based application. The model used anonymised patient records between 2016-2019 of elective orthopaedic procedures from an NHS Trust in England. In this paper, it is used to investigate scenarios including resourcing (beds and theatres) and productivity (lengths-of-stay, delayed discharges, theatre activity) to support planning for meeting new NHS targets aimed at reducing elective orthopaedic surgical backlogs in a proposed ring fenced orthopaedic surgical facility. The simulation is interactive and intended for use by health service planners and clinicians. <h4>Results</h4> A higher number of beds (65-70) than the proposed number (40 beds) will be required if lengths-of-stay and delayed discharge rates remain unchanged. Reducing lengths-of-stay in line with national benchmarks reduces bed utilisation to an estimated 60%, allowing for additional theatre activity such as weekend working. Further, reducing the proportion of patients with a delayed discharge by 75% reduces bed utilisation to below 40%, even with weekend working. A range of other scenarios can also be investigated directly by NHS planners using the interactive web app. <h4>Conclusions</h4> The simulation model is intended to support capacity planning of orthopaedic elective services by identifying a balance of capacity across theatres and beds and predicting the impact of productivity measures on capacity requirements. It is applicable beyond the study site and can be adapted for other specialties. <h4>Strengths and Limitations of this study</h4> The simulation model provides rapid quantitative estimates to support post-COVID elective services recovery toward medium-term elective targets. Parameter combinations include changes to both resourcing and productivity. The interactive web app enables intuitive parameter changes by users while underlying source code can be adapted or re-used for similar applications. Patient attributes such as complexity are not included in the model but are reflected in variables such as length-of-stay and delayed discharge rates. Theatre schedules are simplified, incorporating the five key orthopaedic elective surgical procedures.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2023/06/05/2023.05.31.23290774.full.pdf; doi:https://doi.org/10.1101/2023.05.31.23290774; html:https://europepmc.org/article/PPR/PPR670288; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR670288&type=FILE&fileName=EMS176961-pdf.pdf&mimeType=application/pdf
 PPR425646,https://doi.org/10.1101/2021.11.27.21266930,Dosing interval strategies for two-dose COVID-19 vaccination in 13 low- and middle-income countries of Europe: health impact modelling and benefit-risk analysis,"Liu Y, Pearson CA, Sandmann FG, Barnard RC, Kim J, CMMID COVID-19 Working Group, Flasche S, Jit M, Abbas K.",,No Journal Info,2021,2021-11-28,Y,,,,"<h4>Summary</h4> <h4>Background</h4> In settings where the COVID-19 vaccine supply is constrained, extending the intervals between the first and second doses of the COVID-19 vaccine could let more people receive their first doses earlier. Our aim is to estimate the health impact of COVID-19 vaccination alongside benefit-risk assessment of different dosing intervals for low- and middle-income countries of Europe. <h4>Methods</h4> We fitted a dynamic transmission model to country-level daily reported COVID-19 mortality in 13 low- and middle-income countries in the World Health Organization European Region (Albania, Armenia, Azerbaijan, Belarus, Bosnia and Herzegovina, Bulgaria, Georgia, Republic of Moldova, Russian Federation, Serbia, North Macedonia, Turkey, and Ukraine). A vaccine product with characteristics similar to the Oxford/AstraZeneca COVID-19 (AZD1222) vaccine was used in the base case scenario and was complemented by sensitivity analyses around efficacies related to other COVID-19 vaccines. Both fixed dosing intervals at 4, 8, 12, 16, and 20 weeks and dose-specific intervals that prioritise specific doses for certain age groups were tested. Optimal intervals minimise COVID-19 mortality between March 2021 and December 2022. We incorporated the emergence of variants of concern into the model, and also conducted a benefit-risk assessment to quantify the trade-off between health benefits versus adverse events following immunisation. <h4>Findings</h4> In 12 of the 13 countries, optimal strategies are those that prioritise the first doses among older adults (60+ years) or adults (20-59 years). These strategies lead to dosing intervals longer than six months. In comparison, a four-week fixed dosing interval may incur 10.2% [range: 4.0% - 22.5%; n = 13 (countries)] more deaths. There is generally a negative association between dosing interval and COVID-19 mortality within the range we investigated. Assuming a shorter first dose waning duration of 120 days, as opposed to 360 days in the base case, led to shorter optimal dosing intervals of 8-12 weeks. Benefit-risk ratios were the highest for fixed dosing intervals of 8-12 weeks. <h4>Interpretation</h4> We infer that longer dosing intervals of over six months, which are substantially longer than the current label recommendation for most vaccine products, could reduce COVID-19 mortality in low- and middle-income countries of WHO/Europe. Certain vaccine features, such as fast waning of first doses, significantly shorten the optimal dosing intervals. <h4>Funding</h4> World Health Organization",,doi:https://doi.org/10.1016/j.lanepe.2022.100381; doi:https://doi.org/10.1101/2021.11.27.21266930; html:https://europepmc.org/article/PPR/PPR425646; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR425646&type=FILE&fileName=EMS140311-pdf.pdf&mimeType=application/pdf
-PPR341842,https://doi.org/10.2139/ssrn.3817437,Risk Factors for Developing COVID-19: A Population-Based Longitudinal Study (COVIDENCE UK),"Holt H, Talaei M, Greenig M, Zenner D, Symons J, Relton C, Young KS, Davies MR, Thompson KN, Ashman J, Rajpoot SS, Kayyale AA, Rifai SE, Lloyd PJ, Jolliffe DA, Finer S, Ilidriomiti S, Miners A, Hopkinson NS, Alam B, Pfeffer PE, McCoy D, Davies GA, Lyons RA, Griffiths CJ, Kee F, Sheikh A, Breen G, Shaheen SO, Martineau AR.",,No Journal Info,2021,2021-04-01,N,,,,"Background: Risk factors for severe COVID-19 include older age, male sex, obesity, Black or Asian ethnicity and underlying medical conditions. Whether these factors also influence susceptibility to developing COVID-19 is uncertain.<br><br>Methods: We undertook a prospective, population-based cohort study   (COVIDENCE UK) from 1  st  May 2020 to 5  th  February 2021  . Baseline information on potential risk factors was captured by an online questionnaire. Monthly follow-up questionnaires captured incident COVID-19. We used logistic regression models to estimate multivariable-adjusted odds ratios (aORs) for associations between potential risk factors and risk of COVID-19.<br><br>Findings: We recorded 446 incident cases of COVID-19 in 15,227 participants (2.9%). Increased risk of developing COVID-19 was independently associated with Asian/Asian British  vs  . White ethnicity (aOR 2.31, 95% CI 1.35-3.95), household overcrowding  (aOR per additional 0.5 people/bedroom 1.26, 1.11-1.43)  , any  vs  . no visits to/from other households in previous week (aOR 1.33, 1.07-1.64), number of visits to indoor public places (aOR per extra visit per week 1.05, 1.01-1.09), frontline occupation excluding health/social care  vs.  no frontline occupation (aOR 1.49, 1.12-1.98), and raised body mass index (BMI) (aOR 1.51 [1.20-1.90] for BMI 25.0-30.0 kg/m  2  and 1.38 [1.05-1.82] for BMI >30.0 kg/m  2  vs.  BMI <25.0 kg/m  2  ). Atopic disease was independently associated with decreased risk (aOR 0.76, 0.59-0.98). No independent associations were seen for age, sex, other medical conditions, diet, or micronutrient supplement use.<br><br>Interpretation: After rigorous adjustment for factors influencing exposure to SARS-CoV-2, Asian/Asian British ethnicity and raised BMI were associated with increased risk of developing COVID-19, while atopic disease was associated with decreased risk.<br><br>Trial Registration: It is registered with ClinicalTrials.gov (NCT04330599).<br><br>Funding: Barts Charity, Health Data Research UK<br><br>Declaration of Interest: None to declare. <br><br>Ethical Approval: The study was sponsored by Queen Mary University of London and approved by<br>Leicester South Research Ethics Committee (ref 20/EM/0117).",,pdf:http://pure-oai.bham.ac.uk/ws/files/148236929/holth2021risk.pdf; doi:https://doi.org/10.2139/ssrn.3817437; html:https://europepmc.org/article/PPR/PPR341842; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR341842&type=FILE&fileName=EMS124907-pdf.pdf&mimeType=application/pdf; doi:https://doi.org/10.2139/ssrn.3817437
+PPR670288,https://doi.org/10.1101/2023.05.31.23290774,POST-COVID ORTHOPAEDIC ELECTIVE RESOURCE PLANNING USING SIMULATION MODELLING,"Harper A, Monks T, Wilson R, Redaniel MT, Eyles E, Jones T, Penfold C, Elliott A, Keen T, Pitt M, Blom A, Whitehouse M, Judge A.",,No Journal Info,2023,2023-06-05,Y,,,,"<h4>ABSTRACT</h4> <h4>Objectives</h4> To develop a simulation model to support orthopaedic elective capacity planning. <h4>Methods</h4> An open-source, generalisable discrete-event simulation was developed, including a web-based application. The model used anonymised patient records between 2016-2019 of elective orthopaedic procedures from an NHS Trust in England. In this paper, it is used to investigate scenarios including resourcing (beds and theatres) and productivity (lengths-of-stay, delayed discharges, theatre activity) to support planning for meeting new NHS targets aimed at reducing elective orthopaedic surgical backlogs in a proposed ring fenced orthopaedic surgical facility. The simulation is interactive and intended for use by health service planners and clinicians. <h4>Results</h4> A higher number of beds (65-70) than the proposed number (40 beds) will be required if lengths-of-stay and delayed discharge rates remain unchanged. Reducing lengths-of-stay in line with national benchmarks reduces bed utilisation to an estimated 60%, allowing for additional theatre activity such as weekend working. Further, reducing the proportion of patients with a delayed discharge by 75% reduces bed utilisation to below 40%, even with weekend working. A range of other scenarios can also be investigated directly by NHS planners using the interactive web app. <h4>Conclusions</h4> The simulation model is intended to support capacity planning of orthopaedic elective services by identifying a balance of capacity across theatres and beds and predicting the impact of productivity measures on capacity requirements. It is applicable beyond the study site and can be adapted for other specialties. <h4>Strengths and Limitations of this study</h4> The simulation model provides rapid quantitative estimates to support post-COVID elective services recovery toward medium-term elective targets. Parameter combinations include changes to both resourcing and productivity. The interactive web app enables intuitive parameter changes by users while underlying source code can be adapted or re-used for similar applications. Patient attributes such as complexity are not included in the model but are reflected in variables such as length-of-stay and delayed discharge rates. Theatre schedules are simplified, incorporating the five key orthopaedic elective surgical procedures.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2023/06/05/2023.05.31.23290774.full.pdf; doi:https://doi.org/10.1101/2023.05.31.23290774; html:https://europepmc.org/article/PPR/PPR670288; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR670288&type=FILE&fileName=EMS176961-pdf.pdf&mimeType=application/pdf
 PPR249201,https://doi.org/10.1101/2020.12.02.20240648,The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia,"Pavelka M, Van-Zandvoort K, Abbott S, Sherratt K, Majdan M, CMMID COVID-19 working group, Analýz IZ, Jarčuška P, Krajčí M, Flasche S, Funk S.",,No Journal Info,2020,2020-12-04,Y,,,,"Slovakia conducted multiple rounds of population-wide rapid antigen testing for SARS-CoV-2 in late 2020, combined with a period of additional contact restrictions. Observed prevalence decreased by 58% (95% CI: 57-58%) within one week in the 45 counties that were subject to two rounds of mass testing, an estimate that remained robust when adjusting for multiple potential confounders. Adjusting for epidemic growth of 4.4% (1.1-6.9%) per day preceding the mass testing campaign, the estimated decrease in prevalence compared to a scenario of unmitigated growth was 70% (67-73%). Modelling suggests that this decrease cannot be explained solely by infection control measures, but requires the additional impact of isolation as well as quarantine of household members of those testing positive.",,pdf:https://www.science.org/cms/asset/e974db95-138d-4a9f-aa91-2f8f6c705f36/pap.pdf; doi:https://doi.org/10.1101/2020.12.02.20240648; html:https://europepmc.org/article/PPR/PPR249201; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR249201&type=FILE&fileName=EMS107887-pdf.pdf&mimeType=application/pdf
+PPR341842,https://doi.org/10.2139/ssrn.3817437,Risk Factors for Developing COVID-19: A Population-Based Longitudinal Study (COVIDENCE UK),"Holt H, Talaei M, Greenig M, Zenner D, Symons J, Relton C, Young KS, Davies MR, Thompson KN, Ashman J, Rajpoot SS, Kayyale AA, Rifai SE, Lloyd PJ, Jolliffe DA, Finer S, Ilidriomiti S, Miners A, Hopkinson NS, Alam B, Pfeffer PE, McCoy D, Davies GA, Lyons RA, Griffiths CJ, Kee F, Sheikh A, Breen G, Shaheen SO, Martineau AR.",,No Journal Info,2021,2021-04-01,N,,,,"Background: Risk factors for severe COVID-19 include older age, male sex, obesity, Black or Asian ethnicity and underlying medical conditions. Whether these factors also influence susceptibility to developing COVID-19 is uncertain.<br><br>Methods: We undertook a prospective, population-based cohort study   (COVIDENCE UK) from 1  st  May 2020 to 5  th  February 2021  . Baseline information on potential risk factors was captured by an online questionnaire. Monthly follow-up questionnaires captured incident COVID-19. We used logistic regression models to estimate multivariable-adjusted odds ratios (aORs) for associations between potential risk factors and risk of COVID-19.<br><br>Findings: We recorded 446 incident cases of COVID-19 in 15,227 participants (2.9%). Increased risk of developing COVID-19 was independently associated with Asian/Asian British  vs  . White ethnicity (aOR 2.31, 95% CI 1.35-3.95), household overcrowding  (aOR per additional 0.5 people/bedroom 1.26, 1.11-1.43)  , any  vs  . no visits to/from other households in previous week (aOR 1.33, 1.07-1.64), number of visits to indoor public places (aOR per extra visit per week 1.05, 1.01-1.09), frontline occupation excluding health/social care  vs.  no frontline occupation (aOR 1.49, 1.12-1.98), and raised body mass index (BMI) (aOR 1.51 [1.20-1.90] for BMI 25.0-30.0 kg/m  2  and 1.38 [1.05-1.82] for BMI >30.0 kg/m  2  vs.  BMI <25.0 kg/m  2  ). Atopic disease was independently associated with decreased risk (aOR 0.76, 0.59-0.98). No independent associations were seen for age, sex, other medical conditions, diet, or micronutrient supplement use.<br><br>Interpretation: After rigorous adjustment for factors influencing exposure to SARS-CoV-2, Asian/Asian British ethnicity and raised BMI were associated with increased risk of developing COVID-19, while atopic disease was associated with decreased risk.<br><br>Trial Registration: It is registered with ClinicalTrials.gov (NCT04330599).<br><br>Funding: Barts Charity, Health Data Research UK<br><br>Declaration of Interest: None to declare. <br><br>Ethical Approval: The study was sponsored by Queen Mary University of London and approved by<br>Leicester South Research Ethics Committee (ref 20/EM/0117).",,pdf:http://pure-oai.bham.ac.uk/ws/files/148236929/holth2021risk.pdf; doi:https://doi.org/10.2139/ssrn.3817437; html:https://europepmc.org/article/PPR/PPR341842; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR341842&type=FILE&fileName=EMS124907-pdf.pdf&mimeType=application/pdf; doi:https://doi.org/10.2139/ssrn.3817437
 PPR114828,https://doi.org/10.1101/2020.02.26.20028167,Estimation of country-level basic reproductive ratios for novel Coronavirus (COVID-19) using synthetic contact matrices,"Hilton J, Keeling MJ.",,No Journal Info,2020,2020-02-27,Y,,,,"The outbreak of novel coronavirus (COVID-19) has the potential for global spread, infecting large numbers in all countries. In this case, estimating the country-specific basic reproductive ratio is a vital first step in public-health planning. The basic reproductive ratio ( R 0 ) is determined by both the nature of pathogen and the network of contacts through which the disease can spread - with this network determined by socio-demographics including age-structure and household composition. Here we focus on the age-structured transmission within the population, using data from China to inform age-dependent susceptibility and synthetic age-mixing matrices to inform the contact network. This allows us to determine the country-specific basic reproductive ratio as a multiplicative scaling of the value from China. We predict that R 0 will be highest across Eastern Europe and Japan, and lowest across Africa, Central America and South-Western Asia. This pattern is largely driven by the ratio of children to older adults in each country and the observed propensity of clinical cases in the elderly.","This paper aims to estimate country-specific reproductive ratio, which is determined by the nature of the virus and the network of contacts through which teh disease can spread. The authors predict that the reproductive ratio will be highest across Eastern Europe and Japan, and lowest across Africa, Central America and South-Western Asia. This was based on the ratio of children to older adults in each country, as well as the observed frequency of cases in the elderly.",pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008031&type=printable; doi:https://doi.org/10.1101/2020.02.26.20028167; html:https://europepmc.org/article/PPR/PPR114828; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR114828&type=FILE&fileName=EMS88861-pdf.pdf&mimeType=application/pdf
 PPR290155,https://doi.org/10.1101/2021.02.25.21252402,Racial and ethnic differences in COVID-19 vaccine hesitancy and uptake,"Nguyen LH, Joshi AD, Drew DA, Merino J, Ma W, Lo C, Kwon S, Wang K, Graham MS, Polidori L, Menni C, Sudre CH, Anyane-Yeboa A, Astley CM, Warner ET, Hu CY, Selvachandran S, Davies R, Nash D, Franks PW, Wolf J, Ourselin S, Steves CJ, Spector TD, Chan AT.",,No Journal Info,2021,2021-02-28,Y,,,,"<h4>Background</h4> Racial and ethnic minorities have been disproportionately impacted by COVID-19. In the initial phase of population-based vaccination in the United States (U.S.) and United Kingdom (U.K.), vaccine hesitancy and limited access may result in disparities in uptake. <h4>Methods</h4> We performed a cohort study among U.S. and U.K. participants in the smartphone-based COVID Symptom Study (March 24, 2020-February 16, 2021). We used logistic regression to estimate odds ratios (ORs) of COVID-19 vaccine hesitancy (unsure/not willing) and receipt. <h4>Results</h4> In the U.S. ( n =87,388), compared to White non-Hispanic participants, the multivariable ORs of vaccine hesitancy were 3.15 (95% CI: 2.86 to 3.47) for Black participants, 1.42 (1.28 to 1.58) for Hispanic participants, 1.34 (1.18 to 1.52) for Asian participants, and 2.02 (1.70 to 2.39) for participants reporting more than one race/other. In the U.K. ( n =1,254,294), racial and ethnic minorities had similarly elevated hesitancy: compared to White participants, their corresponding ORs were 2.84 (95% CI: 2.69 to 2.99) for Black participants, 1.66 (1.57 to 1.76) for South Asian participants, 1.84 (1.70 to 1.98) for Middle East/East Asian participants, and 1.48 (1.39 to 1.57) for participants reporting more than one race/other. Among U.S. participants, the OR of vaccine receipt was 0.71 (0.64 to 0.79) for Black participants, a disparity that persisted among individuals who specifically endorsed a willingness to obtain a vaccine. In contrast, disparities in uptake were not observed in the U.K. <h4>Conclusions</h4> COVID-19 vaccine hesitancy was greater among racial and ethnic minorities, and Black participants living in the U.S. were less likely to receive a vaccine than White participants. Lower uptake among Black participants in the U.S. during the initial vaccine rollout is attributable to both hesitancy and disparities in access.",,pdf:https://www.nature.com/articles/s41467-022-28200-3.pdf; doi:https://doi.org/10.1101/2021.02.25.21252402; html:https://europepmc.org/article/PPR/PPR290155; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR290155&type=FILE&fileName=EMS117911-pdf.pdf&mimeType=application/pdf
 PPR174832,https://doi.org/10.1101/2020.06.10.20084715,Estimating the COVID-19 epidemic trajectory and hospital capacity requirements in South West England: a mathematical modelling framework,"Booton RD, MacGregor L, Vass L, Looker KJ, Hyams C, Bright PD, Harding I, Lazarus R, Hamilton F, Lawson D, Danon L, Pratt A, Wood R, Brooks-Pollock E, Turner KM.",,No Journal Info,2020,2020-06-12,Y,,,,"<h4>Objectives</h4> To develop a regional model of COVID-19 dynamics, for use in estimating the number of infections, deaths and required acute and intensive care (IC) beds using the South West of England (SW) as an example case. <h4>Design</h4> Open-source age-structured variant of a susceptible-exposed-infectious-recovered (SEIR) deterministic compartmental mathematical model. Latin hypercube sampling and maximum likelihood estimation were used to calibrate to cumulative cases and cumulative deaths. <h4>Setting</h4> SW at a time considered early in the pandemic, where National Health Service (NHS) authorities required evidence to guide localised planning and support decision-making. <h4>Participants</h4> Publicly-available data on COVID-19 patients. <h4>Primary and secondary outcome measures</h4> The expected numbers of infected cases, deaths due to COVID-19 infection, patient occupancy of acute and IC beds and the reproduction (“R”) number over time. <h4>Results</h4> SW model projections indicate that, as of the 11 th May 2020 (when ‘lockdown’ measures were eased), 5,793 (95% credible interval, CrI, 2,003 – 12,051) individuals were still infectious (0.10% of the total SW England population, 95%CrI 0.04 – 0.22%), and a total of 189,048 (95%CrI 141,580 – 277,955) had been infected with the virus (either asymptomatically or symptomatically), but recovered, which is 3.4% (95%CrI 2.5 – 5.0%) of the SW population. The total number of patients in acute and IC beds in the SW on the 11 th May 2020 was predicted to be 701 (95%CrI 169 – 1,543) and 110 (95%CrI 8 – 464) respectively. The R value in SW England was predicted to be 2.6 (95%CrI 2.0 – 3.2) prior to any interventions, with social distancing reducing this to 2.3 (95%CrI 1.8 – 2.9) and lockdown/ school closures further reducing the R value to 0.6 (95CrI% 0.5 – 0.7). <h4>Conclusions</h4> The developed model has proved a valuable asset for local and regional healthcare services. The model will be used further in the SW as the pandemic evolves, and – as open source software – is portable to healthcare systems in other geographies. <h4>Future work/ applications</h4> Open-source modelling tool available for wider use and re-use. Customisable to a number of granularities such as at the local, regional and national level. Supports a more holistic understanding of intervention efficacy through estimating unobservable quantities, e.g. asymptomatic population. While not presented here, future use of the model could evaluate the effect of various interventions on transmission of COVID-19. Further developments could consider the impact of bedded capacity in terms of resulting excess deaths.",,pdf:https://research-information.bris.ac.uk/ws/files/264998554/e041536.full.pdf; doi:https://doi.org/10.1101/2020.06.10.20084715; html:https://europepmc.org/article/PPR/PPR174832; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR174832&type=FILE&fileName=EMS95901-pdf.pdf&mimeType=application/pdf
@@ -374,8 +374,8 @@ PPR195140,https://doi.org/10.1101/2020.07.30.20165464,Risk stratification of pat
 PPR170310,https://doi.org/10.1101/2020.05.27.20083287,Estimating excess mortality in people with cancer and multimorbidity in the COVID-19 emergency,"Lai AG, Pasea L, Banerjee A, Denaxas S, Katsoulis M, Chang WH, Williams B, Pillay D, Noursadeghi M, Linch D, Hughes D, Forster MD, Turnbull C, Fitzpatrick NK, Boyd K, Foster GR, Cooper M, Jones M, Pritchard-Jones K, Sullivan R, Hall G, Davie C, Lawler M, Hemingway H.",,No Journal Info,2020,2020-06-01,Y,,,,"<h4>Background: </h4> Cancer and multiple non-cancer conditions are considered by the Centers for Disease Control and Prevention (CDC) as high risk conditions in the COVID-19 emergency. Professional societies have recommended changes in cancer service provision to minimize COVID-19 risks to cancer patients and health care workers. However, we do not know the extent to which cancer patients, in whom multi-morbidity is common, may be at higher overall risk of mortality as a net result of multiple factors including COVID-19 infection, changes in health services, and socioeconomic factors. <h4>Methods:</h4> We report multi-center, weekly cancer diagnostic referrals and chemotherapy treatments until April 2020 in England and Northern Ireland. We analyzed population-based health records from 3,862,012 adults in England to estimate 1-year mortality in 24 cancer sites and 15 non-cancer comorbidity clusters (40 conditions) recognized by CDC as high-risk. We estimated overall (direct and indirect) effects of COVID-19 emergency on mortality under different Relative Impact of the Emergency (RIE) and different Proportions of the population Affected by the Emergency (PAE). We applied the same model to the US, using Surveillance, Epidemiology, and End Results (SEER) program data. <h4>Results:</h4> Weekly data until April 2020 demonstrate significant falls in admissions for chemotherapy (45-66% reduction) and urgent referrals for early cancer diagnosis (70-89% reduction), compared to pre-emergency levels. Under conservative assumptions of the emergency affecting only people with newly diagnosed cancer (incident cases) at COVID-19 PAE of 40%, and an RIE of 1.5, the model estimated 6,270 excess deaths at 1 year in England and 33,890 excess deaths in the US. In England, the proportion of patients with incident cancer with ≥1 comorbidity was 65.2%. The number of comorbidities was strongly associated with cancer mortality risk. Across a range of model assumptions, and across incident and prevalent cancer cases, 78% of excess deaths occur in cancer patients with ≥1 comorbidity. <h4>Conclusion:</h4> We provide the first estimates of potential excess mortality among people with cancer and multimorbidity due to the COVID-19 emergency and demonstrate dramatic changes in cancer services. To better inform prioritization of cancer care and guide policy change, there is an urgent need for weekly data on cause-specific excess mortality, cancer diagnosis and treatment provision and better intelligence on the use of effective treatments for comorbidities.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2020/06/01/2020.05.27.20083287.full.pdf; doi:https://doi.org/10.1101/2020.05.27.20083287; html:https://europepmc.org/article/PPR/PPR170310; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR170310&type=FILE&fileName=EMS91512-pdf.pdf&mimeType=application/pdf
 PPR275525,https://doi.org/10.1101/2021.01.28.21250680,"Changes in symptomatology, re-infection and transmissibility associated with SARS-CoV-2 variant B.1.1.7: an ecological study","Graham MS, Sudre CH, May A, Antonelli M, Murray B, Varsavsky T, Kläser K, Canas LS, Molteni E, Modat M, Drew DA, Nguyen LH, Polidori L, Selvachandran S, Hu C, Capdevila J, The COVID-19 Genomics UK (COG-UK) consortium, Hammers A, Chan AT, Wolf J, Spector TD, Steves CJ, Ourselin S.",,No Journal Info,2021,2021-01-29,Y,,,,"<h4>Background</h4> SARS-CoV-2 variant B.1.1.7 was first identified in December 2020 in England. It is not known if the new variant presents with variation in symptoms or disease course, if previously infected individuals may become reinfected with the new variant, or how the variant’s increased transmissibility affects measures to reduce its spread. <h4>Methods</h4> Using longitudinal symptom reports from 36,920 users of the COVID Symptom Study app testing positive for Covid-19 between 28 September and 27 December 2020, we performed an ecological study to examine the association between the regional proportion of B.1.1.7 and reported symptoms, disease course, rates of reinfection, and transmissibility. <h4>Findings</h4> We found no evidence for changes in reported symptoms or disease duration associated with B.1.1.7. We found a likely reinfection rate of 0.7% (95% CI 0.6-0.8), but no evidence that this was higher compared to older strains. We found an increase in R(t) by a factor of 1.35 (95% CI 1.02-1.69). Despite this, we found that R(t) fell below 1 during regional and national lockdowns, even in regions with high proportions of B.1.1.7. <h4>Interpretation</h4> The lack of change in symptoms indicates existing testing and surveillance infrastructure do not need to change specifically for the new variant, and the reinfection findings suggest that vaccines are likely to remain effective against the new variant. <h4>Funding</h4> Zoe Global Limited, Department of Health, Wellcome Trust, EPSRC, NIHR, MRC, Alzheimer’s Society. <h4>Research in context</h4> <h4>Evidence before this study</h4> To identify existing evidence on SARS-CoV-2 variant B.1.1.7 we searched PubMed and Google Scholar for articles between 1 December 2020 and 1 February 2021 using the keywords Covid-19 AND B.1.1.7, finding 281 results. We did not find any studies that investigated B.1.1.7-associated changes in the symptoms experienced, their severity and duration, but found one study showing B.1.1.7 did not change the ratio of symptomatic to asymptomatic infections. We found six articles describing laboratory-based investigations of the responses of B.1.1.7 to vaccine-induced immunity to B.1.1.7, but no work investigating what this means for natural immunity and the likelihood of reinfection outside of the lab. We found five articles demonstrating the increased transmissibility of B.1.1.7. <h4>Added value of this study</h4> To our knowledge, this is the first study to explore changes in symptom type and duration, as well as community reinfection rates, associated with B.1.1.7. The work uses self-reported symptom logs from 36,920 users of the COVID Symptom Study app reporting positive test results between 28 September and 27 December 2020. We find that B.1.1.7 is not associated with changes in the symptoms experienced in Covid-19, nor their duration. Building on existing lab studies, our work suggests that natural immunity developed from previous infection provides similar levels of protection to B.1.1.7. We add to the emerging consensus that B.1.1.7 exhibits increased transmissibility. <h4>Implications of all the available evidence</h4> Our findings suggest that existing criteria for obtaining a Covid-19 test in the community need not change for the rise of B.1.1.7. The fact that immunity developed from infection by wild type variants protects against B.1.1.7 provides an indication that vaccines will remain effective against B.1.1.7. R(t) fell below 1 during the UK’s national lockdown, even in regions with high levels of B.1.1.7, but further investigation is required to establish the factors that enabled this, to facilitate countries seeking to control the spread of B.1.1.7.",,pdf:http://pure-oai.bham.ac.uk/ws/files/134813250/1_s2.0_S2468266721000554_main.pdf; doi:https://doi.org/10.1101/2021.01.28.21250680; html:https://europepmc.org/article/PPR/PPR275525; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR275525&type=FILE&fileName=EMS115539-pdf.pdf&mimeType=application/pdf
 PPR393011,https://doi.org/10.1101/2021.09.03.21262888,Risk of severe COVID-19 outcomes associated with immune-mediated inflammatory diseases and immune modifying therapies: a nationwide cohort study in the OpenSAFELY platform,"MacKenna B, Kennedy NA, Mehkar A, Rowan A, Galloway J, Mansfield KE, Bechman K, Matthewman J, Yates M, Brown J, Schultze A, Norton S, Walker AJ, Morton CE, Harrison D, Bhaskaran K, Rentsch CT, Williamson E, Croker R, Bacon S, Hickman G, Ward T, Davy S, Green A, Fisher L, Hulme W, Bates C, Curtis HJ, Tazare J, Eggo RM, Evans D, Inglesby P, Cockburn J, McDonald HI, Tomlinson LA, Mathur R, Wong AY, Forbes H, Parry J, Hester F, Harper S, Douglas IJ, Smeeth L, Lees CW, Evans SJ, Goldacre B, Smith C, Langan SM.",,No Journal Info,2021,2021-09-10,N,,,,"<h4>ABSTRACT</h4> <h4>Background</h4> It is unclear if people with immune-mediated inflammatory diseases (IMIDs) (joint, bowel and skin) and on immune modifying therapy have increased risk of serious COVID-19 outcomes. <h4>Methods</h4> With the approval of NHS England we conducted a cohort study, using OpenSAFELY, analysingroutinely-collected primary care data linked to hospital admission, death and previously unavailable hospital prescription data. We used Cox regression (adjusting for confounders) to estimate hazard ratios (HR) comparing risk of COVID-19-death, death/critical care admission, and hospitalisation (March to September 2020) in: 1) people with IMIDs compared to the general population; and 2) people with IMIDs on targeted immune modifying drugs (e.g., biologics) compared to standard systemic treatment (e.g., methotrexate). <h4>Findings</h4> We identified 17,672,065 adults; of 1,163,438 (7%) with IMIDs, 19,119 people received targeted immune modifying drugs, and 200,813 received standard systemics. We saw evidence of increased COVID-19-death (HR 1.23, 95%CI 1.20, 1.27), and COVID-19 hospitalisation (HR 1.32, 95%CI 1.29, 1.35) in individuals with IMIDs overall compared to individuals without IMIDs of the same age, sex, deprivation and smoking status. We saw no evidence of increased COVID-19 deaths with targeted compared to standard systemic treatments (HR 1.03, 95%CI 0.80, 1.33). There was no evidence of increased COVID-19-related death in those prescribed TNF inhibitors, IL-12/23, IL7, IL-6 or JAK inhibitors compared to standard systemics. Rituximab was associated with increased COVID-19 death (HR 1.68, 95%CI 1.11, 2.56); however, this finding may relate to confounding. <h4>Interpretation</h4> COVID-19 death and hospitalisation was higher in people with IMIDs. We saw no increased risk of adverse COVID-19 outcomes in those on most targeted immune modifying drugs for IMIDs compared to standard systemics. <h4>RESEARCH IN CONTEXT</h4> <h4>Evidence before this study</h4> We searched PubMed on May 19 th , 2021, using the terms “COVID-19”, “SARS-CoV-2” and “rheumatoid arthritis”, “psoriatic arthritis” “ankylosing spondylitis”, “Crohn’s disease” “ulcerative colitis” “hidradenitis suppurativa” and “psoriasis”, to identify primary research articles examining severe COVID-19 outcome risk in individuals with immune-mediated inflammatory diseases (IMIDs) and those on immune modifying therapy. The studies identified (including matched cohort studies and studies in disease-specific registries) were limited by small sample sizes and number of outcomes. Most studies did not show a signal of increased adverse COVID-19 outcomes in those on targeted therapies, with the exception of rituximab. Additionally, disease-specific registries are subject to selection bias and lack denominator populations. <h4>Added value of the study</h4> In our large population-based study of 17 million individuals, including 1 million people with IMIDs and just under 200,000 receiving immune modifying medications, we saw evidence that people with IMIDs had an increased risk of COVID-19-related death compared to the general population after adjusting for potential confounders (age, sex, deprivation, smoking status) (HR 1.23, 95%CI 1.20, 1.27). We saw differences by IMID type, with COVID-19-related death being increased by the most in people with inflammatory joint disease (HR 1.47, 95%CI 1.40, 1.54). We also saw some evidence that those with IMIDs were more likely, compared to the general population, to have COVID-19-related critical care admission/death (HR 1.24, 95%CI 1.21, 1.28) and hospitalisation (HR 1.32, 95%CI 1.29, 1.35). Compared to people with IMIDs taking standard systemics, we saw no evidence of differences in severe COVID-19-related outcomes with TNF inhibitors, IL-17 inhibitors, IL-12/23 inhibitors, IL-6 inhibitors and JAK inhibitors. However, there was some evidence that rituximab was associated with an increased risk of COVID-19-related death (HR 1.68, 95%CI 1.11, 2.56) and death/critical care admission (HR 1.92, 95%CI 1.31, 2.81). We also saw evidence of an increase in COVID-19-related hospital admissions in people prescribed rituximab (HR 1.59, 95%CI 1.16, 2.18) or JAK inhibition (HR 1.81, 95%CI 1.09, 3.01) compared to those on standard systemics, although this could be related to worse underlying health rather than the drugs themselves, and numbers of events were small. This is the first study to our knowledge to use high-cost drug data on medicines supplied by hospitals at a national scale in England (to identify targeted therapies). The availability of these data fills an important gap in the medication record of those with more specialist conditions treated by hospitals creating an important opportunity to generate insights to these conditions and these medications <h4>Implications of all of the available evidence</h4> Our study offers insights into future risk mitigation strategies and SARS-CoV-2 vaccination priorities for individuals with IMIDs, as it highlights that those with IMIDs and those taking rituximab may be at risk of severe COVID-19 outcomes. Critically, our study does not show a link between most targeted immune modifying medications compared to standard systemics and severe COVID-19 outcomes. However, the increased risk of adverse COVID-19 outcomes that we saw in people with IMIDs and those treated with rituximab merits further study.",,pdf:https://qmro.qmul.ac.uk/xmlui/bitstream/123456789/83106/2/Mathur%20Risk%20of%20severe%20COVID-19%20outcomes%20associated%20with%20immune-mediated%20inflammatory%20diseases%20and%20immune-modifying%20therapies%3a%20a%20nationwide%20cohort%20study%20in%20the%20OpenSAFELY%20platform%202022%20Published.pdf; doi:https://doi.org/10.1101/2021.09.03.21262888; html:https://europepmc.org/article/PPR/PPR393011; doi:https://doi.org/10.1101/2021.09.03.21262888
-PPR304173,https://doi.org/10.1101/2021.03.27.21254452,Risk factors for developing COVID-19: a population-based longitudinal study (COVIDENCE UK),"Holt H, Talaei M, Greenig M, Zenner D, Symons J, Relton C, Young KS, Davies MR, Thompson KN, Ashman J, Rajpoot SS, Kayyale AA, Rifai SE, Lloyd PJ, Jolliffe DA, Finer S, Ilidriomiti S, Miners A, Hopkinson NS, Alam B, Pfeffer PE, McCoy D, Davies GA, Lyons RA, Griffiths CJ, Kee F, Sheikh A, Breen G, Shaheen SO, Martineau AR.",,No Journal Info,2021,2021-03-29,Y,,,,"<h4>Summary</h4> <h4>Background</h4> Risk factors for severe COVID-19 include older age, male sex, obesity, Black or Asian ethnicity and underlying medical conditions. Whether these factors also influence susceptibility to developing COVID-19 is uncertain. <h4>Methods</h4> We undertook a prospective, population-based cohort study (COVIDENCE UK) from 1 st May 2020 to 5 th February 2021. Baseline information on potential risk factors was captured by an online questionnaire. Monthly follow-up questionnaires captured incident COVID-19. We used logistic regression models to estimate multivariable-adjusted odds ratios (aORs) for associations between potential risk factors and risk of COVID-19. <h4>Findings</h4> We recorded 446 incident cases of COVID-19 in 15,227 participants (2.9%). Increased risk of developing COVID-19 was independently associated with Asian/Asian British vs . White ethnicity (aOR 2.31, 95% CI 1.35-3.95), household overcrowding (aOR per additional 0.5 people/bedroom 1.26, 1.11-1.43), any vs . no visits to/from other households in previous week (aOR 1.33, 1.07-1.64), number of visits to indoor public places (aOR per extra visit per week 1.05, 1.01-1.09), frontline occupation excluding health/social care vs . no frontline occupation (aOR 1.49, 1.12-1.98), and raised body mass index (BMI) (aOR 1.51 [1.20-1.90] for BMI 25.0-30.0 kg/m 2 and 1.38 [1.05-1.82] for BMI >30.0 kg/m 2 vs . BMI <25.0 kg/m 2 ). Atopic disease was independently associated with decreased risk (aOR 0.76, 0.59-0.98). No independent associations were seen for age, sex, other medical conditions, diet, or micronutrient supplement use. <h4>Interpretation</h4> After rigorous adjustment for factors influencing exposure to SARS-CoV-2, Asian/Asian British ethnicity and raised BMI were associated with increased risk of developing COVID-19, while atopic disease was associated with decreased risk. <h4>Funding</h4> Barts Charity, Health Data Research UK",,pdf:http://pure-oai.bham.ac.uk/ws/files/148236929/holth2021risk.pdf; doi:https://doi.org/10.1101/2021.03.27.21254452; html:https://europepmc.org/article/PPR/PPR304173; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR304173&type=FILE&fileName=EMS121246-pdf.pdf&mimeType=application/pdf
 PPR172602,https://doi.org/10.1101/2020.06.06.20122689,The impact of COVID-19 control measures on social contacts and transmission in Kenyan informal settlements,"Quaife M, van Zandvoort K, Gimma A, Shah K, McCreesh N, Prem K, Barasa E, Mwanga D, Kangwana B, Pinchoff J, CMMID COVID-19 Working Group, Edmunds WJ, Jarvis CI, Austrian K.",,No Journal Info,2020,2020-06-07,Y,,,,"<h4>Background</h4> Many low- and middle-income countries have implemented control measures against coronavirus disease 2019 (COVID-19). However, it is not clear to what extent these measures explain the low numbers of recorded COVID-19 cases and deaths in Africa. One of the main aims of control measures is to reduce respiratory pathogen transmission through direct contact with others. In this study we collect contact data from residents of informal settlements around Nairobi, Kenya to assess if control measures have changed contact patterns, and estimate the impact of changes on the basic reproduction number ( R 0 ). <h4>Methods</h4> We conducted a social contact survey with 213 residents of five informal settlements around Nairobi in early May 2020, four weeks after the Kenyan government introduced enhanced physical distancing measures and a curfew between 7pm and 5am. Respondents were asked to report all direct physical and non-physical contacts made the previous day, alongside a questionnaire asking about the social and economic impact of COVID-19 and control measures. We examined contact patterns by demographic factors, including socioeconomic status. We described the impact of COVID-19 and control measures on income and food security. We compared contact patterns during control measures to patterns from non-pandemic periods to estimate the change in R 0 . <h4>Findings</h4> We estimate that control measures reduced physical and non-physical contacts, reducing the R 0 from around 2.6 to between 0.5 and 0.7, depending on the pre-COVID-19 comparison matrix used. Masks were worn by at least one person in 92% of contacts. Respondents in the poorest socioeconomic quintile reported 1.5 times more contacts than those in the richest. 86% of respondents reported a total or partial loss of income due to COVID-19, and 74% reported eating less or skipping meals due to having too little money for food. <h4>Interpretation</h4> COVID-19 control measures have had a large impact on direct contacts and therefore transmission, but have also caused considerable economic and food insecurity. Reductions in R 0 are consistent with the linear epidemic growth in Kenya and other sub-Saharan African countries that implemented similar, early control measures. However, negative and inequitable impacts on economic and food security may mean control measures are not sustainable in the longer term. <h4>Research in context</h4> <h4>Evidence before this study</h4> We conducted a PubMed search on 6 June 2020 with no language restrictions for studies published since inception, using the search terms (“social mix*” OR “social cont*” OR “contact pattern*) AND (“covid*”). The search yielded 53 articles, two of which reported changes in social contacts after COVID-19 control measures. The first study reported changes in contact patterns in Wuhan and Shanghai, and the second changes in contact patterns in the UK. We found no studies examining changes in contact patterns due to control measures in sub-Saharan Africa, and no studies disaggregating contacts by socioeconomic status. <h4>Added value of this study</h4> This is the first study to estimate the reproduction number of COVID-19 under control measures in sub-Saharan Africa using primary contact data. This study also moves beyond existing work to i) measure contacts in densely populated informal settlements, ii) explore how social contacts vary across socioeconomic status, and iii) assess the impact of control measures on economic and food security in these areas. <h4>Implications of all the evidence</h4> COVID-19 control measures have substantially reduced social contacts and disease transmission. People of lower socioeconomic status face greater transmission risk as they report more contacts. Control measures have led to considerable economic and food insecurity, and may not be sustainable in the long term without efforts to reduce the burden of control measures on households.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-020-01779-4; doi:https://doi.org/10.1101/2020.06.06.20122689; html:https://europepmc.org/article/PPR/PPR172602; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR172602&type=FILE&fileName=EMS91656-pdf.pdf&mimeType=application/pdf
+PPR304173,https://doi.org/10.1101/2021.03.27.21254452,Risk factors for developing COVID-19: a population-based longitudinal study (COVIDENCE UK),"Holt H, Talaei M, Greenig M, Zenner D, Symons J, Relton C, Young KS, Davies MR, Thompson KN, Ashman J, Rajpoot SS, Kayyale AA, Rifai SE, Lloyd PJ, Jolliffe DA, Finer S, Ilidriomiti S, Miners A, Hopkinson NS, Alam B, Pfeffer PE, McCoy D, Davies GA, Lyons RA, Griffiths CJ, Kee F, Sheikh A, Breen G, Shaheen SO, Martineau AR.",,No Journal Info,2021,2021-03-29,Y,,,,"<h4>Summary</h4> <h4>Background</h4> Risk factors for severe COVID-19 include older age, male sex, obesity, Black or Asian ethnicity and underlying medical conditions. Whether these factors also influence susceptibility to developing COVID-19 is uncertain. <h4>Methods</h4> We undertook a prospective, population-based cohort study (COVIDENCE UK) from 1 st May 2020 to 5 th February 2021. Baseline information on potential risk factors was captured by an online questionnaire. Monthly follow-up questionnaires captured incident COVID-19. We used logistic regression models to estimate multivariable-adjusted odds ratios (aORs) for associations between potential risk factors and risk of COVID-19. <h4>Findings</h4> We recorded 446 incident cases of COVID-19 in 15,227 participants (2.9%). Increased risk of developing COVID-19 was independently associated with Asian/Asian British vs . White ethnicity (aOR 2.31, 95% CI 1.35-3.95), household overcrowding (aOR per additional 0.5 people/bedroom 1.26, 1.11-1.43), any vs . no visits to/from other households in previous week (aOR 1.33, 1.07-1.64), number of visits to indoor public places (aOR per extra visit per week 1.05, 1.01-1.09), frontline occupation excluding health/social care vs . no frontline occupation (aOR 1.49, 1.12-1.98), and raised body mass index (BMI) (aOR 1.51 [1.20-1.90] for BMI 25.0-30.0 kg/m 2 and 1.38 [1.05-1.82] for BMI >30.0 kg/m 2 vs . BMI <25.0 kg/m 2 ). Atopic disease was independently associated with decreased risk (aOR 0.76, 0.59-0.98). No independent associations were seen for age, sex, other medical conditions, diet, or micronutrient supplement use. <h4>Interpretation</h4> After rigorous adjustment for factors influencing exposure to SARS-CoV-2, Asian/Asian British ethnicity and raised BMI were associated with increased risk of developing COVID-19, while atopic disease was associated with decreased risk. <h4>Funding</h4> Barts Charity, Health Data Research UK",,pdf:http://pure-oai.bham.ac.uk/ws/files/148236929/holth2021risk.pdf; doi:https://doi.org/10.1101/2021.03.27.21254452; html:https://europepmc.org/article/PPR/PPR304173; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR304173&type=FILE&fileName=EMS121246-pdf.pdf&mimeType=application/pdf
 PPR289287,https://doi.org/10.2139/ssrn.3786058,Inpatient COVID-19 Mortality Has Reduced Over Time: Results from an Observational Cohort,"Bechman K, Yates M, Mann K, Nagra D, Smith L, Rutherford AI, Periselneris J, Walder D, Dobson RJ, Kraljevic Z, Teo JT, Bernal W, Barker RD, Galloway J, Norton S.",,No Journal Info,2021,2021-02-15,N,,,,"Introduction: The Covid-19 pandemic in the United Kingdom has seen two waves; the first starting in March 2020 and the second in late October 2020.  It is not known whether outcomes were different in the first and second waves.<br><br>Methods: The study population comprised all patients admitted to a 1,500-bed London Hospital Trust between March 2020 and January 2021, who tested positive for Covid-19 by PCR within 3-days of admissions. Primary outcome was death within 28-days of admission. Socio-demographics (age, sex, ethnicity), hypertension, diabetes, obesity, baseline physiological observations, CRP, neutrophil, chest x-ray abnormality, remdesivir and dexamethasone were incorporated as co-variates. Proportional subhazards models compared mortality risk between wave 1 and wave 2. Cox-proportional hazard model with propensity score adjustment were used to compare mortality in patients prescribed remdesivir and dexamethasone.<br><br>Findings: There were 3,457 COVID-19 admissions, 2,494 hospital discharges and 619 deaths. There were notable differences in age, ethnicity, comorbidities, and admission disease severity between wave 1 and wave 2. Twenty-eight-day mortality was higher during wave 1 (25.7% versus 13.2%). Mortality risk adjusted for co-variates was significantly lower in wave 2 compared to wave 1 [adjSHR 0.41(0.30, 0.56)p<0.001]. Analysis of treatment impact did not show statistically different effects of remdesivir [HR 1.22(95%CI 0.91, 1.62),p=0.18] or dexamethasone [HR 1.31(95%CI 0.80, 2.14),p=0.29].<br><br>Interpretation: There has been substantial improvements in COVID-19 mortality in the second wave, even accounting for demographics, comorbidity, and disease severity. Neither dexamethasone nor remdesivir appeared to be key explanatory factors, although there may be unmeasured confounding present.<br><br>Funding: None.<br><br>Conflict of Interest: None declared by authors.<br><br>Ethical Approval: This project operated under London South East Research Ethics Committee (reference 18/LO/2048) approval granted to the King’s Electronic Records Research Interface (KERRI); specific work on COVID-19 research was reviewed with expert patient input on a virtual committee with Caldicott Guardian oversight.",,pdf:https://discovery.ucl.ac.uk/10145214/1/Dobson_journal.pone.0261142.pdf; doi:https://doi.org/10.2139/ssrn.3786058; html:https://europepmc.org/article/PPR/PPR289287; doi:https://doi.org/10.2139/ssrn.3786058
 PPR204757,https://doi.org/10.1101/2020.08.21.20167965,Implications of the school-household network structure on SARS-CoV-2 transmission under different school reopening strategies in England,"Munday JD, Sherratt K, Meakin S, Endo A, Pearson CAB, Hellewell J, Abbott S, Bosse NI, CMMID COVID 1-9 Working Group, Atkins KE, Wallinga J, Edmunds WJ, van Hoek AJ, Funk S.",,No Journal Info,2020,2020-08-24,Y,,,,"<h4>Background</h4> School closures are a well-established non-pharmaceutical intervention in the event of infectious disease outbreaks, and have been implemented in many countries across the world, including the UK, to slow down the spread of SARS-CoV-2. As governments begin to relax restrictions on public life there is a need to understand the potential impact that reopening schools may have on transmission. <h4>Methods</h4> We used data provided by the UK Department for Education to construct a network of English schools, connected through pairs of pupils resident at the same address. We used the network to evaluate the potential for transmission between schools, and for long range propagation across the network, under different reopening scenarios. <h4>Results</h4> Amongst the options evaluated we found that reopening only Reception, Year 1 and Year 6 (4-6 and 10-11 year olds) resulted in the lowest risk of transmission between schools, with outbreaks within a single school unlikely to result in outbreaks in adjacent schools in the network. The additional reopening of Years 10 and 12 (14-15 and 16-17 year olds) resulted in an increase in the risk of transmission between schools comparable to reopening all primary school years (4-11 year olds). However, the majority of schools presented low risk of initiating widespread transmission through the school system. Reopening all secondary school years (11-18 year olds) resulted in large potential outbreak clusters putting up to 50% of households connected to schools at risk of infection if sustained transmission within schools was possible. <h4>Conclusions</h4> Reopening secondary school years is likely to have a greater impact on community transmission than reopening primary schools in England. Keeping transmission within schools limited is essential for reducing the risk of large outbreaks amongst school-aged children and their household members.",,pdf:https://www.nature.com/articles/s41467-021-22213-0.pdf; doi:https://doi.org/10.1101/2020.08.21.20167965; html:https://europepmc.org/article/PPR/PPR204757; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR204757&type=FILE&fileName=EMS95596-pdf.pdf&mimeType=application/pdf
 PPR581420,https://doi.org/10.1101/2022.12.07.22283175,"Apixaban following discharge in hospitalised adults with COVID-19: Preliminary results from a multicentre, open-label, randomised controlled platform clinical trial","Toshner MR, Gamble C, Baillie JK, Best A, Bedson E, Bradley J, Calvert M, Davies EH, Docherty AB, Gkioni E, Hughes DA, Jaki T, Jenkins RG, Jones A, Landray MJ, Mant J, McAuley DF, Openshaw PJ, Richards D, Wicks P, HEAL-COVID Collaboration, Summers C.",,No Journal Info,2022,2022-12-07,Y,,,,"<h4>Summary</h4> <h4>Background</h4> The role of thromboprophylaxis in the post-acute phase of COVID-19 is uncertain due to conflicting results from randomised controlled trials and observational studies. We aimed to determine the effectiveness of post-hospital apixaban in reducing the rate of death and hospital readmission of hospitalised adults with COVID-19. <h4>Methods</h4> HEAL COVID is an adaptive randomised open label multicentre platform trial recruiting participants from National Health Service Hospitals in the United Kingdom. Here we report the preliminary results of apixaban comparison of HEAL-COVID. Participants with a hospital admission related to confirmed COVID-19 and an expected date of discharge in the subsequent five days were randomised to either apixaban 2.5 mg twice daily or standard care (no anticoagulation) for 14 days. The primary outcome was hospital free survival at 12 months obtained through routine data sources. The trial was prospectively registered with ISRCTN (15851697) and Clincialtrials.gov ( NCT04801940 ). <h4>Findings</h4> Between 19 May 2021 and 21 November 2022, 402 participants from 109 sites were randomised to apixaban and 399 to standard care. Seven participants withdrew from the apixaban group and one from the standard care group. Analysis was undertaken on an intention-to-treat basis. The apixaban arm was stopped on the recommendation of the oversight committees following an interim analysis due to no indication of benefit. Of the 402 participants randomised to apixaban, 117 experienced death or rehospitalisation during a median follow-up of 344·5 days (IQR 125 to 365), and 123 participants receiving standard care experienced death or rehospitalisation during a median follow-up of 349 days (IQR 124 to 365). There was no statistical difference in the rate of death and rehospitalisation (HR: 0·96 99%CI 0·69-1·34; p=0·75). Three participants in the apixaban arm experienced clinically significant bleeding during treatment. <h4>Interpretation</h4> Fourteen days of post-hospital anticoagulation with the direct oral anticoagulant apixaban did not reduce the rate of death or rehospitalisation of adults hospitalised with COVID-19. These data do not support the use of prophylactic post-hospital anticoagulation in adults with COVID-19. <h4>Funding</h4> HEAL-COVID is funded by the National Institute for Health and Care Research [NIHR133788] and the NIHR Cambridge Biomedical Research Centre [BRC-1215-20014*].",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/12/07/2022.12.07.22283175.full.pdf; doi:https://doi.org/10.1101/2022.12.07.22283175; html:https://europepmc.org/article/PPR/PPR581420; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR581420&type=FILE&fileName=EMS158329-pdf.pdf&mimeType=application/pdf
@@ -388,7 +388,7 @@ PPR530179,https://doi.org/10.1101/2022.08.08.22278493,Inequalities in colorectal
 PPR291776,https://doi.org/10.1101/2021.03.02.21252444,An overview of the National COVID-19 Chest Imaging Database: data quality and cohort analysis,"Cushnan D, Bennett O, Berka R, Bertolli O, Chopra A, Dorgham S, Favaro A, Ganepola T, Halling-Brown M, Imreh G, Jacob J, Jefferson E, Lemarchand F, Schofield D, Wyatt JC, NCCID Collaborative.",,No Journal Info,2021,2021-03-03,Y,,,,"The National COVID-19 Chest Imaging Database (NCCID) is a centralised database containing chest X-rays, chest Computed Tomography (CT) scans and cardiac Magnetic Resonance Images (MRI) from patients across the UK, jointly established by NHSX, the British Society of Thoracic Imaging (BSTI), Royal Surrey NHS Foundation Trust (RSNFT) and Faculty. The objective of the initiative is to support a better understanding of the coronavirus SARS-CoV-2 disease (COVID-19) and development of machine learning (ML) technologies that will improve care for patients hospitalised with a severe COVID-19 infection. The NCCID is now accumulating data from 20 NHS Trusts and Health Boards across England and Wales, with a total contribution of approximately 25,000 imaging studies in the training set (at time of writing) and is actively being used as a research tool by several organisations. This paper introduces the training dataset, including a snapshot analysis performed by NHSX covering: the completeness of clinical data, the availability of image data for the various use-cases (diagnosis, prognosis and longitudinal risk) and potential model confounders within the imaging data. The aim is to inform both existing and potential data users of the NCCID’s suitability for developing diagnostic/prognostic models. In addition, a cohort analysis was performed to measure the representativeness of the NCCID to the wider COVID-19 affected population. Three major aspects were included: geographic, demographic and temporal coverage, revealing good alignment in some categories, e.g., sex and identifying areas for improvements to data collection methods, particularly with respect to geographic coverage. All analyses and discussions are focused on the implications for building ML tools that will generalise well to the clinical use cases.",,pdf:https://discovery.dundee.ac.uk/files/69908473/giab076.pdf; doi:https://doi.org/10.1101/2021.03.02.21252444; html:https://europepmc.org/article/PPR/PPR291776; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR291776&type=FILE&fileName=EMS118552-pdf.pdf&mimeType=application/pdf
 PPR296523,https://doi.org/10.1101/2021.03.11.21253106,"Clinical presentation, disease course and outcome of COVID-19 in hospitalized patients with and without pre-existing cardiac disease – a cohort study across eighteen countries","CAPACITY-COVID collaborative consortium and LEOSS Study Group, Linschoten M, Uijl A, Schut A, Jakob C, Romão L, Bell R, McFarlane E, Stecher M, Zondag A, van Iperen E, Hermans-van Ast W, Lea N, Schaap J, Jewbali L, Smits P, Patel R, Aujayeb A, Ripley D, Saxena M, Spinner C, McCann G, Moss A, Parker E, Borgmann S, Tessitore E, Rieg S, Kearney M, Byrom-Goulthorp R, Hower M, Al-Ali A, Alshehri A, Alnafie A, Alshahrani M, Almubarak Y, Al-Muhanna F, Al-Rubaish A, Hanses F, Shore A, Ball C, Anning C, Rüthrich M, Nierop P, Vehreschild M, Heymans S, Henkens M, Raafs A, van der Horst I, van Bussel B, Magdelijns F, Lanznaster J, Kopylov P, Blagova O, Wille K, Pinto Y, Offerhaus J, Bleijendaal H, Piepel C, ten Berg J, Bor W, Maarse M, Römmele C, Tio R, Sturkenboom N, Tometten L, den Uil C, Scholte N, Groenendijk A, Dolff S, Zijlstra L, Hilt A, von Bergwelt-Baildon M, Groenemeijer B, Merle U, van der Zee P, van Beek E, Rothfuss K, Tjong F, van der Lingen A, Kolk M, Isberner N, Monraats P, Magro M, Hermans W, Kochanek M, Captur G, Thomson R, Nadalin S, Linssen G, Veneman T, Zaal R, Degenhardt C, Martens F, Badings E, Strauss R, Zaman A, Alkhalil M, Prasad S, Grüner B, Haerkens-Arends H, Eberwein L, Dark P, Lomas D, vom Dahl J, Verschure D, Hellwig K, Mosterd A, Rauschning D, van der Heijden D, Neufang M, van Hessen M, Raichle C, Montagna L, Mazzilli S, Bianco M, Westhoff T, Shafiee A, Hedayat B, Saneei E, Porhosseini H, Jensen B, Gabriel L, Er A, Kietselaer B, Schubert J, Timmermans P, Messiaen P, Friedrichs A, van den Brink F, Woudstra P, Trauth J, Ribeiro M, de With K, van der Linden M, Kielstein J, Macías Ruiz R, Guggemos W, Hellou E, Markart P, van Kesteren H, Heigener D, de Vries J, Stieglitz S, Baltazar J, Voigt I, van de Watering D, Milovanovic M, Redón J, Forner M, Rüddel J, Wu K, Nattermann J, Veldhuis L, Westendorp I, Riedel C, Kwakkel-van Erp J, van Ierssel S, van Craenenbroeck E, Walter L, de Sutter J, Worm M, Drost J, Moriarty A, Salah R, Charlotte N, van Boxem A, Dorman H, Reidinga A, van der Meer P, Wierda E, van Veen H, Delsing C, Meijs M, van de Wal R, Weytjens C, Hermanides R, Emans M, al-Windy N, Koning A, Schellings D, Anthonio R, Bucciarelli-Ducci C, Caputo M, Westendorp P, Kuijper A, van Ofwegen-Hanekamp C, Persoon A, Seelig J, van der Harst P, Siebelink H, van Smeden M, Williams S, Pilgram L, van Gilst W, Tieleman R, Williams B, Asselbergs F.",,No Journal Info,2021,2021-03-12,Y,,,,"<h4>Aims</h4> Patients with cardiac disease are considered high risk for poor outcomes following hospitalization with COVID-19. The primary aim of this study was to evaluate heterogeneity in associations between various heart disease subtypes and in-hospital mortality. <h4>Method and results</h4> We used data from the CAPACITY-COVID registry and LEOSS study. Multivariable Poisson regression models were fitted to assess the association between different types of pre-existent heart disease and in-hospital mortality. 16,511 patients with COVID-19 were included (21.1% aged 66 – 75 years; 40.2% female) and 31.5% had a history of heart disease. Patients with heart disease were older, predominantly male and often had other comorbid conditions when compared to those without. Mortality was higher in patients with cardiac disease (29.7%; n=1545 versus 15.9%; n=1797). However, following multivariable adjustment this difference was not significant (adjusted risk ratio (aRR) 1.08 [95% CI 1.02 – 1.15; p-value 0.12 (corrected for multiple testing)]). Associations with in-hospital mortality by heart disease subtypes differed considerably, with the strongest association for heart failure aRR (1.19 [1.10 – 1.30]; p-value <0.018) particularly for severe NYHA III/IV) heart failure (aRR 1.41 [95% CI 1.20 – 1.64; p-value <0.018]. None of the other heart disease subtypes, including ischemic heart disease, remained significant after multivariable adjustment. Serious cardiac complications were diagnosed in <1% of patients. <h4>Conclusion</h4> Considerable heterogeneity exists in the strength of association between heart disease subtypes and in-hospital mortality. Of all patients with heart disease, those with heart failure are at greatest risk of death when hospitalized with COVID-19. Serious cardiac complications are rare.",,pdf:https://academic.oup.com/eurheartj/article-pdf/43/11/1104/42879968/ehab656.pdf; doi:https://doi.org/10.1101/2021.03.11.21253106; html:https://europepmc.org/article/PPR/PPR296523; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR296523&type=FILE&fileName=EMS119336-pdf.pdf&mimeType=application/pdf
 PPR538641,https://doi.org/10.1101/2022.08.29.22279351,Insights into COVID-19 epidemiology and control from temporal changes in serial interval distributions in Hong Kong,"Ali ST, Chen D, Lim WW, Yeung A, Adam DC, Lau YC, Lau EHY, Wong JY, Xiao J, Ho F, Gao H, Wang L, Xu X, Du Z, Wu P, Leung GM, Cowling BJ.",,No Journal Info,2022,2022-08-30,Y,,,,"The serial interval distribution is used to approximate the generation time distribution, an essential parameter to predict the effective reproductive number “ R t ”, a measure of transmissibility. However, serial interval distributions may change as an epidemic progresses rather than remaining constant. Here we show that serial intervals in Hong Kong varied over time, closely associated with the temporal variation in COVID-19 case profiles and public health and social measures that were implemented in response to surges in community transmission. Quantification of the variation over time in serial intervals led to improved estimation of R t , and provided additional insights into the impact of public health measures on transmission of infections. <h4>One-Sentence Summary</h4> Real-time estimates of serial interval distributions can improve assessment of COVID-19 transmission dynamics and control.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/08/30/2022.08.29.22279351.full.pdf; doi:https://doi.org/10.1101/2022.08.29.22279351; html:https://europepmc.org/article/PPR/PPR538641; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR538641&type=FILE&fileName=EMS153686-pdf.pdf&mimeType=application/pdf
-PPR178438,https://doi.org/10.1101/2020.06.18.20134742,Racial and ethnic determinants of Covid-19 risk,"Lo C, Nguyen LH, Drew DA, Graham MS, Warner ET, Joshi AD, Astley CM, Guo C, Ma W, Mehta RS, Kwon S, Song M, Davies R, Capdevila J, Lee KA, Lochlainn MN, Varsavsky T, Sudre CH, Wolf J, Cozier YC, Rosenberg L, Wilkens LR, Haiman CA, Le Marchand L, Palmer JR, Spector TD, Ourselin S, Steves CJ, Chan AT.",,No Journal Info,2020,2020-06-20,Y,,,,"<h4>ABSTRACT</h4> <h4>Background</h4> Racial and ethnic minorities have disproportionately high hospitalization rates and mortality related to the novel coronavirus disease 2019 (Covid-19). There are comparatively scant data on race and ethnicity as determinants of infection risk. <h4>Methods</h4> We used a smartphone application (beginning March 24, 2020 in the United Kingdom [U.K.] and March 29, 2020 in the United States [U.S.]) to recruit 2,414,601 participants who reported their race/ethnicity through May 25, 2020 and employed logistic regression to determine the adjusted odds ratios (aORs) and 95% confidence intervals (CIs) for a positive Covid-19 test among racial and ethnic groups. <h4>Results</h4> We documented 8,858 self-reported cases of Covid-19 among 2,259,841 non-Hispanic white; 79 among 9,615 Hispanic; 186 among 18,176 Black; 598 among 63,316 Asian; and 347 among 63,653 other racial minority participants. Compared with non-Hispanic white participants, the risk for a positive Covid-19 test was increased across racial minorities (aORs ranging from 1.24 to 3.51). After adjustment for socioeconomic indices and Covid-19 exposure risk factors, the associations (aOR [95% CI]) were attenuated but remained significant for Hispanic (1.58 [1.24-2.02]) and Black participants (2.56 [1.93-3.39]) in the U.S. and South Asian (1.52 [1.38-1.67]) and Middle Eastern participants (1.56 [1.25-1.95]) in the U.K. A higher risk of Covid-19 and seeking or receiving treatment was also observed for several racial/ethnic minority subgroups. <h4>Conclusions</h4> Our results demonstrate an increase in Covid-19 risk among racial and ethnic minorities not completely explained by other risk factors for Covid-19, comorbidities, and sociodemographic characteristics. Further research investigating these disparities are needed to inform public health measures.",,pdf:http://www.thelancet.com/article/S2589537021003096/pdf; doi:https://doi.org/10.1101/2020.06.18.20134742; html:https://europepmc.org/article/PPR/PPR178438; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR178438&type=FILE&fileName=EMS88297-pdf.pdf&mimeType=application/pdf
+PPR178438,https://doi.org/10.1101/2020.06.18.20134742,Racial and ethnic determinants of Covid-19 risk,"Lo C, Nguyen LH, Drew DA, Graham MS, Warner ET, Joshi AD, Astley CM, Guo C, Ma W, Mehta RS, Kwon S, Song M, Davies R, Capdevila J, Lee KA, Lochlainn MN, Varsavsky T, Sudre CH, Wolf J, Cozier YC, Rosenberg L, Wilkens LR, Haiman CA, Le Marchand L, Palmer JR, Spector TD, Ourselin S, Steves CJ, Chan AT.",,No Journal Info,2020,2020-06-20,Y,,,,"<h4>ABSTRACT</h4> <h4>Background</h4> Racial and ethnic minorities have disproportionately high hospitalization rates and mortality related to the novel coronavirus disease 2019 (Covid-19). There are comparatively scant data on race and ethnicity as determinants of infection risk. <h4>Methods</h4> We used a smartphone application (beginning March 24, 2020 in the United Kingdom [U.K.] and March 29, 2020 in the United States [U.S.]) to recruit 2,414,601 participants who reported their race/ethnicity through May 25, 2020 and employed logistic regression to determine the adjusted odds ratios (aORs) and 95% confidence intervals (CIs) for a positive Covid-19 test among racial and ethnic groups. <h4>Results</h4> We documented 8,858 self-reported cases of Covid-19 among 2,259,841 non-Hispanic white; 79 among 9,615 Hispanic; 186 among 18,176 Black; 598 among 63,316 Asian; and 347 among 63,653 other racial minority participants. Compared with non-Hispanic white participants, the risk for a positive Covid-19 test was increased across racial minorities (aORs ranging from 1.24 to 3.51). After adjustment for socioeconomic indices and Covid-19 exposure risk factors, the associations (aOR [95% CI]) were attenuated but remained significant for Hispanic (1.58 [1.24-2.02]) and Black participants (2.56 [1.93-3.39]) in the U.S. and South Asian (1.52 [1.38-1.67]) and Middle Eastern participants (1.56 [1.25-1.95]) in the U.K. A higher risk of Covid-19 and seeking or receiving treatment was also observed for several racial/ethnic minority subgroups. <h4>Conclusions</h4> Our results demonstrate an increase in Covid-19 risk among racial and ethnic minorities not completely explained by other risk factors for Covid-19, comorbidities, and sociodemographic characteristics. Further research investigating these disparities are needed to inform public health measures.",,doi:https://doi.org/10.1101/2020.06.18.20134742; doi:https://doi.org/10.1101/2020.06.18.20134742; html:https://europepmc.org/article/PPR/PPR178438; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR178438&type=FILE&fileName=EMS88297-pdf.pdf&mimeType=application/pdf
 PPR269227,https://doi.org/10.1101/2021.01.15.21249756,Factors associated with deaths due to COVID-19 versus other causes: population-based cohort analysis of UK primary care data and linked national death registrations within the OpenSAFELY platform,"Bhaskaran K, Bacon S, Evans S, Bates C, Rentsch C, MacKenna B, Tomlinson L, Walker A, Schultze A, Morton C, Grint D, Mehrkar A, Eggo R, Inglesby P, Douglas I, McDonald H, Cockburn J, Williamson E, Evans D, Curtis H, Hulme W, Parry J, Hester F, Harper S, Spiegelhalter D, Smeeth L, Goldacre B.",,No Journal Info,2021,2021-01-20,Y,,,,"<h4>ABSTRACT</h4> <h4>Background</h4> Mortality from COVID-19 shows a strong relationship with age and pre-existing medical conditions, as does mortality from other causes. However it is unclear how specific factors are differentially associated with COVID-19 mortality as compared to mortality from other causes. <h4>Methods</h4> Working on behalf of NHS England, we carried out a cohort study within the OpenSAFELY platform. Primary care data from England were linked to national death registrations. We included all adults (aged ≥18 years) in the database on 1 st February 2020 and with >1 year of continuous prior registration, the cut-off date for deaths was 9 th November 2020. Associations between individual-level characteristics and COVID-19 and non-COVID deaths were estimated by fitting age- and sex-adjusted logistic models for these two outcomes. <h4>Results</h4> 17,456,515 individuals were included. 17,063 died from COVID-19 and 134,316 from other causes. Most factors associated with COVID-19 death were similarly associated with non-COVID death, but the magnitudes of association differed. Older age was more strongly associated with COVID-19 death than non-COVID death (e.g. ORs 40.7 [95% CI 37.7-43.8] and 29.6 [28.9-30.3] respectively for ≥80 vs 50-59 years), as was male sex, deprivation, obesity, and some comorbidities. Smoking, history of cancer and chronic liver disease had stronger associations with non-COVID than COVID-19 death. All non-white ethnic groups had higher odds than white of COVID-19 death (OR for Black: 2.20 [1.96-2.47], South Asian: 2.33 [2.16-2.52]), but lower odds than white of non-COVID death (Black: 0.88 [0.83-0.94], South Asian: 0.78 [0.75-0.81]). <h4>Interpretation</h4> Similar associations of most individual-level factors with COVID-19 and non-COVID death suggest that COVID-19 largely multiplies existing risks faced by patients, with some notable exceptions. Identifying the unique factors contributing to the excess COVID-19 mortality risk among non-white groups is a priority to inform efforts to reduce deaths from COVID-19. <h4>Funding</h4> Wellcome, Royal Society, National Institute for Health Research, National Institute for Health Research Oxford Biomedical Research Centre, UK Medical Research Council, Health Data Research UK.",,doi:https://doi.org/10.1016/j.lanepe.2021.100109; doi:https://doi.org/10.1101/2021.01.15.21249756; html:https://europepmc.org/article/PPR/PPR269227; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR269227&type=FILE&fileName=EMS112324-pdf.pdf&mimeType=application/pdf
 PPR204755,https://doi.org/10.1101/2020.08.21.20177808,Quarantine and testing strategies in contact tracing for SARS-CoV-2,"Quilty BJ, Clifford S, Flasche S, Kucharski AJ, CMMID COVID-19 Working Group, Edmunds WJ.",,No Journal Info,2020,2020-08-24,Y,,,,"<h4>Summary</h4> Previous work has indicated that contact tracing and isolation of index case and quarantine of potential secondary cases can, in concert with physical distancing measures, be an effective strategy for reducing transmission of SARS-CoV-2 (1). Currently, contacts traced manually through the NHS Test and Trace scheme in the UK are asked to self-isolate for 14 days from the day they were exposed to the index case, which represents the upper bound for the incubation period (2). However, following previous work on screening strategies for air travellers (3,4) it may be possible that this quarantine period could be reduced if combined with PCR testing. Adapting the simulation model for contact tracing, we find that quarantine periods of at least 10 days combined with a PCR test on day 9 may largely emulate the results from a 14-day quarantine period in terms of the averted transmission potential from secondary cases (72% (95%UI: 3%, 100%) vs 75% (4%, 100%), respectively). These results assume the delays from testing index cases’ and tracing their contacts are minimised (no longer than 4.5 days on average). If secondary cases are traced and quarantined 1 day earlier on average, shorter quarantine periods of 8 days with a test on day 7 (76% (7%, 100%)) approach parity with the 14 day quarantine period with a 1 day longer delay to the index cases’ test. However, the risk of false-negative PCR tests early in a traced case’s infectious period likely prevents the use of testing to reduce quarantine periods further than this, and testing immediately upon tracing, with release if negative, will avert just 17% of transmission potential on average. In conclusion, the use of PCR testing is an effective strategy for reducing quarantine periods for secondary cases, while still reducing transmission of SARS-CoV-2, especially if delays in the test and trace system can be reduced, and may improve quarantine compliance rates.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2020/10/23/2020.08.21.20177808.full.pdf; doi:https://doi.org/10.1101/2020.08.21.20177808; html:https://europepmc.org/article/PPR/PPR204755; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR204755&type=FILE&fileName=EMS95490-pdf.pdf&mimeType=application/pdf
 PPR639769,https://doi.org/10.1101/2023.04.01.23287538,Trends in weight gain recorded in English primary care before and during the Coronavirus-19 pandemic: an observational cohort study using the OpenSAFELY platform,"Samuel M, Park RY, Eastwood SV, Eto F, Morton CE, Stow D, Bacon S, Mehrkar A, Morley J, Dillingham I, Inglesby P, Hulme WJ, Khunti K, Mathur R, Valabhji J, MacKenna B, Finer S, The OpenSAFELY Collaborative.",,No Journal Info,2023,2023-04-03,Y,,,,"<h4>Background</h4> We investigated which clinical and sociodemographic characteristics were associated with unhealthy patterns of weight gain amongst adults living in England during the pandemic. <h4>Methods</h4> With the approval of NHS England we conducted an observational cohort study of Body Mass Index (BMI) changes between March 2015 and March 2022 using the OpenSAFELY-TPP platform. We estimated individual rates of weight gain before and during the pandemic, and identified individuals with rapid weight gain (>0·5kg/m 2 /year) in each period. We also estimated the change in rate of weight gain between the prepandemic and pandemic period and defined extreme-accelerators as the ten percent of individuals with the greatest increase (>1·84kg/m 2 /year). We estimated associations with these outcomes using multivariate logistic regression. <h4>Findings</h4> We extracted data on 17,742,365 adults (50·1% female, 76·1% White British). Median BMI increased from 27·8kg/m 2 [IQR:24·3-32·1] in 2019 (March 2019 to February 2020) to 28·0kg/m 2 [24·4-32·6] in 2021. Rapid pandemic weight gain (n=3,214,155) was associated with female sex (male vs female: aOR 0·76 [95%CI:0·76-0·76]); younger age (50-59-years vs 18–29-years: aOR 0·60 [0·60-0·61]); White British ethnicity (Black Caribbean vs White British: aOR 0·91 [0·89-0·94]); deprivation (least-deprived-IMD-quintile vs most-deprived: aOR 0·77 [0·77-0·78]); and long-term conditions, of which mental health conditions had the greatest effect (e.g. depression (aOR 1·18[1·17-1·18])). Similar characteristics increased risk of extreme acceleration (n=2,768,695). <h4>Interpretation</h4> We found female sex, younger age, deprivation and mental health conditions increased risk of unhealthy patterns of pandemic weight gain. This highlights the need to incorporate sociodemographic, physical, and mental health characteristics when formulating post-pandemic research, policies, and interventions targeting BMI. <h4>Funding</h4> NIHR",,pdf:https://www.medrxiv.org/content/medrxiv/early/2023/04/03/2023.04.01.23287538.full.pdf; doi:https://doi.org/10.1101/2023.04.01.23287538; html:https://europepmc.org/article/PPR/PPR639769; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR639769&type=FILE&fileName=EMS173550-pdf.pdf&mimeType=application/pdf
@@ -398,8 +398,8 @@ PPR273714,https://doi.org/10.1101/2021.01.25.21250356,Trends and clinical charac
 PPR339051,https://doi.org/10.1101/2021.05.06.21256755,Clinical coding of long COVID in English primary care: a federated analysis of 58 million patient records in situ using OpenSAFELY,"The OpenSAFELY Collaborative, Walker AJ, MacKenna B, Inglesby P, Rentsch CT, Curtis HJ, Morton CE, Morley J, Mehrkar A, Bacon S, Hickman G, Bates C, Croker R, Evans D, Ward T, Cockburn J, Davy S, Bhaskaran K, Schultze A, Williamson EJ, Hulme WJ, McDonald HI, Tomlinson L, Mathur R, Eggo RM, Wing K, Wong AY, Forbes H, Tazare J, Parry J, Hester F, Harper S, O’Hanlon S, Eavis A, Jarvis R, Avramov D, Griffiths P, Fowles A, Parkes N, Douglas IJ, Evans SJ, Smeeth L, Goldacre B.",,No Journal Info,2021,2021-05-13,Y,,,,"<h4>Background</h4> Long COVID is a term to describe new or persistent symptoms at least four weeks after onset of acute COVID-19. Clinical codes to describe this phenomenon were released in November 2020 in the UK, but it is not known how these codes have been used in practice. <h4>Methods</h4> Working on behalf of NHS England, we used OpenSAFELY data encompassing 96% of the English population. We measured the proportion of people with a recorded code for long COVID, overall and by demographic factors, electronic health record software system, and week. We also measured variation in recording amongst practices. <h4>Results</h4> Long COVID was recorded for 23,273 people. Coding was unevenly distributed amongst practices, with 26.7% of practices having not used the codes at all. Regional variation was high, ranging between 20.3 per 100,000 people for East of England (95% confidence interval 19.3-21.4) and 55.6 in London (95% CI 54.1-57.1). The rate was higher amongst women (52.1, 95% CI 51.3-52.9) compared to men (28.1, 95% CI 27.5-28.7), and higher amongst practices using EMIS software (53.7, 95% CI 52.9-54.4) compared to TPP software (20.9, 95% CI 20.3-21.4). <h4>Conclusions</h4> Long COVID coding in primary care is low compared with early reports of long COVID prevalence. This may reflect under-coding, sub-optimal communication of clinical terms, under-diagnosis, a true low prevalence of long COVID diagnosed by clinicians, or a combination of factors. We recommend increased awareness of diagnostic codes, to facilitate research and planning of services; and surveys of clinicians’ experiences, to complement ongoing patient surveys.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2021/05/13/2021.05.06.21256755.1.full.pdf; doi:https://doi.org/10.1101/2021.05.06.21256755; html:https://europepmc.org/article/PPR/PPR339051; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR339051&type=FILE&fileName=EMS124533-pdf.pdf&mimeType=application/pdf
 PPR401012,https://doi.org/10.1101/2021.09.27.21264005,“<i>The vaccination is positive; I don’t think it’s the panacea</i>”: A qualitative study on COVID-19 vaccine attitudes among ethnically diverse healthcare workers in the United Kingdom,"Gogoi M, Wobi F, Qureshi I, Al-Oraibi A, Hassan O, Nellums LB, Pareek M.",,No Journal Info,2021,2021-09-28,Y,,,,"<h4>Background</h4> Globally, healthcare workers (HCWs) are prioritised for receiving vaccinations against the coronavirus disease-2019 (COVID-19). Previous research has shown disparities in COVID-19 vaccination uptake among HCWs based on ethnicity, job role, sex, age, and deprivation. However, vaccine attitudes underpinning these variations are yet to be fully explored. <h4>Methods</h4> We conducted a qualitative study with 164 HCWs from different ethnicities, sexes, job roles, migration statuses, and regions in the United Kingdom (UK). Interviews and focus groups were conducted using Microsoft Teams or telephone, and recorded with participants’ permission. Recordings were transcribed and thematically analysed following an inductive approach. <h4>Findings</h4> We conducted an in-depth analysis of 53 randomly selected transcripts (involving 82 participants) to generate rapid evidence. Four different vaccine attitudes were identified: Active Acceptance, Passive Acceptance, Passive Decline, and Active Decline. Factors influencing vaccine acceptance include: knowledge of vaccine; risk perception; positive attitude towards other vaccines; social influences; and considerations about the future. Correspondingly, barriers to vaccine acceptance were identified as, low trust in the vaccine and historical (mis)trust, inadequate communication, and inequities in delivery and access. Opinion on mandatory vaccination was divided. <h4>Interpretation</h4> Our data show that vaccine attitudes are diverse and elements of hesitancy may remain even after vaccine acceptance. This has implications for the sustainability of the vaccine programme, particularly as new components (e.g. boosters) are being added. Based on our findings we recommend trust-building, designing inclusive and accessible information, and addressing structural inequities for improving vaccine uptake among HCWs. <h4>Funding</h4> UKRI-MRC and NIHR.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2021/09/28/2021.09.27.21264005.full.pdf; doi:https://doi.org/10.1101/2021.09.27.21264005; html:https://europepmc.org/article/PPR/PPR401012; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR401012&type=FILE&fileName=EMS136658-pdf.pdf&mimeType=application/pdf
 PPR157839,https://doi.org/10.1101/2020.04.27.20081711,Response strategies for COVID-19 epidemics in African settings: a mathematical modelling study,"Zandvoort Kv, Jarvis CI, Pearson CAB, Davies NG, CMMID COVID-19 working group, Russell TW, Kucharski AJ, Jit M, Flasche S, Eggo RM, Checchi F.",,No Journal Info,2020,2020-05-03,Y,,,,"<h4>Background</h4> The health impact of COVID-19 may differ in African settings as compared to countries in Europe or China due to demographic, epidemiological, environmental and socio-economic factors. We evaluated strategies to reduce SARS-CoV-2 burden in African countries, so as to support decisions that balance minimising mortality, protecting health services and safeguarding livelihoods. <h4>Methods</h4> We used a Susceptible-Exposed-Infectious-Recovered mathematical model, stratified by age, to predict the evolution of COVID-19 epidemics in three countries representing a range of age distributions in Africa (from oldest to youngest average age: Mauritius, Nigeria and Niger), under various effectiveness assumptions for combinations of different non-pharmaceutical interventions: self-isolation of symptomatic people, physical distancing, and ‘shielding’ (physical isolation) of the high-risk population. We adapted model parameters to better represent uncertainty about what might be expected in African populations, in particular by shifting the distribution of severity risk towards younger ages and increasing the case-fatality ratio. <h4>Results</h4> We predicted median clinical attack rates over the first 12 months of 17% (Niger) to 39% (Mauritius), peaking at 2–4 months, if epidemics were unmitigated. Self-isolation while symptomatic had a maximum impact of about 30% on reducing severe cases, while the impact of physical distancing varied widely depending on percent contact reduction and R 0 . The effect of shielding high-risk people, e.g. by rehousing them in physical isolation, was sensitive mainly to residual contact with low-risk people, and to a lesser extent to contact among shielded individuals. Response strategies incorporating self-isolation of symptomatic individuals, moderate physical distancing and high uptake of shielding reduced predicted peak bed demand by 46% to 54% and mortality by 60% to 75%. Lockdowns delayed epidemics by about 3 months. Estimates were sensitive to differences in age-specific social mixing patterns, as published in the literature. <h4>Discussion</h4> In African settings, as elsewhere, current evidence suggests large COVID-19 epidemics are expected. However, African countries have fewer means to suppress transmission and manage cases. We found that self-isolation of symptomatic persons and general physical distancing are unlikely to avert very large epidemics, unless distancing takes the form of stringent lockdown measures. However, both interventions help to mitigate the epidemic. Shielding of high-risk individuals can reduce health service demand and, even more markedly, mortality if it features high uptake and low contact of shielded and unshielded people, with no increase in contact among shielded people. Strategies combining self-isolation, moderate physical distancing and shielding will probably achieve substantial reductions in mortality in African countries. Temporary lockdowns, where socioeconomically acceptable, can help gain crucial time for planning and expanding health service capacity.","Zandvoort et al. used mathematical modelling and simulation methods to predict the impact of various control scenarios on outcome of COVID-19 epidemics in three African countries. They’ve shown that mixed strategies, including moderate physical distancing and shielding are more likely to achieve substantial reductions in mortality in African countries. ",pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-020-01789-2; doi:https://doi.org/10.1101/2020.04.27.20081711; html:https://europepmc.org/article/PPR/PPR157839; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR157839&type=FILE&fileName=EMS91299-pdf.pdf&mimeType=application/pdf
-PPR609122,https://doi.org/10.1101/2023.01.25.23285005,Call detail record aggregation methodology impacts infectious disease models informed by human mobility,"Gibbs H, Musah A, Seidu O, Ampofo W, Asiedu-Bekoe F, Gray J, Adewole WA, Cheshire J, Marks M, Eggo RM.",,No Journal Info,2023,2023-01-28,Y,,,,"This paper demonstrates how two different methods used to calculate population-level mobility from Call Detail Records (CDR) produce varying predictions of the spread of epidemics informed by these data. Our findings are based on one CDR dataset describing inter-district movement in Ghana in 2021, produced using two different aggregation methodologies. One methodology, “all pairs,” is designed to retain long distance network connections while the other, “sequential” methodology is designed to accurately reflect the volume of travel between locations. We show how the choice of methodology feeds through models of human mobility to the predictions of a metapopulation SEIR model of disease transmission. We also show that this impact varies depending on the location of pathogen introduction and transmissibility. For central locations or highly transmissible diseases, we do not observe significant differences between aggregation methodologies on the predicted spread of disease. For less transmissible diseases or those introduced into remote locations, we find that the choice of aggregation methodology influences the speed of spatial spread as well as the size of the peak number of infections in individual districts. Our findings can help researchers and users of epidemiological models to understand how methodological choices at the level of model inputs may influence the results of models of infectious disease transmission, as well as the circumstances in which these choices do not alter model predictions. <h4>Author Summary</h4> Predicting the sub-national spread of infectious disease requires accurate measurements of inter-regional travel networks. Often, this information is derived from the patterns of mobile device connections to the cellular network. This travel data is then used as an input to epidemiological models of infection transmission, defining the likelihood that disease is “exported” between regions. In this paper, we use one mobile device dataset collected in Ghana in 2021, aggregated according to two different methodologies which represent different aspects of inter-regional travel. We show how the choice of aggregation methodology leads to different predicted epidemics, and highlight the conditions under which models of infection transmission may be influenced by methodological choices in the aggregation of travel data used to parameterize these models. For example, we show how aggregation methodology changes predicted epidemics for less-transmissible infections and under certain models of human movement. We also highlight areas of relative stability, where aggregation choices do not alter predicted epidemics, such as cases where an infection is highly transmissible or is introduced into a central location.",,pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011368&type=printable; doi:https://doi.org/10.1101/2023.01.25.23285005; html:https://europepmc.org/article/PPR/PPR609122; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR609122&type=FILE&fileName=EMS163650-pdf.pdf&mimeType=application/pdf
 PPR558613,https://doi.org/10.1101/2022.10.17.22281058,Eleven key measures for monitoring general practice clinical activity during COVID-19 using federated analytics on 48 million adults’ primary care records through OpenSAFELY,"Fisher L, Curtis HJ, Croker R, Wiedemann M, Speed V, Wood C, Brown A, Hopcroft LE, Higgins R, Massey J, Inglesby P, Morton CE, Walker AJ, Morley J, Mehrkar A, Bacon S, Hickman G, Macdonald O, Lewis T, Wood M, Myers M, Samuel M, Conibere R, Baqir W, Sood H, Drury C, Collison K, Bates C, Evans D, Dillingham I, Ward T, Davy S, Smith RM, Hulme W, Green A, Parry J, Hester F, Harper S, Cockburn J, O’Hanlon S, Eavis A, Jarvis R, Avramov D, Griffiths P, Fowles A, Parkes N, MacKenna B, Goldacre B.",,No Journal Info,2022,2022-10-17,Y,,,,"<h4>Background</h4> The COVID-19 pandemic has had a significant impact on delivery of NHS care. We have developed the OpenSAFELY Service Restoration Observatory (SRO) to describe this impact on primary care activity and monitor its recovery. <h4>Objectives</h4> To develop key measures of primary care activity and describe the trends in these measures throughout the COVID-19 pandemic. <h4>Methods</h4> With the approval of NHS England we developed an open source software framework for data management and analysis to describe trends and variation in clinical activity across primary care electronic health record (EHR) data on 48 million adults. We developed SNOMED-CT codelists for key measures of primary care clinical activity selected by a expert clinical advisory group and conducted a population cohort-based study to describe trends and variation in these measures January 2019-December 2021, and pragmatically classified their level of recovery one year into the pandemic using the percentage change in the median practice level rate. <h4>Results</h4> We produced 11 measures reflective of clinical activity in general practice. A substantial drop in activity was observed in all measures at the outset of the COVID-19 pandemic. By April 2021, the median rate had recovered to within 15% of the median rate in April 2019 in six measures. The remaining measures showed a sustained drop, ranging from a 18.5% reduction in medication reviews to a 42.0% reduction in blood pressure monitoring. Three measures continued to show a sustained drop by December 2021. <h4>Conclusions</h4> The COVID-19 pandemic was associated with a substantial change in primary care activity across the measures we developed, with recovery in most measures. We delivered an open source software framework to describe trends and variation in clinical activity across an unprecedented scale of primary care data. We will continue to expand the set of key measures to be routinely monitored using our publicly available NHS OpenSAFELY SRO dashboards with near real-time data.",,doi:https://doi.org/10.1101/2022.10.17.22281058; doi:https://doi.org/10.1101/2022.10.17.22281058; html:https://europepmc.org/article/PPR/PPR558613; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR558613&type=FILE&fileName=EMS155818-pdf.pdf&mimeType=application/pdf
+PPR609122,https://doi.org/10.1101/2023.01.25.23285005,Call detail record aggregation methodology impacts infectious disease models informed by human mobility,"Gibbs H, Musah A, Seidu O, Ampofo W, Asiedu-Bekoe F, Gray J, Adewole WA, Cheshire J, Marks M, Eggo RM.",,No Journal Info,2023,2023-01-28,Y,,,,"This paper demonstrates how two different methods used to calculate population-level mobility from Call Detail Records (CDR) produce varying predictions of the spread of epidemics informed by these data. Our findings are based on one CDR dataset describing inter-district movement in Ghana in 2021, produced using two different aggregation methodologies. One methodology, “all pairs,” is designed to retain long distance network connections while the other, “sequential” methodology is designed to accurately reflect the volume of travel between locations. We show how the choice of methodology feeds through models of human mobility to the predictions of a metapopulation SEIR model of disease transmission. We also show that this impact varies depending on the location of pathogen introduction and transmissibility. For central locations or highly transmissible diseases, we do not observe significant differences between aggregation methodologies on the predicted spread of disease. For less transmissible diseases or those introduced into remote locations, we find that the choice of aggregation methodology influences the speed of spatial spread as well as the size of the peak number of infections in individual districts. Our findings can help researchers and users of epidemiological models to understand how methodological choices at the level of model inputs may influence the results of models of infectious disease transmission, as well as the circumstances in which these choices do not alter model predictions. <h4>Author Summary</h4> Predicting the sub-national spread of infectious disease requires accurate measurements of inter-regional travel networks. Often, this information is derived from the patterns of mobile device connections to the cellular network. This travel data is then used as an input to epidemiological models of infection transmission, defining the likelihood that disease is “exported” between regions. In this paper, we use one mobile device dataset collected in Ghana in 2021, aggregated according to two different methodologies which represent different aspects of inter-regional travel. We show how the choice of aggregation methodology leads to different predicted epidemics, and highlight the conditions under which models of infection transmission may be influenced by methodological choices in the aggregation of travel data used to parameterize these models. For example, we show how aggregation methodology changes predicted epidemics for less-transmissible infections and under certain models of human movement. We also highlight areas of relative stability, where aggregation choices do not alter predicted epidemics, such as cases where an infection is highly transmissible or is introduced into a central location.",,pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011368&type=printable; doi:https://doi.org/10.1101/2023.01.25.23285005; html:https://europepmc.org/article/PPR/PPR609122; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR609122&type=FILE&fileName=EMS163650-pdf.pdf&mimeType=application/pdf
 PPR237625,https://doi.org/10.1101/2020.11.09.20228015,A time-resolved proteomic and diagnostic map characterizes COVID-19 disease progression and predicts outcome,"Demichev V, Tober-Lau P, Nazarenko T, Thibeault C, Whitwell H, Lemke O, Röhl A, Freiwald A, Szyrwiel L, Ludwig D, Correia-Melo C, Helbig ET, Stubbemann P, Grüning N, Blyuss O, Vernardis S, White M, Messner CB, Joannidis M, Sonnweber T, Klein SJ, Pizzini A, Wohlfarter Y, Sahanic S, Hilbe R, Schaefer B, Wagner S, Mittermaier M, Machleidt F, Garcia C, Ruwwe-Glösenkamp C, Lingscheid T, de Jarcy LB, Stegemann MS, Pfeiffer M, Jürgens L, Denker S, Zickler D, Enghard P, Zelezniak A, Campbell A, Hayward C, Porteous DJ, Marioni RE, Uhrig A, Müller-Redetzky H, Zoller H, Löffler-Ragg J, Keller MA, Tancevski I, Timms JF, Zaikin A, Hippenstiel S, Ramharter M, Witzenrath M, Suttorp N, Lilley K, Mülleder M, Sander LE, PA-COVID-19 Study group, Ralser M, Kurth F.",,No Journal Info,2020,2020-11-12,Y,,,,"COVID-19 is highly variable in its clinical presentation, ranging from asymptomatic infection to severe organ damage and death. There is an urgent need for predictive markers that can guide clinical decision-making, inform about the effect of experimental therapies, and point to novel therapeutic targets. Here, we characterize the time-dependent progression of COVID-19 through different stages of the disease, by measuring 86 accredited diagnostic parameters and plasma proteomes at 687 sampling points, in a cohort of 139 patients during hospitalization. We report that the time-resolved patient molecular phenotypes reflect an initial spike in the systemic inflammatory response, which is gradually alleviated and followed by a protein signature indicative of tissue repair, metabolic reconstitution and immunomodulation. Further, we show that the early host response is predictive for the disease trajectory and gives rise to proteomic and diagnostic marker signatures that classify the need for supplemental oxygen therapy and mechanical ventilation, and that predict the time to recovery of mildly ill patients. In severely ill patients, the molecular phenotype of the early host response predicts survival, in two independent cohorts and weeks before outcome. We also identify age-specific molecular response to COVID-19, which involves increased inflammation and lipoprotein dysregulation in older patients. Our study provides a deep and time resolved molecular characterization of COVID-19 disease progression, and reports biomarkers for risk-adapted treatment strategies and molecular disease monitoring. Our study demonstrates accurate prognosis of COVID-19 outcome from proteomic signatures recorded weeks earlier.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2020/11/12/2020.11.09.20228015.full.pdf; doi:https://doi.org/10.1101/2020.11.09.20228015; html:https://europepmc.org/article/PPR/PPR237625; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR237625&type=FILE&fileName=EMS104194-pdf.pdf&mimeType=application/pdf
 PPR139421,https://doi.org/10.1101/2020.04.01.20049908,"The effect of non-pharmaceutical interventions on COVID-19 cases, deaths and demand for hospital services in the UK: a modelling study","Davies NG, Kucharski AJ, Eggo RM, Gimma A, CMMID COVID-19 working group, Edmunds WJ.",,No Journal Info,2020,2020-04-06,Y,,,,"<h4>Background</h4> Non-pharmaceutical interventions have been implemented to reduce transmission of SARS-CoV-2 in the UK. Projecting the size of an unmitigated epidemic and the potential effect of different control measures has been critical to support evidence-based policymaking during the early stages of the epidemic. <h4>Methods</h4> We used a stochastic age-structured transmission model to explore a range of intervention scenarios, including the introduction of school closures, social distancing, shielding of elderly groups, self-isolation of symptomatic cases, and extreme “lockdown”-type restrictions. We simulated different durations of interventions and triggers for introduction, as well as combinations of interventions. For each scenario, we projected estimated new cases over time, patients requiring inpatient and critical care (intensive care unit, ICU) treatment, and deaths. <h4>Findings</h4> We found that mitigation measures aimed at reducing transmission would likely have decreased the reproduction number, but not sufficiently to prevent ICU demand from exceeding NHS availability. To keep ICU bed demand below capacity in the model, more extreme restrictions were necessary. In a scenario where “lockdown”-type interventions were put in place to reduce transmission, these interventions would need to be in place for a large proportion of the coming year in order to prevent healthcare demand exceeding availability. <h4>Interpretation</h4> The characteristics of SARS-CoV-2 mean that extreme measures are likely required to bring the epidemic under control and to prevent very large numbers of deaths and an excess of demand on hospital beds, especially those in ICUs. <h4>Research in Context</h4> <h4>Evidence before this study</h4> As countries have moved from early containment efforts to planning for the introduction of large-scale non-pharmaceutical interventions to control COVID-19 outbreaks, epidemic modelling studies have explored the potential for extensive social distancing measures to curb transmission. However, it remains unclear how different combinations of interventions, timings, and triggers for the introduction and lifting of control measures may affect the impact of the epidemic on health services, and what the range of uncertainty associated with these estimates would be. <h4>Added value of this study</h4> Using a stochastic, age-structured epidemic model, we explored how eight different intervention scenarios could influence the number of new cases and deaths, as well as intensive care beds required over the projected course of the epidemic. We also assessed the potential impact of local versus national targeting of interventions, reduction in leisure events, impact of increased childcare by grandparents, and timing of triggers for different control measures. We simulated multiple realisations for each scenario to reflect uncertainty in possible epidemic trajectories. <h4>Implications of all the available evidence</h4> Our results support early modelling findings, and subsequent empirical observations, that in the absence of control measures, a COVID-19 epidemic could quickly overwhelm a healthcare system. We found that even a combination of moderate interventions – such as school closures, shielding of older groups and self-isolation – would be unlikely to prevent an epidemic that would far exceed available ICU capacity in the UK. Intermittent periods of more intensive lockdown-type measures are predicted to be effective for preventing the healthcare system from being overwhelmed.","It is highly important to know the outcome of different scenarios ahead of critical decisions. Davies et al. shed light on various scenarios considering there is no drug or vaccine for the COVID-19. They’ve looked at interventions such as school closure, social distancing, shielding of the elderly, self-isolation of those with symptoms and shown that all of these reduces the total number of cases by 70-75% and delays the peak of epidemic by 3-8 weeks. Social distancing have the greatest impact in total number of cases while elderly shielding had the greatest impact on number of deaths.",pdf:http://www.thelancet.com/article/S246826672030133X/pdf; doi:https://doi.org/10.1101/2020.04.01.20049908; html:https://europepmc.org/article/PPR/PPR139421; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR139421&type=FILE&fileName=EMS89534-pdf.pdf&mimeType=application/pdf
 PPR362420,https://doi.org/10.1101/2021.06.24.21259374,A proteomic survival predictor for COVID-19 patients in intensive care,"Demichev V, Tober-Lau P, Nazarenko T, Aulakh SK, Whitwell H, Lemke O, Röhl A, Freiwald A, Mittermaier M, Szyrwiel L, Ludwig D, Correia-Melo C, Lippert LJ, Helbig ET, Stubbemann P, Olk N, Thibeault C, Grüning N, Blyuss O, Vernardis S, White M, Messner CB, Joannidis M, Sonnweber T, Klein SJ, Pizzini A, Wohlfarter Y, Sahanic S, Hilbe R, Schaefer B, Wagner S, Machleidt F, Garcia C, Ruwwe-Glösenkamp C, Lingscheid T, de Jarcy LB, Stegemann MS, Pfeiffer M, Jürgens L, Denker S, Zickler D, Spies C, Edel A, Müller NB, Enghard P, Zelezniak A, Bellmann-Weiler R, Weiss G, Campbell A, Hayward C, Porteous DJ, Marioni RE, Uhrig A, Zoller H, Löffler-Ragg J, Keller MA, Tancevski I, Timms JF, Zaikin A, Hippenstiel S, Ramharter M, Müller-Redetzky H, Witzenrath M, Suttorp N, Lilley K, Mülleder M, Sander LE, PA-COVID-19 Study group, Kurth F, Ralser M.",,No Journal Info,2021,2021-06-26,N,,,,"Global healthcare systems are challenged by the COVID-19 pandemic. There is a need to optimize allocation of treatment and resources in intensive care, as clinically established risk assessments such as SOFA and APACHE II scores show only limited performance for predicting the survival of severely ill COVID-19 patients. Comprehensively capturing the host physiology, we speculated that proteomics in combination with new data-driven analysis strategies could produce a new generation of prognostic discriminators. We studied two independent cohorts of patients with severe COVID-19 who required intensive care and invasive mechanical ventilation. SOFA score, Charlson comorbidity index and APACHE II score were poor predictors of survival. Plasma proteomics instead identified 14 proteins that showed concentration trajectories different between survivors and non-survivors. A proteomic predictor trained on single samples obtained at the first time point at maximum treatment level (i.e. WHO grade 7) and weeks before the outcome, achieved accurate classification of survivors in an exploratory (AUROC 0.81) as well as in the independent validation cohort (AUROC of 1.0). The majority of proteins with high relevance in the prediction model belong to the coagulation system and complement cascade. Our study demonstrates that predictors derived from plasma protein levels have the potential to substantially outperform current prognostic markers in intensive care. <h4>Trial registration</h4> German Clinical Trials Register DRKS00021688",,pdf:https://journals.plos.org/digitalhealth/article/file?id=10.1371/journal.pdig.0000007&type=printable; doi:https://doi.org/10.1101/2021.06.24.21259374; html:https://europepmc.org/article/PPR/PPR362420; doi:https://doi.org/10.1101/2021.06.24.21259374
@@ -408,8 +408,8 @@ PPR129796,https://doi.org/10.1101/2020.03.24.20043018,Age-dependent effects in t
 
 Alternative lay summary: This study aimed to explain the differences in the risk of infection with COVID-19 between people of different ages, using data from 6 countries. The authors found that age was a very important factor in showing signs of infection (20% chance of having symptoms aged <10y, 70% in older adults), but that age may not influence the chance of being infected. These findings are important because they suggest that closing schools may be less effective in preventing spread of infection than for infections like influenza where children play a bigger role in spreading the disease.",pdf:https://www.nature.com/articles/s41591-020-0962-9.pdf; doi:https://doi.org/10.1101/2020.03.24.20043018; html:https://europepmc.org/article/PPR/PPR129796; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR129796&type=FILE&fileName=EMS89351-pdf.pdf&mimeType=application/pdf
 PPR645696,https://doi.org/10.1101/2023.04.14.23287661,"Determining prescriptions in electronic healthcare record (EHR) data: methods for development of standardized, reproducible drug codelists","Graul EL, Stone PW, Massen GM, Hatam S, Adamson A, Denaxas S, Peters NS, Quint JK.",,No Journal Info,2023,2023-04-17,Y,,,,"<h4>ABSTRACT</h4> <h4>Objective</h4> Epidemiological research using electronic healthcare records(EHR) informing everyday patient care uses combinations of codes (“codelists”) to define diseases and prescriptions (or phenotypes). Yet methodology for codelist generation varies, manifesting in misclassification bias, while there are drug-specific codelist considerations. <h4>Materials and Methods</h4> We developed methods to generate drug codelists, testing this using the Clinical Practice Research Datalink (CPRD) Aurum database, accounting for missing data in “attribute” search variables. We generated codelists for 1)cardiovascular disease and 2)inhaled Chronic Obstructive Pulmonary Disease (COPD) therapies, applying them to a sample cohort of 335,931 COPD patients. We compared searching on all search variables (A,”gold standard”) to B) chemical and C) ontological information only. <h4>Results</h4> In Search A we determined 165,150 patients prescribed cardiovascular drugs(49.2% of cohort), and 317,963 prescribed COPD inhalers (94.7% of cohort). Considering output per value set, Search C missed substantial prescriptions, including vasodilator anti-hypertensives (A and B:19,696 prescriptions; C:1,145) and SAMA inhalers (A and B:35,310; C:564). <h4>Discussion</h4> We recommend the full methods (A) for comprehensiveness. There are special considerations when generating adaptable and generalizable drug codelists, including fluctuating status, cohort-specific drug indications, underlying hierarchical ontology, and statistical analyses. <h4>Conclusions</h4> <h4>Methods: </h4> must have end-to-end clinical input, and be standardizable, reproducible, and understandable to all researchers across data contexts. <h4>LAY ABSTRACT</h4> Health research using patient records informs everyday medicine, using groups of codes (“codelists”) to define diseases and drugs. Yet methods to create drug codelists are inconsistent, may not include physician expertise, nor be reported. We developed a reproducible method to create drug codelists, testing it using de-identified healthcare records. We generated codelists for 1) heart conditions and 2) inhalers to identify prescriptions in a sample group of 335,931 patients with chronic lung disease. We compared our full methods (Search A) to two restricted searches to show prescriptions can be missed if necessary considerations are not made. In search A, we determined 165,150 people (49.2% of sample group) prescribed drugs from the heart codelist. For lung inhalers, we determined 317,963 prescriptions (94.7% of group). Search C missed substantial prescriptions, for drugs lowering blood pressure by opening vessels (A and B:19,696 prescriptions; C: 1,145), and short-term inhalers opening airways (A and B: 35,310; C:564). We recommend full methods(A) for completeness. Drug codelist methods must be consistent, duplicable, and include physician input at all research stages, and have special considerations including status (eg, new, taken off market), disease, and drug categorical system. Quality methods should be freely accessible and usable across study contexts.",,pdf:https://academic.oup.com/jamiaopen/article-pdf/6/3/ooad078/51279371/ooad078.pdf; doi:https://doi.org/10.1101/2023.04.14.23287661; html:https://europepmc.org/article/PPR/PPR645696; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR645696&type=FILE&fileName=EMS174337-pdf.pdf&mimeType=application/pdf
-PPR704199,https://doi.org/10.2139/ssrn.4547861,Hospital Admission Related to Common Infections in Primary Care in England: Risk Prediction and Evaluation of the Impact of COVID-19 Pandemic Using OpenSAFELY,"Fahmi A, Palin V, Zhong X, Yang Y, Watts S, Ashcroft D, Goldacre B, Mackenna B, Fisher L, Massey J, Mehrkar A, Bacon S, Group OC, Hand K, Staa TPV.",,No Journal Info,2023,2023-08-28,N,,,,"Background: Antimicrobial resistance (AMR) is a multifaceted global challenge, partly driven by inappropriate antibiotic prescribing. The COVID-19 pandemic impacted antibiotic prescribing for common bacterial infections. This highlights the need to examine risk of hospital admissions related to common infections, excluding COVID-19 infections during the pandemic<br><br>Methods: With the approval of NHS England, we accessed electronic health records from The Phoenix Partnership (TPP) through OpenSAFELY platform. We included patients with primary care diagnosis of common infections, including lower respiratory tract infection (LRTI), upper respiratory tract infections (URTI), and lower urinary tract infection (UTI), from January 2019 to August 2022. We excluded patients with a COVID-19 record 90 days before to 30 days after the infection diagnosis. Using Cox proportional-hazard regression models, we predicted risk of infection-related hospital admission in 30 days follow-up period after the diagnosis.<br><br>Findings: We found 12,745,165 infection diagnoses from January 2019 to August 2022. Of them, 80,395 (2·05%) cases were admitted to hospital in the follow-up period. Counts of hospital admission for infections dropped during COVID-19, e.g., LRTI from 3,950 in December 2019 to 520 in April 2020. Comparing those prescribed an antibiotic to those without, reduction in risk of hospital admission were largest with LRTI (adjusted odds ratio (OR) of 0·35; 95% confidence interval (CI), 0·35-0·36) and UTI (adjusted OR 0·45; 95% CI, 0·44-0·46), compared to URTI (adjusted OR 1·04; 95% CI, 1·03-1·06).<br><br>Interpretation: Large effectiveness of antibiotics in preventing complications related to LRTI and UTI can support better targeting of antibiotics to patients with higher complication risks.<br><br>Funding: Health Data Research UK and National Institute for Health Research.<br><br>Declaration of Interest: All authors declare the following: BG and OpenSAFELY has received research funding from the Laura and John Arnold Foundation, the NHS National Institute for Health Research (NIHR), the NIHR School of Primary Care Research, NHS England, the NIHR Oxford Biomedical Research Centre, the Mohn-Westlake Foundation, NIHR Applied Research Collaboration Oxford and Thames Valley, the Wellcome Trust, the Good Thinking Foundation, Health Data Research UK, the Health Foundation, the World Health Organisation, UKRI MRC, Asthma UK, the British Lung Foundation, and the Longitudinal Health and Wellbeing strand of the National Core Studies programme; he is a Non-Executive Director at NHS Digital; he also receives personal income from speaking and writing for lay audiences on the misuse of science. AM has received consultancy fees (from https://inductionhealthcare.com) and is member of RCGP health informatics group and the NHS Digital GP data Professional Advisory Group that advises on access to GP Data for Pandemic Planning and Research (GDPPR). For the latter, he received payment for the GDPPR role.<br><br>Ethical Approval: This study was approved by the Health Research Authority and NHS Research Ethics Committee [REC reference 21/SC/0287].",,doi:https://doi.org/10.2139/ssrn.4547861; html:https://europepmc.org/article/PPR/PPR704199; doi:https://doi.org/10.2139/ssrn.4547861
 PPR291740,https://doi.org/10.1101/2021.03.03.21252737,"Ethnicity and COVID-19 outcomes among healthcare workers in the United Kingdom: UK-REACH ethico-legal research, qualitative research on healthcare workers’ experiences, and stakeholder engagement protocol","Gogoi M, Reed-Berendt R, Al-Oraibi A, Hassan O, Wobi F, Gupta A, Abubakar I, Dove ES, Nellums LB, Pareek M.",,No Journal Info,2021,2021-03-03,Y,,,,"<h4>ABSTRACT</h4> <h4>Introduction</h4> As the world continues to grapple with the COVID-19 pandemic, emerging evidence suggests that individuals from ethnic minority backgrounds may be disproportionately affected. The UK-REACH project has been initiated to understand ethnic differentials in COVID-19 outcomes among healthcare workers (HCWs) in the United Kingdom (UK) through five inter-linked work packages. The ethico-legal work package (Work Package 3) aims to understand and address legal, ethical and acceptability issues around big data research; the healthcare workers’ experiences work package (Work Package 4) is a qualitative study exploring healthcare workers’ experiences during COVID-19 and; the stakeholder engagement work package (Work Package 5) aims to provide feedback and support with the formulation and dissemination of the project recommendations. <h4>Methods and Analysis</h4> Work Package 3 has two different research strands: (a) desk-based doctrinal research; and (b) empirical qualitative research with key opinion leaders. For the empirical research, in-depth interviews will be conducted digitally and recorded with participants’ permission. Recordings will be transcribed, coded and analysed using thematic analysis. In Work Package 4, online in-depth interviews and focus groups will be conducted with approximately 150 HCWs, from across the UK, and these will be recorded with participants’ consent. The recordings will be transcribed, coded and data will be analysed using thematic analysis. Work Package 5 will achieve its objectives through regular group meetings and in-group discussions. <h4>Ethics and Dissemination</h4> Ethical approval has been received from the London - Brighton & Sussex Research Ethics Committee of the Health Research Authority (Ref No. 20/HRA/4718). Results of the study will be published in open access journals, and disseminated through conference presentations, project website, stakeholder organisations, media and scientific advisory groups. <h4>Registration Details</h4> Registered with the International Standard Randomised Controlled Trial Number registry ( ISRCTN11811602 ). <h4>STRENGTHS AND LIMITATIONS OF THIS STUDY</h4> The dual approach of doctrinal and empirical research (Work Package 3) on the use of personal data by UK-REACH will give a comprehensive understanding of the ethical and legal implications of the study, and perceptions about its use of data. Qualitative research with healthcare workers in the UK on their experiences during the COVID-19 pandemic (Work Package 4) will provide insight into personal behaviour, perceptions of risk and coping mechanisms adopted both inside and outside of the work environment. Stakeholder engagement (Work Package 5) from professional regulatory bodies and staff groups is embedded within the UK-REACH study to provide feedback on project activities and support with project recommendations. The target participants (key opinion leaders) for Work Package 3 empirical study will likely come from predominantly White backgrounds which may limit the breadth of views obtained in interviews. This limitation will be mitigated by active recruitment of opinion leaders from a wide variety of ethnic backgrounds and active interaction with Work Package 5. Due to the pandemic restrictions, interviews and focus group discussions will be conducted via online methods as a substitute for face-to-face meetings, posing practical and technological challenges for dynamic interaction with participants.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/7/e049611.full.pdf; doi:https://doi.org/10.1101/2021.03.03.21252737; html:https://europepmc.org/article/PPR/PPR291740; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR291740&type=FILE&fileName=EMS118538-pdf.pdf&mimeType=application/pdf
+PPR704199,https://doi.org/10.2139/ssrn.4547861,Hospital Admission Related to Common Infections in Primary Care in England: Risk Prediction and Evaluation of the Impact of COVID-19 Pandemic Using OpenSAFELY,"Fahmi A, Palin V, Zhong X, Yang Y, Watts S, Ashcroft D, Goldacre B, Mackenna B, Fisher L, Massey J, Mehrkar A, Bacon S, Group OC, Hand K, Staa TPV.",,No Journal Info,2023,2023-08-28,N,,,,"Background: Antimicrobial resistance (AMR) is a multifaceted global challenge, partly driven by inappropriate antibiotic prescribing. The COVID-19 pandemic impacted antibiotic prescribing for common bacterial infections. This highlights the need to examine risk of hospital admissions related to common infections, excluding COVID-19 infections during the pandemic<br><br>Methods: With the approval of NHS England, we accessed electronic health records from The Phoenix Partnership (TPP) through OpenSAFELY platform. We included patients with primary care diagnosis of common infections, including lower respiratory tract infection (LRTI), upper respiratory tract infections (URTI), and lower urinary tract infection (UTI), from January 2019 to August 2022. We excluded patients with a COVID-19 record 90 days before to 30 days after the infection diagnosis. Using Cox proportional-hazard regression models, we predicted risk of infection-related hospital admission in 30 days follow-up period after the diagnosis.<br><br>Findings: We found 12,745,165 infection diagnoses from January 2019 to August 2022. Of them, 80,395 (2·05%) cases were admitted to hospital in the follow-up period. Counts of hospital admission for infections dropped during COVID-19, e.g., LRTI from 3,950 in December 2019 to 520 in April 2020. Comparing those prescribed an antibiotic to those without, reduction in risk of hospital admission were largest with LRTI (adjusted odds ratio (OR) of 0·35; 95% confidence interval (CI), 0·35-0·36) and UTI (adjusted OR 0·45; 95% CI, 0·44-0·46), compared to URTI (adjusted OR 1·04; 95% CI, 1·03-1·06).<br><br>Interpretation: Large effectiveness of antibiotics in preventing complications related to LRTI and UTI can support better targeting of antibiotics to patients with higher complication risks.<br><br>Funding: Health Data Research UK and National Institute for Health Research.<br><br>Declaration of Interest: All authors declare the following: BG and OpenSAFELY has received research funding from the Laura and John Arnold Foundation, the NHS National Institute for Health Research (NIHR), the NIHR School of Primary Care Research, NHS England, the NIHR Oxford Biomedical Research Centre, the Mohn-Westlake Foundation, NIHR Applied Research Collaboration Oxford and Thames Valley, the Wellcome Trust, the Good Thinking Foundation, Health Data Research UK, the Health Foundation, the World Health Organisation, UKRI MRC, Asthma UK, the British Lung Foundation, and the Longitudinal Health and Wellbeing strand of the National Core Studies programme; he is a Non-Executive Director at NHS Digital; he also receives personal income from speaking and writing for lay audiences on the misuse of science. AM has received consultancy fees (from https://inductionhealthcare.com) and is member of RCGP health informatics group and the NHS Digital GP data Professional Advisory Group that advises on access to GP Data for Pandemic Planning and Research (GDPPR). For the latter, he received payment for the GDPPR role.<br><br>Ethical Approval: This study was approved by the Health Research Authority and NHS Research Ethics Committee [REC reference 21/SC/0287].",,doi:https://doi.org/10.2139/ssrn.4547861; html:https://europepmc.org/article/PPR/PPR704199; doi:https://doi.org/10.2139/ssrn.4547861
 PPR290304,https://doi.org/10.1101/2021.02.27.21252593,Surgical activity in England and Wales during the COVID-19 pandemic: a nationwide observational cohort study,"Dobbs TD, Gibson JAG, Fowler AJ, Abbott TE, Shahid T, Torabi F, Griffiths R, Lyons RA, Pearse RM, Whitaker IS.",,No Journal Info,2021,2021-03-01,Y,,,,"<h4>Objectives</h4> To report the volume of surgical activity and the number of cancelled surgical procedures during the COVID-19 pandemic. <h4>Design and setting</h4> Analysis of electronic health record data from the National Health Service (NHS) in England and Wales. <h4>Methods</h4> We used hospital episode statistics for all adult patients undergoing surgery between 1 st January 2020 and 31 st December 2020. We identified surgical procedures using a previously published list of procedure codes. Procedures were stratified by urgency of surgery as defined by NHS England. We calculated the deficit of surgical activity by comparing the expected number of procedures from the years 2016-2019 with the actual number of procedures in 2020. We estimated the cumulative number of cancelled procedures by 31 st December 2021 according patterns of activity in 2020. <h4>Results</h4> The total number of surgical procedures carried out in England and Wales in 2020 was 3,102,674 compared to the predicted number of 4,671,338. This represents a 33.6% reduction in the national volume of surgical activity. There were 763,730 emergency surgical procedures (13.4% reduction), compared to 2,338,944 elective surgical procedures (38.6% reduction). The cumulative number of cancelled or postponed procedures was 1,568,664. We estimate that this will increase to 2,358,420 by 31 st December 2021. <h4>Conclusions</h4> The volume of surgical activity in England and Wales was reduced by 33.6% in 2020, resulting in over 1,568,664 cancelled operations. This deficit will continue to grow in 2021. <h4>Summary boxes</h4> <h4>What is already known on this topic</h4> The COVID-19 pandemic necessitated a rapid change in the provision of care, including the suspension of a large proportion of surgical activity Surgical activity has yet to return to normal and has been further impacted by subsequent waves of the pandemic This will lead to a large backlog of cases <h4>What this study adds</h4> 3,102,674 surgical procedures were performed in England and Wales during 2020, a 33.6% reduction on the expected yearly surgical activity Over 1.5 million procedures were not performed, with this deficit likely to continue to grow to 2.3 million by the end of 2021 This deficit is the equivalent of more than 6 months of pre-pandemic surgical activity, requiring a monumental financial and logistic challenge to manage",,pdf:https://qmro.qmul.ac.uk/xmlui/bitstream/123456789/71298/2/Abbott%20Surgical%20activity%20in%20England%202021%20Published.pdf; doi:https://doi.org/10.1101/2021.02.27.21252593; html:https://europepmc.org/article/PPR/PPR290304; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR290304&type=FILE&fileName=EMS117861-pdf.pdf&mimeType=application/pdf
 PPR370776,https://doi.org/10.1101/2021.07.12.21260385,Estimating the effectiveness of first dose of COVID-19 vaccine against mortality in England: a quasi-experimental study,"Bermingham C, Morgan J, Ayoubkhani D, Glickman M, Islam N, Sheikh A, Sterne J, Walker AS, Nafilyan V.",,No Journal Info,2021,2021-07-16,Y,,,,"<h4>Background</h4> Estimating real-world vaccine effectiveness is vital to assess the impact of the vaccination programme on the pandemic and inform the ongoing policy response. However, estimating vaccine effectiveness using observational data is inherently challenging because of the non-randomised design and the potential for unmeasured confounding. <h4>Methods</h4> We used a Regression Discontinuity Design (RDD) to estimate vaccine effectiveness against COVID-19 mortality in England, exploiting the discontinuity in vaccination rates resulting from the UK’s age-based vaccination priority groups. We used the fact that people aged 80 or over were prioritised for the vaccine roll-out in the UK to compare the risk of COVID-19 and non-COVID-19 death in people aged 75–79 and 80–84. <h4>Findings</h4> The prioritisation of vaccination of people aged 80 or above led to a large discrepancy in vaccination rates in people 80–84 compared to those 75–79 at the beginning of the vaccination campaign. We found a corresponding difference in COVID-19 mortality, but not in non-COVID-19 mortality, suggesting that our approach appropriately addresses the issue of unmeasured confounding factors. Our results suggest that the first vaccine dose reduced the risk of COVID-19 death by 52.6% (95% Cl 26.6–84.2) in those aged 80. <h4>Interpretations</h4> Our results support existing evidence that a first dose of a COVID-19 vaccine has a strong protective effect against COVID-19 mortality in older adults. The RDD estimate of vaccine effectiveness is comparable to previously published studies using different methods, suggesting that unmeasured confounding factors are unlikely to substantially bias these studies. <h4>Funding</h4> Office for National Statistics. <h4>Research in Context</h4> <h4>Evidence before this study</h4> We searched PubMed for studies reporting on the ‘real-world’ effectiveness of the COVID-19 vaccination on risk of death using terms such as “COVID-19”, “vaccine effectiveness”, “mortality” and “death”. The relevant published studies on this topic report vaccine effectiveness estimates against risk of death ranging from 64.2% to 98.7%, for varying times post-vaccination. All of these are observational studies and therefore potentially subject to bias from unmeasured confounding. We found no studies that used a quasi-experimental method such as regression discontinuity design, which is not subject to bias from unmeasured confounding, to calculate the effectiveness of the COVID-19 vaccination on risk of COVID-19 death, or on other outcomes such as hospitalisation or infection. <h4>Added value of this study</h4> The estimates of vaccine effectiveness based on observational data may be biased by unmeasured confounding. This study uses a regression discontinuity design to estimate vaccine effectiveness, exploiting the fact that the vaccination campaign in the UK was rolled out following age-based priority groups. This enables the calculation of an unbiased estimate of the effectiveness of the COVID-19 vaccine against risk of death. The vaccine effectiveness estimate of 52.6% (95% Cl 26.6–84.2) is slightly lower but similar to previously published estimates, therefore suggesting that these estimates are not substantially affected by unmeasured confounding factors and confirming the effectiveness of the COVID-19 vaccine against risk of COVID-19 death. <h4>Implications of all the available evidence</h4> Obtaining an unbiased estimate of COVID-19 vaccine effectiveness is of vital importance in informing policy for lifting COVID-19 related measures. The regression discontinuity design provides confidence that the existing estimates from observational studies are unlikely to be substantially biased by unmeasured confounding.",,pdf:https://academic.oup.com/aje/article-pdf/192/2/267/49088247/kwac157.pdf; doi:https://doi.org/10.1101/2021.07.12.21260385; html:https://europepmc.org/article/PPR/PPR370776; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR370776&type=FILE&fileName=EMS130767-pdf.pdf&mimeType=application/pdf
 PPR410412,https://doi.org/10.1101/2021.10.18.21264686,Regional excess mortality during the 2020 COVID-19 pandemic: a study of five European countries,"Konstantinoudis G, Cameletti M, Gómez-Rubio V, León Gómez I, Pirani M, Baio G, Larrauri A, Riou J, Egger M, Vineis P, Blangiardo M.",,No Journal Info,2021,2021-10-23,Y,,,,"The impact of the COVID-19 pandemic on excess mortality from all causes in 2020 varied across and within European countries. Using data for 2015-2019, we applied Bayesian spatio-temporal models to quantify the expected weekly deaths at the regional level had the pandemic not occurred in England, Greece, Italy, Spain, and Switzerland. With around 30%, Madrid, Castile-La Mancha, Castile-Leon (Spain) and Lombardia (Italy) were the regions with the highest excess mortality. In England, Greece and Switzerland, the regions most affected were Outer London and the West Midlands (England), Eastern, Western and Central Macedonia (Greece), and Ticino (Switzerland), with 15-20% excess mortality in 2020. Our study highlights the importance of the large transportation hubs for establishing community transmission in the first stages of the pandemic. Acting promptly to limit transmission around these hubs is essential to prevent spread to other regions and countries.",,pdf:https://www.nature.com/articles/s41467-022-28157-3.pdf; doi:https://doi.org/10.1101/2021.10.18.21264686; html:https://europepmc.org/article/PPR/PPR410412; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR410412&type=FILE&fileName=EMS137364-pdf.pdf&mimeType=application/pdf
@@ -428,14 +428,14 @@ PPR185844,https://doi.org/10.1101/2020.07.08.20148965,A case-control and cohort
 PPR607510,https://doi.org/10.2139/ssrn.4060371,Epidemiologic Information Discovery from Open-Access COVID-19 Case Reports Via Pretrained Language Model,"Wang Z, Liu XF, Du Z, Wang L, Wu Y, Holme P, Lachmann M, lin h, Wong ZSY, Xu X, Sun Y.",,No Journal Info,2022,2022-03-17,N,,,,"Although open-access data are increasing common and useful to epidemiological research, curation  of such datasets is resource-intensive and time-consuming. Despite a major source of COVID-19 data, the regularly disclosed case reports were often written in natural language with unstructured format. Here we propose a computational framework that can automatically extract epidemiological information from open-access COVID-19 case reports. We develop this framework by coupling language model developed using deep neural networks with training samples compiled using an optimized data annotation strategy. When applying to the COVID-19 case reports collected from mainland China, our novel framework outstrips all other state-of-the-art deep learning models. The information extracted from our approach is highly consistent with that obtained from the gold-standard manual coding, with a matching rate of 80%. To implement our algorithm, we provide an open-access online platform that can accurately estimate epidemiological statistics in real-time with substantially reduced burden in data curation.",,pdf:https://www.repository.cam.ac.uk/bitstream/1810/342099/2/article.pdf; doi:https://doi.org/10.2139/ssrn.4060371; html:https://europepmc.org/article/PPR/PPR607510; doi:https://doi.org/10.2139/ssrn.4060371
 PPR602769,https://doi.org/10.2139/ssrn.3615999,Diabetes and COVID-19 Related Mortality in the Critical Care Setting: A Real-Time National Cohort Study in England,"Dennis JM, Mateen BA, Sonabend R, Thomas NJ, Patel KA, Hattersley AT, Denaxas S, McGovern AP, Vollmer SJ.",,No Journal Info,2020,2020-06-05,N,,,,"Background:The importance of diabetes as a prognostic factor in people admitted to hospital critical care with COVID-19 is poorly understood and has not been quantified.  <br><br>Methods:We used a real-time national database (COVID-19 Hospitalisation in England Surveillance System; CHESS), comprising data on COVID-19 related admissions to hospital in England requiring admission to a high dependency unit (HDU) or intensive care unit (ICU) between March 1, 2020 and May 17, 2020. The objective was to describe the relationship between diabetes and all-cause in-hospital mortality in adults, using Cox proportional hazard models adjusted for age, sex, ethnicity, obesity, and other comorbidities. The primary analysis was restricted to a subset with sufficiently complete comorbidity status recording. Several sensitivity analyses, including on the unrestricted dataset, were carried out to verify the results.  <br><br>Findings:  Diabetes was independently associated with mortality in people admitted to critical care settings with COVID-19 in England; the proportion of 30-day mortality attributable to diabetes, after adjusting for age, sex, ethnicity, obesity, and other comorbidities, was 4·8% (95%CI 2·5-7·0). 14,639 COVID-19 related HDU and ICU admissions were reported during the study period, of which 6,142 were included in primary analysis, including 3,311 HDU (mean age 72), and 2,831 ICU admissions (mean age 58). 1,439 (23·4%) had diabetes. 1,847 individuals (30·1%) died during the study period. 30 day mortality was higher in people with diabetes than without (p < 0·001). People with diabetes were at increased risk of death (adjusted hazard ratio (HR) 1·28 [1·14, 1·42]). Results were consistent in subsets admitted to HDU only (adjusted HR 1·27 [1·09, 1·48]) and ICU (adjusted HR 1·31 [1·12, 1·54]). Sensitivity analyses were consistent with the primary analysis.  <br><br>Interpretation:Diabetes is an independent prognostic factor for mortality in people with COVID-19 requiring HDU or ICU treatment. Quantification of this diabetes associated risk enables appropriate treatment decisions in people with diabetes and severe COVID-19.  <br><br>Funding Statement: This study received no funding.<br><br>Declaration of Interests: APM declares previous research funding from Eli Lilly and Company, Pfizer, and AstraZeneca. SJV declares funding from IQVIA. All other authors declare no competing interests.<br><br>Ethics Approval Statement: The study was reviewed and approved by the Warwick BSREC (BSREC 119/19-20) and sponsorship is being provided by University of Warwick (SOC.28/19-20).",,doi:https://doi.org/10.2139/ssrn.3615999; html:https://europepmc.org/article/PPR/PPR602769; doi:https://doi.org/10.2139/ssrn.3615999
 PPR186560,https://doi.org/10.1101/2020.07.10.20151118,The 4C Initiative (Clinical Care for Cardiovascular disease in the COVID-19 pandemic) – monitoring the indirect impact of the coronavirus pandemic on services for cardiovascular diseases in the UK,"4C Initiative of the CVD-COVID-UK consortium, Ball S, Banerjee A, Berry C, Boyle J, Bray B, Bradlow W, Chaudhry A, Crawley R, Danesh J, Denniston A, Falter F, Figueroa J, Hall C, Hemingway H, Jefferson E, Johnson T, King G, Lee K, McKean P, Mason S, Mills N, Pearson E, Pirmohamed M, Poon M, Priedon R, Shah A, Sofat R, Sterne J, Strachan F, Sudlow C, Szarka Z, Whiteley W, Wyatt M.",,No Journal Info,2020,2020-07-11,Y,,,,"<h4>ABSTRACT</h4> <h4>Background</h4> The coronavirus (COVID-19) pandemic affects cardiovascular diseases (CVDs) directly through infection and indirectly through health service reorganisation and public health policy. Real-time data are needed to quantify direct and indirect effects. We aimed to monitor hospital activity for presentation, diagnosis and treatment of CVDs during the pandemic to inform on indirect effects. <h4>Methods</h4> We analysed aggregate data on presentations, diagnoses and treatments or procedures for selected CVDs (acute coronary syndromes, heart failure, stroke and transient ischaemic attack, venous thromboembolism, peripheral arterial disease and aortic aneurysm) in UK hospitals before and during the COVID-19 epidemic. We produced an online visualisation tool to enable near real-time monitoring of trends. <h4>Findings</h4> Nine hospitals across England and Scotland contributed hospital activity data from 28 Oct 2019 (pre-COVID-19) to 10 May 2020 (pre-easing of lockdown), and for the same weeks during 2018-2019. Across all hospitals, total admissions and emergency department (ED) attendances decreased after lockdown (23 March 2020) by 57.9% (57.1-58.6%) and 52.9% (52.2-53.5%) respectively compared with the previous year. Activity for cardiac, cerebrovascular and other vascular conditions started to decline 1-2 weeks before lockdown, and fell by 31-88% after lockdown, with the greatest reductions observed for coronary artery bypass grafts, carotid endarterectomy, aortic aneurysm repair and peripheral arterial disease procedures. Compared with before the first UK COVID-19 (31 January 2020), activity declined across diseases and specialties between the first case and lockdown (total ED attendances RR 0.94, 0.93-0.95; total hospital admissions RR 0.96, 0.95-0.97) and after lockdown (attendances RR 0.63, 0.62-0.64; admissions RR 0.59, 0.57-0.60). There was limited recovery towards usual levels of some activities from mid-April 2020. <h4>Interpretation</h4> Substantial reductions in total and cardiovascular activities are likely to contribute to a major burden of indirect effects of the pandemic, suggesting they should be monitored and mitigated urgently. <h4>Funding</h4> British Heart Foundation, Health Data Research UK",,pdf:https://www.medrxiv.org/content/medrxiv/early/2020/07/11/2020.07.10.20151118.full.pdf; doi:https://doi.org/10.1101/2020.07.10.20151118; html:https://europepmc.org/article/PPR/PPR186560; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR186560&type=FILE&fileName=EMS87270-pdf.pdf&mimeType=application/pdf
-PPR534818,https://doi.org/10.1101/2022.08.23.22279112,Prognostic accuracy of triage tools for adults with suspected COVID-19 in a middle-income setting: an observational cohort study,"Marincowitz C, Sbaffi L, Hodkinson P, McAlpine D, Fuller G, Goodacre S, Bath PA, Bath PA, Hasan M, Omer Y, Wallis L.",,No Journal Info,2022,2022-08-23,Y,,,,"<h4>Study Objective</h4> Tools proposed to triage acuity in suspected COVID-19 in the ED have been derived and validated in higher-income settings during early waves of the pandemic. We estimated the accuracy of seven risk-stratification tools recommended to predict severe illness in the Western Cape, South Africa. <h4>Methods</h4> An observational cohort study using routinely collected data from EDs across the Western Cape, from the 27 th of August 2020 to 11 th March 2022 was conducted to assess performance of the PRIEST tool, NEWS2, TEWS, the WHO algorithm, CRB-65, Quick COVID-19 Severity Index and PMEWS in suspected COVID-19. The primary outcome was death or ICU admission. <h4>Results</h4> Of 446,084 patients, 15,397 patients (3.45%, 95% CI:34% to 35.1%) experienced the primary outcome. Clinical decision-making for inpatient admission achieved a sensitivity of 0.77 (95% CI 0.76 to 0.78), specificity 0.88 (95% CI 0.87 to 0.88) and the negative predictive value (NPV) 0.99 (95% CI 0.99 to 0.99). NEWS2, PMEWS and PRIEST tool algorithm identified patients at risk of adverse outcomes at recommended cut-offs with moderate sensitivity (>0.8) and specificity ranging from 0.47 (NEWS2) to 0.65 (PRIEST tool). Use of the tools at recommended thresholds would have more than doubled admissions with only a 0.01% reduction in false negative triage. <h4>Conclusion</h4> Use of the PRIEST score, NEWS2 and PMEWS at a threshold of a point higher would achieve similar accuracy to current clinical admission decision, with possible gains in transparency and speed of decision-making.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/08/23/2022.08.23.22279112.full.pdf; doi:https://doi.org/10.1101/2022.08.23.22279112; html:https://europepmc.org/article/PPR/PPR534818; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR534818&type=FILE&fileName=EMS153216-pdf.pdf&mimeType=application/pdf
 PPR237477,https://doi.org/10.1101/2020.11.11.20220962,Short-term forecasts to inform the response to the Covid-19 epidemic in the UK,"Funk S, Abbott S, Atkins B, Baguelin M, Baillie J, Birrell P, Blake J, Bosse N, Burton J, Carruthers J, Davies N, De Angelis D, Dyson L, Edmunds W, Eggo R, Ferguson N, Gaythorpe K, Gorsich E, Guyver-Fletcher G, Hellewell J, Hill E, Holmes A, House T, Jewell C, Jit M, Jombart T, Joshi I, Keeling M, Kendall E, Knock E, Kucharski A, Lythgoe K, Meakin S, Munday J, Openshaw P, Overton C, Pagani F, Pearson J, Perez-Guzman P, Pellis L, Scarabel F, Semple M, Sherratt K, Tang M, Tildesley M, Van Leeuwen E, Whittles L, CMMID COVID-19 Working Group, Imperial College COVID-19 Response Team, ISARIC4C Investigators.",,No Journal Info,2020,2020-11-13,Y,,,,"<h4>Background</h4> Short-term forecasts of infectious disease can aid situational awareness and planning for outbreak response. Here, we report on multi-model forecasts of Covid-19 in the UK that were generated at regular intervals starting at the end of March 2020, in order to monitor expected healthcare utilisation and population impacts in real time. <h4>Methods</h4> We evaluated the performance of individual model forecasts generated between 24 March and 14 July 2020, using a variety of metrics including the weighted interval score as well as metrics that assess the calibration, sharpness, bias and absolute error of forecasts separately. We further combined the predictions from individual models into ensemble forecasts using a simple mean as well as a quantile regression average that aimed to maximise performance. We compared model performance to a null model of no change. <h4>Results</h4> In most cases, individual models performed better than the null model, and ensembles models were well calibrated and performed comparatively to the best individual models. The quantile regression average did not noticeably outperform the mean ensemble. <h4>Conclusions</h4> Ensembles of multi-model forecasts can inform the policy response to the Covid-19 pandemic by assessing future resource needs and expected population impact of morbidity and mortality.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2020/12/04/2020.11.11.20220962.full.pdf; doi:https://doi.org/10.1101/2020.11.11.20220962; html:https://europepmc.org/article/PPR/PPR237477; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR237477&type=FILE&fileName=EMS104159-pdf.pdf&mimeType=application/pdf
+PPR534818,https://doi.org/10.1101/2022.08.23.22279112,Prognostic accuracy of triage tools for adults with suspected COVID-19 in a middle-income setting: an observational cohort study,"Marincowitz C, Sbaffi L, Hodkinson P, McAlpine D, Fuller G, Goodacre S, Bath PA, Bath PA, Hasan M, Omer Y, Wallis L.",,No Journal Info,2022,2022-08-23,Y,,,,"<h4>Study Objective</h4> Tools proposed to triage acuity in suspected COVID-19 in the ED have been derived and validated in higher-income settings during early waves of the pandemic. We estimated the accuracy of seven risk-stratification tools recommended to predict severe illness in the Western Cape, South Africa. <h4>Methods</h4> An observational cohort study using routinely collected data from EDs across the Western Cape, from the 27 th of August 2020 to 11 th March 2022 was conducted to assess performance of the PRIEST tool, NEWS2, TEWS, the WHO algorithm, CRB-65, Quick COVID-19 Severity Index and PMEWS in suspected COVID-19. The primary outcome was death or ICU admission. <h4>Results</h4> Of 446,084 patients, 15,397 patients (3.45%, 95% CI:34% to 35.1%) experienced the primary outcome. Clinical decision-making for inpatient admission achieved a sensitivity of 0.77 (95% CI 0.76 to 0.78), specificity 0.88 (95% CI 0.87 to 0.88) and the negative predictive value (NPV) 0.99 (95% CI 0.99 to 0.99). NEWS2, PMEWS and PRIEST tool algorithm identified patients at risk of adverse outcomes at recommended cut-offs with moderate sensitivity (>0.8) and specificity ranging from 0.47 (NEWS2) to 0.65 (PRIEST tool). Use of the tools at recommended thresholds would have more than doubled admissions with only a 0.01% reduction in false negative triage. <h4>Conclusion</h4> Use of the PRIEST score, NEWS2 and PMEWS at a threshold of a point higher would achieve similar accuracy to current clinical admission decision, with possible gains in transparency and speed of decision-making.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2022/08/23/2022.08.23.22279112.full.pdf; doi:https://doi.org/10.1101/2022.08.23.22279112; html:https://europepmc.org/article/PPR/PPR534818; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR534818&type=FILE&fileName=EMS153216-pdf.pdf&mimeType=application/pdf
 PPR624483,https://doi.org/10.1101/2023.03.02.23286669,Use of a digital application to enhance communication and triage between care homes and National Health Service community services in the United Kingdom: a qualitative evaluation,"Russell S, Stocker R, Cockshott Z, Mason S, Knight J, Hanratty B, Preston N.",,No Journal Info,2023,2023-03-02,N,,,,"Recent years have seen a rise in digital interventions to improve coordination between care homes and NHS services, supporting remote sharing of data on the health of care home residents. Such interventions were key components in the response to the COVID-19 pandemic. This paper presents findings from the qualitative component of an evaluation of an implementation of the HealthCall Digital Care Homes application, across sites in northern England. The implementation commenced prior to the pandemic and continued throughout. Semi-structured, qualitative interviews were held with stakeholders. Interviews were conducted remotely (October 2020 -June 2021). Data were analysed via a reflexive thematic analysis then mapped against Normalization Process Theory (NPT) constructs (coherence, collective action, cognitive participation, and reflexive monitoring) providing a framework to assess implementation success. Thirty-five participants were recruited: 16 care home staff, six NHS community nurses, five relatives of care home residents, four HealthCall team members, three care home residents, and one local authority commissioner. Despite facing challenges such as apprehension towards digital technology among care home staff, the application was viewed positively across stakeholder groups. The HealthCall team maintained formal and informal feedback loop with stakeholders. This resulted in revisions to the intervention and implementation. Appropriate training and problem solving from the HealthCall team and buy-in from care home and NHS staff were key to achieving success across NPT constructs. While this implementation appears broadly successful, establishing rapport and maintaining ongoing support requires significant time, financial backing, and the right individuals in place across stakeholder groups to drive implementation and intervention evolution. The digital literacy of care home staff requires encouragement to enhance their readiness for digital interventions. The COVID-19 pandemic has pushed this agenda forward. Problems with stability across the workforce within care homes need to be addressed to avoid skill loss and support embeddedness of digital interventions. <h4>What is known about this topic?</h4> Improving healthcare delivery in UK care homes is a health policy priority. Digital interventions designed to enhance the referral process between care homes and NHS services and improve the healthcare delivery in care homes have become increasingly common in the UK. The HealthCall Digital Care Homes application is one such intervention. These interventions and their implementations require evaluation to ensure that they operate as intended, function coherently and are considered appropriate and legitimate to the care home setting. <h4>What this paper adds?</h4> The HealthCall Digital Care Homes app is a feasible, appropriate and legitimate intervention for referral, triage and health care support for non-urgent health care needs of care home residents. The ongoing involvement of end users in further developing the intervention, and the level of monitoring and support provided by the implementation team appears to be key to the implementation’s success. The digital preparedness of UK care homes is limited. Ensuring that care homes are digitally enabled, with a digitally literate workforce, should be a policy and research priority.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2023/03/02/2023.03.02.23286669.full.pdf; doi:https://doi.org/10.1101/2023.03.02.23286669; html:https://europepmc.org/article/PPR/PPR624483; doi:https://doi.org/10.1101/2023.03.02.23286669
 PPR153348,https://doi.org/10.1101/2020.04.18.20064774,"How many are at increased risk of severe COVID-19 disease? Rapid global, regional and national estimates for 2020","Clark A, Jit M, Warren-Gash C, Guthrie B, Wang HH, Mercer SW, Sanderson C, McKee M, Troeger C, Ong KI, Checchi F, Perel P, Joseph S, Gibbs HP, Banerjee A, CMMID COVID-19 working group, Eggo RM.",,No Journal Info,2020,2020-04-22,Y,,,,"<h4>Background</h4> The risk of severe COVID-19 disease is known to be higher in older individuals and those with underlying health conditions. Understanding the number of individuals at increased risk of severe COVID-19 illness, and how this varies between countries may inform the design of possible strategies to shield those at highest risk. <h4>Methods</h4> We estimated the number of individuals at increased risk of severe COVID-19 disease by age (5-year age groups), sex and country (n=188) based on prevalence data from the Global Burden of Disease (GBD) study for 2017 and United Nations population estimates for 2020. We also calculated the number of individuals without an underlying condition that could be considered at-risk because of their age, using thresholds from 50-70 years. The list of underlying conditions relevant to COVID-19 disease was determined by mapping conditions listed in GBD to the guidelines published by WHO and public health agencies in the UK and US. We analysed data from two large multimorbidity studies to determine appropriate adjustment factors for clustering and multimorbidity. <h4>Results</h4> We estimate that 1.7 (1.0 - 2.4) billion individuals (22% [15-28%] of the global population) are at increased risk of severe COVID-19 disease. The share of the population at increased risk ranges from 16% in Africa to 31% in Europe. Chronic kidney disease (CKD), cardiovascular disease (CVD), diabetes and chronic respiratory disease (CRD) were the most prevalent conditions in males and females aged 50+ years. African countries with a high prevalence of HIV/AIDS and Island countries with a high prevalence of diabetes, also had a high share of the population at increased risk. The prevalence of multimorbidity (>1 underlying conditions) was three times higher in Europe than in Africa (10% vs 3%). <h4>Conclusion</h4> Based on current guidelines and prevalence data from GBD, we estimate that one in five individuals worldwide has a condition that is on the list of those at increased risk of severe COVID-19 disease. However, for many of these individuals the underlying condition will be undiagnosed or not severe enough to be captured in health systems, and in some cases the increase in risk may be quite modest. There is an urgent need for robust analyses of the risks associated with different underlying conditions so that countries can identify the highest risk groups and develop targeted shielding policies to mitigate the effects of the COVID-19 pandemic. <h4>Research in context</h4> <h4>Evidence before this study</h4> As the COVID-19 pandemic evolves, countries are considering policies of ‘shielding’ the most vulnerable, but there is currently very limited evidence on the number of individuals that might need to be shielded. Guidelines on who is currently believed to be at increased risk of severe COVID-19 illness have been published online by the WHO and public health agencies in the UK and US. We searched PubMed (“Risk factors” AND “COVID-19”) without language restrictions, from database inception until April 5, 2020, and identified 62 studies published between Feb 15, 2020 and March 20, 2020. Evidence from China, Italy and the USA indicates that older individuals, males and those with underlying conditions, such as CVD, diabetes and CRD, are at greater risk of severe COVID-19 illness and death. <h4>Added value of this study</h4> This study combines evidence from large international databases and new analysis of large multimorbidity studies to inform policymakers about the number of individuals that may be at increased risk of severe COVID-19 illness in different countries. We developed a tool for rapid assessments of the number and percentage of country populations that would need to be targeted under different shielding policies. <h4>Implications of all the available evidence</h4> Quantifying how many and who is at increased risk of severe COVID-19 illness is critical to help countries design more effective interventions to protect vulnerable individuals and reduce pressure on health systems. This information can also inform a broader assessment of the health, social and economic implications of shielding various groups.","""This paper estimates the likely number of global population that would be at increased risk of severe COVID-19 disease. They estimate that 1.7 (1.0 - 2.4) billion individuals (22% [15-28%] of the global population) are at  increased risk of severe COVID-19 disease. The share of the population at increased risk ranges from 16% in Africa to 31% in Europe.""",pdf:https://www.medrxiv.org/content/medrxiv/early/2020/04/22/2020.04.18.20064774.full.pdf; doi:https://doi.org/10.1101/2020.04.18.20064774; html:https://europepmc.org/article/PPR/PPR153348; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR153348&type=FILE&fileName=EMS90450-pdf.pdf&mimeType=application/pdf
 PPR667569,https://doi.org/10.1101/2023.05.23.23290408,Complex patterns of multimorbidity associated with severe COVID-19 and Long COVID,"Pietzner M, Denaxas S, Yasmeen S, Ulmer MA, Nakanishi T, Arnold M, Kastenmüller G, Hemingway H, Langenberg C.",,No Journal Info,2023,2023-05-28,Y,,,,"<h4>ABSTRACT</h4> Early evidence that patients with (multiple) pre-existing diseases are at highest risk for severe COVID-19 has been instrumental in the pandemic to allocate critical care resources and later vaccination schemes. However, systematic studies exploring the breadth of medical diagnoses, including common, but non-fatal diseases are scarce, but may help to understand severe COVID-19 among patients at supposedly low risk. Here, we systematically harmonized >12 million primary care and hospitalisation health records from ∼500,000 UK Biobank participants into 1448 collated disease terms to systematically identify diseases predisposing to severe COVID-19 (requiring hospitalisation or death) and its post-acute sequalae, Long COVID. We identified a total of 679 diseases associated with an increased risk for severe COVID-19 (n=672) and/or Long COVID (n=72) that spanned almost all clinical specialties and were strongly enriched in clusters of cardio-respiratory and endocrine-renal diseases. For 57 diseases, we established consistent evidence to predispose to severe COVID-19 based on survival and genetic susceptibility analyses. This included a possible role of symptoms of malaise and fatigue as a so far largely overlooked risk factor for severe COVID-19. We finally observed partially opposing risk estimates at known risk loci for severe COVID-19 for etiologically related diseases, such as post-inflammatory pulmonary fibrosis (e.g., MUC5B , NPNT , and PSMD3 ) or rheumatoid arthritis (e.g., TYK2 ), possibly indicating a segregation of disease mechanisms. Our results provide a unique reference that demonstrates how 1) complex co-occurrence of multiple – including non-fatal – conditions predispose to increased COVID-19 severity and 2) how incorporating the whole breadth of medical diagnosis can guide the interpretation of genetic risk loci.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2023/05/28/2023.05.23.23290408.full.pdf; doi:https://doi.org/10.1101/2023.05.23.23290408; html:https://europepmc.org/article/PPR/PPR667569; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR667569&type=FILE&fileName=EMS176610-pdf.pdf&mimeType=application/pdf
 PPR697706,https://doi.org/10.1101/2023.07.20.23292883,Impact of COVID-19 on recorded blood pressure screening and hypertension management in England: An analysis of monthly changes in Quality and Outcomes Framework indicators in OpenSAFELY,"Wiedemann M, Speed V, Cunningham C, Higgins R, Curtis HJ, Andrews C, Fisher L, Hopcroft LEM, Rentsch CT, Mahalingasivam V, Tomlinson L, Morton CE, Samuel M, Green ACA, Wood C, Brown A, Massey J, Walters C, Smith R, Inglesby P, Evans D, Maude S, Dillingham I, Walker AJ, Morley J, Mehrkar A, Bacon SCJ, Bates C, Cockburn J, Parry J, Hester F, Harper S, McManus RJ, Goldacre B, MacKenna B.",,No Journal Info,2023,2023-07-26,Y,,,,"<h4>Background</h4> Cardiovascular disease management in primary care in England was disrupted during the COVID-19 pandemic. <h4>Objective</h4> To describe the impact of the COVID-19 pandemic on blood pressure screening and hypertension management, based upon a national quality of care scheme (Quality and Outcomes Framework, QOF) across key demographic, regional, and clinical subgroups. To this end, we translated complex clinical quality of care schemes from text descriptions into reusable analytic code. <h4>Methods</h4> With the approval of NHS England, a population based cohort study was conducted on 25.2 million patient records in situ using OpenSAFELY-TPP. We included all NHS patients registered at general practices using TPP software between March 2019 and March 2023. Individuals that were eligible for blood pressure screening and with a diagnosis of hypertension were identified according to the QOF 2021/22 business rules. We examined monthly changes in recorded blood pressure screening in the preceding 5 years in patients aged ≥ 45, recorded hypertension prevalence, and the recorded percentage of patients treated to target (i.e., ≤ 140/90 mmHg for patients ≤ 79 years and ≤ 150/90 mmHg for patients ≥ 80 years) in the preceding 12 months, within demographic, regional, and clinical subgroups as well as the variation across practices. <h4>Results</h4> The overall percentage of patients aged ≥ 45 who had blood pressure screening recorded in the preceding 5 years decreased from 90% in March 2019 to 85% in March 2023. Recorded hypertension prevalence was relatively stable at 15% throughout the study period. The percentage of patients with a record of hypertension treated to target in the preceding 12 months reduced from a maximum of 71% in March 2020 to a minimum of 47% in February 2021 in patients aged ≤ 79 years, and from 85% in March 2020 to a minimum of 58% in February 2021 in patients aged ≥ 80 years before recovering. Blood pressure screening rates in the preceding 5 years remained stable in older age groups, patients with a record of learning disability, or care home status. <h4>Conclusions</h4> There was substantial disruption to hypertension management QOF indicators during the pandemic, which can likely be attributed to a general reduction of blood pressure measurement including screening. OpenSAFELY can be used to continuously monitor monthly changes in national quality of care schemes to identify changes in key clinical subgroups early and support prioritisation of recovery from disrupted care caused by COVID-19.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2023/07/31/2023.07.20.23292883.full.pdf; doi:https://doi.org/10.1101/2023.07.20.23292883; html:https://europepmc.org/article/PPR/PPR697706; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR697706&type=FILE&fileName=EMS181988-pdf.pdf&mimeType=application/pdf
-PPR644063,https://doi.org/10.1101/2023.04.06.23288168,Identification of a specific inflammatory protein biosignature in coronary and peripheral blood associated with increased risk of future cardiovascular events,"Proudfoot D, Gigante B, West NE, Hoole SP, Strawbridge RJ, Tremoli E, Baldassarre D, Williams S.",,No Journal Info,2023,2023-04-12,Y,,,,"<h4>Background and rationale</h4> As an adjunct to coronary intervention, the Liquid Biopsy System (LBS, PlaqueTec, UK) enables accurate intracoronary blood sampling at discrete sites simultaneously. We investigated variation between local coronary and remote (peripheral) blood levels of a panel of atherosclerosis-associated proteins and examined how this might relate to cardiovascular risk assessment. <h4>Methods and Results</h4> In a previous proof-of-concept trial, coronary blood samples were collected using the LBS in 28 patients. For 12 of these patients, sampling was conducted across the uninstrumented lesion, prior to percutaneous coronary intervention (PCI). Peripheral blood samples were also collected, at baseline and after PCI. Protein levels in coronary and peripheral plasma samples were analysed by proximity extension assay (PEA, Olink). Before PCI, in 10 out of 12 patients, coronary levels of hepatocyte growth factor (HGF), pappalysin-1 (PAPPA) and spondin-1 (SPON1) were elevated compared with peripheral levels, in some cases >10-fold. Following PCI, involving iatrogenic plaque rupture prior to stenting, peripheral levels of these proteins were elevated to a similar degree as coronary levels. In 2 patients, peripheral elevations of HGF, PAPPA and SPON1 (all >90 th centile) were observed at baseline, prior to PCI. The protein pattern that was identified, consisting of high levels of a combination of HGF, PAPPA and SPON1 was absent in healthy control peripheral blood, but when investigated in baseline peripheral blood samples from reference cardiovascular and COVID-19 patient cohorts, was associated with the occurrence of major adverse cardiovascular events (MACE) and mortality. <h4>Conclusions</h4> From investigation of coronary and peripheral blood samples, we identified a novel inflammatory protein signature, which when present in peripheral blood appears to portend worse outcomes. Measurement of these proteins could therefore aid identification of individuals at high risk of cardiovascular events or death. <h4>Translational Perspective</h4> Through sampling of local coronary blood, we discovered a novel protein biosignature consisting of a combination of elevated levels of HGF, PAPPA and SPON1. When this biosignature was assessed in peripheral samples from reference cardiovascular and COVID-19 cohorts, it associated with the occurrence of MACE and mortality. The biosignature protein levels correlated with markers of mast cell and neutrophil activity but not with CRP, possibly indicating a specific inflammatory status. Early detection of this protein signal has potential clinical utility to identify specific patients at increased risk of poor outcomes. <h4>Graphical Abstract</h4>",,pdf:https://www.medrxiv.org/content/medrxiv/early/2023/04/12/2023.04.06.23288168.full.pdf; doi:https://doi.org/10.1101/2023.04.06.23288168; html:https://europepmc.org/article/PPR/PPR644063; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR644063&type=FILE&fileName=EMS174291-pdf.pdf&mimeType=application/pdf
 PPR172592,https://doi.org/10.1101/2020.06.05.20121962,TRACKing Excess Deaths (TRACKED) – an interactive online tool to monitor excess deaths associated with COVID-19 pandemic in the United Kingdom,"Poon MT, Brennan PM, Jin K, Figueroa JD, Sudlow CL.",,No Journal Info,2020,2020-06-07,Y,,,,"<h4>Background</h4> We aimed to describe trends of excess mortality in the United Kingdom (UK) stratified by nation and cause of death, and to develop an online tool for reporting the most up to date data on excess mortality. <h4>Methods</h4> Population statistics agencies in the UK including the Office for National Statistics (ONS), National Records of Scotland (NRS), and Northern Ireland Statistics and Research Agency (NISRA) publish weekly data on deaths. We used mortality data up to 22 nd May in the ONS and the NISRA and 24 th May in the NRS. Crude mortality for non-COVID deaths (where there is no mention of COVID-19 on the death certificate) calculated. Excess mortality defined as difference between observed mortality and expected average of mortality from previous 5 years. <h4>Results</h4> There were 56,961 excess deaths and 8,986 were non-COVID excess deaths. England had the highest number of excess deaths per 100,000 population (85) and Northern Ireland the lowest (34). Non-COVID mortality increased from 23rd March and returned to the 5-year average on 10th May. In Scotland, where underlying cause mortality data besides COVID-related deaths was available, the percentage excess over the 8-week period when COVID-related mortality peaked was: dementia 49%, other causes 21%, circulatory diseases 10%, and cancer 5%. We developed an online tool (TRACKing Excess Deaths - TRACKED) to allow dynamic exploration and visualisation of the latest mortality trends ( http://trackingexcessdeaths.com ). <h4>Conclusions</h4> Continuous monitoring of excess mortality trends and further integration of age- and gender-stratified and underlying cause of death data beyond COVID-19 will allow dynamic assessment of the impacts of indirect and direct mortality of the COVID-19 pandemic.",,doi:https://doi.org/10.12688/wellcomeopenres.16058.1; doi:https://doi.org/10.1101/2020.06.05.20121962; html:https://europepmc.org/article/PPR/PPR172592; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR172592&type=FILE&fileName=EMS91985-pdf.pdf&mimeType=application/pdf
+PPR644063,https://doi.org/10.1101/2023.04.06.23288168,Identification of a specific inflammatory protein biosignature in coronary and peripheral blood associated with increased risk of future cardiovascular events,"Proudfoot D, Gigante B, West NE, Hoole SP, Strawbridge RJ, Tremoli E, Baldassarre D, Williams S.",,No Journal Info,2023,2023-04-12,Y,,,,"<h4>Background and rationale</h4> As an adjunct to coronary intervention, the Liquid Biopsy System (LBS, PlaqueTec, UK) enables accurate intracoronary blood sampling at discrete sites simultaneously. We investigated variation between local coronary and remote (peripheral) blood levels of a panel of atherosclerosis-associated proteins and examined how this might relate to cardiovascular risk assessment. <h4>Methods and Results</h4> In a previous proof-of-concept trial, coronary blood samples were collected using the LBS in 28 patients. For 12 of these patients, sampling was conducted across the uninstrumented lesion, prior to percutaneous coronary intervention (PCI). Peripheral blood samples were also collected, at baseline and after PCI. Protein levels in coronary and peripheral plasma samples were analysed by proximity extension assay (PEA, Olink). Before PCI, in 10 out of 12 patients, coronary levels of hepatocyte growth factor (HGF), pappalysin-1 (PAPPA) and spondin-1 (SPON1) were elevated compared with peripheral levels, in some cases >10-fold. Following PCI, involving iatrogenic plaque rupture prior to stenting, peripheral levels of these proteins were elevated to a similar degree as coronary levels. In 2 patients, peripheral elevations of HGF, PAPPA and SPON1 (all >90 th centile) were observed at baseline, prior to PCI. The protein pattern that was identified, consisting of high levels of a combination of HGF, PAPPA and SPON1 was absent in healthy control peripheral blood, but when investigated in baseline peripheral blood samples from reference cardiovascular and COVID-19 patient cohorts, was associated with the occurrence of major adverse cardiovascular events (MACE) and mortality. <h4>Conclusions</h4> From investigation of coronary and peripheral blood samples, we identified a novel inflammatory protein signature, which when present in peripheral blood appears to portend worse outcomes. Measurement of these proteins could therefore aid identification of individuals at high risk of cardiovascular events or death. <h4>Translational Perspective</h4> Through sampling of local coronary blood, we discovered a novel protein biosignature consisting of a combination of elevated levels of HGF, PAPPA and SPON1. When this biosignature was assessed in peripheral samples from reference cardiovascular and COVID-19 cohorts, it associated with the occurrence of MACE and mortality. The biosignature protein levels correlated with markers of mast cell and neutrophil activity but not with CRP, possibly indicating a specific inflammatory status. Early detection of this protein signal has potential clinical utility to identify specific patients at increased risk of poor outcomes. <h4>Graphical Abstract</h4>",,pdf:https://www.medrxiv.org/content/medrxiv/early/2023/04/12/2023.04.06.23288168.full.pdf; doi:https://doi.org/10.1101/2023.04.06.23288168; html:https://europepmc.org/article/PPR/PPR644063; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR644063&type=FILE&fileName=EMS174291-pdf.pdf&mimeType=application/pdf
 PPR428677,https://doi.org/10.1101/2021.12.03.21266112,Brain Injury in COVID-19 is Associated with Autoinflammation and Autoimmunity,"Needham E, Ren A, Digby R, Outtrim J, Chatfield D, Manktelow A, Newcombe V, Doffinger R, Barcenas-Morales G, Fonseca C, Taussig M, Burnstein R, Dunai C, Sithole N, Ashton N, Zetterberg H, Gisslen M, Edén A, Marklund E, Griffiths M, Cavanagh J, Breen G, Irani S, Elmer A, Kingston N, Bradley J, Taams L, Michael B, Bullmore E, Smith K, Lyons P, Coles A, Menon D, the Cambridge NeuroCOVID Group, the NIHR COVID-19 BioResource, Cambridge NIHR Clinical Research Facility.",,No Journal Info,2021,2021-12-05,Y,,,,"COVID-19 has been associated with many neurological complications including stroke, delirium and encephalitis. Furthermore, many individuals experience a protracted post-viral syndrome which is dominated by neuropsychiatric symptoms, and is seemingly unrelated to COVID-19 severity. The true frequency and underlying mechanisms of neurological injury are unknown, but exaggerated host inflammatory responses appear to be a key driver of severe COVID-19 more broadly. We sought to investigate the dynamics of, and relationship between, serum markers of brain injury (neurofilament light [NfL], Glial Fibrillary Acidic Protein [GFAP] and total Tau) and markers of dysregulated host response including measures of autoinflammation (proinflammatory cytokines) and autoimmunity. Brain injury biomarkers were measured using the Quanterix Simoa HDx platform, cytokine profiling by Luminex (R&D) and autoantibodies by a custom protein microarray. During hospitalisation, patients with COVID-19 demonstrated elevations of NfL and GFAP in a severity-dependant manner, and there was evidence of ongoing active brain injury at follow-up 4 months later. Raised NfL and GFAP were associated with both elevations of pro-inflammatory cytokines and the presence of autoantibodies; autoantibodies were commonly seen against lung surfactant proteins as well as brain proteins such as myelin associated glycoprotein, but reactivity was seen to a large number of different antigens. Furthermore, a distinct process characterised by elevation of serum total Tau was seen in patients at follow-up, which appeared to be independent of initial disease severity and was not associated with dysregulated immune responses in the same manner as NfL and GFAP.",,pdf:https://www.repository.cam.ac.uk/bitstream/1810/343727/3/awac321.pdf; doi:https://doi.org/10.1101/2021.12.03.21266112; html:https://europepmc.org/article/PPR/PPR428677; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR428677&type=FILE&fileName=EMS141610-pdf.pdf&mimeType=application/pdf
 PPR187554,https://doi.org/10.1101/2020.07.14.20152629,COVID-19 infection and attributable mortality in UK care homes: Cohort study using active surveillance and electronic records (March-June 2020),"Dutey-Magni PF, Williams H, Jhass A, Rait G, Lorencatto F, Hemingway H, Hemingway H, Hayward A, Shallcross L.",,No Journal Info,2020,2020-07-15,Y,,,,"<h4>Background</h4> Epidemiological data on COVID-19 infection in care homes are scarce. We analysed data from a large provider of long-term care for older people to investigate infection and mortality during the first wave of the pandemic. <h4>Methods</h4> Cohort study of 179 UK care homes with 9,339 residents and 11,604 staff.We used manager-reported daily tallies to estimate the incidence of suspected and confirmed infection and mortality in staff and residents. Individual-level electronic health records from 8,713 residents were used to model risk factors for confirmed infection, mortality, and estimate attributable mortality. <h4>Results</h4> 2,075/9,339 residents developed COVID-19 symptoms (22.2% [95% confidence interval: 21.4%; 23.1%]), while 951 residents (10.2% [9.6%; 10.8%]) and 585 staff (5.0% [4.7%; 5.5%]) had laboratory-confirmed infections. The incidence of confirmed infection was 152.6 [143.1; 162.6] and 62.3 [57.3; 67.5] per 100,000 person-days in residents and staff respectively. 121/179 (67.6%) care homes had at least one COVID-19 infection or COVID-19-related death. Lower staffing ratios and higher occupancy rates were independent risk factors for infection. 217/607 residents with confirmed infection died (case-fatality rate: 35.7% [31.9%; 39.7%]). Mortality in residents with no direct evidence of infection was two-fold higher in care homes with outbreaks versus those without (adjusted HR 2.2 [1.8; 2.6]). <h4>Conclusions</h4> <h4>Findingss: </h4>uggest many deaths occurred in people who were infected with COVID-19, but not tested. Higher occupancy and lower staffing levels were independently associated with risks of infection. Protecting staff and residents from infection requires regular testing for COVID-19 and fundamental changes to staffing and care home occupancy.",,pdf:https://discovery.ucl.ac.uk/10122604/10/Dutey-Magni_afab060.pdf; doi:https://doi.org/10.1101/2020.07.14.20152629; html:https://europepmc.org/article/PPR/PPR187554; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR187554&type=FILE&fileName=EMS87167-pdf.pdf&mimeType=application/pdf
 PPR263081,https://doi.org/10.1101/2021.01.06.21249352,OpenSAFELY NHS Service Restoration Observatory 1: describing trends and variation in primary care clinical activity for 23.3 million patients in England during the first wave of COVID-19,"The OpenSAFELY Collaborative, Curtis HJ, MacKenna B, MacKenna B, Croker R, Inglesby P, Walker AJ, Morley J, Mehrkar A, Morton CE, Bacon S, Hickman G, Bates C, Morley J, Evans D, Ward T, Cockburn J, Davy S, Bhaskaran K, Schultze A, Rentsch CT, Williamson E, Hulme W, McDonald HI, Tomlinson L, Mathur R, Drysdale H, Eggo RM, Wing K, Wong AY, Forbes H, Parry J, Hester F, Harper S, Evans SJ, Douglas IJ, Smeeth L, Goldacre B.",,No Journal Info,2021,2021-01-08,Y,,,,"<h4>Background</h4> The COVID-19 pandemic has disrupted healthcare activity globally. The NHS in England stopped most non-urgent work by March 2020, but later recommended that services should be restored to near-normal levels before winter where possible. The authors are developing the OpenSAFELY NHS Service Restoration Observatory , using data to describe changes in service activity during COVID-19, and reviewing signals for action with commissioners, researchers and clinicians. Here we report phase one: generating, managing, and describing the data. <h4>Objective</h4> To describe the volume and variation of coded clinical activity in English primary care across 23.8 million patients’ records, taking respiratory disease and laboratory procedures as key examples. <h4>Methods</h4> Working on behalf of NHS England we developed an open source software framework for data management and analysis to describe trends and variation in clinical activity across primary care EHR data on 23.8 million patients; and conducted a population cohort-based study to describe activity using CTV3 coding hierarchy and keyword searches from January 2019-September 2020. <h4>Results</h4> Much activity recorded in general practice declined to some extent during the pandemic, but largely recovered by September 2020, with some exceptions. There was a large drop in coded activity for commonly used laboratory tests, with broad recovery to pre-pandemic levels by September. One exception was blood coagulation tests such as International Normalised Ratio (INR), with a smaller reduction (median tests per 1000 patients in 2020: February 8.0; April 6.2; September 7.0). The overall pattern of recording for respiratory symptoms was less affected, following an expected seasonal pattern and classified as “no change” from the previous year. Respiratory tract infections exhibited a sustained drop compared with pre-pandemic levels, not returning to pre-pandemic levels by September 2020. Various COVID-19 codes increased through the period. We observed a small decline associated with high level codes for long-term respiratory conditions such as chronic obstructive pulmonary disease (COPD) and asthma. Asthma annual reviews experienced a small drop but since recovered, while COPD annual reviews remain below baseline. <h4>Conclusions</h4> We successfully delivered an open source software framework to describe trends and variation in clinical activity across an unprecedented scale of primary care data. The COVD-19 pandemic led to a substantial change in healthcare activity. Most laboratory tests showed substantial reduction, largely recovering to near-normal levels by September 2020, with some important tests less affected. Records of respiratory infections decreased with the exception of codes related to COVID-19, whilst activity of other respiratory disease codes was mixed. We are expanding the NHS Service Restoration Observatory in collaboration with clinicians, commissioners and researchers and welcome feedback.",,pdf:https://bjgp.org/content/bjgp/72/714/e63.full.pdf; doi:https://doi.org/10.1101/2021.01.06.21249352; html:https://europepmc.org/article/PPR/PPR263081; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR263081&type=FILE&fileName=EMS110198-pdf.pdf&mimeType=application/pdf
@@ -460,8 +460,8 @@ PPR141100,https://doi.org/10.1101/2020.04.05.20054528,"Estimating number of case
 PPR436245,https://doi.org/10.1101/2021.12.23.21268279,Remote Covid Assessment in Primary Care (RECAP) risk prediction tool: derivation and real-world validation studies,"Espinosa-Gonzalez A, Prociuk D, Fiorentino F, Ramtale C, Mi E, Mi E, Glampson B, Neves AL, Okusi C, Hussain L, Macartney J, Brown M, Browne B, Warren C, Chowla R, Heaversedge J, Greenhalgh T, de Lusignan S, Mayer E, Delaney B.",,No Journal Info,2021,2021-12-25,N,,,,"<h4>Background</h4> Accurate assessment of COVID-19 severity in the community is essential for best patient care and efficient use of services and requires a risk prediction score that is COVID-19 specific and adequately validated in a community setting. Following a qualitative phase to identify signs, symptoms and risk factors, we sought to develop and validate two COVID-19-specific risk prediction scores RECAP-GP (without peripheral oxygen saturation (SpO2)) and RECAP-O2 (with SpO2). <h4>Methods</h4> Prospective cohort study using multivariable logistic regression for model development. Data on signs and symptoms (model predictors) were collected on community-based patients with suspected COVID-19 via primary care electronic health records systems and linked with secondary data on hospital admission (primary outcome) within 28 days of symptom onset. Data sources: RECAP-GP: Oxford-Royal College of General Practitioners Research and Surveillance Centre (RSC) primary care practices (development), Northwest London (NWL) primary care practices, NHS COVID-19 Clinical Assessment Service (CCAS) (validation). RECAP-O2: Doctaly Assist platform (development, and validation in subsequent sample). Estimated sample size was 2,880 per model. <h4>Findings</h4> Data were available from 8,311 individuals. Observations, such SpO2, were mostly missing in NWL, RSC, and CCAS data; however, SpO2 was available for around 70% of Doctaly patients. In the final predictive models, RECAP-GP included sex, age, degree of breathlessness, temperature symptoms, and presence of hypertension (Area Under the Curve (AUC): 0.802, Validation Negative Predictive Value (NPV) of ‘low risk’ 98.8%. RECAP-O2 included age, degree of breathlessness, fatigue, and SpO2 at rest (AUC: 0.843), Validation NPV of ‘low risk’ 99.4%. <h4>Interpretation</h4> Both RECAP models are a valid tool in the assessment of COVID-19 patients in the community. RECAP-GP can be used initially, without need for observations, to identify patients who require monitoring. If the patient is monitored at home and SpO2 is available, RECAP-O2 is useful to assess the need for further treatment escalation. <h4>Research in context panel</h4> <h4>Evidence before the study</h4> This study was conceived during the first COVID-19 wave in the UK (March - April 2020), as members of the research team contributed to the development of national clinical guidelines for COVID-19 management in the community and to the Oxford COVID-19 rapid review to track signs and symptoms of COVID-19 internationally. The review was carried out according to Cochrane Collaboration standards for rapid reviews and identified systematic reviews and large-scale observational studies describing the signs and symptoms of COVID-19. Evidence gathered showed worsening of COVID-19 symptoms around the 7th day of disease and challenges in identifying patients with higher likelihood of severity to increase their monitoring. To this end, tools such NEWS2 have been used in the UK to assess COVID-19 patients in primary care, but they do not capture the characteristics of COVID-19 infection and/or are not suitable for community remote assessment. Several COVID-19 risk scores have been developed. QCOVID provides a risk of mortality considering patients’ existing risk factors but does not include acute signs and symptoms. ISARIC 4C Deterioration model has been specifically developed for hospital settings. In England, the NHS has implemented the Oximetry @home strategy to monitor patients with acute COVID-19 deemed at risk (older than 64 years old or with comorbidities) by providing pulse oximeters; however, the criteria for monitoring or for escalation of care have not been validated. There is, therefore, the need to develop a risk prediction score to establish COVID-19 patients’ risk of deterioration to be used in the community for both face to face or remote consultation. <h4>Added value of this study</h4> We developed and validated two COVID-19 specific risk prediction scores. One to be used in the initial remote assessment of patients with acute COVID-19 to assess need for monitoring (RECAP-GP). The second one to assess the need for further treatment escalation and includes peripheral saturation of oxygen among the model predictors (RECAP-O2). To our knowledge, this is the first COVID-19 specific risk prediction score to assess and monitor COVID-19 patients’ risk of deterioration remotely. This will be a valuable resource to complement the use of oximetry in the community clinical decision-making when assessing a patient with acute COVID-19. <h4>Implications of all available evidence</h4> To manage pandemic waves and their demand on healthcare, acute COVID-19 patients require close monitoring in the community and prompt escalation of their treatment. Guidance available so far relies on unvalidated tools and clinician judgement to assess deterioration. COVID-19 specific community-based risk prediction scores such as RECAP may contribute to reducing the uncertainty in the assessment and monitoring of COVID-19 patients, increase safety in clinical practice and improve outcomes by facilitating appropriate treatment escalation.",,doi:https://doi.org/10.1016/s2589-7500(22)00123-6; doi:https://doi.org/10.1101/2021.12.23.21268279; html:https://europepmc.org/article/PPR/PPR436245; doi:https://doi.org/10.1101/2021.12.23.21268279
 PPR516555,https://doi.org/10.1101/2022.07.08.22277317,A national audit of pancreatic enzyme prescribing in pancreatic cancer from 2015 to 2023 in England using OpenSAFELY-TPP,"Lemanska A, Andrews C, Fisher L, Butler-Cole B, Mehrkar A, Roberts KJ, Goldacre B, Walker AJ, The OpenSAFELY Collaborative, MacKenna B.",,No Journal Info,2022,2022-07-10,Y,,,,"<h4>Objectives</h4> Cancer treatments were variably disrupted during the COVID-19 pandemic. UK guidelines recommend pancreatic enzyme replacement therapy (PERT) to all people with unresectable pancreatic cancer. The aim was to investigate the impact of COVID-19 on PERT prescribing to people with unresectable pancreatic cancer and to investigate the national and regional rates from January 2015 to January 2023. <h4>Data sources</h4> With the approval of NHS England, we conducted this study using 24 million electronic healthcare records of people within the OpenSAFELY-TPP research platform. There were 22,860 people diagnosed with pancreatic cancer in the study cohort. We visualised the trends over time and modelled the effect of COVID-19 with the interrupted time series analysis. <h4>Conclusions</h4> In contrast to many other treatments, prescribing of PERT was not affected during the pandemic. Overall, since 2015, the rates increased steadily over time by 1% every year. The national rates ranged from 41% in 2015 to 48% in early 2023. There was substantial regional variation with the highest rates of 50% to 60% in West Midlands. <h4>Implications for Nursing Practice</h4> In pancreatic cancer, if PERT is prescribed, it is usually initiated in hospitals by clinical nurse specialists and continued after discharge by primary care. At just under 50% in early 2023, the rates were still below the recommended 100% standard. More research is needed to understand barriers to prescribing of PERT and geographic variation to improve quality of care. Prior work relied on manual audits. With OpenSAFELY, we developed an automated audit allowing for regular updates.",,doi:https://doi.org/10.1101/2022.07.08.22277317; html:https://europepmc.org/article/PPR/PPR516555; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR516555&type=FILE&fileName=EMS150145-pdf.pdf&mimeType=application/pdf
 PPR886242,https://doi.org/10.1101/2024.07.23.24310853,Genomics of chronic cough unravels neurological pathways,"Coley K, John C, Ghouse J, Shepherd DJ, Shrine N, Izquierdo AG, Kanoni S, Magavern EF, Packer R, McGarvey L, Smith JA, Bundgaard H, Ostrowski SR, Erikstrup C, Pedersen OBV, van Heel DA, Hennah W, Marttila M, Free RC, Hollox EJ, Wain LV, Tobin MD, Batini C, Genes & Health Research Team.",,No Journal Info,2024,2024-07-24,Y,,,,"<h4>Background</h4> Chronic cough is a symptom of common lung conditions, occurs as a side effect of ACE inhibitors (ACEis), or may be unexplained. Despite chronic cough representing a substantial health burden, its biological mechanisms remain unclear. We hypothesised shared genetic architecture between chronic dry cough and ACEi-induced cough and aimed to identify causal genes underlying both phenotypes. <h4>Methods</h4> We performed multi-ancestry genome-wide association studies (GWAS) of chronic dry cough and ACEi-induced cough, and a multi-trait GWAS of both phenotypes, utilising data from five cohort studies. Chronic dry cough was defined by questionnaire responses, and ACEi-induced cough by treatment switches or clinical diagnosis in electronic health records. We mapped putative causal genes and performed phenome-wide association studies (PheWAS) of associated variants and genetic risk scores (GRS) for these phenotypes to identify pleotropic effects. <h4>Findings</h4> We found seven novel genetic association signals reaching p -value <5×10 −8 in the multi-trait or single-trait analyses of chronic dry cough and ACEi-induced cough. The novel variants mapped to 10 novel genes, and we mapped an additional three novel genes to known risk variants, many of which implicating neurological functions ( CTNNA1, KCNA10, MAPKAP1, OR4C12, OR4C13, SIL1 ). The GRS-PheWAS highlighted associations with increased risk of several conditions reported as comorbidities of chronic cough, including fibromyalgia pain, and with spirometry measurements. <h4>Interpretation</h4> Our findings advance the understanding of neuronal dysfunction underlying cough hypersensitivity in chronic dry cough and ACEi-induced cough at the population-level, and the identification of comorbidities associated with genetic predisposition to cough could inform drug target discovery. <h4>Funding</h4> Medical Research Council, Wellcome Trust, National Institute for Health and Care Research, Orion Pharma. <h4>Research in context</h4> <h4>Evidence before this study</h4> We searched the National Human Genome Research Institute-European Bioinformatic Institute Catalog of human genome-wide association studies (GWAS) from inception through to 21 st May 2024, using the search term “cough” to identify publications which tested association between genetic variants and cough. Additionally, we searched PubMed for English language articles published before 21 st May 2024 using the terms “cough” or “ACE inhibitor” combined with “genome-wide association” to find relevant publications. We manually filtered the results from both searches to ensure the cough-related publications related to a dry, unproductive cough. To date, there have been no GWAS of unexplained dry cough, while several for ACE inhibitor (ACEi)-induced cough have identified 11 associated genetic loci at genome-wide significance ( p -value <5×10 −8 ). These loci have implicated genes involved in neuronal excitability and the bradykinin pathway. <h4>Added value of this study</h4> We present the first multi-ancestry GWAS of chronic dry cough, defined using questionnaire responses, and the largest multi-ancestry GWAS of ACEi-induced cough, characterised by either a medication switch from an ACEi to an angiotensin-II receptor blocker or a clinical diagnosis. By leveraging the clinical and genetic overlap between these two traits, we conducted a multi-trait GWAS to identify novel associated loci. Across the multi-trait and single-trait analyses, we identified seven novel associated loci at genome-wide significance ( p -value <5×10 −8 ), mapped to 10 genes which have not previously been linked to cough phenotypes. <h4>Implications of all the available evidence</h4> We identified novel genes involved in neurological processes ( CTNNA1, KCNA10, OR4C12, OR4C13 ) or implicated in neurological or neurodegenerative conditions ( SIL1 and MAPKAP1 ). The genes we implicate from all genetic associations with cough to date support the role of neurobiological processes underlying dry cough biology, and highlight potential therapeutic targets.",,doi:https://doi.org/10.1101/2024.07.23.24310853; doi:https://doi.org/10.1101/2024.07.23.24310853; html:https://europepmc.org/article/PPR/PPR886242; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR886242&type=FILE&fileName=EMS197791-pdf.pdf&mimeType=application/pdf
-PPR755427,https://doi.org/10.21203/rs.3.rs-3568389/v1,Stigma relating to tuberculosis infection prevention and control implementation in rural health facilities in South Africa – a theoretical analysis with opportunities for mitigation,"Westhuizen H, Ehrlich R, Somdyala N, Greenhalgh T, Tonkin-Crine S, Butler CC.",,No Journal Info,2023,2023-11-08,Y,,,,"<h4>Background: </h4> Tuberculosis (TB) is a stigmatised disease due to its associations with poverty, HIV, transmission risk and mortality. The use of visible TB infection prevention and control (IPC) measures, such as masks or isolation, can contribute to stigma. Methods  To explore stigma in this condition, we conducted in-depth individual interviews with 18 health workers and 15 patients in the rural Eastern Cape of South Africa using a semi-structured interview guide and narrative approach. We used reflexive thematic analysis and applied Link and Phelan’s theoretical model of stigma. Results  Participants shared poignant narratives of TB stigma, often entailing TB IPC, with some feeling ‘less than human’. We found TB IPC measures sometimes exacerbated stigma, for example through introducing physical isolation that became prolonged, or through a mask marking the person out as being ill with TB. In this context, stigma emerged from the narrow definition of what mask-wearing symbolises, in contrast with broader uses of masks as a preventative measure. In this way, the health facility itself was shown to play an important role in generating and perpetuating IPC related stigma. We applied ‘ubuntu’ as African humanist conceptual framework to develop recommendations of how TB IPC implementation could be destigmatised. Conclusion  Health facilities may unwittingly perpetuate stigma, but they also have the potential to reduce it. Ubuntu emphases shared humanity and collective wellbeing and could engage with some of the deep-rooted contributors to TB stigma. An ubuntu-informed approach could underpin a local policy change to universal masking, thereby destigmatising an important IPC practice.",,pdf:https://www.researchsquare.com/article/rs-3568389/latest.pdf; doi:https://doi.org/10.21203/rs.3.rs-3568389/v1; html:https://europepmc.org/article/PPR/PPR755427; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR755427&type=FILE&fileName=EMS191184-pdf.pdf&mimeType=application/pdf
 PPR207614,https://doi.org/10.1101/2020.08.25.20181198,The importance of supplementary immunisation activities to prevent measles outbreaks during the COVID-19 pandemic in Kenya,"Mburu C, Ojal J, Chebet R, Akech D, Karia B, Tuju J, Sigilai A, Abbas K, Jit M, Funk S, Smits G, van Gageldonk P, van der Klis F, Tabu C, Nokes D, LSHTM CMMID COVID-19 Working Group, Scott J, Flasche S, Adetifa I.",,No Journal Info,2020,2020-08-31,N,,,,"<h4>Background</h4> The COVID-19 pandemic has disrupted routine measles immunisation and supplementary immunisation activities (SIAs) in most countries including Kenya. We assessed the risk of measles outbreaks during the pandemic in Kenya as a case study for the African Region. <h4>Methods</h4> Combining measles serological data, local contact patterns, and vaccination coverage into a cohort model, we predicted the age-adjusted population immunity in Kenya and estimated the probability of outbreaks when contact-reducing COVID-19 interventions are lifted. We considered various scenarios for reduced measles vaccination coverage from April 2020. <h4>Findings</h4> In February 2020, when a scheduled SIA was postponed, population immunity was close to the herd immunity threshold and the probability of a large outbreak was 22% (0-46). As the COVID-19 restrictions to physical contact are lifted, from December 2020, the probability of a large measles outbreak increased to 31% (8-51), 35% (16-52) and 43% (31-56) assuming a 15%, 50% and 100% reduction in measles vaccination coverage. By December 2021, this risk increases further to 37% (17-54), 44% (29-57) and 57% (48-65) for the same coverage scenarios respectively. However, the increased risk of a measles outbreak following the lifting of restrictions on contact can be overcome by conducting an SIA with ≥ 95% coverage in under-fives. <h4>Interpretation</h4> While contact restrictions sufficient for SAR-CoV-2 control temporarily reduce measles transmissibility and the risk of an outbreak from a measles immunity gap, this risk rises rapidly once physical distancing is relaxed. Implementing delayed SIAs will be critical for prevention of measles outbreaks once contact restrictions are fully lifted in Kenya. <h4>Funding</h4> The United Kingdom’s Medical Research Council and the Department for International Development",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-021-01906-9; doi:https://doi.org/10.1101/2020.08.25.20181198; html:https://europepmc.org/article/PPR/PPR207614; doi:https://doi.org/10.1101/2020.08.25.20181198
+PPR755427,https://doi.org/10.21203/rs.3.rs-3568389/v1,Stigma relating to tuberculosis infection prevention and control implementation in rural health facilities in South Africa – a theoretical analysis with opportunities for mitigation,"Westhuizen H, Ehrlich R, Somdyala N, Greenhalgh T, Tonkin-Crine S, Butler CC.",,No Journal Info,2023,2023-11-08,Y,,,,"<h4>Background: </h4> Tuberculosis (TB) is a stigmatised disease due to its associations with poverty, HIV, transmission risk and mortality. The use of visible TB infection prevention and control (IPC) measures, such as masks or isolation, can contribute to stigma. Methods  To explore stigma in this condition, we conducted in-depth individual interviews with 18 health workers and 15 patients in the rural Eastern Cape of South Africa using a semi-structured interview guide and narrative approach. We used reflexive thematic analysis and applied Link and Phelan’s theoretical model of stigma. Results  Participants shared poignant narratives of TB stigma, often entailing TB IPC, with some feeling ‘less than human’. We found TB IPC measures sometimes exacerbated stigma, for example through introducing physical isolation that became prolonged, or through a mask marking the person out as being ill with TB. In this context, stigma emerged from the narrow definition of what mask-wearing symbolises, in contrast with broader uses of masks as a preventative measure. In this way, the health facility itself was shown to play an important role in generating and perpetuating IPC related stigma. We applied ‘ubuntu’ as African humanist conceptual framework to develop recommendations of how TB IPC implementation could be destigmatised. Conclusion  Health facilities may unwittingly perpetuate stigma, but they also have the potential to reduce it. Ubuntu emphases shared humanity and collective wellbeing and could engage with some of the deep-rooted contributors to TB stigma. An ubuntu-informed approach could underpin a local policy change to universal masking, thereby destigmatising an important IPC practice.",,pdf:https://www.researchsquare.com/article/rs-3568389/latest.pdf; doi:https://doi.org/10.21203/rs.3.rs-3568389/v1; html:https://europepmc.org/article/PPR/PPR755427; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR755427&type=FILE&fileName=EMS191184-pdf.pdf&mimeType=application/pdf
 PPR308166,https://doi.org/10.1101/2021.04.01.21254789,Mendelian randomisation identifies alternative splicing of the FAS death receptor as a mediator of severe COVID-19,"Klaric L, Gisby JS, Papadaki A, Muckian MD, Macdonald-Dunlop E, Zhao JH, Tokolyi A, Persyn E, Pairo-Castineira E, Morris AP, Kalnapenkis A, Richmond A, Landini A, Hedman ÅK, Prins B, Zanetti D, Wheeler E, Kooperberg C, Yao C, Petrie JR, Fu J, Folkersen L, Walker M, Magnusson M, Eriksson N, Mattsson-Carlgren N, Timmers PR, Hwang S, Enroth S, Gustafsson S, Vosa U, Chen Y, Siegbahn A, Reiner A, Johansson Å, Thorand B, Gigante B, Hayward C, Herder C, Gieger C, Langenberg C, Levy D, Zhernakova DV, Smith JG, Campbell H, Sundstrom J, Danesh J, Michaëlsson K, Suhre K, Lind L, Wallentin L, Padyukov L, Landén M, Wareham NJ, Göteson A, Hansson O, Eriksson P, Strawbridge RJ, Assimes TL, Esko T, Gyllensten U, Baillie JK, Paul DS, Joshi PK, Butterworth AS, Mälarstig A, Pirastu N, Wilson JF, Peters JE.",,No Journal Info,2021,2021-04-07,Y,,,,"Severe COVID-19 is characterised by immunopathology and epithelial injury. Proteomic studies have identified circulating proteins that are biomarkers of severe COVID-19, but cannot distinguish correlation from causation. To address this, we performed Mendelian randomisation (MR) to identify proteins that mediate severe COVID-19. Using protein quantitative trait loci (pQTL) data from the SCALLOP consortium, involving meta-analysis of up to 26,494 individuals, and COVID-19 genome-wide association data from the Host Genetics Initiative, we performed MR for 157 COVID-19 severity protein biomarkers. We identified significant MR results for five proteins: FAS, TNFRSF10A, CCL2, EPHB4 and LGALS9. Further evaluation of these candidates using sensitivity analyses and colocalization testing provided strong evidence to implicate the apoptosis-associated cytokine receptor FAS as a causal mediator of severe COVID-19. This effect was specific to severe disease. Using RNA-seq data from 4,778 individuals, we demonstrate that the pQTL at the FAS locus results from genetically influenced alternate splicing causing skipping of exon 6. We show that the risk allele for very severe COVID-19 increases the proportion of transcripts lacking exon 6, and thereby increases soluble FAS. Soluble FAS acts as a decoy receptor for FAS-ligand, inhibiting apoptosis induced through membrane-bound FAS. In summary, we demonstrate a novel genetic mechanism that contributes to risk of severe of COVID-19, highlighting a pathway that may be a promising therapeutic target.",,doi:https://doi.org/10.1101/2021.04.01.21254789; html:https://europepmc.org/article/PPR/PPR308166; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR308166&type=FILE&fileName=EMS121852-pdf.pdf&mimeType=application/pdf
 PPR183540,https://doi.org/10.1101/2020.07.03.20145839,"The Impact of COVID-19 on Adjusted Mortality Risk in Care Homes for Older Adults in Wales, United Kingdom: A retrospective population-based cohort study for mortality in 2016-2020","Hollinghurst J, Lyons J, Fry R, Akbari A, Gravenor M, Watkins A, Verity F, Lyons RA.",,No Journal Info,2020,2020-07-04,Y,,,,"<h4>ABSTRACT</h4> <h4>Background</h4> Mortality in care homes has had a prominent focus during the COVID-19 outbreak. Multiple and interconnected challenges face the care home sector in the prevention and management of outbreaks of COVID-19, including adequate supply of personal protective equipment, staff shortages, and insufficient or lack of timely COVID-19 testing. Care homes are particularly vulnerable to infectious diseases. <h4>Aim</h4> To analyse the mortality of older care home residents in Wales during COVID-19 lockdown and compare this across the population of Wales and the previous 4-years. <h4>Study Design and Setting</h4> We used anonymised Electronic Health Records (EHRs) and administrative data from the Secure Anonymised Information Linkage (SAIL) Databank to create a cross-sectional cohort study. We anonymously linked data for Welsh residents to mortality data up to the 14 th June 2020. <h4>Methods</h4> We calculated survival curves and adjusted Cox proportional hazards models to estimate hazard ratios (HRs) for the risk of mortality. We adjusted hazard ratios for age, gender, social economic status and prior health conditions. <h4>Results</h4> Survival curves show an increased proportion of deaths between 23 rd March and 14 th June 2020 in care homes for older people, with an adjusted HR of 1·72 (1·55, 1·90) compared to 2016. Compared to the general population in 2016-2019, adjusted care home mortality HRs for older adults rose from 2·15 (2·11,2·20) in 2016-2019 to 2·94 (2·81,3·08) in 2020. <h4>Conclusions</h4> The survival curves and increased HRs show a significantly increased risk of death in the 2020 study periods.",,pdf:https://academic.oup.com/ageing/article-pdf/50/1/25/42362959/afaa207.pdf; doi:https://doi.org/10.1101/2020.07.03.20145839; html:https://europepmc.org/article/PPR/PPR183540; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR183540&type=FILE&fileName=EMS87632-pdf.pdf&mimeType=application/pdf
 PPR362272,https://doi.org/10.1101/2021.06.22.21259336,Population disruption: estimating changes in population distribution of the UK during the COVID-19 pandemic,"Gibbs H, Waterlow NR, Cheshire J, Danon L, Liu Y, Grundy C, Kucharski AJ, LSHTM CMMID COVID-19 Working Group, Eggo RM.",,No Journal Info,2021,2021-06-24,Y,,,,"Mobility data have demonstrated major changes in human movement patterns in response to COVID-19 and associated interventions in many countries. This can involve sub-national redistribution, short-term relocations as well as international migration. In this paper, we combine detailed location data from Facebook measuring the location of approximately 6 million daily active Facebook users in 5km 2 tiles in the UK with census-derived population estimates to measure population mobility and redistribution. We provide time-varying population estimates and assess spatial population changes with respect to population density and four key reference dates in 2020 (First lockdown, End of term, Beginning of term, Christmas). We also show how population estimates derived from the distribution of Facebook users vary compared to mid-2020 small area population estimates by the UK national statistics agencies. We estimate that between March 2020 and March 2021, the total population of the UK declined and we identify important spatial variations in this population change, showing that low-density areas have experienced lower population decreases than urban areas. We estimate that, for the top 10% highest population tiles, the population has decreased by 6.6%. Further, we provide evidence that geographic redistributions of population within the UK coincide with dates of non-pharmaceutical interventions including lockdowns and movement restrictions, as well as seasonal patterns of migration around holiday dates. The methods used in this study reveal significant changes in population distribution at high spatial and temporal resolutions that have not previously been quantified by available demographic surveys in the UK. We found early indicators of potential longer-term changes in the population distribution of the UK although it is not clear if these changes may persist after the COVID-19 pandemic.",,doi:https://doi.org/10.1101/2021.06.22.21259336; html:https://europepmc.org/article/PPR/PPR362272; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR362272&type=FILE&fileName=EMS129221-pdf.pdf&mimeType=application/pdf
@@ -472,8 +472,8 @@ PPR254227,https://doi.org/10.1101/2020.12.14.20248155,Investigating mental and p
 PPR264211,https://doi.org/10.1101/2021.01.11.21249461,A national retrospective cohort study of mechanical ventilator availability and its association with mortality risk in intensive care patients with COVID-19,"Wilde H, Mellan TA, Hawryluk I, Dennis J, Denaxas S, Pagel C, Duncan A, Bhatt S, Flaxman S, Mateen BA, Vollmer S.",,No Journal Info,2021,2021-01-13,Y,,,,"<h4>Objectives: </h4> To determine if there is an association between survival rates in intensive care units (ICU) and occupancy of the unit on the day of admission. <h4>Design:</h4> National retrospective observational cohort study during the COVID-19 pandemic. <h4>Setting:</h4> 90 English hospital trusts (i.e. groups of hospitals functioning as single operational units).  Participants: 6,686 adults admitted to an ICU in England between 2nd April and 1st December, 2020 (inclusive), with presumed or confirmed COVID-19, for whom data was submitted to the national surveillance programme and met study inclusion criteria.  Interventions: N/A  Main Outcomes and Measures: A Bayesian hierarchical approach was used to model the association between hospital trust level (mechanical ventilation compatible) bed occupancy, and in-hospital all-cause mortality. Results were adjusted for unit characteristics (pre-pandemic size), individual patient-level demographic characteristics (age, sex, ethnicity, time-to-ICU admission), and recorded chronic comorbidities (obesity, diabetes, respiratory disease, liver disease, heart disease, hypertension, immunosuppression, neurological disease, renal disease). <h4>Results:</h4> 121,151 patient-days were observed, with a mortality rate of 20.8 per 1,000 patient days. Adjusting for patient-level factors, mortality was higher for admissions during periods of high occupancy (>85% occupancy versus the baseline of 45 to 85%) [OR 1.18 (95% posterior credible interval (PCI): 1.00 to 1.38)]. In contrast, mortality was decreased for admissions during periods of low occupancy (<45% relative to the baseline) [OR 0.79 (95% PCI: 0.69 to 0.90)].  Conclusion and Relevance: Increasing occupancy of beds compatible with mechanical ventilation, a proxy for operational strain, is associated with a higher mortality risk for individuals admitted to ICU. Public health interventions (such as expeditious vaccination programmes and non-pharmaceutical interventions) to control both incidence and prevalence of COVID-19, and therefore keep ICU occupancy low in the context of the pandemic, are necessary to mitigate the impact of this type of resource saturation.  Trial Registration: N/A",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-021-02096-0; doi:https://doi.org/10.1101/2021.01.11.21249461; html:https://europepmc.org/article/PPR/PPR264211; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR264211&type=FILE&fileName=EMS110554-pdf.pdf&mimeType=application/pdf
 PPR250078,https://doi.org/10.1101/2020.12.03.20242941,Contrasting factors associated with COVID-19-related ICU admission and death outcomes in hospitalised patients by means of Shapley values,"Cavallaro M, Moiz H, Keeling MJ, McCarthy ND.",,No Journal Info,2020,2020-12-07,Y,,,,"Identification of those at greatest risk of death due to the substantial threat of COVID-19 can benefit from novel approaches to epidemiology that leverage large datasets and complex machine-learning models, provide data-driven intelligence, and guide decisions such as intensive-care unit admission (ICUA). The objective of this study is two-fold, one substantive and one methodological: substantively to evaluate the association of demographic and health records with two related, yet different, outcomes of severe COVID-19 (viz., death and ICUA); methodologically to compare interpretations based on logistic regression and on gradient-boosted decision tree (GBDT) predictions interpreted by means of the Shapley impacts of covariates. Very different association of some factors, e.g., obesity and chronic respiratory diseases, with death and ICUA may guide review of practice. Shapley explanation of GBDTs identified varying effects of some factors among patients, thus emphasising the importance of individual patient assessment. The results of this study are also relevant for the evaluation of complex automated clinical decision systems, which should optimise prediction scores whilst remaining interpretable to clinicians and mitigating potential biases. <h4>Author summary</h4> The design is a retrospective cohort study of 13954 in-patients of ages ranging from 1 to 105 year (IQR: 56, 70, 81) with a confirmed diagnosis of COVID-19 by 28th June 2020. This study used multivariable logistic regression to generate odd ratios (ORs) multiply adjusted for 37 covariates (comorbidities, demographic, and others) selected on the basis of clinical interest and prior findings. Results were supplemented by gradient-boosted decision tree (GBDT) classification to generate Shapley values in order to evaluate the impact of the covariates on model output for all patients. Factors are differentially associated with death and ICUA and among patients. Deaths due to COVID-19 were associated with immunosuppression due to disease (OR 1.39, 95% CI 1.10-1.76), type-2 diabetes (OR 1.31, 95% CI 1.17-1.46), chronic respiratory disease (OR 1.19, 95% CI 1.05-1.35), age (OR 1.56/10-year increment, 95% CI 1.52-1.61), and male sex (OR 1.54, 95% CI1.42-1.68). Associations of ICUA with some factors differed in direction (e.g., age, chronic respiratory disease). Self-reported ethnicities were strongly but variably associated with both outcomes. GBDTs had similar performance (ROC-AUC, ICUA 0.83, death 0.68 for GBDT; 0.80 and 0.68 for logistic regression). We derived importance scores based on Shapley values which were consistent with the ORs, despite the underlying machine-learning model being intrinsically different to the logistic regression. Chronic heart disease, hypertension, other comorbidities, and some ethnicities had Shapley impacts on death ranging from positive to negative among different patients, although consistently associated with ICUA for all. Immunosuppressive disease, type-2 diabetes, and chronic liver and respiratory diseases had positive impacts on death with either positive or negative on ICUA. We highlight the complexity of informing clinical practice and public-health interventions. We recommend that clinical support systems should not only predict patients at risk, but also yield interpretable outputs for validation by domain experts.",,pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009121&type=printable; doi:https://doi.org/10.1101/2020.12.03.20242941; html:https://europepmc.org/article/PPR/PPR250078; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR250078&type=FILE&fileName=EMS108093-pdf.pdf&mimeType=application/pdf
 PPR167046,https://doi.org/10.1101/2020.05.19.20106641,Study Data Element Mapping: Feasibility of Defining Common Data Elements Across COVID-19 Studies,"Mathewson P, Gordon B, Snowley K, Fennessy C, Denniston A, Sebire N.",,No Journal Info,2020,2020-05-26,N,,,,"<h4>Background: </h4> Numerous clinical studies are now underway investigating aspects of COVID-19. The aim of this study was to identify a selection of national and/or multicentre clinical COVID-19 studies in the United Kingdom to examine the feasibility and outcomes of documenting the most frequent data elements common across studies to rapidly inform future study design and demonstrate proof-of-concept for further subject-specific study data element mapping to improve research data management. <h4>Methods:</h4> 25 COVID-19 studies were included. For each, information regarding the specific data elements being collected was recorded. Data elements collated were arbitrarily divided into categories for ease of visualisation. Elements which were most frequently and consistently recorded across studies are presented in relation to their relative commonality. <h4>Results:</h4> Across the 25 studies, 261 data elements were recorded in total. The most frequently recorded 100 data elements were identified across all studies and are presented with relative frequencies. Categories with the largest numbers of common elements included demographics, admission criteria, medical history and investigations. Mortality and need for specific respiratory support were the most common outcome measures, but with specific studies including a range of other outcome measures. <h4>Conclusion:</h4> The findings of this study have demonstrated that it is feasible to collate specific data elements recorded across a range of studies investigating a specific clinical condition in order to identify those elements which are most common among studies. These data may be of value for those establishing new studies and to allow researchers to rapidly identify studies collecting data of potential use hence minimising duplication and increasing data re-use and interoperability",,pdf:https://discovery.ucl.ac.uk/10108130/1/2020.05.19.20106641v1.full.pdf; doi:https://doi.org/10.1101/2020.05.19.20106641; html:https://europepmc.org/article/PPR/PPR167046; doi:https://doi.org/10.1101/2020.05.19.20106641
-PPR594314,https://doi.org/10.1101/2023.01.06.23284202,Long Covid symptoms and diagnosis in primary care: a cohort study using structured and unstructured data in The Health Improvement Network primary care database,"Shah AD, Subramanian A, Lewis J, Dhalla S, Ford E, Haroon S, Kuan V, Nirantharakumar K.",,No Journal Info,2023,2023-01-09,Y,,,,"<h4>BACKGROUND</h4> Long Covid is a widely recognised consequence of COVID-19 infection, but little is known about the burden of symptoms that patients present with in primary care, as these are typically recorded only in free text clinical notes. Our objectives were to compare symptoms in patients with and without a history of COVID-19, and investigate symptoms associated with a Long Covid diagnosis. <h4>METHODS</h4> We used primary care electronic health record data from The Health Improvement Network (THIN), a Cegedim database. We included adults registered with participating practices in England, Scotland or Wales. We extracted information about 89 symptoms and ‘Long Covid’ diagnoses from free text using natural language processing. We calculated hazard ratios (adjusted for age, sex, baseline medical conditions and prior symptoms) for each symptom from 12 weeks after the COVID-19 diagnosis. <h4>FINDINGS</h4> We compared 11,015 patients with confirmed COVID-19 and 18,098 unexposed controls. Only 20% of symptom records were coded, with 80% in free text. A wide range of symptoms were associated with COVID-19 at least 12 weeks post-infection, with strongest associations for fatigue (adjusted hazard ratio (aHR) 3.99, 95% confidence interval (CI) 3.59, 4.44), shortness of breath (aHR 3.14, 95% CI 2.88, 3.42), palpitations (aHR 2.75, 95% CI 2.28, 3.32), and phlegm (aHR 2.88, 95% CI 2.30, 3.61). However, a limited subset of symptoms were recorded within 7 days prior to a Long Covid diagnosis in more than 20% of cases: shortness of breath, chest pain, pain, fatigue, cough, and anxiety / depression. <h4>CONCLUSION</h4> Numerous symptoms are reported to primary care at least 12 weeks after COVID-19 infection, but only a subset are commonly associated with a GP diagnosis of Long Covid.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2023/01/09/2023.01.06.23284202.full.pdf; doi:https://doi.org/10.1101/2023.01.06.23284202; html:https://europepmc.org/article/PPR/PPR594314; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR594314&type=FILE&fileName=EMS159579-pdf.pdf&mimeType=application/pdf
 PPR138670,https://doi.org/10.1101/2020.03.31.20049023,Quantifying the impact of physical distance measures on the transmission of COVID-19 in the UK,"Jarvis CI, Van Zandvoort K, Gimma A, Prem K, CMMID COVID-19 working group, Klepac P, Rubin GJ, Edmunds WJ.",,No Journal Info,2020,2020-04-03,Y,,,,"<h4>Background</h4> To mitigate and slow the spread of COVID-19, many countries have adopted unprecedented physical distancing policies, including the UK. We evaluate whether these measures might be sufficient to control the epidemic by estimating their impact on the reproduction number ( R 0 , the average number of secondary cases generated per case). <h4>Methods</h4> We asked a representative sample of UK adults about their contact patterns on the previous day. The questionnaire documents the age and location of contacts and as well as a measure of their intimacy (whether physical contact was made or not). In addition, we asked about adherence to different physical distancing measures. The first surveys were sent on Tuesday 24th March, one day after a “ lockdown” was implemented across the UK. We compared measured contact patterns during the “ lockdown” to patterns of social contact made during a non-epidemic period. By comparing these, we estimated the change in reproduction number as a consequence of the physical distancing measures imposed. We used a meta-analysis of published estimates to inform our estimates of the reproduction number before interventions were put in place. <h4>Findings</h4> We found a 73% reduction in the average daily number of contacts observed per participant (from 10.2 to 2.9). This would be sufficient to reduce R 0 from 2.6 prior to lockdown to 0.62 (95% confidence interval [CI] 0.37 - 0.89) after the lockdown, based on all types of contact and 0.37 (95% CI = 0.22 - 0.53) for physical contacts only. <h4>Interpretation</h4> The physical distancing measures adopted by the UK public have substantially reduced contact levels and will likely lead to a substantial impact and a decline in cases in the coming weeks. However, this projected decline in incidence will not occur immediately as there are significant delays between infection, the onset of symptomatic disease and hospitalisation, as well as further delays to these events being reported. Tracking behavioural change can give a more rapid assessment of the impact of physical distancing measures than routine epidemiological surveillance. <h4>Research in context</h4> <h4>Evidence before this study</h4> Many governments have adopted physical distancing measures to mitigate the impact of the COVID-19 pandemic. However, it is unclear to what extent these measures reduce the number of contacts and therefore transmission. We searched PubMed and medRxiv on March 28, 2020, with the terms “ (coronavirus OR COVID-19 OR influenza) AND ((school OR work) AND (closure OR holiday)) AND (contact OR mixing)” and identified 59 and 17 results, respectively. Only one study conducted in China during the COVID-19 pandemic reported a reduction in daily contacts outside the home during the period of “ lockdown”. We found no other published articles that empirically quantify the impact of these measures on age- and location-specific mixing patterns. <h4>Added value of this study</h4> By surveying adults’ behaviour in the UK during a period of stringent physical distancing (“ lockdown”) and comparing the results to previously collected data, we found a large reduction in daily contacts particularly outside the home, resulting in a marked reduction in the estimated reproduction number from 2.6 to 0.62 (95% bootstrapped confidence interval [CI] 0.37 - 0.89). This method allows for rapid assessment of changes in the reproduction number that is unaffected by reporting delays. <h4>Implications of all the available evidence</h4> Changes in human contact behaviour drive respiratory infection rates. Understanding these changes at different stages of the COVID-19 pandemic allows us to rapidly quantify the impact of physical distancing measures on the transmission of pathogens.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-020-01597-8; doi:https://doi.org/10.1101/2020.03.31.20049023; html:https://europepmc.org/article/PPR/PPR138670; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR138670&type=FILE&fileName=EMS89599-pdf.pdf&mimeType=application/pdf
+PPR594314,https://doi.org/10.1101/2023.01.06.23284202,Long Covid symptoms and diagnosis in primary care: a cohort study using structured and unstructured data in The Health Improvement Network primary care database,"Shah AD, Subramanian A, Lewis J, Dhalla S, Ford E, Haroon S, Kuan V, Nirantharakumar K.",,No Journal Info,2023,2023-01-09,Y,,,,"<h4>BACKGROUND</h4> Long Covid is a widely recognised consequence of COVID-19 infection, but little is known about the burden of symptoms that patients present with in primary care, as these are typically recorded only in free text clinical notes. Our objectives were to compare symptoms in patients with and without a history of COVID-19, and investigate symptoms associated with a Long Covid diagnosis. <h4>METHODS</h4> We used primary care electronic health record data from The Health Improvement Network (THIN), a Cegedim database. We included adults registered with participating practices in England, Scotland or Wales. We extracted information about 89 symptoms and ‘Long Covid’ diagnoses from free text using natural language processing. We calculated hazard ratios (adjusted for age, sex, baseline medical conditions and prior symptoms) for each symptom from 12 weeks after the COVID-19 diagnosis. <h4>FINDINGS</h4> We compared 11,015 patients with confirmed COVID-19 and 18,098 unexposed controls. Only 20% of symptom records were coded, with 80% in free text. A wide range of symptoms were associated with COVID-19 at least 12 weeks post-infection, with strongest associations for fatigue (adjusted hazard ratio (aHR) 3.99, 95% confidence interval (CI) 3.59, 4.44), shortness of breath (aHR 3.14, 95% CI 2.88, 3.42), palpitations (aHR 2.75, 95% CI 2.28, 3.32), and phlegm (aHR 2.88, 95% CI 2.30, 3.61). However, a limited subset of symptoms were recorded within 7 days prior to a Long Covid diagnosis in more than 20% of cases: shortness of breath, chest pain, pain, fatigue, cough, and anxiety / depression. <h4>CONCLUSION</h4> Numerous symptoms are reported to primary care at least 12 weeks after COVID-19 infection, but only a subset are commonly associated with a GP diagnosis of Long Covid.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2023/01/09/2023.01.06.23284202.full.pdf; doi:https://doi.org/10.1101/2023.01.06.23284202; html:https://europepmc.org/article/PPR/PPR594314; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR594314&type=FILE&fileName=EMS159579-pdf.pdf&mimeType=application/pdf
 PPR630660,https://doi.org/10.1101/2023.03.10.23286918,Medical history predicts phenome-wide disease onset and enables the rapid response to emerging health threats,"Steinfeldt J, Wild B, Buergel T, Pietzner M, Upmeier zu Belzen J, Vauvelle A, Hegselmann S, Denaxas S, Hemingway H, Langenberg C, Landmesser U, Deanfield J, Eils R.",,No Journal Info,2023,2023-03-15,Y,,,,"The COVID-19 pandemic exposed, with few exceptions, a global deficiency in delivering systematic, data-driven guidance to protect citizens and coordinate vaccination programs. At the same time, medical histories are routinely recorded in most healthcare systems and are instantly available for risk assessment. Here, we demonstrate the utility of medical history in determining the risk for 1,883 diseases across clinical specialties and facilitating the rapid response to emerging health threats at the example of COVID-19. We developed a neural network to learn disease-specific risk states from routinely collected health records of 502,460 UK Biobank participants, demonstrating risk stratification for nearly all conditions, and validated this model on 229,830 individuals from the All of US cohort. When integrated into Cox Proportional Hazard Models, we observed significant discriminative improvements over basic demographic predictors for 1,774 (94.3%). After transferring the unmodified risk models to the All of US cohort, the discriminate improvements were replicated for 1,347 (89.8%) of 1,500 investigated endpoints, demonstrating model generalizability across healthcare systems and historically underrepresented groups. We then show that these risk states can be used to identify individuals vulnerable to severe COVID-19 and mortality. Our study demonstrates the currently underused potential of medical history to rapidly respond to emerging health threats by systematically estimating risk for thousands of diseases at once at minimal cost.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2023/03/16/2023.03.10.23286918.full.pdf; doi:https://doi.org/10.1101/2023.03.10.23286918; html:https://europepmc.org/article/PPR/PPR630660; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR630660&type=FILE&fileName=EMS188640-pdf.pdf&mimeType=application/pdf
 PPR230607,https://doi.org/10.1101/2020.10.26.20219576,Impact of the COVID-19 pandemic on remote mental healthcare and prescribing in psychiatry,"Patel R, Irving J, Brinn A, Broadbent M, Shetty H, Pritchard M, Downs J, Stewart R, Harland R, McGuire P.",,No Journal Info,2020,2020-10-27,Y,,,,"<h4>Objectives</h4> The recent COVID-19 pandemic has disrupted mental healthcare delivery, with many services shifting from in- person to remote patient contact. We investigated the impact of the pandemic on the use of remote consultation and on the prescribing of psychiatric medications. <h4>Design and setting</h4> The Clinical Record Interactive Search tool (CRIS) was used to examine de-identified electronic health records (EHRs) of people receiving mental healthcare from the South London and Maudsley (SLaM) NHS Foundation Trust. Data from the period before and after the onset of the pandemic were analysed using linear regression, and visualised using locally estimated scatterplot smoothing (LOESS). <h4>Participants</h4> All patients receiving care from SLaM between 7 th January 2019 and 20 th September 2020 (around 37,500 patients per week). <h4>Outcome measures</h4> The number of clinical contacts (in-person, remote or non-attended) with mental healthcare professionals per week Prescribing of antipsychotic and mood stabiliser medications per week <h4>Results</h4> Following the onset of the pandemic, the frequency of in-person contacts was significantly reduced compared to that in the previous year (β coefficient: −5829.6 contacts, 95% CI −6919.5 to −4739.6, p<0.001), while the frequency of remote contacts significantly increased (β coefficient: 3338.5 contacts, 95% CI 3074.4 to 3602.7, p<0.001). Rates of remote consultation were lower in older adults than in working age adults, children and adolescents. Despite this change in the type of patient contact, antipsychotic and mood stabiliser prescribing remained at similar levels. <h4>Conclusions</h4> The COVID-19 pandemic has been associated with a marked increase in remote consultation, particularly among younger patients. However, there was no evidence that this has led to changes in psychiatric prescribing. Nevertheless, further work is needed to ensure that older patients are able to access mental healthcare remotely.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2020/10/27/2020.10.26.20219576.full.pdf; doi:https://doi.org/10.1101/2020.10.26.20219576; html:https://europepmc.org/article/PPR/PPR230607; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR230607&type=FILE&fileName=EMS101579-pdf.pdf&mimeType=application/pdf
 PPR208637,https://doi.org/10.1101/2020.09.02.20186502,Real-time monitoring of COVID-19 dynamics using automated trend fitting and anomaly detection,"Jombart T, Ghozzi S, Schumacher D, Leclerc QJ, Jit M, Flasche S, Greaves F, Ward T, Eggo RM, Nightingale E, Meakin S, Brady OJ, Centre for Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Medley GF, Höhle M, Edmunds WJ.",,No Journal Info,2020,2020-09-03,Y,,,,"As several countries gradually release social distancing measures, rapid detection of new localised COVID-19 hotspots and subsequent intervention will be key to avoiding large-scale resurgence of transmission. We introduce ASMODEE (Automatic Selection of Models and Outlier Detection for Epidemics), a new tool for detecting sudden changes in COVID-19 incidence. Our approach relies on automatically selecting the best (fitting or predicting) model from a range of user-defined time series models, excluding the most recent data points, to characterise the main trend in an incidence. We then derive prediction intervals and classify data points outside this interval as outliers, which provides an objective criterion for identifying departures from previous trends. We also provide a method for selecting the optimal breakpoints, used to define how many recent data points are to be excluded from the trend fitting procedure. The analysis of simulated COVID-19 outbreaks suggest ASMODEE compares favourably with a state-of-art outbreak-detection algorithm while being simpler and more flexible. We illustrate our method using publicly available data of NHS Pathways reporting potential COVID-19 cases in England at a fine spatial scale, for which we provide a template automated analysis pipeline. ASMODEE is implemented in the free R package trendbreaker .",,pdf:https://royalsocietypublishing.org/doi/pdf/10.1098/rstb.2020.0266; doi:https://doi.org/10.1101/2020.09.02.20186502; html:https://europepmc.org/article/PPR/PPR208637; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR208637&type=FILE&fileName=EMS94645-pdf.pdf&mimeType=application/pdf
@@ -523,8 +523,8 @@ PPR760658,https://doi.org/10.1101/2023.11.17.23298682,Estimating Demand for Pote
 PPR290370,https://doi.org/10.1101/2021.02.25.21252433,Predicting COVID-19 related death using the OpenSAFELY platform,"The OpenSAFELY Collaborative, Williamson EJ, Tazare J, Bhaskaran K, Bhaskaran K, McDonald HI, Walker AJ, Tomlinson L, Wing K, Bacon S, Bates C, Bates C, Curtis HJ, Forbes H, Minassian C, Morton CE, Nightingale E, Mehrkar A, Evans D, Nicholson BD, Leon D, Inglesby P, MacKenna B, Davies NG, DeVito NJ, Drysdale H, Cockburn J, Hulme W, Morley J, Douglas I, Rentsch CT, Mathur R, Wong A, Schultze A, Croker R, Parry J, Hester F, Harper S, Grieve R, Harrison DA, Steyerberg EW, Eggo RM, Diaz-Ordaz K, Keogh R, Evans SJ, Smeeth L, Goldacre B.",,No Journal Info,2021,2021-03-01,Y,,,,"<h4>Objectives</h4> To compare approaches for obtaining relative and absolute estimates of risk of 28-day COVID-19 mortality for adults in the general population of England in the context of changing levels of circulating infection. <h4>Design</h4> Three designs were compared. (A) case-cohort which does not explicitly account for the time-changing prevalence of COVID-19 infection, (B) 28-day landmarking, a series of sequential overlapping sub-studies incorporating time-updating proxy measures of the prevalence of infection, and (C) daily landmarking. Regression models were fitted to predict 28-day COVID-19 mortality. <h4>Setting</h4> Working on behalf of NHS England, we used clinical data from adult patients from all regions of England held in the TPP SystmOne electronic health record system, linked to Office for National Statistics (ONS) mortality data, using the OpenSAFELY platform. <h4>Participants</h4> Eligible participants were adults aged 18 or over, registered at a general practice using TPP software on 1 st March 2020 with recorded sex, postcode and ethnicity. 11,972,947 individuals were included, and 7,999 participants experienced a COVID-19 related death. The study period lasted 100 days, ending 8 th June 2020. <h4>Predictors</h4> A range of demographic characteristics and comorbidities were used as potential predictors. Local infection prevalence was estimated with three proxies: modelled based on local prevalence and other key factors; rate of A&E COVID-19 related attendances; and rate of suspected COVID-19 cases in primary care. <h4>Main outcome measures</h4> COVID-19 related death. <h4>Results</h4> All models discriminated well between patients who did and did not experience COVID-19 related death, with C-statistics ranging from 0.92-0.94. Accurate estimates of absolute risk required data on local infection prevalence, with modelled estimates providing the best performance. <h4>Conclusions</h4> Reliable estimates of absolute risk need to incorporate changing local prevalence of infection. Simple models can provide very good discrimination and may simplify implementation of risk prediction tools in practice.",,pdf:https://diagnprognres.biomedcentral.com/track/pdf/10.1186/s41512-022-00120-2; doi:https://doi.org/10.1101/2021.02.25.21252433; html:https://europepmc.org/article/PPR/PPR290370; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR290370&type=FILE&fileName=EMS117896-pdf.pdf&mimeType=application/pdf
 PPR409881,https://doi.org/10.1101/2021.10.16.21265095,"One-dose ChAdOx1 nCoV-19 Vaccine Effectiveness Against Symptomatic COVID-19 in a vulnerable community in Rio de Janeiro, Brazil: test-negative design study","Ranzani OT, Silva AAB, Peres IT, Antunes BBP, Gonzaga-da-Silva TW, Soranz DR, Cerbino-Neto J, Hamacher S, Bozza FA.",,No Journal Info,2021,2021-10-20,Y,,,,"<h4>ABSTRACT</h4> We conducted a test-negative study design at the community “Complexo da Maré”, the largest group of favelas in Rio de Janeiro, Brazil, when Gamma and Delta were the predominant variants circulating. We estimated 42.4% (95% CI, 24.6, 56.0) protection against symptomatic COVID-19 after 21 days of one dose of ChAdOx1.",,doi:https://doi.org/10.1016/j.cmi.2022.01.032; doi:https://doi.org/10.1101/2021.10.16.21265095; html:https://europepmc.org/article/PPR/PPR409881; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR409881&type=FILE&fileName=EMS137340-pdf.pdf&mimeType=application/pdf
 PPR683580,https://doi.org/10.1101/2023.06.28.23291704,Data-driven identification of potentially successful intervention implementations: a proof of concept using five years of opioid prescribing data from over 7000 practices in England,"Hopcroft LEM, Curtis HJ, Croker R, Pretis F, Inglesby P, Evans D, Bacon S, Goldacre B, Walker AJ, MacKenna B.",,No Journal Info,2023,2023-06-29,Y,,,,"<h4>Background</h4> We have previously demonstrated that opioid prescribing increased by 127% between 1998 and 2016. New policies aimed at tackling this increasing trend have been recommended by public health bodies and there is some evidence that progress is being made. We sought to extend our previous work and develop an unbiased, data-driven approach to identify general practices and clinical commissioning groups (CCGs) whose prescribing data suggest that interventions to reduce the prescribing of opioids may have been successfully implemented. <h4>Methods</h4> We analysed five years of prescribing data for three opioid prescribing measures: one capturing total opioid prescribing and two capturing regular prescribing of high dose opioids. Using a data-driven approach, we applied a modified version of our change detection Python library to identify changes in these measures over time, consistent with the successful implementation of an intervention. This analysis was carried out for general practices and CCGs, and organisations were ranked according to the change in prescribing rate. <h4>Results</h4> We present data for the three CCGs and practices demonstrating the biggest reduction in opioid prescribing across the three opioid prescribing measures. We observed a 40% drop in the regular prescribing of high dose opioids (measured as a percentage of regular opioids) in the highest ranked CCG (North Tyneside); a 99% drop in this same measure was found in several practices. Decile plots demonstrate that CCGs exhibiting large reductions in opioid prescribing do so via slow and gradual reductions over a long period of time (typically over two years); in contrast, practices exhibiting large reductions do so rapidly over a much shorter period of time. <h4>Conclusions</h4> By applying one of our existing analysis tools to a national dataset, we were able to rank NHS organisations by reduction in opioid prescribing rates. Highly ranked organisations are candidates for further qualitative research into intervention design and implementation. <h4>Contributions to the literature</h4> Demonstrating that a data-driven approach can identify and quantify changes in important clinical measures in publicly available NHS data Identifying changes in this way allows the unbiased identification of candidates for further qualitative research into intervention design and implementation Large reductions observed at the CCG level (which are more robust to local circumstances) demonstrate that it is possible to reduce opioid prescribing and that continued and wider success in reducing opioid prescribing is dependent, at least in part, to closing an implementation gap",,doi:https://doi.org/10.1101/2023.06.28.23291704; html:https://europepmc.org/article/PPR/PPR683580; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR683580&type=FILE&fileName=EMS178309-pdf.pdf&mimeType=application/pdf
-PPR277488,https://doi.org/10.1101/2021.02.02.21250989,Short report: Ethnicity and COVID-19 death in the early part of the COVID-19 second wave in England: an analysis of OpenSAFELY data from 1<sup>st</sup> September to 9<sup>th</sup> November 2020,"Bhaskaran K, Mathur R, Rentsch CT, Morton CE, Hulme WJ, Schultze A, MacKenna B, Eggo RM, Wong AY, Williamson EJ, Forbes H, Wing K, McDonald HI, Bates C, Bacon S, Walker AJ, Evans D, Inglesby P, Mehrkar A, Curtis HJ, DeVito NJ, Croker R, Drysdale H, Cockburn J, Parry J, Hester F, Harper S, Douglas IJ, Tomlinson L, Evans SJ, Grieve R, Smeeth L, Goldacre B.",,No Journal Info,2021,2021-02-03,Y,,,,"<h4>Summary</h4> Black and minority ethnic groups were at raised risk of dying from COVID-19 during the first few months of the COVID-19 epidemic in England. We aimed to investigate whether ethnic inequalities in COVID-19 deaths were similar in the more recent “second wave” of the epidemic. Working on behalf of NHS England, we used primary care and linked ONS mortality data within the OpenSAFELY platform. All adults in the database at 1st September 2020 and with at least 1 year of prior follow-up and a record of ethnicity were included. The outcome was COVID-19-related death (death with COVID-19 listed as a cause of death on the death certificate). Follow-up was to 9th November 2020. Hazard ratios for ethnicity were calculated using Cox regression models adjusted for age and sex, and then further adjusted for deprivation. 13,223,154 people were included. During the study period, people of South Asian ethnicity were at higher risk of death due to COVID-19 than white people after adjusting for age and sex (HR = 3.47, 95% CI 2.99-4.03); the association attenuated somewhat on further adjustment for index of multiple deprivation (HR = 2.86, 2.46-3.33, Table 2). In contrast with the first wave of the epidemic, we found little evidence of a raised risk in black or other ethnic groups compared to white (HR for black vs white = 1.28, 0.87-1.88 adjusted for age and sex; and 1.01, 0.69-1.49 further adjusted for deprivation). Our findings suggest that ethnic inequalities in the risk of dying COVID-19-related death have changed between the first and early second wave of the epidemic in England.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2021/02/03/2021.02.02.21250989.full.pdf; doi:https://doi.org/10.1101/2021.02.02.21250989; html:https://europepmc.org/article/PPR/PPR277488; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR277488&type=FILE&fileName=EMS115851-pdf.pdf&mimeType=application/pdf
 PPR574413,https://doi.org/10.21203/rs.3.rs-2210654/v1,Response to Medicines and Healthcare products Regulatory Agency’s “Consultation on proposals for legislative changes for clinical trials”,"Law M, Couturier D, Choodari-Oskooei B, Crout P, Gamble C, Pallmann P, Pilling M, Robertson D, Robling M, Sydes MR, Villar SS, Wason J, Wheeler G, Williamson SF, Yap C, Jaki T.",,No Journal Info,2022,2022-11-22,Y,,,,"In the United Kingdom, the Medicines and Healthcare products Regulatory Agency consulted on proposals “to improve and strengthen the UK clinical trials legislation to help us make the UK the best place to research and develop safe and innovative medicines”. The purpose of the consultation was to help finalise the proposals and contribute to the drafting of secondary legislation. We discussed these proposals as members of the Trials Methodology Research Partnership Adaptive Designs Working Group, which is jointly funded by the Medical Research Council and the National Institute for Health and Care Research. Two topics arose frequently in the discussion: the emphasis on legislation, and data sharing. It is our opinion that the proposals rely heavily on legislation to change practice. However, clinical trials are heterogeneous, and as a result some trials will struggle to comply with all of the proposed legislation. Furthermore, adaptive design clinical trials are even more heterogeneous than their non-adaptive counterparts, and face more challenges. Consequently, it is possible that increased legislation could have a greater negative impact on adaptive designs than non-adaptive designs. Overall, we are skeptical that the introduction of legislation will achieve the desired outcomes, with some exceptions. Meanwhile the topic of data sharing – making anonymised individual-level clinical trial data available to other investigators for further use – is entirely absent from the proposals. However, as an aspect of the wider concept of open science and reproducible research, data sharing is an increasingly important aspect of clinical trials. The benefits of data sharing include faster innovation, improved surveillance of drug safety and effectiveness and decreasing participant exposure to unnecessary risk. There are already a number of UK-focused documents that discuss and encourage data sharing, for example, the Concordat on Open Research Data and the Medical Research Council’s Data Sharing Policy. We strongly suggest that data sharing should be the norm rather than the exception, and hope that the forthcoming proposals on clinical trials
 address this important topic.",,pdf:https://www.researchsquare.com/article/rs-2210654/latest.pdf; doi:https://doi.org/10.21203/rs.3.rs-2210654/v1; html:https://europepmc.org/article/PPR/PPR574413; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR574413&type=FILE&fileName=EMS157568-pdf.pdf&mimeType=application/pdf
+PPR277488,https://doi.org/10.1101/2021.02.02.21250989,Short report: Ethnicity and COVID-19 death in the early part of the COVID-19 second wave in England: an analysis of OpenSAFELY data from 1<sup>st</sup> September to 9<sup>th</sup> November 2020,"Bhaskaran K, Mathur R, Rentsch CT, Morton CE, Hulme WJ, Schultze A, MacKenna B, Eggo RM, Wong AY, Williamson EJ, Forbes H, Wing K, McDonald HI, Bates C, Bacon S, Walker AJ, Evans D, Inglesby P, Mehrkar A, Curtis HJ, DeVito NJ, Croker R, Drysdale H, Cockburn J, Parry J, Hester F, Harper S, Douglas IJ, Tomlinson L, Evans SJ, Grieve R, Smeeth L, Goldacre B.",,No Journal Info,2021,2021-02-03,Y,,,,"<h4>Summary</h4> Black and minority ethnic groups were at raised risk of dying from COVID-19 during the first few months of the COVID-19 epidemic in England. We aimed to investigate whether ethnic inequalities in COVID-19 deaths were similar in the more recent “second wave” of the epidemic. Working on behalf of NHS England, we used primary care and linked ONS mortality data within the OpenSAFELY platform. All adults in the database at 1st September 2020 and with at least 1 year of prior follow-up and a record of ethnicity were included. The outcome was COVID-19-related death (death with COVID-19 listed as a cause of death on the death certificate). Follow-up was to 9th November 2020. Hazard ratios for ethnicity were calculated using Cox regression models adjusted for age and sex, and then further adjusted for deprivation. 13,223,154 people were included. During the study period, people of South Asian ethnicity were at higher risk of death due to COVID-19 than white people after adjusting for age and sex (HR = 3.47, 95% CI 2.99-4.03); the association attenuated somewhat on further adjustment for index of multiple deprivation (HR = 2.86, 2.46-3.33, Table 2). In contrast with the first wave of the epidemic, we found little evidence of a raised risk in black or other ethnic groups compared to white (HR for black vs white = 1.28, 0.87-1.88 adjusted for age and sex; and 1.01, 0.69-1.49 further adjusted for deprivation). Our findings suggest that ethnic inequalities in the risk of dying COVID-19-related death have changed between the first and early second wave of the epidemic in England.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2021/02/03/2021.02.02.21250989.full.pdf; doi:https://doi.org/10.1101/2021.02.02.21250989; html:https://europepmc.org/article/PPR/PPR277488; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR277488&type=FILE&fileName=EMS115851-pdf.pdf&mimeType=application/pdf
 PPR164426,https://doi.org/10.1101/2020.05.14.20101626,A semi-supervised approach for rapidly creating clinical biomarker phenotypes in the UK Biobank using different primary care EHR and clinical terminology systems,"Denaxas S, Shah AD, Mateen BA, Kuan V, Quint JK, Fitzpatrick N, Torralbo A, Fatemifar G, Hemingway H.",,No Journal Info,2020,2020-05-19,Y,,,,"<h4>Objectives</h4> The UK Biobank (UKB) is making primary care Electronic Health Records (EHR) for 500,000 participants available for COVID-19-related research. Data are extracted from four sources, recorded using five clinical terminologies and stored in different schemas. The aims of our research were to: a) develop a semi-supervised approach for bootstrapping EHR phenotyping algorithms in UKB EHR, and b) to evaluate our approach by implementing and evaluating phenotypes for 31 common biomarkers. <h4>Materials and Methods</h4> We describe an algorithmic approach to phenotyping biomarkers in primary care EHR involving a) bootstrapping definitions using existing phenotypes, b) excluding generic, rare or semantically distant terms, c) forward-mapping terminology terms, d) expert review, and e) data extraction. We evaluated the phenotypes by assessing the ability to reproduce known epidemiological associations with all-cause mortality using Cox proportional hazards models. <h4>Results</h4> We created and evaluated phenotyping algorithms for 31 biomarkers many of which are directly related to COVID–19 complications e.g. diabetes, cardiovascular disease, respiratory disease. Our algorithm identified 1651 Read v2 and Clinical Terms Version 3 terms and automatically excluded 1228 terms. Clinical review excluded 103 terms and included 44 terms, resulting in 364 terms for data extraction (sensitivity 0.89, specificity 0.92). We extracted 38,190,682 events and identified 220,978 participants with at least one biomarker measured. <h4>Discussion and conclusion</h4> Bootstrapping phenotyping algorithms from similar EHR can potentially address pre-existing methodological concerns that undermine the outputs of biomarker discovery pipelines and provide research-quality phenotyping algorithms.",,pdf:https://academic.oup.com/jamiaopen/article-pdf/3/4/545/36625793/ooaa047.pdf; doi:https://doi.org/10.1101/2020.05.14.20101626; html:https://europepmc.org/article/PPR/PPR164426; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR164426&type=FILE&fileName=EMS92414-pdf.pdf&mimeType=application/pdf
 PPR367589,https://doi.org/10.1101/2021.07.07.21253295,Mortality among Care Home Residents in England during the first and second waves of the COVID-19 pandemic: an analysis of 4.3 million adults over the age of 65,"Schultze A, Nightingale E, Evans D, Hulme W, Rosello A, Bates C, Cockburn J, MacKenna B, Curtis HJ, Morton CE, Croker R, Bacon S, McDonald HI, Rentsch CT, Bhaskaran K, Mathur R, Tomlinson LA, Williamson EJ, Forbes H, Tazare J, Grint D, Walker AJ, Inglesby P, DeVito NJ, Mehrkar A, Hickman G, Davy S, Ward T, Fisher L, Green AC, Wing K, Wong AY, McManus R, Parry J, Hester F, Harper S, Evans SJ, Douglas IJ, Smeeth L, Eggo RM, Goldacre B, Leon DA.",,No Journal Info,2021,2021-07-08,Y,,,,"<h4>Background</h4> Residents in care homes have been severely impacted by the COVID-19 pandemic. We describe trends in risk of mortality among care home residents compared to residents in private homes in England. <h4>Methods</h4> On behalf of NHS England, we used OpenSAFELY-TPP, an analytics platform running across the linked electronic health records of approximately a third of the English population, to calculate monthly age-standardised risks of death due to all causes and COVID-19 among adults aged >=65 years between 1/2/2019 and 31/03/2021. Care home residents were identified using linkage to the Care and Quality Commission. <h4>Findings</h4> We included 4,329,078 people aged 65 years or older on the 1st of February 2019, 2.2% of whom were classified as residing in a care or nursing home. Age-standardised mortality risks were approximately 10 times higher among care home residents compared to non-residents in February 2019 residents (CMF = 10.59, 95%CI = 9.51, 11.81 among women, CMF = 10.82, 95%CI = 9.89, 11.84 among men). This increased to more than 17 times in April 2020 (CMF = 17.52, 95%CI = 16.38, 18.74 among women, CMF = 18.12, 95%CI = 17.17 – 19.12 among men) before returning to pre-pandemic levels in June 2020. CMFs did not increase during the second wave, despite a rise in the absolute age-standardised COVID-19 mortality risks. <h4>Interpretation</h4> The first COVID-19 wave had a disproportionate impact on care home residents in England compared to older private home residents. A degree of immunity, improved protective measures or changes in the underlying frailty of the populations may explain the lack of an increase in the relative mortality risks during the second wave. The care home population should be prioritised for measures aimed at controlling the spread of COVID-19. <h4>Funding</h4> Medical Research Council MR/V015737/1",,doi:https://doi.org/10.1016/j.lanepe.2021.100295; doi:https://doi.org/10.1101/2021.07.07.21253295; html:https://europepmc.org/article/PPR/PPR367589; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR367589&type=FILE&fileName=EMS130305-pdf.pdf&mimeType=application/pdf
 PPR276352,https://doi.org/10.1101/2021.01.30.21250083,Increasing but inadequate intention to receive Covid-19 vaccination over the first 50 days of impact of the more infectious variant and roll-out of vaccination in UK: indicators for public health messaging,"Bachtiger P, Adamson A, Maclean WA, Quint JK, Peters NS.",,No Journal Info,2021,2021-02-01,Y,,,,"<h4>ABSTRACT</h4> <h4>Objectives</h4> To inform critical public health messaging by determining how changes in Covid-19 vaccine hesitancy, attitudes to the priorities for administration, the emergence of new variants and availability of vaccines may affect the trajectory and achievement of herd immunity. <h4>Methods</h4> >9,000 respondents in an ongoing cross-sectional participatory longitudinal epidemiology study (LoC-19, n=18,581) completed a questionnaire within their personal electronic health record in the week reporting first effective Covid-19 vaccines, and then again after widespread publicity of the increased transmissibility of a new variant (November 13th and December 31st 2020 respectively). Questions covered willingness to receive Covid-19 vaccination and attitudes to prioritisation. Descriptive statistics, unadjusted and adjusted odds ratios (ORs) and natural language processing of free-text responses are reported, and how changes over the first 50 days of both vaccination roll-out and new-variant impact modelling of anticipated transmission rates and the likelihood and time to herd immunity. <h4>Findings</h4> Compared with the week reporting the first efficacious vaccine there was a 15% increase in acceptance of Covid-19 vaccination, attributable in one third to the impact of the new variant, with 75% of respondents “shielding” – staying at home and not leaving unless essential – regardless of health status or tier rules. 12.5% of respondents plan to change their behaviour two weeks after completing vaccination compared with 45% intending to do so only when cases have reduced to a low level. Despite the increase from 71% to 86% over this critical 50-day period, modelling of planned uptake of vaccination remains below that required for rapid effective herd immunity – now estimated to be 90 percent in the presence of a new variant escalating R 0 to levels requiring further lockdowns. To inform the public messaging essential therefore to improve uptake, age and female gender were, respectively, strongly positively and negatively associated with wanting a vaccine. 22.7% disagreed with the prioritisation list, though 70.3% were against being able to expedite vaccination through payment. Teachers (988, 12.6%) and Black, Asian and Minority Ethnic (BAME) (837, 10.7%) groups were most cited by respondents for prioritisation. <h4>Interpretation</h4> In this sample, the growing impact of personal choice among the increasingly informed public highlights a decrease in Covid-19 vaccine hesitancy over time, with news of a new variant motivating increased willingness for vaccination but at levels below what may be required for effective herd immunity. We identify public preferences for next-in-line priorities, headed by teachers and BAME groups, consideration of which will help build trust and community engagement critical for maximising compliance with not only the vaccination programme but also all other public health measures.",,pdf:https://www.medrxiv.org/content/medrxiv/early/2021/02/01/2021.01.30.21250083.full.pdf; doi:https://doi.org/10.1101/2021.01.30.21250083; html:https://europepmc.org/article/PPR/PPR276352; pdf:https://europepmc.org/api/fulltextRepo?pprId=PPR276352&type=FILE&fileName=EMS115671-pdf.pdf&mimeType=application/pdf
diff --git a/data/covid/papers.csv b/data/covid/papers.csv
index b622147b..2eaeed31 100644
--- a/data/covid/papers.csv
+++ b/data/covid/papers.csv
@@ -7,8 +7,8 @@ id,doi,title,authorString,authorAffiliations,journalTitle,pubYear,date,isOpenAcc
 39011273,https://doi.org/10.34133/hds.0159,The Time-Varying Impact of COVID-19 on the Acute Kidney Disorders: A Historical Matched Cohort Study and Mendelian Randomization Analysis.,"Li C, Zhang C, Chen J, Chen Y, Ying Z, Hu Y, Song H, Fu P, Zeng X.",,Health data science,2024,2024-07-15,Y,,,,"<b>Background:</b> This study aimed to explore the time-varying impact of COVID-19 on acute kidney disorders, including acute kidney injury and other acute kidney diseases. <b>Methods:</b> From the UK Biobank, 10,121 participants with COVID-19 were matched with up to 3 historically unexposed controls by age, sex, Townsend deprivation index, and the status of hospitalization or receiving critical care. We investigated the association between COVID-19 and incidence of acute kidney disorders, within the first 4 weeks after infection, using conditional and time-varying Cox proportional hazard regression. In addition, one-sample Mendelian randomization, utilizing the polygenic risk score for COVID-19 as an instrumental variable, was conducted to explore the potential causality of the association. <b>Results:</b> In the matched cohort study, we observed a significant association between COVID-19 and acute kidney disorders predominantly within the first 3 weeks. The impact of COVID-19 was time dependent, peaking in the second week (hazard ratio, 12.77; 95% confidence interval, 5.93 to 27.70) and decreasing by the fourth week (hazard ratio, 2.28; 95% confidence interval, 0.75 to 6.93). In subgroup analyses, only moderate to severe COVID-19 cases were associated with acute worsening of renal function in a time-dependent pattern. One-sample Mendelian randomization analyses further showed that COVID-19 might exert a ""short-term"" causal effect on the risk of acute kidney disorders, primarily confined to the first week after infection. <b>Conclusions:</b> The risk of acute kidney disorders following COVID-19 demonstrates a time-varying pattern. Hazard effects were observed only in patients with moderate or severe but not mild COVID-19.",,doi:https://doi.org/10.34133/hds.0159; doi:https://doi.org/10.34133/hds.0159; html:https://europepmc.org/articles/PMC11246837; pdf:https://europepmc.org/articles/PMC11246837?pdf=render
 37875536,https://doi.org/10.1038/s41467-023-41879-2,"Long-term health impacts of COVID-19 among 242,712 adults in England.","Atchison CJ, Davies B, Cooper E, Lound A, Whitaker M, Hampshire A, Azor A, Donnelly CA, Chadeau-Hyam M, Cooke GS, Ward H, Elliott P.",,Nature communications,2023,2023-10-24,Y,,,,"The COVID-19 pandemic is having a lasting impact on health and well-being. We compare current self-reported health, quality of life and symptom profiles for people with ongoing symptoms following COVID-19 to those who have never tested positive for SARS-CoV-2 infection and those who have recovered from COVID-19. Overall, 276,840/800,000 (34·6%) of invited participants took part. Mental health and health-related quality of life were worse among participants with ongoing persistent symptoms post-COVID compared with those who had never had COVID-19 or had recovered. In this study, median duration of COVID-related symptoms (N = 130,251) was 1·3 weeks (inter-quartile range 6 days to 2 weeks), with 7·5% and 5·2% reporting ongoing symptoms ≥12 weeks and ≥52 weeks respectively. Female sex, ≥1 comorbidity and being infected when Wild-type variant was dominant were associated with higher probability of symptoms lasting ≥12 weeks and longer recovery time in those with persistent symptoms. Although COVID-19 is usually of short duration, some adults experience persistent and burdensome illness.",,pdf:https://www.nature.com/articles/s41467-023-41879-2.pdf; doi:https://doi.org/10.1038/s41467-023-41879-2; html:https://europepmc.org/articles/PMC10598213; pdf:https://europepmc.org/articles/PMC10598213?pdf=render
 38345538,https://doi.org/10.1177/01410768231223584,Risk of winter hospitalisation and death from acute respiratory infections in Scotland: national retrospective cohort study.,"Shi T, Millington T, Robertson C, Jeffrey K, Katikireddi SV, McCowan C, Simpson CR, Woolford L, Daines L, Kerr S, Swallow B, Fagbamigbe A, Vallejos CA, Weatherill D, Jayacodi S, Marsh K, McMenamin J, Rudan I, Ritchie LD, Mueller T, Kurdi A, Sheikh A, Public Health Scotland and the EAVE II Collaborators.",,Journal of the Royal Society of Medicine,2024,2024-02-12,N,epidemiology; Respiratory Medicine; Health Informatics,,,"<h4>Objectives</h4>We undertook a national analysis to characterise and identify risk factors for acute respiratory infections (ARIs) resulting in hospitalisation during the winter period in Scotland.<h4>Design</h4>A population-based retrospective cohort analysis.<h4>Setting</h4>Scotland.<h4>Participants</h4>The study involved 5.4 million residents in Scotland.<h4>Main outcome measures</h4>Cox proportional hazard models were used to estimate adjusted hazard ratios (aHRs) and 95% confidence intervals (CIs) for the association between risk factors and ARI hospitalisation.<h4>Results</h4>Between 1 September 2022 and 31 January 2023, there were 22,284 (10.9% of 203,549 with any emergency hospitalisation) ARI hospitalisations (1759 in children and 20,525 in adults) in Scotland. Compared with the reference group of children aged 6-17 years, the risk of ARI hospitalisation was higher in children aged 3-5 years (aHR = 4.55; 95% CI: 4.11-5.04). Compared with those aged 25-29 years, the risk of ARI hospitalisation was highest among the oldest adults aged ≥80 years (aHR = 7.86; 95% CI: 7.06-8.76). Adults from more deprived areas (most deprived vs. least deprived, aHR = 1.64; 95% CI: 1.57-1.72), with existing health conditions (≥5 vs. 0 health conditions, aHR = 4.84; 95% CI: 4.53-5.18) or with history of all-cause emergency admissions (≥6 vs. 0 previous emergency admissions, aHR = 7.53; 95% CI: 5.48-10.35) were at a higher risk of ARI hospitalisations. The risk increased by the number of existing health conditions and previous emergency admission. Similar associations were seen in children.<h4>Conclusions</h4>Younger children, older adults, those from more deprived backgrounds and individuals with greater numbers of pre-existing conditions and previous emergency admission were at increased risk for winter hospitalisations for ARI.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/01410768231223584; doi:https://doi.org/10.1177/01410768231223584; html:https://europepmc.org/articles/PMC11450722; pdf:https://europepmc.org/articles/PMC11450722?pdf=render; doi:https://doi.org/10.1177/01410768231223584
-37880687,https://doi.org/10.1186/s12889-023-16993-x,Understanding covid-19 outcomes among people with intellectual disabilities in England.,"Sosenko F, Mackay D, Pell JP, Hatton C, Jani BD, Cairns D, Ward L, Henderson A, Fleming M, Nijhof D, Melville C, CVD-COVID-UK/COVID-IMPACT Consortium.",,BMC public health,2023,2023-10-25,Y,Learning Disabilities; Intellectual Disabilities; Covid-19,,,"<h4>Background</h4>Evidence from the UK from the early stages of the covid-19 pandemic showed that people with Intellectual Disabilities (ID) had higher rates of covid-19 mortality than people without ID. However, estimates of the magnitude of risk vary widely; different studies used different time periods; and only early stages of the pandemic have been analysed. Existing analyses of risk factors have also been limited. The objective of this study was to investigate covid-19 mortality rates, hospitalisation rates, and risk factors in people with ID in England up to the end of 2021.<h4>Methods</h4>Retrospective cohort study of all people with a laboratory-confirmed SARS-CoV-2 infection or death involving covid-19. Datasets covering primary care, secondary care, covid-19 tests and vaccinations, prescriptions, and deaths were linked at individual level.<h4>Results</h4>Covid-19 carries a disproportionately higher risk of death for people with ID, above their already higher risk of dying from other causes, in comparison to those without ID. Around 2,000 people with ID had a death involving covid-19 in England up to the end of 2021; approximately 1 in 180. The covid-19 standardized mortality ratio was 5.6 [95% CI 5.4, 5.9]. People with ID were also more likely to be hospitalised for covid-19 than people without ID. The main determinants of severe covid-19 outcomes (deaths and/or hospitalisations) in both populations were age, multimorbidity and vaccination status. The key factor responsible for the higher risk of severe covid-19 in the ID population was a much higher prevalence of multimorbidity in this population. AstraZeneca vaccine was slightly less effective in preventing severe covid-19 outcomes among people with ID than among people without ID.<h4>Conclusions</h4>People with ID should be considered a priority group in future pandemics, such as shielding and vaccinations.",,pdf:https://bmcpublichealth.biomedcentral.com/counter/pdf/10.1186/s12889-023-16993-x; doi:https://doi.org/10.1186/s12889-023-16993-x; html:https://europepmc.org/articles/PMC10601171; pdf:https://europepmc.org/articles/PMC10601171?pdf=render
 37921538,https://doi.org/10.1177/01410768231205430,Adverse events after first and second doses of COVID-19 vaccination in England: a national vaccine surveillance platform self-controlled case series study.,"Tsang RS, Agrawal U, Joy M, Byford R, Robertson C, Anand SN, Hinton W, Mayor N, Kar D, Williams J, Victor W, Akbari A, Bradley DT, Murphy S, O'Reilly D, Owen RK, Chuter A, Beggs J, Howsam G, Sheikh A, Richard Hobbs FD, Lusignan S.",,Journal of the Royal Society of Medicine,2024,2023-11-03,Y,epidemiology; Public Health; Vaccination Programmes,,,"<h4>Objectives</h4>To estimate the incidence of adverse events of interest (AEIs) after receiving their first and second doses of coronavirus disease 2019 (COVID-19) vaccinations, and to report the safety profile differences between the different COVID-19 vaccines.<h4>Design</h4>We used a self-controlled case series design to estimate the relative incidence (RI) of AEIs reported to the Oxford-Royal College of General Practitioners national sentinel network. We compared the AEIs that occurred seven days before and after receiving the COVID-19 vaccinations to background levels between 1 October 2020 and 12 September 2021.<h4>Setting</h4>England, UK.<h4>Participants</h4>Individuals experiencing AEIs after receiving first and second doses of COVID-19 vaccines.<h4>Main outcome measures</h4>AEIs determined based on events reported in clinical trials and in primary care during post-license surveillance.<h4>Results</h4>A total of 7,952,861 individuals were vaccinated with COVID-19 vaccines within the study period. Among them, 781,200 individuals (9.82%) presented to general practice with 1,482,273 AEIs. Within the first seven days post-vaccination, 4.85% of all the AEIs were reported. There was a 3-7% decrease in the overall RI of AEIs in the seven days after receiving both doses of Pfizer-BioNTech BNT162b2 (RI = 0.93; 95% CI: 0.91-0.94) and 0.96; 95% CI: 0.94-0.98), respectively) and Oxford-AstraZeneca ChAdOx1 (RI = 0.97; 95% CI: 0.95-0.98) for both doses), but a 20% increase after receiving the first dose of Moderna mRNA-1273 (RI = 1.20; 95% CI: 1.00-1.44)).<h4>Conclusions</h4>COVID-19 vaccines are associated with a small decrease in the incidence of medically attended AEIs. Sentinel networks could routinely report common AEI rates, which could contribute to reporting vaccine safety.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/01410768231205430; doi:https://doi.org/10.1177/01410768231205430; html:https://europepmc.org/articles/PMC11100448; pdf:https://europepmc.org/articles/PMC11100448?pdf=render
+37880687,https://doi.org/10.1186/s12889-023-16993-x,Understanding covid-19 outcomes among people with intellectual disabilities in England.,"Sosenko F, Mackay D, Pell JP, Hatton C, Jani BD, Cairns D, Ward L, Henderson A, Fleming M, Nijhof D, Melville C, CVD-COVID-UK/COVID-IMPACT Consortium.",,BMC public health,2023,2023-10-25,Y,Learning Disabilities; Intellectual Disabilities; Covid-19,,,"<h4>Background</h4>Evidence from the UK from the early stages of the covid-19 pandemic showed that people with Intellectual Disabilities (ID) had higher rates of covid-19 mortality than people without ID. However, estimates of the magnitude of risk vary widely; different studies used different time periods; and only early stages of the pandemic have been analysed. Existing analyses of risk factors have also been limited. The objective of this study was to investigate covid-19 mortality rates, hospitalisation rates, and risk factors in people with ID in England up to the end of 2021.<h4>Methods</h4>Retrospective cohort study of all people with a laboratory-confirmed SARS-CoV-2 infection or death involving covid-19. Datasets covering primary care, secondary care, covid-19 tests and vaccinations, prescriptions, and deaths were linked at individual level.<h4>Results</h4>Covid-19 carries a disproportionately higher risk of death for people with ID, above their already higher risk of dying from other causes, in comparison to those without ID. Around 2,000 people with ID had a death involving covid-19 in England up to the end of 2021; approximately 1 in 180. The covid-19 standardized mortality ratio was 5.6 [95% CI 5.4, 5.9]. People with ID were also more likely to be hospitalised for covid-19 than people without ID. The main determinants of severe covid-19 outcomes (deaths and/or hospitalisations) in both populations were age, multimorbidity and vaccination status. The key factor responsible for the higher risk of severe covid-19 in the ID population was a much higher prevalence of multimorbidity in this population. AstraZeneca vaccine was slightly less effective in preventing severe covid-19 outcomes among people with ID than among people without ID.<h4>Conclusions</h4>People with ID should be considered a priority group in future pandemics, such as shielding and vaccinations.",,pdf:https://bmcpublichealth.biomedcentral.com/counter/pdf/10.1186/s12889-023-16993-x; doi:https://doi.org/10.1186/s12889-023-16993-x; html:https://europepmc.org/articles/PMC10601171; pdf:https://europepmc.org/articles/PMC10601171?pdf=render
 38818129,https://doi.org/10.12688/wellcomeopenres.20750.1,Anti-nucleocapsid antibody levels following initial and repeat SARS-CoV-2 infections in a cohort of long-term care facility residents in England (VIVALDI).,"Stirrup O, Tut G, Krutikov M, Bone D, Lancaster T, Azmi B, Monakhov I, Moss P, Hayward A, Copas A, Shallcross L.",,Wellcome open research,2024,2024-02-19,Y,Immunoglobulin G; Nucleocapsid; Covid-19; Sars-cov-2; Omicron,,,"<h4>Background</h4>We have previously demonstrated that older residents of long-term care facilities (LTCF) in the UK show levels of anti-spike antibodies that are comparable to the general population following primary series and booster vaccination for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, data on the humoral response to other SARS-CoV-2 proteins associated with natural infection are scarce in this vulnerable population.<h4>Methods</h4>We measured quantitative levels of anti-nucleocapsid antibodies in blood samples taken from LTCF residents and staff after initial and repeat SARS-CoV-2 infections, between December 2020 and March 2023. Data on SARS-CoV-2 infection and vaccination were obtained through linkage to national datasets. Linear mixed effects models were used to investigate anti-nucleocapsid antibody levels, using log10 scale, in relation to time from most recent infection. This included evaluation of associations between repeat infection, staff/resident status, age, sex, Omicron infection and vaccination history and peak antibody level and slope of decline with time.<h4>Results</h4>We analysed 405 antibody observations from 220 residents and 396 observations from 215 staff. Repeat infection was associated with 8.5-fold (95%CI 4.9-14.8-fold) higher initial (peak) median anti-nucleocapsid antibody level, with steeper subsequent slope of decline. There were no significant differences in antibody level associated with resident (vs. staff) status or age, but Omicron infection was associated with 3.6-fold (95%CI 2.4-5.4-fold) higher levels. There was stronger evidence of waning of antibody levels over time in a sensitivity analysis in which observations were censored in cases with suspected undetected repeat infection.<h4>Conclusions</h4>We found similar levels of anti-nucleocapsid antibody in residents and staff of LTCFs. Repeat infection and infection with an Omicron strain were associated with higher peak values. There was evidence of waning of anti-nucleocapsid antibody levels over time.",,doi:https://doi.org/10.12688/wellcomeopenres.20750.1; html:https://europepmc.org/articles/PMC11137476; pdf:https://europepmc.org/articles/PMC11137476?pdf=render
 37169862,https://doi.org/10.1038/s41591-023-02343-2,Accelerated waning of the humoral response to COVID-19 vaccines in obesity.,"van der Klaauw AA, Horner EC, Pereyra-Gerber P, Agrawal U, Foster WS, Spencer S, Vergese B, Smith M, Henning E, Ramsay ID, Smith JA, Guillaume SM, Sharpe HJ, Hay IM, Thompson S, Innocentin S, Booth LH, Robertson C, McCowan C, Kerr S, Mulroney TE, O'Reilly MJ, Gurugama TP, Gurugama LP, Rust MA, Ferreira A, Ebrahimi S, Ceron-Gutierrez L, Scotucci J, Kronsteiner B, Dunachie SJ, Klenerman P, PITCH Consortium, Park AJ, Rubino F, Lamikanra AA, Stark H, Kingston N, Estcourt L, Harvala H, Roberts DJ, Doffinger R, Linterman MA, Matheson NJ, Sheikh A, Farooqi IS, Thaventhiran JED.",,Nature medicine,2023,2023-05-11,Y,,,,"Obesity is associated with an increased risk of severe Coronavirus Disease 2019 (COVID-19) infection and mortality. COVID-19 vaccines reduce the risk of serious COVID-19 outcomes; however, their effectiveness in people with obesity is incompletely understood. We studied the relationship among body mass index (BMI), hospitalization and mortality due to COVID-19 among 3.6 million people in Scotland using the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) surveillance platform. We found that vaccinated individuals with severe obesity (BMI > 40 kg/m<sup>2</sup>) were 76% more likely to experience hospitalization or death from COVID-19 (adjusted rate ratio of 1.76 (95% confidence interval (CI), 1.60-1.94). We also conducted a prospective longitudinal study of a cohort of 28 individuals with severe obesity compared to 41 control individuals with normal BMI (BMI 18.5-24.9 kg/m<sup>2</sup>). We found that 55% of individuals with severe obesity had unquantifiable titers of neutralizing antibody against authentic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus compared to 12% of individuals with normal BMI (P = 0.0003) 6 months after their second vaccine dose. Furthermore, we observed that, for individuals with severe obesity, at any given anti-spike and anti-receptor-binding domain (RBD) antibody level, neutralizing capacity was lower than that of individuals with a normal BMI. Neutralizing capacity was restored by a third dose of vaccine but again declined more rapidly in people with severe obesity. We demonstrate that waning of COVID-19 vaccine-induced humoral immunity is accelerated in individuals with severe obesity. As obesity is associated with increased hospitalization and mortality from breakthrough infections, our findings have implications for vaccine prioritization policies.",,pdf:https://www.nature.com/articles/s41591-023-02343-2.pdf; doi:https://doi.org/10.1038/s41591-023-02343-2; html:https://europepmc.org/articles/PMC10202802; pdf:https://europepmc.org/articles/PMC10202802?pdf=render
 38912714,https://doi.org/10.1097/ede.0000000000001747,Effectiveness of mRNA COVID-19 Vaccines as First Booster Doses in England: An Observational Study in OpenSAFELY-TPP.,"Horne EMF, Hulme WJ, Parker EPK, Keogh RH, Williamson EJ, Williamson EJ, Walker VM, Palmer TM, Denholm R, Knight R, Curtis HJ, Walker AJ, Andrews CD, Mehrkar A, Morley J, MacKenna B, Bacon SCJ, Goldacre B, Hernán MA, Sterne JAC, and the OpenSAFELY collaborative.",,"Epidemiology (Cambridge, Mass.)",2024,2024-06-24,Y,,,,"<h4>Background</h4>The UK delivered its first ""booster"" COVID-19 vaccine doses in September 2021, initially to individuals at high risk of severe disease, then to all adults. The BNT162b2 Pfizer-BioNTech vaccine was used initially, then also Moderna mRNA-1273.<h4>Methods</h4>With the approval of the National Health Service England, we used routine clinical data to estimate the effectiveness of boosting with BNT162b2 or mRNA-1273 compared with no boosting in eligible adults who had received two primary course vaccine doses. We matched each booster recipient with an unboosted control on factors relating to booster priority status and prior COVID-19 immunization. We adjusted for additional factors in Cox models, estimating hazard ratios up to 182 days (6 months) following booster dose. We estimated hazard ratios overall and within the following periods: 1-14, 15-42, 43-69, 70-97, 98-126, 127-152, and 155-182 days. Outcomes included a positive SARS-CoV-2 test, COVID-19 hospitalization, COVID-19 death, non-COVID-19 death, and fracture.<h4>Results</h4>We matched 8,198,643 booster recipients with unboosted controls. Adjusted hazard ratios over 6-month follow-up were: positive SARS-CoV-2 test 0.75 (0.74, 0.75); COVID-19 hospitalization 0.30 (0.29, 0.31); COVID-19 death 0.11 (0.10, 0.14); non-COVID-19 death 0.22 (0.21, 0.23); and fracture 0.77 (0.75, 0.78). Estimated effectiveness of booster vaccines against severe COVID-19-related outcomes peaked during the first 3 months following the booster dose. By 6 months, the cumulative incidence of positive SARS-CoV-2 test was higher in boosted than unboosted individuals.<h4>Conclusions</h4>We estimate that COVID-19 booster vaccination, compared with no booster vaccination, provided substantial protection against COVID-19 hospitalization and COVID-19 death but only limited protection against positive SARS-CoV-2 test. Lower rates of fracture in boosted than unboosted individuals may suggest unmeasured confounding. Observational studies should report estimated vaccine effectiveness against nontarget and negative control outcomes.",,html:https://journals.lww.com/epidem/fulltext/2024/07000/effectiveness_of_mrna_covid_19_vaccines_as_first.18.aspx; doi:https://doi.org/10.1097/EDE.0000000000001747; html:https://europepmc.org/articles/PMC11191555; pdf:https://europepmc.org/articles/PMC11191555?pdf=render
@@ -29,15 +29,15 @@ PMC11201135,https://doi.org/,Exploring Prior Antibiotic Exposure Characteristics
 38053867,https://doi.org/10.1016/j.heliyon.2023.e21734,Wastewater-based surveillance models for COVID-19: A focused review on spatio-temporal models.,"Torabi F, Li G, Mole C, Nicholson G, Rowlingson B, Smith CR, Jersakova R, Diggle PJ, Blangiardo M.",,Heliyon,2023,2023-11-08,Y,Wastewater-based Epidemiology; Covid-19; Wastewater-Based Surveillance; Spatio-Temporal Statistical Modelling,,,"The evident shedding of the SARS-CoV-2 RNA particles from infected individuals into the wastewater opened up a tantalizing array of possibilities for prediction of COVID-19 prevalence prior to symptomatic case identification through community testing. Many countries have therefore explored the use of wastewater metrics as a surveillance tool, replacing traditional direct measurement of prevalence with cost-effective approaches based on SARS-CoV-2 RNA concentrations in wastewater samples. Two important aspects in building prediction models are: time over which the prediction occurs and space for which the predicted case numbers is shown. In this review, our main focus was on finding mathematical models which take into the account both the time-varying and spatial nature of wastewater-based metrics into account. We used six main characteristics as our assessment criteria: i) modelling approach; ii) temporal coverage; iii) spatial coverage; iv) sample size; v) wastewater sampling method; and vi) covariates included in the modelling. The majority of studies in the early phases of the pandemic recognized the temporal association of SARS-CoV-2 RNA concentration level in wastewater with the number of COVID-19 cases, ignoring their spatial context. We examined 15 studies up to April 2023, focusing on models considering both temporal and spatial aspects of wastewater metrics. Most early studies correlated temporal SARS-CoV-2 RNA levels with COVID-19 cases but overlooked spatial factors. Linear regression and SEIR models were commonly used (n = 10, 66.6 % of studies), along with machine learning (n = 1, 6.6 %) and Bayesian approaches (n = 1, 6.6 %) in some cases. Three studies employed spatio-temporal modelling approach (n = 3, 20.0 %). We conclude that the development, validation and calibration of further spatio-temporally explicit models should be done in parallel with the advancement of wastewater metrics before the potential of wastewater as a surveillance tool can be fully realised.",,doi:https://doi.org/10.1016/j.heliyon.2023.e21734; html:https://europepmc.org/articles/PMC10694161; pdf:https://europepmc.org/articles/PMC10694161?pdf=render
 36180455,https://doi.org/10.1038/s41598-022-20118-6,"Risk of thrombocytopenic, haemorrhagic and thromboembolic disorders following COVID-19 vaccination and positive test: a self-controlled case series analysis in Wales.","Torabi F, Bedston S, Lowthian E, Akbari A, Owen RK, Bradley DT, Agrawal U, Collins P, Fry R, Griffiths LJ, Beggs J, Davies G, Hollinghurst J, Lyons J, Abbasizanjani H, Cottrell S, Perry M, Roberts R, Azcoaga-Lorenzo A, Fagbamigbe AF, Shi T, Tsang RSM, Robertson C, Hobbs FDR, de Lusignan S, McCowan C, Gravenor M, Simpson CR, Sheikh A, Lyons RA.",,Scientific reports,2022,2022-09-30,Y,,,,"There is a need for better understanding of the risk of thrombocytopenic, haemorrhagic, thromboembolic disorders following first, second and booster vaccination doses and testing positive for SARS-CoV-2. Self-controlled cases series analysis of 2.1 million linked patient records in Wales between 7th December 2020 and 31st December 2021. Outcomes were the first diagnosis of thrombocytopenic, haemorrhagic and thromboembolic events in primary or secondary care datasets, exposure was defined as 0-28 days post-vaccination or a positive reverse transcription polymerase chain reaction test for SARS-CoV-2. 36,136 individuals experienced either a thrombocytopenic, haemorrhagic or thromboembolic event during the study period. Relative to baseline, our observations show greater risk of outcomes in the periods post-first dose of BNT162b2 for haemorrhagic (IRR 1.47, 95%CI: 1.04-2.08) and idiopathic thrombocytopenic purpura (IRR 2.80, 95%CI: 1.21-6.49) events; post-second dose of ChAdOx1 for arterial thrombosis (IRR 1.14, 95%CI: 1.01-1.29); post-booster greater risk of venous thromboembolic (VTE) (IRR-Moderna 3.62, 95%CI: 0.99-13.17) (IRR-BNT162b2 1.39, 95%CI: 1.04-1.87) and arterial thrombosis (IRR-Moderna 3.14, 95%CI: 1.14-8.64) (IRR-BNT162b2 1.34, 95%CI: 1.15-1.58). Similarly, post SARS-CoV-2 infection the risk was increased for haemorrhagic (IRR 1.49, 95%CI: 1.15-1.92), VTE (IRR 5.63, 95%CI: 4.91, 6.4), arterial thrombosis (IRR 2.46, 95%CI: 2.22-2.71). We found that there was a measurable risk of thrombocytopenic, haemorrhagic, thromboembolic events after COVID-19 vaccination and infection.",,pdf:https://www.nature.com/articles/s41598-022-20118-6.pdf; doi:https://doi.org/10.1038/s41598-022-20118-6; html:https://europepmc.org/articles/PMC9524320; pdf:https://europepmc.org/articles/PMC9524320?pdf=render
 38467603,https://doi.org/10.1038/s41467-024-46497-0,Impact of vaccination on the association of COVID-19 with cardiovascular diseases: An OpenSAFELY cohort study.,"Cezard GI, Denholm RE, Knight R, Wei Y, Teece L, Toms R, Forbes HJ, Walker AJ, Fisher L, Massey J, Hopcroft LEM, Horne EMF, Taylor K, Palmer T, Arab MA, Cuitun Coronado JI, Ip SHY, Davy S, Dillingham I, Bacon S, Mehrkar A, Morton CE, Greaves F, Hyams C, Davey Smith G, Macleod J, Chaturvedi N, Goldacre B, Whiteley WN, Wood AM, Sterne JAC, Walker V, Longitudinal Health and Wellbeing and Data and Connectivity UK COVID-19 National Core Studies, CONVALESCENCE study and the OpenSAFELY collaborative.",,Nature communications,2024,2024-03-11,Y,,,,"Infection with SARS-CoV-2 is associated with an increased risk of arterial and venous thrombotic events, but the implications of vaccination for this increased risk are uncertain. With the approval of NHS England, we quantified associations between COVID-19 diagnosis and cardiovascular diseases in different vaccination and variant eras using linked electronic health records for ~40% of the English population. We defined a 'pre-vaccination' cohort (18,210,937 people) in the wild-type/Alpha variant eras (January 2020-June 2021), and 'vaccinated' and 'unvaccinated' cohorts (13,572,399 and 3,161,485 people respectively) in the Delta variant era (June-December 2021). We showed that the incidence of each arterial thrombotic, venous thrombotic and other cardiovascular outcomes was substantially elevated during weeks 1-4 after COVID-19, compared with before or without COVID-19, but less markedly elevated in time periods beyond week 4. Hazard ratios were higher after hospitalised than non-hospitalised COVID-19 and higher in the pre-vaccination and unvaccinated cohorts than the vaccinated cohort. COVID-19 vaccination reduces the risk of cardiovascular events after COVID-19 infection. People who had COVID-19 before or without being vaccinated are at higher risk of cardiovascular events for at least two years.",,pdf:https://www.nature.com/articles/s41467-024-46497-0.pdf; doi:https://doi.org/10.1038/s41467-024-46497-0; html:https://europepmc.org/articles/PMC10928172; pdf:https://europepmc.org/articles/PMC10928172?pdf=render
+37056776,https://doi.org/10.3389/fimmu.2023.1146702,"SARS-CoV-2 antibody responses associate with sex, age and disease severity in previously uninfected people admitted to hospital with COVID-19: An ISARIC4C prospective study.","Parker E, Thomas J, Roper KJ, Ijaz S, Edwards T, Marchesin F, Katsanovskaja K, Lett L, Jones C, Hardwick HE, Davis C, Vink E, McDonald SE, Moore SC, Dicks S, Jegatheesan K, Cook NJ, Hope J, Cherepanov P, McClure MO, Baillie JK, Openshaw PJM, Turtle L, Ho A, Semple MG, Paxton WA, Tedder RS, Pollakis G, ISARIC4C Investigators.",,Frontiers in immunology,2023,2023-03-15,Y,Serology; Virus; Disease; immunology; Neutralisation; Covid-19; Sars-cov-2,,,"The SARS-CoV-2 pandemic enables the analysis of immune responses induced against a novel coronavirus infecting immunologically naïve individuals. This provides an opportunity for analysis of immune responses and associations with age, sex and disease severity. Here we measured an array of solid-phase binding antibody and viral neutralising Ab (nAb) responses in participants (n=337) of the ISARIC4C cohort and characterised their correlation with peak disease severity during acute infection and early convalescence. Overall, the responses in a Double Antigen Binding Assay (DABA) for antibody to the receptor binding domain (anti-RBD) correlated well with IgM as well as IgG responses against viral spike, S1 and nucleocapsid protein (NP) antigens. DABA reactivity also correlated with nAb. As we and others reported previously, there is greater risk of severe disease and death in older men, whilst the sex ratio was found to be equal within each severity grouping in younger people. In older males with severe disease (mean age 68 years), peak antibody levels were found to be delayed by one to two weeks compared with women, and nAb responses were delayed further. Additionally, we demonstrated that solid-phase binding antibody responses reached higher levels in males as measured <i>via</i> DABA and IgM binding against Spike, NP and S1 antigens. In contrast, this was not observed for nAb responses. When measuring SARS-CoV-2 RNA transcripts (as a surrogate for viral shedding) in nasal swabs at recruitment, we saw no significant differences by sex or disease severity status. However, we have shown higher antibody levels associated with low nasal viral RNA indicating a role of antibody responses in controlling viral replication and shedding in the upper airway. In this study, we have shown discernible differences in the humoral immune responses between males and females and these differences associate with age as well as with resultant disease severity.",,pdf:https://www.frontiersin.org/articles/10.3389/fimmu.2023.1146702/pdf; doi:https://doi.org/10.3389/fimmu.2023.1146702; html:https://europepmc.org/articles/PMC10087108; pdf:https://europepmc.org/articles/PMC10087108?pdf=render
 38491011,https://doi.org/10.1038/s41467-024-46451-0,"Uptake of COVID-19 vaccinations amongst 3,433,483 children and young people: meta-analysis of UK prospective cohorts.","Aldridge SJ, Agrawal U, Murphy S, Millington T, Akbari A, Almaghrabi F, Anand SN, Bedston S, Goudie R, Griffiths R, Joy M, Lowthian E, de Lusignan S, Patterson L, Robertson C, Rudan I, Bradley DT, Lyons RA, Sheikh A, Owen RK.",,Nature communications,2024,2024-03-15,Y,,,,"SARS-CoV-2 infection in children and young people (CYP) can lead to life-threatening COVID-19, transmission within households and schools, and the development of long COVID. Using linked health and administrative data, we investigated vaccine uptake among 3,433,483 CYP aged 5-17 years across all UK nations between 4th August 2021 and 31st May 2022. We constructed national cohorts and undertook multi-state modelling and meta-analysis to identify associations between demographic variables and vaccine uptake. We found that uptake of the first COVID-19 vaccine among CYP was low across all four nations compared to other age groups and diminished with subsequent doses. Age and vaccination status of adults living in the same household were identified as important risk factors associated with vaccine uptake in CYP. For example, 5-11 year-olds were less likely to receive their first vaccine compared to 16-17 year-olds (adjusted Hazard Ratio [aHR]: 0.10 (95%CI: 0.06-0.19)), and CYP in unvaccinated households were less likely to receive their first vaccine compared to CYP in partially vaccinated households (aHR: 0.19, 95%CI 0.13-0.29).",,doi:https://doi.org/10.1038/s41467-024-46451-0; html:https://europepmc.org/articles/PMC10943015; pdf:https://europepmc.org/articles/PMC10943015?pdf=render
 36669966,https://doi.org/10.1016/j.vaccine.2023.01.023,COVID-19 booster vaccination uptake and infection breakthrough amongst health care workers in Wales: A national prospective cohort study.,"Bedston S, Lowthian E, Jarvis CI, Akbari A, Beggs J, Bradley D, de Lusignan S, Griffiths R, Herbert L, Hobbs R, Kerr S, Lyons J, Midgley W, Owen RK, Quint JK, Tsang R, Torabi F, Sheikh A, Lyons RA.",,Vaccine,2023,2023-01-13,Y,Uptake; Vaccination; Health care workers; Booster; Breakthrough; Covid-19,,,"<h4>Background</h4>From September 2021, Health Care Workers (HCWs) in Wales began receiving a COVID-19 booster vaccination. This is the first dose beyond the primary vaccination schedule. Given the emergence of new variants, vaccine waning vaccine, and increasing vaccination hesitancy, there is a need to understand booster vaccine uptake and subsequent breakthrough in this high-risk population.<h4>Methods</h4>We conducted a prospective, national-scale, observational cohort study of HCWs in Wales using anonymised, linked data from the SAIL Databank. We analysed uptake of COVID-19 booster vaccinations from September 2021 to February 2022, with comparisons against uptake of the initial primary vaccination schedule. We also analysed booster breakthrough, in the form of PCR-confirmed SARS-Cov-2 infection, comparing to the second primary dose. Cox proportional hazard models were used to estimate associations for vaccination uptake and breakthrough regarding staff roles, socio-demographics, household composition, and other factors.<h4>Results</h4>We derived a cohort of 73,030 HCWs living in Wales (78% female, 60% 18-49 years old). Uptake was quickest amongst HCWs aged 60 + years old (aHR 2.54, 95%CI 2.45-2.63), compared with those aged 18-29. Asian HCWs had quicker uptake (aHR 1.18, 95%CI 1.14-1.22), whilst Black HCWs had slower uptake (aHR 0.67, 95%CI 0.61-0.74), compared to white HCWs. HCWs residing in the least deprived areas were slightly quicker to have received a booster dose (aHR 1.12, 95%CI 1.09-1.16), compared with those in the most deprived areas. Strongest associations with breakthrough infections were found for those living with children (aHR 1.52, 95%CI 1.41-1.63), compared to two-adult only households. HCWs aged 60 + years old were less likely to get breakthrough infections, compared to those aged 18-29 (aHR 0.42, 95%CI 0.38-0.47).<h4>Conclusion</h4>Vaccination uptake was consistently lower among black HCWs, as well as those from deprived areas. Whilst breakthrough infections were highest in households with children.",,doi:https://doi.org/10.1016/j.vaccine.2023.01.023; doi:https://doi.org/10.1016/j.vaccine.2023.01.023; html:https://europepmc.org/articles/PMC9837216; pdf:https://europepmc.org/articles/PMC9837216?pdf=render
-37056776,https://doi.org/10.3389/fimmu.2023.1146702,"SARS-CoV-2 antibody responses associate with sex, age and disease severity in previously uninfected people admitted to hospital with COVID-19: An ISARIC4C prospective study.","Parker E, Thomas J, Roper KJ, Ijaz S, Edwards T, Marchesin F, Katsanovskaja K, Lett L, Jones C, Hardwick HE, Davis C, Vink E, McDonald SE, Moore SC, Dicks S, Jegatheesan K, Cook NJ, Hope J, Cherepanov P, McClure MO, Baillie JK, Openshaw PJM, Turtle L, Ho A, Semple MG, Paxton WA, Tedder RS, Pollakis G, ISARIC4C Investigators.",,Frontiers in immunology,2023,2023-03-15,Y,Serology; Virus; Disease; immunology; Neutralisation; Covid-19; Sars-cov-2,,,"The SARS-CoV-2 pandemic enables the analysis of immune responses induced against a novel coronavirus infecting immunologically naïve individuals. This provides an opportunity for analysis of immune responses and associations with age, sex and disease severity. Here we measured an array of solid-phase binding antibody and viral neutralising Ab (nAb) responses in participants (n=337) of the ISARIC4C cohort and characterised their correlation with peak disease severity during acute infection and early convalescence. Overall, the responses in a Double Antigen Binding Assay (DABA) for antibody to the receptor binding domain (anti-RBD) correlated well with IgM as well as IgG responses against viral spike, S1 and nucleocapsid protein (NP) antigens. DABA reactivity also correlated with nAb. As we and others reported previously, there is greater risk of severe disease and death in older men, whilst the sex ratio was found to be equal within each severity grouping in younger people. In older males with severe disease (mean age 68 years), peak antibody levels were found to be delayed by one to two weeks compared with women, and nAb responses were delayed further. Additionally, we demonstrated that solid-phase binding antibody responses reached higher levels in males as measured <i>via</i> DABA and IgM binding against Spike, NP and S1 antigens. In contrast, this was not observed for nAb responses. When measuring SARS-CoV-2 RNA transcripts (as a surrogate for viral shedding) in nasal swabs at recruitment, we saw no significant differences by sex or disease severity status. However, we have shown higher antibody levels associated with low nasal viral RNA indicating a role of antibody responses in controlling viral replication and shedding in the upper airway. In this study, we have shown discernible differences in the humoral immune responses between males and females and these differences associate with age as well as with resultant disease severity.",,pdf:https://www.frontiersin.org/articles/10.3389/fimmu.2023.1146702/pdf; doi:https://doi.org/10.3389/fimmu.2023.1146702; html:https://europepmc.org/articles/PMC10087108; pdf:https://europepmc.org/articles/PMC10087108?pdf=render
 35042645,https://doi.org/10.1016/j.vaccine.2021.11.061,"COVID-19 vaccine uptake, effectiveness, and waning in 82,959 health care workers: A national prospective cohort study in Wales.","Bedston S, Akbari A, Jarvis CI, Lowthian E, Torabi F, North L, Lyons J, Perry M, Griffiths LJ, Owen RK, Beggs J, Chuter A, Bradley DT, de Lusignan S, Fry R, Richard Hobbs FD, Hollinghurst J, Katikireddi SV, Murphy S, O'Reily D, Robertson C, Shi T, Tsang RSM, Sheikh A, Lyons RA.",,Vaccine,2022,2022-01-15,Y,Vaccines; Health care workers; Pandemic; Covid-19,,,"<h4>Background</h4>While population estimates suggest high vaccine effectiveness against SARS-CoV-2 infection, the protection for health care workers, who are at higher risk of SARS-CoV-2 exposure, is less understood.<h4>Methods</h4>We conducted a national cohort study of health care workers in Wales (UK) from 7 December 2020 to 30 September 2021. We examined uptake of any COVID-19 vaccine, and the effectiveness of BNT162b2 mRNA (Pfizer-BioNTech) against polymerase chain reaction (PCR) confirmed SARS-CoV-2 infection. We used linked and routinely collected national-scale data within the SAIL Databank. Data were available on 82,959 health care workers in Wales, with exposure extending to 26 weeks after second doses.<h4>Results</h4>Overall vaccine uptake was high (90%), with most health care workers receiving theBNT162b2 vaccine (79%). Vaccine uptake differed by age, staff role, socioeconomic status; those aged 50-59 and 60+ years old were 1.6 times more likely to get vaccinated than those aged 16-29. Medical and dental staff, and Allied Health Practitioners were 1.5 and 1.1 times more likely to get vaccinated, compared to nursing and midwifery staff. The effectiveness of the BNT162b2 vaccine was found to be strong and consistent across the characteristics considered; 52% three to six weeks after first dose, 86% from two weeks after second dose, though this declined to 53% from 22 weeks after the second dose.<h4>Conclusions</h4>With some variation in rate of uptake, those who were vaccinated had a reduced risk of PCR-confirmed SARS-CoV-2 infection, compared to those unvaccinated. Second dose has provided stronger protection for longer than first dose but our study is consistent with waning from seven weeks onwards.",,doi:https://doi.org/10.1016/j.vaccine.2021.11.061; doi:https://doi.org/10.1016/j.vaccine.2021.11.061; html:https://europepmc.org/articles/PMC8760602
-38778017,https://doi.org/10.1038/s41541-024-00878-0,Influence of individuals' determinants including vaccine type on cellular and humoral responses to SARS-CoV-2 vaccination.,"Chambers ES, Cai W, Vivaldi G, Jolliffe DA, Perdek N, Li W, Faustini SE, Gibbons JM, Pade C, Richter AG, Coussens AK, Martineau AR.",,NPJ vaccines,2024,2024-05-22,Y,,,,"Vaccine development targeting SARS-CoV-2 in 2020 was of critical importance in reducing COVID-19 severity and mortality. In the U.K. during the initial roll-out most individuals either received two doses of Pfizer COVID-19 vaccine (BNT162b2) or the adenovirus-based vaccine from Oxford/AstraZeneca (ChAdOx1-nCoV-19). There are conflicting data as to the impact of age, sex and body habitus on cellular and humoral responses to vaccination, and most studies in this area have focused on determinants of mRNA vaccine immunogenicity. Here, we studied a cohort of participants in a population-based longitudinal study (COVIDENCE UK) to determine the influence of age, sex, body mass index (BMI) and pre-vaccination anti-Spike (anti-S) antibody status on vaccine-induced humoral and cellular immune responses to two doses of BNT162b2 or ChAdOx-n-CoV-19 vaccination. Younger age and pre-vaccination anti-S seropositivity were both associated with stronger antibody responses to vaccination. BNT162b2 generated higher neutralising and anti-S antibody titres to vaccination than ChAdOx1-nCoV-19, but cellular responses to the two vaccines were no different. Irrespective of vaccine type, increasing age was also associated with decreased frequency of cytokine double-positive CD4+T cells. Increasing BMI was associated with reduced frequency of SARS-CoV-2-specific TNF+CD8% T cells for both vaccines. Together, our findings demonstrate that increasing age and BMI are associated with attenuated cellular and humoral responses to SARS-CoV-2 vaccination. Whilst both vaccines induced T cell responses, BNT162b2 induced significantly elevated humoral immune response as compared to ChAdOx-n-CoV-19.",,pdf:https://www.nature.com/articles/s41541-024-00878-0.pdf; doi:https://doi.org/10.1038/s41541-024-00878-0; html:https://europepmc.org/articles/PMC11111746; pdf:https://europepmc.org/articles/PMC11111746?pdf=render
 37228015,https://doi.org/10.1371/journal.pbio.3002118,Dynamics of SARS-CoV-2 infection hospitalisation and infection fatality ratios over 23 months in England.,"Eales O, Haw D, Wang H, Atchison C, Ashby D, Cooke GS, Barclay W, Ward H, Darzi A, Donnelly CA, Chadeau-Hyam M, Elliott P, Riley S.",,PLoS biology,2023,2023-05-25,Y,,,,"The relationship between prevalence of infection and severe outcomes such as hospitalisation and death changed over the course of the COVID-19 pandemic. Reliable estimates of the infection fatality ratio (IFR) and infection hospitalisation ratio (IHR) along with the time-delay between infection and hospitalisation/death can inform forecasts of the numbers/timing of severe outcomes and allow healthcare services to better prepare for periods of increased demand. The REal-time Assessment of Community Transmission-1 (REACT-1) study estimated swab positivity for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in England approximately monthly from May 2020 to March 2022. Here, we analyse the changing relationship between prevalence of swab positivity and the IFR and IHR over this period in England, using publicly available data for the daily number of deaths and hospitalisations, REACT-1 swab positivity data, time-delay models, and Bayesian P-spline models. We analyse data for all age groups together, as well as in 2 subgroups: those aged 65 and over and those aged 64 and under. Additionally, we analysed the relationship between swab positivity and daily case numbers to estimate the case ascertainment rate of England's mass testing programme. During 2020, we estimated the IFR to be 0.67% and the IHR to be 2.6%. By late 2021/early 2022, the IFR and IHR had both decreased to 0.097% and 0.76%, respectively. The average case ascertainment rate over the entire duration of the study was estimated to be 36.1%, but there was some significant variation in continuous estimates of the case ascertainment rate. Continuous estimates of the IFR and IHR of the virus were observed to increase during the periods of Alpha and Delta's emergence. During periods of vaccination rollout, and the emergence of the Omicron variant, the IFR and IHR decreased. During 2020, we estimated a time-lag of 19 days between hospitalisation and swab positivity, and 26 days between deaths and swab positivity. By late 2021/early 2022, these time-lags had decreased to 7 days for hospitalisations and 18 days for deaths. Even though many populations have high levels of immunity to SARS-CoV-2 from vaccination and natural infection, waning of immunity and variant emergence will continue to be an upwards pressure on the IHR and IFR. As investments in community surveillance of SARS-CoV-2 infection are scaled back, alternative methods are required to accurately track the ever-changing relationship between infection, hospitalisation, and death and hence provide vital information for healthcare provision and utilisation.",,pdf:https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.3002118&type=printable; doi:https://doi.org/10.1371/journal.pbio.3002118; html:https://europepmc.org/articles/PMC10212114; pdf:https://europepmc.org/articles/PMC10212114?pdf=render
+38778017,https://doi.org/10.1038/s41541-024-00878-0,Influence of individuals' determinants including vaccine type on cellular and humoral responses to SARS-CoV-2 vaccination.,"Chambers ES, Cai W, Vivaldi G, Jolliffe DA, Perdek N, Li W, Faustini SE, Gibbons JM, Pade C, Richter AG, Coussens AK, Martineau AR.",,NPJ vaccines,2024,2024-05-22,Y,,,,"Vaccine development targeting SARS-CoV-2 in 2020 was of critical importance in reducing COVID-19 severity and mortality. In the U.K. during the initial roll-out most individuals either received two doses of Pfizer COVID-19 vaccine (BNT162b2) or the adenovirus-based vaccine from Oxford/AstraZeneca (ChAdOx1-nCoV-19). There are conflicting data as to the impact of age, sex and body habitus on cellular and humoral responses to vaccination, and most studies in this area have focused on determinants of mRNA vaccine immunogenicity. Here, we studied a cohort of participants in a population-based longitudinal study (COVIDENCE UK) to determine the influence of age, sex, body mass index (BMI) and pre-vaccination anti-Spike (anti-S) antibody status on vaccine-induced humoral and cellular immune responses to two doses of BNT162b2 or ChAdOx-n-CoV-19 vaccination. Younger age and pre-vaccination anti-S seropositivity were both associated with stronger antibody responses to vaccination. BNT162b2 generated higher neutralising and anti-S antibody titres to vaccination than ChAdOx1-nCoV-19, but cellular responses to the two vaccines were no different. Irrespective of vaccine type, increasing age was also associated with decreased frequency of cytokine double-positive CD4+T cells. Increasing BMI was associated with reduced frequency of SARS-CoV-2-specific TNF+CD8% T cells for both vaccines. Together, our findings demonstrate that increasing age and BMI are associated with attenuated cellular and humoral responses to SARS-CoV-2 vaccination. Whilst both vaccines induced T cell responses, BNT162b2 induced significantly elevated humoral immune response as compared to ChAdOx-n-CoV-19.",,pdf:https://www.nature.com/articles/s41541-024-00878-0.pdf; doi:https://doi.org/10.1038/s41541-024-00878-0; html:https://europepmc.org/articles/PMC11111746; pdf:https://europepmc.org/articles/PMC11111746?pdf=render
 35057841,https://doi.org/10.1186/s13063-021-05965-4,Development and evaluation of rapid data-enabled access to routine clinical information to enhance early recruitment to the national clinical platform trial of COVID-19 community treatments.,"Cake C, Ogburn E, Pinches H, Coleman G, Seymour D, Woodard F, Manohar S, Monsur M, Landray M, Dalton G, Morris AD, Chinnery PF, UK COVID-19 National Core Studies Consortium, Hobbs FDR, Butler C.",,Trials,2022,2022-01-20,Y,Recruitment; Data; Clinical Trials; Primary Care; Healthcare; Covid-19; Public And Patient Involvement And Engagement,,,"<h4>Background</h4>The COVID-19 pandemic has presented unique challenges for rapidly designing, initiating, and delivering therapeutic clinical trials. PRINCIPLE (Platform Randomised Trial of Treatments in the Community for Epidemic and Pandemic Illnesses) is the UK national platform investigating repurposed therapies for COVID-19 treatment of older people in the community at high risk of complications. Standard methods of patient recruitment were failing to meet the required pace and scale of enrolment. This paper describes the development and appraisal of a near real-time, data-driven, ethical approach for enhancing recruitment in community care by contacting people with a recent COVID-19 positive test result from the central NHS Test and Trace service within approximately 24-48 h of their test result.<h4>Methods</h4>A multi-disciplinary team was formed to solve the technical, ethical, public perception, logistical and information governance issues required to provide a near-real time (approximately within 24-48 h of receiving a positive test) feed of potential trial participants from test result data to the research team. PRINCIPLE was also given unique access to the Summary Care Record (SCR) to ensure safe prescribing, and to enable the trial team to quickly and safely bring consented patients into the trial. A survey of the public was used to understand public perceptions of the use of test data for this proposed methodology.<h4>Results</h4>Prior to establishing the data service, PRINCIPLE registered on average 87 participants per week. This increased by up to 87 additional people registered per week from the test data, contributing to an increase from 1013 recruits to PRINCIPLE at the start of October 2020 to 2802 recruits by 20 December 2020. Whilst procedural caveats were identified by the public consultation, out of 2639 people contacted by PRINCIPLE following a positive test result, no one raised a concern about being approached.<h4>Conclusions</h4>This paper describes a novel approach to using near-real time NHS operational data to recruit community-based patients within a few days of presentation with acute illness. This approach increased recruitment and reduced time between positive test and randomisation, allowing more rapid evaluation of treatments and increased safety for participants. End-to-end public and patient involvement in the design of the approach provided evidence to inform information governance decisions.<h4>Trial registration</h4>PRINCIPLE is funded by UK Research and Innovation and the Department of Health and Social Care through the National Institute for Health Research. EudraCT number: 2020-001209-22 . 26/03/2020 ISRCTN registry: ISRCTN86534580 . 20/03/2020 REC number: 20/SC/058 IRAS number: 281958.",,pdf:https://trialsjournal.biomedcentral.com/counter/pdf/10.1186/s13063-021-05965-4; doi:https://doi.org/10.1186/s13063-021-05965-4; html:https://europepmc.org/articles/PMC8771189; pdf:https://europepmc.org/articles/PMC8771189?pdf=render
-37243092,https://doi.org/10.3390/vaccines11050988,A Methodological Framework for Assessing the Benefit of SARS-CoV-2 Vaccination following Previous Infection: Case Study of Five- to Eleven-Year-Olds.,"Pagel C, Wilde H, Tomlinson C, Mateen B, Brown K.",,Vaccines,2023,2023-05-16,Y,Health Policy; Mathematical Modelling; Covid-19; Paediatric Vaccines,,,"Vaccination rates against SARS-CoV-2 in children aged five to eleven years remain low in many countries. The current benefit of vaccination in this age group has been questioned given that the large majority of children have now experienced at least one SARS-CoV-2 infection. However, protection from infection, vaccination or both wanes over time. National decisions on offering vaccines to this age group have tended to be made without considering time since infection. There is an urgent need to evaluate the additional benefits of vaccination in previously infected children and under what circumstances those benefits accrue. We present a novel methodological framework for estimating the potential benefits of COVID-19 vaccination in previously infected children aged five to eleven, accounting for waning. We apply this framework to the UK context and for two adverse outcomes: hospitalisation related to SARS-CoV-2 infection and Long Covid. We show that the most important drivers of benefit are: the degree of protection provided by previous infection; the protection provided by vaccination; the time since previous infection; and future attack rates. Vaccination can be very beneficial for previously infected children if future attack rates are high and several months have elapsed since the previous major wave in this group. Benefits are generally larger for Long Covid than hospitalisation, because Long Covid is both more common than hospitalisation and previous infection offers less protection against it. Our framework provides a structure for policy makers to explore the additional benefit of vaccination across a range of adverse outcomes and different parameter assumptions. It can be easily updated as new evidence emerges.",,pdf:https://www.mdpi.com/2076-393X/11/5/988/pdf?version=1684231380; doi:https://doi.org/10.3390/vaccines11050988; html:https://europepmc.org/articles/PMC10220644; pdf:https://europepmc.org/articles/PMC10220644?pdf=render
 34151246,https://doi.org/10.1016/j.cjco.2021.05.020,Cardiovascular and Renal Risk Factors and Complications Associated With COVID-19.,"Touyz RM, Boyd MOE, Guzik T, Padmanabhan S, McCallum L, Delles C, Mark PB, Petrie JR, Rios F, Montezano AC, Sykes R, Berry C.",,CJC open,2021,2021-06-16,Y,,,,"The current COVID-19 pandemic, caused by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) virus, represents the largest medical challenge in decades. It has exposed unexpected cardiovascular vulnerabilities at all stages of the disease (pre-infection, acute phase, and subsequent chronic phase). The major cardiometabolic drivers identified as having epidemiologic and mechanistic associations with COVID-19 are abnormal adiposity, dysglycemia, dyslipidemia, and hypertension. Hypertension is of particular interest, because components of the renin-angiotensin system (RAS), which are critically involved in the pathophysiology of hypertension, are also implicated in COVID-19. Specifically, angiotensin-converting enzyme-2 (ACE2), a multifunctional protein of the RAS, which is part of the protective axis of the RAS, is also the receptor through which SARS-CoV-2 enters host cells, causing viral infection. Cardiovascular and cardiometabolic comorbidities not only predispose people to COVID-19, but also are complications of SARS-CoV-2 infection. In addition, increasing evidence indicates that acute kidney injury is common in COVID-19, occurs early and in temporal association with respiratory failure, and is associated with poor prognosis, especially in the presence of cardiovascular risk factors. Here, we discuss cardiovascular and kidney disease in the context of COVID-19 and provide recent advances on putative pathophysiological mechanisms linking cardiovascular disease and COVID-19, focusing on the RAS and ACE2, as well as the immune system and inflammation. We provide up-to-date information on the relationships among hypertension, diabetes, and COVID-19 and emphasize the major cardiovascular diseases associated with COVID-19. We also briefly discuss emerging cardiovascular complications associated with long COVID-19, notably postural tachycardia syndrome (POTS).",,pdf:http://www.cjcopen.ca/article/S2589790X21001554/pdf; doi:https://doi.org/10.1016/j.cjco.2021.05.020; html:https://europepmc.org/articles/PMC8205551; pdf:https://europepmc.org/articles/PMC8205551?pdf=render
+37243092,https://doi.org/10.3390/vaccines11050988,A Methodological Framework for Assessing the Benefit of SARS-CoV-2 Vaccination following Previous Infection: Case Study of Five- to Eleven-Year-Olds.,"Pagel C, Wilde H, Tomlinson C, Mateen B, Brown K.",,Vaccines,2023,2023-05-16,Y,Health Policy; Mathematical Modelling; Covid-19; Paediatric Vaccines,,,"Vaccination rates against SARS-CoV-2 in children aged five to eleven years remain low in many countries. The current benefit of vaccination in this age group has been questioned given that the large majority of children have now experienced at least one SARS-CoV-2 infection. However, protection from infection, vaccination or both wanes over time. National decisions on offering vaccines to this age group have tended to be made without considering time since infection. There is an urgent need to evaluate the additional benefits of vaccination in previously infected children and under what circumstances those benefits accrue. We present a novel methodological framework for estimating the potential benefits of COVID-19 vaccination in previously infected children aged five to eleven, accounting for waning. We apply this framework to the UK context and for two adverse outcomes: hospitalisation related to SARS-CoV-2 infection and Long Covid. We show that the most important drivers of benefit are: the degree of protection provided by previous infection; the protection provided by vaccination; the time since previous infection; and future attack rates. Vaccination can be very beneficial for previously infected children if future attack rates are high and several months have elapsed since the previous major wave in this group. Benefits are generally larger for Long Covid than hospitalisation, because Long Covid is both more common than hospitalisation and previous infection offers less protection against it. Our framework provides a structure for policy makers to explore the additional benefit of vaccination across a range of adverse outcomes and different parameter assumptions. It can be easily updated as new evidence emerges.",,pdf:https://www.mdpi.com/2076-393X/11/5/988/pdf?version=1684231380; doi:https://doi.org/10.3390/vaccines11050988; html:https://europepmc.org/articles/PMC10220644; pdf:https://europepmc.org/articles/PMC10220644?pdf=render
 37124948,https://doi.org/10.1016/j.lanepe.2023.100638,Severity of Omicron BA.5 variant and protective effect of vaccination: national cohort and matched analyses in Scotland.,"Robertson C, Kerr S, Sheikh A.",,The Lancet regional health. Europe,2023,2023-04-14,Y,,,,,,doi:https://doi.org/10.1016/j.lanepe.2023.100638; doi:https://doi.org/10.1016/j.lanepe.2023.100638; html:https://europepmc.org/articles/PMC10139952; pdf:https://europepmc.org/articles/PMC10139952?pdf=render
 39167370,https://doi.org/10.1001/jamapsychiatry.2024.2339,COVID-19 and Mental Illnesses in Vaccinated and Unvaccinated People.,"Walker VM, Patalay P, Cuitun Coronado JI, Denholm R, Forbes H, Stafford J, Moltrecht B, Palmer T, Walker A, Thompson EJ, Taylor K, Cezard G, Horne EMF, Wei Y, Al Arab M, Knight R, Fisher L, Massey J, Davy S, Mehrkar A, Bacon S, Goldacre B, Wood A, Chaturvedi N, Macleod J, John A, Sterne JAC, Longitudinal Health and Wellbeing COVID-19 National Core Study.",,JAMA psychiatry,2024,2024-08-21,Y,,,,"<h4>Importance</h4>Associations have been found between COVID-19 and subsequent mental illness in both hospital- and population-based studies. However, evidence regarding which mental illnesses are associated with COVID-19 by vaccination status in these populations is limited.<h4>Objective</h4>To determine which mental illnesses are associated with diagnosed COVID-19 by vaccination status in both hospitalized patients and the general population.<h4>Design, setting, and participants</h4>This study was conducted in 3 cohorts, 1 before vaccine availability followed during the wild-type/Alpha variant eras (January 2020-June 2021) and 2 (vaccinated and unvaccinated) during the Delta variant era (June-December 2021). With National Health Service England approval, OpenSAFELY-TPP was used to access linked data from 24 million people registered with general practices in England using TPP SystmOne. People registered with a GP in England for at least 6 months and alive with known age between 18 and 110 years, sex, deprivation index information, and region at baseline were included. People were excluded if they had COVID-19 before baseline. Data were analyzed from July 2022 to June 2024.<h4>Exposure</h4>Confirmed COVID-19 diagnosis recorded in primary care secondary care, testing data, or the death registry.<h4>Main outcomes and measures</h4>Adjusted hazard ratios (aHRs) comparing the incidence of mental illnesses after diagnosis of COVID-19 with the incidence before or without COVID-19 for depression, serious mental illness, general anxiety, posttraumatic stress disorder, eating disorders, addiction, self-harm, and suicide.<h4>Results</h4>The largest cohort, the pre-vaccine availability cohort, included 18 648 606 people (9 363 710 [50.2%] female and 9 284 896 [49.8%] male) with a median (IQR) age of 49 (34-64) years. The vaccinated cohort included 14 035 286 individuals (7 308 556 [52.1%] female and 6 726 730 [47.9%] male) with a median (IQR) age of 53 (38-67) years. The unvaccinated cohort included 3 242 215 individuals (1 363 401 [42.1%] female and 1 878 814 [57.9%] male) with a median (IQR) age of 35 (27-46) years. Incidence of most outcomes was elevated during weeks 1 through 4 after COVID-19 diagnosis, compared with before or without COVID-19, in each cohort. Incidence of mental illnesses was lower in the vaccinated cohort compared with the pre-vaccine availability and unvaccinated cohorts: aHRs for depression and serious mental illness during weeks 1 through 4 after COVID-19 were 1.93 (95% CI, 1.88-1.98) and 1.49 (95% CI, 1.41-1.57) in the pre-vaccine availability cohort and 1.79 (95% CI, 1.68-1.90) and 1.45 (95% CI, 1.27-1.65) in the unvaccinated cohort compared with 1.16 (95% CI, 1.12-1.20) and 0.91 (95% CI, 0.85-0.98) in the vaccinated cohort. Elevation in incidence was higher and persisted longer after hospitalization for COVID-19.<h4>Conclusions and relevance</h4>In this study, incidence of mental illnesses was elevated for up to a year following severe COVID-19 in unvaccinated people. These findings suggest that vaccination may mitigate the adverse effects of COVID-19 on mental health.",,doi:https://doi.org/10.1001/jamapsychiatry.2024.2339; html:https://europepmc.org/articles/PMC11339697
 38388690,https://doi.org/10.1038/s41597-024-02958-1,"Ethnicity data resource in population-wide health records: completeness, coverage and granularity of diversity.","Pineda-Moncusí M, Allery F, Delmestri A, Bolton T, Nolan J, Thygesen JH, Handy A, Banerjee A, Denaxas S, Tomlinson C, Denniston AK, Sudlow C, Akbari A, Wood A, Collins GS, Petersen I, Coates LC, Khunti K, Prieto-sAlhambra D, Khalid S, CVD-COVID-UK/COVID-IMPACT Consortium.",,Scientific data,2024,2024-02-22,Y,,,,"Intersectional social determinants including ethnicity are vital in health research. We curated a population-wide data resource of self-identified ethnicity data from over 60 million individuals in England primary care, linking it to hospital records. We assessed ethnicity data in terms of completeness, consistency, and granularity and found one in ten individuals do not have ethnicity information recorded in primary care. By linking to hospital records, ethnicity data were completed for 94% of individuals. By reconciling SNOMED-CT concepts and census-level categories into a consistent hierarchy, we organised more than 250 ethnicity sub-groups including and beyond ""White"", ""Black"", ""Asian"", ""Mixed"" and ""Other, and found them to be distributed in proportions similar to the general population. This large observational dataset presents an algorithmic hierarchy to represent self-identified ethnicity data collected across heterogeneous healthcare settings. Accurate and easily accessible ethnicity data can lead to a better understanding of population diversity, which is important to address disparities and influence policy recommendations that can translate into better, fairer health for all.",,pdf:https://www.nature.com/articles/s41597-024-02958-1.pdf; doi:https://doi.org/10.1038/s41597-024-02958-1; html:https://europepmc.org/articles/PMC10883937; pdf:https://europepmc.org/articles/PMC10883937?pdf=render
@@ -55,8 +55,8 @@ PMC11201135,https://doi.org/,Exploring Prior Antibiotic Exposure Characteristics
 37644002,https://doi.org/10.1038/s41467-023-40965-9,Neonatal and maternal outcomes following SARS-CoV-2 infection and COVID-19 vaccination: a population-based matched cohort study.,"Lindsay L, Calvert C, Shi T, Carruthers J, Denny C, Donaghy J, Hopcroft LEM, Hopkins L, Goulding A, McLaughlin T, Moore E, Taylor B, Bhaskaran K, Katikireddi SV, McCabe R, McCowan C, Simpson CR, Robertson C, Sheikh A, Wood R, Stock SJ.",,Nature communications,2023,2023-08-29,Y,,,,"Understanding the impact of SARS-CoV-2 infection and COVID-19 vaccination in pregnancy on neonatal and maternal outcomes informs clinical decision-making. Here we report a national, population-based, matched cohort study to investigate associations between SARS-CoV-2 infection and, separately, COVID-19 vaccination just before or during pregnancy and the risk of adverse neonatal and maternal outcomes among women in Scotland with a singleton pregnancy ending at ≥20 weeks gestation. Neonatal outcomes are stillbirth, neonatal death, extended perinatal mortality, preterm birth (overall, spontaneous, and provider-initiated), small-for-gestational age, and low Apgar score. Maternal outcomes are admission to critical care or death, venous thromboembolism, hypertensive disorders of pregnancy, and pregnancy-related bleeding. We use conditional logistic regression to derive odds ratios adjusted for socio-demographic and clinical characteristics (aORs). We find that infection is associated with an increased risk of preterm (aOR=1.36, 95% Confidence Interval [CI] = 1.16-1.59) and very preterm birth (aOR = 1.90, 95% CI 1.20-3.02), maternal admission to critical care or death (aOR=1.72, 95% CI = 1.39-2.12), and venous thromboembolism (aOR = 2.53, 95% CI = 1.47-4.35). We find no evidence of increased risk for any of our outcomes following vaccination. These data suggest SARS-CoV-2 infection during pregnancy is associated with adverse neonatal and maternal outcomes, and COVID-19 vaccination remains a safe way for pregnant women to protect themselves and their babies against infection.",,pdf:https://www.nature.com/articles/s41467-023-40965-9.pdf; doi:https://doi.org/10.1038/s41467-023-40965-9; html:https://europepmc.org/articles/PMC10465539; pdf:https://europepmc.org/articles/PMC10465539?pdf=render
 36958018,https://doi.org/10.1111/anae.16001,Postoperative mortality and complications in patients with and without pre-operative SARS-CoV-2 infection: a service evaluation of 24 million linked records using OpenSAFELY.,"McInerney CD, Kotzé A, Bacon S, Cutting JE, Fisher L, Goldacre B, Johnson OA, Kua J, McGuckin D, Mehrkar A, OpenSAFELY Collaborative, Moonesinghe SR.",,Anaesthesia,2023,2023-03-23,Y,"Public Health; Patient Safety; Surgical Procedures, Operative; Covid-19; Sars-cov-2",,,"Surgical decision-making after SARS-CoV-2 infection is influenced by the presence of comorbidity, infection severity and whether the surgical problem is time-sensitive. Contemporary surgical policy to delay surgery is informed by highly heterogeneous country-specific guidance. We evaluated surgical provision in England during the COVID-19 pandemic to assess real-world practice and whether deferral remains necessary. Using the OpenSAFELY platform, we adapted the COVIDSurg protocol for a service evaluation of surgical procedures that took place within the English NHS from 17 March 2018 to 17 March 2022. We assessed whether hospitals adhered to guidance not to operate on patients within 7 weeks of an indication of SARS-CoV-2 infection. Additional outcomes were postoperative all-cause mortality (30 days, 6 months) and complications (pulmonary, cardiac, cerebrovascular). The exposure was the interval between the most recent indication of SARS-CoV-2 infection and subsequent surgery. In any 6-month window, < 3% of surgical procedures were conducted within 7 weeks of an indication of SARS-CoV-2 infection. Mortality for surgery conducted within 2 weeks of a positive test in the era since widespread SARS-CoV-2 vaccine availability was 1.1%, declining to 0.3% by 4 weeks. Compared with the COVIDSurg study cohort, outcomes for patients in the English NHS cohort were better during the COVIDSurg data collection period and the pandemic era before vaccines became available. Clinicians within the English NHS followed national guidance by operating on very few patients within 7 weeks of a positive indication of SARS-CoV-2 infection. In England, surgical patients' overall risk following an indication of SARS-CoV-2 infection is lower than previously thought.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/anae.16001; doi:https://doi.org/10.1111/anae.16001; html:https://europepmc.org/articles/PMC7616145; pdf:https://europepmc.org/articles/PMC7616145?pdf=render
 34487522,https://doi.org/10.1093/cid/ciab754,Severity of Severe Acute Respiratory System Coronavirus 2 (SARS-CoV-2) Alpha Variant (B.1.1.7) in England.,"Grint DJ, Wing K, Houlihan C, Gibbs HP, Evans SJW, Williamson E, McDonald HI, Bhaskaran K, Evans D, Walker AJ, Hickman G, Nightingale E, Schultze A, Rentsch CT, Bates C, Cockburn J, Curtis HJ, Morton CE, Bacon S, Davy S, Wong AYS, Mehrkar A, Tomlinson L, Douglas IJ, Mathur R, MacKenna B, Ingelsby P, Croker R, Parry J, Hester F, Harper S, DeVito NJ, Hulme W, Tazare J, Smeeth L, Goldacre B, Eggo RM.",,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2022,2022-08-01,Y,Alpha; Hospital Admission; Case Fatality; Sars-cov-2,,,"<h4>Background</h4>The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) alpha variant (B.1.1.7) is associated with higher transmissibility than wild-type virus, becoming the dominant variant in England by January 2021. We aimed to describe the severity of the alpha variant in terms of the pathway of disease from testing positive to hospital admission and death.<h4>Methods</h4>With the approval of NHS England, we linked individual-level data from primary care with SARS-CoV-2 community testing, hospital admission, and Office for National Statistics all-cause death data. We used testing data with S-gene target failure as a proxy for distinguishing alpha and wild-type cases, and stratified Cox proportional hazards regression to compare the relative severity of alpha cases with wild-type diagnosed from 16 November 2020 to 11 January 2021.<h4>Results</h4>Using data from 185 234 people who tested positive for SARS-CoV-2 in the community (alpha = 93 153; wild-type = 92 081), in fully adjusted analysis accounting for individual-level demographics and comorbidities as well as regional variation in infection incidence, we found alpha associated with 73% higher hazards of all-cause death (adjusted hazard ratio [aHR]: 1.73; 95% confidence interval [CI]: 1.41-2.13; P < .0001) and 62% higher hazards of hospital admission (1.62; 1.48-1.78; P < .0001) compared with wild-type virus. Among patients already admitted to the intensive care unit, the association between alpha and increased all-cause mortality was smaller and the CI included the null (aHR: 1.20; 95% CI: .74-1.95; P = .45).<h4>Conclusions</h4>The SARS-CoV-2 alpha variant is associated with an increased risk of both hospitalization and mortality than wild-type virus.",,pdf:https://academic.oup.com/cid/article-pdf/75/1/e1120/45513976/ciab754.pdf; doi:https://doi.org/10.1093/cid/ciab754; html:https://europepmc.org/articles/PMC8522415; pdf:https://europepmc.org/articles/PMC8522415?pdf=render
-36719907,https://doi.org/10.1371/journal.pmed.1004086,Outcome of COVID-19 in hospitalised immunocompromised patients: An analysis of the WHO ISARIC CCP-UK prospective cohort study.,"Turtle L, Thorpe M, Drake TM, Swets M, Palmieri C, Russell CD, Ho A, Aston S, Wootton DG, Richter A, de Silva TI, Hardwick HE, Leeming G, Law A, Openshaw PJM, Harrison EM, ISARIC4C investigators, Baillie JK, Semple MG, Docherty AB.",,PLoS medicine,2023,2023-01-31,Y,,,,"<h4>Background</h4>Immunocompromised patients may be at higher risk of mortality if hospitalised with Coronavirus Disease 2019 (COVID-19) compared with immunocompetent patients. However, previous studies have been contradictory. We aimed to determine whether immunocompromised patients were at greater risk of in-hospital death and how this risk changed over the pandemic.<h4>Methods and findings</h4>We included patients > = 19 years with symptomatic community-acquired COVID-19 recruited to the ISARIC WHO Clinical Characterisation Protocol UK prospective cohort study. We defined immunocompromise as immunosuppressant medication preadmission, cancer treatment, organ transplant, HIV, or congenital immunodeficiency. We used logistic regression to compare the risk of death in both groups, adjusting for age, sex, deprivation, ethnicity, vaccination, and comorbidities. We used Bayesian logistic regression to explore mortality over time. Between 17 January 2020 and 28 February 2022, we recruited 156,552 eligible patients, of whom 21,954 (14%) were immunocompromised. In total, 29% (n = 6,499) of immunocompromised and 21% (n = 28,608) of immunocompetent patients died in hospital. The odds of in-hospital mortality were elevated for immunocompromised patients (adjusted OR 1.44, 95% CI [1.39, 1.50], p < 0.001). Not all immunocompromising conditions had the same risk, for example, patients on active cancer treatment were less likely to have their care escalated to intensive care (adjusted OR 0.77, 95% CI [0.7, 0.85], p < 0.001) or ventilation (adjusted OR 0.65, 95% CI [0.56, 0.76], p < 0.001). However, cancer patients were more likely to die (adjusted OR 2.0, 95% CI [1.87, 2.15], p < 0.001). Analyses were adjusted for age, sex, socioeconomic deprivation, comorbidities, and vaccination status. As the pandemic progressed, in-hospital mortality reduced more slowly for immunocompromised patients than for immunocompetent patients. This was particularly evident with increasing age: the probability of the reduction in hospital mortality being less for immunocompromised patients aged 50 to 69 years was 88% for men and 83% for women, and for those >80 years was 99% for men and 98% for women. The study is limited by a lack of detailed drug data prior to admission, including steroid doses, meaning that we may have incorrectly categorised some immunocompromised patients as immunocompetent.<h4>Conclusions</h4>Immunocompromised patients remain at elevated risk of death from COVID-19. Targeted measures such as additional vaccine doses, monoclonal antibodies, and nonpharmaceutical preventive interventions should be continually encouraged for this patient group.<h4>Trial registration</h4>ISRCTN 66726260.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004086&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004086; html:https://europepmc.org/articles/PMC9928075; pdf:https://europepmc.org/articles/PMC9928075?pdf=render
 36272418,https://doi.org/10.1093/ije/dyac199,"Waning of first- and second-dose ChAdOx1 and BNT162b2 COVID-19 vaccinations: a pooled target trial study of 12.9 million individuals in England, Northern Ireland, Scotland and Wales.","Kerr S, Bedston S, Bradley DT, Joy M, Lowthian E, Mulholland RM, Akbari A, Hobbs FDR, Katikireddi SV, de Lusignan S, Rudan I, Torabi F, Tsang RSM, Lyons RA, Robertson C, Sheikh A.",,International journal of epidemiology,2023,2023-02-01,Y,Vaccine Effectiveness; Vaccine Waning; Covid-19,,,"<h4>Background</h4>Several SARS-CoV-2 vaccines have been shown to provide protection against COVID-19 hospitalization and death. However, some evidence suggests that notable waning in effectiveness against these outcomes occurs within months of vaccination. We undertook a pooled analysis across the four nations of the UK to investigate waning in vaccine effectiveness (VE) and relative vaccine effectiveness (rVE) against severe COVID-19 outcomes.<h4>Methods</h4>We carried out a target trial design for first/second doses of ChAdOx1(Oxford-AstraZeneca) and BNT162b2 (Pfizer-BioNTech) with a composite outcome of COVID-19 hospitalization or death over the period 8 December 2020 to 30 June 2021. Exposure groups were matched by age, local authority area and propensity for vaccination. We pooled event counts across the four UK nations.<h4>Results</h4>For Doses 1 and 2 of ChAdOx1 and Dose 1 of BNT162b2, VE/rVE reached zero by approximately Days 60-80 and then went negative. By Day 70, VE/rVE was -25% (95% CI: -80 to 14) and 10% (95% CI: -32 to 39) for Doses 1 and 2 of ChAdOx1, respectively, and 42% (95% CI: 9 to 64) and 53% (95% CI: 26 to 70) for Doses 1 and 2 of BNT162b2, respectively. rVE for Dose 2 of BNT162b2 remained above zero throughout and reached 46% (95% CI: 13 to 67) after 98 days of follow-up.<h4>Conclusions</h4>We found strong evidence of waning in VE/rVE for Doses 1 and 2 of ChAdOx1, as well as Dose 1 of BNT162b2. This evidence may be used to inform policies on timings of additional doses of vaccine.",,pdf:https://academic.oup.com/ije/article-pdf/52/1/22/49127317/dyac199.pdf; doi:https://doi.org/10.1093/ije/dyac199; html:https://europepmc.org/articles/PMC9620314; pdf:https://europepmc.org/articles/PMC9620314?pdf=render
+36719907,https://doi.org/10.1371/journal.pmed.1004086,Outcome of COVID-19 in hospitalised immunocompromised patients: An analysis of the WHO ISARIC CCP-UK prospective cohort study.,"Turtle L, Thorpe M, Drake TM, Swets M, Palmieri C, Russell CD, Ho A, Aston S, Wootton DG, Richter A, de Silva TI, Hardwick HE, Leeming G, Law A, Openshaw PJM, Harrison EM, ISARIC4C investigators, Baillie JK, Semple MG, Docherty AB.",,PLoS medicine,2023,2023-01-31,Y,,,,"<h4>Background</h4>Immunocompromised patients may be at higher risk of mortality if hospitalised with Coronavirus Disease 2019 (COVID-19) compared with immunocompetent patients. However, previous studies have been contradictory. We aimed to determine whether immunocompromised patients were at greater risk of in-hospital death and how this risk changed over the pandemic.<h4>Methods and findings</h4>We included patients > = 19 years with symptomatic community-acquired COVID-19 recruited to the ISARIC WHO Clinical Characterisation Protocol UK prospective cohort study. We defined immunocompromise as immunosuppressant medication preadmission, cancer treatment, organ transplant, HIV, or congenital immunodeficiency. We used logistic regression to compare the risk of death in both groups, adjusting for age, sex, deprivation, ethnicity, vaccination, and comorbidities. We used Bayesian logistic regression to explore mortality over time. Between 17 January 2020 and 28 February 2022, we recruited 156,552 eligible patients, of whom 21,954 (14%) were immunocompromised. In total, 29% (n = 6,499) of immunocompromised and 21% (n = 28,608) of immunocompetent patients died in hospital. The odds of in-hospital mortality were elevated for immunocompromised patients (adjusted OR 1.44, 95% CI [1.39, 1.50], p < 0.001). Not all immunocompromising conditions had the same risk, for example, patients on active cancer treatment were less likely to have their care escalated to intensive care (adjusted OR 0.77, 95% CI [0.7, 0.85], p < 0.001) or ventilation (adjusted OR 0.65, 95% CI [0.56, 0.76], p < 0.001). However, cancer patients were more likely to die (adjusted OR 2.0, 95% CI [1.87, 2.15], p < 0.001). Analyses were adjusted for age, sex, socioeconomic deprivation, comorbidities, and vaccination status. As the pandemic progressed, in-hospital mortality reduced more slowly for immunocompromised patients than for immunocompetent patients. This was particularly evident with increasing age: the probability of the reduction in hospital mortality being less for immunocompromised patients aged 50 to 69 years was 88% for men and 83% for women, and for those >80 years was 99% for men and 98% for women. The study is limited by a lack of detailed drug data prior to admission, including steroid doses, meaning that we may have incorrectly categorised some immunocompromised patients as immunocompetent.<h4>Conclusions</h4>Immunocompromised patients remain at elevated risk of death from COVID-19. Targeted measures such as additional vaccine doses, monoclonal antibodies, and nonpharmaceutical preventive interventions should be continually encouraged for this patient group.<h4>Trial registration</h4>ISRCTN 66726260.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004086&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004086; html:https://europepmc.org/articles/PMC9928075; pdf:https://europepmc.org/articles/PMC9928075?pdf=render
 36469089,https://doi.org/10.1093/ageing/afac250,"The impact of dementia, frailty and care home characteristics on SARS-CoV-2 incidence in a national cohort of Welsh care home residents during a period of high community prevalence.","Emmerson C, Hollinghurst J, North L, Fry R, Akbari A, Humphreys C, Gravenor MB, Lyons RA.",,Age and ageing,2022,2022-12-01,Y,Frailty; Dementia; Older People; Care Homes; Covid-19; Sars-cov-2,,,"<h4>Background</h4>dementia may increase care home residents' risk of COVID-19, but there is a lack of evidence on this effect and on interactions with individual and care home-level factors.<h4>Methods</h4>we created a national cross-sectional retrospective cohort of care home residents in Wales for 1 September to 31 December 2020. Risk factors were analysed using multi-level logistic regression to model the likelihood of SARS-CoV-2 infection and mortality.<h4>Results</h4>the cohort included 9,571 individuals in 673 homes. Dementia was diagnosed in 5,647 individuals (59%); 1,488 (15.5%) individuals tested positive for SARS-CoV-2. We estimated the effects of age, dementia, frailty, care home size, proportion of residents with dementia, nursing and dementia services, communal space and region. The final model included the proportion of residents with dementia (OR for positive test 4.54 (95% CIs 1.55-13.27) where 75% of residents had dementia compared to no residents with dementia) and frailty (OR 1.29 (95% CIs 1.05-1.59) for severe frailty compared with no frailty). Analysis suggested 76% of the variation was due to setting rather than individual factors. Additional analysis suggested severe frailty and proportion of residents with dementia was associated with all-cause mortality, as was dementia diagnosis. Mortality analyses were challenging to interpret.<h4>Discussion</h4>whilst individual frailty increased the risk of COVID-19 infection, dementia was a risk factor at care home but not individual level. These findings suggest whole-setting interventions, particularly in homes with high proportions of residents with dementia and including those with low/no individual risk factors may reduce the impact of COVID-19.",,doi:https://doi.org/10.1093/ageing/afac250; doi:https://doi.org/10.1093/ageing/afac250; html:https://europepmc.org/articles/PMC9721242; pdf:https://europepmc.org/articles/PMC9721242?pdf=render
 37347268,https://doi.org/10.1177/01410768231181268,"Trends in SARS-CoV-2 infection and vaccination in school staff, students and their household members from 2020 to 2022 in Wales, UK: an electronic cohort study.","Lowthian E, Abbasizanjani H, Bedston S, Akbari A, Cowley L, Fry R, Owen RK, Hollinghurst J, Rudan I, Beggs J, Marchant E, Torabi F, Lusignan S, Crick T, Moore G, Sheikh A, Lyons RA.",,Journal of the Royal Society of Medicine,2023,2023-06-22,Y,Pandemic; Schools; Population Health; Covid-19; Social Restrictions,,,"<h4>Objectives</h4>We investigated SARS-CoV-2 infection trends, risk of SARS-CoV-2 infection and COVID-19 vaccination uptake among school staff, students and their household members in Wales, UK.<h4>Design</h4>Seven-day average of SARS-CoV-2 infections and polymerase chain reaction tests per 1000 people daily, cumulative incidence of COVID-19 vaccination uptake and multi-level Poisson models with time-varying covariates.<h4>Setting</h4>National electronic cohort between September 2020 and May 2022 when several variants were predominant in the UK (Alpha, Delta and Omicron).<h4>Participants</h4>School students aged 4 to 10/11 years (primary school and younger middle school, <i>n</i> = 238,163), and 11 to 15/16 years (secondary school and older middle school, <i>n</i> = 182,775), school staff in Wales (<i>n</i> = 47,963) and the household members of students and staff (<i>n</i> = 697,659).<h4>Main outcome measures</h4>SARS-CoV-2 infection and COVID-19 vaccination uptake.<h4>Results</h4>School students had a sustained period of high infection rates compared with household members after August 2021. Primary schedule vaccination uptake was highest among staff (96.3%) but lower for household members (72.2%), secondary and older middle school students (59.8%), and primary and younger middle school students (3.3%). Multi-level Poisson models showed that vaccination was associated with a lower risk of SARS-CoV-2 infection. The Delta variant posed a greater infection risk for students than the Alpha variant. However, Omicron was a larger risk for staff and household members.<h4>Conclusions</h4>Public health bodies should be informed of the protection COVID-19 vaccines afford, with more research being required for younger populations. Furthermore, schools require additional support in managing new, highly transmissible variants. Further research should examine the mechanisms between child deprivation and SARS-CoV-2 infection.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/01410768231181268; doi:https://doi.org/10.1177/01410768231181268; html:https://europepmc.org/articles/PMC10767617; pdf:https://europepmc.org/articles/PMC10767617?pdf=render
 38429458,https://doi.org/10.1038/s41590-024-01754-8,Iron dysregulation and inflammatory stress erythropoiesis associates with long-term outcome of COVID-19.,"Hanson AL, Mulè MP, Ruffieux H, Mescia F, Bergamaschi L, Pelly VS, Turner L, Kotagiri P, Cambridge Institute of Therapeutic Immunology and Infectious Disease–National Institute for Health Research (CITIID–NIHR) COVID BioResource Collaboration, Göttgens B, Hess C, Gleadall N, Bradley JR, Nathan JA, Lyons PA, Drakesmith H, Smith KGC.",,Nature immunology,2024,2024-03-01,Y,,,,"Persistent symptoms following SARS-CoV-2 infection are increasingly reported, although the drivers of post-acute sequelae (PASC) of COVID-19 are unclear. Here we assessed 214 individuals infected with SARS-CoV-2, with varying disease severity, for one year from COVID-19 symptom onset to determine the early correlates of PASC. A multivariate signature detected beyond two weeks of disease, encompassing unresolving inflammation, anemia, low serum iron, altered iron-homeostasis gene expression and emerging stress erythropoiesis; differentiated those who reported PASC months later, irrespective of COVID-19 severity. A whole-blood heme-metabolism signature, enriched in hospitalized patients at month 1-3 post onset, coincided with pronounced iron-deficient reticulocytosis. Lymphopenia and low numbers of dendritic cells persisted in those with PASC, and single-cell analysis reported iron maldistribution, suggesting monocyte iron loading and increased iron demand in proliferating lymphocytes. Thus, defects in iron homeostasis, dysregulated erythropoiesis and immune dysfunction due to COVID-19 possibly contribute to inefficient oxygen transport, inflammatory disequilibrium and persisting symptomatology, and may be therapeutically tractable.",,doi:https://doi.org/10.1038/s41590-024-01754-8; doi:https://doi.org/10.1038/s41590-024-01754-8; html:https://europepmc.org/articles/PMC10907301; pdf:https://europepmc.org/articles/PMC10907301?pdf=render
@@ -67,8 +67,8 @@ PMC11201135,https://doi.org/,Exploring Prior Antibiotic Exposure Characteristics
 37543047,https://doi.org/10.1016/s2666-7568(23)00105-8,"Antipsychotic drug prescribing and mortality in people with dementia before and during the COVID-19 pandemic: a retrospective cohort study in Wales, UK.","Schnier C, McCarthy A, Morales DR, Akbari A, Sofat R, Dale C, Takhar R, Mamas MA, Khunti K, Zaccardi F, Sudlow CL, Wilkinson T, CVD-COVID-UK/COVID-IMPACT Consortium.",,The lancet. Healthy longevity,2023,2023-08-01,N,,,,"<h4>Background</h4>Concerns have been raised that antipsychotic drug prescribing, which has been associated with increased mortality in people with dementia, might have increased during the COVID-19 pandemic due to social restrictions imposed to limit the spread of SARS-CoV-2. We used multisource, routinely collected health-care data from Wales, UK to investigate prescribing and mortality variations in people with dementia before and during the COVID-19 pandemic.<h4>Methods</h4>In this retrospective cohort study, we used individual-level, anonymised, population-scale linked health data to identify adults aged 60 years and older with a diagnosis of dementia in Wales, UK. We used the CVD-COVID-UK initiative to access Welsh routinely collected electronic health record data from the Secure Anonymised Information Linkage (SAIL) Databank. Patients who were alive and registered with a SAIL general practice on Jan 1, 2016, and who received a dementia diagnosis before the age of 60 years and before or during the study period were included. We explored antipsychotic drug prescribing rate changes over 67 months, between Jan 1, 2016, and Aug 1, 2021, overall and stratified by age and dementia subtype. We used time-series analyses to examine all-cause and myocardial infarction and stroke mortality over the study period and identified the leading causes of death in people with dementia between Jan 1, 2020, and Aug 1, 2021.<h4>Findings</h4>Of 3 106 690 participants in SAIL between Jan 1, 2016 and Aug 1, 2021, 57 396 people (35 148 [61·2%] women and 22 248 [38·8%] men) met inclusion criteria for this study and contributed 101 428 person-years of follow-up. Of the 57 396 people with dementia, 11 929 (20·8%) were prescribed an antipsychotic drug at any point during follow-up. Accounting for seasonality, antipsychotic drug prescribing increased during the second half of 2019 and throughout 2020. However, the absolute difference in prescribing rates was small, ranging from 1253 prescriptions per 10 000 person-months in March, 2019, to 1305 per 10 000 person-months in September, 2020. All-cause mortality and stroke mortality increased throughout 2020, while myocardial infarction mortality declined. From Jan 1, 2020, to Aug 1, 2021, 1286 (17·1%) of 7508 participants who died had COVID-19 recorded as the underlying cause of death.<h4>Interpretation</h4>During the COVID-19 pandemic, antipsychotic drug prescribing in people with dementia in the UK increased slightly; however, it is unlikely that this was solely related to the pandemic and this increase was unlikely to be a major factor in the substantial increase in mortality during 2020. The long-term increase in antipsychotic drug prescribing in younger people and in those with Alzheimer's disease warrants further investigation using resources with access to more granular clinical data. Although deprescribing antipsychotic medications remains an essential aspect of dementia care, the results of this study suggest that changes in prescribing and deprescribing practices as a result of the COVID-19 pandemic are not required.<h4>Funding</h4>British Heart Foundation (via the British Heart Foundation Data Science Centre led by Health Data Research UK), and the Scottish Neurological Research Fund.",,doi:https://doi.org/10.1016/S2666-7568(23)00105-8
 35798890,https://doi.org/10.1038/s41564-022-01143-7,SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway.,"Willett BJ, Grove J, MacLean OA, Wilkie C, De Lorenzo G, Furnon W, Cantoni D, Scott S, Logan N, Ashraf S, Manali M, Szemiel A, Cowton V, Vink E, Harvey WT, Davis C, Asamaphan P, Smollett K, Tong L, Orton R, Hughes J, Holland P, Silva V, Pascall DJ, Puxty K, da Silva Filipe A, Yebra G, Shaaban S, Holden MTG, Pinto RM, Gunson R, Templeton K, Murcia PR, Patel AH, Klenerman P, Dunachie S, PITCH Consortium, COVID-19 Genomics UK (COG-UK) Consortium, Haughney J, Robertson DL, Palmarini M, Ray S, Thomson EC.",,Nature microbiology,2022,2022-07-07,Y,,,,"Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant.",,pdf:https://www.nature.com/articles/s41564-022-01143-7.pdf; doi:https://doi.org/10.1038/s41564-022-01143-7; html:https://europepmc.org/articles/PMC9352574; pdf:https://europepmc.org/articles/PMC9352574?pdf=render
 38237625,https://doi.org/10.1016/s0140-6736(23)02467-4,"Undervaccination and severe COVID-19 outcomes: meta-analysis of national cohort studies in England, Northern Ireland, Scotland, and Wales.",HDR UK COALESCE Consortium.,,"Lancet (London, England)",2024,2024-01-15,N,,,,"<h4>Background</h4>Undervaccination (receiving fewer than the recommended number of SARS-CoV-2 vaccine doses) could be associated with increased risk of severe COVID-19 outcomes-ie, COVID-19 hospitalisation or death-compared with full vaccination (receiving the recommended number of SARS-CoV-2 vaccine doses). We sought to determine the factors associated with undervaccination, and to investigate the risk of severe COVID-19 outcomes in people who were undervaccinated in each UK nation and across the UK.<h4>Methods</h4>We used anonymised, harmonised electronic health record data with whole population coverage to carry out cohort studies in England, Northern Ireland, Scotland, and Wales. Participants were required to be at least 5 years of age to be included in the cohorts. We estimated adjusted odds ratios for undervaccination as of June 1, 2022. We also estimated adjusted hazard ratios (aHRs) for severe COVID-19 outcomes during the period June 1 to Sept 30, 2022, with undervaccination as a time-dependent exposure. We combined results from nation-specific analyses in a UK-wide fixed-effect meta-analysis. We estimated the reduction in severe COVID-19 outcomes associated with a counterfactual scenario in which everyone in the UK was fully vaccinated on June 1, 2022.<h4>Findings</h4>The numbers of people undervaccinated on June 1, 2022 were 26 985 570 (45·8%) of 58 967 360 in England, 938 420 (49·8%) of 1 885 670 in Northern Ireland, 1 709 786 (34·2%) of 4 992 498 in Scotland, and 773 850 (32·8%) of 2 358 740 in Wales. People who were younger, from more deprived backgrounds, of non-White ethnicity, or had a lower number of comorbidities were less likely to be fully vaccinated. There was a total of 40 393 severe COVID-19 outcomes in the cohorts, with 14 156 of these in undervaccinated participants. We estimated the reduction in severe COVID-19 outcomes in the UK over 4 months of follow-up associated with a counterfactual scenario in which everyone was fully vaccinated on June 1, 2022 as 210 (95% CI 94-326) in the 5-15 years age group, 1544 (1399-1689) in those aged 16-74 years, and 5426 (5340-5512) in those aged 75 years or older. aHRs for severe COVID-19 outcomes in the meta-analysis for the age group of 75 years or older were 2·70 (2·61-2·78) for one dose fewer than recommended, 3·13 (2·93-3·34) for two fewer, 3·61 (3·13-4·17) for three fewer, and 3·08 (2·89-3·29) for four fewer.<h4>Interpretation</h4>Rates of undervaccination against COVID-19 ranged from 32·8% to 49·8% across the four UK nations in summer, 2022. Undervaccination was associated with an elevated risk of severe COVID-19 outcomes.<h4>Funding</h4>UK Research and Innovation National Core Studies: Data and Connectivity.",,pdf:http://www.thelancet.com/article/S0140673623024674/pdf; doi:https://doi.org/10.1016/S0140-6736(23)02467-4
-35690576,https://doi.org/10.1016/s2589-7500(22)00091-7,COVID-19 trajectories among 57 million adults in England: a cohort study using electronic health records.,"Thygesen JH, Tomlinson C, Hollings S, Mizani MA, Handy A, Akbari A, Banerjee A, Cooper J, Lai AG, Li K, Mateen BA, Sattar N, Sofat R, Torralbo A, Wu H, Wood A, Sterne JAC, Pagel C, Whiteley WN, Sudlow C, Hemingway H, Denaxas S, Longitudinal Health and Wellbeing COVID-19 National Core Study and the CVD-COVID-UK/COVID-IMPACT Consortium.",,The Lancet. Digital health,2022,2022-06-09,Y,,,,"<h4>Background</h4>Updatable estimates of COVID-19 onset, progression, and trajectories underpin pandemic mitigation efforts. To identify and characterise disease trajectories, we aimed to define and validate ten COVID-19 phenotypes from nationwide linked electronic health records (EHR) using an extensible framework.<h4>Methods</h4>In this cohort study, we used eight linked National Health Service (NHS) datasets for people in England alive on Jan 23, 2020. Data on COVID-19 testing, vaccination, primary and secondary care records, and death registrations were collected until Nov 30, 2021. We defined ten COVID-19 phenotypes reflecting clinically relevant stages of disease severity and encompassing five categories: positive SARS-CoV-2 test, primary care diagnosis, hospital admission, ventilation modality (four phenotypes), and death (three phenotypes). We constructed patient trajectories illustrating transition frequency and duration between phenotypes. Analyses were stratified by pandemic waves and vaccination status.<h4>Findings</h4>Among 57 032 174 individuals included in the cohort, 13 990 423 COVID-19 events were identified in 7 244 925 individuals, equating to an infection rate of 12·7% during the study period. Of 7 244 925 individuals, 460 737 (6·4%) were admitted to hospital and 158 020 (2·2%) died. Of 460 737 individuals who were admitted to hospital, 48 847 (10·6%) were admitted to the intensive care unit (ICU), 69 090 (15·0%) received non-invasive ventilation, and 25 928 (5·6%) received invasive ventilation. Among 384 135 patients who were admitted to hospital but did not require ventilation, mortality was higher in wave 1 (23 485 [30·4%] of 77 202 patients) than wave 2 (44 220 [23·1%] of 191 528 patients), but remained unchanged for patients admitted to the ICU. Mortality was highest among patients who received ventilatory support outside of the ICU in wave 1 (2569 [50·7%] of 5063 patients). 15 486 (9·8%) of 158 020 COVID-19-related deaths occurred within 28 days of the first COVID-19 event without a COVID-19 diagnoses on the death certificate. 10 884 (6·9%) of 158 020 deaths were identified exclusively from mortality data with no previous COVID-19 phenotype recorded. We observed longer patient trajectories in wave 2 than wave 1.<h4>Interpretation</h4>Our analyses illustrate the wide spectrum of disease trajectories as shown by differences in incidence, survival, and clinical pathways. We have provided a modular analytical framework that can be used to monitor the impact of the pandemic and generate evidence of clinical and policy relevance using multiple EHR sources.<h4>Funding</h4>British Heart Foundation Data Science Centre, led by Health Data Research UK.",,pdf:http://www.thelancet.com/article/S2589750022000917/pdf; doi:https://doi.org/10.1016/S2589-7500(22)00091-7; html:https://europepmc.org/articles/PMC9179175; pdf:https://europepmc.org/articles/PMC9179175?pdf=render
 35110546,https://doi.org/10.1038/s41467-022-28248-1,"A population-based cohort study of obesity, ethnicity and COVID-19 mortality in 12.6 million adults in England.","Yates T, Summerfield A, Razieh C, Banerjee A, Chudasama Y, Davies MJ, Gillies C, Islam N, Lawson C, Mirkes E, Zaccardi F, Khunti K, Nafilyan V.",,Nature communications,2022,2022-02-02,Y,,,,"Obesity and ethnicity are known risk factors for COVID-19 outcomes, but their combination has not been extensively examined. We investigate the association between body mass index (BMI) and COVID-19 mortality across different ethnic groups using linked national Census, electronic health records and mortality data for adults in England from the start of pandemic (January 2020) to December 2020. There were 30,067 (0.27%), 1,208 (0.29%), 1,831 (0.29%), 845 (0.18%) COVID-19 deaths in white, Black, South Asian and other ethnic minority groups, respectively. Here we show that BMI was more strongly associated with COVID-19 mortality in ethnic minority groups, resulting in an ethnic risk of COVID-19 mortality that was dependant on BMI. The estimated risk of COVID-19 mortality at a BMI of 40 kg/m<sup>2</sup> in white ethnicities was equivalent to the risk observed at a BMI of 30.1 kg/m<sup>2</sup>, 27.0 kg/m<sup>2</sup>, and 32.2 kg/m<sup>2</sup> in Black, South Asian and other ethnic minority groups, respectively.",,pdf:https://www.nature.com/articles/s41467-022-28248-1.pdf; doi:https://doi.org/10.1038/s41467-022-28248-1; html:https://europepmc.org/articles/PMC8810846; pdf:https://europepmc.org/articles/PMC8810846?pdf=render
+35690576,https://doi.org/10.1016/s2589-7500(22)00091-7,COVID-19 trajectories among 57 million adults in England: a cohort study using electronic health records.,"Thygesen JH, Tomlinson C, Hollings S, Mizani MA, Handy A, Akbari A, Banerjee A, Cooper J, Lai AG, Li K, Mateen BA, Sattar N, Sofat R, Torralbo A, Wu H, Wood A, Sterne JAC, Pagel C, Whiteley WN, Sudlow C, Hemingway H, Denaxas S, Longitudinal Health and Wellbeing COVID-19 National Core Study and the CVD-COVID-UK/COVID-IMPACT Consortium.",,The Lancet. Digital health,2022,2022-06-09,Y,,,,"<h4>Background</h4>Updatable estimates of COVID-19 onset, progression, and trajectories underpin pandemic mitigation efforts. To identify and characterise disease trajectories, we aimed to define and validate ten COVID-19 phenotypes from nationwide linked electronic health records (EHR) using an extensible framework.<h4>Methods</h4>In this cohort study, we used eight linked National Health Service (NHS) datasets for people in England alive on Jan 23, 2020. Data on COVID-19 testing, vaccination, primary and secondary care records, and death registrations were collected until Nov 30, 2021. We defined ten COVID-19 phenotypes reflecting clinically relevant stages of disease severity and encompassing five categories: positive SARS-CoV-2 test, primary care diagnosis, hospital admission, ventilation modality (four phenotypes), and death (three phenotypes). We constructed patient trajectories illustrating transition frequency and duration between phenotypes. Analyses were stratified by pandemic waves and vaccination status.<h4>Findings</h4>Among 57 032 174 individuals included in the cohort, 13 990 423 COVID-19 events were identified in 7 244 925 individuals, equating to an infection rate of 12·7% during the study period. Of 7 244 925 individuals, 460 737 (6·4%) were admitted to hospital and 158 020 (2·2%) died. Of 460 737 individuals who were admitted to hospital, 48 847 (10·6%) were admitted to the intensive care unit (ICU), 69 090 (15·0%) received non-invasive ventilation, and 25 928 (5·6%) received invasive ventilation. Among 384 135 patients who were admitted to hospital but did not require ventilation, mortality was higher in wave 1 (23 485 [30·4%] of 77 202 patients) than wave 2 (44 220 [23·1%] of 191 528 patients), but remained unchanged for patients admitted to the ICU. Mortality was highest among patients who received ventilatory support outside of the ICU in wave 1 (2569 [50·7%] of 5063 patients). 15 486 (9·8%) of 158 020 COVID-19-related deaths occurred within 28 days of the first COVID-19 event without a COVID-19 diagnoses on the death certificate. 10 884 (6·9%) of 158 020 deaths were identified exclusively from mortality data with no previous COVID-19 phenotype recorded. We observed longer patient trajectories in wave 2 than wave 1.<h4>Interpretation</h4>Our analyses illustrate the wide spectrum of disease trajectories as shown by differences in incidence, survival, and clinical pathways. We have provided a modular analytical framework that can be used to monitor the impact of the pandemic and generate evidence of clinical and policy relevance using multiple EHR sources.<h4>Funding</h4>British Heart Foundation Data Science Centre, led by Health Data Research UK.",,pdf:http://www.thelancet.com/article/S2589750022000917/pdf; doi:https://doi.org/10.1016/S2589-7500(22)00091-7; html:https://europepmc.org/articles/PMC9179175; pdf:https://europepmc.org/articles/PMC9179175?pdf=render
 39143081,https://doi.org/10.1038/s41541-024-00934-9,COVID-19 and influenza vaccine uptake among pregnant women in national cohorts of England and Wales.,"Gu X, Agrawal U, Midgley W, Bedston S, Anand SN, Goudie R, Byford R, Joy M, Jamie G, Hoang U, Ordóñez-Mena JM, Robertson C, Hobbs FDR, Akbari A, Sheikh A, de Lusignan S.",,NPJ vaccines,2024,2024-08-14,Y,,,,"Vaccines against COVID-19 and influenza can reduce the adverse outcomes caused by infections during pregnancy, but vaccine uptake among pregnant women has been suboptimal. We examined the COVID-19 and influenza vaccine uptake and disparities in pregnant women during the COVID-19 pandemic to inform vaccination interventions. We used data from the Oxford-Royal College of General Practitioners Research and Surveillance Centre database in England and the Secure Anonymised Information Linkage Databank in Wales. The uptake of at least one dose of vaccine was 40.2% for COVID-19 and 41.8% for influenza among eligible pregnant women. We observed disparities in COVID-19 and influenza vaccine uptake, with socioeconomically deprived and ethnic minority groups showing lower vaccination rates. The suboptimal uptake of COVID-19 and influenza vaccines, especially in those from socioeconomically deprived backgrounds and Black, mixed or other ethnic groups, underscores the necessity for interventions to reduce vaccine hesitancy and enhance acceptance in pregnant women.",,doi:https://doi.org/10.1038/s41541-024-00934-9; doi:https://doi.org/10.1038/s41541-024-00934-9; html:https://europepmc.org/articles/PMC11324884; pdf:https://europepmc.org/articles/PMC11324884?pdf=render
 34994801,https://doi.org/10.1093/pubmed/fdab400,COVID-19 vaccination uptake amongst ethnic minority communities in England: a linked study exploring the drivers of differential vaccination rates.,"Gaughan CH, Razieh C, Khunti K, Banerjee A, Chudasama YV, Davies MJ, Dolby T, Gillies CL, Lawson C, Mirkes EM, Morgan J, Tingay K, Zaccardi F, Yates T, Nafilyan V.",,"Journal of public health (Oxford, England)",2023,2023-03-01,Y,Vaccination; Cultural; Ethnicity; Social; Sociodemographic Factors; Demographic; Covid-19,,,"<h4>Background</h4>Despite generally high coronavirus disease 2019 (COVID-19) vaccination rates in the UK, vaccination hesitancy and lower take-up rates have been reported in certain ethnic minority communities.<h4>Methods</h4>We used vaccination data from the National Immunisation Management System (NIMS) linked to the 2011 Census and individual health records for subjects aged ≥40 years (n = 24 094 186). We estimated age-standardized vaccination rates, stratified by ethnic group and key sociodemographic characteristics, such as religious affiliation, deprivation, educational attainment, geography, living conditions, country of birth, language skills and health status. To understand the association of ethnicity with lower vaccination rates, we conducted a logistic regression model adjusting for differences in geographic, sociodemographic and health characteristics. ResultsAll ethnic groups had lower age-standardized rates of vaccination compared with the white British population, whose vaccination rate of at least one dose was 94% (95% CI: 94%-94%). Black communities had the lowest rates, with 75% (74-75%) of black African and 66% (66-67%) of black Caribbean individuals having received at least one dose. The drivers of these lower rates were partly explained by accounting for sociodemographic differences. However, modelled estimates showed significant differences remained for all minority ethnic groups, compared with white British individuals.<h4>Conclusions</h4>Lower COVID-19 vaccination rates are consistently observed amongst all ethnic minorities.",,pdf:https://academic.oup.com/jpubhealth/article-pdf/45/1/e65/49527132/fdab400.pdf; doi:https://doi.org/10.1093/pubmed/fdab400; html:https://europepmc.org/articles/PMC8755382; pdf:https://europepmc.org/articles/PMC8755382?pdf=render
 36825398,https://doi.org/10.1097/mcp.0000000000000948,Effectiveness and safety of coronavirus disease 2019 vaccines.,"Shi T, Robertson C, Sheikh A.",,Current opinion in pulmonary medicine,2023,2023-02-24,Y,,,,"<h4>Purpose of review</h4>To review and summarise recent evidence on the effectiveness of coronavirus disease 2019 (COVID-19) vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and COVID-19 hospitalisation and death in adults as well as in specific population groups, namely pregnant women, and children and adolescents. We also sought to summarise evidence on vaccine safety in relation to cardiovascular and neurological complications. In order to do so, we drew primarily on evidence from two our own data platforms and supplement these with insights from related large population-based studies and systematic reviews.<h4>Recent findings</h4>All studies showed high vaccine effectiveness against confirmed SARS-CoV-2 infection and in particular against COVID-19 hospitalisation and death. However, vaccine effectiveness against symptomatic COVID-19 infection waned over time. These studies also found that booster vaccines would be needed to maintain high vaccine effectiveness against severe COVID-19 outcomes. Rare cardiovascular and neurological complications have been reported in association with COVID-19 vaccines.<h4>Summary</h4>The findings from this paper support current recommendations that vaccination remains the safest way for adults, pregnant women, children and adolescents to be protected against COVID-19. There is a need to continue to monitor the effectiveness and safety of COVID-19 vaccines as these continue to be deployed in the evolving pandemic.",,html:https://journals.lww.com/co-pulmonarymedicine/Fulltext/9900/Effectiveness_and_safety_of_coronavirus_disease.53.aspx; doi:https://doi.org/10.1097/MCP.0000000000000948; html:https://europepmc.org/articles/PMC10090353; pdf:https://europepmc.org/articles/PMC10090353?pdf=render
@@ -78,11 +78,11 @@ PMC11201135,https://doi.org/,Exploring Prior Antibiotic Exposure Characteristics
 34148733,https://doi.org/10.1016/j.bja.2021.05.018,Mortality after surgery with SARS-CoV-2 infection in England: a population-wide epidemiological study.,"Abbott TEF, Fowler AJ, Dobbs TD, Gibson J, Shahid T, Dias P, Akbari A, Whitaker IS, Pearse RM.",,British journal of anaesthesia,2021,2021-06-11,Y,Surgery; Anaesthesia; epidemiology; Public Policy; Covid-19,,,"<h4>Background</h4>The COVID-19 pandemic has heavily impacted elective and emergency surgery around the world. We aimed to confirm the incidence of perioperative severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and associated mortality after surgery.<h4>Methods</h4>Analysis of routine electronic health record data from NHS hospitals in England. We extracted data from Hospital Episode Statistics in England describing adult patients undergoing surgery between January 1, 2020 and February 28, 2021. The exposure was SARS-CoV-2 infection defined by International Classification of Diseases (ICD)-10 codes. The primary outcome measure was 90 day in-hospital mortality. Data were analysed using multivariable logistic regression adjusted for age, sex, Charlson Comorbidity Index, Index of Multiple Deprivation, presence of cancer, surgical procedure type and admission acuity. Results are presented as n (%) and odds ratios (OR) with 95% confidence intervals (CI).<h4>Results</h4>We identified 2 666 978 patients undergoing surgery of whom 28 777 (1.1%) had SARS-CoV-2 infection. In total, 26 364 (1.0%) patients died in hospital. SARS-CoV-2 infection was associated with a much greater risk of death (SARS-CoV-2: 6153/28 777 [21.4%] vs no SARS-CoV-2: 20 211/2 638 201 [0.8%]; OR=5.7 [95% CI, 5.5-5.9]; P<0.001). Amongst patients undergoing elective surgery, 2412/1 857 586 (0.1%) had SARS-CoV-2, of whom 172/2412 (7.1%) died, compared with 1414/1 857 586 (0.1%) patients without SARS-CoV-2 (OR=25.8 [95% CI, 21.7-30.9]; P<0.001). Amongst patients undergoing emergency surgery, 22 918/582 292 (3.9%) patients had SARS-CoV-2, of whom 5752/22 918 (25.1%) died, compared with 18 060/559 374 (3.4%) patients without SARS-CoV-2 (OR=5.5 [95% CI, 5.3-5.7]; P<0.001).<h4>Conclusions</h4>The low incidence of SARS-CoV-2 infection in NHS surgical pathways suggests current infection prevention and control policies are highly effective. However, the high mortality amongst patients with SARS-CoV-2 suggests these precautions cannot be safely relaxed.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8192173; doi:https://doi.org/10.1016/j.bja.2021.05.018; html:https://europepmc.org/articles/PMC8192173; pdf:https://europepmc.org/articles/PMC8192173?pdf=render
 38106559,https://doi.org/10.1016/j.eclinm.2023.102251,Long-term symptom profiles after COVID-19 <i>vs</i> other acute respiratory infections: an analysis of data from the COVIDENCE UK study.,"Vivaldi G, Pfeffer PE, Talaei M, Basera TJ, Shaheen SO, Martineau AR.",,EClinicalMedicine,2023,2023-10-06,Y,Acute respiratory infections; Sars-cov-2; Long Covid; Post-acute Sequelae,,,"<h4>Background</h4>Long COVID is a well recognised, if heterogeneous, entity. Acute respiratory infections (ARIs) due to other pathogens may cause long-term symptoms, but few studies compare post-acute sequelae between SARS-CoV-2 and other ARIs. We aimed to compare symptom profiles between people with previous SARS-CoV-2 infection, people with previous non-COVID-19 ARIs, and contemporaneous controls, and to identify clusters of long-term symptoms.<h4>Methods</h4>COVIDENCE UK is a prospective, population-based UK study of ARIs in adults. We analysed data for 16 potential long COVID symptoms and health-related quality of life (HRQoL), reported between January 21 and February 15, 2021, by participants unvaccinated against SARS-CoV-2. We classified participants as having previous SARS-CoV-2 infection or previous non-COVID-19 ARI (≥4 weeks prior) or no reported ARI. We compared symptoms by infection status using logistic and fractional regression, and identified symptom clusters using latent class analysis (LCA). This study is registered with ClinicalTrials.gov, NCT04330599.<h4>Findings</h4>We included 10,171 participants (1311 [12.9%] with SARS-CoV-2 infection, 472 [4.6%] with non-COVID-19 ARI). Both types of infection were associated with increased prevalence/severity of most symptoms and decreased HRQoL compared with no infection. Participants with SARS-CoV-2 infection had increased odds of problems with taste/smell (odds ratio 19.74, 95% CI 10.53-37.00) and lightheadedness or dizziness (1.74, 1.18-2.56) compared with participants with non-COVID-19 ARIs. Separate LCA models identified three symptom severity groups for each infection type. In the most severe groups (representing 22% of participants for both SARS-CoV-2 and non-COVID-19 ARI), SARS-CoV-2 infection presented with a higher probability of problems with taste/smell (probability 0.41 <i>vs</i> 0.04), hair loss (0.25 <i>vs</i> 0.16), unusual sweating (0.38 <i>vs</i> 0.25), unusual racing of the heart (0.43 <i>vs</i> 0.33), and memory problems (0.70 <i>vs</i> 0.55) than non-COVID-19 ARI.<h4>Interpretation</h4>Both SARS-CoV-2 and non-COVID-19 ARIs are associated with a wide range of symptoms more than 4 weeks after the acute infection. Research on post-acute sequelae of ARIs should extend from SARS-CoV-2 to include other pathogens.<h4>Funding</h4>Barts Charity.",,doi:https://doi.org/10.1016/j.eclinm.2023.102251; html:https://europepmc.org/articles/PMC10721552; pdf:https://europepmc.org/articles/PMC10721552?pdf=render
 36576189,https://doi.org/10.1136/bmjopen-2022-064320,Assessing medication use patterns in patients hospitalised with COVID-19: a retrospective study.,"Mueller T, Kurdi A, Hall E, Bullard I, Wapshott J, Goodfellow A, Platt N, Proud E, McTaggart S, Bennie M, Sheikh A, EAVE II Collaboration.",,BMJ open,2022,2022-12-05,Y,Therapeutics; clinical pharmacology; Health Informatics; Covid-19,,,"<h4>Objective</h4>To describe patterns of medication use-that is, dexamethasone; remdesivir; and tocilizumab-in the management of patients hospitalised with COVID-19.<h4>Design and setting</h4>Retrospective observational study, using routinely collected, linked electronic data from clinical practice in Scotland. Data on drug exposure in secondary care has been obtained from the Hospital Electronic Prescribing and Medicines Administration System.<h4>Participants</h4>Patients being treated with the drugs of interest and hospitalised for COVID-19 between 1 March 2020 and 10 November 2021.<h4>Outcomes</h4>Identification of patients subject to the treatments of interest; summary of patients' baseline characteristics; description of medication use patterns and treatment episodes. Analyses were descriptive in nature.<h4>Results</h4>Overall, 4063 patients matching the inclusion criteria were identified in Scotland, with a median (IQR) age of 64 years (52-76). Among all patients, 81.4% (n=3307) and 17.8% (n=725) were treated with one or two medicines, respectively; dexamethasone monotherapy accounted for the majority (n=3094, 76.2%) followed by dexamethasone in combination with tocilizumab (n=530, 13.0%). Treatment patterns were variable over time but roughly followed the waves of COVID-19 infections; however, the different drugs were used to varying degrees during the study period.The median (IQR) treatment duration differed by medicine: dexamethasone 5 days (2-9); remdesivir 5 days (2-5); and tocilizumab 1 day (1-1). The overall median (IQR) length of hospital stay among all patients included in the study cohort was 9 days (5-17); 24.7% of patients died in hospital.<h4>Conclusion</h4>The use of adjuvant medicines in patients hospitalised with COVID-19 appears in line with evolving evidence and changing treatment guidelines. In-hospital electronic prescribing systems are a valuable source of information, providing detailed patient-level data on in-hospital drug use.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/12/e064320.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-064320; html:https://europepmc.org/articles/PMC9723413; pdf:https://europepmc.org/articles/PMC9723413?pdf=render
+36658423,https://doi.org/10.1038/s41591-022-02158-7,The impact of the COVID-19 pandemic on cardiovascular disease prevention and management.,"Dale CE, Takhar R, Carragher R, Katsoulis M, Torabi F, Duffield S, Kent S, Mueller T, Kurdi A, Le Anh TN, McTaggart S, Abbasizanjani H, Hollings S, Scourfield A, Lyons RA, Griffiths R, Lyons J, Davies G, Harris D, Handy A, Mizani MA, Tomlinson C, Thygesen JH, Ashworth M, Denaxas S, Banerjee A, Sterne JAC, Brown P, Bullard I, Priedon R, Mamas MA, Slee A, Lorgelly P, Pirmohamed M, Khunti K, Morris AD, Sudlow C, Akbari A, Bennie M, Sattar N, Sofat R, CVD-COVID-UK Consortium.",,Nature medicine,2023,2023-01-19,N,,,,"How the Coronavirus Disease 2019 (COVID-19) pandemic has affected prevention and management of cardiovascular disease (CVD) is not fully understood. In this study, we used medication data as a proxy for CVD management using routinely collected, de-identified, individual-level data comprising 1.32 billion records of community-dispensed CVD medications from England, Scotland and Wales between April 2018 and July 2021. Here we describe monthly counts of prevalent and incident medications dispensed, as well as percentage changes compared to the previous year, for several CVD-related indications, focusing on hypertension, hypercholesterolemia and diabetes. We observed a decline in the dispensing of antihypertensive medications between March 2020 and July 2021, with 491,306 fewer individuals initiating treatment than expected. This decline was predicted to result in 13,662 additional CVD events, including 2,281 cases of myocardial infarction and 3,474 cases of stroke, should individuals remain untreated over their lifecourse. Incident use of lipid-lowering medications decreased by 16,744 patients per month during the first half of 2021 as compared to 2019. By contrast, incident use of medications to treat type 2 diabetes mellitus, other than insulin, increased by approximately 623 patients per month for the same time period. In light of these results, methods to identify and treat individuals who have missed treatment for CVD risk factors and remain undiagnosed are urgently required to avoid large numbers of excess future CVD events, an indirect impact of the COVID-19 pandemic.",,pdf:https://www.nature.com/articles/s41591-022-02158-7.pdf; doi:https://doi.org/10.1038/s41591-022-02158-7
 36543718,https://doi.org/10.1016/j.ebiom.2022.104402,SARS-CoV-2-specific nasal IgA wanes 9 months after hospitalisation with COVID-19 and is not induced by subsequent vaccination.,"Liew F, Talwar S, Cross A, Willett BJ, Scott S, Logan N, Siggins MK, Swieboda D, Sidhu JK, Efstathiou C, Moore SC, Davis C, Mohamed N, Nunag J, King C, Thompson AAR, Rowland-Jones SL, Docherty AB, Chalmers JD, Ho LP, Horsley A, Raman B, Poinasamy K, Marks M, Kon OM, Howard L, Wootton DG, Dunachie S, Quint JK, Evans RA, Wain LV, Fontanella S, de Silva TI, Ho A, Harrison E, Baillie JK, Semple MG, Brightling C, Thwaites RS, Turtle L, Openshaw PJM, ISARIC4C Investigators, PHOSP-COVID collaborative group.",,EBioMedicine,2023,2022-12-19,Y,Vaccination; Mucosal immunity; Convalescent; Covid-19; Sars-cov-2 Immunity; Sars-cov-2 Variants; Nasal Antibody,,,"<h4>Background</h4>Most studies of immunity to SARS-CoV-2 focus on circulating antibody, giving limited insights into mucosal defences that prevent viral replication and onward transmission. We studied nasal and plasma antibody responses one year after hospitalisation for COVID-19, including a period when SARS-CoV-2 vaccination was introduced.<h4>Methods</h4>In this follow up study, plasma and nasosorption samples were prospectively collected from 446 adults hospitalised for COVID-19 between February 2020 and March 2021 via the ISARIC4C and PHOSP-COVID consortia. IgA and IgG responses to NP and S of ancestral SARS-CoV-2, Delta and Omicron (BA.1) variants were measured by electrochemiluminescence and compared with plasma neutralisation data.<h4>Findings</h4>Strong and consistent nasal anti-NP and anti-S IgA responses were demonstrated, which remained elevated for nine months (p < 0.0001). Nasal and plasma anti-S IgG remained elevated for at least 12 months (p < 0.0001) with plasma neutralising titres that were raised against all variants compared to controls (p < 0.0001). Of 323 with complete data, 307 were vaccinated between 6 and 12 months; coinciding with rises in nasal and plasma IgA and IgG anti-S titres for all SARS-CoV-2 variants, although the change in nasal IgA was minimal (1.46-fold change after 10 months, p = 0.011) and the median remained below the positive threshold determined by pre-pandemic controls. Samples 12 months after admission showed no association between nasal IgA and plasma IgG anti-S responses (R = 0.05, p = 0.18), indicating that nasal IgA responses are distinct from those in plasma and minimally boosted by vaccination.<h4>Interpretation</h4>The decline in nasal IgA responses 9 months after infection and minimal impact of subsequent vaccination may explain the lack of long-lasting nasal defence against reinfection and the limited effects of vaccination on transmission. These findings highlight the need to develop vaccines that enhance nasal immunity.<h4>Funding</h4>This study has been supported by ISARIC4C and PHOSP-COVID consortia. ISARIC4C is supported by grants from the National Institute for Health and Care Research and the Medical Research Council. Liverpool Experimental Cancer Medicine Centre provided infrastructure support for this research. The PHOSP-COVD study is jointly funded by UK Research and Innovation and National Institute of Health and Care Research. The funders were not involved in the study design, interpretation of data or the writing of this manuscript.",,pdf:http://bura.brunel.ac.uk/bitstream/2438/26835/1/FullText.pdf; doi:https://doi.org/10.1016/j.ebiom.2022.104402; html:https://europepmc.org/articles/PMC9762734; pdf:https://europepmc.org/articles/PMC9762734?pdf=render
 38162515,https://doi.org/10.1016/j.lanepe.2023.100816,"Risk of severe COVID-19 outcomes after autumn 2022 COVID-19 booster vaccinations: a pooled analysis of national prospective cohort studies involving 7.4 million adults in England, Northern Ireland, Scotland and Wales.","Bedston S, Almaghrabi F, Patterson L, Agrawal U, Woolford L, Anand SN, Joy M, Crawford A, Goudie R, Byford R, Abbasizanjani H, Smith D, Laidlaw L, Akbari A, Sullivan C, Bradley DT, Lyons RA, de Lusignan S, Hobbs FDR, Robertson C, Sheikh SA, Shi T.",,The Lancet regional health. Europe,2024,2023-12-12,Y,Vaccine; Hospital Admission; Booster Dose; Vaccine Breakthrough; Covid-19,,,"<h4>Background</h4>UK COVID-19 vaccination policy has evolved to offering COVID-19 booster doses to individuals at increased risk of severe Illness from COVID-19. Building on our analyses of vaccine effectiveness of first, second and initial booster doses, we aimed to identify individuals at increased risk of severe outcomes (i.e., COVID-19 related hospitalisation or death) post the autumn 2022 booster dose.<h4>Methods</h4>We undertook a national population-based cohort analysis across all four UK nations through linked primary care, vaccination, hospitalisation and mortality data. We included individuals who received autumn 2022 booster doses of BNT162b2 (Comirnaty) or mRNA-1273 (Spikevax) during the period September 1, 2022 to December 31, 2022 to investigate the risk of severe COVID-19 outcomes. Cox proportional hazard models were used to estimate adjusted hazard ratios (aHR) and 95% confidence intervals (CIs) for the association between demographic and clinical factors and severe COVID-19 outcomes after the autumn booster dose. Analyses were adjusted for age, sex, body mass index (BMI), deprivation, urban/rural areas and comorbidities. Stratified analyses were conducted by vaccine type. We then conducted a fixed-effect meta-analysis to combine results across the four UK nations.<h4>Findings</h4>Between September 1, 2022 and December 31, 2022, 7,451,890 individuals ≥18 years received an autumn booster dose. 3500 had severe COVID-19 outcomes (2.9 events per 1000 person-years). Being male (male vs female, aHR 1.41 (1.32-1.51)), older adults (≥80 years vs 18-49 years; 10.43 (8.06-13.50)), underweight (BMI <18.5 vs BMI 25.0-29.9; 2.94 (2.51-3.44)), those with comorbidities (≥5 comorbidities vs none; 9.45 (8.15-10.96)) had a higher risk of COVID-19 hospitalisation or death after the autumn booster dose. Those with a larger household size (≥11 people within household vs 2 people; 1.56 (1.23-1.98)) and from more deprived areas (most deprived vs least deprived quintile; 1.35 (1.21-1.51)) had modestly higher risks. We also observed at least a two-fold increase in risk for those with various chronic neurological conditions, including Down's syndrome, immunodeficiency, chronic kidney disease, cancer, chronic respiratory disease, or cardiovascular disease.<h4>Interpretation</h4>Males, older individuals, underweight individuals, those with an increasing number of comorbidities, from a larger household or more deprived areas, and those with specific underlying health conditions remained at increased risk of COVID-19 hospitalisation and death after the autumn 2022 vaccine booster dose. There is now a need to focus on these risk groups for investigating immunogenicity and efficacy of further booster doses or therapeutics.<h4>Funding</h4>National Core Studies-Immunity, UK Research and Innovation (Medical Research Council and Economic and Social Research Council), Health Data Research UK, the Scottish Government, and the University of Edinburgh.",,doi:https://doi.org/10.1016/j.lanepe.2023.100816; html:https://europepmc.org/articles/PMC10757260; pdf:https://europepmc.org/articles/PMC10757260?pdf=render
 38023948,https://doi.org/10.18332/ejm/171802,A qualitative study exploring healthcare workers' lived experiences of the impacts of COVID-19 policies and guidelines on maternal and reproductive healthcare services in the United Kingdom.,"Chaloner J, Qureshi I, Gogoi M, Ekezie WC, Al-Oraibi A, Wobi F, Agbonmwandolor JO, Nellums LB, Pareek M.",,European journal of midwifery,2023,2023-11-08,Y,Healthcare Workers; Vaccine Hesitancy; Redeployment; Infection Controls; Covid-19; Policies And Guidelines,,,"<h4>Introduction</h4>During the COVID-19 pandemic, pregnant women were regarded as vulnerable to poor health outcomes if infected with the SARS-CoV-2 (COVID-19) virus. To protect the United Kingdom's (UK) National Health Service (NHS) and pregnant patients, strict infection control policies and regulations were implemented. This study aimed to understand the impact of the COVID-19 policies and guidelines on maternal and reproductive health services during the pandemic from the experiences of healthcare workers (HCWs) caring for these patients.<h4>Methods</h4>This qualitative study involved HCWs from the United Kingdom Research study into Ethnicity and COVID-19 outcomes in Healthcare workers (UK-REACH) project. Semi-structured interviews and focus groups were conducted online or by telephone with 44 diverse HCWs. Transcripts were thematically analyzed following Braun and Clarke's principles of qualitative analysis.<h4>Results</h4>Three key themes were identified during analysis. First, infection control policies impacted appointment availability, resulting in many cancellations and delays to treatment. Telemedicine was also used extensively to reduce risks from face-to-face consultations, disadvantaging patients from minoritized ethnicities. Secondly, staff shortages and redeployments reduced availability of consultations, appointments, and sonography scans. Finally, staff and patients reported challenges accessing timely, reliable and accurate information and guidance.<h4>Conclusions</h4>COVID-19 demonstrated how a global health crisis can impact maternal and reproductive health services, leading to reduced service quality and surgical delays due to staff redeployment policies. Our findings underscore the implications of policy and future health crises preparedness. This includes tailored infection control policies, addressing elective surgery backlogs early and improved dissemination of relevant vaccine information.",,pdf:https://www.europeanjournalofmidwifery.eu/pdf-171802-96110?filename=A qualitative study.pdf; doi:https://doi.org/10.18332/ejm/171802; html:https://europepmc.org/articles/PMC10630987; pdf:https://europepmc.org/articles/PMC10630987?pdf=render
 35239462,https://doi.org/10.1080/21645515.2022.2031774,COVID-19 vaccine uptake and effectiveness in adults aged 50 years and older in Wales UK: a 1.2m population data-linkage cohort approach.,"Perry M, Gravenor MB, Cottrell S, Bedston S, Roberts R, Williams C, Salmon J, Lyons J, Akbari A, Lyons RA, Torabi F, Griffiths LJ.",,Human vaccines & immunotherapeutics,2022,2022-03-03,Y,Immunization; Adult; Vaccination; Effectiveness; Wales; Sars-cov-2; Covid-19 Vaccines,,,"Vaccination programs against COVID-19 vary globally with estimates of vaccine effectiveness (VE) affected by vaccine type, schedule, strain, outcome, and recipient characteristics. This study assessed VE of BNT162b2 and ChAdOx1 vaccines against PCR positive SARS-CoV-2 infection, hospital admission, and death among adults aged 50 years and older in Wales, UK during the period 7 December 2020 to 18 July 2021, when Alpha, followed by Delta, were the predominant variants. We used individual-level linked routinely collected data within the Secure Anonymized Information Linkage (SAIL) Databank. Data were available for 1,262,689 adults aged 50 years and over; coverage of one dose of any COVID-19 vaccine in this population was 92.6%, with coverage of two doses 90.4%. VE against PCR positive infection at 28-days or more post first dose of any COVID-19 vaccine was 16.0% (95%CI 9.6-22.0), and 42.0% (95%CI 36.5-47.1) seven or more days after a second dose. VE against hospital admission was higher at 72.9% (95%CI 63.6-79.8) 28 days or more post vaccination with one dose of any vaccine type, and 84.9% (95%CI 78.2-89.5) at 7 or more days post two doses. VE for one dose against death was estimated to be 80.9% (95%CI 72.1-86.9). VE against PCR positive infection and hospital admission was higher for BNT162b2 compared to ChAdOx1. In conclusion, vaccine uptake has been high among adults in Wales and VE estimates are encouraging, with two doses providing considerable protection against severe outcomes. Continued roll-out of the vaccination programme within Wales, and globally, is crucial in our fight against COVID-19.",,pdf:https://www.tandfonline.com/doi/pdf/10.1080/21645515.2022.2031774?needAccess=true; doi:https://doi.org/10.1080/21645515.2022.2031774; html:https://europepmc.org/articles/PMC8993055; pdf:https://europepmc.org/articles/PMC8993055?pdf=render
-36658423,https://doi.org/10.1038/s41591-022-02158-7,The impact of the COVID-19 pandemic on cardiovascular disease prevention and management.,"Dale CE, Takhar R, Carragher R, Katsoulis M, Torabi F, Duffield S, Kent S, Mueller T, Kurdi A, Le Anh TN, McTaggart S, Abbasizanjani H, Hollings S, Scourfield A, Lyons RA, Griffiths R, Lyons J, Davies G, Harris D, Handy A, Mizani MA, Tomlinson C, Thygesen JH, Ashworth M, Denaxas S, Banerjee A, Sterne JAC, Brown P, Bullard I, Priedon R, Mamas MA, Slee A, Lorgelly P, Pirmohamed M, Khunti K, Morris AD, Sudlow C, Akbari A, Bennie M, Sattar N, Sofat R, CVD-COVID-UK Consortium.",,Nature medicine,2023,2023-01-19,N,,,,"How the Coronavirus Disease 2019 (COVID-19) pandemic has affected prevention and management of cardiovascular disease (CVD) is not fully understood. In this study, we used medication data as a proxy for CVD management using routinely collected, de-identified, individual-level data comprising 1.32 billion records of community-dispensed CVD medications from England, Scotland and Wales between April 2018 and July 2021. Here we describe monthly counts of prevalent and incident medications dispensed, as well as percentage changes compared to the previous year, for several CVD-related indications, focusing on hypertension, hypercholesterolemia and diabetes. We observed a decline in the dispensing of antihypertensive medications between March 2020 and July 2021, with 491,306 fewer individuals initiating treatment than expected. This decline was predicted to result in 13,662 additional CVD events, including 2,281 cases of myocardial infarction and 3,474 cases of stroke, should individuals remain untreated over their lifecourse. Incident use of lipid-lowering medications decreased by 16,744 patients per month during the first half of 2021 as compared to 2019. By contrast, incident use of medications to treat type 2 diabetes mellitus, other than insulin, increased by approximately 623 patients per month for the same time period. In light of these results, methods to identify and treat individuals who have missed treatment for CVD risk factors and remain undiagnosed are urgently required to avoid large numbers of excess future CVD events, an indirect impact of the COVID-19 pandemic.",,pdf:https://www.nature.com/articles/s41591-022-02158-7.pdf; doi:https://doi.org/10.1038/s41591-022-02158-7
 38589621,https://doi.org/10.1038/s41590-024-01778-0,Large-scale phenotyping of patients with long COVID post-hospitalization reveals mechanistic subtypes of disease.,"Liew F, Efstathiou C, Fontanella S, Richardson M, Saunders R, Swieboda D, Sidhu JK, Ascough S, Moore SC, Mohamed N, Nunag J, King C, Leavy OC, Elneima O, McAuley HJC, Shikotra A, Singapuri A, Sereno M, Harris VC, Houchen-Wolloff L, Greening NJ, Lone NI, Thorpe M, Thompson AAR, Rowland-Jones SL, Docherty AB, Chalmers JD, Ho LP, Horsley A, Raman B, Poinasamy K, Marks M, Kon OM, Howard LS, Wootton DG, Quint JK, de Silva TI, Ho A, Chiu C, Harrison EM, Greenhalf W, Baillie JK, Semple MG, Turtle L, Evans RA, Wain LV, Brightling C, Thwaites RS, Openshaw PJM, PHOSP-COVID collaborative group, ISARIC investigators.",,Nature immunology,2024,2024-04-08,Y,,,,"One in ten severe acute respiratory syndrome coronavirus 2 infections result in prolonged symptoms termed long coronavirus disease (COVID), yet disease phenotypes and mechanisms are poorly understood<sup>1</sup>. Here we profiled 368 plasma proteins in 657 participants ≥3 months following hospitalization. Of these, 426 had at least one long COVID symptom and 233 had fully recovered. Elevated markers of myeloid inflammation and complement activation were associated with long COVID. IL-1R2, MATN2 and COLEC12 were associated with cardiorespiratory symptoms, fatigue and anxiety/depression; MATN2, CSF3 and C1QA were elevated in gastrointestinal symptoms and C1QA was elevated in cognitive impairment. Additional markers of alterations in nerve tissue repair (SPON-1 and NFASC) were elevated in those with cognitive impairment and SCG3, suggestive of brain-gut axis disturbance, was elevated in gastrointestinal symptoms. Severe acute respiratory syndrome coronavirus 2-specific immunoglobulin G (IgG) was persistently elevated in some individuals with long COVID, but virus was not detected in sputum. Analysis of inflammatory markers in nasal fluids showed no association with symptoms. Our study aimed to understand inflammatory processes that underlie long COVID and was not designed for biomarker discovery. Our findings suggest that specific inflammatory pathways related to tissue damage are implicated in subtypes of long COVID, which might be targeted in future therapeutic trials.",,doi:https://doi.org/10.1038/s41590-024-01778-0; html:https://europepmc.org/articles/PMC11003868; pdf:https://europepmc.org/articles/PMC11003868?pdf=render
 39374974,https://doi.org/10.1136/bmj-2024-080528,Non-pharmaceutical interventions: evaluating challenges and priorities for future health shocks.,"Majeed A, Quint JK, Bhatt S, Davies F, Islam N.",,BMJ (Clinical research ed.),2024,2024-10-07,Y,,,,,,doi:https://doi.org/10.1136/bmj-2024-080528; html:https://europepmc.org/articles/PMC11450877
 36216011,https://doi.org/10.1016/s2213-2600(22)00360-5,Pregnancy outcomes after SARS-CoV-2 infection in periods dominated by delta and omicron variants in Scotland: a population-based cohort study.,"Stock SJ, Moore E, Calvert C, Carruthers J, Denny C, Donaghy J, Hillman S, Hopcroft LEM, Hopkins L, Goulding A, Lindsay L, McLaughlin T, Taylor B, Auyeung B, Katikireddi SV, McCowan C, Ritchie LD, Rudan I, Simpson CR, Robertson C, Sheikh A, Wood R.",,The Lancet. Respiratory medicine,2022,2022-10-07,Y,,,,"<h4>Background</h4>Evidence suggests that the SARS-CoV-2 omicron (B.1·1.529) is associated with lower risks of adverse outcomes than the delta (B.1.617.2) variant among the general population. However, little is known about outcomes after omicron infection in pregnancy. We aimed to assess and compare short-term pregnancy outcomes after SARS-CoV-2 delta and omicron infection in pregnancy.<h4>Methods</h4>We did a national population-based cohort study of women who had SARS-CoV-2 infection in pregnancy between May 17, 2021, and Jan 31, 2022. The primary maternal outcome was admission to critical care within 21 days of infection or death within 28 days of date of infection. Pregnancy outcomes were preterm birth and stillbirth within 28 days of infection. Neonatal outcomes were death within 28 days of birth, and low Apgar score (<7 of 10, for babies born at term) or neonatal SARS-CoV-2 infection in births occurring within 28 days of maternal infection. We used periods when variants were dominant in the general Scottish population, based on 50% or more of cases being S-gene positive (delta variant, from May 17 to Dec 14, 2021) or S-gene negative (omicron variant, from Dec 15, 2021, to Jan 31, 2022) as surrogates for variant infections. Analyses used logistic regression, adjusting for maternal age, deprivation quintile, ethnicity, weeks of gestation, and vaccination status. Sensitivity analyses included restricting the analysis to those with first confirmed SARS-CoV-2 infection and using periods when delta or omicron had 90% or more predominance.<h4>Findings</h4>Between May 17, 2021, and Jan 31, 2022, there were 9923 SARS-CoV-2 infections in 9823 pregnancies, in 9817 women in Scotland. Compared with infections in the delta-dominant period, SARS-CoV-2 infections in pregnancy in the omicron-dominant period were associated with lower maternal critical care admission risk (0·3% [13 of 4968] vs 1·8% [89 of 4955]; adjusted odds ratio 0·25, 95% CI 0·14-0·44) and lower preterm birth within 28 days of infection (1·8% [37 of 2048] vs 4·2% [98 of 2338]; 0·57, 95% CI 0·38-0·87). There were no maternal deaths within 28 days of infection. Estimates of low Apgar scores were imprecise due to low numbers (5 [1·2%] of 423 with omicron vs 11 [2·1%] of 528 with delta, adjusted odds ratio 0·72, 0·23-2·32). There were fewer stillbirths in the omicron-dominant period than in the delta-dominant period (4·3 [2 of 462] per 1000 births vs 20·3 [13 of 639] per 1000) and no neonatal deaths during the omicron-dominant period (0 [0 of 460] per 1000 births vs 6·3 [4 of 626] per 1000 births), thus numbers were too small to support adjusted analyses. Rates of neonatal infection were low in births within 28 days of maternal SARS-CoV-2 infection, with 11 cases of neonatal SARS-CoV-2 in the delta-dominant period, and 1 case in the omicron-dominant period. Of the 15 stillbirths, 12 occurred in women who had not received two or more doses of COVID-19 vaccination at the time of SARS-CoV-2 infection in pregnancy. All 12 cases of neonatal SARS-CoV-2 infection occurred in women who had not received two or more doses of vaccine at the time of maternal infection. Findings in sensitivity analyses were similar to those in the main analyses.<h4>Interpretation</h4>Pregnant women infected with SARS-CoV-2 were substantially less likely to have a preterm birth or maternal critical care admission during the omicron-dominant period than during the delta-dominant period.<h4>Funding</h4>Wellcome Trust, Tommy's charity, Medical Research Council, UK Research and Innovation, Health Data Research UK, National Core Studies-Data and Connectivity, Public Health Scotland, Scottish Government Health and Social Care, Scottish Government Chief Scientist Office, National Research Scotland.",,doi:https://doi.org/10.1016/s2213-2600(22)00360-5; doi:https://doi.org/10.1016/S2213-2600(22)00360-5; html:https://europepmc.org/articles/PMC9708088; pdf:https://europepmc.org/articles/PMC9708088?pdf=render
@@ -92,29 +92,29 @@ PMC11201135,https://doi.org/,Exploring Prior Antibiotic Exposure Characteristics
 34697502,https://doi.org/10.1038/s41591-021-01556-7,Neurological complications after first dose of COVID-19 vaccines and SARS-CoV-2 infection.,"Patone M, Handunnetthi L, Saatci D, Pan J, Katikireddi SV, Razvi S, Hunt D, Mei XW, Dixon S, Zaccardi F, Khunti K, Watkinson P, Coupland CAC, Doidge J, Harrison DA, Ravanan R, Sheikh A, Robertson C, Hippisley-Cox J.",,Nature medicine,2021,2021-10-25,Y,,,,"Emerging reports of rare neurological complications associated with COVID-19 infection and vaccinations are leading to regulatory, clinical and public health concerns. We undertook a self-controlled case series study to investigate hospital admissions from neurological complications in the 28 days after a first dose of ChAdOx1nCoV-19 (n = 20,417,752) or BNT162b2 (n = 12,134,782), and after a SARS-CoV-2-positive test (n = 2,005,280). There was an increased risk of Guillain-Barré syndrome (incidence rate ratio (IRR), 2.90; 95% confidence interval (CI): 2.15-3.92 at 15-21 days after vaccination) and Bell's palsy (IRR, 1.29; 95% CI: 1.08-1.56 at 15-21 days) with ChAdOx1nCoV-19. There was an increased risk of hemorrhagic stroke (IRR, 1.38; 95% CI: 1.12-1.71 at 15-21 days) with BNT162b2. An independent Scottish cohort provided further support for the association between ChAdOx1nCoV and Guillain-Barré syndrome (IRR, 2.32; 95% CI: 1.08-5.02 at 1-28 days). There was a substantially higher risk of all neurological outcomes in the 28 days after a positive SARS-CoV-2 test including Guillain-Barré syndrome (IRR, 5.25; 95% CI: 3.00-9.18). Overall, we estimated 38 excess cases of Guillain-Barré syndrome per 10 million people receiving ChAdOx1nCoV-19 and 145 excess cases per 10 million people after a positive SARS-CoV-2 test. In summary, although we find an increased risk of neurological complications in those who received COVID-19 vaccines, the risk of these complications is greater following a positive SARS-CoV-2 test.",,pdf:https://www.nature.com/articles/s41591-021-01556-7.pdf; doi:https://doi.org/10.1038/s41591-021-01556-7; html:https://europepmc.org/articles/PMC8629105; pdf:https://europepmc.org/articles/PMC8629105?pdf=render
 33413610,https://doi.org/10.1186/s13073-020-00822-6,An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets.,"Ward D, Higgins M, Phelan JE, Hibberd ML, Campino S, Clark TG.",,Genome medicine,2021,2021-01-07,Y,Mutation; Epitopes; Surveillance; cross-reactivity; Immuno-informatics; Sars-cov-2; Covid; Human-coronavirus,,,"During COVID-19, diagnostic serological tools and vaccines have been developed. To inform control activities in a post-vaccine surveillance setting, we have developed an online ""immuno-analytics"" resource that combines epitope, sequence, protein and SARS-CoV-2 mutation analysis. SARS-CoV-2 spike and nucleocapsid proteins are both vaccine and serological diagnostic targets. Using the tool, the nucleocapsid protein appears to be a sub-optimal target for use in serological platforms. Spike D614G (and nsp12 L314P) mutations were most frequent (> 86%), whilst spike A222V/L18F have recently increased. Also, Orf3a proteins may be a suitable target for serology. The tool can accessed from: http://genomics.lshtm.ac.uk/immuno (online); https://github.com/dan-ward-bio/COVID-immunoanalytics (source code).",,pdf:https://genomemedicine.biomedcentral.com/counter/pdf/10.1186/s13073-020-00822-6; doi:https://doi.org/10.1186/s13073-020-00822-6; html:https://europepmc.org/articles/PMC7790334; pdf:https://europepmc.org/articles/PMC7790334?pdf=render
 38850276,https://doi.org/10.1093/ije/dyae068,Risk of cardiovascular events following COVID-19 in people with and without pre-existing chronic respiratory disease.,"Whittaker H, Kallis C, Bolton T, Wood A, Walker S, Sheikh A, Brownrigg A, Akbari A, Sterniczuk K, Quint JK, CVD-COVID-UK/COVID-IMPACT Consortium.",,International journal of epidemiology,2024,2024-04-01,N,Asthma; Cardiovascular disease; COPD; Covid-19,,,"<h4>Background</h4>COVID-19 is associated with cardiovascular outcomes in the general population, but it is unknown whether people with chronic respiratory disease (CRD) have a higher risk of cardiovascular events post-COVID-19 compared with the general population and, if so, what respiratory-related factors may modify this risk in these people.<h4>Methods</h4>Primary and secondary care data from the National Health Service England were used to define a population of adults in England with COVID-19 (index date) between 1 January 2020 and 30 November 2021. Adjusted Cox proportional hazard regression was used to quantify the association between CRD, asthma-related factors, chronic obstructive pulmonary disease (COPD)-related factors, and risk of cardiovascular events. Asthma-specific factors included baseline asthma control, exacerbations, and inhaled corticosteroid (ICS) dose. COPD-specific risk factors included baseline ICS and exacerbations. Secondary objectives quantified the impact of COVID-19 hospitalisation and vaccine dose on cardiovascular outcomes.<h4>Results</h4>Of 3 670 455 people, those with CRD had a higher risk of cardiovascular events [adjusted hazard ratio (HRadj), 1.08; 95% confidence interval (CI) 1.06-1.11], heart failure (HRadj, 1.17; 95% CI, 1.12-1.22), angina (HRadj, 1.13; 95% CI, 1.06-1.20) and pulmonary emboli (HRadj, 1.24; 95% CI, 1.15-1.33) compared with people without CRD. In people with asthma or COPD, baseline exacerbations were associated with a higher risk of cardiovascular outcomes (HRadj, 1.36; 95% CI, 1.27-1.00 and HRadj, 1.35; 95% CI, 1.24-1.46, respectively). Regardless of CRD, the risk of cardiovascular events was lower with increasing COVID-19 vaccine dose.<h4>Conclusions</h4>Higher risk of cardiovascular events post-COVID-19 might be explained by the underlying severity of the CRD, and COVID-19 vaccines were beneficial to both people with and those without CRD with regards to cardiovascualr events.",,doi:https://doi.org/10.1093/ije/dyae068; doi:https://doi.org/10.1093/ije/dyae068
-34514500,https://doi.org/10.1093/infdis/jiab459,The Impact of Cocirculating Pathogens on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/Coronavirus Disease 2019 Surveillance: How Concurrent Epidemics May Introduce Bias and Decrease the Observed SARS-CoV-2 Percentage Positivity.,"Kovacevic A, Eggo RM, Baguelin M, Domenech de Cellès M, Opatowski L.",,The Journal of infectious diseases,2022,2022-01-01,Y,Mathematical Modeling; Multiplex Testing; Sars-cov-2; Covid-19 Surveillance; Cocirculating Respiratory Viruses,,,"<h4>Background</h4>Circulation of seasonal non-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) respiratory viruses with syndromic overlap during the coronavirus disease 2019 (COVID-19) pandemic may alter the quality of COVID-19 surveillance, with possible consequences for real-time analysis and delay in implementation of control measures.<h4>Methods</h4>Using a multipathogen susceptible-exposed-infectious-recovered (SEIR) transmission model formalizing cocirculation of SARS-CoV-2 and another respiratory virus, we assessed how an outbreak of secondary virus may affect 2 COVID-19 surveillance indicators: testing demand and positivity. Using simulation, we assessed to what extent the use of multiplex polymerase chain reaction tests on a subsample of symptomatic individuals can help correct the observed SARS-CoV-2 percentage positivity and improve surveillance quality.<h4>Results</h4>We find that a non-SARS-CoV-2 epidemic strongly increases SARS-CoV-2 daily testing demand and artificially reduces the observed SARS-CoV-2 percentage positivity for the duration of the outbreak. We estimate that performing 1 multiplex test for every 1000 COVID-19 tests on symptomatic individuals could be sufficient to maintain surveillance of other respiratory viruses in the population and correct the observed SARS-CoV-2 percentage positivity.<h4>Conclusions</h4>This study showed that cocirculating respiratory viruses can distort SARS-CoV-2 surveillance. Correction of the positivity rate can be achieved by using multiplex polymerase chain reaction tests, and a low number of samples is sufficient to avoid bias in SARS-CoV-2 surveillance.",,pdf:https://academic.oup.com/jid/article-pdf/225/2/199/42224165/jiab459.pdf; doi:https://doi.org/10.1093/infdis/jiab459; html:https://europepmc.org/articles/PMC8763960; pdf:https://europepmc.org/articles/PMC8763960?pdf=render
 35038629,https://doi.org/10.1016/j.puhe.2021.12.010,Investigating the association between COVID-19 vaccination and care home outbreak frequency and duration.,"Bradley DT, Murphy S, McWilliams P, Arnold S, Lavery S, Murphy J, de Lusignan S, Hobbs R, Tsang RSM, Akbari A, Torabi F, Beggs J, Chuter A, Shi T, Vasileiou E, Robertson C, Sheikh A, Reid H, O'Reilly D.",,Public health,2022,2021-12-18,Y,Vaccination; outbreak; Care Homes; Covid-19; Sars-cov-2,,,"<h4>Objectives</h4>At the end of 2020, many countries commenced a vaccination programme against SARS-CoV-2. Public health authorities aim to prevent and interrupt outbreaks of infectious disease in social care settings. We aimed to investigate the association between the introduction of the vaccination programme and the frequency and duration of COVID-19 outbreaks in Northern Ireland (NI).<h4>Study design</h4>We undertook an ecological study using routinely available national data.<h4>Methods</h4>We used Poisson regression to measure the relationship between the number of RT-PCR confirmed COVID-19 outbreaks in care homes, and as a measure of community COVID-19 prevalence, the Office for National Statistics COVID-19 Infection Survey estimated the number of people testing positive for COVID-19 in NI. We estimated the change in this relationship and estimated the expected number of care home outbreaks in the absence of the vaccination programme. A Cox proportional hazards model estimated the hazard ratio of a confirmed COVID-19 care home outbreak closure.<h4>Results</h4>Care home outbreaks reduced by two-thirds compared to expected following the introduction of the vaccination programme, from a projected 1625 COVID-19 outbreaks (95% prediction interval 1553-1694) between 7 December 2020 and 28 October 2021 to an observed 501. We estimated an adjusted hazard ratio of 2.53 of the outbreak closure assuming a 21-day lag for immunity.<h4>Conclusions</h4>These findings describe the association of the vaccination with a reduction in outbreak frequency and duration across NI care homes. This indicates probable reduced harm and disruption from COVID-19 in social care settings following vaccination. Future research using individual level data from care home residents will be needed to investigate the effectiveness of the vaccines and the duration of their effects.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa59048/Download/59048__22075__e4bbc8a7cad6434abac5984eb2422e06.pdf; doi:https://doi.org/10.1016/j.puhe.2021.12.010; html:https://europepmc.org/articles/PMC8683272; pdf:https://europepmc.org/articles/PMC8683272?pdf=render
+34514500,https://doi.org/10.1093/infdis/jiab459,The Impact of Cocirculating Pathogens on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/Coronavirus Disease 2019 Surveillance: How Concurrent Epidemics May Introduce Bias and Decrease the Observed SARS-CoV-2 Percentage Positivity.,"Kovacevic A, Eggo RM, Baguelin M, Domenech de Cellès M, Opatowski L.",,The Journal of infectious diseases,2022,2022-01-01,Y,Mathematical Modeling; Multiplex Testing; Sars-cov-2; Covid-19 Surveillance; Cocirculating Respiratory Viruses,,,"<h4>Background</h4>Circulation of seasonal non-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) respiratory viruses with syndromic overlap during the coronavirus disease 2019 (COVID-19) pandemic may alter the quality of COVID-19 surveillance, with possible consequences for real-time analysis and delay in implementation of control measures.<h4>Methods</h4>Using a multipathogen susceptible-exposed-infectious-recovered (SEIR) transmission model formalizing cocirculation of SARS-CoV-2 and another respiratory virus, we assessed how an outbreak of secondary virus may affect 2 COVID-19 surveillance indicators: testing demand and positivity. Using simulation, we assessed to what extent the use of multiplex polymerase chain reaction tests on a subsample of symptomatic individuals can help correct the observed SARS-CoV-2 percentage positivity and improve surveillance quality.<h4>Results</h4>We find that a non-SARS-CoV-2 epidemic strongly increases SARS-CoV-2 daily testing demand and artificially reduces the observed SARS-CoV-2 percentage positivity for the duration of the outbreak. We estimate that performing 1 multiplex test for every 1000 COVID-19 tests on symptomatic individuals could be sufficient to maintain surveillance of other respiratory viruses in the population and correct the observed SARS-CoV-2 percentage positivity.<h4>Conclusions</h4>This study showed that cocirculating respiratory viruses can distort SARS-CoV-2 surveillance. Correction of the positivity rate can be achieved by using multiplex polymerase chain reaction tests, and a low number of samples is sufficient to avoid bias in SARS-CoV-2 surveillance.",,pdf:https://academic.oup.com/jid/article-pdf/225/2/199/42224165/jiab459.pdf; doi:https://doi.org/10.1093/infdis/jiab459; html:https://europepmc.org/articles/PMC8763960; pdf:https://europepmc.org/articles/PMC8763960?pdf=render
 38531661,https://doi.org/10.1111/bcp.16030,The impact of COVID-19 on medication reviews in English primary care. An OpenSAFELY-TPP analysis of 20 million adult electronic health records.,"OpenSAFELY Collaborative, Wood C, Speed V, Fisher L, Curtis HJ, Schaffer AL, Walker AJ, Croker R, Brown AD, Cunningham C, Hulme WJ, Andrews CD, Butler-Cole BFC, Evans D, Inglesby P, Dillingham I, Bacon SCJ, Davy S, Ward T, Hickman G, Bridges L, O'Dwyer T, Maude S, Smith RM, Mehrkar A, Bates C, Cockburn J, Parry J, Hester F, Harper S, Goldacre B, MacKenna B.",,British journal of clinical pharmacology,2024,2024-03-26,Y,General Practice; Prescribing; Primary Care,,,"<h4>Aims</h4>The COVID-19 pandemic caused significant disruption to routine activity in primary care. Medication reviews are an important primary care activity ensuring safety and appropriateness of prescribing. A disruption could have significant negative implications for patient care. Using routinely collected data, our aim was first to describe codes used to record medication review activity and then to report the impact of COVID-19 on the rates of medication reviews.<h4>Methods</h4>With the approval of NHS England, we conducted a cohort study of 20 million adult patient records in general practice, in-situ using the OpenSAFELY platform. For each month, between April 2019 and March 2022, we report the percentage of patients with a medication review coded monthly and in the previous 12 months with breakdowns by regional, clinical and demographic subgroups and those prescribed high-risk medications.<h4>Results</h4>In April 2019, 32.3% of patients had a medication review coded in the previous 12 months. During the first COVID-19 lockdown, monthly activity decreased (-21.1% April 2020), but the 12-month rate was not substantially impacted (-10.5% March 2021). The rate of structured medication review in the last 12 months reached 2.9% by March 2022, with higher percentages in high-risk groups (care home residents 34.1%, age 90+ years 13.1%, high-risk medications 10.2%). The most used medication review code was Medication review done 314530002 (59.5%).<h4>Conclusions</h4>There was a substantial reduction in the monthly rate of medication reviews during the pandemic but rates recovered by the end of the study period. Structured medication reviews were prioritized for high-risk patients.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/bcp.16030; doi:https://doi.org/10.1111/bcp.16030; html:https://europepmc.org/articles/PMC7616229; pdf:https://europepmc.org/articles/PMC7616229?pdf=render
-38942167,https://doi.org/10.1016/j.ijid.2024.107155,"Vaccinations, cardiovascular drugs, hospitalization, and mortality in COVID-19 and Long COVID.","Dashtban A, Mizani MA, Pasea L, Tomlinson C, Mu Y, Islam N, Rafferty S, Warren-Gash C, Denaxas S, Horstmanshof K, Kontopantelis E, Petersen S, Sudlow C, Khunti K, Banerjee A, CVD-COVID-UK/COVID-IMPACT Consortium.",,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2024,2024-06-26,N,Vaccination; Cardiovascular disease; Covid-19; Long Covid,,,"<h4>Objective</h4>To identify highest-risk subgroups for COVID-19 and Long COVID(LC), particularly in contexts of influenza and cardiovascular disease(CVD).<h4>Methods</h4>Using national, linked electronic health records for England (NHS England Secure Data Environment via CVD-COVID-UK/COVID-IMPACT Consortium), we studied individuals (of all ages) with COVID-19 and LC (2020-2023). We compared all-cause hospitalization and mortality by prior CVD, high CV risk, vaccination status (COVID-19/influenza), and CVD drugs, investigating impact of vaccination and CVD prevention using population preventable fractions.<h4>Results</h4>Hospitalization and mortality were 15.3% and 2.0% among 17,373,850 individuals with COVID-19 (LC rate 1.3%), and 16.8% and 1.4% among 301,115 with LC. Adjusted risk of mortality and hospitalization were reduced with COVID-19 vaccination ≥ 2 doses(COVID-19:HR 0.36 and 0.69; LC:0.44 and 0.90). With influenza vaccination, mortality was reduced, but not hospitalization (COVID-19:0.86 and 1.01, and LC:0.72 and 1.05). Mortality and hospitalization were reduced by CVD prevention in those with CVD, e.g., anticoagulants- COVID:19:0.69 and 0.92; LC:0.59 and 0.88; lipid lowering- COVID-19:0.69 and 0.86; LC:0.68 and 0.90. COVID-19 vaccination averted 245044 of 321383 and 7586 of 8738 preventable deaths after COVID-19 and LC, respectively.<h4>Interpretation</h4>Prior CVD and high CV risk are associated with increased hospitalization and mortality in COVID-19 and LC. Targeted COVID-19 vaccination and CVD prevention are priority interventions.<h4>Funding</h4>NIHR. HDR UK.",,doi:https://doi.org/10.1016/j.ijid.2024.107155
 36874571,https://doi.org/10.12688/wellcomeopenres.17981.1,Settings for non-household transmission of SARS-CoV-2 during the second lockdown in England and Wales - analysis of the Virus Watch household community cohort study.,"Hoskins S, Beale S, Nguyen V, Fragaszy E, Navaratnam AMD, Smith C, French C, Kovar J, Byrne T, Fong WLE, Geismar C, Patel P, Yavlinksy A, Johnson AM, Aldridge RW, Hayward A, Virus Watch Collaborative.",,Wellcome open research,2022,2022-08-03,Y,Transmission; Activities; Pandemic; Work; Public Transport; Shopping; Lockdown; Covid-19; Sars-cov-2,,,"<b>Background</b>: ""Lockdowns"" to control serious respiratory virus pandemics were widely used during the coronavirus disease 2019 (COVID-19) pandemic.  However, there is limited information to understand the settings in which most transmission occurs during lockdowns, to support refinement of similar policies for future pandemics.  <b>Methods</b>: Among Virus Watch household cohort participants we identified those infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outside the household.  Using survey activity data, we undertook multivariable logistic regressions assessing the contribution of activities on non-household infection risk.  We calculated adjusted population attributable fractions (APAF) to estimate which activity accounted for the greatest proportion of non-household infections during the pandemic's second wave. <b>Results</b>: Among 10,858 adults, 18% of cases were likely due to household transmission.  Among 10,475 participants (household-acquired cases excluded), including 874 non-household-acquired infections, infection was associated with: leaving home for work or education (AOR 1.20 (1.02 - 1.42), APAF 6.9%); public transport (more than once per week AOR 1.82 (1.49 - 2.23), public transport APAF 12.42%); and shopping (more than once per week AOR 1.69 (1.29 - 2.21), shopping APAF 34.56%).  Other non-household activities were rare and not significantly associated with infection. <b>Conclusions:</b> During lockdown, going to work and using public or shared transport independently increased infection risk, however only a minority did these activities.  Most participants visited shops, accounting for one-third of non-household transmission.  Transmission in restricted hospitality and leisure settings was minimal suggesting these restrictions were effective.   If future respiratory infection pandemics emerge these findings highlight the value of working from home, using forms of transport that minimise exposure to others, minimising exposure to shops and restricting non-essential activities.",,doi:https://doi.org/10.12688/wellcomeopenres.17981.1; html:https://europepmc.org/articles/PMC9975411; pdf:https://europepmc.org/articles/PMC9975411?pdf=render
+38942167,https://doi.org/10.1016/j.ijid.2024.107155,"Vaccinations, cardiovascular drugs, hospitalization, and mortality in COVID-19 and Long COVID.","Dashtban A, Mizani MA, Pasea L, Tomlinson C, Mu Y, Islam N, Rafferty S, Warren-Gash C, Denaxas S, Horstmanshof K, Kontopantelis E, Petersen S, Sudlow C, Khunti K, Banerjee A, CVD-COVID-UK/COVID-IMPACT Consortium.",,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2024,2024-06-26,N,Vaccination; Cardiovascular disease; Covid-19; Long Covid,,,"<h4>Objective</h4>To identify highest-risk subgroups for COVID-19 and Long COVID(LC), particularly in contexts of influenza and cardiovascular disease(CVD).<h4>Methods</h4>Using national, linked electronic health records for England (NHS England Secure Data Environment via CVD-COVID-UK/COVID-IMPACT Consortium), we studied individuals (of all ages) with COVID-19 and LC (2020-2023). We compared all-cause hospitalization and mortality by prior CVD, high CV risk, vaccination status (COVID-19/influenza), and CVD drugs, investigating impact of vaccination and CVD prevention using population preventable fractions.<h4>Results</h4>Hospitalization and mortality were 15.3% and 2.0% among 17,373,850 individuals with COVID-19 (LC rate 1.3%), and 16.8% and 1.4% among 301,115 with LC. Adjusted risk of mortality and hospitalization were reduced with COVID-19 vaccination ≥ 2 doses(COVID-19:HR 0.36 and 0.69; LC:0.44 and 0.90). With influenza vaccination, mortality was reduced, but not hospitalization (COVID-19:0.86 and 1.01, and LC:0.72 and 1.05). Mortality and hospitalization were reduced by CVD prevention in those with CVD, e.g., anticoagulants- COVID:19:0.69 and 0.92; LC:0.59 and 0.88; lipid lowering- COVID-19:0.69 and 0.86; LC:0.68 and 0.90. COVID-19 vaccination averted 245044 of 321383 and 7586 of 8738 preventable deaths after COVID-19 and LC, respectively.<h4>Interpretation</h4>Prior CVD and high CV risk are associated with increased hospitalization and mortality in COVID-19 and LC. Targeted COVID-19 vaccination and CVD prevention are priority interventions.<h4>Funding</h4>NIHR. HDR UK.",,doi:https://doi.org/10.1016/j.ijid.2024.107155
 38977844,https://doi.org/10.1038/s43856-024-00506-x,Complex patterns of multimorbidity associated with severe COVID-19 and long COVID.,"Pietzner M, Denaxas S, Yasmeen S, Ulmer MA, Nakanishi T, Arnold M, Kastenmüller G, Hemingway H, Langenberg C.",,Communications medicine,2024,2024-07-08,Y,,,,"<h4>Background</h4>Early evidence that patients with (multiple) pre-existing diseases are at highest risk for severe COVID-19 has been instrumental in the pandemic to allocate critical care resources and later vaccination schemes. However, systematic studies exploring the breadth of medical diagnoses are scarce but may help to understand severe COVID-19 among patients at supposedly low risk.<h4>Methods</h4>We systematically harmonized >12 million primary care and hospitalisation health records from ~500,000 UK Biobank participants into 1448 collated disease terms to systematically identify diseases predisposing to severe COVID-19 (requiring hospitalisation or death) and its post-acute sequalae, Long COVID.<h4>Results</h4>Here we identify 679 diseases associated with an increased risk for severe COVID-19 (n = 672) and/or Long COVID (n = 72) that span almost all clinical specialties and are strongly enriched in clusters of cardio-respiratory and endocrine-renal diseases. For 57 diseases, we establish consistent evidence to predispose to severe COVID-19 based on survival and genetic susceptibility analyses. This includes a possible role of symptoms of malaise and fatigue as a so far largely overlooked risk factor for severe COVID-19. We finally observe partially opposing risk estimates at known risk loci for severe COVID-19 for etiologically related diseases, such as post-inflammatory pulmonary fibrosis or rheumatoid arthritis, possibly indicating a segregation of disease mechanisms.<h4>Conclusions</h4>Our results provide a unique reference that demonstrates how 1) complex co-occurrence of multiple - including non-fatal - conditions predispose to increased COVID-19 severity and 2) how incorporating the whole breadth of medical diagnosis can guide the interpretation of genetic risk loci.",,doi:https://doi.org/10.1038/s43856-024-00506-x; html:https://europepmc.org/articles/PMC11231221; pdf:https://europepmc.org/articles/PMC11231221?pdf=render
 33845766,https://doi.org/10.1186/s12879-021-05992-1,"Informing the public health response to COVID-19: a systematic review of risk factors for disease, severity, and mortality.","Flook M, Jackson C, Vasileiou E, Simpson CR, Muckian MD, Agrawal U, McCowan C, Jia Y, Murray JLK, Ritchie LD, Robertson C, Stock SJ, Wang X, Woolhouse MEJ, Sheikh A, Stagg HR.",,BMC infectious diseases,2021,2021-04-12,Y,Mortality; Review; Morbidity; Coronavirus; Systematic review; risk factors; Covid-19,,,"<h4>Background</h4>Severe Acute Respiratory Syndrome coronavirus-2 (SARS-CoV-2) has challenged public health agencies globally. In order to effectively target government responses, it is critical to identify the individuals most at risk of coronavirus disease-19 (COVID-19), developing severe clinical signs, and mortality. We undertook a systematic review of the literature to present the current status of scientific knowledge in these areas and describe the need for unified global approaches, moving forwards, as well as lessons learnt for future pandemics.<h4>Methods</h4>Medline, Embase and Global Health were searched to the end of April 2020, as well as the Web of Science. Search terms were specific to the SARS-CoV-2 virus and COVID-19. Comparative studies of risk factors from any setting, population group and in any language were included. Titles, abstracts and full texts were screened by two reviewers and extracted in duplicate into a standardised form. Data were extracted on risk factors for COVID-19 disease, severe disease, or death and were narratively and descriptively synthesised.<h4>Results</h4>One thousand two hundred and thirty-eight papers were identified post-deduplication. Thirty-three met our inclusion criteria, of which 26 were from China. Six assessed the risk of contracting the disease, 20 the risk of having severe disease and ten the risk of dying. Age, gender and co-morbidities were commonly assessed as risk factors. The weight of evidence showed increasing age to be associated with severe disease and mortality, and general comorbidities with mortality. Only seven studies presented multivariable analyses and power was generally limited. A wide range of definitions were used for disease severity.<h4>Conclusions</h4>The volume of literature generated in the short time since the appearance of SARS-CoV-2 has been considerable. Many studies have sought to document the risk factors for COVID-19 disease, disease severity and mortality; age was the only risk factor based on robust studies and with a consistent body of evidence. Mechanistic studies are required to understand why age is such an important risk factor. At the start of pandemics, large, standardised, studies that use multivariable analyses are urgently needed so that the populations most at risk can be rapidly protected.<h4>Registration</h4>This review was registered on PROSPERO as CRD42020177714 .",,pdf:https://bmcinfectdis.biomedcentral.com/counter/pdf/10.1186/s12879-021-05992-1; doi:https://doi.org/10.1186/s12879-021-05992-1; html:https://europepmc.org/articles/PMC8040367; pdf:https://europepmc.org/articles/PMC8040367?pdf=render
 35275994,https://doi.org/10.2337/dc21-1709,Admission Blood Glucose Level and Its Association With Cardiovascular and Renal Complications in Patients Hospitalized With COVID-19.,"Norris T, Razieh C, Yates T, Zaccardi F, Gillies CL, Chudasama YV, Rowlands A, Davies MJ, McCann GP, Banerjee A, Docherty AB, Openshaw PJM, Baillie JK, Semple MG, Lawson CA, Khunti K.",,Diabetes care,2022,2022-05-01,N,,,,"<h4>Objective</h4>To investigate the association between admission blood glucose levels and risk of in-hospital cardiovascular and renal complications.<h4>Research design and methods</h4>In this multicenter prospective study of 36,269 adults hospitalized with COVID-19 between 6 February 2020 and 16 March 2021 (N = 143,266), logistic regression models were used to explore associations between admission glucose level (mmol/L and mg/dL) and odds of in-hospital complications, including heart failure, arrhythmia, cardiac ischemia, cardiac arrest, coagulation complications, stroke, and renal injury. Nonlinearity was investigated using restricted cubic splines. Interaction models explored whether associations between glucose levels and complications were modified by clinically relevant factors.<h4>Results</h4>Cardiovascular and renal complications occurred in 10,421 (28.7%) patients; median admission glucose level was 6.7 mmol/L (interquartile range 5.8-8.7) (120.6 mg/dL [104.4-156.6]). While accounting for confounders, for all complications except cardiac ischemia and stroke, there was a nonlinear association between glucose and cardiovascular and renal complications. For example, odds of heart failure, arrhythmia, coagulation complications, and renal injury decreased to a nadir at 6.4 mmol/L (115 mg/dL), 4.9 mmol/L (88.2 mg/dL), 4.7 mmol/L (84.6 mg/dL), and 5.8 mmol/L (104.4 mg/dL), respectively, and increased thereafter until 26.0 mmol/L (468 mg/dL), 50.0 mmol/L (900 mg/dL), 8.5 mmol/L (153 mg/dL), and 32.4 mmol/L (583.2 mg/dL). Compared with 5 mmol/L (90 mg/dL), odds ratios at these glucose levels were 1.28 (95% CI 0.96, 1.69) for heart failure, 2.23 (1.03, 4.81) for arrhythmia, 1.59 (1.36, 1.86) for coagulation complications, and 2.42 (2.01, 2.92) for renal injury. For most complications, a modifying effect of age was observed, with higher odds of complications at higher glucose levels for patients age <69 years. Preexisting diabetes status had a similar modifying effect on odds of complications, but evidence was strongest for renal injury, cardiac ischemia, and any cardiovascular/renal complication.<h4>Conclusions</h4>Increased odds of cardiovascular or renal complications were observed for admission glucose levels indicative of both hypo- and hyperglycemia. Admission glucose could be used as a marker for risk stratification of high-risk patients. Further research should evaluate interventions to optimize admission glucose on improving COVID-19 outcomes.",,pdf:https://diabetesjournals.org/care/article-pdf/45/5/1132/678515/dc211709.pdf; doi:https://doi.org/10.2337/dc21-1709; html:https://europepmc.org/articles/PMC9174963; pdf:https://europepmc.org/articles/PMC9174963?pdf=render; doi:https://doi.org/10.2337/dc21-1709
 37311808,https://doi.org/10.1038/s41467-023-39193-y,"Natural history of long-COVID in a nationwide, population cohort study.","Hastie CE, Lowe DJ, McAuley A, Mills NL, Winter AJ, Black C, Scott JT, O'Donnell CA, Blane DN, Browne S, Ibbotson TR, Pell JP.",,Nature communications,2023,2023-06-13,Y,,,,"Previous studies on the natural history of long-COVID have been few and selective. Without comparison groups, disease progression cannot be differentiated from symptoms originating from other causes. The Long-COVID in Scotland Study (Long-CISS) is a Scotland-wide, general population cohort of adults who had laboratory-confirmed SARS-CoV-2 infection matched to PCR-negative adults. Serial, self-completed, online questionnaires collected information on pre-existing health conditions and current health six, 12 and 18 months after index test. Of those with previous symptomatic infection, 35% reported persistent incomplete/no recovery, 12% improvement and 12% deterioration. At six and 12 months, one or more symptom was reported by 71.5% and 70.7% respectively of those previously infected, compared with 53.5% and 56.5% of those never infected. Altered taste, smell and confusion improved over time compared to the never infected group and adjusted for confounders. Conversely, late onset dry and productive cough, and hearing problems were more likely following SARS-CoV-2 infection.",,pdf:https://www.nature.com/articles/s41467-023-39193-y.pdf; doi:https://doi.org/10.1038/s41467-023-39193-y; html:https://europepmc.org/articles/PMC10263377; pdf:https://europepmc.org/articles/PMC10263377?pdf=render
 37067859,https://doi.org/10.1136/bmjmed-2022-000245,Sex differences in cardiovascular complications and mortality in hospital patients with covid-19: registry based observational study.,"Hockham C, Linschoten M, Asselbergs FW, Ghossein C, Woodward M, Peters SAE, CAPACITY-COVID Collaborative Consortium .",,BMJ medicine,2023,2023-02-14,Y,epidemiology; Heart Failure; Cardiology; Covid-19,,,"<h4>Objective</h4>To assess whether the risk of cardiovascular complications of covid-19 differ between the sexes and to determine whether any sex differences in risk are reduced in individuals with pre-existing cardiovascular disease.<h4>Design</h4>Registry based observational study.<h4>Setting</h4>74 hospitals across 13 countries (eight European) participating in CAPACITY-COVID (Cardiac complicAtions in Patients With SARS Corona vIrus 2 regisTrY), from March 2020 to May 2021.<h4>Participants</h4>All adults (aged ≥18 years), predominantly European, admitted to hospital with highly suspected covid-19 disease or covid-19 disease confirmed by positive laboratory test results (n=11 167 patients).<h4>Main outcome measures</h4>Any cardiovascular complication during admission to hospital. Secondary outcomes were in-hospital mortality and individual cardiovascular complications with ≥20 events for each sex. Logistic regression was used to examine sex differences in the risk of cardiovascular outcomes, overall and grouped by pre-existing cardiovascular disease.<h4>Results</h4>Of 11 167 adults (median age 68 years, 40% female participants) included, 3423 (36% of whom were female participants) had pre-existing cardiovascular disease. In both sexes, the most common cardiovascular complications were supraventricular tachycardias (4% of female participants, 6% of male participants), pulmonary embolism (3% and 5%), and heart failure (decompensated or de novo) (2% in both sexes). After adjusting for age, ethnic group, pre-existing cardiovascular disease, and risk factors for cardiovascular disease, female individuals were less likely than male individuals to have a cardiovascular complication (odds ratio 0.72, 95% confidence interval 0.64 to 0.80) or die (0.65, 0.59 to 0.72). Differences between the sexes were not modified by pre-existing cardiovascular disease; for the primary outcome, the female-to-male ratio of the odds ratio in those without, compared with those with, pre-existing cardiovascular disease was 0.84 (0.67 to 1.07).<h4>Conclusions</h4>In patients admitted to hospital for covid-19, female participants were less likely than male participants to have a cardiovascular complication. The differences between the sexes could not be attributed to the lower prevalence of pre-existing cardiovascular disease in female individuals. The reasons for this advantage in female individuals requires further research.",,pdf:https://bmjmedicine.bmj.com/content/bmjmed/2/1/e000245.full.pdf; doi:https://doi.org/10.1136/bmjmed-2022-000245; html:https://europepmc.org/articles/PMC10083523; pdf:https://europepmc.org/articles/PMC10083523?pdf=render
 35380004,https://doi.org/10.1042/bcj20220105,Development of a colorimetric assay for the detection of SARS-CoV-2 3CLpro activity.,"Garland GD, Harvey RF, Mulroney TE, Monti M, Fuller S, Haigh R, Gerber PP, Barer MR, Matheson NJ, Willis AE.",,The Biochemical journal,2022,2022-04-01,Y,Coronavirus; Assay Development; Covid 19,,,"Diagnostic testing continues to be an integral component of the strategy to contain the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) global pandemic, the causative agent of Coronavirus Disease 2019 (COVID-19). The SARS-CoV-2 genome encodes the 3C-like protease (3CLpro) which is essential for coronavirus replication. This study adapts an in vitro colorimetric gold nanoparticle (AuNP) based protease assay to specifically detect the activity of SARS-CoV-2 3CLpro as a purified recombinant protein and as a cellular protein exogenously expressed in HEK293T human cells. We also demonstrate that the specific sensitivity of the assay for SARS-CoV-2 3CLpro can be improved by use of an optimised peptide substrate and through hybrid dimerisation with inactive 3CLpro mutant monomers. These findings highlight the potential for further development of the AuNP protease assay to detect SARS-CoV-2 3CLpro activity as a novel, accessible and cost-effective diagnostic test for SARS-CoV-2 infection at the point-of-care. Importantly, this versatile assay could also be easily adapted to detect specific protease activity associated with other viruses or diseases conditions.",,pdf:https://portlandpress.com/biochemj/article-pdf/479/8/901/932114/bcj-2022-0105.pdf; doi:https://doi.org/10.1042/BCJ20220105; html:https://europepmc.org/articles/PMC9162461; pdf:https://europepmc.org/articles/PMC9162461?pdf=render
-36609574,https://doi.org/10.1038/s41467-022-35771-8,A population-based matched cohort study of major congenital anomalies following COVID-19 vaccination and SARS-CoV-2 infection.,"Calvert C, Carruthers J, Denny C, Donaghy J, Hopcroft LEM, Hopkins L, Goulding A, Lindsay L, McLaughlin T, Moore E, Taylor B, Loane M, Dolk H, Morris J, Auyeung B, Bhaskaran K, Gibbons CL, Katikireddi SV, O'Leary M, McAllister D, Shi T, Simpson CR, Robertson C, Sheikh A, Stock SJ, Wood R.",,Nature communications,2023,2023-01-06,Y,,,,"Evidence on associations between COVID-19 vaccination or SARS-CoV-2 infection and the risk of congenital anomalies is limited. Here we report a national, population-based, matched cohort study using linked electronic health records from Scotland (May 2020-April 2022) to estimate the association between COVID-19 vaccination and, separately, SARS-CoV-2 infection between six weeks pre-conception and 19 weeks and six days gestation and the risk of [1] any major congenital anomaly and [2] any non-genetic major congenital anomaly. Mothers vaccinated in this pregnancy exposure period mostly received an mRNA vaccine (73.7% Pfizer-BioNTech BNT162b2 and 7.9% Moderna mRNA-1273). Of the 6731 babies whose mothers were vaccinated in the pregnancy exposure period, 153 had any anomaly and 120 had a non-genetic anomaly. Primary analyses find no association between any vaccination and any anomaly (adjusted Odds Ratio [aOR] = 1.01, 95% Confidence Interval [CI] = 0.83-1.24) or non-genetic anomalies (aOR = 1.00, 95% CI = 0.81-1.22). Primary analyses also find no association between SARS-CoV-2 infection and any anomaly (aOR = 1.02, 95% CI = 0.66-1.60) or non-genetic anomalies (aOR = 0.94, 95% CI = 0.57-1.54). Findings are robust to sensitivity analyses. These data provide reassurance on the safety of vaccination, in particular mRNA vaccines, just before or in early pregnancy.",,pdf:https://www.nature.com/articles/s41467-022-35771-8.pdf; doi:https://doi.org/10.1038/s41467-022-35771-8; html:https://europepmc.org/articles/PMC9821346; pdf:https://europepmc.org/articles/PMC9821346?pdf=render
 37729117,https://doi.org/10.1371/journal.pdig.0000309,Training and testing of a gradient boosted machine learning model to predict adverse outcome in patients presenting to emergency departments with suspected covid-19 infection in a middle-income setting.,"Fuller GW, Hasan M, Hodkinson P, McAlpine D, Goodacre S, Bath PA, Sbaffi L, Omer Y, Wallis L, Marincowitz C.",,PLOS digital health,2023,2023-09-20,Y,,,,"COVID-19 infection rates remain high in South Africa. Clinical prediction models may be helpful for rapid triage, and supporting clinical decision making, for patients with suspected COVID-19 infection. The Western Cape, South Africa, has integrated electronic health care data facilitating large-scale linked routine datasets. The aim of this study was to develop a machine learning model to predict adverse outcome in patients presenting with suspected COVID-19 suitable for use in a middle-income setting. A retrospective cohort study was conducted using linked, routine data, from patients presenting with suspected COVID-19 infection to public-sector emergency departments (EDs) in the Western Cape, South Africa between 27th August 2020 and 31st October 2021. The primary outcome was death or critical care admission at 30 days. An XGBoost machine learning model was trained and internally tested using split-sample validation. External validation was performed in 3 test cohorts: Western Cape patients presenting during the Omicron COVID-19 wave, a UK cohort during the ancestral COVID-19 wave, and a Sudanese cohort during ancestral and Eta waves. A total of 282,051 cases were included in a complete case training dataset. The prevalence of 30-day adverse outcome was 4.0%. The most important features for predicting adverse outcome were the requirement for supplemental oxygen, peripheral oxygen saturations, level of consciousness and age. Internal validation using split-sample test data revealed excellent discrimination (C-statistic 0.91, 95% CI 0.90 to 0.91) and calibration (CITL of 1.05). The model achieved C-statistics of 0.84 (95% CI 0.84 to 0.85), 0.72 (95% CI 0.71 to 0.73), and 0.62, (95% CI 0.59 to 0.65) in the Omicron, UK, and Sudanese test cohorts. Results were materially unchanged in sensitivity analyses examining missing data. An XGBoost machine learning model achieved good discrimination and calibration in prediction of adverse outcome in patients presenting with suspected COVID19 to Western Cape EDs. Performance was reduced in temporal and geographical external validation.",,pdf:https://journals.plos.org/digitalhealth/article/file?id=10.1371/journal.pdig.0000309&type=printable; doi:https://doi.org/10.1371/journal.pdig.0000309; html:https://europepmc.org/articles/PMC10511129; pdf:https://europepmc.org/articles/PMC10511129?pdf=render
-37118525,https://doi.org/10.1038/s43587-022-00328-3,Strong peak immunogenicity but rapid antibody waning following third vaccine dose in older residents of care homes.,"Tut G, Lancaster T, Krutikov M, Sylla P, Bone D, Spalkova E, Bentley C, Amin U, Jadir A, Hulme S, Kaur N, Tut E, Bruton R, Wu MY, Harvey R, Carr EJ, Crick COVID Immunity Pipeline, Beale R, Stirrup O, Shrotri M, Azmi B, Fuller C, Baynton V, Irwin-Singer A, Hayward A, Copas A, Shallcross L, Moss P.",,Nature aging,2023,2023-01-20,Y,,,,"Third-dose coronavirus disease 2019 vaccines are being deployed widely but their efficacy has not been assessed adequately in vulnerable older people who exhibit suboptimal responses after primary vaccination series. This observational study, which was carried out by the VIVALDI study based in England, looked at spike-specific immune responses in 341 staff and residents in long-term care facilities who received an mRNA vaccine following dual primary series vaccination with BNT162b2 or ChAdOx1. Third-dose vaccination strongly increased antibody responses with preferential relative enhancement in older people and was required to elicit neutralization of Omicron. Cellular immune responses were also enhanced with strong cross-reactive recognition of Omicron. However, antibody titers fell 21-78% within 100 d after vaccine and 27% of participants developed a breakthrough Omicron infection. These findings reveal strong immunogenicity of a third vaccine in one of the most vulnerable population groups and endorse an approach for widespread delivery across this population. Ongoing assessment will be required to determine the stability of immune protection.",,pdf:https://www.nature.com/articles/s43587-022-00328-3.pdf; doi:https://doi.org/10.1038/s43587-022-00328-3; html:https://europepmc.org/articles/PMC10154221; pdf:https://europepmc.org/articles/PMC10154221?pdf=render
+36609574,https://doi.org/10.1038/s41467-022-35771-8,A population-based matched cohort study of major congenital anomalies following COVID-19 vaccination and SARS-CoV-2 infection.,"Calvert C, Carruthers J, Denny C, Donaghy J, Hopcroft LEM, Hopkins L, Goulding A, Lindsay L, McLaughlin T, Moore E, Taylor B, Loane M, Dolk H, Morris J, Auyeung B, Bhaskaran K, Gibbons CL, Katikireddi SV, O'Leary M, McAllister D, Shi T, Simpson CR, Robertson C, Sheikh A, Stock SJ, Wood R.",,Nature communications,2023,2023-01-06,Y,,,,"Evidence on associations between COVID-19 vaccination or SARS-CoV-2 infection and the risk of congenital anomalies is limited. Here we report a national, population-based, matched cohort study using linked electronic health records from Scotland (May 2020-April 2022) to estimate the association between COVID-19 vaccination and, separately, SARS-CoV-2 infection between six weeks pre-conception and 19 weeks and six days gestation and the risk of [1] any major congenital anomaly and [2] any non-genetic major congenital anomaly. Mothers vaccinated in this pregnancy exposure period mostly received an mRNA vaccine (73.7% Pfizer-BioNTech BNT162b2 and 7.9% Moderna mRNA-1273). Of the 6731 babies whose mothers were vaccinated in the pregnancy exposure period, 153 had any anomaly and 120 had a non-genetic anomaly. Primary analyses find no association between any vaccination and any anomaly (adjusted Odds Ratio [aOR] = 1.01, 95% Confidence Interval [CI] = 0.83-1.24) or non-genetic anomalies (aOR = 1.00, 95% CI = 0.81-1.22). Primary analyses also find no association between SARS-CoV-2 infection and any anomaly (aOR = 1.02, 95% CI = 0.66-1.60) or non-genetic anomalies (aOR = 0.94, 95% CI = 0.57-1.54). Findings are robust to sensitivity analyses. These data provide reassurance on the safety of vaccination, in particular mRNA vaccines, just before or in early pregnancy.",,pdf:https://www.nature.com/articles/s41467-022-35771-8.pdf; doi:https://doi.org/10.1038/s41467-022-35771-8; html:https://europepmc.org/articles/PMC9821346; pdf:https://europepmc.org/articles/PMC9821346?pdf=render
 35756853,https://doi.org/10.1016/j.lanepe.2022.100428,"Impact of COVID-19 pandemic on asthma exacerbations: Retrospective cohort study of over 500,000 patients in a national English primary care database.","Shah SA, Quint JK, Sheikh A.",,The Lancet regional health. Europe,2022,2022-06-15,Y,Asthma; Pandemic; Asthma Exacerbations; Covid-19,,,"<h4>Background</h4>Several countries reported a substantial reduction in asthma exacerbations associated with COVID-19 pandemic-related restrictions. However, it is not known if these early reported declines were short-term and if these have rebounded to pre-pandemic levels following easing of lockdown restrictions.<h4>Methods</h4>We undertook a retrospective, cohort study of all asthma patients in a national primary care database of almost 10 million patients, Optimum Patient Care Database (OPCRD), identified from January 1, 2010, to December 31, 2015, using a previously validated algorithm. We subsequently followed the identified cohort of asthma patients from January 1, 2016, to October 3, 2021, and identified every asthma exacerbation episode with a validated algorithm. To quantify any pandemic-related change in exacerbations, we created a control time-series (mean of 2016-2019) and then compared the change in exacerbation rate in 2020-2021 over quarterly periods when compared with the control period (the pre-pandemic period). We undertook overall and stratified analyses by age group, sex, and English region.<h4>Findings</h4>We identified 100,362 asthma patients (502,669 patient-years) from across England who experienced at least one exacerbation episode (298,390 exacerbation episodes during the entire follow-up). Except for the first quarter of 2020, the exacerbation rates were substantially lower (>25%) during all quarters in 2020-2021 when compared with the rates during 2016-2019 (39.7% (95% Confidence Interval (CI): 34.6, 44.9) in quarter-2, 2020; 46.5% (95%CI: 36.7, 56.4) in quarter-3, 2020; 56.3% (95%CI: 48.7, 63.9) in quarter-4, 2020; 63.2% (95%CI: 53.9, 72.5) in quarter-1, 2021; 57.7% (95%CI: 52.9, 62.4) in quarter-2, 2021; 53.3% (95%CI: 43.8, 62.8) in quarter-3, 2021).<h4>Interpretation</h4>There was a substantial and persistent reduction in asthma exacerbations across England over the first 18 months after the first lockdown. This is unlikely to be adequately explained by changes in health-seeking behaviour, pandemic-related healthcare service disruption, or any air-quality improvements.<h4>Funding</h4>Asthma UK, Health Data Research UK (HDR UK), Medical Research Council (MRC), National Institute for Health Research (NIHR).",,doi:https://doi.org/10.1016/j.lanepe.2022.100428; doi:https://doi.org/10.1016/j.lanepe.2022.100428; html:https://europepmc.org/articles/PMC9213032; pdf:https://europepmc.org/articles/PMC9213032?pdf=render
+37118525,https://doi.org/10.1038/s43587-022-00328-3,Strong peak immunogenicity but rapid antibody waning following third vaccine dose in older residents of care homes.,"Tut G, Lancaster T, Krutikov M, Sylla P, Bone D, Spalkova E, Bentley C, Amin U, Jadir A, Hulme S, Kaur N, Tut E, Bruton R, Wu MY, Harvey R, Carr EJ, Crick COVID Immunity Pipeline, Beale R, Stirrup O, Shrotri M, Azmi B, Fuller C, Baynton V, Irwin-Singer A, Hayward A, Copas A, Shallcross L, Moss P.",,Nature aging,2023,2023-01-20,Y,,,,"Third-dose coronavirus disease 2019 vaccines are being deployed widely but their efficacy has not been assessed adequately in vulnerable older people who exhibit suboptimal responses after primary vaccination series. This observational study, which was carried out by the VIVALDI study based in England, looked at spike-specific immune responses in 341 staff and residents in long-term care facilities who received an mRNA vaccine following dual primary series vaccination with BNT162b2 or ChAdOx1. Third-dose vaccination strongly increased antibody responses with preferential relative enhancement in older people and was required to elicit neutralization of Omicron. Cellular immune responses were also enhanced with strong cross-reactive recognition of Omicron. However, antibody titers fell 21-78% within 100 d after vaccine and 27% of participants developed a breakthrough Omicron infection. These findings reveal strong immunogenicity of a third vaccine in one of the most vulnerable population groups and endorse an approach for widespread delivery across this population. Ongoing assessment will be required to determine the stability of immune protection.",,pdf:https://www.nature.com/articles/s43587-022-00328-3.pdf; doi:https://doi.org/10.1038/s43587-022-00328-3; html:https://europepmc.org/articles/PMC10154221; pdf:https://europepmc.org/articles/PMC10154221?pdf=render
 37429634,https://doi.org/10.3399/bjgpo.2023.0057,UK research data resources based on primary care electronic health records: review and summary for potential users.,"Edwards L, Pickett J, Ashcroft DM, Dambha-Miller H, Majeed A, Mallen C, Petersen I, Qureshi N, van Staa T, Abel G, Carvalho C, Denholm R, Kontopantelis E, Macaulay A, Macleod J.",,BJGP open,2023,2023-09-19,Y,Population; Primary Health Care; Electronic Health Records; Primary Care Databases; Population Level Linked Data,,,"<h4>Background</h4>The range and scope of electronic health record (EHR) data assets in the UK has recently increased, which has been mainly in response to the COVID-19 pandemic. Summarising and comparing the large primary care resources will help researchers to choose the data resources most suited to their needs.<h4>Aim</h4>To describe the current landscape of UK EHR databases and considerations of access and use of these resources relevant to researchers.<h4>Design & setting</h4>Narrative review of EHR databases in the UK.<h4>Method</h4>Information was collected from the Health Data Research Innovation Gateway, publicly available websites and other published data, and from key informants. The eligibility criteria were population-based open-access databases sampling EHRs across the whole population of one or more countries in the UK. Published database characteristics were extracted and summarised, and these were corroborated with resource providers. Results were synthesised narratively.<h4>Results</h4>Nine large national primary care EHR data resources were identified and summarised. These resources are enhanced by linkage to other administrative data to a varying extent. Resources are mainly intended to support observational research, although some can support experimental studies. There is considerable overlap of populations covered. While all resources are accessible to bona fide researchers, access mechanisms, costs, timescales, and other considerations vary across databases.<h4>Conclusion</h4>Researchers are currently able to access primary care EHR data from several sources. Choice of data resource is likely to be driven by project needs and access considerations. The landscape of data resources based on primary care EHRs in the UK continues to evolve.",,pdf:https://bjgpopen.org/content/bjgpoa/early/2023/07/10/BJGPO.2023.0057.full.pdf; doi:https://doi.org/10.3399/BJGPO.2023.0057; html:https://europepmc.org/articles/PMC10646196; pdf:https://europepmc.org/articles/PMC10646196?pdf=render
 35875883,https://doi.org/10.1093/cvr/cvac115,Long COVID and the cardiovascular system-elucidating causes and cellular mechanisms in order to develop targeted diagnostic and therapeutic strategies: a joint Scientific Statement of the ESC Working Groups on Cellular Biology of the Heart and Myocardial and Pericardial Diseases.,"Gyöngyösi M, Alcaide P, Asselbergs FW, Brundel BJJM, Camici GG, Martins PDC, Ferdinandy P, Fontana M, Girao H, Gnecchi M, Gollmann-Tepeköylü C, Kleinbongard P, Krieg T, Madonna R, Paillard M, Pantazis A, Perrino C, Pesce M, Schiattarella GG, Sluijter JPG, Steffens S, Tschöpe C, Van Linthout S, Davidson SM.",,Cardiovascular research,2023,2023-03-01,Y,Cardiac; cardiovascular; Covid-19; Long Covid; Post Covid,,,"Long COVID has become a world-wide, non-communicable epidemic, caused by long-lasting multiorgan symptoms that endure for weeks or months after SARS-CoV-2 infection has already subsided. This scientific document aims to provide insight into the possible causes and therapeutic options available for the cardiovascular manifestations of long COVID. In addition to chronic fatigue, which is a common symptom of long COVID, patients may present with chest pain, ECG abnormalities, postural orthostatic tachycardia, or newly developed supraventricular or ventricular arrhythmias. Imaging of the heart and vessels has provided evidence of chronic, post-infectious perimyocarditis with consequent left or right ventricular failure, arterial wall inflammation, or microthrombosis in certain patient populations. Better understanding of the underlying cellular and molecular mechanisms of long COVID will aid in the development of effective treatment strategies for its cardiovascular manifestations. A number of mechanisms have been proposed, including those involving direct effects on the myocardium, microthrombotic damage to vessels or endothelium, or persistent inflammation. Unfortunately, existing circulating biomarkers, coagulation, and inflammatory markers, are not highly predictive for either the presence or outcome of long COVID when measured 3 months after SARS-CoV-2 infection. Further studies are needed to understand underlying mechanisms, identify specific biomarkers, and guide future preventive strategies or treatments to address long COVID and its cardiovascular sequelae.",,pdf:https://academic.oup.com/cardiovascres/advance-article-pdf/doi/10.1093/cvr/cvac115/46855438/cvac115.pdf; doi:https://doi.org/10.1093/cvr/cvac115; html:https://europepmc.org/articles/PMC9384470; pdf:https://europepmc.org/articles/PMC9384470?pdf=render
 35858680,https://doi.org/10.1136/bmj-2021-068946,Comparative effectiveness of ChAdOx1 versus BNT162b2 covid-19 vaccines in health and social care workers in England: cohort study using OpenSAFELY.,"Hulme WJ, Williamson EJ, Green ACA, Bhaskaran K, McDonald HI, Rentsch CT, Schultze A, Tazare J, Curtis HJ, Walker AJ, Tomlinson LA, Palmer T, Horne EMF, MacKenna B, Morton CE, Mehrkar A, Morley J, Fisher L, Bacon SCJ, Evans D, Inglesby P, Hickman G, Davy S, Ward T, Croker R, Eggo RM, Wong AYS, Mathur R, Wing K, Forbes H, Grint DJ, Douglas IJ, Evans SJW, Smeeth L, Bates C, Cockburn J, Parry J, Hester F, Harper S, Sterne JAC, Hernán MA, Goldacre B.",,BMJ (Clinical research ed.),2022,2022-07-20,Y,,,,"<h4>Objective</h4>To compare the effectiveness of the BNT162b2 mRNA (Pfizer-BioNTech) and the ChAdOx1 (Oxford-AstraZeneca) covid-19 vaccines against infection and covid-19 disease in health and social care workers.<h4>Design</h4>Cohort study, emulating a comparative effectiveness trial, on behalf of NHS England.<h4>Setting</h4>Linked primary care, hospital, and covid-19 surveillance records available within the OpenSAFELY-TPP research platform, covering a period when the SARS-CoV-2 Alpha variant was dominant.<h4>Participants</h4>317 341 health and social care workers vaccinated between 4 January and 28 February 2021, registered with a general practice using the TPP SystmOne clinical information system in England, and not clinically extremely vulnerable.<h4>Interventions</h4>Vaccination with either BNT162b2 or ChAdOx1 administered as part of the national covid-19 vaccine roll-out.<h4>Main outcome measures</h4>Recorded SARS-CoV-2 positive test, or covid-19 related attendance at an accident and emergency (A&E) department or hospital admission occurring within 20 weeks of receipt of the first vaccine dose.<h4>Results</h4>Over the duration of 118 771 person-years of follow-up there were 6962 positive SARS-CoV-2 tests, 282 covid-19 related A&E attendances, and 166 covid-19 related hospital admissions. The cumulative incidence of each outcome was similar for both vaccines during the first 20 weeks after vaccination. The cumulative incidence of recorded SARS-CoV-2 infection 20 weeks after first-dose vaccination with BNT162b2 was 21.7 per 1000 people (95% confidence interval 20.9 to 22.4) and with ChAdOx1 was 23.7 (21.8 to 25.6), representing a difference of 2.04 per 1000 people (0.04 to 4.04). The difference in the cumulative incidence per 1000 people of covid-19 related A&E attendance at 20 weeks was 0.06 per 1000 people (95% CI -0.31 to 0.43). For covid-19 related hospital admission, this difference was 0.11 per 1000 people (-0.22 to 0.44).<h4>Conclusions</h4>In this cohort of healthcare workers where we would not anticipate vaccine type to be related to health status, we found no substantial differences in the incidence of SARS-CoV-2 infection or covid-19 disease up to 20 weeks after vaccination. Incidence dropped sharply at 3-4 weeks after vaccination, and there were few covid-19 related hospital attendance and admission events after this period. This is in line with expected onset of vaccine induced immunity and suggests strong protection against Alpha variant covid-19 disease for both vaccines in this relatively young and healthy population of healthcare workers.",,pdf:https://www.bmj.com/content/bmj/378/bmj-2021-068946.full.pdf; doi:https://doi.org/10.1136/bmj-2021-068946; html:https://europepmc.org/articles/PMC9295078; pdf:https://europepmc.org/articles/PMC9295078?pdf=render
 35192597,https://doi.org/10.1371/journal.pmed.1003926,"Association of COVID-19 vaccines ChAdOx1 and BNT162b2 with major venous, arterial, or thrombocytopenic events: A population-based cohort study of 46 million adults in England.","Whiteley WN, Ip S, Cooper JA, Bolton T, Keene S, Walker V, Denholm R, Akbari A, Omigie E, Hollings S, Di Angelantonio E, Denaxas S, Wood A, Sterne JAC, Sudlow C, CVD-COVID-UK consortium.",,PLoS medicine,2022,2022-02-22,Y,,,,"<h4>Background</h4>Thromboses in unusual locations after the Coronavirus Disease 2019 (COVID-19) vaccine ChAdOx1-S have been reported, although their frequency with vaccines of different types is uncertain at a population level. The aim of this study was to estimate the population-level risks of hospitalised thrombocytopenia and major arterial and venous thromboses after COVID-19 vaccination.<h4>Methods and findings</h4>In this whole-population cohort study, we analysed linked electronic health records from adults living in England, from 8 December 2020 to 18 March 2021. We estimated incidence rates and hazard ratios (HRs) for major arterial, venous, and thrombocytopenic outcomes 1 to 28 and >28 days after first vaccination dose for ChAdOx1-S and BNT162b2 vaccines. Analyses were performed separately for ages <70 and ≥70 years and adjusted for age, age2, sex, ethnicity, and deprivation. We also prespecified adjustment for anticoagulant medication, combined oral contraceptive medication, hormone replacement therapy medication, history of pulmonary embolism or deep vein thrombosis, and history of coronavirus infection in analyses of venous thrombosis; and diabetes, hypertension, smoking, antiplatelet medication, blood pressure lowering medication, lipid lowering medication, anticoagulant medication, history of stroke, and history of myocardial infarction in analyses of arterial thromboses. We selected further covariates with backward selection. Of 46 million adults, 23 million (51%) were women; 39 million (84%) were <70; and 3.7 million (8.1%) Asian or Asian British, 1.6 million (3.5%) Black or Black British, 36 million (79%) White, 0.7 million (1.5%) mixed ethnicity, and 1.5 million (3.2%) were of another ethnicity. Approximately 21 million (46%) adults had their first vaccination between 8 December 2020 and 18 March 2021. The crude incidence rates (per 100,000 person-years) of all venous events were as follows: prevaccination, 140 [95% confidence interval (CI): 138 to 142]; ≤28 days post-ChAdOx1-S, 294 (281 to 307); >28 days post-ChAdOx1-S, 359 (338 to 382), ≤28 days post-BNT162b2-S, 241 (229 to 253); >28 days post-BNT162b2-S 277 (263 to 291). The crude incidence rates (per 100,000 person-years) of all arterial events were as follows: prevaccination, 546 (95% CI: 541 to 555); ≤28 days post-ChAdOx1-S, 1,211 (1,185 to 1,237); >28 days post-ChAdOx1-S, 1678 (1,630 to 1,726), ≤28 days post-BNT162b2-S, 1,242 (1,214 to 1,269); >28 days post-BNT162b2-S, 1,539 (1,507 to 1,572). Adjusted HRs (aHRs) 1 to 28 days after ChAdOx1-S, compared with unvaccinated rates, at ages <70 and ≥70 years, respectively, were 0.97 (95% CI: 0.90 to 1.05) and 0.58 (0.53 to 0.63) for venous thromboses, and 0.90 (0.86 to 0.95) and 0.76 (0.73 to 0.79) for arterial thromboses. Corresponding aHRs for BNT162b2 were 0.81 (0.74 to 0.88) and 0.57 (0.53 to 0.62) for venous thromboses, and 0.94 (0.90 to 0.99) and 0.72 (0.70 to 0.75) for arterial thromboses. aHRs for thrombotic events were higher at younger ages for venous thromboses after ChAdOx1-S, and for arterial thromboses after both vaccines. Rates of intracranial venous thrombosis (ICVT) and of thrombocytopenia in adults aged <70 years were higher 1 to 28 days after ChAdOx1-S (aHRs 2.27, 95% CI: 1.33 to 3.88 and 1.71, 1.35 to 2.16, respectively), but not after BNT162b2 (0.59, 0.24 to 1.45 and 1.00, 0.75 to 1.34) compared with unvaccinated. The corresponding absolute excess risks of ICVT 1 to 28 days after ChAdOx1-S were 0.9 to 3 per million, varying by age and sex. The main limitations of the study are as follows: (i) it relies on the accuracy of coded healthcare data to identify exposures, covariates, and outcomes; (ii) the use of primary reason for hospital admission to measure outcome, which improves the positive predictive value but may lead to an underestimation of incidence; and (iii) potential unmeasured confounding.<h4>Conclusions</h4>In this study, we observed increases in rates of ICVT and thrombocytopenia after ChAdOx1-S vaccination in adults aged <70 years that were small compared with its effect in reducing COVID-19 morbidity and mortality, although more precise estimates for adults aged <40 years are needed. For people aged ≥70 years, rates of arterial or venous thrombotic events were generally lower after either vaccine compared with unvaccinated, suggesting that either vaccine is suitable in this age group.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003926&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003926; html:https://europepmc.org/articles/PMC8863280; pdf:https://europepmc.org/articles/PMC8863280?pdf=render
 35429382,https://doi.org/10.1093/infdis/jiac146,Severe Acute Respiratory Syndrome Coronavirus 2 Anti-Spike Antibody Levels Following Second Dose of ChAdOx1 nCov-19 or BNT162b2 Vaccine in Residents of Long-term Care Facilities in England (VIVALDI).,"Stirrup O, Krutikov M, Tut G, Palmer T, Bone D, Bruton R, Fuller C, Azmi B, Lancaster T, Sylla P, Kaur N, Spalkova E, Bentley C, Amin U, Jadir A, Hulme S, Giddings R, Nacer-Laidi H, Baynton V, Irwin-Singer A, Hayward A, Moss P, Copas A, Shallcross L.",,The Journal of infectious diseases,2022,2022-11-01,Y,Antibodies; Vaccination; Waning; Long-term Care Facilities; Covid-19,,,"General population studies have shown strong humoral response following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination with subsequent waning of anti-spike antibody levels. Vaccine-induced immune responses are often attenuated in frail and older populations, but published data are scarce. We measured SARS-CoV-2 anti-spike antibody levels in long-term care facility residents and staff following a second vaccination dose with Oxford-AstraZeneca or Pfizer-BioNTech. Vaccination elicited robust antibody responses in older residents, suggesting comparable levels of vaccine-induced immunity to that in the general population. Antibody levels are higher after Pfizer-BioNTech vaccination but fall more rapidly compared to Oxford-AstraZeneca recipients and are enhanced by prior infection in both groups.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9047242; doi:https://doi.org/10.1093/infdis/jiac146; html:https://europepmc.org/articles/PMC9047242; pdf:https://europepmc.org/articles/PMC9047242?pdf=render
 38803829,https://doi.org/10.1136/bmjmed-2023-000791,Incidence and treatment of group A streptococcal infections during covid-19 pandemic and 2022 outbreak: retrospective cohort study in England using OpenSAFELY-TPP.,"Cunningham C, Fisher L, Wood C, Speed V, Brown AD, Curtis H, Higgins R, Croker R, Butler-Cole BF, Evans D, Inglesby P, Dillingham I, Bacon SC, Beech E, Hand K, Davy S, Ward T, Hickman G, Bridges L, O'Dwyer T, Maude S, Smith RM, Mehrkar A, Hart LC, Bates C, Cockburn J, Parry J, Hester F, Harper S, Goldacre B, MacKenna B.",,BMJ medicine,2024,2024-05-24,Y,Primary Health Care; Infectious Disease Medicine; Covid-19,,,"<h4>Objective</h4>To investigate the effect of the covid-19 pandemic on the number of patients with group A streptococcal infections and related antibiotic prescriptions.<h4>Design</h4>Retrospective cohort study in England using OpenSAFELY-TPP.<h4>Setting</h4>Primary care practices in England that used TPP SystmOne software, 1 January 2018 to 31 March 2023, with the approval of NHS England.<h4>Participants</h4>Patients registered at a TPP practice at the start of each month of the study period. Patients with missing data for sex or age were excluded, resulting in a population of 23 816 470 in January 2018, increasing to 25 541 940 by March 2023.<h4>Main outcome measures</h4>Monthly counts and crude rates of patients with group A streptococcal infections (sore throat or tonsillitis, scarlet fever, and invasive group A streptococcal infections), and recommended firstline, alternative, and reserved antibiotic prescriptions linked with a group A streptococcal infection before (pre-April 2020), during, and after (post-April 2021) covid-19 restrictions. Maximum and minimum count and rate for each infectious season (time from September to August), as well as the rate ratio of the 2022-23 season compared with the last comparably high season (2017-18).<h4>Results</h4>The number of patients with group A streptococcal infections, and antibiotic prescriptions linked to an indication of group A streptococcal infection, peaked in December 2022, higher than the peak in 2017-18. The rate ratios for monthly sore throat or tonsillitis (possible group A streptococcal throat infection), scarlet fever, and invasive group A streptococcal infection in 2022-23 relative to 2017-18 were 1.39 (95% confidence interval (CI) 1.38 to 1.40), 2.68 (2.59 to 2.77), and 4.37 (2.94 to 6.48), respectively. The rate ratio for prescriptions of first line, alternative, and reserved antibiotics to patients with group A streptococcal infections in 2022-23 relative to 2017-18 were 1.37 (95% CI 1.35 to 1.38), 2.30 (2.26 to 2.34), and 2.42 (2.24 to 2.61), respectively. For individual antibiotic prescriptions in 2022-23, azithromycin showed the greatest relative increase versus 2017-18, with a rate ratio of 7.37 (6.22 to 8.74). This finding followed a marked decrease in the recording of patients with group A streptococcal infections and associated prescriptions during the period of covid-19 restrictions where the maximum count and rates were lower than any minimum rates before the covid-19 pandemic.<h4>Conclusions</h4>Recording of rates of scarlet fever, sore throat or tonsillitis, and invasive group A streptococcal infections, and associated antibiotic prescribing, peaked in December 2022. Primary care data can supplement existing infectious disease surveillance through linkages with relevant prescribing data and detailed analysis of clinical and demographic subgroups.",,doi:https://doi.org/10.1136/bmjmed-2023-000791; html:https://europepmc.org/articles/PMC11129040; pdf:https://europepmc.org/articles/PMC11129040?pdf=render
-36253471,https://doi.org/10.1038/s41467-022-33937-y,A population-based matched cohort study of early pregnancy outcomes following COVID-19 vaccination and SARS-CoV-2 infection.,"Calvert C, Carruthers J, Denny C, Donaghy J, Hillman S, Hopcroft LEM, Hopkins L, Goulding A, Lindsay L, McLaughlin T, Moore E, Pan J, Taylor B, Almaghrabi F, Auyeung B, Bhaskaran K, Gibbons CL, Katikireddi SV, McCowan C, Murray J, O'Leary M, Ritchie LD, Shah SA, Simpson CR, Robertson C, Sheikh A, Stock SJ, Wood R.",,Nature communications,2022,2022-10-17,Y,,,,"Data on the safety of COVID-19 vaccines in early pregnancy are limited. We conducted a national, population-based, matched cohort study assessing associations between COVID-19 vaccination and miscarriage prior to 20 weeks gestation and, separately, ectopic pregnancy. We identified women in Scotland vaccinated between 6 weeks preconception and 19 weeks 6 days gestation (for miscarriage; n = 18,780) or 2 weeks 6 days gestation (for ectopic; n = 10,570). Matched, unvaccinated women from the pre-pandemic and, separately, pandemic periods were used as controls. Here we show no association between vaccination and miscarriage (adjusted Odds Ratio [aOR], pre-pandemic controls = 1.02, 95% Confidence Interval [CI] = 0.96-1.09) or ectopic pregnancy (aOR = 1.13, 95% CI = 0.92-1.38). We undertook additional analyses examining confirmed SARS-CoV-2 infection as the exposure and similarly found no association with miscarriage or ectopic pregnancy. Our findings support current recommendations that vaccination remains the safest way for pregnant women to protect themselves and their babies from COVID-19.",,pdf:https://www.nature.com/articles/s41467-022-33937-y.pdf; doi:https://doi.org/10.1038/s41467-022-33937-y; html:https://europepmc.org/articles/PMC9574832; pdf:https://europepmc.org/articles/PMC9574832?pdf=render
 32565483,https://doi.org/10.1136/bmjopen-2020-039097,Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II): protocol for an observational study using linked Scottish national data.,"Simpson CR, Robertson C, Vasileiou E, McMenamin J, Gunson R, Ritchie LD, Woolhouse M, Morrice L, Kelly D, Stagg HR, Marques D, Murray J, Sheikh A.",,BMJ open,2020,2020-06-21,Y,epidemiology; Public Health; Respiratory Medicine (See Thoracic Medicine),,,"<h4>Introduction</h4>Following the emergence of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019 and the ensuing COVID-19 pandemic, population-level surveillance and rapid assessment of the effectiveness of existing or new therapeutic or preventive interventions are required to ensure that interventions are targeted to those at highest risk of serious illness or death from COVID-19. We aim to repurpose and expand an existing pandemic reporting platform to determine the attack rate of SARS-CoV-2, the uptake and effectiveness of any new pandemic vaccine (once available) and any protective effect conferred by existing or new antimicrobial drugs and other therapies.<h4>Methods and analysis</h4>A prospective observational cohort will be used to monitor daily/weekly the progress of the COVID-19 epidemic and to evaluate the effectiveness of therapeutic interventions in approximately 5.4 million individuals registered in general practices across Scotland. A national linked dataset of patient-level primary care data, out-of-hours, hospitalisation, mortality and laboratory data will be assembled. The primary outcomes will measure association between: (A) laboratory confirmed SARS-CoV-2 infection, morbidity and mortality, and demographic, socioeconomic and clinical population characteristics; and (B) healthcare burden of COVID-19 and demographic, socioeconomic and clinical population characteristics. The secondary outcomes will estimate: (A) the uptake (for vaccines only); (B) effectiveness; and (C) safety of new or existing therapies, vaccines and antimicrobials against SARS-CoV-2 infection. The association between population characteristics and primary outcomes will be assessed via multivariate logistic regression models. The effectiveness of therapies, vaccines and antimicrobials will be assessed from time-dependent Cox models or Poisson regression models. Self-controlled study designs will be explored to estimate the risk of therapeutic and prophylactic-related adverse events.<h4>Ethics and dissemination</h4>We obtained approval from the National Research Ethics Service Committee, Southeast Scotland 02. The study findings will be presented at international conferences and published in peer-reviewed journals.",,pdf:https://bmjopen.bmj.com/content/bmjopen/10/6/e039097.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-039097; html:https://europepmc.org/articles/PMC7311023; pdf:https://europepmc.org/articles/PMC7311023?pdf=render
+36253471,https://doi.org/10.1038/s41467-022-33937-y,A population-based matched cohort study of early pregnancy outcomes following COVID-19 vaccination and SARS-CoV-2 infection.,"Calvert C, Carruthers J, Denny C, Donaghy J, Hillman S, Hopcroft LEM, Hopkins L, Goulding A, Lindsay L, McLaughlin T, Moore E, Pan J, Taylor B, Almaghrabi F, Auyeung B, Bhaskaran K, Gibbons CL, Katikireddi SV, McCowan C, Murray J, O'Leary M, Ritchie LD, Shah SA, Simpson CR, Robertson C, Sheikh A, Stock SJ, Wood R.",,Nature communications,2022,2022-10-17,Y,,,,"Data on the safety of COVID-19 vaccines in early pregnancy are limited. We conducted a national, population-based, matched cohort study assessing associations between COVID-19 vaccination and miscarriage prior to 20 weeks gestation and, separately, ectopic pregnancy. We identified women in Scotland vaccinated between 6 weeks preconception and 19 weeks 6 days gestation (for miscarriage; n = 18,780) or 2 weeks 6 days gestation (for ectopic; n = 10,570). Matched, unvaccinated women from the pre-pandemic and, separately, pandemic periods were used as controls. Here we show no association between vaccination and miscarriage (adjusted Odds Ratio [aOR], pre-pandemic controls = 1.02, 95% Confidence Interval [CI] = 0.96-1.09) or ectopic pregnancy (aOR = 1.13, 95% CI = 0.92-1.38). We undertook additional analyses examining confirmed SARS-CoV-2 infection as the exposure and similarly found no association with miscarriage or ectopic pregnancy. Our findings support current recommendations that vaccination remains the safest way for pregnant women to protect themselves and their babies from COVID-19.",,pdf:https://www.nature.com/articles/s41467-022-33937-y.pdf; doi:https://doi.org/10.1038/s41467-022-33937-y; html:https://europepmc.org/articles/PMC9574832; pdf:https://europepmc.org/articles/PMC9574832?pdf=render
 35047182,https://doi.org/10.7189/jogh.11.01010,"The COVID-19 pandemic in children and young people during 2020-2021: Learning about clinical presentation, patterns of spread, viral load, diagnosis and treatment.","Rudan I, Adeloye D, Katikireddi SV, Murray J, Simpson C, Shah SA, Robertson C, Sheikh A, EAVE II collaboration.",,Journal of global health,2021,2021-12-25,Y,,,,,,doi:https://doi.org/10.7189/jogh.11.01010; doi:https://doi.org/10.7189/jogh.11.01010; html:https://europepmc.org/articles/PMC8763336; pdf:https://europepmc.org/articles/PMC8763336?pdf=render
 36834176,https://doi.org/10.3390/ijerph20043477,"Non-Pharmacological Therapies for Post-Viral Syndromes, Including Long COVID: A Systematic Review.","Chandan JS, Brown KR, Simms-Williams N, Bashir NZ, Camaradou J, Heining D, Turner GM, Rivera SC, Hotham R, Minhas S, Nirantharakumar K, Sivan M, Khunti K, Raindi D, Marwaha S, Hughes SE, McMullan C, Marshall T, Calvert MJ, Haroon S, Aiyegbusi OL, TLC Study.",,International journal of environmental research and public health,2023,2023-02-16,Y,Rehabilitation; Systematic review; Pvs; Non-pharmacological Intervention; Covid-19; Long Covid; Post-covid-19 Condition; Post-acute Sequelae Of Sars-cov-2 Infection (Pasc); Post-Viral Syndromes,,,"<h4>Background</h4>Post-viral syndromes (PVS), including Long COVID, are symptoms sustained from weeks to years following an acute viral infection. Non-pharmacological treatments for these symptoms are poorly understood. This review summarises the evidence for the effectiveness of non-pharmacological treatments for PVS.<h4>Methods</h4>We conducted a systematic review to evaluate the effectiveness of non-pharmacological interventions for PVS, as compared to either standard care, alternative non-pharmacological therapy, or placebo. The outcomes of interest were changes in symptoms, exercise capacity, quality of life (including mental health and wellbeing), and work capability. We searched five databases (Embase, MEDLINE, PsycINFO, CINAHL, MedRxiv) for randomised controlled trials (RCTs) published between 1 January 2001 to 29 October 2021. The relevant outcome data were extracted, the study quality was appraised using the Cochrane risk-of-bias tool, and the findings were synthesised narratively.<h4>Findings</h4>Overall, five studies of five different interventions (Pilates, music therapy, telerehabilitation, resistance exercise, neuromodulation) met the inclusion criteria. Aside from music-based intervention, all other selected interventions demonstrated some support in the management of PVS in some patients.<h4>Interpretation</h4>In this study, we observed a lack of robust evidence evaluating the non-pharmacological treatments for PVS, including Long COVID. Considering the prevalence of prolonged symptoms following acute viral infections, there is an urgent need for clinical trials evaluating the effectiveness and cost-effectiveness of non-pharmacological treatments for patients with PVS.<h4>Registration</h4>The study protocol was registered with PROSPERO [CRD42021282074] in October 2021 and published in BMJ Open in 2022.",,pdf:https://www.mdpi.com/1660-4601/20/4/3477/pdf?version=1677135187; doi:https://doi.org/10.3390/ijerph20043477; html:https://europepmc.org/articles/PMC9967466; pdf:https://europepmc.org/articles/PMC9967466?pdf=render
 34582457,https://doi.org/10.1371/journal.pmed.1003777,Predictive symptoms for COVID-19 in the community: REACT-1 study of over 1 million people.,"Elliott J, Whitaker M, Bodinier B, Eales O, Riley S, Ward H, Cooke G, Darzi A, Chadeau-Hyam M, Elliott P.",,PLoS medicine,2021,2021-09-28,Y,,,,"<h4>Background</h4>Rapid detection, isolation, and contact tracing of community COVID-19 cases are essential measures to limit the community spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aimed to identify a parsimonious set of symptoms that jointly predict COVID-19 and investigated whether predictive symptoms differ between the B.1.1.7 (Alpha) lineage (predominating as of April 2021 in the US, UK, and elsewhere) and wild type.<h4>Methods and findings</h4>We obtained throat and nose swabs with valid SARS-CoV-2 PCR test results from 1,147,370 volunteers aged 5 years and above (6,450 positive cases) in the REal-time Assessment of Community Transmission-1 (REACT-1) study. This study involved repeated community-based random surveys of prevalence in England (study rounds 2 to 8, June 2020 to January 2021, response rates 22%-27%). Participants were asked about symptoms occurring in the week prior to testing. Viral genome sequencing was carried out for PCR-positive samples with N-gene cycle threshold value < 34 (N = 1,079) in round 8 (January 2021). In univariate analysis, all 26 surveyed symptoms were associated with PCR positivity compared with non-symptomatic people. Stability selection (1,000 penalized logistic regression models with 50% subsampling) among people reporting at least 1 symptom identified 7 symptoms as jointly and positively predictive of PCR positivity in rounds 2-7 (June to December 2020): loss or change of sense of smell, loss or change of sense of taste, fever, new persistent cough, chills, appetite loss, and muscle aches. The resulting model (rounds 2-7) predicted PCR positivity in round 8 with area under the curve (AUC) of 0.77. The same 7 symptoms were selected as jointly predictive of B.1.1.7 infection in round 8, although when comparing B.1.1.7 with wild type, new persistent cough and sore throat were more predictive of B.1.1.7 infection while loss or change of sense of smell was more predictive of the wild type. The main limitations of our study are (i) potential participation bias despite random sampling of named individuals from the National Health Service register and weighting designed to achieve a representative sample of the population of England and (ii) the necessary reliance on self-reported symptoms, which may be prone to recall bias and may therefore lead to biased estimates of symptom prevalence in England.<h4>Conclusions</h4>Where testing capacity is limited, it is important to use tests in the most efficient way possible. We identified a set of 7 symptoms that, when considered together, maximize detection of COVID-19 in the community, including infection with the B.1.1.7 lineage.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003777&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003777; html:https://europepmc.org/articles/PMC8478234; pdf:https://europepmc.org/articles/PMC8478234?pdf=render
@@ -136,19 +136,19 @@ PMC10929454,https://doi.org/,Optimising data curation pipelines for population-l
 36189425,https://doi.org/10.1016/j.lanepe.2022.100513,"BNT162b2 COVID-19 vaccination uptake, safety, effectiveness and waning in children and young people aged 12-17 years in Scotland.","Rudan I, Millington T, Antal K, Grange Z, Fenton L, Sullivan C, Buelo A, Wood R, Woolford L, Swann OV, Murray JLK, Cullen LA, Moore E, Haider F, Almaghrabi F, McMenamin J, Agrawal U, Shah SA, Kerr S, Simpson CR, Katikireddi SV, Ritchie SLD, Robertson C, Sheikh SA.",,The Lancet regional health. Europe,2022,2022-09-28,Y,Scotland; United Kingdom; Children And Young People; Vaccine Effectiveness; Vaccine Uptake; Vaccine Safety; Vaccine Waning; Age Group 12-15 Years; Covid-19; Age Group 16-17 Years; National Prospective Cohort Study; Bnt162b2 Covid-19 Vaccination,,,"<h4>Background</h4>The two-dose BNT162b2 (Pfizer-BioNTech) vaccine has demonstrated high efficacy against COVID-19 disease in clinical trials of children and young people (CYP). Consequently, we investigated the uptake, safety, effectiveness and waning of the protective effect of the BNT162b2 against symptomatic COVID-19 in CYP aged 12-17 years in Scotland.<h4>Methods</h4>The analysis of the vaccine uptake was based on information from the Turas Vaccination Management Tool, inclusive of Mar 1, 2022. Vaccine safety was evaluated using national data on hospital admissions and General Practice (GP) consultations, through a self-controlled case series (SCCS) design, investigating 17 health outcomes of interest. Vaccine effectiveness (VE) against symptomatic COVID-19 disease for Delta and Omicron variants was estimated using a test-negative design (TND) and S-gene status in a prospective cohort study using the Scotland-wide Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) surveillance platform. The waning of the VE following each dose of BNT162b2 was assessed using a matching process followed by conditional logistic regression.<h4>Findings</h4>Between Aug 6, 2021 and Mar 1, 2022, 75.9% of the 112,609 CYP aged 16-17 years received the first and 49.0% the second COVID-19 vaccine dose. Among 237,681 CYP aged 12-15 years, the uptake was 64.5% and 37.2%, respectively. For 12-17-year-olds, BNT162b2 showed an excellent safety record, with no increase in hospital stays following vaccination for any of the 17 investigated health outcomes. In the 16-17-year-old group, VE against symptomatic COVID-19 during the Delta period was 64.2% (95% confidence interval [CI] 59.2-68.5) at 2-5 weeks after the first dose and 95.6% (77.0-99.1) at 2-5 weeks after the second dose. The respective VEs against symptomatic COVID-19 in the Omicron period were 22.8% (95% CI -6.4-44.0) and 65.5% (95% CI 56.0-73.0). In children aged 12-15 years, VE against symptomatic COVID-19 during the Delta period was 65.4% (95% CI 61.5-68.8) at 2-5 weeks after the first dose, with no observed cases at 2-5 weeks after the second dose. The corresponding VE against symptomatic COVID-19 during the Omicron period were 30.2% (95% CI 18.4-40.3) and 81.2% (95% CI 77.7-84.2). The waning of the protective effect against the symptomatic disease began after five weeks post-first and post-second dose.<h4>Interpretation</h4>During the study period, uptake of BNT162b2 in Scotland has covered more than two-thirds of CYP aged 12-17 years with the first dose and about 40% with the second dose. We found no increased likelihood of admission to hospital with a range of health outcomes in the period after vaccination. Vaccination with both doses was associated with a substantial reduction in the risk of COVID-19 symptomatic disease during both the Delta and Omicron periods, but this protection began to wane after five weeks.<h4>Funding</h4>UK Research and Innovation (Medical Research Council); Research and Innovation Industrial Strategy Challenge Fund; Chief Scientist's Office of the Scottish Government; Health Data Research UK; National Core Studies - Data and Connectivity.",,pdf:https://aura.abdn.ac.uk/bitstream/2164/19244/1/Rudan_etal_LRHE_BNT162b2_COVID_19_VOR.pdf; doi:https://doi.org/10.1016/j.lanepe.2022.100513; html:https://europepmc.org/articles/PMC9514975; pdf:https://europepmc.org/articles/PMC9514975?pdf=render
 34430954,https://doi.org/10.1016/s2666-7568(21)00168-9,Profile of humoral and cellular immune responses to single doses of BNT162b2 or ChAdOx1 nCoV-19 vaccines in residents and staff within residential care homes (VIVALDI): an observational study.,"Tut G, Lancaster T, Krutikov M, Sylla P, Bone D, Kaur N, Spalkova E, Bentley C, Amin U, Jadir AT, Hulme S, Butler MS, Ayodele M, Bruton R, Shrotri M, Azmi B, Fuller C, Irwin-Singer A, Hayward A, Copas A, Shallcross L, Moss P.",,The lancet. Healthy longevity,2021,2021-08-19,Y,,,,"<h4>Background</h4>Residents of long-term care facilities (LTCFs) have been prioritised for COVID-19 vaccination because of the high COVID-19 mortality in this population. Several countries have implemented an extended interval of up to 12 weeks between the first and second vaccine doses to increase population coverage of single-dose vaccination. We aimed to assess the magnitude and quality of adaptive immune responses following a single dose of COVID-19 vaccine in LTCF residents and staff.<h4>Methods</h4>From the LTCFs participating in the ongoing VIVALDI study (ISRCTN14447421), staff and residents who had received a first dose of COVID-19 vaccine (BNT162b2 [tozinameran] or ChAdOx1 nCoV-19), had pre-vaccination and post-vaccination blood samples (collected between Dec 11, 2020, and Feb 16, 2021), and could be linked to a pseudoidentifier in the COVID-19 Data Store were included in our cohort. Past infection with SARS-CoV-2 was defined on the basis of nucleocapsid-specific IgG antibodies being detected through a semiquantitative immunoassay, and participants who tested positive on this assay after but not before vaccination were excluded from the study. Processed blood samples were assessed for spike-specific immune responses, including spike-specific IgG antibody titres, T-cell responses to spike protein peptide mixes, and inhibition of ACE2 binding by spike protein from four variants of SARS-CoV-2 (the original strain as well as the B.1.1.7, B.1.351, and P.1 variants). Responses before and after vaccination were compared on the basis of age, previous infection status, role (staff or resident), and time since vaccination.<h4>Findings</h4>Our cohort comprised 124 participants from 14 LTCFs: 89 (72%) staff (median age 48 years [IQR 35·5-56]) and 35 (28%) residents (87 years [77-90]). Blood samples were collected a median 40 days (IQR 25-47; range 6-52) after vaccination. 30 (24%) participants (18 [20%] staff and 12 [34%] residents) had serological evidence of previous SARS-CoV-2 infection. All participants with previous infection had high antibody titres following vaccination that were independent of age (<i>r</i> <sub>s</sub>=0·076, p=0·70). In participants without evidence of previous infection, titres were negatively correlated with age (<i>r</i> <sub>s</sub>=-0·434, p<0·0001) and were 8·2-times lower in residents than in staff. This effect appeared to result from a kinetic delay antibody generation in older infection-naive participants, with the negative age correlation disappearing only in samples taken more than 42 days post-vaccination (<i>r</i> <sub>s</sub>=-0·207, p=0·20; n=40), in contrast to samples taken after 0-21 days (<i>r</i> <sub>s</sub>=-0·774, p=0·0043; n=12) or 22-42 days (<i>r</i> <sub>s</sub>=-0·437, p=0·0034; n=43). Spike-specific cellular responses were similar between older and younger participants. In infection-naive participants, antibody inhibition of ACE2 binding by spike protein from the original SARS-CoV-2 strain was negatively correlated with age (<i>r</i> <sub>s</sub>=-0·439, p<0·0001), and was significantly lower against spike protein from the B.1.351 variant (median inhibition 31% [14-100], p=0·010) and the P.1 variant (23% [14-97], p<0·0001) than against the original strain (58% [27-100]). By contrast, a single dose of vaccine resulted in around 100% inhibition of the spike-ACE2 interaction against all variants in people with a history of infection.<h4>Interpretation</h4>History of SARS-CoV-2 infection impacts the magnitude and quality of antibody response after a single dose of COVID-19 vaccine in LTCF residents. Residents who are infection-naive have delayed antibody responses to the first dose of vaccine and should be considered for an early second dose where possible.<h4>Funding</h4>UK Government Department of Health and Social Care.",,pdf:https://discovery.ucl.ac.uk/10133388/1/1-s2.0-S2666756821001689-main.pdf; doi:https://doi.org/10.1016/S2666-7568(21)00168-9; html:https://europepmc.org/articles/PMC8376213
 39054034,https://doi.org/10.1016/s2213-8587(24)00159-1,Incidence of diabetes after SARS-CoV-2 infection in England and the implications of COVID-19 vaccination: a retrospective cohort study of 16 million people.,"Taylor K, Eastwood S, Walker V, Cezard G, Knight R, Al Arab M, Wei Y, Horne EMF, Teece L, Forbes H, Walker A, Fisher L, Massey J, Hopcroft LEM, Palmer T, Cuitun Coronado J, Ip S, Davy S, Dillingham I, Morton C, Greaves F, Macleod J, Goldacre B, Wood A, Chaturvedi N, Sterne JAC, Denholm R, Longitudinal Health and Wellbeing and Data and Connectivity UK COVID-19 National Core Studies, CONVALESCENCE study, OpenSAFELY collaborative.",,The lancet. Diabetes & endocrinology,2024,2024-08-01,N,,,,"<h4>Background</h4>Some studies have shown that the incidence of type 2 diabetes increases after a diagnosis of COVID-19, although the evidence is not conclusive. However, the effects of the COVID-19 vaccine on this association, or the effect on other diabetes subtypes, are not clear. We aimed to investigate the association between COVID-19 and incidence of type 2, type 1, gestational and non-specific diabetes, and the effect of COVID- 19 vaccination, up to 52 weeks after diagnosis.<h4>Methods</h4>In this retrospective cohort study, we investigated the diagnoses of incident diabetes following COVID-19 diagnosis in England in a pre-vaccination, vaccinated, and unvaccinated cohort using linked electronic health records. People alive and aged between 18 years and 110 years, registered with a general practitioner for at least 6 months before baseline, and with available data for sex, region, and area deprivation were included. Those with a previous COVID-19 diagnosis were excluded. We estimated adjusted hazard ratios (aHRs) comparing diabetes incidence after COVID-19 diagnosis with diabetes incidence before or in the absence of COVID-19 up to 102 weeks after diagnosis. Results were stratified by COVID-19 severity (categorised as hospitalised or non-hospitalised) and diabetes type.<h4>Findings</h4>16 669 943 people were included in the pre-vaccination cohort (Jan 1, 2020-Dec 14, 2021), 12 279 669 in the vaccinated cohort, and 3 076 953 in the unvaccinated cohort (both June 1-Dec 14, 2021). In the pre-vaccination cohort, aHRs for the incidence of type 2 diabetes after COVID-19 (compared with before or in the absence of diagnosis) declined from 4·30 (95% CI 4·06-4·55) in weeks 1-4 to 1·24 (1·14-1.35) in weeks 53-102. aHRs were higher in unvaccinated people (8·76 [7·49-10·25]) than in vaccinated people (1·66 [1·50-1·84]) in weeks 1-4 and in patients hospitalised with COVID-19 (pre-vaccination cohort 28·3 [26·2-30·5]) in weeks 1-4 declining to 2·04 [1·72-2·42] in weeks 53-102) than in those who were not hospitalised (1·95 [1·78-2·13] in weeks 1-4 declining to 1·11 [1·01-1·22] in weeks 53-102). Type 2 diabetes persisted for 4 months after COVID-19 in around 60% of those diagnosed. Patterns were similar for type 1 diabetes, although excess incidence did not persist beyond 1 year after a COVID-19 diagnosis.<h4>Interpretation</h4>Elevated incidence of type 2 diabetes after COVID-19 is greater, and persists for longer, in people who were hospitalised with COVID-19 than in those who were not, and is markedly less apparent in people who have been vaccinated against COVID-19. Testing for type 2 diabetes after severe COVID-19 and the promotion of vaccination are important tools in addressing this public health problem.<h4>Funding</h4>UK National Institute for Health and Care Research, UK Research and Innovation (UKRI) Medical Research Council, UKRI Engineering and Physical Sciences Research Council, Health Data Research UK, Diabetes UK, British Heart Foundation, and the Stroke Association.",,doi:https://doi.org/10.1016/S2213-8587(24)00159-1
-36369151,https://doi.org/10.1038/s41467-022-34244-2,"Variant-specific symptoms of COVID-19 in a study of 1,542,510 adults in England.","Whitaker M, Elliott J, Bodinier B, Barclay W, Ward H, Cooke G, Donnelly CA, Chadeau-Hyam M, Elliott P.",,Nature communications,2022,2022-11-11,Y,,,,"Infection with SARS-CoV-2 virus is associated with a wide range of symptoms. The REal-time Assessment of Community Transmission -1 (REACT-1) study monitored the spread and clinical manifestation of SARS-CoV-2 among random samples of the population in England from 1 May 2020 to 31 March 2022. We show changing symptom profiles associated with the different variants over that period, with lower reporting of loss of sense of smell or taste for Omicron compared to previous variants, and higher reporting of cold-like and influenza-like symptoms, controlling for vaccination status. Contrary to the perception that recent variants have become successively milder, Omicron BA.2 was associated with reporting more symptoms, with greater disruption to daily activities, than BA.1. With restrictions lifted and routine testing limited in many countries, monitoring the changing symptom profiles associated with SARS-CoV-2 infection and effects on daily activities will become increasingly important.",,pdf:https://www.nature.com/articles/s41467-022-34244-2.pdf; doi:https://doi.org/10.1038/s41467-022-34244-2; html:https://europepmc.org/articles/PMC9651890; pdf:https://europepmc.org/articles/PMC9651890?pdf=render
-38902726,https://doi.org/10.1186/s12916-024-03477-x,Healthcare utilisation in people with long COVID: an OpenSAFELY cohort study.,"Lin LY, Henderson AD, Carlile O, Dillingham I, Butler-Cole BFC, Marks M, Briggs A, Jit M, Tomlinson LA, Bates C, Parry J, Bacon SCJ, Goldacre B, Mehrkar A, MacKenna B, OpenSAFELY Collaborative, Eggo RM, Herrett E.",,BMC medicine,2024,2024-06-20,Y,Health Care Costs; Electronic Health Records; Facilities And Services Utilization; Long Covid,,,"<h4>Background</h4>Long COVID potentially increases healthcare utilisation and costs. However, its impact on the NHS remains to be determined.<h4>Methods</h4>This study aims to assess the healthcare utilisation of individuals with long COVID. With the approval of NHS England, we conducted a matched cohort study using primary and secondary care data via OpenSAFELY, a platform for analysing anonymous electronic health records. The long COVID exposure group, defined by diagnostic codes, was matched with five comparators without long COVID between Nov 2020 and Jan 2023. We compared their total healthcare utilisation from GP consultations, prescriptions, hospital admissions, A&E visits, and outpatient appointments. Healthcare utilisation and costs were evaluated using a two-part model adjusting for covariates. Using a difference-in-difference model, we also compared healthcare utilisation after long COVID with pre-pandemic records.<h4>Results</h4>We identified 52,988 individuals with a long COVID diagnosis, matched to 264,867 comparators without a diagnosis. In the 12 months post-diagnosis, there was strong evidence that those with long COVID were more likely to use healthcare resources (OR: 8.29, 95% CI: 7.74-8.87), and have 49% more healthcare utilisation (RR: 1.49, 95% CI: 1.48-1.51). Our model estimated that the long COVID group had 30 healthcare visits per year (predicted mean: 29.23, 95% CI: 28.58-29.92), compared to 16 in the comparator group (predicted mean visits: 16.04, 95% CI: 15.73-16.36). Individuals with long COVID were more likely to have non-zero healthcare expenditures (OR = 7.66, 95% CI = 7.20-8.15), with costs being 44% higher than the comparator group (cost ratio = 1.44, 95% CI: 1.39-1.50). The long COVID group costs approximately £2500 per person per year (predicted mean cost: £2562.50, 95% CI: £2335.60-£2819.22), and the comparator group costs £1500 (predicted mean cost: £1527.43, 95% CI: £1404.33-1664.45). Historically, individuals with long COVID utilised healthcare resources more frequently, but their average healthcare utilisation increased more after being diagnosed with long COVID, compared to the comparator group.<h4>Conclusions</h4>Long COVID increases healthcare utilisation and costs. Public health policies should allocate more resources towards preventing, treating, and supporting individuals with long COVID.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-024-03477-x; doi:https://doi.org/10.1186/s12916-024-03477-x; html:https://europepmc.org/articles/PMC11188519; pdf:https://europepmc.org/articles/PMC11188519?pdf=render
 35780805,https://doi.org/10.1016/s2213-8587(22)00158-9,"Associations of BMI with COVID-19 vaccine uptake, vaccine effectiveness, and risk of severe COVID-19 outcomes after vaccination in England: a population-based cohort study.","Piernas C, Patone M, Astbury NM, Gao M, Sheikh A, Khunti K, Shankar-Hari M, Dixon S, Coupland C, Aveyard P, Hippisley-Cox J, Jebb SA.",,The lancet. Diabetes & endocrinology,2022,2022-07-01,Y,,,,"<h4>Background</h4>A high BMI has been associated with a reduced immune response to vaccination against influenza. We aimed to investigate the association between BMI and COVID-19 vaccine uptake, vaccine effectiveness, and risk of severe COVID-19 outcomes after vaccination by using a large, representative population-based cohort from England.<h4>Methods</h4>In this population-based cohort study, we used the QResearch database of general practice records and included patients aged 18 years or older who were registered at a practice that was part of the database in England between Dec 8, 2020 (date of the first vaccination in the UK), to Nov 17, 2021, with available data on BMI. Uptake was calculated as the proportion of people with zero, one, two, or three doses of the vaccine across BMI categories. Effectiveness was assessed through a nested matched case-control design to estimate odds ratios (OR) for severe COVID-19 outcomes (ie, admission to hospital or death) in people who had been vaccinated versus those who had not, considering vaccine dose and time periods since vaccination. Vaccine effectiveness against infection with SARS-CoV-2 was also investigated. Multivariable Cox proportional hazard models estimated the risk of severe COVID-19 outcomes associated with BMI (reference BMI 23 kg/m<sup>2</sup>) after vaccination.<h4>Findings</h4>Among 9 171 524 participants (mean age 52 [SD 19] years; BMI 26·7 [5·6] kg/m<sup>2</sup>), 566 461 tested positive for SARS-CoV-2 during follow-up, of whom 32 808 were admitted to hospital and 14 389 died. Of the total study sample, 19·2% (1 758 689) were unvaccinated, 3·1% (287 246) had one vaccine dose, 52·6% (4 828 327) had two doses, and 25·0% (2 297 262) had three doses. In people aged 40 years and older, uptake of two or three vaccine doses was more than 80% among people with overweight or obesity, which was slightly lower in people with underweight (70-83%). Although significant heterogeneity was found across BMI groups, protection against severe COVID-19 disease (comparing people who were vaccinated vs those who were not) was high after 14 days or more from the second dose for hospital admission (underweight: OR 0·51 [95% CI 0·41-0·63]; healthy weight: 0·34 [0·32-0·36]; overweight: 0·32 [0·30-0·34]; and obesity: 0·32 [0·30-0·34]) and death (underweight: 0·60 [0·36-0·98]; healthy weight: 0·39 [0·33-0·47]; overweight: 0·30 [0·25-0·35]; and obesity: 0·26 [0·22-0·30]). In the vaccinated cohort, there were significant linear associations between BMI and COVID-19 hospitalisation and death after the first dose, and J-shaped associations after the second dose.<h4>Interpretation</h4>Using BMI categories, there is evidence of protection against severe COVID-19 in people with overweight or obesity who have been vaccinated, which was of a similar magnitude to that of people of healthy weight. Vaccine effectiveness was slightly lower in people with underweight, in whom vaccine uptake was also the lowest for all ages. In the vaccinated cohort, there were increased risks of severe COVID-19 outcomes for people with underweight or obesity compared with the vaccinated population with a healthy weight. These results suggest the need for targeted efforts to increase uptake in people with low BMI (<18·5 kg/m<sup>2</sup>), in whom uptake is lower and vaccine effectiveness seems to be reduced. Strategies to achieve and maintain a healthy weight should be prioritised at the population level, which could help reduce the burden of COVID-19 disease.<h4>Funding</h4>UK Research and Innovation and National Institute for Health Research Oxford Biomedical Research Centre.",,pdf:http://www.thelancet.com/article/S2213858722001589/pdf; doi:https://doi.org/10.1016/S2213-8587(22)00158-9; html:https://europepmc.org/articles/PMC9246477; pdf:https://europepmc.org/articles/PMC9246477?pdf=render
+38902726,https://doi.org/10.1186/s12916-024-03477-x,Healthcare utilisation in people with long COVID: an OpenSAFELY cohort study.,"Lin LY, Henderson AD, Carlile O, Dillingham I, Butler-Cole BFC, Marks M, Briggs A, Jit M, Tomlinson LA, Bates C, Parry J, Bacon SCJ, Goldacre B, Mehrkar A, MacKenna B, OpenSAFELY Collaborative, Eggo RM, Herrett E.",,BMC medicine,2024,2024-06-20,Y,Health Care Costs; Electronic Health Records; Facilities And Services Utilization; Long Covid,,,"<h4>Background</h4>Long COVID potentially increases healthcare utilisation and costs. However, its impact on the NHS remains to be determined.<h4>Methods</h4>This study aims to assess the healthcare utilisation of individuals with long COVID. With the approval of NHS England, we conducted a matched cohort study using primary and secondary care data via OpenSAFELY, a platform for analysing anonymous electronic health records. The long COVID exposure group, defined by diagnostic codes, was matched with five comparators without long COVID between Nov 2020 and Jan 2023. We compared their total healthcare utilisation from GP consultations, prescriptions, hospital admissions, A&E visits, and outpatient appointments. Healthcare utilisation and costs were evaluated using a two-part model adjusting for covariates. Using a difference-in-difference model, we also compared healthcare utilisation after long COVID with pre-pandemic records.<h4>Results</h4>We identified 52,988 individuals with a long COVID diagnosis, matched to 264,867 comparators without a diagnosis. In the 12 months post-diagnosis, there was strong evidence that those with long COVID were more likely to use healthcare resources (OR: 8.29, 95% CI: 7.74-8.87), and have 49% more healthcare utilisation (RR: 1.49, 95% CI: 1.48-1.51). Our model estimated that the long COVID group had 30 healthcare visits per year (predicted mean: 29.23, 95% CI: 28.58-29.92), compared to 16 in the comparator group (predicted mean visits: 16.04, 95% CI: 15.73-16.36). Individuals with long COVID were more likely to have non-zero healthcare expenditures (OR = 7.66, 95% CI = 7.20-8.15), with costs being 44% higher than the comparator group (cost ratio = 1.44, 95% CI: 1.39-1.50). The long COVID group costs approximately £2500 per person per year (predicted mean cost: £2562.50, 95% CI: £2335.60-£2819.22), and the comparator group costs £1500 (predicted mean cost: £1527.43, 95% CI: £1404.33-1664.45). Historically, individuals with long COVID utilised healthcare resources more frequently, but their average healthcare utilisation increased more after being diagnosed with long COVID, compared to the comparator group.<h4>Conclusions</h4>Long COVID increases healthcare utilisation and costs. Public health policies should allocate more resources towards preventing, treating, and supporting individuals with long COVID.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-024-03477-x; doi:https://doi.org/10.1186/s12916-024-03477-x; html:https://europepmc.org/articles/PMC11188519; pdf:https://europepmc.org/articles/PMC11188519?pdf=render
+36369151,https://doi.org/10.1038/s41467-022-34244-2,"Variant-specific symptoms of COVID-19 in a study of 1,542,510 adults in England.","Whitaker M, Elliott J, Bodinier B, Barclay W, Ward H, Cooke G, Donnelly CA, Chadeau-Hyam M, Elliott P.",,Nature communications,2022,2022-11-11,Y,,,,"Infection with SARS-CoV-2 virus is associated with a wide range of symptoms. The REal-time Assessment of Community Transmission -1 (REACT-1) study monitored the spread and clinical manifestation of SARS-CoV-2 among random samples of the population in England from 1 May 2020 to 31 March 2022. We show changing symptom profiles associated with the different variants over that period, with lower reporting of loss of sense of smell or taste for Omicron compared to previous variants, and higher reporting of cold-like and influenza-like symptoms, controlling for vaccination status. Contrary to the perception that recent variants have become successively milder, Omicron BA.2 was associated with reporting more symptoms, with greater disruption to daily activities, than BA.1. With restrictions lifted and routine testing limited in many countries, monitoring the changing symptom profiles associated with SARS-CoV-2 infection and effects on daily activities will become increasingly important.",,pdf:https://www.nature.com/articles/s41467-022-34244-2.pdf; doi:https://doi.org/10.1038/s41467-022-34244-2; html:https://europepmc.org/articles/PMC9651890; pdf:https://europepmc.org/articles/PMC9651890?pdf=render
 36139476,https://doi.org/10.3390/cells11182901,Dysregulated Neutrophil Phenotype and Function in Hospitalised Non-ICU COVID-19 Pneumonia.,"Belchamber KBR, Thein OS, Hazeldine J, Grudzinska FS, Faniyi AA, Hughes MJ, Jasper AE, Yip KP, Crowley LE, Lugg ST, Sapey E, Parekh D, Thickett DR, Scott A.",,Cells,2022,2022-09-16,Y,Inflammation; neutrophil; innate immunity; Covid-19,,,"<b>Rationale</b>: Infection with the SARS-CoV2 virus is associated with elevated neutrophil counts. Evidence of neutrophil dysfunction in COVID-19 is based on transcriptomics or single functional assays. Cell functions are interwoven pathways, and understanding the effect across the spectrum of neutrophil function may identify therapeutic targets. <b>Objectives</b>: Examine neutrophil phenotype and function in 41 hospitalised, non-ICU COVID-19 patients versus 23 age-matched controls (AMC) and 26 community acquired pneumonia patients (CAP). <b>Methods</b>: Isolated neutrophils underwent ex vivo analyses for migration, bacterial phagocytosis, ROS generation, NETosis and receptor expression. Circulating DNAse 1 activity, levels of cfDNA, MPO, VEGF, IL-6 and sTNFRI were measured and correlated to clinical outcome. Serial sampling on day three to five post hospitalization were also measured. The effect of ex vivo PI3K inhibition was measured in a further cohort of 18 COVID-19 patients. <b>Results</b>: Compared to AMC and CAP, COVID-19 neutrophils demonstrated elevated transmigration (<i>p</i> = 0.0397) and NETosis (<i>p</i> = 0.0332), and impaired phagocytosis (<i>p</i> = 0.0036) associated with impaired ROS generation (<i>p</i> < 0.0001). The percentage of CD54+ neutrophils (<i>p</i> < 0.001) was significantly increased, while surface expression of CD11b (<i>p</i> = 0.0014) and PD-L1 (<i>p</i> = 0.006) were significantly decreased in COVID-19. COVID-19 and CAP patients showed increased systemic markers of NETosis including increased cfDNA (<i>p</i> = 0.0396) and impaired DNAse activity (<i>p</i> < 0.0001). The ex vivo inhibition of PI3K γ and δ reduced NET release by COVID-19 neutrophils (<i>p</i> = 0.0129). <b>Conclusions</b>: COVID-19 is associated with neutrophil dysfunction across all main effector functions, with altered phenotype, elevated migration and NETosis, and impaired antimicrobial responses. These changes highlight that targeting neutrophil function may help modulate COVID-19 severity.",,pdf:https://www.mdpi.com/2073-4409/11/18/2901/pdf?version=1663743438; doi:https://doi.org/10.3390/cells11182901; html:https://europepmc.org/articles/PMC9496854; pdf:https://europepmc.org/articles/PMC9496854?pdf=render
 36717723,https://doi.org/10.1038/s41590-022-01380-2,A patient-centric modeling framework captures recovery from SARS-CoV-2 infection.,"Ruffieux H, Hanson AL, Lodge S, Lawler NG, Whiley L, Gray N, Nolan TH, Bergamaschi L, Mescia F, Turner L, de Sa A, Pelly VS, Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) BioResource COVID-19 Collaboration, Kotagiri P, Kingston N, Bradley JR, Holmes E, Wist J, Nicholson JK, Lyons PA, Smith KGC, Richardson S, Bantug GR, Hess C.",,Nature immunology,2023,2023-01-30,Y,,,,"The biology driving individual patient responses to severe acute respiratory syndrome coronavirus 2 infection remains ill understood. Here, we developed a patient-centric framework leveraging detailed longitudinal phenotyping data and covering a year after disease onset, from 215 infected individuals with differing disease severities. Our analyses revealed distinct 'systemic recovery' profiles, with specific progression and resolution of the inflammatory, immune cell, metabolic and clinical responses. In particular, we found a strong inter-patient and intra-patient temporal covariation of innate immune cell numbers, kynurenine metabolites and lipid metabolites, which highlighted candidate immunologic and metabolic pathways influencing the restoration of homeostasis, the risk of death and that of long COVID. Based on these data, we identified a composite signature predictive of systemic recovery, using a joint model on cellular and molecular parameters measured soon after disease onset. New predictions can be generated using the online tool http://shiny.mrc-bsu.cam.ac.uk/apps/covid-19-systemic-recovery-prediction-app , designed to test our findings prospectively.",,pdf:https://www.nature.com/articles/s41590-022-01380-2.pdf; doi:https://doi.org/10.1038/s41590-022-01380-2; html:https://europepmc.org/articles/PMC9892000; pdf:https://europepmc.org/articles/PMC9892000?pdf=render
-36145196,https://doi.org/10.3390/nu14183821,Vitamin D Supplementation Does Not Influence SARS-CoV-2 Vaccine Efficacy or Immunogenicity: Sub-Studies Nested within the CORONAVIT Randomised Controlled Trial.,"Jolliffe DA, Vivaldi G, Chambers ES, Cai W, Li W, Faustini SE, Gibbons JM, Pade C, Coussens AK, Richter AG, McKnight Á, Martineau AR.",,Nutrients,2022,2022-09-16,Y,Interferon gamma; Vitamin D; Antibody; Randomised Controlled Trial; Breakthrough Sars-cov-2 Infection; Bnt162b2 Pfizer; Chadox1 Ncov-19 Oxford–astrazeneca,,,"Vitamin D deficiency has been reported to associate with the impaired development of antigen-specific responses following vaccination. We aimed to determine whether vitamin D supplements might boost the immunogenicity and efficacy of SARS-CoV-2 vaccination by conducting three sub-studies nested within the CORONAVIT randomised controlled trial, which investigated the effects of offering vitamin D supplements at a dose of 800 IU/day or 3200 IU/day vs. no offer on risk of acute respiratory infections in UK adults with circulating 25-hydroxyvitamin D concentrations <75 nmol/L. Sub-study 1 (n = 2808) investigated the effects of vitamin D supplementation on the risk of breakthrough SARS-CoV-2 infection following two doses of SARS-CoV-2 vaccine. Sub-study 2 (n = 1853) investigated the effects of vitamin D supplementation on titres of combined IgG, IgA and IgM (IgGAM) anti-Spike antibodies in eluates of dried blood spots collected after SARS-CoV-2 vaccination. Sub-study 3 (n = 100) investigated the effects of vitamin D supplementation on neutralising antibody and cellular responses in venous blood samples collected after SARS-CoV-2 vaccination. In total, 1945/2808 (69.3%) sub-study 1 participants received two doses of ChAdOx1 nCoV-19 (Oxford−AstraZeneca); the remainder received two doses of BNT162b2 (Pfizer). Mean follow-up 25(OH)D concentrations were significantly elevated in the 800 IU/day vs. no-offer group (82.5 vs. 53.6 nmol/L; mean difference 28.8 nmol/L, 95% CI 22.8−34.8) and in the 3200 IU/day vs. no offer group (105.4 vs. 53.6 nmol/L; mean difference 51.7 nmol/L, 45.1−58.4). Vitamin D supplementation did not influence the risk of breakthrough SARS-CoV-2 infection in vaccinated participants (800 IU/day vs. no offer: adjusted hazard ratio 1.28, 95% CI 0.89 to 1.84; 3200 IU/day vs. no offer: 1.17, 0.81 to 1.70). Neither did it influence IgGAM anti-Spike titres, neutralising antibody titres or IFN-γ concentrations in the supernatants of S peptide-stimulated whole blood. In conclusion, vitamin D replacement at a dose of 800 or 3200 IU/day effectively elevated 25(OH)D concentrations, but it did not influence the protective efficacy or immunogenicity of SARS-CoV-2 vaccination when given to adults who had a sub-optimal vitamin D status at baseline.",,pdf:https://www.mdpi.com/2072-6643/14/18/3821/pdf?version=1663570353; doi:https://doi.org/10.3390/nu14183821; html:https://europepmc.org/articles/PMC9506404; pdf:https://europepmc.org/articles/PMC9506404?pdf=render
 37363797,https://doi.org/10.1016/j.lanepe.2023.100653,Impact of COVID-19 on broad-spectrum antibiotic prescribing for common infections in primary care in England: a time-series analyses using OpenSAFELY and effects of predictors including deprivation.,"Zhong X, Pate A, Yang YT, Fahmi A, Ashcroft DM, Goldacre B, MacKenna B, Mehrkar A, Bacon SC, Massey J, Fisher L, Inglesby P, OpenSAFELY collaborative, Hand K, van Staa T, Palin V.",,The Lancet regional health. Europe,2023,2023-05-16,Y,Antimicrobial resistance; Primary Care; Broad-spectrum Antibiotics; Covid-19 Pandemic,,,"<h4>Background</h4>The COVID-19 pandemic impacted the healthcare systems, adding extra pressure to reduce antimicrobial resistance. Therefore, we aimed to evaluate changes in antibiotic prescription patterns after COVID-19 started.<h4>Methods</h4>With the approval of NHS England, we used the OpenSAFELY platform to access the TPP SystmOne electronic health record (EHR) system in primary care and selected patients prescribed antibiotics from 2019 to 2021. To evaluate the impact of COVID-19 on broad-spectrum antibiotic prescribing, we evaluated prescribing rates and its predictors and used interrupted time series analysis by fitting binomial logistic regression models.<h4>Findings</h4>Over 32 million antibiotic prescriptions were extracted over the study period; 8.7% were broad-spectrum. The study showed increases in broad-spectrum antibiotic prescribing (odds ratio [OR] 1.37; 95% confidence interval [CI] 1.36-1.38) as an immediate impact of the pandemic, followed by a gradual recovery with a 1.1-1.2% decrease in odds of broad-spectrum prescription per month. The same pattern was found within subgroups defined by age, sex, region, ethnicity, and socioeconomic deprivation quintiles. More deprived patients were more likely to receive broad-spectrum antibiotics, which differences remained stable over time. The most significant increase in broad-spectrum prescribing was observed for lower respiratory tract infection (OR 2.33; 95% CI 2.1-2.50) and otitis media (OR 1.96; 95% CI 1.80-2.13).<h4>Interpretation</h4>An immediate reduction in antibiotic prescribing and an increase in the proportion of broad-spectrum antibiotic prescribing in primary care was observed. The trends recovered to pre-pandemic levels, but the consequence of the COVID-19 pandemic on AMR needs further investigation.<h4>Funding</h4>This work was supported by Health Data Research UK and by National Institute for Health Research.",,doi:https://doi.org/10.1016/j.lanepe.2023.100653; doi:https://doi.org/10.1016/j.lanepe.2023.100653; html:https://europepmc.org/articles/PMC10186397; pdf:https://europepmc.org/articles/PMC10186397?pdf=render
+36145196,https://doi.org/10.3390/nu14183821,Vitamin D Supplementation Does Not Influence SARS-CoV-2 Vaccine Efficacy or Immunogenicity: Sub-Studies Nested within the CORONAVIT Randomised Controlled Trial.,"Jolliffe DA, Vivaldi G, Chambers ES, Cai W, Li W, Faustini SE, Gibbons JM, Pade C, Coussens AK, Richter AG, McKnight Á, Martineau AR.",,Nutrients,2022,2022-09-16,Y,Interferon gamma; Vitamin D; Antibody; Randomised Controlled Trial; Breakthrough Sars-cov-2 Infection; Bnt162b2 Pfizer; Chadox1 Ncov-19 Oxford–astrazeneca,,,"Vitamin D deficiency has been reported to associate with the impaired development of antigen-specific responses following vaccination. We aimed to determine whether vitamin D supplements might boost the immunogenicity and efficacy of SARS-CoV-2 vaccination by conducting three sub-studies nested within the CORONAVIT randomised controlled trial, which investigated the effects of offering vitamin D supplements at a dose of 800 IU/day or 3200 IU/day vs. no offer on risk of acute respiratory infections in UK adults with circulating 25-hydroxyvitamin D concentrations <75 nmol/L. Sub-study 1 (n = 2808) investigated the effects of vitamin D supplementation on the risk of breakthrough SARS-CoV-2 infection following two doses of SARS-CoV-2 vaccine. Sub-study 2 (n = 1853) investigated the effects of vitamin D supplementation on titres of combined IgG, IgA and IgM (IgGAM) anti-Spike antibodies in eluates of dried blood spots collected after SARS-CoV-2 vaccination. Sub-study 3 (n = 100) investigated the effects of vitamin D supplementation on neutralising antibody and cellular responses in venous blood samples collected after SARS-CoV-2 vaccination. In total, 1945/2808 (69.3%) sub-study 1 participants received two doses of ChAdOx1 nCoV-19 (Oxford−AstraZeneca); the remainder received two doses of BNT162b2 (Pfizer). Mean follow-up 25(OH)D concentrations were significantly elevated in the 800 IU/day vs. no-offer group (82.5 vs. 53.6 nmol/L; mean difference 28.8 nmol/L, 95% CI 22.8−34.8) and in the 3200 IU/day vs. no offer group (105.4 vs. 53.6 nmol/L; mean difference 51.7 nmol/L, 45.1−58.4). Vitamin D supplementation did not influence the risk of breakthrough SARS-CoV-2 infection in vaccinated participants (800 IU/day vs. no offer: adjusted hazard ratio 1.28, 95% CI 0.89 to 1.84; 3200 IU/day vs. no offer: 1.17, 0.81 to 1.70). Neither did it influence IgGAM anti-Spike titres, neutralising antibody titres or IFN-γ concentrations in the supernatants of S peptide-stimulated whole blood. In conclusion, vitamin D replacement at a dose of 800 or 3200 IU/day effectively elevated 25(OH)D concentrations, but it did not influence the protective efficacy or immunogenicity of SARS-CoV-2 vaccination when given to adults who had a sub-optimal vitamin D status at baseline.",,pdf:https://www.mdpi.com/2072-6643/14/18/3821/pdf?version=1663570353; doi:https://doi.org/10.3390/nu14183821; html:https://europepmc.org/articles/PMC9506404; pdf:https://europepmc.org/articles/PMC9506404?pdf=render
 37697235,https://doi.org/10.1186/s12879-023-08555-8,"COVID-19 vaccination in pregnancy: the impact of multimorbidity and smoking status on vaccine hesitancy, a cohort study of 25,111 women in Wales, UK.","Mhereeg M, Jones H, Kennedy J, Seaborne M, Parker M, Kennedy N, Akbari A, Zuccolo L, Azcoaga-Lorenzo A, Davies A, Nirantharakumar K, Brophy S.",,BMC infectious diseases,2023,2023-09-11,Y,Pregnancy; Smoking Status; Vaccine Uptake; Multimorbidity; Vaccine Hesitancy; Sail Databank; Covid-19 Vaccination,,,"<h4>Background</h4>Multimorbidity, smoking status, and pregnancy are identified as three risk factors associated with more severe outcomes following a SARS-CoV-2 infection, thus vaccination uptake is crucial for pregnant women living with multimorbidity and a history of smoking. This study aimed to examine the impact of multimorbidity, smoking status, and demographics (age, ethnic group, area of deprivation) on vaccine hesitancy among pregnant women in Wales using electronic health records (EHR) linkage.<h4>Methods</h4>This cohort study utilised routinely collected, individual-level, anonymised population-scale linked data within the Secure Anonymised Information Linkage (SAIL) Databank. Pregnant women were identified from 13th April 2021 to 31st December 2021. Survival analysis was employed to examine and compare the length of time to vaccination uptake in pregnancy by considering multimorbidity, smoking status, as well as depression, diabetes, asthma, and cardiovascular conditions independently. The study also assessed the variation in uptake by multimorbidity, smoking status, and demographics, both jointly and separately for the independent conditions, using hazard ratios (HR) derived from the Cox regression model.<h4>Results</h4>Within the population cohort, 8,203 (32.7%) received at least one dose of the COVID-19 vaccine during pregnancy, with 8,572 (34.1%) remaining unvaccinated throughout the follow-up period, and 8,336 (33.2%) receiving the vaccine postpartum. Women aged 30 years or older were more likely to have the vaccine in pregnancy. Those who had depression were slightly but significantly more likely to have the vaccine compared to those without depression (HR = 1.08, 95% CI 1.03 to 1.14, p = 0.002). Women living with multimorbidity were 1.12 times more likely to have the vaccine compared to those living without multimorbidity (HR = 1.12, 95% CI 1.04 to 1.19, p = 0.001). Vaccine uptakes were significantly lower among both current smokers and former smokers compared to never smokers (HR = 0.87, 95% CI 0.81 to 0.94, p < 0.001 and HR = 0.92, 95% CI 0.85 to 0.98, p = 0.015 respectively). Uptake was also lower among those living in the most deprived areas compared to those living in the most affluent areas (HR = 0.89, 95% CI 0.83 to 0.96, p = 0.002).<h4>Conclusion</h4>Younger women, living without multimorbidity, current and former smokers, and those living in the more deprived areas are less likely to have the vaccine, thus, a targeted approach to vaccinations may be required for these groups. Pregnant individuals living with multimorbidity exhibit a slight but statistically significant reduction in vaccine hesitancy towards COVID-19 during pregnancy.",,pdf:https://bmcinfectdis.biomedcentral.com/counter/pdf/10.1186/s12879-023-08555-8; doi:https://doi.org/10.1186/s12879-023-08555-8; html:https://europepmc.org/articles/PMC10496238; pdf:https://europepmc.org/articles/PMC10496238?pdf=render
 34238721,https://doi.org/10.1016/s2589-7500(21)00105-9,Temporal trends and forecasting of COVID-19 hospitalisations and deaths in Scotland using a national real-time patient-level data platform: a statistical modelling study.,"Simpson CR, Robertson C, Vasileiou E, Moore E, McCowan C, Agrawal U, Stagg HR, Docherty A, Mulholland R, Murray JLK, Ritchie LD, McMenamin J, Sheikh A.",,The Lancet. Digital health,2021,2021-07-05,Y,,,,"<h4>Background</h4>As the COVID-19 pandemic continues, national-level surveillance platforms with real-time individual person-level data are required to monitor and predict the epidemiological and clinical profile of COVID-19 and inform public health policy. We aimed to create a national dataset of patient-level data in Scotland to identify temporal trends and COVID-19 risk factors, and to develop a novel statistical prediction model to forecast COVID-19-related deaths and hospitalisations during the second wave.<h4>Methods</h4>We established a surveillance platform to monitor COVID-19 temporal trends using person-level primary care data (including age, sex, socioeconomic status, urban or rural residence, care home residence, and clinical risk factors) linked to data on SARS-CoV-2 RT-PCR tests, hospitalisations, and deaths for all individuals resident in Scotland who were registered with a general practice on Feb 23, 2020. A Cox proportional hazards model was used to estimate the association between clinical risk groups and time to hospitalisation and death. A survival prediction model derived from data from March 1 to June 23, 2020, was created to forecast hospital admissions and deaths from October to December, 2020. We fitted a generalised additive spline model to daily SARS-CoV-2 cases over the previous 10 weeks and used this to create a 28-day forecast of the number of daily cases. The age and risk group pattern of cases in the previous 3 weeks was then used to select a stratified sample of individuals from our cohort who had not previously tested positive, with future cases in each group sampled from a multinomial distribution. We then used their patient characteristics (including age, sex, comorbidities, and socioeconomic status) to predict their probability of hospitalisation or death.<h4>Findings</h4>Our cohort included 5 384 819 people, representing 98·6% of the entire estimated population residing in Scotland during 2020. Hospitalisation and death among those testing positive for SARS-CoV-2 between March 1 and June 23, 2020, were associated with several patient characteristics, including male sex (hospitalisation hazard ratio [HR] 1·47, 95% CI 1·38-1·57; death HR 1·62, 1·49-1·76) and various comorbidities, with the highest hospitalisation HR found for transplantation (4·53, 1·87-10·98) and the highest death HR for myoneural disease (2·33, 1·46-3·71). For those testing positive, there were decreasing temporal trends in hospitalisation and death rates. The proportion of positive tests among older age groups (>40 years) and those with at-risk comorbidities increased during October, 2020. On Nov 10, 2020, the projected number of hospitalisations for Dec 8, 2020 (28 days later) was 90 per day (95% prediction interval 55-125) and the projected number of deaths was 21 per day (12-29).<h4>Interpretation</h4>The estimated incidence of SARS-CoV-2 infection based on positive tests recorded in this unique data resource has provided forecasts of hospitalisation and death rates for the whole of Scotland. These findings were used by the Scottish Government to inform their response to reduce COVID-19-related morbidity and mortality.<h4>Funding</h4>Medical Research Council, National Institute for Health Research Health Technology Assessment Programme, UK Research and Innovation Industrial Strategy Challenge Fund, Health Data Research UK, Scottish Government Director General Health and Social Care.",,doi:https://doi.org/10.1016/s2589-7500(21)00105-9; doi:https://doi.org/10.1016/S2589-7500(21)00105-9; html:https://europepmc.org/articles/PMC8257056
 36417468,https://doi.org/10.1371/journal.pcbi.1010724,"Trends in SARS-CoV-2 infection prevalence during England's roadmap out of lockdown, January to July 2021.","Eales O, Wang H, Haw D, Ainslie KEC, Walters CE, Atchison C, Cooke G, Barclay W, Ward H, Darzi A, Ashby D, Donnelly CA, Elliott P, Riley S.",,PLoS computational biology,2022,2022-11-23,Y,,,,"<h4>Background</h4>Following rapidly rising COVID-19 case numbers, England entered a national lockdown on 6 January 2021, with staged relaxations of restrictions from 8 March 2021 onwards.<h4>Aim</h4>We characterise how the lockdown and subsequent easing of restrictions affected trends in SARS-CoV-2 infection prevalence.<h4>Methods</h4>On average, risk of infection is proportional to infection prevalence. The REal-time Assessment of Community Transmission-1 (REACT-1) study is a repeat cross-sectional study of over 98,000 people every round (rounds approximately monthly) that estimates infection prevalence in England. We used Bayesian P-splines to estimate prevalence and the time-varying reproduction number (Rt) nationally, regionally and by age group from round 8 (beginning 6 January 2021) to round 13 (ending 12 July 2021) of REACT-1. As a comparator, a separate segmented-exponential model was used to quantify the impact on Rt of each relaxation of restrictions.<h4>Results</h4>Following an initial plateau of 1.54% until mid-January, infection prevalence decreased until 13 May when it reached a minimum of 0.09%, before increasing until the end of the study to 0.76%. Following the first easing of restrictions, which included schools reopening, the reproduction number Rt increased by 82% (55%, 108%), but then decreased by 61% (82%, 53%) at the second easing of restrictions, which was timed to match the Easter school holidays. Following further relaxations of restrictions, the observed Rt increased steadily, though the increase due to these restrictions being relaxed was offset by the effects of vaccination and also affected by the rapid rise of Delta. There was a high degree of synchrony in the temporal patterns of prevalence between regions and age groups.<h4>Conclusion</h4>High-resolution prevalence data fitted to P-splines allowed us to show that the lockdown was effective at reducing risk of infection with school holidays/closures playing a significant part.",,pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010724&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1010724; html:https://europepmc.org/articles/PMC9728904; pdf:https://europepmc.org/articles/PMC9728904?pdf=render
 35468332,https://doi.org/10.1016/s1473-3099(22)00141-4,Severity of omicron variant of concern and effectiveness of vaccine boosters against symptomatic disease in Scotland (EAVE II): a national cohort study with nested test-negative design.,"Sheikh A, Kerr S, Woolhouse M, McMenamin J, Robertson C, EAVE II Collaborators.",,The Lancet. Infectious diseases,2022,2022-04-22,Y,,,,"<h4>Background</h4>Since its emergence in November, 2021, in southern Africa, the SARS-CoV-2 omicron variant of concern (VOC) has rapidly spread across the world. We aimed to investigate the severity of omicron and the extent to which booster vaccines are effective in preventing symptomatic infection.<h4>Methods</h4>In this study, using the Scotland-wide Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) platform, we did a cohort analysis with a nested test-negative design incident case-control study covering the period Nov 1-Dec 19, 2021, to provide initial estimates of omicron severity and the effectiveness of vaccine boosters against symptomatic disease relative to 25 weeks or more after the second vaccine dose. Primary care data derived from 940 general practices across Scotland were linked to laboratory data and hospital admission data. We compared outcomes between infection with the delta VOC (defined as S-gene positive) and the omicron VOC (defined as S-gene negative). We assessed effectiveness against symptomatic SARS-CoV-2 infection, with infection confirmed through a positive RT-PCR.<h4>Findings</h4>By Dec 19, 2021, there were 23 840 S-gene-negative cases in Scotland, which were predominantly among those aged 20-39 years (11 732 [49·2%]). The proportion of S-gene-negative cases that were possible reinfections was more than ten times that of S-gene-positive cases (7·6% vs 0·7%; p<0·0001). There were 15 hospital admissions in S-gene-negative individuals, giving an adjusted observed-to-expected admissions ratio of 0·32 (95% CI 0·19-0·52). The booster vaccine dose was associated with a 57% (54-60) reduction in the risk of symptomatic S-gene-negative infection relative to individuals who tested positive 25 weeks or more after the second vaccine dose.<h4>Interpretation</h4>These early national data suggest that omicron is associated with a two-thirds reduction in the risk of COVID-19 hospitalisation compared with delta. Although offering the greatest protection against delta, the booster dose of vaccination offers substantial additional protection against the risk of symptomatic COVID-19 for omicron compared with 25 weeks or more after the second vaccine dose.<h4>Funding</h4>Health Data Research UK, National Core Studies, Public Health Scotland, Scottish Government, UK Research and Innovation, and University of Edinburgh.",,pdf:https://aura.abdn.ac.uk/bitstream/2164/18748/1/Sheikh_etal_LID_Severity_Omicron_Variant_VOR.pdf; doi:https://doi.org/10.1016/S1473-3099(22)00141-4; html:https://europepmc.org/articles/PMC9033213
-38642613,https://doi.org/10.1016/j.clinme.2024.100209,Addressing ethnic disparities in neurological research in the United Kingdom: An example from the prospective multicentre COVID-19 Clinical Neuroscience Study.,"van Wamelen DJ, Rota S, Hartmann M, Martin NH, Alam AM, Thomas RH, Dodd KC, Jenkins T, Smith CJ, Zandi MS, Easton A, Carr G, Benjamin LA, Lilleker JB, Saucer D, Coles AJ, Wood N, Ray Chaudhuri K, Breen G, Michael BD, COVID-CNS consortium.",,"Clinical medicine (London, England)",2024,2024-04-19,Y,Diversity; Recruitment; Neurology; Ethnicity; Covid-19,,,"<h4>Background</h4>Minority ethnic groups have often been underrepresented in research, posing a problem in relation to external validity and extrapolation of findings. Here, we aimed to assess recruitment and retainment strategies in a large observational study assessing neurological complications following SARS-CoV-2 infection.<h4>Methods</h4>Participants were recruited following confirmed infection with SARS-CoV-2 and hospitalisation. Self-reported ethnicity was recorded alongside other demographic data to identify potential barriers to recruitment.<h4>Results</h4>807 participants were recruited to COVID-CNS, and ethnicity data were available for 93.2%. We identified a proportionate representation of self-reported ethnicity categories, and distribution of broad ethnicity categories mirrored individual centres' catchment areas. White ethnicity within individual centres ranged between 44.5% and 89.1%, with highest percentage of participants with non-White ethnicity in London-based centres. Examples are provided how to reach potentially underrepresented minority ethnic groups.<h4>Conclusions</h4>Recruitment barriers in relation to potentially underrepresented ethnic groups may be overcome with strategies identified here.",,doi:https://doi.org/10.1016/j.clinme.2024.100209; doi:https://doi.org/10.1016/j.clinme.2024.100209; html:https://europepmc.org/articles/PMC11091497; pdf:https://europepmc.org/articles/PMC11091497?pdf=render
 36647111,https://doi.org/10.1186/s12911-022-02093-0,"Harmonising electronic health records for reproducible research: challenges, solutions and recommendations from a UK-wide COVID-19 research collaboration.","Abbasizanjani H, Torabi F, Bedston S, Bolton T, Davies G, Denaxas S, Griffiths R, Herbert L, Hollings S, Keene S, Khunti K, Lowthian E, Lyons J, Mizani MA, Nolan J, Sudlow C, Walker V, Whiteley W, Wood A, Akbari A, CVD-COVID-UK/COVID-IMPACT Consortium.",,BMC medical informatics and decision making,2023,2023-01-16,Y,Population Health; Electronic Health Record; Reproducible Research; Common Data Model; Data Harmonisation; Sail Databank; Covid-19; Nhs Digital Tre For England; Trusted Research Environments,,,"<h4>Background</h4>The CVD-COVID-UK consortium was formed to understand the relationship between COVID-19 and cardiovascular diseases through analyses of harmonised electronic health records (EHRs) across the four UK nations. Beyond COVID-19, data harmonisation and common approaches enable analysis within and across independent Trusted Research Environments. Here we describe the reproducible harmonisation method developed using large-scale EHRs in Wales to accommodate the fast and efficient implementation of cross-nation analysis in England and Wales as part of the CVD-COVID-UK programme. We characterise current challenges and share lessons learnt.<h4>Methods</h4>Serving the scope and scalability of multiple study protocols, we used linked, anonymised individual-level EHR, demographic and administrative data held within the SAIL Databank for the population of Wales. The harmonisation method was implemented as a four-layer reproducible process, starting from raw data in the first layer. Then each of the layers two to four is framed by, but not limited to, the characterised challenges and lessons learnt. We achieved curated data as part of our second layer, followed by extracting phenotyped data in the third layer. We captured any project-specific requirements in the fourth layer.<h4>Results</h4>Using the implemented four-layer harmonisation method, we retrieved approximately 100 health-related variables for the 3.2 million individuals in Wales, which are harmonised with corresponding variables for > 56 million individuals in England. We processed 13 data sources into the first layer of our harmonisation method: five of these are updated daily or weekly, and the rest at various frequencies providing sufficient data flow updates for frequent capturing of up-to-date demographic, administrative and clinical information.<h4>Conclusions</h4>We implemented an efficient, transparent, scalable, and reproducible harmonisation method that enables multi-nation collaborative research. With a current focus on COVID-19 and its relationship with cardiovascular outcomes, the harmonised data has supported a wide range of research activities across the UK.",,pdf:https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-022-02093-0; doi:https://doi.org/10.1186/s12911-022-02093-0; html:https://europepmc.org/articles/PMC9842203; pdf:https://europepmc.org/articles/PMC9842203?pdf=render
+38642613,https://doi.org/10.1016/j.clinme.2024.100209,Addressing ethnic disparities in neurological research in the United Kingdom: An example from the prospective multicentre COVID-19 Clinical Neuroscience Study.,"van Wamelen DJ, Rota S, Hartmann M, Martin NH, Alam AM, Thomas RH, Dodd KC, Jenkins T, Smith CJ, Zandi MS, Easton A, Carr G, Benjamin LA, Lilleker JB, Saucer D, Coles AJ, Wood N, Ray Chaudhuri K, Breen G, Michael BD, COVID-CNS consortium.",,"Clinical medicine (London, England)",2024,2024-04-19,Y,Diversity; Recruitment; Neurology; Ethnicity; Covid-19,,,"<h4>Background</h4>Minority ethnic groups have often been underrepresented in research, posing a problem in relation to external validity and extrapolation of findings. Here, we aimed to assess recruitment and retainment strategies in a large observational study assessing neurological complications following SARS-CoV-2 infection.<h4>Methods</h4>Participants were recruited following confirmed infection with SARS-CoV-2 and hospitalisation. Self-reported ethnicity was recorded alongside other demographic data to identify potential barriers to recruitment.<h4>Results</h4>807 participants were recruited to COVID-CNS, and ethnicity data were available for 93.2%. We identified a proportionate representation of self-reported ethnicity categories, and distribution of broad ethnicity categories mirrored individual centres' catchment areas. White ethnicity within individual centres ranged between 44.5% and 89.1%, with highest percentage of participants with non-White ethnicity in London-based centres. Examples are provided how to reach potentially underrepresented minority ethnic groups.<h4>Conclusions</h4>Recruitment barriers in relation to potentially underrepresented ethnic groups may be overcome with strategies identified here.",,doi:https://doi.org/10.1016/j.clinme.2024.100209; doi:https://doi.org/10.1016/j.clinme.2024.100209; html:https://europepmc.org/articles/PMC11091497; pdf:https://europepmc.org/articles/PMC11091497?pdf=render
 36701357,https://doi.org/10.1371/journal.pone.0280943,Awareness and perceptions of Long COVID among people in the REACT programme: Early insights from a pilot interview study.,"Cooper E, Lound A, Atchison CJ, Whitaker M, Eccles C, Cooke GS, Elliott P, Ward H.",,PloS one,2023,2023-01-26,Y,,,,"<h4>Background</h4>Long COVID is a patient-made term describing new or persistent symptoms experienced following SARS-CoV-2 infection. The Real-time Assessment of Community Transmission-Long COVID (REACT-LC) study aims to understand variation in experiences following infection, and to identify biological, social, and environmental factors associated with Long COVID. We undertook a pilot interview study to inform the design, recruitment approach, and topic guide for the REACT-LC qualitative study. We sought to gain initial insights into the experience and attribution of new or persistent symptoms and the awareness or perceived applicability of the term Long COVID.<h4>Methods</h4>People were invited to REACT-LC assessment centres if they had taken part in REACT, a random community-based prevalence study, and had a documented history of SARS-CoV-2 infection. We invited people from REACT-LC assessment centres who had reported experiencing persistent symptoms for more than 12 weeks to take part in an interview. We conducted face to face and online semi-structured interviews which were transcribed and analysed using Thematic Analysis.<h4>Results</h4>We interviewed 13 participants (6 female, 7 male, median age 31). Participants reported a wide variation in both new and persistent symptoms which were often fluctuating or unpredictable in nature. Some participants were confident about the link between their persistent symptoms and COVID-19; however, others were unclear about the underlying cause of symptoms or felt that the impact of public health measures (such as lockdowns) played a role. We found differences in awareness and perceived applicability of the term Long COVID.<h4>Conclusion</h4>This pilot has informed the design, recruitment approach and topic guide for our qualitative study. It offers preliminary insights into the varied experiences of people living with persistent symptoms including differences in symptom attribution and perceived applicability of the term Long COVID. This variation shows the value of recruiting from a nationally representative sample of participants who are experiencing persistent symptoms.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0280943&type=printable; doi:https://doi.org/10.1371/journal.pone.0280943; html:https://europepmc.org/articles/PMC9879384; pdf:https://europepmc.org/articles/PMC9879384?pdf=render
 33722197,https://doi.org/10.1186/s12879-021-05951-w,Renin-angiotensin system inhibitors and susceptibility to COVID-19 in patients with hypertension: a propensity score-matched cohort study in primary care.,"Haroon S, Subramanian A, Cooper J, Anand A, Gokhale K, Byne N, Dhalla S, Acosta-Mena D, Taverner T, Okoth K, Wang J, Chandan JS, Sainsbury C, Zemedikun DT, Thomas GN, Parekh D, Marshall T, Sapey E, Adderley NJ, Nirantharakumar K.",,BMC infectious diseases,2021,2021-03-15,Y,,,,"<h4>Introduction</h4>Renin-angiotensin system (RAS) inhibitors have been postulated to influence susceptibility to Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). This study investigated whether there is an association between their prescription and the incidence of COVID-19 and all-cause mortality.<h4>Methods</h4>We conducted a propensity-score matched cohort study comparing the incidence of COVID-19 among patients with hypertension prescribed angiotensin-converting enzyme I (ACE) inhibitors or angiotensin II type-1 receptor blockers (ARBs) to those treated with calcium channel blockers (CCBs) in a large UK-based primary care database (The Health Improvement Network). We estimated crude incidence rates for confirmed/suspected COVID-19 in each drug exposure group. We used Cox proportional hazards models to produce adjusted hazard ratios for COVID-19. We assessed all-cause mortality as a secondary outcome.<h4>Results</h4>The incidence rate of COVID-19 among users of ACE inhibitors and CCBs was 9.3 per 1000 person-years (83 of 18,895 users [0.44%]) and 9.5 per 1000 person-years (85 of 18,895 [0.45%]), respectively. The adjusted hazard ratio was 0.92 (95% CI 0.68 to 1.26). The incidence rate among users of ARBs was 15.8 per 1000 person-years (79 out of 10,623 users [0.74%]). The adjusted hazard ratio was 1.38 (95% CI 0.98 to 1.95). There were no significant associations between use of RAS inhibitors and all-cause mortality.<h4>Conclusion</h4>Use of ACE inhibitors was not associated with the risk of COVID-19 whereas use of ARBs was associated with a statistically non-significant increase compared to the use of CCBs. However, no significant associations were observed between prescription of either ACE inhibitors or ARBs and all-cause mortality.",,pdf:https://bmcinfectdis.biomedcentral.com/counter/pdf/10.1186/s12879-021-05951-w; doi:https://doi.org/10.1186/s12879-021-05951-w; html:https://europepmc.org/articles/PMC7957446; pdf:https://europepmc.org/articles/PMC7957446?pdf=render
 36863848,https://doi.org/10.1136/archdischild-2022-325152,Characteristics and predictors of persistent symptoms post-COVID-19 in children and young people: a large community cross-sectional study in England.,"Atchison CJ, Whitaker M, Donnelly CA, Chadeau-Hyam M, Riley S, Darzi A, Ashby D, Barclay W, Cooke GS, Elliott P, Ward H.",,Archives of disease in childhood,2023,2023-03-02,Y,epidemiology; Paediatrics; Adolescent Health; Infectious Disease Medicine; Covid-19,,,"<h4>Objective</h4>To estimate the prevalence of, and associated risk factors for, persistent symptoms post-COVID-19 among children aged 5-17 years in England.<h4>Design</h4>Serial cross-sectional study.<h4>Setting</h4>Rounds 10-19 (March 2021 to March 2022) of the REal-time Assessment of Community Transmission-1 study (monthly cross-sectional surveys of random samples of the population in England).<h4>Study population</h4>Children aged 5-17 years in the community.<h4>Predictors</h4>Age, sex, ethnicity, presence of a pre-existing health condition, index of multiple deprivation, COVID-19 vaccination status and dominant UK circulating SARS-CoV-2 variant at time of symptom onset.<h4>Main outcome measures</h4>Prevalence of persistent symptoms, reported as those lasting ≥3 months post-COVID-19.<h4>Results</h4>Overall, 4.4% (95% CI 3.7 to 5.1) of 3173 5-11 year-olds and 13.3% (95% CI 12.5 to 14.1) of 6886 12-17 year-olds with prior symptomatic infection reported at least one symptom lasting ≥3 months post-COVID-19, of whom 13.5% (95% CI 8.4 to 20.9) and 10.9% (95% CI 9.0 to 13.2), respectively, reported their ability to carry out day-to-day activities was reduced 'a lot' due to their symptoms. The most common symptoms among participants with persistent symptoms were persistent coughing (27.4%) and headaches (25.4%) in children aged 5-11 years and loss or change of sense of smell (52.2%) and taste (40.7%) in participants aged 12-17 years. Higher age and having a pre-existing health condition were associated with higher odds of reporting persistent symptoms.<h4>Conclusions</h4>One in 23 5-11 year-olds and one in eight 12-17 year-olds post-COVID-19 report persistent symptoms lasting ≥3 months, of which one in nine report a large impact on performing day-to-day activities.",,pdf:https://adc.bmj.com/content/archdischild/early/2023/03/01/archdischild-2022-325152.full.pdf; doi:https://doi.org/10.1136/archdischild-2022-325152; html:https://europepmc.org/articles/PMC10313975; pdf:https://europepmc.org/articles/PMC10313975?pdf=render
@@ -157,16 +157,16 @@ PMC10929454,https://doi.org/,Optimising data curation pipelines for population-l
 34670038,https://doi.org/10.1056/nejmc2113864,BNT162b2 and ChAdOx1 nCoV-19 Vaccine Effectiveness against Death from the Delta Variant.,"Sheikh A, Robertson C, Taylor B.",,The New England journal of medicine,2021,2021-10-20,Y,,,,,,doi:https://doi.org/10.1056/nejmc2113864; doi:https://doi.org/10.1056/NEJMc2113864; html:https://europepmc.org/articles/PMC8552534; pdf:https://europepmc.org/articles/PMC8552534?pdf=render
 38135686,https://doi.org/10.1038/s41467-023-42320-4,Para-infectious brain injury in COVID-19 persists at follow-up despite attenuated cytokine and autoantibody responses.,"Michael BD, Dunai C, Needham EJ, Tharmaratnam K, Williams R, Huang Y, Boardman SA, Clark JJ, Sharma P, Subramaniam K, Wood GK, Collie C, Digby R, Ren A, Norton E, Leibowitz M, Ebrahimi S, Fower A, Fox H, Tato E, Ellul MA, Sunderland G, Held M, Hetherington C, Egbe FN, Palmos A, Stirrups K, Grundmann A, Chiollaz AC, Sanchez JC, Stewart JP, Griffiths M, Solomon T, Breen G, Coles AJ, Kingston N, Bradley JR, Chinnery PF, Cavanagh J, Irani SR, Vincent A, Baillie JK, Openshaw PJ, Semple MG, ISARIC4C Investigators, COVID-CNS Consortium, Taams LS, Menon DK.",,Nature communications,2023,2023-12-22,Y,,,,"To understand neurological complications of COVID-19 better both acutely and for recovery, we measured markers of brain injury, inflammatory mediators, and autoantibodies in 203 hospitalised participants; 111 with acute sera (1-11 days post-admission) and 92 convalescent sera (56 with COVID-19-associated neurological diagnoses). Here we show that compared to 60 uninfected controls, tTau, GFAP, NfL, and UCH-L1 are increased with COVID-19 infection at acute timepoints and NfL and GFAP are significantly higher in participants with neurological complications. Inflammatory mediators (IL-6, IL-12p40, HGF, M-CSF, CCL2, and IL-1RA) are associated with both altered consciousness and markers of brain injury. Autoantibodies are more common in COVID-19 than controls and some (including against MYL7, UCH-L1, and GRIN3B) are more frequent with altered consciousness. Additionally, convalescent participants with neurological complications show elevated GFAP and NfL, unrelated to attenuated systemic inflammatory mediators and to autoantibody responses. Overall, neurological complications of COVID-19 are associated with evidence of neuroglial injury in both acute and late disease and these correlate with dysregulated innate and adaptive immune responses acutely.",,pdf:https://www.nature.com/articles/s41467-023-42320-4.pdf; doi:https://doi.org/10.1038/s41467-023-42320-4; html:https://europepmc.org/articles/PMC10746705; pdf:https://europepmc.org/articles/PMC10746705?pdf=render
 38064420,https://doi.org/10.1371/journal.pgph.0002022,"Using electronic medical records to understand the impact of SARS-CoV-2 lockdown measures on maternal and neonatal outcomes in Kampala, Uganda.","Ouma J, Hookham L, Akera LA, Rukundo G, Kyohere M, Kakande A, Nakyesige R, Musoke P, Le Doare K.",,PLOS global public health,2023,2023-12-08,Y,,,,"Kawempe National Referral Hospital (KNRH) is a tertiary facility with over 21,000 pregnant or postpartum women admitted annually. The hospital, located in Kampala, Uganda, uses an Electronic Medical Records (EMR) system to capture patient data. Used since 2017, this readily available electronic health record (EHR) has the benefit of informing real-time clinical care, especially during pandemics such as COVID-19. We investigated the use of EHR to assess risk factors for adverse pregnancy and infant outcomes that can be incorporated into a data visualization dashboard for real time decision making during pandemics. This study analysed data from the UgandaEMR collected at pre-, during- and post-lockdown timepoints of the COVID-19 pandemic to determine its use in monitoring risk factors for adverse pregnancy and neonatal outcomes. Logistic regression models were used to identify the risk factors for adverse pregnancy and maternal outcomes including prematurity, obstetric complications, still births and neonatal deaths. Pearson chi-square test was used for pair-wise comparison of the outcomes at the various stages of the pandemic. Data analysis was performed in R, within the International COVID-19 Data Alliance (ICODA) workbench. A visualisation dashboard was developed based on the risk factors, to support decision making and improved healthcare delivery. Comparison of pre-and post-lockdown variables showed an increased risk of pre-term birth (adjusted Odds Ratio (aOR = 1.67, 95% confidence interval (CI) 1.38-2.01)); obstetric complications (aOR = 2.77, 95% CI: 2.53-3.03); immediate neonatal death (aOR = 3.89, 95% CI 2.65-5.72) and Caesarean section (aOR = 1.22, 95% CI 1.11-1.34). The significant risk factors for adverse outcomes were younger maternal age and gestational age <32weeks at labour. This study demonstrates the feasibility of using EHR to identify and monitor at-risk subpopulation groups accessing health services in real time. This information is critical for the development of timely and appropriate interventions in outbreaks and pandemic situations.",,doi:https://doi.org/10.1371/journal.pgph.0002022; html:https://europepmc.org/articles/PMC10707482; pdf:https://europepmc.org/articles/PMC10707482?pdf=render
+38162022,https://doi.org/10.1016/j.isci.2023.108526,"Hospital-treated prevalent infections, the plasma proteome and incident dementia among UK older adults.","Beydoun MA, Beydoun HA, Noren Hooten N, Meirelles O, Li Z, El-Hajj ZW, Weiss J, Maino Vieytes CA, Launer LJ, Evans MK, Zonderman AB.",,iScience,2023,2023-11-23,Y,Neurology; Public Health; Microbiome,,,"The plasma proteome can mediate the association of hospital-treated infections with dementia incidence. We screened up to 37,269 UK Biobank participants aged 50-74 years for the presence of a prevalent hospital-treated infection, subsequently tested as a predictor for ≤1,463 plasma proteins and dementia incidence. Four-way decomposition models decomposed infection-dementia total effect into pure mediation, pure interaction, neither or both through the plasma proteome. Hospital-treated infections increased dementia two-fold. The strongest mediation effect was through the growth differentiation factor 15 (GDF15) protein. Top 17 proteomic mediators explained collectively 5% of the total effect, while pathway analysis of all mediators (k = 221 plasma proteins) revealed top pathways including the immune system, signal transduction, metabolism, disease and metabolism of proteins, with the GDF15 cluster reflecting most strongly the ""transmembrane receptor protein tyrosine kinase signaling pathway"". The association of hospital-treated infections with dementia was partially mediated through GDF15 and other plasma proteomic markers.",,pdf:http://www.cell.com/article/S2589004223026032/pdf; doi:https://doi.org/10.1016/j.isci.2023.108526; html:https://europepmc.org/articles/PMC10755048; pdf:https://europepmc.org/articles/PMC10755048?pdf=render
 37302069,https://doi.org/10.1016/j.celrep.2023.112613,Proteomic analysis of circulating immune cells identifies cellular phenotypes associated with COVID-19 severity.,"Potts M, Fletcher-Etherington A, Nightingale K, Mescia F, Bergamaschi L, Calero-Nieto FJ, Antrobus R, Williamson J, Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID BioResource Collaboration, Parsons H, Huttlin EL, Kingston N, Göttgens B, Bradley JR, Lehner PJ, Matheson NJ, Smith KGC, Wills MR, Lyons PA, Weekes MP.",,Cell reports,2023,2023-05-29,Y,Cp: Immunology,,,"Certain serum proteins, including C-reactive protein (CRP) and D-dimer, have prognostic value in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Nonetheless, these factors are non-specific, providing limited mechanistic insight into the peripheral blood mononuclear cell (PBMC) populations that drive the pathogenesis of severe COVID-19. To identify cellular phenotypes associated with disease, we performed a comprehensive, unbiased analysis of total and plasma-membrane PBMC proteomes from 40 unvaccinated individuals with SARS-CoV-2, spanning the whole disease spectrum. Combined with RNA sequencing (RNA-seq) and flow cytometry from the same donors, we define a comprehensive multi-omic profile for each severity level, revealing that immune-cell dysregulation progresses with increasing disease. The cell-surface proteins CEACAMs1, 6, and 8, CD177, CD63, and CD89 are strongly associated with severe COVID-19, corresponding to the emergence of atypical CD3<sup>+</sup>CD4<sup>+</sup>CEACAM1/6/8<sup>+</sup>CD177<sup>+</sup>CD63<sup>+</sup>CD89<sup>+</sup> and CD16<sup>+</sup>CEACAM1/6/8<sup>+</sup> mononuclear cells. Utilization of these markers may facilitate real-time patient assessment by flow cytometry and identify immune populations that could be targeted to ameliorate immunopathology.",,pdf:http://www.cell.com/article/S2211124723006241/pdf; doi:https://doi.org/10.1016/j.celrep.2023.112613; html:https://europepmc.org/articles/PMC10243220; pdf:https://europepmc.org/articles/PMC10243220?pdf=render
 34977922,https://doi.org/10.1093/ije/dyab243,Cohort Profile: The COVID-19 in Pregnancy in Scotland (COPS) dynamic cohort of pregnant women to assess effects of viral and vaccine exposures on pregnancy.,"Stock SJ, Carruthers J, Denny C, Donaghy J, Goulding A, Hopcroft LEM, Hopkins L, Mulholland R, Agrawal U, Auyeung B, Katikireddi SV, McCowan C, Murray J, Robertson C, Sheikh A, Shi T, Simpson CR, Vasileiou E, Wood R.",,International journal of epidemiology,2022,2022-10-01,Y,,,,,,pdf:https://academic.oup.com/ije/article-pdf/51/5/e245/46495259/dyab243.pdf; doi:https://doi.org/10.1093/ije/dyab243; html:https://europepmc.org/articles/PMC9557859; pdf:https://europepmc.org/articles/PMC9557859?pdf=render
-38162022,https://doi.org/10.1016/j.isci.2023.108526,"Hospital-treated prevalent infections, the plasma proteome and incident dementia among UK older adults.","Beydoun MA, Beydoun HA, Noren Hooten N, Meirelles O, Li Z, El-Hajj ZW, Weiss J, Maino Vieytes CA, Launer LJ, Evans MK, Zonderman AB.",,iScience,2023,2023-11-23,Y,Neurology; Public Health; Microbiome,,,"The plasma proteome can mediate the association of hospital-treated infections with dementia incidence. We screened up to 37,269 UK Biobank participants aged 50-74 years for the presence of a prevalent hospital-treated infection, subsequently tested as a predictor for ≤1,463 plasma proteins and dementia incidence. Four-way decomposition models decomposed infection-dementia total effect into pure mediation, pure interaction, neither or both through the plasma proteome. Hospital-treated infections increased dementia two-fold. The strongest mediation effect was through the growth differentiation factor 15 (GDF15) protein. Top 17 proteomic mediators explained collectively 5% of the total effect, while pathway analysis of all mediators (k = 221 plasma proteins) revealed top pathways including the immune system, signal transduction, metabolism, disease and metabolism of proteins, with the GDF15 cluster reflecting most strongly the ""transmembrane receptor protein tyrosine kinase signaling pathway"". The association of hospital-treated infections with dementia was partially mediated through GDF15 and other plasma proteomic markers.",,pdf:http://www.cell.com/article/S2589004223026032/pdf; doi:https://doi.org/10.1016/j.isci.2023.108526; html:https://europepmc.org/articles/PMC10755048; pdf:https://europepmc.org/articles/PMC10755048?pdf=render
 36572492,https://doi.org/10.1136/bmjopen-2022-065862,"Variability and performance of NHS England's 'reason to reside' criteria in predicting hospital discharge in acute hospitals in England: a retrospective, observational cohort study.","Sapey E, Gallier S, Evison F, McNulty D, Reeves K, Ball S.",,BMJ open,2022,2022-12-26,Y,Information management; Health Policy; Quality In Health Care,,,"<h4>Objectives</h4>NHS England (NHSE) advocates 'reason to reside' (R2R) criteria to support discharge planning. The proportion of patients without R2R and their rate of discharge are reported daily by acute hospitals in England. R2R has no interoperable standardised data model (SDM), and its performance has not been validated. We aimed to understand the degree of intercentre and intracentre variation in R2R-related metrics reported to NHSE, define an SDM implemented within a single centre Electronic Health Record to generate an electronic R2R (eR2R) and evaluate its performance in predicting subsequent discharge.<h4>Design</h4>Retrospective observational cohort study using routinely collected health data.<h4>Setting</h4>122 NHS Trusts in England for national reporting and an acute hospital in England for local reporting.<h4>Participants</h4>6 602 706 patient-days were analysed using 3-month national data and 1 039 592 patient-days, using 3-year single centre data.<h4>Main outcome measures</h4>Variability in R2R-related metrics reported to NHSE. Performance of eR2R in predicting discharge within 24 hours.<h4>Results</h4>There were high levels of intracentre and intercentre variability in R2R-related metrics (p<0.0001) but not in eR2R. Informedness of eR2R for discharge within 24 hours was low (J-statistic 0.09-0.12 across three consecutive years). In those remaining in hospital without eR2R, 61.2% met eR2R criteria on subsequent days (76% within 24 hours), most commonly due to increased NEWS2 (21.9%) or intravenous therapy administration (32.8%).<h4>Conclusions</h4>Reported R2R metrics are highly variable between and within acute Trusts in England. Although case-mix or community care provision may account for some variability, the absence of a SDM prevents standardised reporting. Following the development of a SDM in one acute Trust, the variability reduced. However, the performance of eR2R was poor, prone to change even when negative and unable to meaningfully contribute to discharge planning.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/12/e065862.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-065862; html:https://europepmc.org/articles/PMC9805825; pdf:https://europepmc.org/articles/PMC9805825?pdf=render
 35813280,https://doi.org/10.1016/s2666-7568(22)00118-0,Antibody and cellular immune responses following dual COVID-19 vaccination within infection-naive residents of long-term care facilities: an observational cohort study.,"Tut G, Lancaster T, Sylla P, Butler MS, Kaur N, Spalkova E, Bentley C, Amin U, Jadir A, Hulme S, Ayodele M, Bone D, Tut E, Bruton R, Krutikov M, Giddings R, Shrotri M, Azmi B, Fuller C, Baynton V, Irwin-Singer A, Hayward A, Copas A, Shallcross L, Moss P.",,The lancet. Healthy longevity,2022,2022-07-04,Y,,,,"<h4>Background</h4>Older age and frailty are risk factors for poor clinical outcomes following SARS-CoV-2 infection. As such, COVID-19 vaccination has been prioritised for individuals with these factors, but there is concern that immune responses might be impaired due to age-related immune dysregulation and comorbidity. We aimed to study humoral and cellular responses to COVID-19 vaccines in residents of long-term care facilities (LTCFs).<h4>Methods</h4>In this observational cohort study, we assessed antibody and cellular immune responses following COVID-19 vaccination in members of staff and residents at 74 LTCFs across the UK. Staff and residents were eligible for inclusion if it was possible to link them to a pseudo-identifier in the COVID-19 datastore, if they had received two vaccine doses, and if they had given a blood sample 6 days after vaccination at the earliest. There were no comorbidity exclusion criteria. Participants were stratified by age (<65 years or ≥65 years) and infection status (previous SARS-CoV-2 infection [infection-primed group] or SARS-CoV-2 naive [infection-naive group]). Anticoagulated edetic acid (EDTA) blood samples were assessed and humoral and cellular responses were quantified.<h4>Findings</h4>Between Dec 11, 2020, and June 27, 2021, blood samples were taken from 220 people younger than 65 years (median age 51 years [IQR 39-61]; 103 [47%] had previously had a SARS-CoV-2 infection) and 268 people aged 65 years or older of LTCFs (median age 87 years [80-92]; 144 [43%] had a previous SARS-CoV-2 infection). Samples were taken a median of 82 days (IQR 72-100) after the second vaccination. Antibody responses following dual vaccination were strong and equivalent between participants younger then 65 years and those aged 65 years and older in the infection-primed group (median 125 285 Au/mL [1128 BAU/mL] for <65 year olds <i>vs</i> 157 979 Au/mL [1423 BAU/mL] for ≥65 year olds; p=0·47). The antibody response was reduced by 2·4-times (467 BAU/mL; p≤0·0001) in infection-naive people younger than 65 years and 8·1-times (174 BAU/mL; p≤0·0001) in infection-naive residents compared with their infection-primed counterparts. Antibody response was 2·6-times lower in infection-naive residents than in infection-naive people younger than 65 years (p=0·0006). Impaired neutralisation of delta (1.617.2) variant spike binding was also apparent in infection-naive people younger than 65 years and in those aged 65 years and older. Spike-specific T-cell responses were also significantly enhanced in the infection-primed group. Infection-naive people aged 65 years and older (203 SFU per million [IQR 89-374]) had a 52% lower T-cell response compared with infection-naive people younger than 65 years (85 SFU per million [30-206]; p≤0·0001). Post-vaccine spike-specific CD4 T-cell responses displayed single or dual production of IFN-γ and IL-2 were similar across infection status groups, whereas the infection-primed group had an extended functional profile with TNFα and CXCL10 production.<h4>Interpretation</h4>These data reveal suboptimal post-vaccine immune responses within infection-naive residents of LTCFs, and they suggest the need for optimisation of immune protection through the use of booster vaccination.<h4>Funding</h4>UK Government Department of Health and Social Care.",,pdf:http://pure-oai.bham.ac.uk/ws/files/173553190/1_s2.0_S2666756822001180_main.pdf; doi:https://doi.org/10.1016/S2666-7568(22)00118-0; html:https://europepmc.org/articles/PMC9252532; pdf:https://europepmc.org/articles/PMC9252532?pdf=render
 36244382,https://doi.org/10.1016/s0140-6736(22)01656-7,"Severe COVID-19 outcomes after full vaccination of primary schedule and initial boosters: pooled analysis of national prospective cohort studies of 30 million individuals in England, Northern Ireland, Scotland, and Wales.","Agrawal U, Bedston S, McCowan C, Oke J, Patterson L, Robertson C, Akbari A, Azcoaga-Lorenzo A, Bradley DT, Fagbamigbe AF, Grange Z, Hall ECR, Joy M, Katikireddi SV, Kerr S, Ritchie L, Murphy S, Owen RK, Rudan I, Shah SA, Simpson CR, Torabi F, Tsang RSM, de Lusignan S, Lyons RA, O'Reilly D, Sheikh A.",,"Lancet (London, England)",2022,2022-10-01,Y,,,,"<h4>Background</h4>Current UK vaccination policy is to offer future COVID-19 booster doses to individuals at high risk of serious illness from COVID-19, but it is still uncertain which groups of the population could benefit most. In response to an urgent request from the UK Joint Committee on Vaccination and Immunisation, we aimed to identify risk factors for severe COVID-19 outcomes (ie, COVID-19-related hospitalisation or death) in individuals who had completed their primary COVID-19 vaccination schedule and had received the first booster vaccine.<h4>Methods</h4>We constructed prospective cohorts across all four UK nations through linkages of primary care, RT-PCR testing, vaccination, hospitalisation, and mortality data on 30 million people. We included individuals who received primary vaccine doses of BNT162b2 (tozinameran; Pfizer-BioNTech) or ChAdOx1 nCoV-19 (Oxford-AstraZeneca) vaccines in our initial analyses. We then restricted analyses to those given a BNT162b2 or mRNA-1273 (elasomeran; Moderna) booster and had a severe COVID-19 outcome between Dec 20, 2021, and Feb 28, 2022 (when the omicron (B.1.1.529) variant was dominant). We fitted time-dependent Poisson regression models and calculated adjusted rate ratios (aRRs) and 95% CIs for the associations between risk factors and COVID-19-related hospitalisation or death. We adjusted for a range of potential covariates, including age, sex, comorbidities, and previous SARS-CoV-2 infection. Stratified analyses were conducted by vaccine type. We then did pooled analyses across UK nations using fixed-effect meta-analyses.<h4>Findings</h4>Between Dec 8, 2020, and Feb 28, 2022, 16 208 600 individuals completed their primary vaccine schedule and 13 836 390 individuals received a booster dose. Between Dec 20, 2021, and Feb 28, 2022, 59 510 (0·4%) of the primary vaccine group and 26 100 (0·2%) of those who received their booster had severe COVID-19 outcomes. The risk of severe COVID-19 outcomes reduced after receiving the booster (rate change: 8·8 events per 1000 person-years to 7·6 events per 1000 person-years). Older adults (≥80 years vs 18-49 years; aRR 3·60 [95% CI 3·45-3·75]), those with comorbidities (≥5 comorbidities vs none; 9·51 [9·07-9·97]), being male (male vs female; 1·23 [1·20-1·26]), and those with certain underlying health conditions-in particular, individuals receiving immunosuppressants (yes vs no; 5·80 [5·53-6·09])-and those with chronic kidney disease (stage 5 vs no; 3·71 [2·90-4·74]) remained at high risk despite the initial booster. Individuals with a history of COVID-19 infection were at reduced risk (infected ≥9 months before booster dose vs no previous infection; aRR 0·41 [95% CI 0·29-0·58]).<h4>Interpretation</h4>Older people, those with multimorbidity, and those with specific underlying health conditions remain at increased risk of COVID-19 hospitalisation and death after the initial vaccine booster and should, therefore, be prioritised for additional boosters, including novel optimised versions, and the increasing array of COVID-19 therapeutics.<h4>Funding</h4>National Core Studies-Immunity, UK Research and Innovation (Medical Research Council), Health Data Research UK, the Scottish Government, and the University of Edinburgh.",,pdf:http://www.thelancet.com/article/S0140673622016567/pdf; doi:https://doi.org/10.1016/S0140-6736(22)01656-7; html:https://europepmc.org/articles/PMC9560746; pdf:https://europepmc.org/articles/PMC9560746?pdf=render
 35033224,https://doi.org/10.1016/s2213-2600(21)00543-9,Risk of serious COVID-19 outcomes among adults with asthma in Scotland: a national incident cohort study.,"Shi T, Pan J, Vasileiou E, Robertson C, Sheikh A, Public Health Scotland and the EAVE II Collaborators.",,The Lancet. Respiratory medicine,2022,2022-01-13,Y,,,,"<h4>Background</h4>There is considerable uncertainty over whether adults with asthma should be offered booster vaccines against SARS-CoV-2 and, if so, who should be prioritised for booster vaccination. We were asked by the UK's Joint Commission on Vaccination and Immunisation to undertake an urgent analysis to identify which adults with asthma were at an increased risk of serious COVID-19 outcomes to inform deliberations on booster COVID-19 vaccines.<h4>Methods</h4>This national incident cohort study was done in all adults in Scotland aged 18 years and older who were included in the linked dataset of Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II). We used data from EAVE II to investigate the risk of COVID-19 hospitalisation and the composite outcome of intensive care unit (ICU) admission or death from COVID-19 among adults with asthma. A Cox proportional hazard model was used to derive adjusted hazard ratios (HRs) and 95% CIs for the association between asthma and COVID-19 hospital admission and ICU admission or death, stratified by markers of history of an asthma attack defined by either oral corticosteroid prescription (prednisolone, prednisone, and dexamethasone) in the 2 years before March 1, 2020, or hospitalisation for asthma before March 1, 2020. Analyses were adjusted for age, sex, socioeconomic status, comorbidity, previous hospitalisation, and vaccine status.<h4>Findings</h4>Between March 1, 2020, and July 27, 2021, 561 279 (12·7%) of 4 421 663 adults in Scotland had clinician-diagnosed-and-recorded-asthma. Among adults with asthma, 39 253 (7·0%) had confirmed SARS-CoV-2 infections, of whom 4828 (12·3%) were admitted to hospital for COVID-19 (among them, an estimated 600 [12·4%] might have been due to nosocomial infections). Adults with asthma were found to be at an increased risk of COVID-19 hospital admission (adjusted HR 1·27, 95% CI 1·23-1·32) compared with those without asthma. When using oral corticosteroid prescribing in the preceding 2 years as a marker for history of an asthma attack, the adjusted HR was 1·54 (95% CI 1·46-1·61) for those with three or more prescribed courses of oral corticosteroids, 1·37 (1·26-1·48) for those with two prescribed courses, 1·30 (1·23-1·37) for those with one prescribed course, and 1·15 (1·11-1·21) for those without any courses, compared with those aged 18 years or older without asthma. Adults with asthma were found to be at an increased risk of COVID-19 ICU admission or death compared with those without asthma (adjusted HR 1·13, 95 % CI 1·05-1·22). The adjusted HR was 1·44 (95% CI 1·31-1·58) for those with three or more prescribed courses of oral corticosteroids, 1·27 (1·09-1·48) for those with two prescribed courses, 1·04 (0·93-1·16) for those with one prescribed course, and 1·06 (0·97-1·17) for those without any course, compared with adults without asthma.<h4>Interpretation</h4>Adults with asthma who have required two or more courses of oral corticosteroids in the previous 2 years or a hospital admission for asthma before March 1, 2020, are at increased risk of both COVID-19 hospitalisation and ICU admission or death. Patients with a recent asthma attack should be considered a priority group for booster COVID-19 vaccines.<h4>Funding</h4>UK Research and Innovation (Medical Research Council), Research and Innovation Industrial Strategy Challenge Fund, Health Data Research UK, and Scottish Government.",,pdf:http://www.thelancet.com/article/S2213260021005439/pdf; doi:https://doi.org/10.1016/S2213-2600(21)00543-9; html:https://europepmc.org/articles/PMC8758152
-37343968,https://doi.org/10.1136/bmj-2022-072976,Risk prediction of covid-19 related death or hospital admission in adults testing positive for SARS-CoV-2 infection during the omicron wave in England (QCOVID4): cohort study.,"Hippisley-Cox J, Khunti K, Sheikh A, Nguyen-Van-Tam JS, Coupland CAC.",,BMJ (Clinical research ed.),2023,2023-06-21,Y,,,,"<h4>Objectives</h4>To derive and validate risk prediction algorithms (QCOVID4) to estimate the risk of covid-19 related death and hospital admission in people with a positive SARS-CoV-2 test result during the period when the omicron variant of the virus was predominant in England, and to evaluate performance compared with a high risk cohort from NHS Digital.<h4>Design</h4>Cohort study.<h4>Setting</h4>QResearch database linked to English national data on covid-19 vaccinations, SARS-CoV-2 test results, hospital admissions, and cancer and mortality data, 11 December 2021 to 31 March 2022, with follow-up to 30 June 2022.<h4>Participants</h4>1.3 million adults in the derivation cohort and 0.15 million adults in the validation cohort, aged 18-100 years, with a positive test result for SARS-CoV-2 infection.<h4>Main outcome measures</h4>Primary outcome was covid-19 related death and secondary outcome was hospital admission for covid-19. Risk equations with predictor variables were derived from models fitted in the derivation cohort. Performance was evaluated in a separate validation cohort.<h4>Results</h4>Of 1 297 922 people with a positive test result for SARS-CoV-2 infection in the derivation cohort, 18 756 (1.5%) had a covid-19 related hospital admission and 3878 (0.3%) had a covid-19 related death during follow-up. The final QCOVID4 models included age, deprivation score and a range of health and sociodemographic factors, number of covid-19 vaccinations, and previous SARS-CoV-2 infection. The risk of death related to covid-19 was lower among those who had received a covid-19 vaccine, with evidence of a dose-response relation (42% risk reduction associated with one vaccine dose and 92% reduction with four or more doses in men). Previous SARS-CoV-2 infection was associated with a reduction in the risk of covid-19 related death (49% reduction in men). The QCOVID4 algorithm for covid-19 explained 76.0% (95% confidence interval 73.9% to 78.2%) of the variation in time to covid-19 related death in men with a D statistic of 3.65 (3.43 to 3.86) and Harrell's C statistic of 0.970 (0.962 to 0.979). Results were similar for women. QCOVID4 was well calibrated. QCOVID4 was substantially more efficient than the NHS Digital algorithm for correctly identifying patients at high risk of covid-19 related death. Of the 461 covid-19 related deaths in the validation cohort, 333 (72.2%) were in the QCOVID4 high risk group and 95 (20.6%) in the NHS Digital high risk group.<h4>Conclusion</h4>The QCOVID4 risk algorithm, modelled from data during the period when the omicron variant of the SARS-CoV-2 virus was predominant in England, now includes vaccination dose and previous SARS-CoV-2 infection, and predicted covid-19 related death among people with a positive test result. QCOVID4 more accurately identified individuals at the highest levels of absolute risk for targeted interventions than the approach adopted by NHS Digital. QCOVID4 performed well and could be used for targeting treatments for covid-19 disease.",,pdf:https://www.bmj.com/content/bmj/381/bmj-2022-072976.full.pdf; doi:https://doi.org/10.1136/bmj-2022-072976; html:https://europepmc.org/articles/PMC10282241; pdf:https://europepmc.org/articles/PMC10282241?pdf=render
-35104837,https://doi.org/10.1038/s41586-022-04474-x,Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity.,"Meng B, Abdullahi A, Ferreira IATM, Goonawardane N, Saito A, Kimura I, Yamasoba D, Gerber PP, Fatihi S, Rathore S, Zepeda SK, Papa G, Kemp SA, Ikeda T, Toyoda M, Tan TS, Kuramochi J, Mitsunaga S, Ueno T, Shirakawa K, Takaori-Kondo A, Brevini T, Mallery DL, Charles OJ, CITIID-NIHR BioResource COVID-19 Collaboration, Genotype to Phenotype Japan (G2P-Japan) Consortium, Ecuador-COVID19 Consortium, Bowen JE, Joshi A, Walls AC, Jackson L, Martin D, Smith KGC, Bradley J, Briggs JAG, Choi J, Madissoon E, Meyer KB, Mlcochova P, Ceron-Gutierrez L, Doffinger R, Teichmann SA, Fisher AJ, Pizzuto MS, de Marco A, Corti D, Hosmillo M, Lee JH, James LC, Thukral L, Veesler D, Sigal A, Sampaziotis F, Goodfellow IG, Matheson NJ, Sato K, Gupta RK.",,Nature,2022,2022-02-01,Y,,,,"The SARS-CoV-2 Omicron BA.1 variant emerged in 2021<sup>1</sup> and has multiple mutations in its spike protein<sup>2</sup>. Here we show that the spike protein of Omicron has a higher affinity for ACE2 compared with Delta, and a marked change in its antigenicity increases Omicron's evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralizing antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralization. Importantly, the antiviral drugs remdesivir and molnupiravir retain efficacy against Omicron BA.1. Replication was similar for Omicron and Delta virus isolates in human nasal epithelial cultures. However, in lung cells and gut cells, Omicron demonstrated lower replication. Omicron spike protein was less efficiently cleaved compared with Delta. The differences in replication were mapped to the entry efficiency of the virus on the basis of spike-pseudotyped virus assays. The defect in entry of Omicron pseudotyped virus to specific cell types effectively correlated with higher cellular RNA expression of TMPRSS2, and deletion of TMPRSS2 affected Delta entry to a greater extent than Omicron. Furthermore, drug inhibitors targeting specific entry pathways<sup>3</sup> demonstrated that the Omicron spike inefficiently uses the cellular protease TMPRSS2, which promotes cell entry through plasma membrane fusion, with greater dependency on cell entry through the endocytic pathway. Consistent with suboptimal S1/S2 cleavage and inability to use TMPRSS2, syncytium formation by the Omicron spike was substantially impaired compared with the Delta spike. The less efficient spike cleavage of Omicron at S1/S2 is associated with a shift in cellular tropism away from TMPRSS2-expressing cells, with implications for altered pathogenesis.",,pdf:https://www.nature.com/articles/s41586-022-04474-x.pdf; doi:https://doi.org/10.1038/s41586-022-04474-x; html:https://europepmc.org/articles/PMC8942856; pdf:https://europepmc.org/articles/PMC8942856?pdf=render
 35027756,https://doi.org/10.1038/s41591-021-01666-2,SARS-CoV-2 infection and COVID-19 vaccination rates in pregnant women in Scotland.,"Stock SJ, Carruthers J, Calvert C, Denny C, Donaghy J, Goulding A, Hopcroft LEM, Hopkins L, McLaughlin T, Pan J, Shi T, Taylor B, Agrawal U, Auyeung B, Katikireddi SV, McCowan C, Murray J, Simpson CR, Robertson C, Vasileiou E, Sheikh A, Wood R.",,Nature medicine,2022,2022-01-13,Y,,,,"Population-level data on COVID-19 vaccine uptake in pregnancy and SARS-CoV-2 infection outcomes are lacking. We describe COVID-19 vaccine uptake and SARS-CoV-2 infection in pregnant women in Scotland, using whole-population data from a national, prospective cohort. Between the start of a COVID-19 vaccine program in Scotland, on 8 December 2020 and 31 October 2021, 25,917 COVID-19 vaccinations were given to 18,457 pregnant women. Vaccine coverage was substantially lower in pregnant women than in the general female population of 18-44 years; 32.3% of women giving birth in October 2021 had two doses of vaccine compared to 77.4% in all women. The extended perinatal mortality rate for women who gave birth within 28 d of a COVID-19 diagnosis was 22.6 per 1,000 births (95% CI 12.9-38.5; pandemic background rate 5.6 per 1,000 births; 452 out of 80,456; 95% CI 5.1-6.2). Overall, 77.4% (3,833 out of 4,950; 95% CI 76.2-78.6) of SARS-CoV-2 infections, 90.9% (748 out of 823; 95% CI 88.7-92.7) of SARS-CoV-2 associated with hospital admission and 98% (102 out of 104; 95% CI 92.5-99.7) of SARS-CoV-2 associated with critical care admission, as well as all baby deaths, occurred in pregnant women who were unvaccinated at the time of COVID-19 diagnosis. Addressing low vaccine uptake rates in pregnant women is imperative to protect the health of women and babies in the ongoing pandemic.",,pdf:https://www.nature.com/articles/s41591-021-01666-2.pdf; doi:https://doi.org/10.1038/s41591-021-01666-2; html:https://europepmc.org/articles/PMC8938271; pdf:https://europepmc.org/articles/PMC8938271?pdf=render
+35104837,https://doi.org/10.1038/s41586-022-04474-x,Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity.,"Meng B, Abdullahi A, Ferreira IATM, Goonawardane N, Saito A, Kimura I, Yamasoba D, Gerber PP, Fatihi S, Rathore S, Zepeda SK, Papa G, Kemp SA, Ikeda T, Toyoda M, Tan TS, Kuramochi J, Mitsunaga S, Ueno T, Shirakawa K, Takaori-Kondo A, Brevini T, Mallery DL, Charles OJ, CITIID-NIHR BioResource COVID-19 Collaboration, Genotype to Phenotype Japan (G2P-Japan) Consortium, Ecuador-COVID19 Consortium, Bowen JE, Joshi A, Walls AC, Jackson L, Martin D, Smith KGC, Bradley J, Briggs JAG, Choi J, Madissoon E, Meyer KB, Mlcochova P, Ceron-Gutierrez L, Doffinger R, Teichmann SA, Fisher AJ, Pizzuto MS, de Marco A, Corti D, Hosmillo M, Lee JH, James LC, Thukral L, Veesler D, Sigal A, Sampaziotis F, Goodfellow IG, Matheson NJ, Sato K, Gupta RK.",,Nature,2022,2022-02-01,Y,,,,"The SARS-CoV-2 Omicron BA.1 variant emerged in 2021<sup>1</sup> and has multiple mutations in its spike protein<sup>2</sup>. Here we show that the spike protein of Omicron has a higher affinity for ACE2 compared with Delta, and a marked change in its antigenicity increases Omicron's evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralizing antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralization. Importantly, the antiviral drugs remdesivir and molnupiravir retain efficacy against Omicron BA.1. Replication was similar for Omicron and Delta virus isolates in human nasal epithelial cultures. However, in lung cells and gut cells, Omicron demonstrated lower replication. Omicron spike protein was less efficiently cleaved compared with Delta. The differences in replication were mapped to the entry efficiency of the virus on the basis of spike-pseudotyped virus assays. The defect in entry of Omicron pseudotyped virus to specific cell types effectively correlated with higher cellular RNA expression of TMPRSS2, and deletion of TMPRSS2 affected Delta entry to a greater extent than Omicron. Furthermore, drug inhibitors targeting specific entry pathways<sup>3</sup> demonstrated that the Omicron spike inefficiently uses the cellular protease TMPRSS2, which promotes cell entry through plasma membrane fusion, with greater dependency on cell entry through the endocytic pathway. Consistent with suboptimal S1/S2 cleavage and inability to use TMPRSS2, syncytium formation by the Omicron spike was substantially impaired compared with the Delta spike. The less efficient spike cleavage of Omicron at S1/S2 is associated with a shift in cellular tropism away from TMPRSS2-expressing cells, with implications for altered pathogenesis.",,pdf:https://www.nature.com/articles/s41586-022-04474-x.pdf; doi:https://doi.org/10.1038/s41586-022-04474-x; html:https://europepmc.org/articles/PMC8942856; pdf:https://europepmc.org/articles/PMC8942856?pdf=render
+37343968,https://doi.org/10.1136/bmj-2022-072976,Risk prediction of covid-19 related death or hospital admission in adults testing positive for SARS-CoV-2 infection during the omicron wave in England (QCOVID4): cohort study.,"Hippisley-Cox J, Khunti K, Sheikh A, Nguyen-Van-Tam JS, Coupland CAC.",,BMJ (Clinical research ed.),2023,2023-06-21,Y,,,,"<h4>Objectives</h4>To derive and validate risk prediction algorithms (QCOVID4) to estimate the risk of covid-19 related death and hospital admission in people with a positive SARS-CoV-2 test result during the period when the omicron variant of the virus was predominant in England, and to evaluate performance compared with a high risk cohort from NHS Digital.<h4>Design</h4>Cohort study.<h4>Setting</h4>QResearch database linked to English national data on covid-19 vaccinations, SARS-CoV-2 test results, hospital admissions, and cancer and mortality data, 11 December 2021 to 31 March 2022, with follow-up to 30 June 2022.<h4>Participants</h4>1.3 million adults in the derivation cohort and 0.15 million adults in the validation cohort, aged 18-100 years, with a positive test result for SARS-CoV-2 infection.<h4>Main outcome measures</h4>Primary outcome was covid-19 related death and secondary outcome was hospital admission for covid-19. Risk equations with predictor variables were derived from models fitted in the derivation cohort. Performance was evaluated in a separate validation cohort.<h4>Results</h4>Of 1 297 922 people with a positive test result for SARS-CoV-2 infection in the derivation cohort, 18 756 (1.5%) had a covid-19 related hospital admission and 3878 (0.3%) had a covid-19 related death during follow-up. The final QCOVID4 models included age, deprivation score and a range of health and sociodemographic factors, number of covid-19 vaccinations, and previous SARS-CoV-2 infection. The risk of death related to covid-19 was lower among those who had received a covid-19 vaccine, with evidence of a dose-response relation (42% risk reduction associated with one vaccine dose and 92% reduction with four or more doses in men). Previous SARS-CoV-2 infection was associated with a reduction in the risk of covid-19 related death (49% reduction in men). The QCOVID4 algorithm for covid-19 explained 76.0% (95% confidence interval 73.9% to 78.2%) of the variation in time to covid-19 related death in men with a D statistic of 3.65 (3.43 to 3.86) and Harrell's C statistic of 0.970 (0.962 to 0.979). Results were similar for women. QCOVID4 was well calibrated. QCOVID4 was substantially more efficient than the NHS Digital algorithm for correctly identifying patients at high risk of covid-19 related death. Of the 461 covid-19 related deaths in the validation cohort, 333 (72.2%) were in the QCOVID4 high risk group and 95 (20.6%) in the NHS Digital high risk group.<h4>Conclusion</h4>The QCOVID4 risk algorithm, modelled from data during the period when the omicron variant of the SARS-CoV-2 virus was predominant in England, now includes vaccination dose and previous SARS-CoV-2 infection, and predicted covid-19 related death among people with a positive test result. QCOVID4 more accurately identified individuals at the highest levels of absolute risk for targeted interventions than the approach adopted by NHS Digital. QCOVID4 performed well and could be used for targeting treatments for covid-19 disease.",,pdf:https://www.bmj.com/content/bmj/381/bmj-2022-072976.full.pdf; doi:https://doi.org/10.1136/bmj-2022-072976; html:https://europepmc.org/articles/PMC10282241; pdf:https://europepmc.org/articles/PMC10282241?pdf=render
 38589944,https://doi.org/10.1111/bcp.16062,"OpenSAFELY: The impact of COVID-19 on azathioprine, leflunomide and methotrexate monitoring, and factors associated with change in monitoring rate.","Brown AD, Fisher L, Curtis HJ, Wiedemann M, Hulme WJ, Speed V, Hopcroft LEM, Cunningham C, Costello RE, Galloway JB, Russell MD, Bechman K, Kurt Z, Croker R, Wood C, Walker AJ, Schaffer AL, Bacon SCJ, Mehrkar A, Hickman G, Bates C, Cockburn J, Parry J, Hester F, Harper S, Goldacre B, OpenSAFELY Collaborative, MacKenna B.",,British journal of clinical pharmacology,2024,2024-04-08,Y,Methotrexate; General Practice; Azathioprine; Leflunomide; Electronic Health Records; Antirheumatic Agents; Covid‐19,,,"<h4>Aims</h4>The COVID-19 pandemic created unprecedented pressure on healthcare services. This study investigates whether disease-modifying antirheumatic drug (DMARD) safety monitoring was affected during the COVID-19 pandemic.<h4>Methods</h4>A population-based cohort study was conducted using the OpenSAFELY platform to access electronic health record data from 24.2 million patients registered at general practices using TPP's SystmOne software. Patients were included for further analysis if prescribed azathioprine, leflunomide or methotrexate between November 2019 and July 2022. Outcomes were assessed as monthly trends and variation between various sociodemographic and clinical groups for adherence with standard safety monitoring recommendations.<h4>Results</h4>An acute increase in the rate of missed monitoring occurred across the study population (+12.4 percentage points) when lockdown measures were implemented in March 2020. This increase was more pronounced for some patient groups (70-79 year-olds: +13.7 percentage points; females: +12.8 percentage points), regions (North West: +17.0 percentage points), medications (leflunomide: +20.7 percentage points) and monitoring tests (blood pressure: +24.5 percentage points). Missed monitoring rates decreased substantially for all groups by July 2022. Consistent differences were observed in overall missed monitoring rates between several groups throughout the study.<h4>Conclusion</h4>DMARD monitoring rates temporarily deteriorated during the COVID-19 pandemic. Deterioration coincided with the onset of lockdown measures, with monitoring rates recovering rapidly as lockdown measures were eased. Differences observed in monitoring rates between medications, tests, regions and patient groups highlight opportunities to tackle potential inequalities in the provision or uptake of monitoring services. Further research should evaluate the causes of the differences identified between groups.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/bcp.16062; doi:https://doi.org/10.1111/bcp.16062; html:https://europepmc.org/articles/PMC7616619; pdf:https://europepmc.org/articles/PMC7616619?pdf=render
 36481043,https://doi.org/10.1016/s2468-1253(22)00389-2,Neutralising antibody potency against SARS-CoV-2 wild-type and omicron BA.1 and BA.4/5 variants in patients with inflammatory bowel disease treated with infliximab and vedolizumab after three doses of COVID-19 vaccine (CLARITY IBD): an analysis of a prospective multicentre cohort study.,"Liu Z, Le K, Zhou X, Alexander JL, Lin S, Bewshea C, Chanchlani N, Nice R, McDonald TJ, Lamb CA, Sebastian S, Kok K, Lees CW, Hart AL, Pollok RC, Boyton RJ, Altmann DM, Pollock KM, Goodhand JR, Kennedy NA, Ahmad T, Powell N, CLARITY study investigators.",,The lancet. Gastroenterology & hepatology,2023,2022-12-05,Y,,,,"<h4>Background</h4>Anti-TNF drugs, such as infliximab, are associated with attenuated antibody responses after SARS-CoV-2 vaccination. We aimed to determine how the anti-TNF drug infliximab and the anti-integrin drug vedolizumab affect vaccine-induced neutralising antibodies against highly transmissible omicron (B.1.1.529) BA.1, and BA.4 and BA.5 (hereafter BA.4/5) SARS-CoV-2 variants, which possess the ability to evade host immunity and, together with emerging sublineages, are now the dominating variants causing current waves of infection.<h4>Methods</h4>CLARITY IBD is a prospective, multicentre, observational cohort study investigating the effect of infliximab and vedolizumab on SARS-CoV-2 infection and vaccination in patients with inflammatory bowel disease (IBD). Patients aged 5 years and older with a diagnosis of IBD and being treated with infliximab or vedolizumab for 6 weeks or longer were recruited from infusion units at 92 hospitals in the UK. In this analysis, we included participants who had received uninterrupted biological therapy since recruitment and without a previous SARS-CoV-2 infection. The primary outcome was neutralising antibody responses against SARS-CoV-2 wild-type and omicron subvariants BA.1 and BA.4/5 after three doses of SARS-CoV-2 vaccine. We constructed Cox proportional hazards models to investigate the risk of breakthrough infection in relation to neutralising antibody titres. The study is registered with the ISRCTN registry, ISRCTN45176516, and is closed to accrual.<h4>Findings</h4>Between Sept 22 and Dec 23, 2020, 7224 patients with IBD were recruited to the CLARITY IBD study, of whom 1288 had no previous SARS-CoV-2 infection after three doses of SARS-CoV-2 vaccine and were established on either infliximab (n=871) or vedolizumab (n=417) and included in this study (median age was 46·1 years [IQR 33·6-58·2], 610 [47·4%] were female, 671 [52·1%] were male, 1209 [93·9%] were White, and 46 [3·6%] were Asian). After three doses of SARS-CoV-2 vaccine, 50% neutralising titres (NT50s) were significantly lower in patients treated with infliximab than in those treated with vedolizumab, against wild-type (geometric mean 2062 [95% CI 1720-2473] vs 3440 [2939-4026]; p<0·0001), BA.1 (107·3 [86·40-133·2] vs 648·9 [523·5-804·5]; p<0·0001), and BA.4/5 (40·63 [31·99-51·60] vs 223·0 [183·1-271·4]; p<0·0001) variants. Breakthrough infection was significantly more frequent in patients treated with infliximab (119 [13·7%; 95% CI 11·5-16·2] of 871) than in those treated with vedolizumab (29 [7·0% [4·8-10·0] of 417; p=0·00040). Cox proportional hazards models of time to breakthrough infection after the third dose of vaccine showed infliximab treatment to be associated with a higher hazard risk than treatment with vedolizumab (hazard ratio [HR] 1·71 [95% CI 1·08-2·71]; p=0·022). Among participants who had a breakthrough infection, we found that higher neutralising antibody titres against BA.4/5 were associated with a lower hazard risk and, hence, a longer time to breakthrough infection (HR 0·87 [0·79-0·95]; p=0·0028).<h4>Interpretation</h4>Our findings underline the importance of continued SARS-CoV-2 vaccination programmes, including second-generation bivalent vaccines, especially in patient subgroups where vaccine immunogenicity and efficacy might be reduced, such as those on anti-TNF therapies.<h4>Funding</h4>Royal Devon University Healthcare NHS Foundation Trust; Hull University Teaching Hospital NHS Trust; NIHR Imperial Biomedical Research Centre; Crohn's and Colitis UK; Guts UK; National Core Studies Immunity Programme, UK Research and Innovation; and unrestricted educational grants from F Hoffmann-La Roche, Biogen, Celltrion Healthcare, Takeda, and Galapagos.",,doi:https://doi.org/10.1016/s2468-1253(22)00389-2; doi:https://doi.org/10.1016/S2468-1253(22)00389-2; html:https://europepmc.org/articles/PMC9757903; pdf:https://europepmc.org/articles/PMC9757903?pdf=render
 37363796,https://doi.org/10.1016/j.lanepe.2023.100636,Comparative effectiveness of two- and three-dose COVID-19 vaccination schedules involving AZD1222 and BNT162b2 in people with kidney disease: a linked OpenSAFELY and UK Renal Registry cohort study.,"OpenSAFELY Collaborative, Parker EPK, Horne EMF, Hulme WJ, Tazare J, Zheng B, Carr EJ, Loud F, Lyon S, Mahalingasivam V, MacKenna B, Mehrkar A, Scanlon M, Santhakumaran S, Steenkamp R, Goldacre B, Sterne JAC, Nitsch D, Tomlinson LA, LH&W NCS (or CONVALESCENCE) Collaborative.",,The Lancet regional health. Europe,2023,2023-05-03,Y,Vaccination; Effectiveness; Chronic Kidney Disease; Nhs England; Covid-19; Sars-cov-2,,,"<h4>Background</h4>Kidney disease is a key risk factor for COVID-19-related mortality and suboptimal vaccine response. Optimising vaccination strategies is essential to reduce the disease burden in this vulnerable population. We therefore compared the effectiveness of two- and three-dose schedules involving AZD1222 (AZ; ChAdOx1-S) and BNT162b2 (BNT) among people with kidney disease in England.<h4>Methods</h4>With the approval of NHS England, we performed a retrospective cohort study among people with moderate-to-severe kidney disease. Using linked primary care and UK Renal Registry records in the OpenSAFELY-TPP platform, we identified adults with stage 3-5 chronic kidney disease, dialysis recipients, and kidney transplant recipients. We used Cox proportional hazards models to compare COVID-19-related outcomes and non-COVID-19 death after two-dose (AZ-AZ vs BNT-BNT) and three-dose (AZ-AZ-BNT vs BNT-BNT-BNT) schedules.<h4>Findings</h4>After two doses, incidence during the Delta wave was higher in AZ-AZ (n = 257,580) than BNT-BNT recipients (n = 169,205; adjusted hazard ratios [95% CIs] 1.43 [1.37-1.50], 1.59 [1.43-1.77], 1.44 [1.12-1.85], and 1.09 [1.02-1.17] for SARS-CoV-2 infection, COVID-19-related hospitalisation, COVID-19-related death, and non-COVID-19 death, respectively). Findings were consistent across disease subgroups, including dialysis and transplant recipients. After three doses, there was little evidence of differences between AZ-AZ-BNT (n = 220,330) and BNT-BNT-BNT recipients (n = 157,065) for any outcome during a period of Omicron dominance.<h4>Interpretation</h4>Among individuals with moderate-to-severe kidney disease, two doses of BNT conferred stronger protection than AZ against SARS-CoV-2 infection and severe disease. A subsequent BNT dose levelled the playing field, emphasising the value of heterologous RNA doses in vulnerable populations.<h4>Funding</h4>National Core Studies, Wellcome Trust, MRC, and Health Data Research UK.",,doi:https://doi.org/10.1016/j.lanepe.2023.100636; doi:https://doi.org/10.1016/j.lanepe.2023.100636; html:https://europepmc.org/articles/PMC10155829; pdf:https://europepmc.org/articles/PMC10155829?pdf=render
@@ -187,36 +187,36 @@ PMC10929454,https://doi.org/,Optimising data curation pipelines for population-l
 35970827,https://doi.org/10.1038/s41467-022-32264-6,"Second-dose ChAdOx1 and BNT162b2 COVID-19 vaccines and thrombocytopenic, thromboembolic and hemorrhagic events in Scotland.","Simpson CR, Kerr S, Katikireddi SV, McCowan C, Ritchie LD, Pan J, Stock SJ, Rudan I, Tsang RSM, de Lusignan S, Hobbs FDR, Akbari A, Lyons RA, Robertson C, Sheikh A.",,Nature communications,2022,2022-08-15,Y,,,,"We investigated thrombocytopenic, thromboembolic and hemorrhagic events following a second dose of ChAdOx1 and BNT162b2 using a self-controlled case series analysis. We used a national prospective cohort with 2.0 million(m) adults vaccinated with two doses of ChAdOx or 1.6 m with BNT162b2. The incidence rate ratio (IRR) for idiopathic thrombocytopenic purpura (ITP) 14-20 days post-ChAdOx1 second dose was 2.14, 95% confidence interval (CI) 0.90-5.08. The incidence of ITP post-second dose ChAdOx1 was 0.59 (0.37-0.89) per 100,000 doses. No evidence of an increased risk of CVST was found for the 0-27 day risk period (IRR 0.83, 95% CI 0.16 to 4.26). However, few (≤5) events arose within this risk period. It is perhaps noteworthy that these events all clustered in the 7-13 day period (IRR 4.06, 95% CI 0.94 to 17.51). No other associations were found for second dose ChAdOx1, or any association for second dose BNT162b2 vaccination. Second dose ChAdOx1 vaccination was associated with increased borderline risks of ITP and CVST events. However, these events were rare thus providing reassurance about the safety of these vaccines. Further analyses including more cases are required to determine more precisely the risk profile for ITP and CVST after a second dose of ChAdOx1 vaccine.",,pdf:https://www.nature.com/articles/s41467-022-32264-6.pdf; doi:https://doi.org/10.1038/s41467-022-32264-6; html:https://europepmc.org/articles/PMC9377297; pdf:https://europepmc.org/articles/PMC9377297?pdf=render
 38951929,https://doi.org/10.1186/s13063-024-08273-9,"Clinical trial results in context: comparison of baseline characteristics and outcomes of 38,510 RECOVERY trial participants versus a reference population of 346,271 people hospitalised with COVID-19 in England.","Pessoa-Amorim G, Goldacre R, Crichton C, Stevens W, Nunn M, King A, Murray D, Welsh R, Pinches H, Rees A, Morris EJA, Landray MJ, Haynes R, Horby P, Wallendszus K, Peto L, Campbell M, Harper C, Mafham M.",,Trials,2024,2024-06-29,Y,Recovery; Randomised Trials; Evidence Translation; Covid-19,,,"<h4>Background</h4>Randomised trials are essential to reliably assess medical interventions. Nevertheless, interpretation of such studies, particularly when considering absolute effects, is enhanced by understanding how the trial population may differ from the populations it aims to represent.<h4>Methods</h4>We compared baseline characteristics and mortality of RECOVERY participants recruited in England (n = 38,510) with a reference population hospitalised with COVID-19 in England (n = 346,271) from March 2020 to November 2021. We used linked hospitalisation and mortality data for both cohorts to extract demographics, comorbidity/frailty scores, and crude and age- and sex-adjusted 28-day all-cause mortality.<h4>Results</h4>Demographics of RECOVERY participants were broadly similar to the reference population, but RECOVERY participants were younger (mean age [standard deviation]: RECOVERY 62.6 [15.3] vs reference 65.7 [18.5] years) and less frequently female (37% vs 45%). Comorbidity and frailty scores were lower in RECOVERY, but differences were attenuated after age stratification. Age- and sex-adjusted 28-day mortality declined over time but was similar between cohorts across the study period (RECOVERY 23.7% [95% confidence interval: 23.3-24.1%]; vs reference 24.8% [24.6-25.0%]), except during the first pandemic wave in the UK (March-May 2020) when adjusted mortality was lower in RECOVERY.<h4>Conclusions</h4>Adjusted 28-day mortality in RECOVERY was similar to a nationwide reference population of patients admitted with COVID-19 in England during the same period but varied substantially over time in both cohorts. Therefore, the absolute effect estimates from RECOVERY were broadly applicable to the target population at the time but should be interpreted in the light of current mortality estimates.<h4>Trial registration</h4>ISRCTN50189673- Feb. 04, 2020, NCT04381936- May 11, 2020.",,doi:https://doi.org/10.1186/s13063-024-08273-9; doi:https://doi.org/10.1186/s13063-024-08273-9; html:https://europepmc.org/articles/PMC11218071; pdf:https://europepmc.org/articles/PMC11218071?pdf=render
 38670744,https://doi.org/10.1016/s2589-7500(24)00028-1,Data challenges for international health emergencies: lessons learned from ten international COVID-19 driver projects.,"Boylan S, Arsenault C, Barreto M, Bozza FA, Fonseca A, Forde E, Hookham L, Humphreys GS, Ichihara MY, Le Doare K, Liu XF, McNamara E, Mugunga JC, Oliveira JF, Ouma J, Postlethwaite N, Retford M, Reyes LF, Morris AD, Wozencraft A.",,The Lancet. Digital health,2024,2024-05-01,N,,,,"The COVID-19 pandemic highlighted the importance of international data sharing and access to improve health outcomes for all. The International COVID-19 Data Alliance (ICODA) programme enabled 12 exemplar or driver projects to use existing health-related data to address major research questions relating to the pandemic, and developed data science approaches that helped each research team to overcome challenges, accelerate the data research cycle, and produce rapid insights and outputs. These approaches also sought to address inequity in data access and use, test approaches to ethical health data use, and make summary datasets and outputs accessible to a wider group of researchers. This Health Policy paper focuses on the challenges and lessons learned from ten of the ICODA driver projects, involving researchers from 19 countries and a range of health-related datasets. The ICODA programme reviewed the time taken for each project to complete stages of the health data research cycle and identified common challenges in areas such as data sharing agreements and data curation. Solutions included provision of standard data sharing templates, additional data curation expertise at an early stage, and a trusted research environment that facilitated data sharing across national boundaries and reduced risk. These approaches enabled the driver projects to rapidly produce research outputs, including publications, shared code, dashboards, and innovative resources, which can all be accessed and used by other research teams to address global health challenges.",,doi:https://doi.org/10.1016/s2589-7500(24)00028-1; doi:https://doi.org/10.1016/S2589-7500(24)00028-1
+34301672,https://doi.org/10.1136/bmjopen-2021-053402,Sociodemographic inequality in COVID-19 vaccination coverage among elderly adults in England: a national linked data study.,"Nafilyan V, Dolby T, Razieh C, Gaughan CH, Morgan J, Ayoubkhani D, Walker S, Khunti K, Glickman M, Yates T.",,BMJ open,2021,2021-07-23,Y,Infection control; epidemiology; Covid-19,,,"<h4>Objective</h4>To examine inequalities in COVID-19 vaccination rates among elderly adults in England.<h4>Design</h4>Cohort study.<h4>Setting</h4>People living in private households and communal establishments in England.<h4>Participants</h4>6 655 672 adults aged ≥70 years (mean 78.8 years, 55.2% women) who were alive on 15 March 2021.<h4>Main outcome measures</h4>Having received the first dose of a vaccine against COVID-19 by 15 March 2021. We calculated vaccination rates and estimated unadjusted and adjusted ORs using logistic regression models.<h4>Results</h4>By 15 March 2021, 93.2% of people living in England aged 70 years and over had received at least one dose of a COVID-19 vaccine. While vaccination rates differed across all factors considered apart from sex, the greatest disparities were seen between ethnic and religious groups. The lowest rates were in people of black African and black Caribbean ethnic backgrounds, where only 67.2% and 73.8% had received a vaccine, with adjusted odds of not being vaccinated at 5.01 (95% CI 4.86 to 5.16) and 4.85 (4.75 to 4.96) times greater than the white British group. The proportion of individuals self-identifying as Muslim and Buddhist who had received a vaccine was 79.1% and 84.1%, respectively. Older age, greater area deprivation, less advantaged socioeconomic position (proxied by living in a rented home), being disabled and living either alone or in a multigenerational household were also associated with higher odds of not having received the vaccine.<h4>Conclusion</h4>Research is now urgently needed to understand why disparities exist in these groups and how they can best be addressed through public health policy and community engagement.",,doi:https://doi.org/10.1136/bmjopen-2021-053402; doi:https://doi.org/10.1136/bmjopen-2021-053402; html:https://europepmc.org/articles/PMC8313303; pdf:https://europepmc.org/articles/PMC8313303?pdf=render
 38419914,https://doi.org/10.23889/ijpds.v8i4.2169,Towards a standardised cross-sectoral data access agreement template for research: a core set of principles for data access within trusted research environments.,"Brophy R, Bellavia E, Bluemink MG, Evans K, Hashimi M, Macaulay Y, McNamara E, Noble A, Quattroni P, Rudczenko A, Morris AD, Smith C, Boyd A.",,International journal of population data science,2023,2023-10-09,Y,"Health Data; Pie; Data Governance; Tres; Sdes; Public Involvement And Engagement; Trusted Research Environments; Daa, Data Sharing Agreement; Keywords Data Access Agreement; Secure Data Environments",,,"<h4>Introduction</h4>Trusted Research Environments (TREs) are secure computing environments that provide access to data for approved researchers to use in studies that can save and improve lives. TREs rely on Data Access Agreements (DAAs) to bind researchers and their organisations to the terms and conditions of accessing the infrastructure and data use. However, DAAs can be overly lengthy, complex, and can contain outdated terms from historical data sharing agreements for physical exchange of data. This is often cited as a cause of significant delays to legal review and research projects starting.<h4>Objectives</h4>The aim was to develop a standardised DAA optimised for data science in TREs across the UK and framed around the 'Five Safes framework' for trustworthy data use. The DAA is underpinned by principles of data access in TREs, the development of which is described in this paper.<h4>Methods</h4>The Pan-UK Data Governance Steering Group of the UK Health Data Research Alliance led the development of a core set of data access principles. This was informed by a benchmarking exercise of DAAs used by established TREs and consultation with public members and stakeholders.<h4>Results</h4>We have defined a core set of principles for TRE data access that can be mapped to a common set of DAA terms for UK-based TREs. Flexibility will be ensured by including terms specific to TREs or specific data/data owners in customisable annexes. Public views obtained through public involvement and engagement (PIE) activities are also reported.<h4>Conclusions</h4>These principles provide the foundation for a standardised UK TRE DAA template, designed to support the growing ecosystem of TREs. By providing a familiar structure and terms, this template aims to build trust among data owners and the UK public and to provide clarity to researchers on their obligations to protect the data. Widespread adoption is intended to accelerate health data research by enabling faster approval of projects, ultimately enabling more timely and effective research.",,doi:https://doi.org/10.23889/ijpds.v8i4.2169; html:https://europepmc.org/articles/PMC10900295; pdf:https://europepmc.org/articles/PMC10900295?pdf=render
 37200350,https://doi.org/10.1371/journal.pone.0285979,"An external validation of the QCOVID3 risk prediction algorithm for risk of hospitalisation and death from COVID-19: An observational, prospective cohort study of 1.66m vaccinated adults in Wales, UK.","Lyons J, Nafilyan V, Akbari A, Bedston S, Harrison E, Hayward A, Hippisley-Cox J, Kee F, Khunti K, Rahman S, Sheikh A, Torabi F, Lyons RA.",,PloS one,2023,2023-05-18,Y,,,,"<h4>Introduction</h4>At the start of the COVID-19 pandemic there was an urgent need to identify individuals at highest risk of severe outcomes, such as hospitalisation and death following infection. The QCOVID risk prediction algorithms emerged as key tools in facilitating this which were further developed during the second wave of the COVID-19 pandemic to identify groups of people at highest risk of severe COVID-19 related outcomes following one or two doses of vaccine.<h4>Objectives</h4>To externally validate the QCOVID3 algorithm based on primary and secondary care records for Wales, UK.<h4>Methods</h4>We conducted an observational, prospective cohort based on electronic health care records for 1.66m vaccinated adults living in Wales on 8th December 2020, with follow-up until 15th June 2021. Follow-up started from day 14 post vaccination to allow the full effect of the vaccine.<h4>Results</h4>The scores produced by the QCOVID3 risk algorithm showed high levels of discrimination for both COVID-19 related deaths and hospital admissions and good calibration (Harrell C statistic: ≥ 0.828).<h4>Conclusion</h4>This validation of the updated QCOVID3 risk algorithms in the adult vaccinated Welsh population has shown that the algorithms are valid for use in the Welsh population, and applicable on a population independent of the original study, which has not been previously reported. This study provides further evidence that the QCOVID algorithms can help inform public health risk management on the ongoing surveillance and intervention to manage COVID-19 related risks.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0285979&type=printable; doi:https://doi.org/10.1371/journal.pone.0285979; html:https://europepmc.org/articles/PMC10194890; pdf:https://europepmc.org/articles/PMC10194890?pdf=render
-34301672,https://doi.org/10.1136/bmjopen-2021-053402,Sociodemographic inequality in COVID-19 vaccination coverage among elderly adults in England: a national linked data study.,"Nafilyan V, Dolby T, Razieh C, Gaughan CH, Morgan J, Ayoubkhani D, Walker S, Khunti K, Glickman M, Yates T.",,BMJ open,2021,2021-07-23,Y,Infection control; epidemiology; Covid-19,,,"<h4>Objective</h4>To examine inequalities in COVID-19 vaccination rates among elderly adults in England.<h4>Design</h4>Cohort study.<h4>Setting</h4>People living in private households and communal establishments in England.<h4>Participants</h4>6 655 672 adults aged ≥70 years (mean 78.8 years, 55.2% women) who were alive on 15 March 2021.<h4>Main outcome measures</h4>Having received the first dose of a vaccine against COVID-19 by 15 March 2021. We calculated vaccination rates and estimated unadjusted and adjusted ORs using logistic regression models.<h4>Results</h4>By 15 March 2021, 93.2% of people living in England aged 70 years and over had received at least one dose of a COVID-19 vaccine. While vaccination rates differed across all factors considered apart from sex, the greatest disparities were seen between ethnic and religious groups. The lowest rates were in people of black African and black Caribbean ethnic backgrounds, where only 67.2% and 73.8% had received a vaccine, with adjusted odds of not being vaccinated at 5.01 (95% CI 4.86 to 5.16) and 4.85 (4.75 to 4.96) times greater than the white British group. The proportion of individuals self-identifying as Muslim and Buddhist who had received a vaccine was 79.1% and 84.1%, respectively. Older age, greater area deprivation, less advantaged socioeconomic position (proxied by living in a rented home), being disabled and living either alone or in a multigenerational household were also associated with higher odds of not having received the vaccine.<h4>Conclusion</h4>Research is now urgently needed to understand why disparities exist in these groups and how they can best be addressed through public health policy and community engagement.",,doi:https://doi.org/10.1136/bmjopen-2021-053402; doi:https://doi.org/10.1136/bmjopen-2021-053402; html:https://europepmc.org/articles/PMC8313303; pdf:https://europepmc.org/articles/PMC8313303?pdf=render
+33728401,https://doi.org/10.1038/s42254-020-0178-4,Modelling COVID-19.,"Vespignani A, Tian H, Dye C, Lloyd-Smith JO, Eggo RM, Shrestha M, Scarpino SV, Gutierrez B, Kraemer MUG, Wu J, Leung K, Leung GM.",,Nature reviews. Physics,2020,2020-05-06,Y,Applied Mathematics; Complex Networks,,,"As the COVID-19 pandemic continues, mathematical epidemiologists share their views on what models reveal about how the disease has spread, the current state of play and what work still needs to be done.",Vespignani et al. used mathematical models to model the epidemic of covid-19 and to predict future scenarios for possible interventions and inform policy and practice.,pdf:https://www.nature.com/articles/s42254-020-0178-4.pdf; doi:https://doi.org/10.1038/s42254-020-0178-4; html:https://europepmc.org/articles/PMC7201389; pdf:https://europepmc.org/articles/PMC7201389?pdf=render
 37120260,https://doi.org/10.1016/s2468-2667(23)00079-8,Changes in COVID-19-related mortality across key demographic and clinical subgroups in England from 2020 to 2022: a retrospective cohort study using the OpenSAFELY platform.,"Nab L, Parker EPK, Andrews CD, Hulme WJ, Fisher L, Morley J, Mehrkar A, MacKenna B, Inglesby P, Morton CE, Bacon SCJ, Hickman G, Evans D, Ward T, Smith RM, Davy S, Dillingham I, Maude S, Butler-Cole BFC, O'Dwyer T, Stables CL, Bridges L, Bates C, Cockburn J, Parry J, Hester F, Harper S, Zheng B, Williamson EJ, Eggo RM, Evans SJW, Goldacre B, Tomlinson LA, Walker AJ, OpenSAFELY Collaborative.",,The Lancet. Public health,2023,2023-05-01,Y,,,,"<h4>Background</h4>COVID-19 has been shown to differently affect various demographic and clinical population subgroups. We aimed to describe trends in absolute and relative COVID-19-related mortality risks across clinical and demographic population subgroups during successive SARS-CoV-2 pandemic waves.<h4>Methods</h4>We did a retrospective cohort study in England using the OpenSAFELY platform with the approval of National Health Service England, covering the first five SARS-CoV-2 pandemic waves (wave one [wild-type] from March 23 to May 30, 2020; wave two [alpha (B.1.1.7)] from Sept 7, 2020, to April 24, 2021; wave three [delta (B.1.617.2)] from May 28 to Dec 14, 2021; wave four [omicron (B.1.1.529)] from Dec 15, 2021, to April 29, 2022; and wave five [omicron] from June 24 to Aug 3, 2022). In each wave, we included people aged 18-110 years who were registered with a general practice on the first day of the wave and who had at least 3 months of continuous general practice registration up to this date. We estimated crude and sex-standardised and age-standardised wave-specific COVID-19-related death rates and relative risks of COVID-19-related death in population subgroups.<h4>Findings</h4>18 895 870 adults were included in wave one, 19 014 720 in wave two, 18 932 050 in wave three, 19 097 970 in wave four, and 19 226 475 in wave five. Crude COVID-19-related death rates per 1000 person-years decreased from 4·48 deaths (95% CI 4·41-4·55) in wave one to 2·69 (2·66-2·72) in wave two, 0·64 (0·63-0·66) in wave three, 1·01 (0·99-1·03) in wave four, and 0·67 (0·64-0·71) in wave five. In wave one, the standardised COVID-19-related death rates were highest in people aged 80 years or older, people with chronic kidney disease stage 5 or 4, people receiving dialysis, people with dementia or learning disability, and people who had received a kidney transplant (ranging from 19·85 deaths per 1000 person-years to 44·41 deaths per 1000 person-years, compared with from 0·05 deaths per 1000 person-years to 15·93 deaths per 1000 person-years in other subgroups). In wave two compared with wave one, in a largely unvaccinated population, the decrease in COVID-19-related mortality was evenly distributed across population subgroups. In wave three compared with wave one, larger decreases in COVID-19-related death rates were seen in groups prioritised for primary SARS-CoV-2 vaccination, including people aged 80 years or older and people with neurological disease, learning disability, or severe mental illness (90-91% decrease). Conversely, smaller decreases in COVID-19-related death rates were observed in younger age groups, people who had received organ transplants, and people with chronic kidney disease, haematological malignancies, or immunosuppressive conditions (0-25% decrease). In wave four compared with wave one, the decrease in COVID-19-related death rates was smaller in groups with lower vaccination coverage (including younger age groups) and conditions associated with impaired vaccine response, including people who had received organ transplants and people with immunosuppressive conditions (26-61% decrease).<h4>Interpretation</h4>There was a substantial decrease in absolute COVID-19-related death rates over time in the overall population, but demographic and clinical relative risk profiles persisted and worsened for people with lower vaccination coverage or impaired immune response. Our findings provide an evidence base to inform UK public health policy for protecting these vulnerable population subgroups.<h4>Funding</h4>UK Research and Innovation, Wellcome Trust, UK Medical Research Council, National Institute for Health and Care Research, and Health Data Research UK.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10139026; doi:https://doi.org/10.1016/S2468-2667(23)00079-8; html:https://europepmc.org/articles/PMC10139026; pdf:https://europepmc.org/articles/PMC10139026?pdf=render
 32873607,https://doi.org/10.1136/bmjresp-2020-000644,Ethnicity and risk of death in patients hospitalised for COVID-19 infection in the UK: an observational cohort study in an urban catchment area.,"Sapey E, Gallier S, Mainey C, Nightingale P, McNulty D, Crothers H, Evison F, Reeves K, Pagano D, Denniston AK, Nirantharakumar K, Diggle P, Ball S, All clinicians and students at University Hospitals Birmingham NHS Foundation Trust.",,BMJ open respiratory research,2020,2020-09-01,Y,Viral infection; respiratory infection; Clinical Epidemiology,,,"<h4>Background</h4>Studies suggest that certain black and Asian minority ethnic groups experience poorer outcomes from COVID-19, but these studies have not provided insight into potential reasons for this. We hypothesised that outcomes would be poorer for those of South Asian ethnicity hospitalised from a confirmed SARS-CoV-2 infection, once confounding factors, health-seeking behaviours and community demographics were considered, and that this might reflect a more aggressive disease course in these patients.<h4>Methods</h4>Patients with confirmed SARS-CoV-2 infection requiring admission to University Hospitals Birmingham NHS Foundation Trust (UHB) in Birmingham, UK between 10 March 2020 and 17 April 2020 were included. Standardised admission ratio (SAR) and standardised mortality ratio (SMR) were calculated using observed COVID-19 admissions/deaths and 2011 census data. Adjusted HR for mortality was estimated using Cox proportional hazard model adjusting and propensity score matching.<h4>Results</h4>All patients admitted to UHB with COVID-19 during the study period were included (2217 in total). 58% were male, 69.5% were white and the majority (80.2%) had comorbidities. 18.5% were of South Asian ethnicity, and these patients were more likely to be younger and have no comorbidities, but twice the prevalence of diabetes than white patients. SAR and SMR suggested more admissions and deaths in South Asian patients than would be predicted and they were more likely to present with severe disease despite no delay in presentation since symptom onset. South Asian ethnicity was associated with an increased risk of death, both by Cox regression (HR 1.4, 95% CI 1.2 to 1.8), after adjusting for age, sex, deprivation and comorbidities, and by propensity score matching, matching for the same factors but categorising ethnicity into South Asian or not (HR 1.3, 95% CI 1.0 to 1.6).<h4>Conclusions</h4>Those of South Asian ethnicity appear at risk of worse COVID-19 outcomes. Further studies need to establish the underlying mechanistic pathways.",,pdf:https://bmjopenrespres.bmj.com/content/bmjresp/7/1/e000644.full.pdf; doi:https://doi.org/10.1136/bmjresp-2020-000644; html:https://europepmc.org/articles/PMC7467523; pdf:https://europepmc.org/articles/PMC7467523?pdf=render
-33728401,https://doi.org/10.1038/s42254-020-0178-4,Modelling COVID-19.,"Vespignani A, Tian H, Dye C, Lloyd-Smith JO, Eggo RM, Shrestha M, Scarpino SV, Gutierrez B, Kraemer MUG, Wu J, Leung K, Leung GM.",,Nature reviews. Physics,2020,2020-05-06,Y,Applied Mathematics; Complex Networks,,,"As the COVID-19 pandemic continues, mathematical epidemiologists share their views on what models reveal about how the disease has spread, the current state of play and what work still needs to be done.",Vespignani et al. used mathematical models to model the epidemic of covid-19 and to predict future scenarios for possible interventions and inform policy and practice.,pdf:https://www.nature.com/articles/s42254-020-0178-4.pdf; doi:https://doi.org/10.1038/s42254-020-0178-4; html:https://europepmc.org/articles/PMC7201389; pdf:https://europepmc.org/articles/PMC7201389?pdf=render
 39364338,https://doi.org/10.12688/wellcomeopenres.20278.2,"VIVALDI Cohort Profile: Using linked, routinely collected data and longitudinal blood sampling to characterise COVID-19 infections, vaccinations, and related outcomes in care home staff and residents in England.","Krutikov M, Bone D, Stirrup O, Bruton R, Azmi B, Fuller C, Lau M, Low J, Rastogi S, Monakhov I, Tut G, Fink D, Moss P, Hayward A, Copas A, Shallcross L.",,Wellcome open research,2023,2023-01-01,Y,Infection; Data Linkage; Care Homes; Older Adults; Covid-19,,,"VIVALDI (ISRCTN14447421) is a government-funded longitudinal open observational cohort study of staff and residents in care homes for older people in England. The study aimed to describe epidemiology (including seroprevalence) and immune responses to COVID-19 in a subset of care homes, in the context of extremely high mortality in this setting, in the first 12-18 months of the pandemic. Data linkage to routine health data was undertaken for all staff and residents and a subset of individuals who consented to sequential blood sampling to investigate SARS-CoV-2 immunity. This paper aims to describe the samples stored within the VIVALDI biobank and associated linked data, available for use by researchers. Over 70,000 individuals from 346 care homes were included in the data linkage cohort (1 <sup>st</sup> March 2020-31 <sup>st</sup> March 2023). 4971 samples from 2264 individuals (1415 staff, 827 residents) collected between 29 <sup>th</sup> October 2020 and 10 <sup>th</sup> March 2023 are stored. Amongst these samples, there was a maximum of seven per participant however, 217 (26.2%) residents and 551 (38.9%) staff participated in one round only. Key study findings include high COVID-19 seroprevalence among surviving residents, exceeding rates in community-dwelling peers. COVID-19 vaccinations generated robust immune responses in staff and residents which waned, supporting the need for booster vaccination, particularly in response to new variants. Prior infection significantly improved vaccine-induced immune responses, however protection from infection declined following Omicron variant emergence. This is a unique cohort of pre- and post-infection samples linked to data on COVID-19 infections, vaccinations, and outcomes. The cohort spans host immune response evolution to infection and vaccination in this rarely sampled population of frail older care home residents who are especially vulnerable to infection and severe outcomes. These samples can be used to investigate biological mechanisms behind disparate infection responses in older people and make a valuable contribution to research into ageing.",,doi:https://doi.org/10.12688/wellcomeopenres.20278.2; html:https://europepmc.org/articles/PMC11447437; pdf:https://europepmc.org/articles/PMC11447437?pdf=render
 34132940,https://doi.org/10.1007/s10654-021-00765-1,Ethnic differences in COVID-19 mortality during the first two waves of the Coronavirus Pandemic: a nationwide cohort study of 29 million adults in England.,"Nafilyan V, Islam N, Mathur R, Ayoubkhani D, Banerjee A, Glickman M, Humberstone B, Diamond I, Khunti K.",,European journal of epidemiology,2021,2021-06-16,Y,Mortality; Ethnicity; Covid-19,,,"Ethnic minorities have experienced disproportionate COVID-19 mortality rates in the UK and many other countries. We compared the differences in the risk of COVID-19 related death between ethnic groups in the first and second waves the of COVID-19 pandemic in England. We also investigated whether the factors explaining differences in COVID-19 death between ethnic groups changed between the two waves. Using data from the Office for National Statistics Public Health Data Asset, a linked dataset combining the 2011 Census with primary care and hospital records and death registrations, we conducted an observational cohort study to examine differences in the risk of death involving COVID-19 between ethnic groups in the first wave (from 24th January 2020 until 31st August 2020) and the first part of the second wave (from 1st September to 28th December 2020). We estimated age-standardised mortality rates (ASMR) in the two waves stratified by ethnic groups and sex. We also estimated hazard ratios (HRs) for ethnic-minority groups compared with the White British population, adjusted for geographical factors, socio-demographic characteristics, and pre-pandemic health conditions. The study population included over 28.9 million individuals aged 30-100 years living in private households. In the first wave, all ethnic minority groups had a higher risk of COVID-19 related death compared to the White British population. In the second wave, the risk of COVID-19 death remained elevated for people from Pakistani (ASMR: 339.9 [95% CI: 303.7-376.2] and 166.8 [141.7-191.9] deaths per 100,000 population in men and women) and Bangladeshi (318.7 [247.4-390.1] and 127.1 [91.1-171.3] in men and women) background but not for people from Black ethnic groups. Adjustment for geographical factors explained a large proportion of the differences in COVID-19 mortality in the first wave but not in the second wave. Despite an attenuation of the elevated risk of COVID-19 mortality after adjusting for sociodemographic characteristics and health status, the risk was substantially higher in people from Bangladeshi and Pakistani background in both the first and the second waves. Between the first and second waves of the pandemic, the reduction in the difference in COVID-19 mortality between people from Black ethnic background and people from the White British group shows that ethnic inequalities in COVID-19 mortality can be addressed. The continued higher rate of mortality in people from Bangladeshi and Pakistani background is alarming and requires focused public health campaign and policy changes.",,pdf:https://link.springer.com/content/pdf/10.1007/s10654-021-00765-1.pdf; doi:https://doi.org/10.1007/s10654-021-00765-1; html:https://europepmc.org/articles/PMC8206182; pdf:https://europepmc.org/articles/PMC8206182?pdf=render
-36224173,https://doi.org/10.1038/s41467-022-33415-5,Outcomes among confirmed cases and a matched comparison group in the Long-COVID in Scotland study.,"Hastie CE, Lowe DJ, McAuley A, Winter AJ, Mills NL, Black C, Scott JT, O'Donnell CA, Blane DN, Browne S, Ibbotson TR, Pell JP.",,Nature communications,2022,2022-10-12,Y,,,,"With increasing numbers infected by SARS-CoV-2, understanding long-COVID is essential to inform health and social care support. A Scottish population cohort of 33,281 laboratory-confirmed SARS-CoV-2 infections and 62,957 never-infected individuals were followed-up via 6, 12 and 18-month questionnaires and linkage to hospitalization and death records. Of the 31,486 symptomatic infections,1,856 (6%) had not recovered and 13,350 (42%) only partially. No recovery was associated with hospitalized infection, age, female sex, deprivation, respiratory disease, depression and multimorbidity. Previous symptomatic infection was associated with poorer quality of life, impairment across all daily activities and 24 persistent symptoms including breathlessness (OR 3.43, 95% CI 3.29-3.58), palpitations (OR 2.51, OR 2.36-2.66), chest pain (OR 2.09, 95% CI 1.96-2.23), and confusion (OR 2.92, 95% CI 2.78-3.07). Asymptomatic infection was not associated with adverse outcomes. Vaccination was associated with reduced risk of seven symptoms. Here we describe the nature of long-COVID and the factors associated with it.",,pdf:https://researchonline.gcu.ac.uk/files/64233779/s41467_022_33415_5.pdf; doi:https://doi.org/10.1038/s41467-022-33415-5; html:https://europepmc.org/articles/PMC9556711; pdf:https://europepmc.org/articles/PMC9556711?pdf=render
 37128667,https://doi.org/10.1111/bjhp.12666,A qualitative process evaluation using the behaviour change wheel approach: Did a whole genome sequence report form (SRF) used to reduce nosocomial SARS-CoV-2 within UK hospitals operate as anticipated?,"Flowers P, Leiser R, Mapp F, McLeod J, Stirrup O, Illingworth CJR, Blackstone J, Breuer J.",,British journal of health psychology,2023,2023-05-01,Y,Hospital; Behaviour Change; Infection Prevention And Control; Behaviour Change Wheel; Covid-19; Sequence Report Form,,,"<h4>Purpose</h4>The aim of this study was to conduct a process evaluation of a whole-genome sequence report form (SRF) used to reduce nosocomial SARS-CoV-2 through changing infection prevention and control (IPC) behaviours within the COVID-19 pandemic.<h4>Methods</h4>We used a three-staged design. Firstly, we described and theorized the purported content of the SRF using the behaviour change wheel (BCW). Secondly, we used inductive thematic analysis of one-to-one interviews (n = 39) to explore contextual accounts of using the SRF. Thirdly, further deductive analysis gauged support for the intervention working as earlier anticipated.<h4>Results</h4>It was possible to theorize the SRF using the BCW approach and visualize it within a simple logic model. Inductive thematic analyses identified the SRF's acceptability, ease of use and perceived effectiveness. However, major challenges to embedding it in routine practice during the unfolding COVID-19 crisis were reported. Notwithstanding this insight, deductive analysis showed support for the putative intervention functions 'Education', 'Persuasion' and 'Enablement'; behaviour change techniques '1.2 Problem solving', '2.6 Biofeedback', '2.7 Feedback on outcomes of behaviour' and '7.1 Prompts and cues'; and theoretical domains framework domains 'Knowledge' and 'Behavioural regulation'.<h4>Conclusions</h4>Our process evaluation of the SRF, using the BCW approach to describe and theorize its content, provided granular support for the SRF working to change IPC behaviours as anticipated. However, our complementary inductive thematic analysis highlighted the importance of the local context in constraining its routine use. For SRFs to reach their full potential in reducing nosocomial infections, further implementation research is needed.",,doi:https://doi.org/10.1111/bjhp.12666; doi:https://doi.org/10.1111/bjhp.12666; html:https://europepmc.org/articles/PMC11497355; pdf:https://europepmc.org/articles/PMC11497355?pdf=render
-35189888,https://doi.org/10.1186/s12916-022-02286-4,Determinants of pre-vaccination antibody responses to SARS-CoV-2: a population-based longitudinal study (COVIDENCE UK).,"Talaei M, Faustini S, Holt H, Jolliffe DA, Vivaldi G, Greenig M, Perdek N, Maltby S, Bigogno CM, Symons J, Davies GA, Lyons RA, Griffiths CJ, Kee F, Sheikh A, Richter AG, Shaheen SO, Martineau AR.",,BMC medicine,2022,2022-02-22,Y,Obesity; Diet; Serology; Alcohol; Exercise; Micronutrients; Lifestyle; Ethnicity; Occupation; Sars-cov-2,,,"<h4>Background</h4>Prospective population-based studies investigating multiple determinants of pre-vaccination antibody responses to SARS-CoV-2 are lacking.<h4>Methods</h4>We did a prospective population-based study in SARS-CoV-2 vaccine-naive UK adults recruited between May 1 and November 2, 2020, without a positive swab test result for SARS-CoV-2 prior to enrolment. Information on 88 potential sociodemographic, behavioural, nutritional, clinical and pharmacological risk factors was obtained through online questionnaires, and combined IgG/IgA/IgM responses to SARS-CoV-2 spike glycoprotein were determined in dried blood spots obtained between November 6, 2020, and April 18, 2021. We used logistic and linear regression to estimate adjusted odds ratios (aORs) and adjusted geometric mean ratios (aGMRs) for potential determinants of SARS-CoV-2 seropositivity (all participants) and antibody titres (seropositive participants only), respectively.<h4>Results</h4>Of 11,130 participants, 1696 (15.2%) were seropositive. Factors independently associated with  higher risk of SARS-CoV-2 seropositivity included frontline health/care occupation (aOR 1.86, 95% CI 1.48-2.33), international travel (1.20, 1.07-1.35), number of visits to shops and other indoor public places (≥ 5 vs. 0/week: 1.29, 1.06-1.57, P-trend = 0.01), body mass index (BMI) ≥ 25 vs. < 25 kg/m<sup>2</sup> (1.24, 1.11-1.39), South Asian vs. White ethnicity (1.65, 1.10-2.49) and alcohol consumption ≥15 vs. 0 units/week (1.23, 1.04-1.46). Light physical exercise associated with  lower risk (0.80, 0.70-0.93, for ≥ 10 vs. 0-4 h/week). Among seropositive participants, higher titres of anti-Spike antibodies associated with factors including BMI ≥ 30 vs. < 25 kg/m<sup>2</sup> (aGMR 1.10, 1.02-1.19), South Asian vs. White ethnicity (1.22, 1.04-1.44), frontline health/care occupation (1.24, 95% CI 1.11-1.39), international travel (1.11, 1.05-1.16) and number of visits to shops and other indoor public places (≥ 5 vs. 0/week: 1.12, 1.02-1.23, P-trend = 0.01); these associations were not substantially attenuated by adjustment for COVID-19 disease severity.<h4>Conclusions</h4>Higher alcohol consumption and lower light physical exercise represent new modifiable risk factors for SARS-CoV-2 infection. Recognised associations between South Asian ethnic origin and obesity and higher risk of SARS-CoV-2 seropositivity were independent of other sociodemographic, behavioural, nutritional, clinical, and pharmacological factors investigated. Among seropositive participants, higher titres of anti-Spike antibodies in people of South Asian ancestry and in obese people were not explained by greater COVID-19 disease severity in these groups.",,pdf:https://bmcmedicine.biomedcentral.com/track/pdf/10.1186/s12916-022-02286-4; doi:https://doi.org/10.1186/s12916-022-02286-4; html:https://europepmc.org/articles/PMC8860623; pdf:https://europepmc.org/articles/PMC8860623?pdf=render
+36224173,https://doi.org/10.1038/s41467-022-33415-5,Outcomes among confirmed cases and a matched comparison group in the Long-COVID in Scotland study.,"Hastie CE, Lowe DJ, McAuley A, Winter AJ, Mills NL, Black C, Scott JT, O'Donnell CA, Blane DN, Browne S, Ibbotson TR, Pell JP.",,Nature communications,2022,2022-10-12,Y,,,,"With increasing numbers infected by SARS-CoV-2, understanding long-COVID is essential to inform health and social care support. A Scottish population cohort of 33,281 laboratory-confirmed SARS-CoV-2 infections and 62,957 never-infected individuals were followed-up via 6, 12 and 18-month questionnaires and linkage to hospitalization and death records. Of the 31,486 symptomatic infections,1,856 (6%) had not recovered and 13,350 (42%) only partially. No recovery was associated with hospitalized infection, age, female sex, deprivation, respiratory disease, depression and multimorbidity. Previous symptomatic infection was associated with poorer quality of life, impairment across all daily activities and 24 persistent symptoms including breathlessness (OR 3.43, 95% CI 3.29-3.58), palpitations (OR 2.51, OR 2.36-2.66), chest pain (OR 2.09, 95% CI 1.96-2.23), and confusion (OR 2.92, 95% CI 2.78-3.07). Asymptomatic infection was not associated with adverse outcomes. Vaccination was associated with reduced risk of seven symptoms. Here we describe the nature of long-COVID and the factors associated with it.",,pdf:https://researchonline.gcu.ac.uk/files/64233779/s41467_022_33415_5.pdf; doi:https://doi.org/10.1038/s41467-022-33415-5; html:https://europepmc.org/articles/PMC9556711; pdf:https://europepmc.org/articles/PMC9556711?pdf=render
 35502909,https://doi.org/10.1177/01410768221095239,Impact on emergency and elective hospital-based care in Scotland over the first 12 months of the pandemic: interrupted time-series analysis of national lockdowns.,"Shah SA, Mulholland RH, Wilkinson S, Katikireddi SV, Pan J, Shi T, Kerr S, Agrawal U, Rudan I, Simpson CR, Stock SJ, Macleod J, Murray JL, McCowan C, Ritchie L, Woolhouse M, Sheikh A.",,Journal of the Royal Society of Medicine,2022,2022-05-03,Y,Public Health; Statistics And Research Methods; Population Trends,,,"<h4>Objectives</h4>COVID-19 has resulted in the greatest disruption to National Health Service (NHS) care in its over 70-year history. Building on our previous work, we assessed the ongoing impact of pandemic-related disruption on provision of emergency and elective hospital-based care across Scotland over the first year of the pandemic.<h4>Design</h4>We undertook interrupted time-series analyses to evaluate the impact of ongoing pandemic-related disruption on hospital NHS care provision at national level and across demographics and clinical specialties spanning the period 29 March 2020-28 March 2021.<h4>Setting</h4>Scotland, UK.<h4>Participants</h4>Patients receiving hospital care from NHS Scotland.<h4>Main outcome measures</h4>We used the percentage change of accident and emergency attendances, and emergency and planned hospital admissions during the pandemic compared to the average admission rate for equivalent weeks in 2018-2019.<h4>Results</h4>As restrictions were gradually lifted in Scotland after the first lockdown, hospital-based admissions increased approaching pre-pandemic levels. Subsequent tightening of restrictions in September 2020 were associated with a change in slope of relative weekly admissions rate: -1.98% (-2.38, -1.58) in accident and emergency attendance, -1.36% (-1.68, -1.04) in emergency admissions and -2.31% (-2.95, -1.66) in planned admissions. A similar pattern was seen across sex, socioeconomic status and most age groups, except children (0-14 years) where accident and emergency attendance, and emergency admissions were persistently low over the study period.<h4>Conclusions</h4>We found substantial disruption to urgent and planned inpatient healthcare provision in hospitals across NHS Scotland. There is the need for urgent policy responses to address continuing unmet health needs and to ensure resilience in the context of future pandemics.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/01410768221095239; doi:https://doi.org/10.1177/01410768221095239; html:https://europepmc.org/articles/PMC9723811; pdf:https://europepmc.org/articles/PMC9723811?pdf=render
+35189888,https://doi.org/10.1186/s12916-022-02286-4,Determinants of pre-vaccination antibody responses to SARS-CoV-2: a population-based longitudinal study (COVIDENCE UK).,"Talaei M, Faustini S, Holt H, Jolliffe DA, Vivaldi G, Greenig M, Perdek N, Maltby S, Bigogno CM, Symons J, Davies GA, Lyons RA, Griffiths CJ, Kee F, Sheikh A, Richter AG, Shaheen SO, Martineau AR.",,BMC medicine,2022,2022-02-22,Y,Obesity; Diet; Serology; Alcohol; Exercise; Micronutrients; Lifestyle; Ethnicity; Occupation; Sars-cov-2,,,"<h4>Background</h4>Prospective population-based studies investigating multiple determinants of pre-vaccination antibody responses to SARS-CoV-2 are lacking.<h4>Methods</h4>We did a prospective population-based study in SARS-CoV-2 vaccine-naive UK adults recruited between May 1 and November 2, 2020, without a positive swab test result for SARS-CoV-2 prior to enrolment. Information on 88 potential sociodemographic, behavioural, nutritional, clinical and pharmacological risk factors was obtained through online questionnaires, and combined IgG/IgA/IgM responses to SARS-CoV-2 spike glycoprotein were determined in dried blood spots obtained between November 6, 2020, and April 18, 2021. We used logistic and linear regression to estimate adjusted odds ratios (aORs) and adjusted geometric mean ratios (aGMRs) for potential determinants of SARS-CoV-2 seropositivity (all participants) and antibody titres (seropositive participants only), respectively.<h4>Results</h4>Of 11,130 participants, 1696 (15.2%) were seropositive. Factors independently associated with  higher risk of SARS-CoV-2 seropositivity included frontline health/care occupation (aOR 1.86, 95% CI 1.48-2.33), international travel (1.20, 1.07-1.35), number of visits to shops and other indoor public places (≥ 5 vs. 0/week: 1.29, 1.06-1.57, P-trend = 0.01), body mass index (BMI) ≥ 25 vs. < 25 kg/m<sup>2</sup> (1.24, 1.11-1.39), South Asian vs. White ethnicity (1.65, 1.10-2.49) and alcohol consumption ≥15 vs. 0 units/week (1.23, 1.04-1.46). Light physical exercise associated with  lower risk (0.80, 0.70-0.93, for ≥ 10 vs. 0-4 h/week). Among seropositive participants, higher titres of anti-Spike antibodies associated with factors including BMI ≥ 30 vs. < 25 kg/m<sup>2</sup> (aGMR 1.10, 1.02-1.19), South Asian vs. White ethnicity (1.22, 1.04-1.44), frontline health/care occupation (1.24, 95% CI 1.11-1.39), international travel (1.11, 1.05-1.16) and number of visits to shops and other indoor public places (≥ 5 vs. 0/week: 1.12, 1.02-1.23, P-trend = 0.01); these associations were not substantially attenuated by adjustment for COVID-19 disease severity.<h4>Conclusions</h4>Higher alcohol consumption and lower light physical exercise represent new modifiable risk factors for SARS-CoV-2 infection. Recognised associations between South Asian ethnic origin and obesity and higher risk of SARS-CoV-2 seropositivity were independent of other sociodemographic, behavioural, nutritional, clinical, and pharmacological factors investigated. Among seropositive participants, higher titres of anti-Spike antibodies in people of South Asian ancestry and in obese people were not explained by greater COVID-19 disease severity in these groups.",,pdf:https://bmcmedicine.biomedcentral.com/track/pdf/10.1186/s12916-022-02286-4; doi:https://doi.org/10.1186/s12916-022-02286-4; html:https://europepmc.org/articles/PMC8860623; pdf:https://europepmc.org/articles/PMC8860623?pdf=render
 36745545,https://doi.org/10.1099/mgen.0.000887,The use of representative community samples to assess SARS-CoV-2 lineage competition: Alpha outcompetes Beta and wild-type in England from January to March 2021.,"Eales O, Page AJ, Tang SN, Walters CE, Wang H, Haw D, Trotter AJ, Le Viet T, Foster-Nyarko E, Prosolek S, Atchison C, Ashby D, Cooke G, Barclay W, Donnelly CA, O'Grady J, Volz E, The Covid-Genomics Uk Cog-Uk Consortium, Darzi A, Ward H, Elliott P, Riley S.",,Microbial genomics,2023,2023-02-01,Y,,,,"Genomic surveillance for SARS-CoV-2 lineages informs our understanding of possible future changes in transmissibility and vaccine efficacy and will be a high priority for public health for the foreseeable future. However, small changes in the frequency of one lineage over another are often difficult to interpret because surveillance samples are obtained using a variety of methods all of which are known to contain biases. As a case study, using an approach which is largely free of biases, we here describe lineage dynamics and phylogenetic relationships of the Alpha and Beta variant in England during the first 3 months of 2021 using sequences obtained from a random community sample who provided a throat and nose swab for rt-PCR as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. Overall, diversity decreased during the first quarter of 2021, with the Alpha variant (first identified in Kent) becoming predominant, driven by a reproduction number 0.3 higher than for the prior wild-type. During January, positive samples were more likely to be Alpha in those aged 18 to 54 years old. Although individuals infected with the Alpha variant were no more likely to report one or more classic COVID-19 symptoms compared to those infected with wild-type, they were more likely to be antibody-positive 6 weeks after infection. Further, viral load was higher in those infected with the Alpha variant as measured by cycle threshold (Ct) values. The presence of infections with non-imported Beta variant (first identified in South Africa) during January, but not during February or March, suggests initial establishment in the community followed by fade-out. However, this occurred during a period of stringent social distancing. These results highlight how sequence data from representative community surveys such as REACT-1 can augment routine genomic surveillance during periods of lineage diversity.",,doi:https://doi.org/10.1099/mgen.0.000887; html:https://europepmc.org/articles/PMC9997751; pdf:https://europepmc.org/articles/PMC9997751?pdf=render
 34861180,https://doi.org/10.1016/s2213-2600(21)00491-4,Risk of COVID-19 hospital admission among children aged 5-17 years with asthma in Scotland: a national incident cohort study.,"Shi T, Pan J, Katikireddi SV, McCowan C, Kerr S, Agrawal U, Shah SA, Simpson CR, Ritchie LD, Robertson C, Sheikh A, Public Health Scotland and the EAVE II Collaborators.",,The Lancet. Respiratory medicine,2022,2021-11-30,Y,,,,"<h4>Background</h4>There is an urgent need to inform policy deliberations about whether children with asthma should be vaccinated against SARS-CoV-2 and, if so, which subset of children with asthma should be prioritised. We were asked by the UK's Joint Commission on Vaccination and Immunisation to undertake an urgent analysis to identify which children with asthma were at increased risk of serious COVID-19 outcomes.<h4>Methods</h4>This national incident cohort study was done in all children in Scotland aged 5-17 years who were included in the linked dataset of Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II). We used data from EAVE II to investigate the risk of COVID-19 hospitalisation among children with markers of uncontrolled asthma defined by either previous asthma hospital admission or oral corticosteroid prescription in the previous 2 years. A Cox proportional hazard model was used to derive hazard ratios (HRs) and 95% CIs for the association between asthma and COVID-19 hospital admission, stratified by markers of asthma control (previous asthma hospital admission and number of previous prescriptions for oral corticosteroids within 2 years of the study start date). Analyses were adjusted for age, sex, socioeconomic status, comorbidity, and previous hospital admission.<h4>Findings</h4>Between March 1, 2020, and July 27, 2021, 752 867 children were included in the EAVE II dataset, 63 463 (8·4%) of whom had clinician-diagnosed-and-recorded asthma. Of these, 4339 (6·8%) had RT-PCR confirmed SARS-CoV-2 infection. In those with confirmed infection, 67 (1·5%) were admitted to hospital with COVID-19. Among the 689 404 children without asthma, 40 231 (5·8%) had confirmed SARS-CoV-2 infections, of whom 382 (0·9%) were admitted to hospital with COVID-19. The rate of COVID-19 hospital admission was higher in children with poorly controlled asthma than in those with well controlled asthma or without asthma. When using previous hospital admission for asthma as the marker of uncontrolled asthma, the adjusted HR was 6·40 (95% CI 3·27-12·53) for those with poorly controlled asthma and 1·36 (1·02-1·80) for those with well controlled asthma, compared with those with no asthma. When using oral corticosteroid prescriptions as the marker of uncontrolled asthma, the adjusted HR was 3·38 (1·84-6·21) for those with three or more prescribed courses of corticosteroids, 3·53 (1·87-6·67) for those with two prescribed courses of corticosteroids, 1·52 (0·90-2·57) for those with one prescribed course of corticosteroids, and 1·34 (0·98-1·82) for those with no prescribed course, compared with those with no asthma.<h4>Interpretation</h4>School-aged children with asthma with previous recent hospital admission or two or more courses of oral corticosteroids are at markedly increased risk of COVID-19 hospital admission and should be considered a priority for vaccinations. This would translate into 9124 children across Scotland and an estimated 109 448 children across the UK.<h4>Funding</h4>UK Research and Innovation (Medical Research Council), Research and Innovation Industrial Strategy Challenge Fund, Health Data Research UK, and Scottish Government.",,pdf:https://aura.abdn.ac.uk/bitstream/2164/18431/1/Shi_etal_Lancet_Risk_COVID19_Hospital_VOR.pdf; doi:https://doi.org/10.1016/S2213-2600(21)00491-4; html:https://europepmc.org/articles/PMC8631918
 34850818,https://doi.org/10.1093/ageing/afab223,"COVID-19 infection risk amongst 14,104 vaccinated care home residents: a national observational longitudinal cohort study in Wales, UK, December 2020-March 2021.","Hollinghurst J, North L, Perry M, Akbari A, Gravenor MB, Lyons RA, Fry R.",,Age and ageing,2022,2022-01-01,Y,Vaccination; Older People; Care Homes; Covid-19; Sars-cov-2,,,"<h4>Background</h4>vaccinations for COVID-19 have been prioritised for older people living in care homes. However, vaccination trials included limited numbers of older people.<h4>Aim</h4>we aimed to study infection rates of SARS-CoV-2 for older care home residents following vaccination and identify factors associated with increased risk of infection.<h4>Study design and setting</h4>we conducted an observational data-linkage study including 14,104 vaccinated older care home residents in Wales (UK) using anonymised electronic health records and administrative data.<h4>Methods</h4>we used Cox proportional hazards models to estimate hazard ratios (HRs) for the risk of testing positive for SARS-CoV-2 infection following vaccination, after landmark times of either 7 or 21 days post-vaccination. We adjusted HRs for age, sex, frailty, prior SARS-CoV-2 infections and vaccination type.<h4>Results</h4>we observed a small proportion of care home residents with positive polymerase chain reaction (tests following vaccination 1.05% (N = 148), with 90% of infections occurring within 28 days. For the 7-day landmark analysis we found a reduced risk of SARS-CoV-2 infection for vaccinated individuals who had a previous infection; HR (95% confidence interval) 0.54 (0.30, 0.95). For the 21-day landmark analysis, we observed high HRs for individuals with low and intermediate frailty compared with those without; 4.59 (1.23, 17.12) and 4.85 (1.68, 14.04), respectively.<h4>Conclusions</h4>increased risk of infection after 21 days was associated with frailty. We found most infections occurred within 28 days of vaccination, suggesting extra precautions to reduce transmission risk should be taken in this time frame.",,pdf:https://academic.oup.com/ageing/article-pdf/51/1/afab223/42083726/afab223.pdf; doi:https://doi.org/10.1093/ageing/afab223; html:https://europepmc.org/articles/PMC8690013; pdf:https://europepmc.org/articles/PMC8690013?pdf=render
 37308303,https://doi.org/10.3399/bjgp.2023.0044,Diagnostic windows in non-neoplastic diseases: a systematic review.,"Whitfield E, White B, Denaxas S, Lyratzopoulos G.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2023,2023-08-31,Y,Diagnosis; Primary Health Care; Electronic Health Records,,,"<h4>Background</h4>Investigating changes in prediagnostic healthcare utilisation can help identify how much earlier conditions could be diagnosed. Such 'diagnostic windows' are established for cancer but remain relatively unexplored for non-neoplastic conditions.<h4>Aim</h4>To extract evidence on the presence and length of diagnostic windows for non-neoplastic conditions.<h4>Design and setting</h4>A systematic review of studies of prediagnostic healthcare utilisation was carried out.<h4>Method</h4>A search strategy was developed to identify relevant studies from PubMed and Connected Papers. Data were extracted on prediagnostic healthcare use, and evidence of diagnostic window presence and length was assessed.<h4>Results</h4>Of 4340 studies screened, 27 were included, covering 17 non-neoplastic conditions, including both chronic (for example, Parkinson's disease) and acute conditions (for example, stroke). Prediagnostic healthcare events included primary care encounters and presentations with relevant symptoms. For 10 conditions, sufficient evidence to determine diagnostic window presence and length was available, ranging from 28 days (herpes simplex encephalitis) to 9 years (ulcerative colitis). For the remaining conditions, diagnostic windows were likely to be present, but insufficient study duration was often a barrier to robustly determining their length, meaning that diagnostic window length may exceed 10 years for coeliac disease, for example.<h4>Conclusion</h4>Evidence of changing healthcare use before diagnosis exists for many non-neoplastic conditions, establishing that early diagnosis is possible, in principle. In particular, some conditions may be detectable many years earlier than they are currently diagnosed. Further research is required to accurately estimate diagnostic windows and to determine how much earlier diagnosis may be possible, and how this might be achieved.",,pdf:https://bjgp.org/content/bjgp/early/2023/04/04/BJGP.2023.0044.full.pdf; doi:https://doi.org/10.3399/BJGP.2023.0044; html:https://europepmc.org/articles/PMC10285689; pdf:https://europepmc.org/articles/PMC10285689?pdf=render
-32975552,https://doi.org/10.1001/jamapediatrics.2020.4573,Susceptibility to SARS-CoV-2 Infection Among Children and Adolescents Compared With Adults: A Systematic Review and Meta-analysis.,"Viner RM, Mytton OT, Bonell C, Melendez-Torres GJ, Ward J, Hudson L, Waddington C, Thomas J, Russell S, van der Klis F, Koirala A, Ladhani S, Panovska-Griffiths J, Davies NG, Booy R, Eggo RM.",,JAMA pediatrics,2021,2021-02-01,N,,,,"<h4>Importance</h4>The degree to which children and adolescents are infected by and transmit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unclear. The role of children and adolescents in transmission of SARS-CoV-2 is dependent on susceptibility, symptoms, viral load, social contact patterns, and behavior.<h4>Objective</h4>To systematically review the susceptibility to and transmission of SARS-CoV-2 among children and adolescents compared with adults.<h4>Data sources</h4>PubMed and medRxiv were searched from database inception to July 28, 2020, and a total of 13 926 studies were identified, with additional studies identified through hand searching of cited references and professional contacts.<h4>Study selection</h4>Studies that provided data on the prevalence of SARS-CoV-2 in children and adolescents (younger than 20 years) compared with adults (20 years and older) derived from contact tracing or population screening were included. Single-household studies were excluded.<h4>Data extraction and synthesis</h4>PRISMA guidelines for abstracting data were followed, which was performed independently by 2 reviewers. Quality was assessed using a critical appraisal checklist for prevalence studies. Random-effects meta-analysis was undertaken.<h4>Main outcomes and measures</h4>Secondary infection rate (contact-tracing studies) or prevalence or seroprevalence (population screening studies) among children and adolescents compared with adults.<h4>Results</h4>A total of 32 studies comprising 41 640 children and adolescents and 268 945 adults met inclusion criteria, including 18 contact-tracing studies and 14 population screening studies. The pooled odds ratio of being an infected contact in children compared with adults was 0.56 (95% CI, 0.37-0.85), with substantial heterogeneity (I2 = 94.6%). Three school-based contact-tracing studies found minimal transmission from child or teacher index cases. Findings from population screening studies were heterogenous and were not suitable for meta-analysis. Most studies were consistent with lower seroprevalence in children compared with adults, although seroprevalence in adolescents appeared similar to adults.<h4>Conclusions and relevance</h4>In this meta-analysis, there is preliminary evidence that children and adolescents have lower susceptibility to SARS-CoV-2, with an odds ratio of 0.56 for being an infected contact compared with adults. There is weak evidence that children and adolescents play a lesser role than adults in transmission of SARS-CoV-2 at a population level. This study provides no information on the infectivity of children.",,html:https://europepmc.org/articles/pmc7519436; doi:https://doi.org/10.1001/jamapediatrics.2020.4573; html:https://europepmc.org/articles/PMC7519436; doi:https://doi.org/10.1001/jamapediatrics.2020.4573
 33222494,https://doi.org/10.1177/2048872620974605,Cardiac complications in patients hospitalised with COVID-19.,"Linschoten M, Peters S, van Smeden M, Jewbali LS, Schaap J, Siebelink HM, Smits PC, Tieleman RG, van der Harst P, van Gilst WH, Asselbergs FW, CAPACITY-COVID collaborative consortium.",,European heart journal. Acute cardiovascular care,2020,2020-11-21,Y,Pulmonary embolism; Cohorts; Cardiac Complications; Patient Registry; Covid-19/coronavirus,,,"<h4>Aims</h4>To determine the frequency and pattern of cardiac complications in patients hospitalised with coronavirus disease (COVID-19).<h4>Methods and results</h4>CAPACITY-COVID is an international patient registry established to determine the role of cardiovascular disease in the COVID-19 pandemic. In this registry, data generated during routine clinical practice are collected in a standardised manner for patients with a (highly suspected) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection requiring hospitalisation. For the current analysis, consecutive patients with laboratory confirmed COVID-19 registered between 28 March and 3 July 2020 were included. Patients were followed for the occurrence of cardiac complications and pulmonary embolism from admission to discharge. In total, 3011 patients were included, of which 1890 (62.8%) were men. The median age was 67 years (interquartile range 56-76); 937 (31.0%) patients had a history of cardiac disease, with pre-existent coronary artery disease being most common (<i>n</i>=463, 15.4%). During hospitalisation, 595 (19.8%) patients died, including 16 patients (2.7%) with cardiac causes. Cardiac complications were diagnosed in 349 (11.6%) patients, with atrial fibrillation (<i>n</i>=142, 4.7%) being most common. The incidence of other cardiac complications was 1.8% for heart failure (<i>n</i>=55), 0.5% for acute coronary syndrome (<i>n</i>=15), 0.5% for ventricular arrhythmia (<i>n</i>=14), 0.1% for bacterial endocarditis (<i>n</i>=4) and myocarditis (<i>n</i>=3), respectively, and 0.03% for pericarditis (<i>n</i>=1). Pulmonary embolism was diagnosed in 198 (6.6%) patients.<h4>Conclusion</h4>This large study among 3011 hospitalised patients with COVID-19 shows that the incidence of cardiac complications during hospital admission is low, despite a frequent history of cardiovascular disease. Long-term cardiac outcomes and the role of pre-existing cardiovascular disease in COVID-19 outcome warrants further investigation.",,pdf:https://academic.oup.com/ehjacc/article-pdf/9/8/817/49790126/ehjacc0817.pdf; doi:https://doi.org/10.1177/2048872620974605; html:https://europepmc.org/articles/PMC7734244; pdf:https://europepmc.org/articles/PMC7734244?pdf=render
+32975552,https://doi.org/10.1001/jamapediatrics.2020.4573,Susceptibility to SARS-CoV-2 Infection Among Children and Adolescents Compared With Adults: A Systematic Review and Meta-analysis.,"Viner RM, Mytton OT, Bonell C, Melendez-Torres GJ, Ward J, Hudson L, Waddington C, Thomas J, Russell S, van der Klis F, Koirala A, Ladhani S, Panovska-Griffiths J, Davies NG, Booy R, Eggo RM.",,JAMA pediatrics,2021,2021-02-01,N,,,,"<h4>Importance</h4>The degree to which children and adolescents are infected by and transmit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unclear. The role of children and adolescents in transmission of SARS-CoV-2 is dependent on susceptibility, symptoms, viral load, social contact patterns, and behavior.<h4>Objective</h4>To systematically review the susceptibility to and transmission of SARS-CoV-2 among children and adolescents compared with adults.<h4>Data sources</h4>PubMed and medRxiv were searched from database inception to July 28, 2020, and a total of 13 926 studies were identified, with additional studies identified through hand searching of cited references and professional contacts.<h4>Study selection</h4>Studies that provided data on the prevalence of SARS-CoV-2 in children and adolescents (younger than 20 years) compared with adults (20 years and older) derived from contact tracing or population screening were included. Single-household studies were excluded.<h4>Data extraction and synthesis</h4>PRISMA guidelines for abstracting data were followed, which was performed independently by 2 reviewers. Quality was assessed using a critical appraisal checklist for prevalence studies. Random-effects meta-analysis was undertaken.<h4>Main outcomes and measures</h4>Secondary infection rate (contact-tracing studies) or prevalence or seroprevalence (population screening studies) among children and adolescents compared with adults.<h4>Results</h4>A total of 32 studies comprising 41 640 children and adolescents and 268 945 adults met inclusion criteria, including 18 contact-tracing studies and 14 population screening studies. The pooled odds ratio of being an infected contact in children compared with adults was 0.56 (95% CI, 0.37-0.85), with substantial heterogeneity (I2 = 94.6%). Three school-based contact-tracing studies found minimal transmission from child or teacher index cases. Findings from population screening studies were heterogenous and were not suitable for meta-analysis. Most studies were consistent with lower seroprevalence in children compared with adults, although seroprevalence in adolescents appeared similar to adults.<h4>Conclusions and relevance</h4>In this meta-analysis, there is preliminary evidence that children and adolescents have lower susceptibility to SARS-CoV-2, with an odds ratio of 0.56 for being an infected contact compared with adults. There is weak evidence that children and adolescents play a lesser role than adults in transmission of SARS-CoV-2 at a population level. This study provides no information on the infectivity of children.",,html:https://europepmc.org/articles/pmc7519436; doi:https://doi.org/10.1001/jamapediatrics.2020.4573; html:https://europepmc.org/articles/PMC7519436; doi:https://doi.org/10.1001/jamapediatrics.2020.4573
 38645891,https://doi.org/10.1136/bmjmed-2023-000807,Identification of patients undergoing chronic kidney replacement therapy in primary and secondary care data: validation study based on OpenSAFELY and UK Renal Registry.,"Santhakumaran S, Fisher L, Zheng B, Mahalingasivam V, Plumb L, Parker EP, Steenkamp R, Morton C, Mehrkar A, Bacon S, Lyon S, Konstant-Hambling R, Goldacre B, MacKenna B, Tomlinson LA, Nitsch D.",,BMJ medicine,2024,2024-04-18,Y,"Dialysis; Kidney transplantation; Kidney failure, chronic; epidemiology; Covid-19",,,"<h4>Objective</h4>To validate primary and secondary care codes in electronic health records to identify people receiving chronic kidney replacement therapy based on gold standard registry data.<h4>Design</h4>Validation study using data from OpenSAFELY and the UK Renal Registry, with the approval of NHS England.<h4>Setting</h4>Primary and secondary care electronic health records from people registered at 45% of general practices in England on 1 January 2020, linked to data from the UK Renal Registry (UKRR) within the OpenSAFELY-TPP platform, part of the NHS England OpenSAFELY covid-19 service.<h4>Participants</h4>38 745 prevalent patients (recorded as receiving kidney replacement therapy on 1 January 2020 in UKRR data, or primary or secondary care data) and 10 730 incident patients (starting kidney replacement therapy during 2020), from a population of 19 million people alive and registered with a general practice in England on 1 January 2020.<h4>Main outcome measures</h4>Sensitivity and positive predictive values of primary and secondary care code lists for identifying prevalent and incident kidney replacement therapy cohorts compared with the gold standard UKRR data on chronic kidney replacement therapy. Agreement across the data sources overall, and by treatment modality (transplantation or dialysis) and personal characteristics.<h4>Results</h4>Primary and secondary care code lists were sensitive for identifying the UKRR prevalent cohort (91.2% (95% confidence interval (CI) 90.8% to 91.6%) and 92.0% (91.6% to 92.4%), respectively), but not the incident cohort (52.3% (50.3% to 54.3%) and 67.9% (66.1% to 69.7%)). Positive predictive values were low (77.7% (77.2% to 78.2%) for primary care data and 64.7% (64.1% to 65.3%) for secondary care data), particularly for chronic dialysis (53.7% (52.9% to 54.5%) for primary care data and 49.1% (48.0% to 50.2%) for secondary care data). Sensitivity decreased with age and index of multiple deprivation in primary care data, but the opposite was true in secondary care data. Agreement was lower in children, with 30% (295/980) featuring in all three datasets. Half (1165/2315) of the incident patients receiving dialysis in UKRR data had a kidney replacement therapy code in the primary care data within three months of the start date of the kidney replacement therapy. No codes existed whose exclusion would substantially improve the positive predictive value without a decrease in sensitivity.<h4>Conclusions</h4>Codes used in primary and secondary care data failed to identify a small proportion of prevalent patients receiving kidney replacement therapy. Codes also identified many patients who were not recipients of chronic kidney replacement therapy in UKRR data, particularly dialysis codes. Linkage with UKRR kidney replacement therapy data facilitated more accurate identification of incident and prevalent kidney replacement therapy cohorts for research into this vulnerable population. Poor coding has implications for any patient care (including eligibility for vaccination, resourcing, and health policy responses in future pandemics) that relies on accurate reporting of kidney replacement therapy in primary and secondary care data.",,doi:https://doi.org/10.1136/bmjmed-2023-000807; html:https://europepmc.org/articles/PMC11029353; pdf:https://europepmc.org/articles/PMC11029353?pdf=render
 35501391,https://doi.org/10.1038/s41416-022-01830-6,"Impact of the SARS-CoV-2 pandemic on female breast, colorectal and non-small cell lung cancer incidence, stage and healthcare pathway to diagnosis during 2020 in Wales, UK, using a national cancer clinical record system.","Greene G, Griffiths R, Han J, Akbari A, Jones M, Lyons J, Lyons RA, Rolles M, Torabi F, Warlow J, Morris ERA, Lawler M, Huws DW.",,British journal of cancer,2022,2022-05-02,Y,,,,"<h4>Background</h4>COVID-19 pandemic responses impacted behaviour and health services. We estimated the impact on incidence, stage and healthcare pathway to diagnosis for female breast, colorectal and non-small cell lung cancers at population level in Wales.<h4>Methods</h4>Cancer e-record and hospital admission data linkage identified adult cases, stage and healthcare pathway to diagnosis (population ~2.5 million). Using multivariate Poisson regressions, we compared 2019 and 2020 counts and estimated incidence rate ratios (IRR).<h4>Results</h4>Cases decreased 15.2% (n = -1011) overall. Female breast annual IRR was 0.81 (95% CI: 0.76-0.86, p < 0.001), colorectal 0.80 (95% CI: 0.79-0.81, p < 0.001) and non-small cell lung 0.91 (95% CI: 0.90-0.92, p < 0.001). Decreases were largest in 50-69 year olds for female breast and 80+ year olds for all cancers. Stage I female breast cancer declined 41.6%, but unknown stage increased 55.8%. Colorectal stages I-IV declined (range 26.6-29.9%), while unknown stage increased 803.6%. Colorectal Q2-2020 GP-urgent suspected cancer diagnoses decreased 50.0%, and 53.9% for non-small cell lung cancer. Annual screen-detected female breast and colorectal cancers fell 47.8% and 13.3%, respectively. Non-smal -cell lung cancer emergency presentation diagnoses increased 9.5% (Q2-2020) and 16.3% (Q3-2020).<h4>Conclusion</h4>Significantly fewer cases of three common cancers were diagnosed in 2020. Detrimental impacts on outcomes varied between cancers. Ongoing surveillance with health service optimisation will be needed to mitigate impacts.",,pdf:https://www.nature.com/articles/s41416-022-01830-6.pdf; doi:https://doi.org/10.1038/s41416-022-01830-6; html:https://europepmc.org/articles/PMC9060409; pdf:https://europepmc.org/articles/PMC9060409?pdf=render
 35104687,https://doi.org/10.1016/j.retram.2022.103333,A common TMPRSS2 variant has a protective effect against severe COVID-19.,"David A, Parkinson N, Peacock TP, Pairo-Castineira E, Khanna T, Cobat A, Tenesa A, Sancho-Shimizu V, GenOMICC Consortium, ISARIC4C Investigators, Casanova JL, Abel L, Barclay WS, Baillie JK, Sternberg MJ.",,Current research in translational medicine,2022,2022-01-10,Y,Tmprss2; Covid-19; Sars-cov-2; Targeting The Host To Prevent Covid19 Severity,,,"<h4>Background</h4>The human protein transmembrane protease serine type 2 (TMPRSS2) plays a key role in SARS-CoV-2 infection, as it is required to activate the virus' spike protein, facilitating entry into target cells. We hypothesized that naturally-occurring TMPRSS2 human genetic variants affecting the structure and function of the TMPRSS2 protein may modulate the severity of SARS-CoV-2 infection.<h4>Methods</h4>We focused on the only common TMPRSS2 non-synonymous variant predicted to be damaging (rs12329760 C>T, p.V160M), which has a minor allele frequency ranging from 0.14 in Ashkenazi Jewish to 0.38 in East Asians. We analysed the association between the rs12329760 and COVID-19 severity in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units recruited as part of the GenOMICC (Genetics Of Mortality In Critical Care) study. Logistic regression analyses were adjusted for sex, age and deprivation index. For in vitro studies, HEK293 cells were co-transfected with ACE2 and either TMPRSS2 wild type or mutant (TMPRSS2<sub>V160M</sub>). A SARS-CoV-2 pseudovirus entry assay was used to investigate the ability of TMPRSS2<sub>V160M</sub> to promote viral entry.<h4>Results</h4>We show that the T allele of rs12329760 is associated with a reduced likelihood of developing severe COVID-19 (OR 0.87, 95%CI:0.79-0.97, p = 0.01). This association was stronger in homozygous individuals when compared to the general population (OR 0.65, 95%CI:0.50-0.84, p = 1.3 × 10<sup>-3</sup>). We demonstrate in vitro that this variant, which causes the amino acid substitution valine to methionine, affects the catalytic activity of TMPRSS2 and is less able to support SARS-CoV-2 spike-mediated entry into cells.<h4>Conclusion</h4>TMPRSS2 rs12329760 is a common variant associated with a significantly decreased risk of severe COVID-19. Further studies are needed to assess the expression of TMPRSS2 across different age groups. Moreover, our results identify TMPRSS2 as a promising drug target, with a potential role for camostat mesilate, a drug approved for the treatment of chronic pancreatitis and postoperative reflux esophagitis, in the treatment of COVID-19. Clinical trials are needed to confirm this.",,doi:https://doi.org/10.1016/j.retram.2022.103333; doi:https://doi.org/10.1016/j.retram.2022.103333; html:https://europepmc.org/articles/PMC8743599; pdf:https://europepmc.org/articles/PMC8743599?pdf=render
 33243817,https://doi.org/10.1136/bmjopen-2020-042813,COVID-19 in Pregnancy in Scotland (COPS): protocol for an observational study using linked Scottish national data.,"Stock SJ, McAllister D, Vasileiou E, Simpson CR, Stagg HR, Agrawal U, McCowan C, Hopkins L, Donaghy J, Ritchie L, Robertson C, Sheikh A, Wood R.",,BMJ open,2020,2020-11-26,Y,Obstetrics; epidemiology; Neonatology; Perinatology; Covid-19,,,"<h4>Introduction</h4>The effects of SARS-CoV-2 in pregnancy are not fully delineated. We will describe the incidence of COVID-19 in pregnancy at population level in Scotland, in a prospective cohort study using linked data. We will determine associations between COVID-19 and adverse pregnancy, neonatal and maternal outcomes and the proportion of confirmed cases of SARS-CoV-2 infection in neonates associated with maternal COVID-19.<h4>Methods and analysis</h4>Prospective cohort study using national linked data sets. We will include all women in Scotland, UK, who were pregnant on or became pregnant after, 1 March 2020 (the date of the first confirmed case of SARS-CoV-2 infection in Scotland) and all births in Scotland from 1 March 2020 onwards. Individual-level data will be extracted from data sets containing details of all livebirths, stillbirth, terminations of pregnancy and miscarriages and ectopic pregnancies treated in hospital or attending general practice. Records will be linked within the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) platform, which includes primary care records, virology and serology results and details of COVID-19 Community Hubs and Assessment Centre contacts and deaths. We will perform analyses using definitions for confirmed, probable and possible COVID-19 and report serology results (where available). Outcomes will include congenital anomaly, miscarriage, stillbirth, termination of pregnancy, preterm birth, neonatal infection, severe maternal disease and maternal deaths. We will perform descriptive analyses and appropriate modelling, adjusting for demographic and pregnancy characteristics and the presence of comorbidities. The cohort will provide a platform for future studies of the effectiveness and safety of therapeutic interventions and immunisations for COVID-19 and their effects on childhood and developmental outcomes.<h4>Ethics and dissemination</h4>COVID-19 in Pregnancy in Scotland is a substudy of EAVE II(, which has approval from the National Research Ethics Service Committee. Findings will be reported to Scottish Government, Public Health Scotland and published in peer-reviewed journals.",,pdf:https://bmjopen.bmj.com/content/bmjopen/10/11/e042813.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-042813; html:https://europepmc.org/articles/PMC7691999; pdf:https://europepmc.org/articles/PMC7691999?pdf=render
-36350810,https://doi.org/10.1371/journal.pone.0276781,"Primary hypertension, anti-hypertensive medications and the risk of severe COVID-19 in UK Biobank.","Pavey H, Kulkarni S, Wood A, Ben-Shlomo Y, Sever P, McEniery C, Wilkinson I.",,PloS one,2022,2022-11-09,Y,,,,"Hypertension appears to be one of the commonest comorbidities in COVID-19 patients, although whether hypertensive individuals have a higher risk of severe COVID-19 compared with non-hypertensives is unclear. It is also unclear whether the absolute level of systolic blood pressure, or the type of anti-hypertensive medication is related to this risk. Analyses were conducted using data from the UK Biobank and linked health records. Logistic regression models were fitted to assess the impact of hypertension, systolic blood pressure (SBP) and medications on the risk of severe COVID-19. 16,134 individuals tested positive for severe acute respiratory syndrome-coronavirus, 22% (n = 3,584) developed severe COVID-19 and 40% (n = 6,517) were hypertensive. Hypertension was associated with 22% higher odds of severe COVID-19 (Odds ratio (OR) 1.22; 95% confidence interval (CI) 1.12, 1.33), compared with normotension after adjusting for confounding variables. In those taking anti-hypertensive medications, elevated SBP showed a dose-response relationship with severe COVID-19 (150-159mmHg versus 120-129mmHg (OR 1.91; 95% CI 1.44, 2.53), &gt;180+mmHg versus 120-129mmHg (OR 1.93; 95% CI 1.06, 3.51)). SBP &lt;120mmHg was associated with greater odds of severe COVID-19 (OR 1.40; 95% CI 1.11, 1.78). Angiotensin-converting enzyme inhibitors or angiotensin-II receptor blockers were not associated with altered risk of severe COVID-19. Hypertension is an important risk factor for COVID-19. A better understanding of the underlying mechanisms is warranted in case of more severe strains or other viruses in the future.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0276781&type=printable; doi:https://doi.org/10.1371/journal.pone.0276781; html:https://europepmc.org/articles/PMC9645600; pdf:https://europepmc.org/articles/PMC9645600?pdf=render
 38783412,https://doi.org/10.1002/pds.5815,OpenSAFELY: A platform for analysing electronic health records designed for reproducible research.,"Nab L, Schaffer AL, Hulme W, DeVito NJ, Dillingham I, Wiedemann M, Andrews CD, Curtis H, Fisher L, Green A, Massey J, Walters CE, Higgins R, Cunningham C, Morley J, Mehrkar A, Hart L, Davy S, Evans D, Hickman G, Inglesby P, Morton CE, Smith RM, Ward T, O'Dwyer T, Maude S, Bridges L, Butler-Cole BFC, Stables CL, Stokes P, Bates C, Cockburn J, Hester F, Parry J, Bhaskaran K, Schultze A, Rentsch CT, Mathur R, Tomlinson LA, Williamson EJ, Smeeth L, Walker A, Bacon S, MacKenna B, Goldacre B.",,Pharmacoepidemiology and drug safety,2024,2024-06-01,Y,Reproducibility; Electronic Health Records; Open Science; Research Platform; Opensafely,,,"Electronic health records (EHRs) and other administrative health data are increasingly used in research to generate evidence on the effectiveness, safety, and utilisation of medical products and services, and to inform public health guidance and policy. Reproducibility is a fundamental step for research credibility and promotes trust in evidence generated from EHRs. At present, ensuring research using EHRs is reproducible can be challenging for researchers. Research software platforms can provide technical solutions to enhance the reproducibility of research conducted using EHRs. In response to the COVID-19 pandemic, we developed the secure, transparent, analytic open-source software platform OpenSAFELY designed with reproducible research in mind. OpenSAFELY mitigates common barriers to reproducible research by: standardising key workflows around data preparation; removing barriers to code-sharing in secure analysis environments; enforcing public sharing of programming code and codelists; ensuring the same computational environment is used everywhere; integrating new and existing tools that encourage and enable the use of reproducible working practices; and providing an audit trail for all code that is run against the real data to increase transparency. This paper describes OpenSAFELY's reproducibility-by-design approach in detail.",,doi:https://doi.org/10.1002/pds.5815; html:https://europepmc.org/articles/PMC7616137; pdf:https://europepmc.org/articles/PMC7616137?pdf=render
+36350810,https://doi.org/10.1371/journal.pone.0276781,"Primary hypertension, anti-hypertensive medications and the risk of severe COVID-19 in UK Biobank.","Pavey H, Kulkarni S, Wood A, Ben-Shlomo Y, Sever P, McEniery C, Wilkinson I.",,PloS one,2022,2022-11-09,Y,,,,"Hypertension appears to be one of the commonest comorbidities in COVID-19 patients, although whether hypertensive individuals have a higher risk of severe COVID-19 compared with non-hypertensives is unclear. It is also unclear whether the absolute level of systolic blood pressure, or the type of anti-hypertensive medication is related to this risk. Analyses were conducted using data from the UK Biobank and linked health records. Logistic regression models were fitted to assess the impact of hypertension, systolic blood pressure (SBP) and medications on the risk of severe COVID-19. 16,134 individuals tested positive for severe acute respiratory syndrome-coronavirus, 22% (n = 3,584) developed severe COVID-19 and 40% (n = 6,517) were hypertensive. Hypertension was associated with 22% higher odds of severe COVID-19 (Odds ratio (OR) 1.22; 95% confidence interval (CI) 1.12, 1.33), compared with normotension after adjusting for confounding variables. In those taking anti-hypertensive medications, elevated SBP showed a dose-response relationship with severe COVID-19 (150-159mmHg versus 120-129mmHg (OR 1.91; 95% CI 1.44, 2.53), &gt;180+mmHg versus 120-129mmHg (OR 1.93; 95% CI 1.06, 3.51)). SBP &lt;120mmHg was associated with greater odds of severe COVID-19 (OR 1.40; 95% CI 1.11, 1.78). Angiotensin-converting enzyme inhibitors or angiotensin-II receptor blockers were not associated with altered risk of severe COVID-19. Hypertension is an important risk factor for COVID-19. A better understanding of the underlying mechanisms is warranted in case of more severe strains or other viruses in the future.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0276781&type=printable; doi:https://doi.org/10.1371/journal.pone.0276781; html:https://europepmc.org/articles/PMC9645600; pdf:https://europepmc.org/articles/PMC9645600?pdf=render
 34104901,https://doi.org/10.1016/s2666-7568(21)00093-3,Incidence of SARS-CoV-2 infection according to baseline antibody status in staff and residents of 100 long-term care facilities (VIVALDI): a prospective cohort study.,"Krutikov M, Palmer T, Tut G, Fuller C, Shrotri M, Williams H, Davies D, Irwin-Singer A, Robson J, Hayward A, Moss P, Copas A, Shallcross L.",,The lancet. Healthy longevity,2021,2021-06-03,Y,,,,"<h4>Background</h4>SARS-CoV-2 infection represents a major challenge for long-term care facilities (LTCFs) and many residents and staff are seropositive following persistent outbreaks. We aimed to investigate the association between the SARS-CoV-2 antibody status at baseline and subsequent infection in this population.<h4>Methods</h4>We did a prospective cohort study of SARS-CoV-2 infection in staff (aged <65 years) and residents (aged >65 years) at 100 LTCFs in England between Oct 1, 2020, and Feb 1, 2021. Blood samples were collected between June and November, 2020, at baseline, and 2 and 4 months thereafter and tested for IgG antibodies to SARS-CoV-2 nucleocapsid and spike proteins. PCR testing for SARS-CoV-2 was done weekly in staff and monthly in residents. Cox regression was used to estimate hazard ratios (HRs) of a PCR-positive test by baseline antibody status, adjusted for age and sex, and stratified by LTCF.<h4>Findings</h4>682 residents from 86 LCTFs and 1429 staff members from 97 LTCFs met study inclusion criteria. At baseline, IgG antibodies to nucleocapsid were detected in 226 (33%) of 682 residents and 408 (29%) of 1429 staff members. 93 (20%) of 456 residents who were antibody-negative at baseline had a PCR-positive test (infection rate 0·054 per month at risk) compared with four (2%) of 226 residents who were antibody-positive at baseline (0·007 per month at risk). 111 (11%) of 1021 staff members who were antibody-negative at baseline had PCR-positive tests (0·042 per month at risk) compared with ten (2%) of 408 staff members who were antibody-positive staff at baseline (0·009 per month at risk). The risk of PCR-positive infection was higher for residents who were antibody-negative at baseline than residents who were antibody-positive at baseline (adjusted HR [aHR] 0·15, 95% CI 0·05-0·44, p=0·0006), and the risk of a PCR-positive infection was also higher for staff who were antibody-negative at baseline compared with staff who were antibody-positive at baseline (aHR 0·39, 0·19-0·82; p=0·012). 12 of 14 reinfected participants had available data on symptoms, and 11 of these participants were symptomatic. Antibody titres to spike and nucleocapsid proteins were comparable in PCR-positive and PCR-negative cases.<h4>Interpretation</h4>The presence of IgG antibodies to nucleocapsid protein was associated with substantially reduced risk of reinfection in staff and residents for up to 10 months after primary infection.<h4>Funding</h4>UK Government Department of Health and Social Care.",,pdf:http://www.thelancet.com/article/S2666756821000933/pdf; doi:https://doi.org/10.1016/S2666-7568(21)00093-3; html:https://europepmc.org/articles/PMC8175048; pdf:https://europepmc.org/articles/PMC8175048?pdf=render
 38302156,https://doi.org/10.3399/bjgpo.2023.0163,Safety of direct-acting oral anticoagulant (DOAC) prescribing: OpenSAFELY-TPP analysis of 20.5 million adults' electronic health records.,"Homan K, Seeley R, Fisher L, Khatri S, Smith K, Jamieson T, Speed V, Roberts CA, Mehrkar A, Bacon S, MacKenna B, Goldacre B.",,BJGP open,2024,2024-07-29,Y,creatinine clearance; Patient Safety; Electronic Health Records; Doac; Covid-19,,,"<h4>Background</h4>During the COVID-19 pandemic many patients were switched from warfarin to direct-acting oral anticoagulants (DOACs), which require the creatinine clearance (CrCl) calculated to ensure the correct dose is prescribed to avoid bleeding or reduced efficacy.<h4>Aim</h4>To identify the study population proportion prescribed a DOAC. Of these, the proportion with recorded: weight, estimated glomerular filtration rate (eGFR), creatinine, CrCl and atrial fibrillation (AF). To analyse the proportion of patients with recorded AF and CrCl prescribed a recommended DOAC dose.<h4>Design & setting</h4>A retrospective cohort study of 20.5 million adult NHS patients' electronic health records (EHRs) in England in the OpenSAFELY-TPP platform (January 2018-February 2023).<h4>Method</h4>Patients on DOACs were analysed for age, sex, recorded weight, eGFR, creatinine, CrCl and AF. Prescribed DOAC doses in patients with recorded AF were compared with recommended doses for recorded CrCl and determined as either recommended, higher than recommended (overdose), or lower than recommended (underdose).<h4>Results</h4>In February 2023, weight, eGFR, creatinine, CrCl, and AF were recorded in 72.8%, 92.4%, 94.3%, 73.5%, and 73.9% of study population, respectively. Both AF and CrCl were recorded for 56.7% of patients. Of these, 86.2% received the recommended, and 13.8% non-recommended, DOAC doses.<h4>Conclusion</h4>CrCl is not recorded for a substantial number of patients on DOACs. We recommend that national organisations tasked with safety, collectively update guidance on the appropriate weight to use in the Cockcroft-Gault equation, clarify that CrCl is not equivalent to eGFR, and work with GP clinical system suppliers to standardise the calculation of CrCl in the EHR.",,pdf:https://bjgpopen.org/content/bjgpoa/early/2024/01/30/BJGPO.2023.0163.full.pdf; doi:https://doi.org/10.3399/BJGPO.2023.0163; html:https://europepmc.org/articles/PMC7616327; pdf:https://europepmc.org/articles/PMC7616327?pdf=render
 36210437,https://doi.org/10.1186/s12916-022-02588-7,Hesitancy for receiving regular SARS-CoV-2 vaccination in UK healthcare workers: a cross-sectional analysis from the UK-REACH study.,"Veli N, Martin CA, Woolf K, Nazareth J, Pan D, Al-Oraibi A, Baggaley RF, Bryant L, Nellums LB, Gray LJ, Khunti K, Pareek M, UK-REACH Study Collaborative Group.",,BMC medicine,2022,2022-10-10,Y,Vaccination; Ethnicity; Healthcare; Hesitancy; Covid-19; Sars-cov-2,,,"<h4>Background</h4>Regular vaccination against SARS-CoV-2 may be needed to maintain immunity in 'at-risk' populations, which include healthcare workers (HCWs). However, little is known about the proportion of HCWs who might be hesitant about receiving a hypothetical regular SARS-CoV-2 vaccination or the factors associated with this hesitancy.<h4>Methods</h4>Cross-sectional analysis of questionnaire data collected as part of UK-REACH, a nationwide, longitudinal cohort study of HCWs. The outcome measure was binary, either a participant indicated they would definitely accept regular SARS-CoV-2 vaccination if recommended or they indicated some degree of hesitancy regarding acceptance (probably accept or less likely). We used logistic regression to identify factors associated with hesitancy for receiving regular vaccination.<h4>Results</h4>A total of 5454 HCWs were included in the analysed cohort, 23.5% of whom were hesitant about regular SARS-CoV-2 vaccination. Black HCWs were more likely to be hesitant than White HCWs (aOR 2.60, 95%CI 1.80-3.72) as were those who reported a previous episode of COVID-19 (1.33, 1.13-1.57 [vs those who tested negative]). Those who received influenza vaccination in the previous two seasons were over five times less likely to report hesitancy for regular SARS-CoV-2 vaccination than those not vaccinated against influenza in either season (0.18, 0.14-0.21). HCWs who trusted official sources of vaccine information (such as NHS or government adverts or websites) were less likely to report hesitancy for a regular vaccination programme. Those who had been exposed to information advocating against vaccination from friends and family were more likely to be hesitant.<h4>Conclusions</h4>In this study, nearly a quarter of UK HCWs were hesitant about receiving a regular SARS-CoV-2 vaccination. We have identified key factors associated with hesitancy for regular SARS-CoV-2 vaccination, which can be used to identify groups of HCWs at the highest risk of vaccine hesitancy and tailor interventions accordingly. Family and friends of HCWs may influence decisions about regular vaccination. This implies that working with HCWs and their social networks to allay concerns about SARS-CoV-2 vaccination could improve uptake in a regular vaccination programme.<h4>Trial registration</h4>ISRCTN Registry, ISRCTN11811602.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-022-02588-7; doi:https://doi.org/10.1186/s12916-022-02588-7; html:https://europepmc.org/articles/PMC9548389; pdf:https://europepmc.org/articles/PMC9548389?pdf=render
 36720568,https://doi.org/10.1136/bmjopen-2022-066164,Factors associated with COVID-19 vaccine uptake in people with kidney disease: an OpenSAFELY cohort study.,"OpenSAFELY Collaborative, Parker EP, Tazare J, Hulme WJ, Bates C, Carr EJ, Cockburn J, Curtis HJ, Fisher L, Green AC, Harper S, Hester F, Horne EM, Loud F, Lyon S, Mahalingasivam V, Mehrkar A, Nab L, Parry J, Santhakumaran S, Steenkamp R, Sterne JA, Walker AJ, Williamson EJ, Willicombe M, Zheng B, Goldacre B, Nitsch D, Tomlinson LA.",,BMJ open,2023,2023-01-31,Y,Public Health; Kidney & Urinary Tract Disorders; Covid-19,,,"<h4>Objective</h4>To characterise factors associated with COVID-19 vaccine uptake among people with kidney disease in England.<h4>Design</h4>Retrospective cohort study using the OpenSAFELY-TPP platform, performed with the approval of NHS England.<h4>Setting</h4>Individual-level routine clinical data from 24 million people across GPs in England using TPP software. Primary care data were linked directly with COVID-19 vaccine records up to 31 August 2022 and with renal replacement therapy (RRT) status via the UK Renal Registry (UKRR).<h4>Participants</h4>A cohort of adults with stage 3-5 chronic kidney disease (CKD) or receiving RRT at the start of the COVID-19 vaccine roll-out was identified based on evidence of reduced estimated glomerular filtration rate (eGFR) or inclusion in the UKRR.<h4>Main outcome measures</h4>Dose-specific vaccine coverage over time was determined from 1 December 2020 to 31 August 2022. Individual-level factors associated with receipt of a 3-dose or 4-dose vaccine series were explored via Cox proportional hazards models.<h4>Results</h4>992 205 people with stage 3-5 CKD or receiving RRT were included. Cumulative vaccine coverage as of 31 August 2022 was 97.5%, 97.0% and 93.9% for doses 1, 2 and 3, respectively, and 81.9% for dose 4 among individuals with one or more indications for eligibility. Delayed 3-dose vaccine uptake was associated with younger age, minority ethnicity, social deprivation and severe mental illness-associations that were consistent across CKD severity subgroups, dialysis patients and kidney transplant recipients. Similar associations were observed for 4-dose uptake.<h4>Conclusion</h4>Although high primary vaccine and booster dose coverage has been achieved among people with kidney disease in England, key disparities in vaccine uptake remain across clinical and demographic groups and 4-dose coverage is suboptimal. Targeted interventions are needed to identify barriers to vaccine uptake among under-vaccinated subgroups identified in the present study.",,pdf:https://bmjopen.bmj.com/content/bmjopen/13/1/e066164.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-066164; html:https://europepmc.org/articles/PMC9890277; pdf:https://europepmc.org/articles/PMC9890277?pdf=render
-36058413,https://doi.org/10.1016/j.jinf.2022.08.030,A prospective study of risk factors associated with seroprevalence of SARS-CoV-2 antibodies in healthcare workers at a large UK teaching hospital.,"Cooper DJ, Lear S, Watson L, Shaw A, Ferris M, Doffinger R, Bousfield R, Sharrocks K, Weekes MP, Warne B, Sparkes D, Jones NK, Rivett L, Routledge M, Chaudhry A, Dempsey K, Matson M, Lakha A, Gathercole G, O'Connor O, Wilson E, Shahzad O, Toms K, Thompson R, Halsall I, Halsall D, Houghton S, Papadia S, Kingston N, Stirrups KE, Graves B, Townsend P, Walker N, Stark H, CITIID-NIHR BioResource COVID-19 Collaboration, De Angelis D, Seaman S, Dougan G, Bradley JR, Török ME, Goodfellow I, Baker S.",,The Journal of infection,2022,2022-09-02,Y,Healthcare Workers; Sero-epidemiology; Risk Factor Analysis; Covid-19; Sars-cov-2,,,"<h4>Objectives</h4>To describe the risk factors for SARS-CoV-2 infection in UK healthcare workers (HCWs).<h4>Methods</h4>We conducted a prospective sero-epidemiological study of HCWs at a major UK teaching hospital using a SARS-CoV-2 immunoassay. Risk factors for seropositivity were analysed using multivariate logistic regression.<h4>Results</h4>410/5,698 (7·2%) staff tested positive for SARS-CoV-2 antibodies. Seroprevalence was higher in those working in designated COVID-19 areas compared with other areas (9·47% versus 6·16%) Healthcare assistants (aOR 2·06 [95%CI 1·14-3·71]; p=0·016) and domestic and portering staff (aOR 3·45 [95% CI 1·07-11·42]; p=0·039) had significantly higher seroprevalence than other staff groups after adjusting for age, sex, ethnicity and COVID-19 working location. Staff working in acute medicine and medical sub-specialities were also at higher risk (aOR 2·07 [95% CI 1·31-3·25]; p<0·002). Staff from Black, Asian and minority ethnic (BAME) backgrounds had an aOR of 1·65 (95% CI 1·32 - 2·07; p<0·001) compared to white staff; this increased risk was independent of COVID-19 area working. The only symptoms significantly associated with seropositivity in a multivariable model were loss of sense of taste or smell, fever, and myalgia; 31% of staff testing positive reported no prior symptoms.<h4>Conclusions</h4>Risk of SARS-CoV-2 infection amongst HCWs is highly heterogeneous and influenced by COVID-19 working location, role, age and ethnicity. Increased risk amongst BAME staff cannot be accounted for solely by occupational factors.",,pdf:https://www.repository.cam.ac.uk/bitstream/1810/341240/2/1-s2.0-S016344532200514X-main.pdf; doi:https://doi.org/10.1016/j.jinf.2022.08.030; html:https://europepmc.org/articles/PMC9436870; pdf:https://europepmc.org/articles/PMC9436870?pdf=render
 35572721,https://doi.org/10.1016/j.eclinm.2022.101419,Breakthrough SARS-CoV-2 infections in double and triple vaccinated adults and single dose vaccine effectiveness among children in Autumn 2021 in England: REACT-1 study.,"Chadeau-Hyam M, Eales O, Bodinier B, Wang H, Haw D, Whitaker M, Elliott J, Walters CE, Jonnerby J, Atchison C, Diggle PJ, Page AJ, Ashby D, Barclay W, Taylor G, Cooke G, Ward H, Darzi A, Donnelly CA, Elliott P.",,EClinicalMedicine,2022,2022-05-06,Y,School-aged children; Vaccine Effectiveness; Booster Dose; Children Vaccination; Sars-cov-2 Prevalence,,,"<h4>Background</h4>Prevalence of SARS-CoV-2 infection with Delta variant was increasing in England in late summer 2021 among children aged 5 to 17 years, and adults who had received two vaccine doses. In September 2021, a third (booster) dose was offered to vaccinated adults aged 50 years and over, vulnerable adults and healthcare/care-home workers, and a single vaccine dose already offered to 16 and 17 year-olds was extended to children aged 12 to 15 years.<h4>Methods</h4>SARS-CoV-2 community prevalence in England was available from self-administered throat and nose swabs using reverse transcriptase polymerase chain reaction (RT-PCR) in round 13 (24 June to 12 July 2021, <i>N</i> = 98,233), round 14 (9 to 27 September 2021, <i>N</i> = 100,527) and round 15 (19 October to 5 November 2021, <i>N</i> = 100,112) from the REACT-1 study randomised community surveys. Linking to National Health Service (NHS) vaccination data for consenting participants, we estimated vaccine effectiveness in children aged 12 to 17 years and compared swab-positivity rates in adults who received a third dose with those who received two doses.<h4>Findings</h4>Weighted SARS-CoV-2 prevalence was 1.57% (1.48%, 1.66%) in round 15 compared with 0.83% (0.76%, 0.89%) in round 14, and the previously observed link between infections and hospitalisations and deaths had weakened. Vaccine effectiveness against infection in children aged 12 to 17 years was estimated (round 15) at 64.0% (50.9%, 70.6%) and 67.7% (53.8%, 77.5%) for symptomatic infections. Adults who received a third vaccine dose were less likely to test positive compared to those who received two doses, with adjusted OR of 0.36 (0.25, 0.53).<h4>Interpretation</h4>Vaccination of children aged 12 to 17 years and third (booster) doses in adults were effective at reducing infection risk. High rates of vaccination, including booster doses, are a key part of the strategy to reduce infection rates in the community.<h4>Funding</h4>Department of Health and Social Care, England.",,pdf:http://www.thelancet.com/article/S2589537022001493/pdf; doi:https://doi.org/10.1016/j.eclinm.2022.101419; html:https://europepmc.org/articles/PMC9076030; pdf:https://europepmc.org/articles/PMC9076030?pdf=render
+36058413,https://doi.org/10.1016/j.jinf.2022.08.030,A prospective study of risk factors associated with seroprevalence of SARS-CoV-2 antibodies in healthcare workers at a large UK teaching hospital.,"Cooper DJ, Lear S, Watson L, Shaw A, Ferris M, Doffinger R, Bousfield R, Sharrocks K, Weekes MP, Warne B, Sparkes D, Jones NK, Rivett L, Routledge M, Chaudhry A, Dempsey K, Matson M, Lakha A, Gathercole G, O'Connor O, Wilson E, Shahzad O, Toms K, Thompson R, Halsall I, Halsall D, Houghton S, Papadia S, Kingston N, Stirrups KE, Graves B, Townsend P, Walker N, Stark H, CITIID-NIHR BioResource COVID-19 Collaboration, De Angelis D, Seaman S, Dougan G, Bradley JR, Török ME, Goodfellow I, Baker S.",,The Journal of infection,2022,2022-09-02,Y,Healthcare Workers; Sero-epidemiology; Risk Factor Analysis; Covid-19; Sars-cov-2,,,"<h4>Objectives</h4>To describe the risk factors for SARS-CoV-2 infection in UK healthcare workers (HCWs).<h4>Methods</h4>We conducted a prospective sero-epidemiological study of HCWs at a major UK teaching hospital using a SARS-CoV-2 immunoassay. Risk factors for seropositivity were analysed using multivariate logistic regression.<h4>Results</h4>410/5,698 (7·2%) staff tested positive for SARS-CoV-2 antibodies. Seroprevalence was higher in those working in designated COVID-19 areas compared with other areas (9·47% versus 6·16%) Healthcare assistants (aOR 2·06 [95%CI 1·14-3·71]; p=0·016) and domestic and portering staff (aOR 3·45 [95% CI 1·07-11·42]; p=0·039) had significantly higher seroprevalence than other staff groups after adjusting for age, sex, ethnicity and COVID-19 working location. Staff working in acute medicine and medical sub-specialities were also at higher risk (aOR 2·07 [95% CI 1·31-3·25]; p<0·002). Staff from Black, Asian and minority ethnic (BAME) backgrounds had an aOR of 1·65 (95% CI 1·32 - 2·07; p<0·001) compared to white staff; this increased risk was independent of COVID-19 area working. The only symptoms significantly associated with seropositivity in a multivariable model were loss of sense of taste or smell, fever, and myalgia; 31% of staff testing positive reported no prior symptoms.<h4>Conclusions</h4>Risk of SARS-CoV-2 infection amongst HCWs is highly heterogeneous and influenced by COVID-19 working location, role, age and ethnicity. Increased risk amongst BAME staff cannot be accounted for solely by occupational factors.",,pdf:https://www.repository.cam.ac.uk/bitstream/1810/341240/2/1-s2.0-S016344532200514X-main.pdf; doi:https://doi.org/10.1016/j.jinf.2022.08.030; html:https://europepmc.org/articles/PMC9436870; pdf:https://europepmc.org/articles/PMC9436870?pdf=render
 35077449,https://doi.org/10.1371/journal.pmed.1003871,"Overall and cause-specific hospitalisation and death after COVID-19 hospitalisation in England: A cohort study using linked primary care, secondary care, and death registration data in the OpenSAFELY platform.","Bhaskaran K, Rentsch CT, Hickman G, Hulme WJ, Schultze A, Curtis HJ, Wing K, Warren-Gash C, Tomlinson L, Bates CJ, Mathur R, MacKenna B, Mahalingasivam V, Wong A, Walker AJ, Morton CE, Grint D, Mehrkar A, Eggo RM, Inglesby P, Douglas IJ, McDonald HI, Cockburn J, Williamson EJ, Evans D, Parry J, Hester F, Harper S, Evans SJ, Bacon S, Smeeth L, Goldacre B.",,PLoS medicine,2022,2022-01-25,Y,,,,"<h4>Background</h4>There is concern about medium to long-term adverse outcomes following acute Coronavirus Disease 2019 (COVID-19), but little relevant evidence exists. We aimed to investigate whether risks of hospital admission and death, overall and by specific cause, are raised following discharge from a COVID-19 hospitalisation.<h4>Methods and findings</h4>With the approval of NHS-England, we conducted a cohort study, using linked primary care and hospital data in OpenSAFELY to compare risks of hospital admission and death, overall and by specific cause, between people discharged from COVID-19 hospitalisation (February to December 2020) and surviving at least 1 week, and (i) demographically matched controls from the 2019 general population; and (ii) people discharged from influenza hospitalisation in 2017 to 2019. We used Cox regression adjusted for age, sex, ethnicity, obesity, smoking status, deprivation, and comorbidities considered potential risk factors for severe COVID-19 outcomes. We included 24,673 postdischarge COVID-19 patients, 123,362 general population controls, and 16,058 influenza controls, followed for ≤315 days. COVID-19 patients had median age of 66 years, 13,733 (56%) were male, and 19,061 (77%) were of white ethnicity. Overall risk of hospitalisation or death (30,968 events) was higher in the COVID-19 group than general population controls (fully adjusted hazard ratio [aHR] 2.22, 2.14 to 2.30, p < 0.001) but slightly lower than the influenza group (aHR 0.95, 0.91 to 0.98, p = 0.004). All-cause mortality (7,439 events) was highest in the COVID-19 group (aHR 4.82, 4.48 to 5.19 versus general population controls [p < 0.001] and 1.74, 1.61 to 1.88 versus influenza controls [p < 0.001]). Risks for cause-specific outcomes were higher in COVID-19 survivors than in general population controls and largely similar or lower in COVID-19 compared with influenza patients. However, COVID-19 patients were more likely than influenza patients to be readmitted or die due to their initial infection or other lower respiratory tract infection (aHR 1.37, 1.22 to 1.54, p < 0.001) and to experience mental health or cognitive-related admission or death (aHR 1.37, 1.02 to 1.84, p = 0.039); in particular, COVID-19 survivors with preexisting dementia had higher risk of dementia hospitalisation or death (age- and sex-adjusted HR 2.47, 1.37 to 4.44, p = 0.002). Limitations of our study were that reasons for hospitalisation or death may have been misclassified in some cases due to inconsistent use of codes, and we did not have data to distinguish COVID-19 variants.<h4>Conclusions</h4>In this study, we observed that people discharged from a COVID-19 hospital admission had markedly higher risks for rehospitalisation and death than the general population, suggesting a substantial extra burden on healthcare. Most risks were similar to those observed after influenza hospitalisations, but COVID-19 patients had higher risks of all-cause mortality, readmission or death due to the initial infection, and dementia death, highlighting the importance of postdischarge monitoring.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003871&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003871; html:https://europepmc.org/articles/PMC8789178; pdf:https://europepmc.org/articles/PMC8789178?pdf=render
 36522333,https://doi.org/10.1038/s41467-022-35454-4,Multi-omics identify falling LRRC15 as a COVID-19 severity marker and persistent pro-thrombotic signals in convalescence.,"Gisby JS, Buang NB, Papadaki A, Clarke CL, Malik TH, Medjeral-Thomas N, Pinheiro D, Mortimer PM, Lewis S, Sandhu E, McAdoo SP, Prendecki MF, Willicombe M, Pickering MC, Botto M, Thomas DC, Peters JE.",,Nature communications,2022,2022-12-15,Y,,,,"Patients with end-stage kidney disease (ESKD) are at high risk of severe COVID-19. Here, we perform longitudinal blood sampling of ESKD haemodialysis patients with COVID-19, collecting samples pre-infection, serially during infection, and after clinical recovery. Using plasma proteomics, and RNA-sequencing and flow cytometry of immune cells, we identify transcriptomic and proteomic signatures of COVID-19 severity, and find distinct temporal molecular profiles in patients with severe disease. Supervised learning reveals that the plasma proteome is a superior indicator of clinical severity than the PBMC transcriptome. We show that a decreasing trajectory of plasma LRRC15, a proposed co-receptor for SARS-CoV-2, is associated with a more severe clinical course. We observe that two months after the acute infection, patients still display dysregulated gene expression related to vascular, platelet and coagulation pathways, including PF4 (platelet factor 4), which may explain the prolonged thrombotic risk following COVID-19.",,pdf:https://www.nature.com/articles/s41467-022-35454-4.pdf; doi:https://doi.org/10.1038/s41467-022-35454-4; html:https://europepmc.org/articles/PMC9753891; pdf:https://europepmc.org/articles/PMC9753891?pdf=render
 34018481,https://doi.org/10.2807/1560-7917.es.2021.26.20.2100428,The potential for vaccination-induced herd immunity against the SARS-CoV-2 B.1.1.7 variant.,"Hodgson D, Flasche S, Jit M, Kucharski AJ, CMMID COVID-19 Working Group, Centre for Mathematical Modelling of Infectious Disease (CMMID) COVID-19 Working Group.",,Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin,2021,2021-05-01,Y,Vaccination; Herd immunity; Seroprevalence; Sars-cov-2,,,"We assess the feasibility of reaching the herd immunity threshold against SARS-CoV-2 through vaccination, considering vaccine effectiveness (VE), transmissibility of the virus and the level of pre-existing immunity in populations, as well as their age structure. If highly transmissible variants of concern become dominant in areas with low levels of naturally-acquired immunity and/or in populations with large proportions of < 15 year-olds, control of infection without non-pharmaceutical interventions may only be possible with a VE ≥ 80%, and coverage extended to children.",,pdf:https://www.eurosurveillance.org/deliver/fulltext/eurosurveillance/26/20/eurosurv-26-20-1.pdf?itemId=%2Fcontent%2F10.2807%2F1560-7917.ES.2021.26.20.2100428&mimeType=pdf&containerItemId=content/eurosurveillance; doi:https://doi.org/10.2807/1560-7917.ES.2021.26.20.2100428; html:https://europepmc.org/articles/PMC8138959; pdf:https://europepmc.org/articles/PMC8138959?pdf=render
@@ -226,50 +226,50 @@ PMC10929454,https://doi.org/,Optimising data curation pipelines for population-l
 35793922,https://doi.org/10.1136/bmjopen-2021-059385,Deriving and validating a risk prediction model for long COVID-19: protocol for an observational cohort study using linked Scottish data.,"Daines L, Mulholland RH, Vasileiou E, Hammersley V, Weatherill D, Katikireddi SV, Kerr S, Moore E, Pesenti E, Quint JK, Shah SA, Shi T, Simpson CR, Robertson C, Sheikh A.",,BMJ open,2022,2022-07-06,Y,Public Health; Protocols & Guidelines; Covid-19,,,"<h4>Introduction</h4>COVID-19 is commonly experienced as an acute illness, yet some people continue to have symptoms that persist for weeks, or months (commonly referred to as 'long-COVID'). It remains unclear which patients are at highest risk of developing long-COVID. In this protocol, we describe plans to develop a prediction model to identify individuals at risk of developing long-COVID.<h4>Methods and analysis</h4>We will use the national Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) platform, a population-level linked dataset of routine electronic healthcare data from 5.4 million individuals in Scotland. We will identify potential indicators for long-COVID by identifying patterns in primary care data linked to information from out-of-hours general practitioner encounters, accident and emergency visits, hospital admissions, outpatient visits, medication prescribing/dispensing and mortality. We will investigate the potential indicators of long-COVID by performing a matched analysis between those with a positive reverse transcriptase PCR (RT-PCR) test for SARS-CoV-2 infection and two control groups: (1) individuals with at least one negative RT-PCR test and never tested positive; (2) the general population (everyone who did not test positive) of Scotland. Cluster analysis will then be used to determine the final definition of the outcome measure for long-COVID. We will then derive, internally and externally validate a prediction model to identify the epidemiological risk factors associated with long-COVID.<h4>Ethics and dissemination</h4>The EAVE II study has obtained approvals from the Research Ethics Committee (reference: 12/SS/0201), and the Public Benefit and Privacy Panel for Health and Social Care (reference: 1920-0279). Study findings will be published in peer-reviewed journals and presented at conferences. Understanding the predictors for long-COVID and identifying the patient groups at greatest risk of persisting symptoms will inform future treatments and preventative strategies for long-COVID.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/7/e059385.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-059385; html:https://europepmc.org/articles/PMC9260199; pdf:https://europepmc.org/articles/PMC9260199?pdf=render
 35003715,https://doi.org/10.7189/jogh.11.05026,"Uptake, effectiveness and safety of COVID-19 vaccines in children and young people in Scotland: Protocol for early pandemic evaluation and enhanced surveillance of COVID-19 (EAVE II).","Adeloye D, Katikireddi SV, Woolford L, Simpson CR, Shah SA, Agrawal U, Richie LD, Swann OV, Stock SJ, Robertson C, Sheikh A, Rudan I.",,Journal of global health,2021,2021-12-25,Y,,,,"<h4>Background</h4>The dynamics of acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and severity of disease among children and young people (CYP) across different settings are of considerable clinical, public health and societal interest. Severe COVID-19 cases, requiring hospitalisations, and deaths have been reported in some CYP suggesting a need to extend vaccinations to these age groups. As part of the ongoing Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) study, we aim to investigate the uptake, effectiveness and safety of COVID-19 vaccines in children and young people (CYP) aged 0 to 17 years in Scotland. Specifically, we will estimate: (i) uptake of vaccines against COVID-19, (ii) vaccine effectiveness (VE) against the outcomes of symptomatic SARS-CoV-2 infection, hospitalisation, intensive care unit (ICU) admissions, and death; (iii) VE for first/second dose timing among different age groups and risk groups; and (iv) the safety of vaccines.<h4>Methods and analysis</h4>We will conduct an open prospective cohort study classifying exposure as time-varying. We will compare outcomes amongst first dose vaccinated and second dose vaccinated CYP to those not yet vaccinated. A Test Negative Design (TND) case control study will be nested within this national cohort to investigate VE against symptomatic infection. The primary outcomes will be (i) uptake of vaccines against COVID-19, (ii) time to COVID-19 infection, hospitalisation, ICU admissions or death, and (iii) adverse events related to vaccines. Vaccination status (unvaccinated, one dose and two doses) will be defined as a time-varying exposure. Data from multiple sources will be linked using a unique identifier. We will conduct descriptive analyses to explore trends in vaccine uptake, and association between different exposure variables and vaccine uptake will be determined using multivariable logistic regression models. VE will be assessed from time-dependent Cox models or Poisson regression models, adjusted for relevant confounders, including age, sex, socioeconomic status, and comorbidities. We will employ self-controlled study designs to determine the risk of adverse events following COVID-19 vaccination.<h4>Ethics and dissemination</h4>Ethics approval was obtained from the National Research Ethics Committee, South East Scotland 02. We will present findings of this study at international conferences, in peer-reviewed journals and to policy-makers.",,doi:https://doi.org/10.7189/jogh.11.05026; doi:https://doi.org/10.7189/jogh.11.05026; html:https://europepmc.org/articles/PMC8709900; pdf:https://europepmc.org/articles/PMC8709900?pdf=render
 35902613,https://doi.org/10.1038/s41467-022-32096-4,Dynamics of competing SARS-CoV-2 variants during the Omicron epidemic in England.,"Eales O, de Oliveira Martins L, Page AJ, Wang H, Bodinier B, Tang D, Haw D, Jonnerby J, Atchison C, Ashby D, Barclay W, Taylor G, Cooke G, Ward H, Darzi A, Riley S, Elliott P, Donnelly CA, Chadeau-Hyam M.",,Nature communications,2022,2022-07-28,Y,,,,"The SARS-CoV-2 pandemic has been characterised by the regular emergence of genomic variants. With natural and vaccine-induced population immunity at high levels, evolutionary pressure favours variants better able to evade SARS-CoV-2 neutralising antibodies. The Omicron variant (first detected in November 2021) exhibited a high degree of immune evasion, leading to increased infection rates worldwide. However, estimates of the magnitude of this Omicron wave have often relied on routine testing data, which are prone to several biases. Using data from the REal-time Assessment of Community Transmission-1 (REACT-1) study, a series of cross-sectional surveys assessing prevalence of SARS-CoV-2 infection in England, we estimated the dynamics of England's Omicron wave (from 9 September 2021 to 1 March 2022). We estimate an initial peak in national Omicron prevalence of 6.89% (5.34%, 10.61%) during January 2022, followed by a resurgence in SARS-CoV-2 infections as the more transmissible Omicron sub-lineage, BA.2 replaced BA.1 and BA.1.1. Assuming the emergence of further distinct variants, intermittent epidemics of similar magnitudes may become the 'new normal'.",,pdf:https://www.nature.com/articles/s41467-022-32096-4.pdf; doi:https://doi.org/10.1038/s41467-022-32096-4; html:https://europepmc.org/articles/PMC9330949; pdf:https://europepmc.org/articles/PMC9330949?pdf=render
-35813279,https://doi.org/10.1016/s2666-7568(22)00147-7,"Duration of vaccine effectiveness against SARS-CoV-2 infection, hospitalisation, and death in residents and staff of long-term care facilities in England (VIVALDI): a prospective cohort study.","Shrotri M, Krutikov M, Nacer-Laidi H, Azmi B, Palmer T, Giddings R, Fuller C, Irwin-Singer A, Baynton V, Tut G, Moss P, Hayward A, Copas A, Shallcross L.",,The lancet. Healthy longevity,2022,2022-07-04,Y,,,,"<h4>Background</h4>Residents and staff in long-term care facilities have been prioritised for vaccination against SARS-CoV-2, but data on potential waning of vaccine effectiveness and the effect of booster doses in this vulnerable population are scarce. We aimed to evaluate effectiveness of one, two, and three vaccine doses against infection and severe clinical outcomes in staff and residents of long-term care facilities in England over the first year following vaccine roll-out.<h4>Methods</h4>The VIVALDI study is a prospective cohort study done in 331 long-term care facilities in England. Residents aged 65 years or older and staff aged 18 years or older were eligible for participation. Participants had routine PCR testing throughout the study period between Dec 8, 2020, and Dec 11, 2021. We retrieved all PCR results and cycle threshold values for PCR-positive samples from routine testing in long-term care facilities, and positive PCR results from clinical testing in hospitals through the UK's COVID-19 Datastore. PCR results were linked to participants using pseudo-identifiers based on individuals' unique UK National Health Service (NHS) numbers, which were also used to retrieve vaccination records from the National Immunisation Management Service, hospitalisation records from NHS England, and deaths data from the Office for National Statistics through the COVID-19 Datastore. In a Cox proportional hazards regression, we estimated vaccine effectiveness against SARS-CoV-2 infection, COVID-19-related hospitalisation, and COVID-19-related death after one, two, and three vaccine doses, separately by previous SARS-CoV-2 exposure. This study is registered with the ISRCTN Registry, ISRCTN 14447421.<h4>Findings</h4>80 186 residents and staff of long-term care facilities had records available for the study period, of whom 15 518 eligible residents and 19 515 eligible staff were included in the analysis. For residents without evidence of previous SARS-CoV-2 exposure, vaccine effectiveness decreased from 61·7% (95% CI 35·1 to 77·4) to 22·0% (-14·9 to 47·0) against infection; from 89·0% (70·6 to 95·9) to 56·3% (30·1 to 72·6) against hospitalisation; and from 96·4% (84·3 to 99·2) to 64·4% (36·1 to 80·1) against death, when comparing 14-83 days after dose two and 84 days or more after dose two. For staff without evidence of previous exposure, vaccine effectiveness against infection decreased slightly from 57·9% (43·1 to 68·9) at 14-83 days after dose two to 42·1% (29·9 to 52·2) at 84 days or more after dose two. There were no hospitalisations or deaths among unexposed staff at 14-83 days, but seven hospitalisations (vaccine effectiveness 91·0% [95% CI 74·3 to 96·8]) and one death were observed at 84 days or more after dose two. High vaccine effectiveness was restored following a third vaccine dose, with vaccine effectiveness in unexposed residents of 72·7% (55·8 to 83·1) against infection, 90·1% (80·6 to 95·0) against hospitalisation, and 97·5% (88·1 to 99·5) against death; and vaccine effectiveness in unexposed staff of 78·2% (70·0 to 84·1) against infection and 95·8% (49·9 to 99·6) against hospitalisation. There were no COVID-19-related deaths among unexposed staff after the third vaccine dose.<h4>Interpretation</h4>Our findings showed substantial waning of SARS-CoV-2 vaccine effectiveness against all outcomes in residents of long-term care facilities from 12 weeks after a primary course of ChAdOx1-S or mRNA vaccines. Boosters restored protection, and maximised immunity across all outcomes. These findings show the importance of boosting and the need for ongoing surveillance in this vulnerable cohort.<h4>Funding</h4>UK Government Department of Health and Social Care.",,pdf:http://www.thelancet.com/article/S2666756822001477/pdf; doi:https://doi.org/10.1016/S2666-7568(22)00147-7; html:https://europepmc.org/articles/PMC9252508; pdf:https://europepmc.org/articles/PMC9252508?pdf=render
 37528841,https://doi.org/10.1016/j.eclinm.2023.102064,Repeated antibiotic exposure and risk of hospitalisation and death following COVID-19 infection (OpenSAFELY): a matched case-control study.,"Yang YT, Wong D, Ashcroft DM, Massey J, MacKenna B, Fisher L, Mehrkar A, Bacon SC, OpenSAFELY collaborative, Hand K, Zhong X, Fahmi A, Goldacre B, van Staa T, Palin V.",,EClinicalMedicine,2023,2023-07-05,Y,Antibiotics; Primary Care; Severe Outcome; Covid-19,,,"<h4>Background</h4>Identifying potential risk factors related to severe COVID-19 outcomes is important. Repeated intermittent antibiotic use is known be associated with adverse outcomes. This study aims to examine whether prior frequent antibiotic exposure is associated with severe COVID-19 outcomes.<h4>Methods</h4>With the approval of NHS England, we used the OpenSAFELY platform, which integrated primary and secondary care, COVID-19 test, and death registration data. This matched case-control study included 0.67 million patients (aged 18-110 years) from an eligible 2.47 million patients with incident COVID-19 by matching with replacement. Inclusion criteria included registration within one general practice for at least 3 years and infection with incident COVID-19. Cases were identified according to different severity of COVID-19 outcomes. Cases and eligible controls were 1:6 matched on age, sex, region of GP practice, and index year and month of COVID-19 infection. Five quintile groups, based on the number of previous 3-year antibiotic prescriptions, were created to indicate the frequency of prior antibiotic exposure. Conditional logistic regression used to compare the differences between case and control groups, adjusting for ethnicity, body mass index, comorbidities, vaccination history, deprivation, and care home status. Sensitivity analyses were done to explore potential confounding and the effects of missing data.<h4>Findings</h4>Based on our inclusion criteria, between February 1, 2020 and December 31, 2021, 98,420 patients were admitted to hospitals and 22,660 died. 55 unique antibiotics were prescribed. A dose-response relationship between number of antibiotic prescriptions and risk of severe COVID-19 outcome was observed. Patients in the highest quintile with history of prior antibiotic exposure had 1.80 times greater odds of hospitalisation compared to patients without antibiotic exposure (adjusted odds ratio [OR] 1.80, 95% Confidence Interval [CI] 1.75-1.84). Similarly, the adjusted OR for hospitalised patients with death outcomes was 1.34 (95% CI 1.28-1.41). Larger number of prior antibiotic type was also associated with more severe COVID-19 related hospital admission. The adjusted OR of quintile 5 exposure (the most frequent) with more than 3 antibiotic types was around 2 times larger than quintile 1 (only 1 type; OR 1.80, 95% CI 1.75-1.84 vs. OR 1.03, 95% CI 1.01-1.05).<h4>Interpretation</h4>Our observational study has provided evidence that antibiotic exposure frequency and diversity may be associated with COVID-19 severity, potentially suggesting adverse effects of repeated intermittent antibiotic use. Future work could work to elucidate causal links and potential mechanisms. Antibiotic stewardship should put more emphasis on long-term antibiotic exposure and its adverse outcome to increase the awareness of appropriate antibiotics use.<h4>Funding</h4>Health Data Research UK and National Institute for Health Research.",,doi:https://doi.org/10.1016/j.eclinm.2023.102064; html:https://europepmc.org/articles/PMC10388579; pdf:https://europepmc.org/articles/PMC10388579?pdf=render
 34446426,https://doi.org/10.1136/bmj.n1931,Risk of thrombocytopenia and thromboembolism after covid-19 vaccination and SARS-CoV-2 positive testing: self-controlled case series study.,"Hippisley-Cox J, Patone M, Mei XW, Saatci D, Dixon S, Khunti K, Zaccardi F, Watkinson P, Shankar-Hari M, Doidge J, Harrison DA, Griffin SJ, Sheikh A, Coupland CAC.",,BMJ (Clinical research ed.),2021,2021-08-26,Y,,,,"<h4>Objective</h4>To assess the association between covid-19 vaccines and risk of thrombocytopenia and thromboembolic events in England among adults.<h4>Design</h4>Self-controlled case series study using national data on covid-19 vaccination and hospital admissions.<h4>Setting</h4>Patient level data were obtained for approximately 30 million people vaccinated in England between 1 December 2020 and 24 April 2021. Electronic health records were linked with death data from the Office for National Statistics, SARS-CoV-2 positive test data, and hospital admission data from the United Kingdom's health service (NHS).<h4>Participants</h4>29 121 633 people were vaccinated with first doses (19 608 008 with Oxford-AstraZeneca (ChAdOx1 nCoV-19) and 9 513 625 with Pfizer-BioNTech (BNT162b2 mRNA)) and 1 758 095 people had a positive SARS-CoV-2 test. People aged ≥16 years who had first doses of the ChAdOx1 nCoV-19 or BNT162b2 mRNA vaccines and any outcome of interest were included in the study.<h4>Main outcome measures</h4>The primary outcomes were hospital admission or death associated with thrombocytopenia, venous thromboembolism, and arterial thromboembolism within 28 days of three exposures: first dose of the ChAdOx1 nCoV-19 vaccine; first dose of the BNT162b2 mRNA vaccine; and a SARS-CoV-2 positive test. Secondary outcomes were subsets of the primary outcomes: cerebral venous sinus thrombosis (CVST), ischaemic stroke, myocardial infarction, and other rare arterial thrombotic events.<h4>Results</h4>The study found increased risk of thrombocytopenia after ChAdOx1 nCoV-19 vaccination (incidence rate ratio 1.33, 95% confidence interval 1.19 to 1.47 at 8-14 days) and after a positive SARS-CoV-2 test (5.27, 4.34 to 6.40 at 8-14 days); increased risk of venous thromboembolism after ChAdOx1 nCoV-19 vaccination (1.10, 1.02 to 1.18 at 8-14 days) and after SARS-CoV-2 infection (13.86, 12.76 to 15.05 at 8-14 days); and increased risk of arterial thromboembolism after BNT162b2 mRNA vaccination (1.06, 1.01 to 1.10 at 15-21 days) and after SARS-CoV-2 infection (2.02, 1.82 to 2.24 at 15-21 days). Secondary analyses found increased risk of CVST after ChAdOx1 nCoV-19 vaccination (4.01, 2.08 to 7.71 at 8-14 days), after BNT162b2 mRNA vaccination (3.58, 1.39 to 9.27 at 15-21 days), and after a positive SARS-CoV-2 test; increased risk of ischaemic stroke after BNT162b2 mRNA vaccination (1.12, 1.04 to 1.20 at 15-21 days) and after a positive SARS-CoV-2 test; and increased risk of other rare arterial thrombotic events after ChAdOx1 nCoV-19 vaccination (1.21, 1.02 to 1.43 at 8-14 days) and after a positive SARS-CoV-2 test.<h4>Conclusion</h4>Increased risks of haematological and vascular events that led to hospital admission or death were observed for short time intervals after first doses of the ChAdOx1 nCoV-19 and BNT162b2 mRNA vaccines. The risks of most of these events were substantially higher and more prolonged after SARS-CoV-2 infection than after vaccination in the same population.",,pdf:https://www.bmj.com/content/bmj/374/bmj.n1931.full.pdf; doi:https://doi.org/10.1136/bmj.n1931; html:https://europepmc.org/articles/PMC8388189; pdf:https://europepmc.org/articles/PMC8388189?pdf=render
+35813279,https://doi.org/10.1016/s2666-7568(22)00147-7,"Duration of vaccine effectiveness against SARS-CoV-2 infection, hospitalisation, and death in residents and staff of long-term care facilities in England (VIVALDI): a prospective cohort study.","Shrotri M, Krutikov M, Nacer-Laidi H, Azmi B, Palmer T, Giddings R, Fuller C, Irwin-Singer A, Baynton V, Tut G, Moss P, Hayward A, Copas A, Shallcross L.",,The lancet. Healthy longevity,2022,2022-07-04,Y,,,,"<h4>Background</h4>Residents and staff in long-term care facilities have been prioritised for vaccination against SARS-CoV-2, but data on potential waning of vaccine effectiveness and the effect of booster doses in this vulnerable population are scarce. We aimed to evaluate effectiveness of one, two, and three vaccine doses against infection and severe clinical outcomes in staff and residents of long-term care facilities in England over the first year following vaccine roll-out.<h4>Methods</h4>The VIVALDI study is a prospective cohort study done in 331 long-term care facilities in England. Residents aged 65 years or older and staff aged 18 years or older were eligible for participation. Participants had routine PCR testing throughout the study period between Dec 8, 2020, and Dec 11, 2021. We retrieved all PCR results and cycle threshold values for PCR-positive samples from routine testing in long-term care facilities, and positive PCR results from clinical testing in hospitals through the UK's COVID-19 Datastore. PCR results were linked to participants using pseudo-identifiers based on individuals' unique UK National Health Service (NHS) numbers, which were also used to retrieve vaccination records from the National Immunisation Management Service, hospitalisation records from NHS England, and deaths data from the Office for National Statistics through the COVID-19 Datastore. In a Cox proportional hazards regression, we estimated vaccine effectiveness against SARS-CoV-2 infection, COVID-19-related hospitalisation, and COVID-19-related death after one, two, and three vaccine doses, separately by previous SARS-CoV-2 exposure. This study is registered with the ISRCTN Registry, ISRCTN 14447421.<h4>Findings</h4>80 186 residents and staff of long-term care facilities had records available for the study period, of whom 15 518 eligible residents and 19 515 eligible staff were included in the analysis. For residents without evidence of previous SARS-CoV-2 exposure, vaccine effectiveness decreased from 61·7% (95% CI 35·1 to 77·4) to 22·0% (-14·9 to 47·0) against infection; from 89·0% (70·6 to 95·9) to 56·3% (30·1 to 72·6) against hospitalisation; and from 96·4% (84·3 to 99·2) to 64·4% (36·1 to 80·1) against death, when comparing 14-83 days after dose two and 84 days or more after dose two. For staff without evidence of previous exposure, vaccine effectiveness against infection decreased slightly from 57·9% (43·1 to 68·9) at 14-83 days after dose two to 42·1% (29·9 to 52·2) at 84 days or more after dose two. There were no hospitalisations or deaths among unexposed staff at 14-83 days, but seven hospitalisations (vaccine effectiveness 91·0% [95% CI 74·3 to 96·8]) and one death were observed at 84 days or more after dose two. High vaccine effectiveness was restored following a third vaccine dose, with vaccine effectiveness in unexposed residents of 72·7% (55·8 to 83·1) against infection, 90·1% (80·6 to 95·0) against hospitalisation, and 97·5% (88·1 to 99·5) against death; and vaccine effectiveness in unexposed staff of 78·2% (70·0 to 84·1) against infection and 95·8% (49·9 to 99·6) against hospitalisation. There were no COVID-19-related deaths among unexposed staff after the third vaccine dose.<h4>Interpretation</h4>Our findings showed substantial waning of SARS-CoV-2 vaccine effectiveness against all outcomes in residents of long-term care facilities from 12 weeks after a primary course of ChAdOx1-S or mRNA vaccines. Boosters restored protection, and maximised immunity across all outcomes. These findings show the importance of boosting and the need for ongoing surveillance in this vulnerable cohort.<h4>Funding</h4>UK Government Department of Health and Social Care.",,pdf:http://www.thelancet.com/article/S2666756822001477/pdf; doi:https://doi.org/10.1016/S2666-7568(22)00147-7; html:https://europepmc.org/articles/PMC9252508; pdf:https://europepmc.org/articles/PMC9252508?pdf=render
 35790970,https://doi.org/10.1186/s12913-022-08202-z,Access to personal protective equipment in healthcare workers during the COVID-19 pandemic in the United Kingdom: results from a nationwide cohort study (UK-REACH).,"Martin CA, Pan D, Nazareth J, Aujayeb A, Bryant L, Carr S, Gray LJ, Gregary B, Gupta A, Guyatt AL, Gopal A, Hine T, John C, McManus IC, Melbourne C, Nellums LB, Reza R, Simpson S, Tobin MD, Woolf K, Zingwe S, Khunti K, Pareek M, UK-REACH Study Collaborative Group.",,BMC health services research,2022,2022-07-05,Y,Personal Protective Equipment; Ethnicity; Healthcare Worker; Ppe; Covid-19,,,"<h4>Background</h4>Healthcare workers (HCWs) are at high risk of SARS-CoV-2 infection. Effective use of personal protective equipment (PPE) reduces this risk. We sought to determine the prevalence and predictors of self-reported access to appropriate PPE (aPPE) for HCWs in the UK during the COVID-19 pandemic.<h4>Methods</h4>We conducted cross sectional analyses using data from a nationwide questionnaire-based cohort study administered between December 2020-February 2021. The outcome was a binary measure of self-reported aPPE (access all of the time vs access most of the time or less frequently) at two timepoints: the first national lockdown in the UK in March 2020 (primary analysis) and at the time of questionnaire response (secondary analysis).<h4>Results</h4>Ten thousand five hundred eight HCWs were included in the primary analysis, and 12,252 in the secondary analysis. 35.2% of HCWs reported aPPE at all times in the primary analysis; 83.9% reported aPPE at all times in the secondary analysis. In the primary analysis, after adjustment (for age, sex, ethnicity, migration status, occupation, aerosol generating procedure exposure, work sector and region, working hours, night shift frequency and trust in employing organisation), older HCWs and those working in Intensive Care Units were more likely to report aPPE at all times. Asian HCWs (aOR:0.77, 95%CI 0.67-0.89 [vs White]), those in allied health professional and dental roles (vs those in medical roles), and those who saw a higher number of COVID-19 patients compared to those who saw none (≥ 21 patients/week 0.74, 0.61-0.90) were less likely to report aPPE at all times. Those who trusted their employing organisation to deal with concerns about unsafe clinical practice, compared to those who did not, were twice as likely to report aPPE at all times. Significant predictors were largely unchanged in the secondary analysis.<h4>Conclusions</h4>Only a third of HCWs in the UK reported aPPE at all times during the first lockdown and that aPPE had improved later in the pandemic. We also identified key determinants of aPPE during the first UK lockdown, which have mostly persisted since lockdown was eased. These findings have important implications for the safe delivery of healthcare during the pandemic.",,pdf:https://bmchealthservres.biomedcentral.com/counter/pdf/10.1186/s12913-022-08202-z; doi:https://doi.org/10.1186/s12913-022-08202-z; html:https://europepmc.org/articles/PMC9255515; pdf:https://europepmc.org/articles/PMC9255515?pdf=render
 35879616,https://doi.org/10.1038/s41591-022-01909-w,Symptoms and risk factors for long COVID in non-hospitalized adults.,"Subramanian A, Nirantharakumar K, Hughes S, Myles P, Williams T, Gokhale KM, Taverner T, Chandan JS, Brown K, Simms-Williams N, Shah AD, Singh M, Kidy F, Okoth K, Hotham R, Bashir N, Cockburn N, Lee SI, Turner GM, Gkoutos GV, Aiyegbusi OL, McMullan C, Denniston AK, Sapey E, Lord JM, Wraith DC, Leggett E, Iles C, Marshall T, Price MJ, Marwaha S, Davies EH, Jackson LJ, Matthews KL, Camaradou J, Calvert M, Haroon S.",,Nature medicine,2022,2022-07-25,Y,,,,"Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is associated with a range of persistent symptoms impacting everyday functioning, known as post-COVID-19 condition or long COVID. We undertook a retrospective matched cohort study using a UK-based primary care database, Clinical Practice Research Datalink Aurum, to determine symptoms that are associated with confirmed SARS-CoV-2 infection beyond 12 weeks in non-hospitalized adults and the risk factors associated with developing persistent symptoms. We selected 486,149 adults with confirmed SARS-CoV-2 infection and 1,944,580 propensity score-matched adults with no recorded evidence of SARS-CoV-2 infection. Outcomes included 115 individual symptoms, as well as long COVID, defined as a composite outcome of 33 symptoms by the World Health Organization clinical case definition. Cox proportional hazards models were used to estimate adjusted hazard ratios (aHRs) for the outcomes. A total of 62 symptoms were significantly associated with SARS-CoV-2 infection after 12 weeks. The largest aHRs were for anosmia (aHR 6.49, 95% CI 5.02-8.39), hair loss (3.99, 3.63-4.39), sneezing (2.77, 1.40-5.50), ejaculation difficulty (2.63, 1.61-4.28) and reduced libido (2.36, 1.61-3.47). Among the cohort of patients infected with SARS-CoV-2, risk factors for long COVID included female sex, belonging to an ethnic minority, socioeconomic deprivation, smoking, obesity and a wide range of comorbidities. The risk of developing long COVID was also found to be increased along a gradient of decreasing age. SARS-CoV-2 infection is associated with a plethora of symptoms that are associated with a range of sociodemographic and clinical risk factors.",,pdf:https://www.nature.com/articles/s41591-022-01909-w.pdf; doi:https://doi.org/10.1038/s41591-022-01909-w; html:https://europepmc.org/articles/PMC9388369; pdf:https://europepmc.org/articles/PMC9388369?pdf=render
-36384890,https://doi.org/10.1136/bmj-2022-071932,Comparative effectiveness of sotrovimab and molnupiravir for prevention of severe covid-19 outcomes in patients in the community: observational cohort study with the OpenSAFELY platform.,"Zheng B, Green ACA, Tazare J, Curtis HJ, Fisher L, Nab L, Schultze A, Mahalingasivam V, Parker EPK, Hulme WJ, Bacon SCJ, DeVito NJ, Bates C, Evans D, Inglesby P, Drysdale H, Davy S, Cockburn J, Morton CE, Hickman G, Ward T, Smith RM, Parry J, Hester F, Harper S, Mehrkar A, Eggo RM, Walker AJ, Evans SJW, Douglas IJ, MacKenna B, Goldacre B, Tomlinson LA.",,BMJ (Clinical research ed.),2022,2022-11-16,Y,,,,"<h4>Objective</h4>To compare the effectiveness of sotrovimab (a neutralising monoclonal antibody) with molnupiravir (an antiviral) in preventing severe outcomes of covid-19 in adult patients infected with SARS-CoV-2 in the community and at high risk of severe outcomes from covid-19.<h4>Design</h4>Observational cohort study with the OpenSAFELY platform.<h4>Setting</h4>With the approval of NHS England, a real world cohort study was conducted with the OpenSAFELY-TPP platform (a secure, transparent, open source software platform for analysis of NHS electronic health records), and patient level electronic health record data were obtained from 24 million people registered with a general practice in England that uses TPP software. The primary care data were securely linked with data on SARS-CoV-2 infection and treatments, hospital admission, and death, over a period when both drug treatments were frequently prescribed in community settings.<h4>Participants</h4>Adult patients with covid-19 in the community at high risk of severe outcomes from covid-19, treated with sotrovimab or molnupiravir from 16 December 2021.<h4>Interventions</h4>Sotrovimab or molnupiravir given in the community by covid-19 medicine delivery units.<h4>Main outcome measures</h4>Admission to hospital with covid-19 (ie, with covid-19 as the primary diagnosis) or death from covid-19 (ie, with covid-19 as the underlying or contributing cause of death) within 28 days of the start of treatment.<h4>Results</h4>Between 16 December 2021 and 10 February 2022, 3331 and 2689 patients were treated with sotrovimab and molnupiravir, respectively, with no substantial differences in baseline characteristics. Mean age of all 6020 patients was 52 (standard deviation 16) years; 59% were women, 89% were white, and 88% had received three or more covid-19 vaccinations. Within 28 days of the start of treatment, 87 (1.4%) patients were admitted to hospital or died of infection from SARS-CoV-2 (32 treated with sotrovimab and 55 with molnupiravir). Cox proportional hazards models stratified by area showed that after adjusting for demographic information, high risk cohort categories, vaccination status, calendar time, body mass index, and other comorbidities, treatment with sotrovimab was associated with a substantially lower risk than treatment with molnupiravir (hazard ratio 0.54, 95% confidence interval 0.33 to 0.88, P=0.01). Consistent results were found from propensity score weighted Cox models (0.50, 0.31 to 0.81, P=0.005) and when restricted to people who were fully vaccinated (0.53, 0.31 to 0.90, P=0.02). No substantial effect modifications by other characteristics were detected (all P values for interaction >0.10). The findings were similar in an exploratory analysis of patients treated between 16 February and 1 May 2022 when omicron BA.2 was the predominant variant in England.<h4>Conclusions</h4>In routine care of adult patients in England with covid-19 in the community, at high risk of severe outcomes from covid-19, those who received sotrovimab were at lower risk of severe outcomes of covid-19 than those treated with molnupiravir.",,pdf:https://www.bmj.com/content/bmj/379/bmj-2022-071932.full.pdf; doi:https://doi.org/10.1136/bmj-2022-071932; html:https://europepmc.org/articles/PMC9667468
 35296643,https://doi.org/10.1038/s41467-022-28517-z,"Antibody decay, T cell immunity and breakthrough infections following two SARS-CoV-2 vaccine doses in inflammatory bowel disease patients treated with infliximab and vedolizumab.","Lin S, Kennedy NA, Saifuddin A, Sandoval DM, Reynolds CJ, Seoane RC, Kottoor SH, Pieper FP, Lin KM, Butler DK, Chanchlani N, Nice R, Chee D, Bewshea C, Janjua M, McDonald TJ, Sebastian S, Alexander JL, Constable L, Lee JC, Murray CD, Hart AL, Irving PM, Jones GR, Kok KB, Lamb CA, Lees CW, Altmann DM, Boyton RJ, Goodhand JR, Powell N, Ahmad T, CLARITY IBD study.",,Nature communications,2022,2022-03-16,Y,,,,"Anti tumour necrosis factor (anti-TNF) drugs increase the risk of serious respiratory infection and impair protective immunity following pneumococcal and influenza vaccination. Here we report SARS-CoV-2 vaccine-induced immune responses and breakthrough infections in patients with inflammatory bowel disease, who are treated either with the anti-TNF antibody, infliximab, or with vedolizumab targeting a gut-specific anti-integrin that does not impair systemic immunity. Geometric mean [SD] anti-S RBD antibody concentrations are lower and half-lives shorter in patients treated with infliximab than vedolizumab, following two doses of BNT162b2 (566.7 U/mL [6.2] vs 4555.3 U/mL [5.4], p <0.0001; 26.8 days [95% CI 26.2 - 27.5] vs 47.6 days [45.5 - 49.8], p <0.0001); similar results are also observed with ChAdOx1 nCoV-19 vaccination (184.7 U/mL [5.0] vs 784.0 U/mL [3.5], p <0.0001; 35.9 days [34.9 - 36.8] vs 58.0 days [55.0 - 61.3], p value < 0.0001). One fifth of patients fail to mount a T cell response in both treatment groups. Breakthrough SARS-CoV-2 infections are more frequent (5.8% (201/3441) vs 3.9% (66/1682), p = 0.0039) in patients treated with infliximab than vedolizumab, and the risk of breakthrough SARS-CoV-2 infection is predicted by peak anti-S RBD antibody concentration after two vaccine doses. Irrespective of the treatments, higher, more sustained antibody levels are observed in patients with a history of SARS-CoV-2 infection prior to vaccination. Our results thus suggest that adapted vaccination schedules may be required to induce immunity in at-risk, anti-TNF-treated patients.",,pdf:https://www.nature.com/articles/s41467-022-28517-z.pdf; doi:https://doi.org/10.1038/s41467-022-28517-z; html:https://europepmc.org/articles/PMC8927425; pdf:https://europepmc.org/articles/PMC8927425?pdf=render
+36384890,https://doi.org/10.1136/bmj-2022-071932,Comparative effectiveness of sotrovimab and molnupiravir for prevention of severe covid-19 outcomes in patients in the community: observational cohort study with the OpenSAFELY platform.,"Zheng B, Green ACA, Tazare J, Curtis HJ, Fisher L, Nab L, Schultze A, Mahalingasivam V, Parker EPK, Hulme WJ, Bacon SCJ, DeVito NJ, Bates C, Evans D, Inglesby P, Drysdale H, Davy S, Cockburn J, Morton CE, Hickman G, Ward T, Smith RM, Parry J, Hester F, Harper S, Mehrkar A, Eggo RM, Walker AJ, Evans SJW, Douglas IJ, MacKenna B, Goldacre B, Tomlinson LA.",,BMJ (Clinical research ed.),2022,2022-11-16,Y,,,,"<h4>Objective</h4>To compare the effectiveness of sotrovimab (a neutralising monoclonal antibody) with molnupiravir (an antiviral) in preventing severe outcomes of covid-19 in adult patients infected with SARS-CoV-2 in the community and at high risk of severe outcomes from covid-19.<h4>Design</h4>Observational cohort study with the OpenSAFELY platform.<h4>Setting</h4>With the approval of NHS England, a real world cohort study was conducted with the OpenSAFELY-TPP platform (a secure, transparent, open source software platform for analysis of NHS electronic health records), and patient level electronic health record data were obtained from 24 million people registered with a general practice in England that uses TPP software. The primary care data were securely linked with data on SARS-CoV-2 infection and treatments, hospital admission, and death, over a period when both drug treatments were frequently prescribed in community settings.<h4>Participants</h4>Adult patients with covid-19 in the community at high risk of severe outcomes from covid-19, treated with sotrovimab or molnupiravir from 16 December 2021.<h4>Interventions</h4>Sotrovimab or molnupiravir given in the community by covid-19 medicine delivery units.<h4>Main outcome measures</h4>Admission to hospital with covid-19 (ie, with covid-19 as the primary diagnosis) or death from covid-19 (ie, with covid-19 as the underlying or contributing cause of death) within 28 days of the start of treatment.<h4>Results</h4>Between 16 December 2021 and 10 February 2022, 3331 and 2689 patients were treated with sotrovimab and molnupiravir, respectively, with no substantial differences in baseline characteristics. Mean age of all 6020 patients was 52 (standard deviation 16) years; 59% were women, 89% were white, and 88% had received three or more covid-19 vaccinations. Within 28 days of the start of treatment, 87 (1.4%) patients were admitted to hospital or died of infection from SARS-CoV-2 (32 treated with sotrovimab and 55 with molnupiravir). Cox proportional hazards models stratified by area showed that after adjusting for demographic information, high risk cohort categories, vaccination status, calendar time, body mass index, and other comorbidities, treatment with sotrovimab was associated with a substantially lower risk than treatment with molnupiravir (hazard ratio 0.54, 95% confidence interval 0.33 to 0.88, P=0.01). Consistent results were found from propensity score weighted Cox models (0.50, 0.31 to 0.81, P=0.005) and when restricted to people who were fully vaccinated (0.53, 0.31 to 0.90, P=0.02). No substantial effect modifications by other characteristics were detected (all P values for interaction >0.10). The findings were similar in an exploratory analysis of patients treated between 16 February and 1 May 2022 when omicron BA.2 was the predominant variant in England.<h4>Conclusions</h4>In routine care of adult patients in England with covid-19 in the community, at high risk of severe outcomes from covid-19, those who received sotrovimab were at lower risk of severe outcomes of covid-19 than those treated with molnupiravir.",,pdf:https://www.bmj.com/content/bmj/379/bmj-2022-071932.full.pdf; doi:https://doi.org/10.1136/bmj-2022-071932; html:https://europepmc.org/articles/PMC9667468
 37018139,https://doi.org/10.1093/rheumatology/kead150,"COVID-19 infection, admission and death and the impact of corticosteroids among people with rare autoimmune rheumatic disease during the second wave of COVID-19 in England: results from the RECORDER Project.","Rutter M, Lanyon PC, Grainge MJ, Hubbard R, Bythell M, Stilwell P, Aston J, McPhail S, Stevens S, Pearce FA.",,"Rheumatology (Oxford, England)",2023,2023-12-01,Y,Infection; Mortality; Coronavirus; epidemiology; Shielding; Covid-19; Rare Autoimmune Rheumatic Diseases,,,"<h4>Objectives</h4>To calculate the rates of COVID-19 infection and COVID-19-related death among people with rare autoimmune rheumatic diseases (RAIRD) during the second wave of the COVID-19 pandemic in England, and describe the impact of corticosteroids on outcomes.<h4>Methods</h4>Hospital Episode Statistics data were used to identify people alive on 1 August 2020 with ICD-10 codes for RAIRD from the whole population of England. Linked national health records were used to calculate rates and rate ratios of COVID-19 infection and death up to 30 April 2021. Primary definition of COVID-19-related death was mention of COVID-19 on the death certificate. NHS Digital and Office for National Statistics general population data were used for comparison. The association between 30-day corticosteroid usage and COVID-19-related death, COVID-19-related hospital admissions and all-cause deaths was also described.<h4>Results</h4>Of 168 330 people with RAIRD, 9961 (5.92%) had a positive COVID-19 PCR test. The age-standardized infection rate ratio between RAIRD and the general population was 0.99 (95% CI: 0.97, 1.00). 1342 (0.80%) people with RAIRD died with COVID-19 on their death certificate and the age-sex-standardized mortality rate for COVID-19-related death was 2.76 (95% CI: 2.63, 2.89) times higher than in the general population. There was a dose-dependent relationship between 30-day corticosteroid usage and COVID-19-related death. There was no increase in deaths due to other causes.<h4>Conclusions</h4>During the second wave of COVID-19 in England, people with RAIRD had the same risk of COVID-19 infection but a 2.76-fold increased risk of COVID-19-related death compared with the general population, with corticosteroids associated with increased risk.",,pdf:https://academic.oup.com/rheumatology/advance-article-pdf/doi/10.1093/rheumatology/kead150/49769320/kead150.pdf; doi:https://doi.org/10.1093/rheumatology/kead150; html:https://europepmc.org/articles/PMC10691923; pdf:https://europepmc.org/articles/PMC10691923?pdf=render
 38448987,https://doi.org/10.1186/s13033-024-00623-z,Can computer simulation support strategic service planning? Modelling a large integrated mental health system on recovery from COVID-19.,"Pierotti L, Cooper J, James C, Cassels K, Gara E, Denholm R, Wood R.",,International journal of mental health systems,2024,2024-03-07,Y,Computer simulation; Coronavirus; Mental Health Services; Computer Modelling; Service Design; Covid-19,,,"<h4>Background</h4>COVID-19 has had a significant impact on people's mental health and mental health services. During the first year of the pandemic, existing demand was not fully met while new demand was generated, resulting in large numbers of people requiring support. To support mental health services to recover without being overwhelmed, it was important to know where services will experience increased pressure, and what strategies could be implemented to mitigate this.<h4>Methods</h4>We implemented a computer simulation model of patient flow through an integrated mental health service in Southwest England covering General Practice (GP), community-based 'talking therapies' (IAPT), acute hospital care, and specialist care settings. The model was calibrated on data from 1 April 2019 to 1 April 2021. Model parameters included patient demand, service-level length of stay, and probabilities of transitioning to other care settings. We used the model to compare 'do nothing' (baseline) scenarios to 'what if' (mitigation) scenarios, including increasing capacity and reducing length of stay, for two future demand trajectories from 1 April 2021 onwards.<h4>Results</h4>The results from the simulation model suggest that, without mitigation, the impact of COVID-19 will be an increase in pressure on GP and specialist community based services by 50% and 50-100% respectively. Simulating the impact of possible mitigation strategies, results show that increasing capacity in lower-acuity services, such as GP, causes a shift in demand to other parts of the mental health system while decreasing length of stay in higher acuity services is insufficient to mitigate the impact of increased demand.<h4>Conclusion</h4>In capturing the interrelation of patient flow related dynamics between various mental health care settings, we demonstrate the value of computer simulation for assessing the impact of interventions on system flow.",,pdf:https://ijmhs.biomedcentral.com/counter/pdf/10.1186/s13033-024-00623-z; doi:https://doi.org/10.1186/s13033-024-00623-z; html:https://europepmc.org/articles/PMC10918932; pdf:https://europepmc.org/articles/PMC10918932?pdf=render
 36806073,https://doi.org/10.1136/bmjopen-2022-071261,Protocol for an OpenSAFELY cohort study collecting patient-reported outcome measures using the TPP Airmid smartphone application and linked big data to quantify the health and economic costs of long COVID (OpenPROMPT).,"Herrett E, Tomlin K, Lin LY, Tomlinson LA, Jit M, Briggs A, Marks M, Sandmann F, Parry J, Bates C, Morley J, Bacon S, Butler-Cole B, Mahalingasivam V, Dennison A, Smith D, Gabriel E, Mehrkar A, Goldacre B, Smeeth L, Eggo RMM.",,BMJ open,2023,2023-02-17,Y,Quality of life; Health Economics; Covid-19,,,"<h4>Introduction</h4>The impact of long COVID on health-related quality of-life (HRQoL) and productivity is not currently known. It is important to understand who is worst affected by long COVID and the cost to the National Health Service (NHS) and society, so that strategies like booster vaccines can be prioritised to the right people. OpenPROMPT aims to understand the impact of long COVID on HRQoL in adults attending English primary care.<h4>Methods and analysis</h4>We will ask people to participate in this cohort study through a smartphone app (Airmid), and completing a series of questionnaires held within the app. Questionnaires will ask about HRQoL, productivity and symptoms of long COVID. Participants will be asked to fill in the questionnaires once a month, for 90 days. Questionnaire responses will be linked, where possible, to participants' existing health records from primary care, secondary care, and COVID testing and vaccination data. Analysis will take place using the OpenSAFELY data platform and will estimate the impact of long COVID on HRQoL, productivity and cost to the NHS.<h4>Ethics and dissemination</h4>The Proportionate Review Sub-Committee of the South Central-Berkshire B Research Ethics Committee has reviewed and approved the study and have agreed that we can ask people to take part (22/SC/0198). Our results will provide information to support long-term care, and make recommendations for prevention of long COVID in the future.<h4>Trial registration number</h4>NCT05552612.",,pdf:https://bmjopen.bmj.com/content/bmjopen/13/2/e071261.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-071261; html:https://europepmc.org/articles/PMC9943695; pdf:https://europepmc.org/articles/PMC9943695?pdf=render
 37182748,https://doi.org/10.1016/j.jinf.2023.05.010,The impact of COVID-19 on antibiotic prescribing in primary care in England: Evaluation and risk prediction of appropriateness of type and repeat prescribing.,"Zhong X, Pate A, Yang YT, Fahmi A, Ashcroft DM, Goldacre B, MacKenna B, Mehrkar A, Bacon SCJ, Massey J, Fisher L, Inglesby P, OpenSAFELY collaborative, Hand K, van Staa T, Palin V.",,The Journal of infection,2023,2023-05-12,Y,Infection; Antibiotics; Primary Care; Antibiotic Stewardship; Covid-19 Pandemic,,,"<h4>Background</h4>This study aimed to predict risks of potentially inappropriate antibiotic type and repeat prescribing and assess changes during COVID-19.<h4>Methods</h4>With the approval of NHS England, we used OpenSAFELY platform to access the TPP SystmOne electronic health record (EHR) system and selected patients prescribed antibiotics from 2019 to 2021. Multinomial logistic regression models predicted patient's probability of receiving inappropriate antibiotic type or repeat antibiotic course for each common infection.<h4>Results</h4>The population included 9.1 million patients with 29.2 million antibiotic prescriptions. 29.1% of prescriptions were identified as repeat prescribing. Those with same day incident infection coded in the EHR had considerably lower rates of repeat prescribing (18.0%) and 8.6% had potentially inappropriate type. No major changes in the rates of repeat antibiotic prescribing during COVID-19 were found. In the 10 risk prediction models, good levels of calibration and moderate levels of discrimination were found.<h4>Conclusions</h4>Our study found no evidence of changes in level of inappropriate or repeat antibiotic prescribing after the start of COVID-19. Repeat antibiotic prescribing was frequent and varied according to regional and patient characteristics. There is a need for treatment guidelines to be developed around antibiotic failure and clinicians provided with individualised patient information.",,pdf:http://www.journalofinfection.com/article/S0163445323002888/pdf; doi:https://doi.org/10.1016/j.jinf.2023.05.010; html:https://europepmc.org/articles/PMC10176893; pdf:https://europepmc.org/articles/PMC10176893?pdf=render
+36098502,https://doi.org/10.7554/elife.78427,"Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study.","Stirrup O, Blackstone J, Mapp F, MacNeil A, Panca M, Holmes A, Machin N, Shin GY, Mahungu T, Saeed K, Saluja T, Taha Y, Mahida N, Pope C, Chawla A, Cutino-Moguel MT, Tamuri A, Williams R, Darby A, Robertson DL, Flaviani F, Nastouli E, Robson S, Smith D, Loose M, Laing K, Monahan I, Kele B, Haldenby S, George R, Bashton M, Witney AA, Byott M, Coll F, Chapman M, Peacock SJ, COG-UK HOCI Investigators, COVID-19 Genomics UK (COG-UK) consortium, Hughes J, Nebbia G, Partridge DG, Parker M, Price JR, Peters C, Roy S, Snell LB, de Silva TI, Thomson E, Flowers P, Copas A, Breuer J.",,eLife,2022,2022-09-13,Y,Human; Microbiology; Infectious disease; Molecular epidemiology; Infection control; epidemiology; Global Health; Hospital-acquired Infection; Infection Prevention; Viral Genomics; Healthcare-associated Infection; Covid-19,,,"<h4>Background</h4>Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings.<h4>Methods</h4>We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data collection period, followed by intervention periods comprising 8 weeks of 'rapid' (<48 hr) and 4 weeks of 'longer-turnaround' (5-10 days) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital-onset COVID-19 infections (HOCIs; detected ≥48 hr from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on the incidence of probable/definite hospital-acquired infections (HAIs), was evaluated.<h4>Results</h4>A total of 2170 HOCI cases were recorded from October 2020 to April 2021, corresponding to a period of extreme strain on the health service, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (incidence rate ratio 1.60, 95% CI 0.85-3.01; p<i>=</i>0.14) or rapid (0.85, 0.48-1.50; p<i>=</i>0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8 and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2 and 11.6% of cases where the report was returned. In a 'per-protocol' sensitivity analysis, there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. Capacity to respond effectively to insights from sequencing was breached in most sites by the volume of cases and limited resources.<h4>Conclusions</h4>While we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days.<h4>Funding</h4>COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) (grant code: MC_PC_19027), and Genome Research Limited, operating as the Wellcome Sanger Institute.<h4>Clinical trial number</h4>NCT04405934.",,doi:https://doi.org/10.7554/elife.78427; doi:https://doi.org/10.7554/eLife.78427; html:https://europepmc.org/articles/PMC9596156; pdf:https://europepmc.org/articles/PMC9596156?pdf=render
 PMC9023380,https://doi.org/,Assessing the spread risk of COVID-19 associated with multi-mode transportation networks in China,"Xu X, Liu X, Wang L, Wu Y, Lu X, Wang X, Pei S.",,Fundamental research,2022,2022-04-22,Y,Complex Network; Spatial Spread; Human Mobility; Transportation Networks; Covid-19,,,"The spatial spread of COVID-19 during early 2020 in China was primarily driven by outbound travelers leaving the epicenter, Wuhan, Hubei province. Existing studies focus on the influence of aggregated out-bound population flows originating from Wuhan; however, the impacts of different modes of transportation and the network structure of transportation systems on the early spread of COVID-19 in China are not well understood. Here, we assess the roles of the road, railway, and air transportation networks in driving the spatial spread of COVID-19 in China. We find that the short-range spread within Hubei province was dominated by ground traffic, notably, the railway transportation. In contrast, long-range spread to cities in other provinces was mediated by multiple factors, including a higher risk of case importation associated with air transportation and a larger outbreak size in hub cities located at the center of transportation networks. We further show that, although the dissemination of SARS-CoV-2 across countries and continents is determined by the worldwide air transportation network, the early geographic dispersal of COVID-19 within China is better predicted by the railway traffic. Given the recent emergence of multiple more transmissible variants of SARS-CoV-2, our findings can support a better assessment of the spread risk of those variants and improve future pandemic preparedness and responses. Graphical abstract Image, graphical abstract.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9023380/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9023380/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC9023380; pdf:https://europepmc.org/articles/PMC9023380?pdf=render
 35051442,https://doi.org/10.1016/j.jviromet.2022.114471,Reduced amplification efficiency of the RNA-dependent-RNA-polymerase target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests.,"Valley-Omar Z, Marais G, Iranzadeh A, Naidoo M, Korsman S, Maponga T, Hussey H, Davies MA, Boulle A, Doolabh D, Laubscher M, Wojno J, Deetlefs JD, Maritz J, Scott L, Msomi N, Naicker C, Tegally H, de Oliveira T, Bhiman J, Williamson C, Preiser W, Hardie D, Hsiao NY.",,Journal of virological methods,2022,2022-01-18,Y,Surveillance; Diagnostic test; South Africa; Covid-19; Sars-cov-2; Delta Variant,,,"Routine SARS-CoV-2 surveillance in the Western Cape region of South Africa (January-August 2021) found a reduced RT-PCR amplification efficiency of the RdRp-gene target of the Seegene, Allplex 2019-nCoV diagnostic assay from June 2021 when detecting the Delta variant. We investigated whether the reduced amplification efficiency denoted by an increased RT-PCR cycle threshold value (RΔE) can be used as an indirect measure of SARS-CoV-2 Delta variant prevalence. We found a significant increase in the median RΔE for patient samples tested from June 2021, which coincided with the emergence of the SARS-CoV-2 Delta variant within our sample set. Whole genome sequencing on a subset of patient samples identified a highly conserved G15451A, non-synonymous mutation exclusively within the RdRp gene of Delta variants, which may cause reduced RT-PCR amplification efficiency. While whole genome sequencing plays an important in identifying novel SARS-CoV-2 variants, monitoring RΔE value can serve as a useful surrogate for rapid tracking of Delta variant prevalence.",,doi:https://doi.org/10.1016/j.jviromet.2022.114471; doi:https://doi.org/10.1016/j.jviromet.2022.114471; html:https://europepmc.org/articles/PMC8763409; pdf:https://europepmc.org/articles/PMC8763409?pdf=render
-36098502,https://doi.org/10.7554/elife.78427,"Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study.","Stirrup O, Blackstone J, Mapp F, MacNeil A, Panca M, Holmes A, Machin N, Shin GY, Mahungu T, Saeed K, Saluja T, Taha Y, Mahida N, Pope C, Chawla A, Cutino-Moguel MT, Tamuri A, Williams R, Darby A, Robertson DL, Flaviani F, Nastouli E, Robson S, Smith D, Loose M, Laing K, Monahan I, Kele B, Haldenby S, George R, Bashton M, Witney AA, Byott M, Coll F, Chapman M, Peacock SJ, COG-UK HOCI Investigators, COVID-19 Genomics UK (COG-UK) consortium, Hughes J, Nebbia G, Partridge DG, Parker M, Price JR, Peters C, Roy S, Snell LB, de Silva TI, Thomson E, Flowers P, Copas A, Breuer J.",,eLife,2022,2022-09-13,Y,Human; Microbiology; Infectious disease; Molecular epidemiology; Infection control; epidemiology; Global Health; Hospital-acquired Infection; Infection Prevention; Viral Genomics; Healthcare-associated Infection; Covid-19,,,"<h4>Background</h4>Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings.<h4>Methods</h4>We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data collection period, followed by intervention periods comprising 8 weeks of 'rapid' (<48 hr) and 4 weeks of 'longer-turnaround' (5-10 days) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital-onset COVID-19 infections (HOCIs; detected ≥48 hr from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on the incidence of probable/definite hospital-acquired infections (HAIs), was evaluated.<h4>Results</h4>A total of 2170 HOCI cases were recorded from October 2020 to April 2021, corresponding to a period of extreme strain on the health service, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (incidence rate ratio 1.60, 95% CI 0.85-3.01; p<i>=</i>0.14) or rapid (0.85, 0.48-1.50; p<i>=</i>0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8 and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2 and 11.6% of cases where the report was returned. In a 'per-protocol' sensitivity analysis, there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. Capacity to respond effectively to insights from sequencing was breached in most sites by the volume of cases and limited resources.<h4>Conclusions</h4>While we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days.<h4>Funding</h4>COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) (grant code: MC_PC_19027), and Genome Research Limited, operating as the Wellcome Sanger Institute.<h4>Clinical trial number</h4>NCT04405934.",,doi:https://doi.org/10.7554/elife.78427; doi:https://doi.org/10.7554/eLife.78427; html:https://europepmc.org/articles/PMC9596156; pdf:https://europepmc.org/articles/PMC9596156?pdf=render
 35131989,https://doi.org/10.1097/mcp.0000000000000863,A clinical review of long-COVID with a focus on the respiratory system.,"Daines L, Zheng B, Pfeffer P, Hurst JR, Sheikh A.",,Current opinion in pulmonary medicine,2022,2022-02-07,N,,,,"<h4>Purpose of review</h4>Persistence of symptoms after acute coronavirus disease 2019 (COVID-19), often described as long- COVID, is common and debilitating. In this article, we review the epidemiology, clinical features, and research priorities for long-COVID focusing on the respiratory system.<h4>Recent findings</h4>Breathlessness, cough and chest pain were the most commonly reported respiratory symptoms associated with long-COVID. In hospitalised patients, abnormalities on lung function testing or chest imaging were observed less commonly at 12 months compared to six months since discharge. Clinical assessment of patients with persisting symptoms after acute COVID-19 requires a comprehensive evaluation to exclude other possible causes for symptoms. With no robust current evidence for interventions to treat long-COVID respiratory symptoms, symptomatic treatment, supported self-management and pulmonary rehabilitation should be considered to help individuals with respiratory symptoms associated with long-COVID.<h4>Summary</h4>Long-COVID is a debilitating syndrome that often includes persisting respiratory symptoms and to a lesser degree, abnormalities in lung physiology or imaging. Respiratory features of long-COVID may reduce over time, yet resolution is not seen in all cases. Future research is needed to understand the natural history of long-COVID, identify factors associated with spontaneous improvement/persistence, investigate mechanisms for persisting symptoms, and test interventions to prevent and treat long-COVID.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7612723; doi:https://doi.org/10.1097/MCP.0000000000000863; html:https://europepmc.org/articles/PMC7612723; pdf:https://europepmc.org/articles/PMC7612723?pdf=render; doi:https://doi.org/10.1097/mcp.0000000000000863
 36901540,https://doi.org/10.3390/ijerph20054534,Socioeconomic Background and Self-Reported Sleep Quality in Older Adults during the COVID-19 Pandemic: An Analysis of the English Longitudinal Study of Ageing (ELSA).,"Collinge AN, Bath PA, Bath PA.",,International journal of environmental research and public health,2023,2023-03-03,Y,Mental health; Health Promotion; Wellness; Physical Health; Health Disparities; Health Behaviors; Older Adults; Sleep Quality; Socioeconomic Background; Covid-19,,,"The COVID-19 pandemic negatively impacted sleep quality. However, research regarding older adults' sleep quality during the pandemic has been limited. This study examined the association between socioeconomic background (SEB) and older adults' sleep quality during the COVID-19 pandemic. Data on 7040 adults aged ≥50 were acquired from a COVID-19 sub-study of the English Longitudinal Study of Ageing (ELSA). SEB was operationalized using educational attainment, previous financial situation, and concern about the future financial situation. Sociodemographic, mental health, physical health, and health behavior variables were included as covariates. Chi-squared tests and binary logistic regression were used to examine associations between SEB and sleep quality. Lower educational attainment and greater financial hardship and concerns were associated with poor sleep quality. The relationship between educational attainment and sleep quality was explained by the financial variables, while the relationship between previous financial difficulties and sleep quality was explained by physical health and health behavior variables. Greater financial concerns about the future, poor mental health, and poor physical health were independent risk factors for poor sleep quality in older adults during the pandemic. Healthcare professionals and service providers should consider these issues when supporting older patients with sleep problems and in promoting health and wellness.",,pdf:https://www.mdpi.com/1660-4601/20/5/4534/pdf?version=1677842613; doi:https://doi.org/10.3390/ijerph20054534; html:https://europepmc.org/articles/PMC10001974; pdf:https://europepmc.org/articles/PMC10001974?pdf=render
 37434746,https://doi.org/10.1016/j.eclinm.2023.102077,"Ethnic differences in the indirect effects of the COVID-19 pandemic on clinical monitoring and hospitalisations for non-COVID conditions in England: a population-based, observational cohort study using the OpenSAFELY platform.","Costello RE, Tazare J, Piehlmaier D, Herrett E, Parker EPK, Zheng B, Mansfield KE, Henderson AD, Carreira H, Bidulka P, Wong AYS, Warren-Gash C, Hayes JF, Quint JK, MacKenna B, Mehrkar A, Eggo RM, Katikireddi SV, Tomlinson L, Langan SM, Mathur R, LH&W NCS (or CONVALESCENCE) Collaborative, OpenSAFELY collaborative.",,EClinicalMedicine,2023,2023-06-29,Y,Pandemic; Healthcare Utilisation; Ethnic Differences,,,"<h4>Background</h4>The COVID-19 pandemic disrupted healthcare and may have impacted ethnic inequalities in healthcare. We aimed to describe the impact of pandemic-related disruption on ethnic differences in clinical monitoring and hospital admissions for non-COVID conditions in England.<h4>Methods</h4>In this population-based, observational cohort study we used primary care electronic health record data with linkage to hospital episode statistics data and mortality data within OpenSAFELY, a data analytics platform created, with approval of NHS England, to address urgent COVID-19 research questions. We included adults aged 18 years and over registered with a TPP practice between March 1, 2018, and April 30, 2022. We excluded those with missing age, sex, geographic region, or Index of Multiple Deprivation. We grouped ethnicity (exposure), into five categories: White, Asian, Black, Other, and Mixed. We used interrupted time-series regression to estimate ethnic differences in clinical monitoring frequency (blood pressure and Hba1c measurements, chronic obstructive pulmonary disease and asthma annual reviews) before and after March 23, 2020. We used multivariable Cox regression to quantify ethnic differences in hospitalisations related to diabetes, cardiovascular disease, respiratory disease, and mental health before and after March 23, 2020.<h4>Findings</h4>Of 33,510,937 registered with a GP as of 1st January 2020, 19,064,019 were adults, alive and registered for at least 3 months, 3,010,751 met the exclusion criteria and 1,122,912 were missing ethnicity. This resulted in 14,930,356 adults with known ethnicity (92% of sample): 86.6% were White, 7.3% Asian, 2.6% Black, 1.4% Mixed ethnicity, and 2.2% Other ethnicities. Clinical monitoring did not return to pre-pandemic levels for any ethnic group. Ethnic differences were apparent pre-pandemic, except for diabetes monitoring, and remained unchanged, except for blood pressure monitoring in those with mental health conditions where differences narrowed during the pandemic. For those of Black ethnicity, there were seven additional admissions for diabetic ketoacidosis per month during the pandemic, and relative ethnic differences narrowed during the pandemic compared to the White ethnic group (Pre-pandemic hazard ratio (HR): 0.50, 95% confidence interval (CI) 0.41, 0.60, Pandemic HR: 0.75, 95% CI: 0.65, 0.87). There was increased admissions for heart failure during the pandemic for all ethnic groups, though highest in those of White ethnicity (heart failure risk difference: 5.4). Relatively, ethnic differences narrowed for heart failure admission in those of Asian (Pre-pandemic HR 1.56, 95% CI 1.49, 1.64, Pandemic HR 1.24, 95% CI 1.19, 1.29) and Black ethnicity (Pre-pandemic HR 1.41, 95% CI: 1.30, 1.53, Pandemic HR: 1.16, 95% CI 1.09, 1.25) compared with White ethnicity. For other outcomes the pandemic had minimal impact on ethnic differences.<h4>Interpretation</h4>Our study suggests that ethnic differences in clinical monitoring and hospitalisations remained largely unchanged during the pandemic for most conditions. Key exceptions were hospitalisations for diabetic ketoacidosis and heart failure, which warrant further investigation to understand the causes.<h4>Funding</h4>LSHTM COVID-19 Response Grant (DONAT15912).",,pdf:http://www.thelancet.com/article/S2589537023002547/pdf; doi:https://doi.org/10.1016/j.eclinm.2023.102077; html:https://europepmc.org/articles/PMC10331810; pdf:https://europepmc.org/articles/PMC10331810?pdf=render
 37263685,https://doi.org/10.1136/bmjopen-2022-070637,"Impact of the COVID-19 pandemic on domiciliary care workers in Wales, UK: a data linkage cohort study using the SAIL Databank.","Cannings-John R, Schoenbuchner S, Jones H, Lugg-Widger FV, Akbari A, Brookes-Howell L, Hood K, John A, Thomas DR, Prout H, Robling M.",,BMJ open,2023,2023-06-01,Y,Mental health; Social Medicine; Covid-19,,,"<h4>Objectives</h4>To quantify population health risks for domiciliary care workers (DCWs) in Wales, UK, working during the COVID-19 pandemic.<h4>Design</h4>A population-level retrospective study linking occupational registration data to anonymised electronic health records maintained by the Secure Anonymised Information Linkage Databank in a privacy-protecting trusted research environment.<h4>Setting</h4>Registered DCW population in Wales.<h4>Participants</h4>Records for all linked DCWs from 1 March 2020 to 30 November 2021.<h4>Primary and secondary outcome measures</h4>Our primary outcome was confirmed COVID-19 infection; secondary outcomes included contacts for suspected COVID-19, mental health including self-harm, fit notes, respiratory infections not necessarily recorded as COVID-19, deaths involving COVID-19 and all-cause mortality.<h4>Results</h4>Confirmed and suspected COVID-19 infection rates increased over the study period to 24% by 30 November 2021. Confirmed COVID-19 varied by sex (males: 19% vs females: 24%) and age (>55 years: 19% vs <35 years: 26%) and were higher for care workers employed by local authority social services departments compared with the private sector (27% and 23%, respectively). 34% of DCWs required support for a mental health condition, with mental health-related prescribing increasing in frequency when compared with the prepandemic period. Events for self-harm increased from 0.2% to 0.4% over the study period as did the issuing of fit notes. There was no evidence to suggest a miscoding of COVID-19 infection with non-COVID-19 respiratory conditions. COVID-19-related and all-cause mortality were no greater than for the general population aged 15-64 years in Wales (0.1% and 0.034%, respectively). A comparable DCW workforce in Scotland and England would result in a comparable rate of COVID-19 infection, while the younger workforce in Northern Ireland may result in a greater infection rate.<h4>Conclusions</h4>While initial concerns about excess mortality are alleviated, the substantial pre-existing and increased mental health burden for DCWs will require investment to provide long-term support to the sector's workforce.",,pdf:https://bmjopen.bmj.com/content/bmjopen/13/6/e070637.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-070637; html:https://europepmc.org/articles/PMC10255029; pdf:https://europepmc.org/articles/PMC10255029?pdf=render
-37562853,https://doi.org/10.1136/bmjment-2023-300842,Living alone and mental health: parallel analyses in UK longitudinal population surveys and electronic health records prior to and during the COVID-19 pandemic.,"McElroy E, Herrett E, Patel K, Piehlmaier DM, Gessa GD, Huggins C, Green MJ, Kwong ASF, Thompson EJ, Zhu J, Mansfield KE, Silverwood RJ, Mansfield R, Maddock J, Mathur R, Costello RE, Matthews A, Tazare J, Henderson A, Wing K, Bridges L, Bacon S, Mehrkar A, OpenSAFELY Collaborative, Shaw RJ, Wels J, Katikireddi SV, Chaturvedi N, Tomlinson LA, Patalay P, Longitudinal Health and Wellbeing Collaborative.",,BMJ mental health,2023,2023-08-01,Y,Psychiatry; Anxiety Disorders; Covid-19,,,"<h4>Background</h4>People who live alone experience greater levels of mental illness; however, it is unclear whether the COVID-19 pandemic had a disproportionately negative impact on this demographic.<h4>Objective</h4>To describe the mental health gap between those who live alone and with others in the UK prior to and during the COVID-19 pandemic.<h4>Methods</h4>Self-reported psychological distress and life satisfaction in 10 prospective longitudinal population surveys (LPSs) assessed in the nearest pre-pandemic sweep and three periods during the pandemic. Recorded diagnosis of common and severe mental illnesses between March 2018 and January 2022 in electronic healthcare records (EHRs) within the OpenSAFELY-TPP.<h4>Findings</h4>In 37 544 LPS participants, pooled models showed greater psychological distress (standardised mean difference (SMD): 0.09 (95% CI: 0.04; 0.14); relative risk: 1.25 (95% CI: 1.12; 1.39)) and lower life satisfaction (SMD: -0.22 (95% CI: -0.30; -0.15)) for those living alone pre-pandemic. This gap did not change during the pandemic. In the EHR analysis of c.16 million records, mental health conditions were more common in those who lived alone (eg, depression 26 (95% CI: 18 to 33) and severe mental illness 58 (95% CI: 54 to 62) more cases more per 100 000). For common mental health disorders, the gap in recorded cases in EHRs narrowed during the pandemic.<h4>Conclusions</h4>People living alone have poorer mental health and lower life satisfaction. During the pandemic, this gap in self-reported distress remained; however, there was a narrowing of the gap in service use.<h4>Clinical implications</h4>Greater mental health need and potentially greater barriers to mental healthcare access for those who live alone need to be considered in healthcare planning.",,pdf:https://mentalhealth.bmj.com/content/ebmental/26/1/e300842.full.pdf; doi:https://doi.org/10.1136/bmjment-2023-300842; html:https://europepmc.org/articles/PMC10577768; pdf:https://europepmc.org/articles/PMC10577768?pdf=render
 32656368,https://doi.org/10.12688/wellcomeopenres.15889.2,What settings have been linked to SARS-CoV-2 transmission clusters?,"Leclerc QJ, Fuller NM, Knight LE, CMMID COVID-19 Working Group, Funk S, Knight GM.",,Wellcome open research,2020,2020-06-05,Y,Transmission; Cluster; Coronavirus; Settings; Lockdown; Covid-19; Sars-cov-2,,,"<b>Background</b>: Concern about the health impact of novel coronavirus SARS-CoV-2 has resulted in widespread enforced reductions in people's movement (""lockdowns""). However, there are increasing concerns about the severe economic and wider societal consequences of these measures. Some countries have begun to lift some of the rules on physical distancing in a stepwise manner, with differences in what these ""exit strategies"" entail and their timeframes. The aim of this work was to inform such exit strategies by exploring the types of indoor and outdoor settings where transmission of SARS-CoV-2 has been reported to occur and result in clusters of cases. Identifying potential settings that result in transmission clusters allows these to be kept under close surveillance and/or to remain closed as part of strategies that aim to avoid a resurgence in transmission following the lifting of lockdown measures. <b>Methods</b>: We performed a systematic review of available literature and media reports to find settings reported in peer reviewed articles and media with these characteristics. These sources are curated and made available in an editable online database. <b>Results</b>: We found many examples of SARS-CoV-2 clusters linked to a wide range of mostly indoor settings. Few reports came from schools, many from households, and an increasing number were reported in hospitals and elderly care settings across Europe. <b>Conclusions:</b> We identified possible places that are linked to clusters of COVID-19 cases and could be closely monitored and/or remain closed in the first instance following the progressive removal of lockdown restrictions. However, in part due to the limits in surveillance capacities in many settings, the gathering of information such as cluster sizes and attack rates is limited in several ways: inherent recall bias, biased media reporting and missing data.",,doi:https://doi.org/10.12688/wellcomeopenres.15889.2; html:https://europepmc.org/articles/PMC7327724; pdf:https://europepmc.org/articles/PMC7327724?pdf=render
+37562853,https://doi.org/10.1136/bmjment-2023-300842,Living alone and mental health: parallel analyses in UK longitudinal population surveys and electronic health records prior to and during the COVID-19 pandemic.,"McElroy E, Herrett E, Patel K, Piehlmaier DM, Gessa GD, Huggins C, Green MJ, Kwong ASF, Thompson EJ, Zhu J, Mansfield KE, Silverwood RJ, Mansfield R, Maddock J, Mathur R, Costello RE, Matthews A, Tazare J, Henderson A, Wing K, Bridges L, Bacon S, Mehrkar A, OpenSAFELY Collaborative, Shaw RJ, Wels J, Katikireddi SV, Chaturvedi N, Tomlinson LA, Patalay P, Longitudinal Health and Wellbeing Collaborative.",,BMJ mental health,2023,2023-08-01,Y,Psychiatry; Anxiety Disorders; Covid-19,,,"<h4>Background</h4>People who live alone experience greater levels of mental illness; however, it is unclear whether the COVID-19 pandemic had a disproportionately negative impact on this demographic.<h4>Objective</h4>To describe the mental health gap between those who live alone and with others in the UK prior to and during the COVID-19 pandemic.<h4>Methods</h4>Self-reported psychological distress and life satisfaction in 10 prospective longitudinal population surveys (LPSs) assessed in the nearest pre-pandemic sweep and three periods during the pandemic. Recorded diagnosis of common and severe mental illnesses between March 2018 and January 2022 in electronic healthcare records (EHRs) within the OpenSAFELY-TPP.<h4>Findings</h4>In 37 544 LPS participants, pooled models showed greater psychological distress (standardised mean difference (SMD): 0.09 (95% CI: 0.04; 0.14); relative risk: 1.25 (95% CI: 1.12; 1.39)) and lower life satisfaction (SMD: -0.22 (95% CI: -0.30; -0.15)) for those living alone pre-pandemic. This gap did not change during the pandemic. In the EHR analysis of c.16 million records, mental health conditions were more common in those who lived alone (eg, depression 26 (95% CI: 18 to 33) and severe mental illness 58 (95% CI: 54 to 62) more cases more per 100 000). For common mental health disorders, the gap in recorded cases in EHRs narrowed during the pandemic.<h4>Conclusions</h4>People living alone have poorer mental health and lower life satisfaction. During the pandemic, this gap in self-reported distress remained; however, there was a narrowing of the gap in service use.<h4>Clinical implications</h4>Greater mental health need and potentially greater barriers to mental healthcare access for those who live alone need to be considered in healthcare planning.",,pdf:https://mentalhealth.bmj.com/content/ebmental/26/1/e300842.full.pdf; doi:https://doi.org/10.1136/bmjment-2023-300842; html:https://europepmc.org/articles/PMC10577768; pdf:https://europepmc.org/articles/PMC10577768?pdf=render
 36227072,https://doi.org/10.1093/jamia/ocac203,Transforming and evaluating the UK Biobank to the OMOP Common Data Model for COVID-19 research and beyond.,"Papez V, Moinat M, Voss EA, Bazakou S, Van Winzum A, Peviani A, Payralbe S, Kallfelz M, Asselbergs FW, Prieto-Alhambra D, Dobson RJB, Denaxas S.",,Journal of the American Medical Informatics Association : JAMIA,2022,2022-12-01,Y,Phenotyping; Electronic Health Records; Omop; Common Data Model; Medical Ontologies,,,"<h4>Objective</h4>The coronavirus disease 2019 (COVID-19) pandemic has demonstrated the value of real-world data for public health research. International federated analyses are crucial for informing policy makers. Common data models (CDMs) are critical for enabling these studies to be performed efficiently. Our objective was to convert the UK Biobank, a study of 500 000 participants with rich genetic and phenotypic data to the Observational Medical Outcomes Partnership (OMOP) CDM.<h4>Materials and methods</h4>We converted UK Biobank data to OMOP CDM v. 5.3. We transformedparticipant research data on diseases collected at recruitment and electronic health records (EHRs) from primary care, hospitalizations, cancer registrations, and mortality from providers in England, Scotland, and Wales. We performed syntactic and semantic validations and compared comorbidities and risk factors between source and transformed data.<h4>Results</h4>We identified 502 505 participants (3086 with COVID-19) and transformed 690 fields (1 373 239 555 rows) to the OMOP CDM using 8 different controlled clinical terminologies and bespoke mappings. Specifically, we transformed self-reported noncancer illnesses 946 053 (83.91% of all source entries), cancers 37 802 (70.81%), medications 1 218 935 (88.25%), and prescriptions 864 788 (86.96%). In EHR, we transformed 13 028 182 (99.95%) hospital diagnoses, 6 465 399 (89.2%) procedures, 337 896 333 primary care diagnoses (CTV3, SNOMED-CT), 139 966 587 (98.74%) prescriptions (dm+d) and 77 127 (99.95%) deaths (ICD-10). We observed good concordance across demographic, risk factor, and comorbidity factors between source and transformed data.<h4>Discussion and conclusion</h4>Our study demonstrated that the OMOP CDM can be successfully leveraged to harmonize complex large-scale biobanked studies combining rich multimodal phenotypic data. Our study uncovered several challenges when transforming data from questionnaires to the OMOP CDM which require further research. The transformed UK Biobank resource is a valuable tool that can enable federated research, like COVID-19 studies.",,pdf:https://academic.oup.com/jamia/article-pdf/30/1/103/47829607/ocac203.pdf; doi:https://doi.org/10.1093/jamia/ocac203; html:https://europepmc.org/articles/PMC9619789; pdf:https://europepmc.org/articles/PMC9619789?pdf=render
+33658326,https://doi.org/10.1126/science.abg3055,Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England.,"Davies NG, Abbott S, Barnard RC, Jarvis CI, Kucharski AJ, Munday JD, Pearson CAB, Russell TW, Tully DC, Washburne AD, Wenseleers T, Gimma A, Waites W, Wong KLM, van Zandvoort K, Silverman JD, CMMID COVID-19 Working Group, COVID-19 Genomics UK (COG-UK) Consortium, Diaz-Ordaz K, Keogh R, Eggo RM, Funk S, Jit M, Atkins KE, Edmunds WJ.",,"Science (New York, N.Y.)",2021,2021-03-03,Y,,,,"A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, VOC 202012/01 (lineage B.1.1.7), emerged in southeast England in September 2020 and is rapidly spreading toward fixation. Using a variety of statistical and dynamic modeling approaches, we estimate that this variant has a 43 to 90% (range of 95% credible intervals, 38 to 130%) higher reproduction number than preexisting variants. A fitted two-strain dynamic transmission model shows that VOC 202012/01 will lead to large resurgences of COVID-19 cases. Without stringent control measures, including limited closure of educational institutions and a greatly accelerated vaccine rollout, COVID-19 hospitalizations and deaths across England in the first 6 months of 2021 were projected to exceed those in 2020. VOC 202012/01 has spread globally and exhibits a similar transmission increase (59 to 74%) in Denmark, Switzerland, and the United States.",,pdf:https://www.science.org/cms/asset/9064b3e4-39f9-402c-8fa2-b689efda98b4/pap.pdf; doi:https://doi.org/10.1126/science.abg3055; html:https://europepmc.org/articles/PMC8128288; pdf:https://europepmc.org/articles/PMC8128288?pdf=render
 34942103,https://doi.org/10.1016/s0140-6736(21)02754-9,"Two-dose ChAdOx1 nCoV-19 vaccine protection against COVID-19 hospital admissions and deaths over time: a retrospective, population-based cohort study in Scotland and Brazil.","Katikireddi SV, Cerqueira-Silva T, Vasileiou E, Robertson C, Amele S, Pan J, Taylor B, Boaventura V, Werneck GL, Flores-Ortiz R, Agrawal U, Docherty AB, McCowan C, McMenamin J, Moore E, Ritchie LD, Rudan I, Shah SA, Shi T, Simpson CR, Barreto ML, Oliveira VA, Barral-Netto M, Sheikh A.",,"Lancet (London, England)",2022,2021-12-20,Y,,,,"<h4>Background</h4>Reports suggest that COVID-19 vaccine effectiveness is decreasing, but whether this reflects waning or new SARS-CoV-2 variants-especially delta (B.1.617.2)-is unclear. We investigated the association between time since two doses of ChAdOx1 nCoV-19 vaccine and risk of severe COVID-19 outcomes in Scotland (where delta was dominant), with comparative analyses in Brazil (where delta was uncommon).<h4>Methods</h4>In this retrospective, population-based cohort study in Brazil and Scotland, we linked national databases from the EAVE II study in Scotland; and the COVID-19 Vaccination Campaign, Acute Respiratory Infection Suspected Cases, and Severe Acute Respiratory Infection/Illness datasets in Brazil) for vaccination, laboratory testing, clinical, and mortality data. We defined cohorts of adults (aged ≥18 years) who received two doses of ChAdOx1 nCoV-19 and compared rates of severe COVID-19 outcomes (ie, COVID-19 hospital admission or death) across fortnightly periods, relative to 2-3 weeks after the second dose. Entry to the Scotland cohort started from May 19, 2021, and entry to the Brazil cohort started from Jan 18, 2021. Follow-up in both cohorts was until Oct 25, 2021. Poisson regression was used to estimate rate ratios (RRs) and vaccine effectiveness, with 95% CIs.<h4>Findings</h4>1 972 454 adults received two doses of ChAdOx1 nCoV-19 in Scotland and 42 558 839 in Brazil, with longer follow-up in Scotland because two-dose vaccination began earlier in Scotland than in Brazil. In Scotland, RRs for severe COVID-19 increased to 2·01 (95% CI 1·54-2·62) at 10-11 weeks, 3·01 (2·26-3·99) at 14-15 weeks, and 5·43 (4·00-7·38) at 18-19 weeks after the second dose. The pattern of results was similar in Brazil, with RRs of 2·29 (2·01-2·61) at 10-11 weeks, 3·10 (2·63-3·64) at 14-15 weeks, and 4·71 (3·83-5·78) at 18-19 weeks after the second dose. In Scotland, vaccine effectiveness decreased from 83·7% (95% CI 79·7-87·0) at 2-3 weeks, to 75·9% (72·9-78·6) at 14-15 weeks, and 63·7% (59·6-67·4) at 18-19 weeks after the second dose. In Brazil, vaccine effectiveness decreased from 86·4% (85·4-87·3) at 2-3 weeks, to 59·7% (54·6-64·2) at 14-15 weeks, and 42·2% (32·4-50·6) at 18-19 weeks.<h4>Interpretation</h4>We found waning vaccine protection of ChAdOx1 nCoV-19 against COVID-19 hospital admissions and deaths in both Scotland and Brazil, this becoming evident within three months of the second vaccine dose. Consideration needs to be given to providing booster vaccine doses for people who have received ChAdOx1 nCoV-19.<h4>Funding</h4>UK Research and Innovation (Medical Research Council), Scottish Government, Research and Innovation Industrial Strategy Challenge Fund, Health Data Research UK, Fiocruz, Fazer o Bem Faz Bem Programme; Conselho Nacional de Desenvolvimento Científico e Tecnológico, Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro.<h4>Translation</h4>For the Portuguese translation of the abstract see Supplementary Materials section.",,pdf:http://www.thelancet.com/article/S0140673621027549/pdf; doi:https://doi.org/10.1016/S0140-6736(21)02754-9; html:https://europepmc.org/articles/PMC8687670
 37340474,https://doi.org/10.1186/s12916-023-02877-9,Antidepressant drug prescription and incidence of COVID-19 in mental health outpatients: a retrospective cohort study.,"Glebov OO, Mueller C, Stewart R, Aarsland D, Perera G.",,BMC medicine,2023,2023-06-21,Y,Antidepressants; Ssri; respiratory infection; Drug Repurposing; Covid-19; Sars-cov-2,,,"<h4>Background</h4>Currently, the main pharmaceutical intervention for COVID-19 is vaccination. While antidepressant (AD) drugs have shown some efficacy in treatment of symptomatic COVID-19, their preventative potential remains largely unexplored. Analysis of association between prescription of ADs and COVID-19 incidence in the population would be beneficial for assessing the utility of ADs in COVID-19 prevention.<h4>Methods</h4>Retrospective study of association between AD prescription and COVID-19 diagnosis was performed in a cohort of community-dwelling adult mental health outpatients during the 1st wave of COVID-19 pandemic in the UK. Clinical record interactive search (CRIS) was performed for mentions of ADs within 3 months preceding admission to inpatient care of the South London and Maudsley (SLaM) NHS Foundation Trust. Incidence of positive COVID-19 tests upon admission and during inpatient treatment was the primary outcome measure.<h4>Results</h4>AD mention was associated with approximately 40% lower incidence of positive COVID-19 test results when adjusted for socioeconomic parameters and physical health. This association was also observed for prescription of ADs of the selective serotonin reuptake inhibitor (SSRI) class.<h4>Conclusions</h4>This preliminary study suggests that ADs, and SSRIs in particular, may be of benefit for preventing COVID-19 infection spread in the community. The key limitations of the study are its retrospective nature and the focus on a mental health patient cohort. A more definitive assessment of AD and SSRI preventative potential warrants prospective studies in the wider demographic.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-023-02877-9; doi:https://doi.org/10.1186/s12916-023-02877-9; html:https://europepmc.org/articles/PMC10283271; pdf:https://europepmc.org/articles/PMC10283271?pdf=render
-33658326,https://doi.org/10.1126/science.abg3055,Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England.,"Davies NG, Abbott S, Barnard RC, Jarvis CI, Kucharski AJ, Munday JD, Pearson CAB, Russell TW, Tully DC, Washburne AD, Wenseleers T, Gimma A, Waites W, Wong KLM, van Zandvoort K, Silverman JD, CMMID COVID-19 Working Group, COVID-19 Genomics UK (COG-UK) Consortium, Diaz-Ordaz K, Keogh R, Eggo RM, Funk S, Jit M, Atkins KE, Edmunds WJ.",,"Science (New York, N.Y.)",2021,2021-03-03,Y,,,,"A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, VOC 202012/01 (lineage B.1.1.7), emerged in southeast England in September 2020 and is rapidly spreading toward fixation. Using a variety of statistical and dynamic modeling approaches, we estimate that this variant has a 43 to 90% (range of 95% credible intervals, 38 to 130%) higher reproduction number than preexisting variants. A fitted two-strain dynamic transmission model shows that VOC 202012/01 will lead to large resurgences of COVID-19 cases. Without stringent control measures, including limited closure of educational institutions and a greatly accelerated vaccine rollout, COVID-19 hospitalizations and deaths across England in the first 6 months of 2021 were projected to exceed those in 2020. VOC 202012/01 has spread globally and exhibits a similar transmission increase (59 to 74%) in Denmark, Switzerland, and the United States.",,pdf:https://www.science.org/cms/asset/9064b3e4-39f9-402c-8fa2-b689efda98b4/pap.pdf; doi:https://doi.org/10.1126/science.abg3055; html:https://europepmc.org/articles/PMC8128288; pdf:https://europepmc.org/articles/PMC8128288?pdf=render
 35511729,https://doi.org/10.1093/ageing/afac084,"COVID-19 risk factors amongst 14,786 care home residents: an observational longitudinal analysis including daily community positive test rates of COVID-19, hospital stays and vaccination status in Wales (UK) between 1 September 2020 and 1 May 2021.","Hollinghurst J, Hollinghurst R, North L, Mizen A, Akbari A, Long S, Lyons RA, Fry R.",,Age and ageing,2022,2022-05-01,Y,Vaccination; Hospital infection; Older People; Care Homes; Covid-19; Pcr Tests,,,"<h4>Background</h4>COVID-19 vaccinations have been prioritised for high risk individuals.<h4>Aim</h4>Determine individual-level risk factors for care home residents testing positive for SARS-CoV-2.<h4>Study design</h4>Longitudinal observational cohort study using individual-level linked data from the Secure Anonymised Information Linkage (SAIL) databank.<h4>Setting</h4>Fourteen thousand seven hundred and eighty-six older care home residents (aged 65+) living in Wales between 1 September 2020 and 1 May 2021. Our dataset consisted of 2,613,341 individual-level daily observations within 697 care homes.<h4>Methods</h4>We estimated odds ratios (ORs [95% confidence interval]) using multilevel logistic regression models. Our outcome of interest was a positive SARS-CoV-2 PCR test. We included time-dependent covariates for the estimated community positive test rate of COVID-19, hospital inpatient status, vaccination status and frailty. Additional covariates were included for age, sex and specialist care home services.<h4>Results</h4>The multivariable regression model indicated an increase in age (OR 1.01 [1.00,1.01] per year), community positive test rate (OR 1.13 [1.12,1.13] per percent increase), hospital inpatients (OR 7.40 [6.54,8.36]), and residents in care homes with non-specialist dementia care (OR 1.42 [1.01,1.99]) had an increased odds of a positive test. Having a positive test prior to the observation period (OR 0.58 [0.49,0.68]) and either one or two doses of a vaccine (0.21 [0.17,0.25] and 0.05 [0.02,0.09], respectively) were associated with a decreased odds.<h4>Conclusions</h4>Care providers need to remain vigilant despite the vaccination rollout, and extra precautions should be taken when caring for the most vulnerable. Minimising potential COVID-19 infection for care home residents when admitted to hospital should be prioritised.",,pdf:https://academic.oup.com/ageing/article-pdf/51/5/afac084/43520659/afac084.pdf; doi:https://doi.org/10.1093/ageing/afac084; html:https://europepmc.org/articles/PMC9070807; pdf:https://europepmc.org/articles/PMC9070807?pdf=render
 35922409,https://doi.org/10.1038/s41467-022-32121-6,Dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022 in England.,"Elliott P, Eales O, Bodinier B, Tang D, Wang H, Jonnerby J, Haw D, Elliott J, Whitaker M, Walters CE, Atchison C, Diggle PJ, Page AJ, Trotter AJ, Ashby D, Barclay W, Taylor G, Ward H, Darzi A, Cooke GS, Chadeau-Hyam M, Donnelly CA.",,Nature communications,2022,2022-08-03,Y,,,,"Rapid transmission of the SARS-CoV-2 Omicron variant has led to record-breaking case incidence rates around the world. Since May 2020, the REal-time Assessment of Community Transmission-1 (REACT-1) study tracked the spread of SARS-CoV-2 infection in England through RT-PCR of self-administered throat and nose swabs from randomly-selected participants aged 5 years and over. In January 2022, we found an overall weighted prevalence of 4.41% (n = 102,174), three-fold higher than in November to December 2021; we sequenced 2,374 (99.2%) Omicron infections (19 BA.2), and only 19 (0.79%) Delta, with a growth rate advantage for BA.2 compared to BA.1 or BA.1.1. Prevalence was decreasing overall (reproduction number R = 0.95, 95% credible interval [CrI], 0.93, 0.97), but increasing in children aged 5 to 17 years (R = 1.13, 95% CrI, 1.09, 1.18). In England during January 2022, we observed unprecedented levels of SARS-CoV-2 infection, especially among children, driven by almost complete replacement of Delta by Omicron.",,pdf:https://www.nature.com/articles/s41467-022-32121-6.pdf; doi:https://doi.org/10.1038/s41467-022-32121-6; html:https://europepmc.org/articles/PMC9349208; pdf:https://europepmc.org/articles/PMC9349208?pdf=render
 35192598,https://doi.org/10.1371/journal.pmed.1003927,"First dose ChAdOx1 and BNT162b2 COVID-19 vaccinations and cerebral venous sinus thrombosis: A pooled self-controlled case series study of 11.6 million individuals in England, Scotland, and Wales.","Kerr S, Joy M, Torabi F, Bedston S, Akbari A, Agrawal U, Beggs J, Bradley D, Chuter A, Docherty AB, Ford D, Hobbs R, Katikireddi SV, Lowthian E, de Lusignan S, Lyons R, Marple J, McCowan C, McGagh D, McMenamin J, Moore E, Murray JK, Owen RK, Pan J, Ritchie L, Shah SA, Shi T, Stock S, Tsang RSM, Vasileiou E, Woolhouse M, Simpson CR, Robertson C, Sheikh A.",,PLoS medicine,2022,2022-02-22,Y,,,,"<h4>Background</h4>Several countries restricted the administration of ChAdOx1 to older age groups in 2021 over safety concerns following case reports and observed versus expected analyses suggesting a possible association with cerebral venous sinus thrombosis (CVST). Large datasets are required to precisely estimate the association between Coronavirus Disease 2019 (COVID-19) vaccination and CVST due to the extreme rarity of this event. We aimed to accomplish this by combining national data from England, Scotland, and Wales.<h4>Methods and findings</h4>We created data platforms consisting of linked primary care, secondary care, mortality, and virological testing data in each of England, Scotland, and Wales, with a combined cohort of 11,637,157 people and 6,808,293 person years of follow-up. The cohort start date was December 8, 2020, and the end date was June 30, 2021. The outcome measure we examined was incident CVST events recorded in either primary or secondary care records. We carried out a self-controlled case series (SCCS) analysis of this outcome following first dose vaccination with ChAdOx1 and BNT162b2. The observation period consisted of an initial 90-day reference period, followed by a 2-week prerisk period directly prior to vaccination, and a 4-week risk period following vaccination. Counts of CVST cases from each country were tallied, then expanded into a full dataset with 1 row for each individual and observation time period. There was a combined total of 201 incident CVST events in the cohorts (29.5 per million person years). There were 81 CVST events in the observation period among those who a received first dose of ChAdOx1 (approximately 16.34 per million doses) and 40 for those who received a first dose of BNT162b2 (approximately 12.60 per million doses). We fitted conditional Poisson models to estimate incidence rate ratios (IRRs). Vaccination with ChAdOx1 was associated with an elevated risk of incident CVST events in the 28 days following vaccination, IRR = 1.93 (95% confidence interval (CI) 1.20 to 3.11). We did not find an association between BNT162b2 and CVST in the 28 days following vaccination, IRR = 0.78 (95% CI 0.34 to 1.77). Our study had some limitations. The SCCS study design implicitly controls for variables that are constant over the observation period, but also assumes that outcome events are independent of exposure. This assumption may not be satisfied in the case of CVST, firstly because it is a serious adverse event, and secondly because the vaccination programme in the United Kingdom prioritised the clinically extremely vulnerable and those with underlying health conditions, which may have caused a selection effect for individuals more prone to CVST. Although we pooled data from several large datasets, there was still a low number of events, which may have caused imprecision in our estimates.<h4>Conclusions</h4>In this study, we observed a small elevated risk of CVST events following vaccination with ChAdOx1, but not BNT162b2. Our analysis pooled information from large datasets from England, Scotland, and Wales. This evidence may be useful in risk-benefit analyses of vaccine policies and in providing quantification of risks associated with vaccination to the general public.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003927&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003927; html:https://europepmc.org/articles/PMC8863261; pdf:https://europepmc.org/articles/PMC8863261?pdf=render
-38049846,https://doi.org/10.1186/s13012-023-01321-z,Implementing Germ Defence digital behaviour change intervention via all primary care practices in England to reduce respiratory infections during the COVID-19 pandemic: an efficient cluster randomised controlled trial using the OpenSAFELY platform.,"Ainsworth B, Horwood J, Walter SR, Miller S, Chalder M, De Vocht F, Denison-Day J, Elwenspoek MMC, Curtis HJ, Bates C, Mehrkar A, Bacon S, Goldacre B, OpenSAFELY Collaborative, Craggs P, Amlôt R, Francis N, Little P, Macleod J, Moore M, Morton K, Rice C, Sterne J, Stuart B, Towler L, Willcox ML, Yardley L.",,Implementation science : IS,2023,2023-12-04,Y,Infection control; Respiratory Tract Infections; Primary Care; Rct; Behaviour Change; Ehealth; Digital Medicine; Covid-19; Efficient Trial Design,,,"<h4>Background</h4>Germ Defence ( www.germdefence.org ) is an evidence-based interactive website that promotes behaviour change for infection control within households. To maximise the potential of Germ Defence to effectively reduce the spread of COVID-19, the intervention needed to be implemented at scale rapidly.<h4>Methods</h4>With NHS England approval, we conducted an efficient two-arm (1:1 ratio) cluster randomised controlled trial (RCT) to examine the effectiveness of randomising implementation of Germ Defence via general practitioner (GP) practices across England, UK, compared with usual care to disseminate Germ Defence to patients. GP practices randomised to the intervention arm (n = 3292) were emailed and asked to disseminate Germ Defence to all adult patients via mobile phone text, email or social media. Usual care arm GP practices (n = 3287) maintained standard management for the 4-month trial period and then asked to share Germ Defence with their adult patients. The primary outcome was the rate of GP presentations for respiratory tract infections (RTI) per patient. Secondary outcomes comprised rates of acute RTIs, confirmed COVID-19 diagnoses and suspected COVID-19 diagnoses, COVID-19 symptoms, gastrointestinal infection diagnoses, antibiotic usage and hospital admissions. The impact of the intervention on outcome rates was assessed using negative binomial regression modelling within the OpenSAFELY platform. The uptake of the intervention by GP practice and by patients was measured via website analytics.<h4>Results</h4>Germ Defence was used 310,731 times. The average website satisfaction score was 7.52 (0-10 not at all to very satisfied, N = 9933). There was no evidence of a difference in the rate of RTIs between intervention and control practices (rate ratio (RR) 1.01, 95% CI 0.96, 1.06, p = 0.70). This was similar to all other eight health outcomes. Patient engagement within intervention arm practices ranged from 0 to 48% of a practice list.<h4>Conclusions</h4>While the RCT did not demonstrate a difference in health outcomes, we demonstrated that rapid large-scale implementation of a digital behavioural intervention is possible and can be evaluated with a novel efficient prospective RCT methodology analysing routinely collected patient data entirely within a trusted research environment.<h4>Trial registration</h4>This trial was registered in the ISRCTN registry (14602359) on 12 August 2020.",,pdf:https://implementationscience.biomedcentral.com/counter/pdf/10.1186/s13012-023-01321-z; doi:https://doi.org/10.1186/s13012-023-01321-z; html:https://europepmc.org/articles/PMC10694966; pdf:https://europepmc.org/articles/PMC10694966?pdf=render
 33123364,https://doi.org/10.1093/ckj/sfaa192,Temporal changes in complement activation in haemodialysis patients with COVID-19 as a predictor of disease progression.,"Prendecki M, Clarke C, Medjeral-Thomas N, McAdoo SP, Sandhu E, Peters JE, Thomas DC, Willicombe M, Botto M, Pickering MC.",,Clinical kidney journal,2020,2020-10-02,Y,Complement; Haemodialysis; Covid-19,,,"<h4>Background</h4>Complement activation may play a pathogenic role in patients with severe coronavirus disease 2019 (COVID-19) by contributing to tissue inflammation and microvascular thrombosis.<h4>Methods</h4>Serial samples were collected from patients receiving maintenance haemodialysis (HD). Thirty-nine patients had confirmed COVID-19 and 10 patients had no evidence of COVID-19. Plasma C5a and C3a levels were measured using enzyme-linked immunosorbent assay.<h4>Results</h4>We identified elevated levels of plasma C3a and C5a in HD patients with severe COVID-19 compared with controls. Serial sampling identified that C5a levels were elevated prior to clinical deterioration in patients who developed severe disease. C3a more closely mirrored both clinical and biochemical disease severity.<h4>Conclusions</h4>Our findings suggest that activation of complement plays a role in the pathogenesis of COVID-19, leading to endothelial injury and lung damage. C5a may be an earlier biomarker of disease severity than conventional parameters such as C-reactive protein and this warrants further investigation in dedicated biomarker studies. Our data support the testing of complement inhibition as a therapeutic strategy for patients with severe COVID-19.",,pdf:https://academic.oup.com/ckj/article-pdf/13/5/889/33980535/sfaa192.pdf; doi:https://doi.org/10.1093/ckj/sfaa192; html:https://europepmc.org/articles/PMC7577776; pdf:https://europepmc.org/articles/PMC7577776?pdf=render
 33391794,https://doi.org/10.1098/rsos.200958,"ACE inhibition and cardiometabolic risk factors, lung <i>ACE2</i> and <i>TMPRSS2</i> gene expression, and plasma ACE2 levels: a Mendelian randomization study.","Gill D, Arvanitis M, Carter P, Hernández Cordero AI, Jo B, Karhunen V, Larsson SC, Li X, Lockhart SM, Mason A, Pashos E, Saha A, Tan VY, Zuber V, Bossé Y, Fahle S, Hao K, Jiang T, Joubert P, Lunt AC, Ouwehand WH, Roberts DJ, Timens W, van den Berge M, Watkins NA, Battle A, Butterworth AS, Danesh J, Di Angelantonio E, Engelhardt BE, Peters JE, Sin DD, Burgess S.",,Royal Society open science,2020,2020-11-18,Y,Genetic epidemiology; Angiotensin-converting enzyme inhibitors; Mendelian Randomization; Covid-19,,,"Angiotensin-converting enzyme 2 (ACE2) and serine protease TMPRSS2 have been implicated in cell entry for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19). The expression of <i>ACE2</i> and <i>TMPRSS2</i> in the lung epithelium might have implications for the risk of SARS-CoV-2 infection and severity of COVID-19. We use human genetic variants that proxy angiotensin-converting enzyme (ACE) inhibitor drug effects and cardiovascular risk factors to investigate whether these exposures affect lung <i>ACE2</i> and <i>TMPRSS2</i> gene expression and circulating ACE2 levels. We observed no consistent evidence of an association of genetically predicted serum ACE levels with any of our outcomes. There was weak evidence for an association of genetically predicted serum ACE levels with <i>ACE2</i> gene expression in the Lung eQTL Consortium (<i>p</i> = 0.014), but this finding did not replicate. There was evidence of a positive association of genetic liability to type 2 diabetes mellitus with lung <i>ACE2</i> gene expression in the Gene-Tissue Expression (GTEx) study (<i>p</i> = 4 × 10<sup>-4</sup>) and with circulating plasma ACE2 levels in the INTERVAL study (<i>p</i> = 0.03), but not with lung <i>ACE2</i> expression in the Lung eQTL Consortium study (<i>p</i> = 0.68). There were no associations of genetically proxied liability to the other cardiometabolic traits with any outcome. This study does not provide consistent evidence to support an effect of serum ACE levels (as a proxy for ACE inhibitors) or cardiometabolic risk factors on lung <i>ACE2</i> and <i>TMPRSS2</i> expression or plasma ACE2 levels.",,pdf:https://royalsocietypublishing.org/doi/pdf/10.1098/rsos.200958; doi:https://doi.org/10.1098/rsos.200958; html:https://europepmc.org/articles/PMC7735342; pdf:https://europepmc.org/articles/PMC7735342?pdf=render
+38049846,https://doi.org/10.1186/s13012-023-01321-z,Implementing Germ Defence digital behaviour change intervention via all primary care practices in England to reduce respiratory infections during the COVID-19 pandemic: an efficient cluster randomised controlled trial using the OpenSAFELY platform.,"Ainsworth B, Horwood J, Walter SR, Miller S, Chalder M, De Vocht F, Denison-Day J, Elwenspoek MMC, Curtis HJ, Bates C, Mehrkar A, Bacon S, Goldacre B, OpenSAFELY Collaborative, Craggs P, Amlôt R, Francis N, Little P, Macleod J, Moore M, Morton K, Rice C, Sterne J, Stuart B, Towler L, Willcox ML, Yardley L.",,Implementation science : IS,2023,2023-12-04,Y,Infection control; Respiratory Tract Infections; Primary Care; Rct; Behaviour Change; Ehealth; Digital Medicine; Covid-19; Efficient Trial Design,,,"<h4>Background</h4>Germ Defence ( www.germdefence.org ) is an evidence-based interactive website that promotes behaviour change for infection control within households. To maximise the potential of Germ Defence to effectively reduce the spread of COVID-19, the intervention needed to be implemented at scale rapidly.<h4>Methods</h4>With NHS England approval, we conducted an efficient two-arm (1:1 ratio) cluster randomised controlled trial (RCT) to examine the effectiveness of randomising implementation of Germ Defence via general practitioner (GP) practices across England, UK, compared with usual care to disseminate Germ Defence to patients. GP practices randomised to the intervention arm (n = 3292) were emailed and asked to disseminate Germ Defence to all adult patients via mobile phone text, email or social media. Usual care arm GP practices (n = 3287) maintained standard management for the 4-month trial period and then asked to share Germ Defence with their adult patients. The primary outcome was the rate of GP presentations for respiratory tract infections (RTI) per patient. Secondary outcomes comprised rates of acute RTIs, confirmed COVID-19 diagnoses and suspected COVID-19 diagnoses, COVID-19 symptoms, gastrointestinal infection diagnoses, antibiotic usage and hospital admissions. The impact of the intervention on outcome rates was assessed using negative binomial regression modelling within the OpenSAFELY platform. The uptake of the intervention by GP practice and by patients was measured via website analytics.<h4>Results</h4>Germ Defence was used 310,731 times. The average website satisfaction score was 7.52 (0-10 not at all to very satisfied, N = 9933). There was no evidence of a difference in the rate of RTIs between intervention and control practices (rate ratio (RR) 1.01, 95% CI 0.96, 1.06, p = 0.70). This was similar to all other eight health outcomes. Patient engagement within intervention arm practices ranged from 0 to 48% of a practice list.<h4>Conclusions</h4>While the RCT did not demonstrate a difference in health outcomes, we demonstrated that rapid large-scale implementation of a digital behavioural intervention is possible and can be evaluated with a novel efficient prospective RCT methodology analysing routinely collected patient data entirely within a trusted research environment.<h4>Trial registration</h4>This trial was registered in the ISRCTN registry (14602359) on 12 August 2020.",,pdf:https://implementationscience.biomedcentral.com/counter/pdf/10.1186/s13012-023-01321-z; doi:https://doi.org/10.1186/s13012-023-01321-z; html:https://europepmc.org/articles/PMC10694966; pdf:https://europepmc.org/articles/PMC10694966?pdf=render
 37714668,https://doi.org/10.1136/bmjment-2023-300775,"Impact of the COVID-19 pandemic on antipsychotic prescribing in individuals with autism, dementia, learning disability, serious mental illness or living in a care home: a federated analysis of 59 million patients' primary care records in situ using OpenSAFELY.","Macdonald O, Green A, Walker A, Curtis H, Croker R, Brown A, Butler-Cole B, Andrews C, Massey J, Inglesby P, Morton C, Fisher L, Morley J, Mehrkar A, Bacon S, Davy S, Evans D, Dillingham I, Ward T, Hulme W, Bates C, Cockburn J, Parry J, Hester F, Harper S, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Parkes N, Wood I, Goldacre B, Mackenna B.",,BMJ mental health,2023,2023-09-01,Y,Impulse Control Disorders; Adult Psychiatry; Delirium & Cognitive Disorders; Covid-19,,,"<h4>Background</h4>The COVID-19 pandemic affected how care was delivered to vulnerable patients, such as those with dementia or learning disability.<h4>Objective</h4>To explore whether this affected antipsychotic prescribing in at-risk populations.<h4>Methods</h4>With the approval of NHS England, we completed a retrospective cohort study, using the OpenSAFELY platform to explore primary care data of 59 million patients. We identified patients in five at-risk groups: autism, dementia, learning disability, serious mental illness and care home residents. We calculated the monthly prevalence of antipsychotic prescribing in these groups, as well as the incidence of new prescriptions in each month.<h4>Findings</h4>The average monthly rate of antipsychotic prescribing increased in dementia from 82.75 patients prescribed an antipsychotic per 1000 patients (95% CI 82.30 to 83.19) in January-March 2019 to 90.1 (95% CI 89.68 to 90.60) in October-December 2021 and from 154.61 (95% CI 153.79 to 155.43) to 166.95 (95% CI 166.23 to 167.67) in care homes. There were notable spikes in the rate of new prescriptions issued to patients with dementia and in care homes. In learning disability and autism groups, the rate of prescribing per 1000 decreased from 122.97 (95% CI 122.29 to 123.66) to 119.29 (95% CI 118.68 to 119.91) and from 54.91 (95% CI 54.52 to 55.29) to 51.04 (95% CI 50.74 to 51.35), respectively.<h4>Conclusion and implications</h4>We observed a spike in antipsychotic prescribing in the dementia and care home groups, which correlated with lockdowns and was likely due to prescribing of antipsychotics for palliative care. We observed gradual increases in antipsychotic use in dementia and care home patients and decreases in their use in patients with learning disability or autism.",,pdf:https://mentalhealth.bmj.com/content/ebmental/26/1/e300775.full.pdf; doi:https://doi.org/10.1136/bmjment-2023-300775; html:https://europepmc.org/articles/PMC11146375; pdf:https://europepmc.org/articles/PMC11146375?pdf=render
 35192611,https://doi.org/10.1371/journal.pmed.1003916,Uptake of infant and preschool immunisations in Scotland and England during the COVID-19 pandemic: An observational study of routinely collected data.,"McQuaid F, Mulholland R, Sangpang Rai Y, Agrawal U, Bedford H, Cameron JC, Gibbons C, Roy P, Sheikh A, Shi T, Simpson CR, Tait J, Tessier E, Turner S, Villacampa Ortega J, White J, Wood R.",,PLoS medicine,2022,2022-02-22,Y,,,,"<h4>Background</h4>In 2020, the SARS-CoV-2 (COVID-19) pandemic and lockdown control measures threatened to disrupt routine childhood immunisation programmes with early reports suggesting uptake would fall. In response, public health bodies in Scotland and England collected national data for childhood immunisations on a weekly or monthly basis to allow for rapid analysis of trends. The aim of this study was to use these data to assess the impact of different phases of the pandemic on infant and preschool immunisation uptake rates.<h4>Methods and findings</h4>We conducted an observational study using routinely collected data for the year prior to the pandemic (2019) and immediately before (22 January to March 2020), during (23 March to 26 July), and after (27 July to 4 October) the first UK ""lockdown"". Data were obtained for Scotland from the Public Health Scotland ""COVID19 wider impacts on the health care system"" dashboard and for England from ImmForm. Five vaccinations delivered at different ages were evaluated; 3 doses of ""6-in-1"" diphtheria, tetanus, pertussis, polio, Haemophilus influenzae type b, and hepatitis B vaccine (DTaP/IPV/Hib/HepB) and 2 doses of measles, mumps, and rubella (MMR) vaccine. This represented 439,754 invitations to be vaccinated in Scotland and 4.1 million for England. Uptake during the 2020 periods was compared to the previous year (2019) using binary logistic regression analysis. For Scotland, uptake within 4 weeks of a child becoming eligible by age was analysed along with geographical region and indices of deprivation. For Scotland and England, we assessed whether immunisations were up-to-date at approximately 6 months (all doses 6-in-1) and 16 to 18 months (first MMR) of age. We found that uptake within 4 weeks of eligibility in Scotland for all the 5 vaccines was higher during lockdown than in 2019. Differences ranged from 1.3% for first dose 6-in-1 vaccine (95.3 versus 94%, odds ratio [OR] compared to 2019 1.28, 95% confidence intervals [CIs] 1.18 to 1.39) to 14.3% for second MMR dose (66.1 versus 51.8%, OR compared to 2019 1.8, 95% CI 1.74 to 1.87). Significant increases in uptake were seen across all deprivation levels. In England, fewer children due to receive their immunisations during the lockdown period were up to date at 6 months (6-in-1) or 18 months (first dose MMR). The fall in percentage uptake ranged from 0.5% for first 6-in-1 (95.8 versus 96.3%, OR compared to 2019 0.89, 95% CI 0.86- to 0.91) to 2.1% for third 6-in-1 (86.6 versus 88.7%, OR compared to 2019 0.82, 95% CI 0.81 to 0.83). The use of routinely collected data used in this study was a limiting factor as detailed information on potential confounding factors were not available and we were unable to eliminate the possibility of seasonal trends in immunisation uptake.<h4>Conclusions</h4>In this study, we observed that the national lockdown in Scotland was associated with an increase in timely childhood immunisation uptake; however, in England, uptake fell slightly. Reasons for the improved uptake in Scotland may include active measures taken to promote immunisation at local and national levels during this period and should be explored further. Promoting immunisation uptake and addressing potential vaccine hesitancy is particularly important given the ongoing pandemic and COVID-19 vaccination campaigns.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003916&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003916; html:https://europepmc.org/articles/PMC8863286; pdf:https://europepmc.org/articles/PMC8863286?pdf=render
-36921681,https://doi.org/10.1016/j.cca.2023.117271,"Letter to the editor regarding: ""A haemochromatosis-causing HFE mutation is associated with SARS-CoV-2 susceptibility in the Czech population"" clinica chimica acta 538 (2023) 211-215.","Atkins JL, Lucas MR, Pilling LC, Melzer D.",,Clinica chimica acta; international journal of clinical chemistry,2023,2023-03-13,Y,Iron; Haemochromatosis; Hfe; Covd-19,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10009995; doi:https://doi.org/10.1016/j.cca.2023.117271; html:https://europepmc.org/articles/PMC10009995; pdf:https://europepmc.org/articles/PMC10009995?pdf=render
 34726481,https://doi.org/10.1126/science.abl9551,"Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant.","Elliott P, Haw D, Wang H, Eales O, Walters CE, Ainslie KEC, Atchison C, Fronterre C, Diggle PJ, Page AJ, Trotter AJ, Prosolek SJ, COVID-19 Genomics UK (COG-UK) Consortium11‡, Ashby D, Donnelly CA, Barclay W, Taylor G, Cooke G, Ward H, Darzi A, Riley S.",,"Science (New York, N.Y.)",2021,2021-12-17,Y,,,,"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections were rising during early summer 2021 in many countries as a result of the Delta variant. We assessed reverse transcription polymerase chain reaction swab positivity in the Real-time Assessment of Community Transmission–1 (REACT-1) study in England. During June and July 2021, we observed sustained exponential growth with an average doubling time of 25 days, driven by complete replacement of the Alpha variant by Delta and by high prevalence at younger, less-vaccinated ages. Prevalence among unvaccinated people [1.21% (95% credible interval 1.03%, 1.41%)] was three times that among double-vaccinated people [0.40% (95% credible interval 0.34%, 0.48%)]. However, after adjusting for age and other variables, vaccine effectiveness for double-vaccinated people was estimated at between ~50% and ~60% during this period in England. Increased social mixing in the presence of Delta had the potential to generate sustained growth in infections, even at high levels of vaccination.",,pdf:http://pure-oai.bham.ac.uk/ws/files/154666227/science.abl9551.pdf; doi:https://doi.org/10.1126/science.abl9551; html:https://europepmc.org/articles/PMC10763627; pdf:https://europepmc.org/articles/PMC10763627?pdf=render
+36921681,https://doi.org/10.1016/j.cca.2023.117271,"Letter to the editor regarding: ""A haemochromatosis-causing HFE mutation is associated with SARS-CoV-2 susceptibility in the Czech population"" clinica chimica acta 538 (2023) 211-215.","Atkins JL, Lucas MR, Pilling LC, Melzer D.",,Clinica chimica acta; international journal of clinical chemistry,2023,2023-03-13,Y,Iron; Haemochromatosis; Hfe; Covd-19,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10009995; doi:https://doi.org/10.1016/j.cca.2023.117271; html:https://europepmc.org/articles/PMC10009995; pdf:https://europepmc.org/articles/PMC10009995?pdf=render
 35814295,https://doi.org/10.1038/s43856-022-00146-z,Machine learning to support visual auditing of home-based lateral flow immunoassay self-test results for SARS-CoV-2 antibodies.,"Wong NCK, Meshkinfamfard S, Turbé V, Whitaker M, Moshe M, Bardanzellu A, Dai T, Pignatelli E, Barclay W, Darzi A, Elliott P, Ward H, Tanaka RJ, Cooke GS, McKendry RA, Atchison CJ, Bharath AA.",,Communications medicine,2022,2022-07-06,Y,Databases; Public Health,,,"<h4>Background</h4>Lateral flow immunoassays (LFIAs) are being used worldwide for COVID-19 mass testing and antibody prevalence studies. Relatively simple to use and low cost, these tests can be self-administered at home, but rely on subjective interpretation of a test line by eye, risking false positives and false negatives. Here, we report on the development of ALFA (Automated Lateral Flow Analysis) to improve reported sensitivity and specificity.<h4>Methods</h4>Our computational pipeline uses machine learning, computer vision techniques and signal processing algorithms to analyse images of the Fortress LFIA SARS-CoV-2 antibody self-test, and subsequently classify results as invalid, IgG negative and IgG positive. A large image library of 595,339 participant-submitted test photographs was created as part of the REACT-2 community SARS-CoV-2 antibody prevalence study in England, UK. Alongside ALFA, we developed an analysis toolkit which could also detect device blood leakage issues.<h4>Results</h4>Automated analysis showed substantial agreement with human experts (Cohen's kappa 0.90-0.97) and performed consistently better than study participants, particularly for weak positive IgG results. Specificity (98.7-99.4%) and sensitivity (90.1-97.1%) were high compared with visual interpretation by human experts (ranges due to the varying prevalence of weak positive IgG tests in datasets).<h4>Conclusions</h4>Given the potential for LFIAs to be used at scale in the COVID-19 response (for both antibody and antigen testing), even a small improvement in the accuracy of the algorithms could impact the lives of millions of people by reducing the risk of false-positive and false-negative result read-outs by members of the public. Our findings support the use of machine learning-enabled automated reading of at-home antibody lateral flow tests as a tool for improved accuracy for population-level community surveillance.",,pdf:https://www.nature.com/articles/s43856-022-00146-z.pdf; doi:https://doi.org/10.1038/s43856-022-00146-z; html:https://europepmc.org/articles/PMC9259560; pdf:https://europepmc.org/articles/PMC9259560?pdf=render
 34432797,https://doi.org/10.1371/journal.pone.0255748,Regional performance variation in external validation of four prediction models for severity of COVID-19 at hospital admission: An observational multi-centre cohort study.,"Wickstrøm KE, Vitelli V, Carr E, Holten AR, Bendayan R, Reiner AH, Bean D, Searle T, Shek A, Kraljevic Z, Teo J, Dobson R, Tonby K, Köhn-Luque A, Amundsen EK.",,PloS one,2021,2021-08-25,Y,,,,"<h4>Background</h4>Prediction models should be externally validated to assess their performance before implementation. Several prediction models for coronavirus disease-19 (COVID-19) have been published. This observational cohort study aimed to validate published models of severity for hospitalized patients with COVID-19 using clinical and laboratory predictors.<h4>Methods</h4>Prediction models fitting relevant inclusion criteria were chosen for validation. The outcome was either mortality or a composite outcome of mortality and ICU admission (severe disease). 1295 patients admitted with symptoms of COVID-19 at Kings Cross Hospital (KCH) in London, United Kingdom, and 307 patients at Oslo University Hospital (OUH) in Oslo, Norway were included. The performance of the models was assessed in terms of discrimination and calibration.<h4>Results</h4>We identified two models for prediction of mortality (referred to as Xie and Zhang1) and two models for prediction of severe disease (Allenbach and Zhang2). The performance of the models was variable. For prediction of mortality Xie had good discrimination at OUH with an area under the receiver-operating characteristic (AUROC) 0.87 [95% confidence interval (CI) 0.79-0.95] and acceptable discrimination at KCH, AUROC 0.79 [0.76-0.82]. In prediction of severe disease, Allenbach had acceptable discrimination (OUH AUROC 0.81 [0.74-0.88] and KCH AUROC 0.72 [0.68-0.75]). The Zhang models had moderate to poor discrimination. Initial calibration was poor for all models but improved with recalibration.<h4>Conclusions</h4>The performance of the four prediction models was variable. The Xie model had the best discrimination for mortality, while the Allenbach model had acceptable results for prediction of severe disease.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0255748&type=printable; doi:https://doi.org/10.1371/journal.pone.0255748; html:https://europepmc.org/articles/PMC8386866; pdf:https://europepmc.org/articles/PMC8386866?pdf=render
-35567479,https://doi.org/10.1093/rheumatology/keac283,Shielding reduced incidence of COVID-19 in patients with inflammatory arthritis but vulnerability is associated with increased mortality.,"Cooksey R, Underwood J, Brophy S, Atkinson M, Kennedy J, Choy E.",,"Rheumatology (Oxford, England)",2022,2022-06-01,Y,RA; As; PSA; Electronic Health Records; Inflammatory Arthritis; Covid-19,,,"<h4>Objectives</h4>Investigate whether individuals with inflammatory arthritis (IA), their treatments and shielding status affect the risk of adverse outcomes from COVID-19 for the entire population of Wales, UK.<h4>Methods</h4>Retrospective, population-based cohort study using linked, anonymized electronic health data from SAIL Databank, including primary/secondary care, rheumatology, Office for National Statistics Mortality and COVID-19 laboratory data. Individuals aged 18 years and over testing positive for COVID-19 between March 2020 and May 2021 with READ Codes present for rheumatoid arthritis, psoriatic arthritis and ankylosing spondylitis formed the study cases.<h4>Results</h4>A total of 1966 people with IA and 166 602 without tested positive for COVID-19. The incidence rate was 3.5% (1966/56 914) in IA, vs 6% in the general population (166 602/2 760 442), (difference: 2.5%, 95% CI: 2.4%, 2.7%, P ≤0.001). In an adjusted Cox proportional hazard model, IA was not associated with higher mortality (HR: 0.56, 95% CI: 0.18, 1.64, P=0.286). Significant risk factors included shielding (HR: 1.52, 95% CI: 1.40, 1.64, P ≤0.001), hospitalization for previous infections (HR: 1.20, 95% CI: 1.12, 1.28, P ≤0.001), hospitalizations one year pre-pandemic (HR: 1.34, 95% CI: 1.25, 1.44, P ≤0.001) and glucocorticoid use (HR: 1.17, 95% CI: 1.09, 1.25, P ≤0.001).<h4>Conclusions</h4>Individuals with IA had a lower incidence of COVID-19, probably due to shielding. IA was not associated with increased mortality following COVID-19 infection; being vulnerable (shielded), comorbidities and other factors were associated with increased risk. These key risk factors can identify individuals with IA at greater risk from COVID-19 and advised to shield during high community prevalence.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa62372/Download/62372__26337__5539f4f995224d80a2156218d11a03cb.pdf; doi:https://doi.org/10.1093/rheumatology/keac283; html:https://europepmc.org/articles/PMC9248059; pdf:https://europepmc.org/articles/PMC9248059?pdf=render
 37720555,https://doi.org/10.1016/j.xops.2023.100388,A Datasheet for the INSIGHT University Hospitals Birmingham Retinal Vein Occlusion Data Set.,"Bilton EJ, Guggenheim EJ, Baranyi B, Radovanovic C, Williams RL, Bradlow W, Denniston AK, Mollan SP.",,Ophthalmology science,2023,2023-08-22,Y,Myocardial infarction; Retinal Vein Occlusion; Major Cardiovascular Events; Data Set; Biomedical Data,,,"<h4>Purpose</h4>Retinal vein occlusion (RVO) is the second leading cause of visual loss due to retinal disease. Retinal vein occlusion increases the risk of cardiovascular mortality and the risk of stroke. This article describes the data contained within the INSIGHT eye health data set for RVO and cardiovascular disease.<h4>Design</h4>Data set descriptor for routinely collected eye and systemic disease data.<h4>Participants</h4>All people who had suffered an RVO aged ≥ 18 years old, attending the Ophthalmology Clinic at Queen Elizabeth Hospital, University Hospitals Birmingham (UHB) National Health Service (NHS) Trust were included.<h4>Methods</h4>The INSIGHT Health Data Research Hub for Eye Health is an NHS-led ophthalmic bioresource. It provides researchers with safe access to anonymized routinely collected data from contributing NHS hospitals to advance research for patient benefit. This report describes the INSIGHT UHB RVO and major adverse cardiovascular events data set, a data set of ophthalmology and systemic data derived from the United Kingdom's largest acute care trust.<h4>Main outcome measures</h4>This data set consists of routinely collected data from the hospital's electronic patient records. The data set primarily includes structured data (relating to their hospital eye care and any cardiovascular data held for the individual) and OCT ocular images. Further details regarding the available data points are available in the supplementary information.<h4>Results</h4>At the time point of this analysis (September 30, 2022) the data set was composed of clinical data from 1521 patients, from Medisoft records inception. The data set includes 2196 occurrences of RVO affecting 2026 eyes, longitudinal eye follow-up clinical parameters, over 6217 eye-related procedures, and 982 encountered complications. The data set contains information on 2534 major adverse cardiovascular event occurrences, their subtype, number experienced per patient, and chronological relation to RVO event. Longitudinal follow-up data including laboratory results, regular medications, and all-cause mortality are also available within the data set.<h4>Conclusions</h4>This data set descriptor article summarizes the data set contents, the process of its curation, and potential uses. The data set is available through the structured application process that ensures research studies are for patient benefit. Further information regarding the data repository and contact details can be found at https://www.insight.hdrhub.org/.<h4>Financial disclosures</h4>Proprietary or commercial disclosure may be found after the references.",,doi:https://doi.org/10.1016/j.xops.2023.100388; html:https://europepmc.org/articles/PMC10500462; pdf:https://europepmc.org/articles/PMC10500462?pdf=render
+35567479,https://doi.org/10.1093/rheumatology/keac283,Shielding reduced incidence of COVID-19 in patients with inflammatory arthritis but vulnerability is associated with increased mortality.,"Cooksey R, Underwood J, Brophy S, Atkinson M, Kennedy J, Choy E.",,"Rheumatology (Oxford, England)",2022,2022-06-01,Y,RA; As; PSA; Electronic Health Records; Inflammatory Arthritis; Covid-19,,,"<h4>Objectives</h4>Investigate whether individuals with inflammatory arthritis (IA), their treatments and shielding status affect the risk of adverse outcomes from COVID-19 for the entire population of Wales, UK.<h4>Methods</h4>Retrospective, population-based cohort study using linked, anonymized electronic health data from SAIL Databank, including primary/secondary care, rheumatology, Office for National Statistics Mortality and COVID-19 laboratory data. Individuals aged 18 years and over testing positive for COVID-19 between March 2020 and May 2021 with READ Codes present for rheumatoid arthritis, psoriatic arthritis and ankylosing spondylitis formed the study cases.<h4>Results</h4>A total of 1966 people with IA and 166 602 without tested positive for COVID-19. The incidence rate was 3.5% (1966/56 914) in IA, vs 6% in the general population (166 602/2 760 442), (difference: 2.5%, 95% CI: 2.4%, 2.7%, P ≤0.001). In an adjusted Cox proportional hazard model, IA was not associated with higher mortality (HR: 0.56, 95% CI: 0.18, 1.64, P=0.286). Significant risk factors included shielding (HR: 1.52, 95% CI: 1.40, 1.64, P ≤0.001), hospitalization for previous infections (HR: 1.20, 95% CI: 1.12, 1.28, P ≤0.001), hospitalizations one year pre-pandemic (HR: 1.34, 95% CI: 1.25, 1.44, P ≤0.001) and glucocorticoid use (HR: 1.17, 95% CI: 1.09, 1.25, P ≤0.001).<h4>Conclusions</h4>Individuals with IA had a lower incidence of COVID-19, probably due to shielding. IA was not associated with increased mortality following COVID-19 infection; being vulnerable (shielded), comorbidities and other factors were associated with increased risk. These key risk factors can identify individuals with IA at greater risk from COVID-19 and advised to shield during high community prevalence.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa62372/Download/62372__26337__5539f4f995224d80a2156218d11a03cb.pdf; doi:https://doi.org/10.1093/rheumatology/keac283; html:https://europepmc.org/articles/PMC9248059; pdf:https://europepmc.org/articles/PMC9248059?pdf=render
 33837377,https://doi.org/10.1038/s41591-021-01310-z,Actionable druggable genome-wide Mendelian randomization identifies repurposing opportunities for COVID-19.,"Gaziano L, Giambartolomei C, Pereira AC, Gaulton A, Posner DC, Swanson SA, Ho YL, Iyengar SK, Kosik NM, Vujkovic M, Gagnon DR, Bento AP, Barrio-Hernandez I, Rönnblom L, Hagberg N, Lundtoft C, Langenberg C, Pietzner M, Valentine D, Gustincich S, Tartaglia GG, Allara E, Surendran P, Burgess S, Zhao JH, Peters JE, Prins BP, Angelantonio ED, Devineni P, Shi Y, Lynch KE, DuVall SL, Garcon H, Thomann LO, Zhou JJ, Gorman BR, Huffman JE, O'Donnell CJ, Tsao PS, Beckham JC, Pyarajan S, Muralidhar S, Huang GD, Ramoni R, Beltrao P, Danesh J, Hung AM, Chang KM, Sun YV, Joseph J, Leach AR, Edwards TL, Cho K, Gaziano JM, Butterworth AS, Casas JP, VA Million Veteran Program COVID-19 Science Initiative.",,Nature medicine,2021,2021-04-09,Y,,,,"Drug repurposing provides a rapid approach to meet the urgent need for therapeutics to address COVID-19. To identify therapeutic targets relevant to COVID-19, we conducted Mendelian randomization analyses, deriving genetic instruments based on transcriptomic and proteomic data for 1,263 actionable proteins that are targeted by approved drugs or in clinical phase of drug development. Using summary statistics from the Host Genetics Initiative and the Million Veteran Program, we studied 7,554 patients hospitalized with COVID-19 and >1 million controls. We found significant Mendelian randomization results for three proteins (ACE2, P = 1.6 × 10<sup>-6</sup>; IFNAR2, P = 9.8 × 10<sup>-11</sup> and IL-10RB, P = 2.3 × 10<sup>-14</sup>) using cis-expression quantitative trait loci genetic instruments that also had strong evidence for colocalization with COVID-19 hospitalization. To disentangle the shared expression quantitative trait loci signal for IL10RB and IFNAR2, we conducted phenome-wide association scans and pathway enrichment analysis, which suggested that IFNAR2 is more likely to play a role in COVID-19 hospitalization. Our findings prioritize trials of drugs targeting IFNAR2 and ACE2 for early management of COVID-19.",,pdf:https://www.nature.com/articles/s41591-021-01310-z.pdf; doi:https://doi.org/10.1038/s41591-021-01310-z; html:https://europepmc.org/articles/PMC7612986; pdf:https://europepmc.org/articles/PMC7612986?pdf=render
-35143473,https://doi.org/10.1371/journal.pbio.3001531,SARS-CoV-2 antibodies protect against reinfection for at least 6 months in a multicentre seroepidemiological workplace cohort.,"Finch E, Lowe R, Fischinger S, de St Aubin M, Siddiqui SM, Dayal D, Loesche MA, Rhee J, Beger S, Hu Y, Gluck MJ, Mormann B, Hasdianda MA, Musk ER, Alter G, Menon AS, Nilles EJ, Kucharski AJ, CMMID COVID-19 working group and the SpaceX COVID-19 Cohort Collaborative.",,PLoS biology,2022,2022-02-10,Y,,,,"Identifying the potential for SARS-CoV-2 reinfection is crucial for understanding possible long-term epidemic dynamics. We analysed longitudinal PCR and serological testing data from a prospective cohort of 4,411 United States employees in 4 states between April 2020 and February 2021. We conducted a multivariable logistic regression investigating the association between baseline serological status and subsequent PCR test result in order to calculate an odds ratio for reinfection. We estimated an odds ratio for reinfection ranging from 0.14 (95% CI: 0.019 to 0.63) to 0.28 (95% CI: 0.05 to 1.1), implying that the presence of SARS-CoV-2 antibodies at baseline is associated with around 72% to 86% reduced odds of a subsequent PCR positive test based on our point estimates. This suggests that primary infection with SARS-CoV-2 provides protection against reinfection in the majority of individuals, at least over a 6-month time period. We also highlight 2 major sources of bias and uncertainty to be considered when estimating the relative risk of reinfection, confounders and the choice of baseline time point, and show how to account for both in reinfection analysis.",,pdf:https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.3001531&type=printable; doi:https://doi.org/10.1371/journal.pbio.3001531; html:https://europepmc.org/articles/PMC8865659; pdf:https://europepmc.org/articles/PMC8865659?pdf=render
 34345715,https://doi.org/10.23889/ijpds.v5i4.1656,Establishing the impact of COVID-19 on the health outcomes of domiciliary care workers in Wales using routine data: a protocol for the OSCAR study.,"Lugg-Widger F, Cannings-John R, Akbari A, Brookes-Howell L, Hood K, John A, Jones H, Prout H, Schoenbuchner S, Thomas D, Robling M.",,International journal of population data science,2020,2020-01-01,Y,Mortality; Administrative Data; Natural Experiment; Domiciliary Care Worker; Covid-19,,,"<h4>Introduction</h4>Domiciliary care workers (DCWs) continued providing social care to adults in their own homes throughout the COVID-19 pandemic. Evidence of the impact of COVID-19 on health outcomes of DCWs is currently mixed, probably reflecting methodological limitations of existing studies. The risk of COVID-19 to workers providing care in people's homes remains unknown.<h4>Objectives</h4>To quantify the impact of COVID-19 upon health outcomes of DCWs in Wales, to explore causes of variation, and to extrapolate to the rest of the UK DCW population.<h4>Methods</h4>Mixed methods design comprising cohort study of DCWs and exploratory qualitative interviews. Data for all registered DCWs in Wales is available via the SAIL Databank using a secured, privacy-protecting encrypted anonymisation process. Occupational registration data for DCWs working during the pandemic will be combined with EHR outcome data within the SAIL Databank including clinical codes that identify suspected and confirmed COVID-19 cases. We will report rates of suspected and confirmed COVID-19 infections and key health outcomes including mortality and explore variation (by factors such as age, sex, ethnicity, deprivation quintile, rurality, employer, comorbidities) using regression modelling, adjusting for clustering of outcome within Health Board, region and employer. A maximum variation sample of Welsh DCWs will be approached for qualitative interview using a strategy to include participants that vary across factors such as sex, age, ethnicity and employer. The interviews will inform the quantitative analysis modelling. We will generalise the quantitative findings to other UK nations.<h4>Discussion</h4>Using anonymised linked occupational and EHR data and qualitative interviews, the OSCAR study will quantify the risk of COVID-19 on DCWs' health and explore sources of variation. This will provide a secure base for informing public health policy and occupational guidance.",,pdf:https://ijpds.org/article/download/1656/3219; doi:https://doi.org/10.23889/ijpds.v5i4.1656; html:https://europepmc.org/articles/PMC8280712; pdf:https://europepmc.org/articles/PMC8280712?pdf=render
+35143473,https://doi.org/10.1371/journal.pbio.3001531,SARS-CoV-2 antibodies protect against reinfection for at least 6 months in a multicentre seroepidemiological workplace cohort.,"Finch E, Lowe R, Fischinger S, de St Aubin M, Siddiqui SM, Dayal D, Loesche MA, Rhee J, Beger S, Hu Y, Gluck MJ, Mormann B, Hasdianda MA, Musk ER, Alter G, Menon AS, Nilles EJ, Kucharski AJ, CMMID COVID-19 working group and the SpaceX COVID-19 Cohort Collaborative.",,PLoS biology,2022,2022-02-10,Y,,,,"Identifying the potential for SARS-CoV-2 reinfection is crucial for understanding possible long-term epidemic dynamics. We analysed longitudinal PCR and serological testing data from a prospective cohort of 4,411 United States employees in 4 states between April 2020 and February 2021. We conducted a multivariable logistic regression investigating the association between baseline serological status and subsequent PCR test result in order to calculate an odds ratio for reinfection. We estimated an odds ratio for reinfection ranging from 0.14 (95% CI: 0.019 to 0.63) to 0.28 (95% CI: 0.05 to 1.1), implying that the presence of SARS-CoV-2 antibodies at baseline is associated with around 72% to 86% reduced odds of a subsequent PCR positive test based on our point estimates. This suggests that primary infection with SARS-CoV-2 provides protection against reinfection in the majority of individuals, at least over a 6-month time period. We also highlight 2 major sources of bias and uncertainty to be considered when estimating the relative risk of reinfection, confounders and the choice of baseline time point, and show how to account for both in reinfection analysis.",,pdf:https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.3001531&type=printable; doi:https://doi.org/10.1371/journal.pbio.3001531; html:https://europepmc.org/articles/PMC8865659; pdf:https://europepmc.org/articles/PMC8865659?pdf=render
 35047183,https://doi.org/10.7189/jogh.11.01011,The COVID-19 pandemic in children and young people during 2020-2021: A complex discussion on vaccination.,"Rudan I, Adeloye D, Katikireddi V, Murray J, Simpson C, Shah SA, Robertson C, Sheikh A, EAVE II collaboration.",,Journal of global health,2021,2021-12-25,Y,,,,,,doi:https://doi.org/10.7189/jogh.11.01011; doi:https://doi.org/10.7189/jogh.11.01011; html:https://europepmc.org/articles/PMC8763337; pdf:https://europepmc.org/articles/PMC8763337?pdf=render
-33737413,https://doi.org/10.1136/bmj.n628,Association between living with children and outcomes from covid-19: OpenSAFELY cohort study of 12 million adults in England.,"Forbes H, Morton CE, Bacon S, McDonald HI, Minassian C, Brown JP, Rentsch CT, Mathur R, Schultze A, DeVito NJ, MacKenna B, Hulme WJ, Croker R, Walker AJ, Williamson EJ, Bates C, Mehrkar A, Curtis HJ, Evans D, Wing K, Inglesby P, Drysdale H, Wong AYS, Cockburn J, McManus R, Parry J, Hester F, Harper S, Douglas IJ, Smeeth L, Evans SJW, Bhaskaran K, Eggo RM, Goldacre B, Tomlinson LA.",,BMJ (Clinical research ed.),2021,2021-03-18,Y,,,,"<h4>Objective</h4>To investigate whether risk of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and outcomes of coronavirus disease 2019 (covid-19) differed between adults living with and without children during the first two waves of the UK pandemic.<h4>Design</h4>Population based cohort study, on behalf of NHS England.<h4>Setting</h4>Primary care data and pseudonymously linked hospital and intensive care admissions and death records from England, during wave 1 (1 February to 31 August 2020) and wave 2 (1 September to 18 December 2020).<h4>Participants</h4>Two cohorts of adults (18 years and over) registered at a general practice on 1 February 2020 and 1 September 2020.<h4>Main outcome measures</h4>Adjusted hazard ratios for SARS-CoV-2 infection, covid-19 related admission to hospital or intensive care, or death from covid-19, by presence of children in the household.<h4>Results</h4>Among 9 334 392adults aged 65 years and under, during wave 1, living with children was not associated with materially increased risks of recorded SARS-CoV-2 infection, covid-19 related hospital or intensive care admission, or death from covid-19. In wave 2, among adults aged 65 years and under, living with children of any age was associated with an increased risk of recorded SARS-CoV-2 infection (hazard ratio 1.06 (95% confidence interval 1.05 to 1.08) for living with children aged 0-11 years; 1.22 (1.20 to 1.24) for living with children aged 12-18 years) and covid-19 related hospital admission (1.18 (1.06 to 1.31) for living with children aged 0-11; 1.26 (1.12 to 1.40) for living with children aged 12-18). Living with children aged 0-11 was associated with reduced risk of death from both covid-19 and non-covid-19 causes in both waves; living with children of any age was also associated with lower risk of dying from non-covid-19 causes. For adults 65 years and under during wave 2, living with children aged 0-11 years was associated with an increased absolute risk of having SARS-CoV-2 infection recorded of 40-60 per 10 000 people, from 810 to between 850 and 870, and an increase in the number of hospital admissions of 1-5 per 10 000 people, from 160 to between 161 and 165. Living with children aged 12-18 years was associated with an increase of 160-190 per 10 000 in the number of SARS-CoV-2 infections and an increase of 2-6 per 10 000 in the number of hospital admissions.<h4>Conclusions</h4>In contrast to wave 1, evidence existed of increased risk of reported SARS-CoV-2 infection and covid-19 outcomes among adults living with children during wave 2. However, this did not translate into a materially increased risk of covid-19 mortality, and absolute increases in risk were small.",,pdf:https://www.bmj.com/content/bmj/372/bmj.n628.full.pdf; doi:https://doi.org/10.1136/bmj.n628; html:https://europepmc.org/articles/PMC7970340; pdf:https://europepmc.org/articles/PMC7970340?pdf=render
 38877563,https://doi.org/10.1186/s12911-024-02563-7,Collaborative learning from distributed data with differentially private synthetic data.,"Prediger L, Jälkö J, Honkela A, Kaski S.",,BMC medical informatics and decision making,2024,2024-06-14,Y,Collaborative Learning; Health Informatics; Differential Privacy; Synthetic Data,,,"<h4>Background</h4>Consider a setting where multiple parties holding sensitive data aim to collaboratively learn population level statistics, but pooling the sensitive data sets is not possible due to privacy concerns and parties are unable to engage in centrally coordinated joint computation. We study the feasibility of combining privacy preserving synthetic data sets in place of the original data for collaborative learning on real-world health data from the UK Biobank.<h4>Methods</h4>We perform an empirical evaluation based on an existing prospective cohort study from the literature. Multiple parties were simulated by splitting the UK Biobank cohort along assessment centers, for which we generate synthetic data using differentially private generative modelling techniques. We then apply the original study's Poisson regression analysis on the combined synthetic data sets and evaluate the effects of 1) the size of local data set, 2) the number of participating parties, and 3) local shifts in distributions, on the obtained likelihood scores.<h4>Results</h4>We discover that parties engaging in the collaborative learning via shared synthetic data obtain more accurate estimates of the regression parameters compared to using only their local data. This finding extends to the difficult case of small heterogeneous data sets. Furthermore, the more parties participate, the larger and more consistent the improvements become up to a certain limit. Finally, we find that data sharing can especially help parties whose data contain underrepresented groups to perform better-adjusted analysis for said groups.<h4>Conclusions</h4>Based on our results we conclude that sharing of synthetic data is a viable method for enabling learning from sensitive data without violating privacy constraints even if individual data sets are small or do not represent the overall population well. Lack of access to distributed sensitive data is often a bottleneck in biomedical research, which our study shows can be alleviated with privacy-preserving collaborative learning methods.",,doi:https://doi.org/10.1186/s12911-024-02563-7; html:https://europepmc.org/articles/PMC11179391; pdf:https://europepmc.org/articles/PMC11179391?pdf=render
+33737413,https://doi.org/10.1136/bmj.n628,Association between living with children and outcomes from covid-19: OpenSAFELY cohort study of 12 million adults in England.,"Forbes H, Morton CE, Bacon S, McDonald HI, Minassian C, Brown JP, Rentsch CT, Mathur R, Schultze A, DeVito NJ, MacKenna B, Hulme WJ, Croker R, Walker AJ, Williamson EJ, Bates C, Mehrkar A, Curtis HJ, Evans D, Wing K, Inglesby P, Drysdale H, Wong AYS, Cockburn J, McManus R, Parry J, Hester F, Harper S, Douglas IJ, Smeeth L, Evans SJW, Bhaskaran K, Eggo RM, Goldacre B, Tomlinson LA.",,BMJ (Clinical research ed.),2021,2021-03-18,Y,,,,"<h4>Objective</h4>To investigate whether risk of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and outcomes of coronavirus disease 2019 (covid-19) differed between adults living with and without children during the first two waves of the UK pandemic.<h4>Design</h4>Population based cohort study, on behalf of NHS England.<h4>Setting</h4>Primary care data and pseudonymously linked hospital and intensive care admissions and death records from England, during wave 1 (1 February to 31 August 2020) and wave 2 (1 September to 18 December 2020).<h4>Participants</h4>Two cohorts of adults (18 years and over) registered at a general practice on 1 February 2020 and 1 September 2020.<h4>Main outcome measures</h4>Adjusted hazard ratios for SARS-CoV-2 infection, covid-19 related admission to hospital or intensive care, or death from covid-19, by presence of children in the household.<h4>Results</h4>Among 9 334 392adults aged 65 years and under, during wave 1, living with children was not associated with materially increased risks of recorded SARS-CoV-2 infection, covid-19 related hospital or intensive care admission, or death from covid-19. In wave 2, among adults aged 65 years and under, living with children of any age was associated with an increased risk of recorded SARS-CoV-2 infection (hazard ratio 1.06 (95% confidence interval 1.05 to 1.08) for living with children aged 0-11 years; 1.22 (1.20 to 1.24) for living with children aged 12-18 years) and covid-19 related hospital admission (1.18 (1.06 to 1.31) for living with children aged 0-11; 1.26 (1.12 to 1.40) for living with children aged 12-18). Living with children aged 0-11 was associated with reduced risk of death from both covid-19 and non-covid-19 causes in both waves; living with children of any age was also associated with lower risk of dying from non-covid-19 causes. For adults 65 years and under during wave 2, living with children aged 0-11 years was associated with an increased absolute risk of having SARS-CoV-2 infection recorded of 40-60 per 10 000 people, from 810 to between 850 and 870, and an increase in the number of hospital admissions of 1-5 per 10 000 people, from 160 to between 161 and 165. Living with children aged 12-18 years was associated with an increase of 160-190 per 10 000 in the number of SARS-CoV-2 infections and an increase of 2-6 per 10 000 in the number of hospital admissions.<h4>Conclusions</h4>In contrast to wave 1, evidence existed of increased risk of reported SARS-CoV-2 infection and covid-19 outcomes among adults living with children during wave 2. However, this did not translate into a materially increased risk of covid-19 mortality, and absolute increases in risk were small.",,pdf:https://www.bmj.com/content/bmj/372/bmj.n628.full.pdf; doi:https://doi.org/10.1136/bmj.n628; html:https://europepmc.org/articles/PMC7970340; pdf:https://europepmc.org/articles/PMC7970340?pdf=render
 33739254,https://doi.org/10.2807/1560-7917.es.2021.26.11.2100256,"Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England, 16 November to 5 February.","Grint DJ, Wing K, Williamson E, McDonald HI, Bhaskaran K, Evans D, Evans SJ, Walker AJ, Hickman G, Nightingale E, Schultze A, Rentsch CT, Bates C, Cockburn J, Curtis HJ, Morton CE, Bacon S, Davy S, Wong AY, Mehrkar A, Tomlinson L, Douglas IJ, Mathur R, Blomquist P, MacKenna B, Ingelsby P, Croker R, Parry J, Hester F, Harper S, DeVito NJ, Hulme W, Tazare J, Goldacre B, Smeeth L, Eggo RM.",,Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin,2021,2021-03-01,Y,Mortality; Coronavirus; Cfr; Case Fatality Risk; Covid-19; Sars-cov-2; Variant Of Concern,,,The SARS-CoV-2 B.1.1.7 variant of concern (VOC) is increasing in prevalence across Europe. Accurate estimation of disease severity associated with this VOC is critical for pandemic planning. We found increased risk of death for VOC compared with non-VOC cases in England (hazard ratio: 1.67; 95% confidence interval: 1.34-2.09; p < 0.0001). Absolute risk of death by 28 days increased with age and comorbidities. This VOC has potential to spread faster with higher mortality than the pandemic to date.,,pdf:https://www.eurosurveillance.org/deliver/fulltext/eurosurveillance/26/11/eurosurv-26-11-2.pdf?itemId=%2Fcontent%2F10.2807%2F1560-7917.ES.2021.26.11.2100256&mimeType=pdf&containerItemId=content/eurosurveillance; doi:https://doi.org/10.2807/1560-7917.ES.2021.26.11.2100256; html:https://europepmc.org/articles/PMC7976383; pdf:https://europepmc.org/articles/PMC7976383?pdf=render
 35595824,https://doi.org/10.1038/s41598-022-12517-6,Transmission dynamics of SARS-CoV-2 in a strictly-Orthodox Jewish community in the UK.,"Waites W, Pearson CAB, Gaskell KM, House T, Pellis L, Johnson M, Gould V, Hunt A, Stone NRH, Kasstan B, Chantler T, Lal S, Roberts CH, Goldblatt D, CMMID COVID-19 Working Group, Marks M, Eggo RM.",,Scientific reports,2022,2022-05-20,Y,,,,"Some social settings such as households and workplaces, have been identified as high risk for SARS-CoV-2 transmission. Identifying and quantifying the importance of these settings is critical for designing interventions. A tightly-knit religious community in the UK experienced a very large COVID-19 epidemic in 2020, reaching 64.3% seroprevalence within 10 months, and we surveyed this community both for serological status and individual-level attendance at particular settings. Using these data, and a network model of people and places represented as a stochastic graph rewriting system, we estimated the relative contribution of transmission in households, schools and religious institutions to the epidemic, and the relative risk of infection in each of these settings. All congregate settings were important for transmission, with some such as primary schools and places of worship having a higher share of transmission than others. We found that the model needed a higher general-community transmission rate for women (3.3-fold), and lower susceptibility to infection in children to recreate the observed serological data. The precise share of transmission in each place was related to assumptions about the internal structure of those places. Identification of key settings of transmission can allow public health interventions to be targeted at these locations.",,pdf:https://www.nature.com/articles/s41598-022-12517-6.pdf; doi:https://doi.org/10.1038/s41598-022-12517-6; html:https://europepmc.org/articles/PMC9121858; pdf:https://europepmc.org/articles/PMC9121858?pdf=render
 35210596,https://doi.org/10.1038/s41591-022-01736-z,Modeling comparative cost-effectiveness of SARS-CoV-2 vaccine dose fractionation in India.,"Du Z, Wang L, Pandey A, Lim WW, Chinazzi M, Piontti APY, Lau EHY, Wu P, Malani A, Cobey S, Cowling BJ.",,Nature medicine,2022,2022-02-24,Y,,,,"Given global Coronavirus Disease 2019 (COVID-19) vaccine shortages and inequity of vaccine distributions, fractionation of vaccine doses might be an effective strategy for reducing public health and economic burden, notwithstanding the emergence of new variants of concern. In this study, we developed a multi-scale model incorporating population-level transmission and individual-level vaccination to estimate the costs of hospitalization and vaccination and the economic benefits of reducing COVID-19 deaths due to dose-fractionation strategies in India. We used large-scale survey data of the willingness to pay together with data of vaccine and hospital admission costs to build the model. We found that fractional doses of vaccines could be an economically viable vaccination strategy compared to alternatives of either full-dose vaccination or no vaccination. Dose-sparing strategies could save a large number of lives, even with the emergence of new variants with higher transmissibility.",,pdf:https://www.nature.com/articles/s41591-022-01736-z.pdf; doi:https://doi.org/10.1038/s41591-022-01736-z; html:https://europepmc.org/articles/PMC9117137; pdf:https://europepmc.org/articles/PMC9117137?pdf=render
@@ -283,39 +283,39 @@ PMC9023380,https://doi.org/,Assessing the spread risk of COVID-19 associated wit
 36112916,https://doi.org/10.1177/09622802211055853,Inferring risks of coronavirus transmission from community household data.,"House T, Riley H, Pellis L, Pouwels KB, Bacon S, Eidukas A, Jahanshahi K, Eggo RM, Sarah Walker A.",,Statistical methods in medical research,2022,2022-09-01,Y,Infection; Model; epidemic; risk factors; Covid-19,,,"The response of many governments to the COVID-19 pandemic has involved measures to control within- and between-household transmission, providing motivation to improve understanding of the absolute and relative risks in these contexts. Here, we perform exploratory, residual-based, and transmission-dynamic household analysis of the Office for National Statistics COVID-19 Infection Survey data from 26 April 2020 to 15 July 2021 in England. This provides evidence for: (i) temporally varying rates of introduction of infection into households broadly following the trajectory of the overall epidemic and vaccination programme; (ii) susceptible-Infectious transmission probabilities of within-household transmission in the 15-35% range; (iii) the emergence of the Alpha and Delta variants, with the former being around 50% more infectious than wildtype and 35% less infectious than Delta within households; (iv) significantly (in the range of 25-300%) more risk of bringing infection into the household for workers in patient-facing roles pre-vaccine; (v) increased risk for secondary school-age children of bringing the infection into the household when schools are open; (vi) increased risk for primary school-age children of bringing the infection into the household when schools were open since the emergence of new variants.",,doi:https://doi.org/10.1177/09622802211055853; doi:https://doi.org/10.1177/09622802211055853; html:https://europepmc.org/articles/PMC9465559; pdf:https://europepmc.org/articles/PMC9465559?pdf=render
 38763986,https://doi.org/10.1038/s41467-024-48568-8,Medical history predicts phenome-wide disease onset and enables the rapid response to emerging health threats.,"Steinfeldt J, Wild B, Buergel T, Pietzner M, Upmeier Zu Belzen J, Vauvelle A, Hegselmann S, Denaxas S, Hemingway H, Langenberg C, Landmesser U, Deanfield J, Eils R.",,Nature communications,2024,2024-05-20,Y,,,,"The COVID-19 pandemic exposed a global deficiency of systematic, data-driven guidance to identify high-risk individuals. Here, we illustrate the utility of routinely recorded medical history to predict the risk for 1883 diseases across clinical specialties and support the rapid response to emerging health threats such as COVID-19. We developed a neural network to learn from health records of 502,460 UK Biobank. Importantly, we observed discriminative improvements over basic demographic predictors for 1774 (94.3%) endpoints. After transferring the unmodified risk models to the All of US cohort, we replicated these improvements for 1347 (89.8%) of 1500 investigated endpoints, demonstrating generalizability across healthcare systems and historically underrepresented groups. Ultimately, we showed how this approach could have been used to identify individuals vulnerable to severe COVID-19. Our study demonstrates the potential of medical history to support guidance for emerging pandemics by systematically estimating risk for thousands of diseases at once at minimal cost.",,pdf:https://www.nature.com/articles/s41467-024-48568-8.pdf; doi:https://doi.org/10.1038/s41467-024-48568-8; html:https://europepmc.org/articles/PMC11102902; pdf:https://europepmc.org/articles/PMC11102902?pdf=render
 38330197,https://doi.org/10.7189/jogh.14.03006,Caveats in reporting of national vaccine uptake.,"Millington T, Morrison K, Jeffrey K, Sullivan C, Kurdi A, Fagbamigbe AF, Swallow B, Shi T, Shah SA, Kerr S, Simpson CR, Ritchie LD, Robertson C, Sheikh A, Rudan I.",,Journal of global health,2024,2024-02-09,Y,,,,,,doi:https://doi.org/10.7189/jogh.14.03006; html:https://europepmc.org/articles/PMC10852533; pdf:https://europepmc.org/articles/PMC10852533?pdf=render
-36691218,https://doi.org/10.1136/bmjopen-2021-059813,Evaluation of the shielding initiative in Wales (EVITE Immunity): protocol for a quasiexperimental study.,"Evans BA, Akbari A, Bailey R, Bethell L, Bufton S, Carson-Stevens A, Dixon L, Edwards A, John A, Jolles S, Kingston MR, Lyons J, Lyons R, Porter A, Sewell B, Thornton CA, Watkins A, Whiffen T, Snooks H.",,BMJ open,2022,2022-09-08,Y,immunology; Public Health; Health Policy; Covid-19,,,"<h4>Introduction</h4>Shielding aimed to protect those predicted to be at highest risk from COVID-19 and was uniquely implemented in the UK during the COVID-19 pandemic. Clinically extremely vulnerable people identified through algorithms and screening of routine National Health Service (NHS) data were individually and strongly advised to stay at home and strictly self-isolate even from others in their household. This study will generate a logic model of the intervention and evaluate the effects and costs of shielding to inform policy development and delivery during future pandemics.<h4>Methods and analysis</h4>This is a quasiexperimental study undertaken in Wales where records for people who were identified for shielding were already anonymously linked into integrated data systems for public health decision-making. We will: interview policy-makers to understand rationale for shielding advice to inform analysis and interpretation of results; use anonymised individual-level data to select people identified for shielding advice in March 2020 and a matched cohort, from routine electronic health data sources, to compare outcomes; survey a stratified random sample of each group about activities and quality of life at 12 months; use routine and newly collected blood data to assess immunity; interview people who were identified for shielding and their carers and NHS staff who delivered healthcare during shielding, to explore compliance and experiences; collect healthcare resource use data to calculate implementation costs and cost-consequences. Our team includes people who were shielding, who used their experience to help design and deliver this study.<h4>Ethics and dissemination</h4>The study has received approval from the Newcastle North Tyneside 2 Research Ethics Committee (IRAS 295050). We will disseminate results directly to UK government policy-makers, publish in peer-reviewed journals, present at scientific and policy conferences and share accessible summaries of results online and through public and patient networks.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/9/e059813.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-059813; html:https://europepmc.org/articles/PMC9461087; pdf:https://europepmc.org/articles/PMC9461087?pdf=render
 37034358,https://doi.org/10.1016/j.eclinm.2023.101932,Contextualising adverse events of special interest to characterise the baseline incidence rates in 24 million patients with COVID-19 across 26 databases: a multinational retrospective cohort study.,"Voss EA, Shoaibi A, Yin Hui Lai L, Blacketer C, Alshammari T, Makadia R, Haynes K, Sena AG, Rao G, van Sandijk S, Fraboulet C, Boyer L, Le Carrour T, Horban S, Morales DR, Martínez Roldán J, Ramírez-Anguita JM, Mayer MA, de Wilde M, John LH, Duarte-Salles T, Roel E, Pistillo A, Kolde R, Maljković F, Denaxas S, Papez V, Kahn MG, Natarajan K, Reich C, Secora A, Minty EP, Shah NH, Posada JD, Garcia Morales MT, Bosca D, Cadenas Juanino H, Diaz Holgado A, Pedrera Jiménez M, Serrano Balazote P, García Barrio N, Şen S, Üresin AY, Erdogan B, Belmans L, Byttebier G, Malbrain MLNG, Dedman DJ, Cuccu Z, Vashisht R, Butte AJ, Patel A, Dahm L, Han C, Bu F, Arshad F, Ostropolets A, Nyberg F, Hripcsak G, Suchard MA, Prieto-Alhambra D, Rijnbeek PR, Schuemie MJ, Ryan PB.",,EClinicalMedicine,2023,2023-04-04,Y,Observational Research; Omop Cdm; Covid-19; Adverse Events Of Special Interest,,,"<h4>Background</h4>Adverse events of special interest (AESIs) were pre-specified to be monitored for the COVID-19 vaccines. Some AESIs are not only associated with the vaccines, but with COVID-19. Our aim was to characterise the incidence rates of AESIs following SARS-CoV-2 infection in patients and compare these to historical rates in the general population.<h4>Methods</h4>A multi-national cohort study with data from primary care, electronic health records, and insurance claims mapped to a common data model. This study's evidence was collected between Jan 1, 2017 and the conclusion of each database (which ranged from Jul 2020 to May 2022). The 16 pre-specified prevalent AESIs were: acute myocardial infarction, anaphylaxis, appendicitis, Bell's palsy, deep vein thrombosis, disseminated intravascular coagulation, encephalomyelitis, Guillain- Barré syndrome, haemorrhagic stroke, non-haemorrhagic stroke, immune thrombocytopenia, myocarditis/pericarditis, narcolepsy, pulmonary embolism, transverse myelitis, and thrombosis with thrombocytopenia. Age-sex standardised incidence rate ratios (SIR) were estimated to compare post-COVID-19 to pre-pandemic rates in each of the databases.<h4>Findings</h4>Substantial heterogeneity by age was seen for AESI rates, with some clearly increasing with age but others following the opposite trend. Similarly, differences were also observed across databases for same health outcome and age-sex strata. All studied AESIs appeared consistently more common in the post-COVID-19 compared to the historical cohorts, with related meta-analytic SIRs ranging from 1.32 (1.05 to 1.66) for narcolepsy to 11.70 (10.10 to 13.70) for pulmonary embolism.<h4>Interpretation</h4>Our findings suggest all AESIs are more common after COVID-19 than in the general population. Thromboembolic events were particularly common, and over 10-fold more so. More research is needed to contextualise post-COVID-19 complications in the longer term.<h4>Funding</h4>None.",,doi:https://doi.org/10.1016/j.eclinm.2023.101932; doi:https://doi.org/10.1016/j.eclinm.2023.101932; html:https://europepmc.org/articles/PMC10072853; pdf:https://europepmc.org/articles/PMC10072853?pdf=render
+36691218,https://doi.org/10.1136/bmjopen-2021-059813,Evaluation of the shielding initiative in Wales (EVITE Immunity): protocol for a quasiexperimental study.,"Evans BA, Akbari A, Bailey R, Bethell L, Bufton S, Carson-Stevens A, Dixon L, Edwards A, John A, Jolles S, Kingston MR, Lyons J, Lyons R, Porter A, Sewell B, Thornton CA, Watkins A, Whiffen T, Snooks H.",,BMJ open,2022,2022-09-08,Y,immunology; Public Health; Health Policy; Covid-19,,,"<h4>Introduction</h4>Shielding aimed to protect those predicted to be at highest risk from COVID-19 and was uniquely implemented in the UK during the COVID-19 pandemic. Clinically extremely vulnerable people identified through algorithms and screening of routine National Health Service (NHS) data were individually and strongly advised to stay at home and strictly self-isolate even from others in their household. This study will generate a logic model of the intervention and evaluate the effects and costs of shielding to inform policy development and delivery during future pandemics.<h4>Methods and analysis</h4>This is a quasiexperimental study undertaken in Wales where records for people who were identified for shielding were already anonymously linked into integrated data systems for public health decision-making. We will: interview policy-makers to understand rationale for shielding advice to inform analysis and interpretation of results; use anonymised individual-level data to select people identified for shielding advice in March 2020 and a matched cohort, from routine electronic health data sources, to compare outcomes; survey a stratified random sample of each group about activities and quality of life at 12 months; use routine and newly collected blood data to assess immunity; interview people who were identified for shielding and their carers and NHS staff who delivered healthcare during shielding, to explore compliance and experiences; collect healthcare resource use data to calculate implementation costs and cost-consequences. Our team includes people who were shielding, who used their experience to help design and deliver this study.<h4>Ethics and dissemination</h4>The study has received approval from the Newcastle North Tyneside 2 Research Ethics Committee (IRAS 295050). We will disseminate results directly to UK government policy-makers, publish in peer-reviewed journals, present at scientific and policy conferences and share accessible summaries of results online and through public and patient networks.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/9/e059813.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-059813; html:https://europepmc.org/articles/PMC9461087; pdf:https://europepmc.org/articles/PMC9461087?pdf=render
 35266090,https://doi.org/10.1007/s12471-022-01677-9,The benefit of vaccination against COVID-19 outweighs the potential risk of myocarditis and pericarditis.,"Klamer TA, Linschoten M, Asselbergs FW.",,Netherlands heart journal : monthly journal of the Netherlands Society of Cardiology and the Netherlands Heart Foundation,2022,2022-03-09,Y,Side effect; Myocarditis; pericarditis; Covid-19; Coronavirus Disease 2019; Covid-19 Vaccination,,,"Vaccines against coronavirus 2019 disease (COVID-19) have shown to be greatly effective in preventing viral spread, serious illness and death from this infectious disease and are therefore critical for the management of the COVID-19 pandemic. However, the listing of myocarditis and pericarditis as possible rare side effects of the messenger RNA (mRNA) vaccines against COVID-19 by regulatory agencies has sparked discussion on the vaccines' safety. The most important published cohort studies to date demonstrat that myocarditis is a very rare side effect after COVID-19 mRNA vaccination, with an incidence of approximately 1-4 cases per 100,000 vaccinated persons. Young males (16-29 years) appear to be at highest risk, predominantly after receiving the second dose. The disease course is self-limiting in a vast majority of cases: 95% of patients show a rapid resolution of symptoms and normalisation of cardiac biomarkers, electro- and echocardiographic findings within days. Importantly, the available data suggest that the incidence rate of myocarditis in the context of COVID-19 is much greater than the risk of this side effect following vaccination. We conclude that the benefit of vaccination against COVID-19 outweighs the potential risk of myocarditis and pericarditis in both adolescents and adults. Prospective follow-up of patients who have developed these complications after vaccination is required to assess long-term outcomes.",,pdf:https://link.springer.com/content/pdf/10.1007/s12471-022-01677-9.pdf; doi:https://doi.org/10.1007/s12471-022-01677-9; html:https://europepmc.org/articles/PMC8906525; pdf:https://europepmc.org/articles/PMC8906525?pdf=render
 39379679,https://doi.org/10.1038/s43856-024-00625-5,Disease coverage of human genome-wide association studies and pharmaceutical research and development.,"Gordillo-Marañón M, Schmidt AF, Warwick A, Tomlinson C, Ytsma C, Engmann J, Torralbo A, Maclean R, Sofat R, Langenberg C, Shah AD, Denaxas S, Pirmohamed M, Hemingway H, Hingorani AD, Finan C.",,Communications medicine,2024,2024-10-08,Y,,,,"<h4>Background</h4>Despite the growing interest in the use of human genomic data for drug target identification and validation, the extent to which the spectrum of human disease has been addressed by genome-wide association studies (GWAS), or by drug development, and the degree to which these efforts overlap remain unclear.<h4>Methods</h4>In this study we harmonize and integrate different data sources to create a sample space of all the human drug targets and diseases and identify points of convergence or divergence of GWAS and drug development efforts.<h4>Results</h4>We show that only 612 of 11,158 diseases listed in Human Disease Ontology have an approved drug treatment in at least one region of the world. Of the 1414 diseases that are the subject of preclinical or clinical phase drug development, only 666 have been investigated in GWAS. Conversely, of the 1914 human diseases that have been the subject of GWAS, 1121 have yet to be investigated in drug development.<h4>Conclusions</h4>We produce target-disease indication lists to help the pharmaceutical industry to prioritize future drug development efforts based on genetic evidence, academia to prioritize future GWAS for diseases without effective treatments, and both sectors to harness genetic evidence to expand the indications for licensed drugs or to identify repurposing opportunities for clinical candidates that failed in their originally intended indication.",,doi:https://doi.org/10.1038/s43856-024-00625-5; doi:https://doi.org/10.1038/s43856-024-00625-5; html:https://europepmc.org/articles/PMC11461613; pdf:https://europepmc.org/articles/PMC11461613?pdf=render
 38693557,https://doi.org/10.1186/s12913-024-10931-2,The cost of keeping patients waiting: retrospective treatment-control study of additional healthcare utilisation for UK patients awaiting elective treatment.,"James C, Denholm R, Wood R.",,BMC health services research,2024,2024-04-30,Y,Utilisation; Waiting Times; Waitlist; Elective Recovery; Failure-demand,,,"<h4>Objective</h4>Long waiting times for elective hospital treatments are common in many countries. This study seeks to address a deficit in the literature concerning the effect of long waits on the wider consumption of healthcare resources.<h4>Methods</h4>We carried out a retrospective treatment-control study in a healthcare system in South West England from 15 June 2021 to 15 December 2021. We compared weekly contacts with health services of patients waiting over 18 weeks for treatment ('Treatments') and people not on a waiting list ('Controls'). Controls were matched to Treatments based on age, sex, deprivation and multimorbidity. Treatments were stratified by the clinical specialty of the awaited hospital treatment, with healthcare usage assessed over various healthcare settings. Wilcoxon signed-rank tests assessed whether there was an increase in healthcare utilisation and bootstrap resampling was used to estimate the magnitude of any differences.<h4>Results</h4>A total of 44,616 patients were waiting over 18 weeks (the constitutional target in England) for treatment during the study period. There was an increase (p < 0.0004) in healthcare utilisation for all specialties. Patients in the Cardiothoracic Surgery specialty had the largest increase, with 17.9 [interquartile-range: 4.3, 33.8] additional contacts with secondary care and 17.3 [-1.1, 34.1] additional prescriptions per year.<h4>Conclusion</h4>People waiting for treatment consume higher levels of healthcare than comparable individuals not on a waiting list. These findings are relevant for clinicians and managers in better understanding patient need and reducing harm. Results also highlight the possible 'false economy' in failing to promptly resolve long elective waits.",,doi:https://doi.org/10.1186/s12913-024-10931-2; html:https://europepmc.org/articles/PMC11061904; pdf:https://europepmc.org/articles/PMC11061904?pdf=render
-35538704,https://doi.org/10.1177/1357633x221093434,"The development, validation and application of remote blood sample collection in telehealth programmes.","Koulman A, Rennie KL, Parkington D, Tyrrell CS, Catt M, Gkrania-Klotsas E, Wareham NJ.",,Journal of telemedicine and telecare,2024,2022-05-10,Y,Pathology; Self-care; Telehealth; Blood Sampling; Home Telecare,,,"<h4>Introduction</h4>The ability to collect blood samples remotely without the involvement of healthcare professionals is a key element of future telehealth applications. We developed and validated the application of the Drawbridge OneDraw device for use at home for blood sample collection. The device was then applied in a large population-based remote monitoring study to assess changes in SARS-CoV-2 IgG antibody levels.<h4>Methods</h4>We tested: (1) feasibility of participants using the device at home without a healthcare professional on the upper arm and thigh sites (2) stability of the dried blood sample collected remotely (3) participant acceptability of the device compared with finger-prick and venous blood samples and the validity of SARS-CoV-2 virus antibody measurement versus venous blood sample (4) application to the Fenland COVID-19 study in which 4023 participants at 3 timepoints across 6 months.<h4>Results</h4>Participant acceptability was high, with a significantly lower median perceived pain score and 76% of participants preferring the OneDraw device over the other blood collection methods. There was high level of agreement in SARS-CoV-2 virus antibody results with venous blood samples in 120 participants (Cohen's kappa 0.68 (95% CI 0.56, 0.83). In the Fenland COVID-19 study, 92% of participants returned a sample at baseline (3702/4023), 89% at 3 months (3492/3918) and 93% at 6 months (3453/3731), with almost all samples received successfully processed (99.9%).<h4>Discussion</h4>The OneDraw device enables a standardised blood sample collection at home by participants themselves. Due to its ease-of-use and acceptability the OneDraw device is particularly useful in telehealth approaches where multiple samples need to be collected.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/1357633X221093434; doi:https://doi.org/10.1177/1357633X221093434; html:https://europepmc.org/articles/PMC11027437; pdf:https://europepmc.org/articles/PMC11027437?pdf=render
 34911741,https://doi.org/10.1136/heartjnl-2021-320047,Impact of cardiometabolic multimorbidity and ethnicity on cardiovascular/renal complications in patients with COVID-19.,"Norris T, Razieh C, Zaccardi F, Yates T, Islam N, Gillies CL, Chudasama YV, Rowlands AV, Davies MJ, McCann GP, Banerjee A, Lam CSP, Docherty AB, Openshaw PJ, Baillie JK, Semple MG, Lawson CA, Khunti K, ISARIC4C investigators.",,Heart (British Cardiac Society),2022,2022-07-13,Y,epidemiology; risk factors; Covid-19,,,"<h4>Objective</h4>Using a large national database of people hospitalised with COVID-19, we investigated the contribution of cardio-metabolic conditions, multi-morbidity and ethnicity on the risk of in-hospital cardiovascular complications and death.<h4>Methods</h4>A multicentre, prospective cohort study in 302 UK healthcare facilities of adults hospitalised with COVID-19 between 6 February 2020 and 16 March 2021. Logistic models were used to explore associations between baseline patient ethnicity, cardiometabolic conditions and multimorbidity (0, 1, 2, >2 conditions), and in-hospital cardiovascular complications (heart failure, arrhythmia, cardiac ischaemia, cardiac arrest, coagulation complications, stroke), renal injury and death.<h4>Results</h4>Of 65 624 patients hospitalised with COVID-19, 44 598 (68.0%) reported at least one cardiometabolic condition on admission. Cardiovascular/renal complications or death occurred in 24 609 (38.0%) patients. Baseline cardiometabolic conditions were independently associated with increased odds of in-hospital complications and this risk increased in the presence of cardiometabolic multimorbidity. For example, compared with having no cardiometabolic conditions, 1, 2 or ≥3 conditions was associated with 1.46 (95% CI 1.39 to 1.54), 2.04 (95% CI 1.93 to 2.15) and 3.10 (95% CI 2.92 to 3.29) times higher odds of any cardiovascular/renal complication, respectively. A similar pattern was observed for all-cause death. Compared with the white group, the South Asian (OR 1.19, 95% CI 1.10 to 1.29) and black (OR 1.53 to 95% CI 1.37 to 1.72) ethnic groups had higher risk of any cardiovascular/renal complication.<h4>Conclusions</h4>In hospitalised patients with COVID-19, cardiovascular complications or death impacts just under half of all patients, with the highest risk in those of South Asian or Black ethnicity and in patients with cardiometabolic multimorbidity.",,pdf:https://heart.bmj.com/content/heartjnl/108/15/1200.full.pdf; doi:https://doi.org/10.1136/heartjnl-2021-320047; html:https://europepmc.org/articles/PMC8678560; pdf:https://europepmc.org/articles/PMC8678560?pdf=render
+35538704,https://doi.org/10.1177/1357633x221093434,"The development, validation and application of remote blood sample collection in telehealth programmes.","Koulman A, Rennie KL, Parkington D, Tyrrell CS, Catt M, Gkrania-Klotsas E, Wareham NJ.",,Journal of telemedicine and telecare,2024,2022-05-10,Y,Pathology; Self-care; Telehealth; Blood Sampling; Home Telecare,,,"<h4>Introduction</h4>The ability to collect blood samples remotely without the involvement of healthcare professionals is a key element of future telehealth applications. We developed and validated the application of the Drawbridge OneDraw device for use at home for blood sample collection. The device was then applied in a large population-based remote monitoring study to assess changes in SARS-CoV-2 IgG antibody levels.<h4>Methods</h4>We tested: (1) feasibility of participants using the device at home without a healthcare professional on the upper arm and thigh sites (2) stability of the dried blood sample collected remotely (3) participant acceptability of the device compared with finger-prick and venous blood samples and the validity of SARS-CoV-2 virus antibody measurement versus venous blood sample (4) application to the Fenland COVID-19 study in which 4023 participants at 3 timepoints across 6 months.<h4>Results</h4>Participant acceptability was high, with a significantly lower median perceived pain score and 76% of participants preferring the OneDraw device over the other blood collection methods. There was high level of agreement in SARS-CoV-2 virus antibody results with venous blood samples in 120 participants (Cohen's kappa 0.68 (95% CI 0.56, 0.83). In the Fenland COVID-19 study, 92% of participants returned a sample at baseline (3702/4023), 89% at 3 months (3492/3918) and 93% at 6 months (3453/3731), with almost all samples received successfully processed (99.9%).<h4>Discussion</h4>The OneDraw device enables a standardised blood sample collection at home by participants themselves. Due to its ease-of-use and acceptability the OneDraw device is particularly useful in telehealth approaches where multiple samples need to be collected.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/1357633X221093434; doi:https://doi.org/10.1177/1357633X221093434; html:https://europepmc.org/articles/PMC11027437; pdf:https://europepmc.org/articles/PMC11027437?pdf=render
 38360481,https://doi.org/10.1016/j.ebiom.2024.105000,Phenome-wide analysis reveals epistatic associations between APOL1 variants and chronic kidney disease and multiple other disorders.,"Adamson WE, Noyes H, Johnson P, Cooper A, Monckton DG, Ogunsola J, Beckett-Hill G, Sullivan M, Mark P, Parekh RS, MacLeod A.",,EBioMedicine,2024,2024-02-14,Y,Chronic Kidney Disease; Phenome; Apol1; Uk Biobank; Covid-19,,,"<h4>Background</h4>APOL1 variants G1 and G2 are common in populations with recent African ancestry. They are associated with protection from African sleeping sickness, however homozygosity or compound heterozygosity for these variants is associated with chronic kidney disease (CKD) and related conditions. What is not clear is the extent of associations with non-kidney-related disorders, and whether there are clusters of diseases associated with individual APOL1 genotypes.<h4>Methods</h4>Using a cohort of 7462 UK Biobank participants with recent African ancestry, we conducted a phenome-wide association study investigating associations between individual APOL1 genotypes and conditions identified by the International Classification of Disease phenotypes.<h4>Findings</h4>We identified 27 potential associations between individual APOL1 genotypes and a diverse range of conditions. G1/G2 compound heterozygotes were specifically associated with 26 of these conditions (all deleteriously), with an over-representation of infectious diseases (including hospitalisation and death resulting from COVID-19). The analysis also exposed complexities in the relationship between APOL1 and CKD that are not evident when risk variants are grouped together: G1 homozygosity, G2 homozygosity, and G1/G2 compound heterozygosity were each shown to be associated with distinct CKD phenotypes. The multi-locus nature of the G1/G2 genotype means that its associations would go undetected in a standard genome-wide association study.<h4>Interpretation</h4>Our findings have implications for understanding health risks and better-targeted detection, intervention, and therapeutic strategies, particularly in populations where APOL1 G1 and G2 are common such as in sub-Saharan Africa and its diaspora.<h4>Funding</h4>This study was funded by the Wellcome Trust (209511/Z/17/Z) and H3Africa (H3A/18/004).",,doi:https://doi.org/10.1016/j.ebiom.2024.105000; html:https://europepmc.org/articles/PMC10944146; pdf:https://europepmc.org/articles/PMC10944146?pdf=render
 35024157,https://doi.org/10.1177/20552076211059350,Digitally enabled flash glucose monitoring for inpatients with COVID-19: Feasibility and pilot implementation in a teaching NHS Hospital in the UK.,"Robbins T, Hopper A, Brophy J, Pearson E, Suthantirakumar R, Vankad M, Igharo N, Baitule S, Clark CC, Arvanitis TN, Sankar S, Kyrou I, Randeva H.",,Digital health,2022,2022-01-07,Y,Diabetes; Inpatient Care; Digital Health; Flash Glucose Monitoring; Covid-19,,,"<h4>Background</h4>COVID-19 placed significant challenges on healthcare systems. People with diabetes are at high risk of severe COVID-19 with poor outcomes. We describe the first reported use of inpatient digital flash glucose monitoring devices in a UK NHS hospital to support management of people with diabetes hospitalized for COVID-19.<h4>Methods</h4>Inpatients at University Hospitals Coventry & Warwickshire (UHCW) NHS Trust with COVID-19 and diabetes were considered for digitally enabled flash glucose monitoring during their hospitalization. Glucose monitoring data were analysed, and potential associations were explored between relevant parameters, including time in hypoglycaemia, hyperglycaemia, and in range, glycated haemoglobin (HbA1c), average glucose, body mass index (BMI), and length of stay.<h4>Results</h4>During this pilot, digital flash glucose monitoring devices were offered to 25 inpatients, of whom 20 (type 2/type 1: 19/1; mean age: 70.6 years; mean HbA1c: 68.2 mmol/mol; mean BMI: 28.2 kg/m<sup>2</sup>) accepted and used these (80% uptake). In total, over 2788 h of flash glucose monitoring were recorded for these inpatients with COVID-19 and diabetes. Length of stay was not associated with any of the studied variables (all p-values >0.05). Percentage of time in hyperglycaemia exhibited significant associations with both percentage of time in hypoglycaemia and percentage of time in range, as well as with HbA1c (all p-values <0.05). The average glucose was significantly associated with percentage of time in hypoglycaemia, percentage of time in range, and HbA1c (all p-values <0.05).<h4>Discussion</h4>We report the first pilot inpatient use of digital flash glucose monitors in an NHS hospital to support care of inpatients with diabetes and COVID-19. Overall, there are strong arguments for the inpatient use of these devices in the COVID-19 setting, and the findings of this pilot demonstrate feasibility of this digitally enabled approach and support wider use for inpatients with diabetes and COVID-19.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/20552076211059350; doi:https://doi.org/10.1177/20552076211059350; html:https://europepmc.org/articles/PMC8744149; pdf:https://europepmc.org/articles/PMC8744149?pdf=render
-37674175,https://doi.org/10.1186/s12884-023-05958-y,Using the COM-B framework to elucidate facilitators and barriers to COVID-19 vaccine uptake in pregnant women: a qualitative study.,"Patterson L, Berry E, Parsons C, Clarke B, Little A, Beggs J, Chuter A, Jackson T, Hsia Y, McGrath H, Millman C, Murphy S, Bradley DT, Milligan S.",,BMC pregnancy and childbirth,2023,2023-09-06,Y,Pregnancy; Qualitative; Barriers; Facilitators; Com-b; Covid-19 Vaccination,,,"Since April 2021, COVID-19 vaccines have been recommended for pregnant women. Despite this, COVID-19 vaccine uptake in this group is low compared to the non-pregnant population of childbearing age. Our aim was to understand barriers and facilitators to COVID-19 vaccine uptake among pregnant women in Northern Ireland using the COM-B framework, and so to make recommendations for public health interventions. The COM-B proposes that human behaviour is influenced by the extent to which a person has the capability, opportunity, and motivation to enact that behaviour. Understanding the factors underpinning behaviour through this lens helps discern what needs to change to change behaviour, therefore supporting the development of targeted interventions.This study consisted of eight semi-structured interviews with new/expectant mothers who did not receive a COVID-19 vaccine dose while pregnant since April 2021, and a focus group with five participants who received at least one COVID-19 vaccine dose while pregnant. Interview and focus group data were analysed using semi-deductive reflexive thematic analysis framed by a subtle realist approach. The COM-B was used to categorise codes and subthemes were developed within each COM-B construct.Within Psychological Capability, subthemes captured the need for consistent and reliable COVID-19 vaccine information and access to balanced and jargon-free, risk-benefit information that is tailored to the pregnant individual. The behaviour/opinions of family, friends, and local healthcare providers had a powerful influence on COVID-19 vaccine decisions (Social Opportunity). Integrating the COVID-19 vaccine as part of routine antenatal pathways was believed to support access and sense of familiarity (Physical Opportunity). Participants valued health autonomy, however experienced internal conflict driven by concerns about long-term side effects for their baby (Reflective Motivation). Feelings of fear, lack of empathy from healthcare providers, and anticipated guilt commonly underpinned indecision as to whether to get the vaccine (Automatic Motivation).Our study highlighted that the choice to accept a vaccine during pregnancy generates internal conflict and worry. Several participants cited their concern was primarily around the safety for their baby. Healthcare professionals (HCPs) play a significant part when it comes to decision making about COVID-19 vaccines among pregnant women. HCPs and pregnant women should be involved in the development of interventions to improve the delivery and communication of information.",,pdf:https://bmcpregnancychildbirth.biomedcentral.com/counter/pdf/10.1186/s12884-023-05958-y; doi:https://doi.org/10.1186/s12884-023-05958-y; html:https://europepmc.org/articles/PMC10481472; pdf:https://europepmc.org/articles/PMC10481472?pdf=render
 38251486,https://doi.org/10.1016/s2665-9913(23)00206-0,"Gout incidence and management during the COVID-19 pandemic in England, UK: a nationwide observational study using OpenSAFELY.","Russell MD, Massey J, Roddy E, MacKenna B, Bacon S, Goldacre B, Andrews CD, Hickman G, Mehrkar A, Mahto A, Rutherford AI, Patel S, Adas MA, Alveyn E, Nagra D, Bechman K, Ledingham JM, Hudson J, Norton S, Cope AP, Galloway JB.",,The Lancet. Rheumatology,2023,2023-08-31,Y,,,,"<h4>Background</h4>Gout is the most prevalent inflammatory arthritis, yet one of the worst managed. Our objective was to assess how the COVID-19 pandemic impacted incidence and quality of care for people with gout in England, UK.<h4>Methods</h4>With the approval of National Health Service England, we did a population-level cohort study using primary care and hospital electronic health record data for 17·9 million adults registered with general practices using TPP health record software, via the OpenSAFELY platform. The study period was from March 1, 2015, to Feb 28, 2023. Individuals aged 18-110 years were defined as having incident gout if they were assigned index diagnostic codes for gout, were registered with TPP practices in England for at least 12 months before diagnosis, did not receive prescriptions for urate-lowering therapy more than 30 days before diagnosis, and had not been admitted to hospital or attended an emergency department for gout flares more than 30 days before diagnosis. Outcomes assessed were incidence and prevalence of people with recorded gout diagnoses, incidence of gout hospitalisations, initiation of urate-lowering therapy, and attainment of serum urate targets (≤360 μmol/L).<h4>Findings</h4>From a reference population of 17 865 145 adults, 246 695 individuals were diagnosed with incident gout. The mean age of individuals with incident gout was 61·3 years (SD 16·2). 66 265 (26·9%) of 246 695 individuals were female, 180 430 (73·1%) were male, and 189 035 (90·9%) of 208 050 individuals with available ethnicity data were White. Incident gout diagnoses decreased by 30·9% in the year beginning March, 2020, compared with the preceding year (1·23 diagnoses vs 1·78 diagnoses per 1000 adults). Gout prevalence was 3·07% in 2015-16, and 3·21% in 2022-23. Gout hospitalisations decreased by 30·1% in the year commencing March, 2020, compared with the preceding year (9·6 admissions vs 13·7 admissions per 100 000 adults). Of 228 095 people with incident gout and available follow-up, 66 560 (29·2%) were prescribed urate-lowering therapy within 6 months. Of 65 305 individuals who initiated urate-lowering therapy with available follow-up, 16 790 (25·7%) attained a serum urate concentration of 360 μmol/L or less within 6 months of urate-lowering therapy initiation. In interrupted time-series analyses, urate-lowering therapy prescribing improved modestly during the pandemic, compared with pre-pandemic, whereas urate target attainment was similar.<h4>Interpretation</h4>Using gout as an exemplar disease, we showed the complexity of how health care was impacted during the COVID-19 pandemic. We observed a reduction in gout diagnoses but no effect on treatment metrics. We showed how country-wide, routinely collected data can be used to map disease epidemiology and monitor care quality.<h4>Funding</h4>None.",,pdf:http://www.thelancet.com/article/S2665991323002060/pdf; doi:https://doi.org/10.1016/S2665-9913(23)00206-0; html:https://europepmc.org/articles/PMC7616140; pdf:https://europepmc.org/articles/PMC7616140?pdf=render
+37674175,https://doi.org/10.1186/s12884-023-05958-y,Using the COM-B framework to elucidate facilitators and barriers to COVID-19 vaccine uptake in pregnant women: a qualitative study.,"Patterson L, Berry E, Parsons C, Clarke B, Little A, Beggs J, Chuter A, Jackson T, Hsia Y, McGrath H, Millman C, Murphy S, Bradley DT, Milligan S.",,BMC pregnancy and childbirth,2023,2023-09-06,Y,Pregnancy; Qualitative; Barriers; Facilitators; Com-b; Covid-19 Vaccination,,,"Since April 2021, COVID-19 vaccines have been recommended for pregnant women. Despite this, COVID-19 vaccine uptake in this group is low compared to the non-pregnant population of childbearing age. Our aim was to understand barriers and facilitators to COVID-19 vaccine uptake among pregnant women in Northern Ireland using the COM-B framework, and so to make recommendations for public health interventions. The COM-B proposes that human behaviour is influenced by the extent to which a person has the capability, opportunity, and motivation to enact that behaviour. Understanding the factors underpinning behaviour through this lens helps discern what needs to change to change behaviour, therefore supporting the development of targeted interventions.This study consisted of eight semi-structured interviews with new/expectant mothers who did not receive a COVID-19 vaccine dose while pregnant since April 2021, and a focus group with five participants who received at least one COVID-19 vaccine dose while pregnant. Interview and focus group data were analysed using semi-deductive reflexive thematic analysis framed by a subtle realist approach. The COM-B was used to categorise codes and subthemes were developed within each COM-B construct.Within Psychological Capability, subthemes captured the need for consistent and reliable COVID-19 vaccine information and access to balanced and jargon-free, risk-benefit information that is tailored to the pregnant individual. The behaviour/opinions of family, friends, and local healthcare providers had a powerful influence on COVID-19 vaccine decisions (Social Opportunity). Integrating the COVID-19 vaccine as part of routine antenatal pathways was believed to support access and sense of familiarity (Physical Opportunity). Participants valued health autonomy, however experienced internal conflict driven by concerns about long-term side effects for their baby (Reflective Motivation). Feelings of fear, lack of empathy from healthcare providers, and anticipated guilt commonly underpinned indecision as to whether to get the vaccine (Automatic Motivation).Our study highlighted that the choice to accept a vaccine during pregnancy generates internal conflict and worry. Several participants cited their concern was primarily around the safety for their baby. Healthcare professionals (HCPs) play a significant part when it comes to decision making about COVID-19 vaccines among pregnant women. HCPs and pregnant women should be involved in the development of interventions to improve the delivery and communication of information.",,pdf:https://bmcpregnancychildbirth.biomedcentral.com/counter/pdf/10.1186/s12884-023-05958-y; doi:https://doi.org/10.1186/s12884-023-05958-y; html:https://europepmc.org/articles/PMC10481472; pdf:https://europepmc.org/articles/PMC10481472?pdf=render
 34596018,https://doi.org/10.2807/1560-7917.es.2021.26.39.2001440,"Strategies to reduce the risk of SARS-CoV-2 importation from international travellers: modelling estimations for the United Kingdom, July 2020.","Clifford S, Quilty BJ, Russell TW, Liu Y, Chan YD, Pearson CAB, Eggo RM, Endo A, CMMID COVID-19 Working Group, Flasche S, Edmunds WJ, Centre for Mathematical Modelling of Infectious Diseases (CMMID) COVID-19 Working Group.",,Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin,2021,2021-09-01,Y,Quarantine; Pcr Testing; Travel Screening; Covid-19; Sars-cov-2,,,"BackgroundTo mitigate SARS-CoV-2 transmission risks from international air travellers, many countries implemented a combination of up to 14 days of self-quarantine upon arrival plus PCR testing in the early stages of the COVID-19 pandemic in 2020.AimTo assess the effectiveness of quarantine and testing of international travellers to reduce risk of onward SARS-CoV-2 transmission into a destination country in the pre-COVID-19 vaccination era.MethodsWe used a simulation model of air travellers arriving in the United Kingdom from the European Union or the United States, incorporating timing of infection stages while varying quarantine duration and timing and number of PCR tests.ResultsQuarantine upon arrival with a PCR test on day 7 plus a 1-day delay for results can reduce the number of infectious arriving travellers released into the community by a median 94% (95% uncertainty interval (UI): 89-98) compared with a no quarantine/no test scenario. This reduction is similar to that achieved by a 14-day quarantine period (median > 99%; 95% UI: 98-100). Even shorter quarantine periods can prevent a substantial amount of transmission; all strategies in which travellers spend at least 5 days (mean incubation period) in quarantine and have at least one negative test before release are highly effective (median reduction 89%; 95% UI: 83-95)).ConclusionThe effect of different screening strategies impacts asymptomatic and symptomatic individuals differently. The choice of an optimal quarantine and testing strategy for unvaccinated air travellers may vary based on the number of possible imported infections relative to domestic incidence.",,pdf:https://www.eurosurveillance.org/deliver/fulltext/eurosurveillance/26/39/eurosurv-26-39-5.pdf?itemId=%2Fcontent%2F10.2807%2F1560-7917.ES.2021.26.39.2001440&mimeType=pdf&containerItemId=content/eurosurveillance; doi:https://doi.org/10.2807/1560-7917.ES.2021.26.39.2001440; html:https://europepmc.org/articles/PMC8485583; pdf:https://europepmc.org/articles/PMC8485583?pdf=render
 33560344,https://doi.org/10.1210/clinem/dgab067,Association of Metformin with Susceptibility to COVID-19 in People with Type 2 Diabetes.,"Wang J, Cooper JM, Gokhale K, Acosta-Mena D, Dhalla S, Byne N, Chandan JS, Anand A, Okoth K, Subramanian A, Bangash MN, Jackson T, Zemedikun D, Taverner T, Hanif W, Ghosh S, Narendran P, Toulis KA, Tahrani AA, Surenthirakumaran R, Adderley NJ, Haroon S, Khunti K, Sainsbury C, Thomas GN, Nirantharakumar K.",,The Journal of clinical endocrinology and metabolism,2021,2021-04-01,Y,Type 2 diabetes mellitus; Metformin; Covid-19; Sars-cov-2 Infection,,,"<h4>Objective</h4>Diabetes has emerged as an important risk factor for mortality from COVID-19. Metformin, the most commonly prescribed glucose-lowering agent, has been proposed to influence susceptibility to and outcomes of COVID-19 via multiple mechanisms. We investigated whether, in patients with diabetes, metformin is associated with susceptibility to COVID-19 and its outcomes.<h4>Research design and methods</h4>We performed a propensity score-matched cohort study with active comparators using a large UK primary care dataset. Adults with type 2 diabetes patients and a current prescription for metformin and other glucose-lowering agents (MF+) were compared to those with a current prescription for glucose-lowering agents that did not include metformin (MF-). Outcomes were confirmed COVID-19, suspected/confirmed COVID-19, and associated mortality. A negative control outcome analysis (back pain) was also performed.<h4>Results</h4>There were 29 558 and 10 271 patients in the MF+ and MF- groups, respectively, who met the inclusion criteria. In the propensity score-matched analysis, the adjusted hazard ratios for suspected/confirmed COVID-19, confirmed COVID-19, and COVID-19-related mortality were 0.85 (95% CI 0.67, 1.08), 0.80 (95% CI 0.49, 1.30), and 0.87 (95% CI 0.34, 2.20) respectively. The negative outcome control analysis did not suggest unobserved confounding.<h4>Conclusion</h4>Current prescription of metformin was not associated with the risk of COVID-19 or COVID-19-related mortality. It is safe to continue prescribing metformin to improve glycemic control in patients with.",,pdf:https://academic.oup.com/jcem/article-pdf/106/5/1255/41848481/dgab067.pdf; doi:https://doi.org/10.1210/clinem/dgab067; html:https://europepmc.org/articles/PMC7928949
 37498081,https://doi.org/10.7554/elife.84673,Eleven key measures for monitoring general practice clinical activity during COVID-19: A retrospective cohort study using 48 million adults' primary care records in England through OpenSAFELY.,"Fisher L, Curtis HJ, Croker R, Wiedemann M, Speed V, Wood C, Brown A, Hopcroft LEM, Higgins R, Massey J, Inglesby P, Morton CE, Walker AJ, Morley J, Mehrkar A, Bacon S, Hickman G, Macdonald O, Lewis T, Wood M, Myers M, Samuel M, Conibere R, Baqir W, Sood H, Drury C, Collison K, Bates C, Evans D, Dillingham I, Ward T, Davy S, Smith RM, Hulme W, Green A, Parry J, Hester F, Harper S, Cockburn J, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Griffiths P, Fowles A, Parkes N, MacKenna B, Goldacre B.",,eLife,2023,2023-07-27,Y,Human; epidemiology; Public Health; Primary Care; Global Health; Health Informatics,,,"<h4>Background</h4>The COVID-19 pandemic has had a significant impact on delivery of NHS care. We have developed the OpenSAFELY Service Restoration Observatory (SRO) to develop key measures of primary care activity and describe the trends in these measures throughout the COVID-19 pandemic.<h4>Methods</h4>With the approval of NHS England, we developed an open source software framework for data management and analysis to describe trends and variation in clinical activity across primary care electronic health record (EHR) data on 48 million adults.We developed SNOMED-CT codelists for key measures of primary care clinical activity such as blood pressure monitoring and asthma reviews, selected by an expert clinical advisory group and conducted a population cohort-based study to describe trends and variation in these measures January 2019-December 2021, and pragmatically classified their level of recovery one year into the pandemic using the percentage change in the median practice level rate.<h4>Results</h4>We produced 11 measures reflective of clinical activity in general practice. A substantial drop in activity was observed in all measures at the outset of the COVID-19 pandemic. By April 2021, the median rate had recovered to within 15% of the median rate in April 2019 in six measures. The remaining measures showed a sustained drop, ranging from a 18.5% reduction in medication reviews to a 42.0% reduction in blood pressure monitoring. Three measures continued to show a sustained drop by December 2021.<h4>Conclusions</h4>The COVID-19 pandemic was associated with a substantial change in primary care activity across the measures we developed, with recovery in most measures. We delivered an open source software framework to describe trends and variation in clinical activity across an unprecedented scale of primary care data. We will continue to expand the set of key measures to be routinely monitored using our publicly available NHS OpenSAFELY SRO dashboards with near real-time data.<h4>Funding</h4>This research used data assets made available as part of the Data and Connectivity National Core Study, led by Health Data Research UK in partnership with the Office for National Statistics and funded by UK Research and Innovation (grant ref MC_PC_20058).The OpenSAFELY Platform is supported by grants from the Wellcome Trust (222097/Z/20/Z); MRC (MR/V015757/1, MC_PC-20059, MR/W016729/1); NIHR (NIHR135559, COV-LT2-0073), and Health Data Research UK (HDRUK2021.000, 2021.0157).",,doi:https://doi.org/10.7554/eLife.84673; html:https://europepmc.org/articles/PMC10374277; pdf:https://europepmc.org/articles/PMC10374277?pdf=render
-32735547,https://doi.org/10.2196/20169,Can Robots Improve Testing Capacity for SARS-CoV-2?,"Cresswell K, Ramalingam S, Sheikh A.",,Journal of medical Internet research,2020,2020-08-12,Y,Virus; Infectious disease; Testing; Robotics; Pandemic; Covid-19; Sars-cov-2,,,"There is currently increasing interest internationally in deploying robotic applications for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing, as these can help to reduce the risk of transmission of the virus to health care staff and patients. We provide an overview of key recent developments in this area. We argue that, although there is some potential for deploying robots to help with SARS-CoV-2 testing, the potential of patient-facing applications is likely to be limited. This is due to the high costs associated with patient-facing functionality, and risks of potentially adverse impacts on health care staff work practices and patient interactions. In contrast, back-end laboratory-based robots dealing with sample extraction and amplification, that effectively integrate with established processes, software, and interfaces to process samples, are much more likely to result in safety and efficiency gains. Consideration should therefore be given to deploying these at scale.",,pdf:https://www.jmir.org/2020/8/e20169/PDF; doi:https://doi.org/10.2196/20169; html:https://europepmc.org/articles/PMC7450371
 34056579,https://doi.org/10.3389/frai.2021.652669,"The Promise of AI in Detection, Diagnosis, and Epidemiology for Combating COVID-19: Beyond the Hype.","Abdulkareem M, Petersen SE.",,Frontiers in artificial intelligence,2021,2021-05-14,Y,Artificial intelligence; Detection; Diagnosis; Medical imaging; epidemiology; Contact tracing; Social Control; Covid-19,,,"COVID-19 has created enormous suffering, affecting lives, and causing deaths. The ease with which this type of coronavirus can spread has exposed weaknesses of many healthcare systems around the world. Since its emergence, many governments, research communities, commercial enterprises, and other institutions and stakeholders around the world have been fighting in various ways to curb the spread of the disease. Science and technology have helped in the implementation of policies of many governments that are directed toward mitigating the impacts of the pandemic and in diagnosing and providing care for the disease. Recent technological tools, artificial intelligence (AI) tools in particular, have also been explored to track the spread of the coronavirus, identify patients with high mortality risk and diagnose patients for the disease. In this paper, areas where AI techniques are being used in the detection, diagnosis and epidemiological predictions, forecasting and social control for combating COVID-19 are discussed, highlighting areas of successful applications and underscoring issues that need to be addressed to achieve significant progress in battling COVID-19 and future pandemics. Several AI systems have been developed for diagnosing COVID-19 using medical imaging modalities such as chest CT and X-ray images. These AI systems mainly differ in their choices of the algorithms for image segmentation, classification and disease diagnosis. Other AI-based systems have focused on predicting mortality rate, long-term patient hospitalization and patient outcomes for COVID-19. AI has huge potential in the battle against the COVID-19 pandemic but successful practical deployments of these AI-based tools have so far been limited due to challenges such as limited data accessibility, the need for external evaluation of AI models, the lack of awareness of AI experts of the regulatory landscape governing the deployment of AI tools in healthcare, the need for clinicians and other experts to work with AI experts in a multidisciplinary context and the need to address public concerns over data collection, privacy, and protection. Having a dedicated team with expertise in medical data collection, privacy, access and sharing, using federated learning whereby AI scientists hand over training algorithms to the healthcare institutions to train models locally, and taking full advantage of biomedical data stored in biobanks can alleviate some of problems posed by these challenges. Addressing these challenges will ultimately accelerate the translation of AI research into practical and useful solutions for combating pandemics.",,doi:https://doi.org/10.3389/frai.2021.652669; doi:https://doi.org/10.3389/frai.2021.652669; html:https://europepmc.org/articles/PMC8160471; pdf:https://europepmc.org/articles/PMC8160471?pdf=render
+32735547,https://doi.org/10.2196/20169,Can Robots Improve Testing Capacity for SARS-CoV-2?,"Cresswell K, Ramalingam S, Sheikh A.",,Journal of medical Internet research,2020,2020-08-12,Y,Virus; Infectious disease; Testing; Robotics; Pandemic; Covid-19; Sars-cov-2,,,"There is currently increasing interest internationally in deploying robotic applications for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing, as these can help to reduce the risk of transmission of the virus to health care staff and patients. We provide an overview of key recent developments in this area. We argue that, although there is some potential for deploying robots to help with SARS-CoV-2 testing, the potential of patient-facing applications is likely to be limited. This is due to the high costs associated with patient-facing functionality, and risks of potentially adverse impacts on health care staff work practices and patient interactions. In contrast, back-end laboratory-based robots dealing with sample extraction and amplification, that effectively integrate with established processes, software, and interfaces to process samples, are much more likely to result in safety and efficiency gains. Consideration should therefore be given to deploying these at scale.",,pdf:https://www.jmir.org/2020/8/e20169/PDF; doi:https://doi.org/10.2196/20169; html:https://europepmc.org/articles/PMC7450371
 38939225,https://doi.org/10.3389/fpsyg.2024.1395668,Social media users' attitudes toward cyberbullying during the COVID-19 pandemic: associations with gender and verification status.,"Li L, Zhou J, McManus S, Stewart R, Roberts A.",,Frontiers in psychology,2024,2024-06-13,Y,Gender; Emotional Responses; Cyberbullying; Covid; Verification Status,,,"<h4>Introduction</h4>Social media platforms such as Twitter and Weibo facilitate both positive and negative communication, including cyberbullying. Empirical evidence has revealed that cyberbullying increases when public crises occur, that such behavior is gendered, and that social media user account verification may deter it. However, the association of gender and verification status with cyberbullying is underexplored. This study aims to address this gap by examining how Weibo users' gender, verification status, and expression of affect and anger in posts influence cyberbullying attitudes. Specifically, it investigates how these factors differ between posts pro- and anti-cyberbullying of COVID-19 cases during the pandemic.<h4>Methods</h4>This study utilized social role theory, the Barlett and Gentile Cyberbullying Model, and general strain theory as theoretical frameworks. We applied text classification techniques to identify pro-cyberbullying and anti-cyberbullying posts on Weibo. Subsequently, we used a standardized mean difference method to compare the emotional content of these posts. Our analysis focused on the prevalence of affective and anger-related expressions, particularly examining variations across gender and verification status of the users.<h4>Results</h4>Our text classification identified distinct pro-cyberbullying and anti-cyberbullying posts. The standardized mean difference analysis revealed that pro-cyberbullying posts contained significantly more emotional content compared to anti-cyberbullying posts. Further, within the pro-cyberbullying category, posts by verified female users exhibited a higher frequency of anger-related words than those by other users.<h4>Discussion</h4>The findings from this study can enhance researchers' algorithms for identifying cyberbullying attitudes, refine the characterization of cyberbullying behavior using real-world social media data through the integration of the mentioned theories, and help government bodies improve their cyberbullying monitoring especially in the context of public health crises.",,pdf:https://www.frontiersin.org/journals/psychology/articles/10.3389/fpsyg.2024.1395668/pdf; doi:https://doi.org/10.3389/fpsyg.2024.1395668; html:https://europepmc.org/articles/PMC11210603; pdf:https://europepmc.org/articles/PMC11210603?pdf=render
 34376451,https://doi.org/10.1136/bmjopen-2021-048852,Ethnic and social inequalities in COVID-19 outcomes in Scotland: protocol for early pandemic evaluation and enhanced surveillance of COVID-19 (EAVE II).,"Henery P, Vasileiou E, Hainey KJ, Buchanan D, Harrison E, Leyland AH, Alexis T, Robertson C, Agrawal U, Ritchie L, Stock SJ, McCowan C, Docherty A, Kerr S, Marple J, Wood R, Moore E, Simpson CR, Sheikh A, Katikireddi SV.",,BMJ open,2021,2021-08-10,Y,epidemiology; Public Health; Protocols & Guidelines; Covid-19,,,"<h4>Introduction</h4>Evidence from previous pandemics, and the current COVID-19 pandemic, has found that risk of infection/severity of disease is disproportionately higher for ethnic minority groups, and those in lower socioeconomic positions. It is imperative that interventions to prevent the spread of COVID-19 are targeted towards high-risk populations. We will investigate the associations between social characteristics (such as ethnicity, occupation and socioeconomic position) and COVID-19 outcomes and the extent to which characteristics/risk factors might explain observed relationships in Scotland.The primary objective of this study is to describe the epidemiology of COVID-19 by social factors. Secondary objectives are to (1) examine receipt of treatment and prevention of COVID-19 by social factors; (2) quantify ethnic/social differences in adverse COVID-19 outcomes; (3) explore potential mediators of relationships between social factors and SARS-CoV-2 infection/COVID-19 prognosis; (4) examine whether occupational COVID-19 differences differ by other social factors and (5) assess quality of ethnicity coding within National Health Service datasets.<h4>Methods and analysis</h4>We will use a national cohort comprising the adult population of Scotland who completed the 2011 Census and were living in Scotland on 31 March 2020 (~4.3 million people). Census data will be linked to the Early Assessment of Vaccine and Anti-Viral Effectiveness II cohort consisting of primary/secondary care, laboratory data and death records. Sensitivity/specificity and positive/negative predictive values will be used to assess coding quality of ethnicity. Descriptive statistics will be used to examine differences in treatment and prevention of COVID-19. Poisson/Cox regression analyses and mediation techniques will examine ethnic and social differences, and drivers of inequalities in COVID-19. Effect modification (on additive and multiplicative scales) between key variables (such as ethnicity and occupation) will be assessed.<h4>Ethics and dissemination</h4>Ethical approval was obtained from the National Research Ethics Committee, South East Scotland 02. We will present findings of this study at international conferences, in peer-reviewed journals and to policy-makers.",,doi:https://doi.org/10.1136/bmjopen-2021-048852; doi:https://doi.org/10.1136/bmjopen-2021-048852; html:https://europepmc.org/articles/PMC8359861; pdf:https://europepmc.org/articles/PMC8359861?pdf=render
-32485082,https://doi.org/10.1002/ejhf.1924,Angiotensin-converting enzyme inhibitors and angiotensin II receptor blockers are not associated with severe COVID-19 infection in a multi-site UK acute hospital trust.,"Bean DM, Kraljevic Z, Searle T, Bendayan R, Kevin O, Pickles A, Folarin A, Roguski L, Noor K, Shek A, Zakeri R, Shah AM, Teo JTH, Dobson RJB.",,European journal of heart failure,2020,2020-06-01,Y,Hypertension; Angiotensin-converting enzyme inhibitors; Disease Outcome; Covid-19,,,"<h4>Aims</h4>The SARS-CoV-2 virus binds to the angiotensin-converting enzyme 2 (ACE2) receptor for cell entry. It has been suggested that angiotensin-converting enzyme inhibitors (ACEi) and angiotensin II receptor blockers (ARB), which are commonly used in patients with hypertension or diabetes and may raise tissue ACE2 levels, could increase the risk of severe COVID-19 infection.<h4>Methods and results</h4>We evaluated this hypothesis in a consecutive cohort of 1200 acute inpatients with COVID-19 at two hospitals with a multi-ethnic catchment population in London (UK). The mean age was 68 ± 17 years (57% male) and 74% of patients had at least one comorbidity. Overall, 415 patients (34.6%) reached the primary endpoint of death or transfer to a critical care unit for organ support within 21 days of symptom onset. A total of 399 patients (33.3%) were taking ACEi or ARB. Patients on ACEi/ARB were significantly older and had more comorbidities. The odds ratio for the primary endpoint in patients on ACEi and ARB, after adjustment for age, sex and co-morbidities, was 0.63 (95% confidence interval 0.47-0.84, P < 0.01).<h4>Conclusions</h4>There was no evidence for increased severity of COVID-19 in hospitalised patients on chronic treatment with ACEi or ARB. A trend towards a beneficial effect of ACEi/ARB requires further evaluation in larger meta-analyses and randomised clinical trials.","This study aimed to determine whether or not two specific types of medication (ACE inhibitors and angiotensin-2 blockers - ACEi/ARB) used for hypertension or diabetes are associated with increased risk of severe COVID-19 infection in a sample of 1,200 inpatients (one third of whom were taking the medications under investigation) in two London hospitals. The researchers used data from electonic medical notes and electronic health records. The patients who were taking the medication were, on average, older and had more underlying health conditions than patients who were not. After accounting for these differences in patient health the researchers found that the risk of severe COVID infection was not higher for patients taking ACEi/ARB. This finding is important for patients because it suggests that they should continue to take ACEi/ARB that have been presecribed to them.",doi:https://doi.org/10.1002/ejhf.1924; doi:https://doi.org/10.1002/ejhf.1924; html:https://europepmc.org/articles/PMC7301045; pdf:https://europepmc.org/articles/PMC7301045?pdf=render
 34864250,https://doi.org/10.1016/j.seizure.2021.11.017,Epilepsy mortality in Wales during COVID-19.,"Daniels H, Lacey AS, Mikadze D, Akbari A, Fonferko-Shadrach B, Hollinghurst J, Lyons RA, Rees MI, Sawhney IM, Powell RH, Kerr MP, Pickrell WO.",,Seizure,2022,2021-11-27,Y,Pandemic; Data Linkage; Electronic Health Records; Covid-19,,,"<h4>Purpose</h4>The COVID-19 pandemic has increased mortality worldwide and those with chronic conditions may have been disproportionally affected. However, it is unknown whether the pandemic has changed mortality rates for people with epilepsy. We aimed to compare mortality rates in people with epilepsy in Wales during the pandemic with pre-pandemic rates.<h4>Methods</h4>We performed a retrospective study using individual-level linked population-scale anonymised electronic health records. We identified deaths in people with epilepsy (DPWE), i.e. those with a diagnosis of epilepsy, and deaths associated with epilepsy (DAE), where epilepsy was recorded as a cause of death on death certificates. We compared death rates in 2020 with average rates in 2015-2019 using Poisson models to calculate death rate ratios.<h4>Results</h4>There were 188 DAE and 628 DPWE in Wales in 2020 (death rates: 7.7/100,000/year and 25.7/100,000/year). The average rates for DAE and DPWE from 2015 to 2019 were 5.8/100,000/year and 23.8/100,000/year, respectively. Death rate ratios (2020 compared to 2015-2019) for DAE were 1.34 (95%CI 1.14-1.57, p<0.001) and for DPWE were 1.08 (0.99-1.17, p = 0.09). The death rate ratios for non-COVID deaths (deaths without COVID mentioned on death certificates) for DAE were 1.17 (0.99-1.39, p = 0.06) and for DPWE were 0.96 (0.87-1.05, p = 0.37).<h4>Conclusions</h4>The significant increase in DAE in Wales during 2020 could be explained by the direct effect of COVID-19 infection. Non-COVID-19 deaths have not increased significantly but further work is needed to assess the longer-term impact.",,pdf:http://www.seizure-journal.com/article/S1059131121003757/pdf; doi:https://doi.org/10.1016/j.seizure.2021.11.017; html:https://europepmc.org/articles/PMC8626872
+32485082,https://doi.org/10.1002/ejhf.1924,Angiotensin-converting enzyme inhibitors and angiotensin II receptor blockers are not associated with severe COVID-19 infection in a multi-site UK acute hospital trust.,"Bean DM, Kraljevic Z, Searle T, Bendayan R, Kevin O, Pickles A, Folarin A, Roguski L, Noor K, Shek A, Zakeri R, Shah AM, Teo JTH, Dobson RJB.",,European journal of heart failure,2020,2020-06-01,Y,Hypertension; Angiotensin-converting enzyme inhibitors; Disease Outcome; Covid-19,,,"<h4>Aims</h4>The SARS-CoV-2 virus binds to the angiotensin-converting enzyme 2 (ACE2) receptor for cell entry. It has been suggested that angiotensin-converting enzyme inhibitors (ACEi) and angiotensin II receptor blockers (ARB), which are commonly used in patients with hypertension or diabetes and may raise tissue ACE2 levels, could increase the risk of severe COVID-19 infection.<h4>Methods and results</h4>We evaluated this hypothesis in a consecutive cohort of 1200 acute inpatients with COVID-19 at two hospitals with a multi-ethnic catchment population in London (UK). The mean age was 68 ± 17 years (57% male) and 74% of patients had at least one comorbidity. Overall, 415 patients (34.6%) reached the primary endpoint of death or transfer to a critical care unit for organ support within 21 days of symptom onset. A total of 399 patients (33.3%) were taking ACEi or ARB. Patients on ACEi/ARB were significantly older and had more comorbidities. The odds ratio for the primary endpoint in patients on ACEi and ARB, after adjustment for age, sex and co-morbidities, was 0.63 (95% confidence interval 0.47-0.84, P < 0.01).<h4>Conclusions</h4>There was no evidence for increased severity of COVID-19 in hospitalised patients on chronic treatment with ACEi or ARB. A trend towards a beneficial effect of ACEi/ARB requires further evaluation in larger meta-analyses and randomised clinical trials.","This study aimed to determine whether or not two specific types of medication (ACE inhibitors and angiotensin-2 blockers - ACEi/ARB) used for hypertension or diabetes are associated with increased risk of severe COVID-19 infection in a sample of 1,200 inpatients (one third of whom were taking the medications under investigation) in two London hospitals. The researchers used data from electonic medical notes and electronic health records. The patients who were taking the medication were, on average, older and had more underlying health conditions than patients who were not. After accounting for these differences in patient health the researchers found that the risk of severe COVID infection was not higher for patients taking ACEi/ARB. This finding is important for patients because it suggests that they should continue to take ACEi/ARB that have been presecribed to them.",doi:https://doi.org/10.1002/ejhf.1924; doi:https://doi.org/10.1002/ejhf.1924; html:https://europepmc.org/articles/PMC7301045; pdf:https://europepmc.org/articles/PMC7301045?pdf=render
 35173150,https://doi.org/10.1038/s41467-022-28527-x,"Population antibody responses following COVID-19 vaccination in 212,102 individuals.","Ward H, Whitaker M, Flower B, Tang SN, Atchison C, Darzi A, Donnelly CA, Cann A, Diggle PJ, Ashby D, Riley S, Barclay WS, Elliott P, Cooke GS.",,Nature communications,2022,2022-02-16,Y,,,,"Population antibody surveillance helps track immune responses to COVID-19 vaccinations at scale, and identify host factors that may affect antibody production. We analyse data from 212,102 vaccinated individuals within the REACT-2 programme in England, which uses self-administered lateral flow antibody tests in sequential cross-sectional community samples; 71,923 (33.9%) received at least one dose of BNT162b2 vaccine and 139,067 (65.6%) received ChAdOx1. For both vaccines, antibody positivity peaks 4-5 weeks after first dose and then declines. At least 21 days after second dose of BNT162b2, close to 100% of respondents test positive, while for ChAdOx1, this is significantly reduced, particularly in the oldest age groups (72.7% [70.9-74.4] at ages 75 years and above). For both vaccines, antibody positivity decreases with age, and is higher in females and those with previous infection. Antibody positivity is lower in transplant recipients, obese individuals, smokers and those with specific comorbidities. These groups will benefit from additional vaccine doses.",,pdf:https://www.nature.com/articles/s41467-022-28527-x.pdf; doi:https://doi.org/10.1038/s41467-022-28527-x; html:https://europepmc.org/articles/PMC8850615; pdf:https://europepmc.org/articles/PMC8850615?pdf=render
 37994361,https://doi.org/10.12688/gatesopenres.13654.1,"Higher mortality associated with the SARS-CoV-2 Delta variant in the Western Cape, South Africa, using RdRp target delay as a proxy: a cross-sectional study.","Hussey H, Davies MA, Heekes A, Williamson C, Valley-Omar Z, Hardie D, Korsman S, Doolabh D, Preiser W, Maponga T, Iranzadeh A, Engelbrecht S, Wasserman S, Schrueder N, Boloko L, Symons G, Raubenheimer P, Viljoen A, Parker A, Cohen C, Jasat W, Lessells R, Wilkinson RJ, Boulle A, Hsiao M.",,Gates open research,2022,2022-08-31,Y,DELTA; South Africa; Clinical Severity; Sars-cov-2; B.1.617.2; Rdrp Target Delay,,,"<b>Background:</b> The SARS-CoV-2 Delta variant (B.1.617.2) has been associated with more severe disease, particularly when compared to the Alpha variant. Most of this data, however, is from high income countries and less is understood about the variant's disease severity in other settings, particularly in an African context, and when compared to the Beta variant. <b>Methods:</b> A novel proxy marker, RNA-dependent RNA polymerase (RdRp) target delay in the Seegene Allplex <sup>TM</sup> 2019-nCoV (polymerase chain reaction) PCR assay, was used to identify suspected Delta variant infection in routine laboratory data. All cases diagnosed on this assay in the public sector in the Western Cape, South Africa, from 1 April to 31 July 2021, were included in the dataset provided by the Western Cape Provincial Health Data Centre (PHDC). The PHDC collates information on all COVID-19 related laboratory tests, hospital admissions and deaths for the province. Odds ratios for the association between the proxy marker and death were calculated, adjusted for prior diagnosed infection and vaccination status. <b>Results:</b> A total of 11,355 cases with 700 deaths were included in this study. RdRp target delay (suspected Delta variant) was associated with higher mortality (adjusted odds ratio [aOR] 1.45; 95% confidence interval [CI]: 1.13-1.86), compared to presumptive Beta infection. Prior diagnosed infection during the previous COVID-19 wave, which was driven by the Beta variant, was protective (aOR 0.32; 95%CI: 0.11-0.92) as was vaccination (aOR [95%CI] 0.15 [0.03-0.62] for complete vaccination [≥28 days post a single dose of Ad26.COV2.S or ≥14 days post second BNT162b2 dose]). <b>Conclusion:</b> RdRp target delay, a proxy for infection with the Delta variant, is associated with an increased risk of mortality amongst those who were tested for COVID-19 in our setting.",,doi:https://doi.org/10.12688/gatesopenres.13654.1; html:https://europepmc.org/articles/PMC10663174; pdf:https://europepmc.org/articles/PMC10663174?pdf=render
 36721385,https://doi.org/10.1002/pul2.12192,Reduced circulating BMP9 and pBMP10 in hospitalized COVID-19 patients.,"Dunmore BJ, Upton PD, Auckland K, Samanta RJ, CITIID‐NIHR BioResource COVID‐19 Collaboration, EpiCov Database, Lyons PA, Smith KGC, Gräf S, Summers C, Morrell NW.",,Pulmonary circulation,2023,2023-01-01,Y,Endothelial Cell Dysfunction; Bmps; Viral Infections And Pathogenesis,,,"Similar to other causes of acute respiratory distress syndrome, coronavirus disease 2019 (COVID-19) is characterized by the aberrant expression of vascular injury biomarkers. We present the first report that circulating plasma bone morphogenetic proteins (BMPs), BMP9 and pBMP10, involved in vascular protection, are reduced in hospitalized patients with COVID-19.",,pdf:https://www.repository.cam.ac.uk/bitstream/1810/345820/2/pul2.12192.pdf; doi:https://doi.org/10.1002/pul2.12192; html:https://europepmc.org/articles/PMC9881210; pdf:https://europepmc.org/articles/PMC9881210?pdf=render
 39107017,https://doi.org/10.1136/bmjopen-2023-083497,COVID-19 pandemic impact on hypertension management in North East London: an observational cohort study using electronic health records.,"Rison SCG, Redfern OC, Mathur R, Dostal I, Carvalho C, Raisi-Estabragh Z, Robson J.",,BMJ open,2024,2024-08-06,Y,Hypertension; Blood pressure; Cardiovascular disease; Public Health; Primary Care; Health Equity,,,"<h4>Objective</h4>There are established inequities in the monitoring and management of hypertension in England. The COVID-19 pandemic had a major impact on primary care management of long-term conditions such as hypertension. This study investigated the possible disproportionate impact of the pandemic across patient groups.<h4>Design</h4>Open cohort of people with diagnosed hypertension.<h4>Settings</h4>North East London primary care practices from January 2019 to October 2022.<h4>Participants</h4>All 224 329 adults with hypertension registered in 193 primary care practices.<h4>Outcomes</h4>Monitoring and management of hypertension were assessed using two indicators: (i) blood pressure recorded within 1 year of the index date and (ii) blood pressure control to national clinical practice guidelines.<h4>Results</h4>The proportion of patients with a contemporaneous blood pressure recording fell from a 91% pre-pandemic peak to 62% at the end of the pandemic lockdown and improved to 77% by the end of the study. This was paralleled by the proportion of individuals with controlled hypertension which fell from a 73% pre-pandemic peak to 50% at the end of the pandemic lockdown and improved to 60% by the end of the study. However, when excluding patients without a recent blood pressure recording, the proportions of patients with controlled hypertension increased to 81%, 80% and 78% respectively.Throughout the study, in comparison to the White ethnic group, the Black ethnic group was less likely to achieve adequate blood pressure control (ORs 0.81 (95% CI 0.78 to 0.85, p<0.001) to 0.87 (95% CI 0.84 to 0.91, p<0.001)). Conversely, the Asian ethnic group was more likely to have controlled blood pressure (ORs 1.09 (95% CI 1.05 to 1.14, p<0.001) to 1.28 (95% CI 1.23 to 1.32, p<0.001)). Men, younger individuals, more affluent individuals, individuals with unknown or unrecorded ethnicity or those untreated were also less likely to have blood pressure control to target throughout the study.<h4>Conclusion</h4>The COVID-19 pandemic had a greater impact on blood pressure recording than on blood pressure control. Inequities in blood pressure control persisted during the pandemic and remain outstanding.",,doi:https://doi.org/10.1136/bmjopen-2023-083497; html:https://europepmc.org/articles/PMC11308888; pdf:https://europepmc.org/articles/PMC11308888?pdf=render
-38964793,https://doi.org/10.1136/bmjopen-2023-072314,Impact of the first year of COVID-19 vaccination strategy in Brazil: an ecological study.,"Aguilar S, Bastos LSL, Maçaira P, Baião F, Simões P, Cerbino-Neto J, Ranzani O, Hamacher S, Bozza FA.",,BMJ open,2024,2024-07-04,Y,epidemiology; Public Health; Covid-19,,,"<h4>Objectives</h4>No consensus exists about the best COVID-19 vaccination strategy to be adopted by low-income and middle-income countries. Brazil adopted an age-based calendar strategy to reduce mortality and the burden on the healthcare system. This study evaluates the impact of the vaccination campaign in Brazil on the progression of the reported COVID-19 deaths.<h4>Methods</h4>This ecological study analyses the dynamic of vaccination coverage and COVID-19 deaths in hospitalised adults (≥20 years) during the first year of the COVID-19 vaccination roll-out (January to December 2021) using nationwide data (DATASUS). We stratified the adult population into 20-49, 50-59, 60-69 and 70+ years. The dynamic effect of the vaccination campaign on mortality rates was estimated by applying a negative binomial regression. The prevented and possible preventable deaths (observed deaths higher than expected) and potential years of life lost (PYLL) for each age group were obtained in a counterfactual analysis.<h4>Results</h4>During the first year of COVID-19 vaccination, 266 153 517 doses were administered, achieving 91% first-dose coverage. A total of 380 594 deaths were reported, 154 091 (40%) in 70+ years and 136 804 (36%) from 50-59 or 20-49 years. The mortality rates of 70+ decreased by 52% (rate ratio [95% CI]: 0.48 [0.43-0.53]) in 6 months, whereas rates for 20-49 were still increasing due to low coverage (52%). The vaccination roll-out strategy prevented 59 618 deaths, 53 088 (89%) from those aged 70+ years. However, the strategy did not prevent 54 797 deaths, 85% from those under 60 years, being 26 344 (45%) only in 20-49, corresponding to 1 589 271 PYLL, being 1 080 104 PYLL (68%) from those aged 20-49 years.<h4>Conclusion</h4>The adopted aged-based calendar vaccination strategy initially reduced mortality in the oldest but did not prevent the deaths of the youngest as effectively as compared with the older age group. Countries with a high burden, limited vaccine supply and young populations should consider other factors beyond the age to prioritise who should be vaccinated first.",,doi:https://doi.org/10.1136/bmjopen-2023-072314; html:https://europepmc.org/articles/PMC11227766; pdf:https://europepmc.org/articles/PMC11227766?pdf=render
 36849590,https://doi.org/10.1038/s41562-023-01522-y,Changes in preterm birth and stillbirth during COVID-19 lockdowns in 26 countries.,"Calvert C, Brockway MM, Zoega H, Miller JE, Been JV, Amegah AK, Racine-Poon A, Oskoui SE, Abok II, Aghaeepour N, Akwaowo CD, Alshaikh BN, Ayede AI, Bacchini F, Barekatain B, Barnes R, Bebak K, Berard A, Bhutta ZA, Brook JR, Bryan LR, Cajachagua-Torres KN, Campbell-Yeo M, Chu DT, Connor KL, Cornette L, Cortés S, Daly M, Debauche C, Dedeke IOF, Einarsdóttir K, Engjom H, Estrada-Gutierrez G, Fantasia I, Fiorentino NM, Franklin M, Fraser A, Gachuno OW, Gallo LA, Gissler M, Håberg SE, Habibelahi A, Häggström J, Hookham L, Hui L, Huicho L, Hunter KJ, Huq S, Kc A, Kadambari S, Kelishadi R, Khalili N, Kippen J, Le Doare K, Llorca J, Magee LA, Magnus MC, Man KKC, Mburugu PM, Mediratta RP, Morris AD, Muhajarine N, Mulholland RH, Bonnard LN, Nakibuuka V, Nassar N, Nyadanu SD, Oakley L, Oladokun A, Olayemi OO, Olutekunbi OA, Oluwafemi RO, Ogunkunle TO, Orton C, Örtqvist AK, Ouma J, Oyapero O, Palmer KR, Pedersen LH, Pereira G, Pereyra I, Philip RK, Pruski D, Przybylski M, Quezada-Pinedo HG, Regan AK, Rhoda NR, Rihs TA, Riley T, Rocha TAH, Rolnik DL, Saner C, Schneuer FJ, Souter VL, Stephansson O, Sun S, Swift EM, Szabó M, Temmerman M, Tooke L, Urquia ML, von Dadelszen P, Wellenius GA, Whitehead C, Wong ICK, Wood R, Wróblewska-Seniuk K, Yeboah-Antwi K, Yilgwan CS, Zawiejska A, Sheikh A, Rodriguez N, Burgner D, Stock SJ, Azad MB.",,Nature human behaviour,2023,2023-02-27,Y,,,,"Preterm birth (PTB) is the leading cause of infant mortality worldwide. Changes in PTB rates, ranging from -90% to +30%, were reported in many countries following early COVID-19 pandemic response measures ('lockdowns'). It is unclear whether this variation reflects real differences in lockdown impacts, or perhaps differences in stillbirth rates and/or study designs. Here we present interrupted time series and meta-analyses using harmonized data from 52 million births in 26 countries, 18 of which had representative population-based data, with overall PTB rates ranging from 6% to 12% and stillbirth ranging from 2.5 to 10.5 per 1,000 births. We show small reductions in PTB in the first (odds ratio 0.96, 95% confidence interval 0.95-0.98, P value <0.0001), second (0.96, 0.92-0.99, 0.03) and third (0.97, 0.94-1.00, 0.09) months of lockdown, but not in the fourth month of lockdown (0.99, 0.96-1.01, 0.34), although there were some between-country differences after the first month. For high-income countries in this study, we did not observe an association between lockdown and stillbirths in the second (1.00, 0.88-1.14, 0.98), third (0.99, 0.88-1.12, 0.89) and fourth (1.01, 0.87-1.18, 0.86) months of lockdown, although we have imprecise estimates due to stillbirths being a relatively rare event. We did, however, find evidence of increased risk of stillbirth in the first month of lockdown in high-income countries (1.14, 1.02-1.29, 0.02) and, in Brazil, we found evidence for an association between lockdown and stillbirth in the second (1.09, 1.03-1.15, 0.002), third (1.10, 1.03-1.17, 0.003) and fourth (1.12, 1.05-1.19, <0.001) months of lockdown. With an estimated 14.8 million PTB annually worldwide, the modest reductions observed during early pandemic lockdowns translate into large numbers of PTB averted globally and warrant further research into causal pathways.",,pdf:https://www.nature.com/articles/s41562-023-01522-y.pdf; doi:https://doi.org/10.1038/s41562-023-01522-y; html:https://europepmc.org/articles/PMC10129868; pdf:https://europepmc.org/articles/PMC10129868?pdf=render
+38964793,https://doi.org/10.1136/bmjopen-2023-072314,Impact of the first year of COVID-19 vaccination strategy in Brazil: an ecological study.,"Aguilar S, Bastos LSL, Maçaira P, Baião F, Simões P, Cerbino-Neto J, Ranzani O, Hamacher S, Bozza FA.",,BMJ open,2024,2024-07-04,Y,epidemiology; Public Health; Covid-19,,,"<h4>Objectives</h4>No consensus exists about the best COVID-19 vaccination strategy to be adopted by low-income and middle-income countries. Brazil adopted an age-based calendar strategy to reduce mortality and the burden on the healthcare system. This study evaluates the impact of the vaccination campaign in Brazil on the progression of the reported COVID-19 deaths.<h4>Methods</h4>This ecological study analyses the dynamic of vaccination coverage and COVID-19 deaths in hospitalised adults (≥20 years) during the first year of the COVID-19 vaccination roll-out (January to December 2021) using nationwide data (DATASUS). We stratified the adult population into 20-49, 50-59, 60-69 and 70+ years. The dynamic effect of the vaccination campaign on mortality rates was estimated by applying a negative binomial regression. The prevented and possible preventable deaths (observed deaths higher than expected) and potential years of life lost (PYLL) for each age group were obtained in a counterfactual analysis.<h4>Results</h4>During the first year of COVID-19 vaccination, 266 153 517 doses were administered, achieving 91% first-dose coverage. A total of 380 594 deaths were reported, 154 091 (40%) in 70+ years and 136 804 (36%) from 50-59 or 20-49 years. The mortality rates of 70+ decreased by 52% (rate ratio [95% CI]: 0.48 [0.43-0.53]) in 6 months, whereas rates for 20-49 were still increasing due to low coverage (52%). The vaccination roll-out strategy prevented 59 618 deaths, 53 088 (89%) from those aged 70+ years. However, the strategy did not prevent 54 797 deaths, 85% from those under 60 years, being 26 344 (45%) only in 20-49, corresponding to 1 589 271 PYLL, being 1 080 104 PYLL (68%) from those aged 20-49 years.<h4>Conclusion</h4>The adopted aged-based calendar vaccination strategy initially reduced mortality in the oldest but did not prevent the deaths of the youngest as effectively as compared with the older age group. Countries with a high burden, limited vaccine supply and young populations should consider other factors beyond the age to prioritise who should be vaccinated first.",,doi:https://doi.org/10.1136/bmjopen-2023-072314; html:https://europepmc.org/articles/PMC11227766; pdf:https://europepmc.org/articles/PMC11227766?pdf=render
 35673545,https://doi.org/10.12688/wellcomeopenres.17231.2,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody lateral flow assay for antibody prevalence studies following vaccination: a diagnostic accuracy study.,"Cann A, Clarke C, Brown J, Thomson T, Prendecki M, Moshe M, Badhan A, Simmons B, Klaber B, Elliott P, Darzi A, Riley S, Ashby D, Martin P, Gleeson S, Willicombe M, Kelleher P, Ward H, Barclay WS, Cooke GS.",,Wellcome open research,2021,2021-01-01,Y,Antibodies; Seroprevalence; Lateral Flow; Neutralisation; Lfia; Covid-19; Sars-cov-2,,,"<b>Background:</b> Lateral flow immunoassays (LFIAs) are able to achieve affordable, large scale antibody testing and provide rapid results without the support of central laboratories. As part of the development of the REACT programme extensive evaluation of LFIA performance was undertaken with individuals following natural infection. Here we assess the performance of the selected LFIA to detect antibody responses in individuals who have received at least one dose of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine. <b>Methods:</b> This was a prospective diagnostic accuracy study. Sampling was carried out at renal outpatient clinic and healthcare worker testing sites at Imperial College London NHS Trust. Two cohorts of patients were recruited; the first was a cohort of 108 renal transplant patients attending clinic following two doses of SARS-CoV-2 vaccine, the second cohort comprised 40 healthcare workers attending for first SARS-CoV-2 vaccination and subsequent follow up. During the participants visit, finger-prick blood samples were analysed on LFIA device, while paired venous sampling was sent for serological assessment of antibodies to the spike protein (anti-S) antibodies. Anti-S IgG was detected using the Abbott Architect SARS-CoV-2 IgG Quant II CMIA. A total of 186 paired samples were collected. The accuracy of Fortress LFIA in detecting IgG antibodies to SARS-CoV-2 compared to anti-spike protein detection on Abbott Assay <b>Results:</b> The LFIA had an estimated sensitivity of 92.0% (114/124; 95% confidence interval [CI] 85.7% to 96.1%) and specificity of 93.6% (58/62; 95% CI 84.3% to 98.2%) using the Abbott assay as reference standard (using the threshold for positivity of 7.10 BAU/ml) <b>Conclusions:</b> Fortress LFIA performs well in the detection of antibody responses for intended purpose of population level surveillance but does not meet criteria for individual testing.",,doi:https://doi.org/10.12688/wellcomeopenres.17231.2; html:https://europepmc.org/articles/PMC9152464; pdf:https://europepmc.org/articles/PMC9152464?pdf=render
 36503414,https://doi.org/10.1186/s12879-022-07856-8,"COVID-19 vaccination in pregnancy: views and vaccination uptake rates in pregnancy, a mixed methods analysis from SAIL and the Born-In-Wales Birth Cohort.","Mhereeg M, Jones H, Kennedy J, Seaborne M, Parker M, Kennedy N, Beeson S, Akbari A, Zuccolo L, Davies A, Brophy S.",,BMC infectious diseases,2022,2022-12-12,Y,Pregnancy; Vaccine Uptake; Vaccine Hesitancy; Sail; Covid-19 Vaccination,,,"<h4>Background</h4>Vaccine hesitancy amongst pregnant women has been found to be a concern during past epidemics. This study aimed to (1) estimate COVID-19 vaccination rates among pregnant women in Wales and their association with age, ethnicity, and area of deprivation, using electronic health record (EHR) data linkage, and (2) explore pregnant women's views on receiving the COVID-19 vaccine during pregnancy using data from a survey recruiting via social media (Facebook, Twitter), through midwives, and posters in hospitals (Born-In-Wales Cohort).<h4>Methods</h4>This was a mixed-methods study utilising routinely collected linked data from the Secure Anonymised Information Linkage (SAIL) Databank (Objective 1) and the Born-In-Wales Birth Cohort participants (Objective 2). Pregnant women were identified from 13th April 2021 to 31st December 2021. Survival analysis was utilised to examine and compare the length of time to vaccination uptake in pregnancy, and variation in uptake by; age, ethnic group, and deprivation area was examined using hazard ratios (HR) from Cox regression. Survey respondents were women who had a baby during the COVID-19 pandemic or were pregnant between 1st November 2021 and 24th March 2022 and participating in Born-In-Wales. Codebook thematic analysis was used to generate themes from an open-ended question on the survey.<h4>Results</h4>Population-level data linkage (objective 1): Within the population cohort, 8203 (32.7%) received at least one dose of the COVID-19 vaccine during pregnancy, 8572 (34.1%) remained unvaccinated throughout the follow-up period, and 8336 (33.2%) received the vaccine postpartum. Younger women (< 30 years) were less likely to have the vaccine, and those living in areas of high deprivation were also less likely to have the vaccine (HR = 0.88, 95% CI 0.82 to 0.95). Asian and Other ethnic groups were 1.12 and 1.18 times more likely to have the vaccine in pregnancy compared with White women (HR = 1.12, 95% CI 1.00 to 1.25) and (HR = 1.18, 95% CI 1.03 to 1.37) respectively. Survey responses (objective 2): 207 (69%) of participants stated that they would be happy to have the vaccine during pregnancy. The remaining 94 (31%) indicated they would not have the vaccine during pregnancy. Reasons for having the vaccine included protecting self and baby, perceived risk level, and receipt of sufficient evidence and advice. Reasons for vaccine refusal included lack of research about long-term outcomes for the baby, anxiety about vaccines, inconsistent advice/information, and preference to wait until after the pregnancy.<h4>Conclusion</h4>Potentially only 1 in 3 pregnant women would have the COVID-19 vaccine during pregnancy, even though 2 in 3 reported they would have the vaccination, thus it is critical to develop tailored strategies to increase its acceptance rate and decrease vaccine hesitancy. A targeted approach to vaccinations may be required for groups such as younger people and those living in higher deprivation areas.",,pdf:https://bmcinfectdis.biomedcentral.com/counter/pdf/10.1186/s12879-022-07856-8; doi:https://doi.org/10.1186/s12879-022-07856-8; html:https://europepmc.org/articles/PMC9742024; pdf:https://europepmc.org/articles/PMC9742024?pdf=render
 33185672,https://doi.org/10.1093/jamia/ocaa295,Ensemble learning for poor prognosis predictions: A case study on SARS-CoV-2.,"Wu H, Zhang H, Karwath A, Ibrahim Z, Shi T, Zhang X, Wang K, Sun J, Dhaliwal K, Bean D, Cardoso VR, Li K, Teo JT, Banerjee A, Gao-Smith F, Whitehouse T, Veenith T, Gkoutos GV, Wu X, Dobson R, Guthrie B.",,Journal of the American Medical Informatics Association : JAMIA,2021,2021-03-01,Y,Decision Support; Risk Prediction; Ensemble Learning; Covid-19; Model Synergy,,,"<h4>Objective</h4>Risk prediction models are widely used to inform evidence-based clinical decision making. However, few models developed from single cohorts can perform consistently well at population level where diverse prognoses exist (such as the SARS-CoV-2 [severe acute respiratory syndrome coronavirus 2] pandemic). This study aims at tackling this challenge by synergizing prediction models from the literature using ensemble learning.<h4>Materials and methods</h4>In this study, we selected and reimplemented 7 prediction models for COVID-19 (coronavirus disease 2019) that were derived from diverse cohorts and used different implementation techniques. A novel ensemble learning framework was proposed to synergize them for realizing personalized predictions for individual patients. Four diverse international cohorts (2 from the United Kingdom and 2 from China; N = 5394) were used to validate all 8 models on discrimination, calibration, and clinical usefulness.<h4>Results</h4>Results showed that individual prediction models could perform well on some cohorts while poorly on others. Conversely, the ensemble model achieved the best performances consistently on all metrics quantifying discrimination, calibration, and clinical usefulness. Performance disparities were observed in cohorts from the 2 countries: all models achieved better performances on the China cohorts.<h4>Discussion</h4>When individual models were learned from complementary cohorts, the synergized model had the potential to achieve better performances than any individual model. Results indicate that blood parameters and physiological measurements might have better predictive powers when collected early, which remains to be confirmed by further studies.<h4>Conclusions</h4>Combining a diverse set of individual prediction models, the ensemble method can synergize a robust and well-performing model by choosing the most competent ones for individual patients.",,pdf:https://academic.oup.com/jamia/article-pdf/28/4/791/41182395/ocaa295.pdf; doi:https://doi.org/10.1093/jamia/ocaa295; html:https://europepmc.org/articles/PMC7717299; pdf:https://europepmc.org/articles/PMC7717299?pdf=render
 34599903,https://doi.org/10.1016/s2213-2600(21)00380-5,COVID-19 hospital admissions and deaths after BNT162b2 and ChAdOx1 nCoV-19 vaccinations in 2·57 million people in Scotland (EAVE II): a prospective cohort study.,"Agrawal U, Katikireddi SV, McCowan C, Mulholland RH, Azcoaga-Lorenzo A, Amele S, Fagbamigbe AF, Vasileiou E, Grange Z, Shi T, Kerr S, Moore E, Murray JLK, Shah SA, Ritchie L, O'Reilly D, Stock SJ, Beggs J, Chuter A, Torabi F, Akbari A, Bedston S, McMenamin J, Wood R, Tang RSM, de Lusignan S, Hobbs FDR, Woolhouse M, Simpson CR, Robertson C, Sheikh A.",,The Lancet. Respiratory medicine,2021,2021-09-29,Y,,,,"<h4>Background</h4>The UK COVID-19 vaccination programme has prioritised vaccination of those at the highest risk of COVID-19 mortality and hospitalisation. The programme was rolled out in Scotland during winter 2020-21, when SARS-CoV-2 infection rates were at their highest since the pandemic started, despite social distancing measures being in place. We aimed to estimate the frequency of COVID-19 hospitalisation or death in people who received at least one vaccine dose and characterise these individuals.<h4>Methods</h4>We conducted a prospective cohort study using the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) national surveillance platform, which contained linked vaccination, primary care, RT-PCR testing, hospitalisation, and mortality records for 5·4 million people (around 99% of the population) in Scotland. Individuals were followed up from receiving their first dose of the BNT162b2 (Pfizer-BioNTech) or ChAdOx1 nCoV-19 (Oxford-AstraZeneca) COVID-19 vaccines until admission to hospital for COVID-19, death, or the end of the study period on April 18, 2021. We used a time-dependent Poisson regression model to estimate rate ratios (RRs) for demographic and clinical factors associated with COVID-19 hospitalisation or death 14 days or more after the first vaccine dose, stratified by vaccine type.<h4>Findings</h4>Between Dec 8, 2020, and April 18, 2021, 2 572 008 individuals received their first dose of vaccine-841 090 (32·7%) received BNT162b2 and 1 730 918 (67·3%) received ChAdOx1. 1196 (<0·1%) individuals were admitted to hospital or died due to COVID-19 illness (883 hospitalised, of whom 228 died, and 313 who died due to COVID-19 without hospitalisation) 14 days or more after their first vaccine dose. These severe COVID-19 outcomes were associated with older age (≥80 years vs 18-64 years adjusted RR 4·75, 95% CI 3·85-5·87), comorbidities (five or more risk groups vs less than five risk groups 4·24, 3·34-5·39), hospitalisation in the previous 4 weeks (3·00, 2·47-3·65), high-risk occupations (ten or more previous COVID-19 tests vs less than ten previous COVID-19 tests 2·14, 1·62-2·81), care home residence (1·63, 1·32-2·02), socioeconomic deprivation (most deprived quintile vs least deprived quintile 1·57, 1·30-1·90), being male (1·27, 1·13-1·43), and being an ex-smoker (ex-smoker vs non-smoker 1·18, 1·01-1·38). A history of COVID-19 before vaccination was protective (0·40, 0·29-0·54).<h4>Interpretation</h4>COVID-19 hospitalisations and deaths were uncommon 14 days or more after the first vaccine dose in this national analysis in the context of a high background incidence of SARS-CoV-2 infection and with extensive social distancing measures in place. Sociodemographic and clinical features known to increase the risk of severe disease in unvaccinated populations were also associated with severe outcomes in people receiving their first dose of vaccine and could help inform case management and future vaccine policy formulation.<h4>Funding</h4>UK Research and Innovation (Medical Research Council), Research and Innovation Industrial Strategy Challenge Fund, Scottish Government, and Health Data Research UK.",,pdf:https://aura.abdn.ac.uk/bitstream/2164/17801/1/Agrawal_etal_LRM_COVID19_Hospital_Admissions_VOR.pdf; doi:https://doi.org/10.1016/S2213-2600(21)00380-5; html:https://europepmc.org/articles/PMC8480963
 32564639,https://doi.org/10.1177/0300060520931298,Mortality statistics in England and Wales: the SARS-CoV-2 paradox.,"Harrison G, Newport D, Robbins T, Arvanitis TN, Stein A.",,The Journal of international medical research,2020,2020-06-01,Y,Respiratory disease; United Kingdom; Mortality Rate; Paradox; Covid-19; Sars-cov-2,,,"<h4>Objective</h4>To analyse mortality statistics in the United Kingdom during the initial phases of the severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic and to understand the impact of the pandemic on national mortality.<h4>Methods</h4>Retrospective review of weekly national mortality statistics in the United Kingdom over the past 5 years, including subgroup analysis of respiratory mortality rates.<h4>Results</h4>During the early phases of the SARS-CoV-2 pandemic in the first months of 2020, there were consistently fewer deaths per week compared with the preceding 5 years. This pattern was not observed at any other time within the past 5 years. We have termed this phenomenon the ""SARS-CoV-2 paradox."" We postulate potential explanations for this seeming paradox and explore the implications of these data.<h4>Conclusions</h4>Paradoxically, but potentially importantly, lower rather than higher weekly mortality rates were observed during the early stages of the SARS-CoV-2 pandemic. This paradox may have implications for current and future healthcare utilisation. A rebound increase in non-SARS-CoV-2 mortality later this year might coincide with the peak of SARS-CoV-2 admissions and mortality.",,doi:https://doi.org/10.1177/0300060520931298; doi:https://doi.org/10.1177/0300060520931298; html:https://europepmc.org/articles/PMC7307394; pdf:https://europepmc.org/articles/PMC7307394?pdf=render
-34642622,https://doi.org/10.1016/j.hlpt.2021.100568,Rapid adaptation of a local healthcare digital system to COVID-19: The experience in Birmingham (UK).,"Pankhurst T, Atia J, Evison F, Gallier S, Lewis JM, McKee D, Ryan S, Sapey E, Ball S, Coleman JJ.",,Health policy and technology,2021,2021-10-08,Y,Clinical Decision Support Systems; Medical Informatics; Electronic Health Records; Ehr; Covid-19,,,"<h4>Background</h4>The COVID-19 pandemic created unprecedented pressure on hospitals globally. Digital tools developed before the crisis provided novel aspects of management, and new digital tools were rapidly developed as the crisis progressed. In our institution, a digitally mature NHS Trust in England which builds software systems, development during the early months of the crisis allowed increased patient safety and care, efficient management of the hospital and publication of data. The aim of this paper is to present this experience as a case study, describing development and lessons learned applicable to wider electronic healthcare record development.<h4>Methods</h4>Request, triage, build and test processes for the digital systems were altered in response to the pandemic. Senior Responsible Officers appointed for the emergency triaged all changes and were supported by expert opinion and research active clinicians. Build and test cycles were compressed. New tools were built or existing ones modified in the central Electronic Healthcare Record, PICS (Prescribing, Information and Communication System), Clinical Dashboards and video platforms for remote consultation were developed.<h4>Findings</h4>2236 patients were admitted to UHB with suspected COVID-19 between March and May 2020. Dashboards and visualisation tools enabled by efficient real-time data collection for all new patients, contributed to strategic, operational and clinical decision making.Over 70 urgent changes were made to digital systems, including a screening proforma, improved infection control functions, help and order panels, data dashboards, and updated prescribing features. Novel uses were found for existing functions.<h4>Interpretation</h4>Digital tools contributed to a co-ordinated response to COVID-19 in an area with a high disease burden. Change management processes were modified during the pandemic and successfully delivered rapid software modifications and new tools. Principal benefits came from the ability to adapt systems to rapidly changing clinical situations. Lessons learned from this intense development period are widely applicable to EHR development.<h4>Lay summary</h4>Digital tools, which are well designed, can help clinicians and safeguard patients. Health crises such as the COVID pandemic drove rapid development of digital tools. This case study outlines accelerated development within a governance framework that successfully reused existing tools and built new ones. The lessons from this development are generalizable to digital developments in healthcare.",,doi:https://doi.org/10.1016/j.hlpt.2021.100568; doi:https://doi.org/10.1016/j.hlpt.2021.100568; html:https://europepmc.org/articles/PMC8498783; pdf:https://europepmc.org/articles/PMC8498783?pdf=render
 32393804,https://doi.org/10.1038/s41591-020-0916-2,Real-time tracking of self-reported symptoms to predict potential COVID-19.,"Menni C, Valdes AM, Freidin MB, Sudre CH, Nguyen LH, Drew DA, Ganesh S, Varsavsky T, Cardoso MJ, El-Sayed Moustafa JS, Visconti A, Hysi P, Bowyer RCE, Mangino M, Falchi M, Wolf J, Ourselin S, Chan AT, Steves CJ, Spector TD.",,Nature medicine,2020,2020-05-11,N,,,,"A total of 2,618,862 participants reported their potential symptoms of COVID-19 on a smartphone-based app. Among the 18,401 who had undergone a SARS-CoV-2 test, the proportion of participants who reported loss of smell and taste was higher in those with a positive test result (4,668 of 7,178 individuals; 65.03%) than in those with a negative test result (2,436 of 11,223 participants; 21.71%) (odds ratio = 6.74; 95% confidence interval = 6.31-7.21). A model combining symptoms to predict probable infection was applied to the data from all app users who reported symptoms (805,753) and predicted that 140,312 (17.42%) participants are likely to have COVID-19.",,pdf:https://www.nature.com/articles/s41591-020-0916-2.pdf; doi:https://doi.org/10.1038/s41591-020-0916-2; html:https://europepmc.org/articles/PMC7751267; pdf:https://europepmc.org/articles/PMC7751267?pdf=render; doi:https://doi.org/10.1038/s41591-020-0916-2
+34642622,https://doi.org/10.1016/j.hlpt.2021.100568,Rapid adaptation of a local healthcare digital system to COVID-19: The experience in Birmingham (UK).,"Pankhurst T, Atia J, Evison F, Gallier S, Lewis JM, McKee D, Ryan S, Sapey E, Ball S, Coleman JJ.",,Health policy and technology,2021,2021-10-08,Y,Clinical Decision Support Systems; Medical Informatics; Electronic Health Records; Ehr; Covid-19,,,"<h4>Background</h4>The COVID-19 pandemic created unprecedented pressure on hospitals globally. Digital tools developed before the crisis provided novel aspects of management, and new digital tools were rapidly developed as the crisis progressed. In our institution, a digitally mature NHS Trust in England which builds software systems, development during the early months of the crisis allowed increased patient safety and care, efficient management of the hospital and publication of data. The aim of this paper is to present this experience as a case study, describing development and lessons learned applicable to wider electronic healthcare record development.<h4>Methods</h4>Request, triage, build and test processes for the digital systems were altered in response to the pandemic. Senior Responsible Officers appointed for the emergency triaged all changes and were supported by expert opinion and research active clinicians. Build and test cycles were compressed. New tools were built or existing ones modified in the central Electronic Healthcare Record, PICS (Prescribing, Information and Communication System), Clinical Dashboards and video platforms for remote consultation were developed.<h4>Findings</h4>2236 patients were admitted to UHB with suspected COVID-19 between March and May 2020. Dashboards and visualisation tools enabled by efficient real-time data collection for all new patients, contributed to strategic, operational and clinical decision making.Over 70 urgent changes were made to digital systems, including a screening proforma, improved infection control functions, help and order panels, data dashboards, and updated prescribing features. Novel uses were found for existing functions.<h4>Interpretation</h4>Digital tools contributed to a co-ordinated response to COVID-19 in an area with a high disease burden. Change management processes were modified during the pandemic and successfully delivered rapid software modifications and new tools. Principal benefits came from the ability to adapt systems to rapidly changing clinical situations. Lessons learned from this intense development period are widely applicable to EHR development.<h4>Lay summary</h4>Digital tools, which are well designed, can help clinicians and safeguard patients. Health crises such as the COVID pandemic drove rapid development of digital tools. This case study outlines accelerated development within a governance framework that successfully reused existing tools and built new ones. The lessons from this development are generalizable to digital developments in healthcare.",,doi:https://doi.org/10.1016/j.hlpt.2021.100568; doi:https://doi.org/10.1016/j.hlpt.2021.100568; html:https://europepmc.org/articles/PMC8498783; pdf:https://europepmc.org/articles/PMC8498783?pdf=render
 34750106,https://doi.org/10.3399/bjgp.2021.0376,Trends and clinical characteristics of COVID-19 vaccine recipients: a federated analysis of 57.9 million patients’ primary care records in situ using OpenSAFELY.,"Curtis HJ, Inglesby P, Morton CE, MacKenna B, Green A, Hulme W, Walker AJ, Morley J, Mehrkar A, Bacon S, Hickman G, Bates C, Croker R, Evans D, Ward T, Cockburn J, Davy S, Bhaskaran K, Schultze A, Rentsch CT, Williamson EJ, Rowan A, Fisher L, McDonald HI, Tomlinson L, Mathur R, Drysdale H, Eggo RM, Wing K, Wong AY, Forbes H, Parry J, Hester F, Harper S, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Griffiths P, Fowles A, Parkes N, Douglas IJ, Evans SJ, Smeeth L, Goldacre B, (The OpenSAFELY Collaborative).",,The British journal of general practice : the journal of the Royal College of General Practitioners,2022,2021-12-31,Y,Ethnic Groups; Vaccination; General Practice; Nhs England; Covid-19; Sars-cov-2,,,"<h4>Background</h4>On 8 December 2020 NHS England administered the first COVID-19 vaccination.<h4>Aim</h4>To describe trends and variation in vaccine coverage in different clinical and demographic groups in the first 100 days of the vaccine rollout.<h4>Design and setting</h4>With the approval of NHS England, a cohort study was conducted of 57.9 million patient records in general practice in England, <i>in situ</i> and within the infrastructure of the electronic health record software vendors EMIS and TPP using OpenSAFELY.<h4>Method</h4>Vaccine coverage across various subgroups of Joint Committee on Vaccination and Immunisation (JCVI) priority cohorts is described.<h4>Results</h4>A total of 20 852 692 patients (36.0%) received a vaccine between 8 December 2020 and 17 March 2021. Of patients aged ≥80 years not in a care home (JCVI group 2) 94.7% received a vaccine, but with substantial variation by ethnicity (White 96.2%, Black 68.3%) and deprivation (least deprived 96.6%, most deprived 90.7%). Patients with pre-existing medical conditions were more likely to be vaccinated with two exceptions: severe mental illness (89.5%) and learning disability (91.4%). There were 275 205 vaccine recipients who were identified as care home residents (JCVI group 1; 91.2% coverage). By 17 March, 1 257 914 (6.0%) recipients had a second dose.<h4>Conclusion</h4>The NHS rapidly delivered mass vaccination. In this study a data-monitoring framework was deployed using publicly auditable methods and a secure <i>in situ</i> processing model, using linked but pseudonymised patient-level NHS data for 57.9 million patients. Targeted activity may be needed to address lower vaccination coverage observed among certain key groups.",,doi:https://doi.org/10.3399/bjgp.2021.0376; doi:https://doi.org/10.3399/BJGP.2021.0376; html:https://europepmc.org/articles/PMC8589463; pdf:https://europepmc.org/articles/PMC8589463?pdf=render
 35440446,https://doi.org/10.1136/bmjopen-2021-052514,Protocol for the COG-UK hospital-onset COVID-19 infection (HOCI) multicentre interventional clinical study: evaluating the efficacy of rapid genome sequencing of SARS-CoV-2 in limiting the spread of COVID-19 in UK NHS hospitals.,"Blackstone J, Stirrup O, Mapp F, Panca M, Copas A, Flowers P, Hockey L, Price J, Partridge D, Peters C, de Silva T, Nebbia G, Snell LB, McComish R, COVID-19 Genomics UK (COG-UK) Consortium, Breuer J.",,BMJ open,2022,2022-04-19,Y,Molecular biology; Infection control; epidemiology; Covid-19,,,"<h4>Objectives</h4>Nosocomial transmission of SARS-CoV-2 has been a significant cause of mortality in National Health Service (NHS) hospitals during the COVID-19 pandemic. The COG-UK Consortium Hospital-Onset COVID-19 Infections (COG-UK HOCI) study aims to evaluate whether the use of rapid whole-genome sequencing of SARS-CoV-2, supported by a novel probabilistic reporting methodology, can inform infection prevention and control (IPC) practice within NHS hospital settings.<h4>Design</h4>Multicentre, prospective, interventional, superiority study.<h4>Setting</h4>14 participating NHS hospitals over winter-spring 2020/2021 in the UK.<h4>Participants</h4>Eligible patients must be admitted to hospital with first-confirmed SARS-CoV-2 PCR-positive test result >48 hour from time of admission, where COVID-19 diagnosis not suspected on admission. The projected sample size is 2380 patients.<h4>Intervention</h4>The intervention is the return of a sequence report, within 48 hours in one phase (rapid local lab processing) and within 5-10 days in a second phase (mimicking central lab), comparing the viral genome from an eligible study participant with others within and outside the hospital site.<h4>Primary and secondary outcome measures</h4>The primary outcomes are incidence of Public Health England (PHE)/IPC-defined SARS-CoV-2 hospital-acquired infection during the baseline and two interventional phases, and proportion of hospital-onset cases with genomic evidence of transmission linkage following implementation of the intervention where such linkage was not suspected by initial IPC investigation. Secondary outcomes include incidence of hospital outbreaks, with and without sequencing data; actual and desirable changes to IPC actions; periods of healthcare worker (HCW) absence. Health economic analysis will be conducted to determine cost benefit of the intervention. A process evaluation using qualitative interviews with HCWs will be conducted alongside the study.<h4>Trial registration number</h4>ISRCTN50212645. Pre-results stage. This manuscript is based on protocol V.6.0. 2 September 2021.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/4/e052514.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-052514; html:https://europepmc.org/articles/PMC9019828; pdf:https://europepmc.org/articles/PMC9019828?pdf=render
 37712381,https://doi.org/10.7189/jogh.13.04101,Understanding and reporting odds ratios as rate-ratio estimates in case-control studies.,"Kerr S, Greenland S, Jeffrey K, Millington T, Bedston S, Ritchie L, Simpson CR, Fagbamigbe AF, Kurdi A, Robertson C, Sheikh A, Rudan I.",,Journal of global health,2023,2023-09-15,Y,,,,"<h4>Background</h4>We noted that there remains some confusion in the health-science literature on reporting sample odds ratios as estimated rate ratios in case-control studies.<h4>Methods</h4>We recap historical literature that definitively answered the question of when sample odds ratios (ORs) from a case-control study are consistent estimators for population rate ratios. We use numerical examples to illustrate the magnitude of the disparity between sample ORs in a case-control study and population rate ratios when sufficient conditions for them to be equal are not satisfied.<h4>Results</h4>We stress that in a case-control study, sampling controls from those still at risk at the time of outcome event of the index case is not sufficient for a sample OR to be a consistent estimator for an intelligible rate ratio. In such studies, constancy of the exposure prevalence together with constancy of the hazard ratio (HR) (i.e., the instantaneous rate ratio) over time is sufficient for this result if sampling time is not controlled; if time is controlled, constancy of the HR will suffice. We present numerical examples to illustrate how failure to satisfy these conditions adds a small systematic error to sample ORs as estimates of population rate ratios.<h4>Conclusions</h4>We recommend that researchers understand and critically evaluate all conditions used to interpret their estimates as consistent for a population parameter in case-control studies.",,pdf:https://jogh.org/wp-content/uploads/2023/09/jogh-13-04101.pdf; doi:https://doi.org/10.7189/jogh.13.04101; html:https://europepmc.org/articles/PMC10502767; pdf:https://europepmc.org/articles/PMC10502767?pdf=render
@@ -329,27 +329,27 @@ PMC9023380,https://doi.org/,Assessing the spread risk of COVID-19 associated wit
 36882868,https://doi.org/10.1186/s12916-023-02784-z,"Assessing the impacts of COVID-19 vaccination programme's timing and speed on health benefits, cost-effectiveness, and relative affordability in 27 African countries.","Liu Y, Procter SR, Pearson CAB, Montero AM, Torres-Rueda S, Asfaw E, Uzochukwu B, Drake T, Bergren E, Eggo RM, Ruiz F, Ndembi N, Nonvignon J, Jit M, Vassall A.",,BMC medicine,2023,2023-03-08,Y,Mathematical models; Vaccination; Economic evaluation; decision-making; Affordability; Programme Evaluation; Public Health Interventions; Covid-19 | Sars-cov-2,,,"<h4>Background</h4>The COVID-19 vaccine supply shortage in 2021 constrained roll-out efforts in Africa while populations experienced waves of epidemics. As supply improves, a key question is whether vaccination remains an impactful and cost-effective strategy given changes in the timing of implementation.<h4>Methods</h4>We assessed the impact of vaccination programme timing using an epidemiological and economic model. We fitted an age-specific dynamic transmission model to reported COVID-19 deaths in 27 African countries to approximate existing immunity resulting from infection before substantial vaccine roll-out. We then projected health outcomes (from symptomatic cases to overall disability-adjusted life years (DALYs) averted) for different programme start dates (01 January to 01 December 2021, n = 12) and roll-out rates (slow, medium, fast; 275, 826, and 2066 doses/million population-day, respectively) for viral vector and mRNA vaccines by the end of 2022. Roll-out rates used were derived from observed uptake trajectories in this region. Vaccination programmes were assumed to prioritise those above 60 years before other adults. We collected data on vaccine delivery costs, calculated incremental cost-effectiveness ratios (ICERs) compared to no vaccine use, and compared these ICERs to GDP per capita. We additionally calculated a relative affordability measure of vaccination programmes to assess potential nonmarginal budget impacts.<h4>Results</h4>Vaccination programmes with early start dates yielded the most health benefits and lowest ICERs compared to those with late starts. While producing the most health benefits, fast vaccine roll-out did not always result in the lowest ICERs. The highest marginal effectiveness within vaccination programmes was found among older adults. High country income groups, high proportions of populations over 60 years or non-susceptible at the start of vaccination programmes are associated with low ICERs relative to GDP per capita. Most vaccination programmes with small ICERs relative to GDP per capita were also relatively affordable.<h4>Conclusion</h4>Although ICERs increased significantly as vaccination programmes were delayed, programmes starting late in 2021 may still generate low ICERs and manageable affordability measures. Looking forward, lower vaccine purchasing costs and vaccines with improved efficacies can help increase the economic value of COVID-19 vaccination programmes.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-023-02784-z; doi:https://doi.org/10.1186/s12916-023-02784-z; html:https://europepmc.org/articles/PMC9991879; pdf:https://europepmc.org/articles/PMC9991879?pdf=render
 36150783,https://doi.org/10.1016/s2589-7500(22)00147-9,Data capture and sharing in the COVID-19 pandemic: a cause for concern.,"Dron L, Kalatharan V, Gupta A, Haggstrom J, Zariffa N, Morris AD, Arora P, Park J.",,The Lancet. Digital health,2022,2022-10-01,Y,,,,"Routine health care and research have been profoundly influenced by digital-health technologies. These technologies range from primary data collection in electronic health records (EHRs) and administrative claims to web-based artificial-intelligence-driven analyses. There has been increased use of such health technologies during the COVID-19 pandemic, driven in part by the availability of these data. In some cases, this has resulted in profound and potentially long-lasting positive effects on medical research and routine health-care delivery. In other cases, high profile shortcomings have been evident, potentially attenuating the effect of-or representing a decreased appetite for-digital-health transformation. In this Series paper, we provide an overview of how facets of health technologies in routinely collected medical data (including EHRs and digital data sharing) have been used for COVID-19 research and tracking, and how these technologies might influence future pandemics and health-care research. We explore the strengths and weaknesses of digital-health research during the COVID-19 pandemic and discuss how learnings from COVID-19 might translate into new approaches in a post-pandemic era.",,doi:https://doi.org/10.1016/s2589-7500(22)00147-9; doi:https://doi.org/10.1016/S2589-7500(22)00147-9; html:https://europepmc.org/articles/PMC9489064; pdf:https://europepmc.org/articles/PMC9489064?pdf=render
 34011491,https://doi.org/10.1136/bmj.n1137,Excess deaths associated with covid-19 pandemic in 2020: age and sex disaggregated time series analysis in 29 high income countries.,"Islam N, Shkolnikov VM, Acosta RJ, Klimkin I, Kawachi I, Irizarry RA, Alicandro G, Khunti K, Yates T, Jdanov DA, White M, Lewington S, Lacey B.",,BMJ (Clinical research ed.),2021,2021-05-19,Y,,,,"<h4>Objective</h4>To estimate the direct and indirect effects of the covid-19 pandemic on mortality in 2020 in 29 high income countries with reliable and complete age and sex disaggregated mortality data.<h4>Design</h4>Time series study of high income countries.<h4>Setting</h4>Austria, Belgium, Czech Republic, Denmark, England and Wales, Estonia, Finland, France, Germany, Greece, Hungary, Israel, Italy, Latvia, Lithuania, the Netherlands, New Zealand, Northern Ireland, Norway, Poland, Portugal, Scotland, Slovakia, Slovenia, South Korea, Spain, Sweden, Switzerland, and United States.<h4>Participants</h4>Mortality data from the Short-term Mortality Fluctuations data series of the Human Mortality Database for 2016-20, harmonised and disaggregated by age and sex.<h4>Interventions</h4>Covid-19 pandemic and associated policy measures.<h4>Main outcome measures</h4>Weekly excess deaths (observed deaths versus expected deaths predicted by model) in 2020, by sex and age (0-14, 15-64, 65-74, 75-84, and ≥85 years), estimated using an over-dispersed Poisson regression model that accounts for temporal trends and seasonal variability in mortality.<h4>Results</h4>An estimated 979 000 (95% confidence interval 954 000 to 1 001 000) excess deaths occurred in 2020 in the 29 high income countries analysed. All countries had excess deaths in 2020, except New Zealand, Norway, and Denmark. The five countries with the highest absolute number of excess deaths were the US (458 000, 454 000 to 461 000), Italy (89 100, 87 500 to 90 700), England and Wales (85 400, 83 900 to 86 800), Spain (84 100, 82 800 to 85 300), and Poland (60 100, 58 800 to 61 300). New Zealand had lower overall mortality than expected (-2500, -2900 to -2100). In many countries, the estimated number of excess deaths substantially exceeded the number of reported deaths from covid-19. The highest excess death rates (per 100 000) in men were in Lithuania (285, 259 to 311), Poland (191, 184 to 197), Spain (179, 174 to 184), Hungary (174, 161 to 188), and Italy (168, 163 to 173); the highest rates in women were in Lithuania (210, 185 to 234), Spain (180, 175 to 185), Hungary (169, 156 to 182), Slovenia (158, 132 to 184), and Belgium (151, 141 to 162). Little evidence was found of subsequent compensatory reductions following excess mortality.<h4>Conclusion</h4>Approximately one million excess deaths occurred in 2020 in these 29 high income countries. Age standardised excess death rates were higher in men than women in almost all countries. Excess deaths substantially exceeded reported deaths from covid-19 in many countries, indicating that determining the full impact of the pandemic on mortality requires assessment of excess deaths. Many countries had lower deaths than expected in children <15 years. Sex inequality in mortality widened further in most countries in 2020.",,pdf:https://www.bmj.com/content/bmj/373/bmj.n1137.full.pdf; doi:https://doi.org/10.1136/bmj.n1137; html:https://europepmc.org/articles/PMC8132017; pdf:https://europepmc.org/articles/PMC8132017?pdf=render
-34265229,https://doi.org/10.1177/01410768211032850,"Symptoms, complications and management of long COVID: a review.","Aiyegbusi OL, Hughes SE, Turner G, Rivera SC, McMullan C, Chandan JS, Haroon S, Price G, Davies EH, Nirantharakumar K, Sapey E, Calvert MJ, TLC Study Group.",,Journal of the Royal Society of Medicine,2021,2021-07-15,Y,Infectious diseases; epidemiology; Public Health; Respiratory Medicine; Health Service Research; Covid-19; Long Covid; Post-Covid-19 Syndrome; Persistent Covid-19 Symptoms,,,"Globally, there are now over 160 million confirmed cases of COVID-19 and more than 3 million deaths. While the majority of infected individuals recover, a significant proportion continue to experience symptoms and complications after their acute illness. Patients with 'long COVID' experience a wide range of physical and mental/psychological symptoms. Pooled prevalence data showed the 10 most prevalent reported symptoms were fatigue, shortness of breath, muscle pain, joint pain, headache, cough, chest pain, altered smell, altered taste and diarrhoea. Other common symptoms were cognitive impairment, memory loss, anxiety and sleep disorders. Beyond symptoms and complications, people with long COVID often reported impaired quality of life, mental health and employment issues. These individuals may require multidisciplinary care involving the long-term monitoring of symptoms, to identify potential complications, physical rehabilitation, mental health and social services support. Resilient healthcare systems are needed to ensure efficient and effective responses to future health challenges.",,doi:https://doi.org/10.1177/01410768211032850; doi:https://doi.org/10.1177/01410768211032850; html:https://europepmc.org/articles/PMC8450986; pdf:https://europepmc.org/articles/PMC8450986?pdf=render
+34265229,https://doi.org/10.1177/01410768211032850,"Symptoms, complications and management of long COVID: a review.","Aiyegbusi OL, Hughes SE, Turner G, Rivera SC, McMullan C, Chandan JS, Haroon S, Price G, Davies EH, Nirantharakumar K, Sapey E, Calvert MJ, TLC Study Group.",,Journal of the Royal Society of Medicine,2021,2021-07-15,Y,Infectious diseases; epidemiology; Public Health; Respiratory Medicine; Health Service Research; Covid-19; Long Covid; Persistent Covid-19 Symptoms; Post-Covid-19 Syndrome,,,"Globally, there are now over 160 million confirmed cases of COVID-19 and more than 3 million deaths. While the majority of infected individuals recover, a significant proportion continue to experience symptoms and complications after their acute illness. Patients with 'long COVID' experience a wide range of physical and mental/psychological symptoms. Pooled prevalence data showed the 10 most prevalent reported symptoms were fatigue, shortness of breath, muscle pain, joint pain, headache, cough, chest pain, altered smell, altered taste and diarrhoea. Other common symptoms were cognitive impairment, memory loss, anxiety and sleep disorders. Beyond symptoms and complications, people with long COVID often reported impaired quality of life, mental health and employment issues. These individuals may require multidisciplinary care involving the long-term monitoring of symptoms, to identify potential complications, physical rehabilitation, mental health and social services support. Resilient healthcare systems are needed to ensure efficient and effective responses to future health challenges.",,doi:https://doi.org/10.1177/01410768211032850; doi:https://doi.org/10.1177/01410768211032850; html:https://europepmc.org/articles/PMC8450986; pdf:https://europepmc.org/articles/PMC8450986?pdf=render
 35915500,https://doi.org/10.1186/s12911-022-01947-x,The impact of changes in coding on mortality reports using the example of sepsis.,"Atkin C, Pankhurst T, McNulty D, Keogh A, Gallier S, Pagano D, Sapey E, Ball S.",,BMC medical informatics and decision making,2022,2022-08-01,Y,Mortality; Sepsis; Morbidity; epidemiology; Clinical Coding; Real World Data,,,"<h4>Objectives</h4>NHS Digital issued new guidance on sepsis coding in April 2017 which was further modified in April 2018. During these timeframes some centres reported increased sepsis associated mortality, whilst others reported reduced mortality, in some cases coincident with specific quality improvement programmes. We hypothesised that changes in reported mortality could not be separated from changes in coding practice.<h4>Methods</h4>Hospital Episode Statistics from the Admitted Patient Care dataset for NHS hospitals in England, from April 2016 to March 2020 were analysed. Admissions of adults with sepsis: an International Classification of Diseases 10 (ICD-10) code associated with the Agency for Healthcare Research and Quality Clinical Classifications Software class 'Septicaemia (except in labour)', were assessed. Patient comorbidities were defined by other ICD-10 codes recorded within the admission episode.<h4>Results</h4>1,081,565 hospital episodes with a coded diagnosis of sepsis were studied. After April 2017 there was a significant increase in admission episodes with sepsis coded as the primary reason for admission. There were significant changes in the case-mix of patients with a primary diagnosis of sepsis after April 2017. An analysis of case-mix, hospital and year treated as random effects, defined a small reduction in sepsis associated mortality across England following the first change in coding guidance. No centre specific improvement in outcome could be separated from these random-effects.<h4>Conclusion</h4>Changes in sepsis coding practice altered case-mix and case selection, in ways that varied between centres. This was associated with changes in centre-specific sepsis associated mortality, over time. According to the direction of change these may be interpreted either as requiring local investigation for cause or as supporting coincident changes in clinical practice. A whole system analysis showed that centre specific changes in mortality cannot be separated from system-wide changes. Caution is therefore required when interpreting sepsis outcomes in England, particularly when using single centre studies to inform or support guidance or policy.",,pdf:https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-022-01947-x; doi:https://doi.org/10.1186/s12911-022-01947-x; html:https://europepmc.org/articles/PMC9341053; pdf:https://europepmc.org/articles/PMC9341053?pdf=render
 35151371,https://doi.org/10.1016/j.immuni.2022.01.017,Immuno-proteomic profiling reveals aberrant immune cell regulation in the airways of individuals with ongoing post-COVID-19 respiratory disease.,"Vijayakumar B, Boustani K, Ogger PP, Papadaki A, Tonkin J, Orton CM, Ghai P, Suveizdyte K, Hewitt RJ, Desai SR, Devaraj A, Snelgrove RJ, Molyneaux PL, Garner JL, Peters JE, Shah PL, Lloyd CM, Harker JA.",,Immunity,2022,2022-01-26,Y,T cells; Proteomics; Respiratory Tract; Airways; Respiratory Viral Infection; Tissue-resident Memory; Covid-19; Sars-cov-2; Long Covid,,,"Some patients hospitalized with acute COVID-19 suffer respiratory symptoms that persist for many months. We delineated the immune-proteomic landscape in the airways and peripheral blood of healthy controls and post-COVID-19 patients 3 to 6 months after hospital discharge. Post-COVID-19 patients showed abnormal airway (but not plasma) proteomes, with an elevated concentration of proteins associated with apoptosis, tissue repair, and epithelial injury versus healthy individuals. Increased numbers of cytotoxic lymphocytes were observed in individuals with greater airway dysfunction, while increased B cell numbers and altered monocyte subsets were associated with more widespread lung abnormalities. A one-year follow-up of some post-COVID-19 patients indicated that these abnormalities resolved over time. In summary, COVID-19 causes a prolonged change to the airway immune landscape in those with persistent lung disease, with evidence of cell death and tissue repair linked to the ongoing activation of cytotoxic T cells.",,pdf:http://www.cell.com/article/S1074761322000462/pdf; doi:https://doi.org/10.1016/j.immuni.2022.01.017; html:https://europepmc.org/articles/PMC8789571; pdf:https://europepmc.org/articles/PMC8789571?pdf=render
 32880390,https://doi.org/10.1210/clinem/dgaa627,"Systemic Corticosteroids and Mortality in Severe and Critical COVID-19 Patients in Wuhan, China.","Wu J, Huang J, Zhu G, Liu Y, Xiao H, Zhou Q, Si X, Yi H, Wang C, Yang D, Chen S, Liu X, Liu Z, Wang Q, Lv Q, Huang Y, Yu Y, Guan X, Li Y, Nirantharakumar K, Cheng K, Peng S, Xiao H.",,The Journal of clinical endocrinology and metabolism,2020,2020-12-01,N,Mortality; Systemic Corticosteroids; Covid-19; Severe And Critical,,,"<h4>Background</h4>Systemic corticosteroids are now recommended in many treatment guidelines, although supporting evidence is limited to 1 randomized controlled clinical trial (RECOVERY).<h4>Objective</h4>To identify whether corticosteroids were beneficial to COVID-19 patients.<h4>Methods</h4>A total of 1514 severe and 249 critical hospitalized COVID-19 patients from 2 medical centers in Wuhan, China. Multivariable Cox models, Cox model with time-varying exposure and propensity score analysis (inverse-probability-of-treatment-weighting [IPTW] and propensity score matching [PSM]) were used to estimate the association of corticosteroid use with risk of in-hospital mortality in severe and critical cases.<h4>Results</h4>Corticosteroids were administered in 531 (35.1%) severe and 159 (63.9%) critical patients. Compared to the non-corticosteroid group, systemic corticosteroid use was not associated with beneficial effect in reducing in-hospital mortality in either severe cases (HR = 1.77; 95% CI, 1.08-2.89; P = 0.023), or critical cases (HR = 2.07; 95% CI, 1.08-3.98; P = 0.028). Findings were similar in time-varying Cox analysis. For patients with severe COVID-19 at admission, corticosteroid use was not associated with improved or harmful outcome in either PSM or IPTW analysis. For critical COVID-19 patients at admission, results were consistent with multivariable Cox model analysis.<h4>Conclusion</h4>Corticosteroid use was not associated with beneficial effect in reducing in-hospital mortality for severe or critical cases in Wuhan. Absence of the beneficial effect in our study in contrast to that observed in the RECOVERY clinical trial may be due to biases in observational data, in particular prescription by indication bias, differences in clinical characteristics of patients, choice of corticosteroid used, timing of initiation of treatment, and duration of treatment.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7499588; doi:https://doi.org/10.1210/clinem/dgaa627; html:https://europepmc.org/articles/PMC7499588; pdf:https://europepmc.org/articles/PMC7499588?pdf=render; doi:https://doi.org/10.1210/clinem/dgaa627
 35255491,https://doi.org/10.1038/s41586-022-04569-5,SARS-CoV-2 is associated with changes in brain structure in UK Biobank.,"Douaud G, Lee S, Alfaro-Almagro F, Arthofer C, Wang C, McCarthy P, Lange F, Andersson JLR, Griffanti L, Duff E, Jbabdi S, Taschler B, Keating P, Winkler AM, Collins R, Matthews PM, Allen N, Miller KL, Nichols TE, Smith SM.",,Nature,2022,2022-03-07,Y,,,,"There is strong evidence of brain-related abnormalities in COVID-19<sup>1-13</sup>. However, it remains unknown whether the impact of SARS-CoV-2 infection can be detected in milder cases, and whether this can reveal possible mechanisms contributing to brain pathology. Here we investigated brain changes in 785 participants of UK Biobank (aged 51-81 years) who were imaged twice using magnetic resonance imaging, including 401 cases who tested positive for infection with SARS-CoV-2 between their two scans-with 141 days on average separating their diagnosis and the second scan-as well as 384 controls. The availability of pre-infection imaging data reduces the likelihood of pre-existing risk factors being misinterpreted as disease effects. We identified significant longitudinal effects when comparing the two groups, including (1) a greater reduction in grey matter thickness and tissue contrast in the orbitofrontal cortex and parahippocampal gyrus; (2) greater changes in markers of tissue damage in regions that are functionally connected to the primary olfactory cortex; and (3) a greater reduction in global brain size in the SARS-CoV-2 cases. The participants who were infected with SARS-CoV-2 also showed on average a greater cognitive decline between the two time points. Importantly, these imaging and cognitive longitudinal effects were still observed after excluding the 15 patients who had been hospitalised. These mainly limbic brain imaging results may be the in vivo hallmarks of a degenerative spread of the disease through olfactory pathways, of neuroinflammatory events, or of the loss of sensory input due to anosmia. Whether this deleterious effect can be partially reversed, or whether these effects will persist in the long term, remains to be investigated with additional follow-up.",,pdf:https://www.nature.com/articles/s41586-022-04569-5.pdf; doi:https://doi.org/10.1038/s41586-022-04569-5; html:https://europepmc.org/articles/PMC9046077; pdf:https://europepmc.org/articles/PMC9046077?pdf=render
-36773891,https://doi.org/10.1016/j.jinf.2023.02.012,"Real-world effectiveness of molnupiravir, nirmatrelvir-ritonavir, and sotrovimab on preventing hospital admission among higher-risk patients with COVID-19 in Wales: A retrospective cohort study.","Evans A, Qi C, Adebayo JO, Underwood J, Coulson J, Bailey R, Lyons R, Edwards A, Cooper A, John G, Akbari A.",,The Journal of infection,2023,2023-02-10,Y,Health protection; Public Health; Covid-19,,,"<h4>Objective</h4>To compare the effectiveness of molnupiravir, nirmatrelvir-ritonavir, and sotrovimab with no treatment in preventing hospital admission or death in higher-risk patients infected with SARS-CoV-2 in the community.<h4>Design</h4>Retrospective cohort study of non-hospitalized adult patients with COVID-19 using the Secure Anonymised Information Linkage (SAIL) Databank.<h4>Setting</h4>A real-world cohort study was conducted within the SAIL Databank (a secure trusted research environment containing anonymised, individual, population-scale electronic health record (EHR) data) for the population of Wales, UK.<h4>Participants</h4>Adult patients with COVID-19 in the community, at higher risk of hospitalization and death, testing positive for SARS-CoV-2 between 16th December 2021 and 22nd April 2022.<h4>Interventions</h4>Molnupiravir, nirmatrelvir-ritonavir, and sotrovimab given in the community by local health boards and the National Antiviral Service in Wales.<h4>Main outcome measures</h4>All-cause admission to hospital or death within 28 days of a positive test for SARS-CoV-2.<h4>Statistical analysis</h4>Cox proportional hazard model with treatment status (treated/untreated) as a time-dependent covariate and adjusted for age, sex, number of comorbidities, Welsh Index of Multiple Deprivation, and vaccination status. Secondary subgroup analyses were by treatment type, number of comorbidities, and before and on or after 20th February 2022, when omicron BA.1 and omicron BA.2 were the dominant subvariants in Wales.<h4>Results</h4>Between 16th December 2021 and 22nd April 2022, 7013 higher-risk patients were eligible for inclusion in the study. Of these, 2040 received treatment with molnupiravir (359, 17.6%), nirmatrelvir-ritonavir (602, 29.5%), or sotrovimab (1079, 52.9%). Patients in the treatment group were younger (mean age 53 vs 57 years), had fewer comorbidities, and a higher proportion had received four or more doses of the COVID-19 vaccine (36.3% vs 17.6%). Within 28 days of a positive test, 628 (9.0%) patients were admitted to hospital or died (84 treated and 544 untreated). The primary analysis indicated a lower risk of hospitalization or death at any point within 28 days in treated participants compared to those not receiving treatment. The adjusted hazard rate was 35% (95% CI: 18-49%) lower in treated than untreated participants. There was no indication of the superiority of one treatment over another and no evidence of a reduction in risk of hospitalization or death within 28 days for patients with no or only one comorbidity. In patients treated with sotrovimab, the event rates before and on or after 20th February 2022 were similar (5.0% vs 4.9%) with no significant difference in the hazard ratios for sotrovimab between the time periods.<h4>Conclusions</h4>In higher-risk adult patients in the community with COVID-19, those who received treatment with molnupiravir, nirmatrelvir-ritonavir, or sotrovimab were at lower risk of hospitalization or death than those not receiving treatment.",,pdf:http://www.journalofinfection.com/article/S0163445323000828/pdf; doi:https://doi.org/10.1016/j.jinf.2023.02.012; html:https://europepmc.org/articles/PMC9911979; pdf:https://europepmc.org/articles/PMC9911979?pdf=render
 39292500,https://doi.org/10.2196/46485,The Use of Online Consultation Systems or Remote Consulting in England Characterized Through the Primary Care Health Records of 53 Million People in the OpenSAFELY Platform: Retrospective Cohort Study.,"Fonseca M, MacKenna B, Mehrkar A, OpenSAFELY Collaborative, Walters CE, Hickman G, Pearson J, Fisher L, Inglesby P, Bacon S, Davy S, Hulme W, Goldacre B, Koffman O, Bakhai M.",,JMIR public health and surveillance,2024,2024-09-18,Y,General Practice; Primary Care Research; Remote Monitoring; Health Informatics; Triage; Online Consultation System; Opensafely; Trusted Research Environment; Digital Primary Care; Electronic Health Record Coding,,,"<h4>Background</h4>The National Health Service (NHS) Long Term Plan, published in 2019, committed to ensuring that every patient in England has the right to digital-first primary care by 2023-2024. The COVID-19 pandemic and infection prevention and control measures accelerated work by the NHS to enable and stimulate the use of online consultation (OC) systems across all practices for improved access to primary care.<h4>Objective</h4>We aimed to explore general practice coding activity associated with the use of OC systems in terms of trends, COVID-19 effect, variation, and quality.<h4>Methods</h4>With the approval of NHS England, the OpenSAFELY platform was used to query and analyze the in situ electronic health records of suppliers The Phoenix Partnership (TPP) and Egton Medical Information Systems, covering >53 million patients in >6400 practices, mainly in 2019-2020. Systematized Medical Nomenclature for Medicine-Clinical Terminology (SNOMED-CT) codes relevant to OC systems and written OCs were identified including eConsultation. Events were described by volumes and population rates, practice coverage, and trends before and after the COVID-19 pandemic. Variation was characterized among practices, by sociodemographics, and by clinical history of long-term conditions.<h4>Results</h4>Overall, 3,550,762 relevant coding events were found in practices using TPP, with the code eConsultation detected in 84.56% (2157/2551) of practices. Activity related to digital forms of interaction increased rapidly from March 2020, the onset of the pandemic; namely, in the second half of 2020, >9 monthly eConsultation coding events per 1000 registered population were registered compared to <1 a year prior. However, we found large variations among regions and practices: December 2020 saw the median practice have 0.9 coded instances per 1000 population compared to at least 36 for the highest decile of practices. On sociodemographics, the TPP cohort with OC instances, when compared (univariate analysis) to the cohort with general practitioner consultations, was more predominantly female (661,235/1,087,919, 60.78% vs 9,172,833/17,166,765, 53.43%), aged 18 to 40 years (349,162/1,080,589, 32.31% vs 4,295,711/17,000,942, 25.27%), White (730,389/1,087,919, 67.14% vs 10,887,858/17,166,765, 63.42%), and less deprived (167,889/1,068,887, 15.71% vs 3,376,403/16,867,074, 20.02%). Looking at the eConsultation code through multivariate analysis, it was more commonly recorded among patients with a history of asthma (adjusted odds ratio [aOR] 1.131, 95% CI 1.124-1.137), depression (aOR 1.144, 95% CI 1.138-1.151), or atrial fibrillation (aOR 1.119, 95% CI 1.099-1.139) when compared to other patients with general practitioner consultations, adjusted for long-term conditions, age, and gender.<h4>Conclusions</h4>We successfully queried general practice coding activity relevant to the use of OC systems, showing increased adoption and key areas of variation during the pandemic at both sociodemographic and clinical levels. The work can be expanded to support monitoring of coding quality and underlying activity. This study suggests that large-scale impact evaluation studies can be implemented within the OpenSAFELY platform, namely looking at patient outcomes.",,doi:https://doi.org/10.2196/46485; html:https://europepmc.org/articles/PMC11447420
+36773891,https://doi.org/10.1016/j.jinf.2023.02.012,"Real-world effectiveness of molnupiravir, nirmatrelvir-ritonavir, and sotrovimab on preventing hospital admission among higher-risk patients with COVID-19 in Wales: A retrospective cohort study.","Evans A, Qi C, Adebayo JO, Underwood J, Coulson J, Bailey R, Lyons R, Edwards A, Cooper A, John G, Akbari A.",,The Journal of infection,2023,2023-02-10,Y,Health protection; Public Health; Covid-19,,,"<h4>Objective</h4>To compare the effectiveness of molnupiravir, nirmatrelvir-ritonavir, and sotrovimab with no treatment in preventing hospital admission or death in higher-risk patients infected with SARS-CoV-2 in the community.<h4>Design</h4>Retrospective cohort study of non-hospitalized adult patients with COVID-19 using the Secure Anonymised Information Linkage (SAIL) Databank.<h4>Setting</h4>A real-world cohort study was conducted within the SAIL Databank (a secure trusted research environment containing anonymised, individual, population-scale electronic health record (EHR) data) for the population of Wales, UK.<h4>Participants</h4>Adult patients with COVID-19 in the community, at higher risk of hospitalization and death, testing positive for SARS-CoV-2 between 16th December 2021 and 22nd April 2022.<h4>Interventions</h4>Molnupiravir, nirmatrelvir-ritonavir, and sotrovimab given in the community by local health boards and the National Antiviral Service in Wales.<h4>Main outcome measures</h4>All-cause admission to hospital or death within 28 days of a positive test for SARS-CoV-2.<h4>Statistical analysis</h4>Cox proportional hazard model with treatment status (treated/untreated) as a time-dependent covariate and adjusted for age, sex, number of comorbidities, Welsh Index of Multiple Deprivation, and vaccination status. Secondary subgroup analyses were by treatment type, number of comorbidities, and before and on or after 20th February 2022, when omicron BA.1 and omicron BA.2 were the dominant subvariants in Wales.<h4>Results</h4>Between 16th December 2021 and 22nd April 2022, 7013 higher-risk patients were eligible for inclusion in the study. Of these, 2040 received treatment with molnupiravir (359, 17.6%), nirmatrelvir-ritonavir (602, 29.5%), or sotrovimab (1079, 52.9%). Patients in the treatment group were younger (mean age 53 vs 57 years), had fewer comorbidities, and a higher proportion had received four or more doses of the COVID-19 vaccine (36.3% vs 17.6%). Within 28 days of a positive test, 628 (9.0%) patients were admitted to hospital or died (84 treated and 544 untreated). The primary analysis indicated a lower risk of hospitalization or death at any point within 28 days in treated participants compared to those not receiving treatment. The adjusted hazard rate was 35% (95% CI: 18-49%) lower in treated than untreated participants. There was no indication of the superiority of one treatment over another and no evidence of a reduction in risk of hospitalization or death within 28 days for patients with no or only one comorbidity. In patients treated with sotrovimab, the event rates before and on or after 20th February 2022 were similar (5.0% vs 4.9%) with no significant difference in the hazard ratios for sotrovimab between the time periods.<h4>Conclusions</h4>In higher-risk adult patients in the community with COVID-19, those who received treatment with molnupiravir, nirmatrelvir-ritonavir, or sotrovimab were at lower risk of hospitalization or death than those not receiving treatment.",,pdf:http://www.journalofinfection.com/article/S0163445323000828/pdf; doi:https://doi.org/10.1016/j.jinf.2023.02.012; html:https://europepmc.org/articles/PMC9911979; pdf:https://europepmc.org/articles/PMC9911979?pdf=render
 36936592,https://doi.org/10.1136/bmjmed-2022-000151,Covid-19 variants of concern and pregnancy.,"Stock SJ, Harmer C, Calvert C.",,BMJ medicine,2022,2022-03-02,Y,Pregnancy complications; Covid-19,,,,,pdf:https://bmjmedicine.bmj.com/content/bmjmed/1/1/e000151.full.pdf; doi:https://doi.org/10.1136/bmjmed-2022-000151; html:https://europepmc.org/articles/PMC9951363; pdf:https://europepmc.org/articles/PMC9951363?pdf=render
 36168404,https://doi.org/10.1016/j.lanepe.2022.100501,Risk factors for SARS-CoV-2 infection after primary vaccination with ChAdOx1 nCoV-19 or BNT162b2 and after booster vaccination with BNT162b2 or mRNA-1273: A population-based cohort study (COVIDENCE UK).,"Vivaldi G, Jolliffe DA, Holt H, Tydeman F, Talaei M, Davies GA, Lyons RA, Griffiths CJ, Kee F, Sheikh A, Shaheen SO, Martineau AR.",,The Lancet regional health. Europe,2022,2022-09-23,Y,Vaccination; Breakthrough Infection; Chadox1; Sars-cov-2; Mrna-1273; Bnt162b2,,,"<h4>Background</h4>Little is known about how demographic, behavioural, and vaccine-related factors affect risk of post-vaccination SARS-CoV-2 infection. We aimed to identify risk factors for SARS-CoV-2 infection after primary and booster vaccinations.<h4>Methods</h4>This prospective, population-based, UK study in adults (≥16 years) vaccinated against SARS-CoV-2 assessed risk of breakthrough SARS-CoV-2 infection up to February, 2022, for participants who completed a primary vaccination course (ChAdOx1 nCoV-19 or BNT162b2) and those who received a booster dose (BNT162b2 or mRNA-1273). Cox regression models explored associations between sociodemographic, behavioural, clinical, pharmacological, and nutritional factors and test-positive breakthrough infection, adjusted for local weekly SARS-CoV-2 incidence.<h4>Findings</h4>1051 (7·1%) of 14 713 post-primary participants and 1009 (9·5%) of 10 665 post-booster participants reported breakthrough infection, over a median follow-up of 203 days (IQR 195-216) and 85 days (66-103), respectively. Primary vaccination with ChAdOx1 (<i>vs</i> BNT162b2) was associated with higher risk of infection in both post-primary analysis (adjusted hazard ratio 1·63, 95% CI 1·41-1·88) and after an mRNA-1273 booster (1·26 [1·00-1·57] <i>vs</i> BNT162b2 primary and booster). Lower risk of infection was associated with older age (post-primary: 0·97 [0·96-0·97] per year; post-booster: 0·97 [0·97-0·98]), whereas higher risk of infection was associated with lower educational attainment (post-primary: 1·78 [1·44-2·20] for primary/secondary <i>vs</i> postgraduate; post-booster: 1·46 [1·16-1·83]) and at least three weekly visits to indoor public places (post-primary: 1·36 [1·13-1·63] <i>vs</i> none; post-booster: 1·29 [1·07-1·56]).<h4>Interpretation</h4>Vaccine type, socioeconomic status, age, and behaviours affect risk of breakthrough infection after primary and booster vaccinations.<h4>Funding</h4>Barts Charity, UK Research and Innovation Industrial Strategy Challenge Fund.",,doi:https://doi.org/10.1016/j.lanepe.2022.100501; doi:https://doi.org/10.1016/j.lanepe.2022.100501; html:https://europepmc.org/articles/PMC9499825; pdf:https://europepmc.org/articles/PMC9499825?pdf=render
-33220850,https://doi.org/10.1016/s0140-6736(20)32465-x,Urgent actions and policies needed to address COVID-19 among UK ethnic minorities.,"Mathur R, Bear L, Khunti K, Eggo RM.",,"Lancet (London, England)",2020,2020-11-19,Y,,,,,,pdf:http://www.thelancet.com/article/S014067362032465X/pdf; doi:https://doi.org/10.1016/S0140-6736(20)32465-X; html:https://europepmc.org/articles/PMC7831890; pdf:https://europepmc.org/articles/PMC7831890?pdf=render
 36322788,https://doi.org/10.2196/40035,A Hybrid Architecture (CO-CONNECT) to Facilitate Rapid Discovery and Access to Data Across the United Kingdom in Response to the COVID-19 Pandemic: Development Study.,"Jefferson E, Cole C, Mumtaz S, Cox S, Giles TC, Adejumo S, Urwin E, Lea D, Macdonald C, Best J, Masood E, Milligan G, Johnston J, Horban S, Birced I, Hall C, Jackson AS, Collins C, Rising S, Dodsley C, Hampton J, Hadfield A, Santos R, Tarr S, Panagi V, Lavagna J, Jackson T, Chuter A, Beggs J, Martinez-Queipo M, Ward H, von Ziegenweidt J, Burns F, Martin J, Sebire N, Morris C, Bradley D, Baxter R, Ahonen-Bishopp A, Smith P, Shoemark A, Valdes AM, Ollivere B, Manisty C, Eyre D, Gallant S, Joy G, McAuley A, Connell D, Northstone K, Jeffery K, Di Angelantonio E, McMahon A, Walker M, Semple MG, Sims JM, Lawrence E, Davies B, Baillie JK, Tang M, Leeming G, Power L, Breeze T, Murray D, Orton C, Pierce I, Hall I, Ladhani S, Gillson N, Whitaker M, Shallcross L, Seymour D, Varma S, Reilly G, Morris A, Hopkins S, Sheikh A, Quinlan P.",,Journal of medical Internet research,2022,2022-12-27,Y,Meta-analysis; Health care; Public Health; Clinical Care; Data Extraction; Data Privacy; Health Data; Federated Network; Data Governance; Infrastructure Model; Covid-19; Health Care Record,,,"<h4>Background</h4>COVID-19 data have been generated across the United Kingdom as a by-product of clinical care and public health provision, as well as numerous bespoke and repurposed research endeavors. Analysis of these data has underpinned the United Kingdom's response to the pandemic, and informed public health policies and clinical guidelines. However, these data are held by different organizations, and this fragmented landscape has presented challenges for public health agencies and researchers as they struggle to find relevant data to access and interrogate the data they need to inform the pandemic response at pace.<h4>Objective</h4>We aimed to transform UK COVID-19 diagnostic data sets to be findable, accessible, interoperable, and reusable (FAIR).<h4>Methods</h4>A federated infrastructure model (COVID - Curated and Open Analysis and Research Platform [CO-CONNECT]) was rapidly built to enable the automated and reproducible mapping of health data partners' pseudonymized data to the Observational Medical Outcomes Partnership Common Data Model without the need for any data to leave the data controllers' secure environments, and to support federated cohort discovery queries and meta-analysis.<h4>Results</h4>A total of 56 data sets from 19 organizations are being connected to the federated network. The data include research cohorts and COVID-19 data collected through routine health care provision linked to longitudinal health care records and demographics. The infrastructure is live, supporting aggregate-level querying of data across the United Kingdom.<h4>Conclusions</h4>CO-CONNECT was developed by a multidisciplinary team. It enables rapid COVID-19 data discovery and instantaneous meta-analysis across data sources, and it is researching streamlined data extraction for use in a Trusted Research Environment for research and public health analysis. CO-CONNECT has the potential to make UK health data more interconnected and better able to answer national-level research questions while maintaining patient confidentiality and local governance procedures.",,pdf:https://www.jmir.org/2022/12/e40035/PDF; doi:https://doi.org/10.2196/40035; html:https://europepmc.org/articles/PMC9822177
+33220850,https://doi.org/10.1016/s0140-6736(20)32465-x,Urgent actions and policies needed to address COVID-19 among UK ethnic minorities.,"Mathur R, Bear L, Khunti K, Eggo RM.",,"Lancet (London, England)",2020,2020-11-19,Y,,,,,,pdf:http://www.thelancet.com/article/S014067362032465X/pdf; doi:https://doi.org/10.1016/S0140-6736(20)32465-X; html:https://europepmc.org/articles/PMC7831890; pdf:https://europepmc.org/articles/PMC7831890?pdf=render
 35780515,https://doi.org/10.1016/j.epidem.2022.100604,Appropriately smoothing prevalence data to inform estimates of growth rate and reproduction number.,"Eales O, Ainslie KEC, Walters CE, Wang H, Atchison C, Ashby D, Donnelly CA, Cooke G, Barclay W, Ward H, Darzi A, Elliott P, Riley S.",,Epidemics,2022,2022-06-22,Y,Cross-sectional study; Reproduction Number; Covid-19; Sars-cov-2; Bayesian P-Spline,,,"The time-varying reproduction number (R<sub>t</sub>) can change rapidly over the course of a pandemic due to changing restrictions, behaviours, and levels of population immunity. Many methods exist that allow the estimation of R<sub>t</sub> from case data. However, these are not easily adapted to point prevalence data nor can they infer R<sub>t</sub> across periods of missing data. We developed a Bayesian P-spline model suitable for fitting to a wide range of epidemic time-series, including point-prevalence data. We demonstrate the utility of the model by fitting to periodic daily SARS-CoV-2 swab-positivity data in England from the first 7 rounds (May 2020-December 2020) of the REal-time Assessment of Community Transmission-1 (REACT-1) study. Estimates of R<sub>t</sub> over the period of two subsequent rounds (6-8 weeks) and single rounds (2-3 weeks) inferred using the Bayesian P-spline model were broadly consistent with estimates from a simple exponential model, with overlapping credible intervals. However, there were sometimes substantial differences in point estimates. The Bayesian P-spline model was further able to infer changes in R<sub>t</sub> over shorter periods tracking a temporary increase above one during late-May 2020, a gradual increase in R<sub>t</sub> over the summer of 2020 as restrictions were eased, and a reduction in R<sub>t</sub> during England's second national lockdown followed by an increase as the Alpha variant surged. The model is robust against both under-fitting and over-fitting and is able to interpolate between periods of available data; it is a particularly versatile model when growth rate can change over small timescales, as in the current SARS-CoV-2 pandemic. This work highlights the importance of pairing robust methods with representative samples to track pandemics.",,doi:https://doi.org/10.1016/j.epidem.2022.100604; doi:https://doi.org/10.1016/j.epidem.2022.100604; html:https://europepmc.org/articles/PMC9220254; pdf:https://europepmc.org/articles/PMC9220254?pdf=render
 34796246,https://doi.org/10.1093/ofid/ofab496,"Acceptability, Usability, and Performance of Lateral Flow Immunoassay Tests for Severe Acute Respiratory Syndrome Coronavirus 2 Antibodies: REACT-2 Study of Self-Testing in Nonhealthcare Key Workers.","Davies B, Araghi M, Moshe M, Gao H, Bennet K, Jenkins J, Atchison C, Darzi A, Ashby D, Riley S, Barclay W, Elliott P, Ward H, Cooke G.",,Open forum infectious diseases,2021,2021-10-04,Y,Sensitivity and specificity; Antibody testing; Sars-cov-2; Covid-19 Diagnostic Testing,,,"<h4>Background</h4>Seroprevalence studies are essential to understand the epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Various technologies, including laboratory assays and point-of-care self-tests, are available for antibody testing. The interpretation of seroprevalence studies requires comparative data on the performance of antibody tests.<h4>Methods</h4>In June 2020, current and former members of the United Kingdom police forces and fire service performed a self-test lateral flow immunoassay (LFIA), had a nurse-performed LFIA, and provided a venous blood sample for enzyme-linked immunosorbent assay (ELISA). We present the prevalence of antibodies to SARS-CoV-2 and the acceptability and usability of self-test LFIAs, and we determine the sensitivity and specificity of LFIAs compared with laboratory ELISA.<h4>Results</h4>In this cohort of 5189 current and former members of the police service and 263 members of the fire service, 7.4% (396 of 5348; 95% confidence interval [CI], 6.7-8.1) were antibody positive. Seroprevalence was 8.9% (95% CI, 6.9-11.4) in those under 40 years, 11.5% (95% CI, 8.8-15.0) in those of nonwhite ethnicity, and 7.8% (95% CI, 7.1-8.7) in those currently working. Self-test LFIA had an acceptability of 97.7% and a usability of 90.0%. There was substantial agreement between within-participant LFIA results (kappa 0.80; 95% CI, 0.77-0.83). The LFIAs had a similar performance: compared with ELISA, sensitivity was 82.1% (95% CI, 77.7-86.0) self-test and 76.4% (95% CI, 71.9-80.5) nurse-performed with specificity of 97.8% (95% CI, 97.3-98.2) and 98.5% (95% CI, 98.1-98.8), respectively.<h4>Conclusions</h4>A greater proportion of this nonhealthcare key worker cohort showed evidence of previous infection with SARS-CoV-2 than the general population at 6.0% (95% CI, 5.8-6.1) after the first wave in England. The high acceptability and usability reported by participants and similar performance of self-test and nurse-performed LFIAs indicate that the self-test LFIA is fit for purpose for home testing in occupational and community prevalence studies.",,pdf:https://academic.oup.com/ofid/article-pdf/8/11/ofab496/41174715/ofab496.pdf; doi:https://doi.org/10.1093/ofid/ofab496; html:https://europepmc.org/articles/PMC8522420; pdf:https://europepmc.org/articles/PMC8522420?pdf=render
 36134546,https://doi.org/10.7189/jogh.12.05044,Risk of COVID-19 hospitalizations among school-aged children in Scotland: A national incident cohort study.,"Shi T, Pan J, Moore E, Katikireddi SV, Docherty AB, Fenton L, McCowan C, Agrawal U, Kerr S, Shah SA, Stock SJ, Simpson CR, Robertson C, Sheikh A, Public Health Scotland and the EAVE II Collaborators.",,Journal of global health,2022,2022-09-23,Y,,,,"<h4>Background</h4>There is considerable policy, clinical and public interest about whether children should be vaccinated against SARS-CoV-2 and, if so, which children should be prioritised (particularly if vaccine resources are limited). To inform such deliberations, we sought to identify children and young people at highest risk of hospitalization from COVID-19.<h4>Methods</h4>We used the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) platform to undertake a national incident cohort analysis to investigate the risk of hospitalization among 5-17 years old living in Scotland in risk groups defined by the living risk prediction algorithm (QCOVID). A Cox proportional hazard model was used to derive hazard ratios (HR) and 95% confidence intervals (CIs) for the association between risk groups and COVID-19 hospital admission. Adjustments were made for age, sex, socioeconomic status, co-morbidity, and prior hospitalization.<h4>Results</h4>Between March 1, 2020 and November 22, 2021, there were 146 183 (19.4% of all 752 867 children in Scotland) polymerase chain reaction (PCR) confirmed SARS-CoV-2 infections among 5-17 years old. Of those with confirmed infection, 973 (0.7%) were admitted to hospital with COVID-19. The rate of COVID-19 hospitalization was higher in those within each QCOVID risk group compared to those without the condition. Similar results were found in age stratified analyses (5-11 and 12-17 years old). Risk groups associated with an increased risk of COVID-19 hospital admission, included (adjusted HR, 95% CIs): sickle cell disease 14.35 (8.48-24.28), chronic kidney disease 11.34 (4.61-27.87), blood cancer 6.32 (3.24-12.35), rare pulmonary diseases 5.04 (2.58-9.86), type 2 diabetes 3.04 (1.34-6.92), epilepsy 2.54 (1.69-3.81), type 1 diabetes 2.48 (1.47-4.16), Down syndrome 2.45 (0.96-6.25), cerebral palsy 2.37 (1.26-4.47), severe mental illness 1.43 (0.63-3.24), fracture 1.41 (1.02-1.95), congenital heart disease 1.35 (0.82-2.23), asthma 1.28 (1.06-1.55), and learning disability (excluding Down syndrome) 1.08 (0.82-1.42), when compared to those without these conditions. Although our Cox models were adjusted for a number of potential confounders, residual confounding remains a possibility.<h4>Conclusions</h4>In this national study, we observed an increased risk of COVID-19 hospital admissions among school-aged children with specific underlying long-term health conditions compared with children without these conditions.",,pdf:https://jogh.org/wp-content/uploads/2022/10/jogh-12-05044.pdf; doi:https://doi.org/10.7189/jogh.12.05044; html:https://europepmc.org/articles/PMC9494196; pdf:https://europepmc.org/articles/PMC9494196?pdf=render
 39113083,https://doi.org/10.1186/s12916-024-03399-8,History of childhood maltreatment associated with hospitalization or death due to COVID-19: a cohort study.,"Wang Y, Ge F, Aspelund T, Ask H, Hauksdóttir A, Hu K, Jakobsdóttir J, Zoega H, Shen Q, Whalley HC, Pedersen OBV, Lehto K, Andreassen OA, Fang F, Song H, Valdimarsdóttir UA.",,BMC medicine,2024,2024-08-07,Y,Mortality; Psychiatric disorders; Hospitalization; Childhood Maltreatment; Covid-19,,,"<h4>Background</h4>Childhood maltreatment (CM) has been indicated in adverse health outcomes across the lifespan, including severe infection-related outcomes. Yet, data are scarce on the potential role of CM in severe COVID-19-related outcomes as well as on mechanisms underlying this association.<h4>Methods</h4>We included 151,427 individuals in the UK Biobank who responded to questions on the history of CM in 2016 and 2017 and were alive on January 31, 2020. Binomial logistic regression models were performed to estimate the association between a history of CM and severe COVID-19 outcomes (i.e. hospitalization or death due to COVID-19), as well as COVID-19 diagnosis and vaccination as secondary outcomes. We then explored the potential mediating roles of socio-economic status, lifestyle and pre-pandemic comorbidities, and the effect modification by polygenic risk score for severe COVID-19 outcomes.<h4>Results</h4>The mean age of the study population at the start of the pandemic was 67.7 (SD = 7.72) years, and 56.5% were female. We found the number of CM types was associated with the risk of severe COVID-19 outcomes in a graded manner (p<sub>for trend</sub> < 0.01). Compared to individuals with no history of CM, individuals exposed to any CM were more likely to be hospitalized or die due to COVID-19 (odds ratio [OR] = 1.54 [95%CI 1.31-1.81]), particularly after physical neglect (2.04 [1.57-2.62]). Largely comparable risk patterns were observed across groups of high vs. low genetic risks for severe COVID-19 outcomes (p<sub>for difference</sub> > 0.05). Mediation analysis revealed that 50.9% of the association between CM and severe COVID-19 outcomes was explained by suboptimal socio-economic status, lifestyle, and pre-pandemic diagnosis of psychiatric disorders or other chronic medical conditions. In contrast, any CM exposure was only weakly associated with COVID-19 diagnosis (1.06 [1.01-1.12]) while significantly associated with not being vaccinated for COVID-19 (1.21 [1.13-1.29]).<h4>Conclusions</h4>Our results add to the growing knowledge base indicating the role of childhood maltreatment in negative health outcomes across the lifespan, including severe COVID-19-related outcomes. The identified factors underlying this association represent potential intervention targets for mitigating the harmful effects of childhood maltreatment in COVID-19 and similar future pandemics.",,doi:https://doi.org/10.1186/s12916-024-03399-8; html:https://europepmc.org/articles/PMC11304908; pdf:https://europepmc.org/articles/PMC11304908?pdf=render
 35717168,https://doi.org/10.1186/s12879-022-07490-4,The contribution of hospital-acquired infections to the COVID-19 epidemic in England in the first half of 2020.,"Knight GM, Pham TM, Stimson J, Funk S, Jafari Y, Pople D, Evans S, Yin M, Brown CS, Bhattacharya A, Hope R, Semple MG, ISARIC4C Investigators, CMMID COVID-19 Working Group, Read JM, Cooper BS, Robotham JV.",,BMC infectious diseases,2022,2022-06-18,Y,Mathematical Modelling; Nosocomial Transmission; Covid-19; Sars-cov-2,,,"<h4>Background</h4>SARS-CoV-2 is known to transmit in hospital settings, but the contribution of infections acquired in hospitals to the epidemic at a national scale is unknown.<h4>Methods</h4>We used comprehensive national English datasets to determine the number of COVID-19 patients with identified hospital-acquired infections (with symptom onset > 7 days after admission and before discharge) in acute English hospitals up to August 2020. As patients may leave the hospital prior to detection of infection or have rapid symptom onset, we combined measures of the length of stay and the incubation period distribution to estimate how many hospital-acquired infections may have been missed. We used simulations to estimate the total number (identified and unidentified) of symptomatic hospital-acquired infections, as well as infections due to onward community transmission from missed hospital-acquired infections, to 31st July 2020.<h4>Results</h4>In our dataset of hospitalised COVID-19 patients in acute English hospitals with a recorded symptom onset date (n = 65,028), 7% were classified as hospital-acquired. We estimated that only 30% (range across weeks and 200 simulations: 20-41%) of symptomatic hospital-acquired infections would be identified, with up to 15% (mean, 95% range over 200 simulations: 14.1-15.8%) of cases currently classified as community-acquired COVID-19 potentially linked to hospital transmission. We estimated that 26,600 (25,900 to 27,700) individuals acquired a symptomatic SARS-CoV-2 infection in an acute Trust in England before 31st July 2020, resulting in 15,900 (15,200-16,400) or 20.1% (19.2-20.7%) of all identified hospitalised COVID-19 cases.<h4>Conclusions</h4>Transmission of SARS-CoV-2 to hospitalised patients likely caused approximately a fifth of identified cases of hospitalised COVID-19 in the ""first wave"" in England, but less than 1% of all infections in England. Using time to symptom onset from admission for inpatients as a detection method likely misses a substantial proportion (> 60%) of hospital-acquired infections.",,pdf:https://bmcinfectdis.biomedcentral.com/counter/pdf/10.1186/s12879-022-07490-4; doi:https://doi.org/10.1186/s12879-022-07490-4; html:https://europepmc.org/articles/PMC9206097; pdf:https://europepmc.org/articles/PMC9206097?pdf=render
-35440469,https://doi.org/10.3399/bjgp.2022.0083,"Colchicine for COVID-19 in the community (PRINCIPLE): a randomised, controlled, adaptive platform trial.","Dorward J, Yu LM, Hayward G, Saville BR, Gbinigie O, Van Hecke O, Ogburn E, Evans PH, Thomas NP, Patel MG, Richards D, Berry N, Detry MA, Saunders C, Fitzgerald M, Harris V, Shanyinde M, de Lusignan S, Andersson MI, Butler CC, Hobbs FR, PRINCIPLE Trial Collaborative Group.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2022,2022-06-30,Y,Colchicine; Community; Primary Health Care; Randomised Controlled Trial; Covid-19,,,"<h4>Background</h4>Colchicine has been proposed as a COVID-19 treatment.<h4>Aim</h4>To determine whether colchicine reduces time to recovery and COVID-19-related admissions to hospital and/or deaths among people in the community.<h4>Design and setting</h4>Prospective, multicentre, open-label, multi-arm, randomised, controlled, adaptive platform trial (PRINCIPLE).<h4>Method</h4>Adults aged ≥65 years or ≥18 years with comorbidities or shortness of breath, and unwell for ≤14 days with suspected COVID-19 in the community, were randomised to usual care, usual care plus colchicine (500 µg daily for 14 days), or usual care plus other interventions. The co-primary endpoints were time to first self-reported recovery and admission to hospital/death related to COVID-19, within 28 days, analysed using Bayesian models.<h4>Results</h4>The trial opened on 2 April 2020. Randomisation to colchicine started on 4 March 2021 and stopped on 26 May 2021 because the prespecified time to recovery futility criterion was met. The primary analysis model included 2755 participants who were SARS-CoV-2 positive, randomised to colchicine (<i>n</i> = 156), usual care (<i>n</i> = 1145), and other treatments (<i>n</i> = 1454). Time to first self-reported recovery was similar in the colchicine group compared with usual care with an estimated hazard ratio of 0.92 (95% credible interval (CrI) = 0.72 to 1.16) and an estimated increase of 1.4 days in median time to self-reported recovery for colchicine versus usual care. The probability of meaningful benefit in time to recovery was very low at 1.8%. COVID-19-related admissions to hospital/deaths were similar in the colchicine group versus usual care, with an estimated odds ratio of 0.76 (95% CrI = 0.28 to 1.89) and an estimated difference of -0.4% (95% CrI = -2.7 to 2.4).<h4>Conclusion</h4>Colchicine did not improve time to recovery in people at higher risk of complications with COVID-19 in the community.",,pdf:https://bjgp.org/content/bjgp/72/720/e446.full.pdf; doi:https://doi.org/10.3399/BJGP.2022.0083; html:https://europepmc.org/articles/PMC9037186; pdf:https://europepmc.org/articles/PMC9037186?pdf=render
 34708157,https://doi.org/10.12688/wellcomeopenres.16701.3,Estimating the duration of seropositivity of human seasonal coronaviruses using seroprevalence studies.,"Rees EM, Waterlow NR, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Lowe R, Kucharski AJ.",,Wellcome open research,2021,2021-12-21,Y,Catalytic model; Seroprevalence; Waning Immunity; Seasonal Coronavirus,,,"<b>Background:</b> The duration of immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still uncertain, but it is of key clinical and epidemiological importance. Seasonal human coronaviruses (HCoV) have been circulating for longer and, therefore, may offer insights into the long-term dynamics of reinfection for such viruses. <b>Methods:</b> Combining historical seroprevalence data from five studies covering the four circulating HCoVs with an age-structured reverse catalytic model, we estimated the likely duration of seropositivity following seroconversion. <b>Results:</b> We estimated that antibody persistence lasted between 0.9 (95% Credible interval: 0.6 - 1.6) and 3.8 (95% CrI: 2.0 - 7.4) years. Furthermore, we found the force of infection in older children and adults (those over 8.5 [95% CrI: 7.5 - 9.9] years) to be higher compared with young children in the majority of studies. <b>Conclusions:</b> These estimates of endemic HCoV dynamics could provide an indication of the future long-term infection and reinfection patterns of SARS-CoV-2.",,doi:https://doi.org/10.12688/wellcomeopenres.16701.3; html:https://europepmc.org/articles/PMC8517721; pdf:https://europepmc.org/articles/PMC8517721?pdf=render
+35440469,https://doi.org/10.3399/bjgp.2022.0083,"Colchicine for COVID-19 in the community (PRINCIPLE): a randomised, controlled, adaptive platform trial.","Dorward J, Yu LM, Hayward G, Saville BR, Gbinigie O, Van Hecke O, Ogburn E, Evans PH, Thomas NP, Patel MG, Richards D, Berry N, Detry MA, Saunders C, Fitzgerald M, Harris V, Shanyinde M, de Lusignan S, Andersson MI, Butler CC, Hobbs FR, PRINCIPLE Trial Collaborative Group.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2022,2022-06-30,Y,Colchicine; Community; Primary Health Care; Randomised Controlled Trial; Covid-19,,,"<h4>Background</h4>Colchicine has been proposed as a COVID-19 treatment.<h4>Aim</h4>To determine whether colchicine reduces time to recovery and COVID-19-related admissions to hospital and/or deaths among people in the community.<h4>Design and setting</h4>Prospective, multicentre, open-label, multi-arm, randomised, controlled, adaptive platform trial (PRINCIPLE).<h4>Method</h4>Adults aged ≥65 years or ≥18 years with comorbidities or shortness of breath, and unwell for ≤14 days with suspected COVID-19 in the community, were randomised to usual care, usual care plus colchicine (500 µg daily for 14 days), or usual care plus other interventions. The co-primary endpoints were time to first self-reported recovery and admission to hospital/death related to COVID-19, within 28 days, analysed using Bayesian models.<h4>Results</h4>The trial opened on 2 April 2020. Randomisation to colchicine started on 4 March 2021 and stopped on 26 May 2021 because the prespecified time to recovery futility criterion was met. The primary analysis model included 2755 participants who were SARS-CoV-2 positive, randomised to colchicine (<i>n</i> = 156), usual care (<i>n</i> = 1145), and other treatments (<i>n</i> = 1454). Time to first self-reported recovery was similar in the colchicine group compared with usual care with an estimated hazard ratio of 0.92 (95% credible interval (CrI) = 0.72 to 1.16) and an estimated increase of 1.4 days in median time to self-reported recovery for colchicine versus usual care. The probability of meaningful benefit in time to recovery was very low at 1.8%. COVID-19-related admissions to hospital/deaths were similar in the colchicine group versus usual care, with an estimated odds ratio of 0.76 (95% CrI = 0.28 to 1.89) and an estimated difference of -0.4% (95% CrI = -2.7 to 2.4).<h4>Conclusion</h4>Colchicine did not improve time to recovery in people at higher risk of complications with COVID-19 in the community.",,pdf:https://bjgp.org/content/bjgp/72/720/e446.full.pdf; doi:https://doi.org/10.3399/BJGP.2022.0083; html:https://europepmc.org/articles/PMC9037186; pdf:https://europepmc.org/articles/PMC9037186?pdf=render
 36936265,https://doi.org/10.1136/bmjmed-2022-000276,"Trends, variation, and clinical characteristics of recipients of antiviral drugs and neutralising monoclonal antibodies for covid-19 in community settings: retrospective, descriptive cohort study of 23.4 million people in OpenSAFELY.","Green ACA, Curtis HJ, Higgins R, Nab L, Mahalingasivam V, Smith RM, Mehrkar A, Inglesby P, Drysdale H, DeVito NJ, Croker R, Rentsch CT, Bhaskaran K, Tazare J, Zheng B, Andrews CD, Bacon SCJ, Davy S, Dillingham I, Evans D, Fisher L, Hickman G, Hopcroft LEM, Hulme WJ, Massey J, MacDonald O, Morley J, Morton CE, Park RY, Walker AJ, Ward T, Wiedemann M, Bates C, Cockburn J, Parry J, Hester F, Harper S, Douglas IJ, Evans SJW, Goldacre B, Tomlinson LA, MacKenna B.",,BMJ medicine,2023,2023-01-13,Y,Therapeutics; Community health services; Public Health; Covid-19,,,"<h4>Objective</h4>To ascertain patient eligibility status and describe coverage of antiviral drugs and neutralising monoclonal antibodies (nMAB) as treatment for covid-19 in community settings in England.<h4>Design</h4>Retrospective, descriptive cohort study, approved by NHS England.<h4>Setting</h4>Routine clinical data from 23.4 million people linked to data on covid-19 infection and treatment, within the OpenSAFELY-TPP database.<h4>Participants</h4>Outpatients with covid-19 at high risk of severe outcomes.<h4>Interventions</h4>Nirmatrelvir/ritonavir (paxlovid), sotrovimab, molnupiravir, casirivimab/imdevimab, or remdesivir, used in the community by covid-19 medicine delivery units.<h4>Results</h4>93 870 outpatients with covid-19 were identified between 11 December 2021 and 28 April 2022 to be at high risk of severe outcomes and therefore potentially eligible for antiviral or nMAB treatment (or both). Of these patients, 19 040 (20%) received treatment (sotrovimab, 9660 (51%); molnupiravir, 4620 (24%); paxlovid, 4680 (25%); casirivimab/imdevimab, 50 (<1%); and remdesivir, 30 (<1%)). The proportion of patients treated increased from 9% (190/2220) in the first week of treatment availability to 29% (460/1600) in the latest week. The proportion treated varied by high risk group, being lowest in those with liver disease (16%; 95% confidence interval 15% to 17%); by treatment type, with sotrovimab favoured over molnupiravir and paxlovid in all but three high risk groups (Down's syndrome (35%; 30% to 39%), rare neurological conditions (45%; 43% to 47%), and immune deficiencies (48%; 47% to 50%)); by age, ranging from ≥80 years (13%; 12% to 14%) to 50-59 years (23%; 22% to 23%); by ethnic group, ranging from black (11%; 10% to 12%) to white (21%; 21% to 21%); by NHS region, ranging from 13% (12% to 14%) in Yorkshire and the Humber to 25% (24% to 25%) in the East of England); and by deprivation level, ranging from 15% (14% to 15%) in the most deprived areas to 23% (23% to 24%) in the least deprived areas. Groups that also had lower coverage included unvaccinated patients (7%; 6% to 9%), those with dementia (6%; 5% to 7%), and care home residents (6%; 6% to 7%).<h4>Conclusions</h4>Using the OpenSAFELY platform, we were able to identify patients with covid-19 at high risk of severe outcomes who were potentially eligible to receive treatment and assess the coverage of these new treatments among these patients. In the context of a rapid deployment of a new service, the NHS analytical code used to determine eligibility could have been over-inclusive and some of the eligibility criteria not fully captured in healthcare data. However targeted activity might be needed to resolve apparent lower treatment coverage observed among certain groups, in particular (at present): different NHS regions, ethnic groups, people aged ≥80 years, those living in socioeconomically deprived areas, and care home residents.",,pdf:https://bmjmedicine.bmj.com/content/bmjmed/2/1/e000276.full.pdf; doi:https://doi.org/10.1136/bmjmed-2022-000276; html:https://europepmc.org/articles/PMC9951378; pdf:https://europepmc.org/articles/PMC9951378?pdf=render
-38166330,https://doi.org/10.1148/ryai.220266,The Scottish Medical Imaging Archive: 57.3 Million Radiology Studies Linked to Their Medical Records.,"Baxter R, Nind T, Sutherland J, McAllister G, Hardy D, Hume A, MacLeod R, Caldwell J, Krueger S, Tramma L, Teviotdale R, Gillen K, Scobbie D, Baillie I, Brooks A, Prodan B, Kerr W, Sloan-Murphy D, Herrera JFR, van Beek EJR, Reel PS, Reel S, Mansouri-Benssassi E, Mudie R, Steele D, Doney A, Trucco E, Morris C, Wallace R, Morris A, Parsons M, Jefferson E.",,Radiology. Artificial intelligence,2024,2024-01-01,Y,MRI; CT; ultrasound; angiography; Conventional Radiography; mammography; Imaging Sequences,,,"<b>Keywords:</b> MRI, Imaging Sequences, Ultrasound, Mammography, CT, Angiography, Conventional Radiography Published under a CC BY 4.0 license. See also the commentary by Whitman and Vining in this issue.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10831519; doi:https://doi.org/10.1148/ryai.220266; html:https://europepmc.org/articles/PMC10831519; pdf:https://europepmc.org/articles/PMC10831519?pdf=render
 34145260,https://doi.org/10.1038/s41467-021-23935-x,Community factors and excess mortality in first wave of the COVID-19 pandemic in England.,"Davies B, Parkes BL, Bennett J, Fecht D, Blangiardo M, Ezzati M, Elliott P.",,Nature communications,2021,2021-06-18,Y,,,,"Risk factors for increased risk of death from COVID-19 have been identified, but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality in people aged 40 years and older at the community level during the first wave of the pandemic in England, March-May 2020 compared with 2015-2019. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or with a non-white ethnicity. We found no association between population density or air pollution and excess mortality. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed to avoid further widening of inequalities in mortality patterns as the pandemic progresses.",,pdf:https://www.nature.com/articles/s41467-021-23935-x.pdf; doi:https://doi.org/10.1038/s41467-021-23935-x; html:https://europepmc.org/articles/PMC8213785; pdf:https://europepmc.org/articles/PMC8213785?pdf=render
+38166330,https://doi.org/10.1148/ryai.220266,The Scottish Medical Imaging Archive: 57.3 Million Radiology Studies Linked to Their Medical Records.,"Baxter R, Nind T, Sutherland J, McAllister G, Hardy D, Hume A, MacLeod R, Caldwell J, Krueger S, Tramma L, Teviotdale R, Gillen K, Scobbie D, Baillie I, Brooks A, Prodan B, Kerr W, Sloan-Murphy D, Herrera JFR, van Beek EJR, Reel PS, Reel S, Mansouri-Benssassi E, Mudie R, Steele D, Doney A, Trucco E, Morris C, Wallace R, Morris A, Parsons M, Jefferson E.",,Radiology. Artificial intelligence,2024,2024-01-01,Y,MRI; CT; ultrasound; angiography; Conventional Radiography; mammography; Imaging Sequences,,,"<b>Keywords:</b> MRI, Imaging Sequences, Ultrasound, Mammography, CT, Angiography, Conventional Radiography Published under a CC BY 4.0 license. See also the commentary by Whitman and Vining in this issue.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10831519; doi:https://doi.org/10.1148/ryai.220266; html:https://europepmc.org/articles/PMC10831519; pdf:https://europepmc.org/articles/PMC10831519?pdf=render
 35226680,https://doi.org/10.1371/journal.pone.0264023,"COVID-19 mitigation measures in primary schools and association with infection and school staff wellbeing: An observational survey linked with routine data in Wales, UK.","Marchant E, Griffiths L, Crick T, Fry R, Hollinghurst J, James M, Cowley L, Abbasizanjani H, Torabi F, Thompson DA, Kennedy J, Akbari A, Gravenor MB, Lyons RA, Brophy S.",,PloS one,2022,2022-02-28,Y,,,,"<h4>Introduction</h4>School-based COVID-19 mitigation strategies have greatly impacted the primary school day (children aged 3-11) including: wearing face coverings, two metre distancing, no mixing of children, and no breakfast clubs or extra-curricular activities. This study examines these mitigation measures and association with COVID-19 infection, respiratory infection, and school staff wellbeing between October to December 2020 in Wales, UK.<h4>Methods</h4>A school staff survey captured self-reported COVID-19 mitigation measures in the school, participant anxiety and depression, and open-text responses regarding experiences of teaching and implementing measures. These survey responses were linked to national-scale COVID-19 test results data to examine association of measures in the school and the likelihood of a positive (staff or pupil) COVID-19 case in the school (clustered by school, adjusted for school size and free school meals using logistic regression). Linkage was conducted through the SAIL (Secure Anonymised Information Linkage) Databank.<h4>Results</h4>Responses were obtained from 353 participants from 59 primary schools within 15 of 22 local authorities. Having more direct non-household contacts was associated with a higher likelihood of COVID-19 positive case in the school (1-5 contacts compared to none, OR 2.89 (1.01, 8.31)) and a trend to more self-reported cold symptoms. Staff face covering was not associated with a lower odds of school COVID-19 cases (mask vs. no covering OR 2.82 (1.11, 7.14)) and was associated with higher self-reported cold symptoms. School staff reported the impacts of wearing face coverings on teaching, including having to stand closer to pupils and raise their voices to be heard. 67.1% were not able to implement two metre social distancing from pupils. We did not find evidence that maintaining a two metre distance was associated with lower rates of COVID-19 in the school.<h4>Conclusions</h4>Implementing, adhering to and evaluating COVID-19 mitigation guidelines is challenging in primary school settings. Our findings suggest that reducing non-household direct contacts lowers infection rates. There was no evidence that face coverings, two metre social distancing or stopping children mixing was associated with lower odds of COVID-19 or cold infection rates in the school. Primary school staff found teaching challenging during COVID-19 restrictions, especially for younger learners and those with additional learning needs.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0264023&type=printable; doi:https://doi.org/10.1371/journal.pone.0264023; html:https://europepmc.org/articles/PMC8884508; pdf:https://europepmc.org/articles/PMC8884508?pdf=render
 34304048,https://doi.org/10.1016/j.ebiom.2021.103485,Shorter leukocyte telomere length is associated with adverse COVID-19 outcomes: A cohort study in UK Biobank.,"Wang Q, Codd V, Raisi-Estabragh Z, Musicha C, Bountziouka V, Kaptoge S, Allara E, Angelantonio ED, Butterworth AS, Wood AM, Thompson JR, Petersen SE, Harvey NC, Danesh JN, Samani NJ, Nelson CP.",,EBioMedicine,2021,2021-07-23,Y,,,,"Background Older age is the most powerful risk factor for adverse coronavirus disease-19 (COVID-19) outcomes. It is uncertain whether leucocyte telomere length (LTL), previously proposed as a marker of biological age, is also associated with COVID-19 outcomes. Methods We associated LTL values obtained from participants recruited into UK Biobank (UKB) during 2006-2010 with adverse COVID-19 outcomes recorded by 30 November 2020, defined as a composite of any of the following: hospital admission, need for critical care, respiratory support, or mortality. Using information on 130 LTL-associated genetic variants, we conducted exploratory Mendelian randomisation (MR) analyses in UKB to evaluate whether observational associations might reflect cause-and-effect relationships. Findings Of 6775 participants in UKB who tested positive for infection with SARS-CoV-2 in the community, there were 914 (13.5%) with adverse COVID-19 outcomes. The odds ratio (OR) for adverse COVID-19 outcomes was 1·17 (95% CI 1·05-1·30; P = 0·004) per 1-SD shorter usual LTL, after adjustment for age, sex and ethnicity. Similar ORs were observed in analyses that: adjusted for additional risk factors; disaggregated the composite outcome and reduced the scope for selection or collider bias. In MR analyses, the OR for adverse COVID-19 outcomes was directionally concordant but non-significant. Interpretation Shorter LTL is associated with higher risk of adverse COVID-19 outcomes, independent of several major risk factors for COVID-19 including age. Further data are needed to determine whether this association reflects causality. Funding UK Medical Research Council, Biotechnology and Biological Sciences Research Council and British Heart Foundation.",,pdf:http://www.thelancet.com/article/S2352396421002784/pdf; doi:https://doi.org/10.1016/j.ebiom.2021.103485; html:https://europepmc.org/articles/PMC8299112; pdf:https://europepmc.org/articles/PMC8299112?pdf=render
 32220655,https://doi.org/10.1016/s2468-2667(20)30073-6,"The effect of control strategies to reduce social mixing on outcomes of the COVID-19 epidemic in Wuhan, China: a modelling study.","Prem K, Liu Y, Russell TW, Kucharski AJ, Eggo RM, Davies N, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Jit M, Klepac P.",,The Lancet. Public health,2020,2020-03-25,Y,,,,"<h4>Background</h4>In December, 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus, emerged in Wuhan, China. Since then, the city of Wuhan has taken unprecedented measures in response to the outbreak, including extended school and workplace closures. We aimed to estimate the effects of physical distancing measures on the progression of the COVID-19 epidemic, hoping to provide some insights for the rest of the world.<h4>Methods</h4>To examine how changes in population mixing have affected outbreak progression in Wuhan, we used synthetic location-specific contact patterns in Wuhan and adapted these in the presence of school closures, extended workplace closures, and a reduction in mixing in the general community. Using these matrices and the latest estimates of the epidemiological parameters of the Wuhan outbreak, we simulated the ongoing trajectory of an outbreak in Wuhan using an age-structured susceptible-exposed-infected-removed (SEIR) model for several physical distancing measures. We fitted the latest estimates of epidemic parameters from a transmission model to data on local and internationally exported cases from Wuhan in an age-structured epidemic framework and investigated the age distribution of cases. We also simulated lifting of the control measures by allowing people to return to work in a phased-in way and looked at the effects of returning to work at different stages of the underlying outbreak (at the beginning of March or April).<h4>Findings</h4>Our projections show that physical distancing measures were most effective if the staggered return to work was at the beginning of April; this reduced the median number of infections by more than 92% (IQR 66-97) and 24% (13-90) in mid-2020 and end-2020, respectively. There are benefits to sustaining these measures until April in terms of delaying and reducing the height of the peak, median epidemic size at end-2020, and affording health-care systems more time to expand and respond. However, the modelled effects of physical distancing measures vary by the duration of infectiousness and the role school children have in the epidemic.<h4>Interpretation</h4>Restrictions on activities in Wuhan, if maintained until April, would probably help to delay the epidemic peak. Our projections suggest that premature and sudden lifting of interventions could lead to an earlier secondary peak, which could be flattened by relaxing the interventions gradually. However, there are limitations to our analysis, including large uncertainties around estimates of R<sub>0</sub> and the duration of infectiousness.<h4>Funding</h4>Bill & Melinda Gates Foundation, National Institute for Health Research, Wellcome Trust, and Health Data Research UK.",,pdf:https://repository.publisso.de/resource/frl:6420088/data; doi:https://doi.org/10.1016/S2468-2667(20)30073-6; html:https://europepmc.org/articles/PMC7158905
@@ -360,8 +360,8 @@ PMC9023380,https://doi.org/,Assessing the spread risk of COVID-19 associated wit
 34598993,https://doi.org/10.1136/bmjopen-2021-054410,"Changes in neonatal admissions, care processes and outcomes in England and Wales during the COVID-19 pandemic: a whole population cohort study.","Greenbury SF, Longford N, Ougham K, Angelini ED, Battersby C, Uthaya S, Modi N.",,BMJ open,2021,2021-10-01,Y,Public Health; Neonatology; Neonatal Intensive & Critical Care,,,"<h4>Objectives</h4>The COVID-19 pandemic instigated multiple societal and healthcare interventions with potential to affect perinatal practice. We evaluated population-level changes in preterm and full-term admissions to neonatal units, care processes and outcomes.<h4>Design</h4>Observational cohort study using the UK National Neonatal Research Database.<h4>Setting</h4>England and Wales.<h4>Participants</h4>Admissions to National Health Service neonatal units from 2012 to 2020.<h4>Main outcome measures</h4>Admissions by gestational age, ethnicity and Index of Multiple Deprivation, and key care processes and outcomes.<h4>Methods</h4>We calculated differences in numbers and rates between April and June 2020 (spring), the first 3 months of national lockdown (COVID-19 period), and December 2019-February 2020 (winter), prior to introduction of mitigation measures, and compared them with the corresponding differences in the previous 7 years. We considered the COVID-19 period highly unusual if the spring-winter difference was smaller or larger than all previous corresponding differences, and calculated the level of confidence in this conclusion.<h4>Results</h4>Marked fluctuations occurred in all measures over the 8 years with several highly unusual changes during the COVID-19 period. Total admissions fell, having risen over all previous years (COVID-19 difference: -1492; previous 7-year difference range: +100, +1617; p<0.001); full-term black admissions rose (+66; -64, +35; p<0.001) whereas Asian (-137; -14, +101; p<0.001) and white (-319; -235, +643: p<0.001) admissions fell. Transfers to higher and lower designation neonatal units increased (+129; -4, +88; p<0.001) and decreased (-47; -25, +12; p<0.001), respectively. Total preterm admissions decreased (-350; -26, +479; p<0.001). The fall in extremely preterm admissions was most marked in the two lowest socioeconomic quintiles.<h4>Conclusions</h4>Our findings indicate substantial changes occurred in care pathways and clinical thresholds, with disproportionate effects on black ethnic groups, during the immediate COVID-19 period, and raise the intriguing possibility that non-healthcare interventions may reduce extremely preterm births.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/10/e054410.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-054410; html:https://europepmc.org/articles/PMC8488283; pdf:https://europepmc.org/articles/PMC8488283?pdf=render
 34544601,https://doi.org/10.1016/j.vaccine.2021.09.019,"Inequalities in coverage of COVID-19 vaccination: A population register based cross-sectional study in Wales, UK.","Perry M, Akbari A, Cottrell S, Gravenor MB, Roberts R, Lyons RA, Bedston S, Torabi F, Griffiths L.",,Vaccine,2021,2021-09-08,Y,Ethnic Groups; Vaccination; Socioeconomic Factors; Immunisation; Covid-19 Vaccines,,,"The COVID-19 pandemic has highlighted existing health inequalities for ethnic minority groups and those living in more socioeconomically deprived areas in the UK. With higher levels of severe outcomes in these groups, equitable vaccination coverage should be prioritised. The aim of this study was to identify inequalities in coverage of COVID-19 vaccination in Wales, UK and to highlight areas which may benefit from routine enhanced surveillance and targeted interventions. Records within the Wales Immunisation System (WIS) population register were linked to the Welsh Demographic Service Dataset (WDSD) and central list of shielding patients, held within the Secure Anonymised Information Linkage (SAIL) Databank. Ethnic group was derived from the 2011 census and over 20 administrative electronic health record (EHR) data sources. Uptake of first dose of any COVID-19 vaccine was analysed over time, with the odds of being vaccinated as at 25th April 2021 by sex, health board of residence, rural/urban classification, deprivation quintile and ethnic group presented. Using logistic regression models, analyses were adjusted for age group, care home resident status, health and social care worker status and shielding status. This study included 1,256,412 individuals aged 50 years and over. Vaccine coverage increased steadily from 8th December 2020 until mid-April 2021. Overall uptake of first dose of COVID-19 vaccine in this group was 92.1%. After adjustment the odds of being vaccinated were lower for individuals who were male, resident in the most deprived areas, resident in an urban area and an ethnic group other than White. The largest inequality was seen between ethnic groups, with the odds of being vaccinated 0.22 (95 %CI 0.21-0.24) if in any Black ethnic group compared to any White ethnic group. Ongoing monitoring of inequity in uptake of vaccinations is required, with better targeted interventions and engagement with deprived and ethnic communities to improve vaccination uptake.",,doi:https://doi.org/10.1016/j.vaccine.2021.09.019; doi:https://doi.org/10.1016/j.vaccine.2021.09.019; html:https://europepmc.org/articles/PMC8423991
 34782484,https://doi.org/10.1136/thoraxjnl-2021-217580,External validation of the QCovid risk prediction algorithm for risk of COVID-19 hospitalisation and mortality in adults: national validation cohort study in Scotland.,"Simpson CR, Robertson C, Kerr S, Shi T, Vasileiou E, Moore E, McCowan C, Agrawal U, Docherty A, Mulholland R, Murray J, Ritchie LD, McMenamin J, Hippisley-Cox J, Sheikh A.",,Thorax,2022,2021-11-15,Y,Clinical Epidemiology; Covid-19,,,"<h4>Background</h4>The QCovid algorithm is a risk prediction tool that can be used to stratify individuals by risk of COVID-19 hospitalisation and mortality. Version 1 of the algorithm was trained using data covering 10.5 million patients in England in the period 24 January 2020 to 30 April 2020. We carried out an external validation of version 1 of the QCovid algorithm in Scotland.<h4>Methods</h4>We established a national COVID-19 data platform using individual level data for the population of Scotland (5.4 million residents). Primary care data were linked to reverse-transcription PCR (RT-PCR) virology testing, hospitalisation and mortality data. We assessed the performance of the QCovid algorithm in predicting COVID-19 hospitalisations and deaths in our dataset for two time periods matching the original study: 1 March 2020 to 30 April 2020, and 1 May 2020 to 30 June 2020.<h4>Results</h4>Our dataset comprised 5 384 819 individuals, representing 99% of the estimated population (5 463 300) resident in Scotland in 2020. The algorithm showed good calibration in the first period, but systematic overestimation of risk in the second period, prior to temporal recalibration. Harrell's C for deaths in females and males in the first period was 0.95 (95% CI 0.94 to 0.95) and 0.93 (95% CI 0.92 to 0.93), respectively. Harrell's C for hospitalisations in females and males in the first period was 0.81 (95% CI 0.80 to 0.82) and 0.82 (95% CI 0.81 to 0.82), respectively.<h4>Conclusions</h4>Version 1 of the QCovid algorithm showed high levels of discrimination in predicting the risk of COVID-19 hospitalisations and deaths in adults resident in Scotland for the original two time periods studied, but is likely to need ongoing recalibration prospectively.",,pdf:https://thorax.bmj.com/content/thoraxjnl/77/5/497.full.pdf; doi:https://doi.org/10.1136/thoraxjnl-2021-217580; html:https://europepmc.org/articles/PMC8595052; pdf:https://europepmc.org/articles/PMC8595052?pdf=render
-34870142,https://doi.org/10.1016/j.infpip.2021.100192,"Effectiveness of infection prevention and control interventions, excluding personal protective equipment, to prevent nosocomial transmission of SARS-CoV-2: a systematic review and call for action.","Jafari Y, Yin M, Lim C, Pople D, Evans S, Stimson J, Pham TM, LSHTM CMMID COVID-19 working group, Read JM, Robotham JV, Cooper BS, Knight GM.",,Infection prevention in practice,2022,2021-11-29,Y,,,,"Many infection prevention and control (IPC) interventions have been adopted by hospitals to limit nosocomial transmission of SARS-CoV-2. The aim of this systematic review is to identify evidence on the effectiveness of these interventions. We conducted a literature search of five databases (OVID MEDLINE, Embase, CENTRAL, COVID-19 Portfolio (pre-print), Web of Science). SWIFT ActiveScreener software was used to screen English titles and abstracts published between 1st January 2020 and 6th April 2021. Intervention studies, defined by Cochrane Effective Practice and Organisation of Care, that evaluated IPC interventions with an outcome of SARS-CoV-2 infection in either patients or healthcare workers were included. Personal protective equipment (PPE) was excluded as this intervention had been previously reviewed. Risks of bias were assessed using the Cochrane tool for randomised trials (RoB2) and non-randomized studies of interventions (ROBINS-I). From 23,156 screened articles, we identified seven articles that met the inclusion criteria, all of which evaluated interventions to prevent infections in healthcare workers and the majority of which were focused on effectiveness of prophylaxes. Due to heterogeneity in interventions, we did not conduct a meta-analysis. All agents used for prophylaxes have little to no evidence of effectiveness against SARS-CoV-2 infections. We did not find any studies evaluating the effectiveness of interventions including but not limited to screening, isolation and improved ventilation. There is limited evidence from interventional studies, excluding PPE, evaluating IPC measures for SARS-CoV-2. This review calls for urgent action to implement such studies to inform policies to protect our most vulnerable populations and healthcare workers.",,doi:https://doi.org/10.1016/j.infpip.2021.100192; doi:https://doi.org/10.1016/j.infpip.2021.100192; html:https://europepmc.org/articles/PMC8628369; pdf:https://europepmc.org/articles/PMC8628369?pdf=render
 37142468,https://doi.org/10.1016/j.soncn.2023.151439,A National Audit of Pancreatic Enzyme Prescribing in Pancreatic Cancer from 2015 to 2023 in England Using OpenSAFELY-TPP.,"Lemanska A, Andrews C, Fisher L, Butler-Cole B, Mehrkar A, Roberts KJ, Goldacre B, Walker AJ, MacKenna B, OpenSAFELY Collaborative.",,Seminars in oncology nursing,2023,2023-05-02,N,Pancreatic cancer; Quality Of Care; Electronic Health Records; Prescribing Audit; Covid-19; Pancreatic Cancer Enzyme Replacement; Pancreatic Enzyme Insufficiency,,,"<h4>Objectives</h4>Cancer treatments were variably disrupted during the coronavirus disease 2019 (COVID-19) pandemic. UK guidelines recommend pancreatic enzyme replacement therapy (PERT) to all people with unresectable pancreatic cancer. The aim was to investigate the impact of the COVID-19 pandemic on PERT prescribing to people with unresectable pancreatic cancer and to investigate the national and regional rates from January 2015 to January 2023.<h4>Data sources</h4>With the approval of NHS England, we conducted this study using 24 million electronic health records of people within the OpenSAFELY-TPP research platform. There were 22,860 people diagnosed with pancreatic cancer in the study cohort. We visualized the trends over time and modeled the effect of the COVID-19 pandemic with the interrupted time-series analysis.<h4>Conclusion</h4>In contrast to many other treatments, prescribing of PERT was not affected during the pandemic. Overall, since 2015, the rates increased steadily over time by 1% every year. The national rates ranged from 41% in 2015 to 48% in early 2023. There was substantial regional variation, with the highest rates of 50% to 60% in West Midlands.<h4>Implications for nursing practice</h4>In pancreatic cancer, if PERT is prescribed, it is usually initiated in hospitals by clinical nurse specialists and continued after discharge by primary care practitioners. At just under 50% in early 2023, the rates were still below the recommended 100% standard. More research is needed to understand barriers to prescribing of PERT and geographic variation to improve quality of care. Prior work relied on manual audits. With OpenSAFELY, we developed an automated audit that allows for regular updates (https://doi.org/10.53764/rpt.a0b1b51c7a).",,doi:https://doi.org/10.1016/j.soncn.2023.151439; doi:https://doi.org/10.1016/j.soncn.2023.151439; html:https://europepmc.org/articles/PMC7616357; pdf:https://europepmc.org/articles/PMC7616357?pdf=render; doi:https://doi.org/10.1016/j.soncn.2023.151439
+34870142,https://doi.org/10.1016/j.infpip.2021.100192,"Effectiveness of infection prevention and control interventions, excluding personal protective equipment, to prevent nosocomial transmission of SARS-CoV-2: a systematic review and call for action.","Jafari Y, Yin M, Lim C, Pople D, Evans S, Stimson J, Pham TM, LSHTM CMMID COVID-19 working group, Read JM, Robotham JV, Cooper BS, Knight GM.",,Infection prevention in practice,2022,2021-11-29,Y,,,,"Many infection prevention and control (IPC) interventions have been adopted by hospitals to limit nosocomial transmission of SARS-CoV-2. The aim of this systematic review is to identify evidence on the effectiveness of these interventions. We conducted a literature search of five databases (OVID MEDLINE, Embase, CENTRAL, COVID-19 Portfolio (pre-print), Web of Science). SWIFT ActiveScreener software was used to screen English titles and abstracts published between 1st January 2020 and 6th April 2021. Intervention studies, defined by Cochrane Effective Practice and Organisation of Care, that evaluated IPC interventions with an outcome of SARS-CoV-2 infection in either patients or healthcare workers were included. Personal protective equipment (PPE) was excluded as this intervention had been previously reviewed. Risks of bias were assessed using the Cochrane tool for randomised trials (RoB2) and non-randomized studies of interventions (ROBINS-I). From 23,156 screened articles, we identified seven articles that met the inclusion criteria, all of which evaluated interventions to prevent infections in healthcare workers and the majority of which were focused on effectiveness of prophylaxes. Due to heterogeneity in interventions, we did not conduct a meta-analysis. All agents used for prophylaxes have little to no evidence of effectiveness against SARS-CoV-2 infections. We did not find any studies evaluating the effectiveness of interventions including but not limited to screening, isolation and improved ventilation. There is limited evidence from interventional studies, excluding PPE, evaluating IPC measures for SARS-CoV-2. This review calls for urgent action to implement such studies to inform policies to protect our most vulnerable populations and healthcare workers.",,doi:https://doi.org/10.1016/j.infpip.2021.100192; doi:https://doi.org/10.1016/j.infpip.2021.100192; html:https://europepmc.org/articles/PMC8628369; pdf:https://europepmc.org/articles/PMC8628369?pdf=render
 35715350,https://doi.org/10.1016/j.vaccine.2022.06.010,Safety of COVID-19 vaccination and acute neurological events: A self-controlled case series in England using the OpenSAFELY platform.,"Walker JL, Schultze A, Tazare J, Tamborska A, Singh B, Donegan K, Stowe J, Morton CE, Hulme WJ, Curtis HJ, Williamson EJ, Mehrkar A, Eggo RM, Rentsch CT, Mathur R, Bacon S, Walker AJ, Davy S, Evans D, Inglesby P, Hickman G, MacKenna B, Tomlinson L, Ca Green A, Fisher L, Cockburn J, Parry J, Hester F, Harper S, Bates C, Evans SJ, Solomon T, Andrews NJ, Douglas IJ, Goldacre B, Smeeth L, McDonald HI.",,Vaccine,2022,2022-06-07,Y,Transverse Myelitis; Guillain-barré Syndrome; Vaccine Safety; Self-controlled Case Series; Bell’s Palsy; Covid-19 Vaccines,,,"<h4>Introduction</h4>We investigated the potential association of COVID-19 vaccination with three acute neurological events: Guillain-Barré syndrome (GBS), transverse myelitis and Bell's palsy.<h4>Methods</h4>With the approval of NHS England we analysed primary care data from >17 million patients in England linked to emergency care, hospital admission and mortality records in the OpenSAFELY platform. Separately for each vaccine brand, we used a self-controlled case series design to estimate the incidence rate ratio for each outcome in the period following vaccination (4-42 days for GBS, 4-28 days for transverse myelitis and Bell's palsy) compared to a within-person baseline, using conditional Poisson regression.<h4>Results</h4>Among 7,783,441 ChAdOx1 vaccinees, there was an increased rate of GBS (N = 517; incidence rate ratio 2·85; 95% CI2·33-3·47) and Bell's palsy (N = 5,350; 1·39; 1·27-1·53) following a first dose of ChAdOx1 vaccine, corresponding to 11.0 additional cases of GBS and 17.9 cases of Bell's palsy per 1 million vaccinees if causal. For GBS this applied to the first, but not the second, dose. There was no clear evidence of an association of ChAdOx1 vaccination with transverse myelitis (N = 199; 1·51; 0·96-2·37). Among 5,729,152 BNT162b2 vaccinees, there was no evidence of any association with GBS (N = 283; 1·09; 0·75-1·57), transverse myelitis (N = 109; 1·62; 0·86-3·03) or Bell's palsy (N = 3,609; 0·89; 0·76-1·03). Among 255,446 mRNA-1273 vaccine recipients there was no evidence of an association with Bell's palsy (N = 78; 0·88, 0·32-2·42).<h4>Conclusions</h4>COVID-19 vaccines save lives, but it is important to understand rare adverse events. We observed a short-term increased rate of Guillain-Barré syndrome and Bell's palsy after first dose of ChAdOx1 vaccine. The absolute risk, assuming a causal effect attributable to vaccination, was low.",,doi:https://doi.org/10.1016/j.vaccine.2022.06.010; doi:https://doi.org/10.1016/j.vaccine.2022.06.010; html:https://europepmc.org/articles/PMC9170533; pdf:https://europepmc.org/articles/PMC9170533?pdf=render
 37346822,https://doi.org/10.12688/wellcomeopenres.18735.2,First dose COVID-19 vaccine coverage amongst adolescents and children in England: an analysis of 3.21 million patients' primary care records in situ using OpenSAFELY.,"Hopcroft LE, Curtis HJ, Brown AD, Hulme WJ, Andrews CD, Morton CE, Inglesby P, Morley J, Mehrkar A, Bacon SC, Eggo RM, Mahalingasivam V, Parker EPK, Tomlinson LA, Bates C, Cockburn J, Parry J, Hester F, Harper S, Goldacre B, Walker AJ, MacKenna B.",,Wellcome open research,2023,2023-06-09,Y,Vaccine; Primary Health Care; Public Health; Covid-19,,,"<b>Background:</b> The coronavirus disease 2019 (COVID-19) vaccination programme in England was extended to include all adolescents and children by April 2022. The aim of this paper is to describe trends and variation in vaccine coverage in different clinical and demographic groups amongst adolescents and children in England by August 2022. <b>Methods:</b> With the approval of NHS England, a cohort study was conducted of 3.21 million children and adolescents' records in general practice in England,  <i>in situ</i> and within the infrastructure of the electronic health record software vendor TPP using OpenSAFELY. Vaccine coverage across various demographic (sex, deprivation index and ethnicity) and clinical (risk status) populations is described. <b>Results:</b> Coverage is higher amongst adolescents than it is amongst children, with 53.5% adolescents and 10.8% children having received their first dose of the COVID-19 vaccine. Within those groups, coverage varies by ethnicity, deprivation index and risk status; there is no evidence of variation by sex. <b>Conclusion:</b> First dose COVID-19 vaccine coverage is shown to vary amongst various demographic and clinical groups of children and adolescents.",,doi:https://doi.org/10.12688/wellcomeopenres.18735.2; html:https://europepmc.org/articles/PMC10280033; pdf:https://europepmc.org/articles/PMC10280033?pdf=render
 34384736,https://doi.org/10.1016/s2589-7500(21)00175-8,"Predicted COVID-19 positive cases, hospitalisations, and deaths associated with the Delta variant of concern, June-July, 2021.","Shah SA, Moore E, Robertson C, McMenamin J, Katikireddi SV, Simpson CR, Shi T, Agrawal U, McCowan C, Stock S, Ritchie LD, Sheikh A, Public Health Scotland and the EAVE II Collaborators.",,The Lancet. Digital health,2021,2021-08-09,Y,,,,,,pdf:https://aura.abdn.ac.uk/bitstream/2164/21105/1/Shah_etal_Predicted_Covid_19_Positive_VOR.pdf; doi:https://doi.org/10.1016/S2589-7500(21)00175-8; html:https://europepmc.org/articles/PMC8352493; pdf:https://europepmc.org/articles/PMC8352493?pdf=render
@@ -378,26 +378,26 @@ PMC9023380,https://doi.org/,Assessing the spread risk of COVID-19 associated wit
 33082154,https://doi.org/10.1136/bmj.m3731,Living risk prediction algorithm (QCOVID) for risk of hospital admission and mortality from coronavirus 19 in adults: national derivation and validation cohort study.,"Clift AK, Coupland CAC, Keogh RH, Diaz-Ordaz K, Williamson E, Harrison EM, Hayward A, Hemingway H, Horby P, Mehta N, Benger J, Khunti K, Spiegelhalter D, Sheikh A, Valabhji J, Lyons RA, Robson J, Semple MG, Kee F, Johnson P, Jebb S, Williams T, Hippisley-Cox J.",,BMJ (Clinical research ed.),2020,2020-10-20,Y,,,,"<h4>Objective</h4>To derive and validate a risk prediction algorithm to estimate hospital admission and mortality outcomes from coronavirus disease 2019 (covid-19) in adults.<h4>Design</h4>Population based cohort study.<h4>Setting and participants</h4>QResearch database, comprising 1205 general practices in England with linkage to covid-19 test results, Hospital Episode Statistics, and death registry data. 6.08 million adults aged 19-100 years were included in the derivation dataset and 2.17 million in the validation dataset. The derivation and first validation cohort period was 24 January 2020 to 30 April 2020. The second temporal validation cohort covered the period 1 May 2020 to 30 June 2020.<h4>Main outcome measures</h4>The primary outcome was time to death from covid-19, defined as death due to confirmed or suspected covid-19 as per the death certification or death occurring in a person with confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the period 24 January to 30 April 2020. The secondary outcome was time to hospital admission with confirmed SARS-CoV-2 infection. Models were fitted in the derivation cohort to derive risk equations using a range of predictor variables. Performance, including measures of discrimination and calibration, was evaluated in each validation time period.<h4>Results</h4>4384 deaths from covid-19 occurred in the derivation cohort during follow-up and 1722 in the first validation cohort period and 621 in the second validation cohort period. The final risk algorithms included age, ethnicity, deprivation, body mass index, and a range of comorbidities. The algorithm had good calibration in the first validation cohort. For deaths from covid-19 in men, it explained 73.1% (95% confidence interval 71.9% to 74.3%) of the variation in time to death (R<sup>2</sup>); the D statistic was 3.37 (95% confidence interval 3.27 to 3.47), and Harrell's C was 0.928 (0.919 to 0.938). Similar results were obtained for women, for both outcomes, and in both time periods. In the top 5% of patients with the highest predicted risks of death, the sensitivity for identifying deaths within 97 days was 75.7%. People in the top 20% of predicted risk of death accounted for 94% of all deaths from covid-19.<h4>Conclusion</h4>The QCOVID population based risk algorithm performed well, showing very high levels of discrimination for deaths and hospital admissions due to covid-19. The absolute risks presented, however, will change over time in line with the prevailing SARS-C0V-2 infection rate and the extent of social distancing measures in place, so they should be interpreted with caution. The model can be recalibrated for different time periods, however, and has the potential to be dynamically updated as the pandemic evolves.",,pdf:https://www.bmj.com/content/bmj/371/bmj.m3731.full.pdf; doi:https://doi.org/10.1136/bmj.m3731; html:https://europepmc.org/articles/PMC7574532; pdf:https://europepmc.org/articles/PMC7574532?pdf=render
 33875444,https://doi.org/10.1136/bmjopen-2020-045077,COVID-19 in patients with hepatobiliary and pancreatic diseases: a single-centre cross-sectional study in East London.,"Dayem Ullah AZM, Sivapalan L, Kocher HM, Chelala C.",,BMJ open,2021,2021-04-19,Y,Pancreatic Disease; Hepatobiliary Disease; Covid-19,,,"<h4>Objective</h4>To explore risk factors associated with COVID-19 susceptibility and survival in patients with pre-existing hepato-pancreato-biliary (HPB) conditions.<h4>Design</h4>Cross-sectional study.<h4>Setting</h4>East London Pancreatic Cancer Epidemiology (EL-PaC-Epidem) Study at Barts Health National Health Service Trust, UK. Linked electronic health records were interrogated on a cohort of participants (age ≥18 years), reported with HPB conditions between 1 April 2008 and 6 March 2020.<h4>Participants</h4>EL-PaC-Epidem Study participants, alive on 12 February 2020, and living in East London within the previous 6 months (n=15 440). The cohort represents a multi-ethnic population with 51.7% belonging to the non-White background.<h4>Main outcome measure</h4>COVID-19 incidence and mortality.<h4>Results</h4>Some 226 (1.5%) participants had confirmed COVID-19 diagnosis between 12 February and 12 June 2020, with increased odds for men (OR 1.56; 95% CI 1.2 to 2.04) and Black ethnicity (2.04; 1.39 to 2.95) as well as patients with moderate to severe liver disease (2.2; 1.35 to 3.59). Each additional comorbidity increased the odds of infection by 62%. Substance misusers were at more risk of infection, so were patients on vitamin D treatment. The higher ORs in patients with chronic pancreatic or mild liver conditions, age >70, and a history of smoking or obesity were due to coexisting comorbidities. Increased odds of death were observed for men (3.54; 1.68 to 7.85) and Black ethnicity (3.77; 1.38 to 10.7). Patients having respiratory complications from COVID-19 without a history of chronic respiratory disease also had higher odds of death (5.77; 1.75 to 19).<h4>Conclusions</h4>In this large population-based study of patients with HPB conditions, men, Black ethnicity, pre-existing moderate to severe liver conditions, six common medical multimorbidities, substance misuse and a history of vitamin D treatment independently posed higher odds of acquiring COVID-19 compared with their respective counterparts. The odds of death were significantly high for men and Black people.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/4/e045077.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-045077; html:https://europepmc.org/articles/PMC8057071; pdf:https://europepmc.org/articles/PMC8057071?pdf=render
 33541353,https://doi.org/10.1186/s12916-020-01872-8,The impact of non-pharmaceutical interventions on SARS-CoV-2 transmission across 130 countries and territories.,"Liu Y, Morgenstern C, Kelly J, Lowe R, CMMID COVID-19 Working Group, Jit M.",,BMC medicine,2021,2021-02-05,Y,Quantitative; Pandemic; Health Impact Assessment; Public Health Intervention; Longitudinal Analysis; Policy Evaluation; Non-pharmaceutical Interventions; Covid-19; Sars-cov-2,,,"<h4>Background</h4>Non-pharmaceutical interventions (NPIs) are used to reduce transmission of SARS coronavirus 2 (SARS-CoV-2) that causes coronavirus disease 2019 (COVID-19). However, empirical evidence of the effectiveness of specific NPIs has been inconsistent. We assessed the effectiveness of NPIs around internal containment and closure, international travel restrictions, economic measures, and health system actions on SARS-CoV-2 transmission in 130 countries and territories.<h4>Methods</h4>We used panel (longitudinal) regression to estimate the effectiveness of 13 categories of NPIs in reducing SARS-CoV-2 transmission using data from January to June 2020. First, we examined the temporal association between NPIs using hierarchical cluster analyses. We then regressed the time-varying reproduction number (R<sub>t</sub>) of COVID-19 against different NPIs. We examined different model specifications to account for the temporal lag between NPIs and changes in R<sub>t</sub>, levels of NPI intensity, time-varying changes in NPI effect, and variable selection criteria. Results were interpreted taking into account both the range of model specifications and temporal clustering of NPIs.<h4>Results</h4>There was strong evidence for an association between two NPIs (school closure, internal movement restrictions) and reduced R<sub>t</sub>. Another three NPIs (workplace closure, income support, and debt/contract relief) had strong evidence of effectiveness when ignoring their level of intensity, while two NPIs (public events cancellation, restriction on gatherings) had strong evidence of their effectiveness only when evaluating their implementation at maximum capacity (e.g. restrictions on 1000+ people gathering were not effective, restrictions on < 10 people gathering were). Evidence about the effectiveness of the remaining NPIs (stay-at-home requirements, public information campaigns, public transport closure, international travel controls, testing, contact tracing) was inconsistent and inconclusive. We found temporal clustering between many of the NPIs. Effect sizes varied depending on whether or not we included data after peak NPI intensity.<h4>Conclusion</h4>Understanding the impact that specific NPIs have had on SARS-CoV-2 transmission is complicated by temporal clustering, time-dependent variation in effects, and differences in NPI intensity. However, the effectiveness of school closure and internal movement restrictions appears robust across different model specifications, with some evidence that other NPIs may also be effective under particular conditions. This provides empirical evidence for the potential effectiveness of many, although not all, actions policy-makers are taking to respond to the COVID-19 pandemic.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-020-01872-8; doi:https://doi.org/10.1186/s12916-020-01872-8; html:https://europepmc.org/articles/PMC7861967; pdf:https://europepmc.org/articles/PMC7861967?pdf=render
-34174193,https://doi.org/10.1016/s1473-3099(21)00289-9,Vaccine effectiveness of the first dose of ChAdOx1 nCoV-19 and BNT162b2 against SARS-CoV-2 infection in residents of long-term care facilities in England (VIVALDI): a prospective cohort study.,"Shrotri M, Krutikov M, Palmer T, Giddings R, Azmi B, Subbarao S, Fuller C, Irwin-Singer A, Davies D, Tut G, Lopez Bernal J, Moss P, Hayward A, Copas A, Shallcross L.",,The Lancet. Infectious diseases,2021,2021-06-23,Y,,,,"<h4>Background</h4>The effectiveness of SARS-CoV-2 vaccines in older adults living in long-term care facilities is uncertain. We investigated the protective effect of the first dose of the Oxford-AstraZeneca non-replicating viral-vectored vaccine (ChAdOx1 nCoV-19; AZD1222) and the Pfizer-BioNTech mRNA-based vaccine (BNT162b2) in residents of long-term care facilities in terms of PCR-confirmed SARS-CoV-2 infection over time since vaccination.<h4>Methods</h4>The VIVALDI study is a prospective cohort study that commenced recruitment on June 11, 2020, to investigate SARS-CoV-2 transmission, infection outcomes, and immunity in residents and staff in long-term care facilities in England that provide residential or nursing care for adults aged 65 years and older. In this cohort study, we included long-term care facility residents undergoing routine asymptomatic SARS-CoV-2 testing between Dec 8, 2020 (the date the vaccine was first deployed in a long-term care facility), and March 15, 2021, using national testing data linked within the COVID-19 Datastore. Using Cox proportional hazards regression, we estimated the relative hazard of PCR-positive infection at 0-6 days, 7-13 days, 14-20 days, 21-27 days, 28-34 days, 35-48 days, and 49 days and beyond after vaccination, comparing unvaccinated and vaccinated person-time from the same cohort of residents, adjusting for age, sex, previous infection, local SARS-CoV-2 incidence, long-term care facility bed capacity, and clustering by long-term care facility. We also compared mean PCR cycle threshold (Ct) values for positive swabs obtained before and after vaccination. The study is registered with ISRCTN, number 14447421.<h4>Findings</h4>10 412 care home residents aged 65 years and older from 310 LTCFs were included in this analysis. The median participant age was 86 years (IQR 80-91), 7247 (69·6%) of 10 412 residents were female, and 1155 residents (11·1%) had evidence of previous SARS-CoV-2 infection. 9160 (88·0%) residents received at least one vaccine dose, of whom 6138 (67·0%) received ChAdOx1 and 3022 (33·0%) received BNT162b2. Between Dec 8, 2020, and March 15, 2021, there were 36 352 PCR results in 670 628 person-days, and 1335 PCR-positive infections (713 in unvaccinated residents and 612 in vaccinated residents) were included. Adjusted hazard ratios (HRs) for PCR-positive infection relative to unvaccinated residents declined from 28 days after the first vaccine dose to 0·44 (95% CI 0·24-0·81) at 28-34 days and 0·38 (0·19-0·77) at 35-48 days. Similar effect sizes were seen for ChAdOx1 (adjusted HR 0·32, 95% CI 0·15-0·66) and BNT162b2 (0·35, 0·17-0·71) vaccines at 35-48 days. Mean PCR Ct values were higher for infections that occurred at least 28 days after vaccination than for those occurring before vaccination (31·3 [SD 8·7] in 107 PCR-positive tests vs 26·6 [6·6] in 552 PCR-positive tests; p<0·0001).<h4>Interpretation</h4>Single-dose vaccination with BNT162b2 and ChAdOx1 vaccines provides substantial protection against infection in older adults from 4-7 weeks after vaccination and might reduce SARS-CoV-2 transmission. However, the risk of infection is not eliminated, highlighting the ongoing need for non-pharmaceutical interventions to prevent transmission in long-term care facilities.<h4>Funding</h4>UK Government Department of Health and Social Care.",,pdf:http://www.thelancet.com/article/S1473309921002899/pdf; doi:https://doi.org/10.1016/S1473-3099(21)00289-9; html:https://europepmc.org/articles/PMC8221738
-34732073,https://doi.org/10.1161/strokeaha.121.034787,"Risk, Clinical Course, and Outcome of Ischemic Stroke in Patients Hospitalized With COVID-19: A Multicenter Cohort Study.","Sluis WM, Linschoten M, Buijs JE, Biesbroek JM, den Hertog HM, Ribbers T, Nieuwkamp DJ, van Houwelingen RC, Dias A, van Uden IWM, Kerklaan JP, Bienfait HP, Vermeer SE, de Jong SW, Ali M, Wermer MJH, de Graaf MT, Brouwers PJAM, Asselbergs FW, Kappelle LJ, van der Worp HB, Algra AM, CAPACITY-COVID Collaborative Consortium*.",,Stroke,2021,2021-11-04,N,Intensive care units; Pulmonary embolism; incidence; Hospital Mortality; Patient Discharge; Covid-19,,,"<h4>Background and purpose</h4>The frequency of ischemic stroke in patients with coronavirus disease 2019 (COVID-19) varies in the current literature, and risk factors are unknown. We assessed the incidence, risk factors, and outcomes of acute ischemic stroke in hospitalized patients with COVID-19.<h4>Methods</h4>We included patients with a laboratory-confirmed SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) infection admitted in 16 Dutch hospitals participating in the international CAPACITY-COVID registry between March 1 and August 1, 2020. Patients were screened for the occurrence of acute ischemic stroke. We calculated the cumulative incidence of ischemic stroke and compared risk factors, cardiovascular complications, and in-hospital mortality in patients with and without ischemic stroke.<h4>Results</h4>We included 2147 patients with COVID-19, of whom 586 (27.3%) needed treatment at an intensive care unit. Thirty-eight patients (1.8%) had an ischemic stroke. Patients with stroke were older but did not differ in sex or cardiovascular risk factors. Median time between the onset of COVID-19 symptoms and diagnosis of stroke was 2 weeks. The incidence of ischemic stroke was higher among patients who were treated at an intensive care unit (16/586; 2.7% versus nonintensive care unit, 22/1561; 1.4%; <i>P</i>=0.039). Pulmonary embolism was more common in patients with (8/38; 21.1%) than in those without stroke (160/2109; 7.6%; adjusted risk ratio, 2.08 [95% CI, 1.52-2.84]). Twenty-seven patients with ischemic stroke (71.1%) died during admission or were functionally dependent at discharge. Patients with ischemic stroke were at a higher risk of in-hospital mortality (adjusted risk ratio, 1.56 [95% CI, 1.13-2.15]) than patients without stroke.<h4>Conclusions</h4>In this multicenter cohort study, the cumulative incidence of acute ischemic stroke in hospitalized patients with COVID-19 was ≈2%, with a higher risk in patients treated at an intensive care unit. The majority of stroke patients had a poor outcome. The association between ischemic stroke and pulmonary embolism warrants further investigation.",,pdf:https://europepmc.org/articles/pmc8607920?pdf=render; doi:https://doi.org/10.1161/STROKEAHA.121.034787; html:https://europepmc.org/articles/PMC8607920; pdf:https://europepmc.org/articles/PMC8607920?pdf=render; doi:https://doi.org/10.1161/strokeaha.121.034787
 35609019,https://doi.org/10.1371/journal.pone.0267176,Population birth outcomes in 2020 and experiences of expectant mothers during the COVID-19 pandemic: A 'born in Wales' mixed methods study using routine data.,"Jones H, Seaborne M, Cowley L, Odd D, Paranjothy S, Akbari A, Brophy S.",,PloS one,2022,2022-05-24,Y,,,,"<h4>Background</h4>Pregnancy can be a stressful time and the COVID-19 pandemic has affected all aspects of life. This study aims to investigate the pandemic impact on pregnancy experience, rates of primary childhood immunisations and the differences in birth outcomes in during 2020 to those of previous years.<h4>Methods</h4>Self-reported pregnancy experience: 215 expectant mothers (aged 16+) in Wales completed an online survey about their experiences of pregnancy during the pandemic. The qualitative survey data was analysed using codebook thematic analysis. Population-level birth outcomes in Wales: Stillbirths, prematurity, birth weight and Caesarean section births before (2016-2019) and during (2020) the pandemic were compared using anonymised individual-level, population-scale routine data held in the Secure Anonymised Information Linkage (SAIL) Databank. Uptake of the first three scheduled primary childhood immunisations were compared between 2019 and 2020.<h4>Findings</h4>The pandemic had a negative impact on the mental health of 71% of survey respondents, who reported anxiety, stress and loneliness; this was associated with attending scans without their partner, giving birth alone, and minimal contact with midwives. There was no significant difference in annual outcomes including gestation and birth weight, stillbirths, and Caesarean sections for infants born in 2020 compared to 2016-2019. There was an increase in late term births (≥42 weeks gestation) during the first lockdown (OR: 1.28, p = 0.019) and a decrease in moderate to late preterm births (32-36 weeks gestation) during the second lockdown (OR: 0.74, p = 0.001). Fewer babies were born in 2020 (N = 29,031) compared to 2016-2019 (average N = 32,582). All babies received their immunisations in 2020, but there were minor delays in the timings of immunisations. Those due at 8-weeks were 8% less likely to be on time (within 28-days) and at 16-weeks, they were 19% less likely to be on time.<h4>Interpretation</h4>Whilst the pandemic had a negative impact on mothers' experiences of pregnancy. Population-level data suggests that this did not translate to adverse birth outcomes for babies born during the pandemic.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0267176&type=printable; doi:https://doi.org/10.1371/journal.pone.0267176; html:https://europepmc.org/articles/PMC9129046; pdf:https://europepmc.org/articles/PMC9129046?pdf=render
+34732073,https://doi.org/10.1161/strokeaha.121.034787,"Risk, Clinical Course, and Outcome of Ischemic Stroke in Patients Hospitalized With COVID-19: A Multicenter Cohort Study.","Sluis WM, Linschoten M, Buijs JE, Biesbroek JM, den Hertog HM, Ribbers T, Nieuwkamp DJ, van Houwelingen RC, Dias A, van Uden IWM, Kerklaan JP, Bienfait HP, Vermeer SE, de Jong SW, Ali M, Wermer MJH, de Graaf MT, Brouwers PJAM, Asselbergs FW, Kappelle LJ, van der Worp HB, Algra AM, CAPACITY-COVID Collaborative Consortium*.",,Stroke,2021,2021-11-04,N,Intensive care units; Pulmonary embolism; incidence; Hospital Mortality; Patient Discharge; Covid-19,,,"<h4>Background and purpose</h4>The frequency of ischemic stroke in patients with coronavirus disease 2019 (COVID-19) varies in the current literature, and risk factors are unknown. We assessed the incidence, risk factors, and outcomes of acute ischemic stroke in hospitalized patients with COVID-19.<h4>Methods</h4>We included patients with a laboratory-confirmed SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) infection admitted in 16 Dutch hospitals participating in the international CAPACITY-COVID registry between March 1 and August 1, 2020. Patients were screened for the occurrence of acute ischemic stroke. We calculated the cumulative incidence of ischemic stroke and compared risk factors, cardiovascular complications, and in-hospital mortality in patients with and without ischemic stroke.<h4>Results</h4>We included 2147 patients with COVID-19, of whom 586 (27.3%) needed treatment at an intensive care unit. Thirty-eight patients (1.8%) had an ischemic stroke. Patients with stroke were older but did not differ in sex or cardiovascular risk factors. Median time between the onset of COVID-19 symptoms and diagnosis of stroke was 2 weeks. The incidence of ischemic stroke was higher among patients who were treated at an intensive care unit (16/586; 2.7% versus nonintensive care unit, 22/1561; 1.4%; <i>P</i>=0.039). Pulmonary embolism was more common in patients with (8/38; 21.1%) than in those without stroke (160/2109; 7.6%; adjusted risk ratio, 2.08 [95% CI, 1.52-2.84]). Twenty-seven patients with ischemic stroke (71.1%) died during admission or were functionally dependent at discharge. Patients with ischemic stroke were at a higher risk of in-hospital mortality (adjusted risk ratio, 1.56 [95% CI, 1.13-2.15]) than patients without stroke.<h4>Conclusions</h4>In this multicenter cohort study, the cumulative incidence of acute ischemic stroke in hospitalized patients with COVID-19 was ≈2%, with a higher risk in patients treated at an intensive care unit. The majority of stroke patients had a poor outcome. The association between ischemic stroke and pulmonary embolism warrants further investigation.",,pdf:https://europepmc.org/articles/pmc8607920?pdf=render; doi:https://doi.org/10.1161/STROKEAHA.121.034787; html:https://europepmc.org/articles/PMC8607920; pdf:https://europepmc.org/articles/PMC8607920?pdf=render; doi:https://doi.org/10.1161/strokeaha.121.034787
+34174193,https://doi.org/10.1016/s1473-3099(21)00289-9,Vaccine effectiveness of the first dose of ChAdOx1 nCoV-19 and BNT162b2 against SARS-CoV-2 infection in residents of long-term care facilities in England (VIVALDI): a prospective cohort study.,"Shrotri M, Krutikov M, Palmer T, Giddings R, Azmi B, Subbarao S, Fuller C, Irwin-Singer A, Davies D, Tut G, Lopez Bernal J, Moss P, Hayward A, Copas A, Shallcross L.",,The Lancet. Infectious diseases,2021,2021-06-23,Y,,,,"<h4>Background</h4>The effectiveness of SARS-CoV-2 vaccines in older adults living in long-term care facilities is uncertain. We investigated the protective effect of the first dose of the Oxford-AstraZeneca non-replicating viral-vectored vaccine (ChAdOx1 nCoV-19; AZD1222) and the Pfizer-BioNTech mRNA-based vaccine (BNT162b2) in residents of long-term care facilities in terms of PCR-confirmed SARS-CoV-2 infection over time since vaccination.<h4>Methods</h4>The VIVALDI study is a prospective cohort study that commenced recruitment on June 11, 2020, to investigate SARS-CoV-2 transmission, infection outcomes, and immunity in residents and staff in long-term care facilities in England that provide residential or nursing care for adults aged 65 years and older. In this cohort study, we included long-term care facility residents undergoing routine asymptomatic SARS-CoV-2 testing between Dec 8, 2020 (the date the vaccine was first deployed in a long-term care facility), and March 15, 2021, using national testing data linked within the COVID-19 Datastore. Using Cox proportional hazards regression, we estimated the relative hazard of PCR-positive infection at 0-6 days, 7-13 days, 14-20 days, 21-27 days, 28-34 days, 35-48 days, and 49 days and beyond after vaccination, comparing unvaccinated and vaccinated person-time from the same cohort of residents, adjusting for age, sex, previous infection, local SARS-CoV-2 incidence, long-term care facility bed capacity, and clustering by long-term care facility. We also compared mean PCR cycle threshold (Ct) values for positive swabs obtained before and after vaccination. The study is registered with ISRCTN, number 14447421.<h4>Findings</h4>10 412 care home residents aged 65 years and older from 310 LTCFs were included in this analysis. The median participant age was 86 years (IQR 80-91), 7247 (69·6%) of 10 412 residents were female, and 1155 residents (11·1%) had evidence of previous SARS-CoV-2 infection. 9160 (88·0%) residents received at least one vaccine dose, of whom 6138 (67·0%) received ChAdOx1 and 3022 (33·0%) received BNT162b2. Between Dec 8, 2020, and March 15, 2021, there were 36 352 PCR results in 670 628 person-days, and 1335 PCR-positive infections (713 in unvaccinated residents and 612 in vaccinated residents) were included. Adjusted hazard ratios (HRs) for PCR-positive infection relative to unvaccinated residents declined from 28 days after the first vaccine dose to 0·44 (95% CI 0·24-0·81) at 28-34 days and 0·38 (0·19-0·77) at 35-48 days. Similar effect sizes were seen for ChAdOx1 (adjusted HR 0·32, 95% CI 0·15-0·66) and BNT162b2 (0·35, 0·17-0·71) vaccines at 35-48 days. Mean PCR Ct values were higher for infections that occurred at least 28 days after vaccination than for those occurring before vaccination (31·3 [SD 8·7] in 107 PCR-positive tests vs 26·6 [6·6] in 552 PCR-positive tests; p<0·0001).<h4>Interpretation</h4>Single-dose vaccination with BNT162b2 and ChAdOx1 vaccines provides substantial protection against infection in older adults from 4-7 weeks after vaccination and might reduce SARS-CoV-2 transmission. However, the risk of infection is not eliminated, highlighting the ongoing need for non-pharmaceutical interventions to prevent transmission in long-term care facilities.<h4>Funding</h4>UK Government Department of Health and Social Care.",,pdf:http://www.thelancet.com/article/S1473309921002899/pdf; doi:https://doi.org/10.1016/S1473-3099(21)00289-9; html:https://europepmc.org/articles/PMC8221738
 35216844,https://doi.org/10.1016/j.vaccine.2022.02.056,Localising vaccination services: Qualitative insights on public health and minority group collaborations to co-deliver coronavirus vaccines.,"Kasstan B, Mounier-Jack S, Letley L, Gaskell KM, Roberts CH, Stone NRH, Lal S, Eggo RM, Marks M, Chantler T.",,Vaccine,2022,2022-02-17,Y,Qualitative Research; Ethnic Minorities; Coronavirus Vaccine; Localising Services; Public Health Collaboration,,,"Ethnic and religious minorities have been disproportionately affected by the SARS-CoV-2 pandemic and are less likely to accept coronavirus vaccinations. Orthodox (Haredi) Jewish neighbourhoods in England experienced high incidences of SARS-CoV-2 in 2020-21 and measles outbreaks (2018-19) due to suboptimal childhood vaccination coverage. The objective of our study was to explore how the coronavirus vaccination programme (CVP) was co-delivered between public health services and an Orthodox Jewish health organisation. Methods included 28 semi-structured interviews conducted virtually with public health professionals, community welfare and religious representatives, and household members. We examined CVP delivery from the perspectives of those involved in organising services and vaccine beneficiaries. Interview data was contextualised within debates of the CVP in Orthodox (Haredi) Jewish print and social media. Thematic analysis generated five considerations: i) Prior immunisation-related collaboration with public health services carved a role for Jewish health organisations to host and promote coronavirus vaccination sessions, distribute appointments, and administer vaccines ii) Public health services maintained responsibility for training, logistics, and maintaining vaccination records; iii) The localised approach to service delivery promoted vaccination in a minority with historically suboptimal levels of coverage; iv) Co-delivery promoted trust in the CVP, though a minority of participants maintained concerns around safety; v) Provision of CVP information and stakeholders' response to situated (context-specific) challenges and concerns. Drawing on this example of CVP co-delivery, we propose that a localised approach to delivering immunisation programmes could address service provision gaps in ways that involve trusted community organisations. Localisation of vaccination services can include communication or implementation strategies, but both approaches involve consideration of investment, engagement and coordination, which are not cost-neutral. Localising vaccination services in collaboration with welfare groups raises opportunities for the on-going CVP and other immunisation programmes, and constitutes an opportunity for ethnic and religious minorities to collaborate in safeguarding community health.",,doi:https://doi.org/10.1016/j.vaccine.2022.02.056; doi:https://doi.org/10.1016/j.vaccine.2022.02.056; html:https://europepmc.org/articles/PMC8849863
-33085509,https://doi.org/10.7326/m20-4986,COVID-19 Mortality Risk in Down Syndrome: Results From a Cohort Study of 8 Million Adults.,"Clift AK, Coupland CAC, Keogh RH, Hemingway H, Hippisley-Cox J.",,Annals of internal medicine,2021,2020-10-21,Y,,,,,,pdf:https://europepmc.org/articles/pmc7592804?pdf=render; doi:https://doi.org/10.7326/M20-4986; html:https://europepmc.org/articles/PMC7592804; pdf:https://europepmc.org/articles/PMC7592804?pdf=render
 34340970,https://doi.org/10.3399/bjgp.2021.0301,Clinical coding of long COVID in English primary care: a federated analysis of 58 million patient records <i>in situ</i> using OpenSAFELY.,"Walker AJ, MacKenna B, Inglesby P, Tomlinson L, Rentsch CT, Curtis HJ, Morton CE, Morley J, Mehrkar A, Bacon S, Hickman G, Bates C, Croker R, Evans D, Ward T, Cockburn J, Davy S, Bhaskaran K, Schultze A, Williamson EJ, Hulme WJ, McDonald HI, Mathur R, Eggo RM, Wing K, Wong AY, Forbes H, Tazare J, Parry J, Hester F, Harper S, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Griffiths P, Fowles A, Parkes N, Douglas IJ, Evans SJ, (The OpenSAFELY Collaborative).",,The British journal of general practice : the journal of the Royal College of General Practitioners,2021,2021-10-28,Y,Primary Health Care; General Practice; Electronic Health Records; Covid-19; Long Covid,,,"<h4>Background</h4>Long COVID describes new or persistent symptoms at least 4 weeks after onset of acute COVID-19. Clinical codes to describe this phenomenon were recently created.<h4>Aim</h4>To describe the use of long-COVID codes, and variation of use by general practice, demographic variables, and over time.<h4>Design and setting</h4>Population-based cohort study in English primary care.<h4>Method</h4>Working on behalf of NHS England, OpenSAFELY data were used encompassing 96% of the English population between 1 February 2020 and 25 May 2021. The proportion of people with a recorded code for long COVID was measured overall and by demographic factors, electronic health record software system (EMIS or TPP), and week.<h4>Results</h4>Long COVID was recorded for 23 273 people. Coding was unevenly distributed among practices, with 26.7% of practices having never used the codes. Regional variation ranged between 20.3 per 100 000 people for East of England (95% confidence interval [CI] = 19.3 to 21.4) and 55.6 per 100 000 people in London (95% CI = 54.1 to 57.1). Coding was higher among females (52.1, 95% CI = 51.3 to 52.9) than males (28.1, 95% CI = 27.5 to 28.7), and higher among practices using EMIS (53.7, 95% CI = 52.9 to 54.4) than those using TPP (20.9, 95% CI = 20.3 to 21.4).<h4>Conclusion</h4>Current recording of long COVID in primary care is very low, and variable between practices. This may reflect patients not presenting; clinicians and patients holding different diagnostic thresholds; or challenges with the design and communication of diagnostic codes. Increased awareness of diagnostic codes is recommended to facilitate research and planning of services, and also surveys with qualitative work to better evaluate clinicians' understanding of the diagnosis.",,pdf:https://bjgp.org/content/bjgp/71/712/e806.full.pdf; doi:https://doi.org/10.3399/BJGP.2021.0301; html:https://europepmc.org/articles/PMC8340730; pdf:https://europepmc.org/articles/PMC8340730?pdf=render
+33085509,https://doi.org/10.7326/m20-4986,COVID-19 Mortality Risk in Down Syndrome: Results From a Cohort Study of 8 Million Adults.,"Clift AK, Coupland CAC, Keogh RH, Hemingway H, Hippisley-Cox J.",,Annals of internal medicine,2021,2020-10-21,Y,,,,,,pdf:https://europepmc.org/articles/pmc7592804?pdf=render; doi:https://doi.org/10.7326/M20-4986; html:https://europepmc.org/articles/PMC7592804; pdf:https://europepmc.org/articles/PMC7592804?pdf=render
 35964473,https://doi.org/10.1016/j.socscimed.2022.115237,"""We've all got the virus inside us now"": Disaggregating public health relations and responsibilities for health protection in pandemic London.","Kasstan B, Mounier-Jack S, Gaskell KM, Eggo RM, Marks M, Chantler T.",,Social science & medicine (1982),2022,2022-08-07,Y,Pandemic; Public Health; Judaism; Responsibility; London; Covid-19,,,"The COVID-19 pandemic has disproportionately impacted ethnic minorities in the global north, evidenced by higher rates of transmission, morbidity, and mortality relative to population sizes. Orthodox Jewish neighbourhoods in London had extremely high SARS-CoV-2 seroprevalence rates, reflecting patterns in Israel and the US. The aim of this paper is to examine how responsibilities over health protection are conveyed, and to what extent responsibility is sought by, and shared between, state services, and 'community' stakeholders or representative groups, and families in public health emergencies. The study investigates how public health and statutory services stakeholders, Orthodox Jewish communal custodians and households sought to enact health protection in London during the first year of the pandemic (March 2020-March 2021). Twenty-eight semi-structured interviews were conducted across these cohorts. Findings demonstrate that institutional relations - both their formation and at times fragmentation - were directly shaped by issues surrounding COVID-19 control measures. Exchanges around protective interventions (whether control measures, contact tracing technologies, or vaccines) reveal diverse and diverging attributions of responsibility and authority. The paper develops a framework of public health relations to understand negotiations between statutory services and minority groups over responsiveness and accountability in health protection. Disaggregating public health relations can help social scientists to critique who and what characterises institutional relationships with minority groups, and what ideas of responsibility and responsiveness are projected by differently-positioned stakeholders in health protection.",,doi:https://doi.org/10.1016/j.socscimed.2022.115237; doi:https://doi.org/10.1016/j.socscimed.2022.115237; html:https://europepmc.org/articles/PMC9357441; pdf:https://europepmc.org/articles/PMC9357441?pdf=render
-35440465,https://doi.org/10.3399/bjgp.2021.0689,Association between oral anticoagulants and COVID-19-related outcomes: a population-based cohort study.,"Wong AY, Tomlinson L, Brown JP, Elson W, Walker AJ, Schultze A, Morton CE, Evans D, Inglesby P, MacKenna B, Bhaskaran K, Rentsch CT, Powell E, Williamson E, Croker R, Bacon S, Hulme W, Bates C, Curtis HJ, Mehrkar A, Cockburn J, McDonald HI, Mathur R, Wing K, Forbes H, Eggo RM, Evans SJ, Smeeth L, Goldacre B, Douglas IJ, (The OpenSAFELY Collaborative).",,The British journal of general practice : the journal of the Royal College of General Practitioners,2022,2022-06-30,Y,Warfarin; Factor Xa Inhibitors; Dabigatran; Covid-19,,,"<h4>Background</h4>Early evidence has shown that anticoagulant reduces the risk of thrombotic events in those infected with COVID-19. However, evidence of the role of routinely prescribed oral anticoagulants (OACs) in COVID-19 outcomes is limited.<h4>Aim</h4>To investigate the association between OACs and COVID-19 outcomes in those with atrial fibrillation and a CHA<sub>2</sub>DS<sub>2</sub>-VASc score of 2.<h4>Design and setting</h4>On behalf of NHS England, a population-based cohort study was conducted.<h4>Method</h4>The study used primary care data and pseudonymously-linked SARS-CoV-2 antigen testing data, hospital admissions, and death records from England. Cox regression was used to estimate hazard ratios (HRs) for COVID-19 outcomes comparing people with current OAC use versus non-use, accounting for age, sex, comorbidities, other medications, deprivation, and general practice.<h4>Results</h4>Of 71 103 people with atrial fibrillation and a CHA<sub>2</sub>DS<sub>2</sub>-VASc score of 2, there were 52 832 current OAC users and 18 271 non-users. No difference in risk of being tested for SARS-CoV-2 was associated with current use (adjusted HR [aHR] 0.99, 95% confidence interval [CI] = 0.95 to 1.04) versus non-use. A lower risk of testing positive for SARS-CoV-2 (aHR 0.77, 95% CI = 0.63 to 0.95) and a marginally lower risk of COVID-19-related death (aHR, 0.74, 95% CI = 0.53 to 1.04) were associated with current use versus non-use.<h4>Conclusion</h4>Among those at low baseline stroke risk, people receiving OACs had a lower risk of testing positive for SARS-CoV-2 and severe COVID-19 outcomes than non-users; this might be explained by a causal effect of OACs in preventing severe COVID-19 outcomes or unmeasured confounding, including more cautious behaviours leading to reduced infection risk.",,pdf:https://bjgp.org/content/bjgp/early/2022/04/19/BJGP.2021.0689.full.pdf; doi:https://doi.org/10.3399/BJGP.2021.0689; html:https://europepmc.org/articles/PMC9037187; pdf:https://europepmc.org/articles/PMC9037187?pdf=render
 34089614,https://doi.org/10.1093/ije/dyab028,Cohort Profile: Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) Database.,"Mulholland RH, Vasileiou E, Simpson CR, Robertson C, Ritchie LD, Agrawal U, Woolhouse M, Murray JL, Stagg HR, Docherty AB, McCowan C, Wood R, Stock SJ, Sheikh A.",,International journal of epidemiology,2021,2021-08-01,N,,,,,,pdf:https://academic.oup.com/ije/article-pdf/50/4/1064/40146583/dyab028.pdf; doi:https://doi.org/10.1093/ije/dyab028; html:https://europepmc.org/articles/PMC8195245; pdf:https://europepmc.org/articles/PMC8195245?pdf=render; doi:https://doi.org/10.1093/ije/dyab028
+35440465,https://doi.org/10.3399/bjgp.2021.0689,Association between oral anticoagulants and COVID-19-related outcomes: a population-based cohort study.,"Wong AY, Tomlinson L, Brown JP, Elson W, Walker AJ, Schultze A, Morton CE, Evans D, Inglesby P, MacKenna B, Bhaskaran K, Rentsch CT, Powell E, Williamson E, Croker R, Bacon S, Hulme W, Bates C, Curtis HJ, Mehrkar A, Cockburn J, McDonald HI, Mathur R, Wing K, Forbes H, Eggo RM, Evans SJ, Smeeth L, Goldacre B, Douglas IJ, (The OpenSAFELY Collaborative).",,The British journal of general practice : the journal of the Royal College of General Practitioners,2022,2022-06-30,Y,Warfarin; Factor Xa Inhibitors; Dabigatran; Covid-19,,,"<h4>Background</h4>Early evidence has shown that anticoagulant reduces the risk of thrombotic events in those infected with COVID-19. However, evidence of the role of routinely prescribed oral anticoagulants (OACs) in COVID-19 outcomes is limited.<h4>Aim</h4>To investigate the association between OACs and COVID-19 outcomes in those with atrial fibrillation and a CHA<sub>2</sub>DS<sub>2</sub>-VASc score of 2.<h4>Design and setting</h4>On behalf of NHS England, a population-based cohort study was conducted.<h4>Method</h4>The study used primary care data and pseudonymously-linked SARS-CoV-2 antigen testing data, hospital admissions, and death records from England. Cox regression was used to estimate hazard ratios (HRs) for COVID-19 outcomes comparing people with current OAC use versus non-use, accounting for age, sex, comorbidities, other medications, deprivation, and general practice.<h4>Results</h4>Of 71 103 people with atrial fibrillation and a CHA<sub>2</sub>DS<sub>2</sub>-VASc score of 2, there were 52 832 current OAC users and 18 271 non-users. No difference in risk of being tested for SARS-CoV-2 was associated with current use (adjusted HR [aHR] 0.99, 95% confidence interval [CI] = 0.95 to 1.04) versus non-use. A lower risk of testing positive for SARS-CoV-2 (aHR 0.77, 95% CI = 0.63 to 0.95) and a marginally lower risk of COVID-19-related death (aHR, 0.74, 95% CI = 0.53 to 1.04) were associated with current use versus non-use.<h4>Conclusion</h4>Among those at low baseline stroke risk, people receiving OACs had a lower risk of testing positive for SARS-CoV-2 and severe COVID-19 outcomes than non-users; this might be explained by a causal effect of OACs in preventing severe COVID-19 outcomes or unmeasured confounding, including more cautious behaviours leading to reduced infection risk.",,pdf:https://bjgp.org/content/bjgp/early/2022/04/19/BJGP.2021.0689.full.pdf; doi:https://doi.org/10.3399/BJGP.2021.0689; html:https://europepmc.org/articles/PMC9037187; pdf:https://europepmc.org/articles/PMC9037187?pdf=render
 35369709,https://doi.org/10.1128/jcm.02408-21,SARS-CoV-2 Testing in the Community: Testing Positive Samples with the TaqMan SARS-CoV-2 Mutation Panel To Find Variants in Real Time.,"Ashford F, Best A, Dunn SJ, Ahmed Z, Siddiqui H, Melville J, Wilkinson S, Mirza J, Cumley N, Stockton J, Ferguson J, Wheatley L, Ratcliffe E, Casey A, Plant T, COVID-19 Genomics UK (COG-UK) Consortium, Quick J, Richter A, Loman N, McNally A.",,Journal of clinical microbiology,2022,2022-04-04,Y,PCR; Genotyping; Genome sequencing; SNPs; real time; Sars-cov-2; Variants Of Concern,,,"Genome sequencing is a powerful tool for identifying SARS-CoV-2 variant lineages; however, there can be limitations due to sequence dropout when used to identify specific key mutations. Recently, ThermoFisher Scientific has developed genotyping assays to help bridge the gap between testing capacity and sequencing capability to generate real-time genotyping results based on specific variants. Over a 6-week period during the months of April and May 2021, we set out to assess the ThermoFisher TaqMan mutation panel genotyping assay, initially for three mutations of concern and then for an additional two mutations of concern, against SARS-CoV-2-positive clinical samples and the corresponding COVID-19 Genomics UK Consortium (COG-UK) sequencing data. We demonstrate that genotyping is a powerful in-depth technique for identifying specific mutations, is an excellent complement to genome sequencing, and has real clinical health value potential, allowing laboratories to report and take action on variants of concern much more quickly.",,pdf:https://escholarship.org/content/qt5cn7258j/qt5cn7258j.pdf?t=ry5bq6; doi:https://doi.org/10.1128/jcm.02408-21; html:https://europepmc.org/articles/PMC9020355; pdf:https://europepmc.org/articles/PMC9020355?pdf=render
 34328624,https://doi.org/10.1007/s11695-021-05493-9,30-Day Morbidity and Mortality of Bariatric Surgery During the COVID-19 Pandemic: a Multinational Cohort Study of 7704 Patients from 42 Countries.,"Singhal R, Ludwig C, Rudge G, Gkoutos GV, Tahrani A, Mahawar K, GENEVA Collaborators, Pędziwiatr M, Major P, Zarzycki P, Pantelis A, Lapatsanis DP, Stravodimos G, Matthys C, Focquet M, Vleeschouwers W, Spaventa AG, Zerrweck C, Vitiello A, Berardi G, Musella M, Sanchez-Meza A, Cantu FJ, Mora F, Cantu MA, Katakwar A, Reddy DN, Elmaleh H, Hassan M, Elghandour A, Elbanna M, Osman A, Khan A, Layani L, Kiran N, Velikorechin A, Solovyeva M, Melali H, Shahabi S, Agrawal A, Shrivastava A, Sharma A, Narwaria B, Narwaria M, Raziel A, Sakran N, Susmallian S, Karagöz L, Akbaba M, Pişkin SZ, Balta AZ, Senol Z, Manno E, Iovino MG, Osman A, Qassem M, Arana-Garza S, Povoas HP, Vilas-Boas ML, Naumann D, Super J, Li A, Ammori BJ, Balamoun H, Salman M, Nasta AM, Goel R, Sánchez-Aguilar H, Herrera MF, Abou-Mrad A, Cloix L, Mazzini GS, Kristem L, Lazaro A, Campos J, Bernardo J, González J, Trindade C, Viveiros O, Ribeiro R, Goitein D, Hazzan D, Segev L, Beck T, Reyes H, Monterrubio J, García P, Benois M, Kassir R, Contine A, Elshafei M, Aktas S, Weiner S, Heidsieck T, Level L, Pinango S, Ortega PM, Moncada R, Valenti V, Vlahović I, Boras Z, Liagre A, Martini F, Juglard G, Motwani M, Saggu SS, Al Moman H, López LAA, Cortez MAC, Zavala RA, D'Haese C, Kempeneers I, Himpens J, Lazzati A, Paolino L, Bathaei S, Bedirli A, Yavuz A, Büyükkasap Ç, Özaydın S, Kwiatkowski A, Bartosiak K, Walędziak M, Santonicola A, Angrisani L, Iovino P, Palma R, Iossa A, Boru CE, De Angelis F, Silecchia G, Hussain A, Balchandra S, Coltell IB, Pérez JL, Bohra A, Awan AK, Madhok B, Leeder PC, Awad S, Al-Khyatt W, Shoma A, Elghadban H, Ghareeb S, Mathews B, Kurian M, Larentzakis A, Vrakopoulou GZ, Albanopoulos K, Bozdag A, Lale A, Kirkil C, Dincer M, Bashir A, Haddad A, Hijleh LA, Zilberstein B, de Marchi DD, Souza WP, Brodén CM, Gislason H, Shah K, Ambrosi A, Pavone G, Tartaglia N, Kona SLK, Kalyan K, Perez CEG, Botero MAF, Covic A, Timofte D, Maxim M, Faraj D, Tseng L, Liem R, Ören G, Dilektasli E, Yalcin I, AlMukhtar H, Al Hadad M, Mohan R, Arora N, Bedi D, Rives-Lange C, Chevallier JM, Poghosyan T, Sebbag H, Zinaï L, Khaldi S, Mauchien C, Mazza D, Dinescu G, Rea B, Pérez-Galaz F, Zavala L, Besa A, Curell A, Balibrea JM, Vaz C, Galindo L, Silva N, Caballero JLE, Sebastian SO, Marchesini JCD, da Fonseca Pereira RA, Sobottka WH, Fiolo FE, Turchi M, Coelho ACJ, Zacaron AL, Barbosa A, Quinino R, Menaldi G, Paleari N, Martinez-Duartez P, de Aragon Ramírez de Esparza GM, Esteban VS, Torres A, Garcia-Galocha JL, Josa M, Pacheco-Garcia JM, Mayo-Ossorio MA, Chowbey P, Soni V, de Vasconcelos Cunha HA, Castilho MV, Ferreira RMA, Barreiro TA, Charalabopoulos A, Sdralis E, Davakis S, Bomans B, Dapri G, Van Belle K, Takieddine M, Vaneukem P, Karaca ESA, Karaca FC, Sumer A, Peksen C, Savas OA, Chousleb E, Elmokayed F, Fakhereldin I, Aboshanab HM, Swelium T, Gudal A, Gamloo L, Ugale A, Ugale S, Boeker C, Reetz C, Hakami IA, Mall J, Alexandrou A, Baili E, Bodnar Z, Maleckas A, Gudaityte R, Guldogan CE, Gundogdu E, Ozmen MM, Thakkar D, Dukkipati N, Shah PS, Shah SS, Shah SS, Adil MT, Jambulingam P, Mamidanna R, Whitelaw D, Adil MT, Jain V, Veetil DK, Wadhawan R, Torres A, Torres M, Tinoco T, Leclercq W, Romeijn M, van de Pas K, Alkhazraji AK, Taha SA, Ustun M, Yigit T, Inam A, Burhanulhaq M, Pazouki A, Eghbali F, Kermansaravi M, Jazi AHD, Mahmoudieh M, Mogharehabed N, Tsiotos G, Stamou K, Barrera Rodriguez FJ, Rojas Navarro MA, Torres OM, Martinez SL, Tamez ERM, Millan Cornejo GA, Flores JEG, Mohammed DA, Elfawal MH, Shabbir A, Guowei K, So JB, Kaplan ET, Kaplan M, Kaplan T, Pham D, Rana G, Kappus M, Gadani R, Kahitan M, Pokharel K, Osborne A, Pournaras D, Hewes J, Napolitano E, Chiappetta S, Bottino V, Dorado E, Schoettler A, Gaertner D, Fedtke K, Aguilar-Espinosa F, Aceves-Lozano S, Balani A, Nagliati C, Pennisi D, Rizzi A, Frattini F, Foschi D, Benuzzi L, Parikh C, Shah H, Pinotti E, Montuori M, Borrelli V, Dargent J, Copaescu CA, Hutopila I, Smeu B, Witteman B, Hazebroek E, Deden L, Heusschen L, Okkema S, Aufenacker T, den Hengst W, Vening W, van der Burgh Y, Ghazal A, Ibrahim H, Niazi M, Alkhaffaf B, Altarawni M, Cesana GC, Anselmino M, Uccelli M, Olmi S, Stier C, Akmanlar T, Sonnenberg T, Schieferbein U, Marcolini A, Awruch D, Vicentin M, de Souza Bastos EL, Gregorio SA, Ahuja A, Mittal T, Bolckmans R, Wiggins T, Baratte C, Wisnewsky JA, Genser L, Chong L, Taylor L, Ward S, Chong L, Taylor L, Hi MW, Heneghan H, Fearon N, Plamper A, Rheinwalt K, Heneghan H, Geoghegan J, Ng KC, Fearon N, Kaseja K, Kotowski M, Samarkandy TA, Leyva-Alvizo A, Corzo-Culebro L, Wang C, Yang W, Dong Z, Riera M, Jain R, Hamed H, Said M, Zarzar K, Garcia M, Türkçapar AG, Şen O, Baldini E, Conti L, Wietzycoski C, Lopes E, Pintar T, Salobir J, Aydin C, Atici SD, Ergin A, Ciyiltepe H, Bozkurt MA, Kizilkaya MC, Onalan NBD, Zuber MNBA, Wong WJ, Garcia A, Vidal L, Beisani M, Pasquier J, Vilallonga R, Sharma S, Parmar C, Lee L, Sufi P, Sinan H, Saydam M.",,Obesity surgery,2021,2021-07-30,Y,Pandemic; Obesity Surgery; Bariatric Surgery; Revisional Surgery; Covid-19; Sars-cov-2,,,"<h4>Background</h4>There are data on the safety of cancer surgery and the efficacy of preventive strategies on the prevention of postoperative symptomatic COVID-19 in these patients. But there is little such data for any elective surgery. The main objectives of this study were to examine the safety of bariatric surgery (BS) during the coronavirus disease 2019 (COVID-19) pandemic and to determine the efficacy of perioperative COVID-19 protective strategies on postoperative symptomatic COVID-19 rates.<h4>Methods</h4>We conducted an international cohort study to determine all-cause and COVID-19-specific 30-day morbidity and mortality of BS performed between 01/05/2020 and 31/10/2020.<h4>Results</h4>Four hundred ninety-nine surgeons from 185 centres in 42 countries provided data on 7704 patients. Elective primary BS (n = 7084) was associated with a 30-day morbidity of 6.76% (n = 479) and a 30-day mortality of 0.14% (n = 10). Emergency BS, revisional BS, insulin-treated type 2 diabetes, and untreated obstructive sleep apnoea were associated with increased complications on multivariable analysis. Forty-three patients developed symptomatic COVID-19 postoperatively, with a higher risk in non-whites. Preoperative self-isolation, preoperative testing for SARS-CoV-2, and surgery in institutions not concurrently treating COVID-19 patients did not reduce the incidence of postoperative COVID-19. Postoperative symptomatic COVID-19 was more likely if the surgery was performed during a COVID-19 peak in that country.<h4>Conclusions</h4>BS can be performed safely during the COVID-19 pandemic with appropriate perioperative protocols. There was no relationship between preoperative testing for COVID-19 and self-isolation with symptomatic postoperative COVID-19. The risk of postoperative COVID-19 risk was greater in non-whites or if BS was performed during a local peak.",,pdf:https://link.springer.com/content/pdf/10.1007/s11695-021-05493-9.pdf; doi:https://doi.org/10.1007/s11695-021-05493-9; html:https://europepmc.org/articles/PMC8323543; pdf:https://europepmc.org/articles/PMC8323543?pdf=render
 32119825,https://doi.org/10.1016/s2214-109x(20)30074-7,Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts.,"Hellewell J, Abbott S, Gimma A, Bosse NI, Jarvis CI, Russell TW, Munday JD, Kucharski AJ, Edmunds WJ, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Funk S, Eggo RM.",,The Lancet. Global health,2020,2020-02-28,Y,,Improving Public Health,COVID-19,"<h4>Background</h4>Isolation of cases and contact tracing is used to control outbreaks of infectious diseases, and has been used for coronavirus disease 2019 (COVID-19). Whether this strategy will achieve control depends on characteristics of both the pathogen and the response. Here we use a mathematical model to assess if isolation and contact tracing are able to control onwards transmission from imported cases of COVID-19.<h4>Methods</h4>We developed a stochastic transmission model, parameterised to the COVID-19 outbreak. We used the model to quantify the potential effectiveness of contact tracing and isolation of cases at controlling a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-like pathogen. We considered scenarios that varied in the number of initial cases, the basic reproduction number (R<sub>0</sub>), the delay from symptom onset to isolation, the probability that contacts were traced, the proportion of transmission that occurred before symptom onset, and the proportion of subclinical infections. We assumed isolation prevented all further transmission in the model. Outbreaks were deemed controlled if transmission ended within 12 weeks or before 5000 cases in total. We measured the success of controlling outbreaks using isolation and contact tracing, and quantified the weekly maximum number of cases traced to measure feasibility of public health effort.<h4>Findings</h4>Simulated outbreaks starting with five initial cases, an R<sub>0</sub> of 1·5, and 0% transmission before symptom onset could be controlled even with low contact tracing probability; however, the probability of controlling an outbreak decreased with the number of initial cases, when R<sub>0</sub> was 2·5 or 3·5 and with more transmission before symptom onset. Across different initial numbers of cases, the majority of scenarios with an R<sub>0</sub> of 1·5 were controllable with less than 50% of contacts successfully traced. To control the majority of outbreaks, for R<sub>0</sub> of 2·5 more than 70% of contacts had to be traced, and for an R<sub>0</sub> of 3·5 more than 90% of contacts had to be traced. The delay between symptom onset and isolation had the largest role in determining whether an outbreak was controllable when R<sub>0</sub> was 1·5. For R<sub>0</sub> values of 2·5 or 3·5, if there were 40 initial cases, contact tracing and isolation were only potentially feasible when less than 1% of transmission occurred before symptom onset.<h4>Interpretation</h4>In most scenarios, highly effective contact tracing and case isolation is enough to control a new outbreak of COVID-19 within 3 months. The probability of control decreases with long delays from symptom onset to isolation, fewer cases ascertained by contact tracing, and increasing transmission before symptoms. This model can be modified to reflect updated transmission characteristics and more specific definitions of outbreak control to assess the potential success of local response efforts.<h4>Funding</h4>Wellcome Trust, Global Challenges Research Fund, and Health Data Research UK.",,pdf:https://europepmc.org/articles/pmc7097845?pdf=render; doi:https://doi.org/10.1016/S2214-109X(20)30074-7; html:https://europepmc.org/articles/PMC7097845; pdf:https://europepmc.org/articles/PMC7097845?pdf=render
 34108714,https://doi.org/10.1038/s41591-021-01408-4,"First-dose ChAdOx1 and BNT162b2 COVID-19 vaccines and thrombocytopenic, thromboembolic and hemorrhagic events in Scotland.","Simpson CR, Shi T, Vasileiou E, Katikireddi SV, Kerr S, Moore E, McCowan C, Agrawal U, Shah SA, Ritchie LD, Murray J, Pan J, Bradley DT, Stock SJ, Wood R, Chuter A, Beggs J, Stagg HR, Joy M, Tsang RSM, de Lusignan S, Hobbs R, Lyons RA, Torabi F, Bedston S, O'Leary M, Akbari A, McMenamin J, Robertson C, Sheikh A.",,Nature medicine,2021,2021-06-09,Y,,,,"Reports of ChAdOx1 vaccine-associated thrombocytopenia and vascular adverse events have led to some countries restricting its use. Using a national prospective cohort, we estimated associations between exposure to first-dose ChAdOx1 or BNT162b2 vaccination and hematological and vascular adverse events using a nested incident-matched case-control study and a confirmatory self-controlled case series (SCCS) analysis. An association was found between ChAdOx1 vaccination and idiopathic thrombocytopenic purpura (ITP) (0-27 d after vaccination; adjusted rate ratio (aRR) = 5.77, 95% confidence interval (CI), 2.41-13.83), with an estimated incidence of 1.13 (0.62-1.63) cases per 100,000 doses. An SCCS analysis confirmed that this was unlikely due to bias (RR = 1.98 (1.29-3.02)). There was also an increased risk for arterial thromboembolic events (aRR = 1.22, 1.12-1.34) 0-27 d after vaccination, with an SCCS RR of 0.97 (0.93-1.02). For hemorrhagic events 0-27 d after vaccination, the aRR was 1.48 (1.12-1.96), with an SCCS RR of 0.95 (0.82-1.11). A first dose of ChAdOx1 was found to be associated with small increased risks of ITP, with suggestive evidence of an increased risk of arterial thromboembolic and hemorrhagic events. The attenuation of effect found in the SCCS analysis means that there is the potential for overestimation of the reported results, which might indicate the presence of some residual confounding or confounding by indication. Public health authorities should inform their jurisdictions of these relatively small increased risks associated with ChAdOx1. No positive associations were seen between BNT162b2 and thrombocytopenic, thromboembolic and hemorrhagic events.",,pdf:https://www.nature.com/articles/s41591-021-01408-4.pdf; doi:https://doi.org/10.1038/s41591-021-01408-4; html:https://europepmc.org/articles/PMC8282499; pdf:https://europepmc.org/articles/PMC8282499?pdf=render
-34190735,https://doi.org/,The changing characteristics of COVID-19 presentations. A regional comparison of SARS-CoV-2 hospitalised patients during the first and second wave.,"Atkin C, Kamwa V, Reddy-Kolanu V, Parekh D, Evison F, Nightingale P, Gallier S, Ball S, Sapey E.",,Acute medicine,2021,2021-01-01,N,,,,"<h4>Background</h4>This study assesses COVID-19 hospitalised patient demography and outcomes during wave 1 and wave 2, prior to new variants of the virus.<h4>Methods</h4>All patients with a positive SARS-CoV-2 swab between 10th March 2020 and 5th July 2020 (wave 1) and 1st September 2020 and 16th November 2020 (wave 2) admitted to University Hospitals Birmingham NHS Foundation Trust were included (n=4856), followed for 28 days.<h4>Results</h4>Wave 2 patients were younger, more ethnically diverse, had less co-morbidities and disease presentation was milder on presentation. After matching for these factors, mortality was reduced, but without differences in intensive care admissions.<h4>Conclusion</h4>Prior to new SARS-CoV-2 variants, outcomes for hospitalised patients with COVID-19 were improving but with similar intensive care needs.",,
 33587202,https://doi.org/10.1007/s10654-021-00722-y,COVID-19 mortality in the UK Biobank cohort: revisiting and evaluating risk factors.,"Elliott J, Bodinier B, Whitaker M, Delpierre C, Vermeulen R, Tzoulaki I, Elliott P, Chadeau-Hyam M.",,European journal of epidemiology,2021,2021-02-15,Y,Risk factor; Prospective Cohort; Uk Biobank; Sars-cov-2; Covid-19 Mortality,,,"Most studies of severe/fatal COVID-19 risk have used routine/hospitalisation data without detailed pre-morbid characterisation. Using the community-based UK Biobank cohort, we investigate risk factors for COVID-19 mortality in comparison with non-COVID-19 mortality. We investigated demographic, social (education, income, housing, employment), lifestyle (smoking, drinking, body mass index), biological (lipids, cystatin C, vitamin D), medical (comorbidities, medications) and environmental (air pollution) data from UK Biobank (N = 473,550) in relation to 459 COVID-19 and 2626 non-COVID-19 deaths to 21 September 2020. We used univariate, multivariable and penalised regression models. Age (OR = 2.76 [2.18-3.49] per S.D. [8.1 years], p = 2.6 × 10<sup>-17</sup>), male sex (OR = 1.47 [1.26-1.73], p = 1.3 × 10<sup>-6</sup>) and Black versus White ethnicity (OR = 1.21 [1.12-1.29], p = 3.0 × 10<sup>-7</sup>) were independently associated with and jointly explanatory of (area under receiver operating characteristic curve, AUC = 0.79) increased risk of COVID-19 mortality. In multivariable regression, alongside demographic covariates, being a healthcare worker, current smoker, having cardiovascular disease, hypertension, diabetes, autoimmune disease, and oral steroid use at enrolment were independently associated with COVID-19 mortality. Penalised regression models selected income, cardiovascular disease, hypertension, diabetes, cystatin C, and oral steroid use as jointly contributing to COVID-19 mortality risk; Black ethnicity, hypertension and oral steroid use contributed to COVID-19 but not non-COVID-19 mortality. Age, male sex and Black ethnicity, as well as comorbidities and oral steroid use at enrolment were associated with increased risk of COVID-19 death. Our results suggest that previously reported associations of COVID-19 mortality with body mass index, low vitamin D, air pollutants, renin-angiotensin-aldosterone system inhibitors may be explained by the aforementioned factors.",,pdf:https://link.springer.com/content/pdf/10.1007/s10654-021-00722-y.pdf; doi:https://doi.org/10.1007/s10654-021-00722-y; html:https://europepmc.org/articles/PMC7882869; pdf:https://europepmc.org/articles/PMC7882869?pdf=render
+34190735,https://doi.org/,The changing characteristics of COVID-19 presentations. A regional comparison of SARS-CoV-2 hospitalised patients during the first and second wave.,"Atkin C, Kamwa V, Reddy-Kolanu V, Parekh D, Evison F, Nightingale P, Gallier S, Ball S, Sapey E.",,Acute medicine,2021,2021-01-01,N,,,,"<h4>Background</h4>This study assesses COVID-19 hospitalised patient demography and outcomes during wave 1 and wave 2, prior to new variants of the virus.<h4>Methods</h4>All patients with a positive SARS-CoV-2 swab between 10th March 2020 and 5th July 2020 (wave 1) and 1st September 2020 and 16th November 2020 (wave 2) admitted to University Hospitals Birmingham NHS Foundation Trust were included (n=4856), followed for 28 days.<h4>Results</h4>Wave 2 patients were younger, more ethnically diverse, had less co-morbidities and disease presentation was milder on presentation. After matching for these factors, mortality was reduced, but without differences in intensive care admissions.<h4>Conclusion</h4>Prior to new SARS-CoV-2 variants, outcomes for hospitalised patients with COVID-19 were improving but with similar intensive care needs.",,
 33939953,https://doi.org/10.1016/s0140-6736(21)00634-6,"Ethnic differences in SARS-CoV-2 infection and COVID-19-related hospitalisation, intensive care unit admission, and death in 17 million adults in England: an observational cohort study using the OpenSAFELY platform.","Mathur R, Rentsch CT, Morton CE, Hulme WJ, Schultze A, MacKenna B, Eggo RM, Bhaskaran K, Wong AYS, Williamson EJ, Forbes H, Wing K, McDonald HI, Bates C, Bacon S, Walker AJ, Evans D, Inglesby P, Mehrkar A, Curtis HJ, DeVito NJ, Croker R, Drysdale H, Cockburn J, Parry J, Hester F, Harper S, Douglas IJ, Tomlinson L, Evans SJW, Grieve R, Harrison D, Rowan K, Khunti K, Chaturvedi N, Smeeth L, Goldacre B, OpenSAFELY Collaborative.",,"Lancet (London, England)",2021,2021-04-30,Y,,,,"<h4>Background</h4>COVID-19 has disproportionately affected minority ethnic populations in the UK. Our aim was to quantify ethnic differences in SARS-CoV-2 infection and COVID-19 outcomes during the first and second waves of the COVID-19 pandemic in England.<h4>Methods</h4>We conducted an observational cohort study of adults (aged ≥18 years) registered with primary care practices in England for whom electronic health records were available through the OpenSAFELY platform, and who had at least 1 year of continuous registration at the start of each study period (Feb 1 to Aug 3, 2020 [wave 1], and Sept 1 to Dec 31, 2020 [wave 2]). Individual-level primary care data were linked to data from other sources on the outcomes of interest: SARS-CoV-2 testing and positive test results and COVID-19-related hospital admissions, intensive care unit (ICU) admissions, and death. The exposure was self-reported ethnicity as captured on the primary care record, grouped into five high-level census categories (White, South Asian, Black, other, and mixed) and 16 subcategories across these five categories, as well as an unknown ethnicity category. We used multivariable Cox regression to examine ethnic differences in the outcomes of interest. Models were adjusted for age, sex, deprivation, clinical factors and comorbidities, and household size, with stratification by geographical region.<h4>Findings</h4>Of 17 288 532 adults included in the study (excluding care home residents), 10 877 978 (62·9%) were White, 1 025 319 (5·9%) were South Asian, 340 912 (2·0%) were Black, 170 484 (1·0%) were of mixed ethnicity, 320 788 (1·9%) were of other ethnicity, and 4 553 051 (26·3%) were of unknown ethnicity. In wave 1, the likelihood of being tested for SARS-CoV-2 infection was slightly higher in the South Asian group (adjusted hazard ratio 1·08 [95% CI 1·07-1·09]), Black group (1·08 [1·06-1·09]), and mixed ethnicity group (1·04 [1·02-1·05]) and was decreased in the other ethnicity group (0·77 [0·76-0·78]) relative to the White group. The risk of testing positive for SARS-CoV-2 infection was higher in the South Asian group (1·99 [1·94-2·04]), Black group (1·69 [1·62-1·77]), mixed ethnicity group (1·49 [1·39-1·59]), and other ethnicity group (1·20 [1·14-1·28]). Compared with the White group, the four remaining high-level ethnic groups had an increased risk of COVID-19-related hospitalisation (South Asian group 1·48 [1·41-1·55], Black group 1·78 [1·67-1·90], mixed ethnicity group 1·63 [1·45-1·83], other ethnicity group 1·54 [1·41-1·69]), COVID-19-related ICU admission (2·18 [1·92-2·48], 3·12 [2·65-3·67], 2·96 [2·26-3·87], 3·18 [2·58-3·93]), and death (1·26 [1·15-1·37], 1·51 [1·31-1·71], 1·41 [1·11-1·81], 1·22 [1·00-1·48]). In wave 2, the risks of hospitalisation, ICU admission, and death relative to the White group were increased in the South Asian group but attenuated for the Black group compared with these risks in wave 1. Disaggregation into 16 ethnicity groups showed important heterogeneity within the five broader categories.<h4>Interpretation</h4>Some minority ethnic populations in England have excess risks of testing positive for SARS-CoV-2 and of adverse COVID-19 outcomes compared with the White population, even after accounting for differences in sociodemographic, clinical, and household characteristics. Causes are likely to be multifactorial, and delineating the exact mechanisms is crucial. Tackling ethnic inequalities will require action across many fronts, including reducing structural inequalities, addressing barriers to equitable care, and improving uptake of testing and vaccination.<h4>Funding</h4>Medical Research Council.",,pdf:https://researchonline.lshtm.ac.uk/id/eprint/4659476/13/PIIS0140673621006346.pdf; doi:https://doi.org/10.1016/S0140-6736(21)00634-6; html:https://europepmc.org/articles/PMC8087292; pdf:https://europepmc.org/articles/PMC8087292?pdf=render
 35265823,https://doi.org/10.1016/j.eclinm.2022.101317,Variation in global COVID-19 symptoms by geography and by chronic disease: A global survey using the COVID-19 Symptom Mapper.,"Kadirvelu B, Burcea G, Quint JK, Costelloe CE, Faisal AA.",,EClinicalMedicine,2022,2022-03-06,Y,"Comorbidities; Pcr, Polymerase Chain Reaction; Covid-19; Covid-19 Symptoms; Covid Symptom Profile; Covid Symptoms Mapper; Covid Symptoms Survey; Covid-19, The Coronavirus Disease That First Appeared In 2019 Caused By The Sars-cov-2 Coronavirus.; Who, World Health Organization, A Specialized Agency Of The United Nations Responsible For International Public Health.",,,"<h4>Background</h4>COVID-19 is typically characterised by a triad of symptoms: cough, fever and loss of taste and smell, however, this varies globally. This study examines variations in COVID-19 symptom profiles based on underlying chronic disease and geographical location.<h4>Methods</h4>Using a global online symptom survey of 78,299 responders in 190 countries between 09/04/2020 and 22/09/2020, we conducted an exploratory study to examine symptom profiles associated with a positive COVID-19 test result by country and underlying chronic disease (single, co- or multi-morbidities) using statistical and machine learning methods.<h4>Findings</h4>From the results of 7980 COVID-19 tested positive responders, we find that symptom patterns differ by country. For example, India reported a lower proportion of headache (22.8% vs 47.8%, p<1e-13) and itchy eyes (7.3% vs. 16.5%, p=2e-8) than other countries. As with geographic location, we find people differed in their reported symptoms if they suffered from specific chronic diseases. For example, COVID-19 positive responders with asthma (25.3% vs. 13.7%, p=7e-6) were more likely to report shortness of breath compared to those with no underlying chronic disease.<h4>Interpretation</h4>We have identified variation in COVID-19 symptom profiles depending on geographic location and underlying chronic disease. Failure to reflect this symptom variation in public health messaging may contribute to asymptomatic COVID-19 spread and put patients with chronic diseases at a greater risk of infection. Future work should focus on symptom profile variation in the emerging variants of the SARS-CoV-2 virus. This is crucial to speed up clinical diagnosis, predict prognostic outcomes and target treatment.<h4>Funding</h4>We acknowledge funding to AAF by a UKRI Turing AI Fellowship and to CEC by a personal NIHR Career Development Fellowship (grant number NIHR-2016-090-015). JKQ has received grants from The Health Foundation, MRC, GSK, Bayer, BI, Asthma UK-British Lung Foundation, IQVIA, Chiesi AZ, and Insmed. This work is supported by BREATHE - The Health Data Research Hub for Respiratory Health [MC_PC_19004]. BREATHE is funded through the UK Research and Innovation Industrial Strategy Challenge Fund and delivered through Health Data Research UK. Imperial College London is grateful for the support from the Northwest London NIHR Applied Research Collaboration. The views expressed in this publication are those of the authors and not necessarily those of the NIHR or the Department of Health and Social Care.",,pdf:http://www.thelancet.com/article/S2589537022000475/pdf; doi:https://doi.org/10.1016/j.eclinm.2022.101317; html:https://europepmc.org/articles/PMC8898170; pdf:https://europepmc.org/articles/PMC8898170?pdf=render
 36385522,https://doi.org/10.1093/ehjqcco/qcac077,Effects of the COVID-19 pandemic on secondary care for cardiovascular disease in the UK: an electronic health record analysis across three countries.,"Wright FL, Cheema K, Goldacre R, Hall N, Herz N, Islam N, Karim Z, Moreno-Martos D, Morales DR, O'Connell D, Spata E, Akbari A, Ashworth M, Barber M, Briffa N, Canoy D, Denaxas S, Khunti K, Kurdi A, Mamas M, Priedon R, Sudlow C, Morris EJA, Lacey B, Banerjee A.",,European heart journal. Quality of care & clinical outcomes,2023,2023-06-01,Y,,,,"<h4>Background</h4>Although morbidity and mortality from COVID-19 have been widely reported, the indirect effects of the pandemic beyond 2020 on other major diseases and health service activity have not been well described.<h4>Methods and results</h4>Analyses used national administrative electronic hospital records in England, Scotland, and Wales for 2016-21. Admissions and procedures during the pandemic (2020-21) related to six major cardiovascular conditions [acute coronary syndrome (ACS), heart failure (HF), stroke/transient ischaemic attack (TIA), peripheral arterial disease (PAD), aortic aneurysm (AA), and venous thromboembolism(VTE)] were compared with the annual average in the pre-pandemic period (2016-19). Differences were assessed by time period and urgency of care.In 2020, there were 31 064 (-6%) fewer hospital admissions [14 506 (-4%) fewer emergencies, 16 560 (-23%) fewer elective admissions] compared with 2016-19 for the six major cardiovascular diseases (CVDs) combined. The proportional reduction in admissions was similar in all three countries. Overall, hospital admissions returned to pre-pandemic levels in 2021. Elective admissions remained substantially below expected levels for almost all conditions in all three countries [-10 996 (-15%) fewer admissions]. However, these reductions were offset by higher than expected total emergency admissions [+25 878 (+6%) higher admissions], notably for HF and stroke in England, and for VTE in all three countries. Analyses for procedures showed similar temporal variations to admissions.<h4>Conclusion</h4>The present study highlights increasing emergency cardiovascular admissions during the pandemic, in the context of a substantial and sustained reduction in elective admissions and procedures. This is likely to increase further the demands on cardiovascular services over the coming years.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa62054/Download/62054__26063__5453b00901174a7d9a0797547f023fba.pdf; doi:https://doi.org/10.1093/ehjqcco/qcac077; html:https://europepmc.org/articles/PMC10284263; pdf:https://europepmc.org/articles/PMC10284263?pdf=render
-37726825,https://doi.org/10.1186/s13063-023-07606-4,Correction: Development and evaluation of rapid data-enabled access to routine clinical information to enhance early recruitment to the national clinical platform trial of COVID-19 community treatments.,"Cake C, Ogburn E, Pinches H, Coleman G, Seymour D, Woodard F, Manohar S, Monsur M, Landray M, Dalton G, Morris AD, Chinnery PF, UK COVID-19 National Core Studies Consortium, Hobbs FDR, Butler C.",,Trials,2023,2023-09-19,Y,,,,,,pdf:https://trialsjournal.biomedcentral.com/counter/pdf/10.1186/s13063-023-07606-4; doi:https://doi.org/10.1186/s13063-023-07606-4; html:https://europepmc.org/articles/PMC10507817; pdf:https://europepmc.org/articles/PMC10507817?pdf=render
 35308309,https://doi.org/10.1016/j.eclinm.2022.101346,"Healthcare workers' views on mandatory SARS-CoV-2 vaccination in the UK: A cross-sectional, mixed-methods analysis from the UK-REACH study.","Woolf K, Gogoi M, Martin CA, Papineni P, Lagrata S, Nellums LB, McManus IC, Guyatt AL, Melbourne C, Bryant L, Gupta A, John C, Carr S, Tobin MD, Simpson S, Gregary B, Aujayeb A, Zingwe S, Reza R, Gray LJ, Khunti K, Pareek M, UK-REACH Study Collaborative Group.",,EClinicalMedicine,2022,2022-03-15,Y,,,,"<h4>Background</h4>Several countries now have mandatory SARS-CoV-2 vaccination for healthcare workers (HCWs) or the general population. HCWs' views on this are largely unknown. Using data from the nationwide UK-REACH study we aimed to understand UK HCW's views on improving SARS-CoV-2 vaccination coverage, including mandatory vaccination.<h4>Methods</h4>Between 21st April and 26th June 2021, we administered an online questionnaire via email to 17 891 UK HCWs recruited as part of a longitudinal cohort from across the UK who had previously responded to a baseline questionnaire (primarily recruited through email) as part of the United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers (UK-REACH) nationwide prospective cohort study. We categorised responses to a free-text question ""What should society do if people do not get vaccinated against COVID-19?"" using qualitative content analysis. We collapsed categories into a binary variable: favours mandatory vaccination or not, using logistic regression to calculate its demographic predictors, and its occupational, health, and attitudinal predictors adjusted for demographics.<h4>Findings</h4>Of 5633 questionnaire respondents, 3235 answered the free text question. Median age of free text responders was 47 years (IQR 36-56) and 2705 (74.3%) were female. 18% (<i>n</i> = 578) favoured mandatory vaccination (201 [6%] participants for HCWs and others working with vulnerable populations; 377 [12%] for the general population), but the most frequent suggestion was education (32%, <i>n</i> = 1047). Older HCWs (OR 1.84; 95% CI 1.44-2.34 [≥55 years vs 16 years to <40 years]), HCWs vaccinated against influenza (OR 1.49; 95% CI 1.11-2.01 [2 vaccines vs none]), and with more positive vaccination attitudes generally (OR 1.10; 95% CI 1.06-1.15) were more likely to favour mandatory vaccination, whereas female HCWs (OR= 0.79, 95% CI 0.63-0.96, vs male HCWs) and Black HCWs (OR=0.46, 95% CI 0.25-0.85, vs white HCWs) were less likely to.<h4>Interpretation</h4>Only one in six of the HCWs in this large, diverse, UK-wide sample favoured mandatory vaccination. Building trust, educating, and supporting HCWs who are hesitant about vaccination may be more acceptable, effective, and equitable.<h4>Funding</h4>MRC-UK Research and Innovation grant (MR/V027549/1) and the Department of Health and Social Care (DHSC) via the National Institute for Health Research (NIHR). Core funding was also provided by NIHR Biomedical Research Centres.",,pdf:http://www.thelancet.com/article/S2589537022000761/pdf; doi:https://doi.org/10.1016/j.eclinm.2022.101346; html:https://europepmc.org/articles/PMC8923694; pdf:https://europepmc.org/articles/PMC8923694?pdf=render
+37726825,https://doi.org/10.1186/s13063-023-07606-4,Correction: Development and evaluation of rapid data-enabled access to routine clinical information to enhance early recruitment to the national clinical platform trial of COVID-19 community treatments.,"Cake C, Ogburn E, Pinches H, Coleman G, Seymour D, Woodard F, Manohar S, Monsur M, Landray M, Dalton G, Morris AD, Chinnery PF, UK COVID-19 National Core Studies Consortium, Hobbs FDR, Butler C.",,Trials,2023,2023-09-19,Y,,,,,,pdf:https://trialsjournal.biomedcentral.com/counter/pdf/10.1186/s13063-023-07606-4; doi:https://doi.org/10.1186/s13063-023-07606-4; html:https://europepmc.org/articles/PMC10507817; pdf:https://europepmc.org/articles/PMC10507817?pdf=render
 36436752,https://doi.org/10.1016/j.ijid.2022.11.024,"Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa.","Davies MA, Morden E, Rousseau P, Arendse J, Bam JL, Boloko L, Cloete K, Cohen C, Chetty N, Dane P, Heekes A, Hsiao NY, Hunter M, Hussey H, Jacobs T, Jassat W, Kariem S, Kassanjee R, Laenen I, Roux SL, Lessells R, Mahomed H, Maughan D, Meintjes G, Mendelson M, Mnguni A, Moodley M, Murie K, Naude J, Ntusi NAB, Paleker M, Parker A, Pienaar D, Preiser W, Prozesky H, Raubenheimer P, Rossouw L, Schrueder N, Smith B, Smith M, Solomon W, Symons G, Taljaard J, Wasserman S, Wilkinson RJ, Wolmarans M, Wolter N, Boulle A.",,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2023,2022-11-24,Y,"Covid-19; Omicron; Ba.4; Ba.5; Death, Severe Hospitalization",,,"<h4>Objectives</h4>We aimed to compare the clinical severity of Omicron BA.4/BA.5 infection with BA.1 and earlier variant infections among laboratory-confirmed SARS-CoV-2 cases in the Western Cape, South Africa, using timing of infection to infer the lineage/variant causing infection.<h4>Methods</h4>We included public sector patients aged ≥20 years with laboratory-confirmed COVID-19 between May 01-May 21, 2022 (BA.4/BA.5 wave) and equivalent previous wave periods. We compared the risk between waves of (i) death and (ii) severe hospitalization/death (all within 21 days of diagnosis) using Cox regression adjusted for demographics, comorbidities, admission pressure, vaccination, and previous infection.<h4>Results</h4>Among 3793 patients from the BA.4/BA.5 wave and 190,836 patients from previous waves, the risk of severe hospitalization/death was similar in the BA.4/BA.5 and BA.1 waves (adjusted hazard ratio [aHR] 1.12; 95% confidence interval [CI] 0.93; 1.34). Both Omicron waves had a lower risk of severe outcomes than previous waves. Previous infection (aHR 0.29, 95% CI 0.24; 0.36) and vaccination (aHR 0.17; 95% CI 0.07; 0.40 for at least three doses vs no vaccine) were protective.<h4>Conclusion</h4>Disease severity was similar among diagnosed COVID-19 cases in the BA.4/BA.5 and BA.1 periods in the context of growing immunity against SARS-CoV-2 due to previous infection and vaccination, both of which were strongly protective.",,doi:https://doi.org/10.1016/j.ijid.2022.11.024; doi:https://doi.org/10.1016/j.ijid.2022.11.024; html:https://europepmc.org/articles/PMC9686046; pdf:https://europepmc.org/articles/PMC9686046?pdf=render
 35411997,https://doi.org/10.1111/tmi.13752,"Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa.","Davies MA, Kassanjee R, Rousseau P, Morden E, Johnson L, Solomon W, Hsiao NY, Hussey H, Meintjes G, Paleker M, Jacobs T, Raubenheimer P, Heekes A, Dane P, Bam JL, Smith M, Preiser W, Pienaar D, Mendelson M, Naude J, Schrueder N, Mnguni A, Le Roux S, Murie K, Prozesky H, Mahomed H, Rossouw L, Wasserman S, Maughan D, Boloko L, Smith B, Taljaard J, Symons G, Ntusi NAB, Parker A, Wolter N, Jassat W, Cohen C, Lessells R, Wilkinson RJ, Arendse J, Kariem S, Moodley M, Wolmarans M, Cloete K, Boulle A, Western Cape and South African National Departments of Health in collaboration with the National Institute for Communicable Diseases in South Africa Affiliations.",,Tropical medicine & international health : TM & IH,2022,2022-05-10,Y,Vaccination; Immunity; DELTA; Sub-Saharan Africa; Covid-19; Prior Infection; Omicron,,,"<h4>Objectives</h4>The objective was to compare COVID-19 outcomes in the Omicron-driven fourth wave with prior waves in the Western Cape, assess the contribution of undiagnosed prior infection to differences in outcomes in a context of high seroprevalence due to prior infection and determine whether protection against severe disease conferred by prior infection and/or vaccination was maintained.<h4>Methods</h4>In this cohort study, we included public sector patients aged ≥20 years with a laboratory-confirmed COVID-19 diagnosis between 14 November and 11 December 2021 (wave four) and equivalent prior wave periods. We compared the risk between waves of the following outcomes using Cox regression: death, severe hospitalisation or death and any hospitalisation or death (all ≤14 days after diagnosis) adjusted for age, sex, comorbidities, geography, vaccination and prior infection.<h4>Results</h4>We included 5144 patients from wave four and 11,609 from prior waves. The risk of all outcomes was lower in wave four compared to the Delta-driven wave three (adjusted hazard ratio (aHR) [95% confidence interval (CI)] for death 0.27 [0.19; 0.38]. Risk reduction was lower when adjusting for vaccination and prior diagnosed infection (aHR: 0.41, 95% CI: 0.29; 0.59) and reduced further when accounting for unascertained prior infections (aHR: 0.72). Vaccine protection was maintained in wave four (aHR for outcome of death: 0.24; 95% CI: 0.10; 0.58).<h4>Conclusions</h4>In the Omicron-driven wave, severe COVID-19 outcomes were reduced mostly due to protection conferred by prior infection and/or vaccination, but intrinsically reduced virulence may account for a modest reduction in risk of severe hospitalisation or death compared to the Delta-driven wave.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/tmi.13752; doi:https://doi.org/10.1111/tmi.13752; html:https://europepmc.org/articles/PMC9115442; pdf:https://europepmc.org/articles/PMC9115442?pdf=render
 38192590,https://doi.org/10.1016/j.eclinm.2023.102321,Clinical and health inequality risk factors for non-COVID-related sepsis during the global COVID-19 pandemic: a national case-control and cohort study.,"Zhong X, Ashiru-Oredope D, Pate A, Martin GP, Sharma A, Dark P, Felton T, Lake C, MacKenna B, Mehrkar A, Bacon SCJ, Massey J, Inglesby P, Goldacre B, OpenSAFELY Collaborative, Hand K, Bladon S, Cunningham N, Gilham E, Brown CS, Mirfenderesky M, Palin V, van Staa TP.",,EClinicalMedicine,2023,2023-11-23,Y,Sepsis; Morbidity; Primary Care; Deprivation; Health Inequality; Covid-19 Pandemic,,,"<h4>Background</h4>Sepsis, characterised by significant morbidity and mortality, is intricately linked to socioeconomic disparities and pre-admission clinical histories. This study aspires to elucidate the association between non-COVID-19 related sepsis and health inequality risk factors amidst the pandemic in England, with a secondary focus on their association with 30-day sepsis mortality.<h4>Methods</h4>With the approval of NHS England, we harnessed the OpenSAFELY platform to execute a cohort study and a 1:6 matched case-control study. A sepsis diagnosis was identified from the incident hospital admissions record using ICD-10 codes. This encompassed 248,767 cases with non-COVID-19 sepsis from a cohort of 22.0 million individuals spanning January 1, 2019, to June 31, 2022. Socioeconomic deprivation was gauged using the Index of Multiple Deprivation score, reflecting indicators like income, employment, and education. Hospitalisation-related sepsis diagnoses were categorised as community-acquired or hospital-acquired. Cases were matched to controls who had no recorded diagnosis of sepsis, based on age (stepwise), sex, and calendar month. The eligibility criteria for controls were established primarily on the absence of a recorded sepsis diagnosis. Associations between potential predictors and odds of developing non-COVID-19 sepsis underwent assessment through conditional logistic regression models, with multivariable regression determining odds ratios (ORs) for 30-day mortality.<h4>Findings</h4>The study included 224,361 (10.2%) cases with non-COVID-19 sepsis and 1,346,166 matched controls. The most socioeconomic deprived quintile was associated with higher odds of developing non-COVID-19 sepsis than the least deprived quintile (crude OR 1.80 [95% CI 1.77-1.83]). Other risk factors (after adjusting comorbidities) such as learning disability (adjusted OR 3.53 [3.35-3.73]), chronic liver disease (adjusted OR 3.08 [2.97-3.19]), chronic kidney disease (stage 4: adjusted OR 2.62 [2.55-2.70], stage 5: adjusted OR 6.23 [5.81-6.69]), cancer, neurological disease, immunosuppressive conditions were also associated with developing non-COVID-19 sepsis. The incidence rate of non-COVID-19 sepsis decreased during the COVID-19 pandemic and rebounded to pre-pandemic levels (April 2021) after national lockdowns had been lifted. The 30-day mortality risk in cases with non-COVID-19 sepsis was higher for the most deprived quintile across all periods.<h4>Interpretation</h4>Socioeconomic deprivation, comorbidity and learning disabilities were associated with an increased odds of developing non-COVID-19 related sepsis and 30-day mortality in England. This study highlights the need to improve the prevention of sepsis, including more precise targeting of antimicrobials to higher-risk patients.<h4>Funding</h4>The UK Health Security Agency, Health Data Research UK, and National Institute for Health Research.",,doi:https://doi.org/10.1016/j.eclinm.2023.102321; html:https://europepmc.org/articles/PMC10772239; pdf:https://europepmc.org/articles/PMC10772239?pdf=render
@@ -405,22 +405,22 @@ PMC9023380,https://doi.org/,Assessing the spread risk of COVID-19 associated wit
 33611594,https://doi.org/10.1093/eurjpc/zwaa155,Excess deaths in people with cardiovascular diseases during the COVID-19 pandemic.,"Banerjee A, Chen S, Pasea L, Lai AG, Katsoulis M, Denaxas S, Nafilyan V, Williams B, Wong WK, Bakhai A, Khunti K, Pillay D, Noursadeghi M, Wu H, Pareek N, Bromage D, McDonagh TA, Byrne J, Teo JTH, Shah AM, Humberstone B, Tang LV, Shah ASV, Rubboli A, Guo Y, Hu Y, Sudlow CLM, Lip GYH, Hemingway H.",,European journal of preventive cardiology,2021,2021-12-01,Y,Cardiovascular disease; Public Health; Health Policy; Global Health; Coronavirus-2019,,,"<h4>Aims</h4>Cardiovascular diseases (CVDs) increase mortality risk from coronavirus infection (COVID-19). There are also concerns that the pandemic has affected supply and demand of acute cardiovascular care. We estimated excess mortality in specific CVDs, both 'direct', through infection, and 'indirect', through changes in healthcare.<h4>Methods and results</h4>We used (i) national mortality data for England and Wales to investigate trends in non-COVID-19 and CVD excess deaths; (ii) routine data from hospitals in England (n = 2), Italy (n = 1), and China (n = 5) to assess indirect pandemic effects on referral, diagnosis, and treatment services for CVD; and (iii) population-based electronic health records from 3 862 012 individuals in England to investigate pre- and post-COVID-19 mortality for people with incident and prevalent CVD. We incorporated pre-COVID-19 risk (by age, sex, and comorbidities), estimated population COVID-19 prevalence, and estimated relative risk (RR) of mortality in those with CVD and COVID-19 compared with CVD and non-infected (RR: 1.2, 1.5, 2.0, and 3.0).Mortality data suggest indirect effects on CVD will be delayed rather than contemporaneous (peak RR 1.14). CVD service activity decreased by 60-100% compared with pre-pandemic levels in eight hospitals across China, Italy, and England. In China, activity remained below pre-COVID-19 levels for 2-3 months even after easing lockdown and is still reduced in Italy and England. For total CVD (incident and prevalent), at 10% COVID-19 prevalence, we estimated direct impact of 31 205 and 62 410 excess deaths in England (RR 1.5 and 2.0, respectively), and indirect effect of 49 932 to 99 865 deaths.<h4>Conclusion</h4>Supply and demand for CVD services have dramatically reduced across countries with potential for substantial, but avoidable, excess mortality during and after the pandemic.",,pdf:https://academic.oup.com/eurjpc/article-pdf/28/14/1599/41827245/zwaa155.pdf; doi:https://doi.org/10.1093/eurjpc/zwaa155; html:https://europepmc.org/articles/PMC7928969; pdf:https://europepmc.org/articles/PMC7928969?pdf=render
 35365070,https://doi.org/10.1186/s12879-022-07268-8,Impact of non-pharmaceutical interventions on SARS-CoV-2 outbreaks in English care homes: a modelling study.,"Rosello A, Barnard RC, Smith DRM, Evans S, Grimm F, Davies NG, Centre for Mathematical Modelling of Infectious Diseases COVID-19 Modelling Working Group, Deeny SR, Knight GM, Edmunds WJ.",,BMC infectious diseases,2022,2022-04-01,Y,PCR; Testing; mathematical model; Long-term Care Facility; Care Home; Non-pharmaceutical Interventions; Covid-19; Sars-cov-2,,,"<h4>Background</h4>COVID-19 outbreaks still occur in English care homes despite the interventions in place.<h4>Methods</h4>We developed a stochastic compartmental model to simulate the spread of SARS-CoV-2 within an English care home. We quantified the outbreak risk with baseline non-pharmaceutical interventions (NPIs) already in place, the role of community prevalence in driving outbreaks, and the relative contribution of all importation routes into a fully susceptible care home. We also considered the potential impact of additional control measures in care homes with and without immunity, namely: increasing staff and resident testing frequency, using lateral flow antigen testing (LFD) tests instead of polymerase chain reaction (PCR), enhancing infection prevention and control (IPC), increasing the proportion of residents isolated, shortening the delay to isolation, improving the effectiveness of isolation, restricting visitors and limiting staff to working in one care home. We additionally present a Shiny application for users to apply this model to their facility of interest, specifying care home, outbreak and intervention characteristics.<h4>Results</h4>The model suggests that importation of SARS-CoV-2 by staff, from the community, is the main driver of outbreaks, that importation by visitors or from hospitals is rare, and that the past testing strategy (monthly testing of residents and daily testing of staff by PCR) likely provides negligible benefit in preventing outbreaks. Daily staff testing by LFD was 39% (95% 18-55%) effective in preventing outbreaks at 30 days compared to no testing.<h4>Conclusions</h4>Increasing the frequency of testing in staff and enhancing IPC are important to preventing importations to the care home. Further work is needed to understand the impact of vaccination in this population, which is likely to be very effective in preventing outbreaks.",,pdf:https://bmcinfectdis.biomedcentral.com/track/pdf/10.1186/s12879-022-07268-8; doi:https://doi.org/10.1186/s12879-022-07268-8; html:https://europepmc.org/articles/PMC8972713; pdf:https://europepmc.org/articles/PMC8972713?pdf=render
 33635829,https://doi.org/10.1530/eje-20-1163,Increased COVID-19 infections in women with polycystic ovary syndrome: a population-based study.,"Subramanian A, Anand A, Adderley NJ, Okoth K, Toulis KA, Gokhale K, Sainsbury C, O'Reilly MW, Arlt W, Nirantharakumar K.",,European journal of endocrinology,2021,2021-05-01,Y,,,,"<h4>Objective</h4>Several recent observational studies have linked metabolic comorbidities to an increased risk from COVID-19. Here we investigated whether women with PCOS are at an increased risk of COVID-19 infection.<h4>Design</h4>Population-based closed cohort study between 31 January 2020 and 22 July 2020 in the setting of a UK primary care database (The Health Improvement Network, THIN).<h4>Methods</h4>The main outcome was the incidence of COVID-19 coded as suspected or confirmed by the primary care provider. We used Cox proportional hazards regression model with stepwise inclusion of explanatory variables (age, BMI, impaired glucose regulation, androgen excess, anovulation, vitamin D deficiency, hypertension, and cardiovascular disease) to provide unadjusted and adjusted hazard risks (HR) of COVID-19 infection among women with PCOS compared to women without PCOS.<h4>Results</h4>We identified 21 292 women with a coded diagnosis of PCO/PCOS and randomly selected 78 310 aged and general practice matched control women. The crude COVID-19 incidence was 18.1 and 11.9 per 1000 person-years among women with and without PCOS, respectively. Age-adjusted Cox regression analysis suggested a 51% higher risk of COVID-19 among women with PCOS compared to women without PCOS (HR: 1.51 (95% CI: 1.27-1.80), P < 0.001). After adjusting for age and BMI, HR reduced to 1.36 (1.14-1.63)], P = 0.001. In the fully adjusted model, women with PCOS had a 28% increased risk of COVID-19 (aHR: 1.28 (1.05-1.56), P = 0.015).<h4>Conclusion</h4>Women with PCOS are at an increased risk of COVID-19 infection and should be specifically encouraged to adhere to infection control measures during the COVID-19 pandemic.<h4>Significance statement</h4>Women with polycystic ovary syndrome (PCOS) have an increased risk of cardio-metabolic disease, which have been identified as a risk factor for COVID-19. To investigate whether the increased metabolic risk in PCOS translates into an increased risk of COVID-19 infection, we carried out a population-based closed cohort study in the UK during its first wave of the SARS-CoV-2 pandemic (January to July 2020), including 21 292 women with PCOS and 78 310 controls matched for sex, age and general practice location. Results revealed a 52% increased risk of COVID-19 infection in women with PCOS, which remained increased at 28% above controls after adjustment for age, BMI, impaired glucose regulation and other explanatory variables.",,pdf:https://academic.oup.com/ejendo/article-pdf/184/5/637/45221794/eje-20-1163.pdf; doi:https://doi.org/10.1530/EJE-20-1163; html:https://europepmc.org/articles/PMC8052516; pdf:https://europepmc.org/articles/PMC8052516?pdf=render
+34645794,https://doi.org/10.1038/s41467-021-25914-8,A cross-sectional analysis of meteorological factors and SARS-CoV-2 transmission in 409 cities across 26 countries.,"Sera F, Armstrong B, Abbott S, Meakin S, O'Reilly K, von Borries R, Schneider R, Royé D, Hashizume M, Pascal M, Tobias A, Vicedo-Cabrera AM, MCC Collaborative Research Network, CMMID COVID-19 Working Group, Gasparrini A, Lowe R.",,Nature communications,2021,2021-10-13,Y,,,,"There is conflicting evidence on the influence of weather on COVID-19 transmission. Our aim is to estimate weather-dependent signatures in the early phase of the pandemic, while controlling for socio-economic factors and non-pharmaceutical interventions. We identify a modest non-linear association between mean temperature and the effective reproduction number (R<sub>e</sub>) in 409 cities in 26 countries, with a decrease of 0.087 (95% CI: 0.025; 0.148) for a 10 °C increase. Early interventions have a greater effect on R<sub>e</sub> with a decrease of 0.285 (95% CI 0.223; 0.347) for a 5th - 95th percentile increase in the government response index. The variation in the effective reproduction number explained by government interventions is 6 times greater than for mean temperature. We find little evidence of meteorological conditions having influenced the early stages of local epidemics and conclude that population behaviour and government interventions are more important drivers of transmission.",,doi:https://doi.org/10.1038/s41467-021-25914-8; doi:https://doi.org/10.1038/s41467-021-25914-8; html:https://europepmc.org/articles/PMC8514574; pdf:https://europepmc.org/articles/PMC8514574?pdf=render
 39174061,https://doi.org/10.1136/bmjopen-2023-078108,Risk factors for prolonged length of hospital stay following elective hip replacement surgery: a retrospective longitudinal observational study.,"Wilson R, Margelyte R, Redaniel MT, Eyles E, Jones T, Penfold C, Blom A, Elliott A, Harper A, Keen T, Pitt M, Judge A.",,BMJ open,2024,2024-08-21,Y,Hip; Primary Health Care; Hospitalization; Adult Orthopaedics,,,"<h4>Objectives</h4>Our aim was to identify which patients are likely to stay in hospital longer following total hip replacement surgery.<h4>Design</h4>Longitudinal, observational study used routinely collected data.<h4>Setting</h4>Data were collected from an NHS Trust in South-West England between 2016 and 2019.<h4>Participants</h4>2352 hip replacement patients had complete data and were included in analysis.<h4>Primary and secondary outcome measures</h4>Three measures of length of stay were used: a count measure of number of days spent in hospital, a binary measure of ≤7 days/>7 days in hospital and a binary measure of remaining in hospital when medically fit for discharge.<h4>Results</h4>The mean length of stay was 5.4 days following surgery, with 18% in hospital for more than 7 days, and 11% staying in hospital when medically fit for discharge. Longer hospital stay was associated with older age (OR=1.06, 95% CI 1.05 to 1.08), being female (OR=1.42, 95% CI 1.12 to 1.81) and more comorbidities (OR=3.52, 95% CI 1.45 to 8.55) and shorter length of stay with not having had a recent hospital admission (OR=0.44, 95% CI 0.32 to 0.60). Results were similar for remaining in hospital when medically fit for discharge, with the addition of an association with highest socioeconomic deprivation (OR=2.08, 95% CI 1.37 to 3.16).<h4>Conclusions</h4>Older, female patients with more comorbidities and from more socioeconomically deprived areas are likely to remain in hospital for longer following surgery. This study produced regression models demonstrating consistent results across three measures of prolonged hospital stay following hip replacement surgery. These findings could be used to inform surgery planning and when supporting patient discharge following surgery.",,doi:https://doi.org/10.1136/bmjopen-2023-078108; html:https://europepmc.org/articles/PMC11340698; pdf:https://europepmc.org/articles/PMC11340698?pdf=render
 34173614,https://doi.org/10.1016/s2666-7568(20)30012-x,Evolution and effects of COVID-19 outbreaks in care homes: a population analysis in 189 care homes in one geographical region of the UK.,"Burton JK, Bayne G, Evans C, Garbe F, Gorman D, Honhold N, McCormick D, Othieno R, Stevenson JE, Swietlik S, Templeton KE, Tranter M, Willocks L, Guthrie B.",,The lancet. Healthy longevity,2020,2020-10-20,Y,,,,"<h4>Background</h4>COVID-19 has affected care home residents internationally, but detailed information on outbreaks is scarce. We aimed to describe the evolution of outbreaks of COVID-19 in all care homes in one large health region in Scotland.<h4>Methods</h4>We did a population analysis of testing, cases, and deaths in care homes in the National Health Service (NHS) Lothian health region of the UK. We obtained data for COVID-19 testing (PCR testing of nasopharyngeal swabs for severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) and deaths (COVID-19-related and non-COVID-19-related), and we analysed data by several variables including type of care home, number of beds, and locality. Outcome measures were timing of outbreaks, number of confirmed cases of COVID-19 in care home residents, care home characteristics associated with the presence of an outbreak, and deaths of residents in both care homes and hospitals. We calculated excess deaths (both COVID-19-related and non-COVID-19-related), which we defined as the sum of deaths over and above the historical average in the same period over the past 5 years.<h4>Findings</h4>Between March 10 and Aug 2, 2020, residents at 189 care homes (5843 beds) were tested for COVID-19 when symptomatic. A COVID-19 outbreak was confirmed at 69 (37%) care homes, of which 66 (96%) were care homes for older people. The size of care homes for older people was strongly associated with a COVID-19 outbreak (odds ratio per 20-bed increase 3·35, 95% CI 1·99-5·63). 907 confirmed cases of SARS-CoV-2 infection were recorded during the study period, and 432 COVID-19-related deaths. 229 (25%) COVID-19-related cases and 99 (24%) COVID-related deaths occurred in five (3%) of 189 care homes, and 441 (49%) cases and 207 (50%) deaths were in 13 (7%) care homes. 411 (95%) COVID-19-related deaths occurred in the 69 care homes with a confirmed COVID-19 outbreak, 19 (4%) deaths were in hospital, and two (<1%) were in one of the 120 care homes without a confirmed COVID-19 outbreak. At the 69 care homes with a confirmed COVID-19 outbreak, 74 excess non-COVID-19-related deaths were reported, whereas ten non-COVID-19-related excess deaths were observed in the 120 care homes without a confirmed COVID-19 outbreak. 32 fewer non-COVID-19-related deaths than expected were reported among care home residents in hospital.<h4>Interpretation</h4>The effect of COVID-19 on care homes has been substantial but concentrated in care homes with known outbreaks. A key implication from our findings is that, if community incidence of COVID-19 increases again, many care home residents will be susceptible. Shielding care home residents from potential sources of SARS-CoV-2 infection, and ensuring rapid action to minimise outbreak size if infection is introduced, will be important for any second wave.<h4>Funding</h4>None.",,doi:https://doi.org/10.1016/s2666-7568(20)30012-x; doi:https://doi.org/10.1016/S2666-7568(20)30012-X; html:https://europepmc.org/articles/PMC7574931; pdf:https://europepmc.org/articles/PMC7574931?pdf=render
-34645794,https://doi.org/10.1038/s41467-021-25914-8,A cross-sectional analysis of meteorological factors and SARS-CoV-2 transmission in 409 cities across 26 countries.,"Sera F, Armstrong B, Abbott S, Meakin S, O'Reilly K, von Borries R, Schneider R, Royé D, Hashizume M, Pascal M, Tobias A, Vicedo-Cabrera AM, MCC Collaborative Research Network, CMMID COVID-19 Working Group, Gasparrini A, Lowe R.",,Nature communications,2021,2021-10-13,Y,,,,"There is conflicting evidence on the influence of weather on COVID-19 transmission. Our aim is to estimate weather-dependent signatures in the early phase of the pandemic, while controlling for socio-economic factors and non-pharmaceutical interventions. We identify a modest non-linear association between mean temperature and the effective reproduction number (R<sub>e</sub>) in 409 cities in 26 countries, with a decrease of 0.087 (95% CI: 0.025; 0.148) for a 10 °C increase. Early interventions have a greater effect on R<sub>e</sub> with a decrease of 0.285 (95% CI 0.223; 0.347) for a 5th - 95th percentile increase in the government response index. The variation in the effective reproduction number explained by government interventions is 6 times greater than for mean temperature. We find little evidence of meteorological conditions having influenced the early stages of local epidemics and conclude that population behaviour and government interventions are more important drivers of transmission.",,doi:https://doi.org/10.1038/s41467-021-25914-8; doi:https://doi.org/10.1038/s41467-021-25914-8; html:https://europepmc.org/articles/PMC8514574; pdf:https://europepmc.org/articles/PMC8514574?pdf=render
 32384159,https://doi.org/10.1093/jtm/taaa068,Effectiveness of interventions targeting air travellers for delaying local outbreaks of SARS-CoV-2.,"Clifford S, Pearson CAB, Klepac P, Van Zandvoort K, Quilty BJ, CMMID COVID-19 working group, Eggo RM, Flasche S.",,Journal of travel medicine,2020,2020-08-01,Y,Coronavirus; Public Health Emergency Of International Concern; Covid-19; Travel Screening,,,"<h4>Background</h4>We evaluated if interventions aimed at air travellers can delay local severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) community transmission in a previously unaffected country.<h4>Methods</h4>We simulated infected air travellers arriving into countries with no sustained SARS-CoV-2 transmission or other introduction routes from affected regions. We assessed the effectiveness of syndromic screening at departure and/or arrival and traveller sensitisation to the COVID-2019-like symptoms with the aim to trigger rapid self-isolation and reporting on symptom onset to enable contact tracing. We assumed that syndromic screening would reduce the number of infected arrivals and that traveller sensitisation reduces the average number of secondary cases. We use stochastic simulations to account for uncertainty in both arrival and secondary infections rates, and present sensitivity analyses on arrival rates of infected travellers and the effectiveness of traveller sensitisation. We report the median expected delay achievable in each scenario and an inner 50% interval.<h4>Results</h4>Under baseline assumptions, introducing exit and entry screening in combination with traveller sensitisation can delay a local SARS-CoV-2 outbreak by 8 days (50% interval: 3-14 days) when the rate of importation is 1 infected traveller per week at time of introduction. The additional benefit of entry screening is small if exit screening is effective: the combination of only exit screening and traveller sensitisation can delay an outbreak by 7 days (50% interval: 2-13 days). In the absence of screening, with less effective sensitisation, or a higher rate of importation, these delays shrink rapidly to <4 days.<h4>Conclusion</h4>Syndromic screening and traveller sensitisation in combination may have marginally delayed SARS-CoV-2 outbreaks in unaffected countries.",,pdf:https://academic.oup.com/jtm/article-pdf/27/5/taaa068/33666000/taaa068.pdf; doi:https://doi.org/10.1093/jtm/taaa068; html:https://europepmc.org/articles/PMC7239177; pdf:https://europepmc.org/articles/PMC7239177?pdf=render
 35235826,https://doi.org/10.1016/j.ijid.2022.02.051,"Assessing the clinical severity of the Omicron variant in the Western Cape Province, South Africa, using the diagnostic PCR proxy marker of RdRp target delay to distinguish between Omicron and Delta infections - a survival analysis.","Hussey H, Davies MA, Heekes A, Williamson C, Valley-Omar Z, Hardie D, Korsman S, Doolabh D, Preiser W, Maponga T, Iranzadeh A, Wasserman S, Boloko L, Symons G, Raubenheimer P, Parker A, Schrueder N, Solomon W, Rousseau P, Wolter N, Jassat W, Cohen C, Lessells R, Wilkinson RJ, Boulle A, Hsiao NY.",,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2022,2022-02-27,Y,South Africa; Clinical Severity; Sars-cov-2; Omicron Variant; Rdrp Target Delay,,,"<h4>Background</h4>At present, it is unclear whether the extent of reduced risk of severe disease seen with SARS-Cov-2 Omicron variant infection is caused by a decrease in variant virulence or by higher levels of population immunity.<h4>Methods</h4>RdRp target delay (RTD) in the Seegene Allplex<sup>TM</sup> 2019-nCoV PCR assay is a proxy marker for the Delta variant. The absence of this proxy marker in the transition period was used to identify suspected Omicron infections. Cox regression was performed for the outcome of hospital admission in those who tested positive for SARS-CoV-2 on the Seegene Allplex<sup>TM</sup> assay from November 1 to December 14, 2021 in the Western Cape Province, South Africa, in the public sector. Adjustments were made for vaccination status and prior diagnosis of infection.<h4>Results</h4>A total of 150 cases with RTD and 1486 cases without RTD were included. Cases without RTD had a lower hazard of admission (adjusted hazard ratio [aHR], 0.56; 95% confidence interval [CI], 0.34-0.91). Complete vaccination was protective against admission, with an aHR of 0.45 (95% CI, 0.26-0.77).<h4>Conclusion</h4>Omicron has resulted in a lower risk of hospital admission compared with contemporaneous Delta infection, when using the proxy marker of RTD. Under-ascertainment of reinfections with an immune escape variant remains a challenge to accurately assessing variant virulence.",,pdf:http://spiral.imperial.ac.uk/bitstream/10044/1/95846/7/1-s2.0-S1201971222001291-main.pdf; doi:https://doi.org/10.1016/j.ijid.2022.02.051; html:https://europepmc.org/articles/PMC8882068; pdf:https://europepmc.org/articles/PMC8882068?pdf=render
 38296965,https://doi.org/10.1038/s41467-023-43644-x,"Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial.","RECOVERY Collaborative Group, Horby PW, Peto L, Staplin N, Campbell M, Pessoa-Amorim G, Mafham M, Emberson JR, Stewart R, Prudon B, Uriel A, Green CA, Dhasmana DJ, Malein F, Majumdar J, Collini P, Shurmer J, Yates B, Baillie JK, Buch MH, Day J, Faust SN, Jaki T, Jeffery K, Juszczak E, Knight M, Lim WS, Montgomery A, Mumford A, Rowan K, Thwaites G, Haynes R, Landray MJ.",,Nature communications,2024,2024-01-31,Y,,,,"Dimethyl fumarate (DMF) inhibits inflammasome-mediated inflammation and has been proposed as a treatment for patients hospitalised with COVID-19. This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple treatments in patients hospitalised for COVID-19 (NCT04381936, ISRCTN50189673). In this assessment of DMF performed at 27 UK hospitals, adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. Between 2 March 2021 and 18 November 2021, 713 patients were enroled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients received corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.86-1.47; p = 0.40). There was no significant effect of DMF on any secondary outcome.",,pdf:https://www.nature.com/articles/s41467-023-43644-x.pdf; doi:https://doi.org/10.1038/s41467-023-43644-x; html:https://europepmc.org/articles/PMC10831058; pdf:https://europepmc.org/articles/PMC10831058?pdf=render
 37730605,https://doi.org/10.1186/s12889-023-16523-9,Inequalities and mental health during the Coronavirus pandemic in the UK: a mixed-methods exploration.,"Lombardo C, Guo L, Solomon S, Crepaz-Keay D, McDaid S, Thorpe L, Martin S, John A, Morton A, Davidson G, Kousoulis AA, Van Bortel T.",,BMC public health,2023,2023-09-20,Y,Coronavirus; Mental health; Pandemic; United Kingdom; Inequalities; Social Determinants; Inequity; Adult Population; Covid-19,,,"<h4>Background</h4>The World Health Organisation declared the novel Coronavirus disease (COVID-19) a global pandemic on 11th March 2020. Since then, the world has been firmly in its grip. At the time of writing, there were more than 767,972,961 million confirmed cases and over 6,950,655 million deaths. While the main policy focus has been on controlling the virus and ensuring vaccine roll-out and uptake, the population mental health impacts of the pandemic are expected to be long-term, with certain population groups affected more than others.<h4>Methods</h4>The overall objectives of our 'Coronavirus: Mental Health and the Pandemic' study were to explore UK adults' experiences of the Coronavirus pandemic and to gain insights into the mental health impacts, population-level changes over time, current and future mental health needs, and how these can best be addressed. The wider mixed-methods study consisted of repeated cross-sectional surveys and embedded qualitative sub-studies including in-depth interviews and focus group discussions with the wider UK adult population. For this particular inequalities and mental health sub-study, we used mixed methods data from our cross-sectional surveys and we carried out three Focus Group Discussions with a maximum variation sample from across the UK adult population. The discussions covered the broader topic of 'Inequalities and mental health during the Coronavirus pandemic in the UK' and took place online between April and August 2020. Focus Groups transcripts were analysed using thematic analysis in NVIVO. Cross-sectional survey data were analysed using STATA for descriptive statistics.<h4>Results</h4>Three broad main themes emerged, each supporting a number of sub-themes: (1) Impacts of the pandemic; (2) Moving forward: needs and recommendations; (3) Coping mechanisms and resilience. Findings showed that participants described their experiences of the pandemic in relation to its impact on themselves and on different groups of people. Their experiences illustrated how the pandemic and subsequent measures had exacerbated existing inequalities and created new ones, and triggered various emotional responses. Participants also described their coping strategies and what worked and did not work for them, as well as support needs and recommendations for moving forward through, and out of, the pandemic; all of which are valuable learnings to be considered in policy making for improving mental health and for ensuring future preparedness.<h4>Conclusions</h4>The pandemic is taking a long-term toll on the nations' mental health which will continue to have impacts for years to come. It is therefore crucial to learn the vital lessons learned from this pandemic. Specific as well as whole-government policies need to respond to this, address inequalities and the different needs across the life-course and across society, and take a holistic approach to mental health improvement across the UK.",,pdf:https://bmcpublichealth.biomedcentral.com/counter/pdf/10.1186/s12889-023-16523-9; doi:https://doi.org/10.1186/s12889-023-16523-9; html:https://europepmc.org/articles/PMC10510114; pdf:https://europepmc.org/articles/PMC10510114?pdf=render
-35585575,https://doi.org/10.1186/s12889-022-13219-4,The impact of COVID-19 vaccination in prisons in England and Wales: a metapopulation model.,"McCarthy CV, O'Mara O, van Leeuwen E, CMMID COVID-19 Working Group, Jit M, Sandmann F.",,BMC public health,2022,2022-05-18,Y,Vaccination; mathematical model; Public Health; Prisons; Covid-19,,,"<h4>Background</h4>High incidence of cases and deaths due to coronavirus disease 2019 (COVID-19) have been reported in prisons worldwide. This study aimed to evaluate the impact of different COVID-19 vaccination strategies in epidemiologically semi-enclosed settings such as prisons, where staff interact regularly with those incarcerated and the wider community.<h4>Methods</h4>We used a metapopulation transmission-dynamic model of a local prison in England and Wales. Two-dose vaccination strategies included no vaccination, vaccination of all individuals who are incarcerated and/or staff, and an age-based approach. Outcomes were quantified in terms of COVID-19-related symptomatic cases, losses in quality-adjusted life-years (QALYs), and deaths.<h4>Results</h4>Compared to no vaccination, vaccinating all people living and working in prison reduced cases, QALY loss and deaths over a one-year period by 41%, 32% and 36% respectively. However, if vaccine introduction was delayed until the start of an outbreak, the impact was negligible. Vaccinating individuals who are incarcerated and staff over 50 years old averted one death for every 104 vaccination courses administered. All-staff-only strategies reduced cases by up to 5%. Increasing coverage from 30 to 90% among those who are incarcerated reduced cases by around 30 percentage points.<h4>Conclusions</h4>The impact of vaccination in prison settings was highly dependent on early and rapid vaccine delivery. If administered to both those living and working in prison prior to an outbreak occurring, vaccines could substantially reduce COVID-19-related morbidity and mortality in prison settings.",,pdf:https://bmcpublichealth.biomedcentral.com/track/pdf/10.1186/s12889-022-13219-4; doi:https://doi.org/10.1186/s12889-022-13219-4; html:https://europepmc.org/articles/PMC9115545; pdf:https://europepmc.org/articles/PMC9115545?pdf=render
 35611160,https://doi.org/10.1016/j.eclinm.2022.101462,Impact of first UK COVID-19 lockdown on hospital admissions: Interrupted time series study of 32 million people.,"Shah SA, Brophy S, Kennedy J, Fisher L, Walker A, Mackenna B, Curtis H, Inglesby P, Davy S, Bacon S, Goldacre B, Agrawal U, Moore E, Simpson CR, Macleod J, Cooksey R, Sheikh A, Katikireddi SV.",,EClinicalMedicine,2022,2022-05-20,Y,Pandemic; Healthcare Inequalities; Interrupted Time Series Analysis; Covid-19; Sars-cov-2; Healthcare Disruption,,,"<h4>Background</h4>Uncontrolled infection and lockdown measures introduced in response have resulted in an unprecedented challenge for health systems internationally. Whether such unprecedented impact was due to lockdown itself and recedes when such measures are lifted is unclear. We assessed the short- and medium-term impacts of the first lockdown measures on hospital care for tracer non-COVID-19 conditions in England, Scotland and Wales across diseases, sexes, and socioeconomic and ethnic groups.<h4>Methods</h4>We used OpenSAFELY (for England), EAVEII (Scotland), and SAIL Databank (Wales) to extract weekly hospital admission rates for cancer, cardiovascular and respiratory conditions (excluding COVID-19) from the pre-pandemic period until 25/10/2020 and conducted a controlled interrupted time series analysis. We undertook stratified analyses and assessed admission rates over seven months during which lockdown restrictions were gradually lifted.<h4>Findings</h4>Our combined dataset included 32 million people who contributed over 74 million person-years. Admission rates for all three conditions fell by 34.2% (Confidence Interval (CI): -43.0, -25.3) in England, 20.9% (CI: -27.8, -14.1) in Scotland, and 24.7% (CI: -36.7, -12.7) in Wales, with falls across every stratum considered. In all three nations, cancer-related admissions fell the most while respiratory-related admissions fell the least (e.g., rates fell by 40.5% (CI: -47.4, -33.6), 21.9% (CI: -35.4, -8.4), and 19.0% (CI: -30.6, -7.4) in England for cancer, cardiovascular-related, and respiratory-related admissions respectively). Unscheduled admissions rates fell more in the most than the least deprived quintile across all three nations. Some ethnic minority groups experienced greater falls in admissions (e.g., in England, unscheduled admissions fell by 9.5% (CI: -20.2, 1.2) for Whites, but 44.3% (CI: -71.0, -17.6), 34.6% (CI: -63.8, -5.3), and 25.6% (CI: -45.0, -6.3) for Mixed, Other and Black ethnic groups respectively). Despite easing of restrictions, the overall admission rates remained lower in England, Scotland, and Wales by 20.8%, 21.6%, and 22.0%, respectively when compared to the same period (August-September) during the pre-pandemic years. This corresponds to a reduction of 26.2, 23.8 and 30.2 admissions per 100,000 people in England, Scotland, and Wales respectively.<h4>Interpretation</h4>Hospital care for non-COVID diseases fell substantially across England, Scotland, and Wales during the first lockdown, with reductions persisting for at least six months. The most deprived and minority ethnic groups were impacted more severely.<h4>Funding</h4>This work was funded by the Medical Research Council as part of the Lifelong Health and Wellbeing study as part of National Core Studies (MC_PC_20030). SVK acknowledges funding from the Medical Research Council (MC_UU_00022/2), and the Scottish Government Chief Scientist Office (SPHSU17). EAVE II is funded by the Medical Research Council (MR/R008345/1) with the support of BREATHE - The Health Data Research Hub for Respiratory Health (MC_PC_19004), which is funded through the UK Research and Innovation Industrial Strategy Challenge Fund and delivered through Health Data Research UK. BG has received research funding from the NHS National Institute for Health Research (NIHR), the Wellcome Trust, Health Data Research UK, Asthma UK, the British Lung Foundation, and the Longitudinal Health and Wellbeing strand of the National Core Studies programme.",,pdf:http://www.thelancet.com/article/S2589537022001924/pdf; doi:https://doi.org/10.1016/j.eclinm.2022.101462; html:https://europepmc.org/articles/PMC9121886; pdf:https://europepmc.org/articles/PMC9121886?pdf=render
+35585575,https://doi.org/10.1186/s12889-022-13219-4,The impact of COVID-19 vaccination in prisons in England and Wales: a metapopulation model.,"McCarthy CV, O'Mara O, van Leeuwen E, CMMID COVID-19 Working Group, Jit M, Sandmann F.",,BMC public health,2022,2022-05-18,Y,Vaccination; mathematical model; Public Health; Prisons; Covid-19,,,"<h4>Background</h4>High incidence of cases and deaths due to coronavirus disease 2019 (COVID-19) have been reported in prisons worldwide. This study aimed to evaluate the impact of different COVID-19 vaccination strategies in epidemiologically semi-enclosed settings such as prisons, where staff interact regularly with those incarcerated and the wider community.<h4>Methods</h4>We used a metapopulation transmission-dynamic model of a local prison in England and Wales. Two-dose vaccination strategies included no vaccination, vaccination of all individuals who are incarcerated and/or staff, and an age-based approach. Outcomes were quantified in terms of COVID-19-related symptomatic cases, losses in quality-adjusted life-years (QALYs), and deaths.<h4>Results</h4>Compared to no vaccination, vaccinating all people living and working in prison reduced cases, QALY loss and deaths over a one-year period by 41%, 32% and 36% respectively. However, if vaccine introduction was delayed until the start of an outbreak, the impact was negligible. Vaccinating individuals who are incarcerated and staff over 50 years old averted one death for every 104 vaccination courses administered. All-staff-only strategies reduced cases by up to 5%. Increasing coverage from 30 to 90% among those who are incarcerated reduced cases by around 30 percentage points.<h4>Conclusions</h4>The impact of vaccination in prison settings was highly dependent on early and rapid vaccine delivery. If administered to both those living and working in prison prior to an outbreak occurring, vaccines could substantially reduce COVID-19-related morbidity and mortality in prison settings.",,pdf:https://bmcpublichealth.biomedcentral.com/track/pdf/10.1186/s12889-022-13219-4; doi:https://doi.org/10.1186/s12889-022-13219-4; html:https://europepmc.org/articles/PMC9115545; pdf:https://europepmc.org/articles/PMC9115545?pdf=render
 33879890,https://doi.org/10.1038/s41591-021-01329-2,Single-cell multi-omics analysis of the immune response in COVID-19.,"Stephenson E, Reynolds G, Botting RA, Calero-Nieto FJ, Morgan MD, Tuong ZK, Bach K, Sungnak W, Worlock KB, Yoshida M, Kumasaka N, Kania K, Engelbert J, Olabi B, Spegarova JS, Wilson NK, Mende N, Jardine L, Gardner LCS, Goh I, Horsfall D, McGrath J, Webb S, Mather MW, Lindeboom RGH, Dann E, Huang N, Polanski K, Prigmore E, Gothe F, Scott J, Payne RP, Baker KF, Hanrath AT, Schim van der Loeff ICD, Barr AS, Sanchez-Gonzalez A, Bergamaschi L, Mescia F, Barnes JL, Kilich E, de Wilton A, Saigal A, Saleh A, Janes SM, Smith CM, Gopee N, Wilson C, Coupland P, Coxhead JM, Kiselev VY, van Dongen S, Bacardit J, King HW, Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID-19 BioResource Collaboration, Rostron AJ, Simpson AJ, Hambleton S, Laurenti E, Lyons PA, Meyer KB, Nikolić MZ, Duncan CJA, Smith KGC, Teichmann SA, Clatworthy MR, Marioni JC, Göttgens B, Haniffa M.",,Nature medicine,2021,2021-04-20,Y,,,,"Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19. We identified expansion of nonclassical monocytes expressing complement transcripts (CD16<sup>+</sup>C1QA/B/C<sup>+</sup>) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34<sup>+</sup> hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8<sup>+</sup> T cells and an increased ratio of CD8<sup>+</sup> effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease. We observed a relative loss of IgA2 in symptomatic disease despite an overall expansion of plasmablasts and plasma cells. Our study highlights the coordinated immune response that contributes to COVID-19 pathogenesis and reveals discrete cellular components that can be targeted for therapy.",,pdf:https://www.nature.com/articles/s41591-021-01329-2.pdf; doi:https://doi.org/10.1038/s41591-021-01329-2; html:https://europepmc.org/articles/PMC8121667; pdf:https://europepmc.org/articles/PMC8121667?pdf=render
 38135323,https://doi.org/10.1136/bmjopen-2023-076221,Development and application of simulation modelling for orthopaedic elective resource planning in England.,"Harper A, Monks T, Wilson R, Redaniel MT, Eyles E, Jones T, Penfold C, Elliott A, Keen T, Pitt M, Blom A, Whitehouse MR, Judge A.",,BMJ open,2023,2023-12-22,Y,Information management; Orthopaedic & Trauma Surgery; Organisation Of Health Services; World Wide Web Technology,,,"<h4>Objectives</h4>This study aimed to develop a simulation model to support orthopaedic elective capacity planning.<h4>Methods</h4>An open-source, generalisable discrete-event simulation was developed, including a web-based application. The model used anonymised patient records between 2016 and 2019 of elective orthopaedic procedures from a National Health Service (NHS) Trust in England. In this paper, it is used to investigate scenarios including resourcing (beds and theatres) and productivity (lengths of stay, delayed discharges and theatre activity) to support planning for meeting new NHS targets aimed at reducing elective orthopaedic surgical backlogs in a proposed ring-fenced orthopaedic surgical facility. The simulation is interactive and intended for use by health service planners and clinicians.<h4>Results</h4>A higher number of beds (65-70) than the proposed number (40 beds) will be required if lengths of stay and delayed discharge rates remain unchanged. Reducing lengths of stay in line with national benchmarks reduces bed utilisation to an estimated 60%, allowing for additional theatre activity such as weekend working. Further, reducing the proportion of patients with a delayed discharge by 75% reduces bed utilisation to below 40%, even with weekend working. A range of other scenarios can also be investigated directly by NHS planners using the interactive web app.<h4>Conclusions</h4>The simulation model is intended to support capacity planning of orthopaedic elective services by identifying a balance of capacity across theatres and beds and predicting the impact of productivity measures on capacity requirements. It is applicable beyond the study site and can be adapted for other specialties.",,doi:https://doi.org/10.1136/bmjopen-2023-076221; html:https://europepmc.org/articles/PMC10748981; pdf:https://europepmc.org/articles/PMC10748981?pdf=render
 37119604,https://doi.org/10.1016/j.canep.2023.102367,"Whole-population trends in pathology-confirmed cancer incidence in Northern Ireland, Scotland and Wales during the SARS-CoV-2 pandemic: A retrospective observational study.","Greene GJ, Thomson CS, Donnelly D, Chung D, Bhatti L, Gavin AT, Lawler M, Huws DW, Rolles MJ, Bennée F, Morrison DS.",,Cancer epidemiology,2023,2023-04-21,Y,Pandemic; Population-based Incidence; Covid-19; Sars-cov-2; Pathology-Confirmed Cancer,,,"<h4>Introduction</h4>The COVID-19 epidemic interrupted normal cancer diagnosis procedures. Population-based cancer registries report incidence at least 18 months after it happens. Our goal was to make more timely estimates by using pathologically confirmed cancers (PDC) as a proxy for incidence. We compared the 2020 and 2021 PDC with the 2019 pre-pandemic baseline in Scotland, Wales, and Northern Ireland (NI).<h4>Methods</h4>Numbers of female breast (ICD-10 C50), lung (C33-34), colorectal (C18-20), gynaecological (C51-58), prostate (C61), head and neck (C00-C14, C30-32), upper gastro-intestinal (C15-16), urological (C64-68), malignant melanoma (C43), and non-melanoma skin (NMSC) (C44) cancers were counted. Multiple pairwise comparisons generated incidence rate ratios (IRR).<h4>Results</h4>Data were accessible within 5 months of the pathological diagnosis date. Between 2019 and 2020, the number of pathologically confirmed malignancies (excluding NMSC) decreased by 7315 (14.1 %). Scotland experienced early monthly declines of up to 64 % (colorectal cancers, April 2020 versus April 2019). Wales experienced the greatest overall change in 2020, but Northern Ireland experienced the quickest recovery. The pandemic's effects varied by cancer type, with no significant change in lung cancer diagnoses in Wales in 2020 (IRR 0.97 (95 % CI 0.90-1.05)), followed by an increase in 2021 (IRR 1.11 (1.03-1.20).<h4>Conclusion</h4>PDC are useful in reporting cancer incidence quicker than cancer registrations. Temporal and geographical differences between participating countries mirrored differences in responses to the COVID-19 pandemic, indicating face validity and the potential for quick cancer diagnosis assessment. To verify their sensitivity and specificity against the gold standard of cancer registrations, however, additional research is required.",,doi:https://doi.org/10.1016/j.canep.2023.102367; html:https://europepmc.org/articles/PMC10121133; pdf:https://europepmc.org/articles/PMC10121133?pdf=render
 36374585,https://doi.org/10.1177/01410768221131897,Using national electronic health records for pandemic preparedness: validation of a parsimonious model for predicting excess deaths among those with COVID-19-a data-driven retrospective cohort study.,"Mizani MA, Dashtban A, Pasea L, Lai AG, Thygesen J, Tomlinson C, Handy A, Mamza JB, Morris T, Khalid S, Zaccardi F, Macleod MJ, Torabi F, Canoy D, Akbari A, Berry C, Bolton T, Nolan J, Khunti K, Denaxas S, Hemingway H, Sudlow C, Banerjee A, CVD-COVID-UK Consortium.",,Journal of the Royal Society of Medicine,2023,2022-11-14,N,Infectious diseases; Clinical; epidemiology; Public Health; Health Informatics,,,"<h4>Objectives</h4>To use national, pre- and post-pandemic electronic health records (EHR) to develop and validate a scenario-based model incorporating baseline mortality risk, infection rate (IR) and relative risk (RR) of death for prediction of excess deaths.<h4>Design</h4>An EHR-based, retrospective cohort study.<h4>Setting</h4>Linked EHR in Clinical Practice Research Datalink (CPRD); and linked EHR and COVID-19 data in England provided in NHS Digital Trusted Research Environment (TRE).<h4>Participants</h4>In the development (CPRD) and validation (TRE) cohorts, we included 3.8 million and 35.1 million individuals aged ≥30 years, respectively.<h4>Main outcome measures</h4>One-year all-cause excess deaths related to COVID-19 from March 2020 to March 2021.<h4>Results</h4>From 1 March 2020 to 1 March 2021, there were 127,020 observed excess deaths. Observed RR was 4.34% (95% CI, 4.31-4.38) and IR was 6.27% (95% CI, 6.26-6.28). In the validation cohort, predicted one-year excess deaths were 100,338 compared with the observed 127,020 deaths with a ratio of predicted to observed excess deaths of 0.79.<h4>Conclusions</h4>We show that a simple, parsimonious model incorporating baseline mortality risk, one-year IR and RR of the pandemic can be used for scenario-based prediction of excess deaths in the early stages of a pandemic. Our analyses show that EHR could inform pandemic planning and surveillance, despite limited use in emergency preparedness to date. Although infection dynamics are important in the prediction of mortality, future models should take greater account of underlying conditions.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/01410768221131897; doi:https://doi.org/10.1177/01410768221131897; html:https://europepmc.org/articles/PMC9909113; pdf:https://europepmc.org/articles/PMC9909113?pdf=render; doi:https://doi.org/10.1177/01410768221131897
 35896970,https://doi.org/10.1186/s12879-022-07628-4,SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2.,"Eales O, Page AJ, de Oliveira Martins L, Wang H, Bodinier B, Haw D, Jonnerby J, Atchison C, COVID-19 Genomics UK (COG-UK) Consortium, Ashby D, Barclay W, Taylor G, Cooke G, Ward H, Darzi A, Riley S, Chadeau-Hyam M, Donnelly CA, Elliott P.",,BMC infectious diseases,2022,2022-07-27,Y,Mutation; Genetic diversity; Transmission Advantage; Covid-19; Sars-cov-2; Delta Variant,,,"<h4>Background</h4>Since the emergence of SARS-CoV-2, evolutionary pressure has driven large increases in the transmissibility of the virus. However, with increasing levels of immunity through vaccination and natural infection the evolutionary pressure will switch towards immune escape. Genomic surveillance in regions of high immunity is crucial in detecting emerging variants that can more successfully navigate the immune landscape.<h4>Methods</h4>We present phylogenetic relationships and lineage dynamics within England (a country with high levels of immunity), as inferred from a random community sample of individuals who provided a self-administered throat and nose swab for rt-PCR testing as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. During round 14 (9 September-27 September 2021) and 15 (19 October-5 November 2021) lineages were determined for 1322 positive individuals, with 27.1% of those which reported their symptom status reporting no symptoms in the previous month.<h4>Results</h4>We identified 44 unique lineages, all of which were Delta or Delta sub-lineages, and found a reduction in their mutation rate over the study period. The proportion of the Delta sub-lineage AY.4.2 was increasing, with a reproduction number 15% (95% CI 8-23%) greater than the most prevalent lineage, AY.4. Further, AY.4.2 was less associated with the most predictive COVID-19 symptoms (p = 0.029) and had a reduced mutation rate (p = 0.050). Both AY.4.2 and AY.4 were found to be geographically clustered in September but this was no longer the case by late October/early November, with only the lineage AY.6 exhibiting clustering towards the South of England.<h4>Conclusions</h4>As SARS-CoV-2 moves towards endemicity and new variants emerge, genomic data obtained from random community samples can augment routine surveillance data without the potential biases introduced due to higher sampling rates of symptomatic individuals.",,pdf:https://bmcinfectdis.biomedcentral.com/counter/pdf/10.1186/s12879-022-07628-4; doi:https://doi.org/10.1186/s12879-022-07628-4; html:https://europepmc.org/articles/PMC9326417; pdf:https://europepmc.org/articles/PMC9326417?pdf=render
-39015764,https://doi.org/10.1093/braincomms/fcae220,"Head motion in the UK Biobank imaging subsample: longitudinal stability, associations with psychological and physical health, and risk of incomplete data.","Ward J, Cox SR, Quinn T, Lyall LM, Strawbridge RJ, Russell E, Pell JP, Stewart W, Cullen B, Whalley H, Lyall DM.",,Brain communications,2024,2024-07-02,Y,Motion; Imaging; Bias; epidemiology; Uk Biobank,,,"Participant motion in brain magnetic resonance imaging is associated with processing problems including potentially non-useable/incomplete data. This has implications for representativeness in research. Few large studies have investigated predictors of increased motion in the first instance. We exploratively tested for association between multiple psychological and physical health traits with concurrent motion during T<sub>1</sub> structural, diffusion, average resting-state and task functional magnetic resonance imaging in <i>N</i> = 52 951 UK Biobank imaging subsample participants. These traits included history of cardiometabolic, inflammatory, neurological and psychiatric conditions, as well as concurrent cognitive test scores and anthropometric traits. We tested for stability in motion in participants with longitudinal imaging data (<i>n</i> = 5305, average 2.64 years later). All functional and T<sub>1</sub> structural motion variables were significantly intercorrelated (Pearson <i>r</i> range 0.3-0.8, all <i>P</i> < 0.001). Diffusion motion variables showed weaker correlations around <i>r</i> = 0.1. Most physical and psychological phenotypes showed significant association with at least one measure of increased motion including specifically in participants with complete useable data (highest β = 0.66 for diabetes versus resting-state functional magnetic resonance imaging motion). Poorer values in most health traits predicted lower odds of complete imaging data, with the largest association for history of traumatic brain injury (odds ratio = 0.720, 95% confidence interval = 0.562 to 0.923, <i>P</i> = 0.009). Worse psychological and physical health are consistent predictors of increased average functional and structural motion during brain imaging and associated with lower odds of complete data. Average motion levels were largely consistent across modalities and longitudinally in participants with repeat data. Together, these findings have implications for representativeness and bias in imaging studies of generally healthy population samples.",,doi:https://doi.org/10.1093/braincomms/fcae220; html:https://europepmc.org/articles/PMC11249925; pdf:https://europepmc.org/articles/PMC11249925?pdf=render
 35698725,https://doi.org/10.1016/s2665-9913(22)00098-4,Risk of severe COVID-19 outcomes associated with immune-mediated inflammatory diseases and immune-modifying therapies: a nationwide cohort study in the OpenSAFELY platform.,"MacKenna B, Kennedy NA, Mehrkar A, Rowan A, Galloway J, Matthewman J, Mansfield KE, Bechman K, Yates M, Brown J, Schultze A, Norton S, Walker AJ, Morton CE, Harrison D, Bhaskaran K, Rentsch CT, Williamson E, Croker R, Bacon S, Hickman G, Ward T, Davy S, Green A, Fisher L, Hulme W, Bates C, Curtis HJ, Tazare J, Eggo RM, Evans D, Inglesby P, Cockburn J, McDonald HI, Tomlinson LA, Mathur R, Wong AYS, Forbes H, Parry J, Hester F, Harper S, Douglas IJ, Smeeth L, Lees CW, Evans SJW, Goldacre B, Smith CH, Langan SM.",,The Lancet. Rheumatology,2022,2022-06-09,Y,,,,"<h4>Background</h4>The risk of severe COVID-19 outcomes in people with immune-mediated inflammatory diseases and on immune-modifying drugs might not be fully mediated by comorbidities and might vary by factors such as ethnicity. We aimed to assess the risk of severe COVID-19 in adults with immune-mediated inflammatory diseases and in those on immune-modifying therapies.<h4>Methods</h4>We did a cohort study, using OpenSAFELY (an analytics platform for electronic health records) and TPP (a software provider for general practitioners), analysing routinely collected primary care data linked to hospital admission, death, and previously unavailable hospital prescription data. We included people aged 18 years or older on March 1, 2020, who were registered with TPP practices with at least 12 months of primary care records before March, 2020. We used Cox regression (adjusting for confounders and mediators) to estimate hazard ratios (HRs) comparing the risk of COVID-19-related death, critical care admission or death, and hospital admission (from March 1 to Sept 30, 2020) in people with immune-mediated inflammatory diseases compared with the general population, and in people with immune-mediated inflammatory diseases on targeted immune-modifying drugs (eg, biologics) compared with those on standard systemic treatment (eg, methotrexate).<h4>Findings</h4>We identified 17 672 065 adults; 1 163 438 adults (640 164 [55·0%] women and 523 274 [45·0%] men, and 827 457 [71·1%] of White ethnicity) had immune-mediated inflammatory diseases, and 16 508 627 people (8 215 020 [49·8%] women and 8 293 607 [50·2%] men, and 10 614 096 [64·3%] of White ethnicity) were included as the general population. Of 1 163 438 adults with immune-mediated inflammatory diseases, 19 119 (1·6%) received targeted immune-modifying therapy and 181 694 (15·6%) received standard systemic therapy. Compared with the general population, adults with immune-mediated inflammatory diseases had an increased risk of COVID-19-related death after adjusting for confounders (age, sex, deprivation, and smoking status; HR 1·23, 95% CI 1·20-1·27) and further adjusting for mediators (body-mass index [BMI], cardiovascular disease, diabetes, and current glucocorticoid use; 1·15, 1·11-1·18). Adults with immune-mediated inflammatory diseases also had an increased risk of COVID-19-related critical care admission or death (confounder-adjusted HR 1·24, 95% CI 1·21-1·28; mediator-adjusted 1·16, 1·12-1·19) and hospital admission (confounder-adjusted 1·32, 1·29-1·35; mediator-adjusted 1·20, 1·17-1·23). In post-hoc analyses, the risk of severe COVID-19 outcomes in people with immune-mediated inflammatory diseases was higher in non-White ethnic groups than in White ethnic groups (as it was in the general population). We saw no evidence of increased COVID-19-related death in adults on targeted, compared with those on standard systemic, therapy after adjusting for confounders (age, sex, deprivation, BMI, immune-mediated inflammatory diseases [bowel, joint, and skin], cardiovascular disease, cancer [excluding non-melanoma skin cancer], stroke, and diabetes (HR 1·03, 95% CI 0·80-1·33), and after additionally adjusting for current glucocorticoid use (1·01, 0·78-1·30). There was no evidence of increased COVID-19-related death in adults prescribed tumour necrosis factor inhibitors, interleukin (IL)-12/IL‑23 inhibitors, IL-17 inhibitors, IL-6 inhibitors, or Janus kinase inhibitors compared with those on standard systemic therapy. Rituximab was associated with increased COVID-19-related death (HR 1·68, 95% CI 1·11-2·56), with some attenuation after excluding people with haematological malignancies or organ transplants (1·<b>54, 0</b>·<b>95</b>-<b>2</b>·<b>49</b>).<h4>Interpretation</h4>COVID-19 deaths and hospital admissions were higher in people with immune-mediated inflammatory diseases. We saw no increased risk of adverse COVID-19 outcomes in those on most targeted immune-modifying drugs for immune-mediated inflammatory diseases compared with those on standard systemic therapy.<h4>Funding</h4>UK Medical Research Council, NIHR Biomedical Research Centre at King's College London and Guy's and St Thomas' NHS Foundation Trust, and Wellcome Trust.",,pdf:http://www.thelancet.com/article/S2665991322000984/pdf; doi:https://doi.org/10.1016/S2665-9913(22)00098-4; html:https://europepmc.org/articles/PMC9179144; pdf:https://europepmc.org/articles/PMC9179144?pdf=render
+39015764,https://doi.org/10.1093/braincomms/fcae220,"Head motion in the UK Biobank imaging subsample: longitudinal stability, associations with psychological and physical health, and risk of incomplete data.","Ward J, Cox SR, Quinn T, Lyall LM, Strawbridge RJ, Russell E, Pell JP, Stewart W, Cullen B, Whalley H, Lyall DM.",,Brain communications,2024,2024-07-02,Y,Motion; Imaging; Bias; epidemiology; Uk Biobank,,,"Participant motion in brain magnetic resonance imaging is associated with processing problems including potentially non-useable/incomplete data. This has implications for representativeness in research. Few large studies have investigated predictors of increased motion in the first instance. We exploratively tested for association between multiple psychological and physical health traits with concurrent motion during T<sub>1</sub> structural, diffusion, average resting-state and task functional magnetic resonance imaging in <i>N</i> = 52 951 UK Biobank imaging subsample participants. These traits included history of cardiometabolic, inflammatory, neurological and psychiatric conditions, as well as concurrent cognitive test scores and anthropometric traits. We tested for stability in motion in participants with longitudinal imaging data (<i>n</i> = 5305, average 2.64 years later). All functional and T<sub>1</sub> structural motion variables were significantly intercorrelated (Pearson <i>r</i> range 0.3-0.8, all <i>P</i> < 0.001). Diffusion motion variables showed weaker correlations around <i>r</i> = 0.1. Most physical and psychological phenotypes showed significant association with at least one measure of increased motion including specifically in participants with complete useable data (highest β = 0.66 for diabetes versus resting-state functional magnetic resonance imaging motion). Poorer values in most health traits predicted lower odds of complete imaging data, with the largest association for history of traumatic brain injury (odds ratio = 0.720, 95% confidence interval = 0.562 to 0.923, <i>P</i> = 0.009). Worse psychological and physical health are consistent predictors of increased average functional and structural motion during brain imaging and associated with lower odds of complete data. Average motion levels were largely consistent across modalities and longitudinally in participants with repeat data. Together, these findings have implications for representativeness and bias in imaging studies of generally healthy population samples.",,doi:https://doi.org/10.1093/braincomms/fcae220; html:https://europepmc.org/articles/PMC11249925; pdf:https://europepmc.org/articles/PMC11249925?pdf=render
 34784292,https://doi.org/10.2196/32587,Investigating the Use of Digital Health Technology to Monitor COVID-19 and Its Effects: Protocol for an Observational Study (Covid Collab Study).,"Stewart C, Ranjan Y, Conde P, Rashid Z, Sankesara H, Bai X, Dobson RJB, Folarin AA.",,JMIR research protocols,2021,2021-12-08,Y,Monitoring; Infectious disease; Recovery; Mobile phone; Feasibility; Surveillance; Data; Mental health; Observational; Smartphone; Wearable; Mobile Health; Wearable Devices; Digital Health; Crowdsourced; Covid-19,,,"<h4>Background</h4>The ubiquity of mobile phones and increasing use of wearable fitness trackers offer a wide-ranging window into people's health and well-being. There are clear advantages in using remote monitoring technologies to gain an insight into health, particularly under the shadow of the COVID-19 pandemic.<h4>Objective</h4>Covid Collab is a crowdsourced study that was set up to investigate the feasibility of identifying, monitoring, and understanding the stratification of SARS-CoV-2 infection and recovery through remote monitoring technologies. Additionally, we will assess the impacts of the COVID-19 pandemic and associated social measures on people's behavior, physical health, and mental well-being.<h4>Methods</h4>Participants will remotely enroll in the study through the Mass Science app to donate historic and prospective mobile phone data, fitness tracking wearable data, and regular COVID-19-related and mental health-related survey data. The data collection period will cover a continuous period (ie, both before and after any reported infections), so that comparisons to a participant's own baseline can be made. We plan to carry out analyses in several areas, which will cover symptomatology; risk factors; the machine learning-based classification of illness; and trajectories of recovery, mental well-being, and activity.<h4>Results</h4>As of June 2021, there are over 17,000 participants-largely from the United Kingdom-and enrollment is ongoing.<h4>Conclusions</h4>This paper introduces a crowdsourced study that will include remotely enrolled participants to record mobile health data throughout the COVID-19 pandemic. The data collected may help researchers investigate a variety of areas, including COVID-19 progression; mental well-being during the pandemic; and the adherence of remote, digitally enrolled participants.<h4>International registered report identifier (irrid)</h4>DERR1-10.2196/32587.",,doi:https://doi.org/10.2196/32587; doi:https://doi.org/10.2196/32587; html:https://europepmc.org/articles/PMC8658240
 35189575,https://doi.org/10.1016/j.ebiom.2022.103878,The impact of hypoxia on B cells in COVID-19.,"Kotagiri P, Mescia F, Hanson AL, Turner L, Bergamaschi L, Peñalver A, Richoz N, Moore SD, Ortmann BM, Dunmore BJ, Morgan MD, Tuong ZK, Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID BioResource Collaboration, Göttgens B, Toshner M, Hess C, Maxwell PH, Clatworthy MR, Nathan JA, Bradley JR, Lyons PA, Burrows N, Smith KGC.",,EBioMedicine,2022,2022-02-19,Y,Hypoxia; B cells; Lymphopenia; Covid-19,,,"<h4>Background</h4>Prominent early features of COVID-19 include severe, often clinically silent, hypoxia and a pronounced reduction in B cells, the latter important in defence against SARS-CoV-2. This presentation resembles the phenotype of mice with VHL-deficient B cells, in which Hypoxia-Inducible Factors are constitutively active, suggesting hypoxia might drive B cell abnormalities in COVID-19.<h4>Methods</h4>Detailed B cell phenotyping was undertaken by flow-cytometry on longitudinal samples from patients with COVID-19 across a range of severities (NIHR Cambridge BioResource). The impact of hypoxia on the transcriptome was assessed by single-cell and whole blood RNA sequencing analysis. The direct effect of hypoxia on B cells was determined through immunisation studies in genetically modified and hypoxia-exposed mice.<h4>Findings</h4>We demonstrate the breadth of early and persistent defects in B cell subsets in moderate/severe COVID-19, including reduced marginal zone-like, memory and transitional B cells, changes also observed in B cell VHL-deficient mice. These findings were associated with hypoxia-related transcriptional changes in COVID-19 patient B cells, and similar B cell abnormalities were seen in mice kept in hypoxic conditions.<h4>Interpretation</h4>Hypoxia may contribute to the pronounced and persistent B cell pathology observed in acute COVID-19 pneumonia. Assessment of the impact of early oxygen therapy on these immune defects should be considered, as their correction could contribute to improved outcomes.<h4>Funding</h4>Evelyn Trust, Addenbrooke's Charitable Trust, UKRI/NIHR, Wellcome Trust.",,pdf:http://www.thelancet.com/article/S2352396422000627/pdf; doi:https://doi.org/10.1016/j.ebiom.2022.103878; html:https://europepmc.org/articles/PMC8856886; pdf:https://europepmc.org/articles/PMC8856886?pdf=render
 36498739,https://doi.org/10.3390/jcm11237163,Biopsychosocial Response to the COVID-19 Lockdown in People with Major Depressive Disorder and Multiple Sclerosis.,"Siddi S, Giné-Vázquez I, Bailon R, Matcham F, Lamers F, Kontaxis S, Laporta E, Garcia E, Arranz B, Dalla Costa G, Guerrero AI, Zabalza A, Buron MD, Comi G, Leocani L, Annas P, Hotopf M, Penninx BWJH, Magyari M, Sørensen PS, Montalban X, Lavelle G, Ivan A, Oetzmann C, White KM, Difrancesco S, Locatelli P, Mohr DC, Aguiló J, Narayan V, Folarin A, Dobson RJB, Dineley J, Leightley D, Cummins N, Vairavan S, Ranjan Y, Rashid Z, Rintala A, Girolamo G, Preti A, Simblett S, Wykes T, Pab Members, Myin-Germeys I, Haro JM, On Behalf Of The Radar-Cns Consortium.",,Journal of clinical medicine,2022,2022-12-01,Y,Stress; Heart rate; Multiple sclerosis; Physical Activity; Social Activity; Major Depressive Disorder; Depression Severity; Decentralized; Covid-19; Sars-cov-2,,,"<h4>Background</h4>Changes in lifestyle, finances and work status during COVID-19 lockdowns may have led to biopsychosocial changes in people with pre-existing vulnerabilities such as Major Depressive Disorders (MDDs) and Multiple Sclerosis (MS).<h4>Methods</h4>Data were collected as a part of the RADAR-CNS (Remote Assessment of Disease and Relapse-Central Nervous System) program. We analyzed the following data from long-term participants in a decentralized multinational study: symptoms of depression, heart rate (HR) during the day and night; social activity; sedentary state, steps and physical activity of varying intensity. Linear mixed-effects regression analyses with repeated measures were fitted to assess the changes among three time periods (pre, during and post-lockdown) across the groups, adjusting for depression severity before the pandemic and gender.<h4>Results</h4>Participants with MDDs (N = 255) and MS (N = 214) were included in the analyses. Overall, depressive symptoms remained stable across the three periods in both groups. A lower mean HR and HR variation were observed between pre and during lockdown during the day for MDDs and during the night for MS. HR variation during rest periods also decreased between pre- and post-lockdown in both clinical conditions. We observed a reduction in physical activity for MDDs and MS upon the introduction of lockdowns. The group with MDDs exhibited a net increase in social interaction via social network apps over the three periods.<h4>Conclusions</h4>Behavioral responses to the lockdown measured by social activity, physical activity and HR may reflect changes in stress in people with MDDs and MS. Remote technology monitoring might promptly activate an early warning of physical and social alterations in these stressful situations. Future studies must explore how stress does or does not impact depression severity.",,pdf:https://www.mdpi.com/2077-0383/11/23/7163/pdf?version=1670311452; doi:https://doi.org/10.3390/jcm11237163; html:https://europepmc.org/articles/PMC9738639; pdf:https://europepmc.org/articles/PMC9738639?pdf=render
@@ -433,8 +433,8 @@ PMC9023380,https://doi.org/,Assessing the spread risk of COVID-19 associated wit
 34935001,https://doi.org/10.1016/s2666-7568(21)00282-8,Prevalence and duration of detectable SARS-CoV-2 nucleocapsid antibodies in staff and residents of long-term care facilities over the first year of the pandemic (VIVALDI study): prospective cohort study in England.,"Krutikov M, Palmer T, Tut G, Fuller C, Azmi B, Giddings R, Shrotri M, Kaur N, Sylla P, Lancaster T, Irwin-Singer A, Hayward A, Moss P, Copas A, Shallcross L.",,The lancet. Healthy longevity,2022,2021-12-16,Y,,,,"<h4>Background</h4>Long-term care facilities (LTCFs) have reported high SARS-CoV-2 infection rates and related mortality, but the proportion of infected people among those who have survived, and duration of the antibody response to natural infection, is unknown. We determined the prevalence and stability of nucleocapsid antibodies (the standard assay for detection of previous infection) in staff and residents in LTCFs in England.<h4>Methods</h4>This was a prospective cohort study of residents 65 years or older and of staff 65 years or younger in 201 LTCFs in England between March 1, 2020, and May 7, 2021. Participants were linked to a unique pseudo-identifier based on their UK National Health Service identification number. Serial blood samples were tested for IgG antibodies against SARS-CoV-2 nucleocapsid protein using the Abbott ARCHITECT i-system (Abbott, Maidenhead, UK) immunoassay. Primary endpoints were prevalence and cumulative incidence of antibody positivity, which were weighted to the LTCF population. Incidence rate of loss of antibodies (seroreversion) was estimated from Kaplan-Meier curves.<h4>Findings</h4>9488 samples were included, 8636 (91·0%) of which could be individually linked to 1434 residents and 3288 staff members. The cumulative incidence of nucleocapsid seropositivity was 34·6% (29·6-40·0) in residents and 26·1% (23·0-29·5) in staff over 11 months. 239 (38·6%) residents and 503 women (81·3%) were included in the antibody-waning analysis, and median follow-up was 149 days (IQR 107-169). The incidence rate of seroreversion was 2·1 per 1000 person-days at risk, and median time to reversion was 242·5 days.<h4>Interpretation</h4>At least a quarter of staff and a third of surviving residents were infected with SAR-CoV-2 during the first two waves of the pandemic in England. Nucleocapsid-specific antibodies often become undetectable within the first year following infection, which is likely to lead to marked underestimation of the true proportion of people with previous infection. Given that natural infection might act to boost vaccine responses, better assays to identify natural infection should be developed.<h4>Funding</h4>UK Government Department of Health and Social Care.",,pdf:http://www.thelancet.com/article/S2666756821002828/pdf; doi:https://doi.org/10.1016/S2666-7568(21)00282-8; html:https://europepmc.org/articles/PMC8676418
 34308406,https://doi.org/10.1016/j.lanepe.2021.100180,Ethnic differences in SARS-CoV-2 vaccine hesitancy in United Kingdom healthcare workers: Results from the UK-REACH prospective nationwide cohort study.,"Woolf K, McManus IC, Martin CA, Nellums LB, Guyatt AL, Melbourne C, Bryant L, Gogoi M, Wobi F, Al-Oraibi A, Hassan O, Gupta A, John C, Tobin MD, Carr S, Simpson S, Gregary B, Aujayeb A, Zingwe S, Reza R, Gray LJ, Khunti K, Pareek M, UK-REACH Study Collaborative Group.",,The Lancet regional health. Europe,2021,2021-07-19,Y,,,,"<h4>Background</h4>In most countries, healthcare workers (HCWs) represent a priority group for vaccination against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) due to their elevated risk of COVID-19 and potential contribution to nosocomial SARS-CoV-2 transmission. Concerns have been raised that HCWs from ethnic minority groups are more likely to be vaccine hesitant (defined by the World Health Organisation as refusing or delaying a vaccination) than those of White ethnicity, but there are limited data on SARS-CoV-2 vaccine hesitancy and its predictors in UK HCWs.<h4>Methods</h4>Nationwide prospective cohort study and qualitative study in a multi-ethnic cohort of clinical and non-clinical UK HCWs. We analysed ethnic differences in SARS-CoV-2 vaccine hesitancy adjusting for demographics, vaccine trust, and perceived risk of COVID-19. We explored reasons for hesitancy in qualitative data using a framework analysis.<h4>Findings</h4>11,584 HCWs were included in the cohort analysis. 23% (2704) reported vaccine hesitancy. Compared to White British HCWs (21.3% hesitant), HCWs from Black Caribbean (54.2%), Mixed White and Black Caribbean (38.1%), Black African (34.4%), Chinese (33.1%), Pakistani (30.4%), and White Other (28.7%) ethnic groups were significantly more likely to be hesitant. In adjusted analysis, Black Caribbean (aOR 3.37, 95% CI 2.11 - 5.37), Black African (aOR 2.05, 95% CI 1.49 - 2.82), White Other ethnic groups (aOR 1.48, 95% CI 1.19 - 1.84) were significantly more likely to be hesitant. Other independent predictors of hesitancy were younger age, female sex, higher score on a COVID-19 conspiracy beliefs scale, lower trust in employer, lack of influenza vaccine uptake in the previous season, previous COVID-19, and pregnancy. Qualitative data from 99 participants identified the following contributors to hesitancy: lack of trust in government and employers, safety concerns due to the speed of vaccine development, lack of ethnic diversity in vaccine studies, and confusing and conflicting information. Participants felt uptake in ethnic minority communities might be improved through inclusive communication, involving HCWs in the vaccine rollout, and promoting vaccination through trusted networks.<h4>Interpretation</h4>Despite increased risk of COVID-19, HCWs from some ethnic minority groups are more likely to be vaccine hesitant than their White British colleagues. Strategies to build trust and dispel myths surrounding the COVID-19 vaccine in these communities are urgently required. Emphasis should be placed on the safety and benefit of SARS-CoV-2 vaccination in pregnancy and in those with previous COVID-19. Public health communications should be inclusive, non-stigmatising and utilise trusted networks.<h4>Funding</h4>UKRI-MRC and NIHR.",,doi:https://doi.org/10.1016/j.lanepe.2021.100180; doi:https://doi.org/10.1016/j.lanepe.2021.100180; html:https://europepmc.org/articles/PMC8287519; pdf:https://europepmc.org/articles/PMC8287519?pdf=render
 32951042,https://doi.org/10.1093/ageing/afaa207,"The impact of COVID-19 on adjusted mortality risk in care homes for older adults in Wales, UK: a retrospective population-based cohort study for mortality in 2016-2020.","Hollinghurst J, Lyons J, Fry R, Akbari A, Gravenor M, Watkins A, Verity F, Lyons RA.",,Age and ageing,2021,2021-01-01,Y,Mortality; Frailty; Older People; Care Homes; Covid-19,,,"<h4>Background</h4>mortality in care homes has had a prominent focus during the COVID-19 outbreak. Care homes are particularly vulnerable to the spread of infectious diseases, which may lead to increased mortality risk. Multiple and interconnected challenges face the care home sector in the prevention and management of outbreaks of COVID-19, including adequate supply of personal protective equipment, staff shortages and insufficient or lack of timely COVID-19 testing.<h4>Aim</h4>to analyse the mortality of older care home residents in Wales during COVID-19 lockdown and compare this across the population of Wales and the previous 4 years.<h4>Study design and setting</h4>we used anonymised electronic health records and administrative data from the secure anonymised information linkage databank to create a cross-sectional cohort study. We anonymously linked data for Welsh residents to mortality data up to the 14th June 2020.<h4>Methods</h4>we calculated survival curves and adjusted Cox proportional hazards models to estimate hazard ratios (HRs) for the risk of mortality. We adjusted HRs for age, gender, social economic status and prior health conditions.<h4>Results</h4>survival curves show an increased proportion of deaths between 23rd March and 14th June 2020 in care homes for older people, with an adjusted HR of 1.72 (1.55, 1.90) compared with 2016. Compared with the general population in 2016-2019, adjusted care home mortality HRs for older adults rose from 2.15 (2.11, 2.20) in 2016-2019 to 2.94 (2.81, 3.08) in 2020.<h4>Conclusions</h4>the survival curves and increased HRs show a significantly increased risk of death in the 2020 study periods.",,pdf:https://academic.oup.com/ageing/article-pdf/50/1/25/42362959/afaa207.pdf; doi:https://doi.org/10.1093/ageing/afaa207; html:https://europepmc.org/articles/PMC7546151; pdf:https://europepmc.org/articles/PMC7546151?pdf=render
-35255492,https://doi.org/10.1038/s41586-022-04576-6,Whole-genome sequencing reveals host factors underlying critical COVID-19.,"Kousathanas A, Pairo-Castineira E, Rawlik K, Stuckey A, Odhams CA, Walker S, Russell CD, Malinauskas T, Wu Y, Millar J, Shen X, Elliott KS, Griffiths F, Oosthuyzen W, Morrice K, Keating S, Wang B, Rhodes D, Klaric L, Zechner M, Parkinson N, Siddiq A, Goddard P, Donovan S, Maslove D, Nichol A, Semple MG, Zainy T, Maleady-Crowe F, Todd L, Salehi S, Knight J, Elgar G, Chan G, Arumugam P, Patch C, Rendon A, Bentley D, Kingsley C, Kosmicki JA, Horowitz JE, Baras A, Abecasis GR, Ferreira MAR, Justice A, Mirshahi T, Oetjens M, Rader DJ, Ritchie MD, Verma A, Fowler TA, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Elliott P, Walsh T, Tenesa A, GenOMICC investigators, 23andMe investigators, COVID-19 Human Genetics Initiative, Fawkes A, Murphy L, Rowan K, Ponting CP, Vitart V, Wilson JF, Yang J, Bretherick AD, Scott RH, Hendry SC, Moutsianas L, Law A, Caulfield MJ, Baillie JK.",,Nature,2022,2022-03-07,Y,,,,"Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care<sup>1</sup> or hospitalization<sup>2-4</sup> after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.",,pdf:https://www.nature.com/articles/s41586-022-04576-6.pdf; doi:https://doi.org/10.1038/s41586-022-04576-6; html:https://europepmc.org/articles/PMC9259496; pdf:https://europepmc.org/articles/PMC9259496?pdf=render
 34972825,https://doi.org/10.1038/s41564-021-01029-0,Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework.,"Nicholson G, Lehmann B, Padellini T, Pouwels KB, Jersakova R, Lomax J, King RE, Mallon AM, Diggle PJ, Richardson S, Blangiardo M, Holmes C.",,Nature microbiology,2022,2021-12-31,Y,,,,"Global and national surveillance of SARS-CoV-2 epidemiology is mostly based on targeted schemes focused on testing individuals with symptoms. These tested groups are often unrepresentative of the wider population and exhibit test positivity rates that are biased upwards compared with the true population prevalence. Such data are routinely used to infer infection prevalence and the effective reproduction number, R<sub>t</sub>, which affects public health policy. Here, we describe a causal framework that provides debiased fine-scale spatiotemporal estimates by combining targeted test counts with data from a randomized surveillance study in the United Kingdom called REACT. Our probabilistic model includes a bias parameter that captures the increased probability of an infected individual being tested, relative to a non-infected individual, and transforms observed test counts to debiased estimates of the true underlying local prevalence and R<sub>t</sub>. We validated our approach on held-out REACT data over a 7-month period. Furthermore, our local estimates of R<sub>t</sub> are indicative of 1-week- and 2-week-ahead changes in SARS-CoV-2-positive case numbers. We also observed increases in estimated local prevalence and R<sub>t</sub> that reflect the spread of the Alpha and Delta variants. Our results illustrate how randomized surveys can augment targeted testing to improve statistical accuracy in monitoring the spread of emerging and ongoing infectious disease.",,pdf:https://www.nature.com/articles/s41564-021-01029-0.pdf; doi:https://doi.org/10.1038/s41564-021-01029-0; html:https://europepmc.org/articles/PMC8727294; pdf:https://europepmc.org/articles/PMC8727294?pdf=render
+35255492,https://doi.org/10.1038/s41586-022-04576-6,Whole-genome sequencing reveals host factors underlying critical COVID-19.,"Kousathanas A, Pairo-Castineira E, Rawlik K, Stuckey A, Odhams CA, Walker S, Russell CD, Malinauskas T, Wu Y, Millar J, Shen X, Elliott KS, Griffiths F, Oosthuyzen W, Morrice K, Keating S, Wang B, Rhodes D, Klaric L, Zechner M, Parkinson N, Siddiq A, Goddard P, Donovan S, Maslove D, Nichol A, Semple MG, Zainy T, Maleady-Crowe F, Todd L, Salehi S, Knight J, Elgar G, Chan G, Arumugam P, Patch C, Rendon A, Bentley D, Kingsley C, Kosmicki JA, Horowitz JE, Baras A, Abecasis GR, Ferreira MAR, Justice A, Mirshahi T, Oetjens M, Rader DJ, Ritchie MD, Verma A, Fowler TA, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Elliott P, Walsh T, Tenesa A, GenOMICC investigators, 23andMe investigators, COVID-19 Human Genetics Initiative, Fawkes A, Murphy L, Rowan K, Ponting CP, Vitart V, Wilson JF, Yang J, Bretherick AD, Scott RH, Hendry SC, Moutsianas L, Law A, Caulfield MJ, Baillie JK.",,Nature,2022,2022-03-07,Y,,,,"Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care<sup>1</sup> or hospitalization<sup>2-4</sup> after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.",,pdf:https://www.nature.com/articles/s41586-022-04576-6.pdf; doi:https://doi.org/10.1038/s41586-022-04576-6; html:https://europepmc.org/articles/PMC9259496; pdf:https://europepmc.org/articles/PMC9259496?pdf=render
 32781946,https://doi.org/10.1098/rspb.2020.1405,Key questions for modelling COVID-19 exit strategies.,"Thompson RN, Hollingsworth TD, Isham V, Arribas-Bel D, Ashby B, Britton T, Challenor P, Chappell LHK, Clapham H, Cunniffe NJ, Dawid AP, Donnelly CA, Eggo RM, Funk S, Gilbert N, Glendinning P, Gog JR, Hart WS, Heesterbeek H, House T, Keeling M, Kiss IZ, Kretzschmar ME, Lloyd AL, McBryde ES, McCaw JM, McKinley TJ, Miller JC, Morris M, O'Neill PD, Parag KV, Pearson CAB, Pellis L, Pulliam JRC, Ross JV, Tomba GS, Silverman BW, Struchiner CJ, Tildesley MJ, Trapman P, Webb CR, Mollison D, Restif O.",,Proceedings. Biological sciences,2020,2020-08-12,Y,Uncertainty; Mathematical Modelling; Epidemic Control; Exit Strategy; Covid-19; Sars-cov-2,,,"Combinations of intense non-pharmaceutical interventions (lockdowns) were introduced worldwide to reduce SARS-CoV-2 transmission. Many governments have begun to implement exit strategies that relax restrictions while attempting to control the risk of a surge in cases. Mathematical modelling has played a central role in guiding interventions, but the challenge of designing optimal exit strategies in the face of ongoing transmission is unprecedented. Here, we report discussions from the Isaac Newton Institute 'Models for an exit strategy' workshop (11-15 May 2020). A diverse community of modellers who are providing evidence to governments worldwide were asked to identify the main questions that, if answered, would allow for more accurate predictions of the effects of different exit strategies. Based on these questions, we propose a roadmap to facilitate the development of reliable models to guide exit strategies. This roadmap requires a global collaborative effort from the scientific community and policymakers, and has three parts: (i) improve estimation of key epidemiological parameters; (ii) understand sources of heterogeneity in populations; and (iii) focus on requirements for data collection, particularly in low-to-middle-income countries. This will provide important information for planning exit strategies that balance socio-economic benefits with public health.",,doi:https://doi.org/10.1098/rspb.2020.1405; doi:https://doi.org/10.1098/rspb.2020.1405; html:https://europepmc.org/articles/PMC7575516; pdf:https://europepmc.org/articles/PMC7575516?pdf=render
 38827086,https://doi.org/,Mechanisms for Integrating Real Data into Search Game Simulations: An Application to Winter Health Service Pressures and Preventative Policies.,"Chapman M, G-Medhin A, Daneshi K, Bramwell T, Durbaba S, Curcin V, Parmar D, Boulding H, Becares L, Morgan C, Molokhia M, McBurney P, Harding S, Wolfe I, Ashworth M, Poston L.",,AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science,2024,2024-05-31,N,,,,"While modelling and simulation are powerful techniques for exploring complex phenomena, if they are not coupled with suitable real-world data any results obtained are likely to require extensive validation. We consider this problem in the context of search game modelling, and suggest that both demographic and behaviour data are used to configure certain model parameters. We show this integration in practice by using a combined dataset of over 150,000 individuals to configure a specific search game model that captures the environment, population, interventions and individual behaviours relating to winter health service pressures. The presence of this data enables us to more accurately explore the potential impact of service pressure interventions, which we do across 33,000 simulations using a computational version of the model. We find government advice to be the best-performing intervention in simulation, in respect of improved health, reduced health inequalities, and thus reduced pressure on health service utilisation.",,html:https://europepmc.org/articles/PMC11141793; pdf:https://europepmc.org/articles/PMC11141793?pdf=render
 34210356,https://doi.org/10.1186/s13059-021-02395-y,CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance.,"Nicholls SM, Poplawski R, Bull MJ, Underwood A, Chapman M, Abu-Dahab K, Taylor B, Colquhoun RM, Rowe WPM, Jackson B, Hill V, O'Toole Á, Rey S, Southgate J, Amato R, Livett R, Gonçalves S, Harrison EM, Peacock SJ, Aanensen DM, Rambaut A, Connor TR, Loman NJ, COVID-19 Genomics UK (COG-UK) Consortium.",,Genome biology,2021,2021-07-01,Y,,,,"In response to the ongoing SARS-CoV-2 pandemic in the UK, the COVID-19 Genomics UK (COG-UK) consortium was formed to rapidly sequence SARS-CoV-2 genomes as part of a national-scale genomic surveillance strategy. The network consists of universities, academic institutes, regional sequencing centres and the four UK Public Health Agencies. We describe the development and deployment of CLIMB-COVID, an encompassing digital infrastructure to address the challenge of collecting and integrating both genomic sequencing data and sample-associated metadata produced across the COG-UK network.",,pdf:https://genomebiology.biomedcentral.com/counter/pdf/10.1186/s13059-021-02395-y; doi:https://doi.org/10.1186/s13059-021-02395-y; html:https://europepmc.org/articles/PMC8247108; pdf:https://europepmc.org/articles/PMC8247108?pdf=render
@@ -442,15 +442,15 @@ PMC9023380,https://doi.org/,Assessing the spread risk of COVID-19 associated wit
 33827854,https://doi.org/10.1136/bmj.n826,Linked electronic health records for research on a nationwide cohort of more than 54 million people in England: data resource.,"Wood A, Denholm R, Hollings S, Cooper J, Ip S, Walker V, Denaxas S, Akbari A, Banerjee A, Whiteley W, Lai A, Sterne J, Sudlow C, CVD-COVID-UK consortium.",,BMJ (Clinical research ed.),2021,2021-04-07,Y,,,,"<h4>Objective</h4>To describe a novel England-wide electronic health record (EHR) resource enabling whole population research on covid-19 and cardiovascular disease while ensuring data security and privacy and maintaining public trust.<h4>Design</h4>Data resource comprising linked person level records from national healthcare settings for the English population, accessible within NHS Digital's new trusted research environment.<h4>Setting</h4>EHRs from primary care, hospital episodes, death registry, covid-19 laboratory test results, and community dispensing data, with further enrichment planned from specialist intensive care, cardiovascular, and covid-19 vaccination data.<h4>Participants</h4>54.4 million people alive on 1 January 2020 and registered with an NHS general practitioner in England.<h4>Main measures of interest</h4>Confirmed and suspected covid-19 diagnoses, exemplar cardiovascular conditions (incident stroke or transient ischaemic attack and incident myocardial infarction) and all cause mortality between 1 January and 31 October 2020.<h4>Results</h4>The linked cohort includes more than 96% of the English population. By combining person level data across national healthcare settings, data on age, sex, and ethnicity are complete for around 95% of the population. Among 53.3 million people with no previous diagnosis of stroke or transient ischaemic attack, 98 721 had a first ever incident stroke or transient ischaemic attack between 1 January and 31 October 2020, of which 30% were recorded only in primary care and 4% only in death registry records. Among 53.2 million people with no previous diagnosis of myocardial infarction, 62 966 had an incident myocardial infarction during follow-up, of which 8% were recorded only in primary care and 12% only in death registry records. A total of 959 470 people had a confirmed or suspected covid-19 diagnosis (714 162 in primary care data, 126 349 in hospital admission records, 776 503 in covid-19 laboratory test data, and 50 504 in death registry records). Although 58% of these were recorded in both primary care and covid-19 laboratory test data, 15% and 18%, respectively, were recorded in only one.<h4>Conclusions</h4>This population-wide resource shows the importance of linking person level data across health settings to maximise completeness of key characteristics and to ascertain cardiovascular events and covid-19 diagnoses. Although this resource was initially established to support research on covid-19 and cardiovascular disease to benefit clinical care and public health and to inform healthcare policy, it can broaden further to enable a wide range of research.",,pdf:https://www.bmj.com/content/bmj/373/bmj.n826.full.pdf; doi:https://doi.org/10.1136/bmj.n826; html:https://europepmc.org/articles/PMC8413899; pdf:https://europepmc.org/articles/PMC8413899?pdf=render
 37570411,https://doi.org/10.3390/healthcare11152171,Patient Experiences of Communication with Healthcare Professionals on Their Healthcare Management around Chronic Respiratory Diseases.,"Zhang X, Buttery SC, Sterniczuk K, Brownrigg A, Kennington E, Quint JK.",,"Healthcare (Basel, Switzerland)",2023,2023-07-31,Y,Communication; experience; Healthcare Professionals; Chronic Respiratory Disease,,,"<h4>Background</h4>Communication is an important clinical tool for the prevention and control of diseases, to advise and inform patients and the public, providing them with essential knowledge regarding healthcare and disease management. This study explored the experience of communication between healthcare professionals (HCPs) and people with long-term lung conditions, from the patient perspective.<h4>Methods</h4>This qualitative study analyzed the experience of people with chronic lung disease, recruited via Asthma & Lung UK (A&LUK) and COPD research databases. A&LUK invited people who had expressed a desire to be involved in research associated with their condition via their Expert Patient Panel and associated patients' groups. Two focus group interviews (12 participants) and one individual interview (1 participant) were conducted. Thematic analysis was used for data analysis.<h4>Results</h4>Two main themes were identified and we named them 'involving communication' and 'communication needs to be improved. 'They included seven subthemes: community-led support increased the patients' social interaction with peers; allied-HCP-led support increased patients' satisfaction; disliking being repeatedly asked the same basic information; feeling communication was unengaging, lacking personal specifics and the use of medical terminology and jargon.<h4>Conclusions</h4>The study has identified what most matters in the process of communication with HCPs in people with long-term respiratory diseases of their healthcare management. The findings of the study can be used to improve the patient-healthcare professional relationship and facilitate a better communication flow in long-term healthcare management.",,pdf:https://www.mdpi.com/2227-9032/11/15/2171/pdf?version=1690788413; doi:https://doi.org/10.3390/healthcare11152171; html:https://europepmc.org/articles/PMC10418967; pdf:https://europepmc.org/articles/PMC10418967?pdf=render
 33714592,https://doi.org/10.1016/j.mayocp.2021.02.007,"Place and Underlying Cause of Death During the COVID-19 Pandemic: Retrospective Cohort Study of 3.5 Million Deaths in England and Wales, 2014 to 2020.","Wu J, Mafham M, Mamas MA, Rashid M, Kontopantelis E, Deanfield JE, de Belder MA, Gale CP.",,Mayo Clinic proceedings,2021,2021-02-16,Y,,,,"<h4>Objective</h4>To describe the place and cause of death during the coronavirus disease 2019 (COVID-19) pandemic to assess its impact on excess mortality.<h4>Methods</h4>This national death registry included all adult (aged ≥18 years) deaths in England and Wales between January 1, 2014, and June 30, 2020. Daily deaths during the COVID-19 pandemic were compared against the expected daily deaths, estimated with use of the Farrington surveillance algorithm for daily historical data between 2014 and 2020 by place and cause of death.<h4>Results</h4>Between March 2 and June 30, 2020, there was an excess mortality of 57,860 (a proportional increase of 35%) compared with the expected deaths, of which 50,603 (87%) were COVID-19 related. At home, only 14% (2267) of the 16,190 excess deaths were related to COVID-19, with 5963 deaths due to cancer and 2485 deaths due to cardiac disease, few of which involved COVID-19. In care homes or hospices, 61% (15,623) of the 25,611 excess deaths were related to COVID-19, 5539 of which were due to respiratory disease, and most of these (4315 deaths) involved COVID-19. In the hospital, there were 16,174 fewer deaths than expected that did not involve COVID-19, with 4088 fewer deaths due to cancer and 1398 fewer deaths due to cardiac disease than expected.<h4>Conclusion</h4>The COVID-19 pandemic has resulted in a large excess of deaths in care homes that were poorly characterized and likely to be the result of undiagnosed COVID-19. There was a smaller but important and ongoing excess in deaths at home, particularly from cancer and cardiac disease, suggesting public avoidance of hospital care for non-COVID-19 conditions.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7885692; doi:https://doi.org/10.1016/j.mayocp.2021.02.007; html:https://europepmc.org/articles/PMC7885692; pdf:https://europepmc.org/articles/PMC7885692?pdf=render
+37198478,https://doi.org/10.1038/s41586-023-06034-3,GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19.,"Pairo-Castineira E, Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, Oosthuyzen W, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Morrice K, Keating S, Maslove D, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Begg C, Walsh T, Tenesa A, Flores C, Riancho JA, Rojas-Martinez A, Lapunzina P, GenOMICC Investigators, SCOURGE Consortium, ISARICC Investigators, 23andMe COVID-19 Team, Yang J, Ponting CP, Wilson JF, Vitart V, Abedalthagafi M, Luchessi AD, Parra EJ, Cruz R, Carracedo A, Fawkes A, Murphy L, Rowan K, Pereira AC, Law A, Fairfax B, Hendry SC, Baillie JK.",,Nature,2023,2023-05-17,Y,,,,"Critical illness in COVID-19 is an extreme and clinically homogeneous disease phenotype that we have previously shown<sup>1</sup> to be highly efficient for discovery of genetic associations<sup>2</sup>. Despite the advanced stage of illness at presentation, we have shown that host genetics in patients who are critically ill with COVID-19 can identify immunomodulatory therapies with strong beneficial effects in this group<sup>3</sup>. Here we analyse 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously. To investigate the therapeutic implications of these findings, we infer the structural consequences of protein-coding variants, and combine our GWAS results with gene expression data using a monocyte transcriptome-wide association study (TWAS) model, as well as gene and protein expression using Mendelian randomization. We identify potentially druggable targets in multiple systems, including inflammatory signalling (JAK1), monocyte-macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).",,pdf:https://www.nature.com/articles/s41586-023-06034-3.pdf; doi:https://doi.org/10.1038/s41586-023-06034-3; html:https://europepmc.org/articles/PMC10208981; pdf:https://europepmc.org/articles/PMC10208981?pdf=render
 35085490,https://doi.org/10.1016/s2213-2600(21)00542-7,SARS-CoV-2 infection and vaccine effectiveness in England (REACT-1): a series of cross-sectional random community surveys.,"Chadeau-Hyam M, Wang H, Eales O, Haw D, Bodinier B, Whitaker M, Walters CE, Ainslie KEC, Atchison C, Fronterre C, Diggle PJ, Page AJ, Trotter AJ, Ashby D, Barclay W, Taylor G, Cooke G, Ward H, Darzi A, Riley S, Donnelly CA, Elliott P, COVID-19 Genomics UK consortium.",,The Lancet. Respiratory medicine,2022,2022-01-24,Y,,,,"<h4>Background</h4>England has experienced a third wave of the COVID-19 epidemic since the end of May, 2021, coinciding with the rapid spread of the delta (B.1.617.2) variant, despite high levels of vaccination among adults. Vaccination rates (single dose) in England are lower among children aged 16-17 years and 12-15 years, whose vaccination in England commenced in August and September, 2021, respectively. We aimed to analyse the underlying dynamics driving patterns in SARS-CoV-2 prevalence during September, 2021, in England.<h4>Methods</h4>The REal-time Assessment of Community Transmission-1 (REACT-1) study, which commenced data collection in May, 2020, involves a series of random cross-sectional surveys in the general population of England aged 5 years and older. Using RT-PCR swab positivity data from 100 527 participants with valid throat and nose swabs in round 14 of REACT-1 (Sept 9-27, 2021), we estimated community-based prevalence of SARS-CoV-2 and vaccine effectiveness against infection by combining round 14 data with data from round 13 (June 24 to July 12, 2021; n=172 862).<h4>Findings</h4>During September, 2021, we estimated a mean RT-PCR positivity rate of 0·83% (95% CrI 0·76-0·89), with a reproduction number (R) overall of 1·03 (95% CrI 0·94-1·14). Among the 475 (62·2%) of 764 sequenced positive swabs, all were of the delta variant; 22 (4·63%; 95% CI 3·07-6·91) included the Tyr145His mutation in the spike protein associated with the AY.4 sublineage, and there was one Glu484Lys mutation. Age, region, key worker status, and household size jointly contributed to the risk of swab positivity. The highest weighted prevalence was observed among children aged 5-12 years, at 2·32% (95% CrI 1·96-2·73) and those aged 13-17 years, at 2·55% (2·11-3·08). The SARS-CoV-2 epidemic grew in those aged 5-11 years, with an R of 1·42 (95% CrI 1·18-1·68), but declined in those aged 18-54 years, with an R of 0·81 (0·68-0·97). At ages 18-64 years, the adjusted vaccine effectiveness against infection was 62·8% (95% CI 49·3-72·7) after two doses compared to unvaccinated people, for all vaccines combined, 44·8% (22·5-60·7) for the ChAdOx1 nCov-19 (Oxford-AstraZeneca) vaccine, and 71·3% (56·6-81·0) for the BNT162b2 (Pfizer-BioNTech) vaccine. In individuals aged 18 years and older, the weighted prevalence of swab positivity was 0·35% (95% CrI 0·31-0·40) if the second dose was administered up to 3 months before their swab but 0·55% (0·50-0·61) for those who received their second dose 3-6 months before their swab, compared to 1·76% (1·60-1·95) among unvaccinated individuals.<h4>Interpretation</h4>In September, 2021, at the start of the autumn school term in England, infections were increasing exponentially in children aged 5-17 years, at a time when vaccination rates were low in this age group. In adults, compared to those who received their second dose less than 3 months ago, the higher prevalence of swab positivity at 3-6 months following two doses of the COVID-19 vaccine suggests an increased risk of breakthrough infections during this period. The vaccination programme needs to reach children as well as unvaccinated and partially vaccinated adults to reduce SARS-CoV-2 transmission and associated disruptions to work and education.<h4>Funding</h4>Department of Health and Social Care, England.",,pdf:http://www.thelancet.com/article/S2213260021005427/pdf; doi:https://doi.org/10.1016/S2213-2600(21)00542-7; html:https://europepmc.org/articles/PMC8786320
 32851419,https://doi.org/10.1007/s00394-020-02372-4,Vitamin D and COVID-19 infection and mortality in UK Biobank.,"Hastie CE, Pell JP, Sattar N.",,European journal of nutrition,2021,2020-08-26,Y,Vitamin D; Mortality; Covid-19,,,"<h4>Purpose</h4>Low blood 25-hydroxyvitamin D (25(OH)D) concentration has been proposed as a potential causal factor in COVID-19 risk. We aimed to establish whether baseline serum 25(OH)D concentration was associated with COVID-19 mortality, and inpatient confirmed COVID-19 infection, in UK Biobank participants.<h4>Methods</h4>UK Biobank recruited 502,624 participants aged 37-73 years between 2006 and 2010. Baseline exposure data, including serum 25(OH)D concentration, were linked to COVID-19 mortality. Univariable and multivariable Cox proportional hazards regression analyses were performed for the association between 25(OH)D and COVID-19 death, and Poisson regression analyses for the association between 25(OH)D and severe COVID-19 infection.<h4>Results</h4>Complete data were available for 341,484 UK Biobank participants, of which 656 had inpatient confirmed COVID-19 infection and 203 died of COVID-19 infection. 25(OH)D concentration was associated with severe COVID-19 infection and mortality univariably (mortality per 10 nmol/L 25(OH)D HR  0.92; 95% CI 0.86-0.98; p = 0.016), but not after adjustment for confounders (mortality per 10 nmol/L 25(OH)D HR 0.98; 95% CI = 0.91-1.06; p = 0.696). Vitamin D insufficiency or deficiency was also not independently associated with either COVID-19 infection or linked mortality.<h4>Conclusions</h4>Our findings do not support a potential link between 25(OH)D concentrations and risk of severe COVID-19 infection and mortality. Randomised trials are needed to prove a beneficial role for vitamin D in the prevention of severe COVID-19 reactions or death.",,pdf:https://link.springer.com/content/pdf/10.1007/s00394-020-02372-4.pdf; doi:https://doi.org/10.1007/s00394-020-02372-4; html:https://europepmc.org/articles/PMC7449523; pdf:https://europepmc.org/articles/PMC7449523?pdf=render
-37198478,https://doi.org/10.1038/s41586-023-06034-3,GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19.,"Pairo-Castineira E, Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, Oosthuyzen W, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Morrice K, Keating S, Maslove D, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Begg C, Walsh T, Tenesa A, Flores C, Riancho JA, Rojas-Martinez A, Lapunzina P, GenOMICC Investigators, SCOURGE Consortium, ISARICC Investigators, 23andMe COVID-19 Team, Yang J, Ponting CP, Wilson JF, Vitart V, Abedalthagafi M, Luchessi AD, Parra EJ, Cruz R, Carracedo A, Fawkes A, Murphy L, Rowan K, Pereira AC, Law A, Fairfax B, Hendry SC, Baillie JK.",,Nature,2023,2023-05-17,Y,,,,"Critical illness in COVID-19 is an extreme and clinically homogeneous disease phenotype that we have previously shown<sup>1</sup> to be highly efficient for discovery of genetic associations<sup>2</sup>. Despite the advanced stage of illness at presentation, we have shown that host genetics in patients who are critically ill with COVID-19 can identify immunomodulatory therapies with strong beneficial effects in this group<sup>3</sup>. Here we analyse 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously. To investigate the therapeutic implications of these findings, we infer the structural consequences of protein-coding variants, and combine our GWAS results with gene expression data using a monocyte transcriptome-wide association study (TWAS) model, as well as gene and protein expression using Mendelian randomization. We identify potentially druggable targets in multiple systems, including inflammatory signalling (JAK1), monocyte-macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).",,pdf:https://www.nature.com/articles/s41586-023-06034-3.pdf; doi:https://doi.org/10.1038/s41586-023-06034-3; html:https://europepmc.org/articles/PMC10208981; pdf:https://europepmc.org/articles/PMC10208981?pdf=render
 35144240,https://doi.org/10.2196/32543,Artificial Intelligence-Enabled Social Media Analysis for Pharmacovigilance of COVID-19 Vaccinations in the United Kingdom: Observational Study.,"Hussain Z, Sheikh Z, Tahir A, Dashtipour K, Gogate M, Sheikh A, Hussain A.",,JMIR public health and surveillance,2022,2022-05-27,Y,Artificial intelligence; Vaccination; Public Health; Health Informatics; Natural Language Processing; Facebook; Social Media; Twitter; Sentiment Analysis; Infodemiology; Deep Learning; Covid-19,,,"<h4>Background</h4>The rollout of vaccines for COVID-19 in the United Kingdom started in December 2020. Uptake has been high, and there has been a subsequent reduction in infections, hospitalizations, and deaths among vaccinated individuals. However, vaccine hesitancy remains a concern, in particular relating to adverse effects following immunization (AEFIs). Social media analysis has the potential to inform policy makers about AEFIs being discussed by the public as well as public attitudes toward the national immunization campaign.<h4>Objective</h4>We sought to assess the frequency and nature of AEFI-related mentions on social media in the United Kingdom and to provide insights on public sentiments toward COVID-19 vaccines.<h4>Methods</h4>We extracted and analyzed over 121,406 relevant Twitter and Facebook posts, from December 8, 2020, to April 30, 2021. These were thematically filtered using a 2-step approach, initially using COVID-19-related keywords and then using vaccine- and manufacturer-related keywords. We identified AEFI-related keywords and modeled their word frequency to monitor their trends over 2-week periods. We also adapted and utilized our recently developed hybrid ensemble model, which combines state-of-the-art lexicon rule-based and deep learning-based approaches, to analyze sentiment trends relating to the main vaccines available in the United Kingdom.<h4>Results</h4>Our COVID-19 AEFI search strategy identified 46,762 unique Facebook posts by 14,346 users and 74,644 tweets (excluding retweets) by 36,446 users over the 4-month period. We identified an increasing trend in the number of mentions for each AEFI on social media over the study period. The most frequent AEFI mentions were found to be symptoms related to appetite (n=79,132, 14%), allergy (n=53,924, 9%), injection site (n=56,152, 10%), and clots (n=43,907, 8%). We also found some rarely reported AEFIs such as Bell palsy (n=11,909, 2%) and Guillain-Barre syndrome (n=9576, 2%) being discussed as frequently as more well-known side effects like headache (n=10,641, 2%), fever (n=12,707, 2%), and diarrhea (n=16,559, 3%). Overall, we found public sentiment toward vaccines and their manufacturers to be largely positive (58%), with a near equal split between negative (22%) and neutral (19%) sentiments. The sentiment trend was relatively steady over time and had minor variations, likely based on political and regulatory announcements and debates.<h4>Conclusions</h4>The most frequently discussed COVID-19 AEFIs on social media were found to be broadly consistent with those reported in the literature and by government pharmacovigilance. We also detected potential safety signals from our analysis that have been detected elsewhere and are currently being investigated. As such, we believe our findings support the use of social media analysis to provide a complementary data source to conventional knowledge sources being used for pharmacovigilance purposes.",,pdf:https://publichealth.jmir.org/2022/5/e32543/PDF; doi:https://doi.org/10.2196/32543; html:https://europepmc.org/articles/PMC9150729
 36029521,https://doi.org/10.1093/ije/dyac171,Cohort Profile: The United Kingdom Research study into Ethnicity and COVID-19 outcomes in Healthcare workers (UK-REACH).,"Bryant L, Free RC, Woolf K, Melbourne C, Guyatt AL, John C, Gupta A, Gray LJ, Nellums L, Martin CA, McManus IC, Garwood C, Modhawdia V, Carr S, Wain LV, Tobin MD, Khunti K, Akubakar I, Pareek M, UK-REACH Collaborative Group+.",,International journal of epidemiology,2023,2023-02-01,Y,,,,,,pdf:https://academic.oup.com/ije/article-pdf/52/1/e38/49127215/dyac171.pdf; doi:https://doi.org/10.1093/ije/dyac171; html:https://europepmc.org/articles/PMC9452183; pdf:https://europepmc.org/articles/PMC9452183?pdf=render
 34862222,https://doi.org/10.7861/clinmed.2021-0386,'What is the risk to me from COVID-19?': Public involvement in providing mortality risk information for people with 'high-risk' conditions for COVID-19 (OurRisk.CoV).,"Banerjee A, Pasea L, Manohar S, Lai AG, Hemingway E, Sofer I, Katsoulis M, Sood H, Morris A, Cake C, Fitzpatrick NK, Williams B, Denaxas S, Hemingway H, and members of the Health Data Research UK COVID-19 Patient and Public Involvement and Engagement Panel.",,"Clinical medicine (London, England)",2021,2021-11-01,N,Mortality; Coronavirus; Patient And Public Involvement; Risk Information,,,"Patients and public have sought mortality risk information throughout the pandemic, but their needs may not be served by current risk prediction tools. Our mixed methods study involved: (1) systematic review of published risk tools for prognosis, (2) provision and patient testing of new mortality risk estimates for people with high-risk conditions and (3) iterative patient and public involvement and engagement with qualitative analysis. Only one of 53 (2%) previously published risk tools involved patients or the public, while 11/53 (21%) had publicly accessible portals, but all for use by clinicians and researchers.Among people with a wide range of underlying conditions, there has been sustained interest and engagement in accessible and tailored, pre- and postpandemic mortality information. Informed by patient feedback, we provide such information in 'five clicks' (https://covid19-phenomics.org/OurRiskCoV.html), as context for decision making and discussions with health professionals and family members. Further development requires curation and regular updating of NHS data and wider patient and public engagement.",,pdf:https://www.rcpjournals.org/content/clinmedicine/21/6/e620.full.pdf; doi:https://doi.org/10.7861/clinmed.2021-0386; html:https://europepmc.org/articles/PMC8806292; pdf:https://europepmc.org/articles/PMC8806292?pdf=render; doi:https://doi.org/10.7861/clinmed.2021-0386
 38512523,https://doi.org/10.1007/s00415-024-12284-6,Prevalence and temporal relationship of clinical co-morbidities in idiopathic dystonia: a UK linkage-based study.,"Bailey GA, Rawlings A, Torabi F, Pickrell WO, Peall KJ.",,Journal of neurology,2024,2024-03-21,Y,epidemiology; Dystonia; Co-morbidity; Linked Clinical Data,,,"While motor and psychiatric phenotypes in idiopathic dystonia are increasingly well understood, a few studies have examined the rate, type, and temporal pattern of other clinical co-morbidities in dystonia. Here, we determine the rates of clinical diagnoses across 13 broad systems-based diagnostic groups, comparing an overall idiopathic dystonia cohort, and sub-cohorts of cervical dystonia, blepharospasm, and dystonic tremor, to a matched-control cohort. Using the SAIL databank, we undertook a longitudinal population-based cohort study (January 1st 1994-December 31st 2017) using anonymised electronic healthcare records for individuals living in Wales (UK), identifying those diagnosed with dystonia through use of a previously validated algorithm. Clinical co-morbid diagnoses were identified from primary health care records, with a 10% prevalence threshold required for onward analysis. Using this approach, 54,166 dystonia cases were identified together with 216,574 matched controls. Within this cohort, ten of the main ICD-10 diagnostic codes exceeded the 10% prevalence threshold over the 20-year period (infection, neurological, respiratory, gastrointestinal, genitourinary, dermatological, musculoskeletal, circulatory, neoplastic, and endocrinological). In the overall dystonia cohort, musculoskeletal (aOR: 1.89, aHR: 1.74), respiratory (aOR: 1.84; aHR: 1.65), and gastrointestinal (aOR: 1.72; aHR: 1.6) disorders had the strongest associations both pre- and post-dystonia diagnosis. However, variation in the rate of association of individual clinical co-morbidities was observed across the cervical, blepharospasm, and tremor dystonia groups. This study suggests an increased rate of specific co-morbid clinical disorders both pre- and post-dystonia diagnosis which should be considered during clinical assessment of those with dystonia to enable optimum symptomatic management.",,pdf:https://link.springer.com/content/pdf/10.1007/s00415-024-12284-6.pdf; doi:https://doi.org/10.1007/s00415-024-12284-6; html:https://europepmc.org/articles/PMC11136734; pdf:https://europepmc.org/articles/PMC11136734?pdf=render
-35909058,https://doi.org/10.1016/s2589-7500(22)00123-6,Remote COVID-19 Assessment in Primary Care (RECAP) risk prediction tool: derivation and real-world validation studies.,"Espinosa-Gonzalez A, Prociuk D, Fiorentino F, Ramtale C, Mi E, Mi E, Glampson B, Neves AL, Okusi C, Husain L, Macartney J, Brown M, Browne B, Warren C, Chowla R, Heaversedge J, Greenhalgh T, de Lusignan S, Mayer E, Delaney BC.",,The Lancet. Digital health,2022,2022-07-28,Y,,,,"<h4>Background</h4>Accurate assessment of COVID-19 severity in the community is essential for patient care and requires COVID-19-specific risk prediction scores adequately validated in a community setting. Following a qualitative phase to identify signs, symptoms, and risk factors, we aimed to develop and validate two COVID-19-specific risk prediction scores. Remote COVID-19 Assessment in Primary Care-General Practice score (RECAP-GP; without peripheral oxygen saturation [SpO<sub>2</sub>]) and RECAP-oxygen saturation score (RECAP-O2; with SpO<sub>2</sub>).<h4>Methods</h4>RECAP was a prospective cohort study that used multivariable logistic regression. Data on signs and symptoms (predictors) of disease were collected from community-based patients with suspected COVID-19 via primary care electronic health records and linked with secondary data on hospital admission (outcome) within 28 days of symptom onset. Data sources for RECAP-GP were Oxford-Royal College of General Practitioners Research and Surveillance Centre (RCGP-RSC) primary care practices (development set), northwest London primary care practices (validation set), and the NHS COVID-19 Clinical Assessment Service (CCAS; validation set). The data source for RECAP-O2 was the Doctaly Assist platform (development set and validation set in subsequent sample). The two probabilistic risk prediction models were built by backwards elimination using the development sets and validated by application to the validation datasets. Estimated sample size per model, including the development and validation sets was 2880 people.<h4>Findings</h4>Data were available from 8311 individuals. Observations, such as SpO<sub>2</sub>, were mostly missing in the northwest London, RCGP-RSC, and CCAS data; however, SpO<sub>2</sub> was available for 1364 (70·0%) of 1948 patients who used Doctaly. In the final predictive models, RECAP-GP (n=1863) included sex (male and female), age (years), degree of breathlessness (three point scale), temperature symptoms (two point scale), and presence of hypertension (yes or no); the area under the curve was 0·80 (95% CI 0·76-0·85) and on validation the negative predictive value of a low risk designation was 99% (95% CI 98·1-99·2; 1435 of 1453). RECAP-O2 included age (years), degree of breathlessness (two point scale), fatigue (two point scale), and SpO<sub>2</sub> at rest (as a percentage); the area under the curve was 0·84 (0·78-0·90) and on validation the negative predictive value of low risk designation was 99% (95% CI 98·9-99·7; 1176 of 1183).<h4>Interpretation</h4>Both RECAP models are valid tools to assess COVID-19 patients in the community. RECAP-GP can be used initially, without need for observations, to identify patients who require monitoring. If the patient is monitored and SpO<sub>2</sub> is available, RECAP-O2 is useful to assess the need for treatment escalation.<h4>Funding</h4>Community Jameel and the Imperial College President's Excellence Fund, the Economic and Social Research Council, UK Research and Innovation, and Health Data Research UK.",,doi:https://doi.org/10.1016/s2589-7500(22)00123-6; doi:https://doi.org/10.1016/S2589-7500(22)00123-6; html:https://europepmc.org/articles/PMC9333950; pdf:https://europepmc.org/articles/PMC9333950?pdf=render
 35151397,https://doi.org/10.1016/s0140-6736(22)00163-5,"Casirivimab and imdevimab in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial.",RECOVERY Collaborative Group.,,"Lancet (London, England)",2022,2022-02-01,Y,,,,"<h4>Background</h4>Casirivimab and imdevimab are non-competing monoclonal antibodies that bind to two different sites on the receptor binding domain of the SARS-CoV-2 spike glycoprotein, blocking viral entry into host cells. We aimed to evaluate the efficacy and safety of casirivimab and imdevimab administered in combination in patients admitted to hospital with COVID-19.<h4>Methods</h4>RECOVERY is a randomised, controlled, open-label platform trial comparing several possible treatments with usual care in patients admitted to hospital with COVID-19. 127 UK hospitals took part in the evaluation of casirivimab and imdevimab. Eligible participants were any patients aged at least 12 years admitted to hospital with clinically suspected or laboratory-confirmed SARS-CoV-2 infection. Participants were randomly assigned (1:1) to either usual standard of care alone or usual care plus casirivimab 4 g and imdevimab 4 g administered together in a single intravenous infusion. Investigators and data assessors were masked to analyses of the outcome data during the trial. The primary outcome was 28-day all-cause mortality assessed by intention to treat, first only in patients without detectable antibodies to SARS-CoV-2 infection at randomisation (ie, those who were seronegative) and then in the overall population. Safety was assessed in all participants who received casirivimab and imdevimab. The trial is registered with ISRCTN (50189673) and ClinicalTrials.gov (NCT04381936).<h4>Findings</h4>Between Sept 18, 2020, and May 22, 2021, 9785 patients enrolled in RECOVERY were eligible for casirivimab and imdevimab, of which 4839 were randomly assigned to casirivimab and imdevimab plus usual care and 4946 to usual care alone. 3153 (32%) of 9785 patients were seronegative, 5272 (54%) were seropositive, and 1360 (14%) had unknown baseline antibody status. 812 (8%) patients were known to have received at least one dose of a SARS-CoV-2 vaccine. In the primary efficacy population of seronegative patients, 396 (24%) of 1633 patients allocated to casirivimab and imdevimab versus 452 (30%) of 1520 patients allocated to usual care died within 28 days (rate ratio [RR] 0·79, 95% CI 0·69-0·91; p=0·0009). In an analysis of all randomly assigned patients (regardless of baseline antibody status), 943 (19%) of 4839 patients allocated to casirivimab and imdevimab versus 1029 (21%) of 4946 patients allocated to usual care died within 28 days (RR 0·94, 95% CI 0·86-1·02; p=0·14). The proportional effect of casirivimab and imdevimab on mortality differed significantly between seropositive and seronegative patients (p value for heterogeneity=0·002). There were no deaths attributed to the treatment, or meaningful between-group differences in the pre-specified safety outcomes of cause-specific mortality, cardiac arrhythmia, thrombosis, or major bleeding events. Serious adverse reactions reported in seven (<1%) participants were believed by the local investigator to be related to treatment with casirivimab and imdevimab.<h4>Interpretation</h4>In patients admitted to hospital with COVID-19, the monoclonal antibody combination of casirivimab and imdevimab reduced 28-day mortality in patients who were seronegative (and therefore had not mounted their own humoral immune response) at baseline but not in those who were seropositive at baseline.<h4>Funding</h4>UK Research and Innovation (Medical Research Council) and National Institute of Health Research.",,pdf:https://aura.abdn.ac.uk/bitstream/2164/18986/1/Recovery_etal_TL_Casirivimab_And_Imdevimab_VoR.pdf; doi:https://doi.org/10.1016/S0140-6736(22)00163-5; html:https://europepmc.org/articles/PMC8830904
+35909058,https://doi.org/10.1016/s2589-7500(22)00123-6,Remote COVID-19 Assessment in Primary Care (RECAP) risk prediction tool: derivation and real-world validation studies.,"Espinosa-Gonzalez A, Prociuk D, Fiorentino F, Ramtale C, Mi E, Mi E, Glampson B, Neves AL, Okusi C, Husain L, Macartney J, Brown M, Browne B, Warren C, Chowla R, Heaversedge J, Greenhalgh T, de Lusignan S, Mayer E, Delaney BC.",,The Lancet. Digital health,2022,2022-07-28,Y,,,,"<h4>Background</h4>Accurate assessment of COVID-19 severity in the community is essential for patient care and requires COVID-19-specific risk prediction scores adequately validated in a community setting. Following a qualitative phase to identify signs, symptoms, and risk factors, we aimed to develop and validate two COVID-19-specific risk prediction scores. Remote COVID-19 Assessment in Primary Care-General Practice score (RECAP-GP; without peripheral oxygen saturation [SpO<sub>2</sub>]) and RECAP-oxygen saturation score (RECAP-O2; with SpO<sub>2</sub>).<h4>Methods</h4>RECAP was a prospective cohort study that used multivariable logistic regression. Data on signs and symptoms (predictors) of disease were collected from community-based patients with suspected COVID-19 via primary care electronic health records and linked with secondary data on hospital admission (outcome) within 28 days of symptom onset. Data sources for RECAP-GP were Oxford-Royal College of General Practitioners Research and Surveillance Centre (RCGP-RSC) primary care practices (development set), northwest London primary care practices (validation set), and the NHS COVID-19 Clinical Assessment Service (CCAS; validation set). The data source for RECAP-O2 was the Doctaly Assist platform (development set and validation set in subsequent sample). The two probabilistic risk prediction models were built by backwards elimination using the development sets and validated by application to the validation datasets. Estimated sample size per model, including the development and validation sets was 2880 people.<h4>Findings</h4>Data were available from 8311 individuals. Observations, such as SpO<sub>2</sub>, were mostly missing in the northwest London, RCGP-RSC, and CCAS data; however, SpO<sub>2</sub> was available for 1364 (70·0%) of 1948 patients who used Doctaly. In the final predictive models, RECAP-GP (n=1863) included sex (male and female), age (years), degree of breathlessness (three point scale), temperature symptoms (two point scale), and presence of hypertension (yes or no); the area under the curve was 0·80 (95% CI 0·76-0·85) and on validation the negative predictive value of a low risk designation was 99% (95% CI 98·1-99·2; 1435 of 1453). RECAP-O2 included age (years), degree of breathlessness (two point scale), fatigue (two point scale), and SpO<sub>2</sub> at rest (as a percentage); the area under the curve was 0·84 (0·78-0·90) and on validation the negative predictive value of low risk designation was 99% (95% CI 98·9-99·7; 1176 of 1183).<h4>Interpretation</h4>Both RECAP models are valid tools to assess COVID-19 patients in the community. RECAP-GP can be used initially, without need for observations, to identify patients who require monitoring. If the patient is monitored and SpO<sub>2</sub> is available, RECAP-O2 is useful to assess the need for treatment escalation.<h4>Funding</h4>Community Jameel and the Imperial College President's Excellence Fund, the Economic and Social Research Council, UK Research and Innovation, and Health Data Research UK.",,doi:https://doi.org/10.1016/s2589-7500(22)00123-6; doi:https://doi.org/10.1016/S2589-7500(22)00123-6; html:https://europepmc.org/articles/PMC9333950; pdf:https://europepmc.org/articles/PMC9333950?pdf=render
 35448463,https://doi.org/10.3390/metabo12040276,MetaboListem and TABoLiSTM: Two Deep Learning Algorithms for Metabolite Named Entity Recognition.,"Yeung CS, Beck T, Posma JM.",,Metabolites,2022,2022-03-22,Y,Natural Language Processing; Named Entity Recognition; Deep Learning,,,"Reviewing the metabolomics literature is becoming increasingly difficult because of the rapid expansion of relevant journal literature. Text-mining technologies are therefore needed to facilitate more efficient literature reviews. Here we contribute a standardised corpus of full-text publications from metabolomics studies and describe the development of two metabolite named entity recognition (NER) methods. These methods are based on Bidirectional Long Short-Term Memory (BiLSTM) networks and each incorporate different transfer learning techniques (for tokenisation and word embedding). Our first model (MetaboListem) follows prior methodology using GloVe word embeddings. Our second model exploits BERT and BioBERT for embedding and is named TABoLiSTM (Transformer-Affixed BiLSTM). The methods are trained on a novel corpus annotated using rule-based methods, and evaluated on manually annotated metabolomics articles. MetaboListem (F1-score 0.890, precision 0.892, recall 0.888) and TABoLiSTM (BioBERT version: F1-score 0.909, precision 0.926, recall 0.893) have achieved state-of-the-art performance on metabolite NER. A training corpus with full-text sentences from >1000 full-text Open Access metabolomics publications with 105,335 annotated metabolites was created, as well as a manually annotated test corpus (19,138 annotations). This work demonstrates that deep learning algorithms are capable of identifying metabolite names accurately and efficiently in text. The proposed corpus and NER algorithms can be used for metabolomics text-mining tasks such as information retrieval, document classification and literature-based discovery and are available from the omicsNLP GitHub repository.",,pdf:https://www.mdpi.com/2218-1989/12/4/276/pdf?version=1647939572; doi:https://doi.org/10.3390/metabo12040276; html:https://europepmc.org/articles/PMC9031427; pdf:https://europepmc.org/articles/PMC9031427?pdf=render
 37192798,https://doi.org/10.1136/bmjopen-2022-066398,Impact of pausing elective hip and knee replacement surgery during winter 2017 on subsequent service provision at a major NHS Trust: a descriptive observational study using interrupted time series.,"Jones T, Penfold C, Redaniel MT, Eyles E, Keen T, Elliott A, Blom AW, Judge A.",,BMJ open,2023,2023-05-16,Y,Knee; Hip; Human Resource Management; Orthopaedic & Trauma Surgery,,,"<h4>Objectives</h4>To explore the impact of a temporary cancellation of elective surgery in winter 2017 on trends in primary hip and knee replacement at a major National Health Service (NHS) Trust, and whether lessons can be learnt about efficient surgery provision.<h4>Design and setting</h4>Observational descriptive study using interrupted time series analysis of hospital records to explore trends in primary hip and knee replacement surgery at a major NHS Trust, as well as patient characteristics, 2016-2019.<h4>Intervention</h4>A temporary cancellation of elective services for 2 months in winter 2017.<h4>Outcomes</h4>NHS-funded hospital admissions for primary hip or knee replacement, length of stay and bed occupancy. Additionally, we explored the ratio of elective to emergency admissions at the Trust as a measure of elective capacity, and the ratio of public to private provision of NHS-funded hip and knee surgery.<h4>Results</h4>After winter 2017, there was a sustained reduction in the number of knee replacements, a decrease in the proportion of most deprived people having knee replacements and an increase in average age for knee replacement and comorbidity for both types of surgery. The ratio of public to private provision dropped after winter 2017, and elective capacity generally has reduced over time. There was clear seasonality in provision of elective surgery, with less complex patients admitted during winter.<h4>Conclusions</h4>Declining elective capacity and seasonality has a marked effect on the provision of joint replacement, despite efficiency improvements in hospital treatment. The Trust has outsourced less complex patients to independent providers, and/or treated them during winter when capacity is most limited. There is a need to explore whether these are strategies that could be used explicitly to maximise the use of limited elective capacity, provide benefit to patients and value for money for taxpayers.",,pdf:https://bmjopen.bmj.com/content/bmjopen/13/5/e066398.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-066398; html:https://europepmc.org/articles/PMC10193088; pdf:https://europepmc.org/articles/PMC10193088?pdf=render
 37303488,https://doi.org/10.1136/bmjmed-2022-000392,"Changes in medication safety indicators in England throughout the covid-19 pandemic using OpenSAFELY: population based, retrospective cohort study of 57 million patients using federated analytics.","Fisher L, Hopcroft LE, Rodgers S, Barrett J, Oliver K, Avery AJ, Evans D, Curtis H, Croker R, Macdonald O, Morley J, Mehrkar A, Bacon S, Davy S, Dillingham I, Evans D, Hickman G, Inglesby P, Morton CE, Smith B, Ward T, Hulme W, Green A, Massey J, Walker AJ, Bates C, Cockburn J, Parry J, Hester F, Harper S, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Griffiths P, Fowles A, Parkes N, Goldacre B, MacKenna B.",,BMJ medicine,2023,2023-05-11,Y,Primary Health Care; Medical Informatics; Covid-19,,,"<h4>Objective</h4>To implement complex, PINCER (pharmacist led information technology intervention) prescribing indicators, on a national scale with general practice data to describe the impact of the covid-19 pandemic on safe prescribing.<h4>Design</h4>Population based, retrospective cohort study using federated analytics.<h4>Setting</h4>Electronic general practice health record data from 56.8 million NHS patients by use of the OpenSAFELY platform, with the approval of the National Health Service (NHS) England.<h4>Participants</h4>NHS patients (aged 18-120 years) who were alive and registered at a general practice that used TPP or EMIS computer systems and were recorded as at risk of at least one potentially hazardous PINCER indicator.<h4>Main outcome measure</h4>Between 1 September 2019 and 1 September 2021, monthly trends and between practice variation for compliance with 13 PINCER indicators, as calculated on the first of every month, were reported. Prescriptions that do not adhere to these indicators are potentially hazardous and can cause gastrointestinal bleeds; are cautioned against in specific conditions (specifically heart failure, asthma, and chronic renal failure); or require blood test monitoring. The percentage for each indicator is formed of a numerator of patients deemed to be at risk of a potentially hazardous prescribing event and the denominator is of patients for which assessment of the indicator is clinically meaningful. Higher indicator percentages represent potentially poorer performance on medication safety.<h4>Results</h4>The PINCER indicators were successfully implemented across general practice data for 56.8 million patient records from 6367 practices in OpenSAFELY. Hazardous prescribing remained largely unchanged during the covid-19 pandemic, with no evidence of increases in indicators of harm as captured by the PINCER indicators. The percentage of patients at risk of potentially hazardous prescribing, as defined by each PINCER indicator, at mean quarter 1 (Q1) 2020 (representing before the pandemic) ranged from 1.11% (age ≥65 years and non-steroidal anti-inflammatory drugs) to 36.20% (amiodarone and no thyroid function test), while Q1 2021 (representing after the pandemic) percentages ranged from 0.75% (age ≥65 years and non-steroidal anti-inflammatory drugs) to 39.23% (amiodarone and no thyroid function test). Transient delays occurred in blood test monitoring for some medications, particularly angiotensin-converting enzyme inhibitors (where blood monitoring worsened from a mean of 5.16% in Q1 2020 to 12.14% in Q1 2021, and began to recover in June 2021). All indicators substantially recovered by September 2021. We identified 1 813 058 patients (3.1%) at risk of at least one potentially hazardous prescribing event.<h4>Conclusion</h4>NHS data from general practices can be analysed at national scale to generate insights into service delivery. Potentially hazardous prescribing was largely unaffected by the covid-19 pandemic in primary care health records in England.",,pdf:https://bmjmedicine.bmj.com/content/bmjmed/2/1/e000392.full.pdf; doi:https://doi.org/10.1136/bmjmed-2022-000392; html:https://europepmc.org/articles/PMC10254692; pdf:https://europepmc.org/articles/PMC10254692?pdf=render
@@ -460,9 +460,9 @@ PMC9023380,https://doi.org/,Assessing the spread risk of COVID-19 associated wit
 33185016,https://doi.org/10.1002/art.41593,Nonsteroidal Antiinflammatory Drugs and Susceptibility to COVID-19.,"Chandan JS, Zemedikun DT, Thayakaran R, Byne N, Dhalla S, Acosta-Mena D, Gokhale KM, Thomas T, Sainsbury C, Subramanian A, Cooper J, Anand A, Okoth KO, Wang J, Adderley NJ, Taverner T, Denniston AK, Lord J, Thomas GN, Buckley CD, Raza K, Bhala N, Nirantharakumar K, Haroon S.",,"Arthritis & rheumatology (Hoboken, N.J.)",2021,2021-05-01,Y,,,,"<h4>Objective</h4>To identify whether active use of nonsteroidal antiinflammatory drugs (NSAIDs) increases susceptibility to developing suspected or confirmed coronavirus disease 2019 (COVID-19) compared to the use of other common analgesics.<h4>Methods</h4>We performed a propensity score-matched cohort study with active comparators, using a large UK primary care data set. The cohort consisted of adult patients age ≥18 years with osteoarthritis (OA) who were followed up from January 30 to July 31, 2020. Patients prescribed an NSAID (excluding topical preparations) were compared to those prescribed either co-codamol (paracetamol and codeine) or co-dydramol (paracetamol and dihydrocodeine). A total of 13,202 patients prescribed NSAIDs were identified, compared to 12,457 patients prescribed the comparator drugs. The primary outcome measure was the documentation of suspected or confirmed COVID-19, and the secondary outcome measure was all-cause mortality.<h4>Results</h4>During follow-up, the incidence rates of suspected/confirmed COVID-19 were 15.4 and 19.9 per 1,000 person-years in the NSAID-exposed group and comparator group, respectively. Adjusted hazard ratios for suspected or confirmed COVID-19 among the unmatched and propensity score-matched OA cohorts, using data from clinical consultations in primary care settings, were 0.82 (95% confidence interval [95% CI] 0.62-1.10) and 0.79 (95% CI 0.57-1.11), respectively, and adjusted hazard ratios for the risk of all-cause mortality were 0.97 (95% CI 0.75-1.27) and 0.85 (95% CI 0.61-1.20), respectively. There was no effect modification by age or sex.<h4>Conclusion</h4>No increase in the risk of suspected or confirmed COVID-19 or mortality was observed among patients with OA in a primary care setting who were prescribed NSAIDs as compared to those who received comparator drugs. These results are reassuring and suggest that in the absence of acute illness, NSAIDs can be safely prescribed during the ongoing pandemic.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/art.41593; doi:https://doi.org/10.1002/art.41593; html:https://europepmc.org/articles/PMC8252419; pdf:https://europepmc.org/articles/PMC8252419?pdf=render
 35022215,https://doi.org/10.1136/bmj-2021-067519,Indirect effects of the covid-19 pandemic on childhood infection in England: population based observational study.,"Kadambari S, Goldacre R, Morris E, Goldacre MJ, Pollard AJ.",,BMJ (Clinical research ed.),2022,2022-01-12,Y,,,,"<h4>Objective</h4>To assess the impact of the covid-19 pandemic on hospital admission rates and mortality outcomes for childhood respiratory infections, severe invasive infections, and vaccine preventable disease in England.<h4>Design</h4>Population based observational study of 19 common childhood respiratory, severe invasive, and vaccine preventable infections, comparing hospital admission rates and mortality outcomes before and after the onset of the pandemic in England.<h4>Setting</h4>Hospital admission data from every NHS hospital in England from 1 March 2017 to 30 June 2021 with record linkage to national mortality data.<h4>Population</h4>Children aged 0-14 years admitted to an NHS hospital with a selected childhood infection from 1 March 2017 to 30 June 2021.<h4>Main outcome measures</h4>For each infection, numbers of hospital admissions every month from 1 March 2017 to 30 June 2021, percentage changes in the number of hospital admissions before and after 1 March 2020, and adjusted odds ratios to compare 60 day case fatality outcomes before and after 1 March 2020.<h4>Results</h4>After 1 March 2020, substantial and sustained reductions in hospital admissions were found for all but one of the 19 infective conditions studied. Among the respiratory infections, the greatest percentage reductions were for influenza (mean annual number admitted between 1 March 2017 and 29 February 2020 was 5379 and number of children admitted from 1 March 2020 to 28 February 2021 was 304, 94% reduction, 95% confidence interval 89% to 97%), and bronchiolitis (from 51 655 to 9423, 82% reduction, 95% confidence interval 79% to 84%). Among the severe invasive infections, the greatest reduction was for meningitis (50% reduction, 47% to 52%). For the vaccine preventable infections, reductions ranged from 53% (32% to 68%) for mumps to 90% (80% to 95%) for measles. Reductions were seen across all demographic subgroups and in children with underlying comorbidities. Corresponding decreases were also found for the absolute numbers of 60 day case fatalities, although the proportion of children admitted for pneumonia who died within 60 days increased (age-sex adjusted odds ratio 1.71, 95% confidence interval 1.43 to 2.05). More recent data indicate that some respiratory infections increased to higher levels than usual after May 2021.<h4>Conclusions</h4>During the covid-19 pandemic, a range of behavioural changes (adoption of non-pharmacological interventions) and societal strategies (school closures, lockdowns, and restricted travel) were used to reduce transmission of SARS-CoV-2, which also reduced admissions for common and severe childhood infections. Continued monitoring of these infections is required as social restrictions evolve.",,pdf:https://www.bmj.com/content/bmj/376/bmj-2021-067519.full.pdf; doi:https://doi.org/10.1136/bmj-2021-067519; html:https://europepmc.org/articles/PMC8753487; pdf:https://europepmc.org/articles/PMC8753487?pdf=render
 33316211,https://doi.org/10.1016/s2352-3018(20)30305-2,HIV infection and COVID-19 death: a population-based cohort analysis of UK primary care data and linked national death registrations within the OpenSAFELY platform.,"Bhaskaran K, Rentsch CT, MacKenna B, Schultze A, Mehrkar A, Bates CJ, Eggo RM, Morton CE, Bacon SCJ, Inglesby P, Douglas IJ, Walker AJ, McDonald HI, Cockburn J, Williamson EJ, Evans D, Forbes HJ, Curtis HJ, Hulme WJ, Parry J, Hester F, Harper S, Evans SJW, Smeeth L, Goldacre B.",,The lancet. HIV,2021,2020-12-11,Y,,,,"<h4>Background</h4>Whether HIV infection is associated with risk of death due to COVID-19 is unclear. We aimed to investigate this association in a large-scale population-based study in England.<h4>Methods</h4>We did a retrospective cohort study. Working on behalf of NHS England, we used the OpenSAFELY platform to analyse routinely collected electronic primary care data linked to national death registrations. We included all adults (aged ≥18 years) alive and in follow-up on Feb 1, 2020, and with at least 1 year of continuous registration with a general practitioner before this date. People with a primary care record for HIV infection were compared with people without HIV. The outcome was COVID-19 death, defined as the presence of International Classification of Diseases 10 codes U07.1 or U07.2 anywhere on the death certificate. Cox regression models were used to estimate the association between HIV infection and COVID-19 death; they were initially adjusted for age and sex, then we added adjustment for index of multiple deprivation and ethnicity, and then for a broad range of comorbidities. Interaction terms were added to assess effect modification by age, sex, ethnicity, comorbidities, and calendar time.<h4>Results</h4>17 282 905 adults were included, of whom 27 480 (0·16%) had HIV recorded. People living with HIV were more likely to be male, of Black ethnicity, and from a more deprived geographical area than the general population. 14 882 COVID-19 deaths occurred during the study period, with 25 among people with HIV. People living with HIV had higher risk of COVID-19 death than those without HIV after adjusting for age and sex: hazard ratio (HR) 2·90 (95% CI 1·96-4·30; p<0·0001). The association was attenuated, but risk remained high, after adjustment for deprivation, ethnicity, smoking and obesity: adjusted HR 2·59 (95% CI 1·74-3·84; p<0·0001). There was some evidence that the association was larger among people of Black ethnicity: HR 4·31 (95% CI 2·42-7·65) versus 1·84 (1·03-3·26) in non-Black individuals (p-interaction=0·044).<h4>Interpretation</h4>People with HIV in the UK seem to be at increased risk of COVID-19 mortality. Targeted policies should be considered to address this raised risk as the pandemic response evolves.<h4>Funding</h4>Wellcome, Royal Society, National Institute for Health Research, National Institute for Health Research Oxford Biomedical Research Centre, UK Medical Research Council, Health Data Research UK.",,pdf:http://www.thelancet.com/article/S2352301820303052/pdf; doi:https://doi.org/10.1016/S2352-3018(20)30305-2; html:https://europepmc.org/articles/PMC7773630; pdf:https://europepmc.org/articles/PMC7773630?pdf=render
-37088955,https://doi.org/10.1177/02692163231167212,"Deaths at home, area-based deprivation and the effect of the Covid-19 pandemic: An analysis of mortality data across four nations.","Leniz J, Davies JM, Bone AE, Hocaoglu M, Verne J, Barclay S, Murtagh FEM, Fraser LK, Higginson IJ, Sleeman KE.",,Palliative medicine,2023,2023-04-23,Y,Mortality; Palliative care; Terminal Care; Inequalities; Place Of Death; Deprivation; Pandemics; Socio-economic Position; Covid-19,,,"<h4>Background</h4>The number and proportion of home deaths in the UK increased during the Covid-19 pandemic. It is not known whether these changes were experienced disproportionately by people from different socioeconomic groups.<h4>Aim</h4>To examine the association between home death and socioeconomic position during the Covid-19 pandemic, and how this changed between 2019 and 2020.<h4>Design</h4>Retrospective cohort study using population-based individual-level mortality data.<h4>Setting/participants</h4>All registered deaths in England, Wales, Scotland and Northern Ireland. The proportion of home deaths between 28th March and 31st December 2020 was compared with the same period in 2019. We used Poisson regression models to evaluate the association between decedent's area-based level of deprivation and risk of home death, as well as the interaction between deprivation and year of death, for each nation separately.<h4>Results</h4>Between the 28th March and 31st December 2020, 409,718 deaths were recorded in England, 46,372 in Scotland, 26,410 in Wales and 13,404 in Northern Ireland. All four nations showed an increase in the adjusted proportion of home deaths between 2019 and 2020, ranging from 21 to 28%. This increase was lowest for people living in the most deprived areas in all nations, with evidence of a deprivation gradient in England.<h4>Conclusions</h4>The Covid-19 pandemic exacerbated a previously described socioeconomic inequality in place of death in the UK. Further research to understand the reasons for this change and if this inequality has been sustained is needed.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10125882; doi:https://doi.org/10.1177/02692163231167212; html:https://europepmc.org/articles/PMC10125882; pdf:https://europepmc.org/articles/PMC10125882?pdf=render
-39301141,https://doi.org/10.12688/wellcomeopenres.16058.2,Tracking Excess Deaths (TRACKED) - an interactive online tool to monitor excess deaths associated with the COVID-19 pandemic in the United Kingdom.,"Poon MTC, Brennan PM, Jin K, Figueroa JD, Sudlow CLM.",,Wellcome open research,2020,2020-11-20,Y,Mortality; Coronavirus; Web Application; Excess Deaths; Covid-19,,,"<b>Background:</b> We aimed to describe trends of excess mortality in the United Kingdom (UK) stratified by nation and cause of death, and to develop an online tool for reporting the most up to date data on excess mortality <b>Methods:</b> Population statistics agencies in the UK including the Office for National Statistics (ONS), National Records of Scotland (NRS), and Northern Ireland Statistics and Research Agency (NISRA) publish weekly mortality data. We used mortality data up to 22 <sup>nd</sup> May in the ONS and the NISRA and 24 <sup>th</sup> May in the NRS. The main outcome measures were crude mortality for non-COVID deaths (where there is no mention of COVID-19 on the death certificate) calculated, and excess mortality defined as difference between observed mortality and expected average of mortality from previous 5 years. <b>Results:</b> There were 56,961 excess deaths, of which 8,986 were non-COVID excess deaths. England had the highest number of excess deaths per 100,000 population (85) and Northern Ireland the lowest (34). Non-COVID mortality increased from 23 <sup>rd</sup> March and returned to the 5-year average on 10 <sup>th</sup> May. In Scotland, where underlying cause mortality data besides COVID-related deaths was available, the percentage excess over the 8-week period when COVID-related mortality peaked was: dementia 49%, other causes 21%, circulatory diseases 10%, and cancer 5%. We developed an online tool (TRACKing Excess Deaths - TRACKED) to allow dynamic exploration and visualisation of the latest mortality trends. <b>Conclusions:</b> Continuous monitoring of excess mortality trends and further integration of age- and gender-stratified and underlying cause of death data beyond COVID-19 will allow dynamic assessment of the impacts of indirect and direct mortality of the COVID-19 pandemic.",,doi:https://doi.org/10.12688/wellcomeopenres.16058.2; html:https://europepmc.org/articles/PMC11411238; pdf:https://europepmc.org/articles/PMC11411238?pdf=render
 36276403,https://doi.org/10.3389/fpubh.2022.875198,The mental health experiences of ethnic minorities in the UK during the Coronavirus pandemic: A qualitative exploration.,"Van Bortel T, Lombardo C, Guo L, Solomon S, Martin S, Hughes K, Weeks L, Crepaz-Keay D, McDaid S, Chantler O, Thorpe L, Morton A, Davidson G, John A, Kousoulis AA.",,Frontiers in public health,2022,2022-10-06,Y,Mental health; United Kingdom; Inequalities; Ethnic Minorities; Covid-19; Coronavirus Pandemic; Bame Ethnicity,,,"<h4>Background</h4>Worldwide, the Coronavirus pandemic has had a major impact on people's health, lives, and livelihoods. However, this impact has not been felt equally across various population groups. People from ethnic minority backgrounds in the UK have been more adversely affected by the pandemic, especially in terms of their physical health. Their mental health, on the other hand, has received less attention. This study aimed to explore the mental health experiences of UK adults from ethnic minorities during the Coronavirus pandemic. This work forms part of our wider long-term UK population study ""Mental Health in the Pandemic.""<h4>Methods</h4>We conducted an exploratory qualitative study with people from ethnic minority communities across the UK. A series of in-depth interviews were conducted with 15 women, 14 men and 1 non-binary person from ethnic minority backgrounds, aged between 18 and 65 years old (mean age = 40). We utilized purposefully selected maximum variation sampling in order to capture as wide a variety of views, perceptions and experiences as possible. Inclusion criteria: adults (18+) from ethnic minorities across the UK; able to provide full consent to participate; able to participate in a video- or phone-call interview. All interviews took place <i>via</i> MS Teams or Zoom. The gathered data were transcribed verbatim and underwent thematic analysis following Braun and Clarke carried out using NVivo 12 software.<h4>Results</h4>The qualitative data analysis yielded seven overarching themes: (1) pandemic-specific mental health and wellbeing experiences; (2) issues relating to the media; (3) coping mechanisms; (4) worries around and attitudes toward vaccination; (5) suggestions for support in moving forward; (6) best and worst experiences during pandemic and lockdowns; (7) biggest areas of change in personal life. Generally, participants' mental health experiences varied with some not being affected by the pandemic in a way related to their ethnicity, some sharing positive experiences and coping strategies (exercising more, spending more time with family, community cohesion), and some expressing negative experiences (eating or drinking more, feeling more isolated, or even racism and abuse, especially toward Asian communities). Concerns were raised around trust issues in relation to the media, the inadequate representation of ethnic minorities, and the spread of fake news especially on social media. Attitudes toward vaccinations varied too, with some people more willing to have the vaccine than others.<h4>Conclusion</h4>This study's findings highlight the diversity in the pandemic mental health experiences of ethnic minorities in the UK and has implications for policy, practice and further research. To enable moving forward beyond the pandemic, our study surfaced the need for culturally appropriate mental health support, financial support (as a key mental health determinant), accurate media representation, and clear communication messaging from the Governments of the UK.",,pdf:https://www.frontiersin.org/articles/10.3389/fpubh.2022.875198/pdf; doi:https://doi.org/10.3389/fpubh.2022.875198; html:https://europepmc.org/articles/PMC9582845; pdf:https://europepmc.org/articles/PMC9582845?pdf=render
+39301141,https://doi.org/10.12688/wellcomeopenres.16058.2,Tracking Excess Deaths (TRACKED) - an interactive online tool to monitor excess deaths associated with the COVID-19 pandemic in the United Kingdom.,"Poon MTC, Brennan PM, Jin K, Figueroa JD, Sudlow CLM.",,Wellcome open research,2020,2020-11-20,Y,Mortality; Coronavirus; Web Application; Excess Deaths; Covid-19,,,"<b>Background:</b> We aimed to describe trends of excess mortality in the United Kingdom (UK) stratified by nation and cause of death, and to develop an online tool for reporting the most up to date data on excess mortality <b>Methods:</b> Population statistics agencies in the UK including the Office for National Statistics (ONS), National Records of Scotland (NRS), and Northern Ireland Statistics and Research Agency (NISRA) publish weekly mortality data. We used mortality data up to 22 <sup>nd</sup> May in the ONS and the NISRA and 24 <sup>th</sup> May in the NRS. The main outcome measures were crude mortality for non-COVID deaths (where there is no mention of COVID-19 on the death certificate) calculated, and excess mortality defined as difference between observed mortality and expected average of mortality from previous 5 years. <b>Results:</b> There were 56,961 excess deaths, of which 8,986 were non-COVID excess deaths. England had the highest number of excess deaths per 100,000 population (85) and Northern Ireland the lowest (34). Non-COVID mortality increased from 23 <sup>rd</sup> March and returned to the 5-year average on 10 <sup>th</sup> May. In Scotland, where underlying cause mortality data besides COVID-related deaths was available, the percentage excess over the 8-week period when COVID-related mortality peaked was: dementia 49%, other causes 21%, circulatory diseases 10%, and cancer 5%. We developed an online tool (TRACKing Excess Deaths - TRACKED) to allow dynamic exploration and visualisation of the latest mortality trends. <b>Conclusions:</b> Continuous monitoring of excess mortality trends and further integration of age- and gender-stratified and underlying cause of death data beyond COVID-19 will allow dynamic assessment of the impacts of indirect and direct mortality of the COVID-19 pandemic.",,doi:https://doi.org/10.12688/wellcomeopenres.16058.2; html:https://europepmc.org/articles/PMC11411238; pdf:https://europepmc.org/articles/PMC11411238?pdf=render
+37088955,https://doi.org/10.1177/02692163231167212,"Deaths at home, area-based deprivation and the effect of the Covid-19 pandemic: An analysis of mortality data across four nations.","Leniz J, Davies JM, Bone AE, Hocaoglu M, Verne J, Barclay S, Murtagh FEM, Fraser LK, Higginson IJ, Sleeman KE.",,Palliative medicine,2023,2023-04-23,Y,Mortality; Palliative care; Terminal Care; Inequalities; Place Of Death; Deprivation; Pandemics; Socio-economic Position; Covid-19,,,"<h4>Background</h4>The number and proportion of home deaths in the UK increased during the Covid-19 pandemic. It is not known whether these changes were experienced disproportionately by people from different socioeconomic groups.<h4>Aim</h4>To examine the association between home death and socioeconomic position during the Covid-19 pandemic, and how this changed between 2019 and 2020.<h4>Design</h4>Retrospective cohort study using population-based individual-level mortality data.<h4>Setting/participants</h4>All registered deaths in England, Wales, Scotland and Northern Ireland. The proportion of home deaths between 28th March and 31st December 2020 was compared with the same period in 2019. We used Poisson regression models to evaluate the association between decedent's area-based level of deprivation and risk of home death, as well as the interaction between deprivation and year of death, for each nation separately.<h4>Results</h4>Between the 28th March and 31st December 2020, 409,718 deaths were recorded in England, 46,372 in Scotland, 26,410 in Wales and 13,404 in Northern Ireland. All four nations showed an increase in the adjusted proportion of home deaths between 2019 and 2020, ranging from 21 to 28%. This increase was lowest for people living in the most deprived areas in all nations, with evidence of a deprivation gradient in England.<h4>Conclusions</h4>The Covid-19 pandemic exacerbated a previously described socioeconomic inequality in place of death in the UK. Further research to understand the reasons for this change and if this inequality has been sustained is needed.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10125882; doi:https://doi.org/10.1177/02692163231167212; html:https://europepmc.org/articles/PMC10125882; pdf:https://europepmc.org/articles/PMC10125882?pdf=render
 33079204,https://doi.org/10.1093/ehjqcco/qcaa079,Impact of COVID-19 on cardiac procedure activity in England and associated 30-day mortality.,"Mohamed MO, Banerjee A, Clarke S, de Belder M, Patwala A, Goodwin AT, Kwok CS, Rashid M, Gale CP, Curzen N, Mamas MA.",,European heart journal. Quality of care & clinical outcomes,2021,2021-05-01,Y,Mortality; Cardiac; England; Procedures; Covid-19,,,"<h4>Aims</h4>Limited data exist on the impact of COVID-19 on national changes in cardiac procedure activity, including patient characteristics and clinical outcomes before and during the COVID-19 pandemic.<h4>Methods and results</h4>All major cardiac procedures (n = 374 899) performed between 1 January and 31 May for the years 2018, 2019, and 2020 were analysed, stratified by procedure type and time-period (pre-COVID: January-May 2018 and 2019 and January-February 2020 and COVID: March-May 2020). Multivariable logistic regression was performed to examine the odds ratio (OR) of 30-day mortality for procedures performed in the COVID period. Overall, there was a deficit of 45 501 procedures during the COVID period compared to the monthly averages (March-May) in 2018-2019. Cardiac catheterization and device implantations were the most affected in terms of numbers (n = 19 637 and n = 10 453), whereas surgical procedures such as mitral valve replacement, other valve replacement/repair, atrioseptal defect/ventriculoseptal defect repair, and coronary artery bypass grafting were the most affected as a relative percentage difference (Δ) to previous years' averages. Transcatheter aortic valve replacement was the least affected (Δ -10.6%). No difference in 30-day mortality was observed between pre-COVID and COVID time-periods for all cardiac procedures except cardiac catheterization [OR 1.25 95% confidence interval (CI) 1.07-1.47, P = 0.006] and cardiac device implantation (OR 1.35 95% CI 1.15-1.58, P < 0.001).<h4>Conclusion</h4>Cardiac procedural activity has significantly declined across England during the COVID-19 pandemic, with a deficit in excess of 45 000 procedures, without an increase in risk of mortality for most cardiac procedures performed during the pandemic. Major restructuring of cardiac services is necessary to deal with this deficit, which would inevitably impact long-term morbidity and mortality.",,pdf:https://academic.oup.com/ehjqcco/article-pdf/7/3/247/37776880/qcaa079.pdf; doi:https://doi.org/10.1093/ehjqcco/qcaa079; html:https://europepmc.org/articles/PMC7665465; pdf:https://europepmc.org/articles/PMC7665465?pdf=render
 35434685,https://doi.org/10.1016/j.lanepe.2022.100381,Dosing interval strategies for two-dose COVID-19 vaccination in 13 middle-income countries of Europe: Health impact modelling and benefit-risk analysis.,"Liu Y, Pearson CAB, Sandmann FG, Barnard RC, Kim JH, CMMID COVID-19 Working Group, Flasche S, Jit M, Abbas K.",,The Lancet regional health. Europe,2022,2022-04-11,Y,"Quantitative Methods; Mathematical Modelling; Public Health Intervention; Vaccine Policy; Ve, Vaccine Efficacy; Covid-19; Sars-cov-2; Voc, Variant Of Concern; Aefi, Adverse Events Following Immunisation; Mic, Middle Income Country",,,"<h4>Background</h4>In settings where the COVID-19 vaccine supply is constrained, extending the intervals between the first and second doses of the COVID-19 vaccine may allow more people receive their first doses earlier. Our aim is to estimate the health impact of COVID-19 vaccination alongside benefit-risk assessment of different dosing intervals in 13 middle-income countries (MICs) of Europe.<h4>Methods</h4>We fitted a dynamic transmission model to country-level daily reported COVID-19 mortality in 13 MICs in Europe (Albania, Armenia, Azerbaijan, Belarus, Bosnia and Herzegovina, Bulgaria, Georgia, Republic of Moldova, Russian Federation, Serbia, North Macedonia, Turkey, and Ukraine). A vaccine product with characteristics similar to those of the Oxford/AstraZeneca COVID-19 (AZD1222) vaccine was used in the base case scenario and was complemented by sensitivity analyses around efficacies similar to other COVID-19 vaccines. Both fixed dosing intervals at 4, 8, 12, 16, and 20 weeks and dose-specific intervals that prioritise specific doses for certain age groups were tested. Optimal intervals minimise COVID-19 mortality between March 2021 and December 2022. We incorporated the emergence of variants of concern (VOCs) into the model and conducted a benefit-risk assessment to quantify the tradeoff between health benefits versus adverse events following immunisation.<h4>Findings</h4>In all countries modelled, optimal strategies are those that prioritise the first doses among older adults (60+ years) or adults (20+ years), which lead to dosing intervals longer than six months. In comparison, a four-week fixed dosing interval may incur 10.1% [range: 4.3% - 19.0%; n = 13 (countries)] more deaths. The rapid waning of the immunity induced by the first dose (i.e. with means ranging 60-120 days as opposed to 360 days in the base case) resulted in shorter optimal dosing intervals of 8-20 weeks. Benefit-risk ratios were the highest for fixed dosing intervals of 8-12 weeks.<h4>Interpretation</h4>We infer that longer dosing intervals of over six months could reduce COVID-19 mortality in MICs of Europe. Certain parameters, such as rapid waning of first-dose induced immunity and increased immune escape through the emergence of VOCs, could significantly shorten the optimal dosing intervals.<h4>Funding</h4>World Health Organization.",,doi:https://doi.org/10.1016/j.lanepe.2022.100381; doi:https://doi.org/10.1016/j.lanepe.2022.100381; html:https://europepmc.org/articles/PMC8996067; pdf:https://europepmc.org/articles/PMC8996067?pdf=render
 32835195,https://doi.org/10.1016/s2589-7500(20)30134-5,The effects of physical distancing on population mobility during the COVID-19 pandemic in the UK.,"Drake TM, Docherty AB, Weiser TG, Yule S, Sheikh A, Harrison EM.",,The Lancet. Digital health,2020,2020-06-12,Y,,,,,,doi:https://doi.org/10.1016/s2589-7500(20)30134-5; doi:https://doi.org/10.1016/S2589-7500(20)30134-5; html:https://europepmc.org/articles/PMC7292602; pdf:https://europepmc.org/articles/PMC7292602?pdf=render
@@ -481,13 +481,13 @@ PMC9023380,https://doi.org/,Assessing the spread risk of COVID-19 associated wit
 36476601,https://doi.org/10.1186/s12911-022-02055-6,Neural-signature methods for structured EHR prediction.,"Vauvelle A, Creed P, Denaxas S.",,BMC medical informatics and decision making,2022,2022-12-07,Y,Machine Learning; Electronic Healthcare Records; Signature Methods,,,"Models that can effectively represent structured Electronic Healthcare Records (EHR) are central to an increasing range of applications in healthcare. Due to the sequential nature of health data, Recurrent Neural Networks have emerged as the dominant component within state-of-the-art architectures. The signature transform represents an alternative modelling paradigm for sequential data. This transform provides a non-learnt approach to creating a fixed vector representation of temporal features and has shown strong performances across an increasing number of domains, including medical data. However, the signature method has not yet been applied to structured EHR data. To this end, we follow recent work that enables the signature to be used as a differentiable layer within a neural architecture enabling application in high dimensional domains where calculation would have previously been intractable. Using a heart failure prediction task as an exemplar, we provide an empirical evaluation of different variations of the signature method and compare against state-of-the-art baselines. This first application of neural-signature methods in real-world healthcare data shows a competitive performance when compared to strong baselines and thus warrants further investigation within the health domain.",,pdf:https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-022-02055-6; doi:https://doi.org/10.1186/s12911-022-02055-6; html:https://europepmc.org/articles/PMC9730578; pdf:https://europepmc.org/articles/PMC9730578?pdf=render
 32619549,https://doi.org/10.1016/j.cels.2020.05.012,Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection.,"Messner CB, Demichev V, Wendisch D, Michalick L, White M, Freiwald A, Textoris-Taube K, Vernardis SI, Egger AS, Kreidl M, Ludwig D, Kilian C, Agostini F, Zelezniak A, Thibeault C, Pfeiffer M, Hippenstiel S, Hocke A, von Kalle C, Campbell A, Hayward C, Porteous DJ, Marioni RE, Langenberg C, Lilley KS, Kuebler WM, Mülleder M, Drosten C, Suttorp N, Witzenrath M, Kurth F, Sander LE, Ralser M.",,Cell systems,2020,2020-06-02,Y,Mass spectrometry; High-throughput Proteomics; Swath-ms; Antiviral Immune Response; Clinical Classifiers; Covid-19 Infection,,,"The COVID-19 pandemic is an unprecedented global challenge, and point-of-care diagnostic classifiers are urgently required. Here, we present a platform for ultra-high-throughput serum and plasma proteomics that builds on ISO13485 standardization to facilitate simple implementation in regulated clinical laboratories. Our low-cost workflow handles up to 180 samples per day, enables high precision quantification, and reduces batch effects for large-scale and longitudinal studies. We use our platform on samples collected from a cohort of early hospitalized cases of the SARS-CoV-2 pandemic and identify 27 potential biomarkers that are differentially expressed depending on the WHO severity grade of COVID-19. They include complement factors, the coagulation system, inflammation modulators, and pro-inflammatory factors upstream and downstream of interleukin 6. All protocols and software for implementing our approach are freely available. In total, this work supports the development of routine proteomic assays to aid clinical decision making and generate hypotheses about potential COVID-19 therapeutic targets.",,pdf:http://www.cell.com/article/S2405471220301976/pdf; doi:https://doi.org/10.1016/j.cels.2020.05.012; html:https://europepmc.org/articles/PMC7264033
 33012285,https://doi.org/10.1186/s12916-020-01779-4,The impact of COVID-19 control measures on social contacts and transmission in Kenyan informal settlements.,"Quaife M, van Zandvoort K, Gimma A, Shah K, McCreesh N, Prem K, Barasa E, Mwanga D, Kangwana B, Pinchoff J, CMMID COVID-19 Working Group, Edmunds WJ, Jarvis CI, Austrian K.",,BMC medicine,2020,2020-10-05,Y,Social Contacts; Covid-19; Sars-cov-2; Physical Distancing,,,"<h4>Background</h4>Many low- and middle-income countries have implemented control measures against coronavirus disease 2019 (COVID-19). However, it is not clear to what extent these measures explain the low numbers of recorded COVID-19 cases and deaths in Africa. One of the main aims of control measures is to reduce respiratory pathogen transmission through direct contact with others. In this study, we collect contact data from residents of informal settlements around Nairobi, Kenya, to assess if control measures have changed contact patterns, and estimate the impact of changes on the basic reproduction number (R<sub>0</sub>).<h4>Methods</h4>We conducted a social contact survey with 213 residents of five informal settlements around Nairobi in early May 2020, 4 weeks after the Kenyan government introduced enhanced physical distancing measures and a curfew between 7 pm and 5 am. Respondents were asked to report all direct physical and non-physical contacts made the previous day, alongside a questionnaire asking about the social and economic impact of COVID-19 and control measures. We examined contact patterns by demographic factors, including socioeconomic status. We described the impact of COVID-19 and control measures on income and food security. We compared contact patterns during control measures to patterns from non-pandemic periods to estimate the change in R<sub>0</sub>.<h4>Results</h4>We estimate that control measures reduced physical contacts by 62% and non-physical contacts by either 63% or 67%, depending on the pre-COVID-19 comparison matrix used. Masks were worn by at least one person in 92% of contacts. Respondents in the poorest socioeconomic quintile reported 1.5 times more contacts than those in the richest. Eighty-six percent of respondents reported a total or partial loss of income due to COVID-19, and 74% reported eating less or skipping meals due to having too little money for food.<h4>Conclusion</h4>COVID-19 control measures have had a large impact on direct contacts and therefore transmission, but have also caused considerable economic and food insecurity. Reductions in R<sub>0</sub> are consistent with the comparatively low epidemic growth in Kenya and other sub-Saharan African countries that implemented similar, early control measures. However, negative and inequitable impacts on economic and food security may mean control measures are not sustainable in the longer term.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-020-01779-4; doi:https://doi.org/10.1186/s12916-020-01779-4; html:https://europepmc.org/articles/PMC7533154; pdf:https://europepmc.org/articles/PMC7533154?pdf=render
-36426419,https://doi.org/10.1111/hsc.14109,"""I don't mean to be rude, but could you put a mask on while I'm here?"" A qualitative study of risks experienced by domiciliary care workers in Wales during the COVID-19 pandemic.","Prout H, Lugg-Widger FV, Brookes-Howell L, Cannings-John R, Akbari A, John A, Thomas DR, Robling M.",,Health & social care in the community,2022,2022-11-24,Y,Qualitative; risk; Social Care; Covid-19; Domiciliary Care Workers,,,"Domiciliary care workers (DCWs) continued to provide care to adults in their own homes throughout the COVID-19 pandemic. The evidence of the impact of COVID-19 on health outcomes of DCWs is currently mixed. The OSCAR study will quantify the impact of COVID-19 upon health outcomes of DCWs in Wales, explore causes of variation and extrapolate to the rest of the UK DCW population. An embedded qualitative study aimed to explore DCW experiences during the pandemic, including factors that may have varied risk of exposure to COVID-19 and adverse health and wellbeing outcomes. Registered DCWs working throughout Wales were invited to participate in a semi-structured telephone interview. 24 DCWs were interviewed between February and July 2021. Themes were identified through inductive analysis using thematic coding. Several themes emerged relating to risk of exposure to COVID-19. First, general changes to the role of the DCW during the pandemic were identified. Second, practical challenges for DCWs in the workplace were reported, including staff shortages, clients and families not following safety procedures, initial shortages of personal protective equipment (PPE), DCW criticism of standard use PPE, client difficulty with PPE and management of rapid antigen testing. Third, lack of government/employer preparation for a pandemic was described, including the reorganisation of staff clients and services, inadequate or confusing information for many DCWs, COVID-19 training and the need for improved practical instruction and limited official standard risk assessments for DCWs. Pressure to attend work and perceptions of COVID-19 risk and vaccination was also reported. In summary, this paper describes the risk factors associated with working during the pandemic. We have mapped recommendations for each problem using these qualitative findings including tailored training and better support for isolated team members and identified the required changes at several socio-ecological levels.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/hsc.14109; doi:https://doi.org/10.1111/hsc.14109; html:https://europepmc.org/articles/PMC10100139; pdf:https://europepmc.org/articles/PMC10100139?pdf=render
 32991065,https://doi.org/10.1111/dom.14203,Sodium-glucose co-transporter-2 inhibitors and susceptibility to COVID-19: A population-based retrospective cohort study.,"Sainsbury C, Wang J, Gokhale K, Acosta-Mena D, Dhalla S, Byne N, Chandan JS, Anand A, Cooper J, Okoth K, Subramanian A, Bangash MN, Taverner T, Hanif W, Ghosh S, Narendran P, Cheng KK, Marshall T, Gkoutos G, Toulis K, Thomas N, Tahrani A, Adderley NJ, Haroon S, Nirantharakumar K.",,"Diabetes, obesity & metabolism",2021,2020-10-19,Y,Type 2 diabetes; Dpp-4 Inhibitor; Pharmaco-epidemiology; Sglt2 Inhibitor; Antidiabetic Drug,,,"Sodium-glucose co-transporter-2 (SGLT2) inhibitors are widely prescribed in people with type 2 diabetes. We aimed to investigate whether SGLT2 inhibitor prescription is associated with COVID-19, when compared with an active comparator. We performed a propensity-score-matched cohort study with active comparators and a negative control outcome in a large UK-based primary care dataset. Participants prescribed SGLT2 inhibitors (n = 9948) and a comparator group prescribed dipeptidyl peptidase-4 (DPP-4) inhibitors (n = 14 917) were followed up from January 30 to July 27, 2020. The primary outcome was confirmed or clinically suspected COVID-19. The incidence rate of COVID-19 was 19.7/1000 person-years among users of SGLT2 inhibitors and 24.7/1000 person-years among propensity-score-matched users of DPP-4 inhibitors. The adjusted hazard ratio was 0.92 (95% confidence interval 0.66 to 1.29), and there was no evidence of residual confounding in the negative control analysis. We did not observe an increased risk of COVID-19 in primary care amongst those prescribed SGLT2 inhibitors compared to DPP-4 inhibitors, suggesting that clinicians may safely use these agents in the everyday care of people with type 2 diabetes during the COVID-19 pandemic.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/dom.14203; doi:https://doi.org/10.1111/dom.14203; html:https://europepmc.org/articles/PMC7537530; pdf:https://europepmc.org/articles/PMC7537530?pdf=render
+36426419,https://doi.org/10.1111/hsc.14109,"""I don't mean to be rude, but could you put a mask on while I'm here?"" A qualitative study of risks experienced by domiciliary care workers in Wales during the COVID-19 pandemic.","Prout H, Lugg-Widger FV, Brookes-Howell L, Cannings-John R, Akbari A, John A, Thomas DR, Robling M.",,Health & social care in the community,2022,2022-11-24,Y,Qualitative; risk; Social Care; Covid-19; Domiciliary Care Workers,,,"Domiciliary care workers (DCWs) continued to provide care to adults in their own homes throughout the COVID-19 pandemic. The evidence of the impact of COVID-19 on health outcomes of DCWs is currently mixed. The OSCAR study will quantify the impact of COVID-19 upon health outcomes of DCWs in Wales, explore causes of variation and extrapolate to the rest of the UK DCW population. An embedded qualitative study aimed to explore DCW experiences during the pandemic, including factors that may have varied risk of exposure to COVID-19 and adverse health and wellbeing outcomes. Registered DCWs working throughout Wales were invited to participate in a semi-structured telephone interview. 24 DCWs were interviewed between February and July 2021. Themes were identified through inductive analysis using thematic coding. Several themes emerged relating to risk of exposure to COVID-19. First, general changes to the role of the DCW during the pandemic were identified. Second, practical challenges for DCWs in the workplace were reported, including staff shortages, clients and families not following safety procedures, initial shortages of personal protective equipment (PPE), DCW criticism of standard use PPE, client difficulty with PPE and management of rapid antigen testing. Third, lack of government/employer preparation for a pandemic was described, including the reorganisation of staff clients and services, inadequate or confusing information for many DCWs, COVID-19 training and the need for improved practical instruction and limited official standard risk assessments for DCWs. Pressure to attend work and perceptions of COVID-19 risk and vaccination was also reported. In summary, this paper describes the risk factors associated with working during the pandemic. We have mapped recommendations for each problem using these qualitative findings including tailored training and better support for isolated team members and identified the required changes at several socio-ecological levels.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/hsc.14109; doi:https://doi.org/10.1111/hsc.14109; html:https://europepmc.org/articles/PMC10100139; pdf:https://europepmc.org/articles/PMC10100139?pdf=render
 37745706,https://doi.org/10.3389/fendo.2023.1266557,"Editorial: Integrative multi-modal, multi-omics analytics for the better understanding of metabolic diseases.","Acharjee A, Agarwal P, Gkoutos GV.",,Frontiers in endocrinology,2023,2023-09-08,Y,Biomarker; Therapeutic; Diagnostic; Metabolic Disease; Omics,,,,,doi:https://doi.org/10.3389/fendo.2023.1266557; html:https://europepmc.org/articles/PMC10516571; pdf:https://europepmc.org/articles/PMC10516571?pdf=render
 37067557,https://doi.org/10.1007/s00134-023-07039-2,Variants of concern and clinical outcomes in critically ill COVID-19 patients.,DP-EFFECT-BRAZIL investigators.,,Intensive care medicine,2023,2023-04-17,Y,,,,,,pdf:https://link.springer.com/content/pdf/10.1007/s00134-023-07039-2.pdf; doi:https://doi.org/10.1007/s00134-023-07039-2; html:https://europepmc.org/articles/PMC10108805; pdf:https://europepmc.org/articles/PMC10108805?pdf=render
-38905569,https://doi.org/10.1056/evidoa2400179,Effect of Fenofibrate on Progression of Diabetic Retinopathy.,"Preiss D, Logue J, Sammons E, Zayed M, Emberson J, Wade R, Wallendszus K, Stevens W, Cretney R, Harding S, Leese G, Currie G, Armitage J.",,NEJM evidence,2024,2024-06-21,Y,,,,"<h4>Background</h4>Findings from cardiovascular outcome trials suggest that fenofibrate therapy may reduce the progression of diabetic retinopathy.<h4>Methods</h4>We recruited and followed adults with nonreferable diabetic retinopathy or maculopathy using the national Diabetic Eye Screening (DES) program in Scotland. We randomly assigned participants to receive 145-mg fenofibrate tablets or placebo (taken daily or, in those with impaired renal function, on alternate days). The primary outcome was a composite of developing referable diabetic retinopathy or maculopathy (based on Scotland's DES grading scheme) or treatment (intravitreal injection, retinal laser, vitrectomy) for retinopathy or maculopathy.<h4>Results</h4>A total of 1151 participants were randomly assigned to treatment. During a median of 4.0 years, progression to referable diabetic retinopathy or maculopathy, or treatment thereof, occurred in 131 (22.7%) of 576 participants in the fenofibrate group and 168 (29.2%) of 575 in the placebo group (hazard ratio, 0.73; 95% confidence interval [CI], 0.58 to 0.91; P=0.006). In the fenofibrate group compared with the placebo group, the frequencies for any progression of retinopathy or maculopathy were 185 (32.1%) vs. 231 (40.2%); hazard ratio, 0.74; 95% CI, 0.61 to 0.90 and for the development of macular edema were 22 (3.8%) vs. 43 (7.5%); hazard ratio, 0.50; 95% CI, 0.30 to 0.84. Seventeen (3.0%) participants assigned fenofibrate and 28 (4.9%) assigned placebo were given treatment for retinopathy (hazard ratio, 0.58; 95% CI, 0.31 to 1.06). There was no effect on visual function, quality of life, or visual acuity. Trial-averaged estimated glomerular filtration rate was 7.9 (95% CI, 6.8 to 9.1) ml/min/1.73 m<sup>2</sup> lower in participants in the fenofibrate group compared with the placebo group. Serious adverse events occurred in 208 (36.1%) participants allocated fenofibrate and 204 (35.5%) participants allocated placebo.<h4>Conclusions</h4>Fenofibrate reduced progression of diabetic retinopathy compared with placebo among participants with early retinal changes. (Funded by the National Institute for Health and Care Research; ClinicalTrials.gov number, NCT03439345; ISRCTN number, ISRCTN15073006.).",,doi:https://doi.org/10.1056/EVIDoa2400179; html:https://europepmc.org/articles/PMC7616293; pdf:https://europepmc.org/articles/PMC7616293?pdf=render
 32997638,https://doi.org/10.1109/jbhi.2020.3027987,A Novel Intelligent Computational Approach to Model Epidemiological Trends and Assess the Impact of Non-Pharmacological Interventions for COVID-19.,"Ren J, Yan Y, Zhao H, Ma P, Zabalza J, Hussain Z, Luo S, Dai Q, Zhao S, Sheikh A, Hussain A, Li H.",,IEEE journal of biomedical and health informatics,2020,2020-12-04,Y,,,,"The novel coronavirus disease 2019 (COVID-19) pandemic has led to a worldwide crisis in public health. It is crucial we understand the epidemiological trends and impact of non-pharmacological interventions (NPIs), such as lockdowns for effective management of the disease and control of its spread. We develop and validate a novel intelligent computational model to predict epidemiological trends of COVID-19, with the model parameters enabling an evaluation of the impact of NPIs. By representing the number of daily confirmed cases (NDCC) as a time-series, we assume that, with or without NPIs, the pattern of the pandemic satisfies a series of Gaussian distributions according to the central limit theorem. The underlying pandemic trend is first extracted using a singular spectral analysis (SSA) technique, which decomposes the NDCC time series into the sum of a small number of independent and interpretable components such as a slow varying trend, oscillatory components and structureless noise. We then use a mixture of Gaussian fitting (GF) to derive a novel predictive model for the SSA extracted NDCC incidence trend, with the overall model termed SSA-GF. Our proposed model is shown to accurately predict the NDCC trend, peak daily cases, the length of the pandemic period, the total confirmed cases and the associated dates of the turning points on the cumulated NDCC curve. Further, the three key model parameters, specifically, the amplitude (alpha), mean (mu), and standard deviation (sigma) are linked to the underlying pandemic patterns, and enable a directly interpretable evaluation of the impact of NPIs, such as strict lockdowns and travel restrictions. The predictive model is validated using available data from China and South Korea, and new predictions are made, partially requiring future validation, for the cases of Italy, Spain, the UK and the USA. Comparative results demonstrate that the introduction of consistent control measures across countries can lead to development of similar parametric models, reflected in particular by relative variations in their underlying sigma, alpha and mu values. The paper concludes with a number of open questions and outlines future research directions.",,pdf:https://ieeexplore.ieee.org/ielx7/6221020/9281055/09210178.pdf; doi:https://doi.org/10.1109/JBHI.2020.3027987; html:https://europepmc.org/articles/PMC8545177; pdf:https://europepmc.org/articles/PMC8545177?pdf=render
-32814572,https://doi.org/10.1186/s12916-020-01712-9,The effect of travel restrictions on the geographical spread of COVID-19 between large cities in China: a modelling study.,"Quilty BJ, Diamond C, Liu Y, Gibbs H, Russell TW, Jarvis CI, Prem K, Pearson CAB, Clifford S, Flasche S, CMMID COVID-19 working group, Klepac P, Eggo RM, Jit M.",,BMC medicine,2020,2020-08-19,Y,China; Wuhan; Mobility; Delay; Outbreaks; Modelling; Travel Restrictions; Covid-19; Sars-cov-2; Cordon Sanitaire,,,"<h4>Background</h4>To contain the spread of COVID-19, a cordon sanitaire was put in place in Wuhan prior to the Lunar New Year, on 23 January 2020. We assess the efficacy of the cordon sanitaire to delay the introduction and onset of local transmission of COVID-19 in other major cities in mainland China.<h4>Methods</h4>We estimated the number of infected travellers from Wuhan to other major cities in mainland China from November 2019 to February 2020 using previously estimated COVID-19 prevalence in Wuhan and publicly available mobility data. We focused on Beijing, Chongqing, Hangzhou, and Shenzhen as four representative major cities to identify the potential independent contribution of the cordon sanitaire and holiday travel. To do this, we simulated outbreaks generated by infected arrivals in these destination cities using stochastic branching processes. We also modelled the effect of the cordon sanitaire in combination with reduced transmissibility scenarios to simulate the effect of local non-pharmaceutical interventions.<h4>Results</h4>We find that in the four cities, given the potentially high prevalence of COVID-19 in Wuhan between December 2019 and early January 2020, local transmission may have been seeded as early as 1-8 January 2020. By the time the cordon sanitaire was imposed, infections were likely in the thousands. The cordon sanitaire alone did not substantially affect the epidemic progression in these cities, although it may have had some effect in smaller cities. Reduced transmissibility resulted in a notable decrease in the incidence of infection in the four studied cities.<h4>Conclusions</h4>Our results indicate that sustained transmission was likely occurring several weeks prior to the implementation of the cordon sanitaire in four major cities of mainland China and that the observed decrease in incidence was likely attributable to other non-pharmaceutical, transmission-reducing interventions.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-020-01712-9; doi:https://doi.org/10.1186/s12916-020-01712-9; html:https://europepmc.org/articles/PMC7437104; pdf:https://europepmc.org/articles/PMC7437104?pdf=render
+32814572,https://doi.org/10.1186/s12916-020-01712-9,The effect of travel restrictions on the geographical spread of COVID-19 between large cities in China: a modelling study.,"Quilty BJ, Diamond C, Liu Y, Gibbs H, Russell TW, Jarvis CI, Prem K, Pearson CAB, Clifford S, Flasche S, CMMID COVID-19 working group, Klepac P, Eggo RM, Jit M.",,BMC medicine,2020,2020-08-19,Y,China; Wuhan; Mobility; Delay; Outbreaks; Modelling; Travel Restrictions; Covid-19; Sars-cov-2; Cordon Sanitaire,,,"<h4>Background</h4>To contain the spread of COVID-19, a cordon sanitaire was put in place in Wuhan prior to the Lunar New Year, on 23 January 2020. We assess the efficacy of the cordon sanitaire to delay the introduction and onset of local transmission of COVID-19 in other major cities in mainland China.<h4>Methods</h4>We estimated the number of infected travellers from Wuhan to other major cities in mainland China from November 2019 to February 2020 using previously estimated COVID-19 prevalence in Wuhan and publicly available mobility data. We focused on Beijing, Chongqing, Hangzhou, and Shenzhen as four representative major cities to identify the potential independent contribution of the cordon sanitaire and holiday travel. To do this, we simulated outbreaks generated by infected arrivals in these destination cities using stochastic branching processes. We also modelled the effect of the cordon sanitaire in combination with reduced transmissibility scenarios to simulate the effect of local non-pharmaceutical interventions.<h4>Results</h4>We find that in the four cities, given the potentially high prevalence of COVID-19 in Wuhan between December 2019 and early January 2020, local transmission may have been seeded as early as 1-8 January 2020. By the time the cordon sanitaire was imposed, infections were likely in the thousands. The cordon sanitaire alone did not substantially affect the epidemic progression in these cities, although it may have had some effect in smaller cities. Reduced transmissibility resulted in a notable decrease in the incidence of infection in the four studied cities.<h4>Conclusions</h4>Our results indicate that sustained transmission was likely occurring several weeks prior to the implementation of the cordon sanitaire in four major cities of mainland China and that the observed decrease in incidence was likely attributable to other non-pharmaceutical, transmission-reducing interventions.",,doi:https://doi.org/10.1186/s12916-020-01712-9; doi:https://doi.org/10.1186/s12916-020-01712-9; html:https://europepmc.org/articles/PMC7437104; pdf:https://europepmc.org/articles/PMC7437104?pdf=render
+38905569,https://doi.org/10.1056/evidoa2400179,Effect of Fenofibrate on Progression of Diabetic Retinopathy.,"Preiss D, Logue J, Sammons E, Zayed M, Emberson J, Wade R, Wallendszus K, Stevens W, Cretney R, Harding S, Leese G, Currie G, Armitage J.",,NEJM evidence,2024,2024-06-21,Y,,,,"<h4>Background</h4>Findings from cardiovascular outcome trials suggest that fenofibrate therapy may reduce the progression of diabetic retinopathy.<h4>Methods</h4>We recruited and followed adults with nonreferable diabetic retinopathy or maculopathy using the national Diabetic Eye Screening (DES) program in Scotland. We randomly assigned participants to receive 145-mg fenofibrate tablets or placebo (taken daily or, in those with impaired renal function, on alternate days). The primary outcome was a composite of developing referable diabetic retinopathy or maculopathy (based on Scotland's DES grading scheme) or treatment (intravitreal injection, retinal laser, vitrectomy) for retinopathy or maculopathy.<h4>Results</h4>A total of 1151 participants were randomly assigned to treatment. During a median of 4.0 years, progression to referable diabetic retinopathy or maculopathy, or treatment thereof, occurred in 131 (22.7%) of 576 participants in the fenofibrate group and 168 (29.2%) of 575 in the placebo group (hazard ratio, 0.73; 95% confidence interval [CI], 0.58 to 0.91; P=0.006). In the fenofibrate group compared with the placebo group, the frequencies for any progression of retinopathy or maculopathy were 185 (32.1%) vs. 231 (40.2%); hazard ratio, 0.74; 95% CI, 0.61 to 0.90 and for the development of macular edema were 22 (3.8%) vs. 43 (7.5%); hazard ratio, 0.50; 95% CI, 0.30 to 0.84. Seventeen (3.0%) participants assigned fenofibrate and 28 (4.9%) assigned placebo were given treatment for retinopathy (hazard ratio, 0.58; 95% CI, 0.31 to 1.06). There was no effect on visual function, quality of life, or visual acuity. Trial-averaged estimated glomerular filtration rate was 7.9 (95% CI, 6.8 to 9.1) ml/min/1.73 m<sup>2</sup> lower in participants in the fenofibrate group compared with the placebo group. Serious adverse events occurred in 208 (36.1%) participants allocated fenofibrate and 204 (35.5%) participants allocated placebo.<h4>Conclusions</h4>Fenofibrate reduced progression of diabetic retinopathy compared with placebo among participants with early retinal changes. (Funded by the National Institute for Health and Care Research; ClinicalTrials.gov number, NCT03439345; ISRCTN number, ISRCTN15073006.).",,doi:https://doi.org/10.1056/EVIDoa2400179; html:https://europepmc.org/articles/PMC7616293; pdf:https://europepmc.org/articles/PMC7616293?pdf=render
 32371477,https://doi.org/10.1126/science.abc0473,Rapid implementation of mobile technology for real-time epidemiology of COVID-19.,"Drew DA, Nguyen LH, Steves CJ, Menni C, Freydin M, Varsavsky T, Sudre CH, Cardoso MJ, Ourselin S, Wolf J, Spector TD, Chan AT, COPE Consortium.",,"Science (New York, N.Y.)",2020,2020-05-05,Y,,,,"The rapid pace of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents challenges to the robust collection of population-scale data to address this global health crisis. We established the COronavirus Pandemic Epidemiology (COPE) Consortium to unite scientists with expertise in big data research and epidemiology to develop the COVID Symptom Study, previously known as the COVID Symptom Tracker, mobile application. This application-which offers data on risk factors, predictive symptoms, clinical outcomes, and geographical hotspots-was launched in the United Kingdom on 24 March 2020 and the United States on 29 March 2020 and has garnered more than 2.8 million users as of 2 May 2020. Our initiative offers a proof of concept for the repurposing of existing approaches to enable rapidly scalable epidemiologic data collection and analysis, which is critical for a data-driven response to this public health challenge.","Drew et al. decribe the use of a smart-phone App to track Covid-19 symptoms reported by users to track, in real time, information on newly infected individuals. It has been launched in the UK and US and has 2.8 million users and is used to rapidly identify emerging hot spots for infection.",pdf:https://www.science.org/cms/asset/fb31d61b-4be3-483a-b040-2ee970dfb432/pap.pdf; doi:https://doi.org/10.1126/science.abc0473; html:https://europepmc.org/articles/PMC7200009; pdf:https://europepmc.org/articles/PMC7200009?pdf=render
 35291009,https://doi.org/10.1093/ageing/afac072,Intensity of COVID-19 in care homes following hospital discharge in the early stages of the UK epidemic.,"Hollinghurst J, North L, Emmerson C, Akbari A, Torabi F, Williams C, Lyons RA, Hawkes AG, Bennett E, Gravenor MB, Fry R.",,Age and ageing,2022,2022-05-01,Y,Older People; Care Homes; Hospital Discharge; Linked Data; Hawkes Process; Multi-level Model; Covid-19,,,"<h4>Background</h4>defining features of the COVID-19 pandemic in many countries were the tragic extent to which care home residents were affected and the difficulty in preventing the introduction and subsequent spread of infection. Management of risk in care homes requires good evidence on the most important transmission pathways. One hypothesised route at the start of the pandemic, prior to widespread testing, was the transfer of patients from hospitals that were experiencing high levels of nosocomial events.<h4>Methods</h4>we tested the hypothesis that hospital discharge events increased the intensity of care home cases using a national individually linked health record cohort in Wales, UK. We monitored 186,772 hospital discharge events over the period from March to July 2020, tracking individuals to 923 care homes and recording the daily case rate in the homes populated by 15,772 residents. We estimated the risk of an increase in case rates following exposure to a hospital discharge using multi-level hierarchical logistic regression and a novel stochastic Hawkes process outbreak model.<h4>Findings</h4>in regression analysis, after adjusting for care home size, we found no significant association between hospital discharge and subsequent increases in care home case numbers (odds ratio: 0.99, 95% CI: 0.82, 1.90). Risk factors for increased cases included care home size, care home resident density and provision of nursing care. Using our outbreak model, we found a significant effect of hospital discharge on the subsequent intensity of cases. However, the effect was small and considerably less than the effect of care home size, suggesting the highest risk of introduction came from interaction with the community. We estimated that approximately 1.8% of hospital discharged patients may have been infected.<h4>Interpretation</h4>there is growing evidence in the UK that the risk of transfer of COVID-19 from the high-risk hospital setting to the high-risk care home setting during the early stages of the pandemic was relatively small. Although access to testing was limited to initial symptomatic cases in each care home at this time, our results suggest that reduced numbers of discharges, selection of patients and action taken within care homes following transfer all may have contributed to the mitigation. The precise key transmission routes from the community remain to be quantified.",,pdf:https://academic.oup.com/ageing/article-pdf/51/5/afac072/43616755/afac072.pdf; doi:https://doi.org/10.1093/ageing/afac072; html:https://europepmc.org/articles/PMC8992303; pdf:https://europepmc.org/articles/PMC8992303?pdf=render
 37253531,https://doi.org/10.1136/bmjgh-2022-009997,Effectiveness of a multicomponent intervention to face the COVID-19 pandemic in Rio de Janeiro's favelas: difference-in-differences analysis.,"Batista-da-Silva AA, Moraes CB, Bozza HR, Bastos LDSL, Ranzani OT, Hamacher S, Bozza FA, Comitê Gestor Conexão Saúde.",,BMJ global health,2023,2023-05-01,Y,"Control strategies; Public Health; Intervention Study; Infections, Diseases, Disorders, Injuries; Covid-19",,,"<h4>Introduction</h4>Few community-based interventions addressing the transmission control and clinical management of COVID-19 cases have been reported, especially in poor urban communities from low-income and middle-income countries. Here, we analyse the impact of a multicomponent intervention that combines community engagement, mobile surveillance, massive testing and telehealth on COVID-19 cases detection and mortality rates in a large vulnerable community (<i>Complexo da Maré</i>) in Rio de Janeiro, Brazil.<h4>Methods</h4>We performed a difference-in-differences (DID) analysis to estimate the impact of the multicomponent intervention in <i>Maré,</i> before (March-August 2020) and after the intervention (September 2020 to April 2021), compared with equivalent local vulnerable communities. We applied a negative binomial regression model to estimate the intervention effect in weekly cases and mortality rates in <i>Maré</i>.<h4>Results</h4>Before the intervention, <i>Maré</i> presented lower rates of reported COVID-19 cases compared with the control group (1373 vs 1579 cases/100 000 population), comparable mortality rates (309 vs 287 deaths/100 000 population) and higher case fatality rates (13.7% vs 12.2%). After the intervention, <i>Maré</i> displayed a 154% (95% CI 138.6% to 170.4%) relative increase in reported case rates. Relative changes in reported death rates were -60% (95% CI -69.0% to -47.9%) in Maré and -28% (95% CI -42.0% to -9.8%) in the control group. The case fatality rate was reduced by 77% (95% CI -93.1% to -21.1%) in <i>Maré</i> and 52% (95% CI -81.8% to -29.4%) in the control group. The DID showed a reduction of 46% (95% CI 17% to 65%) of weekly reported deaths and an increased 23% (95% CI 5% to 44%) of reported cases in <i>Maré</i> after intervention onset.<h4>Conclusion</h4>An integrated intervention combining communication, surveillance and telehealth, with a strong community engagement component, could reduce COVID-19 mortality and increase case detection in a large vulnerable community in Rio de Janeiro. These findings show that investment in community-based interventions may reduce mortality and improve pandemic control in poor communities from low-income and middle-income countries.",,doi:https://doi.org/10.1136/bmjgh-2022-009997; doi:https://doi.org/10.1136/bmjgh-2022-009997; html:https://europepmc.org/articles/PMC10230340; pdf:https://europepmc.org/articles/PMC10230340?pdf=render
@@ -497,16 +497,16 @@ PMC9023380,https://doi.org/,Assessing the spread risk of COVID-19 associated wit
 33710281,https://doi.org/10.1093/ageing/afab060,COVID-19 infection and attributable mortality in UK care homes: cohort study using active surveillance and electronic records (March-June 2020).,"Dutey-Magni PF, Williams H, Jhass A, Rait G, Lorencatto F, Hemingway H, Hayward A, Shallcross L.",,Age and ageing,2021,2021-06-01,Y,Mortality; Morbidity; Older People; Long-term Care; Covid-19; Sars-cov-2,,,"<h4>Background</h4>epidemiological data on COVID-19 infection in care homes are scarce. We analysed data from a large provider of long-term care for older people to investigate infection and mortality during the first wave of the pandemic.<h4>Methods</h4>cohort study of 179 UK care homes with 9,339 residents and 11,604 staff. We used manager-reported daily tallies to estimate the incidence of suspected and confirmed infection and mortality in staff and residents. Individual-level electronic health records from 8,713 residents were used to model risk factors for confirmed infection, mortality and estimate attributable mortality.<h4>Results</h4>2,075/9,339 residents developed COVID-19 symptoms (22.2% [95% confidence interval: 21.4%; 23.1%]), while 951 residents (10.2% [9.6%; 10.8%]) and 585 staff (5.0% [4.7%; 5.5%]) had laboratory-confirmed infections. The incidence of confirmed infection was 152.6 [143.1; 162.6] and 62.3 [57.3; 67.5] per 100,000 person-days in residents and staff, respectively. Sixty-eight percent (121/179) of care homes had at least one COVID-19 infection or COVID-19-related death. Lower staffing ratios and higher occupancy rates were independent risk factors for infection.Out of 607 residents with confirmed infection, 217 died (case fatality rate: 35.7% [31.9%; 39.7%]). Mortality in residents with no direct evidence of infection was twofold higher in care homes with outbreaks versus those without (adjusted hazard ratio: 2.2 [1.8; 2.6]).<h4>Conclusions</h4>findings suggest many deaths occurred in people who were infected with COVID-19, but not tested. Higher occupancy and lower staffing levels were independently associated with risks of infection. Protecting staff and residents from infection requires regular testing for COVID-19 and fundamental changes to staffing and care home occupancy.",,pdf:https://academic.oup.com/ageing/article-pdf/50/4/1019/40971734/afab060.pdf; doi:https://doi.org/10.1093/ageing/afab060; html:https://europepmc.org/articles/PMC7989651; pdf:https://europepmc.org/articles/PMC7989651?pdf=render
 38238056,https://doi.org/10.1136/bmjopen-2023-076711,"Cohort profile: Born in Wales-a birth cohort with maternity, parental and child data linkage for life course research in Wales, UK.","Jones H, Seaborne MJ, Kennedy NL, James M, Dredge S, Bandyopadhyay A, Battaglia A, Davies S, Brophy S.",,BMJ open,2024,2024-01-18,Y,epidemiology; Public Health; Community Child Health; Surveys And Questionnaires,,,"<h4>Purpose</h4>Using Wales's national dataset for maternity and births as a core dataset, we have linked related datasets to create a more complete and comprehensive entire country birth cohort. Data of anonymised identified persons are linked on the individual level to data from health, social care and education data within the Secure Anonymised Information Linkage (SAIL) Databank. Each individual is assigned an encrypted Anonymised Linking Field; this field is used to link anonymised individuals across datasets. We present the descriptive data available in the core dataset, and the future expansion plans for the database beyond its initial development stage.<h4>Participants</h4>Descriptive information from 2011 to 2023 has been gathered from the National Community Child Health Database (NCCHD) in SAIL. This comprehensive dataset comprises over 400 000 child electronic records. Additionally, survey responses about health and well-being from a cross-section of the population including 2500 parents and 30 000 primary school children have been collected for enriched personal responses and linkage to the data spine.<h4>Findings to date</h4>The electronic cohort comprises all children born in Wales since 2011, with follow-up conducted until they finish primary school at age 11. The child cohort is 51%: 49% female: male, and 7.8% are from ethnic minority backgrounds. When considering age distribution, 26.8% of children are under the age of 5, while 63.2% fall within the age range of 5-11.<h4>Future plans</h4>Born in Wales will expand by 30 000 new births annually in Wales (in NCCHD), while including follow-up data of children and parents already in the database. Supplementary datasets complement the existing linkage, including primary care, hospital data, educational attainment and social care. Future research includes exploring the long-term implications of COVID-19 on child health and development, and examining the impact of parental work environment on child health and development.",,pdf:https://bmjopen.bmj.com/content/bmjopen/14/1/e076711.full.pdf; doi:https://doi.org/10.1136/bmjopen-2023-076711; html:https://europepmc.org/articles/PMC10806724; pdf:https://europepmc.org/articles/PMC10806724?pdf=render
 33995410,https://doi.org/10.3389/fimmu.2021.671052,Plasma Lectin Pathway Complement Proteins in Patients With COVID-19 and Renal Disease.,"Medjeral-Thomas NR, Troldborg A, Hansen AG, Gisby J, Clarke CL, Prendecki M, McAdoo SP, Sandhu E, Lightstone L, Thomas DC, Willicombe M, Botto M, Peters JE, Pickering MC, Thiel S.",,Frontiers in immunology,2021,2021-04-29,Y,Complement; Lectin; Coronavirus; Chronic Kidney Disease; Covid-19,,,"We do not understand why non-white ethnicity and chronic kidney disease increase susceptibility to COVID-19. The lectin pathway of complement activation is a key contributor to innate immunity and inflammation. Concentrations of plasma lectin pathway proteins influence pathway activity and vary with ethnicity. We measured circulating lectin proteins in a multi-ethnic cohort of chronic kidney disease patients with and without COVID19 infection to determine if lectin pathway activation was contributing to COVID19 severity. We measured 11 lectin proteins in serial samples from a cohort of 33 patients with chronic kidney impairment and COVID19. Controls were single plasma samples from 32 patients on dialysis and 32 healthy individuals. We demonstrated multiple associations between recognition molecules and associated proteases of the lectin pathway and COVID-19, including COVID-19 severity. Some of these associations were unique to patients of Asian and White ethnicity. Our novel findings demonstrate that COVID19 infection alters the concentration of plasma lectin proteins and some of these changes were linked to ethnicity. This suggests a role for the lectin pathway in the host response to COVID-19 and suggest that variability within this pathway may contribute to ethnicity-associated differences in susceptibility to severe COVID-19.",,pdf:https://www.frontiersin.org/articles/10.3389/fimmu.2021.671052/pdf; doi:https://doi.org/10.3389/fimmu.2021.671052; html:https://europepmc.org/articles/PMC8118695; pdf:https://europepmc.org/articles/PMC8118695?pdf=render
+36812516,https://doi.org/10.1371/journal.pdig.0000007,A proteomic survival predictor for COVID-19 patients in intensive care.,"Demichev V, Tober-Lau P, Nazarenko T, Lemke O, Kaur Aulakh S, Whitwell HJ, Röhl A, Freiwald A, Mittermaier M, Szyrwiel L, Ludwig D, Correia-Melo C, Lippert LJ, Helbig ET, Stubbemann P, Olk N, Thibeault C, Grüning NM, Blyuss O, Vernardis S, White M, Messner CB, Joannidis M, Sonnweber T, Klein SJ, Pizzini A, Wohlfarter Y, Sahanic S, Hilbe R, Schaefer B, Wagner S, Machleidt F, Garcia C, Ruwwe-Glösenkamp C, Lingscheid T, Bosquillon de Jarcy L, Stegemann MS, Pfeiffer M, Jürgens L, Denker S, Zickler D, Spies C, Edel A, Müller NB, Enghard P, Zelezniak A, Bellmann-Weiler R, Weiss G, Campbell A, Hayward C, Porteous DJ, Marioni RE, Uhrig A, Zoller H, Löffler-Ragg J, Keller MA, Tancevski I, Timms JF, Zaikin A, Hippenstiel S, Ramharter M, Müller-Redetzky H, Witzenrath M, Suttorp N, Lilley K, Mülleder M, Sander LE, PA-COVID-19 Study group, Kurth F, Ralser M.",,PLOS digital health,2022,2022-01-18,Y,,,,"Global healthcare systems are challenged by the COVID-19 pandemic. There is a need to optimize allocation of treatment and resources in intensive care, as clinically established risk assessments such as SOFA and APACHE II scores show only limited performance for predicting the survival of severely ill COVID-19 patients. Additional tools are also needed to monitor treatment, including experimental therapies in clinical trials. Comprehensively capturing human physiology, we speculated that proteomics in combination with new data-driven analysis strategies could produce a new generation of prognostic discriminators. We studied two independent cohorts of patients with severe COVID-19 who required intensive care and invasive mechanical ventilation. SOFA score, Charlson comorbidity index, and APACHE II score showed limited performance in predicting the COVID-19 outcome. Instead, the quantification of 321 plasma protein groups at 349 timepoints in 50 critically ill patients receiving invasive mechanical ventilation revealed 14 proteins that showed trajectories different between survivors and non-survivors. A predictor trained on proteomic measurements obtained at the first time point at maximum treatment level (i.e. WHO grade 7), which was weeks before the outcome, achieved accurate classification of survivors (AUROC 0.81). We tested the established predictor on an independent validation cohort (AUROC 1.0). The majority of proteins with high relevance in the prediction model belong to the coagulation system and complement cascade. Our study demonstrates that plasma proteomics can give rise to prognostic predictors substantially outperforming current prognostic markers in intensive care.",,pdf:https://journals.plos.org/digitalhealth/article/file?id=10.1371/journal.pdig.0000007&type=printable; doi:https://doi.org/10.1371/journal.pdig.0000007; html:https://europepmc.org/articles/PMC9931303; pdf:https://europepmc.org/articles/PMC9931303?pdf=render
 33745917,https://doi.org/10.1016/j.jinf.2021.03.011,"The dynamics of procalcitonin in COVID-19 patients admitted to Intensive care unit - a multi-centre cohort study in the South West of England, UK.","Williams P, McWilliams C, Soomro K, Harding I, Gurney S, Thomas M, Albur M, Martin Williams O.",,The Journal of infection,2021,2021-03-18,Y,,,,,,pdf:http://www.journalofinfection.com/article/S0163445321001286/pdf; doi:https://doi.org/10.1016/j.jinf.2021.03.011; html:https://europepmc.org/articles/PMC7970419; pdf:https://europepmc.org/articles/PMC7970419?pdf=render
 36987388,https://doi.org/10.1177/08862605231163885,Characterizing the Differences in Descriptions of Violence on Reddit During the COVID-19 Pandemic.,"Li L, Neubauer L, Stewart R, Roberts A.",,Journal of interpersonal violence,2023,2023-03-28,Y,Increase rate; Data Classification; Reddit; Violence Types,,,"Concerns have been raised over the experiences of violence such as domestic violence (DV) and intimate partner violence (IPV) during the COVID-19 pandemic. Social media such as Reddit represent an alternative outlet for reporting experiences of violence where healthcare access has been limited. This study analyzed seven violence-related subreddits to investigate the trends of different violence patterns from January 2018 to February 2022 to enhance the health-service providers' existing service or provide some new perspective for existing violence research. Specifically, we collected violence-related texts from Reddit using keyword searching and identified six major types with supervised machine learning classifiers: DV, IPV, physical violence, sexual violence, emotional violence, and nonspecific violence or others. The increase rate (IR) of each violence type was calculated and temporally compared in five phases of the pandemic. The phases include one pre-pandemic phase (<i>Phase 0</i>, the date before February 26, 2020) and four pandemic phases (<i>Phases 1-4</i>) with separation dates of June 17, 2020, September 7, 2020, and June 4, 2021. We found that the number of IPV-related posts increased most in the earliest phase; however, that for COVID-citing IPV was highest in the mid-pandemic phase. IRs for DV, IPV, and emotional violence also showed increases across all pandemic phases, with IRs of 26.9%, 58.8%, and 28.8%, respectively, from the pre-pandemic to the first pandemic phase. In the other three pandemic phases, all the IRs for these three types of violence were positive, though lower than the IRs in the first pandemic phase. The findings highlight the importance of identifying and providing help to those who suffer from such violent experiences and support the role of social media site monitoring as a means of informative surveillance for help-providing authorities and violence research groups.",,doi:https://doi.org/10.1177/08862605231163885; doi:https://doi.org/10.1177/08862605231163885; html:https://europepmc.org/articles/PMC10064198; pdf:https://europepmc.org/articles/PMC10064198?pdf=render
-36812516,https://doi.org/10.1371/journal.pdig.0000007,A proteomic survival predictor for COVID-19 patients in intensive care.,"Demichev V, Tober-Lau P, Nazarenko T, Lemke O, Kaur Aulakh S, Whitwell HJ, Röhl A, Freiwald A, Mittermaier M, Szyrwiel L, Ludwig D, Correia-Melo C, Lippert LJ, Helbig ET, Stubbemann P, Olk N, Thibeault C, Grüning NM, Blyuss O, Vernardis S, White M, Messner CB, Joannidis M, Sonnweber T, Klein SJ, Pizzini A, Wohlfarter Y, Sahanic S, Hilbe R, Schaefer B, Wagner S, Machleidt F, Garcia C, Ruwwe-Glösenkamp C, Lingscheid T, Bosquillon de Jarcy L, Stegemann MS, Pfeiffer M, Jürgens L, Denker S, Zickler D, Spies C, Edel A, Müller NB, Enghard P, Zelezniak A, Bellmann-Weiler R, Weiss G, Campbell A, Hayward C, Porteous DJ, Marioni RE, Uhrig A, Zoller H, Löffler-Ragg J, Keller MA, Tancevski I, Timms JF, Zaikin A, Hippenstiel S, Ramharter M, Müller-Redetzky H, Witzenrath M, Suttorp N, Lilley K, Mülleder M, Sander LE, PA-COVID-19 Study group, Kurth F, Ralser M.",,PLOS digital health,2022,2022-01-18,Y,,,,"Global healthcare systems are challenged by the COVID-19 pandemic. There is a need to optimize allocation of treatment and resources in intensive care, as clinically established risk assessments such as SOFA and APACHE II scores show only limited performance for predicting the survival of severely ill COVID-19 patients. Additional tools are also needed to monitor treatment, including experimental therapies in clinical trials. Comprehensively capturing human physiology, we speculated that proteomics in combination with new data-driven analysis strategies could produce a new generation of prognostic discriminators. We studied two independent cohorts of patients with severe COVID-19 who required intensive care and invasive mechanical ventilation. SOFA score, Charlson comorbidity index, and APACHE II score showed limited performance in predicting the COVID-19 outcome. Instead, the quantification of 321 plasma protein groups at 349 timepoints in 50 critically ill patients receiving invasive mechanical ventilation revealed 14 proteins that showed trajectories different between survivors and non-survivors. A predictor trained on proteomic measurements obtained at the first time point at maximum treatment level (i.e. WHO grade 7), which was weeks before the outcome, achieved accurate classification of survivors (AUROC 0.81). We tested the established predictor on an independent validation cohort (AUROC 1.0). The majority of proteins with high relevance in the prediction model belong to the coagulation system and complement cascade. Our study demonstrates that plasma proteomics can give rise to prognostic predictors substantially outperforming current prognostic markers in intensive care.",,pdf:https://journals.plos.org/digitalhealth/article/file?id=10.1371/journal.pdig.0000007&type=printable; doi:https://doi.org/10.1371/journal.pdig.0000007; html:https://europepmc.org/articles/PMC9931303; pdf:https://europepmc.org/articles/PMC9931303?pdf=render
 33725121,https://doi.org/10.1093/rheumatology/keab250,COVID-19 in patients with autoimmune diseases: characteristics and outcomes in a multinational network of cohorts across three countries.,"Tan EH, Sena AG, Prats-Uribe A, You SC, Ahmed WU, Kostka K, Reich C, Duvall SL, Lynch KE, Matheny ME, Duarte-Salles T, Bertolin SF, Hripcsak G, Natarajan K, Falconer T, Spotnitz M, Ostropolets A, Blacketer C, Alshammari TM, Alghoul H, Alser O, Lane JCE, Dawoud DM, Shah K, Yang Y, Zhang L, Areia C, Golozar A, Recalde M, Casajust P, Jonnagaddala J, Subbian V, Vizcaya D, Lai LYH, Nyberg F, Morales DR, Posada JD, Shah NH, Gong M, Vivekanantham A, Abend A, Minty EP, Suchard M, Rijnbeek P, Ryan PB, Prieto-Alhambra D.",,"Rheumatology (Oxford, England)",2021,2021-10-01,Y,Mortality; Hospitalization; Open Science; Autoimmune Condition; Observational Health Data Sciences And Informatics (Ohdsi); Observational Medical Outcomes Partnership (Omop); Covid-19,,,"<h4>Objective</h4>Patients with autoimmune diseases were advised to shield to avoid coronavirus disease 2019 (COVID-19), but information on their prognosis is lacking. We characterized 30-day outcomes and mortality after hospitalization with COVID-19 among patients with prevalent autoimmune diseases, and compared outcomes after hospital admissions among similar patients with seasonal influenza.<h4>Methods</h4>A multinational network cohort study was conducted using electronic health records data from Columbia University Irving Medical Center [USA, Optum (USA), Department of Veterans Affairs (USA), Information System for Research in Primary Care-Hospitalization Linked Data (Spain) and claims data from IQVIA Open Claims (USA) and Health Insurance and Review Assessment (South Korea). All patients with prevalent autoimmune diseases, diagnosed and/or hospitalized between January and June 2020 with COVID-19, and similar patients hospitalized with influenza in 2017-18 were included. Outcomes were death and complications within 30 days of hospitalization.<h4>Results</h4>We studied 133 589 patients diagnosed and 48 418 hospitalized with COVID-19 with prevalent autoimmune diseases. Most patients were female, aged ≥50 years with previous comorbidities. The prevalence of hypertension (45.5-93.2%), chronic kidney disease (14.0-52.7%) and heart disease (29.0-83.8%) was higher in hospitalized vs diagnosed patients with COVID-19. Compared with 70 660 hospitalized with influenza, those admitted with COVID-19 had more respiratory complications including pneumonia and acute respiratory distress syndrome, and higher 30-day mortality (2.2-4.3% vs 6.32-24.6%).<h4>Conclusion</h4>Compared with influenza, COVID-19 is a more severe disease, leading to more complications and higher mortality.",,pdf:https://academic.oup.com/rheumatology/article-pdf/60/SI/SI37/40544680/keab250.pdf; doi:https://doi.org/10.1093/rheumatology/keab250; html:https://europepmc.org/articles/PMC7989171; pdf:https://europepmc.org/articles/PMC7989171?pdf=render
 38783292,https://doi.org/10.1186/s12939-024-02198-0,"Discrimination, disadvantage and disempowerment during COVID-19: a qualitative intrasectional analysis of the lived experiences of an ethnically diverse healthcare workforce in the United Kingdom.","Gogoi M, Qureshi I, Chaloner J, Al-Oraibi A, Reilly H, Wobi F, Agbonmwandolor JO, Ekezie W, Hassan O, Lal Z, Kapilashrami A, Nellums L, Pareek M, UK-REACH Study Collaborative Group Members.",,International journal for equity in health,2024,2024-05-23,Y,Discrimination; Healthcare Workers; Disadvantage; Disempowerment; Covid-19 Pandemic; Intersectionality; Intrasectionalism,,,"<h4>Background</h4>Healthcare workers (HCWs) in the United Kingdom (UK) have faced many challenges during the COVID-19 pandemic, some of these arising out of their social positions. Existing literature explicating these challenges (e.g., lack of appropriate PPE, redeployment, understaffing) have highlighted inequities in how these have been experienced by HCWs based on ethnicity, gender or, job role. In this paper, we move a step ahead and examine how the intersection of these social positions have impacted HCWs' experiences of challenges during the pandemic.<h4>Methods</h4>We collected qualitative data, using interviews and focus groups, from 164 HCWs from different ethnicities, gender, job roles, migration statuses, and regions in the United Kingdom (UK) between December 2020 and July 2021. Interviews and focus groups were conducted online or by telephone, and recorded with participants' permission. Recordings were transcribed and a hybrid thematic analytical approach integrating inductive data-driven codes with deductive ones informed by an intersectional framework was adopted to analyse the transcripts.<h4>Results</h4>Thematic analysis of transcripts identified disempowerment, disadvantage and, discrimination as the three main themes around which HCWs' experiences of challenges were centred, based on their intersecting identities (e.g., ethnicity gender, and/or migration status). Our analysis also acknowledges that disadvantages faced by HCWs were linked to systemic and structural factors at the micro, meso and macro ecosystemic levels. This merging of analysis which is grounded in intersectionality and considers the ecosystemic levels has been termed as 'intrasectionalism'.<h4>Discussion</h4>Our research demonstrates how an intrasectional lens can help better understand how different forms of mutually reinforcing inequities exist at all levels within the healthcare workforce and how these impact HCWs from certain backgrounds who face greater disadvantage, discrimination and disempowerment, particularly during times of crisis like the COVID-19 pandemic.",,pdf:https://equityhealthj.biomedcentral.com/counter/pdf/10.1186/s12939-024-02198-0; doi:https://doi.org/10.1186/s12939-024-02198-0; html:https://europepmc.org/articles/PMC11118759; pdf:https://europepmc.org/articles/PMC11118759?pdf=render
 33203640,https://doi.org/10.1136/bmjopen-2020-043828,"Estimated impact of the COVID-19 pandemic on cancer services and excess 1-year mortality in people with cancer and multimorbidity: near real-time data on cancer care, cancer deaths and a population-based cohort study.","Lai AG, Pasea L, Banerjee A, Hall G, Denaxas S, Chang WH, Katsoulis M, Williams B, Pillay D, Noursadeghi M, Linch D, Hughes D, Forster MD, Turnbull C, Fitzpatrick NK, Boyd K, Foster GR, Enver T, Nafilyan V, Humberstone B, Neal RD, Cooper M, Jones M, Pritchard-Jones K, Sullivan R, Davie C, Lawler M, Hemingway H.",,BMJ open,2020,2020-11-17,Y,Oncology; Health Informatics; Covid-19,,,"<h4>Objectives</h4>To estimate the impact of the COVID-19 pandemic on cancer care services and overall (direct and indirect) excess deaths in people with cancer.<h4>Methods</h4>We employed near real-time weekly data on cancer care to determine the adverse effect of the pandemic on cancer services. We also used these data, together with national death registrations until June 2020 to model deaths, in excess of background (pre-COVID-19) mortality, in people with cancer. Background mortality risks for 24 cancers with and without COVID-19-relevant comorbidities were obtained from population-based primary care cohort (Clinical Practice Research Datalink) on 3 862 012 adults in England.<h4>Results</h4>Declines in urgent referrals (median=-70.4%) and chemotherapy attendances (median=-41.5%) to a nadir (lowest point) in the pandemic were observed. By 31 May, these declines have only partially recovered; urgent referrals (median=-44.5%) and chemotherapy attendances (median=-31.2%). There were short-term excess death registrations for cancer (without COVID-19), with peak relative risk (RR) of 1.17 at week ending on 3 April. The peak RR for all-cause deaths was 2.1 from week ending on 17 April. Based on these findings and recent literature, we modelled 40% and 80% of cancer patients being affected by the pandemic in the long-term. At 40% affected, we estimated 1-year total (direct and indirect) excess deaths in people with cancer as between 7165 and 17 910, using RRs of 1.2 and 1.5, respectively, where 78% of excess deaths occured in patients with ≥1 comorbidity.<h4>Conclusions</h4>Dramatic reductions were detected in the demand for, and supply of, cancer services which have not fully recovered with lockdown easing. These may contribute, over a 1-year time horizon, to substantial excess mortality among people with cancer and multimorbidity. It is urgent to understand how the recovery of general practitioner, oncology and other hospital services might best mitigate these long-term excess mortality risks.",,pdf:https://bmjopen.bmj.com/content/bmjopen/10/11/e043828.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-043828; html:https://europepmc.org/articles/PMC7674020; pdf:https://europepmc.org/articles/PMC7674020?pdf=render
 35476839,https://doi.org/10.1371/journal.pone.0266967,"Healthcare contacts with self-harm during COVID-19: An e-cohort whole-population-based study using individual-level linked routine electronic health records in Wales, UK, 2016-March 2021.","DelPozo-Banos M, Lee SC, Friedmann Y, Akbari A, Torabi F, Lloyd K, Lyons RA, John A.",,PloS one,2022,2022-04-27,Y,,,,"<h4>Introduction</h4>Reduced rates of help seeking by those who self-harmed during the COVID-19 pandemic have been reported.<h4>Objectives</h4>To understand changes in healthcare service contacts for self-harm during the COVID-19 pandemic across primary, emergency and secondary care.<h4>Methods</h4>This retrospective cohort study used routine electronic healthcare data for Wales, United Kingdom, from 2016 to March 14, 2021. Population-based data from primary care, emergency departments and hospital admissions were linked at individual-level. All Welsh residents aged ≥10 years over the study period were included in the study. Primary, emergency and secondary care contacts with self-harm at any time between 2016 and March 14, 2021 were identified. Outcomes were counts, incidence, prevalence and proportion of self-harm contacts relative to all contacts in each and all settings, as well as the proportion of people contacting one or more settings with self-harm. Weekly trends were modelled using generalised estimated equations, with differences between 2020 (to March 2021) and comparison years 2016-2018 (to March 2017-2019) quantified using difference in differences, from which mean rate of odds ratios (μROR) across years was reported.<h4>Results</h4>The study included 3,552,210 individuals over the study period. Self-harm contacts reduced across services in March and December 2020 compared to previous years. Primary care contacts with self-harm reduced disproportionately compared to non-self-harm contacts (μROR = 0.7, p<0.05), while their proportion increased in emergency departments during April 2020 (μROR = 1.3, p<0.05 in 2/3 comparison years) and hospital admissions during April-May 2020 (μROR = 1.2, p<0.05 in 2/3 comparison years). Despite this, those who self-harmed in April 2020 were more likely to be seen in primary care than other settings compared to previous years (μROR = 1.2, p<0.05). A lower proportion of those with self-harm contacts in emergency departments were subsequently admitted to hospital in December 2020 compared to previous years (μROR = 0.5, p<0.05).<h4>Conclusions</h4>These findings suggest that those who self-harmed during the COVID-19 pandemic may have been less likely to seek help, and those who did so faced more stringent criteria for admission. Communications encouraging those who self-harm to seek help during pandemics may be beneficial. However, this needs to be supported by maintained provision of mental health services.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0266967&type=printable; doi:https://doi.org/10.1371/journal.pone.0266967; html:https://europepmc.org/articles/PMC9045644; pdf:https://europepmc.org/articles/PMC9045644?pdf=render
 38747160,https://doi.org/10.1111/acel.14195,Proteomic aging clock (PAC) predicts age-related outcomes in middle-aged and older adults.,"Kuo CL, Chen Z, Liu P, Pilling LC, Atkins JL, Fortinsky RH, Kuchel GA, Diniz BS.",,Aging cell,2024,2024-05-15,Y,Leukocyte Telomere Length; Phenoage; Accelerated Biological Aging; Uk Biobank Pharma Proteomics Project; Biological Age Deviation; Composite Aging Biomarkers; Bioage,,,"Beyond mere prognostication, optimal biomarkers of aging provide insights into qualitative and quantitative features of biological aging and might, therefore, offer useful information for the testing and, ultimately, clinical use of gerotherapeutics. We aimed to develop a proteomic aging clock (PAC) for all-cause mortality risk as a proxy of biological age. Data were from the UK Biobank Pharma Proteomics Project, including 53,021 participants aged between 39 and 70 years and 2923 plasma proteins assessed using the Olink Explore 3072 assay®. 10.9% of the participants died during a mean follow-up of 13.3 years, with the mean age at death of 70.1 years. The Spearman correlation between PAC proteomic age and chronological age was 0.77. PAC showed robust age-adjusted associations and predictions for all-cause mortality and the onset of various diseases in general and disease-free participants. The proteins associated with PAC proteomic age deviation were enriched in several processes related to the hallmarks of biological aging. Our results expand previous findings by showing that biological age acceleration, based on PAC, strongly predicts all-cause mortality and several incident disease outcomes. Particularly, it facilitates the evaluation of risk for multiple conditions in a disease-free population, thereby, contributing to the prevention of initial diseases, which vary among individuals and may subsequently lead to additional comorbidities.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/acel.14195; doi:https://doi.org/10.1111/acel.14195; html:https://europepmc.org/articles/PMC11320350; pdf:https://europepmc.org/articles/PMC11320350?pdf=render
-39049868,https://doi.org/10.1016/j.lanepe.2024.100994,"Trends in incidence of pneumothorax in England before, during and after the COVID-19 pandemic (2017-2023): a population-based observational study.","Zhong X, Goldacre R, Morris EJA, Hallifax RJ.",,The Lancet regional health. Europe,2024,2024-07-01,Y,epidemiology; Pneumothorax; incidence; Covid,,,"<h4>Background</h4>COVID-19 is a risk factor for pneumothorax. The pandemic may have influenced healthcare-seeking behaviour for pneumothorax. This study aimed to investigate recent trends in the incidence of pneumothorax in England.<h4>Methods</h4>A population-based epidemiological study was conducted using an English national dataset of hospital admissions (Hospital Episode Statistics) from 2017 to 2023. Record-linkage was used to identify multiple admissions per person and co-morbidity. Pneumothoraces co-occurring with COVID-19 were identified by concurrent COVID-19 diagnostic coding. The pre-pandemic (January 2017-February 2020), pandemic (March-2020-February-2021) and post-pandemic periods (March 2021-March 2023) were compared.<h4>Findings</h4>From 2017 to 2023, there were 72,275 hospital admissions for spontaneous pneumothorax among 59,130 patients. Admissions showed marked variability, peaking in January 2021 when the rate of admissions was about two-thirds higher than that of the pre-pandemic level (Incidence rate ratio [IRR] 1.65, 95% CI: 1.48-1.84). However, when excluding patients with a concurrent COVID-19 diagnosis, the overall trend shifted to a reduction during the pandemic period. Post-pandemic rates were not significantly different from pre-pandemic levels (IRR = 0.96, 95% CI: 0.89-1.04). The incidence of spontaneous pneumothorax was significantly higher in males (rate ratio compared to females: 2.29, 95% CI: 2.19-2.39). However, the trends were consistent in both males and females.<h4>Interpretation</h4>This study highlights a significant peak in COVID-19 related cases but a corresponding trough in non-COVID-related cases (end 2020, early 2021). Despite a previous report of increasing incidence of (non-COVID-related) hospitalised spontaneous pneumothorax over the long-term between 1968 and 2016, we did not observe any continued increase throughout this study period, prompting further investigation into the impact of recent guidelines.<h4>Funding</h4>Authors are supported by the NIHR Oxford BRC, Li Ka Shing and Robertson Foundations, MRC, and HDR UK.",,doi:https://doi.org/10.1016/j.lanepe.2024.100994; html:https://europepmc.org/articles/PMC11267084; pdf:https://europepmc.org/articles/PMC11267084?pdf=render
 35027740,https://doi.org/10.1038/s41588-021-00996-8,Multi-ancestry fine mapping implicates OAS1 splicing in risk of severe COVID-19.,"Huffman JE, Butler-Laporte G, Khan A, Pairo-Castineira E, Drivas TG, Peloso GM, Nakanishi T, COVID-19 Host Genetics Initiative, Ganna A, Verma A, Baillie JK, Kiryluk K, Richards JB, Zeberg H.",,Nature genetics,2022,2022-01-13,Y,,,,"The OAS1/2/3 cluster has been identified as a risk locus for severe COVID-19 among individuals of European ancestry, with a protective haplotype of approximately 75 kilobases (kb) derived from Neanderthals in the chromosomal region 12q24.13. This haplotype contains a splice variant of OAS1, which occurs in people of African ancestry independently of gene flow from Neanderthals. Using trans-ancestry fine-mapping approaches in 20,779 hospitalized cases, we demonstrate that this splice variant is likely to be the SNP responsible for the association at this locus, thus strongly implicating OAS1 as an effector gene influencing COVID-19 severity.",,pdf:https://www.nature.com/articles/s41588-021-00996-8.pdf; doi:https://doi.org/10.1038/s41588-021-00996-8; html:https://europepmc.org/articles/PMC8837537; pdf:https://europepmc.org/articles/PMC8837537?pdf=render
+39049868,https://doi.org/10.1016/j.lanepe.2024.100994,"Trends in incidence of pneumothorax in England before, during and after the COVID-19 pandemic (2017-2023): a population-based observational study.","Zhong X, Goldacre R, Morris EJA, Hallifax RJ.",,The Lancet regional health. Europe,2024,2024-07-01,Y,epidemiology; Pneumothorax; incidence; Covid,,,"<h4>Background</h4>COVID-19 is a risk factor for pneumothorax. The pandemic may have influenced healthcare-seeking behaviour for pneumothorax. This study aimed to investigate recent trends in the incidence of pneumothorax in England.<h4>Methods</h4>A population-based epidemiological study was conducted using an English national dataset of hospital admissions (Hospital Episode Statistics) from 2017 to 2023. Record-linkage was used to identify multiple admissions per person and co-morbidity. Pneumothoraces co-occurring with COVID-19 were identified by concurrent COVID-19 diagnostic coding. The pre-pandemic (January 2017-February 2020), pandemic (March-2020-February-2021) and post-pandemic periods (March 2021-March 2023) were compared.<h4>Findings</h4>From 2017 to 2023, there were 72,275 hospital admissions for spontaneous pneumothorax among 59,130 patients. Admissions showed marked variability, peaking in January 2021 when the rate of admissions was about two-thirds higher than that of the pre-pandemic level (Incidence rate ratio [IRR] 1.65, 95% CI: 1.48-1.84). However, when excluding patients with a concurrent COVID-19 diagnosis, the overall trend shifted to a reduction during the pandemic period. Post-pandemic rates were not significantly different from pre-pandemic levels (IRR = 0.96, 95% CI: 0.89-1.04). The incidence of spontaneous pneumothorax was significantly higher in males (rate ratio compared to females: 2.29, 95% CI: 2.19-2.39). However, the trends were consistent in both males and females.<h4>Interpretation</h4>This study highlights a significant peak in COVID-19 related cases but a corresponding trough in non-COVID-related cases (end 2020, early 2021). Despite a previous report of increasing incidence of (non-COVID-related) hospitalised spontaneous pneumothorax over the long-term between 1968 and 2016, we did not observe any continued increase throughout this study period, prompting further investigation into the impact of recent guidelines.<h4>Funding</h4>Authors are supported by the NIHR Oxford BRC, Li Ka Shing and Robertson Foundations, MRC, and HDR UK.",,doi:https://doi.org/10.1016/j.lanepe.2024.100994; html:https://europepmc.org/articles/PMC11267084; pdf:https://europepmc.org/articles/PMC11267084?pdf=render
 35879886,https://doi.org/10.1017/s0033291722002501,"Depression, anxiety and PTSD symptoms before and during the COVID-19 pandemic in the UK.","Young KS, Purves KL, Hübel C, Davies MR, Thompson KN, Bristow S, Krebs G, Danese A, Hirsch C, Parsons CE, Vassos E, Adey BN, Bright S, Hegemann L, Lee YT, Kalsi G, Monssen D, Mundy J, Peel AJ, Rayner C, Rogers HC, Ter Kuile A, Ward C, York K, Lin Y, Palmos AB, Schmidt U, Veale D, Nicholson TR, Pollak TA, Stevelink SAM, Moukhtarian T, Martineau AR, Holt H, Maughan B, Al-Chalabi A, Chaudhuri KR, Richardson MP, Bradley JR, Chinnery PF, Kingston N, Papadia S, Stirrups KE, Linger R, Hotopf M, Eley TC, Breen G.",,Psychological medicine,2023,2022-07-26,Y,Depression; Anxiety; Ptsd; Covid-19,,,"<h4>Background</h4>The impact of the coronavirus disease 2019 (COVID-19) pandemic on mental health is still being unravelled. It is important to identify which individuals are at greatest risk of worsening symptoms. This study aimed to examine changes in depression, anxiety and post-traumatic stress disorder (PTSD) symptoms using prospective and retrospective symptom change assessments, and to find and examine the effect of key risk factors.<h4>Method</h4>Online questionnaires were administered to 34 465 individuals (aged 16 years or above) in April/May 2020 in the UK, recruited from existing cohorts or via social media. Around one-third (<i>n</i> = 12 718) of included participants had prior diagnoses of depression or anxiety and had completed pre-pandemic mental health assessments (between September 2018 and February 2020), allowing prospective investigation of symptom change.<h4>Results</h4>Prospective symptom analyses showed small decreases in depression (PHQ-9: -0.43 points) and anxiety [generalised anxiety disorder scale - 7 items (GAD)-7: -0.33 points] and increases in PTSD (PCL-6: 0.22 points). Conversely, retrospective symptom analyses demonstrated significant large increases (PHQ-9: 2.40; GAD-7 = 1.97), with 55% reported worsening mental health since the beginning of the pandemic on a global change rating. Across both prospective and retrospective measures of symptom change, worsening depression, anxiety and PTSD symptoms were associated with prior mental health diagnoses, female gender, young age and unemployed/student status.<h4>Conclusions</h4>We highlight the effect of prior mental health diagnoses on worsening mental health during the pandemic and confirm previously reported sociodemographic risk factors. Discrepancies between prospective and retrospective measures of changes in mental health may be related to recall bias-related underestimation of prior symptom severity.",,pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/8C3760ED596F1ED8B80F729AC5E47B9B/S0033291722002501a.pdf/div-class-title-depression-anxiety-and-ptsd-symptoms-before-and-during-the-covid-19-pandemic-in-the-uk-div.pdf; doi:https://doi.org/10.1017/S0033291722002501; html:https://europepmc.org/articles/PMC10482709; pdf:https://europepmc.org/articles/PMC10482709?pdf=render
 33711543,https://doi.org/10.1016/j.jbi.2021.103728,Explainable automated coding of clinical notes using hierarchical label-wise attention networks and label embedding initialisation.,"Dong H, Suárez-Paniagua V, Whiteley W, Wu H.",,Journal of biomedical informatics,2021,2021-03-09,N,Natural Language Processing; Multi-label Classification; Deep Learning; Attention Mechanisms; Automated Medical Coding; Explainability; Label Correlation,,,"<h4>Background</h4>Diagnostic or procedural coding of clinical notes aims to derive a coded summary of disease-related information about patients. Such coding is usually done manually in hospitals but could potentially be automated to improve the efficiency and accuracy of medical coding. Recent studies on deep learning for automated medical coding achieved promising performances. However, the explainability of these models is usually poor, preventing them to be used confidently in supporting clinical practice. Another limitation is that these models mostly assume independence among labels, ignoring the complex correlations among medical codes which can potentially be exploited to improve the performance.<h4>Methods</h4>To address the issues of model explainability and label correlations, we propose a Hierarchical Label-wise Attention Network (HLAN), which aimed to interpret the model by quantifying importance (as attention weights) of words and sentences related to each of the labels. Secondly, we propose to enhance the major deep learning models with a label embedding (LE) initialisation approach, which learns a dense, continuous vector representation and then injects the representation into the final layers and the label-wise attention layers in the models. We evaluated the methods using three settings on the MIMIC-III discharge summaries: full codes, top-50 codes, and the UK NHS (National Health Service) COVID-19 (Coronavirus disease 2019) shielding codes. Experiments were conducted to compare the HLAN model and label embedding initialisation to the state-of-the-art neural network based methods, including variants of Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNNs).<h4>Results</h4>HLAN achieved the best Micro-level AUC and F<sub>1</sub> on the top-50 code prediction, 91.9% and 64.1%, respectively; and comparable results on the NHS COVID-19 shielding code prediction to other models: around 97% Micro-level AUC. More importantly, in the analysis of model explanations, by highlighting the most salient words and sentences for each label, HLAN showed more meaningful and comprehensive model interpretation compared to the CNN-based models and its downgraded baselines, HAN and HA-GRU. Label embedding (LE) initialisation significantly boosted the previous state-of-the-art model, CNN with attention mechanisms, on the full code prediction to 52.5% Micro-level F<sub>1</sub>. The analysis of the layers initialised with label embeddings further explains the effect of this initialisation approach. The source code of the implementation and the results are openly available at https://github.com/acadTags/Explainable-Automated-Medical-Coding.<h4>Conclusion</h4>We draw the conclusion from the evaluation results and analyses. First, with hierarchical label-wise attention mechanisms, HLAN can provide better or comparable results for automated coding to the state-of-the-art, CNN-based models. Second, HLAN can provide more comprehensive explanations for each label by highlighting key words and sentences in the discharge summaries, compared to the n-grams in the CNN-based models and the downgraded baselines, HAN and HA-GRU. Third, the performance of deep learning based multi-label classification for automated coding can be consistently boosted by initialising label embeddings that captures the correlations among labels. We further discuss the advantages and drawbacks of the overall method regarding its potential to be deployed to a hospital and suggest areas for future studies.",,doi:https://doi.org/10.1016/j.jbi.2021.103728; doi:https://doi.org/10.1016/j.jbi.2021.103728
 34606520,https://doi.org/10.1371/journal.pmed.1003815,"COVID-19 vaccination in Sindh Province, Pakistan: A modelling study of health impact and cost-effectiveness.","Pearson CAB, Bozzani F, Procter SR, Davies NG, Huda M, Jensen HT, Keogh-Brown M, Khalid M, Sweeney S, Torres-Rueda S, CHiL COVID-19 Working Group, CMMID COVID-19 Working Group, Eggo RM, Vassall A, Jit M.",,PLoS medicine,2021,2021-10-04,Y,,,,"<h4>Background</h4>Multiple Coronavirus Disease 2019 (COVID-19) vaccines appear to be safe and efficacious, but only high-income countries have the resources to procure sufficient vaccine doses for most of their eligible populations. The World Health Organization has published guidelines for vaccine prioritisation, but most vaccine impact projections have focused on high-income countries, and few incorporate economic considerations. To address this evidence gap, we projected the health and economic impact of different vaccination scenarios in Sindh Province, Pakistan (population: 48 million).<h4>Methods and findings</h4>We fitted a compartmental transmission model to COVID-19 cases and deaths in Sindh from 30 April to 15 September 2020. We then projected cases, deaths, and hospitalisation outcomes over 10 years under different vaccine scenarios. Finally, we combined these projections with a detailed economic model to estimate incremental costs (from healthcare and partial societal perspectives), disability-adjusted life years (DALYs), and incremental cost-effectiveness ratio (ICER) for each scenario. We project that 1 year of vaccine distribution, at delivery rates consistent with COVAX projections, using an infection-blocking vaccine at $3/dose with 70% efficacy and 2.5-year duration of protection is likely to avert around 0.9 (95% credible interval (CrI): 0.9, 1.0) million cases, 10.1 (95% CrI: 10.1, 10.3) thousand deaths, and 70.1 (95% CrI: 69.9, 70.6) thousand DALYs, with an ICER of $27.9 per DALY averted from the health system perspective. Under a broad range of alternative scenarios, we find that initially prioritising the older (65+) population generally prevents more deaths. However, unprioritised distribution has almost the same cost-effectiveness when considering all outcomes, and both prioritised and unprioritised programmes can be cost-effective for low per-dose costs. High vaccine prices ($10/dose), however, may not be cost-effective, depending on the specifics of vaccine performance, distribution programme, and future pandemic trends. The principal drivers of the health outcomes are the fitted values for the overall transmission scaling parameter and disease natural history parameters from other studies, particularly age-specific probabilities of infection and symptomatic disease, as well as social contact rates. Other parameters are investigated in sensitivity analyses. This study is limited by model approximations, available data, and future uncertainty. Because the model is a single-population compartmental model, detailed impacts of nonpharmaceutical interventions (NPIs) such as household isolation cannot be practically represented or evaluated in combination with vaccine programmes. Similarly, the model cannot consider prioritising groups like healthcare or other essential workers. The model is only fitted to the reported case and death data, which are incomplete and not disaggregated by, e.g., age. Finally, because the future impact and implementation cost of NPIs are uncertain, how these would interact with vaccination remains an open question.<h4>Conclusions</h4>COVID-19 vaccination can have a considerable health impact and is likely to be cost-effective if more optimistic vaccine scenarios apply. Preventing severe disease is an important contributor to this impact. However, the advantage of prioritising older, high-risk populations is smaller in generally younger populations. This reduction is especially true in populations with more past transmission, and if the vaccine is likely to further impede transmission rather than just disease. Those conditions are typical of many low- and middle-income countries.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003815&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003815; html:https://europepmc.org/articles/PMC8523052; pdf:https://europepmc.org/articles/PMC8523052?pdf=render
@@ -519,14 +519,14 @@ PMC9023380,https://doi.org/,Assessing the spread risk of COVID-19 associated wit
 33177070,https://doi.org/10.1136/bmj.m4262,"Accuracy of UK Rapid Test Consortium (UK-RTC) ""AbC-19 Rapid Test"" for detection of previous SARS-CoV-2 infection in key workers: test accuracy study.","Mulchandani R, Jones HE, Taylor-Phillips S, Shute J, Perry K, Jamarani S, Brooks T, Charlett A, Hickman M, Oliver I, Kaptoge S, Danesh J, Di Angelantonio E, Ades AE, Wyllie DH, EDSAB-HOME and COMPARE Investigators.",,BMJ (Clinical research ed.),2020,2020-11-11,Y,,,,"<h4>Objective</h4>To assess the accuracy of the AbC-19 Rapid Test lateral flow immunoassay for the detection of previous severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection.<h4>Design</h4>Test accuracy study.<h4>Setting</h4>Laboratory based evaluation.<h4>Participants</h4>2847 key workers (healthcare staff, fire and rescue officers, and police officers) in England in June 2020 (268 with a previous polymerase chain reaction (PCR) positive result (median 63 days previously), 2579 with unknown previous infection status); and 1995 pre-pandemic blood donors.<h4>Main outcome measures</h4>AbC-19 sensitivity and specificity, estimated using known negative (pre-pandemic) and known positive (PCR confirmed) samples as reference standards and secondly using the Roche Elecsys anti-nucleoprotein assay, a highly sensitive laboratory immunoassay, as a reference standard in samples from key workers.<h4>Results</h4>Test result bands were often weak, with positive/negative discordance by three trained laboratory staff for 3.9% of devices. Using consensus readings, for known positive and negative samples sensitivity was 92.5% (95% confidence interval 88.8% to 95.1%) and specificity was 97.9% (97.2% to 98.4%). Using an immunoassay reference standard, sensitivity was 94.2% (90.7% to 96.5%) among PCR confirmed cases but 84.7% (80.6% to 88.1%) among other people with antibodies. This is consistent with AbC-19 being more sensitive when antibody concentrations are higher, as people with PCR confirmation tended to have more severe disease whereas only 62% (218/354) of seropositive participants had had symptoms. If 1 million key workers were tested with AbC-19 and 10% had actually been previously infected, 84 700 true positive and 18 900 false positive results would be projected. The probability that a positive result was correct would be 81.7% (76.8% to 85.8%).<h4>Conclusions</h4>AbC-19 sensitivity was lower among unselected populations than among PCR confirmed cases of SARS-CoV-2, highlighting the scope for overestimation of assay performance in studies involving only PCR confirmed cases, owing to ""spectrum bias."" Assuming that 10% of the tested population have had SARS-CoV-2 infection, around one in five key workers testing positive with AbC-19 would be false positives.<h4>Study registration</h4>ISRCTN 56609224.",,pdf:https://www.bmj.com/content/bmj/371/bmj.m4262.full.pdf; doi:https://doi.org/10.1136/bmj.m4262; html:https://europepmc.org/articles/PMC7656121; pdf:https://europepmc.org/articles/PMC7656121?pdf=render
 34518162,https://doi.org/10.1136/bjophthalmol-2021-319383,Predicting the immediate impact of national lockdown on neovascular age-related macular degeneration and associated visual morbidity: an INSIGHT Health Data Research Hub for Eye Health report.,"Mollan SP, Fu DJ, Chuo CY, Gannon JG, Lee WH, Hopkins JJ, Hughes C, Denniston AK, Keane PA, Cantrell R.",,The British journal of ophthalmology,2023,2021-09-13,Y,Clinical Trial; Neovascularisation; Covid-19,,,"<h4>Objective</h4>Predicting the impact of neovascular age-related macular degeneration (nAMD) service disruption on visual outcomes following national lockdown in the UK to contain SARS-CoV-2.<h4>Methods and analysis</h4>This retrospective cohort study includes deidentified data from 2229 UK patients from the INSIGHT Health Data Research digital hub. We forecasted the number of treatment-naïve nAMD patients requiring anti-vascular endothelial growth factor (anti-VEGF) initiation during UK lockdown (16 March 2020 through 31 July 2020) at Moorfields Eye Hospital (MEH) and University Hospitals Birmingham (UHB). Best-measured visual acuity (VA) changes without anti-VEGF therapy were predicted using post hoc analysis of Minimally Classic/Occult Trial of the Anti-VEGF Antibody Ranibizumab in the Treatment of Neovascular AMD trial sham-control arm data (n=238).<h4>Results</h4>At our centres, 376 patients were predicted to require anti-VEGF initiation during lockdown (MEH: 325; UHB: 51). Without treatment, mean VA was projected to decline after 12 months. The proportion of eyes in the MEH cohort predicted to maintain the key positive visual outcome of ≥70 ETDRS letters (Snellen equivalent 6/12) fell from 25.5% at baseline to 5.8% at 12 months (UHB: 9.8%-7.8%). Similarly, eyes with VA <25 ETDRS letters (6/96) were predicted to increase from 4.3% to 14.2% at MEH (UHB: 5.9%-7.8%) after 12 months without treatment.<h4>Conclusions</h4>Here, we demonstrate how combining data from a recently founded national digital health data repository with historical industry-funded clinical trial data can enhance predictive modelling in nAMD. The demonstrated detrimental effects of prolonged treatment delay should incentivise healthcare providers to support nAMD patients accessing care in safe environments.<h4>Trial registration number</h4>NCT00056836.",,pdf:https://discovery.ucl.ac.uk/10164981/1/267.full.pdf; doi:https://doi.org/10.1136/bjophthalmol-2021-319383; html:https://europepmc.org/articles/PMC9887382; pdf:https://europepmc.org/articles/PMC9887382?pdf=render
 36526323,https://doi.org/10.1136/bmjopen-2022-068252,"Identification of risk factors associated with prolonged hospital stay following primary knee replacement surgery: a retrospective, longitudinal observational study.","Wilson R, Margelyte R, Redaniel MT, Eyles E, Jones T, Penfold C, Blom A, Elliott A, Harper A, Keen T, Pitt M, Judge A.",,BMJ open,2022,2022-12-16,Y,Knee; Rheumatology; Statistics & Research Methods; Orthopaedic & Trauma Surgery; Adult Orthopaedics,,,"<h4>Objectives</h4>To identify risk factors associated with prolonged length of hospital stay and staying in hospital longer than medically necessary following primary knee replacement surgery.<h4>Design</h4>Retrospective, longitudinal observational study.<h4>Setting</h4>Elective knee replacement surgeries between 2016 and 2019 were identified using routinely collected data from an NHS Trust in England.<h4>Participants</h4>There were 2295 knee replacement patients with complete data included in analysis. The mean age was 68 (SD 11) and 60% were female.<h4>Outcome measures</h4>We assessed a binary length of stay outcome (>7 days), a continuous length of stay outcome (≤30 days) and a binary measure of whether patients remained in hospital when they were medically fit for discharge.<h4>Results</h4>The mean length of stay was 5.0 days (SD 3.9), 15.4% of patients were in hospital for >7 days and 7.1% remained in hospital when they were medically fit for discharge. Longer length of stay was associated with older age (<i>b=</i>0.08, 95% CI 0.07 to 0.09), female sex (<i>b</i>=0.36, 95% CI 0.06 to 0.67), high deprivation (<i>b</i>=0.98, 95% CI 0.47 to 1.48) and more comorbidities (<i>b</i>=2.48, 95% CI 0.15 to 4.81). Remaining in hospital beyond being medically fit for discharge was associated with older age (OR=1.07, 95% CI 1.05 to 1.09), female sex (OR=1.71, 95% CI 1.19 to 2.47) and high deprivation (OR=2.27, 95% CI 1.27 to 4.06).<h4>Conclusions</h4>The regression models could be used to identify which patients are likely to occupy hospital beds for longer. This could be helpful in scheduling operations to aid hospital efficiency by planning these patients' operations for when the hospital is less busy.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/12/e068252.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-068252; html:https://europepmc.org/articles/PMC9764602; pdf:https://europepmc.org/articles/PMC9764602?pdf=render
-37124165,https://doi.org/10.1016/j.ufug.2023.127934,"Effects of the onset of the COVID-19 pandemic restrictions on park crime in London, England: An interrupted time series analysis.","Hajna S, Cummins S.",,Urban forestry & urban greening,2023,2023-04-11,Y,Parks; Crimes; Covid-19,,,"<h4>Introduction</h4>Park crimes may have increased during the COVID-19 pandemic as a result of lockdowns that limited the number of capable guardians in public spaces. Despite this, the impacts of the lockdowns on park crimes remain unknown. To help us understand the societal impacts of policies implemented during this period, we assessed how the onset of the COVID-19 restrictions impacted urban park crime levels in London, England.<h4>Methods</h4>We identified crimes that occurred in publicly accessible parks and gardens in the Greater London Authority (England, UK) between March 1, 2019 and February 28, 2021 by overlaying open-access crime data with greenspace data supplied by the Greater Information for Greater London service. Using interrupted time series analyses, we estimated seasonality-adjusted associations between the onset of COVID-19 restrictions and park crimes.<h4>Results</h4>Overall (1565.7, 95% confidence intervals [CI] 1021.9 to 2109.5) and antisocial behaviour crimes (1772.7, 95% CI 823.6-2721.7) increased in London parks during the first full month of COVID-19 restrictions (April 2020). There were no notable trends in park crimes in London prior to the onset of restrictions, but overall and antisocial behaviour crimes decreased after the onset of restrictions at a rate of 156.4 (95% CI -220.25 to -92.51) and 164.7 (95% CI -280.68 to -48.74) crimes/months, respectively.<h4>Conclusions</h4>Overall park crimes increased during the first full month of the COVID-19 restrictions, largely driven by an increase in antisocial behaviours. Additional research is needed to identify the specific misdemeanours that accounted for this rise in antisocial behaviours and to investigate their downstream impacts (e.g. increases in policing costs or decreases in perceived park safety).",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10088280; doi:https://doi.org/10.1016/j.ufug.2023.127934; html:https://europepmc.org/articles/PMC10088280; pdf:https://europepmc.org/articles/PMC10088280?pdf=render
 34810237,https://doi.org/10.1136/thoraxjnl-2021-217629,Prospective validation of the 4C prognostic models for adults hospitalised with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol.,"Knight SR, Gupta RK, Ho A, Pius R, Buchan I, Carson G, Drake TM, Dunning J, Fairfield CJ, Gamble C, Green CA, Halpin S, Hardwick HE, Holden KA, Horby PW, Jackson C, Mclean KA, Merson L, Nguyen-Van-Tam JS, Norman L, Olliaro PL, Pritchard MG, Russell CD, Shaw CA, Sheikh A, Solomon T, Sudlow C, Swann OV, Turtle LCW, Openshaw PJM, Baillie JK, Docherty A, Semple MG, Noursadeghi M, Harrison EM, ISARIC Coronavirus Clinical Characterisation Consortium (ISARIC4C) Investigators, ISARIC4C investigators.",,Thorax,2022,2021-11-22,Y,Covid-19,,,"<h4>Purpose</h4>To prospectively validate two risk scores to predict mortality (4C Mortality) and in-hospital deterioration (4C Deterioration) among adults hospitalised with COVID-19.<h4>Methods</h4>Prospective observational cohort study of adults (age ≥18 years) with confirmed or highly suspected COVID-19 recruited into the International Severe Acute Respiratory and emerging Infections Consortium (ISARIC) WHO Clinical Characterisation Protocol UK (CCP-UK) study in 306 hospitals across England, Scotland and Wales. Patients were recruited between 27 August 2020 and 17 February 2021, with at least 4 weeks follow-up before final data extraction. The main outcome measures were discrimination and calibration of models for in-hospital deterioration (defined as any requirement of ventilatory support or critical care, or death) and mortality, incorporating predefined subgroups.<h4>Results</h4>76 588 participants were included, of whom 27 352 (37.4%) deteriorated and 12 581 (17.4%) died. Both the 4C Mortality (0.78 (0.77 to 0.78)) and 4C Deterioration scores (pooled C-statistic 0.76 (95% CI 0.75 to 0.77)) demonstrated consistent discrimination across all nine National Health Service regions, with similar performance metrics to the original validation cohorts. Calibration remained stable (4C Mortality: pooled slope 1.09, pooled calibration-in-the-large 0.12; 4C Deterioration: 1.00, -0.04), with no need for temporal recalibration during the second UK pandemic wave of hospital admissions.<h4>Conclusion</h4>Both 4C risk stratification models demonstrate consistent performance to predict clinical deterioration and mortality in a large prospective second wave validation cohort of UK patients. Despite recent advances in the treatment and management of adults hospitalised with COVID-19, both scores can continue to inform clinical decision making.<h4>Trial registration number</h4>ISRCTN66726260.",,pdf:https://thorax.bmj.com/content/thoraxjnl/77/6/606.full.pdf; doi:https://doi.org/10.1136/thoraxjnl-2021-217629; html:https://europepmc.org/articles/PMC8610617; pdf:https://europepmc.org/articles/PMC8610617?pdf=render
+37124165,https://doi.org/10.1016/j.ufug.2023.127934,"Effects of the onset of the COVID-19 pandemic restrictions on park crime in London, England: An interrupted time series analysis.","Hajna S, Cummins S.",,Urban forestry & urban greening,2023,2023-04-11,Y,Parks; Crimes; Covid-19,,,"<h4>Introduction</h4>Park crimes may have increased during the COVID-19 pandemic as a result of lockdowns that limited the number of capable guardians in public spaces. Despite this, the impacts of the lockdowns on park crimes remain unknown. To help us understand the societal impacts of policies implemented during this period, we assessed how the onset of the COVID-19 restrictions impacted urban park crime levels in London, England.<h4>Methods</h4>We identified crimes that occurred in publicly accessible parks and gardens in the Greater London Authority (England, UK) between March 1, 2019 and February 28, 2021 by overlaying open-access crime data with greenspace data supplied by the Greater Information for Greater London service. Using interrupted time series analyses, we estimated seasonality-adjusted associations between the onset of COVID-19 restrictions and park crimes.<h4>Results</h4>Overall (1565.7, 95% confidence intervals [CI] 1021.9 to 2109.5) and antisocial behaviour crimes (1772.7, 95% CI 823.6-2721.7) increased in London parks during the first full month of COVID-19 restrictions (April 2020). There were no notable trends in park crimes in London prior to the onset of restrictions, but overall and antisocial behaviour crimes decreased after the onset of restrictions at a rate of 156.4 (95% CI -220.25 to -92.51) and 164.7 (95% CI -280.68 to -48.74) crimes/months, respectively.<h4>Conclusions</h4>Overall park crimes increased during the first full month of the COVID-19 restrictions, largely driven by an increase in antisocial behaviours. Additional research is needed to identify the specific misdemeanours that accounted for this rise in antisocial behaviours and to investigate their downstream impacts (e.g. increases in policing costs or decreases in perceived park safety).",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10088280; doi:https://doi.org/10.1016/j.ufug.2023.127934; html:https://europepmc.org/articles/PMC10088280; pdf:https://europepmc.org/articles/PMC10088280?pdf=render
 33087179,https://doi.org/10.1186/s12916-020-01790-9,Reconstructing the early global dynamics of under-ascertained COVID-19 cases and infections.,"Russell TW, Golding N, Hellewell J, Abbott S, Wright L, Pearson CAB, van Zandvoort K, Jarvis CI, Gibbs H, Liu Y, Eggo RM, Edmunds WJ, Kucharski AJ, CMMID COVID-19 working group.",,BMC medicine,2020,2020-10-22,Y,Surveillance; Situational Awareness; Under-reporting; Case Ascertainment; Outbreak Analysis; Covid-19; Sars-cov-2,,,"<h4>Background</h4>Asymptomatic or subclinical SARS-CoV-2 infections are often unreported, which means that confirmed case counts may not accurately reflect underlying epidemic dynamics. Understanding the level of ascertainment (the ratio of confirmed symptomatic cases to the true number of symptomatic individuals) and undetected epidemic progression is crucial to informing COVID-19 response planning, including the introduction and relaxation of control measures. Estimating case ascertainment over time allows for accurate estimates of specific outcomes such as seroprevalence, which is essential for planning control measures.<h4>Methods</h4>Using reported data on COVID-19 cases and fatalities globally, we estimated the proportion of symptomatic cases (i.e. any person with any of fever ≥ 37.5 °C, cough, shortness of breath, sudden onset of anosmia, ageusia or dysgeusia illness) that were reported in 210 countries and territories, given those countries had experienced more than ten deaths. We used published estimates of the baseline case fatality ratio (CFR), which was adjusted for delays and under-ascertainment, then calculated the ratio of this baseline CFR to an estimated local delay-adjusted CFR to estimate the level of under-ascertainment in a particular location. We then fit a Bayesian Gaussian process model to estimate the temporal pattern of under-ascertainment.<h4>Results</h4>Based on reported cases and deaths, we estimated that, during March 2020, the median percentage of symptomatic cases detected across the 84 countries which experienced more than ten deaths ranged from 2.4% (Bangladesh) to 100% (Chile). Across the ten countries with the highest number of total confirmed cases as of 6 July 2020, we estimated that the peak number of symptomatic cases ranged from 1.4 times (Chile) to 18 times (France) larger than reported. Comparing our model with national and regional seroprevalence data where available, we find that our estimates are consistent with observed values. Finally, we estimated seroprevalence for each country. As of 7 June, our seroprevalence estimates range from 0% (many countries) to 13% (95% CrI 5.6-24%) (Belgium).<h4>Conclusions</h4>We found substantial under-ascertainment of symptomatic cases, particularly at the peak of the first wave of the SARS-CoV-2 pandemic, in many countries. Reported case counts will therefore likely underestimate the rate of outbreak growth initially and underestimate the decline in the later stages of an epidemic. Although there was considerable under-reporting in many locations, our estimates were consistent with emerging serological data, suggesting that the proportion of each country's population infected with SARS-CoV-2 worldwide is generally low.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-020-01790-9; doi:https://doi.org/10.1186/s12916-020-01790-9; html:https://europepmc.org/articles/PMC7577796; pdf:https://europepmc.org/articles/PMC7577796?pdf=render
 34870256,https://doi.org/10.1016/j.lanepe.2021.100267,Optimising health and economic impacts of COVID-19 vaccine prioritisation strategies in the WHO European Region: a mathematical modelling study.,"Liu Y, Sandmann FG, Barnard RC, Pearson CAB, Pastore R, Pebody R, Flasche S, Jit M.",,The Lancet regional health. Europe,2022,2021-11-30,Y,Europe; Health Economics; Mathematical Modelling; Policy Evaluation; Vaccine Policy; Multicountry Analysis; Covid-19,,,"<h4>Background</h4>Countries in the World Health Organization (WHO) European Region differ in terms of the COVID-19 vaccine supply conditions. We evaluated the health and economic impact of different age-based vaccine prioritisation strategies across this demographically and socio-economically diverse region.<h4>Methods</h4>We fitted age-specific compartmental models to the reported daily COVID-19 mortality in 2020 to inform the immunity level before vaccine roll-out. Models capture country-specific differences in population structures, contact patterns, epidemic history, life expectancy, and GDP per capita.We examined four strategies that prioritise: all adults (V+), younger (20-59 year-olds) followed by older adults (60+) (V20), older followed by younger adults (V60), and the oldest adults (75+) (V75) followed by incrementally younger age groups. We explored four roll-out scenarios (R1-4) - the slowest scenario (R1) reached 30% coverage by December 2022 and the fastest (R4) 80% by December 2021. Five decision-making metrics were summarised over 2021-22: mortality, morbidity, and losses in comorbidity-adjusted life expectancy, comorbidity- and quality-adjusted life years, and human capital. Six vaccine profiles were tested - the highest performing vaccine has 95% efficacy against both infection and disease, and the lowest 50% against diseases and 0% against infection.<h4>Findings</h4>Of the 20 decision-making metrics and roll-out scenario combinations, the same optimal strategy applied to all countries in only one combination; V60 was more or similarly desirable than V75 in 19 combinations. Of the 38 countries with fitted models, 11-37 countries had variable optimal strategies by decision-making metrics or roll-out scenarios. There are greater benefits in prioritising older adults when roll-out is slow and when vaccine profiles are less favourable.<h4>Interpretation</h4>The optimal age-based vaccine prioritisation strategies were sensitive to country characteristics, decision-making metrics, and roll-out speeds. A prioritisation strategy involving more age-based stages (V75) does not necessarily lead to better health and economic outcomes than targeting broad age groups (V60). Countries expecting a slow vaccine roll-out may particularly benefit from prioritising older adults.<h4>Funding</h4>World Health Organization, Bill and Melinda Gates Foundation, the Medical Research Council (United Kingdom), the National Institute of Health Research (United Kingdom), the European Commission, the Foreign, Commonwealth and Development Office (United Kingdom), Wellcome Trust.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8288152; doi:https://doi.org/10.1016/j.lanepe.2021.100267; html:https://europepmc.org/articles/PMC8629724; pdf:https://europepmc.org/articles/PMC8629724?pdf=render
 35671273,https://doi.org/10.1371/journal.pone.0268837,Optimising the balance of acute and intermediate care capacity for the complex discharge pathway: Computer modelling study during COVID-19 recovery in England.,"Onen-Dumlu Z, Harper AL, Forte PG, Powell AL, Pitt M, Vasilakis C, Wood RM.",,PloS one,2022,2022-06-07,Y,,,,"<h4>Objectives</h4>While there has been significant research on the pressures facing acute hospitals during the COVID-19 pandemic, there has been less interest in downstream community services which have also been challenged in meeting demand. This study aimed to estimate the theoretical cost-optimal capacity requirement for 'step down' intermediate care services within a major healthcare system in England, at a time when considerable uncertainty remained regarding vaccination uptake and the easing of societal restrictions.<h4>Methods</h4>Demand for intermediate care was projected using an epidemiological model (for COVID-19 demand) and regressing upon public mobility (for non-COVID-19 demand). These were inputted to a computer simulation model of patient flow from acute discharge readiness to bedded and home-based Discharge to Assess (D2A) intermediate care services. Cost-optimal capacity was defined as that which yielded the lowest total cost of intermediate care provision and corresponding acute discharge delays.<h4>Results</h4>Increased intermediate care capacity is likely to bring about lower system-level costs, with the additional D2A investment more than offset by substantial reductions in costly acute discharge delays (leading also to improved patient outcome and experience). Results suggest that completely eliminating acute 'bed blocking' is unlikely economical (requiring large amounts of downstream capacity), and that health systems should instead target an appropriate tolerance based upon the specific characteristics of the pathway.<h4>Conclusions</h4>Computer modelling can be a valuable asset for determining optimal capacity allocation along the complex care pathway. With results supporting a Business Case for increased downstream capacity, this study demonstrates how modelling can be applied in practice and provides a blueprint for use alongside the freely-available model code.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0268837&type=printable; doi:https://doi.org/10.1371/journal.pone.0268837; html:https://europepmc.org/articles/PMC9173611; pdf:https://europepmc.org/articles/PMC9173611?pdf=render
 34161326,https://doi.org/10.1371/journal.pcbi.1009121,Contrasting factors associated with COVID-19-related ICU admission and death outcomes in hospitalised patients by means of Shapley values.,"Cavallaro M, Moiz H, Keeling MJ, McCarthy ND.",,PLoS computational biology,2021,2021-06-23,Y,,,,"Identification of those at greatest risk of death due to the substantial threat of COVID-19 can benefit from novel approaches to epidemiology that leverage large datasets and complex machine-learning models, provide data-driven intelligence, and guide decisions such as intensive-care unit admission (ICUA). The objective of this study is two-fold, one substantive and one methodological: substantively to evaluate the association of demographic and health records with two related, yet different, outcomes of severe COVID-19 (viz., death and ICUA); methodologically to compare interpretations based on logistic regression and on gradient-boosted decision tree (GBDT) predictions interpreted by means of the Shapley impacts of covariates. Very different association of some factors, e.g., obesity and chronic respiratory diseases, with death and ICUA may guide review of practice. Shapley explanation of GBDTs identified varying effects of some factors among patients, thus emphasising the importance of individual patient assessment. The results of this study are also relevant for the evaluation of complex automated clinical decision systems, which should optimise prediction scores whilst remaining interpretable to clinicians and mitigating potential biases.",,pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009121&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1009121; html:https://europepmc.org/articles/PMC8259985; pdf:https://europepmc.org/articles/PMC8259985?pdf=render
-37080124,https://doi.org/10.1016/j.seizure.2023.04.006,COVID-19 vaccination uptake in people with epilepsy in wales.,"Strafford H, Lacey AS, Hollinghurst J, Akbari A, Watkins A, Paterson J, Jennings D, Lyons RA, Powell HR, Kerr MP, Chin RW, Pickrell WO.",,Seizure,2023,2023-04-06,Y,"Epilepsy; Vaccination; Data Linkage; Electronic Health Records; Pandemic, Covid-19",,,"<h4>Purpose</h4>People with epilepsy (PWE) are at increased risk of severe COVID-19. Assessing COVID-19 vaccine uptake is therefore important. We compared COVID-19 vaccination uptake for PWE in Wales with a matched control cohort.<h4>Methods</h4>We performed a retrospective, population, cohort study using linked, anonymised, Welsh electronic health records within the Secure Anonymised Information Linkage (SAIL) Databank (Welsh population=3.1 million).We identified PWE in Wales between 1st March 2020 and 31st December 2021 and created a control cohort using exact 5:1 matching (sex, age and socioeconomic status). We recorded 1st, 2nd and booster COVID-19 vaccinations.<h4>Results</h4>There were 25,404 adults with epilepsy (127,020 controls). 23,454 (92.3%) had a first vaccination, 22,826 (89.9%) a second, and 17,797 (70.1%) a booster. Comparative figures for controls were: 112,334 (87.8%), 109,057 (85.2%) and 79,980 (62.4%).PWE had higher vaccination rates in all age, sex and socioeconomic subgroups apart from booster uptake in older subgroups. Vaccination rates were higher in older subgroups, women and less deprived areas for both cohorts. People with intellectual disability and epilepsy had higher vaccination rates when compared with controls with intellectual disability.<h4>Conclusions</h4>COVID-19 vaccination uptake for PWE in Wales was higher than that for a matched control group.",,pdf:http://www.seizure-journal.com/article/S1059131123001000/pdf; doi:https://doi.org/10.1016/j.seizure.2023.04.006; html:https://europepmc.org/articles/PMC10076248; pdf:https://europepmc.org/articles/PMC10076248?pdf=render
 34310590,https://doi.org/10.1371/journal.pcbi.1009098,Projecting contact matrices in 177 geographical regions: An update and comparison with empirical data for the COVID-19 era.,"Prem K, Zandvoort KV, Klepac P, Eggo RM, Davies NG, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Cook AR, Jit M.",,PLoS computational biology,2021,2021-07-26,Y,,,,"Mathematical models have played a key role in understanding the spread of directly-transmissible infectious diseases such as Coronavirus Disease 2019 (COVID-19), as well as the effectiveness of public health responses. As the risk of contracting directly-transmitted infections depends on who interacts with whom, mathematical models often use contact matrices to characterise the spread of infectious pathogens. These contact matrices are usually generated from diary-based contact surveys. However, the majority of places in the world do not have representative empirical contact studies, so synthetic contact matrices have been constructed using more widely available setting-specific survey data on household, school, classroom, and workplace composition combined with empirical data on contact patterns in Europe. In 2017, the largest set of synthetic contact matrices to date were published for 152 geographical locations. In this study, we update these matrices with the most recent data and extend our analysis to 177 geographical locations. Due to the observed geographic differences within countries, we also quantify contact patterns in rural and urban settings where data is available. Further, we compare both the 2017 and 2020 synthetic matrices to out-of-sample empirically-constructed contact matrices, and explore the effects of using both the empirical and synthetic contact matrices when modelling physical distancing interventions for the COVID-19 pandemic. We found that the synthetic contact matrices show qualitative similarities to the contact patterns in the empirically-constructed contact matrices. Models parameterised with the empirical and synthetic matrices generated similar findings with few differences observed in age groups where the empirical matrices have missing or aggregated age groups. This finding means that synthetic contact matrices may be used in modelling outbreaks in settings for which empirical studies have yet to be conducted.",,pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009098&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1009098; html:https://europepmc.org/articles/PMC8354454; pdf:https://europepmc.org/articles/PMC8354454?pdf=render
+37080124,https://doi.org/10.1016/j.seizure.2023.04.006,COVID-19 vaccination uptake in people with epilepsy in wales.,"Strafford H, Lacey AS, Hollinghurst J, Akbari A, Watkins A, Paterson J, Jennings D, Lyons RA, Powell HR, Kerr MP, Chin RW, Pickrell WO.",,Seizure,2023,2023-04-06,Y,"Epilepsy; Vaccination; Data Linkage; Electronic Health Records; Pandemic, Covid-19",,,"<h4>Purpose</h4>People with epilepsy (PWE) are at increased risk of severe COVID-19. Assessing COVID-19 vaccine uptake is therefore important. We compared COVID-19 vaccination uptake for PWE in Wales with a matched control cohort.<h4>Methods</h4>We performed a retrospective, population, cohort study using linked, anonymised, Welsh electronic health records within the Secure Anonymised Information Linkage (SAIL) Databank (Welsh population=3.1 million).We identified PWE in Wales between 1st March 2020 and 31st December 2021 and created a control cohort using exact 5:1 matching (sex, age and socioeconomic status). We recorded 1st, 2nd and booster COVID-19 vaccinations.<h4>Results</h4>There were 25,404 adults with epilepsy (127,020 controls). 23,454 (92.3%) had a first vaccination, 22,826 (89.9%) a second, and 17,797 (70.1%) a booster. Comparative figures for controls were: 112,334 (87.8%), 109,057 (85.2%) and 79,980 (62.4%).PWE had higher vaccination rates in all age, sex and socioeconomic subgroups apart from booster uptake in older subgroups. Vaccination rates were higher in older subgroups, women and less deprived areas for both cohorts. People with intellectual disability and epilepsy had higher vaccination rates when compared with controls with intellectual disability.<h4>Conclusions</h4>COVID-19 vaccination uptake for PWE in Wales was higher than that for a matched control group.",,pdf:http://www.seizure-journal.com/article/S1059131123001000/pdf; doi:https://doi.org/10.1016/j.seizure.2023.04.006; html:https://europepmc.org/articles/PMC10076248; pdf:https://europepmc.org/articles/PMC10076248?pdf=render
 36716318,https://doi.org/10.1371/journal.pmed.1004174,Therapeutic potential of IL6R blockade for the treatment of sepsis and sepsis-related death: A Mendelian randomisation study.,"Hamilton FW, Thomas M, Arnold D, Palmer T, Moran E, Mentzer AJ, Maskell N, Baillie K, Summers C, Hingorani A, MacGowan A, Khandaker GM, Mitchell R, Davey Smith G, Ghazal P, Timpson NJ.",,PLoS medicine,2023,2023-01-30,Y,,,,"<h4>Background</h4>Sepsis is characterised by dysregulated, life-threatening immune responses, which are thought to be driven by cytokines such as interleukin 6 (IL-6). Genetic variants in IL6R known to down-regulate IL-6 signalling are associated with improved Coronavirus Disease 2019 (COVID-19) outcomes, a finding later confirmed in randomised trials of IL-6 receptor antagonists (IL6RAs). We hypothesised that blockade of IL6R could also improve outcomes in sepsis.<h4>Methods and findings</h4>We performed a Mendelian randomisation (MR) analysis using single nucleotide polymorphisms (SNPs) in and near IL6R to evaluate the likely causal effects of IL6R blockade on sepsis (primary outcome), sepsis severity, other infections, and COVID-19 (secondary outcomes). We weighted SNPs by their effect on CRP and combined results across them in inverse variance weighted meta-analysis, proxying the effect of IL6RA. Our outcomes were measured in UK Biobank, FinnGen, the COVID-19 Host Genetics Initiative (HGI), and the GenOSept and GainS consortium. We performed several sensitivity analyses to test assumptions of our methods, including utilising variants around CRP and gp130 in a similar analysis. In the UK Biobank cohort (N = 486,484, including 11,643 with sepsis), IL6R blockade was associated with a decreased risk of our primary outcome, sepsis (odds ratio (OR) = 0.80; 95% confidence interval (CI) 0.66 to 0.96, per unit of natural log-transformed CRP decrease). The size of this effect increased with severity, with larger effects on 28-day sepsis mortality (OR = 0.74; 95% CI 0.47 to 1.15); critical care admission with sepsis (OR = 0.48, 95% CI 0.30 to 0.78) and critical care death with sepsis (OR = 0.37, 95% CI 0.14 to 0.98). Similar associations were seen with severe respiratory infection: OR for pneumonia in critical care 0.69 (95% CI 0.49 to 0.97) and for sepsis survival in critical care (OR = 0.22; 95% CI 0.04 to 1.31) in the GainS and GenOSept consortium, although this result had a large degree of imprecision. We also confirm the previously reported protective effect of IL6R blockade on severe COVID-19 (OR = 0.69, 95% CI 0.57 to 0.84) in the COVID-19 HGI, which was of similar magnitude to that seen in sepsis. Sensitivity analyses did not alter our primary results. These results are subject to the limitations and assumptions of MR, which in this case reflects interpretation of these SNP effects as causally acting through blockade of IL6R, and reflect lifetime exposure to IL6R blockade, rather than the effect of therapeutic IL6R blockade.<h4>Conclusions</h4>IL6R blockade is causally associated with reduced incidence of sepsis. Similar but imprecisely estimated results supported a causal effect also on sepsis related mortality and critical care admission with sepsis. These effects are comparable in size to the effect seen in severe COVID-19, where IL-6 receptor antagonists were shown to improve survival. These data suggest that a randomised trial of IL-6 receptor antagonists in sepsis should be considered.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004174&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004174; html:https://europepmc.org/articles/PMC9925069; pdf:https://europepmc.org/articles/PMC9925069?pdf=render
 33782396,https://doi.org/10.1038/s41467-021-22213-0,Implications of the school-household network structure on SARS-CoV-2 transmission under school reopening strategies in England.,"Munday JD, Sherratt K, Meakin S, Endo A, Pearson CAB, Hellewell J, Abbott S, Bosse NI, CMMID COVID-19 Working Group, Atkins KE, Wallinga J, Edmunds WJ, van Hoek AJ, Funk S.",,Nature communications,2021,2021-03-29,Y,,,,"In early 2020 many countries closed schools to mitigate the spread of SARS-CoV-2. Since then, governments have sought to relax the closures, engendering a need to understand associated risks. Using address records, we construct a network of schools in England connected through pupils who share households. We evaluate the risk of transmission between schools under different reopening scenarios. We show that whilst reopening select year-groups causes low risk of large-scale transmission, reopening secondary schools could result in outbreaks affecting up to 2.5 million households if unmitigated, highlighting the importance of careful monitoring and within-school infection control to avoid further school closures or other restrictions.",,pdf:https://www.nature.com/articles/s41467-021-22213-0.pdf; doi:https://doi.org/10.1038/s41467-021-22213-0; html:https://europepmc.org/articles/PMC8007691; pdf:https://europepmc.org/articles/PMC8007691?pdf=render
 39319350,https://doi.org/10.3389/fpsyt.2024.1181739,Applying neural network algorithms to ascertain reported experiences of violence in routine mental healthcare records and distributions of reports by diagnosis.,"Mason AJC, Bhavsar V, Botelle R, Chandran D, Li L, Mascio A, Sanyal J, Kadra-Scalzo G, Roberts A, Williams M, Stewart R.",,Frontiers in psychiatry,2024,2024-09-10,Y,Violence; Victimisation; Natural Language Processing; Cris; Mental Health Records,,,"<h4>Introduction</h4>Experiences of violence are important risk factors for worse outcome in people with mental health conditions; however, they are not routinely collected be mental health services, so their ascertainment depends on extraction from text fields with natural language processing (NLP) algorithms.<h4>Methods</h4>Applying previously developed neural network algorithms to routine mental healthcare records, we sought to describe the distribution of recorded violence victimisation by demographic and diagnostic characteristics. We ascertained recorded violence victimisation from the records of 60,021 patients receiving care from a large south London NHS mental healthcare provider during 2019. Descriptive and regression analyses were conducted to investigate variation by age, sex, ethnic group, and diagnostic category (ICD-10 F chapter sub-headings plus post-traumatic stress disorder (PTSD) as a specific condition).<h4>Results</h4>Patients with a mood disorder (adjusted odds ratio 1.63, 1.55-1.72), personality disorder (4.03, 3.65-4.45), schizophrenia spectrum disorder (1.84, 1.74-1.95) or PTSD (2.36, 2.08-2.69) had a significantly increased likelihood of victimisation compared to those with other mental health diagnoses. Additionally, patients from minority ethnic groups (1.10 (1.02-1.20) for Black, 1.40 (1.31-1.49) for Asian compared to White groups) had significantly higher likelihood of recorded violence victimisation. Males were significantly less likely to have reported recorded violence victimisation (0.44, 0.42-0.45) than females.<h4>Discussion</h4>We thus demonstrate the successful deployment of machine learning based NLP algorithms to ascertain important entities for outcome prediction in mental healthcare. The observed distributions highlight which sex, ethnicity and diagnostic groups had more records of violence victimisation. Further development of these algorithms could usefully capture broader experiences, such as differentiating more efficiently between witnessed, perpetrated and experienced violence and broader violence experiences like emotional abuse.",,doi:https://doi.org/10.3389/fpsyt.2024.1181739; html:https://europepmc.org/articles/PMC11420987; pdf:https://europepmc.org/articles/PMC11420987?pdf=render
@@ -534,35 +534,35 @@ PMC9023380,https://doi.org/,Assessing the spread risk of COVID-19 associated wit
 34644365,https://doi.org/10.1371/journal.pone.0258484,Cohort profile: The UK COVID-19 Public Experiences (COPE) prospective longitudinal mixed-methods study of health and well-being during the SARSCoV2 coronavirus pandemic.,"Phillips R, Taiyari K, Torrens-Burton A, Cannings-John R, Williams D, Peddle S, Campbell S, Hughes K, Gillespie D, Sellars P, Pell B, Ashfield-Watt P, Akbari A, Seage CH, Perham N, Joseph-Williams N, Harrop E, Blaxland J, Wood F, Poortinga W, Wahl-Jorgensen K, James DH, Crone D, Thomas-Jones E, Hallingberg B.",,PloS one,2021,2021-10-13,Y,,,,"Public perceptions of pandemic viral threats and government policies can influence adherence to containment, delay, and mitigation policies such as physical distancing, hygienic practices, use of physical barriers, uptake of testing, contact tracing, and vaccination programs. The UK COVID-19 Public Experiences (COPE) study aims to identify determinants of health behaviour using the Capability, Opportunity, Motivation (COM-B) model using a longitudinal mixed-methods approach. Here, we provide a detailed description of the demographic and self-reported health characteristics of the COPE cohort at baseline assessment, an overview of data collected, and plans for follow-up of the cohort. The COPE baseline survey was completed by 11,113 UK adult residents (18+ years of age). Baseline data collection started on the 13th of March 2020 (10-days before the introduction of the first national COVID-19 lockdown in the UK) and finished on the 13th of April 2020. Participants were recruited via the HealthWise Wales (HWW) research registry and through social media snowballing and advertising (Facebook®, Twitter®, Instagram®). Participants were predominantly female (69%), over 50 years of age (68%), identified as white (98%), and were living with their partner (68%). A large proportion (67%) had a college/university level education, and half reported a pre-existing health condition (50%). Initial follow-up plans for the cohort included in-depth surveys at 3-months and 12-months after the first UK national lockdown to assess short and medium-term effects of the pandemic on health behaviour and subjective health and well-being. Additional consent will be sought from participants at follow-up for data linkage and surveys at 18 and 24-months after the initial UK national lockdown. A large non-random sample was recruited to the COPE cohort during the early stages of the COVID-19 pandemic, which will enable longitudinal analysis of the determinants of health behaviour and changes in subjective health and well-being over the course of the pandemic.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0258484&type=printable; doi:https://doi.org/10.1371/journal.pone.0258484; html:https://europepmc.org/articles/PMC8513913; pdf:https://europepmc.org/articles/PMC8513913?pdf=render
 33939952,https://doi.org/10.1016/s0140-6736(21)00949-1,COVID-19 and disparities affecting ethnic minorities.,"Morales DR, Ali SN.",,"Lancet (London, England)",2021,2021-04-30,Y,,,,,,pdf:http://www.thelancet.com/article/S0140673621009491/pdf; doi:https://doi.org/10.1016/S0140-6736(21)00949-1; html:https://europepmc.org/articles/PMC9755653; pdf:https://europepmc.org/articles/PMC9755653?pdf=render
 35983770,https://doi.org/10.2807/1560-7917.es.2022.27.33.2100885,"Recording of 'COVID-19 vaccine declined': a cohort study on 57.9 million National Health Service patients' records in situ using OpenSAFELY, England, 8 December 2020 to 25 May 2021.","Curtis HJ, Inglesby P, MacKenna B, Croker R, Hulme WJ, Rentsch CT, Bhaskaran K, Mathur R, Morton CE, Bacon SC, Smith RM, Evans D, Mehrkar A, Tomlinson L, Walker AJ, Bates C, Hickman G, Ward T, Morley J, Cockburn J, Davy S, Williamson EJ, Eggo RM, Parry J, Hester F, Harper S, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Griffiths P, Fowles A, Parkes N, Evans SJ, Douglas IJ, Smeeth L, Goldacre B.",,Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin,2022,2022-08-01,Y,Vaccination; Vaccine Hesitancy; Nhs England; Covid-19; Sars-cov-2,,,"BackgroundPriority patients in England were offered COVID-19 vaccination by mid-April 2021. Codes in clinical record systems can denote the vaccine being declined.AimWe describe records of COVID-19 vaccines being declined, according to clinical and demographic factors.MethodsWith the approval of NHS England, we conducted a retrospective cohort study between 8 December 2020 and 25 May 2021 with primary care records for 57.9 million patients using OpenSAFELY, a secure health analytics platform. COVID-19 vaccination priority patients were those aged ≥ 50 years or ≥ 16 years clinically extremely vulnerable (CEV) or 'at risk'. We describe the proportion recorded as declining vaccination for each group and stratified by clinical and demographic subgroups, subsequent vaccination and distribution of clinical code usage across general practices.ResultsOf 24.5 million priority patients, 663,033 (2.7%) had a decline recorded, while 2,155,076 (8.8%) had neither a vaccine nor decline recorded. Those recorded as declining, who were subsequently vaccinated (n = 125,587; 18.9%) were overrepresented in the South Asian population (32.3% vs 22.8% for other ethnicities aged ≥ 65 years). The proportion of declining unvaccinated patients was highest in CEV (3.3%), varied strongly with ethnicity (black 15.3%, South Asian 5.6%, white 1.5% for ≥ 80 years) and correlated positively with increasing deprivation.ConclusionsClinical codes indicative of COVID-19 vaccinations being declined are commonly used in England, but substantially more common among black and South Asian people, and in more deprived areas. Qualitative research is needed to determine typical reasons for recorded declines, including to what extent they reflect patients actively declining.",,pdf:https://www.eurosurveillance.org/deliver/fulltext/eurosurveillance/27/33/eurosurv-27-33-5.pdf?itemId=%2Fcontent%2F10.2807%2F1560-7917.ES.2022.27.33.2100885&mimeType=pdf&containerItemId=content/eurosurveillance; doi:https://doi.org/10.2807/1560-7917.ES.2022.27.33.2100885; html:https://europepmc.org/articles/PMC9389857
-36446465,https://doi.org/10.1136/bmjopen-2022-065142,"Prevalence, pathophysiology, prediction and health-related quality of life of long COVID: study protocol of the longitudinal multiple cohort CORona Follow Up (CORFU) study.","Ghossein-Doha C, Wintjens MSJN, Janssen EBNJ, Klein D, Heemskerk SCM, Asselbergs FW, Birnie E, Bonsel GJ, van Bussel BCT, Cals JWL, Ten Cate H, Haagsma J, Hemmen B, van der Horst ICC, Kietselaer BLJH, Klok FA, de Kruif MD, Linschoten M, van Santen S, Vernooy K, Willems LH, Westerborg R, Warle M, van Kuijk SMJ.",,BMJ open,2022,2022-11-29,Y,epidemiology; Public Health; Protocols & Guidelines; Covid-19,,,"<h4>Introduction</h4>The variety, time patterns and long-term prognosis of persistent COVID-19 symptoms (long COVID-19) in patients who suffered from mild to severe acute COVID-19 are incompletely understood. Cohort studies will be combined to describe the prevalence of long COVID-19 symptoms, and to explore the pathophysiological mechanisms and impact on health-related quality of life. A prediction model for long COVID-19 will be developed and internally validated to guide care in future patients.<h4>Methods and analysis</h4>Data from seven COVID-19 cohorts will be aggregated in the longitudinal multiple cohort CORona Follow Up (CORFU) study. CORFU includes Dutch patients who suffered from COVID-19 at home, were hospitalised without or with intensive care unit treatment, needed inpatient or outpatient rehabilitation and controls who did not suffer from COVID-19. Individual cohort study designs were aligned and follow-up has been synchronised. Cohort participants will be followed up for a maximum of 24 months after acute infection. Next to the clinical characteristics measured in individual cohorts, the CORFU questionnaire on long COVID-19 outcomes and determinants will be administered digitally at 3, 6, 12, 18 and 24 months after the infection. The primary outcome is the prevalence of long COVID-19 symptoms up to 2 years after acute infection. Secondary outcomes are health-related quality of life (eg, EQ-5D), physical functioning, and the prevalence of thromboembolic complications, respiratory complications, cardiovascular diseases and endothelial dysfunction. A prediction model and a patient platform prototype will be developed.<h4>Ethics and dissemination</h4>Approval was obtained from the medical research ethics committee of Maastricht University Medical Center+ and Maastricht University (METC 2021-2990) and local committees of the participating cohorts. The project is supported by ZonMW and EuroQol Research Foundation. Results will be published in open access peer-reviewed scientific journals and presented at (inter)national conferences.<h4>Trial registration number</h4>NCT05240742.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/11/e065142.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-065142; html:https://europepmc.org/articles/PMC9709810; pdf:https://europepmc.org/articles/PMC9709810?pdf=render
 33821553,https://doi.org/10.1002/jia2.25697,The impact of disruptions due to COVID-19 on HIV transmission and control among men who have sex with men in China.,"Booton RD, Fu G, MacGregor L, Li J, Ong JJ, Tucker JD, Turner KM, Tang W, Vickerman P, Mitchell KM.",,Journal of the International AIDS Society,2021,2021-04-01,Y,Modelling; Hiv Transmission; Men Who Have Sex With Men; People’s Republic Of China; Key And Vulnerable Populations; Covid-19 Pandemic,,,"<h4>Introduction</h4>The COVID-19 pandemic is impacting HIV care globally, with gaps in HIV treatment expected to increase HIV transmission and HIV-related mortality. We estimated how COVID-19-related disruptions could impact HIV transmission and mortality among men who have sex with men (MSM) in four cities in China, over a one- and five-year time horizon.<h4>Methods</h4>Regional data from China indicated that the number of MSM undergoing facility-based HIV testing reduced by 59% during the COVID-19 pandemic, alongside reductions in ART initiation (34%), numbers of all sexual partners (62%) and consistency of condom use (25%), but initial data indicated no change in viral suppression. A mathematical model of HIV transmission/treatment among MSM was used to estimate the impact of disruptions on HIV infections/HIV-related deaths. Disruption scenarios were assessed for their individual and combined impact over one and five years for 3/4/6-month disruption periods, starting from 1 January 2020.<h4>Results</h4>Our model predicted new HIV infections and HIV-related deaths would be increased most by disruptions to viral suppression, with 25% reductions (25% virally suppressed MSM stop taking ART) for a three-month period increasing HIV infections by 5% to 14% over one year and deaths by 7% to 12%. Observed reductions in condom use increased HIV infections by 5% to 14% but had minimal impact (<1%) on deaths. Smaller impacts on infections and deaths (<3%) were seen for disruptions to facility HIV testing and ART initiation, but reduced partner numbers resulted in 11% to 23% fewer infections and 0.4% to 1.0% fewer deaths. Longer disruption periods (4/6 months) amplified the impact of disruption scenarios. When realistic disruptions were modelled simultaneously, an overall decrease in new HIV infections occurred over one year (3% to 17%), but not for five years (1% increase to 4% decrease), whereas deaths mostly increased over one year (1% to 2%) and five years (1.2 increase to 0.3 decrease).<h4>Conclusions</h4>The overall impact of COVID-19 on new HIV infections and HIV-related deaths is dependent on the nature, scale and length of the various disruptions. Resources should be directed to ensuring levels of viral suppression and condom use are maintained to mitigate any adverse effects of COVID-19-related disruption on HIV transmission and control among MSM in China.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jia2.25697; doi:https://doi.org/10.1002/jia2.25697; html:https://europepmc.org/articles/PMC8022092; pdf:https://europepmc.org/articles/PMC8022092?pdf=render
+36446465,https://doi.org/10.1136/bmjopen-2022-065142,"Prevalence, pathophysiology, prediction and health-related quality of life of long COVID: study protocol of the longitudinal multiple cohort CORona Follow Up (CORFU) study.","Ghossein-Doha C, Wintjens MSJN, Janssen EBNJ, Klein D, Heemskerk SCM, Asselbergs FW, Birnie E, Bonsel GJ, van Bussel BCT, Cals JWL, Ten Cate H, Haagsma J, Hemmen B, van der Horst ICC, Kietselaer BLJH, Klok FA, de Kruif MD, Linschoten M, van Santen S, Vernooy K, Willems LH, Westerborg R, Warle M, van Kuijk SMJ.",,BMJ open,2022,2022-11-29,Y,epidemiology; Public Health; Protocols & Guidelines; Covid-19,,,"<h4>Introduction</h4>The variety, time patterns and long-term prognosis of persistent COVID-19 symptoms (long COVID-19) in patients who suffered from mild to severe acute COVID-19 are incompletely understood. Cohort studies will be combined to describe the prevalence of long COVID-19 symptoms, and to explore the pathophysiological mechanisms and impact on health-related quality of life. A prediction model for long COVID-19 will be developed and internally validated to guide care in future patients.<h4>Methods and analysis</h4>Data from seven COVID-19 cohorts will be aggregated in the longitudinal multiple cohort CORona Follow Up (CORFU) study. CORFU includes Dutch patients who suffered from COVID-19 at home, were hospitalised without or with intensive care unit treatment, needed inpatient or outpatient rehabilitation and controls who did not suffer from COVID-19. Individual cohort study designs were aligned and follow-up has been synchronised. Cohort participants will be followed up for a maximum of 24 months after acute infection. Next to the clinical characteristics measured in individual cohorts, the CORFU questionnaire on long COVID-19 outcomes and determinants will be administered digitally at 3, 6, 12, 18 and 24 months after the infection. The primary outcome is the prevalence of long COVID-19 symptoms up to 2 years after acute infection. Secondary outcomes are health-related quality of life (eg, EQ-5D), physical functioning, and the prevalence of thromboembolic complications, respiratory complications, cardiovascular diseases and endothelial dysfunction. A prediction model and a patient platform prototype will be developed.<h4>Ethics and dissemination</h4>Approval was obtained from the medical research ethics committee of Maastricht University Medical Center+ and Maastricht University (METC 2021-2990) and local committees of the participating cohorts. The project is supported by ZonMW and EuroQol Research Foundation. Results will be published in open access peer-reviewed scientific journals and presented at (inter)national conferences.<h4>Trial registration number</h4>NCT05240742.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/11/e065142.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-065142; html:https://europepmc.org/articles/PMC9709810; pdf:https://europepmc.org/articles/PMC9709810?pdf=render
 35967893,https://doi.org/10.1080/20008066.2022.2105577,Factors influencing the mental health of an ethnically diverse healthcare workforce during COVID-19: a qualitative study in the United Kingdom.,"Qureshi I, Gogoi M, Al-Oraibi A, Wobi F, Chaloner J, Gray L, Guyatt AL, Hassan O, Nellums LB, Pareek M, UK-REACH Collaborative Group.",,European journal of psychotraumatology,2022,2022-08-09,Y,Stress; Trauma; Anxiety; Mental health; Workforce; Healthcare; Ethnic Minority; Covid-19,,,"<b>Background:</b> Healthcare workers (HCWs) have been reported to be experiencing a deterioration in their mental health due to COVID-19. In addition, ethnic minority populations in the United Kingdom are disproportionately affected by COVID-19. It is imperative that HCWs are appropriately supported and protected from mental harm during the pandemic. Our research aims to add to the evidence base by providing greater insight into the lived experience of HCWs from diverse ethnic backgrounds during the pandemic that had an impact on their mental health. <b>Methods:</b> We undertook a qualitative work package as part of the United Kingdom Research study into Ethnicity And COVID-19 outcomes among Healthcare workers (UK-REACH). As part of the qualitative research, we carried out 16 focus groups with a total of 61 HCWs between December 2020 and July 2021. The aim of the study was to explore topics such as their experiences, fears and concerns, while working during the pandemic. The purposive sample included ancillary healthcare workers, doctors, nurses, midwives and allied health professionals from diverse ethnic backgrounds to ensure inclusion of underrepresented and disproportionately impacted individuals. We conducted discussions using Microsoft Teams. Recordings were transcribed and thematically analysed. <b>Results:</b> Several factors were identified which impacted on the mental health of HCWs during this period including anxiety (due to inconsistent protocols and policy); fear (of infection); trauma (due to increased exposure to severe illness and death); guilt (of potentially infecting loved ones); and stress (due to longer working hours and increased workload). <b>Conclusion:</b> COVID-19 has affected the mental health of HCWs. We identified a number of factors which may be contributing to a deterioration in mental health for participants from diverse ethnic backgrounds. Healthcare organisations should consider developing strategies to counter the negative impact of these factors, including recommendations made by HCWs themselves.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9364733; doi:https://doi.org/10.1080/20008066.2022.2105577; html:https://europepmc.org/articles/PMC9364733; pdf:https://europepmc.org/articles/PMC9364733?pdf=render
 33743846,https://doi.org/10.1016/s1473-3099(21)00079-7,The potential health and economic value of SARS-CoV-2 vaccination alongside physical distancing in the UK: a transmission model-based future scenario analysis and economic evaluation.,"Sandmann FG, Davies NG, Vassall A, Edmunds WJ, Jit M, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 working group.",,The Lancet. Infectious diseases,2021,2021-03-18,Y,,,,"<h4>Background</h4>In response to the COVID-19 pandemic, the UK first adopted physical distancing measures in March, 2020. Vaccines against SARS-CoV-2 became available in December, 2020. We explored the health and economic value of introducing SARS-CoV-2 immunisation alongside physical distancing in the UK to gain insights about possible future scenarios in a post-vaccination era.<h4>Methods</h4>We used an age-structured dynamic transmission and economic model to explore different scenarios of UK mass immunisation programmes over 10 years. We compared vaccinating 75% of individuals aged 15 years or older (and annually revaccinating 50% of individuals aged 15-64 years and 75% of individuals aged 65 years or older) to no vaccination. We assumed either 50% vaccine efficacy against disease and 45-week protection (worst-case scenario) or 95% vaccine efficacy against infection and 3-year protection (best-case scenario). Natural immunity was assumed to wane within 45 weeks. We also explored the additional impact of physical distancing on vaccination by assuming either an initial lockdown followed by voluntary physical distancing, or an initial lockdown followed by increased physical distancing mandated above a certain threshold of incident daily infections. We considered benefits in terms of quality-adjusted life-years (QALYs) and costs, both to the health-care payer and the national economy. We discounted future costs and QALYs at 3·5% annually and assumed a monetary value per QALY of £20 000 and a conservative long-run cost per vaccine dose of £15. We explored and varied these parameters in sensitivity analyses. We expressed the health and economic benefits of each scenario with the net monetary value: QALYs × (monetary value per QALY) - costs.<h4>Findings</h4>Without the initial lockdown, vaccination, and increased physical distancing, we estimated 148·0 million (95% uncertainty interval 48·5-198·8) COVID-19 cases and 3·1 million (0·84-4·5) deaths would occur in the UK over 10 years. In the best-case scenario, vaccination minimises community transmission without future periods of increased physical distancing, whereas SARS-CoV-2 becomes endemic with biannual epidemics in the worst-case scenario. Ongoing transmission is also expected in intermediate scenarios with vaccine efficacy similar to published clinical trial data. From a health-care perspective, introducing vaccination leads to incremental net monetary values ranging from £12·0 billion to £334·7 billion in the best-case scenario and from -£1·1 billion to £56·9 billion in the worst-case scenario. Incremental net monetary values of increased physical distancing might be negative from a societal perspective if national economy losses are persistent and large.<h4>Interpretation</h4>Our model findings highlight the substantial health and economic value of introducing SARS-CoV-2 vaccination. Smaller outbreaks could continue even with vaccines, but population-wide implementation of increased physical distancing might no longer be justifiable. Our study provides early insights about possible future post-vaccination scenarios from an economic and epidemiological perspective.<h4>Funding</h4>National Institute for Health Research, European Commission, Bill & Melinda Gates Foundation.",,pdf:http://www.thelancet.com/article/S1473309921000797/pdf; doi:https://doi.org/10.1016/S1473-3099(21)00079-7; html:https://europepmc.org/articles/PMC7972313
 34139154,https://doi.org/10.1016/j.cels.2021.05.005,A time-resolved proteomic and prognostic map of COVID-19.,"Demichev V, Tober-Lau P, Lemke O, Nazarenko T, Thibeault C, Whitwell H, Röhl A, Freiwald A, Szyrwiel L, Ludwig D, Correia-Melo C, Aulakh SK, Helbig ET, Stubbemann P, Lippert LJ, Grüning NM, Blyuss O, Vernardis S, White M, Messner CB, Joannidis M, Sonnweber T, Klein SJ, Pizzini A, Wohlfarter Y, Sahanic S, Hilbe R, Schaefer B, Wagner S, Mittermaier M, Machleidt F, Garcia C, Ruwwe-Glösenkamp C, Lingscheid T, Bosquillon de Jarcy L, Stegemann MS, Pfeiffer M, Jürgens L, Denker S, Zickler D, Enghard P, Zelezniak A, Campbell A, Hayward C, Porteous DJ, Marioni RE, Uhrig A, Müller-Redetzky H, Zoller H, Löffler-Ragg J, Keller MA, Tancevski I, Timms JF, Zaikin A, Hippenstiel S, Ramharter M, Witzenrath M, Suttorp N, Lilley K, Mülleder M, Sander LE, PA-COVID-19 Study group, Ralser M, Kurth F.",,Cell systems,2021,2021-06-14,Y,Proteomics; Biomarkers; Physiological parameters; Machine Learning; Disease Prognosis; Clinical Disease Progression; Patient Trajectories; Longitudinal Profiling; Covid-19,,,"COVID-19 is highly variable in its clinical presentation, ranging from asymptomatic infection to severe organ damage and death. We characterized the time-dependent progression of the disease in 139 COVID-19 inpatients by measuring 86 accredited diagnostic parameters, such as blood cell counts and enzyme activities, as well as untargeted plasma proteomes at 687 sampling points. We report an initial spike in a systemic inflammatory response, which is gradually alleviated and followed by a protein signature indicative of tissue repair, metabolic reconstitution, and immunomodulation. We identify prognostic marker signatures for devising risk-adapted treatment strategies and use machine learning to classify therapeutic needs. We show that the machine learning models based on the proteome are transferable to an independent cohort. Our study presents a map linking routinely used clinical diagnostic parameters to plasma proteomes and their dynamics in an infectious disease.",,doi:https://doi.org/10.1016/j.cels.2021.05.005; doi:https://doi.org/10.1016/j.cels.2021.05.005; html:https://europepmc.org/articles/PMC8201874
 33493433,https://doi.org/10.1016/s1470-2045(20)30743-9,"The impact of the COVID-19 pandemic on radiotherapy services in England, UK: a population-based study.","Spencer K, Jones CM, Girdler R, Roe C, Sharpe M, Lawton S, Miller L, Lewis P, Evans M, Sebag-Montefiore D, Roques T, Smittenaar R, Morris E.",,The Lancet. Oncology,2021,2021-01-22,Y,,,,"<h4>Background</h4>The indirect impact of the COVID-19 pandemic on cancer outcomes is of increasing concern. However, the extent to which key treatment modalities have been affected is unclear. We aimed to assess the impact of the pandemic on radiotherapy activity in England.<h4>Methods</h4>In this population-based study, data relating to all radiotherapy delivered for cancer in the English NHS, between Feb 4, 2019, and June 28, 2020, were extracted from the National Radiotherapy Dataset. Changes in mean weekly radiotherapy courses, attendances (reflecting fractions), and fractionation patterns following the start of the UK lockdown were compared with corresponding months in 2019 overall, for specific diagnoses, and across age groups. The significance of changes in radiotherapy activity during lockdown was examined using interrupted time-series (ITS) analysis.<h4>Findings</h4>In 2020, mean weekly radiotherapy courses fell by 19·9% in April, 6·2% in May, and 11·6% in June compared with corresponding months in 2019. A relatively greater fall was observed for attendances (29·1% in April, 31·4% in May, and 31·5% in June). These changes were significant on ITS analysis (p<0·0001). A greater reduction in treatment courses between 2019 and 2020 was seen for patients aged 70 years or older compared with those aged younger than 70 years (34·4% vs 7·3% in April). By diagnosis, the largest reduction from 2019 to 2020 in treatment courses was for prostate cancer (77·0% in April) and non-melanoma skin cancer (72·4% in April). Conversely, radiotherapy courses in April, 2020, compared with April, 2019, increased by 41·2% in oesophageal cancer, 64·2% in bladder cancer, and 36·3% in rectal cancer. Increased use of ultra-hypofractionated (26 Gy in five fractions) breast radiotherapy as a percentage of all courses (0·2% in April, 2019, to 60·6% in April, 2020; ITS p<0·0001) contributed to the substantial reduction in attendances.<h4>Interpretation</h4>Radiotherapy activity fell significantly, but use of hypofractionated regimens rapidly increased in the English NHS during the first peak of the COVID-19 pandemic. An increase in treatments for some cancers suggests that radiotherapy compensated for reduced surgical activity. These data will assist health-care providers in understanding the indirect consequences of the pandemic and the role of radiotherapy services in minimising these consequences.<h4>Funding</h4>None.",,pdf:https://eprints.whiterose.ac.uk/171109/2/Supplementary%20material_v3.pdf; doi:https://doi.org/10.1016/S1470-2045(20)30743-9; html:https://europepmc.org/articles/PMC7825861; pdf:https://europepmc.org/articles/PMC7825861?pdf=render
 35477524,https://doi.org/10.1136/bmj-2022-070230,Development and validation of the symptom burden questionnaire for long covid (SBQ-LC): Rasch analysis.,"Hughes SE, Haroon S, Subramanian A, McMullan C, Aiyegbusi OL, Turner GM, Jackson L, Davies EH, Frost C, McNamara G, Price G, Matthews K, Camaradou J, Ormerod J, Walker A, Calvert MJ.",,BMJ (Clinical research ed.),2022,2022-04-27,Y,,,,"<h4>Objective</h4>To describe the development and validation of a novel patient reported outcome measure for symptom burden from long covid, the symptom burden questionnaire for long covid (SBQ-LC).<h4>Design</h4>Multiphase, prospective mixed methods study.<h4>Setting</h4>Remote data collection and social media channels in the United Kingdom, 14 April to 1 August 2021.<h4>Participants</h4>13 adults (aged ≥18 years) with self-reported long covid and 10 clinicians evaluated content validity. 274 adults with long covid field tested the draft questionnaire.<h4>Main outcome measures</h4>Published systematic reviews informed development of SBQ-LC's conceptual framework and initial item pool. Thematic analysis of transcripts from cognitive debriefing interviews and online clinician surveys established content validity. Consensus discussions with the patient and public involvement group of the Therapies for Long COVID in non-hospitalised individuals: From symptoms, patient reported outcomes and immunology to targeted therapies (TLC Study) confirmed face validity. Rasch analysis of field test data guided item and scale refinement and provided initial evidence of the SBQ-LC's measurement properties.<h4>Results</h4>SBQ-LC (version 1.0) is a modular instrument measuring patient reported outcomes and is composed of 17 independent scales with promising psychometric properties. Respondents rate their symptom burden during the past seven days using a dichotomous response or 4 point rating scale. Each scale provides coverage of a different symptom domain and returns a summed raw score that can be transformed to a linear (0-100) score. Higher scores represent higher symptom burden. After rating scale refinement and item reduction, all scales satisfied the Rasch model requirements for unidimensionality (principal component analysis of residuals: first residual contrast values <2.00 eigenvalue units) and item fit (outfit mean square values within 0.5 -1.5 logits). Rating scale categories were ordered with acceptable category fit statistics (outfit mean square values <2.0 logits). 14 item pairs had evidence of local dependency (residual correlation values >0.4). Across the 17 scales, person reliability ranged from 0.34 to 0.87, person separation ranged from 0.71 to 2.56, item separation ranged from 1.34 to 13.86, and internal consistency reliability (Cronbach's alpha) ranged from 0.56 to 0.91.<h4>Conclusions</h4>SBQ-LC (version 1.0) is a comprehensive patient reported outcome instrument developed using modern psychometric methods. It measures symptoms of long covid important to people with lived experience of the condition and may be used to evaluate the impact of interventions and inform best practice in clinical management.",,pdf:https://www.bmj.com/content/bmj/377/bmj-2022-070230.full.pdf; doi:https://doi.org/10.1136/bmj-2022-070230; html:https://europepmc.org/articles/PMC9043395; pdf:https://europepmc.org/articles/PMC9043395?pdf=render
 35247983,https://doi.org/10.1186/s12877-021-02673-1,"Age is the main determinant of COVID-19 related in-hospital mortality with minimal impact of pre-existing comorbidities, a retrospective cohort study.","Henkens MTHM, Raafs AG, Verdonschot JAJ, Linschoten M, van Smeden M, Wang P, van der Hooft BHM, Tieleman R, Janssen MLF, Ter Bekke RMA, Hazebroek MR, van der Horst ICC, Asselbergs FW, Magdelijns FJH, Heymans SRB, CAPACITY-COVID collaborative consortium.",,BMC geriatrics,2022,2022-03-05,Y,Mortality; Hospitalization; Netherlands; Mediation Analysis; Covid-19,,,"<h4>Background</h4>Age and comorbidities increase COVID-19 related in-hospital mortality risk, but the extent by which comorbidities mediate the impact of age remains unknown.<h4>Methods</h4>In this multicenter retrospective cohort study with data from 45 Dutch hospitals, 4806 proven COVID-19 patients hospitalized in Dutch hospitals (between February and July 2020) from the CAPACITY-COVID registry were included (age 69[58-77]years, 64% men). The primary outcome was defined as a combination of in-hospital mortality or discharge with palliative care. Logistic regression analysis was performed to analyze the associations between sex, age, and comorbidities with the primary outcome. The effect of comorbidities on the relation of age with the primary outcome was evaluated using mediation analysis.<h4>Results</h4>In-hospital COVID-19 related mortality occurred in 1108 (23%) patients, 836 (76%) were aged ≥70 years (70+). Both age 70+ and female sex were univariably associated with outcome (odds ratio [OR]4.68, 95%confidence interval [4.02-5.45], OR0.68[0.59-0.79], respectively;both p<  0.001). All comorbidities were univariably associated with outcome (p<0.001), and all but dyslipidemia remained significant after adjustment for age70+ and sex. The impact of comorbidities was attenuated after age-spline adjustment, only leaving female sex, diabetes mellitus (DM), chronic kidney disease (CKD), and chronic pulmonary obstructive disease (COPD) significantly associated (female OR0.65[0.55-0.75], DM OR1.47[1.26-1.72], CKD OR1.61[1.32-1.97], COPD OR1.30[1.07-1.59]). Pre-existing comorbidities in older patients negligibly (<6% in all comorbidities) mediated the association between higher age and outcome.<h4>Conclusions</h4>Age is the main determinant of COVID-19 related in-hospital mortality, with negligible mediation effect of pre-existing comorbidities.<h4>Trial registration</h4>CAPACITY-COVID ( NCT04325412 ).",,doi:https://doi.org/10.1186/s12877-021-02673-1; doi:https://doi.org/10.1186/s12877-021-02673-1; html:https://europepmc.org/articles/PMC8897728; pdf:https://europepmc.org/articles/PMC8897728?pdf=render
-34252085,https://doi.org/10.1371/journal.pcbi.1009162,Detecting behavioural changes in human movement to inform the spatial scale of interventions against COVID-19.,"Gibbs H, Nightingale E, Liu Y, Cheshire J, Danon L, Smeeth L, Pearson CAB, Grundy C, LSHTM CMMID COVID-19 working group, Kucharski AJ, Eggo RM.",,PLoS computational biology,2021,2021-07-12,Y,,,,"On March 23 2020, the UK enacted an intensive, nationwide lockdown to mitigate transmission of COVID-19. As restrictions began to ease, more localized interventions were used to target resurgences in transmission. Understanding the spatial scale of networks of human interaction, and how these networks change over time, is critical to targeting interventions at the most at-risk areas without unnecessarily restricting areas at low risk of resurgence. We use detailed human mobility data aggregated from Facebook users to determine how the spatially-explicit network of movements changed before and during the lockdown period, in response to the easing of restrictions, and to the introduction of locally-targeted interventions. We also apply community detection techniques to the weighted, directed network of movements to identify geographically-explicit movement communities and measure the evolution of these community structures through time. We found that the mobility network became more sparse and the number of mobility communities decreased under the national lockdown, a change that disproportionately affected long distance connections central to the mobility network. We also found that the community structure of areas in which locally-targeted interventions were implemented following epidemic resurgence did not show reorganization of community structure but did show small decreases in indicators of travel outside of local areas. We propose that communities detected using Facebook or other mobility data be used to assess the impact of spatially-targeted restrictions and may inform policymakers about the spatial extent of human movement patterns in the UK. These data are available in near real-time, allowing quantification of changes in the distribution of the population across the UK, as well as changes in travel patterns to inform our understanding of the impact of geographically-targeted interventions.",,pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009162&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1009162; html:https://europepmc.org/articles/PMC8297940; pdf:https://europepmc.org/articles/PMC8297940?pdf=render
 35706489,https://doi.org/10.1016/j.eclinm.2022.101428,Impact of ethnicity on the accuracy of measurements of oxygen saturations: A retrospective observational cohort study.,"Bangash MN, Hodson J, Evison F, Patel JM, Johnston AM, Gallier S, Sapey E, Parekh D.",,EClinicalMedicine,2022,2022-05-06,Y,Inequalities; Ethnicity; Oxygen Saturations,,,"<h4>Background</h4>Pulse oximeters are routinely used in community and hospital settings worldwide as a rapid, non-invasive, and readily available bedside tool to approximate blood oxygenation. Potential racial biases in peripheral oxygen saturation (SpO2) measurements may influence the accuracy of pulse oximetry readings and impact clinical decision making. We aimed to assess whether the accuracy of oxygen saturation measured by SpO2, relative to arterial blood gas (SaO2), varies by ethnicity.<h4>Methods</h4>In this large retrospective observational cohort study covering four NHS Hospitals serving a large urban population in Birmingham, United Kingdom, consecutive pairs of SpO2 and SaO2 measurements taken on the same patient within an interval of less than 20 min were identified from electronic patient records. Where multiple pairs of measurements were recorded in a spell, only the first was included in the analysis. The differences between SpO2 and SaO2 measurements were compared across groups of self-identified ethnicity. These differences were subsequently adjusted for age, sex, bilirubin, systolic blood pressure, carboxyhaemaglobin saturations and the time interval between SpO2 and SaO2 measurements.<h4>Findings</h4>Paired O2 saturation measurements from 16,818 inpatient spells between 1st January 2017 and 18th February 2021 were analysed. The cohort self-identified as being of White (81.2%), Asian (11.7%), Black (4.0%), or Other (3.2%) ethnicities. Across the cohort, SpO2 was statistically significantly higher than SaO2 (<i>p</i> < 0.0001), with medians of 98% (interquartile range [IQR]: 95-100%) vs. 97% (IQR: 96-99%), and a median difference of 0.5% points (pps; 95% confidence interval [CI]: 0.5-0.6). However, the size of this difference varied considerably with the magnitude of SaO2, with SpO2 overestimating by a median by 3.8pp (IQR: 0.4, 8.8) for SaO2 values <90% but underestimating by a median of 0.4pp (IQR: -2.0, 1.4) for an SaO2 of 95%. The differences between SpO2 and SaO2 were also found to vary by ethnicity, with this difference being 0.8pp (95% CI: 0.6-1.0, <i>p</i> < 0.0001) greater in those of Black vs. White ethnicity. These differences resulted in 8.7% vs. 6.1% of Black vs. White patients who were classified as normoxic on SpO2 actually being hypoxic on the gold standard SaO2 (odds ratio: 1.47, 95% CI: 1.09-1.98, <i>p</i> = 0.012).<h4>Interpretation</h4>Pulse oximetry may overestimate O2 saturation, and this is possibly more pronounced in patients of Black ethnicity. Prospective studies are urgently warranted to assess the impact of ethnicity on the accuracy of pulse oximetry, to ensure care is optimised for all.<h4>Funding</h4>PIONEER, the Health Data Research UK (HDR-UK) Health Data Research Hub in acute care.",,pdf:http://www.thelancet.com/article/S2589537022001584/pdf; doi:https://doi.org/10.1016/j.eclinm.2022.101428; html:https://europepmc.org/articles/PMC9096912; pdf:https://europepmc.org/articles/PMC9096912?pdf=render
+34252085,https://doi.org/10.1371/journal.pcbi.1009162,Detecting behavioural changes in human movement to inform the spatial scale of interventions against COVID-19.,"Gibbs H, Nightingale E, Liu Y, Cheshire J, Danon L, Smeeth L, Pearson CAB, Grundy C, LSHTM CMMID COVID-19 working group, Kucharski AJ, Eggo RM.",,PLoS computational biology,2021,2021-07-12,Y,,,,"On March 23 2020, the UK enacted an intensive, nationwide lockdown to mitigate transmission of COVID-19. As restrictions began to ease, more localized interventions were used to target resurgences in transmission. Understanding the spatial scale of networks of human interaction, and how these networks change over time, is critical to targeting interventions at the most at-risk areas without unnecessarily restricting areas at low risk of resurgence. We use detailed human mobility data aggregated from Facebook users to determine how the spatially-explicit network of movements changed before and during the lockdown period, in response to the easing of restrictions, and to the introduction of locally-targeted interventions. We also apply community detection techniques to the weighted, directed network of movements to identify geographically-explicit movement communities and measure the evolution of these community structures through time. We found that the mobility network became more sparse and the number of mobility communities decreased under the national lockdown, a change that disproportionately affected long distance connections central to the mobility network. We also found that the community structure of areas in which locally-targeted interventions were implemented following epidemic resurgence did not show reorganization of community structure but did show small decreases in indicators of travel outside of local areas. We propose that communities detected using Facebook or other mobility data be used to assess the impact of spatially-targeted restrictions and may inform policymakers about the spatial extent of human movement patterns in the UK. These data are available in near real-time, allowing quantification of changes in the distribution of the population across the UK, as well as changes in travel patterns to inform our understanding of the impact of geographically-targeted interventions.",,pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009162&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1009162; html:https://europepmc.org/articles/PMC8297940; pdf:https://europepmc.org/articles/PMC8297940?pdf=render
 34535484,https://doi.org/10.1136/bmjopen-2021-050647,The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers (UK-REACH): protocol for a prospective longitudinal cohort study of healthcare and ancillary workers in UK healthcare settings.,"Woolf K, Melbourne C, Bryant L, Guyatt AL, McManus IC, Gupta A, Free RC, Nellums L, Carr S, John C, Martin CA, Wain LV, Gray LJ, Garwood C, Modhwadia V, Abrams KR, Tobin MD, Khunti K, Pareek M, UK-REACH Study Collaborative Group+.",,BMJ open,2021,2021-09-17,Y,Mental health; Public Health; Covid-19,,,"<h4>Introduction</h4>The COVID-19 pandemic has resulted in significant morbidity and mortality and devastated economies globally. Among groups at increased risk are healthcare workers (HCWs) and ethnic minority groups. Emerging evidence suggests that HCWs from ethnic minority groups are at increased risk of adverse COVID-19-related outcomes. To date, there has been no large-scale analysis of these risks in UK HCWs or ancillary workers in healthcare settings, stratified by ethnicity or occupation, and adjusted for confounders. This paper reports the protocol for a prospective longitudinal questionnaire study of UK HCWs, as part of the UK-REACH programme (The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers).<h4>Methods and analysis</h4>A baseline questionnaire will be administered to a national cohort of UK HCWs and ancillary workers in healthcare settings, and those registered with UK healthcare regulators, with follow-up questionnaires administered at 4 and 8 months. With consent, questionnaire data will be linked to health records with 25-year follow-up. Univariate associations between ethnicity and clinical COVID-19 outcomes, physical and mental health, and key confounders/explanatory variables will be tested. Multivariable analyses will test for associations between ethnicity and key outcomes adjusted for the confounder/explanatory variables. We will model changes over time by ethnic group, facilitating understanding of absolute and relative risks in different ethnic groups, and generalisability of findings.<h4>Ethics and dissemination</h4>The study is approved by Health Research Authority (reference 20/HRA/4718), and carries minimal risk. We aim to manage the small risk of participant distress about questions on sensitive topics by clearly participant information that the questionnaire covers sensitive topics and there is no obligation to answer these or any other questions, and by providing support organisation links. Results will be disseminated with reports to Government and papers submitted to pre-print servers and peer reviewed journals.<h4>Trial registration number</h4>ISRCTN11811602; Pre-results.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/9/e050647.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-050647; html:https://europepmc.org/articles/PMC8450967; pdf:https://europepmc.org/articles/PMC8450967?pdf=render
 34183745,https://doi.org/10.1038/s41598-021-92874-w,Frailty assessed by administrative tools and mortality in patients with pneumonia admitted to the hospital and ICU in Wales.,"Szakmany T, Hollinghurst J, Pugh R, Akbari A, Griffiths R, Bailey R, Lyons RA.",,Scientific reports,2021,2021-06-28,Y,,,,"The ideal method of identifying frailty is uncertain, and data on long-term outcomes is relatively limited. We examined frailty indices derived from population-scale linked data on Intensive Care Unit (ICU) and hospitalised non-ICU patients with pneumonia to elucidate the influence of frailty on mortality. Longitudinal cohort study between 2010-2018 using population-scale anonymised data linkage of healthcare records for adults admitted to hospital with pneumonia in Wales. Primary outcome was in-patient mortality. Odds Ratios (ORs [95% confidence interval]) for age, hospital frailty risk score (HFRS), electronic frailty index (eFI), Charlson comorbidity index (CCI), and social deprivation index were estimated using multivariate logistic regression models. The area under the receiver operating characteristic curve (AUC) was estimated to determine the best fitting models. Of the 107,188 patients, mean (SD) age was 72.6 (16.6) years, 50% were men. The models adjusted for the two frailty indices and the comorbidity index had an increased odds of in-patient mortality for individuals with an ICU admission (ORs for ICU admission in the eFI model 2.67 [2.55, 2.79], HFRS model 2.30 [2.20, 2.41], CCI model 2.62 [2.51, 2.75]). Models indicated advancing age, increased frailty and comorbidity were also associated with an increased odds of in-patient mortality (eFI, baseline fit, ORs: mild 1.09 [1.04, 1.13], moderate 1.13 [1.08, 1.18], severe 1.17 [1.10, 1.23]. HFRS, baseline low, ORs: intermediate 2.65 [2.55, 2.75], high 3.31 [3.17, 3.45]). CCI, baseline < 1, ORs: '1-10' 1.15 [1.11, 1.20], > 10 2.50 [2.41, 2.60]). For predicting inpatient deaths, the CCI and HFRS based models were similar, however for longer term outcomes the CCI based model was superior. Frailty and comorbidity are significant risk factors for patients admitted to hospital with pneumonia. Frailty and comorbidity scores based on administrative data have only moderate ability to predict outcome.",,pdf:https://www.nature.com/articles/s41598-021-92874-w.pdf; doi:https://doi.org/10.1038/s41598-021-92874-w; html:https://europepmc.org/articles/PMC8239046; pdf:https://europepmc.org/articles/PMC8239046?pdf=render
 39323985,https://doi.org/10.1214/23-aoas1849,"A BAYESIAN HIERARCHICAL SMALL AREA POPULATION MODEL ACCOUNTING FOR DATA SOURCE SPECIFIC METHODOLOGIES FROM AMERICAN COMMUNITY SURVEY, POPULATION ESTIMATES PROGRAM, AND DECENNIAL CENSUS DATA.","Peterson EN, Nethery RC, Padellini T, Chen JT, Coull BA, Piel FB, Wakefield J, Blangiardo M, Waller LA.",,The annals of applied statistics,2024,2024-04-05,N,Bayesian Methods; American Community Survey; Sampling And Nonsampling Errors; Small Area Population Estimates; Decennial Census,,,"Small area population counts are necessary for many epidemiological studies, yet their quality and accuracy are often not assessed. In the United States, small area population counts are published by the United States Census Bureau (USCB) in the form of the decennial census counts, intercensal population projections (PEP), and American Community Survey (ACS) estimates. Although there are significant relationships between these three data sources, there are important contrasts in data collection, data availability, and processing methodologies such that each set of reported population counts may be subject to different sources and magnitudes of error. Additionally, these data sources do not report identical small area population counts due to post-survey adjustments specific to each data source. Consequently, in public health studies, small area disease/mortality rates may differ depending on which data source is used for denominator data. To accurately estimate annual small area population counts <i>and their</i> associated uncertainties, we present a Bayesian population (BPop) model, which fuses information from all three USCB sources, accounting for data source specific methodologies and associated errors. We produce comprehensive small area race-stratified estimates of the true population, and associated uncertainties, given the observed trends in all three USCB population estimates. The main features of our framework are: (1) a single model integrating multiple data sources, (2) accounting for data source specific data generating mechanisms and specifically accounting for data source specific errors, and (3) prediction of population counts for years without USCB reported data. We focus our study on the Black and White only populations for 159 counties of Georgia and produce estimates for years 2006-2023. We compare BPop population estimates to decennial census counts, PEP annual counts, and ACS multi-year estimates. Additionally, we illustrate and explain the different types of data source specific errors. Lastly, we compare model performance using simulations and validation exercises. Our Bayesian population model can be extended to other applications at smaller spatial granularity and for demographic subpopulations defined further by race, age, and sex, and/or for other geographical regions.",,doi:https://doi.org/10.1214/23-aoas1849; html:https://europepmc.org/articles/PMC11423836; pdf:https://europepmc.org/articles/PMC11423836?pdf=render; doi:https://doi.org/10.1214/23-aoas1849
 35168181,https://doi.org/10.1016/j.thromres.2022.01.023,Potentially inappropriate prescribing of DOACs to people with mechanical heart valves: A federated analysis of 57.9 million patients' primary care records in situ using OpenSAFELY.,"OpenSAFELY Collaborative, Fisher L, Speed V, Curtis HJ, Rentsch CT, Wong AYS, Schultze A, Massey J, Inglesby P, Morton CE, Wood M, Walker AJ, Morley J, Mehrkar A, Bacon S, Hickman G, Bates C, Croker R, Evans D, Ward T, Cockburn J, Davy S, Bhaskaran K, Smith B, Williamson E, Hulme W, Green A, Eggo RM, Forbes H, Tazare J, Parry J, Hester F, Harper S, Meadows J, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Griffiths P, Fowles A, Parkes N, Douglas IJ, Evans SJW, Smeeth L, MacKenna B, Tomlinson L, Goldacre B.",,Thrombosis research,2022,2022-01-29,N,Anticoagulants; Thrombosis; Heart valve prosthesis; Patient Safety; Electronic Health Records,,,,,pdf:https://ora.ox.ac.uk/objects/uuid:aa50f867-d3a4-45ff-9173-1c9677a7ba4f/files/r3x816n268; doi:https://doi.org/10.1016/j.thromres.2022.01.023; html:https://europepmc.org/articles/PMC7616146; pdf:https://europepmc.org/articles/PMC7616146?pdf=render; doi:https://doi.org/10.1016/j.thromres.2022.01.023
 36240828,https://doi.org/10.1016/s2214-109x(22)00358-8,Prediction of upcoming global infection burden of influenza seasons after relaxation of public health and social measures during the COVID-19 pandemic: a modelling study.,"Ali ST, Lau YC, Shan S, Ryu S, Du Z, Wang L, Xu XK, Chen D, Xiong J, Tae J, Tsang TK, Wu P, Lau EHY, Cowling BJ.",,The Lancet. Global health,2022,2022-11-01,Y,,,,"<h4>Background</h4>The transmission dynamics of influenza were affected by public health and social measures (PHSMs) implemented globally since early 2020 to mitigate the COVID-19 pandemic. We aimed to assess the effect of COVID-19 PHSMs on the transmissibility of influenza viruses and to predict upcoming influenza epidemics.<h4>Methods</h4>For this modelling study, we used surveillance data on influenza virus activity for 11 different locations and countries in 2017-22. We implemented a data-driven mechanistic predictive modelling framework to predict future influenza seasons on the basis of pre-COVID-19 dynamics and the effect of PHSMs during the COVID-19 pandemic. We simulated the potential excess burden of upcoming influenza epidemics in terms of fold rise in peak magnitude and epidemic size compared with pre-COVID-19 levels. We also examined how a proactive influenza vaccination programme could mitigate this effect.<h4>Findings</h4>We estimated that COVID-19 PHSMs reduced influenza transmissibility by a maximum of 17·3% (95% CI 13·3-21·4) to 40·6% (35·2-45·9) and attack rate by 5·1% (1·5-7·2) to 24·8% (20·8-27·5) in the 2019-20 influenza season. We estimated a 10-60% increase in the population susceptibility for influenza, which might lead to a maximum of 1-5-fold rise in peak magnitude and 1-4-fold rise in epidemic size for the upcoming 2022-23 influenza season across locations, with a significantly higher fold rise in Singapore and Taiwan. The infection burden could be mitigated by additional proactive one-off influenza vaccination programmes.<h4>Interpretation</h4>Our results suggest the potential for substantial increases in infection burden in upcoming influenza seasons across the globe. Strengthening influenza vaccination programmes is the best preventive measure to reduce the effect of influenza virus infections in the community.<h4>Funding</h4>Health and Medical Research Fund, Hong Kong.",,pdf:https://www.repository.cam.ac.uk/bitstreams/bb5465bd-c08f-4c3d-ab0e-87fee39fc92b/download; doi:https://doi.org/10.1016/S2214-109X(22)00358-8; html:https://europepmc.org/articles/PMC9573849
 32685698,https://doi.org/10.12688/wellcomeopenres.15842.3,Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China.,"Endo A, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Abbott S, Kucharski AJ, Funk S.",,Wellcome open research,2020,2020-07-10,Y,Branching Process; Overdispersion; Novel Coronavirus; Covid-19; Sars-cov-2; Superspreading,,,"<b>Background:</b> A novel coronavirus disease (COVID-19) outbreak has now spread to a number of countries worldwide. While sustained transmission chains of human-to-human transmission suggest high basic reproduction number <i>R</i> <sub>0</sub>, variation in the number of secondary transmissions (often characterised by so-called superspreading events) may be large as some countries have observed fewer local transmissions than others. <b>Methods:</b> We quantified individual-level variation in COVID-19 transmission by applying a mathematical model to observed outbreak sizes in affected countries. We extracted the number of imported and local cases in the affected countries from the World Health Organization situation report and applied a branching process model where the number of secondary transmissions was assumed to follow a negative-binomial distribution. <b>Results:</b> Our model suggested a high degree of individual-level variation in the transmission of COVID-19. Within the current consensus range of <i>R</i> <sub>0</sub> (2-3), the overdispersion parameter <i>k</i> of a negative-binomial distribution was estimated to be around 0.1 (median estimate 0.1; 95% CrI: 0.05-0.2 for R0 = 2.5), suggesting that 80% of secondary transmissions may have been caused by a small fraction of infectious individuals (~10%). A joint estimation yielded likely ranges for <i>R</i> <sub>0</sub> and <i>k</i> (95% CrIs: <i>R</i> <sub>0</sub> 1.4-12; <i>k</i> 0.04-0.2); however, the upper bound of <i>R</i> <sub>0</sub> was not well informed by the model and data, which did not notably differ from that of the prior distribution. <b>Conclusions:</b> Our finding of a highly-overdispersed offspring distribution highlights a potential benefit to focusing intervention efforts on superspreading. As most infected individuals do not contribute to the expansion of an epidemic, the effective reproduction number could be drastically reduced by preventing relatively rare superspreading events.",,doi:https://doi.org/10.12688/wellcomeopenres.15842.3; html:https://europepmc.org/articles/PMC7338915; pdf:https://europepmc.org/articles/PMC7338915?pdf=render
-37468148,https://doi.org/10.1136/bmj-2023-075133,Associations between self-reported healthcare disruption due to covid-19 and avoidable hospital admission: evidence from seven linked longitudinal studies for England.,"Green MA, McKee M, Hamilton OK, Shaw RJ, Macleod J, Boyd A, Katikireddi SV, LH&W NCS Collaborative.",,BMJ (Clinical research ed.),2023,2023-07-19,Y,,,,"<h4>Objectives</h4>To examine whether there is an association between people who experienced disrupted access to healthcare during the covid-19 pandemic and risk of an avoidable hospital admission.<h4>Design</h4>Observational analysis using evidence from seven linked longitudinal cohort studies for England.<h4>Setting</h4>Studies linked to electronic health records from NHS Digital from 1 March 2020 to 25 August 2022. Data were accessed using the UK Longitudinal Linkage Collaboration trusted research environment.<h4>Participants</h4>Individual level records for 29 276 people.<h4>Main outcome measures</h4>Avoidable hospital admissions defined as emergency hospital admissions for ambulatory care sensitive and emergency urgent care sensitive conditions.<h4>Results</h4>9742 participants (weighted percentage 35%, adjusted for sample structure of longitudinal cohorts) self-reported some form of disrupted access to healthcare during the covid-19 pandemic. People with disrupted access were at increased risk of any (odds ratio 1.80, 95% confidence interval 1.39 to 2.34), acute (2.01, 1.39 to 2.92), and chronic (1.80, 1.31 to 2.48) ambulatory care sensitive hospital admissions. For people who experienced disrupted access to appointments (eg, visiting their doctor or an outpatient department) and procedures (eg, surgery, cancer treatment), positive associations were found with measures of avoidable hospital admissions.<h4>Conclusions</h4>Evidence from linked individual level data shows that people whose access to healthcare was disrupted were more likely to have a potentially preventable hospital admission. The findings highlight the need to increase healthcare investment to tackle the short and long term implications of the pandemic, and to protect treatments and procedures during future pandemics.",,doi:https://doi.org/10.1136/bmj-2023-075133; html:https://europepmc.org/articles/PMC10354595; pdf:https://europepmc.org/articles/PMC10354595?pdf=render
 36962513,https://doi.org/10.1371/journal.pgph.0000502,"Association between mobility, non-pharmaceutical interventions, and COVID-19 transmission in Ghana: A modelling study using mobile phone data.","Gibbs H, Liu Y, Abbott S, Baffoe-Nyarko I, Laryea DO, Akyereko E, Kuma-Aboagye P, Asante IA, Mitjà O, LSHTM CMMID COVID-19 Working Group, Ampofo W, Asiedu-Bekoe F, Marks M, Eggo RM.",,PLOS global public health,2022,2022-09-13,Y,,,,"Governments around the world have implemented non-pharmaceutical interventions to limit the transmission of COVID-19. Here we assess if increasing NPI stringency was associated with a reduction in COVID-19 cases in Ghana. While lockdowns and physical distancing have proven effective for reducing COVID-19 transmission, there is still limited understanding of how NPI measures are reflected in indicators of human mobility. Further, there is a lack of understanding about how findings from high-income settings correspond to low and middle-income contexts. In this study, we assess the relationship between indicators of human mobility, NPIs, and estimates of Rt, a real-time measure of the intensity of COVID-19 transmission. We construct a multilevel generalised linear mixed model, combining local disease surveillance data from subnational districts of Ghana with the timing of NPIs and indicators of human mobility from Google and Vodafone Ghana. We observe a relationship between reductions in human mobility and decreases in Rt during the early stages of the COVID-19 epidemic in Ghana. We find that the strength of this relationship varies through time, decreasing after the most stringent period of interventions in the early epidemic. Our findings demonstrate how the association of NPI and mobility indicators with COVID-19 transmission may vary through time. Further, we demonstrate the utility of combining local disease surveillance data with large scale human mobility data to augment existing surveillance capacity to monitor the impact of NPI policies.",,pdf:https://journals.plos.org/globalpublichealth/article/file?id=10.1371/journal.pgph.0000502&type=printable; doi:https://doi.org/10.1371/journal.pgph.0000502; html:https://europepmc.org/articles/PMC10021296; pdf:https://europepmc.org/articles/PMC10021296?pdf=render
-36497616,https://doi.org/10.3390/ijerph192315544,Association between Internet Usage and Quality of Life of Elderly People in England: Evidence from the English Longitudinal Study of Ageing (ELSA).,"Vidiasratri AR, Bath PA, Bath PA.",,International journal of environmental research and public health,2022,2022-11-23,Y,Internet; Quality of life; Older People,,,"The WHO has stated that the number of senior citizens above age 65 across the world will double by the year 2050: in the UK, the whole population is projected to grow by about 2.5% over a decade, from mid-2018. Although people are living longer, they are not healthier in old age, and there is an increasing number of illnesses and disabilities in the ageing population, which have an impact on their overall well-being and quality of life (QoL). Alongside these trends, Internet technologies have improved and provide a wide range of information, including on medical and health issues. This study aimed to examine the association between the utilisation of the internet among older people in England and their QoL. This study utilised the English Longitudinal Study of Aging (ELSA), a longitudinal study of a representative sample of people aged 50 and over in England. The data from Wave 9 were analysed using bivariate analysis and logistic regression. The results show a strong association between QoL and utilisation of the Internet in older people, even when adjusting for demographic variables and health. Higher use of the internet was associated with older people being less likely to have higher QoL. The excessive use of the internet for communication and gathering information also contributed to lower QoL. From the findings, poorer QoL was also found in people in older age groups, in those who are married, and those who never suffer from chronic diseases. Our findings suggest that the quality of life in older people might not only be associated with the frequency of usage but also the purpose for which the internet is used; however, this relationship is complex and further research should explore this in greater depth. Further research should also investigate how older people's use of the Internet changed during the COVID-19 pandemic and the effects of this on the QoL in older age.",,pdf:https://www.mdpi.com/1660-4601/19/23/15544/pdf?version=1669349785; doi:https://doi.org/10.3390/ijerph192315544; html:https://europepmc.org/articles/PMC9738189; pdf:https://europepmc.org/articles/PMC9738189?pdf=render
+37468148,https://doi.org/10.1136/bmj-2023-075133,Associations between self-reported healthcare disruption due to covid-19 and avoidable hospital admission: evidence from seven linked longitudinal studies for England.,"Green MA, McKee M, Hamilton OK, Shaw RJ, Macleod J, Boyd A, Katikireddi SV, LH&W NCS Collaborative.",,BMJ (Clinical research ed.),2023,2023-07-19,Y,,,,"<h4>Objectives</h4>To examine whether there is an association between people who experienced disrupted access to healthcare during the covid-19 pandemic and risk of an avoidable hospital admission.<h4>Design</h4>Observational analysis using evidence from seven linked longitudinal cohort studies for England.<h4>Setting</h4>Studies linked to electronic health records from NHS Digital from 1 March 2020 to 25 August 2022. Data were accessed using the UK Longitudinal Linkage Collaboration trusted research environment.<h4>Participants</h4>Individual level records for 29 276 people.<h4>Main outcome measures</h4>Avoidable hospital admissions defined as emergency hospital admissions for ambulatory care sensitive and emergency urgent care sensitive conditions.<h4>Results</h4>9742 participants (weighted percentage 35%, adjusted for sample structure of longitudinal cohorts) self-reported some form of disrupted access to healthcare during the covid-19 pandemic. People with disrupted access were at increased risk of any (odds ratio 1.80, 95% confidence interval 1.39 to 2.34), acute (2.01, 1.39 to 2.92), and chronic (1.80, 1.31 to 2.48) ambulatory care sensitive hospital admissions. For people who experienced disrupted access to appointments (eg, visiting their doctor or an outpatient department) and procedures (eg, surgery, cancer treatment), positive associations were found with measures of avoidable hospital admissions.<h4>Conclusions</h4>Evidence from linked individual level data shows that people whose access to healthcare was disrupted were more likely to have a potentially preventable hospital admission. The findings highlight the need to increase healthcare investment to tackle the short and long term implications of the pandemic, and to protect treatments and procedures during future pandemics.",,doi:https://doi.org/10.1136/bmj-2023-075133; html:https://europepmc.org/articles/PMC10354595; pdf:https://europepmc.org/articles/PMC10354595?pdf=render
 32790708,https://doi.org/10.1371/journal.pone.0237298,Clinical academic research in the time of Corona: A simulation study in England and a call for action.,"Banerjee A, Katsoulis M, Lai AG, Pasea L, Treibel TA, Manisty C, Denaxas S, Quarta G, Hemingway H, Cavalcante JL, Noursadeghi M, Moon JC.",,PloS one,2020,2020-08-13,Y,,,,"<h4>Objectives</h4>We aimed to model the impact of coronavirus (COVID-19) on the clinical academic response in England, and to provide recommendations for COVID-related research.<h4>Design</h4>A stochastic model to determine clinical academic capacity in England, incorporating the following key factors which affect the ability to conduct research in the COVID-19 climate: (i) infection growth rate and population infection rate (from UK COVID-19 statistics and WHO); (ii) strain on the healthcare system (from published model); and (iii) availability of clinical academic staff with appropriate skillsets affected by frontline clinical activity and sickness (from UK statistics).<h4>Setting</h4>Clinical academics in primary and secondary care in England.<h4>Participants</h4>Equivalent of 3200 full-time clinical academics in England.<h4>Interventions</h4>Four policy approaches to COVID-19 with differing population infection rates: ""Italy model"" (6%), ""mitigation"" (10%), ""relaxed mitigation"" (40%) and ""do-nothing"" (80%) scenarios. Low and high strain on the health system (no clinical academics able to do research at 10% and 5% infection rate, respectively.<h4>Main outcome measures</h4>Number of full-time clinical academics available to conduct clinical research during the pandemic in England.<h4>Results</h4>In the ""Italy model"", ""mitigation"", ""relaxed mitigation"" and ""do-nothing"" scenarios, from 5 March 2020 the duration (days) and peak infection rates (%) are 95(2.4%), 115(2.5%), 240(5.3%) and 240(16.7%) respectively. Near complete attrition of academia (87% reduction, <400 clinical academics) occurs 35 days after pandemic start for 11, 34, 62, 76 days respectively-with no clinical academics at all for 37 days in the ""do-nothing"" scenario. Restoration of normal academic workforce (80% of normal capacity) takes 11, 12, 30 and 26 weeks respectively.<h4>Conclusions</h4>Pandemic COVID-19 crushes the science needed at system level. National policies mitigate, but the academic community needs to adapt. We highlight six key strategies: radical prioritisation (eg 3-4 research ideas per institution), deep resourcing, non-standard leadership (repurposing of key non-frontline teams), rationalisation (profoundly simple approaches), careful site selection (eg protected sites with large academic backup) and complete suspension of academic competition with collaborative approaches.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0237298&type=printable; doi:https://doi.org/10.1371/journal.pone.0237298; html:https://europepmc.org/articles/PMC7425844; pdf:https://europepmc.org/articles/PMC7425844?pdf=render
+36497616,https://doi.org/10.3390/ijerph192315544,Association between Internet Usage and Quality of Life of Elderly People in England: Evidence from the English Longitudinal Study of Ageing (ELSA).,"Vidiasratri AR, Bath PA, Bath PA.",,International journal of environmental research and public health,2022,2022-11-23,Y,Internet; Quality of life; Older People,,,"The WHO has stated that the number of senior citizens above age 65 across the world will double by the year 2050: in the UK, the whole population is projected to grow by about 2.5% over a decade, from mid-2018. Although people are living longer, they are not healthier in old age, and there is an increasing number of illnesses and disabilities in the ageing population, which have an impact on their overall well-being and quality of life (QoL). Alongside these trends, Internet technologies have improved and provide a wide range of information, including on medical and health issues. This study aimed to examine the association between the utilisation of the internet among older people in England and their QoL. This study utilised the English Longitudinal Study of Aging (ELSA), a longitudinal study of a representative sample of people aged 50 and over in England. The data from Wave 9 were analysed using bivariate analysis and logistic regression. The results show a strong association between QoL and utilisation of the Internet in older people, even when adjusting for demographic variables and health. Higher use of the internet was associated with older people being less likely to have higher QoL. The excessive use of the internet for communication and gathering information also contributed to lower QoL. From the findings, poorer QoL was also found in people in older age groups, in those who are married, and those who never suffer from chronic diseases. Our findings suggest that the quality of life in older people might not only be associated with the frequency of usage but also the purpose for which the internet is used; however, this relationship is complex and further research should explore this in greater depth. Further research should also investigate how older people's use of the Internet changed during the COVID-19 pandemic and the effects of this on the QoL in older age.",,pdf:https://www.mdpi.com/1660-4601/19/23/15544/pdf?version=1669349785; doi:https://doi.org/10.3390/ijerph192315544; html:https://europepmc.org/articles/PMC9738189; pdf:https://europepmc.org/articles/PMC9738189?pdf=render
 36315390,https://doi.org/10.1002/eat.23834,"Risk and protective factors for new-onset binge eating, low weight, and self-harm symptoms in >35,000 individuals in the UK during the COVID-19 pandemic.","Davies HL, Hübel C, Herle M, Kakar S, Mundy J, Peel AJ, Ter Kuile AR, Zvrskovec J, Monssen D, Lim KX, Davies MR, Palmos AB, Lin Y, Kalsi G, Rogers HC, Bristow S, Glen K, Malouf CM, Kelly EJ, Purves KL, Young KS, Hotopf M, Armour C, McIntosh AM, Eley TC, Treasure J, Breen G.",,The International journal of eating disorders,2023,2022-10-31,Y,Mental health; Psychiatric disorders; Eating Disorders; Comorbidity; Suicidal Ideation,,,"<h4>Objective</h4>The disruption caused by the COVID-19 pandemic has been associated with poor mental health, including increases in eating disorders and self-harm symptoms. We investigated risk and protective factors for the new onset of these symptoms during the pandemic.<h4>Method</h4>Data were from the COVID-19 Psychiatry and Neurological Genetics study and the Repeated Assessment of Mental health in Pandemics Study (n = 36,715). Exposures were socio-demographic characteristics, lifetime psychiatric disorder, and COVID-related variables, including SARS-CoV-2 infection/illness with COVID-19. We identified four subsamples of participants without pre-pandemic experience of our outcomes: binge eating (n = 24,211), low weight (n = 24,364), suicidal and/or self-harm ideation (n = 18,040), and self-harm (n = 29,948). Participants reported on our outcomes at frequent intervals (fortnightly to monthly). We fitted multiple logistic regression models to identify factors associated with the new onset of our outcomes.<h4>Results</h4>Within each subsample, new onset was reported by: 21% for binge eating, 10.8% for low weight, 23.5% for suicidal and/or self-harm ideation, and 3.5% for self-harm. Shared risk factors included having a lifetime psychiatric disorder, not being in paid employment, higher pandemic worry scores, and being racially minoritized. Conversely, infection with SARS-CoV-2/illness with COVID-19 was linked to lower odds of binge eating, low weight, and suicidal and/or self-harm ideation.<h4>Discussion</h4>Overall, we detected shared risk factors that may drive the comorbidity between eating disorders and self-harm. Subgroups of individuals with these risk factors may require more frequent monitoring during future pandemics.<h4>Public significance</h4>In a sample of 35,000 UK residents, people who had a psychiatric disorder, identified as being part of a racially minoritized group, were not in paid employment, or were more worried about the pandemic were more likely to experience binge eating, low weight, suicidal and/or self-harm ideation, and self-harm for the first time during the pandemic. People with these risk factors may need particular attention during future pandemics to enable early identification of new psychiatric symptoms.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/eat.23834; doi:https://doi.org/10.1002/eat.23834; html:https://europepmc.org/articles/PMC9874817; pdf:https://europepmc.org/articles/PMC9874817?pdf=render
 34847950,https://doi.org/10.1186/s12916-021-02190-3,Models of COVID-19 vaccine prioritisation: a systematic literature search and narrative review.,"Saadi N, Chi YL, Ghosh S, Eggo RM, McCarthy CV, Quaife M, Dawa J, Jit M, Vassall A.",,BMC medicine,2021,2021-12-01,Y,"Covid-19, Vaccination, Mathematical Modelling",,,"<h4>Background</h4>How best to prioritise COVID-19 vaccination within and between countries has been a public health and an ethical challenge for decision-makers globally. We reviewed epidemiological and economic modelling evidence on population priority groups to minimise COVID-19 mortality, transmission, and morbidity outcomes.<h4>Methods</h4>We searched the National Institute of Health iSearch COVID-19 Portfolio (a database of peer-reviewed and pre-print articles), Econlit, the Centre for Economic Policy Research, and the National Bureau of Economic Research for mathematical modelling studies evaluating the impact of prioritising COVID-19 vaccination to population target groups. The first search was conducted on March 3, 2021, and an updated search on the LMIC literature was conducted from March 3, 2021, to September 24, 2021. We narratively synthesised the main study conclusions on prioritisation and the conditions under which the conclusions changed.<h4>Results</h4>The initial search identified 1820 studies and 36 studies met the inclusion criteria. The updated search on LMIC literature identified 7 more studies. 43 studies in total were narratively synthesised. 74% of studies described outcomes in high-income countries (single and multi-country). We found that for countries seeking to minimise deaths, prioritising vaccination of senior adults was the optimal strategy and for countries seeking to minimise cases the young were prioritised. There were several exceptions to the main conclusion, notably that reductions in deaths could be increased if groups at high risk of both transmission and death could be further identified. Findings were also sensitive to the level of vaccine coverage.<h4>Conclusion</h4>The evidence supports WHO SAGE recommendations on COVID-19 vaccine prioritisation. There is, however, an evidence gap on optimal prioritisation for low- and middle-income countries, studies that included an economic evaluation, and studies that explore prioritisation strategies if the aim is to reduce overall health burden including morbidity.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-021-02190-3; doi:https://doi.org/10.1186/s12916-021-02190-3; html:https://europepmc.org/articles/PMC8632563; pdf:https://europepmc.org/articles/PMC8632563?pdf=render
 32702311,https://doi.org/10.1016/s1470-2045(20)30392-2,Effect of delays in the 2-week-wait cancer referral pathway during the COVID-19 pandemic on cancer survival in the UK: a modelling study.,"Sud A, Torr B, Jones ME, Broggio J, Scott S, Loveday C, Garrett A, Gronthoud F, Nicol DL, Jhanji S, Boyce SA, Williams M, Riboli E, Muller DC, Kipps E, Larkin J, Navani N, Swanton C, Lyratzopoulos G, McFerran E, Lawler M, Houlston R, Turnbull C.",,The Lancet. Oncology,2020,2020-07-20,Y,,,,"<h4>Background</h4>During the COVID-19 lockdown, referrals via the 2-week-wait urgent pathway for suspected cancer in England, UK, are reported to have decreased by up to 84%. We aimed to examine the impact of different scenarios of lockdown-accumulated backlog in cancer referrals on cancer survival, and the impact on survival per referred patient due to delayed referral versus risk of death from nosocomial infection with severe acute respiratory syndrome coronavirus 2.<h4>Methods</h4>In this modelling study, we used age-stratified and stage-stratified 10-year cancer survival estimates for patients in England, UK, for 20 common tumour types diagnosed in 2008-17 at age 30 years and older from Public Health England. We also used data for cancer diagnoses made via the 2-week-wait referral pathway in 2013-16 from the Cancer Waiting Times system from NHS Digital. We applied per-day hazard ratios (HRs) for cancer progression that we generated from observational studies of delay to treatment. We quantified the annual numbers of cancers at stage I-III diagnosed via the 2-week-wait pathway using 2-week-wait age-specific and stage-specific breakdowns. From these numbers, we estimated the aggregate number of lives and life-years lost in England for per-patient delays of 1-6 months in presentation, diagnosis, or cancer treatment, or a combination of these. We assessed three scenarios of a 3-month period of lockdown during which 25%, 50%, and 75% of the normal monthly volumes of symptomatic patients delayed their presentation until after lockdown. Using referral-to-diagnosis conversion rates and COVID-19 case-fatality rates, we also estimated the survival increment per patient referred.<h4>Findings</h4>Across England in 2013-16, an average of 6281 patients with stage I-III cancer were diagnosed via the 2-week-wait pathway per month, of whom 1691 (27%) would be predicted to die within 10 years from their disease. Delays in presentation via the 2-week-wait pathway over a 3-month lockdown period (with an average presentational delay of 2 months per patient) would result in 181 additional lives and 3316 life-years lost as a result of a backlog of referrals of 25%, 361 additional lives and 6632 life-years lost for a 50% backlog of referrals, and 542 additional lives and 9948 life-years lost for a 75% backlog in referrals. Compared with all diagnostics for the backlog being done in month 1 after lockdown, additional capacity across months 1-3 would result in 90 additional lives and 1662 live-years lost due to diagnostic delays for the 25% backlog scenario, 183 additional lives and 3362 life-years lost under the 50% backlog scenario, and 276 additional lives and 5075 life-years lost under the 75% backlog scenario. However, a delay in additional diagnostic capacity with provision spread across months 3-8 after lockdown would result in 401 additional lives and 7332 life-years lost due to diagnostic delays under the 25% backlog scenario, 811 additional lives and 14 873 life-years lost under the 50% backlog scenario, and 1231 additional lives and 22 635 life-years lost under the 75% backlog scenario. A 2-month delay in 2-week-wait investigatory referrals results in an estimated loss of between 0·0 and 0·7 life-years per referred patient, depending on age and tumour type.<h4>Interpretation</h4>Prompt provision of additional capacity to address the backlog of diagnostics will minimise deaths as a result of diagnostic delays that could add to those predicted due to expected presentational delays. Prioritisation of patient groups for whom delay would result in most life-years lost warrants consideration as an option for mitigating the aggregate burden of mortality in patients with cancer.<h4>Funding</h4>None.",,pdf:http://www.thelancet.com/article/S1470204520303922/pdf; doi:https://doi.org/10.1016/S1470-2045(20)30392-2; html:https://europepmc.org/articles/PMC7116538; pdf:https://europepmc.org/articles/PMC7116538?pdf=render
 36992188,https://doi.org/10.3390/vaccines11030604,"Household Composition and Inequalities in COVID-19 Vaccination in Wales, UK.","Lench A, Perry M, Johnson RD, Fry R, Richardson G, Lyons RA, Akbari A, Edwards A, Collins B, Joseph-Williams N, Cooper A, Cottrell S.",,Vaccines,2023,2023-03-07,Y,Vaccines; Vaccination; Households; Inequalities; Immunisation; Household Composition; Inequities; Covid-19,,,"The uptake of COVID-19 vaccination in Wales is high at a population level but many inequalities exist. Household composition may be an important factor in COVID-19 vaccination uptake due to the practical, social, and psychological implications associated with different living arrangements. In this study, the role of household composition in the uptake of COVID-19 vaccination in Wales was examined with the aim of identifying areas for intervention to address inequalities. Records within the Wales Immunisation System (WIS) COVID-19 vaccination register were linked to the Welsh Demographic Service Dataset (WDSD; a population register for Wales) held within the Secure Anonymised Information Linkage (SAIL) databank. Eight household types were defined based on household size, the presence or absence of children, and the presence of single or multiple generations. Uptake of the second dose of any COVID-19 vaccine was analysed using logistic regression. Gender, age group, health board, rural/urban residential classification, ethnic group, and deprivation quintile were included as covariates for multivariable regression. Compared to two-adult households, all other household types were associated with lower uptake. The most significantly reduced uptake was observed for large, multigenerational, adult group households (aOR 0.45, 95%CI 0.43-0.46). Comparing multivariable regression with and without incorporation of household composition as a variable produced significant differences in odds of vaccination for health board, age group, and ethnic group categories. These results indicate that household composition is an important factor for the uptake of COVID-19 vaccination and consideration of differences in household composition is necessary to mitigate vaccination inequalities.",,pdf:https://www.mdpi.com/2076-393X/11/3/604/pdf?version=1678670919; doi:https://doi.org/10.3390/vaccines11030604; html:https://europepmc.org/articles/PMC10055803; pdf:https://europepmc.org/articles/PMC10055803?pdf=render
 35013731,https://doi.org/10.1016/j.lanepe.2021.100299,Persistent hesitancy for SARS-CoV-2 vaccines among healthcare workers in the United Kingdom: analysis of longitudinal data from the UK-REACH cohort study.,"Martin CA, Woolf K, Bryant L, Carr S, Gray LJ, Gupta A, Guyatt AL, John C, Melbourne C, McManus IC, Nazareth J, Nellums LB, Tobin MD, Pan D, Khunti K, Pareek M, UK-REACH Study Collaborative Group.",,The Lancet regional health. Europe,2022,2022-01-04,Y,,,,,,doi:https://doi.org/10.1016/j.lanepe.2021.100299; doi:https://doi.org/10.1016/j.lanepe.2021.100299; html:https://europepmc.org/articles/PMC8730737; pdf:https://europepmc.org/articles/PMC8730737?pdf=render
+38529358,https://doi.org/10.1093/braincomms/fcae088,"<i>Helicobacter pylori</i>, persistent infection burden and structural brain imaging markers.","Beydoun MA, Beydoun HA, Hu YH, El-Hajj ZW, Georgescu MF, Noren Hooten N, Li Z, Weiss J, Lyall DM, Waldstein SR, Hedges DW, Gale SD, Launer LJ, Evans MK, Zonderman AB.",,Brain communications,2024,2024-03-13,N,Helicobacter Pylori; Persistent infection; Brain imaging; Cognitive Aging,,,"Persistent infections, whether viral, bacterial or parasitic, including <i>Helicobacter pylori</i> infection, have been implicated in non-communicable diseases, including dementia and other neurodegenerative diseases. In this cross-sectional study, data on 635 cognitively normal participants from the UK Biobank study (2006-21, age range: 40-70 years) were used to examine whether <i>H. pylori</i> seropositivity (e.g. presence of antibodies), serointensities of five <i>H. pylori</i> antigens and a measure of total persistent infection burden were associated with selected brain volumetric structural MRI (total, white, grey matter, frontal grey matter (left/right), white matter hyperintensity as percent intracranial volume and bi-lateral sub-cortical volumes) and diffusion-weighted MRI measures (global and tract-specific bi-lateral fractional anisotropy and mean diffusivity), after an average 9-10 years of lag time. Persistent infection burden was calculated as a cumulative score of seropositivity for over 20 different pathogens. Multivariable-adjusted linear regression analyses were conducted, whereby selected potential confounders (all measures) and intracranial volume (sub-cortical volumes) were adjusted, with stratification by Alzheimer's disease polygenic risk score tertile when exposures were <i>H. pylori</i> antigen serointensities. Type I error was adjusted to 0.007. We report little evidence of an association between <i>H. pylori</i> seropositivity and persistent infection burden with various volumetric outcomes (<i>P</i> > 0.007, from multivariable regression models), unlike previously reported in past research. However, <i>H. pylori</i> antigen serointensities, particularly immunoglobulin G against the vacuolating cytotoxin A, GroEL and outer membrane protein antigens, were associated with poorer tract-specific white matter integrity (<i>P</i> < 0.007), with outer membrane protein serointensity linked to worse outcomes in cognition-related tracts such as the external capsule, the anterior limb of the internal capsule and the cingulum, specifically at low Alzheimer's disease polygenic risk. Vacuolating cytotoxin A serointensity was associated with greater white matter hyperintensity volume among individuals with mid-level Alzheimer's disease polygenic risk, while among individuals with the highest Alzheimer's disease polygenic risk, the urease serointensity was consistently associated with reduced bi-lateral caudate volumes and the vacuolating cytotoxin A serointensity was linked to reduced right putamen volume (<i>P</i> < 0.007). Outer membrane protein and urease were associated with larger sub-cortical volumes (e.g. left putamen and right nucleus accumbens) at middle Alzheimer's disease polygenic risk levels (<i>P</i> < 0.007). Our results shed light on the relationship between <i>H. pylori</i> seropositivity, <i>H. pylori</i> antigen levels and persistent infection burden with brain volumetric structural measures. These data are important given the links between infectious agents and neurodegenerative diseases, including Alzheimer's disease, and can be used for the development of drugs and preventive interventions that would reduce the burden of those diseases.",,doi:https://doi.org/10.1093/braincomms/fcae088; html:https://europepmc.org/articles/PMC10961948; pdf:https://europepmc.org/articles/PMC10961948?pdf=render; doi:https://doi.org/10.1093/braincomms/fcae088
 35354646,https://doi.org/10.1136/thoraxjnl-2021-218629,Relationship between asthma and severe COVID-19: a national cohort study.,"Dolby T, Nafilyan V, Morgan A, Kallis C, Sheikh A, Quint JK.",,Thorax,2023,2022-03-30,Y,Asthma; Covid-19,,,"<h4>Background</h4>We aimed to determine whether children and adults with poorly controlled or more severe asthma have greater risk of hospitalisation and/or death from COVID-19.<h4>Methods</h4>We used individual-level data from the Office for National Statistics Public Health Data Asset, based on the 2011 census in England, and the General Practice Extraction Service data for pandemic planning and research linked to death registration records and Hospital Episode Statistics admission data. Adults were followed from 1 January 2020 to 30 September 2021 for hospitalisation or death from COVID-19. For children, only hospitalisation was included.<h4>Results</h4>Our cohort comprised 35 202 533 adults and 2 996 503 children aged 12-17 years. After controlling for sociodemographic factors, pre-existing health conditions and vaccine status, the risk of death involving COVID-19 for adults with asthma prescribed low dose inhaled corticosteroids (ICS) was not significantly different from those without asthma. Adults with asthma prescribed medium and high dosage ICS had an elevated risk of COVID-19 death; HRs 1.18 (95% CI 1.14 to 1.23) and 1.36 (95% CI 1.28 to 1.44), respectively. A similar pattern was observed for COVID-19 hospitalisation; fully adjusted HRs 1.53 (95% CI 1.50 to 1.56) and 1.52 (95% CI 1.46 to 1.56) for adults with asthma prescribed medium and high-dosage ICS, respectively. Risk of hospitalisation was greater for children with asthma prescribed one (2.58 (95% CI 1.82 to 3.66)) or two or more (3.80 (95% CI 2.41 to 5.95)) courses of oral corticosteroids in the year prior to the pandemic.<h4>Discussion</h4>People with mild and/or well-controlled asthma are neither at significantly increased risk of hospitalisation with nor more likely to die from COVID-19 than adults without asthma.",,pdf:https://thorax.bmj.com/content/thoraxjnl/early/2022/03/29/thoraxjnl-2021-218629.full.pdf; doi:https://doi.org/10.1136/thoraxjnl-2021-218629; html:https://europepmc.org/articles/PMC8983409; pdf:https://europepmc.org/articles/PMC8983409?pdf=render
 37717030,https://doi.org/10.1186/s13756-023-01280-6,The impact of the COVID-19 pandemic on the treatment of common infections in primary care and the change to antibiotic prescribing in England.,"Yang YT, Zhong X, Fahmi A, Watts S, Ashcroft DM, Massey J, Fisher L, MacKenna B, Mehrkar A, Bacon SCJ, Goldacre B, Hand K, van Staa T, Palin V.",,Antimicrobial resistance and infection control,2023,2023-09-16,Y,Infection; Antibiotics; Primary Care; Antibiotic Stewardship; Covid-19 Pandemic,,,"<h4>Background</h4>There is concern that the COVID-19 pandemic altered the management of common infections in primary care. This study aimed to evaluate infection-coded consultation rates and antibiotic use during the pandemic and how any change may have affected clinical outcomes.<h4>Methods</h4>With the approval of NHS England, a retrospective cohort study using the OpenSAFELY platform analysed routinely collected electronic health data from GP practices in England between January 2019 and December 2021. Infection coded consultations and antibiotic prescriptions were used estimate multiple measures over calendar months, including age-sex adjusted prescribing rates, prescribing by infection and antibiotic type, infection consultation rates, coding quality and rate of same-day antibiotic prescribing for COVID-19 infections. Interrupted time series (ITS) estimated the effect of COVID-19 pandemic on infection-coded consultation rates. The impact of the pandemic on non- COVID-19 infection-related hospitalisations was also estimated.<h4>Results</h4>Records from 24 million patients were included. The rate of infection-related consultations fell for all infections (mean reduction of 39% in 2020 compared to 2019 mean rate), except for UTI which remained stable. Modelling infection-related consultation rates highlighted this with an incidence rate ratio of 0.44 (95% CI 0.36-0.53) for incident consultations and 0.43 (95% CI 0.33-0.54) for prevalent consultations. Lower respiratory tract infections (LRTI) saw the largest reduction of 0.11 (95% CI 0.07-0.17). Antibiotic prescribing rates fell with a mean reduction of 118.4 items per 1000 patients in 2020, returning to pre-pandemic rates by summer 2021. Prescribing for LRTI decreased 20% and URTI increased 15.9%. Over 60% of antibiotics were issued without an associated same-day infection code, which increased during the pandemic. Infection-related hospitalisations reduced (by 62%), with the largest reduction observed for pneumonia infections (72.9%). Same-day antibiotic prescribing for COVID-19 infection increased from 1 to 10.5% between the second and third national lockdowns and rose again during 2022.<h4>Conclusions</h4>Changes to consultations and hospital admissions may be driven by reduced transmission of non-COVID-19 infections due to reduced social mixing and lockdowns. Inconsistencies in coding practice emphasises the need for improvement to inform new antibiotic stewardship policies and prevent resistance to novel infections.",,pdf:https://aricjournal.biomedcentral.com/counter/pdf/10.1186/s13756-023-01280-6; doi:https://doi.org/10.1186/s13756-023-01280-6; html:https://europepmc.org/articles/PMC10504725; pdf:https://europepmc.org/articles/PMC10504725?pdf=render
 38895652,https://doi.org/10.1093/jamiaopen/ooae049,Creating a next-generation phenotype library: the health data research UK Phenotype Library.,"Thayer DS, Mumtaz S, Elmessary MA, Scanlon I, Zinnurov A, Coldea AI, Scanlon J, Chapman M, Curcin V, John A, DelPozo-Banos M, Davies H, Karwath A, Gkoutos GV, Fitzpatrick NK, Quint JK, Varma S, Milner C, Oliveira C, Parkinson H, Denaxas S, Hemingway H, Jefferson E.",,JAMIA open,2024,2024-06-17,Y,Phenotyping; Medical Informatics; Algorithms; Public Health Informatics; Electronic Health Records; Application Programming Interface,,,"<h4>Objective</h4>To enable reproducible research at scale by creating a platform that enables health data users to find, access, curate, and re-use electronic health record phenotyping algorithms.<h4>Materials and methods</h4>We undertook a structured approach to identifying requirements for a phenotype algorithm platform by engaging with key stakeholders. User experience analysis was used to inform the design, which we implemented as a web application featuring a novel metadata standard for defining phenotyping algorithms, access via Application Programming Interface (API), support for computable data flows, and version control. The application has creation and editing functionality, enabling researchers to submit phenotypes directly.<h4>Results</h4>We created and launched the Phenotype Library in October 2021. The platform currently hosts 1049 phenotype definitions defined against 40 health data sources and >200K terms across 16 medical ontologies. We present several case studies demonstrating its utility for supporting and enabling research: the library hosts curated phenotype collections for the BREATHE respiratory health research hub and the Adolescent Mental Health Data Platform, and it is supporting the development of an informatics tool to generate clinical evidence for clinical guideline development groups.<h4>Discussion</h4>This platform makes an impact by being open to all health data users and accepting all appropriate content, as well as implementing key features that have not been widely available, including managing structured metadata, access via an API, and support for computable phenotypes.<h4>Conclusions</h4>We have created the first openly available, programmatically accessible resource enabling the global health research community to store and manage phenotyping algorithms. Removing barriers to describing, sharing, and computing phenotypes will help unleash the potential benefit of health data for patients and the public.",,pdf:https://academic.oup.com/jamiaopen/article-pdf/7/2/ooae049/58255810/ooae049.pdf; doi:https://doi.org/10.1093/jamiaopen/ooae049; html:https://europepmc.org/articles/PMC11182945; pdf:https://europepmc.org/articles/PMC11182945?pdf=render
-38529358,https://doi.org/10.1093/braincomms/fcae088,"<i>Helicobacter pylori</i>, persistent infection burden and structural brain imaging markers.","Beydoun MA, Beydoun HA, Hu YH, El-Hajj ZW, Georgescu MF, Noren Hooten N, Li Z, Weiss J, Lyall DM, Waldstein SR, Hedges DW, Gale SD, Launer LJ, Evans MK, Zonderman AB.",,Brain communications,2024,2024-03-13,N,Helicobacter Pylori; Persistent infection; Brain imaging; Cognitive Aging,,,"Persistent infections, whether viral, bacterial or parasitic, including <i>Helicobacter pylori</i> infection, have been implicated in non-communicable diseases, including dementia and other neurodegenerative diseases. In this cross-sectional study, data on 635 cognitively normal participants from the UK Biobank study (2006-21, age range: 40-70 years) were used to examine whether <i>H. pylori</i> seropositivity (e.g. presence of antibodies), serointensities of five <i>H. pylori</i> antigens and a measure of total persistent infection burden were associated with selected brain volumetric structural MRI (total, white, grey matter, frontal grey matter (left/right), white matter hyperintensity as percent intracranial volume and bi-lateral sub-cortical volumes) and diffusion-weighted MRI measures (global and tract-specific bi-lateral fractional anisotropy and mean diffusivity), after an average 9-10 years of lag time. Persistent infection burden was calculated as a cumulative score of seropositivity for over 20 different pathogens. Multivariable-adjusted linear regression analyses were conducted, whereby selected potential confounders (all measures) and intracranial volume (sub-cortical volumes) were adjusted, with stratification by Alzheimer's disease polygenic risk score tertile when exposures were <i>H. pylori</i> antigen serointensities. Type I error was adjusted to 0.007. We report little evidence of an association between <i>H. pylori</i> seropositivity and persistent infection burden with various volumetric outcomes (<i>P</i> > 0.007, from multivariable regression models), unlike previously reported in past research. However, <i>H. pylori</i> antigen serointensities, particularly immunoglobulin G against the vacuolating cytotoxin A, GroEL and outer membrane protein antigens, were associated with poorer tract-specific white matter integrity (<i>P</i> < 0.007), with outer membrane protein serointensity linked to worse outcomes in cognition-related tracts such as the external capsule, the anterior limb of the internal capsule and the cingulum, specifically at low Alzheimer's disease polygenic risk. Vacuolating cytotoxin A serointensity was associated with greater white matter hyperintensity volume among individuals with mid-level Alzheimer's disease polygenic risk, while among individuals with the highest Alzheimer's disease polygenic risk, the urease serointensity was consistently associated with reduced bi-lateral caudate volumes and the vacuolating cytotoxin A serointensity was linked to reduced right putamen volume (<i>P</i> < 0.007). Outer membrane protein and urease were associated with larger sub-cortical volumes (e.g. left putamen and right nucleus accumbens) at middle Alzheimer's disease polygenic risk levels (<i>P</i> < 0.007). Our results shed light on the relationship between <i>H. pylori</i> seropositivity, <i>H. pylori</i> antigen levels and persistent infection burden with brain volumetric structural measures. These data are important given the links between infectious agents and neurodegenerative diseases, including Alzheimer's disease, and can be used for the development of drugs and preventive interventions that would reduce the burden of those diseases.",,doi:https://doi.org/10.1093/braincomms/fcae088; html:https://europepmc.org/articles/PMC10961948; pdf:https://europepmc.org/articles/PMC10961948?pdf=render; doi:https://doi.org/10.1093/braincomms/fcae088
 32234121,https://doi.org/10.2807/1560-7917.es.2020.25.12.2000256,"Estimating the infection and case fatality ratio for coronavirus disease (COVID-19) using age-adjusted data from the outbreak on the Diamond Princess cruise ship, February 2020.","Russell TW, Hellewell J, Jarvis CI, van Zandvoort K, Abbott S, Ratnayake R, CMMID COVID-19 working group, Flasche S, Eggo RM, Edmunds WJ, Kucharski AJ.",,Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin,2020,2020-03-01,Y,Coronavirus; outbreak; Severity; Asymptomatic; Case Fatality Ratio; Cruise Ship; Covid-19; Infection Fatality Ratio,"COVID-19, Improving Public Health","COVID-19, infection","Adjusting for delay from confirmation to death, we estimated case and infection fatality ratios (CFR, IFR) for coronavirus disease (COVID-19) on the Diamond Princess ship as 2.6% (95% confidence interval (CI): 0.89-6.7) and 1.3% (95% CI: 0.38-3.6), respectively. Comparing deaths on board with expected deaths based on naive CFR estimates from China, we estimated CFR and IFR in China to be 1.2% (95% CI: 0.3-2.7) and 0.6% (95% CI: 0.2-1.3), respectively.",,pdf:https://www.eurosurveillance.org/deliver/fulltext/eurosurveillance/25/12/eurosurv-25-12-3.pdf?itemId=%2Fcontent%2F10.2807%2F1560-7917.ES.2020.25.12.2000256&mimeType=pdf&containerItemId=content/eurosurveillance; doi:https://doi.org/10.2807/1560-7917.ES.2020.25.12.2000256; html:https://europepmc.org/articles/PMC7118348; pdf:https://europepmc.org/articles/PMC7118348?pdf=render
 34672950,https://doi.org/10.1016/s2213-2600(21)00435-5,"Colchicine in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial.",RECOVERY Collaborative Group.,,The Lancet. Respiratory medicine,2021,2021-10-18,Y,,,,"<h4>Background</h4>Colchicine has been proposed as a treatment for COVID-19 based on its anti-inflammatory actions. We aimed to evaluate the efficacy and safety of colchicine in patients admitted to hospital with COVID-19.<h4>Methods</h4>In this streamlined, randomised, controlled, open-label trial, underway at 177 hospitals in the UK, two hospitals in Indonesia, and two hospitals in Nepal, several possible treatments were compared with usual care in patients hospitalised with COVID-19. Patients were eligible for inclusion in the study if they were admitted to hospital with clinically suspected or laboratory confirmed SARS-CoV-2 infection and had no medical history that might, in the opinion of the attending clinician, put the patient at significant risk if they were to participate in the trial. Eligible and consenting adults were randomly assigned (1:1) to receive either usual standard of care alone (usual care group) or usual standard of care plus colchicine (colchicine group) using web-based simple (unstratified) randomisation with allocation concealment. Participants received colchicine 1 mg after randomisation followed by 500 μg 12 h later and then 500 μg twice a day by mouth or nasogastric tube for 10 days in total or until discharge. Dose frequency was halved for patients receiving a moderate CYP3A4 inhibitor (eg, diltiazem), patients with an estimated glomerular filtration rate of less than 30 mL/min per 1·73m<sup>2</sup>, and those with an estimated bodyweight of less than 70 kg. The primary outcome was 28-day mortality, secondary endpoints included time to discharge, the proportion of patients discharged from hospital within 28 days, and, in patients not on invasive mechanical ventilation at randomisation, a composite endpoint of invasive mechanical ventilation or death. All analyses were by intention-to-treat. The trial is registered with ISRCTN, 50189673, and ClinicalTrials.gov, NCT04381936.<h4>Findings</h4>Between Nov 27, 2020, and March 4, 2021, 11 340 (58%) of 19 423 patients enrolled into the RECOVERY trial were eligible to receive colchicine; 5610 (49%) patients were randomly assigned to the colchicine group and 5730 (51%) to the usual care group. Overall, 1173 (21%) patients in the colchicine group and 1190 (21%) patients in the usual care group died within 28 days (rate ratio 1·01 [95% CI 0·93 to 1·10]; p=0·77). Consistent results were seen in all prespecified subgroups of patients. Median time to discharge alive (10 days [IQR 5 to >28]) was the same in both groups, and there was no significant difference in the proportion of patients discharged from hospital alive within 28 days (3901 [70%] patients in the colchicine group and 4032 [70%] usual care group; rate ratio 0·98 [95% CI 0·94 to 1·03]; p=0·44). In those not on invasive mechanical ventilation at baseline, there was no significant difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (1344 [25%] in the colchicine group vs 1343 [25%] patients in the usual care group; risk ratio 1·02 [95% CI 0·96 to 1·09]; p=0·47).<h4>Interpretation</h4>In adults hospitalised with COVID-19, colchicine was not associated with reductions in 28-day mortality, duration of hospital stay, or risk of progressing to invasive mechanical ventilation or death.<h4>Funding</h4>UK Research and Innovation (Medical Research Council), National Institute of Health Research, and Wellcome Trust.",,pdf:http://www.thelancet.com/article/S2213260021004355/pdf; doi:https://doi.org/10.1016/S2213-2600(21)00435-5; html:https://europepmc.org/articles/PMC8523117
 32046816,https://doi.org/10.2807/1560-7917.es.2020.25.5.2000080,Effectiveness of airport screening at detecting travellers infected with novel coronavirus (2019-nCoV).,"Quilty BJ, Clifford S, CMMID nCoV working group2, Flasche S, Eggo RM.",,Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin,2020,2020-02-01,Y,Surveillance; Effectiveness; Interventions; Emerging Infections; 2019-Ncov; Airport Screening; Thermal Scanning,,,"We evaluated effectiveness of thermal passenger screening for 2019-nCoV infection at airport exit and entry to inform public health decision-making. In our baseline scenario, we estimated that 46% (95% confidence interval: 36 to 58) of infected travellers would not be detected, depending on incubation period, sensitivity of exit and entry screening, and proportion of asymptomatic cases. Airport screening is unlikely to detect a sufficient proportion of 2019-nCoV infected travellers to avoid entry of infected travellers.",,pdf:https://www.eurosurveillance.org/deliver/fulltext/eurosurveillance/25/5/eurosurv-25-5-2.pdf?itemId=%2Fcontent%2F10.2807%2F1560-7917.ES.2020.25.5.2000080&mimeType=pdf&containerItemId=content/eurosurveillance; doi:https://doi.org/10.2807/1560-7917.ES.2020.25.5.2000080; html:https://europepmc.org/articles/PMC7014668; pdf:https://europepmc.org/articles/PMC7014668?pdf=render
@@ -579,12 +579,12 @@ PMC9023380,https://doi.org/,Assessing the spread risk of COVID-19 associated wit
 36769519,https://doi.org/10.3390/jcm12030872,Patterns of Healthcare Resource Utilisation of Critical Care Survivors between 2006 and 2017 in Wales: A Population-Based Study.,"Alsallakh M, Tan L, Pugh R, Akbari A, Bailey R, Griffiths R, Lyons RA, Szakmany T.",,Journal of clinical medicine,2023,2023-01-21,Y,Wales; Healthcare Resource Utilisation; Critical Care Survivorship,,,"In this retrospective cohort study, we used the Secure Anonymised Information Linkage (SAIL) Databank to characterise and identify predictors of the one-year post-discharge healthcare resource utilisation (HRU) of adults who were admitted to critical care units in Wales between 1 April 2006 and 31 December 2017. We modelled one-year post-critical-care HRU using negative binomial models and used linear models for the difference from one-year pre-critical-care HRU. We estimated the association between critical illness and post-hospitalisation HRU using multilevel negative binomial models among people hospitalised in 2015. We studied 55,151 patients. Post-critical-care HRU was 11-87% greater than pre-critical-care levels, whereas emergency department (ED) attendances decreased by 30%. Age ≥50 years was generally associated with greater post-critical-care HRU; those over 80 had three times longer hospital readmissions than those younger than 50 (incidence rate ratio (IRR): 2.96, 95% CI: 2.84, 3.09). However, ED attendances were higher in those younger than 50. High comorbidity was associated with 22-62% greater post-critical-care HRU than no or low comorbidity. The most socioeconomically deprived quintile was associated with 24% more ED attendances (IRR: 1.24 [1.16, 1.32]) and 13% longer hospital stays (IRR: 1.13 [1.09, 1.17]) than the least deprived quintile. Critical care survivors had greater 1-year post-discharge HRU than non-critical inpatients, including 68% longer hospital stays (IRR: 1.68 [1.63, 1.74]). Critical care survivors, particularly those with older ages, high comorbidity, and socioeconomic deprivation, used significantly more primary and secondary care resources after discharge compared with their baseline and non-critical inpatients. Interventions are needed to ensure that key subgroups are identified and adequately supported.",,pdf:https://www.mdpi.com/2077-0383/12/3/872/pdf?version=1674984751; doi:https://doi.org/10.3390/jcm12030872; html:https://europepmc.org/articles/PMC9917699; pdf:https://europepmc.org/articles/PMC9917699?pdf=render
 PMC10686417,https://doi.org/,The impact of restricted provision of publicly funded elective hip and knee joints replacement during the COVID-19 pandemic in England,"Penfold C, Blom A, Redaniel M, Jones T, Eyles E, Keen T, Elliott A, Judge A.",,PloS one,2023,2023-01-01,Y,,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10686417/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10686417/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC10686417; pdf:https://europepmc.org/articles/PMC10686417?pdf=render
 33655079,https://doi.org/10.12688/wellcomeopenres.16304.2,Impact of baseline cases of cough and fever on UK COVID-19 diagnostic testing rates: estimates from the Bug Watch community cohort study.,"Eyre MT, Burns R, Kirkby V, Smith C, Denaxas S, Nguyen V, Hayward A, Shallcross L, Fragaszy E, Aldridge RW.",,Wellcome open research,2020,2020-01-01,Y,Fever; Cough; United Kingdom; Diagnostic Testing Capacity; Swab Test; Covid-19,,,"<b>Background:</b> Diagnostic testing forms a major part of the UK's response to the current coronavirus disease 2019 (COVID-19) pandemic with tests offered to anyone with a continuous cough, high temperature or anosmia. Testing capacity must be sufficient during the winter respiratory season when levels of cough and fever are high due to non-COVID-19 causes. This study aims to make predictions about the contribution of baseline cough or fever to future testing demand in the UK. <b>Methods:</b> In this analysis of the Bug Watch community cohort study, we estimated the incidence of cough or fever in England in 2018-2019. We then estimated the COVID-19 diagnostic testing rates required in the UK for baseline cough or fever cases for the period July 2020-June 2021. This was explored for different rates of the population requesting tests, four COVID-19 second wave scenarios and high and low baseline cough or fever incidence scenarios. <b>Results:</b> Under the high baseline cough or fever scenario, incidence in the UK is expected to rise rapidly from 250,708 (95%CI 181,095 - 347,080) cases per day in September to a peak of 444,660 (95%CI 353,084 - 559,988) in December. If 80% of these cases request tests, testing demand would exceed 1.4 million tests per week for five consecutive months. Demand was significantly lower in the low cough or fever incidence scenario, with 129,115 (95%CI 111,596 - 151,679) tests per day in January 2021, compared to 340,921 (95%CI 276,039 - 424,491) tests per day in the higher incidence scenario. <b>Conclusions:</b> Our results show that national COVID-19 testing demand is highly dependent on background cough or fever incidence. This study highlights that the UK's response to the COVID-19 pandemic must ensure that a high proportion of people with symptoms request tests, and that testing capacity is sufficient to meet the high predicted demand.",,doi:https://doi.org/10.12688/wellcomeopenres.16304.2; html:https://europepmc.org/articles/PMC7890379; pdf:https://europepmc.org/articles/PMC7890379?pdf=render
-37248229,https://doi.org/10.1038/s41467-023-38756-3,Evidence-driven spatiotemporal COVID-19 hospitalization prediction with Ising dynamics.,"Gao J, Heintz J, Mack C, Glass L, Cross A, Sun J.",,Nature communications,2023,2023-05-29,Y,,,,"In this work, we aim to accurately predict the number of hospitalizations during the COVID-19 pandemic by developing a spatiotemporal prediction model. We propose HOIST, an Ising dynamics-based deep learning model for spatiotemporal COVID-19 hospitalization prediction. By drawing the analogy between locations and lattice sites in statistical mechanics, we use the Ising dynamics to guide the model to extract and utilize spatial relationships across locations and model the complex influence of granular information from real-world clinical evidence. By leveraging rich linked databases, including insurance claims, census information, and hospital resource usage data across the U.S., we evaluate the HOIST model on the large-scale spatiotemporal COVID-19 hospitalization prediction task for 2299 counties in the U.S. In the 4-week hospitalization prediction task, HOIST achieves 368.7 mean absolute error, 0.6 [Formula: see text] and 0.89 concordance correlation coefficient score on average. Our detailed number needed to treat (NNT) and cost analysis suggest that future COVID-19 vaccination efforts may be most impactful in rural areas. This model may serve as a resource for future county and state-level vaccination efforts.",,doi:https://doi.org/10.1038/s41467-023-38756-3; doi:https://doi.org/10.1038/s41467-023-38756-3; html:https://europepmc.org/articles/PMC10226446; pdf:https://europepmc.org/articles/PMC10226446?pdf=render
-32907855,https://doi.org/10.1136/bmj.m3339,Risk stratification of patients admitted to hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: development and validation of the 4C Mortality Score.,"Knight SR, Ho A, Pius R, Buchan I, Carson G, Drake TM, Dunning J, Fairfield CJ, Gamble C, Green CA, Gupta R, Halpin S, Hardwick HE, Holden KA, Horby PW, Jackson C, Mclean KA, Merson L, Nguyen-Van-Tam JS, Norman L, Noursadeghi M, Olliaro PL, Pritchard MG, Russell CD, Shaw CA, Sheikh A, Solomon T, Sudlow C, Swann OV, Turtle LC, Openshaw PJ, Baillie JK, Semple MG, Docherty AB, Harrison EM, ISARIC4C investigators.",,BMJ (Clinical research ed.),2020,2020-09-09,Y,,,,"<h4>Objective</h4>To develop and validate a pragmatic risk score to predict mortality in patients admitted to hospital with coronavirus disease 2019 (covid-19).<h4>Design</h4>Prospective observational cohort study.<h4>Setting</h4>International Severe Acute Respiratory and emerging Infections Consortium (ISARIC) World Health Organization (WHO) Clinical Characterisation Protocol UK (CCP-UK) study (performed by the ISARIC Coronavirus Clinical Characterisation Consortium-ISARIC-4C) in 260 hospitals across England, Scotland, and Wales. Model training was performed on a cohort of patients recruited between 6 February and 20 May 2020, with validation conducted on a second cohort of patients recruited after model development between 21 May and 29 June 2020<i>.</i> PARTICIPANTS: Adults (age ≥18 years) admitted to hospital with covid-19 at least four weeks before final data extraction.<h4>Main outcome measure</h4>In-hospital mortality.<h4>Results</h4>35 463 patients were included in the derivation dataset (mortality rate 32.2%) and 22 361 in the validation dataset (mortality rate 30.1%). The final 4C Mortality Score included eight variables readily available at initial hospital assessment: age, sex, number of comorbidities, respiratory rate, peripheral oxygen saturation, level of consciousness, urea level, and C reactive protein (score range 0-21 points). The 4C Score showed high discrimination for mortality (derivation cohort: area under the receiver operating characteristic curve 0.79, 95% confidence interval 0.78 to 0.79; validation cohort: 0.77, 0.76 to 0.77) with excellent calibration (validation: calibration-in-the-large=0, slope=1.0). Patients with a score of at least 15 (n=4158, 19%) had a 62% mortality (positive predictive value 62%) compared with 1% mortality for those with a score of 3 or less (n=1650, 7%; negative predictive value 99%). Discriminatory performance was higher than 15 pre-existing risk stratification scores (area under the receiver operating characteristic curve range 0.61-0.76), with scores developed in other covid-19 cohorts often performing poorly (range 0.63-0.73).<h4>Conclusions</h4>An easy-to-use risk stratification score has been developed and validated based on commonly available parameters at hospital presentation. The 4C Mortality Score outperformed existing scores, showed utility to directly inform clinical decision making, and can be used to stratify patients admitted to hospital with covid-19 into different management groups. The score should be further validated to determine its applicability in other populations.<h4>Study registration</h4>ISRCTN66726260.",,pdf:https://www.bmj.com/content/bmj/370/bmj.m3339.full.pdf; doi:https://doi.org/10.1136/bmj.m3339; html:https://europepmc.org/articles/PMC7116472; pdf:https://europepmc.org/articles/PMC7116472?pdf=render
 33024096,https://doi.org/10.1038/s41467-020-18783-0,Changing travel patterns in China during the early stages of the COVID-19 pandemic.,"Gibbs H, Liu Y, Pearson CAB, Jarvis CI, Grundy C, Quilty BJ, Diamond C, LSHTM CMMID COVID-19 working group, Eggo RM.",,Nature communications,2020,2020-10-06,Y,,,,"Understanding changes in human mobility in the early stages of the COVID-19 pandemic is crucial for assessing the impacts of travel restrictions designed to reduce disease spread. Here, relying on data from mainland China, we investigate the spatio-temporal characteristics of human mobility between 1st January and 1st March 2020, and discuss their public health implications. An outbound travel surge from Wuhan before travel restrictions were implemented was also observed across China due to the Lunar New Year, indicating that holiday travel may have played a larger role in mobility changes compared to impending travel restrictions. Holiday travel also shifted healthcare pressure related to COVID-19 towards locations with lower healthcare capacity. Network analyses showed no sign of major changes in the transportation network after Lunar New Year. Changes observed were temporary and did not lead to structural reorganisation of the transportation network during the study period.",,pdf:https://www.nature.com/articles/s41467-020-18783-0.pdf; doi:https://doi.org/10.1038/s41467-020-18783-0; html:https://europepmc.org/articles/PMC7538915; pdf:https://europepmc.org/articles/PMC7538915?pdf=render
+32907855,https://doi.org/10.1136/bmj.m3339,Risk stratification of patients admitted to hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: development and validation of the 4C Mortality Score.,"Knight SR, Ho A, Pius R, Buchan I, Carson G, Drake TM, Dunning J, Fairfield CJ, Gamble C, Green CA, Gupta R, Halpin S, Hardwick HE, Holden KA, Horby PW, Jackson C, Mclean KA, Merson L, Nguyen-Van-Tam JS, Norman L, Noursadeghi M, Olliaro PL, Pritchard MG, Russell CD, Shaw CA, Sheikh A, Solomon T, Sudlow C, Swann OV, Turtle LC, Openshaw PJ, Baillie JK, Semple MG, Docherty AB, Harrison EM, ISARIC4C investigators.",,BMJ (Clinical research ed.),2020,2020-09-09,Y,,,,"<h4>Objective</h4>To develop and validate a pragmatic risk score to predict mortality in patients admitted to hospital with coronavirus disease 2019 (covid-19).<h4>Design</h4>Prospective observational cohort study.<h4>Setting</h4>International Severe Acute Respiratory and emerging Infections Consortium (ISARIC) World Health Organization (WHO) Clinical Characterisation Protocol UK (CCP-UK) study (performed by the ISARIC Coronavirus Clinical Characterisation Consortium-ISARIC-4C) in 260 hospitals across England, Scotland, and Wales. Model training was performed on a cohort of patients recruited between 6 February and 20 May 2020, with validation conducted on a second cohort of patients recruited after model development between 21 May and 29 June 2020<i>.</i> PARTICIPANTS: Adults (age ≥18 years) admitted to hospital with covid-19 at least four weeks before final data extraction.<h4>Main outcome measure</h4>In-hospital mortality.<h4>Results</h4>35 463 patients were included in the derivation dataset (mortality rate 32.2%) and 22 361 in the validation dataset (mortality rate 30.1%). The final 4C Mortality Score included eight variables readily available at initial hospital assessment: age, sex, number of comorbidities, respiratory rate, peripheral oxygen saturation, level of consciousness, urea level, and C reactive protein (score range 0-21 points). The 4C Score showed high discrimination for mortality (derivation cohort: area under the receiver operating characteristic curve 0.79, 95% confidence interval 0.78 to 0.79; validation cohort: 0.77, 0.76 to 0.77) with excellent calibration (validation: calibration-in-the-large=0, slope=1.0). Patients with a score of at least 15 (n=4158, 19%) had a 62% mortality (positive predictive value 62%) compared with 1% mortality for those with a score of 3 or less (n=1650, 7%; negative predictive value 99%). Discriminatory performance was higher than 15 pre-existing risk stratification scores (area under the receiver operating characteristic curve range 0.61-0.76), with scores developed in other covid-19 cohorts often performing poorly (range 0.63-0.73).<h4>Conclusions</h4>An easy-to-use risk stratification score has been developed and validated based on commonly available parameters at hospital presentation. The 4C Mortality Score outperformed existing scores, showed utility to directly inform clinical decision making, and can be used to stratify patients admitted to hospital with covid-19 into different management groups. The score should be further validated to determine its applicability in other populations.<h4>Study registration</h4>ISRCTN66726260.",,pdf:https://www.bmj.com/content/bmj/370/bmj.m3339.full.pdf; doi:https://doi.org/10.1136/bmj.m3339; html:https://europepmc.org/articles/PMC7116472; pdf:https://europepmc.org/articles/PMC7116472?pdf=render
+37248229,https://doi.org/10.1038/s41467-023-38756-3,Evidence-driven spatiotemporal COVID-19 hospitalization prediction with Ising dynamics.,"Gao J, Heintz J, Mack C, Glass L, Cross A, Sun J.",,Nature communications,2023,2023-05-29,Y,,,,"In this work, we aim to accurately predict the number of hospitalizations during the COVID-19 pandemic by developing a spatiotemporal prediction model. We propose HOIST, an Ising dynamics-based deep learning model for spatiotemporal COVID-19 hospitalization prediction. By drawing the analogy between locations and lattice sites in statistical mechanics, we use the Ising dynamics to guide the model to extract and utilize spatial relationships across locations and model the complex influence of granular information from real-world clinical evidence. By leveraging rich linked databases, including insurance claims, census information, and hospital resource usage data across the U.S., we evaluate the HOIST model on the large-scale spatiotemporal COVID-19 hospitalization prediction task for 2299 counties in the U.S. In the 4-week hospitalization prediction task, HOIST achieves 368.7 mean absolute error, 0.6 [Formula: see text] and 0.89 concordance correlation coefficient score on average. Our detailed number needed to treat (NNT) and cost analysis suggest that future COVID-19 vaccination efforts may be most impactful in rural areas. This model may serve as a resource for future county and state-level vaccination efforts.",,doi:https://doi.org/10.1038/s41467-023-38756-3; doi:https://doi.org/10.1038/s41467-023-38756-3; html:https://europepmc.org/articles/PMC10226446; pdf:https://europepmc.org/articles/PMC10226446?pdf=render
+36333839,https://doi.org/10.1002/gps.5834,The impact of the first UK COVID-19 lockdown on presentations with psychosis to mental health services for older adults: An electronic health records study in South London.,"Simkin L, Yung P, Greig F, Perera G, Tsamakis K, Rizos E, Stewart R, Velayudhan L, Mueller C.",,International journal of geriatric psychiatry,2022,2022-12-01,Y,Dementia; Hallucinations; Delusions; Psychosis; Older Adults; Lockdown; Covid‐19; Non‐white Ethnicity,,,"<h4>Objectives</h4>Social distancing restrictions in the COVID-19 pandemic may have had adverse effects on older adults' mental health. Whereby the impact on mood is well-described, less is known about psychotic symptoms. The aim of this study was to compare characteristics associated with psychotic symptoms during the first UK lockdown and a pre-pandemic comparison period.<h4>Methods</h4>In this retrospective observational study we analysed anonymised records from patients referred to mental health services for older adults in South London in the 16-week period of the UK lockdown starting in March 2020, and in the comparable pre-pandemic period in 2019. We used logistic regression models to compare the associations of different patient characteristics with increased odds of presenting with any psychotic symptom (defined as hallucinations and/or delusion), hallucinations, or delusions, during lockdown and the corresponding pre-pandemic period.<h4>Results</h4>1991 referrals were identified. There were fewer referrals during lockdown but a higher proportion of presentations with any psychotic symptom (48.7% vs. 42.8%, p = 0.018), particularly hallucinations (41.0% vs. 27.8%, p < 0.001). Patients of non-White ethnicity (adjusted odds ratio (OR): 1.83; 95% confidence interval (CI): 1.13-2.99) and patients with dementia (adjusted OR: 3.09; 95% CI: 1.91-4.99) were more likely to be referred with psychotic symptoms during lockdown. While a weaker association between dementia and psychotic symptoms was found in the pre-COVID period (adjusted OR: 1.55; 95% CI: 1.19-2.03), interaction terms indicated higher odds of patients of non-White ethnicity or dementia to present with psychosis during the lockdown period.<h4>Conclusions</h4>During lockdown, referrals to mental health services for adults decreased, but contained a higher proportion with psychotic symptoms. The stronger association with psychotic symptoms in non-White ethnic groups and patients with dementia during lockdown suggests that barriers in accessing care might have increased during the COVID-19 pandemic.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/gps.5834; doi:https://doi.org/10.1002/gps.5834; html:https://europepmc.org/articles/PMC9828419; pdf:https://europepmc.org/articles/PMC9828419?pdf=render
 33319712,https://doi.org/10.1186/s12911-020-01336-2,Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies.,"Slater LT, Gkoutos GV, Hoehndorf R.",,BMC medical informatics and decision making,2020,2020-12-15,Y,Automated Reasoning; Ontology Interoperability,,,"<h4>Background</h4>Ontologies are widely used throughout the biomedical domain. These ontologies formally represent the classes and relations assumed to exist within a domain. As scientific domains are deeply interlinked, so too are their representations. While individual ontologies can be tested for consistency and coherency using automated reasoning methods, systematically combining ontologies of multiple domains together may reveal previously hidden contradictions.<h4>Methods</h4>We developed a method that tests for hidden unsatisfiabilities in an ontology that arise when combined with other ontologies. For this purpose, we combined sets of ontologies and use automated reasoning to determine whether unsatisfiable classes are present. In addition, we designed and implemented a novel algorithm that can determine justifications for contradictions across extremely large and complicated ontologies, and use these justifications to semi-automatically repair ontologies by identifying a small set of axioms that, when removed, result in a consistent and coherent set of ontologies.<h4>Results</h4>We tested the mutual consistency of the OBO Foundry and the OBO ontologies and find that the combined OBO Foundry gives rise to at least 636 unsatisfiable classes, while the OBO ontologies give rise to more than 300,000 unsatisfiable classes. We also applied our semi-automatic repair algorithm to each combination of OBO ontologies that resulted in unsatisfiable classes, finding that only 117 axioms could be removed to account for all cases of unsatisfiability across all OBO ontologies.<h4>Conclusions</h4>We identified a large set of hidden unsatisfiability across a broad range of biomedical ontologies, and we find that this large set of unsatisfiable classes is the result of a relatively small amount of axiomatic disagreements. Our results show that hidden unsatisfiability is a serious problem in ontology interoperability; however, our results also provide a way towards more consistent ontologies by addressing the issues we identified.",,pdf:https://bmcmedinformdecismak.biomedcentral.com/track/pdf/10.1186/s12911-020-01336-2; doi:https://doi.org/10.1186/s12911-020-01336-2; html:https://europepmc.org/articles/PMC7736131; pdf:https://europepmc.org/articles/PMC7736131?pdf=render
 33531486,https://doi.org/10.1038/s41467-021-21370-6,Author Correction: Genetic architecture of host proteins involved in SARS-CoV-2 infection.,"Pietzner M, Wheeler E, Carrasco-Zanini J, Raffler J, Kerrison ND, Oerton E, Auyeung VPW, Luan J, Finan C, Casas JP, Ostroff R, Williams SA, Kastenmüller G, Ralser M, Gamazon ER, Wareham NJ, Hingorani AD, Langenberg C.",,Nature communications,2021,2021-02-02,Y,,,,,,pdf:https://www.nature.com/articles/s41467-021-21370-6.pdf; doi:https://doi.org/10.1038/s41467-021-21370-6; html:https://europepmc.org/articles/PMC7854714; pdf:https://europepmc.org/articles/PMC7854714?pdf=render
-36333839,https://doi.org/10.1002/gps.5834,The impact of the first UK COVID-19 lockdown on presentations with psychosis to mental health services for older adults: An electronic health records study in South London.,"Simkin L, Yung P, Greig F, Perera G, Tsamakis K, Rizos E, Stewart R, Velayudhan L, Mueller C.",,International journal of geriatric psychiatry,2022,2022-12-01,Y,Dementia; Hallucinations; Delusions; Psychosis; Older Adults; Lockdown; Covid‐19; Non‐white Ethnicity,,,"<h4>Objectives</h4>Social distancing restrictions in the COVID-19 pandemic may have had adverse effects on older adults' mental health. Whereby the impact on mood is well-described, less is known about psychotic symptoms. The aim of this study was to compare characteristics associated with psychotic symptoms during the first UK lockdown and a pre-pandemic comparison period.<h4>Methods</h4>In this retrospective observational study we analysed anonymised records from patients referred to mental health services for older adults in South London in the 16-week period of the UK lockdown starting in March 2020, and in the comparable pre-pandemic period in 2019. We used logistic regression models to compare the associations of different patient characteristics with increased odds of presenting with any psychotic symptom (defined as hallucinations and/or delusion), hallucinations, or delusions, during lockdown and the corresponding pre-pandemic period.<h4>Results</h4>1991 referrals were identified. There were fewer referrals during lockdown but a higher proportion of presentations with any psychotic symptom (48.7% vs. 42.8%, p = 0.018), particularly hallucinations (41.0% vs. 27.8%, p < 0.001). Patients of non-White ethnicity (adjusted odds ratio (OR): 1.83; 95% confidence interval (CI): 1.13-2.99) and patients with dementia (adjusted OR: 3.09; 95% CI: 1.91-4.99) were more likely to be referred with psychotic symptoms during lockdown. While a weaker association between dementia and psychotic symptoms was found in the pre-COVID period (adjusted OR: 1.55; 95% CI: 1.19-2.03), interaction terms indicated higher odds of patients of non-White ethnicity or dementia to present with psychosis during the lockdown period.<h4>Conclusions</h4>During lockdown, referrals to mental health services for adults decreased, but contained a higher proportion with psychotic symptoms. The stronger association with psychotic symptoms in non-White ethnic groups and patients with dementia during lockdown suggests that barriers in accessing care might have increased during the COVID-19 pandemic.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/gps.5834; doi:https://doi.org/10.1002/gps.5834; html:https://europepmc.org/articles/PMC9828419; pdf:https://europepmc.org/articles/PMC9828419?pdf=render
 34503493,https://doi.org/10.1186/s12916-021-02107-0,"Estimating the impact of reopening schools on the reproduction number of SARS-CoV-2 in England, using weekly contact survey data.","Munday JD, Jarvis CI, Gimma A, Wong KLM, van Zandvoort K, CMMID COVID-19 Working Group, Funk S, Edmunds WJ.",,BMC medicine,2021,2021-09-10,Y,School Closure; Reproduction Number; Social Contacts; Covid-19; Sars-cov-2; Comix,,,"<h4>Background</h4>Schools were closed in England on 4 January 2021 as part of increased national restrictions to curb transmission of SARS-CoV-2. The UK government reopened schools on 8 March. Although there was evidence of lower individual-level transmission risk amongst children compared to adults, the combined effects of this with increased contact rates in school settings and the resulting impact on the overall transmission rate in the population were not clear.<h4>Methods</h4>We measured social contacts of > 5000 participants weekly from March 2020, including periods when schools were both open and closed, amongst other restrictions. We combined these data with estimates of the susceptibility and infectiousness of children compared with adults to estimate the impact of reopening schools on the reproduction number.<h4>Results</h4>Our analysis indicates that reopening all schools under the same measures as previous periods that combined lockdown with face-to-face schooling would be likely to increase the reproduction number substantially. Assuming a baseline of 0.8, we estimated a likely increase to between 1.0 and 1.5 with the reopening of all schools or to between 0.9 and 1.2 reopening primary or secondary schools alone.<h4>Conclusion</h4>Our results suggest that reopening schools would likely halt the fall in cases observed between January and March 2021 and would risk a return to rising infections, but these estimates relied heavily on the latest estimates or reproduction number and the validity of the susceptibility and infectiousness profiles we used at the time of reopening.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-021-02107-0; doi:https://doi.org/10.1186/s12916-021-02107-0; html:https://europepmc.org/articles/PMC8428960; pdf:https://europepmc.org/articles/PMC8428960?pdf=render
 39414270,https://doi.org/10.1136/bmjopen-2024-088600,What is the carbon footprint of academic clinical trials? A study of hotspots in 10 trials.,"Griffiths J, Adshead F, Al-Shahi Salman R, Anderson C, Bedson E, Bliss J, Boshoff A, Chen X, Cranley D, Doran P, Dunne F, Gamble C, Gillies K, Hood K, Kavanagh C, Malone J, McGregor N, McNamara C, Midha E, Moore K, Murphy L, Newman C, O'Reilly S, Perkins AM, Pett S, Sydes MR, Whitty L, You F, Fox L, Williamson PR.",,BMJ open,2024,2024-10-16,Y,Climate change; Randomized controlled trial; Clinical Trial; Statistics & Research Methods,,,"<h4>Background</h4>Clinical trials are fundamental to healthcare, however, they also contribute to anthropogenic climate change. Following previous work to develop and test a method and guidance to calculate the carbon footprint of clinical trials, we have now applied the guidance to 10 further UK and international, academically sponsored clinical trials to continue the identification of hotspots and opportunities for lower carbon trial design.<h4>Methods</h4>10 collaborating clinical trial units (CTUs) self-identified and a trial was selected from their portfolio to represent a variety of designs, health areas and interventions. Trial activity data was collated by trial teams across 10 modules spanning trial setup through to closure, then multiplied by emission factors provided in the guidance to calculate the carbon footprint. Feedback was collected from trial teams on the process, experience and ease of use of the guidance.<h4>Results</h4>We footprinted 10 trials: 6 investigational medicinal product trials, 1 nutritional, 1 surgical, 1 health surveillance and one complex intervention trial. Six of these were completed and four ongoing (two in follow-up and two recruiting). The carbon footprint of the 10 trials ranged from 16 to 765 tonnes CO<sub>2</sub>e. Common hotspots were identified as CTU emissions, trial-specific patient assessments and trial team meetings and travel. Hotspots for specific trial designs were also identified. The time taken to collate activity data and complete carbon calculations ranged from 5 to 60 hours. The draft guidance was updated to include new activities identified from the 10 trials and in response to user feedback.<h4>Discussion</h4>There are opportunities to reduce the impact of trials across all modules, particularly trial-specific meetings and travel, patient assessments and laboratory practice. A trial's carbon footprint should be considered at the design stage, but work is required to make this common place.",,doi:https://doi.org/10.1136/bmjopen-2024-088600; html:https://europepmc.org/articles/PMC11487931; pdf:https://europepmc.org/articles/PMC11487931?pdf=render
 37193316,https://doi.org/10.1016/j.xops.2023.100293,"A Datasheet for the INSIGHT Birmingham, Solihull, and Black Country Diabetic Retinopathy Screening Dataset.","Kale AU, Mills A, Guggenheim E, Gee D, Bodza S, Anumakonda A, Doal R, Williams R, Gallier S, Lee WH, Galsworthy P, Benning M, Fanning H, Keane PA, Denniston AK, Mollan SP.",,Ophthalmology science,2023,2023-02-26,Y,Diabetes mellitus; Diabetic retinopathy; Imaging; Dataset; Biomedical Data,,,"<h4>Purpose</h4>Diabetic retinopathy (DR) is the most common microvascular complication associated with diabetes mellitus (DM), affecting approximately 40% of this patient population. Early detection of DR is vital to ensure monitoring of disease progression and prompt sight saving treatments as required. This article describes the data contained within the INSIGHT Birmingham, Solihull, and Black Country Diabetic Retinopathy Dataset.<h4>Design</h4>Dataset descriptor for routinely collected eye screening data.<h4>Participants</h4>All diabetic patients aged 12 years and older, attending annual digital retinal photography-based screening within the Birmingham, Solihull, and Black Country Eye Screening Programme.<h4>Methods</h4>The INSIGHT Health Data Research Hub for Eye Health is a National Health Service (NHS)-led ophthalmic bioresource that provides researchers with safe access to anonymized, routinely collected data from contributing NHS hospitals to advance research for patient benefit. This report describes the INSIGHT Birmingham, Solihull, and Black Country DR Screening Dataset, a dataset of anonymized images and linked screening data derived from the United Kingdom's largest regional DR screening program.<h4>Main outcome measures</h4>This dataset consists of routinely collected data from the eye screening program. The data primarily include retinal photographs with the associated DR grading data. Additional data such as corresponding demographic details, information regarding patients' diabetic status, and visual acuity data are also available. Further details regarding available data points are available in the supplementary information, in addition to the INSIGHT webpage included below.<h4>Results</h4>At the time point of this analysis (December 31, 2019), the dataset comprised 6 202 161 images from 246 180 patients, with a dataset inception date of January 1, 2007. The dataset includes 1 360 547 grading episodes between R0M0 and R3M1.<h4>Conclusions</h4>This dataset descriptor article summarizes the content of the dataset, how it has been curated, and what its potential uses are. Data are available through a structured application process for research studies that support discovery, clinical evidence analyses, and innovation in artificial intelligence technologies for patient benefit. Further information regarding the data repository and contact details can be found at https://www.insight.hdrhub.org/.<h4>Financial disclosures</h4>Proprietary or commercial disclosure may be found after the references.",,pdf:http://www.ophthalmologyscience.org/article/S2666914523000258/pdf; doi:https://doi.org/10.1016/j.xops.2023.100293; html:https://europepmc.org/articles/PMC10182318; pdf:https://europepmc.org/articles/PMC10182318?pdf=render
@@ -595,16 +595,16 @@ PMC10686417,https://doi.org/,The impact of restricted provision of publicly fund
 38626948,https://doi.org/10.1136/bmj-2023-078378,TRIPOD+AI statement: updated guidance for reporting clinical prediction models that use regression or machine learning methods.,"Collins GS, Moons KGM, Dhiman P, Riley RD, Beam AL, Van Calster B, Ghassemi M, Liu X, Reitsma JB, van Smeden M, Boulesteix AL, Camaradou JC, Celi LA, Denaxas S, Denniston AK, Glocker B, Golub RM, Harvey H, Heinze G, Hoffman MM, Kengne AP, Lam E, Lee N, Loder EW, Maier-Hein L, Mateen BA, McCradden MD, Oakden-Rayner L, Ordish J, Parnell R, Rose S, Singh K, Wynants L, Logullo P.",,BMJ (Clinical research ed.),2024,2024-04-16,Y,,,,,,pdf:https://www.bmj.com/content/bmj/385/bmj-2023-078378.full.pdf; doi:https://doi.org/10.1136/bmj-2023-078378; html:https://europepmc.org/articles/PMC11019967
 37068964,https://doi.org/10.3399/bjgp.2022.0301,OpenSAFELY NHS Service Restoration Observatory 2: changes in primary care clinical activity in England during the COVID-19 pandemic.,"Curtis HJ, MacKenna B, Wiedemann M, Fisher L, Croker R, Morton CE, Inglesby P, Walker AJ, Morley J, Mehrkar A, Bacon SC, Hickman G, Evans D, Ward T, Davy S, Hulme WJ, Macdonald O, Conibere R, Lewis T, Myers M, Wanninayake S, Collison K, Drury C, Samuel M, Sood H, Cipriani A, Fazel S, Sharma M, Baqir W, Bates C, Parry J, Goldacre B, OpenSAFELY Collaborative.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2023,2023-04-27,Y,Primary Health Care; General Practice; Electronic Health Records; Covid-19,,,"<h4>Background</h4>The COVID-19 pandemic has disrupted healthcare activity across a broad range of clinical services. The NHS stopped non-urgent work in March 2020, later recommending services be restored to near-normal levels before winter where possible.<h4>Aim</h4>To describe changes in the volume and variation of coded clinical activity in general practice across six clinical areas: cardiovascular disease, diabetes, mental health, female and reproductive health, screening and related procedures, and processes related to medication.<h4>Design and setting</h4>With the approval of NHS England, a cohort study was conducted of 23.8 million patient records in general practice, in situ using OpenSAFELY.<h4>Method</h4>Common primary care activities were analysed using Clinical Terms Version 3 codes and keyword searches from January 2019 to December 2020, presenting median and deciles of code usage across practices per month.<h4>Results</h4>Substantial and widespread changes in clinical activity in primary care were identified since the onset of the COVID-19 pandemic, with generally good recovery by December 2020. A few exceptions showed poor recovery and warrant further investigation, such as mental health (for example, for 'Depression interim review' the median occurrences across practices in December 2020 was down by 41.6% compared with December 2019).<h4>Conclusion</h4>Granular NHS general practice data at population-scale can be used to monitor disruptions to healthcare services and guide the development of mitigation strategies. The authors are now developing real-time monitoring dashboards for the key measures identified in this study, as well as further studies using primary care data to monitor and mitigate the indirect health impacts of COVID-19 on the NHS.",,pdf:https://bjgp.org/content/bjgp/early/2023/01/31/BJGP.2022.0301.full.pdf; doi:https://doi.org/10.3399/BJGP.2022.0301; html:https://europepmc.org/articles/PMC10131234; pdf:https://europepmc.org/articles/PMC10131234?pdf=render
 33612430,https://doi.org/10.1016/s2589-7500(21)00017-0,Indirect acute effects of the COVID-19 pandemic on physical and mental health in the UK: a population-based study.,"Mansfield KE, Mathur R, Tazare J, Henderson AD, Mulick AR, Carreira H, Matthews AA, Bidulka P, Gayle A, Forbes H, Cook S, Wong AYS, Strongman H, Wing K, Warren-Gash C, Cadogan SL, Smeeth L, Hayes JF, Quint JK, McKee M, Langan SM.",,The Lancet. Digital health,2021,2021-02-18,Y,,,,"<h4>Background</h4>There are concerns that the response to the COVID-19 pandemic in the UK might have worsened physical and mental health, and reduced use of health services. However, the scale of the problem is unquantified, impeding development of effective mitigations. We aimed to ascertain what has happened to general practice contacts for acute physical and mental health outcomes during the pandemic.<h4>Methods</h4>Using de-identified electronic health records from the Clinical Research Practice Datalink (CPRD) Aurum (covering 13% of the UK population), between 2017 and 2020, we calculated weekly primary care contacts for selected acute physical and mental health conditions: anxiety, depression, self-harm (fatal and non-fatal), severe mental illness, eating disorder, obsessive-compulsive disorder, acute alcohol-related events, asthma exacerbation, chronic obstructive pulmonary disease exacerbation, acute cardiovascular events (cerebrovascular accident, heart failure, myocardial infarction, transient ischaemic attacks, unstable angina, and venous thromboembolism), and diabetic emergency. Primary care contacts included remote and face-to-face consultations, diagnoses from hospital discharge letters, and secondary care referrals, and conditions were identified through primary care records for diagnoses, symptoms, and prescribing. Our overall study population included individuals aged 11 years or older who had at least 1 year of registration with practices contributing to CPRD Aurum in the specified period, but denominator populations varied depending on the condition being analysed. We used an interrupted time-series analysis to formally quantify changes in conditions after the introduction of population-wide restrictions (defined as March 29, 2020) compared with the period before their introduction (defined as Jan 1, 2017 to March 7, 2020), with data excluded for an adjustment-to-restrictions period (March 8-28).<h4>Findings</h4>The overall population included 9 863 903 individuals on Jan 1, 2017, and increased to 10 226 939 by Jan 1, 2020. Primary care contacts for almost all conditions dropped considerably after the introduction of population-wide restrictions. The largest reductions were observed for contacts for diabetic emergencies (odds ratio 0·35 [95% CI 0·25-0·50]), depression (0·53 [0·52-0·53]), and self-harm (0·56 [0·54-0·58]). In the interrupted time-series analysis, with the exception of acute alcohol-related events (0·98 [0·89-1·10]), there was evidence of a reduction in contacts for all conditions (anxiety 0·67 [0·66-0·67], eating disorders 0·62 [0·59-0·66], obsessive-compulsive disorder [0·69 [0·64-0·74]], self-harm 0·56 [0·54-0·58], severe mental illness 0·80 [0·78-0·83], stroke 0·59 [0·56-0·62], transient ischaemic attack 0·63 [0·58-0·67], heart failure 0·62 [0·60-0·64], myocardial infarction 0·72 [0·68-0·77], unstable angina 0·72 [0·60-0·87], venous thromboembolism 0·94 [0·90-0·99], and asthma exacerbation 0·88 [0·86-0·90]). By July, 2020, except for unstable angina and acute alcohol-related events, contacts for all conditions had not recovered to pre-lockdown levels.<h4>Interpretation</h4>There were substantial reductions in primary care contacts for acute physical and mental conditions following the introduction of restrictions, with limited recovery by July, 2020. Further research is needed to ascertain whether these reductions reflect changes in disease frequency or missed opportunities for care. Maintaining health-care access should be a key priority in future public health planning, including further restrictions. The conditions we studied are sufficiently severe that any unmet need will have substantial ramifications for the people with the conditions as well as health-care provision.<h4>Funding</h4>Wellcome Trust Senior Fellowship, Health Data Research UK.",,pdf:http://www.thelancet.com/article/S2589750021000170/pdf; doi:https://doi.org/10.1016/S2589-7500(21)00017-0; html:https://europepmc.org/articles/PMC7985613; pdf:https://europepmc.org/articles/PMC7985613?pdf=render
-36749628,https://doi.org/10.2196/42449,Charting a Course for Smartphones and Wearables to Transform Population Health Research.,"Dixon WG, van der Veer SN, Ali SM, Laidlaw L, Dobson RJB, Sudlow C, Chico T, MacArthur JAL, Doherty A.",,Journal of medical Internet research,2023,2023-02-07,Y,Research; Health; Clinical; Data; Digital; Devices; Wearable; Mhealth; Mobile Health; Person-generated Health Data; Population Health Research,,,"The use of data from smartphones and wearable devices has huge potential for population health research, given the high level of device ownership; the range of novel health-relevant data types available from consumer devices; and the frequency and duration with which data are, or could be, collected. Yet, the uptake and success of large-scale mobile health research in the last decade have not met this intensely promoted opportunity. We make the argument that digital person-generated health data are required and necessary to answer many top priority research questions, using illustrative examples taken from the James Lind Alliance Priority Setting Partnerships. We then summarize the findings from 2 UK initiatives that considered the challenges and possible solutions for what needs to be done and how such solutions can be implemented to realize the future opportunities of digital person-generated health data for clinically important population health research. Examples of important areas that must be addressed to advance the field include digital inequality and possible selection bias; easy access for researchers to the appropriate data collection tools, including how best to harmonize data items; analysis methodologies for time series data; patient and public involvement and engagement methods for optimizing recruitment, retention, and public trust; and methods for providing research participants with greater control over their data. There is also a major opportunity, provided through the linkage of digital person-generated health data to routinely collected data, to support novel population health research, bringing together clinician-reported and patient-reported measures. We recognize that well-conducted studies need a wide range of diverse challenges to be skillfully addressed in unison (eg, challenges regarding epidemiology, data science and biostatistics, psychometrics, behavioral and social science, software engineering, user interface design, information governance, data management, and patient and public involvement and engagement). Consequently, progress would be accelerated by the establishment of a new interdisciplinary community where all relevant and necessary skills are brought together to allow for excellence throughout the life cycle of a research study. This will require a partnership of diverse people, methods, and technologies. If done right, the synergy of such a partnership has the potential to transform many millions of people's lives for the better.",,pdf:https://www.jmir.org/2023/1/e42449/PDF; doi:https://doi.org/10.2196/42449; html:https://europepmc.org/articles/PMC11334374; html:https://europepmc.org/articles/PMC7614184; pdf:https://europepmc.org/articles/PMC7614184?pdf=render
 33444539,https://doi.org/10.1016/s2213-2600(20)30559-2,Development and validation of the ISARIC 4C Deterioration model for adults hospitalised with COVID-19: a prospective cohort study.,"Gupta RK, Harrison EM, Ho A, Docherty AB, Knight SR, van Smeden M, Abubakar I, Lipman M, Quartagno M, Pius R, Buchan I, Carson G, Drake TM, Dunning J, Fairfield CJ, Gamble C, Green CA, Halpin S, Hardwick HE, Holden KA, Horby PW, Jackson C, Mclean KA, Merson L, Nguyen-Van-Tam JS, Norman L, Olliaro PL, Pritchard MG, Russell CD, Scott-Brown J, Shaw CA, Sheikh A, Solomon T, Sudlow C, Swann OV, Turtle L, Openshaw PJM, Baillie JK, Semple MG, Noursadeghi M, ISARIC4C Investigators.",,The Lancet. Respiratory medicine,2021,2021-01-11,Y,,,,"<h4>Background</h4>Prognostic models to predict the risk of clinical deterioration in acute COVID-19 cases are urgently required to inform clinical management decisions.<h4>Methods</h4>We developed and validated a multivariable logistic regression model for in-hospital clinical deterioration (defined as any requirement of ventilatory support or critical care, or death) among consecutively hospitalised adults with highly suspected or confirmed COVID-19 who were prospectively recruited to the International Severe Acute Respiratory and Emerging Infections Consortium Coronavirus Clinical Characterisation Consortium (ISARIC4C) study across 260 hospitals in England, Scotland, and Wales. Candidate predictors that were specified a priori were considered for inclusion in the model on the basis of previous prognostic scores and emerging literature describing routinely measured biomarkers associated with COVID-19 prognosis. We used internal-external cross-validation to evaluate discrimination, calibration, and clinical utility across eight National Health Service (NHS) regions in the development cohort. We further validated the final model in held-out data from an additional NHS region (London).<h4>Findings</h4>74 944 participants (recruited between Feb 6 and Aug 26, 2020) were included, of whom 31 924 (43·2%) of 73 948 with available outcomes met the composite clinical deterioration outcome. In internal-external cross-validation in the development cohort of 66 705 participants, the selected model (comprising 11 predictors routinely measured at the point of hospital admission) showed consistent discrimination, calibration, and clinical utility across all eight NHS regions. In held-out data from London (n=8239), the model showed a similarly consistent performance (C-statistic 0·77 [95% CI 0·76 to 0·78]; calibration-in-the-large 0·00 [-0·05 to 0·05]); calibration slope 0·96 [0·91 to 1·01]), and greater net benefit than any other reproducible prognostic model.<h4>Interpretation</h4>The 4C Deterioration model has strong potential for clinical utility and generalisability to predict clinical deterioration and inform decision making among adults hospitalised with COVID-19.<h4>Funding</h4>National Institute for Health Research (NIHR), UK Medical Research Council, Wellcome Trust, Department for International Development, Bill & Melinda Gates Foundation, EU Platform for European Preparedness Against (Re-)emerging Epidemics, NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool, NIHR HPRU in Respiratory Infections at Imperial College London.",,pdf:https://www.pure.ed.ac.uk/ws/files/194098304/1_s2.0_S2213260020305592_main.pdf; doi:https://doi.org/10.1016/S2213-2600(20)30559-2; html:https://europepmc.org/articles/PMC7832571
 38809392,https://doi.org/10.1007/s11357-024-01202-3,Mediating and moderating effects of plasma proteomic biomarkers on the association between poor oral health problems and incident dementia: The UK Biobank study.,"Beydoun HA, Beydoun MA, Noren Hooten N, Weiss J, Li Z, Georgescu MF, Maino Vieytes CA, Meirelles O, Launer LJ, Evans MK, Zonderman AB.",,GeroScience,2024,2024-05-29,N,Aging; Dementia; periodontal disease; Tooth loss; Poor Oral Health; Plasma Proteomic Biomarkers,,,"The plasma proteome can mediate poor oral health problems (POHP)'s link to incident dementia. We screened 37,269 UK Biobank participants 50-74 years old (2006-2010) for prevalent POHP, further tested against 1463 plasma proteins and incident dementia over up to 15 years of follow-up. Total effect (TE) of POHP-dementia through plasma proteomic markers was decomposed into pure indirect effect (PIE), interaction referent (INTREF), controlled direct effect (CDE), or mediated interaction (INTMED). POHP increased the risk of all-cause dementia by 17% (P < 0.05). Growth differentiation factor 15 (GDF15) exhibited the strongest mediating effects (PIE > 0, P < 0.001), explaining 28% the total effect of POHP on dementia, as a pure indirect effect. A first principal component encompassing top 4 mediators (GDF15, IL19, MMP12, and ACVRL1), explained 11% of the POHP-dementia effect as a pure indirect effect. Pathway analysis including all mediators (k = 173 plasma proteins) revealed the involvement of the immune system, signal transduction, metabolism, disease, and gene expression, while STRING analysis indicated that top mediators within the first principal component were also represented in the two largest proteomic clusters. The dominant biological GO pathway for the GDF15 cluster was GO:0007169 labeled as ""transmembrane receptor protein tyrosine kinase signaling pathway."" Dementia is linked to POHP mediated by GDF15 among several proteomic markers.",,doi:https://doi.org/10.1007/s11357-024-01202-3; html:https://europepmc.org/articles/PMC11336161; pdf:https://europepmc.org/articles/PMC11336161?pdf=render; doi:https://doi.org/10.1007/s11357-024-01202-3
+36749628,https://doi.org/10.2196/42449,Charting a Course for Smartphones and Wearables to Transform Population Health Research.,"Dixon WG, van der Veer SN, Ali SM, Laidlaw L, Dobson RJB, Sudlow C, Chico T, MacArthur JAL, Doherty A.",,Journal of medical Internet research,2023,2023-02-07,Y,Research; Health; Clinical; Data; Digital; Devices; Wearable; Mhealth; Mobile Health; Person-generated Health Data; Population Health Research,,,"The use of data from smartphones and wearable devices has huge potential for population health research, given the high level of device ownership; the range of novel health-relevant data types available from consumer devices; and the frequency and duration with which data are, or could be, collected. Yet, the uptake and success of large-scale mobile health research in the last decade have not met this intensely promoted opportunity. We make the argument that digital person-generated health data are required and necessary to answer many top priority research questions, using illustrative examples taken from the James Lind Alliance Priority Setting Partnerships. We then summarize the findings from 2 UK initiatives that considered the challenges and possible solutions for what needs to be done and how such solutions can be implemented to realize the future opportunities of digital person-generated health data for clinically important population health research. Examples of important areas that must be addressed to advance the field include digital inequality and possible selection bias; easy access for researchers to the appropriate data collection tools, including how best to harmonize data items; analysis methodologies for time series data; patient and public involvement and engagement methods for optimizing recruitment, retention, and public trust; and methods for providing research participants with greater control over their data. There is also a major opportunity, provided through the linkage of digital person-generated health data to routinely collected data, to support novel population health research, bringing together clinician-reported and patient-reported measures. We recognize that well-conducted studies need a wide range of diverse challenges to be skillfully addressed in unison (eg, challenges regarding epidemiology, data science and biostatistics, psychometrics, behavioral and social science, software engineering, user interface design, information governance, data management, and patient and public involvement and engagement). Consequently, progress would be accelerated by the establishment of a new interdisciplinary community where all relevant and necessary skills are brought together to allow for excellence throughout the life cycle of a research study. This will require a partnership of diverse people, methods, and technologies. If done right, the synergy of such a partnership has the potential to transform many millions of people's lives for the better.",,pdf:https://www.jmir.org/2023/1/e42449/PDF; doi:https://doi.org/10.2196/42449; html:https://europepmc.org/articles/PMC11334374; html:https://europepmc.org/articles/PMC7614184; pdf:https://europepmc.org/articles/PMC7614184?pdf=render
 34868617,https://doi.org/10.1177/20552076211048654,Towards nationally curated data archives for clinical radiology image analysis at scale: Learnings from national data collection in response to a pandemic.,"Cushnan D, Berka R, Bertolli O, Williams P, Schofield D, Joshi I, Favaro A, Halling-Brown M, Imreh G, Jefferson E, Sebire NJ, Reilly G, Rodrigues JCL, Robinson G, Copley S, Malik R, Bloomfield C, Gleeson F, Crotty M, Denton E, Dickson J, Leeming G, Hardwick HE, Baillie K, Openshaw PJ, Semple MG, Rubin C, Howlett A, Rockall AG, Bhayat A, Fascia D, Sudlow C, NCCID Collaborative, Jacob J.",,Digital health,2021,2021-01-01,Y,Artificial intelligence; Medicine; Imaging; general; Radiology; Respiratory; Machine Learning; Coronavirus Sars-Cov-2 Disease,,,"The prevalence of the coronavirus SARS-CoV-2 disease has resulted in the unprecedented collection of health data to support research. Historically, coordinating the collation of such datasets on a national scale has been challenging to execute for several reasons, including issues with data privacy, the lack of data reporting standards, interoperable technologies, and distribution methods. The coronavirus SARS-CoV-2 disease pandemic has highlighted the importance of collaboration between government bodies, healthcare institutions, academic researchers and commercial companies in overcoming these issues during times of urgency. The National COVID-19 Chest Imaging Database, led by NHSX, British Society of Thoracic Imaging, Royal Surrey NHS Foundation Trust and Faculty, is an example of such a national initiative. Here, we summarise the experiences and challenges of setting up the National COVID-19 Chest Imaging Database, and the implications for future ambitions of national data curation in medical imaging to advance the safe adoption of artificial intelligence in healthcare.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/20552076211048654; doi:https://doi.org/10.1177/20552076211048654; html:https://europepmc.org/articles/PMC8637703; pdf:https://europepmc.org/articles/PMC8637703?pdf=render
 34270458,https://doi.org/10.4269/ajtmh.21-0482,The Need for a Practical Approach to Evaluate the Effectiveness of COVID-19 Vaccines for Low- and Middle-Income Countries.,"Nsanzimana S, Gupta A, Uwizihiwe JP, Haggstrom J, Dron L, Arora P, Park JJH.",,The American journal of tropical medicine and hygiene,2021,2021-07-16,Y,,,,"The global demand for coronavirus disease 2019 (COVID-19) vaccines currently far outweighs the available global supply and manufacturing capacity. As a result, securing doses of vaccines for low- and middle-income countries has been challenging, particularly for African countries. Clinical trial investigation for COVID-19 vaccines has been rare in Africa, with the only randomized clinical trials (RCTs) for COVID-19 vaccines having been conducted in South Africa. In addition to addressing the current inequities in the vaccine roll-out for low- and middle-income countries, there is a need to monitor the real-world effectiveness of COVID-19 vaccines in these regions. Although RCTs are the superior method for evaluating vaccine efficacy, the feasibility of conducting RCTs to monitor COVID-19 vaccine effectiveness during mass vaccine campaigns will likely be low. There is still a need to evaluate the effectiveness of mass COVID-19 vaccine distribution in a practical manner. We discuss how target trial emulation, the application of trial design principles from RCTs to the analysis of observational data, can be used as a practical, cost-effective way to evaluate real-world effectiveness for COVID-19 vaccines. There are several study design considerations that need to be made in the analyses of observational data, such as uncontrolled confounders and selection biases. Target trial emulation accounts for these considerations to improve the analyses of observational data. The framework of target trial emulation provides a practical way to monitor the effectiveness of mass vaccine campaigns for COVID-19 using observational data.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8592367; doi:https://doi.org/10.4269/ajtmh.21-0482; html:https://europepmc.org/articles/PMC8592367; pdf:https://europepmc.org/articles/PMC8592367?pdf=render
 33472631,https://doi.org/10.1186/s12916-020-01893-3,Evaluation and improvement of the National Early Warning Score (NEWS2) for COVID-19: a multi-hospital study.,"Carr E, Bendayan R, Bean D, Stammers M, Wang W, Zhang H, Searle T, Kraljevic Z, Shek A, Phan HTT, Muruet W, Gupta RK, Shinton AJ, Wyatt M, Shi T, Zhang X, Pickles A, Stahl D, Zakeri R, Noursadeghi M, O'Gallagher K, Rogers M, Folarin A, Karwath A, Wickstrøm KE, Köhn-Luque A, Slater L, Cardoso VR, Bourdeaux C, Holten AR, Ball S, McWilliams C, Roguski L, Borca F, Batchelor J, Amundsen EK, Wu X, Gkoutos GV, Sun J, Pinto A, Guthrie B, Breen C, Douiri A, Wu H, Curcin V, Teo JT, Shah AM, Dobson RJB.",,BMC medicine,2021,2021-01-21,Y,Prediction model; Blood parameters; Covid-19; News2 Score,,,"<h4>Background</h4>The National Early Warning Score (NEWS2) is currently recommended in the UK for the risk stratification of COVID-19 patients, but little is known about its ability to detect severe cases. We aimed to evaluate NEWS2 for the prediction of severe COVID-19 outcome and identify and validate a set of blood and physiological parameters routinely collected at hospital admission to improve upon the use of NEWS2 alone for medium-term risk stratification.<h4>Methods</h4>Training cohorts comprised 1276 patients admitted to King's College Hospital National Health Service (NHS) Foundation Trust with COVID-19 disease from 1 March to 30 April 2020. External validation cohorts included 6237 patients from five UK NHS Trusts (Guy's and St Thomas' Hospitals, University Hospitals Southampton, University Hospitals Bristol and Weston NHS Foundation Trust, University College London Hospitals, University Hospitals Birmingham), one hospital in Norway (Oslo University Hospital), and two hospitals in Wuhan, China (Wuhan Sixth Hospital and Taikang Tongji Hospital). The outcome was severe COVID-19 disease (transfer to intensive care unit (ICU) or death) at 14 days after hospital admission. Age, physiological measures, blood biomarkers, sex, ethnicity, and comorbidities (hypertension, diabetes, cardiovascular, respiratory and kidney diseases) measured at hospital admission were considered in the models.<h4>Results</h4>A baseline model of 'NEWS2 + age' had poor-to-moderate discrimination for severe COVID-19 infection at 14 days (area under receiver operating characteristic curve (AUC) in training cohort = 0.700, 95% confidence interval (CI) 0.680, 0.722; Brier score = 0.192, 95% CI 0.186, 0.197). A supplemented model adding eight routinely collected blood and physiological parameters (supplemental oxygen flow rate, urea, age, oxygen saturation, C-reactive protein, estimated glomerular filtration rate, neutrophil count, neutrophil/lymphocyte ratio) improved discrimination (AUC = 0.735; 95% CI 0.715, 0.757), and these improvements were replicated across seven UK and non-UK sites. However, there was evidence of miscalibration with the model tending to underestimate risks in most sites.<h4>Conclusions</h4>NEWS2 score had poor-to-moderate discrimination for medium-term COVID-19 outcome which raises questions about its use as a screening tool at hospital admission. Risk stratification was improved by including readily available blood and physiological parameters measured at hospital admission, but there was evidence of miscalibration in external sites. This highlights the need for a better understanding of the use of early warning scores for COVID.",,doi:https://doi.org/10.1186/s12916-020-01893-3; doi:https://doi.org/10.1186/s12916-020-01893-3; html:https://europepmc.org/articles/PMC7817348; pdf:https://europepmc.org/articles/PMC7817348?pdf=render
 36997856,https://doi.org/10.1186/s12882-023-03126-0,A clinical frailty scale obtained from MDT discussion performs poorly in assessing frailty in haemodialysis recipients.,"Anderson BM, Qasim M, Correa G, Evison F, Gallier S, Ferro CJ, Jackson TA, Sharif A.",,BMC nephrology,2023,2023-03-30,Y,Mortality; Frailty; Haemodialysis; Hospitalisation; Clinical Frailty Scale,,,"<h4>Background</h4>The Clinical Frailty Scale (CFS) is a commonly utilised frailty screening tool that has been associated with hospitalisation and mortality in haemodialysis recipients, but is subject to heterogenous methodologies including subjective clinician opinion. The aims of this study were to (i) examine the accuracy of a subjective, multidisciplinary assessment of CFS at haemodialysis Quality Assurance (QA) meetings (CFS-MDT), compared with a standard CFS score via clinical interview, and (ii) ascertain the associations of these scores with hospitalisation and mortality.<h4>Methods</h4>We performed a prospective cohort study of prevalent haemodialysis recipients linked to national datasets for outcomes including mortality and hospitalisation. Frailty was assessed using the CFS after structured clinical interview. The CFS-MDT was derived from consensus at haemodialysis QA meetings, involving dialysis nurses, dietitians, and nephrologists.<h4>Results</h4>453 participants were followed-up for a median of 685 days (IQR 544-812), during which there were 96 (21.2%) deaths and 1136 hospitalisations shared between 327 (72.1%) participants. Frailty was identified in 246 (54.3%) participants via CFS, but only 120 (26.5%) via CFS-MDT. There was weak correlation (Spearman Rho 0.485, P < 0.001) on raw frailty scores and minimal agreement (Cohen's κ = 0.274, P < 0.001) on categorisation of frail, vulnerable and robust between the CFS and CFS-MDT. Increasing frailty was associated with higher rates of hospitalisation for the CFS (IRR 1.26, 95% C.I. 1.17-1.36, P = 0.016) and CFS-MDT (IRR 1.10, 1.02-1.19, P = 0.02), but only the CFS-MDT was associated with nights spent in hospital (IRR 1.22, 95% C.I. 1.08-1.38, P = 0.001). Both scores were associated with mortality (CFS HR 1.31, 95% C.I. 1.09-1.57, P = 0.004; CFS-MDT HR 1.36, 95% C.I. 1.16-1.59, P < 0.001).<h4>Conclusions</h4>Assessment of CFS is deeply affected by the underlying methodology, with the potential to profoundly affect decision-making. The CFS-MDT appears to be a weak alternative to conventional CFS. Standardisation of CFS use is of paramount importance in clinical and research practice in haemodialysis.<h4>Trial registration</h4>Clinicaltrials.gov : NCT03071107 registered 06/03/2017.",,pdf:https://bmcnephrol.biomedcentral.com/counter/pdf/10.1186/s12882-023-03126-0; doi:https://doi.org/10.1186/s12882-023-03126-0; html:https://europepmc.org/articles/PMC10062243; pdf:https://europepmc.org/articles/PMC10062243?pdf=render
 32613083,https://doi.org/10.12688/wellcomeopenres.15922.2,"Black, Asian and Minority Ethnic groups in England are at increased risk of death from COVID-19: indirect standardisation of NHS mortality data.","Aldridge RW, Lewer D, Katikireddi SV, Mathur R, Pathak N, Burns R, Fragaszy EB, Johnson AM, Devakumar D, Abubakar I, Hayward A.",,Wellcome open research,2020,2020-06-24,Y,Mortality; Minority Ethnic Groups; Covid-19; Sars-cov-2,,,"<b>Background</b>: International and UK data suggest that Black, Asian and Minority Ethnic (BAME) groups are at increased risk of infection and death from COVID-19. We aimed to explore the risk of death in minority ethnic groups in England using data reported by NHS England. <b>Methods</b>: We used NHS data on patients with a positive COVID-19 test who died in hospitals in England published on 28th April, with deaths by ethnicity available from 1st March 2020 up to 5pm on 21 April 2020. We undertook indirect standardisation of these data (using the whole population of England as the reference) to produce ethnic specific standardised mortality ratios (SMRs) adjusted for age and geographical region. <b>Results</b>: The largest total number of deaths in minority ethnic groups were Indian (492 deaths) and Black Caribbean (460 deaths) groups. Adjusting for region we found a lower risk of death for White Irish (SMR 0.52; 95%CIs 0.45-0.60) and White British ethnic groups (0.88; 95%CIs 0.86-0.0.89), but increased risk of death for Black African (3.24; 95%CIs 2.90-3.62), Black Caribbean (2.21; 95%CIs 2.02-2.41), Pakistani (3.29; 95%CIs 2.96-3.64), Bangladeshi (2.41; 95%CIs 1.98-2.91) and Indian (1.70; 95%CIs 1.56-1.85) minority ethnic groups. <b>Conclusion:</b> Our analysis adds to the evidence that BAME people are at increased risk of death from COVID-19 even after adjusting for geographical region, but was limited by the lack of data on deaths outside of NHS settings and ethnicity denominator data being based on the 2011 census. Despite these limitations, we believe there is an urgent need to take action to reduce the risk of death for BAME groups and better understand why some ethnic groups experience greater risk. Actions that are likely to reduce these inequities include ensuring adequate income protection, reducing occupational risks, reducing barriers in accessing healthcare and providing culturally and linguistically appropriate public health communications.",,doi:https://doi.org/10.12688/wellcomeopenres.15922.2; html:https://europepmc.org/articles/PMC7317462; pdf:https://europepmc.org/articles/PMC7317462?pdf=render
-38941600,https://doi.org/10.2196/55302,Longitudinal Assessment of Seasonal Impacts and Depression Associations on Circadian Rhythm Using Multimodal Wearable Sensing: Retrospective Analysis.,"Zhang Y, Folarin AA, Sun S, Cummins N, Ranjan Y, Rashid Z, Stewart C, Conde P, Sankesara H, Laiou P, Matcham F, White KM, Oetzmann C, Lamers F, Siddi S, Simblett S, Vairavan S, Myin-Germeys I, Mohr DC, Wykes T, Haro JM, Annas P, Penninx BW, Narayan VA, Hotopf M, Dobson RJ, RADAR-CNS consortium.",,Journal of medical Internet research,2024,2024-06-28,Y,Circadian rhythm; Monitoring; Mental health; Major Depressive Disorder; Biological Rhythms; Mdd; Wearable; Mhealth; Mobile Health; Digital Health,,,"<h4>Background</h4>Previous mobile health (mHealth) studies have revealed significant links between depression and circadian rhythm features measured via wearables. However, the comprehensive impact of seasonal variations was not fully considered in these studies, potentially biasing interpretations in real-world settings.<h4>Objective</h4>This study aims to explore the associations between depression severity and wearable-measured circadian rhythms while accounting for seasonal impacts.<h4>Methods</h4>Data were sourced from a large longitudinal mHealth study, wherein participants' depression severity was assessed biweekly using the 8-item Patient Health Questionnaire (PHQ-8), and participants' behaviors, including sleep, step count, and heart rate (HR), were tracked via Fitbit devices for up to 2 years. We extracted 12 circadian rhythm features from the 14-day Fitbit data preceding each PHQ-8 assessment, including cosinor variables, such as HR peak timing (HR acrophase), and nonparametric features, such as the onset of the most active continuous 10-hour period (M10 onset). To investigate the association between depression severity and circadian rhythms while also assessing the seasonal impacts, we used three nested linear mixed-effects models for each circadian rhythm feature: (1) incorporating the PHQ-8 score as an independent variable, (2) adding seasonality, and (3) adding an interaction term between season and the PHQ-8 score.<h4>Results</h4>Analyzing 10,018 PHQ-8 records alongside Fitbit data from 543 participants (n=414, 76.2% female; median age 48, IQR 32-58 years), we found that after adjusting for seasonal effects, higher PHQ-8 scores were associated with reduced daily steps (β=-93.61, P<.001), increased sleep variability (β=0.96, P<.001), and delayed circadian rhythms (ie, sleep onset: β=0.55, P=.001; sleep offset: β=1.12, P<.001; M10 onset: β=0.73, P=.003; HR acrophase: β=0.71, P=.001). Notably, the negative association with daily steps was more pronounced in spring (β of PHQ-8 × spring = -31.51, P=.002) and summer (β of PHQ-8 × summer = -42.61, P<.001) compared with winter. Additionally, the significant correlation with delayed M10 onset was observed solely in summer (β of PHQ-8 × summer = 1.06, P=.008). Moreover, compared with winter, participants experienced a shorter sleep duration by 16.6 minutes, an increase in daily steps by 394.5, a delay in M10 onset by 20.5 minutes, and a delay in HR peak time by 67.9 minutes during summer.<h4>Conclusions</h4>Our findings highlight significant seasonal influences on human circadian rhythms and their associations with depression, underscoring the importance of considering seasonal variations in mHealth research for real-world applications. This study also indicates the potential of wearable-measured circadian rhythms as digital biomarkers for depression.",,doi:https://doi.org/10.2196/55302; html:https://europepmc.org/articles/PMC11245656
 33661754,https://doi.org/10.2196/21547,Implementation of the COVID-19 Vulnerability Index Across an International Network of Health Care Data Sets: Collaborative External Validation Study.,"Reps JM, Kim C, Williams RD, Markus AF, Yang C, Duarte-Salles T, Falconer T, Jonnagaddala J, Williams A, Fernández-Bertolín S, DuVall SL, Kostka K, Rao G, Shoaibi A, Ostropolets A, Spotnitz ME, Zhang L, Casajust P, Steyerberg EW, Nyberg F, Kaas-Hansen BS, Choi YH, Morales D, Liaw ST, Abrahão MTF, Areia C, Matheny ME, Lynch KE, Aragón M, Park RW, Hripcsak G, Reich CG, Suchard MA, You SC, Ryan PB, Prieto-Alhambra D, Rijnbeek PR.",,JMIR medical informatics,2021,2021-04-05,Y,Prediction; Modeling; Observation; decision-making; Bias; Hospitalization; risk; Transportability; Prognostic Model; Datasets; External Validation; Covid-19; C-19,,,"<h4>Background</h4>SARS-CoV-2 is straining health care systems globally. The burden on hospitals during the pandemic could be reduced by implementing prediction models that can discriminate patients who require hospitalization from those who do not. The COVID-19 vulnerability (C-19) index, a model that predicts which patients will be admitted to hospital for treatment of pneumonia or pneumonia proxies, has been developed and proposed as a valuable tool for decision-making during the pandemic. However, the model is at high risk of bias according to the ""prediction model risk of bias assessment"" criteria, and it has not been externally validated.<h4>Objective</h4>The aim of this study was to externally validate the C-19 index across a range of health care settings to determine how well it broadly predicts hospitalization due to pneumonia in COVID-19 cases.<h4>Methods</h4>We followed the Observational Health Data Sciences and Informatics (OHDSI) framework for external validation to assess the reliability of the C-19 index. We evaluated the model on two different target populations, 41,381 patients who presented with SARS-CoV-2 at an outpatient or emergency department visit and 9,429,285 patients who presented with influenza or related symptoms during an outpatient or emergency department visit, to predict their risk of hospitalization with pneumonia during the following 0-30 days. In total, we validated the model across a network of 14 databases spanning the United States, Europe, Australia, and Asia.<h4>Results</h4>The internal validation performance of the C-19 index had a C statistic of 0.73, and the calibration was not reported by the authors. When we externally validated it by transporting it to SARS-CoV-2 data, the model obtained C statistics of 0.36, 0.53 (0.473-0.584) and 0.56 (0.488-0.636) on Spanish, US, and South Korean data sets, respectively. The calibration was poor, with the model underestimating risk. When validated on 12 data sets containing influenza patients across the OHDSI network, the C statistics ranged between 0.40 and 0.68.<h4>Conclusions</h4>Our results show that the discriminative performance of the C-19 index model is low for influenza cohorts and even worse among patients with COVID-19 in the United States, Spain, and South Korea. These results suggest that C-19 should not be used to aid decision-making during the COVID-19 pandemic. Our findings highlight the importance of performing external validation across a range of settings, especially when a prediction model is being extrapolated to a different population. In the field of prediction, extensive validation is required to create appropriate trust in a model.",,pdf:https://medinform.jmir.org/2021/4/e21547/PDF; doi:https://doi.org/10.2196/21547; html:https://europepmc.org/articles/PMC8023380
+38941600,https://doi.org/10.2196/55302,Longitudinal Assessment of Seasonal Impacts and Depression Associations on Circadian Rhythm Using Multimodal Wearable Sensing: Retrospective Analysis.,"Zhang Y, Folarin AA, Sun S, Cummins N, Ranjan Y, Rashid Z, Stewart C, Conde P, Sankesara H, Laiou P, Matcham F, White KM, Oetzmann C, Lamers F, Siddi S, Simblett S, Vairavan S, Myin-Germeys I, Mohr DC, Wykes T, Haro JM, Annas P, Penninx BW, Narayan VA, Hotopf M, Dobson RJ, RADAR-CNS consortium.",,Journal of medical Internet research,2024,2024-06-28,Y,Circadian rhythm; Monitoring; Mental health; Major Depressive Disorder; Biological Rhythms; Mdd; Wearable; Mhealth; Mobile Health; Digital Health,,,"<h4>Background</h4>Previous mobile health (mHealth) studies have revealed significant links between depression and circadian rhythm features measured via wearables. However, the comprehensive impact of seasonal variations was not fully considered in these studies, potentially biasing interpretations in real-world settings.<h4>Objective</h4>This study aims to explore the associations between depression severity and wearable-measured circadian rhythms while accounting for seasonal impacts.<h4>Methods</h4>Data were sourced from a large longitudinal mHealth study, wherein participants' depression severity was assessed biweekly using the 8-item Patient Health Questionnaire (PHQ-8), and participants' behaviors, including sleep, step count, and heart rate (HR), were tracked via Fitbit devices for up to 2 years. We extracted 12 circadian rhythm features from the 14-day Fitbit data preceding each PHQ-8 assessment, including cosinor variables, such as HR peak timing (HR acrophase), and nonparametric features, such as the onset of the most active continuous 10-hour period (M10 onset). To investigate the association between depression severity and circadian rhythms while also assessing the seasonal impacts, we used three nested linear mixed-effects models for each circadian rhythm feature: (1) incorporating the PHQ-8 score as an independent variable, (2) adding seasonality, and (3) adding an interaction term between season and the PHQ-8 score.<h4>Results</h4>Analyzing 10,018 PHQ-8 records alongside Fitbit data from 543 participants (n=414, 76.2% female; median age 48, IQR 32-58 years), we found that after adjusting for seasonal effects, higher PHQ-8 scores were associated with reduced daily steps (β=-93.61, P<.001), increased sleep variability (β=0.96, P<.001), and delayed circadian rhythms (ie, sleep onset: β=0.55, P=.001; sleep offset: β=1.12, P<.001; M10 onset: β=0.73, P=.003; HR acrophase: β=0.71, P=.001). Notably, the negative association with daily steps was more pronounced in spring (β of PHQ-8 × spring = -31.51, P=.002) and summer (β of PHQ-8 × summer = -42.61, P<.001) compared with winter. Additionally, the significant correlation with delayed M10 onset was observed solely in summer (β of PHQ-8 × summer = 1.06, P=.008). Moreover, compared with winter, participants experienced a shorter sleep duration by 16.6 minutes, an increase in daily steps by 394.5, a delay in M10 onset by 20.5 minutes, and a delay in HR peak time by 67.9 minutes during summer.<h4>Conclusions</h4>Our findings highlight significant seasonal influences on human circadian rhythms and their associations with depression, underscoring the importance of considering seasonal variations in mHealth research for real-world applications. This study also indicates the potential of wearable-measured circadian rhythms as digital biomarkers for depression.",,doi:https://doi.org/10.2196/55302; html:https://europepmc.org/articles/PMC11245656
 39385845,https://doi.org/10.1093/ehjimp/qyae094,"Quality control of cardiac magnetic resonance imaging segmentation, feature tracking, aortic flow, and native T1 analysis using automated batch processing in the UK Biobank study.","Chadalavada S, Rauseo E, Salih A, Naderi H, Khanji M, Vargas JD, Lee AM, Amir-Kalili A, Lockhart L, Graham B, Chirvasa M, Fung K, Paiva J, Sanghvi MM, Slabaugh GG, Jensen MT, Aung N, Petersen SE.",,European heart journal. Imaging methods and practice,2024,2024-07-01,Y,Quality control; Machine Learning; Cardiac Magnetic Resonance Imaging; Automated Image Analysis; Shiny App,,,"<h4>Aims</h4>Automated algorithms are regularly used to analyse cardiac magnetic resonance (CMR) images. Validating data output reliability from this method is crucial for enabling widespread adoption. We outline a visual quality control (VQC) process for image analysis using automated batch processing. We assess the performance of automated analysis and the reliability of replacing visual checks with statistical outlier (SO) removal approach in UK Biobank CMR scans.<h4>Methods and results</h4>We included 1987 CMR scans from the UK Biobank COVID-19 imaging study. We used batch processing software (Circle Cardiovascular Imaging Inc.-CVI42) to automatically extract chamber volumetric data, strain, native T1, and aortic flow data. The automated analysis outputs (∼62 000 videos and 2000 images) were visually checked by six experienced clinicians using a standardized approach and a custom-built R Shiny app. Inter-observer variability was assessed. Data from scans passing VQC were compared with a SO removal QC method in a subset of healthy individuals (<i>n</i> = 1069). Automated segmentation was highly rated, with over 95% of scans passing VQC. Overall inter-observer agreement was very good (Gwet's AC2 0.91; 95% confidence interval 0.84, 0.94). No difference in overall data derived from VQC or SO removal in healthy individuals was observed.<h4>Conclusion</h4>Automated image analysis using CVI42 prototypes for UK Biobank CMR scans demonstrated high quality. Larger UK Biobank data sets analysed using these automated algorithms do not require in-depth VQC. SO removal is sufficient as a QC measure, with operator discretion for visual checks based on population or research objectives.",,doi:https://doi.org/10.1093/ehjimp/qyae094; html:https://europepmc.org/articles/PMC11462446; pdf:https://europepmc.org/articles/PMC11462446?pdf=render
 37432340,https://doi.org/10.1093/rheumatology/kead346,Trends for opioid prescribing and the impact of the COVID-19 pandemic in patients with rheumatic and musculoskeletal diseases between 2006 and 2021.,"Huang YT, Jenkins DA, Yimer BB, Benitez-Aurioles J, Peek N, Lunt M, Dixon WG, Jani M.",,"Rheumatology (Oxford, England)",2024,2024-04-01,Y,RA; SLE; Trend; PSA; Opioids; Oa; Axial Spondyloarthritis; Fm; Covid-19,,,"<h4>Objective</h4>To investigate opioid prescribing trends and assess the impact of the COVID-19 pandemic on opioid prescribing in rheumatic and musculoskeletal diseases (RMDs).<h4>Methods</h4>Adult patients with RA, PsA, axial spondyloarthritis (AxSpA), SLE, OA and FM with opioid prescriptions between 1 January 2006 and 31 August 2021 without cancer in UK primary care were included. Age- and gender-standardized yearly rates of new and prevalent opioid users were calculated between 2006 and 2021. For prevalent users, monthly measures of mean morphine milligram equivalents (MME)/day were calculated between 2006 and 2021. To assess the impact of the pandemic, we fitted regression models to the monthly number of prevalent opioid users between January 2015 and August 2021. The time coefficient reflects the trend pre-pandemic and the interaction term coefficient represents the change in the trend during the pandemic.<h4>Results</h4>The study included 1 313 519 RMD patients. New opioid users for RA, PsA and FM increased from 2.6, 1.0 and 3.4/10 000 persons in 2006 to 4.5, 1.8 and 8.7, respectively, in 2018 or 2019. This was followed by a fall to 2.4, 1.2 and 5.9, respectively, in 2021. Prevalent opioid users for all RMDs increased from 2006 but plateaued or dropped beyond 2018, with a 4.5-fold increase in FM between 2006 and 2021. In this period, MME/day increased for all RMDs, with the highest for FM (≥35). During COVID-19 lockdowns, RA, PsA and FM showed significant changes in the trend of prevalent opioid users. The trend for FM increased pre-pandemic and started decreasing during the pandemic.<h4>Conclusion</h4>The plateauing or decreasing trend of opioid users for RMDs after 2018 may reflect the efforts to tackle rising opioid prescribing in the UK. The pandemic led to fewer people on opioids for most RMDs, providing reassurance that there was no sudden increase in opioid prescribing during the pandemic.",,pdf:https://academic.oup.com/rheumatology/advance-article-pdf/doi/10.1093/rheumatology/kead346/50930066/kead346.pdf; doi:https://doi.org/10.1093/rheumatology/kead346; html:https://europepmc.org/articles/PMC10986805; pdf:https://europepmc.org/articles/PMC10986805?pdf=render
 37123891,https://doi.org/10.1016/j.heliyon.2023.e15143,Disclosure control of machine learning models from trusted research environments (TRE): New challenges and opportunities.,"Mansouri-Benssassi E, Rogers S, Reel S, Malone M, Smith J, Ritchie F, Jefferson E.",,Heliyon,2023,2023-04-03,Y,AI; Machine Learning; Data Privacy; Safe Haven; Disclosure Control; Trusted Research Environment,,,"<h4>Introduction</h4>Artificial intelligence (AI) applications in healthcare and medicine have increased in recent years. To enable access to personal data, Trusted Research Environments (TREs) (otherwise known as Safe Havens) provide safe and secure environments in which researchers can access sensitive personal data and develop AI (in particular machine learning (ML)) models. However, currently few TREs support the training of ML models in part due to a gap in the practical decision-making guidance for TREs in handling model disclosure. Specifically, the training of ML models creates a need to disclose new types of outputs from TREs. Although TREs have clear policies for the disclosure of statistical outputs, the extent to which trained models can leak personal training data once released is not well understood.<h4>Background</h4>We review, for a general audience, different types of ML models and their applicability within healthcare. We explain the outputs from training a ML model and how trained ML models can be vulnerable to external attacks to discover personal data encoded within the model.<h4>Risks</h4>We present the challenges for disclosure control of trained ML models in the context of training and exporting models from TREs. We provide insights and analyse methods that could be introduced within TREs to mitigate the risk of privacy breaches when disclosing trained models.<h4>Discussion</h4>Although specific guidelines and policies exist for statistical disclosure controls in TREs, they do not satisfactorily address these new types of output requests; i.e., trained ML models. There is significant potential for new interdisciplinary research opportunities in developing and adapting policies and tools for safely disclosing ML outputs from TREs.",,pdf:http://www.cell.com/article/S2405844023023502/pdf; doi:https://doi.org/10.1016/j.heliyon.2023.e15143; html:https://europepmc.org/articles/PMC10130764; pdf:https://europepmc.org/articles/PMC10130764?pdf=render
@@ -633,8 +633,9 @@ PMC10686417,https://doi.org/,The impact of restricted provision of publicly fund
 34244281,https://doi.org/10.1136/bmjopen-2021-049611,"Ethnicity and COVID-19 outcomes among healthcare workers in the UK: UK-REACH ethico-legal research, qualitative research on healthcare workers' experiences and stakeholder engagement protocol.","Gogoi M, Reed-Berendt R, Al-Oraibi A, Hassan O, Wobi F, Gupta A, Abubakar I, Dove E, Nellums LB, Pareek M, UK-REACH Collaborative Group.",,BMJ open,2021,2021-07-09,Y,Medical Ethics; Qualitative Research; Medical Law; Covid-19,,,"<h4>Introduction</h4>As the world continues to grapple with the COVID-19 pandemic, emerging evidence suggests that individuals from ethnic minority backgrounds may be disproportionately affected. The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers (UK-REACH) project has been initiated to generate rapid evidence on whether and why ethnicity affects COVID-19 diagnosis and clinical outcomes in healthcare workers (HCWs) in the UK, through five interlinked work packages/work streams, three of which form the basis of this protocol. The ethico-legal work (Work Package 3) aims to understand and address legal, ethical and acceptability issues around big data research; the HCWs' experiences study (Work Package 4) explores their work and personal experiences, perceptions of risk, support and coping mechanisms; the stakeholder engagement work (Work Package 5) aims to provide feedback and support with the formulation and dissemination of the project recommendations.<h4>Methods and analysis</h4>Work Package 3 has two different research strands: (A) desk-based doctrinal research; and (B) empirical qualitative research with key opinion leaders. For the empirical research, in-depth interviews will be conducted digitally and recorded with participants' permission. Recordings will be transcribed, coded and analysed using thematic analysis. In Work Package 4, online in-depth interviews and focus groups will be conducted with approximately 150 HCWs, from across the UK, and these will be recorded with participants' consent. The recordings will be transcribed and coded and data will be analysed using thematic analysis. Work Package 5 will achieve its objectives through regular group meetings and in-group discussions.<h4>Ethics and dissemination</h4>Ethical approval has been received from the London-Brighton & Sussex Research Ethics Committee of the Health Research Authority (Ref No 20/HRA/4718). Results of the study will be published in open-access journals, and disseminated through conference presentations, project website, stakeholder organisations, media and scientific advisory groups.<h4>Trial registration number</h4>ISRCTN11811602.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/7/e049611.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-049611; html:https://europepmc.org/articles/PMC8275361; pdf:https://europepmc.org/articles/PMC8275361?pdf=render
 32355555,https://doi.org/10.7189/jogh.10.010104,COVID-19 must catalyse key global natural experiments.,"Been JV, Sheikh A.",,Journal of global health,2020,2020-06-01,Y,,,,,"""Been and Sheikh’s editorial about COVID-19, outlines the importance of two natural experiments: a- how different countries responded to the pandemic and its effects and b- impact of improvements in air quality on human and planetary health.""",doi:https://doi.org/10.7189/jogh.10.010104; doi:https://doi.org/10.7189/jogh.10.010104; html:https://europepmc.org/articles/PMC7179980; pdf:https://europepmc.org/articles/PMC7179980?pdf=render
 36648008,https://doi.org/10.1111/iwj.14088,"Evaluating the cost of managing patients with cellulitis in Wales, UK: A 20-year population-scale study.","Humphreys I, Akbari A, Griffiths R, Graham-Woollard D, Morgan K, Noble-Jones R, Gabe-Walters M, Thomas M.",,International wound journal,2023,2023-01-17,Y,Longitudinal data; Cellulitis; Lymphoedema; Economic Burden; Sail Databank,,,"This study aimed to estimate costs associated with managing patients with cellulitis from the UK National Health Service (NHS) perspective. The analysis was undertaken through the Secure Anonymised Information Linkage Databank, which brings together population-scale, individual-level anonymised linked data from a wide range of sources, including 80% of primary care general practices within Wales (population coverage ~3.2 million). The data covered a 20-year period from 1999 to 2019. All patients linked to the relevant codes were tracked through primary care settings, recording the number of general practice visits (number of days with an event recorded) and number of in-patient stays. Resources were valued in monetary terms (£ sterling), with costs determined from national published sources of unit costs. These resources were then extrapolated out to reflect UK NHS costs. This is the first attempt to estimate the financial burden of cellulitis using routine data sources on a national scale. The estimated direct annual costs to the Welsh NHS (£28 554 338) are considerable. In-Patient events and length of stay costs are the main cost drivers, with annual Welsh NHS estimates of £19 664 126 with primary care events costing £8 890 212. Initiatives to support patients and healthcare professionals in identifying early signs/risks of cellulitis, improve the accuracy of initial diagnosis, prevent cellulitis recurrence, and improve evidence-based treatment pathways would result in major financial savings, to both the Welsh and UK NHS. In light of these findings, Wales has developed the innovative National Lymphoedema cellulitis Improvement Programme to address these burdens; providing a proactive model of cellulitis care.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/iwj.14088; doi:https://doi.org/10.1111/iwj.14088; html:https://europepmc.org/articles/PMC10333041; pdf:https://europepmc.org/articles/PMC10333041?pdf=render
-37561812,https://doi.org/10.1371/journal.pcbi.1011368,Call detail record aggregation methodology impacts infectious disease models informed by human mobility.,"Gibbs H, Musah A, Seidu O, Ampofo W, Asiedu-Bekoe F, Gray J, Adewole WA, Cheshire J, Marks M, Eggo RM.",,PLoS computational biology,2023,2023-08-10,Y,,,,"This paper demonstrates how two different methods used to calculate population-level mobility from Call Detail Records (CDR) produce varying predictions of the spread of epidemics informed by these data. Our findings are based on one CDR dataset describing inter-district movement in Ghana in 2021, produced using two different aggregation methodologies. One methodology, ""all pairs,"" is designed to retain long distance network connections while the other, ""sequential"" methodology is designed to accurately reflect the volume of travel between locations. We show how the choice of methodology feeds through models of human mobility to the predictions of a metapopulation SEIR model of disease transmission. We also show that this impact varies depending on the location of pathogen introduction and the transmissibility of infections. For central locations or highly transmissible diseases, we do not observe significant differences between aggregation methodologies on the predicted spread of disease. For less transmissible diseases or those introduced into remote locations, we find that the choice of aggregation methodology influences the speed of spatial spread as well as the size of the peak number of infections in individual districts. Our findings can help researchers and users of epidemiological models to understand how methodological choices at the level of model inputs may influence the results of models of infectious disease transmission, as well as the circumstances in which these choices do not alter model predictions.",,pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011368&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1011368; html:https://europepmc.org/articles/PMC10443843; pdf:https://europepmc.org/articles/PMC10443843?pdf=render
+39486903,https://doi.org/10.1016/s2468-2667(24)00215-9,"Contemporary epidemiology of hospitalised heart failure with reduced versus preserved ejection fraction in England: a retrospective, cohort study of whole-population electronic health records.","Fletcher RA, Rockenschaub P, Neuen BL, Walter IJ, Conrad N, Mizani MA, Bolton T, Lawson CA, Tomlinson C, Logothetis SB, Petitjean C, Brizzi LF, Kaptoge S, Raffetti E, Calvert PA, Di Angelantonio E, Banerjee A, Mamas MA, Squire I, Denaxas S, McDonagh TA, Sudlow C, Petersen SE, Chertow GM, Khunti K, Sundström J, Arnott C, Cleland JGF, Danesh J, McMurray JJV, Vaduganathan M, Wood AM, CVD-COVID-UK/COVID-IMPACT Consortium.",,The Lancet. Public health,2024,2024-11-01,N,,,,"<h4>Background</h4>Heart failure is common, complex, and often associated with coexisting chronic medical conditions and a high mortality. We aimed to assess the epidemiology of people admitted to hospital with heart failure with reduced ejection fraction (HFrEF) and heart failure with preserved ejection fraction (HFpEF), including the period covering the COVID-19 pandemic, which was previously not well characterised.<h4>Methods</h4>In this retrospective, cohort study, we used whole-population electronic health records with 57 million individuals in England to identify patients hospitalised with heart failure as the primary diagnosis in any consultant episode of an in-patient admission to a National Health Service (NHS) hospital. We excluded individuals with less than 1 year of medical history records in primary or secondary care; admissions to NHS hospitals for which less than 10% of heart failure cases were linkable to the National Heart Failure Audit (NHFA); individuals younger than 18 years at the time of the heart failure hospitalisation; and patients who died in hospital during the index heart failure admission. For patients with new onset heart failure, we assessed incidence rates of 30-day and 1-year all-cause and cause-specific (cardiovascular, non-cardiovascular, and heart failure-related) emergency rehospitalisation and mortality after discharge, and dispensed guideline-recommended medical therapy (GRMT). Follow-up occurred from the index admission to the earliest occurrence of the event of interest, death, or end of data coverage. We estimated adjusted hazard ratios (HRs) to compare HFrEF with HFpEF. We computed population-attributable fractions to quantify the percentage of outcomes attributable to coexisting chronic medical conditions.<h4>Findings</h4>Among 233 320 patients identified who survived the index heart failure admission across 335 NHS hospitals between Jan 1, 2019, and Dec 31, 2022, 101 320 (43·4%) had HFrEF, 71 910 (30·8%) had HFpEF, and 60 090 (25·8%) had an unknown classification. In patients with new onset heart failure, there were reductions in all-cause 30-day (-5·2% [95% CI -7·7 to -2·6] in 2019-22) and 1-year rehospitalisation rates (-3·9% [-6·6 to -1·2]). Declining 30-day rehospitalisation rates affected patients with HFpEF (-4·8% [-9·2 to -0·2]) and HFrEF (-6·2% [-10·5 to -1·6]), although 1-year rates were not statistically significant for patients with HFpEF (-2·2% [-6·6 to 2·3] vs -5·7% [-10·6 to -0·5] for HFrEF). There were no temporal trends in incidence rates of 30-day or 1-year mortality after discharge. The rates of all-cause (HR 1·20 [1·18-1·22]) and cause-specific rehospitalisation were uniformly higher in those with HFpEF than those with HFrEF. Patients with HFpEF also had higher rates of 1-year all-cause mortality after discharge (HR 1·07 [1·05-1·09]), driven by excess risk of non-cardiovascular death (HR 1·25 [1·21-1·29]). Rates of rehospitalisation and mortality were highest in patients with coexisting chronic kidney disease, chronic obstructive pulmonary disease, dementia, and liver disease. Chronic kidney disease contributed to 6·5% (5·6-7·4) of rehospitalisations within 1 year for HFrEF and 5·0% (4·1-5·9) of rehospitalisations for HFpEF, double that of any other coexisting condition. There was swift implementation of newer GRMT, but markedly lower dispensing of these medications in patients with coexisting chronic kidney disease.<h4>Interpretation</h4>Rates of rehospitalisation in patients with heart failure in England have decreased during 2019-22. Further population health improvements could be reached through enhanced implementation of GRMT, particularly in patients with coexisting chronic kidney disease, who, despite being at high risk, remain undertreated.<h4>Funding</h4>Wellcome Trust, Health Data Research UK, British Heart Foundation Data Science Centre.",,doi:https://doi.org/10.1016/S2468-2667(24)00215-9
 37587484,https://doi.org/10.1186/s12874-023-02000-9,Implementation of the trial emulation approach in medical research: a scoping review.,"Scola G, Chis Ster A, Bean D, Pareek N, Emsley R, Landau S.",,BMC medical research methodology,2023,2023-08-16,Y,Causal Inference; Observational Data; Target Trial; Trial Emulation,,,"<h4>Background</h4>When conducting randomised controlled trials is impractical, an alternative is to carry out an observational study. However, making valid causal inferences from observational data is challenging because of the risk of several statistical biases. In 2016 Hernán and Robins put forward the 'target trial framework' as a guide to best design and analyse observational studies whilst preventing the most common biases. This framework consists of (1) clearly defining a causal question about an intervention, (2) specifying the protocol of the hypothetical trial, and (3) explaining how the observational data will be used to emulate it.<h4>Methods</h4>The aim of this scoping review was to identify and review all explicit attempts of trial emulation studies across all medical fields. Embase, Medline and Web of Science were searched for trial emulation studies published in English from database inception to February 25, 2021. The following information was extracted from studies that were deemed eligible for review: the subject area, the type of observational data that they leveraged, and the statistical methods they used to address the following biases: (A) confounding bias, (B) immortal time bias, and (C) selection bias.<h4>Results</h4>The search resulted in 617 studies, 38 of which we deemed eligible for review. Of those 38 studies, most focused on cardiology, infectious diseases or oncology and the majority used electronic health records/electronic medical records data and cohort studies data. Different statistical methods were used to address confounding at baseline and selection bias, predominantly conditioning on the confounders (N = 18/49, 37%) and inverse probability of censoring weighting (N = 7/20, 35%) respectively. Different approaches were used to address immortal time bias, assigning individuals to treatment strategies at start of follow-up based on their data available at that specific time (N = 21, 55%), using the sequential trial emulations approach (N = 11, 29%) or the cloning approach (N = 6, 16%).<h4>Conclusion</h4>Different methods can be leveraged to address (A) confounding bias, (B) immortal time bias, and (C) selection bias. When working with observational data, and if possible, the 'target trial' framework should be used as it provides a structured conceptual approach to observational research.",,doi:https://doi.org/10.1186/s12874-023-02000-9; html:https://europepmc.org/articles/PMC10428565; pdf:https://europepmc.org/articles/PMC10428565?pdf=render
+37561812,https://doi.org/10.1371/journal.pcbi.1011368,Call detail record aggregation methodology impacts infectious disease models informed by human mobility.,"Gibbs H, Musah A, Seidu O, Ampofo W, Asiedu-Bekoe F, Gray J, Adewole WA, Cheshire J, Marks M, Eggo RM.",,PLoS computational biology,2023,2023-08-10,Y,,,,"This paper demonstrates how two different methods used to calculate population-level mobility from Call Detail Records (CDR) produce varying predictions of the spread of epidemics informed by these data. Our findings are based on one CDR dataset describing inter-district movement in Ghana in 2021, produced using two different aggregation methodologies. One methodology, ""all pairs,"" is designed to retain long distance network connections while the other, ""sequential"" methodology is designed to accurately reflect the volume of travel between locations. We show how the choice of methodology feeds through models of human mobility to the predictions of a metapopulation SEIR model of disease transmission. We also show that this impact varies depending on the location of pathogen introduction and the transmissibility of infections. For central locations or highly transmissible diseases, we do not observe significant differences between aggregation methodologies on the predicted spread of disease. For less transmissible diseases or those introduced into remote locations, we find that the choice of aggregation methodology influences the speed of spatial spread as well as the size of the peak number of infections in individual districts. Our findings can help researchers and users of epidemiological models to understand how methodological choices at the level of model inputs may influence the results of models of infectious disease transmission, as well as the circumstances in which these choices do not alter model predictions.",,pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011368&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1011368; html:https://europepmc.org/articles/PMC10443843; pdf:https://europepmc.org/articles/PMC10443843?pdf=render
 34740937,https://doi.org/10.1136/bmjopen-2021-056601,Analysis of mental and physical disorders associated with COVID-19 in online health forums: a natural language processing study.,"Patel R, Smeraldi F, Abdollahyan M, Irving J, Bessant C.",,BMJ open,2021,2021-11-05,Y,information technology; Health Informatics; Covid-19,,,"<h4>Objectives</h4>Online health forums provide rich and untapped real-time data on population health. Through novel data extraction and natural language processing (NLP) techniques, we characterise the evolution of mental and physical health concerns relating to the COVID-19 pandemic among online health forum users.<h4>Setting and design</h4>We obtained data from three leading online health forums: HealthBoards, Inspire and HealthUnlocked, from the period 1 January 2020 to 31 May 2020. Using NLP, we analysed the content of posts related to COVID-19.<h4>Primary outcome measures</h4>(1) Proportion of forum posts containing COVID-19 keywords; (2) proportion of forum users making their very first post about COVID-19; (3) proportion of COVID-19-related posts containing content related to physical and mental health comorbidities.<h4>Results</h4>Data from 739 434 posts created by 53 134 unique users were analysed. A total of 35 581 posts (4.8%) contained a COVID-19 keyword. Posts discussing COVID-19 and related comorbid disorders spiked in early March to mid-March around the time of global implementation of lockdowns prompting a large number of users to post on online health forums for the first time. Over a quarter of COVID-19-related thread titles mentioned a physical or mental health comorbidity.<h4>Conclusions</h4>We demonstrate that it is feasible to characterise the content of online health forum user posts regarding COVID-19 and measure changes over time. The pandemic and corresponding public response has had a significant impact on posters' queries regarding mental health. Social media data sources such as online health forums can be harnessed to strengthen population-level mental health surveillance.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/11/e056601.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-056601; html:https://europepmc.org/articles/PMC8573296; pdf:https://europepmc.org/articles/PMC8573296?pdf=render
 34859617,https://doi.org/10.1002/edm2.309,The clinical profile and associated mortality in people with and without diabetes with Coronavirus disease 2019 on admission to acute hospital services.,"Gokhale K, Mostafa SA, Wang J, Tahrani AA, Sainsbury CA, Toulis KA, Thomas GN, Hassan-Smith Z, Sapey E, Gallier S, Adderley NJ, Narendran P, Bellary S, Taverner T, Ghosh S, Nirantharakumar K, Hanif W.",,"Endocrinology, diabetes & metabolism",2022,2021-12-03,Y,Diabetes; Complications; Covid-19,,,"<h4>Introduction</h4>To assess if in adults with COVID-19, whether those with diabetes and complications (DM+C) present with a more severe clinical profile and if that relates to increased mortality, compared to those with diabetes with no complications (DM-NC) and those without diabetes.<h4>Methods</h4>Service-level data was used from 996 adults with laboratory confirmed COVID-19 who presented to the Queen Elizabeth Hospital Birmingham, UK, from March to June 2020. All individuals were categorized into DM+C, DM-NC, and non-diabetes groups. Physiological and laboratory measurements in the first 5 days after admission were collated and compared among groups. Cox proportional hazards regression models were used to evaluate associations between diabetes status and the risk of mortality.<h4>Results</h4>Among the 996 individuals, 104 (10.4%) were DM+C, 295 (29.6%) DM-NC and 597 (59.9%) non-diabetes. There were 309 (31.0%) in-hospital deaths documented, 40 (4.0% of total cohort) were DM+C, 99 (9.9%) DM-NC and 170 (17.0%) non-diabetes. Individuals with DM+C were more likely to present with high anion gap/metabolic acidosis, features of renal impairment, and low albumin/lymphocyte count than those with DM-NC or those without diabetes. There was no significant difference in mortality rates among the groups: compared to individuals without diabetes, the adjusted HRs were 1.39 (95% CI 0.95-2.03, p = 0.093) and 1.18 (95% CI 0.90-1.54, p = 0.226) in DM+C and DM-C, respectively.<h4>Conclusions</h4>Those with COVID-19 and DM+C presented with a more severe clinical and biochemical profile, but this did not associate with increased mortality in this study.",,doi:https://doi.org/10.1002/edm2.309; doi:https://doi.org/10.1002/edm2.309; html:https://europepmc.org/articles/PMC8754243; pdf:https://europepmc.org/articles/PMC8754243?pdf=render
 33299071,https://doi.org/10.1038/s41746-020-00357-5,Belief of having had unconfirmed Covid-19 infection reduces willingness to participate in app-based contact tracing.,"Bachtiger P, Adamson A, Quint JK, Peters NS.",,NPJ digital medicine,2020,2020-11-06,Y,,,,"Contact tracing and lockdown are health policies being used worldwide to combat the coronavirus (COVID-19). The UK National Health Service (NHS) Track and Trace Service has plans for a nationwide app that notifies the need for self-isolation to those in contact with a person testing positive for COVID-19. To be successful, such an app will require high uptake, the determinants and willingness for which are unclear but essential to understand for effective public health benefit. The objective of this study was to measure the determinants of willingness to participate in an NHS app-based contact-tracing programme using a questionnaire within the Care Information Exchange (CIE)-the largest patient-facing electronic health record in the NHS. Among 47,708 registered NHS users of the CIE, 27% completed a questionnaire asking about willingness to participate in app-based contact tracing, understanding of government advice, mental and physical wellbeing and their healthcare utilisation-related or not to COVID-19. Descriptive statistics are reported alongside univariate and multivariable logistic regression models, with positive or negative responses to a question on app-based contact tracing as the dependent variable. 26.1% of all CIE participants were included in the analysis (N = 12,434, 43.0% male, mean age 55.2). 60.3% of respondents were willing to participate in app-based contact tracing. Out of those who responded 'no', 67.2% stated that this was due to privacy concerns. In univariate analysis, worsening mood, fear and anxiety in relation to changes in government rules around lockdown were associated with lower willingness to participate. Multivariable analysis showed that difficulty understanding government rules was associated with a decreased inclination to download the app, with those scoring 1-2 and 3-4 in their understanding of the new government rules being 45% and 27% less inclined to download the contact-tracing app, respectively; when compared to those who rated their understanding as 5-6/10 (OR for 1-2/10 = 0.57 [CI 0.48-0.67]; OR for 3-4/10 = 0.744 [CI 0.64-0.87]), whereas scores of 7-8 and 9-10 showed a 43% and 31% respective increase. Those reporting an unconfirmed belief of having previously had and recovered from COVID-19 were 27% less likely to be willing to download the app; belief of previous recovery from COVID-19 infection OR 0.727 [0.585-0.908]). In this large UK-wide questionnaire of wellbeing in lockdown, a willingness for app-based contact tracing over an appropriate age range is 60%-close to the estimated 56% population uptake, and substantially less than the smartphone-user uptake considered necessary for an app-based contact tracing to be an effective intervention to help suppress an epidemic. Difficulty comprehending government advice and uncertainty of diagnosis, based on a public health policy of not testing to confirm self-reported COVID-19 infection during lockdown, therefore reduce willingness to adopt a government contact-tracing app to a level below the threshold for effectiveness as a tool to suppress an epidemic.",,pdf:https://www.nature.com/articles/s41746-020-00357-5.pdf; doi:https://doi.org/10.1038/s41746-020-00357-5; html:https://europepmc.org/articles/PMC7648058; pdf:https://europepmc.org/articles/PMC7648058?pdf=render
@@ -644,9 +645,9 @@ PMC10686417,https://doi.org/,The impact of restricted provision of publicly fund
 35288697,https://doi.org/10.1038/s41591-022-01750-1,COVID-19 and resilience of healthcare systems in ten countries.,"Arsenault C, Gage A, Kim MK, Kapoor NR, Akweongo P, Amponsah F, Aryal A, Asai D, Awoonor-Williams JK, Ayele W, Bedregal P, Doubova SV, Dulal M, Gadeka DD, Gordon-Strachan G, Mariam DH, Hensman D, Joseph JP, Kaewkamjornchai P, Eshetu MK, Gelaw SK, Kubota S, Leerapan B, Margozzini P, Mebratie AD, Mehata S, Moshabela M, Mthethwa L, Nega A, Oh J, Park S, Passi-Solar Á, Pérez-Cuevas R, Phengsavanh A, Reddy T, Rittiphairoj T, Sapag JC, Thermidor R, Tlou B, Valenzuela Guiñez F, Bauhoff S, Kruk ME.",,Nature medicine,2022,2022-03-14,Y,,,,"Declines in health service use during the Coronavirus Disease 2019 (COVID-19) pandemic could have important effects on population health. In this study, we used an interrupted time series design to assess the immediate effect of the pandemic on 31 health services in two low-income (Ethiopia and Haiti), six middle-income (Ghana, Lao People's Democratic Republic, Mexico, Nepal, South Africa and Thailand) and high-income (Chile and South Korea) countries. Despite efforts to maintain health services, disruptions of varying magnitude and duration were found in every country, with no clear patterns by country income group or pandemic intensity. Disruptions in health services often preceded COVID-19 waves. Cancer screenings, TB screening and detection and HIV testing were most affected (26-96% declines). Total outpatient visits declined by 9-40% at national levels and remained lower than predicted by the end of 2020. Maternal health services were disrupted in approximately half of the countries, with declines ranging from 5% to 33%. Child vaccinations were disrupted for shorter periods, but we estimate that catch-up campaigns might not have reached all children missed. By contrast, provision of antiretrovirals for HIV was not affected. By the end of 2020, substantial disruptions remained in half of the countries. Preliminary data for 2021 indicate that disruptions likely persisted. Although a portion of the declines observed might result from decreased needs during lockdowns (from fewer infectious illnesses or injuries), a larger share likely reflects a shortfall of health system resilience. Countries must plan to compensate for missed healthcare during the current pandemic and invest in strategies for better health system resilience for future emergencies.",,pdf:https://www.nature.com/articles/s41591-022-01750-1.pdf; doi:https://doi.org/10.1038/s41591-022-01750-1; html:https://europepmc.org/articles/PMC9205770; pdf:https://europepmc.org/articles/PMC9205770?pdf=render
 32679111,https://doi.org/10.1016/s0140-6736(20)31356-8,COVID-19 pandemic and admission rates for and management of acute coronary syndromes in England.,"Mafham MM, Spata E, Goldacre R, Gair D, Curnow P, Bray M, Hollings S, Roebuck C, Gale CP, Mamas MA, Deanfield JE, de Belder MA, Luescher TF, Denwood T, Landray MJ, Emberson JR, Collins R, Morris EJA, Casadei B, Baigent C.",,"Lancet (London, England)",2020,2020-07-14,Y,,,,"<h4>Background</h4>Several countries affected by the COVID-19 pandemic have reported a substantial drop in the number of patients attending the emergency department with acute coronary syndromes and a reduced number of cardiac procedures. We aimed to understand the scale, nature, and duration of changes to admissions for different types of acute coronary syndrome in England and to evaluate whether in-hospital management of patients has been affected as a result of the COVID-19 pandemic.<h4>Methods</h4>We analysed data on hospital admissions in England for types of acute coronary syndrome from Jan 1, 2019, to May 24, 2020, that were recorded in the Secondary Uses Service Admitted Patient Care database. Admissions were classified as ST-elevation myocardial infarction (STEMI), non-STEMI (NSTEMI), myocardial infarction of unknown type, or other acute coronary syndromes (including unstable angina). We identified revascularisation procedures undertaken during these admissions (ie, coronary angiography without percutaneous coronary intervention [PCI], PCI, and coronary artery bypass graft surgery). We calculated the numbers of weekly admissions and procedures undertaken; percentage reductions in weekly admissions and across subgroups were also calculated, with 95% CIs.<h4>Findings</h4>Hospital admissions for acute coronary syndrome declined from mid-February, 2020, falling from a 2019 baseline rate of 3017 admissions per week to 1813 per week by the end of March, 2020, a reduction of 40% (95% CI 37-43). This decline was partly reversed during April and May, 2020, such that by the last week of May, 2020, there were 2522 admissions, representing a 16% (95% CI 13-20) reduction from baseline. During the period of declining admissions, there were reductions in the numbers of admissions for all types of acute coronary syndrome, including both STEMI and NSTEMI, but relative and absolute reductions were larger for NSTEMI, with 1267 admissions per week in 2019 and 733 per week by the end of March, 2020, a percent reduction of 42% (95% CI 38-46). In parallel, reductions were recorded in the number of PCI procedures for patients with both STEMI (438 PCI procedures per week in 2019 vs 346 by the end of March, 2020; percent reduction 21%, 95% CI 12-29) and NSTEMI (383 PCI procedures per week in 2019 vs 240 by the end of March, 2020; percent reduction 37%, 29-45). The median length of stay among patients with acute coronary syndrome fell from 4 days (IQR 2-9) in 2019 to 3 days (1-5) by the end of March, 2020.<h4>Interpretation</h4>Compared with the weekly average in 2019, there was a substantial reduction in the weekly numbers of patients with acute coronary syndrome who were admitted to hospital in England by the end of March, 2020, which had been partly reversed by the end of May, 2020. The reduced number of admissions during this period is likely to have resulted in increases in out-of-hospital deaths and long-term complications of myocardial infarction and missed opportunities to offer secondary prevention treatment for patients with coronary heart disease. The full extent of the effect of COVID-19 on the management of patients with acute coronary syndrome will continue to be assessed by updating these analyses.<h4>Funding</h4>UK Medical Research Council, British Heart Foundation, Public Health England, Health Data Research UK, and the National Institute for Health Research Oxford Biomedical Research Centre.",,doi:https://doi.org/10.1016/s0140-6736(20)31356-8; doi:https://doi.org/10.1016/S0140-6736(20)31356-8; html:https://europepmc.org/articles/PMC7429983; pdf:https://europepmc.org/articles/PMC7429983?pdf=render
 35260393,https://doi.org/10.1136/bmjgh-2021-008099,Overcoming disruptions in essential health services during the COVID-19 pandemic in Mexico.,"Doubova SV, Robledo-Aburto ZA, Duque-Molina C, Borrayo-Sánchez G, González-León M, Avilés-Hernández R, Contreras-Sánchez SE, Leslie HH, Kruk M, Pérez-Cuevas R, Arsenault C.",,BMJ global health,2022,2022-03-01,Y,Health Policy; Health Systems; Covid-19,,,,,pdf:https://gh.bmj.com/content/bmjgh/7/3/e008099.full.pdf; doi:https://doi.org/10.1136/bmjgh-2021-008099; html:https://europepmc.org/articles/PMC8905410; pdf:https://europepmc.org/articles/PMC8905410?pdf=render
-PMC9644982,https://doi.org/,Assessing the impacts of COVID-19 on Care Homes in Wales.,"Fry R, Hollinghurst J, North L, Emmerson C, Long S, Akbari A, Gravenor M, Lyons R.",,International journal of population data science,,2022-11-21,Y,,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9644982/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9644982/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC9644982; pdf:https://europepmc.org/articles/PMC9644982?pdf=render
-34053271,https://doi.org/10.1098/rstb.2020.0266,Real-time monitoring of COVID-19 dynamics using automated trend fitting and anomaly detection.,"Jombart T, Ghozzi S, Schumacher D, Taylor TJ, Leclerc QJ, Jit M, Flasche S, Greaves F, Ward T, Eggo RM, Nightingale E, Meakin S, Brady OJ, Centre for Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Medley GF, Höhle M, Edmunds WJ.",,"Philosophical transactions of the Royal Society of London. Series B, Biological sciences",2021,2021-05-31,Y,Algorithm; Surveillance; outbreak; Machine Learning; Asmodee; Trendbreaker,,,"As several countries gradually release social distancing measures, rapid detection of new localized COVID-19 hotspots and subsequent intervention will be key to avoiding large-scale resurgence of transmission. We introduce ASMODEE (automatic selection of models and outlier detection for epidemics), a new tool for detecting sudden changes in COVID-19 incidence. Our approach relies on automatically selecting the best (fitting or predicting) model from a range of user-defined time series models, excluding the most recent data points, to characterize the main trend in an incidence. We then derive prediction intervals and classify data points outside this interval as outliers, which provides an objective criterion for identifying departures from previous trends. We also provide a method for selecting the optimal breakpoints, used to define how many recent data points are to be excluded from the trend fitting procedure. The analysis of simulated COVID-19 outbreaks suggests ASMODEE compares favourably with a state-of-art outbreak-detection algorithm while being simpler and more flexible. As such, our method could be of wider use for infectious disease surveillance. We illustrate ASMODEE using publicly available data of National Health Service (NHS) Pathways reporting potential COVID-19 cases in England at a fine spatial scale, showing that the method would have enabled the early detection of the flare-ups in Leicester and Blackburn with Darwen, two to three weeks before their respective lockdown. ASMODEE is implemented in the free R package <i>trendbreaker</i>. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.",,pdf:https://royalsocietypublishing.org/doi/pdf/10.1098/rstb.2020.0266; doi:https://doi.org/10.1098/rstb.2020.0266; html:https://europepmc.org/articles/PMC8165581; pdf:https://europepmc.org/articles/PMC8165581?pdf=render
 36526319,https://doi.org/10.1136/bmjopen-2022-064910,Performance of scoring systems in selecting short stay medical admissions suitable for assessment in same day emergency care: an analysis of diagnostic accuracy in a UK hospital setting.,"Atkin C, Gallier S, Wallin E, Reddy-Kolanu V, Sapey E.",,BMJ open,2022,2022-12-16,Y,Internal Medicine; General Medicine (See Internal Medicine); Organisation Of Health Services,,,"<h4>Objectives</h4>To assess the performance of the Amb score and Glasgow Admission Prediction Score (GAPS) in identifying acute medical admissions suitable for same day emergency care (SDEC) in a large urban secondary centre.<h4>Design</h4>Retrospective assessment of routinely collected data from electronic healthcare records.<h4>Setting</h4>Single large urban tertiary care centre.<h4>Participants</h4>All unplanned admissions to general medicine on Monday-Friday, episodes starting 08:00-16:59 hours and lasting up to 48 hours, between 1 April 2019 and 9 March 2020.<h4>Main outcome measures</h4>Sensitivity, specificity, positive and negative predictive value of the Amb score and GAPS in identifying patients discharged within 12 hours of arrival.<h4>Results</h4>7365 episodes were assessed. 94.6% of episodes had an Amb score suggesting suitability for SDEC. The positive predictive value of the Amb score in identifying those discharged within 12 hours was 54.5% (95% CI 53.3% to 55.8%). The area under the receiver operating characteristic curve (AUROC) for the Amb score was 0.612 (95% CI 0.599 to 0.625).42.4% of episodes had a GAPS suggesting suitability for SDEC. The positive predictive value of the GAPS in identifying those discharged within 12 hours was 50.5% (95% CI 48.4% to 52.7%). The AUROC for the GAPS was 0.606 (95% CI 0.590 to 0.622).41.4% of the population had both an Amb and GAPS score suggestive of suitability for SDEC and 5.7% of the population had both and Amb and GAPS score suggestive of a lack of suitability for SDEC.<h4>Conclusions</h4>The Amb score and GAPS had poor discriminatory ability to identify acute medical admissions suitable for discharge within 12 hours, limiting their utility in selecting patients for assessment within SDEC services within this diverse patient population.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/12/e064910.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-064910; html:https://europepmc.org/articles/PMC9764605; pdf:https://europepmc.org/articles/PMC9764605?pdf=render
+34053271,https://doi.org/10.1098/rstb.2020.0266,Real-time monitoring of COVID-19 dynamics using automated trend fitting and anomaly detection.,"Jombart T, Ghozzi S, Schumacher D, Taylor TJ, Leclerc QJ, Jit M, Flasche S, Greaves F, Ward T, Eggo RM, Nightingale E, Meakin S, Brady OJ, Centre for Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Medley GF, Höhle M, Edmunds WJ.",,"Philosophical transactions of the Royal Society of London. Series B, Biological sciences",2021,2021-05-31,Y,Algorithm; Surveillance; outbreak; Machine Learning; Asmodee; Trendbreaker,,,"As several countries gradually release social distancing measures, rapid detection of new localized COVID-19 hotspots and subsequent intervention will be key to avoiding large-scale resurgence of transmission. We introduce ASMODEE (automatic selection of models and outlier detection for epidemics), a new tool for detecting sudden changes in COVID-19 incidence. Our approach relies on automatically selecting the best (fitting or predicting) model from a range of user-defined time series models, excluding the most recent data points, to characterize the main trend in an incidence. We then derive prediction intervals and classify data points outside this interval as outliers, which provides an objective criterion for identifying departures from previous trends. We also provide a method for selecting the optimal breakpoints, used to define how many recent data points are to be excluded from the trend fitting procedure. The analysis of simulated COVID-19 outbreaks suggests ASMODEE compares favourably with a state-of-art outbreak-detection algorithm while being simpler and more flexible. As such, our method could be of wider use for infectious disease surveillance. We illustrate ASMODEE using publicly available data of National Health Service (NHS) Pathways reporting potential COVID-19 cases in England at a fine spatial scale, showing that the method would have enabled the early detection of the flare-ups in Leicester and Blackburn with Darwen, two to three weeks before their respective lockdown. ASMODEE is implemented in the free R package <i>trendbreaker</i>. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.",,pdf:https://royalsocietypublishing.org/doi/pdf/10.1098/rstb.2020.0266; doi:https://doi.org/10.1098/rstb.2020.0266; html:https://europepmc.org/articles/PMC8165581; pdf:https://europepmc.org/articles/PMC8165581?pdf=render
+PMC9644982,https://doi.org/,Assessing the impacts of COVID-19 on Care Homes in Wales.,"Fry R, Hollinghurst J, North L, Emmerson C, Long S, Akbari A, Gravenor M, Lyons R.",,International journal of population data science,,2022-11-21,Y,,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9644982/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9644982/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC9644982; pdf:https://europepmc.org/articles/PMC9644982?pdf=render
 34053260,https://doi.org/10.1098/rstb.2020.0283,Exploring surveillance data biases when estimating the reproduction number: with insights into subpopulation transmission of COVID-19 in England.,"Sherratt K, Abbott S, Meakin SR, Hellewell J, Munday JD, Bosse N, CMMID COVID-19 Working Group, Jit M, Funk S.",,"Philosophical transactions of the Royal Society of London. Series B, Biological sciences",2021,2021-05-31,Y,Transmission; Surveillance; Bias; Covid-19; Sars-cov-2; Time-varying Reproduction Number,,,"The time-varying reproduction number (<i>R<sub>t</sub></i>: the average number of secondary infections caused by each infected person) may be used to assess changes in transmission potential during an epidemic. While new infections are not usually observed directly, they can be estimated from data. However, data may be delayed and potentially biased. We investigated the sensitivity of <i>R<sub>t</sub></i> estimates to different data sources representing COVID-19 in England, and we explored how this sensitivity could track epidemic dynamics in population sub-groups. We sourced public data on test-positive cases, hospital admissions and deaths with confirmed COVID-19 in seven regions of England over March through August 2020. We estimated <i>R<sub>t</sub></i> using a model that mapped unobserved infections to each data source. We then compared differences in <i>R<sub>t</sub></i> with the demographic and social context of surveillance data over time. Our estimates of transmission potential varied for each data source, with the relative inconsistency of estimates varying across regions and over time. <i>R<sub>t</sub></i> estimates based on hospital admissions and deaths were more spatio-temporally synchronous than when compared to estimates from all test positives. We found these differences may be linked to biased representations of subpopulations in each data source. These included spatially clustered testing, and where outbreaks in hospitals, care homes, and young age groups reflected the link between age and severity of the disease. We highlight that policy makers could better target interventions by considering the source populations of <i>R<sub>t</sub></i> estimates. Further work should clarify the best way to combine and interpret <i>R<sub>t</sub></i> estimates from different data sources based on the desired use. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.",,pdf:https://royalsocietypublishing.org/doi/pdf/10.1098/rstb.2020.0283; doi:https://doi.org/10.1098/rstb.2020.0283; html:https://europepmc.org/articles/PMC8165604; pdf:https://europepmc.org/articles/PMC8165604?pdf=render
 36529825,https://doi.org/10.1007/s40258-022-00777-2,The False Economy of Seeking to Eliminate Delayed Transfers of Care: Some Lessons from Queueing Theory.,"Wood RM, Harper AL, Onen-Dumlu Z, Forte PG, Pitt M, Vasilakis C.",,Applied health economics and health policy,2023,2022-12-18,Y,,,,"<h4>Background</h4>It is a stated ambition of many healthcare systems to eliminate delayed transfers of care (DTOCs) between acute and step-down community services.<h4>Objective</h4>This study aims to demonstrate how, counter to intuition, pursual of such a policy is likely to be uneconomical, as it would require large amounts of community capacity to accommodate even the rarest of demand peaks, leaving much capacity unused for much of the time.<h4>Methods</h4>Some standard results from queueing theory-a mathematical discipline for considering the dynamics of queues and queueing systems-are used to provide a model of patient flow from the acute to community setting. While queueing models have a track record of application in healthcare, they have not before been used to address this question.<h4>Results</h4>Results show that 'eliminating' DTOCs is a false economy: the additional community costs required are greater than the possible acute cost saving. While a substantial proportion of DTOCs can be attributed to inefficient use of resources, the remainder can be considered economically essential to ensuring cost-efficient service operation. For England's National Health Service (NHS), our modelling estimates annual cost savings of £117m if DTOCs are reduced to the 12% of current levels that can be regarded as economically essential.<h4>Conclusion</h4>This study discourages the use of 'zero DTOC' targets and instead supports an assessment based on the specific characteristics of the healthcare system considered.",,pdf:https://link.springer.com/content/pdf/10.1007/s40258-022-00777-2.pdf; doi:https://doi.org/10.1007/s40258-022-00777-2; html:https://europepmc.org/articles/PMC9760184; pdf:https://europepmc.org/articles/PMC9760184?pdf=render
 35210898,https://doi.org/10.2147/por.s353400,Deriving a Standardised Recommended Respiratory Disease Codelist Repository for Future Research.,"MacRae C, Whittaker H, Mukherjee M, Daines L, Morgan A, Iwundu C, Alsallakh M, Vasileiou E, O'Rourke E, Williams AT, Stone PW, Sheikh A, Quint JK.",,Pragmatic and observational research,2022,2022-02-16,Y,Asthma; COPD; Respiratory Tract Infections; Electronic Healthcare Records,,,"<h4>Background</h4>Electronic health record (EHR) databases provide rich, longitudinal data on interactions with healthcare providers and can be used to advance research into respiratory conditions. However, since these data are primarily collected to support health care delivery, clinical coding can be inconsistent, resulting in inherent challenges in using these data for research purposes.<h4>Methods</h4>We systematically searched existing international literature and UK code repositories to find respiratory disease codelists for asthma from January 2018, and chronic obstructive pulmonary disease and respiratory tract infections from January 2020, based on prior searches. Medline searches using key terms provided in article lists. Full-text articles, supplementary files, and reference lists were examined for codelists, and codelists repositories were searched. A reproducible methodology for codelists creation was developed with recommended lists for each disease created based on multidisciplinary expert opinion and previously published literature.<h4>Results</h4>Medline searches returned 1126 asthma articles, 70 COPD articles, and 90 respiratory infection articles, with 3%, 22% and 5% including codelists, respectively. Repository searching returned 12 asthma, 23 COPD, and 64 respiratory infection codelists. We have systematically compiled respiratory disease codelists and from these derived recommended lists for use by researchers to find the most up-to-date and relevant respiratory disease codelists that can be tailored to individual research questions.<h4>Conclusion</h4>Few published papers include codelists, and where published diverse codelists were used, even when answering similar research questions. Whilst some advances have been made, greater consistency and transparency across studies using routine data to study respiratory diseases are needed.",,pdf:https://www.dovepress.com/getfile.php?fileID=78337; doi:https://doi.org/10.2147/POR.S353400; html:https://europepmc.org/articles/PMC8859726; pdf:https://europepmc.org/articles/PMC8859726?pdf=render
@@ -655,17 +656,17 @@ PMC9644982,https://doi.org/,Assessing the impacts of COVID-19 on Care Homes in W
 33521768,https://doi.org/10.1016/s2666-7568(20)30011-8,Tackling immunosenescence to improve COVID-19 outcomes and vaccine response in older adults.,"Cox LS, Bellantuono I, Lord JM, Sapey E, Mannick JB, Partridge L, Gordon AL, Steves CJ, Witham MD.",,The lancet. Healthy longevity,2020,2020-11-09,Y,,,,,,pdf:https://eprint.ncl.ac.uk/fulltext.aspx?url=271502/147E40FC-6152-4060-81B1-702AE3B1D66A.pdf&pub_id=271502; doi:https://doi.org/10.1016/S2666-7568(20)30011-8; html:https://europepmc.org/articles/PMC7834195; pdf:https://europepmc.org/articles/PMC7834195?pdf=render
 36093379,https://doi.org/10.1016/j.isci.2022.105079,Epidemiologic information discovery from open-access COVID-19 case reports via pretrained language model.,"Wang Z, Liu XF, Du Z, Wang L, Wu Y, Holme P, Lachmann M, Lin H, Wong ZSY, Xu XK, Sun Y.",,iScience,2022,2022-09-05,Y,Artificial intelligence; Virology; Machine Learning; Health Sciences,,,"Although open-access data are increasingly common and useful to epidemiological research, the curation of such datasets is resource-intensive and time-consuming. Despite the existence of a major source of COVID-19 data, the regularly disclosed case reports were often written in natural language with an unstructured format. Here, we propose a computational framework that can automatically extract epidemiological information from open-access COVID-19 case reports. We develop this framework by coupling a language model developed using deep neural networks with training samples compiled using an optimized data annotation strategy. When applied to the COVID-19 case reports collected from mainland China, our framework outperforms all other state-of-the-art deep learning models. The information extracted from our approach is highly consistent with that obtained from the gold-standard manual coding, with a matching rate of 80%. To disseminate our algorithm, we provide an open-access online platform that is able to estimate key epidemiological statistics in real time, with much less effort for data curation.",,pdf:http://www.cell.com/article/S2589004222013517/pdf; doi:https://doi.org/10.1016/j.isci.2022.105079; html:https://europepmc.org/articles/PMC9441477; pdf:https://europepmc.org/articles/PMC9441477?pdf=render
 33782080,https://doi.org/10.1136/thoraxjnl-2020-216512,Impact of COVID-19 national lockdown on asthma exacerbations: interrupted time-series analysis of English primary care data.,"Shah SA, Quint JK, Nwaru BI, Sheikh A.",,Thorax,2021,2021-03-29,Y,Asthma; Asthma Epidemiology; Covid-19,,,"<h4>Background</h4>The impact of COVID-19 and ensuing national lockdown on asthma exacerbations is unclear.<h4>Methods</h4>We conducted an interrupted time-series (lockdown on 23 March 2020 as point of interruption) analysis in asthma cohort identified using a validated algorithm from a national-level primary care database, the Optimum Patient Care Database. We derived asthma exacerbation rates for every week and compared exacerbation rates in the period: January to August 2020 with a pre-COVID-19 period and January to August 2016-2019. Exacerbations were defined as asthma-related hospital attendance/admission (including accident and emergency visit), or an acute course of oral corticosteroids with evidence of respiratory review, as recorded in primary care. We used a generalised least squares modelling approach and stratified the analyses by age, sex, English region and healthcare setting.<h4>Results</h4>From a database of 9 949 387 patients, there were 100 165 patients with asthma who experienced at least one exacerbation during 2016-2020. Of 278 996 exacerbation episodes, 49 938 (17.9%) required hospital visit. Comparing pre-lockdown to post-lockdown period, we observed a statistically significant reduction in the level (-0.196 episodes per person-year; p<0.001; almost 20 episodes for every 100 patients with asthma per year) of exacerbation rates across all patients. The reductions in level in stratified analyses were: 0.005-0.244 (healthcare setting, only those without hospital attendance/admission were significant), 0.210-0.277 (sex), 0.159-0.367 (age), 0.068-0.590 (region).<h4>Conclusions</h4>There has been a significant reduction in attendance to primary care for asthma exacerbations during the pandemic. This reduction was observed in all age groups, both sexes and across most regions in England.",,pdf:https://thorax.bmj.com/content/thoraxjnl/76/9/860.full.pdf; doi:https://doi.org/10.1136/thoraxjnl-2020-216512; html:https://europepmc.org/articles/PMC8011425; pdf:https://europepmc.org/articles/PMC8011425?pdf=render
-PMC9645061,https://doi.org/,Using population-scale medication data to evaluate the impact of the COVID-19 pandemic on the usage of analgesics by cancer patients.,"Han J, Akbari A, Torabi F, Griffiths R, Lyons J, Rolles M, Arnold C, Huws D, Lawler M, Lyons R.",,International journal of population data science,,2022-11-25,Y,,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9645061/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9645061/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC9645061; pdf:https://europepmc.org/articles/PMC9645061?pdf=render
 34785588,https://doi.org/10.1136/openhrt-2021-001784,OpenSAFELY: impact of national guidance on switching anticoagulant therapy during COVID-19 pandemic.,"OpenSAFELY Collaborative, Curtis HJ, MacKenna B, Walker AJ, Croker R, Mehrkar A, Morton C, Bacon S, Hickman G, Inglesby P, Bates C, Evans D, Ward T, Cockburn J, Davy S, Bhaskaran K, Schultze A, Rentsch CT, Williamson E, Hulme W, Tomlinson L, Mathur R, Drysdale H, Eggo RM, Wong AY, Forbes H, Parry J, Hester F, Harper S, Douglas I, Smeeth L, Goldacre B.",,Open heart,2021,2021-11-01,Y,Stroke; Medication Adherence; Healthcare Economics And Organisations; Covid-19,,,"<h4>Background</h4>Early in the COVID-19 pandemic, the National Health Service (NHS) recommended that appropriate patients anticoagulated with warfarin should be switched to direct-acting oral anticoagulants (DOACs), requiring less frequent blood testing. Subsequently, a national safety alert was issued regarding patients being inappropriately coprescribed two anticoagulants following a medication change and associated monitoring.<h4>Objective</h4>To describe which people were switched from warfarin to DOACs; identify potentially unsafe coprescribing of anticoagulants; and assess whether abnormal clotting results have become more frequent during the pandemic.<h4>Methods</h4>With the approval of NHS England, we conducted a cohort study using routine clinical data from 24 million NHS patients in England.<h4>Results</h4>20 000 of 164 000 warfarin patients (12.2%) switched to DOACs between March and May 2020, most commonly to edoxaban and apixaban. Factors associated with switching included: older age, recent renal function test, higher number of recent INR tests recorded, atrial fibrillation diagnosis and care home residency. There was a sharp rise in coprescribing of warfarin and DOACs from typically 50-100 per month to 246 in April 2020, 0.06% of all people receiving a DOAC or warfarin. International normalised ratio (INR) testing fell by 14% to 506.8 patients tested per 1000 warfarin patients each month. We observed a very small increase in elevated INRs (n=470) during April compared with January (n=420).<h4>Conclusions</h4>Increased switching of anticoagulants from warfarin to DOACs was observed at the outset of the COVID-19 pandemic in England following national guidance. There was a small but substantial number of people coprescribed warfarin and DOACs during this period. Despite a national safety alert on the issue, a widespread rise in elevated INR test results was not found. Primary care has responded rapidly to changes in patient care during the COVID-19 pandemic.",,pdf:https://openheart.bmj.com/content/openhrt/8/2/e001784.full.pdf; doi:https://doi.org/10.1136/openhrt-2021-001784; html:https://europepmc.org/articles/PMC8595296; pdf:https://europepmc.org/articles/PMC8595296?pdf=render
+PMC9645061,https://doi.org/,Using population-scale medication data to evaluate the impact of the COVID-19 pandemic on the usage of analgesics by cancer patients.,"Han J, Akbari A, Torabi F, Griffiths R, Lyons J, Rolles M, Arnold C, Huws D, Lawler M, Lyons R.",,International journal of population data science,,2022-11-25,Y,,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9645061/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9645061/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC9645061; pdf:https://europepmc.org/articles/PMC9645061?pdf=render
 36434299,https://doi.org/10.1007/s00127-022-02393-w,Adverse outcomes associated with recorded victimization in mental health electronic records during the first UK COVID-19 lockdown.,"Kadra-Scalzo G, Kornblum D, Stewart R, Howard LM.",,Social psychiatry and psychiatric epidemiology,2023,2022-11-24,Y,Mental health; Domestic Violence; Victimisation; Adverse Outcomes; Covid-19,,,"<h4>Purpose</h4>The impact of COVID-19 pandemic policies on vulnerable groups such as people with mental health problems who experience violence remains unknown. This study aimed to investigate the prevalence of victimization recorded in mental healthcare records during the first UK lockdown, and associations with subsequent adverse outcomes.<h4>Methods</h4>Using a large mental healthcare database, we identified all adult patients receiving services between 16.12.2019 and 15.06.2020 and extracted records of victimisation between 16.03.2020 and 15.06.2020 (first UK COVID-19 lockdown). We investigated adverse outcomes including acute care, emergency department referrals and all-cause mortality in the year following the lockdown (16.06.2020- 01.11.2021). Multivariable Cox regressions models were constructed, adjusting for socio-demographic, socioeconomic, clinical, and service use factors.<h4>Results</h4>Of 21,037 adults receiving mental healthcare over the observation period, 3,610 (17.2%) had victimisation mentioned between 16.03.2020 and 15.06.2020 (first UK COVID-19 lockdown). Service users with mentions of victimisation in their records had an elevated risk for all outcomes: acute care (adjusted HR: 2.1; 95%CI 1.9-2.3, p < 0.001), emergency department referrals (aHR: 2.0; 95%CI 1.8-2.2; p < 0.001), and all-cause mortality (aHR: 1.5; 95%CI 1.1-1.9; p = 0.003), when compared to service users with no recorded victimisation. We did not observe a statistically significant interaction with gender; however, after adjusting for possible confounders, men had slightly higher hazard ratios for all-cause mortality and emergency department referrals than women.<h4>Conclusion</h4>Patients with documented victimisation during the first UK lockdown were at increased risk for acute care, emergency department referrals and all-cause mortality. Further research is needed into mediating mechanisms.",,pdf:https://link.springer.com/content/pdf/10.1007/s00127-022-02393-w.pdf; doi:https://doi.org/10.1007/s00127-022-02393-w; html:https://europepmc.org/articles/PMC9702612; pdf:https://europepmc.org/articles/PMC9702612?pdf=render
 34261639,https://doi.org/10.1136/bmj.n1592,Risks of covid-19 hospital admission and death for people with learning disability: population based cohort study using the OpenSAFELY platform.,"Williamson EJ, McDonald HI, Bhaskaran K, Walker AJ, Bacon S, Davy S, Schultze A, Tomlinson L, Bates C, Ramsay M, Curtis HJ, Forbes H, Wing K, Minassian C, Tazare J, Morton CE, Nightingale E, Mehrkar A, Evans D, Inglesby P, MacKenna B, Cockburn J, Rentsch CT, Mathur R, Wong AYS, Eggo RM, Hulme W, Croker R, Parry J, Hester F, Harper S, Douglas IJ, Evans SJW, Smeeth L, Goldacre B, Kuper H.",,BMJ (Clinical research ed.),2021,2021-07-14,Y,,,,"<h4>Objective</h4>To assess the association between learning disability and risk of hospital admission and death from covid-19 in England among adults and children.<h4>Design</h4>Population based cohort study on behalf of NHS England using the OpenSAFELY platform.<h4>Setting</h4>Patient level data were obtained for more than 17 million people registered with a general practice in England that uses TPP software. Electronic health records were linked with death data from the Office for National Statistics and hospital admission data from NHS Secondary Uses Service.<h4>Participants</h4>Adults (aged 16-105 years) and children (<16 years) from two cohorts: wave 1 (registered with a TPP practice as of 1 March 2020 and followed until 31 August 2020); and wave 2 (registered 1 September 2020 and followed until 8 February 2021). The main exposure group consisted of people on a general practice learning disability register; a subgroup was defined as those having profound or severe learning disability. People with Down's syndrome and cerebral palsy were identified (whether or not they were on the learning disability register).<h4>Main outcome measure</h4>Covid-19 related hospital admission and covid-19 related death. Non-covid-19 deaths were also explored.<h4>Results</h4>For wave 1, 14 312 023 adults aged ≥16 years were included, and 90 307 (0.63%) were on the learning disability register. Among adults on the register, 538 (0.6%) had a covid-19 related hospital admission; there were 222 (0.25%) covid-19 related deaths and 602 (0.7%) non-covid deaths. Among adults not on the register, 29 781 (0.2%) had a covid-19 related hospital admission; there were 13 737 (0.1%) covid-19 related deaths and 69 837 (0.5%) non-covid deaths. Wave 1 hazard ratios for adults on the learning disability register (adjusted for age, sex, ethnicity, and geographical location) were 5.3 (95% confidence interval 4.9 to 5.8) for covid-19 related hospital admission and 8.2 (7.2 to 9.4) for covid-19 related death. Wave 2 produced similar estimates. Associations were stronger among those classified as having severe to profound learning disability, and among those in residential care. For both waves, Down's syndrome and cerebral palsy were associated with increased hazards for both events; Down's syndrome to a greater extent. Hazard ratios for non-covid deaths followed similar patterns with weaker associations. Similar patterns of increased relative risk were seen for children, but covid-19 related deaths and hospital admissions were rare, reflecting low event rates among children.<h4>Conclusions</h4>People with learning disability have markedly increased risks of hospital admission and death from covid-19, over and above the risks observed for non-covid causes of death. Prompt access to covid-19 testing and healthcare is warranted for this vulnerable group, and prioritisation for covid-19 vaccination and other targeted preventive measures should be considered.",,pdf:https://www.bmj.com/content/bmj/374/bmj.n1592.full.pdf; doi:https://doi.org/10.1136/bmj.n1592; html:https://europepmc.org/articles/PMC8278652; pdf:https://europepmc.org/articles/PMC8278652?pdf=render
 37393057,https://doi.org/10.1016/j.bbi.2023.06.028,"Cardiovascular health, infection burden and their interactive association with brain volumetric and white matter integrity outcomes in the UK Biobank.","Beydoun MA, Beydoun HA, Gale SD, Hedges D, Weiss J, Li Z, Erickson LD, Noren Hooten N, Launer LJ, Evans MK, Zonderman AB.",,"Brain, behavior, and immunity",2023,2023-06-29,N,Infection; Aging; White Matter Integrity; Brain Volumes; Brain Magnetic Resonance Imaging,,,"<h4>Background</h4>Cardiovascular health is associated with brain magnetic resonance imaging (MRI) markers of pathology and infections may modulate this association.<h4>Methods</h4>Using data from 38,803 adults (aged 40-70 years) and followed-up for 5-15 years, we tested associations of prevalent total (47.5%) and hospital-treated infection burden (9.7%) with brain structural and diffusion-weighted MRI (i.e., sMRI and dMRI, respectively) common in dementia phenome. Poor white matter tissue integrity was operationalized with lower global and tract-specific fractional anisotropy (FA) and higher mean diffusivity (MD). Volumetric sMRI outcomes included total, gray matter (GM), white matter (WM), frontal bilateral GM, white matter hyperintensity (WMH), and selected based on previous associations with dementia. Cardiovascular health was measured with Life's Essential 8 score (LE8) converted to tertiles. Multiple linear regression models were used, adjusting for intracranial volumes (ICV) for subcortical structures, and for demographic, socio-economic, and the Alzheimer's Disease polygenic risk score for all outcomes, among potential confounders.<h4>Results</h4>In fully adjusted models, hospital-treated infections were inversely related to GM (β ± SE: -1042 ± 379, p = 0.006) and directly related to WMH as percent of ICV (Log<sub>e</sub> transformed) (β ± SE:+0.026 ± 0.007, p < 0.001). Both total and hospital-treated infections were associated with poor WMI, while the latter was inversely related to FA within the lowest LE8 tertile (β ± SE:-0.0011 ± 0.0003, p < 0.001, P<sub>LE8×IB</sub> < 0.05), a pattern detected for GM, Right Frontal GM, left accumbens and left hippocampus volumes. Within the uppermost LE8 tertile, total infection burden was linked to smaller right amygdala while being associated with larger left frontal GM and right putamen volumes, in the overall sample. Within that uppermost tertile of LE8, caudate volumes were also positively associated with hospital-treated infections.<h4>Conclusions</h4>Hospital-treated infections had more consistent deleterious effects on volumetric and white matter integrity brain neuroimaging outcomes compared with total infectious burden, particularly in poorer cardiovascular health groups. Further studies are needed in comparable populations, including longitudinal studies with multiple repeats on neuroimaging markers.",,doi:https://doi.org/10.1016/j.bbi.2023.06.028; html:https://europepmc.org/articles/PMC11040741; pdf:https://europepmc.org/articles/PMC11040741?pdf=render; doi:https://doi.org/10.1016/j.bbi.2023.06.028
-33545096,https://doi.org/10.1016/s0140-6736(21)00149-5,"Azithromycin in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial.",RECOVERY Collaborative Group.,,"Lancet (London, England)",2021,2021-02-02,Y,,,,"<h4>Background</h4>Azithromycin has been proposed as a treatment for COVID-19 on the basis of its immunomodulatory actions. We aimed to evaluate the safety and efficacy of azithromycin in patients admitted to hospital with COVID-19.<h4>Methods</h4>In this randomised, controlled, open-label, adaptive platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), several possible treatments were compared with usual care in patients admitted to hospital with COVID-19 in the UK. The trial is underway at 176 hospitals in the UK. Eligible and consenting patients were randomly allocated to either usual standard of care alone or usual standard of care plus azithromycin 500 mg once per day by mouth or intravenously for 10 days or until discharge (or allocation to one of the other RECOVERY treatment groups). Patients were assigned via web-based simple (unstratified) randomisation with allocation concealment and were twice as likely to be randomly assigned to usual care than to any of the active treatment groups. Participants and local study staff were not masked to the allocated treatment, but all others involved in the trial were masked to the outcome data during the trial. The primary outcome was 28-day all-cause mortality, assessed in the intention-to-treat population. The trial is registered with ISRCTN, 50189673, and ClinicalTrials.gov, NCT04381936.<h4>Findings</h4>Between April 7 and Nov 27, 2020, of 16 442 patients enrolled in the RECOVERY trial, 9433 (57%) were eligible and 7763 were included in the assessment of azithromycin. The mean age of these study participants was 65·3 years (SD 15·7) and approximately a third were women (2944 [38%] of 7763). 2582 patients were randomly allocated to receive azithromycin and 5181 patients were randomly allocated to usual care alone. Overall, 561 (22%) patients allocated to azithromycin and 1162 (22%) patients allocated to usual care died within 28 days (rate ratio 0·97, 95% CI 0·87-1·07; p=0·50). No significant difference was seen in duration of hospital stay (median 10 days [IQR 5 to >28] vs 11 days [5 to >28]) or the proportion of patients discharged from hospital alive within 28 days (rate ratio 1·04, 95% CI 0·98-1·10; p=0·19). Among those not on invasive mechanical ventilation at baseline, no significant difference was seen in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (risk ratio 0·95, 95% CI 0·87-1·03; p=0·24).<h4>Interpretation</h4>In patients admitted to hospital with COVID-19, azithromycin did not improve survival or other prespecified clinical outcomes. Azithromycin use in patients admitted to hospital with COVID-19 should be restricted to patients in whom there is a clear antimicrobial indication.<h4>Funding</h4>UK Research and Innovation (Medical Research Council) and National Institute of Health Research.",,pdf:http://www.thelancet.com/article/S0140673621001495/pdf; doi:https://doi.org/10.1016/S0140-6736(21)00149-5; html:https://europepmc.org/articles/PMC7884931; pdf:https://europepmc.org/articles/PMC7884931?pdf=render
 33952557,https://doi.org/10.1136/bmjopen-2021-049964,Study protocol of the Edinburgh and Lothian Virus Intervention Study in Kids: a randomised controlled trial of hypertonic saline nose drops in children with upper respiratory tract infections (ELVIS Kids).,"Ramalingam S, Graham C, Oatey K, Rayson P, Stoddart A, Sheikh A, Cunningham S, ELVIS Kids Trial Investigators.",,BMJ open,2021,2021-05-05,Y,Virology; Community Child Health; Neonatology; Primary Care; Paediatric Infectious Disease & Immunisation,,,"<h4>Introduction</h4>Edinburgh and Lothians' Viral Intervention Study Kids is a parallel, open-label, randomised controlled trial of hypertonic saline (HS) nose drops (~2.6% sodium chloride) vs standard care in children <7 years of age with symptoms of an upper respiratory tract infection (URTI).<h4>Methods and analysis</h4>Children are recruited prior to URTI or within 48 hours of developing URTI symptoms by advertising in areas such as local schools/nurseries, health centres/hospitals, recreational facilities, public events, workplaces, local/social media. Willing parents/guardians, of children <7 years of age will be asked to contact the research team at their local site. Children will be randomised to either a control arm (standard symptomatic care), or intervention arm (three drops/nostril of HS, at least four times a day, until 24 hours after asymptomatic or a maximum of 28 days). All participants are requested to provide a nasal swab at the start of the study (intervention arm: before HS drops) and then daily for four more days. Parent/guardian complete a validated daily diary, an end of illness diary, a satisfaction questionnaire and a wheeze questionnaire (day 28). The parent/guardian of a child in the intervention arm is taught to prepare HS nose drops. Parent/guardian of children asymptomatic at recruitment are requested to inform the research team within 48 hours of their child developing an URTI and follow the instructions already provided. The day 28 questionnaire determines if the child experienced a wheeze following illness. Participation in the study ends on day 28.<h4>Ethics and dissemination</h4>The study has been approved by the West of Scotland Research Ethics Service (18/WS/0080). It is cosponsored by Academic and Clinical Central Office for Research and Development-a partnership between the University of Edinburgh and National Health Service Lothian Health Board. The findings will be disseminated through peer-reviewed publications, conference presentations and via the study website.<h4>Trial registration number</h4>NCT03463694.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/5/e049964.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-049964; html:https://europepmc.org/articles/PMC8103393; pdf:https://europepmc.org/articles/PMC8103393?pdf=render
+33545096,https://doi.org/10.1016/s0140-6736(21)00149-5,"Azithromycin in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial.",RECOVERY Collaborative Group.,,"Lancet (London, England)",2021,2021-02-02,Y,,,,"<h4>Background</h4>Azithromycin has been proposed as a treatment for COVID-19 on the basis of its immunomodulatory actions. We aimed to evaluate the safety and efficacy of azithromycin in patients admitted to hospital with COVID-19.<h4>Methods</h4>In this randomised, controlled, open-label, adaptive platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), several possible treatments were compared with usual care in patients admitted to hospital with COVID-19 in the UK. The trial is underway at 176 hospitals in the UK. Eligible and consenting patients were randomly allocated to either usual standard of care alone or usual standard of care plus azithromycin 500 mg once per day by mouth or intravenously for 10 days or until discharge (or allocation to one of the other RECOVERY treatment groups). Patients were assigned via web-based simple (unstratified) randomisation with allocation concealment and were twice as likely to be randomly assigned to usual care than to any of the active treatment groups. Participants and local study staff were not masked to the allocated treatment, but all others involved in the trial were masked to the outcome data during the trial. The primary outcome was 28-day all-cause mortality, assessed in the intention-to-treat population. The trial is registered with ISRCTN, 50189673, and ClinicalTrials.gov, NCT04381936.<h4>Findings</h4>Between April 7 and Nov 27, 2020, of 16 442 patients enrolled in the RECOVERY trial, 9433 (57%) were eligible and 7763 were included in the assessment of azithromycin. The mean age of these study participants was 65·3 years (SD 15·7) and approximately a third were women (2944 [38%] of 7763). 2582 patients were randomly allocated to receive azithromycin and 5181 patients were randomly allocated to usual care alone. Overall, 561 (22%) patients allocated to azithromycin and 1162 (22%) patients allocated to usual care died within 28 days (rate ratio 0·97, 95% CI 0·87-1·07; p=0·50). No significant difference was seen in duration of hospital stay (median 10 days [IQR 5 to >28] vs 11 days [5 to >28]) or the proportion of patients discharged from hospital alive within 28 days (rate ratio 1·04, 95% CI 0·98-1·10; p=0·19). Among those not on invasive mechanical ventilation at baseline, no significant difference was seen in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (risk ratio 0·95, 95% CI 0·87-1·03; p=0·24).<h4>Interpretation</h4>In patients admitted to hospital with COVID-19, azithromycin did not improve survival or other prespecified clinical outcomes. Azithromycin use in patients admitted to hospital with COVID-19 should be restricted to patients in whom there is a clear antimicrobial indication.<h4>Funding</h4>UK Research and Innovation (Medical Research Council) and National Institute of Health Research.",,pdf:http://www.thelancet.com/article/S0140673621001495/pdf; doi:https://doi.org/10.1016/S0140-6736(21)00149-5; html:https://europepmc.org/articles/PMC7884931; pdf:https://europepmc.org/articles/PMC7884931?pdf=render
 36280346,https://doi.org/10.1136/heartjnl-2022-321492,Cardiovascular disease and mortality sequelae of COVID-19 in the UK Biobank.,"Raisi-Estabragh Z, Cooper J, Salih A, Raman B, Lee AM, Neubauer S, Harvey NC, Petersen SE.",,Heart (British Cardiac Society),2022,2022-12-22,Y,epidemiology; Covid-19,,,"<h4>Objective</h4>To examine association of COVID-19 with incident cardiovascular events in 17 871 UK Biobank cases between March 2020 and 2021.<h4>Methods</h4>COVID-19 cases were defined using health record linkage. Each case was propensity score-matched to two uninfected controls on age, sex, deprivation, body mass index, ethnicity, diabetes, prevalent ischaemic heart disease (IHD), smoking, hypertension and high cholesterol. We included the following incident outcomes: myocardial infarction, stroke, heart failure, atrial fibrillation, venous thromboembolism (VTE), pericarditis, all-cause death, cardiovascular death, IHD death. Cox proportional hazards regression was used to estimate associations of COVID-19 with each outcome over an average of 141 days (range 32-395) of prospective follow-up.<h4>Results</h4>Non-hospitalised cases (n=14 304) had increased risk of incident VTE (HR 2.74 (95% CI 1.38 to 5.45), p=0.004) and death (HR 10.23 (95% CI 7.63 to 13.70), p<0.0001). Individuals with primary COVID-19 hospitalisation (n=2701) had increased risk of all outcomes considered. The largest effect sizes were with VTE (HR 27.6 (95% CI 14.5 to 52.3); p<0.0001), heart failure (HR 21.6 (95% CI 10.9 to 42.9); p<0.0001) and stroke (HR 17.5 (95% CI 5.26 to 57.9); p<0.0001). Those hospitalised with COVID-19 as a secondary diagnosis (n=866) had similarly increased cardiovascular risk. The associated risks were greatest in the first 30 days after infection but remained higher than controls even after this period.<h4>Conclusions</h4>Individuals hospitalised with COVID-19 have increased risk of incident cardiovascular events across a range of disease and mortality outcomes. The risk of most events is highest in the early postinfection period. Individuals not requiring hospitalisation have increased risk of VTE, but not of other cardiovascular-specific outcomes.",,pdf:https://heart.bmj.com/content/heartjnl/109/2/119.full.pdf; doi:https://doi.org/10.1136/heartjnl-2022-321492; html:https://europepmc.org/articles/PMC9811071; pdf:https://europepmc.org/articles/PMC9811071?pdf=render
 33052324,https://doi.org/10.1016/j.eclinm.2020.100574,A case-control and cohort study to determine the relationship between ethnic background and severe COVID-19.,"Zakeri R, Bendayan R, Ashworth M, Bean DM, Dodhia H, Durbaba S, O'Gallagher K, Palmer C, Curcin V, Aitken E, Bernal W, Barker RD, Norton S, Gulliford M, Teo JTH, Galloway J, Dobson RJB, Shah AM.",,EClinicalMedicine,2020,2020-10-09,Y,Case-control study; Ethnicity; Deprivation; Comorbidities; Covid-19,,,"<h4>Background</h4>People of minority ethnic backgrounds may be disproportionately affected by severe COVID-19. Whether this relates to increased infection risk, more severe disease progression, or worse in-hospital survival is unknown. The contribution of comorbidities or socioeconomic deprivation to ethnic patterning of outcomes is also unclear.<h4>Methods</h4>We conducted a case-control and a cohort study in an inner city primary and secondary care setting to examine whether ethnic background affects the risk of hospital admission with severe COVID-19 and/or in-hospital mortality. Inner city adult residents admitted to hospital with confirmed COVID-19 (<i>n</i> = 872 cases) were compared with 3,488 matched controls randomly sampled from a primary healthcare database comprising 344,083 people residing in the same region. For the cohort study, we studied 1827 adults consecutively admitted with COVID-19. The primary exposure variable was self-defined ethnicity. Analyses were adjusted for socio-demographic and clinical variables.<h4>Findings</h4>The 872 cases comprised 48.1% Black, 33.7% White, 12.6% Mixed/Other and 5.6% Asian patients. In conditional logistic regression analyses, Black and Mixed/Other ethnicity were associated with higher admission risk than white (OR 3.12 [95% CI 2.63-3.71] and 2.97 [2.30-3.85] respectively). Adjustment for comorbidities and deprivation modestly attenuated the association (OR 2.24 [1.83-2.74] for Black, 2.70 [2.03-3.59] for Mixed/Other). Asian ethnicity was not associated with higher admission risk (adjusted OR 1.01 [0.70-1.46]). In the cohort study of 1827 patients, 455 (28.9%) died over a median (IQR) of 8 (4-16) days. Age and male sex, but not Black (adjusted HR 1.06 [0.82-1.37]) or Mixed/Other ethnicity (adjusted HR 0.72 [0.47-1.10]), were associated with in-hospital mortality. Asian ethnicity was associated with higher in-hospital mortality but with a large confidence interval (adjusted HR 1.71 [1.15-2.56]).<h4>Interpretation</h4>Black and Mixed ethnicity are independently associated with greater admission risk with COVID-19 and may be risk factors for development of severe disease, but do not affect in-hospital mortality risk. Comorbidities and socioeconomic factors only partly account for this and additional ethnicity-related factors may play a large role. The impact of COVID-19 may be different in Asians.<h4>Funding</h4>British Heart Foundation; the National Institute for Health Research; Health Data Research UK.",,pdf:http://www.thelancet.com/article/S2589537020303187/pdf; doi:https://doi.org/10.1016/j.eclinm.2020.100574; html:https://europepmc.org/articles/PMC7545271; pdf:https://europepmc.org/articles/PMC7545271?pdf=render
-33478953,https://doi.org/10.1136/annrheumdis-2020-219517,Use of non-steroidal anti-inflammatory drugs and risk of death from COVID-19: an OpenSAFELY cohort analysis based on two cohorts.,"Wong AY, MacKenna B, Morton CE, Schultze A, Walker AJ, Bhaskaran K, Brown JP, Rentsch CT, Williamson E, Drysdale H, Croker R, Bacon S, Hulme W, Bates C, Curtis HJ, Mehrkar A, Evans D, Inglesby P, Cockburn J, McDonald HI, Tomlinson L, Mathur R, Wing K, Forbes H, Eggo RM, Parry J, Hester F, Harper S, Evans SJ, Smeeth L, Douglas IJ, Goldacre B, OpenSAFELY Collaborative.",,Annals of the rheumatic diseases,2021,2021-01-21,Y,Arthritis; Rheumatoid; Osteoarthritis; epidemiology; Covid-19,,,"<h4>Objectives</h4>To assess the association between routinely prescribed non-steroidal anti-inflammatory drugs (NSAIDs) and deaths from COVID-19 using OpenSAFELY, a secure analytical platform.<h4>Methods</h4>We conducted two cohort studies from 1 March to 14 June 2020. Working on behalf of National Health Service England, we used routine clinical data in England linked to death data. In study 1, we identified people with an NSAID prescription in the last 3 years from the general population. In study 2, we identified people with rheumatoid arthritis/osteoarthritis. We defined exposure as current NSAID prescription within the 4 months before 1 March 2020. We used Cox regression to estimate HRs for COVID-19 related death in people currently prescribed NSAIDs, compared with those not currently prescribed NSAIDs, accounting for age, sex, comorbidities, other medications and geographical region.<h4>Results</h4>In study 1, we included 536 423 current NSAID users and 1 927 284 non-users in the general population. We observed no evidence of difference in risk of COVID-19 related death associated with current use (HR 0.96, 95% CI 0.80 to 1.14) in the multivariable-adjusted model. In study 2, we included 1 708 781 people with rheumatoid arthritis/osteoarthritis, of whom 175 495 (10%) were current NSAID users. In the multivariable-adjusted model, we observed a lower risk of COVID-19 related death (HR 0.78, 95% CI 0.64 to 0.94) associated with current use of NSAID versus non-use.<h4>Conclusions</h4>We found no evidence of a harmful effect of routinely prescribed NSAIDs on COVID-19 related deaths. Risks of COVID-19 do not need to influence decisions about the routine therapeutic use of NSAIDs.",,pdf:https://ard.bmj.com/content/annrheumdis/80/7/943.full.pdf; doi:https://doi.org/10.1136/annrheumdis-2020-219517; html:https://europepmc.org/articles/PMC7823433; pdf:https://europepmc.org/articles/PMC7823433?pdf=render
 37006328,https://doi.org/10.1093/braincomms/fcad065,"Infections among individuals with multiple sclerosis, Alzheimer's disease and Parkinson's disease.","Hu Y, Hu K, Song H, Pawitan Y, Piehl F, Fang F.",,Brain communications,2023,2023-03-16,Y,Multiple sclerosis; Alzheimer’s disease; Infections; Parkinson’s Disease,,,"A link between neurodegenerative diseases and infections has been previously reported. However, it is not clear to what extent such link is caused by confounding factors or to what extent it is intimately connected with the underlying conditions. Further, studies on the impact of infections on mortality risk following neurodegenerative diseases are rare. We analysed two data sets with different characteristics: (i) a community-based cohort from the UK Biobank with 2023 patients with multiple sclerosis, 2200 patients with Alzheimer's disease, 3050 patients with Parkinson's disease diagnosed before 1 March 2020 and 5 controls per case who were randomly selected and individually matched to the case; (ii) a Swedish Twin Registry cohort with 230 patients with multiple sclerosis, 885 patients with Alzheimer's disease and 626 patients with Parkinson's disease diagnosed before 31 December 2016 and their disease-free co-twins. The relative risk of infections after a diagnosis of neurodegenerative disease was estimated using stratified Cox models, with adjustment for differences in baseline characteristics. Causal mediation analyses of survival outcomes based on Cox models were performed to assess the impact of infections on mortality. Compared with matched controls or unaffected co-twins, we observed an elevated infection risk after diagnosis of neurodegenerative diseases, with a fully adjusted hazard ratio (95% confidence interval) of 2.45 (2.24-2.69) for multiple sclerosis, 5.06 (4.58-5.59) for Alzheimer's disease and 3.72 (3.44-4.01) for Parkinson's disease in the UK Biobank cohort, and 1.78 (1.21-2.62) for multiple sclerosis, 1.50 (1.19-1.88) for Alzheimer's disease and 2.30 (1.79-2.95) for Parkinson's disease in the twin cohort. Similar risk increases were observed when we analysed infections during the 5 years before diagnosis of the respective disease. Occurrence of infections after diagnosis had, however, relatively little impact on mortality, as mediation of infections on mortality (95% confidence interval) was estimated as 31.89% (26.83-37.11%) for multiple sclerosis, 13.38% (11.49-15.29%) for Alzheimer's disease and 18.85% (16.95-20.97%) for Parkinson's disease in the UK Biobank cohort, whereas it was 6.56% (-3.59 to 16.88%) for multiple sclerosis, -2.21% (-0.21 to 4.65%) for Parkinson's disease and -3.89% (-7.27 to -0.51%) for Alzheimer's disease in the twin cohort. Individuals with studied neurodegenerative diseases display an increased risk of infections independently of genetic and familial environment factors. A similar magnitude of risk increase is present prior to confirmed diagnosis, which may indicate a modulating effect of the studied neurological conditions on immune defences.",,pdf:https://academic.oup.com/braincomms/advance-article-pdf/doi/10.1093/braincomms/fcad065/49588224/fcad065.pdf; doi:https://doi.org/10.1093/braincomms/fcad065; html:https://europepmc.org/articles/PMC10053639; pdf:https://europepmc.org/articles/PMC10053639?pdf=render
+33478953,https://doi.org/10.1136/annrheumdis-2020-219517,Use of non-steroidal anti-inflammatory drugs and risk of death from COVID-19: an OpenSAFELY cohort analysis based on two cohorts.,"Wong AY, MacKenna B, Morton CE, Schultze A, Walker AJ, Bhaskaran K, Brown JP, Rentsch CT, Williamson E, Drysdale H, Croker R, Bacon S, Hulme W, Bates C, Curtis HJ, Mehrkar A, Evans D, Inglesby P, Cockburn J, McDonald HI, Tomlinson L, Mathur R, Wing K, Forbes H, Eggo RM, Parry J, Hester F, Harper S, Evans SJ, Smeeth L, Douglas IJ, Goldacre B, OpenSAFELY Collaborative.",,Annals of the rheumatic diseases,2021,2021-01-21,Y,Arthritis; Rheumatoid; Osteoarthritis; epidemiology; Covid-19,,,"<h4>Objectives</h4>To assess the association between routinely prescribed non-steroidal anti-inflammatory drugs (NSAIDs) and deaths from COVID-19 using OpenSAFELY, a secure analytical platform.<h4>Methods</h4>We conducted two cohort studies from 1 March to 14 June 2020. Working on behalf of National Health Service England, we used routine clinical data in England linked to death data. In study 1, we identified people with an NSAID prescription in the last 3 years from the general population. In study 2, we identified people with rheumatoid arthritis/osteoarthritis. We defined exposure as current NSAID prescription within the 4 months before 1 March 2020. We used Cox regression to estimate HRs for COVID-19 related death in people currently prescribed NSAIDs, compared with those not currently prescribed NSAIDs, accounting for age, sex, comorbidities, other medications and geographical region.<h4>Results</h4>In study 1, we included 536 423 current NSAID users and 1 927 284 non-users in the general population. We observed no evidence of difference in risk of COVID-19 related death associated with current use (HR 0.96, 95% CI 0.80 to 1.14) in the multivariable-adjusted model. In study 2, we included 1 708 781 people with rheumatoid arthritis/osteoarthritis, of whom 175 495 (10%) were current NSAID users. In the multivariable-adjusted model, we observed a lower risk of COVID-19 related death (HR 0.78, 95% CI 0.64 to 0.94) associated with current use of NSAID versus non-use.<h4>Conclusions</h4>We found no evidence of a harmful effect of routinely prescribed NSAIDs on COVID-19 related deaths. Risks of COVID-19 do not need to influence decisions about the routine therapeutic use of NSAIDs.",,pdf:https://ard.bmj.com/content/annrheumdis/80/7/943.full.pdf; doi:https://doi.org/10.1136/annrheumdis-2020-219517; html:https://europepmc.org/articles/PMC7823433; pdf:https://europepmc.org/articles/PMC7823433?pdf=render
 36949447,https://doi.org/10.1186/s12889-023-15345-z,Inequalities in colorectal cancer screening uptake in Wales: an examination of the impact of the temporary suspension of the screening programme during the COVID-19 pandemic.,"Bright D, Hillier S, Song J, Huws DW, Greene G, Hodgson K, Akbari A, Griffiths R, Davies AR, Gjini A.",,BMC public health,2023,2023-03-22,Y,Colorectal Cancer; Inequalities; Bowel; Ethnicity; Cancer Screening; Covid-19,,,"<h4>Background</h4>Response to the early stages of the COVID-19 pandemic resulted in the temporary disruption of cancer screening in the UK, and strong public messaging to stay safe and to protect NHS capacity. Following reintroduction in services, we explored the impact on inequalities in uptake of the Bowel Screening Wales (BSW) programme to identify groups who may benefit from tailored interventions.<h4>Methods</h4>Records within the BSW were linked to electronic health records (EHR) and administrative data within the Secured Anonymised Information Linkage (SAIL) Databank. Ethnic group was obtained from a linked data method available within SAIL. We examined uptake for the first 3 months of invitations (August to October) following the reintroduction of BSW programme in 2020, compared to the same period in the preceding 3 years. Uptake was measured across a 6 month follow-up period. Logistic models were conducted to analyse variations in uptake by sex, age group, income deprivation quintile, urban/rural location, ethnic group, and clinically extremely vulnerable (CEV) status in each period; and to compare uptake within sociodemographic groups between different periods.<h4>Results</h4>Uptake during August to October 2020 (period 2020/21; 60.4%) declined compared to the same period in 2019/20 (62.7%) but remained above the 60% Welsh standard. Variation by sex, age, income deprivation, and ethnic groups was observed in all periods studied. Compared to the pre-pandemic period in 2019/20, uptake declined for most demographic groups, except for older individuals (70-74 years) and those in the most income deprived group. Uptake continues to be lower in males, younger individuals, people living in the most income deprived areas and those of Asian and unknown ethnic backgrounds.<h4>Conclusion</h4>Our findings are encouraging with overall uptake achieving the 60% Welsh standard during the first three months after the programme restarted in 2020 despite the disruption. Inequalities did not worsen after the programme resumed activities but variations in CRC screening in Wales associated with sex, age, deprivation and ethnic group remain. This needs to be considered in targeting strategies to improve uptake and informed choice in CRC screening to avoid exacerbating disparities in CRC outcomes as screening services recover from the pandemic.",,pdf:https://bmcpublichealth.biomedcentral.com/counter/pdf/10.1186/s12889-023-15345-z; doi:https://doi.org/10.1186/s12889-023-15345-z; html:https://europepmc.org/articles/PMC10031708; pdf:https://europepmc.org/articles/PMC10031708?pdf=render
 33075408,https://doi.org/10.1016/j.jaci.2020.10.007,Factors associated with adverse COVID-19 outcomes in patients with psoriasis-insights from a global registry-based study.,"Mahil SK, Dand N, Mason KJ, Yiu ZZN, Tsakok T, Meynell F, Coker B, McAteer H, Moorhead L, Mackenzie T, Rossi MT, Rivera R, Mahe E, Carugno A, Magnano M, Rech G, Balogh EA, Feldman SR, De La Cruz C, Choon SE, Naldi L, Lambert J, Spuls P, Jullien D, Bachelez H, McMahon DE, Freeman EE, Gisondi P, Puig L, Warren RB, Di Meglio P, Langan SM, Capon F, Griffiths CEM, Barker JN, Smith CH, PsoProtect study group.",,The Journal of allergy and clinical immunology,2021,2020-10-16,Y,Psoriasis; Immunosuppressants; risk factors; Hospitalization; Biologics; Covid-19,,,"<h4>Background</h4>The multimorbid burden and use of systemic immunosuppressants in people with psoriasis may confer greater risk of adverse outcomes of coronavirus disease 2019 (COVID-19), but the data are limited.<h4>Objective</h4>Our aim was to characterize the course of COVID-19 in patients with psoriasis and identify factors associated with hospitalization.<h4>Methods</h4>Clinicians reported patients with psoriasis with confirmed/suspected COVID-19 via an international registry, Psoriasis Patient Registry for Outcomes, Therapy and Epidemiology of COVID-19 Infection. Multiple logistic regression was used to assess the association between clinical and/or demographic characteristics and hospitalization. A separate patient-facing registry characterized risk-mitigating behaviors.<h4>Results</h4>Of 374 clinician-reported patients from 25 countries, 71% were receiving a biologic, 18% were receiving a nonbiologic, and 10% were not receiving any systemic treatment for psoriasis. In all, 348 patients (93%) were fully recovered from COVID-19, 77 (21%) were hospitalized, and 9 (2%) died. Increased hospitalization risk was associated with older age (multivariable-adjusted odds ratio [OR] = 1.59 per 10 years; 95% CI = 1.19-2.13), male sex (OR = 2.51; 95% CI = 1.23-5.12), nonwhite ethnicity (OR = 3.15; 95% CI = 1.24-8.03), and comorbid chronic lung disease (OR = 3.87; 95% CI = 1.52-9.83). Hospitalization was more frequent in patients using nonbiologic systemic therapy than in those using biologics (OR = 2.84; 95% CI = 1.31-6.18). No significant differences were found between classes of biologics. Independent patient-reported data (n = 1626 across 48 countries) suggested lower levels of social isolation in individuals receiving nonbiologic systemic therapy than in those receiving biologics (OR = 0.68; 95% CI = 0.50-0.94).<h4>Conclusion</h4>In this international case series of patients with moderate-to-severe psoriasis, biologic use was associated with lower risk of COVID-19-related hospitalization than with use of nonbiologic systemic therapies; however, further investigation is warranted on account of potential selection bias and unmeasured confounding. Established risk factors (being older, being male, being of nonwhite ethnicity, and having comorbidities) were associated with higher hospitalization rates.",,pdf:https://researchonline.lshtm.ac.uk/id/eprint/4659367/1/Factors%20associated%20with%20adverse%20COVID-19%20outcomes%20in%20patients%20with%20psoriasis-insights%20from%20a%20global%20registry-based%20study.pdf; doi:https://doi.org/10.1016/j.jaci.2020.10.007; html:https://europepmc.org/articles/PMC7566694; pdf:https://europepmc.org/articles/PMC7566694?pdf=render
 38296292,https://doi.org/10.1136/bmjopen-2023-078135,"Risk factor associations for severe COVID-19, influenza and pneumonia in people with diabetes to inform future pandemic preparations: UK population-based cohort study.","Hopkins R, Young KG, Thomas NJ, Godwin J, Raja D, Mateen BA, Challen RJ, Vollmer SJ, Shields BM, McGovern AP, Dennis JM.",,BMJ open,2024,2024-01-31,Y,risk factors; Electronic Health Records; Diabetes & Endocrinology; Covid-19,,,"<h4>Objective</h4>This study aimed to compare clinical and sociodemographic risk factors for severe COVID-19, influenza and pneumonia, in people with diabetes.<h4>Design</h4>Population-based cohort study.<h4>Setting</h4>UK primary care records (Clinical Practice Research Datalink) linked to mortality and hospital records.<h4>Participants</h4>Individuals with type 1 and type 2 diabetes (COVID-19 cohort: n=43 033 type 1 diabetes and n=584 854 type 2 diabetes, influenza and pneumonia cohort: n=42 488 type 1 diabetes and n=585 289 type 2 diabetes).<h4>Primary and secondary outcome measures</h4>COVID-19 hospitalisation from 1 February 2020 to 31 October 2020 (pre-COVID-19 vaccination roll-out), and influenza and pneumonia hospitalisation from 1 September 2016 to 31 May 2019 (pre-COVID-19 pandemic). Secondary outcomes were COVID-19 and pneumonia mortality. Associations between clinical and sociodemographic risk factors and each outcome were assessed using multivariable Cox proportional hazards models. In people with type 2 diabetes, we explored modifying effects of glycated haemoglobin (HbA1c) and body mass index (BMI) by age, sex and ethnicity.<h4>Results</h4>In type 2 diabetes, poor glycaemic control and severe obesity were consistently associated with increased risk of hospitalisation for COVID-19, influenza and pneumonia. The highest HbA1c and BMI-associated relative risks were observed in people aged under 70 years. Sociodemographic-associated risk differed markedly by respiratory infection, particularly for ethnicity. Compared with people of white ethnicity, black and south Asian groups had a greater risk of COVID-19 hospitalisation, but a lesser risk of pneumonia hospitalisation. Risk factor associations for type 1 diabetes and for type 2 diabetes mortality were broadly consistent with the primary analysis.<h4>Conclusions</h4>Clinical risk factors of high HbA1c and severe obesity are consistently associated with severe outcomes from COVID-19, influenza and pneumonia, especially in younger people. In contrast, associations with sociodemographic risk factors differed by type of respiratory infection. This emphasises that risk stratification should be specific to individual respiratory infections.",,pdf:https://bmjopen.bmj.com/content/bmjopen/14/1/e078135.full.pdf; doi:https://doi.org/10.1136/bmjopen-2023-078135; html:https://europepmc.org/articles/PMC10831438; pdf:https://europepmc.org/articles/PMC10831438?pdf=render
@@ -682,8 +683,8 @@ PMC9645061,https://doi.org/,Using population-scale medication data to evaluate t
 33310109,https://doi.org/10.1016/j.ijid.2020.12.006,"Response to ""Early hydroxychloroquine but not chloroquine use reduces ICU admission in COVID-19 patients"".","Linschoten M, Nab L, van der Horst ICC, Tieleman R, Asselbergs FW.",,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2021,2020-12-09,Y,,,,,,pdf:http://www.ijidonline.com/article/S1201971220325297/pdf; doi:https://doi.org/10.1016/j.ijid.2020.12.006; html:https://europepmc.org/articles/PMC7725132; pdf:https://europepmc.org/articles/PMC7725132?pdf=render
 32413819,https://doi.org/10.1016/j.dsx.2020.04.050,Vitamin D concentrations and COVID-19 infection in UK Biobank.,"Hastie CE, Mackay DF, Ho F, Celis-Morales CA, Katikireddi SV, Niedzwiedz CL, Jani BD, Welsh P, Mair FS, Gray SR, O'Donnell CA, Gill JM, Sattar N, Pell JP.",,Diabetes & metabolic syndrome,2020,2020-05-07,Y,Vitamin D; Ethnicity; Covid-19,,,"<h4>Background and aims</h4>COVID-19 and low levels of vitamin D appear to disproportionately affect black and minority ethnic individuals. We aimed to establish whether blood 25-hydroxyvitamin D (25(OH)D) concentration was associated with COVID-19 risk, and whether it explained the higher incidence of COVID-19 in black and South Asian people.<h4>Methods</h4>UK Biobank recruited 502,624 participants aged 37-73 years between 2006 and 2010. Baseline exposure data, including 25(OH)D concentration and ethnicity, were linked to COVID-19 test results. Univariable and multivariable logistic regression analyses were performed for the association between 25(OH)D and confirmed COVID-19, and the association between ethnicity and both 25(OH)D and COVID-19.<h4>Results</h4>Complete data were available for 348,598 UK Biobank participants. Of these, 449 had confirmed COVID-19 infection. Vitamin D was associated with COVID-19 infection univariably (OR = 0.99; 95% CI 0.99-0.999; p = 0.013), but not after adjustment for confounders (OR = 1.00; 95% CI = 0.998-1.01; p = 0.208). Ethnicity was associated with COVID-19 infection univariably (blacks versus whites OR = 5.32, 95% CI = 3.68-7.70, p-value<0.001; South Asians versus whites OR = 2.65, 95% CI = 1.65-4.25, p-value<0.001). Adjustment for 25(OH)D concentration made little difference to the magnitude of the association.<h4>Conclusions</h4>Our findings do not support a potential link between vitamin D concentrations and risk of COVID-19 infection, nor that vitamin D concentration may explain ethnic differences in COVID-19 infection.","This study aimed to investigate if low levels of vitamin D were associated with a higher likelihood of having COVID-19, which could be a cause of higher rates of COVID infection amoung black and South Asian people.",doi:https://doi.org/10.1016/j.dsx.2020.04.050; doi:https://doi.org/10.1016/j.dsx.2020.04.050; html:https://europepmc.org/articles/PMC7204679
 38519155,https://doi.org/10.1016/s2589-7500(24)00025-6,Foresight-a generative pretrained transformer for modelling of patient timelines using electronic health records: a retrospective modelling study.,"Kraljevic Z, Bean D, Shek A, Bendayan R, Hemingway H, Yeung JA, Deng A, Baston A, Ross J, Idowu E, Teo JT, Dobson RJB.",,The Lancet. Digital health,2024,2024-04-01,Y,,,,"<h4>Background</h4>An electronic health record (EHR) holds detailed longitudinal information about a patient's health status and general clinical history, a large portion of which is stored as unstructured, free text. Existing approaches to model a patient's trajectory focus mostly on structured data and a subset of single-domain outcomes. This study aims to evaluate the effectiveness of Foresight, a generative transformer in temporal modelling of patient data, integrating both free text and structured formats, to predict a diverse array of future medical outcomes, such as disorders, substances (eg, to do with medicines, allergies, or poisonings), procedures, and findings (eg, relating to observations, judgements, or assessments).<h4>Methods</h4>Foresight is a novel transformer-based pipeline that uses named entity recognition and linking tools to convert EHR document text into structured, coded concepts, followed by providing probabilistic forecasts for future medical events, such as disorders, substances, procedures, and findings. The Foresight pipeline has four main components: (1) CogStack (data retrieval and preprocessing); (2) the Medical Concept Annotation Toolkit (structuring of the free-text information from EHRs); (3) Foresight Core (deep-learning model for biomedical concept modelling); and (4) the Foresight web application. We processed the entire free-text portion from three different hospital datasets (King's College Hospital [KCH], South London and Maudsley [SLaM], and the US Medical Information Mart for Intensive Care III [MIMIC-III]), resulting in information from 811 336 patients and covering both physical and mental health institutions. We measured the performance of models using custom metrics derived from precision and recall.<h4>Findings</h4>Foresight achieved a precision@10 (ie, of 10 forecasted candidates, at least one is correct) of 0·68 (SD 0·0027) for the KCH dataset, 0·76 (0·0032) for the SLaM dataset, and 0·88 (0·0018) for the MIMIC-III dataset, for forecasting the next new disorder in a patient timeline. Foresight also achieved a precision@10 value of 0·80 (0·0013) for the KCH dataset, 0·81 (0·0026) for the SLaM dataset, and 0·91 (0·0011) for the MIMIC-III dataset, for forecasting the next new biomedical concept. In addition, Foresight was validated on 34 synthetic patient timelines by five clinicians and achieved a relevancy of 33 (97% [95% CI 91-100]) of 34 for the top forecasted candidate disorder. As a generative model, Foresight can forecast follow-on biomedical concepts for as many steps as required.<h4>Interpretation</h4>Foresight is a general-purpose model for biomedical concept modelling that can be used for real-world risk forecasting, virtual trials, and clinical research to study the progression of disorders, to simulate interventions and counterfactuals, and for educational purposes.<h4>Funding</h4>National Health Service Artificial Intelligence Laboratory, National Institute for Health and Care Research Biomedical Research Centre, and Health Data Research UK.",,doi:https://doi.org/10.1016/S2589-7500(24)00025-6; html:https://europepmc.org/articles/PMC11220626
-36802769,https://doi.org/10.1259/bjr.20201465,Applying machine learning classifiers to automate quality assessment of paediatric dynamic susceptibility contrast (DSC-) MRI data.,"Powell SJ, Withey SB, Sun Y, Grist JT, Novak J, MacPherson L, Abernethy L, Pizer B, Grundy R, Morgan PS, Jaspan T, Bailey S, Mitra D, Auer DP, Avula S, Arvanitis TN, Peet A.",,The British journal of radiology,2023,2023-02-20,Y,,,,"<h4>Objective</h4>Investigate the performance of qualitative review (QR) for assessing dynamic susceptibility contrast (DSC-) MRI data quality in paediatric normal brain and develop an automated alternative to QR.<h4>Methods</h4>1027 signal-time courses were assessed by Reviewer 1 using QR. 243 were additionally assessed by Reviewer 2 and % disagreements and Cohen's κ (κ) were calculated. The signal drop-to-noise ratio (SDNR), root mean square error (RMSE), full width half maximum (FWHM) and percentage signal recovery (PSR) were calculated for the 1027 signal-time courses. Data quality thresholds for each measure were determined using QR results. The measures and QR results trained machine learning classifiers. Sensitivity, specificity, precision, classification error and area under the curve from a receiver operating characteristic curve were calculated for each threshold and classifier.<h4>Results</h4>Comparing reviewers gave 7% disagreements and κ = 0.83. Data quality thresholds of: 7.6 for SDNR; 0.019 for RMSE; 3 s and 19 s for FWHM; and 42.9 and 130.4% for PSR were produced. SDNR gave the best sensitivity, specificity, precision, classification error and area under the curve values of 0.86, 0.86, 0.93, 14.2% and 0.83. Random forest was the best machine learning classifier, giving sensitivity, specificity, precision, classification error and area under the curve of 0.94, 0.83, 0.93, 9.3% and 0.89.<h4>Conclusion</h4>The reviewers showed good agreement. Machine learning classifiers trained on signal-time course measures and QR can assess quality. Combining multiple measures reduces misclassification.<h4>Advances in knowledge</h4>A new automated quality control method was developed, which trained machine learning classifiers using QR results.",,doi:https://doi.org/10.1259/bjr.20201465; doi:https://doi.org/10.1259/bjr.20201465; html:https://europepmc.org/articles/PMC10161906; pdf:https://europepmc.org/articles/PMC10161906?pdf=render
 33531015,https://doi.org/10.1186/s12916-021-01906-9,The importance of supplementary immunisation activities to prevent measles outbreaks during the COVID-19 pandemic in Kenya.,"Mburu CN, Ojal J, Chebet R, Akech D, Karia B, Tuju J, Sigilai A, Abbas K, Jit M, Funk S, Smits G, van Gageldonk PGM, van der Klis FRM, Tabu C, Nokes DJ, LSHTM CMMID COVID-19 Working Group, Scott J, Flasche S, Adetifa I.",,BMC medicine,2021,2021-02-03,Y,outbreak; Measles; Vaccination Coverage; Supplementary Immunisation Activities; Covid-19,,,"<h4>Background</h4>The COVID-19 pandemic has disrupted routine measles immunisation and supplementary immunisation activities (SIAs) in most countries including Kenya. We assessed the risk of measles outbreaks during the pandemic in Kenya as a case study for the African Region.<h4>Methods</h4>Combining measles serological data, local contact patterns, and vaccination coverage into a cohort model, we predicted the age-adjusted population immunity in Kenya and estimated the probability of outbreaks when contact-reducing COVID-19 interventions are lifted. We considered various scenarios for reduced measles vaccination coverage from April 2020.<h4>Results</h4>In February 2020, when a scheduled SIA was postponed, population immunity was close to the herd immunity threshold and the probability of a large outbreak was 34% (8-54). As the COVID-19 contact restrictions are nearly fully eased, from December 2020, the probability of a large measles outbreak will increase to 38% (19-54), 46% (30-59), and 54% (43-64) assuming a 15%, 50%, and 100% reduction in measles vaccination coverage. By December 2021, this risk increases further to 43% (25-56), 54% (43-63), and 67% (59-72) for the same coverage scenarios respectively. However, the increased risk of a measles outbreak following the lifting of all restrictions can be overcome by conducting a SIA with ≥ 95% coverage in under-fives.<h4>Conclusion</h4>While contact restrictions sufficient for SAR-CoV-2 control temporarily reduce measles transmissibility and the risk of an outbreak from a measles immunity gap, this risk rises rapidly once these restrictions are lifted. Implementing delayed SIAs will be critical for prevention of measles outbreaks given the roll-back of contact restrictions in Kenya.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-021-01906-9; doi:https://doi.org/10.1186/s12916-021-01906-9; html:https://europepmc.org/articles/PMC7854026; pdf:https://europepmc.org/articles/PMC7854026?pdf=render
+36802769,https://doi.org/10.1259/bjr.20201465,Applying machine learning classifiers to automate quality assessment of paediatric dynamic susceptibility contrast (DSC-) MRI data.,"Powell SJ, Withey SB, Sun Y, Grist JT, Novak J, MacPherson L, Abernethy L, Pizer B, Grundy R, Morgan PS, Jaspan T, Bailey S, Mitra D, Auer DP, Avula S, Arvanitis TN, Peet A.",,The British journal of radiology,2023,2023-02-20,Y,,,,"<h4>Objective</h4>Investigate the performance of qualitative review (QR) for assessing dynamic susceptibility contrast (DSC-) MRI data quality in paediatric normal brain and develop an automated alternative to QR.<h4>Methods</h4>1027 signal-time courses were assessed by Reviewer 1 using QR. 243 were additionally assessed by Reviewer 2 and % disagreements and Cohen's κ (κ) were calculated. The signal drop-to-noise ratio (SDNR), root mean square error (RMSE), full width half maximum (FWHM) and percentage signal recovery (PSR) were calculated for the 1027 signal-time courses. Data quality thresholds for each measure were determined using QR results. The measures and QR results trained machine learning classifiers. Sensitivity, specificity, precision, classification error and area under the curve from a receiver operating characteristic curve were calculated for each threshold and classifier.<h4>Results</h4>Comparing reviewers gave 7% disagreements and κ = 0.83. Data quality thresholds of: 7.6 for SDNR; 0.019 for RMSE; 3 s and 19 s for FWHM; and 42.9 and 130.4% for PSR were produced. SDNR gave the best sensitivity, specificity, precision, classification error and area under the curve values of 0.86, 0.86, 0.93, 14.2% and 0.83. Random forest was the best machine learning classifier, giving sensitivity, specificity, precision, classification error and area under the curve of 0.94, 0.83, 0.93, 9.3% and 0.89.<h4>Conclusion</h4>The reviewers showed good agreement. Machine learning classifiers trained on signal-time course measures and QR can assess quality. Combining multiple measures reduces misclassification.<h4>Advances in knowledge</h4>A new automated quality control method was developed, which trained machine learning classifiers using QR results.",,doi:https://doi.org/10.1259/bjr.20201465; doi:https://doi.org/10.1259/bjr.20201465; html:https://europepmc.org/articles/PMC10161906; pdf:https://europepmc.org/articles/PMC10161906?pdf=render
 36065116,https://doi.org/10.1093/brain/awac321,Brain injury in COVID-19 is associated with dysregulated innate and adaptive immune responses.,"Needham EJ, Ren AL, Digby RJ, Norton EJ, Ebrahimi S, Outtrim JG, Chatfield DA, Manktelow AE, Leibowitz MM, Newcombe VFJ, Doffinger R, Barcenas-Morales G, Fonseca C, Taussig MJ, Burnstein RM, Samanta RJ, Dunai C, Sithole N, Ashton NJ, Zetterberg H, Gisslén M, Edén A, Marklund E, Openshaw PJM, Dunning J, Griffiths MJ, Cavanagh J, Breen G, Irani SR, Elmer A, Kingston N, Summers C, Bradley JR, Taams LS, Michael BD, Bullmore ET, Smith KGC, Lyons PA, Coles AJ, Menon DK, Cambridge NeuroCOVID Group, CITIID-NIHR COVID-19 BioResource Collaboration, Cambridge NIHR Clinical Research Facility.",,Brain : a journal of neurology,2022,2022-11-01,Y,Autoantibodies; Brain injury; neuroinflammation; Covid-19,,,"COVID-19 is associated with neurological complications including stroke, delirium and encephalitis. Furthermore, a post-viral syndrome dominated by neuropsychiatric symptoms is common, and is seemingly unrelated to COVID-19 severity. The true frequency and underlying mechanisms of neurological injury are unknown, but exaggerated host inflammatory responses appear to be a key driver of COVID-19 severity. We investigated the dynamics of, and relationship between, serum markers of brain injury [neurofilament light (NfL), glial fibrillary acidic protein (GFAP) and total tau] and markers of dysregulated host response (autoantibody production and cytokine profiles) in 175 patients admitted with COVID-19 and 45 patients with influenza. During hospitalization, sera from patients with COVID-19 demonstrated elevations of NfL and GFAP in a severity-dependent manner, with evidence of ongoing active brain injury at follow-up 4 months later. These biomarkers were associated with elevations of pro-inflammatory cytokines and the presence of autoantibodies to a large number of different antigens. Autoantibodies were commonly seen against lung surfactant proteins but also brain proteins such as myelin associated glycoprotein. Commensurate findings were seen in the influenza cohort. A distinct process characterized by elevation of serum total tau was seen in patients at follow-up, which appeared to be independent of initial disease severity and was not associated with dysregulated immune responses unlike NfL and GFAP. These results demonstrate that brain injury is a common consequence of both COVID-19 and influenza, and is therefore likely to be a feature of severe viral infection more broadly. The brain injury occurs in the context of dysregulation of both innate and adaptive immune responses, with no single pathogenic mechanism clearly responsible.",,pdf:https://academic.oup.com/brain/article-pdf/145/11/4097/47170622/awac321.pdf; doi:https://doi.org/10.1093/brain/awac321; html:https://europepmc.org/articles/PMC9494359; pdf:https://europepmc.org/articles/PMC9494359?pdf=render
 37269003,https://doi.org/10.1186/s13643-023-02261-x,Non-adherence and non-persistence to intravitreal anti-vascular endothelial growth factor (anti-VEGF) therapy: a systematic review and meta-analysis.,"Shahzad H, Mahmood S, McGee S, Hubbard J, Haque S, Paudyal V, Denniston AK, Hill LJ, Jalal Z.",,Systematic reviews,2023,2023-06-02,Y,Meta-analysis; Intravitreal; Anti-vegf; Non-adherence; Macular; Non-persistence; Covid-19,,,"<h4>Background</h4>Intravitreal anti-vascular endothelial growth factor (anti-VEGF) injections play a key role in treating a range of macular diseases. The effectiveness of these therapies is dependent on patients' adherence (the extent to which a patient takes their medicines as per agreed recommendations from the healthcare provider) and persistence (continuation of the treatment for the prescribed duration) to their prescribed treatment regimens. The aim of this systematic review was to demonstrate the need for further investigation into the prevalence of, and factors contributing to, patient-led non-adherence and non-persistence, thus facilitating improved clinical outcomes.<h4>Methods</h4>Systematic searches were conducted in Google Scholar, Web of Science, PubMed, MEDLINE, and the Cochrane Library. Studies in English conducted before February 2023 that reported the level of, and/or barriers to, non-adherence or non-persistence to intravitreal anti-VEGF ocular disease therapy were included. Duplicate papers, literature reviews, expert opinion articles, case studies, and case series were excluded following screening by two independent authors.<h4>Results</h4>Data from a total of 409,215 patients across 52 studies were analysed. Treatment regimens included pro re nata, monthly and treat-and-extend protocols; study durations ranged from 4 months to 8 years. Of the 52 studies, 22 included a breakdown of reasons for patient non-adherence/non-persistence. Patient-led non-adherence varied between 17.5 and 35.0% depending on the definition used. Overall pooled prevalence of patient-led treatment non-persistence was 30.0% (P = 0.000). Reasons for non-adherence/non-persistence included dissatisfaction with treatment results (29.9%), financial burden (19%), older age/comorbidities (15.5%), difficulty booking appointments (8.5%), travel distance/social isolation (7.9%), lack of time (5.8%), satisfaction with the perceived improvement in their condition (4.4%), fear of injection (4.0%), loss of motivation (4.0%), apathy towards eyesight (2.5%), dissatisfaction with facilities 2.3%, and discomfort/pain (0.3%). Three studies found non-adherence rates between 51.6 and 68.8% during the COVID-19 pandemic, in part due to fear of exposure to COVID-19 and difficulties travelling during lockdown.<h4>Discussion</h4>Results suggest high levels of patient-led non-adherence/non-persistence to anti-VEGF therapy, mostly due to dissatisfaction with treatment results, a combination of comorbidities, loss of motivation and the burden of travel. This study provides key information on prevalence and factors contributing to non-adherence/non-persistence in anti-VEGF treatment for macular diseases, aiding identification of at-risk individuals to improve real-world visual outcomes. Improvements in the literature can be achieved by establishing uniform definitions and standard timescales for what constitutes non-adherence/non-persistence.<h4>Systematic review registration</h4>PROSPERO CRD42020216205.",,doi:https://doi.org/10.1186/s13643-023-02261-x; doi:https://doi.org/10.1186/s13643-023-02261-x; html:https://europepmc.org/articles/PMC10237080; pdf:https://europepmc.org/articles/PMC10237080?pdf=render
 33780469,https://doi.org/10.1371/journal.pone.0248195,Deriving household composition using population-scale electronic health record data-A reproducible methodology.,"Johnson RD, Griffiths LJ, Hollinghurst JP, Akbari A, Lee A, Thompson DA, Lyons RA, Fry R.",,PloS one,2021,2021-03-29,Y,,,,"<h4>Background</h4>Physical housing and household composition have an important role in the lives of individuals and drive health and social outcomes, and inequalities. Most methods to understand housing composition are based on survey or census data, and there is currently no reproducible methodology for creating population-level household composition measures using linked administrative data.<h4>Methods</h4>Using existing, and more recent enhancements to the address-data linkage methods in the SAIL Databank using Residential Anonymised Linking Fields we linked individuals to properties using the anonymised Welsh Demographic Service data in the SAIL Databank. We defined households, household size, and household composition measures based on adult to child relationships, and age differences between residents to create relative age measures.<h4>Results</h4>Two relative age-based algorithms were developed and returned similar results when applied to population and household-level data, describing household composition for 3.1 million individuals within 1.2 million households in Wales. Developed methods describe binary, and count level generational household composition measures.<h4>Conclusions</h4>Improved residential anonymised linkage field methods in SAIL have led to improved property-level data linkage, allowing the design and application of household composition measures that assign individuals to shared residences and allow the description of household composition across Wales. The reproducible methods create longitudinal, household-level composition measures at a population-level using linked administrative data. Such measures are important to help understand more detail about an individual's home and area environment and how that may affect the health and wellbeing of the individual, other residents, and potentially into the wider community.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0248195&type=printable; doi:https://doi.org/10.1371/journal.pone.0248195; html:https://europepmc.org/articles/PMC8007012; pdf:https://europepmc.org/articles/PMC8007012?pdf=render
@@ -694,8 +695,8 @@ PMC9645061,https://doi.org/,Using population-scale medication data to evaluate t
 38627354,https://doi.org/10.1007/s15010-024-02235-8,"Sepsis and case fatality rates and associations with deprivation, ethnicity, and clinical characteristics: population-based case-control study with linked primary care and hospital data in England.","van Staa TP, Pate A, Martin GP, Sharma A, Dark P, Felton T, Zhong X, Bladon S, Cunningham N, Gilham EL, Brown CS, Mirfenderesky M, Palin V, Ashiru-Oredope D.",,Infection,2024,2024-04-16,Y,Sepsis; RACE; Frailty; Primary Care; Deprivation,,,"<h4>Purpose</h4>Sepsis is a life-threatening organ dysfunction caused by dysregulated host response to infection. The purpose of the study was to measure the associations of specific exposures (deprivation, ethnicity, and clinical characteristics) with incident sepsis and case fatality.<h4>Methods</h4>Two research databases in England were used including anonymized patient-level records from primary care linked to hospital admission, death certificate, and small-area deprivation. Sepsis cases aged 65-100 years were matched to up to six controls. Predictors for sepsis (including 60 clinical conditions) were evaluated using logistic and random forest models; case fatality rates were analyzed using logistic models.<h4>Results</h4>108,317 community-acquired sepsis cases were analyzed. Severe frailty was strongly associated with the risk of developing sepsis (crude odds ratio [OR] 14.93; 95% confidence interval [CI] 14.37-15.52). The quintile with most deprived patients showed an increased sepsis risk (crude OR 1.48; 95% CI 1.45-1.51) compared to least deprived quintile. Strong predictors for sepsis included antibiotic exposure in prior 2 months, being house bound, having cancer, learning disability, and diabetes mellitus. Severely frail patients had a case fatality rate of 42.0% compared to 24.0% in non-frail patients (adjusted OR 1.53; 95% CI 1.41-1.65). Sepsis cases with recent prior antibiotic exposure died less frequently compared to non-users (adjusted OR 0.7; 95% CI 0.72-0.76). Case fatality strongly decreased over calendar time.<h4>Conclusion</h4>Given the variety of predictors and their level of associations for developing sepsis, there is a need for prediction models for risk of developing sepsis that can help to target preventative antibiotic therapy.",,pdf:https://link.springer.com/content/pdf/10.1007/s15010-024-02235-8.pdf; doi:https://doi.org/10.1007/s15010-024-02235-8; html:https://europepmc.org/articles/PMC11288984; pdf:https://europepmc.org/articles/PMC11288984?pdf=render
 36446449,https://doi.org/10.1136/bmjopen-2022-061849,Effect of lifting COVID-19 restrictions on utilisation of primary care services in Nepal: a difference-in-differences analysis.,"Kapoor NR, Aryal A, Mehata S, Dulal M, Kruk ME, Bauhoff S, Arsenault C.",,BMJ open,2022,2022-11-29,Y,Primary Care; Health Policy; Covid-19,,,"<h4>Introduction</h4>An increasing number of studies have reported disruptions in health service utilisation due to the COVID-19 pandemic and its associated restrictions. However, little is known about the effect of lifting COVID-19 restrictions on health service utilisation. The objective of this study was to estimate the effect of lifting COVID-19 restrictions on primary care service utilisation in Nepal.<h4>Methods</h4>Data on utilisation of 10 primary care services were extracted from the Health Management Information System across all health facilities in Nepal. We used a difference-in-differences design and linear fixed effects regressions to estimate the effect of lifting COVID-19 restrictions. The treatment group included palikas that had lifted restrictions in place from 17 August 2020 to 16 September 2020 (Bhadra 2077) and the control group included palikas that had maintained restrictions during that period. The pre-period included the 4 months of national lockdown from 24 March 2020 to 22 July 2020 (Chaitra 2076 to Ashar 2077). Models included month and palika fixed effects and controlled for COVID-19 incidence.<h4>Results</h4>We found that lifting COVID-19 restrictions was associated with an average increase per palika of 57.5 contraceptive users (95% CI 14.6 to 100.5), 15.6 antenatal care visits (95% CI 5.3 to 25.9) and 1.6 child pneumonia visits (95% CI 0.2 to 2.9). This corresponded to a 9.4% increase in contraceptive users, 34.2% increase in antenatal care visits and 15.6% increase in child pneumonia visits. Utilisation of most other primary care services also increased after lifting restrictions, but coefficients were not statistically significant.<h4>Conclusions</h4>Despite the ongoing pandemic, lifting restrictions can lead to an increase in some primary care services. Our results point to a causal link between restrictions and health service utilisation and call for policy makers in low- and middle-income countries to carefully consider the trade-offs of strict lockdowns during future COVID-19 waves or future pandemics.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/11/e061849.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-061849; html:https://europepmc.org/articles/PMC9709811; pdf:https://europepmc.org/articles/PMC9709811?pdf=render
 35410184,https://doi.org/10.1186/s12889-022-13069-0,The local burden of disease during the first wave of the COVID-19 epidemic in England: estimation using different data sources from changing surveillance practices.,"Nightingale ES, Abbott S, Russell TW, CMMID Covid-19 Working Group, Lowe R, Medley GF, Brady OJ.",,BMC public health,2022,2022-04-11,Y,,,,"<h4>Background</h4>The COVID-19 epidemic has differentially impacted communities across England, with regional variation in rates of confirmed cases, hospitalisations and deaths. Measurement of this burden changed substantially over the first months, as surveillance was expanded to accommodate the escalating epidemic. Laboratory confirmation was initially restricted to clinical need (""pillar 1"") before expanding to community-wide symptomatics (""pillar 2""). This study aimed to ascertain whether inconsistent measurement of case data resulting from varying testing coverage could be reconciled by drawing inference from COVID-19-related deaths.<h4>Methods</h4>We fit a Bayesian spatio-temporal model to weekly COVID-19-related deaths per local authority (LTLA) throughout the first wave (1 January 2020-30 June 2020), adjusting for the local epidemic timing and the age, deprivation and ethnic composition of its population. We combined predictions from this model with case data under community-wide, symptomatic testing and infection prevalence estimates from the ONS infection survey, to infer the likely trajectory of infections implied by the deaths in each LTLA.<h4>Results</h4>A model including temporally- and spatially-correlated random effects was found to best accommodate the observed variation in COVID-19-related deaths, after accounting for local population characteristics. Predicted case counts under community-wide symptomatic testing suggest a total of 275,000-420,000 cases over the first wave - a median of over 100,000 additional to the total confirmed in practice under varying testing coverage. This translates to a peak incidence of around 200,000 total infections per week across England. The extent to which estimated total infections are reflected in confirmed case counts was found to vary substantially across LTLAs, ranging from 7% in Leicester to 96% in Gloucester with a median of 23%.<h4>Conclusions</h4>Limitations in testing capacity biased the observed trajectory of COVID-19 infections throughout the first wave. Basing inference on COVID-19-related mortality and higher-coverage testing later in the time period, we could explore the extent of this bias more explicitly. Evidence points towards substantial under-representation of initial growth and peak magnitude of infections nationally, to which different parts of the country contribute unequally.",,pdf:https://bmcpublichealth.biomedcentral.com/track/pdf/10.1186/s12889-022-13069-0; doi:https://doi.org/10.1186/s12889-022-13069-0; html:https://europepmc.org/articles/PMC8996221; pdf:https://europepmc.org/articles/PMC8996221?pdf=render
-35642867,https://doi.org/10.1111/bjhp.12606,"Perceived threat of COVID-19, attitudes towards vaccination, and vaccine hesitancy: A prospective longitudinal study in the UK.","Phillips R, Gillespie D, Hallingberg B, Evans J, Taiyari K, Torrens-Burton A, Cannings-John R, Williams D, Sheils E, Ashfield-Watt P, Akbari A, Hughes K, Thomas-Jones E, James D, Wood F.",,British journal of health psychology,2022,2022-06-01,Y,Risk Perception; Behaviour Change; Vaccine Hesitancy; Covid-19; Sars Cov2,,,"<h4>Objectives</h4>Using the Health Belief Model as a conceptual framework, we investigated the association between attitudes towards COVID-19, COVID-19 vaccinations, and vaccine hesitancy and change in these variables over a 9-month period in a UK cohort.<h4>Methods</h4>The COPE study cohort (n = 11,113) was recruited via an online survey at enrolment in March/April 2020. The study was advertised via the HealthWise Wales research registry and social media. Follow-up data were available for 6942 people at 3 months (June/July 2020) and 5037 at 12 months (March/April 2021) post-enrolment. Measures included demographics, perceived threat of COVID-19, perceived control, intention to accept or decline a COVID-19 vaccination, and attitudes towards vaccination. Logistic regression models were fitted cross-sectionally at 3 and 12 months to assess the association between motivational factors and vaccine hesitancy. Longitudinal changes in motivational variables for vaccine-hesitant and non-hesitant groups were examined using mixed-effect analysis of variance models.<h4>Results</h4>Fear of COVID-19, perceived susceptibility to COVID-19, and perceived personal control over COVID-19 infection transmission decreased between the 3- and 12-month surveys. Vaccine hesitancy at 12 months was independently associated with low fear of the disease and more negative attitudes towards COVID-19 vaccination. Specific barriers to COVID-19 vaccine uptake included concerns about safety and efficacy in light of its rapid development, mistrust of government and pharmaceutical companies, dislike of coercive policies, and perceived lack of relaxation in COVID-19-related restrictions as the vaccination programme progressed.<h4>Conclusions</h4>Decreasing fear of COVID-19, perceived susceptibility to the disease, and perceptions of personal control over reducing infection-transmission may impact future COVID-19 vaccination uptake.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa60128/Download/60128__24479__4d74009536e649b0b17180e2bfd80435.pdf; doi:https://doi.org/10.1111/bjhp.12606; html:https://europepmc.org/articles/PMC9347957; pdf:https://europepmc.org/articles/PMC9347957?pdf=render
 37315048,https://doi.org/10.1371/journal.pone.0287091,LMIC-PRIEST: Derivation and validation of a clinical severity score for acutely ill adults with suspected COVID-19 in a middle-income setting.,"Marincowitz C, Hodkinson P, McAlpine D, Fuller G, Goodacre S, Bath PA, Bath PA, Sbaffi L, Hasan M, Omer Y, Wallis L.",,PloS one,2023,2023-06-14,Y,,,,"<h4>Background</h4>Uneven vaccination and less resilient health care systems mean hospitals in LMICs are at risk of being overwhelmed during periods of increased COVID-19 infection. Risk-scores proposed for rapid triage of need for admission from the emergency department (ED) have been developed in higher-income settings during initial waves of the pandemic.<h4>Methods</h4>Routinely collected data for public hospitals in the Western Cape, South Africa from the 27th August 2020 to 11th March 2022 were used to derive a cohort of 446,084 ED patients with suspected COVID-19. The primary outcome was death or ICU admission at 30 days. The cohort was divided into derivation and Omicron variant validation sets. We developed the LMIC-PRIEST score based on the coefficients from multivariable analysis in the derivation cohort and existing triage practices. We externally validated accuracy in the Omicron period and a UK cohort.<h4>Results</h4>We analysed 305,564 derivation, 140,520 Omicron and 12,610 UK validation cases. Over 100 events per predictor parameter were modelled. Multivariable analyses identified eight predictor variables retained across models. We used these findings and clinical judgement to develop a score based on South African Triage Early Warning Scores and also included age, sex, oxygen saturation, inspired oxygen, diabetes and heart disease. The LMIC-PRIEST score achieved C-statistics: 0.82 (95% CI: 0.82 to 0.83) development cohort; 0.79 (95% CI: 0.78 to 0.80) Omicron cohort; and 0.79 (95% CI: 0.79 to 0.80) UK cohort. Differences in prevalence of outcomes led to imperfect calibration in external validation. However, use of the score at thresholds of three or less would allow identification of very low-risk patients (NPV ≥0.99) who could be rapidly discharged using information collected at initial assessment.<h4>Conclusion</h4>The LMIC-PRIEST score shows good discrimination and high sensitivity at lower thresholds and can be used to rapidly identify low-risk patients in LMIC ED settings.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0287091&type=printable; doi:https://doi.org/10.1371/journal.pone.0287091; html:https://europepmc.org/articles/PMC10266677; pdf:https://europepmc.org/articles/PMC10266677?pdf=render
+35642867,https://doi.org/10.1111/bjhp.12606,"Perceived threat of COVID-19, attitudes towards vaccination, and vaccine hesitancy: A prospective longitudinal study in the UK.","Phillips R, Gillespie D, Hallingberg B, Evans J, Taiyari K, Torrens-Burton A, Cannings-John R, Williams D, Sheils E, Ashfield-Watt P, Akbari A, Hughes K, Thomas-Jones E, James D, Wood F.",,British journal of health psychology,2022,2022-06-01,Y,Risk Perception; Behaviour Change; Vaccine Hesitancy; Covid-19; Sars Cov2,,,"<h4>Objectives</h4>Using the Health Belief Model as a conceptual framework, we investigated the association between attitudes towards COVID-19, COVID-19 vaccinations, and vaccine hesitancy and change in these variables over a 9-month period in a UK cohort.<h4>Methods</h4>The COPE study cohort (n = 11,113) was recruited via an online survey at enrolment in March/April 2020. The study was advertised via the HealthWise Wales research registry and social media. Follow-up data were available for 6942 people at 3 months (June/July 2020) and 5037 at 12 months (March/April 2021) post-enrolment. Measures included demographics, perceived threat of COVID-19, perceived control, intention to accept or decline a COVID-19 vaccination, and attitudes towards vaccination. Logistic regression models were fitted cross-sectionally at 3 and 12 months to assess the association between motivational factors and vaccine hesitancy. Longitudinal changes in motivational variables for vaccine-hesitant and non-hesitant groups were examined using mixed-effect analysis of variance models.<h4>Results</h4>Fear of COVID-19, perceived susceptibility to COVID-19, and perceived personal control over COVID-19 infection transmission decreased between the 3- and 12-month surveys. Vaccine hesitancy at 12 months was independently associated with low fear of the disease and more negative attitudes towards COVID-19 vaccination. Specific barriers to COVID-19 vaccine uptake included concerns about safety and efficacy in light of its rapid development, mistrust of government and pharmaceutical companies, dislike of coercive policies, and perceived lack of relaxation in COVID-19-related restrictions as the vaccination programme progressed.<h4>Conclusions</h4>Decreasing fear of COVID-19, perceived susceptibility to the disease, and perceptions of personal control over reducing infection-transmission may impact future COVID-19 vaccination uptake.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa60128/Download/60128__24479__4d74009536e649b0b17180e2bfd80435.pdf; doi:https://doi.org/10.1111/bjhp.12606; html:https://europepmc.org/articles/PMC9347957; pdf:https://europepmc.org/articles/PMC9347957?pdf=render
 36544046,https://doi.org/10.1038/s41746-022-00730-6,A survey on clinical natural language processing in the United Kingdom from 2007 to 2022.,"Wu H, Wang M, Wu J, Francis F, Chang YH, Shavick A, Dong H, Poon MTC, Fitzpatrick N, Levine AP, Slater LT, Handy A, Karwath A, Gkoutos GV, Chelala C, Shah AD, Stewart R, Collier N, Alex B, Whiteley W, Sudlow C, Roberts A, Dobson RJB.",,NPJ digital medicine,2022,2022-12-21,Y,,,,"Much of the knowledge and information needed for enabling high-quality clinical research is stored in free-text format. Natural language processing (NLP) has been used to extract information from these sources at scale for several decades. This paper aims to present a comprehensive review of clinical NLP for the past 15 years in the UK to identify the community, depict its evolution, analyse methodologies and applications, and identify the main barriers. We collect a dataset of clinical NLP projects (n = 94; £ = 41.97 m) funded by UK funders or the European Union's funding programmes. Additionally, we extract details on 9 funders, 137 organisations, 139 persons and 431 research papers. Networks are created from timestamped data interlinking all entities, and network analysis is subsequently applied to generate insights. 431 publications are identified as part of a literature review, of which 107 are eligible for final analysis. Results show, not surprisingly, clinical NLP in the UK has increased substantially in the last 15 years: the total budget in the period of 2019-2022 was 80 times that of 2007-2010. However, the effort is required to deepen areas such as disease (sub-)phenotyping and broaden application domains. There is also a need to improve links between academia and industry and enable deployments in real-world settings for the realisation of clinical NLP's great potential in care delivery. The major barriers include research and development access to hospital data, lack of capable computational resources in the right places, the scarcity of labelled data and barriers to sharing of pretrained models.",,pdf:https://www.nature.com/articles/s41746-022-00730-6.pdf; doi:https://doi.org/10.1038/s41746-022-00730-6; html:https://europepmc.org/articles/PMC9770568; pdf:https://europepmc.org/articles/PMC9770568?pdf=render
 37751239,https://doi.org/10.2196/49438,Design and Evaluation of an Intensive Care Unit Dashboard Built in Response to the COVID-19 Pandemic: Semistructured Interview Study.,"Wac M, Craddock I, Chantziara S, Campbell T, Santos-Rodriguez R, Davidson B, McWilliams C.",,JMIR human factors,2023,2023-09-26,Y,Design; Health; ICU; EPR; intensive care unit; Interview; Intensive Care; Critical Care; Electronic Patient Record; Participatory Design; Ehr; Electronic Health Record; Software Engineering; Clinical Information System; Cis; Thematic Analysis; Dashboard; Human-centered Design; Covid-19; Interactive Display,,,"<h4>Background</h4>Dashboards and interactive displays are becoming increasingly prevalent in most health care settings and have the potential to streamline access to information, consolidate disparate data sources and deliver new insights. Our research focuses on intensive care units (ICUs) which are heavily instrumented, critical care environments that generate vast amounts of data and frequently require individualized support for each patient. Consequently, clinicians experience a high cognitive load, which can translate to suboptimal performance. The global COVID-19 pandemic exacerbated this problem by generating a large number of additional hospitalizations, which necessitated a new tool that would help manage ICUs' census. In a previous study, we interviewed clinicians at the University Hospitals Bristol and Weston National Health Service Foundation Trust to capture the requirements for bespoke dashboards that would alleviate this problem.<h4>Objective</h4>This study aims to design, implement, and evaluate an ICU dashboard to allow for monitoring of the high volume of patients in need of critical care, particularly tailored to high-demand situations, such as those seen during the COVID-19 pandemic.<h4>Methods</h4>Building upon the previously gathered requirements, we developed a dashboard, integrated it within the ICU of a National Health Service trust, and allowed all staff to access our tool. For evaluation purposes, participants were recruited and interviewed following a 25-day period during which they were able to use the dashboard clinically. The semistructured interviews followed a topic guide aimed at capturing the usability of the dashboard, supplemented with additional questions asked post hoc to probe themes established during the interview. Interview transcripts were analyzed using a thematic analysis framework that combined inductive and deductive approaches and integrated the Technology Acceptance Model.<h4>Results</h4>A total of 10 participants with 4 different roles in the ICU (6 consultants, 2 junior doctors, 1 nurse, and 1 advanced clinical practitioner) participated in the interviews. Our analysis generated 4 key topics that prevailed across the data: our dashboard met the usability requirements of the participants and was found useful and intuitive; participants perceived that it impacted their delivery of patient care by improving the access to the information and better equipping them to do their job; the tool was used in a variety of ways and for different reasons and tasks; and there were barriers to integration of our dashboard into practice, including familiarity with existing systems, which stifled the adoption of our tool.<h4>Conclusions</h4>Our findings show that the perceived utility of the dashboard had a positive impact on the clinicians' workflows in the ICU. Improving access to information translated into more efficient patient care and transformed some of the existing processes. The introduction of our tool was met with positive reception, but its integration during the COVID-19 pandemic limited its adoption into practice.",,doi:https://doi.org/10.2196/49438; doi:https://doi.org/10.2196/49438; html:https://europepmc.org/articles/PMC10565627
 37060915,https://doi.org/10.1016/s0140-6736(23)00510-x,"Higher dose corticosteroids in patients admitted to hospital with COVID-19 who are hypoxic but not requiring ventilatory support (RECOVERY): a randomised, controlled, open-label, platform trial.","RECOVERY Collaborative Group. Electronic address: recoverytrial@ndph.ox.ac.uk, RECOVERY Collaborative Group.",,"Lancet (London, England)",2023,2023-04-13,Y,,,,"<h4>Background</h4>Low-dose corticosteroids have been shown to reduce mortality for patients with COVID-19 requiring oxygen or ventilatory support (non-invasive mechanical ventilation, invasive mechanical ventilation, or extracorporeal membrane oxygenation). We evaluated the use of a higher dose of corticosteroids in this patient group.<h4>Methods</h4>This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]) is assessing multiple possible treatments in patients hospitalised for COVID-19. Eligible and consenting adult patients with clinical evidence of hypoxia (ie, receiving oxygen or with oxygen saturation <92% on room air) were randomly allocated (1:1) to either usual care with higher dose corticosteroids (dexamethasone 20 mg once daily for 5 days followed by 10 mg dexamethasone once daily for 5 days or until discharge if sooner) or usual standard of care alone (which included dexamethasone 6 mg once daily for 10 days or until discharge if sooner). The primary outcome was 28-day mortality among all randomised participants. On May 11, 2022, the independent data monitoring committee recommended stopping recruitment of patients receiving no oxygen or simple oxygen only due to safety concerns. We report the results for these participants only. Recruitment of patients receiving ventilatory support is ongoing. The RECOVERY trial is registered with ISRCTN (50189673) and ClinicalTrials.gov (NCT04381936).<h4>Findings</h4>Between May 25, 2021, and May 13, 2022, 1272 patients with COVID-19 and hypoxia receiving no oxygen (eight [1%]) or simple oxygen only (1264 [99%]) were randomly allocated to receive usual care plus higher dose corticosteroids (659 patients) versus usual care alone (613 patients, of whom 87% received low-dose corticosteroids during the follow-up period). Of those randomly assigned, 745 (59%) were in Asia, 512 (40%) in the UK, and 15 (1%) in Africa. 248 (19%) had diabetes and 769 (60%) were male. Overall, 123 (19%) of 659 patients allocated to higher dose corticosteroids versus 75 (12%) of 613 patients allocated to usual care died within 28 days (rate ratio 1·59 [95% CI 1·20-2·10]; p=0·0012). There was also an excess of pneumonia reported to be due to non-COVID infection (64 cases [10%] vs 37 cases [6%]; absolute difference 3·7% [95% CI 0·7-6·6]) and an increase in hyperglycaemia requiring increased insulin dose (142 [22%] vs 87 [14%]; absolute difference 7·4% [95% CI 3·2-11·5]).<h4>Interpretation</h4>In patients hospitalised for COVID-19 with clinical hypoxia who required either no oxygen or simple oxygen only, higher dose corticosteroids significantly increased the risk of death compared with usual care, which included low-dose corticosteroids. The RECOVERY trial continues to assess the effects of higher dose corticosteroids in patients hospitalised with COVID-19 who require non-invasive ventilation, invasive mechanical ventilation, or extracorporeal membrane oxygenation.<h4>Funding</h4>UK Research and Innovation (Medical Research Council), National Institute of Health and Care Research, and Wellcome Trust.",,doi:https://doi.org/10.1016/s0140-6736(23)00510-x; doi:https://doi.org/10.1016/S0140-6736(23)00510-X; html:https://europepmc.org/articles/PMC10156147; pdf:https://europepmc.org/articles/PMC10156147?pdf=render
@@ -723,8 +724,8 @@ PMC9645061,https://doi.org/,Using population-scale medication data to evaluate t
 36808078,https://doi.org/10.1136/pn-2021-003286,Outpatient neurology diagnostic coding: a proposed scheme for standardised implementation.,"Biggin F, Knight J, Dayanandan R, Marson A, Wilson M, Nitkunan A, Rog D, Kipps C, Mummery C, Williams A, Emsley HCA.",,Practical neurology,2023,2023-02-20,Y,Clinical Neurology,,,"Clinical coding uses a classification system to assign standard codes to clinical terms and so facilitates good clinical practice through audit, service design and research. However, despite clinical coding being mandatory for inpatient activity, this is often not so for outpatient services, where most neurological care is delivered. Recent reports by the UK National Neurosciences Advisory Group and NHS England's 'Getting It Right First Time' initiative recommend implementing outpatient coding. The UK currently has no standardised system for outpatient neurology diagnostic coding. However, most new attendances at general neurology clinics appear to be classifiable with a limited number of diagnostic terms. We present the rationale for diagnostic coding and its benefits, and the need for clinical engagement to develop a system that is pragmatic, quick and easy to use. We outline a scheme developed in the UK that could be used elsewhere.",,pdf:https://pn.bmj.com/content/practneurol/early/2023/02/19/pn-2021-003286.full.pdf; doi:https://doi.org/10.1136/pn-2021-003286; html:https://europepmc.org/articles/PMC10423506; pdf:https://europepmc.org/articles/PMC10423506?pdf=render
 PMC8855010,https://doi.org/,POS-894 PREDICTING PANDEMIC-RELATED EXCESS-DEATH USING PRE-PANDEMIC RISK OF MORTALITY IN INDIVIDUALS WITH CHRONIC KIDNEY DISEASE,"Dashtban M, Mizani M, Gonazalez-Izquierdo A, Corbett R, Denaxas S, Quint J, Mamza J, Morris T, Hemingway H, Sudlow C, Banerjee A.",,Kidney international reports,2022,2022-02-01,Y,,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8855010/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8855010/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC8855010; pdf:https://europepmc.org/articles/PMC8855010?pdf=render
 34107928,https://doi.org/10.1186/s12913-021-06509-x,Importance of patient bed pathways and length of stay differences in predicting COVID-19 hospital bed occupancy in England.,"Leclerc QJ, Fuller NM, Keogh RH, Diaz-Ordaz K, Sekula R, Semple MG, ISARIC4C Investigators, CMMID COVID-19 Working Group, Atkins KE, Procter SR, Knight GM.",,BMC health services research,2021,2021-06-09,Y,Length Of Stay; Hospitalisation; Bed Occupancy; Covid-19; Sars-cov-2; Bed Pathway,,,"<h4>Background</h4>Predicting bed occupancy for hospitalised patients with COVID-19 requires understanding of length of stay (LoS) in particular bed types. LoS can vary depending on the patient's ""bed pathway"" - the sequence of transfers of individual patients between bed types during a hospital stay. In this study, we characterise these pathways, and their impact on predicted hospital bed occupancy.<h4>Methods</h4>We obtained data from University College Hospital (UCH) and the ISARIC4C COVID-19 Clinical Information Network (CO-CIN) on hospitalised patients with COVID-19 who required care in general ward or critical care (CC) beds to determine possible bed pathways and LoS. We developed a discrete-time model to examine the implications of using either bed pathways or only average LoS by bed type to forecast bed occupancy. We compared model-predicted bed occupancy to publicly available bed occupancy data on COVID-19 in England between March and August 2020.<h4>Results</h4>In both the UCH and CO-CIN datasets, 82% of hospitalised patients with COVID-19 only received care in general ward beds. We identified four other bed pathways, present in both datasets: ""Ward, CC, Ward"", ""Ward, CC"", ""CC"" and ""CC, Ward"". Mean LoS varied by bed type, pathway, and dataset, between 1.78 and 13.53 days. For UCH, we found that using bed pathways improved the accuracy of bed occupancy predictions, while only using an average LoS for each bed type underestimated true bed occupancy. However, using the CO-CIN LoS dataset we were not able to replicate past data on bed occupancy in England, suggesting regional LoS heterogeneities.<h4>Conclusions</h4>We identified five bed pathways, with substantial variation in LoS by bed type, pathway, and geography. This might be caused by local differences in patient characteristics, clinical care strategies, or resource availability, and suggests that national LoS averages may not be appropriate for local forecasts of bed occupancy for COVID-19.<h4>Trial registration</h4>The ISARIC WHO CCP-UK study ISRCTN66726260 was retrospectively registered on 21/04/2020 and designated an Urgent Public Health Research Study by NIHR.",,pdf:https://bmchealthservres.biomedcentral.com/counter/pdf/10.1186/s12913-021-06509-x; doi:https://doi.org/10.1186/s12913-021-06509-x; html:https://europepmc.org/articles/PMC8188158; pdf:https://europepmc.org/articles/PMC8188158?pdf=render
-36715329,https://doi.org/10.1093/bjd/ljac090,"The epidemiology, healthcare and societal burden of basal cell carcinoma in Wales 2000-2018: a retrospective nationwide analysis.","Ibrahim N, Jovic M, Ali S, Williams N, Gibson JAG, Griffiths R, Dobbs TD, Akbari A, Lyons RA, Hutchings HA, Whitaker IS.",,The British journal of dermatology,2023,2023-02-01,N,,,,"<h4>Background</h4>Basal cell carcinoma (BCC) represents the most commonly occurring cancer worldwide within the white population. Reports predict 298 308 cases of BCC in the UK by 2025, at a cost of £265-366 million to the National Health Service (NHS). Despite the morbidity, societal and healthcare pressures brought about by BCC, routinely collected healthcare data and global registration remain limited.<h4>Objectives</h4>To calculate the incidence of BCC in Wales between 2000 and 2018 and to establish the related healthcare utilization and estimated cost of care.<h4>Methods</h4>The Secure Anonymised Information Linkage (SAIL) databank is one of the largest and most robust health and social care data repositories in the UK. Cancer registry data were linked to routinely collected healthcare databases between 2000 and 2018. Pathological data from Swansea Bay University Health Board (SBUHB) were used for internal validation.<h4>Results</h4>A total of 61 404 histologically proven BCCs were identified within the SAIL Databank during the study period. The European age-standardized incidence for BCC in 2018 was 224.6 per 100 000 person-years. Based on validated regional data, a 45% greater incidence was noted within SBUHB pathology vs. matched regions within SAIL between 2016 and 2018. A negative association between deprivation and incidence was noted with a higher incidence in the least socially deprived and rural dwellers. Approximately 2% travelled 25-50 miles for dermatological services compared with 37% for plastic surgery. Estimated NHS costs of surgically managed lesions for 2002-2019 equated to £119.2-164.4 million.<h4>Conclusions</h4>Robust epidemiological data that are internationally comparable and representative are scarce for nonmelanoma skin cancer. The rising global incidence coupled with struggling healthcare systems in the post-COVID-19 recovery period serve to intensify the societal and healthcare impact. This study is the first to demonstrate the incidence of BCC in Wales and is one of a small number in the UK using internally validated large cohort datasets. Furthermore, our findings demonstrate one of the highest published incidences within the UK and Europe.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa62055/Download/62055__26915__ae11794993454389b6ceddbb7f50caaa.pdf; doi:https://doi.org/10.1093/bjd/ljac090
 34716166,https://doi.org/10.1136/bmjopen-2021-053268,Electronic reminders and rewards to improve adherence to inhaled asthma treatment in adolescents: a non-randomised feasibility study in tertiary care.,"De Simoni A, Fleming L, Holliday L, Horne R, Priebe S, Bush A, Sheikh A, Griffiths C.",,BMJ open,2021,2021-10-29,Y,Asthma; Respiratory Medicine (See Thoracic Medicine); Paediatric Thoracic Medicine,,,"<h4>Objective</h4>To test the feasibility and acceptability of a short-term reminder and incentives intervention in adolescents with low adherence to asthma medications.<h4>Methods</h4>Mixed-methods feasibility study in a tertiary care clinic. Adolescents recruited to a 24-week programme with three 8-weekly visits, receiving electronic reminders to prompt inhaled corticosteroid (ICS) inhalation through a mobile app coupled with electronic monitoring devices (EMD). From the second visit, monetary incentives based on adherence of ICS inhalation: £1 per dose, maximum £2 /day, up to £112/study, collected as gift cards at the third visit. End of study interviews and questionnaires assessing perceptions of asthma and ICS, analysed using the Perceptions and Practicalities Framework.<h4>Participants</h4>Adolescents (11-18 years) with documented low ICS adherence (<80% by EMD), and poor asthma control at the first clinic visit.<h4>Results</h4>10 out of 12 adolescents approached were recruited (7 males, 3 females, 12-16 years). Eight participants provided adherence measures up to the fourth visits and received rewards. Mean study duration was 281 days, with 7/10 participants unable to attend their fourth visit due to COVID-19 lockdown. Only 3/10 participants managed to pair the app/EMD up to the fourth visit, which was associated with improved ICS adherence (from 0.51, SD 0.07 to 0.86, SD 0.05). Adherence did not change in adolescents unable to pair the app/EMD. The intervention was acceptable to participants and parents/guardians. Exit interviews showed that participants welcomed reminders and incentives, though expressed frustration with app/EMD technological difficulties. Participants stated the intervention helped through reminding ICS doses, promoting self-monitoring and increasing motivation to take inhalers.<h4>Conclusions</h4>An intervention using electronic reminders and incentives through an app coupled with an EMD was feasible and acceptable to adolescents with asthma. A pilot randomised controlled trial is warranted to better estimate the effect size on adherence, with improved technical support for the EMD.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/10/e053268.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-053268; html:https://europepmc.org/articles/PMC8559117; pdf:https://europepmc.org/articles/PMC8559117?pdf=render
+36715329,https://doi.org/10.1093/bjd/ljac090,"The epidemiology, healthcare and societal burden of basal cell carcinoma in Wales 2000-2018: a retrospective nationwide analysis.","Ibrahim N, Jovic M, Ali S, Williams N, Gibson JAG, Griffiths R, Dobbs TD, Akbari A, Lyons RA, Hutchings HA, Whitaker IS.",,The British journal of dermatology,2023,2023-02-01,N,,,,"<h4>Background</h4>Basal cell carcinoma (BCC) represents the most commonly occurring cancer worldwide within the white population. Reports predict 298 308 cases of BCC in the UK by 2025, at a cost of £265-366 million to the National Health Service (NHS). Despite the morbidity, societal and healthcare pressures brought about by BCC, routinely collected healthcare data and global registration remain limited.<h4>Objectives</h4>To calculate the incidence of BCC in Wales between 2000 and 2018 and to establish the related healthcare utilization and estimated cost of care.<h4>Methods</h4>The Secure Anonymised Information Linkage (SAIL) databank is one of the largest and most robust health and social care data repositories in the UK. Cancer registry data were linked to routinely collected healthcare databases between 2000 and 2018. Pathological data from Swansea Bay University Health Board (SBUHB) were used for internal validation.<h4>Results</h4>A total of 61 404 histologically proven BCCs were identified within the SAIL Databank during the study period. The European age-standardized incidence for BCC in 2018 was 224.6 per 100 000 person-years. Based on validated regional data, a 45% greater incidence was noted within SBUHB pathology vs. matched regions within SAIL between 2016 and 2018. A negative association between deprivation and incidence was noted with a higher incidence in the least socially deprived and rural dwellers. Approximately 2% travelled 25-50 miles for dermatological services compared with 37% for plastic surgery. Estimated NHS costs of surgically managed lesions for 2002-2019 equated to £119.2-164.4 million.<h4>Conclusions</h4>Robust epidemiological data that are internationally comparable and representative are scarce for nonmelanoma skin cancer. The rising global incidence coupled with struggling healthcare systems in the post-COVID-19 recovery period serve to intensify the societal and healthcare impact. This study is the first to demonstrate the incidence of BCC in Wales and is one of a small number in the UK using internally validated large cohort datasets. Furthermore, our findings demonstrate one of the highest published incidences within the UK and Europe.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa62055/Download/62055__26915__ae11794993454389b6ceddbb7f50caaa.pdf; doi:https://doi.org/10.1093/bjd/ljac090
 36962800,https://doi.org/10.1371/journal.pgph.0000843,Effect of the COVID-19 pandemic on health service utilization across regions of Ethiopia: An interrupted time series analysis of health information system data from 2019-2020.,"Mebratie AD, Nega A, Gage A, Mariam DH, Eshetu MK, Arsenault C.",,PLOS global public health,2022,2022-09-12,Y,,,,"The spread of COVID-19 and associated deaths have remained low in Ethiopia. However, the pandemic could pose a public health crisis indirectly through disruptions in essential health services. The aim of this study was to examine disruptions in health service utilization during the first nine months of the COVID-19 pandemic across 10 regions in Ethiopia. We analyzed utilization of 21 different health services across all of Ethiopia (except the Tigray region) for the period of January 2019 to December 2020. Data were extracted from the Ethiopian district health information system (DHIS2). Monthly visits in 2020 were graphed relative to the same months in 2019. Interrupted time series analysis was used to estimate the effect of the pandemic on service utilization in each region. We found that disruptions in health services were generally higher in urban regions which were most affected by COVID. Outpatient visits declined by 52%, 54%, and 58%, specifically in Dire Dawa, Addis Ababa and Harari, the three urban regions. Similarly, there was a 47% reduction in inpatient admissions in Addis Ababa. In agrarian regions, the pandemic caused an 11% to 17% reduction in outpatient visits and a 10% to 27% decline in inpatient admissions. Visits for children with diarrhea, pneumonia and malnutrition also declined substantially while maternal health services were less affected. Our study indicates that disruptions in health services were more pronounced in areas that were relatively harder hit by the pandemic. Our results show that the Ethiopian health system has a limited capacity to absorb shocks. During future waves of COVID or future pandemics, the Ethiopian health system must be better prepared to maintain essential services and mitigate the indirect impact of the pandemic on public health, particularly in urban areas.",,pdf:https://journals.plos.org/globalpublichealth/article/file?id=10.1371/journal.pgph.0000843&type=printable; doi:https://doi.org/10.1371/journal.pgph.0000843; html:https://europepmc.org/articles/PMC10021875; pdf:https://europepmc.org/articles/PMC10021875?pdf=render
 32877352,https://doi.org/10.2196/19992,Using Smartphones and Wearable Devices to Monitor Behavioral Changes During COVID-19.,"Sun S, Folarin AA, Ranjan Y, Rashid Z, Conde P, Stewart C, Cummins N, Matcham F, Dalla Costa G, Simblett S, Leocani L, Lamers F, Sørensen PS, Buron M, Zabalza A, Guerrero Pérez AI, Penninx BW, Siddi S, Haro JM, Myin-Germeys I, Rintala A, Wykes T, Narayan VA, Comi G, Hotopf M, Dobson RJ, RADAR-CNS Consortium.",,Journal of medical Internet research,2020,2020-09-25,Y,Mobility; Smartphones; Mobile Health; Behavioral Monitoring; Wearable Devices; Phone Use; Covid-19,,,"<h4>Background</h4>In the absence of a vaccine or effective treatment for COVID-19, countries have adopted nonpharmaceutical interventions (NPIs) such as social distancing and full lockdown. An objective and quantitative means of passively monitoring the impact and response of these interventions at a local level is needed.<h4>Objective</h4>We aim to explore the utility of the recently developed open-source mobile health platform Remote Assessment of Disease and Relapse (RADAR)-base as a toolbox to rapidly test the effect and response to NPIs intended to limit the spread of COVID-19.<h4>Methods</h4>We analyzed data extracted from smartphone and wearable devices, and managed by the RADAR-base from 1062 participants recruited in Italy, Spain, Denmark, the United Kingdom, and the Netherlands. We derived nine features on a daily basis including time spent at home, maximum distance travelled from home, the maximum number of Bluetooth-enabled nearby devices (as a proxy for physical distancing), step count, average heart rate, sleep duration, bedtime, phone unlock duration, and social app use duration. We performed Kruskal-Wallis tests followed by post hoc Dunn tests to assess differences in these features among baseline, prelockdown, and during lockdown periods. We also studied behavioral differences by age, gender, BMI, and educational background.<h4>Results</h4>We were able to quantify expected changes in time spent at home, distance travelled, and the number of nearby Bluetooth-enabled devices between prelockdown and during lockdown periods (P<.001 for all five countries). We saw reduced sociality as measured through mobility features and increased virtual sociality through phone use. People were more active on their phones (P<.001 for Italy, Spain, and the United Kingdom), spending more time using social media apps (P<.001 for Italy, Spain, the United Kingdom, and the Netherlands), particularly around major news events. Furthermore, participants had a lower heart rate (P<.001 for Italy and Spain; P=.02 for Denmark), went to bed later (P<.001 for Italy, Spain, the United Kingdom, and the Netherlands), and slept more (P<.001 for Italy, Spain, and the United Kingdom). We also found that young people had longer homestay than older people during the lockdown and fewer daily steps. Although there was no significant difference between the high and low BMI groups in time spent at home, the low BMI group walked more.<h4>Conclusions</h4>RADAR-base, a freely deployable data collection platform leveraging data from wearables and mobile technologies, can be used to rapidly quantify and provide a holistic view of behavioral changes in response to public health interventions as a result of infectious outbreaks such as COVID-19. RADAR-base may be a viable approach to implementing an early warning system for passively assessing the local compliance to interventions in epidemics and pandemics, and could help countries ease out of lockdown.",,pdf:https://www.jmir.org/2020/9/e19992/PDF; doi:https://doi.org/10.2196/19992; html:https://europepmc.org/articles/PMC7527031
 33785494,https://doi.org/10.1136/bmjopen-2020-046365,Impact of the COVID-19 pandemic on remote mental healthcare and prescribing in psychiatry: an electronic health record study.,"Patel R, Irving J, Brinn A, Broadbent M, Shetty H, Pritchard M, Downs J, Stewart R, Harland R, McGuire P.",,BMJ open,2021,2021-03-30,Y,Psychiatry; Mental health; epidemiology; Telemedicine; Health Informatics,,,"<h4>Objectives</h4>The recent COVID-19 pandemic has disrupted mental healthcare delivery, with many services shifting from in-person to remote patient contact. We investigated the impact of the pandemic on the use of remote consultation and on the prescribing of psychiatric medications.<h4>Design and setting</h4>The Clinical Record Interactive Search tool was used to examine deidentified electronic health records of people receiving mental healthcare from the South London and Maudsley (SLaM) NHS Foundation Trust. Data from the period before and after the onset of the pandemic were analysed using linear regression, and visualised using locally estimated scatterplot smoothing.<h4>Participants</h4>All patients receiving care from SLaM between 7 January 2019 and 20 September 2020 (around 37 500 patients per week).<h4>Outcome measures</h4>(i) The number of clinical contacts (in-person, remote or non-attended) with mental healthcare professionals per week.(ii) Prescribing of antipsychotic and mood stabiliser medications per week.<h4>Results</h4>Following the onset of the pandemic, the frequency of in-person contacts was significantly reduced compared with that in the previous year (β coefficient: -5829.6 contacts, 95% CI -6919.5 to -4739.6, p<0.001), while the frequency of remote contacts significantly increased (β coefficient: 3338.5 contacts, 95% CI 3074.4 to 3602.7, p<0.001). Rates of remote consultation were lower in older adults than in working age adults, children and adolescents. Despite this change in the type of patient contact, antipsychotic and mood stabiliser prescribing remained at similar levels.<h4>Conclusions</h4>The COVID-19 pandemic has been associated with a marked increase in remote consultation, particularly among younger patients. However, there was no evidence that this has led to changes in psychiatric prescribing. Nevertheless, further work is needed to ensure that older patients are able to access mental healthcare remotely.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/3/e046365.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-046365; html:https://europepmc.org/articles/PMC8728386; pdf:https://europepmc.org/articles/PMC8728386?pdf=render
@@ -736,14 +737,14 @@ PMC8855010,https://doi.org/,POS-894 PREDICTING PANDEMIC-RELATED EXCESS-DEATH USI
 34470746,https://doi.org/10.1136/bmjgh-2021-006204,Disruption in essential health services in Mexico during COVID-19: an interrupted time series analysis of health information system data.,"Doubova SV, Leslie HH, Kruk ME, Pérez-Cuevas R, Arsenault C.",,BMJ global health,2021,2021-09-01,Y,Hypertension; Cancer; Diabetes; Maternal Health; Health Systems Evaluation,,,"<h4>Introduction</h4>The COVID-19 pandemic has disrupted health systems around the world. The objectives of this study are to estimate the overall effect of the pandemic on essential health service use and outcomes in Mexico, describe observed and predicted trends in services over 24 months, and to estimate the number of visits lost through December 2020.<h4>Methods</h4>We used health information system data for January 2019 to December 2020 from the Mexican Institute of Social Security (IMSS), which provides health services for more than half of Mexico's population-65 million people. Our analysis includes nine indicators of service use and three outcome indicators for reproductive, maternal and child health and non-communicable disease services. We used an interrupted time series design and linear generalised estimating equation models to estimate the change in service use and outcomes from April to December 2020. Estimates were expressed using average marginal effects on the risk ratio scale.<h4>Results</h4>The study found that across nine health services, an estimated 8.74 million patient visits were lost in Mexico. This included a decline of over two thirds for breast and cervical cancer screenings (79% and 68%, respectively), over half for sick child visits and female contraceptive services, approximately one-third for childhood vaccinations, diabetes, hypertension and antenatal care consultations, and a decline of 10% for deliveries performed at IMSS. In terms of patient outcomes, the proportion of patients with diabetes and hypertension with controlled conditions declined by 22% and 17%, respectively. Caesarean section rate did not change.<h4>Conclusion</h4>Significant disruptions in health services show that the pandemic has strained the resilience of the Mexican health system and calls for urgent efforts to resume essential services and plan for catching up on missed preventive care even as the COVID-19 crisis continues in Mexico.",,pdf:https://gh.bmj.com/content/bmjgh/6/9/e006204.full.pdf; doi:https://doi.org/10.1136/bmjgh-2021-006204; html:https://europepmc.org/articles/PMC8413469; pdf:https://europepmc.org/articles/PMC8413469?pdf=render
 36936594,https://doi.org/10.1136/bmjmed-2022-000247,Measuring multimorbidity in research: Delphi consensus study.,"Ho ISS, Azcoaga-Lorenzo A, Akbari A, Davies J, Khunti K, Kadam UT, Lyons RA, McCowan C, Mercer SW, Nirantharakumar K, Staniszewska S, Guthrie B.",,BMJ medicine,2022,2022-07-27,Y,Medicine; epidemiology; Primary Health Care; Public Health; Research Design,,,"<h4>Objective</h4>To develop international consensus on the definition and measurement of multimorbidity in research.<h4>Design</h4>Delphi consensus study.<h4>Setting</h4>International consensus; data collected in three online rounds from participants between 30 November 2020 and 18 May 2021.<h4>Participants</h4>Professionals interested in multimorbidity and people with long term conditions were recruited to professional and public panels.<h4>Results</h4>150 professional and 25 public participants completed the first survey round. Response rates for rounds 2/3 were 83%/92% for professionals and 88%/93% in the public panel, respectively. Across both panels, the consensus was that multimorbidity should be defined as two or more long term conditions. Complex multimorbidity was perceived to be a useful concept, but the panels were unable to agree on how to define it. Both panels agreed that conditions should be included in a multimorbidity measure if they were one or more of the following: currently active; permanent in their effects; requiring current treatment, care, or therapy; requiring surveillance; or relapsing-remitting conditions requiring ongoing care. Consensus was reached for 24 conditions to always include in multimorbidity measures, and 35 conditions to usually include unless a good reason not to existed. Simple counts were preferred for estimating prevalence and examining clustering or trajectories, and weighted measures were preferred for risk adjustment and outcome prediction.<h4>Conclusions</h4>Previous multimorbidity research is limited by inconsistent definitions and approaches to measuring multimorbidity. This Delphi study identifies professional and public panel consensus guidance to facilitate consistency of definition and measurement, and to improve study comparability and reproducibility.",,pdf:https://bmjmedicine.bmj.com/content/bmjmed/1/1/e000247.full.pdf; doi:https://doi.org/10.1136/bmjmed-2022-000247; html:https://europepmc.org/articles/PMC9978673; pdf:https://europepmc.org/articles/PMC9978673?pdf=render
 37433797,https://doi.org/10.1038/s41467-023-38816-8,The role of vaccination and public awareness in forecasts of Mpox incidence in the United Kingdom.,"Brand SPC, Cavallaro M, Cumming F, Turner C, Florence I, Blomquist P, Hilton J, Guzman-Rincon LM, House T, Nokes DJ, Keeling MJ.",,Nature communications,2023,2023-07-11,Y,,,,"Beginning in May 2022, Mpox virus spread rapidly in high-income countries through close human-to-human contact primarily amongst communities of gay, bisexual and men who have sex with men (GBMSM). Behavioural change arising from increased knowledge and health warnings may have reduced the rate of transmission and modified Vaccinia-based vaccination is likely to be an effective longer-term intervention. We investigate the UK epidemic presenting 26-week projections using a stochastic discrete-population transmission model which includes GBMSM status, rate of formation of new sexual partnerships, and clique partitioning of the population. The Mpox cases peaked in mid-July; our analysis is that the decline was due to decreased transmission rate per infected individual and infection-induced immunity among GBMSM, especially those with the highest rate of new partners. Vaccination did not cause Mpox incidence to turn over, however, we predict that a rebound in cases due to behaviour reversion was prevented by high-risk group-targeted vaccination.",,pdf:https://www.nature.com/articles/s41467-023-38816-8.pdf; doi:https://doi.org/10.1038/s41467-023-38816-8; html:https://europepmc.org/articles/PMC10336136; pdf:https://europepmc.org/articles/PMC10336136?pdf=render
-35337642,https://doi.org/10.1016/s2589-7500(22)00018-8,"Implementation of corticosteroids in treatment of COVID-19 in the ISARIC WHO Clinical Characterisation Protocol UK: prospective, cohort study.","Närhi F, Moonesinghe SR, Shenkin SD, Drake TM, Mulholland RH, Donegan C, Dunning J, Fairfield CJ, Girvan M, Hardwick HE, Ho A, Leeming G, Nguyen-Van-Tam JS, Pius R, Russell CD, Shaw CA, Spencer RG, Turtle L, Openshaw PJM, Baillie JK, Harrison EM, Semple MG, Docherty AB, ISARIC4C investigators.",,The Lancet. Digital health,2022,2022-04-01,Y,,,,"<h4>Background</h4>Dexamethasone was the first intervention proven to reduce mortality in patients with COVID-19 being treated in hospital. We aimed to evaluate the adoption of corticosteroids in the treatment of COVID-19 in the UK after the RECOVERY trial publication on June 16, 2020, and to identify discrepancies in care.<h4>Methods</h4>We did an audit of clinical implementation of corticosteroids in a prospective, observational, cohort study in 237 UK acute care hospitals between March 16, 2020, and April 14, 2021, restricted to patients aged 18 years or older with proven or high likelihood of COVID-19, who received supplementary oxygen. The primary outcome was administration of dexamethasone, prednisolone, hydrocortisone, or methylprednisolone. This study is registered with ISRCTN, ISRCTN66726260.<h4>Findings</h4>Between June 17, 2020, and April 14, 2021, 47 795 (75·2%) of 63 525 of patients on supplementary oxygen received corticosteroids, higher among patients requiring critical care than in those who received ward care (11 185 [86·6%] of 12 909 vs 36 415 [72·4%] of 50 278). Patients 50 years or older were significantly less likely to receive corticosteroids than those younger than 50 years (adjusted odds ratio 0·79 [95% CI 0·70-0·89], p=0·0001, for 70-79 years; 0·52 [0·46-0·58], p<0·0001, for >80 years), independent of patient demographics and illness severity. 84 (54·2%) of 155 pregnant women received corticosteroids. Rates of corticosteroid administration increased from 27·5% in the week before June 16, 2020, to 75-80% in January, 2021.<h4>Interpretation</h4>Implementation of corticosteroids into clinical practice in the UK for patients with COVID-19 has been successful, but not universal. Patients older than 70 years, independent of illness severity, chronic neurological disease, and dementia, were less likely to receive corticosteroids than those who were younger, as were pregnant women. This could reflect appropriate clinical decision making, but the possibility of inequitable access to life-saving care should be considered.<h4>Funding</h4>UK National Institute for Health Research and UK Medical Research Council.",,pdf:http://www.thelancet.com/article/S2589750022000188/pdf; doi:https://doi.org/10.1016/S2589-7500(22)00018-8; html:https://europepmc.org/articles/PMC8940185
 34240696,https://doi.org/10.2807/1560-7917.es.2021.26.27.2000004,"Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season.","Xu Y, Lewandowski K, Downs LO, Kavanagh J, Hender T, Lumley S, Jeffery K, Foster D, Sanderson ND, Vaughan A, Morgan M, Vipond R, Carroll M, Peto T, Crook D, Walker AS, Matthews PC, Pullan ST.",,Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin,2021,2021-07-01,Y,Genetic diversity; Influenza; Diagnosis; Metagenomics; Antiviral Drug Resistance; Nanopore; Respiratory Viruses; Nosocomial Transmission,,,"BackgroundInfluenza virus presents a considerable challenge to public health by causing seasonal epidemics and occasional pandemics. Nanopore metagenomic sequencing has the potential to be deployed for near-patient testing, providing rapid infection diagnosis, rationalising antimicrobial therapy, and supporting infection-control interventions.AimTo evaluate the applicability of this sequencing approach as a routine laboratory test for influenza in clinical settings.MethodsWe conducted Oxford Nanopore Technologies (Oxford, United Kingdom (UK)) metagenomic sequencing for 180 respiratory samples from a UK hospital during the 2018/19 influenza season, and compared results to routine molecular diagnostic standards (Xpert Xpress Flu/RSV assay; BioFire FilmArray Respiratory Panel 2 assay). We investigated drug resistance, genetic diversity, and nosocomial transmission using influenza sequence data.ResultsCompared to standard testing, Nanopore metagenomic sequencing was 83% (75/90) sensitive and 93% (84/90) specific for detecting influenza A viruses. Of 59 samples with haemagglutinin subtype determined, 40 were H1 and 19 H3. We identified an influenza A(H3N2) genome encoding the oseltamivir resistance S331R mutation in neuraminidase, potentially associated with an emerging distinct intra-subtype reassortant. Whole genome phylogeny refuted suspicions of a transmission cluster in a ward, but identified two other clusters that likely reflected nosocomial transmission, associated with a predominant community-circulating strain. We also detected other potentially pathogenic viruses and bacteria from the metagenome.ConclusionNanopore metagenomic sequencing can detect the emergence of novel variants and drug resistance, providing timely insights into antimicrobial stewardship and vaccine design. Full genome generation can help investigate and manage nosocomial outbreaks.",,pdf:https://www.eurosurveillance.org/deliver/fulltext/eurosurveillance/26/27/eurosurv-26-27-4.pdf?itemId=%2Fcontent%2F10.2807%2F1560-7917.ES.2021.26.27.2000004&mimeType=pdf&containerItemId=content/eurosurveillance; doi:https://doi.org/10.2807/1560-7917.ES.2021.26.27.2000004; html:https://europepmc.org/articles/PMC8268652; pdf:https://europepmc.org/articles/PMC8268652?pdf=render
+35337642,https://doi.org/10.1016/s2589-7500(22)00018-8,"Implementation of corticosteroids in treatment of COVID-19 in the ISARIC WHO Clinical Characterisation Protocol UK: prospective, cohort study.","Närhi F, Moonesinghe SR, Shenkin SD, Drake TM, Mulholland RH, Donegan C, Dunning J, Fairfield CJ, Girvan M, Hardwick HE, Ho A, Leeming G, Nguyen-Van-Tam JS, Pius R, Russell CD, Shaw CA, Spencer RG, Turtle L, Openshaw PJM, Baillie JK, Harrison EM, Semple MG, Docherty AB, ISARIC4C investigators.",,The Lancet. Digital health,2022,2022-04-01,Y,,,,"<h4>Background</h4>Dexamethasone was the first intervention proven to reduce mortality in patients with COVID-19 being treated in hospital. We aimed to evaluate the adoption of corticosteroids in the treatment of COVID-19 in the UK after the RECOVERY trial publication on June 16, 2020, and to identify discrepancies in care.<h4>Methods</h4>We did an audit of clinical implementation of corticosteroids in a prospective, observational, cohort study in 237 UK acute care hospitals between March 16, 2020, and April 14, 2021, restricted to patients aged 18 years or older with proven or high likelihood of COVID-19, who received supplementary oxygen. The primary outcome was administration of dexamethasone, prednisolone, hydrocortisone, or methylprednisolone. This study is registered with ISRCTN, ISRCTN66726260.<h4>Findings</h4>Between June 17, 2020, and April 14, 2021, 47 795 (75·2%) of 63 525 of patients on supplementary oxygen received corticosteroids, higher among patients requiring critical care than in those who received ward care (11 185 [86·6%] of 12 909 vs 36 415 [72·4%] of 50 278). Patients 50 years or older were significantly less likely to receive corticosteroids than those younger than 50 years (adjusted odds ratio 0·79 [95% CI 0·70-0·89], p=0·0001, for 70-79 years; 0·52 [0·46-0·58], p<0·0001, for >80 years), independent of patient demographics and illness severity. 84 (54·2%) of 155 pregnant women received corticosteroids. Rates of corticosteroid administration increased from 27·5% in the week before June 16, 2020, to 75-80% in January, 2021.<h4>Interpretation</h4>Implementation of corticosteroids into clinical practice in the UK for patients with COVID-19 has been successful, but not universal. Patients older than 70 years, independent of illness severity, chronic neurological disease, and dementia, were less likely to receive corticosteroids than those who were younger, as were pregnant women. This could reflect appropriate clinical decision making, but the possibility of inequitable access to life-saving care should be considered.<h4>Funding</h4>UK National Institute for Health Research and UK Medical Research Council.",,pdf:http://www.thelancet.com/article/S2589750022000188/pdf; doi:https://doi.org/10.1016/S2589-7500(22)00018-8; html:https://europepmc.org/articles/PMC8940185
 36721180,https://doi.org/10.1186/s12961-022-00956-6,Tracking health system performance in times of crisis using routine health data: lessons learned from a multicountry consortium.,"Turcotte-Tremblay AM, Leerapan B, Akweongo P, Amponsah F, Aryal A, Asai D, Awoonor-Williams JK, Ayele W, Bauhoff S, Doubova SV, Gadeka DD, Dulal M, Gage A, Gordon-Strachan G, Haile-Mariam D, Joseph JP, Kaewkamjornchai P, Kapoor NR, Gelaw SK, Kim MK, Kruk ME, Kubota S, Margozzini P, Mehata S, Mthethwa L, Nega A, Oh J, Park SK, Passi-Solar A, Perez Cuevas RE, Reddy T, Rittiphairoj T, Sapag JC, Thermidor R, Tlou B, Arsenault C.",,Health research policy and systems,2023,2023-01-31,Y,Quality Of Care; Health Systems; Routine Health Information Systems; Covid-19,,,"COVID-19 has prompted the use of readily available administrative data to track health system performance in times of crisis and to monitor disruptions in essential healthcare services. In this commentary we describe our experience working with these data and lessons learned across countries. Since April 2020, the Quality Evidence for Health System Transformation (QuEST) network has used administrative data and routine health information systems (RHIS) to assess health system performance during COVID-19 in Chile, Ethiopia, Ghana, Haiti, Lao People's Democratic Republic, Mexico, Nepal, South Africa, Republic of Korea and Thailand. We compiled a large set of indicators related to common health conditions for the purpose of multicountry comparisons. The study compiled 73 indicators. A total of 43% of the indicators compiled pertained to reproductive, maternal, newborn and child health (RMNCH). Only 12% of the indicators were related to hypertension, diabetes or cancer care. We also found few indicators related to mental health services and outcomes within these data systems. Moreover, 72% of the indicators compiled were related to volume of services delivered, 18% to health outcomes and only 10% to the quality of processes of care. While several datasets were complete or near-complete censuses of all health facilities in the country, others excluded some facility types or population groups. In some countries, RHIS did not capture services delivered through non-visit or nonconventional care during COVID-19, such as telemedicine. We propose the following recommendations to improve the analysis of administrative and RHIS data to track health system performance in times of crisis: ensure the scope of health conditions covered is aligned with the burden of disease, increase the number of indicators related to quality of care and health outcomes; incorporate data on nonconventional care such as telehealth; continue improving data quality and expand reporting from private sector facilities; move towards collecting patient-level data through electronic health records to facilitate quality-of-care assessment and equity analyses; implement more resilient and standardized health information technologies; reduce delays and loosen restrictions for researchers to access the data; complement routine data with patient-reported data; and employ mixed methods to better understand the underlying causes of service disruptions.",,pdf:https://health-policy-systems.biomedcentral.com/counter/pdf/10.1186/s12961-022-00956-6; doi:https://doi.org/10.1186/s12961-022-00956-6; html:https://europepmc.org/articles/PMC9888332; pdf:https://europepmc.org/articles/PMC9888332?pdf=render
 33934335,https://doi.org/10.1111/anae.15466,Long-term trends in critical care admissions in Wales*.,"Pugh RJ, Bailey R, Szakmany T, Al Sallakh M, Hollinghurst J, Akbari A, Griffiths R, Battle C, Thorpe C, Subbe CP, Lyons RA.",,Anaesthesia,2021,2021-05-02,Y,Ageing; Frailty; Outcomes; Comorbidity; Critical Care Capacity,,,"As national populations age, demands on critical care services are expected to increase. In many healthcare settings, longitudinal trends indicate rising numbers and proportions of patients admitted to ICU who are older; elsewhere, including some parts of the UK, a decrease has raised concerns with regard to rationing according to age. Our aim was to investigate admission trends in Wales, where critical care capacity has not risen in the last decade. We used the Secure Anonymised Information Linkage Databank to identify and characterise critical care admissions in patients aged ≥ 18 years from 1 January 2008 to 31 December 2017. We categorised 85,629 ICU admissions as youngest (18-64 years), older (65-79 years) and oldest (≥ 80 years). The oldest group accounted for 15% of admissions, the older age group 39% and the youngest group 46%. Relative to the national population, the incidence of admission rates per 10,000 population in the oldest group decreased significantly over the study period from 91.5/10,000 in 2008 to 77.5/10,000 (a relative decrease of 15%), and among the older group from 89.2/10,000 in 2008 to 75.3/10,000 in 2017 (a relative decrease of 16%). We observed significant decreases in admissions with high comorbidity (modified Charlson comorbidity index); increases in the proportion of older patients admitted who were considered 'fit' rather than frail (electronic frailty index); and decreases in admissions with a medical diagnosis. In contrast to other healthcare settings, capacity constraints and surgical imperatives appear to have contributed to a relative exclusion of older patients presenting with acute medical illness.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa56830/Download/56830__24941__ed34d96421c74ecca52d5a3aaf9afc85.pdf; doi:https://doi.org/10.1111/anae.15466; html:https://europepmc.org/articles/PMC10138728; pdf:https://europepmc.org/articles/PMC10138728?pdf=render
 33500288,https://doi.org/10.1136/bmjopen-2020-042945,Hospital bed capacity and usage across secondary healthcare providers in England during the first wave of the COVID-19 pandemic: a descriptive analysis.,"Mateen BA, Wilde H, Dennis JM, Duncan A, Thomas N, McGovern A, Denaxas S, Keeling M, Vollmer S.",,BMJ open,2021,2021-01-26,Y,Public Health; Health Policy; Intensive & Critical Care; Covid-19,,,"<h4>Objective</h4>In this study, we describe the pattern of bed occupancy across England during the peak of the first wave of the COVID-19 pandemic.<h4>Design</h4>Descriptive survey.<h4>Setting</h4>All non-specialist secondary care providers in England from 27 March27to 5 June 2020.<h4>Participants</h4>Acute (non-specialist) trusts with a type 1 (ie, 24 hours/day, consultant-led) accident and emergency department (n=125), Nightingale (field) hospitals (n=7) and independent sector secondary care providers (n=195).<h4>Main outcome measures</h4>Two thresholds for 'safe occupancy' were used: 85% as per the Royal College of Emergency Medicine and 92% as per NHS Improvement.<h4>Results</h4>At peak availability, there were 2711 additional beds compatible with mechanical ventilation across England, reflecting a 53% increase in capacity, and occupancy never exceeded 62%. A consequence of the repurposing of beds meant that at the trough there were 8.7% (8508) fewer general and acute beds across England, but occupancy never exceeded 72%. The closest to full occupancy of general and acute bed (surge) capacity that any trust in England reached was 99.8% . For beds compatible with mechanical ventilation there were 326 trust-days (3.7%) spent above 85% of surge capacity and 154 trust-days (1.8%) spent above 92%. 23 trusts spent a cumulative 81 days at 100% saturation of their surge ventilator bed capacity (median number of days per trust=1, range: 1-17). However, only three sustainability and transformation partnerships (aggregates of geographically co-located trusts) reached 100% saturation of their mechanical ventilation beds.<h4>Conclusions</h4>Throughout the first wave of the pandemic, an adequate supply of all bed types existed at a national level. However, due to an unequal distribution of bed utilisation, many trusts spent a significant period operating above 'safe-occupancy' thresholds despite substantial capacity in geographically co-located trusts, a key operational issue to address in preparing for future waves.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/1/e042945.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-042945; html:https://europepmc.org/articles/PMC7843315; pdf:https://europepmc.org/articles/PMC7843315?pdf=render
 36472984,https://doi.org/10.1371/journal.pmed.1004124,Association between antidementia medication use and mortality in people diagnosed with dementia with Lewy bodies in the UK: A retrospective cohort study.,"Chen S, Price AC, Cardinal RN, Moylett S, Kershenbaum AD, Fitzgerald J, Mueller C, Stewart R, O'Brien JT.",,PLoS medicine,2022,2022-12-06,Y,,,,"<h4>Background</h4>Dementia with Lewy bodies (DLBs) is a common cause of dementia but has higher mortality than Alzheimer's disease (AD). The reasons for this are unclear, but antidementia drugs (including acetylcholinesterase inhibitors [AChEIs] and memantine) symptomatically benefit people with DLB and might improve outcomes. We investigated whether AChEIs and/or memantine were associated with reduced hospital admissions and mortality.<h4>Methods and findings</h4>We performed a retrospective cohort study of those diagnosed with DLB between 1 January 2005 and 31 December 2019, using data from electronic clinical records of secondary care mental health services in Cambridgeshire and Peterborough NHS Foundation Trust (CPFT), United Kingdom (catchment area population approximately 0.86 million), as well as linked records from national Hospital Episode Statistics (HES) data. Eligible patients were those who started AChEIs or memantine within 3 months of their diagnosis (cases) and those who never used AChEIs or memantine (controls). Outcomes included admission, length of stay, and mortality. Cox proportional hazard and linear regression models were used. Of 592 patients with DLB, 219 never took AChEIs or memantine, 100 took AChEIs only, and 273 took both AChEIs and memantine. The cohorts were followed up for an average of 896 days, 981 days, and 1,004 days, respectively. There were no significant differences in the cohorts' baseline characteristics, except for socioeconomic status that was lower in patients who never took AChEIs or memantine (χ2 = 23.34, P = 0.003). After controlling for confounding by sociodemographic factors (age, sex, marital status, ethnicity, socioeconomic status), antipsychotic use, antidepressant use, cognitive status, physical comorbidity, anticholinergic burden, and global health performance, compared with patients who never took AChEIs or memantine, patients taking AChEIs only or taking both had a significantly lower risk of death (adjusted hazard ratio (HR) = 0.67, 95% CI = 0.48 to 0.93, p = 0.02; adjusted HR = 0.64, 95% CI = 0.50 to 0.83, P = 0.001, respectively). Those taking AChEIs or both AChEIs and memantine had significantly shorter periods of unplanned hospital admission for physical disorders (adjusted coefficient -13.48, 95% CI = [-26.87, -0.09], P = 0.049; adjusted coefficient -14.21, 95% CI = [-24.58, -3.85], P = 0.007, respectively), but no difference in length of stay for planned admissions for physical disorders, or for admissions for mental health disorders. No significant additional associations of memantine on admission, length of stay, and mortality were found (all P > 0.05). The main limitation was that this was a naturalistic study and possible confounds cannot be fully controlled, and there may be selection bias resulting from nonrandom prescription behaviour in clinical practice. However, we mimicked the intention-to-treat design of clinical trials, and the majority of baseline characters were balanced between cohorts. In addition, our series of sensitivity analyses confirmed the consistency of our results.<h4>Conclusion</h4>In this study, we observed that use of AChEIs with or without memantine in DLB was associated with shorter duration of hospital admissions and decreased risk of mortality. Although our study was naturalistic, it supports further the use of AChEIs in DLB.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004124&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004124; html:https://europepmc.org/articles/PMC9725132; pdf:https://europepmc.org/articles/PMC9725132?pdf=render
-35471746,https://doi.org/10.1186/s13613-022-01011-x,The resilient intensive care unit.,"Salluh JIF, Kurtz P, Bastos LSL, Quintairos A, Zampieri FG, Bozza FA.",,Annals of intensive care,2022,2022-04-26,Y,,,,"<h4>Background</h4>The COVID-19 pandemic tested the capacity of intensive care units (ICU) to respond to a crisis and demonstrated their fragility. Unsurprisingly, higher than usual mortality rates, lengths of stay (LOS), and ICU-acquired complications occurred during the pandemic. However, worse outcomes were not universal nor constant across ICUs and significant variation in outcomes was reported, demonstrating that some ICUs could adequately manage the surge of COVID-19.<h4>Methods</h4>In the present editorial, we discuss the concept of a resilient Intensive Care Unit, including which metrics can be used to address the capacity to respond, sustain results and incorporate new practices that lead to improvement.<h4>Results</h4>We believe that a resiliency analysis adds a component of preparedness to the usual ICU performance evaluation and outcomes metrics to be used during the crisis and in regular times.<h4>Conclusions</h4>The COVID-19 pandemic demonstrated the need for a resilient health system. Although this concept has been discussed for health systems, it was not tested in intensive care. Future studies should evaluate this concept to improve ICU organization for standard and pandemic times.",,pdf:https://annalsofintensivecare.springeropen.com/track/pdf/10.1186/s13613-022-01011-x; doi:https://doi.org/10.1186/s13613-022-01011-x; html:https://europepmc.org/articles/PMC9038989; pdf:https://europepmc.org/articles/PMC9038989?pdf=render
 33628949,https://doi.org/10.12688/wellcomeopenres.16020.2,The Avon Longitudinal Study of Parents and Children - A resource for COVID-19 research: Questionnaire data capture April-May 2020.,"Northstone K, Howarth S, Smith D, Bowring C, Wells N, Timpson NJ.",,Wellcome open research,2020,2020-11-20,Y,Coronavirus; Mental health; Alspac; Birth Cohort Study; Online Questionnaire; Children Of The 90S; Covid-19,,,"The Avon Longitudinal Study of Parents and Children (ALSPAC) is a prospective population-based cohort study which recruited pregnant women in 1990-1992. The resource provides an informative and efficient setting for collecting data on the current coronavirus 2019 (COVID-19) pandemic. In early March 2020, a questionnaire was developed in collaboration with other longitudinal population studies to ensure cross-cohort comparability. It targeted retrospective and current COVID-19 infection information (exposure assessment, symptom tracking and reported clinical outcomes) and the impact of both disease and mitigating measures implemented to manage the COVID-19 crisis more broadly. Data were collected on symptoms of COVID-19 and seasonal flu, travel prior to the pandemic, mental health and social, behavioural and lifestyle factors. The online questionnaire was deployed across parent (G0) and offspring (G1) generations between 9 <sup>th</sup> April and 15 <sup>th</sup> May 2020. 6807 participants completed the questionnaire (2706 original mothers, 1014 original fathers/partners, 2973 offspring (mean age ~28 years) and 114 offspring partners). Eight (0.01%) participants (4 G0 and 4 G1) reported a positive test for COVID-19, 77 (1.13%; 28 G0 and 49 G1) reported that they had been told by a doctor they likely had COVID-19 and 865 (12.7%; 426 G0 and 439 G1) suspected that they have had COVID-19.  Using algorithmically defined cases, we estimate that the predicted proportion of COVID-19 cases ranged from 1.03% - 4.19% depending on timing during the period of reporting (October 2019-March 2020). Data from this first questionnaire will be complemented with at least two more follow-up questionnaires, linkage to health records and results of biological testing as they become available. Data has been released as: 1) a standard dataset containing <i>all</i> participant responses with key sociodemographic factors and 2) as a composite release coordinating data from the existing resource, thus enabling bespoke research across all areas supported by the study.",,doi:https://doi.org/10.12688/wellcomeopenres.16020.2; html:https://europepmc.org/articles/PMC7883314; pdf:https://europepmc.org/articles/PMC7883314?pdf=render
+35471746,https://doi.org/10.1186/s13613-022-01011-x,The resilient intensive care unit.,"Salluh JIF, Kurtz P, Bastos LSL, Quintairos A, Zampieri FG, Bozza FA.",,Annals of intensive care,2022,2022-04-26,Y,,,,"<h4>Background</h4>The COVID-19 pandemic tested the capacity of intensive care units (ICU) to respond to a crisis and demonstrated their fragility. Unsurprisingly, higher than usual mortality rates, lengths of stay (LOS), and ICU-acquired complications occurred during the pandemic. However, worse outcomes were not universal nor constant across ICUs and significant variation in outcomes was reported, demonstrating that some ICUs could adequately manage the surge of COVID-19.<h4>Methods</h4>In the present editorial, we discuss the concept of a resilient Intensive Care Unit, including which metrics can be used to address the capacity to respond, sustain results and incorporate new practices that lead to improvement.<h4>Results</h4>We believe that a resiliency analysis adds a component of preparedness to the usual ICU performance evaluation and outcomes metrics to be used during the crisis and in regular times.<h4>Conclusions</h4>The COVID-19 pandemic demonstrated the need for a resilient health system. Although this concept has been discussed for health systems, it was not tested in intensive care. Future studies should evaluate this concept to improve ICU organization for standard and pandemic times.",,pdf:https://annalsofintensivecare.springeropen.com/track/pdf/10.1186/s13613-022-01011-x; doi:https://doi.org/10.1186/s13613-022-01011-x; html:https://europepmc.org/articles/PMC9038989; pdf:https://europepmc.org/articles/PMC9038989?pdf=render
 36084076,https://doi.org/10.1371/journal.pone.0273687,"""The vaccination is positive; I don't think it's the panacea"": A qualitative study on COVID-19 vaccine attitudes among ethnically diverse healthcare workers in the United Kingdom.","Gogoi M, Wobi F, Qureshi I, Al-Oraibi A, Hassan O, Chaloner J, Nellums LB, Pareek M, UK-REACH Collaborative Group.",,PloS one,2022,2022-09-09,Y,,,,"<h4>Background</h4>Globally, healthcare workers (HCWs) were prioritised for receiving vaccinations against the coronavirus disease-2019 (COVID-19). Previous research has shown disparities in COVID-19 vaccination uptake among HCWs based on ethnicity, job role, sex, age, and deprivation. However, vaccine attitudes underpinning these variations and factors influencing these attitudes are yet to be fully explored.<h4>Methods</h4>We conducted a qualitative study with 164 HCWs from different ethnicities, sexes, job roles, migration statuses, and regions in the United Kingdom (UK). Interviews and focus groups were conducted online or telephonically, and recorded with participants' permission. Recordings were transcribed and a two-pronged analytical approach was adopted: content analysis for categorising vaccine attitudes and thematic analysis for identifying factors influencing vaccine attitudes.<h4>Findings</h4>We identified four different COVID-19 vaccine attitudes among HCWs: Active Acceptance, Passive Acceptance, Passive Decline, and Active Decline. Content analysis of the transcripts showed that HCWs from ethnic minority communities and female HCWs were more likely to either decline (actively/passively) or passively accept vaccination-reflecting hesitancy. Factors influencing these attitudes included: trust; risk perception; social influences; access and equity; considerations about the future.<h4>Interpretation</h4>Our data show that attitudes towards COVID-19 vaccine are diverse, and elements of hesitancy may persist even after uptake. This has implications for the sustainability of the COVID-19 vaccine programme, particularly as new components (for example boosters) are being offered. We also found that vaccine attitudes differed by ethnicity, sex and job role, which calls for an intersectional and dynamic approach for improving vaccine uptake among HCWs. Trust, risk perception, social influences, access and equity and future considerations all influence vaccine attitudes and have a bearing on HCWs' decision about accepting or declining the COVID-19 vaccine. Based on our findings, we recommend building trust, addressing structural inequities and, designing inclusive and accessible information to address hesitancy.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0273687&type=printable; doi:https://doi.org/10.1371/journal.pone.0273687; html:https://europepmc.org/articles/PMC9462779; pdf:https://europepmc.org/articles/PMC9462779?pdf=render
 35726508,https://doi.org/10.1177/10398562221103117,Improving quantification of anticholinergic burden using the Anticholinergic Effect on Cognition Scale - a healthcare improvement study in a geriatric ward setting.,"Balasundaram B, Ang WST, Stewart R, Bishara D, Ooi CH, Li F, Akram F, Eu Kwek AB.",,Australasian psychiatry : bulletin of Royal Australian and New Zealand College of Psychiatrists,2022,2022-06-21,Y,Dementia; Delirium; Anticholinergic drugs; Anticholinergic Burden Scales; Anticholinergic Effect On Cognition Scale,,,"<h4>Objective</h4>Anticholinergic burden refers to the cumulative effects of taking multiple medications with anticholinergic effects. This study was carried out in a public hospital in Singapore, aimed to improve and achieve a 100% comprehensive identification and review of measured, anticholinergic burden in a geriatric psychiatry liaison service to geriatric wards. We evaluated changes in pre-to post-assessment anticholinergic burden scores and trainee feedback.<h4>Method</h4>Plan Do Study Act methodology was employed, and Anticholinergic Effect on Cognition scale (AEC) was implemented as the study intervention. A survey instrument evaluated trainee feedback.<h4>Results</h4>There was no measured anticholinergic burden in a baseline of 170 assessments. 75 liaison psychiatry assessments were conducted between June and November 2021 in two cycles. 94.7% of pre-assessments (at the time of assessment) and 71.1% of post-assessments (following assessment) had a record of AEC scores in clinical documentation in cycle one, improving in the second cycle to 100%, 94.6%, respectively. A high post-assessment AEC score of 3 and over reduced from 15.8% in cycle one to 5.4% in cycle two. The trainee feedback suggested an enriching educational experience.<h4>Conclusions</h4>Using the AEC scale, the findings support the feasibility of comprehensive identification and review of measured anticholinergic burden in older people with neurocognitive disorders.",,doi:https://doi.org/10.1177/10398562221103117; doi:https://doi.org/10.1177/10398562221103117; html:https://europepmc.org/articles/PMC9379386; pdf:https://europepmc.org/articles/PMC9379386?pdf=render
 35443953,https://doi.org/10.1136/bmjopen-2021-056523,Can we accurately forecast non-elective bed occupancy and admissions in the NHS? A time-series MSARIMA analysis of longitudinal data from an NHS Trust.,"Eyles E, Redaniel MT, Jones T, Prat M, Keen T.",,BMJ open,2022,2022-04-20,Y,epidemiology; Statistics & Research Methods; Health Services Administration & Management; Accident & Emergency Medicine,,,"<h4>Objectives</h4>The main objective of the study was to develop more accurate and precise short-term forecasting models for admissions and bed occupancy for an NHS Trust located in Bristol, England. Subforecasts for the medical and surgical specialties, and for different lengths of stay were realised DESIGN: Autoregressive integrated moving average models were specified on a training dataset of daily count data, then tested on a 6-week forecast horizon. Explanatory variables were included in the models: day of the week, holiday days, lagged temperature and precipitation.<h4>Setting</h4>A secondary care hospital in an NHS Trust in South West England.<h4>Participants</h4>Hospital admissions between September 2016 and March 2020, comprising 1291 days.<h4>Primary and secondary outcome measures</h4>The accuracy of the forecasts was assessed through standard measures, as well as compared with the actual data using accuracy thresholds of 10% and 20% of the mean number of admissions or occupied beds.<h4>Results</h4>The overall Autoregressive Integrated Moving Average (ARIMA) admissions forecast was compared with the Trust's forecast, and found to be more accurate, namely, being closer to the actual value 95.6% of the time. Furthermore, it was more precise than the Trust's. The subforecasts, as well as those for bed occupancy, tended to be less accurate compared with the overall forecasts. All of the explanatory variables improved the forecasts.<h4>Conclusions</h4>ARIMA models can forecast non-elective admissions in an NHS Trust accurately on a 6-week horizon, which is an improvement on the current predictive modelling in the Trust. These models can be readily applied to other contexts, improving patient flow.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/4/e056523.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-056523; html:https://europepmc.org/articles/PMC9021768; pdf:https://europepmc.org/articles/PMC9021768?pdf=render
@@ -766,18 +767,18 @@ PMC8855010,https://doi.org/,POS-894 PREDICTING PANDEMIC-RELATED EXCESS-DEATH USI
 35634533,https://doi.org/10.12688/wellcomeopenres.17360.1,A comprehensive high cost drugs dataset from the NHS in England - An OpenSAFELY-TPP Short Data Report.,"Rowan A, Bates C, Hulme W, Evans D, Davy S, A Kennedy N, Galloway J, E Mansfield K, Bechman K, Matthewman J, Yates M, Brown J, Schultze A, Norton S, J Walker A, E Morton C, Bhaskaran K, T Rentsch C, Williamson E, Croker R, Bacon S, Hickman G, Ward T, Green A, Fisher L, J Curtis H, Tazare J, M Eggo R, Inglesby P, Cockburn J, I McDonald H, Mathur R, Ys Wong A, Forbes H, Parry J, Hester F, Harper S, J Douglas I, Smeeth L, A Tomlinson L, W Lees C, Evans S, Smith C, M Langan S, Mehkar A, MacKenna B, Goldacre B.",,Wellcome open research,2021,2021-12-22,Y,Medications; Biosimilars; Healthcare Administration; Opensafely,,,"<b>Background:</b> At the outset of the COVID-19 pandemic, there was no routine comprehensive hospital medicines data from the UK available to researchers. These records can be important for many analyses including the effect of certain medicines on the risk of severe COVID-19 outcomes. With the approval of NHS England, we set out to obtain data on one specific group of medicines, ""high-cost drugs"" (HCD) which are typically specialist medicines for the management of long-term conditions, prescribed by hospitals to patients. Additionally, we aimed to make these data available to all approved researchers in OpenSAFELY-TPP. This report is intended to support all studies carried out in OpenSAFELY-TPP, and those elsewhere, working with this dataset or similar data. <b>Methods:</b> Working with the North East Commissioning Support Unit and NHS Digital, we arranged for collation of a single national HCD dataset to help inform responses to the COVID-19 pandemic. The dataset was developed from payment submissions from hospitals to commissioners. <b>Results:</b> In the financial year (FY) 2018/19 there were 2.8 million submissions for 1.1 million unique patient IDs recorded in the HCD. The average number of submissions per patient over the year was 2.6. In FY 2019/20 there were 4.0 million submissions for 1.3 million unique patient IDs. The average number of submissions per patient over the year was 3.1. Of the 21 variables in the dataset, three are now available for analysis in OpenSafely-TPP: Financial year and month of drug being dispensed; drug name; and a description of the drug dispensed. <b>Conclusions:</b> We have described the process for sourcing a national HCD dataset, making these data available for COVID-19-related analysis through OpenSAFELY-TPP and provided information on the variables included in the dataset, data coverage and an initial descriptive analysis.",,doi:https://doi.org/10.12688/wellcomeopenres.17360.1; html:https://europepmc.org/articles/PMC9120928; pdf:https://europepmc.org/articles/PMC9120928?pdf=render
 36036238,https://doi.org/10.1002/clt2.12180,Mixed-methods evaluation of a nurse-led allergy clinic model in primary care: Feasibility trial.,"Hammersley V, Kelman M, Morrice L, Kendall M, Mukerjhee M, Harley S, Schwarze J, Sheikh A.",,Clinical and translational allergy,2022,2022-08-01,Y,Allergy; Quality of life; Primary Care,,,"<h4>Introduction</h4>It is now widely acknowledged that there are serious shortcomings in allergy care provision for patients seen in primary care. We sought to assess the feasibility of delivering and evaluating a new nurse-led allergy service in primary care, measured by recruitment, retention and estimates of the potential impact of the intervention on disease-specific quality of life.<h4>Methods</h4>Mixed-methods evaluation of a nurse-led primary care-based allergy clinic in Edinburgh, UK undertaken during the period 2017-2021 with a focus on suspected food allergy and atopic eczema in young children, allergic rhinitis in children and young people, and suspected anaphylaxis in adults. Prior to March 2020, patients were seen face-to-face (Phase 1). Due to COVID-19 pandemic restrictions, recruitment was halted between March-August 2020, and a remote clinic was restarted in September 2020 (Phase 2). Disease-specific quality of life was measured at baseline and 6-12 weeks post intervention using validated instruments. Quantitative data were descriptively analysed. We undertook interviews with 16 carers/patients and nine healthcare professionals, which were thematically analysed.<h4>Results</h4>During Phase 1, 426/506 (84%) referred patients met the eligibility criteria; 40/46 (87%) of Phase 2 referrals were eligible. Males and females were recruited in approximately equal numbers. The majority (83%) of referrals were for possible food allergy or anaphylaxis. Complete data were available for 338/426 (79%) patients seen in Phase 1 and 30/40 (75%) in Phase 2. Compared with baseline assessments, there were improvements in disease-specific quality of life for most categories of patients. Patients/carers and healthcare professionals reported high levels of satisfaction, this being reinforced by the qualitative interviews in which convenience and speed of access to expert opinion, the quality of the consultation, and patient/care empowerment were particularly emphasised.<h4>Conclusion</h4>This large feasibility trial has demonstrated that it is possible to recruit, deliver and retain individuals into a nurse-led allergy clinic with both face-to-face and remote consultations. Our data indicate that the intervention was considered acceptable to patients/carers and healthcare professionals. The before-after data of disease-specific quality of life suggest that the intervention may prove effective, but this now needs to be confirmed through a formal randomised controlled trial.<h4>Trial registration</h4>ClinicalTrials.gov reference NCT03826953.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9362986; doi:https://doi.org/10.1002/clt2.12180; html:https://europepmc.org/articles/PMC9362986; pdf:https://europepmc.org/articles/PMC9362986?pdf=render
 33664493,https://doi.org/10.1038/s41591-021-01275-z,The need for ethical guidance for the use of patient-reported outcomes in research and clinical practice.,"Cruz Rivera S, Mercieca-Bebber R, Aiyegbusi OL, Scott J, Hunn A, Fernandez C, Ives J, Ells C, Price G, Draper H, Calvert MJ.",,Nature medicine,2021,2021-04-01,N,,,,,,pdf:https://www.nature.com/articles/s41591-021-01275-z.pdf; doi:https://doi.org/10.1038/s41591-021-01275-z
-34230034,https://doi.org/10.1136/bmjresp-2021-000967,Increase in recruitment upon integration of trial into a clinical care pathway: an observational study.,"Yip KP, Gompertz S, Snelson C, Willson J, Madathil S, Huq SS, Rauf F, Salmon N, Tengende J, Tracey J, Cooper B, Filby K, Ball S, Parekh D, Dosanjh DPS.",,BMJ open respiratory research,2021,2021-07-01,Y,Covid-19,,,"<h4>Introduction</h4>Many respiratory clinical trials fail to reach their recruitment target and this problem exacerbates existing funding issues. Integration of the clinical trial recruitment process into a clinical care pathway (CCP) may represent an effective way to significantly increase recruitment numbers.<h4>Methods</h4>A respiratory support unit and a CCP for escalation of patients with severe COVID-19 were established on 11 January 2021. The recruitment process for the Randomised Evaluation of COVID-19 Therapy-Respiratory Support trial was integrated into the CCP on the same date. Recruitment data for the trial were collected before and after integration into the CCP.<h4>Results</h4>On integration of the recruitment process into a CCP, there was a significant increase in recruitment numbers. Fifty patients were recruited over 266 days before this process occurred whereas 108 patients were recruited over 49 days after this process. There was a statistically significant increase in both the proportion of recruited patients relative to the number of COVID-19 hospital admissions (change from 2.8% to 9.1%, p<0.0001) and intensive therapy unit admissions (change from 17.8% to 50.2%, p<0.001) over the same period, showing that this increase in recruitment was independent of COVID-19 prevalence.<h4>Discussion</h4>Integrating the trial recruitment process into a CCP can significantly boost recruitment numbers. This represents an innovative model that can be used to maximise recruitment without impacting on the financial and labour costs associated with the running of a respiratory clinical trial.",,pdf:https://bmjopenrespres.bmj.com/content/bmjresp/8/1/e000967.full.pdf; doi:https://doi.org/10.1136/bmjresp-2021-000967; html:https://europepmc.org/articles/PMC8261886; pdf:https://europepmc.org/articles/PMC8261886?pdf=render
 37143610,https://doi.org/10.1093/ehjopen/oead037,"SAIL study of stroke, systemic embolism and bleeding outcomes with warfarin anticoagulation in non-valvular atrial fibrillation (S<sup>4</sup>-BOW-AF).","Harris DE, Torabi F, Mallory D, Akbari A, Thayer D, Wang T, Grundy S, Gravenor M, Alikhan R, Lister S, Halcox J.",,European heart journal open,2023,2023-04-13,Y,Bleeding; Atrial fibrillation; Stroke; Warfarin; Pharmacotherapy; Inr Control,,,"<h4>Aims</h4>In patients with non-valvular atrial fibrillation (NVAF) prescribed warfarin, the association between guideline defined international normalised ratio (INR) control and adverse outcomes in unknown. We aimed to (i) determine stroke and systemic embolism (SSE) and bleeding events in NVAF patients prescribed warfarin; and (ii) estimate the increased risk of these adverse events associated with poor INR control in this population.<h4>Methods and results</h4>Individual-level population-scale linked patient data were used to investigate the association between INR control and both SSE and bleeding events using (i) the National Institute for Health and Care Excellence (NICE) criteria of poor INR control [time in therapeutic range (TTR) <65%, two INRs <1.5 or two INRs >5 in a 6-month period or any INR >8]. A total of 35 891 patients were included for SSE and 35 035 for bleeding outcome analyses. Mean CHA<sub>2</sub>DS<sub>2</sub>-VASc score was 3.5 (SD = 1.7), and the mean follow up was 4.3 years for both analyses. Mean TTR was 71.9%, with 34% of time spent in poor INR control according to NICE criteria.SSE and bleeding event rates (per 100 patient years) were 1.01 (95%CI 0.95-1.08) and 3.4 (95%CI 3.3-3.5), respectively, during adequate INR control, rising to 1.82 (95%CI 1.70-1.94) and 4.8 (95% CI 4.6-5.0) during poor INR control.Poor INR control was independently associated with increased risk of both SSE [HR = 1.69 (95%CI = 1.54-1.86), <i>P</i> < 0.001] and bleeding [HR = 1.40 (95%CI 1.33-1.48), <i>P</i> < 0.001] in Cox-multivariable models.<h4>Conclusion</h4>Guideline-defined poor INR control is associated with significantly higher SSE and bleeding event rates, independent of recognised risk factors for stroke or bleeding.",,pdf:https://academic.oup.com/ehjopen/advance-article-pdf/doi/10.1093/ehjopen/oead037/49878718/oead037.pdf; doi:https://doi.org/10.1093/ehjopen/oead037; html:https://europepmc.org/articles/PMC10153743; pdf:https://europepmc.org/articles/PMC10153743?pdf=render
-37321240,https://doi.org/10.1016/s2215-0366(23)00113-x,Mental health in Europe during the COVID-19 pandemic: a systematic review.,"Ahmed N, Barnett P, Greenburgh A, Pemovska T, Stefanidou T, Lyons N, Ikhtabi S, Talwar S, Francis ER, Harris SM, Shah P, Machin K, Jeffreys S, Mitchell L, Lynch C, Foye U, Schlief M, Appleton R, Saunders KRK, Baldwin H, Allan SM, Sheridan-Rains L, Kharboutly O, Kular A, Goldblatt P, Stewart R, Kirkbride JB, Lloyd-Evans B, Johnson S.",,The lancet. Psychiatry,2023,2023-06-12,Y,,,,"The COVID-19 pandemic caused immediate and far-reaching disruption to society, the economy, and health-care services. We synthesised evidence on the effect of the pandemic on mental health and mental health care in high-income European countries. We included 177 longitudinal and repeated cross-sectional studies comparing prevalence or incidence of mental health problems, mental health symptom severity in people with pre-existing mental health conditions, or mental health service use before versus during the pandemic, or between different timepoints of the pandemic. We found that epidemiological studies reported higher prevalence of some mental health problems during the pandemic compared with before it, but that in most cases this increase reduced over time. Conversely, studies of health records showed reduced incidence of new diagnoses at the start of the pandemic, which further declined during 2020. Mental health service use also declined at the onset of the pandemic but increased later in 2020 and through 2021, although rates of use did not return to pre-pandemic levels for some services. We found mixed patterns of effects of the pandemic on mental health and social outcome for adults already living with mental health conditions.",,pdf:http://www.thelancet.com/article/S221503662300113X/pdf; doi:https://doi.org/10.1016/S2215-0366(23)00113-X; html:https://europepmc.org/articles/PMC10259832; pdf:https://europepmc.org/articles/PMC10259832?pdf=render
+34230034,https://doi.org/10.1136/bmjresp-2021-000967,Increase in recruitment upon integration of trial into a clinical care pathway: an observational study.,"Yip KP, Gompertz S, Snelson C, Willson J, Madathil S, Huq SS, Rauf F, Salmon N, Tengende J, Tracey J, Cooper B, Filby K, Ball S, Parekh D, Dosanjh DPS.",,BMJ open respiratory research,2021,2021-07-01,Y,Covid-19,,,"<h4>Introduction</h4>Many respiratory clinical trials fail to reach their recruitment target and this problem exacerbates existing funding issues. Integration of the clinical trial recruitment process into a clinical care pathway (CCP) may represent an effective way to significantly increase recruitment numbers.<h4>Methods</h4>A respiratory support unit and a CCP for escalation of patients with severe COVID-19 were established on 11 January 2021. The recruitment process for the Randomised Evaluation of COVID-19 Therapy-Respiratory Support trial was integrated into the CCP on the same date. Recruitment data for the trial were collected before and after integration into the CCP.<h4>Results</h4>On integration of the recruitment process into a CCP, there was a significant increase in recruitment numbers. Fifty patients were recruited over 266 days before this process occurred whereas 108 patients were recruited over 49 days after this process. There was a statistically significant increase in both the proportion of recruited patients relative to the number of COVID-19 hospital admissions (change from 2.8% to 9.1%, p<0.0001) and intensive therapy unit admissions (change from 17.8% to 50.2%, p<0.001) over the same period, showing that this increase in recruitment was independent of COVID-19 prevalence.<h4>Discussion</h4>Integrating the trial recruitment process into a CCP can significantly boost recruitment numbers. This represents an innovative model that can be used to maximise recruitment without impacting on the financial and labour costs associated with the running of a respiratory clinical trial.",,pdf:https://bmjopenrespres.bmj.com/content/bmjresp/8/1/e000967.full.pdf; doi:https://doi.org/10.1136/bmjresp-2021-000967; html:https://europepmc.org/articles/PMC8261886; pdf:https://europepmc.org/articles/PMC8261886?pdf=render
 34458913,https://doi.org/10.1093/ije/dyab172,Potential test-negative design study bias in outbreak settings: application to Ebola vaccination in Democratic Republic of Congo.,"Pearson CAB, Edmunds WJ, Hladish TJ, Eggo RM.",,International journal of epidemiology,2022,2022-02-01,Y,Mathematical Modelling; Ebola; Outbreak Response; Drc; Test-negative Design,,,"<h4>Background</h4>Infectious disease outbreaks present unique challenges to study designs for vaccine evaluation. Test-negative design (TND) studies have previously been used to estimate vaccine effectiveness and have been proposed for Ebola virus disease (EVD) vaccines. However, there are key differences in how cases and controls are recruited during outbreaks and pandemics of novel pathogens, whcih have implications for the reliability of effectiveness estimates using this design.<h4>Methods</h4>We use a modelling approach to quantify TND bias for a prophylactic vaccine under varying study and epidemiological scenarios. Our model accounts for heterogeneity in vaccine distribution and for two potential routes to testing and recruitment into the study: self-reporting and contact-tracing. We derive conventional and hybrid TND estimators for this model and suggest ways to translate public health response data into the parameters of the model.<h4>Results</h4>Using a conventional TND study, our model finds biases in vaccine effectiveness estimates. Bias arises due to differential recruitment from self-reporting and contact-tracing, and due to clustering of vaccination. We estimate the degree of bias when recruitment route is not available, and propose a study design to eliminate the bias if recruitment route is recorded.<h4>Conclusions</h4>Hybrid TND studies can resolve the design bias with conventional TND studies applied to outbreak and pandemic response testing data, if those efforts collect individuals' routes to testing. Without route to testing, other epidemiological data will be required to estimate the magnitude of potential bias in a conventional TND study. Since these studies may need to be conducted retrospectively, public health responses should obtain these data, and generic protocols for outbreak and pandemic response studies should emphasize the need to record routes to testing.",,pdf:https://academic.oup.com/ije/article-pdf/51/1/265/42555506/dyab172.pdf; doi:https://doi.org/10.1093/ije/dyab172; html:https://europepmc.org/articles/PMC8855996; pdf:https://europepmc.org/articles/PMC8855996?pdf=render
+37321240,https://doi.org/10.1016/s2215-0366(23)00113-x,Mental health in Europe during the COVID-19 pandemic: a systematic review.,"Ahmed N, Barnett P, Greenburgh A, Pemovska T, Stefanidou T, Lyons N, Ikhtabi S, Talwar S, Francis ER, Harris SM, Shah P, Machin K, Jeffreys S, Mitchell L, Lynch C, Foye U, Schlief M, Appleton R, Saunders KRK, Baldwin H, Allan SM, Sheridan-Rains L, Kharboutly O, Kular A, Goldblatt P, Stewart R, Kirkbride JB, Lloyd-Evans B, Johnson S.",,The lancet. Psychiatry,2023,2023-06-12,Y,,,,"The COVID-19 pandemic caused immediate and far-reaching disruption to society, the economy, and health-care services. We synthesised evidence on the effect of the pandemic on mental health and mental health care in high-income European countries. We included 177 longitudinal and repeated cross-sectional studies comparing prevalence or incidence of mental health problems, mental health symptom severity in people with pre-existing mental health conditions, or mental health service use before versus during the pandemic, or between different timepoints of the pandemic. We found that epidemiological studies reported higher prevalence of some mental health problems during the pandemic compared with before it, but that in most cases this increase reduced over time. Conversely, studies of health records showed reduced incidence of new diagnoses at the start of the pandemic, which further declined during 2020. Mental health service use also declined at the onset of the pandemic but increased later in 2020 and through 2021, although rates of use did not return to pre-pandemic levels for some services. We found mixed patterns of effects of the pandemic on mental health and social outcome for adults already living with mental health conditions.",,pdf:http://www.thelancet.com/article/S221503662300113X/pdf; doi:https://doi.org/10.1016/S2215-0366(23)00113-X; html:https://europepmc.org/articles/PMC10259832; pdf:https://europepmc.org/articles/PMC10259832?pdf=render
 34227657,https://doi.org/10.1093/bjs/znab183,Machine learning risk prediction of mortality for patients undergoing surgery with perioperative SARS-CoV-2: the COVIDSurg mortality score.,"COVIDSurg Collaborative
 .",,The British journal of surgery,2021,2021-11-01,Y,,,,,,pdf:https://academic.oup.com/bjs/article-pdf/108/11/1274/47371055/znab183.pdf; doi:https://doi.org/10.1093/bjs/znab183; html:https://europepmc.org/articles/PMC8344569; pdf:https://europepmc.org/articles/PMC8344569?pdf=render
 37159441,https://doi.org/10.1371/journal.pdig.0000218,Hospital-wide natural language processing summarising the health data of 1 million patients.,"Bean DM, Kraljevic Z, Shek A, Teo J, Dobson RJB.",,PLOS digital health,2023,2023-05-09,Y,,,,"Electronic health records (EHRs) represent a major repository of real world clinical trajectories, interventions and outcomes. While modern enterprise EHR's try to capture data in structured standardised formats, a significant bulk of the available information captured in the EHR is still recorded only in unstructured text format and can only be transformed into structured codes by manual processes. Recently, Natural Language Processing (NLP) algorithms have reached a level of performance suitable for large scale and accurate information extraction from clinical text. Here we describe the application of open-source named-entity-recognition and linkage (NER+L) methods (CogStack, MedCAT) to the entire text content of a large UK hospital trust (King's College Hospital, London). The resulting dataset contains 157M SNOMED concepts generated from 9.5M documents for 1.07M patients over a period of 9 years. We present a summary of prevalence and disease onset as well as a patient embedding that captures major comorbidity patterns at scale. NLP has the potential to transform the health data lifecycle, through large-scale automation of a traditionally manual task.",,doi:https://doi.org/10.1371/journal.pdig.0000218; doi:https://doi.org/10.1371/journal.pdig.0000218; html:https://europepmc.org/articles/PMC10168555; pdf:https://europepmc.org/articles/PMC10168555?pdf=render
-35308999,https://doi.org/,Axes of Prognosis: Identifying Subtypes of COVID-19 Outcomes.,"Whitfield E, Coffey C, Zhang H, Shi T, Wu X, Li Q, Wu H.",,AMIA ... Annual Symposium proceedings. AMIA Symposium,2021,2021-01-01,N,,,,"COVID-19 is a disease with vast impact, yet much remains unclear about patient outcomes. Most approaches to risk prediction of COVID-19 focus on binary or tertiary severity outcomes, despite the heterogeneity of the disease. In this work, we identify heterogeneous subtypes of COVID-19 outcomes by considering 'axes' of prognosis. We propose two innovative clustering approaches - 'Layered Axes' and 'Prognosis Space' - to apply on patients' outcome data. We then show how these clusters can help predict a patient's deterioration pathway on their hospital admission, using random forest classification. We illustrate this methodology on a cohort from Wuhan in early 2020. We discover interesting subgroups of poor prognosis, particularly within respiratory patients, and predict respiratory subgroup membership with high accuracy. This work could assist clinicians in identifying appropriate treatments at patients' hospital admission. Moreover, our method could be used to explore subtypes of 'long COVID' and other diseases with heterogeneous outcomes.",,html:https://europepmc.org/articles/PMC8861682; pdf:https://europepmc.org/articles/PMC8861682?pdf=render
 38383380,https://doi.org/10.1186/s12939-024-02114-6,Rapid systematic review on risks and outcomes of sepsis: the influence of risk factors associated with health inequalities.,"Bladon S, Ashiru-Oredope D, Cunningham N, Pate A, Martin GP, Zhong X, Gilham EL, Brown CS, Mirfenderesky M, Palin V, van Staa TP.",,International journal for equity in health,2024,2024-02-21,Y,Sepsis; Antimicrobial resistance; communities; Socioeconomic status; Ethnicity; Deprivation; Health Inequalities; Maternal,,,"<h4>Background and aims</h4>Sepsis is a serious and life-threatening condition caused by a dysregulated immune response to an infection. Recent guidance issued in the UK gave recommendations around recognition and antibiotic treatment of sepsis, but did not consider factors relating to health inequalities. The aim of this study was to summarise the literature investigating associations between health inequalities and sepsis.<h4>Methods</h4>Searches were conducted in Embase for peer-reviewed articles published since 2010 that included sepsis in combination with one of the following five areas: socioeconomic status, race/ethnicity, community factors, medical needs and pregnancy/maternity.<h4>Results</h4>Five searches identified 1,402 studies, with 50 unique studies included in the review after screening (13 sociodemographic, 14 race/ethnicity, 3 community, 3 care/medical needs and 20 pregnancy/maternity; 3 papers examined multiple health inequalities). Most of the studies were conducted in the USA (31/50), with only four studies using UK data (all pregnancy related). Socioeconomic factors associated with increased sepsis incidence included lower socioeconomic status, unemployment and lower education level, although findings were not consistent across studies. For ethnicity, mixed results were reported. Living in a medically underserved area or being resident in a nursing home increased risk of sepsis. Mortality rates after sepsis were found to be higher in people living in rural areas or in those discharged to skilled nursing facilities while associations with ethnicity were mixed. Complications during delivery, caesarean-section delivery, increased deprivation and black and other ethnic minority race were associated with post-partum sepsis.<h4>Conclusion</h4>There are clear correlations between sepsis morbidity and mortality and the presence of factors associated with health inequalities. To inform local guidance and drive public health measures, there is a need for studies conducted across more diverse setting and countries.",,doi:https://doi.org/10.1186/s12939-024-02114-6; html:https://europepmc.org/articles/PMC10882893; pdf:https://europepmc.org/articles/PMC10882893?pdf=render
+35308999,https://doi.org/,Axes of Prognosis: Identifying Subtypes of COVID-19 Outcomes.,"Whitfield E, Coffey C, Zhang H, Shi T, Wu X, Li Q, Wu H.",,AMIA ... Annual Symposium proceedings. AMIA Symposium,2021,2021-01-01,N,,,,"COVID-19 is a disease with vast impact, yet much remains unclear about patient outcomes. Most approaches to risk prediction of COVID-19 focus on binary or tertiary severity outcomes, despite the heterogeneity of the disease. In this work, we identify heterogeneous subtypes of COVID-19 outcomes by considering 'axes' of prognosis. We propose two innovative clustering approaches - 'Layered Axes' and 'Prognosis Space' - to apply on patients' outcome data. We then show how these clusters can help predict a patient's deterioration pathway on their hospital admission, using random forest classification. We illustrate this methodology on a cohort from Wuhan in early 2020. We discover interesting subgroups of poor prognosis, particularly within respiratory patients, and predict respiratory subgroup membership with high accuracy. This work could assist clinicians in identifying appropriate treatments at patients' hospital admission. Moreover, our method could be used to explore subtypes of 'long COVID' and other diseases with heterogeneous outcomes.",,html:https://europepmc.org/articles/PMC8861682; pdf:https://europepmc.org/articles/PMC8861682?pdf=render
 35802687,https://doi.org/10.1371/journal.pone.0270668,"Association between tocilizumab, sarilumab and all-cause mortality at 28 days in hospitalised patients with COVID-19: A network meta-analysis.","Godolphin PJ, Fisher DJ, Berry LR, Derde LPG, Diaz JV, Gordon AC, Lorenzi E, Marshall JC, Murthy S, Shankar-Hari M, Sterne JAC, Tierney JF, Vale CL.",,PloS one,2022,2022-07-08,Y,,,,"<h4>Background</h4>A recent prospective meta-analysis demonstrated that interleukin-6 antagonists are associated with lower all-cause mortality in hospitalised patients with COVID-19, compared with usual care or placebo. However, emerging evidence suggests that clinicians are favouring the use of tocilizumab over sarilumab. A new randomised comparison of these agents from the REMAP-CAP trial shows similar effects on in-hospital mortality. Therefore, we initiated a network meta-analysis, to estimate pairwise associations between tocilizumab, sarilumab and usual care or placebo with 28-day mortality, in COVID-19 patients receiving concomitant corticosteroids and ventilation, based on all available direct and indirect evidence.<h4>Methods</h4>Eligible trials randomised hospitalised patients with COVID-19 that compared tocilizumab or sarilumab with usual care or placebo in the prospective meta-analysis or that directly compared tocilizumab with sarilumab. Data were restricted to patients receiving corticosteroids and either non-invasive or invasive ventilation at randomisation. Pairwise associations between tocilizumab, sarilumab and usual care or placebo for all-cause mortality 28 days after randomisation were estimated using a frequentist contrast-based network meta-analysis of odds ratios (ORs), implementing multivariate fixed-effects models that assume consistency between the direct and indirect evidence.<h4>Findings</h4>One trial (REMAP-CAP) was identified that directly compared tocilizumab with sarilumab and supplied results on all-cause mortality at 28-days. This network meta-analysis was based on 898 eligible patients (278 deaths) from REMAP-CAP and 3710 eligible patients from 18 trials (1278 deaths) from the prospective meta-analysis. Summary ORs were similar for tocilizumab [0·82 [0·71-0·95, p = 0·008]] and sarilumab [0·80 [0·61-1·04, p = 0·09]] compared with usual care or placebo. The summary OR for 28-day mortality comparing tocilizumab with sarilumab was 1·03 [95%CI 0·81-1·32, p = 0·80]. The p-value for the global test of inconsistency was 0·28.<h4>Conclusions</h4>Administration of either tocilizumab or sarilumab was associated with lower 28-day all-cause mortality compared with usual care or placebo. The association is not dependent on the choice of interleukin-6 receptor antagonist.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0270668&type=printable; doi:https://doi.org/10.1371/journal.pone.0270668; html:https://europepmc.org/articles/PMC9269978; pdf:https://europepmc.org/articles/PMC9269978?pdf=render
-36777997,https://doi.org/10.1016/j.xgen.2022.100181,Leveraging global multi-ancestry meta-analysis in the study of idiopathic pulmonary fibrosis genetics.,"Partanen JJ, Häppölä P, Zhou W, Lehisto AA, Ainola M, Sutinen E, Allen RJ, Stockwell AD, Leavy OC, Oldham JM, Guillen-Guio B, Cox NJ, Hirbo JB, Schwartz DA, Fingerlin TE, Flores C, Noth I, Yaspan BL, Jenkins RG, Wain LV, Ripatti S, Pirinen M, International IPF Genetics Consortium, Global Biobank Meta-Analysis Initiative (GBMI), Laitinen T, Kaarteenaho R, Myllärniemi M, Daly MJ, Koskela JT.",,Cell genomics,2022,2022-10-12,Y,Meta-analysis; idiopathic pulmonary fibrosis; Gwas; Ancestry; Muc5b; Fine-mapping; Cross-population Analysis; Covid-19; Global Biobank Meta-Analysis Initiative,,,"The research of rare and devastating orphan diseases, such as idiopathic pulmonary fibrosis (IPF) has been limited by the rarity of the disease itself. The prognosis is poor-the prevalence of IPF is only approximately four times the incidence, limiting the recruitment of patients to trials and studies of the underlying biology. Global biobanking efforts can dramatically alter the future of IPF research. We describe a large-scale meta-analysis of IPF, with 8,492 patients and 1,355,819 population controls from 13 biobanks around the globe. Finally, we combine this meta-analysis with the largest available meta-analysis of IPF, reaching 11,160 patients and 1,364,410 population controls. We identify seven novel genome-wide significant loci, only one of which would have been identified if the analysis had been limited to European ancestry individuals. We observe notable pleiotropy across IPF susceptibility and severe COVID-19 infection and note an unexplained sex-heterogeneity effect at the strongest IPF locus <i>MUC5B</i>.",,pdf:https://helda.helsinki.fi/bitstream/10138/355828/1/Leveraging_global_multi_ancestry_meta_a...pdf; doi:https://doi.org/10.1016/j.xgen.2022.100181; html:https://europepmc.org/articles/PMC9903787; pdf:https://europepmc.org/articles/PMC9903787?pdf=render
 32685697,https://doi.org/10.12688/wellcomeopenres.15788.1,The contribution of pre-symptomatic infection to the transmission dynamics of COVID-2019.,"Liu Y, Centre for Mathematical Modelling of Infectious Diseases nCoV Working Group, Funk S, Flasche S.",,Wellcome open research,2020,2020-04-01,Y,Incubation period; Serial Interval; Covid-19; Pre-symptomatic Transmission,,,"<b>Background:</b> Pre-symptomatic transmission can be a key determinant of the effectiveness of containment and mitigation strategies for infectious diseases, particularly if interventions rely on syndromic case finding. For COVID-19, infections in the absence of apparent symptoms have been reported frequently alongside circumstantial evidence for asymptomatic or pre-symptomatic transmission. We estimated the potential contribution of pre-symptomatic cases to COVID-19 transmission. <b>Methods:</b> Using the probability for symptom onset on a given day inferred from the incubation period, we attributed the serial interval reported from Shenzen, China, into likely pre-symptomatic and symptomatic transmission. We used the serial interval derived for cases isolated more than 6 days after symptom onset as the no active case finding scenario and the unrestricted serial interval as the active case finding scenario. We reported the estimate assuming no correlation between the incubation period and the serial interval alongside a range indicating alternative assumptions of positive and negative correlation. <b>Results:</b> We estimated that 23% (range accounting for correlation: 12 - 28%) of transmissions in Shenzen may have originated from pre-symptomatic infections. Through accelerated case isolation following symptom onset, this percentage increased to 46% (21 - 46%), implying that about 35% of secondary infections among symptomatic cases have been prevented. These results were robust to using reported incubation periods and serial intervals from other settings. <b>Conclusions:</b> Pre-symptomatic transmission may be essential to consider for containment and mitigation strategies for COVID-19.",,doi:https://doi.org/10.12688/wellcomeopenres.15788.1; html:https://europepmc.org/articles/PMC7324944; pdf:https://europepmc.org/articles/PMC7324944?pdf=render
+36777997,https://doi.org/10.1016/j.xgen.2022.100181,Leveraging global multi-ancestry meta-analysis in the study of idiopathic pulmonary fibrosis genetics.,"Partanen JJ, Häppölä P, Zhou W, Lehisto AA, Ainola M, Sutinen E, Allen RJ, Stockwell AD, Leavy OC, Oldham JM, Guillen-Guio B, Cox NJ, Hirbo JB, Schwartz DA, Fingerlin TE, Flores C, Noth I, Yaspan BL, Jenkins RG, Wain LV, Ripatti S, Pirinen M, International IPF Genetics Consortium, Global Biobank Meta-Analysis Initiative (GBMI), Laitinen T, Kaarteenaho R, Myllärniemi M, Daly MJ, Koskela JT.",,Cell genomics,2022,2022-10-12,Y,Meta-analysis; idiopathic pulmonary fibrosis; Gwas; Ancestry; Muc5b; Fine-mapping; Cross-population Analysis; Covid-19; Global Biobank Meta-Analysis Initiative,,,"The research of rare and devastating orphan diseases, such as idiopathic pulmonary fibrosis (IPF) has been limited by the rarity of the disease itself. The prognosis is poor-the prevalence of IPF is only approximately four times the incidence, limiting the recruitment of patients to trials and studies of the underlying biology. Global biobanking efforts can dramatically alter the future of IPF research. We describe a large-scale meta-analysis of IPF, with 8,492 patients and 1,355,819 population controls from 13 biobanks around the globe. Finally, we combine this meta-analysis with the largest available meta-analysis of IPF, reaching 11,160 patients and 1,364,410 population controls. We identify seven novel genome-wide significant loci, only one of which would have been identified if the analysis had been limited to European ancestry individuals. We observe notable pleiotropy across IPF susceptibility and severe COVID-19 infection and note an unexplained sex-heterogeneity effect at the strongest IPF locus <i>MUC5B</i>.",,pdf:https://helda.helsinki.fi/bitstream/10138/355828/1/Leveraging_global_multi_ancestry_meta_a...pdf; doi:https://doi.org/10.1016/j.xgen.2022.100181; html:https://europepmc.org/articles/PMC9903787; pdf:https://europepmc.org/articles/PMC9903787?pdf=render
 34850874,https://doi.org/10.1093/gigascience/giab083,Erratum to: An overview of the National COVID-19 Chest Imaging Database: data quality and cohort analysis.,"Cushnan D, Bennett O, Berka R, Bertolli O, Chopra A, Dorgham S, Favaro A, Ganepola T, Halling-Brown M, Imreh G, Jacob J, Jefferson E, Lemarchand F, Schofield D, Wyatt JC, Collaborative NCCID.",,GigaScience,2021,2021-12-01,Y,,,,,,pdf:https://academic.oup.com/gigascience/article-pdf/10/12/giab083/41395049/giab083.pdf; doi:https://doi.org/10.1093/gigascience/giab083; html:https://europepmc.org/articles/PMC8634578; pdf:https://europepmc.org/articles/PMC8634578?pdf=render
 PMC8718341,https://doi.org/,"Loneliness, coping, suicidal thoughts and self-harm during the COVID-19 pandemic: a repeat cross-sectional UK population survey","John A, Lee S, Solomon S, Crepaz-Keay D, McDaid S, Morton A, Davidson G, Van Bortel T, Kousoulis A.",,BMJ open,2021,2021-01-01,Y,Mental health; Public Health; Suicide & Self-harm; Covid-19,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8718341/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8718341/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC8718341; pdf:https://europepmc.org/articles/PMC8718341?pdf=render
 34693751,https://doi.org/10.1177/14799731211053332,The diagnosis of asthma. Can physiological tests of small airways function help?,"Almeshari MA, Stockley J, Sapey E.",,Chronic respiratory disease,2021,2021-01-01,Y,Diagnosis; Asthma; Spirometry; Oscillometry; Small Airways Function,,,"Asthma is a common, chronic, and heterogeneous disease with a global impact and substantial economic costs. It is also associated with significant mortality and morbidity and the burden of undiagnosed asthma is significant. Asthma can be difficult to diagnose as there is no gold standard test and, while spirometry is central in diagnosing asthma, it may not be sufficient to confirm or exclude the diagnosis. The most commonly reported spirometric measures (forced expiratory volume in one second (FEV<sub>1</sub>) and forced vital capacity assess function in the larger airways. However, small airway dysfunction is highly prevalent in asthma and some studies suggest small airway involvement is one of the earliest disease manifestations. Moreover, there are new inhaled therapies with ultrafine particles that are specifically designed to target the small airways. Potentially, tests of small airways may more accurately diagnose early or mild asthma and assess the response to treatment than spirometry. Furthermore, some assessment techniques do not rely on forced ventilatory manoeuvres and may, therefore, be easier for certain groups to perform. This review discusses the current evidence of small airways tests in asthma and future research that may be needed to further assess their utility.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/14799731211053332; doi:https://doi.org/10.1177/14799731211053332; html:https://europepmc.org/articles/PMC8543738; pdf:https://europepmc.org/articles/PMC8543738?pdf=render
@@ -786,8 +787,8 @@ PMC8718341,https://doi.org/,"Loneliness, coping, suicidal thoughts and self-harm
 36050271,https://doi.org/10.1016/s2589-7500(22)00151-0,CODE-EHR best-practice framework for the use of structured electronic health-care records in clinical research.,"Kotecha D, Asselbergs FW, Achenbach S, Anker SD, Atar D, Baigent C, Banerjee A, Beger B, Brobert G, Casadei B, Ceccarelli C, Cowie MR, Crea F, Cronin M, Denaxas S, Derix A, Fitzsimons D, Fredriksson M, Gale CP, Gkoutos GV, Goettsch W, Hemingway H, Ingvar M, Jonas A, Kazmierski R, Løgstrup S, Lumbers RT, Lüscher TF, McGreavy P, Piña IL, Roessig L, Steinbeisser C, Sundgren M, Tyl B, Thiel GV, Bochove KV, Vardas PE, Villanueva T, Vrana M, Weber W, Weidinger F, Windecker S, Wood A, Grobbee DE, Innovative Medicines Initiative BigData@Heart Consortium, European Society of Cardiology, and CODE-EHR International Consensus Group.",,The Lancet. Digital health,2022,2022-08-29,N,,,,"Big data is important to new developments in global clinical science that aim to improve the lives of patients. Technological advances have led to the regular use of structured electronic health-care records with the potential to address key deficits in clinical evidence that could improve patient care. The COVID-19 pandemic has shown this potential in big data and related analytics but has also revealed important limitations. Data verification, data validation, data privacy, and a mandate from the public to conduct research are important challenges to effective use of routine health-care data. The European Society of Cardiology and the BigData@Heart consortium have brought together a range of international stakeholders, including representation from patients, clinicians, scientists, regulators, journal editors, and industry members. In this Review, we propose the CODE-EHR minimum standards framework to be used by researchers and clinicians to improve the design of studies and enhance transparency of study methods. The CODE-EHR framework aims to develop robust and effective utilisation of health-care data for research purposes.",,doi:https://doi.org/10.1016/s2589-7500(22)00151-0; doi:https://doi.org/10.1016/S2589-7500(22)00151-0
 35923560,https://doi.org/10.1016/j.lanepe.2022.100475,Equity of access to NHS-funded hip replacements in England and Wales: Trends from 2006 to 2016.,"Wyatt S, Bailey R, Moore P, Revell M.",,The Lancet regional health. Europe,2022,2022-07-29,Y,trends; Equity; Hip Replacements; Socio-economic Deprivation,,,"<h4>Background</h4>Elective hip replacement is a cost-effective means of improving hip function. Previous research has suggested that the supply of hip replacements in the NHS is governed by the inverse care law. We examine whether inequities in supply improved in England and Wales between 2006 and 2016.<h4>Methods</h4>We compare levels of need and supply of NHS funded hip replacements to adults aged 50+ years, across quintiles of deprivation in England and Wales between 2006 and 2016. We use data from routine health records and a large longitudinal study and adjust for age and sex using general additive negative-binomial regression.<h4>Findings</h4>The number of NHS-funded hip replacements per 100,000 population rose substantially from 272.6 and 266.7 in 2002, to 539.7 and 466.3 in 2018 in England and Wales respectively. Having adjusted for age and sex, people living in the most deprived quintile were 2.36 (95% CI, 1.69 to 3.29) times more likely to need a hip replacement in 2006 than those living in quintile 3, whereas those living in the least deprived quintile were 0.45 (95% CI, 0.39 to 0.69) as likely. Despite this, people living in the most deprived quintile were 0.81 (95% CI, 0.78 to 0.83) times as likely in England and 0.93 (95% CI, 0.84 to 1.04) as likely in Wales to receive an NHS-funded hip replacement in 2006 than those living in quintile 3. We found no evidence that these substantial inequities had reduced between 2006 and 2016.<h4>Interpretation</h4>With respect to hip-replacement surgery in England and Wales, policy ambitions to reduce healthcare inequities have not been realised.<h4>Funding</h4>This work was supported by Health Data Research UK.",,doi:https://doi.org/10.1016/j.lanepe.2022.100475; doi:https://doi.org/10.1016/j.lanepe.2022.100475; html:https://europepmc.org/articles/PMC9340533; pdf:https://europepmc.org/articles/PMC9340533?pdf=render
 35304633,https://doi.org/10.1007/s00520-022-06976-w,An exploration of wellbeing in men diagnosed with prostate cancer undergoing active surveillance: a qualitative study.,"Eymech O, Brunckhorst O, Fox L, Jawaid A, Van Hemelrijck M, Stewart R, Dasgupta P, Ahmed K.",,Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer,2022,2022-03-19,Y,Quality of life; Mental health; prostate cancer; Active Surveillance; Mental Wellbeing; Psa Anxiety,,,"<h4>Purpose</h4>There is a growing emphasis on improving quality of life of people with prostate cancer. However, those undergoing active surveillance remain underrepresented in the literature with less known about their unique challenges. Therefore, we aimed to explore their lived experiences post diagnosis and its effect on their mental, social, and physical wellbeing.<h4>Methods</h4>Qualitative semi-structured interviews were conducted with 13 men undergoing active surveillance for low-risk disease. Thematic analysis was used to inductively co-construct themes through the lens of the biopsychosocial model.<h4>Results</h4>Mental wellbeing was strongly affected in our participants due to the overwhelming emotional impact of their diagnosis resulting in an 'Emotional Diagnostic Disequilibrium'. Informational awareness and education about prostate cancer helped patients with 'Recognition of the Impact'. Patients experienced an 'Unsettling Monitoring Cycle' due to the increased fear and anxiety around PSA monitoring appointments, with some men ignoring their mental wellbeing needs as their disease is 'A Future Problem'. 'Concealment of Diagnosis' left many feeling isolated and highlighted an important coping mechanisms in the 'Importance of a Social Support Network' theme. Finally, physical health mostly changed through alterations in health behaviour, leading to 'A Healthier Lifestyle' with increasing attribution of physical symptoms to age through 'Symptomatic Overshadowing'.<h4>Conclusion</h4>The greatest disease impact on men's wellbeing was at the time of diagnosis, with a subsequent cyclical anxiety and fear of disease progression prominent around monitoring appointments. Future research should explore ways to better support patients with these issues and at these times, improving their quality of life.",,pdf:https://link.springer.com/content/pdf/10.1007/s00520-022-06976-w.pdf; doi:https://doi.org/10.1007/s00520-022-06976-w; html:https://europepmc.org/articles/PMC8933126; pdf:https://europepmc.org/articles/PMC8933126?pdf=render
-37596262,https://doi.org/10.1038/s41467-023-40679-y,A genome-wide association study of blood cell morphology identifies cellular proteins implicated in disease aetiology.,"Akbari P, Vuckovic D, Stefanucci L, Jiang T, Kundu K, Kreuzhuber R, Bao EL, Collins JH, Downes K, Grassi L, Guerrero JA, Kaptoge S, Knight JC, Meacham S, Sambrook J, Seyres D, Stegle O, Verboon JM, Walter K, Watkins NA, Danesh J, Roberts DJ, Di Angelantonio E, Sankaran VG, Frontini M, Burgess S, Kuijpers T, Peters JE, Butterworth AS, Ouwehand WH, Soranzo N, Astle WJ.",,Nature communications,2023,2023-08-18,Y,,,,"Blood cells contain functionally important intracellular structures, such as granules, critical to immunity and thrombosis. Quantitative variation in these structures has not been subjected previously to large-scale genetic analysis. We perform genome-wide association studies of 63 flow-cytometry derived cellular phenotypes-including cell-type specific measures of granularity, nucleic acid content and reactivity-in 41,515 participants in the INTERVAL study. We identify 2172 distinct variant-trait associations, including associations near genes coding for proteins in organelles implicated in inflammatory and thrombotic diseases. By integrating with epigenetic data we show that many intracellular structures are likely to be determined in immature precursor cells. By integrating with proteomic data we identify the transcription factor FOG2 as an early regulator of platelet formation and α-granularity. Finally, we show that colocalisation of our associations with disease risk signals can suggest aetiological cell-types-variants in IL2RA and ITGA4 respectively mirror the known effects of daclizumab in multiple sclerosis and vedolizumab in inflammatory bowel disease.",,doi:https://doi.org/10.1038/s41467-023-40679-y; html:https://europepmc.org/articles/PMC10439125; pdf:https://europepmc.org/articles/PMC10439125?pdf=render
 38633019,https://doi.org/10.1002/lrh2.10391,ROAD2H: Development and evaluation of an open-source explainable artificial intelligence approach for managing co-morbidity and clinical guidelines.,"Domínguez J, Prociuk D, Marović B, Čyras K, Cocarascu O, Ruiz F, Mi E, Mi E, Ramtale C, Rago A, Darzi A, Toni F, Curcin V, Delaney B.",,Learning health systems,2024,2023-09-12,Y,Clinical Decision Support Systems; Argumentation; Fhir; Cds Hooks; Transition‐based Medical Recommendation Model; Co‐morbidity,,,"<h4>Introduction</h4>Clinical decision support (CDS) systems (CDSSs) that integrate clinical guidelines need to reflect real-world co-morbidity. In patient-specific clinical contexts, transparent recommendations that allow for contraindications and other conflicts arising from co-morbidity are a requirement. In this work, we develop and evaluate a non-proprietary, standards-based approach to the deployment of computable guidelines with explainable argumentation, integrated with a commercial electronic health record (EHR) system in Serbia, a middle-income country in West Balkans.<h4>Methods</h4>We used an ontological framework, the Transition-based Medical Recommendation (TMR) model, to represent, and reason about, guideline concepts, and chose the 2017 International global initiative for chronic obstructive lung disease (GOLD) guideline and a Serbian hospital as the deployment and evaluation site, respectively. To mitigate potential guideline conflicts, we used a TMR-based implementation of the Assumptions-Based Argumentation framework extended with preferences and Goals (ABA+G). Remote EHR integration of computable guidelines was via a microservice architecture based on HL7 FHIR and CDS Hooks. A prototype integration was developed to manage chronic obstructive pulmonary disease (COPD) with comorbid cardiovascular or chronic kidney diseases, and a mixed-methods evaluation was conducted with 20 simulated cases and five pulmonologists.<h4>Results</h4>Pulmonologists agreed 97% of the time with the GOLD-based COPD symptom severity assessment assigned to each patient by the CDSS, and 98% of the time with one of the proposed COPD care plans. Comments were favourable on the principles of explainable argumentation; inclusion of additional co-morbidities was suggested in the future along with customisation of the level of explanation with expertise.<h4>Conclusion</h4>An ontological model provided a flexible means of providing argumentation and explainable artificial intelligence for a long-term condition. Extension to other guidelines and multiple co-morbidities is needed to test the approach further.",,doi:https://doi.org/10.1002/lrh2.10391; html:https://europepmc.org/articles/PMC11019374; pdf:https://europepmc.org/articles/PMC11019374?pdf=render
+37596262,https://doi.org/10.1038/s41467-023-40679-y,A genome-wide association study of blood cell morphology identifies cellular proteins implicated in disease aetiology.,"Akbari P, Vuckovic D, Stefanucci L, Jiang T, Kundu K, Kreuzhuber R, Bao EL, Collins JH, Downes K, Grassi L, Guerrero JA, Kaptoge S, Knight JC, Meacham S, Sambrook J, Seyres D, Stegle O, Verboon JM, Walter K, Watkins NA, Danesh J, Roberts DJ, Di Angelantonio E, Sankaran VG, Frontini M, Burgess S, Kuijpers T, Peters JE, Butterworth AS, Ouwehand WH, Soranzo N, Astle WJ.",,Nature communications,2023,2023-08-18,Y,,,,"Blood cells contain functionally important intracellular structures, such as granules, critical to immunity and thrombosis. Quantitative variation in these structures has not been subjected previously to large-scale genetic analysis. We perform genome-wide association studies of 63 flow-cytometry derived cellular phenotypes-including cell-type specific measures of granularity, nucleic acid content and reactivity-in 41,515 participants in the INTERVAL study. We identify 2172 distinct variant-trait associations, including associations near genes coding for proteins in organelles implicated in inflammatory and thrombotic diseases. By integrating with epigenetic data we show that many intracellular structures are likely to be determined in immature precursor cells. By integrating with proteomic data we identify the transcription factor FOG2 as an early regulator of platelet formation and α-granularity. Finally, we show that colocalisation of our associations with disease risk signals can suggest aetiological cell-types-variants in IL2RA and ITGA4 respectively mirror the known effects of daclizumab in multiple sclerosis and vedolizumab in inflammatory bowel disease.",,doi:https://doi.org/10.1038/s41467-023-40679-y; html:https://europepmc.org/articles/PMC10439125; pdf:https://europepmc.org/articles/PMC10439125?pdf=render
 37650026,https://doi.org/10.23889/ijpds.v7i1.1727,An overview of synthetic administrative data for research.,"Kokosi T, De Stavola B, Mitra R, Frayling L, Doherty A, Dove I, Sonnenberg P, Harron K.",,International journal of population data science,2022,2022-05-23,Y,Data Linkage; Statistical Disclosure Control; Data Utility; Synthetic Data; Data Confidentiality; Administrative Datasets,,,"Use of administrative data for research and for planning services has increased over recent decades due to the value of the large, rich information available. However, concerns about the release of sensitive or personal data and the associated disclosure risk can lead to lengthy approval processes and restricted data access. This can delay or prevent the production of timely evidence. A promising solution to facilitate more efficient data access is to create synthetic versions of the original datasets which are less likely to hold confidential information and can minimise disclosure risk. Such data may be used as an interim solution, allowing researchers to develop their analysis plans on non-disclosive data, whilst waiting for access to the real data. We aim to provide an overview of the background and uses of synthetic data and describe common methods used to generate synthetic data in the context of UK administrative research. We propose a simplified terminology for categories of synthetic data (univariate, multivariate, and complex modality synthetic data) as well as a more comprehensive description of the terminology used in the existing literature and illustrate challenges and future directions for research.",,pdf:https://ijpds.org/article/download/1727/3395; doi:https://doi.org/10.23889/ijpds.v7i1.1727; html:https://europepmc.org/articles/PMC10464868; pdf:https://europepmc.org/articles/PMC10464868?pdf=render
 34173574,https://doi.org/10.1016/j.puhip.2020.100039,Schools and COVID-19: Reopening Pandora's box?,"Ziauddeen N, Woods-Townsend K, Saxena S, Gilbert R, Alwan NA.",,"Public health in practice (Oxford, England)",2020,2020-11-01,Y,Safety; Covid-19; School Re-Opening,,,"Schools in countries across the world are reopening as lockdown to slow progression of COVID-19 is eased. The UK government ordered school closures in England from March 20, 2020, later than the rest of Europe. A temporary and limited return for some year groups was trialled from June 2020. Teachers, school governors, the public and doctors have openly challenged the decision. The UK government has struggled to provide enough detailed information to convince the public, teachers and health practitioners, that effective systems for protection, including test, trace and isolate, are in place to prevent and manage outbreaks in schools. Risks of infection on reopening to children, staff and families must be weighed against the harms of closure to children's education and social development. The potential consequences, if the re-opening of schools is managed badly, is subsequent waves of COVID-19 infection leading to more deaths, further school closures and prolonged restrictions, losing any ground gained thus far. This article weighs the evidence for risks and benefits of reopening schools during the pandemic.",,doi:https://doi.org/10.1016/j.puhip.2020.100039; doi:https://doi.org/10.1016/j.puhip.2020.100039; html:https://europepmc.org/articles/PMC7486860; pdf:https://europepmc.org/articles/PMC7486860?pdf=render
 34800427,https://doi.org/10.1016/s0140-6736(21)01825-0,"Aspirin in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial.",RECOVERY Collaborative Group.,,"Lancet (London, England)",2022,2021-11-17,Y,,,,"<h4>Background</h4>Aspirin has been proposed as a treatment for COVID-19 on the basis of its anti-thrombotic properties. We aimed to evaluate the efficacy and safety of aspirin in patients admitted to hospital with COVID-19.<h4>Methods</h4>In this randomised, controlled, open-label, platform trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19. The trial took place at 177 hospitals in the UK, two hospitals in Indonesia, and two hospitals in Nepal. Eligible and consenting adults were randomly allocated in a 1:1 ratio to either usual standard of care plus 150 mg aspirin once per day until discharge or usual standard of care alone using web-based simple (unstratified) randomisation with allocation concealment. The primary outcome was 28 day mortality. All analyses were done by intention to treat. The trial is registered with ISRCTN (50189673) and ClinicalTrials.gov (NCT04381936).<h4>Findings</h4>Between Nov 1, 2020, and March 21, 2021, 14 892 (66%) of 22 560 patients enrolled into the RECOVERY trial were eligible to be randomly allocated to aspirin. 7351 patients were randomly allocated (1:1) to receive aspirin and 7541 patients to receive usual care alone. Overall, 1222 (17%) of 7351 patients allocated to aspirin and 1299 (17%) of 7541 patients allocated to usual care died within 28 days (rate ratio 0·96, 95% CI 0·89-1·04; p=0·35). Consistent results were seen in all prespecified subgroups of patients. Patients allocated to aspirin had a slightly shorter duration of hospitalisation (median 8 days, IQR 5 to >28, vs 9 days, IQR 5 to >28) and a higher proportion were discharged from hospital alive within 28 days (75% vs 74%; rate ratio 1·06, 95% CI 1·02-1·10; p=0·0062). Among patients not on invasive mechanical ventilation at baseline, there was no significant difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (21% vs 22%; risk ratio 0·96, 95% CI 0·90-1·03; p=0·23). Aspirin use was associated with a reduction in thrombotic events (4·6% vs 5·3%; absolute reduction 0·6%, SE 0·4%) and an increase in major bleeding events (1·6% vs 1·0%; absolute increase 0·6%, SE 0·2%).<h4>Interpretation</h4>In patients hospitalised with COVID-19, aspirin was not associated with reductions in 28 day mortality or in the risk of progressing to invasive mechanical ventilation or death, but was associated with a small increase in the rate of being discharged alive within 28 days.<h4>Funding</h4>UK Research and Innovation (Medical Research Council), National Institute of Health Research, and the Wellcome Trust through the COVID-19 Therapeutics Accelerator.",,doi:https://doi.org/10.1016/s0140-6736(21)01825-0; doi:https://doi.org/10.1016/S0140-6736(21)01825-0; html:https://europepmc.org/articles/PMC8598213
@@ -804,8 +805,8 @@ PMC8718341,https://doi.org/,"Loneliness, coping, suicidal thoughts and self-harm
 36992264,https://doi.org/10.3390/vaccines11030680,"Determinants of Equity in Coverage of Measles-Containing Vaccines in Wales, UK, during the Elimination Era.","Perry M, Cottrell S, Gravenor MB, Griffiths L.",,Vaccines,2023,2023-03-17,Y,"Vaccination; Measles; Socioeconomic Factors; Immunisation; Mmr; Measles, Mumps And Rubella Vaccine",,,"In the context of the WHO's measles and rubella elimination targets and European Immunization Agenda 2030, this large cross-sectional study aimed to identify inequalities in measles vaccination coverage in Wales, UK. The vaccination status of individuals aged 2 to 25 years of age, alive and resident in Wales as of 31 August 2021, was ascertained through linkage of the National Community Child Health Database and primary care data. A series of predictor variables were derived from five national datasets and all analysis was carried out in the Secure Anonymised Information Linkage Databank at Swansea University. In these 648,895 individuals, coverage of the first dose of measles-containing vaccine (due at 12-13 months of age) was 97.1%, and coverage of the second dose (due at 3 years and 4 months) in 4 to 25-year-olds was 93.8%. In multivariable analysis, excluding 0.7% with known refusal, the strongest association with being unvaccinated was birth order (families with six or more children) and being born outside of the UK. Living in a deprived area, being eligible for free school meals, a lower level of maternal education, and having a recorded language other than English or Welsh were also associated with lower coverage. Some of these factors may also be associated with refusal. This knowledge can be used to target future interventions and prioritise areas for catch up in a time of limited resource.",,pdf:https://www.mdpi.com/2076-393X/11/3/680/pdf?version=1679031223; doi:https://doi.org/10.3390/vaccines11030680; html:https://europepmc.org/articles/PMC10057771; pdf:https://europepmc.org/articles/PMC10057771?pdf=render
 35835543,https://doi.org/10.1136/heartjnl-2022-321196,Eligibility for early rhythm control in patients with atrial fibrillation in the UK Biobank.,"Kany S, Cardoso VR, Bravo L, Williams JA, Schnabel R, Fabritz L, Gkoutos GV, Kirchhof P.",,Heart (British Cardiac Society),2022,2022-11-10,Y,Atrial fibrillation; Stroke; Catheter ablation,,,"<h4>Objective</h4>The Early Treatment of Atrial Fibrillation for Stroke Prevention (EAST-AFNET4) trial showed a clinical benefit of early rhythm-control therapy in patients with recently diagnosed atrial fibrillation (AF). The generalisability of the results in the general population is not known.<h4>Methods</h4>Participants in the population-based UK Biobank were assessed for eligibility based on the EAST-AFNET4 inclusion/exclusion criteria. Treatment of all eligible participants was classified as early rhythm-control (antiarrhythmic drug therapy or AF ablation) or usual care. To assess treatment effects, primary care data and Hospital Episode Statistics were merged with UK Biobank data.Efficacy and safety outcomes were compared between groups in the entire cohort and in a propensity-matched data set.<h4>Results</h4>AF was present in 35 526/502 493 (7.1%) participants, including 8340 (988 with AF <1 year) with AF at enrolment and 27 186 with incident AF during follow-up. Most participants (22 003/27 186; 80.9%) with incident AF were eligible for early rhythm-control.Eligible participants were older (70 years vs 63 years) and more likely to be female (42% vs 21%) compared with ineligible patients. Of 9004 participants with full primary care data, 874 (9.02%) received early rhythm-control. Safety outcomes were not different between patients receiving early rhythm-control and controls. The primary outcome of EAST-AFNET 4, a composite of cardiovascular death, stroke/transient ischaemic attack and hospitalisation for heart failure or acute coronary syndrome occurred less often in participants receiving early rhythm-control compared with controls in the entire cohort (HR 0.82, 95% CI 0.71 to 0.94, p=0.005). In the propensity-score matched analysis, early rhythm-control did not significantly decrease of the primary outcome compared with usual care (HR 0.87, 95% CI 0.72 to 1.04, p=0.124).<h4>Conclusion</h4>Around 80% of participants diagnosed with AF in the UK population are eligible for early rhythm-control. Early rhythm-control therapy was safe in routine care.",,pdf:https://heart.bmj.com/content/heartjnl/early/2022/07/13/heartjnl-2022-321196.full.pdf; doi:https://doi.org/10.1136/heartjnl-2022-321196; html:https://europepmc.org/articles/PMC9664114; pdf:https://europepmc.org/articles/PMC9664114?pdf=render
 38838327,https://doi.org/10.2196/51323,Data-Driven Identification of Potentially Successful Intervention Implementations Using 5 Years of Opioid Prescribing Data: Retrospective Database Study.,"Hopcroft LE, Curtis HJ, Croker R, Pretis F, Inglesby P, Evans D, Bacon S, Goldacre B, Walker AJ, MacKenna B.",,JMIR public health and surveillance,2024,2024-06-05,Y,Identification; Opioid; intervention; General Practice; Primary Care; Opioid Analgesics; Electronic Health Records; Implementations; Implementation Science; Proof Of Concept; Data-driven; Data Science; Unbiased; Analysis Tool; Prescribing Data,,,"<h4>Background</h4>We have previously demonstrated that opioid prescribing increased by 127% between 1998 and 2016. New policies aimed at tackling this increasing trend have been recommended by public health bodies, and there is some evidence that progress is being made.<h4>Objective</h4>We sought to extend our previous work and develop a data-driven approach to identify general practices and clinical commissioning groups (CCGs) whose prescribing data suggest that interventions to reduce the prescribing of opioids may have been successfully implemented.<h4>Methods</h4>We analyzed 5 years of prescribing data (December 2014 to November 2019) for 3 opioid prescribing measures-total opioid prescribing as oral morphine equivalent per 1000 registered population, the number of high-dose opioids prescribed per 1000 registered population, and the number of high-dose opioids as a percentage of total opioids prescribed. Using a data-driven approach, we applied a modified version of our change detection Python library to identify reductions in these measures over time, which may be consistent with the successful implementation of an intervention to reduce opioid prescribing. This analysis was carried out for general practices and CCGs, and organizations were ranked according to the change in prescribing rate.<h4>Results</h4>We identified a reduction in total opioid prescribing in 94 (49.2%) out of 191 CCGs, with a median reduction of 15.1 (IQR 11.8-18.7; range 9.0-32.8) in total oral morphine equivalence per 1000 patients. We present data for the 3 CCGs and practices demonstrating the biggest reduction in opioid prescribing for each of the 3 opioid prescribing measures. We observed a 40% proportional drop (8.9% absolute reduction) in the regular prescribing of high-dose opioids (measured as a percentage of regular opioids) in the highest-ranked CCG (North Tyneside); a 99% drop in this same measure was found in several practices (44%-95% absolute reduction). Decile plots demonstrate that CCGs exhibiting large reductions in opioid prescribing do so via slow and gradual reductions over a long period of time (typically over a period of 2 years); in contrast, practices exhibiting large reductions do so rapidly over a much shorter period of time.<h4>Conclusions</h4>By applying 1 of our existing analysis tools to a national data set, we were able to identify rapid and maintained changes in opioid prescribing within practices and CCGs and rank organizations by the magnitude of reduction. Highly ranked organizations are candidates for further qualitative research into intervention design and implementation.",,doi:https://doi.org/10.2196/51323; doi:https://doi.org/10.2196/51323; html:https://europepmc.org/articles/PMC11187509
-36669843,https://doi.org/10.1136/bmjopen-2022-064364,Implementation of a quality improvement programme using the Active Patient Link call and recall system to improve timeliness and equity of childhood vaccinations: protocol for a mixed-methods evaluation.,"Marszalek M, Hawking MKD, Gutierrez A, Dostal I, Ahmed Z, Firman N, Robson J, Bedford H, Billington A, Moss N, Dezateux C.",,BMJ open,2023,2023-01-20,Y,immunology; Public Health; Preventive Medicine; Community Child Health; Quality In Health Care; Paediatric Infectious Disease & Immunisation,,,"<h4>Introduction</h4>Call and recall systems provide actionable intelligence to improve equity and timeliness of childhood vaccinations, which have been disrupted during the COVID-19 pandemic. We will evaluate the effectiveness, fidelity and sustainability of a data-enabled quality improvement programme delivered in primary care using an Active Patient Link Immunisation (APL-Imms) call and recall system to improve timeliness and equity of uptake in a multiethnic disadvantaged urban population. We will use qualitative methods to evaluate programme delivery, focusing on uptake and use, implementation barriers and service improvements for clinical and non-clinical primary care staff, its fidelity and sustainability.<h4>Methods and analysis</h4>This is a mixed-methods observational study in 284 general practices in north east London (NEL). The target population will be preschool-aged children eligible to receive diphtheria, tetanus and pertussis (DTaP) or measles, mumps and rubella (MMR) vaccinations and registered with an NEL general practice. The intervention comprises an in-practice call and recall tool, facilitation and training, and financial incentives. The quantitative evaluation will include interrupted time Series analyses and Slope Index of Inequality. The primary outcomes will be the proportion of children receiving at least one dose of a DTaP-containing or MMR vaccination defined, respectively, as administered between age 6 weeks and 6 months or between 12 and 18 months of age. The qualitative evaluation will involve a 'Think Aloud' method and semistructured interviews of stakeholders to assess impact, fidelity and sustainability of the APL-Imms tool, and fidelity of the implementation by facilitators.<h4>Ethics and dissemination</h4>The research team has been granted permission from data controllers in participating practices to use deidentified data for audit purposes. As findings will be specific to the local context, research ethics approval is not required. Results will be disseminated in a peer-reviewed journal and to stakeholders, including parents, health providers and commissioners.",,pdf:https://bmjopen.bmj.com/content/bmjopen/13/1/e064364.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-064364; html:https://europepmc.org/articles/PMC9872487; pdf:https://europepmc.org/articles/PMC9872487?pdf=render
 37393924,https://doi.org/10.1016/s0140-6736(23)00860-7,"The unfinished agenda of communicable diseases among children and adolescents before the COVID-19 pandemic, 1990-2019: a systematic analysis of the Global Burden of Disease Study 2019.",GBD 2019 Child and Adolescent Communicable Disease Collaborators.,,"Lancet (London, England)",2023,2023-06-29,Y,,,,"<h4>Background</h4>Communicable disease control has long been a focus of global health policy. There have been substantial reductions in the burden and mortality of communicable diseases among children younger than 5 years, but we know less about this burden in older children and adolescents, and it is unclear whether current programmes and policies remain aligned with targets for intervention. This knowledge is especially important for policy and programmes in the context of the COVID-19 pandemic. We aimed to use the Global Burden of Disease (GBD) Study 2019 to systematically characterise the burden of communicable diseases across childhood and adolescence.<h4>Methods</h4>In this systematic analysis of the GBD study from 1990 to 2019, all communicable diseases and their manifestations as modelled within GBD 2019 were included, categorised as 16 subgroups of common diseases or presentations. Data were reported for absolute count, prevalence, and incidence across measures of cause-specific mortality (deaths and years of life lost), disability (years lived with disability [YLDs]), and disease burden (disability-adjusted life-years [DALYs]) for children and adolescents aged 0-24 years. Data were reported across the Socio-demographic Index (SDI) and across time (1990-2019), and for 204 countries and territories. For HIV, we reported the mortality-to-incidence ratio (MIR) as a measure of health system performance.<h4>Findings</h4>In 2019, there were 3·0 million deaths and 30·0 million years of healthy life lost to disability (as measured by YLDs), corresponding to 288·4 million DALYs from communicable diseases among children and adolescents globally (57·3% of total communicable disease burden across all ages). Over time, there has been a shift in communicable disease burden from young children to older children and adolescents (largely driven by the considerable reductions in children younger than 5 years and slower progress elsewhere), although children younger than 5 years still accounted for most of the communicable disease burden in 2019. Disease burden and mortality were predominantly in low-SDI settings, with high and high-middle SDI settings also having an appreciable burden of communicable disease morbidity (4·0 million YLDs in 2019 alone). Three cause groups (enteric infections, lower-respiratory-tract infections, and malaria) accounted for 59·8% of the global communicable disease burden in children and adolescents, with tuberculosis and HIV both emerging as important causes during adolescence. HIV was the only cause for which disease burden increased over time, particularly in children and adolescents older than 5 years, and especially in females. Excess MIRs for HIV were observed for males aged 15-19 years in low-SDI settings.<h4>Interpretation</h4>Our analysis supports continued policy focus on enteric infections and lower-respiratory-tract infections, with orientation to children younger than 5 years in settings of low socioeconomic development. However, efforts should also be targeted to other conditions, particularly HIV, given its increased burden in older children and adolescents. Older children and adolescents also experience a large burden of communicable disease, further highlighting the need for efforts to extend beyond the first 5 years of life. Our analysis also identified substantial morbidity caused by communicable diseases affecting child and adolescent health across the world.<h4>Funding</h4>The Australian National Health and Medical Research Council Centre for Research Excellence for Driving Investment in Global Adolescent Health and the Bill & Melinda Gates Foundation.",,pdf:http://www.thelancet.com/article/S0140673623008607/pdf; doi:https://doi.org/10.1016/S0140-6736(23)00860-7; html:https://europepmc.org/articles/PMC10375221; pdf:https://europepmc.org/articles/PMC10375221?pdf=render
+36669843,https://doi.org/10.1136/bmjopen-2022-064364,Implementation of a quality improvement programme using the Active Patient Link call and recall system to improve timeliness and equity of childhood vaccinations: protocol for a mixed-methods evaluation.,"Marszalek M, Hawking MKD, Gutierrez A, Dostal I, Ahmed Z, Firman N, Robson J, Bedford H, Billington A, Moss N, Dezateux C.",,BMJ open,2023,2023-01-20,Y,immunology; Public Health; Preventive Medicine; Community Child Health; Quality In Health Care; Paediatric Infectious Disease & Immunisation,,,"<h4>Introduction</h4>Call and recall systems provide actionable intelligence to improve equity and timeliness of childhood vaccinations, which have been disrupted during the COVID-19 pandemic. We will evaluate the effectiveness, fidelity and sustainability of a data-enabled quality improvement programme delivered in primary care using an Active Patient Link Immunisation (APL-Imms) call and recall system to improve timeliness and equity of uptake in a multiethnic disadvantaged urban population. We will use qualitative methods to evaluate programme delivery, focusing on uptake and use, implementation barriers and service improvements for clinical and non-clinical primary care staff, its fidelity and sustainability.<h4>Methods and analysis</h4>This is a mixed-methods observational study in 284 general practices in north east London (NEL). The target population will be preschool-aged children eligible to receive diphtheria, tetanus and pertussis (DTaP) or measles, mumps and rubella (MMR) vaccinations and registered with an NEL general practice. The intervention comprises an in-practice call and recall tool, facilitation and training, and financial incentives. The quantitative evaluation will include interrupted time Series analyses and Slope Index of Inequality. The primary outcomes will be the proportion of children receiving at least one dose of a DTaP-containing or MMR vaccination defined, respectively, as administered between age 6 weeks and 6 months or between 12 and 18 months of age. The qualitative evaluation will involve a 'Think Aloud' method and semistructured interviews of stakeholders to assess impact, fidelity and sustainability of the APL-Imms tool, and fidelity of the implementation by facilitators.<h4>Ethics and dissemination</h4>The research team has been granted permission from data controllers in participating practices to use deidentified data for audit purposes. As findings will be specific to the local context, research ethics approval is not required. Results will be disseminated in a peer-reviewed journal and to stakeholders, including parents, health providers and commissioners.",,pdf:https://bmjopen.bmj.com/content/bmjopen/13/1/e064364.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-064364; html:https://europepmc.org/articles/PMC9872487; pdf:https://europepmc.org/articles/PMC9872487?pdf=render
 37773956,https://doi.org/10.1371/journal.pone.0292240,Prioritising cardiovascular disease risk assessment to high risk individuals based on primary care records.,"Chung R, Xu Z, Arnold M, Stevens D, Keogh R, Barrett J, Harrison H, Pennells L, Kim LG, DiAngelantonio E, Paige E, Usher-Smith JA, Wood AM.",,PloS one,2023,2023-09-29,Y,,,,"<h4>Objective</h4>To provide quantitative evidence for systematically prioritising individuals for full formal cardiovascular disease (CVD) risk assessment using primary care records with a novel tool (eHEART) with age- and sex- specific risk thresholds.<h4>Methods and analysis</h4>eHEART was derived using landmark Cox models for incident CVD with repeated measures of conventional CVD risk predictors in 1,642,498 individuals from the Clinical Practice Research Datalink. Using 119,137 individuals from UK Biobank, we modelled the implications of initiating guideline-recommended statin therapy using eHEART with age- and sex-specific prioritisation thresholds corresponding to 5% false negative rates to prioritise adults aged 40-69 years in a population in England for invitation to a formal CVD risk assessment.<h4>Results</h4>Formal CVD risk assessment on all adults would identify 76% and 49% of future CVD events amongst men and women respectively, and 93 (95% CI: 90, 95) men and 279 (95% CI: 259, 297) women would need to be screened (NNS) to prevent one CVD event. In contrast, if eHEART was first used to prioritise individuals for formal CVD risk assessment, we would identify 73% and 47% of future events amongst men and women respectively, and a NNS of 75 (95% CI: 72, 77) men and 162 (95% CI: 150, 172) women. Replacing the age- and sex-specific prioritisation thresholds with a 10% threshold identify around 10% less events.<h4>Conclusions</h4>The use of prioritisation tools with age- and sex-specific thresholds could lead to more efficient CVD assessment programmes with only small reductions in effectiveness at preventing new CVD events.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0292240&type=printable; doi:https://doi.org/10.1371/journal.pone.0292240; html:https://europepmc.org/articles/PMC10540947; pdf:https://europepmc.org/articles/PMC10540947?pdf=render
 33619467,https://doi.org/10.1093/jamiaopen/ooaa047,A semi-supervised approach for rapidly creating clinical biomarker phenotypes in the UK Biobank using different primary care EHR and clinical terminology systems.,"Denaxas S, Shah AD, Mateen BA, Kuan V, Quint JK, Fitzpatrick N, Torralbo A, Fatemifar G, Hemingway H.",,JAMIA open,2020,2020-12-05,Y,Phenotyping; Medical Informatics; Electronic Health Records; Uk Biobank,,,"<h4>Objectives</h4>The UK Biobank (UKB) is making primary care electronic health records (EHRs) for 500 000 participants available for COVID-19-related research. Data are extracted from four sources, recorded using five clinical terminologies and stored in different schemas. The aims of our research were to: (a) develop a semi-supervised approach for bootstrapping EHR phenotyping algorithms in UKB EHR, and (b) to evaluate our approach by implementing and evaluating phenotypes for 31 common biomarkers.<h4>Materials and methods</h4>We describe an algorithmic approach to phenotyping biomarkers in primary care EHR involving (a) bootstrapping definitions using existing phenotypes, (b) excluding generic, rare, or semantically distant terms, (c) forward-mapping terminology terms, (d) expert review, and (e) data extraction. We evaluated the phenotypes by assessing the ability to reproduce known epidemiological associations with all-cause mortality using Cox proportional hazards models.<h4>Results</h4>We created and evaluated phenotyping algorithms for 31 biomarkers many of which are directly related to COVID-19 complications, for example diabetes, cardiovascular disease, respiratory disease. Our algorithm identified 1651 Read v2 and Clinical Terms Version 3 terms and automatically excluded 1228 terms. Clinical review excluded 103 terms and included 44 terms, resulting in 364 terms for data extraction (sensitivity 0.89, specificity 0.92). We extracted 38 190 682 events and identified 220 978 participants with at least one biomarker measured.<h4>Discussion and conclusion</h4>Bootstrapping phenotyping algorithms from similar EHR can potentially address pre-existing methodological concerns that undermine the outputs of biomarker discovery pipelines and provide research-quality phenotyping algorithms.",,pdf:https://academic.oup.com/jamiaopen/article-pdf/3/4/545/36625793/ooaa047.pdf; doi:https://doi.org/10.1093/jamiaopen/ooaa047; html:https://europepmc.org/articles/PMC7717266; pdf:https://europepmc.org/articles/PMC7717266?pdf=render
 34939832,https://doi.org/10.1308/rcsann.2021.0206,"Projections for primary hip and knee replacement surgery up to the year 2060: an analysis based on data from The National Joint Registry for England, Wales, Northern Ireland and the Isle of Man.","Matharu GS, Culliford DJ, Blom AW, Judge A.",,Annals of the Royal College of Surgeons of England,2022,2021-12-23,N,Total hip replacement; Total Knee Replacement; Demand; Future Numbers,,,"<h4>Introduction</h4>We estimated the number of primary total hip and knee replacements (THR and TKR) that will need to be performed up to the year 2060.<h4>Methods</h4>We used data from The National Joint Registry for England, Wales, Northern Ireland and the Isle of Man on the volume of primary THRs (<i>n</i>=94,936) and TKRs (<i>n</i>=100,547) performed in 2018. We projected future numbers of THR and TKR using a static estimated rate from 2018 applied to population growth forecast data from the UK Office for National Statistics up to 2060.<h4>Results</h4>By 2060, THR and TKR volume would increase from 2018 levels by an estimated 37.7% (<i>n</i>=130,766) and 36.6% (<i>n</i>=137,341), respectively. For both males and females demand for surgery was also higher for patients aged 70 and over, with older patients having the biggest relative increase in volume over time: 70-79 years (44.6% males, 41.2% females); 80-89 years (112.4% males, 85.6% females); 90 years and older (348.0% males, 198.2% females).<h4>Conclusion</h4>By 2060 demand for hip and knee joint replacement is estimated to increase by almost 40%. Demand will be greatest in older patients (70+ years), which will have significant implications for the health service requiring forward planning given that morbidity and resource use is higher in this population. These issues, coupled with two waves of COVID-19, will impact the ability of health services to deliver timely joint replacement to many patients for a number of years, requiring urgent planning.",,doi:https://doi.org/10.1308/rcsann.2021.0206; html:https://europepmc.org/articles/PMC9157920; pdf:https://europepmc.org/articles/PMC9157920?pdf=render; doi:https://doi.org/10.1308/rcsann.2021.0206
@@ -813,16 +814,16 @@ PMC8718341,https://doi.org/,"Loneliness, coping, suicidal thoughts and self-harm
 33602244,https://doi.org/10.1186/s12916-021-01924-7,The impact of local and national restrictions in response to COVID-19 on social contacts in England: a longitudinal natural experiment.,"Jarvis CI, Gimma A, van Zandvoort K, Wong KLM, CMMID COVID-19 working group, Edmunds WJ.",,BMC medicine,2021,2021-02-19,Y,Pandemic; England; United Kingdom; Disease Outbreak; Non-pharmaceutical Interventions; Covid-19; Contact Survey; Lockdowns,,,"<h4>Background</h4>England's COVID-19 response transitioned from a national lockdown to localised interventions. In response to rising cases, these were supplemented by national restrictions on contacts (the Rule of Six), then 10 pm closing for bars and restaurants, and encouragement to work from home. These were quickly followed by a 3-tier system applying different restrictions in different localities. As cases continued to rise, a second national lockdown was declared. We used a national survey to quantify the impact of these restrictions on epidemiologically relevant contacts.<h4>Methods</h4>We compared paired measures on setting-specific contacts before and after each restriction started and tested for differences using paired permutation tests on the mean change in contacts and the proportion of individuals decreasing their contacts.<h4>Results</h4>Following the imposition of each measure, individuals tended to report fewer contacts than they had before. However, the magnitude of the changes was relatively small and variable. For instance, although early closure of bars and restaurants appeared to have no measurable effect on contacts, the work from home directive reduced mean daily work contacts by 0.99 (95% confidence interval CI] 0.03-1.94), and the Rule of Six reduced non-work and school contacts by a mean of 0.25 (0.01-0.5) per day. Whilst Tier 3 appeared to also reduce non-work and school contacts, the evidence for an effect of the lesser restrictions (Tiers 1 and 2) was much weaker. There may also have been some evidence of saturation of effects, with those who were in Tier 1 (least restrictive) reducing their contacts markedly when they entered lockdown, which was not reflected in similar changes in those who were already under tighter restrictions (Tiers 2 and 3).<h4>Conclusions</h4>The imposition of various local and national measures in England during the summer and autumn of 2020 has gradually reduced contacts. However, these changes are smaller than the initial lockdown in March. This may partly be because many individuals were already starting from a lower number of contacts.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-021-01924-7; doi:https://doi.org/10.1186/s12916-021-01924-7; html:https://europepmc.org/articles/PMC7892289; pdf:https://europepmc.org/articles/PMC7892289?pdf=render
 39453837,https://doi.org/10.1056/nejmoa2409183,Long-Term Effects of Empagliflozin in Patients with Chronic Kidney Disease.,"EMPA-KIDNEY Collaborative Group, Herrington WG, Staplin N, Agrawal N, Wanner C, Green JB, Hauske SJ, Emberson JR, Preiss D, Judge P, Zhu D, Dayanandan R, Arimoto R, Mayne KJ, Ng SYA, Sammons E, Hill M, Stevens W, Wallendszus K, Brenner S, Cheung AK, Liu ZH, Li J, Hooi LS, Liu W, Kadowaki T, Nangaku M, Levin A, Cherney DZI, Maggioni AP, Pontremoli R, Deo R, Goto S, Rossello X, Tuttle KR, Steubl D, Massey D, Brueckmann M, Landray MJ, Baigent C, Haynes R.",,The New England journal of medicine,2024,2024-10-25,Y,,,,"<h4>Background</h4>In the EMPA-KIDNEY trial, empagliflozin, a sodium-glucose cotransporter 2 (SGLT2) inhibitor, had positive cardiorenal effects in patients with chronic kidney disease who were at risk for disease progression. Post-trial follow-up was designed to assess how the effects of empagliflozin would evolve after the discontinuation of the trial drug.<h4>Methods</h4>In the active trial, patients with chronic kidney disease were randomly assigned to receive either empagliflozin (10 mg once daily) or matching placebo and were followed for a median of 2 years. All the patients had an estimated glomerular filtration rate (eGFR) of at least 20 but less than 45 ml per minute per 1.73 m<sup>2</sup> of body-surface area or an eGFR of at least 45 but less than 90 ml per minute per 1.73 m<sup>2</sup> with a urinary albumin-to-creatinine ratio (with albumin measured in milligrams and creatinine measured in grams) of at least 200. Subsequently, surviving patients who consented were observed for 2 additional years. No trial empagliflozin or placebo was administered during the post-trial period, but local practitioners could prescribe open-label SGLT2 inhibitors, including open-label empagliflozin. The primary composite outcome was kidney disease progression or cardiovascular death as assessed from the start of the active-trial period to the end of the post-trial period.<h4>Results</h4>Of the 6609 patients who had undergone randomization in the active trial, 4891 (74%) were enrolled in the post-trial period. During this period, the use of open-label SGLT2 inhibitors was similar in the two groups (43% in the empagliflozin group and 40% in the placebo group). During the combined active- and post-trial periods, a primary-outcome event occurred in 865 of 3304 patients (26.2%) in the empagliflozin group and in 1001 of 3305 patients (30.3%) in the placebo group (hazard ratio, 0.79; 95% confidence interval [CI], 0.72 to 0.87). During the post-trial period only, the hazard ratio for a primary-outcome event was 0.87 (95% CI, 0.76 to 0.99). During the combined periods, the risk of kidney disease progression was 23.5% in the empagliflozin group and 27.1% in the placebo group; the risk of the composite of death or end-stage kidney disease was 16.9% and 19.6%, respectively; and the risk of cardiovascular death was 3.8% and 4.9%, respectively. There was no effect of empagliflozin on death from noncardiovascular causes (5.3% in both groups).<h4>Conclusions</h4>In a broad range of patients with chronic kidney disease at risk for progression, empagliflozin continued to have additional cardiorenal benefits for up to 12 months after it was discontinued. (Funded by Boehringer Ingelheim and others; EMPA-KIDNEY ClinicalTrials.gov number, NCT03594110; EuDRACT number, 2017-002971-24.).",,doi:https://doi.org/10.1056/NEJMoa2409183; html:https://europepmc.org/articles/PMC7616743; pdf:https://europepmc.org/articles/PMC7616743?pdf=render
 34562388,https://doi.org/10.1016/s0140-6736(21)01258-7,"Tracking development assistance for health and for COVID-19: a review of development assistance, government, out-of-pocket, and other private spending on health for 204 countries and territories, 1990-2050.",Global Burden of Disease 2020 Health Financing Collaborator Network.,,"Lancet (London, England)",2021,2021-09-22,Y,,,,"<h4>Background</h4>The rapid spread of COVID-19 renewed the focus on how health systems across the globe are financed, especially during public health emergencies. Development assistance is an important source of health financing in many low-income countries, yet little is known about how much of this funding was disbursed for COVID-19. We aimed to put development assistance for health for COVID-19 in the context of broader trends in global health financing, and to estimate total health spending from 1995 to 2050 and development assistance for COVID-19 in 2020.<h4>Methods</h4>We estimated domestic health spending and development assistance for health to generate total health-sector spending estimates for 204 countries and territories. We leveraged data from the WHO Global Health Expenditure Database to produce estimates of domestic health spending. To generate estimates for development assistance for health, we relied on project-level disbursement data from the major international development agencies' online databases and annual financial statements and reports for information on income sources. To adjust our estimates for 2020 to include disbursements related to COVID-19, we extracted project data on commitments and disbursements from a broader set of databases (because not all of the data sources used to estimate the historical series extend to 2020), including the UN Office of Humanitarian Assistance Financial Tracking Service and the International Aid Transparency Initiative. We reported all the historic and future spending estimates in inflation-adjusted 2020 US$, 2020 US$ per capita, purchasing-power parity-adjusted US$ per capita, and as a proportion of gross domestic product. We used various models to generate future health spending to 2050.<h4>Findings</h4>In 2019, health spending globally reached $8·8 trillion (95% uncertainty interval [UI] 8·7-8·8) or $1132 (1119-1143) per person. Spending on health varied within and across income groups and geographical regions. Of this total, $40·4 billion (0·5%, 95% UI 0·5-0·5) was development assistance for health provided to low-income and middle-income countries, which made up 24·6% (UI 24·0-25·1) of total spending in low-income countries. We estimate that $54·8 billion in development assistance for health was disbursed in 2020. Of this, $13·7 billion was targeted toward the COVID-19 health response. $12·3 billion was newly committed and $1·4 billion was repurposed from existing health projects. $3·1 billion (22·4%) of the funds focused on country-level coordination and $2·4 billion (17·9%) was for supply chain and logistics. Only $714·4 million (7·7%) of COVID-19 development assistance for health went to Latin America, despite this region reporting 34·3% of total recorded COVID-19 deaths in low-income or middle-income countries in 2020. Spending on health is expected to rise to $1519 (1448-1591) per person in 2050, although spending across countries is expected to remain varied.<h4>Interpretation</h4>Global health spending is expected to continue to grow, but remain unequally distributed between countries. We estimate that development organisations substantially increased the amount of development assistance for health provided in 2020. Continued efforts are needed to raise sufficient resources to mitigate the pandemic for the most vulnerable, and to help curtail the pandemic for all.<h4>Funding</h4>Bill & Melinda Gates Foundation.",,pdf:http://www.thelancet.com/article/S0140673621012587/pdf; doi:https://doi.org/10.1016/S0140-6736(21)01258-7; html:https://europepmc.org/articles/PMC8457757; pdf:https://europepmc.org/articles/PMC8457757?pdf=render
-36001371,https://doi.org/10.2196/38122,Deployment of a Free-Text Analytics Platform at a UK National Health Service Research Hospital: CogStack at University College London Hospitals.,"Noor K, Roguski L, Bai X, Handy A, Klapaukh R, Folarin A, Romao L, Matteson J, Lea N, Zhu L, Asselbergs FW, Wong WK, Shah A, Dobson RJ.",,JMIR medical informatics,2022,2022-08-24,Y,Information Retrieval; Natural Language Processing; Text Mining; Electronic Health Record System; Clinical Support,,,"<h4>Background</h4>As more health care organizations transition to using electronic health record (EHR) systems, it is important for these organizations to maximize the secondary use of their data to support service improvement and clinical research. These organizations will find it challenging to have systems capable of harnessing the unstructured data fields in the record (clinical notes, letters, etc) and more practically have such systems interact with all of the hospital data systems (legacy and current).<h4>Objective</h4>We describe the deployment of the EHR interfacing information extraction and retrieval platform CogStack at University College London Hospitals (UCLH).<h4>Methods</h4>At UCLH, we have deployed the CogStack platform, an information retrieval platform with natural language processing capabilities. The platform addresses the problem of data ingestion and harmonization from multiple data sources using the Apache NiFi module for managing complex data flows. The platform also facilitates the extraction of structured data from free-text records through use of the MedCAT natural language processing library. Finally, data science tools are made available to support data scientists and the development of downstream applications dependent upon data ingested and analyzed by CogStack.<h4>Results</h4>The platform has been deployed at the hospital, and in particular, it has facilitated a number of research and service evaluation projects. To date, we have processed over 30 million records, and the insights produced from CogStack have informed a number of clinical research use cases at the hospital.<h4>Conclusions</h4>The CogStack platform can be configured to handle the data ingestion and harmonization challenges faced by a hospital. More importantly, the platform enables the hospital to unlock important clinical information from the unstructured portion of the record using natural language processing technology.",,pdf:https://medinform.jmir.org/2022/8/e38122/PDF; doi:https://doi.org/10.2196/38122; html:https://europepmc.org/articles/PMC9453582
 34912046,https://doi.org/10.1038/s41366-021-01048-1,"30-day morbidity and mortality of sleeve gastrectomy, Roux-en-Y gastric bypass and one anastomosis gastric bypass: a propensity score-matched analysis of the GENEVA data.","Singhal R, Cardoso VR, Wiggins T, Super J, Ludwig C, Gkoutos GV, Mahawar K, GENEVA Collaborators.",,International journal of obesity (2005),2022,2021-12-15,Y,,,,"<h4>Background</h4>There is a paucity of data comparing 30-day morbidity and mortality of sleeve gastrectomy (SG), Roux-en-Y gastric bypass (RYGB), and one anastomosis gastric bypass (OAGB). This study aimed to compare the 30-day safety of SG, RYGB, and OAGB in propensity score-matched cohorts.<h4>Materials and methods</h4>This analysis utilised data collected from the GENEVA study which was a multicentre observational cohort study of bariatric and metabolic surgery (BMS) in 185 centres across 42 countries between 01/05/2022 and 31/10/2020 during the Coronavirus Disease-2019 (COVID-19) pandemic. 30-day complications were categorised according to the Clavien-Dindo classification. Patients receiving SG, RYGB, or OAGB were propensity-matched according to baseline characteristics and 30-day complications were compared between groups.<h4>Results</h4>In total, 6770 patients (SG 3983; OAGB 702; RYGB 2085) were included in this analysis. Prior to matching, RYGB was associated with highest 30-day complication rate (SG 5.8%; OAGB 7.5%; RYGB 8.0% (p = 0.006)). On multivariate regression modelling, Insulin-dependent type 2 diabetes mellitus and hypercholesterolaemia were associated with increased 30-day complications. Being a non-smoker was associated with reduced complication rates. When compared to SG as a reference category, RYGB, but not OAGB, was associated with an increased rate of 30-day complications. A total of 702 pairs of SG and OAGB were propensity score-matched. The complication rate in the SG group was 7.3% (n = 51) as compared to 7.5% (n = 53) in the OAGB group (p = 0.68). Similarly, 2085 pairs of SG and RYGB were propensity score-matched. The complication rate in the SG group was 6.1% (n = 127) as compared to 7.9% (n = 166) in the RYGB group (p = 0.09). And, 702 pairs of OAGB and RYGB were matched. The complication rate in both groups was the same at 7.5 % (n = 53; p = 0.07).<h4>Conclusions</h4>This global study found no significant difference in the 30-day morbidity and mortality of SG, RYGB, and OAGB in propensity score-matched cohorts.",,pdf:https://www.nature.com/articles/s41366-021-01048-1.pdf; doi:https://doi.org/10.1038/s41366-021-01048-1; html:https://europepmc.org/articles/PMC8671878; pdf:https://europepmc.org/articles/PMC8671878?pdf=render
+36001371,https://doi.org/10.2196/38122,Deployment of a Free-Text Analytics Platform at a UK National Health Service Research Hospital: CogStack at University College London Hospitals.,"Noor K, Roguski L, Bai X, Handy A, Klapaukh R, Folarin A, Romao L, Matteson J, Lea N, Zhu L, Asselbergs FW, Wong WK, Shah A, Dobson RJ.",,JMIR medical informatics,2022,2022-08-24,Y,Information Retrieval; Natural Language Processing; Text Mining; Electronic Health Record System; Clinical Support,,,"<h4>Background</h4>As more health care organizations transition to using electronic health record (EHR) systems, it is important for these organizations to maximize the secondary use of their data to support service improvement and clinical research. These organizations will find it challenging to have systems capable of harnessing the unstructured data fields in the record (clinical notes, letters, etc) and more practically have such systems interact with all of the hospital data systems (legacy and current).<h4>Objective</h4>We describe the deployment of the EHR interfacing information extraction and retrieval platform CogStack at University College London Hospitals (UCLH).<h4>Methods</h4>At UCLH, we have deployed the CogStack platform, an information retrieval platform with natural language processing capabilities. The platform addresses the problem of data ingestion and harmonization from multiple data sources using the Apache NiFi module for managing complex data flows. The platform also facilitates the extraction of structured data from free-text records through use of the MedCAT natural language processing library. Finally, data science tools are made available to support data scientists and the development of downstream applications dependent upon data ingested and analyzed by CogStack.<h4>Results</h4>The platform has been deployed at the hospital, and in particular, it has facilitated a number of research and service evaluation projects. To date, we have processed over 30 million records, and the insights produced from CogStack have informed a number of clinical research use cases at the hospital.<h4>Conclusions</h4>The CogStack platform can be configured to handle the data ingestion and harmonization challenges faced by a hospital. More importantly, the platform enables the hospital to unlock important clinical information from the unstructured portion of the record using natural language processing technology.",,pdf:https://medinform.jmir.org/2022/8/e38122/PDF; doi:https://doi.org/10.2196/38122; html:https://europepmc.org/articles/PMC9453582
 36962407,https://doi.org/10.1371/journal.pgph.0000292,Health worker experiences of implementing TB infection prevention and control: A qualitative evidence synthesis to inform implementation recommendations.,"van der Westhuizen HM, Dorward J, Roberts N, Greenhalgh T, Ehrlich R, Butler CC, Tonkin-Crine S.",,PLOS global public health,2022,2022-07-07,Y,,,,"Implementation of TB infection prevention and control (IPC) measures in health facilities is frequently inadequate, despite nosocomial TB transmission to patients and health workers causing harm. We aimed to review qualitative evidence of the complexity associated with implementing TB IPC, to help guide the development of TB IPC implementation plans. We undertook a qualitative evidence synthesis of studies that used qualitative methods to explore the experiences of health workers implementing TB IPC in health facilities. We searched eight databases in November 2021, complemented by citation tracking. Two reviewers screened titles and abstracts and reviewed full texts of potentially eligible papers. We used the Critical Appraisals Skills Programme checklist for quality appraisal, thematic synthesis to identify key findings and the GRADE-CERQual method to appraise the certainty of review findings. The review protocol was pre-registered on PROSPERO, ID CRD42020165314. We screened 1062 titles and abstracts and reviewed 102 full texts, with 37 studies included in the synthesis. We developed 10 key findings, five of which we had high confidence in. We describe several components of TB IPC as a complex intervention. Health workers were influenced by their personal occupational TB risk perceptions when deciding whether to implement TB IPC and neglected the contribution of TB IPC to patient safety. Health workers and researchers expressed multiple uncertainties (for example the duration of infectiousness of people with TB), assumptions and misconceptions about what constitutes effective TB IPC, including focussing TB IPC on patients known with TB on treatment who pose a small risk of transmission. Instead, TB IPC resources should target high risk areas for transmission (crowded, poorly ventilated spaces). Furthermore, TB IPC implementation plans should support health workers to translate TB IPC guidelines to local contexts, including how to navigate unintended stigma caused by IPC, and using limited IPC resources effectively.",,pdf:https://journals.plos.org/globalpublichealth/article/file?id=10.1371/journal.pgph.0000292&type=printable; doi:https://doi.org/10.1371/journal.pgph.0000292; html:https://europepmc.org/articles/PMC10021216; pdf:https://europepmc.org/articles/PMC10021216?pdf=render
 32838035,https://doi.org/10.1002/lrh2.10236,Rapid translation of clinical guidelines into executable knowledge: A case study of COVID-19 and online demonstration.,"Fox J, Khan O, Curtis H, Wright A, Pal C, Cockburn N, Cooper J, Chandan JS, Nirantharakumar K.",,Learning health systems,2021,2020-07-14,Y,Artificial intelligence; Covid‐19; Rapid Learning Systems,,,"<h4>Introduction</h4>We report a pathfinder study of AI/knowledge engineering methods to rapidly formalise COVID-19 guidelines into an executable model of decision making and care pathways. The knowledge source for the study was material published by BMJ Best Practice in March 2020.<h4>Methods</h4>The <i>PROforma</i> guideline modelling language and OpenClinical.net authoring and publishing platform were used to create a data model for care of COVID-19 patients together with executable models of rules, decisions and plans that interpret patient data and give personalised care advice.<h4>Results</h4><i>PROforma</i> and OpenClinical.net proved to be an effective combination for rapidly creating the COVID-19 model; the Pathfinder 1 demonstrator is available for assessment at https://www.openclinical.net/index.php?id=746.<h4>Conclusions</h4>This is believed to be the first use of AI/knowledge engineering methods for disseminating best-practice in COVID-19 care. It demonstrates a novel and promising approach to the rapid translation of clinical guidelines into point of care services, and a foundation for rapid learning systems in many areas of healthcare.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/lrh2.10236; doi:https://doi.org/10.1002/lrh2.10236; html:https://europepmc.org/articles/PMC7323421; pdf:https://europepmc.org/articles/PMC7323421?pdf=render
 37706486,https://doi.org/10.1080/09638288.2023.2254235,Stepped collaborative care for pain and posttraumatic stress disorder after major trauma: a randomized controlled feasibility trial.,"Giummarra MJ, Reeder S, Williams S, Devlin A, Knol R, Ponsford J, Arnold CA, Konstantatos A, Gabbe BJ, Clarke H, Katz J, Mitchell F, Robinson E, Zatzick D.",,Disability and rehabilitation,2024,2023-09-14,Y,Trauma; Injury; Recovery; Pain; Hospitalization; Ptsd; Brief Intervention,,,"<h4>Purpose</h4>To examine feasibility and acceptability of providing stepped collaborative care case management targeting posttraumatic stress disorder (PTSD) and pain symptoms after major traumatic injury.<h4>Materials and methods</h4>Participants were major trauma survivors in Victoria, Australia, at risk of persistent pain or PTSD with high baseline symptoms. Participants were block-randomized, stratified by compensation-status, to the usual care (<i>n</i> = 15) or intervention (<i>n</i> = 17) group (46% of eligible patients). The intervention was adapted from existing stepped collaborative care interventions with input from interdisciplinary experts and people with lived experience in trauma and disability. The proactive case management intervention targeted PTSD and pain management for 6-months using motivational interviewing, cognitive behavioral therapy strategies, and collaborative care. Qualitative interviews explored intervention acceptability.<h4>Results</h4>Intervention participants received a median of 7 h case manager contact and reported that they valued the supportive and non-judgmental listening, and timely access to effective strategies, resources, and treatments post-injury from the case manager. Participants reported few disadvantages from participation, and positive impacts on symptoms and recovery outcomes consistent with the reduction in PTSD and pain symptoms measured at 1-, 3- and 6-months.<h4>Conclusions</h4>Stepped collaborative care was low-cost, feasible, and acceptable to people at risk of PTSD or pain after major trauma.IMPLICATIONS FOR REHABILITATIONAfter hospitalization for injury, people can experience difficulty accessing timely support to manage posttraumatic stress, pain and other concerns.Stepped case management-based interventions that provide individualized support and collaborative care have reduced posttraumatic stress symptom severity for patients admitted to American trauma centers.We showed that this model of care could be adapted to target pain and mental health in the trauma system in Victoria, Australia.The intervention was low cost, acceptable and highly valued by most participants who perceived that it helped them use strategies to better manage post-traumatic symptoms, and to access clinicians and treatments relevant to their needs.",,pdf:https://www.tandfonline.com/doi/pdf/10.1080/09638288.2023.2254235?needAccess=true; doi:https://doi.org/10.1080/09638288.2023.2254235; html:https://europepmc.org/articles/PMC10937328; pdf:https://europepmc.org/articles/PMC10937328?pdf=render
 37850214,https://doi.org/10.1183/23120541.00110-2023,Mapping inpatient care pathways for patients with COPD: an observational study using routinely collected electronic hospital record data.,"Evison F, Cooper R, Gallier S, Missier P, Sayer AA, Sapey E, Witham MD.",,ERJ open research,2023,2023-09-01,Y,,,,"<h4>Introduction</h4>Respiratory specialist ward care is associated with better outcomes for patients with COPD exacerbations. We assessed patient pathways and associated factors for people admitted to hospital with COPD exacerbations.<h4>Methods</h4>We analysed routinely collected electronic health data for patients admitted with COPD exacerbation in 2018 to Queen Elizabeth Hospital, Birmingham, UK. We extracted data on demographics, deprivation index, Elixhauser comorbidities, ward moves, length of stay, and in-hospital and 1-year mortality. We compared care pathways with recommended care pathways (transition from initial assessment area to respiratory wards or discharge). We used Markov state transition models to derive probabilities of following recommended pathways for patient subgroups.<h4>Results</h4>Of 42 555 patients with unplanned admissions during 2018, 571 patients were admitted at least once with an exacerbation of COPD. The mean±sd age was 51±11 years; 313 (55%) were women, 337 (59%) lived in the most deprived neighbourhoods and 45 (9%) were from non-white ethnic backgrounds. 428 (75.0%) had ≥4 comorbidities. Age >70 years was associated with higher in-hospital and 1-year mortality, more places of care (wards) and longer length of stay; having ≥4 comorbidities was associated with higher mortality and longer length of stay. Older age was associated with a significantly lower probability of following a recommended pathway (>70 years: 0.514, 95% CI 0.458-0.571; ≤70 years: 0.636, 95% CI 0.572-0.696; p=0.004).<h4>Conclusions</h4>Only older age was associated with a lower chance of following recommended hospital pathways of care. Such analyses could help refine appropriate care pathways for patients with COPD exacerbations.",,pdf:https://openres.ersjournals.com/content/erjor/early/2023/08/24/23120541.00110-2023.full.pdf; doi:https://doi.org/10.1183/23120541.00110-2023; html:https://europepmc.org/articles/PMC10577591; pdf:https://europepmc.org/articles/PMC10577591?pdf=render
 39039249,https://doi.org/10.1038/s41591-024-03142-z,Proteomic signatures improve risk prediction for common and rare diseases.,"Carrasco-Zanini J, Pietzner M, Davitte J, Surendran P, Croteau-Chonka DC, Robins C, Torralbo A, Tomlinson C, Grünschläger F, Fitzpatrick N, Ytsma C, Kanno T, Gade S, Freitag D, Ziebell F, Haas S, Denaxas S, Betts JC, Wareham NJ, Hemingway H, Scott RA, Langenberg C.",,Nature medicine,2024,2024-07-22,Y,,,,"For many diseases there are delays in diagnosis due to a lack of objective biomarkers for disease onset. Here, in 41,931 individuals from the United Kingdom Biobank Pharma Proteomics Project, we integrated measurements of ~3,000 plasma proteins with clinical information to derive sparse prediction models for the 10-year incidence of 218 common and rare diseases (81-6,038 cases). We then compared prediction models developed using proteomic data with models developed using either basic clinical information alone or clinical information combined with data from 37 clinical assays. The predictive performance of sparse models including as few as 5 to 20 proteins was superior to the performance of models developed using basic clinical information for 67 pathologically diverse diseases (median delta C-index = 0.07; range = 0.02-0.31). Sparse protein models further outperformed models developed using basic information combined with clinical assay data for 52 diseases, including multiple myeloma, non-Hodgkin lymphoma, motor neuron disease, pulmonary fibrosis and dilated cardiomyopathy. For multiple myeloma, single-cell RNA sequencing from bone marrow in newly diagnosed patients showed that four of the five predictor proteins were expressed specifically in plasma cells, consistent with the strong predictive power of these proteins. External replication of sparse protein models in the EPIC-Norfolk study showed good generalizability for prediction of the six diseases tested. These findings show that sparse plasma protein signatures, including both disease-specific proteins and protein predictors shared across several diseases, offer clinically useful prediction of common and rare diseases.",,doi:https://doi.org/10.1038/s41591-024-03142-z; html:https://europepmc.org/articles/PMC11405273; pdf:https://europepmc.org/articles/PMC11405273?pdf=render
 37798805,https://doi.org/10.1186/s13063-023-07576-7,"Medicines and Healthcare products Regulatory Agency's ""Consultation on proposals for legislative changes for clinical trials"": a response from the Trials Methodology Research Partnership Adaptive Designs Working Group, with a focus on data sharing.","Law M, Couturier DL, Choodari-Oskooei B, Crout P, Gamble C, Jacko P, Pallmann P, Pilling M, Robertson DS, Robling M, Sydes MR, Villar SS, Wason J, Wheeler G, Williamson SF, Yap C, Jaki T.",,Trials,2023,2023-10-05,Y,Legislation; data sharing; Consultation,,,"In the UK, the Medicines and Healthcare products Regulatory Agency consulted on proposals ""to improve and strengthen the UK clinical trials legislation to help us make the UK the best place to research and develop safe and innovative medicines"". The purpose of the consultation was to help finalise the proposals and contribute to the drafting of secondary legislation. We discussed these proposals as members of the Trials Methodology Research Partnership Adaptive Designs Working Group, which is jointly funded by the Medical Research Council and the National Institute for Health and Care Research. Two topics arose frequently in the discussion: the emphasis on legislation, and the absence of questions on data sharing. It is our opinion that the proposals rely heavily on legislation to change practice. However, clinical trials are heterogeneous, and as a result some trials will struggle to comply with all of the proposed legislation. Furthermore, adaptive design clinical trials are even more heterogeneous than their non-adaptive counterparts, and face more challenges. Consequently, it is possible that increased legislation could have a greater negative impact on adaptive designs than non-adaptive designs. Overall, we are sceptical that the introduction of legislation will achieve the desired outcomes, with some exceptions. Meanwhile the topic of data sharing - making anonymised individual-level clinical trial data available to other investigators for further use - is entirely absent from the proposals and the consultation in general. However, as an aspect of the wider concept of open science and reproducible research, data sharing is an increasingly important aspect of clinical trials. The benefits of data sharing include faster innovation, improved surveillance of drug safety and effectiveness and decreasing participant exposure to unnecessary risk. There are already a number of UK-focused documents that discuss and encourage data sharing, for example, the Concordat on Open Research Data and the Medical Research Council's Data Sharing Policy. We strongly suggest that data sharing should be the norm rather than the exception, and hope that the forthcoming proposals on clinical trials invite discussion on this important topic.",,pdf:https://trialsjournal.biomedcentral.com/counter/pdf/10.1186/s13063-023-07576-7; doi:https://doi.org/10.1186/s13063-023-07576-7; html:https://europepmc.org/articles/PMC10552399; pdf:https://europepmc.org/articles/PMC10552399?pdf=render
-37578823,https://doi.org/10.2196/45233,Challenges in Using mHealth Data From Smartphones and Wearable Devices to Predict Depression Symptom Severity: Retrospective Analysis.,"Sun S, Folarin AA, Zhang Y, Cummins N, Garcia-Dias R, Stewart C, Ranjan Y, Rashid Z, Conde P, Laiou P, Sankesara H, Matcham F, Leightley D, White KM, Oetzmann C, Ivan A, Lamers F, Siddi S, Simblett S, Nica R, Rintala A, Mohr DC, Myin-Germeys I, Wykes T, Haro JM, Penninx BWJH, Vairavan S, Narayan VA, Annas P, Hotopf M, Dobson RJB, RADAR-CNS Consortium.",,Journal of medical Internet research,2023,2023-08-14,Y,Depression; Mobile phone; Missing Data; Smartphones; Mobile Health; Wearable Devices; Behavioral Patterns; Digital Phenotypes,,,"<h4>Background</h4>Major depressive disorder (MDD) affects millions of people worldwide, but timely treatment is not often received owing in part to inaccurate subjective recall and variability in the symptom course. Objective and frequent MDD monitoring can improve subjective recall and help to guide treatment selection. Attempts have been made, with varying degrees of success, to explore the relationship between the measures of depression and passive digital phenotypes (features) extracted from smartphones and wearables devices to remotely and continuously monitor changes in symptomatology. However, a number of challenges exist for the analysis of these data. These include maintaining participant engagement over extended time periods and therefore understanding what constitutes an acceptable threshold of missing data; distinguishing between the cross-sectional and longitudinal relationships for different features to determine their utility in tracking within-individual longitudinal variation or screening individuals at high risk; and understanding the heterogeneity with which depression manifests itself in behavioral patterns quantified by the passive features.<h4>Objective</h4>We aimed to address these 3 challenges to inform future work in stratified analyses.<h4>Methods</h4>Using smartphone and wearable data collected from 479 participants with MDD, we extracted 21 features capturing mobility, sleep, and smartphone use. We investigated the impact of the number of days of available data on feature quality using the intraclass correlation coefficient and Bland-Altman analysis. We then examined the nature of the correlation between the 8-item Patient Health Questionnaire (PHQ-8) depression scale (measured every 14 days) and the features using the individual-mean correlation, repeated measures correlation, and linear mixed effects model. Furthermore, we stratified the participants based on their behavioral difference, quantified by the features, between periods of high (depression) and low (no depression) PHQ-8 scores using the Gaussian mixture model.<h4>Results</h4>We demonstrated that at least 8 (range 2-12) days were needed for reliable calculation of most of the features in the 14-day time window. We observed that features such as sleep onset time correlated better with PHQ-8 scores cross-sectionally than longitudinally, whereas features such as wakefulness after sleep onset correlated well with PHQ-8 longitudinally but worse cross-sectionally. Finally, we found that participants could be separated into 3 distinct clusters according to their behavioral difference between periods of depression and periods of no depression.<h4>Conclusions</h4>This work contributes to our understanding of how these mobile health-derived features are associated with depression symptom severity to inform future work in stratified analyses.",,pdf:https://www.jmir.org/2023/1/e45233/PDF; doi:https://doi.org/10.2196/45233; html:https://europepmc.org/articles/PMC10463088
 37456658,https://doi.org/10.12688/hrbopenres.13667.1,Qualitative data sharing practices in clinical trials in the UK and Ireland: towards the production of good practice guidance.,"McCarthy M, Gillies K, Rousseau N, Wade J, Gamble C, Toomey E, Matvienko-Sikar K, Sydes M, Dowling M, Bryant V, Biesty L, Houghton C.",,HRB open research,2023,2023-02-06,Y,data sharing; Qualitative; trials; Focus Groups,,,"<b>Background</b>: Data sharing enables researchers to conduct novel research with previously collected datasets, thus maximising scientific findings and cost effectiveness, and reducing research waste. The value of sharing, even de-identified, quantitative data from clinical trials is well recognised with a moderated access approach recommended. While substantial challenges to sharing quantitative data remain, there are additional challenges for sharing qualitative data in trials. Incorporating the necessary information about how qualitative data will be shared into already complex trial recruitment and consent processes proves challenging. The aim of this study was to explore whether and how trial teams share qualitative data collected as part of the design, conduct, analysis, or delivery of clinical trials. <b>Methods: </b>Phase 1 involved semi-structured, in-depth qualitative interviews and focus groups with key trial stakeholder groups including trial managers and clinical trialists (n=3), qualitative researchers in trials (n=9), members of research funding bodies (n=2) and trial participants (n=1). Data were analysed using thematic analysis. In Phase 2, we conducted a content analysis of 16 participant information leaflets (PIL) and consent forms (CF) for trials that collected qualitative data. <b>Results:</b> Three key themes were identified from our Phase 1 findings: ' <i>Understanding and experiences of the potential benefits of sharing qualitative data from trials', 'Concerns about qualitative data sharing'</i>, and ' <i>Future guidance and funding</i>'. In phase 2, the PILs and CFs received revealed that the benefits of data sharing for participants were only explained in two of the study documents. <b>Conclusions:</b> The value of sharing qualitative data was acknowledged, but there are many uncertainties as to how, when, and where to share this data. In addition, there were ethical concerns in relation to the consent process required for qualitative data sharing in trials. This study provides insight into the existing practice of qualitative data sharing in trials.",,pdf:https://hrbopenresearch.org/articles/6-10/pdf; doi:https://doi.org/10.12688/hrbopenres.13667.1; html:https://europepmc.org/articles/PMC10345597; pdf:https://europepmc.org/articles/PMC10345597?pdf=render
+37578823,https://doi.org/10.2196/45233,Challenges in Using mHealth Data From Smartphones and Wearable Devices to Predict Depression Symptom Severity: Retrospective Analysis.,"Sun S, Folarin AA, Zhang Y, Cummins N, Garcia-Dias R, Stewart C, Ranjan Y, Rashid Z, Conde P, Laiou P, Sankesara H, Matcham F, Leightley D, White KM, Oetzmann C, Ivan A, Lamers F, Siddi S, Simblett S, Nica R, Rintala A, Mohr DC, Myin-Germeys I, Wykes T, Haro JM, Penninx BWJH, Vairavan S, Narayan VA, Annas P, Hotopf M, Dobson RJB, RADAR-CNS Consortium.",,Journal of medical Internet research,2023,2023-08-14,Y,Depression; Mobile phone; Missing Data; Smartphones; Mobile Health; Wearable Devices; Behavioral Patterns; Digital Phenotypes,,,"<h4>Background</h4>Major depressive disorder (MDD) affects millions of people worldwide, but timely treatment is not often received owing in part to inaccurate subjective recall and variability in the symptom course. Objective and frequent MDD monitoring can improve subjective recall and help to guide treatment selection. Attempts have been made, with varying degrees of success, to explore the relationship between the measures of depression and passive digital phenotypes (features) extracted from smartphones and wearables devices to remotely and continuously monitor changes in symptomatology. However, a number of challenges exist for the analysis of these data. These include maintaining participant engagement over extended time periods and therefore understanding what constitutes an acceptable threshold of missing data; distinguishing between the cross-sectional and longitudinal relationships for different features to determine their utility in tracking within-individual longitudinal variation or screening individuals at high risk; and understanding the heterogeneity with which depression manifests itself in behavioral patterns quantified by the passive features.<h4>Objective</h4>We aimed to address these 3 challenges to inform future work in stratified analyses.<h4>Methods</h4>Using smartphone and wearable data collected from 479 participants with MDD, we extracted 21 features capturing mobility, sleep, and smartphone use. We investigated the impact of the number of days of available data on feature quality using the intraclass correlation coefficient and Bland-Altman analysis. We then examined the nature of the correlation between the 8-item Patient Health Questionnaire (PHQ-8) depression scale (measured every 14 days) and the features using the individual-mean correlation, repeated measures correlation, and linear mixed effects model. Furthermore, we stratified the participants based on their behavioral difference, quantified by the features, between periods of high (depression) and low (no depression) PHQ-8 scores using the Gaussian mixture model.<h4>Results</h4>We demonstrated that at least 8 (range 2-12) days were needed for reliable calculation of most of the features in the 14-day time window. We observed that features such as sleep onset time correlated better with PHQ-8 scores cross-sectionally than longitudinally, whereas features such as wakefulness after sleep onset correlated well with PHQ-8 longitudinally but worse cross-sectionally. Finally, we found that participants could be separated into 3 distinct clusters according to their behavioral difference between periods of depression and periods of no depression.<h4>Conclusions</h4>This work contributes to our understanding of how these mobile health-derived features are associated with depression symptom severity to inform future work in stratified analyses.",,pdf:https://www.jmir.org/2023/1/e45233/PDF; doi:https://doi.org/10.2196/45233; html:https://europepmc.org/articles/PMC10463088
 35485805,https://doi.org/10.1017/s003329172200109x,Multimorbidity clusters among people with serious mental illness: a representative primary and secondary data linkage cohort study.,"Ma R, Romano E, Ashworth M, Yadegarfar ME, Dregan A, Ronaldson A, de Oliveira C, Jacobs R, Stewart R, Stubbs B.",,Psychological medicine,2023,2022-04-29,Y,Mortality; Schizophrenia; Psychosis; Physical Health; Multimorbidity,,,"<h4>Background</h4>People with serious mental illness (SMI) experience higher mortality partially attributable to higher long-term condition (LTC) prevalence. However, little is known about multiple LTCs (MLTCs) clustering in this population.<h4>Methods</h4>People from South London with SMI and two or more existing LTCs aged 18+ at diagnosis were included using linked primary and mental healthcare records, 2012-2020. Latent class analysis (LCA) determined MLTC classes and multinominal logistic regression examined associations between demographic/clinical characteristics and latent class membership.<h4>Results</h4>The sample included 1924 patients (mean (s.d.) age 48.2 (17.3) years). Five latent classes were identified: 'substance related' (24.9%), 'atopic' (24.2%), 'pure affective' (30.4%), 'cardiovascular' (14.1%), and 'complex multimorbidity' (6.4%). Patients had on average 7-9 LTCs in each cluster. Males were at increased odds of MLTCs in all four clusters, compared to the 'pure affective'. Compared to the largest cluster ('pure affective'), the 'substance related' and the 'atopic' clusters were younger [odds ratios (OR) per year increase 0.99 (95% CI 0.98-1.00) and 0.96 (0.95-0.97) respectively], and the 'cardiovascular' and 'complex multimorbidity' clusters were older (ORs 1.09 (1.07-1.10) and 1.16 (1.14-1.18) respectively). The 'substance related' cluster was more likely to be White, the 'cardiovascular' cluster more likely to be Black (compared to White; OR 1.75, 95% CI 1.10-2.79), and both more likely to have schizophrenia, compared to other clusters.<h4>Conclusion</h4>The current study identified five latent class MLTC clusters among patients with SMI. An integrated care model for treating MLTCs in this population is recommended to improve multimorbidity care.",,pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/BDE3DC6059EB59B00B2E0CD892963804/S003329172200109Xa.pdf/div-class-title-multimorbidity-clusters-among-people-with-serious-mental-illness-a-representative-primary-and-secondary-data-linkage-cohort-study-div.pdf; doi:https://doi.org/10.1017/S003329172200109X; html:https://europepmc.org/articles/PMC10388332; pdf:https://europepmc.org/articles/PMC10388332?pdf=render
 36644660,https://doi.org/10.1177/20552076221128677,Evaluation of prototype risk prediction tools for clinicians and people living with type 2 diabetes in North West London using the think aloud method.,"Gardner C, Wake D, Brodie D, Silverstein A, Young S, Cunningham S, Sainsbury C, Ilia M, Lucas A, Willis T, Halligan J.",,Digital health,2023,2023-01-08,Y,Artificial intelligence; Internet; Diabetes; Qualitative; risk factors; Machine Learning; Health Informatics; Behaviour Change; Personalised Medicine; Digital Health,,,"The prevalence of type 2 diabetes in North West London (NWL) is relatively high compared to other parts of the United Kingdom with outcomes suboptimal. This presents a need for more effective strategies to identify people living with type 2 diabetes who need additional support. An emerging subset of web-based interventions for diabetes self-management and population management has used artificial intelligence and machine learning models to stratify the risk of complications from diabetes and identify patients in need of immediate support. In this study, two prototype risk prediction tools on the MyWay Diabetes and MyWay Clinical platforms were evaluated with six clinicians and six people living with type 2 diabetes in NWL using the think aloud method. The results of the sessions with people living with type 2 diabetes showed that the concept of the tool was intuitive, however, more instruction on how to correctly use the risk prediction tool would be valuable. The feedback from the sessions with clinicians was that the data presented in the tool aligned with the key diabetes targets in NWL, and that this would be useful for identifying and inviting patients to the practice who are overdue for tests and at risk of complications. The findings of the evaluation have been used to support the development of the prototype risk predictions tools. This study demonstrates the value of conducting usability testing on web-based interventions designed to support the targeted management of type 2 diabetes in local communities.",,doi:https://doi.org/10.1177/20552076221128677; doi:https://doi.org/10.1177/20552076221128677; html:https://europepmc.org/articles/PMC9834412; pdf:https://europepmc.org/articles/PMC9834412?pdf=render
 34468322,https://doi.org/10.2196/30083,An Early Warning Risk Prediction Tool (RECAP-V1) for Patients Diagnosed With COVID-19: Protocol for a Statistical Analysis Plan.,"Fiorentino F, Prociuk D, Espinosa Gonzalez AB, Neves AL, Husain L, Ramtale SC, Mi E, Mi E, Macartney J, Anand SN, Sherlock J, Saravanakumar K, Mayer E, de Lusignan S, Greenhalgh T, Delaney BC.",,JMIR research protocols,2021,2021-10-05,Y,Modeling; Early warning; Risk Score; Remote Assessment; Covid-19,,,"<h4>Background</h4>Since the start of the COVID-19 pandemic, efforts have been made to develop early warning risk scores to help clinicians decide which patient is likely to deteriorate and require hospitalization. The RECAP (Remote COVID-19 Assessment in Primary Care) study investigates the predictive risk of hospitalization, deterioration, and death of patients with confirmed COVID-19, based on a set of parameters chosen through a Delphi process performed by clinicians. We aim to use rich data collected remotely through the use of electronic data templates integrated in the electronic health systems of several general practices across the United Kingdom to construct accurate predictive models. The models will be based on preexisting conditions and monitoring data of a patient's clinical parameters (eg, blood oxygen saturation) to make reliable predictions as to the patient's risk of hospital admission, deterioration, and death.<h4>Objective</h4>This statistical analysis plan outlines the statistical methods to build the prediction model to be used in the prioritization of patients in the primary care setting. The statistical analysis plan for the RECAP study includes the development and validation of the RECAP-V1 prediction model as a primary outcome. This prediction model will be adapted as a three-category risk score split into red (high risk), amber (medium risk), and green (low risk) for any patient with suspected COVID-19. The model will predict the risk of deterioration and hospitalization.<h4>Methods</h4>After the data have been collected, we will assess the degree of missingness and use a combination of traditional data imputation using multiple imputation by chained equations, as well as more novel machine-learning approaches to impute the missing data for the final analysis. For predictive model development, we will use multiple logistic regression analyses to construct the model. We aim to recruit a minimum of 1317 patients for model development and validation. We will then externally validate the model on an independent dataset of 1400 patients. The model will also be applied for multiple different datasets to assess both its performance in different patient groups and its applicability for different methods of data collection.<h4>Results</h4>As of May 10, 2021, we have recruited 3732 patients. A further 2088 patients have been recruited through the National Health Service Clinical Assessment Service, and approximately 5000 patients have been recruited through the DoctalyHealth platform.<h4>Conclusions</h4>The methodology for the development of the RECAP-V1 prediction model as well as the risk score will provide clinicians with a statistically robust tool to help prioritize COVID-19 patients.<h4>Trial registration</h4>ClinicalTrials.gov NCT04435041; https://clinicaltrials.gov/ct2/show/NCT04435041.<h4>International registered report identifier (irrid)</h4>DERR1-10.2196/30083.",,doi:https://doi.org/10.2196/30083; doi:https://doi.org/10.2196/30083; html:https://europepmc.org/articles/PMC8494068
@@ -833,12 +834,12 @@ PMC8718341,https://doi.org/,"Loneliness, coping, suicidal thoughts and self-harm
 37918923,https://doi.org/10.1136/bmjopen-2023-072531,Evaluation of variation in special educational needs provision and its impact on health and education using administrative records for England: umbrella protocol for a mixed-methods research programme.,"Zylbersztejn A, Lewis K, Nguyen V, Matthews J, Winterburn I, Karwatowska L, Barnes S, Lilliman M, Saxton J, Stone A, Boddy K, Downs J, Logan S, Rahi J, Black-Hawkins K, Dearden L, Ford T, Harron K, De Stavola B, Gilbert R.",,BMJ open,2023,2023-11-02,Y,epidemiology; Public Health; Qualitative Research; Health Informatics; Statistics & Research Methods; Health Equity,,,"<h4>Introduction</h4>One-third of children in England have special educational needs (SEN) provision recorded during their school career. The proportion of children with SEN provision varies between schools and demographic groups, which may reflect variation in need, inequitable provision and/or systemic factors. There is scant evidence on whether SEN provision improves health and education outcomes.<h4>Methods</h4>The Health Outcomes of young People in Education (HOPE) research programme uses administrative data from the Education and Child Health Insights from Linked Data-ECHILD-which contains data from all state schools, and contacts with National Health Service hospitals in England, to explore variation in SEN provision and its impact on health and education outcomes. This umbrella protocol sets out analyses across four work packages (WP). WP1 defined a range of 'health phenotypes', that is health conditions expected to need SEN provision in primary school. Next, we describe health and education outcomes (WP1) and individual, school-level and area-level factors affecting variation in SEN provision across different phenotypes (WP2). WP3 assesses the impact of SEN provision on health and education outcomes for specific health phenotypes using a range of causal inference methods to account for confounding factors and possible selection bias. In WP4 we review local policies and synthesise findings from surveys, interviews and focus groups of service users and providers to understand factors associated with variation in and experiences of identification, assessment and provision for SEN. Triangulation of findings on outcomes, variation and impact of SEN provision for different health phenotypes in ECHILD, with experiences of SEN provision will inform interpretation of findings for policy, practice and families and methods for future evaluation.<h4>Ethics and dissemination</h4>Research ethics committees have approved the use of the ECHILD database and, separately, the survey, interviews and focus groups of young people, parents and service providers. These stakeholders will contribute to the design, interpretation and communication of findings.",,doi:https://doi.org/10.1136/bmjopen-2023-072531; html:https://europepmc.org/articles/PMC10626865; pdf:https://europepmc.org/articles/PMC10626865?pdf=render
 36810190,https://doi.org/10.1136/bmjebm-2023-112253,Digitally enabled decentralised research: opportunities to improve the efficiency of clinical trials and observational studies.,"Aiyegbusi OL, Davies EH, Myles P, Williams T, Frost C, Haroon S, Hughes SE, Wilson R, McMullan C, Subramanian A, Nirantharakumar K, Calvert MJ.",,BMJ evidence-based medicine,2023,2023-02-21,Y,information technology; drug discovery; Drug Development; Covid-19,,,,,pdf:https://ebm.bmj.com/content/ebmed/early/2023/02/20/bmjebm-2023-112253.full.pdf; doi:https://doi.org/10.1136/bmjebm-2023-112253; html:https://europepmc.org/articles/PMC10579468; pdf:https://europepmc.org/articles/PMC10579468?pdf=render
 37185641,https://doi.org/10.1136/bmjopen-2022-070022,EXAcerbations of COPD and their OutcomeS on CardioVascular diseases (EXACOS-CV) Programme: protocol of multicountry observational cohort studies.,"Nordon C, Rhodes K, Quint JK, Vogelmeier CF, Simons SO, Hawkins NM, Marshall J, Ouwens M, Garbe E, Müllerová H.",,BMJ open,2023,2023-04-26,Y,epidemiology; Cardiology; Vascular Medicine; Chronic Airways Disease,,,"<h4>Introduction</h4>In patients with chronic obstructive pulmonary disease (COPD), the risk of certain cardiovascular (CV) events is increased by threefold to fivefold in the year following acute exacerbation of COPD (AECOPD), compared with a non-exacerbation period. While the effect of severe AECOPD is well established, the relationship of moderate exacerbation or prior exacerbation to elevated risk of CV events is less clear. We will conduct cohort studies in multiple countries to further characterise the association between AECOPD and CV events.<h4>Methods and analysis</h4>Retrospective longitudinal cohort studies will be conducted within routinely collected electronic healthcare records or claims databases. The study cohorts will include patients meeting inclusion criteria for COPD between 1 January 2014 and 31 December 2018. Moderate exacerbation is defined as an outpatient visit and/or medication dispensation/prescription for exacerbation; severe exacerbation is defined as hospitalisation for COPD. The primary outcomes of interest are the time to (1) first hospitalisation for a CV event (including acute coronary syndrome, heart failure, arrhythmias or cerebral ischaemia) since cohort entry or (2) death. Time-dependent Cox proportional hazards models will compare the hazard of a CV event between exposed periods following exacerbation (split into these periods: 1-7, 8-14, 15-30, 31-180 and 181-365 days) and the unexposed reference time period, adjusted on time-fixed and time-varying confounders.<h4>Ethics and dissemination</h4>Studies have been approved in Canada, Japan, the Netherlands, Spain and the UK, where an institutional review board is mandated. For each study, the results will be published in peer-reviewed journals.",,pdf:https://bmjopen.bmj.com/content/bmjopen/13/4/e070022.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-070022; html:https://europepmc.org/articles/PMC10151875; pdf:https://europepmc.org/articles/PMC10151875?pdf=render
-35105585,https://doi.org/10.1136/bmjopen-2021-054376,Development of an algorithm to classify primary care electronic health records of alcohol consumption: experience using data linkage from UK Biobank and primary care electronic health data sources.,"Fraile-Navarro D, Azcoaga-Lorenzo A, Agrawal U, Jani B, Fagbamigbe A, Currie D, Baldacchino A, Sullivan F.",,BMJ open,2022,2022-02-01,Y,Public Health; Primary Care; Health Informatics,,,"<h4>Objectives</h4>Develop a novel algorithm to categorise alcohol consumption using primary care electronic health records (EHRs) and asses its reliability by comparing this classification with self-reported alcohol consumption data obtained from the UK Biobank (UKB) cohort.<h4>Design</h4>Cross-sectional study.<h4>Setting</h4>The UKB, a population-based cohort with participants aged between 40 and 69 years recruited across the UK between 2006 and 2010.<h4>Participants</h4>UKB participants from Scotland with linked primary care data.<h4>Primary and secondary outcome measures</h4>Create a rule-based multiclass algorithm to classify alcohol consumption reported by Scottish UKB participants and compare it with their classification using data present in primary care EHRs based on Read Codes. We evaluated agreement metrics (simple agreement and kappa statistic).<h4>Results</h4>Among the Scottish UKB participants, 18 838 (69%) had at least one Read Code related to alcohol consumption and were used in the classification. The agreement of alcohol consumption categories between UKB and primary care data, including assessments within 5 years was 59.6%, and kappa was 0.23 (95% CI 0.21 to 0.24). Differences in classification between the two sources were statistically significant (p<0.001); More individuals were classified as 'sensible drinkers' and in lower alcohol consumption levels in primary care records compared with the UKB. Agreement improved slightly when using only numerical values (k=0.29; 95% CI 0.27 to 0.31) and decreased when using qualitative descriptors only (k=0.18;95% CI 0.16 to 0.20).<h4>Conclusion</h4>Our algorithm classifies alcohol consumption recorded in Primary Care EHRs into discrete meaningful categories. These results suggest that alcohol consumption may be underestimated in primary care EHRs. Using numerical values (alcohol units) may improve classification when compared with qualitative descriptors.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/2/e054376.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-054376; html:https://europepmc.org/articles/PMC8808438; pdf:https://europepmc.org/articles/PMC8808438?pdf=render
 36525457,https://doi.org/10.1371/journal.pone.0279250,Undergoing radical treatment for prostate cancer and its impact on wellbeing: A qualitative study exploring men's experiences.,"Vyas N, Brunckhorst O, Fox L, Van Hemelrijck M, Muir G, Stewart R, Dasgupta P, Ahmed K.",,PloS one,2022,2022-12-16,Y,,,,"<h4>Introduction</h4>Quality of life in prostate cancer survivorship is becoming increasingly important, with mental and social wellbeing recognised as key components. However, limited global evaluation of psychosocial challenges experienced after treatment exists. Therefore, we aimed to explore the lived experiences of men who underwent radical treatment, and its psychosocial impact.<h4>Material and methods</h4>This qualitative study was conducted using 19 men who had undergone radical treatment (prostatectomy or radiotherapy) for their cancer. Semi-structured interviews were conducted exploring lived experiences of men after treatment. A Structured thematic analysis of collected data was undertaken, with an inductive co-construction of themes through the lens of the biopsychosocial model. Themes generated were considered within a psychological, social, and physical wellbeing framework.<h4>Results</h4>An initial knowledge gap meant mental wellbeing was strongly impacted initially leading to a 'Diagnostic Blow and the Search for Clarity'. Doubt over individuals' future resulted in 'An Uncertain Future' in many men. Once treatment was completed a 'Reflective journey' began, with men considering their outcomes and decisions made. Social wellbeing was also impacted with many identifying the 'Emotional Repercussions' on their relationships and the impact their diagnosis had on their partner and family. Many subsequently sought to increase their support through 'The Social Network and Advocacy', while physical changes led to an increased need for 'Social Planning'. Finally, physical wellbeing was highlighted by a continual acknowledgement of the 'Natural process of ageing' leading to a reluctancy to seek help, whilst simultaneously attempting to improve existing health via 'The Health Kick'.<h4>Conclusions</h4>Radical treatments have a considerable impact on mental and social wellbeing of individuals. Anxiety after diagnosis and significant uncertainty over individual futures exist, with physical complications of treatment leading to social repercussions. Future research should aim to identify forms of support to improve quality of life of these men.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0279250&type=printable; doi:https://doi.org/10.1371/journal.pone.0279250; html:https://europepmc.org/articles/PMC9757548; pdf:https://europepmc.org/articles/PMC9757548?pdf=render
+35105585,https://doi.org/10.1136/bmjopen-2021-054376,Development of an algorithm to classify primary care electronic health records of alcohol consumption: experience using data linkage from UK Biobank and primary care electronic health data sources.,"Fraile-Navarro D, Azcoaga-Lorenzo A, Agrawal U, Jani B, Fagbamigbe A, Currie D, Baldacchino A, Sullivan F.",,BMJ open,2022,2022-02-01,Y,Public Health; Primary Care; Health Informatics,,,"<h4>Objectives</h4>Develop a novel algorithm to categorise alcohol consumption using primary care electronic health records (EHRs) and asses its reliability by comparing this classification with self-reported alcohol consumption data obtained from the UK Biobank (UKB) cohort.<h4>Design</h4>Cross-sectional study.<h4>Setting</h4>The UKB, a population-based cohort with participants aged between 40 and 69 years recruited across the UK between 2006 and 2010.<h4>Participants</h4>UKB participants from Scotland with linked primary care data.<h4>Primary and secondary outcome measures</h4>Create a rule-based multiclass algorithm to classify alcohol consumption reported by Scottish UKB participants and compare it with their classification using data present in primary care EHRs based on Read Codes. We evaluated agreement metrics (simple agreement and kappa statistic).<h4>Results</h4>Among the Scottish UKB participants, 18 838 (69%) had at least one Read Code related to alcohol consumption and were used in the classification. The agreement of alcohol consumption categories between UKB and primary care data, including assessments within 5 years was 59.6%, and kappa was 0.23 (95% CI 0.21 to 0.24). Differences in classification between the two sources were statistically significant (p<0.001); More individuals were classified as 'sensible drinkers' and in lower alcohol consumption levels in primary care records compared with the UKB. Agreement improved slightly when using only numerical values (k=0.29; 95% CI 0.27 to 0.31) and decreased when using qualitative descriptors only (k=0.18;95% CI 0.16 to 0.20).<h4>Conclusion</h4>Our algorithm classifies alcohol consumption recorded in Primary Care EHRs into discrete meaningful categories. These results suggest that alcohol consumption may be underestimated in primary care EHRs. Using numerical values (alcohol units) may improve classification when compared with qualitative descriptors.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/2/e054376.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-054376; html:https://europepmc.org/articles/PMC8808438; pdf:https://europepmc.org/articles/PMC8808438?pdf=render
 35577541,https://doi.org/10.1136/archdischild-2021-323616,Changes in adolescents' planned hospital care during the COVID-19 pandemic: analysis of linked administrative data.,"Mc Grath-Lone L, Etoori D, Gilbert R, Harron KL, Woodman J, Blackburn R.",,Archives of disease in childhood,2022,2022-09-20,Y,Social Work; Child Health Services; Adolescent Health; Covid-19,,,"<h4>Objective</h4>To describe changes in planned hospital care during the pandemic for vulnerable adolescents receiving children's social care (CSC) services or special educational needs (SEN) support, relative to their peers.<h4>Design</h4>Observational cohort in the Education and Child Health Insights from Linked Data database (linked de-identified administrative health, education and social care records of all children in England).<h4>Study population</h4>All secondary school pupils in years 7-11 in academic year 2019/2020 (N=3 030 235).<h4>Main exposure</h4>Receiving SEN support or CSC services.<h4>Main outcomes</h4>Changes in outpatient attendances and planned hospital admissions during the first 9 months of the pandemic (23 March-31 December 2020), estimated by comparing predicted with observed numbers and rates per 1000 child-years.<h4>Results</h4>A fifth of pupils (20.5%) received some form of statutory support: 14.2% received SEN support only, 3.6% received CSC services only and 2.7% received both. Decreases in planned hospital care were greater for these vulnerable adolescents than their peers: -290 vs -225 per 1000 child-years for outpatient attendances and -36 vs -16 per 1000 child-years for planned admissions. Overall, 21% of adolescents who were vulnerable disproportionately bore 25% of the decrease in outpatient attendances and 37% of the decrease in planned hospital admissions. Vulnerable adolescents were less likely than their peers to have face-to-face outpatient care.<h4>Conclusion</h4>These findings indicate that socially vulnerable groups of children have high health needs, which may need to be prioritised to ensure equitable provision, including for catch-up of planned care postpandemic.",,pdf:https://adc.bmj.com/content/archdischild/107/10/e29.full.pdf; doi:https://doi.org/10.1136/archdischild-2021-323616; html:https://europepmc.org/articles/PMC9157329; pdf:https://europepmc.org/articles/PMC9157329?pdf=render
 38383544,https://doi.org/10.1038/s41467-024-45761-7,The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies.,"Lipworth S, Matlock W, Shaw L, Vihta KD, Rodger G, Chau K, Barker L, George S, Kavanagh J, Davies T, Vaughan A, Andersson M, Jeffery K, Oakley S, Morgan M, Hopkins S, Peto T, Crook D, Walker AS, Stoesser N.",,Nature communications,2024,2024-02-22,Y,,,,"Plasmids carry genes conferring antimicrobial resistance and other clinically important traits, and contribute to the rapid dissemination of such genes. Previous studies using complete plasmid assemblies, which are essential for reliable inference, have been small and/or limited to plasmids carrying antimicrobial resistance genes (ARGs). In this study, we sequenced 1,880 complete plasmids from 738 isolates from bloodstream infections in Oxfordshire, UK. The bacteria had been originally isolated in 2009 (194 isolates) and 2018 (368 isolates), plus a stratified selection from intervening years (176 isolates). We demonstrate that plasmids are largely, but not entirely, constrained to a single host species, although there is substantial overlap between species of plasmid gene-repertoire. Most ARGs are carried by a relatively small number of plasmid groups with biological features that are predictable. Plasmids carrying ARGs (including those encoding carbapenemases) share a putative 'backbone' of core genes with those carrying no such genes. These findings suggest that future surveillance should, in addition to tracking plasmids currently associated with clinically important genes, focus on identifying and monitoring the dissemination of high-risk plasmid groups with the potential to rapidly acquire and disseminate these genes.",,doi:https://doi.org/10.1038/s41467-024-45761-7; html:https://europepmc.org/articles/PMC10881496; pdf:https://europepmc.org/articles/PMC10881496?pdf=render
-37063605,https://doi.org/10.1111/rssa.12955,Estimation of reproduction numbers in real time: Conceptual and statistical challenges.,"Pellis L, Birrell PJ, Blake J, Overton CE, Scarabel F, Stage HB, Brooks-Pollock E, Danon L, Hall I, House TA, Keeling MJ, Read JM, JUNIPER Consortium, De Angelis D.",,"Journal of the Royal Statistical Society. Series A, (Statistics in Society)",2022,2022-11-22,Y,Growth Rate; Reproduction Numbers; Real‐Time Estimation,,,"The reproduction number R has been a central metric of the COVID-19 pandemic response, published weekly by the UK government and regularly reported in the media. Here, we provide a formal definition and discuss the advantages and most common misconceptions around this quantity. We consider the intuition behind different formulations of R , the complexities in its estimation (including the unavoidable lags involved), and its value compared to other indicators (e.g. the growth rate) that can be directly observed from aggregate surveillance data and react more promptly to changes in epidemic trend. As models become more sophisticated, with age and/or spatial structure, formulating R becomes increasingly complicated and inevitably model-dependent. We present some models currently used in the UK pandemic response as examples. Ultimately, limitations in the available data streams, data quality and time constraints force pragmatic choices to be made on a quantity that is an average across time, space, social structure and settings. Effectively communicating these challenges is important but often difficult in an emergency.",,pdf:https://academic.oup.com/jrsssa/article-pdf/185/Supplement_1/S112/49420672/jrsssa_185_supplement_1_s112.pdf; doi:https://doi.org/10.1111/rssa.12955; html:https://europepmc.org/articles/PMC10100071; pdf:https://europepmc.org/articles/PMC10100071?pdf=render
 39145103,https://doi.org/10.3310/nihropenres.13558.1,Planned and unplanned hospital admissions and health-related school absence rates in children with neurodisability: Protocol for a population-based study using linked education and hospital data from England.,"Gimeno L, Zylbersztejn A, Cant A, Harron K, Gilbert R.",,NIHR open research,2024,2024-05-01,Y,Electronic Health Records; Hospital Admissions; Linked Data; School Absence; Neurodisability,,,"<h4>Background</h4>Neurodisability describes a broad set of conditions affecting the brain and nervous system which result in functional limitations. Children with neurodisability have more hospital admissions than their peers without neurodisability and higher rates of school absence. However, longitudinal evidence comparing rates of hospital admission and school absence in children with neurodisability to peers without neurodisability throughout school is limited, as is understanding about whether differences are greatest for planned care (e.g., scheduled appointments) or unplanned care. This study will describe rates of planned and unplanned hospital admissions and school absence due to illness and medical reasons throughout primary school (Reception to Year 6, ages 4 to 11 in England) for children with neurodisability and all other children, using linked individual-level health and education data.<h4>Methods</h4>We will use the ECHILD (Education and Child Insights from Linked Data) database, which links educational and health records across England. We will define a primary school cohort of children who were born in National Health Service-funded hospitals in England between 1 <sup>st</sup> September 2003 and 31 <sup>st</sup> August 2008, and who were enrolled in Reception (age 4/5) at state-funded schools. We will use hospital admissions records to identify children who have recorded indicators of neurodisability from birth up to the end of primary school (Year 6, age 10/11).<h4>Results</h4>We will describe rates of planned and unplanned hospital admissions and health-related school absence for three groups of children: those with a neurodisability indicator first recorded before beginning primary school, those with neurodisability first recorded during primary school, and those without a record of neurodisability before end of primary school.<h4>Conclusions</h4>We will further explore whether differences between these group vary across primary school years and by socioeconomic and demographic characteristics.",,doi:https://doi.org/10.3310/nihropenres.13558.1; html:https://europepmc.org/articles/PMC11319901; pdf:https://europepmc.org/articles/PMC11319901?pdf=render
+37063605,https://doi.org/10.1111/rssa.12955,Estimation of reproduction numbers in real time: Conceptual and statistical challenges.,"Pellis L, Birrell PJ, Blake J, Overton CE, Scarabel F, Stage HB, Brooks-Pollock E, Danon L, Hall I, House TA, Keeling MJ, Read JM, JUNIPER Consortium, De Angelis D.",,"Journal of the Royal Statistical Society. Series A, (Statistics in Society)",2022,2022-11-22,Y,Growth Rate; Reproduction Numbers; Real‐Time Estimation,,,"The reproduction number R has been a central metric of the COVID-19 pandemic response, published weekly by the UK government and regularly reported in the media. Here, we provide a formal definition and discuss the advantages and most common misconceptions around this quantity. We consider the intuition behind different formulations of R , the complexities in its estimation (including the unavoidable lags involved), and its value compared to other indicators (e.g. the growth rate) that can be directly observed from aggregate surveillance data and react more promptly to changes in epidemic trend. As models become more sophisticated, with age and/or spatial structure, formulating R becomes increasingly complicated and inevitably model-dependent. We present some models currently used in the UK pandemic response as examples. Ultimately, limitations in the available data streams, data quality and time constraints force pragmatic choices to be made on a quantity that is an average across time, space, social structure and settings. Effectively communicating these challenges is important but often difficult in an emergency.",,pdf:https://academic.oup.com/jrsssa/article-pdf/185/Supplement_1/S112/49420672/jrsssa_185_supplement_1_s112.pdf; doi:https://doi.org/10.1111/rssa.12955; html:https://europepmc.org/articles/PMC10100071; pdf:https://europepmc.org/articles/PMC10100071?pdf=render
 35130878,https://doi.org/10.1186/s12916-022-02234-2,"Lifetime risk of cardiovascular-renal disease in type 2 diabetes: a population-based study in 473,399 individuals.","Zhang R, Mamza JB, Morris T, Godfrey G, Asselbergs FW, Denaxas S, Hemingway H, Banerjee A.",,BMC medicine,2022,2022-02-07,Y,Kidney; Type 2 diabetes; lifetime; Attributable Risk; Population Health; cardiovascular,,,"<h4>Background</h4>Cardiovascular and renal diseases (CVRD) are major causes of mortality in individuals with type 2 diabetes (T2D). Studies of lifetime risk have neither considered all CVRD together nor the relative contribution of major risk factors to combined disease burden.<h4>Methods</h4>In a population-based cohort study using national electronic health records, we studied 473,399 individuals with T2D in England 2007-2018. Lifetime risk of individual and combined major adverse renal cardiovascular events, MARCE (including CV death and CVRD: heart failure; chronic kidney disease; myocardial infarction; stroke or peripheral artery disease), were estimated, accounting for baseline CVRD status and competing risk of death. We calculated population attributable risk for individual CVRD components. Ideal cardiovascular health was defined by blood pressure, cholesterol, glucose, smoking, physical activity, diet, and body mass index (i.e. modifiable risk factors).<h4>Results</h4>In individuals with T2D, lifetime risk of MARCE was 80% in those free from CVRD and was 97%, 93%, 98%, 89% and 91% in individuals with heart failure, chronic kidney disease, myocardial infarction, stroke and peripheral arterial disease, respectively at baseline. Among CVRD-free individuals, lifetime risk of chronic kidney disease was highest (54%), followed by CV death (41%), heart failure (29%), stroke (20%), myocardial infarction (19%) and peripheral arterial disease (9%). In those with HF only, 75% of MARCE after index T2D can be attributed to HF after adjusting for age, gender, and comorbidities. Compared with those with > 1, < 3 and ≥3 modifiable health risk behaviours, achieving ideal cardiovascular health could reduce MARCE by approximately 41.5%, 23.6% and 17.2%, respectively, in the T2D population.<h4>Conclusions</h4>Four out of five individuals with T2D free from CVRD, and nearly all those with history of CVRD, will develop MARCE over their lifetime. Early preventive measures in T2D patients are clinical, public health and policy priorities.",,pdf:https://bmcmedicine.biomedcentral.com/track/pdf/10.1186/s12916-022-02234-2; doi:https://doi.org/10.1186/s12916-022-02234-2; html:https://europepmc.org/articles/PMC8822817; pdf:https://europepmc.org/articles/PMC8822817?pdf=render
 38113090,https://doi.org/10.2196/41540,Association Between Household Online Grocery Delivery Service Use and Food and Drink Purchase Behavior in England: Cross-Sectional Analysis.,"Yau A, Law C, Cornelsen L, Adams J, Boyland E, Burgoine T, de Vocht F, White M, Cummins S.",,JMIR public health and surveillance,2023,2023-12-19,Y,Delivery; Diet; Internet; Public Health; Lifestyle; Consumer Behavior; Inequality; Sociodemographic Factors; Online; Food Preferences; Food Purchase; Supermarkets; Food And Beverages; Online Purchase; Grocery Purchase; Grocery; Online Grocery,,,"<h4>Background</h4>Online grocery delivery services (OGDSs) are a popular way of acquiring food. However, it is unclear whether OGDS use is associated with the healthiness of purchases and whether there are sociodemographic differences in OGDS use. If so, the increased prevalence of OGDS use may have implications for population diet, and differential OGDS use could contribute to diet inequalities.<h4>Objective</h4>This study aimed to examine whether OGDS use varies by sociodemographic characteristics and is associated with the amount and types of groceries purchased.<h4>Methods</h4>Item-level take-home food and drink purchase data (n=3,233,920 items) from households in London and the North of England were available from the 2019 UK Kantar fast-moving consumer goods panel (N=1911). Purchases were categorized as being bought online or in-store. We used logistic regression to estimate the likelihood of an above-median frequency of OGDS use by sociodemographic characteristics. We used Poisson regression to estimate the differences in energy and nutrients purchased by households that had above- and below-median OGDS use and the proportion of energy purchased from products high in fat, salt, and sugar (HFSS) online versus in-store among households that used both shopping methods (n=665).<h4>Results</h4>In total, 668 (35%) households used OGDSs at least once in 2019. Of the households that used OGDSs, the median use was 5 occasions in 2019. Households were more likely to have above-median use in London versus in the North of England (odds ratio 1.29, 95% CI 1.01-1.65) and if they had a higher annual household income (odds ratio 1.56, 95% CI 1.02-2.38 for ≥£50,000 [US $64,000] vs <£20,000 [$25,600]). Households with above-median OGDS use had a higher weekly mean purchase of energy by 1461 (95% CI 1448-1474) kcal per person compared with households with below-median OGDS use. For households that used a combination of in-store and online shopping, HFSS products made up a lower proportion (-10.1%, 95% CI -12% to -8.1%) of energy purchased online compared to in-store.<h4>Conclusions</h4>Differences in grocery purchases between households with above- and below-median OGDS use could have positive or negative consequences. The extra energy purchased among households with above-median OGDS use could lead to overconsumption or food waste, which has negative consequences for population and environmental health. Alternatively, this extra energy may be replacing out-of-home purchasing, which tends to be less healthy, and may be beneficial for the population diet. Households made fewer HFSS purchases when shopping online compared to in-store, which may be due to differences in the shopping environment or experience, such as fewer promotions and advertisements when shopping online or not having to transport and carry purchases home. As higher-income households used OGDS more frequently, the implications of this sociodemographic pattern on dietary inequalities must be explored.",,doi:https://doi.org/10.2196/41540; html:https://europepmc.org/articles/PMC10762614
 37827807,https://doi.org/10.1136/bmjresp-2023-001806,Observational cohort study protocol: neutrophil function and energetics in adults with pneumonia and sepsis - Pneumonia Metabolism in Ageing (PUMA).,"Grudzinska FS, Faniyi AA, Scott A, Sapey E, Thickett DR.",,BMJ open respiratory research,2023,2023-10-01,Y,Pneumonia; innate immunity; Bacterial Infection; respiratory infection; Neutrophil Biology,,,"<h4>Introduction</h4>Community-acquired pneumonia has high mortality and is associated with significant healthcare costs. In older adults with community-acquired pneumonia neutrophil dysfunction has been identified and is associated with poor outcomes for patients. Immunometabolism is a rapidly developing field which links immune cell function to metabolism. This study aims to explore neutrophil metabolism in community-acquired pneumonia.<h4>Methods and analysis</h4>Pneumonia Metabolism in Ageing study is a prospective observational study recruiting older adults hospitalised with community-acquired pneumonia to examine neutrophil function and metabolic status. Controls will be older adults with no acute illness. The primary endpoint is neutrophil chemotaxis.<h4>Ethics and dissemination</h4>The study has ethical approval from the Research Ethics Committee Wales, reference 19/WA/0299. This study involves participants who may lack the capacity to consent to research involvement, in this situation, personal or professional assent will be sought. The results from this study will be submitted for publication in peer-reviewed journals and disseminated at local and international conferences.",,pdf:https://bmjopenrespres.bmj.com/content/bmjresp/10/1/e001806.full.pdf; doi:https://doi.org/10.1136/bmjresp-2023-001806; html:https://europepmc.org/articles/PMC10582892; pdf:https://europepmc.org/articles/PMC10582892?pdf=render
@@ -865,8 +866,8 @@ PMC8718341,https://doi.org/,"Loneliness, coping, suicidal thoughts and self-harm
 34765951,https://doi.org/10.1016/j.eclinm.2021.101163,Net effects of sodium-glucose co-transporter-2 inhibition in different patient groups: a meta-analysis of large placebo-controlled randomized trials.,"Staplin N, Roddick AJ, Emberson J, Reith C, Riding A, Wonnacott A, Kuverji A, Bhandari S, Baigent C, Haynes R, Herrington WG.",,EClinicalMedicine,2021,2021-10-26,Y,Safety; Heart Failure; Randomized Trials; Ckd; Sodium-glucose Co-transporter 2 Inhibitors,,,"<h4>Background</h4>The net absolute effects of sodium-glucose co-transporter-2 (SGLT-2) inhibitors across different patient groups have not been quantified.<h4>Methods</h4>We performed a meta-analysis of published large (>500 participants/arm) placebo-controlled SGLT-2 inhibitor trials after systematically searching MEDLINE and Embase databases from inception to 28th August 2021 (PROSPERO 2021 CRD42021240468).<h4>Findings</h4>Four heart failure trials (n=15,684 participants), four trials in type 2 diabetes mellitus at high atherosclerotic cardiovascular risk (n=42,568), and three trials in chronic kidney disease (n=19,289) were included. Relative risks (RRs) for all cardiovascular, renal and safety outcomes were broadly similar across these three patient groups, and between people with or without diabetes. Overall, compared to placebo, allocation to SGLT-2 inhibition reduced risk of hospitalization for heart failure or cardiovascular death by 23% (RR=0.77, 95%CI 0.73-0.80; n=6658), cardiovascular death by 14% (0.86, 0.81-0.92; n=3962), major adverse cardiovascular events by 11% (0.89, 0.84-0.94; n=5703), kidney disease progression by 36% (0.64, 0.59-0.70; n=2275), acute kidney injury by 30% (0.70, 0.62-0.79; n=1013 events) and severe hypoglycaemia by 13% (0.87, 0.79-0.97; n=1484). There was no effect of SGLT-2 inhibition on risk of non-cardiovascular death (0.93, 0.86-1.01; n=2226), but a net 12% reduction in all-cause mortality remained evident (0.88, 0.84-0.93; n=6188). However, the risk of ketoacidosis was 2-times higher among those allocated SGLT-2 inhibitors compared to placebo (2.03, 1.41-2.93; n=159; absolute excess in people with diabetes ∼0.3/1000 patient years). A small increased risk of urinary tract infection was evident (1.07, 1.02-1.13; n=5384) alongside a known increased risk of mycotic genital infections. Overall, risk of lower limb amputations was increased by 16% (1.16, 1.02-1.31; n=1074), but this risk was largely driven by a single outlying trial (CANVAS).<h4>Interpretations</h4>The relative effects of SGLT-2 inhibition on key safety and efficacy outcomes are consistent across the different studied groups of patient. Consequently, absolute benefits and harms are determined by the absolute baseline risk of particular outcomes, with absolute benefits on mortality and on non-fatal serious cardiac/renal outcomes substantially exceeding the risks of amputation and ketoacidosis in the main patient groups studied to date.<h4>Funding</h4>MRC-UK & KRUK.",,doi:https://doi.org/10.1016/j.eclinm.2021.101163; doi:https://doi.org/10.1016/j.eclinm.2021.101163; html:https://europepmc.org/articles/PMC8571171; pdf:https://europepmc.org/articles/PMC8571171?pdf=render
 34038519,https://doi.org/10.1093/ageing/afab084,Developing a UK sarcopenia registry: recruitment and baseline characteristics of the SarcNet pilot.,"Witham MD, Heslop P, Dodds RM, Clegg AP, Hope SV, McDonald C, Smithard D, Storey B, Tan AL, Thornhill A, Sayer AA.",,Age and ageing,2021,2021-09-01,Y,Recruitment; Older People; Registry; Sarcopenia,,,"<h4>Background</h4>sarcopenia registries are a potential method to meet the challenge of recruitment to sarcopenia trials. We tested the feasibility of setting up a UK sarcopenia registry, the feasibility of recruitment methods and sought to characterise the pilot registry population.<h4>Methods</h4>six diverse UK sites took part, with potential participants aged 65 and over approached via mailshots from local primary care practices. Telephone pre-screening using the SARC-F score was followed by in-person screening and baseline visit. Co-morbidities, medications, grip strength, Short Physical Performance Battery, bioimpedance analysis, Geriatric Depression Score, Montreal Cognitive Assessment, Sarcopenia Quality of Life score were performed and permission sought for future recontact. Descriptive statistics for recruitment rates and baseline measures were generated; an embedded randomised trial examined the effect of a University logo on the primary care mailshot on recruitment rates.<h4>Results</h4>sixteen practices contributed a total of 3,508 letters. In total, 428 replies were received (12% response rate); 380 underwent telephone pre-screening of whom 215 (57%) were eligible to attend a screening visit; 150 participants were recruited (40% of those pre-screened) with 147 contributing baseline data. No significant difference was seen in response rates between mailshots with and without the logo (between-group difference 1.1% [95% confidence interval -1.0% to 3.4%], P = 0.31). The mean age of enrollees was 78 years; 72 (49%) were women. In total, 138/147 (94%) had probable sarcopenia on European Working Group on Sarcopenia 2019 criteria and 145/147 (98%) agreed to be recontacted about future studies.<h4>Conclusion</h4>recruitment to a multisite UK sarcopenia registry is feasible, with high levels of consent for recontact.",,pdf:https://academic.oup.com/ageing/article-pdf/50/5/1762/40349116/afab084.pdf; doi:https://doi.org/10.1093/ageing/afab084; html:https://europepmc.org/articles/PMC8437066; pdf:https://europepmc.org/articles/PMC8437066?pdf=render
 33017023,https://doi.org/10.1001/jamaneurol.2020.3502,Trends in Optic Neuritis Incidence and Prevalence in the UK and Association With Systemic and Neurologic Disease.,"Braithwaite T, Subramanian A, Petzold A, Galloway J, Adderley NJ, Mollan SP, Plant GT, Nirantharakumar K, Denniston AK.",,JAMA neurology,2020,2020-12-01,N,,,,"<h4>Importance</h4>Epidemiologic data on optic neuritis (ON) incidence and associations with immune-mediated inflammatory diseases (IMIDs) are sparse.<h4>Objective</h4>To estimate 22-year trends in ON prevalence and incidence and association with IMIDs in the United Kingdom.<h4>Design, setting, and participants</h4>This cohort study analyzed data from The Health Improvement Network from January 1, 1995, to September 1, 2019. The study included 10 937 511 patients 1 year or older with 75.2 million person-years' follow-up. Annual ON incidence rates were estimated yearly (January 1, 1997, to December 31, 2018), and annual ON prevalence was estimated by performing sequential cross-sectional studies on data collected on January 1 each year for the same period. Data for 1995, 1996, and 2019 were excluded as incomplete. Risk factors for ON were explored in a cohort analysis from January 1, 1997, to December 31, 2018. Matched case-control and retrospective cohort studies were performed using data from January 1, 1995, to September 1, 2019, to explore the odds of antecedent diagnosis and hazard of incident diagnosis of 66 IMIDs in patients compared with controls.<h4>Exposures</h4>Optic neuritis.<h4>Main outcomes and measures</h4>Annual point prevalence and incidence rates of ON, adjusted incident rate ratios (IRRs) for risk factors, and adjusted odds ratios (ORs) and adjusted hazard ratios (HRs) for 66 IMIDs.<h4>Results</h4>A total of 10 937 511 patients (median [IQR] age at cohort entry, 32.6 [18.0-50.4] years; 5 571 282 [50.9%] female) were studied. A total of 1962 of 2826 patients (69.4%) with incident ON were female and 1192 of 1290 92.4%) were White, with a mean (SD) age of 35.6 (15.6) years. Overall incidence across 22 years was stable at 3.7 (95% CI, 3.6-3.9) per 100 000 person-years. Annual point prevalence (per 100 000 population) increased with database maturity, from 69.3 (95% CI, 57.2-81.3) in 1997 to 114.8 (95% CI, 111.0-118.6) in 2018. The highest risk of incident ON was associated with female sex, obesity, reproductive age, smoking, and residence at higher latitude, with significantly lower risk in South Asian or mixed race/ethnicity compared with White people. Patients with ON had significantly higher odds of prior multiple sclerosis (MS) (OR, 98.22; 95% CI, 65.40-147.52), syphilis (OR, 5.76; 95% CI, 1.39-23.96), Mycoplasma (OR, 3.90; 95% CI, 1.09-13.93), vasculitis (OR, 3.70; 95% CI, 1.68-8.15), sarcoidosis (OR, 2.50; 95% CI, 1.21-5.18), Epstein-Barr virus (OR, 2.29; 95% CI, 1.80-2.92), Crohn disease (OR, 1.97; 95% CI, 1.13-3.43), and psoriasis (OR, 1.28; 95% CI, 1.03-1.58). Patients with ON had a significantly higher hazard of incident MS (HR, 284.97; 95% CI, 167.85-483.81), Behçet disease (HR, 17.39; 95% CI, 1.55-195.53), sarcoidosis (HR, 14.80; 95% CI, 4.86-45.08), vasculitis (HR, 4.89; 95% CI, 1.82-13.10), Sjögren syndrome (HR, 3.48; 95% CI, 1.38-8.76), and herpetic infection (HR, 1.68; 95% CI, 1.24-2.28).<h4>Conclusions and relevance</h4>The UK incidence of ON is stable. Even though predominantly associated with MS, ON has numerous other associations with IMIDs. Although individually rare, together these associations outnumber MS-associated ON and typically require urgent management to preserve sight.",,pdf:http://pure-oai.bham.ac.uk/ws/files/100688542/NEU20_1602R_Merged_PDF.pdf; doi:https://doi.org/10.1001/jamaneurol.2020.3502; html:https://europepmc.org/articles/PMC7536630; doi:https://doi.org/10.1001/jamaneurol.2020.3502
-38595770,https://doi.org/10.2147/clep.s437937,"A Harmonised Approach to Curating Research-Ready Datasets for Asthma, Chronic Obstructive Pulmonary Disease (COPD) and Interstitial Lung Disease (ILD) in England, Wales and Scotland Using Clinical Practice Research Datalink (CPRD), Secure Anonymised Information Linkage (SAIL) Databank and DataLoch.","Hatam S, Scully ST, Cook S, Evans HT, Hume A, Kallis C, Farr I, Orton C, Sheikh A, Quint JK.",,Clinical epidemiology,2024,2024-04-04,Y,Asthma; COPD; Harmonisation; Data Curation; Her; Ild,,,"<h4>Background</h4>Electronic healthcare records (EHRs) are an important resource for health research that can be used to improve patient outcomes in chronic respiratory diseases. However, consistent approaches in the analysis of these datasets are needed for coherent messaging, and when undertaking comparative studies across different populations.<h4>Methods and results</h4>We developed a harmonised curation approach to generate comparable patient cohorts for asthma, chronic obstructive pulmonary disease (COPD) and interstitial lung disease (ILD) using datasets from within Clinical Practice Research Datalink (CPRD; for England), Secure Anonymised Information Linkage (SAIL; for Wales) and DataLoch (for Scotland) by defining commonly derived variables consistently between the datasets. By working in parallel on the curation methodology used for CPRD, SAIL and DataLoch for asthma, COPD and ILD, we were able to highlight key differences in coding and recording between the databases and identify solutions to enable valid comparisons.<h4>Conclusion</h4>Codelists and metadata generated have been made available to help re-create the asthma, COPD and ILD cohorts in CPRD, SAIL and DataLoch for different time periods, and provide a starting point for the curation of respiratory datasets in other EHR databases, expediting further comparable respiratory research.",,pdf:https://www.dovepress.com/getfile.php?fileID=98087; doi:https://doi.org/10.2147/CLEP.S437937; html:https://europepmc.org/articles/PMC11002787; pdf:https://europepmc.org/articles/PMC11002787?pdf=render
 37263751,https://doi.org/10.1183/13993003.01667-2022,Genome-wide association study of chronic sputum production implicates loci involved in mucus production and infection.,"Packer RJ, Shrine N, Hall R, Melbourne CA, Thompson R, Williams AT, Paynton ML, Guyatt AL, Allen RJ, Lee PH, John C, Campbell A, Hayward C, de Vries M, Vonk JM, Davitte J, Hessel E, Michalovich D, Betts JC, Sayers I, Yeo A, Hall IP, Tobin MD, Wain LV.",,The European respiratory journal,2023,2023-06-15,Y,,,,"<h4>Background</h4>Chronic sputum production impacts on quality of life and is a feature of many respiratory diseases. Identification of the genetic variants associated with chronic sputum production in a disease agnostic sample could improve understanding of its causes and identify new molecular targets for treatment.<h4>Methods</h4>We conducted a genome-wide association study (GWAS) of chronic sputum production in UK Biobank. Signals meeting genome-wide significance (p<5×10<sup>-8</sup>) were investigated in additional independent studies, were fine-mapped and putative causal genes identified by gene expression analysis. GWASs of respiratory traits were interrogated to identify whether the signals were driven by existing respiratory disease among the cases and variants were further investigated for wider pleiotropic effects using phenome-wide association studies (PheWASs).<h4>Results</h4>From a GWAS of 9714 cases and 48 471 controls, we identified six novel genome-wide significant signals for chronic sputum production including signals in the human leukocyte antigen (HLA) locus, chromosome 11 mucin locus (containing <i>MUC2</i>, <i>MUC5AC</i> and <i>MUC5B</i>) and <i>FUT2</i> locus. The four common variant associations were supported by independent studies with a combined sample size of up to 2203 cases and 17 627 controls. The mucin locus signal had previously been reported for association with moderate-to-severe asthma. The HLA signal was fine-mapped to an amino acid change of threonine to arginine (frequency 36.8%) in HLA-DRB1 (<i>HLA-DRB1*03:147</i>). The signal near <i>FUT2</i> was associated with expression of several genes including <i>FUT2</i>, for which the direction of effect was tissue dependent. Our PheWAS identified a wide range of associations including blood cell traits, liver biomarkers, infections, gastrointestinal and thyroid-associated diseases, and respiratory disease.<h4>Conclusions</h4>Novel signals at the <i>FUT2</i> and mucin loci suggest that mucin fucosylation may be a driver of chronic sputum production even in the absence of diagnosed respiratory disease and provide genetic support for this pathway as a target for therapeutic intervention.",,pdf:https://erj.ersjournals.com/content/erj/61/6/2201667.full.pdf; doi:https://doi.org/10.1183/13993003.01667-2022; html:https://europepmc.org/articles/PMC10284065; pdf:https://europepmc.org/articles/PMC10284065?pdf=render
+38595770,https://doi.org/10.2147/clep.s437937,"A Harmonised Approach to Curating Research-Ready Datasets for Asthma, Chronic Obstructive Pulmonary Disease (COPD) and Interstitial Lung Disease (ILD) in England, Wales and Scotland Using Clinical Practice Research Datalink (CPRD), Secure Anonymised Information Linkage (SAIL) Databank and DataLoch.","Hatam S, Scully ST, Cook S, Evans HT, Hume A, Kallis C, Farr I, Orton C, Sheikh A, Quint JK.",,Clinical epidemiology,2024,2024-04-04,Y,Asthma; COPD; Harmonisation; Data Curation; Her; Ild,,,"<h4>Background</h4>Electronic healthcare records (EHRs) are an important resource for health research that can be used to improve patient outcomes in chronic respiratory diseases. However, consistent approaches in the analysis of these datasets are needed for coherent messaging, and when undertaking comparative studies across different populations.<h4>Methods and results</h4>We developed a harmonised curation approach to generate comparable patient cohorts for asthma, chronic obstructive pulmonary disease (COPD) and interstitial lung disease (ILD) using datasets from within Clinical Practice Research Datalink (CPRD; for England), Secure Anonymised Information Linkage (SAIL; for Wales) and DataLoch (for Scotland) by defining commonly derived variables consistently between the datasets. By working in parallel on the curation methodology used for CPRD, SAIL and DataLoch for asthma, COPD and ILD, we were able to highlight key differences in coding and recording between the databases and identify solutions to enable valid comparisons.<h4>Conclusion</h4>Codelists and metadata generated have been made available to help re-create the asthma, COPD and ILD cohorts in CPRD, SAIL and DataLoch for different time periods, and provide a starting point for the curation of respiratory datasets in other EHR databases, expediting further comparable respiratory research.",,pdf:https://www.dovepress.com/getfile.php?fileID=98087; doi:https://doi.org/10.2147/CLEP.S437937; html:https://europepmc.org/articles/PMC11002787; pdf:https://europepmc.org/articles/PMC11002787?pdf=render
 33971933,https://doi.org/10.1186/s13063-021-05295-5,Accessing routinely collected health data to improve clinical trials: recent experience of access.,"Macnair A, Love SB, Murray ML, Gilbert DC, Parmar MKB, Denwood T, Carpenter J, Sydes MR, Langley RE, Cafferty FH.",,Trials,2021,2021-05-10,Y,Clinical Trials; Electronic Health Records; Data Accessibility; Routinely Collected Data,,,"<h4>Background</h4>Routinely collected electronic health records (EHRs) have the potential to enhance randomised controlled trials (RCTs) by facilitating recruitment and follow-up. Despite this, current EHR use is minimal in UK RCTs, in part due to ongoing concerns about the utility (reliability, completeness, accuracy) and accessibility of the data. The aim of this manuscript is to document the process, timelines and challenges of the application process to help improve the service both for the applicants and data holders.<h4>Methods</h4>This is a qualitative paper providing a descriptive narrative from one UK clinical trials unit (MRC CTU at UCL) on the experience of two trial teams' application process to access data from three large English national datasets: National Cancer Registration and Analysis Service (NCRAS), National Institute for Cardiovascular Outcomes Research (NICOR) and NHS Digital to establish themes for discussion. The underpinning reason for applying for the data was to compare EHRs with data collected through case report forms in two RCTs, Add-Aspirin (ISRCTN 74358648) and PATCH (ISRCTN 70406718).<h4>Results</h4>The Add-Aspirin trial, which had a pre-planned embedded sub-study to assess EHR, received data from NCRAS 13 months after the first application. In the PATCH trial, the decision to request data was made whilst the trial was recruiting. The study received data after 8 months from NICOR and 15 months for NHS Digital following final application submission. This concluded in May 2020. Prior to application submission, significant time and effort was needed particularly in relation to the PATCH trial where negotiations over consent and data linkage took many years.<h4>Conclusions</h4>Our experience demonstrates that data access can be a prolonged and complex process. This is compounded if multiple data sources are required for the same project. This needs to be factored in when planning to use EHR within RCTs and is best considered prior to conception of the trial. Data holders and researchers are endeavouring to simplify and streamline the application process so that the potential of EHR can be realised for clinical trials.",,pdf:https://trialsjournal.biomedcentral.com/counter/pdf/10.1186/s13063-021-05295-5; doi:https://doi.org/10.1186/s13063-021-05295-5; html:https://europepmc.org/articles/PMC8108438; pdf:https://europepmc.org/articles/PMC8108438?pdf=render
 34481555,https://doi.org/10.1016/s2213-8587(21)00207-2,"Identifying adults at high-risk for change in weight and BMI in England: a longitudinal, large-scale, population-based cohort study using electronic health records.","Katsoulis M, Lai AG, Diaz-Ordaz K, Gomes M, Pasea L, Banerjee A, Denaxas S, Tsilidis K, Lagiou P, Misirli G, Bhaskaran K, Wannamethee G, Dobson R, Batterham RL, Kipourou DK, Lumbers RT, Wen L, Wareham N, Langenberg C, Hemingway H.",,The lancet. Diabetes & endocrinology,2021,2021-09-02,Y,,,,"<h4>Background</h4>Targeted obesity prevention policies would benefit from the identification of population groups with the highest risk of weight gain. The relative importance of adult age, sex, ethnicity, geographical region, and degree of social deprivation on weight gain is not known. We aimed to identify high-risk groups for changes in weight and BMI using electronic health records (EHR).<h4>Methods</h4>In this longitudinal, population-based cohort study we used linked EHR data from 400 primary care practices (via the Clinical Practice Research Datalink) in England, accessed via the CALIBER programme. Eligible participants were aged 18-74 years, were registered at a general practice clinic, and had BMI and weight measurements recorded between Jan 1, 1998, and June 30, 2016, during the period when they had eligible linked data with at least 1 year of follow-up time. We calculated longitudinal changes in BMI over 1, 5, and 10 years, and investigated the absolute risk and odds ratios (ORs) of transitioning between BMI categories (underweight, normal weight, overweight, obesity class 1 and 2, and severe obesity [class 3]), as defined by WHO. The associations of demographic factors with BMI transitions were estimated by use of logistic regression analysis, adjusting for baseline BMI, family history of cardiovascular disease, use of diuretics, and prevalent chronic conditions.<h4>Findings</h4>We included 2 092 260 eligible individuals with more than 9 million BMI measurements in our study. Young adult age was the strongest risk factor for weight gain at 1, 5, and 10 years of follow-up. Compared with the oldest age group (65-74 years), adults in the youngest age group (18-24 years) had the highest OR (4·22 [95% CI 3·86-4·62]) and greatest absolute risk (37% vs 24%) of transitioning from normal weight to overweight or obesity at 10 years. Likewise, adults in the youngest age group with overweight or obesity at baseline were also at highest risk to transition to a higher BMI category; OR 4·60 (4·06-5·22) and absolute risk (42% vs 18%) of transitioning from overweight to class 1 and 2 obesity, and OR 5·87 (5·23-6·59) and absolute risk (22% vs 5%) of transitioning from class 1 and 2 obesity to class 3 obesity. Other demographic factors were consistently less strongly associated with these transitions; for example, the OR of transitioning from normal weight to overweight or obesity in people living in the most socially deprived versus least deprived areas was 1·23 (1·18-1·27), for men versus women was 1·12 (1·08-1·16), and for Black individuals versus White individuals was 1·13 (1·04-1·24). We provide an open access online risk calculator, and present high-resolution obesity risk charts over a 1-year, 5-year, and 10-year follow-up period.<h4>Interpretation</h4>A radical shift in policy is required to focus on individuals at the highest risk of weight gain (ie, young adults aged 18-24 years) for individual-level and population-level prevention of obesity and its long-term consequences for health and health care.<h4>Funding</h4>The British Hearth Foundation, Health Data Research UK, the UK Medical Research Council, and the National Institute for Health Research.",,pdf:http://www.thelancet.com/article/S2213858721002072/pdf; doi:https://doi.org/10.1016/S2213-8587(21)00207-2; html:https://europepmc.org/articles/PMC8440227; pdf:https://europepmc.org/articles/PMC8440227?pdf=render
 36654802,https://doi.org/10.1002/lrh2.10315,"A framework for understanding, designing, developing and evaluating learning health systems.","Foley T, Vale L.",,Learning health systems,2023,2022-05-20,Y,Quality improvement; Informatics; Implementation Science; Learning Health Systems; Learning Healthcare Systems,,,"<h4>Introduction</h4>A Learning Health System is not a technical project. It is the evolution of an existing health system into one capable of learning from every patient. This paper outlines a recently published framework intended to aid the understanding, design, development and evaluation of Learning Health Systems.<h4>Methods</h4>This work extended an existing repository of Learning Health System evidence, adding five more workshops. The total was subjected to thematic analysis, yielding a framework of elements important to understanding, designing, developing and evaluating Learning Health Systems. Purposeful literature reviews were conducted on each element. The findings were revised following a review by a group of international experts.<h4>Results</h4>The resulting framework was arranged around four questions:What is our rationale for developing a Learning Health System?There can be many reasons for developing a Learning Health System. Understanding these will guide its development.What sources of complexity exist at the system and the intervention level?An understanding of complexity is central to making Learning Health Systems work. The non-adoption, abandonment, scale-up, spread and sustainability framework was utilised to help understand and manage it.What strategic approaches to change do we need to consider?A range of strategic issues must be addressed to enable successful change in a Learning Health System. These include, strategy, organisational structure, culture, workforce, implementation science, behaviour change, co-design and evaluation.What technical building blocks will we need?A Learning Health System must capture data from practice, turn it into knowledge and apply it back into practice. There are many methods to achieve this and a range of platforms to help.<h4>Discussion</h4>The results form a framework for understanding, designing, developing and evaluating Learning Health Systems at any scale.<h4>Conclusion</h4>It is hoped that this framework will evolve with use and feedback.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9835047; doi:https://doi.org/10.1002/lrh2.10315; html:https://europepmc.org/articles/PMC9835047; pdf:https://europepmc.org/articles/PMC9835047?pdf=render
@@ -891,8 +892,8 @@ PMC8718341,https://doi.org/,"Loneliness, coping, suicidal thoughts and self-harm
 37293269,https://doi.org/10.1140/epjds/s13688-023-00394-6,Do poverty and wealth look the same the world over? A comparative study of 12 cities from five high-income countries using street images.,"Suel E, Muller E, Bennett JE, Blakely T, Doyle Y, Lynch J, Mackenbach JD, Middel A, Mizdrak A, Nathvani R, Brauer M, Ezzati M.",,EPJ data science,2023,2023-06-07,Y,Computer vision; Visual Similarity; Urban Inequalities; Street Images,,,"Urbanization and inequalities are two of the major policy themes of our time, intersecting in large cities where social and economic inequalities are particularly pronounced. Large scale street-level images are a source of city-wide visual information and allow for comparative analyses of multiple cities. Computer vision methods based on deep learning applied to street images have been shown to successfully measure inequalities in socioeconomic and environmental features, yet existing work has been within specific geographies and have not looked at how visual environments compare across different cities and countries. In this study, we aim to apply existing methods to understand whether, and to what extent, poor and wealthy groups live in visually similar neighborhoods across cities and countries. We present novel insights on similarity of neighborhoods using street-level images and deep learning methods. We analyzed 7.2 million images from 12 cities in five high-income countries, home to more than 85 million people: Auckland (New Zealand), Sydney (Australia), Toronto and Vancouver (Canada), Atlanta, Boston, Chicago, Los Angeles, New York, San Francisco, and Washington D.C. (United States of America), and London (United Kingdom). Visual features associated with neighborhood disadvantage are more distinct and unique to each city than those associated with affluence. For example, from what is visible from street images, high density poor neighborhoods located near the city center (e.g., in London) are visually distinct from poor suburban neighborhoods characterized by lower density and lower accessibility (e.g., in Atlanta). This suggests that differences between two cities is also driven by historical factors, policies, and local geography. Our results also have implications for image-based measures of inequality in cities especially when trained on data from cities that are visually distinct from target cities. We showed that these are more prone to errors for disadvantaged areas especially when transferring across cities, suggesting more attention needs to be paid to improving methods for capturing heterogeneity in poor environment across cities around the world.<h4>Supplementary information</h4>The online version contains supplementary material available at 10.1140/epjds/s13688-023-00394-6.",,pdf:https://epjdatascience.springeropen.com/counter/pdf/10.1140/epjds/s13688-023-00394-6; doi:https://doi.org/10.1140/epjds/s13688-023-00394-6; html:https://europepmc.org/articles/PMC10245348; pdf:https://europepmc.org/articles/PMC10245348?pdf=render
 37308319,https://doi.org/10.1111/bdi.13355,The network structure of mania symptoms differs between people with and without binge eating.,"Davies HL, Peel AJ, Mundy J, Monssen D, Kakar S, Davies MR, Adey BN, Armour C, Kalsi G, Lin Y, Marsh I, Rogers HC, Walters JTR, Herle M, Glen K, Malouf CM, Kelly EJ, Eley TC, Treasure J, Breen G, Hübel C.",,Bipolar disorders,2023,2023-06-12,Y,Diagnosis; Bipolar disorder; Signs And Symptoms; Anorexia Nervosa; Bulimia Nervosa; Network Analysis; Binge-eating Disorder,,,"<h4>Objectives</h4>People with bipolar disorder who also report binge eating have increased psychopathology and greater impairment than those without binge eating. Whether this co-occurrence is related to binge eating as a symptom or presents differently across full-syndrome eating disorders with binge eating is unclear.<h4>Methods</h4>We first compared networks of 13 lifetime mania symptoms in 34,226 participants from the United Kingdom's National Institute for Health and Care Research BioResource with (n = 12,104) and without (n = 22,122) lifetime binge eating. Second, in the subsample with binge eating, we compared networks of mania symptoms in participants with lifetime anorexia nervosa binge-eating/purging (n = 825), bulimia nervosa (n = 3737), and binge-eating disorder (n = 3648).<h4>Results</h4>People with binge eating endorsed every mania symptom significantly more often than those without binge eating. Within the subsample, people with bulimia nervosa most often had the highest endorsement rate of each mania symptom. We found significant differences in network parameter statistics, including network structure (M = 0.25, p = 0.001) and global strength (S = 1.84, p = 0.002) when comparing the binge eating with no binge-eating participants. However, network structure differences were sensitive to reductions in sample size and the greater density of the latter network was explained by the large proportion of participants (34%) without mania symptoms. The structure of the anorexia nervosa binge-eating/purging network differed from the bulimia nervosa network (M = 0.66, p = 0.001), but the result was unstable.<h4>Conclusions</h4>Our results suggest that the presence and structure of mania symptoms may be more associated with binge eating as a symptom rather than any specific binge-type eating disorder. Further research with larger sample sizes is required to confirm our findings.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/bdi.13355; doi:https://doi.org/10.1111/bdi.13355; html:https://europepmc.org/articles/PMC10768381; pdf:https://europepmc.org/articles/PMC10768381?pdf=render
 33043790,https://doi.org/10.1177/0141076820961776,Advancing UK regulatory science and innovation in healthcare.,"Calvert MJ, Marston E, Samuels M, Rivera SC, Torlinska B, Oliver K, Denniston AK, Hoare S.",,Journal of the Royal Society of Medicine,2021,2020-10-12,Y,,,,,,pdf:https://journals.sagepub.com/doi/pdf/10.1177/0141076820961776; doi:https://doi.org/10.1177/0141076820961776; html:https://europepmc.org/articles/PMC7809339; pdf:https://europepmc.org/articles/PMC7809339?pdf=render
-34653419,https://doi.org/10.1016/s2468-2667(21)00205-x,Life expectancy and risk of death in 6791 communities in England from 2002 to 2019: high-resolution spatiotemporal analysis of civil registration data.,"Rashid T, Bennett JE, Paciorek CJ, Doyle Y, Pearson-Stuttard J, Flaxman S, Fecht D, Toledano MB, Li G, Daby HI, Johnson E, Davies B, Ezzati M.",,The Lancet. Public health,2021,2021-10-13,Y,,,,"<h4>Background</h4>High-resolution data for how mortality and longevity have changed in England, UK are scarce. We aimed to estimate trends from 2002 to 2019 in life expectancy and probabilities of death at different ages for all 6791 middle-layer super output areas (MSOAs) in England.<h4>Methods</h4>We performed a high-resolution spatiotemporal analysis of civil registration data from the UK Small Area Health Statistics Unit research database using de-identified data for all deaths in England from 2002 to 2019, with information on age, sex, and MSOA of residence, and population counts by age, sex, and MSOA. We used a Bayesian hierarchical model to obtain estimates of age-specific death rates by sharing information across age groups, MSOAs, and years. We used life table methods to calculate life expectancy at birth and probabilities of death in different ages by sex and MSOA.<h4>Findings</h4>In 2002-06 and 2006-10, all but a few (0-1%) MSOAs had a life expectancy increase for female and male sexes. In 2010-14, female life expectancy decreased in 351 (5·2%) of 6791 MSOAs. By 2014-19, the number of MSOAs with declining life expectancy was 1270 (18·7%) for women and 784 (11·5%) for men. The life expectancy increase from 2002 to 2019 was smaller in MSOAs where life expectancy had been lower in 2002 (mostly northern urban MSOAs), and larger in MSOAs where life expectancy had been higher in 2002 (mostly MSOAs in and around London). As a result of these trends, the gap between the first and 99th percentiles of MSOA life expectancy for women increased from 10·7 years (95% credible interval 10·4-10·9) in 2002 to reach 14·2 years (13·9-14·5) in 2019, and for men increased from 11·5 years (11·3-11·7) in 2002 to 13·6 years (13·4-13·9) in 2019.<h4>Interpretation</h4>In the decade before the COVID-19 pandemic, life expectancy declined in increasing numbers of communities in England. To ensure that this trend does not continue or worsen, there is a need for pro-equity economic and social policies, and greater investment in public health and health care throughout the entire country.<h4>Funding</h4>Wellcome Trust, Imperial College London, Medical Research Council, Health Data Research UK, and National Institutes of Health Research.",,pdf:http://www.thelancet.com/article/S246826672100205X/pdf; doi:https://doi.org/10.1016/S2468-2667(21)00205-X; html:https://europepmc.org/articles/PMC8554392
 34446501,https://doi.org/10.1136/bmjopen-2021-052629,Using patient-reported outcome measures during the management of patients with end-stage kidney disease requiring treatment with haemodialysis (PROM-HD): a qualitative study.,"Anderson NE, McMullan C, Calvert M, Dutton M, Cockwell P, Aiyegbusi OL, Kyte D.",,BMJ open,2021,2021-08-26,Y,Dialysis; Nephrology; Telemedicine; Qualitative Research; End Stage Renal Failure,,,"<h4>Objectives</h4>Patients undergoing haemodialysis report elevated symptoms and reduced health-related quality of life, and often prioritise improvements in psychosocial well-being over long-term survival. Systematic collection and use of patient-reported outcomes (PROs) may help support tailored healthcare and improve outcomes. This study investigates the methodological basis for routine PRO assessment, particularly using electronic formats (ePROs), to maximise the potential of PRO use, through exploration of the experiences, views and perceptions of patients and healthcare professionals (HCPs) on implementation and use of PROs in haemodialysis settings.<h4>Study design</h4>Qualitative study.<h4>Setting and participants</h4>Semistructured interviews with 22 patients undergoing haemodialysis, and 17 HCPs in the UK.<h4>Analytical approach</h4>Transcripts were analysed deductively using the Consolidated Framework for Implementation Research (CFIR) and inductively using thematic analysis.<h4>Results</h4>For effective implementation, the potential value of PROs needs to be demonstrated empirically to stakeholders. Any intervention must remain flexible enough for individual and aggregate use, measuring outcomes that matter to patients and clinicians, while maintaining operational simplicity. Any implementation must sit within a wider framework of education and support for both patients and clinicians who demonstrate varying previous experience of using PROs and often confuse related concepts. Implementation plans must recognise the multidimensionality of end-stage kidney disease and treatment by haemodialysis, while acknowledging the associated challenges of delivering care in a highly specialised environment. To support implementation, careful consideration needs to be given to barriers and facilitators including effective leadership, the role of champions, effective launch and ongoing evaluation.<h4>Conclusions</h4>Using the CFIR to explore the experiences, views and perceptions of key stakeholders, this study identified key factors at organisational and individual levels which could assist effective implementation of ePROs in haemodialysis settings. Further research will be required to evaluate subsequent ePRO interventions to demonstrate the impact and benefit to the dialysis community.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/8/e052629.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-052629; html:https://europepmc.org/articles/PMC8395280; pdf:https://europepmc.org/articles/PMC8395280?pdf=render
+34653419,https://doi.org/10.1016/s2468-2667(21)00205-x,Life expectancy and risk of death in 6791 communities in England from 2002 to 2019: high-resolution spatiotemporal analysis of civil registration data.,"Rashid T, Bennett JE, Paciorek CJ, Doyle Y, Pearson-Stuttard J, Flaxman S, Fecht D, Toledano MB, Li G, Daby HI, Johnson E, Davies B, Ezzati M.",,The Lancet. Public health,2021,2021-10-13,Y,,,,"<h4>Background</h4>High-resolution data for how mortality and longevity have changed in England, UK are scarce. We aimed to estimate trends from 2002 to 2019 in life expectancy and probabilities of death at different ages for all 6791 middle-layer super output areas (MSOAs) in England.<h4>Methods</h4>We performed a high-resolution spatiotemporal analysis of civil registration data from the UK Small Area Health Statistics Unit research database using de-identified data for all deaths in England from 2002 to 2019, with information on age, sex, and MSOA of residence, and population counts by age, sex, and MSOA. We used a Bayesian hierarchical model to obtain estimates of age-specific death rates by sharing information across age groups, MSOAs, and years. We used life table methods to calculate life expectancy at birth and probabilities of death in different ages by sex and MSOA.<h4>Findings</h4>In 2002-06 and 2006-10, all but a few (0-1%) MSOAs had a life expectancy increase for female and male sexes. In 2010-14, female life expectancy decreased in 351 (5·2%) of 6791 MSOAs. By 2014-19, the number of MSOAs with declining life expectancy was 1270 (18·7%) for women and 784 (11·5%) for men. The life expectancy increase from 2002 to 2019 was smaller in MSOAs where life expectancy had been lower in 2002 (mostly northern urban MSOAs), and larger in MSOAs where life expectancy had been higher in 2002 (mostly MSOAs in and around London). As a result of these trends, the gap between the first and 99th percentiles of MSOA life expectancy for women increased from 10·7 years (95% credible interval 10·4-10·9) in 2002 to reach 14·2 years (13·9-14·5) in 2019, and for men increased from 11·5 years (11·3-11·7) in 2002 to 13·6 years (13·4-13·9) in 2019.<h4>Interpretation</h4>In the decade before the COVID-19 pandemic, life expectancy declined in increasing numbers of communities in England. To ensure that this trend does not continue or worsen, there is a need for pro-equity economic and social policies, and greater investment in public health and health care throughout the entire country.<h4>Funding</h4>Wellcome Trust, Imperial College London, Medical Research Council, Health Data Research UK, and National Institutes of Health Research.",,pdf:http://www.thelancet.com/article/S246826672100205X/pdf; doi:https://doi.org/10.1016/S2468-2667(21)00205-X; html:https://europepmc.org/articles/PMC8554392
 37280096,https://doi.org/10.1136/thorax-2023-220057,"Asthma symptoms, spirometry and air pollution exposure in schoolchildren in an informal settlement and an affluent area of Nairobi, Kenya.","Meme H, Amukoye E, Bowyer C, Chakaya J, Das D, Dobson R, Dragosits U, Fuld J, Gray C, Hahn M, Kiplimo R, Lesosky M, Loh MM, McKendree J, Mortimer K, Ndombi A, Netter L, Obasi A, Orina F, Pearson C, Price H, Quint JK, Semple S, Twigg M, Waelde C, Walnycki A, Warwick M, Wendler J, West SE, Wilson M, Zurba L, Devereux G.",,Thorax,2023,2023-06-06,Y,Asthma; Paediatric Asthma; Asthma Epidemiology,,,"<h4>Background</h4>Although 1 billion people live in informal (slum) settlements, the consequences for respiratory health of living in these settlements remain largely unknown. This study investigated whether children living in an informal settlement in Nairobi, Kenya are at increased risk of asthma symptoms.<h4>Methods</h4>Children attending schools in Mukuru (an informal settlement in Nairobi) and a more affluent area (Buruburu) were compared. Questionnaires quantified respiratory symptoms and environmental exposures; spirometry was performed; personal exposure to particulate matter (PM<sub>2.5</sub>) was estimated.<h4>Results</h4>2373 children participated, 1277 in Mukuru (median age, IQR 11, 9-13 years, 53% girls), and 1096 in Buruburu (10, 8-12 years, 52% girls). Mukuru schoolchildren were from less affluent homes, had greater exposure to pollution sources and PM<sub>2.5</sub>. When compared with Buruburu schoolchildren, Mukuru schoolchildren had a greater prevalence of symptoms, 'current wheeze' (9.5% vs 6.4%, p=0.007) and 'trouble breathing' (16.3% vs 12.6%, p=0.01), and these symptoms were more severe and problematic. Diagnosed asthma was more common in Buruburu (2.8% vs 1.2%, p=0.004). Spirometry did not differ between Mukuru and Buruburu. Regardless of community, significant adverse associations were observed with self-reported exposure to 'vapours, dusts, gases, fumes', mosquito coil burning, adult smoker(s) in the home, refuse burning near homes and residential proximity to roads.<h4>Conclusion</h4>Children living in informal settlements are more likely to develop wheezing symptoms consistent with asthma that are more severe but less likely to be diagnosed as asthma. Self-reported but not objectively measured air pollution exposure was associated with increased risk of asthma symptoms.",,pdf:https://thorax.bmj.com/content/thoraxjnl/early/2023/05/24/thorax-2023-220057.full.pdf; doi:https://doi.org/10.1136/thorax-2023-220057; html:https://europepmc.org/articles/PMC10715514; pdf:https://europepmc.org/articles/PMC10715514?pdf=render
 36426221,https://doi.org/10.3389/fcvm.2022.1016032,Clinician's guide to trustworthy and responsible artificial intelligence in cardiovascular imaging.,"Szabo L, Raisi-Estabragh Z, Salih A, McCracken C, Ruiz Pujadas E, Gkontra P, Kiss M, Maurovich-Horvath P, Vago H, Merkely B, Lee AM, Lekadir K, Petersen SE.",,Frontiers in cardiovascular medicine,2022,2022-11-08,Y,Artificial intelligence; Trustworthiness; Cardiovascular Imaging; Machine Learning (Ml); Ai Risk,,,"A growing number of artificial intelligence (AI)-based systems are being proposed and developed in cardiology, driven by the increasing need to deal with the vast amount of clinical and imaging data with the ultimate aim of advancing patient care, diagnosis and prognostication. However, there is a critical gap between the development and clinical deployment of AI tools. A key consideration for implementing AI tools into real-life clinical practice is their ""trustworthiness"" by end-users. Namely, we must ensure that AI systems can be trusted and adopted by all parties involved, including clinicians and patients. Here we provide a summary of the concepts involved in developing a ""trustworthy AI system."" We describe the main risks of AI applications and potential mitigation techniques for the wider application of these promising techniques in the context of cardiovascular imaging. Finally, we show why trustworthy AI concepts are important governing forces of AI development.",,pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2022.1016032/pdf; doi:https://doi.org/10.3389/fcvm.2022.1016032; html:https://europepmc.org/articles/PMC9681217; pdf:https://europepmc.org/articles/PMC9681217?pdf=render
 37563721,https://doi.org/10.1186/s13063-023-07473-z,Evaluation of interventions to prevent vasovagal reactions among whole blood donors: rationale and design of a large cluster randomised trial.,"McMahon A, Kaptoge S, Walker M, Mehenny S, Gilchrist PT, Sambrook J, Akhtar N, Sweeting M, Wood AM, Stirrups K, Chung R, Fahle S, Johnson E, Cullen D, Godfrey R, Duthie S, Allen L, Harvey P, Berkson M, Allen E, Watkins NA, Bradley JR, Kingston N, Miflin G, Armitage J, Roberts DJ, Danesh J, Di Angelantonio E.",,Trials,2023,2023-08-10,Y,Cross-over; Blood donors; Blood Donation; Factorial Design; Vasovagal Reactions; Cluster Randomised Trial; Stepped-wedge,,,"<h4>Background</h4>Vasovagal reactions (VVRs) are the most common acute complications of blood donation. Responsible for substantial morbidity, they also reduce the likelihood of repeated donations and are disruptive and costly for blood services. Although blood establishments worldwide have adopted different strategies to prevent VVRs (including water loading and applied muscle tension [AMT]), robust evidence is limited. The Strategies to Improve Donor Experiences (STRIDES) trial aims to reliably assess the impact of four different interventions to prevent VVRs among blood donors.<h4>Methods</h4>STRIDES is a cluster-randomised cross-over/stepped-wedge factorial trial of four interventions to reduce VVRs involving about 1.4 million whole blood donors enrolled from all 73 blood donation sites (mobile teams and donor centres) of National Health Service Blood and Transplant (NHSBT) in England. Each site (""cluster"") has been randomly allocated to receive one or more interventions during a 36-month period, using principles of cross-over, stepped-wedge and factorial trial design to assign the sequence of interventions. Each of the four interventions is compared to NHSBT's current practices: (i) 500-ml isotonic drink before donation (vs current 500-ml plain water); (ii) 3-min rest on donation chair after donation (vs current 2 min); (iii) new modified AMT (vs current practice of AMT); and (iv) psychosocial intervention using preparatory materials (vs current practice of nothing). The primary outcome is the number of in-session VVRs with loss of consciousness (i.e. episodes involving loss of consciousness of any duration, with or without additional complications). Secondary outcomes include all in-session VVRs (i.e. with and without loss of consciousness), all delayed VVRs (i.e. those occurring after leaving the venue) and any in-session non-VVR adverse events or reactions.<h4>Discussion</h4>The STRIDES trial should yield novel information about interventions, singly and in combination, for the prevention of VVRs, with the aim of generating policy-shaping evidence to help inform blood services to improve donor health, donor experience, and service efficiency.<h4>Trial registration</h4>ISRCTN: 10412338. Registration date: October 24, 2019.",,doi:https://doi.org/10.1186/s13063-023-07473-z; html:https://europepmc.org/articles/PMC10413586; pdf:https://europepmc.org/articles/PMC10413586?pdf=render
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@@ -13,8 +13,8 @@ PMC10809876,https://doi.org/,Analysis of translesion polymerases in colorectal c
 35057841,https://doi.org/10.1186/s13063-021-05965-4,Development and evaluation of rapid data-enabled access to routine clinical information to enhance early recruitment to the national clinical platform trial of COVID-19 community treatments.,"Cake C, Ogburn E, Pinches H, Coleman G, Seymour D, Woodard F, Manohar S, Monsur M, Landray M, Dalton G, Morris AD, Chinnery PF, UK COVID-19 National Core Studies Consortium, Hobbs FDR, Butler C.",,Trials,2022,2022-01-20,Y,Recruitment; Data; Clinical Trials; Primary Care; Healthcare; Covid-19; Public And Patient Involvement And Engagement,,,"<h4>Background</h4>The COVID-19 pandemic has presented unique challenges for rapidly designing, initiating, and delivering therapeutic clinical trials. PRINCIPLE (Platform Randomised Trial of Treatments in the Community for Epidemic and Pandemic Illnesses) is the UK national platform investigating repurposed therapies for COVID-19 treatment of older people in the community at high risk of complications. Standard methods of patient recruitment were failing to meet the required pace and scale of enrolment. This paper describes the development and appraisal of a near real-time, data-driven, ethical approach for enhancing recruitment in community care by contacting people with a recent COVID-19 positive test result from the central NHS Test and Trace service within approximately 24-48 h of their test result.<h4>Methods</h4>A multi-disciplinary team was formed to solve the technical, ethical, public perception, logistical and information governance issues required to provide a near-real time (approximately within 24-48 h of receiving a positive test) feed of potential trial participants from test result data to the research team. PRINCIPLE was also given unique access to the Summary Care Record (SCR) to ensure safe prescribing, and to enable the trial team to quickly and safely bring consented patients into the trial. A survey of the public was used to understand public perceptions of the use of test data for this proposed methodology.<h4>Results</h4>Prior to establishing the data service, PRINCIPLE registered on average 87 participants per week. This increased by up to 87 additional people registered per week from the test data, contributing to an increase from 1013 recruits to PRINCIPLE at the start of October 2020 to 2802 recruits by 20 December 2020. Whilst procedural caveats were identified by the public consultation, out of 2639 people contacted by PRINCIPLE following a positive test result, no one raised a concern about being approached.<h4>Conclusions</h4>This paper describes a novel approach to using near-real time NHS operational data to recruit community-based patients within a few days of presentation with acute illness. This approach increased recruitment and reduced time between positive test and randomisation, allowing more rapid evaluation of treatments and increased safety for participants. End-to-end public and patient involvement in the design of the approach provided evidence to inform information governance decisions.<h4>Trial registration</h4>PRINCIPLE is funded by UK Research and Innovation and the Department of Health and Social Care through the National Institute for Health Research. EudraCT number: 2020-001209-22 . 26/03/2020 ISRCTN registry: ISRCTN86534580 . 20/03/2020 REC number: 20/SC/058 IRAS number: 281958.",,pdf:https://trialsjournal.biomedcentral.com/counter/pdf/10.1186/s13063-021-05965-4; doi:https://doi.org/10.1186/s13063-021-05965-4; html:https://europepmc.org/articles/PMC8771189; pdf:https://europepmc.org/articles/PMC8771189?pdf=render
 37880687,https://doi.org/10.1186/s12889-023-16993-x,Understanding covid-19 outcomes among people with intellectual disabilities in England.,"Sosenko F, Mackay D, Pell JP, Hatton C, Jani BD, Cairns D, Ward L, Henderson A, Fleming M, Nijhof D, Melville C, CVD-COVID-UK/COVID-IMPACT Consortium.",,BMC public health,2023,2023-10-25,Y,Learning Disabilities; Intellectual Disabilities; Covid-19,,,"<h4>Background</h4>Evidence from the UK from the early stages of the covid-19 pandemic showed that people with Intellectual Disabilities (ID) had higher rates of covid-19 mortality than people without ID. However, estimates of the magnitude of risk vary widely; different studies used different time periods; and only early stages of the pandemic have been analysed. Existing analyses of risk factors have also been limited. The objective of this study was to investigate covid-19 mortality rates, hospitalisation rates, and risk factors in people with ID in England up to the end of 2021.<h4>Methods</h4>Retrospective cohort study of all people with a laboratory-confirmed SARS-CoV-2 infection or death involving covid-19. Datasets covering primary care, secondary care, covid-19 tests and vaccinations, prescriptions, and deaths were linked at individual level.<h4>Results</h4>Covid-19 carries a disproportionately higher risk of death for people with ID, above their already higher risk of dying from other causes, in comparison to those without ID. Around 2,000 people with ID had a death involving covid-19 in England up to the end of 2021; approximately 1 in 180. The covid-19 standardized mortality ratio was 5.6 [95% CI 5.4, 5.9]. People with ID were also more likely to be hospitalised for covid-19 than people without ID. The main determinants of severe covid-19 outcomes (deaths and/or hospitalisations) in both populations were age, multimorbidity and vaccination status. The key factor responsible for the higher risk of severe covid-19 in the ID population was a much higher prevalence of multimorbidity in this population. AstraZeneca vaccine was slightly less effective in preventing severe covid-19 outcomes among people with ID than among people without ID.<h4>Conclusions</h4>People with ID should be considered a priority group in future pandemics, such as shielding and vaccinations.",,pdf:https://bmcpublichealth.biomedcentral.com/counter/pdf/10.1186/s12889-023-16993-x; doi:https://doi.org/10.1186/s12889-023-16993-x; html:https://europepmc.org/articles/PMC10601171; pdf:https://europepmc.org/articles/PMC10601171?pdf=render
 36669966,https://doi.org/10.1016/j.vaccine.2023.01.023,COVID-19 booster vaccination uptake and infection breakthrough amongst health care workers in Wales: A national prospective cohort study.,"Bedston S, Lowthian E, Jarvis CI, Akbari A, Beggs J, Bradley D, de Lusignan S, Griffiths R, Herbert L, Hobbs R, Kerr S, Lyons J, Midgley W, Owen RK, Quint JK, Tsang R, Torabi F, Sheikh A, Lyons RA.",,Vaccine,2023,2023-01-13,Y,Uptake; Vaccination; Health care workers; Booster; Breakthrough; Covid-19,,,"<h4>Background</h4>From September 2021, Health Care Workers (HCWs) in Wales began receiving a COVID-19 booster vaccination. This is the first dose beyond the primary vaccination schedule. Given the emergence of new variants, vaccine waning vaccine, and increasing vaccination hesitancy, there is a need to understand booster vaccine uptake and subsequent breakthrough in this high-risk population.<h4>Methods</h4>We conducted a prospective, national-scale, observational cohort study of HCWs in Wales using anonymised, linked data from the SAIL Databank. We analysed uptake of COVID-19 booster vaccinations from September 2021 to February 2022, with comparisons against uptake of the initial primary vaccination schedule. We also analysed booster breakthrough, in the form of PCR-confirmed SARS-Cov-2 infection, comparing to the second primary dose. Cox proportional hazard models were used to estimate associations for vaccination uptake and breakthrough regarding staff roles, socio-demographics, household composition, and other factors.<h4>Results</h4>We derived a cohort of 73,030 HCWs living in Wales (78% female, 60% 18-49 years old). Uptake was quickest amongst HCWs aged 60 + years old (aHR 2.54, 95%CI 2.45-2.63), compared with those aged 18-29. Asian HCWs had quicker uptake (aHR 1.18, 95%CI 1.14-1.22), whilst Black HCWs had slower uptake (aHR 0.67, 95%CI 0.61-0.74), compared to white HCWs. HCWs residing in the least deprived areas were slightly quicker to have received a booster dose (aHR 1.12, 95%CI 1.09-1.16), compared with those in the most deprived areas. Strongest associations with breakthrough infections were found for those living with children (aHR 1.52, 95%CI 1.41-1.63), compared to two-adult only households. HCWs aged 60 + years old were less likely to get breakthrough infections, compared to those aged 18-29 (aHR 0.42, 95%CI 0.38-0.47).<h4>Conclusion</h4>Vaccination uptake was consistently lower among black HCWs, as well as those from deprived areas. Whilst breakthrough infections were highest in households with children.",,doi:https://doi.org/10.1016/j.vaccine.2023.01.023; doi:https://doi.org/10.1016/j.vaccine.2023.01.023; html:https://europepmc.org/articles/PMC9837216; pdf:https://europepmc.org/articles/PMC9837216?pdf=render
-38562403,https://doi.org/10.1016/j.ssmph.2024.101655,Pathways explaining racial/ethnic and socio-economic disparities in brain white matter integrity outcomes in the UK Biobank study.,"Weiss J, Beydoun MA, Beydoun HA, Georgescu MF, Hu YH, Noren Hooten N, Banerjee S, Launer LJ, Evans MK, Zonderman AB.",,SSM - population health,2024,2024-03-20,Y,Aging; Magnetic Resonance Imaging; Racial Disparities; Socio-economic Status; White Matter Integrity,,,"Pathways explaining racial/ethnic and socio-economic status (SES) disparities in white matter integrity (WMI) reflecting brain health, remain underexplored, particularly in the UK population. We examined racial/ethnic and SES disparities in diffusion tensor brain magnetic resonance imaging (dMRI) markers, namely global and tract-specific mean fractional anisotropy (FA), and tested total, direct and indirect effects through lifestyle, health-related and cognition factors using a structural equations modeling approach among 36,184 UK Biobank participants aged 40-70 y at baseline assessment (47% men). Multiple linear regression models were conducted, testing independent associations of race/ethnicity, socio-economic and other downstream factors in relation to global mean FA, while stratifying by Alzheimer's Disease polygenic Risk Score (AD PRS) tertiles. Race (Non-White vs. White) and lower SES predicted poorer WMI (i.e. lower global mean FA) at follow-up, with racial/ethnic disparities in FA<sub>mean</sub> involving multiple pathways and SES playing a central role in those pathways. Mediational patterns differed across tract-specific FA outcomes, with SES-FA<sub>mean</sub> total effect being partially mediated (41% of total effect = indirect effect). Furthermore, the association of poor cognition with FA<sub>mean</sub> was markedly stronger in the two uppermost AD PRS tertiles compared to the lower tertile (T<sub>2</sub> and T<sub>3</sub>: β±SE: -0.0009 ± 0.0001 vs. T<sub>1</sub>: β±SE: -0.0005 ± 0.0001, <i>P</i> < 0.001), independently of potentially confounding factors. Race and lower SES were generally important determinants of adverse WMI outcomes, with partial mediation of socio-economic disparities in global mean FA through lifestyle, health-related and cognition factors. The association of poor cognition with lower global mean FA was stronger at higher AD polygenic risk.",,doi:https://doi.org/10.1016/j.ssmph.2024.101655; html:https://europepmc.org/articles/PMC10982559; pdf:https://europepmc.org/articles/PMC10982559?pdf=render
 34994801,https://doi.org/10.1093/pubmed/fdab400,COVID-19 vaccination uptake amongst ethnic minority communities in England: a linked study exploring the drivers of differential vaccination rates.,"Gaughan CH, Razieh C, Khunti K, Banerjee A, Chudasama YV, Davies MJ, Dolby T, Gillies CL, Lawson C, Mirkes EM, Morgan J, Tingay K, Zaccardi F, Yates T, Nafilyan V.",,"Journal of public health (Oxford, England)",2023,2023-03-01,Y,Vaccination; Cultural; Ethnicity; Social; Sociodemographic Factors; Demographic; Covid-19,,,"<h4>Background</h4>Despite generally high coronavirus disease 2019 (COVID-19) vaccination rates in the UK, vaccination hesitancy and lower take-up rates have been reported in certain ethnic minority communities.<h4>Methods</h4>We used vaccination data from the National Immunisation Management System (NIMS) linked to the 2011 Census and individual health records for subjects aged ≥40 years (n = 24 094 186). We estimated age-standardized vaccination rates, stratified by ethnic group and key sociodemographic characteristics, such as religious affiliation, deprivation, educational attainment, geography, living conditions, country of birth, language skills and health status. To understand the association of ethnicity with lower vaccination rates, we conducted a logistic regression model adjusting for differences in geographic, sociodemographic and health characteristics. ResultsAll ethnic groups had lower age-standardized rates of vaccination compared with the white British population, whose vaccination rate of at least one dose was 94% (95% CI: 94%-94%). Black communities had the lowest rates, with 75% (74-75%) of black African and 66% (66-67%) of black Caribbean individuals having received at least one dose. The drivers of these lower rates were partly explained by accounting for sociodemographic differences. However, modelled estimates showed significant differences remained for all minority ethnic groups, compared with white British individuals.<h4>Conclusions</h4>Lower COVID-19 vaccination rates are consistently observed amongst all ethnic minorities.",,pdf:https://academic.oup.com/jpubhealth/article-pdf/45/1/e65/49527132/fdab400.pdf; doi:https://doi.org/10.1093/pubmed/fdab400; html:https://europepmc.org/articles/PMC8755382; pdf:https://europepmc.org/articles/PMC8755382?pdf=render
+38562403,https://doi.org/10.1016/j.ssmph.2024.101655,Pathways explaining racial/ethnic and socio-economic disparities in brain white matter integrity outcomes in the UK Biobank study.,"Weiss J, Beydoun MA, Beydoun HA, Georgescu MF, Hu YH, Noren Hooten N, Banerjee S, Launer LJ, Evans MK, Zonderman AB.",,SSM - population health,2024,2024-03-20,Y,Aging; Magnetic Resonance Imaging; Racial Disparities; Socio-economic Status; White Matter Integrity,,,"Pathways explaining racial/ethnic and socio-economic status (SES) disparities in white matter integrity (WMI) reflecting brain health, remain underexplored, particularly in the UK population. We examined racial/ethnic and SES disparities in diffusion tensor brain magnetic resonance imaging (dMRI) markers, namely global and tract-specific mean fractional anisotropy (FA), and tested total, direct and indirect effects through lifestyle, health-related and cognition factors using a structural equations modeling approach among 36,184 UK Biobank participants aged 40-70 y at baseline assessment (47% men). Multiple linear regression models were conducted, testing independent associations of race/ethnicity, socio-economic and other downstream factors in relation to global mean FA, while stratifying by Alzheimer's Disease polygenic Risk Score (AD PRS) tertiles. Race (Non-White vs. White) and lower SES predicted poorer WMI (i.e. lower global mean FA) at follow-up, with racial/ethnic disparities in FA<sub>mean</sub> involving multiple pathways and SES playing a central role in those pathways. Mediational patterns differed across tract-specific FA outcomes, with SES-FA<sub>mean</sub> total effect being partially mediated (41% of total effect = indirect effect). Furthermore, the association of poor cognition with FA<sub>mean</sub> was markedly stronger in the two uppermost AD PRS tertiles compared to the lower tertile (T<sub>2</sub> and T<sub>3</sub>: β±SE: -0.0009 ± 0.0001 vs. T<sub>1</sub>: β±SE: -0.0005 ± 0.0001, <i>P</i> < 0.001), independently of potentially confounding factors. Race and lower SES were generally important determinants of adverse WMI outcomes, with partial mediation of socio-economic disparities in global mean FA through lifestyle, health-related and cognition factors. The association of poor cognition with lower global mean FA was stronger at higher AD polygenic risk.",,doi:https://doi.org/10.1016/j.ssmph.2024.101655; html:https://europepmc.org/articles/PMC10982559; pdf:https://europepmc.org/articles/PMC10982559?pdf=render
 37124948,https://doi.org/10.1016/j.lanepe.2023.100638,Severity of Omicron BA.5 variant and protective effect of vaccination: national cohort and matched analyses in Scotland.,"Robertson C, Kerr S, Sheikh A.",,The Lancet regional health. Europe,2023,2023-04-14,Y,,,,,,doi:https://doi.org/10.1016/j.lanepe.2023.100638; doi:https://doi.org/10.1016/j.lanepe.2023.100638; html:https://europepmc.org/articles/PMC10139952; pdf:https://europepmc.org/articles/PMC10139952?pdf=render
 39349692,https://doi.org/10.1038/s41746-024-01257-8,Talking about diseases; developing a model of patient and public-prioritised disease phenotypes.,"Slater K, Schofield PN, Wright J, Clift P, Irani A, Bradlow W, Aziz F, Gkoutos GV.",,NPJ digital medicine,2024,2024-09-30,Y,,,,"Deep phenotyping describes the use of standardised terminologies to create comprehensive phenotypic descriptions of biomedical phenomena. These characterisations facilitate secondary analysis, evidence synthesis, and practitioner awareness, thereby guiding patient care. The vast majority of this knowledge is derived from sources that describe an academic understanding of disease, including academic literature and experimental databases. Previous work indicates a gulf between the priorities, perspectives, and perceptions held by different healthcare stakeholders. Using social media data, we develop a phenotype model that represents a public perspective on disease and compare this with a model derived from a combination of existing academic phenotype databases. We identified 52,198 positive disease-phenotype associations from social media across 311 diseases. We further identified 24,618 novel phenotype associations not shared by the biomedical and literature-derived phenotype model across 304 diseases, of which we considered 14,531 significant. Manifestations of disease affecting quality of life, and concerning endocrine, digestive, and reproductive diseases were over-represented in the social media phenotype model. An expert clinical review found that social media-derived associations were considered similarly well-established to those derived from literature, and were seen significantly more in patient clinical encounters. The phenotype model recovered from social media presents a significantly different perspective than existing resources derived from biomedical databases and literature, providing a large number of associations novel to the latter dataset. We propose that the integration and interrogation of these public perspectives on the disease can inform clinical awareness, improve secondary analysis, and bridge understanding and priorities across healthcare stakeholders.",,doi:https://doi.org/10.1038/s41746-024-01257-8; doi:https://doi.org/10.1038/s41746-024-01257-8; html:https://europepmc.org/articles/PMC11443070; pdf:https://europepmc.org/articles/PMC11443070?pdf=render
 37751591,https://doi.org/10.18632/aging.205058,Pathways explaining racial/ethnic and socio-economic disparities in dementia incidence: the UK Biobank study.,"Beydoun MA, Beydoun HA, Fanelli-Kuczmarski MT, Weiss J, Georgescu MF, Meirelles O, Lyall DM, Evans MK, Zonderman AB.",,Aging,2023,2023-09-25,Y,Alzheimer’s disease; Dementia; Health Disparities; Socio-economic Status; Structural Equations Modeling,,,"<h4>Background</h4>Pathways explaining racial/ethnic disparities in dementia risk are under-evaluated.<h4>Methods</h4>We examine those disparities and their related pathways among UK Biobank study respondents (50-74 y, <i>N</i> = 323,483; 3.6% non-White minorities) using a series of Cox proportional hazards and generalized structural equations models (GSEM).<h4>Results</h4>After ≤15 years, 5,491 all-cause dementia cases were diagnosed. Racial minority status (RACE_ETHN, Non-White vs. White) increased dementia risk by 24% (HR = 1.24, 95% CI: 1.07-1.45, <i>P</i> = 0.005), an association attenuated by socio-economic status (SES), (HR = 1.12, 95% CI: 0.96-1.31). Total race-dementia effect was mediated through both SES and Life's Essential 8 lifestyle sub-score (LE8<sub>LIFESTYLE</sub>), combining diet, smoking, physical activity, and sleep factors. SES was inversely related to dementia risk (HR = 0.69, 95% CI: 0.67, 0.72, <i>P</i> < 0.001). Pathways explaining excess dementia risk among racial minorities included 'RACE_ETHN(-) → SES(-) → DEMENTIA', 'RACE_ETHN(-) → SES(-) → Poor cognitive performance, COGN(+) → DEMENTIA' and 'RACE_ETHN(-) → SES(+) → LE8<sub>LIFESTYLE</sub>(-) → DEMENTIA'.<h4>Conclusions</h4>Pending future interventions, lifestyle factors including diet, smoking, physical activity, and sleep are crucial for reducing racial and socio-economic disparities in dementia.",,pdf:https://www.aging-us.com/article/205058/pdf; doi:https://doi.org/10.18632/aging.205058; html:https://europepmc.org/articles/PMC10564412; pdf:https://europepmc.org/articles/PMC10564412?pdf=render
@@ -36,8 +36,8 @@ PMC10809876,https://doi.org/,Analysis of translesion polymerases in colorectal c
 37875536,https://doi.org/10.1038/s41467-023-41879-2,"Long-term health impacts of COVID-19 among 242,712 adults in England.","Atchison CJ, Davies B, Cooper E, Lound A, Whitaker M, Hampshire A, Azor A, Donnelly CA, Chadeau-Hyam M, Cooke GS, Ward H, Elliott P.",,Nature communications,2023,2023-10-24,Y,,,,"The COVID-19 pandemic is having a lasting impact on health and well-being. We compare current self-reported health, quality of life and symptom profiles for people with ongoing symptoms following COVID-19 to those who have never tested positive for SARS-CoV-2 infection and those who have recovered from COVID-19. Overall, 276,840/800,000 (34·6%) of invited participants took part. Mental health and health-related quality of life were worse among participants with ongoing persistent symptoms post-COVID compared with those who had never had COVID-19 or had recovered. In this study, median duration of COVID-related symptoms (N = 130,251) was 1·3 weeks (inter-quartile range 6 days to 2 weeks), with 7·5% and 5·2% reporting ongoing symptoms ≥12 weeks and ≥52 weeks respectively. Female sex, ≥1 comorbidity and being infected when Wild-type variant was dominant were associated with higher probability of symptoms lasting ≥12 weeks and longer recovery time in those with persistent symptoms. Although COVID-19 is usually of short duration, some adults experience persistent and burdensome illness.",,pdf:https://www.nature.com/articles/s41467-023-41879-2.pdf; doi:https://doi.org/10.1038/s41467-023-41879-2; html:https://europepmc.org/articles/PMC10598213; pdf:https://europepmc.org/articles/PMC10598213?pdf=render
 36180455,https://doi.org/10.1038/s41598-022-20118-6,"Risk of thrombocytopenic, haemorrhagic and thromboembolic disorders following COVID-19 vaccination and positive test: a self-controlled case series analysis in Wales.","Torabi F, Bedston S, Lowthian E, Akbari A, Owen RK, Bradley DT, Agrawal U, Collins P, Fry R, Griffiths LJ, Beggs J, Davies G, Hollinghurst J, Lyons J, Abbasizanjani H, Cottrell S, Perry M, Roberts R, Azcoaga-Lorenzo A, Fagbamigbe AF, Shi T, Tsang RSM, Robertson C, Hobbs FDR, de Lusignan S, McCowan C, Gravenor M, Simpson CR, Sheikh A, Lyons RA.",,Scientific reports,2022,2022-09-30,Y,,,,"There is a need for better understanding of the risk of thrombocytopenic, haemorrhagic, thromboembolic disorders following first, second and booster vaccination doses and testing positive for SARS-CoV-2. Self-controlled cases series analysis of 2.1 million linked patient records in Wales between 7th December 2020 and 31st December 2021. Outcomes were the first diagnosis of thrombocytopenic, haemorrhagic and thromboembolic events in primary or secondary care datasets, exposure was defined as 0-28 days post-vaccination or a positive reverse transcription polymerase chain reaction test for SARS-CoV-2. 36,136 individuals experienced either a thrombocytopenic, haemorrhagic or thromboembolic event during the study period. Relative to baseline, our observations show greater risk of outcomes in the periods post-first dose of BNT162b2 for haemorrhagic (IRR 1.47, 95%CI: 1.04-2.08) and idiopathic thrombocytopenic purpura (IRR 2.80, 95%CI: 1.21-6.49) events; post-second dose of ChAdOx1 for arterial thrombosis (IRR 1.14, 95%CI: 1.01-1.29); post-booster greater risk of venous thromboembolic (VTE) (IRR-Moderna 3.62, 95%CI: 0.99-13.17) (IRR-BNT162b2 1.39, 95%CI: 1.04-1.87) and arterial thrombosis (IRR-Moderna 3.14, 95%CI: 1.14-8.64) (IRR-BNT162b2 1.34, 95%CI: 1.15-1.58). Similarly, post SARS-CoV-2 infection the risk was increased for haemorrhagic (IRR 1.49, 95%CI: 1.15-1.92), VTE (IRR 5.63, 95%CI: 4.91, 6.4), arterial thrombosis (IRR 2.46, 95%CI: 2.22-2.71). We found that there was a measurable risk of thrombocytopenic, haemorrhagic, thromboembolic events after COVID-19 vaccination and infection.",,pdf:https://www.nature.com/articles/s41598-022-20118-6.pdf; doi:https://doi.org/10.1038/s41598-022-20118-6; html:https://europepmc.org/articles/PMC9524320; pdf:https://europepmc.org/articles/PMC9524320?pdf=render
 37620452,https://doi.org/10.1007/s13300-023-01456-8,Sars-Cov-2 Infection in People with Type 1 Diabetes and Hospital Admission: An Analysis of Risk Factors for England.,"Heald AH, Jenkins DA, Williams R, Mudaliar RN, Khan A, Syed A, Sattar N, Khunti K, Naseem A, Bowden-Davies KA, Gibson JM, Ollier W, CVD-COVID-UK/COVID-IMPACT Consortium.",,"Diabetes therapy : research, treatment and education of diabetes and related disorders",2023,2023-08-25,Y,type 1 diabetes; Outcome; Covid-19; Sars-cov-2,,,"<h4>Introduction</h4>The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus (coronavirus disease 2019 [COVID-19]) pandemic revealed the vulnerability of specific population groups in relation to susceptibility to acute deterioration in their health, including hospital admission and mortality. There is less data on outcomes for people with type 1 diabetes (T1D) following SARS-CoV-2 infection than for those with type 2 diabetes (T2D). In this study we set out to determine the relative likelihood of hospital admission following SARS-CoV-2 infection in people with T1D when compared to those without T1D.<h4>Methods</h4>This study was conducted as a retrospective cohort study and utilised an all-England dataset. Electronic health record data relating to people in a national England database (NHS England's Secure Data Environment, accessed via the BHF Data Science Centre's CVD-COVID-UK/COVID-IMPACT consortium) were analysed. The cohort consisted of patients with a confirmed SARS-CoV-2 infection, and the exposure was whether or not an individual had T1D prior to infection (77,392 patients with T1D). The patients without T1D were matched for sex, age and approximate date of the positive COVID-19 test, with three SARS-CoV-2-infected people living without diabetes (n = 223,995). Potential factors influencing the relative likelihood of the outcome of hospital admission within 28 days were ascertained using univariable and multivariable logistic regression.<h4>Results</h4>Median age of the people living with T1D was 37 (interquartile range 25-52) years, 47.4% were female and 89.6% were of white ethnicity. Mean body mass index was 27 (standard error [SE] 0.022) kg/m<sup>2</sup>, and mean glycated haemoglobin (HbA1c) was 67.3 (SE 0.069) mmol/mol (8.3%). A significantly higher proportion of people with T1D (10.7%) versus matched non-diabetes individuals (3.9%) were admitted to hospital. In combined analysis including individuals with T1D and matched controls, multiple regression modelling indicated that the factors independently relating to a higher likelihood of hospital admission were: T1D (odds ratio [OR] 1.71, 95% confidence interval [CI] 1.62-1.80]), age (OR 1.02, 95% CI 1.02-1.03), social deprivation (higher Townsend deprivation score: OR 1.07, 95% CI 1.06-1.08), lower estimated glomerular filtration rate (eGFR) value (OR 0.975, 95% CI 0.974-0.976), non-white ethnicity (OR black 1.19, 95% CI 1.06-1.33/OR Asian 1.21, 95% CI 1.05-1.39) and having asthma (OR 1.27, 95% CI 1.19-1.35]), chronic obstructive pulmonary disease (OR 2.10, 95% CI 1.89-2.32), severe mental illness (OR 1.83, 95% CI 1.57-2.12) or hypertension (OR 1.44, 95% CI 1.37-1.52).<h4>Conclusion</h4>In this all-England study, we describe that, following confirmed infection with SARS-CoV-2, the risk factors for hospital admission for people living with T1D are similar to people without diabetes following confirmed SARS-CoV-2 infection, although the former were more likely to be admitted to hospital. The younger age of individuals with T1D in relation to risk stratification must be taken into account in any ongoing risk reduction strategies regarding COVID-19/future viral pandemics.",,doi:https://doi.org/10.1007/s13300-023-01456-8; doi:https://doi.org/10.1007/s13300-023-01456-8; html:https://europepmc.org/articles/PMC10597906; pdf:https://europepmc.org/articles/PMC10597906?pdf=render
-37308303,https://doi.org/10.3399/bjgp.2023.0044,Diagnostic windows in non-neoplastic diseases: a systematic review.,"Whitfield E, White B, Denaxas S, Lyratzopoulos G.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2023,2023-08-31,Y,Diagnosis; Primary Health Care; Electronic Health Records,,,"<h4>Background</h4>Investigating changes in prediagnostic healthcare utilisation can help identify how much earlier conditions could be diagnosed. Such 'diagnostic windows' are established for cancer but remain relatively unexplored for non-neoplastic conditions.<h4>Aim</h4>To extract evidence on the presence and length of diagnostic windows for non-neoplastic conditions.<h4>Design and setting</h4>A systematic review of studies of prediagnostic healthcare utilisation was carried out.<h4>Method</h4>A search strategy was developed to identify relevant studies from PubMed and Connected Papers. Data were extracted on prediagnostic healthcare use, and evidence of diagnostic window presence and length was assessed.<h4>Results</h4>Of 4340 studies screened, 27 were included, covering 17 non-neoplastic conditions, including both chronic (for example, Parkinson's disease) and acute conditions (for example, stroke). Prediagnostic healthcare events included primary care encounters and presentations with relevant symptoms. For 10 conditions, sufficient evidence to determine diagnostic window presence and length was available, ranging from 28 days (herpes simplex encephalitis) to 9 years (ulcerative colitis). For the remaining conditions, diagnostic windows were likely to be present, but insufficient study duration was often a barrier to robustly determining their length, meaning that diagnostic window length may exceed 10 years for coeliac disease, for example.<h4>Conclusion</h4>Evidence of changing healthcare use before diagnosis exists for many non-neoplastic conditions, establishing that early diagnosis is possible, in principle. In particular, some conditions may be detectable many years earlier than they are currently diagnosed. Further research is required to accurately estimate diagnostic windows and to determine how much earlier diagnosis may be possible, and how this might be achieved.",,pdf:https://bjgp.org/content/bjgp/early/2023/04/04/BJGP.2023.0044.full.pdf; doi:https://doi.org/10.3399/BJGP.2023.0044; html:https://europepmc.org/articles/PMC10285689; pdf:https://europepmc.org/articles/PMC10285689?pdf=render
 38803829,https://doi.org/10.1136/bmjmed-2023-000791,Incidence and treatment of group A streptococcal infections during covid-19 pandemic and 2022 outbreak: retrospective cohort study in England using OpenSAFELY-TPP.,"Cunningham C, Fisher L, Wood C, Speed V, Brown AD, Curtis H, Higgins R, Croker R, Butler-Cole BF, Evans D, Inglesby P, Dillingham I, Bacon SC, Beech E, Hand K, Davy S, Ward T, Hickman G, Bridges L, O'Dwyer T, Maude S, Smith RM, Mehrkar A, Hart LC, Bates C, Cockburn J, Parry J, Hester F, Harper S, Goldacre B, MacKenna B.",,BMJ medicine,2024,2024-05-24,Y,Primary Health Care; Infectious Disease Medicine; Covid-19,,,"<h4>Objective</h4>To investigate the effect of the covid-19 pandemic on the number of patients with group A streptococcal infections and related antibiotic prescriptions.<h4>Design</h4>Retrospective cohort study in England using OpenSAFELY-TPP.<h4>Setting</h4>Primary care practices in England that used TPP SystmOne software, 1 January 2018 to 31 March 2023, with the approval of NHS England.<h4>Participants</h4>Patients registered at a TPP practice at the start of each month of the study period. Patients with missing data for sex or age were excluded, resulting in a population of 23 816 470 in January 2018, increasing to 25 541 940 by March 2023.<h4>Main outcome measures</h4>Monthly counts and crude rates of patients with group A streptococcal infections (sore throat or tonsillitis, scarlet fever, and invasive group A streptococcal infections), and recommended firstline, alternative, and reserved antibiotic prescriptions linked with a group A streptococcal infection before (pre-April 2020), during, and after (post-April 2021) covid-19 restrictions. Maximum and minimum count and rate for each infectious season (time from September to August), as well as the rate ratio of the 2022-23 season compared with the last comparably high season (2017-18).<h4>Results</h4>The number of patients with group A streptococcal infections, and antibiotic prescriptions linked to an indication of group A streptococcal infection, peaked in December 2022, higher than the peak in 2017-18. The rate ratios for monthly sore throat or tonsillitis (possible group A streptococcal throat infection), scarlet fever, and invasive group A streptococcal infection in 2022-23 relative to 2017-18 were 1.39 (95% confidence interval (CI) 1.38 to 1.40), 2.68 (2.59 to 2.77), and 4.37 (2.94 to 6.48), respectively. The rate ratio for prescriptions of first line, alternative, and reserved antibiotics to patients with group A streptococcal infections in 2022-23 relative to 2017-18 were 1.37 (95% CI 1.35 to 1.38), 2.30 (2.26 to 2.34), and 2.42 (2.24 to 2.61), respectively. For individual antibiotic prescriptions in 2022-23, azithromycin showed the greatest relative increase versus 2017-18, with a rate ratio of 7.37 (6.22 to 8.74). This finding followed a marked decrease in the recording of patients with group A streptococcal infections and associated prescriptions during the period of covid-19 restrictions where the maximum count and rates were lower than any minimum rates before the covid-19 pandemic.<h4>Conclusions</h4>Recording of rates of scarlet fever, sore throat or tonsillitis, and invasive group A streptococcal infections, and associated antibiotic prescribing, peaked in December 2022. Primary care data can supplement existing infectious disease surveillance through linkages with relevant prescribing data and detailed analysis of clinical and demographic subgroups.",,doi:https://doi.org/10.1136/bmjmed-2023-000791; html:https://europepmc.org/articles/PMC11129040; pdf:https://europepmc.org/articles/PMC11129040?pdf=render
+37308303,https://doi.org/10.3399/bjgp.2023.0044,Diagnostic windows in non-neoplastic diseases: a systematic review.,"Whitfield E, White B, Denaxas S, Lyratzopoulos G.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2023,2023-08-31,Y,Diagnosis; Primary Health Care; Electronic Health Records,,,"<h4>Background</h4>Investigating changes in prediagnostic healthcare utilisation can help identify how much earlier conditions could be diagnosed. Such 'diagnostic windows' are established for cancer but remain relatively unexplored for non-neoplastic conditions.<h4>Aim</h4>To extract evidence on the presence and length of diagnostic windows for non-neoplastic conditions.<h4>Design and setting</h4>A systematic review of studies of prediagnostic healthcare utilisation was carried out.<h4>Method</h4>A search strategy was developed to identify relevant studies from PubMed and Connected Papers. Data were extracted on prediagnostic healthcare use, and evidence of diagnostic window presence and length was assessed.<h4>Results</h4>Of 4340 studies screened, 27 were included, covering 17 non-neoplastic conditions, including both chronic (for example, Parkinson's disease) and acute conditions (for example, stroke). Prediagnostic healthcare events included primary care encounters and presentations with relevant symptoms. For 10 conditions, sufficient evidence to determine diagnostic window presence and length was available, ranging from 28 days (herpes simplex encephalitis) to 9 years (ulcerative colitis). For the remaining conditions, diagnostic windows were likely to be present, but insufficient study duration was often a barrier to robustly determining their length, meaning that diagnostic window length may exceed 10 years for coeliac disease, for example.<h4>Conclusion</h4>Evidence of changing healthcare use before diagnosis exists for many non-neoplastic conditions, establishing that early diagnosis is possible, in principle. In particular, some conditions may be detectable many years earlier than they are currently diagnosed. Further research is required to accurately estimate diagnostic windows and to determine how much earlier diagnosis may be possible, and how this might be achieved.",,pdf:https://bjgp.org/content/bjgp/early/2023/04/04/BJGP.2023.0044.full.pdf; doi:https://doi.org/10.3399/BJGP.2023.0044; html:https://europepmc.org/articles/PMC10285689; pdf:https://europepmc.org/articles/PMC10285689?pdf=render
 39068671,https://doi.org/10.18632/aging.206033,mTORC1 activation in presumed classical monocytes: observed correlation with human size variation and neuropsychiatric disease.,"Berner K, Oz N, Kaya A, Acharjee A, Berner J.",,Aging,2024,2024-07-26,Y,Monocyte; ketamine; Rapamycin; lithium; Mtorc1,,,"<h4>Background</h4>Gain of function disturbances in nutrient sensing are likely the largest component in human age-related disease. Mammalian target of rapamycin complex 1 (mTORC1) activity affects health span and longevity. The drugs ketamine and rapamycin are effective against chronic pain and depression, and both affect mTORC1 activity. Our objective was to measure phosphorylated p70S6K, a marker for mTORC1 activity, in individuals with psychiatric disease to determine whether phosphorylated p70S6K could predict medication response.<h4>Methods</h4>Twenty-seven females provided blood samples in which p70S6K and phosphorylated p70S6K were analyzed. Chart review gathered biometric measurements, clinical phenotypes, and medication response. Questionnaires assessed anxiety, depression, autism traits, and mitochondrial dysfunction, to determine neuropsychiatric disease profiles. Univariate and multivariate statistical analyses were used to identify predictors of medication response.<h4>Results</h4>mTORC1 activity correlated highly with both classical biometrics (height, macrocephaly, pupil distance) and specific neuropsychiatric disease profiles (anxiety and autism). Across all cases, phosphorylated p70S6K was the best predictor for ketamine response, and also the best predictor for rapamycin response in a single instance.<h4>Conclusions</h4>The data illustrate the importance of mTORC1 activity in both observable body structure and medication response. This report suggests that a simple assay may allow cost-effective prediction of medication response.",,doi:https://doi.org/10.18632/aging.206033; html:https://europepmc.org/articles/PMC11315394; pdf:https://europepmc.org/articles/PMC11315394?pdf=render
 36205023,https://doi.org/10.1002/cam4.5323,Role of microbiota and microbiota-derived short-chain fatty acids in PDAC.,"Temel HY, Kaymak Ö, Kaplan S, Bahcivanci B, Gkoutos GV, Acharjee A.",,Cancer medicine,2023,2022-10-07,Y,Inflammation; Microbiota; Pancreatic Ductal Adenocarcinoma; Microbiome; Host-microbe Interactions; Scfa,,,"Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive lethal diseases among other cancer types. Gut microbiome and its metabolic regulation play a crucial role in PDAC. Metabolic regulation in the gut is a complex process that involves microbiome and microbiome-derived short-chain fatty acids (SCFAs). SCFAs regulate inflammation, as well as lipid and glucose metabolism, through different pathways. This review aims to summarize recent developments in PDAC in the context of gut and oral microbiota and their associations with short-chain fatty acid (SCFA). In addition to this, we discuss possible therapeutic applications using microbiota in PDAC.",,doi:https://doi.org/10.1002/cam4.5323; doi:https://doi.org/10.1002/cam4.5323; html:https://europepmc.org/articles/PMC10028056; pdf:https://europepmc.org/articles/PMC10028056?pdf=render
 39112676,https://doi.org/10.1007/s11657-024-01435-x,Body fat distribution and bone mineral density in a multi-ethnic sample of postmenopausal women in The Malaysian Cohort.,"Bihun H, Abdullah N, Abdul Murad NA, Chin SF, Arifin ASK, Khuzaimi AN, Karpe F, Lewington S, Carter J, Bragg F, Jamal R.",,Archives of osteoporosis,2024,2024-08-07,Y,Adiposity; bone mineral density; cross-sectional; Ethnicity; Dual X-ray Absorptiometry; Postmenopausal Women,,,"In this study of postmenopausal women in Malaysia, total adiposity was inversely associated with total BMD, while regional associations varied. No differences were detected across Malay, Chinese, and Indian ethnicities. Low BMD contributes substantially to morbidity and mortality, and increasing adiposity levels globally may be contributing to this.<h4>Purpose</h4>To investigate associations of total and regional adiposity with bone mineral density (BMD) among a multi-ethnic cohort of postmenopausal women.<h4>Methods</h4>Dual X-ray absorptiometry (DXA) imaging was undertaken for 1990 postmenopausal women without prior chronic diseases (30% Malay, 53% Chinese, and 17% Indian) from The Malaysian Cohort (TMC). The strength of the associations between standardized total and regional body fat percentages with total and regional BMD was examined using linear regression models adjusted for age, height, lean mass, ethnicity, education, and diabetes. Effect modification was assessed for ethnicity.<h4>Results</h4>Women with a higher total body fat percentage were more likely to be Indian or Malay. Mean (SD) BMD for the whole-body total, lumbar spine, leg, and arm were 1.08 (0.11), 0.96 (0.15), 2.21 (0.22), and 1.36 (0.12) g/cm<sup>2</sup>, respectively. Total body and visceral fat percentage were inversely associated with total BMD (- 0.02 [95% CI - 0.03, - 0.01] and - 0.01 [- 0.02, - 0.006] g/cm<sup>2</sup> per 1 SD, respectively). In contrast, subcutaneous and gynoid fat percentages were positively associated with BMD (0.007 [0.002, 0.01] and 0.01 [0.006, 0.02] g/cm<sup>2</sup>, respectively). Total body fat percentage showed a weak positive association with lumbar BMD (0.01 [0.004, 0.02]) and inverse associations with leg (- 0.04 [- 0.06, - 0.03]) and arm (- 0.02 [- 0.03, - 0.02]) BMD in the highest four quintiles. There was no effect modification by ethnicity (p<sub>hetero</sub> > 0.05).<h4>Conclusion</h4>Total adiposity was inversely associated with total BMD, although regional associations varied. There was no heterogeneity across ethnic groups suggesting adiposity may be a risk factor for low BMD across diverse populations.",,doi:https://doi.org/10.1007/s11657-024-01435-x; html:https://europepmc.org/articles/PMC11306509; pdf:https://europepmc.org/articles/PMC11306509?pdf=render
@@ -47,8 +47,8 @@ PMC10809876,https://doi.org/,Analysis of translesion polymerases in colorectal c
 38783412,https://doi.org/10.1002/pds.5815,OpenSAFELY: A platform for analysing electronic health records designed for reproducible research.,"Nab L, Schaffer AL, Hulme W, DeVito NJ, Dillingham I, Wiedemann M, Andrews CD, Curtis H, Fisher L, Green A, Massey J, Walters CE, Higgins R, Cunningham C, Morley J, Mehrkar A, Hart L, Davy S, Evans D, Hickman G, Inglesby P, Morton CE, Smith RM, Ward T, O'Dwyer T, Maude S, Bridges L, Butler-Cole BFC, Stables CL, Stokes P, Bates C, Cockburn J, Hester F, Parry J, Bhaskaran K, Schultze A, Rentsch CT, Mathur R, Tomlinson LA, Williamson EJ, Smeeth L, Walker A, Bacon S, MacKenna B, Goldacre B.",,Pharmacoepidemiology and drug safety,2024,2024-06-01,Y,Reproducibility; Electronic Health Records; Open Science; Research Platform; Opensafely,,,"Electronic health records (EHRs) and other administrative health data are increasingly used in research to generate evidence on the effectiveness, safety, and utilisation of medical products and services, and to inform public health guidance and policy. Reproducibility is a fundamental step for research credibility and promotes trust in evidence generated from EHRs. At present, ensuring research using EHRs is reproducible can be challenging for researchers. Research software platforms can provide technical solutions to enhance the reproducibility of research conducted using EHRs. In response to the COVID-19 pandemic, we developed the secure, transparent, analytic open-source software platform OpenSAFELY designed with reproducible research in mind. OpenSAFELY mitigates common barriers to reproducible research by: standardising key workflows around data preparation; removing barriers to code-sharing in secure analysis environments; enforcing public sharing of programming code and codelists; ensuring the same computational environment is used everywhere; integrating new and existing tools that encourage and enable the use of reproducible working practices; and providing an audit trail for all code that is run against the real data to increase transparency. This paper describes OpenSAFELY's reproducibility-by-design approach in detail.",,doi:https://doi.org/10.1002/pds.5815; html:https://europepmc.org/articles/PMC7616137; pdf:https://europepmc.org/articles/PMC7616137?pdf=render
 35690576,https://doi.org/10.1016/s2589-7500(22)00091-7,COVID-19 trajectories among 57 million adults in England: a cohort study using electronic health records.,"Thygesen JH, Tomlinson C, Hollings S, Mizani MA, Handy A, Akbari A, Banerjee A, Cooper J, Lai AG, Li K, Mateen BA, Sattar N, Sofat R, Torralbo A, Wu H, Wood A, Sterne JAC, Pagel C, Whiteley WN, Sudlow C, Hemingway H, Denaxas S, Longitudinal Health and Wellbeing COVID-19 National Core Study and the CVD-COVID-UK/COVID-IMPACT Consortium.",,The Lancet. Digital health,2022,2022-06-09,Y,,,,"<h4>Background</h4>Updatable estimates of COVID-19 onset, progression, and trajectories underpin pandemic mitigation efforts. To identify and characterise disease trajectories, we aimed to define and validate ten COVID-19 phenotypes from nationwide linked electronic health records (EHR) using an extensible framework.<h4>Methods</h4>In this cohort study, we used eight linked National Health Service (NHS) datasets for people in England alive on Jan 23, 2020. Data on COVID-19 testing, vaccination, primary and secondary care records, and death registrations were collected until Nov 30, 2021. We defined ten COVID-19 phenotypes reflecting clinically relevant stages of disease severity and encompassing five categories: positive SARS-CoV-2 test, primary care diagnosis, hospital admission, ventilation modality (four phenotypes), and death (three phenotypes). We constructed patient trajectories illustrating transition frequency and duration between phenotypes. Analyses were stratified by pandemic waves and vaccination status.<h4>Findings</h4>Among 57 032 174 individuals included in the cohort, 13 990 423 COVID-19 events were identified in 7 244 925 individuals, equating to an infection rate of 12·7% during the study period. Of 7 244 925 individuals, 460 737 (6·4%) were admitted to hospital and 158 020 (2·2%) died. Of 460 737 individuals who were admitted to hospital, 48 847 (10·6%) were admitted to the intensive care unit (ICU), 69 090 (15·0%) received non-invasive ventilation, and 25 928 (5·6%) received invasive ventilation. Among 384 135 patients who were admitted to hospital but did not require ventilation, mortality was higher in wave 1 (23 485 [30·4%] of 77 202 patients) than wave 2 (44 220 [23·1%] of 191 528 patients), but remained unchanged for patients admitted to the ICU. Mortality was highest among patients who received ventilatory support outside of the ICU in wave 1 (2569 [50·7%] of 5063 patients). 15 486 (9·8%) of 158 020 COVID-19-related deaths occurred within 28 days of the first COVID-19 event without a COVID-19 diagnoses on the death certificate. 10 884 (6·9%) of 158 020 deaths were identified exclusively from mortality data with no previous COVID-19 phenotype recorded. We observed longer patient trajectories in wave 2 than wave 1.<h4>Interpretation</h4>Our analyses illustrate the wide spectrum of disease trajectories as shown by differences in incidence, survival, and clinical pathways. We have provided a modular analytical framework that can be used to monitor the impact of the pandemic and generate evidence of clinical and policy relevance using multiple EHR sources.<h4>Funding</h4>British Heart Foundation Data Science Centre, led by Health Data Research UK.",,pdf:http://www.thelancet.com/article/S2589750022000917/pdf; doi:https://doi.org/10.1016/S2589-7500(22)00091-7; html:https://europepmc.org/articles/PMC9179175; pdf:https://europepmc.org/articles/PMC9179175?pdf=render
 38531661,https://doi.org/10.1111/bcp.16030,The impact of COVID-19 on medication reviews in English primary care. An OpenSAFELY-TPP analysis of 20 million adult electronic health records.,"OpenSAFELY Collaborative, Wood C, Speed V, Fisher L, Curtis HJ, Schaffer AL, Walker AJ, Croker R, Brown AD, Cunningham C, Hulme WJ, Andrews CD, Butler-Cole BFC, Evans D, Inglesby P, Dillingham I, Bacon SCJ, Davy S, Ward T, Hickman G, Bridges L, O'Dwyer T, Maude S, Smith RM, Mehrkar A, Bates C, Cockburn J, Parry J, Hester F, Harper S, Goldacre B, MacKenna B.",,British journal of clinical pharmacology,2024,2024-03-26,Y,General Practice; Prescribing; Primary Care,,,"<h4>Aims</h4>The COVID-19 pandemic caused significant disruption to routine activity in primary care. Medication reviews are an important primary care activity ensuring safety and appropriateness of prescribing. A disruption could have significant negative implications for patient care. Using routinely collected data, our aim was first to describe codes used to record medication review activity and then to report the impact of COVID-19 on the rates of medication reviews.<h4>Methods</h4>With the approval of NHS England, we conducted a cohort study of 20 million adult patient records in general practice, in-situ using the OpenSAFELY platform. For each month, between April 2019 and March 2022, we report the percentage of patients with a medication review coded monthly and in the previous 12 months with breakdowns by regional, clinical and demographic subgroups and those prescribed high-risk medications.<h4>Results</h4>In April 2019, 32.3% of patients had a medication review coded in the previous 12 months. During the first COVID-19 lockdown, monthly activity decreased (-21.1% April 2020), but the 12-month rate was not substantially impacted (-10.5% March 2021). The rate of structured medication review in the last 12 months reached 2.9% by March 2022, with higher percentages in high-risk groups (care home residents 34.1%, age 90+ years 13.1%, high-risk medications 10.2%). The most used medication review code was Medication review done 314530002 (59.5%).<h4>Conclusions</h4>There was a substantial reduction in the monthly rate of medication reviews during the pandemic but rates recovered by the end of the study period. Structured medication reviews were prioritized for high-risk patients.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/bcp.16030; doi:https://doi.org/10.1111/bcp.16030; html:https://europepmc.org/articles/PMC7616229; pdf:https://europepmc.org/articles/PMC7616229?pdf=render
-37243092,https://doi.org/10.3390/vaccines11050988,A Methodological Framework for Assessing the Benefit of SARS-CoV-2 Vaccination following Previous Infection: Case Study of Five- to Eleven-Year-Olds.,"Pagel C, Wilde H, Tomlinson C, Mateen B, Brown K.",,Vaccines,2023,2023-05-16,Y,Health Policy; Mathematical Modelling; Covid-19; Paediatric Vaccines,,,"Vaccination rates against SARS-CoV-2 in children aged five to eleven years remain low in many countries. The current benefit of vaccination in this age group has been questioned given that the large majority of children have now experienced at least one SARS-CoV-2 infection. However, protection from infection, vaccination or both wanes over time. National decisions on offering vaccines to this age group have tended to be made without considering time since infection. There is an urgent need to evaluate the additional benefits of vaccination in previously infected children and under what circumstances those benefits accrue. We present a novel methodological framework for estimating the potential benefits of COVID-19 vaccination in previously infected children aged five to eleven, accounting for waning. We apply this framework to the UK context and for two adverse outcomes: hospitalisation related to SARS-CoV-2 infection and Long Covid. We show that the most important drivers of benefit are: the degree of protection provided by previous infection; the protection provided by vaccination; the time since previous infection; and future attack rates. Vaccination can be very beneficial for previously infected children if future attack rates are high and several months have elapsed since the previous major wave in this group. Benefits are generally larger for Long Covid than hospitalisation, because Long Covid is both more common than hospitalisation and previous infection offers less protection against it. Our framework provides a structure for policy makers to explore the additional benefit of vaccination across a range of adverse outcomes and different parameter assumptions. It can be easily updated as new evidence emerges.",,pdf:https://www.mdpi.com/2076-393X/11/5/988/pdf?version=1684231380; doi:https://doi.org/10.3390/vaccines11050988; html:https://europepmc.org/articles/PMC10220644; pdf:https://europepmc.org/articles/PMC10220644?pdf=render
 36261315,https://doi.org/10.1002/ana.26536,Fewer COVID-19 Neurological Complications with Dexamethasone and Remdesivir.,"Grundmann A, Wu CH, Hardwick M, Baillie JK, Openshaw PJM, Semple MG, Böhning D, Pett S, Michael BD, Thomas RH, Galea I, ISARIC4C investigators.",,Annals of neurology,2023,2022-11-09,Y,,,,"<h4>Objective</h4>The objective of this study was to assess the impact of treatment with dexamethasone, remdesivir or both on neurological complications in acute coronavirus diease 2019 (COVID-19).<h4>Methods</h4>We used observational data from the International Severe Acute and emerging Respiratory Infection Consortium World Health Organization (WHO) Clinical Characterization Protocol, United Kingdom. Hospital inpatients aged ≥18 years with laboratory-confirmed severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection admitted between January 31, 2020, and June 29, 2021, were included. Treatment allocation was non-blinded and performed by reporting clinicians. A propensity scoring methodology was used to minimize confounding. Treatment with remdesivir, dexamethasone, or both was assessed against the standard of care. The primary outcome was a neurological complication occurring at the point of death, discharge, or resolution of the COVID-19 clinical episode.<h4>Results</h4>Out of 89,297 hospital inpatients, 64,088 had severe COVID-19 and 25,209 had non-hypoxic COVID-19. Neurological complications developed in 4.8% and 4.5%, respectively. In both groups, neurological complications were associated with increased mortality, intensive care unit (ICU) admission, worse self-care on discharge, and time to recovery. In patients with severe COVID-19, treatment with dexamethasone (n = 21,129), remdesivir (n = 1,428), and both combined (n = 10,846) were associated with a lower frequency of neurological complications: OR = 0.76 (95% confidence interval [CI] = 0.69-0.83), OR = 0.69 (95% CI = 0.51-0.90), and OR = 0.54 (95% CI = 0.47-0.61), respectively. In patients with non-hypoxic COVID-19, dexamethasone (n = 2,580) was associated with less neurological complications (OR = 0.78, 95% CI = 0.62-0.97), whereas the dexamethasone/remdesivir combination (n = 460) showed a similar trend (OR = 0.63, 95% CI = 0.31-1.15).<h4>Interpretation</h4>Treatment with dexamethasone, remdesivir, or both in patients hospitalized with COVID-19 was associated with a lower frequency of neurological complications in an additive manner, such that the greatest benefit was observed in patients who received both drugs together. ANN NEUROL 2023;93:88-102.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ana.26536; doi:https://doi.org/10.1002/ana.26536; html:https://europepmc.org/articles/PMC9874556; pdf:https://europepmc.org/articles/PMC9874556?pdf=render
+37243092,https://doi.org/10.3390/vaccines11050988,A Methodological Framework for Assessing the Benefit of SARS-CoV-2 Vaccination following Previous Infection: Case Study of Five- to Eleven-Year-Olds.,"Pagel C, Wilde H, Tomlinson C, Mateen B, Brown K.",,Vaccines,2023,2023-05-16,Y,Health Policy; Mathematical Modelling; Covid-19; Paediatric Vaccines,,,"Vaccination rates against SARS-CoV-2 in children aged five to eleven years remain low in many countries. The current benefit of vaccination in this age group has been questioned given that the large majority of children have now experienced at least one SARS-CoV-2 infection. However, protection from infection, vaccination or both wanes over time. National decisions on offering vaccines to this age group have tended to be made without considering time since infection. There is an urgent need to evaluate the additional benefits of vaccination in previously infected children and under what circumstances those benefits accrue. We present a novel methodological framework for estimating the potential benefits of COVID-19 vaccination in previously infected children aged five to eleven, accounting for waning. We apply this framework to the UK context and for two adverse outcomes: hospitalisation related to SARS-CoV-2 infection and Long Covid. We show that the most important drivers of benefit are: the degree of protection provided by previous infection; the protection provided by vaccination; the time since previous infection; and future attack rates. Vaccination can be very beneficial for previously infected children if future attack rates are high and several months have elapsed since the previous major wave in this group. Benefits are generally larger for Long Covid than hospitalisation, because Long Covid is both more common than hospitalisation and previous infection offers less protection against it. Our framework provides a structure for policy makers to explore the additional benefit of vaccination across a range of adverse outcomes and different parameter assumptions. It can be easily updated as new evidence emerges.",,pdf:https://www.mdpi.com/2076-393X/11/5/988/pdf?version=1684231380; doi:https://doi.org/10.3390/vaccines11050988; html:https://europepmc.org/articles/PMC10220644; pdf:https://europepmc.org/articles/PMC10220644?pdf=render
 37407076,https://doi.org/10.1136/bmj-2022-073639,Hospital admissions linked to SARS-CoV-2 infection in children and adolescents: cohort study of 3.2 million first ascertained infections in England.,"Wilde H, Tomlinson C, Mateen BA, Selby D, Kanthimathinathan HK, Ramnarayan P, Du Pre P, Johnson M, Pathan N, Pathan N, Gonzalez-Izquierdo A, Lai AG, Gurdasani D, Pagel C, Denaxas S, Vollmer S, Brown K, CVD-COVID-UK/COVID-IMPACT consortium.",,BMJ (Clinical research ed.),2023,2023-07-05,Y,,,,"<h4>Objective</h4>To describe hospital admissions associated with SARS-CoV-2 infection in children and adolescents.<h4>Design</h4>Cohort study of 3.2 million first ascertained SARS-CoV-2 infections using electronic health care record data.<h4>Setting</h4>England, July 2020 to February 2022.<h4>Participants</h4>About 12 million children and adolescents (age <18 years) who were resident in England.<h4>Main outcome measures</h4>Ascertainment of a first SARS-CoV-2 associated hospital admissions: due to SARS-CoV-2, with SARS-CoV-2 as a contributory factor, incidental to SARS-CoV-2 infection, and hospital acquired SARS-CoV-2.<h4>Results</h4>3 226 535 children and adolescents had a recorded first SARS-CoV-2 infection during the observation period, and 29 230 (0.9%) infections involved a SARS-CoV-2 associated hospital admission. The median length of stay was 2 (interquartile range 1-4) days) and 1710 of 29 230 (5.9%) SARS-CoV-2 associated admissions involved paediatric critical care. 70 deaths occurred in which covid-19 or paediatric inflammatory multisystem syndrome was listed as a cause, of which 55 (78.6%) were in participants with a SARS-CoV-2 associated hospital admission. SARS-CoV-2 was the cause or a contributory factor in 21 000 of 29 230 (71.8%) participants who were admitted to hospital and only 380 (1.3%) participants acquired infection as an inpatient and 7855 (26.9%) participants were admitted with incidental SARS-CoV-2 infection. Boys, younger children (<5 years), and those from ethnic minority groups or areas of high deprivation were more likely to be admitted to hospital (all P<0.001). The covid-19 vaccination programme in England has identified certain conditions as representing a higher risk of admission to hospital with SARS-CoV-2: 11 085 (37.9%) of participants admitted to hospital had evidence of such a condition, and a further 4765 (16.3%) of participants admitted to hospital had a medical or developmental health condition not included in the vaccination programme's list.<h4>Conclusions</h4>Most SARS-CoV-2 associated hospital admissions in children and adolescents in England were due to SARS-CoV-2 or SARS-CoV-2 was a contributory factor. These results should inform future public health initiatives and research.",,pdf:https://www.bmj.com/content/bmj/382/bmj-2022-073639.full.pdf; doi:https://doi.org/10.1136/bmj-2022-073639; html:https://europepmc.org/articles/PMC10318942; pdf:https://europepmc.org/articles/PMC10318942?pdf=render
 36469089,https://doi.org/10.1093/ageing/afac250,"The impact of dementia, frailty and care home characteristics on SARS-CoV-2 incidence in a national cohort of Welsh care home residents during a period of high community prevalence.","Emmerson C, Hollinghurst J, North L, Fry R, Akbari A, Humphreys C, Gravenor MB, Lyons RA.",,Age and ageing,2022,2022-12-01,Y,Frailty; Dementia; Older People; Care Homes; Covid-19; Sars-cov-2,,,"<h4>Background</h4>dementia may increase care home residents' risk of COVID-19, but there is a lack of evidence on this effect and on interactions with individual and care home-level factors.<h4>Methods</h4>we created a national cross-sectional retrospective cohort of care home residents in Wales for 1 September to 31 December 2020. Risk factors were analysed using multi-level logistic regression to model the likelihood of SARS-CoV-2 infection and mortality.<h4>Results</h4>the cohort included 9,571 individuals in 673 homes. Dementia was diagnosed in 5,647 individuals (59%); 1,488 (15.5%) individuals tested positive for SARS-CoV-2. We estimated the effects of age, dementia, frailty, care home size, proportion of residents with dementia, nursing and dementia services, communal space and region. The final model included the proportion of residents with dementia (OR for positive test 4.54 (95% CIs 1.55-13.27) where 75% of residents had dementia compared to no residents with dementia) and frailty (OR 1.29 (95% CIs 1.05-1.59) for severe frailty compared with no frailty). Analysis suggested 76% of the variation was due to setting rather than individual factors. Additional analysis suggested severe frailty and proportion of residents with dementia was associated with all-cause mortality, as was dementia diagnosis. Mortality analyses were challenging to interpret.<h4>Discussion</h4>whilst individual frailty increased the risk of COVID-19 infection, dementia was a risk factor at care home but not individual level. These findings suggest whole-setting interventions, particularly in homes with high proportions of residents with dementia and including those with low/no individual risk factors may reduce the impact of COVID-19.",,doi:https://doi.org/10.1093/ageing/afac250; doi:https://doi.org/10.1093/ageing/afac250; html:https://europepmc.org/articles/PMC9721242; pdf:https://europepmc.org/articles/PMC9721242?pdf=render
 35715992,https://doi.org/10.1002/cam4.4941,Associating transcriptomics data with inflammatory markers to understand tumour microenvironment in hepatocellular carcinoma.,"Bahcivanci B, Shafiha R, Gkoutos GV, Acharjee A.",,Cancer medicine,2023,2022-06-18,Y,Hepatocellular carcinoma; Tumor Microenvironment; Gene Signature; Immune Deconvolution,,,"<h4>Background</h4>Liver cancer is the fourth leading cause of cancer-related death globally which is estimated to reach more than 1 million deaths a year by 2030. Among liver cancer types, hepatocellular carcinoma (HCC) accounts for approximately 90% of the cases and is known to have a tumour promoting inflammation regardless of its underlying aetiology. However, current promising treatment approaches, such as immunotherapy, are partially effective for most of the patients due to the immunosuppressive nature of the tumour microenvironment (TME). Therefore, there is an urgent need to fully understand TME in HCC and discover new immune markers to eliminate resistance to immunotherapy.<h4>Methods</h4>We analyse three microarray datasets, using unsupervised and supervised methods, in an effort to discover signature genes. First, univariate, and multivariate, feature selection methods, such as the Boruta algorithm, are applied. Subsequently, an optimisation procedure, which utilises random forest algorithm with three dataset pairs combinations, is performed. The resulting optimal gene sets are then combined and further subjected to network analysis and pathway enrichment analysis so as to obtain information related to their biological relevance. The microarray datasets were analysed via the MCP-counter, CIBERSORT, TIMER, EPIC, and quanTIseq deconvolution methods and an estimation of cell type abundances for each dataset sample were identified. The differences in the cell type abundances, between the adjacent and tumour sample groups, were then assessed using a Wilcoxon Rank Sum test (p-value < 0.05).<h4>Results</h4>The optimal gene signature sets, derived from each of the data pairs combination, achieved AUC values ranging from 0.959 to 0.988 in external validation sets using Random Forest model. CLEC1B and PTTG1 genes are retrieved across each optimal set. Among the signature genes, PTTG1, AURKA, and UBE2C genes are found to be involved in the regulation of mitotic sister chromatid separation and anaphase-promoting complex (APC) dependent catabolic process (adjusted p-value < 0.001). Additionally, the application of deconvolution algorithms revealed significant changes in cell type abundances of Regulatory T (Treg) cells, M0 and M1 macrophages, and T CD8<sup>+</sup> cells between adjacent and tumour samples.<h4>Conclusion</h4>We identified ECM1 gene as a potential immune-related marker acting through immune cell migration and macrophage polarisation. Our results indicate that macrophages, such as M0 macrophage and M1 macrophage cells, undergo significant changes in HCC TME. Moreover, our immune deconvolution approach revealed significant infiltration of Treg cells and M0 macrophages, and a significant decrease in T CD8<sup>+</sup> cells and M1 macrophages in tumour samples.",,pdf:http://pure-oai.bham.ac.uk/ws/files/172896799/Cancer_Medicine_2022_Bahcivanci_Associating_transcriptomics_data_with_inflammatory_markers_to_understand_tumour.pdf; doi:https://doi.org/10.1002/cam4.4941; html:https://europepmc.org/articles/PMC9844659; pdf:https://europepmc.org/articles/PMC9844659?pdf=render
@@ -57,27 +57,27 @@ PMC10809876,https://doi.org/,Analysis of translesion polymerases in colorectal c
 35724769,https://doi.org/10.1016/j.kint.2022.05.015,A retrospective cohort study predicting and validating impact of the COVID-19 pandemic in individuals with chronic kidney disease.,"Dashtban A, Mizani MA, Denaxas S, Nitsch D, Quint J, Corbett R, Mamza JB, Morris T, Mamas M, Lawlor DA, Khunti K, CVD-COVID-UK Consortium, Sudlow C, Hemingway H, Banerjee A.",,Kidney international,2022,2022-06-17,Y,Mortality; Chronic Kidney Disease; Sars-cov-2,,,"Chronic kidney disease (CKD) is associated with increased risk of baseline mortality and severe COVID-19, but analyses across CKD stages, and comorbidities are lacking. In prevalent and incident CKD, we investigated comorbidities, baseline risk, COVID-19 incidence, and predicted versus observed one-year excess death. In a national dataset (NHS Digital Trusted Research Environment [NHSD TRE]) for England encompassing 56 million individuals), we conducted a retrospective cohort study (March 2020 to March 2021) for prevalence of comorbidities by incident and prevalent CKD, SARS-CoV-2 infection and mortality. Baseline mortality risk, incidence and outcome of infection by comorbidities, controlling for age, sex and vaccination were assessed. Observed versus predicted one-year mortality at varying population infection rates and pandemic-related relative risks using our published model in pre-pandemic CKD cohorts (NHSD TRE and Clinical Practice Research Datalink [CPRD]) were compared. Among individuals with CKD (prevalent:1,934,585, incident:144,969), comorbidities were common (73.5% and 71.2% with one or more condition[s] in respective data sets, and 13.2% and 11.2% with three or more conditions, in prevalent and incident CKD), and associated with SARS-CoV-2 infection, particularly dialysis/transplantation (odds ratio 2.08, 95% confidence interval 2.04-2.13) and heart failure (1.73, 1.71-1.76), but not cancer (1.01, 1.01-1.04). One-year all-cause mortality varied by age, sex, multi-morbidity and CKD stage. Compared with 34,265 observed excess deaths, in the NHSD-TRE and CPRD databases respectively, we predicted 28,746 and 24,546 deaths (infection rates 10% and relative risks 3.0), and 23,754 and 20,283 deaths (observed infection rates 6.7% and relative risks 3.7). Thus, in this largest, national-level study, individuals with CKD have a high burden of comorbidities and multi-morbidity, and high risk of pre-pandemic and pandemic mortality. Hence, treatment of comorbidities, non-pharmaceutical measures, and vaccination are priorities for people with CKD and management of long-term conditions is important during and beyond the pandemic.",,doi:https://doi.org/10.1016/j.kint.2022.05.015; doi:https://doi.org/10.1016/j.kint.2022.05.015; html:https://europepmc.org/articles/PMC9212366; pdf:https://europepmc.org/articles/PMC9212366?pdf=render
 38589944,https://doi.org/10.1111/bcp.16062,"OpenSAFELY: The impact of COVID-19 on azathioprine, leflunomide and methotrexate monitoring, and factors associated with change in monitoring rate.","Brown AD, Fisher L, Curtis HJ, Wiedemann M, Hulme WJ, Speed V, Hopcroft LEM, Cunningham C, Costello RE, Galloway JB, Russell MD, Bechman K, Kurt Z, Croker R, Wood C, Walker AJ, Schaffer AL, Bacon SCJ, Mehrkar A, Hickman G, Bates C, Cockburn J, Parry J, Hester F, Harper S, Goldacre B, OpenSAFELY Collaborative, MacKenna B.",,British journal of clinical pharmacology,2024,2024-04-08,Y,Methotrexate; General Practice; Azathioprine; Leflunomide; Electronic Health Records; Antirheumatic Agents; Covid‐19,,,"<h4>Aims</h4>The COVID-19 pandemic created unprecedented pressure on healthcare services. This study investigates whether disease-modifying antirheumatic drug (DMARD) safety monitoring was affected during the COVID-19 pandemic.<h4>Methods</h4>A population-based cohort study was conducted using the OpenSAFELY platform to access electronic health record data from 24.2 million patients registered at general practices using TPP's SystmOne software. Patients were included for further analysis if prescribed azathioprine, leflunomide or methotrexate between November 2019 and July 2022. Outcomes were assessed as monthly trends and variation between various sociodemographic and clinical groups for adherence with standard safety monitoring recommendations.<h4>Results</h4>An acute increase in the rate of missed monitoring occurred across the study population (+12.4 percentage points) when lockdown measures were implemented in March 2020. This increase was more pronounced for some patient groups (70-79 year-olds: +13.7 percentage points; females: +12.8 percentage points), regions (North West: +17.0 percentage points), medications (leflunomide: +20.7 percentage points) and monitoring tests (blood pressure: +24.5 percentage points). Missed monitoring rates decreased substantially for all groups by July 2022. Consistent differences were observed in overall missed monitoring rates between several groups throughout the study.<h4>Conclusion</h4>DMARD monitoring rates temporarily deteriorated during the COVID-19 pandemic. Deterioration coincided with the onset of lockdown measures, with monitoring rates recovering rapidly as lockdown measures were eased. Differences observed in monitoring rates between medications, tests, regions and patient groups highlight opportunities to tackle potential inequalities in the provision or uptake of monitoring services. Further research should evaluate the causes of the differences identified between groups.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/bcp.16062; doi:https://doi.org/10.1111/bcp.16062; html:https://europepmc.org/articles/PMC7616619; pdf:https://europepmc.org/articles/PMC7616619?pdf=render
 34301672,https://doi.org/10.1136/bmjopen-2021-053402,Sociodemographic inequality in COVID-19 vaccination coverage among elderly adults in England: a national linked data study.,"Nafilyan V, Dolby T, Razieh C, Gaughan CH, Morgan J, Ayoubkhani D, Walker S, Khunti K, Glickman M, Yates T.",,BMJ open,2021,2021-07-23,Y,Infection control; epidemiology; Covid-19,,,"<h4>Objective</h4>To examine inequalities in COVID-19 vaccination rates among elderly adults in England.<h4>Design</h4>Cohort study.<h4>Setting</h4>People living in private households and communal establishments in England.<h4>Participants</h4>6 655 672 adults aged ≥70 years (mean 78.8 years, 55.2% women) who were alive on 15 March 2021.<h4>Main outcome measures</h4>Having received the first dose of a vaccine against COVID-19 by 15 March 2021. We calculated vaccination rates and estimated unadjusted and adjusted ORs using logistic regression models.<h4>Results</h4>By 15 March 2021, 93.2% of people living in England aged 70 years and over had received at least one dose of a COVID-19 vaccine. While vaccination rates differed across all factors considered apart from sex, the greatest disparities were seen between ethnic and religious groups. The lowest rates were in people of black African and black Caribbean ethnic backgrounds, where only 67.2% and 73.8% had received a vaccine, with adjusted odds of not being vaccinated at 5.01 (95% CI 4.86 to 5.16) and 4.85 (4.75 to 4.96) times greater than the white British group. The proportion of individuals self-identifying as Muslim and Buddhist who had received a vaccine was 79.1% and 84.1%, respectively. Older age, greater area deprivation, less advantaged socioeconomic position (proxied by living in a rented home), being disabled and living either alone or in a multigenerational household were also associated with higher odds of not having received the vaccine.<h4>Conclusion</h4>Research is now urgently needed to understand why disparities exist in these groups and how they can best be addressed through public health policy and community engagement.",,doi:https://doi.org/10.1136/bmjopen-2021-053402; doi:https://doi.org/10.1136/bmjopen-2021-053402; html:https://europepmc.org/articles/PMC8313303; pdf:https://europepmc.org/articles/PMC8313303?pdf=render
-37587102,https://doi.org/10.1038/s41467-023-40643-w,"SARS-CoV-2 rapid antibody test results and subsequent risk of hospitalisation and death in 361,801 people.","Whitaker M, Davies B, Atchison C, Barclay W, Ashby D, Darzi A, Riley S, Cooke G, Donnelly CA, Chadeau-Hyam M, Elliott P, Ward H.",,Nature communications,2023,2023-08-16,Y,,,,"The value of SARS-CoV-2 lateral flow immunoassay (LFIA) tests for estimating individual disease risk is unclear. The REACT-2 study in England, UK, obtained self-administered SARS-CoV-2 LFIA test results from 361,801 adults in January-May 2021. Here, we link to routine data on subsequent hospitalisation (to September 2021), and death (to December 2021). Among those who had received one or more vaccines, a negative LFIA is associated with increased risk of hospitalisation with COVID-19 (HR: 2.73 [95% confidence interval: 1.15,6.48]), death (all-cause) (HR: 1.59, 95% CI:1.07, 2.37), and death with COVID-19 as underlying cause (20.6 [1.83,232]). For people designated at high risk from COVID-19, who had received one or more vaccines, there is an additional risk of all-cause mortality of 1.9 per 1000 for those testing antibody negative compared to positive. However, the LFIA does not provide substantial predictive information over and above that which is available from detailed sociodemographic and health-related variables. Nonetheless, this simple test provides a marker which could be a valuable addition to understanding population and individual-level risk.",,doi:https://doi.org/10.1038/s41467-023-40643-w; html:https://europepmc.org/articles/PMC10432566; pdf:https://europepmc.org/articles/PMC10432566?pdf=render
+35038629,https://doi.org/10.1016/j.puhe.2021.12.010,Investigating the association between COVID-19 vaccination and care home outbreak frequency and duration.,"Bradley DT, Murphy S, McWilliams P, Arnold S, Lavery S, Murphy J, de Lusignan S, Hobbs R, Tsang RSM, Akbari A, Torabi F, Beggs J, Chuter A, Shi T, Vasileiou E, Robertson C, Sheikh A, Reid H, O'Reilly D.",,Public health,2022,2021-12-18,Y,Vaccination; outbreak; Care Homes; Covid-19; Sars-cov-2,,,"<h4>Objectives</h4>At the end of 2020, many countries commenced a vaccination programme against SARS-CoV-2. Public health authorities aim to prevent and interrupt outbreaks of infectious disease in social care settings. We aimed to investigate the association between the introduction of the vaccination programme and the frequency and duration of COVID-19 outbreaks in Northern Ireland (NI).<h4>Study design</h4>We undertook an ecological study using routinely available national data.<h4>Methods</h4>We used Poisson regression to measure the relationship between the number of RT-PCR confirmed COVID-19 outbreaks in care homes, and as a measure of community COVID-19 prevalence, the Office for National Statistics COVID-19 Infection Survey estimated the number of people testing positive for COVID-19 in NI. We estimated the change in this relationship and estimated the expected number of care home outbreaks in the absence of the vaccination programme. A Cox proportional hazards model estimated the hazard ratio of a confirmed COVID-19 care home outbreak closure.<h4>Results</h4>Care home outbreaks reduced by two-thirds compared to expected following the introduction of the vaccination programme, from a projected 1625 COVID-19 outbreaks (95% prediction interval 1553-1694) between 7 December 2020 and 28 October 2021 to an observed 501. We estimated an adjusted hazard ratio of 2.53 of the outbreak closure assuming a 21-day lag for immunity.<h4>Conclusions</h4>These findings describe the association of the vaccination with a reduction in outbreak frequency and duration across NI care homes. This indicates probable reduced harm and disruption from COVID-19 in social care settings following vaccination. Future research using individual level data from care home residents will be needed to investigate the effectiveness of the vaccines and the duration of their effects.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa59048/Download/59048__22075__e4bbc8a7cad6434abac5984eb2422e06.pdf; doi:https://doi.org/10.1016/j.puhe.2021.12.010; html:https://europepmc.org/articles/PMC8683272; pdf:https://europepmc.org/articles/PMC8683272?pdf=render
 36647111,https://doi.org/10.1186/s12911-022-02093-0,"Harmonising electronic health records for reproducible research: challenges, solutions and recommendations from a UK-wide COVID-19 research collaboration.","Abbasizanjani H, Torabi F, Bedston S, Bolton T, Davies G, Denaxas S, Griffiths R, Herbert L, Hollings S, Keene S, Khunti K, Lowthian E, Lyons J, Mizani MA, Nolan J, Sudlow C, Walker V, Whiteley W, Wood A, Akbari A, CVD-COVID-UK/COVID-IMPACT Consortium.",,BMC medical informatics and decision making,2023,2023-01-16,Y,Population Health; Electronic Health Record; Reproducible Research; Common Data Model; Data Harmonisation; Sail Databank; Covid-19; Nhs Digital Tre For England; Trusted Research Environments,,,"<h4>Background</h4>The CVD-COVID-UK consortium was formed to understand the relationship between COVID-19 and cardiovascular diseases through analyses of harmonised electronic health records (EHRs) across the four UK nations. Beyond COVID-19, data harmonisation and common approaches enable analysis within and across independent Trusted Research Environments. Here we describe the reproducible harmonisation method developed using large-scale EHRs in Wales to accommodate the fast and efficient implementation of cross-nation analysis in England and Wales as part of the CVD-COVID-UK programme. We characterise current challenges and share lessons learnt.<h4>Methods</h4>Serving the scope and scalability of multiple study protocols, we used linked, anonymised individual-level EHR, demographic and administrative data held within the SAIL Databank for the population of Wales. The harmonisation method was implemented as a four-layer reproducible process, starting from raw data in the first layer. Then each of the layers two to four is framed by, but not limited to, the characterised challenges and lessons learnt. We achieved curated data as part of our second layer, followed by extracting phenotyped data in the third layer. We captured any project-specific requirements in the fourth layer.<h4>Results</h4>Using the implemented four-layer harmonisation method, we retrieved approximately 100 health-related variables for the 3.2 million individuals in Wales, which are harmonised with corresponding variables for > 56 million individuals in England. We processed 13 data sources into the first layer of our harmonisation method: five of these are updated daily or weekly, and the rest at various frequencies providing sufficient data flow updates for frequent capturing of up-to-date demographic, administrative and clinical information.<h4>Conclusions</h4>We implemented an efficient, transparent, scalable, and reproducible harmonisation method that enables multi-nation collaborative research. With a current focus on COVID-19 and its relationship with cardiovascular outcomes, the harmonised data has supported a wide range of research activities across the UK.",,pdf:https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-022-02093-0; doi:https://doi.org/10.1186/s12911-022-02093-0; html:https://europepmc.org/articles/PMC9842203; pdf:https://europepmc.org/articles/PMC9842203?pdf=render
+37587102,https://doi.org/10.1038/s41467-023-40643-w,"SARS-CoV-2 rapid antibody test results and subsequent risk of hospitalisation and death in 361,801 people.","Whitaker M, Davies B, Atchison C, Barclay W, Ashby D, Darzi A, Riley S, Cooke G, Donnelly CA, Chadeau-Hyam M, Elliott P, Ward H.",,Nature communications,2023,2023-08-16,Y,,,,"The value of SARS-CoV-2 lateral flow immunoassay (LFIA) tests for estimating individual disease risk is unclear. The REACT-2 study in England, UK, obtained self-administered SARS-CoV-2 LFIA test results from 361,801 adults in January-May 2021. Here, we link to routine data on subsequent hospitalisation (to September 2021), and death (to December 2021). Among those who had received one or more vaccines, a negative LFIA is associated with increased risk of hospitalisation with COVID-19 (HR: 2.73 [95% confidence interval: 1.15,6.48]), death (all-cause) (HR: 1.59, 95% CI:1.07, 2.37), and death with COVID-19 as underlying cause (20.6 [1.83,232]). For people designated at high risk from COVID-19, who had received one or more vaccines, there is an additional risk of all-cause mortality of 1.9 per 1000 for those testing antibody negative compared to positive. However, the LFIA does not provide substantial predictive information over and above that which is available from detailed sociodemographic and health-related variables. Nonetheless, this simple test provides a marker which could be a valuable addition to understanding population and individual-level risk.",,doi:https://doi.org/10.1038/s41467-023-40643-w; html:https://europepmc.org/articles/PMC10432566; pdf:https://europepmc.org/articles/PMC10432566?pdf=render
 38491011,https://doi.org/10.1038/s41467-024-46451-0,"Uptake of COVID-19 vaccinations amongst 3,433,483 children and young people: meta-analysis of UK prospective cohorts.","Aldridge SJ, Agrawal U, Murphy S, Millington T, Akbari A, Almaghrabi F, Anand SN, Bedston S, Goudie R, Griffiths R, Joy M, Lowthian E, de Lusignan S, Patterson L, Robertson C, Rudan I, Bradley DT, Lyons RA, Sheikh A, Owen RK.",,Nature communications,2024,2024-03-15,Y,,,,"SARS-CoV-2 infection in children and young people (CYP) can lead to life-threatening COVID-19, transmission within households and schools, and the development of long COVID. Using linked health and administrative data, we investigated vaccine uptake among 3,433,483 CYP aged 5-17 years across all UK nations between 4th August 2021 and 31st May 2022. We constructed national cohorts and undertook multi-state modelling and meta-analysis to identify associations between demographic variables and vaccine uptake. We found that uptake of the first COVID-19 vaccine among CYP was low across all four nations compared to other age groups and diminished with subsequent doses. Age and vaccination status of adults living in the same household were identified as important risk factors associated with vaccine uptake in CYP. For example, 5-11 year-olds were less likely to receive their first vaccine compared to 16-17 year-olds (adjusted Hazard Ratio [aHR]: 0.10 (95%CI: 0.06-0.19)), and CYP in unvaccinated households were less likely to receive their first vaccine compared to CYP in partially vaccinated households (aHR: 0.19, 95%CI 0.13-0.29).",,doi:https://doi.org/10.1038/s41467-024-46451-0; html:https://europepmc.org/articles/PMC10943015; pdf:https://europepmc.org/articles/PMC10943015?pdf=render
-35038629,https://doi.org/10.1016/j.puhe.2021.12.010,Investigating the association between COVID-19 vaccination and care home outbreak frequency and duration.,"Bradley DT, Murphy S, McWilliams P, Arnold S, Lavery S, Murphy J, de Lusignan S, Hobbs R, Tsang RSM, Akbari A, Torabi F, Beggs J, Chuter A, Shi T, Vasileiou E, Robertson C, Sheikh A, Reid H, O'Reilly D.",,Public health,2022,2021-12-18,Y,Vaccination; outbreak; Care Homes; Covid-19; Sars-cov-2,,,"<h4>Objectives</h4>At the end of 2020, many countries commenced a vaccination programme against SARS-CoV-2. Public health authorities aim to prevent and interrupt outbreaks of infectious disease in social care settings. We aimed to investigate the association between the introduction of the vaccination programme and the frequency and duration of COVID-19 outbreaks in Northern Ireland (NI).<h4>Study design</h4>We undertook an ecological study using routinely available national data.<h4>Methods</h4>We used Poisson regression to measure the relationship between the number of RT-PCR confirmed COVID-19 outbreaks in care homes, and as a measure of community COVID-19 prevalence, the Office for National Statistics COVID-19 Infection Survey estimated the number of people testing positive for COVID-19 in NI. We estimated the change in this relationship and estimated the expected number of care home outbreaks in the absence of the vaccination programme. A Cox proportional hazards model estimated the hazard ratio of a confirmed COVID-19 care home outbreak closure.<h4>Results</h4>Care home outbreaks reduced by two-thirds compared to expected following the introduction of the vaccination programme, from a projected 1625 COVID-19 outbreaks (95% prediction interval 1553-1694) between 7 December 2020 and 28 October 2021 to an observed 501. We estimated an adjusted hazard ratio of 2.53 of the outbreak closure assuming a 21-day lag for immunity.<h4>Conclusions</h4>These findings describe the association of the vaccination with a reduction in outbreak frequency and duration across NI care homes. This indicates probable reduced harm and disruption from COVID-19 in social care settings following vaccination. Future research using individual level data from care home residents will be needed to investigate the effectiveness of the vaccines and the duration of their effects.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa59048/Download/59048__22075__e4bbc8a7cad6434abac5984eb2422e06.pdf; doi:https://doi.org/10.1016/j.puhe.2021.12.010; html:https://europepmc.org/articles/PMC8683272; pdf:https://europepmc.org/articles/PMC8683272?pdf=render
 PMC10929454,https://doi.org/,Optimising data curation pipelines for population-level analytics in secure data environments: Findings from a phenome-wide analysis in the NHS England Secure Data Environment,"Al Arab M, Welshman Z, Allara E, Nolan J, Denholm R.",,International journal of population data science,,2024-03-15,Y,,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10929454/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10929454/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC10929454; pdf:https://europepmc.org/articles/PMC10929454?pdf=render
 38799298,https://doi.org/10.1186/s41231-023-00153-9,Translational research and key aspects to make it successful.,Acharjee A.,,Translational medicine communications,2023,2023-09-18,Y,Communication; Leadership; Translational Research; Project Management,,,,,doi:https://doi.org/10.1186/s41231-023-00153-9; html:https://europepmc.org/articles/PMC11116195; pdf:https://europepmc.org/articles/PMC11116195?pdf=render
 34600327,https://doi.org/10.1016/j.compbiomed.2021.104904,Multi-faceted semantic clustering with text-derived phenotypes.,"Slater K, Williams JA, Karwath A, Fanning H, Ball S, Schofield PN, Hoehndorf R, Gkoutos GV.",,Computers in biology and medicine,2021,2021-09-27,Y,Clustering; Ontology; Semantic Similarity; Mimic-iii; Cluster Explanation,,,"Identification of ontology concepts in clinical narrative text enables the creation of phenotype profiles that can be associated with clinical entities, such as patients or drugs. Constructing patient phenotype profiles using formal ontologies enables their analysis via semantic similarity, in turn enabling the use of background knowledge in clustering or classification analyses. However, traditional semantic similarity approaches collapse complex relationships between patient phenotypes into a unitary similarity scores for each pair of patients. Moreover, single scores may be based only on matching terms with the greatest information content (IC), ignoring other dimensions of patient similarity. This process necessarily leads to a loss of information in the resulting representation of patient similarity, and is especially apparent when using very large text-derived and highly multi-morbid phenotype profiles. Moreover, it renders finding a biological explanation for similarity very difficult; the black box problem. In this article, we explore the generation of multiple semantic similarity scores for patients based on different facets of their phenotypic manifestation, which we define through different sub-graphs in the Human Phenotype Ontology. We further present a new methodology for deriving sets of qualitative class descriptions for groups of entities described by ontology terms. Leveraging this strategy to obtain meaningful explanations for our semantic clusters alongside other evaluation techniques, we show that semantic clustering with ontology-derived facets enables the representation, and thus identification of, clinically relevant phenotype relationships not easily recoverable using overall clustering alone. In this way, we demonstrate the potential of faceted semantic clustering for gaining a deeper and more nuanced understanding of text-derived patient phenotypes.",,doi:https://doi.org/10.1016/j.compbiomed.2021.104904; doi:https://doi.org/10.1016/j.compbiomed.2021.104904; html:https://europepmc.org/articles/PMC8573608
 34939069,https://doi.org/10.3389/fdgth.2021.781227,Effects of Negation and Uncertainty Stratification on Text-Derived Patient Profile Similarity.,"Slater LT, Karwath A, Hoehndorf R, Gkoutos GV.",,Frontiers in digital health,2021,2021-12-06,Y,Differential diagnosis; Ontology; Negation; Semantic Similarity; Context Disambiguation; Phenotype Profiles,,,"Semantic similarity is a useful approach for comparing patient phenotypes, and holds the potential of an effective method for exploiting text-derived phenotypes for differential diagnosis, text and document classification, and outcome prediction. While approaches for context disambiguation are commonly used in text mining applications, forming a standard component of information extraction pipelines, their effects on semantic similarity calculations have not been widely explored. In this work, we evaluate how inclusion and disclusion of negated and uncertain mentions of concepts from text-derived phenotypes affects similarity of patients, and the use of those profiles to predict diagnosis. We report on the effectiveness of these approaches and report a very small, yet significant, improvement in performance when classifying primary diagnosis over MIMIC-III patient visits.",,pdf:https://www.frontiersin.org/articles/10.3389/fdgth.2021.781227/pdf; doi:https://doi.org/10.3389/fdgth.2021.781227; html:https://europepmc.org/articles/PMC8685209; pdf:https://europepmc.org/articles/PMC8685209?pdf=render
 38846423,https://doi.org/10.1016/j.lanepe.2024.100938,Modifiable risk factors for asthma exacerbations during the COVID-19 pandemic: a population-based repeated cross-sectional study using the Research and Surveillance Centre primary care database.,"Mukherjee M, Okusi C, Jamie G, Byford R, Ferreira F, Agarwal U, Weatherill D, Fletcher M, Quint JK, Romel Bhuia M, de Lusignan S, Sheikh SA.",,The Lancet regional health. Europe,2024,2024-05-24,Y,Cluster analysis; Prevalence; Asthma; risk factors; Exacerbations; Covid-19,,,"<h4>Background</h4>There were substantial reductions in asthma exacerbations during the COVID-19 pandemic for reasons that remain poorly understood. We investigated changes in modifiable risk factors which might help explain the reductions in asthma exacerbations.<h4>Methods</h4>Multilevel generalised linear mixed models were fitted to examine changes in modifiable risk factors for asthma exacerbations during 2020-2022, compared to pre-pandemic year (2019), using observational, routine data from general practices in the Oxford-Royal College of General Practitioners Research and Surveillance Centre. Asthma exacerbations were defined as any of GP recorded: asthma exacerbations, prescriptions of prednisolone, accident and emergency department attendance or hospitalisation for asthma. Modifiable risk factors of interest were ownership of asthma self-management plan, asthma annual review, inhaled-corticosteroid (ICS) prescriptions, influenza vaccinations and respiratory-tract-infections (RTI).<h4>Findings</h4>Compared with 2019 (n = 550,995), in 2020 (n = 565,956) and 2022 (n = 562,167) (p < 0.05): asthma exacerbations declined from 67.1% to 51.9% and 61.1%, the proportion of people who had: asthma exacerbations reduced from 20.4% to 15.1% and 18.5%, asthma self-management plans increased from 28.6% to 37.7% and 55.9%; ICS prescriptions increased from 69.9% to 72.0% and 71.1%; influenza vaccinations increased from 14.2% to 25.4% and 55.3%; current smoking declined from 15.0% to 14.5% and 14.7%; lower-RTI declined from 10.5% to 5.3% and 8.1%; upper-RTI reduced from 10.7% to 5.8% and 7.6%. There was cluster effect of GP practices on asthma exacerbations (p = 0.001). People with asthma were more likely (p < 0.05) to have exacerbations if they had LRTI (seven times(x)), had URTI and ILI (both twice), were current smokers (1.4x), PPV vaccinated (1.3x), seasonal flu vaccinated (1.01x), took ICS (1.3x), had asthma reviews (1.09x). People with asthma were less likely to have exacerbations if they had self-management plan (7%), and were partially (4%) than fully COVID-19 vaccinated.<h4>Interpretation</h4>We have identified changes in modifiable risk factors for asthma exacerbation that need to be maintained in the post-pandemic era.<h4>Funding</h4>Asthma UK Centre for Applied Research and Health Data Research UK.",,doi:https://doi.org/10.1016/j.lanepe.2024.100938; html:https://europepmc.org/articles/PMC11153226; pdf:https://europepmc.org/articles/PMC11153226?pdf=render
-38630417,https://doi.org/10.1007/s44192-024-00066-5,Cerebrospinal fluid metabolomes of treatment-resistant depression subtypes and ketamine response: a pilot study.,"Berner J, Acharjee A.",,Discover mental health,2024,2024-04-17,Y,,,,"Depression is a disorder with variable presentation. Selecting treatments and dose-finding is, therefore, challenging and time-consuming. In addition, novel antidepressants such as ketamine have sparse optimization evidence. Insights obtained from metabolomics may improve the management of patients. The objective of this study was to determine whether compounds in the cerebrospinal fluid (CSF) metabolome correlate with scores on questionnaires and response to medication. We performed a retrospective pilot study to evaluate phenotypic and metabolomic variability in patients with treatment-resistant depression using multivariate data compression algorithms. Twenty-nine patients with treatment-resistant depression provided fasting CSF samples. Over 300 metabolites were analyzed in these samples with liquid chromatography-mass spectrometry. Chart review provided basic demographic information, clinical status with self-reported questionnaires, and response to medication. Of the 300 metabolites analyzed, 151 were present in all CSF samples and used in the analyses. Hypothesis-free multivariate analysis compressed the resultant data set into two dimensions using Principal Component (PC) analysis, accounting for ~ 32% of the variance. PC1 accounted for 16.9% of the variance and strongly correlated with age in one direction and 5-methyltetrahydrofolate, homocarnosine, and depression and anxiety scores in the opposite direction. PC2 accounted for 15.4% of the variance, with one end strongly correlated with autism scores, male gender, and cognitive fatigue scores, and the other end with bipolar diagnosis, lithium use, and ethylmalonate disturbance. This small pilot study suggests that complex treatment-resistant depression can be mapped onto a 2-dimensional pathophysiological domain. The results may have implications for treatment selection for depression subtypes.",,pdf:https://link.springer.com/content/pdf/10.1007/s44192-024-00066-5.pdf; doi:https://doi.org/10.1007/s44192-024-00066-5; html:https://europepmc.org/articles/PMC11024073; pdf:https://europepmc.org/articles/PMC11024073?pdf=render
-37794179,https://doi.org/10.1038/s41416-023-02450-4,A taxonomy of early diagnosis research to guide study design and funding prioritisation.,"Whitfield E, White B, Denaxas S, Barclay ME, Renzi C, Lyratzopoulos G.",,British journal of cancer,2023,2023-10-04,Y,,,,"Researchers and research funders aiming to improve diagnosis seek to identify if, when, where, and how earlier diagnosis is possible. This has led to the propagation of research studies using a wide range of methodologies and data sources to explore diagnostic processes. Many such studies use electronic health record data and focus on cancer diagnosis. Based on this literature, we propose a taxonomy to guide the design and support the synthesis of early diagnosis research, focusing on five key questions: Do healthcare use patterns suggest earlier diagnosis could be possible? How does the diagnostic process begin? How do patients progress from presentation to diagnosis? How long does the diagnostic process take? Could anything have been done differently to reach the correct diagnosis sooner? We define families of diagnostic research study designs addressing each of these questions and appraise their unique or complementary contributions and limitations. We identify three further questions on relationships between the families and their relevance for examining patient group inequalities, supported with examples from the cancer literature. Although exemplified through cancer as a disease model, we recognise the framework is also applicable to non-neoplastic disease. The proposed framework can guide future study design and research funding prioritisation.",,pdf:https://www.nature.com/articles/s41416-023-02450-4.pdf; doi:https://doi.org/10.1038/s41416-023-02450-4; html:https://europepmc.org/articles/PMC10645731; pdf:https://europepmc.org/articles/PMC10645731?pdf=render
 39011273,https://doi.org/10.34133/hds.0159,The Time-Varying Impact of COVID-19 on the Acute Kidney Disorders: A Historical Matched Cohort Study and Mendelian Randomization Analysis.,"Li C, Zhang C, Chen J, Chen Y, Ying Z, Hu Y, Song H, Fu P, Zeng X.",,Health data science,2024,2024-07-15,Y,,,,"<b>Background:</b> This study aimed to explore the time-varying impact of COVID-19 on acute kidney disorders, including acute kidney injury and other acute kidney diseases. <b>Methods:</b> From the UK Biobank, 10,121 participants with COVID-19 were matched with up to 3 historically unexposed controls by age, sex, Townsend deprivation index, and the status of hospitalization or receiving critical care. We investigated the association between COVID-19 and incidence of acute kidney disorders, within the first 4 weeks after infection, using conditional and time-varying Cox proportional hazard regression. In addition, one-sample Mendelian randomization, utilizing the polygenic risk score for COVID-19 as an instrumental variable, was conducted to explore the potential causality of the association. <b>Results:</b> In the matched cohort study, we observed a significant association between COVID-19 and acute kidney disorders predominantly within the first 3 weeks. The impact of COVID-19 was time dependent, peaking in the second week (hazard ratio, 12.77; 95% confidence interval, 5.93 to 27.70) and decreasing by the fourth week (hazard ratio, 2.28; 95% confidence interval, 0.75 to 6.93). In subgroup analyses, only moderate to severe COVID-19 cases were associated with acute worsening of renal function in a time-dependent pattern. One-sample Mendelian randomization analyses further showed that COVID-19 might exert a ""short-term"" causal effect on the risk of acute kidney disorders, primarily confined to the first week after infection. <b>Conclusions:</b> The risk of acute kidney disorders following COVID-19 demonstrates a time-varying pattern. Hazard effects were observed only in patients with moderate or severe but not mild COVID-19.",,doi:https://doi.org/10.34133/hds.0159; doi:https://doi.org/10.34133/hds.0159; html:https://europepmc.org/articles/PMC11246837; pdf:https://europepmc.org/articles/PMC11246837?pdf=render
+37794179,https://doi.org/10.1038/s41416-023-02450-4,A taxonomy of early diagnosis research to guide study design and funding prioritisation.,"Whitfield E, White B, Denaxas S, Barclay ME, Renzi C, Lyratzopoulos G.",,British journal of cancer,2023,2023-10-04,Y,,,,"Researchers and research funders aiming to improve diagnosis seek to identify if, when, where, and how earlier diagnosis is possible. This has led to the propagation of research studies using a wide range of methodologies and data sources to explore diagnostic processes. Many such studies use electronic health record data and focus on cancer diagnosis. Based on this literature, we propose a taxonomy to guide the design and support the synthesis of early diagnosis research, focusing on five key questions: Do healthcare use patterns suggest earlier diagnosis could be possible? How does the diagnostic process begin? How do patients progress from presentation to diagnosis? How long does the diagnostic process take? Could anything have been done differently to reach the correct diagnosis sooner? We define families of diagnostic research study designs addressing each of these questions and appraise their unique or complementary contributions and limitations. We identify three further questions on relationships between the families and their relevance for examining patient group inequalities, supported with examples from the cancer literature. Although exemplified through cancer as a disease model, we recognise the framework is also applicable to non-neoplastic disease. The proposed framework can guide future study design and research funding prioritisation.",,pdf:https://www.nature.com/articles/s41416-023-02450-4.pdf; doi:https://doi.org/10.1038/s41416-023-02450-4; html:https://europepmc.org/articles/PMC10645731; pdf:https://europepmc.org/articles/PMC10645731?pdf=render
+38630417,https://doi.org/10.1007/s44192-024-00066-5,Cerebrospinal fluid metabolomes of treatment-resistant depression subtypes and ketamine response: a pilot study.,"Berner J, Acharjee A.",,Discover mental health,2024,2024-04-17,Y,,,,"Depression is a disorder with variable presentation. Selecting treatments and dose-finding is, therefore, challenging and time-consuming. In addition, novel antidepressants such as ketamine have sparse optimization evidence. Insights obtained from metabolomics may improve the management of patients. The objective of this study was to determine whether compounds in the cerebrospinal fluid (CSF) metabolome correlate with scores on questionnaires and response to medication. We performed a retrospective pilot study to evaluate phenotypic and metabolomic variability in patients with treatment-resistant depression using multivariate data compression algorithms. Twenty-nine patients with treatment-resistant depression provided fasting CSF samples. Over 300 metabolites were analyzed in these samples with liquid chromatography-mass spectrometry. Chart review provided basic demographic information, clinical status with self-reported questionnaires, and response to medication. Of the 300 metabolites analyzed, 151 were present in all CSF samples and used in the analyses. Hypothesis-free multivariate analysis compressed the resultant data set into two dimensions using Principal Component (PC) analysis, accounting for ~ 32% of the variance. PC1 accounted for 16.9% of the variance and strongly correlated with age in one direction and 5-methyltetrahydrofolate, homocarnosine, and depression and anxiety scores in the opposite direction. PC2 accounted for 15.4% of the variance, with one end strongly correlated with autism scores, male gender, and cognitive fatigue scores, and the other end with bipolar diagnosis, lithium use, and ethylmalonate disturbance. This small pilot study suggests that complex treatment-resistant depression can be mapped onto a 2-dimensional pathophysiological domain. The results may have implications for treatment selection for depression subtypes.",,pdf:https://link.springer.com/content/pdf/10.1007/s44192-024-00066-5.pdf; doi:https://doi.org/10.1007/s44192-024-00066-5; html:https://europepmc.org/articles/PMC11024073; pdf:https://europepmc.org/articles/PMC11024073?pdf=render
 37562853,https://doi.org/10.1136/bmjment-2023-300842,Living alone and mental health: parallel analyses in UK longitudinal population surveys and electronic health records prior to and during the COVID-19 pandemic.,"McElroy E, Herrett E, Patel K, Piehlmaier DM, Gessa GD, Huggins C, Green MJ, Kwong ASF, Thompson EJ, Zhu J, Mansfield KE, Silverwood RJ, Mansfield R, Maddock J, Mathur R, Costello RE, Matthews A, Tazare J, Henderson A, Wing K, Bridges L, Bacon S, Mehrkar A, OpenSAFELY Collaborative, Shaw RJ, Wels J, Katikireddi SV, Chaturvedi N, Tomlinson LA, Patalay P, Longitudinal Health and Wellbeing Collaborative.",,BMJ mental health,2023,2023-08-01,Y,Psychiatry; Anxiety Disorders; Covid-19,,,"<h4>Background</h4>People who live alone experience greater levels of mental illness; however, it is unclear whether the COVID-19 pandemic had a disproportionately negative impact on this demographic.<h4>Objective</h4>To describe the mental health gap between those who live alone and with others in the UK prior to and during the COVID-19 pandemic.<h4>Methods</h4>Self-reported psychological distress and life satisfaction in 10 prospective longitudinal population surveys (LPSs) assessed in the nearest pre-pandemic sweep and three periods during the pandemic. Recorded diagnosis of common and severe mental illnesses between March 2018 and January 2022 in electronic healthcare records (EHRs) within the OpenSAFELY-TPP.<h4>Findings</h4>In 37 544 LPS participants, pooled models showed greater psychological distress (standardised mean difference (SMD): 0.09 (95% CI: 0.04; 0.14); relative risk: 1.25 (95% CI: 1.12; 1.39)) and lower life satisfaction (SMD: -0.22 (95% CI: -0.30; -0.15)) for those living alone pre-pandemic. This gap did not change during the pandemic. In the EHR analysis of c.16 million records, mental health conditions were more common in those who lived alone (eg, depression 26 (95% CI: 18 to 33) and severe mental illness 58 (95% CI: 54 to 62) more cases more per 100 000). For common mental health disorders, the gap in recorded cases in EHRs narrowed during the pandemic.<h4>Conclusions</h4>People living alone have poorer mental health and lower life satisfaction. During the pandemic, this gap in self-reported distress remained; however, there was a narrowing of the gap in service use.<h4>Clinical implications</h4>Greater mental health need and potentially greater barriers to mental healthcare access for those who live alone need to be considered in healthcare planning.",,pdf:https://mentalhealth.bmj.com/content/ebmental/26/1/e300842.full.pdf; doi:https://doi.org/10.1136/bmjment-2023-300842; html:https://europepmc.org/articles/PMC10577768; pdf:https://europepmc.org/articles/PMC10577768?pdf=render
 35192597,https://doi.org/10.1371/journal.pmed.1003926,"Association of COVID-19 vaccines ChAdOx1 and BNT162b2 with major venous, arterial, or thrombocytopenic events: A population-based cohort study of 46 million adults in England.","Whiteley WN, Ip S, Cooper JA, Bolton T, Keene S, Walker V, Denholm R, Akbari A, Omigie E, Hollings S, Di Angelantonio E, Denaxas S, Wood A, Sterne JAC, Sudlow C, CVD-COVID-UK consortium.",,PLoS medicine,2022,2022-02-22,Y,,,,"<h4>Background</h4>Thromboses in unusual locations after the Coronavirus Disease 2019 (COVID-19) vaccine ChAdOx1-S have been reported, although their frequency with vaccines of different types is uncertain at a population level. The aim of this study was to estimate the population-level risks of hospitalised thrombocytopenia and major arterial and venous thromboses after COVID-19 vaccination.<h4>Methods and findings</h4>In this whole-population cohort study, we analysed linked electronic health records from adults living in England, from 8 December 2020 to 18 March 2021. We estimated incidence rates and hazard ratios (HRs) for major arterial, venous, and thrombocytopenic outcomes 1 to 28 and >28 days after first vaccination dose for ChAdOx1-S and BNT162b2 vaccines. Analyses were performed separately for ages <70 and ≥70 years and adjusted for age, age2, sex, ethnicity, and deprivation. We also prespecified adjustment for anticoagulant medication, combined oral contraceptive medication, hormone replacement therapy medication, history of pulmonary embolism or deep vein thrombosis, and history of coronavirus infection in analyses of venous thrombosis; and diabetes, hypertension, smoking, antiplatelet medication, blood pressure lowering medication, lipid lowering medication, anticoagulant medication, history of stroke, and history of myocardial infarction in analyses of arterial thromboses. We selected further covariates with backward selection. Of 46 million adults, 23 million (51%) were women; 39 million (84%) were <70; and 3.7 million (8.1%) Asian or Asian British, 1.6 million (3.5%) Black or Black British, 36 million (79%) White, 0.7 million (1.5%) mixed ethnicity, and 1.5 million (3.2%) were of another ethnicity. Approximately 21 million (46%) adults had their first vaccination between 8 December 2020 and 18 March 2021. The crude incidence rates (per 100,000 person-years) of all venous events were as follows: prevaccination, 140 [95% confidence interval (CI): 138 to 142]; ≤28 days post-ChAdOx1-S, 294 (281 to 307); >28 days post-ChAdOx1-S, 359 (338 to 382), ≤28 days post-BNT162b2-S, 241 (229 to 253); >28 days post-BNT162b2-S 277 (263 to 291). The crude incidence rates (per 100,000 person-years) of all arterial events were as follows: prevaccination, 546 (95% CI: 541 to 555); ≤28 days post-ChAdOx1-S, 1,211 (1,185 to 1,237); >28 days post-ChAdOx1-S, 1678 (1,630 to 1,726), ≤28 days post-BNT162b2-S, 1,242 (1,214 to 1,269); >28 days post-BNT162b2-S, 1,539 (1,507 to 1,572). Adjusted HRs (aHRs) 1 to 28 days after ChAdOx1-S, compared with unvaccinated rates, at ages <70 and ≥70 years, respectively, were 0.97 (95% CI: 0.90 to 1.05) and 0.58 (0.53 to 0.63) for venous thromboses, and 0.90 (0.86 to 0.95) and 0.76 (0.73 to 0.79) for arterial thromboses. Corresponding aHRs for BNT162b2 were 0.81 (0.74 to 0.88) and 0.57 (0.53 to 0.62) for venous thromboses, and 0.94 (0.90 to 0.99) and 0.72 (0.70 to 0.75) for arterial thromboses. aHRs for thrombotic events were higher at younger ages for venous thromboses after ChAdOx1-S, and for arterial thromboses after both vaccines. Rates of intracranial venous thrombosis (ICVT) and of thrombocytopenia in adults aged <70 years were higher 1 to 28 days after ChAdOx1-S (aHRs 2.27, 95% CI: 1.33 to 3.88 and 1.71, 1.35 to 2.16, respectively), but not after BNT162b2 (0.59, 0.24 to 1.45 and 1.00, 0.75 to 1.34) compared with unvaccinated. The corresponding absolute excess risks of ICVT 1 to 28 days after ChAdOx1-S were 0.9 to 3 per million, varying by age and sex. The main limitations of the study are as follows: (i) it relies on the accuracy of coded healthcare data to identify exposures, covariates, and outcomes; (ii) the use of primary reason for hospital admission to measure outcome, which improves the positive predictive value but may lead to an underestimation of incidence; and (iii) potential unmeasured confounding.<h4>Conclusions</h4>In this study, we observed increases in rates of ICVT and thrombocytopenia after ChAdOx1-S vaccination in adults aged <70 years that were small compared with its effect in reducing COVID-19 morbidity and mortality, although more precise estimates for adults aged <40 years are needed. For people aged ≥70 years, rates of arterial or venous thrombotic events were generally lower after either vaccine compared with unvaccinated, suggesting that either vaccine is suitable in this age group.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003926&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003926; html:https://europepmc.org/articles/PMC8863280; pdf:https://europepmc.org/articles/PMC8863280?pdf=render
 37328267,https://doi.org/10.1515/dx-2023-0062,Explainable AI for gut microbiome-based diagnostics: colorectal cancer as a case study.,Acharjee A.,,"Diagnosis (Berlin, Germany)",2023,2023-06-19,N,Diagnostics; Microbiome; Interpretable Ai,,,,,pdf:https://www.degruyter.com/document/doi/10.1515/dx-2023-0062/pdf; doi:https://doi.org/10.1515/dx-2023-0062
-38345538,https://doi.org/10.1177/01410768231223584,Risk of winter hospitalisation and death from acute respiratory infections in Scotland: national retrospective cohort study.,"Shi T, Millington T, Robertson C, Jeffrey K, Katikireddi SV, McCowan C, Simpson CR, Woolford L, Daines L, Kerr S, Swallow B, Fagbamigbe A, Vallejos CA, Weatherill D, Jayacodi S, Marsh K, McMenamin J, Rudan I, Ritchie LD, Mueller T, Kurdi A, Sheikh A, Public Health Scotland and the EAVE II Collaborators.",,Journal of the Royal Society of Medicine,2024,2024-02-12,N,epidemiology; Respiratory Medicine; Health Informatics,,,"<h4>Objectives</h4>We undertook a national analysis to characterise and identify risk factors for acute respiratory infections (ARIs) resulting in hospitalisation during the winter period in Scotland.<h4>Design</h4>A population-based retrospective cohort analysis.<h4>Setting</h4>Scotland.<h4>Participants</h4>The study involved 5.4 million residents in Scotland.<h4>Main outcome measures</h4>Cox proportional hazard models were used to estimate adjusted hazard ratios (aHRs) and 95% confidence intervals (CIs) for the association between risk factors and ARI hospitalisation.<h4>Results</h4>Between 1 September 2022 and 31 January 2023, there were 22,284 (10.9% of 203,549 with any emergency hospitalisation) ARI hospitalisations (1759 in children and 20,525 in adults) in Scotland. Compared with the reference group of children aged 6-17 years, the risk of ARI hospitalisation was higher in children aged 3-5 years (aHR = 4.55; 95% CI: 4.11-5.04). Compared with those aged 25-29 years, the risk of ARI hospitalisation was highest among the oldest adults aged ≥80 years (aHR = 7.86; 95% CI: 7.06-8.76). Adults from more deprived areas (most deprived vs. least deprived, aHR = 1.64; 95% CI: 1.57-1.72), with existing health conditions (≥5 vs. 0 health conditions, aHR = 4.84; 95% CI: 4.53-5.18) or with history of all-cause emergency admissions (≥6 vs. 0 previous emergency admissions, aHR = 7.53; 95% CI: 5.48-10.35) were at a higher risk of ARI hospitalisations. The risk increased by the number of existing health conditions and previous emergency admission. Similar associations were seen in children.<h4>Conclusions</h4>Younger children, older adults, those from more deprived backgrounds and individuals with greater numbers of pre-existing conditions and previous emergency admission were at increased risk for winter hospitalisations for ARI.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/01410768231223584; doi:https://doi.org/10.1177/01410768231223584; html:https://europepmc.org/articles/PMC11450722; pdf:https://europepmc.org/articles/PMC11450722?pdf=render; doi:https://doi.org/10.1177/01410768231223584
 38296356,https://doi.org/10.3399/bjgp.2023.0492,Weight trends among adults with diabetes or hypertension during the COVID-19 pandemic: an observational study using OpenSAFELY.,"Samuel M, Park RY, Eastwood SV, Eto F, Morton CE, Stow D, Bacon S, Goldacre B, Mehrkar A, Morley J, Dillingham I, Inglesby P, Hulme WJ, Khunti K, Mathur R, Valabhji J, MacKenna B, Finer S, OpenSAFELY Collaborative.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2024,2024-10-31,Y,Hypertension; Type 2 diabetes mellitus; body mass index; Primary Health Care; Health Inequalities; Covid-19,,,"<h4>Background</h4>COVID-19 pandemic restrictions may have influenced behaviours related to weight.<h4>Aim</h4>To describe patterns of weight change among adults living in England with type 2 diabetes (T2D) and/or hypertension during the pandemic.<h4>Design and setting</h4>An observational cohort study using the routinely collected health data of approximately 40% of adults living in England, accessed through the OpenSAFELY service inside TPP.<h4>Method</h4>Clinical and sociodemographic characteristics associated with rapid weight gain (>0.5 kg/m<sup>2</sup>/year) were investigated using multivariable logistic regression.<h4>Results</h4>Data were extracted on adults with T2D (<i>n</i> = 1 231 455, 43.9% female, and 76.0% White British) or hypertension (<i>n</i> = 3 558 405, 49.7% female, and 84.3% White British). Adults with T2D lost weight overall (median δ = -0.1 kg/m<sup>2</sup>/year [interquartile range {IQR} -0.7-0.4]). However, rapid weight gain was common (20.7%) and associated with the following: sex (male versus female: adjusted odds ratio [aOR] 0.78 [95% confidence interval {CI} = 0.77 to 0.79]); age (older age reduced odds, for example, aged 60-69 years versus 18-29 years: aOR 0.66 [95% CI = 0.61 to 0.71]); deprivation (least deprived Index of Multiple Deprivation [IMD] quintile versus most deprived IMD quintile: aOR 0.87 [95% CI = 0.85 to 0.89]); White ethnicity (Black versus White: aOR 0.95 [95% CI = 0.92 to 0.98]); mental health conditions (for example, depression: aOR 1.13 [95% CI = 1.12 to 1.15]); and diabetes treatment (non-insulin treatment versus no pharmacological treatment: aOR 0.68 [95% CI = 0.67 to 0.69]). Adults with hypertension maintained stable weight overall (median δ = 0.0 kg/m<sup>2</sup>/year [IQR -0.6-0.5]); however, rapid weight gain was common (24.7%) and associated with similar characteristics as in T2D.<h4>Conclusion</h4>Among adults living in England with T2D and/or hypertension, rapid pandemic weight gain was more common among females, younger adults, those living in more deprived areas, and those with mental health conditions.",,pdf:https://bjgp.org/content/bjgp/early/2024/01/26/BJGP.2023.0492.full.pdf; doi:https://doi.org/10.3399/BJGP.2023.0492; html:https://europepmc.org/articles/PMC11466294; pdf:https://europepmc.org/articles/PMC11466294?pdf=render
+38345538,https://doi.org/10.1177/01410768231223584,Risk of winter hospitalisation and death from acute respiratory infections in Scotland: national retrospective cohort study.,"Shi T, Millington T, Robertson C, Jeffrey K, Katikireddi SV, McCowan C, Simpson CR, Woolford L, Daines L, Kerr S, Swallow B, Fagbamigbe A, Vallejos CA, Weatherill D, Jayacodi S, Marsh K, McMenamin J, Rudan I, Ritchie LD, Mueller T, Kurdi A, Sheikh A, Public Health Scotland and the EAVE II Collaborators.",,Journal of the Royal Society of Medicine,2024,2024-02-12,N,epidemiology; Respiratory Medicine; Health Informatics,,,"<h4>Objectives</h4>We undertook a national analysis to characterise and identify risk factors for acute respiratory infections (ARIs) resulting in hospitalisation during the winter period in Scotland.<h4>Design</h4>A population-based retrospective cohort analysis.<h4>Setting</h4>Scotland.<h4>Participants</h4>The study involved 5.4 million residents in Scotland.<h4>Main outcome measures</h4>Cox proportional hazard models were used to estimate adjusted hazard ratios (aHRs) and 95% confidence intervals (CIs) for the association between risk factors and ARI hospitalisation.<h4>Results</h4>Between 1 September 2022 and 31 January 2023, there were 22,284 (10.9% of 203,549 with any emergency hospitalisation) ARI hospitalisations (1759 in children and 20,525 in adults) in Scotland. Compared with the reference group of children aged 6-17 years, the risk of ARI hospitalisation was higher in children aged 3-5 years (aHR = 4.55; 95% CI: 4.11-5.04). Compared with those aged 25-29 years, the risk of ARI hospitalisation was highest among the oldest adults aged ≥80 years (aHR = 7.86; 95% CI: 7.06-8.76). Adults from more deprived areas (most deprived vs. least deprived, aHR = 1.64; 95% CI: 1.57-1.72), with existing health conditions (≥5 vs. 0 health conditions, aHR = 4.84; 95% CI: 4.53-5.18) or with history of all-cause emergency admissions (≥6 vs. 0 previous emergency admissions, aHR = 7.53; 95% CI: 5.48-10.35) were at a higher risk of ARI hospitalisations. The risk increased by the number of existing health conditions and previous emergency admission. Similar associations were seen in children.<h4>Conclusions</h4>Younger children, older adults, those from more deprived backgrounds and individuals with greater numbers of pre-existing conditions and previous emergency admission were at increased risk for winter hospitalisations for ARI.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/01410768231223584; doi:https://doi.org/10.1177/01410768231223584; html:https://europepmc.org/articles/PMC11450722; pdf:https://europepmc.org/articles/PMC11450722?pdf=render; doi:https://doi.org/10.1177/01410768231223584
 36356998,https://doi.org/10.1136/bmjopen-2022-063271,"Studying the Long-term Impact of COVID-19 in Kids (SLICK). Healthcare use and costs in children and young people following community-acquired SARS-CoV-2 infection: protocol for an observational study using linked primary and secondary routinely collected healthcare data from England, Scotland and Wales.","Swann OV, Lone NI, Harrison EM, Tomlinson LA, Walker AJ, Seaborne MJ, Pollock L, Farrell J, Hall PS, Seth S, Williams TC, Preston J, Ainsworth JS, Semple FF, Baillie JK, Katikireddi SV, Akbari A, Lyons R, Simpson CR, Semple MG, Goldacre B, Brophy S, Sheikh A, Docherty AB.",,BMJ open,2022,2022-11-10,Y,epidemiology; Health Economics; Covid-19; Paediatric Infectious Disease &Amp; Immunisation,,,"<h4>Introduction</h4>SARS-CoV-2 infection rarely causes hospitalisation in children and young people (CYP), but mild or asymptomatic infections are common. Persistent symptoms following infection have been reported in CYP but subsequent healthcare use is unclear. We aim to describe healthcare use in CYP following community-acquired SARS-CoV-2 infection and identify those at risk of ongoing healthcare needs.<h4>Methods and analysis</h4>We will use anonymised individual-level, population-scale national data linking demographics, comorbidities, primary and secondary care use and mortality between 1 January 2019 and 1 May 2022. SARS-CoV-2 test data will be linked from 1 January 2020 to 1 May 2022. Analyses will use Trusted Research Environments: OpenSAFELY in England, Secure Anonymised Information Linkage (SAIL) Databank in Wales and Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 in Scotland (EAVE-II). CYP aged ≥4 and &lt;18 years who underwent SARS-CoV-2 reverse transcription PCR (RT-PCR) testing between 1 January 2020 and 1 May 2021 and those untested CYP will be examined.The primary outcome measure is cumulative healthcare cost over 12 months following SARS-CoV-2 testing, stratified into primary or secondary care, and physical or mental healthcare. We will estimate the burden of healthcare use attributable to SARS-CoV-2 infections in the 12 months after testing using a matched cohort study of RT-PCR positive, negative or untested CYP matched on testing date, with adjustment for confounders. We will identify factors associated with higher healthcare needs in the 12 months following SARS-CoV-2 infection using an unmatched cohort of RT-PCR positive CYP. Multivariable logistic regression and machine learning approaches will identify risk factors for high healthcare use and characterise patterns of healthcare use post infection.<h4>Ethics and dissemination</h4>This study was approved by the South-Central Oxford C Health Research Authority Ethics Committee (13/SC/0149). Findings will be preprinted and published in peer-reviewed journals. Analysis code and code lists will be available through public GitHub repositories and OpenCodelists with meta-data via HDR-UK Innovation Gateway.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/11/e063271.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-063271; html:https://europepmc.org/articles/PMC9659708; pdf:https://europepmc.org/articles/PMC9659708?pdf=render
 37368983,https://doi.org/10.2337/dc23-0294,"Relationship Among Diabetes, Obesity, and Cardiovascular Disease Phenotypes: A UK Biobank Cohort Study.","Brown OI, Drozd M, McGowan H, Giannoudi M, Conning-Rowland M, Gierula J, Straw S, Wheatcroft SB, Bridge K, Roberts LD, Levelt E, Ajjan R, Griffin KJ, Bailey MA, Kearney MT, Cubbon RM.",,Diabetes care,2023,2023-08-01,Y,,,,"<h4>Objective</h4>Obesity and diabetes frequently coexist, yet their individual contributions to cardiovascular risk remain debated. We explored cardiovascular disease biomarkers, events, and mortality in the UK Biobank stratified by BMI and diabetes.<h4>Research design and methods</h4>A total of 451,355 participants were stratified by ethnicity-specific BMI categories (normal, overweight, obese) and diabetes status. We examined cardiovascular biomarkers including carotid intima-media thickness (CIMT), arterial stiffness, left ventricular ejection fraction (LVEF), and cardiac contractility index (CCI). Poisson regression models estimated adjusted incidence rate ratios (IRRs) for myocardial infarction, ischemic stroke, and cardiovascular death, with normal-weight nondiabetes as comparator.<h4>Results</h4>Five percent of participants had diabetes (10% normal weight, 34% overweight, and 55% obese vs. 34%, 43%, and 23%, respectively, without diabetes). In the nondiabetes group, overweight/obesity was associated with higher CIMT, arterial stiffness, and CCI and lower LVEF (P < 0.005); these relationships were diminished in the diabetes group. Within BMI classes, diabetes was associated with adverse cardiovascular biomarker phenotype (P < 0.005), particularly in the normal-weight group. After 5,323,190 person-years follow-up, incident myocardial infarction, ischemic stroke, and cardiovascular mortality rose across increasing BMI categories without diabetes (P < 0.005); this was comparable in the diabetes groups (P-interaction > 0.05). Normal-weight diabetes had comparable adjusted cardiovascular mortality to obese nondiabetes (IRR 1.22 [95% CI 0.96-1.56]; P = 0.1).<h4>Conclusions</h4>Obesity and diabetes are additively associated with adverse cardiovascular biomarkers and mortality risk. While adiposity metrics are more strongly correlated with cardiovascular biomarkers than diabetes-oriented metrics, both correlate weakly, suggesting that other factors underpin the high cardiovascular risk of normal-weight diabetes.",,pdf:https://diabetesjournals.org/care/article-pdf/46/8/1531/729620/dc230294.pdf; doi:https://doi.org/10.2337/dc23-0294; html:https://europepmc.org/articles/PMC10369123; pdf:https://europepmc.org/articles/PMC10369123?pdf=render
-35273122,https://doi.org/10.1136/heartjnl-2021-320325,Evaluation of antithrombotic use and COVID-19 outcomes in a nationwide atrial fibrillation cohort.,"Handy A, Banerjee A, Wood AM, Dale C, Sudlow CLM, Tomlinson C, Bean D, Thygesen JH, Mizani MA, Katsoulis M, Takhar R, Hollings S, Denaxas S, Walker V, Dobson R, Sofat R, CVD-COVID-UK Consortium.",,Heart (British Cardiac Society),2022,2022-05-25,Y,Atrial fibrillation; epidemiology; Electronic Health Records; drug monitoring; Covid-19,,,"<h4>Objective</h4>To evaluate antithrombotic (AT) use in individuals with atrial fibrillation (AF) and at high risk of stroke (CHA<sub>2</sub>DS<sub>2</sub>-VASc score ≥2) and investigate whether pre-existing AT use may improve COVID-19 outcomes.<h4>Methods</h4>Individuals with AF and CHA<sub>2</sub>DS<sub>2</sub>-VASc score ≥2 on 1 January 2020 were identified using electronic health records for 56 million people in England and were followed up until 1 May 2021. Factors associated with pre-existing AT use were analysed using logistic regression. Differences in COVID-19-related hospitalisation and death were analysed using logistic and Cox regression in individuals with pre-existing AT use versus no AT use, anticoagulants (AC) versus antiplatelets (AP), and direct oral anticoagulants (DOACs) versus warfarin.<h4>Results</h4>From 972 971 individuals with AF (age 79 (±9.3), female 46.2%) and CHA<sub>2</sub>DS<sub>2</sub>-VASc score ≥2, 88.0% (n=856 336) had pre-existing AT use, 3.8% (n=37 418) had a COVID-19 hospitalisation and 2.2% (n=21 116) died, followed up to 1 May 2021. Factors associated with no AT use included comorbidities that may contraindicate AT use (liver disease and history of falls) and demographics (socioeconomic status and ethnicity). Pre-existing AT use was associated with lower odds of death (OR=0.92, 95% CI 0.87 to 0.96), but higher odds of hospitalisation (OR=1.20, 95% CI 1.15 to 1.26). AC versus AP was associated with lower odds of death (OR=0.93, 95% CI 0.87 to 0.98) and higher hospitalisation (OR=1.17, 95% CI 1.11 to 1.24). For DOACs versus warfarin, lower odds were observed for hospitalisation (OR=0.86, 95% CI 0.82 to 0.89) but not for death (OR=1.00, 95% CI 0.95 to 1.05).<h4>Conclusions</h4>Pre-existing AT use may be associated with lower odds of COVID-19 death and, while not evidence of causality, provides further incentive to improve AT coverage for eligible individuals with AF.",,pdf:https://heart.bmj.com/content/heartjnl/108/12/923.full.pdf; doi:https://doi.org/10.1136/heartjnl-2021-320325; html:https://europepmc.org/articles/PMC8931797; pdf:https://europepmc.org/articles/PMC8931797?pdf=render
 34345715,https://doi.org/10.23889/ijpds.v5i4.1656,Establishing the impact of COVID-19 on the health outcomes of domiciliary care workers in Wales using routine data: a protocol for the OSCAR study.,"Lugg-Widger F, Cannings-John R, Akbari A, Brookes-Howell L, Hood K, John A, Jones H, Prout H, Schoenbuchner S, Thomas D, Robling M.",,International journal of population data science,2020,2020-01-01,Y,Mortality; Administrative Data; Natural Experiment; Domiciliary Care Worker; Covid-19,,,"<h4>Introduction</h4>Domiciliary care workers (DCWs) continued providing social care to adults in their own homes throughout the COVID-19 pandemic. Evidence of the impact of COVID-19 on health outcomes of DCWs is currently mixed, probably reflecting methodological limitations of existing studies. The risk of COVID-19 to workers providing care in people's homes remains unknown.<h4>Objectives</h4>To quantify the impact of COVID-19 upon health outcomes of DCWs in Wales, to explore causes of variation, and to extrapolate to the rest of the UK DCW population.<h4>Methods</h4>Mixed methods design comprising cohort study of DCWs and exploratory qualitative interviews. Data for all registered DCWs in Wales is available via the SAIL Databank using a secured, privacy-protecting encrypted anonymisation process. Occupational registration data for DCWs working during the pandemic will be combined with EHR outcome data within the SAIL Databank including clinical codes that identify suspected and confirmed COVID-19 cases. We will report rates of suspected and confirmed COVID-19 infections and key health outcomes including mortality and explore variation (by factors such as age, sex, ethnicity, deprivation quintile, rurality, employer, comorbidities) using regression modelling, adjusting for clustering of outcome within Health Board, region and employer. A maximum variation sample of Welsh DCWs will be approached for qualitative interview using a strategy to include participants that vary across factors such as sex, age, ethnicity and employer. The interviews will inform the quantitative analysis modelling. We will generalise the quantitative findings to other UK nations.<h4>Discussion</h4>Using anonymised linked occupational and EHR data and qualitative interviews, the OSCAR study will quantify the risk of COVID-19 on DCWs' health and explore sources of variation. This will provide a secure base for informing public health policy and occupational guidance.",,pdf:https://ijpds.org/article/download/1656/3219; doi:https://doi.org/10.23889/ijpds.v5i4.1656; html:https://europepmc.org/articles/PMC8280712; pdf:https://europepmc.org/articles/PMC8280712?pdf=render
+35273122,https://doi.org/10.1136/heartjnl-2021-320325,Evaluation of antithrombotic use and COVID-19 outcomes in a nationwide atrial fibrillation cohort.,"Handy A, Banerjee A, Wood AM, Dale C, Sudlow CLM, Tomlinson C, Bean D, Thygesen JH, Mizani MA, Katsoulis M, Takhar R, Hollings S, Denaxas S, Walker V, Dobson R, Sofat R, CVD-COVID-UK Consortium.",,Heart (British Cardiac Society),2022,2022-05-25,Y,Atrial fibrillation; epidemiology; Electronic Health Records; drug monitoring; Covid-19,,,"<h4>Objective</h4>To evaluate antithrombotic (AT) use in individuals with atrial fibrillation (AF) and at high risk of stroke (CHA<sub>2</sub>DS<sub>2</sub>-VASc score ≥2) and investigate whether pre-existing AT use may improve COVID-19 outcomes.<h4>Methods</h4>Individuals with AF and CHA<sub>2</sub>DS<sub>2</sub>-VASc score ≥2 on 1 January 2020 were identified using electronic health records for 56 million people in England and were followed up until 1 May 2021. Factors associated with pre-existing AT use were analysed using logistic regression. Differences in COVID-19-related hospitalisation and death were analysed using logistic and Cox regression in individuals with pre-existing AT use versus no AT use, anticoagulants (AC) versus antiplatelets (AP), and direct oral anticoagulants (DOACs) versus warfarin.<h4>Results</h4>From 972 971 individuals with AF (age 79 (±9.3), female 46.2%) and CHA<sub>2</sub>DS<sub>2</sub>-VASc score ≥2, 88.0% (n=856 336) had pre-existing AT use, 3.8% (n=37 418) had a COVID-19 hospitalisation and 2.2% (n=21 116) died, followed up to 1 May 2021. Factors associated with no AT use included comorbidities that may contraindicate AT use (liver disease and history of falls) and demographics (socioeconomic status and ethnicity). Pre-existing AT use was associated with lower odds of death (OR=0.92, 95% CI 0.87 to 0.96), but higher odds of hospitalisation (OR=1.20, 95% CI 1.15 to 1.26). AC versus AP was associated with lower odds of death (OR=0.93, 95% CI 0.87 to 0.98) and higher hospitalisation (OR=1.17, 95% CI 1.11 to 1.24). For DOACs versus warfarin, lower odds were observed for hospitalisation (OR=0.86, 95% CI 0.82 to 0.89) but not for death (OR=1.00, 95% CI 0.95 to 1.05).<h4>Conclusions</h4>Pre-existing AT use may be associated with lower odds of COVID-19 death and, while not evidence of causality, provides further incentive to improve AT coverage for eligible individuals with AF.",,pdf:https://heart.bmj.com/content/heartjnl/108/12/923.full.pdf; doi:https://doi.org/10.1136/heartjnl-2021-320325; html:https://europepmc.org/articles/PMC8931797; pdf:https://europepmc.org/articles/PMC8931797?pdf=render
 38645891,https://doi.org/10.1136/bmjmed-2023-000807,Identification of patients undergoing chronic kidney replacement therapy in primary and secondary care data: validation study based on OpenSAFELY and UK Renal Registry.,"Santhakumaran S, Fisher L, Zheng B, Mahalingasivam V, Plumb L, Parker EP, Steenkamp R, Morton C, Mehrkar A, Bacon S, Lyon S, Konstant-Hambling R, Goldacre B, MacKenna B, Tomlinson LA, Nitsch D.",,BMJ medicine,2024,2024-04-18,Y,"Dialysis; Kidney transplantation; Kidney failure, chronic; epidemiology; Covid-19",,,"<h4>Objective</h4>To validate primary and secondary care codes in electronic health records to identify people receiving chronic kidney replacement therapy based on gold standard registry data.<h4>Design</h4>Validation study using data from OpenSAFELY and the UK Renal Registry, with the approval of NHS England.<h4>Setting</h4>Primary and secondary care electronic health records from people registered at 45% of general practices in England on 1 January 2020, linked to data from the UK Renal Registry (UKRR) within the OpenSAFELY-TPP platform, part of the NHS England OpenSAFELY covid-19 service.<h4>Participants</h4>38 745 prevalent patients (recorded as receiving kidney replacement therapy on 1 January 2020 in UKRR data, or primary or secondary care data) and 10 730 incident patients (starting kidney replacement therapy during 2020), from a population of 19 million people alive and registered with a general practice in England on 1 January 2020.<h4>Main outcome measures</h4>Sensitivity and positive predictive values of primary and secondary care code lists for identifying prevalent and incident kidney replacement therapy cohorts compared with the gold standard UKRR data on chronic kidney replacement therapy. Agreement across the data sources overall, and by treatment modality (transplantation or dialysis) and personal characteristics.<h4>Results</h4>Primary and secondary care code lists were sensitive for identifying the UKRR prevalent cohort (91.2% (95% confidence interval (CI) 90.8% to 91.6%) and 92.0% (91.6% to 92.4%), respectively), but not the incident cohort (52.3% (50.3% to 54.3%) and 67.9% (66.1% to 69.7%)). Positive predictive values were low (77.7% (77.2% to 78.2%) for primary care data and 64.7% (64.1% to 65.3%) for secondary care data), particularly for chronic dialysis (53.7% (52.9% to 54.5%) for primary care data and 49.1% (48.0% to 50.2%) for secondary care data). Sensitivity decreased with age and index of multiple deprivation in primary care data, but the opposite was true in secondary care data. Agreement was lower in children, with 30% (295/980) featuring in all three datasets. Half (1165/2315) of the incident patients receiving dialysis in UKRR data had a kidney replacement therapy code in the primary care data within three months of the start date of the kidney replacement therapy. No codes existed whose exclusion would substantially improve the positive predictive value without a decrease in sensitivity.<h4>Conclusions</h4>Codes used in primary and secondary care data failed to identify a small proportion of prevalent patients receiving kidney replacement therapy. Codes also identified many patients who were not recipients of chronic kidney replacement therapy in UKRR data, particularly dialysis codes. Linkage with UKRR kidney replacement therapy data facilitated more accurate identification of incident and prevalent kidney replacement therapy cohorts for research into this vulnerable population. Poor coding has implications for any patient care (including eligibility for vaccination, resourcing, and health policy responses in future pandemics) that relies on accurate reporting of kidney replacement therapy in primary and secondary care data.",,doi:https://doi.org/10.1136/bmjmed-2023-000807; html:https://europepmc.org/articles/PMC11029353; pdf:https://europepmc.org/articles/PMC11029353?pdf=render
 PMC11227019,https://doi.org/,Adoption of high-sensitivity cardiac troponin for risk stratification of patients with suspected myocardial infarction: a multicentre cohort study,"McDermott M, Kimenai D, Anand A, Huang Z, Houston A, Williams S, Evison F, Gallier S, Carenzo C, Glampson B, Hasan M, Robertson A, Phillips T, Davis C, Sapey E, Mayer E, Mason S, Stammers M, Mills N.",,The Lancet regional health. Europe,2024,2024-06-13,Y,Myocardial infarction; Data Linkage; High-sensitivity Cardiac Troponin; Healthcare Outcomes; Healthcare Data,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11227019/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11227019/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC11227019; pdf:https://europepmc.org/articles/PMC11227019?pdf=render
 39472985,https://doi.org/10.1186/s13063-024-08580-1,Retraction Note: Development and evaluation of rapid data-enabled access to routine clinical information to enhance early recruitment to the national clinical platform trial of COVID-19 community treatments.,"Cake C, Ogburn E, Pinches H, Coleman G, Seymour D, Woodard F, Manohar S, Monsur M, Landray M, Dalton G, Morris AD, Chinnery PF, UK COVID-19 National Core Studies Consortium, Hobbs FDR, Butler C.",,Trials,2024,2024-10-29,N,,,,,,doi:https://doi.org/10.1186/s13063-024-08580-1
@@ -91,18 +91,18 @@ PMC11227019,https://doi.org/,Adoption of high-sensitivity cardiac troponin for r
 37543047,https://doi.org/10.1016/s2666-7568(23)00105-8,"Antipsychotic drug prescribing and mortality in people with dementia before and during the COVID-19 pandemic: a retrospective cohort study in Wales, UK.","Schnier C, McCarthy A, Morales DR, Akbari A, Sofat R, Dale C, Takhar R, Mamas MA, Khunti K, Zaccardi F, Sudlow CL, Wilkinson T, CVD-COVID-UK/COVID-IMPACT Consortium.",,The lancet. Healthy longevity,2023,2023-08-01,N,,,,"<h4>Background</h4>Concerns have been raised that antipsychotic drug prescribing, which has been associated with increased mortality in people with dementia, might have increased during the COVID-19 pandemic due to social restrictions imposed to limit the spread of SARS-CoV-2. We used multisource, routinely collected health-care data from Wales, UK to investigate prescribing and mortality variations in people with dementia before and during the COVID-19 pandemic.<h4>Methods</h4>In this retrospective cohort study, we used individual-level, anonymised, population-scale linked health data to identify adults aged 60 years and older with a diagnosis of dementia in Wales, UK. We used the CVD-COVID-UK initiative to access Welsh routinely collected electronic health record data from the Secure Anonymised Information Linkage (SAIL) Databank. Patients who were alive and registered with a SAIL general practice on Jan 1, 2016, and who received a dementia diagnosis before the age of 60 years and before or during the study period were included. We explored antipsychotic drug prescribing rate changes over 67 months, between Jan 1, 2016, and Aug 1, 2021, overall and stratified by age and dementia subtype. We used time-series analyses to examine all-cause and myocardial infarction and stroke mortality over the study period and identified the leading causes of death in people with dementia between Jan 1, 2020, and Aug 1, 2021.<h4>Findings</h4>Of 3 106 690 participants in SAIL between Jan 1, 2016 and Aug 1, 2021, 57 396 people (35 148 [61·2%] women and 22 248 [38·8%] men) met inclusion criteria for this study and contributed 101 428 person-years of follow-up. Of the 57 396 people with dementia, 11 929 (20·8%) were prescribed an antipsychotic drug at any point during follow-up. Accounting for seasonality, antipsychotic drug prescribing increased during the second half of 2019 and throughout 2020. However, the absolute difference in prescribing rates was small, ranging from 1253 prescriptions per 10 000 person-months in March, 2019, to 1305 per 10 000 person-months in September, 2020. All-cause mortality and stroke mortality increased throughout 2020, while myocardial infarction mortality declined. From Jan 1, 2020, to Aug 1, 2021, 1286 (17·1%) of 7508 participants who died had COVID-19 recorded as the underlying cause of death.<h4>Interpretation</h4>During the COVID-19 pandemic, antipsychotic drug prescribing in people with dementia in the UK increased slightly; however, it is unlikely that this was solely related to the pandemic and this increase was unlikely to be a major factor in the substantial increase in mortality during 2020. The long-term increase in antipsychotic drug prescribing in younger people and in those with Alzheimer's disease warrants further investigation using resources with access to more granular clinical data. Although deprescribing antipsychotic medications remains an essential aspect of dementia care, the results of this study suggest that changes in prescribing and deprescribing practices as a result of the COVID-19 pandemic are not required.<h4>Funding</h4>British Heart Foundation (via the British Heart Foundation Data Science Centre led by Health Data Research UK), and the Scottish Neurological Research Fund.",,doi:https://doi.org/10.1016/S2666-7568(23)00105-8
 35192598,https://doi.org/10.1371/journal.pmed.1003927,"First dose ChAdOx1 and BNT162b2 COVID-19 vaccinations and cerebral venous sinus thrombosis: A pooled self-controlled case series study of 11.6 million individuals in England, Scotland, and Wales.","Kerr S, Joy M, Torabi F, Bedston S, Akbari A, Agrawal U, Beggs J, Bradley D, Chuter A, Docherty AB, Ford D, Hobbs R, Katikireddi SV, Lowthian E, de Lusignan S, Lyons R, Marple J, McCowan C, McGagh D, McMenamin J, Moore E, Murray JK, Owen RK, Pan J, Ritchie L, Shah SA, Shi T, Stock S, Tsang RSM, Vasileiou E, Woolhouse M, Simpson CR, Robertson C, Sheikh A.",,PLoS medicine,2022,2022-02-22,Y,,,,"<h4>Background</h4>Several countries restricted the administration of ChAdOx1 to older age groups in 2021 over safety concerns following case reports and observed versus expected analyses suggesting a possible association with cerebral venous sinus thrombosis (CVST). Large datasets are required to precisely estimate the association between Coronavirus Disease 2019 (COVID-19) vaccination and CVST due to the extreme rarity of this event. We aimed to accomplish this by combining national data from England, Scotland, and Wales.<h4>Methods and findings</h4>We created data platforms consisting of linked primary care, secondary care, mortality, and virological testing data in each of England, Scotland, and Wales, with a combined cohort of 11,637,157 people and 6,808,293 person years of follow-up. The cohort start date was December 8, 2020, and the end date was June 30, 2021. The outcome measure we examined was incident CVST events recorded in either primary or secondary care records. We carried out a self-controlled case series (SCCS) analysis of this outcome following first dose vaccination with ChAdOx1 and BNT162b2. The observation period consisted of an initial 90-day reference period, followed by a 2-week prerisk period directly prior to vaccination, and a 4-week risk period following vaccination. Counts of CVST cases from each country were tallied, then expanded into a full dataset with 1 row for each individual and observation time period. There was a combined total of 201 incident CVST events in the cohorts (29.5 per million person years). There were 81 CVST events in the observation period among those who a received first dose of ChAdOx1 (approximately 16.34 per million doses) and 40 for those who received a first dose of BNT162b2 (approximately 12.60 per million doses). We fitted conditional Poisson models to estimate incidence rate ratios (IRRs). Vaccination with ChAdOx1 was associated with an elevated risk of incident CVST events in the 28 days following vaccination, IRR = 1.93 (95% confidence interval (CI) 1.20 to 3.11). We did not find an association between BNT162b2 and CVST in the 28 days following vaccination, IRR = 0.78 (95% CI 0.34 to 1.77). Our study had some limitations. The SCCS study design implicitly controls for variables that are constant over the observation period, but also assumes that outcome events are independent of exposure. This assumption may not be satisfied in the case of CVST, firstly because it is a serious adverse event, and secondly because the vaccination programme in the United Kingdom prioritised the clinically extremely vulnerable and those with underlying health conditions, which may have caused a selection effect for individuals more prone to CVST. Although we pooled data from several large datasets, there was still a low number of events, which may have caused imprecision in our estimates.<h4>Conclusions</h4>In this study, we observed a small elevated risk of CVST events following vaccination with ChAdOx1, but not BNT162b2. Our analysis pooled information from large datasets from England, Scotland, and Wales. This evidence may be useful in risk-benefit analyses of vaccine policies and in providing quantification of risks associated with vaccination to the general public.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003927&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003927; html:https://europepmc.org/articles/PMC8863261; pdf:https://europepmc.org/articles/PMC8863261?pdf=render
 39379679,https://doi.org/10.1038/s43856-024-00625-5,Disease coverage of human genome-wide association studies and pharmaceutical research and development.,"Gordillo-Marañón M, Schmidt AF, Warwick A, Tomlinson C, Ytsma C, Engmann J, Torralbo A, Maclean R, Sofat R, Langenberg C, Shah AD, Denaxas S, Pirmohamed M, Hemingway H, Hingorani AD, Finan C.",,Communications medicine,2024,2024-10-08,Y,,,,"<h4>Background</h4>Despite the growing interest in the use of human genomic data for drug target identification and validation, the extent to which the spectrum of human disease has been addressed by genome-wide association studies (GWAS), or by drug development, and the degree to which these efforts overlap remain unclear.<h4>Methods</h4>In this study we harmonize and integrate different data sources to create a sample space of all the human drug targets and diseases and identify points of convergence or divergence of GWAS and drug development efforts.<h4>Results</h4>We show that only 612 of 11,158 diseases listed in Human Disease Ontology have an approved drug treatment in at least one region of the world. Of the 1414 diseases that are the subject of preclinical or clinical phase drug development, only 666 have been investigated in GWAS. Conversely, of the 1914 human diseases that have been the subject of GWAS, 1121 have yet to be investigated in drug development.<h4>Conclusions</h4>We produce target-disease indication lists to help the pharmaceutical industry to prioritize future drug development efforts based on genetic evidence, academia to prioritize future GWAS for diseases without effective treatments, and both sectors to harness genetic evidence to expand the indications for licensed drugs or to identify repurposing opportunities for clinical candidates that failed in their originally intended indication.",,doi:https://doi.org/10.1038/s43856-024-00625-5; doi:https://doi.org/10.1038/s43856-024-00625-5; html:https://europepmc.org/articles/PMC11461613; pdf:https://europepmc.org/articles/PMC11461613?pdf=render
-33969335,https://doi.org/10.1016/j.lanepe.2021.100098,"Prevalence of antibody positivity to SARS-CoV-2 following the first peak of infection in England: Serial cross-sectional studies of 365,000 adults.","Ward H, Cooke GS, Atchison C, Whitaker M, Elliott J, Moshe M, Brown JC, Flower B, Daunt A, Ainslie K, Ashby D, Donnelly CA, Riley S, Darzi A, Barclay W, Elliott P.",,The Lancet regional health. Europe,2021,2021-05-02,Y,,,,"<h4>Background</h4>The time-concentrated nature of the first wave of the COVID-19 epidemic in England in March and April 2020 provides a natural experiment to measure changes in antibody positivity at the population level before onset of the second wave and initiation of the vaccination programme.<h4>Methods</h4>Three cross-sectional national surveys with non-overlapping random samples of the population in England undertaken between late June and September 2020 (REACT-2 study). 365,104 adults completed questionnaires and self-administered lateral flow immunoassay (LFIA) tests for IgG against SARS-CoV-2.<h4>Findings</h4>Overall, 17,576 people had detectable antibodies, a prevalence of 4.9% (95% confidence intervals 4.9, 5.0) when adjusted for test characteristics and weighted to the adult population of England. The prevalence declined from 6.0% (5.8, 6.1), to 4.8% (4.7, 5.0) and 4.4% (4.3, 4.5), over the three rounds of the study a difference of -26.5% (-29.0, -23.8). The highest prevalence and smallest overall decline in positivity was in the youngest age group (18-24 years) at -14.9% (-21.6, -8.1), and lowest prevalence and largest decline in the oldest group (>74 years) at -39.0% (-50.8, -27.2). The decline from June to September 2020 was largest in those who did not report a history of COVID-19 at -64.0% (-75.6, -52.3), compared to -22.3% (-27.0, -17.7) in those with SARS-CoV-2 infection confirmed on PCR.<h4>Interpretation</h4>A large proportion of the population remained susceptible to SARS-CoV-2 infection in England based on naturally acquired immunity from the first wave. Widespread vaccination is needed to confer immunity and control the epidemic at population level.<h4>Funding</h4>This work was funded by the Department of Health and Social Care in England.",,doi:https://doi.org/10.1016/j.lanepe.2021.100098; doi:https://doi.org/10.1016/j.lanepe.2021.100098; html:https://europepmc.org/articles/PMC8088780; pdf:https://europepmc.org/articles/PMC8088780?pdf=render
 36719907,https://doi.org/10.1371/journal.pmed.1004086,Outcome of COVID-19 in hospitalised immunocompromised patients: An analysis of the WHO ISARIC CCP-UK prospective cohort study.,"Turtle L, Thorpe M, Drake TM, Swets M, Palmieri C, Russell CD, Ho A, Aston S, Wootton DG, Richter A, de Silva TI, Hardwick HE, Leeming G, Law A, Openshaw PJM, Harrison EM, ISARIC4C investigators, Baillie JK, Semple MG, Docherty AB.",,PLoS medicine,2023,2023-01-31,Y,,,,"<h4>Background</h4>Immunocompromised patients may be at higher risk of mortality if hospitalised with Coronavirus Disease 2019 (COVID-19) compared with immunocompetent patients. However, previous studies have been contradictory. We aimed to determine whether immunocompromised patients were at greater risk of in-hospital death and how this risk changed over the pandemic.<h4>Methods and findings</h4>We included patients > = 19 years with symptomatic community-acquired COVID-19 recruited to the ISARIC WHO Clinical Characterisation Protocol UK prospective cohort study. We defined immunocompromise as immunosuppressant medication preadmission, cancer treatment, organ transplant, HIV, or congenital immunodeficiency. We used logistic regression to compare the risk of death in both groups, adjusting for age, sex, deprivation, ethnicity, vaccination, and comorbidities. We used Bayesian logistic regression to explore mortality over time. Between 17 January 2020 and 28 February 2022, we recruited 156,552 eligible patients, of whom 21,954 (14%) were immunocompromised. In total, 29% (n = 6,499) of immunocompromised and 21% (n = 28,608) of immunocompetent patients died in hospital. The odds of in-hospital mortality were elevated for immunocompromised patients (adjusted OR 1.44, 95% CI [1.39, 1.50], p < 0.001). Not all immunocompromising conditions had the same risk, for example, patients on active cancer treatment were less likely to have their care escalated to intensive care (adjusted OR 0.77, 95% CI [0.7, 0.85], p < 0.001) or ventilation (adjusted OR 0.65, 95% CI [0.56, 0.76], p < 0.001). However, cancer patients were more likely to die (adjusted OR 2.0, 95% CI [1.87, 2.15], p < 0.001). Analyses were adjusted for age, sex, socioeconomic deprivation, comorbidities, and vaccination status. As the pandemic progressed, in-hospital mortality reduced more slowly for immunocompromised patients than for immunocompetent patients. This was particularly evident with increasing age: the probability of the reduction in hospital mortality being less for immunocompromised patients aged 50 to 69 years was 88% for men and 83% for women, and for those >80 years was 99% for men and 98% for women. The study is limited by a lack of detailed drug data prior to admission, including steroid doses, meaning that we may have incorrectly categorised some immunocompromised patients as immunocompetent.<h4>Conclusions</h4>Immunocompromised patients remain at elevated risk of death from COVID-19. Targeted measures such as additional vaccine doses, monoclonal antibodies, and nonpharmaceutical preventive interventions should be continually encouraged for this patient group.<h4>Trial registration</h4>ISRCTN 66726260.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004086&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004086; html:https://europepmc.org/articles/PMC9928075; pdf:https://europepmc.org/articles/PMC9928075?pdf=render
+33969335,https://doi.org/10.1016/j.lanepe.2021.100098,"Prevalence of antibody positivity to SARS-CoV-2 following the first peak of infection in England: Serial cross-sectional studies of 365,000 adults.","Ward H, Cooke GS, Atchison C, Whitaker M, Elliott J, Moshe M, Brown JC, Flower B, Daunt A, Ainslie K, Ashby D, Donnelly CA, Riley S, Darzi A, Barclay W, Elliott P.",,The Lancet regional health. Europe,2021,2021-05-02,Y,,,,"<h4>Background</h4>The time-concentrated nature of the first wave of the COVID-19 epidemic in England in March and April 2020 provides a natural experiment to measure changes in antibody positivity at the population level before onset of the second wave and initiation of the vaccination programme.<h4>Methods</h4>Three cross-sectional national surveys with non-overlapping random samples of the population in England undertaken between late June and September 2020 (REACT-2 study). 365,104 adults completed questionnaires and self-administered lateral flow immunoassay (LFIA) tests for IgG against SARS-CoV-2.<h4>Findings</h4>Overall, 17,576 people had detectable antibodies, a prevalence of 4.9% (95% confidence intervals 4.9, 5.0) when adjusted for test characteristics and weighted to the adult population of England. The prevalence declined from 6.0% (5.8, 6.1), to 4.8% (4.7, 5.0) and 4.4% (4.3, 4.5), over the three rounds of the study a difference of -26.5% (-29.0, -23.8). The highest prevalence and smallest overall decline in positivity was in the youngest age group (18-24 years) at -14.9% (-21.6, -8.1), and lowest prevalence and largest decline in the oldest group (>74 years) at -39.0% (-50.8, -27.2). The decline from June to September 2020 was largest in those who did not report a history of COVID-19 at -64.0% (-75.6, -52.3), compared to -22.3% (-27.0, -17.7) in those with SARS-CoV-2 infection confirmed on PCR.<h4>Interpretation</h4>A large proportion of the population remained susceptible to SARS-CoV-2 infection in England based on naturally acquired immunity from the first wave. Widespread vaccination is needed to confer immunity and control the epidemic at population level.<h4>Funding</h4>This work was funded by the Department of Health and Social Care in England.",,doi:https://doi.org/10.1016/j.lanepe.2021.100098; doi:https://doi.org/10.1016/j.lanepe.2021.100098; html:https://europepmc.org/articles/PMC8088780; pdf:https://europepmc.org/articles/PMC8088780?pdf=render
 32873607,https://doi.org/10.1136/bmjresp-2020-000644,Ethnicity and risk of death in patients hospitalised for COVID-19 infection in the UK: an observational cohort study in an urban catchment area.,"Sapey E, Gallier S, Mainey C, Nightingale P, McNulty D, Crothers H, Evison F, Reeves K, Pagano D, Denniston AK, Nirantharakumar K, Diggle P, Ball S, All clinicians and students at University Hospitals Birmingham NHS Foundation Trust.",,BMJ open respiratory research,2020,2020-09-01,Y,Viral infection; respiratory infection; Clinical Epidemiology,,,"<h4>Background</h4>Studies suggest that certain black and Asian minority ethnic groups experience poorer outcomes from COVID-19, but these studies have not provided insight into potential reasons for this. We hypothesised that outcomes would be poorer for those of South Asian ethnicity hospitalised from a confirmed SARS-CoV-2 infection, once confounding factors, health-seeking behaviours and community demographics were considered, and that this might reflect a more aggressive disease course in these patients.<h4>Methods</h4>Patients with confirmed SARS-CoV-2 infection requiring admission to University Hospitals Birmingham NHS Foundation Trust (UHB) in Birmingham, UK between 10 March 2020 and 17 April 2020 were included. Standardised admission ratio (SAR) and standardised mortality ratio (SMR) were calculated using observed COVID-19 admissions/deaths and 2011 census data. Adjusted HR for mortality was estimated using Cox proportional hazard model adjusting and propensity score matching.<h4>Results</h4>All patients admitted to UHB with COVID-19 during the study period were included (2217 in total). 58% were male, 69.5% were white and the majority (80.2%) had comorbidities. 18.5% were of South Asian ethnicity, and these patients were more likely to be younger and have no comorbidities, but twice the prevalence of diabetes than white patients. SAR and SMR suggested more admissions and deaths in South Asian patients than would be predicted and they were more likely to present with severe disease despite no delay in presentation since symptom onset. South Asian ethnicity was associated with an increased risk of death, both by Cox regression (HR 1.4, 95% CI 1.2 to 1.8), after adjusting for age, sex, deprivation and comorbidities, and by propensity score matching, matching for the same factors but categorising ethnicity into South Asian or not (HR 1.3, 95% CI 1.0 to 1.6).<h4>Conclusions</h4>Those of South Asian ethnicity appear at risk of worse COVID-19 outcomes. Further studies need to establish the underlying mechanistic pathways.",,pdf:https://bmjopenrespres.bmj.com/content/bmjresp/7/1/e000644.full.pdf; doi:https://doi.org/10.1136/bmjresp-2020-000644; html:https://europepmc.org/articles/PMC7467523; pdf:https://europepmc.org/articles/PMC7467523?pdf=render
-37699667,https://doi.org/10.1136/jech-2023-220801,Predictive value of metabolic profiling in cardiovascular risk scores: analysis of 75 000 adults in UK Biobank.,"Jin D, Trichia E, Islam N, Lewington S, Lacey B.",,Journal of epidemiology and community health,2023,2023-09-12,Y,Cardiovascular diseases; epidemiology; Primary Health Care,,,"<h4>Background</h4>Metabolic profiling (the extensive measurement of circulating metabolites across multiple biological pathways) is increasingly employed in clinical care. However, there is little evidence on the benefit of metabolic profiling as compared with established atherosclerotic cardiovascular disease (CVD) risk scores.<h4>Methods</h4>UK Biobank is a prospective study of 0.5 million participants, aged 40-69 at recruitment. Analyses were restricted to 74 780 participants with metabolic profiling (measured using nuclear magnetic resonance) and without CVD at baseline. Cox regression was used to compare model performance before and after addition of metabolites to QRISK3 (an established CVD risk score used in primary care in England); analyses derived three models, with metabolites selected by association significance or by employing two different machine learning approaches.<h4>Results</h4>We identified 5097 incident CVD events within the 10-year follow-up. Harrell's C-index of QRISK3 was 0.750 (95% CI 0.739 to 0.763) for women and 0.706 (95% CI 0.696 to 0.716) for men. Adding selected metabolites did not significantly improve measures of discrimination in women (Harrell's C-index of three models are 0.759 (0.747 to 0.772), 0.759 (0.746 to 0.770) and 0.759 (0.748 to 0.771), respectively) or men (0.710 (0.701 to 0.720), 0.710 (0.700 to 0.719) and 0.710 (0.701 to 0.719), respectively), and neither did it improve reclassification or calibration.<h4>Conclusion</h4>This large-scale study applied both conventional and machine learning approaches to assess the potential benefit of metabolic profiling to well-established CVD risk scores. However, there was no evidence that metabolic profiling improved CVD risk prediction in this population.",,doi:https://doi.org/10.1136/jech-2023-220801; html:https://europepmc.org/articles/PMC11418003; pdf:https://europepmc.org/articles/PMC11418003?pdf=render
 34127076,https://doi.org/10.1186/s40900-021-00281-2,"Perceptions of anonymised data use and awareness of the NHS data opt-out amongst patients, carers and healthcare staff.","Atkin C, Crosby B, Dunn K, Price G, Marston E, Crawford C, O'Hara M, Morgan C, Levermore M, Gallier S, Modhwadia S, Attwood J, Perks S, Denniston AK, Gkoutos G, Dormer R, Rosser A, Ignatowicz A, Fanning H, Sapey E, PIONEER Data Hub.",,Research involvement and engagement,2021,2021-06-14,Y,data sharing; Commercial; Secondary Data Use; Anonymised Healthcare Data; National Data Opt-out,,,"<h4>Background</h4>England operates a National Data Opt-Out (NDOO) for the secondary use of confidential health data for research and planning. We hypothesised that public awareness and support for the secondary use of health data and the NDOO would vary by participant demography and healthcare experience. We explored patient/public awareness and perceptions of secondary data use, grouping potential researchers into National Health Service (NHS), academia or commercial. We assessed awareness of the NDOO system amongst patients, carers, healthcare staff and the public. We co-developed recommendations to consider when sharing unconsented health data for research.<h4>Methods</h4>A patient and public engagement program, co-created and including patient and public workshops, questionnaires and discussion groups regarding anonymised health data use.<h4>Results</h4>There were 350 participants in total. Central concerns for health data use included unauthorised data re-use, the potential for discrimination and data sharing without patient benefit. 94% of respondents were happy for their data to be used for NHS research, 85% for academic research and 68% by health companies, but less than 50% for non-healthcare companies and opinions varied with demography and participant group. Questionnaires showed that knowledge of the NDOO was low, with 32% of all respondents, 53% of all NHS staff and 29% of all patients aware of the NDOO. Recommendations to guide unconsented secondary health data use included that health data use should benefit patients; data sharing decisions should involve patients/public. That data should remain in close proximity to health services with the principles of data minimisation applied. Further, that there should be transparency in secondary health data use, including publicly available lists of projects, summaries and benefits. Finally, organisations involved in data access decisions should participate in programmes to increase knowledge of the NDOO, to ensure public members were making informed choices about their own data.<h4>Conclusion</h4>The majority of participants in this study reported that the use of healthcare data for secondary purposes was acceptable when accessed by NHS. Academic and health-focused companies. However, awareness was limited, including of the NDOO. Further development of publicly-agreed recommendations for secondary health data use may improve both awareness and confidence in secondary health data use.",,pdf:https://researchinvolvement.biomedcentral.com/track/pdf/10.1186/s40900-021-00281-2; doi:https://doi.org/10.1186/s40900-021-00281-2; html:https://europepmc.org/articles/PMC8201435; pdf:https://europepmc.org/articles/PMC8201435?pdf=render
+37699667,https://doi.org/10.1136/jech-2023-220801,Predictive value of metabolic profiling in cardiovascular risk scores: analysis of 75 000 adults in UK Biobank.,"Jin D, Trichia E, Islam N, Lewington S, Lacey B.",,Journal of epidemiology and community health,2023,2023-09-12,Y,Cardiovascular diseases; epidemiology; Primary Health Care,,,"<h4>Background</h4>Metabolic profiling (the extensive measurement of circulating metabolites across multiple biological pathways) is increasingly employed in clinical care. However, there is little evidence on the benefit of metabolic profiling as compared with established atherosclerotic cardiovascular disease (CVD) risk scores.<h4>Methods</h4>UK Biobank is a prospective study of 0.5 million participants, aged 40-69 at recruitment. Analyses were restricted to 74 780 participants with metabolic profiling (measured using nuclear magnetic resonance) and without CVD at baseline. Cox regression was used to compare model performance before and after addition of metabolites to QRISK3 (an established CVD risk score used in primary care in England); analyses derived three models, with metabolites selected by association significance or by employing two different machine learning approaches.<h4>Results</h4>We identified 5097 incident CVD events within the 10-year follow-up. Harrell's C-index of QRISK3 was 0.750 (95% CI 0.739 to 0.763) for women and 0.706 (95% CI 0.696 to 0.716) for men. Adding selected metabolites did not significantly improve measures of discrimination in women (Harrell's C-index of three models are 0.759 (0.747 to 0.772), 0.759 (0.746 to 0.770) and 0.759 (0.748 to 0.771), respectively) or men (0.710 (0.701 to 0.720), 0.710 (0.700 to 0.719) and 0.710 (0.701 to 0.719), respectively), and neither did it improve reclassification or calibration.<h4>Conclusion</h4>This large-scale study applied both conventional and machine learning approaches to assess the potential benefit of metabolic profiling to well-established CVD risk scores. However, there was no evidence that metabolic profiling improved CVD risk prediction in this population.",,doi:https://doi.org/10.1136/jech-2023-220801; html:https://europepmc.org/articles/PMC11418003; pdf:https://europepmc.org/articles/PMC11418003?pdf=render
 38693557,https://doi.org/10.1186/s12913-024-10931-2,The cost of keeping patients waiting: retrospective treatment-control study of additional healthcare utilisation for UK patients awaiting elective treatment.,"James C, Denholm R, Wood R.",,BMC health services research,2024,2024-04-30,Y,Utilisation; Waiting Times; Waitlist; Elective Recovery; Failure-demand,,,"<h4>Objective</h4>Long waiting times for elective hospital treatments are common in many countries. This study seeks to address a deficit in the literature concerning the effect of long waits on the wider consumption of healthcare resources.<h4>Methods</h4>We carried out a retrospective treatment-control study in a healthcare system in South West England from 15 June 2021 to 15 December 2021. We compared weekly contacts with health services of patients waiting over 18 weeks for treatment ('Treatments') and people not on a waiting list ('Controls'). Controls were matched to Treatments based on age, sex, deprivation and multimorbidity. Treatments were stratified by the clinical specialty of the awaited hospital treatment, with healthcare usage assessed over various healthcare settings. Wilcoxon signed-rank tests assessed whether there was an increase in healthcare utilisation and bootstrap resampling was used to estimate the magnitude of any differences.<h4>Results</h4>A total of 44,616 patients were waiting over 18 weeks (the constitutional target in England) for treatment during the study period. There was an increase (p < 0.0004) in healthcare utilisation for all specialties. Patients in the Cardiothoracic Surgery specialty had the largest increase, with 17.9 [interquartile-range: 4.3, 33.8] additional contacts with secondary care and 17.3 [-1.1, 34.1] additional prescriptions per year.<h4>Conclusion</h4>People waiting for treatment consume higher levels of healthcare than comparable individuals not on a waiting list. These findings are relevant for clinicians and managers in better understanding patient need and reducing harm. Results also highlight the possible 'false economy' in failing to promptly resolve long elective waits.",,doi:https://doi.org/10.1186/s12913-024-10931-2; html:https://europepmc.org/articles/PMC11061904; pdf:https://europepmc.org/articles/PMC11061904?pdf=render
 38049846,https://doi.org/10.1186/s13012-023-01321-z,Implementing Germ Defence digital behaviour change intervention via all primary care practices in England to reduce respiratory infections during the COVID-19 pandemic: an efficient cluster randomised controlled trial using the OpenSAFELY platform.,"Ainsworth B, Horwood J, Walter SR, Miller S, Chalder M, De Vocht F, Denison-Day J, Elwenspoek MMC, Curtis HJ, Bates C, Mehrkar A, Bacon S, Goldacre B, OpenSAFELY Collaborative, Craggs P, Amlôt R, Francis N, Little P, Macleod J, Moore M, Morton K, Rice C, Sterne J, Stuart B, Towler L, Willcox ML, Yardley L.",,Implementation science : IS,2023,2023-12-04,Y,Infection control; Respiratory Tract Infections; Primary Care; Rct; Behaviour Change; Ehealth; Digital Medicine; Covid-19; Efficient Trial Design,,,"<h4>Background</h4>Germ Defence ( www.germdefence.org ) is an evidence-based interactive website that promotes behaviour change for infection control within households. To maximise the potential of Germ Defence to effectively reduce the spread of COVID-19, the intervention needed to be implemented at scale rapidly.<h4>Methods</h4>With NHS England approval, we conducted an efficient two-arm (1:1 ratio) cluster randomised controlled trial (RCT) to examine the effectiveness of randomising implementation of Germ Defence via general practitioner (GP) practices across England, UK, compared with usual care to disseminate Germ Defence to patients. GP practices randomised to the intervention arm (n = 3292) were emailed and asked to disseminate Germ Defence to all adult patients via mobile phone text, email or social media. Usual care arm GP practices (n = 3287) maintained standard management for the 4-month trial period and then asked to share Germ Defence with their adult patients. The primary outcome was the rate of GP presentations for respiratory tract infections (RTI) per patient. Secondary outcomes comprised rates of acute RTIs, confirmed COVID-19 diagnoses and suspected COVID-19 diagnoses, COVID-19 symptoms, gastrointestinal infection diagnoses, antibiotic usage and hospital admissions. The impact of the intervention on outcome rates was assessed using negative binomial regression modelling within the OpenSAFELY platform. The uptake of the intervention by GP practice and by patients was measured via website analytics.<h4>Results</h4>Germ Defence was used 310,731 times. The average website satisfaction score was 7.52 (0-10 not at all to very satisfied, N = 9933). There was no evidence of a difference in the rate of RTIs between intervention and control practices (rate ratio (RR) 1.01, 95% CI 0.96, 1.06, p = 0.70). This was similar to all other eight health outcomes. Patient engagement within intervention arm practices ranged from 0 to 48% of a practice list.<h4>Conclusions</h4>While the RCT did not demonstrate a difference in health outcomes, we demonstrated that rapid large-scale implementation of a digital behavioural intervention is possible and can be evaluated with a novel efficient prospective RCT methodology analysing routinely collected patient data entirely within a trusted research environment.<h4>Trial registration</h4>This trial was registered in the ISRCTN registry (14602359) on 12 August 2020.",,pdf:https://implementationscience.biomedcentral.com/counter/pdf/10.1186/s13012-023-01321-z; doi:https://doi.org/10.1186/s13012-023-01321-z; html:https://europepmc.org/articles/PMC10694966; pdf:https://europepmc.org/articles/PMC10694966?pdf=render
 39165418,https://doi.org/10.1016/j.gastha.2024.03.005,Protein Phosphatase 1 Regulatory Subunit 3 Beta rs4240624 Genotype Is Associated With Gallstones and With Significant Changes in Bile Lipidome.,"Männistö VT, Kaminska D, Haal S, Asteljoki J, Luukkonen PK, Käkelä P, Tavaglione F, van Weeghel M, Neuvonen M, Niemi M, Romeo S, Nieuwdorp M, Pihlajamäki J, Groen AK.",,Gastro hep advances,2024,2024-03-12,Y,Bile; Lipidomics; Gallstone Disease; Ppp1r3b,,,"<h4>Background and aims</h4>Gallstone disease (GSD) associates with significant morbidity and mortality. Decreased secretion of bile acids has been suggested as a driving factor for GSD. Recently, we linked the protein phosphatase 1 regulatory subunit 3 beta (<i>PPP1R3B)</i> rs4240624 genotype to decreased bile acid levels in bile. In this study, we investigated whether these individuals had an increased risk for GSD as well as the differences in the lipid composition of the gallbladder bile of these individuals compared to controls and patients with GSD.<h4>Methods</h4>Bile acids, cholesterol, and phospholipid levels in gallbladder bile samples were enzymatically measured in 46 patients (34 female, age 45.7 ± 9.8 years, BMI 41.3 ± 4.4 kg/m<sup>2</sup>) who underwent elective laparoscopic Roux-en-Y gastric bypass. The lipidome of gallbladder bile was analyzed using high-performance liquid chromatography-mass spectrometry. Gallstone status was evaluated using abdominal ultrasonography before the surgery.<h4>Results</h4>The G allele of <i>PPP1R3B</i> rs4240624 was significantly associated with GSD in patients with obesity. We validated this association in the UK Biobank. Bile lipidomics demonstrated that 13 of the 17 minor lipid classes measured were higher in individuals with the G allele. The concentrations of bile acids, cholesterol, and phospholipids, as well as the cholesterol saturation index, were lower in patients with GSD than in those without gallstones. GSD had an effect similar to that of <i>PPP1R3B</i> genotype on minor lipids.<h4>Conclusion</h4>The <i>PPP1R3B</i> rs4240624 genotype is associated with gallstones and with changes in gallbladder bile similar to those observed in patients with gallstones, suggesting that the <i>PPP1R3B</i> genotype contributes to the risk of gallstones by altering the bile lipidome.",,doi:https://doi.org/10.1016/j.gastha.2024.03.005; html:https://europepmc.org/articles/PMC11330930; pdf:https://europepmc.org/articles/PMC11330930?pdf=render
+38251486,https://doi.org/10.1016/s2665-9913(23)00206-0,"Gout incidence and management during the COVID-19 pandemic in England, UK: a nationwide observational study using OpenSAFELY.","Russell MD, Massey J, Roddy E, MacKenna B, Bacon S, Goldacre B, Andrews CD, Hickman G, Mehrkar A, Mahto A, Rutherford AI, Patel S, Adas MA, Alveyn E, Nagra D, Bechman K, Ledingham JM, Hudson J, Norton S, Cope AP, Galloway JB.",,The Lancet. Rheumatology,2023,2023-08-31,Y,,,,"<h4>Background</h4>Gout is the most prevalent inflammatory arthritis, yet one of the worst managed. Our objective was to assess how the COVID-19 pandemic impacted incidence and quality of care for people with gout in England, UK.<h4>Methods</h4>With the approval of National Health Service England, we did a population-level cohort study using primary care and hospital electronic health record data for 17·9 million adults registered with general practices using TPP health record software, via the OpenSAFELY platform. The study period was from March 1, 2015, to Feb 28, 2023. Individuals aged 18-110 years were defined as having incident gout if they were assigned index diagnostic codes for gout, were registered with TPP practices in England for at least 12 months before diagnosis, did not receive prescriptions for urate-lowering therapy more than 30 days before diagnosis, and had not been admitted to hospital or attended an emergency department for gout flares more than 30 days before diagnosis. Outcomes assessed were incidence and prevalence of people with recorded gout diagnoses, incidence of gout hospitalisations, initiation of urate-lowering therapy, and attainment of serum urate targets (≤360 μmol/L).<h4>Findings</h4>From a reference population of 17 865 145 adults, 246 695 individuals were diagnosed with incident gout. The mean age of individuals with incident gout was 61·3 years (SD 16·2). 66 265 (26·9%) of 246 695 individuals were female, 180 430 (73·1%) were male, and 189 035 (90·9%) of 208 050 individuals with available ethnicity data were White. Incident gout diagnoses decreased by 30·9% in the year beginning March, 2020, compared with the preceding year (1·23 diagnoses vs 1·78 diagnoses per 1000 adults). Gout prevalence was 3·07% in 2015-16, and 3·21% in 2022-23. Gout hospitalisations decreased by 30·1% in the year commencing March, 2020, compared with the preceding year (9·6 admissions vs 13·7 admissions per 100 000 adults). Of 228 095 people with incident gout and available follow-up, 66 560 (29·2%) were prescribed urate-lowering therapy within 6 months. Of 65 305 individuals who initiated urate-lowering therapy with available follow-up, 16 790 (25·7%) attained a serum urate concentration of 360 μmol/L or less within 6 months of urate-lowering therapy initiation. In interrupted time-series analyses, urate-lowering therapy prescribing improved modestly during the pandemic, compared with pre-pandemic, whereas urate target attainment was similar.<h4>Interpretation</h4>Using gout as an exemplar disease, we showed the complexity of how health care was impacted during the COVID-19 pandemic. We observed a reduction in gout diagnoses but no effect on treatment metrics. We showed how country-wide, routinely collected data can be used to map disease epidemiology and monitor care quality.<h4>Funding</h4>None.",,pdf:http://www.thelancet.com/article/S2665991323002060/pdf; doi:https://doi.org/10.1016/S2665-9913(23)00206-0; html:https://europepmc.org/articles/PMC7616140; pdf:https://europepmc.org/articles/PMC7616140?pdf=render
 39047204,https://doi.org/10.1212/wnl.0000000000209659,"Association Between Body Composition Patterns, Cardiovascular Disease, and Risk of Neurodegenerative Disease in the UK Biobank.","Xu S, Wen S, Yang Y, He J, Yang H, Qu Y, Zeng Y, Zhu J, Fang F, Song H.",,Neurology,2024,2024-07-24,Y,,,,"<h4>Background and objectives</h4>Accumulating evidence connects diverse components of body composition (e.g., fat, muscle, and bone) to neurodegenerative disease risk, yet their interplay remains underexplored. This study examines the associations between patterns of body composition and the risk of neurodegenerative diseases, exploring the mediating role of cardiovascular diseases (CVDs).<h4>Methods</h4>This retrospective analysis used data from the UK Biobank, a prospective community-based cohort study. We included participants free of neurodegenerative diseases and with requisite body composition measurements at recruitment, who were followed from 5 years after recruitment until April 1, 2023, to identify incident neurodegenerative diseases. We assessed the associations between different components and major patterns of body composition (identified by principal component analysis) with the risk of neurodegenerative diseases, using multivariable Cox models. Analyses were stratified by disease susceptibility, indexed by polygenetic risk scores for Alzheimer and Parkinson diseases, <i>APOE</i> genotype, and family history of neurodegenerative diseases. Furthermore, we performed mediation analysis to estimate the contribution of CVDs to these associations. In addition, in a subcohort of 40,790 participants, we examined the relationship between body composition patterns and brain aging biomarkers (i.e., brain atrophy and cerebral small vessel disease).<h4>Results</h4>Among 412,691 participants (mean age 56.0 years, 55.1% female), 8,224 new cases of neurodegenerative diseases were identified over an average follow-up of 9.1 years. Patterns identified as ""fat-to-lean mass,"" ""muscle strength,"" ""bone density,"" and ""leg-dominant fat distribution"" were associated with a lower rate of neurodegenerative diseases (hazard ratio [HR] = 0.74-0.94) while ""central obesity"" and ""arm-dominant fat distribution"" patterns were associated with a higher rate (HR = 1.13-1.18). Stratification analysis yielded comparable risk estimates across different susceptibility groups. Notably, 10.7%-35.3% of the observed associations were mediated by CVDs, particularly cerebrovascular diseases. The subcohort analysis of brain aging biomarkers corroborated the findings for ""central obesity,"" ""muscle strength,"" and ""arm-dominant fat distribution"" patterns.<h4>Discussion</h4>Our analyses demonstrated robust associations of body composition patterns featured by ""central obesity,"" ""muscle strength,"" and ""arm-dominant fat distribution"" with both neurodegenerative diseases and brain aging, which were partially mediated by CVDs. These findings underscore the potential of improving body composition and early CVD management in mitigating risk of neurodegenerative diseases.",,doi:https://doi.org/10.1212/WNL.0000000000209659; html:https://europepmc.org/articles/PMC11314951; pdf:https://europepmc.org/articles/PMC11314951?pdf=render
-36901540,https://doi.org/10.3390/ijerph20054534,Socioeconomic Background and Self-Reported Sleep Quality in Older Adults during the COVID-19 Pandemic: An Analysis of the English Longitudinal Study of Ageing (ELSA).,"Collinge AN, Bath PA, Bath PA.",,International journal of environmental research and public health,2023,2023-03-03,Y,Mental health; Health Promotion; Wellness; Physical Health; Health Disparities; Health Behaviors; Older Adults; Sleep Quality; Socioeconomic Background; Covid-19,,,"The COVID-19 pandemic negatively impacted sleep quality. However, research regarding older adults' sleep quality during the pandemic has been limited. This study examined the association between socioeconomic background (SEB) and older adults' sleep quality during the COVID-19 pandemic. Data on 7040 adults aged ≥50 were acquired from a COVID-19 sub-study of the English Longitudinal Study of Ageing (ELSA). SEB was operationalized using educational attainment, previous financial situation, and concern about the future financial situation. Sociodemographic, mental health, physical health, and health behavior variables were included as covariates. Chi-squared tests and binary logistic regression were used to examine associations between SEB and sleep quality. Lower educational attainment and greater financial hardship and concerns were associated with poor sleep quality. The relationship between educational attainment and sleep quality was explained by the financial variables, while the relationship between previous financial difficulties and sleep quality was explained by physical health and health behavior variables. Greater financial concerns about the future, poor mental health, and poor physical health were independent risk factors for poor sleep quality in older adults during the pandemic. Healthcare professionals and service providers should consider these issues when supporting older patients with sleep problems and in promoting health and wellness.",,pdf:https://www.mdpi.com/1660-4601/20/5/4534/pdf?version=1677842613; doi:https://doi.org/10.3390/ijerph20054534; html:https://europepmc.org/articles/PMC10001974; pdf:https://europepmc.org/articles/PMC10001974?pdf=render
 36503414,https://doi.org/10.1186/s12879-022-07856-8,"COVID-19 vaccination in pregnancy: views and vaccination uptake rates in pregnancy, a mixed methods analysis from SAIL and the Born-In-Wales Birth Cohort.","Mhereeg M, Jones H, Kennedy J, Seaborne M, Parker M, Kennedy N, Beeson S, Akbari A, Zuccolo L, Davies A, Brophy S.",,BMC infectious diseases,2022,2022-12-12,Y,Pregnancy; Vaccine Uptake; Vaccine Hesitancy; Sail; Covid-19 Vaccination,,,"<h4>Background</h4>Vaccine hesitancy amongst pregnant women has been found to be a concern during past epidemics. This study aimed to (1) estimate COVID-19 vaccination rates among pregnant women in Wales and their association with age, ethnicity, and area of deprivation, using electronic health record (EHR) data linkage, and (2) explore pregnant women's views on receiving the COVID-19 vaccine during pregnancy using data from a survey recruiting via social media (Facebook, Twitter), through midwives, and posters in hospitals (Born-In-Wales Cohort).<h4>Methods</h4>This was a mixed-methods study utilising routinely collected linked data from the Secure Anonymised Information Linkage (SAIL) Databank (Objective 1) and the Born-In-Wales Birth Cohort participants (Objective 2). Pregnant women were identified from 13th April 2021 to 31st December 2021. Survival analysis was utilised to examine and compare the length of time to vaccination uptake in pregnancy, and variation in uptake by; age, ethnic group, and deprivation area was examined using hazard ratios (HR) from Cox regression. Survey respondents were women who had a baby during the COVID-19 pandemic or were pregnant between 1st November 2021 and 24th March 2022 and participating in Born-In-Wales. Codebook thematic analysis was used to generate themes from an open-ended question on the survey.<h4>Results</h4>Population-level data linkage (objective 1): Within the population cohort, 8203 (32.7%) received at least one dose of the COVID-19 vaccine during pregnancy, 8572 (34.1%) remained unvaccinated throughout the follow-up period, and 8336 (33.2%) received the vaccine postpartum. Younger women (< 30 years) were less likely to have the vaccine, and those living in areas of high deprivation were also less likely to have the vaccine (HR = 0.88, 95% CI 0.82 to 0.95). Asian and Other ethnic groups were 1.12 and 1.18 times more likely to have the vaccine in pregnancy compared with White women (HR = 1.12, 95% CI 1.00 to 1.25) and (HR = 1.18, 95% CI 1.03 to 1.37) respectively. Survey responses (objective 2): 207 (69%) of participants stated that they would be happy to have the vaccine during pregnancy. The remaining 94 (31%) indicated they would not have the vaccine during pregnancy. Reasons for having the vaccine included protecting self and baby, perceived risk level, and receipt of sufficient evidence and advice. Reasons for vaccine refusal included lack of research about long-term outcomes for the baby, anxiety about vaccines, inconsistent advice/information, and preference to wait until after the pregnancy.<h4>Conclusion</h4>Potentially only 1 in 3 pregnant women would have the COVID-19 vaccine during pregnancy, even though 2 in 3 reported they would have the vaccination, thus it is critical to develop tailored strategies to increase its acceptance rate and decrease vaccine hesitancy. A targeted approach to vaccinations may be required for groups such as younger people and those living in higher deprivation areas.",,pdf:https://bmcinfectdis.biomedcentral.com/counter/pdf/10.1186/s12879-022-07856-8; doi:https://doi.org/10.1186/s12879-022-07856-8; html:https://europepmc.org/articles/PMC9742024; pdf:https://europepmc.org/articles/PMC9742024?pdf=render
-38251486,https://doi.org/10.1016/s2665-9913(23)00206-0,"Gout incidence and management during the COVID-19 pandemic in England, UK: a nationwide observational study using OpenSAFELY.","Russell MD, Massey J, Roddy E, MacKenna B, Bacon S, Goldacre B, Andrews CD, Hickman G, Mehrkar A, Mahto A, Rutherford AI, Patel S, Adas MA, Alveyn E, Nagra D, Bechman K, Ledingham JM, Hudson J, Norton S, Cope AP, Galloway JB.",,The Lancet. Rheumatology,2023,2023-08-31,Y,,,,"<h4>Background</h4>Gout is the most prevalent inflammatory arthritis, yet one of the worst managed. Our objective was to assess how the COVID-19 pandemic impacted incidence and quality of care for people with gout in England, UK.<h4>Methods</h4>With the approval of National Health Service England, we did a population-level cohort study using primary care and hospital electronic health record data for 17·9 million adults registered with general practices using TPP health record software, via the OpenSAFELY platform. The study period was from March 1, 2015, to Feb 28, 2023. Individuals aged 18-110 years were defined as having incident gout if they were assigned index diagnostic codes for gout, were registered with TPP practices in England for at least 12 months before diagnosis, did not receive prescriptions for urate-lowering therapy more than 30 days before diagnosis, and had not been admitted to hospital or attended an emergency department for gout flares more than 30 days before diagnosis. Outcomes assessed were incidence and prevalence of people with recorded gout diagnoses, incidence of gout hospitalisations, initiation of urate-lowering therapy, and attainment of serum urate targets (≤360 μmol/L).<h4>Findings</h4>From a reference population of 17 865 145 adults, 246 695 individuals were diagnosed with incident gout. The mean age of individuals with incident gout was 61·3 years (SD 16·2). 66 265 (26·9%) of 246 695 individuals were female, 180 430 (73·1%) were male, and 189 035 (90·9%) of 208 050 individuals with available ethnicity data were White. Incident gout diagnoses decreased by 30·9% in the year beginning March, 2020, compared with the preceding year (1·23 diagnoses vs 1·78 diagnoses per 1000 adults). Gout prevalence was 3·07% in 2015-16, and 3·21% in 2022-23. Gout hospitalisations decreased by 30·1% in the year commencing March, 2020, compared with the preceding year (9·6 admissions vs 13·7 admissions per 100 000 adults). Of 228 095 people with incident gout and available follow-up, 66 560 (29·2%) were prescribed urate-lowering therapy within 6 months. Of 65 305 individuals who initiated urate-lowering therapy with available follow-up, 16 790 (25·7%) attained a serum urate concentration of 360 μmol/L or less within 6 months of urate-lowering therapy initiation. In interrupted time-series analyses, urate-lowering therapy prescribing improved modestly during the pandemic, compared with pre-pandemic, whereas urate target attainment was similar.<h4>Interpretation</h4>Using gout as an exemplar disease, we showed the complexity of how health care was impacted during the COVID-19 pandemic. We observed a reduction in gout diagnoses but no effect on treatment metrics. We showed how country-wide, routinely collected data can be used to map disease epidemiology and monitor care quality.<h4>Funding</h4>None.",,pdf:http://www.thelancet.com/article/S2665991323002060/pdf; doi:https://doi.org/10.1016/S2665-9913(23)00206-0; html:https://europepmc.org/articles/PMC7616140; pdf:https://europepmc.org/articles/PMC7616140?pdf=render
+36901540,https://doi.org/10.3390/ijerph20054534,Socioeconomic Background and Self-Reported Sleep Quality in Older Adults during the COVID-19 Pandemic: An Analysis of the English Longitudinal Study of Ageing (ELSA).,"Collinge AN, Bath PA, Bath PA.",,International journal of environmental research and public health,2023,2023-03-03,Y,Mental health; Health Promotion; Wellness; Physical Health; Health Disparities; Health Behaviors; Older Adults; Sleep Quality; Socioeconomic Background; Covid-19,,,"The COVID-19 pandemic negatively impacted sleep quality. However, research regarding older adults' sleep quality during the pandemic has been limited. This study examined the association between socioeconomic background (SEB) and older adults' sleep quality during the COVID-19 pandemic. Data on 7040 adults aged ≥50 were acquired from a COVID-19 sub-study of the English Longitudinal Study of Ageing (ELSA). SEB was operationalized using educational attainment, previous financial situation, and concern about the future financial situation. Sociodemographic, mental health, physical health, and health behavior variables were included as covariates. Chi-squared tests and binary logistic regression were used to examine associations between SEB and sleep quality. Lower educational attainment and greater financial hardship and concerns were associated with poor sleep quality. The relationship between educational attainment and sleep quality was explained by the financial variables, while the relationship between previous financial difficulties and sleep quality was explained by physical health and health behavior variables. Greater financial concerns about the future, poor mental health, and poor physical health were independent risk factors for poor sleep quality in older adults during the pandemic. Healthcare professionals and service providers should consider these issues when supporting older patients with sleep problems and in promoting health and wellness.",,pdf:https://www.mdpi.com/1660-4601/20/5/4534/pdf?version=1677842613; doi:https://doi.org/10.3390/ijerph20054534; html:https://europepmc.org/articles/PMC10001974; pdf:https://europepmc.org/articles/PMC10001974?pdf=render
 37935988,https://doi.org/10.1093/ije/dyad143,Independent relevance of adiposity measures to coronary heart disease risk among 0.5 million adults in UK Biobank.,"Trichia E, Malden DE, Jin D, Wright N, Taylor H, Karpe F, Sherliker P, Murgia F, Hopewell JC, Lacey B, Emberson J, Bennett D, Lewington S.",,International journal of epidemiology,2023,2023-12-01,Y,Genetics; Obesity; epidemiology; Coronary Heart Disease,,,"<h4>Background</h4>Evidence on body fat distribution shows opposing effects of waist circumference (WC) and hip circumference (HC) for coronary heart disease (CHD). We aimed to investigate the causality and the shape of such associations.<h4>Methods</h4>UK Biobank is a prospective cohort study of 0.5 million adults aged 40-69 years recruited between 2006 and 2010. Adjusted hazard ratios (HRs) for the associations of measured and genetically predicted body mass index (BMI), WC, HC and waist-to-hip ratio with incident CHD were obtained from Cox models. Mendelian randomization (MR) was used to assess causality. The analysis included 456 495 participants (26 225 first-ever CHD events) without prior CHD.<h4>Results</h4>All measures of adiposity demonstrated strong, positive and approximately log-linear associations with CHD risk over a median follow-up of 12.7 years. For HC, however, the association became inverse given the BMI and WC (HR per usual SD 0.95, 95% CI 0.93-0.97). Associations for BMI and WC remained independently positive after adjustment for other adiposity measures and were similar (1.14, 1.13-1.16 and 1.18, 1.15-1.20, respectively), with WC displaying stronger associations among women. Blood pressure, plasma lipids and dysglycaemia accounted for much of the observed excess risk. MR results were generally consistent with the observational, implying causality.<h4>Conclusions</h4>Body fat distribution measures displayed similar associations with CHD risk as BMI except for HC, which was inversely associated with CHD risk (given WC and BMI). These findings suggest that different measures of body fat distribution likely influence CHD risk through both overlapping and independent mechanisms.",,pdf:https://academic.oup.com/ije/advance-article-pdf/doi/10.1093/ije/dyad143/52829486/dyad143.pdf; doi:https://doi.org/10.1093/ije/dyad143; html:https://europepmc.org/articles/PMC10749766; pdf:https://europepmc.org/articles/PMC10749766?pdf=render
 36272418,https://doi.org/10.1093/ije/dyac199,"Waning of first- and second-dose ChAdOx1 and BNT162b2 COVID-19 vaccinations: a pooled target trial study of 12.9 million individuals in England, Northern Ireland, Scotland and Wales.","Kerr S, Bedston S, Bradley DT, Joy M, Lowthian E, Mulholland RM, Akbari A, Hobbs FDR, Katikireddi SV, de Lusignan S, Rudan I, Torabi F, Tsang RSM, Lyons RA, Robertson C, Sheikh A.",,International journal of epidemiology,2023,2023-02-01,Y,Vaccine Effectiveness; Vaccine Waning; Covid-19,,,"<h4>Background</h4>Several SARS-CoV-2 vaccines have been shown to provide protection against COVID-19 hospitalization and death. However, some evidence suggests that notable waning in effectiveness against these outcomes occurs within months of vaccination. We undertook a pooled analysis across the four nations of the UK to investigate waning in vaccine effectiveness (VE) and relative vaccine effectiveness (rVE) against severe COVID-19 outcomes.<h4>Methods</h4>We carried out a target trial design for first/second doses of ChAdOx1(Oxford-AstraZeneca) and BNT162b2 (Pfizer-BioNTech) with a composite outcome of COVID-19 hospitalization or death over the period 8 December 2020 to 30 June 2021. Exposure groups were matched by age, local authority area and propensity for vaccination. We pooled event counts across the four UK nations.<h4>Results</h4>For Doses 1 and 2 of ChAdOx1 and Dose 1 of BNT162b2, VE/rVE reached zero by approximately Days 60-80 and then went negative. By Day 70, VE/rVE was -25% (95% CI: -80 to 14) and 10% (95% CI: -32 to 39) for Doses 1 and 2 of ChAdOx1, respectively, and 42% (95% CI: 9 to 64) and 53% (95% CI: 26 to 70) for Doses 1 and 2 of BNT162b2, respectively. rVE for Dose 2 of BNT162b2 remained above zero throughout and reached 46% (95% CI: 13 to 67) after 98 days of follow-up.<h4>Conclusions</h4>We found strong evidence of waning in VE/rVE for Doses 1 and 2 of ChAdOx1, as well as Dose 1 of BNT162b2. This evidence may be used to inform policies on timings of additional doses of vaccine.",,pdf:https://academic.oup.com/ije/article-pdf/52/1/22/49127317/dyac199.pdf; doi:https://doi.org/10.1093/ije/dyac199; html:https://europepmc.org/articles/PMC9620314; pdf:https://europepmc.org/articles/PMC9620314?pdf=render
 35239462,https://doi.org/10.1080/21645515.2022.2031774,COVID-19 vaccine uptake and effectiveness in adults aged 50 years and older in Wales UK: a 1.2m population data-linkage cohort approach.,"Perry M, Gravenor MB, Cottrell S, Bedston S, Roberts R, Williams C, Salmon J, Lyons J, Akbari A, Lyons RA, Torabi F, Griffiths LJ.",,Human vaccines & immunotherapeutics,2022,2022-03-03,Y,Immunization; Adult; Vaccination; Effectiveness; Wales; Sars-cov-2; Covid-19 Vaccines,,,"Vaccination programs against COVID-19 vary globally with estimates of vaccine effectiveness (VE) affected by vaccine type, schedule, strain, outcome, and recipient characteristics. This study assessed VE of BNT162b2 and ChAdOx1 vaccines against PCR positive SARS-CoV-2 infection, hospital admission, and death among adults aged 50 years and older in Wales, UK during the period 7 December 2020 to 18 July 2021, when Alpha, followed by Delta, were the predominant variants. We used individual-level linked routinely collected data within the Secure Anonymized Information Linkage (SAIL) Databank. Data were available for 1,262,689 adults aged 50 years and over; coverage of one dose of any COVID-19 vaccine in this population was 92.6%, with coverage of two doses 90.4%. VE against PCR positive infection at 28-days or more post first dose of any COVID-19 vaccine was 16.0% (95%CI 9.6-22.0), and 42.0% (95%CI 36.5-47.1) seven or more days after a second dose. VE against hospital admission was higher at 72.9% (95%CI 63.6-79.8) 28 days or more post vaccination with one dose of any vaccine type, and 84.9% (95%CI 78.2-89.5) at 7 or more days post two doses. VE for one dose against death was estimated to be 80.9% (95%CI 72.1-86.9). VE against PCR positive infection and hospital admission was higher for BNT162b2 compared to ChAdOx1. In conclusion, vaccine uptake has been high among adults in Wales and VE estimates are encouraging, with two doses providing considerable protection against severe outcomes. Continued roll-out of the vaccination programme within Wales, and globally, is crucial in our fight against COVID-19.",,pdf:https://www.tandfonline.com/doi/pdf/10.1080/21645515.2022.2031774?needAccess=true; doi:https://doi.org/10.1080/21645515.2022.2031774; html:https://europepmc.org/articles/PMC8993055; pdf:https://europepmc.org/articles/PMC8993055?pdf=render
@@ -115,11 +115,11 @@ PMC11227019,https://doi.org/,Adoption of high-sensitivity cardiac troponin for r
 33836447,https://doi.org/10.1016/j.compbiomed.2021.104360,Towards similarity-based differential diagnostics for common diseases.,"Slater K, Karwath A, Williams JA, Russell S, Makepeace S, Carberry A, Hoehndorf R, Gkoutos GV.",,Computers in biology and medicine,2021,2021-04-01,Y,Differential diagnosis; Ontology; Semantic Web; Semantic Similarity; Mimic-iii,,,"Ontology-based phenotype profiles have been utilised for the purpose of differential diagnosis of rare genetic diseases, and for decision support in specific disease domains. Particularly, semantic similarity facilitates diagnostic hypothesis generation through comparison with disease phenotype profiles. However, the approach has not been applied for differential diagnosis of common diseases, or generalised clinical diagnostics from uncurated text-derived phenotypes. In this work, we describe the development of an approach for deriving patient phenotype profiles from clinical narrative text, and apply this to text associated with MIMIC-III patient visits. We then explore the use of semantic similarity with those text-derived phenotypes to classify primary patient diagnosis, comparing the use of patient-patient similarity and patient-disease similarity using phenotype-disease profiles previously mined from literature. We also consider a combined approach, in which literature-derived phenotypes are extended with the content of text-derived phenotypes we mined from 500 patients. The results reveal a powerful approach, showing that in one setting, uncurated text phenotypes can be used for differential diagnosis of common diseases, making use of information both inside and outside the setting. While the methods themselves should be explored for further optimisation, they could be applied to a variety of clinical tasks, such as differential diagnosis, cohort discovery, document and text classification, and outcome prediction.",,doi:https://doi.org/10.1016/j.compbiomed.2021.104360; doi:https://doi.org/10.1016/j.compbiomed.2021.104360; html:https://europepmc.org/articles/PMC8204262
 36958018,https://doi.org/10.1111/anae.16001,Postoperative mortality and complications in patients with and without pre-operative SARS-CoV-2 infection: a service evaluation of 24 million linked records using OpenSAFELY.,"McInerney CD, Kotzé A, Bacon S, Cutting JE, Fisher L, Goldacre B, Johnson OA, Kua J, McGuckin D, Mehrkar A, OpenSAFELY Collaborative, Moonesinghe SR.",,Anaesthesia,2023,2023-03-23,Y,"Public Health; Patient Safety; Surgical Procedures, Operative; Covid-19; Sars-cov-2",,,"Surgical decision-making after SARS-CoV-2 infection is influenced by the presence of comorbidity, infection severity and whether the surgical problem is time-sensitive. Contemporary surgical policy to delay surgery is informed by highly heterogeneous country-specific guidance. We evaluated surgical provision in England during the COVID-19 pandemic to assess real-world practice and whether deferral remains necessary. Using the OpenSAFELY platform, we adapted the COVIDSurg protocol for a service evaluation of surgical procedures that took place within the English NHS from 17 March 2018 to 17 March 2022. We assessed whether hospitals adhered to guidance not to operate on patients within 7 weeks of an indication of SARS-CoV-2 infection. Additional outcomes were postoperative all-cause mortality (30 days, 6 months) and complications (pulmonary, cardiac, cerebrovascular). The exposure was the interval between the most recent indication of SARS-CoV-2 infection and subsequent surgery. In any 6-month window, < 3% of surgical procedures were conducted within 7 weeks of an indication of SARS-CoV-2 infection. Mortality for surgery conducted within 2 weeks of a positive test in the era since widespread SARS-CoV-2 vaccine availability was 1.1%, declining to 0.3% by 4 weeks. Compared with the COVIDSurg study cohort, outcomes for patients in the English NHS cohort were better during the COVIDSurg data collection period and the pandemic era before vaccines became available. Clinicians within the English NHS followed national guidance by operating on very few patients within 7 weeks of a positive indication of SARS-CoV-2 infection. In England, surgical patients' overall risk following an indication of SARS-CoV-2 infection is lower than previously thought.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/anae.16001; doi:https://doi.org/10.1111/anae.16001; html:https://europepmc.org/articles/PMC7616145; pdf:https://europepmc.org/articles/PMC7616145?pdf=render
 37714668,https://doi.org/10.1136/bmjment-2023-300775,"Impact of the COVID-19 pandemic on antipsychotic prescribing in individuals with autism, dementia, learning disability, serious mental illness or living in a care home: a federated analysis of 59 million patients' primary care records in situ using OpenSAFELY.","Macdonald O, Green A, Walker A, Curtis H, Croker R, Brown A, Butler-Cole B, Andrews C, Massey J, Inglesby P, Morton C, Fisher L, Morley J, Mehrkar A, Bacon S, Davy S, Evans D, Dillingham I, Ward T, Hulme W, Bates C, Cockburn J, Parry J, Hester F, Harper S, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Parkes N, Wood I, Goldacre B, Mackenna B.",,BMJ mental health,2023,2023-09-01,Y,Impulse Control Disorders; Adult Psychiatry; Delirium & Cognitive Disorders; Covid-19,,,"<h4>Background</h4>The COVID-19 pandemic affected how care was delivered to vulnerable patients, such as those with dementia or learning disability.<h4>Objective</h4>To explore whether this affected antipsychotic prescribing in at-risk populations.<h4>Methods</h4>With the approval of NHS England, we completed a retrospective cohort study, using the OpenSAFELY platform to explore primary care data of 59 million patients. We identified patients in five at-risk groups: autism, dementia, learning disability, serious mental illness and care home residents. We calculated the monthly prevalence of antipsychotic prescribing in these groups, as well as the incidence of new prescriptions in each month.<h4>Findings</h4>The average monthly rate of antipsychotic prescribing increased in dementia from 82.75 patients prescribed an antipsychotic per 1000 patients (95% CI 82.30 to 83.19) in January-March 2019 to 90.1 (95% CI 89.68 to 90.60) in October-December 2021 and from 154.61 (95% CI 153.79 to 155.43) to 166.95 (95% CI 166.23 to 167.67) in care homes. There were notable spikes in the rate of new prescriptions issued to patients with dementia and in care homes. In learning disability and autism groups, the rate of prescribing per 1000 decreased from 122.97 (95% CI 122.29 to 123.66) to 119.29 (95% CI 118.68 to 119.91) and from 54.91 (95% CI 54.52 to 55.29) to 51.04 (95% CI 50.74 to 51.35), respectively.<h4>Conclusion and implications</h4>We observed a spike in antipsychotic prescribing in the dementia and care home groups, which correlated with lockdowns and was likely due to prescribing of antipsychotics for palliative care. We observed gradual increases in antipsychotic use in dementia and care home patients and decreases in their use in patients with learning disability or autism.",,pdf:https://mentalhealth.bmj.com/content/ebmental/26/1/e300775.full.pdf; doi:https://doi.org/10.1136/bmjment-2023-300775; html:https://europepmc.org/articles/PMC11146375; pdf:https://europepmc.org/articles/PMC11146375?pdf=render
+39277617,https://doi.org/10.1038/s41467-024-52452-w,Evaluating the cost-effectiveness of polygenic risk score-stratified screening for abdominal aortic aneurysm.,"Kelemen M, Danesh J, Di Angelantonio E, Inouye M, O'Sullivan J, Pennells L, Roychowdhury T, Sweeting MJ, Wood AM, Harrison S, Kim LG.",,Nature communications,2024,2024-09-14,Y,,,,"As the heritability of abdominal aortic aneurysm (AAA) is high and AAA partially shares genetic architecture with other cardiovascular diseases, genetic information could help inform AAA screening strategies. Exploiting pleiotropy and meta-analysing summary data from large studies, we construct a polygenic risk score (PRS) for AAA. Leveraging related traits improves PRS performance (R<sup>2</sup>) by 22.7%, relative to using AAA alone. Compared with the low PRS tertile, intermediate and high tertiles have hazard ratios for AAA of 2.13 (95%CI 1.61, 2.82) and 3.70 (95%CI 2.86, 4.80) respectively, adjusted for clinical risk factors. Using simulation modelling, we compare PRS- and smoking-stratified screening with inviting men at age 65 and not inviting women (current UK strategy). In a futuristic scenario where genomic information is available, our modelling suggests inviting male current smokers with high PRS earlier than 65 and screening female smokers with high/intermediate PRS at 65 and 70 respectively, may improve cost-effectiveness.",,doi:https://doi.org/10.1038/s41467-024-52452-w; html:https://europepmc.org/articles/PMC11401842; pdf:https://europepmc.org/articles/PMC11401842?pdf=render
 33993870,https://doi.org/10.1186/s12916-021-02000-w,Impact of COVID-19 lockdown on the incidence and mortality of acute exacerbations of chronic obstructive pulmonary disease: national interrupted time series analyses for Scotland and Wales.,"Alsallakh MA, Sivakumaran S, Kennedy S, Vasileiou E, Lyons RA, Robertson C, Sheikh A, Davies GA, EAVE II Collaborators.",,BMC medicine,2021,2021-05-17,Y,Acute Exacerbation Of Chronic Obstructive Pulmonary Disease; Covid-19 Lockdown,,,"<h4>Background</h4>The COVID-19 pandemic and ensuing national lockdowns have dramatically changed the healthcare landscape. The pandemic's impact on people with chronic obstructive pulmonary disease (COPD) remains poorly understood. We hypothesised that the UK-wide lockdown restrictions were associated with reductions in severe COPD exacerbations. We provide the first national level analyses of the impact of the COVID-19 pandemic and first lockdown on severe COPD exacerbations resulting in emergency hospital admissions and/or leading to death as well as those recorded in primary care or emergency departments.<h4>Methods</h4>Using data from Public Health Scotland and the Secure Anonymised Information Linkage Databank in Wales, we accessed weekly counts of emergency hospital admissions and deaths due to COPD over the first 30 weeks of 2020 and compared these to the national averages over the preceding 5 years. For both Scotland and Wales, we undertook interrupted time-series analyses to model the impact of instigating lockdown on these outcomes. Using fixed-effect meta-analysis, we derived pooled estimates of the overall changes in trends across the two nations.<h4>Results</h4>Lockdown was associated with 48% pooled reduction in emergency admissions for COPD in both countries (incidence rate ratio, IRR 0.52, 95% CI 0.46 to 0.58), relative to the 5-year averages. There was no statistically significant change in deaths due to COPD (pooled IRR 1.08, 95% CI 0.87 to 1.33). In Wales, lockdown was associated with 39% reduction in primary care consultations for acute exacerbation of COPD (IRR 0.61, 95% CI 0.52 to 0.71) and 46% reduction in COPD-related emergency department attendances (IRR 0.54, 95% CI 0.36 to 0.81).<h4>Conclusions</h4>The UK-wide lockdown was associated with the most substantial reductions in COPD exacerbations ever seen across Scotland and Wales, with no corresponding increase in COPD deaths. This may have resulted from reduced transmission of respiratory infections, reduced exposure to outdoor air pollution and/or improved COPD self-management.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-021-02000-w; doi:https://doi.org/10.1186/s12916-021-02000-w; html:https://europepmc.org/articles/PMC8126470; pdf:https://europepmc.org/articles/PMC8126470?pdf=render
 38549123,https://doi.org/10.1186/s12911-024-02487-2,A novel generative adversarial networks modelling for the class imbalance problem in high dimensional omics data.,"Cusworth S, Gkoutos GV, Acharjee A.",,BMC medical informatics and decision making,2024,2024-03-28,Y,Gan; Multiomics; Synthetic Data; Class Imbalance,,,"Class imbalance remains a large problem in high-throughput omics analyses, causing bias towards the over-represented class when training machine learning-based classifiers. Oversampling is a common method used to balance classes, allowing for better generalization of the training data. More naive approaches can introduce other biases into the data, being especially sensitive to inaccuracies in the training data, a problem considering the characteristically noisy data obtained in healthcare. This is especially a problem with high-dimensional data. A generative adversarial network-based method is proposed for creating synthetic samples from small, high-dimensional data, to improve upon other more naive generative approaches. The method was compared with 'synthetic minority over-sampling technique' (SMOTE) and 'random oversampling' (RO). Generative methods were validated by training classifiers on the balanced data.",,pdf:https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-024-02487-2; doi:https://doi.org/10.1186/s12911-024-02487-2; html:https://europepmc.org/articles/PMC10979623; pdf:https://europepmc.org/articles/PMC10979623?pdf=render
-39015764,https://doi.org/10.1093/braincomms/fcae220,"Head motion in the UK Biobank imaging subsample: longitudinal stability, associations with psychological and physical health, and risk of incomplete data.","Ward J, Cox SR, Quinn T, Lyall LM, Strawbridge RJ, Russell E, Pell JP, Stewart W, Cullen B, Whalley H, Lyall DM.",,Brain communications,2024,2024-07-02,Y,Motion; Imaging; Bias; epidemiology; Uk Biobank,,,"Participant motion in brain magnetic resonance imaging is associated with processing problems including potentially non-useable/incomplete data. This has implications for representativeness in research. Few large studies have investigated predictors of increased motion in the first instance. We exploratively tested for association between multiple psychological and physical health traits with concurrent motion during T<sub>1</sub> structural, diffusion, average resting-state and task functional magnetic resonance imaging in <i>N</i> = 52 951 UK Biobank imaging subsample participants. These traits included history of cardiometabolic, inflammatory, neurological and psychiatric conditions, as well as concurrent cognitive test scores and anthropometric traits. We tested for stability in motion in participants with longitudinal imaging data (<i>n</i> = 5305, average 2.64 years later). All functional and T<sub>1</sub> structural motion variables were significantly intercorrelated (Pearson <i>r</i> range 0.3-0.8, all <i>P</i> < 0.001). Diffusion motion variables showed weaker correlations around <i>r</i> = 0.1. Most physical and psychological phenotypes showed significant association with at least one measure of increased motion including specifically in participants with complete useable data (highest β = 0.66 for diabetes versus resting-state functional magnetic resonance imaging motion). Poorer values in most health traits predicted lower odds of complete imaging data, with the largest association for history of traumatic brain injury (odds ratio = 0.720, 95% confidence interval = 0.562 to 0.923, <i>P</i> = 0.009). Worse psychological and physical health are consistent predictors of increased average functional and structural motion during brain imaging and associated with lower odds of complete data. Average motion levels were largely consistent across modalities and longitudinally in participants with repeat data. Together, these findings have implications for representativeness and bias in imaging studies of generally healthy population samples.",,doi:https://doi.org/10.1093/braincomms/fcae220; html:https://europepmc.org/articles/PMC11249925; pdf:https://europepmc.org/articles/PMC11249925?pdf=render
-39277617,https://doi.org/10.1038/s41467-024-52452-w,Evaluating the cost-effectiveness of polygenic risk score-stratified screening for abdominal aortic aneurysm.,"Kelemen M, Danesh J, Di Angelantonio E, Inouye M, O'Sullivan J, Pennells L, Roychowdhury T, Sweeting MJ, Wood AM, Harrison S, Kim LG.",,Nature communications,2024,2024-09-14,Y,,,,"As the heritability of abdominal aortic aneurysm (AAA) is high and AAA partially shares genetic architecture with other cardiovascular diseases, genetic information could help inform AAA screening strategies. Exploiting pleiotropy and meta-analysing summary data from large studies, we construct a polygenic risk score (PRS) for AAA. Leveraging related traits improves PRS performance (R<sup>2</sup>) by 22.7%, relative to using AAA alone. Compared with the low PRS tertile, intermediate and high tertiles have hazard ratios for AAA of 2.13 (95%CI 1.61, 2.82) and 3.70 (95%CI 2.86, 4.80) respectively, adjusted for clinical risk factors. Using simulation modelling, we compare PRS- and smoking-stratified screening with inviting men at age 65 and not inviting women (current UK strategy). In a futuristic scenario where genomic information is available, our modelling suggests inviting male current smokers with high PRS earlier than 65 and screening female smokers with high/intermediate PRS at 65 and 70 respectively, may improve cost-effectiveness.",,doi:https://doi.org/10.1038/s41467-024-52452-w; html:https://europepmc.org/articles/PMC11401842; pdf:https://europepmc.org/articles/PMC11401842?pdf=render
 37697235,https://doi.org/10.1186/s12879-023-08555-8,"COVID-19 vaccination in pregnancy: the impact of multimorbidity and smoking status on vaccine hesitancy, a cohort study of 25,111 women in Wales, UK.","Mhereeg M, Jones H, Kennedy J, Seaborne M, Parker M, Kennedy N, Akbari A, Zuccolo L, Azcoaga-Lorenzo A, Davies A, Nirantharakumar K, Brophy S.",,BMC infectious diseases,2023,2023-09-11,Y,Pregnancy; Smoking Status; Vaccine Uptake; Multimorbidity; Vaccine Hesitancy; Sail Databank; Covid-19 Vaccination,,,"<h4>Background</h4>Multimorbidity, smoking status, and pregnancy are identified as three risk factors associated with more severe outcomes following a SARS-CoV-2 infection, thus vaccination uptake is crucial for pregnant women living with multimorbidity and a history of smoking. This study aimed to examine the impact of multimorbidity, smoking status, and demographics (age, ethnic group, area of deprivation) on vaccine hesitancy among pregnant women in Wales using electronic health records (EHR) linkage.<h4>Methods</h4>This cohort study utilised routinely collected, individual-level, anonymised population-scale linked data within the Secure Anonymised Information Linkage (SAIL) Databank. Pregnant women were identified from 13th April 2021 to 31st December 2021. Survival analysis was employed to examine and compare the length of time to vaccination uptake in pregnancy by considering multimorbidity, smoking status, as well as depression, diabetes, asthma, and cardiovascular conditions independently. The study also assessed the variation in uptake by multimorbidity, smoking status, and demographics, both jointly and separately for the independent conditions, using hazard ratios (HR) derived from the Cox regression model.<h4>Results</h4>Within the population cohort, 8,203 (32.7%) received at least one dose of the COVID-19 vaccine during pregnancy, with 8,572 (34.1%) remaining unvaccinated throughout the follow-up period, and 8,336 (33.2%) receiving the vaccine postpartum. Women aged 30 years or older were more likely to have the vaccine in pregnancy. Those who had depression were slightly but significantly more likely to have the vaccine compared to those without depression (HR = 1.08, 95% CI 1.03 to 1.14, p = 0.002). Women living with multimorbidity were 1.12 times more likely to have the vaccine compared to those living without multimorbidity (HR = 1.12, 95% CI 1.04 to 1.19, p = 0.001). Vaccine uptakes were significantly lower among both current smokers and former smokers compared to never smokers (HR = 0.87, 95% CI 0.81 to 0.94, p < 0.001 and HR = 0.92, 95% CI 0.85 to 0.98, p = 0.015 respectively). Uptake was also lower among those living in the most deprived areas compared to those living in the most affluent areas (HR = 0.89, 95% CI 0.83 to 0.96, p = 0.002).<h4>Conclusion</h4>Younger women, living without multimorbidity, current and former smokers, and those living in the more deprived areas are less likely to have the vaccine, thus, a targeted approach to vaccinations may be required for these groups. Pregnant individuals living with multimorbidity exhibit a slight but statistically significant reduction in vaccine hesitancy towards COVID-19 during pregnancy.",,pdf:https://bmcinfectdis.biomedcentral.com/counter/pdf/10.1186/s12879-023-08555-8; doi:https://doi.org/10.1186/s12879-023-08555-8; html:https://europepmc.org/articles/PMC10496238; pdf:https://europepmc.org/articles/PMC10496238?pdf=render
+39015764,https://doi.org/10.1093/braincomms/fcae220,"Head motion in the UK Biobank imaging subsample: longitudinal stability, associations with psychological and physical health, and risk of incomplete data.","Ward J, Cox SR, Quinn T, Lyall LM, Strawbridge RJ, Russell E, Pell JP, Stewart W, Cullen B, Whalley H, Lyall DM.",,Brain communications,2024,2024-07-02,Y,Motion; Imaging; Bias; epidemiology; Uk Biobank,,,"Participant motion in brain magnetic resonance imaging is associated with processing problems including potentially non-useable/incomplete data. This has implications for representativeness in research. Few large studies have investigated predictors of increased motion in the first instance. We exploratively tested for association between multiple psychological and physical health traits with concurrent motion during T<sub>1</sub> structural, diffusion, average resting-state and task functional magnetic resonance imaging in <i>N</i> = 52 951 UK Biobank imaging subsample participants. These traits included history of cardiometabolic, inflammatory, neurological and psychiatric conditions, as well as concurrent cognitive test scores and anthropometric traits. We tested for stability in motion in participants with longitudinal imaging data (<i>n</i> = 5305, average 2.64 years later). All functional and T<sub>1</sub> structural motion variables were significantly intercorrelated (Pearson <i>r</i> range 0.3-0.8, all <i>P</i> < 0.001). Diffusion motion variables showed weaker correlations around <i>r</i> = 0.1. Most physical and psychological phenotypes showed significant association with at least one measure of increased motion including specifically in participants with complete useable data (highest β = 0.66 for diabetes versus resting-state functional magnetic resonance imaging motion). Poorer values in most health traits predicted lower odds of complete imaging data, with the largest association for history of traumatic brain injury (odds ratio = 0.720, 95% confidence interval = 0.562 to 0.923, <i>P</i> = 0.009). Worse psychological and physical health are consistent predictors of increased average functional and structural motion during brain imaging and associated with lower odds of complete data. Average motion levels were largely consistent across modalities and longitudinally in participants with repeat data. Together, these findings have implications for representativeness and bias in imaging studies of generally healthy population samples.",,doi:https://doi.org/10.1093/braincomms/fcae220; html:https://europepmc.org/articles/PMC11249925; pdf:https://europepmc.org/articles/PMC11249925?pdf=render
 38112489,https://doi.org/10.1097/hep.0000000000000707,Combined use of the CLivD score and FIB-4 for prediction of liver-related outcomes in the population.,"Åberg F, Asteljoki J, Männistö V, Luukkonen PK.",,"Hepatology (Baltimore, Md.)",2024,2023-12-19,Y,,,,"<h4>Background and aims</h4>A need exists for effective and practical tools to identify individuals at increased risk of liver-related outcomes (LROs) within the general population.<h4>Approach and results</h4>We externally validated the chronic liver disease (CLivD) score for LROs in the UK Biobank cohort. We also investigated the sequential combined use of CLivD and fibrosis-4 (FIB-4) scores. Our analysis included 369,832 adults without baseline liver disease and with available data for CLivD and FIB-4 computation. LROs reflecting compensated or decompensated liver cirrhosis or HCC were ascertained through linkages with electronic health care registries. Discriminatory performance and cumulative incidence were evaluated with competing-risk methodologies. Over a 10-year follow-up, time-dependent AUC values for LRO prediction were 0.80 for CLivD lab (including gamma-glutamyltransferase), 0.72 for CLivD non-lab (excluding laboratory values), and 0.75 for FIB-4. CLivD lab demonstrated AUC values exceeding 0.85 for liver-related death and severe alcohol-associated liver outcomes. The predictive performance of FIB-4 increased with rising CLivD scores; 10-year FIB-4 AUC values ranged from 0.60 within the minimal-risk CLivD subgroup to 0.81 within the high-risk CLivD subgroup. Moreover, in the minimal-risk CLivD subgroup, the cumulative incidence of LRO varied from 0.05% to 0.3% across low-to-high FIB-4 strata. In contrast, within the high-risk CLivD subgroup, the corresponding incidence ranged from 1.7% to 21.1% (up to 33% in individuals with FIB-4 >3.25).<h4>Conclusions</h4>The CLivD score is a valid tool for LRO risk assessment and improves the predictive performance of FIB-4. The combined use of CLivD and FIB-4 identified a subgroup where 1 in 3 individuals developed LROs within 10 years.",,doi:https://doi.org/10.1097/HEP.0000000000000707; html:https://europepmc.org/articles/PMC11191041; pdf:https://europepmc.org/articles/PMC11191041?pdf=render
 39289682,https://doi.org/10.1186/s12916-024-03632-4,Diurnal timing of physical activity and risk of colorectal cancer in the UK Biobank.,"Stein MJ, Baurecht H, Bohmann P, Fervers B, Fontvieille E, Freisling H, Friedenreich CM, Konzok J, Peruchet-Noray L, Sedlmeier AM, Leitzmann MF, Weber A.",,BMC medicine,2024,2024-09-18,Y,Colorectal Cancer; Uk Biobank; Physical Activity Patterns; Raw Accelerometry,,,"<h4>Background</h4>Physical activity reduces colorectal cancer risk, yet the diurnal timing of physical activity in colorectal cancer etiology remains unclear.<h4>Methods</h4>This study used 24-h accelerometry time series from UK Biobank participants aged 42 to 79 years to derive circadian physical activity patterns using functional principal component analysis. Multivariable Cox proportional hazard models were used to examine associations with colorectal cancer risk.<h4>Results</h4>Among 86,252 participants (56% women), 529 colorectal cancer cases occurred during a median 5.3-year follow-up. We identified four physical activity patterns that explained almost 100% of the data variability during the day. A pattern of continuous day-long activity was inversely associated with colorectal cancer risk (hazard ratio (HR) = 0.94, 95% confidence interval (CI) = 0.89-0.99). A second pattern of late-day activity was suggestively inversely related to risk (HR = 0.93, 95% CI = 0.85-1.02). A third pattern of early- plus late-day activity was associated with decreased risk (HR = 0.89, 95% CI = 0.80-0.99). A fourth pattern of mid-day plus night-time activity showed no relation (HR = 1.02, 95% CI = 0.88-1.19). Our results were consistent across various sensitivity analyses, including the restriction to never smokers, the exclusion of the first 2 years of follow-up, and the adjustment for shift work.<h4>Conclusions</h4>A pattern of early- plus late-day activity is related to reduced colorectal cancer risk, beyond the benefits of overall activity. Further research is needed to confirm the role of activity timing in colorectal cancer prevention.",,doi:https://doi.org/10.1186/s12916-024-03632-4; doi:https://doi.org/10.1186/s12916-024-03632-4; html:https://europepmc.org/articles/PMC11409794; pdf:https://europepmc.org/articles/PMC11409794?pdf=render
 38515138,https://doi.org/10.1186/s13023-024-03124-x,Cardiovascular disease in Alpha 1 antitrypsin deficiency: an observational study assessing the role of neutrophil proteinase activity and the suitability of validated screening tools.,"Sapey E, Crowley LE, Edgar RG, Griffiths D, Samanta S, Crisford H, Bolton CE, Hurst JR, Stockley RA.",,Orphanet journal of rare diseases,2024,2024-03-21,Y,Neutrophils; Cardiovascular disease; Emphysema; Arterial stiffness; risk assessment; chronic obstructive pulmonary disease; Alpha 1 Anti-trypsin Deficiency,,,"<h4>Background</h4>Alpha 1 Antitrypsin Deficiency (AATD) is a rare, inherited lung disease which shares features with Chronic Obstructive Pulmonary Disease (COPD) but has a greater burden of proteinase related tissue damage. These proteinases are associated with cardiovascular disease (CVD) in the general population. It is unclear whether patients with AATD have a greater risk of CVD compared to usual COPD, how best to screen for this, and whether neutrophil proteinases are implicated in AATD-associated CVD. This study had three aims. To compare CVD risk in never-augmented AATD patients to non-AATD COPD and healthy controls (HC). To assess relationships between CVD risk and lung physiology. To determine if neutrophil proteinase activity was associated with CVD risk in AATD. Cardiovascular risk was assessed by QRISK2® score and aortic stiffness measurements using carotid-femoral (aortic) pulse wave velocity (aPWV). Medical history, computed tomography scans and post-bronchodilator lung function parameters were reviewed. Systemic proteinase 3 activity was measured. Patients were followed for 4 years, to assess CVD development.<h4>Results</h4>228 patients with AATD, 50 with non-AATD COPD and 51 healthy controls were recruited. In all COPD and HC participants, QRISK2® and aPWV gave concordant results (with both measures either high or in the normal range). This was not the case in AATD. Once aPWV was adjusted for age and smoking history, aPWV was highest and QRISK2® lowest in AATD patients compared to the COPD or HC participants. Higher aPWV was associated with impairments in lung physiology, the presence of emphysema on CT scan and proteinase 3 activity following adjustment for age, smoking status and traditional CVD risk factors (using QRISK2® scores) in AATD. There were no such relationships with QRISK2® in AATD. AATD patients with confirmed CVD at four-year follow up had a higher aPWV but not QRISK2® at baseline assessment.<h4>Conclusion</h4>aPWV measured CVD risk is elevated in AATD. This risk is not captured by QRISK2®. There is a relationship between aPWV, lung disease and proteinase-3 activity. Proteinase-driven breakdown of elastin fibres in large arteries and lungs is a putative mechanism and forms a potential therapeutic target for CVD in AATD.",,pdf:https://ojrd.biomedcentral.com/counter/pdf/10.1186/s13023-024-03124-x; doi:https://doi.org/10.1186/s13023-024-03124-x; html:https://europepmc.org/articles/PMC10956254; pdf:https://europepmc.org/articles/PMC10956254?pdf=render
@@ -149,16 +149,16 @@ PMC11227019,https://doi.org/,Adoption of high-sensitivity cardiac troponin for r
 38747160,https://doi.org/10.1111/acel.14195,Proteomic aging clock (PAC) predicts age-related outcomes in middle-aged and older adults.,"Kuo CL, Chen Z, Liu P, Pilling LC, Atkins JL, Fortinsky RH, Kuchel GA, Diniz BS.",,Aging cell,2024,2024-05-15,Y,Leukocyte Telomere Length; Phenoage; Accelerated Biological Aging; Uk Biobank Pharma Proteomics Project; Biological Age Deviation; Composite Aging Biomarkers; Bioage,,,"Beyond mere prognostication, optimal biomarkers of aging provide insights into qualitative and quantitative features of biological aging and might, therefore, offer useful information for the testing and, ultimately, clinical use of gerotherapeutics. We aimed to develop a proteomic aging clock (PAC) for all-cause mortality risk as a proxy of biological age. Data were from the UK Biobank Pharma Proteomics Project, including 53,021 participants aged between 39 and 70 years and 2923 plasma proteins assessed using the Olink Explore 3072 assay®. 10.9% of the participants died during a mean follow-up of 13.3 years, with the mean age at death of 70.1 years. The Spearman correlation between PAC proteomic age and chronological age was 0.77. PAC showed robust age-adjusted associations and predictions for all-cause mortality and the onset of various diseases in general and disease-free participants. The proteins associated with PAC proteomic age deviation were enriched in several processes related to the hallmarks of biological aging. Our results expand previous findings by showing that biological age acceleration, based on PAC, strongly predicts all-cause mortality and several incident disease outcomes. Particularly, it facilitates the evaluation of risk for multiple conditions in a disease-free population, thereby, contributing to the prevention of initial diseases, which vary among individuals and may subsequently lead to additional comorbidities.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/acel.14195; doi:https://doi.org/10.1111/acel.14195; html:https://europepmc.org/articles/PMC11320350; pdf:https://europepmc.org/articles/PMC11320350?pdf=render
 35909578,https://doi.org/10.23889/ijpds.v7i1.1717,"Health and household environment factors linked with early alcohol use in adolescence: a record-linked, data-driven, longitudinal cohort study.","Bandyopadhyay A, Brophy S, Akbari A, Demmler J, Kennedy J, Paranjothy S, Lyons RA, Moore S.",,International journal of population data science,2022,2022-07-07,Y,Alcohol; Adolescent; Cohort study; Data Linkage; Electronic Health Records (Ehrs),,,"<h4>Introduction</h4>Early alcohol use has significant association with poor health outcomes. Individual risk factors around early alcohol use have been identified, but a holistic, data-driven investigation into health and household environmental factors on early alcohol use is yet to be undertaken.<h4>Objectives</h4>This study aims to investigate the relationship between preceding health events, household exposures and early alcohol use during adolescence using a two-stage data-driven approach.<h4>Methods</h4>In stage one, a study population (N = 1,072) were derived from the Millennium Cohort Study (MCS) Wales (born between 2000-2002). MCS data were first linked with electronic-health records. Factors associated with early (<=eleven years old) alcohol use were identified using feature selection and stepwise logistic regression. In stage two, analogous risk factors from MCS were recreated for whole population (N = 59,231) of children (born between 1998-2002 in the Welsh Demographic Service Dataset) using routine data to predict the alcohol-related health events in hospital or GP records.<h4>Results</h4>Significant risk factors from stage two included poor maternal mental (adjusted odds ratio [aOR] = 1.31) and physical health (aOR = 1.25), living with someone with alcohol-related problem (aOR = 2.16), single-adult household (aOR = 1.45), ever in deprivation (aOR = 1.66), child's high hyperactivity (aOR = 3.57), and conduct disorder (aOR = 3.26). Children with health events, whose health needs are supported (e.g., are taken to the doctor), are at lower risk of early alcohol use.<h4>Conclusion</h4>Health events of the family members and the child can act as modifiable exposures and may therefore inform the development of prevention initiatives. Families with known alcohol problems, living in deprivation, experiencing child behavioural problems and those who are not taken to the doctor are at higher risk of early drinking behaviour and should be prioritised for early years support and interventions to target problem drinking in young people.",,pdf:https://ijpds.org/article/download/1717/3510; doi:https://doi.org/10.23889/ijpds.v7i1.1717; html:https://europepmc.org/articles/PMC9284510; pdf:https://europepmc.org/articles/PMC9284510?pdf=render
 34706900,https://doi.org/10.1136/emermed-2021-211706,Comparative analysis of major incident triage tools in children: a UK population-based analysis.,"Vassallo J, Chernbumroong S, Malik N, Xu Y, Keene D, Gkoutos G, Lyttle MD, Smith J, in collaboration with PERUKI (Paediatric Emergency Research in the UK and Ireland).",,Emergency medicine journal : EMJ,2021,2021-10-27,Y,Planning; Paediatrics; Major Incident; Clinical Care; Triage; Major Incidents,,,"<h4>Introduction</h4>Triage is a key principle in the effective management of major incidents. There is currently a paucity of evidence to guide the triage of children. The aim of this study was to perform a comparative analysis of nine adult and paediatric triage tools, including the novel 'Sheffield Paediatric Triage Tool' (SPTT), assessing their ability in identifying patients needing life-saving interventions (LSIs).<h4>Methods</h4>A 10-year (2008-2017) retrospective database review of the Trauma Audit Research Network (TARN) Database for paediatric patients (<16 years) was performed. Primary outcome was identification of patients receiving one or more LSIs from a previously defined list. Secondary outcomes included mortality and prediction of Injury Severity Score (ISS) >15. Primary analysis was conducted on patients with complete prehospital physiological data with planned secondary analyses using first recorded data. Performance characteristics were evaluated using sensitivity, specificity, undertriage and overtriage.<h4>Results</h4>15 133 patients met TARN inclusion criteria. 4962 (32.8%) had complete prehospital physiological data and 8255 (54.5%) had complete first recorded physiological data. The majority of patients were male (69.5%), with a median age of 11.9 years. The overwhelming majority of patients (95.4%) sustained blunt trauma, yielding a median ISS of 9 and overall, 875 patients (17.6%) received at least one LSI. The SPTT demonstrated the greatest sensitivity of all triage tools at identifying need for LSI (92.2%) but was associated with the highest rate of overtriage (75.0%). Both the Paediatric Triage Tape (sensitivity 34.1%) and JumpSTART (sensitivity 45.0%) performed less well at identifying LSI. By contrast, the adult Modified Physiological Triage Tool-24 (MPTT-24) triage tool had the second highest sensitivity (80.8%) with tolerable rates of overtriage (70.2%).<h4>Conclusion</h4>The SPTT and MPTT-24 outperform existing paediatric triage tools at identifying those patients requiring LSIs. This may necessitate a change in recommended practice. Further work is needed to determine the optimum method of paediatric major incident triage, but consideration should be given to simplifying major incident triage by the use of one generic tool (the MPTT-24) for adults and children.",,pdf:https://emj.bmj.com/content/emermed/early/2022/04/27/emermed-2021-211706.full.pdf; doi:https://doi.org/10.1136/emermed-2021-211706; html:https://europepmc.org/articles/PMC9510399; pdf:https://europepmc.org/articles/PMC9510399?pdf=render
-35501391,https://doi.org/10.1038/s41416-022-01830-6,"Impact of the SARS-CoV-2 pandemic on female breast, colorectal and non-small cell lung cancer incidence, stage and healthcare pathway to diagnosis during 2020 in Wales, UK, using a national cancer clinical record system.","Greene G, Griffiths R, Han J, Akbari A, Jones M, Lyons J, Lyons RA, Rolles M, Torabi F, Warlow J, Morris ERA, Lawler M, Huws DW.",,British journal of cancer,2022,2022-05-02,Y,,,,"<h4>Background</h4>COVID-19 pandemic responses impacted behaviour and health services. We estimated the impact on incidence, stage and healthcare pathway to diagnosis for female breast, colorectal and non-small cell lung cancers at population level in Wales.<h4>Methods</h4>Cancer e-record and hospital admission data linkage identified adult cases, stage and healthcare pathway to diagnosis (population ~2.5 million). Using multivariate Poisson regressions, we compared 2019 and 2020 counts and estimated incidence rate ratios (IRR).<h4>Results</h4>Cases decreased 15.2% (n = -1011) overall. Female breast annual IRR was 0.81 (95% CI: 0.76-0.86, p < 0.001), colorectal 0.80 (95% CI: 0.79-0.81, p < 0.001) and non-small cell lung 0.91 (95% CI: 0.90-0.92, p < 0.001). Decreases were largest in 50-69 year olds for female breast and 80+ year olds for all cancers. Stage I female breast cancer declined 41.6%, but unknown stage increased 55.8%. Colorectal stages I-IV declined (range 26.6-29.9%), while unknown stage increased 803.6%. Colorectal Q2-2020 GP-urgent suspected cancer diagnoses decreased 50.0%, and 53.9% for non-small cell lung cancer. Annual screen-detected female breast and colorectal cancers fell 47.8% and 13.3%, respectively. Non-smal -cell lung cancer emergency presentation diagnoses increased 9.5% (Q2-2020) and 16.3% (Q3-2020).<h4>Conclusion</h4>Significantly fewer cases of three common cancers were diagnosed in 2020. Detrimental impacts on outcomes varied between cancers. Ongoing surveillance with health service optimisation will be needed to mitigate impacts.",,pdf:https://www.nature.com/articles/s41416-022-01830-6.pdf; doi:https://doi.org/10.1038/s41416-022-01830-6; html:https://europepmc.org/articles/PMC9060409; pdf:https://europepmc.org/articles/PMC9060409?pdf=render
 35609019,https://doi.org/10.1371/journal.pone.0267176,Population birth outcomes in 2020 and experiences of expectant mothers during the COVID-19 pandemic: A 'born in Wales' mixed methods study using routine data.,"Jones H, Seaborne M, Cowley L, Odd D, Paranjothy S, Akbari A, Brophy S.",,PloS one,2022,2022-05-24,Y,,,,"<h4>Background</h4>Pregnancy can be a stressful time and the COVID-19 pandemic has affected all aspects of life. This study aims to investigate the pandemic impact on pregnancy experience, rates of primary childhood immunisations and the differences in birth outcomes in during 2020 to those of previous years.<h4>Methods</h4>Self-reported pregnancy experience: 215 expectant mothers (aged 16+) in Wales completed an online survey about their experiences of pregnancy during the pandemic. The qualitative survey data was analysed using codebook thematic analysis. Population-level birth outcomes in Wales: Stillbirths, prematurity, birth weight and Caesarean section births before (2016-2019) and during (2020) the pandemic were compared using anonymised individual-level, population-scale routine data held in the Secure Anonymised Information Linkage (SAIL) Databank. Uptake of the first three scheduled primary childhood immunisations were compared between 2019 and 2020.<h4>Findings</h4>The pandemic had a negative impact on the mental health of 71% of survey respondents, who reported anxiety, stress and loneliness; this was associated with attending scans without their partner, giving birth alone, and minimal contact with midwives. There was no significant difference in annual outcomes including gestation and birth weight, stillbirths, and Caesarean sections for infants born in 2020 compared to 2016-2019. There was an increase in late term births (≥42 weeks gestation) during the first lockdown (OR: 1.28, p = 0.019) and a decrease in moderate to late preterm births (32-36 weeks gestation) during the second lockdown (OR: 0.74, p = 0.001). Fewer babies were born in 2020 (N = 29,031) compared to 2016-2019 (average N = 32,582). All babies received their immunisations in 2020, but there were minor delays in the timings of immunisations. Those due at 8-weeks were 8% less likely to be on time (within 28-days) and at 16-weeks, they were 19% less likely to be on time.<h4>Interpretation</h4>Whilst the pandemic had a negative impact on mothers' experiences of pregnancy. Population-level data suggests that this did not translate to adverse birth outcomes for babies born during the pandemic.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0267176&type=printable; doi:https://doi.org/10.1371/journal.pone.0267176; html:https://europepmc.org/articles/PMC9129046; pdf:https://europepmc.org/articles/PMC9129046?pdf=render
+35501391,https://doi.org/10.1038/s41416-022-01830-6,"Impact of the SARS-CoV-2 pandemic on female breast, colorectal and non-small cell lung cancer incidence, stage and healthcare pathway to diagnosis during 2020 in Wales, UK, using a national cancer clinical record system.","Greene G, Griffiths R, Han J, Akbari A, Jones M, Lyons J, Lyons RA, Rolles M, Torabi F, Warlow J, Morris ERA, Lawler M, Huws DW.",,British journal of cancer,2022,2022-05-02,Y,,,,"<h4>Background</h4>COVID-19 pandemic responses impacted behaviour and health services. We estimated the impact on incidence, stage and healthcare pathway to diagnosis for female breast, colorectal and non-small cell lung cancers at population level in Wales.<h4>Methods</h4>Cancer e-record and hospital admission data linkage identified adult cases, stage and healthcare pathway to diagnosis (population ~2.5 million). Using multivariate Poisson regressions, we compared 2019 and 2020 counts and estimated incidence rate ratios (IRR).<h4>Results</h4>Cases decreased 15.2% (n = -1011) overall. Female breast annual IRR was 0.81 (95% CI: 0.76-0.86, p < 0.001), colorectal 0.80 (95% CI: 0.79-0.81, p < 0.001) and non-small cell lung 0.91 (95% CI: 0.90-0.92, p < 0.001). Decreases were largest in 50-69 year olds for female breast and 80+ year olds for all cancers. Stage I female breast cancer declined 41.6%, but unknown stage increased 55.8%. Colorectal stages I-IV declined (range 26.6-29.9%), while unknown stage increased 803.6%. Colorectal Q2-2020 GP-urgent suspected cancer diagnoses decreased 50.0%, and 53.9% for non-small cell lung cancer. Annual screen-detected female breast and colorectal cancers fell 47.8% and 13.3%, respectively. Non-smal -cell lung cancer emergency presentation diagnoses increased 9.5% (Q2-2020) and 16.3% (Q3-2020).<h4>Conclusion</h4>Significantly fewer cases of three common cancers were diagnosed in 2020. Detrimental impacts on outcomes varied between cancers. Ongoing surveillance with health service optimisation will be needed to mitigate impacts.",,pdf:https://www.nature.com/articles/s41416-022-01830-6.pdf; doi:https://doi.org/10.1038/s41416-022-01830-6; html:https://europepmc.org/articles/PMC9060409; pdf:https://europepmc.org/articles/PMC9060409?pdf=render
 33045103,https://doi.org/10.1002/gps.5446,Socio-economic predictors of time to care home admission in people living with dementia in Wales: A routine data linkage study.,"Giebel C, Hollinghurst J, Akbari A, Schnier C, Wilkinson T, North L, Gabbay M, Rodgers S.",,International journal of geriatric psychiatry,2021,2020-10-19,Y,Dementia; Care Homes; Socio-economic Status; Health Inequalities; Routine Data,,,"<h4>Objectives</h4>Limited research has shown that people with dementia (PwD) from lower socio-economic backgrounds can face difficulties in accessing the right care at the right time. This study examined whether socio-economic status (SES) and rural versus urban living location are associated with the time between diagnosis and care home admission in PwD living in Wales, UK.<h4>Methods/design</h4>This study linked routine health data and an e-cohort of PwD who have been admitted into a care home between 2000 and 2018 living in Wales. Survival analysis explored the effects of SES, living location, living situation, and frailty on the time between diagnosis and care home admission.<h4>Results</h4>In 34,514 PwD, the average time between diagnosis and care home admission was 1.5 (±1.4) years. Cox regression analysis showed that increased age, living alone, frailty, and living in less disadvantaged neighbourhoods were associated with faster rate to care home admission. Living in rural regions predicted a slower rate until care home admission.<h4>Conclusions</h4>This is one of the first studies to show a link between socio-economic factors on time to care home admission in dementia. Future research needs to address variations in care needs between PwD from different socio-economic and geographical backgrounds.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/gps.5446; doi:https://doi.org/10.1002/gps.5446; html:https://europepmc.org/articles/PMC7984448; pdf:https://europepmc.org/articles/PMC7984448?pdf=render
 37227368,https://doi.org/10.1097/ede.0000000000001626,Evaluating Metformin Strategies for Cancer Prevention: A Target Trial Emulation Using Electronic Health Records.,"Dickerman BA, García-Albéniz X, Logan RW, Denaxas S, Hernán MA.",,"Epidemiology (Cambridge, Mass.)",2023,2023-05-23,N,,,,"<h4>Background</h4>Metformin users appear to have a substantially lower risk of cancer than nonusers in many observational studies. These inverse associations may be explained by common flaws in observational analyses that can be avoided by explicitly emulating a target trial.<h4>Methods</h4>We emulated target trials of metformin therapy and cancer risk using population-based linked electronic health records from the UK (2009-2016). We included individuals with diabetes, no history of cancer, no recent prescription for metformin or other glucose-lowering medication, and hemoglobin A1c (HbA1c) <64 mmol/mol (<8.0%). Outcomes included total cancer and 4 site-specific cancers (breast, colorectal, lung, and prostate). We estimated risks using pooled logistic regression with adjustment for risk factors via inverse-probability weighting. We emulated a second target trial among individuals regardless of diabetes status. We compared our estimates with those obtained using previously applied analytic approaches.<h4>Results</h4>Among individuals with diabetes, the estimated 6-year risk differences (metformin - no metformin) were -0.2% (95% CI = -1.6%, 1.3%) in the intention-to-treat analysis and 0.0% (95% CI = -2.1%, 2.3%) in the per-protocol analysis. The corresponding estimates for all site-specific cancers were close to zero. Among individuals regardless of diabetes status, these estimates were also close to zero and more precise. By contrast, previous analytic approaches yielded estimates that appeared strongly protective.<h4>Conclusions</h4>Our findings are consistent with the hypothesis that metformin therapy does not meaningfully influence cancer incidence. The findings highlight the importance of explicitly emulating a target trial to reduce bias in the effect estimates derived from observational analyses.",,doi:https://doi.org/10.1097/EDE.0000000000001626; html:https://europepmc.org/articles/PMC10524586; pdf:https://europepmc.org/articles/PMC10524586?pdf=render; doi:https://doi.org/10.1097/ede.0000000000001626
 37669983,https://doi.org/10.1038/s41598-023-41476-9,Link prediction in complex network using information flow.,"Aziz F, Slater LT, Bravo-Merodio L, Acharjee A, Gkoutos GV.",,Scientific reports,2023,2023-09-05,Y,,,,"Link prediction in complex networks has recently attracted a great deal of attraction in diverse scientific domains, including social and biological sciences. Given a snapshot of a network, the goal is to predict links that are missing in the network or that are likely to occur in the near future. This problem has both theoretical and practical significance; it not only helps us to identify missing links in a network more efficiently by avoiding the expensive and time consuming experimental processes, but also allows us to study the evolution of a network with time. To address the problem of link prediction, numerous attempts have been made over the recent years that exploit the local and the global topological properties of the network to predict missing links in the network. In this paper, we use parametrised matrix forest index (PMFI) to predict missing links in a network. We show that, for small parameter values, this index is linked to a heat diffusion process on a graph and therefore encodes geometric properties of the network. We then develop a framework that combines the PMFI with a local similarity index to predict missing links in the network. The framework is applied to numerous networks obtained from diverse domains such as social network, biological network, and transport network. The results show that the proposed method can predict missing links with higher accuracy when compared to other state-of-the-art link prediction methods.",,doi:https://doi.org/10.1038/s41598-023-41476-9; html:https://europepmc.org/articles/PMC10480459; pdf:https://europepmc.org/articles/PMC10480459?pdf=render
-34817387,https://doi.org/10.2196/29532,Introduction of Systematized Nomenclature of Medicine-Clinical Terms Coding Into an Electronic Health Record and Evaluation of its Impact: Qualitative and Quantitative Study.,"Pankhurst T, Evison F, Atia J, Gallier S, Coleman J, Ball S, McKee D, Ryan S, Black R.",,JMIR medical informatics,2021,2021-11-23,Y,Research; Diagnoses; data sharing; Clinical Decision Support; Population Health; Electronic Health Records; Coding Standards; Problem List; Health Data Exchange; Health Data Research; Clinician Led Design; International Classification Of Diseases Version 10 (Icd-10); National Health Service Blueprint; Systematized Nomenclature Of Medicine–clinical Terms (Snomed-ct); Clinician Reported Experience; Electronic Health Record Standards; Patient Diagnoses; Use Of Electronic Health Data; User-led Design; Clinical Usability,,,"<h4>Background</h4>This study describes the conversion within an existing electronic health record (EHR) from the International Classification of Diseases, Tenth Revision coding system to the SNOMED-CT (Systematized Nomenclature of Medicine-Clinical Terms) for the collection of patient histories and diagnoses. The setting is a large acute hospital that is designing and building its own EHR. Well-designed EHRs create opportunities for continuous data collection, which can be used in clinical decision support rules to drive patient safety. Collected data can be exchanged across health care systems to support patients in all health care settings. Data can be used for research to prevent diseases and protect future populations.<h4>Objective</h4>The aim of this study was to migrate a current EHR, with all relevant patient data, to the SNOMED-CT coding system to optimize clinical use and clinical decision support, facilitate data sharing across organizational boundaries for national programs, and enable remodeling of medical pathways.<h4>Methods</h4>The study used qualitative and quantitative data to understand the successes and gaps in the project, clinician attitudes toward the new tool, and the future use of the tool.<h4>Results</h4>The new coding system (tool) was well received and immediately widely used in all specialties. This resulted in increased, accurate, and clinically relevant data collection. Clinicians appreciated the increased depth and detail of the new coding, welcomed the potential for both data sharing and research, and provided extensive feedback for further development.<h4>Conclusions</h4>Successful implementation of the new system aligned the University Hospitals Birmingham NHS Foundation Trust with national strategy and can be used as a blueprint for similar projects in other health care settings.",,pdf:https://medinform.jmir.org/2021/11/e29532/PDF; doi:https://doi.org/10.2196/29532; html:https://europepmc.org/articles/PMC8663536
 38416166,https://doi.org/10.1007/s00228-024-03656-y,"Use of statins and risks of ovarian, uterine, and cervical diseases: a cohort study in the UK Biobank.","Jiao XF, Li H, Zeng L, Yang H, Hu Y, Qu Y, Chen W, Sun Y, Zhang W, Zeng X, Zhang L.",,European journal of clinical pharmacology,2024,2024-02-28,Y,Cervical cancer; Cohort study; risk; statins; polycystic ovarian syndrome,,,"<h4>Purpose</h4>To examine the associations between use of statins and risks of various ovarian, uterine, and cervical diseases, including ovarian cancer, endometrial cancer, cervical cancer, ovarian cyst, polycystic ovarian syndrome, endometriosis, endometrial hyperplasia, endometrial polyp, and cervical polyp.<h4>Methods</h4>We conducted a cohort study among female participants in the UK Biobank. Information on the use of statins was collected through verbal interview. Outcome information was obtained by linking to national cancer registry data and hospital inpatient data. We used Cox proportional hazards regression to examine the associations.<h4>Results</h4>A total of 180,855 female participants (18,403 statin users and 162,452 non-users) were included. Use of statins was significantly associated with increased risks of cervical cancer (adjusted hazard ratio (HR), 1.55; 95% confidence interval (95% CI), 1.05-2.30) and polycystic ovarian syndrome (adjusted HR, 4.39; 95% CI, 1.68-11.49). However, we observed no significant association between use of statins and risk of ovarian cancer, endometrial cancer, ovarian cyst, endometriosis, endometrial hyperplasia, endometrial polyp, or cervical polyp.<h4>Conclusion</h4>Our findings suggest that use of statins is associated with increased risks of cervical cancer and polycystic ovarian syndrome, but is not associated with increased or decreased risk of ovarian cancer, endometrial cancer, ovarian cyst, endometriosis, endometrial polyp, or cervical polyp.",,pdf:https://link.springer.com/content/pdf/10.1007/s00228-024-03656-y.pdf; doi:https://doi.org/10.1007/s00228-024-03656-y; html:https://europepmc.org/articles/PMC11098902; pdf:https://europepmc.org/articles/PMC11098902?pdf=render
+34817387,https://doi.org/10.2196/29532,Introduction of Systematized Nomenclature of Medicine-Clinical Terms Coding Into an Electronic Health Record and Evaluation of its Impact: Qualitative and Quantitative Study.,"Pankhurst T, Evison F, Atia J, Gallier S, Coleman J, Ball S, McKee D, Ryan S, Black R.",,JMIR medical informatics,2021,2021-11-23,Y,Research; Diagnoses; data sharing; Clinical Decision Support; Population Health; Electronic Health Records; Coding Standards; Problem List; Health Data Exchange; Health Data Research; Clinician Led Design; International Classification Of Diseases Version 10 (Icd-10); National Health Service Blueprint; Systematized Nomenclature Of Medicine–clinical Terms (Snomed-ct); Clinician Reported Experience; Electronic Health Record Standards; Patient Diagnoses; Use Of Electronic Health Data; User-led Design; Clinical Usability,,,"<h4>Background</h4>This study describes the conversion within an existing electronic health record (EHR) from the International Classification of Diseases, Tenth Revision coding system to the SNOMED-CT (Systematized Nomenclature of Medicine-Clinical Terms) for the collection of patient histories and diagnoses. The setting is a large acute hospital that is designing and building its own EHR. Well-designed EHRs create opportunities for continuous data collection, which can be used in clinical decision support rules to drive patient safety. Collected data can be exchanged across health care systems to support patients in all health care settings. Data can be used for research to prevent diseases and protect future populations.<h4>Objective</h4>The aim of this study was to migrate a current EHR, with all relevant patient data, to the SNOMED-CT coding system to optimize clinical use and clinical decision support, facilitate data sharing across organizational boundaries for national programs, and enable remodeling of medical pathways.<h4>Methods</h4>The study used qualitative and quantitative data to understand the successes and gaps in the project, clinician attitudes toward the new tool, and the future use of the tool.<h4>Results</h4>The new coding system (tool) was well received and immediately widely used in all specialties. This resulted in increased, accurate, and clinically relevant data collection. Clinicians appreciated the increased depth and detail of the new coding, welcomed the potential for both data sharing and research, and provided extensive feedback for further development.<h4>Conclusions</h4>Successful implementation of the new system aligned the University Hospitals Birmingham NHS Foundation Trust with national strategy and can be used as a blueprint for similar projects in other health care settings.",,pdf:https://medinform.jmir.org/2021/11/e29532/PDF; doi:https://doi.org/10.2196/29532; html:https://europepmc.org/articles/PMC8663536
 35356660,https://doi.org/10.7189/jogh.12.05008,"BNT162b2 and ChAdOx1 nCoV-19 vaccinations, incidence of SARS-CoV-2 infections and COVID-19 hospitalisations in Scotland in the Delta era.","Shah SA, Robertson C, Rudan I, Murray JL, McCowan C, Grange Z, Buelo A, Sullivan C, Simpson CR, Ritchie LD, Sheikh A.",,Journal of global health,2022,2022-03-26,Y,,,,"<h4>Background</h4>The emergence of the B.1.617.2 Delta variant of concern was associated with increasing numbers of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and COVID-19 hospital admissions. We aim to study national population level SARS-CoV-2 infections and COVID-19 associated hospitalisations by vaccination status to provide insight into the association of vaccination on temporal trends during the time in which the SARS-CoV-2 Delta variant became dominant in Scotland.<h4>Methods</h4>We used the Scotland-wide Early Pandemic Evaluation and Enhanced Surveillance (EAVE II) platform, covering the period when Delta was pervasive (May 01 to October 23, 2021). We performed a cohort analysis of every vaccine-eligible individual aged 20 or over from across Scotland. We determined the vaccination coverage, SARS-CoV-2 incidence rate and COVID-19 associated hospitalisations incidence rate. We then stratified those rates by age group, vaccination status (defined as ""unvaccinated"", ""partially vaccinated"" (1 dose), or ""fully vaccinated"" (2 doses)), vaccine type (BNT162b2 or ChAdOx1 nCoV-19), and coexisting conditions known to be associated with severe COVID-19 outcomes.<h4>Results</h4>During the follow-up of 4 183 022 individuals, there were 407 405 SARS-CoV-2 positive cases with 10 441 (2.6%) associated with a hospital admission. Those vaccinated with two doses (defined as fully vaccinated in the current study) of either vaccine had lower incidence rates of SARS-CoV-2 infections and much lower incidence rates of COVID-19 associated hospitalisations than those unvaccinated in the Delta era in Scotland. Younger age groups were substantially more likely to get infected. In contrast, older age groups were much more likely to be hospitalised. The incidence rates stratified by coexisting conditions were broadly comparable with the overall age group patterns.<h4>Conclusions</h4>This study suggests that national population level vaccination was associated with a reduction in SARS-CoV-2 infections and COVID-19 associated hospitalisation in Scotland throughout the Delta era.",,doi:https://doi.org/10.7189/jogh.12.05008; doi:https://doi.org/10.7189/jogh.12.05008; html:https://europepmc.org/articles/PMC8942298; pdf:https://europepmc.org/articles/PMC8942298?pdf=render
-39152507,https://doi.org/10.1186/s13063-024-08330-3,Towards an understanding of the ethics of electronic consent in clinical trials.,"Sahan K, Wijesurendra R, Preiss D, Mafham M, Sheehan M.",,Trials,2024,2024-08-16,Y,,,,"There are good practical reasons to use electronic consent (e-consent) in randomised trials, especially when conducting large-scale clinical trials to answer population-level health research questions. However, determining ethical reasons for e-consent is not so clear and depends on a proper understanding of what e-consent means when used in clinical trials and its ethical significance. Here we focus on four features of ethical significance which give rise to a range of ethical considerations relating to e-consent and merit further focused ethics research.",,doi:https://doi.org/10.1186/s13063-024-08330-3; html:https://europepmc.org/articles/PMC11329992; pdf:https://europepmc.org/articles/PMC11329992?pdf=render
 38135323,https://doi.org/10.1136/bmjopen-2023-076221,Development and application of simulation modelling for orthopaedic elective resource planning in England.,"Harper A, Monks T, Wilson R, Redaniel MT, Eyles E, Jones T, Penfold C, Elliott A, Keen T, Pitt M, Blom A, Whitehouse MR, Judge A.",,BMJ open,2023,2023-12-22,Y,Information management; Orthopaedic & Trauma Surgery; Organisation Of Health Services; World Wide Web Technology,,,"<h4>Objectives</h4>This study aimed to develop a simulation model to support orthopaedic elective capacity planning.<h4>Methods</h4>An open-source, generalisable discrete-event simulation was developed, including a web-based application. The model used anonymised patient records between 2016 and 2019 of elective orthopaedic procedures from a National Health Service (NHS) Trust in England. In this paper, it is used to investigate scenarios including resourcing (beds and theatres) and productivity (lengths of stay, delayed discharges and theatre activity) to support planning for meeting new NHS targets aimed at reducing elective orthopaedic surgical backlogs in a proposed ring-fenced orthopaedic surgical facility. The simulation is interactive and intended for use by health service planners and clinicians.<h4>Results</h4>A higher number of beds (65-70) than the proposed number (40 beds) will be required if lengths of stay and delayed discharge rates remain unchanged. Reducing lengths of stay in line with national benchmarks reduces bed utilisation to an estimated 60%, allowing for additional theatre activity such as weekend working. Further, reducing the proportion of patients with a delayed discharge by 75% reduces bed utilisation to below 40%, even with weekend working. A range of other scenarios can also be investigated directly by NHS planners using the interactive web app.<h4>Conclusions</h4>The simulation model is intended to support capacity planning of orthopaedic elective services by identifying a balance of capacity across theatres and beds and predicting the impact of productivity measures on capacity requirements. It is applicable beyond the study site and can be adapted for other specialties.",,doi:https://doi.org/10.1136/bmjopen-2023-076221; html:https://europepmc.org/articles/PMC10748981; pdf:https://europepmc.org/articles/PMC10748981?pdf=render
+39152507,https://doi.org/10.1186/s13063-024-08330-3,Towards an understanding of the ethics of electronic consent in clinical trials.,"Sahan K, Wijesurendra R, Preiss D, Mafham M, Sheehan M.",,Trials,2024,2024-08-16,Y,,,,"There are good practical reasons to use electronic consent (e-consent) in randomised trials, especially when conducting large-scale clinical trials to answer population-level health research questions. However, determining ethical reasons for e-consent is not so clear and depends on a proper understanding of what e-consent means when used in clinical trials and its ethical significance. Here we focus on four features of ethical significance which give rise to a range of ethical considerations relating to e-consent and merit further focused ethics research.",,doi:https://doi.org/10.1186/s13063-024-08330-3; html:https://europepmc.org/articles/PMC11329992; pdf:https://europepmc.org/articles/PMC11329992?pdf=render
 34238721,https://doi.org/10.1016/s2589-7500(21)00105-9,Temporal trends and forecasting of COVID-19 hospitalisations and deaths in Scotland using a national real-time patient-level data platform: a statistical modelling study.,"Simpson CR, Robertson C, Vasileiou E, Moore E, McCowan C, Agrawal U, Stagg HR, Docherty A, Mulholland R, Murray JLK, Ritchie LD, McMenamin J, Sheikh A.",,The Lancet. Digital health,2021,2021-07-05,Y,,,,"<h4>Background</h4>As the COVID-19 pandemic continues, national-level surveillance platforms with real-time individual person-level data are required to monitor and predict the epidemiological and clinical profile of COVID-19 and inform public health policy. We aimed to create a national dataset of patient-level data in Scotland to identify temporal trends and COVID-19 risk factors, and to develop a novel statistical prediction model to forecast COVID-19-related deaths and hospitalisations during the second wave.<h4>Methods</h4>We established a surveillance platform to monitor COVID-19 temporal trends using person-level primary care data (including age, sex, socioeconomic status, urban or rural residence, care home residence, and clinical risk factors) linked to data on SARS-CoV-2 RT-PCR tests, hospitalisations, and deaths for all individuals resident in Scotland who were registered with a general practice on Feb 23, 2020. A Cox proportional hazards model was used to estimate the association between clinical risk groups and time to hospitalisation and death. A survival prediction model derived from data from March 1 to June 23, 2020, was created to forecast hospital admissions and deaths from October to December, 2020. We fitted a generalised additive spline model to daily SARS-CoV-2 cases over the previous 10 weeks and used this to create a 28-day forecast of the number of daily cases. The age and risk group pattern of cases in the previous 3 weeks was then used to select a stratified sample of individuals from our cohort who had not previously tested positive, with future cases in each group sampled from a multinomial distribution. We then used their patient characteristics (including age, sex, comorbidities, and socioeconomic status) to predict their probability of hospitalisation or death.<h4>Findings</h4>Our cohort included 5 384 819 people, representing 98·6% of the entire estimated population residing in Scotland during 2020. Hospitalisation and death among those testing positive for SARS-CoV-2 between March 1 and June 23, 2020, were associated with several patient characteristics, including male sex (hospitalisation hazard ratio [HR] 1·47, 95% CI 1·38-1·57; death HR 1·62, 1·49-1·76) and various comorbidities, with the highest hospitalisation HR found for transplantation (4·53, 1·87-10·98) and the highest death HR for myoneural disease (2·33, 1·46-3·71). For those testing positive, there were decreasing temporal trends in hospitalisation and death rates. The proportion of positive tests among older age groups (>40 years) and those with at-risk comorbidities increased during October, 2020. On Nov 10, 2020, the projected number of hospitalisations for Dec 8, 2020 (28 days later) was 90 per day (95% prediction interval 55-125) and the projected number of deaths was 21 per day (12-29).<h4>Interpretation</h4>The estimated incidence of SARS-CoV-2 infection based on positive tests recorded in this unique data resource has provided forecasts of hospitalisation and death rates for the whole of Scotland. These findings were used by the Scottish Government to inform their response to reduce COVID-19-related morbidity and mortality.<h4>Funding</h4>Medical Research Council, National Institute for Health Research Health Technology Assessment Programme, UK Research and Innovation Industrial Strategy Challenge Fund, Health Data Research UK, Scottish Government Director General Health and Social Care.",,doi:https://doi.org/10.1016/s2589-7500(21)00105-9; doi:https://doi.org/10.1016/S2589-7500(21)00105-9; html:https://europepmc.org/articles/PMC8257056
 33252680,https://doi.org/10.1093/ageing/afaa252,A comparison of two national frailty scoring systems.,"Hollinghurst J, Housley G, Watkins A, Clegg A, Gilbert T, Conroy SP.",,Age and ageing,2021,2021-06-01,N,Frailty; Risk stratification; Older People; Primary Care; Secondary Care; Electronic Health Records,,,"<h4>Background</h4>The electronic Frailty Index (eFI) has been developed in primary care settings. The Hospital Frailty Risk Score (HFRS) was derived using secondary care data.<h4>Objective</h4>Compare the two different tools for identifying frailty in older people admitted to hospital.<h4>Design and setting</h4>Retrospective cohort study using the Secure Anonymised Information Linkage Databank, comprising 126,600 people aged 65+ who were admitted as an emergency to hospital in Wales from January 2013 up until December 2017.<h4>Methods</h4>Pearson's correlation coefficient and weighted kappa were used to assess the correlation between the tools. Cox and logistic regression were used to estimate hazard ratios (HRs) and odds ratios (ORs). The Concordance statistic and area under the receiver operating curves (AUROC) were estimated to determine discrimination.<h4>Results</h4>Pearson's correlation coefficient was 0.26 and the weighted kappa was 0.23. Comparing the highest to the least frail categories in the two scores the HRs for 90-day mortality, 90-day emergency readmission and care home admissions within 1-year using the HFRS were 1.41, 1.69 and 4.15 for the eFI 1.16, 1.63 and 1.47. Similarly, the ORs for inpatient death, length of stay greater than 10 days and readmission within 30-days were 1.44, 2.07 and 1.52 for the HFRS, and 1.21, 1.21 and 1.44 for the eFI. AUROC was determined as having no clinically relevant difference between the tools.<h4>Conclusions</h4>The eFI and HFRS have a low correlation between their scores. The HRs and ORs were higher for the increasing frailty categories for both the HFRS and eFI.",,pdf:https://academic.oup.com/ageing/article-pdf/50/4/1208/38839537/afaa252.pdf; doi:https://doi.org/10.1093/ageing/afaa252; html:https://europepmc.org/articles/PMC8244560; pdf:https://europepmc.org/articles/PMC8244560?pdf=render; doi:https://doi.org/10.1093/ageing/afaa252
 36216011,https://doi.org/10.1016/s2213-2600(22)00360-5,Pregnancy outcomes after SARS-CoV-2 infection in periods dominated by delta and omicron variants in Scotland: a population-based cohort study.,"Stock SJ, Moore E, Calvert C, Carruthers J, Denny C, Donaghy J, Hillman S, Hopcroft LEM, Hopkins L, Goulding A, Lindsay L, McLaughlin T, Taylor B, Auyeung B, Katikireddi SV, McCowan C, Ritchie LD, Rudan I, Simpson CR, Robertson C, Sheikh A, Wood R.",,The Lancet. Respiratory medicine,2022,2022-10-07,Y,,,,"<h4>Background</h4>Evidence suggests that the SARS-CoV-2 omicron (B.1·1.529) is associated with lower risks of adverse outcomes than the delta (B.1.617.2) variant among the general population. However, little is known about outcomes after omicron infection in pregnancy. We aimed to assess and compare short-term pregnancy outcomes after SARS-CoV-2 delta and omicron infection in pregnancy.<h4>Methods</h4>We did a national population-based cohort study of women who had SARS-CoV-2 infection in pregnancy between May 17, 2021, and Jan 31, 2022. The primary maternal outcome was admission to critical care within 21 days of infection or death within 28 days of date of infection. Pregnancy outcomes were preterm birth and stillbirth within 28 days of infection. Neonatal outcomes were death within 28 days of birth, and low Apgar score (<7 of 10, for babies born at term) or neonatal SARS-CoV-2 infection in births occurring within 28 days of maternal infection. We used periods when variants were dominant in the general Scottish population, based on 50% or more of cases being S-gene positive (delta variant, from May 17 to Dec 14, 2021) or S-gene negative (omicron variant, from Dec 15, 2021, to Jan 31, 2022) as surrogates for variant infections. Analyses used logistic regression, adjusting for maternal age, deprivation quintile, ethnicity, weeks of gestation, and vaccination status. Sensitivity analyses included restricting the analysis to those with first confirmed SARS-CoV-2 infection and using periods when delta or omicron had 90% or more predominance.<h4>Findings</h4>Between May 17, 2021, and Jan 31, 2022, there were 9923 SARS-CoV-2 infections in 9823 pregnancies, in 9817 women in Scotland. Compared with infections in the delta-dominant period, SARS-CoV-2 infections in pregnancy in the omicron-dominant period were associated with lower maternal critical care admission risk (0·3% [13 of 4968] vs 1·8% [89 of 4955]; adjusted odds ratio 0·25, 95% CI 0·14-0·44) and lower preterm birth within 28 days of infection (1·8% [37 of 2048] vs 4·2% [98 of 2338]; 0·57, 95% CI 0·38-0·87). There were no maternal deaths within 28 days of infection. Estimates of low Apgar scores were imprecise due to low numbers (5 [1·2%] of 423 with omicron vs 11 [2·1%] of 528 with delta, adjusted odds ratio 0·72, 0·23-2·32). There were fewer stillbirths in the omicron-dominant period than in the delta-dominant period (4·3 [2 of 462] per 1000 births vs 20·3 [13 of 639] per 1000) and no neonatal deaths during the omicron-dominant period (0 [0 of 460] per 1000 births vs 6·3 [4 of 626] per 1000 births), thus numbers were too small to support adjusted analyses. Rates of neonatal infection were low in births within 28 days of maternal SARS-CoV-2 infection, with 11 cases of neonatal SARS-CoV-2 in the delta-dominant period, and 1 case in the omicron-dominant period. Of the 15 stillbirths, 12 occurred in women who had not received two or more doses of COVID-19 vaccination at the time of SARS-CoV-2 infection in pregnancy. All 12 cases of neonatal SARS-CoV-2 infection occurred in women who had not received two or more doses of vaccine at the time of maternal infection. Findings in sensitivity analyses were similar to those in the main analyses.<h4>Interpretation</h4>Pregnant women infected with SARS-CoV-2 were substantially less likely to have a preterm birth or maternal critical care admission during the omicron-dominant period than during the delta-dominant period.<h4>Funding</h4>Wellcome Trust, Tommy's charity, Medical Research Council, UK Research and Innovation, Health Data Research UK, National Core Studies-Data and Connectivity, Public Health Scotland, Scottish Government Health and Social Care, Scottish Government Chief Scientist Office, National Research Scotland.",,doi:https://doi.org/10.1016/s2213-2600(22)00360-5; doi:https://doi.org/10.1016/S2213-2600(22)00360-5; html:https://europepmc.org/articles/PMC9708088; pdf:https://europepmc.org/articles/PMC9708088?pdf=render
@@ -170,13 +170,13 @@ PMC11227019,https://doi.org/,Adoption of high-sensitivity cardiac troponin for r
 36102210,https://doi.org/10.1002/prp2.1007,What is the evidence that a pharmacy team working in an acute or emergency medicine department improves outcomes for patients: A systematic review.,"Punj E, Collins A, Agravedi N, Marriott J, Sapey E.",,Pharmacology research & perspectives,2022,2022-10-01,Y,Emergency Medicine; Medication Errors; Medication Reconciliation; Pharmac*,,,"Pharmacy services within hospitals are changing, with more taking on medication reconciliation activities. This systematic review was conducted to determine the measured impacts of Pharmacy teams working in an acute or emergency medicine department. The protocol followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and was prospectively registered on PROSPERO, National Institute for Health and Care Research, UK registration number: CRD42020187487. The systematic review had two co-primary aims: a reduction in the number of incorrect prescriptions on admission by comparing the medication list from primary care to secondary care, and a reduction in the severity of harm caused by these incorrect prescriptions; chosen to determine the impact of pharmacy-led medication reconciliation services in the emergency and acute medicine setting. Seventeen articles were included. Fifteen were non-randomized controlled trials and two were randomized controlled trials. The number of patients combined for all studies was 7630. No studies included were based within the UK. All studies showed benefits in terms of a reduction in medicine errors and patient harm, compared to control arms. Nine articles were included in a statistical analysis comparing the pharmacy intervention arm with the non-pharmacy control arm, with a Chi<sup>2</sup> of 101.10 and I<sup>2</sup> value = 92%. However, studies were heterogenous with different outcome measures and many showed evidence of bias. The included studies consistently indicated that pharmacy services based within acute or emergency medicine departments in hospitals were associated with fewer medication errors. Further studies are needed to understand the health and economic impact of deploying a pharmacy service in acute medical settings including out-of-hours working.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9471999; doi:https://doi.org/10.1002/prp2.1007; html:https://europepmc.org/articles/PMC9471999; pdf:https://europepmc.org/articles/PMC9471999?pdf=render
 39148062,https://doi.org/10.1186/s12889-024-19505-7,Associations of fruit intake with adiposity and cardiometabolic biomarkers in UK Biobank.,"Trichia E, MacLean F, Perez-Cornago A, Tong TYN, Emberson JR, Key TJ, Lewington S, Carter JL.",,BMC public health,2024,2024-08-16,Y,Lipids; Fruit; Blood pressure; Oxidative stress; Inflammation; Adiposity; Glycaemia; Uk Biobank; Cardiometabolic,,,"<h4>Background</h4>Fruit consumption has been associated with a lower cardiovascular disease (CVD) risk but the underlying mechanisms are unclear. We investigated the cross-sectional and prospective associations of fruit consumption with markers of adiposity, blood pressure, lipids, low-grade inflammation, glycaemia, and oxidative stress.<h4>Methods</h4>The main analyses included 365 534 middle-aged adults from the UK Biobank at baseline, of whom 11 510, and 38 988 were included in the first and second follow-up respectively, free from CVD and cancer at baseline. Fruit consumption frequency at baseline was assessed using a questionnaire. We assessed the cross-sectional and prospective associations of fruit with adiposity (body mass index, waist circumference and %body fat), systolic and diastolic blood pressure, lipids (low-density and high-density lipoproteins, triglycerides and apolipoprotein B), glycaemia (haemoglobin A1c), low-grade inflammation (C-reactive protein) and oxidative stress (gamma-glutamyl-transferase) using linear regression models adjusted for socioeconomic and lifestyle factors. Analyses were repeated in a subset with two to five complete 24-h dietary assessments (n = 26 596) allowing for adjustment for total energy intake.<h4>Results</h4>Fruit consumption at baseline generally showed weak inverse associations with adiposity and biomarkers at baseline. Most of these relationships did not persist through follow-up, except for inverse associations with diastolic blood pressure, C-reactive protein, gamma-glutamyl transferase and adiposity. However, for most mechanisms, mean levels varied by less than 0.1 standard deviations (SD) between high and low fruit consumption (> 3 vs < 1 servings/day) in further adjusted models (while the difference was < 0.2 SD for all of them). For example, waist circumference and diastolic blood pressure were 1 cm and 1 mmHg lower in high compared to low fruit intake at the first follow-up (95% confidence interval: -1.8, -0.1 and -1.8, -0.3, respectively). Analyses in the 24-h dietary assessment subset showed overall similar associations.<h4>Conclusions</h4>We observed very small differences in adiposity and cardiometabolic biomarkers between those who reported high fruit consumption vs low, most of which did not persist over follow-up. Future studies on other mechanisms and detailed assessment of confounding might further elucidate the relevance of fruit to cardiovascular disease.",,doi:https://doi.org/10.1186/s12889-024-19505-7; doi:https://doi.org/10.1186/s12889-024-19505-7; html:https://europepmc.org/articles/PMC11328357; pdf:https://europepmc.org/articles/PMC11328357?pdf=render
 36083213,https://doi.org/10.1093/jamia/ocac158,Translating and evaluating historic phenotyping algorithms using SNOMED CT.,"Elkheder M, Gonzalez-Izquierdo A, Qummer Ul Arfeen M, Kuan V, Lumbers RT, Denaxas S, Shah AD.",,Journal of the American Medical Informatics Association : JAMIA,2023,2023-01-01,Y,Terminology; Phenotype; Ontology; Electronic Health Records; Snomed Ct,,,"<h4>Objective</h4>Patient phenotype definitions based on terminologies are required for the computational use of electronic health records. Within UK primary care research databases, such definitions have typically been represented as flat lists of Read terms, but Systematized Nomenclature of Medicine-Clinical Terms (SNOMED CT) (a widely employed international reference terminology) enables the use of relationships between concepts, which could facilitate the phenotyping process. We implemented SNOMED CT-based phenotyping approaches and investigated their performance in the CPRD Aurum primary care database.<h4>Materials and methods</h4>We developed SNOMED CT phenotype definitions for 3 exemplar diseases: diabetes mellitus, asthma, and heart failure, using 3 methods: ""primary"" (primary concept and its descendants), ""extended"" (primary concept, descendants, and additional relations), and ""value set"" (based on text searches of term descriptions). We also derived SNOMED CT codelists in a semiautomated manner for 276 disease phenotypes used in a study of health across the lifecourse. Cohorts selected using each codelist were compared to ""gold standard"" manually curated Read codelists in a sample of 500 000 patients from CPRD Aurum.<h4>Results</h4>SNOMED CT codelists selected a similar set of patients to Read, with F1 scores exceeding 0.93, and age and sex distributions were similar. The ""value set"" and ""extended"" codelists had slightly greater recall but lower precision than ""primary"" codelists. We were able to represent 257 of the 276 phenotypes by a single concept hierarchy, and for 135 phenotypes, the F1 score was greater than 0.9.<h4>Conclusions</h4>SNOMED CT provides an efficient way to define disease phenotypes, resulting in similar patient populations to manually curated codelists.",,pdf:https://discovery.ucl.ac.uk/id/eprint/10155637/1/ocac158.pdf; doi:https://doi.org/10.1093/jamia/ocac158; html:https://europepmc.org/articles/PMC9846670; pdf:https://europepmc.org/articles/PMC9846670?pdf=render
+38783251,https://doi.org/10.1186/s12885-024-12344-0,Prospective associations of leucocyte subtypes and obesity with the risk of developing cutaneous malignant melanoma in the UK Biobank cohort.,"Christakoudi S, Tsilidis KK, Riboli E.",,BMC cancer,2024,2024-05-23,Y,Lymphocytes; Neutrophils; Monocytes; Obesity; BMI; abdominal obesity; Cutaneous Malignant Melanoma; Absi,,,"<h4>Background</h4>Obesity is associated with chronic low-grade inflammation, which is linked to cancer development. Abdominal obesity (a body mass index, ABSI), however, has unusually been associated inversely with cutaneous malignant melanoma (CMM), while general obesity (body mass index, BMI) is associated positively. Leucocytes participate in inflammation and are higher in obesity, but prospective associations of leucocytes with cutaneous malignant melanoma are unclear.<h4>Methods</h4>We examined the prospective associations of neutrophil, lymphocyte, and monocyte counts (each individually), as well as the prospective associations of ABSI and BMI, with cutaneous malignant melanoma in UK Biobank. We used multivariable Cox proportional hazards models and explored heterogeneity according to sex, menopausal status, age (≥ 50 years at recruitment), smoking status, ABSI (dichotomised at the median: ≥73.5 women; ≥79.8 men), BMI (normal weight, overweight, obese), and time to diagnosis.<h4>Results</h4>During a mean follow-up of 10.2 years, 2174 CMM cases were ascertained in 398,450 participants. There was little evidence for associations with neutrophil or lymphocyte counts. Monocyte count, however, was associated inversely in participants overall (HR = 0.928; 95%CI: 0.888-0.971; per one standard deviation increase; SD = 0.144*10<sup>9</sup>/L women; SD = 0.169*10<sup>9</sup>/L men), specifically in older participants (HR = 0.906; 95%CI: 0.862-0.951), and more clearly in participants with low ABSI (HR = 0.880; 95%CI: 0.824-0.939), or with BMI ≥ 25 kg/m<sup>2</sup> (HR = 0.895; 95%CI: 0.837-0.958 for overweight; HR = 0.923; 95%CI: 0.848-1.005 for obese). ABSI was associated inversely in pre-menopausal women (HR = 0.810; 95%CI: 0.702-0.935; SD = 4.95) and men (HR = 0.925; 95%CI: 0.867-0.986; SD = 4.11). BMI was associated positively in men (HR = 1.148; 95%CI: 1.078-1.222; SD = 4.04 kg/m<sup>2</sup>). There was little evidence for heterogeneity according to smoking status. The associations with monocyte count and BMI were retained to at least 8 years prior to diagnosis, but the association with ABSI was observed up to 4 years prior to diagnosis and not for longer follow-up time.<h4>Conclusions</h4>Monocyte count is associated prospectively inversely with the risk of developing CMM in older individuals, while BMI is associated positively in men, suggesting a mechanistic involvement of factors related to monocytes and subcutaneous adipose tissue in melanoma development. An inverse association with ABSI closer to diagnosis may reflect reverse causality or glucocorticoid resistance.",,doi:https://doi.org/10.1186/s12885-024-12344-0; html:https://europepmc.org/articles/PMC11112846; pdf:https://europepmc.org/articles/PMC11112846?pdf=render
 39323985,https://doi.org/10.1214/23-aoas1849,"A BAYESIAN HIERARCHICAL SMALL AREA POPULATION MODEL ACCOUNTING FOR DATA SOURCE SPECIFIC METHODOLOGIES FROM AMERICAN COMMUNITY SURVEY, POPULATION ESTIMATES PROGRAM, AND DECENNIAL CENSUS DATA.","Peterson EN, Nethery RC, Padellini T, Chen JT, Coull BA, Piel FB, Wakefield J, Blangiardo M, Waller LA.",,The annals of applied statistics,2024,2024-04-05,N,Bayesian Methods; American Community Survey; Sampling And Nonsampling Errors; Small Area Population Estimates; Decennial Census,,,"Small area population counts are necessary for many epidemiological studies, yet their quality and accuracy are often not assessed. In the United States, small area population counts are published by the United States Census Bureau (USCB) in the form of the decennial census counts, intercensal population projections (PEP), and American Community Survey (ACS) estimates. Although there are significant relationships between these three data sources, there are important contrasts in data collection, data availability, and processing methodologies such that each set of reported population counts may be subject to different sources and magnitudes of error. Additionally, these data sources do not report identical small area population counts due to post-survey adjustments specific to each data source. Consequently, in public health studies, small area disease/mortality rates may differ depending on which data source is used for denominator data. To accurately estimate annual small area population counts <i>and their</i> associated uncertainties, we present a Bayesian population (BPop) model, which fuses information from all three USCB sources, accounting for data source specific methodologies and associated errors. We produce comprehensive small area race-stratified estimates of the true population, and associated uncertainties, given the observed trends in all three USCB population estimates. The main features of our framework are: (1) a single model integrating multiple data sources, (2) accounting for data source specific data generating mechanisms and specifically accounting for data source specific errors, and (3) prediction of population counts for years without USCB reported data. We focus our study on the Black and White only populations for 159 counties of Georgia and produce estimates for years 2006-2023. We compare BPop population estimates to decennial census counts, PEP annual counts, and ACS multi-year estimates. Additionally, we illustrate and explain the different types of data source specific errors. Lastly, we compare model performance using simulations and validation exercises. Our Bayesian population model can be extended to other applications at smaller spatial granularity and for demographic subpopulations defined further by race, age, and sex, and/or for other geographical regions.",,doi:https://doi.org/10.1214/23-aoas1849; html:https://europepmc.org/articles/PMC11423836; pdf:https://europepmc.org/articles/PMC11423836?pdf=render; doi:https://doi.org/10.1214/23-aoas1849
 38537901,https://doi.org/10.1016/j.cct.2024.107514,Getting our ducks in a row: The need for data utility comparisons of healthcare systems data for clinical trials.,"Sydes MR, Murray ML, Ahmed S, Apostolidou S, Bliss JM, Bloomfield C, Cannings-John R, Carpenter J, Clayton T, Clout M, Cosgriff R, Farrin AJ, Gentry-Maharaj A, Gilbert DC, Harper C, James ND, Langley RE, Lessels S, Lugg-Widger F, Mackenzie IS, Mafham M, Menon U, Mintz H, Pinches H, Robling M, Wright-Hughes A, Yorke-Edwards V, Love SB.",,Contemporary clinical trials,2024,2024-03-26,N,DUCKS; Health Policy; Electronic Health Records; Rcts; Data Utility; Real World Data; Routinely-Collected Data; Healthcare Systems Data; Data Utility Comparison Studies; Routinely-collected Healthcare Data,,,"<h4>Background</h4>Better use of healthcare systems data, collected as part of interactions between patients and the healthcare system, could transform planning and conduct of randomised controlled trials. Multiple challenges to widespread use include whether healthcare systems data captures sufficiently well the data traditionally captured on case report forms. ""Data Utility Comparison Studies"" (DUCkS) assess the utility of healthcare systems data for RCTs by comparison to data collected by the trial. Despite their importance, there are few published UK examples of DUCkS.<h4>Methods-and-results</h4>Building from ongoing and selected recent examples of UK-led DUCkS in the literature, we set out experience-based considerations for the conduct of future DUCkS. Developed through informal iterative discussions in many forums, considerations are offered for planning, protocol development, data, analysis and reporting, with comparisons at ""patient-level"" or ""trial-level"", depending on the item of interest and trial status.<h4>Discussion</h4>DUCkS could be a valuable tool in assessing where healthcare systems data can be used for trials and in which trial teams can play a leading role. There is a pressing need for trials to be more efficient in their delivery and research waste must be reduced. Trials have been making inconsistent use of healthcare systems data, not least because of an absence of evidence of utility. DUCkS can also help to identify challenges in using healthcare systems data, such as linkage (access and timing) and data quality. We encourage trial teams to incorporate and report DUCkS in trials and funders and data providers to support them.",,doi:https://doi.org/10.1016/j.cct.2024.107514
+38529358,https://doi.org/10.1093/braincomms/fcae088,"<i>Helicobacter pylori</i>, persistent infection burden and structural brain imaging markers.","Beydoun MA, Beydoun HA, Hu YH, El-Hajj ZW, Georgescu MF, Noren Hooten N, Li Z, Weiss J, Lyall DM, Waldstein SR, Hedges DW, Gale SD, Launer LJ, Evans MK, Zonderman AB.",,Brain communications,2024,2024-03-13,N,Helicobacter Pylori; Persistent infection; Brain imaging; Cognitive Aging,,,"Persistent infections, whether viral, bacterial or parasitic, including <i>Helicobacter pylori</i> infection, have been implicated in non-communicable diseases, including dementia and other neurodegenerative diseases. In this cross-sectional study, data on 635 cognitively normal participants from the UK Biobank study (2006-21, age range: 40-70 years) were used to examine whether <i>H. pylori</i> seropositivity (e.g. presence of antibodies), serointensities of five <i>H. pylori</i> antigens and a measure of total persistent infection burden were associated with selected brain volumetric structural MRI (total, white, grey matter, frontal grey matter (left/right), white matter hyperintensity as percent intracranial volume and bi-lateral sub-cortical volumes) and diffusion-weighted MRI measures (global and tract-specific bi-lateral fractional anisotropy and mean diffusivity), after an average 9-10 years of lag time. Persistent infection burden was calculated as a cumulative score of seropositivity for over 20 different pathogens. Multivariable-adjusted linear regression analyses were conducted, whereby selected potential confounders (all measures) and intracranial volume (sub-cortical volumes) were adjusted, with stratification by Alzheimer's disease polygenic risk score tertile when exposures were <i>H. pylori</i> antigen serointensities. Type I error was adjusted to 0.007. We report little evidence of an association between <i>H. pylori</i> seropositivity and persistent infection burden with various volumetric outcomes (<i>P</i> > 0.007, from multivariable regression models), unlike previously reported in past research. However, <i>H. pylori</i> antigen serointensities, particularly immunoglobulin G against the vacuolating cytotoxin A, GroEL and outer membrane protein antigens, were associated with poorer tract-specific white matter integrity (<i>P</i> < 0.007), with outer membrane protein serointensity linked to worse outcomes in cognition-related tracts such as the external capsule, the anterior limb of the internal capsule and the cingulum, specifically at low Alzheimer's disease polygenic risk. Vacuolating cytotoxin A serointensity was associated with greater white matter hyperintensity volume among individuals with mid-level Alzheimer's disease polygenic risk, while among individuals with the highest Alzheimer's disease polygenic risk, the urease serointensity was consistently associated with reduced bi-lateral caudate volumes and the vacuolating cytotoxin A serointensity was linked to reduced right putamen volume (<i>P</i> < 0.007). Outer membrane protein and urease were associated with larger sub-cortical volumes (e.g. left putamen and right nucleus accumbens) at middle Alzheimer's disease polygenic risk levels (<i>P</i> < 0.007). Our results shed light on the relationship between <i>H. pylori</i> seropositivity, <i>H. pylori</i> antigen levels and persistent infection burden with brain volumetric structural measures. These data are important given the links between infectious agents and neurodegenerative diseases, including Alzheimer's disease, and can be used for the development of drugs and preventive interventions that would reduce the burden of those diseases.",,doi:https://doi.org/10.1093/braincomms/fcae088; html:https://europepmc.org/articles/PMC10961948; pdf:https://europepmc.org/articles/PMC10961948?pdf=render; doi:https://doi.org/10.1093/braincomms/fcae088
 34706926,https://doi.org/10.1136/jech-2021-217090,Drug prescriptions and dementia incidence: a medication-wide association study of 17000 dementia cases among half a million participants.,"Wilkinson T, Schnier C, Bush K, Rannikmäe K, Lyons RA, McTaggart S, Bennie M, Sudlow CL.",,Journal of epidemiology and community health,2022,2021-10-27,Y,Dementia; Pharmacoepidemiology; Record Linkage; Neuroepidemiology,,,"<h4>Background</h4>Previous studies have suggested that some medications may influence dementia risk. We conducted a hypothesis-generating medication-wide association study to investigate systematically the association between all prescription medications and incident dementia.<h4>Methods</h4>We used a population-based cohort within the Secure Anonymised Information Linkage (SAIL) databank, comprising routinely-collected primary care, hospital admissions and mortality data from Wales, UK. We included all participants born after 1910 and registered with a SAIL general practice at ≤60 years old. Follow-up was from each participant's 60th birthday to the earliest of dementia diagnosis, deregistration from a SAIL general practice, death or the end of 2018. We considered participants exposed to a medication if they received ≥1 prescription for any of 744 medications before or during follow-up. We adjusted for sex, smoking and socioeconomic status. The outcome was any all-cause dementia code in primary care, hospital or mortality data during follow-up. We used Cox regression to calculate hazard ratios and Bonferroni-corrected p values.<h4>Results</h4>Of 551 344 participants, 16 998 (3%) developed dementia (median follow-up was 17 years for people who developed dementia, 10 years for those without dementia). Of 744 medications, 221 (30%) were associated with dementia. Of these, 217 (98%) were associated with increased dementia incidence, many clustering around certain indications. Four medications (all vaccines) were associated with a lower dementia incidence.<h4>Conclusions</h4>Almost a third of medications were associated with dementia. The clustering of many drugs around certain indications may provide insights into early manifestations of dementia. We encourage further investigation of hypotheses generated by these results.",,pdf:https://jech.bmj.com/content/jech/76/3/223.full.pdf; doi:https://doi.org/10.1136/jech-2021-217090; html:https://europepmc.org/articles/PMC8862053; pdf:https://europepmc.org/articles/PMC8862053?pdf=render
-38783251,https://doi.org/10.1186/s12885-024-12344-0,Prospective associations of leucocyte subtypes and obesity with the risk of developing cutaneous malignant melanoma in the UK Biobank cohort.,"Christakoudi S, Tsilidis KK, Riboli E.",,BMC cancer,2024,2024-05-23,Y,Lymphocytes; Neutrophils; Monocytes; Obesity; BMI; abdominal obesity; Cutaneous Malignant Melanoma; Absi,,,"<h4>Background</h4>Obesity is associated with chronic low-grade inflammation, which is linked to cancer development. Abdominal obesity (a body mass index, ABSI), however, has unusually been associated inversely with cutaneous malignant melanoma (CMM), while general obesity (body mass index, BMI) is associated positively. Leucocytes participate in inflammation and are higher in obesity, but prospective associations of leucocytes with cutaneous malignant melanoma are unclear.<h4>Methods</h4>We examined the prospective associations of neutrophil, lymphocyte, and monocyte counts (each individually), as well as the prospective associations of ABSI and BMI, with cutaneous malignant melanoma in UK Biobank. We used multivariable Cox proportional hazards models and explored heterogeneity according to sex, menopausal status, age (≥ 50 years at recruitment), smoking status, ABSI (dichotomised at the median: ≥73.5 women; ≥79.8 men), BMI (normal weight, overweight, obese), and time to diagnosis.<h4>Results</h4>During a mean follow-up of 10.2 years, 2174 CMM cases were ascertained in 398,450 participants. There was little evidence for associations with neutrophil or lymphocyte counts. Monocyte count, however, was associated inversely in participants overall (HR = 0.928; 95%CI: 0.888-0.971; per one standard deviation increase; SD = 0.144*10<sup>9</sup>/L women; SD = 0.169*10<sup>9</sup>/L men), specifically in older participants (HR = 0.906; 95%CI: 0.862-0.951), and more clearly in participants with low ABSI (HR = 0.880; 95%CI: 0.824-0.939), or with BMI ≥ 25 kg/m<sup>2</sup> (HR = 0.895; 95%CI: 0.837-0.958 for overweight; HR = 0.923; 95%CI: 0.848-1.005 for obese). ABSI was associated inversely in pre-menopausal women (HR = 0.810; 95%CI: 0.702-0.935; SD = 4.95) and men (HR = 0.925; 95%CI: 0.867-0.986; SD = 4.11). BMI was associated positively in men (HR = 1.148; 95%CI: 1.078-1.222; SD = 4.04 kg/m<sup>2</sup>). There was little evidence for heterogeneity according to smoking status. The associations with monocyte count and BMI were retained to at least 8 years prior to diagnosis, but the association with ABSI was observed up to 4 years prior to diagnosis and not for longer follow-up time.<h4>Conclusions</h4>Monocyte count is associated prospectively inversely with the risk of developing CMM in older individuals, while BMI is associated positively in men, suggesting a mechanistic involvement of factors related to monocytes and subcutaneous adipose tissue in melanoma development. An inverse association with ABSI closer to diagnosis may reflect reverse causality or glucocorticoid resistance.",,doi:https://doi.org/10.1186/s12885-024-12344-0; html:https://europepmc.org/articles/PMC11112846; pdf:https://europepmc.org/articles/PMC11112846?pdf=render
 33319712,https://doi.org/10.1186/s12911-020-01336-2,Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies.,"Slater LT, Gkoutos GV, Hoehndorf R.",,BMC medical informatics and decision making,2020,2020-12-15,Y,Automated Reasoning; Ontology Interoperability,,,"<h4>Background</h4>Ontologies are widely used throughout the biomedical domain. These ontologies formally represent the classes and relations assumed to exist within a domain. As scientific domains are deeply interlinked, so too are their representations. While individual ontologies can be tested for consistency and coherency using automated reasoning methods, systematically combining ontologies of multiple domains together may reveal previously hidden contradictions.<h4>Methods</h4>We developed a method that tests for hidden unsatisfiabilities in an ontology that arise when combined with other ontologies. For this purpose, we combined sets of ontologies and use automated reasoning to determine whether unsatisfiable classes are present. In addition, we designed and implemented a novel algorithm that can determine justifications for contradictions across extremely large and complicated ontologies, and use these justifications to semi-automatically repair ontologies by identifying a small set of axioms that, when removed, result in a consistent and coherent set of ontologies.<h4>Results</h4>We tested the mutual consistency of the OBO Foundry and the OBO ontologies and find that the combined OBO Foundry gives rise to at least 636 unsatisfiable classes, while the OBO ontologies give rise to more than 300,000 unsatisfiable classes. We also applied our semi-automatic repair algorithm to each combination of OBO ontologies that resulted in unsatisfiable classes, finding that only 117 axioms could be removed to account for all cases of unsatisfiability across all OBO ontologies.<h4>Conclusions</h4>We identified a large set of hidden unsatisfiability across a broad range of biomedical ontologies, and we find that this large set of unsatisfiable classes is the result of a relatively small amount of axiomatic disagreements. Our results show that hidden unsatisfiability is a serious problem in ontology interoperability; however, our results also provide a way towards more consistent ontologies by addressing the issues we identified.",,pdf:https://bmcmedinformdecismak.biomedcentral.com/track/pdf/10.1186/s12911-020-01336-2; doi:https://doi.org/10.1186/s12911-020-01336-2; html:https://europepmc.org/articles/PMC7736131; pdf:https://europepmc.org/articles/PMC7736131?pdf=render
 35275994,https://doi.org/10.2337/dc21-1709,Admission Blood Glucose Level and Its Association With Cardiovascular and Renal Complications in Patients Hospitalized With COVID-19.,"Norris T, Razieh C, Yates T, Zaccardi F, Gillies CL, Chudasama YV, Rowlands A, Davies MJ, McCann GP, Banerjee A, Docherty AB, Openshaw PJM, Baillie JK, Semple MG, Lawson CA, Khunti K.",,Diabetes care,2022,2022-05-01,N,,,,"<h4>Objective</h4>To investigate the association between admission blood glucose levels and risk of in-hospital cardiovascular and renal complications.<h4>Research design and methods</h4>In this multicenter prospective study of 36,269 adults hospitalized with COVID-19 between 6 February 2020 and 16 March 2021 (N = 143,266), logistic regression models were used to explore associations between admission glucose level (mmol/L and mg/dL) and odds of in-hospital complications, including heart failure, arrhythmia, cardiac ischemia, cardiac arrest, coagulation complications, stroke, and renal injury. Nonlinearity was investigated using restricted cubic splines. Interaction models explored whether associations between glucose levels and complications were modified by clinically relevant factors.<h4>Results</h4>Cardiovascular and renal complications occurred in 10,421 (28.7%) patients; median admission glucose level was 6.7 mmol/L (interquartile range 5.8-8.7) (120.6 mg/dL [104.4-156.6]). While accounting for confounders, for all complications except cardiac ischemia and stroke, there was a nonlinear association between glucose and cardiovascular and renal complications. For example, odds of heart failure, arrhythmia, coagulation complications, and renal injury decreased to a nadir at 6.4 mmol/L (115 mg/dL), 4.9 mmol/L (88.2 mg/dL), 4.7 mmol/L (84.6 mg/dL), and 5.8 mmol/L (104.4 mg/dL), respectively, and increased thereafter until 26.0 mmol/L (468 mg/dL), 50.0 mmol/L (900 mg/dL), 8.5 mmol/L (153 mg/dL), and 32.4 mmol/L (583.2 mg/dL). Compared with 5 mmol/L (90 mg/dL), odds ratios at these glucose levels were 1.28 (95% CI 0.96, 1.69) for heart failure, 2.23 (1.03, 4.81) for arrhythmia, 1.59 (1.36, 1.86) for coagulation complications, and 2.42 (2.01, 2.92) for renal injury. For most complications, a modifying effect of age was observed, with higher odds of complications at higher glucose levels for patients age <69 years. Preexisting diabetes status had a similar modifying effect on odds of complications, but evidence was strongest for renal injury, cardiac ischemia, and any cardiovascular/renal complication.<h4>Conclusions</h4>Increased odds of cardiovascular or renal complications were observed for admission glucose levels indicative of both hypo- and hyperglycemia. Admission glucose could be used as a marker for risk stratification of high-risk patients. Further research should evaluate interventions to optimize admission glucose on improving COVID-19 outcomes.",,pdf:https://diabetesjournals.org/care/article-pdf/45/5/1132/678515/dc211709.pdf; doi:https://doi.org/10.2337/dc21-1709; html:https://europepmc.org/articles/PMC9174963; pdf:https://europepmc.org/articles/PMC9174963?pdf=render; doi:https://doi.org/10.2337/dc21-1709
-38529358,https://doi.org/10.1093/braincomms/fcae088,"<i>Helicobacter pylori</i>, persistent infection burden and structural brain imaging markers.","Beydoun MA, Beydoun HA, Hu YH, El-Hajj ZW, Georgescu MF, Noren Hooten N, Li Z, Weiss J, Lyall DM, Waldstein SR, Hedges DW, Gale SD, Launer LJ, Evans MK, Zonderman AB.",,Brain communications,2024,2024-03-13,N,Helicobacter Pylori; Persistent infection; Brain imaging; Cognitive Aging,,,"Persistent infections, whether viral, bacterial or parasitic, including <i>Helicobacter pylori</i> infection, have been implicated in non-communicable diseases, including dementia and other neurodegenerative diseases. In this cross-sectional study, data on 635 cognitively normal participants from the UK Biobank study (2006-21, age range: 40-70 years) were used to examine whether <i>H. pylori</i> seropositivity (e.g. presence of antibodies), serointensities of five <i>H. pylori</i> antigens and a measure of total persistent infection burden were associated with selected brain volumetric structural MRI (total, white, grey matter, frontal grey matter (left/right), white matter hyperintensity as percent intracranial volume and bi-lateral sub-cortical volumes) and diffusion-weighted MRI measures (global and tract-specific bi-lateral fractional anisotropy and mean diffusivity), after an average 9-10 years of lag time. Persistent infection burden was calculated as a cumulative score of seropositivity for over 20 different pathogens. Multivariable-adjusted linear regression analyses were conducted, whereby selected potential confounders (all measures) and intracranial volume (sub-cortical volumes) were adjusted, with stratification by Alzheimer's disease polygenic risk score tertile when exposures were <i>H. pylori</i> antigen serointensities. Type I error was adjusted to 0.007. We report little evidence of an association between <i>H. pylori</i> seropositivity and persistent infection burden with various volumetric outcomes (<i>P</i> > 0.007, from multivariable regression models), unlike previously reported in past research. However, <i>H. pylori</i> antigen serointensities, particularly immunoglobulin G against the vacuolating cytotoxin A, GroEL and outer membrane protein antigens, were associated with poorer tract-specific white matter integrity (<i>P</i> < 0.007), with outer membrane protein serointensity linked to worse outcomes in cognition-related tracts such as the external capsule, the anterior limb of the internal capsule and the cingulum, specifically at low Alzheimer's disease polygenic risk. Vacuolating cytotoxin A serointensity was associated with greater white matter hyperintensity volume among individuals with mid-level Alzheimer's disease polygenic risk, while among individuals with the highest Alzheimer's disease polygenic risk, the urease serointensity was consistently associated with reduced bi-lateral caudate volumes and the vacuolating cytotoxin A serointensity was linked to reduced right putamen volume (<i>P</i> < 0.007). Outer membrane protein and urease were associated with larger sub-cortical volumes (e.g. left putamen and right nucleus accumbens) at middle Alzheimer's disease polygenic risk levels (<i>P</i> < 0.007). Our results shed light on the relationship between <i>H. pylori</i> seropositivity, <i>H. pylori</i> antigen levels and persistent infection burden with brain volumetric structural measures. These data are important given the links between infectious agents and neurodegenerative diseases, including Alzheimer's disease, and can be used for the development of drugs and preventive interventions that would reduce the burden of those diseases.",,doi:https://doi.org/10.1093/braincomms/fcae088; html:https://europepmc.org/articles/PMC10961948; pdf:https://europepmc.org/articles/PMC10961948?pdf=render; doi:https://doi.org/10.1093/braincomms/fcae088
 37193316,https://doi.org/10.1016/j.xops.2023.100293,"A Datasheet for the INSIGHT Birmingham, Solihull, and Black Country Diabetic Retinopathy Screening Dataset.","Kale AU, Mills A, Guggenheim E, Gee D, Bodza S, Anumakonda A, Doal R, Williams R, Gallier S, Lee WH, Galsworthy P, Benning M, Fanning H, Keane PA, Denniston AK, Mollan SP.",,Ophthalmology science,2023,2023-02-26,Y,Diabetes mellitus; Diabetic retinopathy; Imaging; Dataset; Biomedical Data,,,"<h4>Purpose</h4>Diabetic retinopathy (DR) is the most common microvascular complication associated with diabetes mellitus (DM), affecting approximately 40% of this patient population. Early detection of DR is vital to ensure monitoring of disease progression and prompt sight saving treatments as required. This article describes the data contained within the INSIGHT Birmingham, Solihull, and Black Country Diabetic Retinopathy Dataset.<h4>Design</h4>Dataset descriptor for routinely collected eye screening data.<h4>Participants</h4>All diabetic patients aged 12 years and older, attending annual digital retinal photography-based screening within the Birmingham, Solihull, and Black Country Eye Screening Programme.<h4>Methods</h4>The INSIGHT Health Data Research Hub for Eye Health is a National Health Service (NHS)-led ophthalmic bioresource that provides researchers with safe access to anonymized, routinely collected data from contributing NHS hospitals to advance research for patient benefit. This report describes the INSIGHT Birmingham, Solihull, and Black Country DR Screening Dataset, a dataset of anonymized images and linked screening data derived from the United Kingdom's largest regional DR screening program.<h4>Main outcome measures</h4>This dataset consists of routinely collected data from the eye screening program. The data primarily include retinal photographs with the associated DR grading data. Additional data such as corresponding demographic details, information regarding patients' diabetic status, and visual acuity data are also available. Further details regarding available data points are available in the supplementary information, in addition to the INSIGHT webpage included below.<h4>Results</h4>At the time point of this analysis (December 31, 2019), the dataset comprised 6 202 161 images from 246 180 patients, with a dataset inception date of January 1, 2007. The dataset includes 1 360 547 grading episodes between R0M0 and R3M1.<h4>Conclusions</h4>This dataset descriptor article summarizes the content of the dataset, how it has been curated, and what its potential uses are. Data are available through a structured application process for research studies that support discovery, clinical evidence analyses, and innovation in artificial intelligence technologies for patient benefit. Further information regarding the data repository and contact details can be found at https://www.insight.hdrhub.org/.<h4>Financial disclosures</h4>Proprietary or commercial disclosure may be found after the references.",,pdf:http://www.ophthalmologyscience.org/article/S2666914523000258/pdf; doi:https://doi.org/10.1016/j.xops.2023.100293; html:https://europepmc.org/articles/PMC10182318; pdf:https://europepmc.org/articles/PMC10182318?pdf=render
 38686369,https://doi.org/10.3389/fmed.2024.1354070,Development of automated neural network prediction for echocardiographic left ventricular ejection fraction.,"Zhang Y, Liu B, Bunting KV, Brind D, Thorley A, Karwath A, Lu W, Zhou D, Wang X, Mobley AR, Tica O, Gkoutos GV, Kotecha D, Duan J.",,Frontiers in medicine,2024,2024-04-03,Y,Artificial intelligence; Atrial fibrillation; Ejection fraction; Heart Failure; Echocardiogram,,,"<h4>Introduction</h4>The echocardiographic measurement of left ventricular ejection fraction (LVEF) is fundamental to the diagnosis and classification of patients with heart failure (HF).<h4>Methods</h4>This paper aimed to quantify LVEF automatically and accurately with the proposed pipeline method based on deep neural networks and ensemble learning. Within the pipeline, an Atrous Convolutional Neural Network (ACNN) was first trained to segment the left ventricle (LV), before employing the area-length formulation based on the ellipsoid single-plane model to calculate LVEF values. This formulation required inputs of LV area, derived from segmentation using an improved Jeffrey's method, as well as LV length, derived from a novel ensemble learning model. To further improve the pipeline's accuracy, an automated peak detection algorithm was used to identify end-diastolic and end-systolic frames, avoiding issues with human error. Subsequently, single-beat LVEF values were averaged across all cardiac cycles to obtain the final LVEF.<h4>Results</h4>This method was developed and internally validated in an open-source dataset containing 10,030 echocardiograms. The Pearson's correlation coefficient was 0.83 for LVEF prediction compared to expert human analysis (<i>p</i> < 0.001), with a subsequent area under the receiver operator curve (AUROC) of 0.98 (95% confidence interval 0.97 to 0.99) for categorisation of HF with reduced ejection (HFrEF; LVEF<40%). In an external dataset with 200 echocardiograms, this method achieved an AUC of 0.90 (95% confidence interval 0.88 to 0.91) for HFrEF assessment.<h4>Conclusion</h4>The automated neural network-based calculation of LVEF is comparable to expert clinicians performing time-consuming, frame-by-frame manual evaluations of cardiac systolic function.",,pdf:https://www.frontiersin.org/articles/10.3389/fmed.2024.1354070/pdf?isPublishedV2=False; doi:https://doi.org/10.3389/fmed.2024.1354070; html:https://europepmc.org/articles/PMC11057494; pdf:https://europepmc.org/articles/PMC11057494?pdf=render
 38569874,https://doi.org/10.1136/jnnp-2024-333530,"Trends in the prevalence and pharmacological management of migraine during pregnancy in the UK, 2000-2018.","Phillips K, Nirantharakumar K, Wakerley BR, Crowe FL.",,"Journal of neurology, neurosurgery, and psychiatry",2024,2024-09-17,Y,Migraine,,,"<h4>Background</h4>Migraine is common in women of reproductive age. This study aimed to (1) describe the prevalence of migraine in pregnant women in the UK, (2) identify drugs commonly prescribed for migraine during pregnancy and (3) identify characteristics associated with being prescribed medication for migraine during pregnancy.<h4>Methods</h4>The Clinical Practice Research Datalink pregnancy register, a database of pregnancy episodes identified in anonymised primary care health records, was used.Crude and age-standardised prevalence of migraine during pregnancy and the proportion of women with migraine prescribed drugs used for migraine management were calculated for each year between 2000 and 2018.Logistic regression was used to describe the relationship between patient characteristics and being prescribed migraine medication during pregnancy.<h4>Results</h4>1 377 053 pregnancies were included, of which 187 328 were in women with a history of migraine. The age-adjusted prevalence increased from 11.4% in 2000 to 17.2% in 2018. There was an increase in the rates of prescription for numerous medications for the management of migraine.Older women (adjusted OR (aOR) 1.41 (1.20 to 1.66)), women of black (aOR 1.40 (1.32 to 1.48)) and South Asian ethnicity (aOR 1.48 (1.38 to 1.59)), those living in the most deprived areas (aOR 1.60 (1.54 to 1.66)), women who were obese (aOR 1.39 (1.35 to 1.43)), smokers (aOR 1.15 (1.12 to 1.18)) and those with comorbid conditions were more likely to receive a prescription during pregnancy.<h4>Conclusions</h4>Rates of recorded migraine have increased over the past two decades as well as rates of prescribing in women with migraine. Higher prescribing rates are seen in certain groups, which has the potential to exacerbate health inequalities.",,pdf:https://jnnp.bmj.com/content/jnnp/early/2024/04/03/jnnp-2024-333530.full.pdf; doi:https://doi.org/10.1136/jnnp-2024-333530; html:https://europepmc.org/articles/PMC11420713; pdf:https://europepmc.org/articles/PMC11420713?pdf=render
@@ -185,59 +185,59 @@ PMC11227019,https://doi.org/,Adoption of high-sensitivity cardiac troponin for r
 36609412,https://doi.org/10.1136/archdischild-2022-324713,"Confirmed SARS-CoV-2 infection in Scottish neonates 2020-2022: a national, population-based cohort study.","Goulding A, McQuaid F, Lindsay L, Agrawal U, Auyeung B, Calvert C, Carruthers J, Denny C, Donaghy J, Hillman S, Hopcroft L, Hopkins L, McCowan C, McLaughlin T, Moore E, Ritchie L, Simpson CR, Taylor B, Fenton L, Pollock L, Gale C, Kurinczuk JJ, Robertson C, Sheikh A, Stock S, Wood R.",,Archives of disease in childhood. Fetal and neonatal edition,2023,2023-01-06,Y,epidemiology; Neonatology; Covid-19,,,"<h4>Objectives</h4>To examine neonates in Scotland aged 0-27 days with SARS-CoV-2 infection confirmed by viral testing; the risk of confirmed neonatal infection by maternal and infant characteristics; and hospital admissions associated with confirmed neonatal infections.<h4>Design</h4>Population-based cohort study.<h4>Setting and population</h4>All live births in Scotland, 1 March 2020-31 January 2022.<h4>Results</h4>There were 141 neonates with confirmed SARS-CoV-2 infection over the study period, giving an overall infection rate of 153 per 100 000 live births (141/92 009, 0.15%). Among infants born to women with confirmed infection around the time of birth, the confirmed neonatal infection rate was 1812 per 100 000 live births (15/828, 1.8%). Two-thirds (92/141, 65.2%) of neonates with confirmed infection had an associated admission to neonatal or (more commonly) paediatric care. Six of these babies (6/92, 6.5%) were admitted to neonatal and/or paediatric intensive care; however, none of these six had COVID-19 recorded as their main diagnosis. There were no neonatal deaths among babies with confirmed infection.<h4>Implications and relevance</h4>Confirmed neonatal SARS-CoV-2 infection was uncommon over the first 23 months of the pandemic in Scotland. Secular trends in the neonatal confirmed infection rate broadly followed those seen in the general population, although at a lower level. Maternal confirmed infection at birth was associated with an increased risk of neonatal confirmed infection. Two-thirds of neonates with confirmed infection had an associated admission to hospital, with resulting implications for the baby, family and services, although their outcomes were generally good. Ascertainment of confirmed infection depends on the extent of testing, and this is likely to have varied over time and between groups: the extent of unconfirmed infection is inevitably unknown.",,pdf:https://fn.bmj.com/content/fetalneonatal/early/2023/01/05/archdischild-2022-324713.full.pdf; doi:https://doi.org/10.1136/archdischild-2022-324713; html:https://europepmc.org/articles/PMC10313998; pdf:https://europepmc.org/articles/PMC10313998?pdf=render
 35706489,https://doi.org/10.1016/j.eclinm.2022.101428,Impact of ethnicity on the accuracy of measurements of oxygen saturations: A retrospective observational cohort study.,"Bangash MN, Hodson J, Evison F, Patel JM, Johnston AM, Gallier S, Sapey E, Parekh D.",,EClinicalMedicine,2022,2022-05-06,Y,Inequalities; Ethnicity; Oxygen Saturations,,,"<h4>Background</h4>Pulse oximeters are routinely used in community and hospital settings worldwide as a rapid, non-invasive, and readily available bedside tool to approximate blood oxygenation. Potential racial biases in peripheral oxygen saturation (SpO2) measurements may influence the accuracy of pulse oximetry readings and impact clinical decision making. We aimed to assess whether the accuracy of oxygen saturation measured by SpO2, relative to arterial blood gas (SaO2), varies by ethnicity.<h4>Methods</h4>In this large retrospective observational cohort study covering four NHS Hospitals serving a large urban population in Birmingham, United Kingdom, consecutive pairs of SpO2 and SaO2 measurements taken on the same patient within an interval of less than 20 min were identified from electronic patient records. Where multiple pairs of measurements were recorded in a spell, only the first was included in the analysis. The differences between SpO2 and SaO2 measurements were compared across groups of self-identified ethnicity. These differences were subsequently adjusted for age, sex, bilirubin, systolic blood pressure, carboxyhaemaglobin saturations and the time interval between SpO2 and SaO2 measurements.<h4>Findings</h4>Paired O2 saturation measurements from 16,818 inpatient spells between 1st January 2017 and 18th February 2021 were analysed. The cohort self-identified as being of White (81.2%), Asian (11.7%), Black (4.0%), or Other (3.2%) ethnicities. Across the cohort, SpO2 was statistically significantly higher than SaO2 (<i>p</i> < 0.0001), with medians of 98% (interquartile range [IQR]: 95-100%) vs. 97% (IQR: 96-99%), and a median difference of 0.5% points (pps; 95% confidence interval [CI]: 0.5-0.6). However, the size of this difference varied considerably with the magnitude of SaO2, with SpO2 overestimating by a median by 3.8pp (IQR: 0.4, 8.8) for SaO2 values <90% but underestimating by a median of 0.4pp (IQR: -2.0, 1.4) for an SaO2 of 95%. The differences between SpO2 and SaO2 were also found to vary by ethnicity, with this difference being 0.8pp (95% CI: 0.6-1.0, <i>p</i> < 0.0001) greater in those of Black vs. White ethnicity. These differences resulted in 8.7% vs. 6.1% of Black vs. White patients who were classified as normoxic on SpO2 actually being hypoxic on the gold standard SaO2 (odds ratio: 1.47, 95% CI: 1.09-1.98, <i>p</i> = 0.012).<h4>Interpretation</h4>Pulse oximetry may overestimate O2 saturation, and this is possibly more pronounced in patients of Black ethnicity. Prospective studies are urgently warranted to assess the impact of ethnicity on the accuracy of pulse oximetry, to ensure care is optimised for all.<h4>Funding</h4>PIONEER, the Health Data Research UK (HDR-UK) Health Data Research Hub in acute care.",,pdf:http://www.thelancet.com/article/S2589537022001584/pdf; doi:https://doi.org/10.1016/j.eclinm.2022.101428; html:https://europepmc.org/articles/PMC9096912; pdf:https://europepmc.org/articles/PMC9096912?pdf=render
 34148733,https://doi.org/10.1016/j.bja.2021.05.018,Mortality after surgery with SARS-CoV-2 infection in England: a population-wide epidemiological study.,"Abbott TEF, Fowler AJ, Dobbs TD, Gibson J, Shahid T, Dias P, Akbari A, Whitaker IS, Pearse RM.",,British journal of anaesthesia,2021,2021-06-11,Y,Surgery; Anaesthesia; epidemiology; Public Policy; Covid-19,,,"<h4>Background</h4>The COVID-19 pandemic has heavily impacted elective and emergency surgery around the world. We aimed to confirm the incidence of perioperative severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and associated mortality after surgery.<h4>Methods</h4>Analysis of routine electronic health record data from NHS hospitals in England. We extracted data from Hospital Episode Statistics in England describing adult patients undergoing surgery between January 1, 2020 and February 28, 2021. The exposure was SARS-CoV-2 infection defined by International Classification of Diseases (ICD)-10 codes. The primary outcome measure was 90 day in-hospital mortality. Data were analysed using multivariable logistic regression adjusted for age, sex, Charlson Comorbidity Index, Index of Multiple Deprivation, presence of cancer, surgical procedure type and admission acuity. Results are presented as n (%) and odds ratios (OR) with 95% confidence intervals (CI).<h4>Results</h4>We identified 2 666 978 patients undergoing surgery of whom 28 777 (1.1%) had SARS-CoV-2 infection. In total, 26 364 (1.0%) patients died in hospital. SARS-CoV-2 infection was associated with a much greater risk of death (SARS-CoV-2: 6153/28 777 [21.4%] vs no SARS-CoV-2: 20 211/2 638 201 [0.8%]; OR=5.7 [95% CI, 5.5-5.9]; P<0.001). Amongst patients undergoing elective surgery, 2412/1 857 586 (0.1%) had SARS-CoV-2, of whom 172/2412 (7.1%) died, compared with 1414/1 857 586 (0.1%) patients without SARS-CoV-2 (OR=25.8 [95% CI, 21.7-30.9]; P<0.001). Amongst patients undergoing emergency surgery, 22 918/582 292 (3.9%) patients had SARS-CoV-2, of whom 5752/22 918 (25.1%) died, compared with 18 060/559 374 (3.4%) patients without SARS-CoV-2 (OR=5.5 [95% CI, 5.3-5.7]; P<0.001).<h4>Conclusions</h4>The low incidence of SARS-CoV-2 infection in NHS surgical pathways suggests current infection prevention and control policies are highly effective. However, the high mortality amongst patients with SARS-CoV-2 suggests these precautions cannot be safely relaxed.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8192173; doi:https://doi.org/10.1016/j.bja.2021.05.018; html:https://europepmc.org/articles/PMC8192173; pdf:https://europepmc.org/articles/PMC8192173?pdf=render
-38331807,https://doi.org/10.1186/s12916-024-03271-9,Childhood maltreatment and risk of endocrine diseases: an exploration of mediating pathways using sequential mediation analysis.,"Wen S, Zhu J, Han X, Li Y, Liu H, Yang H, Hou C, Xu S, Wang J, Hu Y, Qu Y, Liu D, Aspelund T, Fang F, Valdimarsdóttir UA, Song H.",,BMC medicine,2024,2024-02-08,Y,Endocrine diseases; Childhood Maltreatment; Sequential Mediation Analysis; Psychological Adversities,,,"<h4>Background</h4>Adverse childhood experiences (ACEs), including childhood maltreatment, have been linked with increased risk of diabetes and obesity during adulthood. A comprehensive assessment on the associations between childhood maltreatment and all major endocrine diseases, as well as the relative importance of different proposed mechanistic pathways on these associations, is currently lacking.<h4>Methods</h4>Based on the UK Biobank, we constructed a cohort including 151,659 participants with self-reported data on childhood maltreatment who were 30 years of age or older on/after January 1, 1985. All participants were followed from the index date (i.e., January 1, 1985, or their 30th birthday, whichever came later) until the first diagnosis of any or specific (12 individual diagnoses and 9 subtypes) endocrine diseases, death, or the end of follow-up (December 31, 2019), whichever occurred first. We used Cox models to examine the association of childhood maltreatment, treated as continuous (i.e., the cumulative number of experienced childhood maltreatment), ordinal (i.e., 0, 1 and ≥ 2), or binary (< 2 and ≥ 2) variable, with any and specific endocrine diseases, adjusted for multiple covariates. We further examined the risk of having multiple endocrine diseases using Linear or Logistic Regression models. Then, sequential mediation analyses were performed to assess the contribution of four possible mechanisms (i.e., suboptimal socioeconomic status (SES), psychological adversities, unfavorable lifestyle, and biological alterations) on the observed associations.<h4>Results</h4>During an average follow-up of 30.8 years, 20,885 participants received a diagnosis of endocrine diseases. We observed an association between the cumulative number of experienced childhood maltreatment and increased risk of being diagnosed with any endocrine disease (adjusted hazard ratio (HR) = 1.10, 95% confidence interval 1.09-1.12). The HR was 1.26 (1.22-1.30) when comparing individuals ≥ 2 with those with < 2 experienced childhood maltreatment. We further noted the most pronounced associations for type 2 diabetes (1.40 (1.33-1.48)) and hypothalamic-pituitary-adrenal (HPA)-axis-related endocrine diseases (1.38 (1.17-1.62)), and the association was stronger for having multiple endocrine diseases, compared to having one (odds ratio (95% CI) = 1.24 (1.19-1.30), 1.35 (1.27-1.44), and 1.52 (1.52-1.53) for 1, 2, and ≥ 3, respectively). Sequential mediation analyses showed that the association between childhood maltreatment and endocrine diseases was consistently and most distinctly mediated by psychological adversities (15.38 ~ 44.97%), while unfavorable lifestyle (10.86 ~ 25.32%) was additionally noted for type 2 diabetes whereas suboptimal SES (14.42 ~ 39.33%) for HPA-axis-related endocrine diseases.<h4>Conclusions</h4>Our study demonstrates that adverse psychological sequel of childhood maltreatment constitutes the main pathway to multiple endocrine diseases, particularly type 2 diabetes and HPA-axis-related endocrine diseases. Therefore, increased access to evidence-based mental health services may also be pivotal in reducing the risk of endocrine diseases among childhood maltreatment-exposed individuals.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-024-03271-9; doi:https://doi.org/10.1186/s12916-024-03271-9; html:https://europepmc.org/articles/PMC10854183; pdf:https://europepmc.org/articles/PMC10854183?pdf=render
-34544601,https://doi.org/10.1016/j.vaccine.2021.09.019,"Inequalities in coverage of COVID-19 vaccination: A population register based cross-sectional study in Wales, UK.","Perry M, Akbari A, Cottrell S, Gravenor MB, Roberts R, Lyons RA, Bedston S, Torabi F, Griffiths L.",,Vaccine,2021,2021-09-08,Y,Ethnic Groups; Vaccination; Socioeconomic Factors; Immunisation; Covid-19 Vaccines,,,"The COVID-19 pandemic has highlighted existing health inequalities for ethnic minority groups and those living in more socioeconomically deprived areas in the UK. With higher levels of severe outcomes in these groups, equitable vaccination coverage should be prioritised. The aim of this study was to identify inequalities in coverage of COVID-19 vaccination in Wales, UK and to highlight areas which may benefit from routine enhanced surveillance and targeted interventions. Records within the Wales Immunisation System (WIS) population register were linked to the Welsh Demographic Service Dataset (WDSD) and central list of shielding patients, held within the Secure Anonymised Information Linkage (SAIL) Databank. Ethnic group was derived from the 2011 census and over 20 administrative electronic health record (EHR) data sources. Uptake of first dose of any COVID-19 vaccine was analysed over time, with the odds of being vaccinated as at 25th April 2021 by sex, health board of residence, rural/urban classification, deprivation quintile and ethnic group presented. Using logistic regression models, analyses were adjusted for age group, care home resident status, health and social care worker status and shielding status. This study included 1,256,412 individuals aged 50 years and over. Vaccine coverage increased steadily from 8th December 2020 until mid-April 2021. Overall uptake of first dose of COVID-19 vaccine in this group was 92.1%. After adjustment the odds of being vaccinated were lower for individuals who were male, resident in the most deprived areas, resident in an urban area and an ethnic group other than White. The largest inequality was seen between ethnic groups, with the odds of being vaccinated 0.22 (95 %CI 0.21-0.24) if in any Black ethnic group compared to any White ethnic group. Ongoing monitoring of inequity in uptake of vaccinations is required, with better targeted interventions and engagement with deprived and ethnic communities to improve vaccination uptake.",,doi:https://doi.org/10.1016/j.vaccine.2021.09.019; doi:https://doi.org/10.1016/j.vaccine.2021.09.019; html:https://europepmc.org/articles/PMC8423991
-36332519,https://doi.org/10.1016/j.ijmedinf.2022.104905,Creation of a core competency framework for clinical informatics: From genesis to maintaining relevance.,"Davies A, Hassey A, Williams J, Moulton G.",,International journal of medical informatics,2022,2022-10-30,N,Informatics; Core Competencies; Competency Framework; Healthcare Workforce; Informaticians,,,"<h4>Background</h4>The United Kingdom's Faculty of Clinical Informatics (FCI) embarked on the creation of a core competency framework in response to the need to provide support to those working in clinical and health and social care that also hold informatics roles.<h4>Methods</h4>The work spanned several phases and utilised a mixed-methods approach consisting of interviews, surveys, job listing analysis, expert discussions and a systematic literature review. The work presented here explores the lessons learnt from the process of creating the framework and the next steps for ensuring its use and continued relevance.<h4>Results</h4>A core competency framework was generated with six domains, 36 sub-domains and 111 individual competency statements. A discussion and eight key recommendations are presented based on the development of this framework.<h4>Conclusion</h4>Definition of the target audience is important to manage scope and define purpose. The use of robust reproducible methods helps to establish a strong evidence base. Competency frameworks should be living documents, ideally presented in an accessible digital form to enable easy use and embedding in other tools (e.g. for accreditation or to search competencies).",,doi:https://doi.org/10.1016/j.ijmedinf.2022.104905
-37828061,https://doi.org/10.1038/s41598-023-43193-9,Consistent effects of the genetics of happiness across the lifespan and ancestries in multiple cohorts.,"Ward J, Lyall LM, Cullen B, Strawbridge RJ, Zhu X, Stanciu I, Aman A, Niedzwiedz CL, Anderson J, Bailey MES, Lyall DM, Pell JP.",,Scientific reports,2023,2023-10-12,Y,,,,"Happiness is a fundamental human affective trait, but its biological basis is not well understood. Using a novel approach, we construct LDpred-inf polygenic scores of a general happiness measure in 2 cohorts: the Adolescent Brain Cognitive Development (ABCD) cohort (N = 15,924, age range 9.23-11.8 years), the Add Health cohort (N = 9129, age range 24.5-34.7) to determine associations with several well-being and happiness measures. Additionally, we investigated associations between genetic scores for happiness and brain structure in ABCD (N = 9626, age range (8.9-11) and UK Biobank (N = 16,957, age range 45-83). We detected significant (p.FDR < 0.05) associations between higher genetic scores vs. several well-being measures (best r<sup>2</sup> = 0.019) in children of multiple ancestries in ABCD and small yet significant correlations with a happiness measure in European participants in Add Health (r<sup>2</sup> = 0.004). Additionally, we show significant associations between lower genetic scores for happiness with smaller structural brain phenotypes in a white British subsample of UK Biobank and a white sub-sample group of ABCD. We demonstrate that the genetic basis for general happiness level appears to have a consistent effect on happiness and wellbeing measures throughout the lifespan, across multiple ancestral backgrounds, and multiple brain structures.",,pdf:https://www.nature.com/articles/s41598-023-43193-9.pdf; doi:https://doi.org/10.1038/s41598-023-43193-9; html:https://europepmc.org/articles/PMC10570373; pdf:https://europepmc.org/articles/PMC10570373?pdf=render
 38280379,https://doi.org/10.1016/j.xcrm.2023.101391,Evidence for a causal link between intra-pancreatic fat deposition and pancreatic cancer: A prospective cohort and Mendelian randomization study.,"Yamazaki H, Streicher SA, Wu L, Fukuhara S, Wagner R, Heni M, Grossman SR, Lenz HJ, Setiawan VW, Le Marchand L, Huang BZ.",,Cell reports. Medicine,2024,2024-01-26,Y,Pancreatic adenocarcinoma; Pancreas Cancer; Fatty Pancreas; Pancreatic Fat; Pancreatic Steatosis; Pancreas Fat,,,"Prior observational studies suggest an association between intra-pancreatic fat deposition (IPFD) and pancreatic ductal adenocarcinoma (PDAC); however, the causal relationship is unclear. To elucidate causality, we conduct a prospective observational study using magnetic resonance imaging (MRI)-measured IPFD data and also perform a Mendelian randomization study using genetic instruments for IPFD. In the observational study, we use UK Biobank data (N = 29,463, median follow-up: 4.5 years) and find that high IPFD (>10%) is associated with PDAC risk (adjusted hazard ratio [HR]: 3.35, 95% confidence interval [95% CI]: 1.60-7.00). In the Mendelian randomization study, we leverage eight out of nine IPFD-associated genetic variants (p < 5 × 10<sup>-8</sup>) from a genome-wide association study in the UK Biobank (N = 25,617) and find that genetically determined IPFD is associated with PDAC (odds ratio [OR] per 1-standard deviation [SD] increase in IPFD: 2.46, 95% CI: 1.38-4.40) in the Pancreatic Cancer Cohort Consortium I, II, III (PanScan I-III)/Pancreatic Cancer Case-Control Consortium (PanC4) dataset (8,275 PDAC cases and 6,723 non-cases). This study provides evidence for a potential causal role of IPFD in the pathogenesis of PDAC. Thus, reducing IPFD may lower PDAC risk.",,doi:https://doi.org/10.1016/j.xcrm.2023.101391; html:https://europepmc.org/articles/PMC10897551; pdf:https://europepmc.org/articles/PMC10897551?pdf=render
+34544601,https://doi.org/10.1016/j.vaccine.2021.09.019,"Inequalities in coverage of COVID-19 vaccination: A population register based cross-sectional study in Wales, UK.","Perry M, Akbari A, Cottrell S, Gravenor MB, Roberts R, Lyons RA, Bedston S, Torabi F, Griffiths L.",,Vaccine,2021,2021-09-08,Y,Ethnic Groups; Vaccination; Socioeconomic Factors; Immunisation; Covid-19 Vaccines,,,"The COVID-19 pandemic has highlighted existing health inequalities for ethnic minority groups and those living in more socioeconomically deprived areas in the UK. With higher levels of severe outcomes in these groups, equitable vaccination coverage should be prioritised. The aim of this study was to identify inequalities in coverage of COVID-19 vaccination in Wales, UK and to highlight areas which may benefit from routine enhanced surveillance and targeted interventions. Records within the Wales Immunisation System (WIS) population register were linked to the Welsh Demographic Service Dataset (WDSD) and central list of shielding patients, held within the Secure Anonymised Information Linkage (SAIL) Databank. Ethnic group was derived from the 2011 census and over 20 administrative electronic health record (EHR) data sources. Uptake of first dose of any COVID-19 vaccine was analysed over time, with the odds of being vaccinated as at 25th April 2021 by sex, health board of residence, rural/urban classification, deprivation quintile and ethnic group presented. Using logistic regression models, analyses were adjusted for age group, care home resident status, health and social care worker status and shielding status. This study included 1,256,412 individuals aged 50 years and over. Vaccine coverage increased steadily from 8th December 2020 until mid-April 2021. Overall uptake of first dose of COVID-19 vaccine in this group was 92.1%. After adjustment the odds of being vaccinated were lower for individuals who were male, resident in the most deprived areas, resident in an urban area and an ethnic group other than White. The largest inequality was seen between ethnic groups, with the odds of being vaccinated 0.22 (95 %CI 0.21-0.24) if in any Black ethnic group compared to any White ethnic group. Ongoing monitoring of inequity in uptake of vaccinations is required, with better targeted interventions and engagement with deprived and ethnic communities to improve vaccination uptake.",,doi:https://doi.org/10.1016/j.vaccine.2021.09.019; doi:https://doi.org/10.1016/j.vaccine.2021.09.019; html:https://europepmc.org/articles/PMC8423991
+38331807,https://doi.org/10.1186/s12916-024-03271-9,Childhood maltreatment and risk of endocrine diseases: an exploration of mediating pathways using sequential mediation analysis.,"Wen S, Zhu J, Han X, Li Y, Liu H, Yang H, Hou C, Xu S, Wang J, Hu Y, Qu Y, Liu D, Aspelund T, Fang F, Valdimarsdóttir UA, Song H.",,BMC medicine,2024,2024-02-08,Y,Endocrine diseases; Childhood Maltreatment; Sequential Mediation Analysis; Psychological Adversities,,,"<h4>Background</h4>Adverse childhood experiences (ACEs), including childhood maltreatment, have been linked with increased risk of diabetes and obesity during adulthood. A comprehensive assessment on the associations between childhood maltreatment and all major endocrine diseases, as well as the relative importance of different proposed mechanistic pathways on these associations, is currently lacking.<h4>Methods</h4>Based on the UK Biobank, we constructed a cohort including 151,659 participants with self-reported data on childhood maltreatment who were 30 years of age or older on/after January 1, 1985. All participants were followed from the index date (i.e., January 1, 1985, or their 30th birthday, whichever came later) until the first diagnosis of any or specific (12 individual diagnoses and 9 subtypes) endocrine diseases, death, or the end of follow-up (December 31, 2019), whichever occurred first. We used Cox models to examine the association of childhood maltreatment, treated as continuous (i.e., the cumulative number of experienced childhood maltreatment), ordinal (i.e., 0, 1 and ≥ 2), or binary (< 2 and ≥ 2) variable, with any and specific endocrine diseases, adjusted for multiple covariates. We further examined the risk of having multiple endocrine diseases using Linear or Logistic Regression models. Then, sequential mediation analyses were performed to assess the contribution of four possible mechanisms (i.e., suboptimal socioeconomic status (SES), psychological adversities, unfavorable lifestyle, and biological alterations) on the observed associations.<h4>Results</h4>During an average follow-up of 30.8 years, 20,885 participants received a diagnosis of endocrine diseases. We observed an association between the cumulative number of experienced childhood maltreatment and increased risk of being diagnosed with any endocrine disease (adjusted hazard ratio (HR) = 1.10, 95% confidence interval 1.09-1.12). The HR was 1.26 (1.22-1.30) when comparing individuals ≥ 2 with those with < 2 experienced childhood maltreatment. We further noted the most pronounced associations for type 2 diabetes (1.40 (1.33-1.48)) and hypothalamic-pituitary-adrenal (HPA)-axis-related endocrine diseases (1.38 (1.17-1.62)), and the association was stronger for having multiple endocrine diseases, compared to having one (odds ratio (95% CI) = 1.24 (1.19-1.30), 1.35 (1.27-1.44), and 1.52 (1.52-1.53) for 1, 2, and ≥ 3, respectively). Sequential mediation analyses showed that the association between childhood maltreatment and endocrine diseases was consistently and most distinctly mediated by psychological adversities (15.38 ~ 44.97%), while unfavorable lifestyle (10.86 ~ 25.32%) was additionally noted for type 2 diabetes whereas suboptimal SES (14.42 ~ 39.33%) for HPA-axis-related endocrine diseases.<h4>Conclusions</h4>Our study demonstrates that adverse psychological sequel of childhood maltreatment constitutes the main pathway to multiple endocrine diseases, particularly type 2 diabetes and HPA-axis-related endocrine diseases. Therefore, increased access to evidence-based mental health services may also be pivotal in reducing the risk of endocrine diseases among childhood maltreatment-exposed individuals.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-024-03271-9; doi:https://doi.org/10.1186/s12916-024-03271-9; html:https://europepmc.org/articles/PMC10854183; pdf:https://europepmc.org/articles/PMC10854183?pdf=render
 38877008,https://doi.org/10.1038/s41541-024-00898-w,Association between antibody responses post-vaccination and severe COVID-19 outcomes in Scotland.,"Macdonald C, Palmateer N, McAuley A, Lindsay L, Hasan T, Hameed SS, Hall E, Jeffrey K, Grange Z, Gousias P, Mavin S, Jarvis L, Cameron JC, Daines L, Tibble H, Simpson CR, McCowan C, Katikireddi SV, Rudan I, Fagbamigbe AF, Ritchie L, Swallow B, Moss P, Robertson C, Sheikh A, Murray J.",,NPJ vaccines,2024,2024-06-14,Y,,,,"Several population-level studies have described individual clinical risk factors associated with suboptimal antibody responses following COVID-19 vaccination, but none have examined multimorbidity. Others have shown that suboptimal post-vaccination responses offer reduced protection to subsequent SARS-CoV-2 infection; however, the level of protection from COVID-19 hospitalisation/death remains unconfirmed. We use national Scottish datasets to investigate the association between multimorbidity and testing antibody-negative, examining the correlation between antibody levels and subsequent COVID-19 hospitalisation/death among double-vaccinated individuals. We found that individuals with multimorbidity ( ≥ five conditions) were more likely to test antibody-negative post-vaccination and 13.37 [6.05-29.53] times more likely to be hospitalised/die from COVID-19 than individuals without conditions. We also show a dose-dependent association between post-vaccination antibody levels and COVID-19 hospitalisation or death, with those with undetectable antibody levels at a significantly higher risk (HR 9.21 [95% CI 4.63-18.29]) of these serious outcomes compared to those with high antibody levels.",,pdf:https://www.nature.com/articles/s41541-024-00898-w.pdf; doi:https://doi.org/10.1038/s41541-024-00898-w; html:https://europepmc.org/articles/PMC11178861; pdf:https://europepmc.org/articles/PMC11178861?pdf=render
-37309989,https://doi.org/10.1002/pds.5656,Prevalent new user designs: A literature review of current implementation practice.,"Tazare J, Gibbons DC, Bokern M, Williamson EJ, Gillespie IA, Cunnington M, Logie J, Douglas IJ.",,Pharmacoepidemiology and drug safety,2023,2023-06-22,N,Literature review; Database Research; Prevalent New User Designs,,,"<h4>Purpose</h4>Prevalent new user (PNU) designs extend the active comparator new user design by allowing for the inclusion of initiators of the study drug who were previously on a comparator treatment. We performed a literature review summarising current practice.<h4>Methods</h4>PubMed was searched for studies applying the PNU design since its proposal in 2017. The review focused on three components. First, we extracted information on the overall study design, including the database used. We summarised information on implementation of the PNU design, including key decisions relating to exposure set definition and estimation of time-conditional propensity scores. Finally, we reviewed the analysis strategy of the matched cohort.<h4>Results</h4>Nineteen studies met the criteria for inclusion. Most studies (73%) implemented the PNU design in electronic health record or registry databases, with the remaining using insurance claims databases. Of 15 studies including a class of prevalent users, 40% deviated from the original exposure set definition proposals in favour of a more complex definition. Four studies did not include prevalent new users but used other aspects of the PNU framework. Several studies lacked details on exposure set definition (n = 2), time-conditional propensity score model (n = 2) or integration of complex analytical techniques, such as the high-dimensional propensity score algorithm (n = 3).<h4>Conclusion</h4>PNU designs have been applied in a range of therapeutic and disease areas. However, to encourage more widespread use of this design and help shape best practice, there is a need for improved accessibility, specifically through the provision of analytical code alongside guidance to support implementation and transparent reporting.",,doi:https://doi.org/10.1002/pds.5656; doi:https://doi.org/10.1002/pds.5656
-35796183,https://doi.org/10.1177/01410768221107119,"SARS-CoV-2 infection risk among 77,587 healthcare workers: a national observational longitudinal cohort study in Wales, United Kingdom, April to November 2020.","Hollinghurst J, North L, Szakmany T, Pugh R, Davies GA, Sivakumaran S, Jarvis R, Rolles M, Pickrell WO, Akbari A, Davies G, Griffiths R, Lyons J, Torabi F, Fry R, Gravenor MB, Lyons RA.",,Journal of the Royal Society of Medicine,2022,2022-07-07,Y,Public Health; Healthcare Workers; Infection Risk; Covid-19; Sars-cov-2,,,"<h4>Objectives</h4>To better understand the risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among healthcare workers, leading to recommendations for the prioritisation of personal protective equipment, testing, training and vaccination.<h4>Design</h4>Observational, longitudinal, national cohort study.<h4>Setting</h4>Our cohort were secondary care (hospital-based) healthcare workers employed by NHS Wales (United Kingdom) organisations from 1 April 2020 to 30 November 2020.<h4>Participants</h4>We included 577,756 monthly observations among 77,587 healthcare workers. Using linked anonymised datasets, participants were grouped into 20 staff roles. Additionally, each role was deemed either patient-facing, non-patient-facing or undetermined. This was linked to individual demographic details and dates of positive SARS-CoV-2 PCR tests.<h4>Main outcome measures</h4>We used univariable and multivariable logistic regression models to determine odds ratios (ORs) for the risk of a positive SARS-CoV-2 PCR test.<h4>Results</h4>Patient-facing healthcare workers were at the highest risk of SARS-CoV-2 infection with an adjusted OR (95% confidence interval [CI]) of 2.28 (95% CI 2.10-2.47). We found that after adjustment, foundation year doctors (OR 1.83 [95% CI 1.47-2.27]), healthcare support workers [OR 1.36 [95% CI 1.20-1.54]) and hospital nurses (OR 1.27 [95% CI 1.12-1.44]) were at the highest risk of infection among all staff groups. Younger healthcare workers and those living in more deprived areas were at a higher risk of infection. We also observed that infection rates varied over time and by organisation.<h4>Conclusions</h4>These findings have important policy implications for the prioritisation of vaccination, testing, training and personal protective equipment provision for patient-facing roles and the higher risk staff groups.",,doi:https://doi.org/10.1177/01410768221107119; doi:https://doi.org/10.1177/01410768221107119; html:https://europepmc.org/articles/PMC9747896; pdf:https://europepmc.org/articles/PMC9747896?pdf=render
+37828061,https://doi.org/10.1038/s41598-023-43193-9,Consistent effects of the genetics of happiness across the lifespan and ancestries in multiple cohorts.,"Ward J, Lyall LM, Cullen B, Strawbridge RJ, Zhu X, Stanciu I, Aman A, Niedzwiedz CL, Anderson J, Bailey MES, Lyall DM, Pell JP.",,Scientific reports,2023,2023-10-12,Y,,,,"Happiness is a fundamental human affective trait, but its biological basis is not well understood. Using a novel approach, we construct LDpred-inf polygenic scores of a general happiness measure in 2 cohorts: the Adolescent Brain Cognitive Development (ABCD) cohort (N = 15,924, age range 9.23-11.8 years), the Add Health cohort (N = 9129, age range 24.5-34.7) to determine associations with several well-being and happiness measures. Additionally, we investigated associations between genetic scores for happiness and brain structure in ABCD (N = 9626, age range (8.9-11) and UK Biobank (N = 16,957, age range 45-83). We detected significant (p.FDR < 0.05) associations between higher genetic scores vs. several well-being measures (best r<sup>2</sup> = 0.019) in children of multiple ancestries in ABCD and small yet significant correlations with a happiness measure in European participants in Add Health (r<sup>2</sup> = 0.004). Additionally, we show significant associations between lower genetic scores for happiness with smaller structural brain phenotypes in a white British subsample of UK Biobank and a white sub-sample group of ABCD. We demonstrate that the genetic basis for general happiness level appears to have a consistent effect on happiness and wellbeing measures throughout the lifespan, across multiple ancestral backgrounds, and multiple brain structures.",,pdf:https://www.nature.com/articles/s41598-023-43193-9.pdf; doi:https://doi.org/10.1038/s41598-023-43193-9; html:https://europepmc.org/articles/PMC10570373; pdf:https://europepmc.org/articles/PMC10570373?pdf=render
 38553835,https://doi.org/10.1002/jcsm.13461,Leukocyte telomere length is associated with MRI-thigh fat-free muscle volume: data from 16 356 UK Biobank adults.,"Kirk B, Kuo CL, Liu P, Xiang M, Earp JE, Kositsawat J, Kuchel GA, Duque G.",,"Journal of cachexia, sarcopenia and muscle",2024,2024-03-29,Y,Skeletal muscle; Cellular senescence; Trabecular Bone; Osteosarcopenia,,,"<h4>Background</h4>Telomere attrition may share common biological mechanisms with bone and muscle loss with aging. Here, we investigated the association between these hallmarks of aging using data from UK Biobank, a large observational study.<h4>Methods</h4>Leukocyte telomere length (LTL as T/S ratio) was measured using a multiplex qPCR assay at baseline (2006-2010). Bone mineral density (whole body and regional; via dual-energy X-ray absorptiometry), trabecular bone score (via lumbar-spine dual-energy X-ray absorptiometry images), fat-free muscle volume (thighs; via magnetic resonance imaging), and muscle fat infiltration (thighs; via magnetic resonance imaging) were measured during the imaging visit (2014-2018). Regression models were used to model LTL against a muscle or bone outcome, unadjusted and adjusted for covariates.<h4>Results</h4>A total of 16 356 adults (mean age: 62.8 ± 7.5 years, 50.5% women) were included. In the fully adjusted model, thigh fat-free muscle volume was associated with LTL in the overall sample (adjusted standardized β (aβ) = 0.017, 95% CI 0.009 to 0.026, P < 0.001, per SD increase in LTL), with stronger associations in men (aβ = 0.022, 95% CI 0.010 to 0.034, P < 0.001) than in women (aβ = 0.013, 95% CI 0.000 to 0.025, P = 0.041) (sex-LTL P = 0.028). The adjusted odds ratio (aOR) for low thigh fat-free muscle volume (body mass index-adjusted, sex-specific bottom 20%) was 0.93 per SD increase in LTL (95% CI 0.89 to 0.96, P < 0.001) in the overall sample, with stronger associations in men (aOR = 0.92, 95% CI 0.87 to 0.99, P = 0.008) than women (aOR = 0.93, 95% CI 0.88 to 0.98, P = 0.009), although the sex difference was not statistically significant in this model (sex-LTL P = 0.37). LTL was not associated with bone mineral density, trabecular bone score, or muscle fat infiltration in the overall or subgroup analyses (P > 0.05).<h4>Conclusions</h4>LTL was consistently associated with thigh fat-free muscle volume in men and women. Future research should investigate moderating effects of lifestyle factors (e.g., physical activity, nutrition, or chronic diseases) in the association between LTL and muscle volume.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jcsm.13461; doi:https://doi.org/10.1002/jcsm.13461; html:https://europepmc.org/articles/PMC11154769; pdf:https://europepmc.org/articles/PMC11154769?pdf=render
+36332519,https://doi.org/10.1016/j.ijmedinf.2022.104905,Creation of a core competency framework for clinical informatics: From genesis to maintaining relevance.,"Davies A, Hassey A, Williams J, Moulton G.",,International journal of medical informatics,2022,2022-10-30,N,Informatics; Core Competencies; Competency Framework; Healthcare Workforce; Informaticians,,,"<h4>Background</h4>The United Kingdom's Faculty of Clinical Informatics (FCI) embarked on the creation of a core competency framework in response to the need to provide support to those working in clinical and health and social care that also hold informatics roles.<h4>Methods</h4>The work spanned several phases and utilised a mixed-methods approach consisting of interviews, surveys, job listing analysis, expert discussions and a systematic literature review. The work presented here explores the lessons learnt from the process of creating the framework and the next steps for ensuring its use and continued relevance.<h4>Results</h4>A core competency framework was generated with six domains, 36 sub-domains and 111 individual competency statements. A discussion and eight key recommendations are presented based on the development of this framework.<h4>Conclusion</h4>Definition of the target audience is important to manage scope and define purpose. The use of robust reproducible methods helps to establish a strong evidence base. Competency frameworks should be living documents, ideally presented in an accessible digital form to enable easy use and embedding in other tools (e.g. for accreditation or to search competencies).",,doi:https://doi.org/10.1016/j.ijmedinf.2022.104905
+35796183,https://doi.org/10.1177/01410768221107119,"SARS-CoV-2 infection risk among 77,587 healthcare workers: a national observational longitudinal cohort study in Wales, United Kingdom, April to November 2020.","Hollinghurst J, North L, Szakmany T, Pugh R, Davies GA, Sivakumaran S, Jarvis R, Rolles M, Pickrell WO, Akbari A, Davies G, Griffiths R, Lyons J, Torabi F, Fry R, Gravenor MB, Lyons RA.",,Journal of the Royal Society of Medicine,2022,2022-07-07,Y,Public Health; Healthcare Workers; Infection Risk; Covid-19; Sars-cov-2,,,"<h4>Objectives</h4>To better understand the risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among healthcare workers, leading to recommendations for the prioritisation of personal protective equipment, testing, training and vaccination.<h4>Design</h4>Observational, longitudinal, national cohort study.<h4>Setting</h4>Our cohort were secondary care (hospital-based) healthcare workers employed by NHS Wales (United Kingdom) organisations from 1 April 2020 to 30 November 2020.<h4>Participants</h4>We included 577,756 monthly observations among 77,587 healthcare workers. Using linked anonymised datasets, participants were grouped into 20 staff roles. Additionally, each role was deemed either patient-facing, non-patient-facing or undetermined. This was linked to individual demographic details and dates of positive SARS-CoV-2 PCR tests.<h4>Main outcome measures</h4>We used univariable and multivariable logistic regression models to determine odds ratios (ORs) for the risk of a positive SARS-CoV-2 PCR test.<h4>Results</h4>Patient-facing healthcare workers were at the highest risk of SARS-CoV-2 infection with an adjusted OR (95% confidence interval [CI]) of 2.28 (95% CI 2.10-2.47). We found that after adjustment, foundation year doctors (OR 1.83 [95% CI 1.47-2.27]), healthcare support workers [OR 1.36 [95% CI 1.20-1.54]) and hospital nurses (OR 1.27 [95% CI 1.12-1.44]) were at the highest risk of infection among all staff groups. Younger healthcare workers and those living in more deprived areas were at a higher risk of infection. We also observed that infection rates varied over time and by organisation.<h4>Conclusions</h4>These findings have important policy implications for the prioritisation of vaccination, testing, training and personal protective equipment provision for patient-facing roles and the higher risk staff groups.",,doi:https://doi.org/10.1177/01410768221107119; doi:https://doi.org/10.1177/01410768221107119; html:https://europepmc.org/articles/PMC9747896; pdf:https://europepmc.org/articles/PMC9747896?pdf=render
 38237625,https://doi.org/10.1016/s0140-6736(23)02467-4,"Undervaccination and severe COVID-19 outcomes: meta-analysis of national cohort studies in England, Northern Ireland, Scotland, and Wales.",HDR UK COALESCE Consortium.,,"Lancet (London, England)",2024,2024-01-15,N,,,,"<h4>Background</h4>Undervaccination (receiving fewer than the recommended number of SARS-CoV-2 vaccine doses) could be associated with increased risk of severe COVID-19 outcomes-ie, COVID-19 hospitalisation or death-compared with full vaccination (receiving the recommended number of SARS-CoV-2 vaccine doses). We sought to determine the factors associated with undervaccination, and to investigate the risk of severe COVID-19 outcomes in people who were undervaccinated in each UK nation and across the UK.<h4>Methods</h4>We used anonymised, harmonised electronic health record data with whole population coverage to carry out cohort studies in England, Northern Ireland, Scotland, and Wales. Participants were required to be at least 5 years of age to be included in the cohorts. We estimated adjusted odds ratios for undervaccination as of June 1, 2022. We also estimated adjusted hazard ratios (aHRs) for severe COVID-19 outcomes during the period June 1 to Sept 30, 2022, with undervaccination as a time-dependent exposure. We combined results from nation-specific analyses in a UK-wide fixed-effect meta-analysis. We estimated the reduction in severe COVID-19 outcomes associated with a counterfactual scenario in which everyone in the UK was fully vaccinated on June 1, 2022.<h4>Findings</h4>The numbers of people undervaccinated on June 1, 2022 were 26 985 570 (45·8%) of 58 967 360 in England, 938 420 (49·8%) of 1 885 670 in Northern Ireland, 1 709 786 (34·2%) of 4 992 498 in Scotland, and 773 850 (32·8%) of 2 358 740 in Wales. People who were younger, from more deprived backgrounds, of non-White ethnicity, or had a lower number of comorbidities were less likely to be fully vaccinated. There was a total of 40 393 severe COVID-19 outcomes in the cohorts, with 14 156 of these in undervaccinated participants. We estimated the reduction in severe COVID-19 outcomes in the UK over 4 months of follow-up associated with a counterfactual scenario in which everyone was fully vaccinated on June 1, 2022 as 210 (95% CI 94-326) in the 5-15 years age group, 1544 (1399-1689) in those aged 16-74 years, and 5426 (5340-5512) in those aged 75 years or older. aHRs for severe COVID-19 outcomes in the meta-analysis for the age group of 75 years or older were 2·70 (2·61-2·78) for one dose fewer than recommended, 3·13 (2·93-3·34) for two fewer, 3·61 (3·13-4·17) for three fewer, and 3·08 (2·89-3·29) for four fewer.<h4>Interpretation</h4>Rates of undervaccination against COVID-19 ranged from 32·8% to 49·8% across the four UK nations in summer, 2022. Undervaccination was associated with an elevated risk of severe COVID-19 outcomes.<h4>Funding</h4>UK Research and Innovation National Core Studies: Data and Connectivity.",,pdf:http://www.thelancet.com/article/S0140673623024674/pdf; doi:https://doi.org/10.1016/S0140-6736(23)02467-4
+37309989,https://doi.org/10.1002/pds.5656,Prevalent new user designs: A literature review of current implementation practice.,"Tazare J, Gibbons DC, Bokern M, Williamson EJ, Gillespie IA, Cunnington M, Logie J, Douglas IJ.",,Pharmacoepidemiology and drug safety,2023,2023-06-22,N,Literature review; Database Research; Prevalent New User Designs,,,"<h4>Purpose</h4>Prevalent new user (PNU) designs extend the active comparator new user design by allowing for the inclusion of initiators of the study drug who were previously on a comparator treatment. We performed a literature review summarising current practice.<h4>Methods</h4>PubMed was searched for studies applying the PNU design since its proposal in 2017. The review focused on three components. First, we extracted information on the overall study design, including the database used. We summarised information on implementation of the PNU design, including key decisions relating to exposure set definition and estimation of time-conditional propensity scores. Finally, we reviewed the analysis strategy of the matched cohort.<h4>Results</h4>Nineteen studies met the criteria for inclusion. Most studies (73%) implemented the PNU design in electronic health record or registry databases, with the remaining using insurance claims databases. Of 15 studies including a class of prevalent users, 40% deviated from the original exposure set definition proposals in favour of a more complex definition. Four studies did not include prevalent new users but used other aspects of the PNU framework. Several studies lacked details on exposure set definition (n = 2), time-conditional propensity score model (n = 2) or integration of complex analytical techniques, such as the high-dimensional propensity score algorithm (n = 3).<h4>Conclusion</h4>PNU designs have been applied in a range of therapeutic and disease areas. However, to encourage more widespread use of this design and help shape best practice, there is a need for improved accessibility, specifically through the provision of analytical code alongside guidance to support implementation and transparent reporting.",,doi:https://doi.org/10.1002/pds.5656; doi:https://doi.org/10.1002/pds.5656
 34216888,https://doi.org/10.1016/j.compbiomed.2021.104556,NFnetFu: A novel workflow for microbiome data fusion.,"Bisht V, Acharjee A, Gkoutos GV.",,Computers in biology and medicine,2021,2021-06-08,Y,Clustering; Microbiome; Fuzzy Inference; Network Fusion,,,"Microbiome data analysis and its interpretation into meaningful biological insights remain very challenging for numerous reasons, perhaps most prominently, due to the need to account for multiple factors, including collinearity, sparsity (excessive zeros) and effect size, that the complex experimental workflow and subsequent downstream data analysis require. Moreover, a meaningful microbiome data analysis necessitates the development of interpretable models that incorporate inferences across available data as well as background biomedical knowledge. We developed a multimodal framework that considers sparsity (excessive zeros), lower effect size, intrinsically microbial correlations, i.e., collinearity, as well as background biomedical knowledge in the form of a cluster-infused enriched network architecture. Finally, our framework also provides a candidate taxa/Operational Taxonomic Unit (OTU) that can be targeted for future validation experiments. We have developed a tool, the term NFnetFU (Neuro Fuzzy network Fusion), that encompasses our framework and have made it freely available at https://github.com/VartikaBisht6197/NFnetFu.",,doi:https://doi.org/10.1016/j.compbiomed.2021.104556; doi:https://doi.org/10.1016/j.compbiomed.2021.104556; html:https://europepmc.org/articles/PMC8404037
 35035708,https://doi.org/,Multi-omics-based identification of atopic dermatitis target genes and their potential associations with metabolites and miRNAs.,"Acharjee A, Gribaleva E, Bano S, Gkoutos GV.",,American journal of translational research,2021,2021-12-15,N,Eczema; Translational Research; Machine Learning; Pathway analysis; Atopic Dermatitis (Ad); Multi-omics,,,"Atopic dermatitis (AD), or atopic eczema, is one of the most common inflammatory skin diseases with up to 10% prevalence in adults, and approximately 15-20% in children in industrialized countries. As a result, there is an unmet need for faster, safer, and effective treatments for AD. AD pathogenesis represents a complex interplay between multiple factors, such as environmental factors or stimuli, genetic factors, immune dysfunctions. However, although multi-omics label studies have been very useful in understanding the pathophysiological mechanisms of AD and its clinical manifestations, there have been very few studies that integrate different labels of omics data. Here, we attempted to integrate gene expression and metabolomics datasets from multiple different publicly available AD cohort datasets and conduct an integrated systems-level AD analysis. We used four different GEO transcriptome data sets and, by applying an elastic net machine learning algorithm, identified robust hub genes that can be used as signatures, for example, H2AFX, MCM7, ESR1 and SF3A2. Moreover, we investigated potential associations of those genes by applying a pathway-based approach over metabolomics and miRNA datasets. Our results revealed potential novel associations between fatty acids and peroxisomal lipid metabolism pathways, as well as with several microRNAs.",,html:https://europepmc.org/articles/PMC8748113; pdf:https://europepmc.org/articles/PMC8748113?pdf=render
 35468332,https://doi.org/10.1016/s1473-3099(22)00141-4,Severity of omicron variant of concern and effectiveness of vaccine boosters against symptomatic disease in Scotland (EAVE II): a national cohort study with nested test-negative design.,"Sheikh A, Kerr S, Woolhouse M, McMenamin J, Robertson C, EAVE II Collaborators.",,The Lancet. Infectious diseases,2022,2022-04-22,Y,,,,"<h4>Background</h4>Since its emergence in November, 2021, in southern Africa, the SARS-CoV-2 omicron variant of concern (VOC) has rapidly spread across the world. We aimed to investigate the severity of omicron and the extent to which booster vaccines are effective in preventing symptomatic infection.<h4>Methods</h4>In this study, using the Scotland-wide Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) platform, we did a cohort analysis with a nested test-negative design incident case-control study covering the period Nov 1-Dec 19, 2021, to provide initial estimates of omicron severity and the effectiveness of vaccine boosters against symptomatic disease relative to 25 weeks or more after the second vaccine dose. Primary care data derived from 940 general practices across Scotland were linked to laboratory data and hospital admission data. We compared outcomes between infection with the delta VOC (defined as S-gene positive) and the omicron VOC (defined as S-gene negative). We assessed effectiveness against symptomatic SARS-CoV-2 infection, with infection confirmed through a positive RT-PCR.<h4>Findings</h4>By Dec 19, 2021, there were 23 840 S-gene-negative cases in Scotland, which were predominantly among those aged 20-39 years (11 732 [49·2%]). The proportion of S-gene-negative cases that were possible reinfections was more than ten times that of S-gene-positive cases (7·6% vs 0·7%; p<0·0001). There were 15 hospital admissions in S-gene-negative individuals, giving an adjusted observed-to-expected admissions ratio of 0·32 (95% CI 0·19-0·52). The booster vaccine dose was associated with a 57% (54-60) reduction in the risk of symptomatic S-gene-negative infection relative to individuals who tested positive 25 weeks or more after the second vaccine dose.<h4>Interpretation</h4>These early national data suggest that omicron is associated with a two-thirds reduction in the risk of COVID-19 hospitalisation compared with delta. Although offering the greatest protection against delta, the booster dose of vaccination offers substantial additional protection against the risk of symptomatic COVID-19 for omicron compared with 25 weeks or more after the second vaccine dose.<h4>Funding</h4>Health Data Research UK, National Core Studies, Public Health Scotland, Scottish Government, UK Research and Innovation, and University of Edinburgh.",,pdf:https://aura.abdn.ac.uk/bitstream/2164/18748/1/Sheikh_etal_LID_Severity_Omicron_Variant_VOR.pdf; doi:https://doi.org/10.1016/S1473-3099(22)00141-4; html:https://europepmc.org/articles/PMC9033213
-39119202,https://doi.org/10.1093/ehjopen/oeae059,Ventricular volume asymmetry as a novel imaging biomarker for disease discrimination and outcome prediction.,"McCracken C, Szabo L, Abdulelah ZA, Condurache DG, Vago H, Nichols TE, Petersen SE, Neubauer S, Raisi-Estabragh Z.",,European heart journal open,2024,2024-07-25,Y,Cardiovascular disease; epidemiology; Cardiovascular Risk; Cardiovascular Magnetic Resonance; Imaging Biomarkers; Uk Biobank,,,"<h4>Aims</h4>Disruption of the predictable symmetry of the healthy heart may be an indicator of cardiovascular risk. This study defines the population distribution of ventricular asymmetry and its relationships across a range of prevalent and incident cardiorespiratory diseases.<h4>Methods and results</h4>The analysis includes 44 796 UK Biobank participants (average age 64.1 ± 7.7 years; 51.9% women). Cardiovascular magnetic resonance (CMR) metrics were derived using previously validated automated pipelines. Ventricular asymmetry was expressed as the ratio of left and right ventricular (LV and RV) end-diastolic volumes. Clinical outcomes were defined through linked health records. Incident events were those occurring for the first time after imaging, longitudinally tracked over an average follow-up time of 4.75 ± 1.52 years. The normal range for ventricular symmetry was defined in a healthy subset. Participants with values outside the 5th-95th percentiles of the healthy distribution were classed as either LV dominant (LV/RV > 112%) or RV dominant (LV/RV < 80%) asymmetry. Associations of LV and RV dominant asymmetry with vascular risk factors, CMR features, and prevalent and incident cardiovascular diseases (CVDs) were examined using regression models, adjusting for vascular risk factors, prevalent diseases, and conventional CMR measures. Left ventricular dominance was linked to an array of pre-existing vascular risk factors and CVDs, and a two-fold increased risk of incident heart failure, non-ischaemic cardiomyopathies, and left-sided valvular disorders. Right ventricular dominance was associated with an elevated risk of all-cause mortality.<h4>Conclusion</h4>Ventricular asymmetry has clinical utility for cardiovascular risk assessment, providing information that is incremental to traditional risk factors and conventional CMR metrics.",,doi:https://doi.org/10.1093/ehjopen/oeae059; html:https://europepmc.org/articles/PMC11306927; pdf:https://europepmc.org/articles/PMC11306927?pdf=render
 39411544,https://doi.org/10.1177/20552076241287450,Predicting suicidal behavior in individuals with depression over 50 years of age: Evidence from the UK biobank.,"Zhang J, Liu Y, Zhang C, Chen Y, Hu Y, Yang X, Liu W, Zhang W, Liu D, Song H.",,Digital health,2024,2024-01-01,Y,Depression; Prevention; risk factors; Suicide; Machine Learning,,,"<h4>Objective</h4>To construct applicable models suitable for predicting the risk of suicidal behavior among individuals with depression, particularly on the progression from no history of suicidal behavior to suicide attempts, as well as from suicidal ideation to suicide attempts.<h4>Methods</h4>Based on a prospective cohort from the UK Biobank, a total of 55,139 individuals aged 50 and above with depression were enrolled in the study, among whom 29,528 exhibited suicidal behavior. Specifically, they were divided into control (25,611), suicidal ideation (24,361), and suicide attempt (5167) groups. Least absolute shrinkage and selection operator (LASSO) regression was used to identify a subset of important features for distinguishing suicidal ideation and suicide attempts. We used the Gradient Boosting Decision Tree (GBDT) algorithm with stratified 10-fold cross-validation and grid-search to construct the prediction models for suicidal ideation or suicide attempts. To address the dataset imbalance in classifying suicide attempts, we used random under-sampling. The SHapley Additive exPlanations (SHAP) were used to estimate the important variables in the GBDT model.<h4>Results</h4>Significant differences in sociodemographic, economic, lifestyle, and psychological factors were observed across the three groups. Each classifier optimally utilized 8-11 features. Overall, the algorithms predicting suicide attempts demonstrated slightly higher performance than those predicting suicidal ideation. The GBDT classifier achieved the highest accuracy, with AUROC scores of 0.914 for suicide attempts and 0.803 for suicidal ideation. Distinctive predictive factors were identified for each group: while depression's inherent characteristics crucially distinguished the suicidal ideation group from controls, some key predictors, including the age of depression onset and childhood trauma events, were identified for suicide attempts.<h4>Conclusions</h4>We established applicable machine learning-based models for predicting suicidal behavior, particularly suicide attempts, in individuals with depression, and clarified the differences in predictors between suicidal ideation and suicide attempts.",,doi:https://doi.org/10.1177/20552076241287450; html:https://europepmc.org/articles/PMC11475109; pdf:https://europepmc.org/articles/PMC11475109?pdf=render
+39119202,https://doi.org/10.1093/ehjopen/oeae059,Ventricular volume asymmetry as a novel imaging biomarker for disease discrimination and outcome prediction.,"McCracken C, Szabo L, Abdulelah ZA, Condurache DG, Vago H, Nichols TE, Petersen SE, Neubauer S, Raisi-Estabragh Z.",,European heart journal open,2024,2024-07-25,Y,Cardiovascular disease; epidemiology; Cardiovascular Risk; Cardiovascular Magnetic Resonance; Imaging Biomarkers; Uk Biobank,,,"<h4>Aims</h4>Disruption of the predictable symmetry of the healthy heart may be an indicator of cardiovascular risk. This study defines the population distribution of ventricular asymmetry and its relationships across a range of prevalent and incident cardiorespiratory diseases.<h4>Methods and results</h4>The analysis includes 44 796 UK Biobank participants (average age 64.1 ± 7.7 years; 51.9% women). Cardiovascular magnetic resonance (CMR) metrics were derived using previously validated automated pipelines. Ventricular asymmetry was expressed as the ratio of left and right ventricular (LV and RV) end-diastolic volumes. Clinical outcomes were defined through linked health records. Incident events were those occurring for the first time after imaging, longitudinally tracked over an average follow-up time of 4.75 ± 1.52 years. The normal range for ventricular symmetry was defined in a healthy subset. Participants with values outside the 5th-95th percentiles of the healthy distribution were classed as either LV dominant (LV/RV > 112%) or RV dominant (LV/RV < 80%) asymmetry. Associations of LV and RV dominant asymmetry with vascular risk factors, CMR features, and prevalent and incident cardiovascular diseases (CVDs) were examined using regression models, adjusting for vascular risk factors, prevalent diseases, and conventional CMR measures. Left ventricular dominance was linked to an array of pre-existing vascular risk factors and CVDs, and a two-fold increased risk of incident heart failure, non-ischaemic cardiomyopathies, and left-sided valvular disorders. Right ventricular dominance was associated with an elevated risk of all-cause mortality.<h4>Conclusion</h4>Ventricular asymmetry has clinical utility for cardiovascular risk assessment, providing information that is incremental to traditional risk factors and conventional CMR metrics.",,doi:https://doi.org/10.1093/ehjopen/oeae059; html:https://europepmc.org/articles/PMC11306927; pdf:https://europepmc.org/articles/PMC11306927?pdf=render
 38905569,https://doi.org/10.1056/evidoa2400179,Effect of Fenofibrate on Progression of Diabetic Retinopathy.,"Preiss D, Logue J, Sammons E, Zayed M, Emberson J, Wade R, Wallendszus K, Stevens W, Cretney R, Harding S, Leese G, Currie G, Armitage J.",,NEJM evidence,2024,2024-06-21,Y,,,,"<h4>Background</h4>Findings from cardiovascular outcome trials suggest that fenofibrate therapy may reduce the progression of diabetic retinopathy.<h4>Methods</h4>We recruited and followed adults with nonreferable diabetic retinopathy or maculopathy using the national Diabetic Eye Screening (DES) program in Scotland. We randomly assigned participants to receive 145-mg fenofibrate tablets or placebo (taken daily or, in those with impaired renal function, on alternate days). The primary outcome was a composite of developing referable diabetic retinopathy or maculopathy (based on Scotland's DES grading scheme) or treatment (intravitreal injection, retinal laser, vitrectomy) for retinopathy or maculopathy.<h4>Results</h4>A total of 1151 participants were randomly assigned to treatment. During a median of 4.0 years, progression to referable diabetic retinopathy or maculopathy, or treatment thereof, occurred in 131 (22.7%) of 576 participants in the fenofibrate group and 168 (29.2%) of 575 in the placebo group (hazard ratio, 0.73; 95% confidence interval [CI], 0.58 to 0.91; P=0.006). In the fenofibrate group compared with the placebo group, the frequencies for any progression of retinopathy or maculopathy were 185 (32.1%) vs. 231 (40.2%); hazard ratio, 0.74; 95% CI, 0.61 to 0.90 and for the development of macular edema were 22 (3.8%) vs. 43 (7.5%); hazard ratio, 0.50; 95% CI, 0.30 to 0.84. Seventeen (3.0%) participants assigned fenofibrate and 28 (4.9%) assigned placebo were given treatment for retinopathy (hazard ratio, 0.58; 95% CI, 0.31 to 1.06). There was no effect on visual function, quality of life, or visual acuity. Trial-averaged estimated glomerular filtration rate was 7.9 (95% CI, 6.8 to 9.1) ml/min/1.73 m<sup>2</sup> lower in participants in the fenofibrate group compared with the placebo group. Serious adverse events occurred in 208 (36.1%) participants allocated fenofibrate and 204 (35.5%) participants allocated placebo.<h4>Conclusions</h4>Fenofibrate reduced progression of diabetic retinopathy compared with placebo among participants with early retinal changes. (Funded by the National Institute for Health and Care Research; ClinicalTrials.gov number, NCT03439345; ISRCTN number, ISRCTN15073006.).",,doi:https://doi.org/10.1056/EVIDoa2400179; html:https://europepmc.org/articles/PMC7616293; pdf:https://europepmc.org/articles/PMC7616293?pdf=render
 38086891,https://doi.org/10.1038/s41598-023-48894-9,surviveR: a flexible shiny application for patient survival analysis.,"Sessler T, Quinn GP, Wappett M, Rogan E, Sharkey D, Ahmaderaghi B, Lawler M, Longley DB, McDade SS.",,Scientific reports,2023,2023-12-13,Y,,,,"Kaplan-Meier (KM) survival analyses based on complex patient categorization due to the burgeoning volumes of genomic, molecular and phenotypic data, are an increasingly important aspect of the biomedical researcher's toolkit. Commercial statistics and graphing packages for such analyses are functionally limited, whereas open-source tools have a high barrier-to-entry in terms of understanding of methodologies and computational expertise. We developed surviveR to address this unmet need for a survival analysis tool that can enable users with limited computational expertise to conduct routine but complex analyses. surviveR is a cloud-based Shiny application, that addresses our identified unmet need for an easy-to-use web-based tool that can plot and analyse survival based datasets. Integrated customization options allows a user with limited computational expertise to easily filter patients to enable custom cohort generation, automatically calculate log-rank test and Cox hazard ratios. Continuous datasets can be integrated, such as RNA or protein expression measurements which can be then used as categories for survival plotting. We further demonstrate the utility through exemplifying its application to a clinically relevant colorectal cancer patient dataset. surviveR is a cloud-based web application available at https://generatr.qub.ac.uk/app/surviveR , that can be used by non-experts users to perform complex custom survival analysis.",,pdf:https://www.nature.com/articles/s41598-023-48894-9.pdf; doi:https://doi.org/10.1038/s41598-023-48894-9; html:https://europepmc.org/articles/PMC10716386; pdf:https://europepmc.org/articles/PMC10716386?pdf=render
 36647011,https://doi.org/10.1186/s12882-022-03031-y,Does acute kidney injury alerting improve patient outcomes?,"Atia J, Evison F, Gallier S, Hewins P, Ball S, Gavin J, Coleman J, Garrick M, Pankhurst T.",,BMC nephrology,2023,2023-01-17,Y,Acute Kidney Injury; Referral; Electronic Patient Records; Electronic Health Records; Patient Outcomes,,,"<h4>Background</h4>Electronic alerts (e-alerts) for Acute Kidney Injury (AKI) have been implemented into a variety of different Electronic Health Records (EHR) systems worldwide in order to improve recognition and encourage early appropriate management of AKI. We were interested in the impact on patient safety, specialist referral and clinical management.<h4>Methods</h4>All patients admitted to our institution with AKI were included in the study. We studied AKI progression, dialysis dependency, length of hospital stay, emergency readmission, ICU readmission, and death, before and after the introduction of electronic alerts. The impact on prescription of high risk drugs, fluid administration, and referral to renal services was also analysed.<h4>Results</h4>After the introduction of the e-alert, progression to higher AKI stage, emergency readmission to hospital and death during admission were significantly reduced. More prescriptions were stopped for drugs that adversely affect renal function in AKI and there was a significant increase in the ICU admissions and in the number of patients having dialysis, especially in earlier stages. Longer term mortality, renal referrals, and fluid alteration did not change significantly after the AKI e-alert introduction.<h4>Conclusions</h4>AKI e-alerts can improve clinical outcomes in hospitalised patients.",,pdf:https://bmcnephrol.biomedcentral.com/counter/pdf/10.1186/s12882-022-03031-y; doi:https://doi.org/10.1186/s12882-022-03031-y; html:https://europepmc.org/articles/PMC9843843; pdf:https://europepmc.org/articles/PMC9843843?pdf=render
-35909577,https://doi.org/10.23889/ijpds.v7i1.1725,Educational achievements of children aged 10-11 years with cystic fibrosis. A data linkage study in Wales.,"Schlüter DK, Griffiths R, Akbari A, Taylor-Robinson D.",,International journal of population data science,2022,2022-06-27,Y,Education; Cystic Fibrosis; Data Linkage; Sail Databank,,,"<h4>Introduction</h4>As people with cystic fibrosis (CF) lead longer, healthier lives, educational qualifications and employment prospects are increasingly important. However, little is known about the social consequences of CF, in particular, any impact on educational achievements and the support children with CF receive in schools.<h4>Objectives</h4>To assess the educational achievements of children with CF in Wales compared to the general Welsh population, and the additional learning support children with CF receive in schools.<h4>Methods</h4>We conducted a population-scale data linkage study of all children born in Wales using the Secure Anonymised Information Linkage (SAIL) Databank. We used anonymised individual-level population-scale health and administrative data sources to identify children with CF born between 2000 - 2015, linked to educational attainment records. We calculated the percentage of children that reached expected levels in statutory assessment at age 10-11, Key Stage 2 (KS2), and compared this to educational outcomes in the general population. We also assessed the percentage of children with CF that received extra learning support.<h4>Results</h4>Out of 150 eligible children, 119 had KS2 results. 77% (95% CI: 69%-84%) of children achieved expected levels in English, 81% (95% CI: 73% -87%) in Mathematics and 82% (95% CI: 75% - 88%) in Science. In the comparable general Welsh population, 83.4% to 91.1% achieved the expected level in English, 84.9% to 91.6% in Maths, and 87.1% to 92.2% in Science across the years of the study. 70% of children with CF received extra learning support.<h4>Conclusions</h4>Children with CF in Wales may have worse educational achievements than the general population. More research is needed to inform policies and interventions to better support children with CF to reach their full educational potential and employment opportunities.",,pdf:https://ijpds.org/article/download/1725/3455; doi:https://doi.org/10.23889/ijpds.v7i1.1725; html:https://europepmc.org/articles/PMC9284509; pdf:https://europepmc.org/articles/PMC9284509?pdf=render
 36447940,https://doi.org/10.1016/s2665-9913(22)00305-8,Incidence and management of inflammatory arthritis in England before and during the COVID-19 pandemic: a population-level cohort study using OpenSAFELY.,"Russell MD, Galloway JB, Andrews CD, MacKenna B, Goldacre B, Mehrkar A, Curtis HJ, Butler-Cole B, O'Dwyer T, Qureshi S, Ledingham JM, Mahto A, Rutherford AI, Adas MA, Alveyn E, Norton S, Cope AP, Bechman K, OpenSAFELY Collaborative.",,The Lancet. Rheumatology,2022,2022-11-03,Y,,,,"<h4>Background</h4>The impact of the COVID-19 pandemic on the incidence and management of inflammatory arthritis is not understood. Routinely captured data in secure platforms, such as OpenSAFELY, offer unique opportunities to understand how care for patients with inflammatory arthritis was impacted upon by the pandemic. Our objective was to use OpenSAFELY to assess the effects of the pandemic on diagnostic incidence and care delivery for inflammatory arthritis in England and to replicate key metrics from the National Early Inflammatory Arthritis Audit.<h4>Methods</h4>In this population-level cohort study, we used primary care and hospital data for 17·7 million adults registered with general practices using TPP health record software, to explore the following outcomes between April 1, 2019, and March 31, 2022: (1) incidence of inflammatory arthritis diagnoses (rheumatoid arthritis, psoriatic arthritis, axial spondyloarthritis, and undifferentiated inflammatory arthritis) recorded in primary care; (2) time to first rheumatology assessment; (3) time to first prescription of a disease-modifying antirheumatic drug (DMARD) in primary care; and (4) choice of first DMARD.<h4>Findings</h4>Among 17 683 500 adults, there were 31 280 incident inflammatory arthritis diagnoses recorded between April 1, 2019, and March 31, 2022. The mean age of diagnosed patients was 55·4 years (SD 16·6), 18 615 (59·5%) were female, 12 665 (40·5%) were male, and 22 925 (88·3%) of 25 960 with available ethnicity data were White. New inflammatory arthritis diagnoses decreased by 20·3% in the year commencing April, 2020, relative to the preceding year (5·1 <i>vs</i> 6·4 diagnoses per 10 000 adults). The median time to first rheumatology assessment was shorter during the pandemic (18 days; IQR 8-35) than before (21 days; 9-41). The proportion of patients prescribed DMARDs in primary care was similar before and during the pandemic; however, during the pandemic, fewer people were prescribed methotrexate or leflunomide, and more were prescribed sulfasalazine or hydroxychloroquine.<h4>Interpretation</h4>Inflammatory arthritis diagnoses decreased markedly during the early phase of the pandemic. The impact on rheumatology assessment times and DMARD prescribing in primary care was less marked than might have been anticipated. This study demonstrates the feasibility of using routinely captured, near real-time data in the secure OpenSAFELY platform to benchmark care quality on a national scale, without the need for manual data collection.<h4>Funding</h4>None.",,pdf:https://researchonline.lshtm.ac.uk/id/eprint/4669009/1/Russell_etal_2022_Incidence-and-management-of-inflammatory.pdf; doi:https://doi.org/10.1016/S2665-9913(22)00305-8; html:https://europepmc.org/articles/PMC9691150; pdf:https://europepmc.org/articles/PMC9691150?pdf=render
+35909577,https://doi.org/10.23889/ijpds.v7i1.1725,Educational achievements of children aged 10-11 years with cystic fibrosis. A data linkage study in Wales.,"Schlüter DK, Griffiths R, Akbari A, Taylor-Robinson D.",,International journal of population data science,2022,2022-06-27,Y,Education; Cystic Fibrosis; Data Linkage; Sail Databank,,,"<h4>Introduction</h4>As people with cystic fibrosis (CF) lead longer, healthier lives, educational qualifications and employment prospects are increasingly important. However, little is known about the social consequences of CF, in particular, any impact on educational achievements and the support children with CF receive in schools.<h4>Objectives</h4>To assess the educational achievements of children with CF in Wales compared to the general Welsh population, and the additional learning support children with CF receive in schools.<h4>Methods</h4>We conducted a population-scale data linkage study of all children born in Wales using the Secure Anonymised Information Linkage (SAIL) Databank. We used anonymised individual-level population-scale health and administrative data sources to identify children with CF born between 2000 - 2015, linked to educational attainment records. We calculated the percentage of children that reached expected levels in statutory assessment at age 10-11, Key Stage 2 (KS2), and compared this to educational outcomes in the general population. We also assessed the percentage of children with CF that received extra learning support.<h4>Results</h4>Out of 150 eligible children, 119 had KS2 results. 77% (95% CI: 69%-84%) of children achieved expected levels in English, 81% (95% CI: 73% -87%) in Mathematics and 82% (95% CI: 75% - 88%) in Science. In the comparable general Welsh population, 83.4% to 91.1% achieved the expected level in English, 84.9% to 91.6% in Maths, and 87.1% to 92.2% in Science across the years of the study. 70% of children with CF received extra learning support.<h4>Conclusions</h4>Children with CF in Wales may have worse educational achievements than the general population. More research is needed to inform policies and interventions to better support children with CF to reach their full educational potential and employment opportunities.",,pdf:https://ijpds.org/article/download/1725/3455; doi:https://doi.org/10.23889/ijpds.v7i1.1725; html:https://europepmc.org/articles/PMC9284509; pdf:https://europepmc.org/articles/PMC9284509?pdf=render
 37726825,https://doi.org/10.1186/s13063-023-07606-4,Correction: Development and evaluation of rapid data-enabled access to routine clinical information to enhance early recruitment to the national clinical platform trial of COVID-19 community treatments.,"Cake C, Ogburn E, Pinches H, Coleman G, Seymour D, Woodard F, Manohar S, Monsur M, Landray M, Dalton G, Morris AD, Chinnery PF, UK COVID-19 National Core Studies Consortium, Hobbs FDR, Butler C.",,Trials,2023,2023-09-19,Y,,,,,,pdf:https://trialsjournal.biomedcentral.com/counter/pdf/10.1186/s13063-023-07606-4; doi:https://doi.org/10.1186/s13063-023-07606-4; html:https://europepmc.org/articles/PMC10507817; pdf:https://europepmc.org/articles/PMC10507817?pdf=render
 37142468,https://doi.org/10.1016/j.soncn.2023.151439,A National Audit of Pancreatic Enzyme Prescribing in Pancreatic Cancer from 2015 to 2023 in England Using OpenSAFELY-TPP.,"Lemanska A, Andrews C, Fisher L, Butler-Cole B, Mehrkar A, Roberts KJ, Goldacre B, Walker AJ, MacKenna B, OpenSAFELY Collaborative.",,Seminars in oncology nursing,2023,2023-05-02,N,Pancreatic cancer; Quality Of Care; Electronic Health Records; Prescribing Audit; Covid-19; Pancreatic Cancer Enzyme Replacement; Pancreatic Enzyme Insufficiency,,,"<h4>Objectives</h4>Cancer treatments were variably disrupted during the coronavirus disease 2019 (COVID-19) pandemic. UK guidelines recommend pancreatic enzyme replacement therapy (PERT) to all people with unresectable pancreatic cancer. The aim was to investigate the impact of the COVID-19 pandemic on PERT prescribing to people with unresectable pancreatic cancer and to investigate the national and regional rates from January 2015 to January 2023.<h4>Data sources</h4>With the approval of NHS England, we conducted this study using 24 million electronic health records of people within the OpenSAFELY-TPP research platform. There were 22,860 people diagnosed with pancreatic cancer in the study cohort. We visualized the trends over time and modeled the effect of the COVID-19 pandemic with the interrupted time-series analysis.<h4>Conclusion</h4>In contrast to many other treatments, prescribing of PERT was not affected during the pandemic. Overall, since 2015, the rates increased steadily over time by 1% every year. The national rates ranged from 41% in 2015 to 48% in early 2023. There was substantial regional variation, with the highest rates of 50% to 60% in West Midlands.<h4>Implications for nursing practice</h4>In pancreatic cancer, if PERT is prescribed, it is usually initiated in hospitals by clinical nurse specialists and continued after discharge by primary care practitioners. At just under 50% in early 2023, the rates were still below the recommended 100% standard. More research is needed to understand barriers to prescribing of PERT and geographic variation to improve quality of care. Prior work relied on manual audits. With OpenSAFELY, we developed an automated audit that allows for regular updates (https://doi.org/10.53764/rpt.a0b1b51c7a).",,doi:https://doi.org/10.1016/j.soncn.2023.151439; doi:https://doi.org/10.1016/j.soncn.2023.151439; html:https://europepmc.org/articles/PMC7616357; pdf:https://europepmc.org/articles/PMC7616357?pdf=render; doi:https://doi.org/10.1016/j.soncn.2023.151439
 34649961,https://doi.org/10.1101/cshperspect.a039230,Human Genomics and Drug Development.,"Schmidt AF, Hingorani AD, Finan C.",,Cold Spring Harbor perspectives in medicine,2022,2022-02-01,N,,,,"Insights into the genetic basis of human disease are helping to address some of the key challenges in new drug development including the very high rates of failure. Here we review the recent history of an emerging, genomics-assisted approach to pharmaceutical research and development, and its relationship to Mendelian randomization (MR), a well-established analytical approach to causal inference. We demonstrate how human genomic data linked to pharmaceutically relevant phenotypes can be used for (1) drug target identification (mapping relevant drug targets to diseases), (2) drug target validation (inferring the likely effects of drug target perturbation), (3) evaluation of the effectiveness and specificity of compound-target engagement (inferring the extent to which the effects of a compound are exclusive to the target and distinguishing between on-target and off-target compound effects), and (4) the selection of end points in clinical trials (the diseases or conditions to be evaluated as trial outcomes). We show how genomics can help identify indication expansion opportunities for licensed drugs and repurposing of compounds developed to clinical phase that proved safe but ineffective for the original intended indication. We outline statistical and biological considerations in using MR for drug target validation (drug target MR) and discuss the obstacles and challenges for scaled applications of these genomics-based approaches.",,pdf:https://discovery.ucl.ac.uk/10138810/1/ForUCLDiscovery.pdf; doi:https://doi.org/10.1101/cshperspect.a039230; html:https://europepmc.org/articles/PMC8805642; pdf:https://europepmc.org/articles/PMC8805642?pdf=render; doi:https://doi.org/10.1101/cshperspect.a039230
+37169862,https://doi.org/10.1038/s41591-023-02343-2,Accelerated waning of the humoral response to COVID-19 vaccines in obesity.,"van der Klaauw AA, Horner EC, Pereyra-Gerber P, Agrawal U, Foster WS, Spencer S, Vergese B, Smith M, Henning E, Ramsay ID, Smith JA, Guillaume SM, Sharpe HJ, Hay IM, Thompson S, Innocentin S, Booth LH, Robertson C, McCowan C, Kerr S, Mulroney TE, O'Reilly MJ, Gurugama TP, Gurugama LP, Rust MA, Ferreira A, Ebrahimi S, Ceron-Gutierrez L, Scotucci J, Kronsteiner B, Dunachie SJ, Klenerman P, PITCH Consortium, Park AJ, Rubino F, Lamikanra AA, Stark H, Kingston N, Estcourt L, Harvala H, Roberts DJ, Doffinger R, Linterman MA, Matheson NJ, Sheikh A, Farooqi IS, Thaventhiran JED.",,Nature medicine,2023,2023-05-11,Y,,,,"Obesity is associated with an increased risk of severe Coronavirus Disease 2019 (COVID-19) infection and mortality. COVID-19 vaccines reduce the risk of serious COVID-19 outcomes; however, their effectiveness in people with obesity is incompletely understood. We studied the relationship among body mass index (BMI), hospitalization and mortality due to COVID-19 among 3.6 million people in Scotland using the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) surveillance platform. We found that vaccinated individuals with severe obesity (BMI > 40 kg/m<sup>2</sup>) were 76% more likely to experience hospitalization or death from COVID-19 (adjusted rate ratio of 1.76 (95% confidence interval (CI), 1.60-1.94). We also conducted a prospective longitudinal study of a cohort of 28 individuals with severe obesity compared to 41 control individuals with normal BMI (BMI 18.5-24.9 kg/m<sup>2</sup>). We found that 55% of individuals with severe obesity had unquantifiable titers of neutralizing antibody against authentic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus compared to 12% of individuals with normal BMI (P = 0.0003) 6 months after their second vaccine dose. Furthermore, we observed that, for individuals with severe obesity, at any given anti-spike and anti-receptor-binding domain (RBD) antibody level, neutralizing capacity was lower than that of individuals with a normal BMI. Neutralizing capacity was restored by a third dose of vaccine but again declined more rapidly in people with severe obesity. We demonstrate that waning of COVID-19 vaccine-induced humoral immunity is accelerated in individuals with severe obesity. As obesity is associated with increased hospitalization and mortality from breakthrough infections, our findings have implications for vaccine prioritization policies.",,pdf:https://www.nature.com/articles/s41591-023-02343-2.pdf; doi:https://doi.org/10.1038/s41591-023-02343-2; html:https://europepmc.org/articles/PMC10202802; pdf:https://europepmc.org/articles/PMC10202802?pdf=render
 35915784,https://doi.org/10.1016/j.lanepe.2022.100462,Omicron SARS-CoV-2 epidemic in England during February 2022: A series of cross-sectional community surveys.,"Chadeau-Hyam M, Tang D, Eales O, Bodinier B, Wang H, Jonnerby J, Whitaker M, Elliott J, Haw D, Walters CE, Atchison C, Diggle PJ, Page AJ, Ashby D, Barclay W, Taylor G, Cooke G, Ward H, Darzi A, Donnelly CA, Elliott P.",,The Lancet regional health. Europe,2022,2022-07-28,Y,"Rt-pcr, Reverse Transcription Polymerase Chain Reaction; Ct, Cycle Threshold; Nhs, National Health Service; Covid-19; Sars-cov-2; Omicron Variant; Ba.2 Sublineage; Random Community Surveys; Ltla, Lower-tier Local Authority; P-spline, Penalised Spline; Ukhsa, Uk Health Security Agency; B-spline, Basis Spline; Rim, Random Iterative Method",,,"<h4>Background</h4>The Omicron wave of COVID-19 in England peaked in January 2022 resulting from the rapid transmission of the Omicron BA.1 variant. We investigate the spread and dynamics of the SARS-CoV-2 epidemic in the population of England during February 2022, by region, age and main SARS-CoV-2 sub-lineage.<h4>Methods</h4>In the REal-time Assessment of Community Transmission-1 (REACT-1) study we obtained data from a random sample of 94,950 participants with valid throat and nose swab results by RT-PCR during round 18 (8 February to 1 March 2022).<h4>Findings</h4>We estimated a weighted mean SARS-CoV-2 prevalence of 2.88% (95% credible interval [CrI] 2.76-3.00), with a within-round effective reproduction number (R) overall of 0.94 (0·91-0.96). While within-round weighted prevalence fell among children (aged 5 to 17 years) and adults aged 18 to 54 years, we observed a level or increasing weighted prevalence among those aged 55 years and older with an R of 1.04 (1.00-1.09). Among 1,616 positive samples with sublineages determined, one (0.1% [0.0-0.3]) corresponded to XE BA.1/BA.2 recombinant and the remainder were Omicron: <i>N</i>=1047, 64.8% (62.4-67.2) were BA.1; <i>N</i>=568, 35.2% (32.8-37.6) were BA.2. We estimated an R additive advantage for BA.2 (vs BA.1) of 0.38 (0.34-0.41). The highest proportion of BA.2 among positives was found in London.<h4>Interpretation</h4>In February 2022, infection prevalence in England remained high with level or increasing rates of infection in older people and an uptick in hospitalisations. Ongoing surveillance of both survey and hospitalisations data is required.<h4>Funding</h4>Department of Health and Social Care, England.",,doi:https://doi.org/10.1016/j.lanepe.2022.100462; doi:https://doi.org/10.1016/j.lanepe.2022.100462; html:https://europepmc.org/articles/PMC9330654; pdf:https://europepmc.org/articles/PMC9330654?pdf=render
-38045451,https://doi.org/10.1002/joa3.12927,Using machine learning to enhance prediction of atrial fibrillation recurrence after catheter ablation.,"Brahier MS, Zou F, Abdulkareem M, Kochi S, Migliarese F, Thomaides A, Ma X, Wu C, Sandfort V, Bergquist PJ, Srichai MB, Piccini JP, Petersen SE, Vargas JD.",,Journal of arrhythmia,2023,2023-10-05,Y,Atrial fibrillation; Catheter ablation; Cardiac Computed Tomography; Machine Learning; Left Atrium,,,"<h4>Background</h4>Traditional risk scores for recurrent atrial fibrillation (AF) following catheter ablation utilize readily available clinical and echocardiographic variables and yet have limited discriminatory capacity. Use of data from cardiac imaging and deep learning may help improve accuracy and prediction of recurrent AF after ablation.<h4>Methods</h4>We evaluated patients with symptomatic, drug-refractory AF undergoing catheter ablation. All patients underwent pre-ablation cardiac computed tomography (cCT). LAVi was computed using a deep-learning algorithm. In a two-step analysis, random survival forest (RSF) was used to generate prognostic models with variables of highest importance, followed by Cox proportional hazard regression analysis of the selected variables. Events of interest included early and late recurrence.<h4>Results</h4>Among 653 patients undergoing AF ablation, the most important factors associated with late recurrence by RSF analysis at 24 (+/-18) months follow-up included LAVi and early recurrence. In total, 5 covariates were identified as independent predictors of late recurrence: LAVi (HR per mL/m<sup>2</sup> 1.01 [1.01-1.02]; <i>p</i> < .001), early recurrence (HR 2.42 [1.90-3.09]; <i>p</i> < .001), statin use (HR 1.38 [1.09-1.75]; <i>p</i> = .007), beta-blocker use (HR 1.29 [1.01-1.65]; <i>p</i> = .043), and adjunctive cavotricuspid isthmus ablation [HR 0.74 (0.57-0.96); <i>p</i> = .02]. Survival analysis demonstrated that patients with both LAVi >66.7 mL/m<sup>2</sup> and early recurrence had the highest risk of late recurrence risk compared with those with LAVi <66.7 mL/m<sup>2</sup> and no early recurrence (HR 4.52 [3.36-6.08], <i>p</i> < .001).<h4>Conclusions</h4>Machine learning-derived, full volumetric LAVi from cCT is the most important pre-procedural risk factor for late AF recurrence following catheter ablation. The combination of increased LAVi and early recurrence confers more than a four-fold increased risk of late recurrence.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/joa3.12927; doi:https://doi.org/10.1002/joa3.12927; html:https://europepmc.org/articles/PMC10692862; pdf:https://europepmc.org/articles/PMC10692862?pdf=render
 35780805,https://doi.org/10.1016/s2213-8587(22)00158-9,"Associations of BMI with COVID-19 vaccine uptake, vaccine effectiveness, and risk of severe COVID-19 outcomes after vaccination in England: a population-based cohort study.","Piernas C, Patone M, Astbury NM, Gao M, Sheikh A, Khunti K, Shankar-Hari M, Dixon S, Coupland C, Aveyard P, Hippisley-Cox J, Jebb SA.",,The lancet. Diabetes & endocrinology,2022,2022-07-01,Y,,,,"<h4>Background</h4>A high BMI has been associated with a reduced immune response to vaccination against influenza. We aimed to investigate the association between BMI and COVID-19 vaccine uptake, vaccine effectiveness, and risk of severe COVID-19 outcomes after vaccination by using a large, representative population-based cohort from England.<h4>Methods</h4>In this population-based cohort study, we used the QResearch database of general practice records and included patients aged 18 years or older who were registered at a practice that was part of the database in England between Dec 8, 2020 (date of the first vaccination in the UK), to Nov 17, 2021, with available data on BMI. Uptake was calculated as the proportion of people with zero, one, two, or three doses of the vaccine across BMI categories. Effectiveness was assessed through a nested matched case-control design to estimate odds ratios (OR) for severe COVID-19 outcomes (ie, admission to hospital or death) in people who had been vaccinated versus those who had not, considering vaccine dose and time periods since vaccination. Vaccine effectiveness against infection with SARS-CoV-2 was also investigated. Multivariable Cox proportional hazard models estimated the risk of severe COVID-19 outcomes associated with BMI (reference BMI 23 kg/m<sup>2</sup>) after vaccination.<h4>Findings</h4>Among 9 171 524 participants (mean age 52 [SD 19] years; BMI 26·7 [5·6] kg/m<sup>2</sup>), 566 461 tested positive for SARS-CoV-2 during follow-up, of whom 32 808 were admitted to hospital and 14 389 died. Of the total study sample, 19·2% (1 758 689) were unvaccinated, 3·1% (287 246) had one vaccine dose, 52·6% (4 828 327) had two doses, and 25·0% (2 297 262) had three doses. In people aged 40 years and older, uptake of two or three vaccine doses was more than 80% among people with overweight or obesity, which was slightly lower in people with underweight (70-83%). Although significant heterogeneity was found across BMI groups, protection against severe COVID-19 disease (comparing people who were vaccinated vs those who were not) was high after 14 days or more from the second dose for hospital admission (underweight: OR 0·51 [95% CI 0·41-0·63]; healthy weight: 0·34 [0·32-0·36]; overweight: 0·32 [0·30-0·34]; and obesity: 0·32 [0·30-0·34]) and death (underweight: 0·60 [0·36-0·98]; healthy weight: 0·39 [0·33-0·47]; overweight: 0·30 [0·25-0·35]; and obesity: 0·26 [0·22-0·30]). In the vaccinated cohort, there were significant linear associations between BMI and COVID-19 hospitalisation and death after the first dose, and J-shaped associations after the second dose.<h4>Interpretation</h4>Using BMI categories, there is evidence of protection against severe COVID-19 in people with overweight or obesity who have been vaccinated, which was of a similar magnitude to that of people of healthy weight. Vaccine effectiveness was slightly lower in people with underweight, in whom vaccine uptake was also the lowest for all ages. In the vaccinated cohort, there were increased risks of severe COVID-19 outcomes for people with underweight or obesity compared with the vaccinated population with a healthy weight. These results suggest the need for targeted efforts to increase uptake in people with low BMI (<18·5 kg/m<sup>2</sup>), in whom uptake is lower and vaccine effectiveness seems to be reduced. Strategies to achieve and maintain a healthy weight should be prioritised at the population level, which could help reduce the burden of COVID-19 disease.<h4>Funding</h4>UK Research and Innovation and National Institute for Health Research Oxford Biomedical Research Centre.",,pdf:http://www.thelancet.com/article/S2213858722001589/pdf; doi:https://doi.org/10.1016/S2213-8587(22)00158-9; html:https://europepmc.org/articles/PMC9246477; pdf:https://europepmc.org/articles/PMC9246477?pdf=render
-37169862,https://doi.org/10.1038/s41591-023-02343-2,Accelerated waning of the humoral response to COVID-19 vaccines in obesity.,"van der Klaauw AA, Horner EC, Pereyra-Gerber P, Agrawal U, Foster WS, Spencer S, Vergese B, Smith M, Henning E, Ramsay ID, Smith JA, Guillaume SM, Sharpe HJ, Hay IM, Thompson S, Innocentin S, Booth LH, Robertson C, McCowan C, Kerr S, Mulroney TE, O'Reilly MJ, Gurugama TP, Gurugama LP, Rust MA, Ferreira A, Ebrahimi S, Ceron-Gutierrez L, Scotucci J, Kronsteiner B, Dunachie SJ, Klenerman P, PITCH Consortium, Park AJ, Rubino F, Lamikanra AA, Stark H, Kingston N, Estcourt L, Harvala H, Roberts DJ, Doffinger R, Linterman MA, Matheson NJ, Sheikh A, Farooqi IS, Thaventhiran JED.",,Nature medicine,2023,2023-05-11,Y,,,,"Obesity is associated with an increased risk of severe Coronavirus Disease 2019 (COVID-19) infection and mortality. COVID-19 vaccines reduce the risk of serious COVID-19 outcomes; however, their effectiveness in people with obesity is incompletely understood. We studied the relationship among body mass index (BMI), hospitalization and mortality due to COVID-19 among 3.6 million people in Scotland using the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) surveillance platform. We found that vaccinated individuals with severe obesity (BMI > 40 kg/m<sup>2</sup>) were 76% more likely to experience hospitalization or death from COVID-19 (adjusted rate ratio of 1.76 (95% confidence interval (CI), 1.60-1.94). We also conducted a prospective longitudinal study of a cohort of 28 individuals with severe obesity compared to 41 control individuals with normal BMI (BMI 18.5-24.9 kg/m<sup>2</sup>). We found that 55% of individuals with severe obesity had unquantifiable titers of neutralizing antibody against authentic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus compared to 12% of individuals with normal BMI (P = 0.0003) 6 months after their second vaccine dose. Furthermore, we observed that, for individuals with severe obesity, at any given anti-spike and anti-receptor-binding domain (RBD) antibody level, neutralizing capacity was lower than that of individuals with a normal BMI. Neutralizing capacity was restored by a third dose of vaccine but again declined more rapidly in people with severe obesity. We demonstrate that waning of COVID-19 vaccine-induced humoral immunity is accelerated in individuals with severe obesity. As obesity is associated with increased hospitalization and mortality from breakthrough infections, our findings have implications for vaccine prioritization policies.",,pdf:https://www.nature.com/articles/s41591-023-02343-2.pdf; doi:https://doi.org/10.1038/s41591-023-02343-2; html:https://europepmc.org/articles/PMC10202802; pdf:https://europepmc.org/articles/PMC10202802?pdf=render
+38045451,https://doi.org/10.1002/joa3.12927,Using machine learning to enhance prediction of atrial fibrillation recurrence after catheter ablation.,"Brahier MS, Zou F, Abdulkareem M, Kochi S, Migliarese F, Thomaides A, Ma X, Wu C, Sandfort V, Bergquist PJ, Srichai MB, Piccini JP, Petersen SE, Vargas JD.",,Journal of arrhythmia,2023,2023-10-05,Y,Atrial fibrillation; Catheter ablation; Cardiac Computed Tomography; Machine Learning; Left Atrium,,,"<h4>Background</h4>Traditional risk scores for recurrent atrial fibrillation (AF) following catheter ablation utilize readily available clinical and echocardiographic variables and yet have limited discriminatory capacity. Use of data from cardiac imaging and deep learning may help improve accuracy and prediction of recurrent AF after ablation.<h4>Methods</h4>We evaluated patients with symptomatic, drug-refractory AF undergoing catheter ablation. All patients underwent pre-ablation cardiac computed tomography (cCT). LAVi was computed using a deep-learning algorithm. In a two-step analysis, random survival forest (RSF) was used to generate prognostic models with variables of highest importance, followed by Cox proportional hazard regression analysis of the selected variables. Events of interest included early and late recurrence.<h4>Results</h4>Among 653 patients undergoing AF ablation, the most important factors associated with late recurrence by RSF analysis at 24 (+/-18) months follow-up included LAVi and early recurrence. In total, 5 covariates were identified as independent predictors of late recurrence: LAVi (HR per mL/m<sup>2</sup> 1.01 [1.01-1.02]; <i>p</i> < .001), early recurrence (HR 2.42 [1.90-3.09]; <i>p</i> < .001), statin use (HR 1.38 [1.09-1.75]; <i>p</i> = .007), beta-blocker use (HR 1.29 [1.01-1.65]; <i>p</i> = .043), and adjunctive cavotricuspid isthmus ablation [HR 0.74 (0.57-0.96); <i>p</i> = .02]. Survival analysis demonstrated that patients with both LAVi >66.7 mL/m<sup>2</sup> and early recurrence had the highest risk of late recurrence risk compared with those with LAVi <66.7 mL/m<sup>2</sup> and no early recurrence (HR 4.52 [3.36-6.08], <i>p</i> < .001).<h4>Conclusions</h4>Machine learning-derived, full volumetric LAVi from cCT is the most important pre-procedural risk factor for late AF recurrence following catheter ablation. The combination of increased LAVi and early recurrence confers more than a four-fold increased risk of late recurrence.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/joa3.12927; doi:https://doi.org/10.1002/joa3.12927; html:https://europepmc.org/articles/PMC10692862; pdf:https://europepmc.org/articles/PMC10692862?pdf=render
 36749628,https://doi.org/10.2196/42449,Charting a Course for Smartphones and Wearables to Transform Population Health Research.,"Dixon WG, van der Veer SN, Ali SM, Laidlaw L, Dobson RJB, Sudlow C, Chico T, MacArthur JAL, Doherty A.",,Journal of medical Internet research,2023,2023-02-07,Y,Research; Health; Clinical; Data; Digital; Devices; Wearable; Mhealth; Mobile Health; Person-generated Health Data; Population Health Research,,,"The use of data from smartphones and wearable devices has huge potential for population health research, given the high level of device ownership; the range of novel health-relevant data types available from consumer devices; and the frequency and duration with which data are, or could be, collected. Yet, the uptake and success of large-scale mobile health research in the last decade have not met this intensely promoted opportunity. We make the argument that digital person-generated health data are required and necessary to answer many top priority research questions, using illustrative examples taken from the James Lind Alliance Priority Setting Partnerships. We then summarize the findings from 2 UK initiatives that considered the challenges and possible solutions for what needs to be done and how such solutions can be implemented to realize the future opportunities of digital person-generated health data for clinically important population health research. Examples of important areas that must be addressed to advance the field include digital inequality and possible selection bias; easy access for researchers to the appropriate data collection tools, including how best to harmonize data items; analysis methodologies for time series data; patient and public involvement and engagement methods for optimizing recruitment, retention, and public trust; and methods for providing research participants with greater control over their data. There is also a major opportunity, provided through the linkage of digital person-generated health data to routinely collected data, to support novel population health research, bringing together clinician-reported and patient-reported measures. We recognize that well-conducted studies need a wide range of diverse challenges to be skillfully addressed in unison (eg, challenges regarding epidemiology, data science and biostatistics, psychometrics, behavioral and social science, software engineering, user interface design, information governance, data management, and patient and public involvement and engagement). Consequently, progress would be accelerated by the establishment of a new interdisciplinary community where all relevant and necessary skills are brought together to allow for excellence throughout the life cycle of a research study. This will require a partnership of diverse people, methods, and technologies. If done right, the synergy of such a partnership has the potential to transform many millions of people's lives for the better.",,pdf:https://www.jmir.org/2023/1/e42449/PDF; doi:https://doi.org/10.2196/42449; html:https://europepmc.org/articles/PMC11334374; html:https://europepmc.org/articles/PMC7614184; pdf:https://europepmc.org/articles/PMC7614184?pdf=render
 36121907,https://doi.org/10.1161/circulationaha.122.060785,Association of COVID-19 With Major Arterial and Venous Thrombotic Diseases: A Population-Wide Cohort Study of 48 Million Adults in England and Wales.,"Knight R, Walker V, Ip S, Cooper JA, Bolton T, Keene S, Denholm R, Akbari A, Abbasizanjani H, Torabi F, Omigie E, Hollings S, North TL, Toms R, Jiang X, Angelantonio ED, Denaxas S, Thygesen JH, Tomlinson C, Bray B, Smith CJ, Barber M, Khunti K, Davey Smith G, Chaturvedi N, Sudlow C, Whiteley WN, Wood AM, Sterne JAC, CVD-COVID-UK/COVID-IMPACT Consortium and the Longitudinal Health and Wellbeing COVID-19 National Core Study.",,Circulation,2022,2022-09-19,Y,Thrombosis; Myocardial infarction; Stroke; Pulmonary embolism; Venous thrombosis; Electronic Health Records; Covid-19,,,"<h4>Background</h4>Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces a prothrombotic state, but long-term effects of COVID-19 on incidence of vascular diseases are unclear.<h4>Methods</h4>We studied vascular diseases after COVID-19 diagnosis in population-wide anonymized linked English and Welsh electronic health records from January 1 to December 7, 2020. We estimated adjusted hazard ratios comparing the incidence of arterial thromboses and venous thromboembolic events (VTEs) after diagnosis of COVID-19 with the incidence in people without a COVID-19 diagnosis. We conducted subgroup analyses by COVID-19 severity, demographic characteristics, and previous history.<h4>Results</h4>Among 48 million adults, 125 985 were hospitalized and 1 319 789 were not hospitalized within 28 days of COVID-19 diagnosis. In England, there were 260 279 first arterial thromboses and 59 421 first VTEs during 41.6 million person-years of follow-up. Adjusted hazard ratios for first arterial thrombosis after COVID-19 diagnosis compared with no COVID-19 diagnosis declined from 21.7 (95% CI, 21.0-22.4) in week 1 after COVID-19 diagnosis to 1.34 (95% CI, 1.21-1.48) during weeks 27 to 49. Adjusted hazard ratios for first VTE after COVID-19 diagnosis declined from 33.2 (95% CI, 31.3-35.2) in week 1 to 1.80 (95% CI, 1.50-2.17) during weeks 27 to 49. Adjusted hazard ratios were higher, for longer after diagnosis, after hospitalized versus nonhospitalized COVID-19, among Black or Asian versus White people, and among people without versus with a previous event. The estimated whole-population increases in risk of arterial thromboses and VTEs 49 weeks after COVID-19 diagnosis were 0.5% and 0.25%, respectively, corresponding to 7200 and 3500 additional events, respectively, after 1.4 million COVID-19 diagnoses.<h4>Conclusions</h4>High relative incidence of vascular events soon after COVID-19 diagnosis declines more rapidly for arterial thromboses than VTEs. However, incidence remains elevated up to 49 weeks after COVID-19 diagnosis. These results support policies to prevent severe COVID-19 by means of COVID-19 vaccines, early review after discharge, risk factor control, and use of secondary preventive agents in high-risk patients.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCULATIONAHA.122.060785; doi:https://doi.org/10.1161/CIRCULATIONAHA.122.060785; html:https://europepmc.org/articles/PMC9484653; pdf:https://europepmc.org/articles/PMC9484653?pdf=render
 35033224,https://doi.org/10.1016/s2213-2600(21)00543-9,Risk of serious COVID-19 outcomes among adults with asthma in Scotland: a national incident cohort study.,"Shi T, Pan J, Vasileiou E, Robertson C, Sheikh A, Public Health Scotland and the EAVE II Collaborators.",,The Lancet. Respiratory medicine,2022,2022-01-13,Y,,,,"<h4>Background</h4>There is considerable uncertainty over whether adults with asthma should be offered booster vaccines against SARS-CoV-2 and, if so, who should be prioritised for booster vaccination. We were asked by the UK's Joint Commission on Vaccination and Immunisation to undertake an urgent analysis to identify which adults with asthma were at an increased risk of serious COVID-19 outcomes to inform deliberations on booster COVID-19 vaccines.<h4>Methods</h4>This national incident cohort study was done in all adults in Scotland aged 18 years and older who were included in the linked dataset of Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II). We used data from EAVE II to investigate the risk of COVID-19 hospitalisation and the composite outcome of intensive care unit (ICU) admission or death from COVID-19 among adults with asthma. A Cox proportional hazard model was used to derive adjusted hazard ratios (HRs) and 95% CIs for the association between asthma and COVID-19 hospital admission and ICU admission or death, stratified by markers of history of an asthma attack defined by either oral corticosteroid prescription (prednisolone, prednisone, and dexamethasone) in the 2 years before March 1, 2020, or hospitalisation for asthma before March 1, 2020. Analyses were adjusted for age, sex, socioeconomic status, comorbidity, previous hospitalisation, and vaccine status.<h4>Findings</h4>Between March 1, 2020, and July 27, 2021, 561 279 (12·7%) of 4 421 663 adults in Scotland had clinician-diagnosed-and-recorded-asthma. Among adults with asthma, 39 253 (7·0%) had confirmed SARS-CoV-2 infections, of whom 4828 (12·3%) were admitted to hospital for COVID-19 (among them, an estimated 600 [12·4%] might have been due to nosocomial infections). Adults with asthma were found to be at an increased risk of COVID-19 hospital admission (adjusted HR 1·27, 95% CI 1·23-1·32) compared with those without asthma. When using oral corticosteroid prescribing in the preceding 2 years as a marker for history of an asthma attack, the adjusted HR was 1·54 (95% CI 1·46-1·61) for those with three or more prescribed courses of oral corticosteroids, 1·37 (1·26-1·48) for those with two prescribed courses, 1·30 (1·23-1·37) for those with one prescribed course, and 1·15 (1·11-1·21) for those without any courses, compared with those aged 18 years or older without asthma. Adults with asthma were found to be at an increased risk of COVID-19 ICU admission or death compared with those without asthma (adjusted HR 1·13, 95 % CI 1·05-1·22). The adjusted HR was 1·44 (95% CI 1·31-1·58) for those with three or more prescribed courses of oral corticosteroids, 1·27 (1·09-1·48) for those with two prescribed courses, 1·04 (0·93-1·16) for those with one prescribed course, and 1·06 (0·97-1·17) for those without any course, compared with adults without asthma.<h4>Interpretation</h4>Adults with asthma who have required two or more courses of oral corticosteroids in the previous 2 years or a hospital admission for asthma before March 1, 2020, are at increased risk of both COVID-19 hospitalisation and ICU admission or death. Patients with a recent asthma attack should be considered a priority group for booster COVID-19 vaccines.<h4>Funding</h4>UK Research and Innovation (Medical Research Council), Research and Innovation Industrial Strategy Challenge Fund, Health Data Research UK, and Scottish Government.",,pdf:http://www.thelancet.com/article/S2213260021005439/pdf; doi:https://doi.org/10.1016/S2213-2600(21)00543-9; html:https://europepmc.org/articles/PMC8758152
 32951042,https://doi.org/10.1093/ageing/afaa207,"The impact of COVID-19 on adjusted mortality risk in care homes for older adults in Wales, UK: a retrospective population-based cohort study for mortality in 2016-2020.","Hollinghurst J, Lyons J, Fry R, Akbari A, Gravenor M, Watkins A, Verity F, Lyons RA.",,Age and ageing,2021,2021-01-01,Y,Mortality; Frailty; Older People; Care Homes; Covid-19,,,"<h4>Background</h4>mortality in care homes has had a prominent focus during the COVID-19 outbreak. Care homes are particularly vulnerable to the spread of infectious diseases, which may lead to increased mortality risk. Multiple and interconnected challenges face the care home sector in the prevention and management of outbreaks of COVID-19, including adequate supply of personal protective equipment, staff shortages and insufficient or lack of timely COVID-19 testing.<h4>Aim</h4>to analyse the mortality of older care home residents in Wales during COVID-19 lockdown and compare this across the population of Wales and the previous 4 years.<h4>Study design and setting</h4>we used anonymised electronic health records and administrative data from the secure anonymised information linkage databank to create a cross-sectional cohort study. We anonymously linked data for Welsh residents to mortality data up to the 14th June 2020.<h4>Methods</h4>we calculated survival curves and adjusted Cox proportional hazards models to estimate hazard ratios (HRs) for the risk of mortality. We adjusted HRs for age, gender, social economic status and prior health conditions.<h4>Results</h4>survival curves show an increased proportion of deaths between 23rd March and 14th June 2020 in care homes for older people, with an adjusted HR of 1.72 (1.55, 1.90) compared with 2016. Compared with the general population in 2016-2019, adjusted care home mortality HRs for older adults rose from 2.15 (2.11, 2.20) in 2016-2019 to 2.94 (2.81, 3.08) in 2020.<h4>Conclusions</h4>the survival curves and increased HRs show a significantly increased risk of death in the 2020 study periods.",,pdf:https://academic.oup.com/ageing/article-pdf/50/1/25/42362959/afaa207.pdf; doi:https://doi.org/10.1093/ageing/afaa207; html:https://europepmc.org/articles/PMC7546151; pdf:https://europepmc.org/articles/PMC7546151?pdf=render
-32741245,https://doi.org/10.1177/0954411920946526,Artificial intelligence approaches to predict coronary stenosis severity using non-invasive fractional flow reserve.,"Carson JM, Chakshu NK, Sazonov I, Nithiarasu P.",,"Proceedings of the Institution of Mechanical Engineers. Part H, Journal of engineering in medicine",2020,2020-08-03,Y,Artificial intelligence; Biomedical engineering; Coronary Heart Disease; Fractional Flow Reserve; Computational Mechanics; Haemodynamic Modelling,,,"Fractional flow reserve is the current reference standard in the assessment of the functional impact of a stenosis in coronary heart disease. In this study, three models of artificial intelligence of varying degrees of complexity were compared to fractional flow reserve measurements. The three models are the multivariate polynomial regression, which is a statistical method used primarily for correlation; the feed-forward neural network; and the long short-term memory, which is a type of recurrent neural network that is suited to modelling sequences. The models were initially trained using a virtual patient database that was generated from a validated one-dimensional physics-based model. The feed-forward neural network performed the best for all test cases considered, which were a single vessel case from a virtual patient database, a multi-vessel network from a virtual patient database, and 25 clinically invasive fractional flow reserve measurements from real patients. The feed-forward neural network model achieved around 99% diagnostic accuracy in both tests involving virtual patients, and a respectable 72% diagnostic accuracy when compared to the invasive fractional flow reserve measurements. The multivariate polynomial regression model performed well in the single vessel case, but struggled on network cases as the variation of input features was much larger. The long short-term memory performed well for the single vessel cases, but tended to have a bias towards a positive fractional flow reserve prediction for the virtual multi-vessel case, and for the patient cases. Overall, the feed-forward neural network shows promise in successfully predicting fractional flow reserve in real patients, and could be a viable option if trained using a large enough data set of real patients.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/0954411920946526; doi:https://doi.org/10.1177/0954411920946526; html:https://europepmc.org/articles/PMC7675765; pdf:https://europepmc.org/articles/PMC7675765?pdf=render
 38809392,https://doi.org/10.1007/s11357-024-01202-3,Mediating and moderating effects of plasma proteomic biomarkers on the association between poor oral health problems and incident dementia: The UK Biobank study.,"Beydoun HA, Beydoun MA, Noren Hooten N, Weiss J, Li Z, Georgescu MF, Maino Vieytes CA, Meirelles O, Launer LJ, Evans MK, Zonderman AB.",,GeroScience,2024,2024-05-29,N,Aging; Dementia; periodontal disease; Tooth loss; Poor Oral Health; Plasma Proteomic Biomarkers,,,"The plasma proteome can mediate poor oral health problems (POHP)'s link to incident dementia. We screened 37,269 UK Biobank participants 50-74 years old (2006-2010) for prevalent POHP, further tested against 1463 plasma proteins and incident dementia over up to 15 years of follow-up. Total effect (TE) of POHP-dementia through plasma proteomic markers was decomposed into pure indirect effect (PIE), interaction referent (INTREF), controlled direct effect (CDE), or mediated interaction (INTMED). POHP increased the risk of all-cause dementia by 17% (P < 0.05). Growth differentiation factor 15 (GDF15) exhibited the strongest mediating effects (PIE > 0, P < 0.001), explaining 28% the total effect of POHP on dementia, as a pure indirect effect. A first principal component encompassing top 4 mediators (GDF15, IL19, MMP12, and ACVRL1), explained 11% of the POHP-dementia effect as a pure indirect effect. Pathway analysis including all mediators (k = 173 plasma proteins) revealed the involvement of the immune system, signal transduction, metabolism, disease, and gene expression, while STRING analysis indicated that top mediators within the first principal component were also represented in the two largest proteomic clusters. The dominant biological GO pathway for the GDF15 cluster was GO:0007169 labeled as ""transmembrane receptor protein tyrosine kinase signaling pathway."" Dementia is linked to POHP mediated by GDF15 among several proteomic markers.",,doi:https://doi.org/10.1007/s11357-024-01202-3; html:https://europepmc.org/articles/PMC11336161; pdf:https://europepmc.org/articles/PMC11336161?pdf=render; doi:https://doi.org/10.1007/s11357-024-01202-3
 36936262,https://doi.org/10.1136/bmjmed-2022-000371,Association between coeliac disease and cardiovascular disease: prospective analysis of UK Biobank data.,"Conroy M, Allen N, Lacey B, Soilleux E, Littlejohns T.",,BMJ medicine,2023,2023-01-04,Y,epidemiology; Cardiology; Celiac Disease,,,"<h4>Objectives</h4>To investigate whether people with coeliac disease are at increased risk of cardiovascular disease, including ischaemic heart disease, myocardial infarction, and stroke.<h4>Design</h4>Prospective analysis of a large cohort study.<h4>Setting</h4>UK Biobank database.<h4>Participants</h4>469 095 adults, of which 2083 had coeliac disease, aged 40-69 years from England, Scotland, and Wales between 2006 and 2010 without cardiovascular disease at baseline.<h4>Main outcome measure</h4>A composite primary outcome was relative risk of cardiovascular disease, ischaemic heart disease, myocardial infarction, and stroke in people with coeliac disease compared with people who do not have coeliac disease, assessed using Cox proportional hazard models.<h4>Results</h4>40 687 incident cardiovascular disease events occurred over a median follow-up of 12.4 years (interquartile range 11.5-13.1), with 218 events among people with coeliac disease. Participants with coeliac disease were more likely to have a lower body mass index and systolic blood pressure, less likely to smoke, and more likely to have an ideal cardiovascular risk score than people who do not have coeliac disease. Despite this, participants with coeliac disease had an incidence rate of 9.0 cardiovascular disease cases per 1000 person years (95% confidence interval 7.9 to 10.3) compared with 7.4 per 1000 person years (7.3 to 7.4) in people with no coeliac disease. Coeliac disease was associated with an increased risk of cardiovascular disease (hazard ratio 1.27 (95% confidence interval 1.11 to 1.45)), which was not influenced by adjusting for lifestyle factors (1.27 (1.11 to 1.45)), but was strengthened by further adjusting for other cardiovascular risk factors (1.44 (1.26 to 1.65)). Similar associations were identified for ischaemic heart disease and myocardial infarction but fewer stroke events were reported and no evidence of an association between coeliac disease and risk of stroke.<h4>Conclusions</h4>Individuals with coeliac disease had a lower prevalence of traditional cardiovascular risk factors but had a higher risk of developing cardiovascular disease than did people with no coeliac disease. Cardiovascular risk scores used in clinical practice might therefore not adequately capture the excess risk of cardiovascular disease in people with coeliac disease, and clinicians should be aware of the need to optimise cardiovascular health in this population.",,pdf:https://bmjmedicine.bmj.com/content/bmjmed/2/1/e000371.full.pdf; doi:https://doi.org/10.1136/bmjmed-2022-000371; html:https://europepmc.org/articles/PMC9951384; pdf:https://europepmc.org/articles/PMC9951384?pdf=render
-34713086,https://doi.org/10.3389/fdgth.2021.598916,Markup: A Web-Based Annotation Tool Powered by Active Learning.,"Dobbie S, Strafford H, Pickrell WO, Fonferko-Shadrach B, Jones C, Akbari A, Thompson S, Lacey A.",,Frontiers in digital health,2021,2021-07-26,Y,Active Learning; Annotation; Natural Language Processing; Unstructured Text; Sequence-to-sequence Learning,,,"Across various domains, such as health and social care, law, news, and social media, there are increasing quantities of unstructured texts being produced. These potential data sources often contain rich information that could be used for domain-specific and research purposes. However, the unstructured nature of free-text data poses a significant challenge for its utilisation due to the necessity of substantial manual intervention from domain-experts to label embedded information. Annotation tools can assist with this process by providing functionality that enables the accurate capture and transformation of unstructured texts into structured annotations, which can be used individually, or as part of larger Natural Language Processing (NLP) pipelines. We present Markup (https://www.getmarkup.com/) an open-source, web-based annotation tool that is undergoing continued development for use across all domains. Markup incorporates NLP and Active Learning (AL) technologies to enable rapid and accurate annotation using custom user configurations, predictive annotation suggestions, and automated mapping suggestions to both domain-specific ontologies, such as the Unified Medical Language System (UMLS), and custom, user-defined ontologies. We demonstrate a real-world use case of how Markup has been used in a healthcare setting to annotate structured information from unstructured clinic letters, where captured annotations were used to build and test NLP applications.",,pdf:https://www.frontiersin.org/articles/10.3389/fdgth.2021.598916/pdf; doi:https://doi.org/10.3389/fdgth.2021.598916; html:https://europepmc.org/articles/PMC8521860; pdf:https://europepmc.org/articles/PMC8521860?pdf=render
+32741245,https://doi.org/10.1177/0954411920946526,Artificial intelligence approaches to predict coronary stenosis severity using non-invasive fractional flow reserve.,"Carson JM, Chakshu NK, Sazonov I, Nithiarasu P.",,"Proceedings of the Institution of Mechanical Engineers. Part H, Journal of engineering in medicine",2020,2020-08-03,Y,Artificial intelligence; Biomedical engineering; Coronary Heart Disease; Fractional Flow Reserve; Computational Mechanics; Haemodynamic Modelling,,,"Fractional flow reserve is the current reference standard in the assessment of the functional impact of a stenosis in coronary heart disease. In this study, three models of artificial intelligence of varying degrees of complexity were compared to fractional flow reserve measurements. The three models are the multivariate polynomial regression, which is a statistical method used primarily for correlation; the feed-forward neural network; and the long short-term memory, which is a type of recurrent neural network that is suited to modelling sequences. The models were initially trained using a virtual patient database that was generated from a validated one-dimensional physics-based model. The feed-forward neural network performed the best for all test cases considered, which were a single vessel case from a virtual patient database, a multi-vessel network from a virtual patient database, and 25 clinically invasive fractional flow reserve measurements from real patients. The feed-forward neural network model achieved around 99% diagnostic accuracy in both tests involving virtual patients, and a respectable 72% diagnostic accuracy when compared to the invasive fractional flow reserve measurements. The multivariate polynomial regression model performed well in the single vessel case, but struggled on network cases as the variation of input features was much larger. The long short-term memory performed well for the single vessel cases, but tended to have a bias towards a positive fractional flow reserve prediction for the virtual multi-vessel case, and for the patient cases. Overall, the feed-forward neural network shows promise in successfully predicting fractional flow reserve in real patients, and could be a viable option if trained using a large enough data set of real patients.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/0954411920946526; doi:https://doi.org/10.1177/0954411920946526; html:https://europepmc.org/articles/PMC7675765; pdf:https://europepmc.org/articles/PMC7675765?pdf=render
+34864250,https://doi.org/10.1016/j.seizure.2021.11.017,Epilepsy mortality in Wales during COVID-19.,"Daniels H, Lacey AS, Mikadze D, Akbari A, Fonferko-Shadrach B, Hollinghurst J, Lyons RA, Rees MI, Sawhney IM, Powell RH, Kerr MP, Pickrell WO.",,Seizure,2022,2021-11-27,Y,Pandemic; Data Linkage; Electronic Health Records; Covid-19,,,"<h4>Purpose</h4>The COVID-19 pandemic has increased mortality worldwide and those with chronic conditions may have been disproportionally affected. However, it is unknown whether the pandemic has changed mortality rates for people with epilepsy. We aimed to compare mortality rates in people with epilepsy in Wales during the pandemic with pre-pandemic rates.<h4>Methods</h4>We performed a retrospective study using individual-level linked population-scale anonymised electronic health records. We identified deaths in people with epilepsy (DPWE), i.e. those with a diagnosis of epilepsy, and deaths associated with epilepsy (DAE), where epilepsy was recorded as a cause of death on death certificates. We compared death rates in 2020 with average rates in 2015-2019 using Poisson models to calculate death rate ratios.<h4>Results</h4>There were 188 DAE and 628 DPWE in Wales in 2020 (death rates: 7.7/100,000/year and 25.7/100,000/year). The average rates for DAE and DPWE from 2015 to 2019 were 5.8/100,000/year and 23.8/100,000/year, respectively. Death rate ratios (2020 compared to 2015-2019) for DAE were 1.34 (95%CI 1.14-1.57, p<0.001) and for DPWE were 1.08 (0.99-1.17, p = 0.09). The death rate ratios for non-COVID deaths (deaths without COVID mentioned on death certificates) for DAE were 1.17 (0.99-1.39, p = 0.06) and for DPWE were 0.96 (0.87-1.05, p = 0.37).<h4>Conclusions</h4>The significant increase in DAE in Wales during 2020 could be explained by the direct effect of COVID-19 infection. Non-COVID-19 deaths have not increased significantly but further work is needed to assess the longer-term impact.",,pdf:http://www.seizure-journal.com/article/S1059131121003757/pdf; doi:https://doi.org/10.1016/j.seizure.2021.11.017; html:https://europepmc.org/articles/PMC8626872
 34850818,https://doi.org/10.1093/ageing/afab223,"COVID-19 infection risk amongst 14,104 vaccinated care home residents: a national observational longitudinal cohort study in Wales, UK, December 2020-March 2021.","Hollinghurst J, North L, Perry M, Akbari A, Gravenor MB, Lyons RA, Fry R.",,Age and ageing,2022,2022-01-01,Y,Vaccination; Older People; Care Homes; Covid-19; Sars-cov-2,,,"<h4>Background</h4>vaccinations for COVID-19 have been prioritised for older people living in care homes. However, vaccination trials included limited numbers of older people.<h4>Aim</h4>we aimed to study infection rates of SARS-CoV-2 for older care home residents following vaccination and identify factors associated with increased risk of infection.<h4>Study design and setting</h4>we conducted an observational data-linkage study including 14,104 vaccinated older care home residents in Wales (UK) using anonymised electronic health records and administrative data.<h4>Methods</h4>we used Cox proportional hazards models to estimate hazard ratios (HRs) for the risk of testing positive for SARS-CoV-2 infection following vaccination, after landmark times of either 7 or 21 days post-vaccination. We adjusted HRs for age, sex, frailty, prior SARS-CoV-2 infections and vaccination type.<h4>Results</h4>we observed a small proportion of care home residents with positive polymerase chain reaction (tests following vaccination 1.05% (N = 148), with 90% of infections occurring within 28 days. For the 7-day landmark analysis we found a reduced risk of SARS-CoV-2 infection for vaccinated individuals who had a previous infection; HR (95% confidence interval) 0.54 (0.30, 0.95). For the 21-day landmark analysis, we observed high HRs for individuals with low and intermediate frailty compared with those without; 4.59 (1.23, 17.12) and 4.85 (1.68, 14.04), respectively.<h4>Conclusions</h4>increased risk of infection after 21 days was associated with frailty. We found most infections occurred within 28 days of vaccination, suggesting extra precautions to reduce transmission risk should be taken in this time frame.",,pdf:https://academic.oup.com/ageing/article-pdf/51/1/afab223/42083726/afab223.pdf; doi:https://doi.org/10.1093/ageing/afab223; html:https://europepmc.org/articles/PMC8690013; pdf:https://europepmc.org/articles/PMC8690013?pdf=render
+34713086,https://doi.org/10.3389/fdgth.2021.598916,Markup: A Web-Based Annotation Tool Powered by Active Learning.,"Dobbie S, Strafford H, Pickrell WO, Fonferko-Shadrach B, Jones C, Akbari A, Thompson S, Lacey A.",,Frontiers in digital health,2021,2021-07-26,Y,Active Learning; Annotation; Natural Language Processing; Unstructured Text; Sequence-to-sequence Learning,,,"Across various domains, such as health and social care, law, news, and social media, there are increasing quantities of unstructured texts being produced. These potential data sources often contain rich information that could be used for domain-specific and research purposes. However, the unstructured nature of free-text data poses a significant challenge for its utilisation due to the necessity of substantial manual intervention from domain-experts to label embedded information. Annotation tools can assist with this process by providing functionality that enables the accurate capture and transformation of unstructured texts into structured annotations, which can be used individually, or as part of larger Natural Language Processing (NLP) pipelines. We present Markup (https://www.getmarkup.com/) an open-source, web-based annotation tool that is undergoing continued development for use across all domains. Markup incorporates NLP and Active Learning (AL) technologies to enable rapid and accurate annotation using custom user configurations, predictive annotation suggestions, and automated mapping suggestions to both domain-specific ontologies, such as the Unified Medical Language System (UMLS), and custom, user-defined ontologies. We demonstrate a real-world use case of how Markup has been used in a healthcare setting to annotate structured information from unstructured clinic letters, where captured annotations were used to build and test NLP applications.",,pdf:https://www.frontiersin.org/articles/10.3389/fdgth.2021.598916/pdf; doi:https://doi.org/10.3389/fdgth.2021.598916; html:https://europepmc.org/articles/PMC8521860; pdf:https://europepmc.org/articles/PMC8521860?pdf=render
 35501368,https://doi.org/10.1038/s41431-022-01107-9,"Genetic analysis of the PCSK9 locus in psychological, psychiatric, metabolic and cardiovascular traits in UK Biobank.","Hay R, Cullen B, Graham N, Lyall DM, Aman A, Pell JP, Ward J, Smith DJ, Strawbridge RJ.",,European journal of human genetics : EJHG,2022,2022-05-02,Y,,,,"The association between severe mental illness (SMI) and cardiovascular and metabolic disease (CMD) is poorly understood. PCSK9 is expressed in systems critical to both SMI and CMD and influences lipid homeostasis and brain function. We systematically investigated relationships between genetic variation within the PCSK9 locus and risk for both CMD and SMI. UK Biobank recruited ~500,000 volunteers and assessed a wide range of SMI and CMD phenotypes. We used genetic data from white British ancestry individuals of UK Biobank. Genetic association analyses were conducted in PLINK, with statistical significance defined by the number of independent SNPs. Conditional analyses and linkage disequilibrium assessed the independence of SNPs and the presence of multiple signals. Two genetic risk scores of lipid-lowering alleles were calculated and used as proxies for putative lipid-lowering effects of PCSK9. PCSK9 variants were associated with central adiposity, venous thrombosis embolism, systolic blood pressure, mood instability, and neuroticism (all p < 1.16 × 10<sup>-4</sup>). No secondary signals were identified. Conditional analyses and high linkage disequilibrium (r<sup>2</sup> = 0.98) indicated that mood instability and central obesity may share a genetic signal. Genetic risk scores suggested that the lipid-lowering effects of PCSK9 may be causal for greater mood instability and higher neuroticism. This is the first study to implicate the PCSK9 locus in mood-disorder symptoms and related traits, as well as the shared pathology of SMI and CMD. PCSK9 effects on mood may occur via lipid-lowering mechanisms. Further work is needed to understand whether repurposing PCSK9-targeting therapies might improve SMI symptoms and prevent CMD.",,pdf:https://www.nature.com/articles/s41431-022-01107-9.pdf; doi:https://doi.org/10.1038/s41431-022-01107-9; html:https://europepmc.org/articles/PMC9712543; pdf:https://europepmc.org/articles/PMC9712543?pdf=render
-34864250,https://doi.org/10.1016/j.seizure.2021.11.017,Epilepsy mortality in Wales during COVID-19.,"Daniels H, Lacey AS, Mikadze D, Akbari A, Fonferko-Shadrach B, Hollinghurst J, Lyons RA, Rees MI, Sawhney IM, Powell RH, Kerr MP, Pickrell WO.",,Seizure,2022,2021-11-27,Y,Pandemic; Data Linkage; Electronic Health Records; Covid-19,,,"<h4>Purpose</h4>The COVID-19 pandemic has increased mortality worldwide and those with chronic conditions may have been disproportionally affected. However, it is unknown whether the pandemic has changed mortality rates for people with epilepsy. We aimed to compare mortality rates in people with epilepsy in Wales during the pandemic with pre-pandemic rates.<h4>Methods</h4>We performed a retrospective study using individual-level linked population-scale anonymised electronic health records. We identified deaths in people with epilepsy (DPWE), i.e. those with a diagnosis of epilepsy, and deaths associated with epilepsy (DAE), where epilepsy was recorded as a cause of death on death certificates. We compared death rates in 2020 with average rates in 2015-2019 using Poisson models to calculate death rate ratios.<h4>Results</h4>There were 188 DAE and 628 DPWE in Wales in 2020 (death rates: 7.7/100,000/year and 25.7/100,000/year). The average rates for DAE and DPWE from 2015 to 2019 were 5.8/100,000/year and 23.8/100,000/year, respectively. Death rate ratios (2020 compared to 2015-2019) for DAE were 1.34 (95%CI 1.14-1.57, p<0.001) and for DPWE were 1.08 (0.99-1.17, p = 0.09). The death rate ratios for non-COVID deaths (deaths without COVID mentioned on death certificates) for DAE were 1.17 (0.99-1.39, p = 0.06) and for DPWE were 0.96 (0.87-1.05, p = 0.37).<h4>Conclusions</h4>The significant increase in DAE in Wales during 2020 could be explained by the direct effect of COVID-19 infection. Non-COVID-19 deaths have not increased significantly but further work is needed to assess the longer-term impact.",,pdf:http://www.seizure-journal.com/article/S1059131121003757/pdf; doi:https://doi.org/10.1016/j.seizure.2021.11.017; html:https://europepmc.org/articles/PMC8626872
-37263685,https://doi.org/10.1136/bmjopen-2022-070637,"Impact of the COVID-19 pandemic on domiciliary care workers in Wales, UK: a data linkage cohort study using the SAIL Databank.","Cannings-John R, Schoenbuchner S, Jones H, Lugg-Widger FV, Akbari A, Brookes-Howell L, Hood K, John A, Thomas DR, Prout H, Robling M.",,BMJ open,2023,2023-06-01,Y,Mental health; Social Medicine; Covid-19,,,"<h4>Objectives</h4>To quantify population health risks for domiciliary care workers (DCWs) in Wales, UK, working during the COVID-19 pandemic.<h4>Design</h4>A population-level retrospective study linking occupational registration data to anonymised electronic health records maintained by the Secure Anonymised Information Linkage Databank in a privacy-protecting trusted research environment.<h4>Setting</h4>Registered DCW population in Wales.<h4>Participants</h4>Records for all linked DCWs from 1 March 2020 to 30 November 2021.<h4>Primary and secondary outcome measures</h4>Our primary outcome was confirmed COVID-19 infection; secondary outcomes included contacts for suspected COVID-19, mental health including self-harm, fit notes, respiratory infections not necessarily recorded as COVID-19, deaths involving COVID-19 and all-cause mortality.<h4>Results</h4>Confirmed and suspected COVID-19 infection rates increased over the study period to 24% by 30 November 2021. Confirmed COVID-19 varied by sex (males: 19% vs females: 24%) and age (>55 years: 19% vs <35 years: 26%) and were higher for care workers employed by local authority social services departments compared with the private sector (27% and 23%, respectively). 34% of DCWs required support for a mental health condition, with mental health-related prescribing increasing in frequency when compared with the prepandemic period. Events for self-harm increased from 0.2% to 0.4% over the study period as did the issuing of fit notes. There was no evidence to suggest a miscoding of COVID-19 infection with non-COVID-19 respiratory conditions. COVID-19-related and all-cause mortality were no greater than for the general population aged 15-64 years in Wales (0.1% and 0.034%, respectively). A comparable DCW workforce in Scotland and England would result in a comparable rate of COVID-19 infection, while the younger workforce in Northern Ireland may result in a greater infection rate.<h4>Conclusions</h4>While initial concerns about excess mortality are alleviated, the substantial pre-existing and increased mental health burden for DCWs will require investment to provide long-term support to the sector's workforce.",,pdf:https://bmjopen.bmj.com/content/bmjopen/13/6/e070637.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-070637; html:https://europepmc.org/articles/PMC10255029; pdf:https://europepmc.org/articles/PMC10255029?pdf=render
 35858680,https://doi.org/10.1136/bmj-2021-068946,Comparative effectiveness of ChAdOx1 versus BNT162b2 covid-19 vaccines in health and social care workers in England: cohort study using OpenSAFELY.,"Hulme WJ, Williamson EJ, Green ACA, Bhaskaran K, McDonald HI, Rentsch CT, Schultze A, Tazare J, Curtis HJ, Walker AJ, Tomlinson LA, Palmer T, Horne EMF, MacKenna B, Morton CE, Mehrkar A, Morley J, Fisher L, Bacon SCJ, Evans D, Inglesby P, Hickman G, Davy S, Ward T, Croker R, Eggo RM, Wong AYS, Mathur R, Wing K, Forbes H, Grint DJ, Douglas IJ, Evans SJW, Smeeth L, Bates C, Cockburn J, Parry J, Hester F, Harper S, Sterne JAC, Hernán MA, Goldacre B.",,BMJ (Clinical research ed.),2022,2022-07-20,Y,,,,"<h4>Objective</h4>To compare the effectiveness of the BNT162b2 mRNA (Pfizer-BioNTech) and the ChAdOx1 (Oxford-AstraZeneca) covid-19 vaccines against infection and covid-19 disease in health and social care workers.<h4>Design</h4>Cohort study, emulating a comparative effectiveness trial, on behalf of NHS England.<h4>Setting</h4>Linked primary care, hospital, and covid-19 surveillance records available within the OpenSAFELY-TPP research platform, covering a period when the SARS-CoV-2 Alpha variant was dominant.<h4>Participants</h4>317 341 health and social care workers vaccinated between 4 January and 28 February 2021, registered with a general practice using the TPP SystmOne clinical information system in England, and not clinically extremely vulnerable.<h4>Interventions</h4>Vaccination with either BNT162b2 or ChAdOx1 administered as part of the national covid-19 vaccine roll-out.<h4>Main outcome measures</h4>Recorded SARS-CoV-2 positive test, or covid-19 related attendance at an accident and emergency (A&E) department or hospital admission occurring within 20 weeks of receipt of the first vaccine dose.<h4>Results</h4>Over the duration of 118 771 person-years of follow-up there were 6962 positive SARS-CoV-2 tests, 282 covid-19 related A&E attendances, and 166 covid-19 related hospital admissions. The cumulative incidence of each outcome was similar for both vaccines during the first 20 weeks after vaccination. The cumulative incidence of recorded SARS-CoV-2 infection 20 weeks after first-dose vaccination with BNT162b2 was 21.7 per 1000 people (95% confidence interval 20.9 to 22.4) and with ChAdOx1 was 23.7 (21.8 to 25.6), representing a difference of 2.04 per 1000 people (0.04 to 4.04). The difference in the cumulative incidence per 1000 people of covid-19 related A&E attendance at 20 weeks was 0.06 per 1000 people (95% CI -0.31 to 0.43). For covid-19 related hospital admission, this difference was 0.11 per 1000 people (-0.22 to 0.44).<h4>Conclusions</h4>In this cohort of healthcare workers where we would not anticipate vaccine type to be related to health status, we found no substantial differences in the incidence of SARS-CoV-2 infection or covid-19 disease up to 20 weeks after vaccination. Incidence dropped sharply at 3-4 weeks after vaccination, and there were few covid-19 related hospital attendance and admission events after this period. This is in line with expected onset of vaccine induced immunity and suggests strong protection against Alpha variant covid-19 disease for both vaccines in this relatively young and healthy population of healthcare workers.",,pdf:https://www.bmj.com/content/bmj/378/bmj-2021-068946.full.pdf; doi:https://doi.org/10.1136/bmj-2021-068946; html:https://europepmc.org/articles/PMC9295078; pdf:https://europepmc.org/articles/PMC9295078?pdf=render
-39174061,https://doi.org/10.1136/bmjopen-2023-078108,Risk factors for prolonged length of hospital stay following elective hip replacement surgery: a retrospective longitudinal observational study.,"Wilson R, Margelyte R, Redaniel MT, Eyles E, Jones T, Penfold C, Blom A, Elliott A, Harper A, Keen T, Pitt M, Judge A.",,BMJ open,2024,2024-08-21,Y,Hip; Primary Health Care; Hospitalization; Adult Orthopaedics,,,"<h4>Objectives</h4>Our aim was to identify which patients are likely to stay in hospital longer following total hip replacement surgery.<h4>Design</h4>Longitudinal, observational study used routinely collected data.<h4>Setting</h4>Data were collected from an NHS Trust in South-West England between 2016 and 2019.<h4>Participants</h4>2352 hip replacement patients had complete data and were included in analysis.<h4>Primary and secondary outcome measures</h4>Three measures of length of stay were used: a count measure of number of days spent in hospital, a binary measure of ≤7 days/>7 days in hospital and a binary measure of remaining in hospital when medically fit for discharge.<h4>Results</h4>The mean length of stay was 5.4 days following surgery, with 18% in hospital for more than 7 days, and 11% staying in hospital when medically fit for discharge. Longer hospital stay was associated with older age (OR=1.06, 95% CI 1.05 to 1.08), being female (OR=1.42, 95% CI 1.12 to 1.81) and more comorbidities (OR=3.52, 95% CI 1.45 to 8.55) and shorter length of stay with not having had a recent hospital admission (OR=0.44, 95% CI 0.32 to 0.60). Results were similar for remaining in hospital when medically fit for discharge, with the addition of an association with highest socioeconomic deprivation (OR=2.08, 95% CI 1.37 to 3.16).<h4>Conclusions</h4>Older, female patients with more comorbidities and from more socioeconomically deprived areas are likely to remain in hospital for longer following surgery. This study produced regression models demonstrating consistent results across three measures of prolonged hospital stay following hip replacement surgery. These findings could be used to inform surgery planning and when supporting patient discharge following surgery.",,doi:https://doi.org/10.1136/bmjopen-2023-078108; html:https://europepmc.org/articles/PMC11340698; pdf:https://europepmc.org/articles/PMC11340698?pdf=render
+37263685,https://doi.org/10.1136/bmjopen-2022-070637,"Impact of the COVID-19 pandemic on domiciliary care workers in Wales, UK: a data linkage cohort study using the SAIL Databank.","Cannings-John R, Schoenbuchner S, Jones H, Lugg-Widger FV, Akbari A, Brookes-Howell L, Hood K, John A, Thomas DR, Prout H, Robling M.",,BMJ open,2023,2023-06-01,Y,Mental health; Social Medicine; Covid-19,,,"<h4>Objectives</h4>To quantify population health risks for domiciliary care workers (DCWs) in Wales, UK, working during the COVID-19 pandemic.<h4>Design</h4>A population-level retrospective study linking occupational registration data to anonymised electronic health records maintained by the Secure Anonymised Information Linkage Databank in a privacy-protecting trusted research environment.<h4>Setting</h4>Registered DCW population in Wales.<h4>Participants</h4>Records for all linked DCWs from 1 March 2020 to 30 November 2021.<h4>Primary and secondary outcome measures</h4>Our primary outcome was confirmed COVID-19 infection; secondary outcomes included contacts for suspected COVID-19, mental health including self-harm, fit notes, respiratory infections not necessarily recorded as COVID-19, deaths involving COVID-19 and all-cause mortality.<h4>Results</h4>Confirmed and suspected COVID-19 infection rates increased over the study period to 24% by 30 November 2021. Confirmed COVID-19 varied by sex (males: 19% vs females: 24%) and age (>55 years: 19% vs <35 years: 26%) and were higher for care workers employed by local authority social services departments compared with the private sector (27% and 23%, respectively). 34% of DCWs required support for a mental health condition, with mental health-related prescribing increasing in frequency when compared with the prepandemic period. Events for self-harm increased from 0.2% to 0.4% over the study period as did the issuing of fit notes. There was no evidence to suggest a miscoding of COVID-19 infection with non-COVID-19 respiratory conditions. COVID-19-related and all-cause mortality were no greater than for the general population aged 15-64 years in Wales (0.1% and 0.034%, respectively). A comparable DCW workforce in Scotland and England would result in a comparable rate of COVID-19 infection, while the younger workforce in Northern Ireland may result in a greater infection rate.<h4>Conclusions</h4>While initial concerns about excess mortality are alleviated, the substantial pre-existing and increased mental health burden for DCWs will require investment to provide long-term support to the sector's workforce.",,pdf:https://bmjopen.bmj.com/content/bmjopen/13/6/e070637.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-070637; html:https://europepmc.org/articles/PMC10255029; pdf:https://europepmc.org/articles/PMC10255029?pdf=render
+37347268,https://doi.org/10.1177/01410768231181268,"Trends in SARS-CoV-2 infection and vaccination in school staff, students and their household members from 2020 to 2022 in Wales, UK: an electronic cohort study.","Lowthian E, Abbasizanjani H, Bedston S, Akbari A, Cowley L, Fry R, Owen RK, Hollinghurst J, Rudan I, Beggs J, Marchant E, Torabi F, Lusignan S, Crick T, Moore G, Sheikh A, Lyons RA.",,Journal of the Royal Society of Medicine,2023,2023-06-22,Y,Pandemic; Schools; Population Health; Covid-19; Social Restrictions,,,"<h4>Objectives</h4>We investigated SARS-CoV-2 infection trends, risk of SARS-CoV-2 infection and COVID-19 vaccination uptake among school staff, students and their household members in Wales, UK.<h4>Design</h4>Seven-day average of SARS-CoV-2 infections and polymerase chain reaction tests per 1000 people daily, cumulative incidence of COVID-19 vaccination uptake and multi-level Poisson models with time-varying covariates.<h4>Setting</h4>National electronic cohort between September 2020 and May 2022 when several variants were predominant in the UK (Alpha, Delta and Omicron).<h4>Participants</h4>School students aged 4 to 10/11 years (primary school and younger middle school, <i>n</i> = 238,163), and 11 to 15/16 years (secondary school and older middle school, <i>n</i> = 182,775), school staff in Wales (<i>n</i> = 47,963) and the household members of students and staff (<i>n</i> = 697,659).<h4>Main outcome measures</h4>SARS-CoV-2 infection and COVID-19 vaccination uptake.<h4>Results</h4>School students had a sustained period of high infection rates compared with household members after August 2021. Primary schedule vaccination uptake was highest among staff (96.3%) but lower for household members (72.2%), secondary and older middle school students (59.8%), and primary and younger middle school students (3.3%). Multi-level Poisson models showed that vaccination was associated with a lower risk of SARS-CoV-2 infection. The Delta variant posed a greater infection risk for students than the Alpha variant. However, Omicron was a larger risk for staff and household members.<h4>Conclusions</h4>Public health bodies should be informed of the protection COVID-19 vaccines afford, with more research being required for younger populations. Furthermore, schools require additional support in managing new, highly transmissible variants. Further research should examine the mechanisms between child deprivation and SARS-CoV-2 infection.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/01410768231181268; doi:https://doi.org/10.1177/01410768231181268; html:https://europepmc.org/articles/PMC10767617; pdf:https://europepmc.org/articles/PMC10767617?pdf=render
 37544968,https://doi.org/10.1007/s11357-023-00890-7,"Does physical activity moderate the association between shorter leukocyte telomere length and incident coronary heart disease? Data from 54,180 UK Biobank participants.","Xiang M, Pilling LC, Melzer D, Kirk B, Duque G, Liu R, Kuchel GA, Wood AR, Metcalf B, Diniz BS, Hillsdon M, Kuo CL.",,GeroScience,2024,2023-08-07,Y,Interaction; epidemiology; Population-based Study; Prospective Cohort Study; Accelerometer; Moderation; Accelerometry; Time To Event Survival Data,,,"Telomere shortening is a biological aging hallmark. The effect of short telomere length may be targeted by increased physical activity to reduce the risk of multiple aging-related diseases, including coronary heart disease (CHD). The objective was to assess the moderation effect of accelerometer-based physical activity (aPA) on the association between shorter leukocyte telomere length (LTL) relatively in the population sample and incident CHD. Data were from the UK Biobank participants with well-calibrated accelerometer data for at least 6.5 days (n = 54,180). Relative mean LTL at baseline (5-6 years prior to aPA assessment) was measured in T/S ratio, using a multiplex quantitative polymerase chain reaction (qPCR) technology, by comparing the amount of the telomere amplification product (T) to that of a single-copy gene (S). aPA measures included total number of events (at least 10-s continued physical activity > 32 milligravities [mg]), total volume, mean duration, mean intensity, and peak intensity of all events. LTL, aPA measures, and their interactions were associated with incident CHD (mean follow-up 6.8 years) using Cox proportional hazards models adjusting for covariates. Longer LTL (relative to the sample distribution) was associated with reduced incidence of CHD (adjusted hazard ratio [aHR] = 0.94 per standard deviation [SD] increase in LTL, [95% CI, 0.90 to 0.99], P = .010). Incidence of CHD was reduced by higher total volume of aPA (aHR = 0.82 per SD increase in LTL, [95% CI, 0.71 to 0.95], P = .010) but increased by higher total number of events (aHR = 1.11 per SD increase in LTL, [95% CI, 1.02 to 1.21], P = .020) after controlling for other aPA measures and covariates. However, none of the interactions between LTL and aPA measures was statistically significant (P = .171).",,pdf:https://link.springer.com/content/pdf/10.1007/s11357-023-00890-7.pdf; doi:https://doi.org/10.1007/s11357-023-00890-7; html:https://europepmc.org/articles/PMC10828302; pdf:https://europepmc.org/articles/PMC10828302?pdf=render
+39174061,https://doi.org/10.1136/bmjopen-2023-078108,Risk factors for prolonged length of hospital stay following elective hip replacement surgery: a retrospective longitudinal observational study.,"Wilson R, Margelyte R, Redaniel MT, Eyles E, Jones T, Penfold C, Blom A, Elliott A, Harper A, Keen T, Pitt M, Judge A.",,BMJ open,2024,2024-08-21,Y,Hip; Primary Health Care; Hospitalization; Adult Orthopaedics,,,"<h4>Objectives</h4>Our aim was to identify which patients are likely to stay in hospital longer following total hip replacement surgery.<h4>Design</h4>Longitudinal, observational study used routinely collected data.<h4>Setting</h4>Data were collected from an NHS Trust in South-West England between 2016 and 2019.<h4>Participants</h4>2352 hip replacement patients had complete data and were included in analysis.<h4>Primary and secondary outcome measures</h4>Three measures of length of stay were used: a count measure of number of days spent in hospital, a binary measure of ≤7 days/>7 days in hospital and a binary measure of remaining in hospital when medically fit for discharge.<h4>Results</h4>The mean length of stay was 5.4 days following surgery, with 18% in hospital for more than 7 days, and 11% staying in hospital when medically fit for discharge. Longer hospital stay was associated with older age (OR=1.06, 95% CI 1.05 to 1.08), being female (OR=1.42, 95% CI 1.12 to 1.81) and more comorbidities (OR=3.52, 95% CI 1.45 to 8.55) and shorter length of stay with not having had a recent hospital admission (OR=0.44, 95% CI 0.32 to 0.60). Results were similar for remaining in hospital when medically fit for discharge, with the addition of an association with highest socioeconomic deprivation (OR=2.08, 95% CI 1.37 to 3.16).<h4>Conclusions</h4>Older, female patients with more comorbidities and from more socioeconomically deprived areas are likely to remain in hospital for longer following surgery. This study produced regression models demonstrating consistent results across three measures of prolonged hospital stay following hip replacement surgery. These findings could be used to inform surgery planning and when supporting patient discharge following surgery.",,doi:https://doi.org/10.1136/bmjopen-2023-078108; html:https://europepmc.org/articles/PMC11340698; pdf:https://europepmc.org/articles/PMC11340698?pdf=render
 36526323,https://doi.org/10.1136/bmjopen-2022-068252,"Identification of risk factors associated with prolonged hospital stay following primary knee replacement surgery: a retrospective, longitudinal observational study.","Wilson R, Margelyte R, Redaniel MT, Eyles E, Jones T, Penfold C, Blom A, Elliott A, Harper A, Keen T, Pitt M, Judge A.",,BMJ open,2022,2022-12-16,Y,Knee; Rheumatology; Statistics & Research Methods; Orthopaedic & Trauma Surgery; Adult Orthopaedics,,,"<h4>Objectives</h4>To identify risk factors associated with prolonged length of hospital stay and staying in hospital longer than medically necessary following primary knee replacement surgery.<h4>Design</h4>Retrospective, longitudinal observational study.<h4>Setting</h4>Elective knee replacement surgeries between 2016 and 2019 were identified using routinely collected data from an NHS Trust in England.<h4>Participants</h4>There were 2295 knee replacement patients with complete data included in analysis. The mean age was 68 (SD 11) and 60% were female.<h4>Outcome measures</h4>We assessed a binary length of stay outcome (>7 days), a continuous length of stay outcome (≤30 days) and a binary measure of whether patients remained in hospital when they were medically fit for discharge.<h4>Results</h4>The mean length of stay was 5.0 days (SD 3.9), 15.4% of patients were in hospital for >7 days and 7.1% remained in hospital when they were medically fit for discharge. Longer length of stay was associated with older age (<i>b=</i>0.08, 95% CI 0.07 to 0.09), female sex (<i>b</i>=0.36, 95% CI 0.06 to 0.67), high deprivation (<i>b</i>=0.98, 95% CI 0.47 to 1.48) and more comorbidities (<i>b</i>=2.48, 95% CI 0.15 to 4.81). Remaining in hospital beyond being medically fit for discharge was associated with older age (OR=1.07, 95% CI 1.05 to 1.09), female sex (OR=1.71, 95% CI 1.19 to 2.47) and high deprivation (OR=2.27, 95% CI 1.27 to 4.06).<h4>Conclusions</h4>The regression models could be used to identify which patients are likely to occupy hospital beds for longer. This could be helpful in scheduling operations to aid hospital efficiency by planning these patients' operations for when the hospital is less busy.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/12/e068252.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-068252; html:https://europepmc.org/articles/PMC9764602; pdf:https://europepmc.org/articles/PMC9764602?pdf=render
-37347268,https://doi.org/10.1177/01410768231181268,"Trends in SARS-CoV-2 infection and vaccination in school staff, students and their household members from 2020 to 2022 in Wales, UK: an electronic cohort study.","Lowthian E, Abbasizanjani H, Bedston S, Akbari A, Cowley L, Fry R, Owen RK, Hollinghurst J, Rudan I, Beggs J, Marchant E, Torabi F, Lusignan S, Crick T, Moore G, Sheikh A, Lyons RA.",,Journal of the Royal Society of Medicine,2023,2023-06-22,Y,Pandemic; Schools; Population Health; Covid-19; Social Restrictions,,,"<h4>Objectives</h4>We investigated SARS-CoV-2 infection trends, risk of SARS-CoV-2 infection and COVID-19 vaccination uptake among school staff, students and their household members in Wales, UK.<h4>Design</h4>Seven-day average of SARS-CoV-2 infections and polymerase chain reaction tests per 1000 people daily, cumulative incidence of COVID-19 vaccination uptake and multi-level Poisson models with time-varying covariates.<h4>Setting</h4>National electronic cohort between September 2020 and May 2022 when several variants were predominant in the UK (Alpha, Delta and Omicron).<h4>Participants</h4>School students aged 4 to 10/11 years (primary school and younger middle school, <i>n</i> = 238,163), and 11 to 15/16 years (secondary school and older middle school, <i>n</i> = 182,775), school staff in Wales (<i>n</i> = 47,963) and the household members of students and staff (<i>n</i> = 697,659).<h4>Main outcome measures</h4>SARS-CoV-2 infection and COVID-19 vaccination uptake.<h4>Results</h4>School students had a sustained period of high infection rates compared with household members after August 2021. Primary schedule vaccination uptake was highest among staff (96.3%) but lower for household members (72.2%), secondary and older middle school students (59.8%), and primary and younger middle school students (3.3%). Multi-level Poisson models showed that vaccination was associated with a lower risk of SARS-CoV-2 infection. The Delta variant posed a greater infection risk for students than the Alpha variant. However, Omicron was a larger risk for staff and household members.<h4>Conclusions</h4>Public health bodies should be informed of the protection COVID-19 vaccines afford, with more research being required for younger populations. Furthermore, schools require additional support in managing new, highly transmissible variants. Further research should examine the mechanisms between child deprivation and SARS-CoV-2 infection.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/01410768231181268; doi:https://doi.org/10.1177/01410768231181268; html:https://europepmc.org/articles/PMC10767617; pdf:https://europepmc.org/articles/PMC10767617?pdf=render
 34799365,https://doi.org/10.1136/bmjopen-2021-054861,Retrospective cohort study to evaluate medication use in patients hospitalised with COVID-19 in Scotland: protocol for a national observational study.,"Mueller T, Kerr S, McTaggart S, Kurdi A, Vasileiou E, Docherty A, Fraser K, Shi T, Simpson CR, Bennie M, Sheikh A.",,BMJ open,2021,2021-11-19,Y,Therapeutics; clinical pharmacology; Covid-19,,,"<h4>Introduction</h4>COVID-19 has caused millions of hospitalisations and deaths globally. A range of vaccines have been developed and are being deployed at scale in the UK to prevent SARS-CoV-2 infection, which have reduced risk of infection and severe COVID-19 outcomes. Those with COVID-19 are now being treated with several repurposed drugs based on evidence emerging from recent clinical trials. However, there is currently limited real-world data available related to the use of these drugs in routine clinical practice. The purpose of this study is to address the prevailing knowledge gaps regarding the use of dexamethasone, remdesivir and tocilizumab by conducting an exploratory drug utilisation study, aimed at providing in-depth descriptions of patients receiving these drugs as well as the treatment patterns observed in Scotland.<h4>Methods and analysis</h4>Retrospective cohort study, comprising adult patients admitted to hospital with confirmed or suspected COVID-19 across five Scottish Health Boards using data from in-hospital ePrescribing linked to the Early Estimation of Vaccine and Anti-Viral Effectiveness (EAVE II) COVID-19 surveillance platform. The primary outcome will be exposure to the medicines of interest (dexamethasone, remdesivir, tocilizumab), either alone or in combination; exposure will be described in terms of drug(s) of choice; prescribed and administered dose; treatment duration; and any changes in treatment, for example, dose escalation and/or switching to an alternative drug. Analyses will primarily be descriptive in nature.<h4>Ethics and dissemination</h4>Ethical and information governance approvals have been obtained by the National Research Ethics Service Committee, South East Scotland 02 and the Public Benefit and Privacy Panel for Health and Social Care, respectively. Findings from this study will be presented at academic and clinical conferences, and to the funders and other interested parties as appropriate; study findings will also be published in peer-reviewed journals. Publications will be available on the EAVE II website (https://www.ed.ac.uk/usher/eave-ii/key-outputs/our-publications), alongside lay summaries and infographics aimed at the general public. Press releases will also be considered, if appropriate.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/11/e054861.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-054861; html:https://europepmc.org/articles/PMC8609490; pdf:https://europepmc.org/articles/PMC8609490?pdf=render
 34376975,https://doi.org/10.1177/11779322211035921,Cloud Computing Enabled Big Multi-Omics Data Analytics.,"Koppad S, B A, Gkoutos GV, Acharjee A.",,Bioinformatics and biology insights,2021,2021-07-28,Y,Data integration; Cloud Computing; Big Data; Multi-omics Data; Data Analytics,,,"High-throughput experiments enable researchers to explore complex multifactorial diseases through large-scale analysis of omics data. Challenges for such high-dimensional data sets include storage, analyses, and sharing. Recent innovations in computational technologies and approaches, especially in cloud computing, offer a promising, low-cost, and highly flexible solution in the bioinformatics domain. Cloud computing is rapidly proving increasingly useful in molecular modeling, omics data analytics (eg, RNA sequencing, metabolomics, or proteomics data sets), and for the integration, analysis, and interpretation of phenotypic data. We review the adoption of advanced cloud-based and big data technologies for processing and analyzing omics data and provide insights into state-of-the-art cloud bioinformatics applications.",,doi:https://doi.org/10.1177/11779322211035921; doi:https://doi.org/10.1177/11779322211035921; html:https://europepmc.org/articles/PMC8323418; pdf:https://europepmc.org/articles/PMC8323418?pdf=render
-36600681,https://doi.org/10.1177/17562848221145612,Artificial intelligence-based personalized nutrition and prediction of irritable bowel syndrome patients.,"Acharjee A, Choudhury SP.",,Therapeutic advances in gastroenterology,2022,2022-12-26,Y,,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9806427; doi:https://doi.org/10.1177/17562848221145612; html:https://europepmc.org/articles/PMC9806427; pdf:https://europepmc.org/articles/PMC9806427?pdf=render
 34911741,https://doi.org/10.1136/heartjnl-2021-320047,Impact of cardiometabolic multimorbidity and ethnicity on cardiovascular/renal complications in patients with COVID-19.,"Norris T, Razieh C, Zaccardi F, Yates T, Islam N, Gillies CL, Chudasama YV, Rowlands AV, Davies MJ, McCann GP, Banerjee A, Lam CSP, Docherty AB, Openshaw PJ, Baillie JK, Semple MG, Lawson CA, Khunti K, ISARIC4C investigators.",,Heart (British Cardiac Society),2022,2022-07-13,Y,epidemiology; risk factors; Covid-19,,,"<h4>Objective</h4>Using a large national database of people hospitalised with COVID-19, we investigated the contribution of cardio-metabolic conditions, multi-morbidity and ethnicity on the risk of in-hospital cardiovascular complications and death.<h4>Methods</h4>A multicentre, prospective cohort study in 302 UK healthcare facilities of adults hospitalised with COVID-19 between 6 February 2020 and 16 March 2021. Logistic models were used to explore associations between baseline patient ethnicity, cardiometabolic conditions and multimorbidity (0, 1, 2, >2 conditions), and in-hospital cardiovascular complications (heart failure, arrhythmia, cardiac ischaemia, cardiac arrest, coagulation complications, stroke), renal injury and death.<h4>Results</h4>Of 65 624 patients hospitalised with COVID-19, 44 598 (68.0%) reported at least one cardiometabolic condition on admission. Cardiovascular/renal complications or death occurred in 24 609 (38.0%) patients. Baseline cardiometabolic conditions were independently associated with increased odds of in-hospital complications and this risk increased in the presence of cardiometabolic multimorbidity. For example, compared with having no cardiometabolic conditions, 1, 2 or ≥3 conditions was associated with 1.46 (95% CI 1.39 to 1.54), 2.04 (95% CI 1.93 to 2.15) and 3.10 (95% CI 2.92 to 3.29) times higher odds of any cardiovascular/renal complication, respectively. A similar pattern was observed for all-cause death. Compared with the white group, the South Asian (OR 1.19, 95% CI 1.10 to 1.29) and black (OR 1.53 to 95% CI 1.37 to 1.72) ethnic groups had higher risk of any cardiovascular/renal complication.<h4>Conclusions</h4>In hospitalised patients with COVID-19, cardiovascular complications or death impacts just under half of all patients, with the highest risk in those of South Asian or Black ethnicity and in patients with cardiometabolic multimorbidity.",,pdf:https://heart.bmj.com/content/heartjnl/108/15/1200.full.pdf; doi:https://doi.org/10.1136/heartjnl-2021-320047; html:https://europepmc.org/articles/PMC8678560; pdf:https://europepmc.org/articles/PMC8678560?pdf=render
-37126810,https://doi.org/10.7326/m21-4269,Challenges in Estimating the Effectiveness of COVID-19 Vaccination Using Observational Data.,"Hulme WJ, Williamson E, Horne EMF, Green A, McDonald HI, Walker AJ, Curtis HJ, Morton CE, MacKenna B, Croker R, Mehrkar A, Bacon S, Evans D, Inglesby P, Davy S, Bhaskaran K, Schultze A, Rentsch CT, Tomlinson L, Douglas IJ, Evans SJW, Smeeth L, Palmer T, Goldacre B, Hernán MA, Sterne JAC.",,Annals of internal medicine,2023,2023-05-02,N,,,,"The COVID-19 vaccines were developed and rigorously evaluated in randomized trials during 2020. However, important questions, such as the magnitude and duration of protection, their effectiveness against new virus variants, and the effectiveness of booster vaccination, could not be answered by randomized trials and have therefore been addressed in observational studies. Analyses of observational data can be biased because of confounding and because of inadequate design that does not consider the evolution of the pandemic over time and the rapid uptake of vaccination. Emulating a hypothetical ""target trial"" using observational data assembled during vaccine rollouts can help manage such potential sources of bias. This article describes 2 approaches to target trial emulation. In the sequential approach, on each day, eligible persons who have not yet been vaccinated are matched to a vaccinated person. The single-trial approach sets a single baseline at the start of the rollout and considers vaccination as a time-varying variable. The nature of the confounding depends on the analysis strategy: Estimating ""per-protocol"" effects (accounting for vaccination of initially unvaccinated persons after baseline) may require adjustment for both baseline and ""time-varying"" confounders. These issues are illustrated by using observational data from 2 780 931 persons in the United Kingdom aged 70 years or older to estimate the effect of a first dose of a COVID-19 vaccine. Addressing the issues discussed in this article should help authors of observational studies provide robust evidence to guide clinical and policy decisions.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10152408; doi:https://doi.org/10.7326/M21-4269; html:https://europepmc.org/articles/PMC10152408; pdf:https://europepmc.org/articles/PMC10152408?pdf=render; doi:https://doi.org/10.7326/m21-4269
-34487522,https://doi.org/10.1093/cid/ciab754,Severity of Severe Acute Respiratory System Coronavirus 2 (SARS-CoV-2) Alpha Variant (B.1.1.7) in England.,"Grint DJ, Wing K, Houlihan C, Gibbs HP, Evans SJW, Williamson E, McDonald HI, Bhaskaran K, Evans D, Walker AJ, Hickman G, Nightingale E, Schultze A, Rentsch CT, Bates C, Cockburn J, Curtis HJ, Morton CE, Bacon S, Davy S, Wong AYS, Mehrkar A, Tomlinson L, Douglas IJ, Mathur R, MacKenna B, Ingelsby P, Croker R, Parry J, Hester F, Harper S, DeVito NJ, Hulme W, Tazare J, Smeeth L, Goldacre B, Eggo RM.",,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2022,2022-08-01,Y,Alpha; Hospital Admission; Case Fatality; Sars-cov-2,,,"<h4>Background</h4>The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) alpha variant (B.1.1.7) is associated with higher transmissibility than wild-type virus, becoming the dominant variant in England by January 2021. We aimed to describe the severity of the alpha variant in terms of the pathway of disease from testing positive to hospital admission and death.<h4>Methods</h4>With the approval of NHS England, we linked individual-level data from primary care with SARS-CoV-2 community testing, hospital admission, and Office for National Statistics all-cause death data. We used testing data with S-gene target failure as a proxy for distinguishing alpha and wild-type cases, and stratified Cox proportional hazards regression to compare the relative severity of alpha cases with wild-type diagnosed from 16 November 2020 to 11 January 2021.<h4>Results</h4>Using data from 185 234 people who tested positive for SARS-CoV-2 in the community (alpha = 93 153; wild-type = 92 081), in fully adjusted analysis accounting for individual-level demographics and comorbidities as well as regional variation in infection incidence, we found alpha associated with 73% higher hazards of all-cause death (adjusted hazard ratio [aHR]: 1.73; 95% confidence interval [CI]: 1.41-2.13; P < .0001) and 62% higher hazards of hospital admission (1.62; 1.48-1.78; P < .0001) compared with wild-type virus. Among patients already admitted to the intensive care unit, the association between alpha and increased all-cause mortality was smaller and the CI included the null (aHR: 1.20; 95% CI: .74-1.95; P = .45).<h4>Conclusions</h4>The SARS-CoV-2 alpha variant is associated with an increased risk of both hospitalization and mortality than wild-type virus.",,pdf:https://academic.oup.com/cid/article-pdf/75/1/e1120/45513976/ciab754.pdf; doi:https://doi.org/10.1093/cid/ciab754; html:https://europepmc.org/articles/PMC8522415; pdf:https://europepmc.org/articles/PMC8522415?pdf=render
+36600681,https://doi.org/10.1177/17562848221145612,Artificial intelligence-based personalized nutrition and prediction of irritable bowel syndrome patients.,"Acharjee A, Choudhury SP.",,Therapeutic advances in gastroenterology,2022,2022-12-26,Y,,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9806427; doi:https://doi.org/10.1177/17562848221145612; html:https://europepmc.org/articles/PMC9806427; pdf:https://europepmc.org/articles/PMC9806427?pdf=render
 36860174,https://doi.org/10.1093/ije/dyad022,Proxy gene-by-environment Mendelian randomization study of the association between cigarette smoking during pregnancy and offspring mental health.,"Sallis HM, Wootton RE, Davey Smith G, Munafò MR.",,International journal of epidemiology,2023,2023-10-01,Y,Schizophrenia; Depression; Smoking; Mendelian Randomization,,,"<h4>Background</h4>Smoking prevalence is higher among individuals with schizophrenia or depression, and previous work has suggested this relationship is causal. However, this may be due to dynastic effects, for example reflecting maternal smoking during pregnancy rather than a direct effect of smoking. We used a proxy gene-by-environment Mendelian randomization approach to investigate whether there is a causal effect of maternal heaviness of smoking during pregnancy on offspring mental health.<h4>Methods</h4>Analyses were performed in the UK Biobank cohort. Individuals with data on smoking status, maternal smoking during pregnancy, a diagnosis of schizophrenia or depression, and genetic data were included. We used participants' genotype (rs16969968 in the CHRNA5 gene) as a proxy for their mothers' genotype. Analyses were stratified on participants' own smoking status in order to estimate the effect of maternal smoking heaviness during pregnancy independently of offspring smoking.<h4>Results</h4>The effect of maternal smoking on offspring schizophrenia was in opposing directions when stratifying on offspring smoking status. Among offspring of never smokers, each additional risk allele for maternal smoking heaviness appeared to have a protective effect [odds ratio (OR) = 0.77, 95% confidence interval (CI) 0.62 to 0.95, P = 0.015], whereas among ever smokers the effect of maternal smoking was in the reverse direction (OR = 1.23, 95% CI 1.05 to 1.45, P = 0.011, Pinteraction <0.001). There was no clear evidence of an association between maternal smoking heaviness and offspring depression.<h4>Conclusions</h4>These findings do not provide clear evidence of an effect of maternal smoking during pregnancy on offspring schizophrenia or depression, which implies that any causal effect of smoking on schizophrenia or depression is direct.",,pdf:https://academic.oup.com/ije/advance-article-pdf/doi/10.1093/ije/dyad022/49393500/dyad022.pdf; doi:https://doi.org/10.1093/ije/dyad022; html:https://europepmc.org/articles/PMC10555861; pdf:https://europepmc.org/articles/PMC10555861?pdf=render
-33980500,https://doi.org/10.1136/bmjhci-2020-100303,Development of a data utility framework to support effective health data curation.,"Gordon B, Barrett J, Fennessy C, Cake C, Milward A, Irwin C, Jones M, Sebire N.",,BMJ health & care informatics,2021,2021-05-01,Y,Information management; Information Systems; Health Care Sector; Information Science; Bmj Health Informatics,,,"<h4>Objectives</h4>The value of healthcare data is being increasingly recognised, including the need to improve health dataset utility. There is no established mechanism for evaluating healthcare dataset utility making it difficult to evaluate the effectiveness of activities improving the data. To describe the method for generating and involving the user community in developing a proposed framework for evaluation and communication of healthcare dataset utility for given research areas.<h4>Methods</h4>Aninitial version of a matrix to review datasets across a range of dimensions wasdeveloped based on previous published findings regarding healthcare data. Thiswas used to initiate a design process through interviews and surveys with datausers representing a broad range of user types and use cases, to help develop afocused framework for characterising datasets.<h4>Results</h4>Following 21 interviews, 31 survey responses and testing on 43 datasets, five major categories and 13 subcategories were identified as useful for a dataset, including Data Model, Completeness and Linkage. Each sub-category was graded to facilitate rapid and reproducible evaluation of dataset utility for specific use-cases. Testing of applicability to >40 existing datasets demonstrated potential usefulness for subsequent evaluation in real-world practice.<h4>Discussion</h4>Theresearch has developed an evidenced-based initial approach for a framework tounderstand the utility of a healthcare dataset. It likely to require further refinementfollowing wider application and additional categories may be required.<h4>Conclusion</h4>The process has resulted in a user-centred designed framework for objectively evaluating the likely utility of specific healthcare datasets, and therefore, should be of value both for potential users of health data, and for data custodians to identify the areas to provide the optimal value for data curation investment.",,pdf:https://informatics.bmj.com/content/bmjhci/28/1/e100303.full.pdf; doi:https://doi.org/10.1136/bmjhci-2020-100303; html:https://europepmc.org/articles/PMC8117992; pdf:https://europepmc.org/articles/PMC8117992?pdf=render
+34487522,https://doi.org/10.1093/cid/ciab754,Severity of Severe Acute Respiratory System Coronavirus 2 (SARS-CoV-2) Alpha Variant (B.1.1.7) in England.,"Grint DJ, Wing K, Houlihan C, Gibbs HP, Evans SJW, Williamson E, McDonald HI, Bhaskaran K, Evans D, Walker AJ, Hickman G, Nightingale E, Schultze A, Rentsch CT, Bates C, Cockburn J, Curtis HJ, Morton CE, Bacon S, Davy S, Wong AYS, Mehrkar A, Tomlinson L, Douglas IJ, Mathur R, MacKenna B, Ingelsby P, Croker R, Parry J, Hester F, Harper S, DeVito NJ, Hulme W, Tazare J, Smeeth L, Goldacre B, Eggo RM.",,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2022,2022-08-01,Y,Alpha; Hospital Admission; Case Fatality; Sars-cov-2,,,"<h4>Background</h4>The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) alpha variant (B.1.1.7) is associated with higher transmissibility than wild-type virus, becoming the dominant variant in England by January 2021. We aimed to describe the severity of the alpha variant in terms of the pathway of disease from testing positive to hospital admission and death.<h4>Methods</h4>With the approval of NHS England, we linked individual-level data from primary care with SARS-CoV-2 community testing, hospital admission, and Office for National Statistics all-cause death data. We used testing data with S-gene target failure as a proxy for distinguishing alpha and wild-type cases, and stratified Cox proportional hazards regression to compare the relative severity of alpha cases with wild-type diagnosed from 16 November 2020 to 11 January 2021.<h4>Results</h4>Using data from 185 234 people who tested positive for SARS-CoV-2 in the community (alpha = 93 153; wild-type = 92 081), in fully adjusted analysis accounting for individual-level demographics and comorbidities as well as regional variation in infection incidence, we found alpha associated with 73% higher hazards of all-cause death (adjusted hazard ratio [aHR]: 1.73; 95% confidence interval [CI]: 1.41-2.13; P < .0001) and 62% higher hazards of hospital admission (1.62; 1.48-1.78; P < .0001) compared with wild-type virus. Among patients already admitted to the intensive care unit, the association between alpha and increased all-cause mortality was smaller and the CI included the null (aHR: 1.20; 95% CI: .74-1.95; P = .45).<h4>Conclusions</h4>The SARS-CoV-2 alpha variant is associated with an increased risk of both hospitalization and mortality than wild-type virus.",,pdf:https://academic.oup.com/cid/article-pdf/75/1/e1120/45513976/ciab754.pdf; doi:https://doi.org/10.1093/cid/ciab754; html:https://europepmc.org/articles/PMC8522415; pdf:https://europepmc.org/articles/PMC8522415?pdf=render
+37126810,https://doi.org/10.7326/m21-4269,Challenges in Estimating the Effectiveness of COVID-19 Vaccination Using Observational Data.,"Hulme WJ, Williamson E, Horne EMF, Green A, McDonald HI, Walker AJ, Curtis HJ, Morton CE, MacKenna B, Croker R, Mehrkar A, Bacon S, Evans D, Inglesby P, Davy S, Bhaskaran K, Schultze A, Rentsch CT, Tomlinson L, Douglas IJ, Evans SJW, Smeeth L, Palmer T, Goldacre B, Hernán MA, Sterne JAC.",,Annals of internal medicine,2023,2023-05-02,N,,,,"The COVID-19 vaccines were developed and rigorously evaluated in randomized trials during 2020. However, important questions, such as the magnitude and duration of protection, their effectiveness against new virus variants, and the effectiveness of booster vaccination, could not be answered by randomized trials and have therefore been addressed in observational studies. Analyses of observational data can be biased because of confounding and because of inadequate design that does not consider the evolution of the pandemic over time and the rapid uptake of vaccination. Emulating a hypothetical ""target trial"" using observational data assembled during vaccine rollouts can help manage such potential sources of bias. This article describes 2 approaches to target trial emulation. In the sequential approach, on each day, eligible persons who have not yet been vaccinated are matched to a vaccinated person. The single-trial approach sets a single baseline at the start of the rollout and considers vaccination as a time-varying variable. The nature of the confounding depends on the analysis strategy: Estimating ""per-protocol"" effects (accounting for vaccination of initially unvaccinated persons after baseline) may require adjustment for both baseline and ""time-varying"" confounders. These issues are illustrated by using observational data from 2 780 931 persons in the United Kingdom aged 70 years or older to estimate the effect of a first dose of a COVID-19 vaccine. Addressing the issues discussed in this article should help authors of observational studies provide robust evidence to guide clinical and policy decisions.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10152408; doi:https://doi.org/10.7326/M21-4269; html:https://europepmc.org/articles/PMC10152408; pdf:https://europepmc.org/articles/PMC10152408?pdf=render; doi:https://doi.org/10.7326/m21-4269
 37368589,https://doi.org/10.3390/toxics11060489,Association between Residential Exposure to Air Pollution and Incident Coronary Heart Disease Is Not Mediated by Leukocyte Telomere Length: A UK Biobank Study.,"Kuo CL, Liu R, Godoy LDC, Pilling LC, Fortinsky RH, Brugge D.",,Toxics,2023,2023-05-28,Y,Pm10; Pm2.5; No2; Nox; Pm2.5 Absorbance; Pm2.5–10,,,"Higher air pollution exposure and shorter leukocyte telomere length (LTL) are both associated with increased risk of coronary heart disease (CHD), and share plausible mechanisms, including inflammation. LTL may serve as a biomarker of air pollution exposure and may be intervened with to reduce the risk of CHD. To the best of our knowledge, we are the first to test the mediation effect of LTL in the relationship between air pollution exposure and incident CHD. Using the UK Biobank (UKB) data (<i>n</i> = 317,601), we conducted a prospective study linking residential air pollution exposure (PM<sub>2.5</sub>, PM<sub>10</sub>, NO<sub>2</sub>, NO<sub>x</sub>) and LTL to incident CHD during a mean follow-up of 12.6 years. Cox proportional hazards models and generalized additive models with penalized spline functions were used to model the associations of pollutant concentrations and LTL with incident CHD. We found non-linear associations of air pollution exposure with LTL and CHD. Pollutant concentrations in the lower range were decreasingly associated with longer LTL and reduced risk of CHD. The associations between lower pollutant concentrations and reduced risk of CHD, however, were minimally mediated by LTL (<3%). Our findings suggest that air pollution influences CHD through pathways that do not involve LTL. Replication is needed with improved measurements of air pollution that more accurately assesses personal exposure.",,doi:https://doi.org/10.3390/toxics11060489; html:https://europepmc.org/articles/PMC10301073; pdf:https://europepmc.org/articles/PMC10301073?pdf=render
+33980500,https://doi.org/10.1136/bmjhci-2020-100303,Development of a data utility framework to support effective health data curation.,"Gordon B, Barrett J, Fennessy C, Cake C, Milward A, Irwin C, Jones M, Sebire N.",,BMJ health & care informatics,2021,2021-05-01,Y,Information management; Information Systems; Health Care Sector; Information Science; Bmj Health Informatics,,,"<h4>Objectives</h4>The value of healthcare data is being increasingly recognised, including the need to improve health dataset utility. There is no established mechanism for evaluating healthcare dataset utility making it difficult to evaluate the effectiveness of activities improving the data. To describe the method for generating and involving the user community in developing a proposed framework for evaluation and communication of healthcare dataset utility for given research areas.<h4>Methods</h4>Aninitial version of a matrix to review datasets across a range of dimensions wasdeveloped based on previous published findings regarding healthcare data. Thiswas used to initiate a design process through interviews and surveys with datausers representing a broad range of user types and use cases, to help develop afocused framework for characterising datasets.<h4>Results</h4>Following 21 interviews, 31 survey responses and testing on 43 datasets, five major categories and 13 subcategories were identified as useful for a dataset, including Data Model, Completeness and Linkage. Each sub-category was graded to facilitate rapid and reproducible evaluation of dataset utility for specific use-cases. Testing of applicability to >40 existing datasets demonstrated potential usefulness for subsequent evaluation in real-world practice.<h4>Discussion</h4>Theresearch has developed an evidenced-based initial approach for a framework tounderstand the utility of a healthcare dataset. It likely to require further refinementfollowing wider application and additional categories may be required.<h4>Conclusion</h4>The process has resulted in a user-centred designed framework for objectively evaluating the likely utility of specific healthcare datasets, and therefore, should be of value both for potential users of health data, and for data custodians to identify the areas to provide the optimal value for data curation investment.",,pdf:https://informatics.bmj.com/content/bmjhci/28/1/e100303.full.pdf; doi:https://doi.org/10.1136/bmjhci-2020-100303; html:https://europepmc.org/articles/PMC8117992; pdf:https://europepmc.org/articles/PMC8117992?pdf=render
 35381005,https://doi.org/10.1371/journal.pone.0264828,Reproducible disease phenotyping at scale: Example of coronary artery disease in UK Biobank.,"Patel RS, Denaxas S, Howe LJ, Eggo RM, Shah AD, Allen NE, Danesh J, Hingorani A, Sudlow C, Hemingway H.",,PloS one,2022,2022-04-05,Y,,,,"<h4>Importance</h4>A lack of internationally agreed standards for combining available data sources at scale risks inconsistent disease phenotyping limiting research reproducibility.<h4>Objective</h4>To develop and then evaluate if a rules-based algorithm can identify coronary artery disease (CAD) sub-phenotypes using electronic health records (EHR) and questionnaire data from UK Biobank (UKB).<h4>Design</h4>Case-control and cohort study.<h4>Setting</h4>Prospective cohort study of 502K individuals aged 40-69 years recruited between 2006-2010 into the UK Biobank with linked hospitalization and mortality data and genotyping.<h4>Participants</h4>We included all individuals for phenotyping into 6 predefined CAD phenotypes using hospital admission and procedure codes, mortality records and baseline survey data. Of these, 408,470 unrelated individuals of European descent had a polygenic risk score (PRS) for CAD estimated.<h4>Exposure</h4>CAD Phenotypes.<h4>Main outcomes and measures</h4>Association with baseline risk factors, mortality (n = 14,419 over 7.8 years median f/u), and a PRS for CAD.<h4>Results</h4>The algorithm classified individuals with CAD into prevalent MI (n = 4,900); incident MI (n = 4,621), prevalent CAD without MI (n = 10,910), incident CAD without MI (n = 8,668), prevalent self-reported MI (n = 2,754); prevalent self-reported CAD without MI (n = 5,623), yielding 37,476 individuals with any type of CAD. Risk factors were similar across the six CAD phenotypes, except for fewer men in the self-reported CAD without MI group (46.7% v 70.1% for the overall group). In age- and sex- adjusted survival analyses, mortality was highest following incident MI (HR 6.66, 95% CI 6.07-7.31) and lowest for prevalent self-reported CAD without MI at baseline (HR 1.31, 95% CI 1.15-1.50) compared to disease-free controls. There were similar graded associations across the six phenotypes per SD increase in PRS, with the strongest association for prevalent MI (OR 1.50, 95% CI 1.46-1.55) and the weakest for prevalent self-reported CAD without MI (OR 1.08, 95% CI 1.05-1.12). The algorithm is available in the open phenotype HDR UK phenotype library (https://portal.caliberresearch.org/).<h4>Conclusions</h4>An algorithmic, EHR-based approach distinguished six phenotypes of CAD with distinct survival and PRS associations, supporting adoption of open approaches to help standardize CAD phenotyping and its wider potential value for reproducible research in other conditions.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0264828&type=printable; doi:https://doi.org/10.1371/journal.pone.0264828; html:https://europepmc.org/articles/PMC8982857; pdf:https://europepmc.org/articles/PMC8982857?pdf=render
 38956603,https://doi.org/10.1186/s12916-024-03480-2,Risk of emergency hospital admission related to adverse events after antibiotic treatment in adults with a common infection: impact of COVID-19 and derivation and validation of risk prediction models.,"Zhong X, Palin V, Ashcroft DM, Goldacre B, MacKenna B, Mehrkar A, Bacon SCJ, Massey J, Inglesby P, OpenSAFELY collaborative, Hand K, Pate A, van Staa TP.",,BMC medicine,2024,2024-07-02,Y,Antibiotics; Adverse Event; Common Infection; Covid-19 Pandemic,,,"<h4>Background</h4>With the global challenge of antimicrobial resistance intensified during the COVID-19 pandemic, evaluating adverse events (AEs) post-antibiotic treatment for common infections is crucial. This study aims to examines the changes in incidence rates of AEs during the COVID-19 pandemic and predict AE risk following antibiotic prescriptions for common infections, considering their previous antibiotic exposure and other long-term clinical conditions.<h4>Methods</h4>With the approval of NHS England, we used OpenSAFELY platform and analysed electronic health records from patients aged 18-110, prescribed antibiotics for urinary tract infection (UTI), lower respiratory tract infections (LRTI), upper respiratory tract infections (URTI), sinusitis, otitis externa, and otitis media between January 2019 and June 2023. We evaluated the temporal trends in the incidence rate of AEs for each infection, analysing monthly changes over time. The survival probability of emergency AE hospitalisation was estimated in each COVID-19 period (period 1: 1 January 2019 to 25 March 2020, period 2: 26 March 2020 to 8 March 2021, period 3: 9 March 2021 to 30 June 2023) using the Kaplan-Meier approach. Prognostic models, using Cox proportional hazards regression, were developed and validated to predict AE risk within 30 days post-prescription using the records in Period 1.<h4>Results</h4>Out of 9.4 million patients who received antibiotics, 0.6% of UTI, 0.3% of URTI, and 0.5% of LRTI patients experienced AEs. UTI and LRTI patients demonstrated a higher risk of AEs, with a noted increase in AE incidence during the COVID-19 pandemic. Higher comorbidity and recent antibiotic use emerged as significant AE predictors. The developed models exhibited good calibration and discrimination, especially for UTIs and LRTIs, with a C-statistic above 0.70.<h4>Conclusions</h4>The study reveals a variable incidence of AEs post-antibiotic treatment for common infections, with UTI and LRTI patients facing higher risks. AE risks varied between infections and COVID-19 periods. These findings underscore the necessity for cautious antibiotic prescribing and call for further exploration into the intricate dynamics between antibiotic use, AEs, and the pandemic.",,doi:https://doi.org/10.1186/s12916-024-03480-2; html:https://europepmc.org/articles/PMC11220965; pdf:https://europepmc.org/articles/PMC11220965?pdf=render
 39302250,https://doi.org/10.1111/epi.18105,Excess health care use is significantly and persistently reduced following diagnosis of late-onset epilepsy.,"Berglund M, Gonzalez-Izquierdo A, Denaxas S, Lethebe BC, Sajobi TT, Engbers JDT, Wiebe S, Josephson CB.",,Epilepsia,2024,2024-09-20,N,Cohort study; Electronic Heath Records; Health Care Use; Late‐onset Epilepsy,,,"<h4>Objective</h4>The incidence of late-onset epilepsy (LOE) is rising, and these patients may use an excess of health care resources. This study aimed to measure pre-/post-diagnostic health care use (HCU) for patients with LOE compared to controls.<h4>Methods</h4>This was an observational open cohort study covering years 1998-2019 using UK population-based linked primary care (Clinical Practice Research Datalink [CPRD]) and hospital (HES) electronic health records. The participants included patients with incident LOE enrolled in CPRD and 1:10 age-, sex-, and general practice-matched controls. The exposure was incident LOE (diagnosed at age ≥65) using a 5-year washout. The main outcome was all HCU (primary care [PC], accident and emergency [A&E], admitted patient and outpatient care) using inverse proportional weighting to PC use and HCU by setting. An interrupted time-series analysis was used to examine pre-/post-diagnostic HCU between patients with LOE and controls over 4 years either side of diagnosis/matching date. An adjusted mixed-effects negative binomial regression was used for post-diagnosis HCU interactions.<h4>Results</h4>Of 2 569 874 people ≥65 years of age, 1048 (4%) developed incident LOE. Mean weighted total HCU increased by 32 visits per patient-year (95% confidence interval [95% CI]: 13-50, p = .003) until LOE diagnosis, and then dropped by a mean of 60 visits per patient-year (95% CI: -81 to -40). There was an acute rise and fall over the 1-2 years immediately pre-/post-diagnosis. Incident HCU remained higher for LOE compared to controls post-diagnosis (adjusted incidence rate ratio: 1.72; 95% CI: 1.65-1.70; p < .001), including A&E, outpatient, and admitted care.<h4>Significance</h4>Health care use demonstrates an acute on chronic rise over the 4 years before diagnosis of LOE. To what extent the partial reversal of the acute pre-diagnosis rise, and the mediators of the accelerated increase compared to controls are attributed to epilepsy, comorbid and bidirectional disease states, or a combination of both warrants further exploration.",,doi:https://doi.org/10.1111/epi.18105
@@ -251,67 +251,67 @@ PMC11234640,https://doi.org/,"Evidence of gene-nutrient interaction association
 34071236,https://doi.org/10.3390/ijms22115763,"Integration of the Microbiome, Metabolome and Transcriptomics Data Identified Novel Metabolic Pathway Regulation in Colorectal Cancer.","Bisht V, Nash K, Xu Y, Agarwal P, Bosch S, Gkoutos GV, Acharjee A.",,International journal of molecular sciences,2021,2021-05-28,Y,Microbiota; Biomarkers; Transcriptome; Metabolomics; Colorectal Neoplasms; Omics Integration,,,"Integrative multiomics data analysis provides a unique opportunity for the mechanistic understanding of colorectal cancer (CRC) in addition to the identification of potential novel therapeutic targets. In this study, we used public omics data sets to investigate potential associations between microbiome, metabolome, bulk transcriptomics and single cell RNA sequencing datasets. We identified multiple potential interactions, for example 5-aminovalerate interacting with <i>Adlercreutzia</i>; cholesteryl ester interacting with bacterial genera <i>Staphylococcus</i>, <i>Blautia</i> and <i>Roseburia</i>. Using public single cell and bulk RNA sequencing, we identified 17 overlapping genes involved in epithelial cell pathways, with particular significance of the oxidative phosphorylation pathway and the <i>ACAT1</i> gene that indirectly regulates the esterification of cholesterol. These findings demonstrate that the integration of multiomics data sets from diverse populations can help us in untangling the colorectal cancer pathogenesis as well as postulate the disease pathology mechanisms and therapeutic targets.",,pdf:https://www.mdpi.com/1422-0067/22/11/5763/pdf?version=1622194941; doi:https://doi.org/10.3390/ijms22115763; html:https://europepmc.org/articles/PMC8198673; pdf:https://europepmc.org/articles/PMC8198673?pdf=render
 34497074,https://doi.org/10.1136/bmjopen-2020-042483,Modelling the impact of lockdown-easing measures on cumulative COVID-19 cases and deaths in England.,"Ziauddeen H, Subramaniam N, Gurdasani D.",,BMJ open,2021,2021-09-08,Y,Infection control; epidemiology; Public Health; Health Policy,,,"<h4>Objectives</h4>To assess the potential impacts of successive lockdown-easing measures in England, at a point in the COVID-19 pandemic when community transmission levels were relatively high.<h4>Design</h4>We developed a Bayesian model to infer incident cases and reproduction number (<i>R</i>) in England, from incident death data. We then used this to forecast excess cases and deaths in multiple plausible scenarios in which <i>R</i> increases at one or more time points.<h4>Setting</h4>England.<h4>Participants</h4>Publicly available national incident death data for COVID-19 were examined.<h4>Primary outcome</h4>Excess cumulative cases and deaths forecast at 90 days, in simulated scenarios of plausible increases in <i>R</i> after successive easing of lockdown in England, compared with a baseline scenario where <i>R</i> remained constant.<h4>Results</h4>Our model inferred an <i>R</i> of 0.75 on 13 May when England first started easing lockdown. In the most conservative scenario modelled where <i>R</i> increased to 0.80 as lockdown was eased further on 1 June and then remained constant, the model predicted an excess 257 (95% CI 108 to 492) deaths and 26 447 (95% CI 11 105 to 50 549) cumulative cases over 90 days. In the scenario with maximal increases in <i>R</i> (but staying ≤1), the model predicts 3174 (95% CI 1334 to 6060) excess cumulative deaths and 421 310 (95% CI 177 012 to 804 811) cases. Observed data from the forecasting period aligned most closely to the scenario in which <i>R</i> increased to 0.85 on 1 June, and 0.9 on 4 July.<h4>Conclusions</h4>When levels of transmission are high, even small changes in <i>R</i> with easing of lockdown can have significant impacts on expected cases and deaths, even if <i>R</i> remains ≤1. This will have a major impact on population health, tracing systems and healthcare services in England. Following an elimination strategy rather than one of maintenance of <i>R</i> ≤1 would substantially mitigate the impact of the COVID-19 epidemic within England.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/9/e042483.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-042483; html:https://europepmc.org/articles/PMC8438582; pdf:https://europepmc.org/articles/PMC8438582?pdf=render
 36253471,https://doi.org/10.1038/s41467-022-33937-y,A population-based matched cohort study of early pregnancy outcomes following COVID-19 vaccination and SARS-CoV-2 infection.,"Calvert C, Carruthers J, Denny C, Donaghy J, Hillman S, Hopcroft LEM, Hopkins L, Goulding A, Lindsay L, McLaughlin T, Moore E, Pan J, Taylor B, Almaghrabi F, Auyeung B, Bhaskaran K, Gibbons CL, Katikireddi SV, McCowan C, Murray J, O'Leary M, Ritchie LD, Shah SA, Simpson CR, Robertson C, Sheikh A, Stock SJ, Wood R.",,Nature communications,2022,2022-10-17,Y,,,,"Data on the safety of COVID-19 vaccines in early pregnancy are limited. We conducted a national, population-based, matched cohort study assessing associations between COVID-19 vaccination and miscarriage prior to 20 weeks gestation and, separately, ectopic pregnancy. We identified women in Scotland vaccinated between 6 weeks preconception and 19 weeks 6 days gestation (for miscarriage; n = 18,780) or 2 weeks 6 days gestation (for ectopic; n = 10,570). Matched, unvaccinated women from the pre-pandemic and, separately, pandemic periods were used as controls. Here we show no association between vaccination and miscarriage (adjusted Odds Ratio [aOR], pre-pandemic controls = 1.02, 95% Confidence Interval [CI] = 0.96-1.09) or ectopic pregnancy (aOR = 1.13, 95% CI = 0.92-1.38). We undertook additional analyses examining confirmed SARS-CoV-2 infection as the exposure and similarly found no association with miscarriage or ectopic pregnancy. Our findings support current recommendations that vaccination remains the safest way for pregnant women to protect themselves and their babies from COVID-19.",,pdf:https://www.nature.com/articles/s41467-022-33937-y.pdf; doi:https://doi.org/10.1038/s41467-022-33937-y; html:https://europepmc.org/articles/PMC9574832; pdf:https://europepmc.org/articles/PMC9574832?pdf=render
-37435691,https://doi.org/10.1111/dom.15207,"Testing for associations between HbA1c levels, polygenic risk and brain health in UK Biobank (N = 39 283).","Ranglani S, Ward J, Sattar N, Strawbridge RJ, Lyall DM.",,"Diabetes, obesity & metabolism",2023,2023-07-12,N,Type 2 diabetes; Cohort study; Population Study,,,"<h4>Aim</h4>To investigate whether continuous HbA1c levels and HbA1c-polygenic risk scores (HbA1c-PRS) are significantly associated with worse brain health independent of type 2 diabetes (T2D) diagnosis (vs. not), by examining brain structure and cognitive test score phenotypes.<h4>Methods</h4>Using UK Biobank data (n = 39 283), we tested whether HbA1c levels and/or HbA1c-PRS were associated with cognitive test scores and brain imaging phenotypes. We adjusted for confounders of age, sex, Townsend deprivation score, level of education, genotyping chip, eight genetic principal components, smoking, alcohol intake frequency, cholesterol medication, body mass index, T2D and apolipoprotein (APOE) e4 dosage.<h4>Results</h4>We found an association between higher HbA1c levels and poorer performance on symbol digit substitution scores (standardized beta [β] = -0.022, P = .001) in the fully adjusted model. We also found an association between higher HbA1c levels and worse brain MRI phenotypes of grey matter (GM; fully-adjusted β = -0.026, P < .001), whole brain volume (β = -0.072, P = .0113) and a general factor of frontal lobe GM (β = -0.022, P < .001) in partially and fully adjusted models. HbA1c-PRS were significantly associated with GM volume in the fully adjusted model (β = -0.010, P = .0113); however, when adjusted for HbA1c levels, the association was not significant.<h4>Conclusions</h4>Our findings suggest that measured HbA1c is associated with poorer cognitive health, and that HbA1c-PRS do not add significant information to this.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/dom.15207; doi:https://doi.org/10.1111/dom.15207
 33827854,https://doi.org/10.1136/bmj.n826,Linked electronic health records for research on a nationwide cohort of more than 54 million people in England: data resource.,"Wood A, Denholm R, Hollings S, Cooper J, Ip S, Walker V, Denaxas S, Akbari A, Banerjee A, Whiteley W, Lai A, Sterne J, Sudlow C, CVD-COVID-UK consortium.",,BMJ (Clinical research ed.),2021,2021-04-07,Y,,,,"<h4>Objective</h4>To describe a novel England-wide electronic health record (EHR) resource enabling whole population research on covid-19 and cardiovascular disease while ensuring data security and privacy and maintaining public trust.<h4>Design</h4>Data resource comprising linked person level records from national healthcare settings for the English population, accessible within NHS Digital's new trusted research environment.<h4>Setting</h4>EHRs from primary care, hospital episodes, death registry, covid-19 laboratory test results, and community dispensing data, with further enrichment planned from specialist intensive care, cardiovascular, and covid-19 vaccination data.<h4>Participants</h4>54.4 million people alive on 1 January 2020 and registered with an NHS general practitioner in England.<h4>Main measures of interest</h4>Confirmed and suspected covid-19 diagnoses, exemplar cardiovascular conditions (incident stroke or transient ischaemic attack and incident myocardial infarction) and all cause mortality between 1 January and 31 October 2020.<h4>Results</h4>The linked cohort includes more than 96% of the English population. By combining person level data across national healthcare settings, data on age, sex, and ethnicity are complete for around 95% of the population. Among 53.3 million people with no previous diagnosis of stroke or transient ischaemic attack, 98 721 had a first ever incident stroke or transient ischaemic attack between 1 January and 31 October 2020, of which 30% were recorded only in primary care and 4% only in death registry records. Among 53.2 million people with no previous diagnosis of myocardial infarction, 62 966 had an incident myocardial infarction during follow-up, of which 8% were recorded only in primary care and 12% only in death registry records. A total of 959 470 people had a confirmed or suspected covid-19 diagnosis (714 162 in primary care data, 126 349 in hospital admission records, 776 503 in covid-19 laboratory test data, and 50 504 in death registry records). Although 58% of these were recorded in both primary care and covid-19 laboratory test data, 15% and 18%, respectively, were recorded in only one.<h4>Conclusions</h4>This population-wide resource shows the importance of linking person level data across health settings to maximise completeness of key characteristics and to ascertain cardiovascular events and covid-19 diagnoses. Although this resource was initially established to support research on covid-19 and cardiovascular disease to benefit clinical care and public health and to inform healthcare policy, it can broaden further to enable a wide range of research.",,pdf:https://www.bmj.com/content/bmj/373/bmj.n826.full.pdf; doi:https://doi.org/10.1136/bmj.n826; html:https://europepmc.org/articles/PMC8413899; pdf:https://europepmc.org/articles/PMC8413899?pdf=render
+37435691,https://doi.org/10.1111/dom.15207,"Testing for associations between HbA1c levels, polygenic risk and brain health in UK Biobank (N = 39 283).","Ranglani S, Ward J, Sattar N, Strawbridge RJ, Lyall DM.",,"Diabetes, obesity & metabolism",2023,2023-07-12,N,Type 2 diabetes; Cohort study; Population Study,,,"<h4>Aim</h4>To investigate whether continuous HbA1c levels and HbA1c-polygenic risk scores (HbA1c-PRS) are significantly associated with worse brain health independent of type 2 diabetes (T2D) diagnosis (vs. not), by examining brain structure and cognitive test score phenotypes.<h4>Methods</h4>Using UK Biobank data (n = 39 283), we tested whether HbA1c levels and/or HbA1c-PRS were associated with cognitive test scores and brain imaging phenotypes. We adjusted for confounders of age, sex, Townsend deprivation score, level of education, genotyping chip, eight genetic principal components, smoking, alcohol intake frequency, cholesterol medication, body mass index, T2D and apolipoprotein (APOE) e4 dosage.<h4>Results</h4>We found an association between higher HbA1c levels and poorer performance on symbol digit substitution scores (standardized beta [β] = -0.022, P = .001) in the fully adjusted model. We also found an association between higher HbA1c levels and worse brain MRI phenotypes of grey matter (GM; fully-adjusted β = -0.026, P < .001), whole brain volume (β = -0.072, P = .0113) and a general factor of frontal lobe GM (β = -0.022, P < .001) in partially and fully adjusted models. HbA1c-PRS were significantly associated with GM volume in the fully adjusted model (β = -0.010, P = .0113); however, when adjusted for HbA1c levels, the association was not significant.<h4>Conclusions</h4>Our findings suggest that measured HbA1c is associated with poorer cognitive health, and that HbA1c-PRS do not add significant information to this.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/dom.15207; doi:https://doi.org/10.1111/dom.15207
 36195871,https://doi.org/10.1186/s12916-022-02533-8,Post-mortem examination of high mortality in patients with heart failure and atrial fibrillation.,"Țica O, Țica O, Bunting KV, deBono J, Gkoutos GV, Popescu MI, Kotecha D.",,BMC medicine,2022,2022-10-05,Y,Mortality; Atrial fibrillation; Autopsy; Heart Failure; Post-mortem,,,"<h4>Background</h4>The prevalence of combined heart failure (HF) and atrial fibrillation (AF) is rising, and these patients suffer from high rates of mortality. This study aims to provide robust data on factors associated with death, uniquely supported by post-mortem examination.<h4>Methods</h4>A retrospective cohort study of hospitalized adults with a clinical diagnosis of HF and AF at a tertiary centre in Romania between 2014 and 2017. A standardized post-mortem examination was performed where death occurred within 24 h of admission, when the cause of death was not clear or by physician request. National records were used to collect mortality data, subsequently categorized and analysed as HF-related death, vascular death and non-cardiovascular death using Cox proportional hazards regression.<h4>Results</h4>A total of 1009 consecutive patients with a mean age of 73 ± 11 years, 47% women, NYHA class 3.0 ± 0.9, left ventricular ejection fraction (LVEF) 40.1 ± 11.0% and 100% anticoagulated were followed up for 1.5 ± 0.9 years. A total of 291 (29%) died, with post-mortems performed on 186 (64%). Baseline factors associated with mortality were dependent on the cause of death. HF-related death in 136 (47%) was associated with higher NYHA class (hazard ratio [HR] 2.45 per one class increase, 95% CI 1.73-3.46; p < 0.001) and lower LVEF (0.95 per 1% increase, 0.93-0.97; p < 0.001). Vascular death occurred in 75 (26%) and was associated with hypertension (HR 2.83, 1.36-5.90; p = 0.005) and higher LVEF (1.08 per 1% increase, 1.05-1.11; p < 0.001). Non-cardiovascular death in 80 (28%) was associated with clinical obesity (HR 2.20, 1.21-4.00; p = 0.010) and higher LVEF (1.10 per 1% increase, 1.06-1.13; p < 0.001). Across all causes, there was no relationship between mortality and AF type (p = 0.77), HF type (p = 0.85) or LVEF (p = 0.58).<h4>Conclusions</h4>Supported by post-mortem data, the cause of death in HF and AF patients is heterogeneous, and the relationships with typical markers of mortality are critically dependent on the mode of death. The poor prognosis in this group demands further attention to improve management beyond anticoagulation.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-022-02533-8; doi:https://doi.org/10.1186/s12916-022-02533-8; html:https://europepmc.org/articles/PMC9533594; pdf:https://europepmc.org/articles/PMC9533594?pdf=render
-33901420,https://doi.org/10.1016/s0140-6736(21)00677-2,Interim findings from first-dose mass COVID-19 vaccination roll-out and COVID-19 hospital admissions in Scotland: a national prospective cohort study.,"Vasileiou E, Simpson CR, Shi T, Kerr S, Agrawal U, Akbari A, Bedston S, Beggs J, Bradley D, Chuter A, de Lusignan S, Docherty AB, Ford D, Hobbs FR, Joy M, Katikireddi SV, Marple J, McCowan C, McGagh D, McMenamin J, Moore E, Murray JL, Pan J, Ritchie L, Shah SA, Stock S, Torabi F, Tsang RS, Wood R, Woolhouse M, Robertson C, Sheikh A.",,"Lancet (London, England)",2021,2021-04-23,Y,,,,"<h4>Background</h4>The BNT162b2 mRNA (Pfizer-BioNTech) and ChAdOx1 nCoV-19 (Oxford-AstraZeneca) COVID-19 vaccines have shown high efficacy against disease in phase 3 clinical trials and are now being used in national vaccination programmes in the UK and several other countries. Studying the real-world effects of these vaccines is an urgent requirement. The aim of our study was to investigate the association between the mass roll-out of the first doses of these COVID-19 vaccines and hospital admissions for COVID-19.<h4>Methods</h4>We did a prospective cohort study using the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19-EAVE II-database comprising linked vaccination, primary care, real-time reverse transcription-PCR testing, and hospital admission patient records for 5·4 million people in Scotland (about 99% of the population) registered at 940 general practices. Individuals who had previously tested positive were excluded from the analysis. A time-dependent Cox model and Poisson regression models with inverse propensity weights were fitted to estimate effectiveness against COVID-19 hospital admission (defined as 1-adjusted rate ratio) following the first dose of vaccine.<h4>Findings</h4>Between Dec 8, 2020, and Feb 22, 2021, a total of 1 331 993 people were vaccinated over the study period. The mean age of those vaccinated was 65·0 years (SD 16·2). The first dose of the BNT162b2 mRNA vaccine was associated with a vaccine effect of 91% (95% CI 85-94) for reduced COVID-19 hospital admission at 28-34 days post-vaccination. Vaccine effect at the same time interval for the ChAdOx1 vaccine was 88% (95% CI 75-94). Results of combined vaccine effects against hospital admission due to COVID-19 were similar when restricting the analysis to those aged 80 years and older (83%, 95% CI 72-89 at 28-34 days post-vaccination).<h4>Interpretation</h4>Mass roll-out of the first doses of the BNT162b2 mRNA and ChAdOx1 vaccines was associated with substantial reductions in the risk of hospital admission due to COVID-19 in Scotland. There remains the possibility that some of the observed effects might have been due to residual confounding.<h4>Funding</h4>UK Research and Innovation (Medical Research Council), Research and Innovation Industrial Strategy Challenge Fund, Health Data Research UK.",,pdf:https://aura.abdn.ac.uk/bitstream/2164/17090/1/Vasileiou_etal_Lancet_Interim_Findings_FirstDose_VOR.pdf; doi:https://doi.org/10.1016/S0140-6736(21)00677-2; html:https://europepmc.org/articles/PMC8064669
+37056776,https://doi.org/10.3389/fimmu.2023.1146702,"SARS-CoV-2 antibody responses associate with sex, age and disease severity in previously uninfected people admitted to hospital with COVID-19: An ISARIC4C prospective study.","Parker E, Thomas J, Roper KJ, Ijaz S, Edwards T, Marchesin F, Katsanovskaja K, Lett L, Jones C, Hardwick HE, Davis C, Vink E, McDonald SE, Moore SC, Dicks S, Jegatheesan K, Cook NJ, Hope J, Cherepanov P, McClure MO, Baillie JK, Openshaw PJM, Turtle L, Ho A, Semple MG, Paxton WA, Tedder RS, Pollakis G, ISARIC4C Investigators.",,Frontiers in immunology,2023,2023-03-15,Y,Serology; Virus; Disease; immunology; Neutralisation; Covid-19; Sars-cov-2,,,"The SARS-CoV-2 pandemic enables the analysis of immune responses induced against a novel coronavirus infecting immunologically naïve individuals. This provides an opportunity for analysis of immune responses and associations with age, sex and disease severity. Here we measured an array of solid-phase binding antibody and viral neutralising Ab (nAb) responses in participants (n=337) of the ISARIC4C cohort and characterised their correlation with peak disease severity during acute infection and early convalescence. Overall, the responses in a Double Antigen Binding Assay (DABA) for antibody to the receptor binding domain (anti-RBD) correlated well with IgM as well as IgG responses against viral spike, S1 and nucleocapsid protein (NP) antigens. DABA reactivity also correlated with nAb. As we and others reported previously, there is greater risk of severe disease and death in older men, whilst the sex ratio was found to be equal within each severity grouping in younger people. In older males with severe disease (mean age 68 years), peak antibody levels were found to be delayed by one to two weeks compared with women, and nAb responses were delayed further. Additionally, we demonstrated that solid-phase binding antibody responses reached higher levels in males as measured <i>via</i> DABA and IgM binding against Spike, NP and S1 antigens. In contrast, this was not observed for nAb responses. When measuring SARS-CoV-2 RNA transcripts (as a surrogate for viral shedding) in nasal swabs at recruitment, we saw no significant differences by sex or disease severity status. However, we have shown higher antibody levels associated with low nasal viral RNA indicating a role of antibody responses in controlling viral replication and shedding in the upper airway. In this study, we have shown discernible differences in the humoral immune responses between males and females and these differences associate with age as well as with resultant disease severity.",,pdf:https://www.frontiersin.org/articles/10.3389/fimmu.2023.1146702/pdf; doi:https://doi.org/10.3389/fimmu.2023.1146702; html:https://europepmc.org/articles/PMC10087108; pdf:https://europepmc.org/articles/PMC10087108?pdf=render
+35798890,https://doi.org/10.1038/s41564-022-01143-7,SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway.,"Willett BJ, Grove J, MacLean OA, Wilkie C, De Lorenzo G, Furnon W, Cantoni D, Scott S, Logan N, Ashraf S, Manali M, Szemiel A, Cowton V, Vink E, Harvey WT, Davis C, Asamaphan P, Smollett K, Tong L, Orton R, Hughes J, Holland P, Silva V, Pascall DJ, Puxty K, da Silva Filipe A, Yebra G, Shaaban S, Holden MTG, Pinto RM, Gunson R, Templeton K, Murcia PR, Patel AH, Klenerman P, Dunachie S, PITCH Consortium, COVID-19 Genomics UK (COG-UK) Consortium, Haughney J, Robertson DL, Palmarini M, Ray S, Thomson EC.",,Nature microbiology,2022,2022-07-07,Y,,,,"Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant.",,pdf:https://www.nature.com/articles/s41564-022-01143-7.pdf; doi:https://doi.org/10.1038/s41564-022-01143-7; html:https://europepmc.org/articles/PMC9352574; pdf:https://europepmc.org/articles/PMC9352574?pdf=render
 36720568,https://doi.org/10.1136/bmjopen-2022-066164,Factors associated with COVID-19 vaccine uptake in people with kidney disease: an OpenSAFELY cohort study.,"OpenSAFELY Collaborative, Parker EP, Tazare J, Hulme WJ, Bates C, Carr EJ, Cockburn J, Curtis HJ, Fisher L, Green AC, Harper S, Hester F, Horne EM, Loud F, Lyon S, Mahalingasivam V, Mehrkar A, Nab L, Parry J, Santhakumaran S, Steenkamp R, Sterne JA, Walker AJ, Williamson EJ, Willicombe M, Zheng B, Goldacre B, Nitsch D, Tomlinson LA.",,BMJ open,2023,2023-01-31,Y,Public Health; Kidney & Urinary Tract Disorders; Covid-19,,,"<h4>Objective</h4>To characterise factors associated with COVID-19 vaccine uptake among people with kidney disease in England.<h4>Design</h4>Retrospective cohort study using the OpenSAFELY-TPP platform, performed with the approval of NHS England.<h4>Setting</h4>Individual-level routine clinical data from 24 million people across GPs in England using TPP software. Primary care data were linked directly with COVID-19 vaccine records up to 31 August 2022 and with renal replacement therapy (RRT) status via the UK Renal Registry (UKRR).<h4>Participants</h4>A cohort of adults with stage 3-5 chronic kidney disease (CKD) or receiving RRT at the start of the COVID-19 vaccine roll-out was identified based on evidence of reduced estimated glomerular filtration rate (eGFR) or inclusion in the UKRR.<h4>Main outcome measures</h4>Dose-specific vaccine coverage over time was determined from 1 December 2020 to 31 August 2022. Individual-level factors associated with receipt of a 3-dose or 4-dose vaccine series were explored via Cox proportional hazards models.<h4>Results</h4>992 205 people with stage 3-5 CKD or receiving RRT were included. Cumulative vaccine coverage as of 31 August 2022 was 97.5%, 97.0% and 93.9% for doses 1, 2 and 3, respectively, and 81.9% for dose 4 among individuals with one or more indications for eligibility. Delayed 3-dose vaccine uptake was associated with younger age, minority ethnicity, social deprivation and severe mental illness-associations that were consistent across CKD severity subgroups, dialysis patients and kidney transplant recipients. Similar associations were observed for 4-dose uptake.<h4>Conclusion</h4>Although high primary vaccine and booster dose coverage has been achieved among people with kidney disease in England, key disparities in vaccine uptake remain across clinical and demographic groups and 4-dose coverage is suboptimal. Targeted interventions are needed to identify barriers to vaccine uptake among under-vaccinated subgroups identified in the present study.",,pdf:https://bmjopen.bmj.com/content/bmjopen/13/1/e066164.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-066164; html:https://europepmc.org/articles/PMC9890277; pdf:https://europepmc.org/articles/PMC9890277?pdf=render
+33901420,https://doi.org/10.1016/s0140-6736(21)00677-2,Interim findings from first-dose mass COVID-19 vaccination roll-out and COVID-19 hospital admissions in Scotland: a national prospective cohort study.,"Vasileiou E, Simpson CR, Shi T, Kerr S, Agrawal U, Akbari A, Bedston S, Beggs J, Bradley D, Chuter A, de Lusignan S, Docherty AB, Ford D, Hobbs FR, Joy M, Katikireddi SV, Marple J, McCowan C, McGagh D, McMenamin J, Moore E, Murray JL, Pan J, Ritchie L, Shah SA, Stock S, Torabi F, Tsang RS, Wood R, Woolhouse M, Robertson C, Sheikh A.",,"Lancet (London, England)",2021,2021-04-23,Y,,,,"<h4>Background</h4>The BNT162b2 mRNA (Pfizer-BioNTech) and ChAdOx1 nCoV-19 (Oxford-AstraZeneca) COVID-19 vaccines have shown high efficacy against disease in phase 3 clinical trials and are now being used in national vaccination programmes in the UK and several other countries. Studying the real-world effects of these vaccines is an urgent requirement. The aim of our study was to investigate the association between the mass roll-out of the first doses of these COVID-19 vaccines and hospital admissions for COVID-19.<h4>Methods</h4>We did a prospective cohort study using the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19-EAVE II-database comprising linked vaccination, primary care, real-time reverse transcription-PCR testing, and hospital admission patient records for 5·4 million people in Scotland (about 99% of the population) registered at 940 general practices. Individuals who had previously tested positive were excluded from the analysis. A time-dependent Cox model and Poisson regression models with inverse propensity weights were fitted to estimate effectiveness against COVID-19 hospital admission (defined as 1-adjusted rate ratio) following the first dose of vaccine.<h4>Findings</h4>Between Dec 8, 2020, and Feb 22, 2021, a total of 1 331 993 people were vaccinated over the study period. The mean age of those vaccinated was 65·0 years (SD 16·2). The first dose of the BNT162b2 mRNA vaccine was associated with a vaccine effect of 91% (95% CI 85-94) for reduced COVID-19 hospital admission at 28-34 days post-vaccination. Vaccine effect at the same time interval for the ChAdOx1 vaccine was 88% (95% CI 75-94). Results of combined vaccine effects against hospital admission due to COVID-19 were similar when restricting the analysis to those aged 80 years and older (83%, 95% CI 72-89 at 28-34 days post-vaccination).<h4>Interpretation</h4>Mass roll-out of the first doses of the BNT162b2 mRNA and ChAdOx1 vaccines was associated with substantial reductions in the risk of hospital admission due to COVID-19 in Scotland. There remains the possibility that some of the observed effects might have been due to residual confounding.<h4>Funding</h4>UK Research and Innovation (Medical Research Council), Research and Innovation Industrial Strategy Challenge Fund, Health Data Research UK.",,pdf:https://aura.abdn.ac.uk/bitstream/2164/17090/1/Vasileiou_etal_Lancet_Interim_Findings_FirstDose_VOR.pdf; doi:https://doi.org/10.1016/S0140-6736(21)00677-2; html:https://europepmc.org/articles/PMC8064669
 38539097,https://doi.org/10.1186/s12877-024-04804-w,'In the shower crying…but we came back in the following day and did it all again'. Distress and resilience in care home staff during the COVID-19 pandemic- A qualitative interview study.,"Cockshott Z, Russell S, Stocker R, Knight J, Mason S, Hanratty B, Preston N.",,BMC geriatrics,2024,2024-03-27,Y,Resilience; Nursing Homes; Care Homes; Coping; Long-term Care Facilities; Staff Well-being; Covid-19; Staff Mental Health,,,"<h4>Background</h4>Care homes (long-term care facilities) were profoundly impacted early in the COVID-19 pandemic, both in terms of resident mortality and restrictions for infection control. This study investigated the impact on the emotional well-being of care home staff of challenges faced at this time, and the strategies used to manage them.<h4>Methods</h4>Semi-structured interviews conducted October 2020-June 2021 with care home staff and health service staff working with them explored the impact of the early waves of the COVID-19 pandemic (March 2020-June 2021). Interview data were analysed using reflexive thematic analysis.<h4>Results</h4>Interview participants were 16 care home staff and 10 health service staff. Analysis generated four key themes: 1)Anxiety and distress, 2)Overwhelming workload, 3)Pulling through; and 4)Resilience in a time of crisis. Care home staff experienced Anxiety and distress due to uncertainty of what to expect; witnessing illness and deaths of residents; concerns regarding their own health, and sometimes feeling their work was under-recognised. They also experienced an Overwhelming workload due to infection control measures, caring for sick residents and reduction in external healthcare support. Our theme of Pulling through reflects the peer support and problem-solving strategies with which care home staff managed the impact of the pandemic, along with a sense of responsibility and meaning towards their work. An overarching theme of Resilience in a time of crisis drew on the other three themes and describes how many staff managed, maintained, and often increased their work despite the challenges of the pandemic. Participants also described increasing emotional fatigue as the pandemic continued.<h4>Conclusions</h4>This paper builds on literature on the emotional impact of the pandemic on care home staff, also exploring ways that staff responded to this impact. These findings can help inform planning for future crises including disease outbreaks, and raise important questions for further work to develop pandemic preparedness in care homes and beyond. They also raise wider questions about the current cultural status of care work, which may have exposed care home staff to greater risk of distress, and which contrasts with the professionalism and responsibility shown by staff in response to pandemic challenges.",,pdf:https://bmcgeriatr.biomedcentral.com/counter/pdf/10.1186/s12877-024-04804-w; doi:https://doi.org/10.1186/s12877-024-04804-w; html:https://europepmc.org/articles/PMC10967173; pdf:https://europepmc.org/articles/PMC10967173?pdf=render
 38109175,https://doi.org/10.1249/mss.0000000000003365,Device-Measured Physical Activity in 3506 Individuals with Knee or Hip Arthroplasty.,"Small SR, Khalid S, Price AJ, Doherty A.",,Medicine and science in sports and exercise,2024,2023-12-18,Y,,,,"<h4>Purpose</h4>Hip and knee arthroplasty aims to reduce joint pain and increase functional mobility in patients with osteoarthritis; however, the degree to which arthroplasty is associated with higher physical activity is unclear. The current study sought to assess the association of hip and knee arthroplasty with objectively measured physical activity.<h4>Methods</h4>This cross-sectional study analyzed wrist-worn accelerometer data collected in 2013-2016 from UK Biobank participants (aged 43-78 yr). Multivariable linear regression was performed to assess step count, cadence, overall acceleration, and activity behaviors between nonarthritic controls, end-stage arthritic, and postoperative cohorts, controlling for demographic and behavioral confounders. From a cohort of 94,707 participants with valid accelerometer wear time and complete self-reported data, electronic health records were used to identify 3506 participants having undergone primary or revision hip or knee arthroplasty and 68,389 nonarthritic controls.<h4>Results</h4>End-stage hip or knee arthritis was associated with taking 1129 fewer steps per day (95% confidence interval (CI), 811-1447; P < 0.001) and having 5.8 fewer minutes per day (95% CI, 3.0-8.7; P < 0.001) of moderate-to-vigorous activity compared with nonarthritic controls. Unilateral primary hip and knee arthroplasties were associated with 877 (95% CI, 284-1471; P = 0.004) and 893 (95% CI, 232-1554; P = 0.008) more steps than end-stage osteoarthritic participants, respectively. Postoperative unilateral hip arthroplasty participants demonstrated levels of moderate-to-vigorous physical activity and daily step count equivalent to nonarthritic controls. No difference in physical activity was observed between any cohorts in terms of overall acceleration, or time spent in daily light activity, sedentary behavior, or sleep.<h4>Conclusions</h4>Hip and knee arthroplasties are associated with higher levels of physical activity compared with participants with end-stage arthritis. Unilateral hip arthroplasty patients, in particular, demonstrate equivalence to nonarthritic peers at more than 1 yr after surgery.",,doi:https://doi.org/10.1249/MSS.0000000000003365; html:https://europepmc.org/articles/PMC7615832; pdf:https://europepmc.org/articles/PMC7615832?pdf=render
 32276644,https://doi.org/10.1186/s12942-020-00208-2,GIS-modelled built-environment exposures reflecting daily mobility for applications in child health research.,"Mizen A, Fry R, Rodgers S.",,International journal of health geographics,2020,2020-04-10,Y,Environmental exposure; Child Health; Walking; Weighted Network; Daily Mobility; School Commute,,,"<h4>Background</h4>Inaccurately modelled environmental exposures may have important implications for evidence-based policy targeting health promoting or hazardous facilities. Travel routes modelled using GIS generally use shortest network distances or Euclidean buffers to represent journeys with corresponding built-environment exposures calculated along these routes. These methods, however, are an unreliable proxy for calculating child built-environment exposures as child route choice is more complex than shortest network routes.<h4>Methods</h4>We hypothesised that a GIS model informed by characteristics of the built-environment known to influence child route choice could be developed to more accurately model exposures. Using GPS-derived walking commutes to and from school we used logistic regression models to highlight built-environment features important in child route choice (e.g. road type, traffic light count). We then recalculated walking commute routes using a weighted network to incorporate built-environment features. Multilevel regression analyses were used to validate exposure predictions to the retail food environment along the different routing methods.<h4>Results</h4>Children chose routes with more traffic lights and residential roads compared to the modelled shortest network routes. Compared to standard shortest network routes, the GPS-informed weighted network enabled GIS-based walking commutes to be derived with more than three times greater accuracy (38%) for the route to school and more than 12 times greater accuracy (92%) for the route home.<h4>Conclusions</h4>This research advocates using weighted GIS networks to accurately reflect child walking journeys to school. The improved accuracy in route modelling has in turn improved estimates of children's exposures to potentially hazardous features in the environment. Further research is needed to explore if the built-environment features are important internationally. Route and corresponding exposure estimates can be scaled to the population level which will contribute to a better understanding of built-environment exposures on child health and contribute to mobility-based child health policy.",,pdf:https://ij-healthgeographics.biomedcentral.com/track/pdf/10.1186/s12942-020-00208-2; doi:https://doi.org/10.1186/s12942-020-00208-2; html:https://europepmc.org/articles/PMC7147039; pdf:https://europepmc.org/articles/PMC7147039?pdf=render
-35798890,https://doi.org/10.1038/s41564-022-01143-7,SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway.,"Willett BJ, Grove J, MacLean OA, Wilkie C, De Lorenzo G, Furnon W, Cantoni D, Scott S, Logan N, Ashraf S, Manali M, Szemiel A, Cowton V, Vink E, Harvey WT, Davis C, Asamaphan P, Smollett K, Tong L, Orton R, Hughes J, Holland P, Silva V, Pascall DJ, Puxty K, da Silva Filipe A, Yebra G, Shaaban S, Holden MTG, Pinto RM, Gunson R, Templeton K, Murcia PR, Patel AH, Klenerman P, Dunachie S, PITCH Consortium, COVID-19 Genomics UK (COG-UK) Consortium, Haughney J, Robertson DL, Palmarini M, Ray S, Thomson EC.",,Nature microbiology,2022,2022-07-07,Y,,,,"Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant.",,pdf:https://www.nature.com/articles/s41564-022-01143-7.pdf; doi:https://doi.org/10.1038/s41564-022-01143-7; html:https://europepmc.org/articles/PMC9352574; pdf:https://europepmc.org/articles/PMC9352574?pdf=render
-37056776,https://doi.org/10.3389/fimmu.2023.1146702,"SARS-CoV-2 antibody responses associate with sex, age and disease severity in previously uninfected people admitted to hospital with COVID-19: An ISARIC4C prospective study.","Parker E, Thomas J, Roper KJ, Ijaz S, Edwards T, Marchesin F, Katsanovskaja K, Lett L, Jones C, Hardwick HE, Davis C, Vink E, McDonald SE, Moore SC, Dicks S, Jegatheesan K, Cook NJ, Hope J, Cherepanov P, McClure MO, Baillie JK, Openshaw PJM, Turtle L, Ho A, Semple MG, Paxton WA, Tedder RS, Pollakis G, ISARIC4C Investigators.",,Frontiers in immunology,2023,2023-03-15,Y,Serology; Virus; Disease; immunology; Neutralisation; Covid-19; Sars-cov-2,,,"The SARS-CoV-2 pandemic enables the analysis of immune responses induced against a novel coronavirus infecting immunologically naïve individuals. This provides an opportunity for analysis of immune responses and associations with age, sex and disease severity. Here we measured an array of solid-phase binding antibody and viral neutralising Ab (nAb) responses in participants (n=337) of the ISARIC4C cohort and characterised their correlation with peak disease severity during acute infection and early convalescence. Overall, the responses in a Double Antigen Binding Assay (DABA) for antibody to the receptor binding domain (anti-RBD) correlated well with IgM as well as IgG responses against viral spike, S1 and nucleocapsid protein (NP) antigens. DABA reactivity also correlated with nAb. As we and others reported previously, there is greater risk of severe disease and death in older men, whilst the sex ratio was found to be equal within each severity grouping in younger people. In older males with severe disease (mean age 68 years), peak antibody levels were found to be delayed by one to two weeks compared with women, and nAb responses were delayed further. Additionally, we demonstrated that solid-phase binding antibody responses reached higher levels in males as measured <i>via</i> DABA and IgM binding against Spike, NP and S1 antigens. In contrast, this was not observed for nAb responses. When measuring SARS-CoV-2 RNA transcripts (as a surrogate for viral shedding) in nasal swabs at recruitment, we saw no significant differences by sex or disease severity status. However, we have shown higher antibody levels associated with low nasal viral RNA indicating a role of antibody responses in controlling viral replication and shedding in the upper airway. In this study, we have shown discernible differences in the humoral immune responses between males and females and these differences associate with age as well as with resultant disease severity.",,pdf:https://www.frontiersin.org/articles/10.3389/fimmu.2023.1146702/pdf; doi:https://doi.org/10.3389/fimmu.2023.1146702; html:https://europepmc.org/articles/PMC10087108; pdf:https://europepmc.org/articles/PMC10087108?pdf=render
 38894691,https://doi.org/10.2337/dc24-0537,Association of Metabolic Syndrome With Neuroimaging and Cognitive Outcomes in the UK Biobank.,"Qureshi D, Topiwala A, Al Abid SU, Allen NE, Kuźma E, Littlejohns TJ.",,Diabetes care,2024,2024-08-01,Y,,,,"<h4>Objective</h4>Metabolic syndrome (MetS) has been linked to dementia. In this study, we examined the association of MetS with neuroimaging and cognition in dementia-free adults, offering insight into the impact of MetS on brain health prior to dementia onset.<h4>Research design and methods</h4>We included 37,395 dementia-free adults from the UK Biobank database. MetS was defined as having at least three of the following components: larger waist circumference; elevated levels of triglycerides, blood pressure, HbA1c; or reduced HDL cholesterol levels. Multivariable-adjusted linear regression was used to assess associations of MetS with structural neuroimaging and cognitive domains.<h4>Results</h4>MetS was associated with lower total brain (standardized β: -0.06; 95% CI -0.08, -0.04), gray matter (β: -0.10; 95% CI -0.12, -0.08) and hippocampal (for left side, β: -0.03, 95% CI -0.05, -0.01; for right side, β: -0.04, 95% CI -0.07, -0.02) volumes, and greater white matter hyperintensity (WMH) volume (β: 0.08; 95% CI 0.06, 0.11). Study participants with MetS performed poorer on cognitive tests of working memory (β: -0.10; 95% CI -0.13, -0.07), verbal declarative memory (β: -0.08; 95% CI -0.11, -0.05), processing speed (β: -0.06; 95% CI -0.09, -0.04), verbal and numerical reasoning (β: -0.07; 95% CI -0.09, -0.04), nonverbal reasoning (β: -0.03; 95% CI -0.05, -0.01), and on tests of executive function, where higher scores indicated poorer performance (β: 0.05; 95% CI 0.03, 0.08). More MetS components were also associated with less brain volume, greater WMH, and poorer cognition across all domains.<h4>Conclusions</h4>MetS was associated poorer brain health in dementia-free adults, characterized by less brain volume, greater vascular pathology, and poorer cognition. Further research is necessary to understand whether reversal or improvement of MetS can improve brain health.",,pdf:https://diabetesjournals.org/care/article-pdf/doi/10.2337/dc24-0537/773314/dc240537.pdf; doi:https://doi.org/10.2337/dc24-0537; html:https://europepmc.org/articles/PMC11272984; pdf:https://europepmc.org/articles/PMC11272984?pdf=render
 38902726,https://doi.org/10.1186/s12916-024-03477-x,Healthcare utilisation in people with long COVID: an OpenSAFELY cohort study.,"Lin LY, Henderson AD, Carlile O, Dillingham I, Butler-Cole BFC, Marks M, Briggs A, Jit M, Tomlinson LA, Bates C, Parry J, Bacon SCJ, Goldacre B, Mehrkar A, MacKenna B, OpenSAFELY Collaborative, Eggo RM, Herrett E.",,BMC medicine,2024,2024-06-20,Y,Health Care Costs; Electronic Health Records; Facilities And Services Utilization; Long Covid,,,"<h4>Background</h4>Long COVID potentially increases healthcare utilisation and costs. However, its impact on the NHS remains to be determined.<h4>Methods</h4>This study aims to assess the healthcare utilisation of individuals with long COVID. With the approval of NHS England, we conducted a matched cohort study using primary and secondary care data via OpenSAFELY, a platform for analysing anonymous electronic health records. The long COVID exposure group, defined by diagnostic codes, was matched with five comparators without long COVID between Nov 2020 and Jan 2023. We compared their total healthcare utilisation from GP consultations, prescriptions, hospital admissions, A&E visits, and outpatient appointments. Healthcare utilisation and costs were evaluated using a two-part model adjusting for covariates. Using a difference-in-difference model, we also compared healthcare utilisation after long COVID with pre-pandemic records.<h4>Results</h4>We identified 52,988 individuals with a long COVID diagnosis, matched to 264,867 comparators without a diagnosis. In the 12 months post-diagnosis, there was strong evidence that those with long COVID were more likely to use healthcare resources (OR: 8.29, 95% CI: 7.74-8.87), and have 49% more healthcare utilisation (RR: 1.49, 95% CI: 1.48-1.51). Our model estimated that the long COVID group had 30 healthcare visits per year (predicted mean: 29.23, 95% CI: 28.58-29.92), compared to 16 in the comparator group (predicted mean visits: 16.04, 95% CI: 15.73-16.36). Individuals with long COVID were more likely to have non-zero healthcare expenditures (OR = 7.66, 95% CI = 7.20-8.15), with costs being 44% higher than the comparator group (cost ratio = 1.44, 95% CI: 1.39-1.50). The long COVID group costs approximately £2500 per person per year (predicted mean cost: £2562.50, 95% CI: £2335.60-£2819.22), and the comparator group costs £1500 (predicted mean cost: £1527.43, 95% CI: £1404.33-1664.45). Historically, individuals with long COVID utilised healthcare resources more frequently, but their average healthcare utilisation increased more after being diagnosed with long COVID, compared to the comparator group.<h4>Conclusions</h4>Long COVID increases healthcare utilisation and costs. Public health policies should allocate more resources towards preventing, treating, and supporting individuals with long COVID.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-024-03477-x; doi:https://doi.org/10.1186/s12916-024-03477-x; html:https://europepmc.org/articles/PMC11188519; pdf:https://europepmc.org/articles/PMC11188519?pdf=render
+39045545,https://doi.org/10.1016/j.eclinm.2024.102703,Association of latent class analysis-derived multimorbidity clusters with adverse health outcomes in patients with multiple long-term conditions: comparative results across three UK cohorts.,"Krauth SJ, Steell L, Ahmed S, McIntosh E, Dibben GO, Hanlon P, Lewsey J, Nicholl BI, McAllister DA, Smith SM, Evans R, Ahmed Z, Dean S, Greaves C, Barber S, Doherty P, Gardiner N, Ibbotson T, Jolly K, Ormandy P, Simpson SA, Taylor RS, Singh SJ, Mair FS, Jani BD, PERFORM research team.",,EClinicalMedicine,2024,2024-06-28,Y,Mortality; Clustering; Primary Health Care; Hospitalisation; Service Use; Multimorbidity,,,"<h4>Background</h4>It remains unclear how to meaningfully classify people living with multimorbidity (multiple long-term conditions (MLTCs)), beyond counting the number of conditions. This paper aims to identify clusters of MLTCs in different age groups and associated risks of adverse health outcomes and service use.<h4>Methods</h4>Latent class analysis was used to identify MLTCs clusters in different age groups in three cohorts: Secure Anonymised Information Linkage Databank (SAIL) (n = 1,825,289), UK Biobank (n = 502,363), and the UK Household Longitudinal Study (UKHLS) (n = 49,186). Incidence rate ratios (IRR) for MLTC clusters were computed for: all-cause mortality, hospitalisations, and general practice (GP) use over 10 years, using <2 MLTCs as reference. Information on health outcomes and service use were extracted for a ten year follow up period (between 01<sup>st</sup> Jan 2010 and 31st Dec 2019 for UK Biobank and UKHLS, and between 01<sup>st</sup> Jan 2011 and 31st Dec 2020 for SAIL).<h4>Findings</h4>Clustering MLTCs produced largely similar results across different age groups and cohorts. MLTC clusters had distinct associations with health outcomes and service use after accounting for LTC counts, in fully adjusted models. The largest associations with mortality, hospitalisations and GP use in SAIL were observed for the ""<i>Pain+</i>"" cluster in the age-group 18-36 years (mortality IRR = 4.47, hospitalisation IRR = 1.84; GP use IRR = 2.87) and the ""<i>Hypertension, Diabetes & Heart disease</i>"" cluster in the age-group 37-54 years (mortality IRR = 4.52, hospitalisation IRR = 1.53, GP use IRR = 2.36). In UK Biobank, the ""<i>Cancer, Thyroid disease & Rheumatoid arthritis</i>"" cluster in the age group 37-54 years had the largest association with mortality (IRR = 2.47). Cardiometabolic clusters across all age groups, pain/mental health clusters in younger groups, and cancer and pulmonary related clusters in older age groups had higher risk for all outcomes. In UKHLS, MLTC clusters were not significantly associated with higher risk of adverse outcomes, except for the hospitalisation in the age-group 18-36 years.<h4>Interpretation</h4>Personalising care around MLTC clusters that have higher risk of adverse outcomes may have important implications for practice (in relation to secondary prevention), policy (with allocation of health care resources), and research (intervention development and targeting), for people living with MLTCs.<h4>Funding</h4>This study was funded by the National Institute for Health and Care Research (NIHR; Personalised Exercise-Rehabilitation FOR people with Multiple long-term conditions (multimorbidity)-NIHR202020).",,doi:https://doi.org/10.1016/j.eclinm.2024.102703; html:https://europepmc.org/articles/PMC11261399; pdf:https://europepmc.org/articles/PMC11261399?pdf=render
 38939225,https://doi.org/10.3389/fpsyg.2024.1395668,Social media users' attitudes toward cyberbullying during the COVID-19 pandemic: associations with gender and verification status.,"Li L, Zhou J, McManus S, Stewart R, Roberts A.",,Frontiers in psychology,2024,2024-06-13,Y,Gender; Emotional Responses; Cyberbullying; Covid; Verification Status,,,"<h4>Introduction</h4>Social media platforms such as Twitter and Weibo facilitate both positive and negative communication, including cyberbullying. Empirical evidence has revealed that cyberbullying increases when public crises occur, that such behavior is gendered, and that social media user account verification may deter it. However, the association of gender and verification status with cyberbullying is underexplored. This study aims to address this gap by examining how Weibo users' gender, verification status, and expression of affect and anger in posts influence cyberbullying attitudes. Specifically, it investigates how these factors differ between posts pro- and anti-cyberbullying of COVID-19 cases during the pandemic.<h4>Methods</h4>This study utilized social role theory, the Barlett and Gentile Cyberbullying Model, and general strain theory as theoretical frameworks. We applied text classification techniques to identify pro-cyberbullying and anti-cyberbullying posts on Weibo. Subsequently, we used a standardized mean difference method to compare the emotional content of these posts. Our analysis focused on the prevalence of affective and anger-related expressions, particularly examining variations across gender and verification status of the users.<h4>Results</h4>Our text classification identified distinct pro-cyberbullying and anti-cyberbullying posts. The standardized mean difference analysis revealed that pro-cyberbullying posts contained significantly more emotional content compared to anti-cyberbullying posts. Further, within the pro-cyberbullying category, posts by verified female users exhibited a higher frequency of anger-related words than those by other users.<h4>Discussion</h4>The findings from this study can enhance researchers' algorithms for identifying cyberbullying attitudes, refine the characterization of cyberbullying behavior using real-world social media data through the integration of the mentioned theories, and help government bodies improve their cyberbullying monitoring especially in the context of public health crises.",,pdf:https://www.frontiersin.org/journals/psychology/articles/10.3389/fpsyg.2024.1395668/pdf; doi:https://doi.org/10.3389/fpsyg.2024.1395668; html:https://europepmc.org/articles/PMC11210603; pdf:https://europepmc.org/articles/PMC11210603?pdf=render
 36000189,https://doi.org/10.1515/dx-2022-0052,The diagnostic potential and barriers of microbiome based therapeutics.,"Acharjee A, Singh U, Choudhury SP, Gkoutos GV.",,"Diagnosis (Berlin, Germany)",2022,2022-08-25,N,Microbiota; Biomarker; Diagnostics; Machine Learning,,,"High throughput technological innovations in the past decade have accelerated research into the trillions of commensal microbes in the gut. The 'omics' technologies used for microbiome analysis are constantly evolving, and large-scale datasets are being produced. Despite of the fact that much of the research is still in its early stages, specific microbial signatures have been associated with the promotion of cancer, as well as other diseases such as inflammatory bowel disease, neurogenerative diareses etc. It has been also reported that the diversity of the gut microbiome influences the safety and efficacy of medicines. The availability and declining sequencing costs has rendered the employment of RNA-based diagnostics more common in the microbiome field necessitating improved data-analytical techniques so as to fully exploit all the resulting rich biological datasets, while accounting for their unique characteristics, such as their compositional nature as well their heterogeneity and sparsity. As a result, the gut microbiome is increasingly being demonstrating as an important component of personalised medicine since it not only plays a role in inter-individual variability in health and disease, but it also represents a potentially modifiable entity or feature that may be addressed by treatments in a personalised way. In this context, machine learning and artificial intelligence-based methods may be able to unveil new insights into biomedical analyses through the generation of models that may be used to predict category labels, and continuous values. Furthermore, diagnostic aspects will add value in the identification of the non invasive markers in the critical diseases like cancer.",,pdf:https://www.degruyter.com/document/doi/10.1515/dx-2022-0052/pdf; doi:https://doi.org/10.1515/dx-2022-0052
-39045545,https://doi.org/10.1016/j.eclinm.2024.102703,Association of latent class analysis-derived multimorbidity clusters with adverse health outcomes in patients with multiple long-term conditions: comparative results across three UK cohorts.,"Krauth SJ, Steell L, Ahmed S, McIntosh E, Dibben GO, Hanlon P, Lewsey J, Nicholl BI, McAllister DA, Smith SM, Evans R, Ahmed Z, Dean S, Greaves C, Barber S, Doherty P, Gardiner N, Ibbotson T, Jolly K, Ormandy P, Simpson SA, Taylor RS, Singh SJ, Mair FS, Jani BD, PERFORM research team.",,EClinicalMedicine,2024,2024-06-28,Y,Mortality; Clustering; Primary Health Care; Hospitalisation; Service Use; Multimorbidity,,,"<h4>Background</h4>It remains unclear how to meaningfully classify people living with multimorbidity (multiple long-term conditions (MLTCs)), beyond counting the number of conditions. This paper aims to identify clusters of MLTCs in different age groups and associated risks of adverse health outcomes and service use.<h4>Methods</h4>Latent class analysis was used to identify MLTCs clusters in different age groups in three cohorts: Secure Anonymised Information Linkage Databank (SAIL) (n = 1,825,289), UK Biobank (n = 502,363), and the UK Household Longitudinal Study (UKHLS) (n = 49,186). Incidence rate ratios (IRR) for MLTC clusters were computed for: all-cause mortality, hospitalisations, and general practice (GP) use over 10 years, using <2 MLTCs as reference. Information on health outcomes and service use were extracted for a ten year follow up period (between 01<sup>st</sup> Jan 2010 and 31st Dec 2019 for UK Biobank and UKHLS, and between 01<sup>st</sup> Jan 2011 and 31st Dec 2020 for SAIL).<h4>Findings</h4>Clustering MLTCs produced largely similar results across different age groups and cohorts. MLTC clusters had distinct associations with health outcomes and service use after accounting for LTC counts, in fully adjusted models. The largest associations with mortality, hospitalisations and GP use in SAIL were observed for the ""<i>Pain+</i>"" cluster in the age-group 18-36 years (mortality IRR = 4.47, hospitalisation IRR = 1.84; GP use IRR = 2.87) and the ""<i>Hypertension, Diabetes & Heart disease</i>"" cluster in the age-group 37-54 years (mortality IRR = 4.52, hospitalisation IRR = 1.53, GP use IRR = 2.36). In UK Biobank, the ""<i>Cancer, Thyroid disease & Rheumatoid arthritis</i>"" cluster in the age group 37-54 years had the largest association with mortality (IRR = 2.47). Cardiometabolic clusters across all age groups, pain/mental health clusters in younger groups, and cancer and pulmonary related clusters in older age groups had higher risk for all outcomes. In UKHLS, MLTC clusters were not significantly associated with higher risk of adverse outcomes, except for the hospitalisation in the age-group 18-36 years.<h4>Interpretation</h4>Personalising care around MLTC clusters that have higher risk of adverse outcomes may have important implications for practice (in relation to secondary prevention), policy (with allocation of health care resources), and research (intervention development and targeting), for people living with MLTCs.<h4>Funding</h4>This study was funded by the National Institute for Health and Care Research (NIHR; Personalised Exercise-Rehabilitation FOR people with Multiple long-term conditions (multimorbidity)-NIHR202020).",,doi:https://doi.org/10.1016/j.eclinm.2024.102703; html:https://europepmc.org/articles/PMC11261399; pdf:https://europepmc.org/articles/PMC11261399?pdf=render
 39384575,https://doi.org/10.1093/ehjqcco/qcae086,Standardised and hierarchically classified heart failure and complementary disease monitoring outcome measures: european Unified Registries for heart Care evaluation and randomised trials (EuroHeart).,"Bhatty A, Wilkinson C, Batra G, Aktaa S, Smith AB, Wahab A, Chappell S, Alfredsson J, Erlinge D, Ferreira J, Guðmundsdóttir IJ, Hrafnkelsdóttir ÞJ, Ingimarsdóttir IJ, Irs A, Jánosi A, Járai Z, Oliveira-Santos M, Popescu BA, Vasko P, Vinereanu D, Yap J, Bugiardini R, Cenko E, Nadarajah R, Sydes MR, James S, James S, Maggioni AP, Wallentin L, Casadei B, Gale CP.",,European heart journal. Quality of care & clinical outcomes,2024,2024-10-09,N,,,,"<h4>Aims</h4>The lack of standardised definitions for heart failure outcome measures limits the ability to reliably assess effectiveness of heart failure therapies. The European Unified Registries for Heart Care Evaluation and Randomised Trials (EuroHeart) aimed to produce a catalogue of internationally endorsed data definitions for heart failure outcome measures.<h4>Methods</h4>Following the EuroHeart methods for the development of cardiovascular data standards, a working group was formed of representatives from the European Society of Cardiology Heart Failure Association and other leading heart failure experts. A systematic review of observational and randomised clinical trials identified current outcome measures, which was supplemented by clinical practice guidelines and existing registries for contemporary definitions. A modified Delphi process was employed to gain consensus for variable inclusion and whether collection should be mandatory (Level 1) or optional (Level 2) within EuroHeart. In addition, a set of complementary outcome measures were identified by the Working Group as of scientific and clinical importance for longitudinal monitoring for people with heart failure.<h4>Results</h4>Five Level 1 and two Level 2 outcome measures were selected and defined, alongside five complementary monitoring outcomes for patients with heart failure.<h4>Conclusion</h4>We present a structured, hierarchical catalogue of internationally endorsed heart failure outcome measures. This will facilitate quality improvement, high quality observational research, registry-based trials, and post market surveillance of medical devices.",,doi:https://doi.org/10.1093/ehjqcco/qcae086
 36648008,https://doi.org/10.1111/iwj.14088,"Evaluating the cost of managing patients with cellulitis in Wales, UK: A 20-year population-scale study.","Humphreys I, Akbari A, Griffiths R, Graham-Woollard D, Morgan K, Noble-Jones R, Gabe-Walters M, Thomas M.",,International wound journal,2023,2023-01-17,Y,Longitudinal data; Cellulitis; Lymphoedema; Economic Burden; Sail Databank,,,"This study aimed to estimate costs associated with managing patients with cellulitis from the UK National Health Service (NHS) perspective. The analysis was undertaken through the Secure Anonymised Information Linkage Databank, which brings together population-scale, individual-level anonymised linked data from a wide range of sources, including 80% of primary care general practices within Wales (population coverage ~3.2 million). The data covered a 20-year period from 1999 to 2019. All patients linked to the relevant codes were tracked through primary care settings, recording the number of general practice visits (number of days with an event recorded) and number of in-patient stays. Resources were valued in monetary terms (£ sterling), with costs determined from national published sources of unit costs. These resources were then extrapolated out to reflect UK NHS costs. This is the first attempt to estimate the financial burden of cellulitis using routine data sources on a national scale. The estimated direct annual costs to the Welsh NHS (£28 554 338) are considerable. In-Patient events and length of stay costs are the main cost drivers, with annual Welsh NHS estimates of £19 664 126 with primary care events costing £8 890 212. Initiatives to support patients and healthcare professionals in identifying early signs/risks of cellulitis, improve the accuracy of initial diagnosis, prevent cellulitis recurrence, and improve evidence-based treatment pathways would result in major financial savings, to both the Welsh and UK NHS. In light of these findings, Wales has developed the innovative National Lymphoedema cellulitis Improvement Programme to address these burdens; providing a proactive model of cellulitis care.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/iwj.14088; doi:https://doi.org/10.1111/iwj.14088; html:https://europepmc.org/articles/PMC10333041; pdf:https://europepmc.org/articles/PMC10333041?pdf=render
 36244382,https://doi.org/10.1016/s0140-6736(22)01656-7,"Severe COVID-19 outcomes after full vaccination of primary schedule and initial boosters: pooled analysis of national prospective cohort studies of 30 million individuals in England, Northern Ireland, Scotland, and Wales.","Agrawal U, Bedston S, McCowan C, Oke J, Patterson L, Robertson C, Akbari A, Azcoaga-Lorenzo A, Bradley DT, Fagbamigbe AF, Grange Z, Hall ECR, Joy M, Katikireddi SV, Kerr S, Ritchie L, Murphy S, Owen RK, Rudan I, Shah SA, Simpson CR, Torabi F, Tsang RSM, de Lusignan S, Lyons RA, O'Reilly D, Sheikh A.",,"Lancet (London, England)",2022,2022-10-01,Y,,,,"<h4>Background</h4>Current UK vaccination policy is to offer future COVID-19 booster doses to individuals at high risk of serious illness from COVID-19, but it is still uncertain which groups of the population could benefit most. In response to an urgent request from the UK Joint Committee on Vaccination and Immunisation, we aimed to identify risk factors for severe COVID-19 outcomes (ie, COVID-19-related hospitalisation or death) in individuals who had completed their primary COVID-19 vaccination schedule and had received the first booster vaccine.<h4>Methods</h4>We constructed prospective cohorts across all four UK nations through linkages of primary care, RT-PCR testing, vaccination, hospitalisation, and mortality data on 30 million people. We included individuals who received primary vaccine doses of BNT162b2 (tozinameran; Pfizer-BioNTech) or ChAdOx1 nCoV-19 (Oxford-AstraZeneca) vaccines in our initial analyses. We then restricted analyses to those given a BNT162b2 or mRNA-1273 (elasomeran; Moderna) booster and had a severe COVID-19 outcome between Dec 20, 2021, and Feb 28, 2022 (when the omicron (B.1.1.529) variant was dominant). We fitted time-dependent Poisson regression models and calculated adjusted rate ratios (aRRs) and 95% CIs for the associations between risk factors and COVID-19-related hospitalisation or death. We adjusted for a range of potential covariates, including age, sex, comorbidities, and previous SARS-CoV-2 infection. Stratified analyses were conducted by vaccine type. We then did pooled analyses across UK nations using fixed-effect meta-analyses.<h4>Findings</h4>Between Dec 8, 2020, and Feb 28, 2022, 16 208 600 individuals completed their primary vaccine schedule and 13 836 390 individuals received a booster dose. Between Dec 20, 2021, and Feb 28, 2022, 59 510 (0·4%) of the primary vaccine group and 26 100 (0·2%) of those who received their booster had severe COVID-19 outcomes. The risk of severe COVID-19 outcomes reduced after receiving the booster (rate change: 8·8 events per 1000 person-years to 7·6 events per 1000 person-years). Older adults (≥80 years vs 18-49 years; aRR 3·60 [95% CI 3·45-3·75]), those with comorbidities (≥5 comorbidities vs none; 9·51 [9·07-9·97]), being male (male vs female; 1·23 [1·20-1·26]), and those with certain underlying health conditions-in particular, individuals receiving immunosuppressants (yes vs no; 5·80 [5·53-6·09])-and those with chronic kidney disease (stage 5 vs no; 3·71 [2·90-4·74]) remained at high risk despite the initial booster. Individuals with a history of COVID-19 infection were at reduced risk (infected ≥9 months before booster dose vs no previous infection; aRR 0·41 [95% CI 0·29-0·58]).<h4>Interpretation</h4>Older people, those with multimorbidity, and those with specific underlying health conditions remain at increased risk of COVID-19 hospitalisation and death after the initial vaccine booster and should, therefore, be prioritised for additional boosters, including novel optimised versions, and the increasing array of COVID-19 therapeutics.<h4>Funding</h4>National Core Studies-Immunity, UK Research and Innovation (Medical Research Council), Health Data Research UK, the Scottish Government, and the University of Edinburgh.",,pdf:http://www.thelancet.com/article/S0140673622016567/pdf; doi:https://doi.org/10.1016/S0140-6736(22)01656-7; html:https://europepmc.org/articles/PMC9560746; pdf:https://europepmc.org/articles/PMC9560746?pdf=render
 37547953,https://doi.org/10.1002/alz.13405,"Cardiovascular health, infection burden, and incident dementia in the UK Biobank.","Beydoun HA, Beydoun MA, Meirelles O, Erickson LD, Gamaldo AA, Weiss J, Launer LJ, Evans MK, Zonderman AB.",,Alzheimer's & dementia : the journal of the Alzheimer's Association,2023,2023-08-07,N,Infection; Alzheimer's disease; Dementia; Hospitalization; Cardiovascular Health,,,"<h4>Introduction</h4>Among older adults, total and hospitalized infection may be associated with incidence of all-cause and Alzheimer's disease (AD) dementias, with variation by cardiovascular health (CVH).<h4>Methods</h4>We used Cox proportional hazards (PH) models to examine the relationships between International Classification of Diseases-10th revision (ICD-10)-specific viral and bacterial infectious agents and incident all-cause and AD dementia among 355,046 UK Biobank participants ≥50 years at baseline. Life's Essential 8 (LE8) index reflected CVH.<h4>Results</h4>In both sexes, total infection burden (yes vs. no) was associated with all-cause dementia, with significant interactions by LE8 tertiles, whereby this relationship was significant only in the lowest LE8 tertile. Hospital-treated infection burden (yes vs no) was significantly related to all-cause and AD dementia, with no significant interaction with LE8 tertile. Age group patterns were detected.<h4>Discussion</h4>AD and all-cause dementia were related to hospital-treated infections, while CVH modified the relationship of total infection burden with all-cause dementia. Highlights Secondary analysis on >355,000 UK Biobank participants ≥50 years at baseline. Alzheimer's disease and all-cause dementia are both related to hospital-treated infection. Cardiovascular health modifies association of infection burden with all-cause dementia.",,doi:https://doi.org/10.1002/alz.13405; html:https://europepmc.org/articles/PMC10592296; pdf:https://europepmc.org/articles/PMC10592296?pdf=render; doi:https://doi.org/10.1002/alz.13405
+37123891,https://doi.org/10.1016/j.heliyon.2023.e15143,Disclosure control of machine learning models from trusted research environments (TRE): New challenges and opportunities.,"Mansouri-Benssassi E, Rogers S, Reel S, Malone M, Smith J, Ritchie F, Jefferson E.",,Heliyon,2023,2023-04-03,Y,AI; Machine Learning; Data Privacy; Safe Haven; Disclosure Control; Trusted Research Environment,,,"<h4>Introduction</h4>Artificial intelligence (AI) applications in healthcare and medicine have increased in recent years. To enable access to personal data, Trusted Research Environments (TREs) (otherwise known as Safe Havens) provide safe and secure environments in which researchers can access sensitive personal data and develop AI (in particular machine learning (ML)) models. However, currently few TREs support the training of ML models in part due to a gap in the practical decision-making guidance for TREs in handling model disclosure. Specifically, the training of ML models creates a need to disclose new types of outputs from TREs. Although TREs have clear policies for the disclosure of statistical outputs, the extent to which trained models can leak personal training data once released is not well understood.<h4>Background</h4>We review, for a general audience, different types of ML models and their applicability within healthcare. We explain the outputs from training a ML model and how trained ML models can be vulnerable to external attacks to discover personal data encoded within the model.<h4>Risks</h4>We present the challenges for disclosure control of trained ML models in the context of training and exporting models from TREs. We provide insights and analyse methods that could be introduced within TREs to mitigate the risk of privacy breaches when disclosing trained models.<h4>Discussion</h4>Although specific guidelines and policies exist for statistical disclosure controls in TREs, they do not satisfactorily address these new types of output requests; i.e., trained ML models. There is significant potential for new interdisciplinary research opportunities in developing and adapting policies and tools for safely disclosing ML outputs from TREs.",,pdf:http://www.cell.com/article/S2405844023023502/pdf; doi:https://doi.org/10.1016/j.heliyon.2023.e15143; html:https://europepmc.org/articles/PMC10130764; pdf:https://europepmc.org/articles/PMC10130764?pdf=render
 37494295,https://doi.org/10.1371/journal.pone.0286840,"Educational outcomes in childhood cancer survivors: A Scotland-wide record-linkage study of 766,217 schoolchildren.","Baughan N, Pell JP, Mackay DF, Clark D, King A, Fleming M.",,PloS one,2023,2023-07-26,Y,,,,"<h4>Background</h4>A cancer diagnosis during childhood greatly disrupts the lives of those affected, causing physical and psychological challenges. We aim to investigate educational outcomes among schoolchildren with a previous cancer diagnosis compared to their peers.<h4>Methods</h4>Individual records from four national education databases and three national health databases were linked to construct a cohort of all singleton schoolchildren born in Scotland attending Scottish local-authority schools between 2009-2013. Pupils previously diagnosed with any cancer, haematological cancers, and central nervous system (CNS) cancers, were compared to their unaffected peers with respect to five educational outcomes: special educational need (SEN), absenteeism, school exclusion, academic attainment, and unemployment. Analyses were adjusted for sociodemographic and maternity factors and chronic conditions.<h4>Results</h4>Of 766,217 pupils, 1,313 (0.17%) had a previous cancer diagnosis. Children with any cancer had increased odds of SEN (OR 3.26, 95% CI 2.86-3.71), absenteeism (IRR 1.82, 95% CI 1.70-1.94), and low attainment (OR 2.15, 95% CI 1.52-3.03) compared to their peers. Similar findings were observed for haematological (SEN OR 2.62, 95% CI 2.12-3.24; absenteeism IRR 2.04, 95% CI 1.85-2.25; low attainment OR 2.17, 95% CI 1.31-3.61) and CNS (SEN OR 6.44, 95% CI 4.91-8.46; absenteeism IRR 1.75, 95% CI 1.51-2.04; low attainment OR 3.33, 95% CI 1.52-7.30) cancers. Lower exclusions were observed among children with any cancer (IRR 0.51, 95% CI 0.31-0.83) and CNS cancer (IRR 0.20, 95% CI 0.06-0.61). No associations were observed with unemployment.<h4>Conclusions</h4>This study highlights the wider impacts of childhood cancer on educational outcomes. These children need to be supported, as poor educational outcomes can further impact later health.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0286840&type=printable; doi:https://doi.org/10.1371/journal.pone.0286840; html:https://europepmc.org/articles/PMC10370705; pdf:https://europepmc.org/articles/PMC10370705?pdf=render
 36769519,https://doi.org/10.3390/jcm12030872,Patterns of Healthcare Resource Utilisation of Critical Care Survivors between 2006 and 2017 in Wales: A Population-Based Study.,"Alsallakh M, Tan L, Pugh R, Akbari A, Bailey R, Griffiths R, Lyons RA, Szakmany T.",,Journal of clinical medicine,2023,2023-01-21,Y,Wales; Healthcare Resource Utilisation; Critical Care Survivorship,,,"In this retrospective cohort study, we used the Secure Anonymised Information Linkage (SAIL) Databank to characterise and identify predictors of the one-year post-discharge healthcare resource utilisation (HRU) of adults who were admitted to critical care units in Wales between 1 April 2006 and 31 December 2017. We modelled one-year post-critical-care HRU using negative binomial models and used linear models for the difference from one-year pre-critical-care HRU. We estimated the association between critical illness and post-hospitalisation HRU using multilevel negative binomial models among people hospitalised in 2015. We studied 55,151 patients. Post-critical-care HRU was 11-87% greater than pre-critical-care levels, whereas emergency department (ED) attendances decreased by 30%. Age ≥50 years was generally associated with greater post-critical-care HRU; those over 80 had three times longer hospital readmissions than those younger than 50 (incidence rate ratio (IRR): 2.96, 95% CI: 2.84, 3.09). However, ED attendances were higher in those younger than 50. High comorbidity was associated with 22-62% greater post-critical-care HRU than no or low comorbidity. The most socioeconomically deprived quintile was associated with 24% more ED attendances (IRR: 1.24 [1.16, 1.32]) and 13% longer hospital stays (IRR: 1.13 [1.09, 1.17]) than the least deprived quintile. Critical care survivors had greater 1-year post-discharge HRU than non-critical inpatients, including 68% longer hospital stays (IRR: 1.68 [1.63, 1.74]). Critical care survivors, particularly those with older ages, high comorbidity, and socioeconomic deprivation, used significantly more primary and secondary care resources after discharge compared with their baseline and non-critical inpatients. Interventions are needed to ensure that key subgroups are identified and adequately supported.",,pdf:https://www.mdpi.com/2077-0383/12/3/872/pdf?version=1674984751; doi:https://doi.org/10.3390/jcm12030872; html:https://europepmc.org/articles/PMC9917699; pdf:https://europepmc.org/articles/PMC9917699?pdf=render
 34600486,https://doi.org/10.1186/s12880-021-00671-8,The reporting quality of natural language processing studies: systematic review of studies of radiology reports.,"Davidson EM, Poon MTC, Casey A, Grivas A, Duma D, Dong H, Suárez-Paniagua V, Grover C, Tobin R, Whalley H, Wu H, Alex B, Whiteley W.",,BMC medical imaging,2021,2021-10-02,Y,Systematic review; Natural Language Processing; Radiology Reports,,,"<h4>Background</h4>Automated language analysis of radiology reports using natural language processing (NLP) can provide valuable information on patients' health and disease. With its rapid development, NLP studies should have transparent methodology to allow comparison of approaches and reproducibility. This systematic review aims to summarise the characteristics and reporting quality of studies applying NLP to radiology reports.<h4>Methods</h4>We searched Google Scholar for studies published in English that applied NLP to radiology reports of any imaging modality between January 2015 and October 2019. At least two reviewers independently performed screening and completed data extraction. We specified 15 criteria relating to data source, datasets, ground truth, outcomes, and reproducibility for quality assessment. The primary NLP performance measures were precision, recall and F1 score.<h4>Results</h4>Of the 4,836 records retrieved, we included 164 studies that used NLP on radiology reports. The commonest clinical applications of NLP were disease information or classification (28%) and diagnostic surveillance (27.4%). Most studies used English radiology reports (86%). Reports from mixed imaging modalities were used in 28% of the studies. Oncology (24%) was the most frequent disease area. Most studies had dataset size > 200 (85.4%) but the proportion of studies that described their annotated, training, validation, and test set were 67.1%, 63.4%, 45.7%, and 67.7% respectively. About half of the studies reported precision (48.8%) and recall (53.7%). Few studies reported external validation performed (10.8%), data availability (8.5%) and code availability (9.1%). There was no pattern of performance associated with the overall reporting quality.<h4>Conclusions</h4>There is a range of potential clinical applications for NLP of radiology reports in health services and research. However, we found suboptimal reporting quality that precludes comparison, reproducibility, and replication. Our results support the need for development of reporting standards specific to clinical NLP studies.",,pdf:https://bmcmedimaging.biomedcentral.com/track/pdf/10.1186/s12880-021-00671-8; doi:https://doi.org/10.1186/s12880-021-00671-8; html:https://europepmc.org/articles/PMC8487512; pdf:https://europepmc.org/articles/PMC8487512?pdf=render
-37123891,https://doi.org/10.1016/j.heliyon.2023.e15143,Disclosure control of machine learning models from trusted research environments (TRE): New challenges and opportunities.,"Mansouri-Benssassi E, Rogers S, Reel S, Malone M, Smith J, Ritchie F, Jefferson E.",,Heliyon,2023,2023-04-03,Y,AI; Machine Learning; Data Privacy; Safe Haven; Disclosure Control; Trusted Research Environment,,,"<h4>Introduction</h4>Artificial intelligence (AI) applications in healthcare and medicine have increased in recent years. To enable access to personal data, Trusted Research Environments (TREs) (otherwise known as Safe Havens) provide safe and secure environments in which researchers can access sensitive personal data and develop AI (in particular machine learning (ML)) models. However, currently few TREs support the training of ML models in part due to a gap in the practical decision-making guidance for TREs in handling model disclosure. Specifically, the training of ML models creates a need to disclose new types of outputs from TREs. Although TREs have clear policies for the disclosure of statistical outputs, the extent to which trained models can leak personal training data once released is not well understood.<h4>Background</h4>We review, for a general audience, different types of ML models and their applicability within healthcare. We explain the outputs from training a ML model and how trained ML models can be vulnerable to external attacks to discover personal data encoded within the model.<h4>Risks</h4>We present the challenges for disclosure control of trained ML models in the context of training and exporting models from TREs. We provide insights and analyse methods that could be introduced within TREs to mitigate the risk of privacy breaches when disclosing trained models.<h4>Discussion</h4>Although specific guidelines and policies exist for statistical disclosure controls in TREs, they do not satisfactorily address these new types of output requests; i.e., trained ML models. There is significant potential for new interdisciplinary research opportunities in developing and adapting policies and tools for safely disclosing ML outputs from TREs.",,pdf:http://www.cell.com/article/S2405844023023502/pdf; doi:https://doi.org/10.1016/j.heliyon.2023.e15143; html:https://europepmc.org/articles/PMC10130764; pdf:https://europepmc.org/articles/PMC10130764?pdf=render
+36918541,https://doi.org/10.1038/s41467-023-36997-w,Genetic architecture of spatial electrical biomarkers for cardiac arrhythmia and relationship with cardiovascular disease.,"Young WJ, Haessler J, Benjamins JW, Repetto L, Yao J, Isaacs A, Harper AR, Ramirez J, Garnier S, van Duijvenboden S, Baldassari AR, Concas MP, Duong T, Foco L, Isaksen JL, Mei H, Noordam R, Nursyifa C, Richmond A, Santolalla ML, Sitlani CM, Soroush N, Thériault S, Trompet S, Aeschbacher S, Ahmadizar F, Alonso A, Brody JA, Campbell A, Correa A, Darbar D, De Luca A, Deleuze JF, Ellervik C, Fuchsberger C, Goel A, Grace C, Guo X, Hansen T, Heckbert SR, Jackson RD, Kors JA, Lima-Costa MF, Linneberg A, Macfarlane PW, Morrison AC, Navarro P, Porteous DJ, Pramstaller PP, Reiner AP, Risch L, Schotten U, Shen X, Sinagra G, Soliman EZ, Stoll M, Tarazona-Santos E, Tinker A, Trajanoska K, Villard E, Warren HR, Whitsel EA, Wiggins KL, Arking DE, Avery CL, Conen D, Girotto G, Grarup N, Hayward C, Jukema JW, Mook-Kanamori DO, Olesen MS, Padmanabhan S, Psaty BM, Pattaro C, Ribeiro ALP, Rotter JI, Stricker BH, van der Harst P, van Duijn CM, Verweij N, Wilson JG, Orini M, Charron P, Watkins H, Kooperberg C, Lin HJ, Wilson JF, Kanters JK, Sotoodehnia N, Mifsud B, Lambiase PD, Tereshchenko LG, Munroe PB.",,Nature communications,2023,2023-03-14,Y,,,,"The 3-dimensional spatial and 2-dimensional frontal QRS-T angles are measures derived from the vectorcardiogram. They are independent risk predictors for arrhythmia, but the underlying biology is unknown. Using multi-ancestry genome-wide association studies we identify 61 (58 previously unreported) loci for the spatial QRS-T angle (N = 118,780) and 11 for the frontal QRS-T angle (N = 159,715). Seven out of the 61 spatial QRS-T angle loci have not been reported for other electrocardiographic measures. Enrichments are observed in pathways related to cardiac and vascular development, muscle contraction, and hypertrophy. Pairwise genome-wide association studies with classical ECG traits identify shared genetic influences with PR interval and QRS duration. Phenome-wide scanning indicate associations with atrial fibrillation, atrioventricular block and arterial embolism and genetically determined QRS-T angle measures are associated with fascicular and bundle branch block (and also atrioventricular block for the frontal QRS-T angle). We identify potential biology involved in the QRS-T angle and their genetic relationships with cardiovascular traits and diseases, may inform future research and risk prediction.",,pdf:https://www.nature.com/articles/s41467-023-36997-w.pdf; doi:https://doi.org/10.1038/s41467-023-36997-w; html:https://europepmc.org/articles/PMC10015012; pdf:https://europepmc.org/articles/PMC10015012?pdf=render
 36035235,https://doi.org/10.1212/nxg.0000000000200015,"Frequency and Phenotype Associations of Rare Variants in 5 Monogenic Cerebral Small Vessel Disease Genes in 200,000 UK Biobank Participants.","Ferguson AC, Thrippleton S, Henshall D, Whittaker E, Conway B, MacLeod M, Malik R, Rawlik K, Tenesa A, Sudlow C, Rannikmae K.",,Neurology. Genetics,2022,2022-08-24,Y,,,,"<h4>Background and objectives</h4>Based on previous case reports and disease-based cohorts, a minority of patients with cerebral small vessel disease (cSVD) have a monogenic cause, with many also manifesting extracerebral phenotypes. We investigated the frequency, penetrance, and phenotype associations of putative pathogenic variants in cSVD genes in the UK Biobank (UKB), a large population-based study.<h4>Methods</h4>We used a systematic review of previous literature and ClinVar to identify putative pathogenic rare variants in <i>CTSA</i>, <i>TREX1</i>, <i>HTRA1</i>, and <i>COL4A1/2</i>. We mapped phenotypes previously attributed to these variants (phenotypes-of-interest) to disease coding systems used in the UKB's linked health data from UK hospital admissions, death records, and primary care. Among 199,313 exome-sequenced UKB participants, we assessed the following: the proportion of participants carrying ≥1 variant(s); phenotype-of-interest penetrance; and the association between variant carrier status and phenotypes-of-interest using a binary (any phenotype present/absent) and phenotype burden (linear score of the number of phenotypes a participant possessed) approach.<h4>Results</h4>Among UKB participants, 0.5% had ≥1 variant(s) in studied genes. Using hospital admission and death records, 4%-20% of variant carriers per gene had an associated phenotype. This increased to 7%-55% when including primary care records. Only <i>COL4A1</i> variant carrier status was significantly associated with having ≥1 phenotype-of-interest and a higher phenotype score (OR = 1.29, <i>p</i> = 0.006).<h4>Discussion</h4>While putative pathogenic rare variants in monogenic cSVD genes occur in 1:200 people in the UKB population, only approximately half of variant carriers have a relevant disease phenotype recorded in their linked health data. We could not replicate most previously reported gene-phenotype associations, suggesting lower penetrance rates, overestimated pathogenicity, and/or limited statistical power.",,pdf:https://ng.neurology.org/content/nng/8/5/e200015.full.pdf; doi:https://doi.org/10.1212/NXG.0000000000200015; html:https://europepmc.org/articles/PMC9403885; pdf:https://europepmc.org/articles/PMC9403885?pdf=render
-37303488,https://doi.org/10.1136/bmjmed-2022-000392,"Changes in medication safety indicators in England throughout the covid-19 pandemic using OpenSAFELY: population based, retrospective cohort study of 57 million patients using federated analytics.","Fisher L, Hopcroft LE, Rodgers S, Barrett J, Oliver K, Avery AJ, Evans D, Curtis H, Croker R, Macdonald O, Morley J, Mehrkar A, Bacon S, Davy S, Dillingham I, Evans D, Hickman G, Inglesby P, Morton CE, Smith B, Ward T, Hulme W, Green A, Massey J, Walker AJ, Bates C, Cockburn J, Parry J, Hester F, Harper S, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Griffiths P, Fowles A, Parkes N, Goldacre B, MacKenna B.",,BMJ medicine,2023,2023-05-11,Y,Primary Health Care; Medical Informatics; Covid-19,,,"<h4>Objective</h4>To implement complex, PINCER (pharmacist led information technology intervention) prescribing indicators, on a national scale with general practice data to describe the impact of the covid-19 pandemic on safe prescribing.<h4>Design</h4>Population based, retrospective cohort study using federated analytics.<h4>Setting</h4>Electronic general practice health record data from 56.8 million NHS patients by use of the OpenSAFELY platform, with the approval of the National Health Service (NHS) England.<h4>Participants</h4>NHS patients (aged 18-120 years) who were alive and registered at a general practice that used TPP or EMIS computer systems and were recorded as at risk of at least one potentially hazardous PINCER indicator.<h4>Main outcome measure</h4>Between 1 September 2019 and 1 September 2021, monthly trends and between practice variation for compliance with 13 PINCER indicators, as calculated on the first of every month, were reported. Prescriptions that do not adhere to these indicators are potentially hazardous and can cause gastrointestinal bleeds; are cautioned against in specific conditions (specifically heart failure, asthma, and chronic renal failure); or require blood test monitoring. The percentage for each indicator is formed of a numerator of patients deemed to be at risk of a potentially hazardous prescribing event and the denominator is of patients for which assessment of the indicator is clinically meaningful. Higher indicator percentages represent potentially poorer performance on medication safety.<h4>Results</h4>The PINCER indicators were successfully implemented across general practice data for 56.8 million patient records from 6367 practices in OpenSAFELY. Hazardous prescribing remained largely unchanged during the covid-19 pandemic, with no evidence of increases in indicators of harm as captured by the PINCER indicators. The percentage of patients at risk of potentially hazardous prescribing, as defined by each PINCER indicator, at mean quarter 1 (Q1) 2020 (representing before the pandemic) ranged from 1.11% (age ≥65 years and non-steroidal anti-inflammatory drugs) to 36.20% (amiodarone and no thyroid function test), while Q1 2021 (representing after the pandemic) percentages ranged from 0.75% (age ≥65 years and non-steroidal anti-inflammatory drugs) to 39.23% (amiodarone and no thyroid function test). Transient delays occurred in blood test monitoring for some medications, particularly angiotensin-converting enzyme inhibitors (where blood monitoring worsened from a mean of 5.16% in Q1 2020 to 12.14% in Q1 2021, and began to recover in June 2021). All indicators substantially recovered by September 2021. We identified 1 813 058 patients (3.1%) at risk of at least one potentially hazardous prescribing event.<h4>Conclusion</h4>NHS data from general practices can be analysed at national scale to generate insights into service delivery. Potentially hazardous prescribing was largely unaffected by the covid-19 pandemic in primary care health records in England.",,pdf:https://bmjmedicine.bmj.com/content/bmjmed/2/1/e000392.full.pdf; doi:https://doi.org/10.1136/bmjmed-2022-000392; html:https://europepmc.org/articles/PMC10254692; pdf:https://europepmc.org/articles/PMC10254692?pdf=render
 36581868,https://doi.org/10.1186/s12911-022-02045-8,"Effectiveness of clinical decision support in controlling inappropriate red blood cell and platelet transfusions, speciality specific responses and behavioural change.","Atia J, Evison F, Gallier S, Pettler S, Garrick M, Ball S, Lester W, Morton S, Coleman J, Pankhurst T.",,BMC medical informatics and decision making,2022,2022-12-29,Y,Red blood cells; Platelets; CdS; Transfusion; Clinical Decision Support; Haemoglobin; Electronic Health Records; Ehr; E-alerts; Segmented Linear Regression Of Interrupted Time Series,,,"<h4>Background</h4>Electronic clinical decision support (CDS) within Electronic Health Records has been used to improve patient safety, including reducing unnecessary blood product transfusions. We assessed the effectiveness of CDS in controlling inappropriate red blood cell (RBC) and platelet transfusion in a large acute hospital and how speciality specific behaviours changed in response.<h4>Methods</h4>We used segmented linear regression of interrupted time series models to analyse the instantaneous and long term effect of introducing blood product electronic warnings to prescribers. We studied the impact on transfusions for patients in critical care (CC), haematology/oncology (HO) and elsewhere.<h4>Results</h4>In non-CC or HO, there was significant and sustained decrease in the numbers of RBC transfusions after introduction of alerts. In CC the alerts reduced transfusions but this was not sustained, and in HO there was no impact on RBC transfusion. For platelet transfusions outside of CC and HO, the introduction of alerts stopped a rising trend of administration of platelets above recommended targets. In CC, alerts reduced platelet transfusions, but in HO alerts had little impact on clinician prescribing.<h4>Conclusion</h4>The findings suggest that CDS can result in immediate change in user behaviour which is more obvious outside specialist settings of CC and HO. It is important that this is then sustained. In CC and HO, blood transfusion practices differ. CDS thus needs to take specific circumstances into account. In this case there are acceptable reasons to transfuse outside of these crude targets and CDS should take these into account.",,pdf:https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-022-02045-8; doi:https://doi.org/10.1186/s12911-022-02045-8; html:https://europepmc.org/articles/PMC9798655; pdf:https://europepmc.org/articles/PMC9798655?pdf=render
-36918541,https://doi.org/10.1038/s41467-023-36997-w,Genetic architecture of spatial electrical biomarkers for cardiac arrhythmia and relationship with cardiovascular disease.,"Young WJ, Haessler J, Benjamins JW, Repetto L, Yao J, Isaacs A, Harper AR, Ramirez J, Garnier S, van Duijvenboden S, Baldassari AR, Concas MP, Duong T, Foco L, Isaksen JL, Mei H, Noordam R, Nursyifa C, Richmond A, Santolalla ML, Sitlani CM, Soroush N, Thériault S, Trompet S, Aeschbacher S, Ahmadizar F, Alonso A, Brody JA, Campbell A, Correa A, Darbar D, De Luca A, Deleuze JF, Ellervik C, Fuchsberger C, Goel A, Grace C, Guo X, Hansen T, Heckbert SR, Jackson RD, Kors JA, Lima-Costa MF, Linneberg A, Macfarlane PW, Morrison AC, Navarro P, Porteous DJ, Pramstaller PP, Reiner AP, Risch L, Schotten U, Shen X, Sinagra G, Soliman EZ, Stoll M, Tarazona-Santos E, Tinker A, Trajanoska K, Villard E, Warren HR, Whitsel EA, Wiggins KL, Arking DE, Avery CL, Conen D, Girotto G, Grarup N, Hayward C, Jukema JW, Mook-Kanamori DO, Olesen MS, Padmanabhan S, Psaty BM, Pattaro C, Ribeiro ALP, Rotter JI, Stricker BH, van der Harst P, van Duijn CM, Verweij N, Wilson JG, Orini M, Charron P, Watkins H, Kooperberg C, Lin HJ, Wilson JF, Kanters JK, Sotoodehnia N, Mifsud B, Lambiase PD, Tereshchenko LG, Munroe PB.",,Nature communications,2023,2023-03-14,Y,,,,"The 3-dimensional spatial and 2-dimensional frontal QRS-T angles are measures derived from the vectorcardiogram. They are independent risk predictors for arrhythmia, but the underlying biology is unknown. Using multi-ancestry genome-wide association studies we identify 61 (58 previously unreported) loci for the spatial QRS-T angle (N = 118,780) and 11 for the frontal QRS-T angle (N = 159,715). Seven out of the 61 spatial QRS-T angle loci have not been reported for other electrocardiographic measures. Enrichments are observed in pathways related to cardiac and vascular development, muscle contraction, and hypertrophy. Pairwise genome-wide association studies with classical ECG traits identify shared genetic influences with PR interval and QRS duration. Phenome-wide scanning indicate associations with atrial fibrillation, atrioventricular block and arterial embolism and genetically determined QRS-T angle measures are associated with fascicular and bundle branch block (and also atrioventricular block for the frontal QRS-T angle). We identify potential biology involved in the QRS-T angle and their genetic relationships with cardiovascular traits and diseases, may inform future research and risk prediction.",,pdf:https://www.nature.com/articles/s41467-023-36997-w.pdf; doi:https://doi.org/10.1038/s41467-023-36997-w; html:https://europepmc.org/articles/PMC10015012; pdf:https://europepmc.org/articles/PMC10015012?pdf=render
-34183745,https://doi.org/10.1038/s41598-021-92874-w,Frailty assessed by administrative tools and mortality in patients with pneumonia admitted to the hospital and ICU in Wales.,"Szakmany T, Hollinghurst J, Pugh R, Akbari A, Griffiths R, Bailey R, Lyons RA.",,Scientific reports,2021,2021-06-28,Y,,,,"The ideal method of identifying frailty is uncertain, and data on long-term outcomes is relatively limited. We examined frailty indices derived from population-scale linked data on Intensive Care Unit (ICU) and hospitalised non-ICU patients with pneumonia to elucidate the influence of frailty on mortality. Longitudinal cohort study between 2010-2018 using population-scale anonymised data linkage of healthcare records for adults admitted to hospital with pneumonia in Wales. Primary outcome was in-patient mortality. Odds Ratios (ORs [95% confidence interval]) for age, hospital frailty risk score (HFRS), electronic frailty index (eFI), Charlson comorbidity index (CCI), and social deprivation index were estimated using multivariate logistic regression models. The area under the receiver operating characteristic curve (AUC) was estimated to determine the best fitting models. Of the 107,188 patients, mean (SD) age was 72.6 (16.6) years, 50% were men. The models adjusted for the two frailty indices and the comorbidity index had an increased odds of in-patient mortality for individuals with an ICU admission (ORs for ICU admission in the eFI model 2.67 [2.55, 2.79], HFRS model 2.30 [2.20, 2.41], CCI model 2.62 [2.51, 2.75]). Models indicated advancing age, increased frailty and comorbidity were also associated with an increased odds of in-patient mortality (eFI, baseline fit, ORs: mild 1.09 [1.04, 1.13], moderate 1.13 [1.08, 1.18], severe 1.17 [1.10, 1.23]. HFRS, baseline low, ORs: intermediate 2.65 [2.55, 2.75], high 3.31 [3.17, 3.45]). CCI, baseline < 1, ORs: '1-10' 1.15 [1.11, 1.20], > 10 2.50 [2.41, 2.60]). For predicting inpatient deaths, the CCI and HFRS based models were similar, however for longer term outcomes the CCI based model was superior. Frailty and comorbidity are significant risk factors for patients admitted to hospital with pneumonia. Frailty and comorbidity scores based on administrative data have only moderate ability to predict outcome.",,pdf:https://www.nature.com/articles/s41598-021-92874-w.pdf; doi:https://doi.org/10.1038/s41598-021-92874-w; html:https://europepmc.org/articles/PMC8239046; pdf:https://europepmc.org/articles/PMC8239046?pdf=render
+37303488,https://doi.org/10.1136/bmjmed-2022-000392,"Changes in medication safety indicators in England throughout the covid-19 pandemic using OpenSAFELY: population based, retrospective cohort study of 57 million patients using federated analytics.","Fisher L, Hopcroft LE, Rodgers S, Barrett J, Oliver K, Avery AJ, Evans D, Curtis H, Croker R, Macdonald O, Morley J, Mehrkar A, Bacon S, Davy S, Dillingham I, Evans D, Hickman G, Inglesby P, Morton CE, Smith B, Ward T, Hulme W, Green A, Massey J, Walker AJ, Bates C, Cockburn J, Parry J, Hester F, Harper S, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Griffiths P, Fowles A, Parkes N, Goldacre B, MacKenna B.",,BMJ medicine,2023,2023-05-11,Y,Primary Health Care; Medical Informatics; Covid-19,,,"<h4>Objective</h4>To implement complex, PINCER (pharmacist led information technology intervention) prescribing indicators, on a national scale with general practice data to describe the impact of the covid-19 pandemic on safe prescribing.<h4>Design</h4>Population based, retrospective cohort study using federated analytics.<h4>Setting</h4>Electronic general practice health record data from 56.8 million NHS patients by use of the OpenSAFELY platform, with the approval of the National Health Service (NHS) England.<h4>Participants</h4>NHS patients (aged 18-120 years) who were alive and registered at a general practice that used TPP or EMIS computer systems and were recorded as at risk of at least one potentially hazardous PINCER indicator.<h4>Main outcome measure</h4>Between 1 September 2019 and 1 September 2021, monthly trends and between practice variation for compliance with 13 PINCER indicators, as calculated on the first of every month, were reported. Prescriptions that do not adhere to these indicators are potentially hazardous and can cause gastrointestinal bleeds; are cautioned against in specific conditions (specifically heart failure, asthma, and chronic renal failure); or require blood test monitoring. The percentage for each indicator is formed of a numerator of patients deemed to be at risk of a potentially hazardous prescribing event and the denominator is of patients for which assessment of the indicator is clinically meaningful. Higher indicator percentages represent potentially poorer performance on medication safety.<h4>Results</h4>The PINCER indicators were successfully implemented across general practice data for 56.8 million patient records from 6367 practices in OpenSAFELY. Hazardous prescribing remained largely unchanged during the covid-19 pandemic, with no evidence of increases in indicators of harm as captured by the PINCER indicators. The percentage of patients at risk of potentially hazardous prescribing, as defined by each PINCER indicator, at mean quarter 1 (Q1) 2020 (representing before the pandemic) ranged from 1.11% (age ≥65 years and non-steroidal anti-inflammatory drugs) to 36.20% (amiodarone and no thyroid function test), while Q1 2021 (representing after the pandemic) percentages ranged from 0.75% (age ≥65 years and non-steroidal anti-inflammatory drugs) to 39.23% (amiodarone and no thyroid function test). Transient delays occurred in blood test monitoring for some medications, particularly angiotensin-converting enzyme inhibitors (where blood monitoring worsened from a mean of 5.16% in Q1 2020 to 12.14% in Q1 2021, and began to recover in June 2021). All indicators substantially recovered by September 2021. We identified 1 813 058 patients (3.1%) at risk of at least one potentially hazardous prescribing event.<h4>Conclusion</h4>NHS data from general practices can be analysed at national scale to generate insights into service delivery. Potentially hazardous prescribing was largely unaffected by the covid-19 pandemic in primary care health records in England.",,pdf:https://bmjmedicine.bmj.com/content/bmjmed/2/1/e000392.full.pdf; doi:https://doi.org/10.1136/bmjmed-2022-000392; html:https://europepmc.org/articles/PMC10254692; pdf:https://europepmc.org/articles/PMC10254692?pdf=render
 39167370,https://doi.org/10.1001/jamapsychiatry.2024.2339,COVID-19 and Mental Illnesses in Vaccinated and Unvaccinated People.,"Walker VM, Patalay P, Cuitun Coronado JI, Denholm R, Forbes H, Stafford J, Moltrecht B, Palmer T, Walker A, Thompson EJ, Taylor K, Cezard G, Horne EMF, Wei Y, Al Arab M, Knight R, Fisher L, Massey J, Davy S, Mehrkar A, Bacon S, Goldacre B, Wood A, Chaturvedi N, Macleod J, John A, Sterne JAC, Longitudinal Health and Wellbeing COVID-19 National Core Study.",,JAMA psychiatry,2024,2024-08-21,Y,,,,"<h4>Importance</h4>Associations have been found between COVID-19 and subsequent mental illness in both hospital- and population-based studies. However, evidence regarding which mental illnesses are associated with COVID-19 by vaccination status in these populations is limited.<h4>Objective</h4>To determine which mental illnesses are associated with diagnosed COVID-19 by vaccination status in both hospitalized patients and the general population.<h4>Design, setting, and participants</h4>This study was conducted in 3 cohorts, 1 before vaccine availability followed during the wild-type/Alpha variant eras (January 2020-June 2021) and 2 (vaccinated and unvaccinated) during the Delta variant era (June-December 2021). With National Health Service England approval, OpenSAFELY-TPP was used to access linked data from 24 million people registered with general practices in England using TPP SystmOne. People registered with a GP in England for at least 6 months and alive with known age between 18 and 110 years, sex, deprivation index information, and region at baseline were included. People were excluded if they had COVID-19 before baseline. Data were analyzed from July 2022 to June 2024.<h4>Exposure</h4>Confirmed COVID-19 diagnosis recorded in primary care secondary care, testing data, or the death registry.<h4>Main outcomes and measures</h4>Adjusted hazard ratios (aHRs) comparing the incidence of mental illnesses after diagnosis of COVID-19 with the incidence before or without COVID-19 for depression, serious mental illness, general anxiety, posttraumatic stress disorder, eating disorders, addiction, self-harm, and suicide.<h4>Results</h4>The largest cohort, the pre-vaccine availability cohort, included 18 648 606 people (9 363 710 [50.2%] female and 9 284 896 [49.8%] male) with a median (IQR) age of 49 (34-64) years. The vaccinated cohort included 14 035 286 individuals (7 308 556 [52.1%] female and 6 726 730 [47.9%] male) with a median (IQR) age of 53 (38-67) years. The unvaccinated cohort included 3 242 215 individuals (1 363 401 [42.1%] female and 1 878 814 [57.9%] male) with a median (IQR) age of 35 (27-46) years. Incidence of most outcomes was elevated during weeks 1 through 4 after COVID-19 diagnosis, compared with before or without COVID-19, in each cohort. Incidence of mental illnesses was lower in the vaccinated cohort compared with the pre-vaccine availability and unvaccinated cohorts: aHRs for depression and serious mental illness during weeks 1 through 4 after COVID-19 were 1.93 (95% CI, 1.88-1.98) and 1.49 (95% CI, 1.41-1.57) in the pre-vaccine availability cohort and 1.79 (95% CI, 1.68-1.90) and 1.45 (95% CI, 1.27-1.65) in the unvaccinated cohort compared with 1.16 (95% CI, 1.12-1.20) and 0.91 (95% CI, 0.85-0.98) in the vaccinated cohort. Elevation in incidence was higher and persisted longer after hospitalization for COVID-19.<h4>Conclusions and relevance</h4>In this study, incidence of mental illnesses was elevated for up to a year following severe COVID-19 in unvaccinated people. These findings suggest that vaccination may mitigate the adverse effects of COVID-19 on mental health.",,doi:https://doi.org/10.1001/jamapsychiatry.2024.2339; html:https://europepmc.org/articles/PMC11339697
-35255492,https://doi.org/10.1038/s41586-022-04576-6,Whole-genome sequencing reveals host factors underlying critical COVID-19.,"Kousathanas A, Pairo-Castineira E, Rawlik K, Stuckey A, Odhams CA, Walker S, Russell CD, Malinauskas T, Wu Y, Millar J, Shen X, Elliott KS, Griffiths F, Oosthuyzen W, Morrice K, Keating S, Wang B, Rhodes D, Klaric L, Zechner M, Parkinson N, Siddiq A, Goddard P, Donovan S, Maslove D, Nichol A, Semple MG, Zainy T, Maleady-Crowe F, Todd L, Salehi S, Knight J, Elgar G, Chan G, Arumugam P, Patch C, Rendon A, Bentley D, Kingsley C, Kosmicki JA, Horowitz JE, Baras A, Abecasis GR, Ferreira MAR, Justice A, Mirshahi T, Oetjens M, Rader DJ, Ritchie MD, Verma A, Fowler TA, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Elliott P, Walsh T, Tenesa A, GenOMICC investigators, 23andMe investigators, COVID-19 Human Genetics Initiative, Fawkes A, Murphy L, Rowan K, Ponting CP, Vitart V, Wilson JF, Yang J, Bretherick AD, Scott RH, Hendry SC, Moutsianas L, Law A, Caulfield MJ, Baillie JK.",,Nature,2022,2022-03-07,Y,,,,"Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care<sup>1</sup> or hospitalization<sup>2-4</sup> after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.",,pdf:https://www.nature.com/articles/s41586-022-04576-6.pdf; doi:https://doi.org/10.1038/s41586-022-04576-6; html:https://europepmc.org/articles/PMC9259496; pdf:https://europepmc.org/articles/PMC9259496?pdf=render
-36609574,https://doi.org/10.1038/s41467-022-35771-8,A population-based matched cohort study of major congenital anomalies following COVID-19 vaccination and SARS-CoV-2 infection.,"Calvert C, Carruthers J, Denny C, Donaghy J, Hopcroft LEM, Hopkins L, Goulding A, Lindsay L, McLaughlin T, Moore E, Taylor B, Loane M, Dolk H, Morris J, Auyeung B, Bhaskaran K, Gibbons CL, Katikireddi SV, O'Leary M, McAllister D, Shi T, Simpson CR, Robertson C, Sheikh A, Stock SJ, Wood R.",,Nature communications,2023,2023-01-06,Y,,,,"Evidence on associations between COVID-19 vaccination or SARS-CoV-2 infection and the risk of congenital anomalies is limited. Here we report a national, population-based, matched cohort study using linked electronic health records from Scotland (May 2020-April 2022) to estimate the association between COVID-19 vaccination and, separately, SARS-CoV-2 infection between six weeks pre-conception and 19 weeks and six days gestation and the risk of [1] any major congenital anomaly and [2] any non-genetic major congenital anomaly. Mothers vaccinated in this pregnancy exposure period mostly received an mRNA vaccine (73.7% Pfizer-BioNTech BNT162b2 and 7.9% Moderna mRNA-1273). Of the 6731 babies whose mothers were vaccinated in the pregnancy exposure period, 153 had any anomaly and 120 had a non-genetic anomaly. Primary analyses find no association between any vaccination and any anomaly (adjusted Odds Ratio [aOR] = 1.01, 95% Confidence Interval [CI] = 0.83-1.24) or non-genetic anomalies (aOR = 1.00, 95% CI = 0.81-1.22). Primary analyses also find no association between SARS-CoV-2 infection and any anomaly (aOR = 1.02, 95% CI = 0.66-1.60) or non-genetic anomalies (aOR = 0.94, 95% CI = 0.57-1.54). Findings are robust to sensitivity analyses. These data provide reassurance on the safety of vaccination, in particular mRNA vaccines, just before or in early pregnancy.",,pdf:https://www.nature.com/articles/s41467-022-35771-8.pdf; doi:https://doi.org/10.1038/s41467-022-35771-8; html:https://europepmc.org/articles/PMC9821346; pdf:https://europepmc.org/articles/PMC9821346?pdf=render
+34183745,https://doi.org/10.1038/s41598-021-92874-w,Frailty assessed by administrative tools and mortality in patients with pneumonia admitted to the hospital and ICU in Wales.,"Szakmany T, Hollinghurst J, Pugh R, Akbari A, Griffiths R, Bailey R, Lyons RA.",,Scientific reports,2021,2021-06-28,Y,,,,"The ideal method of identifying frailty is uncertain, and data on long-term outcomes is relatively limited. We examined frailty indices derived from population-scale linked data on Intensive Care Unit (ICU) and hospitalised non-ICU patients with pneumonia to elucidate the influence of frailty on mortality. Longitudinal cohort study between 2010-2018 using population-scale anonymised data linkage of healthcare records for adults admitted to hospital with pneumonia in Wales. Primary outcome was in-patient mortality. Odds Ratios (ORs [95% confidence interval]) for age, hospital frailty risk score (HFRS), electronic frailty index (eFI), Charlson comorbidity index (CCI), and social deprivation index were estimated using multivariate logistic regression models. The area under the receiver operating characteristic curve (AUC) was estimated to determine the best fitting models. Of the 107,188 patients, mean (SD) age was 72.6 (16.6) years, 50% were men. The models adjusted for the two frailty indices and the comorbidity index had an increased odds of in-patient mortality for individuals with an ICU admission (ORs for ICU admission in the eFI model 2.67 [2.55, 2.79], HFRS model 2.30 [2.20, 2.41], CCI model 2.62 [2.51, 2.75]). Models indicated advancing age, increased frailty and comorbidity were also associated with an increased odds of in-patient mortality (eFI, baseline fit, ORs: mild 1.09 [1.04, 1.13], moderate 1.13 [1.08, 1.18], severe 1.17 [1.10, 1.23]. HFRS, baseline low, ORs: intermediate 2.65 [2.55, 2.75], high 3.31 [3.17, 3.45]). CCI, baseline < 1, ORs: '1-10' 1.15 [1.11, 1.20], > 10 2.50 [2.41, 2.60]). For predicting inpatient deaths, the CCI and HFRS based models were similar, however for longer term outcomes the CCI based model was superior. Frailty and comorbidity are significant risk factors for patients admitted to hospital with pneumonia. Frailty and comorbidity scores based on administrative data have only moderate ability to predict outcome.",,pdf:https://www.nature.com/articles/s41598-021-92874-w.pdf; doi:https://doi.org/10.1038/s41598-021-92874-w; html:https://europepmc.org/articles/PMC8239046; pdf:https://europepmc.org/articles/PMC8239046?pdf=render
 38332132,https://doi.org/10.1038/s41467-024-45445-2,Disease clusters subsequent to anxiety and stress-related disorders and their genetic determinants.,"Han X, Shen Q, Hou C, Yang H, Chen W, Zeng Y, Qu Y, Suo C, Ye W, Fang F, Valdimarsdóttir UA, Song H.",,Nature communications,2024,2024-02-08,Y,,,,"Anxiety/stress-related disorders have been associated with multiple diseases, whereas a comprehensive assessment of the structure and interplay of subsequent associated diseases and their genetic underpinnings is lacking. Here, we first identify 136, out of 454 tested, medical conditions associated with incident anxiety/stress-related disorders attended in specialized care using a population-based cohort from the nationwide Swedish Patient Register, comprising 70,026 patients with anxiety/stress-related disorders and 1:10 birth year- and sex-matched unaffected individuals. By combining findings from the comorbidity network and disease trajectory analyses, we identify five robust disease clusters to be associated with a prior diagnosis of anxiety/stress-related disorders, featured by predominance of psychiatric disorders, eye diseases, ear diseases, cardiovascular diseases, and skin and genitourinary diseases. These five clusters and their featured diseases are largely validated in the UK Biobank. GWAS analyses based on the UK Biobank identify 3, 33, 40, 4, and 16 significantly independent single nucleotide polymorphisms for the link to the five disease clusters, respectively, which are mapped to several distinct risk genes and biological pathways. These findings motivate further mechanistic explorations and aid early risk assessment for cluster-based disease prevention among patients with newly diagnosed anxiety/stress-related disorders in specialized care.",,pdf:https://www.nature.com/articles/s41467-024-45445-2.pdf; doi:https://doi.org/10.1038/s41467-024-45445-2; html:https://europepmc.org/articles/PMC10853285; pdf:https://europepmc.org/articles/PMC10853285?pdf=render
 38703040,https://doi.org/10.1093/ije/dyae065,"Data Resource Profile: A national linked mother-baby cohort of health, education and social care data in England (ECHILD-MB).","Feng Q, Ireland G, Gilbert R, Harron K.",,International journal of epidemiology,2024,2024-04-01,Y,Data Linkage; Hospital Episode Statistics; Intergenerational Effects; Mother-baby Cohort; National Pupil Database,,,,,pdf:https://academic.oup.com/ije/article-pdf/53/3/dyae065/57401370/dyae065.pdf; doi:https://doi.org/10.1093/ije/dyae065; html:https://europepmc.org/articles/PMC11069107; pdf:https://europepmc.org/articles/PMC11069107?pdf=render
 38036541,https://doi.org/10.1038/s41467-023-43661-w,"True prevalence of long-COVID in a nationwide, population cohort study.","Hastie CE, Lowe DJ, McAuley A, Mills NL, Winter AJ, Black C, Scott JT, O'Donnell CA, Blane DN, Browne S, Ibbotson TR, Pell JP.",,Nature communications,2023,2023-11-30,Y,,,,"Long-COVID prevalence estimates vary widely and should take account of symptoms that would have occurred anyway. Here we determine the prevalence of symptoms attributable to SARS-CoV-2 infection, taking account of background rates and confounding, in a nationwide population cohort study of 198,096 Scottish adults. 98,666 (49.8%) had symptomatic laboratory-confirmed SARS-CoV-2 infections and 99,430 (50.2%) were age-, sex-, and socioeconomically-matched and never-infected. While 41,775 (64.5%) reported at least one symptom 6 months following SARS-CoV-2 infection, this was also true of 34,600 (50.8%) of those never-infected. The crude prevalence of one or more symptom attributable to SARS-CoV-2 infection was 13.8% (13.2%,14.3%), 12.8% (11.9%,13.6%), and 16.3% (14.4%,18.2%) at 6, 12, and 18 months respectively. Following adjustment for potential confounders, these figures were 6.6% (6.3%, 6.9%), 6.5% (6.0%, 6.9%) and 10.4% (9.1%, 11.6%) respectively. Long-COVID is characterised by a wide range of symptoms that, apart from altered taste and smell, are non-specific. Care should be taken in attributing symptoms to previous SARS-CoV-2 infection.",,pdf:https://www.nature.com/articles/s41467-023-43661-w.pdf; doi:https://doi.org/10.1038/s41467-023-43661-w; html:https://europepmc.org/articles/PMC10689486; pdf:https://europepmc.org/articles/PMC10689486?pdf=render
+36609574,https://doi.org/10.1038/s41467-022-35771-8,A population-based matched cohort study of major congenital anomalies following COVID-19 vaccination and SARS-CoV-2 infection.,"Calvert C, Carruthers J, Denny C, Donaghy J, Hopcroft LEM, Hopkins L, Goulding A, Lindsay L, McLaughlin T, Moore E, Taylor B, Loane M, Dolk H, Morris J, Auyeung B, Bhaskaran K, Gibbons CL, Katikireddi SV, O'Leary M, McAllister D, Shi T, Simpson CR, Robertson C, Sheikh A, Stock SJ, Wood R.",,Nature communications,2023,2023-01-06,Y,,,,"Evidence on associations between COVID-19 vaccination or SARS-CoV-2 infection and the risk of congenital anomalies is limited. Here we report a national, population-based, matched cohort study using linked electronic health records from Scotland (May 2020-April 2022) to estimate the association between COVID-19 vaccination and, separately, SARS-CoV-2 infection between six weeks pre-conception and 19 weeks and six days gestation and the risk of [1] any major congenital anomaly and [2] any non-genetic major congenital anomaly. Mothers vaccinated in this pregnancy exposure period mostly received an mRNA vaccine (73.7% Pfizer-BioNTech BNT162b2 and 7.9% Moderna mRNA-1273). Of the 6731 babies whose mothers were vaccinated in the pregnancy exposure period, 153 had any anomaly and 120 had a non-genetic anomaly. Primary analyses find no association between any vaccination and any anomaly (adjusted Odds Ratio [aOR] = 1.01, 95% Confidence Interval [CI] = 0.83-1.24) or non-genetic anomalies (aOR = 1.00, 95% CI = 0.81-1.22). Primary analyses also find no association between SARS-CoV-2 infection and any anomaly (aOR = 1.02, 95% CI = 0.66-1.60) or non-genetic anomalies (aOR = 0.94, 95% CI = 0.57-1.54). Findings are robust to sensitivity analyses. These data provide reassurance on the safety of vaccination, in particular mRNA vaccines, just before or in early pregnancy.",,pdf:https://www.nature.com/articles/s41467-022-35771-8.pdf; doi:https://doi.org/10.1038/s41467-022-35771-8; html:https://europepmc.org/articles/PMC9821346; pdf:https://europepmc.org/articles/PMC9821346?pdf=render
+35255492,https://doi.org/10.1038/s41586-022-04576-6,Whole-genome sequencing reveals host factors underlying critical COVID-19.,"Kousathanas A, Pairo-Castineira E, Rawlik K, Stuckey A, Odhams CA, Walker S, Russell CD, Malinauskas T, Wu Y, Millar J, Shen X, Elliott KS, Griffiths F, Oosthuyzen W, Morrice K, Keating S, Wang B, Rhodes D, Klaric L, Zechner M, Parkinson N, Siddiq A, Goddard P, Donovan S, Maslove D, Nichol A, Semple MG, Zainy T, Maleady-Crowe F, Todd L, Salehi S, Knight J, Elgar G, Chan G, Arumugam P, Patch C, Rendon A, Bentley D, Kingsley C, Kosmicki JA, Horowitz JE, Baras A, Abecasis GR, Ferreira MAR, Justice A, Mirshahi T, Oetjens M, Rader DJ, Ritchie MD, Verma A, Fowler TA, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Elliott P, Walsh T, Tenesa A, GenOMICC investigators, 23andMe investigators, COVID-19 Human Genetics Initiative, Fawkes A, Murphy L, Rowan K, Ponting CP, Vitart V, Wilson JF, Yang J, Bretherick AD, Scott RH, Hendry SC, Moutsianas L, Law A, Caulfield MJ, Baillie JK.",,Nature,2022,2022-03-07,Y,,,,"Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care<sup>1</sup> or hospitalization<sup>2-4</sup> after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.",,pdf:https://www.nature.com/articles/s41586-022-04576-6.pdf; doi:https://doi.org/10.1038/s41586-022-04576-6; html:https://europepmc.org/articles/PMC9259496; pdf:https://europepmc.org/articles/PMC9259496?pdf=render
 35077449,https://doi.org/10.1371/journal.pmed.1003871,"Overall and cause-specific hospitalisation and death after COVID-19 hospitalisation in England: A cohort study using linked primary care, secondary care, and death registration data in the OpenSAFELY platform.","Bhaskaran K, Rentsch CT, Hickman G, Hulme WJ, Schultze A, Curtis HJ, Wing K, Warren-Gash C, Tomlinson L, Bates CJ, Mathur R, MacKenna B, Mahalingasivam V, Wong A, Walker AJ, Morton CE, Grint D, Mehrkar A, Eggo RM, Inglesby P, Douglas IJ, McDonald HI, Cockburn J, Williamson EJ, Evans D, Parry J, Hester F, Harper S, Evans SJ, Bacon S, Smeeth L, Goldacre B.",,PLoS medicine,2022,2022-01-25,Y,,,,"<h4>Background</h4>There is concern about medium to long-term adverse outcomes following acute Coronavirus Disease 2019 (COVID-19), but little relevant evidence exists. We aimed to investigate whether risks of hospital admission and death, overall and by specific cause, are raised following discharge from a COVID-19 hospitalisation.<h4>Methods and findings</h4>With the approval of NHS-England, we conducted a cohort study, using linked primary care and hospital data in OpenSAFELY to compare risks of hospital admission and death, overall and by specific cause, between people discharged from COVID-19 hospitalisation (February to December 2020) and surviving at least 1 week, and (i) demographically matched controls from the 2019 general population; and (ii) people discharged from influenza hospitalisation in 2017 to 2019. We used Cox regression adjusted for age, sex, ethnicity, obesity, smoking status, deprivation, and comorbidities considered potential risk factors for severe COVID-19 outcomes. We included 24,673 postdischarge COVID-19 patients, 123,362 general population controls, and 16,058 influenza controls, followed for ≤315 days. COVID-19 patients had median age of 66 years, 13,733 (56%) were male, and 19,061 (77%) were of white ethnicity. Overall risk of hospitalisation or death (30,968 events) was higher in the COVID-19 group than general population controls (fully adjusted hazard ratio [aHR] 2.22, 2.14 to 2.30, p < 0.001) but slightly lower than the influenza group (aHR 0.95, 0.91 to 0.98, p = 0.004). All-cause mortality (7,439 events) was highest in the COVID-19 group (aHR 4.82, 4.48 to 5.19 versus general population controls [p < 0.001] and 1.74, 1.61 to 1.88 versus influenza controls [p < 0.001]). Risks for cause-specific outcomes were higher in COVID-19 survivors than in general population controls and largely similar or lower in COVID-19 compared with influenza patients. However, COVID-19 patients were more likely than influenza patients to be readmitted or die due to their initial infection or other lower respiratory tract infection (aHR 1.37, 1.22 to 1.54, p < 0.001) and to experience mental health or cognitive-related admission or death (aHR 1.37, 1.02 to 1.84, p = 0.039); in particular, COVID-19 survivors with preexisting dementia had higher risk of dementia hospitalisation or death (age- and sex-adjusted HR 2.47, 1.37 to 4.44, p = 0.002). Limitations of our study were that reasons for hospitalisation or death may have been misclassified in some cases due to inconsistent use of codes, and we did not have data to distinguish COVID-19 variants.<h4>Conclusions</h4>In this study, we observed that people discharged from a COVID-19 hospital admission had markedly higher risks for rehospitalisation and death than the general population, suggesting a substantial extra burden on healthcare. Most risks were similar to those observed after influenza hospitalisations, but COVID-19 patients had higher risks of all-cause mortality, readmission or death due to the initial infection, and dementia death, highlighting the importance of postdischarge monitoring.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003871&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003871; html:https://europepmc.org/articles/PMC8789178; pdf:https://europepmc.org/articles/PMC8789178?pdf=render
 34082729,https://doi.org/10.1186/s12911-021-01533-7,A systematic review of natural language processing applied to radiology reports.,"Casey A, Davidson E, Poon M, Dong H, Duma D, Grivas A, Grover C, Suárez-Paniagua V, Tobin R, Whiteley W, Wu H, Alex B.",,BMC medical informatics and decision making,2021,2021-06-03,Y,Systematic review; Radiology; Natural Language Processing,,,"<h4>Background</h4>Natural language processing (NLP) has a significant role in advancing healthcare and has been found to be key in extracting structured information from radiology reports. Understanding recent developments in NLP application to radiology is of significance but recent reviews on this are limited. This study systematically assesses and quantifies recent literature in NLP applied to radiology reports.<h4>Methods</h4>We conduct an automated literature search yielding 4836 results using automated filtering, metadata enriching steps and citation search combined with manual review. Our analysis is based on 21 variables including radiology characteristics, NLP methodology, performance, study, and clinical application characteristics.<h4>Results</h4>We present a comprehensive analysis of the 164 publications retrieved with publications in 2019 almost triple those in 2015. Each publication is categorised into one of 6 clinical application categories. Deep learning use increases in the period but conventional machine learning approaches are still prevalent. Deep learning remains challenged when data is scarce and there is little evidence of adoption into clinical practice. Despite 17% of studies reporting greater than 0.85 F1 scores, it is hard to comparatively evaluate these approaches given that most of them use different datasets. Only 14 studies made their data and 15 their code available with 10 externally validating results.<h4>Conclusions</h4>Automated understanding of clinical narratives of the radiology reports has the potential to enhance the healthcare process and we show that research in this field continues to grow. Reproducibility and explainability of models are important if the domain is to move applications into clinical use. More could be done to share code enabling validation of methods on different institutional data and to reduce heterogeneity in reporting of study properties allowing inter-study comparisons. Our results have significance for researchers in the field providing a systematic synthesis of existing work to build on, identify gaps, opportunities for collaboration and avoid duplication.",,pdf:https://bmcmedinformdecismak.biomedcentral.com/track/pdf/10.1186/s12911-021-01533-7; doi:https://doi.org/10.1186/s12911-021-01533-7; html:https://europepmc.org/articles/PMC8176715; pdf:https://europepmc.org/articles/PMC8176715?pdf=render
 35140406,https://doi.org/10.1038/s41591-022-01701-w,Vaccine effectiveness of heterologous CoronaVac plus BNT162b2 in Brazil.,"Cerqueira-Silva T, Katikireddi SV, de Araujo Oliveira V, Flores-Ortiz R, Júnior JB, Paixão ES, Robertson C, Penna GO, Werneck GL, Barreto ML, Pearce N, Sheikh A, Barral-Netto M, Boaventura VS.",,Nature medicine,2022,2022-02-09,Y,,,,"There is considerable interest in the waning of effectiveness of coronavirus disease 2019 (COVID-19) vaccines and vaccine effectiveness (VE) of booster doses. Using linked national Brazilian databases, we undertook a test-negative design study involving almost 14 million people (~16 million tests) to estimate VE of CoronaVac over time and VE of BNT162b2 booster vaccination against RT-PCR-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and severe COVID-19 outcomes (hospitalization or death). Compared with unvaccinated individuals, CoronaVac VE at 14-30 d after the second dose was 55.0% (95% confidence interval (CI): 54.3-55.7) against confirmed infection and 82.1% (95% CI: 81.4-82.8) against severe outcomes. VE decreased to 34.7% (95% CI: 33.1-36.2) against infection and 72.5% (95% CI: 70.9-74.0) against severe outcomes over 180 d after the second dose. A BNT162b2 booster, 6 months after the second dose of CoronaVac, improved VE against infection to 92.7% (95% CI: 91.0-94.0) and VE against severe outcomes to 97.3% (95% CI: 96.1-98.1) 14-30 d after the booster. Compared with younger age groups, individuals 80 years of age or older had lower protection after the second dose but similar protection after the booster. Our findings support a BNT162b2 booster vaccine dose after two doses of CoronaVac, particularly for the elderly.",,pdf:https://www.nature.com/articles/s41591-022-01701-w.pdf; doi:https://doi.org/10.1038/s41591-022-01701-w; html:https://europepmc.org/articles/PMC9018414; pdf:https://europepmc.org/articles/PMC9018414?pdf=render
 32300742,https://doi.org/10.1016/j.eclinm.2020.100296,Violence-related knife injuries in a UK city; epidemiology and impact on secondary care resources.,"Malik NS, Munoz B, de Courcey C, Imran R, Lee KC, Chernbumroong S, Bishop J, Lord JM, Gkoutos G, Bowley DM, Foster MA.",,EClinicalMedicine,2020,2020-03-03,Y,,,,"<h4>Background</h4>The incidence of knife-related injuries is rising across the UK. This study aimed to determine the spectrum of knife-related injuries in a major UK city, with regards to patient and injury characteristics. A secondary aim was to quantify their impact on secondary care resources.<h4>Methods</h4>Observational study of patients aged 16+ years admitted to a major trauma centre following knife-related injuries resulting from interpersonal violence (May 2015 to April 2018). Patients were identified using Emergency Department and discharge coding, blood bank and UK national Trauma Audit and Research prospective registries. Patient and injury characteristics, outcome and resource utilisation were collected from ambulance and hospital records.<h4>Findings</h4>532 patients were identified; 93% male, median age 26 years (IQR 20-35). Median injury severity score was 9 (IQR 3-13). 346 (65%) underwent surgery; 133 (25%) required intensive care; 95 (17·9%) received blood transfusion. Median length of stay was 3·3 days (IQR 1·7-6·0). In-hospital mortality was 10/532 (1·9%). 98 patients (18·5%) had previous attendance with violence-related injuries. 24/37 females (64·9%) were injured in a domestic setting. Intoxication with alcohol (19·2%) and illicit drugs (17·6%) was common. Causative weapon was household knife in 9%, knife (other/unspecified) in 38·0%, machete in 13·9%, small folding blade (2·8%) and, unrecorded in 36·3%.<h4>Interpretation</h4>Knife injuries constitute 12·9% of trauma team workload. Violence recidivism and intoxication are common, and females are predominantly injured in a domestic setting, presenting opportunities for targeted violence reduction interventions. 13·9% of injuries involved machetes, with implications for law enforcement strategies.",,pdf:http://www.thelancet.com/article/S2589537020300407/pdf; doi:https://doi.org/10.1016/j.eclinm.2020.100296; html:https://europepmc.org/articles/PMC7152819; pdf:https://europepmc.org/articles/PMC7152819?pdf=render
-35340900,https://doi.org/10.1177/20552076221074122,Magnetic resonance image-based brain tumour segmentation methods: A systematic review.,"Bhalodiya JM, Lim Choi Keung SN, Arvanitis TN.",,Digital health,2022,2022-01-01,Y,Brain; Artificial intelligence; Segmentation; Systematic review; Magnetic Resonance Imaging; Brain Tumour,,,"<h4>Background</h4>Image segmentation is an essential step in the analysis and subsequent characterisation of brain tumours through magnetic resonance imaging. In the literature, segmentation methods are empowered by open-access magnetic resonance imaging datasets, such as the brain tumour segmentation dataset. Moreover, with the increased use of artificial intelligence methods in medical imaging, access to larger data repositories has become vital in method development.<h4>Purpose</h4>To determine what automated brain tumour segmentation techniques can medical imaging specialists and clinicians use to identify tumour components, compared to manual segmentation.<h4>Methods</h4>We conducted a systematic review of 572 brain tumour segmentation studies during 2015-2020. We reviewed segmentation techniques using T1-weighted, T2-weighted, gadolinium-enhanced T1-weighted, fluid-attenuated inversion recovery, diffusion-weighted and perfusion-weighted magnetic resonance imaging sequences. Moreover, we assessed physics or mathematics-based methods, deep learning methods, and software-based or semi-automatic methods, as applied to magnetic resonance imaging techniques. Particularly, we synthesised each method as per the utilised magnetic resonance imaging sequences, study population, technical approach (such as deep learning) and performance score measures (such as Dice score).<h4>Statistical tests</h4>We compared median Dice score in segmenting the whole tumour, tumour core and enhanced tumour.<h4>Results</h4>We found that T1-weighted, gadolinium-enhanced T1-weighted, T2-weighted and fluid-attenuated inversion recovery magnetic resonance imaging are used the most in various segmentation algorithms. However, there is limited use of perfusion-weighted and diffusion-weighted magnetic resonance imaging. Moreover, we found that the U-Net deep learning technology is cited the most, and has high accuracy (Dice score 0.9) for magnetic resonance imaging-based brain tumour segmentation.<h4>Conclusion</h4>U-Net is a promising deep learning technology for magnetic resonance imaging-based brain tumour segmentation. The community should be encouraged to contribute open-access datasets so training, testing and validation of deep learning algorithms can be improved, particularly for diffusion- and perfusion-weighted magnetic resonance imaging, where there are limited datasets available.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/20552076221074122; doi:https://doi.org/10.1177/20552076221074122; html:https://europepmc.org/articles/PMC8943308; pdf:https://europepmc.org/articles/PMC8943308?pdf=render
 34384736,https://doi.org/10.1016/s2589-7500(21)00175-8,"Predicted COVID-19 positive cases, hospitalisations, and deaths associated with the Delta variant of concern, June-July, 2021.","Shah SA, Moore E, Robertson C, McMenamin J, Katikireddi SV, Simpson CR, Shi T, Agrawal U, McCowan C, Stock S, Ritchie LD, Sheikh A, Public Health Scotland and the EAVE II Collaborators.",,The Lancet. Digital health,2021,2021-08-09,Y,,,,,,pdf:https://aura.abdn.ac.uk/bitstream/2164/21105/1/Shah_etal_Predicted_Covid_19_Positive_VOR.pdf; doi:https://doi.org/10.1016/S2589-7500(21)00175-8; html:https://europepmc.org/articles/PMC8352493; pdf:https://europepmc.org/articles/PMC8352493?pdf=render
-36874571,https://doi.org/10.12688/wellcomeopenres.17981.1,Settings for non-household transmission of SARS-CoV-2 during the second lockdown in England and Wales - analysis of the Virus Watch household community cohort study.,"Hoskins S, Beale S, Nguyen V, Fragaszy E, Navaratnam AMD, Smith C, French C, Kovar J, Byrne T, Fong WLE, Geismar C, Patel P, Yavlinksy A, Johnson AM, Aldridge RW, Hayward A, Virus Watch Collaborative.",,Wellcome open research,2022,2022-08-03,Y,Transmission; Activities; Pandemic; Work; Public Transport; Shopping; Lockdown; Covid-19; Sars-cov-2,,,"<b>Background</b>: ""Lockdowns"" to control serious respiratory virus pandemics were widely used during the coronavirus disease 2019 (COVID-19) pandemic.  However, there is limited information to understand the settings in which most transmission occurs during lockdowns, to support refinement of similar policies for future pandemics.  <b>Methods</b>: Among Virus Watch household cohort participants we identified those infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outside the household.  Using survey activity data, we undertook multivariable logistic regressions assessing the contribution of activities on non-household infection risk.  We calculated adjusted population attributable fractions (APAF) to estimate which activity accounted for the greatest proportion of non-household infections during the pandemic's second wave. <b>Results</b>: Among 10,858 adults, 18% of cases were likely due to household transmission.  Among 10,475 participants (household-acquired cases excluded), including 874 non-household-acquired infections, infection was associated with: leaving home for work or education (AOR 1.20 (1.02 - 1.42), APAF 6.9%); public transport (more than once per week AOR 1.82 (1.49 - 2.23), public transport APAF 12.42%); and shopping (more than once per week AOR 1.69 (1.29 - 2.21), shopping APAF 34.56%).  Other non-household activities were rare and not significantly associated with infection. <b>Conclusions:</b> During lockdown, going to work and using public or shared transport independently increased infection risk, however only a minority did these activities.  Most participants visited shops, accounting for one-third of non-household transmission.  Transmission in restricted hospitality and leisure settings was minimal suggesting these restrictions were effective.   If future respiratory infection pandemics emerge these findings highlight the value of working from home, using forms of transport that minimise exposure to others, minimising exposure to shops and restricting non-essential activities.",,doi:https://doi.org/10.12688/wellcomeopenres.17981.1; html:https://europepmc.org/articles/PMC9975411; pdf:https://europepmc.org/articles/PMC9975411?pdf=render
+35340900,https://doi.org/10.1177/20552076221074122,Magnetic resonance image-based brain tumour segmentation methods: A systematic review.,"Bhalodiya JM, Lim Choi Keung SN, Arvanitis TN.",,Digital health,2022,2022-01-01,Y,Brain; Artificial intelligence; Segmentation; Systematic review; Magnetic Resonance Imaging; Brain Tumour,,,"<h4>Background</h4>Image segmentation is an essential step in the analysis and subsequent characterisation of brain tumours through magnetic resonance imaging. In the literature, segmentation methods are empowered by open-access magnetic resonance imaging datasets, such as the brain tumour segmentation dataset. Moreover, with the increased use of artificial intelligence methods in medical imaging, access to larger data repositories has become vital in method development.<h4>Purpose</h4>To determine what automated brain tumour segmentation techniques can medical imaging specialists and clinicians use to identify tumour components, compared to manual segmentation.<h4>Methods</h4>We conducted a systematic review of 572 brain tumour segmentation studies during 2015-2020. We reviewed segmentation techniques using T1-weighted, T2-weighted, gadolinium-enhanced T1-weighted, fluid-attenuated inversion recovery, diffusion-weighted and perfusion-weighted magnetic resonance imaging sequences. Moreover, we assessed physics or mathematics-based methods, deep learning methods, and software-based or semi-automatic methods, as applied to magnetic resonance imaging techniques. Particularly, we synthesised each method as per the utilised magnetic resonance imaging sequences, study population, technical approach (such as deep learning) and performance score measures (such as Dice score).<h4>Statistical tests</h4>We compared median Dice score in segmenting the whole tumour, tumour core and enhanced tumour.<h4>Results</h4>We found that T1-weighted, gadolinium-enhanced T1-weighted, T2-weighted and fluid-attenuated inversion recovery magnetic resonance imaging are used the most in various segmentation algorithms. However, there is limited use of perfusion-weighted and diffusion-weighted magnetic resonance imaging. Moreover, we found that the U-Net deep learning technology is cited the most, and has high accuracy (Dice score 0.9) for magnetic resonance imaging-based brain tumour segmentation.<h4>Conclusion</h4>U-Net is a promising deep learning technology for magnetic resonance imaging-based brain tumour segmentation. The community should be encouraged to contribute open-access datasets so training, testing and validation of deep learning algorithms can be improved, particularly for diffusion- and perfusion-weighted magnetic resonance imaging, where there are limited datasets available.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/20552076221074122; doi:https://doi.org/10.1177/20552076221074122; html:https://europepmc.org/articles/PMC8943308; pdf:https://europepmc.org/articles/PMC8943308?pdf=render
 34605164,https://doi.org/10.1002/mnfr.202100316,Odd Chain Fatty Acids Are Not Robust Biomarkers for Dietary Intake of Fiber.,"Wu Y, Posma JM, Holmes E, Frost G, Chambers ES, Garcia-Perez I.",,Molecular nutrition & food research,2021,2021-10-22,Y,dietary fiber; Short Chain Fatty Acids; Biomarker Validation; Dietary Biomarker; Odd Chain Fatty Acids,,,"<h4>Scope</h4>Prior investigation has suggested a positive association between increased colonic propionate production and circulating odd-chain fatty acids (OCFAs; pentadecanoic acid [C15:0], heptadecanoic acid [C17:0]). As the major source of propionate in humans is the microbial fermentation of dietary fiber, OCFAs have been proposed as candidate biomarkers of dietary fiber. The objective of this study is to critically assess the plausibility, robustness, reliability, dose-response, time-response aspects of OCFAs as potential biomarkers of fermentable fibers in two independent studies using a validated analytical method.<h4>Methods and results</h4>OCFAs are first assessed in a fiber supplementation study, where 21 participants received 10 g dietary fiber supplementation for 7 days. OCFAs are then assessed in a highly controlled inpatient setting, which 19 participants consumed a high fiber (45.1 g per day) and a low fiber diet (13.6 g per day) for 4 days. Collectively in both studies, dietary intakes of fiber as fiber supplementations or having consumed a high fiber diet do not increase circulating levels of OCFAs. The dose and temporal relations are not observed.<h4>Conclusion</h4>Current study has generated new insight on the utility of OCFAs as fiber biomarkers and highlighted the importance of critical assessment of candidate biomarkers before application.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/mnfr.202100316; doi:https://doi.org/10.1002/mnfr.202100316; html:https://europepmc.org/articles/PMC11475553; pdf:https://europepmc.org/articles/PMC11475553?pdf=render
+36874571,https://doi.org/10.12688/wellcomeopenres.17981.1,Settings for non-household transmission of SARS-CoV-2 during the second lockdown in England and Wales - analysis of the Virus Watch household community cohort study.,"Hoskins S, Beale S, Nguyen V, Fragaszy E, Navaratnam AMD, Smith C, French C, Kovar J, Byrne T, Fong WLE, Geismar C, Patel P, Yavlinksy A, Johnson AM, Aldridge RW, Hayward A, Virus Watch Collaborative.",,Wellcome open research,2022,2022-08-03,Y,Transmission; Activities; Pandemic; Work; Public Transport; Shopping; Lockdown; Covid-19; Sars-cov-2,,,"<b>Background</b>: ""Lockdowns"" to control serious respiratory virus pandemics were widely used during the coronavirus disease 2019 (COVID-19) pandemic.  However, there is limited information to understand the settings in which most transmission occurs during lockdowns, to support refinement of similar policies for future pandemics.  <b>Methods</b>: Among Virus Watch household cohort participants we identified those infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outside the household.  Using survey activity data, we undertook multivariable logistic regressions assessing the contribution of activities on non-household infection risk.  We calculated adjusted population attributable fractions (APAF) to estimate which activity accounted for the greatest proportion of non-household infections during the pandemic's second wave. <b>Results</b>: Among 10,858 adults, 18% of cases were likely due to household transmission.  Among 10,475 participants (household-acquired cases excluded), including 874 non-household-acquired infections, infection was associated with: leaving home for work or education (AOR 1.20 (1.02 - 1.42), APAF 6.9%); public transport (more than once per week AOR 1.82 (1.49 - 2.23), public transport APAF 12.42%); and shopping (more than once per week AOR 1.69 (1.29 - 2.21), shopping APAF 34.56%).  Other non-household activities were rare and not significantly associated with infection. <b>Conclusions:</b> During lockdown, going to work and using public or shared transport independently increased infection risk, however only a minority did these activities.  Most participants visited shops, accounting for one-third of non-household transmission.  Transmission in restricted hospitality and leisure settings was minimal suggesting these restrictions were effective.   If future respiratory infection pandemics emerge these findings highlight the value of working from home, using forms of transport that minimise exposure to others, minimising exposure to shops and restricting non-essential activities.",,doi:https://doi.org/10.12688/wellcomeopenres.17981.1; html:https://europepmc.org/articles/PMC9975411; pdf:https://europepmc.org/articles/PMC9975411?pdf=render
 36891499,https://doi.org/10.1016/j.ssmph.2023.101370,How does the local area deprivation influence life chances for children in poverty in Wales: A record linkage cohort study.,"Bandyopadhyay A, Whiffen T, Fry R, Brophy S.",,SSM - population health,2023,2023-02-23,Y,Resilience; Cohort study; Education; Deprivation; Child Poverty; Record Linkage; Local Area,,,"<h4>Objectives</h4>Children growing up in poverty are less likely to achieve in school and more likely to experience mental health problems. This study examined factors in the local area that can help a child overcome the negative impact of poverty.<h4>Design</h4>A longitudinal record linkage retrospective cohort study.<h4>Participants</h4>This study included 159,131 children who lived in Wales and completed their age 16 exams (Key Stage 4 (KS4)) between 2009 and 2016. Free School Meal (FSM) provision was used as an indicator of household-level deprivation. Area-level deprivation was measured using the Welsh Index of Multiple Deprivation (WIMD) 2011. An encrypted unique Anonymous Linking Field was used to link the children with their health- and educational records.<h4>Outcome measures</h4>The outcome variable 'Profile to Leave Poverty' (PLP) was constructed based on successful completion of age 16 exams, no mental health condition, no substance and alcohol misuse records in routine data. Logistic regression with stepwise model selection was used to investigate the association between local area deprivation and the outcome variable.<h4>Results</h4>22% of children on FSM achieved PLP compared to 54.9% of non-FSM children. FSM Children from least deprived areas were significantly more likely to achieve PLP (adjusted odds ratio (aOR) - 2.20 (1.93, 2.51)) than FSM children from most deprived areas. FSM children, living in areas with higher community safety, higher relative income, higher access to services, were more likely to achieve PLP than their peers.<h4>Conclusion</h4>The findings indicate that community-level improvements such as increasing safety, connectivity and employment might help in child's education attainment, mental health and reduce risk taking behaviours.",,doi:https://doi.org/10.1016/j.ssmph.2023.101370; doi:https://doi.org/10.1016/j.ssmph.2023.101370; html:https://europepmc.org/articles/PMC9986621; pdf:https://europepmc.org/articles/PMC9986621?pdf=render
-37088955,https://doi.org/10.1177/02692163231167212,"Deaths at home, area-based deprivation and the effect of the Covid-19 pandemic: An analysis of mortality data across four nations.","Leniz J, Davies JM, Bone AE, Hocaoglu M, Verne J, Barclay S, Murtagh FEM, Fraser LK, Higginson IJ, Sleeman KE.",,Palliative medicine,2023,2023-04-23,Y,Mortality; Palliative care; Terminal Care; Inequalities; Place Of Death; Deprivation; Pandemics; Socio-economic Position; Covid-19,,,"<h4>Background</h4>The number and proportion of home deaths in the UK increased during the Covid-19 pandemic. It is not known whether these changes were experienced disproportionately by people from different socioeconomic groups.<h4>Aim</h4>To examine the association between home death and socioeconomic position during the Covid-19 pandemic, and how this changed between 2019 and 2020.<h4>Design</h4>Retrospective cohort study using population-based individual-level mortality data.<h4>Setting/participants</h4>All registered deaths in England, Wales, Scotland and Northern Ireland. The proportion of home deaths between 28th March and 31st December 2020 was compared with the same period in 2019. We used Poisson regression models to evaluate the association between decedent's area-based level of deprivation and risk of home death, as well as the interaction between deprivation and year of death, for each nation separately.<h4>Results</h4>Between the 28th March and 31st December 2020, 409,718 deaths were recorded in England, 46,372 in Scotland, 26,410 in Wales and 13,404 in Northern Ireland. All four nations showed an increase in the adjusted proportion of home deaths between 2019 and 2020, ranging from 21 to 28%. This increase was lowest for people living in the most deprived areas in all nations, with evidence of a deprivation gradient in England.<h4>Conclusions</h4>The Covid-19 pandemic exacerbated a previously described socioeconomic inequality in place of death in the UK. Further research to understand the reasons for this change and if this inequality has been sustained is needed.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10125882; doi:https://doi.org/10.1177/02692163231167212; html:https://europepmc.org/articles/PMC10125882; pdf:https://europepmc.org/articles/PMC10125882?pdf=render
 35476839,https://doi.org/10.1371/journal.pone.0266967,"Healthcare contacts with self-harm during COVID-19: An e-cohort whole-population-based study using individual-level linked routine electronic health records in Wales, UK, 2016-March 2021.","DelPozo-Banos M, Lee SC, Friedmann Y, Akbari A, Torabi F, Lloyd K, Lyons RA, John A.",,PloS one,2022,2022-04-27,Y,,,,"<h4>Introduction</h4>Reduced rates of help seeking by those who self-harmed during the COVID-19 pandemic have been reported.<h4>Objectives</h4>To understand changes in healthcare service contacts for self-harm during the COVID-19 pandemic across primary, emergency and secondary care.<h4>Methods</h4>This retrospective cohort study used routine electronic healthcare data for Wales, United Kingdom, from 2016 to March 14, 2021. Population-based data from primary care, emergency departments and hospital admissions were linked at individual-level. All Welsh residents aged ≥10 years over the study period were included in the study. Primary, emergency and secondary care contacts with self-harm at any time between 2016 and March 14, 2021 were identified. Outcomes were counts, incidence, prevalence and proportion of self-harm contacts relative to all contacts in each and all settings, as well as the proportion of people contacting one or more settings with self-harm. Weekly trends were modelled using generalised estimated equations, with differences between 2020 (to March 2021) and comparison years 2016-2018 (to March 2017-2019) quantified using difference in differences, from which mean rate of odds ratios (μROR) across years was reported.<h4>Results</h4>The study included 3,552,210 individuals over the study period. Self-harm contacts reduced across services in March and December 2020 compared to previous years. Primary care contacts with self-harm reduced disproportionately compared to non-self-harm contacts (μROR = 0.7, p<0.05), while their proportion increased in emergency departments during April 2020 (μROR = 1.3, p<0.05 in 2/3 comparison years) and hospital admissions during April-May 2020 (μROR = 1.2, p<0.05 in 2/3 comparison years). Despite this, those who self-harmed in April 2020 were more likely to be seen in primary care than other settings compared to previous years (μROR = 1.2, p<0.05). A lower proportion of those with self-harm contacts in emergency departments were subsequently admitted to hospital in December 2020 compared to previous years (μROR = 0.5, p<0.05).<h4>Conclusions</h4>These findings suggest that those who self-harmed during the COVID-19 pandemic may have been less likely to seek help, and those who did so faced more stringent criteria for admission. Communications encouraging those who self-harm to seek help during pandemics may be beneficial. However, this needs to be supported by maintained provision of mental health services.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0266967&type=printable; doi:https://doi.org/10.1371/journal.pone.0266967; html:https://europepmc.org/articles/PMC9045644; pdf:https://europepmc.org/articles/PMC9045644?pdf=render
-36497616,https://doi.org/10.3390/ijerph192315544,Association between Internet Usage and Quality of Life of Elderly People in England: Evidence from the English Longitudinal Study of Ageing (ELSA).,"Vidiasratri AR, Bath PA, Bath PA.",,International journal of environmental research and public health,2022,2022-11-23,Y,Internet; Quality of life; Older People,,,"The WHO has stated that the number of senior citizens above age 65 across the world will double by the year 2050: in the UK, the whole population is projected to grow by about 2.5% over a decade, from mid-2018. Although people are living longer, they are not healthier in old age, and there is an increasing number of illnesses and disabilities in the ageing population, which have an impact on their overall well-being and quality of life (QoL). Alongside these trends, Internet technologies have improved and provide a wide range of information, including on medical and health issues. This study aimed to examine the association between the utilisation of the internet among older people in England and their QoL. This study utilised the English Longitudinal Study of Aging (ELSA), a longitudinal study of a representative sample of people aged 50 and over in England. The data from Wave 9 were analysed using bivariate analysis and logistic regression. The results show a strong association between QoL and utilisation of the Internet in older people, even when adjusting for demographic variables and health. Higher use of the internet was associated with older people being less likely to have higher QoL. The excessive use of the internet for communication and gathering information also contributed to lower QoL. From the findings, poorer QoL was also found in people in older age groups, in those who are married, and those who never suffer from chronic diseases. Our findings suggest that the quality of life in older people might not only be associated with the frequency of usage but also the purpose for which the internet is used; however, this relationship is complex and further research should explore this in greater depth. Further research should also investigate how older people's use of the Internet changed during the COVID-19 pandemic and the effects of this on the QoL in older age.",,pdf:https://www.mdpi.com/1660-4601/19/23/15544/pdf?version=1669349785; doi:https://doi.org/10.3390/ijerph192315544; html:https://europepmc.org/articles/PMC9738189; pdf:https://europepmc.org/articles/PMC9738189?pdf=render
+37088955,https://doi.org/10.1177/02692163231167212,"Deaths at home, area-based deprivation and the effect of the Covid-19 pandemic: An analysis of mortality data across four nations.","Leniz J, Davies JM, Bone AE, Hocaoglu M, Verne J, Barclay S, Murtagh FEM, Fraser LK, Higginson IJ, Sleeman KE.",,Palliative medicine,2023,2023-04-23,Y,Mortality; Palliative care; Terminal Care; Inequalities; Place Of Death; Deprivation; Pandemics; Socio-economic Position; Covid-19,,,"<h4>Background</h4>The number and proportion of home deaths in the UK increased during the Covid-19 pandemic. It is not known whether these changes were experienced disproportionately by people from different socioeconomic groups.<h4>Aim</h4>To examine the association between home death and socioeconomic position during the Covid-19 pandemic, and how this changed between 2019 and 2020.<h4>Design</h4>Retrospective cohort study using population-based individual-level mortality data.<h4>Setting/participants</h4>All registered deaths in England, Wales, Scotland and Northern Ireland. The proportion of home deaths between 28th March and 31st December 2020 was compared with the same period in 2019. We used Poisson regression models to evaluate the association between decedent's area-based level of deprivation and risk of home death, as well as the interaction between deprivation and year of death, for each nation separately.<h4>Results</h4>Between the 28th March and 31st December 2020, 409,718 deaths were recorded in England, 46,372 in Scotland, 26,410 in Wales and 13,404 in Northern Ireland. All four nations showed an increase in the adjusted proportion of home deaths between 2019 and 2020, ranging from 21 to 28%. This increase was lowest for people living in the most deprived areas in all nations, with evidence of a deprivation gradient in England.<h4>Conclusions</h4>The Covid-19 pandemic exacerbated a previously described socioeconomic inequality in place of death in the UK. Further research to understand the reasons for this change and if this inequality has been sustained is needed.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10125882; doi:https://doi.org/10.1177/02692163231167212; html:https://europepmc.org/articles/PMC10125882; pdf:https://europepmc.org/articles/PMC10125882?pdf=render
 36385522,https://doi.org/10.1093/ehjqcco/qcac077,Effects of the COVID-19 pandemic on secondary care for cardiovascular disease in the UK: an electronic health record analysis across three countries.,"Wright FL, Cheema K, Goldacre R, Hall N, Herz N, Islam N, Karim Z, Moreno-Martos D, Morales DR, O'Connell D, Spata E, Akbari A, Ashworth M, Barber M, Briffa N, Canoy D, Denaxas S, Khunti K, Kurdi A, Mamas M, Priedon R, Sudlow C, Morris EJA, Lacey B, Banerjee A.",,European heart journal. Quality of care & clinical outcomes,2023,2023-06-01,Y,,,,"<h4>Background</h4>Although morbidity and mortality from COVID-19 have been widely reported, the indirect effects of the pandemic beyond 2020 on other major diseases and health service activity have not been well described.<h4>Methods and results</h4>Analyses used national administrative electronic hospital records in England, Scotland, and Wales for 2016-21. Admissions and procedures during the pandemic (2020-21) related to six major cardiovascular conditions [acute coronary syndrome (ACS), heart failure (HF), stroke/transient ischaemic attack (TIA), peripheral arterial disease (PAD), aortic aneurysm (AA), and venous thromboembolism(VTE)] were compared with the annual average in the pre-pandemic period (2016-19). Differences were assessed by time period and urgency of care.In 2020, there were 31 064 (-6%) fewer hospital admissions [14 506 (-4%) fewer emergencies, 16 560 (-23%) fewer elective admissions] compared with 2016-19 for the six major cardiovascular diseases (CVDs) combined. The proportional reduction in admissions was similar in all three countries. Overall, hospital admissions returned to pre-pandemic levels in 2021. Elective admissions remained substantially below expected levels for almost all conditions in all three countries [-10 996 (-15%) fewer admissions]. However, these reductions were offset by higher than expected total emergency admissions [+25 878 (+6%) higher admissions], notably for HF and stroke in England, and for VTE in all three countries. Analyses for procedures showed similar temporal variations to admissions.<h4>Conclusion</h4>The present study highlights increasing emergency cardiovascular admissions during the pandemic, in the context of a substantial and sustained reduction in elective admissions and procedures. This is likely to increase further the demands on cardiovascular services over the coming years.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa62054/Download/62054__26063__5453b00901174a7d9a0797547f023fba.pdf; doi:https://doi.org/10.1093/ehjqcco/qcac077; html:https://europepmc.org/articles/PMC10284263; pdf:https://europepmc.org/articles/PMC10284263?pdf=render
 38467603,https://doi.org/10.1038/s41467-024-46497-0,Impact of vaccination on the association of COVID-19 with cardiovascular diseases: An OpenSAFELY cohort study.,"Cezard GI, Denholm RE, Knight R, Wei Y, Teece L, Toms R, Forbes HJ, Walker AJ, Fisher L, Massey J, Hopcroft LEM, Horne EMF, Taylor K, Palmer T, Arab MA, Cuitun Coronado JI, Ip SHY, Davy S, Dillingham I, Bacon S, Mehrkar A, Morton CE, Greaves F, Hyams C, Davey Smith G, Macleod J, Chaturvedi N, Goldacre B, Whiteley WN, Wood AM, Sterne JAC, Walker V, Longitudinal Health and Wellbeing and Data and Connectivity UK COVID-19 National Core Studies, CONVALESCENCE study and the OpenSAFELY collaborative.",,Nature communications,2024,2024-03-11,Y,,,,"Infection with SARS-CoV-2 is associated with an increased risk of arterial and venous thrombotic events, but the implications of vaccination for this increased risk are uncertain. With the approval of NHS England, we quantified associations between COVID-19 diagnosis and cardiovascular diseases in different vaccination and variant eras using linked electronic health records for ~40% of the English population. We defined a 'pre-vaccination' cohort (18,210,937 people) in the wild-type/Alpha variant eras (January 2020-June 2021), and 'vaccinated' and 'unvaccinated' cohorts (13,572,399 and 3,161,485 people respectively) in the Delta variant era (June-December 2021). We showed that the incidence of each arterial thrombotic, venous thrombotic and other cardiovascular outcomes was substantially elevated during weeks 1-4 after COVID-19, compared with before or without COVID-19, but less markedly elevated in time periods beyond week 4. Hazard ratios were higher after hospitalised than non-hospitalised COVID-19 and higher in the pre-vaccination and unvaccinated cohorts than the vaccinated cohort. COVID-19 vaccination reduces the risk of cardiovascular events after COVID-19 infection. People who had COVID-19 before or without being vaccinated are at higher risk of cardiovascular events for at least two years.",,pdf:https://www.nature.com/articles/s41467-024-46497-0.pdf; doi:https://doi.org/10.1038/s41467-024-46497-0; html:https://europepmc.org/articles/PMC10928172; pdf:https://europepmc.org/articles/PMC10928172?pdf=render
+36497616,https://doi.org/10.3390/ijerph192315544,Association between Internet Usage and Quality of Life of Elderly People in England: Evidence from the English Longitudinal Study of Ageing (ELSA).,"Vidiasratri AR, Bath PA, Bath PA.",,International journal of environmental research and public health,2022,2022-11-23,Y,Internet; Quality of life; Older People,,,"The WHO has stated that the number of senior citizens above age 65 across the world will double by the year 2050: in the UK, the whole population is projected to grow by about 2.5% over a decade, from mid-2018. Although people are living longer, they are not healthier in old age, and there is an increasing number of illnesses and disabilities in the ageing population, which have an impact on their overall well-being and quality of life (QoL). Alongside these trends, Internet technologies have improved and provide a wide range of information, including on medical and health issues. This study aimed to examine the association between the utilisation of the internet among older people in England and their QoL. This study utilised the English Longitudinal Study of Aging (ELSA), a longitudinal study of a representative sample of people aged 50 and over in England. The data from Wave 9 were analysed using bivariate analysis and logistic regression. The results show a strong association between QoL and utilisation of the Internet in older people, even when adjusting for demographic variables and health. Higher use of the internet was associated with older people being less likely to have higher QoL. The excessive use of the internet for communication and gathering information also contributed to lower QoL. From the findings, poorer QoL was also found in people in older age groups, in those who are married, and those who never suffer from chronic diseases. Our findings suggest that the quality of life in older people might not only be associated with the frequency of usage but also the purpose for which the internet is used; however, this relationship is complex and further research should explore this in greater depth. Further research should also investigate how older people's use of the Internet changed during the COVID-19 pandemic and the effects of this on the QoL in older age.",,pdf:https://www.mdpi.com/1660-4601/19/23/15544/pdf?version=1669349785; doi:https://doi.org/10.3390/ijerph192315544; html:https://europepmc.org/articles/PMC9738189; pdf:https://europepmc.org/articles/PMC9738189?pdf=render
 39076659,https://doi.org/10.31083/j.rcm2312412,Quantification of Epicardial Adipose Tissue Volume and Attenuation for Cardiac CT Scans Using Deep Learning in a Single Multi-Task Framework.,"Abdulkareem M, Brahier MS, Zou F, Rauseo E, Uchegbu I, Taylor A, Thomaides A, Bergquist PJ, Srichai MB, Lee AM, Vargas JD, Petersen SE.",,Reviews in cardiovascular medicine,2022,2022-12-20,Y,Density; Volume; CT; Attenuation; Epicardial Adipose Tissue; Eat; Deep Learning,,,"<h4>Background</h4>Recent studies have shown that epicardial adipose tissue (EAT) is an independent atrial fibrillation (AF) prognostic marker and has influence on the myocardial function. In computed tomography (CT), EAT volume (EATv) and density (EATd) are parameters that are often used to quantify EAT. While increased EATv has been found to correlate with the prevalence and the recurrence of AF after ablation therapy, higher EATd correlates with inflammation due to arrest of lipid maturation and with high risk of plaque presence and plaque progression. Automation of the quantification task diminishes the variability in readings introduced by different observers in manual quantification and results in high reproducibility of studies and less time-consuming analysis. Our objective is to develop a fully automated quantification of EATv and EATd using a deep learning (DL) framework.<h4>Methods</h4>We proposed a framework that consists of image classification and segmentation DL models and performs the task of selecting images with EAT from all the CT images acquired for a patient, and the task of segmenting the EAT from the output images of the preceding task. EATv and EATd are estimated using the segmentation masks to define the region of interest. For our experiments, a 300-patient dataset was divided into two subsets, each consisting of 150 patients: Dataset 1 (41,979 CT slices) for training the DL models, and Dataset 2 (36,428 CT slices) for evaluating the quantification of EATv and EATd.<h4>Results</h4>The classification model achieved accuracies of 98% for precision, recall and F1 scores, and the segmentation model achieved accuracies in terms of mean ( ± std.) and median dice similarity coefficient scores of 0.844 ( ± 0.19) and 0.84, respectively. Using the evaluation set (Dataset 2), our approach resulted in a Pearson correlation coefficient of 0.971 ( R2 = 0.943) between the label and predicted EATv, and the correlation coefficient of 0.972 ( R2 = 0.945) between the label and predicted EATd.<h4>Conclusions</h4>We proposed a framework that provides a fast and robust strategy for accurate EAT segmentation, and volume (EATv) and attenuation (EATd) quantification tasks. The framework will be useful to clinicians and other practitioners for carrying out reproducible EAT quantification at patient level or for large cohorts and high-throughput projects.",,doi:https://doi.org/10.31083/j.rcm2312412; html:https://europepmc.org/articles/PMC11270472; pdf:https://europepmc.org/articles/PMC11270472?pdf=render
 38429771,https://doi.org/10.1186/s13643-024-02477-5,Accuracy of heart failure ascertainment using routinely collected healthcare data: a systematic review and meta-analysis.,"Goonasekera MA, Offer A, Karsan W, El-Nayir M, Mallorie AE, Parish S, Haynes RJ, Mafham MM.",,Systematic reviews,2024,2024-03-01,Y,"Meta-analysis; Systematic Review,; Methods Comparison,; Outcome Ascertainment,; Randomized Trials,; Streamlined Clinical Trials,",,,"<h4>Background</h4>Ascertainment of heart failure (HF) hospitalizations in cardiovascular trials is costly and complex, involving processes that could be streamlined by using routinely collected healthcare data (RCD). The utility of coded RCD for HF outcome ascertainment in randomized trials requires assessment. We systematically reviewed studies assessing RCD-based HF outcome ascertainment against ""gold standard"" (GS) methods to study the feasibility of using such methods in clinical trials.<h4>Methods</h4>Studies assessing International Classification of Disease (ICD) coded RCD-based HF outcome ascertainment against GS methods and reporting at least one agreement statistic were identified by searching MEDLINE and Embase from inception to May 2021. Data on study characteristics, details of RCD and GS data sources and definitions, and test statistics were reviewed. Summary sensitivities and specificities for studies ascertaining acute and prevalent HF were estimated using a bivariate random effects meta-analysis. Heterogeneity was evaluated using I<sup>2</sup> statistics and hierarchical summary receiver operating characteristic (HSROC) curves.<h4>Results</h4>A total of 58 studies of 48,643 GS-adjudicated HF events were included in this review. Strategies used to improve case identification included the use of broader coding definitions, combining multiple data sources, and using machine learning algorithms to search free text data, but these methods were not always successful and at times reduced specificity in individual studies. Meta-analysis of 17 acute HF studies showed that RCD algorithms have high specificity (96.2%, 95% confidence interval [CI] 91.5-98.3), but lacked sensitivity (63.5%, 95% CI 51.3-74.1) with similar results for 21 prevalent HF studies. There was considerable heterogeneity between studies.<h4>Conclusions</h4>RCD can correctly identify HF outcomes but may miss approximately one-third of events. Methods used to improve case identification should also focus on minimizing false positives.",,pdf:https://systematicreviewsjournal.biomedcentral.com/counter/pdf/10.1186/s13643-024-02477-5; doi:https://doi.org/10.1186/s13643-024-02477-5; html:https://europepmc.org/articles/PMC10905869; pdf:https://europepmc.org/articles/PMC10905869?pdf=render
-35168181,https://doi.org/10.1016/j.thromres.2022.01.023,Potentially inappropriate prescribing of DOACs to people with mechanical heart valves: A federated analysis of 57.9 million patients' primary care records in situ using OpenSAFELY.,"OpenSAFELY Collaborative, Fisher L, Speed V, Curtis HJ, Rentsch CT, Wong AYS, Schultze A, Massey J, Inglesby P, Morton CE, Wood M, Walker AJ, Morley J, Mehrkar A, Bacon S, Hickman G, Bates C, Croker R, Evans D, Ward T, Cockburn J, Davy S, Bhaskaran K, Smith B, Williamson E, Hulme W, Green A, Eggo RM, Forbes H, Tazare J, Parry J, Hester F, Harper S, Meadows J, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Griffiths P, Fowles A, Parkes N, Douglas IJ, Evans SJW, Smeeth L, MacKenna B, Tomlinson L, Goldacre B.",,Thrombosis research,2022,2022-01-29,N,Anticoagulants; Thrombosis; Heart valve prosthesis; Patient Safety; Electronic Health Records,,,,,pdf:https://ora.ox.ac.uk/objects/uuid:aa50f867-d3a4-45ff-9173-1c9677a7ba4f/files/r3x816n268; doi:https://doi.org/10.1016/j.thromres.2022.01.023; html:https://europepmc.org/articles/PMC7616146; pdf:https://europepmc.org/articles/PMC7616146?pdf=render; doi:https://doi.org/10.1016/j.thromres.2022.01.023
 37468507,https://doi.org/10.1038/s41598-023-37580-5,Biobank-scale methods and projections for sparse polygenic prediction from machine learning.,"Raben TG, Lello L, Widen E, Hsu SDH.",,Scientific reports,2023,2023-07-19,Y,,,,"In this paper we characterize the performance of linear models trained via widely-used sparse machine learning algorithms. We build polygenic scores and examine performance as a function of training set size, genetic ancestral background, and training method. We show that predictor performance is most strongly dependent on size of training data, with smaller gains from algorithmic improvements. We find that LASSO generally performs as well as the best methods, judged by a variety of metrics. We also investigate performance characteristics of predictors trained on one genetic ancestry group when applied to another. Using LASSO, we develop a novel method for projecting AUC and correlation as a function of data size (i.e., for new biobanks) and characterize the asymptotic limit of performance. Additionally, for LASSO (compressed sensing) we show that performance metrics and predictor sparsity are in agreement with theoretical predictions from the Donoho-Tanner phase transition. Specifically, a future predictor trained in the Taiwan Precision Medicine Initiative for asthma can achieve an AUC of [Formula: see text] and for height a correlation of [Formula: see text] for a Taiwanese population. This is above the measured values of [Formula: see text] and [Formula: see text], respectively, for UK Biobank trained predictors applied to a European population.",,pdf:https://www.nature.com/articles/s41598-023-37580-5.pdf; doi:https://doi.org/10.1038/s41598-023-37580-5; html:https://europepmc.org/articles/PMC10356957; pdf:https://europepmc.org/articles/PMC10356957?pdf=render
-36139476,https://doi.org/10.3390/cells11182901,Dysregulated Neutrophil Phenotype and Function in Hospitalised Non-ICU COVID-19 Pneumonia.,"Belchamber KBR, Thein OS, Hazeldine J, Grudzinska FS, Faniyi AA, Hughes MJ, Jasper AE, Yip KP, Crowley LE, Lugg ST, Sapey E, Parekh D, Thickett DR, Scott A.",,Cells,2022,2022-09-16,Y,Inflammation; neutrophil; innate immunity; Covid-19,,,"<b>Rationale</b>: Infection with the SARS-CoV2 virus is associated with elevated neutrophil counts. Evidence of neutrophil dysfunction in COVID-19 is based on transcriptomics or single functional assays. Cell functions are interwoven pathways, and understanding the effect across the spectrum of neutrophil function may identify therapeutic targets. <b>Objectives</b>: Examine neutrophil phenotype and function in 41 hospitalised, non-ICU COVID-19 patients versus 23 age-matched controls (AMC) and 26 community acquired pneumonia patients (CAP). <b>Methods</b>: Isolated neutrophils underwent ex vivo analyses for migration, bacterial phagocytosis, ROS generation, NETosis and receptor expression. Circulating DNAse 1 activity, levels of cfDNA, MPO, VEGF, IL-6 and sTNFRI were measured and correlated to clinical outcome. Serial sampling on day three to five post hospitalization were also measured. The effect of ex vivo PI3K inhibition was measured in a further cohort of 18 COVID-19 patients. <b>Results</b>: Compared to AMC and CAP, COVID-19 neutrophils demonstrated elevated transmigration (<i>p</i> = 0.0397) and NETosis (<i>p</i> = 0.0332), and impaired phagocytosis (<i>p</i> = 0.0036) associated with impaired ROS generation (<i>p</i> < 0.0001). The percentage of CD54+ neutrophils (<i>p</i> < 0.001) was significantly increased, while surface expression of CD11b (<i>p</i> = 0.0014) and PD-L1 (<i>p</i> = 0.006) were significantly decreased in COVID-19. COVID-19 and CAP patients showed increased systemic markers of NETosis including increased cfDNA (<i>p</i> = 0.0396) and impaired DNAse activity (<i>p</i> < 0.0001). The ex vivo inhibition of PI3K γ and δ reduced NET release by COVID-19 neutrophils (<i>p</i> = 0.0129). <b>Conclusions</b>: COVID-19 is associated with neutrophil dysfunction across all main effector functions, with altered phenotype, elevated migration and NETosis, and impaired antimicrobial responses. These changes highlight that targeting neutrophil function may help modulate COVID-19 severity.",,pdf:https://www.mdpi.com/2073-4409/11/18/2901/pdf?version=1663743438; doi:https://doi.org/10.3390/cells11182901; html:https://europepmc.org/articles/PMC9496854; pdf:https://europepmc.org/articles/PMC9496854?pdf=render
+35168181,https://doi.org/10.1016/j.thromres.2022.01.023,Potentially inappropriate prescribing of DOACs to people with mechanical heart valves: A federated analysis of 57.9 million patients' primary care records in situ using OpenSAFELY.,"OpenSAFELY Collaborative, Fisher L, Speed V, Curtis HJ, Rentsch CT, Wong AYS, Schultze A, Massey J, Inglesby P, Morton CE, Wood M, Walker AJ, Morley J, Mehrkar A, Bacon S, Hickman G, Bates C, Croker R, Evans D, Ward T, Cockburn J, Davy S, Bhaskaran K, Smith B, Williamson E, Hulme W, Green A, Eggo RM, Forbes H, Tazare J, Parry J, Hester F, Harper S, Meadows J, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Griffiths P, Fowles A, Parkes N, Douglas IJ, Evans SJW, Smeeth L, MacKenna B, Tomlinson L, Goldacre B.",,Thrombosis research,2022,2022-01-29,N,Anticoagulants; Thrombosis; Heart valve prosthesis; Patient Safety; Electronic Health Records,,,,,pdf:https://ora.ox.ac.uk/objects/uuid:aa50f867-d3a4-45ff-9173-1c9677a7ba4f/files/r3x816n268; doi:https://doi.org/10.1016/j.thromres.2022.01.023; html:https://europepmc.org/articles/PMC7616146; pdf:https://europepmc.org/articles/PMC7616146?pdf=render; doi:https://doi.org/10.1016/j.thromres.2022.01.023
 37254630,https://doi.org/10.1111/acel.13808,"Mid-life leukocyte telomere length and dementia risk: An observational and mendelian randomization study of 435,046 UK Biobank participants.","Liu R, Xiang M, Pilling LC, Melzer D, Wang L, Manning KJ, Steffens DC, Bowden J, Fortinsky RH, Kuchel GA, Rhee TG, Diniz BS, Kuo CL.",,Aging cell,2023,2023-05-30,Y,Cognition; Alzheimer's disease; Vascular dementia; Brain Magnetic Resonance Imaging; Hallmarks Of Biological Aging,,,"Telomere attrition is one of biological aging hallmarks and may be intervened to target multiple aging-related diseases, including Alzheimer's disease and Alzheimer's disease related dementias (AD/ADRD). The objective of this study was to assess associations of leukocyte telomere length (TL) with AD/ADRD and early markers of AD/ADRD, including cognitive performance and brain magnetic resonance imaging (MRI) phenotypes. Data from European-ancestry participants in the UK Biobank (n = 435,046) were used to evaluate whether mid-life leukocyte TL is associated with incident AD/ADRD over a mean follow-up of 12.2 years. In a subsample without AD/ADRD and with brain imaging data (n = 43,390), we associated TL with brain MRI phenotypes related to AD or vascular dementia pathology. Longer TL was associated with a lower risk of incident AD/ADRD (adjusted Hazard Ratio [aHR] per SD = 0.93, 95% CI 0.90-0.96, p = 3.37 × 10<sup>-7</sup> ). Longer TL also was associated with better cognitive performance in specific cognitive domains, larger hippocampus volume, lower total volume of white matter hyperintensities, and higher fractional anisotropy and lower mean diffusivity in the fornix. In conclusion, longer TL is inversely associated with AD/ADRD, cognitive impairment, and brain structural lesions toward the development of AD/ADRD. However, the relationships between genetically determined TL and the outcomes above were not statistically significant based on the results from Mendelian randomization analysis results. Our findings add to the literature of prioritizing risk for AD/ADRD. The causality needs to be ascertained in mechanistic studies.",,doi:https://doi.org/10.1111/acel.13808; doi:https://doi.org/10.1111/acel.13808; html:https://europepmc.org/articles/PMC10352557; pdf:https://europepmc.org/articles/PMC10352557?pdf=render
 38234143,https://doi.org/10.1002/cam4.6918,"Interactions of obesity, body shape, diabetes and sex steroids with respect to prostate cancer risk in the UK Biobank cohort.","Christakoudi S, Tsilidis KK, Evangelou E, Riboli E.",,Cancer medicine,2024,2024-01-17,Y,epidemiology; prostate cancer; Cancer Risk Factors; Cancer Prevention,,,"<h4>Background</h4>Obesity and diabetes are associated inversely with low-grade prostate cancer risk and affect steroid hormone synthesis but whether they modify each other's impact on prostate cancer risk remains unknown.<h4>Methods</h4>We examined the independent associations of diabetes, body mass index (BMI), 'a body shape index' (ABSI), hip index (HI), circulating testosterone, sex hormone binding globulin (SHBG) (per one standard deviation increase) and oestradiol ≥175 pmol/L with total prostate cancer risk using multivariable Cox proportional hazards models for UK Biobank men. We evaluated multiplicative interactions (p<sub>MI</sub> ) and additive interactions (relative excess risk from interaction (p<sub>RERI</sub> ), attributable proportion (p<sub>AR</sub> ), synergy index (p<sub>SI</sub> )) with obese (BMI ≥30 kg/m<sup>2</sup> ) and diabetes.<h4>Results</h4>During a mean follow-up of 10.3 years, 9417 incident prostate cancers were diagnosed in 195,813 men. Diabetes and BMI were associated more strongly inversely with prostate cancer risk when occurring together (p<sub>MI</sub>  = 0.0003, p<sub>RERI</sub>  = 0.032, p<sub>AP</sub>  = 0.020, p<sub>SI</sub>  = 0.002). ABSI was associated positively in obese men (HR = 1.081; 95% CI = 1.030-1.135) and men with diabetes (HR = 1.114; 95% CI = 1.021-1.216). The inverse associations with obesity and diabetes were attenuated for high-ABSI ≥79.8 (p<sub>MI</sub>  = 0.022, p<sub>RERI</sub>  = 0.008, p<sub>AP</sub>  = 0.005, p<sub>SI</sub>  <0.0001 obesity; p<sub>MI</sub>  = 0.017, p<sub>RERI</sub>  = 0.047, p<sub>AP</sub>  = 0.025, p<sub>SI</sub>  = 0.0005 diabetes). HI was associated inversely in men overall (HR = 0.967; 95% CI = 0.947-0.988). Free testosterone (FT) was associated most strongly positively in normal weight men (HR = 1.098; 95% CI = 1.045-1.153) and men with diabetes (HR = 1.189; 95% CI = 1.081-1.308). Oestradiol was associated inversely in obese men (HR = 0.805; 95% CI = 0.682-0.951). The inverse association with obesity was stronger for high-FT ≥243 pmol/L (p<sub>RERI</sub>  = 0.040, p<sub>AP</sub>  = 0.031, p<sub>SI</sub>  = 0.002) and high-oestradiol (p<sub>RERI</sub>  = 0.030, p<sub>AP</sub>  = 0.012, p<sub>SI</sub>  <0.0001). The inverse association with diabetes was attenuated for high-FT (p<sub>MI</sub>  = 0.008, p<sub>RERI</sub>  = 0.015, p<sub>AP</sub>  = 0.009, p<sub>SI</sub>  = 0.0006). SHBG was associated inversely in men overall (HR = 0.918; 95% CI = 0.895-0.941), more strongly for high-HI ≥49.1 (p<sub>MI</sub>  = 0.024).<h4>Conclusions</h4>Obesity and diabetes showed synergistic inverse associations with prostate cancer risk, likely involving testosterone reduction for diabetes and oestrogen generation for obesity, which were attenuated for high-ABSI. HI and SHBG showed synergistic inverse associations with prostate cancer risk.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cam4.6918; doi:https://doi.org/10.1002/cam4.6918; html:https://europepmc.org/articles/PMC10905680; pdf:https://europepmc.org/articles/PMC10905680?pdf=render
-31783849,https://doi.org/10.1186/s12911-019-0953-2,Developing a standardised approach to the aggregation of inpatient episodes into person-based spells in all specialties and psychiatric specialties.,"Rees S, Akbari A, Collins H, Lee SC, Marchant A, Rees A, Thayer D, Wang T, Wood S, John A.",,BMC medical informatics and decision making,2019,2019-11-29,Y,Data Quality; Data Linkage; Electronic Healthcare Record; Spells; Hospital Inpatient Episodes; Routine Health Data,Improving Public Health,,"<h4>Background</h4>Electronic health record (EHR) data are available for research in all UK nations and cross-nation comparative studies are becoming more common. All UK inpatient EHRs are based around episodes, but episode-based analysis may not sufficiently capture the patient journey. There is no UK-wide method for aggregating episodes into standardised person-based spells. This study identifies two data quality issues affecting the creation of person-based spells, and tests four methods to create these spells, for implementation across all UK nations.<h4>Methods</h4>Welsh inpatient EHRs from 2013 to 2017 were analysed. Phase one described two data quality issues; transfers of care and episode sequencing. Phase two compared four methods for creating person spells. Measures were mean length of stay (LOS, expressed in days) and number of episodes per person spell for each method.<h4>Results</h4>3.5% of total admissions were transfers-in and 3.1% of total discharges were transfers-out. 68.7% of total transfers-in and 48.7% of psychiatric transfers-in had an identifiable preceding transfer-out, and 78.2% of total transfers-out and 59.0% of psychiatric transfers-out had an identifiable subsequent transfer-in. 0.2% of total episodes and 4.0% of psychiatric episodes overlapped with at least one other episode of any specialty. Method one (no evidence of transfer required; overlapping episodes grouped together) resulted in the longest mean LOS (4.0 days for all specialties; 48.5 days for psychiatric specialties) and the fewest single episode person spells (82.4% of all specialties; 69.7% for psychiatric specialties). Method three (evidence of transfer required; overlapping episodes separated) resulted in the shortest mean LOS (3.7 days for all specialties; 45.8 days for psychiatric specialties) and the most single episode person spells; (86.9% for all specialties; 86.3% for psychiatric specialties).<h4>Conclusions</h4>Transfers-in appear better recorded than transfers-out. Transfer coding is incomplete, particularly for psychiatric specialties. The proportion of episodes that overlap is small but psychiatric episodes are disproportionately affected. The most successful method for grouping episodes into person spells aggregated overlapping episodes and required no evidence of transfer from admission source/method or discharge destination codes. The least successful method treated overlapping episodes as distinct and required transfer coding. The impact of all four methods was greater for psychiatric specialties.","Rees et al used a Welsh database to examine inpatient episode/transfer coding coding for psychiatric patients. They identified deficiencies in the existing coding system for psychitatrics transfers and unexplained coding mistakes/problems, then they presesnt several different methods for constructing the inpatient spell to improve coding and avoid misclassification.",pdf:https://bmcmedinformdecismak.biomedcentral.com/track/pdf/10.1186/s12911-019-0953-2; doi:https://doi.org/10.1186/s12911-019-0953-2; html:https://europepmc.org/articles/PMC6884917; pdf:https://europepmc.org/articles/PMC6884917?pdf=render
+36139476,https://doi.org/10.3390/cells11182901,Dysregulated Neutrophil Phenotype and Function in Hospitalised Non-ICU COVID-19 Pneumonia.,"Belchamber KBR, Thein OS, Hazeldine J, Grudzinska FS, Faniyi AA, Hughes MJ, Jasper AE, Yip KP, Crowley LE, Lugg ST, Sapey E, Parekh D, Thickett DR, Scott A.",,Cells,2022,2022-09-16,Y,Inflammation; neutrophil; innate immunity; Covid-19,,,"<b>Rationale</b>: Infection with the SARS-CoV2 virus is associated with elevated neutrophil counts. Evidence of neutrophil dysfunction in COVID-19 is based on transcriptomics or single functional assays. Cell functions are interwoven pathways, and understanding the effect across the spectrum of neutrophil function may identify therapeutic targets. <b>Objectives</b>: Examine neutrophil phenotype and function in 41 hospitalised, non-ICU COVID-19 patients versus 23 age-matched controls (AMC) and 26 community acquired pneumonia patients (CAP). <b>Methods</b>: Isolated neutrophils underwent ex vivo analyses for migration, bacterial phagocytosis, ROS generation, NETosis and receptor expression. Circulating DNAse 1 activity, levels of cfDNA, MPO, VEGF, IL-6 and sTNFRI were measured and correlated to clinical outcome. Serial sampling on day three to five post hospitalization were also measured. The effect of ex vivo PI3K inhibition was measured in a further cohort of 18 COVID-19 patients. <b>Results</b>: Compared to AMC and CAP, COVID-19 neutrophils demonstrated elevated transmigration (<i>p</i> = 0.0397) and NETosis (<i>p</i> = 0.0332), and impaired phagocytosis (<i>p</i> = 0.0036) associated with impaired ROS generation (<i>p</i> < 0.0001). The percentage of CD54+ neutrophils (<i>p</i> < 0.001) was significantly increased, while surface expression of CD11b (<i>p</i> = 0.0014) and PD-L1 (<i>p</i> = 0.006) were significantly decreased in COVID-19. COVID-19 and CAP patients showed increased systemic markers of NETosis including increased cfDNA (<i>p</i> = 0.0396) and impaired DNAse activity (<i>p</i> < 0.0001). The ex vivo inhibition of PI3K γ and δ reduced NET release by COVID-19 neutrophils (<i>p</i> = 0.0129). <b>Conclusions</b>: COVID-19 is associated with neutrophil dysfunction across all main effector functions, with altered phenotype, elevated migration and NETosis, and impaired antimicrobial responses. These changes highlight that targeting neutrophil function may help modulate COVID-19 severity.",,pdf:https://www.mdpi.com/2073-4409/11/18/2901/pdf?version=1663743438; doi:https://doi.org/10.3390/cells11182901; html:https://europepmc.org/articles/PMC9496854; pdf:https://europepmc.org/articles/PMC9496854?pdf=render
 36807005,https://doi.org/10.1055/a-2038-0541,Long-term outcomes of pouch surveillance and risk of neoplasia in familial adenomatous polyposis.,"Patel RV, Curtius K, Man R, Fletcher J, Cuthill V, Clark SK, von Roon AC, Latchford A.",,Endoscopy,2023,2023-02-17,Y,,,,"<h4>Background</h4>Long-term pouch surveillance outcomes for familial adenomatous polyposis (FAP) are unknown. We aimed to quantify surveillance outcomes and to determine which of selected possible predictive factors are associated with pouch dysplasia.<h4>Methods</h4>Retrospective analysis of collected data on 249 patients was performed, analyzing potential risk factors for the development of adenomas or advanced lesions ( ≥ 10 mm/high grade dysplasia (HGD)/cancer) in the pouch body and cuff using Cox proportional hazards models. Kaplan-Meier analyses included landmark time-point analyses at 10 years after surgery to predict the future risk of advanced lesions.<h4>Results</h4>Of 249 patients, 76 % developed at least one pouch body adenoma, with 16 % developing an advanced pouch body lesion; 18 % developed an advanced cuff lesion. Kaplan-Meier analysis showed a 10-year lag before most advanced lesions developed; cumulative incidence of 2.8 % and 6.4 % at 10 years in the pouch body and cuff, respectively. Landmark analysis suggested the presence of adenomas prior to the 10-year point was associated with subsequent development of advanced lesions in the pouch body (hazard ratio [HR] 4.8, 95 %CI 1.6-14.1; <i>P</i> = 0.004) and cuff (HR 6.8, 95 %CI 2.5-18.3; <i>P</i> < 0.001). There were two HGD and four cancer cases in the cuff and one pouch body cancer; all cases of cancer/HGD that had prior surveillance were preceded by ≥ 10-mm adenomas.<h4>Conclusions</h4>Pouch adenoma progression is slow and most advanced lesions occur after 10 years. HGD and cancer were rare events. Pouch phenotype in the first decade is associated with the future risk of developing advanced lesions and may guide personalized surveillance beyond 10 years.",,pdf:http://www.thieme-connect.de/products/ejournals/pdf/10.1055/a-2038-0541.pdf; doi:https://doi.org/10.1055/a-2038-0541; html:https://europepmc.org/articles/PMC10465241; pdf:https://europepmc.org/articles/PMC10465241?pdf=render
+31783849,https://doi.org/10.1186/s12911-019-0953-2,Developing a standardised approach to the aggregation of inpatient episodes into person-based spells in all specialties and psychiatric specialties.,"Rees S, Akbari A, Collins H, Lee SC, Marchant A, Rees A, Thayer D, Wang T, Wood S, John A.",,BMC medical informatics and decision making,2019,2019-11-29,Y,Data Quality; Data Linkage; Electronic Healthcare Record; Spells; Hospital Inpatient Episodes; Routine Health Data,Improving Public Health,,"<h4>Background</h4>Electronic health record (EHR) data are available for research in all UK nations and cross-nation comparative studies are becoming more common. All UK inpatient EHRs are based around episodes, but episode-based analysis may not sufficiently capture the patient journey. There is no UK-wide method for aggregating episodes into standardised person-based spells. This study identifies two data quality issues affecting the creation of person-based spells, and tests four methods to create these spells, for implementation across all UK nations.<h4>Methods</h4>Welsh inpatient EHRs from 2013 to 2017 were analysed. Phase one described two data quality issues; transfers of care and episode sequencing. Phase two compared four methods for creating person spells. Measures were mean length of stay (LOS, expressed in days) and number of episodes per person spell for each method.<h4>Results</h4>3.5% of total admissions were transfers-in and 3.1% of total discharges were transfers-out. 68.7% of total transfers-in and 48.7% of psychiatric transfers-in had an identifiable preceding transfer-out, and 78.2% of total transfers-out and 59.0% of psychiatric transfers-out had an identifiable subsequent transfer-in. 0.2% of total episodes and 4.0% of psychiatric episodes overlapped with at least one other episode of any specialty. Method one (no evidence of transfer required; overlapping episodes grouped together) resulted in the longest mean LOS (4.0 days for all specialties; 48.5 days for psychiatric specialties) and the fewest single episode person spells (82.4% of all specialties; 69.7% for psychiatric specialties). Method three (evidence of transfer required; overlapping episodes separated) resulted in the shortest mean LOS (3.7 days for all specialties; 45.8 days for psychiatric specialties) and the most single episode person spells; (86.9% for all specialties; 86.3% for psychiatric specialties).<h4>Conclusions</h4>Transfers-in appear better recorded than transfers-out. Transfer coding is incomplete, particularly for psychiatric specialties. The proportion of episodes that overlap is small but psychiatric episodes are disproportionately affected. The most successful method for grouping episodes into person spells aggregated overlapping episodes and required no evidence of transfer from admission source/method or discharge destination codes. The least successful method treated overlapping episodes as distinct and required transfer coding. The impact of all four methods was greater for psychiatric specialties.","Rees et al used a Welsh database to examine inpatient episode/transfer coding coding for psychiatric patients. They identified deficiencies in the existing coding system for psychitatrics transfers and unexplained coding mistakes/problems, then they presesnt several different methods for constructing the inpatient spell to improve coding and avoid misclassification.",pdf:https://bmcmedinformdecismak.biomedcentral.com/track/pdf/10.1186/s12911-019-0953-2; doi:https://doi.org/10.1186/s12911-019-0953-2; html:https://europepmc.org/articles/PMC6884917; pdf:https://europepmc.org/articles/PMC6884917?pdf=render
 35024157,https://doi.org/10.1177/20552076211059350,Digitally enabled flash glucose monitoring for inpatients with COVID-19: Feasibility and pilot implementation in a teaching NHS Hospital in the UK.,"Robbins T, Hopper A, Brophy J, Pearson E, Suthantirakumar R, Vankad M, Igharo N, Baitule S, Clark CC, Arvanitis TN, Sankar S, Kyrou I, Randeva H.",,Digital health,2022,2022-01-07,Y,Diabetes; Inpatient Care; Digital Health; Flash Glucose Monitoring; Covid-19,,,"<h4>Background</h4>COVID-19 placed significant challenges on healthcare systems. People with diabetes are at high risk of severe COVID-19 with poor outcomes. We describe the first reported use of inpatient digital flash glucose monitoring devices in a UK NHS hospital to support management of people with diabetes hospitalized for COVID-19.<h4>Methods</h4>Inpatients at University Hospitals Coventry & Warwickshire (UHCW) NHS Trust with COVID-19 and diabetes were considered for digitally enabled flash glucose monitoring during their hospitalization. Glucose monitoring data were analysed, and potential associations were explored between relevant parameters, including time in hypoglycaemia, hyperglycaemia, and in range, glycated haemoglobin (HbA1c), average glucose, body mass index (BMI), and length of stay.<h4>Results</h4>During this pilot, digital flash glucose monitoring devices were offered to 25 inpatients, of whom 20 (type 2/type 1: 19/1; mean age: 70.6 years; mean HbA1c: 68.2 mmol/mol; mean BMI: 28.2 kg/m<sup>2</sup>) accepted and used these (80% uptake). In total, over 2788 h of flash glucose monitoring were recorded for these inpatients with COVID-19 and diabetes. Length of stay was not associated with any of the studied variables (all p-values >0.05). Percentage of time in hyperglycaemia exhibited significant associations with both percentage of time in hypoglycaemia and percentage of time in range, as well as with HbA1c (all p-values <0.05). The average glucose was significantly associated with percentage of time in hypoglycaemia, percentage of time in range, and HbA1c (all p-values <0.05).<h4>Discussion</h4>We report the first pilot inpatient use of digital flash glucose monitors in an NHS hospital to support care of inpatients with diabetes and COVID-19. Overall, there are strong arguments for the inpatient use of these devices in the COVID-19 setting, and the findings of this pilot demonstrate feasibility of this digitally enabled approach and support wider use for inpatients with diabetes and COVID-19.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/20552076211059350; doi:https://doi.org/10.1177/20552076211059350; html:https://europepmc.org/articles/PMC8744149; pdf:https://europepmc.org/articles/PMC8744149?pdf=render
+34430796,https://doi.org/10.1016/j.mayocpiqo.2021.08.011,Association Between Accelerometer-Assessed Physical Activity and Severity of COVID-19 in UK Biobank.,"Rowlands AV, Dempsey PC, Gillies C, Kloecker DE, Razieh C, Chudasama Y, Islam N, Zaccardi F, Lawson C, Norris T, Davies MJ, Khunti K, Yates T.",,"Mayo Clinic proceedings. Innovations, quality & outcomes",2021,2021-08-20,Y,"Mvpa, Moderate To Vigorous Physical Activity; Covid-19, Coronavirus Disease 2019; Sars-cov-2, Severe Acute Respiratory Syndrome Coronavirus 2",,,"<h4>Objective</h4>To quantify the association between accelerometer-assessed physical activity and coronavirus disease 2019 (COVID-19) outcomes.<h4>Methods</h4>Data from 82,253 UK Biobank participants with accelerometer data (measured 2013-2015), complete covariate data, and linked COVID-19 data from March 16, 2020, to March 16, 2021, were included. Two outcomes were investigated: severe COVID-19 (positive test result from in-hospital setting or COVID-19 as primary cause of death) and nonsevere COVID-19 (positive test result from community setting). Logistic regressions were used to assess associations with moderate to vigorous physical activity (MVPA), total activity, and intensity gradient. A higher intensity gradient indicates a higher proportion of vigorous activity.<h4>Results</h4>Average MVPA was 48.1 (32.7) min/d. Physical activity was associated with lower odds of severe COVID-19 (adjusted odds ratio per standard deviation increase: MVPA, 0.75 [95% CI, 0.67 to 0.85]; total, 0.83 [0.74 to 0.92]; intensity, 0.77 [0.70 to 0.86]), with stronger associations in women (MVPA, 0.63 [0.52 to 0.77]; total, 0.76 [0.64 to 0.90]; intensity, 0.63 [0.53 to 0.74]) than in men (MVPA, 0.84 [0.73 to 0.97]; total, 0.88 [0.77 to 1.01]; intensity, 0.88 [0.77 to 1.00]). In contrast, when mutually adjusted, total activity was associated with higher odds of a nonsevere infection (1.10 [1.04 to 1.16]), whereas the intensity gradient was associated with lower odds (0.91 [0.86 to 0.97]).<h4>Conclusion</h4>Odds of severe COVID-19 were approximately 25% lower per standard deviation (∼30 min/d) MVPA. A greater proportion of vigorous activity was associated with lower odds of severe and nonsevere infections. The association between total activity and higher odds of a nonsevere infection may be through greater community engagement and thus more exposure to the virus. Results support calls for public health messaging highlighting the potential of MVPA for reducing the odds of severe COVID-19.",,pdf:http://www.mcpiqojournal.org/article/S2542454821001302/pdf; doi:https://doi.org/10.1016/j.mayocpiqo.2021.08.011; html:https://europepmc.org/articles/PMC8376658; pdf:https://europepmc.org/articles/PMC8376658?pdf=render
 37475157,https://doi.org/10.1093/cvr/cvad106,A machine learning based approach to identify carotid subclinical atherosclerosis endotypes.,"Chen QS, Bergman O, Ziegler L, Baldassarre D, Veglia F, Tremoli E, Strawbridge RJ, Gallo A, Pirro M, Smit AJ, Kurl S, Savonen K, Lind L, Eriksson P, Gigante B.",,Cardiovascular research,2023,2023-12-01,Y,Atherosclerosis; Artificial intelligence; biological markers; Endotype; Progression Of Atherosclerosis; Ascvd,,,"<h4>Aims</h4>To define endotypes of carotid subclinical atherosclerosis.<h4>Methods and results</h4>We integrated demographic, clinical, and molecular data (n = 124) with ultrasonographic carotid measurements from study participants in the IMPROVE cohort (n = 3340). We applied a neural network algorithm and hierarchical clustering to identify carotid atherosclerosis endotypes. A measure of carotid subclinical atherosclerosis, the c-IMTmean-max, was used to extract atherosclerosis-related features and SHapley Additive exPlanations (SHAP) to reveal endotypes. The association of endotypes with carotid ultrasonographic measurements at baseline, after 30 months, and with the 3-year atherosclerotic cardiovascular disease (ASCVD) risk was estimated by linear (β, SE) and Cox [hazard ratio (HR), 95% confidence interval (CI)] regression models. Crude estimates were adjusted by common cardiovascular risk factors, and baseline ultrasonographic measures. Improvement in ASCVD risk prediction was evaluated by C-statistic and by net reclassification improvement with reference to SCORE2, c-IMTmean-max, and presence of carotid plaques. An ensemble stacking model was used to predict endotypes in an independent validation cohort, the PIVUS (n = 1061). We identified four endotypes able to differentiate carotid atherosclerosis risk profiles from mild (endotype 1) to severe (endotype 4). SHAP identified endotype-shared variables (age, biological sex, and systolic blood pressure) and endotype-specific biomarkers. In the IMPROVE, as compared to endotype 1, endotype 4 associated with the thickest c-IMT at baseline (β, SE) 0.36 (0.014), the highest number of plaques 1.65 (0.075), the fastest c-IMT progression 0.06 (0.013), and the highest ASCVD risk (HR, 95% CI) (1.95, 1.18-3.23). Baseline and progression measures of carotid subclinical atherosclerosis and ASCVD risk were associated with the predicted endotypes in the PIVUS. Endotypes consistently improved measures of ASCVD risk discrimination and reclassification in both study populations.<h4>Conclusions</h4>We report four replicable subclinical carotid atherosclerosis-endotypes associated with progression of atherosclerosis and ASCVD risk in two independent populations. Our approach based on endotypes can be applied for precision medicine in ASCVD prevention.",,pdf:https://academic.oup.com/cardiovascres/advance-article-pdf/doi/10.1093/cvr/cvad106/50910161/cvad106.pdf; doi:https://doi.org/10.1093/cvr/cvad106; html:https://europepmc.org/articles/PMC10730242; pdf:https://europepmc.org/articles/PMC10730242?pdf=render
 36178783,https://doi.org/10.1167/tvst.11.9.34,Phenotyping of ABCA4 Retinopathy by Machine Learning Analysis of Full-Field Electroretinography.,"Glinton SL, Calcagni A, Lilaonitkul W, Pontikos N, Vermeirsch S, Zhang G, Arno G, Wagner SK, Michaelides M, Keane PA, Webster AR, Mahroo OA, Robson AG.",,Translational vision science & technology,2022,2022-09-01,Y,,,,"<h4>Purpose</h4>Biallelic pathogenic variants in ABCA4 are the commonest cause of monogenic retinal disease. The full-field electroretinogram (ERG) quantifies severity of retinal dysfunction. We explored application of machine learning in ERG interpretation and in genotype-phenotype correlations.<h4>Methods</h4>International standard ERGs in 597 cases of ABCA4 retinopathy were classified into three functional phenotypes by human experts: macular dysfunction alone (group 1), or with additional generalized cone dysfunction (group 2), or both cone and rod dysfunction (group 3). Algorithms were developed for automatic selection and measurement of ERG components and for classification of ERG phenotype. Elastic-net regression was used to quantify severity of specific ABCA4 variants based on effect on retinal function.<h4>Results</h4>Of the cohort, 57.6%, 7.4%, and 35.0% fell into groups 1, 2, and 3 respectively. Compared with human experts, automated classification showed overall accuracy of 91.8% (SE, 0.169), and 96.7%, 39.3%, and 93.8% for groups 1, 2, and 3. When groups 2 and 3 were combined, the average holdout group accuracy was 93.6% (SE, 0.142). A regression model yielded phenotypic severity scores for the 47 commonest ABCA4 variants.<h4>Conclusions</h4>This study quantifies prevalence of phenotypic groups based on retinal function in a uniquely large single-center cohort of patients with electrophysiologically characterized ABCA4 retinopathy and shows applicability of machine learning. Novel regression-based analyses of ABCA4 variant severity could identify individuals predisposed to severe disease.<h4>Translational relevance</h4>Machine learning can yield meaningful classifications of ERG data, and data-driven scoring of genetic variants can identify patients likely to benefit most from future therapies.",,doi:https://doi.org/10.1167/tvst.11.9.34; doi:https://doi.org/10.1167/tvst.11.9.34; html:https://europepmc.org/articles/PMC9527330; pdf:https://europepmc.org/articles/PMC9527330?pdf=render
-34430796,https://doi.org/10.1016/j.mayocpiqo.2021.08.011,Association Between Accelerometer-Assessed Physical Activity and Severity of COVID-19 in UK Biobank.,"Rowlands AV, Dempsey PC, Gillies C, Kloecker DE, Razieh C, Chudasama Y, Islam N, Zaccardi F, Lawson C, Norris T, Davies MJ, Khunti K, Yates T.",,"Mayo Clinic proceedings. Innovations, quality & outcomes",2021,2021-08-20,Y,"Mvpa, Moderate To Vigorous Physical Activity; Covid-19, Coronavirus Disease 2019; Sars-cov-2, Severe Acute Respiratory Syndrome Coronavirus 2",,,"<h4>Objective</h4>To quantify the association between accelerometer-assessed physical activity and coronavirus disease 2019 (COVID-19) outcomes.<h4>Methods</h4>Data from 82,253 UK Biobank participants with accelerometer data (measured 2013-2015), complete covariate data, and linked COVID-19 data from March 16, 2020, to March 16, 2021, were included. Two outcomes were investigated: severe COVID-19 (positive test result from in-hospital setting or COVID-19 as primary cause of death) and nonsevere COVID-19 (positive test result from community setting). Logistic regressions were used to assess associations with moderate to vigorous physical activity (MVPA), total activity, and intensity gradient. A higher intensity gradient indicates a higher proportion of vigorous activity.<h4>Results</h4>Average MVPA was 48.1 (32.7) min/d. Physical activity was associated with lower odds of severe COVID-19 (adjusted odds ratio per standard deviation increase: MVPA, 0.75 [95% CI, 0.67 to 0.85]; total, 0.83 [0.74 to 0.92]; intensity, 0.77 [0.70 to 0.86]), with stronger associations in women (MVPA, 0.63 [0.52 to 0.77]; total, 0.76 [0.64 to 0.90]; intensity, 0.63 [0.53 to 0.74]) than in men (MVPA, 0.84 [0.73 to 0.97]; total, 0.88 [0.77 to 1.01]; intensity, 0.88 [0.77 to 1.00]). In contrast, when mutually adjusted, total activity was associated with higher odds of a nonsevere infection (1.10 [1.04 to 1.16]), whereas the intensity gradient was associated with lower odds (0.91 [0.86 to 0.97]).<h4>Conclusion</h4>Odds of severe COVID-19 were approximately 25% lower per standard deviation (∼30 min/d) MVPA. A greater proportion of vigorous activity was associated with lower odds of severe and nonsevere infections. The association between total activity and higher odds of a nonsevere infection may be through greater community engagement and thus more exposure to the virus. Results support calls for public health messaging highlighting the potential of MVPA for reducing the odds of severe COVID-19.",,pdf:http://www.mcpiqojournal.org/article/S2542454821001302/pdf; doi:https://doi.org/10.1016/j.mayocpiqo.2021.08.011; html:https://europepmc.org/articles/PMC8376658; pdf:https://europepmc.org/articles/PMC8376658?pdf=render
 38162515,https://doi.org/10.1016/j.lanepe.2023.100816,"Risk of severe COVID-19 outcomes after autumn 2022 COVID-19 booster vaccinations: a pooled analysis of national prospective cohort studies involving 7.4 million adults in England, Northern Ireland, Scotland and Wales.","Bedston S, Almaghrabi F, Patterson L, Agrawal U, Woolford L, Anand SN, Joy M, Crawford A, Goudie R, Byford R, Abbasizanjani H, Smith D, Laidlaw L, Akbari A, Sullivan C, Bradley DT, Lyons RA, de Lusignan S, Hobbs FDR, Robertson C, Sheikh SA, Shi T.",,The Lancet regional health. Europe,2024,2023-12-12,Y,Vaccine; Hospital Admission; Booster Dose; Vaccine Breakthrough; Covid-19,,,"<h4>Background</h4>UK COVID-19 vaccination policy has evolved to offering COVID-19 booster doses to individuals at increased risk of severe Illness from COVID-19. Building on our analyses of vaccine effectiveness of first, second and initial booster doses, we aimed to identify individuals at increased risk of severe outcomes (i.e., COVID-19 related hospitalisation or death) post the autumn 2022 booster dose.<h4>Methods</h4>We undertook a national population-based cohort analysis across all four UK nations through linked primary care, vaccination, hospitalisation and mortality data. We included individuals who received autumn 2022 booster doses of BNT162b2 (Comirnaty) or mRNA-1273 (Spikevax) during the period September 1, 2022 to December 31, 2022 to investigate the risk of severe COVID-19 outcomes. Cox proportional hazard models were used to estimate adjusted hazard ratios (aHR) and 95% confidence intervals (CIs) for the association between demographic and clinical factors and severe COVID-19 outcomes after the autumn booster dose. Analyses were adjusted for age, sex, body mass index (BMI), deprivation, urban/rural areas and comorbidities. Stratified analyses were conducted by vaccine type. We then conducted a fixed-effect meta-analysis to combine results across the four UK nations.<h4>Findings</h4>Between September 1, 2022 and December 31, 2022, 7,451,890 individuals ≥18 years received an autumn booster dose. 3500 had severe COVID-19 outcomes (2.9 events per 1000 person-years). Being male (male vs female, aHR 1.41 (1.32-1.51)), older adults (≥80 years vs 18-49 years; 10.43 (8.06-13.50)), underweight (BMI <18.5 vs BMI 25.0-29.9; 2.94 (2.51-3.44)), those with comorbidities (≥5 comorbidities vs none; 9.45 (8.15-10.96)) had a higher risk of COVID-19 hospitalisation or death after the autumn booster dose. Those with a larger household size (≥11 people within household vs 2 people; 1.56 (1.23-1.98)) and from more deprived areas (most deprived vs least deprived quintile; 1.35 (1.21-1.51)) had modestly higher risks. We also observed at least a two-fold increase in risk for those with various chronic neurological conditions, including Down's syndrome, immunodeficiency, chronic kidney disease, cancer, chronic respiratory disease, or cardiovascular disease.<h4>Interpretation</h4>Males, older individuals, underweight individuals, those with an increasing number of comorbidities, from a larger household or more deprived areas, and those with specific underlying health conditions remained at increased risk of COVID-19 hospitalisation and death after the autumn 2022 vaccine booster dose. There is now a need to focus on these risk groups for investigating immunogenicity and efficacy of further booster doses or therapeutics.<h4>Funding</h4>National Core Studies-Immunity, UK Research and Innovation (Medical Research Council and Economic and Social Research Council), Health Data Research UK, the Scottish Government, and the University of Edinburgh.",,doi:https://doi.org/10.1016/j.lanepe.2023.100816; html:https://europepmc.org/articles/PMC10757260; pdf:https://europepmc.org/articles/PMC10757260?pdf=render
 38510243,https://doi.org/10.3389/fimmu.2024.1360629,High hypoxia status in pancreatic cancer is associated with multiple hallmarks of an immunosuppressive tumor microenvironment.,"Sadozai H, Acharjee A, Kayani HZ, Gruber T, Gorczynski RM, Burke B.",,Frontiers in immunology,2024,2024-03-06,Y,Hypoxia; Galectins; Immune Checkpoint; Pancreatic Ductal Adenocarcinoma (Pdac); Tumor Microenvironment (Tme),,,"<h4>Introduction</h4>Pancreatic ductal adenocarcinoma (PDAC), the most common form of pancreatic cancer, is a particularly lethal disease that is often diagnosed late and is refractory to most forms of treatment. Tumour hypoxia is a key hallmark of PDAC and is purported to contribute to multiple facets of disease progression such as treatment resistance, increased invasiveness, metabolic reprogramming, and immunosuppression.<h4>Methods</h4>We used the Buffa gene signature as a hypoxia score to profile transcriptomics datasets from PDAC cases. We performed cell-type deconvolution and gene expression profiling approaches to compare the immunological phenotypes of cases with low and high hypoxia scores. We further supported our findings by qPCR analyses in PDAC cell lines cultured in hypoxic conditions.<h4>Results</h4>First, we demonstrated that this hypoxia score is associated with increased tumour grade and reduced survival suggesting that this score is correlated to disease progression. Subsequently, we compared the immune phenotypes of cases with high versus low hypoxia score expression (Hypoxia<sup>HI</sup> vs. Hypoxia<sup>LOW</sup>) to show that high hypoxia is associated with reduced levels of T cells, NK cells and dendritic cells (DC), including the crucial cDC1 subset. Concomitantly, immune-related gene expression profiling revealed that compared to Hypoxia<sup>LOW</sup> tumours, mRNA levels for multiple immunosuppressive molecules were notably elevated in Hypoxia<sup>HI</sup> cases. Using a Random Forest machine learning approach for variable selection, we identified <i>LGALS3</i> (Galectin-3) as the top gene associated with high hypoxia status and confirmed its expression in hypoxic PDAC cell lines.<h4>Discussion</h4>In summary, we demonstrated novel associations between hypoxia and multiple immunosuppressive mediators in PDAC, highlighting avenues for improving PDAC immunotherapy by targeting these immune molecules in combination with hypoxia-targeted drugs.",,doi:https://doi.org/10.3389/fimmu.2024.1360629; html:https://europepmc.org/articles/PMC10951397; pdf:https://europepmc.org/articles/PMC10951397?pdf=render
 36426419,https://doi.org/10.1111/hsc.14109,"""I don't mean to be rude, but could you put a mask on while I'm here?"" A qualitative study of risks experienced by domiciliary care workers in Wales during the COVID-19 pandemic.","Prout H, Lugg-Widger FV, Brookes-Howell L, Cannings-John R, Akbari A, John A, Thomas DR, Robling M.",,Health & social care in the community,2022,2022-11-24,Y,Qualitative; risk; Social Care; Covid-19; Domiciliary Care Workers,,,"Domiciliary care workers (DCWs) continued to provide care to adults in their own homes throughout the COVID-19 pandemic. The evidence of the impact of COVID-19 on health outcomes of DCWs is currently mixed. The OSCAR study will quantify the impact of COVID-19 upon health outcomes of DCWs in Wales, explore causes of variation and extrapolate to the rest of the UK DCW population. An embedded qualitative study aimed to explore DCW experiences during the pandemic, including factors that may have varied risk of exposure to COVID-19 and adverse health and wellbeing outcomes. Registered DCWs working throughout Wales were invited to participate in a semi-structured telephone interview. 24 DCWs were interviewed between February and July 2021. Themes were identified through inductive analysis using thematic coding. Several themes emerged relating to risk of exposure to COVID-19. First, general changes to the role of the DCW during the pandemic were identified. Second, practical challenges for DCWs in the workplace were reported, including staff shortages, clients and families not following safety procedures, initial shortages of personal protective equipment (PPE), DCW criticism of standard use PPE, client difficulty with PPE and management of rapid antigen testing. Third, lack of government/employer preparation for a pandemic was described, including the reorganisation of staff clients and services, inadequate or confusing information for many DCWs, COVID-19 training and the need for improved practical instruction and limited official standard risk assessments for DCWs. Pressure to attend work and perceptions of COVID-19 risk and vaccination was also reported. In summary, this paper describes the risk factors associated with working during the pandemic. We have mapped recommendations for each problem using these qualitative findings including tailored training and better support for isolated team members and identified the required changes at several socio-ecological levels.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/hsc.14109; doi:https://doi.org/10.1111/hsc.14109; html:https://europepmc.org/articles/PMC10100139; pdf:https://europepmc.org/articles/PMC10100139?pdf=render
@@ -336,33 +336,33 @@ PMC11234640,https://doi.org/,"Evidence of gene-nutrient interaction association
 38912714,https://doi.org/10.1097/ede.0000000000001747,Effectiveness of mRNA COVID-19 Vaccines as First Booster Doses in England: An Observational Study in OpenSAFELY-TPP.,"Horne EMF, Hulme WJ, Parker EPK, Keogh RH, Williamson EJ, Williamson EJ, Walker VM, Palmer TM, Denholm R, Knight R, Curtis HJ, Walker AJ, Andrews CD, Mehrkar A, Morley J, MacKenna B, Bacon SCJ, Goldacre B, Hernán MA, Sterne JAC, and the OpenSAFELY collaborative.",,"Epidemiology (Cambridge, Mass.)",2024,2024-06-24,Y,,,,"<h4>Background</h4>The UK delivered its first ""booster"" COVID-19 vaccine doses in September 2021, initially to individuals at high risk of severe disease, then to all adults. The BNT162b2 Pfizer-BioNTech vaccine was used initially, then also Moderna mRNA-1273.<h4>Methods</h4>With the approval of the National Health Service England, we used routine clinical data to estimate the effectiveness of boosting with BNT162b2 or mRNA-1273 compared with no boosting in eligible adults who had received two primary course vaccine doses. We matched each booster recipient with an unboosted control on factors relating to booster priority status and prior COVID-19 immunization. We adjusted for additional factors in Cox models, estimating hazard ratios up to 182 days (6 months) following booster dose. We estimated hazard ratios overall and within the following periods: 1-14, 15-42, 43-69, 70-97, 98-126, 127-152, and 155-182 days. Outcomes included a positive SARS-CoV-2 test, COVID-19 hospitalization, COVID-19 death, non-COVID-19 death, and fracture.<h4>Results</h4>We matched 8,198,643 booster recipients with unboosted controls. Adjusted hazard ratios over 6-month follow-up were: positive SARS-CoV-2 test 0.75 (0.74, 0.75); COVID-19 hospitalization 0.30 (0.29, 0.31); COVID-19 death 0.11 (0.10, 0.14); non-COVID-19 death 0.22 (0.21, 0.23); and fracture 0.77 (0.75, 0.78). Estimated effectiveness of booster vaccines against severe COVID-19-related outcomes peaked during the first 3 months following the booster dose. By 6 months, the cumulative incidence of positive SARS-CoV-2 test was higher in boosted than unboosted individuals.<h4>Conclusions</h4>We estimate that COVID-19 booster vaccination, compared with no booster vaccination, provided substantial protection against COVID-19 hospitalization and COVID-19 death but only limited protection against positive SARS-CoV-2 test. Lower rates of fracture in boosted than unboosted individuals may suggest unmeasured confounding. Observational studies should report estimated vaccine effectiveness against nontarget and negative control outcomes.",,html:https://journals.lww.com/epidem/fulltext/2024/07000/effectiveness_of_mrna_covid_19_vaccines_as_first.18.aspx; doi:https://doi.org/10.1097/EDE.0000000000001747; html:https://europepmc.org/articles/PMC11191555; pdf:https://europepmc.org/articles/PMC11191555?pdf=render
 36580462,https://doi.org/10.1371/journal.pone.0279381,Investigating the potential impact of PCSK9-inhibitors on mood disorders using eQTL-based Mendelian randomization.,"Aman A, Slob EAW, Ward J, Cullen B, Graham N, Lyall DM, Sattar N, Strawbridge RJ.",,PloS one,2022,2022-12-29,Y,,,,"Prescription of PCSK9-inhibitors has increased in recent years but not much is known about its off-target effects. PCSK9-expression is evident in non-hepatic tissues, notably the brain, and genetic variation in the PCSK9 locus has recently been shown to be associated with mood disorder-related traits. We investigated whether PCSK9 inhibition, proxied by a genetic reduction in expression of PCSK9 mRNA, might have a causal adverse effect on mood disorder-related traits. We used genetic variants in the PCSK9 locus associated with reduced PCSK9 expression (eQTLs) in the European population from GTEx v8 and examined the effect on PCSK9 protein levels and three mood disorder-related traits (major depressive disorder, mood instability, and neuroticism), using summary statistics from the largest European ancestry genome-wide association studies. We conducted summary-based Mendelian randomization analyses to estimate the causal effects, and attempted replication using data from eQTLGen, Brain-eMETA, and the CAGE consortium. We found that genetically reduced PCSK9 gene-expression levels were significantly associated with reduced PCSK9 protein levels but not with increased risk of mood disorder-related traits. Further investigation of nearby genes demonstrated that reduced USP24 gene-expression levels was significantly associated with increased risk of mood instability (p-value range = 5.2x10-5-0.03), and neuroticism score (p-value range = 2.9x10-5-0.02), but not with PCSK9 protein levels. Our results suggest that genetic variation in this region acts on mood disorders through a PCSK9-independent pathway, and therefore PCSK9-inhibitors are unlikely to have an adverse impact on mood disorder-related traits.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0279381&type=printable; doi:https://doi.org/10.1371/journal.pone.0279381; html:https://europepmc.org/articles/PMC9799310; pdf:https://europepmc.org/articles/PMC9799310?pdf=render
 38751343,https://doi.org/10.1093/ced/llae196,Disagreement concerning atopic dermatitis subtypes between an English prospective cohort (ALSPAC) and linked electronic health records.,"Matthewman J, Mulick A, Dand N, Major-Smith D, Henderson A, Pearce N, Denaxas S, Iskandar R, Roberts A, Cornish RP, Brown SJ, Paternoster L, Langan SM.",,Clinical and experimental dermatology,2024,2024-05-16,N,,,,"<h4>Background</h4>Subtypes of atopic dermatitis (AD) have been derived from the Avon Longitudinal Study of Parents and Children (ALSPAC) based on presence and severity of symptoms reported in questionnaires (Severe-Frequent, Moderate-Frequent, Moderate-Declining, Mild-Intermittent, Unaffected/Rare). Good agreement between ALSPAC and linked electronic health records (EHRs) would increase trust in the clinical validity of these subtypes and allow inferring subtypes from EHRs alone, which would enable their study in large primary care databases.<h4>Objectives</h4>1. Explore if presence and number of AD records in EHRs agrees with AD symptom and severity reports from ALSPAC; 2. Explore if EHRs agree with ALSPAC-derived AD subtypes; 3. Construct models to classify ALSPAC-derived AD subtype using EHRs.<h4>Methods</h4>We used data from the ALSPAC prospective cohort study from 11 timepoints until age 14 years (1991-2008), linked to local general practice EHRs. We assessed how far ALSPAC questionnaire responses and derived subtypes agreed with AD as established in EHRs using different AD definitions (e.g., diagnosis and/or prescription) and other AD-related records. We classified AD subtypes using EHRs, fitting multinomial logistic regression models tuning hyperparameters and evaluating performance in the testing set (ROC AUC, accuracy, sensitivity, and specificity).<h4>Results</h4>8,828 individuals out of a total 13,898 had both been assigned an AD subtype and had linked EHRs. The number of AD-related codes in EHRs generally increased with severity of AD subtype, however not all with the Severe-Frequent subtypes had AD in EHRs, and many with the Unaffected/Rare subtype did have AD in EHRs. When predicting ALSPAC AD subtype using EHRs, the best tuned model had ROC AUC of 0.65, sensitivity of 0.29 and specificity of 0.83 (both macro averaged); when different sets of predictors were used, individuals with missing EHR coverage excluded, and subtypes combined, sensitivity was not considerably improved.<h4>Conclusions</h4>ALSPAC and EHRs disagreed not just on AD subtypes, but also on whether children had AD or not. Researchers should be aware that individuals considered as having AD in one source may not be considered as having AD in another.",,doi:https://doi.org/10.1093/ced/llae196; doi:https://doi.org/10.1093/ced/llae196
+35027756,https://doi.org/10.1038/s41591-021-01666-2,SARS-CoV-2 infection and COVID-19 vaccination rates in pregnant women in Scotland.,"Stock SJ, Carruthers J, Calvert C, Denny C, Donaghy J, Goulding A, Hopcroft LEM, Hopkins L, McLaughlin T, Pan J, Shi T, Taylor B, Agrawal U, Auyeung B, Katikireddi SV, McCowan C, Murray J, Simpson CR, Robertson C, Vasileiou E, Sheikh A, Wood R.",,Nature medicine,2022,2022-01-13,Y,,,,"Population-level data on COVID-19 vaccine uptake in pregnancy and SARS-CoV-2 infection outcomes are lacking. We describe COVID-19 vaccine uptake and SARS-CoV-2 infection in pregnant women in Scotland, using whole-population data from a national, prospective cohort. Between the start of a COVID-19 vaccine program in Scotland, on 8 December 2020 and 31 October 2021, 25,917 COVID-19 vaccinations were given to 18,457 pregnant women. Vaccine coverage was substantially lower in pregnant women than in the general female population of 18-44 years; 32.3% of women giving birth in October 2021 had two doses of vaccine compared to 77.4% in all women. The extended perinatal mortality rate for women who gave birth within 28 d of a COVID-19 diagnosis was 22.6 per 1,000 births (95% CI 12.9-38.5; pandemic background rate 5.6 per 1,000 births; 452 out of 80,456; 95% CI 5.1-6.2). Overall, 77.4% (3,833 out of 4,950; 95% CI 76.2-78.6) of SARS-CoV-2 infections, 90.9% (748 out of 823; 95% CI 88.7-92.7) of SARS-CoV-2 associated with hospital admission and 98% (102 out of 104; 95% CI 92.5-99.7) of SARS-CoV-2 associated with critical care admission, as well as all baby deaths, occurred in pregnant women who were unvaccinated at the time of COVID-19 diagnosis. Addressing low vaccine uptake rates in pregnant women is imperative to protect the health of women and babies in the ongoing pandemic.",,pdf:https://www.nature.com/articles/s41591-021-01666-2.pdf; doi:https://doi.org/10.1038/s41591-021-01666-2; html:https://europepmc.org/articles/PMC8938271; pdf:https://europepmc.org/articles/PMC8938271?pdf=render
 36441117,https://doi.org/10.1111/acps.13523,Predictors of hospital readmission for patients diagnosed with delirium: An electronic health record data analysis.,"Friedrich ME, Perera G, Leutgeb L, Haardt D, Frey R, Stewart R, Mueller C.",,Acta psychiatrica Scandinavica,2023,2022-12-28,Y,Dementia; risk factors; Delirium; Readmission,,,"<h4>Introduction</h4>Delirium is an acute and fluctuating change in attention and cognition that increases the risk of functional decline, institutionalisation and death in hospitalised patients. After delirium, patients have a significantly higher risk of readmission to hospital. Our aim was to investigate factors associated with hospital readmission in people with delirium.<h4>Methods</h4>We carried out an observational retrospective cohort study using linked mental health care and hospitalisation records from South London. Logistic regression models were used to predict the odds of 30-day readmission and Cox proportional hazard models to calculate readmission risks when not restricting follow-up time.<h4>Results</h4>Of 2814 patients (mean age 78.9 years SD ±11.8) discharged from hospital after an episode of delirium, 823 (29.3%) were readmitted within 30 days. Depressed mood (odds ratio (OR) 1.34 (95% confidence interval (CI) 1.08-1.66)), moderate-to-severe physical health problems (OR 1.67 (95% CI 1.18-2.2.36)) and a history of serious circulatory disease (OR 1.29 (95% CI 1.07-1.55)) were associated with higher odds of hospital readmission, whereas a diagnosis of delirium superimposed on dementia (OR 0.67 (95% CI 0.53-0.84)) and problematic alcohol/substance (OR 0.54 (95% CI 0.33-0.89)) use were associated with lower odds. Cox proportionate hazard models showed similar results.<h4>Conclusion</h4>Almost one-third of patients with delirium were readmitted within a short period of time, a more detailed understanding of the underlying risk factors could help prevent readmissions. Our findings indicate that the aetiology (as alcohol-related delirium), the recognition that delirium occurred in the context of dementia, as well as potentially modifiable factors, as depressed mood affect readmission risk, and should be assessed in clinical settings.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/acps.13523; doi:https://doi.org/10.1111/acps.13523; html:https://europepmc.org/articles/PMC10463092; pdf:https://europepmc.org/articles/PMC10463092?pdf=render
 37946218,https://doi.org/10.1186/s12916-023-03055-7,Social connection and mortality in UK Biobank: a prospective cohort analysis.,"Foster HME, Gill JMR, Mair FS, Celis-Morales CA, Jani BD, Nicholl BI, Lee D, O'Donnell CA.",,BMC medicine,2023,2023-11-10,Y,epidemiology; Public Health; Loneliness; Social Isolation; Social Determinants Of Health; Social Connection,,,"<h4>Background</h4>Components of social connection are associated with mortality, but research examining their independent and combined effects in the same dataset is lacking. This study aimed to examine the independent and combined associations between functional and structural components of social connection and mortality.<h4>Methods</h4>Analysis of 458,146 participants with full data from the UK Biobank cohort linked to mortality registers. Social connection was assessed using two functional (frequency of ability to confide in someone close and often feeling lonely) and three structural (frequency of friends/family visits, weekly group activities, and living alone) component measures. Cox proportional hazard models were used to examine the associations with all-cause and cardiovascular disease (CVD) mortality.<h4>Results</h4>Over a median of 12.6 years (IQR 11.9-13.3) follow-up, 33,135 (7.2%) participants died, including 5112 (1.1%) CVD deaths. All social connection measures were independently associated with both outcomes. Friends/family visit frequencies < monthly were associated with a higher risk of mortality indicating a threshold effect. There were interactions between living alone and friends/family visits and between living alone and weekly group activity. For example, compared with daily friends/family visits-not living alone, there was higher all-cause mortality for daily visits-living alone (HR 1.19 [95% CI 1.12-1.26]), for never having visits-not living alone (1.33 [1.22-1.46]), and for never having visits-living alone (1.77 [1.61-1.95]). Never having friends/family visits whilst living alone potentially counteracted benefits from other components as mortality risks were highest for those reporting both never having visits and living alone regardless of weekly group activity or functional components. When all measures were combined into overall functional and structural components, there was an interaction between components: compared with participants defined as not isolated by both components, those considered isolated by both components had higher CVD mortality (HR 1.63 [1.51-1.76]) than each component alone (functional isolation 1.17 [1.06-1.29]; structural isolation 1.27 [1.18-1.36]).<h4>Conclusions</h4>This work suggests (1) a potential threshold effect for friends/family visits, (2) that those who live alone with additional concurrent markers of structural isolation may represent a high-risk population, (3) that beneficial associations for some types of social connection might not be felt when other types of social connection are absent, and (4) considering both functional and structural components of social connection may help to identify the most isolated in society.",,doi:https://doi.org/10.1186/s12916-023-03055-7; html:https://europepmc.org/articles/PMC10637015; pdf:https://europepmc.org/articles/PMC10637015?pdf=render
 39301141,https://doi.org/10.12688/wellcomeopenres.16058.2,Tracking Excess Deaths (TRACKED) - an interactive online tool to monitor excess deaths associated with the COVID-19 pandemic in the United Kingdom.,"Poon MTC, Brennan PM, Jin K, Figueroa JD, Sudlow CLM.",,Wellcome open research,2020,2020-11-20,Y,Mortality; Coronavirus; Web Application; Excess Deaths; Covid-19,,,"<b>Background:</b> We aimed to describe trends of excess mortality in the United Kingdom (UK) stratified by nation and cause of death, and to develop an online tool for reporting the most up to date data on excess mortality <b>Methods:</b> Population statistics agencies in the UK including the Office for National Statistics (ONS), National Records of Scotland (NRS), and Northern Ireland Statistics and Research Agency (NISRA) publish weekly mortality data. We used mortality data up to 22 <sup>nd</sup> May in the ONS and the NISRA and 24 <sup>th</sup> May in the NRS. The main outcome measures were crude mortality for non-COVID deaths (where there is no mention of COVID-19 on the death certificate) calculated, and excess mortality defined as difference between observed mortality and expected average of mortality from previous 5 years. <b>Results:</b> There were 56,961 excess deaths, of which 8,986 were non-COVID excess deaths. England had the highest number of excess deaths per 100,000 population (85) and Northern Ireland the lowest (34). Non-COVID mortality increased from 23 <sup>rd</sup> March and returned to the 5-year average on 10 <sup>th</sup> May. In Scotland, where underlying cause mortality data besides COVID-related deaths was available, the percentage excess over the 8-week period when COVID-related mortality peaked was: dementia 49%, other causes 21%, circulatory diseases 10%, and cancer 5%. We developed an online tool (TRACKing Excess Deaths - TRACKED) to allow dynamic exploration and visualisation of the latest mortality trends. <b>Conclusions:</b> Continuous monitoring of excess mortality trends and further integration of age- and gender-stratified and underlying cause of death data beyond COVID-19 will allow dynamic assessment of the impacts of indirect and direct mortality of the COVID-19 pandemic.",,doi:https://doi.org/10.12688/wellcomeopenres.16058.2; html:https://europepmc.org/articles/PMC11411238; pdf:https://europepmc.org/articles/PMC11411238?pdf=render
+38877563,https://doi.org/10.1186/s12911-024-02563-7,Collaborative learning from distributed data with differentially private synthetic data.,"Prediger L, Jälkö J, Honkela A, Kaski S.",,BMC medical informatics and decision making,2024,2024-06-14,Y,Collaborative Learning; Health Informatics; Differential Privacy; Synthetic Data,,,"<h4>Background</h4>Consider a setting where multiple parties holding sensitive data aim to collaboratively learn population level statistics, but pooling the sensitive data sets is not possible due to privacy concerns and parties are unable to engage in centrally coordinated joint computation. We study the feasibility of combining privacy preserving synthetic data sets in place of the original data for collaborative learning on real-world health data from the UK Biobank.<h4>Methods</h4>We perform an empirical evaluation based on an existing prospective cohort study from the literature. Multiple parties were simulated by splitting the UK Biobank cohort along assessment centers, for which we generate synthetic data using differentially private generative modelling techniques. We then apply the original study's Poisson regression analysis on the combined synthetic data sets and evaluate the effects of 1) the size of local data set, 2) the number of participating parties, and 3) local shifts in distributions, on the obtained likelihood scores.<h4>Results</h4>We discover that parties engaging in the collaborative learning via shared synthetic data obtain more accurate estimates of the regression parameters compared to using only their local data. This finding extends to the difficult case of small heterogeneous data sets. Furthermore, the more parties participate, the larger and more consistent the improvements become up to a certain limit. Finally, we find that data sharing can especially help parties whose data contain underrepresented groups to perform better-adjusted analysis for said groups.<h4>Conclusions</h4>Based on our results we conclude that sharing of synthetic data is a viable method for enabling learning from sensitive data without violating privacy constraints even if individual data sets are small or do not represent the overall population well. Lack of access to distributed sensitive data is often a bottleneck in biomedical research, which our study shows can be alleviated with privacy-preserving collaborative learning methods.",,doi:https://doi.org/10.1186/s12911-024-02563-7; html:https://europepmc.org/articles/PMC11179391; pdf:https://europepmc.org/articles/PMC11179391?pdf=render
 36322788,https://doi.org/10.2196/40035,A Hybrid Architecture (CO-CONNECT) to Facilitate Rapid Discovery and Access to Data Across the United Kingdom in Response to the COVID-19 Pandemic: Development Study.,"Jefferson E, Cole C, Mumtaz S, Cox S, Giles TC, Adejumo S, Urwin E, Lea D, Macdonald C, Best J, Masood E, Milligan G, Johnston J, Horban S, Birced I, Hall C, Jackson AS, Collins C, Rising S, Dodsley C, Hampton J, Hadfield A, Santos R, Tarr S, Panagi V, Lavagna J, Jackson T, Chuter A, Beggs J, Martinez-Queipo M, Ward H, von Ziegenweidt J, Burns F, Martin J, Sebire N, Morris C, Bradley D, Baxter R, Ahonen-Bishopp A, Smith P, Shoemark A, Valdes AM, Ollivere B, Manisty C, Eyre D, Gallant S, Joy G, McAuley A, Connell D, Northstone K, Jeffery K, Di Angelantonio E, McMahon A, Walker M, Semple MG, Sims JM, Lawrence E, Davies B, Baillie JK, Tang M, Leeming G, Power L, Breeze T, Murray D, Orton C, Pierce I, Hall I, Ladhani S, Gillson N, Whitaker M, Shallcross L, Seymour D, Varma S, Reilly G, Morris A, Hopkins S, Sheikh A, Quinlan P.",,Journal of medical Internet research,2022,2022-12-27,Y,Meta-analysis; Health care; Public Health; Clinical Care; Data Extraction; Data Privacy; Health Data; Federated Network; Data Governance; Infrastructure Model; Covid-19; Health Care Record,,,"<h4>Background</h4>COVID-19 data have been generated across the United Kingdom as a by-product of clinical care and public health provision, as well as numerous bespoke and repurposed research endeavors. Analysis of these data has underpinned the United Kingdom's response to the pandemic, and informed public health policies and clinical guidelines. However, these data are held by different organizations, and this fragmented landscape has presented challenges for public health agencies and researchers as they struggle to find relevant data to access and interrogate the data they need to inform the pandemic response at pace.<h4>Objective</h4>We aimed to transform UK COVID-19 diagnostic data sets to be findable, accessible, interoperable, and reusable (FAIR).<h4>Methods</h4>A federated infrastructure model (COVID - Curated and Open Analysis and Research Platform [CO-CONNECT]) was rapidly built to enable the automated and reproducible mapping of health data partners' pseudonymized data to the Observational Medical Outcomes Partnership Common Data Model without the need for any data to leave the data controllers' secure environments, and to support federated cohort discovery queries and meta-analysis.<h4>Results</h4>A total of 56 data sets from 19 organizations are being connected to the federated network. The data include research cohorts and COVID-19 data collected through routine health care provision linked to longitudinal health care records and demographics. The infrastructure is live, supporting aggregate-level querying of data across the United Kingdom.<h4>Conclusions</h4>CO-CONNECT was developed by a multidisciplinary team. It enables rapid COVID-19 data discovery and instantaneous meta-analysis across data sources, and it is researching streamlined data extraction for use in a Trusted Research Environment for research and public health analysis. CO-CONNECT has the potential to make UK health data more interconnected and better able to answer national-level research questions while maintaining patient confidentiality and local governance procedures.",,pdf:https://www.jmir.org/2022/12/e40035/PDF; doi:https://doi.org/10.2196/40035; html:https://europepmc.org/articles/PMC9822177
-35027756,https://doi.org/10.1038/s41591-021-01666-2,SARS-CoV-2 infection and COVID-19 vaccination rates in pregnant women in Scotland.,"Stock SJ, Carruthers J, Calvert C, Denny C, Donaghy J, Goulding A, Hopcroft LEM, Hopkins L, McLaughlin T, Pan J, Shi T, Taylor B, Agrawal U, Auyeung B, Katikireddi SV, McCowan C, Murray J, Simpson CR, Robertson C, Vasileiou E, Sheikh A, Wood R.",,Nature medicine,2022,2022-01-13,Y,,,,"Population-level data on COVID-19 vaccine uptake in pregnancy and SARS-CoV-2 infection outcomes are lacking. We describe COVID-19 vaccine uptake and SARS-CoV-2 infection in pregnant women in Scotland, using whole-population data from a national, prospective cohort. Between the start of a COVID-19 vaccine program in Scotland, on 8 December 2020 and 31 October 2021, 25,917 COVID-19 vaccinations were given to 18,457 pregnant women. Vaccine coverage was substantially lower in pregnant women than in the general female population of 18-44 years; 32.3% of women giving birth in October 2021 had two doses of vaccine compared to 77.4% in all women. The extended perinatal mortality rate for women who gave birth within 28 d of a COVID-19 diagnosis was 22.6 per 1,000 births (95% CI 12.9-38.5; pandemic background rate 5.6 per 1,000 births; 452 out of 80,456; 95% CI 5.1-6.2). Overall, 77.4% (3,833 out of 4,950; 95% CI 76.2-78.6) of SARS-CoV-2 infections, 90.9% (748 out of 823; 95% CI 88.7-92.7) of SARS-CoV-2 associated with hospital admission and 98% (102 out of 104; 95% CI 92.5-99.7) of SARS-CoV-2 associated with critical care admission, as well as all baby deaths, occurred in pregnant women who were unvaccinated at the time of COVID-19 diagnosis. Addressing low vaccine uptake rates in pregnant women is imperative to protect the health of women and babies in the ongoing pandemic.",,pdf:https://www.nature.com/articles/s41591-021-01666-2.pdf; doi:https://doi.org/10.1038/s41591-021-01666-2; html:https://europepmc.org/articles/PMC8938271; pdf:https://europepmc.org/articles/PMC8938271?pdf=render
 34670038,https://doi.org/10.1056/nejmc2113864,BNT162b2 and ChAdOx1 nCoV-19 Vaccine Effectiveness against Death from the Delta Variant.,"Sheikh A, Robertson C, Taylor B.",,The New England journal of medicine,2021,2021-10-20,Y,,,,,,doi:https://doi.org/10.1056/nejmc2113864; doi:https://doi.org/10.1056/NEJMc2113864; html:https://europepmc.org/articles/PMC8552534; pdf:https://europepmc.org/articles/PMC8552534?pdf=render
-38877563,https://doi.org/10.1186/s12911-024-02563-7,Collaborative learning from distributed data with differentially private synthetic data.,"Prediger L, Jälkö J, Honkela A, Kaski S.",,BMC medical informatics and decision making,2024,2024-06-14,Y,Collaborative Learning; Health Informatics; Differential Privacy; Synthetic Data,,,"<h4>Background</h4>Consider a setting where multiple parties holding sensitive data aim to collaboratively learn population level statistics, but pooling the sensitive data sets is not possible due to privacy concerns and parties are unable to engage in centrally coordinated joint computation. We study the feasibility of combining privacy preserving synthetic data sets in place of the original data for collaborative learning on real-world health data from the UK Biobank.<h4>Methods</h4>We perform an empirical evaluation based on an existing prospective cohort study from the literature. Multiple parties were simulated by splitting the UK Biobank cohort along assessment centers, for which we generate synthetic data using differentially private generative modelling techniques. We then apply the original study's Poisson regression analysis on the combined synthetic data sets and evaluate the effects of 1) the size of local data set, 2) the number of participating parties, and 3) local shifts in distributions, on the obtained likelihood scores.<h4>Results</h4>We discover that parties engaging in the collaborative learning via shared synthetic data obtain more accurate estimates of the regression parameters compared to using only their local data. This finding extends to the difficult case of small heterogeneous data sets. Furthermore, the more parties participate, the larger and more consistent the improvements become up to a certain limit. Finally, we find that data sharing can especially help parties whose data contain underrepresented groups to perform better-adjusted analysis for said groups.<h4>Conclusions</h4>Based on our results we conclude that sharing of synthetic data is a viable method for enabling learning from sensitive data without violating privacy constraints even if individual data sets are small or do not represent the overall population well. Lack of access to distributed sensitive data is often a bottleneck in biomedical research, which our study shows can be alleviated with privacy-preserving collaborative learning methods.",,doi:https://doi.org/10.1186/s12911-024-02563-7; html:https://europepmc.org/articles/PMC11179391; pdf:https://europepmc.org/articles/PMC11179391?pdf=render
 38818129,https://doi.org/10.12688/wellcomeopenres.20750.1,Anti-nucleocapsid antibody levels following initial and repeat SARS-CoV-2 infections in a cohort of long-term care facility residents in England (VIVALDI).,"Stirrup O, Tut G, Krutikov M, Bone D, Lancaster T, Azmi B, Monakhov I, Moss P, Hayward A, Copas A, Shallcross L.",,Wellcome open research,2024,2024-02-19,Y,Immunoglobulin G; Nucleocapsid; Covid-19; Sars-cov-2; Omicron,,,"<h4>Background</h4>We have previously demonstrated that older residents of long-term care facilities (LTCF) in the UK show levels of anti-spike antibodies that are comparable to the general population following primary series and booster vaccination for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, data on the humoral response to other SARS-CoV-2 proteins associated with natural infection are scarce in this vulnerable population.<h4>Methods</h4>We measured quantitative levels of anti-nucleocapsid antibodies in blood samples taken from LTCF residents and staff after initial and repeat SARS-CoV-2 infections, between December 2020 and March 2023. Data on SARS-CoV-2 infection and vaccination were obtained through linkage to national datasets. Linear mixed effects models were used to investigate anti-nucleocapsid antibody levels, using log10 scale, in relation to time from most recent infection. This included evaluation of associations between repeat infection, staff/resident status, age, sex, Omicron infection and vaccination history and peak antibody level and slope of decline with time.<h4>Results</h4>We analysed 405 antibody observations from 220 residents and 396 observations from 215 staff. Repeat infection was associated with 8.5-fold (95%CI 4.9-14.8-fold) higher initial (peak) median anti-nucleocapsid antibody level, with steeper subsequent slope of decline. There were no significant differences in antibody level associated with resident (vs. staff) status or age, but Omicron infection was associated with 3.6-fold (95%CI 2.4-5.4-fold) higher levels. There was stronger evidence of waning of antibody levels over time in a sensitivity analysis in which observations were censored in cases with suspected undetected repeat infection.<h4>Conclusions</h4>We found similar levels of anti-nucleocapsid antibody in residents and staff of LTCFs. Repeat infection and infection with an Omicron strain were associated with higher peak values. There was evidence of waning of anti-nucleocapsid antibody levels over time.",,doi:https://doi.org/10.12688/wellcomeopenres.20750.1; html:https://europepmc.org/articles/PMC11137476; pdf:https://europepmc.org/articles/PMC11137476?pdf=render
 34104901,https://doi.org/10.1016/s2666-7568(21)00093-3,Incidence of SARS-CoV-2 infection according to baseline antibody status in staff and residents of 100 long-term care facilities (VIVALDI): a prospective cohort study.,"Krutikov M, Palmer T, Tut G, Fuller C, Shrotri M, Williams H, Davies D, Irwin-Singer A, Robson J, Hayward A, Moss P, Copas A, Shallcross L.",,The lancet. Healthy longevity,2021,2021-06-03,Y,,,,"<h4>Background</h4>SARS-CoV-2 infection represents a major challenge for long-term care facilities (LTCFs) and many residents and staff are seropositive following persistent outbreaks. We aimed to investigate the association between the SARS-CoV-2 antibody status at baseline and subsequent infection in this population.<h4>Methods</h4>We did a prospective cohort study of SARS-CoV-2 infection in staff (aged <65 years) and residents (aged >65 years) at 100 LTCFs in England between Oct 1, 2020, and Feb 1, 2021. Blood samples were collected between June and November, 2020, at baseline, and 2 and 4 months thereafter and tested for IgG antibodies to SARS-CoV-2 nucleocapsid and spike proteins. PCR testing for SARS-CoV-2 was done weekly in staff and monthly in residents. Cox regression was used to estimate hazard ratios (HRs) of a PCR-positive test by baseline antibody status, adjusted for age and sex, and stratified by LTCF.<h4>Findings</h4>682 residents from 86 LCTFs and 1429 staff members from 97 LTCFs met study inclusion criteria. At baseline, IgG antibodies to nucleocapsid were detected in 226 (33%) of 682 residents and 408 (29%) of 1429 staff members. 93 (20%) of 456 residents who were antibody-negative at baseline had a PCR-positive test (infection rate 0·054 per month at risk) compared with four (2%) of 226 residents who were antibody-positive at baseline (0·007 per month at risk). 111 (11%) of 1021 staff members who were antibody-negative at baseline had PCR-positive tests (0·042 per month at risk) compared with ten (2%) of 408 staff members who were antibody-positive staff at baseline (0·009 per month at risk). The risk of PCR-positive infection was higher for residents who were antibody-negative at baseline than residents who were antibody-positive at baseline (adjusted HR [aHR] 0·15, 95% CI 0·05-0·44, p=0·0006), and the risk of a PCR-positive infection was also higher for staff who were antibody-negative at baseline compared with staff who were antibody-positive at baseline (aHR 0·39, 0·19-0·82; p=0·012). 12 of 14 reinfected participants had available data on symptoms, and 11 of these participants were symptomatic. Antibody titres to spike and nucleocapsid proteins were comparable in PCR-positive and PCR-negative cases.<h4>Interpretation</h4>The presence of IgG antibodies to nucleocapsid protein was associated with substantially reduced risk of reinfection in staff and residents for up to 10 months after primary infection.<h4>Funding</h4>UK Government Department of Health and Social Care.",,pdf:http://www.thelancet.com/article/S2666756821000933/pdf; doi:https://doi.org/10.1016/S2666-7568(21)00093-3; html:https://europepmc.org/articles/PMC8175048; pdf:https://europepmc.org/articles/PMC8175048?pdf=render
 37247403,https://doi.org/10.1093/ageing/afad077,Attainment of NICE blood pressure targets among older people with newly diagnosed hypertension: nationwide linked electronic health records cohort study.,"Todd O, Johnson O, Wilkinson C, Hollinghurst J, Dondo TB, Yadegarfar ME, Sheppard JP, McManus RJ, Gale CP, Clegg A.",,Age and ageing,2023,2023-05-01,Y,Hypertension; Blood pressure; Frailty; Older People; Treatment Target,,,"<h4>Background</h4>it is not known if clinical practice reflects guideline recommendations for the management of hypertension in older people and whether guideline adherence varies according to overall health status.<h4>Aims</h4>to describe the proportion of older people attaining National Institute for Health and Care Excellence (NICE) guideline blood pressure targets within 1 year of hypertension diagnosis and determine predictors of target attainment.<h4>Methods</h4>a nationwide cohort study of Welsh primary care data from the Secure Anonymised Information Linkage databank including patients aged ≥65 years newly diagnosed with hypertension between 1st June 2011 and 1st June 2016. The primary outcome was attainment of NICE guideline blood pressure targets as measured by the latest blood pressure recording up to 1 year after diagnosis. Predictors of target attainment were investigated using logistic regression.<h4>Results</h4>there were 26,392 patients (55% women, median age 71 [IQR 68-77] years) included, of which 13,939 (52.8%) attained a target blood pressure within a median follow-up of 9 months. Success in attaining target blood pressure was associated with a history of atrial fibrillation (OR 1.26, 95% CI 1.11, 1.43), heart failure (OR 1.25, 95% CI 1.06, 1.49) and myocardial infarction (OR 1.20, 95% CI 1.10, 1.32), all compared to no history of each, respectively. Care home residence, the severity of frailty, and increasing co-morbidity were not associated with target attainment following adjustment for confounder variables.<h4>Conclusions</h4>blood pressure remains insufficiently controlled 1 year after diagnosis in nearly half of older people with newly diagnosed hypertension, but target attainment appears unrelated to baseline frailty, multi-morbidity or care home residence.",,doi:https://doi.org/10.1093/ageing/afad077; doi:https://doi.org/10.1093/ageing/afad077; html:https://europepmc.org/articles/PMC10226747; pdf:https://europepmc.org/articles/PMC10226747?pdf=render
 35756853,https://doi.org/10.1016/j.lanepe.2022.100428,"Impact of COVID-19 pandemic on asthma exacerbations: Retrospective cohort study of over 500,000 patients in a national English primary care database.","Shah SA, Quint JK, Sheikh A.",,The Lancet regional health. Europe,2022,2022-06-15,Y,Asthma; Pandemic; Asthma Exacerbations; Covid-19,,,"<h4>Background</h4>Several countries reported a substantial reduction in asthma exacerbations associated with COVID-19 pandemic-related restrictions. However, it is not known if these early reported declines were short-term and if these have rebounded to pre-pandemic levels following easing of lockdown restrictions.<h4>Methods</h4>We undertook a retrospective, cohort study of all asthma patients in a national primary care database of almost 10 million patients, Optimum Patient Care Database (OPCRD), identified from January 1, 2010, to December 31, 2015, using a previously validated algorithm. We subsequently followed the identified cohort of asthma patients from January 1, 2016, to October 3, 2021, and identified every asthma exacerbation episode with a validated algorithm. To quantify any pandemic-related change in exacerbations, we created a control time-series (mean of 2016-2019) and then compared the change in exacerbation rate in 2020-2021 over quarterly periods when compared with the control period (the pre-pandemic period). We undertook overall and stratified analyses by age group, sex, and English region.<h4>Findings</h4>We identified 100,362 asthma patients (502,669 patient-years) from across England who experienced at least one exacerbation episode (298,390 exacerbation episodes during the entire follow-up). Except for the first quarter of 2020, the exacerbation rates were substantially lower (>25%) during all quarters in 2020-2021 when compared with the rates during 2016-2019 (39.7% (95% Confidence Interval (CI): 34.6, 44.9) in quarter-2, 2020; 46.5% (95%CI: 36.7, 56.4) in quarter-3, 2020; 56.3% (95%CI: 48.7, 63.9) in quarter-4, 2020; 63.2% (95%CI: 53.9, 72.5) in quarter-1, 2021; 57.7% (95%CI: 52.9, 62.4) in quarter-2, 2021; 53.3% (95%CI: 43.8, 62.8) in quarter-3, 2021).<h4>Interpretation</h4>There was a substantial and persistent reduction in asthma exacerbations across England over the first 18 months after the first lockdown. This is unlikely to be adequately explained by changes in health-seeking behaviour, pandemic-related healthcare service disruption, or any air-quality improvements.<h4>Funding</h4>Asthma UK, Health Data Research UK (HDR UK), Medical Research Council (MRC), National Institute for Health Research (NIHR).",,doi:https://doi.org/10.1016/j.lanepe.2022.100428; doi:https://doi.org/10.1016/j.lanepe.2022.100428; html:https://europepmc.org/articles/PMC9213032; pdf:https://europepmc.org/articles/PMC9213032?pdf=render
-32043136,https://doi.org/10.1093/ageing/afaa018,New Horizons in the use of routine data for ageing research.,"Todd OM, Burton JK, Dodds RM, Hollinghurst J, Lyons RA, Quinn TJ, Schneider A, Walesby KE, Wilkinson C, Conroy S, Gale CP, Hall M, Walters K, Clegg AP.",,Age and ageing,2020,2020-08-01,Y,Ageing; Data Linkage; Older People; Big Data; Health Informatics; Electronic Health Records,Improving Public Health,,"The past three decades have seen a steady increase in the availability of routinely collected health and social care data and the processing power to analyse it. These developments represent a major opportunity for ageing research, especially with the integration of different datasets across traditional boundaries of health and social care, for prognostic research and novel evaluations of interventions with representative populations of older people. However, there are considerable challenges in using routine data at the level of coding, data analysis and in the application of findings to everyday care. New Horizons in applying routine data to investigate novel questions in ageing research require a collaborative approach between clinicians, data scientists, biostatisticians, epidemiologists and trial methodologists. This requires building capacity for the next generation of research leaders in this important area. There is a need to develop consensus code lists and standardised, validated algorithms for common conditions and outcomes that are relevant for older people to maximise the potential of routine data research in this group. Lastly, we must help drive the application of routine data to improve the care of older people, through the development of novel methods for evaluation of interventions using routine data infrastructure. We believe that harnessing routine data can help address knowledge gaps for older people living with multiple conditions and frailty, and design interventions and pathways of care to address the complex health issues we face in caring for older people.","This article looks at new horizons in the use of routine data for ageing research. This includes prognostic research, clinical trials, and service evaluations. The authors highlight the need for multidisciplinary collaboration. They identify three key areas where the application of routine data has major benefits for research in ageing - prediction (developing prediction tools to identify levels of future risk of outcomes thereby helping in decision making), clinical trials (routine data can help extend participation in clinical trials), and service evaluation (understanding performace of clinical services by measuring outcomes in routine data).",pdf:https://academic.oup.com/ageing/article-pdf/49/5/716/33676968/afaa018.pdf; doi:https://doi.org/10.1093/ageing/afaa018; html:https://europepmc.org/articles/PMC7444666; pdf:https://europepmc.org/articles/PMC7444666?pdf=render
 37765085,https://doi.org/10.3390/ph16091277,The Effects of CYP2C19 Genotype on Proxies of SSRI Antidepressant Response in the UK Biobank.,"Wong WLE, Fabbri C, Laplace B, Li D, van Westrhenen R, Lewis CM, Dawe GS, Young AH.",,"Pharmaceuticals (Basel, Switzerland)",2023,2023-09-11,Y,Cytochrome p450; Antidepressants; Pharmacogenetics; Treatment Response,,,"Selective serotonin reuptake inhibitors (SSRIs) are the most commonly used psychopharmaceutical treatment for major depressive disorder (MDD), but individual responses to SSRIs vary greatly. CYP2C19 is a key enzyme involved in the metabolism of several drugs, including SSRIs. Variations in the CYP2C19 gene are associated with differential metabolic activity, and thus differential SSRI exposure; accordingly, the CYP2C19 genotype may affect the therapeutic response and clinical outcomes, though existing evidence of this link is not entirely consistent. Therefore, we analysed data from the UK Biobank, a large, deeply phenotyped prospective study, to investigate the effects of CYP2C19 metaboliser phenotypes on several clinical outcomes derived from primary care records, including multiple measures of antidepressant switching, discontinuation, duration, and side effects. In this dataset, 24,729 individuals were prescribed citalopram, 3012 individuals were prescribed escitalopram, and 12,544 individuals were prescribed sertraline. Consistent with pharmacological expectations, CYP2C19 poor metabolisers on escitalopram were more likely to switch antidepressants, have side effects following first prescription, and be on escitalopram for a shorter duration compared to normal metabolisers. CYP2C19 poor and intermediate metabolisers on citalopram also exhibited increased odds of discontinuation and shorter durations relative to normal metabolisers. Generally, no associations were found between metabolic phenotypes and proxies of response to sertraline. Sensitivity analyses in a depression subgroup and metabolic activity scores corroborated results from the primary analysis. In summary, our findings suggest that CYP2C19 genotypes, and thus metabolic phenotypes, may have utility in determining clinical responses to SSRIs, particularly escitalopram and citalopram, though further investigation of such a relationship is warranted.",,doi:https://doi.org/10.3390/ph16091277; html:https://europepmc.org/articles/PMC10535191; pdf:https://europepmc.org/articles/PMC10535191?pdf=render
+32043136,https://doi.org/10.1093/ageing/afaa018,New Horizons in the use of routine data for ageing research.,"Todd OM, Burton JK, Dodds RM, Hollinghurst J, Lyons RA, Quinn TJ, Schneider A, Walesby KE, Wilkinson C, Conroy S, Gale CP, Hall M, Walters K, Clegg AP.",,Age and ageing,2020,2020-08-01,Y,Ageing; Data Linkage; Older People; Big Data; Health Informatics; Electronic Health Records,Improving Public Health,,"The past three decades have seen a steady increase in the availability of routinely collected health and social care data and the processing power to analyse it. These developments represent a major opportunity for ageing research, especially with the integration of different datasets across traditional boundaries of health and social care, for prognostic research and novel evaluations of interventions with representative populations of older people. However, there are considerable challenges in using routine data at the level of coding, data analysis and in the application of findings to everyday care. New Horizons in applying routine data to investigate novel questions in ageing research require a collaborative approach between clinicians, data scientists, biostatisticians, epidemiologists and trial methodologists. This requires building capacity for the next generation of research leaders in this important area. There is a need to develop consensus code lists and standardised, validated algorithms for common conditions and outcomes that are relevant for older people to maximise the potential of routine data research in this group. Lastly, we must help drive the application of routine data to improve the care of older people, through the development of novel methods for evaluation of interventions using routine data infrastructure. We believe that harnessing routine data can help address knowledge gaps for older people living with multiple conditions and frailty, and design interventions and pathways of care to address the complex health issues we face in caring for older people.","This article looks at new horizons in the use of routine data for ageing research. This includes prognostic research, clinical trials, and service evaluations. The authors highlight the need for multidisciplinary collaboration. They identify three key areas where the application of routine data has major benefits for research in ageing - prediction (developing prediction tools to identify levels of future risk of outcomes thereby helping in decision making), clinical trials (routine data can help extend participation in clinical trials), and service evaluation (understanding performace of clinical services by measuring outcomes in routine data).",pdf:https://academic.oup.com/ageing/article-pdf/49/5/716/33676968/afaa018.pdf; doi:https://doi.org/10.1093/ageing/afaa018; html:https://europepmc.org/articles/PMC7444666; pdf:https://europepmc.org/articles/PMC7444666?pdf=render
 39319350,https://doi.org/10.3389/fpsyt.2024.1181739,Applying neural network algorithms to ascertain reported experiences of violence in routine mental healthcare records and distributions of reports by diagnosis.,"Mason AJC, Bhavsar V, Botelle R, Chandran D, Li L, Mascio A, Sanyal J, Kadra-Scalzo G, Roberts A, Williams M, Stewart R.",,Frontiers in psychiatry,2024,2024-09-10,Y,Violence; Victimisation; Natural Language Processing; Cris; Mental Health Records,,,"<h4>Introduction</h4>Experiences of violence are important risk factors for worse outcome in people with mental health conditions; however, they are not routinely collected be mental health services, so their ascertainment depends on extraction from text fields with natural language processing (NLP) algorithms.<h4>Methods</h4>Applying previously developed neural network algorithms to routine mental healthcare records, we sought to describe the distribution of recorded violence victimisation by demographic and diagnostic characteristics. We ascertained recorded violence victimisation from the records of 60,021 patients receiving care from a large south London NHS mental healthcare provider during 2019. Descriptive and regression analyses were conducted to investigate variation by age, sex, ethnic group, and diagnostic category (ICD-10 F chapter sub-headings plus post-traumatic stress disorder (PTSD) as a specific condition).<h4>Results</h4>Patients with a mood disorder (adjusted odds ratio 1.63, 1.55-1.72), personality disorder (4.03, 3.65-4.45), schizophrenia spectrum disorder (1.84, 1.74-1.95) or PTSD (2.36, 2.08-2.69) had a significantly increased likelihood of victimisation compared to those with other mental health diagnoses. Additionally, patients from minority ethnic groups (1.10 (1.02-1.20) for Black, 1.40 (1.31-1.49) for Asian compared to White groups) had significantly higher likelihood of recorded violence victimisation. Males were significantly less likely to have reported recorded violence victimisation (0.44, 0.42-0.45) than females.<h4>Discussion</h4>We thus demonstrate the successful deployment of machine learning based NLP algorithms to ascertain important entities for outcome prediction in mental healthcare. The observed distributions highlight which sex, ethnicity and diagnostic groups had more records of violence victimisation. Further development of these algorithms could usefully capture broader experiences, such as differentiating more efficiently between witnessed, perpetrated and experienced violence and broader violence experiences like emotional abuse.",,doi:https://doi.org/10.3389/fpsyt.2024.1181739; html:https://europepmc.org/articles/PMC11420987; pdf:https://europepmc.org/articles/PMC11420987?pdf=render
 38520142,https://doi.org/10.1093/ageing/afae057,Development and external validation of the eFalls tool: a multivariable prediction model for the risk of ED attendance or hospitalisation with a fall or fracture in older adults.,"Archer L, Relton SD, Akbari A, Best K, Bucknall M, Conroy S, Hattle M, Hollinghurst J, Humphrey S, Lyons RA, Richards S, Walters K, West R, van der Windt D, Riley RD, Clegg A, eFI+ investigators.",,Age and ageing,2024,2024-03-01,Y,Prediction model; Prognosis; Prevention; Falls; Older People; Proactive,,,"<h4>Background</h4>Falls are common in older adults and can devastate personal independence through injury such as fracture and fear of future falls. Methods to identify people for falls prevention interventions are currently limited, with high risks of bias in published prediction models. We have developed and externally validated the eFalls prediction model using routinely collected primary care electronic health records (EHR) to predict risk of emergency department attendance/hospitalisation with fall or fracture within 1 year.<h4>Methods</h4>Data comprised two independent, retrospective cohorts of adults aged ≥65 years: the population of Wales, from the Secure Anonymised Information Linkage Databank (model development); the population of Bradford and Airedale, England, from Connected Bradford (external validation). Predictors included electronic frailty index components, supplemented with variables informed by literature reviews and clinical expertise. Fall/fracture risk was modelled using multivariable logistic regression with a Least Absolute Shrinkage and Selection Operator penalty. Predictive performance was assessed through calibration, discrimination and clinical utility. Apparent, internal-external cross-validation and external validation performance were assessed across general practices and in clinically relevant subgroups.<h4>Results</h4>The model's discrimination performance (c-statistic) was 0.72 (95% confidence interval, CI: 0.68 to 0.76) on internal-external cross-validation and 0.82 (95% CI: 0.80 to 0.83) on external validation. Calibration was variable across practices, with some over-prediction in the validation population (calibration-in-the-large, -0.87; 95% CI: -0.96 to -0.78). Clinical utility on external validation was improved after recalibration.<h4>Conclusion</h4>The eFalls prediction model shows good performance and could support proactive stratification for falls prevention services if appropriately embedded into primary care EHR systems.",,pdf:https://academic.oup.com/ageing/article-pdf/53/3/afae057/57063252/afae057.pdf; doi:https://doi.org/10.1093/ageing/afae057; html:https://europepmc.org/articles/PMC10960070; pdf:https://europepmc.org/articles/PMC10960070?pdf=render
-37363696,https://doi.org/10.1155/2023/5885059,Gender Disparity in Expression of Sarcopenia in Haemodialysis Recipients: Analysis from the FITNESS Cohort.,"Anderson BM, Wilson DV, Qasim M, Correa G, Evison F, Gallier S, Ferro CJ, Jackson TA, Sharif A.",,International journal of nephrology,2023,2023-06-17,Y,,,,"<h4>Background</h4>There has been little exploration of the interplay between sarcopenia and frailty in haemodialysis, particularly regarding gender difference. We aimed to (1) assess whether ultrasound-derived low muscle mass (LMM) and sarcopenia are more common in male or female haemodialysis recipients; (2) assess whether age influences any observed gender difference, and (3) explore the interplay between sarcopenia, frailty, and gender in haemodialysis recipients.<h4>Methods</h4>This was an exploratory analysis of a subgroup of adult prevalent (≥3 months) haemodialysis with frailty phenotype (FP) scores. Bilateral anterior thigh thickness (BATT) was obtained according to an established ultrasound protocol. Associations with frailty were explored via both linear and logistic regressions for BATT, LMM, and sarcopenia with a priori covariables, stratified by gender.<h4>Results</h4>In total of 223 studies, participants had ultrasound measurements. Males showed greater prevalence of LMM. On adjusted analyses, LMM was associated with lower hand grip strength in males (<i>β</i> = -4.17; 95% C.I. -7.57 to -0.77; <i>P</i>=0.02), but not females (<i>β</i> = -1.88; 95% C.I. -5.41 to 1.64; <i>P</i>=0.29). LMM was also associated with slower walking speed in both males (<i>β</i> = -0.115; 95% C.I. -0.258 to -0.013; <i>P</i>=0.03) and females (<i>β</i> = -0.152; 95% C.I. -0.300 to -0.005; <i>P</i>=0.04). Sarcopenia was associated with greater odds of frailty on adjusted models in males (OR = 9.86; 95% C.I. 1.8 to 54.0; <i>P</i>=0.01), but not females (OR = 5.16; 95% C.I. 0.22 to 124; <i>P</i>=0.31).<h4>Conclusions</h4>The clinical expression and significance of sarcopenia differ substantially between males and females on haemodialysis. Further work is required to elucidate underlying mechanisms and guide tailored treatment.",,doi:https://doi.org/10.1155/2023/5885059; html:https://europepmc.org/articles/PMC10290558; pdf:https://europepmc.org/articles/PMC10290558?pdf=render
 35715350,https://doi.org/10.1016/j.vaccine.2022.06.010,Safety of COVID-19 vaccination and acute neurological events: A self-controlled case series in England using the OpenSAFELY platform.,"Walker JL, Schultze A, Tazare J, Tamborska A, Singh B, Donegan K, Stowe J, Morton CE, Hulme WJ, Curtis HJ, Williamson EJ, Mehrkar A, Eggo RM, Rentsch CT, Mathur R, Bacon S, Walker AJ, Davy S, Evans D, Inglesby P, Hickman G, MacKenna B, Tomlinson L, Ca Green A, Fisher L, Cockburn J, Parry J, Hester F, Harper S, Bates C, Evans SJ, Solomon T, Andrews NJ, Douglas IJ, Goldacre B, Smeeth L, McDonald HI.",,Vaccine,2022,2022-06-07,Y,Transverse Myelitis; Guillain-barré Syndrome; Vaccine Safety; Self-controlled Case Series; Bell’s Palsy; Covid-19 Vaccines,,,"<h4>Introduction</h4>We investigated the potential association of COVID-19 vaccination with three acute neurological events: Guillain-Barré syndrome (GBS), transverse myelitis and Bell's palsy.<h4>Methods</h4>With the approval of NHS England we analysed primary care data from >17 million patients in England linked to emergency care, hospital admission and mortality records in the OpenSAFELY platform. Separately for each vaccine brand, we used a self-controlled case series design to estimate the incidence rate ratio for each outcome in the period following vaccination (4-42 days for GBS, 4-28 days for transverse myelitis and Bell's palsy) compared to a within-person baseline, using conditional Poisson regression.<h4>Results</h4>Among 7,783,441 ChAdOx1 vaccinees, there was an increased rate of GBS (N = 517; incidence rate ratio 2·85; 95% CI2·33-3·47) and Bell's palsy (N = 5,350; 1·39; 1·27-1·53) following a first dose of ChAdOx1 vaccine, corresponding to 11.0 additional cases of GBS and 17.9 cases of Bell's palsy per 1 million vaccinees if causal. For GBS this applied to the first, but not the second, dose. There was no clear evidence of an association of ChAdOx1 vaccination with transverse myelitis (N = 199; 1·51; 0·96-2·37). Among 5,729,152 BNT162b2 vaccinees, there was no evidence of any association with GBS (N = 283; 1·09; 0·75-1·57), transverse myelitis (N = 109; 1·62; 0·86-3·03) or Bell's palsy (N = 3,609; 0·89; 0·76-1·03). Among 255,446 mRNA-1273 vaccine recipients there was no evidence of an association with Bell's palsy (N = 78; 0·88, 0·32-2·42).<h4>Conclusions</h4>COVID-19 vaccines save lives, but it is important to understand rare adverse events. We observed a short-term increased rate of Guillain-Barré syndrome and Bell's palsy after first dose of ChAdOx1 vaccine. The absolute risk, assuming a causal effect attributable to vaccination, was low.",,doi:https://doi.org/10.1016/j.vaccine.2022.06.010; doi:https://doi.org/10.1016/j.vaccine.2022.06.010; html:https://europepmc.org/articles/PMC9170533; pdf:https://europepmc.org/articles/PMC9170533?pdf=render
 31469943,https://doi.org/10.1002/cnm.3255,Computational instantaneous wave-free ratio (IFR) for patient-specific coronary artery stenoses using 1D network models.,"Carson JM, Roobottom C, Alcock R, Nithiarasu P.",,International journal for numerical methods in biomedical engineering,2019,2019-11-01,Y,Coronary Arteries; Ffr; Ifr; Haemodynamic Modelling,,cardiovascular,"In this work, we estimate the diagnostic threshold of the instantaneous wave-free ratio (iFR) through the use of a one-dimensional haemodynamic framework. To this end, we first compared the computed fractional flow reserve (cFFR) predicted from a 1D computational framework with invasive clinical measurements. The framework shows excellent promise and utilises minimal patient data from a cohort of 52 patients with a total of 66 stenoses. The diagnostic accuracy of the cFFR model was 75.76%, with a sensitivity of 71.43%, a specificity of 77.78%, a positive predictive value of 60%, and a negative predictive value of 85.37%. The validated model was then used to estimate the diagnostic threshold of iFR. The model determined a quadratic relationship between cFFR and the ciFR. The iFR diagnostic threshold was determined to be 0.8910 from a receiver operating characteristic curve that is in the range of 0.89 to 0.9 that is normally reported in clinical studies.",This study aimed to measure how well an algorithm using data from non-invasive tests was able to predict early signs of heart disease.,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cnm.3255; doi:https://doi.org/10.1002/cnm.3255; html:https://europepmc.org/articles/PMC7003475; pdf:https://europepmc.org/articles/PMC7003475?pdf=render
-36691218,https://doi.org/10.1136/bmjopen-2021-059813,Evaluation of the shielding initiative in Wales (EVITE Immunity): protocol for a quasiexperimental study.,"Evans BA, Akbari A, Bailey R, Bethell L, Bufton S, Carson-Stevens A, Dixon L, Edwards A, John A, Jolles S, Kingston MR, Lyons J, Lyons R, Porter A, Sewell B, Thornton CA, Watkins A, Whiffen T, Snooks H.",,BMJ open,2022,2022-09-08,Y,immunology; Public Health; Health Policy; Covid-19,,,"<h4>Introduction</h4>Shielding aimed to protect those predicted to be at highest risk from COVID-19 and was uniquely implemented in the UK during the COVID-19 pandemic. Clinically extremely vulnerable people identified through algorithms and screening of routine National Health Service (NHS) data were individually and strongly advised to stay at home and strictly self-isolate even from others in their household. This study will generate a logic model of the intervention and evaluate the effects and costs of shielding to inform policy development and delivery during future pandemics.<h4>Methods and analysis</h4>This is a quasiexperimental study undertaken in Wales where records for people who were identified for shielding were already anonymously linked into integrated data systems for public health decision-making. We will: interview policy-makers to understand rationale for shielding advice to inform analysis and interpretation of results; use anonymised individual-level data to select people identified for shielding advice in March 2020 and a matched cohort, from routine electronic health data sources, to compare outcomes; survey a stratified random sample of each group about activities and quality of life at 12 months; use routine and newly collected blood data to assess immunity; interview people who were identified for shielding and their carers and NHS staff who delivered healthcare during shielding, to explore compliance and experiences; collect healthcare resource use data to calculate implementation costs and cost-consequences. Our team includes people who were shielding, who used their experience to help design and deliver this study.<h4>Ethics and dissemination</h4>The study has received approval from the Newcastle North Tyneside 2 Research Ethics Committee (IRAS 295050). We will disseminate results directly to UK government policy-makers, publish in peer-reviewed journals, present at scientific and policy conferences and share accessible summaries of results online and through public and patient networks.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/9/e059813.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-059813; html:https://europepmc.org/articles/PMC9461087; pdf:https://europepmc.org/articles/PMC9461087?pdf=render
+37363696,https://doi.org/10.1155/2023/5885059,Gender Disparity in Expression of Sarcopenia in Haemodialysis Recipients: Analysis from the FITNESS Cohort.,"Anderson BM, Wilson DV, Qasim M, Correa G, Evison F, Gallier S, Ferro CJ, Jackson TA, Sharif A.",,International journal of nephrology,2023,2023-06-17,Y,,,,"<h4>Background</h4>There has been little exploration of the interplay between sarcopenia and frailty in haemodialysis, particularly regarding gender difference. We aimed to (1) assess whether ultrasound-derived low muscle mass (LMM) and sarcopenia are more common in male or female haemodialysis recipients; (2) assess whether age influences any observed gender difference, and (3) explore the interplay between sarcopenia, frailty, and gender in haemodialysis recipients.<h4>Methods</h4>This was an exploratory analysis of a subgroup of adult prevalent (≥3 months) haemodialysis with frailty phenotype (FP) scores. Bilateral anterior thigh thickness (BATT) was obtained according to an established ultrasound protocol. Associations with frailty were explored via both linear and logistic regressions for BATT, LMM, and sarcopenia with a priori covariables, stratified by gender.<h4>Results</h4>In total of 223 studies, participants had ultrasound measurements. Males showed greater prevalence of LMM. On adjusted analyses, LMM was associated with lower hand grip strength in males (<i>β</i> = -4.17; 95% C.I. -7.57 to -0.77; <i>P</i>=0.02), but not females (<i>β</i> = -1.88; 95% C.I. -5.41 to 1.64; <i>P</i>=0.29). LMM was also associated with slower walking speed in both males (<i>β</i> = -0.115; 95% C.I. -0.258 to -0.013; <i>P</i>=0.03) and females (<i>β</i> = -0.152; 95% C.I. -0.300 to -0.005; <i>P</i>=0.04). Sarcopenia was associated with greater odds of frailty on adjusted models in males (OR = 9.86; 95% C.I. 1.8 to 54.0; <i>P</i>=0.01), but not females (OR = 5.16; 95% C.I. 0.22 to 124; <i>P</i>=0.31).<h4>Conclusions</h4>The clinical expression and significance of sarcopenia differ substantially between males and females on haemodialysis. Further work is required to elucidate underlying mechanisms and guide tailored treatment.",,doi:https://doi.org/10.1155/2023/5885059; html:https://europepmc.org/articles/PMC10290558; pdf:https://europepmc.org/articles/PMC10290558?pdf=render
 34385524,https://doi.org/10.1038/s41598-021-95802-0,Multimorbidity prediction using link prediction.,"Aziz F, Cardoso VR, Bravo-Merodio L, Russ D, Pendleton SC, Williams JA, Acharjee A, Gkoutos GV.",,Scientific reports,2021,2021-08-12,Y,,,,"Multimorbidity, frequently associated with aging, can be operationally defined as the presence of two or more chronic conditions. Predicting the likelihood of a patient with multimorbidity to develop a further particular disease in the future is one of the key challenges in multimorbidity research. In this paper we are using a network-based approach to analyze multimorbidity data and develop methods for predicting diseases that a patient is likely to develop. The multimorbidity data is represented using a temporal bipartite network whose nodes represent patients and diseases and a link between these nodes indicates that the patient has been diagnosed with the disease. Disease prediction then is reduced to a problem of predicting those missing links in the network that are likely to appear in the future. We develop a novel link prediction method for static bipartite network and validate the performance of the method on benchmark datasets. By using a probabilistic framework, we then report on the development of a method for predicting future links in the network, where links are labelled with a time-stamp. We apply the proposed method to three different multimorbidity datasets and report its performance measured by different performance metrics including AUC, Precision, Recall, and F-Score.",,pdf:https://www.nature.com/articles/s41598-021-95802-0.pdf; doi:https://doi.org/10.1038/s41598-021-95802-0; html:https://europepmc.org/articles/PMC8360941; pdf:https://europepmc.org/articles/PMC8360941?pdf=render
+36691218,https://doi.org/10.1136/bmjopen-2021-059813,Evaluation of the shielding initiative in Wales (EVITE Immunity): protocol for a quasiexperimental study.,"Evans BA, Akbari A, Bailey R, Bethell L, Bufton S, Carson-Stevens A, Dixon L, Edwards A, John A, Jolles S, Kingston MR, Lyons J, Lyons R, Porter A, Sewell B, Thornton CA, Watkins A, Whiffen T, Snooks H.",,BMJ open,2022,2022-09-08,Y,immunology; Public Health; Health Policy; Covid-19,,,"<h4>Introduction</h4>Shielding aimed to protect those predicted to be at highest risk from COVID-19 and was uniquely implemented in the UK during the COVID-19 pandemic. Clinically extremely vulnerable people identified through algorithms and screening of routine National Health Service (NHS) data were individually and strongly advised to stay at home and strictly self-isolate even from others in their household. This study will generate a logic model of the intervention and evaluate the effects and costs of shielding to inform policy development and delivery during future pandemics.<h4>Methods and analysis</h4>This is a quasiexperimental study undertaken in Wales where records for people who were identified for shielding were already anonymously linked into integrated data systems for public health decision-making. We will: interview policy-makers to understand rationale for shielding advice to inform analysis and interpretation of results; use anonymised individual-level data to select people identified for shielding advice in March 2020 and a matched cohort, from routine electronic health data sources, to compare outcomes; survey a stratified random sample of each group about activities and quality of life at 12 months; use routine and newly collected blood data to assess immunity; interview people who were identified for shielding and their carers and NHS staff who delivered healthcare during shielding, to explore compliance and experiences; collect healthcare resource use data to calculate implementation costs and cost-consequences. Our team includes people who were shielding, who used their experience to help design and deliver this study.<h4>Ethics and dissemination</h4>The study has received approval from the Newcastle North Tyneside 2 Research Ethics Committee (IRAS 295050). We will disseminate results directly to UK government policy-makers, publish in peer-reviewed journals, present at scientific and policy conferences and share accessible summaries of results online and through public and patient networks.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/9/e059813.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-059813; html:https://europepmc.org/articles/PMC9461087; pdf:https://europepmc.org/articles/PMC9461087?pdf=render
 39226549,https://doi.org/10.2196/47882,The Digital Platform and Its Emerging Role in Decentralized Clinical Trials.,"Copland RR, Hanke S, Rogers A, Mpaltadoros L, Lazarou I, Zeltsi A, Nikolopoulos S, MacDonald TM, Mackenzie IS.",,Journal of medical Internet research,2024,2024-09-03,Y,Mobile phone; Clinical Trials; Digitalization; Digital Platform; Decentralized Clinical Trials,,,"Decentralized clinical trials (DCTs) are becoming increasingly popular. Digital clinical trial platforms are software environments where users complete designated clinical trial tasks, providing investigators and trial participants with efficient tools to support trial activities and streamline trial processes. In particular, digital platforms with a modular architecture lend themselves to DCTs, where individual trial activities can correspond to specific platform modules. While design features can allow users to customize their platform experience, the real strengths of digital platforms for DCTs are enabling centralized data capture and remote monitoring of trial participants and in using digital technologies to streamline workflows and improve trial management. When selecting a platform for use in a DCT, sponsors and investigators must consider the specific trial requirements. All digital platforms are limited in their functionality and technical capabilities. Integrating additional functional modules into a central platform may solve these challenges, but few commercial platforms are open to integrating third-party components. The lack of common data standardization protocols for clinical trials will likely limit the development of one-size-fits-all digital platforms for DCTs. This viewpoint summarizes the current role of digital platforms in supporting decentralized trial activities, including a discussion of the potential benefits and challenges of digital platforms for investigators and participants. We will highlight the role of the digital platform in the development of DCTs and emphasize where existing technology is functionally limiting. Finally, we will discuss the concept of the ideal fully integrated and unified DCT and the obstacles developers must address before it can be realized.",,doi:https://doi.org/10.2196/47882; doi:https://doi.org/10.2196/47882; html:https://europepmc.org/articles/PMC11408899
 37393057,https://doi.org/10.1016/j.bbi.2023.06.028,"Cardiovascular health, infection burden and their interactive association with brain volumetric and white matter integrity outcomes in the UK Biobank.","Beydoun MA, Beydoun HA, Gale SD, Hedges D, Weiss J, Li Z, Erickson LD, Noren Hooten N, Launer LJ, Evans MK, Zonderman AB.",,"Brain, behavior, and immunity",2023,2023-06-29,N,Infection; Aging; White Matter Integrity; Brain Volumes; Brain Magnetic Resonance Imaging,,,"<h4>Background</h4>Cardiovascular health is associated with brain magnetic resonance imaging (MRI) markers of pathology and infections may modulate this association.<h4>Methods</h4>Using data from 38,803 adults (aged 40-70 years) and followed-up for 5-15 years, we tested associations of prevalent total (47.5%) and hospital-treated infection burden (9.7%) with brain structural and diffusion-weighted MRI (i.e., sMRI and dMRI, respectively) common in dementia phenome. Poor white matter tissue integrity was operationalized with lower global and tract-specific fractional anisotropy (FA) and higher mean diffusivity (MD). Volumetric sMRI outcomes included total, gray matter (GM), white matter (WM), frontal bilateral GM, white matter hyperintensity (WMH), and selected based on previous associations with dementia. Cardiovascular health was measured with Life's Essential 8 score (LE8) converted to tertiles. Multiple linear regression models were used, adjusting for intracranial volumes (ICV) for subcortical structures, and for demographic, socio-economic, and the Alzheimer's Disease polygenic risk score for all outcomes, among potential confounders.<h4>Results</h4>In fully adjusted models, hospital-treated infections were inversely related to GM (β ± SE: -1042 ± 379, p = 0.006) and directly related to WMH as percent of ICV (Log<sub>e</sub> transformed) (β ± SE:+0.026 ± 0.007, p < 0.001). Both total and hospital-treated infections were associated with poor WMI, while the latter was inversely related to FA within the lowest LE8 tertile (β ± SE:-0.0011 ± 0.0003, p < 0.001, P<sub>LE8×IB</sub> < 0.05), a pattern detected for GM, Right Frontal GM, left accumbens and left hippocampus volumes. Within the uppermost LE8 tertile, total infection burden was linked to smaller right amygdala while being associated with larger left frontal GM and right putamen volumes, in the overall sample. Within that uppermost tertile of LE8, caudate volumes were also positively associated with hospital-treated infections.<h4>Conclusions</h4>Hospital-treated infections had more consistent deleterious effects on volumetric and white matter integrity brain neuroimaging outcomes compared with total infectious burden, particularly in poorer cardiovascular health groups. Further studies are needed in comparable populations, including longitudinal studies with multiple repeats on neuroimaging markers.",,doi:https://doi.org/10.1016/j.bbi.2023.06.028; html:https://europepmc.org/articles/PMC11040741; pdf:https://europepmc.org/articles/PMC11040741?pdf=render; doi:https://doi.org/10.1016/j.bbi.2023.06.028
 34861180,https://doi.org/10.1016/s2213-2600(21)00491-4,Risk of COVID-19 hospital admission among children aged 5-17 years with asthma in Scotland: a national incident cohort study.,"Shi T, Pan J, Katikireddi SV, McCowan C, Kerr S, Agrawal U, Shah SA, Simpson CR, Ritchie LD, Robertson C, Sheikh A, Public Health Scotland and the EAVE II Collaborators.",,The Lancet. Respiratory medicine,2022,2021-11-30,Y,,,,"<h4>Background</h4>There is an urgent need to inform policy deliberations about whether children with asthma should be vaccinated against SARS-CoV-2 and, if so, which subset of children with asthma should be prioritised. We were asked by the UK's Joint Commission on Vaccination and Immunisation to undertake an urgent analysis to identify which children with asthma were at increased risk of serious COVID-19 outcomes.<h4>Methods</h4>This national incident cohort study was done in all children in Scotland aged 5-17 years who were included in the linked dataset of Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II). We used data from EAVE II to investigate the risk of COVID-19 hospitalisation among children with markers of uncontrolled asthma defined by either previous asthma hospital admission or oral corticosteroid prescription in the previous 2 years. A Cox proportional hazard model was used to derive hazard ratios (HRs) and 95% CIs for the association between asthma and COVID-19 hospital admission, stratified by markers of asthma control (previous asthma hospital admission and number of previous prescriptions for oral corticosteroids within 2 years of the study start date). Analyses were adjusted for age, sex, socioeconomic status, comorbidity, and previous hospital admission.<h4>Findings</h4>Between March 1, 2020, and July 27, 2021, 752 867 children were included in the EAVE II dataset, 63 463 (8·4%) of whom had clinician-diagnosed-and-recorded asthma. Of these, 4339 (6·8%) had RT-PCR confirmed SARS-CoV-2 infection. In those with confirmed infection, 67 (1·5%) were admitted to hospital with COVID-19. Among the 689 404 children without asthma, 40 231 (5·8%) had confirmed SARS-CoV-2 infections, of whom 382 (0·9%) were admitted to hospital with COVID-19. The rate of COVID-19 hospital admission was higher in children with poorly controlled asthma than in those with well controlled asthma or without asthma. When using previous hospital admission for asthma as the marker of uncontrolled asthma, the adjusted HR was 6·40 (95% CI 3·27-12·53) for those with poorly controlled asthma and 1·36 (1·02-1·80) for those with well controlled asthma, compared with those with no asthma. When using oral corticosteroid prescriptions as the marker of uncontrolled asthma, the adjusted HR was 3·38 (1·84-6·21) for those with three or more prescribed courses of corticosteroids, 3·53 (1·87-6·67) for those with two prescribed courses of corticosteroids, 1·52 (0·90-2·57) for those with one prescribed course of corticosteroids, and 1·34 (0·98-1·82) for those with no prescribed course, compared with those with no asthma.<h4>Interpretation</h4>School-aged children with asthma with previous recent hospital admission or two or more courses of oral corticosteroids are at markedly increased risk of COVID-19 hospital admission and should be considered a priority for vaccinations. This would translate into 9124 children across Scotland and an estimated 109 448 children across the UK.<h4>Funding</h4>UK Research and Innovation (Medical Research Council), Research and Innovation Industrial Strategy Challenge Fund, Health Data Research UK, and Scottish Government.",,pdf:https://aura.abdn.ac.uk/bitstream/2164/18431/1/Shi_etal_Lancet_Risk_COVID19_Hospital_VOR.pdf; doi:https://doi.org/10.1016/S2213-2600(21)00491-4; html:https://europepmc.org/articles/PMC8631918
-38774381,https://doi.org/10.1093/ehjdh/ztae011,Remote monitoring of atrial fibrillation recurrence using mHealth technology (REMOTE-AF).,"Adasuriya G, Barsky A, Kralj-Hans I, Mohan S, Gill S, Chen Z, Jarman J, Jones D, Valli H, Gkoutos GV, Markides V, Hussain W, Wong T, Kotecha D, Haldar S.",,European heart journal. Digital health,2024,2024-02-12,Y,Atrial fibrillation; Ablation; Remote Monitoring; Digital Health; Wearables,,,"<h4>Aims</h4>This proof-of-concept study sought to evaluate changes in heart rate (HR) obtained from a consumer wearable device and compare against implantable loop recorder (ILR)-detected recurrence of atrial fibrillation (AF) and atrial tachycardia (AT) after AF ablation.<h4>Methods and results</h4>REMOTE-AF (NCT05037136) was a prospectively designed sub-study of the CASA-AF randomized controlled trial (NCT04280042). Participants without a permanent pacemaker had an ILR implanted at their index ablation procedure for longstanding persistent AF. Heart rate and step count were continuously monitored using photoplethysmography (PPG) from a commercially available wrist-worn wearable. Photoplethysmography-recorded HR data were pre-processed with noise filtration and episodes at 1-min interval over 30 min of HR elevations (<i>Z</i>-score = 2) were compared with corresponding ILR data. Thirty-five patients were enrolled, with mean age 70.3 ± 6.8 years and median follow-up 10 months (interquartile range 8-12 months). Implantable loop recorder analysis revealed 17 out of 35 patients (49%) had recurrence of AF/AT. Compared with ILR recurrence, wearable-derived elevations in HR ≥ 110 beats per minute had a sensitivity of 95.3%, specificity 54.1%, positive predictive value (PPV) 15.8%, negative predictive value (NPV) 99.2%, and overall accuracy 57.4%. With PPG-recorded HR elevation spikes (non-exercise related), the sensitivity was 87.5%, specificity 62.2%, PPV 39.2%, NPV 92.3%, and overall accuracy 64.0% in the entire patient cohort. In the AF/AT recurrence only group, sensitivity was 87.6%, specificity 68.3%, PPV 53.6%, NPV 93.0%, and overall accuracy 75.0%.<h4>Conclusion</h4>Consumer wearable devices have the potential to contribute to arrhythmia detection after AF ablation.<h4>Study registration</h4>ClinicalTrials.gov Identifier: NCT05037136 https://clinicaltrials.gov/ct2/show/NCT05037136.",,doi:https://doi.org/10.1093/ehjdh/ztae011; html:https://europepmc.org/articles/PMC11104468; pdf:https://europepmc.org/articles/PMC11104468?pdf=render
-33228632,https://doi.org/10.1186/s12920-020-00826-6,A random forest based biomarker discovery and power analysis framework for diagnostics research.,"Acharjee A, Larkman J, Xu Y, Cardoso VR, Gkoutos GV.",,BMC medical genomics,2020,2020-11-23,Y,Biomarker; Feature Selection; Random Forest; Power Study,,,"<h4>Background</h4>Biomarker identification is one of the major and important goal of functional genomics and translational medicine studies. Large scale -omics data are increasingly being accumulated and can provide vital means for the identification of biomarkers for the early diagnosis of complex disease and/or for advanced patient/diseases stratification. These tasks are clearly interlinked, and it is essential that an unbiased and stable methodology is applied in order to address them. Although, recently, many, primarily machine learning based, biomarker identification approaches have been developed, the exploration of potential associations between biomarker identification and the design of future experiments remains a challenge.<h4>Methods</h4>In this study, using both simulated and published experimentally derived datasets, we assessed the performance of several state-of-the-art Random Forest (RF) based decision approaches, namely the Boruta method, the permutation based feature selection without correction method, the permutation based feature selection with correction method, and the backward elimination based feature selection method. Moreover, we conducted a power analysis to estimate the number of samples required for potential future studies.<h4>Results</h4>We present a number of different RF based stable feature selection methods and compare their performances using simulated, as well as published, experimentally derived, datasets. Across all of the scenarios considered, we found the Boruta method to be the most stable methodology, whilst the Permutation (Raw) approach offered the largest number of relevant features, when allowed to stabilise over a number of iterations. Finally, we developed and made available a web interface ( https://joelarkman.shinyapps.io/PowerTools/ ) to streamline power calculations thereby aiding the design of potential future studies within a translational medicine context.<h4>Conclusions</h4>We developed a RF-based biomarker discovery framework and provide a web interface for our framework, termed PowerTools, that caters the design of appropriate and cost-effective subsequent future omics study.",,pdf:https://bmcmedgenomics.biomedcentral.com/track/pdf/10.1186/s12920-020-00826-6; doi:https://doi.org/10.1186/s12920-020-00826-6; html:https://europepmc.org/articles/PMC7685541; pdf:https://europepmc.org/articles/PMC7685541?pdf=render
 36653750,https://doi.org/10.1186/s12882-022-03043-8,Ultrasound quadriceps muscle thickness is variably associated with frailty in haemodialysis recipients.,"Anderson BM, Wilson DV, Qasim M, Correa G, Evison F, Gallier S, Ferro CJ, Jackson TA, Sharif A.",,BMC nephrology,2023,2023-01-18,Y,Frailty; ultrasound; epidemiology; Sarcopenia,,,"<h4>Background</h4>Ultrasonographic quantitation of quadriceps muscle mass is increasingly used for assessment of sarcopenia, but its relationship with frailty in haemodialysis recipients is not known. This study explores the relationship between ultrasound-derived bilateral anterior thigh thickness (BATT), sarcopenia, and frailty by common frailty tools (Frailty Phenotype [FP], Frailty Index [FI], Edmonton Frailty [EFS], and Clinical Frailty Scale [CFS]).<h4>Methods</h4>This was an exploratory analysis of a subgroup of adult prevalent (≥3 months) haemodialysis recipients deeply phenotyped for frailty. Ultrasound assessment of BATT was obtained with participants at an angle of ≤45°, with legs outstretched and knees resting at 10°-20°, according to an established protocol. Associations with frailty were explored via both linear and logistic regressions for BATT, Low Muscle Mass (LMM), and sarcopenia with stepwise adjustment for a priori covariables.<h4>Results</h4>In total 223 study participants had ultrasound measurements. Frailty ranged from 34% for FP to 58% for FI. BATT was associated with increasing frailty on simple linear regression by all frailty tools, but lost significance on addition of covariables. Upon dichotomising frailty tools into Frail/Not Frail, BATT was associated with frailty by all tools on univariable analyses, but only retained association for EFS on the fully adjusted model (OR 0.97, 95% C.I. 0.94-1.00, P = 0.05).<h4>Conclusions</h4>Ultrasound measures of quadriceps thickness is variably associated with frailty in prevalent haemodialysis recipients, dependent upon the frailty tool used, but not independent of other variables. Further work is required to establish the added value of sarcopenia measurement in frail haemodialysis patients.<h4>Trial registration</h4>Clinicaltrials.gov : NCT03071107 registered 06/03/2017.",,pdf:https://bmcnephrol.biomedcentral.com/counter/pdf/10.1186/s12882-022-03043-8; doi:https://doi.org/10.1186/s12882-022-03043-8; html:https://europepmc.org/articles/PMC9847024; pdf:https://europepmc.org/articles/PMC9847024?pdf=render
+33228632,https://doi.org/10.1186/s12920-020-00826-6,A random forest based biomarker discovery and power analysis framework for diagnostics research.,"Acharjee A, Larkman J, Xu Y, Cardoso VR, Gkoutos GV.",,BMC medical genomics,2020,2020-11-23,Y,Biomarker; Feature Selection; Random Forest; Power Study,,,"<h4>Background</h4>Biomarker identification is one of the major and important goal of functional genomics and translational medicine studies. Large scale -omics data are increasingly being accumulated and can provide vital means for the identification of biomarkers for the early diagnosis of complex disease and/or for advanced patient/diseases stratification. These tasks are clearly interlinked, and it is essential that an unbiased and stable methodology is applied in order to address them. Although, recently, many, primarily machine learning based, biomarker identification approaches have been developed, the exploration of potential associations between biomarker identification and the design of future experiments remains a challenge.<h4>Methods</h4>In this study, using both simulated and published experimentally derived datasets, we assessed the performance of several state-of-the-art Random Forest (RF) based decision approaches, namely the Boruta method, the permutation based feature selection without correction method, the permutation based feature selection with correction method, and the backward elimination based feature selection method. Moreover, we conducted a power analysis to estimate the number of samples required for potential future studies.<h4>Results</h4>We present a number of different RF based stable feature selection methods and compare their performances using simulated, as well as published, experimentally derived, datasets. Across all of the scenarios considered, we found the Boruta method to be the most stable methodology, whilst the Permutation (Raw) approach offered the largest number of relevant features, when allowed to stabilise over a number of iterations. Finally, we developed and made available a web interface ( https://joelarkman.shinyapps.io/PowerTools/ ) to streamline power calculations thereby aiding the design of potential future studies within a translational medicine context.<h4>Conclusions</h4>We developed a RF-based biomarker discovery framework and provide a web interface for our framework, termed PowerTools, that caters the design of appropriate and cost-effective subsequent future omics study.",,pdf:https://bmcmedgenomics.biomedcentral.com/track/pdf/10.1186/s12920-020-00826-6; doi:https://doi.org/10.1186/s12920-020-00826-6; html:https://europepmc.org/articles/PMC7685541; pdf:https://europepmc.org/articles/PMC7685541?pdf=render
 36798088,https://doi.org/10.1177/26335565221148616,Classification of long-term condition patterns in rheumatoid arthritis and associations with adverse health events: a UK Biobank cohort study.,"McLoone P, Jani BD, Siebert S, Morton FR, Canning J, Macdonald S, Mair FS, Nicholl BI.",,Journal of multimorbidity and comorbidity,2023,2023-01-01,Y,Rheumatoid arthritis; Mortality; Comorbidity; Latent Class Analysis; Multimorbidity,,,"<h4>Purpose</h4>We aimed to classify individuals with RA and ≥2 additional long-term conditions (LTCs) and describe the association between different LTC classes, number of LTCs and adverse health outcomes.<h4>Methods</h4>We used UK Biobank participants who reported RA (n=5,625) and employed latent class analysis (LCA) to create classes of LTC combinations for those with ≥2 additional LTCs. Cox-proportional hazard and negative binomial regression were used to compare the risk of all-cause mortality, major adverse cardiac events (MACE), and number of emergency hospitalisations over an 11-year follow-up across the different LTC classes and in those with RA plus one additional LTC. Persons with RA without LTCs were the reference group. Analyses were adjusted for demographic characteristics, smoking, BMI, alcohol consumption and physical activity.<h4>Results</h4>A total of 2,566 (46%) participants reported ≥2 LTCs in addition to RA. This involved 1,138 distinct LTC combinations of which 86% were reported by ≤2 individuals. LCA identified 5 morbidity-classes. The distinctive condition in the class with the highest mortality was cancer (class 5; HR 2.66 95%CI (1.91-3.70)). The highest MACE (HR 2.95 95%CI (2.11-4.14)) and emergency hospitalisations (rate ratio 3.01 (2.56-3.54)) were observed in class 3 which comprised asthma, COPD & CHD. There was an increase in mortality, MACE and emergency hospital admissions within each class as the number of LTCs increased.<h4>Conclusions</h4>The risk of adverse health outcomes in RA varied with different patterns of multimorbidity. The pattern of multimorbidity should be considered in risk assessment and formulating management plans in patients with RA.",,doi:https://doi.org/10.1177/26335565221148616; doi:https://doi.org/10.1177/26335565221148616; html:https://europepmc.org/articles/PMC9926377; pdf:https://europepmc.org/articles/PMC9926377?pdf=render
+38774381,https://doi.org/10.1093/ehjdh/ztae011,Remote monitoring of atrial fibrillation recurrence using mHealth technology (REMOTE-AF).,"Adasuriya G, Barsky A, Kralj-Hans I, Mohan S, Gill S, Chen Z, Jarman J, Jones D, Valli H, Gkoutos GV, Markides V, Hussain W, Wong T, Kotecha D, Haldar S.",,European heart journal. Digital health,2024,2024-02-12,Y,Atrial fibrillation; Ablation; Remote Monitoring; Digital Health; Wearables,,,"<h4>Aims</h4>This proof-of-concept study sought to evaluate changes in heart rate (HR) obtained from a consumer wearable device and compare against implantable loop recorder (ILR)-detected recurrence of atrial fibrillation (AF) and atrial tachycardia (AT) after AF ablation.<h4>Methods and results</h4>REMOTE-AF (NCT05037136) was a prospectively designed sub-study of the CASA-AF randomized controlled trial (NCT04280042). Participants without a permanent pacemaker had an ILR implanted at their index ablation procedure for longstanding persistent AF. Heart rate and step count were continuously monitored using photoplethysmography (PPG) from a commercially available wrist-worn wearable. Photoplethysmography-recorded HR data were pre-processed with noise filtration and episodes at 1-min interval over 30 min of HR elevations (<i>Z</i>-score = 2) were compared with corresponding ILR data. Thirty-five patients were enrolled, with mean age 70.3 ± 6.8 years and median follow-up 10 months (interquartile range 8-12 months). Implantable loop recorder analysis revealed 17 out of 35 patients (49%) had recurrence of AF/AT. Compared with ILR recurrence, wearable-derived elevations in HR ≥ 110 beats per minute had a sensitivity of 95.3%, specificity 54.1%, positive predictive value (PPV) 15.8%, negative predictive value (NPV) 99.2%, and overall accuracy 57.4%. With PPG-recorded HR elevation spikes (non-exercise related), the sensitivity was 87.5%, specificity 62.2%, PPV 39.2%, NPV 92.3%, and overall accuracy 64.0% in the entire patient cohort. In the AF/AT recurrence only group, sensitivity was 87.6%, specificity 68.3%, PPV 53.6%, NPV 93.0%, and overall accuracy 75.0%.<h4>Conclusion</h4>Consumer wearable devices have the potential to contribute to arrhythmia detection after AF ablation.<h4>Study registration</h4>ClinicalTrials.gov Identifier: NCT05037136 https://clinicaltrials.gov/ct2/show/NCT05037136.",,doi:https://doi.org/10.1093/ehjdh/ztae011; html:https://europepmc.org/articles/PMC11104468; pdf:https://europepmc.org/articles/PMC11104468?pdf=render
 35185750,https://doi.org/10.3389/fneur.2021.787107,Physician-Confirmed and Administrative Definitions of Stroke in UK Biobank Reflect the Same Underlying Genetic Trait.,"Rannikmäe K, Rawlik K, Ferguson AC, Avramidis N, Jiang M, Pirastu N, Shen X, Davidson E, Woodfield R, Malik R, Dichgans M, Tenesa A, Sudlow C.",,Frontiers in neurology,2021,2022-02-02,Y,Validation; Genetic correlation; Stroke; Accuracy; Routinely Collected Health Data,,,"<h4>Background</h4>Stroke in UK Biobank (UKB) is ascertained <i>via</i> linkages to coded administrative datasets and self-report. We studied the accuracy of these codes using genetic validation.<h4>Methods</h4>We compiled stroke-specific and broad cerebrovascular disease (CVD) code lists (Read V2/V3, ICD-9/-10) for medical settings (hospital, death record, primary care) and self-report. Among 408,210 UKB participants, we identified all with a relevant code, creating 12 stroke definitions based on the code type and source. We performed genome-wide association studies (GWASs) for each definition, comparing summary results against the largest published stroke GWAS (MEGASTROKE), assessing genetic correlations, and replicating 32 stroke-associated loci.<h4>Results</h4>The stroke case numbers identified varied widely from 3,976 (primary care stroke-specific codes) to 19,449 (all codes, all sources). All 12 UKB stroke definitions were significantly correlated with the MEGASTROKE summary GWAS results (rg.81-1) and each other (rg.4-1). However, Bonferroni-corrected confidence intervals were wide, suggesting limited precision of some results. Six previously reported stroke-associated loci were replicated using ≥1 UKB stroke definition.<h4>Conclusions</h4>Stroke case numbers in UKB depend on the code source and type used, with a 5-fold difference in the maximum case-sample size. All stroke definitions are significantly genetically correlated with the largest stroke GWAS to date.",,pdf:https://www.frontiersin.org/articles/10.3389/fneur.2021.787107/pdf; doi:https://doi.org/10.3389/fneur.2021.787107; html:https://europepmc.org/articles/PMC8847736; pdf:https://europepmc.org/articles/PMC8847736?pdf=render
 38533433,https://doi.org/10.3892/etm.2024.12476,Rates of venous thromboembolism associated with acute psychiatric admission: A retrospective cohort study.,"Codling D, Mueller C, Patel J, Stewart R, Arya R, Roberts L.",,Experimental and therapeutic medicine,2024,2024-03-08,Y,incidence; Venous Thromboembolism; Psychiatric Patients; Hospitalisation,,,"The present study aimed to identify rates of venous thromboembolism (VTE) amongst patients treated in inpatient mental health units using linked primary care and mental health care records. Patients resident in the London Borough of Lambeth admitted to mental health units in Southeast London between January 2008 and March 2019 were included, as well as a control group of patients being treated in the community for mental illness. The primary outcome measure was a diagnosis of VTE being recorded in GP records during or within 3 months of an admission to a mental health unit. For 7,198 psychiatric inpatient admissions, 11 episodes of VTE (1.5/1,000 admissions) were identified, with no VTE cases identified in 4,561 patients being treated in the community for mental illness during an equivalent window. This finding indicates that VTE rates following psychiatric inpatient admission might be similar to those following unselected acute medical admission. Larger scale studies are required to confirm the estimated incidence of VTE in patients with mental health conditions and the contribution of acute psychiatry hospitalisation to VTE risk.",,doi:https://doi.org/10.3892/etm.2024.12476; html:https://europepmc.org/articles/PMC10964734; pdf:https://europepmc.org/articles/PMC10964734?pdf=render
 39292500,https://doi.org/10.2196/46485,The Use of Online Consultation Systems or Remote Consulting in England Characterized Through the Primary Care Health Records of 53 Million People in the OpenSAFELY Platform: Retrospective Cohort Study.,"Fonseca M, MacKenna B, Mehrkar A, OpenSAFELY Collaborative, Walters CE, Hickman G, Pearson J, Fisher L, Inglesby P, Bacon S, Davy S, Hulme W, Goldacre B, Koffman O, Bakhai M.",,JMIR public health and surveillance,2024,2024-09-18,Y,General Practice; Primary Care Research; Remote Monitoring; Health Informatics; Triage; Online Consultation System; Opensafely; Trusted Research Environment; Digital Primary Care; Electronic Health Record Coding,,,"<h4>Background</h4>The National Health Service (NHS) Long Term Plan, published in 2019, committed to ensuring that every patient in England has the right to digital-first primary care by 2023-2024. The COVID-19 pandemic and infection prevention and control measures accelerated work by the NHS to enable and stimulate the use of online consultation (OC) systems across all practices for improved access to primary care.<h4>Objective</h4>We aimed to explore general practice coding activity associated with the use of OC systems in terms of trends, COVID-19 effect, variation, and quality.<h4>Methods</h4>With the approval of NHS England, the OpenSAFELY platform was used to query and analyze the in situ electronic health records of suppliers The Phoenix Partnership (TPP) and Egton Medical Information Systems, covering >53 million patients in >6400 practices, mainly in 2019-2020. Systematized Medical Nomenclature for Medicine-Clinical Terminology (SNOMED-CT) codes relevant to OC systems and written OCs were identified including eConsultation. Events were described by volumes and population rates, practice coverage, and trends before and after the COVID-19 pandemic. Variation was characterized among practices, by sociodemographics, and by clinical history of long-term conditions.<h4>Results</h4>Overall, 3,550,762 relevant coding events were found in practices using TPP, with the code eConsultation detected in 84.56% (2157/2551) of practices. Activity related to digital forms of interaction increased rapidly from March 2020, the onset of the pandemic; namely, in the second half of 2020, >9 monthly eConsultation coding events per 1000 registered population were registered compared to <1 a year prior. However, we found large variations among regions and practices: December 2020 saw the median practice have 0.9 coded instances per 1000 population compared to at least 36 for the highest decile of practices. On sociodemographics, the TPP cohort with OC instances, when compared (univariate analysis) to the cohort with general practitioner consultations, was more predominantly female (661,235/1,087,919, 60.78% vs 9,172,833/17,166,765, 53.43%), aged 18 to 40 years (349,162/1,080,589, 32.31% vs 4,295,711/17,000,942, 25.27%), White (730,389/1,087,919, 67.14% vs 10,887,858/17,166,765, 63.42%), and less deprived (167,889/1,068,887, 15.71% vs 3,376,403/16,867,074, 20.02%). Looking at the eConsultation code through multivariate analysis, it was more commonly recorded among patients with a history of asthma (adjusted odds ratio [aOR] 1.131, 95% CI 1.124-1.137), depression (aOR 1.144, 95% CI 1.138-1.151), or atrial fibrillation (aOR 1.119, 95% CI 1.099-1.139) when compared to other patients with general practitioner consultations, adjusted for long-term conditions, age, and gender.<h4>Conclusions</h4>We successfully queried general practice coding activity relevant to the use of OC systems, showing increased adoption and key areas of variation during the pandemic at both sociodemographic and clinical levels. The work can be expanded to support monitoring of coding quality and underlying activity. This study suggests that large-scale impact evaluation studies can be implemented within the OpenSAFELY platform, namely looking at patient outcomes.",,doi:https://doi.org/10.2196/46485; html:https://europepmc.org/articles/PMC11447420
@@ -370,53 +370,53 @@ PMC11234640,https://doi.org/,"Evidence of gene-nutrient interaction association
 38336700,https://doi.org/10.1186/s12916-023-03179-w,Peripheral vertigo and subsequent risk of depression and anxiety disorders: a prospective cohort study using the UK Biobank.,"Chen X, Wei D, Fang F, Song H, Yin L, Kaijser M, Gurholt TP, Andreassen OA, Valdimarsdóttir U, Hu K, Duan M.",,BMC medicine,2024,2024-02-09,Y,Psychiatric disorders; Fractional Anisotropy; Peripheral Vertigo; Frontal-limbic Network,,,"<h4>Background</h4>Peripheral vertigo is often comorbid with psychiatric disorders. However, no longitudinal study has quantified the association between peripheral vertigo and risk of psychiatric disorders. Furthermore, it remains unknown how the white matter integrity of frontal-limbic network relates to the putative peripheral vertigo-psychiatric disorder link.<h4>Methods</h4>We conducted a cohort study including 452,053 participants of the UK Biobank with a follow-up from 2006 through 2021. We assessed the risks of depression and anxiety disorders in relation to a hospitalization episode involving peripheral vertigo using Cox proportional hazards models. We also examined the associations of peripheral vertigo, depression, and anxiety with MRI fractional anisotropy (FA) in a subsample with brain MRI data (N = 36,087), using multivariable linear regression.<h4>Results</h4>Individuals with an inpatient diagnosis of peripheral vertigo had elevated risks of incident depression (hazard ratio (HR) 2.18; 95% confidence interval (CI) 1.79-2.67) and anxiety (HR 2.11; 95% CI 1.71-2.61), compared to others, particularly within 2 years after hospitalization (HR for depression 2.91; 95% CI 2.04-4.15; HR for anxiety 4.92; 95% CI 3.62-6.69). Depression was associated with lower FA in most studied white matter regions, whereas anxiety and peripheral vertigo did not show statistically significant associations with FA.<h4>Conclusions</h4>Individuals with an inpatient diagnosis of peripheral vertigo have increased subsequent risks of depression and anxiety disorders, especially within 2 years after hospitalization. Our findings further indicate a link between depression and lower microstructural connectivity as well as integrity beyond the frontal-limbic network.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-023-03179-w; doi:https://doi.org/10.1186/s12916-023-03179-w; html:https://europepmc.org/articles/PMC10858592; pdf:https://europepmc.org/articles/PMC10858592?pdf=render
 38008730,https://doi.org/10.1186/s12889-023-17169-3,The cost of implementing the COVID-19 shielding policy in Wales.,"Sewell B, Farr A, Akbari A, Carson-Stevens A, Dale J, Edwards A, Evans BA, John A, Torabi F, Jolles S, Kingston M, Lyons J, Lyons RA, Porter A, Watkins A, Williams V, Snooks H.",,BMC public health,2023,2023-11-26,Y,Resources; Implementation; Cost; Shielding; Covid-19; Clinically Vulnerable; Secure Anonymised Data,,,"<h4>Background</h4>The EVITE Immunity study investigated the effects of shielding Clinically Extremely Vulnerable (CEV) people during the COVID-19 pandemic on health outcomes and healthcare costs in Wales, United Kingdom, to help prepare for future pandemics. Shielding was intended to protect those at highest risk of serious harm from COVID-19. We report the cost of implementing shielding in Wales.<h4>Methods</h4>The number of people shielding was extracted from the Secure Anonymised Information Linkage Databank. Resources supporting shielding between March and June 2020 were mapped using published reports, web pages, freedom of information requests to Welsh Government and personal communications (e.g. with the office of the Chief Medical Officer for Wales).<h4>Results</h4>At the beginning of shielding, 117,415 people were on the shielding list. The total additional cost to support those advised to stay home during the initial 14 weeks of the pandemic was £13,307,654 (£113 per person shielded). This included the new resources required to compile the shielding list, inform CEV people of the shielding intervention and provide medicine and food deliveries. The list was adjusted weekly over the 3-month period (130,000 people identified by June 2020). Therefore the cost per person shielded lies between £102 and £113 per person.<h4>Conclusion</h4>This is the first evaluation of the cost of the measures put in place to support those identified to shield in Wales. However, no data on opportunity cost was available. The true costs of shielding including its budget impact and opportunity costs need to be investigated to decide whether shielding is a worthwhile policy for future health emergencies.",,pdf:https://bmcpublichealth.biomedcentral.com/counter/pdf/10.1186/s12889-023-17169-3; doi:https://doi.org/10.1186/s12889-023-17169-3; html:https://europepmc.org/articles/PMC10680245; pdf:https://europepmc.org/articles/PMC10680245?pdf=render
 37789603,https://doi.org/10.1002/pon.6225,Prognostic factors for mental wellbeing in prostate cancer: A systematic review and meta-analysis.,"Vyas N, Brunckhorst O, Fanshawe JB, Stewart R, Dasgupta P, Ahmed K.",,Psycho-oncology,2023,2023-10-03,Y,Cancer; Depression; Quality of life; Anxiety; Oncology; prostate cancer; Body Image; Masculinity; Mental Wellbeing; Fear Of Cancer Recurrence,,,"<h4>Objectives</h4>To evaluate the evidence base for patient, oncological, and treatment prognostic factors associated with multiple mental wellbeing outcomes in prostate cancer patients.<h4>Methods</h4>We performed a literature search of MEDLINE, EMBASE, and CINAHL databases including studies evaluating patient, oncological, or treatment factors against one of five mental wellbeing outcomes; depression, anxiety, fear of cancer recurrence, masculinity, and body image perception. Data synthesis included a random effects meta-analysis for the prognostic effect of individual factors if sufficient homogenous data was available, with a structured narrative synthesis where this was not possible.<h4>Results</h4>A final 62 articles were included. Older age was associated with a reducing odds of depression (OR 0.97, p = 0.04), with little evidence of effect for other outcomes. Additionally, baseline mental health status was related to depression and increasing time since diagnosis was associated with reducing fear of recurrence, albeith with low certainty of evidence. However, few other patient or oncological factors demonstrated any coherent relationship with any wellbeing outcome. Androgen deprivation therapy was associated with increased depression (HR 1.65, 95% CI 1.41-1.92, p < 0.01) and anxiety, however, little difference was seen between other treatment options. Overall, whilst numerous factors were identified, most were evaluated by single studies with few evaluating masculinity and body image outcomes.<h4>Conclusion</h4>We highlight the existing evidence for prognostic factors in mental wellbeing outcomes in prostate cancer, allowing us to consider high-risk groups of patients for preventative and treatment measures. However, the current evidence is heterogenous with further work required exploring less conclusive factors and outcomes.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pon.6225; doi:https://doi.org/10.1002/pon.6225; html:https://europepmc.org/articles/PMC10946963; pdf:https://europepmc.org/articles/PMC10946963?pdf=render
-34942103,https://doi.org/10.1016/s0140-6736(21)02754-9,"Two-dose ChAdOx1 nCoV-19 vaccine protection against COVID-19 hospital admissions and deaths over time: a retrospective, population-based cohort study in Scotland and Brazil.","Katikireddi SV, Cerqueira-Silva T, Vasileiou E, Robertson C, Amele S, Pan J, Taylor B, Boaventura V, Werneck GL, Flores-Ortiz R, Agrawal U, Docherty AB, McCowan C, McMenamin J, Moore E, Ritchie LD, Rudan I, Shah SA, Shi T, Simpson CR, Barreto ML, Oliveira VA, Barral-Netto M, Sheikh A.",,"Lancet (London, England)",2022,2021-12-20,Y,,,,"<h4>Background</h4>Reports suggest that COVID-19 vaccine effectiveness is decreasing, but whether this reflects waning or new SARS-CoV-2 variants-especially delta (B.1.617.2)-is unclear. We investigated the association between time since two doses of ChAdOx1 nCoV-19 vaccine and risk of severe COVID-19 outcomes in Scotland (where delta was dominant), with comparative analyses in Brazil (where delta was uncommon).<h4>Methods</h4>In this retrospective, population-based cohort study in Brazil and Scotland, we linked national databases from the EAVE II study in Scotland; and the COVID-19 Vaccination Campaign, Acute Respiratory Infection Suspected Cases, and Severe Acute Respiratory Infection/Illness datasets in Brazil) for vaccination, laboratory testing, clinical, and mortality data. We defined cohorts of adults (aged ≥18 years) who received two doses of ChAdOx1 nCoV-19 and compared rates of severe COVID-19 outcomes (ie, COVID-19 hospital admission or death) across fortnightly periods, relative to 2-3 weeks after the second dose. Entry to the Scotland cohort started from May 19, 2021, and entry to the Brazil cohort started from Jan 18, 2021. Follow-up in both cohorts was until Oct 25, 2021. Poisson regression was used to estimate rate ratios (RRs) and vaccine effectiveness, with 95% CIs.<h4>Findings</h4>1 972 454 adults received two doses of ChAdOx1 nCoV-19 in Scotland and 42 558 839 in Brazil, with longer follow-up in Scotland because two-dose vaccination began earlier in Scotland than in Brazil. In Scotland, RRs for severe COVID-19 increased to 2·01 (95% CI 1·54-2·62) at 10-11 weeks, 3·01 (2·26-3·99) at 14-15 weeks, and 5·43 (4·00-7·38) at 18-19 weeks after the second dose. The pattern of results was similar in Brazil, with RRs of 2·29 (2·01-2·61) at 10-11 weeks, 3·10 (2·63-3·64) at 14-15 weeks, and 4·71 (3·83-5·78) at 18-19 weeks after the second dose. In Scotland, vaccine effectiveness decreased from 83·7% (95% CI 79·7-87·0) at 2-3 weeks, to 75·9% (72·9-78·6) at 14-15 weeks, and 63·7% (59·6-67·4) at 18-19 weeks after the second dose. In Brazil, vaccine effectiveness decreased from 86·4% (85·4-87·3) at 2-3 weeks, to 59·7% (54·6-64·2) at 14-15 weeks, and 42·2% (32·4-50·6) at 18-19 weeks.<h4>Interpretation</h4>We found waning vaccine protection of ChAdOx1 nCoV-19 against COVID-19 hospital admissions and deaths in both Scotland and Brazil, this becoming evident within three months of the second vaccine dose. Consideration needs to be given to providing booster vaccine doses for people who have received ChAdOx1 nCoV-19.<h4>Funding</h4>UK Research and Innovation (Medical Research Council), Scottish Government, Research and Innovation Industrial Strategy Challenge Fund, Health Data Research UK, Fiocruz, Fazer o Bem Faz Bem Programme; Conselho Nacional de Desenvolvimento Científico e Tecnológico, Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro.<h4>Translation</h4>For the Portuguese translation of the abstract see Supplementary Materials section.",,pdf:http://www.thelancet.com/article/S0140673621027549/pdf; doi:https://doi.org/10.1016/S0140-6736(21)02754-9; html:https://europepmc.org/articles/PMC8687670
-39192241,https://doi.org/10.1186/s12888-024-06022-5,Developing a validated methodology for identifying clozapine treatment periods in electronic health records.,"Segev A, Govind R, Oloyede E, Morrin H, Jewell A, Jones R, Mangiaterra L, Bonora S, Iqbal E, Stewart R, Broadbent M, MacCabe JH.",,BMC psychiatry,2024,2024-08-27,Y,Databases; Schizophrenia; Algorithm; Clozapine; Psychosis; Ehr; Cris; Maudsley,,,"<h4>Background</h4>Clozapine is the only recommended antipsychotic medication for individuals diagnosed with treatment-resistant schizophrenia. Unfortunately, its wider use is hindered by several possible adverse effects, some of which are rare but potentially life threatening. As such, there is a growing interest in studying clozapine use and safety in routinely collected healthcare data. However, previous attempts to characterise clozapine treatment have had low accuracy.<h4>Aim</h4>To develop a methodology for identifying clozapine treatment dates by combining several data sources and implement this on a large clinical database.<h4>Methods</h4>Non-identifiable electronic health records from a large mental health provider in London and a linked database from a national clozapine blood monitoring service were used to obtain information regarding patients' clozapine treatment status, blood tests and pharmacy dispensing records. A rule-based algorithm was developed to determine the dates of starting and stopping treatment based on these data, and more than 10% of the outcomes were validated by manual review of de-identified case note text.<h4>Results</h4>A total of 3,212 possible clozapine treatment periods were identified, of which 425 (13.2%) were excluded due to insufficient data to verify clozapine administration. Of the 2,787 treatments remaining, 1,902 (68.2%) had an identified start-date. On evaluation, the algorithm identified treatments with 96.4% accuracy; start dates were 96.2% accurate within 15 days, and end dates were 85.1% accurate within 30 days.<h4>Conclusions</h4>The algorithm produced a reliable database of clozapine treatment periods. Beyond underpinning future observational clozapine studies, we envisage it will facilitate similar implementations on additional large clinical databases worldwide.",,doi:https://doi.org/10.1186/s12888-024-06022-5; doi:https://doi.org/10.1186/s12888-024-06022-5; html:https://europepmc.org/articles/PMC11351314; pdf:https://europepmc.org/articles/PMC11351314?pdf=render
 36369736,https://doi.org/10.1080/19490976.2022.2139979,"Integration of stool microbiota, proteome and amino acid profiles to discriminate patients with adenomas and colorectal cancer.","Bosch S, Acharjee A, Quraishi MN, Bijnsdorp IV, Rojas P, Bakkali A, Jansen EE, Stokkers P, Kuijvenhoven J, Pham TV, Beggs AD, Jimenez CR, Struys EA, Gkoutos GV, de Meij TG, de Boer NK.",,Gut microbes,2022,2022-01-01,Y,Screening; Biomarker; Adenoma; Colon cancer; Data integration; stool; Multi Omics,,,"<h4>Background</h4>Screening for colorectal cancer (CRC) reduces its mortality but has limited sensitivity and specificity. Aims We aimed to explore potential biomarker panels for CRC and adenoma detection and to gain insight into the interaction between gut microbiota and human metabolism in the presence of these lesions.<h4>Methods</h4>This multicenter case-control cohort was performed between February 2016 and November 2019. Consecutive patients ≥18 years with a scheduled colonoscopy were asked to participate and divided into three age, gender, body-mass index and smoking status-matched subgroups: CRC (n = 12), adenomas (n = 21) and controls (n = 20). Participants collected fecal samples prior to bowel preparation on which proteome (LC-MS/MS), microbiota (16S rRNA profiling) and amino acid (HPLC) composition were assessed. Best predictive markers were combined to create diagnostic biomarker panels. Pearson correlation-based analysis on selected markers was performed to create networks of all platforms.<h4>Results</h4>Combining omics platforms provided new panels which outperformed hemoglobin in this cohort, currently used for screening (AUC 0.98, 0.95 and 0.87 for CRC vs controls, adenoma vs controls and CRC vs adenoma, respectively). Integration of data sets revealed markers associated with increased blood excretion, stress- and inflammatory responses and pointed toward downregulation of epithelial integrity.<h4>Conclusions</h4>Integrating fecal microbiota, proteome and amino acids platforms provides for new biomarker panels that may improve noninvasive screening for adenomas and CRC, and may subsequently lead to lower incidence and mortality of colon cancer.",,doi:https://doi.org/10.1080/19490976.2022.2139979; doi:https://doi.org/10.1080/19490976.2022.2139979; html:https://europepmc.org/articles/PMC9662191; pdf:https://europepmc.org/articles/PMC9662191?pdf=render
+34942103,https://doi.org/10.1016/s0140-6736(21)02754-9,"Two-dose ChAdOx1 nCoV-19 vaccine protection against COVID-19 hospital admissions and deaths over time: a retrospective, population-based cohort study in Scotland and Brazil.","Katikireddi SV, Cerqueira-Silva T, Vasileiou E, Robertson C, Amele S, Pan J, Taylor B, Boaventura V, Werneck GL, Flores-Ortiz R, Agrawal U, Docherty AB, McCowan C, McMenamin J, Moore E, Ritchie LD, Rudan I, Shah SA, Shi T, Simpson CR, Barreto ML, Oliveira VA, Barral-Netto M, Sheikh A.",,"Lancet (London, England)",2022,2021-12-20,Y,,,,"<h4>Background</h4>Reports suggest that COVID-19 vaccine effectiveness is decreasing, but whether this reflects waning or new SARS-CoV-2 variants-especially delta (B.1.617.2)-is unclear. We investigated the association between time since two doses of ChAdOx1 nCoV-19 vaccine and risk of severe COVID-19 outcomes in Scotland (where delta was dominant), with comparative analyses in Brazil (where delta was uncommon).<h4>Methods</h4>In this retrospective, population-based cohort study in Brazil and Scotland, we linked national databases from the EAVE II study in Scotland; and the COVID-19 Vaccination Campaign, Acute Respiratory Infection Suspected Cases, and Severe Acute Respiratory Infection/Illness datasets in Brazil) for vaccination, laboratory testing, clinical, and mortality data. We defined cohorts of adults (aged ≥18 years) who received two doses of ChAdOx1 nCoV-19 and compared rates of severe COVID-19 outcomes (ie, COVID-19 hospital admission or death) across fortnightly periods, relative to 2-3 weeks after the second dose. Entry to the Scotland cohort started from May 19, 2021, and entry to the Brazil cohort started from Jan 18, 2021. Follow-up in both cohorts was until Oct 25, 2021. Poisson regression was used to estimate rate ratios (RRs) and vaccine effectiveness, with 95% CIs.<h4>Findings</h4>1 972 454 adults received two doses of ChAdOx1 nCoV-19 in Scotland and 42 558 839 in Brazil, with longer follow-up in Scotland because two-dose vaccination began earlier in Scotland than in Brazil. In Scotland, RRs for severe COVID-19 increased to 2·01 (95% CI 1·54-2·62) at 10-11 weeks, 3·01 (2·26-3·99) at 14-15 weeks, and 5·43 (4·00-7·38) at 18-19 weeks after the second dose. The pattern of results was similar in Brazil, with RRs of 2·29 (2·01-2·61) at 10-11 weeks, 3·10 (2·63-3·64) at 14-15 weeks, and 4·71 (3·83-5·78) at 18-19 weeks after the second dose. In Scotland, vaccine effectiveness decreased from 83·7% (95% CI 79·7-87·0) at 2-3 weeks, to 75·9% (72·9-78·6) at 14-15 weeks, and 63·7% (59·6-67·4) at 18-19 weeks after the second dose. In Brazil, vaccine effectiveness decreased from 86·4% (85·4-87·3) at 2-3 weeks, to 59·7% (54·6-64·2) at 14-15 weeks, and 42·2% (32·4-50·6) at 18-19 weeks.<h4>Interpretation</h4>We found waning vaccine protection of ChAdOx1 nCoV-19 against COVID-19 hospital admissions and deaths in both Scotland and Brazil, this becoming evident within three months of the second vaccine dose. Consideration needs to be given to providing booster vaccine doses for people who have received ChAdOx1 nCoV-19.<h4>Funding</h4>UK Research and Innovation (Medical Research Council), Scottish Government, Research and Innovation Industrial Strategy Challenge Fund, Health Data Research UK, Fiocruz, Fazer o Bem Faz Bem Programme; Conselho Nacional de Desenvolvimento Científico e Tecnológico, Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro.<h4>Translation</h4>For the Portuguese translation of the abstract see Supplementary Materials section.",,pdf:http://www.thelancet.com/article/S0140673621027549/pdf; doi:https://doi.org/10.1016/S0140-6736(21)02754-9; html:https://europepmc.org/articles/PMC8687670
 32935051,https://doi.org/10.23889/ijpds.v5i1.1128,A national initiative in data science for health: an evaluation of the UK Farr Institute.,"Hemingway H, Lyons R, Li Q, Buchan I, Ainsworth J, Pell J, Morris A.",,International journal of population data science,2020,2020-04-08,Y,,,,"<h4>Objective</h4>To evaluate the extent to which the inter-institutional, inter-disciplinary mobilisation of data and skills in the Farr Institute contributed to establishing the emerging field of data science for health in the UK.<h4>Design and outcome measures</h4>We evaluated evidence of six domains characterising a new field of science:defining central scientific challenges,demonstrating how the central challenges might be solved,creating novel interactions among groups of scientists,training new types of experts,re-organising universities,demonstrating impacts in society.We carried out citation, network and time trend analyses of publications, and a narrative review of infrastructure, methods and tools.<h4>Setting</h4>Four UK centres in London, North England, Scotland and Wales (23 university partners), 2013-2018.<h4>Results</h4>1. The Farr Institute helped define a central scientific challenge publishing a research corpus, demonstrating insights from electronic health record (EHR) and administrative data at each stage of the translational cycle in 593 papers with at least one Farr Institute author affiliation on PubMed. 2. The Farr Institute offered some demonstrations of how these scientific challenges might be solved: it established the first four ISO27001 certified trusted research environments in the UK, and approved more than 1000 research users, published on 102 unique EHR and administrative data sources, although there was no clear evidence of an increase in novel, sustained record linkages. The Farr Institute established open platforms for the EHR phenotyping algorithms and validations (>70 diseases, CALIBER). Sample sizes showed some evidence of increase but remained less than 10% of the UK population in primary care-hospital care linked studies. 3.The Farr Institute created novel interactions among researchers: the co-author publication network expanded from 944 unique co-authors (based on 67 publications in the first 30 months) to 3839 unique co-authors (545 papers in the final 30 months). 4. Training expanded substantially with 3 new masters courses, training >400 people at masters, short-course and leadership level and 48 PhD students. 5. Universities reorganised with 4/5 Centres established 27 new faculty (tenured) positions, 3 new university institutes. 6. Emerging evidence of impacts included: > 3200 citations for the 10 most cited papers and Farr research informed eight practice-changing clinical guidelines and policies relevant to the health of millions of UK citizens.<h4>Conclusion</h4>The Farr Institute played a major role in establishing and growing the field of data science for health in the UK, with some initial evidence of benefits for health and healthcare. The Farr Institute has now expanded into Health Data Research (HDR) UK but key challenges remain including, how to network such activities internationally.",,pdf:https://ijpds.org/article/download/1128/2865; doi:https://doi.org/10.23889/ijpds.v5i1.1128; html:https://europepmc.org/articles/PMC7480324; pdf:https://europepmc.org/articles/PMC7480324?pdf=render
-38649271,https://doi.org/10.1136/thorax-2023-220856,Rheumatoid arthritis and idiopathic pulmonary fibrosis: a bidirectional Mendelian randomisation study.,"Leavy OC, Kawano-Dourado L, Stewart ID, Quint JK, Solomon JJ, Borie R, Crestani B, Wain LV, Jenkins G, Dieudé P, Minelli C.",,Thorax,2024,2024-05-20,Y,Interstitial fibrosis; idiopathic pulmonary fibrosis; Rheumatoid Lung Disease,,,"<h4>Background</h4>A usual interstitial pneumonia (UIP) pattern of lung injury is a key feature of idiopathic pulmonary fibrosis (IPF) and is also observed in up to 40% of individuals with rheumatoid arthritis (RA)-associated interstitial lung disease (RA-ILD). The RA-UIP phenotype could result from either a causal relationship of RA on UIP or vice versa, or from a simple co-occurrence of RA and IPF due to shared demographic, genetic or environmental risk factors.<h4>Methods</h4>We used two-sample bidirectional Mendelian randomisation (MR) to test the hypothesis of a causal effect of RA on UIP and of UIP on RA, using variants from genome-wide association studies (GWAS) of RA (separately for seropositive (18 019 cases and 991 604 controls) and seronegative (8515 cases and 1 015 471 controls) RA) and of IPF (4125 cases and 20 464 controls) as genetic instruments. Sensitivity analyses were conducted to assess the robustness of the results to violations of the MR assumptions.<h4>Findings</h4>IPF showed a significant causal effect on seropositive RA, with developing IPF increasing the risk of seropositive RA (OR=1.06, 95% CI: 1.04 to 1.08, p<0.001) which was robust under all models. For the MR in the other direction, seropositive RA showed a significant protective effect on IPF (OR=0.93; 95% CI: 0.87 to 0.99; p=0.032), but the effect was not significant when sensitivity analyses were applied. This was likely because of bias due to exclusion of patients with RA from among the cases in the IPF GWAS, or possibly because our genetic instruments did not fully capture the effect of the complex human leucocyte antigen region, the strongest RA genetic risk factor.<h4>Interpretation</h4>Our findings support the hypothesis that RA-UIP may be due to a cause-effect relationship between UIP and RA, rather than due to a coincidental occurrence of IPF in patients with RA. The significant causal effect of IPF on seropositive RA suggests that pathomechanisms involved in the development of UIP may promote RA, and this may help inform future guidelines on screening for ILD in patients with RA.",,pdf:https://thorax.bmj.com/content/thoraxjnl/early/2024/04/21/thorax-2023-220856.full.pdf; doi:https://doi.org/10.1136/thorax-2023-220856; html:https://europepmc.org/articles/PMC11137470; pdf:https://europepmc.org/articles/PMC11137470?pdf=render
+39192241,https://doi.org/10.1186/s12888-024-06022-5,Developing a validated methodology for identifying clozapine treatment periods in electronic health records.,"Segev A, Govind R, Oloyede E, Morrin H, Jewell A, Jones R, Mangiaterra L, Bonora S, Iqbal E, Stewart R, Broadbent M, MacCabe JH.",,BMC psychiatry,2024,2024-08-27,Y,Databases; Schizophrenia; Algorithm; Clozapine; Psychosis; Ehr; Cris; Maudsley,,,"<h4>Background</h4>Clozapine is the only recommended antipsychotic medication for individuals diagnosed with treatment-resistant schizophrenia. Unfortunately, its wider use is hindered by several possible adverse effects, some of which are rare but potentially life threatening. As such, there is a growing interest in studying clozapine use and safety in routinely collected healthcare data. However, previous attempts to characterise clozapine treatment have had low accuracy.<h4>Aim</h4>To develop a methodology for identifying clozapine treatment dates by combining several data sources and implement this on a large clinical database.<h4>Methods</h4>Non-identifiable electronic health records from a large mental health provider in London and a linked database from a national clozapine blood monitoring service were used to obtain information regarding patients' clozapine treatment status, blood tests and pharmacy dispensing records. A rule-based algorithm was developed to determine the dates of starting and stopping treatment based on these data, and more than 10% of the outcomes were validated by manual review of de-identified case note text.<h4>Results</h4>A total of 3,212 possible clozapine treatment periods were identified, of which 425 (13.2%) were excluded due to insufficient data to verify clozapine administration. Of the 2,787 treatments remaining, 1,902 (68.2%) had an identified start-date. On evaluation, the algorithm identified treatments with 96.4% accuracy; start dates were 96.2% accurate within 15 days, and end dates were 85.1% accurate within 30 days.<h4>Conclusions</h4>The algorithm produced a reliable database of clozapine treatment periods. Beyond underpinning future observational clozapine studies, we envisage it will facilitate similar implementations on additional large clinical databases worldwide.",,doi:https://doi.org/10.1186/s12888-024-06022-5; doi:https://doi.org/10.1186/s12888-024-06022-5; html:https://europepmc.org/articles/PMC11351314; pdf:https://europepmc.org/articles/PMC11351314?pdf=render
 36629285,https://doi.org/10.1093/eurheartj/ehac758,Artificial intelligence to enhance clinical value across the spectrum of cardiovascular healthcare.,"Gill SK, Karwath A, Uh HW, Cardoso VR, Gu Z, Barsky A, Slater L, Acharjee A, Duan J, Dall'Olio L, El Bouhaddani S, Chernbumroong S, Stanbury M, Haynes S, Asselbergs FW, Grobbee DE, Eijkemans MJC, Gkoutos GV, Kotecha D, BigData@Heart Consortium and the cardAIc group.",,European heart journal,2023,2023-03-01,Y,Artificial intelligence; Management; Treatment; Healthcare,,,"Artificial intelligence (AI) is increasingly being utilized in healthcare. This article provides clinicians and researchers with a step-wise foundation for high-value AI that can be applied to a variety of different data modalities. The aim is to improve the transparency and application of AI methods, with the potential to benefit patients in routine cardiovascular care. Following a clear research hypothesis, an AI-based workflow begins with data selection and pre-processing prior to analysis, with the type of data (structured, semi-structured, or unstructured) determining what type of pre-processing steps and machine-learning algorithms are required. Algorithmic and data validation should be performed to ensure the robustness of the chosen methodology, followed by an objective evaluation of performance. Seven case studies are provided to highlight the wide variety of data modalities and clinical questions that can benefit from modern AI techniques, with a focus on applying them to cardiovascular disease management. Despite the growing use of AI, further education for healthcare workers, researchers, and the public are needed to aid understanding of how AI works and to close the existing gap in knowledge. In addition, issues regarding data access, sharing, and security must be addressed to ensure full engagement by patients and the public. The application of AI within healthcare provides an opportunity for clinicians to deliver a more personalized approach to medical care by accounting for confounders, interactions, and the rising prevalence of multi-morbidity.",,pdf:https://academic.oup.com/eurheartj/advance-article-pdf/doi/10.1093/eurheartj/ehac758/48602276/ehac758.pdf; doi:https://doi.org/10.1093/eurheartj/ehac758; html:https://europepmc.org/articles/PMC9976986; pdf:https://europepmc.org/articles/PMC9976986?pdf=render
+38649271,https://doi.org/10.1136/thorax-2023-220856,Rheumatoid arthritis and idiopathic pulmonary fibrosis: a bidirectional Mendelian randomisation study.,"Leavy OC, Kawano-Dourado L, Stewart ID, Quint JK, Solomon JJ, Borie R, Crestani B, Wain LV, Jenkins G, Dieudé P, Minelli C.",,Thorax,2024,2024-05-20,Y,Interstitial fibrosis; idiopathic pulmonary fibrosis; Rheumatoid Lung Disease,,,"<h4>Background</h4>A usual interstitial pneumonia (UIP) pattern of lung injury is a key feature of idiopathic pulmonary fibrosis (IPF) and is also observed in up to 40% of individuals with rheumatoid arthritis (RA)-associated interstitial lung disease (RA-ILD). The RA-UIP phenotype could result from either a causal relationship of RA on UIP or vice versa, or from a simple co-occurrence of RA and IPF due to shared demographic, genetic or environmental risk factors.<h4>Methods</h4>We used two-sample bidirectional Mendelian randomisation (MR) to test the hypothesis of a causal effect of RA on UIP and of UIP on RA, using variants from genome-wide association studies (GWAS) of RA (separately for seropositive (18 019 cases and 991 604 controls) and seronegative (8515 cases and 1 015 471 controls) RA) and of IPF (4125 cases and 20 464 controls) as genetic instruments. Sensitivity analyses were conducted to assess the robustness of the results to violations of the MR assumptions.<h4>Findings</h4>IPF showed a significant causal effect on seropositive RA, with developing IPF increasing the risk of seropositive RA (OR=1.06, 95% CI: 1.04 to 1.08, p<0.001) which was robust under all models. For the MR in the other direction, seropositive RA showed a significant protective effect on IPF (OR=0.93; 95% CI: 0.87 to 0.99; p=0.032), but the effect was not significant when sensitivity analyses were applied. This was likely because of bias due to exclusion of patients with RA from among the cases in the IPF GWAS, or possibly because our genetic instruments did not fully capture the effect of the complex human leucocyte antigen region, the strongest RA genetic risk factor.<h4>Interpretation</h4>Our findings support the hypothesis that RA-UIP may be due to a cause-effect relationship between UIP and RA, rather than due to a coincidental occurrence of IPF in patients with RA. The significant causal effect of IPF on seropositive RA suggests that pathomechanisms involved in the development of UIP may promote RA, and this may help inform future guidelines on screening for ILD in patients with RA.",,pdf:https://thorax.bmj.com/content/thoraxjnl/early/2024/04/21/thorax-2023-220856.full.pdf; doi:https://doi.org/10.1136/thorax-2023-220856; html:https://europepmc.org/articles/PMC11137470; pdf:https://europepmc.org/articles/PMC11137470?pdf=render
 31088492,https://doi.org/10.1186/s12967-019-1912-5,-Omics biomarker identification pipeline for translational medicine.,"Bravo-Merodio L, Williams JA, Gkoutos GV, Acharjee A.",,Journal of translational medicine,2019,2019-05-14,Y,Biomarker; Feature Selection; Regularization; -omics; Translational Medicine,,,"<h4>Background</h4>Translational medicine (TM) is an emerging domain that aims to facilitate medical or biological advances efficiently from the scientist to the clinician. Central to the TM vision is to narrow the gap between basic science and applied science in terms of time, cost and early diagnosis of the disease state. Biomarker identification is one of the main challenges within TM. The identification of disease biomarkers from -omics data will not only help the stratification of diverse patient cohorts but will also provide early diagnostic information which could improve patient management and potentially prevent adverse outcomes. However, biomarker identification needs to be robust and reproducible. Hence a robust unbiased computational framework that can help clinicians identify those biomarkers is necessary.<h4>Methods</h4>We developed a pipeline (workflow) that includes two different supervised classification techniques based on regularization methods to identify biomarkers from -omics or other high dimension clinical datasets. The pipeline includes several important steps such as quality control and stability of selected biomarkers. The process takes input files (outcome and independent variables or -omics data) and pre-processes (normalization, missing values) them. After a random division of samples into training and test sets, Least Absolute Shrinkage and Selection Operator and Elastic Net feature selection methods are applied to identify the most important features representing potential biomarker candidates. The penalization parameters are optimised using 10-fold cross validation and the process undergoes 100 iterations and a combinatorial analysis to select the best performing multivariate model. An empirical unbiased assessment of their quality as biomarkers for clinical use is performed through a Receiver Operating Characteristic curve and its Area Under the Curve analysis on both permuted and real data for 1000 different randomized training and test sets. We validated this pipeline against previously published biomarkers.<h4>Results</h4>We applied this pipeline to three different datasets with previously published biomarkers: lipidomics data by Acharjee et al. (Metabolomics 13:25, 2017) and transcriptomics data by Rajamani and Bhasin (Genome Med 8:38, 2016) and Mills et al. (Blood 114:1063-1072, 2009). Our results demonstrate that our method was able to identify both previously published biomarkers as well as new variables that add value to the published results.<h4>Conclusions</h4>We developed a robust pipeline to identify clinically relevant biomarkers that can be applied to different -omics datasets. Such identification reveals potentially novel drug targets and can be used as a part of a machine-learning based patient stratification framework in the translational medicine settings.",,pdf:https://translational-medicine.biomedcentral.com/track/pdf/10.1186/s12967-019-1912-5; doi:https://doi.org/10.1186/s12967-019-1912-5; html:https://europepmc.org/articles/PMC6518609; pdf:https://europepmc.org/articles/PMC6518609?pdf=render
+34446426,https://doi.org/10.1136/bmj.n1931,Risk of thrombocytopenia and thromboembolism after covid-19 vaccination and SARS-CoV-2 positive testing: self-controlled case series study.,"Hippisley-Cox J, Patone M, Mei XW, Saatci D, Dixon S, Khunti K, Zaccardi F, Watkinson P, Shankar-Hari M, Doidge J, Harrison DA, Griffin SJ, Sheikh A, Coupland CAC.",,BMJ (Clinical research ed.),2021,2021-08-26,Y,,,,"<h4>Objective</h4>To assess the association between covid-19 vaccines and risk of thrombocytopenia and thromboembolic events in England among adults.<h4>Design</h4>Self-controlled case series study using national data on covid-19 vaccination and hospital admissions.<h4>Setting</h4>Patient level data were obtained for approximately 30 million people vaccinated in England between 1 December 2020 and 24 April 2021. Electronic health records were linked with death data from the Office for National Statistics, SARS-CoV-2 positive test data, and hospital admission data from the United Kingdom's health service (NHS).<h4>Participants</h4>29 121 633 people were vaccinated with first doses (19 608 008 with Oxford-AstraZeneca (ChAdOx1 nCoV-19) and 9 513 625 with Pfizer-BioNTech (BNT162b2 mRNA)) and 1 758 095 people had a positive SARS-CoV-2 test. People aged ≥16 years who had first doses of the ChAdOx1 nCoV-19 or BNT162b2 mRNA vaccines and any outcome of interest were included in the study.<h4>Main outcome measures</h4>The primary outcomes were hospital admission or death associated with thrombocytopenia, venous thromboembolism, and arterial thromboembolism within 28 days of three exposures: first dose of the ChAdOx1 nCoV-19 vaccine; first dose of the BNT162b2 mRNA vaccine; and a SARS-CoV-2 positive test. Secondary outcomes were subsets of the primary outcomes: cerebral venous sinus thrombosis (CVST), ischaemic stroke, myocardial infarction, and other rare arterial thrombotic events.<h4>Results</h4>The study found increased risk of thrombocytopenia after ChAdOx1 nCoV-19 vaccination (incidence rate ratio 1.33, 95% confidence interval 1.19 to 1.47 at 8-14 days) and after a positive SARS-CoV-2 test (5.27, 4.34 to 6.40 at 8-14 days); increased risk of venous thromboembolism after ChAdOx1 nCoV-19 vaccination (1.10, 1.02 to 1.18 at 8-14 days) and after SARS-CoV-2 infection (13.86, 12.76 to 15.05 at 8-14 days); and increased risk of arterial thromboembolism after BNT162b2 mRNA vaccination (1.06, 1.01 to 1.10 at 15-21 days) and after SARS-CoV-2 infection (2.02, 1.82 to 2.24 at 15-21 days). Secondary analyses found increased risk of CVST after ChAdOx1 nCoV-19 vaccination (4.01, 2.08 to 7.71 at 8-14 days), after BNT162b2 mRNA vaccination (3.58, 1.39 to 9.27 at 15-21 days), and after a positive SARS-CoV-2 test; increased risk of ischaemic stroke after BNT162b2 mRNA vaccination (1.12, 1.04 to 1.20 at 15-21 days) and after a positive SARS-CoV-2 test; and increased risk of other rare arterial thrombotic events after ChAdOx1 nCoV-19 vaccination (1.21, 1.02 to 1.43 at 8-14 days) and after a positive SARS-CoV-2 test.<h4>Conclusion</h4>Increased risks of haematological and vascular events that led to hospital admission or death were observed for short time intervals after first doses of the ChAdOx1 nCoV-19 and BNT162b2 mRNA vaccines. The risks of most of these events were substantially higher and more prolonged after SARS-CoV-2 infection than after vaccination in the same population.",,pdf:https://www.bmj.com/content/bmj/374/bmj.n1931.full.pdf; doi:https://doi.org/10.1136/bmj.n1931; html:https://europepmc.org/articles/PMC8388189; pdf:https://europepmc.org/articles/PMC8388189?pdf=render
 35698725,https://doi.org/10.1016/s2665-9913(22)00098-4,Risk of severe COVID-19 outcomes associated with immune-mediated inflammatory diseases and immune-modifying therapies: a nationwide cohort study in the OpenSAFELY platform.,"MacKenna B, Kennedy NA, Mehrkar A, Rowan A, Galloway J, Matthewman J, Mansfield KE, Bechman K, Yates M, Brown J, Schultze A, Norton S, Walker AJ, Morton CE, Harrison D, Bhaskaran K, Rentsch CT, Williamson E, Croker R, Bacon S, Hickman G, Ward T, Davy S, Green A, Fisher L, Hulme W, Bates C, Curtis HJ, Tazare J, Eggo RM, Evans D, Inglesby P, Cockburn J, McDonald HI, Tomlinson LA, Mathur R, Wong AYS, Forbes H, Parry J, Hester F, Harper S, Douglas IJ, Smeeth L, Lees CW, Evans SJW, Goldacre B, Smith CH, Langan SM.",,The Lancet. Rheumatology,2022,2022-06-09,Y,,,,"<h4>Background</h4>The risk of severe COVID-19 outcomes in people with immune-mediated inflammatory diseases and on immune-modifying drugs might not be fully mediated by comorbidities and might vary by factors such as ethnicity. We aimed to assess the risk of severe COVID-19 in adults with immune-mediated inflammatory diseases and in those on immune-modifying therapies.<h4>Methods</h4>We did a cohort study, using OpenSAFELY (an analytics platform for electronic health records) and TPP (a software provider for general practitioners), analysing routinely collected primary care data linked to hospital admission, death, and previously unavailable hospital prescription data. We included people aged 18 years or older on March 1, 2020, who were registered with TPP practices with at least 12 months of primary care records before March, 2020. We used Cox regression (adjusting for confounders and mediators) to estimate hazard ratios (HRs) comparing the risk of COVID-19-related death, critical care admission or death, and hospital admission (from March 1 to Sept 30, 2020) in people with immune-mediated inflammatory diseases compared with the general population, and in people with immune-mediated inflammatory diseases on targeted immune-modifying drugs (eg, biologics) compared with those on standard systemic treatment (eg, methotrexate).<h4>Findings</h4>We identified 17 672 065 adults; 1 163 438 adults (640 164 [55·0%] women and 523 274 [45·0%] men, and 827 457 [71·1%] of White ethnicity) had immune-mediated inflammatory diseases, and 16 508 627 people (8 215 020 [49·8%] women and 8 293 607 [50·2%] men, and 10 614 096 [64·3%] of White ethnicity) were included as the general population. Of 1 163 438 adults with immune-mediated inflammatory diseases, 19 119 (1·6%) received targeted immune-modifying therapy and 181 694 (15·6%) received standard systemic therapy. Compared with the general population, adults with immune-mediated inflammatory diseases had an increased risk of COVID-19-related death after adjusting for confounders (age, sex, deprivation, and smoking status; HR 1·23, 95% CI 1·20-1·27) and further adjusting for mediators (body-mass index [BMI], cardiovascular disease, diabetes, and current glucocorticoid use; 1·15, 1·11-1·18). Adults with immune-mediated inflammatory diseases also had an increased risk of COVID-19-related critical care admission or death (confounder-adjusted HR 1·24, 95% CI 1·21-1·28; mediator-adjusted 1·16, 1·12-1·19) and hospital admission (confounder-adjusted 1·32, 1·29-1·35; mediator-adjusted 1·20, 1·17-1·23). In post-hoc analyses, the risk of severe COVID-19 outcomes in people with immune-mediated inflammatory diseases was higher in non-White ethnic groups than in White ethnic groups (as it was in the general population). We saw no evidence of increased COVID-19-related death in adults on targeted, compared with those on standard systemic, therapy after adjusting for confounders (age, sex, deprivation, BMI, immune-mediated inflammatory diseases [bowel, joint, and skin], cardiovascular disease, cancer [excluding non-melanoma skin cancer], stroke, and diabetes (HR 1·03, 95% CI 0·80-1·33), and after additionally adjusting for current glucocorticoid use (1·01, 0·78-1·30). There was no evidence of increased COVID-19-related death in adults prescribed tumour necrosis factor inhibitors, interleukin (IL)-12/IL‑23 inhibitors, IL-17 inhibitors, IL-6 inhibitors, or Janus kinase inhibitors compared with those on standard systemic therapy. Rituximab was associated with increased COVID-19-related death (HR 1·68, 95% CI 1·11-2·56), with some attenuation after excluding people with haematological malignancies or organ transplants (1·<b>54, 0</b>·<b>95</b>-<b>2</b>·<b>49</b>).<h4>Interpretation</h4>COVID-19 deaths and hospital admissions were higher in people with immune-mediated inflammatory diseases. We saw no increased risk of adverse COVID-19 outcomes in those on most targeted immune-modifying drugs for immune-mediated inflammatory diseases compared with those on standard systemic therapy.<h4>Funding</h4>UK Medical Research Council, NIHR Biomedical Research Centre at King's College London and Guy's and St Thomas' NHS Foundation Trust, and Wellcome Trust.",,pdf:http://www.thelancet.com/article/S2665991322000984/pdf; doi:https://doi.org/10.1016/S2665-9913(22)00098-4; html:https://europepmc.org/articles/PMC9179144; pdf:https://europepmc.org/articles/PMC9179144?pdf=render
-33683514,https://doi.org/10.1007/s10237-021-01437-5,A framework for incorporating 3D hyperelastic vascular wall models in 1D blood flow simulations.,"Coccarelli A, Carson JM, Aggarwal A, Pant S.",,Biomechanics and modeling in mechanobiology,2021,2021-03-08,Y,Pulse wave velocity; Common carotid artery; Hyperelasticity; Tube Law; Axial Stretching; One-dimensional Blood Flow Modelling,,,"We present a novel framework for investigating the role of vascular structure on arterial haemodynamics in large vessels, with a special focus on the human common carotid artery (CCA). The analysis is carried out by adopting a three-dimensional (3D) derived, fibre-reinforced, hyperelastic structural model, which is coupled with an axisymmetric, reduced order model describing blood flow. The vessel transmural pressure and lumen area are related via a Holzapfel-Ogden type of law, and the residual stresses along the thickness and length of the vessel are also accounted for. After a structural characterization of the adopted hyperelastic model, we investigate the link underlying the vascular wall response and blood-flow dynamics by comparing the proposed framework results against a popular tube law. The comparison shows that the behaviour of the model can be captured by the simpler linear surrogate only if a representative value of compliance is applied. Sobol's multi-variable sensitivity analysis is then carried out in order to identify the extent to which the structural parameters have an impact on the CCA haemodynamics. In this case, the local pulse wave velocity (PWV) is used as index for representing the arterial transmission capacity of blood pressure waveforms. The sensitivity analysis suggests that some geometrical factors, such as the stress-free inner radius and opening angle, play a major role on the system's haemodynamics. Subsequently, we quantified the differences in haemodynamic variables obtained from different virtual CCAs, tube laws and flow conditions. Although each artery presents a distinct vascular response, the differences obtained across different flow regimes are not significant. As expected, the linear tube law is unable to accurately capture all the haemodynamic features characterizing the current model. The findings from the sensitivity analysis are further confirmed by investigating the axial stretching effect on the CCA fluid dynamics. This factor does not seem to alter the pressure and flow waveforms. On the contrary, it is shown that, for an axially stretched vessel, the vascular wall exhibits an attenuation in absolute distension and an increase in circumferential stress, corroborating the findings of previous studies. This analysis shows that the new model offers a good balance between computational complexity and physics captured, making it an ideal framework for studies aiming to investigate the profound link between vascular mechanobiology and blood flow.",,pdf:https://link.springer.com/content/pdf/10.1007/s10237-021-01437-5.pdf; doi:https://doi.org/10.1007/s10237-021-01437-5; html:https://europepmc.org/articles/PMC8298378; pdf:https://europepmc.org/articles/PMC8298378?pdf=render
 37120260,https://doi.org/10.1016/s2468-2667(23)00079-8,Changes in COVID-19-related mortality across key demographic and clinical subgroups in England from 2020 to 2022: a retrospective cohort study using the OpenSAFELY platform.,"Nab L, Parker EPK, Andrews CD, Hulme WJ, Fisher L, Morley J, Mehrkar A, MacKenna B, Inglesby P, Morton CE, Bacon SCJ, Hickman G, Evans D, Ward T, Smith RM, Davy S, Dillingham I, Maude S, Butler-Cole BFC, O'Dwyer T, Stables CL, Bridges L, Bates C, Cockburn J, Parry J, Hester F, Harper S, Zheng B, Williamson EJ, Eggo RM, Evans SJW, Goldacre B, Tomlinson LA, Walker AJ, OpenSAFELY Collaborative.",,The Lancet. Public health,2023,2023-05-01,Y,,,,"<h4>Background</h4>COVID-19 has been shown to differently affect various demographic and clinical population subgroups. We aimed to describe trends in absolute and relative COVID-19-related mortality risks across clinical and demographic population subgroups during successive SARS-CoV-2 pandemic waves.<h4>Methods</h4>We did a retrospective cohort study in England using the OpenSAFELY platform with the approval of National Health Service England, covering the first five SARS-CoV-2 pandemic waves (wave one [wild-type] from March 23 to May 30, 2020; wave two [alpha (B.1.1.7)] from Sept 7, 2020, to April 24, 2021; wave three [delta (B.1.617.2)] from May 28 to Dec 14, 2021; wave four [omicron (B.1.1.529)] from Dec 15, 2021, to April 29, 2022; and wave five [omicron] from June 24 to Aug 3, 2022). In each wave, we included people aged 18-110 years who were registered with a general practice on the first day of the wave and who had at least 3 months of continuous general practice registration up to this date. We estimated crude and sex-standardised and age-standardised wave-specific COVID-19-related death rates and relative risks of COVID-19-related death in population subgroups.<h4>Findings</h4>18 895 870 adults were included in wave one, 19 014 720 in wave two, 18 932 050 in wave three, 19 097 970 in wave four, and 19 226 475 in wave five. Crude COVID-19-related death rates per 1000 person-years decreased from 4·48 deaths (95% CI 4·41-4·55) in wave one to 2·69 (2·66-2·72) in wave two, 0·64 (0·63-0·66) in wave three, 1·01 (0·99-1·03) in wave four, and 0·67 (0·64-0·71) in wave five. In wave one, the standardised COVID-19-related death rates were highest in people aged 80 years or older, people with chronic kidney disease stage 5 or 4, people receiving dialysis, people with dementia or learning disability, and people who had received a kidney transplant (ranging from 19·85 deaths per 1000 person-years to 44·41 deaths per 1000 person-years, compared with from 0·05 deaths per 1000 person-years to 15·93 deaths per 1000 person-years in other subgroups). In wave two compared with wave one, in a largely unvaccinated population, the decrease in COVID-19-related mortality was evenly distributed across population subgroups. In wave three compared with wave one, larger decreases in COVID-19-related death rates were seen in groups prioritised for primary SARS-CoV-2 vaccination, including people aged 80 years or older and people with neurological disease, learning disability, or severe mental illness (90-91% decrease). Conversely, smaller decreases in COVID-19-related death rates were observed in younger age groups, people who had received organ transplants, and people with chronic kidney disease, haematological malignancies, or immunosuppressive conditions (0-25% decrease). In wave four compared with wave one, the decrease in COVID-19-related death rates was smaller in groups with lower vaccination coverage (including younger age groups) and conditions associated with impaired vaccine response, including people who had received organ transplants and people with immunosuppressive conditions (26-61% decrease).<h4>Interpretation</h4>There was a substantial decrease in absolute COVID-19-related death rates over time in the overall population, but demographic and clinical relative risk profiles persisted and worsened for people with lower vaccination coverage or impaired immune response. Our findings provide an evidence base to inform UK public health policy for protecting these vulnerable population subgroups.<h4>Funding</h4>UK Research and Innovation, Wellcome Trust, UK Medical Research Council, National Institute for Health and Care Research, and Health Data Research UK.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10139026; doi:https://doi.org/10.1016/S2468-2667(23)00079-8; html:https://europepmc.org/articles/PMC10139026; pdf:https://europepmc.org/articles/PMC10139026?pdf=render
+33683514,https://doi.org/10.1007/s10237-021-01437-5,A framework for incorporating 3D hyperelastic vascular wall models in 1D blood flow simulations.,"Coccarelli A, Carson JM, Aggarwal A, Pant S.",,Biomechanics and modeling in mechanobiology,2021,2021-03-08,Y,Pulse wave velocity; Common carotid artery; Hyperelasticity; Tube Law; Axial Stretching; One-dimensional Blood Flow Modelling,,,"We present a novel framework for investigating the role of vascular structure on arterial haemodynamics in large vessels, with a special focus on the human common carotid artery (CCA). The analysis is carried out by adopting a three-dimensional (3D) derived, fibre-reinforced, hyperelastic structural model, which is coupled with an axisymmetric, reduced order model describing blood flow. The vessel transmural pressure and lumen area are related via a Holzapfel-Ogden type of law, and the residual stresses along the thickness and length of the vessel are also accounted for. After a structural characterization of the adopted hyperelastic model, we investigate the link underlying the vascular wall response and blood-flow dynamics by comparing the proposed framework results against a popular tube law. The comparison shows that the behaviour of the model can be captured by the simpler linear surrogate only if a representative value of compliance is applied. Sobol's multi-variable sensitivity analysis is then carried out in order to identify the extent to which the structural parameters have an impact on the CCA haemodynamics. In this case, the local pulse wave velocity (PWV) is used as index for representing the arterial transmission capacity of blood pressure waveforms. The sensitivity analysis suggests that some geometrical factors, such as the stress-free inner radius and opening angle, play a major role on the system's haemodynamics. Subsequently, we quantified the differences in haemodynamic variables obtained from different virtual CCAs, tube laws and flow conditions. Although each artery presents a distinct vascular response, the differences obtained across different flow regimes are not significant. As expected, the linear tube law is unable to accurately capture all the haemodynamic features characterizing the current model. The findings from the sensitivity analysis are further confirmed by investigating the axial stretching effect on the CCA fluid dynamics. This factor does not seem to alter the pressure and flow waveforms. On the contrary, it is shown that, for an axially stretched vessel, the vascular wall exhibits an attenuation in absolute distension and an increase in circumferential stress, corroborating the findings of previous studies. This analysis shows that the new model offers a good balance between computational complexity and physics captured, making it an ideal framework for studies aiming to investigate the profound link between vascular mechanobiology and blood flow.",,pdf:https://link.springer.com/content/pdf/10.1007/s10237-021-01437-5.pdf; doi:https://doi.org/10.1007/s10237-021-01437-5; html:https://europepmc.org/articles/PMC8298378; pdf:https://europepmc.org/articles/PMC8298378?pdf=render
 32634370,https://doi.org/10.1098/rsob.200121,Core regulatory circuitries in defining cancer cell identity across the malignant spectrum.,"Jahangiri L, Tsaprouni L, Trigg RM, Williams JA, Gkoutos GV, Turner SD, Pereira J.",,Open biology,2020,2020-07-08,Y,Cell Identity; Super-enhancers; Core Regulatory Circuitry; Liquid And Solid Cancers,,,"Gene expression programmes driving cell identity are established by tightly regulated transcription factors that auto- and cross-regulate in a feed-forward manner, forming core regulatory circuitries (CRCs). CRC transcription factors create and engage super-enhancers by recruiting acetylation writers depositing permissive H3K27ac chromatin marks. These super-enhancers are largely associated with BET proteins, including BRD4, that influence higher-order chromatin structure. The orchestration of these events triggers accessibility of RNA polymerase machinery and the imposition of lineage-specific gene expression. In cancers, CRCs drive cell identity by superimposing developmental programmes on a background of genetic alterations. Further, the establishment and maintenance of oncogenic states are reliant on CRCs that drive factors involved in tumour development. Hence, the molecular dissection of CRC components driving cell identity and cancer state can contribute to elucidating mechanisms of diversion from pre-determined developmental programmes and highlight cancer dependencies. These insights can provide valuable opportunities for identifying and re-purposing drug targets. In this article, we review the current understanding of CRCs across solid and liquid malignancies and avenues of investigation for drug development efforts. We also review techniques used to understand CRCs and elaborate the indication of discussed CRC transcription factors in the wider context of cancer CRC models.",,pdf:https://royalsocietypublishing.org/doi/pdf/10.1098/rsob.200121; doi:https://doi.org/10.1098/rsob.200121; html:https://europepmc.org/articles/PMC7574545; pdf:https://europepmc.org/articles/PMC7574545?pdf=render
-34446426,https://doi.org/10.1136/bmj.n1931,Risk of thrombocytopenia and thromboembolism after covid-19 vaccination and SARS-CoV-2 positive testing: self-controlled case series study.,"Hippisley-Cox J, Patone M, Mei XW, Saatci D, Dixon S, Khunti K, Zaccardi F, Watkinson P, Shankar-Hari M, Doidge J, Harrison DA, Griffin SJ, Sheikh A, Coupland CAC.",,BMJ (Clinical research ed.),2021,2021-08-26,Y,,,,"<h4>Objective</h4>To assess the association between covid-19 vaccines and risk of thrombocytopenia and thromboembolic events in England among adults.<h4>Design</h4>Self-controlled case series study using national data on covid-19 vaccination and hospital admissions.<h4>Setting</h4>Patient level data were obtained for approximately 30 million people vaccinated in England between 1 December 2020 and 24 April 2021. Electronic health records were linked with death data from the Office for National Statistics, SARS-CoV-2 positive test data, and hospital admission data from the United Kingdom's health service (NHS).<h4>Participants</h4>29 121 633 people were vaccinated with first doses (19 608 008 with Oxford-AstraZeneca (ChAdOx1 nCoV-19) and 9 513 625 with Pfizer-BioNTech (BNT162b2 mRNA)) and 1 758 095 people had a positive SARS-CoV-2 test. People aged ≥16 years who had first doses of the ChAdOx1 nCoV-19 or BNT162b2 mRNA vaccines and any outcome of interest were included in the study.<h4>Main outcome measures</h4>The primary outcomes were hospital admission or death associated with thrombocytopenia, venous thromboembolism, and arterial thromboembolism within 28 days of three exposures: first dose of the ChAdOx1 nCoV-19 vaccine; first dose of the BNT162b2 mRNA vaccine; and a SARS-CoV-2 positive test. Secondary outcomes were subsets of the primary outcomes: cerebral venous sinus thrombosis (CVST), ischaemic stroke, myocardial infarction, and other rare arterial thrombotic events.<h4>Results</h4>The study found increased risk of thrombocytopenia after ChAdOx1 nCoV-19 vaccination (incidence rate ratio 1.33, 95% confidence interval 1.19 to 1.47 at 8-14 days) and after a positive SARS-CoV-2 test (5.27, 4.34 to 6.40 at 8-14 days); increased risk of venous thromboembolism after ChAdOx1 nCoV-19 vaccination (1.10, 1.02 to 1.18 at 8-14 days) and after SARS-CoV-2 infection (13.86, 12.76 to 15.05 at 8-14 days); and increased risk of arterial thromboembolism after BNT162b2 mRNA vaccination (1.06, 1.01 to 1.10 at 15-21 days) and after SARS-CoV-2 infection (2.02, 1.82 to 2.24 at 15-21 days). Secondary analyses found increased risk of CVST after ChAdOx1 nCoV-19 vaccination (4.01, 2.08 to 7.71 at 8-14 days), after BNT162b2 mRNA vaccination (3.58, 1.39 to 9.27 at 15-21 days), and after a positive SARS-CoV-2 test; increased risk of ischaemic stroke after BNT162b2 mRNA vaccination (1.12, 1.04 to 1.20 at 15-21 days) and after a positive SARS-CoV-2 test; and increased risk of other rare arterial thrombotic events after ChAdOx1 nCoV-19 vaccination (1.21, 1.02 to 1.43 at 8-14 days) and after a positive SARS-CoV-2 test.<h4>Conclusion</h4>Increased risks of haematological and vascular events that led to hospital admission or death were observed for short time intervals after first doses of the ChAdOx1 nCoV-19 and BNT162b2 mRNA vaccines. The risks of most of these events were substantially higher and more prolonged after SARS-CoV-2 infection than after vaccination in the same population.",,pdf:https://www.bmj.com/content/bmj/374/bmj.n1931.full.pdf; doi:https://doi.org/10.1136/bmj.n1931; html:https://europepmc.org/articles/PMC8388189; pdf:https://europepmc.org/articles/PMC8388189?pdf=render
+36583230,https://doi.org/10.1002/cam4.5556,Circulating gamma-glutamyl transpeptidase and risk of pancreatic cancer: A prospective cohort study in the UK Biobank.,"Liao W, Yang Y, Yang H, Qu Y, Song H, Li Q.",,Cancer medicine,2023,2022-12-29,Y,Prevention; Pancreatic cancer; Gamma-glutamyl Transpeptidase; European Ancestry,,,"<h4>Background</h4>To determine whether serum gamma-glutamyl transpeptidase (GGT) level is associated with pancreatic cancer risk in a large prospective cohort.<h4>Methods</h4>The study analyzed serum GGT concentration at baseline of 421,032 participants recruited in the UK Biobank since 2006 through 2010. Information on incidence of pancreatic cancer was obtained from cancer and death registers, updated until 2015 in Scotland or 2016 in England and Wales. Adjusted Cox proportional hazards models were used to measure the association between serum GGT and pancreatic cancer risk.<h4>Results</h4>The study identified 586 cases of pancreatic cancer over a median follow-up period of 7.16 years. In the multivariable-adjusted Cox model, serum GGT level was associated with 14% higher pancreatic cancer risk (hazard ratio (HR) per one standard deviation increment of log2 GGT level = 1.14, 95% confidence interval (CI) 1.02-1.28, p = 0.025). In the total population, the HR for the highest GGT group was 1.68 (95%CI: 1.22-2.30) versus the lowest GGT group. The HR for the highest GGT group in men (≥50.2 U/L) was 1.72 (95%CI: 1.14-2.61) and that in women (≥31.6 U/L) was 1.75 (95%CI: 1.06-2.88) versus the lowest GGT group.<h4>Conclusion</h4>Our findings suggested a positive association of serum GGT in pancreatic cancer etiology, implying the potential of monitoring GGT level for identifying at-risk individuals for pancreatic cancer.",,doi:https://doi.org/10.1002/cam4.5556; doi:https://doi.org/10.1002/cam4.5556; html:https://europepmc.org/articles/PMC10134379; pdf:https://europepmc.org/articles/PMC10134379?pdf=render
 34829865,https://doi.org/10.3390/biomedicines9111636,Machine Learning-Based Identification of Potentially Novel Non-Alcoholic Fatty Liver Disease Biomarkers.,"Shafiha R, Bahcivanci B, Gkoutos GV, Acharjee A.",,Biomedicines,2021,2021-11-07,Y,Biomarker; Machine Learning; Lipidomics; Transcriptomics; Nafld,,,"Non-alcoholic fatty liver disease (NAFLD) is a chronic liver disease that presents a great challenge for treatment and prevention.. This study aims to implement a machine learning approach that employs such datasets to identify potential biomarker targets. We developed a pipeline to identify potential biomarkers for NAFLD that includes five major processes, namely, a pre-processing step, a feature selection and a generation of a random forest model and, finally, a downstream feature analysis and a provision of a potential biological interpretation. The pre-processing step includes data normalising and variable extraction accompanied by appropriate annotations. A feature selection based on a differential gene expression analysis is then conducted to identify significant features and then employ them to generate a random forest model whose performance is assessed based on a receiver operating characteristic curve. Next, the features are subjected to a downstream analysis, such as univariate analysis, a pathway enrichment analysis, a network analysis and a generation of correlation plots, boxplots and heatmaps. Once the results are obtained, the biological interpretation and the literature validation is conducted over the identified features and results. We applied this pipeline to transcriptomics and lipidomic datasets and concluded that the C4BPA gene could play a role in the development of NAFLD. The activation of the complement pathway, due to the downregulation of the C4BPA gene, leads to an increase in triglyceride content, which might further render the lipid metabolism. This approach identified the C4BPA gene, an inhibitor of the complement pathway, as a potential biomarker for the development of NAFLD.",,pdf:https://www.mdpi.com/2227-9059/9/11/1636/pdf?version=1637024773; doi:https://doi.org/10.3390/biomedicines9111636; html:https://europepmc.org/articles/PMC8615894; pdf:https://europepmc.org/articles/PMC8615894?pdf=render
+35511729,https://doi.org/10.1093/ageing/afac084,"COVID-19 risk factors amongst 14,786 care home residents: an observational longitudinal analysis including daily community positive test rates of COVID-19, hospital stays and vaccination status in Wales (UK) between 1 September 2020 and 1 May 2021.","Hollinghurst J, Hollinghurst R, North L, Mizen A, Akbari A, Long S, Lyons RA, Fry R.",,Age and ageing,2022,2022-05-01,Y,Vaccination; Hospital infection; Older People; Care Homes; Covid-19; Pcr Tests,,,"<h4>Background</h4>COVID-19 vaccinations have been prioritised for high risk individuals.<h4>Aim</h4>Determine individual-level risk factors for care home residents testing positive for SARS-CoV-2.<h4>Study design</h4>Longitudinal observational cohort study using individual-level linked data from the Secure Anonymised Information Linkage (SAIL) databank.<h4>Setting</h4>Fourteen thousand seven hundred and eighty-six older care home residents (aged 65+) living in Wales between 1 September 2020 and 1 May 2021. Our dataset consisted of 2,613,341 individual-level daily observations within 697 care homes.<h4>Methods</h4>We estimated odds ratios (ORs [95% confidence interval]) using multilevel logistic regression models. Our outcome of interest was a positive SARS-CoV-2 PCR test. We included time-dependent covariates for the estimated community positive test rate of COVID-19, hospital inpatient status, vaccination status and frailty. Additional covariates were included for age, sex and specialist care home services.<h4>Results</h4>The multivariable regression model indicated an increase in age (OR 1.01 [1.00,1.01] per year), community positive test rate (OR 1.13 [1.12,1.13] per percent increase), hospital inpatients (OR 7.40 [6.54,8.36]), and residents in care homes with non-specialist dementia care (OR 1.42 [1.01,1.99]) had an increased odds of a positive test. Having a positive test prior to the observation period (OR 0.58 [0.49,0.68]) and either one or two doses of a vaccine (0.21 [0.17,0.25] and 0.05 [0.02,0.09], respectively) were associated with a decreased odds.<h4>Conclusions</h4>Care providers need to remain vigilant despite the vaccination rollout, and extra precautions should be taken when caring for the most vulnerable. Minimising potential COVID-19 infection for care home residents when admitted to hospital should be prioritised.",,pdf:https://academic.oup.com/ageing/article-pdf/51/5/afac084/43520659/afac084.pdf; doi:https://doi.org/10.1093/ageing/afac084; html:https://europepmc.org/articles/PMC9070807; pdf:https://europepmc.org/articles/PMC9070807?pdf=render
 33114263,https://doi.org/10.3390/ijms21217886,Biomarker Prioritisation and Power Estimation Using Ensemble Gene Regulatory Network Inference.,"Aziz F, Acharjee A, Williams JA, Russ D, Bravo-Merodio L, Gkoutos GV.",,International journal of molecular sciences,2020,2020-10-23,Y,Experimental design; Gene Regulatory Network; Causal Modelling; Omics Integration,,,"Inferring the topology of a gene regulatory network (GRN) from gene expression data is a challenging but important undertaking for gaining a better understanding of gene regulation. Key challenges include working with noisy data and dealing with a higher number of genes than samples. Although a number of different methods have been proposed to infer the structure of a GRN, there are large discrepancies among the different inference algorithms they adopt, rendering their meaningful comparison challenging. In this study, we used two methods, namely the MIDER (Mutual Information Distance and Entropy Reduction) and the PLSNET (Partial least square based feature selection) methods, to infer the structure of a GRN directly from data and computationally validated our results. Both methods were applied to different gene expression datasets resulting from inflammatory bowel disease (IBD), pancreatic ductal adenocarcinoma (PDAC), and acute myeloid leukaemia (AML) studies. For each case, gene regulators were successfully identified. For example, for the case of the IBD dataset, the <i>UGT1A</i> family genes were identified as key regulators while upon analysing the PDAC dataset, the <i>SULF1</i> and <i>THBS2</i> genes were depicted. We further demonstrate that an ensemble-based approach, that combines the output of the MIDER and PLSNET algorithms, can infer the structure of a GRN from data with higher accuracy. We have also estimated the number of the samples required for potential future validation studies. Here, we presented our proposed analysis framework that caters not only to candidate regulator genes prediction for potential validation experiments but also an estimation of the number of samples required for these experiments.",,pdf:https://www.mdpi.com/1422-0067/21/21/7886/pdf?version=1604329387; doi:https://doi.org/10.3390/ijms21217886; html:https://europepmc.org/articles/PMC7660606; pdf:https://europepmc.org/articles/PMC7660606?pdf=render
-36583230,https://doi.org/10.1002/cam4.5556,Circulating gamma-glutamyl transpeptidase and risk of pancreatic cancer: A prospective cohort study in the UK Biobank.,"Liao W, Yang Y, Yang H, Qu Y, Song H, Li Q.",,Cancer medicine,2023,2022-12-29,Y,Prevention; Pancreatic cancer; Gamma-glutamyl Transpeptidase; European Ancestry,,,"<h4>Background</h4>To determine whether serum gamma-glutamyl transpeptidase (GGT) level is associated with pancreatic cancer risk in a large prospective cohort.<h4>Methods</h4>The study analyzed serum GGT concentration at baseline of 421,032 participants recruited in the UK Biobank since 2006 through 2010. Information on incidence of pancreatic cancer was obtained from cancer and death registers, updated until 2015 in Scotland or 2016 in England and Wales. Adjusted Cox proportional hazards models were used to measure the association between serum GGT and pancreatic cancer risk.<h4>Results</h4>The study identified 586 cases of pancreatic cancer over a median follow-up period of 7.16 years. In the multivariable-adjusted Cox model, serum GGT level was associated with 14% higher pancreatic cancer risk (hazard ratio (HR) per one standard deviation increment of log2 GGT level = 1.14, 95% confidence interval (CI) 1.02-1.28, p = 0.025). In the total population, the HR for the highest GGT group was 1.68 (95%CI: 1.22-2.30) versus the lowest GGT group. The HR for the highest GGT group in men (≥50.2 U/L) was 1.72 (95%CI: 1.14-2.61) and that in women (≥31.6 U/L) was 1.75 (95%CI: 1.06-2.88) versus the lowest GGT group.<h4>Conclusion</h4>Our findings suggested a positive association of serum GGT in pancreatic cancer etiology, implying the potential of monitoring GGT level for identifying at-risk individuals for pancreatic cancer.",,doi:https://doi.org/10.1002/cam4.5556; doi:https://doi.org/10.1002/cam4.5556; html:https://europepmc.org/articles/PMC10134379; pdf:https://europepmc.org/articles/PMC10134379?pdf=render
 36750952,https://doi.org/10.1186/s12911-023-02109-3,A multi-granular stacked regression for forecasting long-term demand in Emergency Departments.,"James C, Wood R, Denholm R.",,BMC medical informatics and decision making,2023,2023-02-07,Y,Forecasting; Emergency Department; Machine Learning; Population Health; Service Demand,,,"<h4>Background</h4>In the United Kingdom, Emergency Departments (EDs) are under significant pressure due to an ever-increasing number of attendances. Understanding how the capacity of other urgent care services and the health of a population may influence ED attendances is imperative for commissioners and policy makers to develop long-term strategies for reducing this pressure and improving quality and safety.<h4>Methods</h4>We developed a novel multi-granular stacked regression (MGSR) model using publicly available data to predict future mean monthly ED attendances within Clinical Commissioning Group regions in England. The MGSR combines measures of population health and health service capacity in other related settings. We assessed model performance using the R-squared statistic, measuring variance explained, and the Mean Absolute Percentage Error (MAPE), measuring forecasting accuracy. We used the MGSR to forecast ED demand over a 4-year period under hypothetical scenarios where service capacity is increased, or population health is improved.<h4>Results</h4>Measures of service capacity explain 41 ± 4% of the variance in monthly ED attendances and measures of population health explain 62 ± 22%. The MGSR leads to an overall improvement in performance, with an R-squared of 0.79 ± 0.02 and MAPE of 3% when forecasting mean monthly ED attendances per CCG. Using the MGSR to forecast long-term demand under different scenarios, we found improving population health would reduce peak ED attendances per CCG by approximately 1000 per month after 2 years.<h4>Conclusion</h4>Combining models of population health and wider urgent care service capacity for predicting monthly ED attendances leads to an improved performance compared to each model individually. Policies designed to improve population health will reduce ED attendances and enhance quality and safety in the long-term.",,pdf:https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-023-02109-3; doi:https://doi.org/10.1186/s12911-023-02109-3; html:https://europepmc.org/articles/PMC9903450; pdf:https://europepmc.org/articles/PMC9903450?pdf=render
-35511729,https://doi.org/10.1093/ageing/afac084,"COVID-19 risk factors amongst 14,786 care home residents: an observational longitudinal analysis including daily community positive test rates of COVID-19, hospital stays and vaccination status in Wales (UK) between 1 September 2020 and 1 May 2021.","Hollinghurst J, Hollinghurst R, North L, Mizen A, Akbari A, Long S, Lyons RA, Fry R.",,Age and ageing,2022,2022-05-01,Y,Vaccination; Hospital infection; Older People; Care Homes; Covid-19; Pcr Tests,,,"<h4>Background</h4>COVID-19 vaccinations have been prioritised for high risk individuals.<h4>Aim</h4>Determine individual-level risk factors for care home residents testing positive for SARS-CoV-2.<h4>Study design</h4>Longitudinal observational cohort study using individual-level linked data from the Secure Anonymised Information Linkage (SAIL) databank.<h4>Setting</h4>Fourteen thousand seven hundred and eighty-six older care home residents (aged 65+) living in Wales between 1 September 2020 and 1 May 2021. Our dataset consisted of 2,613,341 individual-level daily observations within 697 care homes.<h4>Methods</h4>We estimated odds ratios (ORs [95% confidence interval]) using multilevel logistic regression models. Our outcome of interest was a positive SARS-CoV-2 PCR test. We included time-dependent covariates for the estimated community positive test rate of COVID-19, hospital inpatient status, vaccination status and frailty. Additional covariates were included for age, sex and specialist care home services.<h4>Results</h4>The multivariable regression model indicated an increase in age (OR 1.01 [1.00,1.01] per year), community positive test rate (OR 1.13 [1.12,1.13] per percent increase), hospital inpatients (OR 7.40 [6.54,8.36]), and residents in care homes with non-specialist dementia care (OR 1.42 [1.01,1.99]) had an increased odds of a positive test. Having a positive test prior to the observation period (OR 0.58 [0.49,0.68]) and either one or two doses of a vaccine (0.21 [0.17,0.25] and 0.05 [0.02,0.09], respectively) were associated with a decreased odds.<h4>Conclusions</h4>Care providers need to remain vigilant despite the vaccination rollout, and extra precautions should be taken when caring for the most vulnerable. Minimising potential COVID-19 infection for care home residents when admitted to hospital should be prioritised.",,pdf:https://academic.oup.com/ageing/article-pdf/51/5/afac084/43520659/afac084.pdf; doi:https://doi.org/10.1093/ageing/afac084; html:https://europepmc.org/articles/PMC9070807; pdf:https://europepmc.org/articles/PMC9070807?pdf=render
 37586846,https://doi.org/10.1136/openhrt-2023-002378,Cardiovascular imaging research priorities.,"MacArthur JAL, Yong GL, Dweck MR, Fairbairn TA, Weir-McCall J, Puyol-Antón E, Meldrum J, Blakelock P, Khan S, Morrice L, Sudlow CLM, Williams MC.",,Open heart,2023,2023-08-01,Y,Health Services; Research Design; Diagnostic Imaging,,,"<h4>Objectives</h4>Two interlinked surveys were organised by the British Heart Foundation Data Science Centre, which aimed to establish national priorities for cardiovascular imaging research.<h4>Methods</h4>First a single time point public survey explored their views of cardiovascular imaging research. Subsequently, a three-phase modified Delphi prioritisation exercise was performed by researchers and healthcare professionals. Research questions were submitted by a diverse range of stakeholders to the question 'What are the most important research questions that cardiovascular imaging should be used to address?'. Of these, 100 research questions were prioritised based on their positive impact for patients. The 32 highest rated questions were further prioritised based on three domains: positive impact for patients, potential to reduce inequalities in healthcare and ability to be implemented into UK healthcare practice in a timely manner.<h4>Results</h4>The public survey was completed by 354 individuals, with the highest rated areas relating to improving treatment, quality of life and diagnosis. In the second survey, 506 research questions were submitted by diverse stakeholders. Prioritisation was performed by 90 researchers or healthcare professionals in the first round and 64 in the second round. The highest rated questions were 'How do we ensure patients have equal access to cardiovascular imaging when it is needed?' and 'How can we use cardiovascular imaging to avoid invasive procedures'. There was general agreement between healthcare professionals and researchers regarding priorities for the positive impact for patients and least agreement for their ability to be implemented into UK healthcare practice in a timely manner. There was broad overlap between the prioritised research questions and the results of the public survey.<h4>Conclusions</h4>We have identified priorities for cardiovascular imaging research, incorporating the views of diverse stakeholders. These priorities will be useful for researchers, funders and other organisations planning future research.",,pdf:https://openheart.bmj.com/content/openhrt/10/2/e002378.full.pdf; doi:https://doi.org/10.1136/openhrt-2023-002378; html:https://europepmc.org/articles/PMC10432634; pdf:https://europepmc.org/articles/PMC10432634?pdf=render
 35973468,https://doi.org/10.1016/j.jviromet.2022.114607,Evaluation of the impact of pre-analytical conditions on sample stability for the detection of SARS-CoV-2 RNA.,"Mosscrop L, Watber P, Elliot P, Cooke G, Barclay W, Freemont PS, Rosadas C, Taylor GP.",,Journal of virological methods,2022,2022-08-13,Y,RNA; Diagnosis; Rt-qpcr; Sample Stability; Sars-cov-2,,,"Demand for accurate SARS-CoV-2 diagnostics is high. Most samples in the UK are collected in the community and rely on the postal service for delivery to the laboratories. The current recommendation remains that swabs should be collected in Viral Transport Media (VTM) and transported with a cold chain to the laboratory for RNA extraction and RT-qPCR. This is not always possible. We aimed to test the stability of SARS-CoV-2 RNA subjected to different pre-analytical conditions. Swabs were dipped into PBS containing cultured SARS-CoV-2 and placed in either a dry tube or a tube containing either normal saline or VTM. The tubes were then stored at different temperatures (20-50 °C) for variable periods (8 h to 5 days). Samples were tested by RT-qPCR targeting SARS-CoV-2 E gene. VTM outperformed swabs in saline and dry swabs in all conditions. Samples in VTM were stable, independent of a cold chain, for 5 days, with a maximum increase in cycle threshold (Ct) of 1.34 when held at 40 °C. Using normal saline as the transport media resulted in a loss of sensitivity (increased Ct) over time and with increasing temperature (up to 7.8 cycles compared to VTM). SARS-CoV-2 was not detected in 3/9 samples in normal saline when tested after 120 h incubation. Transportation of samples in VTM provides a high level of confidence in the results despite the potential for considerable, uncontrolled variation in temperature and longer transportation periods. False negative results may be seen after 96 h in saline and viral loads will appear lower.",,doi:https://doi.org/10.1016/j.jviromet.2022.114607; doi:https://doi.org/10.1016/j.jviromet.2022.114607; html:https://europepmc.org/articles/PMC9374597; pdf:https://europepmc.org/articles/PMC9374597?pdf=render
 39324394,https://doi.org/10.1017/s0033291724001922,Characteristics associated with progression to probable dementia with Lewy bodies in a cohort with very late-onset psychosis.,"Gibson LL, Mueller C, Stewart R, Aarsland D.",,Psychological medicine,2024,2024-09-26,Y,Dementia; Dementia With Lewy Bodies; Very Late-onset Psychosis,,,"<h4>Background</h4>Very late-onset psychosis (VLOP) is associated with higher rates of dementia but the proportion who develop dementia with Lewy bodies (DLB) is unknown. We aimed to identify individuals with VLOP who develop dementia and DLB and characterize the risk factors for progression.<h4>Methods</h4>Anonymized data were retrieved from electronic records for individuals with VLOP. Patients developing dementia after psychosis were identified, in addition to those with <u>></u>2 core features of DLB at the time of dementia or DLB identified by a natural language processing application (NLP-DLB). Demographic factors, Health of the National Outcome Scale (HoNOS) and symptoms at index psychosis were explored as predictors of progression to dementia.<h4>Results</h4>In 1425 patients with VLOP over 4.29 years (mean) follow up, 197 (13.8%) received a subsequent diagnosis of dementia. Of these, 24.4% (<i>n</i> = 48) had <u>></u>2 core features of DLB and 6% (<i>n</i> = 12) had NLP-DLB. In cox proportional hazard models, older age and cognitive impairment at the time of psychosis were associated with increased risk of incident dementia. Visual hallucinations and 2+ core features of DLB at index psychosis were associated with increased risk of dementia with 2+ symptoms of DLB but not all-cause dementia. Two or more core features of DLB at index psychosis were associated with 81% specificity and 67% sensitivity for incident NLP-DLB.<h4>Conclusions</h4>In patients with VLOP who develop dementia, core features of DLB are common. Visual hallucinations or two core features of DLB in VLOP should prompt clinicians to consider DLB and support further investigation.",,doi:https://doi.org/10.1017/S0033291724001922; html:https://europepmc.org/articles/PMC11496220; pdf:https://europepmc.org/articles/PMC11496220?pdf=render
 36810667,https://doi.org/10.1210/clinem/dgad103,Morbidity Associated With Primary Hyperparathyroidism-A Population-based Study With a Subanalysis on Vitamin D.,"Soto-Pedre E, Lin YY, Soto-Hernaez J, Newey PJ, Leese GP.",,The Journal of clinical endocrinology and metabolism,2023,2023-08-01,Y,Calcium; Vitamin D; Mortality; Primary Hyperparathyroidism,,,"<h4>Context</h4>Primary hyperparathyroidism (PHPT) is associated with increased risk of morbidity and death, and vitamin D levels are a potentially confounding variable.<h4>Objective</h4>The aim of this study was to assess morbidity and mortality associated with primary hyperparathyroidism (PHPT).<h4>Methods</h4>In this population-based retrospective matched cohort study, data linkage of biochemistry, hospital admissions, prescribing, imaging, pathology, and deaths was used to identify patients across the region of Tayside, Scotland, who had PHPT from 1997 to 2019. Cox proportional hazards models and hazards ratios (HR) were used to explore the relationship between exposure to PHPT and several clinical outcomes. Comparisons were made with an age- and gender-matched cohort.<h4>Results</h4>In 11 616 people with PHPT (66.8% female), with a mean follow-up period of 8.8 years, there was an adjusted HR of death of 2.05 (95% CI, 1.97-2.13) for those exposed to PHPT. There was also an increased risk of cardiovascular disease (HR = 1.34; 95% CI, 1.24-1.45), cerebrovascular disease (HR = 1.29; 95% CI, 1.15-1.45), diabetes (HR = 1.39; 95% CI, 1.26-1.54), renal stones (HR = 3.02; 95% CI, 2.19-4.17) and osteoporosis (HR = 1.31; 95% CI, 1.16-1.49). Following adjustment for serum vitamin D concentrations (n = 2748), increased risks for death, diabetes, renal stones, and osteoporosis persisted, but not for cardiovascular or cerebrovascular disease.<h4>Conclusion</h4>In a large population-based study, PHPT was associated with death, diabetes, renal stones, and osteoporosis, independent of serum vitamin D concentration.",,pdf:https://academic.oup.com/jcem/advance-article-pdf/doi/10.1210/clinem/dgad103/49516503/dgad103.pdf; doi:https://doi.org/10.1210/clinem/dgad103; html:https://europepmc.org/articles/PMC10438903
 35290489,https://doi.org/10.1007/s00247-021-05266-7,Dynamic susceptibility-contrast magnetic resonance imaging with contrast agent leakage correction aids in predicting grade in pediatric brain tumours: a multicenter study.,"Withey SB, MacPherson L, Oates A, Powell S, Novak J, Abernethy L, Pizer B, Grundy R, Morgan PS, Bailey S, Mitra D, Arvanitis TN, Auer DP, Avula S, Peet AC.",,Pediatric radiology,2022,2022-03-15,Y,Brain; Tumor; Children; Perfusion; Magnetic Resonance Imaging; Blood volume; Multicenter; Leakage Correction; Dynamic Susceptibility-contrast Magnetic Resonance Imaging,,,"<h4>Background</h4>Relative cerebral blood volume (rCBV) measured using dynamic susceptibility-contrast MRI can differentiate between low- and high-grade pediatric brain tumors. Multicenter studies are required for translation into clinical practice.<h4>Objective</h4>We compared leakage-corrected dynamic susceptibility-contrast MRI perfusion parameters acquired at multiple centers in low- and high-grade pediatric brain tumors.<h4>Materials and methods</h4>Eighty-five pediatric patients underwent pre-treatment dynamic susceptibility-contrast MRI scans at four centers. MRI protocols were variable. We analyzed data using the Boxerman leakage-correction method producing pixel-by-pixel estimates of leakage-uncorrected (rCBV<sub>uncorr</sub>) and corrected (rCBV<sub>corr</sub>) relative cerebral blood volume, and the leakage parameter, K<sub>2</sub>. Histological diagnoses were obtained. Tumors were classified by high-grade tumor. We compared whole-tumor median perfusion parameters between low- and high-grade tumors and across tumor types.<h4>Results</h4>Forty tumors were classified as low grade, 45 as high grade. Mean whole-tumor median rCBV<sub>uncorr</sub> was higher in high-grade tumors than low-grade tumors (mean ± standard deviation [SD] = 2.37±2.61 vs. -0.14±5.55; P<0.01). Average median rCBV increased following leakage correction (2.54±1.63 vs. 1.68±1.36; P=0.010), remaining higher in high-grade tumors than low grade-tumors. Low-grade tumors, particularly pilocytic astrocytomas, showed T1-dominant leakage effects; high-grade tumors showed T2*-dominance (mean K<sub>2</sub>=0.017±0.049 vs. 0.002±0.017). Parameters varied with tumor type but not center. Median rCBV<sub>uncorr</sub> was higher (mean = 1.49 vs. 0.49; P=0.015) and K<sub>2</sub> lower (mean = 0.005 vs. 0.016; P=0.013) in children who received a pre-bolus of contrast agent compared to those who did not. Leakage correction removed the difference.<h4>Conclusion</h4>Dynamic susceptibility-contrast MRI acquired at multiple centers helped distinguish between children's brain tumors. Relative cerebral blood volume was significantly higher in high-grade compared to low-grade tumors and differed among common tumor types. Vessel leakage correction is required to provide accurate rCBV, particularly in low-grade enhancing tumors.",,pdf:https://link.springer.com/content/pdf/10.1007/s00247-021-05266-7.pdf; doi:https://doi.org/10.1007/s00247-021-05266-7; html:https://europepmc.org/articles/PMC9107460; pdf:https://europepmc.org/articles/PMC9107460?pdf=render
+35913410,https://doi.org/10.1093/cid/ciac629,Validity of Self-testing at Home With Rapid Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Detection by Lateral Flow Immunoassay.,"Atchison CJ, Moshe M, Brown JC, Whitaker M, Wong NCK, Bharath AA, McKendry RA, Darzi A, Ashby D, Donnelly CA, Riley S, Elliott P, Barclay WS, Cooke GS, Ward H.",,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2023,2023-02-01,Y,Antibodies; Lateral Flow Immunoassay; Home-testing; Covid-19; Sars-cov-2,,,"<h4>Background</h4>We explore severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody lateral flow immunoassay (LFIA) performance under field conditions compared to laboratory-based electrochemiluminescence immunoassay (ECLIA) and live virus neutralization.<h4>Methods</h4>In July 2021, 3758 participants performed, at home, a self-administered Fortress LFIA on finger-prick blood, reported and submitted a photograph of the result, and provided a self-collected capillary blood sample for assessment of immunoglobulin G (IgG) antibodies using the Roche Elecsys® Anti-SARS-CoV-2 ECLIA. We compared the self-reported LFIA result to the quantitative ECLIA and checked the reading of the LFIA result with an automated image analysis (ALFA). In a subsample of 250 participants, we compared the results to live virus neutralization.<h4>Results</h4>Almost all participants (3593/3758, 95.6%) had been vaccinated or reported prior infection. Overall, 2777/3758 (73.9%) were positive on self-reported LFIA, 2811/3457 (81.3%) positive by LFIA when ALFA-reported, and 3622/3758 (96.4%) positive on ECLIA (using the manufacturer reference standard threshold for positivity of 0.8 U mL-1). Live virus neutralization was detected in 169 of 250 randomly selected samples (67.6%); 133/169 were positive with self-reported LFIA (sensitivity 78.7%; 95% confidence interval [CI]: 71.8, 84.6), 142/155 (91.6%; 95% CI: 86.1, 95.5) with ALFA, and 169 (100%; 95% CI: 97.8, 100.0) with ECLIA. There were 81 samples with no detectable virus neutralization; 47/81 were negative with self-reported LFIA (specificity 58.0%; 95% CI: 46.5, 68.9), 34/75 (45.3%; 95% CI: 33.8, 57.3) with ALFA, and 0/81 (0%; 95% CI: 0, 4.5) with ECLIA.<h4>Conclusions</h4>Self-administered LFIA is less sensitive than a quantitative antibody test, but the positivity in LFIA correlates better than the quantitative ECLIA with virus neutralization.",,doi:https://doi.org/10.1093/cid/ciac629; doi:https://doi.org/10.1093/cid/ciac629; html:https://europepmc.org/articles/PMC9384551; pdf:https://europepmc.org/articles/PMC9384551?pdf=render
 31799783,https://doi.org/10.1002/cnm.3267,Personalising cardiovascular network models in pregnancy: A two-tiered parameter estimation approach.,"Carson J, Warrander L, Johnstone E, van Loon R.",,International journal for numerical methods in biomedical engineering,2021,2020-01-13,Y,Pregnancy; Parameter estimation; Pre-eclampsia; Personalised Haemodynamic Model; Uterine Artery Waveform,,,"Uterine artery Doppler waveforms are often studied to determine whether a patient is at risk of developing pathologies such as pre-eclampsia. Many uterine waveform indices have been developed, which attempt to relate characteristics of the waveform with the physiological adaptation of the maternal cardiovascular system, and are often suggested to be an indicator of increased placenta resistance and arterial stiffness. Doppler waveforms of four patients, two of whom developed pre-eclampsia, are compared with a comprehensive closed-loop model of pregnancy. The closed-loop model has been previously validated but has been extended to include an improved parameter estimation technique that utilises systolic and diastolic blood pressure, cardiac output, heart rate, and pulse wave velocity measurements to adapt model resistances, compliances, blood volume, and the mean vessel areas in the main systemic arteries. The shape of the model-predicted uterine artery velocity waveforms showed good agreement with the characteristics observed in the patient Doppler waveforms. The personalised models obtained now allow a prediction of the uterine pressure waveforms in addition to the uterine velocity. This allows for a more detailed mechanistic analysis of the waveforms, eg, wave intensity analysis, to study existing clinical indices. The findings indicate that to accurately estimate arterial stiffness, both pulse pressure and pulse wave velocities are required. In addition, the results predict that patients who developed pre-eclampsia later in pregnancy have larger vessel areas in the main systemic arteries compared with the two patients who had normal pregnancy outcomes.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cnm.3267; doi:https://doi.org/10.1002/cnm.3267; html:https://europepmc.org/articles/PMC9286682; pdf:https://europepmc.org/articles/PMC9286682?pdf=render
 35473737,https://doi.org/10.1136/bmjopen-2021-060413,"Therapies for Long COVID in non-hospitalised individuals: from symptoms, patient-reported outcomes and immunology to targeted therapies (The TLC Study).","Haroon S, Nirantharakumar K, Hughes SE, Subramanian A, Aiyegbusi OL, Davies EH, Myles P, Williams T, Turner G, Chandan JS, McMullan C, Lord J, Wraith DC, McGee K, Denniston AK, Taverner T, Jackson LJ, Sapey E, Gkoutos G, Gokhale K, Leggett E, Iles C, Frost C, McNamara G, Bamford A, Marshall T, Zemedikun DT, Price G, Marwaha S, Simms-Williams N, Brown K, Walker A, Jones K, Matthews K, Camaradou J, Saint-Cricq M, Kumar S, Alder Y, Stanton DE, Agyen L, Baber M, Blaize H, Calvert M.",,BMJ open,2022,2022-04-26,Y,Therapeutics; immunology; Public Health; Covid-19,,,"<h4>Introduction</h4>Individuals with COVID-19 frequently experience symptoms and impaired quality of life beyond 4-12 weeks, commonly referred to as Long COVID. Whether Long COVID is one or several distinct syndromes is unknown. Establishing the evidence base for appropriate therapies is needed. We aim to evaluate the symptom burden and underlying pathophysiology of Long COVID syndromes in non-hospitalised individuals and evaluate potential therapies.<h4>Methods and analysis</h4>A cohort of 4000 non-hospitalised individuals with a past COVID-19 diagnosis and 1000 matched controls will be selected from anonymised primary care records from the Clinical Practice Research Datalink, and invited by their general practitioners to participate on a digital platform (Atom5). Individuals will report symptoms, quality of life, work capability and patient-reported outcome measures. Data will be collected monthly for 1 year.Statistical clustering methods will be used to identify distinct Long COVID-19 symptom clusters. Individuals from the four most prevalent clusters and two control groups will be invited to participate in the BioWear substudy which will further phenotype Long COVID symptom clusters by measurement of immunological parameters and actigraphy.We will review existing evidence on interventions for postviral syndromes and Long COVID to map and prioritise interventions for each newly characterised Long COVID syndrome. Recommendations will be made using the cumulative evidence in an expert consensus workshop. A virtual supportive intervention will be coproduced with patients and health service providers for future evaluation.Individuals with lived experience of Long COVID will be involved throughout this programme through a patient and public involvement group.<h4>Ethics and dissemination</h4>Ethical approval was obtained from the Solihull Research Ethics Committee, West Midlands (21/WM/0203). Research findings will be presented at international conferences, in peer-reviewed journals, to Long COVID patient support groups and to policymakers.<h4>Trial registration number</h4>1567490.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/4/e060413.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-060413; html:https://europepmc.org/articles/PMC9044550; pdf:https://europepmc.org/articles/PMC9044550?pdf=render
-35913410,https://doi.org/10.1093/cid/ciac629,Validity of Self-testing at Home With Rapid Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Detection by Lateral Flow Immunoassay.,"Atchison CJ, Moshe M, Brown JC, Whitaker M, Wong NCK, Bharath AA, McKendry RA, Darzi A, Ashby D, Donnelly CA, Riley S, Elliott P, Barclay WS, Cooke GS, Ward H.",,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2023,2023-02-01,Y,Antibodies; Lateral Flow Immunoassay; Home-testing; Covid-19; Sars-cov-2,,,"<h4>Background</h4>We explore severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody lateral flow immunoassay (LFIA) performance under field conditions compared to laboratory-based electrochemiluminescence immunoassay (ECLIA) and live virus neutralization.<h4>Methods</h4>In July 2021, 3758 participants performed, at home, a self-administered Fortress LFIA on finger-prick blood, reported and submitted a photograph of the result, and provided a self-collected capillary blood sample for assessment of immunoglobulin G (IgG) antibodies using the Roche Elecsys® Anti-SARS-CoV-2 ECLIA. We compared the self-reported LFIA result to the quantitative ECLIA and checked the reading of the LFIA result with an automated image analysis (ALFA). In a subsample of 250 participants, we compared the results to live virus neutralization.<h4>Results</h4>Almost all participants (3593/3758, 95.6%) had been vaccinated or reported prior infection. Overall, 2777/3758 (73.9%) were positive on self-reported LFIA, 2811/3457 (81.3%) positive by LFIA when ALFA-reported, and 3622/3758 (96.4%) positive on ECLIA (using the manufacturer reference standard threshold for positivity of 0.8 U mL-1). Live virus neutralization was detected in 169 of 250 randomly selected samples (67.6%); 133/169 were positive with self-reported LFIA (sensitivity 78.7%; 95% confidence interval [CI]: 71.8, 84.6), 142/155 (91.6%; 95% CI: 86.1, 95.5) with ALFA, and 169 (100%; 95% CI: 97.8, 100.0) with ECLIA. There were 81 samples with no detectable virus neutralization; 47/81 were negative with self-reported LFIA (specificity 58.0%; 95% CI: 46.5, 68.9), 34/75 (45.3%; 95% CI: 33.8, 57.3) with ALFA, and 0/81 (0%; 95% CI: 0, 4.5) with ECLIA.<h4>Conclusions</h4>Self-administered LFIA is less sensitive than a quantitative antibody test, but the positivity in LFIA correlates better than the quantitative ECLIA with virus neutralization.",,doi:https://doi.org/10.1093/cid/ciac629; doi:https://doi.org/10.1093/cid/ciac629; html:https://europepmc.org/articles/PMC9384551; pdf:https://europepmc.org/articles/PMC9384551?pdf=render
 35197114,https://doi.org/10.1186/s41512-022-00120-2,Comparison of methods for predicting COVID-19-related death in the general population using the OpenSAFELY platform.,"OpenSAFELY Collaborative, Williamson EJ, Tazare J, Bhaskaran K, McDonald HI, Walker AJ, Tomlinson L, Wing K, Bacon S, Bates C, Curtis HJ, Forbes HJ, Minassian C, Morton CE, Nightingale E, Mehrkar A, Evans D, Nicholson BD, Leon DA, Inglesby P, MacKenna B, Davies NG, DeVito NJ, Drysdale H, Cockburn J, Hulme WJ, Morley J, Douglas I, Rentsch CT, Mathur R, Wong A, Schultze A, Croker R, Parry J, Hester F, Harper S, Grieve R, Harrison DA, Steyerberg EW, Eggo RM, Diaz-Ordaz K, Keogh R, Evans SJW, Smeeth L, Goldacre B.",,Diagnostic and prognostic research,2022,2022-02-24,Y,Mortality; Infectious disease; Risk stratification; Statistical methodology; Risk Prediction; Covid-19,,,"<h4>Background</h4>Obtaining accurate estimates of the risk of COVID-19-related death in the general population is challenging in the context of changing levels of circulating infection.<h4>Methods</h4>We propose a modelling approach to predict 28-day COVID-19-related death which explicitly accounts for COVID-19 infection prevalence using a series of sub-studies from new landmark times incorporating time-updating proxy measures of COVID-19 infection prevalence. This was compared with an approach ignoring infection prevalence. The target population was adults registered at a general practice in England in March 2020. The outcome was 28-day COVID-19-related death. Predictors included demographic characteristics and comorbidities. Three proxies of local infection prevalence were used: model-based estimates, rate of COVID-19-related attendances in emergency care, and rate of suspected COVID-19 cases in primary care. We used data within the TPP SystmOne electronic health record system linked to Office for National Statistics mortality data, using the OpenSAFELY platform, working on behalf of NHS England. Prediction models were developed in case-cohort samples with a 100-day follow-up. Validation was undertaken in 28-day cohorts from the target population. We considered predictive performance (discrimination and calibration) in geographical and temporal subsets of data not used in developing the risk prediction models. Simple models were contrasted to models including a full range of predictors.<h4>Results</h4>Prediction models were developed on 11,972,947 individuals, of whom 7999 experienced COVID-19-related death. All models discriminated well between individuals who did and did not experience the outcome, including simple models adjusting only for basic demographics and number of comorbidities: C-statistics 0.92-0.94. However, absolute risk estimates were substantially miscalibrated when infection prevalence was not explicitly modelled.<h4>Conclusions</h4>Our proposed models allow absolute risk estimation in the context of changing infection prevalence but predictive performance is sensitive to the proxy for infection prevalence. Simple models can provide excellent discrimination and may simplify implementation of risk prediction tools.",,pdf:https://diagnprognres.biomedcentral.com/track/pdf/10.1186/s41512-022-00120-2; doi:https://doi.org/10.1186/s41512-022-00120-2; html:https://europepmc.org/articles/PMC8865947; pdf:https://europepmc.org/articles/PMC8865947?pdf=render
 36174228,https://doi.org/10.1093/ije/dyac189,Cohort Profile: Longitudinal population-based study of COVID-19 in UK adults (COVIDENCE UK).,"Holt H, Relton C, Talaei M, Symons J, Davies MR, Jolliffe DA, Vivaldi G, Tydeman F, Williamson AE, Pfeffer PE, Orton C, Ford DV, Davies GA, Lyons RA, Griffiths CJ, Kee F, Sheikh A, Breen G, Shaheen SO, Martineau AR.",,International journal of epidemiology,2023,2023-02-01,N,,,,,,pdf:https://academic.oup.com/ije/article-pdf/52/1/e46/49127271/dyac189.pdf; doi:https://doi.org/10.1093/ije/dyac189; html:https://europepmc.org/articles/PMC9620716; pdf:https://europepmc.org/articles/PMC9620716?pdf=render; doi:https://doi.org/10.1093/ije/dyac189
-36051279,https://doi.org/10.3389/fcvm.2022.894503,Predicting post-contrast information from contrast agent free cardiac MRI using machine learning: Challenges and methods.,"Abdulkareem M, Kenawy AA, Rauseo E, Lee AM, Sojoudi A, Amir-Khalili A, Lekadir K, Young AA, Barnes MR, Barckow P, Khanji MY, Aung N, Petersen SE.",,Frontiers in cardiovascular medicine,2022,2022-07-27,Y,contrast; Decision tree; Machine Learning; Cmr; support vector machines; Deep Learning; Contrast-free,,,"<h4>Objectives</h4>Currently, administering contrast agents is necessary for accurately visualizing and quantifying presence, location, and extent of myocardial infarction (MI) with cardiac magnetic resonance (CMR). In this study, our objective is to investigate and analyze pre- and post-contrast CMR images with the goal of predicting post-contrast information using pre-contrast information only. We propose methods and identify challenges.<h4>Methods</h4>The study population consists of 272 retrospectively selected CMR studies with diagnoses of MI (<i>n</i> = 108) and healthy controls (<i>n</i> = 164). We describe a pipeline for pre-processing this dataset for analysis. After data feature engineering, 722 cine short-axis (SAX) images and segmentation mask pairs were used for experimentation. This constitutes 506, 108, and 108 pairs for the training, validation, and testing sets, respectively. We use deep learning (DL) segmentation (UNet) and classification (ResNet50) models to discover the extent and location of the scar and classify between the ischemic cases and healthy cases (i.e., cases with no regional myocardial scar) from the pre-contrast cine SAX image frames, respectively. We then capture complex data patterns that represent subtle signal and functional changes in the cine SAX images due to MI using optical flow, rate of change of myocardial area, and radiomics data. We apply this dataset to explore two supervised learning methods, namely, the support vector machines (SVM) and the decision tree (DT) methods, to develop predictive models for classifying pre-contrast cine SAX images as being a case of MI or healthy.<h4>Results</h4>Overall, for the UNet segmentation model, the performance based on the mean Dice score for the test set (<i>n</i> = 108) is 0.75 (±0.20) for the endocardium, 0.51 (±0.21) for the epicardium and 0.20 (±0.17) for the scar. For the classification task, the accuracy, F1 and precision scores of 0.68, 0.69, and 0.64, respectively, were achieved with the SVM model, and of 0.62, 0.63, and 0.72, respectively, with the DT model.<h4>Conclusion</h4>We have presented some promising approaches involving DL, SVM, and DT methods in an attempt to accurately predict contrast information from non-contrast images. While our initial results are modest for this challenging task, this area of research still poses several open problems.",,pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2022.894503/pdf; doi:https://doi.org/10.3389/fcvm.2022.894503; html:https://europepmc.org/articles/PMC9426684; pdf:https://europepmc.org/articles/PMC9426684?pdf=render
 35502909,https://doi.org/10.1177/01410768221095239,Impact on emergency and elective hospital-based care in Scotland over the first 12 months of the pandemic: interrupted time-series analysis of national lockdowns.,"Shah SA, Mulholland RH, Wilkinson S, Katikireddi SV, Pan J, Shi T, Kerr S, Agrawal U, Rudan I, Simpson CR, Stock SJ, Macleod J, Murray JL, McCowan C, Ritchie L, Woolhouse M, Sheikh A.",,Journal of the Royal Society of Medicine,2022,2022-05-03,Y,Public Health; Statistics And Research Methods; Population Trends,,,"<h4>Objectives</h4>COVID-19 has resulted in the greatest disruption to National Health Service (NHS) care in its over 70-year history. Building on our previous work, we assessed the ongoing impact of pandemic-related disruption on provision of emergency and elective hospital-based care across Scotland over the first year of the pandemic.<h4>Design</h4>We undertook interrupted time-series analyses to evaluate the impact of ongoing pandemic-related disruption on hospital NHS care provision at national level and across demographics and clinical specialties spanning the period 29 March 2020-28 March 2021.<h4>Setting</h4>Scotland, UK.<h4>Participants</h4>Patients receiving hospital care from NHS Scotland.<h4>Main outcome measures</h4>We used the percentage change of accident and emergency attendances, and emergency and planned hospital admissions during the pandemic compared to the average admission rate for equivalent weeks in 2018-2019.<h4>Results</h4>As restrictions were gradually lifted in Scotland after the first lockdown, hospital-based admissions increased approaching pre-pandemic levels. Subsequent tightening of restrictions in September 2020 were associated with a change in slope of relative weekly admissions rate: -1.98% (-2.38, -1.58) in accident and emergency attendance, -1.36% (-1.68, -1.04) in emergency admissions and -2.31% (-2.95, -1.66) in planned admissions. A similar pattern was seen across sex, socioeconomic status and most age groups, except children (0-14 years) where accident and emergency attendance, and emergency admissions were persistently low over the study period.<h4>Conclusions</h4>We found substantial disruption to urgent and planned inpatient healthcare provision in hospitals across NHS Scotland. There is the need for urgent policy responses to address continuing unmet health needs and to ensure resilience in the context of future pandemics.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/01410768221095239; doi:https://doi.org/10.1177/01410768221095239; html:https://europepmc.org/articles/PMC9723811; pdf:https://europepmc.org/articles/PMC9723811?pdf=render
+36051279,https://doi.org/10.3389/fcvm.2022.894503,Predicting post-contrast information from contrast agent free cardiac MRI using machine learning: Challenges and methods.,"Abdulkareem M, Kenawy AA, Rauseo E, Lee AM, Sojoudi A, Amir-Khalili A, Lekadir K, Young AA, Barnes MR, Barckow P, Khanji MY, Aung N, Petersen SE.",,Frontiers in cardiovascular medicine,2022,2022-07-27,Y,contrast; Decision tree; Machine Learning; Cmr; support vector machines; Deep Learning; Contrast-free,,,"<h4>Objectives</h4>Currently, administering contrast agents is necessary for accurately visualizing and quantifying presence, location, and extent of myocardial infarction (MI) with cardiac magnetic resonance (CMR). In this study, our objective is to investigate and analyze pre- and post-contrast CMR images with the goal of predicting post-contrast information using pre-contrast information only. We propose methods and identify challenges.<h4>Methods</h4>The study population consists of 272 retrospectively selected CMR studies with diagnoses of MI (<i>n</i> = 108) and healthy controls (<i>n</i> = 164). We describe a pipeline for pre-processing this dataset for analysis. After data feature engineering, 722 cine short-axis (SAX) images and segmentation mask pairs were used for experimentation. This constitutes 506, 108, and 108 pairs for the training, validation, and testing sets, respectively. We use deep learning (DL) segmentation (UNet) and classification (ResNet50) models to discover the extent and location of the scar and classify between the ischemic cases and healthy cases (i.e., cases with no regional myocardial scar) from the pre-contrast cine SAX image frames, respectively. We then capture complex data patterns that represent subtle signal and functional changes in the cine SAX images due to MI using optical flow, rate of change of myocardial area, and radiomics data. We apply this dataset to explore two supervised learning methods, namely, the support vector machines (SVM) and the decision tree (DT) methods, to develop predictive models for classifying pre-contrast cine SAX images as being a case of MI or healthy.<h4>Results</h4>Overall, for the UNet segmentation model, the performance based on the mean Dice score for the test set (<i>n</i> = 108) is 0.75 (±0.20) for the endocardium, 0.51 (±0.21) for the epicardium and 0.20 (±0.17) for the scar. For the classification task, the accuracy, F1 and precision scores of 0.68, 0.69, and 0.64, respectively, were achieved with the SVM model, and of 0.62, 0.63, and 0.72, respectively, with the DT model.<h4>Conclusion</h4>We have presented some promising approaches involving DL, SVM, and DT methods in an attempt to accurately predict contrast information from non-contrast images. While our initial results are modest for this challenging task, this area of research still poses several open problems.",,pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2022.894503/pdf; doi:https://doi.org/10.3389/fcvm.2022.894503; html:https://europepmc.org/articles/PMC9426684; pdf:https://europepmc.org/articles/PMC9426684?pdf=render
+37198478,https://doi.org/10.1038/s41586-023-06034-3,GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19.,"Pairo-Castineira E, Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, Oosthuyzen W, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Morrice K, Keating S, Maslove D, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Begg C, Walsh T, Tenesa A, Flores C, Riancho JA, Rojas-Martinez A, Lapunzina P, GenOMICC Investigators, SCOURGE Consortium, ISARICC Investigators, 23andMe COVID-19 Team, Yang J, Ponting CP, Wilson JF, Vitart V, Abedalthagafi M, Luchessi AD, Parra EJ, Cruz R, Carracedo A, Fawkes A, Murphy L, Rowan K, Pereira AC, Law A, Fairfax B, Hendry SC, Baillie JK.",,Nature,2023,2023-05-17,Y,,,,"Critical illness in COVID-19 is an extreme and clinically homogeneous disease phenotype that we have previously shown<sup>1</sup> to be highly efficient for discovery of genetic associations<sup>2</sup>. Despite the advanced stage of illness at presentation, we have shown that host genetics in patients who are critically ill with COVID-19 can identify immunomodulatory therapies with strong beneficial effects in this group<sup>3</sup>. Here we analyse 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously. To investigate the therapeutic implications of these findings, we infer the structural consequences of protein-coding variants, and combine our GWAS results with gene expression data using a monocyte transcriptome-wide association study (TWAS) model, as well as gene and protein expression using Mendelian randomization. We identify potentially druggable targets in multiple systems, including inflammatory signalling (JAK1), monocyte-macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).",,pdf:https://www.nature.com/articles/s41586-023-06034-3.pdf; doi:https://doi.org/10.1038/s41586-023-06034-3; html:https://europepmc.org/articles/PMC10208981; pdf:https://europepmc.org/articles/PMC10208981?pdf=render
 38554132,https://doi.org/10.1093/database/baae008,Visualization and exploration of linked data using virtual reality.,"Kellmann AJ, Postema M, de Keijser J, Svetachov P, Wilson RC, van Enckevort EJ, Swertz MA.",,Database : the journal of biological databases and curation,2024,2024-02-01,Y,,,,"In this report, we analyse the use of virtual reality (VR) as a method to navigate and explore complex knowledge graphs. Over the past few decades, linked data technologies [Resource Description Framework (RDF) and Web Ontology Language (OWL)] have shown to be valuable to encode such graphs and many tools have emerged to interactively visualize RDF. However, as knowledge graphs get larger, most of these tools struggle with the limitations of 2D screens or 3D projections. Therefore, in this paper, we evaluate the use of VR to visually explore SPARQL Protocol and RDF Query Language (SPARQL) (construct) queries, including a series of tutorial videos that demonstrate the power of VR (see Graph2VR tutorial playlist: https://www.youtube.com/playlist?list=PLRQCsKSUyhNIdUzBNRTmE-_JmuiOEZbdH). We first review existing methods for Linked Data visualization and then report the creation of a prototype, Graph2VR. Finally, we report a first evaluation of the use of VR for exploring linked data graphs. Our results show that most participants enjoyed testing Graph2VR and found it to be a useful tool for graph exploration and data discovery. The usability study also provides valuable insights for potential future improvements to Linked Data visualization in VR.",,doi:https://doi.org/10.1093/database/baae008; html:https://europepmc.org/articles/PMC11184448; pdf:https://europepmc.org/articles/PMC11184448?pdf=render
 37669576,https://doi.org/10.1016/j.schres.2023.08.024,Unraveling ethnic disparities in antipsychotic prescribing among patients with psychosis: A retrospective cohort study based on electronic clinical records.,"Wang T, Codling D, Bhugra D, Msosa Y, Broadbent M, Patel R, Roberts A, McGuire P, Stewart R, Dobson R, Harland R.",,Schizophrenia research,2023,2023-09-03,Y,Psychopharmacology; Psychosis; Ethnicity; Electronic Health Records; Healthcare Inequality; Antipsychotic Prescription,,,"<h4>Background</h4>Previous studies have shown mixed evidence on ethnic disparities in antipsychotic prescribing among patients with psychosis in the UK, partly due to small sample sizes. This study aimed to examine the current state of antipsychotic prescription with respect to patient ethnicity among the entire population known to a large UK mental health trust with non-affective psychosis, adjusting for multiple potential risk factors.<h4>Methods</h4>This retrospective cohort study included all patients (N = 19,291) who were aged 18 years or over at their first diagnoses of non-affective psychosis (identified with the ICD-10 codes of F20-F29) recorded in electronic health records (EHRs) at the South London and Maudsley NHS Trust until March 2021. The most recently recorded antipsychotic treatments and patient attributes were extracted from EHRs, including both structured fields and free-text fields processed using natural language processing applications. Multivariable logistic regression models were used to calculate the odds ratios (OR) for antipsychotic prescription according to patient ethnicity, adjusted for multiple potential contributing factors, including demographic (age and gender), clinical (diagnoses, duration of illness, service use and history of cannabis use), socioeconomic factors (level of deprivation and own-group ethnic density in the area of residence) and temporal changes in clinical guidelines (date of prescription).<h4>Results</h4>The cohort consisted of 43.10 % White, 8.31 % Asian, 40.80 % Black, 2.64 % Mixed, and 5.14 % of patients from Other ethnicity. Among them, 92.62 % had recorded antipsychotic receipt, where 24.05 % for depot antipsychotics and 81.72 % for second-generation antipsychotic (SGA) medications. Most ethnic minority groups were not significantly different from White patients in receiving any antipsychotic. Among those receiving antipsychotic prescribing, Black patients were more likely to be prescribed depot (adjusted OR 1.29, 95 % confidence interval (CI) 1.14-1.47), but less likely to receive SGA (adjusted OR 0.85, 95 % CI 0.74-0.97), olanzapine (OR 0.82, 95 % CI 0.73-0.92) and clozapine (adjusted OR 0.71, 95 % CI 0.6-0.85) than White patients. All the ethnic minority groups were less likely to be prescribed olanzapine than the White group.<h4>Conclusions</h4>Black patients with psychosis had a distinct pattern in antipsychotic prescription, with less use of SGA, including olanzapine and clozapine, but more use of depot antipsychotics, even when adjusting for the effects of multiple demographic, clinical and socioeconomic factors. Further research is required to understand the sources of these ethnic disparities and eliminate care inequalities.",,doi:https://doi.org/10.1016/j.schres.2023.08.024; html:https://europepmc.org/articles/PMC10881407
 35354646,https://doi.org/10.1136/thoraxjnl-2021-218629,Relationship between asthma and severe COVID-19: a national cohort study.,"Dolby T, Nafilyan V, Morgan A, Kallis C, Sheikh A, Quint JK.",,Thorax,2023,2022-03-30,Y,Asthma; Covid-19,,,"<h4>Background</h4>We aimed to determine whether children and adults with poorly controlled or more severe asthma have greater risk of hospitalisation and/or death from COVID-19.<h4>Methods</h4>We used individual-level data from the Office for National Statistics Public Health Data Asset, based on the 2011 census in England, and the General Practice Extraction Service data for pandemic planning and research linked to death registration records and Hospital Episode Statistics admission data. Adults were followed from 1 January 2020 to 30 September 2021 for hospitalisation or death from COVID-19. For children, only hospitalisation was included.<h4>Results</h4>Our cohort comprised 35 202 533 adults and 2 996 503 children aged 12-17 years. After controlling for sociodemographic factors, pre-existing health conditions and vaccine status, the risk of death involving COVID-19 for adults with asthma prescribed low dose inhaled corticosteroids (ICS) was not significantly different from those without asthma. Adults with asthma prescribed medium and high dosage ICS had an elevated risk of COVID-19 death; HRs 1.18 (95% CI 1.14 to 1.23) and 1.36 (95% CI 1.28 to 1.44), respectively. A similar pattern was observed for COVID-19 hospitalisation; fully adjusted HRs 1.53 (95% CI 1.50 to 1.56) and 1.52 (95% CI 1.46 to 1.56) for adults with asthma prescribed medium and high-dosage ICS, respectively. Risk of hospitalisation was greater for children with asthma prescribed one (2.58 (95% CI 1.82 to 3.66)) or two or more (3.80 (95% CI 2.41 to 5.95)) courses of oral corticosteroids in the year prior to the pandemic.<h4>Discussion</h4>People with mild and/or well-controlled asthma are neither at significantly increased risk of hospitalisation with nor more likely to die from COVID-19 than adults without asthma.",,pdf:https://thorax.bmj.com/content/thoraxjnl/early/2022/03/29/thoraxjnl-2021-218629.full.pdf; doi:https://doi.org/10.1136/thoraxjnl-2021-218629; html:https://europepmc.org/articles/PMC8983409; pdf:https://europepmc.org/articles/PMC8983409?pdf=render
 35296643,https://doi.org/10.1038/s41467-022-28517-z,"Antibody decay, T cell immunity and breakthrough infections following two SARS-CoV-2 vaccine doses in inflammatory bowel disease patients treated with infliximab and vedolizumab.","Lin S, Kennedy NA, Saifuddin A, Sandoval DM, Reynolds CJ, Seoane RC, Kottoor SH, Pieper FP, Lin KM, Butler DK, Chanchlani N, Nice R, Chee D, Bewshea C, Janjua M, McDonald TJ, Sebastian S, Alexander JL, Constable L, Lee JC, Murray CD, Hart AL, Irving PM, Jones GR, Kok KB, Lamb CA, Lees CW, Altmann DM, Boyton RJ, Goodhand JR, Powell N, Ahmad T, CLARITY IBD study.",,Nature communications,2022,2022-03-16,Y,,,,"Anti tumour necrosis factor (anti-TNF) drugs increase the risk of serious respiratory infection and impair protective immunity following pneumococcal and influenza vaccination. Here we report SARS-CoV-2 vaccine-induced immune responses and breakthrough infections in patients with inflammatory bowel disease, who are treated either with the anti-TNF antibody, infliximab, or with vedolizumab targeting a gut-specific anti-integrin that does not impair systemic immunity. Geometric mean [SD] anti-S RBD antibody concentrations are lower and half-lives shorter in patients treated with infliximab than vedolizumab, following two doses of BNT162b2 (566.7 U/mL [6.2] vs 4555.3 U/mL [5.4], p <0.0001; 26.8 days [95% CI 26.2 - 27.5] vs 47.6 days [45.5 - 49.8], p <0.0001); similar results are also observed with ChAdOx1 nCoV-19 vaccination (184.7 U/mL [5.0] vs 784.0 U/mL [3.5], p <0.0001; 35.9 days [34.9 - 36.8] vs 58.0 days [55.0 - 61.3], p value < 0.0001). One fifth of patients fail to mount a T cell response in both treatment groups. Breakthrough SARS-CoV-2 infections are more frequent (5.8% (201/3441) vs 3.9% (66/1682), p = 0.0039) in patients treated with infliximab than vedolizumab, and the risk of breakthrough SARS-CoV-2 infection is predicted by peak anti-S RBD antibody concentration after two vaccine doses. Irrespective of the treatments, higher, more sustained antibody levels are observed in patients with a history of SARS-CoV-2 infection prior to vaccination. Our results thus suggest that adapted vaccination schedules may be required to induce immunity in at-risk, anti-TNF-treated patients.",,pdf:https://www.nature.com/articles/s41467-022-28517-z.pdf; doi:https://doi.org/10.1038/s41467-022-28517-z; html:https://europepmc.org/articles/PMC8927425; pdf:https://europepmc.org/articles/PMC8927425?pdf=render
 34445233,https://doi.org/10.3390/ijms22168527,The Contribution of Autophagy and LncRNAs to MYC-Driven Gene Regulatory Networks in Cancers.,"Jahangiri L, Pucci P, Ishola T, Trigg RM, Williams JA, Pereira J, Cavanagh ML, Turner SD, Gkoutos GV, Tsaprouni L.",,International journal of molecular sciences,2021,2021-08-08,Y,MYC; Autophagy; Lncrnas; Gene Regulatory Networks (Grns),,,"MYC is a target of the Wnt signalling pathway and governs numerous cellular and developmental programmes hijacked in cancers. The amplification of MYC is a frequently occurring genetic alteration in cancer genomes, and this transcription factor is implicated in metabolic reprogramming, cell death, and angiogenesis in cancers. In this review, we analyse MYC gene networks in solid cancers. We investigate the interaction of MYC with long non-coding RNAs (lncRNAs). Furthermore, we investigate the role of MYC regulatory networks in inducing changes to cellular processes, including autophagy and mitophagy. Finally, we review the interaction and mutual regulation between MYC and lncRNAs, and autophagic processes and analyse these networks as unexplored areas of targeting and manipulation for therapeutic gain in MYC-driven malignancies.",,pdf:https://www.mdpi.com/1422-0067/22/16/8527/pdf?version=1628431894; doi:https://doi.org/10.3390/ijms22168527; html:https://europepmc.org/articles/PMC8395220; pdf:https://europepmc.org/articles/PMC8395220?pdf=render
-37198478,https://doi.org/10.1038/s41586-023-06034-3,GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19.,"Pairo-Castineira E, Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, Oosthuyzen W, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Morrice K, Keating S, Maslove D, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Begg C, Walsh T, Tenesa A, Flores C, Riancho JA, Rojas-Martinez A, Lapunzina P, GenOMICC Investigators, SCOURGE Consortium, ISARICC Investigators, 23andMe COVID-19 Team, Yang J, Ponting CP, Wilson JF, Vitart V, Abedalthagafi M, Luchessi AD, Parra EJ, Cruz R, Carracedo A, Fawkes A, Murphy L, Rowan K, Pereira AC, Law A, Fairfax B, Hendry SC, Baillie JK.",,Nature,2023,2023-05-17,Y,,,,"Critical illness in COVID-19 is an extreme and clinically homogeneous disease phenotype that we have previously shown<sup>1</sup> to be highly efficient for discovery of genetic associations<sup>2</sup>. Despite the advanced stage of illness at presentation, we have shown that host genetics in patients who are critically ill with COVID-19 can identify immunomodulatory therapies with strong beneficial effects in this group<sup>3</sup>. Here we analyse 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously. To investigate the therapeutic implications of these findings, we infer the structural consequences of protein-coding variants, and combine our GWAS results with gene expression data using a monocyte transcriptome-wide association study (TWAS) model, as well as gene and protein expression using Mendelian randomization. We identify potentially druggable targets in multiple systems, including inflammatory signalling (JAK1), monocyte-macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).",,pdf:https://www.nature.com/articles/s41586-023-06034-3.pdf; doi:https://doi.org/10.1038/s41586-023-06034-3; html:https://europepmc.org/articles/PMC10208981; pdf:https://europepmc.org/articles/PMC10208981?pdf=render
 35165107,https://doi.org/10.1136/bmjopen-2021-050062,"Investigating the uptake, effectiveness and safety of COVID-19 vaccines: protocol for an observational study using linked UK national data.","Vasileiou E, Shi T, Kerr S, Robertson C, Joy M, Tsang R, McGagh D, Williams J, Hobbs R, de Lusignan S, de Lusignan S, Bradley D, OReilly D, Murphy S, Chuter A, Beggs J, Ford D, Orton C, Akbari A, Bedston S, Davies G, Griffiths LJ, Griffiths R, Lowthian E, Lyons J, Lyons RA, North L, Perry M, Torabi F, Pickett J, McMenamin J, McCowan C, Agrawal U, Wood R, Stock SJ, Moore E, Henery P, Simpson CR, Sheikh A.",,BMJ open,2022,2022-02-14,Y,epidemiology; Public Health; Respiratory Infections; Covid-19,,,"<h4>Introduction</h4>The novel coronavirus SARS-CoV-2, which emerged in December 2019, has caused millions of deaths and severe illness worldwide. Numerous vaccines are currently under development of which a few have now been authorised for population-level administration by several countries. As of 20 September 2021, over 48 million people have received their first vaccine dose and over 44 million people have received their second vaccine dose across the UK. We aim to assess the uptake rates, effectiveness, and safety of all currently approved COVID-19 vaccines in the UK.<h4>Methods and analysis</h4>We will use prospective cohort study designs to assess vaccine uptake, effectiveness and safety against clinical outcomes and deaths. Test-negative case-control study design will be used to assess vaccine effectiveness (VE) against laboratory confirmed SARS-CoV-2 infection. Self-controlled case series and retrospective cohort study designs will be carried out to assess vaccine safety against mild-to-moderate and severe adverse events, respectively. Individual-level pseudonymised data from primary care, secondary care, laboratory test and death records will be linked and analysed in secure research environments in each UK nation. Univariate and multivariate logistic regression models will be carried out to estimate vaccine uptake levels in relation to various population characteristics. VE estimates against laboratory confirmed SARS-CoV-2 infection will be generated using a generalised additive logistic model. Time-dependent Cox models will be used to estimate the VE against clinical outcomes and deaths. The safety of the vaccines will be assessed using logistic regression models with an offset for the length of the risk period. Where possible, data will be meta-analysed across the UK nations.<h4>Ethics and dissemination</h4>We obtained approvals from the National Research Ethics Service Committee, Southeast Scotland 02 (12/SS/0201), the Secure Anonymised Information Linkage independent Information Governance Review Panel project number 0911. Concerning English data, University of Oxford is compliant with the General Data Protection Regulation and the National Health Service (NHS) Digital Data Security and Protection Policy. This is an approved study (Integrated Research Application ID 301740, Health Research Authority (HRA) Research Ethics Committee 21/HRA/2786). The Oxford-Royal College of General Practitioners Clinical Informatics Digital Hub meets NHS Digital's Data Security and Protection Toolkit requirements. In Northern Ireland, the project was approved by the Honest Broker Governance Board, project number 0064. Findings will be made available to national policy-makers, presented at conferences and published in peer-reviewed journals.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/2/e050062.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-050062; html:https://europepmc.org/articles/PMC8844955; pdf:https://europepmc.org/articles/PMC8844955?pdf=render
 38942167,https://doi.org/10.1016/j.ijid.2024.107155,"Vaccinations, cardiovascular drugs, hospitalization, and mortality in COVID-19 and Long COVID.","Dashtban A, Mizani MA, Pasea L, Tomlinson C, Mu Y, Islam N, Rafferty S, Warren-Gash C, Denaxas S, Horstmanshof K, Kontopantelis E, Petersen S, Sudlow C, Khunti K, Banerjee A, CVD-COVID-UK/COVID-IMPACT Consortium.",,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2024,2024-06-26,N,Vaccination; Cardiovascular disease; Covid-19; Long Covid,,,"<h4>Objective</h4>To identify highest-risk subgroups for COVID-19 and Long COVID(LC), particularly in contexts of influenza and cardiovascular disease(CVD).<h4>Methods</h4>Using national, linked electronic health records for England (NHS England Secure Data Environment via CVD-COVID-UK/COVID-IMPACT Consortium), we studied individuals (of all ages) with COVID-19 and LC (2020-2023). We compared all-cause hospitalization and mortality by prior CVD, high CV risk, vaccination status (COVID-19/influenza), and CVD drugs, investigating impact of vaccination and CVD prevention using population preventable fractions.<h4>Results</h4>Hospitalization and mortality were 15.3% and 2.0% among 17,373,850 individuals with COVID-19 (LC rate 1.3%), and 16.8% and 1.4% among 301,115 with LC. Adjusted risk of mortality and hospitalization were reduced with COVID-19 vaccination ≥ 2 doses(COVID-19:HR 0.36 and 0.69; LC:0.44 and 0.90). With influenza vaccination, mortality was reduced, but not hospitalization (COVID-19:0.86 and 1.01, and LC:0.72 and 1.05). Mortality and hospitalization were reduced by CVD prevention in those with CVD, e.g., anticoagulants- COVID:19:0.69 and 0.92; LC:0.59 and 0.88; lipid lowering- COVID-19:0.69 and 0.86; LC:0.68 and 0.90. COVID-19 vaccination averted 245044 of 321383 and 7586 of 8738 preventable deaths after COVID-19 and LC, respectively.<h4>Interpretation</h4>Prior CVD and high CV risk are associated with increased hospitalization and mortality in COVID-19 and LC. Targeted COVID-19 vaccination and CVD prevention are priority interventions.<h4>Funding</h4>NIHR. HDR UK.",,doi:https://doi.org/10.1016/j.ijid.2024.107155
-38177425,https://doi.org/10.1038/s43588-023-00461-y,GREENER principles for environmentally sustainable computational science.,"Lannelongue L, Aronson HG, Bateman A, Birney E, Caplan T, Juckes M, McEntyre J, Morris AD, Reilly G, Inouye M.",,Nature computational science,2023,2023-06-26,N,,,,"The carbon footprint of scientific computing is substantial, but environmentally sustainable computational science (ESCS) is a nascent field with many opportunities to thrive. To realize the immense green opportunities and continued, yet sustainable, growth of computer science, we must take a coordinated approach to our current challenges, including greater awareness and transparency, improved estimation and wider reporting of environmental impacts. Here, we present a snapshot of where ESCS stands today and introduce the GREENER set of principles, as well as guidance for best practices moving forward.",,doi:https://doi.org/10.1038/s43588-023-00461-y
 35918110,https://doi.org/10.1136/bmjopen-2021-057433,"Investigating the relationship between thought interference, somatic passivity and outcomes in patients with psychosis: a natural language processing approach using a clinical records search platform in south London.","Magrangeas TT, Kolliakou A, Sanyal J, Patel R, Stewart R.",,BMJ open,2022,2022-08-02,Y,Health Informatics; Adult Psychiatry; Schizophrenia & Psychotic Disorders,,,"<h4>Objectives</h4>We aimed to apply natural language processing algorithms in routine healthcare records to identify reported somatic passivity (external control of sensations, actions and impulses) and thought interference symptoms (thought broadcasting, insertion, withdrawal), first-rank symptoms traditionally central to diagnosing schizophrenia, and determine associations with prognosis by analysing routine outcomes.<h4>Design</h4>Four algorithms were developed on deidentified mental healthcare data and applied to ascertain recorded symptoms over the 3 months following first presentation to a mental healthcare provider in a cohort of patients with a primary schizophreniform disorder (ICD-10 F20-F29) diagnosis.<h4>Setting and participants</h4>From the electronic health records of a large secondary mental healthcare provider in south London, 9323 patients were ascertained from 2007 to the data extraction date (25 February 2020).<h4>Outcomes</h4>The primary binary dependent variable for logistic regression analyses was any negative outcome (Mental Health Act section, >2 antipsychotics prescribed, >22 days spent in crisis care) over the subsequent 2 years.<h4>Results</h4>Final adjusted models indicated significant associations of this composite outcome with baseline somatic passivity (prevalence 4.9%; adjusted OR 1.61, 95% CI 1.37 to 1.88), thought insertion (10.7%; 1.24, 95% CI 1.15 to 1.55) and thought withdrawal (4.9%; 1.36, 95% CI 1.10 to 1.69), but not independently with thought broadcast (10.3%; 1.05, 95% CI 0.91 to 1.22).<h4>Conclusions</h4>Symptoms traditionally central to the diagnosis of schizophrenia, but under-represented in current diagnostic frameworks, were thus identified as important predictors of short-term to medium-term prognosis in schizophreniform disorders.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/8/e057433.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-057433; html:https://europepmc.org/articles/PMC9351333; pdf:https://europepmc.org/articles/PMC9351333?pdf=render
+38177425,https://doi.org/10.1038/s43588-023-00461-y,GREENER principles for environmentally sustainable computational science.,"Lannelongue L, Aronson HG, Bateman A, Birney E, Caplan T, Juckes M, McEntyre J, Morris AD, Reilly G, Inouye M.",,Nature computational science,2023,2023-06-26,N,,,,"The carbon footprint of scientific computing is substantial, but environmentally sustainable computational science (ESCS) is a nascent field with many opportunities to thrive. To realize the immense green opportunities and continued, yet sustainable, growth of computer science, we must take a coordinated approach to our current challenges, including greater awareness and transparency, improved estimation and wider reporting of environmental impacts. Here, we present a snapshot of where ESCS stands today and introduce the GREENER set of principles, as well as guidance for best practices moving forward.",,doi:https://doi.org/10.1038/s43588-023-00461-y
 35336739,https://doi.org/10.3390/biology11030365,Machine Learning-Based Identification of Colon Cancer Candidate Diagnostics Genes.,"Koppad S, Basava A, Nash K, Gkoutos GV, Acharjee A.",,Biology,2022,2022-02-25,Y,Prediction; Variable selection; Machine Learning; Transcriptomics; Biomarker Identification,,,"<h4>Background</h4>Colorectal cancer (CRC) is the third leading cause of cancer-related death and the fourth most commonly diagnosed cancer worldwide. Due to a lack of diagnostic biomarkers and understanding of the underlying molecular mechanisms, CRC's mortality rate continues to grow. CRC occurrence and progression are dynamic processes. The expression levels of specific molecules vary at various stages of CRC, rendering its early detection and diagnosis challenging and the need for identifying accurate and meaningful CRC biomarkers more pressing. The advances in high-throughput sequencing technologies have been used to explore novel gene expression, targeted treatments, and colon cancer pathogenesis. Such approaches are routinely being applied and result in large datasets whose analysis is increasingly becoming dependent on machine learning (ML) algorithms that have been demonstrated to be computationally efficient platforms for the identification of variables across such high-dimensional datasets.<h4>Methods</h4>We developed a novel ML-based experimental design to study CRC gene associations. Six different machine learning methods were employed as classifiers to identify genes that can be used as diagnostics for CRC using gene expression and clinical datasets. The accuracy, sensitivity, specificity, F1 score, and area under receiver operating characteristic (AUROC) curve were derived to explore the differentially expressed genes (DEGs) for CRC diagnosis. Gene ontology enrichment analyses of these DEGs were performed and predicted gene signatures were linked with miRNAs.<h4>Results</h4>We evaluated six machine learning classification methods (Adaboost, ExtraTrees, logistic regression, naïve Bayes classifier, random forest, and XGBoost) across different combinations of training and test datasets over GEO datasets. The accuracy and the AUROC of each combination of training and test data with different algorithms were used as comparison metrics. Random forest (RF) models consistently performed better than other models. In total, 34 genes were identified and used for pathway and gene set enrichment analysis. Further mapping of the 34 genes with miRNA identified interesting miRNA hubs genes.<h4>Conclusions</h4>We identified 34 genes with high accuracy that can be used as a diagnostics panel for CRC.",,pdf:https://www.mdpi.com/2079-7737/11/3/365/pdf?version=1645777713; doi:https://doi.org/10.3390/biology11030365; html:https://europepmc.org/articles/PMC8944988; pdf:https://europepmc.org/articles/PMC8944988?pdf=render
 34879829,https://doi.org/10.1186/s12911-021-01693-6,Identifying and evaluating clinical subtypes of Alzheimer's disease in care electronic health records using unsupervised machine learning.,"Alexander N, Alexander DC, Barkhof F, Denaxas S.",,BMC medical informatics and decision making,2021,2021-12-08,Y,Alzheimer's disease; Clustering; Subtyping; Ehr; K-means,,,"<h4>Background</h4>Alzheimer's disease (AD) is a highly heterogeneous disease with diverse trajectories and outcomes observed in clinical populations. Understanding this heterogeneity can enable better treatment, prognosis and disease management. Studies to date have mainly used imaging or cognition data and have been limited in terms of data breadth and sample size. Here we examine the clinical heterogeneity of Alzheimer's disease patients using electronic health records (EHR) to identify and characterise disease subgroups using multiple clustering methods, identifying clusters which are clinically actionable.<h4>Methods</h4>We identified AD patients in primary care EHR from the Clinical Practice Research Datalink (CPRD) using a previously validated rule-based phenotyping algorithm. We extracted and included a range of comorbidities, symptoms and demographic features as patient features. We evaluated four different clustering methods (k-means, kernel k-means, affinity propagation and latent class analysis) to cluster Alzheimer's disease patients. We compared clusters on clinically relevant outcomes and evaluated each method using measures of cluster structure, stability, efficiency of outcome prediction and replicability in external data sets.<h4>Results</h4>We identified 7,913 AD patients, with a mean age of 82 and 66.2% female. We included 21 features in our analysis. We observed 5, 2, 5 and 6 clusters in k-means, kernel k-means, affinity propagation and latent class analysis respectively. K-means was found to produce the most consistent results based on four evaluative measures. We discovered a consistent cluster found in three of the four methods composed of predominantly female, younger disease onset (43% between ages 42-73) diagnosed with depression and anxiety, with a quicker rate of progression compared to the average across other clusters.<h4>Conclusion</h4>Each clustering approach produced substantially different clusters and K-Means performed the best out of the four methods based on the four evaluative criteria. However, the consistent appearance of one particular cluster across three of the four methods potentially suggests the presence of a distinct disease subtype that merits further exploration. Our study underlines the variability of the results obtained from different clustering approaches and the importance of systematically evaluating different approaches for identifying disease subtypes in complex EHR.",,pdf:https://bmcmedinformdecismak.biomedcentral.com/track/pdf/10.1186/s12911-021-01693-6; doi:https://doi.org/10.1186/s12911-021-01693-6; html:https://europepmc.org/articles/PMC8653614; pdf:https://europepmc.org/articles/PMC8653614?pdf=render
-37147628,https://doi.org/10.1186/s12911-023-02181-9,Ontology-driven and weakly supervised rare disease identification from clinical notes.,"Dong H, Suárez-Paniagua V, Zhang H, Wang M, Casey A, Davidson E, Chen J, Alex B, Whiteley W, Wu H.",,BMC medical informatics and decision making,2023,2023-05-05,Y,Phenotyping; Natural Language Processing; Rare Diseases; Ontology Matching; Clinical Notes; Weak Supervision,,,"<h4>Background</h4>Computational text phenotyping is the practice of identifying patients with certain disorders and traits from clinical notes. Rare diseases are challenging to be identified due to few cases available for machine learning and the need for data annotation from domain experts.<h4>Methods</h4>We propose a method using ontologies and weak supervision, with recent pre-trained contextual representations from Bi-directional Transformers (e.g. BERT). The ontology-driven framework includes two steps: (i) Text-to-UMLS, extracting phenotypes by contextually linking mentions to concepts in Unified Medical Language System (UMLS), with a Named Entity Recognition and Linking (NER+L) tool, SemEHR, and weak supervision with customised rules and contextual mention representation; (ii) UMLS-to-ORDO, matching UMLS concepts to rare diseases in Orphanet Rare Disease Ontology (ORDO). The weakly supervised approach is proposed to learn a phenotype confirmation model to improve Text-to-UMLS linking, without annotated data from domain experts. We evaluated the approach on three clinical datasets, MIMIC-III discharge summaries, MIMIC-III radiology reports, and NHS Tayside brain imaging reports from two institutions in the US and the UK, with annotations.<h4>Results</h4>The improvements in the precision were pronounced (by over 30% to 50% absolute score for Text-to-UMLS linking), with almost no loss of recall compared to the existing NER+L tool, SemEHR. Results on radiology reports from MIMIC-III and NHS Tayside were consistent with the discharge summaries. The overall pipeline processing clinical notes can extract rare disease cases, mostly uncaptured in structured data (manually assigned ICD codes).<h4>Conclusion</h4>The study provides empirical evidence for the task by applying a weakly supervised NLP pipeline on clinical notes. The proposed weak supervised deep learning approach requires no human annotation except for validation and testing, by leveraging ontologies, NER+L tools, and contextual representations. The study also demonstrates that Natural Language Processing (NLP) can complement traditional ICD-based approaches to better estimate rare diseases in clinical notes. We discuss the usefulness and limitations of the weak supervision approach and propose directions for future studies.",,pdf:https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-023-02181-9; doi:https://doi.org/10.1186/s12911-023-02181-9; html:https://europepmc.org/articles/PMC10162001; pdf:https://europepmc.org/articles/PMC10162001?pdf=render
 35572721,https://doi.org/10.1016/j.eclinm.2022.101419,Breakthrough SARS-CoV-2 infections in double and triple vaccinated adults and single dose vaccine effectiveness among children in Autumn 2021 in England: REACT-1 study.,"Chadeau-Hyam M, Eales O, Bodinier B, Wang H, Haw D, Whitaker M, Elliott J, Walters CE, Jonnerby J, Atchison C, Diggle PJ, Page AJ, Ashby D, Barclay W, Taylor G, Cooke G, Ward H, Darzi A, Donnelly CA, Elliott P.",,EClinicalMedicine,2022,2022-05-06,Y,School-aged children; Vaccine Effectiveness; Booster Dose; Children Vaccination; Sars-cov-2 Prevalence,,,"<h4>Background</h4>Prevalence of SARS-CoV-2 infection with Delta variant was increasing in England in late summer 2021 among children aged 5 to 17 years, and adults who had received two vaccine doses. In September 2021, a third (booster) dose was offered to vaccinated adults aged 50 years and over, vulnerable adults and healthcare/care-home workers, and a single vaccine dose already offered to 16 and 17 year-olds was extended to children aged 12 to 15 years.<h4>Methods</h4>SARS-CoV-2 community prevalence in England was available from self-administered throat and nose swabs using reverse transcriptase polymerase chain reaction (RT-PCR) in round 13 (24 June to 12 July 2021, <i>N</i> = 98,233), round 14 (9 to 27 September 2021, <i>N</i> = 100,527) and round 15 (19 October to 5 November 2021, <i>N</i> = 100,112) from the REACT-1 study randomised community surveys. Linking to National Health Service (NHS) vaccination data for consenting participants, we estimated vaccine effectiveness in children aged 12 to 17 years and compared swab-positivity rates in adults who received a third dose with those who received two doses.<h4>Findings</h4>Weighted SARS-CoV-2 prevalence was 1.57% (1.48%, 1.66%) in round 15 compared with 0.83% (0.76%, 0.89%) in round 14, and the previously observed link between infections and hospitalisations and deaths had weakened. Vaccine effectiveness against infection in children aged 12 to 17 years was estimated (round 15) at 64.0% (50.9%, 70.6%) and 67.7% (53.8%, 77.5%) for symptomatic infections. Adults who received a third vaccine dose were less likely to test positive compared to those who received two doses, with adjusted OR of 0.36 (0.25, 0.53).<h4>Interpretation</h4>Vaccination of children aged 12 to 17 years and third (booster) doses in adults were effective at reducing infection risk. High rates of vaccination, including booster doses, are a key part of the strategy to reduce infection rates in the community.<h4>Funding</h4>Department of Health and Social Care, England.",,pdf:http://www.thelancet.com/article/S2589537022001493/pdf; doi:https://doi.org/10.1016/j.eclinm.2022.101419; html:https://europepmc.org/articles/PMC9076030; pdf:https://europepmc.org/articles/PMC9076030?pdf=render
-34007894,https://doi.org/10.23889/ijpds.v6i1.1373,Visualisation and optimisation of alcohol-related hospital admissions ICD-10 codes in Welsh e-cohort data.,"Trefan L, Akbari A, Morgan JS, Farewell DM, Fone D, Lyons RA, Jones Hywel M, Moore SC.",,International journal of population data science,2021,2021-03-24,Y,Alcohol; Hospital Admission; Optimisation; Icd-10 Codes; E-Cohort Data,,,"<h4>Introduction</h4>The excessive consumption of alcohol is detrimental to long term health and increases the likelihood of hospital admission. However, definitions of alcohol-related hospital admission vary, giving rise to uncertainty in the effect of alcohol on alcohol-related health care utilization.<h4>Objectives</h4>To compare diagnostic codes on hospital admission and discharge and to determine the ideal combination of codes necessary for an accurate determination of alcohol-related hospital admission.<h4>Methods</h4>Routine population-linked e-cohort data were extracted from the Secure Anonymised Information Linkage (SAIL) Databank containing all alcohol-related hospital admissions (n,= 92,553) from 2006 to 2011 in Wales, United Kingdom. The distributions of the diagnostic codes recorded at admission and discharge were compared. By calculating a misclassification rate (sensitivity-like measure) the appropriate number of coding fields to examine for alcohol-codes was established.<h4>Results</h4>There was agreement between admission and discharge codes. When more than ten coding fields were used the misclassification rate was less than 1%.<h4>Conclusion</h4>With the data at present and alcohol-related codes used, codes recorded at admission and discharge can be used equivalently to identify alcohol-related admissions. The appropriate number of coding fields to examine was established: fewer than ten is likely to lead to under-reporting of alcohol-related admissions. The methods developed here can be applied to other medical conditions that can be described using a certain set of diagnostic codes, each of which can be a known sole cause of the condition and recorded in multiple positions in e-cohort data.",,pdf:https://ijpds.org/article/download/1373/3264; doi:https://doi.org/10.23889/ijpds.v6i1.1373; html:https://europepmc.org/articles/PMC8103565; pdf:https://europepmc.org/articles/PMC8103565?pdf=render
 34440368,https://doi.org/10.3390/genes12081194,"Genetic Variation in the ASTN2 Locus in Cardiovascular, Metabolic and Psychiatric Traits: Evidence for Pleiotropy Rather Than Shared Biology.","Burt O, Johnston KJA, Graham N, Cullen B, Lyall DM, Lyall LM, Pell JP, Ward J, Smith DJ, Strawbridge RJ.",,Genes,2021,2021-07-31,Y,Blood pressure; BMI; Cardiovascular disease; Metabolic Disease; Psychiatric Illness; Mood Instability; Neuroticism; Central Obesity; Anhedonia; Astn2,,,"<h4>Background</h4>The link between cardiometabolic and psychiatric illness has long been attributed to human behaviour, however recent research highlights shared biological mechanisms. The <i>ASTN2</i> locus has been previously implicated in psychiatric and cardiometabolic traits, therefore this study aimed to systematically investigate the genetic architecture of <i>ASTN2</i> in relation to a wide range of relevant traits.<h4>Methods</h4>Baseline questionnaire, assessment and genetic data of 402111 unrelated white British ancestry individuals from the UK Biobank was analysed. Genetic association analyses were conducted using PLINK 1.07, assuming an additive genetic model and adjusting for age, sex, genotyping chip, and population structure. Conditional analyses and linkage disequilibrium assessment were used to determine whether cardiometabolic and psychiatric signals were independent.<h4>Results</h4>Associations between genetic variants in the ASTN2 locus and blood pressure, total and central obesity, neuroticism, anhedonia and mood instability were identified. All analyses support the independence of the cardiometabolic traits from the psychiatric traits. In silico analyses provide support for the central obesity signal acting through <i>ASTN2</i>, however most of the other signals are likely acting through other genes in the locus.<h4>Conclusions</h4>Our systematic analysis demonstrates that <i>ASTN2</i> has pleiotropic effects on cardiometabolic and psychiatric traits, rather than contributing to shared pathology.",,pdf:https://www.mdpi.com/2073-4425/12/8/1194/pdf?version=1627984735; doi:https://doi.org/10.3390/genes12081194; html:https://europepmc.org/articles/PMC8391428; pdf:https://europepmc.org/articles/PMC8391428?pdf=render
-34108714,https://doi.org/10.1038/s41591-021-01408-4,"First-dose ChAdOx1 and BNT162b2 COVID-19 vaccines and thrombocytopenic, thromboembolic and hemorrhagic events in Scotland.","Simpson CR, Shi T, Vasileiou E, Katikireddi SV, Kerr S, Moore E, McCowan C, Agrawal U, Shah SA, Ritchie LD, Murray J, Pan J, Bradley DT, Stock SJ, Wood R, Chuter A, Beggs J, Stagg HR, Joy M, Tsang RSM, de Lusignan S, Hobbs R, Lyons RA, Torabi F, Bedston S, O'Leary M, Akbari A, McMenamin J, Robertson C, Sheikh A.",,Nature medicine,2021,2021-06-09,Y,,,,"Reports of ChAdOx1 vaccine-associated thrombocytopenia and vascular adverse events have led to some countries restricting its use. Using a national prospective cohort, we estimated associations between exposure to first-dose ChAdOx1 or BNT162b2 vaccination and hematological and vascular adverse events using a nested incident-matched case-control study and a confirmatory self-controlled case series (SCCS) analysis. An association was found between ChAdOx1 vaccination and idiopathic thrombocytopenic purpura (ITP) (0-27 d after vaccination; adjusted rate ratio (aRR) = 5.77, 95% confidence interval (CI), 2.41-13.83), with an estimated incidence of 1.13 (0.62-1.63) cases per 100,000 doses. An SCCS analysis confirmed that this was unlikely due to bias (RR = 1.98 (1.29-3.02)). There was also an increased risk for arterial thromboembolic events (aRR = 1.22, 1.12-1.34) 0-27 d after vaccination, with an SCCS RR of 0.97 (0.93-1.02). For hemorrhagic events 0-27 d after vaccination, the aRR was 1.48 (1.12-1.96), with an SCCS RR of 0.95 (0.82-1.11). A first dose of ChAdOx1 was found to be associated with small increased risks of ITP, with suggestive evidence of an increased risk of arterial thromboembolic and hemorrhagic events. The attenuation of effect found in the SCCS analysis means that there is the potential for overestimation of the reported results, which might indicate the presence of some residual confounding or confounding by indication. Public health authorities should inform their jurisdictions of these relatively small increased risks associated with ChAdOx1. No positive associations were seen between BNT162b2 and thrombocytopenic, thromboembolic and hemorrhagic events.",,pdf:https://www.nature.com/articles/s41591-021-01408-4.pdf; doi:https://doi.org/10.1038/s41591-021-01408-4; html:https://europepmc.org/articles/PMC8282499; pdf:https://europepmc.org/articles/PMC8282499?pdf=render
+34007894,https://doi.org/10.23889/ijpds.v6i1.1373,Visualisation and optimisation of alcohol-related hospital admissions ICD-10 codes in Welsh e-cohort data.,"Trefan L, Akbari A, Morgan JS, Farewell DM, Fone D, Lyons RA, Jones Hywel M, Moore SC.",,International journal of population data science,2021,2021-03-24,Y,Alcohol; Hospital Admission; Optimisation; Icd-10 Codes; E-Cohort Data,,,"<h4>Introduction</h4>The excessive consumption of alcohol is detrimental to long term health and increases the likelihood of hospital admission. However, definitions of alcohol-related hospital admission vary, giving rise to uncertainty in the effect of alcohol on alcohol-related health care utilization.<h4>Objectives</h4>To compare diagnostic codes on hospital admission and discharge and to determine the ideal combination of codes necessary for an accurate determination of alcohol-related hospital admission.<h4>Methods</h4>Routine population-linked e-cohort data were extracted from the Secure Anonymised Information Linkage (SAIL) Databank containing all alcohol-related hospital admissions (n,= 92,553) from 2006 to 2011 in Wales, United Kingdom. The distributions of the diagnostic codes recorded at admission and discharge were compared. By calculating a misclassification rate (sensitivity-like measure) the appropriate number of coding fields to examine for alcohol-codes was established.<h4>Results</h4>There was agreement between admission and discharge codes. When more than ten coding fields were used the misclassification rate was less than 1%.<h4>Conclusion</h4>With the data at present and alcohol-related codes used, codes recorded at admission and discharge can be used equivalently to identify alcohol-related admissions. The appropriate number of coding fields to examine was established: fewer than ten is likely to lead to under-reporting of alcohol-related admissions. The methods developed here can be applied to other medical conditions that can be described using a certain set of diagnostic codes, each of which can be a known sole cause of the condition and recorded in multiple positions in e-cohort data.",,pdf:https://ijpds.org/article/download/1373/3264; doi:https://doi.org/10.23889/ijpds.v6i1.1373; html:https://europepmc.org/articles/PMC8103565; pdf:https://europepmc.org/articles/PMC8103565?pdf=render
 32990744,https://doi.org/10.1093/gigascience/giaa095,An extensible big data software architecture managing a research resource of real-world clinical radiology data linked to other health data from the whole Scottish population.,"Nind T, Sutherland J, McAllister G, Hardy D, Hume A, MacLeod R, Caldwell J, Krueger S, Tramma L, Teviotdale R, Abdelatif M, Gillen K, Ward J, Scobbie D, Baillie I, Brooks A, Prodan B, Kerr W, Sloan-Murphy D, Herrera JFR, McManus D, Morris C, Sinclair C, Baxter R, Parsons M, Morris A, Jefferson E.",,GigaScience,2020,2020-09-01,Y,ML; AI; Radiology; Big Data,,,"<h4>Aim</h4>To enable a world-leading research dataset of routinely collected clinical images linked to other routinely collected data from the whole Scottish national population. This includes more than 30 million different radiological examinations from a population of 5.4 million and >2 PB of data collected since 2010.<h4>Methods</h4>Scotland has a central archive of radiological data used to directly provide clinical care to patients. We have developed an architecture and platform to securely extract a copy of those data, link it to other clinical or social datasets, remove personal data to protect privacy, and make the resulting data available to researchers in a controlled Safe Haven environment.<h4>Results</h4>An extensive software platform has been developed to host, extract, and link data from cohorts to answer research questions. The platform has been tested on 5 different test cases and is currently being further enhanced to support 3 exemplar research projects.<h4>Conclusions</h4>The data available are from a range of radiological modalities and scanner types and were collected under different environmental conditions. These real-world, heterogenous data are valuable for training algorithms to support clinical decision making, especially for deep learning where large data volumes are required. The resource is now available for international research access. The platform and data can support new health research using artificial intelligence and machine learning technologies, as well as enabling discovery science.",,pdf:https://academic.oup.com/gigascience/article-pdf/9/10/giaa095/33802377/giaa095.pdf; doi:https://doi.org/10.1093/gigascience/giaa095; html:https://europepmc.org/articles/PMC7523405; pdf:https://europepmc.org/articles/PMC7523405?pdf=render
+37147628,https://doi.org/10.1186/s12911-023-02181-9,Ontology-driven and weakly supervised rare disease identification from clinical notes.,"Dong H, Suárez-Paniagua V, Zhang H, Wang M, Casey A, Davidson E, Chen J, Alex B, Whiteley W, Wu H.",,BMC medical informatics and decision making,2023,2023-05-05,Y,Phenotyping; Natural Language Processing; Rare Diseases; Ontology Matching; Clinical Notes; Weak Supervision,,,"<h4>Background</h4>Computational text phenotyping is the practice of identifying patients with certain disorders and traits from clinical notes. Rare diseases are challenging to be identified due to few cases available for machine learning and the need for data annotation from domain experts.<h4>Methods</h4>We propose a method using ontologies and weak supervision, with recent pre-trained contextual representations from Bi-directional Transformers (e.g. BERT). The ontology-driven framework includes two steps: (i) Text-to-UMLS, extracting phenotypes by contextually linking mentions to concepts in Unified Medical Language System (UMLS), with a Named Entity Recognition and Linking (NER+L) tool, SemEHR, and weak supervision with customised rules and contextual mention representation; (ii) UMLS-to-ORDO, matching UMLS concepts to rare diseases in Orphanet Rare Disease Ontology (ORDO). The weakly supervised approach is proposed to learn a phenotype confirmation model to improve Text-to-UMLS linking, without annotated data from domain experts. We evaluated the approach on three clinical datasets, MIMIC-III discharge summaries, MIMIC-III radiology reports, and NHS Tayside brain imaging reports from two institutions in the US and the UK, with annotations.<h4>Results</h4>The improvements in the precision were pronounced (by over 30% to 50% absolute score for Text-to-UMLS linking), with almost no loss of recall compared to the existing NER+L tool, SemEHR. Results on radiology reports from MIMIC-III and NHS Tayside were consistent with the discharge summaries. The overall pipeline processing clinical notes can extract rare disease cases, mostly uncaptured in structured data (manually assigned ICD codes).<h4>Conclusion</h4>The study provides empirical evidence for the task by applying a weakly supervised NLP pipeline on clinical notes. The proposed weak supervised deep learning approach requires no human annotation except for validation and testing, by leveraging ontologies, NER+L tools, and contextual representations. The study also demonstrates that Natural Language Processing (NLP) can complement traditional ICD-based approaches to better estimate rare diseases in clinical notes. We discuss the usefulness and limitations of the weak supervision approach and propose directions for future studies.",,pdf:https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-023-02181-9; doi:https://doi.org/10.1186/s12911-023-02181-9; html:https://europepmc.org/articles/PMC10162001; pdf:https://europepmc.org/articles/PMC10162001?pdf=render
+34108714,https://doi.org/10.1038/s41591-021-01408-4,"First-dose ChAdOx1 and BNT162b2 COVID-19 vaccines and thrombocytopenic, thromboembolic and hemorrhagic events in Scotland.","Simpson CR, Shi T, Vasileiou E, Katikireddi SV, Kerr S, Moore E, McCowan C, Agrawal U, Shah SA, Ritchie LD, Murray J, Pan J, Bradley DT, Stock SJ, Wood R, Chuter A, Beggs J, Stagg HR, Joy M, Tsang RSM, de Lusignan S, Hobbs R, Lyons RA, Torabi F, Bedston S, O'Leary M, Akbari A, McMenamin J, Robertson C, Sheikh A.",,Nature medicine,2021,2021-06-09,Y,,,,"Reports of ChAdOx1 vaccine-associated thrombocytopenia and vascular adverse events have led to some countries restricting its use. Using a national prospective cohort, we estimated associations between exposure to first-dose ChAdOx1 or BNT162b2 vaccination and hematological and vascular adverse events using a nested incident-matched case-control study and a confirmatory self-controlled case series (SCCS) analysis. An association was found between ChAdOx1 vaccination and idiopathic thrombocytopenic purpura (ITP) (0-27 d after vaccination; adjusted rate ratio (aRR) = 5.77, 95% confidence interval (CI), 2.41-13.83), with an estimated incidence of 1.13 (0.62-1.63) cases per 100,000 doses. An SCCS analysis confirmed that this was unlikely due to bias (RR = 1.98 (1.29-3.02)). There was also an increased risk for arterial thromboembolic events (aRR = 1.22, 1.12-1.34) 0-27 d after vaccination, with an SCCS RR of 0.97 (0.93-1.02). For hemorrhagic events 0-27 d after vaccination, the aRR was 1.48 (1.12-1.96), with an SCCS RR of 0.95 (0.82-1.11). A first dose of ChAdOx1 was found to be associated with small increased risks of ITP, with suggestive evidence of an increased risk of arterial thromboembolic and hemorrhagic events. The attenuation of effect found in the SCCS analysis means that there is the potential for overestimation of the reported results, which might indicate the presence of some residual confounding or confounding by indication. Public health authorities should inform their jurisdictions of these relatively small increased risks associated with ChAdOx1. No positive associations were seen between BNT162b2 and thrombocytopenic, thromboembolic and hemorrhagic events.",,pdf:https://www.nature.com/articles/s41591-021-01408-4.pdf; doi:https://doi.org/10.1038/s41591-021-01408-4; html:https://europepmc.org/articles/PMC8282499; pdf:https://europepmc.org/articles/PMC8282499?pdf=render
 37949372,https://doi.org/10.1016/j.jhin.2023.10.021,COVID-19-related mortality and hospital admissions in the VIVALDI study cohort: October 2020 to March 2023.,"Stirrup O, Krutikov M, Azmi B, Monakhov I, Hayward A, Copas A, Shallcross L.",,The Journal of hospital infection,2024,2023-11-08,Y,Care Homes; Covid-19; Sars-cov-2; Infection Fatality Ratio; Infection Hospitalization Ratio,,,"<h4>Background</h4>Long-term-care facilities (LTCFs) were heavily affected by COVID-19 early in the pandemic, but the impact of the virus has reduced over time with vaccination campaigns and build-up of immunity from prior infection.<h4>Objectives</h4>To evaluate the mortality and hospital admissions associated with SARS-CoV-2 in LTCFs in England over the course of the VIVALDI study, from October 2020 to March 2023.<h4>Methods</h4>We included residents aged ≥65 years from participating LTCFs who had available follow-up time within the analysis period. We calculated incidence rates (IRs) of COVID-19-linked mortality and hospital admissions per calendar quarter, along with infection fatality ratios (IFRs, within 28 days) and infection hospitalization ratios (IHRs, within 14 days) following positive SARS-CoV-2 test.<h4>Results</h4>A total of 26,286 residents were included, with at least one positive test for SARS-CoV-2 in 8513 (32.4%). The IR of COVID-19-related mortality peaked in the first quarter (Q1) of 2021 at 0.47 per 1000 person-days (1 kpd) (around a third of all deaths), in comparison with 0.10 per 1 kpd for Q1 2023 which had a similar IR of SARS-CoV-2 infections. There was a fall in observed IFR for SARS-CoV-2 infections from 24.9% to 6.7% between these periods, with a fall in IHR from 12.1% to 8.8%. The population had high overall IRs for mortality for each quarter evaluated, corresponding to annual mortality probability of 28.8-41.3%.<h4>Conclusions</h4>Standardized real-time monitoring of hospitalization and mortality following infection in LTCFs could inform policy on the need for non-pharmaceutical interventions to prevent transmission.",,pdf:http://www.journalofhospitalinfection.com/article/S0195670123003572/pdf; doi:https://doi.org/10.1016/j.jhin.2023.10.021; html:https://europepmc.org/articles/PMC10927615; pdf:https://europepmc.org/articles/PMC10927615?pdf=render
 35226680,https://doi.org/10.1371/journal.pone.0264023,"COVID-19 mitigation measures in primary schools and association with infection and school staff wellbeing: An observational survey linked with routine data in Wales, UK.","Marchant E, Griffiths L, Crick T, Fry R, Hollinghurst J, James M, Cowley L, Abbasizanjani H, Torabi F, Thompson DA, Kennedy J, Akbari A, Gravenor MB, Lyons RA, Brophy S.",,PloS one,2022,2022-02-28,Y,,,,"<h4>Introduction</h4>School-based COVID-19 mitigation strategies have greatly impacted the primary school day (children aged 3-11) including: wearing face coverings, two metre distancing, no mixing of children, and no breakfast clubs or extra-curricular activities. This study examines these mitigation measures and association with COVID-19 infection, respiratory infection, and school staff wellbeing between October to December 2020 in Wales, UK.<h4>Methods</h4>A school staff survey captured self-reported COVID-19 mitigation measures in the school, participant anxiety and depression, and open-text responses regarding experiences of teaching and implementing measures. These survey responses were linked to national-scale COVID-19 test results data to examine association of measures in the school and the likelihood of a positive (staff or pupil) COVID-19 case in the school (clustered by school, adjusted for school size and free school meals using logistic regression). Linkage was conducted through the SAIL (Secure Anonymised Information Linkage) Databank.<h4>Results</h4>Responses were obtained from 353 participants from 59 primary schools within 15 of 22 local authorities. Having more direct non-household contacts was associated with a higher likelihood of COVID-19 positive case in the school (1-5 contacts compared to none, OR 2.89 (1.01, 8.31)) and a trend to more self-reported cold symptoms. Staff face covering was not associated with a lower odds of school COVID-19 cases (mask vs. no covering OR 2.82 (1.11, 7.14)) and was associated with higher self-reported cold symptoms. School staff reported the impacts of wearing face coverings on teaching, including having to stand closer to pupils and raise their voices to be heard. 67.1% were not able to implement two metre social distancing from pupils. We did not find evidence that maintaining a two metre distance was associated with lower rates of COVID-19 in the school.<h4>Conclusions</h4>Implementing, adhering to and evaluating COVID-19 mitigation guidelines is challenging in primary school settings. Our findings suggest that reducing non-household direct contacts lowers infection rates. There was no evidence that face coverings, two metre social distancing or stopping children mixing was associated with lower odds of COVID-19 or cold infection rates in the school. Primary school staff found teaching challenging during COVID-19 restrictions, especially for younger learners and those with additional learning needs.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0264023&type=printable; doi:https://doi.org/10.1371/journal.pone.0264023; html:https://europepmc.org/articles/PMC8884508; pdf:https://europepmc.org/articles/PMC8884508?pdf=render
 36629015,https://doi.org/10.1177/17407745221143449,Lack of transparent reporting of trial monitoring approaches in randomised controlled trials: A systematic review of contemporary protocol papers.,"Hsieh SF, Yorke-Edwards V, Murray ML, Diaz-Montana C, Love SB, Sydes MR.",,"Clinical trials (London, England)",2023,2023-01-11,Y,Systematic review; Randomised Controlled Trial; On-site Monitoring; Risk-based Monitoring; Protocol Paper; Central Monitoring; Trial Monitoring; Reporting Monitoring,,,"<h4>Background</h4>Monitoring is essential to ensure patient safety and data integrity in clinical trials as per Good Clinical Practice. The Standard Protocol Items: Recommendations for Interventional Trials Statement and its checklist guides authors to include monitoring in their protocols. We investigated how well monitoring was reported in published 'protocol papers' for contemporary randomised controlled trials.<h4>Methods</h4>A systematic search was conducted in PubMed to identify eligible protocol papers published in selected journals between 1 January 2020 and 31 May 2020. Protocol papers were classified by whether they reported monitoring and, if so, by the details of monitoring. Data were summarised descriptively.<h4>Results</h4>Of 811 protocol papers for randomised controlled trials, 386 (48%; 95% CI: 44%-51%) explicitly reported some monitoring information. Of these, 20% (77/386) reported monitoring information consistent with an on-site monitoring approach, and 39% (152/386) with central monitoring, 26% (101/386) with a mixed approach, while 14% (54/386) did not provide sufficient information to specify an approach. Only 8% (30/386) of randomised controlled trials reported complete details about all of scope, frequency and organisation of monitoring; frequency of monitoring was the least reported. However, 6% (25/386) of papers used the term 'audit' to describe 'monitoring'.<h4>Discussion</h4>Monitoring information was reported in only approximately half of the protocol papers. Suboptimal reporting of monitoring hinders the clinical community from having the full information on which to judge the validity of a trial and jeopardises the value of protocol papers and the credibility of the trial itself. Greater efforts are needed to promote the transparent reporting of monitoring to journal editors and authors.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/17407745221143449; doi:https://doi.org/10.1177/17407745221143449; html:https://europepmc.org/articles/PMC10021127; pdf:https://europepmc.org/articles/PMC10021127?pdf=render
@@ -431,42 +431,42 @@ PMC11234640,https://doi.org/,"Evidence of gene-nutrient interaction association
 37650027,https://doi.org/10.23889/ijpds.v7i1.1724,"A methodology to facilitate critical care research using multiple linked electronic, clinical and administrative health records at population scale.","Griffiths R, Herbert L, Akbari A, Bailey R, Hollinghurst J, Pugh R, Szakmany T, Torabi F, Lyons RA.",,International journal of population data science,2022,2022-07-18,Y,Intensive Care; Critical Care; Electronic Health Records; Icnarc; Linkable Research Data,,,"<h4>Introduction</h4>Critical Care is a specialty in medicine providing a service for severely ill and high-risk patients who, due to the nature of their condition, may require long periods recovering after discharge. Consequently, focus on the routine data collection carried out in Intensive Care Units (ICUs) leads to reporting that is confined to the critical care episode and is typically insensitive to variation in individual patient pathways through critical care to recovery.A resource which facilitates efficient research into interactions with healthcare services surrounding critical admissions, capturing the complete patient's healthcare trajectory from primary care to non-acute hospital care prior to ICU, would provide an important longer-term perspective for critical care research.<h4>Objective</h4>To describe and apply a reproducible methodology that demonstrates how both routine administrative and clinically rich critical care data sources can be integrated with primary and secondary healthcare data to create a single dataset that captures a broader view of patient care.<h4>Method</h4>To demonstrate the INTEGRATE methodology, it was applied to routine administrative and clinical healthcare data sources in the Secure Anonymised Data Linking (SAIL) Databank to create a dataset of patients' complete healthcare trajectory prior to critical care admission. SAIL is a national, data safe haven of anonymised linkable datasets about the population of Wales.<h4>Results</h4>When applying the INTEGRATE methodology in SAIL, between 2010 and 2019 we observed 91,582 critical admissions for 76,019 patients. Of these, 90,632 (99%) had an associated non-acute hospital admission, 48,979 (53%) had an emergency admission, and 64,832 (71%) a primary care interaction in the week prior to the critical care admission.<h4>Conclusion</h4>This methodology, at population scale, integrates two critical care data sources into a single dataset together with data sources on healthcare prior to critical admission, thus providing a key research asset to study critical care pathways.",,pdf:https://ijpds.org/article/download/1724/3569; doi:https://doi.org/10.23889/ijpds.v7i1.1724; html:https://europepmc.org/articles/PMC10464871; pdf:https://europepmc.org/articles/PMC10464871?pdf=render
 36941845,https://doi.org/10.1016/j.xkme.2023.100613,"Cognitive Impairment, Frailty, and Adverse Outcomes Among Prevalent Hemodialysis Recipients: Results From a Large Prospective Cohort Study in the United Kingdom.","Anderson BM, Qasim M, Correa G, Evison F, Gallier S, Ferro CJ, Jackson TA, Sharif A.",,Kidney medicine,2023,2023-02-09,Y,Mortality; Frailty; Dementia; Cognitive impairment; epidemiology; hemodialysis; Hospitalization; End-stage Kidney Disease,,,"<h4>Rationale & objective</h4>Frailty and cognitive impairment are common in hemodialysis recipients and have been associated with high mortality. There is considerable heterogeneity in frailty reporting, with little comparison between commonly used frailty tools and little exploration of the interplay between cognition and frailty. The aims were to explore the relationship between frailty scores and cognition and their associations with hospitalization and mortality.<h4>Study design</h4>Prospective cohort study.<h4>Setting & population</h4>Prevalent hemodialysis recipients linked to national datasets for hospitalization and mortality.<h4>Predictors</h4>Montreal Cognitive Assessment (MoCA), Frailty Phenotype, Frailty Index (FI), Edmonton Frailty Scale, and Clinical Frailty Scale (CFS) were performed at baseline. Cognitive impairment was defined as MoCA scores of <26, or <21 in dexterity impairment, <18 in visual impairment.<h4>Outcomes</h4>Mortality, hospitalization.<h4>Analytical approach</h4>Cox proportional hazards model for mortality, censored for end of follow-up. Negative binomial regression for admission rates, censored for death/end of follow-up.<h4>Results</h4>In total, 448 participants were recruited with valid MoCAs and followed up for a median of 685 days. There were 103 (23%) deaths and 1,120 admissions of at least one night. Cognitive impairment was identified in 346 (77.2%) participants. Increasing frailty by all definitions was associated with poorer cognition. Cognition was not associated with mortality (HR, 0.99; 95% CI, 0.95-1.03; <i>P</i> = 0.41) or hospitalization (IRR, 1.01; 95% CI, 0.99-1.04; <i>P</i> = 0.39) on multivariable analyses. There were interactions between MoCA scores and increasing frailty by FI (<i>P</i> = 0.002) and Clinical Frailty Scale (<i>P</i> = 0.005); admissions were highest when both MoCA and frailty scores were high, and when both scores were low.<h4>Limitations</h4>As frailty is a dynamic state, a single cross-sectional assessment may not accurately reflect its year-to-year variability. In addition, these findings are in maintenance dialysis and may not be transferable to incident hemodialysis. There were small variations in application of frailty tool criteria from other studies, which may have influenced the results.<h4>Conclusions</h4>Cognitive impairment is highly prevalent in this hemodialysis cohort. The interaction between cognition and frailty on rates of admission suggests the MoCA offers value in identifying higher risk hemodialysis populations with both high and low degrees of frailty.",,pdf:http://www.kidneymedicinejournal.org/article/S2590059523000213/pdf; doi:https://doi.org/10.1016/j.xkme.2023.100613; html:https://europepmc.org/articles/PMC10024232; pdf:https://europepmc.org/articles/PMC10024232?pdf=render
 37815053,https://doi.org/10.1161/jaha.123.029552,Lipoprotein Characteristics and Incident Coronary Heart Disease: Prospective Cohort of Nearly 90 000 Individuals in UK Biobank.,"Jin D, Trichia E, Islam N, Bešević J, Lewington S, Lacey B.",,Journal of the American Heart Association,2023,2023-10-10,Y,Apolipoproteins; Cholesterol; Nuclear magnetic resonance; Lipoproteins; Triglycerides; Coronary Heart Disease; Uk biobank,,,"Background Associations of coronary heart disease (CHD) with plasma lipids are well described, but the associations with characteristics of lipoproteins (which transport lipids) remain unclear. Methods and Results UK Biobank is a prospective study of 0.5 million adults. Analyses were restricted to 89 422 participants with plasma lipoprotein and apolipoprotein measures from Nightingale nuclear magnetic resonance spectroscopy and without CHD at baseline. CHD risk was positively associated with concentrations of very-low-density lipoproteins, intermediate-density lipoproteins, and low-density lipoproteins (LDL), and inversely associated with high-density lipoproteins. Hazard ratios (99% CIs) per SD were 1.22 (1.17-1.28), 1.16 (1.11-1.21), 1.20 (1.15-1.25), and 0.90 (0.86-0.95), respectively. Larger subclasses of very-low-density lipoproteins were less strongly associated with CHD risk, but associations did not materially vary by size of LDL or high-density lipoprotein. Given lipoprotein particle concentrations, lipid composition (including cholesterol) was not strongly related to CHD risk, except for triglyceride in LDL particles. Apolipoprotein B was highly correlated with LDL concentration (<i>r</i>=0.99), but after adjustment for apolipoprotein B, concentrations of very-low-density lipoprotein and high-density lipoprotein particles remained strongly related to CHD risk. Conclusions This large-scale study reliably quantifies the associations of nuclear magnetic resonance-defined lipoprotein characteristics with CHD risk. CHD risk was most strongly related to particle concentrations, and separate measurements of lipoprotein concentrations may be of greater value than the measurement by apolipoprotein B, which was largely determined by LDL concentration alone. Furthermore, there was strong evidence of positive association with mean triglyceride molecules per LDL particle but little evidence of associations with total triglycerides or other lipid and lipoprotein fractions after accounting for lipoprotein concentrations.",,doi:https://doi.org/10.1161/JAHA.123.029552; html:https://europepmc.org/articles/PMC10757541; pdf:https://europepmc.org/articles/PMC10757541?pdf=render
-37346822,https://doi.org/10.12688/wellcomeopenres.18735.2,First dose COVID-19 vaccine coverage amongst adolescents and children in England: an analysis of 3.21 million patients' primary care records in situ using OpenSAFELY.,"Hopcroft LE, Curtis HJ, Brown AD, Hulme WJ, Andrews CD, Morton CE, Inglesby P, Morley J, Mehrkar A, Bacon SC, Eggo RM, Mahalingasivam V, Parker EPK, Tomlinson LA, Bates C, Cockburn J, Parry J, Hester F, Harper S, Goldacre B, Walker AJ, MacKenna B.",,Wellcome open research,2023,2023-06-09,Y,Vaccine; Primary Health Care; Public Health; Covid-19,,,"<b>Background:</b> The coronavirus disease 2019 (COVID-19) vaccination programme in England was extended to include all adolescents and children by April 2022. The aim of this paper is to describe trends and variation in vaccine coverage in different clinical and demographic groups amongst adolescents and children in England by August 2022. <b>Methods:</b> With the approval of NHS England, a cohort study was conducted of 3.21 million children and adolescents' records in general practice in England,  <i>in situ</i> and within the infrastructure of the electronic health record software vendor TPP using OpenSAFELY. Vaccine coverage across various demographic (sex, deprivation index and ethnicity) and clinical (risk status) populations is described. <b>Results:</b> Coverage is higher amongst adolescents than it is amongst children, with 53.5% adolescents and 10.8% children having received their first dose of the COVID-19 vaccine. Within those groups, coverage varies by ethnicity, deprivation index and risk status; there is no evidence of variation by sex. <b>Conclusion:</b> First dose COVID-19 vaccine coverage is shown to vary amongst various demographic and clinical groups of children and adolescents.",,doi:https://doi.org/10.12688/wellcomeopenres.18735.2; html:https://europepmc.org/articles/PMC10280033; pdf:https://europepmc.org/articles/PMC10280033?pdf=render
 32565483,https://doi.org/10.1136/bmjopen-2020-039097,Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II): protocol for an observational study using linked Scottish national data.,"Simpson CR, Robertson C, Vasileiou E, McMenamin J, Gunson R, Ritchie LD, Woolhouse M, Morrice L, Kelly D, Stagg HR, Marques D, Murray J, Sheikh A.",,BMJ open,2020,2020-06-21,Y,epidemiology; Public Health; Respiratory Medicine (See Thoracic Medicine),,,"<h4>Introduction</h4>Following the emergence of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019 and the ensuing COVID-19 pandemic, population-level surveillance and rapid assessment of the effectiveness of existing or new therapeutic or preventive interventions are required to ensure that interventions are targeted to those at highest risk of serious illness or death from COVID-19. We aim to repurpose and expand an existing pandemic reporting platform to determine the attack rate of SARS-CoV-2, the uptake and effectiveness of any new pandemic vaccine (once available) and any protective effect conferred by existing or new antimicrobial drugs and other therapies.<h4>Methods and analysis</h4>A prospective observational cohort will be used to monitor daily/weekly the progress of the COVID-19 epidemic and to evaluate the effectiveness of therapeutic interventions in approximately 5.4 million individuals registered in general practices across Scotland. A national linked dataset of patient-level primary care data, out-of-hours, hospitalisation, mortality and laboratory data will be assembled. The primary outcomes will measure association between: (A) laboratory confirmed SARS-CoV-2 infection, morbidity and mortality, and demographic, socioeconomic and clinical population characteristics; and (B) healthcare burden of COVID-19 and demographic, socioeconomic and clinical population characteristics. The secondary outcomes will estimate: (A) the uptake (for vaccines only); (B) effectiveness; and (C) safety of new or existing therapies, vaccines and antimicrobials against SARS-CoV-2 infection. The association between population characteristics and primary outcomes will be assessed via multivariate logistic regression models. The effectiveness of therapies, vaccines and antimicrobials will be assessed from time-dependent Cox models or Poisson regression models. Self-controlled study designs will be explored to estimate the risk of therapeutic and prophylactic-related adverse events.<h4>Ethics and dissemination</h4>We obtained approval from the National Research Ethics Service Committee, Southeast Scotland 02. The study findings will be presented at international conferences and published in peer-reviewed journals.",,pdf:https://bmjopen.bmj.com/content/bmjopen/10/6/e039097.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-039097; html:https://europepmc.org/articles/PMC7311023; pdf:https://europepmc.org/articles/PMC7311023?pdf=render
-38106617,https://doi.org/10.1016/j.patter.2023.100892,Mortality prediction with adaptive feature importance recalibration for peritoneal dialysis patients.,"Ma L, Zhang C, Gao J, Jiao X, Yu Z, Zhu Y, Wang T, Ma X, Wang Y, Tang W, Zhao X, Ruan W, Wang T.",,"Patterns (New York, N.Y.)",2023,2023-12-08,Y,Peritoneal dialysis; PD; End-stage Renal Disease; Electronic Medical Record; Emr; Esrd; Mortality Prediction; Deep Learning; Model Interpretability,,,"The study aims to develop AICare, an interpretable mortality prediction model, using electronic medical records (EMR) from follow-up visits for end-stage renal disease (ESRD) patients. AICare includes a multichannel feature extraction module and an adaptive feature importance recalibration module. It integrates dynamic records and static features to perform personalized health context representation learning. The dataset encompasses 13,091 visits and demographic data of 656 peritoneal dialysis (PD) patients spanning 12 years. An additional public dataset of 4,789 visits from 1,363 hemodialysis (HD) patients is also considered. AICare outperforms traditional deep learning models in mortality prediction while retaining interpretability. It uncovers mortality-feature relationships and variations in feature importance and provides reference values. An AI-doctor interaction system is developed for visualizing patients' health trajectories and risk indicators.",,pdf:http://www.cell.com/article/S2666389923002945/pdf; doi:https://doi.org/10.1016/j.patter.2023.100892; html:https://europepmc.org/articles/PMC10724364; pdf:https://europepmc.org/articles/PMC10724364?pdf=render
+37346822,https://doi.org/10.12688/wellcomeopenres.18735.2,First dose COVID-19 vaccine coverage amongst adolescents and children in England: an analysis of 3.21 million patients' primary care records in situ using OpenSAFELY.,"Hopcroft LE, Curtis HJ, Brown AD, Hulme WJ, Andrews CD, Morton CE, Inglesby P, Morley J, Mehrkar A, Bacon SC, Eggo RM, Mahalingasivam V, Parker EPK, Tomlinson LA, Bates C, Cockburn J, Parry J, Hester F, Harper S, Goldacre B, Walker AJ, MacKenna B.",,Wellcome open research,2023,2023-06-09,Y,Vaccine; Primary Health Care; Public Health; Covid-19,,,"<b>Background:</b> The coronavirus disease 2019 (COVID-19) vaccination programme in England was extended to include all adolescents and children by April 2022. The aim of this paper is to describe trends and variation in vaccine coverage in different clinical and demographic groups amongst adolescents and children in England by August 2022. <b>Methods:</b> With the approval of NHS England, a cohort study was conducted of 3.21 million children and adolescents' records in general practice in England,  <i>in situ</i> and within the infrastructure of the electronic health record software vendor TPP using OpenSAFELY. Vaccine coverage across various demographic (sex, deprivation index and ethnicity) and clinical (risk status) populations is described. <b>Results:</b> Coverage is higher amongst adolescents than it is amongst children, with 53.5% adolescents and 10.8% children having received their first dose of the COVID-19 vaccine. Within those groups, coverage varies by ethnicity, deprivation index and risk status; there is no evidence of variation by sex. <b>Conclusion:</b> First dose COVID-19 vaccine coverage is shown to vary amongst various demographic and clinical groups of children and adolescents.",,doi:https://doi.org/10.12688/wellcomeopenres.18735.2; html:https://europepmc.org/articles/PMC10280033; pdf:https://europepmc.org/articles/PMC10280033?pdf=render
 35050151,https://doi.org/10.3390/metabo12010029,Integration of Metabolomic and Clinical Data Improves the Prediction of Intensive Care Unit Length of Stay Following Major Traumatic Injury.,"Acharjee A, Hazeldine J, Bazarova A, Deenadayalu L, Zhang J, Bentley C, Russ D, Lord JM, Gkoutos GV, Young SP, Foster MA.",,Metabolites,2021,2021-12-31,Y,Inflammation; Metabolomics; Omics Integration; Icu Length Of Stay,,,"Recent advances in emergency medicine and the co-ordinated delivery of trauma care mean more critically-injured patients now reach the hospital alive and survive life-saving operations. Indeed, between 2008 and 2017, the odds of surviving a major traumatic injury in the UK increased by nineteen percent. However, the improved survival rates of severely-injured patients have placed an increased burden on the healthcare system, with major trauma a common cause of intensive care unit (ICU) admissions that last ≥10 days. Improved understanding of the factors influencing patient outcomes is now urgently needed. We investigated the serum metabolomic profile of fifty-five major trauma patients across three post-injury phases: acute (days 0-4), intermediate (days 5-14) and late (days 15-112). Using ICU length of stay (LOS) as a clinical outcome, we aimed to determine whether the serum metabolome measured at days 0-4 post-injury for patients with an extended (≥10 days) ICU LOS differed from that of patients with a short (<10 days) ICU LOS. In addition, we investigated whether combining metabolomic profiles with clinical scoring systems would generate a variable that would identify patients with an extended ICU LOS with a greater degree of accuracy than models built on either variable alone. The number of metabolites unique to and shared across each time segment varied across acute, intermediate and late segments. A one-way ANOVA revealed the most variation in metabolite levels across the different time-points was for the metabolites lactate, glucose, anserine and 3-hydroxybutyrate. A total of eleven features were selected to differentiate between <10 days ICU LOS vs. >10 days ICU LOS. New Injury Severity Score (NISS), testosterone, and the metabolites cadaverine, urea, isoleucine, acetoacetate, dimethyl sulfone, syringate, creatinine, xylitol, and acetone form the integrated biomarker set. Using metabolic enrichment analysis, we found valine, leucine and isoleucine biosynthesis, glutathione metabolism, and glycine, serine and threonine metabolism were the top three pathways differentiating ICU LOS with a <i>p</i> < 0.05. A combined model of NISS and testosterone and all nine selected metabolites achieved an AUROC of 0.824. Differences exist in the serum metabolome of major trauma patients who subsequently experience a short or prolonged ICU LOS in the acute post-injury setting. Combining metabolomic data with anatomical scoring systems allowed us to discriminate between these two groups with a greater degree of accuracy than that of either variable alone.",,pdf:https://www.mdpi.com/2218-1989/12/1/29/pdf?version=1642410547; doi:https://doi.org/10.3390/metabo12010029; html:https://europepmc.org/articles/PMC8780653; pdf:https://europepmc.org/articles/PMC8780653?pdf=render
+38106617,https://doi.org/10.1016/j.patter.2023.100892,Mortality prediction with adaptive feature importance recalibration for peritoneal dialysis patients.,"Ma L, Zhang C, Gao J, Jiao X, Yu Z, Zhu Y, Wang T, Ma X, Wang Y, Tang W, Zhao X, Ruan W, Wang T.",,"Patterns (New York, N.Y.)",2023,2023-12-08,Y,Peritoneal dialysis; PD; End-stage Renal Disease; Electronic Medical Record; Emr; Esrd; Mortality Prediction; Deep Learning; Model Interpretability,,,"The study aims to develop AICare, an interpretable mortality prediction model, using electronic medical records (EMR) from follow-up visits for end-stage renal disease (ESRD) patients. AICare includes a multichannel feature extraction module and an adaptive feature importance recalibration module. It integrates dynamic records and static features to perform personalized health context representation learning. The dataset encompasses 13,091 visits and demographic data of 656 peritoneal dialysis (PD) patients spanning 12 years. An additional public dataset of 4,789 visits from 1,363 hemodialysis (HD) patients is also considered. AICare outperforms traditional deep learning models in mortality prediction while retaining interpretability. It uncovers mortality-feature relationships and variations in feature importance and provides reference values. An AI-doctor interaction system is developed for visualizing patients' health trajectories and risk indicators.",,pdf:http://www.cell.com/article/S2666389923002945/pdf; doi:https://doi.org/10.1016/j.patter.2023.100892; html:https://europepmc.org/articles/PMC10724364; pdf:https://europepmc.org/articles/PMC10724364?pdf=render
 35910710,https://doi.org/10.1093/rap/rkac056,Real-world use of an etanercept biosimilar including selective <i>versus</i> automatic substitution in inflammatory arthritis patients: a UK-based electronic health records study.,"Cooksey R, Brophy S, Kennedy J, Seaborne M, Choy E.",,Rheumatology advances in practice,2022,2022-07-27,Y,RA; As; PSA; Etanercept; Biosimilars,,,"<h4>Objective</h4>Biosimilars are approved as an alternative treatment to their originators. We compared the clinical outcomes of etanercept (ETN) biosimilar compared with ETN originator in real-world practice, from two local health boards in Wales with different policies on switching: automatic <i>vs</i> selective.<h4>Methods</h4>Data from the Secure Anonymised Information Linkage (SAIL) databank in Wales were used to create a retrospective cohort study using linked primary and secondary care data. Patients aged ≥18 years with diagnosis codes for RA, PsA or AS were included. Outcomes included treatment failure and DAS-28 score (for RA). The local health board with a policy of automatic switching (i.e. clinician/nurse involvement not mandated) is labelled as automatic switch area, and the other, which required clinician/nurse supervision, as selective switch.<h4>Results</h4>Of 8925 individuals with inflammatory arthritis, 13.3% (365) received ETN biosimilar and 31.5% (863) ETN originator. The treatment discontinuation rate was similar for ETN biosimilar and originator by Kaplan-Meier analysis. More biosimilar failure patients were treated in the automatic switch area (15 <i>vs</i> 4.8%). In the automatic switch area, 28.8% (75 of 260) of patients switched automatically from ETN originator to biosimilar compared with 10.5% (11 of 105) in the selective switch area. ETN biosimilar reduced DAS-28 by 1.6 ± 1.8 in the selective switch area <i>vs</i> 0.4 ± 0.6 in the automatic switch area.<h4>Conclusion</h4>The ETN biosimilar was well tolerated. Fewer people were switched using selective policy, but this was associated with lower failure rates. Automatic switch policy led to more patients being switched and did not lead to significant worsening of disease.",,pdf:https://academic.oup.com/rheumap/advance-article-pdf/doi/10.1093/rap/rkac056/45095148/rkac056.pdf; doi:https://doi.org/10.1093/rap/rkac056; html:https://europepmc.org/articles/PMC9336562; pdf:https://europepmc.org/articles/PMC9336562?pdf=render
 31878916,https://doi.org/10.1186/s12889-019-7919-2,Sustained adherence to a Mediterranean diet and physical activity on all-cause mortality in the Melbourne Collaborative Cohort Study: application of the g-formula.,"Williamson EJ, Polak J, Simpson JA, Giles GG, English DR, Hodge A, Gurrin L, Forbes AB.",,BMC public health,2019,2019-12-26,Y,G-computation; Time-varying Confounding; Parametric G-formula; G-methods,"Improving Public Health, Understanding the Causes of Disease",,"<h4>Background</h4>Adherence to a traditional Mediterranean diet has been associated with lower mortality and cardiovascular disease risk. The relative importance of diet compared to other lifestyle factors and effects of dietary patterns over time remains unknown.<h4>Methods</h4>We used the parametric G-formula to account for time-dependent confounding, in order to assess the relative importance of diet compared to other lifestyle factors and effects of dietary patterns over time. We included healthy Melbourne Collaborative Cohort Study participants attending a visit during 1995-1999. Questionnaires assessed diet and physical activity at each of three study waves. Deaths were identified by linkage to national registries. We estimated mortality risk over approximately 14 years (1995-2011).<h4>Results</h4>Of 22,213 participants, 2163 (9.7%) died during 13.6 years median follow-up. Sustained high physical activity and adherence to a Mediterranean-style diet resulted in an estimated reduction in all-cause mortality of 1.82 per 100 people (95% confidence interval (CI): 0.03, 3.6). The population attributable fraction was 13% (95% CI: 4, 23%) for sustained high physical activity, 7% (95% CI: - 3, 17%) for sustained adherence to a Mediterranean-style diet and 18% (95% CI: 0, 36%) for their combination.<h4>Conclusions</h4>A small reduction in mortality may be achieved by sustained elevated physical activity levels in healthy middle-aged adults, but there may be comparatively little gain from increasing adherence to a Mediterranean-style diet.",This study aimed to calculate the proportion of deaths that could be prevented over a 14 year period through making long-term changes in lifestyle (diet and physical activity). Over 22K people were included in the study and filled out questionnaires about their lifestyle at three different time points. The authors used statistical methods that take into account how lifestyle measurements change over time and estimated the relative impact that different lifestyle factors have on death. The study suggests that being more physically active in middle age is more likely to reduce mortality than maintaining a Mediterranean-style diet.,pdf:https://bmcpublichealth.biomedcentral.com/track/pdf/10.1186/s12889-019-7919-2; doi:https://doi.org/10.1186/s12889-019-7919-2; html:https://europepmc.org/articles/PMC6933918; pdf:https://europepmc.org/articles/PMC6933918?pdf=render
 32989456,https://doi.org/10.1093/ije/dyaa144,Emulating a target trial in case-control designs: an application to statins and colorectal cancer.,"Dickerman BA, García-Albéniz X, Logan RW, Denaxas S, Hernán MA.",,International journal of epidemiology,2020,2020-10-01,N,Causal Inference; Electronic Health Records; Case-control; Comparative Effectiveness; Target Trial,,,"<h4>Background</h4>Previous case-control studies have reported a strong association between statin use and lower cancer risk. It is unclear whether this association reflects a benefit of statins or is the result of design decisions that cannot be mapped to a (hypothetical) target trial (that would answer the question of interest).<h4>Methods</h4>We outlined the protocol of a target trial to estimate the effect of statins on colorectal cancer incidence among adults with low-density lipoprotein (LDL) cholesterol below 5 mmol/L. We then emulated the target trial using linked electronic health records of 752 469 eligible UK adults (CALIBER 1999-2016) under both a cohort design and a case-control sampling of the cohort. We used pooled logistic regression to estimate intention-to-treat and per-protocol effects of statins on colorectal cancer, with adjustment for baseline and time-varying risk factors via inverse-probability weighting. Finally, we compared our case-control effect estimates with those obtained using previous case-control procedures.<h4>Results</h4>Over the 6-year follow-up, 3596 individuals developed colorectal cancer. Estimated intention-to-treat and per-protocol hazard ratios were 1.00 (95% confidence interval [CI]: 0.87, 1.16) and 0.90 (95% CI: 0.71, 1.12), respectively. As expected, adequate case-control sampling yielded the same estimates. By contrast, previous case-control analytical approaches yielded estimates that appeared strongly protective (odds ratio 0.57, 95% CI: 0.36, 0.91, for ≥5 vs. <5 years of statin use).<h4>Conclusions</h4>Our study demonstrates how to explicitly emulate a target trial using case-control data to reduce discrepancies between observational and randomized trial evidence. This approach may inform future case-control analyses for comparative effectiveness research.",,pdf:https://academic.oup.com/ije/article-pdf/49/5/1637/34947124/dyaa144.pdf; doi:https://doi.org/10.1093/ije/dyaa144; html:https://europepmc.org/articles/PMC7746409; pdf:https://europepmc.org/articles/PMC7746409?pdf=render; doi:https://doi.org/10.1093/ije/dyaa144
-38444664,https://doi.org/10.1183/23120541.00010-2024,Development and evaluation of a tool to optimise inhaler selection prior to hospital discharge following an exacerbation of COPD.,"Price E, Ahmad S, Althobiani MA, Ayoob T, Burgoyne T, De Soyza A, Dobson M, Echevarria C, Martin G, Mendes RG, Preston AM, Rahman NM, Sapey E, Usmani OS, Hurst JR.",,ERJ open research,2024,2024-03-04,N,,,,"<h4>Introduction</h4>Rates of mortality and re-admission after a hospitalised exacerbation of COPD are high and resistant to change. COPD guidelines do not give practical advice about the optimal selection of inhaled drugs and device in this situation. We hypothesised that a failure to optimise inhaled drug and drug delivery prior to discharge from hospital after an exacerbation would be associated with a modifiable increased risk of re-admission and death. We designed a study to 1) develop a practical inhaler selection tool to use at the point of hospital discharge and 2) implement this tool to understand the potential impact on modifying inhaler prescriptions, clinical outcomes, acceptability to clinicians and patients, and the feasibility of delivering a definitive trial to demonstrate potential benefit.<h4>Methods</h4>We iteratively developed an inhaler selection tool for use prior to discharge following a hospitalised exacerbation of COPD using surveys with multiprofessional clinicians and a focus group of people living with COPD. We surveyed clinicians to understand their views on the minimum clinically important difference (MCID) for death and re-admission following a hospitalised exacerbation of COPD. We conducted a mixed-methods implementation feasibility study using the tool at discharge, and collated 30- and 90-day follow-up data including death and re-admissions. Additionally, we observed the tool being used and interviewed clinicians and patients about use of the tool in this setting.<h4>Results</h4>We completed the design of an inhaler selection tool through two rounds of consultations with 94 multiprofessional clinicians, and a focus group of four expert patients. Regarding MCIDs, there was majority consensus for the following reductions from baseline being the MCID: 30-day readmissions 5-10%, 90-day readmissions 10-20%, 30-day mortality 5-10% and 90-day mortality 5-10%. 118 patients were assessed for eligibility and 26 had the tool applied. A change in inhaled medication was recommended in nine (35%) out of 26. Re-admission or death at 30 days was seen in 33% of the switch group and 35% of the no-switch group. Re-admission or death at 90 days was seen in 56% of the switch group and 41% of the no-switch group. Satisfaction with inhalers was generally high, and switching was associated with a small increase in the Feeling of Satisfaction with Inhaler questionnaire of 3 out of 50 points. Delivery of a definitive study would be challenging.<h4>Conclusion</h4>We completed a mixed-methods study to design and implement a tool to aid optimisation of inhaled pharmacotherapy prior to discharge following a hospitalised exacerbation of COPD. This was not associated with fewer re-admissions, but was well received and one-third of people were eligible for a change in inhalers.",,doi:https://doi.org/10.1183/23120541.00010-2024
 34977922,https://doi.org/10.1093/ije/dyab243,Cohort Profile: The COVID-19 in Pregnancy in Scotland (COPS) dynamic cohort of pregnant women to assess effects of viral and vaccine exposures on pregnancy.,"Stock SJ, Carruthers J, Denny C, Donaghy J, Goulding A, Hopcroft LEM, Hopkins L, Mulholland R, Agrawal U, Auyeung B, Katikireddi SV, McCowan C, Murray J, Robertson C, Sheikh A, Shi T, Simpson CR, Vasileiou E, Wood R.",,International journal of epidemiology,2022,2022-10-01,Y,,,,,,pdf:https://academic.oup.com/ije/article-pdf/51/5/e245/46495259/dyab243.pdf; doi:https://doi.org/10.1093/ije/dyab243; html:https://europepmc.org/articles/PMC9557859; pdf:https://europepmc.org/articles/PMC9557859?pdf=render
+38444664,https://doi.org/10.1183/23120541.00010-2024,Development and evaluation of a tool to optimise inhaler selection prior to hospital discharge following an exacerbation of COPD.,"Price E, Ahmad S, Althobiani MA, Ayoob T, Burgoyne T, De Soyza A, Dobson M, Echevarria C, Martin G, Mendes RG, Preston AM, Rahman NM, Sapey E, Usmani OS, Hurst JR.",,ERJ open research,2024,2024-03-04,N,,,,"<h4>Introduction</h4>Rates of mortality and re-admission after a hospitalised exacerbation of COPD are high and resistant to change. COPD guidelines do not give practical advice about the optimal selection of inhaled drugs and device in this situation. We hypothesised that a failure to optimise inhaled drug and drug delivery prior to discharge from hospital after an exacerbation would be associated with a modifiable increased risk of re-admission and death. We designed a study to 1) develop a practical inhaler selection tool to use at the point of hospital discharge and 2) implement this tool to understand the potential impact on modifying inhaler prescriptions, clinical outcomes, acceptability to clinicians and patients, and the feasibility of delivering a definitive trial to demonstrate potential benefit.<h4>Methods</h4>We iteratively developed an inhaler selection tool for use prior to discharge following a hospitalised exacerbation of COPD using surveys with multiprofessional clinicians and a focus group of people living with COPD. We surveyed clinicians to understand their views on the minimum clinically important difference (MCID) for death and re-admission following a hospitalised exacerbation of COPD. We conducted a mixed-methods implementation feasibility study using the tool at discharge, and collated 30- and 90-day follow-up data including death and re-admissions. Additionally, we observed the tool being used and interviewed clinicians and patients about use of the tool in this setting.<h4>Results</h4>We completed the design of an inhaler selection tool through two rounds of consultations with 94 multiprofessional clinicians, and a focus group of four expert patients. Regarding MCIDs, there was majority consensus for the following reductions from baseline being the MCID: 30-day readmissions 5-10%, 90-day readmissions 10-20%, 30-day mortality 5-10% and 90-day mortality 5-10%. 118 patients were assessed for eligibility and 26 had the tool applied. A change in inhaled medication was recommended in nine (35%) out of 26. Re-admission or death at 30 days was seen in 33% of the switch group and 35% of the no-switch group. Re-admission or death at 90 days was seen in 56% of the switch group and 41% of the no-switch group. Satisfaction with inhalers was generally high, and switching was associated with a small increase in the Feeling of Satisfaction with Inhaler questionnaire of 3 out of 50 points. Delivery of a definitive study would be challenging.<h4>Conclusion</h4>We completed a mixed-methods study to design and implement a tool to aid optimisation of inhaled pharmacotherapy prior to discharge following a hospitalised exacerbation of COPD. This was not associated with fewer re-admissions, but was well received and one-third of people were eligible for a change in inhalers.",,doi:https://doi.org/10.1183/23120541.00010-2024
 36526319,https://doi.org/10.1136/bmjopen-2022-064910,Performance of scoring systems in selecting short stay medical admissions suitable for assessment in same day emergency care: an analysis of diagnostic accuracy in a UK hospital setting.,"Atkin C, Gallier S, Wallin E, Reddy-Kolanu V, Sapey E.",,BMJ open,2022,2022-12-16,Y,Internal Medicine; General Medicine (See Internal Medicine); Organisation Of Health Services,,,"<h4>Objectives</h4>To assess the performance of the Amb score and Glasgow Admission Prediction Score (GAPS) in identifying acute medical admissions suitable for same day emergency care (SDEC) in a large urban secondary centre.<h4>Design</h4>Retrospective assessment of routinely collected data from electronic healthcare records.<h4>Setting</h4>Single large urban tertiary care centre.<h4>Participants</h4>All unplanned admissions to general medicine on Monday-Friday, episodes starting 08:00-16:59 hours and lasting up to 48 hours, between 1 April 2019 and 9 March 2020.<h4>Main outcome measures</h4>Sensitivity, specificity, positive and negative predictive value of the Amb score and GAPS in identifying patients discharged within 12 hours of arrival.<h4>Results</h4>7365 episodes were assessed. 94.6% of episodes had an Amb score suggesting suitability for SDEC. The positive predictive value of the Amb score in identifying those discharged within 12 hours was 54.5% (95% CI 53.3% to 55.8%). The area under the receiver operating characteristic curve (AUROC) for the Amb score was 0.612 (95% CI 0.599 to 0.625).42.4% of episodes had a GAPS suggesting suitability for SDEC. The positive predictive value of the GAPS in identifying those discharged within 12 hours was 50.5% (95% CI 48.4% to 52.7%). The AUROC for the GAPS was 0.606 (95% CI 0.590 to 0.622).41.4% of the population had both an Amb and GAPS score suggestive of suitability for SDEC and 5.7% of the population had both and Amb and GAPS score suggestive of a lack of suitability for SDEC.<h4>Conclusions</h4>The Amb score and GAPS had poor discriminatory ability to identify acute medical admissions suitable for discharge within 12 hours, limiting their utility in selecting patients for assessment within SDEC services within this diverse patient population.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/12/e064910.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-064910; html:https://europepmc.org/articles/PMC9764605; pdf:https://europepmc.org/articles/PMC9764605?pdf=render
 PMC10910267,https://doi.org/,Development and evaluation of a tool to optimise inhaler selection prior to hospital discharge following an exacerbation of COPD,"Price E, Ahmad S, Althobiani M, Ayoob T, Burgoyne T, De Soyza A, Dobson M, Echevarria C, Martin G, Mendes R, Preston A, Rahman N, Sapey E, Usmani O, Hurst J.",,ERJ open research,2024,2024-03-01,Y,,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10910267/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10910267/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC10910267; pdf:https://europepmc.org/articles/PMC10910267?pdf=render
 36219788,https://doi.org/10.1093/ije/dyac185,Borrowing strength from clinical trials in analysing longitudinal data from a treated cohort: investigating the effectiveness of acetylcholinesterase inhibitors in the management of dementia.,"Knight R, Stewart R, Khondoker M, Landau S.",,International journal of epidemiology,2023,2023-06-01,Y,Cognition; Dementia; Randomized controlled trial; acetylcholinesterase inhibitors; Electronic Medical Record; Bayesian Modelling,,,"<h4>Background</h4>Health care professionals seek information about effectiveness of treatments in patients who would be offered them in routine clinical practice. Electronic medical records (EMRs) and randomized controlled trials (RCTs) can both provide data on treatment effects; however, each data source has limitations when considered in isolation.<h4>Methods</h4>A novel modelling methodology which incorporates RCT estimates in the analysis of EMR data via informative prior distributions is proposed. A Bayesian mixed modelling approach is used to model outcome trajectories among patients in the EMR dataset receiving the treatment of interest. This model incorporates an estimate of treatment effect based on a meta-analysis of RCTs as an informative prior distribution. This provides a combined estimate of treatment effect based on both data sources.<h4>Results</h4>The superior performance of the novel combined estimator is demonstrated via a simulation study. The new approach is applied to estimate the effectiveness at 12 months after treatment initiation of acetylcholinesterase inhibitors in the management of the cognitive symptoms of dementia in terms of Mini-Mental State Examination scores. This demonstrated that estimates based on either trials data only (1.10, SE = 0.316) or cohort data only (1.56, SE = 0.240) overestimated this compared with the estimate using data from both sources (0.86, SE = 0.327).<h4>Conclusions</h4>It is possible to combine data from EMRs and RCTs in order to provide better estimates of treatment effectiveness.",,pdf:https://academic.oup.com/ije/advance-article-pdf/doi/10.1093/ije/dyac185/47708280/dyac185.pdf; doi:https://doi.org/10.1093/ije/dyac185; html:https://europepmc.org/articles/PMC10244047; pdf:https://europepmc.org/articles/PMC10244047?pdf=render
-39009776,https://doi.org/10.1038/s41591-024-03094-4,Consumer wearable devices for evaluation of heart rate control using digoxin versus beta-blockers: the RATE-AF randomized trial.,"Gill SK, Barsky A, Guan X, Bunting KV, Karwath A, Tica O, Stanbury M, Haynes S, Folarin A, Dobson R, Kurps J, Asselbergs FW, Grobbee DE, Camm AJ, Eijkemans MJC, Gkoutos GV, Kotecha D, BigData@Heart Consortium, cardAIc group, RATE-AF trial team.",,Nature medicine,2024,2024-07-15,Y,,,,"Consumer-grade wearable technology has the potential to support clinical research and patient management. Here, we report results from the RATE-AF trial wearables study, which was designed to compare heart rate in older, multimorbid patients with permanent atrial fibrillation and heart failure who were randomized to treatment with either digoxin or beta-blockers. Heart rate (n = 143,379,796) and physical activity (n = 23,704,307) intervals were obtained from 53 participants (mean age 75.6 years (s.d. 8.4), 40% women) using a wrist-worn wearable linked to a smartphone for 20 weeks. Heart rates in participants treated with digoxin versus beta-blockers were not significantly different (regression coefficient 1.22 (95% confidence interval (CI) -2.82 to 5.27; P = 0.55); adjusted 0.66 (95% CI -3.45 to 4.77; P = 0.75)). No difference in heart rate was observed between the two groups of patients after accounting for physical activity (P = 0.74) or patients with high activity levels (≥30,000 steps per week; P = 0.97). Using a convolutional neural network designed to account for missing data, we found that wearable device data could predict New York Heart Association functional class 5 months after baseline assessment similarly to standard clinical measures of electrocardiographic heart rate and 6-minute walk test (F1 score 0.56 (95% CI 0.41 to 0.70) versus 0.55 (95% CI 0.41 to 0.68); P = 0.88 for comparison). The results of this study indicate that digoxin and beta-blockers have equivalent effects on heart rate in atrial fibrillation at rest and on exertion, and suggest that dynamic monitoring of individuals with arrhythmia using wearable technology could be an alternative to in-person assessment. ClinicalTrials.gov identifier: NCT02391337 .",,doi:https://doi.org/10.1038/s41591-024-03094-4; html:https://europepmc.org/articles/PMC11271403; pdf:https://europepmc.org/articles/PMC11271403?pdf=render
 32635913,https://doi.org/10.1186/s12911-020-01169-z,Application of standardised effect sizes to hospital discharge outcomes for people with diabetes.,"Robbins T, Lim Choi Keung SN, Sankar S, Randeva H, Arvanitis TN.",,BMC medical informatics and decision making,2020,2020-07-07,Y,Mortality; Diabetes; Readmission; Effect Size,,,"<h4>Background</h4>Patients with diabetes are at an increased risk of readmission and mortality when discharged from hospital. Existing research identifies statistically significant risk factors that are thought to underpin these outcomes. Increasingly, these risk factors are being used to create risk prediction models, and target risk modifying interventions. These risk factors are typically reported in the literature accompanied by unstandardized effect sizes, which makes comparisons difficult. We demonstrate an assessment of variation between standardised effect sizes for such risk factors across care outcomes and patient cohorts. Such an approach will support development of more rigorous risk stratification tools and better targeting of intervention measures.<h4>Methods</h4>Data was extracted from the electronic health record of a major tertiary referral centre, over a 3-year period, for all patients discharged from hospital with a concurrent diagnosis of diabetes mellitus. Risk factors selected for extraction were pre-specified according to a systematic review of the research literature. Standardised effect sizes were calculated for all statistically significant risk factors, and compared across patient cohorts and both readmission & mortality outcome measures.<h4>Results</h4>Data was extracted for 46,357 distinct admissions patients, creating a large dataset of approximately 10,281,400 data points. The calculation of standardized effect size measures allowed direct comparison. Effect sizes were noted to be larger for mortality compared to readmission, as well as for being larger for surgical and type 1 diabetes cohorts of patients.<h4>Conclusions</h4>The calculation of standardised effect sizes is an important step in evaluating risk factors for healthcare events. This will improve our understanding of risk and support the development of more effective risk stratification tools to support patients to make better informed decisions at discharge from hospital.",,pdf:https://bmcmedinformdecismak.biomedcentral.com/track/pdf/10.1186/s12911-020-01169-z; doi:https://doi.org/10.1186/s12911-020-01169-z; html:https://europepmc.org/articles/PMC7339522; pdf:https://europepmc.org/articles/PMC7339522?pdf=render
-33745917,https://doi.org/10.1016/j.jinf.2021.03.011,"The dynamics of procalcitonin in COVID-19 patients admitted to Intensive care unit - a multi-centre cohort study in the South West of England, UK.","Williams P, McWilliams C, Soomro K, Harding I, Gurney S, Thomas M, Albur M, Martin Williams O.",,The Journal of infection,2021,2021-03-18,Y,,,,,,pdf:http://www.journalofinfection.com/article/S0163445321001286/pdf; doi:https://doi.org/10.1016/j.jinf.2021.03.011; html:https://europepmc.org/articles/PMC7970419; pdf:https://europepmc.org/articles/PMC7970419?pdf=render
 33517931,https://doi.org/10.1192/j.eurpsy.2021.6,"The association between C-reactive protein, mood disorder, and cognitive function in UK Biobank.","Milton DC, Ward J, Ward E, Lyall DM, Strawbridge RJ, Smith DJ, Cullen B.",,European psychiatry : the journal of the Association of European Psychiatrists,2021,2021-02-01,Y,Inflammation; Cognitive function; C-reactive Protein; Mood Disorder,,,"<h4>Background</h4>Systemic inflammation has been linked with mood disorder and cognitive impairment. The extent of this relationship remains uncertain, with the effects of serum inflammatory biomarkers compared to genetic predisposition toward inflammation yet to be clearly established.<h4>Methods</h4>We investigated the magnitude of associations between C-reactive protein (CRP) measures, lifetime history of bipolar disorder or major depression, and cognitive function (reaction time and visuospatial memory) in 84,268 UK Biobank participants. CRP was measured in serum and a polygenic risk score for CRP was calculated, based on a published genome-wide association study. Multiple regression models adjusted for sociodemographic and clinical confounders.<h4>Results</h4>Increased serum CRP was significantly associated with mood disorder history (Kruskal-Wallis H = 196.06, p < 0.001, η2 = 0.002) but increased polygenic risk for CRP was not (F = 0.668, p = 0.648, η2 < 0.001). Compared to the lowest quintile, the highest serum CRP quintile was significantly associated with both negative and positive differences in cognitive performance (fully adjusted models: reaction time B = -0.030, 95% CI = -0.052, -0.008; visuospatial memory B = 0.066, 95% CI = 0.042, 0.089). More severe mood disorder categories were significantly associated with worse cognitive performance and this was not moderated by serum or genetic CRP level.<h4>Conclusions</h4>In this large cohort study, we found that measured inflammation was associated with mood disorder history, but genetic predisposition to inflammation was not. The association between mood disorder and worse cognitive performance was very small and did not vary by CRP level. The inconsistent relationship between CRP measures and cognitive performance warrants further study.",,pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/DAB4F3EAD33B9437269C92D7A0A5DDC4/S0924933821000067a.pdf/div-class-title-the-association-between-c-reactive-protein-mood-disorder-and-cognitive-function-in-uk-biobank-div.pdf; doi:https://doi.org/10.1192/j.eurpsy.2021.6; html:https://europepmc.org/articles/PMC8057439; pdf:https://europepmc.org/articles/PMC8057439?pdf=render
+33745917,https://doi.org/10.1016/j.jinf.2021.03.011,"The dynamics of procalcitonin in COVID-19 patients admitted to Intensive care unit - a multi-centre cohort study in the South West of England, UK.","Williams P, McWilliams C, Soomro K, Harding I, Gurney S, Thomas M, Albur M, Martin Williams O.",,The Journal of infection,2021,2021-03-18,Y,,,,,,pdf:http://www.journalofinfection.com/article/S0163445321001286/pdf; doi:https://doi.org/10.1016/j.jinf.2021.03.011; html:https://europepmc.org/articles/PMC7970419; pdf:https://europepmc.org/articles/PMC7970419?pdf=render
+39009776,https://doi.org/10.1038/s41591-024-03094-4,Consumer wearable devices for evaluation of heart rate control using digoxin versus beta-blockers: the RATE-AF randomized trial.,"Gill SK, Barsky A, Guan X, Bunting KV, Karwath A, Tica O, Stanbury M, Haynes S, Folarin A, Dobson R, Kurps J, Asselbergs FW, Grobbee DE, Camm AJ, Eijkemans MJC, Gkoutos GV, Kotecha D, BigData@Heart Consortium, cardAIc group, RATE-AF trial team.",,Nature medicine,2024,2024-07-15,Y,,,,"Consumer-grade wearable technology has the potential to support clinical research and patient management. Here, we report results from the RATE-AF trial wearables study, which was designed to compare heart rate in older, multimorbid patients with permanent atrial fibrillation and heart failure who were randomized to treatment with either digoxin or beta-blockers. Heart rate (n = 143,379,796) and physical activity (n = 23,704,307) intervals were obtained from 53 participants (mean age 75.6 years (s.d. 8.4), 40% women) using a wrist-worn wearable linked to a smartphone for 20 weeks. Heart rates in participants treated with digoxin versus beta-blockers were not significantly different (regression coefficient 1.22 (95% confidence interval (CI) -2.82 to 5.27; P = 0.55); adjusted 0.66 (95% CI -3.45 to 4.77; P = 0.75)). No difference in heart rate was observed between the two groups of patients after accounting for physical activity (P = 0.74) or patients with high activity levels (≥30,000 steps per week; P = 0.97). Using a convolutional neural network designed to account for missing data, we found that wearable device data could predict New York Heart Association functional class 5 months after baseline assessment similarly to standard clinical measures of electrocardiographic heart rate and 6-minute walk test (F1 score 0.56 (95% CI 0.41 to 0.70) versus 0.55 (95% CI 0.41 to 0.68); P = 0.88 for comparison). The results of this study indicate that digoxin and beta-blockers have equivalent effects on heart rate in atrial fibrillation at rest and on exertion, and suggest that dynamic monitoring of individuals with arrhythmia using wearable technology could be an alternative to in-person assessment. ClinicalTrials.gov identifier: NCT02391337 .",,doi:https://doi.org/10.1038/s41591-024-03094-4; html:https://europepmc.org/articles/PMC11271403; pdf:https://europepmc.org/articles/PMC11271403?pdf=render
 35448463,https://doi.org/10.3390/metabo12040276,MetaboListem and TABoLiSTM: Two Deep Learning Algorithms for Metabolite Named Entity Recognition.,"Yeung CS, Beck T, Posma JM.",,Metabolites,2022,2022-03-22,Y,Natural Language Processing; Named Entity Recognition; Deep Learning,,,"Reviewing the metabolomics literature is becoming increasingly difficult because of the rapid expansion of relevant journal literature. Text-mining technologies are therefore needed to facilitate more efficient literature reviews. Here we contribute a standardised corpus of full-text publications from metabolomics studies and describe the development of two metabolite named entity recognition (NER) methods. These methods are based on Bidirectional Long Short-Term Memory (BiLSTM) networks and each incorporate different transfer learning techniques (for tokenisation and word embedding). Our first model (MetaboListem) follows prior methodology using GloVe word embeddings. Our second model exploits BERT and BioBERT for embedding and is named TABoLiSTM (Transformer-Affixed BiLSTM). The methods are trained on a novel corpus annotated using rule-based methods, and evaluated on manually annotated metabolomics articles. MetaboListem (F1-score 0.890, precision 0.892, recall 0.888) and TABoLiSTM (BioBERT version: F1-score 0.909, precision 0.926, recall 0.893) have achieved state-of-the-art performance on metabolite NER. A training corpus with full-text sentences from >1000 full-text Open Access metabolomics publications with 105,335 annotated metabolites was created, as well as a manually annotated test corpus (19,138 annotations). This work demonstrates that deep learning algorithms are capable of identifying metabolite names accurately and efficiently in text. The proposed corpus and NER algorithms can be used for metabolomics text-mining tasks such as information retrieval, document classification and literature-based discovery and are available from the omicsNLP GitHub repository.",,pdf:https://www.mdpi.com/2218-1989/12/4/276/pdf?version=1647939572; doi:https://doi.org/10.3390/metabo12040276; html:https://europepmc.org/articles/PMC9031427; pdf:https://europepmc.org/articles/PMC9031427?pdf=render
 38435677,https://doi.org/10.1016/j.abst.2023.10.002,Taurine as a biomarker for aging: A new avenue for translational research.,Acharjee A.,,Advances in biomarker sciences and technology,2023,2023-01-01,Y,Biomarker; Diagnostics; Translational Research,,,"The physiologic and irreversible process of ageing is accompanied by a wide range of structural and functional shifts at multiple different levels. It is also suggested that variations in the blood concentrations of metabolites, hormones, and micronutrients may play a role in the ageing process. Recently, Singh et al. <sup>1,2</sup> investigated a study on Taurine shortage as a driver and biomarker of ageing and its impact on a healthy lifespan.<sup>2</sup> They further proposed that functional abnormalities in numerous organs associated with age-related illnesses have been linked to early-life Taurine insufficiency. Taurine deficiency in the elderly and the possible benefits of Taurine supplements One of the reasons for decreasing Taurine concentration is the loss of endogenous synthesis, which may contribute to the decrease in Taurine levels seen in the elderly. While it was previously believed that the liver was responsible for most Taurine synthesis in humans, new research suggests that other organs or common intermediates may play a larger role. The authors experimented with and analysed a life-span examination of various organisms, for example, mice to assess the impacts of Taurine supplementation. They also analysed after the administration of oral Taurine supplementation in conjunction with other interventions using multi-omics data sets (RNA sequencing, metabolomics etc.) across different species.",,doi:https://doi.org/10.1016/j.abst.2023.10.002; html:https://europepmc.org/articles/PMC10901744
 37180154,https://doi.org/10.3389/fimmu.2023.1083072,Real-time assessment of neutrophil metabolism and oxidative burst using extracellular flux analysis.,"Grudzinska FS, Jasper A, Sapey E, Thickett DR, Mauro C, Scott A, Barlow J.",,Frontiers in immunology,2023,2023-04-25,Y,Neutrophils; Oxidative burst; glycolysis; Immunometabolism; Extracellular Flux Analysis,,,"Neutrophil responses are critical during inflammatory and infective events, and neutrophil dysregulation has been associated with poor patient outcomes. Immunometabolism is a rapidly growing field that has provided insights into cellular functions in health and disease. Neutrophils are highly glycolytic when activated, with inhibition of glycolysis associated with functional deficits. There is currently very limited data available assessing metabolism in neutrophils. Extracellular flux (XF) analysis assesses real time oxygen consumption and the rate of proton efflux in cells. This technology allows for the automated addition of inhibitors and stimulants to visualise the effect on metabolism. We describe optimised protocols for an XFe96 XF Analyser to (i) probe glycolysis in neutrophils under basal and stimulated conditions, (ii) probe phorbol 12-myristate 13-acetate induced oxidative burst, and (iii) highlight challenges of using XF technology to examine mitochondrial function in neutrophils. We provide an overview of how to analyze XF data and identify pitfalls of probing neutrophil metabolism with XF analysis. In summary we describe robust methods for assessing glycolysis and oxidative burst in human neutrophils and discuss the challenges around using this technique to assess mitochondrial respiration. XF technology is a powerful platform with a user-friendly interface and data analysis templates, however we suggest caution when assessing neutrophil mitochondrial respiration.",,pdf:https://www.frontiersin.org/articles/10.3389/fimmu.2023.1083072/pdf; doi:https://doi.org/10.3389/fimmu.2023.1083072; html:https://europepmc.org/articles/PMC10166867; pdf:https://europepmc.org/articles/PMC10166867?pdf=render
 38151278,https://doi.org/10.1136/bmjopen-2023-075958,External validation of the QCovid 2 and 3 risk prediction algorithms for risk of COVID-19 hospitalisation and mortality in adults: a national cohort study in Scotland.,"Kerr S, Millington T, Rudan I, McCowan C, Tibble H, Jeffrey K, Fagbamigbe AF, Simpson CR, Robertson C, Hippisley-Cox J, Sheikh A.",,BMJ open,2023,2023-12-27,Y,epidemiology; Health Informatics; Respiratory Medicine (See Thoracic Medicine),,,"<h4>Objective</h4>The QCovid 2 and 3 algorithms are risk prediction tools developed during the second wave of the COVID-19 pandemic that can be used to predict the risk of COVID-19 hospitalisation and mortality, taking vaccination status into account. In this study, we assess their performance in Scotland.<h4>Methods</h4>We used the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 national data platform consisting of individual-level data for the population of Scotland (5.4 million residents). Primary care data were linked to reverse-transcription PCR virology testing, hospitalisation and mortality data. We assessed the discrimination and calibration of the QCovid 2 and 3 algorithms in predicting COVID-19 hospitalisations and deaths between 8 December 2020 and 15 June 2021.<h4>Results</h4>Our validation dataset comprised 465 058 individuals, aged 19-100. We found the following performance metrics (95% CIs) for QCovid 2 and 3: Harrell's C 0.84 (0.82 to 0.86) for hospitalisation, and 0.92 (0.90 to 0.94) for death, observed-expected ratio of 0.24 for hospitalisation and 0.26 for death (ie, both the number of hospitalisations and the number of deaths were overestimated), and a Brier score of 0.0009 (0.00084 to 0.00096) for hospitalisation and 0.00036 (0.00032 to 0.0004) for death.<h4>Conclusions</h4>We found good discrimination of the QCovid 2 and 3 algorithms in Scotland, although performance was worse in higher age groups. Both the number of hospitalisations and the number of deaths were overestimated.",,pdf:https://bmjopen.bmj.com/content/bmjopen/13/12/e075958.full.pdf; doi:https://doi.org/10.1136/bmjopen-2023-075958; html:https://europepmc.org/articles/PMC10753764; pdf:https://europepmc.org/articles/PMC10753764?pdf=render
 35413949,https://doi.org/10.1038/s41467-022-29521-z,"Persistent COVID-19 symptoms in a community study of 606,434 people in England.","Whitaker M, Elliott J, Chadeau-Hyam M, Riley S, Darzi A, Cooke G, Ward H, Elliott P.",,Nature communications,2022,2022-04-12,Y,,,,"Long COVID remains a broadly defined syndrome, with estimates of prevalence and duration varying widely. We use data from rounds 3-5 of the REACT-2 study (n = 508,707; September 2020 - February 2021), a representative community survey of adults in England, and replication data from round 6 (n = 97,717; May 2021) to estimate the prevalence and identify predictors of persistent symptoms lasting 12 weeks or more; and unsupervised learning to cluster individuals by reported symptoms. At 12 weeks in rounds 3-5, 37.7% experienced at least one symptom, falling to 21.6% in round 6. Female sex, increasing age, obesity, smoking, vaping, hospitalisation with COVID-19, deprivation, and being a healthcare worker are associated with higher probability of persistent symptoms in rounds 3-5, and Asian ethnicity with lower probability. Clustering analysis identifies a subset of participants with predominantly respiratory symptoms. Managing the long-term sequelae of COVID-19 will remain a major challenge for affected individuals and their families and for health services.",,pdf:https://www.nature.com/articles/s41467-022-29521-z.pdf; doi:https://doi.org/10.1038/s41467-022-29521-z; html:https://europepmc.org/articles/PMC9005552; pdf:https://europepmc.org/articles/PMC9005552?pdf=render
-38626948,https://doi.org/10.1136/bmj-2023-078378,TRIPOD+AI statement: updated guidance for reporting clinical prediction models that use regression or machine learning methods.,"Collins GS, Moons KGM, Dhiman P, Riley RD, Beam AL, Van Calster B, Ghassemi M, Liu X, Reitsma JB, van Smeden M, Boulesteix AL, Camaradou JC, Celi LA, Denaxas S, Denniston AK, Glocker B, Golub RM, Harvey H, Heinze G, Hoffman MM, Kengne AP, Lam E, Lee N, Loder EW, Maier-Hein L, Mateen BA, McCradden MD, Oakden-Rayner L, Ordish J, Parnell R, Rose S, Singh K, Wynants L, Logullo P.",,BMJ (Clinical research ed.),2024,2024-04-16,Y,,,,,,pdf:https://www.bmj.com/content/bmj/385/bmj-2023-078378.full.pdf; doi:https://doi.org/10.1136/bmj-2023-078378; html:https://europepmc.org/articles/PMC11019967
-38283541,https://doi.org/10.1016/j.ssmph.2023.101592,Childhood cognitive ability and self-harm and suicide in later life.,"Iveson MH, Ball EL, Whalley HC, Deary IJ, Cox SR, Batty GD, John A, McIntosh AM.",,SSM - population health,2024,2023-12-29,Y,epidemiology; Suicide; Data Linkage; Self-harm; Older Age; Cognitive Ability,,,"<h4>Background</h4>Self-harm and suicide remain prevalent in later life. For younger adults, higher early-life cognitive ability appears to predict lower self-harm and suicide risk. Comparatively little is known about these associations among middle-aged and older adults.<h4>Methods</h4>This study examined the association between childhood (age 11) cognitive ability and self-harm and suicide risk among a Scotland-wide cohort (N = 53037), using hospital admission and mortality records to follow individuals from age 34 to 85. Multistate models examined the association between childhood cognitive ability and transitions between unaffected, self-harm, and then suicide or non-suicide death.<h4>Results</h4>After adjusting for childhood and adulthood socioeconomic conditions, higher childhood cognitive ability was significantly associated with reduced risk of self-harm among both males (451 events; HR = 0.90, 95% CI [0.82, 0.99]) and females (516 events; HR = 0.89, 95% CI [0.81, 0.98]). Childhood cognitive ability was not significantly associated with suicide risk among those with (Male: 16 events, HR = 1.05, 95% CI [0.61, 1.80]; Female: 13 events, HR = 1.08, 95% CI [0.55, 2.15]) or without self-harm events (Male: 118 events, HR = 1.17, 95% CI [0.84, 1.63]; Female: 31 events, HR = 1.30, 95% CI [0.70, 2.41]).<h4>Limitations</h4>The study only includes self-harm events that result in a hospital admission and does not account for self-harm prior to follow-up.<h4>Conclusions</h4>This extends work on cognitive ability and mental health, demonstrating that these associations can span the life course and into middle and older age.",,doi:https://doi.org/10.1016/j.ssmph.2023.101592; html:https://europepmc.org/articles/PMC10821139; pdf:https://europepmc.org/articles/PMC10821139?pdf=render
 37358897,https://doi.org/10.2196/45849,Development of a Corpus Annotated With Mentions of Pain in Mental Health Records: Natural Language Processing Approach.,"Chaturvedi J, Chance N, Mirza L, Vernugopan V, Velupillai S, Stewart R, Roberts A.",,JMIR formative research,2023,2023-06-26,Y,Pain; Mental health; Annotation; Information Extraction; Natural Language Processing,,,"<h4>Background</h4>Pain is a widespread issue, with 20% of adults (1 in 5) experiencing it globally. A strong association has been demonstrated between pain and mental health conditions, and this association is known to exacerbate disability and impairment. Pain is also known to be strongly related to emotions, which can lead to damaging consequences. As pain is a common reason for people to access health care facilities, electronic health records (EHRs) are a potential source of information on this pain. Mental health EHRs could be particularly beneficial since they can show the overlap of pain with mental health. Most mental health EHRs contain the majority of their information within the free-text sections of the records. However, it is challenging to extract information from free text. Natural language processing (NLP) methods are therefore required to extract this information from the text.<h4>Objective</h4>This research describes the development of a corpus of manually labeled mentions of pain and pain-related entities from the documents of a mental health EHR database, for use in the development and evaluation of future NLP methods.<h4>Methods</h4>The EHR database used, Clinical Record Interactive Search, consists of anonymized patient records from The South London and Maudsley National Health Service Foundation Trust in the United Kingdom. The corpus was developed through a process of manual annotation where pain mentions were marked as relevant (ie, referring to physical pain afflicting the patient), negated (ie, indicating absence of pain), or not relevant (ie, referring to pain affecting someone other than the patient, or metaphorical and hypothetical mentions). Relevant mentions were also annotated with additional attributes such as anatomical location affected by pain, pain character, and pain management measures, if mentioned.<h4>Results</h4>A total of 5644 annotations were collected from 1985 documents (723 patients). Over 70% (n=4028) of the mentions found within the documents were annotated as relevant, and about half of these mentions also included the anatomical location affected by the pain. The most common pain character was chronic pain, and the most commonly mentioned anatomical location was the chest. Most annotations (n=1857, 33%) were from patients who had a primary diagnosis of mood disorders (International Classification of Diseases-10th edition, chapter F30-39).<h4>Conclusions</h4>This research has helped better understand how pain is mentioned within the context of mental health EHRs and provided insight into the kind of information that is typically mentioned around pain in such a data source. In future work, the extracted information will be used to develop and evaluate a machine learning-based NLP application to automatically extract relevant pain information from EHR databases.",,pdf:https://formative.jmir.org/2023/1/e45849/PDF; doi:https://doi.org/10.2196/45849; html:https://europepmc.org/articles/PMC10337440; pdf:https://europepmc.org/articles/PMC10337440?pdf=render
+38283541,https://doi.org/10.1016/j.ssmph.2023.101592,Childhood cognitive ability and self-harm and suicide in later life.,"Iveson MH, Ball EL, Whalley HC, Deary IJ, Cox SR, Batty GD, John A, McIntosh AM.",,SSM - population health,2024,2023-12-29,Y,epidemiology; Suicide; Data Linkage; Self-harm; Older Age; Cognitive Ability,,,"<h4>Background</h4>Self-harm and suicide remain prevalent in later life. For younger adults, higher early-life cognitive ability appears to predict lower self-harm and suicide risk. Comparatively little is known about these associations among middle-aged and older adults.<h4>Methods</h4>This study examined the association between childhood (age 11) cognitive ability and self-harm and suicide risk among a Scotland-wide cohort (N = 53037), using hospital admission and mortality records to follow individuals from age 34 to 85. Multistate models examined the association between childhood cognitive ability and transitions between unaffected, self-harm, and then suicide or non-suicide death.<h4>Results</h4>After adjusting for childhood and adulthood socioeconomic conditions, higher childhood cognitive ability was significantly associated with reduced risk of self-harm among both males (451 events; HR = 0.90, 95% CI [0.82, 0.99]) and females (516 events; HR = 0.89, 95% CI [0.81, 0.98]). Childhood cognitive ability was not significantly associated with suicide risk among those with (Male: 16 events, HR = 1.05, 95% CI [0.61, 1.80]; Female: 13 events, HR = 1.08, 95% CI [0.55, 2.15]) or without self-harm events (Male: 118 events, HR = 1.17, 95% CI [0.84, 1.63]; Female: 31 events, HR = 1.30, 95% CI [0.70, 2.41]).<h4>Limitations</h4>The study only includes self-harm events that result in a hospital admission and does not account for self-harm prior to follow-up.<h4>Conclusions</h4>This extends work on cognitive ability and mental health, demonstrating that these associations can span the life course and into middle and older age.",,doi:https://doi.org/10.1016/j.ssmph.2023.101592; html:https://europepmc.org/articles/PMC10821139; pdf:https://europepmc.org/articles/PMC10821139?pdf=render
 33799834,https://doi.org/10.3390/cancers13061239,The Role of Autophagy and lncRNAs in the Maintenance of Cancer Stem Cells.,"Jahangiri L, Ishola T, Pucci P, Trigg RM, Pereira J, Williams JA, Cavanagh ML, Gkoutos GV, Tsaprouni L, Turner SD.",,Cancers,2021,2021-03-11,Y,Autophagy; Haematological Malignancies; Tumour Microenvironment; Lncrnas; Solid Cancers; Cancer Stem Cells (Cscs),,,"Cancer stem cells (CSCs) possess properties such as self-renewal, resistance to apoptotic cues, quiescence, and DNA-damage repair capacity. Moreover, CSCs strongly influence the tumour microenvironment (TME) and may account for cancer progression, recurrence, and relapse. CSCs represent a distinct subpopulation in tumours and the detection, characterisation, and understanding of the regulatory landscape and cellular processes that govern their maintenance may pave the way to improving prognosis, selective targeted therapy, and therapy outcomes. In this review, we have discussed the characteristics of CSCs identified in various cancer types and the role of autophagy and long noncoding RNAs (lncRNAs) in maintaining the homeostasis of CSCs. Further, we have discussed methods to detect CSCs and strategies for treatment and relapse, taking into account the requirement to inhibit CSC growth and survival within the complex backdrop of cellular processes, microenvironmental interactions, and regulatory networks associated with cancer. Finally, we critique the computationally reinforced triangle of factors inclusive of CSC properties, the process of autophagy, and lncRNA and their associated networks with respect to hypoxia, epithelial-to-mesenchymal transition (EMT), and signalling pathways.",,pdf:https://www.mdpi.com/2072-6694/13/6/1239/pdf?version=1615817230; doi:https://doi.org/10.3390/cancers13061239; html:https://europepmc.org/articles/PMC7998932; pdf:https://europepmc.org/articles/PMC7998932?pdf=render
+38626948,https://doi.org/10.1136/bmj-2023-078378,TRIPOD+AI statement: updated guidance for reporting clinical prediction models that use regression or machine learning methods.,"Collins GS, Moons KGM, Dhiman P, Riley RD, Beam AL, Van Calster B, Ghassemi M, Liu X, Reitsma JB, van Smeden M, Boulesteix AL, Camaradou JC, Celi LA, Denaxas S, Denniston AK, Glocker B, Golub RM, Harvey H, Heinze G, Hoffman MM, Kengne AP, Lam E, Lee N, Loder EW, Maier-Hein L, Mateen BA, McCradden MD, Oakden-Rayner L, Ordish J, Parnell R, Rose S, Singh K, Wynants L, Logullo P.",,BMJ (Clinical research ed.),2024,2024-04-16,Y,,,,,,pdf:https://www.bmj.com/content/bmj/385/bmj-2023-078378.full.pdf; doi:https://doi.org/10.1136/bmj-2023-078378; html:https://europepmc.org/articles/PMC11019967
 37181393,https://doi.org/10.1016/j.jacasi.2022.12.006,Ambient Temperature and Myocardial Infarction: Who Is at Risk?,"Lowry MTH, Mills NL, Kimenai DM.",,JACC. Asia,2023,2023-03-14,Y,Myocardial infarction; Ambient temperature; risk factors,,,,,doi:https://doi.org/10.1016/j.jacasi.2022.12.006; doi:https://doi.org/10.1016/j.jacasi.2022.12.006; html:https://europepmc.org/articles/PMC10167505; pdf:https://europepmc.org/articles/PMC10167505?pdf=render
+38192590,https://doi.org/10.1016/j.eclinm.2023.102321,Clinical and health inequality risk factors for non-COVID-related sepsis during the global COVID-19 pandemic: a national case-control and cohort study.,"Zhong X, Ashiru-Oredope D, Pate A, Martin GP, Sharma A, Dark P, Felton T, Lake C, MacKenna B, Mehrkar A, Bacon SCJ, Massey J, Inglesby P, Goldacre B, OpenSAFELY Collaborative, Hand K, Bladon S, Cunningham N, Gilham E, Brown CS, Mirfenderesky M, Palin V, van Staa TP.",,EClinicalMedicine,2023,2023-11-23,Y,Sepsis; Morbidity; Primary Care; Deprivation; Health Inequality; Covid-19 Pandemic,,,"<h4>Background</h4>Sepsis, characterised by significant morbidity and mortality, is intricately linked to socioeconomic disparities and pre-admission clinical histories. This study aspires to elucidate the association between non-COVID-19 related sepsis and health inequality risk factors amidst the pandemic in England, with a secondary focus on their association with 30-day sepsis mortality.<h4>Methods</h4>With the approval of NHS England, we harnessed the OpenSAFELY platform to execute a cohort study and a 1:6 matched case-control study. A sepsis diagnosis was identified from the incident hospital admissions record using ICD-10 codes. This encompassed 248,767 cases with non-COVID-19 sepsis from a cohort of 22.0 million individuals spanning January 1, 2019, to June 31, 2022. Socioeconomic deprivation was gauged using the Index of Multiple Deprivation score, reflecting indicators like income, employment, and education. Hospitalisation-related sepsis diagnoses were categorised as community-acquired or hospital-acquired. Cases were matched to controls who had no recorded diagnosis of sepsis, based on age (stepwise), sex, and calendar month. The eligibility criteria for controls were established primarily on the absence of a recorded sepsis diagnosis. Associations between potential predictors and odds of developing non-COVID-19 sepsis underwent assessment through conditional logistic regression models, with multivariable regression determining odds ratios (ORs) for 30-day mortality.<h4>Findings</h4>The study included 224,361 (10.2%) cases with non-COVID-19 sepsis and 1,346,166 matched controls. The most socioeconomic deprived quintile was associated with higher odds of developing non-COVID-19 sepsis than the least deprived quintile (crude OR 1.80 [95% CI 1.77-1.83]). Other risk factors (after adjusting comorbidities) such as learning disability (adjusted OR 3.53 [3.35-3.73]), chronic liver disease (adjusted OR 3.08 [2.97-3.19]), chronic kidney disease (stage 4: adjusted OR 2.62 [2.55-2.70], stage 5: adjusted OR 6.23 [5.81-6.69]), cancer, neurological disease, immunosuppressive conditions were also associated with developing non-COVID-19 sepsis. The incidence rate of non-COVID-19 sepsis decreased during the COVID-19 pandemic and rebounded to pre-pandemic levels (April 2021) after national lockdowns had been lifted. The 30-day mortality risk in cases with non-COVID-19 sepsis was higher for the most deprived quintile across all periods.<h4>Interpretation</h4>Socioeconomic deprivation, comorbidity and learning disabilities were associated with an increased odds of developing non-COVID-19 related sepsis and 30-day mortality in England. This study highlights the need to improve the prevention of sepsis, including more precise targeting of antimicrobials to higher-risk patients.<h4>Funding</h4>The UK Health Security Agency, Health Data Research UK, and National Institute for Health Research.",,doi:https://doi.org/10.1016/j.eclinm.2023.102321; html:https://europepmc.org/articles/PMC10772239; pdf:https://europepmc.org/articles/PMC10772239?pdf=render
 37624366,https://doi.org/10.1039/d2an01350a,Platform-agnostic electrochemical sensing app and companion potentiostat.,"Manoharan V, Rodrigues R, Sadati S, Swann MJ, Freeman N, Du B, Yildirim E, Tamer U, Arvanitis TN, Isakov D, Asadipour A, Charmet J.",,The Analyst,2023,2023-09-25,Y,,,,"Electrochemical sensing is ubiquitous in a number of fields ranging from biosensing, to environmental monitoring through to food safety and battery or corrosion characterisation. Whereas conventional potentiostats are ideal to develop assays in laboratory settings, they are in general, not well-suited for field work due to their size and power requirements. To address this need, a number of portable battery-operated potentiostats have been proposed over the years. However, most open source solutions do not take full advantage of integrated circuit (IC) potentiostats, a rapidly evolving field. This is partly due to the constraining requirements inherent to the development of dedicated interfaces, such as apps, to address and control a set of common electrochemical sensing parameters. Here we propose the PocketEC, a universal app that has all the functionalities to interface with potentiostat ICs through a user defined property file. The versatility of PocketEC, developed with an assay developer mindset, was demonstrated by interfacing it, <i>via</i> Bluetooth, to the ADuCM355 evaluation board, the open-source DStat potentiostat and the Voyager board, a custom-built, small footprint potentiostat based around the LMP91000 chip. The Voyager board is presented here for the first time. Data obtained using a standard redox probe, Ferrocene Carboxylic Acid (FCA) and a silver ion assay using anodic stripping multi-step amperometry were in good agreement with analogous measurements using a bench top potentiostat. Combined with its Voyager board companion, the PocketEC app can be used directly for a number of wearable or portable electrochemical sensing applications. Importantly, the versatility of the app makes it a candidate of choice for the development of future portable potentiostats. Finally, the app is available to download on the Google Play store and the source codes and design files for the PocketEC app and the Voyager board are shared <i>via</i> Creative Commons license (CC BY-NC 3.0) to promote the development of novel portable or wearable applications based on electrochemical sensing.",,pdf:https://pubs.rsc.org/en/content/articlepdf/2023/an/d2an01350a; doi:https://doi.org/10.1039/d2an01350a; html:https://europepmc.org/articles/PMC10518900
 33780469,https://doi.org/10.1371/journal.pone.0248195,Deriving household composition using population-scale electronic health record data-A reproducible methodology.,"Johnson RD, Griffiths LJ, Hollinghurst JP, Akbari A, Lee A, Thompson DA, Lyons RA, Fry R.",,PloS one,2021,2021-03-29,Y,,,,"<h4>Background</h4>Physical housing and household composition have an important role in the lives of individuals and drive health and social outcomes, and inequalities. Most methods to understand housing composition are based on survey or census data, and there is currently no reproducible methodology for creating population-level household composition measures using linked administrative data.<h4>Methods</h4>Using existing, and more recent enhancements to the address-data linkage methods in the SAIL Databank using Residential Anonymised Linking Fields we linked individuals to properties using the anonymised Welsh Demographic Service data in the SAIL Databank. We defined households, household size, and household composition measures based on adult to child relationships, and age differences between residents to create relative age measures.<h4>Results</h4>Two relative age-based algorithms were developed and returned similar results when applied to population and household-level data, describing household composition for 3.1 million individuals within 1.2 million households in Wales. Developed methods describe binary, and count level generational household composition measures.<h4>Conclusions</h4>Improved residential anonymised linkage field methods in SAIL have led to improved property-level data linkage, allowing the design and application of household composition measures that assign individuals to shared residences and allow the description of household composition across Wales. The reproducible methods create longitudinal, household-level composition measures at a population-level using linked administrative data. Such measures are important to help understand more detail about an individual's home and area environment and how that may affect the health and wellbeing of the individual, other residents, and potentially into the wider community.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0248195&type=printable; doi:https://doi.org/10.1371/journal.pone.0248195; html:https://europepmc.org/articles/PMC8007012; pdf:https://europepmc.org/articles/PMC8007012?pdf=render
-38192590,https://doi.org/10.1016/j.eclinm.2023.102321,Clinical and health inequality risk factors for non-COVID-related sepsis during the global COVID-19 pandemic: a national case-control and cohort study.,"Zhong X, Ashiru-Oredope D, Pate A, Martin GP, Sharma A, Dark P, Felton T, Lake C, MacKenna B, Mehrkar A, Bacon SCJ, Massey J, Inglesby P, Goldacre B, OpenSAFELY Collaborative, Hand K, Bladon S, Cunningham N, Gilham E, Brown CS, Mirfenderesky M, Palin V, van Staa TP.",,EClinicalMedicine,2023,2023-11-23,Y,Sepsis; Morbidity; Primary Care; Deprivation; Health Inequality; Covid-19 Pandemic,,,"<h4>Background</h4>Sepsis, characterised by significant morbidity and mortality, is intricately linked to socioeconomic disparities and pre-admission clinical histories. This study aspires to elucidate the association between non-COVID-19 related sepsis and health inequality risk factors amidst the pandemic in England, with a secondary focus on their association with 30-day sepsis mortality.<h4>Methods</h4>With the approval of NHS England, we harnessed the OpenSAFELY platform to execute a cohort study and a 1:6 matched case-control study. A sepsis diagnosis was identified from the incident hospital admissions record using ICD-10 codes. This encompassed 248,767 cases with non-COVID-19 sepsis from a cohort of 22.0 million individuals spanning January 1, 2019, to June 31, 2022. Socioeconomic deprivation was gauged using the Index of Multiple Deprivation score, reflecting indicators like income, employment, and education. Hospitalisation-related sepsis diagnoses were categorised as community-acquired or hospital-acquired. Cases were matched to controls who had no recorded diagnosis of sepsis, based on age (stepwise), sex, and calendar month. The eligibility criteria for controls were established primarily on the absence of a recorded sepsis diagnosis. Associations between potential predictors and odds of developing non-COVID-19 sepsis underwent assessment through conditional logistic regression models, with multivariable regression determining odds ratios (ORs) for 30-day mortality.<h4>Findings</h4>The study included 224,361 (10.2%) cases with non-COVID-19 sepsis and 1,346,166 matched controls. The most socioeconomic deprived quintile was associated with higher odds of developing non-COVID-19 sepsis than the least deprived quintile (crude OR 1.80 [95% CI 1.77-1.83]). Other risk factors (after adjusting comorbidities) such as learning disability (adjusted OR 3.53 [3.35-3.73]), chronic liver disease (adjusted OR 3.08 [2.97-3.19]), chronic kidney disease (stage 4: adjusted OR 2.62 [2.55-2.70], stage 5: adjusted OR 6.23 [5.81-6.69]), cancer, neurological disease, immunosuppressive conditions were also associated with developing non-COVID-19 sepsis. The incidence rate of non-COVID-19 sepsis decreased during the COVID-19 pandemic and rebounded to pre-pandemic levels (April 2021) after national lockdowns had been lifted. The 30-day mortality risk in cases with non-COVID-19 sepsis was higher for the most deprived quintile across all periods.<h4>Interpretation</h4>Socioeconomic deprivation, comorbidity and learning disabilities were associated with an increased odds of developing non-COVID-19 related sepsis and 30-day mortality in England. This study highlights the need to improve the prevention of sepsis, including more precise targeting of antimicrobials to higher-risk patients.<h4>Funding</h4>The UK Health Security Agency, Health Data Research UK, and National Institute for Health Research.",,doi:https://doi.org/10.1016/j.eclinm.2023.102321; html:https://europepmc.org/articles/PMC10772239; pdf:https://europepmc.org/articles/PMC10772239?pdf=render
-38355631,https://doi.org/10.1186/s12916-024-03284-4,Association between pregnancy-related complications and development of type 2 diabetes and hypertension in women: an umbrella review.,"Wambua S, Singh M, Okoth K, Snell KIE, Riley RD, Yau C, Thangaratinam S, Nirantharakumar K, Crowe FL, MuM-PreDiCT Group.",,BMC medicine,2024,2024-02-14,Y,Hypertension; Type 2 diabetes; Pregnancy complications; Obstetrics And Gynaecology; Umbrella Review,,,"<h4>Background</h4>Despite many systematic reviews and meta-analyses examining the associations of pregnancy complications with risk of type 2 diabetes mellitus (T2DM) and hypertension, previous umbrella reviews have only examined a single pregnancy complication. Here we have synthesised evidence from systematic reviews and meta-analyses on the associations of a wide range of pregnancy-related complications with risk of developing T2DM and hypertension.<h4>Methods</h4>Medline, Embase and Cochrane Database of Systematic Reviews were searched from inception until 26 September 2022 for systematic reviews and meta-analysis examining the association between pregnancy complications and risk of T2DM and hypertension. Screening of articles, data extraction and quality appraisal (AMSTAR2) were conducted independently by two reviewers using Covidence software. Data were extracted for studies that examined the risk of T2DM and hypertension in pregnant women with the pregnancy complication compared to pregnant women without the pregnancy complication. Summary estimates of each review were presented using tables, forest plots and narrative synthesis and reported following Preferred Reporting Items for Overviews of Reviews (PRIOR) guidelines.<h4>Results</h4>Ten systematic reviews were included. Two pregnancy complications were identified. Gestational diabetes mellitus (GDM): One review showed GDM was associated with a 10-fold higher risk of T2DM at least 1 year after pregnancy (relative risk (RR) 9.51 (95% confidence interval (CI) 7.14 to 12.67) and although the association differed by ethnicity (white: RR 16.28 (95% CI 15.01 to 17.66), non-white: RR 10.38 (95% CI 4.61 to 23.39), mixed: RR 8.31 (95% CI 5.44 to 12.69)), the between subgroups difference were not statistically significant at 5% significance level. Another review showed GDM was associated with higher mean blood pressure at least 3 months postpartum (mean difference in systolic blood pressure: 2.57 (95% CI 1.74 to 3.40) mmHg and mean difference in diastolic blood pressure: 1.89 (95% CI 1.32 to 2.46) mmHg). Hypertensive disorders of pregnancy (HDP): Three reviews showed women with a history of HDP were 3 to 6 times more likely to develop hypertension at least 6 weeks after pregnancy compared to women without HDP (meta-analysis with largest number of studies: odds ratio (OR) 4.33 (3.51 to 5.33)) and one review reported a higher rate of T2DM after HDP (hazard ratio (HR) 2.24 (1.95 to 2.58)) at least a year after pregnancy. One of the three reviews and five other reviews reported women with a history of preeclampsia were 3 to 7 times more likely to develop hypertension at least 6 weeks postpartum (meta-analysis with the largest number of studies: OR 3.90 (3.16 to 4.82) with one of these reviews reporting the association was greatest in women from Asia (Asia: OR 7.54 (95% CI 2.49 to 22.81), Europe: OR 2.19 (95% CI 0.30 to 16.02), North and South America: OR 3.32 (95% CI 1.26 to 8.74)).<h4>Conclusions</h4>GDM and HDP are associated with a greater risk of developing T2DM and hypertension. Common confounders adjusted for across the included studies in the reviews were maternal age, body mass index (BMI), socioeconomic status, smoking status, pre-pregnancy and current BMI, parity, family history of T2DM or cardiovascular disease, ethnicity, and time of delivery. Further research is needed to evaluate the value of embedding these pregnancy complications as part of assessment for future risk of T2DM and chronic hypertension.",,doi:https://doi.org/10.1186/s12916-024-03284-4; html:https://europepmc.org/articles/PMC10865714; pdf:https://europepmc.org/articles/PMC10865714?pdf=render
-36217535,https://doi.org/10.1038/s43856-022-00185-6,"Multi-omic phenotyping reveals host-microbe responses to bariatric surgery, glycaemic control and obesity.","Penney NC, Yeung DKT, Garcia-Perez I, Posma JM, Kopytek A, Garratt B, Ashrafian H, Frost G, Marchesi JR, Purkayastha S, Hoyles L, Darzi A, Holmes E.",,Communications medicine,2022,2022-10-07,Y,Obesity; Type 2 diabetes; Dynamical Systems; Microbiome,,,"<h4>Background</h4>Resolution of type 2 diabetes (T2D) is common following bariatric surgery, particularly Roux-en-Y gastric bypass. However, the underlying mechanisms have not been fully elucidated.<h4>Methods</h4>To address this we compare the integrated serum, urine and faecal metabolic profiles of participants with obesity ± T2D (<i>n</i> = 80, T2D = 42) with participants who underwent Roux-en-Y gastric bypass or sleeve gastrectomy (pre and 3-months post-surgery; <i>n</i> = 27), taking diet into account. We co-model these data with shotgun metagenomic profiles of the gut microbiota to provide a comprehensive atlas of host-gut microbe responses to bariatric surgery, weight-loss and glycaemic control at the systems level.<h4>Results</h4>Here we show that bariatric surgery reverses several disrupted pathways characteristic of T2D. The differential metabolite set representative of bariatric surgery overlaps with both diabetes (19.3% commonality) and body mass index (18.6% commonality). However, the percentage overlap between diabetes and body mass index is minimal (4.0% commonality), consistent with weight-independent mechanisms of T2D resolution. The gut microbiota is more strongly correlated to body mass index than T2D, although we identify some pathways such as amino acid metabolism that correlate with changes to the gut microbiota and which influence glycaemic control.<h4>Conclusion</h4>We identify multi-omic signatures associated with responses to surgery, body mass index, and glycaemic control. Improved understanding of gut microbiota - host co-metabolism may lead to novel therapies for weight-loss or diabetes. However, further experiments are required to provide mechanistic insight into the role of the gut microbiota in host metabolism and establish proof of causality.",,pdf:https://www.nature.com/articles/s43856-022-00185-6.pdf; doi:https://doi.org/10.1038/s43856-022-00185-6; html:https://europepmc.org/articles/PMC9546886; pdf:https://europepmc.org/articles/PMC9546886?pdf=render
 38509709,https://doi.org/10.1016/j.xhgg.2024.100284,A power-based sliding window approach to evaluate the clinical impact of rare genetic variants in the nucleotide sequence or the spatial position of the folded protein.,"Cirulli ET, Schiabor Barrett KM, Bolze A, Judge DP, Pawloski PA, Grzymski JJ, Lee W, Washington NL.",,HGG advances,2024,2024-03-19,Y,Genetic analysis; Sliding window; Rare Variants,,,"Systematic determination of novel variant pathogenicity remains a major challenge, even when there is an established association between a gene and phenotype. Here we present Power Window (PW), a sliding window technique that identifies the impactful regions of a gene using population-scale clinico-genomic datasets. By sizing analysis windows on the number of variant carriers, rather than the number of variants or nucleotides, statistical power is held constant, enabling the localization of clinical phenotypes and removal of unassociated gene regions. The windows can be built by sliding across either the nucleotide sequence of the gene (through 1D space) or the positions of the amino acids in the folded protein (through 3D space). Using a training set of 350k exomes from the UK Biobank (UKB), we developed PW models for well-established gene-disease associations and tested their accuracy in two independent cohorts (117k UKB exomes and 65k exomes sequenced at Helix in the Healthy Nevada Project, myGenetics, or In Our DNA SC studies). The significant models retained a median of 49% of the qualifying variant carriers in each gene (range 2%-98%), with quantitative traits showing a median effect size improvement of 66% compared with aggregating variants across the entire gene, and binary traits' odds ratios improving by a median of 2.2-fold. PW showcases that electronic health record-based statistical analyses can accurately distinguish between novel coding variants in established genes that will have high phenotypic penetrance and those that will not, unlocking new potential for human genomics research, drug development, variant interpretation, and precision medicine.",,pdf:https://www.cell.com/article/S266624772400023X/pdf; doi:https://doi.org/10.1016/j.xhgg.2024.100284; html:https://europepmc.org/articles/PMC11004801; pdf:https://europepmc.org/articles/PMC11004801?pdf=render
+38355631,https://doi.org/10.1186/s12916-024-03284-4,Association between pregnancy-related complications and development of type 2 diabetes and hypertension in women: an umbrella review.,"Wambua S, Singh M, Okoth K, Snell KIE, Riley RD, Yau C, Thangaratinam S, Nirantharakumar K, Crowe FL, MuM-PreDiCT Group.",,BMC medicine,2024,2024-02-14,Y,Hypertension; Type 2 diabetes; Pregnancy complications; Obstetrics And Gynaecology; Umbrella Review,,,"<h4>Background</h4>Despite many systematic reviews and meta-analyses examining the associations of pregnancy complications with risk of type 2 diabetes mellitus (T2DM) and hypertension, previous umbrella reviews have only examined a single pregnancy complication. Here we have synthesised evidence from systematic reviews and meta-analyses on the associations of a wide range of pregnancy-related complications with risk of developing T2DM and hypertension.<h4>Methods</h4>Medline, Embase and Cochrane Database of Systematic Reviews were searched from inception until 26 September 2022 for systematic reviews and meta-analysis examining the association between pregnancy complications and risk of T2DM and hypertension. Screening of articles, data extraction and quality appraisal (AMSTAR2) were conducted independently by two reviewers using Covidence software. Data were extracted for studies that examined the risk of T2DM and hypertension in pregnant women with the pregnancy complication compared to pregnant women without the pregnancy complication. Summary estimates of each review were presented using tables, forest plots and narrative synthesis and reported following Preferred Reporting Items for Overviews of Reviews (PRIOR) guidelines.<h4>Results</h4>Ten systematic reviews were included. Two pregnancy complications were identified. Gestational diabetes mellitus (GDM): One review showed GDM was associated with a 10-fold higher risk of T2DM at least 1 year after pregnancy (relative risk (RR) 9.51 (95% confidence interval (CI) 7.14 to 12.67) and although the association differed by ethnicity (white: RR 16.28 (95% CI 15.01 to 17.66), non-white: RR 10.38 (95% CI 4.61 to 23.39), mixed: RR 8.31 (95% CI 5.44 to 12.69)), the between subgroups difference were not statistically significant at 5% significance level. Another review showed GDM was associated with higher mean blood pressure at least 3 months postpartum (mean difference in systolic blood pressure: 2.57 (95% CI 1.74 to 3.40) mmHg and mean difference in diastolic blood pressure: 1.89 (95% CI 1.32 to 2.46) mmHg). Hypertensive disorders of pregnancy (HDP): Three reviews showed women with a history of HDP were 3 to 6 times more likely to develop hypertension at least 6 weeks after pregnancy compared to women without HDP (meta-analysis with largest number of studies: odds ratio (OR) 4.33 (3.51 to 5.33)) and one review reported a higher rate of T2DM after HDP (hazard ratio (HR) 2.24 (1.95 to 2.58)) at least a year after pregnancy. One of the three reviews and five other reviews reported women with a history of preeclampsia were 3 to 7 times more likely to develop hypertension at least 6 weeks postpartum (meta-analysis with the largest number of studies: OR 3.90 (3.16 to 4.82) with one of these reviews reporting the association was greatest in women from Asia (Asia: OR 7.54 (95% CI 2.49 to 22.81), Europe: OR 2.19 (95% CI 0.30 to 16.02), North and South America: OR 3.32 (95% CI 1.26 to 8.74)).<h4>Conclusions</h4>GDM and HDP are associated with a greater risk of developing T2DM and hypertension. Common confounders adjusted for across the included studies in the reviews were maternal age, body mass index (BMI), socioeconomic status, smoking status, pre-pregnancy and current BMI, parity, family history of T2DM or cardiovascular disease, ethnicity, and time of delivery. Further research is needed to evaluate the value of embedding these pregnancy complications as part of assessment for future risk of T2DM and chronic hypertension.",,doi:https://doi.org/10.1186/s12916-024-03284-4; html:https://europepmc.org/articles/PMC10865714; pdf:https://europepmc.org/articles/PMC10865714?pdf=render
 39171430,https://doi.org/10.2196/43173,Impact of the COVID-19 Pandemic on Influenza Hospital Admissions and Deaths in Wales: Descriptive National Time Series Analysis.,"Alsallakh M, Adeloye D, Vasileiou E, Sivakumaran S, Akbari A, Lyons RA, Robertson C, Rudan I, Davies GA, Sheikh A.",,JMIR public health and surveillance,2024,2024-08-21,Y,Mortality; Influenza; Wales; Hospitalization; Community Health; Hospital Admission; Public Health Surveillance; Nonpharmaceutical Interventions; Covid-19; Covid-19 Pandemic; Endemic Virus,,,"<h4>Background</h4>The COVID-19 pandemic and the ensuing implementation of control measures caused widespread societal disruption. These disruptions may also have affected community transmission and seasonal circulation patterns of endemic respiratory viruses.<h4>Objective</h4>We aimed to investigate the impact of COVID-19-related disruption on influenza-related emergency hospital admissions and deaths in Wales in the first 2 years of the pandemic.<h4>Methods</h4>A descriptive analysis of influenza activity was conducted using anonymized pathology, hospitalization, and mortality data from the Secure Anonymised Information Linkage Databank in Wales. The annual incidence of emergency hospitalizations and deaths with influenza-specific diagnosis codes between January 1, 2015, and December 31, 2021, was estimated. Case definitions of emergency hospitalization and death required laboratory confirmation with a polymerase chain reaction test. Trends of admissions and deaths were analyzed monthly and yearly. We conducted 2 sensitivity analyses by extending case definitions to include acute respiratory illnesses with a positive influenza test and by limiting admissions to those with influenza as the primary diagnosis. We also examined yearly influenza testing trends to understand changes in testing behavior during the pandemic.<h4>Results</h4>We studied a population of 3,235,883 Welsh residents in 2020 with a median age of 42.5 (IQR 22.9-61.0) years. Influenza testing in Wales increased notably in the last 2 months of 2020, and particularly in 2021 to 39,720 per 100,000 people, compared to the prepandemic levels (1343 in 2019). The percentage of influenza admissions matched to an influenza polymerase chain reaction test increased from 74.8% (1890/2526) in 2019 to 85.2% (98/115) in 2021. However, admissions with a positive test per 100,000 population decreased from 17.0 in 2019 to 2.7 and 0.6 in 2020 and 2021, respectively. Similarly, deaths due to influenza with a positive influenza test per 100,000 population decreased from 0.4 in 2019 to 0.0 in 2020 and 2021. Sensitivity analyses showed similar patterns of decreasing influenza admissions and deaths in the first 2 years of the COVID-19 pandemic.<h4>Conclusions</h4>Nonpharmaceutical interventions to control COVID-19 were associated with a substantial reduction in the transmission of the influenza virus, with associated substantial reductions in hospital cases and deaths observed. Beyond the pandemic context, consideration should be given to the role of nonpharmaceutical community-driven interventions to reduce the burden of influenza.",,doi:https://doi.org/10.2196/43173; html:https://europepmc.org/articles/PMC11358661
+36217535,https://doi.org/10.1038/s43856-022-00185-6,"Multi-omic phenotyping reveals host-microbe responses to bariatric surgery, glycaemic control and obesity.","Penney NC, Yeung DKT, Garcia-Perez I, Posma JM, Kopytek A, Garratt B, Ashrafian H, Frost G, Marchesi JR, Purkayastha S, Hoyles L, Darzi A, Holmes E.",,Communications medicine,2022,2022-10-07,Y,Obesity; Type 2 diabetes; Dynamical Systems; Microbiome,,,"<h4>Background</h4>Resolution of type 2 diabetes (T2D) is common following bariatric surgery, particularly Roux-en-Y gastric bypass. However, the underlying mechanisms have not been fully elucidated.<h4>Methods</h4>To address this we compare the integrated serum, urine and faecal metabolic profiles of participants with obesity ± T2D (<i>n</i> = 80, T2D = 42) with participants who underwent Roux-en-Y gastric bypass or sleeve gastrectomy (pre and 3-months post-surgery; <i>n</i> = 27), taking diet into account. We co-model these data with shotgun metagenomic profiles of the gut microbiota to provide a comprehensive atlas of host-gut microbe responses to bariatric surgery, weight-loss and glycaemic control at the systems level.<h4>Results</h4>Here we show that bariatric surgery reverses several disrupted pathways characteristic of T2D. The differential metabolite set representative of bariatric surgery overlaps with both diabetes (19.3% commonality) and body mass index (18.6% commonality). However, the percentage overlap between diabetes and body mass index is minimal (4.0% commonality), consistent with weight-independent mechanisms of T2D resolution. The gut microbiota is more strongly correlated to body mass index than T2D, although we identify some pathways such as amino acid metabolism that correlate with changes to the gut microbiota and which influence glycaemic control.<h4>Conclusion</h4>We identify multi-omic signatures associated with responses to surgery, body mass index, and glycaemic control. Improved understanding of gut microbiota - host co-metabolism may lead to novel therapies for weight-loss or diabetes. However, further experiments are required to provide mechanistic insight into the role of the gut microbiota in host metabolism and establish proof of causality.",,pdf:https://www.nature.com/articles/s43856-022-00185-6.pdf; doi:https://doi.org/10.1038/s43856-022-00185-6; html:https://europepmc.org/articles/PMC9546886; pdf:https://europepmc.org/articles/PMC9546886?pdf=render
 37171130,https://doi.org/10.1093/gigascience/giad030,Strategies and techniques for quality control and semantic enrichment with multimodal data: a case study in colorectal cancer with eHDPrep.,"Toner TM, Pancholi R, Miller P, Forster T, Coleman HG, Overton IM.",,GigaScience,2022,2022-12-01,Y,Quality control; Bioinformatics; Data integration; Quality assessment; Colorectal Cancer; Medical Informatics; Ontology; Health Data; Semantic Enrichment,,,"<h4>Background</h4>Integration of data from multiple domains can greatly enhance the quality and applicability of knowledge generated in analysis workflows. However, working with health data is challenging, requiring careful preparation in order to support meaningful interpretation and robust results. Ontologies encapsulate relationships between variables that can enrich the semantic content of health datasets to enhance interpretability and inform downstream analyses.<h4>Findings</h4>We developed an R package for electronic health data preparation, ""eHDPrep,"" demonstrated upon a multimodal colorectal cancer dataset (661 patients, 155 variables; Colo-661); a further demonstrator is taken from The Cancer Genome Atlas (459 patients, 94 variables; TCGA-COAD). eHDPrep offers user-friendly methods for quality control, including internal consistency checking and redundancy removal with information-theoretic variable merging. Semantic enrichment functionality is provided, enabling generation of new informative ""meta-variables"" according to ontological common ancestry between variables, demonstrated with SNOMED CT and the Gene Ontology in the current study. eHDPrep also facilitates numerical encoding, variable extraction from free text, completeness analysis, and user review of modifications to the dataset.<h4>Conclusions</h4>eHDPrep provides effective tools to assess and enhance data quality, laying the foundation for robust performance and interpretability in downstream analyses. Application to multimodal colorectal cancer datasets resulted in improved data quality, structuring, and robust encoding, as well as enhanced semantic information. We make eHDPrep available as an R package from CRAN (https://cran.r-project.org/package = eHDPrep) and GitHub (https://github.com/overton-group/eHDPrep).",,pdf:https://academic.oup.com/gigascience/article-pdf/doi/10.1093/gigascience/giad030/50383140/giad030.pdf; doi:https://doi.org/10.1093/gigascience/giad030; html:https://europepmc.org/articles/PMC10176503; pdf:https://europepmc.org/articles/PMC10176503?pdf=render
-33087383,https://doi.org/10.1136/bmjopen-2020-043010,Understanding and responding to COVID-19 in Wales: protocol for a privacy-protecting data platform for enhanced epidemiology and evaluation of interventions.,"Lyons J, Akbari A, Torabi F, Davies GI, North L, Griffiths R, Bailey R, Hollinghurst J, Fry R, Turner SL, Thompson D, Rafferty J, Mizen A, Orton C, Thompson S, Au-Yeung L, Cross L, Gravenor MB, Brophy S, Lucini B, John A, Szakmany T, Davies J, Davies C, Thomas DR, Williams C, Emmerson C, Cottrell S, Connor TR, Taylor C, Pugh RJ, Diggle P, John G, Scourfield S, Hunt J, Cunningham AM, Helliwell K, Lyons R.",,BMJ open,2020,2020-10-21,Y,epidemiology; Public Health; Health Informatics; Covid-19,,,"<h4>Introduction</h4>The emergence of the novel respiratory SARS-CoV-2 and subsequent COVID-19 pandemic have required rapid assimilation of population-level data to understand and control the spread of infection in the general and vulnerable populations. Rapid analyses are needed to inform policy development and target interventions to at-risk groups to prevent serious health outcomes. We aim to provide an accessible research platform to determine demographic, socioeconomic and clinical risk factors for infection, morbidity and mortality of COVID-19, to measure the impact of COVID-19 on healthcare utilisation and long-term health, and to enable the evaluation of natural experiments of policy interventions.<h4>Methods and analysis</h4>Two privacy-protecting population-level cohorts have been created and derived from multisourced demographic and healthcare data. The C20 cohort consists of 3.2 million people in Wales on the 1 January 2020 with follow-up until 31 May 2020. The complete cohort dataset will be updated monthly with some individual datasets available daily. The C16 cohort consists of 3 million people in Wales on the 1 January 2016 with follow-up to 31 December 2019. C16 is designed as a counterfactual cohort to provide contextual comparative population data on disease, health service utilisation and mortality. Study outcomes will: (a) characterise the epidemiology of COVID-19, (b) assess socioeconomic and demographic influences on infection and outcomes, (c) measure the impact of COVID-19 on short -term and longer-term population outcomes and (d) undertake studies on the transmission and spatial spread of infection.<h4>Ethics and dissemination</h4>The Secure Anonymised Information Linkage-independent Information Governance Review Panel has approved this study. The study findings will be presented to policy groups, public meetings, national and international conferences, and published in peer-reviewed journals.",,pdf:https://bmjopen.bmj.com/content/bmjopen/10/10/e043010.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-043010; html:https://europepmc.org/articles/PMC7580065; pdf:https://europepmc.org/articles/PMC7580065?pdf=render
 32341912,https://doi.org/10.1177/2235042x19893470,Urban-rural and socioeconomic status: Impact on multimorbidity prevalence in hospitalized patients.,"Robertson L, Ayansina D, Johnston M, Marks A, Black C.",,Journal of comorbidity,2020,2020-01-01,Y,Prevalence; Socioeconomic status; Hospitalization; Electronic Health Records; Multimorbidity; Urban–rural,,,"<h4>Objective</h4>The aim of this study was to describe multimorbidity prevalence in hospitalized adults, by urban-rural area of residence and socioeconomic status (SES).<h4>Methods</h4>Linked hospital episode data were used. Adults (≥18 years) admitted to hospital as an inpatient during 2014 in Grampian, Scotland, were included. Conditions were identified from admissions during the 5 years prior to the first admission in 2014. Multimorbidity was defined as ≥2 conditions and measured using Tonelli et al. based on International Classification of Diseases-10 coding (preselected list of 30 conditions). We used proportions and 95% confidence intervals (CIs) to summarize the prevalence of multimorbidity by age group, sex, urban-rural category and deprivation. The association between multimorbidity and patient characteristics was assessed using the <i>χ</i> <sup>2</sup> test.<h4>Results</h4>Forty one thousand five hundred and forty-five patients were included (median age 62, 52.6% female). Overall, 27.4% (95% CI 27.0, 27.8) of patients were multimorbid. Multimorbidity prevalence was 28.8% (95% CI 28.1, 29.5) in large urban versus 22.0% (95% CI 20.9, 23.3) in remote rural areas and 28.7% (95% CI 27.2, 30.3) in the most deprived versus 26.0% (95% CI 25.2, 26.9) in the least deprived areas. This effect was consistent in all age groups, but not statistically significant in the age group 18-29 years. Multimorbidity increased with age but was similar for males and females.<h4>Conclusion</h4>Given the scarcity of research into the effect of urban-rural area and SES on multimorbidity prevalence among hospitalized patients, these findings should inform future research into new models of care, including the consideration of urban-rural area and SES.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/2235042X19893470; doi:https://doi.org/10.1177/2235042X19893470; html:https://europepmc.org/articles/PMC7171988; pdf:https://europepmc.org/articles/PMC7171988?pdf=render
+33087383,https://doi.org/10.1136/bmjopen-2020-043010,Understanding and responding to COVID-19 in Wales: protocol for a privacy-protecting data platform for enhanced epidemiology and evaluation of interventions.,"Lyons J, Akbari A, Torabi F, Davies GI, North L, Griffiths R, Bailey R, Hollinghurst J, Fry R, Turner SL, Thompson D, Rafferty J, Mizen A, Orton C, Thompson S, Au-Yeung L, Cross L, Gravenor MB, Brophy S, Lucini B, John A, Szakmany T, Davies J, Davies C, Thomas DR, Williams C, Emmerson C, Cottrell S, Connor TR, Taylor C, Pugh RJ, Diggle P, John G, Scourfield S, Hunt J, Cunningham AM, Helliwell K, Lyons R.",,BMJ open,2020,2020-10-21,Y,epidemiology; Public Health; Health Informatics; Covid-19,,,"<h4>Introduction</h4>The emergence of the novel respiratory SARS-CoV-2 and subsequent COVID-19 pandemic have required rapid assimilation of population-level data to understand and control the spread of infection in the general and vulnerable populations. Rapid analyses are needed to inform policy development and target interventions to at-risk groups to prevent serious health outcomes. We aim to provide an accessible research platform to determine demographic, socioeconomic and clinical risk factors for infection, morbidity and mortality of COVID-19, to measure the impact of COVID-19 on healthcare utilisation and long-term health, and to enable the evaluation of natural experiments of policy interventions.<h4>Methods and analysis</h4>Two privacy-protecting population-level cohorts have been created and derived from multisourced demographic and healthcare data. The C20 cohort consists of 3.2 million people in Wales on the 1 January 2020 with follow-up until 31 May 2020. The complete cohort dataset will be updated monthly with some individual datasets available daily. The C16 cohort consists of 3 million people in Wales on the 1 January 2016 with follow-up to 31 December 2019. C16 is designed as a counterfactual cohort to provide contextual comparative population data on disease, health service utilisation and mortality. Study outcomes will: (a) characterise the epidemiology of COVID-19, (b) assess socioeconomic and demographic influences on infection and outcomes, (c) measure the impact of COVID-19 on short -term and longer-term population outcomes and (d) undertake studies on the transmission and spatial spread of infection.<h4>Ethics and dissemination</h4>The Secure Anonymised Information Linkage-independent Information Governance Review Panel has approved this study. The study findings will be presented to policy groups, public meetings, national and international conferences, and published in peer-reviewed journals.",,pdf:https://bmjopen.bmj.com/content/bmjopen/10/10/e043010.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-043010; html:https://europepmc.org/articles/PMC7580065; pdf:https://europepmc.org/articles/PMC7580065?pdf=render
 33948220,https://doi.org/10.1177/20552076211007661,Association between glycosylated haemoglobin and outcomes for patients discharged from hospital with diabetes: A health informatics approach.,"Robbins T, Sankaranarayanan S, Randeva H, Keung SNLC, Arvanitis TN.",,Digital health,2021,2021-01-01,Y,Biochemistry; Diabetes; Hospital Discharge; Readmission; Health Informatics,,,"<h4>Aims/objectives</h4>Extensive research considers associations between inpatient glycaemic control and outcomes during hospital admission; this cautions against overly tight glycaemic targets. Little research considers glycaemic control following hospital discharge. This is despite a clear understanding that people with diabetes are at increased risk of negative outcomes, following discharge. We evaluate absolute and relative Hba1c values, and frequency of Hba1c monitoring, on readmission and mortality rates for people discharged from hospital with diabetes.<h4>Methods</h4>All discharges (n = 46,357) with diabetes from a major tertiary referral centre over 3 years were extracted, including biochemistry data. We conducted an evaluation of association between Hba1c, mortality and readmission, statistical significance and standardised Cohen's D effect size calculations.<h4>Results</h4>399 patients had a Hba1c performed during their admission. 3,138 patients had a Hba1c within 1 year of discharge. Mean average Hba1c for readmissions was 57.82 vs 60.39 for not readmitted (p = 0.009, Cohen's D 0.28). Mean average number of days to Hba1c testing in readmitted was 97 vs 113 for those not readmitted (p = 0.00006, Cohen's D 0.39). Further evaluation of mortality outcomes, cohorts of T1DM and T2DM and association of relative change in Hba1c was performed.<h4>Conclusions</h4>Lower Hba1c values following discharge from hospital are significantly associated with increased risk of readmission, as is a shorter duration until testing. Similar patterns observed for mortality. Findings particularly prominent for T1DM. Further research needed to consider underlying causation and design of appropriate risk stratification models.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/20552076211007661; doi:https://doi.org/10.1177/20552076211007661; html:https://europepmc.org/articles/PMC8054217; pdf:https://europepmc.org/articles/PMC8054217?pdf=render
 31984360,https://doi.org/10.1093/jamiaopen/ooz009,Annotating and detecting phenotypic information for chronic obstructive pulmonary disease.,"Ju M, Short AD, Thompson P, Bakerly ND, Gkoutos GV, Tsaprouni L, Ananiadou S.",,JAMIA open,2019,2019-04-26,Y,Phenotype; Information Extraction; Natural Language Processing; chronic obstructive pulmonary disease; Text Mining,The Human Phenome,,"<h4>Objectives</h4>Chronic obstructive pulmonary disease (COPD) phenotypes cover a range of lung abnormalities. To allow text mining methods to identify pertinent and potentially complex information about these phenotypes from textual data, we have developed a novel annotated corpus, which we use to train a neural network-based named entity recognizer to detect fine-grained COPD phenotypic information.<h4>Materials and methods</h4>Since COPD phenotype descriptions often mention other concepts within them (proteins, treatments, etc.), our corpus annotations include both outermost phenotype descriptions and concepts nested within them. Our neural layered bidirectional long short-term memory conditional random field (BiLSTM-CRF) network firstly recognizes nested mentions, which are fed into subsequent BiLSTM-CRF layers, to help to recognize enclosing phenotype mentions.<h4>Results</h4>Our corpus of 30 full papers (available at: http://www.nactem.ac.uk/COPD) is annotated by experts with 27 030 phenotype-related concept mentions, most of which are automatically linked to UMLS Metathesaurus concepts. When trained using the corpus, our BiLSTM-CRF network outperforms other popular approaches in recognizing detailed phenotypic information.<h4>Discussion</h4>Information extracted by our method can facilitate efficient location and exploration of detailed information about phenotypes, for example, those specifically concerning reactions to treatments.<h4>Conclusion</h4>The importance of our corpus for developing methods to extract fine-grained information about COPD phenotypes is demonstrated through its successful use to train a layered BiLSTM-CRF network to extract phenotypic information at various levels of granularity. The minimal human intervention needed for training should permit ready adaption to extracting phenotypic information about other diseases.",COPD is linked with a number of lung abnormalities. This study has developed a computer algorithm to extract information about these abnormalities.,pdf:https://academic.oup.com/jamiaopen/article-pdf/2/2/261/32298683/ooz009.pdf; doi:https://doi.org/10.1093/jamiaopen/ooz009; html:https://europepmc.org/articles/PMC6951876; pdf:https://europepmc.org/articles/PMC6951876?pdf=render
 36530697,https://doi.org/10.3389/fpubh.2022.1035415,Associations between air pollution and multimorbidity in the UK Biobank: A cross-sectional study.,"Ronaldson A, Arias de la Torre J, Ashworth M, Hansell AL, Hotopf M, Mudway I, Stewart R, Dregan A, Bakolis I.",,Frontiers in public health,2022,2022-12-02,Y,Air pollution; Nitrogen dioxide; particulate matter; Health Status; Exploratory Factor Analysis; Multimorbidity,,,"<h4>Background</h4>Long-term exposure to air pollution concentrations is known to be adversely associated with a broad range of single non-communicable diseases, but its role in multimorbidity has not been investigated in the UK. We aimed to assess associations between long-term air pollution exposure and multimorbidity status, severity, and patterns using the UK Biobank cohort.<h4>Methods</h4>Multimorbidity status was calculated based on 41 physical and mental conditions. We assessed cross-sectional associations between annual modeled particulate matter (PM)<sub>2.5</sub>, PM<sub>coarse</sub>, PM<sub>10</sub>, and nitrogen dioxide (NO<sub>2</sub>) concentrations (μg/m<sup>3</sup>-modeled to residential address) and multimorbidity status at the baseline assessment (2006-2010) in 364,144 people (mean age: 52.2 ± 8.1 years, 52.6% female). Air pollutants were categorized into quartiles to assess dose-response associations. Among those with multimorbidity (≥2 conditions; <i>n</i> = 156,395) we assessed associations between air pollutant exposure levels and multimorbidity severity and multimorbidity patterns, which were identified using exploratory factor analysis. Associations were explored using generalized linear models adjusted for sociodemographic, behavioral, and environmental indicators.<h4>Results</h4>Higher exposures to PM<sub>2.5</sub>, and NO<sub>2</sub> were associated with multimorbidity status in a dose-dependent manner. These associations were strongest when we compared the highest air pollution quartile (quartile 4: Q4) with the lowest quartile (Q1) [PM<sub>2.5</sub>: adjusted odds ratio (adjOR) = 1.21 (95% CI = 1.18, 1.24); NO<sub>2</sub>: adjOR = 1.19 (95 % CI = 1.16, 1.23)]. We also observed dose-response associations between air pollutant exposures and multimorbidity severity scores. We identified 11 multimorbidity patterns. Air pollution was associated with several multimorbidity patterns with strongest associations (Q4 vs. Q1) observed for neurological (stroke, epilepsy, alcohol/substance dependency) [PM<sub>2.5</sub>: adjOR = 1.31 (95% CI = 1.14, 1.51); NO<sub>2</sub>: adjOR = 1.33 (95% CI = 1.11, 1.60)] and respiratory patterns (COPD, asthma) [PM<sub>2.5</sub>: adjOR = 1.24 (95% CI = 1.16, 1.33); NO<sub>2</sub>: adjOR = 1.26 (95% CI = 1.15, 1.38)].<h4>Conclusions</h4>This cross-sectional study provides evidence that exposure to air pollution might be associated with having multimorbid, multi-organ conditions. Longitudinal studies are needed to further explore these associations.",,pdf:https://www.frontiersin.org/articles/10.3389/fpubh.2022.1035415/pdf; doi:https://doi.org/10.3389/fpubh.2022.1035415; html:https://europepmc.org/articles/PMC9755180; pdf:https://europepmc.org/articles/PMC9755180?pdf=render
@@ -475,61 +475,61 @@ PMC10910267,https://doi.org/,Development and evaluation of a tool to optimise in
 38781449,https://doi.org/10.1093/infdis/jiae265,Fecal microbiota and volatile metabolome pattern alterations precede late-onset meningitis in preterm neonates.,"Frerichs NM, Deianova N, El Manouni El Hassani S, Acharjee A, Quraishi MN, de Boode WP, Cossey V, Hulzebos CV, van Kaam AH, Kramer BW, d'Haens E, de Jonge WJ, Vijlbrief DC, van Weissenbruch MM, Daulton E, Wicaksono AN, Covington JA, Benninga MA, de Boer NKH, van Goudoever JB, Niemarkt HJ, de Meij TGJ.",,The Journal of infectious diseases,2024,2024-05-23,N,volatile organic compounds; Preterm Neonates; Microbiota Analysis; Late-onset Meningitis,,,"<h4>Objective</h4>The fecal microbiota and metabolome are hypothesized to be altered before late-onset neonatal meningitis (LOM), in analogy to late-onset sepsis (LOS). The present study aimed to identify fecal microbiota composition and volatile metabolomics preceding LOM.<h4>Methods</h4>Cases and gestational age-matched controls were selected from a prospective, longitudinal preterm cohort study (born <30 weeks' gestation) at nine neonatal intensive care units. The microbial composition (16S rRNA sequencing) and volatile metabolome (gas chromatography-ion mobility spectrometry (GC-IMS) and GC-time-of-flight-mass spectrometry (GC-TOF-MS)), were analyzed in fecal samples 1-10 days pre-LOM.<h4>Results</h4>Of 1397 included infants, 21 were diagnosed with LOM (1.5%), and 19 with concomitant LOS (90%). Random Forest classification and MaAsLin2 analysis found similar microbiota features contribute to the discrimination of fecal pre-LOM samples versus controls. A Random Forest model based on six microbiota features accurately predicts LOM 1-3 days before diagnosis with an area under the curve (AUC) of 0.88 (n=147). Pattern recognition analysis by GC-IMS revealed an AUC of 0.70-0.76 (P<0.05) in the three days pre-LOM (n=92). No single discriminative metabolites were identified by GC-TOF-MS (n=66).<h4>Conclusion</h4>Infants with LOM could be accurately discriminated from controls based on preclinical microbiota composition, while alterations in the volatile metabolome were moderately associated with preclinical LOM.",,pdf:https://academic.oup.com/jid/advance-article-pdf/doi/10.1093/infdis/jiae265/57846230/jiae265.pdf; doi:https://doi.org/10.1093/infdis/jiae265
 37363797,https://doi.org/10.1016/j.lanepe.2023.100653,Impact of COVID-19 on broad-spectrum antibiotic prescribing for common infections in primary care in England: a time-series analyses using OpenSAFELY and effects of predictors including deprivation.,"Zhong X, Pate A, Yang YT, Fahmi A, Ashcroft DM, Goldacre B, MacKenna B, Mehrkar A, Bacon SC, Massey J, Fisher L, Inglesby P, OpenSAFELY collaborative, Hand K, van Staa T, Palin V.",,The Lancet regional health. Europe,2023,2023-05-16,Y,Antimicrobial resistance; Primary Care; Broad-spectrum Antibiotics; Covid-19 Pandemic,,,"<h4>Background</h4>The COVID-19 pandemic impacted the healthcare systems, adding extra pressure to reduce antimicrobial resistance. Therefore, we aimed to evaluate changes in antibiotic prescription patterns after COVID-19 started.<h4>Methods</h4>With the approval of NHS England, we used the OpenSAFELY platform to access the TPP SystmOne electronic health record (EHR) system in primary care and selected patients prescribed antibiotics from 2019 to 2021. To evaluate the impact of COVID-19 on broad-spectrum antibiotic prescribing, we evaluated prescribing rates and its predictors and used interrupted time series analysis by fitting binomial logistic regression models.<h4>Findings</h4>Over 32 million antibiotic prescriptions were extracted over the study period; 8.7% were broad-spectrum. The study showed increases in broad-spectrum antibiotic prescribing (odds ratio [OR] 1.37; 95% confidence interval [CI] 1.36-1.38) as an immediate impact of the pandemic, followed by a gradual recovery with a 1.1-1.2% decrease in odds of broad-spectrum prescription per month. The same pattern was found within subgroups defined by age, sex, region, ethnicity, and socioeconomic deprivation quintiles. More deprived patients were more likely to receive broad-spectrum antibiotics, which differences remained stable over time. The most significant increase in broad-spectrum prescribing was observed for lower respiratory tract infection (OR 2.33; 95% CI 2.1-2.50) and otitis media (OR 1.96; 95% CI 1.80-2.13).<h4>Interpretation</h4>An immediate reduction in antibiotic prescribing and an increase in the proportion of broad-spectrum antibiotic prescribing in primary care was observed. The trends recovered to pre-pandemic levels, but the consequence of the COVID-19 pandemic on AMR needs further investigation.<h4>Funding</h4>This work was supported by Health Data Research UK and by National Institute for Health Research.",,doi:https://doi.org/10.1016/j.lanepe.2023.100653; doi:https://doi.org/10.1016/j.lanepe.2023.100653; html:https://europepmc.org/articles/PMC10186397; pdf:https://europepmc.org/articles/PMC10186397?pdf=render
 34750106,https://doi.org/10.3399/bjgp.2021.0376,Trends and clinical characteristics of COVID-19 vaccine recipients: a federated analysis of 57.9 million patients’ primary care records in situ using OpenSAFELY.,"Curtis HJ, Inglesby P, Morton CE, MacKenna B, Green A, Hulme W, Walker AJ, Morley J, Mehrkar A, Bacon S, Hickman G, Bates C, Croker R, Evans D, Ward T, Cockburn J, Davy S, Bhaskaran K, Schultze A, Rentsch CT, Williamson EJ, Rowan A, Fisher L, McDonald HI, Tomlinson L, Mathur R, Drysdale H, Eggo RM, Wing K, Wong AY, Forbes H, Parry J, Hester F, Harper S, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Griffiths P, Fowles A, Parkes N, Douglas IJ, Evans SJ, Smeeth L, Goldacre B, (The OpenSAFELY Collaborative).",,The British journal of general practice : the journal of the Royal College of General Practitioners,2022,2021-12-31,Y,Ethnic Groups; Vaccination; General Practice; Nhs England; Covid-19; Sars-cov-2,,,"<h4>Background</h4>On 8 December 2020 NHS England administered the first COVID-19 vaccination.<h4>Aim</h4>To describe trends and variation in vaccine coverage in different clinical and demographic groups in the first 100 days of the vaccine rollout.<h4>Design and setting</h4>With the approval of NHS England, a cohort study was conducted of 57.9 million patient records in general practice in England, <i>in situ</i> and within the infrastructure of the electronic health record software vendors EMIS and TPP using OpenSAFELY.<h4>Method</h4>Vaccine coverage across various subgroups of Joint Committee on Vaccination and Immunisation (JCVI) priority cohorts is described.<h4>Results</h4>A total of 20 852 692 patients (36.0%) received a vaccine between 8 December 2020 and 17 March 2021. Of patients aged ≥80 years not in a care home (JCVI group 2) 94.7% received a vaccine, but with substantial variation by ethnicity (White 96.2%, Black 68.3%) and deprivation (least deprived 96.6%, most deprived 90.7%). Patients with pre-existing medical conditions were more likely to be vaccinated with two exceptions: severe mental illness (89.5%) and learning disability (91.4%). There were 275 205 vaccine recipients who were identified as care home residents (JCVI group 1; 91.2% coverage). By 17 March, 1 257 914 (6.0%) recipients had a second dose.<h4>Conclusion</h4>The NHS rapidly delivered mass vaccination. In this study a data-monitoring framework was deployed using publicly auditable methods and a secure <i>in situ</i> processing model, using linked but pseudonymised patient-level NHS data for 57.9 million patients. Targeted activity may be needed to address lower vaccination coverage observed among certain key groups.",,doi:https://doi.org/10.3399/bjgp.2021.0376; doi:https://doi.org/10.3399/BJGP.2021.0376; html:https://europepmc.org/articles/PMC8589463; pdf:https://europepmc.org/articles/PMC8589463?pdf=render
-37363796,https://doi.org/10.1016/j.lanepe.2023.100636,Comparative effectiveness of two- and three-dose COVID-19 vaccination schedules involving AZD1222 and BNT162b2 in people with kidney disease: a linked OpenSAFELY and UK Renal Registry cohort study.,"OpenSAFELY Collaborative, Parker EPK, Horne EMF, Hulme WJ, Tazare J, Zheng B, Carr EJ, Loud F, Lyon S, Mahalingasivam V, MacKenna B, Mehrkar A, Scanlon M, Santhakumaran S, Steenkamp R, Goldacre B, Sterne JAC, Nitsch D, Tomlinson LA, LH&W NCS (or CONVALESCENCE) Collaborative.",,The Lancet regional health. Europe,2023,2023-05-03,Y,Vaccination; Effectiveness; Chronic Kidney Disease; Nhs England; Covid-19; Sars-cov-2,,,"<h4>Background</h4>Kidney disease is a key risk factor for COVID-19-related mortality and suboptimal vaccine response. Optimising vaccination strategies is essential to reduce the disease burden in this vulnerable population. We therefore compared the effectiveness of two- and three-dose schedules involving AZD1222 (AZ; ChAdOx1-S) and BNT162b2 (BNT) among people with kidney disease in England.<h4>Methods</h4>With the approval of NHS England, we performed a retrospective cohort study among people with moderate-to-severe kidney disease. Using linked primary care and UK Renal Registry records in the OpenSAFELY-TPP platform, we identified adults with stage 3-5 chronic kidney disease, dialysis recipients, and kidney transplant recipients. We used Cox proportional hazards models to compare COVID-19-related outcomes and non-COVID-19 death after two-dose (AZ-AZ vs BNT-BNT) and three-dose (AZ-AZ-BNT vs BNT-BNT-BNT) schedules.<h4>Findings</h4>After two doses, incidence during the Delta wave was higher in AZ-AZ (n = 257,580) than BNT-BNT recipients (n = 169,205; adjusted hazard ratios [95% CIs] 1.43 [1.37-1.50], 1.59 [1.43-1.77], 1.44 [1.12-1.85], and 1.09 [1.02-1.17] for SARS-CoV-2 infection, COVID-19-related hospitalisation, COVID-19-related death, and non-COVID-19 death, respectively). Findings were consistent across disease subgroups, including dialysis and transplant recipients. After three doses, there was little evidence of differences between AZ-AZ-BNT (n = 220,330) and BNT-BNT-BNT recipients (n = 157,065) for any outcome during a period of Omicron dominance.<h4>Interpretation</h4>Among individuals with moderate-to-severe kidney disease, two doses of BNT conferred stronger protection than AZ against SARS-CoV-2 infection and severe disease. A subsequent BNT dose levelled the playing field, emphasising the value of heterologous RNA doses in vulnerable populations.<h4>Funding</h4>National Core Studies, Wellcome Trust, MRC, and Health Data Research UK.",,doi:https://doi.org/10.1016/j.lanepe.2023.100636; doi:https://doi.org/10.1016/j.lanepe.2023.100636; html:https://europepmc.org/articles/PMC10155829; pdf:https://europepmc.org/articles/PMC10155829?pdf=render
 34340970,https://doi.org/10.3399/bjgp.2021.0301,Clinical coding of long COVID in English primary care: a federated analysis of 58 million patient records <i>in situ</i> using OpenSAFELY.,"Walker AJ, MacKenna B, Inglesby P, Tomlinson L, Rentsch CT, Curtis HJ, Morton CE, Morley J, Mehrkar A, Bacon S, Hickman G, Bates C, Croker R, Evans D, Ward T, Cockburn J, Davy S, Bhaskaran K, Schultze A, Williamson EJ, Hulme WJ, McDonald HI, Mathur R, Eggo RM, Wing K, Wong AY, Forbes H, Tazare J, Parry J, Hester F, Harper S, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Griffiths P, Fowles A, Parkes N, Douglas IJ, Evans SJ, (The OpenSAFELY Collaborative).",,The British journal of general practice : the journal of the Royal College of General Practitioners,2021,2021-10-28,Y,Primary Health Care; General Practice; Electronic Health Records; Covid-19; Long Covid,,,"<h4>Background</h4>Long COVID describes new or persistent symptoms at least 4 weeks after onset of acute COVID-19. Clinical codes to describe this phenomenon were recently created.<h4>Aim</h4>To describe the use of long-COVID codes, and variation of use by general practice, demographic variables, and over time.<h4>Design and setting</h4>Population-based cohort study in English primary care.<h4>Method</h4>Working on behalf of NHS England, OpenSAFELY data were used encompassing 96% of the English population between 1 February 2020 and 25 May 2021. The proportion of people with a recorded code for long COVID was measured overall and by demographic factors, electronic health record software system (EMIS or TPP), and week.<h4>Results</h4>Long COVID was recorded for 23 273 people. Coding was unevenly distributed among practices, with 26.7% of practices having never used the codes. Regional variation ranged between 20.3 per 100 000 people for East of England (95% confidence interval [CI] = 19.3 to 21.4) and 55.6 per 100 000 people in London (95% CI = 54.1 to 57.1). Coding was higher among females (52.1, 95% CI = 51.3 to 52.9) than males (28.1, 95% CI = 27.5 to 28.7), and higher among practices using EMIS (53.7, 95% CI = 52.9 to 54.4) than those using TPP (20.9, 95% CI = 20.3 to 21.4).<h4>Conclusion</h4>Current recording of long COVID in primary care is very low, and variable between practices. This may reflect patients not presenting; clinicians and patients holding different diagnostic thresholds; or challenges with the design and communication of diagnostic codes. Increased awareness of diagnostic codes is recommended to facilitate research and planning of services, and also surveys with qualitative work to better evaluate clinicians' understanding of the diagnosis.",,pdf:https://bjgp.org/content/bjgp/71/712/e806.full.pdf; doi:https://doi.org/10.3399/BJGP.2021.0301; html:https://europepmc.org/articles/PMC8340730; pdf:https://europepmc.org/articles/PMC8340730?pdf=render
+37363796,https://doi.org/10.1016/j.lanepe.2023.100636,Comparative effectiveness of two- and three-dose COVID-19 vaccination schedules involving AZD1222 and BNT162b2 in people with kidney disease: a linked OpenSAFELY and UK Renal Registry cohort study.,"OpenSAFELY Collaborative, Parker EPK, Horne EMF, Hulme WJ, Tazare J, Zheng B, Carr EJ, Loud F, Lyon S, Mahalingasivam V, MacKenna B, Mehrkar A, Scanlon M, Santhakumaran S, Steenkamp R, Goldacre B, Sterne JAC, Nitsch D, Tomlinson LA, LH&W NCS (or CONVALESCENCE) Collaborative.",,The Lancet regional health. Europe,2023,2023-05-03,Y,Vaccination; Effectiveness; Chronic Kidney Disease; Nhs England; Covid-19; Sars-cov-2,,,"<h4>Background</h4>Kidney disease is a key risk factor for COVID-19-related mortality and suboptimal vaccine response. Optimising vaccination strategies is essential to reduce the disease burden in this vulnerable population. We therefore compared the effectiveness of two- and three-dose schedules involving AZD1222 (AZ; ChAdOx1-S) and BNT162b2 (BNT) among people with kidney disease in England.<h4>Methods</h4>With the approval of NHS England, we performed a retrospective cohort study among people with moderate-to-severe kidney disease. Using linked primary care and UK Renal Registry records in the OpenSAFELY-TPP platform, we identified adults with stage 3-5 chronic kidney disease, dialysis recipients, and kidney transplant recipients. We used Cox proportional hazards models to compare COVID-19-related outcomes and non-COVID-19 death after two-dose (AZ-AZ vs BNT-BNT) and three-dose (AZ-AZ-BNT vs BNT-BNT-BNT) schedules.<h4>Findings</h4>After two doses, incidence during the Delta wave was higher in AZ-AZ (n = 257,580) than BNT-BNT recipients (n = 169,205; adjusted hazard ratios [95% CIs] 1.43 [1.37-1.50], 1.59 [1.43-1.77], 1.44 [1.12-1.85], and 1.09 [1.02-1.17] for SARS-CoV-2 infection, COVID-19-related hospitalisation, COVID-19-related death, and non-COVID-19 death, respectively). Findings were consistent across disease subgroups, including dialysis and transplant recipients. After three doses, there was little evidence of differences between AZ-AZ-BNT (n = 220,330) and BNT-BNT-BNT recipients (n = 157,065) for any outcome during a period of Omicron dominance.<h4>Interpretation</h4>Among individuals with moderate-to-severe kidney disease, two doses of BNT conferred stronger protection than AZ against SARS-CoV-2 infection and severe disease. A subsequent BNT dose levelled the playing field, emphasising the value of heterologous RNA doses in vulnerable populations.<h4>Funding</h4>National Core Studies, Wellcome Trust, MRC, and Health Data Research UK.",,doi:https://doi.org/10.1016/j.lanepe.2023.100636; doi:https://doi.org/10.1016/j.lanepe.2023.100636; html:https://europepmc.org/articles/PMC10155829; pdf:https://europepmc.org/articles/PMC10155829?pdf=render
+34598993,https://doi.org/10.1136/bmjopen-2021-054410,"Changes in neonatal admissions, care processes and outcomes in England and Wales during the COVID-19 pandemic: a whole population cohort study.","Greenbury SF, Longford N, Ougham K, Angelini ED, Battersby C, Uthaya S, Modi N.",,BMJ open,2021,2021-10-01,Y,Public Health; Neonatology; Neonatal Intensive & Critical Care,,,"<h4>Objectives</h4>The COVID-19 pandemic instigated multiple societal and healthcare interventions with potential to affect perinatal practice. We evaluated population-level changes in preterm and full-term admissions to neonatal units, care processes and outcomes.<h4>Design</h4>Observational cohort study using the UK National Neonatal Research Database.<h4>Setting</h4>England and Wales.<h4>Participants</h4>Admissions to National Health Service neonatal units from 2012 to 2020.<h4>Main outcome measures</h4>Admissions by gestational age, ethnicity and Index of Multiple Deprivation, and key care processes and outcomes.<h4>Methods</h4>We calculated differences in numbers and rates between April and June 2020 (spring), the first 3 months of national lockdown (COVID-19 period), and December 2019-February 2020 (winter), prior to introduction of mitigation measures, and compared them with the corresponding differences in the previous 7 years. We considered the COVID-19 period highly unusual if the spring-winter difference was smaller or larger than all previous corresponding differences, and calculated the level of confidence in this conclusion.<h4>Results</h4>Marked fluctuations occurred in all measures over the 8 years with several highly unusual changes during the COVID-19 period. Total admissions fell, having risen over all previous years (COVID-19 difference: -1492; previous 7-year difference range: +100, +1617; p<0.001); full-term black admissions rose (+66; -64, +35; p<0.001) whereas Asian (-137; -14, +101; p<0.001) and white (-319; -235, +643: p<0.001) admissions fell. Transfers to higher and lower designation neonatal units increased (+129; -4, +88; p<0.001) and decreased (-47; -25, +12; p<0.001), respectively. Total preterm admissions decreased (-350; -26, +479; p<0.001). The fall in extremely preterm admissions was most marked in the two lowest socioeconomic quintiles.<h4>Conclusions</h4>Our findings indicate substantial changes occurred in care pathways and clinical thresholds, with disproportionate effects on black ethnic groups, during the immediate COVID-19 period, and raise the intriguing possibility that non-healthcare interventions may reduce extremely preterm births.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/10/e054410.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-054410; html:https://europepmc.org/articles/PMC8488283; pdf:https://europepmc.org/articles/PMC8488283?pdf=render
 37387161,https://doi.org/10.1093/bioinformatics/btad240,SynBa: improved estimation of drug combination synergies with uncertainty quantification.,"Zhang H, Ek CH, Rattray M, Milo M.",,"Bioinformatics (Oxford, England)",2023,2023-06-01,Y,,,,"<h4>Motivation</h4>There exists a range of different quantification frameworks to estimate the synergistic effect of drug combinations. The diversity and disagreement in estimates make it challenging to determine which combinations from a large drug screening should be proceeded with. Furthermore, the lack of accurate uncertainty quantification for those estimates precludes the choice of optimal drug combinations based on the most favourable synergistic effect.<h4>Results</h4>In this work, we propose SynBa, a flexible Bayesian approach to estimate the uncertainty of the synergistic efficacy and potency of drug combinations, so that actionable decisions can be derived from the model outputs. The actionability is enabled by incorporating the Hill equation into SynBa, so that the parameters representing the potency and the efficacy can be preserved. Existing knowledge may be conveniently inserted due to the flexibility of the prior, as shown by the empirical Beta prior defined for the normalized maximal inhibition. Through experiments on large combination screenings and comparison against benchmark methods, we show that SynBa provides improved accuracy of dose-response predictions and better-calibrated uncertainty estimation for the parameters and the predictions.<h4>Availability and implementation</h4>The code for SynBa is available at https://github.com/HaotingZhang1/SynBa. The datasets are publicly available (DOI of DREAM: 10.7303/syn4231880; DOI of the NCI-ALMANAC subset: 10.5281/zenodo.4135059).",,pdf:https://academic.oup.com/bioinformatics/article-pdf/39/Supplement_1/i121/50741599/btad240.pdf; doi:https://doi.org/10.1093/bioinformatics/btad240; html:https://europepmc.org/articles/PMC10311304; pdf:https://europepmc.org/articles/PMC10311304?pdf=render
 37595069,https://doi.org/10.1093/ageing/afad141,Effectiveness of successive booster vaccine doses against SARS-CoV-2 related mortality in residents of long-term care facilities in the VIVALDI study.,"Stirrup O, Shrotri M, Adams NL, Krutikov M, Azmi B, Monakhov I, Tut G, Moss P, Hayward A, Copas A, Shallcross L.",,Age and ageing,2023,2023-08-01,Y,Older People; Vaccine Effectiveness; Long-term Care Facilities; Covid-19; Sars-cov-2; Omicron,,,"<h4>Background</h4>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused severe disease in unvaccinated long-term care facility (LTCF) residents. Initial booster vaccination following primary vaccination is known to provide strong short-term protection, but data are limited on duration of protection and the protective effect of further booster vaccinations.<h4>Objective</h4>To evaluate the effectiveness of third, fourth and fifth dose booster vaccination against SARS-CoV-2 related mortality amongst older residents of LTCFs.<h4>Design</h4>Prospective cohort study.<h4>Setting</h4>LTCFs for older people in England participating in the VIVALDI study.<h4>Methods</h4>Residents aged >65 years at participating LTCFs were eligible for inclusion if they had at least one polymerase chain reaction or lateral flow device result within the analysis period 1 January 2022 to 31 December 2022. We excluded individuals who had not received at least two vaccine doses before the analysis period. Cox regression was used to estimate relative hazards of SARS-CoV-2 related mortality following 1-3 booster vaccinations compared with primary vaccination, stratified by previous SARS-CoV-2 infection and adjusting for age, sex and LTCF size (total beds).<h4>Results</h4>A total of 13,407 residents were included. Our results indicate that third, fourth and fifth dose booster vaccination provide additional short-term protection against SARS-CoV-2 related mortality relative to primary vaccination, with consistent stabilisation beyond 112 days to 45-75% reduction in risk relative to primary vaccination.<h4>Conclusions</h4>Successive booster vaccination doses provide additional short-term protection against SARS-CoV-2 related mortality amongst older LTCF residents. However, we did not find evidence of a longer-term reduction in risk beyond that provided by initial booster vaccination.",,pdf:https://academic.oup.com/ageing/article-pdf/52/8/afad141/51124726/afad141.pdf; doi:https://doi.org/10.1093/ageing/afad141; html:https://europepmc.org/articles/PMC10438206; pdf:https://europepmc.org/articles/PMC10438206?pdf=render
-34598993,https://doi.org/10.1136/bmjopen-2021-054410,"Changes in neonatal admissions, care processes and outcomes in England and Wales during the COVID-19 pandemic: a whole population cohort study.","Greenbury SF, Longford N, Ougham K, Angelini ED, Battersby C, Uthaya S, Modi N.",,BMJ open,2021,2021-10-01,Y,Public Health; Neonatology; Neonatal Intensive & Critical Care,,,"<h4>Objectives</h4>The COVID-19 pandemic instigated multiple societal and healthcare interventions with potential to affect perinatal practice. We evaluated population-level changes in preterm and full-term admissions to neonatal units, care processes and outcomes.<h4>Design</h4>Observational cohort study using the UK National Neonatal Research Database.<h4>Setting</h4>England and Wales.<h4>Participants</h4>Admissions to National Health Service neonatal units from 2012 to 2020.<h4>Main outcome measures</h4>Admissions by gestational age, ethnicity and Index of Multiple Deprivation, and key care processes and outcomes.<h4>Methods</h4>We calculated differences in numbers and rates between April and June 2020 (spring), the first 3 months of national lockdown (COVID-19 period), and December 2019-February 2020 (winter), prior to introduction of mitigation measures, and compared them with the corresponding differences in the previous 7 years. We considered the COVID-19 period highly unusual if the spring-winter difference was smaller or larger than all previous corresponding differences, and calculated the level of confidence in this conclusion.<h4>Results</h4>Marked fluctuations occurred in all measures over the 8 years with several highly unusual changes during the COVID-19 period. Total admissions fell, having risen over all previous years (COVID-19 difference: -1492; previous 7-year difference range: +100, +1617; p<0.001); full-term black admissions rose (+66; -64, +35; p<0.001) whereas Asian (-137; -14, +101; p<0.001) and white (-319; -235, +643: p<0.001) admissions fell. Transfers to higher and lower designation neonatal units increased (+129; -4, +88; p<0.001) and decreased (-47; -25, +12; p<0.001), respectively. Total preterm admissions decreased (-350; -26, +479; p<0.001). The fall in extremely preterm admissions was most marked in the two lowest socioeconomic quintiles.<h4>Conclusions</h4>Our findings indicate substantial changes occurred in care pathways and clinical thresholds, with disproportionate effects on black ethnic groups, during the immediate COVID-19 period, and raise the intriguing possibility that non-healthcare interventions may reduce extremely preterm births.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/10/e054410.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-054410; html:https://europepmc.org/articles/PMC8488283; pdf:https://europepmc.org/articles/PMC8488283?pdf=render
 37480048,https://doi.org/10.1186/s12872-023-03394-6,"Associations of circulating fatty acids with incident coronary heart disease: a prospective study of 89,242 individuals in UK Biobank.","Jin D, Trichia E, Islam N, Lewington S, Lacey B.",,BMC cardiovascular disorders,2023,2023-07-21,Y,Fatty acids; Lipids; Nuclear magnetic resonance; Coronary Heart Disease; Uk Biobank,,,"<h4>Background</h4>The role of fatty acids in coronary heart disease (CHD) remains uncertain. There is little evidence from large-scale epidemiological studies on the relevance of circulating fatty acids levels to CHD risk. This study aims to examine the independent associations of the major circulating types of fatty acids with CHD risk.<h4>Methods</h4>UK Biobank is a prospective study of adults aged 40-69 in 2006-2010; in 2012-2013, a subset of the participants were resurveyed. Analyses were restricted to 89,242 participants with baseline plasma fatty acids (measured using nuclear magnetic resonance spectroscopy) and without prior CHD. Cox proportional hazards models were used to estimate hazard ratios (HRs) for the associations with incidence CHD, defined as the first-ever myocardial infarction, unstable angina pectoris, coronary-related death, or relevant procedure. And the major types of fatty acids were mutually adjusted to examine the independent associations. Hazard ratios were corrected for regression dilution using the correlation of baseline and resurvey fatty acids measures.<h4>Results</h4>During a median follow-up of 11.8 years, 3,815 incident cases of CHD occurred. Independently of other fatty acids, CHD risk was positively associated with saturated fatty acids (SFA) and monounsaturated fatty acids (MUFA), inversely associated with omega-3 polyunsaturated fatty acids (PUFA), but there was no strong evidence of an association with omega-6 PUFA: HR per standard deviation higher were 1.14 (95% CI, 1.09-1.20), 1.15 (1.10-1.21), 0.91 (0.87-0.94), and 1.04 (0.99-1.09) respectively. Independently of triglycerides and cholesterol, the inverse association with omega-3 PUFA was not materially changed, but the positive associations with SFA and MUFA attenuated to null after adjusting for triglycerides levels.<h4>Conclusions</h4>This large-scale study has quantitated the independent associations of circulating fatty acids with CHD risk. Omega-3 PUFA was inversely related to CHD risk, independently of other fatty acids and major lipid fractions. By contrast, independently of other fatty acids, the positive associations of circulating SFA and MUFA with CHD risk were mostly attributed to their relationship with triglycerides.",,pdf:https://bmccardiovascdisord.biomedcentral.com/counter/pdf/10.1186/s12872-023-03394-6; doi:https://doi.org/10.1186/s12872-023-03394-6; html:https://europepmc.org/articles/PMC10362581; pdf:https://europepmc.org/articles/PMC10362581?pdf=render
 38519155,https://doi.org/10.1016/s2589-7500(24)00025-6,Foresight-a generative pretrained transformer for modelling of patient timelines using electronic health records: a retrospective modelling study.,"Kraljevic Z, Bean D, Shek A, Bendayan R, Hemingway H, Yeung JA, Deng A, Baston A, Ross J, Idowu E, Teo JT, Dobson RJB.",,The Lancet. Digital health,2024,2024-04-01,Y,,,,"<h4>Background</h4>An electronic health record (EHR) holds detailed longitudinal information about a patient's health status and general clinical history, a large portion of which is stored as unstructured, free text. Existing approaches to model a patient's trajectory focus mostly on structured data and a subset of single-domain outcomes. This study aims to evaluate the effectiveness of Foresight, a generative transformer in temporal modelling of patient data, integrating both free text and structured formats, to predict a diverse array of future medical outcomes, such as disorders, substances (eg, to do with medicines, allergies, or poisonings), procedures, and findings (eg, relating to observations, judgements, or assessments).<h4>Methods</h4>Foresight is a novel transformer-based pipeline that uses named entity recognition and linking tools to convert EHR document text into structured, coded concepts, followed by providing probabilistic forecasts for future medical events, such as disorders, substances, procedures, and findings. The Foresight pipeline has four main components: (1) CogStack (data retrieval and preprocessing); (2) the Medical Concept Annotation Toolkit (structuring of the free-text information from EHRs); (3) Foresight Core (deep-learning model for biomedical concept modelling); and (4) the Foresight web application. We processed the entire free-text portion from three different hospital datasets (King's College Hospital [KCH], South London and Maudsley [SLaM], and the US Medical Information Mart for Intensive Care III [MIMIC-III]), resulting in information from 811 336 patients and covering both physical and mental health institutions. We measured the performance of models using custom metrics derived from precision and recall.<h4>Findings</h4>Foresight achieved a precision@10 (ie, of 10 forecasted candidates, at least one is correct) of 0·68 (SD 0·0027) for the KCH dataset, 0·76 (0·0032) for the SLaM dataset, and 0·88 (0·0018) for the MIMIC-III dataset, for forecasting the next new disorder in a patient timeline. Foresight also achieved a precision@10 value of 0·80 (0·0013) for the KCH dataset, 0·81 (0·0026) for the SLaM dataset, and 0·91 (0·0011) for the MIMIC-III dataset, for forecasting the next new biomedical concept. In addition, Foresight was validated on 34 synthetic patient timelines by five clinicians and achieved a relevancy of 33 (97% [95% CI 91-100]) of 34 for the top forecasted candidate disorder. As a generative model, Foresight can forecast follow-on biomedical concepts for as many steps as required.<h4>Interpretation</h4>Foresight is a general-purpose model for biomedical concept modelling that can be used for real-world risk forecasting, virtual trials, and clinical research to study the progression of disorders, to simulate interventions and counterfactuals, and for educational purposes.<h4>Funding</h4>National Health Service Artificial Intelligence Laboratory, National Institute for Health and Care Research Biomedical Research Centre, and Health Data Research UK.",,doi:https://doi.org/10.1016/S2589-7500(24)00025-6; html:https://europepmc.org/articles/PMC11220626
 38686701,https://doi.org/10.1210/clinem/dgae119,"The Association of Cardiometabolic, Diet and Lifestyle Parameters With Plasma Glucagon-like Peptide-1: An IMI DIRECT Study.","Eriksen R, White MC, Dawed AY, Perez IG, Posma JM, Haid M, Sharma S, Prehn C, Thomas EL, Koivula RW, Bizzotto R, Mari A, Giordano GN, Pavo I, Schwenk JM, De Masi F, Tsirigos KD, Brunak S, Viñuela A, Mahajan A, McDonald TJ, Kokkola T, Rutters F, Beulens J, Muilwijk M, Blom M, Elders P, Hansen TH, Fernandez-Tajes J, Jones A, Jennison C, Walker M, McCarthy MI, Pedersen O, Ruetten H, Forgie I, Holst JJ, Thomsen HS, Ridderstråle M, Bell JD, Adamski J, Franks PW, Hansen T, Holmes E, Frost G, Pearson ER.",,The Journal of clinical endocrinology and metabolism,2024,2024-08-01,Y,Obesity; Diet; Nutrition; Insulin resistance; Type 2 diabetes; Prediabetes; Incretin; Glp-1; Liver Fat; Cardiometabolic Markers,,,"<h4>Context</h4>The role of glucagon-like peptide-1 (GLP-1) in type 2 diabetes (T2D) and obesity is not fully understood.<h4>Objective</h4>We investigate the association of cardiometabolic, diet, and lifestyle parameters on fasting and postprandial GLP-1 in people at risk of, or living with, T2D.<h4>Methods</h4>We analyzed cross-sectional data from the two Innovative Medicines Initiative (IMI) Diabetes Research on Patient Stratification (DIRECT) cohorts, cohort 1 (n = 2127) individuals at risk of diabetes; cohort 2 (n = 789) individuals with new-onset T2D.<h4>Results</h4>Our multiple regression analysis reveals that fasting total GLP-1 is associated with an insulin-resistant phenotype and observe a strong independent relationship with male sex, increased adiposity, and liver fat, particularly in the prediabetes population. In contrast, we showed that incremental GLP-1 decreases with worsening glycemia, higher adiposity, liver fat, male sex, and reduced insulin sensitivity in the prediabetes cohort. Higher fasting total GLP-1 was associated with a low intake of wholegrain, fruit, and vegetables in people with prediabetes, and with a high intake of red meat and alcohol in people with diabetes.<h4>Conclusion</h4>These studies provide novel insights into the association between fasting and incremental GLP-1, metabolic traits of diabetes and obesity, and dietary intake, and raise intriguing questions regarding the relevance of fasting GLP-1 in the pathophysiology T2D.",,doi:https://doi.org/10.1210/clinem/dgae119; html:https://europepmc.org/articles/PMC11318998
-35909058,https://doi.org/10.1016/s2589-7500(22)00123-6,Remote COVID-19 Assessment in Primary Care (RECAP) risk prediction tool: derivation and real-world validation studies.,"Espinosa-Gonzalez A, Prociuk D, Fiorentino F, Ramtale C, Mi E, Mi E, Glampson B, Neves AL, Okusi C, Husain L, Macartney J, Brown M, Browne B, Warren C, Chowla R, Heaversedge J, Greenhalgh T, de Lusignan S, Mayer E, Delaney BC.",,The Lancet. Digital health,2022,2022-07-28,Y,,,,"<h4>Background</h4>Accurate assessment of COVID-19 severity in the community is essential for patient care and requires COVID-19-specific risk prediction scores adequately validated in a community setting. Following a qualitative phase to identify signs, symptoms, and risk factors, we aimed to develop and validate two COVID-19-specific risk prediction scores. Remote COVID-19 Assessment in Primary Care-General Practice score (RECAP-GP; without peripheral oxygen saturation [SpO<sub>2</sub>]) and RECAP-oxygen saturation score (RECAP-O2; with SpO<sub>2</sub>).<h4>Methods</h4>RECAP was a prospective cohort study that used multivariable logistic regression. Data on signs and symptoms (predictors) of disease were collected from community-based patients with suspected COVID-19 via primary care electronic health records and linked with secondary data on hospital admission (outcome) within 28 days of symptom onset. Data sources for RECAP-GP were Oxford-Royal College of General Practitioners Research and Surveillance Centre (RCGP-RSC) primary care practices (development set), northwest London primary care practices (validation set), and the NHS COVID-19 Clinical Assessment Service (CCAS; validation set). The data source for RECAP-O2 was the Doctaly Assist platform (development set and validation set in subsequent sample). The two probabilistic risk prediction models were built by backwards elimination using the development sets and validated by application to the validation datasets. Estimated sample size per model, including the development and validation sets was 2880 people.<h4>Findings</h4>Data were available from 8311 individuals. Observations, such as SpO<sub>2</sub>, were mostly missing in the northwest London, RCGP-RSC, and CCAS data; however, SpO<sub>2</sub> was available for 1364 (70·0%) of 1948 patients who used Doctaly. In the final predictive models, RECAP-GP (n=1863) included sex (male and female), age (years), degree of breathlessness (three point scale), temperature symptoms (two point scale), and presence of hypertension (yes or no); the area under the curve was 0·80 (95% CI 0·76-0·85) and on validation the negative predictive value of a low risk designation was 99% (95% CI 98·1-99·2; 1435 of 1453). RECAP-O2 included age (years), degree of breathlessness (two point scale), fatigue (two point scale), and SpO<sub>2</sub> at rest (as a percentage); the area under the curve was 0·84 (0·78-0·90) and on validation the negative predictive value of low risk designation was 99% (95% CI 98·9-99·7; 1176 of 1183).<h4>Interpretation</h4>Both RECAP models are valid tools to assess COVID-19 patients in the community. RECAP-GP can be used initially, without need for observations, to identify patients who require monitoring. If the patient is monitored and SpO<sub>2</sub> is available, RECAP-O2 is useful to assess the need for treatment escalation.<h4>Funding</h4>Community Jameel and the Imperial College President's Excellence Fund, the Economic and Social Research Council, UK Research and Innovation, and Health Data Research UK.",,doi:https://doi.org/10.1016/s2589-7500(22)00123-6; doi:https://doi.org/10.1016/S2589-7500(22)00123-6; html:https://europepmc.org/articles/PMC9333950; pdf:https://europepmc.org/articles/PMC9333950?pdf=render
 34746717,https://doi.org/10.1016/j.eclinm.2021.101100,Paediatric major incident triage: UK military tool offers best performance in predicting the need for time-critical major surgical and resuscitative intervention.,"Malik NS, Chernbumroong S, Xu Y, Vassallo J, Lee J, Moran CG, Newton T, Arul GS, Lord JM, Belli A, Keene D, Foster M, Hodgetts T, Bowley DM, Gkoutos GV.",,EClinicalMedicine,2021,2021-08-23,Y,,,,"<h4>Background</h4>Children are frequently injured during major incidents (MI), including terrorist attacks, conflict and natural disasters. Triage facilitates healthcare resource allocation in order to maximise overall survival. A critical function of MI triage tools is to identify patients needing time-critical major resuscitative and surgical intervention (Priority 1 (P1) status). This study compares the performance of 11 MI triage tools in predicting P1 status in children from the UK Trauma Audit and Research Network (TARN) registry.<h4>Methods</h4>Patients aged <16 years within TARN (January 2008-December 2017) were included. 11 triage tools were applied to patients' first recorded pre-hospital physiology. Patients were retrospectively assigned triage categories (P1, P2, P3, Expectant or Dead) using predefined intervention-based criteria. Tools' performance in <16s were evaluated within four-yearly age subgroups, comparing tool-predicted and intervention-based priority status.<h4>Findings</h4>Amongst 4962 patients, mortality was 1.1% (<i>n</i> = 53); median Injury Severity Score (ISS) was 9 (IQR 9-16). Blunt injuries predominated (94.4%). 1343 (27.1%) met intervention-based criteria for P1, exhibiting greater intensive care requirement (60.2% vs. 8.5%, <i>p</i> < 0.01) and ISS (median 17 vs 9, <i>p</i> < 0.01) compared with P2 patients. The Battlefield Casualty Drills (BCD) Triage Sieve had greatest sensitivity (75.7%) in predicting P1 status in children <16 years, demonstrating a 38.4-49.8% improvement across all subgroups of children <12 years compared with the UK's current Paediatric Triage Tape (PTT). JumpSTART demonstrated low sensitivity in predicting P1 status in 4 to 8 year olds (35.5%) and 0 to 4 year olds (28.5%), and was outperformed by its adult counterpart START (60.6% and 59.6%).<h4>Interpretation</h4>The BCD Triage Sieve had greatest sensitivity in predicting P1 status in this paediatric trauma registry population: we recommend it replaces the PTT in UK practice. Users of JumpSTART may consider alternative tools. We recommend Lerner's triage category definitions when conducting MI evaluations.",,pdf:http://www.thelancet.com/article/S2589537021003801/pdf; doi:https://doi.org/10.1016/j.eclinm.2021.101100; html:https://europepmc.org/articles/PMC8548919; pdf:https://europepmc.org/articles/PMC8548919?pdf=render
+35909058,https://doi.org/10.1016/s2589-7500(22)00123-6,Remote COVID-19 Assessment in Primary Care (RECAP) risk prediction tool: derivation and real-world validation studies.,"Espinosa-Gonzalez A, Prociuk D, Fiorentino F, Ramtale C, Mi E, Mi E, Glampson B, Neves AL, Okusi C, Husain L, Macartney J, Brown M, Browne B, Warren C, Chowla R, Heaversedge J, Greenhalgh T, de Lusignan S, Mayer E, Delaney BC.",,The Lancet. Digital health,2022,2022-07-28,Y,,,,"<h4>Background</h4>Accurate assessment of COVID-19 severity in the community is essential for patient care and requires COVID-19-specific risk prediction scores adequately validated in a community setting. Following a qualitative phase to identify signs, symptoms, and risk factors, we aimed to develop and validate two COVID-19-specific risk prediction scores. Remote COVID-19 Assessment in Primary Care-General Practice score (RECAP-GP; without peripheral oxygen saturation [SpO<sub>2</sub>]) and RECAP-oxygen saturation score (RECAP-O2; with SpO<sub>2</sub>).<h4>Methods</h4>RECAP was a prospective cohort study that used multivariable logistic regression. Data on signs and symptoms (predictors) of disease were collected from community-based patients with suspected COVID-19 via primary care electronic health records and linked with secondary data on hospital admission (outcome) within 28 days of symptom onset. Data sources for RECAP-GP were Oxford-Royal College of General Practitioners Research and Surveillance Centre (RCGP-RSC) primary care practices (development set), northwest London primary care practices (validation set), and the NHS COVID-19 Clinical Assessment Service (CCAS; validation set). The data source for RECAP-O2 was the Doctaly Assist platform (development set and validation set in subsequent sample). The two probabilistic risk prediction models were built by backwards elimination using the development sets and validated by application to the validation datasets. Estimated sample size per model, including the development and validation sets was 2880 people.<h4>Findings</h4>Data were available from 8311 individuals. Observations, such as SpO<sub>2</sub>, were mostly missing in the northwest London, RCGP-RSC, and CCAS data; however, SpO<sub>2</sub> was available for 1364 (70·0%) of 1948 patients who used Doctaly. In the final predictive models, RECAP-GP (n=1863) included sex (male and female), age (years), degree of breathlessness (three point scale), temperature symptoms (two point scale), and presence of hypertension (yes or no); the area under the curve was 0·80 (95% CI 0·76-0·85) and on validation the negative predictive value of a low risk designation was 99% (95% CI 98·1-99·2; 1435 of 1453). RECAP-O2 included age (years), degree of breathlessness (two point scale), fatigue (two point scale), and SpO<sub>2</sub> at rest (as a percentage); the area under the curve was 0·84 (0·78-0·90) and on validation the negative predictive value of low risk designation was 99% (95% CI 98·9-99·7; 1176 of 1183).<h4>Interpretation</h4>Both RECAP models are valid tools to assess COVID-19 patients in the community. RECAP-GP can be used initially, without need for observations, to identify patients who require monitoring. If the patient is monitored and SpO<sub>2</sub> is available, RECAP-O2 is useful to assess the need for treatment escalation.<h4>Funding</h4>Community Jameel and the Imperial College President's Excellence Fund, the Economic and Social Research Council, UK Research and Innovation, and Health Data Research UK.",,doi:https://doi.org/10.1016/s2589-7500(22)00123-6; doi:https://doi.org/10.1016/S2589-7500(22)00123-6; html:https://europepmc.org/articles/PMC9333950; pdf:https://europepmc.org/articles/PMC9333950?pdf=render
 36701357,https://doi.org/10.1371/journal.pone.0280943,Awareness and perceptions of Long COVID among people in the REACT programme: Early insights from a pilot interview study.,"Cooper E, Lound A, Atchison CJ, Whitaker M, Eccles C, Cooke GS, Elliott P, Ward H.",,PloS one,2023,2023-01-26,Y,,,,"<h4>Background</h4>Long COVID is a patient-made term describing new or persistent symptoms experienced following SARS-CoV-2 infection. The Real-time Assessment of Community Transmission-Long COVID (REACT-LC) study aims to understand variation in experiences following infection, and to identify biological, social, and environmental factors associated with Long COVID. We undertook a pilot interview study to inform the design, recruitment approach, and topic guide for the REACT-LC qualitative study. We sought to gain initial insights into the experience and attribution of new or persistent symptoms and the awareness or perceived applicability of the term Long COVID.<h4>Methods</h4>People were invited to REACT-LC assessment centres if they had taken part in REACT, a random community-based prevalence study, and had a documented history of SARS-CoV-2 infection. We invited people from REACT-LC assessment centres who had reported experiencing persistent symptoms for more than 12 weeks to take part in an interview. We conducted face to face and online semi-structured interviews which were transcribed and analysed using Thematic Analysis.<h4>Results</h4>We interviewed 13 participants (6 female, 7 male, median age 31). Participants reported a wide variation in both new and persistent symptoms which were often fluctuating or unpredictable in nature. Some participants were confident about the link between their persistent symptoms and COVID-19; however, others were unclear about the underlying cause of symptoms or felt that the impact of public health measures (such as lockdowns) played a role. We found differences in awareness and perceived applicability of the term Long COVID.<h4>Conclusion</h4>This pilot has informed the design, recruitment approach and topic guide for our qualitative study. It offers preliminary insights into the varied experiences of people living with persistent symptoms including differences in symptom attribution and perceived applicability of the term Long COVID. This variation shows the value of recruiting from a nationally representative sample of participants who are experiencing persistent symptoms.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0280943&type=printable; doi:https://doi.org/10.1371/journal.pone.0280943; html:https://europepmc.org/articles/PMC9879384; pdf:https://europepmc.org/articles/PMC9879384?pdf=render
+35079067,https://doi.org/10.1038/s41598-022-05414-5,Asthma in paediatric intensive care in England residents: observational study.,"Mukherjee M, Cunningham S, Bhuia MR, Lo TM, Been JV, Sheikh A.",,Scientific reports,2022,2022-01-25,Y,,,,"Despite high prevalence of asthma in children in the UK, there were no prior report on asthma admissions in paediatric intensive care units (PICU). We investigated the epidemiology and healthcare resource utilisation in children with asthma presenting to PICUs in England. PICANet, a UK national PICU database, was queried for asthma as the primary reason for admission, of children resident in England from April 2006 until March 2013. There were 2195 admissions to PICU for a median stay of 1.4 days. 59% were males and 51% aged 0-4 years. The fourth and fifth most deprived quintiles represented 61% (1329) admissions and 73% (11) of the 15 deaths. Deaths were most frequent in 10-14 years age (n = 11, 73%), with no deaths in less than 5 years age. 38% of admissions (828/2193) received invasive ventilation, which was more frequent with increasing deprivation (13% (108/828) in least deprived to 31% (260/828) in most deprived) and with decreasing age (0-4-year-olds: 49%, 409/828). This first multi-centre PICU study in England found that children from more deprived neighbourhoods represented the majority of asthma admissions, invasive ventilation and deaths in PICU. Children experiencing socioeconomic deprivation could benefit from enhanced asthma support in the community.",,pdf:https://www.nature.com/articles/s41598-022-05414-5.pdf; doi:https://doi.org/10.1038/s41598-022-05414-5; html:https://europepmc.org/articles/PMC8789863; pdf:https://europepmc.org/articles/PMC8789863?pdf=render
 37607793,https://doi.org/10.1136/bmjopen-2023-076296,"Knowledge support for optimising antibiotic prescribing for common infections in general practices: evaluation of the effectiveness of periodic feedback, decision support during consultations and peer comparisons in a cluster randomised trial (BRIT2) - study protocol.","van Staa T, Sharma A, Palin V, Fahmi A, Cant H, Zhong X, Jury F, Gold N, Welfare W, Ashcroft D, Tsang JY, Elliott RA, Sutton C, Armitage C, Couch P, Moulton G, Tempest E, Buchan IE.",,BMJ open,2023,2023-08-22,Y,Infectious diseases; Randomized controlled trial; Primary Care; Electronic Health Records,,,"<h4>Introduction</h4>This project applies a Learning Healthcare System (LHS) approach to antibiotic prescribing for common infections in primary care. The approach involves iterations of data analysis, feedback to clinicians and implementation of quality improvement activities by the clinicians. The main research question is, can a knowledge support system (KSS) intervention within an LHS implementation improve antibiotic prescribing without increasing the risk of complications?<h4>Methods and analysis</h4>A pragmatic cluster randomised controlled trial will be conducted, with randomisation of at least 112 general practices in North-West England. General practices participating in the trial will be randomised to the following interventions: periodic practice-level and individual prescriber feedback using dashboards; or the same dashboards plus a KSS. Data from large databases of healthcare records are used to characterise heterogeneity in antibiotic uses, and to calculate risk scores for clinical outcomes and for the effectiveness of different treatment strategies. The results provide the baseline content for the dashboards and KSS. The KSS comprises a display within the electronic health record used during the consultation; the prescriber (general practitioner or allied health professional) will answer standard questions about the patient's presentation and will then be presented with information (eg, patient's risk of complications from the infection) to guide decision making. The KSS can generate information sheets for patients, conveyed by the clinicians during consultations. The primary outcome is the practice-level rate of antibiotic prescribing (per 1000 patients) with secondary safety outcomes. The data from practices participating in the trial and the dashboard infrastructure will be held within regional shared care record systems of the National Health Service in the UK.<h4>Ethics and dissemination</h4>Approved by National Health Service Ethics Committee IRAS 290050. The research results will be published in peer-reviewed journals and also disseminated to participating clinical staff and policy and guideline developers.<h4>Trial registration number</h4>ISRCTN16230629.",,doi:https://doi.org/10.1136/bmjopen-2023-076296; doi:https://doi.org/10.1136/bmjopen-2023-076296; html:https://europepmc.org/articles/PMC10445367; pdf:https://europepmc.org/articles/PMC10445367?pdf=render
-35595824,https://doi.org/10.1038/s41598-022-12517-6,Transmission dynamics of SARS-CoV-2 in a strictly-Orthodox Jewish community in the UK.,"Waites W, Pearson CAB, Gaskell KM, House T, Pellis L, Johnson M, Gould V, Hunt A, Stone NRH, Kasstan B, Chantler T, Lal S, Roberts CH, Goldblatt D, CMMID COVID-19 Working Group, Marks M, Eggo RM.",,Scientific reports,2022,2022-05-20,Y,,,,"Some social settings such as households and workplaces, have been identified as high risk for SARS-CoV-2 transmission. Identifying and quantifying the importance of these settings is critical for designing interventions. A tightly-knit religious community in the UK experienced a very large COVID-19 epidemic in 2020, reaching 64.3% seroprevalence within 10 months, and we surveyed this community both for serological status and individual-level attendance at particular settings. Using these data, and a network model of people and places represented as a stochastic graph rewriting system, we estimated the relative contribution of transmission in households, schools and religious institutions to the epidemic, and the relative risk of infection in each of these settings. All congregate settings were important for transmission, with some such as primary schools and places of worship having a higher share of transmission than others. We found that the model needed a higher general-community transmission rate for women (3.3-fold), and lower susceptibility to infection in children to recreate the observed serological data. The precise share of transmission in each place was related to assumptions about the internal structure of those places. Identification of key settings of transmission can allow public health interventions to be targeted at these locations.",,pdf:https://www.nature.com/articles/s41598-022-12517-6.pdf; doi:https://doi.org/10.1038/s41598-022-12517-6; html:https://europepmc.org/articles/PMC9121858; pdf:https://europepmc.org/articles/PMC9121858?pdf=render
 34862222,https://doi.org/10.7861/clinmed.2021-0386,'What is the risk to me from COVID-19?': Public involvement in providing mortality risk information for people with 'high-risk' conditions for COVID-19 (OurRisk.CoV).,"Banerjee A, Pasea L, Manohar S, Lai AG, Hemingway E, Sofer I, Katsoulis M, Sood H, Morris A, Cake C, Fitzpatrick NK, Williams B, Denaxas S, Hemingway H, and members of the Health Data Research UK COVID-19 Patient and Public Involvement and Engagement Panel.",,"Clinical medicine (London, England)",2021,2021-11-01,N,Mortality; Coronavirus; Patient And Public Involvement; Risk Information,,,"Patients and public have sought mortality risk information throughout the pandemic, but their needs may not be served by current risk prediction tools. Our mixed methods study involved: (1) systematic review of published risk tools for prognosis, (2) provision and patient testing of new mortality risk estimates for people with high-risk conditions and (3) iterative patient and public involvement and engagement with qualitative analysis. Only one of 53 (2%) previously published risk tools involved patients or the public, while 11/53 (21%) had publicly accessible portals, but all for use by clinicians and researchers.Among people with a wide range of underlying conditions, there has been sustained interest and engagement in accessible and tailored, pre- and postpandemic mortality information. Informed by patient feedback, we provide such information in 'five clicks' (https://covid19-phenomics.org/OurRiskCoV.html), as context for decision making and discussions with health professionals and family members. Further development requires curation and regular updating of NHS data and wider patient and public engagement.",,pdf:https://www.rcpjournals.org/content/clinmedicine/21/6/e620.full.pdf; doi:https://doi.org/10.7861/clinmed.2021-0386; html:https://europepmc.org/articles/PMC8806292; pdf:https://europepmc.org/articles/PMC8806292?pdf=render; doi:https://doi.org/10.7861/clinmed.2021-0386
-35079067,https://doi.org/10.1038/s41598-022-05414-5,Asthma in paediatric intensive care in England residents: observational study.,"Mukherjee M, Cunningham S, Bhuia MR, Lo TM, Been JV, Sheikh A.",,Scientific reports,2022,2022-01-25,Y,,,,"Despite high prevalence of asthma in children in the UK, there were no prior report on asthma admissions in paediatric intensive care units (PICU). We investigated the epidemiology and healthcare resource utilisation in children with asthma presenting to PICUs in England. PICANet, a UK national PICU database, was queried for asthma as the primary reason for admission, of children resident in England from April 2006 until March 2013. There were 2195 admissions to PICU for a median stay of 1.4 days. 59% were males and 51% aged 0-4 years. The fourth and fifth most deprived quintiles represented 61% (1329) admissions and 73% (11) of the 15 deaths. Deaths were most frequent in 10-14 years age (n = 11, 73%), with no deaths in less than 5 years age. 38% of admissions (828/2193) received invasive ventilation, which was more frequent with increasing deprivation (13% (108/828) in least deprived to 31% (260/828) in most deprived) and with decreasing age (0-4-year-olds: 49%, 409/828). This first multi-centre PICU study in England found that children from more deprived neighbourhoods represented the majority of asthma admissions, invasive ventilation and deaths in PICU. Children experiencing socioeconomic deprivation could benefit from enhanced asthma support in the community.",,pdf:https://www.nature.com/articles/s41598-022-05414-5.pdf; doi:https://doi.org/10.1038/s41598-022-05414-5; html:https://europepmc.org/articles/PMC8789863; pdf:https://europepmc.org/articles/PMC8789863?pdf=render
-37795045,https://doi.org/10.1177/26320843221147855,Monitoring metrics over time: Why clinical trialists need to systematically collect site performance metrics.,"Yorke-Edwards V, Diaz-Montana C, Murray ML, Sydes MR, Love SB.",,Research methods in medicine & health sciences,2023,2022-12-21,N,Clinical Trials; Risk-based Monitoring; Central Monitoring; Centralised Monitoring; Study-Within-A-Trial (Swat),,,"<h4>Background</h4>Over the last decade, there has been an increasing interest in risk-based monitoring (RBM) in clinical trials, resulting in a number of guidelines from regulators and its inclusion in ICH GCP. However, there is a lack of detail on how to approach RBM from a practical perspective, and insufficient understanding of best practice.<h4>Purpose</h4>We present a method for clinical trials units to track their metrics within clinical trials using descriptive statistics and visualisations.<h4>Research design</h4>We suggest descriptive statistics and visualisations within a SWAT methodology.<h4>Study sample</h4>We illustrate this method using the metrics from TEMPER, a monitoring study carried out in three trials at the MRC Clinical Trials Unit at UCL.<h4>Data collection</h4>The data collection for TEMPER is described in <i>DOI: 10.1177/1740774518793379</i>.<h4>Results</h4>We show the results and discuss a protocol for a Study-Within-A-Trial (SWAT 167) for those wishing to use the method.<h4>Conclusions</h4>The potential benefits metric tracking brings to clinical trials include enhanced assessment of sites for potential corrective action, improved evaluation and contextualisation of the influence of metrics and their thresholds, and the establishment of best practice in RBM. The standardisation of the collection of such monitoring data would benefit both individual trials and the clinical trials community.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/26320843221147855; doi:https://doi.org/10.1177/26320843221147855; html:https://europepmc.org/articles/PMC7615148; pdf:https://europepmc.org/articles/PMC7615148?pdf=render; doi:https://doi.org/10.1177/26320843221147855
+35595824,https://doi.org/10.1038/s41598-022-12517-6,Transmission dynamics of SARS-CoV-2 in a strictly-Orthodox Jewish community in the UK.,"Waites W, Pearson CAB, Gaskell KM, House T, Pellis L, Johnson M, Gould V, Hunt A, Stone NRH, Kasstan B, Chantler T, Lal S, Roberts CH, Goldblatt D, CMMID COVID-19 Working Group, Marks M, Eggo RM.",,Scientific reports,2022,2022-05-20,Y,,,,"Some social settings such as households and workplaces, have been identified as high risk for SARS-CoV-2 transmission. Identifying and quantifying the importance of these settings is critical for designing interventions. A tightly-knit religious community in the UK experienced a very large COVID-19 epidemic in 2020, reaching 64.3% seroprevalence within 10 months, and we surveyed this community both for serological status and individual-level attendance at particular settings. Using these data, and a network model of people and places represented as a stochastic graph rewriting system, we estimated the relative contribution of transmission in households, schools and religious institutions to the epidemic, and the relative risk of infection in each of these settings. All congregate settings were important for transmission, with some such as primary schools and places of worship having a higher share of transmission than others. We found that the model needed a higher general-community transmission rate for women (3.3-fold), and lower susceptibility to infection in children to recreate the observed serological data. The precise share of transmission in each place was related to assumptions about the internal structure of those places. Identification of key settings of transmission can allow public health interventions to be targeted at these locations.",,pdf:https://www.nature.com/articles/s41598-022-12517-6.pdf; doi:https://doi.org/10.1038/s41598-022-12517-6; html:https://europepmc.org/articles/PMC9121858; pdf:https://europepmc.org/articles/PMC9121858?pdf=render
 38096890,https://doi.org/10.1016/s1470-2045(23)00530-2,"Mortality from leading cancers in districts of England from 2002 to 2019: a population-based, spatiotemporal study.","Rashid T, Bennett JE, Muller DC, Cross AJ, Pearson-Stuttard J, Asaria P, Daby HI, Fecht D, Davies B, Ezzati M.",,The Lancet. Oncology,2024,2023-12-11,Y,,,,"<h4>Background</h4>Cancers are the leading cause of death in England. We aimed to estimate trends in mortality from leading cancers from 2002 to 2019 for the 314 districts in England.<h4>Methods</h4>We did a high-resolution spatiotemporal analysis of vital registration data from the UK Office for National Statistics using data on all deaths from the ten leading cancers in England from 2002 to 2019. We used a Bayesian hierarchical model to obtain robust estimates of age-specific and cause-specific death rates. We used life table methods to calculate the primary outcome, the unconditional probability of dying between birth and age 80 years by sex, cancer cause of death, local district, and year. We reported Spearman rank correlations between the probability of dying from a cancer and district-level poverty in 2019.<h4>Findings</h4>In 2019, the probability of dying from a cancer before age 80 years ranged from 0·10 (95% credible interval [CrI] 0·10-0·11) to 0·17 (0·16-0·18) for women and from 0·12 (0·12-0·13) to 0·22 (0·21-0·23) for men. Variation in the probability of dying was largest for lung cancer among women, being 3·7 times (95% CrI 3·2-4·4) higher in the district with the highest probability than in the district with the lowest probability; and for stomach cancer for men, being 3·2 times (2·6-4·1) higher in the district with the highest probability than in the one with the lowest probability. The variation in the probability of dying was smallest across districts for lymphoma and multiple myeloma (95% CrI 1·2 times [1·1-1·4] higher in the district with the highest probability than the lowest probability for women and 1·2 times [1·0-1·4] for men), and leukaemia (1·1 times [1·0-1·4] for women and 1·2 times [1·0-1·5] for men). The Spearman rank correlation between probability of dying from a cancer and district poverty was 0·74 (95% CrI 0·72-0·76) for women and 0·79 (0·78-0·81) for men. From 2002 to 2019, the overall probability of dying from a cancer declined in all districts: the reductions ranged from 6·6% (95% CrI 0·3-13·1) to 30·1% (25·6-34·5) for women and from 12·8% (7·1-18·8) to 36·7% (32·2-41·2) for men. However, there were increases in mortality for liver cancer among men, lung cancer and corpus uteri cancer among women, and pancreatic cancer in both sexes in some or all districts with posterior probability greater than 0·80.<h4>Interpretation</h4>Cancers with modifiable risk factors and potential for screening for precancerous lesions had heterogeneous trends and the greatest geographical inequality. To reduce these inequalities, factors affecting both incidence and survival need to be addressed at the local level.<h4>Funding</h4>Wellcome Trust, Imperial College London, UK Medical Research Council, and the National Institute of Health Research.",,pdf:http://www.thelancet.com/article/S1470204523005302/pdf; doi:https://doi.org/10.1016/S1470-2045(23)00530-2; html:https://europepmc.org/articles/PMC7615518; pdf:https://europepmc.org/articles/PMC7615518?pdf=render
-33079204,https://doi.org/10.1093/ehjqcco/qcaa079,Impact of COVID-19 on cardiac procedure activity in England and associated 30-day mortality.,"Mohamed MO, Banerjee A, Clarke S, de Belder M, Patwala A, Goodwin AT, Kwok CS, Rashid M, Gale CP, Curzen N, Mamas MA.",,European heart journal. Quality of care & clinical outcomes,2021,2021-05-01,Y,Mortality; Cardiac; England; Procedures; Covid-19,,,"<h4>Aims</h4>Limited data exist on the impact of COVID-19 on national changes in cardiac procedure activity, including patient characteristics and clinical outcomes before and during the COVID-19 pandemic.<h4>Methods and results</h4>All major cardiac procedures (n = 374 899) performed between 1 January and 31 May for the years 2018, 2019, and 2020 were analysed, stratified by procedure type and time-period (pre-COVID: January-May 2018 and 2019 and January-February 2020 and COVID: March-May 2020). Multivariable logistic regression was performed to examine the odds ratio (OR) of 30-day mortality for procedures performed in the COVID period. Overall, there was a deficit of 45 501 procedures during the COVID period compared to the monthly averages (March-May) in 2018-2019. Cardiac catheterization and device implantations were the most affected in terms of numbers (n = 19 637 and n = 10 453), whereas surgical procedures such as mitral valve replacement, other valve replacement/repair, atrioseptal defect/ventriculoseptal defect repair, and coronary artery bypass grafting were the most affected as a relative percentage difference (Δ) to previous years' averages. Transcatheter aortic valve replacement was the least affected (Δ -10.6%). No difference in 30-day mortality was observed between pre-COVID and COVID time-periods for all cardiac procedures except cardiac catheterization [OR 1.25 95% confidence interval (CI) 1.07-1.47, P = 0.006] and cardiac device implantation (OR 1.35 95% CI 1.15-1.58, P < 0.001).<h4>Conclusion</h4>Cardiac procedural activity has significantly declined across England during the COVID-19 pandemic, with a deficit in excess of 45 000 procedures, without an increase in risk of mortality for most cardiac procedures performed during the pandemic. Major restructuring of cardiac services is necessary to deal with this deficit, which would inevitably impact long-term morbidity and mortality.",,pdf:https://academic.oup.com/ehjqcco/article-pdf/7/3/247/37776880/qcaa079.pdf; doi:https://doi.org/10.1093/ehjqcco/qcaa079; html:https://europepmc.org/articles/PMC7665465; pdf:https://europepmc.org/articles/PMC7665465?pdf=render
+37795045,https://doi.org/10.1177/26320843221147855,Monitoring metrics over time: Why clinical trialists need to systematically collect site performance metrics.,"Yorke-Edwards V, Diaz-Montana C, Murray ML, Sydes MR, Love SB.",,Research methods in medicine & health sciences,2023,2022-12-21,N,Clinical Trials; Risk-based Monitoring; Central Monitoring; Centralised Monitoring; Study-Within-A-Trial (Swat),,,"<h4>Background</h4>Over the last decade, there has been an increasing interest in risk-based monitoring (RBM) in clinical trials, resulting in a number of guidelines from regulators and its inclusion in ICH GCP. However, there is a lack of detail on how to approach RBM from a practical perspective, and insufficient understanding of best practice.<h4>Purpose</h4>We present a method for clinical trials units to track their metrics within clinical trials using descriptive statistics and visualisations.<h4>Research design</h4>We suggest descriptive statistics and visualisations within a SWAT methodology.<h4>Study sample</h4>We illustrate this method using the metrics from TEMPER, a monitoring study carried out in three trials at the MRC Clinical Trials Unit at UCL.<h4>Data collection</h4>The data collection for TEMPER is described in <i>DOI: 10.1177/1740774518793379</i>.<h4>Results</h4>We show the results and discuss a protocol for a Study-Within-A-Trial (SWAT 167) for those wishing to use the method.<h4>Conclusions</h4>The potential benefits metric tracking brings to clinical trials include enhanced assessment of sites for potential corrective action, improved evaluation and contextualisation of the influence of metrics and their thresholds, and the establishment of best practice in RBM. The standardisation of the collection of such monitoring data would benefit both individual trials and the clinical trials community.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/26320843221147855; doi:https://doi.org/10.1177/26320843221147855; html:https://europepmc.org/articles/PMC7615148; pdf:https://europepmc.org/articles/PMC7615148?pdf=render; doi:https://doi.org/10.1177/26320843221147855
 35192611,https://doi.org/10.1371/journal.pmed.1003916,Uptake of infant and preschool immunisations in Scotland and England during the COVID-19 pandemic: An observational study of routinely collected data.,"McQuaid F, Mulholland R, Sangpang Rai Y, Agrawal U, Bedford H, Cameron JC, Gibbons C, Roy P, Sheikh A, Shi T, Simpson CR, Tait J, Tessier E, Turner S, Villacampa Ortega J, White J, Wood R.",,PLoS medicine,2022,2022-02-22,Y,,,,"<h4>Background</h4>In 2020, the SARS-CoV-2 (COVID-19) pandemic and lockdown control measures threatened to disrupt routine childhood immunisation programmes with early reports suggesting uptake would fall. In response, public health bodies in Scotland and England collected national data for childhood immunisations on a weekly or monthly basis to allow for rapid analysis of trends. The aim of this study was to use these data to assess the impact of different phases of the pandemic on infant and preschool immunisation uptake rates.<h4>Methods and findings</h4>We conducted an observational study using routinely collected data for the year prior to the pandemic (2019) and immediately before (22 January to March 2020), during (23 March to 26 July), and after (27 July to 4 October) the first UK ""lockdown"". Data were obtained for Scotland from the Public Health Scotland ""COVID19 wider impacts on the health care system"" dashboard and for England from ImmForm. Five vaccinations delivered at different ages were evaluated; 3 doses of ""6-in-1"" diphtheria, tetanus, pertussis, polio, Haemophilus influenzae type b, and hepatitis B vaccine (DTaP/IPV/Hib/HepB) and 2 doses of measles, mumps, and rubella (MMR) vaccine. This represented 439,754 invitations to be vaccinated in Scotland and 4.1 million for England. Uptake during the 2020 periods was compared to the previous year (2019) using binary logistic regression analysis. For Scotland, uptake within 4 weeks of a child becoming eligible by age was analysed along with geographical region and indices of deprivation. For Scotland and England, we assessed whether immunisations were up-to-date at approximately 6 months (all doses 6-in-1) and 16 to 18 months (first MMR) of age. We found that uptake within 4 weeks of eligibility in Scotland for all the 5 vaccines was higher during lockdown than in 2019. Differences ranged from 1.3% for first dose 6-in-1 vaccine (95.3 versus 94%, odds ratio [OR] compared to 2019 1.28, 95% confidence intervals [CIs] 1.18 to 1.39) to 14.3% for second MMR dose (66.1 versus 51.8%, OR compared to 2019 1.8, 95% CI 1.74 to 1.87). Significant increases in uptake were seen across all deprivation levels. In England, fewer children due to receive their immunisations during the lockdown period were up to date at 6 months (6-in-1) or 18 months (first dose MMR). The fall in percentage uptake ranged from 0.5% for first 6-in-1 (95.8 versus 96.3%, OR compared to 2019 0.89, 95% CI 0.86- to 0.91) to 2.1% for third 6-in-1 (86.6 versus 88.7%, OR compared to 2019 0.82, 95% CI 0.81 to 0.83). The use of routinely collected data used in this study was a limiting factor as detailed information on potential confounding factors were not available and we were unable to eliminate the possibility of seasonal trends in immunisation uptake.<h4>Conclusions</h4>In this study, we observed that the national lockdown in Scotland was associated with an increase in timely childhood immunisation uptake; however, in England, uptake fell slightly. Reasons for the improved uptake in Scotland may include active measures taken to promote immunisation at local and national levels during this period and should be explored further. Promoting immunisation uptake and addressing potential vaccine hesitancy is particularly important given the ongoing pandemic and COVID-19 vaccination campaigns.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003916&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003916; html:https://europepmc.org/articles/PMC8863286; pdf:https://europepmc.org/articles/PMC8863286?pdf=render
-39185668,https://doi.org/10.1002/hbm.70003,Measuring and reducing the carbon footprint of fMRI preprocessing in fMRIPrep.,"Souter NE, Bhagwat N, Racey C, Wilkinson R, Duncan NW, Samuel G, Lannelongue L, Selvan R, Rae CL.",,Human brain mapping,2024,2024-08-01,Y,Carbon; fMRI; Computing; Footprint; Neuroimaging; Preprocessing; Fmriprep,,,"Computationally expensive data processing in neuroimaging research places demands on energy consumption-and the resulting carbon emissions contribute to the climate crisis. We measured the carbon footprint of the functional magnetic resonance imaging (fMRI) preprocessing tool fMRIPrep, testing the effect of varying parameters on estimated carbon emissions and preprocessing performance. Performance was quantified using (a) statistical individual-level task activation in regions of interest and (b) mean smoothness of preprocessed data. Eight variants of fMRIPrep were run with 257 participants who had completed an fMRI stop signal task (the same data also used in the original validation of fMRIPrep). Some variants led to substantial reductions in carbon emissions without sacrificing data quality: for instance, disabling FreeSurfer surface reconstruction reduced carbon emissions by 48%. We provide six recommendations for minimising emissions without compromising performance. By varying parameters and computational resources, neuroimagers can substantially reduce the carbon footprint of their preprocessing. This is one aspect of our research carbon footprint over which neuroimagers have control and agency to act upon.",,doi:https://doi.org/10.1002/hbm.70003; html:https://europepmc.org/articles/PMC11345634; pdf:https://europepmc.org/articles/PMC11345634?pdf=render
 34232969,https://doi.org/10.23889/ijpds.v5i1.1151,How effective are population health surveys for estimating prevalence of chronic conditions compared to anonymised clinical data?,"Whiffen T, Akbari A, Paget T, Lowe S, Lyons R.",,International journal of population data science,2020,2020-06-12,Y,,,,"<h4>Introduction</h4>Population health surveys are used to record person-reported outcome measures for chronic health conditions and provide a useful source of data when evaluating potential disease burdens. The reliability of survey-based prevalence estimates for chronic diseases is unclear nonetheless. This study applied methodological triangulation via a data linkage method to validate prevalence of selected chronic conditions (angina, myocardial infarction, heart failure, and asthma).<h4>Methods</h4>Linked healthcare records were used for a combined cohort of 11,323 adults from the 2013 and 2014 sweeps of the Welsh Health Survey (WHS). The approach utilised consented survey data linked to primary and secondary care electronic health record (EHR) data back to 2002 within the Secure Anonymised Information Linkage (SAIL) Databank.<h4>Results</h4>This descriptive study demonstrates validation of survey and clinical data using data linkage for selected chronic cardiovascular conditions and asthma with varied success. The results indicate that identifying cases for separate cardiovascular conditions was limited without specific medication codes for each condition, but more straightforward for asthma, where there was an extensive list of medications available. For asthma there was better agreement between prevalence estimates based on survey and clinical data as a result.<h4>Conclusion</h4>Whilst the results provide external validity for the WHS as an instrument for estimating the burden of chronic disease, they also indicate that a data linkage appproach can be used to produce comparable prevalence estimates using clinical data if a defined condition-specific set of clinical codes are available.",,pdf:https://ijpds.org/article/download/1151/2553; doi:https://doi.org/10.23889/ijpds.v5i1.1151; html:https://europepmc.org/articles/PMC7473295; pdf:https://europepmc.org/articles/PMC7473295?pdf=render
+39185668,https://doi.org/10.1002/hbm.70003,Measuring and reducing the carbon footprint of fMRI preprocessing in fMRIPrep.,"Souter NE, Bhagwat N, Racey C, Wilkinson R, Duncan NW, Samuel G, Lannelongue L, Selvan R, Rae CL.",,Human brain mapping,2024,2024-08-01,Y,Carbon; fMRI; Computing; Footprint; Neuroimaging; Preprocessing; Fmriprep,,,"Computationally expensive data processing in neuroimaging research places demands on energy consumption-and the resulting carbon emissions contribute to the climate crisis. We measured the carbon footprint of the functional magnetic resonance imaging (fMRI) preprocessing tool fMRIPrep, testing the effect of varying parameters on estimated carbon emissions and preprocessing performance. Performance was quantified using (a) statistical individual-level task activation in regions of interest and (b) mean smoothness of preprocessed data. Eight variants of fMRIPrep were run with 257 participants who had completed an fMRI stop signal task (the same data also used in the original validation of fMRIPrep). Some variants led to substantial reductions in carbon emissions without sacrificing data quality: for instance, disabling FreeSurfer surface reconstruction reduced carbon emissions by 48%. We provide six recommendations for minimising emissions without compromising performance. By varying parameters and computational resources, neuroimagers can substantially reduce the carbon footprint of their preprocessing. This is one aspect of our research carbon footprint over which neuroimagers have control and agency to act upon.",,doi:https://doi.org/10.1002/hbm.70003; html:https://europepmc.org/articles/PMC11345634; pdf:https://europepmc.org/articles/PMC11345634?pdf=render
+33079204,https://doi.org/10.1093/ehjqcco/qcaa079,Impact of COVID-19 on cardiac procedure activity in England and associated 30-day mortality.,"Mohamed MO, Banerjee A, Clarke S, de Belder M, Patwala A, Goodwin AT, Kwok CS, Rashid M, Gale CP, Curzen N, Mamas MA.",,European heart journal. Quality of care & clinical outcomes,2021,2021-05-01,Y,Mortality; Cardiac; England; Procedures; Covid-19,,,"<h4>Aims</h4>Limited data exist on the impact of COVID-19 on national changes in cardiac procedure activity, including patient characteristics and clinical outcomes before and during the COVID-19 pandemic.<h4>Methods and results</h4>All major cardiac procedures (n = 374 899) performed between 1 January and 31 May for the years 2018, 2019, and 2020 were analysed, stratified by procedure type and time-period (pre-COVID: January-May 2018 and 2019 and January-February 2020 and COVID: March-May 2020). Multivariable logistic regression was performed to examine the odds ratio (OR) of 30-day mortality for procedures performed in the COVID period. Overall, there was a deficit of 45 501 procedures during the COVID period compared to the monthly averages (March-May) in 2018-2019. Cardiac catheterization and device implantations were the most affected in terms of numbers (n = 19 637 and n = 10 453), whereas surgical procedures such as mitral valve replacement, other valve replacement/repair, atrioseptal defect/ventriculoseptal defect repair, and coronary artery bypass grafting were the most affected as a relative percentage difference (Δ) to previous years' averages. Transcatheter aortic valve replacement was the least affected (Δ -10.6%). No difference in 30-day mortality was observed between pre-COVID and COVID time-periods for all cardiac procedures except cardiac catheterization [OR 1.25 95% confidence interval (CI) 1.07-1.47, P = 0.006] and cardiac device implantation (OR 1.35 95% CI 1.15-1.58, P < 0.001).<h4>Conclusion</h4>Cardiac procedural activity has significantly declined across England during the COVID-19 pandemic, with a deficit in excess of 45 000 procedures, without an increase in risk of mortality for most cardiac procedures performed during the pandemic. Major restructuring of cardiac services is necessary to deal with this deficit, which would inevitably impact long-term morbidity and mortality.",,pdf:https://academic.oup.com/ehjqcco/article-pdf/7/3/247/37776880/qcaa079.pdf; doi:https://doi.org/10.1093/ehjqcco/qcaa079; html:https://europepmc.org/articles/PMC7665465; pdf:https://europepmc.org/articles/PMC7665465?pdf=render
 37674175,https://doi.org/10.1186/s12884-023-05958-y,Using the COM-B framework to elucidate facilitators and barriers to COVID-19 vaccine uptake in pregnant women: a qualitative study.,"Patterson L, Berry E, Parsons C, Clarke B, Little A, Beggs J, Chuter A, Jackson T, Hsia Y, McGrath H, Millman C, Murphy S, Bradley DT, Milligan S.",,BMC pregnancy and childbirth,2023,2023-09-06,Y,Pregnancy; Qualitative; Barriers; Facilitators; Com-b; Covid-19 Vaccination,,,"Since April 2021, COVID-19 vaccines have been recommended for pregnant women. Despite this, COVID-19 vaccine uptake in this group is low compared to the non-pregnant population of childbearing age. Our aim was to understand barriers and facilitators to COVID-19 vaccine uptake among pregnant women in Northern Ireland using the COM-B framework, and so to make recommendations for public health interventions. The COM-B proposes that human behaviour is influenced by the extent to which a person has the capability, opportunity, and motivation to enact that behaviour. Understanding the factors underpinning behaviour through this lens helps discern what needs to change to change behaviour, therefore supporting the development of targeted interventions.This study consisted of eight semi-structured interviews with new/expectant mothers who did not receive a COVID-19 vaccine dose while pregnant since April 2021, and a focus group with five participants who received at least one COVID-19 vaccine dose while pregnant. Interview and focus group data were analysed using semi-deductive reflexive thematic analysis framed by a subtle realist approach. The COM-B was used to categorise codes and subthemes were developed within each COM-B construct.Within Psychological Capability, subthemes captured the need for consistent and reliable COVID-19 vaccine information and access to balanced and jargon-free, risk-benefit information that is tailored to the pregnant individual. The behaviour/opinions of family, friends, and local healthcare providers had a powerful influence on COVID-19 vaccine decisions (Social Opportunity). Integrating the COVID-19 vaccine as part of routine antenatal pathways was believed to support access and sense of familiarity (Physical Opportunity). Participants valued health autonomy, however experienced internal conflict driven by concerns about long-term side effects for their baby (Reflective Motivation). Feelings of fear, lack of empathy from healthcare providers, and anticipated guilt commonly underpinned indecision as to whether to get the vaccine (Automatic Motivation).Our study highlighted that the choice to accept a vaccine during pregnancy generates internal conflict and worry. Several participants cited their concern was primarily around the safety for their baby. Healthcare professionals (HCPs) play a significant part when it comes to decision making about COVID-19 vaccines among pregnant women. HCPs and pregnant women should be involved in the development of interventions to improve the delivery and communication of information.",,pdf:https://bmcpregnancychildbirth.biomedcentral.com/counter/pdf/10.1186/s12884-023-05958-y; doi:https://doi.org/10.1186/s12884-023-05958-y; html:https://europepmc.org/articles/PMC10481472; pdf:https://europepmc.org/articles/PMC10481472?pdf=render
-35289755,https://doi.org/10.2196/31021,Concept Libraries for Repeatable and Reusable Research: Qualitative Study Exploring the Needs of Users.,"Almowil Z, Zhou SM, Brophy S, Croxall J.",,JMIR human factors,2022,2022-03-15,Y,Electronic Health Records; Record Linkage; Reproducible Research; Clinical Codes; Concept Libraries,,,"<h4>Background</h4>Big data research in the field of health sciences is hindered by a lack of agreement on how to identify and define different conditions and their medications. This means that researchers and health professionals often have different phenotype definitions for the same condition. This lack of agreement makes it difficult to compare different study findings and hinders the ability to conduct repeatable and reusable research.<h4>Objective</h4>This study aims to examine the requirements of various users, such as researchers, clinicians, machine learning experts, and managers, in the development of a data portal for phenotypes (a concept library).<h4>Methods</h4>This was a qualitative study using interviews and focus group discussion. One-to-one interviews were conducted with researchers, clinicians, machine learning experts, and senior research managers in health data science (N=6) to explore their specific needs in the development of a concept library. In addition, a focus group discussion with researchers (N=14) working with the Secured Anonymized Information Linkage databank, a national eHealth data linkage infrastructure, was held to perform a SWOT (strengths, weaknesses, opportunities, and threats) analysis for the phenotyping system and the proposed concept library. The interviews and focus group discussion were transcribed verbatim, and 2 thematic analyses were performed.<h4>Results</h4>Most of the participants thought that the prototype concept library would be a very helpful resource for conducting repeatable research, but they specified that many requirements are needed before its development. Although all the participants stated that they were aware of some existing concept libraries, most of them expressed negative perceptions about them. The participants mentioned several facilitators that would stimulate them to share their work and reuse the work of others, and they pointed out several barriers that could inhibit them from sharing their work and reusing the work of others. The participants suggested some developments that they would like to see to improve reproducible research output using routine data.<h4>Conclusions</h4>The study indicated that most interviewees valued a concept library for phenotypes. However, only half of the participants felt that they would contribute by providing definitions for the concept library, and they reported many barriers regarding sharing their work on a publicly accessible platform. Analysis of interviews and the focus group discussion revealed that different stakeholders have different requirements, facilitators, barriers, and concerns about a prototype concept library.",,doi:https://doi.org/10.2196/31021; doi:https://doi.org/10.2196/31021; html:https://europepmc.org/articles/PMC8965669
 38977844,https://doi.org/10.1038/s43856-024-00506-x,Complex patterns of multimorbidity associated with severe COVID-19 and long COVID.,"Pietzner M, Denaxas S, Yasmeen S, Ulmer MA, Nakanishi T, Arnold M, Kastenmüller G, Hemingway H, Langenberg C.",,Communications medicine,2024,2024-07-08,Y,,,,"<h4>Background</h4>Early evidence that patients with (multiple) pre-existing diseases are at highest risk for severe COVID-19 has been instrumental in the pandemic to allocate critical care resources and later vaccination schemes. However, systematic studies exploring the breadth of medical diagnoses are scarce but may help to understand severe COVID-19 among patients at supposedly low risk.<h4>Methods</h4>We systematically harmonized >12 million primary care and hospitalisation health records from ~500,000 UK Biobank participants into 1448 collated disease terms to systematically identify diseases predisposing to severe COVID-19 (requiring hospitalisation or death) and its post-acute sequalae, Long COVID.<h4>Results</h4>Here we identify 679 diseases associated with an increased risk for severe COVID-19 (n = 672) and/or Long COVID (n = 72) that span almost all clinical specialties and are strongly enriched in clusters of cardio-respiratory and endocrine-renal diseases. For 57 diseases, we establish consistent evidence to predispose to severe COVID-19 based on survival and genetic susceptibility analyses. This includes a possible role of symptoms of malaise and fatigue as a so far largely overlooked risk factor for severe COVID-19. We finally observe partially opposing risk estimates at known risk loci for severe COVID-19 for etiologically related diseases, such as post-inflammatory pulmonary fibrosis or rheumatoid arthritis, possibly indicating a segregation of disease mechanisms.<h4>Conclusions</h4>Our results provide a unique reference that demonstrates how 1) complex co-occurrence of multiple - including non-fatal - conditions predispose to increased COVID-19 severity and 2) how incorporating the whole breadth of medical diagnosis can guide the interpretation of genetic risk loci.",,doi:https://doi.org/10.1038/s43856-024-00506-x; html:https://europepmc.org/articles/PMC11231221; pdf:https://europepmc.org/articles/PMC11231221?pdf=render
+35289755,https://doi.org/10.2196/31021,Concept Libraries for Repeatable and Reusable Research: Qualitative Study Exploring the Needs of Users.,"Almowil Z, Zhou SM, Brophy S, Croxall J.",,JMIR human factors,2022,2022-03-15,Y,Electronic Health Records; Record Linkage; Reproducible Research; Clinical Codes; Concept Libraries,,,"<h4>Background</h4>Big data research in the field of health sciences is hindered by a lack of agreement on how to identify and define different conditions and their medications. This means that researchers and health professionals often have different phenotype definitions for the same condition. This lack of agreement makes it difficult to compare different study findings and hinders the ability to conduct repeatable and reusable research.<h4>Objective</h4>This study aims to examine the requirements of various users, such as researchers, clinicians, machine learning experts, and managers, in the development of a data portal for phenotypes (a concept library).<h4>Methods</h4>This was a qualitative study using interviews and focus group discussion. One-to-one interviews were conducted with researchers, clinicians, machine learning experts, and senior research managers in health data science (N=6) to explore their specific needs in the development of a concept library. In addition, a focus group discussion with researchers (N=14) working with the Secured Anonymized Information Linkage databank, a national eHealth data linkage infrastructure, was held to perform a SWOT (strengths, weaknesses, opportunities, and threats) analysis for the phenotyping system and the proposed concept library. The interviews and focus group discussion were transcribed verbatim, and 2 thematic analyses were performed.<h4>Results</h4>Most of the participants thought that the prototype concept library would be a very helpful resource for conducting repeatable research, but they specified that many requirements are needed before its development. Although all the participants stated that they were aware of some existing concept libraries, most of them expressed negative perceptions about them. The participants mentioned several facilitators that would stimulate them to share their work and reuse the work of others, and they pointed out several barriers that could inhibit them from sharing their work and reusing the work of others. The participants suggested some developments that they would like to see to improve reproducible research output using routine data.<h4>Conclusions</h4>The study indicated that most interviewees valued a concept library for phenotypes. However, only half of the participants felt that they would contribute by providing definitions for the concept library, and they reported many barriers regarding sharing their work on a publicly accessible platform. Analysis of interviews and the focus group discussion revealed that different stakeholders have different requirements, facilitators, barriers, and concerns about a prototype concept library.",,doi:https://doi.org/10.2196/31021; doi:https://doi.org/10.2196/31021; html:https://europepmc.org/articles/PMC8965669
 37400731,https://doi.org/10.1007/s10802-023-01086-5,Maternal Mental Health and Children's Problem Behaviours: A Bi-directional Relationship?,"Lowthian E, Bedston S, Kristensen SM, Akbari A, Fry R, Huxley K, Johnson R, Kim HS, Owen RK, Taylor C, Griffiths L.",,Research on child and adolescent psychopathology,2023,2023-07-04,Y,Child Development; Bayesian analysis; Structural Equation Modelling; Maternal Mental Health; Millennium Cohort Study,,,"Transactional theory and the coercive family process model have illustrated how the parent-child relationship is reciprocal. Emerging research using advanced statistical methods has examined these theories, but further investigations are necessary. In this study, we utilised linked health data on maternal mental health disorders and explored their relationship with child problem behaviours via the Strengths and Difficulties Questionnaire for over 13 years. We accessed data from the Millennium Cohort Study, linked to anonymised individual-level population-scale health and administrative data within the Secure Anonymised Information Linkage (SAIL) Databank. We used Bayesian Structural Equation Modelling, specifically Random-Intercept Cross-Lagged Panel Models, to analyse the relationships between mothers and their children. We then explored these models with the addition of time-invariant covariates. We found that a mother's mental health was strongly associated over time, as were children's problem behaviours. We found mixed evidence for bi-directional relationships, with only emotional problems showing bi-directional associations in mid to late childhood. Only child-to-mother pathways were identified for the overall problem behaviour score and peer problems; no associations were found for conduct problems or hyperactivity. All models had strong between-effects and clear socioeconomic and sex differences. We encourage the use of whole family-based support for mental health and problem behaviours, and recommend that socioeconomic, sex and wider differences should be considered as factors in tailoring family-based interventions and support.",,pdf:https://link.springer.com/content/pdf/10.1007/s10802-023-01086-5.pdf; doi:https://doi.org/10.1007/s10802-023-01086-5; html:https://europepmc.org/articles/PMC10628040; pdf:https://europepmc.org/articles/PMC10628040?pdf=render
 36944118,https://doi.org/10.2337/dc22-1238,Cardiovascular Safety in Type 2 Diabetes With Sulfonylureas as Second-line Drugs: A Nationwide Population-Based Comparative Safety Study.,"Wang H, Cordiner RLM, Huang Y, Donnelly L, Hapca S, Collier A, McKnight J, Kennon B, Gibb F, McKeigue P, Wild SH, Colhoun H, Chalmers J, Petrie J, Sattar N, MacDonald T, McCrimmon RJ, Morales DR, Pearson ER, Scottish Diabetes Research Network Epidemiology Group.",,Diabetes care,2023,2023-05-01,Y,,,,"<h4>Objective</h4>To assess the real-world cardiovascular (CV) safety for sulfonylureas (SU), in comparison with dipeptidyl peptidase 4 inhibitors (DPP4i) and thiazolidinediones (TZD), through development of robust methodology for causal inference in a whole nation study.<h4>Research design and methods</h4>A cohort study was performed including people with type 2 diabetes diagnosed in Scotland before 31 December 2017, who failed to reach HbA1c 48 mmol/mol despite metformin monotherapy and initiated second-line pharmacotherapy (SU/DPP4i/TZD) on or after 1 January 2010. The primary outcome was composite major adverse cardiovascular events (MACE), including hospitalization for myocardial infarction, ischemic stroke, heart failure, and CV death. Secondary outcomes were each individual end point and all-cause death. Multivariable Cox proportional hazards regression and an instrumental variable (IV) approach were used to control confounding in a similar way to the randomization process in a randomized control trial.<h4>Results</h4>Comparing SU to non-SU (DPP4i/TZD), the hazard ratio (HR) for MACE was 1.00 (95% CI: 0.91-1.09) from the multivariable Cox regression and 1.02 (0.91-1.13) and 1.03 (0.91-1.16) using two different IVs. For all-cause death, the HR from Cox regression and the two IV analyses was 1.03 (0.94-1.13), 1.04 (0.93-1.17), and 1.03 (0.90-1.17).<h4>Conclusions</h4>Our findings contribute to the understanding that second-line SU for glucose lowering are unlikely to increase CV risk or all-cause mortality. Given their potent efficacy, microvascular benefits, cost effectiveness, and widespread use, this study supports that SU should remain a part of the global diabetes treatment portfolio.",,pdf:https://diabetesjournals.org/care/article-pdf/46/5/967/702262/dc221238.pdf; doi:https://doi.org/10.2337/dc22-1238; html:https://europepmc.org/articles/PMC10154665; pdf:https://europepmc.org/articles/PMC10154665?pdf=render
 35607618,https://doi.org/10.1016/j.patter.2022.100471,"Relevance, redundancy, and complementarity trade-off (RRCT): A principled, generic, robust feature-selection tool.",Tsanas A.,,"Patterns (New York, N.Y.)",2022,2022-03-31,Y,Information theory; Variable selection; Feature Selection; Statistical Learning; Dimensionality Reduction; Curse Of Dimensionality; Principle Of Parsimony,,,"We present a new heuristic feature-selection (FS) algorithm that integrates in a principled algorithmic framework the three key FS components: relevance, redundancy, and complementarity. Thus, we call it relevance, redundancy, and complementarity trade-off (RRCT). The association strength between each feature and the response and between feature pairs is quantified via an information theoretic transformation of rank correlation coefficients, and the feature complementarity is quantified using partial correlation coefficients. We empirically benchmark the performance of RRCT against 19 FS algorithms across four synthetic and eight real-world datasets in indicative challenging settings evaluating the following: (1) matching the true feature set and (2) out-of-sample performance in binary and multi-class classification problems when presenting selected features into a random forest. RRCT is very competitive in both tasks, and we tentatively make suggestions on the generalizability and application of the best-performing FS algorithms across settings where they may operate effectively.",,pdf:http://www.cell.com/article/S2666389922000514/pdf; doi:https://doi.org/10.1016/j.patter.2022.100471; html:https://europepmc.org/articles/PMC9122960; pdf:https://europepmc.org/articles/PMC9122960?pdf=render
-34474011,https://doi.org/10.1016/s0140-6736(21)01638-x,Redefining β-blocker response in heart failure patients with sinus rhythm and atrial fibrillation: a machine learning cluster analysis.,"Karwath A, Bunting KV, Gill SK, Tica O, Pendleton S, Aziz F, Barsky AD, Chernbumroong S, Duan J, Mobley AR, Cardoso VR, Slater K, Williams JA, Bruce EJ, Wang X, Flather MD, Coats AJS, Gkoutos GV, Kotecha D, card AIc group and the Beta-blockers in Heart Failure Collaborative Group.",,"Lancet (London, England)",2021,2021-08-30,Y,,,,"<h4>Background</h4>Mortality remains unacceptably high in patients with heart failure and reduced left ventricular ejection fraction (LVEF) despite advances in therapeutics. We hypothesised that a novel artificial intelligence approach could better assess multiple and higher-dimension interactions of comorbidities, and define clusters of β-blocker efficacy in patients with sinus rhythm and atrial fibrillation.<h4>Methods</h4>Neural network-based variational autoencoders and hierarchical clustering were applied to pooled individual patient data from nine double-blind, randomised, placebo-controlled trials of β blockers. All-cause mortality during median 1·3 years of follow-up was assessed by intention to treat, stratified by electrocardiographic heart rhythm. The number of clusters and dimensions was determined objectively, with results validated using a leave-one-trial-out approach. This study was prospectively registered with ClinicalTrials.gov (NCT00832442) and the PROSPERO database of systematic reviews (CRD42014010012).<h4>Findings</h4>15 659 patients with heart failure and LVEF of less than 50% were included, with median age 65 years (IQR 56-72) and LVEF 27% (IQR 21-33). 3708 (24%) patients were women. In sinus rhythm (n=12 822), most clusters demonstrated a consistent overall mortality benefit from β blockers, with odds ratios (ORs) ranging from 0·54 to 0·74. One cluster in sinus rhythm of older patients with less severe symptoms showed no significant efficacy (OR 0·86, 95% CI 0·67-1·10; p=0·22). In atrial fibrillation (n=2837), four of five clusters were consistent with the overall neutral effect of β blockers versus placebo (OR 0·92, 0·77-1·10; p=0·37). One cluster of younger atrial fibrillation patients at lower mortality risk but similar LVEF to average had a statistically significant reduction in mortality with β blockers (OR 0·57, 0·35-0·93; p=0·023). The robustness and consistency of clustering was confirmed for all models (p<0·0001 vs random), and cluster membership was externally validated across the nine independent trials.<h4>Interpretation</h4>An artificial intelligence-based clustering approach was able to distinguish prognostic response from β blockers in patients with heart failure and reduced LVEF. This included patients in sinus rhythm with suboptimal efficacy, as well as a cluster of patients with atrial fibrillation where β blockers did reduce mortality.<h4>Funding</h4>Medical Research Council, UK, and EU/EFPIA Innovative Medicines Initiative BigData@Heart.",,doi:https://doi.org/10.1016/s0140-6736(21)01638-x; doi:https://doi.org/10.1016/S0140-6736(21)01638-X; html:https://europepmc.org/articles/PMC8542730; pdf:https://europepmc.org/articles/PMC8542730?pdf=render
-37678881,https://doi.org/10.1093/ageing/afad157,Survival and critical care use among people with dementia in a large English cohort.,"Yorganci E, Sleeman KE, Sampson EL, Stewart R, EMBED-Care Programme.",,Age and ageing,2023,2023-09-01,Y,Survival; Dementia; Intensive Care; Older People; Critical Care; Routine Data,,,"<h4>Background</h4>Admitting people with dementia to critical care units may not always lead to a clear survival benefit. Critical care admissions of people with dementia vary across countries. Little is known about the use and trends of critical care admissions of people with dementia in England.<h4>Objective</h4>To investigate critical care use and survival among people with dementia in a large London catchment area.<h4>Methods</h4>A retrospective cohort study using data from dementia assessment services in south London, UK (2007-20) linked with national hospitalisation data to ascertain critical care admissions. Outcomes included age-sex-standardised critical care use and 1-year post-critical care admission survival by dementia severity (binary: mild versus moderate/severe). We used logistic regression and Kaplan-Meier survival plots for investigating 1-year survival following a critical care admission and linear regressions for time trends.<h4>Results</h4>Of 19,787 people diagnosed with dementia, 726 (3.7%) had ≥1 critical care admission at any time after receiving their dementia diagnosis. The overall 1-year survival of people with dementia, who had a CCA, was 47.5% (n = 345). Dementia severity was not associated with 1-year survival following a critical care admission (mild dementia versus moderate-severe dementia odds of 1-year mortality OR: 0.90, 95% CI [0.66-1.22]). Over the 12-year period from 2008 to 2019, overall critical care use decreased (β = -0.05; 95% CI = -0.01, -0.0003; P = 0.03), while critical care admissions occurring during the last year of life increased (β = 0.11, 95% CI = 0.01, 0.20, P = 0.03).<h4>Conclusions</h4>In this cohort, while critical care use among people with dementia declined overall, its use increased among those in their last year of life. Survival remains comparable to that observed in general older populations.",,doi:https://doi.org/10.1093/ageing/afad157; html:https://europepmc.org/articles/PMC10484725; pdf:https://europepmc.org/articles/PMC10484725?pdf=render
 31757986,https://doi.org/10.1038/s41598-019-53454-1,Ontology-based prediction of cancer driver genes.,"Althubaiti S, Karwath A, Dallol A, Noor A, Alkhayyat SS, Alwassia R, Mineta K, Gojobori T, Beggs AD, Schofield PN, Gkoutos GV, Hoehndorf R.",,Scientific reports,2019,2019-11-22,Y,,Applied Analytics,,"Identifying and distinguishing cancer driver genes among thousands of candidate mutations remains a major challenge. Accurate identification of driver genes and driver mutations is critical for advancing cancer research and personalizing treatment based on accurate stratification of patients. Due to inter-tumor genetic heterogeneity many driver mutations within a gene occur at low frequencies, which make it challenging to distinguish them from non-driver mutations. We have developed a novel method for identifying cancer driver genes. Our approach utilizes multiple complementary types of information, specifically cellular phenotypes, cellular locations, functions, and whole body physiological phenotypes as features. We demonstrate that our method can accurately identify known cancer driver genes and distinguish between their role in different types of cancer. In addition to confirming known driver genes, we identify several novel candidate driver genes. We demonstrate the utility of our method by validating its predictions in nasopharyngeal cancer and colorectal cancer using whole exome and whole genome sequencing.",This study investigated which genes encourage cancer tumors to grow. The study identifies genes and distinguishes their role in different types of cancers. Their method is validated using whole exome and whole genome sequencing,pdf:https://www.nature.com/articles/s41598-019-53454-1.pdf; doi:https://doi.org/10.1038/s41598-019-53454-1; html:https://europepmc.org/articles/PMC6874647; pdf:https://europepmc.org/articles/PMC6874647?pdf=render
-37536152,https://doi.org/10.1016/j.seizure.2023.07.016,Association of comorbid-socioeconomic clusters with mortality in late onset epilepsy derived through unsupervised machine learning.,"Josephson CB, Gonzalez-Izquierdo A, Engbers JDT, Denaxas S, Delgado-Garcia G, Sajobi TT, Wang M, Keezer MR, Wiebe S.",,Seizure,2023,2023-07-29,N,Epilepsy; Elderly; Cohort study; Electronic Health Records; Unsupervised Machine Learning; Late-onset Epilepsy,,,"<h4>Background and objectives</h4>Late-onset epilepsy is a heterogenous entity associated with specific aetiologies and an elevated risk of premature mortality. Specific multimorbid-socioeconomic profiles and their unique prognostic trajectories have not been described. We sought to determine if specific clusters of late onset epilepsy exist, and whether they have unique hazards of premature mortality.<h4>Methods</h4>We performed a retrospective observational cohort study linking primary and hospital-based UK electronic health records with vital statistics data (covering years 1998-2019) to identify all cases of incident late onset epilepsy (from people aged ≥65) and 1:10 age, sex, and GP practice-matched controls. We applied hierarchical agglomerative clustering using common aetiologies identified at baseline to define multimorbid-socioeconomic profiles, compare hazards of early mortality, and tabulating causes of death stratified by cluster.<h4>Results</h4>From 1,032,129 people aged ≥65, we identified 1048 cases of late onset epilepsy who were matched to 10,259 controls. Median age at epilepsy diagnosis was 68 (interquartile range: 66-72) and 474 (45%) were female. The hazard of premature mortality related to late-onset epilepsy was higher than matched controls (hazard ratio [HR] 1.73; 95% confidence interval [95%CI] 1.51-1.99). Ten unique phenotypic clusters were identified, defined by 'healthy' males and females, ischaemic stroke, intracerebral haemorrhage (ICH), ICH and alcohol misuse, dementia and anxiety, anxiety, depression in males and females, and brain tumours. Cluster-specific hazards were often similar to that derived for late-onset epilepsy as a whole. Clusters that differed significantly from the base late-onset epilepsy hazard were 'dementia and anxiety' (HR 5.36; 95%CI 3.31-8.68), 'brain tumour' (HR 4.97; 95%CI 2.89-8.56), 'ICH and alcohol misuse' (HR 2.91; 95%CI 1.76-4.81), and 'ischaemic stroke' (HR 2.83; 95%CI 1.83-4.04). These cluster-specific risks were also elevated compared to those derived for tumours, dementia, ischaemic stroke, and ICH in the whole population. Seizure-related cause of death was uncommon and restricted to the ICH, ICH and alcohol misuse, and healthy female clusters.<h4>Significance</h4>Late-onset epilepsy is an amalgam of unique phenotypic clusters that can be quantitatively defined. Late-onset epilepsy and cluster-specific comorbid profiles have complex effects on premature mortality above and beyond the base rates attributed to epilepsy and cluster-defining comorbidities alone.",,doi:https://doi.org/10.1016/j.seizure.2023.07.016
+37678881,https://doi.org/10.1093/ageing/afad157,Survival and critical care use among people with dementia in a large English cohort.,"Yorganci E, Sleeman KE, Sampson EL, Stewart R, EMBED-Care Programme.",,Age and ageing,2023,2023-09-01,Y,Survival; Dementia; Intensive Care; Older People; Critical Care; Routine Data,,,"<h4>Background</h4>Admitting people with dementia to critical care units may not always lead to a clear survival benefit. Critical care admissions of people with dementia vary across countries. Little is known about the use and trends of critical care admissions of people with dementia in England.<h4>Objective</h4>To investigate critical care use and survival among people with dementia in a large London catchment area.<h4>Methods</h4>A retrospective cohort study using data from dementia assessment services in south London, UK (2007-20) linked with national hospitalisation data to ascertain critical care admissions. Outcomes included age-sex-standardised critical care use and 1-year post-critical care admission survival by dementia severity (binary: mild versus moderate/severe). We used logistic regression and Kaplan-Meier survival plots for investigating 1-year survival following a critical care admission and linear regressions for time trends.<h4>Results</h4>Of 19,787 people diagnosed with dementia, 726 (3.7%) had ≥1 critical care admission at any time after receiving their dementia diagnosis. The overall 1-year survival of people with dementia, who had a CCA, was 47.5% (n = 345). Dementia severity was not associated with 1-year survival following a critical care admission (mild dementia versus moderate-severe dementia odds of 1-year mortality OR: 0.90, 95% CI [0.66-1.22]). Over the 12-year period from 2008 to 2019, overall critical care use decreased (β = -0.05; 95% CI = -0.01, -0.0003; P = 0.03), while critical care admissions occurring during the last year of life increased (β = 0.11, 95% CI = 0.01, 0.20, P = 0.03).<h4>Conclusions</h4>In this cohort, while critical care use among people with dementia declined overall, its use increased among those in their last year of life. Survival remains comparable to that observed in general older populations.",,doi:https://doi.org/10.1093/ageing/afad157; html:https://europepmc.org/articles/PMC10484725; pdf:https://europepmc.org/articles/PMC10484725?pdf=render
+34474011,https://doi.org/10.1016/s0140-6736(21)01638-x,Redefining β-blocker response in heart failure patients with sinus rhythm and atrial fibrillation: a machine learning cluster analysis.,"Karwath A, Bunting KV, Gill SK, Tica O, Pendleton S, Aziz F, Barsky AD, Chernbumroong S, Duan J, Mobley AR, Cardoso VR, Slater K, Williams JA, Bruce EJ, Wang X, Flather MD, Coats AJS, Gkoutos GV, Kotecha D, card AIc group and the Beta-blockers in Heart Failure Collaborative Group.",,"Lancet (London, England)",2021,2021-08-30,Y,,,,"<h4>Background</h4>Mortality remains unacceptably high in patients with heart failure and reduced left ventricular ejection fraction (LVEF) despite advances in therapeutics. We hypothesised that a novel artificial intelligence approach could better assess multiple and higher-dimension interactions of comorbidities, and define clusters of β-blocker efficacy in patients with sinus rhythm and atrial fibrillation.<h4>Methods</h4>Neural network-based variational autoencoders and hierarchical clustering were applied to pooled individual patient data from nine double-blind, randomised, placebo-controlled trials of β blockers. All-cause mortality during median 1·3 years of follow-up was assessed by intention to treat, stratified by electrocardiographic heart rhythm. The number of clusters and dimensions was determined objectively, with results validated using a leave-one-trial-out approach. This study was prospectively registered with ClinicalTrials.gov (NCT00832442) and the PROSPERO database of systematic reviews (CRD42014010012).<h4>Findings</h4>15 659 patients with heart failure and LVEF of less than 50% were included, with median age 65 years (IQR 56-72) and LVEF 27% (IQR 21-33). 3708 (24%) patients were women. In sinus rhythm (n=12 822), most clusters demonstrated a consistent overall mortality benefit from β blockers, with odds ratios (ORs) ranging from 0·54 to 0·74. One cluster in sinus rhythm of older patients with less severe symptoms showed no significant efficacy (OR 0·86, 95% CI 0·67-1·10; p=0·22). In atrial fibrillation (n=2837), four of five clusters were consistent with the overall neutral effect of β blockers versus placebo (OR 0·92, 0·77-1·10; p=0·37). One cluster of younger atrial fibrillation patients at lower mortality risk but similar LVEF to average had a statistically significant reduction in mortality with β blockers (OR 0·57, 0·35-0·93; p=0·023). The robustness and consistency of clustering was confirmed for all models (p<0·0001 vs random), and cluster membership was externally validated across the nine independent trials.<h4>Interpretation</h4>An artificial intelligence-based clustering approach was able to distinguish prognostic response from β blockers in patients with heart failure and reduced LVEF. This included patients in sinus rhythm with suboptimal efficacy, as well as a cluster of patients with atrial fibrillation where β blockers did reduce mortality.<h4>Funding</h4>Medical Research Council, UK, and EU/EFPIA Innovative Medicines Initiative BigData@Heart.",,doi:https://doi.org/10.1016/s0140-6736(21)01638-x; doi:https://doi.org/10.1016/S0140-6736(21)01638-X; html:https://europepmc.org/articles/PMC8542730; pdf:https://europepmc.org/articles/PMC8542730?pdf=render
 36333839,https://doi.org/10.1002/gps.5834,The impact of the first UK COVID-19 lockdown on presentations with psychosis to mental health services for older adults: An electronic health records study in South London.,"Simkin L, Yung P, Greig F, Perera G, Tsamakis K, Rizos E, Stewart R, Velayudhan L, Mueller C.",,International journal of geriatric psychiatry,2022,2022-12-01,Y,Dementia; Hallucinations; Delusions; Psychosis; Older Adults; Lockdown; Covid‐19; Non‐white Ethnicity,,,"<h4>Objectives</h4>Social distancing restrictions in the COVID-19 pandemic may have had adverse effects on older adults' mental health. Whereby the impact on mood is well-described, less is known about psychotic symptoms. The aim of this study was to compare characteristics associated with psychotic symptoms during the first UK lockdown and a pre-pandemic comparison period.<h4>Methods</h4>In this retrospective observational study we analysed anonymised records from patients referred to mental health services for older adults in South London in the 16-week period of the UK lockdown starting in March 2020, and in the comparable pre-pandemic period in 2019. We used logistic regression models to compare the associations of different patient characteristics with increased odds of presenting with any psychotic symptom (defined as hallucinations and/or delusion), hallucinations, or delusions, during lockdown and the corresponding pre-pandemic period.<h4>Results</h4>1991 referrals were identified. There were fewer referrals during lockdown but a higher proportion of presentations with any psychotic symptom (48.7% vs. 42.8%, p = 0.018), particularly hallucinations (41.0% vs. 27.8%, p < 0.001). Patients of non-White ethnicity (adjusted odds ratio (OR): 1.83; 95% confidence interval (CI): 1.13-2.99) and patients with dementia (adjusted OR: 3.09; 95% CI: 1.91-4.99) were more likely to be referred with psychotic symptoms during lockdown. While a weaker association between dementia and psychotic symptoms was found in the pre-COVID period (adjusted OR: 1.55; 95% CI: 1.19-2.03), interaction terms indicated higher odds of patients of non-White ethnicity or dementia to present with psychosis during the lockdown period.<h4>Conclusions</h4>During lockdown, referrals to mental health services for adults decreased, but contained a higher proportion with psychotic symptoms. The stronger association with psychotic symptoms in non-White ethnic groups and patients with dementia during lockdown suggests that barriers in accessing care might have increased during the COVID-19 pandemic.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/gps.5834; doi:https://doi.org/10.1002/gps.5834; html:https://europepmc.org/articles/PMC9828419; pdf:https://europepmc.org/articles/PMC9828419?pdf=render
-36755846,https://doi.org/10.1093/ckj/sfac241,"Depression is associated with frailty and lower quality of life in haemodialysis recipients, but not with mortality or hospitalization.","Anderson BM, Qasim M, Correa G, Evison F, Gallier S, Ferro CJ, Jackson TA, Sharif A.",,Clinical kidney journal,2023,2022-10-31,Y,Mortality; Depression; Frailty; Haemodialysis; Hospitalization; Health-related Quality Of Life,,,"<h4>Background</h4>Frailty and depression are highly prevalent in haemodialysis recipients, exhibit a reciprocal relationship, and are associated with increased mortality and hospitalization, and lower quality of life. Despite this, there has been little exploration of the relationship between depression and frailty upon patient outcomes. We aimed to explore the relationship between depression and frailty, and their associations with mortality, hospitalization and quality of life.<h4>Methods</h4>We performed a prospective cohort study of prevalent haemodialysis recipients linked to national datasets for outcomes including mortality and hospitalization. Depression was assessed using the Patient Health Questionnaire-9 (PHQ-9), frailty using the Clinical Frailty Scale (CFS) and quality of life using the EuroQol 5-Dimension (EQ-5D) Summary Index.<h4>Results</h4>A total of 485 prevalent haemodialysis recipients were recruited, with 111 deaths and 1241 hospitalizations during follow-up. CFS was independently associated with mortality [hazard ratio (HR) 1.31; 95% confidence interval (CI) 1.08, 1.59; <i>P</i> = .006], hospitalization [incidence rate ratio (IRR) 1.13; 95% CI 1.03, 1.25; <i>P</i> = .010] and lower quality of life (Coef. -0.401; 95% CI -0.511, -0.292; <i>P</i> < .001). PHQ-9 score was independently associated with lower quality of life (Coef. -0.042; 95% CI -0.063, -0.021; <i>P</i> < .001), but not mortality (HR 1.00; 95% CI 0.96, 1.04; <i>P</i> = .901) or hospitalization (IRR 0.99; 95% CI 0.97, 1.01; <i>P</i> = .351). In an adjusted model including CFS, moderate depression was associated with reduced hospitalization (IRR 0.72; 95% CI 0.56, 0.93; <i>P</i> = .013).<h4>Conclusions</h4>With the addition of frailty, depression was associated with lower hospital admissions, but poorer quality of life. The relationship between frailty and depression, and their influence on outcomes is complex, requiring further study.",,pdf:https://academic.oup.com/ckj/article-pdf/16/2/342/49100412/sfac241.pdf; doi:https://doi.org/10.1093/ckj/sfac241; html:https://europepmc.org/articles/PMC9900564; pdf:https://europepmc.org/articles/PMC9900564?pdf=render
+37536152,https://doi.org/10.1016/j.seizure.2023.07.016,Association of comorbid-socioeconomic clusters with mortality in late onset epilepsy derived through unsupervised machine learning.,"Josephson CB, Gonzalez-Izquierdo A, Engbers JDT, Denaxas S, Delgado-Garcia G, Sajobi TT, Wang M, Keezer MR, Wiebe S.",,Seizure,2023,2023-07-29,N,Epilepsy; Elderly; Cohort study; Electronic Health Records; Unsupervised Machine Learning; Late-onset Epilepsy,,,"<h4>Background and objectives</h4>Late-onset epilepsy is a heterogenous entity associated with specific aetiologies and an elevated risk of premature mortality. Specific multimorbid-socioeconomic profiles and their unique prognostic trajectories have not been described. We sought to determine if specific clusters of late onset epilepsy exist, and whether they have unique hazards of premature mortality.<h4>Methods</h4>We performed a retrospective observational cohort study linking primary and hospital-based UK electronic health records with vital statistics data (covering years 1998-2019) to identify all cases of incident late onset epilepsy (from people aged ≥65) and 1:10 age, sex, and GP practice-matched controls. We applied hierarchical agglomerative clustering using common aetiologies identified at baseline to define multimorbid-socioeconomic profiles, compare hazards of early mortality, and tabulating causes of death stratified by cluster.<h4>Results</h4>From 1,032,129 people aged ≥65, we identified 1048 cases of late onset epilepsy who were matched to 10,259 controls. Median age at epilepsy diagnosis was 68 (interquartile range: 66-72) and 474 (45%) were female. The hazard of premature mortality related to late-onset epilepsy was higher than matched controls (hazard ratio [HR] 1.73; 95% confidence interval [95%CI] 1.51-1.99). Ten unique phenotypic clusters were identified, defined by 'healthy' males and females, ischaemic stroke, intracerebral haemorrhage (ICH), ICH and alcohol misuse, dementia and anxiety, anxiety, depression in males and females, and brain tumours. Cluster-specific hazards were often similar to that derived for late-onset epilepsy as a whole. Clusters that differed significantly from the base late-onset epilepsy hazard were 'dementia and anxiety' (HR 5.36; 95%CI 3.31-8.68), 'brain tumour' (HR 4.97; 95%CI 2.89-8.56), 'ICH and alcohol misuse' (HR 2.91; 95%CI 1.76-4.81), and 'ischaemic stroke' (HR 2.83; 95%CI 1.83-4.04). These cluster-specific risks were also elevated compared to those derived for tumours, dementia, ischaemic stroke, and ICH in the whole population. Seizure-related cause of death was uncommon and restricted to the ICH, ICH and alcohol misuse, and healthy female clusters.<h4>Significance</h4>Late-onset epilepsy is an amalgam of unique phenotypic clusters that can be quantitatively defined. Late-onset epilepsy and cluster-specific comorbid profiles have complex effects on premature mortality above and beyond the base rates attributed to epilepsy and cluster-defining comorbidities alone.",,doi:https://doi.org/10.1016/j.seizure.2023.07.016
 36544046,https://doi.org/10.1038/s41746-022-00730-6,A survey on clinical natural language processing in the United Kingdom from 2007 to 2022.,"Wu H, Wang M, Wu J, Francis F, Chang YH, Shavick A, Dong H, Poon MTC, Fitzpatrick N, Levine AP, Slater LT, Handy A, Karwath A, Gkoutos GV, Chelala C, Shah AD, Stewart R, Collier N, Alex B, Whiteley W, Sudlow C, Roberts A, Dobson RJB.",,NPJ digital medicine,2022,2022-12-21,Y,,,,"Much of the knowledge and information needed for enabling high-quality clinical research is stored in free-text format. Natural language processing (NLP) has been used to extract information from these sources at scale for several decades. This paper aims to present a comprehensive review of clinical NLP for the past 15 years in the UK to identify the community, depict its evolution, analyse methodologies and applications, and identify the main barriers. We collect a dataset of clinical NLP projects (n = 94; £ = 41.97 m) funded by UK funders or the European Union's funding programmes. Additionally, we extract details on 9 funders, 137 organisations, 139 persons and 431 research papers. Networks are created from timestamped data interlinking all entities, and network analysis is subsequently applied to generate insights. 431 publications are identified as part of a literature review, of which 107 are eligible for final analysis. Results show, not surprisingly, clinical NLP in the UK has increased substantially in the last 15 years: the total budget in the period of 2019-2022 was 80 times that of 2007-2010. However, the effort is required to deepen areas such as disease (sub-)phenotyping and broaden application domains. There is also a need to improve links between academia and industry and enable deployments in real-world settings for the realisation of clinical NLP's great potential in care delivery. The major barriers include research and development access to hospital data, lack of capable computational resources in the right places, the scarcity of labelled data and barriers to sharing of pretrained models.",,pdf:https://www.nature.com/articles/s41746-022-00730-6.pdf; doi:https://doi.org/10.1038/s41746-022-00730-6; html:https://europepmc.org/articles/PMC9770568; pdf:https://europepmc.org/articles/PMC9770568?pdf=render
-37528841,https://doi.org/10.1016/j.eclinm.2023.102064,Repeated antibiotic exposure and risk of hospitalisation and death following COVID-19 infection (OpenSAFELY): a matched case-control study.,"Yang YT, Wong D, Ashcroft DM, Massey J, MacKenna B, Fisher L, Mehrkar A, Bacon SC, OpenSAFELY collaborative, Hand K, Zhong X, Fahmi A, Goldacre B, van Staa T, Palin V.",,EClinicalMedicine,2023,2023-07-05,Y,Antibiotics; Primary Care; Severe Outcome; Covid-19,,,"<h4>Background</h4>Identifying potential risk factors related to severe COVID-19 outcomes is important. Repeated intermittent antibiotic use is known be associated with adverse outcomes. This study aims to examine whether prior frequent antibiotic exposure is associated with severe COVID-19 outcomes.<h4>Methods</h4>With the approval of NHS England, we used the OpenSAFELY platform, which integrated primary and secondary care, COVID-19 test, and death registration data. This matched case-control study included 0.67 million patients (aged 18-110 years) from an eligible 2.47 million patients with incident COVID-19 by matching with replacement. Inclusion criteria included registration within one general practice for at least 3 years and infection with incident COVID-19. Cases were identified according to different severity of COVID-19 outcomes. Cases and eligible controls were 1:6 matched on age, sex, region of GP practice, and index year and month of COVID-19 infection. Five quintile groups, based on the number of previous 3-year antibiotic prescriptions, were created to indicate the frequency of prior antibiotic exposure. Conditional logistic regression used to compare the differences between case and control groups, adjusting for ethnicity, body mass index, comorbidities, vaccination history, deprivation, and care home status. Sensitivity analyses were done to explore potential confounding and the effects of missing data.<h4>Findings</h4>Based on our inclusion criteria, between February 1, 2020 and December 31, 2021, 98,420 patients were admitted to hospitals and 22,660 died. 55 unique antibiotics were prescribed. A dose-response relationship between number of antibiotic prescriptions and risk of severe COVID-19 outcome was observed. Patients in the highest quintile with history of prior antibiotic exposure had 1.80 times greater odds of hospitalisation compared to patients without antibiotic exposure (adjusted odds ratio [OR] 1.80, 95% Confidence Interval [CI] 1.75-1.84). Similarly, the adjusted OR for hospitalised patients with death outcomes was 1.34 (95% CI 1.28-1.41). Larger number of prior antibiotic type was also associated with more severe COVID-19 related hospital admission. The adjusted OR of quintile 5 exposure (the most frequent) with more than 3 antibiotic types was around 2 times larger than quintile 1 (only 1 type; OR 1.80, 95% CI 1.75-1.84 vs. OR 1.03, 95% CI 1.01-1.05).<h4>Interpretation</h4>Our observational study has provided evidence that antibiotic exposure frequency and diversity may be associated with COVID-19 severity, potentially suggesting adverse effects of repeated intermittent antibiotic use. Future work could work to elucidate causal links and potential mechanisms. Antibiotic stewardship should put more emphasis on long-term antibiotic exposure and its adverse outcome to increase the awareness of appropriate antibiotics use.<h4>Funding</h4>Health Data Research UK and National Institute for Health Research.",,doi:https://doi.org/10.1016/j.eclinm.2023.102064; html:https://europepmc.org/articles/PMC10388579; pdf:https://europepmc.org/articles/PMC10388579?pdf=render
+36755846,https://doi.org/10.1093/ckj/sfac241,"Depression is associated with frailty and lower quality of life in haemodialysis recipients, but not with mortality or hospitalization.","Anderson BM, Qasim M, Correa G, Evison F, Gallier S, Ferro CJ, Jackson TA, Sharif A.",,Clinical kidney journal,2023,2022-10-31,Y,Mortality; Depression; Frailty; Haemodialysis; Hospitalization; Health-related Quality Of Life,,,"<h4>Background</h4>Frailty and depression are highly prevalent in haemodialysis recipients, exhibit a reciprocal relationship, and are associated with increased mortality and hospitalization, and lower quality of life. Despite this, there has been little exploration of the relationship between depression and frailty upon patient outcomes. We aimed to explore the relationship between depression and frailty, and their associations with mortality, hospitalization and quality of life.<h4>Methods</h4>We performed a prospective cohort study of prevalent haemodialysis recipients linked to national datasets for outcomes including mortality and hospitalization. Depression was assessed using the Patient Health Questionnaire-9 (PHQ-9), frailty using the Clinical Frailty Scale (CFS) and quality of life using the EuroQol 5-Dimension (EQ-5D) Summary Index.<h4>Results</h4>A total of 485 prevalent haemodialysis recipients were recruited, with 111 deaths and 1241 hospitalizations during follow-up. CFS was independently associated with mortality [hazard ratio (HR) 1.31; 95% confidence interval (CI) 1.08, 1.59; <i>P</i> = .006], hospitalization [incidence rate ratio (IRR) 1.13; 95% CI 1.03, 1.25; <i>P</i> = .010] and lower quality of life (Coef. -0.401; 95% CI -0.511, -0.292; <i>P</i> < .001). PHQ-9 score was independently associated with lower quality of life (Coef. -0.042; 95% CI -0.063, -0.021; <i>P</i> < .001), but not mortality (HR 1.00; 95% CI 0.96, 1.04; <i>P</i> = .901) or hospitalization (IRR 0.99; 95% CI 0.97, 1.01; <i>P</i> = .351). In an adjusted model including CFS, moderate depression was associated with reduced hospitalization (IRR 0.72; 95% CI 0.56, 0.93; <i>P</i> = .013).<h4>Conclusions</h4>With the addition of frailty, depression was associated with lower hospital admissions, but poorer quality of life. The relationship between frailty and depression, and their influence on outcomes is complex, requiring further study.",,pdf:https://academic.oup.com/ckj/article-pdf/16/2/342/49100412/sfac241.pdf; doi:https://doi.org/10.1093/ckj/sfac241; html:https://europepmc.org/articles/PMC9900564; pdf:https://europepmc.org/articles/PMC9900564?pdf=render
 37046692,https://doi.org/10.3390/cancers15072031,"Breast, Prostate, Colorectal, and Lung Cancer Incidence and Risk Factors in Women Who Have Sex with Women and Men Who Have Sex with Men: A Cross-Sectional and Longitudinal Analysis Using UK Biobank.","Underwood S, Lyratzopoulos G, Saunders CL.",,Cancers,2023,2023-03-29,Y,Inequalities; Cancer Incidence; Cancer Risk; Cancer Epidemiology; Sexual Minority Health,,,"<h4>Background</h4>There is limited evidence about cancer incidence for lesbian, gay and bisexual women and men, although the prevalence of cancer risk factors may be higher.<h4>Aim</h4>To describe cancer incidence for four common cancers (breast, lung, colorectal and prostate).<h4>Methods</h4>This project used UK Biobank participant data. We explored risk factor prevalence (age, deprivation, ethnicity, smoking, alcohol intake, obesity, parity, and sexual history), and calculated cancer risk, for six groups defined based on sexual history; women who have sex exclusively with men (WSEM), or women (WSEW), women who have sex with men and women (WSWM); men who have sex exclusively with women (MSEW), or men (MSEM), and men who have sex with women and men (MSWM).<h4>Results</h4>WSEW, WSWM, MSEM, and MSMW were younger, more likely to smoke, and to live in more deprived neighbourhoods. We found no evidence of an association between sexual history and breast, colorectal, or prostate cancer in age-adjusted models. Lung cancer incidence was higher for WSWM compared with WSEM, HR (95%CI) 1.78 (1.28-2.48), <i>p</i> = 0.0005, and MSWM compared with MSEW, 1.43 (1.03-1.99), <i>p</i> = 0.031; after adjustment for smoking, this difference was no longer significant.<h4>Conclusions</h4>Sexual minority groups have a higher risk for lung cancer, due to greater exposure to smoking.",,pdf:https://www.mdpi.com/2072-6694/15/7/2031/pdf?version=1680080044; doi:https://doi.org/10.3390/cancers15072031; html:https://europepmc.org/articles/PMC10093616; pdf:https://europepmc.org/articles/PMC10093616?pdf=render
+37528841,https://doi.org/10.1016/j.eclinm.2023.102064,Repeated antibiotic exposure and risk of hospitalisation and death following COVID-19 infection (OpenSAFELY): a matched case-control study.,"Yang YT, Wong D, Ashcroft DM, Massey J, MacKenna B, Fisher L, Mehrkar A, Bacon SC, OpenSAFELY collaborative, Hand K, Zhong X, Fahmi A, Goldacre B, van Staa T, Palin V.",,EClinicalMedicine,2023,2023-07-05,Y,Antibiotics; Primary Care; Severe Outcome; Covid-19,,,"<h4>Background</h4>Identifying potential risk factors related to severe COVID-19 outcomes is important. Repeated intermittent antibiotic use is known be associated with adverse outcomes. This study aims to examine whether prior frequent antibiotic exposure is associated with severe COVID-19 outcomes.<h4>Methods</h4>With the approval of NHS England, we used the OpenSAFELY platform, which integrated primary and secondary care, COVID-19 test, and death registration data. This matched case-control study included 0.67 million patients (aged 18-110 years) from an eligible 2.47 million patients with incident COVID-19 by matching with replacement. Inclusion criteria included registration within one general practice for at least 3 years and infection with incident COVID-19. Cases were identified according to different severity of COVID-19 outcomes. Cases and eligible controls were 1:6 matched on age, sex, region of GP practice, and index year and month of COVID-19 infection. Five quintile groups, based on the number of previous 3-year antibiotic prescriptions, were created to indicate the frequency of prior antibiotic exposure. Conditional logistic regression used to compare the differences between case and control groups, adjusting for ethnicity, body mass index, comorbidities, vaccination history, deprivation, and care home status. Sensitivity analyses were done to explore potential confounding and the effects of missing data.<h4>Findings</h4>Based on our inclusion criteria, between February 1, 2020 and December 31, 2021, 98,420 patients were admitted to hospitals and 22,660 died. 55 unique antibiotics were prescribed. A dose-response relationship between number of antibiotic prescriptions and risk of severe COVID-19 outcome was observed. Patients in the highest quintile with history of prior antibiotic exposure had 1.80 times greater odds of hospitalisation compared to patients without antibiotic exposure (adjusted odds ratio [OR] 1.80, 95% Confidence Interval [CI] 1.75-1.84). Similarly, the adjusted OR for hospitalised patients with death outcomes was 1.34 (95% CI 1.28-1.41). Larger number of prior antibiotic type was also associated with more severe COVID-19 related hospital admission. The adjusted OR of quintile 5 exposure (the most frequent) with more than 3 antibiotic types was around 2 times larger than quintile 1 (only 1 type; OR 1.80, 95% CI 1.75-1.84 vs. OR 1.03, 95% CI 1.01-1.05).<h4>Interpretation</h4>Our observational study has provided evidence that antibiotic exposure frequency and diversity may be associated with COVID-19 severity, potentially suggesting adverse effects of repeated intermittent antibiotic use. Future work could work to elucidate causal links and potential mechanisms. Antibiotic stewardship should put more emphasis on long-term antibiotic exposure and its adverse outcome to increase the awareness of appropriate antibiotics use.<h4>Funding</h4>Health Data Research UK and National Institute for Health Research.",,doi:https://doi.org/10.1016/j.eclinm.2023.102064; html:https://europepmc.org/articles/PMC10388579; pdf:https://europepmc.org/articles/PMC10388579?pdf=render
 39145098,https://doi.org/10.3310/nihropenres.13530.1,"Protocol for VIVALDI social care: Pilot study to reduce infections, outbreaks and antimicrobial resistance in care homes for older adults.","Krutikov M, Fry Z, Azmi B, Lezard C, Thorn K, Patefield G, Childe G, Hudson J, Stirrup O, Jhass A, Turner N, Cassell J, Flowers P, Hayward A, Copas A, Green M, Shallcross L.",,NIHR open research,2024,2024-02-15,Y,Infection; Antimicrobial resistance; Surveillance; data sharing; Outbreaks; Data Linkage; Care Homes,,,"Care home residents are vulnerable to severe outcomes from infections such as COVID-19 and influenza. However, measures to control outbreaks, such as care home closures to visitors and new admissions, have a detrimental impact on their quality of life. Many infections and outbreaks could be prevented but the first step is to measure them reliably. This is challenging in care homes due to the lack of data and research infrastructure. During the pandemic, the VIVALDI study measured COVID-19 infections in residents and staff by partnering with care providers and using routinely collected data. This study aims to establish sentinel surveillance and a research database to enable observational and future interventional studies in care homes. The project has been co-produced with care providers, staff, residents, relatives, and researchers. The study (October 2023 to March 2025) will explore the feasibility of establishing a network of 500-1500 care homes for older adults in England that is underpinned by a linked data platform. No data will be collected from staff. The cohort will be created by regularly extracting resident identifiers from Digital Social Care Records (DSCR), followed by pseudonymisation and linkage to routinely collected datasets. Following extensive consultation, we decided not to seek informed consent from residents for data collection, but they can 'opt out' of the study. Our goal is to be inclusive, and it is challenging to give every resident the opportunity to 'opt in' due to cognitive impairment and the requirement for consultees. The project, and all requests to use the data will be overseen by relatives, residents, staff, and care providers. The study has been approved by the Health Research Authority Confidentiality Advisory Group (23/CAG/0134&0135) and the South-West Frenchay Research Ethics Committee (23/SW/0105). It is funded by the UK Health Security Agency.",,doi:https://doi.org/10.3310/nihropenres.13530.1; html:https://europepmc.org/articles/PMC11319897; pdf:https://europepmc.org/articles/PMC11319897?pdf=render
-32946449,https://doi.org/10.1371/journal.pone.0237676,"Proton pump inhibitors and dementia risk: Evidence from a cohort study using linked routinely collected national health data in Wales, UK.","Cooksey R, Kennedy J, Dennis MS, Escott-Price V, Lyons RA, Seaborne M, Brophy S.",,PloS one,2020,2020-09-18,Y,,,,"<h4>Objectives</h4>Proton pump inhibitors (PPIs) are commonly prescribed for prevention and treatment of gastrointestinal conditions or for gastroprotection from other drugs. Research suggests they are linked to increased dementia risk. We use linked national health data to examine the association between PPI use and the development of incident dementia.<h4>Methods and findings</h4>A population-based study using electronic health-data from the Secure Anonymised Information Linkage (SAIL) Databank, Wales (UK) from 1999 to 2015. Of data available on 3,765,744 individuals, a cohort who had ever been prescribed a PPI was developed (n = 183,968) for people aged 55 years and over and compared to non-PPI exposed individuals (131,110). Those with prior dementia, mild-cognitive-impairment or delirium codes were excluded. Confounding factors included comorbidities and/or drugs associated with them. Comorbidities might include head injury and some examples of medications include antidepressants, antiplatelets and anticoagulants. These commonly prescribed drugs were investigated as it was not feasible to explore all drugs in this study. The main outcome was a diagnosis of incident dementia. Cox proportional hazard regression modelling was used to calculate the Hazard ratio (HR) of developing dementia in PPI-exposed compared to unexposed individuals while controlling for potential confounders. The mean age of the PPI exposed individuals was 69.9 years and 39.8% male while the mean age of the unexposed individuals was 72.1 years and 41.1% male. The rate of PPI usage was 58.4% (183,968) and incident dementia rate was 11.8% (37,148/315,078). PPI use was associated with decreased dementia risk (HR: 0.67, 95% CI: 0.65 to 0.67, p<0.01).<h4>Conclusions</h4>This study, using large-scale, multi-centre health-data was unable to confirm an association between PPI use and increased dementia risk. Previously reported links may be associated with confounders of people using PPI's, such as increased risk of cardiovascular disease and/or depression and their associated medications which may be responsible for any increased risk of developing dementia.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0237676&type=printable; doi:https://doi.org/10.1371/journal.pone.0237676; html:https://europepmc.org/articles/PMC7500586; pdf:https://europepmc.org/articles/PMC7500586?pdf=render
 34089614,https://doi.org/10.1093/ije/dyab028,Cohort Profile: Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) Database.,"Mulholland RH, Vasileiou E, Simpson CR, Robertson C, Ritchie LD, Agrawal U, Woolhouse M, Murray JL, Stagg HR, Docherty AB, McCowan C, Wood R, Stock SJ, Sheikh A.",,International journal of epidemiology,2021,2021-08-01,N,,,,,,pdf:https://academic.oup.com/ije/article-pdf/50/4/1064/40146583/dyab028.pdf; doi:https://doi.org/10.1093/ije/dyab028; html:https://europepmc.org/articles/PMC8195245; pdf:https://europepmc.org/articles/PMC8195245?pdf=render; doi:https://doi.org/10.1093/ije/dyab028
-36992188,https://doi.org/10.3390/vaccines11030604,"Household Composition and Inequalities in COVID-19 Vaccination in Wales, UK.","Lench A, Perry M, Johnson RD, Fry R, Richardson G, Lyons RA, Akbari A, Edwards A, Collins B, Joseph-Williams N, Cooper A, Cottrell S.",,Vaccines,2023,2023-03-07,Y,Vaccines; Vaccination; Households; Inequalities; Immunisation; Household Composition; Inequities; Covid-19,,,"The uptake of COVID-19 vaccination in Wales is high at a population level but many inequalities exist. Household composition may be an important factor in COVID-19 vaccination uptake due to the practical, social, and psychological implications associated with different living arrangements. In this study, the role of household composition in the uptake of COVID-19 vaccination in Wales was examined with the aim of identifying areas for intervention to address inequalities. Records within the Wales Immunisation System (WIS) COVID-19 vaccination register were linked to the Welsh Demographic Service Dataset (WDSD; a population register for Wales) held within the Secure Anonymised Information Linkage (SAIL) databank. Eight household types were defined based on household size, the presence or absence of children, and the presence of single or multiple generations. Uptake of the second dose of any COVID-19 vaccine was analysed using logistic regression. Gender, age group, health board, rural/urban residential classification, ethnic group, and deprivation quintile were included as covariates for multivariable regression. Compared to two-adult households, all other household types were associated with lower uptake. The most significantly reduced uptake was observed for large, multigenerational, adult group households (aOR 0.45, 95%CI 0.43-0.46). Comparing multivariable regression with and without incorporation of household composition as a variable produced significant differences in odds of vaccination for health board, age group, and ethnic group categories. These results indicate that household composition is an important factor for the uptake of COVID-19 vaccination and consideration of differences in household composition is necessary to mitigate vaccination inequalities.",,pdf:https://www.mdpi.com/2076-393X/11/3/604/pdf?version=1678670919; doi:https://doi.org/10.3390/vaccines11030604; html:https://europepmc.org/articles/PMC10055803; pdf:https://europepmc.org/articles/PMC10055803?pdf=render
+32946449,https://doi.org/10.1371/journal.pone.0237676,"Proton pump inhibitors and dementia risk: Evidence from a cohort study using linked routinely collected national health data in Wales, UK.","Cooksey R, Kennedy J, Dennis MS, Escott-Price V, Lyons RA, Seaborne M, Brophy S.",,PloS one,2020,2020-09-18,Y,,,,"<h4>Objectives</h4>Proton pump inhibitors (PPIs) are commonly prescribed for prevention and treatment of gastrointestinal conditions or for gastroprotection from other drugs. Research suggests they are linked to increased dementia risk. We use linked national health data to examine the association between PPI use and the development of incident dementia.<h4>Methods and findings</h4>A population-based study using electronic health-data from the Secure Anonymised Information Linkage (SAIL) Databank, Wales (UK) from 1999 to 2015. Of data available on 3,765,744 individuals, a cohort who had ever been prescribed a PPI was developed (n = 183,968) for people aged 55 years and over and compared to non-PPI exposed individuals (131,110). Those with prior dementia, mild-cognitive-impairment or delirium codes were excluded. Confounding factors included comorbidities and/or drugs associated with them. Comorbidities might include head injury and some examples of medications include antidepressants, antiplatelets and anticoagulants. These commonly prescribed drugs were investigated as it was not feasible to explore all drugs in this study. The main outcome was a diagnosis of incident dementia. Cox proportional hazard regression modelling was used to calculate the Hazard ratio (HR) of developing dementia in PPI-exposed compared to unexposed individuals while controlling for potential confounders. The mean age of the PPI exposed individuals was 69.9 years and 39.8% male while the mean age of the unexposed individuals was 72.1 years and 41.1% male. The rate of PPI usage was 58.4% (183,968) and incident dementia rate was 11.8% (37,148/315,078). PPI use was associated with decreased dementia risk (HR: 0.67, 95% CI: 0.65 to 0.67, p<0.01).<h4>Conclusions</h4>This study, using large-scale, multi-centre health-data was unable to confirm an association between PPI use and increased dementia risk. Previously reported links may be associated with confounders of people using PPI's, such as increased risk of cardiovascular disease and/or depression and their associated medications which may be responsible for any increased risk of developing dementia.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0237676&type=printable; doi:https://doi.org/10.1371/journal.pone.0237676; html:https://europepmc.org/articles/PMC7500586; pdf:https://europepmc.org/articles/PMC7500586?pdf=render
 33240522,https://doi.org/10.1177/2055207620965046,Electronic-prescribing tools improve N-acetylcysteine prescription accuracy and timeliness for patients who present following a paracetamol overdose: A digital innovation quality-improvement project.,"McCulloch A, Sarwar A, Bate T, Thompson D, McDowell P, Sharif Q, Sapey E, Seccombe A.",,Digital health,2020,2020-01-01,Y,Antidote; Digital; paracetamol; Prescription Errors; Electronic Health Systems,,,"<h4>Objectives</h4>Prescription error rates and delays in treatment provision are high for N-acetylcysteine (NAC) when prescribed for paracetamol overdose (POD). We hypothesised that an electronic tool which proposed the complete NAC regimen would reduce prescription errors and improve the timeliness of NAC provision. Error rates and delays in the provision of NAC were assessed following POD, before and after the implementation of an electronic prescribing tool.<h4>Methods</h4>The NAC electronic prescribing tool proposed the three NAC infusions (dosed for weight) following entry of the patient's weight. All NAC prescriptions were reviewed during a three-month period prior to and after the tool's implementation. Error rates were divided into dose, infusion volume or infusion rate. Delays in NAC provision were identified using national Emergency Medicine guidelines.<h4>Results</h4>108 NAC prescriptions were analysed for all adult patients admitted to the emergency department of a secondary care hospital in the UK between July-September 2017 and August-October 2018, respectively. There were no differences in the demographics of patients or the seniority of the prescribing clinician before or after the introduction of the electronic tool. The electronic prescribing tool was associated with a decrease in prescribing errors (25% to 0%, p < 0.0071) and an increase in the provision of NAC within recommended times (11.1% to 47.4%, p = 0.029).<h4>Conclusions</h4>An electronic prescribing tool improved prescription errors and the timeliness of NAC provision following POD. Further studies will determine the effect of this on length of stay and the benefit of wider implementation in other secondary care hospitals.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/2055207620965046; doi:https://doi.org/10.1177/2055207620965046; html:https://europepmc.org/articles/PMC7675911; pdf:https://europepmc.org/articles/PMC7675911?pdf=render
+36992188,https://doi.org/10.3390/vaccines11030604,"Household Composition and Inequalities in COVID-19 Vaccination in Wales, UK.","Lench A, Perry M, Johnson RD, Fry R, Richardson G, Lyons RA, Akbari A, Edwards A, Collins B, Joseph-Williams N, Cooper A, Cottrell S.",,Vaccines,2023,2023-03-07,Y,Vaccines; Vaccination; Households; Inequalities; Immunisation; Household Composition; Inequities; Covid-19,,,"The uptake of COVID-19 vaccination in Wales is high at a population level but many inequalities exist. Household composition may be an important factor in COVID-19 vaccination uptake due to the practical, social, and psychological implications associated with different living arrangements. In this study, the role of household composition in the uptake of COVID-19 vaccination in Wales was examined with the aim of identifying areas for intervention to address inequalities. Records within the Wales Immunisation System (WIS) COVID-19 vaccination register were linked to the Welsh Demographic Service Dataset (WDSD; a population register for Wales) held within the Secure Anonymised Information Linkage (SAIL) databank. Eight household types were defined based on household size, the presence or absence of children, and the presence of single or multiple generations. Uptake of the second dose of any COVID-19 vaccine was analysed using logistic regression. Gender, age group, health board, rural/urban residential classification, ethnic group, and deprivation quintile were included as covariates for multivariable regression. Compared to two-adult households, all other household types were associated with lower uptake. The most significantly reduced uptake was observed for large, multigenerational, adult group households (aOR 0.45, 95%CI 0.43-0.46). Comparing multivariable regression with and without incorporation of household composition as a variable produced significant differences in odds of vaccination for health board, age group, and ethnic group categories. These results indicate that household composition is an important factor for the uptake of COVID-19 vaccination and consideration of differences in household composition is necessary to mitigate vaccination inequalities.",,pdf:https://www.mdpi.com/2076-393X/11/3/604/pdf?version=1678670919; doi:https://doi.org/10.3390/vaccines11030604; html:https://europepmc.org/articles/PMC10055803; pdf:https://europepmc.org/articles/PMC10055803?pdf=render
 38269898,https://doi.org/10.3233/shti231054,Identifying Mentions of Pain in Mental Health Records Text: A Natural Language Processing Approach.,"Chaturvedi J, Velupillai S, Stewart R, Roberts A.",,Studies in health technology and informatics,2024,2024-01-01,N,Pain; Mental health; Electronic Health Records; Natural Language Processing; Transformers,,,"Pain is a common reason for accessing healthcare resources and is a growing area of research, especially in its overlap with mental health. Mental health electronic health records are a good data source to study this overlap. However, much information on pain is held in the free text of these records, where mentions of pain present a unique natural language processing problem due to its ambiguous nature. This project uses data from an anonymised mental health electronic health records database. A machine learning based classification algorithm is trained to classify sentences as discussing patient pain or not. This will facilitate the extraction of relevant pain information from large databases. 1,985 documents were manually triple-annotated for creation of gold standard training data, which was used to train four classification algorithms. The best performing model achieved an F1-score of 0.98 (95% CI 0.98-0.99).",,pdf:https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI231054; doi:https://doi.org/10.3233/SHTI231054
 36529825,https://doi.org/10.1007/s40258-022-00777-2,The False Economy of Seeking to Eliminate Delayed Transfers of Care: Some Lessons from Queueing Theory.,"Wood RM, Harper AL, Onen-Dumlu Z, Forte PG, Pitt M, Vasilakis C.",,Applied health economics and health policy,2023,2022-12-18,Y,,,,"<h4>Background</h4>It is a stated ambition of many healthcare systems to eliminate delayed transfers of care (DTOCs) between acute and step-down community services.<h4>Objective</h4>This study aims to demonstrate how, counter to intuition, pursual of such a policy is likely to be uneconomical, as it would require large amounts of community capacity to accommodate even the rarest of demand peaks, leaving much capacity unused for much of the time.<h4>Methods</h4>Some standard results from queueing theory-a mathematical discipline for considering the dynamics of queues and queueing systems-are used to provide a model of patient flow from the acute to community setting. While queueing models have a track record of application in healthcare, they have not before been used to address this question.<h4>Results</h4>Results show that 'eliminating' DTOCs is a false economy: the additional community costs required are greater than the possible acute cost saving. While a substantial proportion of DTOCs can be attributed to inefficient use of resources, the remainder can be considered economically essential to ensuring cost-efficient service operation. For England's National Health Service (NHS), our modelling estimates annual cost savings of £117m if DTOCs are reduced to the 12% of current levels that can be regarded as economically essential.<h4>Conclusion</h4>This study discourages the use of 'zero DTOC' targets and instead supports an assessment based on the specific characteristics of the healthcare system considered.",,pdf:https://link.springer.com/content/pdf/10.1007/s40258-022-00777-2.pdf; doi:https://doi.org/10.1007/s40258-022-00777-2; html:https://europepmc.org/articles/PMC9760184; pdf:https://europepmc.org/articles/PMC9760184?pdf=render
-37558806,https://doi.org/10.1038/s41598-023-40215-4,"Associations of the serotonin transporter gene polymorphism, 5-HTTLPR, and adverse life events with late life depression in the elderly Lithuanian population.","Simonyte S, Grabauskyte I, Macijauskiene J, Lesauskaite V, Lesauskaite V, Kvaal KS, Stewart R.",,Scientific reports,2023,2023-08-09,Y,,,,"Late-life depression (LLD) is a multifactorial disorder, with susceptibility and vulnerability potentially influenced by gene-environment interaction. The aim of this study was to investigate whether the 5-HTTLPR polymorphism is associated with LLD. The sample of 353 participants aged 65 years and over was randomly selected from the list of Kaunas city inhabitants by Residents' Register Service of Lithuania. Depressive symptoms were ascertained using the EURO-D scale. The List of Threatening Events Questionnaire was used to identify stressful life events that happened over the last 6 months and during lifetime. A 5-HTTLPR and lifetime stressful events interaction was indicated by higher odds of depression in those with s/s genotype who experienced high stress compared to l/l carriers with low or medium stress, while 5-HTTLPR and current stressful events interaction analysis revealed that carriers of either one or two copies of the s allele had increased odds of depressive symptoms associated with stress compared to participants with the l/l genotype not exposed to stressful situations. Although no significant direct association was found between the 5-HTTLPR short allele and depression, our findings demonstrated that lifetime or current stressful life events and their modification by 5-HTTLPR genotype are risk factors for late-life depression.",,pdf:https://www.nature.com/articles/s41598-023-40215-4.pdf; doi:https://doi.org/10.1038/s41598-023-40215-4; html:https://europepmc.org/articles/PMC10412533; pdf:https://europepmc.org/articles/PMC10412533?pdf=render
 34582457,https://doi.org/10.1371/journal.pmed.1003777,Predictive symptoms for COVID-19 in the community: REACT-1 study of over 1 million people.,"Elliott J, Whitaker M, Bodinier B, Eales O, Riley S, Ward H, Cooke G, Darzi A, Chadeau-Hyam M, Elliott P.",,PLoS medicine,2021,2021-09-28,Y,,,,"<h4>Background</h4>Rapid detection, isolation, and contact tracing of community COVID-19 cases are essential measures to limit the community spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aimed to identify a parsimonious set of symptoms that jointly predict COVID-19 and investigated whether predictive symptoms differ between the B.1.1.7 (Alpha) lineage (predominating as of April 2021 in the US, UK, and elsewhere) and wild type.<h4>Methods and findings</h4>We obtained throat and nose swabs with valid SARS-CoV-2 PCR test results from 1,147,370 volunteers aged 5 years and above (6,450 positive cases) in the REal-time Assessment of Community Transmission-1 (REACT-1) study. This study involved repeated community-based random surveys of prevalence in England (study rounds 2 to 8, June 2020 to January 2021, response rates 22%-27%). Participants were asked about symptoms occurring in the week prior to testing. Viral genome sequencing was carried out for PCR-positive samples with N-gene cycle threshold value < 34 (N = 1,079) in round 8 (January 2021). In univariate analysis, all 26 surveyed symptoms were associated with PCR positivity compared with non-symptomatic people. Stability selection (1,000 penalized logistic regression models with 50% subsampling) among people reporting at least 1 symptom identified 7 symptoms as jointly and positively predictive of PCR positivity in rounds 2-7 (June to December 2020): loss or change of sense of smell, loss or change of sense of taste, fever, new persistent cough, chills, appetite loss, and muscle aches. The resulting model (rounds 2-7) predicted PCR positivity in round 8 with area under the curve (AUC) of 0.77. The same 7 symptoms were selected as jointly predictive of B.1.1.7 infection in round 8, although when comparing B.1.1.7 with wild type, new persistent cough and sore throat were more predictive of B.1.1.7 infection while loss or change of sense of smell was more predictive of the wild type. The main limitations of our study are (i) potential participation bias despite random sampling of named individuals from the National Health Service register and weighting designed to achieve a representative sample of the population of England and (ii) the necessary reliance on self-reported symptoms, which may be prone to recall bias and may therefore lead to biased estimates of symptom prevalence in England.<h4>Conclusions</h4>Where testing capacity is limited, it is important to use tests in the most efficient way possible. We identified a set of 7 symptoms that, when considered together, maximize detection of COVID-19 in the community, including infection with the B.1.1.7 lineage.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003777&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003777; html:https://europepmc.org/articles/PMC8478234; pdf:https://europepmc.org/articles/PMC8478234?pdf=render
+37558806,https://doi.org/10.1038/s41598-023-40215-4,"Associations of the serotonin transporter gene polymorphism, 5-HTTLPR, and adverse life events with late life depression in the elderly Lithuanian population.","Simonyte S, Grabauskyte I, Macijauskiene J, Lesauskaite V, Lesauskaite V, Kvaal KS, Stewart R.",,Scientific reports,2023,2023-08-09,Y,,,,"Late-life depression (LLD) is a multifactorial disorder, with susceptibility and vulnerability potentially influenced by gene-environment interaction. The aim of this study was to investigate whether the 5-HTTLPR polymorphism is associated with LLD. The sample of 353 participants aged 65 years and over was randomly selected from the list of Kaunas city inhabitants by Residents' Register Service of Lithuania. Depressive symptoms were ascertained using the EURO-D scale. The List of Threatening Events Questionnaire was used to identify stressful life events that happened over the last 6 months and during lifetime. A 5-HTTLPR and lifetime stressful events interaction was indicated by higher odds of depression in those with s/s genotype who experienced high stress compared to l/l carriers with low or medium stress, while 5-HTTLPR and current stressful events interaction analysis revealed that carriers of either one or two copies of the s allele had increased odds of depressive symptoms associated with stress compared to participants with the l/l genotype not exposed to stressful situations. Although no significant direct association was found between the 5-HTTLPR short allele and depression, our findings demonstrated that lifetime or current stressful life events and their modification by 5-HTTLPR genotype are risk factors for late-life depression.",,pdf:https://www.nature.com/articles/s41598-023-40215-4.pdf; doi:https://doi.org/10.1038/s41598-023-40215-4; html:https://europepmc.org/articles/PMC10412533; pdf:https://europepmc.org/articles/PMC10412533?pdf=render
 37006328,https://doi.org/10.1093/braincomms/fcad065,"Infections among individuals with multiple sclerosis, Alzheimer's disease and Parkinson's disease.","Hu Y, Hu K, Song H, Pawitan Y, Piehl F, Fang F.",,Brain communications,2023,2023-03-16,Y,Multiple sclerosis; Alzheimer’s disease; Infections; Parkinson’s Disease,,,"A link between neurodegenerative diseases and infections has been previously reported. However, it is not clear to what extent such link is caused by confounding factors or to what extent it is intimately connected with the underlying conditions. Further, studies on the impact of infections on mortality risk following neurodegenerative diseases are rare. We analysed two data sets with different characteristics: (i) a community-based cohort from the UK Biobank with 2023 patients with multiple sclerosis, 2200 patients with Alzheimer's disease, 3050 patients with Parkinson's disease diagnosed before 1 March 2020 and 5 controls per case who were randomly selected and individually matched to the case; (ii) a Swedish Twin Registry cohort with 230 patients with multiple sclerosis, 885 patients with Alzheimer's disease and 626 patients with Parkinson's disease diagnosed before 31 December 2016 and their disease-free co-twins. The relative risk of infections after a diagnosis of neurodegenerative disease was estimated using stratified Cox models, with adjustment for differences in baseline characteristics. Causal mediation analyses of survival outcomes based on Cox models were performed to assess the impact of infections on mortality. Compared with matched controls or unaffected co-twins, we observed an elevated infection risk after diagnosis of neurodegenerative diseases, with a fully adjusted hazard ratio (95% confidence interval) of 2.45 (2.24-2.69) for multiple sclerosis, 5.06 (4.58-5.59) for Alzheimer's disease and 3.72 (3.44-4.01) for Parkinson's disease in the UK Biobank cohort, and 1.78 (1.21-2.62) for multiple sclerosis, 1.50 (1.19-1.88) for Alzheimer's disease and 2.30 (1.79-2.95) for Parkinson's disease in the twin cohort. Similar risk increases were observed when we analysed infections during the 5 years before diagnosis of the respective disease. Occurrence of infections after diagnosis had, however, relatively little impact on mortality, as mediation of infections on mortality (95% confidence interval) was estimated as 31.89% (26.83-37.11%) for multiple sclerosis, 13.38% (11.49-15.29%) for Alzheimer's disease and 18.85% (16.95-20.97%) for Parkinson's disease in the UK Biobank cohort, whereas it was 6.56% (-3.59 to 16.88%) for multiple sclerosis, -2.21% (-0.21 to 4.65%) for Parkinson's disease and -3.89% (-7.27 to -0.51%) for Alzheimer's disease in the twin cohort. Individuals with studied neurodegenerative diseases display an increased risk of infections independently of genetic and familial environment factors. A similar magnitude of risk increase is present prior to confirmed diagnosis, which may indicate a modulating effect of the studied neurological conditions on immune defences.",,pdf:https://academic.oup.com/braincomms/advance-article-pdf/doi/10.1093/braincomms/fcad065/49588224/fcad065.pdf; doi:https://doi.org/10.1093/braincomms/fcad065; html:https://europepmc.org/articles/PMC10053639; pdf:https://europepmc.org/articles/PMC10053639?pdf=render
-36649943,https://doi.org/10.1136/bmjoq-2021-001704,Benefits of electronic charts in intensive care and during a world health pandemic: advantages of the technology age.,"Pankhurst T, Lucas L, Ryan S, Ragdale C, Gyves H, Denner L, Young I, Rathbone L, Shah A, McKee D, Coleman JJ, Evison F, Atia J, Rosser D, Garrick M, Baker R, Gallier S, Ball S.",,BMJ open quality,2023,2023-01-01,Y,Evaluation Methodology; Critical Care; Electronic Health Records,,,"<h4>Aims and objectives</h4>This study sets out to describe benefits from the implementation of electronic observation charting in intensive care units (ICU). This was an extension to the existing hospital wide digital health system. We evaluated error reduction, time-savings and the costs associated with conversion from paper to digital records. The world health emergency of COVID-19 placed extraordinary strain on ICU and staff opinion was evaluated to test how well the electronic system performed.<h4>Methods</h4>A clinically led project group working directly with programmers developed an electronic patient record for intensive care. Data error rates, time to add data and to make calculations were studied before and after the introduction of electronic charts. User feedback was sought pre and post go-live (during the COVID-19 pandemic) and financial implications were calculated by the hospital finance teams.<h4>Results</h4>Error rates equating to 219 000/year were avoided by conversion to electronic charts. Time saved was the equivalent of a nursing shift each day. Recurrent cost savings per year were estimated to be £257k. Staff were overwhelmingly positive about electronic charts in ICU, even during a health pandemic and despite redeployment into intensive care where they were using the electronic charts for the first time.<h4>Discussion</h4>Electronic ICU charts have been successfully introduced into our institution with benefits in terms of patient safety through error reduction and improved care through release of nursing time. Costs have been reduced. Staff feel supported by the digital system and report it to be helpful even during redeployment and in the unfamiliar environment of intensive care.",,pdf:https://bmjopenquality.bmj.com/content/bmjqir/12/1/e001704.full.pdf; doi:https://doi.org/10.1136/bmjoq-2021-001704; html:https://europepmc.org/articles/PMC9853220; pdf:https://europepmc.org/articles/PMC9853220?pdf=render
 34599903,https://doi.org/10.1016/s2213-2600(21)00380-5,COVID-19 hospital admissions and deaths after BNT162b2 and ChAdOx1 nCoV-19 vaccinations in 2·57 million people in Scotland (EAVE II): a prospective cohort study.,"Agrawal U, Katikireddi SV, McCowan C, Mulholland RH, Azcoaga-Lorenzo A, Amele S, Fagbamigbe AF, Vasileiou E, Grange Z, Shi T, Kerr S, Moore E, Murray JLK, Shah SA, Ritchie L, O'Reilly D, Stock SJ, Beggs J, Chuter A, Torabi F, Akbari A, Bedston S, McMenamin J, Wood R, Tang RSM, de Lusignan S, Hobbs FDR, Woolhouse M, Simpson CR, Robertson C, Sheikh A.",,The Lancet. Respiratory medicine,2021,2021-09-29,Y,,,,"<h4>Background</h4>The UK COVID-19 vaccination programme has prioritised vaccination of those at the highest risk of COVID-19 mortality and hospitalisation. The programme was rolled out in Scotland during winter 2020-21, when SARS-CoV-2 infection rates were at their highest since the pandemic started, despite social distancing measures being in place. We aimed to estimate the frequency of COVID-19 hospitalisation or death in people who received at least one vaccine dose and characterise these individuals.<h4>Methods</h4>We conducted a prospective cohort study using the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) national surveillance platform, which contained linked vaccination, primary care, RT-PCR testing, hospitalisation, and mortality records for 5·4 million people (around 99% of the population) in Scotland. Individuals were followed up from receiving their first dose of the BNT162b2 (Pfizer-BioNTech) or ChAdOx1 nCoV-19 (Oxford-AstraZeneca) COVID-19 vaccines until admission to hospital for COVID-19, death, or the end of the study period on April 18, 2021. We used a time-dependent Poisson regression model to estimate rate ratios (RRs) for demographic and clinical factors associated with COVID-19 hospitalisation or death 14 days or more after the first vaccine dose, stratified by vaccine type.<h4>Findings</h4>Between Dec 8, 2020, and April 18, 2021, 2 572 008 individuals received their first dose of vaccine-841 090 (32·7%) received BNT162b2 and 1 730 918 (67·3%) received ChAdOx1. 1196 (<0·1%) individuals were admitted to hospital or died due to COVID-19 illness (883 hospitalised, of whom 228 died, and 313 who died due to COVID-19 without hospitalisation) 14 days or more after their first vaccine dose. These severe COVID-19 outcomes were associated with older age (≥80 years vs 18-64 years adjusted RR 4·75, 95% CI 3·85-5·87), comorbidities (five or more risk groups vs less than five risk groups 4·24, 3·34-5·39), hospitalisation in the previous 4 weeks (3·00, 2·47-3·65), high-risk occupations (ten or more previous COVID-19 tests vs less than ten previous COVID-19 tests 2·14, 1·62-2·81), care home residence (1·63, 1·32-2·02), socioeconomic deprivation (most deprived quintile vs least deprived quintile 1·57, 1·30-1·90), being male (1·27, 1·13-1·43), and being an ex-smoker (ex-smoker vs non-smoker 1·18, 1·01-1·38). A history of COVID-19 before vaccination was protective (0·40, 0·29-0·54).<h4>Interpretation</h4>COVID-19 hospitalisations and deaths were uncommon 14 days or more after the first vaccine dose in this national analysis in the context of a high background incidence of SARS-CoV-2 infection and with extensive social distancing measures in place. Sociodemographic and clinical features known to increase the risk of severe disease in unvaccinated populations were also associated with severe outcomes in people receiving their first dose of vaccine and could help inform case management and future vaccine policy formulation.<h4>Funding</h4>UK Research and Innovation (Medical Research Council), Research and Innovation Industrial Strategy Challenge Fund, Scottish Government, and Health Data Research UK.",,pdf:https://aura.abdn.ac.uk/bitstream/2164/17801/1/Agrawal_etal_LRM_COVID19_Hospital_Admissions_VOR.pdf; doi:https://doi.org/10.1016/S2213-2600(21)00380-5; html:https://europepmc.org/articles/PMC8480963
+36649943,https://doi.org/10.1136/bmjoq-2021-001704,Benefits of electronic charts in intensive care and during a world health pandemic: advantages of the technology age.,"Pankhurst T, Lucas L, Ryan S, Ragdale C, Gyves H, Denner L, Young I, Rathbone L, Shah A, McKee D, Coleman JJ, Evison F, Atia J, Rosser D, Garrick M, Baker R, Gallier S, Ball S.",,BMJ open quality,2023,2023-01-01,Y,Evaluation Methodology; Critical Care; Electronic Health Records,,,"<h4>Aims and objectives</h4>This study sets out to describe benefits from the implementation of electronic observation charting in intensive care units (ICU). This was an extension to the existing hospital wide digital health system. We evaluated error reduction, time-savings and the costs associated with conversion from paper to digital records. The world health emergency of COVID-19 placed extraordinary strain on ICU and staff opinion was evaluated to test how well the electronic system performed.<h4>Methods</h4>A clinically led project group working directly with programmers developed an electronic patient record for intensive care. Data error rates, time to add data and to make calculations were studied before and after the introduction of electronic charts. User feedback was sought pre and post go-live (during the COVID-19 pandemic) and financial implications were calculated by the hospital finance teams.<h4>Results</h4>Error rates equating to 219 000/year were avoided by conversion to electronic charts. Time saved was the equivalent of a nursing shift each day. Recurrent cost savings per year were estimated to be £257k. Staff were overwhelmingly positive about electronic charts in ICU, even during a health pandemic and despite redeployment into intensive care where they were using the electronic charts for the first time.<h4>Discussion</h4>Electronic ICU charts have been successfully introduced into our institution with benefits in terms of patient safety through error reduction and improved care through release of nursing time. Costs have been reduced. Staff feel supported by the digital system and report it to be helpful even during redeployment and in the unfamiliar environment of intensive care.",,pdf:https://bmjopenquality.bmj.com/content/bmjqir/12/1/e001704.full.pdf; doi:https://doi.org/10.1136/bmjoq-2021-001704; html:https://europepmc.org/articles/PMC9853220; pdf:https://europepmc.org/articles/PMC9853220?pdf=render
 34461893,https://doi.org/10.1186/s12916-021-02096-0,The association between mechanical ventilator compatible bed occupancy and mortality risk in intensive care patients with COVID-19: a national retrospective cohort study.,"Wilde H, Mellan T, Hawryluk I, Dennis JM, Denaxas S, Pagel C, Duncan A, Bhatt S, Flaxman S, Mateen BA, Vollmer SJ.",,BMC medicine,2021,2021-08-30,Y,Critical Care; Hospital Mortality; Quality Of Healthcare; Public Health Surveillance; Coronavirus Infection,,,"<h4>Background</h4>The literature paints a complex picture of the association between mortality risk and ICU strain. In this study, we sought to determine if there is an association between mortality risk in intensive care units (ICU) and occupancy of beds compatible with mechanical ventilation, as a proxy for strain.<h4>Methods</h4>A national retrospective observational cohort study of 89 English hospital trusts (i.e. groups of hospitals functioning as single operational units). Seven thousand one hundred thirty-three adults admitted to an ICU in England between 2 April and 1 December, 2020 (inclusive), with presumed or confirmed COVID-19, for whom data was submitted to the national surveillance programme and met study inclusion criteria. A Bayesian hierarchical approach was used to model the association between hospital trust level (mechanical ventilation compatible), bed occupancy, and in-hospital all-cause mortality. Results were adjusted for unit characteristics (pre-pandemic size), individual patient-level demographic characteristics (age, sex, ethnicity, deprivation index, time-to-ICU admission), and recorded chronic comorbidities (obesity, diabetes, respiratory disease, liver disease, heart disease, hypertension, immunosuppression, neurological disease, renal disease).<h4>Results</h4>One hundred thirty-five thousand six hundred patient days were observed, with a mortality rate of 19.4 per 1000 patient days. Adjusting for patient-level factors, mortality was higher for admissions during periods of high occupancy (> 85% occupancy versus the baseline of 45 to 85%) [OR 1.23 (95% posterior credible interval (PCI): 1.08 to 1.39)]. In contrast, mortality was decreased for admissions during periods of low occupancy (< 45% relative to the baseline) [OR 0.83 (95% PCI 0.75 to 0.94)].<h4>Conclusion</h4>Increasing occupancy of beds compatible with mechanical ventilation, a proxy for operational strain, is associated with a higher mortality risk for individuals admitted to ICU. Further research is required to establish if this is a causal relationship or whether it reflects strain on other operational factors such as staff. If causal, the result highlights the importance of strategies to keep ICU occupancy low to mitigate the impact of this type of resource saturation.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-021-02096-0; doi:https://doi.org/10.1186/s12916-021-02096-0; html:https://europepmc.org/articles/PMC8404408; pdf:https://europepmc.org/articles/PMC8404408?pdf=render
+37415095,https://doi.org/10.1186/s12889-023-16202-9,Multi-morbidity and its association with common cancer diagnoses: a UK Biobank prospective study.,"Conroy MC, Reeves GK, Allen NE.",,BMC public health,2023,2023-07-06,Y,Cancer Risk; Uk Biobank; Multi-morbidity,,,"<h4>Background</h4>Whilst multi-morbidity is known to be a concern in people with cancer, very little is known about the risk of cancer in multi-morbid patients. This study aims to investigate the risk of being diagnosed with lung, colorectal, breast and prostate cancer associated with multi-morbidity.<h4>Methods</h4>We investigated the association between multi-morbidity and subsequent risk of cancer diagnosis in UK Biobank. Cox models were used to estimate the relative risks of each cancer of interest in multi-morbid participants, using the Cambridge Multimorbidity Score. The extent to which reverse causation, residual confounding and ascertainment bias may have impacted on the findings was robustly investigated.<h4>Results</h4>Of the 436,990 participants included in the study who were cancer-free at baseline, 21.6% (99,965) were multi-morbid (≥ 2 diseases). Over a median follow-up time of 10.9 [IQR 10.0-11.7] years, 9,019 prostate, 7,994 breast, 5,241 colorectal, and 3,591 lung cancers were diagnosed. After exclusion of the first year of follow-up, there was no clear association between multi-morbidity and risk of colorectal, prostate or breast cancer diagnosis. Those with ≥ 4 diseases at recruitment had double the risk of a subsequent lung cancer diagnosis compared to those with no diseases (HR 2.00 [95% CI 1.70-2.35] p for trend < 0.001). These findings were robust to sensitivity analyses aimed at reducing the impact of reverse causation, residual confounding from known cancer risk factors and ascertainment bias.<h4>Conclusions</h4>Individuals with multi-morbidity are at an increased risk of lung cancer diagnosis. While this association did not appear to be due to common sources of bias in observational studies, further research is needed to understand what underlies this association.",,pdf:https://bmcpublichealth.biomedcentral.com/counter/pdf/10.1186/s12889-023-16202-9; doi:https://doi.org/10.1186/s12889-023-16202-9; html:https://europepmc.org/articles/PMC10326925; pdf:https://europepmc.org/articles/PMC10326925?pdf=render
 34209840,https://doi.org/10.3390/cancers13133257,Dying to Survive-The p53 Paradox.,"Lees A, Sessler T, McDade S.",,Cancers,2021,2021-06-29,Y,Apoptosis; p53; Cell death; Targeted Therapy,,,"The p53 tumour suppressor is best known for its canonical role as ""guardian of the genome"", activating cell cycle arrest and DNA repair in response to DNA damage which, if irreparable or sustained, triggers activation of cell death. However, despite an enormous amount of work identifying the breadth of the gene regulatory networks activated directly and indirectly in response to p53 activation, how p53 activation results in different cell fates in response to different stress signals in homeostasis and in response to p53 activating anti-cancer treatments remains relatively poorly understood. This is likely due to the complex interaction between cell death mechanisms in which p53 has been activated, their neighbouring stressed or unstressed cells and the local stromal and immune microenvironment in which they reside. In this review, we evaluate our understanding of the burgeoning number of cell death pathways affected by p53 activation and how these may paradoxically suppress cell death to ensure tissue integrity and organismal survival. We also discuss how these functions may be advantageous to tumours that maintain wild-type p53, the understanding of which may provide novel opportunity to enhance treatment efficacy.",,pdf:https://www.mdpi.com/2072-6694/13/13/3257/pdf?version=1624967006; doi:https://doi.org/10.3390/cancers13133257; html:https://europepmc.org/articles/PMC8268032; pdf:https://europepmc.org/articles/PMC8268032?pdf=render
 36332942,https://doi.org/10.1136/openhrt-2022-002142,Development of algorithms for determining heart failure with reduced and preserved ejection fraction using nationwide electronic healthcare records in the UK.,"Sundaram V, Zakeri R, Witte KK, Quint JK.",,Open heart,2022,2022-11-01,Y,epidemiology; Heart Failure; Electronic Health Records,,,"<h4>Background</h4>Determining heart failure (HF) phenotypes in routine electronic health records (EHR) is challenging. We aimed to develop and validate EHR algorithms for identification of specific HF phenotypes, using Read codes in combination with selected patient characteristics.<h4>Methods</h4>We used The Healthcare Improvement Network (THIN). The study population included a random sample of individuals with HF diagnostic codes (HF with reduced ejection fraction (HFrEF), HF with preserved ejection fraction (HFpEF) and non-specific HF) selected from all participants registered in the THIN database between 1 January 2015 and 30 September 2017. Confirmed diagnoses were determined in a randomly selected subgroup of 500 patients via GP questionnaires including a review of all available cardiovascular investigations. Confirmed diagnoses of HFrEF and HFpEF were based on four criteria. Based on these data, we calculated a positive predictive value (PPV) of predefined algorithms which consisted of a combination of Read codes and additional information such as echocardiogram results and HF medication records.<h4>Results</h4>The final cohort from which we drew the 500 patient random sample consisted of 10 275 patients. Response rate to the questionnaire was 77.2%. A small proportion (18%) of the overall HF patient population were coded with specific HF phenotype Read codes. For HFrEF, algorithms achieving over 80% PPV included definite, possible or non-specific HF HFrEF codes when combined with at least two of the drugs used to treat HFrEF. Only in non-specific HF coding did the use of three drugs (rather than two) contribute to an improvement of the PPV for HFrEF. HFpEF was only accurately defined with specific codes. In the absence of specific coding for HFpEF, the PPV was consistently below 50%.<h4>Conclusions</h4>Prescription for HF medication can reliably be used to find HFrEF patients in the UK, even in the absence of a specific Read code for HFrEF. Algorithms using non-specific coding could not reliably find HFpEF patients.",,pdf:https://openheart.bmj.com/content/openhrt/9/2/e002142.full.pdf; doi:https://doi.org/10.1136/openhrt-2022-002142; html:https://europepmc.org/articles/PMC9639145; pdf:https://europepmc.org/articles/PMC9639145?pdf=render
+38233744,https://doi.org/10.1186/s12874-024-02143-3,Novel linkage approach to join community-acquired and national data.,"Tochel C, Pead E, McTrusty A, Buckmaster F, MacGillivray T, Tatham AJ, Strang NC, Dhillon B, Bernabeu MO.",,BMC medical research methodology,2024,2024-01-17,Y,Image analysis; Longitudinal data; Data Linkage; Early Disease Detection; Community Optometry,,,"<h4>Background</h4>Community optometrists in Scotland have performed regular free-at-point-of-care eye examinations for all, for over 15 years. Eye examinations include retinal imaging but image storage is fragmented and they are not used for research. The Scottish Collaborative Optometry-Ophthalmology Network e-research project aimed to collect these images and create a repository linked to routinely collected healthcare data, supporting the development of pre-symptomatic diagnostic tools.<h4>Methods</h4>As the image record was usually separate from the patient record and contained minimal patient information, we developed an efficient matching algorithm using a combination of deterministic and probabilistic steps which minimised the risk of false positives, to facilitate national health record linkage. We visited two practices and assessed the data contained in their image device and Practice Management Systems. Practice activities were explored to understand the context of data collection processes. Iteratively, we tested a series of matching rules which captured a high proportion of true positive records compared to manual matches. The approach was validated by testing manual matching against automated steps in three further practices.<h4>Results</h4>A sequence of deterministic rules successfully matched 95% of records in the three test practices compared to manual matching. Adding two probabilistic rules to the algorithm successfully matched 99% of records.<h4>Conclusions</h4>The potential value of community-acquired retinal images can be harnessed only if they are linked to centrally-held healthcare care data. Despite the lack of interoperability between systems within optometry practices and inconsistent use of unique identifiers, data linkage is possible using robust, almost entirely automated processes.",,pdf:https://bmcmedresmethodol.biomedcentral.com/counter/pdf/10.1186/s12874-024-02143-3; doi:https://doi.org/10.1186/s12874-024-02143-3; html:https://europepmc.org/articles/PMC10792819; pdf:https://europepmc.org/articles/PMC10792819?pdf=render
 36857859,https://doi.org/10.1016/j.ebiom.2023.104489,"Identifying subtypes of chronic kidney disease with machine learning: development, internal validation and prognostic validation using linked electronic health records in 350,067 individuals.","Dashtban A, Mizani MA, Pasea L, Denaxas S, Corbett R, Mamza JB, Gao H, Morris T, Hemingway H, Banerjee A.",,EBioMedicine,2023,2023-02-27,Y,Cluster analysis; Survival analysis; Machine Learning; Unsupervised Clustering; Ckd Subtype,,,"<h4>Background</h4>Although chronic kidney disease (CKD) is associated with high multimorbidity, polypharmacy, morbidity and mortality, existing classification systems (mild to severe, usually based on estimated glomerular filtration rate, proteinuria or urine albumin-creatinine ratio) and risk prediction models largely ignore the complexity of CKD, its risk factors and its outcomes. Improved subtype definition could improve prediction of outcomes and inform effective interventions.<h4>Methods</h4>We analysed individuals ≥18 years with incident and prevalent CKD (n = 350,067 and 195,422 respectively) from a population-based electronic health record resource (2006-2020; Clinical Practice Research Datalink, CPRD). We included factors (n = 264 with 2670 derived variables), e.g. demography, history, examination, blood laboratory values and medications. Using a published framework, we identified subtypes through seven unsupervised machine learning (ML) methods (K-means, Diana, HC, Fanny, PAM, Clara, Model-based) with 66 (of 2670) variables in each dataset. We evaluated subtypes for: (i) internal validity (within dataset, across methods); (ii) prognostic validity (predictive accuracy for 5-year all-cause mortality and admissions); and (iii) medications (new and existing by British National Formulary chapter).<h4>Findings</h4>After identifying five clusters across seven approaches, we labelled CKD subtypes: 1. Early-onset, 2. Late-onset, 3. Cancer, 4. Metabolic, and 5. Cardiometabolic. Internal validity: We trained a high performing model (using XGBoost) that could predict disease subtypes with 95% accuracy for incident and prevalent CKD (Sensitivity: 0.81-0.98, F1 score:0.84-0.97). Prognostic validity: 5-year all-cause mortality, hospital admissions, and incidence of new chronic diseases differed across CKD subtypes. The 5-year risk of mortality and admissions in the overall incident CKD population were highest in cardiometabolic subtype: 43.3% (42.3-42.8%) and 29.5% (29.1-30.0%), respectively, and lowest in the early-onset subtype: 5.7% (5.5-5.9%) and 18.7% (18.4-19.1%).<h4>Medications</h4>Across CKD subtypes, the distribution of prescription medication classes at baseline varied, with highest medication burden in cardiometabolic and metabolic subtypes, and higher burden in prevalent than incident CKD.<h4>Interpretation</h4>In the largest CKD study using ML, to-date, we identified five distinct subtypes in individuals with incident and prevalent CKD. These subtypes have relevance to study of aetiology, therapeutics and risk prediction.<h4>Funding</h4>AstraZeneca UK Ltd, Health Data Research UK.",,pdf:http://www.thelancet.com/article/S2352396423000543/pdf; doi:https://doi.org/10.1016/j.ebiom.2023.104489; html:https://europepmc.org/articles/PMC9989643; pdf:https://europepmc.org/articles/PMC9989643?pdf=render
 32935048,https://doi.org/10.23889/ijpds.v5i1.1121,The Secure Anonymised Information Linkage databank Dementia e-cohort (SAIL-DeC).,"Schnier C, Wilkinson T, Akbari A, Orton C, Sleegers K, Gallacher J, Lyons RA, Sudlow C.",,International journal of population data science,2020,2020-02-25,Y,,,,"<h4>Introduction</h4>The rising burden of dementia is a global concern, and there is a need to study its causes, natural history and outcomes. The Secure Anonymised Information Linkage (SAIL) Databank contains anonymised, routinely-collected healthcare data for the population of Wales, UK. It has potential to be a valuable resource for dementia research owing to its size, long follow-up time and prospective collection of data during clinical care.<h4>Objectives</h4>We aimed to apply reproducible methods to create the SAIL dementia e-cohort (SAIL-DeC). We created SAIL-DeC with a view to maximising its utility for a broad range of research questions whilst minimising duplication of effort for researchers.<h4>Methods</h4>SAIL contains individual-level, linked primary care, hospital admission, mortality and demographic data. Data are currently available until 2018 and future updates will extend participant follow-up time. We included participants who were born between 1st January 1900 and 1st January 1958 and for whom primary care data were available. We applied algorithms consisting of International Classification of Diseases (versions 9 and 10) and Read (version 2) codes to identify participants with and without all-cause dementia and dementia subtypes. We also created derived variables for comorbidities and risk factors.<h4>Results</h4>From 4.4 million unique participants in SAIL, 1.2 million met the cohort inclusion criteria, resulting in 18.8 million person-years of follow-up. Of these, 129,650 (10%) developed all-cause dementia, with 77,978 (60%) having dementia subtype codes. Alzheimer's disease was the most common subtype diagnosis (62%). Among the dementia cases, the median duration of observation time was 14 years.<h4>Conclusion</h4>We have created a generalisable, national dementia e-cohort, aimed at facilitating epidemiological dementia research.",,pdf:https://ijpds.org/article/download/1121/2984; doi:https://doi.org/10.23889/ijpds.v5i1.1121; html:https://europepmc.org/articles/PMC7473277; pdf:https://europepmc.org/articles/PMC7473277?pdf=render
-38233744,https://doi.org/10.1186/s12874-024-02143-3,Novel linkage approach to join community-acquired and national data.,"Tochel C, Pead E, McTrusty A, Buckmaster F, MacGillivray T, Tatham AJ, Strang NC, Dhillon B, Bernabeu MO.",,BMC medical research methodology,2024,2024-01-17,Y,Image analysis; Longitudinal data; Data Linkage; Early Disease Detection; Community Optometry,,,"<h4>Background</h4>Community optometrists in Scotland have performed regular free-at-point-of-care eye examinations for all, for over 15 years. Eye examinations include retinal imaging but image storage is fragmented and they are not used for research. The Scottish Collaborative Optometry-Ophthalmology Network e-research project aimed to collect these images and create a repository linked to routinely collected healthcare data, supporting the development of pre-symptomatic diagnostic tools.<h4>Methods</h4>As the image record was usually separate from the patient record and contained minimal patient information, we developed an efficient matching algorithm using a combination of deterministic and probabilistic steps which minimised the risk of false positives, to facilitate national health record linkage. We visited two practices and assessed the data contained in their image device and Practice Management Systems. Practice activities were explored to understand the context of data collection processes. Iteratively, we tested a series of matching rules which captured a high proportion of true positive records compared to manual matches. The approach was validated by testing manual matching against automated steps in three further practices.<h4>Results</h4>A sequence of deterministic rules successfully matched 95% of records in the three test practices compared to manual matching. Adding two probabilistic rules to the algorithm successfully matched 99% of records.<h4>Conclusions</h4>The potential value of community-acquired retinal images can be harnessed only if they are linked to centrally-held healthcare care data. Despite the lack of interoperability between systems within optometry practices and inconsistent use of unique identifiers, data linkage is possible using robust, almost entirely automated processes.",,pdf:https://bmcmedresmethodol.biomedcentral.com/counter/pdf/10.1186/s12874-024-02143-3; doi:https://doi.org/10.1186/s12874-024-02143-3; html:https://europepmc.org/articles/PMC10792819; pdf:https://europepmc.org/articles/PMC10792819?pdf=render
-37415095,https://doi.org/10.1186/s12889-023-16202-9,Multi-morbidity and its association with common cancer diagnoses: a UK Biobank prospective study.,"Conroy MC, Reeves GK, Allen NE.",,BMC public health,2023,2023-07-06,Y,Cancer Risk; Uk Biobank; Multi-morbidity,,,"<h4>Background</h4>Whilst multi-morbidity is known to be a concern in people with cancer, very little is known about the risk of cancer in multi-morbid patients. This study aims to investigate the risk of being diagnosed with lung, colorectal, breast and prostate cancer associated with multi-morbidity.<h4>Methods</h4>We investigated the association between multi-morbidity and subsequent risk of cancer diagnosis in UK Biobank. Cox models were used to estimate the relative risks of each cancer of interest in multi-morbid participants, using the Cambridge Multimorbidity Score. The extent to which reverse causation, residual confounding and ascertainment bias may have impacted on the findings was robustly investigated.<h4>Results</h4>Of the 436,990 participants included in the study who were cancer-free at baseline, 21.6% (99,965) were multi-morbid (≥ 2 diseases). Over a median follow-up time of 10.9 [IQR 10.0-11.7] years, 9,019 prostate, 7,994 breast, 5,241 colorectal, and 3,591 lung cancers were diagnosed. After exclusion of the first year of follow-up, there was no clear association between multi-morbidity and risk of colorectal, prostate or breast cancer diagnosis. Those with ≥ 4 diseases at recruitment had double the risk of a subsequent lung cancer diagnosis compared to those with no diseases (HR 2.00 [95% CI 1.70-2.35] p for trend < 0.001). These findings were robust to sensitivity analyses aimed at reducing the impact of reverse causation, residual confounding from known cancer risk factors and ascertainment bias.<h4>Conclusions</h4>Individuals with multi-morbidity are at an increased risk of lung cancer diagnosis. While this association did not appear to be due to common sources of bias in observational studies, further research is needed to understand what underlies this association.",,pdf:https://bmcpublichealth.biomedcentral.com/counter/pdf/10.1186/s12889-023-16202-9; doi:https://doi.org/10.1186/s12889-023-16202-9; html:https://europepmc.org/articles/PMC10326925; pdf:https://europepmc.org/articles/PMC10326925?pdf=render
 36882868,https://doi.org/10.1186/s12916-023-02784-z,"Assessing the impacts of COVID-19 vaccination programme's timing and speed on health benefits, cost-effectiveness, and relative affordability in 27 African countries.","Liu Y, Procter SR, Pearson CAB, Montero AM, Torres-Rueda S, Asfaw E, Uzochukwu B, Drake T, Bergren E, Eggo RM, Ruiz F, Ndembi N, Nonvignon J, Jit M, Vassall A.",,BMC medicine,2023,2023-03-08,Y,Mathematical models; Vaccination; Economic evaluation; decision-making; Affordability; Programme Evaluation; Public Health Interventions; Covid-19 | Sars-cov-2,,,"<h4>Background</h4>The COVID-19 vaccine supply shortage in 2021 constrained roll-out efforts in Africa while populations experienced waves of epidemics. As supply improves, a key question is whether vaccination remains an impactful and cost-effective strategy given changes in the timing of implementation.<h4>Methods</h4>We assessed the impact of vaccination programme timing using an epidemiological and economic model. We fitted an age-specific dynamic transmission model to reported COVID-19 deaths in 27 African countries to approximate existing immunity resulting from infection before substantial vaccine roll-out. We then projected health outcomes (from symptomatic cases to overall disability-adjusted life years (DALYs) averted) for different programme start dates (01 January to 01 December 2021, n = 12) and roll-out rates (slow, medium, fast; 275, 826, and 2066 doses/million population-day, respectively) for viral vector and mRNA vaccines by the end of 2022. Roll-out rates used were derived from observed uptake trajectories in this region. Vaccination programmes were assumed to prioritise those above 60 years before other adults. We collected data on vaccine delivery costs, calculated incremental cost-effectiveness ratios (ICERs) compared to no vaccine use, and compared these ICERs to GDP per capita. We additionally calculated a relative affordability measure of vaccination programmes to assess potential nonmarginal budget impacts.<h4>Results</h4>Vaccination programmes with early start dates yielded the most health benefits and lowest ICERs compared to those with late starts. While producing the most health benefits, fast vaccine roll-out did not always result in the lowest ICERs. The highest marginal effectiveness within vaccination programmes was found among older adults. High country income groups, high proportions of populations over 60 years or non-susceptible at the start of vaccination programmes are associated with low ICERs relative to GDP per capita. Most vaccination programmes with small ICERs relative to GDP per capita were also relatively affordable.<h4>Conclusion</h4>Although ICERs increased significantly as vaccination programmes were delayed, programmes starting late in 2021 may still generate low ICERs and manageable affordability measures. Looking forward, lower vaccine purchasing costs and vaccines with improved efficacies can help increase the economic value of COVID-19 vaccination programmes.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-023-02784-z; doi:https://doi.org/10.1186/s12916-023-02784-z; html:https://europepmc.org/articles/PMC9991879; pdf:https://europepmc.org/articles/PMC9991879?pdf=render
 37798357,https://doi.org/10.1038/s41598-023-42331-7,"An angiopoietin 2, FGF23, and BMP10 biomarker signature differentiates atrial fibrillation from other concomitant cardiovascular conditions.","Chua W, Cardoso VR, Guasch E, Sinner MF, Al-Taie C, Brady P, Casadei B, Crijns HJGM, Dudink EAMP, Hatem SN, Kääb S, Kastner P, Mont L, Nehaj F, Purmah Y, Reyat JS, Schotten U, Sommerfeld LC, Zeemering S, Ziegler A, Gkoutos GV, Kirchhof P, Fabritz L.",,Scientific reports,2023,2023-10-05,Y,,,,"Early detection of atrial fibrillation (AF) enables initiation of anticoagulation and early rhythm control therapy to reduce stroke, cardiovascular death, and heart failure. In a cross-sectional, observational study, we aimed to identify a combination of circulating biomolecules reflecting different biological processes to detect prevalent AF in patients with cardiovascular conditions presenting to hospital. Twelve biomarkers identified by reviewing literature and patents were quantified on a high-precision, high-throughput platform in 1485 consecutive patients with cardiovascular conditions (median age 69 years [Q1, Q3 60, 78]; 60% male). Patients had either known AF (45%) or AF ruled out by 7-day ECG-monitoring. Logistic regression with backward elimination and a neural network approach considering 7 key clinical characteristics and 12 biomarker concentrations were applied to a randomly sampled discovery cohort (n = 933) and validated in the remaining patients (n = 552). In addition to age, sex, and body mass index (BMI), BMP10, ANGPT2, and FGF23 identified patients with prevalent AF (AUC 0.743 [95% CI 0.712, 0.775]). These circulating biomolecules represent distinct pathways associated with atrial cardiomyopathy and AF. Neural networks identified the same variables as the regression-based approach. The validation using regression yielded an AUC of 0.719 (95% CI 0.677, 0.762), corroborated using deep neural networks (AUC 0.784 [95% CI 0.745, 0.822]). Age, sex, BMI and three circulating biomolecules (BMP10, ANGPT2, FGF23) are associated with prevalent AF in unselected patients presenting to hospital. Findings should be externally validated. Results suggest that age and different disease processes approximated by these three biomolecules contribute to AF in patients. Our findings have the potential to improve screening programs for AF after external validation.",,pdf:https://www.nature.com/articles/s41598-023-42331-7.pdf; doi:https://doi.org/10.1038/s41598-023-42331-7; html:https://europepmc.org/articles/PMC10556075; pdf:https://europepmc.org/articles/PMC10556075?pdf=render
 36606535,https://doi.org/10.1111/jdv.18841,The association between atopic eczema and lymphopenia: Results from a UK cohort study with replication in US survey data.,"Hollestein LM, Ye MYF, Ang KL, Forbes H, Mansfield KE, Abuabara K, Smeeth L, Langan SM.",,Journal of the European Academy of Dermatology and Venereology : JEADV,2023,2023-01-25,Y,,,,"<h4>Background</h4>Lymphocyte skin homing in atopic eczema (AE) may induce lymphopenia.<h4>Objective</h4>To determine if AE is associated with lymphopenia.<h4>Methods</h4>We used UK primary care electronic health records (Clinical Practice Research Datalink GOLD) for a matched cohort study in adults (18 years+) (1997-2015) with at least one recorded lymphocyte count. We matched people with AE to up to five people without. We used multivariable logistic regression to estimate the association between AE and lymphopenia (two low lymphocyte counts within 3 months) and linear mixed effects regression to estimate the association with absolute lymphocyte counts using all available counts. Cox proportional hazard models were used to investigate the effect of lymphopenia on common infections. We replicated the study using US survey data (National Health and Nutrition Examination Survey [NHANES]).<h4>Results</h4>Among 71,731 adults with AE and 126,349 adults without AE, we found an adjusted odds ratio (OR) for lymphopenia of 1.16 (95% CI: 1.09-1.23); the strength of association increased with increasing eczema severity. When comparing all recorded lymphocyte counts from adults with AE (n = 1,497,306) to those of people without AE (n = 4,035,870) we saw a lower mean lymphocyte (adjusted mean difference -0.047 × 10<sup>9</sup> /L [95% CI: -0.051 to -0.043]) in those with AE. The difference was larger for men, with increasing age, and with increasing AE severity and was present among people with AE not treated with immunosuppressive drugs. In NHANES (n = 22,624), the adjusted OR for lymphopenia in adults with AE was 1.30 (95% CI: 0.80-2.11), and the adjusted mean lymphocyte count difference was -0.03 × 10<sup>9</sup> /L (95% CI: -0.07 to 0.02). Despite having a lower lymphocyte count, adjusting for time with lymphopenia, did not alter risk estimates of infections.<h4>Conclusion</h4>Atopic eczema, including increasing AE severity, is associated with a decreased lymphocyte count, regardless of immunosuppressive drug use. Whether the lower lymphocyte count has wider health implications for people with severe eczema warrants further investigation.",,pdf:https://pure.eur.nl/files/97319410/Acad_Dermatol_Venereol_-_2023_-_Hollestein_-_The_association_between_atopic_eczema_and_lymphopenia_Results_from_a_UK.pdf; doi:https://doi.org/10.1111/jdv.18841; html:https://europepmc.org/articles/PMC10947025; pdf:https://europepmc.org/articles/PMC10947025?pdf=render
@@ -551,22 +551,22 @@ PMC10910267,https://doi.org/,Development and evaluation of a tool to optimise in
 33846368,https://doi.org/10.1038/s41598-021-86324-w,Intake of food rich in saturated fat in relation to subclinical atherosclerosis and potential modulating effects from single genetic variants.,"Laguzzi F, Maitusong B, Strawbridge RJ, Baldassarre D, Veglia F, Humphries SE, Rauramaa R, Kurl S, Smit AJ, Giral P, Silveira A, Tremoli E, Hamsten A, de Faire U, Gigante B, Leander K, IMPROVE Study group.",,Scientific reports,2021,2021-04-12,Y,,,,"The relationship between intake of saturated fats and subclinical atherosclerosis, as well as the possible influence of genetic variants, is poorly understood and investigated. We aimed to investigate this relationship, with a hypothesis that it would be positive, and to explore whether genetics may modulate it, using data from a European cohort including 3,407 participants aged 54-79 at high risk of cardiovascular disease. Subclinical atherosclerosis was assessed by carotid intima-media thickness (C-IMT), measured at baseline and after 30 months. Logistic regression (OR; 95% CI) was employed to assess the association between high intake of food rich in saturated fat (vs. low) and: (1) the mean and the maximum values of C-IMT in the whole carotid artery (C-IMT<sub>mean</sub>, C-IMT<sub>max</sub>), in the bifurcation (Bif-), the common (CC-) and internal (ICA-) carotid arteries at baseline (binary, cut-point ≥ 75th), and (2) C-IMT progression (binary, cut-point > zero). For the genetic-diet interaction analyses, we considered 100,350 genetic variants. We defined interaction as departure from additivity of effects. After age- and sex-adjustment, high intake of saturated fat was associated with increased C-IMT<sub>mean</sub> (OR:1.27;1.06-1.47), CC-IMT<sub>mean</sub> (OR:1.22;1.04-1.44) and ICA-IMT<sub>mean</sub> (OR:1.26;1.07-1.48). However, in multivariate analysis results were no longer significant. No clear associations were observed between high intake of saturated fat and risk of atherosclerotic progression. There was no evidence of interactions between high intake of saturated fat and any of the genetic variants considered, after multiple testing corrections. High intake of saturated fats was not independently associated with subclinical atherosclerosis. Moreover, we did not identify any significant genetic-dietary fat interactions in relation to risk of subclinical atherosclerosis.",,pdf:https://www.nature.com/articles/s41598-021-86324-w.pdf; doi:https://doi.org/10.1038/s41598-021-86324-w; html:https://europepmc.org/articles/PMC8042105; pdf:https://europepmc.org/articles/PMC8042105?pdf=render
 32499256,https://doi.org/10.1136/bmjopen-2019-033424,Point-of-care tests for urinary tract infections: protocol for a systematic review and meta-analysis of diagnostic test accuracy.,"Fraile Navarro D, Sullivan F, Azcoaga-Lorenzo A, Hernandez Santiago V.",,BMJ open,2020,2020-06-03,Y,Urinary tract infections; epidemiology; Molecular Diagnostics; Diagnostic Microbiology,,,"<h4>Introduction</h4>Urinary tract infections (UTIs) are the second most common type of infection worldwide, accounting for a large number of primary care consultations and antibiotic prescribing. Current diagnosis is based on an empirical approach, relying on symptoms and occasional use of urine dipsticks. The diagnostic reference standard is still urine culture, although it is not routinely recommended for uncomplicated UTIs in the community, due to time to diagnosis (48 hours). Faster point-of-care tests have been developed, but their diagnostic accuracy has not been compared. Our objective is to systematically review and meta-analyse the diagnostic accuracy of currently available point-of-care tests for UTIs.<h4>Methods and analysis</h4>Studies evaluating the diagnostic accuracy of point-of-care tests for UTIs will be included. PubMed, Web of Science, Embase and Cochrane Database of Systematic Reviews were searched from inception to 1 June 2019. Data extraction and risk-of-bias assessment will be assessed using the Quality Assessment of Diagnostic Accuracy Studies tool. Meta-analysis will be performed depending on data availability and heterogeneity.<h4>Ethics and dissemination</h4>This is a systematic review protocol and therefore formal ethical approval is not required, as no primary, identifiable, personal data will be collected. Patients or the public were not involved in the design of our research. However, the findings from this review will be shared with key stakeholders, including patient groups, clinicians and guideline developers, and will also be presented and national and international conferences.<h4>Prospero registration number</h4>CRD42018112019.",,pdf:https://bmjopen.bmj.com/content/bmjopen/10/6/e033424.full.pdf; doi:https://doi.org/10.1136/bmjopen-2019-033424; html:https://europepmc.org/articles/PMC7282288; pdf:https://europepmc.org/articles/PMC7282288?pdf=render
 31658860,https://doi.org/10.1161/jaha.119.012812,Early Discontinuation of P2Y<sub>12</sub> Antagonists and Adverse Clinical Events Post-Percutaneous Coronary Intervention: A Hospital and Primary Care Linked Cohort.,"Harris DE, Lacey A, Akbari A, Obaid DR, Smith DA, Jenkins GH, Barry JP, Gravenor MB, Halcox JP.",,Journal of the American Heart Association,2019,2019-10-29,Y,Adherence; Percutaneous coronary intervention; Clopidogrel; Discontinuation; Discharge Therapy,"Improving Public Health, Understanding the Causes of Disease",,"Background Early discontinuation of P2Y<sub>12</sub> antagonists post-percutaneous coronary intervention may increase risk of stent thrombosis or nonstent recurrent myocardial infarction. Our aims were to (1) analyze the early discontinuation rate of P2Y<sub>12</sub> antagonists post-percutaneous coronary intervention, (2) explore factors associated with early discontinuation, and (3) analyze the risk of major adverse cardiovascular events (death, acute coronary syndrome, revascularization, or stroke) associated with discontinuation from a prespecified prescribing instruction of 1 year. Method and Results We studied 2090 patients (2011-2015) who were recommended for clopidogrel for 12 months (+aspirin) post-percutaneous coronary intervention within a retrospective observational population cohort. Relationships between clopidogrel discontinuation and major adverse cardiac events were evaluated over 18-month follow-up. Discontinuation of clopidogrel in the first 4 quarters was low at 1.1%, 2.6%, 3.7%, and 6.1%, respectively. Previous revascularization, previous ischemic stroke, and age >80 years were independent predictors of early discontinuation. In a time-dependent multiple regression model, clopidogrel discontinuation and bleeding (hazard ratio=1.82 [1.01-3.30] and hazard ratio=5.30 [3.14-8.94], respectively) were independent predictors of major adverse cardiac events as were age <49 and ≥70 years (versus those aged 50-59 years), hypertension, chronic kidney disease stage 4+, previous revascularization, ischemic stroke, and thromboembolism. Furthermore, in those with both bleeding and clopidogrel discontinuation, hazard ratio for major adverse cardiac events was 9.34 (3.39-25.70). Conclusions Discontinuation of clopidogrel is low in the first year post-percutaneous coronary intervention, where a clear discharge instruction to treat for 1 year is provided. Whereas this is reassuring from the population level, at an individual level discontinuation earlier than the intended duration is associated with an increased rate of adverse events, most notably in those with both bleeding and discontinuation.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.119.012812; doi:https://doi.org/10.1161/JAHA.119.012812; html:https://europepmc.org/articles/PMC6898825; pdf:https://europepmc.org/articles/PMC6898825?pdf=render
+38434747,https://doi.org/10.12688/wellcomeopenres.19858.1,"Interpreting pathology test result values with comparators (< , >) in Electronic Health Records research: an OpenSAFELY short data report.","Curtis HJ, Fisher L, Evans D, OpenSAFELY Collaborative, Bacon S, Mehrkar A, Goldacre B, MacKenna B.",,Wellcome open research,2023,2023-01-01,Y,Pathology; Kidney function tests; Electronic Health Records,,,"<h4>Background</h4>Numeric results of pathology tests are sometimes returned as a range rather than a precise value, e.g. ""<10"". In health data research, test result values above or below clinical threshold values are often used to categorise patients into groups; however comparators (<, > etc) are typically stored separately to the numeric values and often ignored, but may influence interpretation.<h4>Methods</h4>With the approval of NHS England we used routine clinical data from 24 million patients in OpenSAFELY to identify pathology tests with comparators commonly attached to result values. For each test we report: the proportion returned with comparators present, split by comparator type and geographic region; the specific numeric result values returned with comparators, and the associated reference limits.<h4>Results</h4>We identified 11 common test codes where at least one in four results had comparators. Three codes related to glomerular filtration rate (GFR) tests/calculations, with 31-45% of results returned with ""≥"" comparators. At least 90% of tests with numeric values 60 and 90 represented ranges (≥60 and ≥90 respectively) rather than exact values. The other tests - four blood tests (Nucleated red blood cell count, Plasma C reactive protein, Tissue transglutaminase immunoglobulin A, and Rheumatoid factor), two urine tests (albumin/microalbumin) and two faecal tests (calprotectin and quantitative faecal immunochemical test) - were returned with ""≤"" comparators (29-86%).<h4>Conclusions</h4>Comparators appear commonly in certain pathology tests in electronic health records. For most common affected tests, we expect there to be minimal implications for researchers for most use-cases. However, care should be taken around whether results falling exactly on clinical threshold values should be considered ""normal"" or ""abnormal"". Results from GFR tests/calculations cannot reliably distinguish between mild kidney disease (stage G2, 60-<90) versus healthy kidney function (90+). More broadly, health data researchers using numeric test result values should consider the impact of comparators.",,doi:https://doi.org/10.12688/wellcomeopenres.19858.1; html:https://europepmc.org/articles/PMC10904973; pdf:https://europepmc.org/articles/PMC10904973?pdf=render
+34599527,https://doi.org/10.1111/dme.14707,Comparing survival outcomes for kidney transplant recipients with pre-existing diabetes versus those who develop post-transplantation diabetes.,"Hussain A, Culliford A, Phagura N, Evison F, Gallier S, Sharif A.",,Diabetic medicine : a journal of the British Diabetic Association,2022,2021-10-08,N,Survival; Management; Diabetes; Kidney Transplant; Post-transplant Diabetes,,,"<h4>Introduction</h4>The aim of this study was to compare the management strategy and clinical outcomes for kidney transplant recipients with pre-transplant versus post-transplantation diabetes (PTDM) in a contemporary cohort.<h4>Methods</h4>This is a single-centre, retrospective. observational study of kidney transplant recipients between 2007 and 2018 with follow-up to 31 December 2020. Data were extracted from hospital electronic patient records, with clinical outcomes linked to national data sets. PTDM was diagnosed by international consensus guidelines. Unadjusted and adjusted survival outcomes were assessed with Kaplan-Meier curves and Cox regression models, respectively, with PTDM handled as a time-varying covariate.<h4>Results</h4>Data were analysed for 1,757 kidney transplant recipients, of whom 11.8% (n = 207) had pre-transplant diabetes, and 13.8% (n = 243) developed PTDM with median time to onset 108 days (IQR 46-549 days). Median follow-up was 1,839 days (IQR 928-2985 days). Disparate management strategies were observed, although insulin was the commonest glucose-lowering therapy for all patients with diabetes. In adjusted models, PTDM was associated with lower mortality (HR 0.663, 95% CI 0.543-0.810) and pre-diabetes with higher mortality (HR 1.675, 95% CI 1.396-2.011). However, if analyses are restricted to those with at least 5-year follow-up, then PTDM has no association with mortality (HR 0.771, 95% CI 0.419-1.096), but pre-transplant diabetes remains associated with higher mortality (HR 2.029, 95% CI 1.367-3.012).<h4>Conclusions</h4>Pre-transplant diabetes remains associated with increased mortality risk after kidney transplantation, but PTDM effects are time dependent. Development of PTDM should be encouraged as a mandated registry return to study the long-term impact on survival outcomes.",,doi:https://doi.org/10.1111/dme.14707
 33004880,https://doi.org/10.1038/s41598-020-73228-4,"Predicting pattern formation in embryonic stem cells using a minimalist, agent-based probabilistic model.","Wang M, Tsanas A, Blin G, Robertson D.",,Scientific reports,2020,2020-10-01,Y,,,,"The mechanisms of pattern formation during embryonic development remain poorly understood. Embryonic stem cells in culture self-organise to form spatial patterns of gene expression upon geometrical confinement indicating that patterning is an emergent phenomenon that results from the many interactions between the cells. Here, we applied an agent-based modelling approach in order to identify plausible biological rules acting at the meso-scale within stem cell collectives that may explain spontaneous patterning. We tested different models involving differential motile behaviours with or without biases due to neighbour interactions. We introduced a new metric, termed stem cell aggregate pattern distance (SCAPD) to probabilistically assess the fitness of our models with empirical data. The best of our models improves fitness by 70% and 77% over the random models for a discoidal or an ellipsoidal stem cell confinement respectively. Collectively, our findings show that a parsimonious mechanism that involves differential motility is sufficient to explain the spontaneous patterning of the cells upon confinement. Our work also defines a region of the parameter space that is compatible with patterning. We hope that our approach will be applicable to many biological systems and will contribute towards facilitating progress by reducing the need for extensive and costly experiments.",,pdf:https://www.nature.com/articles/s41598-020-73228-4.pdf; doi:https://doi.org/10.1038/s41598-020-73228-4; html:https://europepmc.org/articles/PMC7529768; pdf:https://europepmc.org/articles/PMC7529768?pdf=render
 35534084,https://doi.org/10.1136/bmjopen-2021-054186,Evaluation of freely available data profiling tools for health data research application: a functional evaluation review.,"Gordon B, Fennessy C, Varma S, Barrett J, McCondochie E, Heritage T, Duroe O, Jeffery R, Rajamani V, Earlam K, Banda V, Sebire N.",,BMJ open,2022,2022-05-09,Y,Information management; information technology; Health Informatics,,,"<h4>Objectives</h4>To objectively evaluate freely available data profiling software tools using healthcare data.<h4>Design</h4>Data profiling tools were evaluated for their capabilities using publicly available information and data sheets. From initial assessment, several underwent further detailed evaluation for application on healthcare data using a synthetic dataset of 1000 patients and associated data using a common health data model, and tools scored based on their functionality with this dataset.<h4>Setting</h4>Improving the quality of healthcare data for research use is a priority. Profiling tools can assist by evaluating datasets across a range of quality dimensions. Several freely available software packages with profiling capabilities are available but healthcare organisations often have limited data engineering capability and expertise.<h4>Participants</h4>28 profiling tools, 8 undergoing evaluation on synthetic dataset of 1000 patients.<h4>Results</h4>Of 28 potential profiling tools initially identified, 8 showed high potential for applicability with healthcare datasets based on available documentation, of which two performed consistently well for these purposes across multiple tasks including determination of completeness, consistency, uniqueness, validity, accuracy and provision of distribution metrics.<h4>Conclusions</h4>Numerous freely available profiling tools are serviceable for potential use with health datasets, of which at least two demonstrated high performance across a range of technical data quality dimensions based on testing with synthetic health dataset and common data model. The appropriate tool choice depends on factors including underlying organisational infrastructure, level of data engineering and coding expertise, but there are freely available tools helping profile health datasets for research use and inform curation activity.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/5/e054186.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-054186; html:https://europepmc.org/articles/PMC9086620; pdf:https://europepmc.org/articles/PMC9086620?pdf=render
-34599527,https://doi.org/10.1111/dme.14707,Comparing survival outcomes for kidney transplant recipients with pre-existing diabetes versus those who develop post-transplantation diabetes.,"Hussain A, Culliford A, Phagura N, Evison F, Gallier S, Sharif A.",,Diabetic medicine : a journal of the British Diabetic Association,2022,2021-10-08,N,Survival; Management; Diabetes; Kidney Transplant; Post-transplant Diabetes,,,"<h4>Introduction</h4>The aim of this study was to compare the management strategy and clinical outcomes for kidney transplant recipients with pre-transplant versus post-transplantation diabetes (PTDM) in a contemporary cohort.<h4>Methods</h4>This is a single-centre, retrospective. observational study of kidney transplant recipients between 2007 and 2018 with follow-up to 31 December 2020. Data were extracted from hospital electronic patient records, with clinical outcomes linked to national data sets. PTDM was diagnosed by international consensus guidelines. Unadjusted and adjusted survival outcomes were assessed with Kaplan-Meier curves and Cox regression models, respectively, with PTDM handled as a time-varying covariate.<h4>Results</h4>Data were analysed for 1,757 kidney transplant recipients, of whom 11.8% (n = 207) had pre-transplant diabetes, and 13.8% (n = 243) developed PTDM with median time to onset 108 days (IQR 46-549 days). Median follow-up was 1,839 days (IQR 928-2985 days). Disparate management strategies were observed, although insulin was the commonest glucose-lowering therapy for all patients with diabetes. In adjusted models, PTDM was associated with lower mortality (HR 0.663, 95% CI 0.543-0.810) and pre-diabetes with higher mortality (HR 1.675, 95% CI 1.396-2.011). However, if analyses are restricted to those with at least 5-year follow-up, then PTDM has no association with mortality (HR 0.771, 95% CI 0.419-1.096), but pre-transplant diabetes remains associated with higher mortality (HR 2.029, 95% CI 1.367-3.012).<h4>Conclusions</h4>Pre-transplant diabetes remains associated with increased mortality risk after kidney transplantation, but PTDM effects are time dependent. Development of PTDM should be encouraged as a mandated registry return to study the long-term impact on survival outcomes.",,doi:https://doi.org/10.1111/dme.14707
-38434747,https://doi.org/10.12688/wellcomeopenres.19858.1,"Interpreting pathology test result values with comparators (< , >) in Electronic Health Records research: an OpenSAFELY short data report.","Curtis HJ, Fisher L, Evans D, OpenSAFELY Collaborative, Bacon S, Mehrkar A, Goldacre B, MacKenna B.",,Wellcome open research,2023,2023-01-01,Y,Pathology; Kidney function tests; Electronic Health Records,,,"<h4>Background</h4>Numeric results of pathology tests are sometimes returned as a range rather than a precise value, e.g. ""<10"". In health data research, test result values above or below clinical threshold values are often used to categorise patients into groups; however comparators (<, > etc) are typically stored separately to the numeric values and often ignored, but may influence interpretation.<h4>Methods</h4>With the approval of NHS England we used routine clinical data from 24 million patients in OpenSAFELY to identify pathology tests with comparators commonly attached to result values. For each test we report: the proportion returned with comparators present, split by comparator type and geographic region; the specific numeric result values returned with comparators, and the associated reference limits.<h4>Results</h4>We identified 11 common test codes where at least one in four results had comparators. Three codes related to glomerular filtration rate (GFR) tests/calculations, with 31-45% of results returned with ""≥"" comparators. At least 90% of tests with numeric values 60 and 90 represented ranges (≥60 and ≥90 respectively) rather than exact values. The other tests - four blood tests (Nucleated red blood cell count, Plasma C reactive protein, Tissue transglutaminase immunoglobulin A, and Rheumatoid factor), two urine tests (albumin/microalbumin) and two faecal tests (calprotectin and quantitative faecal immunochemical test) - were returned with ""≤"" comparators (29-86%).<h4>Conclusions</h4>Comparators appear commonly in certain pathology tests in electronic health records. For most common affected tests, we expect there to be minimal implications for researchers for most use-cases. However, care should be taken around whether results falling exactly on clinical threshold values should be considered ""normal"" or ""abnormal"". Results from GFR tests/calculations cannot reliably distinguish between mild kidney disease (stage G2, 60-<90) versus healthy kidney function (90+). More broadly, health data researchers using numeric test result values should consider the impact of comparators.",,doi:https://doi.org/10.12688/wellcomeopenres.19858.1; html:https://europepmc.org/articles/PMC10904973; pdf:https://europepmc.org/articles/PMC10904973?pdf=render
 37018139,https://doi.org/10.1093/rheumatology/kead150,"COVID-19 infection, admission and death and the impact of corticosteroids among people with rare autoimmune rheumatic disease during the second wave of COVID-19 in England: results from the RECORDER Project.","Rutter M, Lanyon PC, Grainge MJ, Hubbard R, Bythell M, Stilwell P, Aston J, McPhail S, Stevens S, Pearce FA.",,"Rheumatology (Oxford, England)",2023,2023-12-01,Y,Infection; Mortality; Coronavirus; epidemiology; Shielding; Covid-19; Rare Autoimmune Rheumatic Diseases,,,"<h4>Objectives</h4>To calculate the rates of COVID-19 infection and COVID-19-related death among people with rare autoimmune rheumatic diseases (RAIRD) during the second wave of the COVID-19 pandemic in England, and describe the impact of corticosteroids on outcomes.<h4>Methods</h4>Hospital Episode Statistics data were used to identify people alive on 1 August 2020 with ICD-10 codes for RAIRD from the whole population of England. Linked national health records were used to calculate rates and rate ratios of COVID-19 infection and death up to 30 April 2021. Primary definition of COVID-19-related death was mention of COVID-19 on the death certificate. NHS Digital and Office for National Statistics general population data were used for comparison. The association between 30-day corticosteroid usage and COVID-19-related death, COVID-19-related hospital admissions and all-cause deaths was also described.<h4>Results</h4>Of 168 330 people with RAIRD, 9961 (5.92%) had a positive COVID-19 PCR test. The age-standardized infection rate ratio between RAIRD and the general population was 0.99 (95% CI: 0.97, 1.00). 1342 (0.80%) people with RAIRD died with COVID-19 on their death certificate and the age-sex-standardized mortality rate for COVID-19-related death was 2.76 (95% CI: 2.63, 2.89) times higher than in the general population. There was a dose-dependent relationship between 30-day corticosteroid usage and COVID-19-related death. There was no increase in deaths due to other causes.<h4>Conclusions</h4>During the second wave of COVID-19 in England, people with RAIRD had the same risk of COVID-19 infection but a 2.76-fold increased risk of COVID-19-related death compared with the general population, with corticosteroids associated with increased risk.",,pdf:https://academic.oup.com/rheumatology/advance-article-pdf/doi/10.1093/rheumatology/kead150/49769320/kead150.pdf; doi:https://doi.org/10.1093/rheumatology/kead150; html:https://europepmc.org/articles/PMC10691923; pdf:https://europepmc.org/articles/PMC10691923?pdf=render
 36987388,https://doi.org/10.1177/08862605231163885,Characterizing the Differences in Descriptions of Violence on Reddit During the COVID-19 Pandemic.,"Li L, Neubauer L, Stewart R, Roberts A.",,Journal of interpersonal violence,2023,2023-03-28,Y,Increase rate; Data Classification; Reddit; Violence Types,,,"Concerns have been raised over the experiences of violence such as domestic violence (DV) and intimate partner violence (IPV) during the COVID-19 pandemic. Social media such as Reddit represent an alternative outlet for reporting experiences of violence where healthcare access has been limited. This study analyzed seven violence-related subreddits to investigate the trends of different violence patterns from January 2018 to February 2022 to enhance the health-service providers' existing service or provide some new perspective for existing violence research. Specifically, we collected violence-related texts from Reddit using keyword searching and identified six major types with supervised machine learning classifiers: DV, IPV, physical violence, sexual violence, emotional violence, and nonspecific violence or others. The increase rate (IR) of each violence type was calculated and temporally compared in five phases of the pandemic. The phases include one pre-pandemic phase (<i>Phase 0</i>, the date before February 26, 2020) and four pandemic phases (<i>Phases 1-4</i>) with separation dates of June 17, 2020, September 7, 2020, and June 4, 2021. We found that the number of IPV-related posts increased most in the earliest phase; however, that for COVID-citing IPV was highest in the mid-pandemic phase. IRs for DV, IPV, and emotional violence also showed increases across all pandemic phases, with IRs of 26.9%, 58.8%, and 28.8%, respectively, from the pre-pandemic to the first pandemic phase. In the other three pandemic phases, all the IRs for these three types of violence were positive, though lower than the IRs in the first pandemic phase. The findings highlight the importance of identifying and providing help to those who suffer from such violent experiences and support the role of social media site monitoring as a means of informative surveillance for help-providing authorities and violence research groups.",,doi:https://doi.org/10.1177/08862605231163885; doi:https://doi.org/10.1177/08862605231163885; html:https://europepmc.org/articles/PMC10064198; pdf:https://europepmc.org/articles/PMC10064198?pdf=render
-36691170,https://doi.org/10.1136/bmjopen-2022-061344,"Pre-COVID-19 pandemic health-related behaviours in children (2018-2020) and association with being tested for SARS-CoV-2 and testing positive for SARS-CoV-2 (2020-2021): a retrospective cohort study using survey data linked with routine health data in Wales, UK.","Marchant E, Lowthian E, Crick T, Griffiths LJ, Fry R, Dadaczynski K, Okan O, James M, Cowley L, Torabi F, Kennedy J, Akbari A, Lyons R, Brophy S.",,BMJ open,2022,2022-09-07,Y,epidemiology; Public Health; Community Child Health; Covid-19,,,"<h4>Objectives</h4>Examine if pre-COVID-19 pandemic (prior March 2020) health-related behaviours during primary school are associated with (1) being tested for SARS-CoV-2 and (2) testing positive between 1 March 2020 and 31 August 2021.<h4>Design</h4>Retrospective cohort study using an online cohort survey (January 2018 to February 2020) linked with routine PCR SARS-CoV-2 test results.<h4>Setting</h4>Children attending primary schools in Wales (2018-2020), UK, who were part of the Health and Attainment of Pupils in a Primary Education Network (HAPPEN)_school network.<h4>Participants</h4>Complete linked records of eligible participants were obtained for n=7062 individuals. 39.1% (n=2764) were tested (age 10.6±0.9; 48.9% girls) and 8.1% (n=569) tested positive for SARS-CoV-2 (age 10.6±1.0; 54.5% girls).<h4>Main outcome measures</h4>Logistic regression of health-related behaviours and demographics were used to determine the ORs of factors associated with (1) being tested for SARS-CoV-2 and (2) testing positive for SARS-CoV-2.<h4>Results</h4>Consuming sugary snacks (1-2 days/week OR=1.24, 95% CI 1.04 to 1.49; 5-6 days/week OR=1.31, 95% CI 1.07 to 1.61; reference 0 days), can swim 25 m (OR=1.21, 95% CI 1.06 to 1.39) and age (OR=1.25, 95% CI 1.16 to 1.35) were associated with an increased likelihood of being tested for SARS-CoV-2. Eating breakfast (OR=1.52, 95% CI 1.01 to 2.27), weekly physical activity ≥60 min (1-2 days OR=1.69, 95% CI 1.04 to 2.74; 3-4 days OR=1.76, 95% CI 1.10 to 2.82; reference 0 days), out-of-school club participation (OR=1.06, 95% CI 1.02 to 1.10), can ride a bike (OR=1.39, 95% CI 1.00 to 1.93), age (OR=1.16, 95% CI 1.05 to 1.28) and girls (OR=1.21, 95% CI 1.00 to 1.46) were associated with an increased likelihood of testing positive for SARS-CoV-2. Living in least deprived areas (quintile 4 OR=0.64, 95% CI 0.46 to 0.90; quintile 5 OR=0.64, 95% CI 0.46 to 0.89) compared with the most deprived (quintile 1) was associated with a decreased likelihood.<h4>Conclusions</h4>Associations may be related to parental health literacy and monitoring behaviours. Physically active behaviours may include coparticipation with others and exposure to SARS-CoV-2. A risk-versus-benefit approach must be considered in relation to promoting these health behaviours, given the importance of health-related behaviours such as childhood physical activity for development.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/9/e061344.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-061344; html:https://europepmc.org/articles/PMC9453425; pdf:https://europepmc.org/articles/PMC9453425?pdf=render
 37068964,https://doi.org/10.3399/bjgp.2022.0301,OpenSAFELY NHS Service Restoration Observatory 2: changes in primary care clinical activity in England during the COVID-19 pandemic.,"Curtis HJ, MacKenna B, Wiedemann M, Fisher L, Croker R, Morton CE, Inglesby P, Walker AJ, Morley J, Mehrkar A, Bacon SC, Hickman G, Evans D, Ward T, Davy S, Hulme WJ, Macdonald O, Conibere R, Lewis T, Myers M, Wanninayake S, Collison K, Drury C, Samuel M, Sood H, Cipriani A, Fazel S, Sharma M, Baqir W, Bates C, Parry J, Goldacre B, OpenSAFELY Collaborative.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2023,2023-04-27,Y,Primary Health Care; General Practice; Electronic Health Records; Covid-19,,,"<h4>Background</h4>The COVID-19 pandemic has disrupted healthcare activity across a broad range of clinical services. The NHS stopped non-urgent work in March 2020, later recommending services be restored to near-normal levels before winter where possible.<h4>Aim</h4>To describe changes in the volume and variation of coded clinical activity in general practice across six clinical areas: cardiovascular disease, diabetes, mental health, female and reproductive health, screening and related procedures, and processes related to medication.<h4>Design and setting</h4>With the approval of NHS England, a cohort study was conducted of 23.8 million patient records in general practice, in situ using OpenSAFELY.<h4>Method</h4>Common primary care activities were analysed using Clinical Terms Version 3 codes and keyword searches from January 2019 to December 2020, presenting median and deciles of code usage across practices per month.<h4>Results</h4>Substantial and widespread changes in clinical activity in primary care were identified since the onset of the COVID-19 pandemic, with generally good recovery by December 2020. A few exceptions showed poor recovery and warrant further investigation, such as mental health (for example, for 'Depression interim review' the median occurrences across practices in December 2020 was down by 41.6% compared with December 2019).<h4>Conclusion</h4>Granular NHS general practice data at population-scale can be used to monitor disruptions to healthcare services and guide the development of mitigation strategies. The authors are now developing real-time monitoring dashboards for the key measures identified in this study, as well as further studies using primary care data to monitor and mitigate the indirect health impacts of COVID-19 on the NHS.",,pdf:https://bjgp.org/content/bjgp/early/2023/01/31/BJGP.2022.0301.full.pdf; doi:https://doi.org/10.3399/BJGP.2022.0301; html:https://europepmc.org/articles/PMC10131234; pdf:https://europepmc.org/articles/PMC10131234?pdf=render
 37263602,https://doi.org/10.1093/eurpub/ckad075,"Community factors and excess mortality in the COVID-19 pandemic in England, Italy and Sweden.","Parkes B, Stafoggia M, Fecht D, Davies B, Bonander C, De' Donato F, Michelozzi P, Piel FB, Strömberg U, Blangiardo M.",,European journal of public health,2023,2023-08-01,Y,,,,"<h4>Background</h4>Analyses of coronavirus disease 19 suggest specific risk factors make communities more or less vulnerable to pandemic-related deaths within countries. What is unclear is whether the characteristics affecting vulnerability of small communities within countries produce similar patterns of excess mortality across countries with different demographics and public health responses to the pandemic. Our aim is to quantify community-level variations in excess mortality within England, Italy and Sweden and identify how such spatial variability was driven by community-level characteristics.<h4>Methods</h4>We applied a two-stage Bayesian model to quantify inequalities in excess mortality in people aged 40 years and older at the community level in England, Italy and Sweden during the first year of the pandemic (March 2020-February 2021). We used community characteristics measuring deprivation, air pollution, living conditions, population density and movement of people as covariates to quantify their associations with excess mortality.<h4>Results</h4>We found just under half of communities in England (48.1%) and Italy (45.8%) had an excess mortality of over 300 per 100 000 males over the age of 40, while for Sweden that covered 23.1% of communities. We showed that deprivation is a strong predictor of excess mortality across the three countries, and communities with high levels of overcrowding were associated with higher excess mortality in England and Sweden.<h4>Conclusion</h4>These results highlight some international similarities in factors affecting mortality that will help policy makers target public health measures to increase resilience to the mortality impacts of this and future pandemics.",,pdf:https://academic.oup.com/eurpub/advance-article-pdf/doi/10.1093/eurpub/ckad075/50504334/ckad075.pdf; doi:https://doi.org/10.1093/eurpub/ckad075; html:https://europepmc.org/articles/PMC10393497; pdf:https://europepmc.org/articles/PMC10393497?pdf=render
+36691170,https://doi.org/10.1136/bmjopen-2022-061344,"Pre-COVID-19 pandemic health-related behaviours in children (2018-2020) and association with being tested for SARS-CoV-2 and testing positive for SARS-CoV-2 (2020-2021): a retrospective cohort study using survey data linked with routine health data in Wales, UK.","Marchant E, Lowthian E, Crick T, Griffiths LJ, Fry R, Dadaczynski K, Okan O, James M, Cowley L, Torabi F, Kennedy J, Akbari A, Lyons R, Brophy S.",,BMJ open,2022,2022-09-07,Y,epidemiology; Public Health; Community Child Health; Covid-19,,,"<h4>Objectives</h4>Examine if pre-COVID-19 pandemic (prior March 2020) health-related behaviours during primary school are associated with (1) being tested for SARS-CoV-2 and (2) testing positive between 1 March 2020 and 31 August 2021.<h4>Design</h4>Retrospective cohort study using an online cohort survey (January 2018 to February 2020) linked with routine PCR SARS-CoV-2 test results.<h4>Setting</h4>Children attending primary schools in Wales (2018-2020), UK, who were part of the Health and Attainment of Pupils in a Primary Education Network (HAPPEN)_school network.<h4>Participants</h4>Complete linked records of eligible participants were obtained for n=7062 individuals. 39.1% (n=2764) were tested (age 10.6±0.9; 48.9% girls) and 8.1% (n=569) tested positive for SARS-CoV-2 (age 10.6±1.0; 54.5% girls).<h4>Main outcome measures</h4>Logistic regression of health-related behaviours and demographics were used to determine the ORs of factors associated with (1) being tested for SARS-CoV-2 and (2) testing positive for SARS-CoV-2.<h4>Results</h4>Consuming sugary snacks (1-2 days/week OR=1.24, 95% CI 1.04 to 1.49; 5-6 days/week OR=1.31, 95% CI 1.07 to 1.61; reference 0 days), can swim 25 m (OR=1.21, 95% CI 1.06 to 1.39) and age (OR=1.25, 95% CI 1.16 to 1.35) were associated with an increased likelihood of being tested for SARS-CoV-2. Eating breakfast (OR=1.52, 95% CI 1.01 to 2.27), weekly physical activity ≥60 min (1-2 days OR=1.69, 95% CI 1.04 to 2.74; 3-4 days OR=1.76, 95% CI 1.10 to 2.82; reference 0 days), out-of-school club participation (OR=1.06, 95% CI 1.02 to 1.10), can ride a bike (OR=1.39, 95% CI 1.00 to 1.93), age (OR=1.16, 95% CI 1.05 to 1.28) and girls (OR=1.21, 95% CI 1.00 to 1.46) were associated with an increased likelihood of testing positive for SARS-CoV-2. Living in least deprived areas (quintile 4 OR=0.64, 95% CI 0.46 to 0.90; quintile 5 OR=0.64, 95% CI 0.46 to 0.89) compared with the most deprived (quintile 1) was associated with a decreased likelihood.<h4>Conclusions</h4>Associations may be related to parental health literacy and monitoring behaviours. Physically active behaviours may include coparticipation with others and exposure to SARS-CoV-2. A risk-versus-benefit approach must be considered in relation to promoting these health behaviours, given the importance of health-related behaviours such as childhood physical activity for development.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/9/e061344.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-061344; html:https://europepmc.org/articles/PMC9453425; pdf:https://europepmc.org/articles/PMC9453425?pdf=render
 37340474,https://doi.org/10.1186/s12916-023-02877-9,Antidepressant drug prescription and incidence of COVID-19 in mental health outpatients: a retrospective cohort study.,"Glebov OO, Mueller C, Stewart R, Aarsland D, Perera G.",,BMC medicine,2023,2023-06-21,Y,Antidepressants; Ssri; respiratory infection; Drug Repurposing; Covid-19; Sars-cov-2,,,"<h4>Background</h4>Currently, the main pharmaceutical intervention for COVID-19 is vaccination. While antidepressant (AD) drugs have shown some efficacy in treatment of symptomatic COVID-19, their preventative potential remains largely unexplored. Analysis of association between prescription of ADs and COVID-19 incidence in the population would be beneficial for assessing the utility of ADs in COVID-19 prevention.<h4>Methods</h4>Retrospective study of association between AD prescription and COVID-19 diagnosis was performed in a cohort of community-dwelling adult mental health outpatients during the 1st wave of COVID-19 pandemic in the UK. Clinical record interactive search (CRIS) was performed for mentions of ADs within 3 months preceding admission to inpatient care of the South London and Maudsley (SLaM) NHS Foundation Trust. Incidence of positive COVID-19 tests upon admission and during inpatient treatment was the primary outcome measure.<h4>Results</h4>AD mention was associated with approximately 40% lower incidence of positive COVID-19 test results when adjusted for socioeconomic parameters and physical health. This association was also observed for prescription of ADs of the selective serotonin reuptake inhibitor (SSRI) class.<h4>Conclusions</h4>This preliminary study suggests that ADs, and SSRIs in particular, may be of benefit for preventing COVID-19 infection spread in the community. The key limitations of the study are its retrospective nature and the focus on a mental health patient cohort. A more definitive assessment of AD and SSRI preventative potential warrants prospective studies in the wider demographic.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-023-02877-9; doi:https://doi.org/10.1186/s12916-023-02877-9; html:https://europepmc.org/articles/PMC10283271; pdf:https://europepmc.org/articles/PMC10283271?pdf=render
 36145196,https://doi.org/10.3390/nu14183821,Vitamin D Supplementation Does Not Influence SARS-CoV-2 Vaccine Efficacy or Immunogenicity: Sub-Studies Nested within the CORONAVIT Randomised Controlled Trial.,"Jolliffe DA, Vivaldi G, Chambers ES, Cai W, Li W, Faustini SE, Gibbons JM, Pade C, Coussens AK, Richter AG, McKnight Á, Martineau AR.",,Nutrients,2022,2022-09-16,Y,Interferon gamma; Vitamin D; Antibody; Randomised Controlled Trial; Breakthrough Sars-cov-2 Infection; Bnt162b2 Pfizer; Chadox1 Ncov-19 Oxford–astrazeneca,,,"Vitamin D deficiency has been reported to associate with the impaired development of antigen-specific responses following vaccination. We aimed to determine whether vitamin D supplements might boost the immunogenicity and efficacy of SARS-CoV-2 vaccination by conducting three sub-studies nested within the CORONAVIT randomised controlled trial, which investigated the effects of offering vitamin D supplements at a dose of 800 IU/day or 3200 IU/day vs. no offer on risk of acute respiratory infections in UK adults with circulating 25-hydroxyvitamin D concentrations <75 nmol/L. Sub-study 1 (n = 2808) investigated the effects of vitamin D supplementation on the risk of breakthrough SARS-CoV-2 infection following two doses of SARS-CoV-2 vaccine. Sub-study 2 (n = 1853) investigated the effects of vitamin D supplementation on titres of combined IgG, IgA and IgM (IgGAM) anti-Spike antibodies in eluates of dried blood spots collected after SARS-CoV-2 vaccination. Sub-study 3 (n = 100) investigated the effects of vitamin D supplementation on neutralising antibody and cellular responses in venous blood samples collected after SARS-CoV-2 vaccination. In total, 1945/2808 (69.3%) sub-study 1 participants received two doses of ChAdOx1 nCoV-19 (Oxford−AstraZeneca); the remainder received two doses of BNT162b2 (Pfizer). Mean follow-up 25(OH)D concentrations were significantly elevated in the 800 IU/day vs. no-offer group (82.5 vs. 53.6 nmol/L; mean difference 28.8 nmol/L, 95% CI 22.8−34.8) and in the 3200 IU/day vs. no offer group (105.4 vs. 53.6 nmol/L; mean difference 51.7 nmol/L, 45.1−58.4). Vitamin D supplementation did not influence the risk of breakthrough SARS-CoV-2 infection in vaccinated participants (800 IU/day vs. no offer: adjusted hazard ratio 1.28, 95% CI 0.89 to 1.84; 3200 IU/day vs. no offer: 1.17, 0.81 to 1.70). Neither did it influence IgGAM anti-Spike titres, neutralising antibody titres or IFN-γ concentrations in the supernatants of S peptide-stimulated whole blood. In conclusion, vitamin D replacement at a dose of 800 or 3200 IU/day effectively elevated 25(OH)D concentrations, but it did not influence the protective efficacy or immunogenicity of SARS-CoV-2 vaccination when given to adults who had a sub-optimal vitamin D status at baseline.",,pdf:https://www.mdpi.com/2072-6643/14/18/3821/pdf?version=1663570353; doi:https://doi.org/10.3390/nu14183821; html:https://europepmc.org/articles/PMC9506404; pdf:https://europepmc.org/articles/PMC9506404?pdf=render
 35927670,https://doi.org/10.1186/s12882-022-02902-8,Pre-operative Waterlow score and outcomes after kidney transplantation.,"Brotherton A, Evison F, Gallier S, Sharif A.",,BMC nephrology,2022,2022-08-04,Y,Mortality; Kidney transplantation; Length Of Stay; Readmission; Surrogate; Waterlow,,,"<h4>Background</h4>Waterlow scoring was introduced in the 1980s as a nursing tool to risk stratify for development of decubitus ulcers (pressure sores) and is commonly used in UK hospitals. Recent interest has focussed on its value as a pre-op surrogate marker for adverse surgical outcomes, but utility after kidney transplantation has never been explored.<h4>Methods</h4>In this single-centre observational study, data was extracted from hospital informatics systems for all kidney allograft recipients transplanted between 1<sup>st</sup> January 2007 and 30<sup>th</sup> June 2020. Waterlow scores were categorised as per national standards; 0-9 (low risk), 10-14 (at risk), 15-19 (high risk) and ≥ 20 (very high risk). Multiple imputation was used to replace missing data with substituted values. Primary outcomes of interest were post-operative length of stay, emergency re-admission within 90-days and mortality analysed by linear, logistic or Cox regression models respectively.<h4>Results</h4>Data was available for 2,041 kidney transplant patients, with baseline demographics significantly different across Waterlow categories. As a continuous variable, the median Waterlow score across the study cohort was 10 (interquartile range 8-13). As a categorical variable, Waterlow scores pre-operatively were classified as low risk (n = 557), at risk (n = 543), high risk (n = 120), very high risk (n = 27) and a large proportion of missing data (n = 794). Median length of stay in days varied significantly with pre-op Waterlow category scores, progressively getting longer with increasing severity of Waterlow category. However, no difference was observed in risk for emergency readmission within 90-days of surgery with severity of Waterlow category. Patients with 'very high risk' Waterlow scores had increased risk for mortality at 41.9% versus high risk (23.7%), at risk (17.4%) and low risk (13.4%). In adjusted analyses, 'very high risk' Waterlow group (as a categorical variable) or Waterlow score (as a continuous variable) had an independent association with increase length of stay after transplant surgery only. No association was observed between any Waterlow risk group/score with emergency 90-day readmission rates or post-transplant mortality after adjustment.<h4>Conclusions</h4>Pre-operative Waterlow scoring is a poor surrogate marker to identify kidney transplant patients at risk of emergency readmission or death and should not be utilised outside its intended use.",,pdf:https://bmcnephrol.biomedcentral.com/counter/pdf/10.1186/s12882-022-02902-8; doi:https://doi.org/10.1186/s12882-022-02902-8; html:https://europepmc.org/articles/PMC9351155; pdf:https://europepmc.org/articles/PMC9351155?pdf=render
 34158305,https://doi.org/10.1136/bmjopen-2020-048333,Association between community-based self-reported COVID-19 symptoms and social deprivation explored using symptom tracker apps: a repeated cross-sectional study in Northern Ireland.,"McKinley JM, Cutting D, Anderson N, Graham C, Johnston B, Mueller U, Atkinson PM, Van Woerden H, Bradley DT, Kee F.",,BMJ open,2021,2021-06-22,Y,Public Health; Statistics & Research Methods; Covid-19,,,"<h4>Objectives</h4>The aim of the study was to investigate the spatial and temporal relationships between the prevalence of COVID-19 symptoms in the community-level and area-level social deprivation.<h4>Design</h4>Spatial mapping, generalised linear models, using time as a factor and spatial-lag models were used to explore the relationship between self-reported COVID-19 symptom prevalence as recorded through two smartphone symptom tracker apps and a range of socioeconomic factors using a repeated cross-sectional study design.<h4>Setting</h4>In the community in Northern Ireland, UK. The analysis period included the earliest stages of non-pharmaceutical interventions and societal restrictions or 'lockdown' in 2020.<h4>Participants</h4>Users of two smartphone symptom tracker apps recording self-reported health information who recorded their location as Northern Ireland, UK.<h4>Primary outcome measures</h4>Population standardised self-reported COVID-19 symptoms and correlation between population standardised self-reported COVID-19 symptoms and area-level characteristics from measures of multiple deprivation including employment levels and population housing density, derived as the mean number of residents per household for each census super output area.<h4>Results</h4>Higher self-reported prevalence of COVID-19 symptoms was associated with the most deprived areas (p<0.001) and with those areas with the lowest employment levels (p<0.001). Higher rates of self-reported COVID-19 symptoms within the age groups, 18-24 and 25-34 years were found within the most deprived areas during the earliest stages of non-pharmaceutical interventions and societal restrictions ('lockdown').<h4>Conclusions</h4>Through spatial regression of self-reporting COVID-19 smartphone data in the community, this research shows how a lens of social deprivation can deepen our understanding of COVID-19 transmission and prevention. Our findings indicate that social inequality, as measured by area-level deprivation, is associated with disparities in potential COVID-19 infection, with higher prevalence of self-reported COVID-19 symptoms in urban areas associated with area-level social deprivation, housing density and age.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/6/e048333.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-048333; html:https://europepmc.org/articles/PMC8228811; pdf:https://europepmc.org/articles/PMC8228811?pdf=render
+36863848,https://doi.org/10.1136/archdischild-2022-325152,Characteristics and predictors of persistent symptoms post-COVID-19 in children and young people: a large community cross-sectional study in England.,"Atchison CJ, Whitaker M, Donnelly CA, Chadeau-Hyam M, Riley S, Darzi A, Ashby D, Barclay W, Cooke GS, Elliott P, Ward H.",,Archives of disease in childhood,2023,2023-03-02,Y,epidemiology; Paediatrics; Adolescent Health; Infectious Disease Medicine; Covid-19,,,"<h4>Objective</h4>To estimate the prevalence of, and associated risk factors for, persistent symptoms post-COVID-19 among children aged 5-17 years in England.<h4>Design</h4>Serial cross-sectional study.<h4>Setting</h4>Rounds 10-19 (March 2021 to March 2022) of the REal-time Assessment of Community Transmission-1 study (monthly cross-sectional surveys of random samples of the population in England).<h4>Study population</h4>Children aged 5-17 years in the community.<h4>Predictors</h4>Age, sex, ethnicity, presence of a pre-existing health condition, index of multiple deprivation, COVID-19 vaccination status and dominant UK circulating SARS-CoV-2 variant at time of symptom onset.<h4>Main outcome measures</h4>Prevalence of persistent symptoms, reported as those lasting ≥3 months post-COVID-19.<h4>Results</h4>Overall, 4.4% (95% CI 3.7 to 5.1) of 3173 5-11 year-olds and 13.3% (95% CI 12.5 to 14.1) of 6886 12-17 year-olds with prior symptomatic infection reported at least one symptom lasting ≥3 months post-COVID-19, of whom 13.5% (95% CI 8.4 to 20.9) and 10.9% (95% CI 9.0 to 13.2), respectively, reported their ability to carry out day-to-day activities was reduced 'a lot' due to their symptoms. The most common symptoms among participants with persistent symptoms were persistent coughing (27.4%) and headaches (25.4%) in children aged 5-11 years and loss or change of sense of smell (52.2%) and taste (40.7%) in participants aged 12-17 years. Higher age and having a pre-existing health condition were associated with higher odds of reporting persistent symptoms.<h4>Conclusions</h4>One in 23 5-11 year-olds and one in eight 12-17 year-olds post-COVID-19 report persistent symptoms lasting ≥3 months, of which one in nine report a large impact on performing day-to-day activities.",,pdf:https://adc.bmj.com/content/archdischild/early/2023/03/01/archdischild-2022-325152.full.pdf; doi:https://doi.org/10.1136/archdischild-2022-325152; html:https://europepmc.org/articles/PMC10313975; pdf:https://europepmc.org/articles/PMC10313975?pdf=render
 38627354,https://doi.org/10.1007/s15010-024-02235-8,"Sepsis and case fatality rates and associations with deprivation, ethnicity, and clinical characteristics: population-based case-control study with linked primary care and hospital data in England.","van Staa TP, Pate A, Martin GP, Sharma A, Dark P, Felton T, Zhong X, Bladon S, Cunningham N, Gilham EL, Brown CS, Mirfenderesky M, Palin V, Ashiru-Oredope D.",,Infection,2024,2024-04-16,Y,Sepsis; RACE; Frailty; Primary Care; Deprivation,,,"<h4>Purpose</h4>Sepsis is a life-threatening organ dysfunction caused by dysregulated host response to infection. The purpose of the study was to measure the associations of specific exposures (deprivation, ethnicity, and clinical characteristics) with incident sepsis and case fatality.<h4>Methods</h4>Two research databases in England were used including anonymized patient-level records from primary care linked to hospital admission, death certificate, and small-area deprivation. Sepsis cases aged 65-100 years were matched to up to six controls. Predictors for sepsis (including 60 clinical conditions) were evaluated using logistic and random forest models; case fatality rates were analyzed using logistic models.<h4>Results</h4>108,317 community-acquired sepsis cases were analyzed. Severe frailty was strongly associated with the risk of developing sepsis (crude odds ratio [OR] 14.93; 95% confidence interval [CI] 14.37-15.52). The quintile with most deprived patients showed an increased sepsis risk (crude OR 1.48; 95% CI 1.45-1.51) compared to least deprived quintile. Strong predictors for sepsis included antibiotic exposure in prior 2 months, being house bound, having cancer, learning disability, and diabetes mellitus. Severely frail patients had a case fatality rate of 42.0% compared to 24.0% in non-frail patients (adjusted OR 1.53; 95% CI 1.41-1.65). Sepsis cases with recent prior antibiotic exposure died less frequently compared to non-users (adjusted OR 0.7; 95% CI 0.72-0.76). Case fatality strongly decreased over calendar time.<h4>Conclusion</h4>Given the variety of predictors and their level of associations for developing sepsis, there is a need for prediction models for risk of developing sepsis that can help to target preventative antibiotic therapy.",,pdf:https://link.springer.com/content/pdf/10.1007/s15010-024-02235-8.pdf; doi:https://doi.org/10.1007/s15010-024-02235-8; html:https://europepmc.org/articles/PMC11288984; pdf:https://europepmc.org/articles/PMC11288984?pdf=render
 38633209,https://doi.org/10.3389/fepid.2024.1326306,Making predictions under interventions: a case study from the PREDICT-CVD cohort in New Zealand primary care.,"Lin L, Poppe K, Wood A, Martin GP, Peek N, Sperrin M.",,Frontiers in epidemiology,2024,2024-04-03,Y,Cardiovascular diseases; Prevention; Treatment; Causal Inference; Clinical Prediction Model,,,"<h4>Background</h4>Most existing clinical prediction models do not allow predictions under interventions. Such predictions allow predicted risk under different proposed strategies to be compared and are therefore useful to support clinical decision making. We aimed to compare methodological approaches for predicting individual level cardiovascular risk under three interventions: smoking cessation, reducing blood pressure, and reducing cholesterol.<h4>Methods</h4>We used data from the PREDICT prospective cohort study in New Zealand to calculate cardiovascular risk in a primary care setting. We compared three strategies to estimate absolute risk under intervention: (a) conditioning on hypothetical interventions in non-causal models; (b) combining existing prediction models with causal effects estimated using observational causal inference methods; and (c) combining existing prediction models with causal effects reported in published literature.<h4>Results</h4>The median absolute cardiovascular risk among smokers was 3.9%; our approaches predicted that smoking cessation reduced this to a median between a non-causal estimate of 2.5% and a causal estimate of 2.8%, depending on estimation methods. For reducing blood pressure, the proposed approaches estimated a reduction of absolute risk from a median of 4.9% to a median between 3.2% and 4.5% (both derived from causal estimation). Reducing cholesterol was estimated to reduce median absolute risk from 3.1% to between 2.2% (non-causal estimate) and 2.8% (causal estimate).<h4>Conclusions</h4>Estimated absolute risk reductions based on non-causal methods were different to those based on causal methods, and there was substantial variation in estimates within the causal methods. Researchers wishing to estimate risk under intervention should be explicit about their causal modelling assumptions and conduct sensitivity analysis by considering a range of possible approaches.",,doi:https://doi.org/10.3389/fepid.2024.1326306; html:https://europepmc.org/articles/PMC11021700; pdf:https://europepmc.org/articles/PMC11021700?pdf=render
-36863848,https://doi.org/10.1136/archdischild-2022-325152,Characteristics and predictors of persistent symptoms post-COVID-19 in children and young people: a large community cross-sectional study in England.,"Atchison CJ, Whitaker M, Donnelly CA, Chadeau-Hyam M, Riley S, Darzi A, Ashby D, Barclay W, Cooke GS, Elliott P, Ward H.",,Archives of disease in childhood,2023,2023-03-02,Y,epidemiology; Paediatrics; Adolescent Health; Infectious Disease Medicine; Covid-19,,,"<h4>Objective</h4>To estimate the prevalence of, and associated risk factors for, persistent symptoms post-COVID-19 among children aged 5-17 years in England.<h4>Design</h4>Serial cross-sectional study.<h4>Setting</h4>Rounds 10-19 (March 2021 to March 2022) of the REal-time Assessment of Community Transmission-1 study (monthly cross-sectional surveys of random samples of the population in England).<h4>Study population</h4>Children aged 5-17 years in the community.<h4>Predictors</h4>Age, sex, ethnicity, presence of a pre-existing health condition, index of multiple deprivation, COVID-19 vaccination status and dominant UK circulating SARS-CoV-2 variant at time of symptom onset.<h4>Main outcome measures</h4>Prevalence of persistent symptoms, reported as those lasting ≥3 months post-COVID-19.<h4>Results</h4>Overall, 4.4% (95% CI 3.7 to 5.1) of 3173 5-11 year-olds and 13.3% (95% CI 12.5 to 14.1) of 6886 12-17 year-olds with prior symptomatic infection reported at least one symptom lasting ≥3 months post-COVID-19, of whom 13.5% (95% CI 8.4 to 20.9) and 10.9% (95% CI 9.0 to 13.2), respectively, reported their ability to carry out day-to-day activities was reduced 'a lot' due to their symptoms. The most common symptoms among participants with persistent symptoms were persistent coughing (27.4%) and headaches (25.4%) in children aged 5-11 years and loss or change of sense of smell (52.2%) and taste (40.7%) in participants aged 12-17 years. Higher age and having a pre-existing health condition were associated with higher odds of reporting persistent symptoms.<h4>Conclusions</h4>One in 23 5-11 year-olds and one in eight 12-17 year-olds post-COVID-19 report persistent symptoms lasting ≥3 months, of which one in nine report a large impact on performing day-to-day activities.",,pdf:https://adc.bmj.com/content/archdischild/early/2023/03/01/archdischild-2022-325152.full.pdf; doi:https://doi.org/10.1136/archdischild-2022-325152; html:https://europepmc.org/articles/PMC10313975; pdf:https://europepmc.org/articles/PMC10313975?pdf=render
 34376451,https://doi.org/10.1136/bmjopen-2021-048852,Ethnic and social inequalities in COVID-19 outcomes in Scotland: protocol for early pandemic evaluation and enhanced surveillance of COVID-19 (EAVE II).,"Henery P, Vasileiou E, Hainey KJ, Buchanan D, Harrison E, Leyland AH, Alexis T, Robertson C, Agrawal U, Ritchie L, Stock SJ, McCowan C, Docherty A, Kerr S, Marple J, Wood R, Moore E, Simpson CR, Sheikh A, Katikireddi SV.",,BMJ open,2021,2021-08-10,Y,epidemiology; Public Health; Protocols & Guidelines; Covid-19,,,"<h4>Introduction</h4>Evidence from previous pandemics, and the current COVID-19 pandemic, has found that risk of infection/severity of disease is disproportionately higher for ethnic minority groups, and those in lower socioeconomic positions. It is imperative that interventions to prevent the spread of COVID-19 are targeted towards high-risk populations. We will investigate the associations between social characteristics (such as ethnicity, occupation and socioeconomic position) and COVID-19 outcomes and the extent to which characteristics/risk factors might explain observed relationships in Scotland.The primary objective of this study is to describe the epidemiology of COVID-19 by social factors. Secondary objectives are to (1) examine receipt of treatment and prevention of COVID-19 by social factors; (2) quantify ethnic/social differences in adverse COVID-19 outcomes; (3) explore potential mediators of relationships between social factors and SARS-CoV-2 infection/COVID-19 prognosis; (4) examine whether occupational COVID-19 differences differ by other social factors and (5) assess quality of ethnicity coding within National Health Service datasets.<h4>Methods and analysis</h4>We will use a national cohort comprising the adult population of Scotland who completed the 2011 Census and were living in Scotland on 31 March 2020 (~4.3 million people). Census data will be linked to the Early Assessment of Vaccine and Anti-Viral Effectiveness II cohort consisting of primary/secondary care, laboratory data and death records. Sensitivity/specificity and positive/negative predictive values will be used to assess coding quality of ethnicity. Descriptive statistics will be used to examine differences in treatment and prevention of COVID-19. Poisson/Cox regression analyses and mediation techniques will examine ethnic and social differences, and drivers of inequalities in COVID-19. Effect modification (on additive and multiplicative scales) between key variables (such as ethnicity and occupation) will be assessed.<h4>Ethics and dissemination</h4>Ethical approval was obtained from the National Research Ethics Committee, South East Scotland 02. We will present findings of this study at international conferences, in peer-reviewed journals and to policy-makers.",,doi:https://doi.org/10.1136/bmjopen-2021-048852; doi:https://doi.org/10.1136/bmjopen-2021-048852; html:https://europepmc.org/articles/PMC8359861; pdf:https://europepmc.org/articles/PMC8359861?pdf=render
 32704561,https://doi.org/10.1002/edm2.140,"Prevalence of admission plasma glucose in 'diabetes' or 'at risk' ranges in hospital emergencies with no prior diagnosis of diabetes by gender, age and ethnicity.","Ghosh S, Manley SE, Nightingale PG, Williams JA, Susarla R, Alonso-Perez I, Stratton IM, Gkoutos GV, Webber J, Luzio SD, Hanif W, Roberts GA.",,"Endocrinology, diabetes & metabolism",2020,2020-05-15,Y,Hyperglycaemia; Undiagnosed Diabetes; Emergency Admissions,,,"<h4>Aims</h4>To establish the prevalence of admission plasma glucose in 'diabetes' and 'at risk' ranges in emergency hospital admissions with no prior diagnosis of diabetes; characteristics of people with hyperglycaemia; and factors influencing glucose measurement.<h4>Methods</h4>Electronic patient records for 113 097 hospital admissions over 1 year from 2014 to 2015 included 43 201 emergencies with glucose available for 31 927 (74%) admissions, comprising 22 045 people. Data are presented for 18 965 people with no prior diagnosis of diabetes and glucose available on first attendance.<h4>Results</h4>Three quarters (14 214) were White Europeans aged 62 (43-78) years, median (IQ range); 12% (2241) South Asians 46 (32-64) years; 9% (1726) Unknown/Other ethnicities 43 (29-61) years; and 4% (784) Afro-Caribbeans 49 (33-63) years, <i>P</i> < .001. Overall, 5% (1003) had glucose in the 'diabetes' range (≥11.1 mmol/L) higher at 8% (175) for South Asians; 16% (3042) were 'at risk' (7.8-11.0 mmol/L), that is 17% (2379) White Europeans, 15% (338) South Asians, 14% (236) Unknown/Others and 11% (89) Afro-Caribbeans, <i>P</i> < .001. The prevalence for South Asians aged <30 years was 2.1% and 5.2%, respectively, 2.6% and 8.6% for Afro-Caribbeans <30 years, and 2.0% and 8.4% for White Europeans <40 years. Glucose increased with age and was more often in the 'diabetes' range for South Asians than White Europeans with South Asian men particularly affected. One third of all emergency admissions were for <24 hours with 58% of these having glucose measured compared to 82% with duration >24 hours.<h4>Conclusions</h4>Hyperglycaemia was evident in 21% of adults admitted as an emergency; various aspects related to follow-up and initial testing, age and ethnicity need to be considered by professional bodies addressing undiagnosed diabetes in hospital admissions.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/edm2.140; doi:https://doi.org/10.1002/edm2.140; html:https://europepmc.org/articles/PMC7375073; pdf:https://europepmc.org/articles/PMC7375073?pdf=render
 36536453,https://doi.org/10.1186/s41512-022-00137-7,Protocol for development and validation of postpartum cardiovascular disease (CVD) risk prediction model incorporating reproductive and pregnancy-related candidate predictors.,"Wambua S, Crowe F, Thangaratinam S, O'Reilly D, McCowan C, Brophy S, Yau C, Nirantharakumar K, Riley R, MuM-PreDiCT Group.",,Diagnostic and prognostic research,2022,2022-12-19,Y,Prognosis; Cardiovascular disease; Pregnant women; Pregnancy complications; Prediction Modeling,,,"<h4>Background</h4>Cardiovascular disease (CVD) is a leading cause of death among women. CVD is associated with reduced quality of life, significant treatment and management costs, and lost productivity. Estimating the risk of CVD would help patients at a higher risk of CVD to initiate preventive measures to reduce risk of disease. The Framingham risk score and the QRISK® score are two risk prediction models used to evaluate future CVD risk in the UK. Although the algorithms perform well in the general population, they do not take into account pregnancy complications, which are well known risk factors for CVD in women and have been highlighted in a recent umbrella review. We plan to develop a robust CVD risk prediction model to assess the additional value of pregnancy risk factors in risk prediction of CVD in women postpartum.<h4>Methods</h4>Using candidate predictors from QRISK®-3, the umbrella review identified from literature and from discussions with clinical experts and patient research partners, we will use time-to-event Cox proportional hazards models to develop and validate a 10-year risk prediction model for CVD postpartum using Clinical Practice Research Datalink (CPRD) primary care database for development and internal validation of the algorithm and the Secure Anonymised Information Linkage (SAIL) databank for external validation. We will then assess the value of additional candidate predictors to the QRISK®-3 in our internal and external validations.<h4>Discussion</h4>The developed risk prediction model will incorporate pregnancy-related factors which have been shown to be associated with future risk of CVD but have not been taken into account in current risk prediction models. Our study will therefore highlight the importance of incorporating pregnancy-related risk factors into risk prediction modeling for CVD postpartum.",,pdf:https://diagnprognres.biomedcentral.com/counter/pdf/10.1186/s41512-022-00137-7; doi:https://doi.org/10.1186/s41512-022-00137-7; html:https://europepmc.org/articles/PMC9761974; pdf:https://europepmc.org/articles/PMC9761974?pdf=render
@@ -574,74 +574,74 @@ PMC10910267,https://doi.org/,Development and evaluation of a tool to optimise in
 34458913,https://doi.org/10.1093/ije/dyab172,Potential test-negative design study bias in outbreak settings: application to Ebola vaccination in Democratic Republic of Congo.,"Pearson CAB, Edmunds WJ, Hladish TJ, Eggo RM.",,International journal of epidemiology,2022,2022-02-01,Y,Mathematical Modelling; Ebola; Outbreak Response; Drc; Test-negative Design,,,"<h4>Background</h4>Infectious disease outbreaks present unique challenges to study designs for vaccine evaluation. Test-negative design (TND) studies have previously been used to estimate vaccine effectiveness and have been proposed for Ebola virus disease (EVD) vaccines. However, there are key differences in how cases and controls are recruited during outbreaks and pandemics of novel pathogens, whcih have implications for the reliability of effectiveness estimates using this design.<h4>Methods</h4>We use a modelling approach to quantify TND bias for a prophylactic vaccine under varying study and epidemiological scenarios. Our model accounts for heterogeneity in vaccine distribution and for two potential routes to testing and recruitment into the study: self-reporting and contact-tracing. We derive conventional and hybrid TND estimators for this model and suggest ways to translate public health response data into the parameters of the model.<h4>Results</h4>Using a conventional TND study, our model finds biases in vaccine effectiveness estimates. Bias arises due to differential recruitment from self-reporting and contact-tracing, and due to clustering of vaccination. We estimate the degree of bias when recruitment route is not available, and propose a study design to eliminate the bias if recruitment route is recorded.<h4>Conclusions</h4>Hybrid TND studies can resolve the design bias with conventional TND studies applied to outbreak and pandemic response testing data, if those efforts collect individuals' routes to testing. Without route to testing, other epidemiological data will be required to estimate the magnitude of potential bias in a conventional TND study. Since these studies may need to be conducted retrospectively, public health responses should obtain these data, and generic protocols for outbreak and pandemic response studies should emphasize the need to record routes to testing.",,pdf:https://academic.oup.com/ije/article-pdf/51/1/265/42555506/dyab172.pdf; doi:https://doi.org/10.1093/ije/dyab172; html:https://europepmc.org/articles/PMC8855996; pdf:https://europepmc.org/articles/PMC8855996?pdf=render
 35902613,https://doi.org/10.1038/s41467-022-32096-4,Dynamics of competing SARS-CoV-2 variants during the Omicron epidemic in England.,"Eales O, de Oliveira Martins L, Page AJ, Wang H, Bodinier B, Tang D, Haw D, Jonnerby J, Atchison C, Ashby D, Barclay W, Taylor G, Cooke G, Ward H, Darzi A, Riley S, Elliott P, Donnelly CA, Chadeau-Hyam M.",,Nature communications,2022,2022-07-28,Y,,,,"The SARS-CoV-2 pandemic has been characterised by the regular emergence of genomic variants. With natural and vaccine-induced population immunity at high levels, evolutionary pressure favours variants better able to evade SARS-CoV-2 neutralising antibodies. The Omicron variant (first detected in November 2021) exhibited a high degree of immune evasion, leading to increased infection rates worldwide. However, estimates of the magnitude of this Omicron wave have often relied on routine testing data, which are prone to several biases. Using data from the REal-time Assessment of Community Transmission-1 (REACT-1) study, a series of cross-sectional surveys assessing prevalence of SARS-CoV-2 infection in England, we estimated the dynamics of England's Omicron wave (from 9 September 2021 to 1 March 2022). We estimate an initial peak in national Omicron prevalence of 6.89% (5.34%, 10.61%) during January 2022, followed by a resurgence in SARS-CoV-2 infections as the more transmissible Omicron sub-lineage, BA.2 replaced BA.1 and BA.1.1. Assuming the emergence of further distinct variants, intermittent epidemics of similar magnitudes may become the 'new normal'.",,pdf:https://www.nature.com/articles/s41467-022-32096-4.pdf; doi:https://doi.org/10.1038/s41467-022-32096-4; html:https://europepmc.org/articles/PMC9330949; pdf:https://europepmc.org/articles/PMC9330949?pdf=render
 35133177,https://doi.org/10.1126/science.abn8347,Rapid increase in Omicron infections in England during December 2021: REACT-1 study.,"Elliott P, Bodinier B, Eales O, Wang H, Haw D, Elliott J, Whitaker M, Jonnerby J, Tang D, Walters CE, Atchison C, Diggle PJ, Page AJ, Trotter AJ, Ashby D, Barclay W, Taylor G, Ward H, Darzi A, Cooke GS, Chadeau-Hyam M, Donnelly CA.",,"Science (New York, N.Y.)",2022,2022-02-08,Y,,,,"The unprecedented rise in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections during December 2021 was concurrent with rapid spread of the Omicron variant in England and globally. We analyzed the prevalence of SARS-CoV-2 and its dynamics in England from the end of November to mid-December 2021 among almost 100,000 participants in the REACT-1 study. Prevalence was high with rapid growth nationally and particularly in London during December 2021, with an increasing proportion of infections due to Omicron. We observed large decreases in swab positivity among mostly vaccinated older children (12 to 17 years) relative to unvaccinated younger children (5 to 11 years), and in adults who received a third (booster) vaccine dose versus two doses. Our results reinforce the importance of vaccination and booster campaigns, although additional measures have been needed to control the rapid growth of the Omicron variant.",,pdf:http://spiral.imperial.ac.uk/bitstream/10044/1/94586/2/science.abn8347.pdf; doi:https://doi.org/10.1126/science.abn8347; html:https://europepmc.org/articles/PMC8939772; pdf:https://europepmc.org/articles/PMC8939772?pdf=render
-38373998,https://doi.org/10.1186/s13073-024-01304-9,"Recent advances in polygenic scores: translation, equitability, methods and FAIR tools.","Xiang R, Kelemen M, Xu Y, Harris LW, Parkinson H, Inouye M, Lambert SA.",,Genome medicine,2024,2024-02-19,Y,transferability; Clinical Utility; Genome-wide Association Studies (Gwas); Open-access; Accessible; Interoperable; Responsible Use; Polygenic Score (Pgs); Fair (Findable; And Reusable),,,"Polygenic scores (PGS) can be used for risk stratification by quantifying individuals' genetic predisposition to disease, and many potentially clinically useful applications have been proposed. Here, we review the latest potential benefits of PGS in the clinic and challenges to implementation. PGS could augment risk stratification through combined use with traditional risk factors (demographics, disease-specific risk factors, family history, etc.), to support diagnostic pathways, to predict groups with therapeutic benefits, and to increase the efficiency of clinical trials. However, there exist challenges to maximizing the clinical utility of PGS, including FAIR (Findable, Accessible, Interoperable, and Reusable) use and standardized sharing of the genomic data needed to develop and recalculate PGS, the equitable performance of PGS across populations and ancestries, the generation of robust and reproducible PGS calculations, and the responsible communication and interpretation of results. We outline how these challenges may be overcome analytically and with more diverse data as well as highlight sustained community efforts to achieve equitable, impactful, and responsible use of PGS in healthcare.",,pdf:https://genomemedicine.biomedcentral.com/counter/pdf/10.1186/s13073-024-01304-9; doi:https://doi.org/10.1186/s13073-024-01304-9; html:https://europepmc.org/articles/PMC10875792; pdf:https://europepmc.org/articles/PMC10875792?pdf=render
-38895652,https://doi.org/10.1093/jamiaopen/ooae049,Creating a next-generation phenotype library: the health data research UK Phenotype Library.,"Thayer DS, Mumtaz S, Elmessary MA, Scanlon I, Zinnurov A, Coldea AI, Scanlon J, Chapman M, Curcin V, John A, DelPozo-Banos M, Davies H, Karwath A, Gkoutos GV, Fitzpatrick NK, Quint JK, Varma S, Milner C, Oliveira C, Parkinson H, Denaxas S, Hemingway H, Jefferson E.",,JAMIA open,2024,2024-06-17,Y,Phenotyping; Medical Informatics; Algorithms; Public Health Informatics; Electronic Health Records; Application Programming Interface,,,"<h4>Objective</h4>To enable reproducible research at scale by creating a platform that enables health data users to find, access, curate, and re-use electronic health record phenotyping algorithms.<h4>Materials and methods</h4>We undertook a structured approach to identifying requirements for a phenotype algorithm platform by engaging with key stakeholders. User experience analysis was used to inform the design, which we implemented as a web application featuring a novel metadata standard for defining phenotyping algorithms, access via Application Programming Interface (API), support for computable data flows, and version control. The application has creation and editing functionality, enabling researchers to submit phenotypes directly.<h4>Results</h4>We created and launched the Phenotype Library in October 2021. The platform currently hosts 1049 phenotype definitions defined against 40 health data sources and >200K terms across 16 medical ontologies. We present several case studies demonstrating its utility for supporting and enabling research: the library hosts curated phenotype collections for the BREATHE respiratory health research hub and the Adolescent Mental Health Data Platform, and it is supporting the development of an informatics tool to generate clinical evidence for clinical guideline development groups.<h4>Discussion</h4>This platform makes an impact by being open to all health data users and accepting all appropriate content, as well as implementing key features that have not been widely available, including managing structured metadata, access via an API, and support for computable phenotypes.<h4>Conclusions</h4>We have created the first openly available, programmatically accessible resource enabling the global health research community to store and manage phenotyping algorithms. Removing barriers to describing, sharing, and computing phenotypes will help unleash the potential benefit of health data for patients and the public.",,pdf:https://academic.oup.com/jamiaopen/article-pdf/7/2/ooae049/58255810/ooae049.pdf; doi:https://doi.org/10.1093/jamiaopen/ooae049; html:https://europepmc.org/articles/PMC11182945; pdf:https://europepmc.org/articles/PMC11182945?pdf=render
 33611594,https://doi.org/10.1093/eurjpc/zwaa155,Excess deaths in people with cardiovascular diseases during the COVID-19 pandemic.,"Banerjee A, Chen S, Pasea L, Lai AG, Katsoulis M, Denaxas S, Nafilyan V, Williams B, Wong WK, Bakhai A, Khunti K, Pillay D, Noursadeghi M, Wu H, Pareek N, Bromage D, McDonagh TA, Byrne J, Teo JTH, Shah AM, Humberstone B, Tang LV, Shah ASV, Rubboli A, Guo Y, Hu Y, Sudlow CLM, Lip GYH, Hemingway H.",,European journal of preventive cardiology,2021,2021-12-01,Y,Cardiovascular disease; Public Health; Health Policy; Global Health; Coronavirus-2019,,,"<h4>Aims</h4>Cardiovascular diseases (CVDs) increase mortality risk from coronavirus infection (COVID-19). There are also concerns that the pandemic has affected supply and demand of acute cardiovascular care. We estimated excess mortality in specific CVDs, both 'direct', through infection, and 'indirect', through changes in healthcare.<h4>Methods and results</h4>We used (i) national mortality data for England and Wales to investigate trends in non-COVID-19 and CVD excess deaths; (ii) routine data from hospitals in England (n = 2), Italy (n = 1), and China (n = 5) to assess indirect pandemic effects on referral, diagnosis, and treatment services for CVD; and (iii) population-based electronic health records from 3 862 012 individuals in England to investigate pre- and post-COVID-19 mortality for people with incident and prevalent CVD. We incorporated pre-COVID-19 risk (by age, sex, and comorbidities), estimated population COVID-19 prevalence, and estimated relative risk (RR) of mortality in those with CVD and COVID-19 compared with CVD and non-infected (RR: 1.2, 1.5, 2.0, and 3.0).Mortality data suggest indirect effects on CVD will be delayed rather than contemporaneous (peak RR 1.14). CVD service activity decreased by 60-100% compared with pre-pandemic levels in eight hospitals across China, Italy, and England. In China, activity remained below pre-COVID-19 levels for 2-3 months even after easing lockdown and is still reduced in Italy and England. For total CVD (incident and prevalent), at 10% COVID-19 prevalence, we estimated direct impact of 31 205 and 62 410 excess deaths in England (RR 1.5 and 2.0, respectively), and indirect effect of 49 932 to 99 865 deaths.<h4>Conclusion</h4>Supply and demand for CVD services have dramatically reduced across countries with potential for substantial, but avoidable, excess mortality during and after the pandemic.",,pdf:https://academic.oup.com/eurjpc/article-pdf/28/14/1599/41827245/zwaa155.pdf; doi:https://doi.org/10.1093/eurjpc/zwaa155; html:https://europepmc.org/articles/PMC7928969; pdf:https://europepmc.org/articles/PMC7928969?pdf=render
 35418418,https://doi.org/10.1136/bmjopen-2021-049441,"Health checks for adults with intellectual disability and association with survival rates: a linked electronic records matched cohort study in Wales, UK.","Kennedy N, Kennedy J, Kerr M, Dredge S, Brophy S.",,BMJ open,2022,2022-04-13,Y,epidemiology; Quality In Health Care; General Medicine (See Internal Medicine),,,"<h4>Objective</h4>To examine if mortality rates are lower in people with intellectual disability who have had a health check compared with those who have not had health checks.<h4>Setting</h4>General practice records of 26 954 people with an intellectual disability in Wales between 2005-2017, of which 7650 (28.4%) with a health check were matched 1:2 with those without a health check.<h4>Primary outcome measure</h4>Office of National Statistics mortality data; a Cox regression was utilised to examine time to death adjusted for comorbidities and gender.<h4>Results</h4>Patients who had a health check were stratified by those who (1) had a confirmed health check, that is, Read Code for a health check (n=7650 (28.4 %)) and (2) had no evidence of receiving a health check in their medical record. Patients with a health check were matched for age at time of health check with two people who did not have a health check. The health check was associated with improved survival for those with autism or Down's Syndrome (HR 0.58 (95% CI 0.37 to 0.91) and HR 0.76 (95% CI 0.64 to 0.91), respectively). There was no evidence of improved survival for those diagnosed with diabetes or cancer. The people who had a health check were more likely to be older, have epilepsy and less likely to have autism or Down's syndrome.<h4>Conclusions</h4>Health checks are likely to influence survival if started before a person is diagnosed with a chronic condition, especially for people with autism or Down's syndrome.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/4/e049441.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-049441; html:https://europepmc.org/articles/PMC9013997; pdf:https://europepmc.org/articles/PMC9013997?pdf=render
+38895652,https://doi.org/10.1093/jamiaopen/ooae049,Creating a next-generation phenotype library: the health data research UK Phenotype Library.,"Thayer DS, Mumtaz S, Elmessary MA, Scanlon I, Zinnurov A, Coldea AI, Scanlon J, Chapman M, Curcin V, John A, DelPozo-Banos M, Davies H, Karwath A, Gkoutos GV, Fitzpatrick NK, Quint JK, Varma S, Milner C, Oliveira C, Parkinson H, Denaxas S, Hemingway H, Jefferson E.",,JAMIA open,2024,2024-06-17,Y,Phenotyping; Medical Informatics; Algorithms; Public Health Informatics; Electronic Health Records; Application Programming Interface,,,"<h4>Objective</h4>To enable reproducible research at scale by creating a platform that enables health data users to find, access, curate, and re-use electronic health record phenotyping algorithms.<h4>Materials and methods</h4>We undertook a structured approach to identifying requirements for a phenotype algorithm platform by engaging with key stakeholders. User experience analysis was used to inform the design, which we implemented as a web application featuring a novel metadata standard for defining phenotyping algorithms, access via Application Programming Interface (API), support for computable data flows, and version control. The application has creation and editing functionality, enabling researchers to submit phenotypes directly.<h4>Results</h4>We created and launched the Phenotype Library in October 2021. The platform currently hosts 1049 phenotype definitions defined against 40 health data sources and >200K terms across 16 medical ontologies. We present several case studies demonstrating its utility for supporting and enabling research: the library hosts curated phenotype collections for the BREATHE respiratory health research hub and the Adolescent Mental Health Data Platform, and it is supporting the development of an informatics tool to generate clinical evidence for clinical guideline development groups.<h4>Discussion</h4>This platform makes an impact by being open to all health data users and accepting all appropriate content, as well as implementing key features that have not been widely available, including managing structured metadata, access via an API, and support for computable phenotypes.<h4>Conclusions</h4>We have created the first openly available, programmatically accessible resource enabling the global health research community to store and manage phenotyping algorithms. Removing barriers to describing, sharing, and computing phenotypes will help unleash the potential benefit of health data for patients and the public.",,pdf:https://academic.oup.com/jamiaopen/article-pdf/7/2/ooae049/58255810/ooae049.pdf; doi:https://doi.org/10.1093/jamiaopen/ooae049; html:https://europepmc.org/articles/PMC11182945; pdf:https://europepmc.org/articles/PMC11182945?pdf=render
+38373998,https://doi.org/10.1186/s13073-024-01304-9,"Recent advances in polygenic scores: translation, equitability, methods and FAIR tools.","Xiang R, Kelemen M, Xu Y, Harris LW, Parkinson H, Inouye M, Lambert SA.",,Genome medicine,2024,2024-02-19,Y,transferability; Clinical Utility; Genome-wide Association Studies (Gwas); Open-access; Accessible; Interoperable; Responsible Use; Polygenic Score (Pgs); Fair (Findable; And Reusable),,,"Polygenic scores (PGS) can be used for risk stratification by quantifying individuals' genetic predisposition to disease, and many potentially clinically useful applications have been proposed. Here, we review the latest potential benefits of PGS in the clinic and challenges to implementation. PGS could augment risk stratification through combined use with traditional risk factors (demographics, disease-specific risk factors, family history, etc.), to support diagnostic pathways, to predict groups with therapeutic benefits, and to increase the efficiency of clinical trials. However, there exist challenges to maximizing the clinical utility of PGS, including FAIR (Findable, Accessible, Interoperable, and Reusable) use and standardized sharing of the genomic data needed to develop and recalculate PGS, the equitable performance of PGS across populations and ancestries, the generation of robust and reproducible PGS calculations, and the responsible communication and interpretation of results. We outline how these challenges may be overcome analytically and with more diverse data as well as highlight sustained community efforts to achieve equitable, impactful, and responsible use of PGS in healthcare.",,pdf:https://genomemedicine.biomedcentral.com/counter/pdf/10.1186/s13073-024-01304-9; doi:https://doi.org/10.1186/s13073-024-01304-9; html:https://europepmc.org/articles/PMC10875792; pdf:https://europepmc.org/articles/PMC10875792?pdf=render
 35197134,https://doi.org/10.1192/bjo.2022.24,Birth without intervention in women with severe mental illness: cohort study.,"Taylor C, Stewart R, Gibson R, Pasupathy D, Shetty H, Howard L.",,BJPsych open,2022,2022-02-24,Y,Schizophrenia; epidemiology; Perinatal Psychiatry; Bipolar Affective Disorders; Birth Without Intervention,,,"<h4>Summary</h4>The rate of normal birth outcomes (i.e. full-term births without intervention) for women with severe mental illness (SMI - psychotic and bipolar disorders) is not known. We examined rates of birth without intervention (spontaneous labour onset, spontaneous vaginal delivery without instruments, no episiotomy and no indication of pre- or post-delivery anaesthesia) in women with SMI (584 pregnancies) compared with a control population (70 942 pregnancies). Outcome ratios were calculated standardising for age. Women with SMI were less likely to have a birth without intervention (29.5%) relative to the control population (36.8%) (standardised outcome ratio 0.74, 95% CI 0.63-0.87).",,pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/4FEB5E5A08973A5347ABA87F440CF09B/S2056472422000242a.pdf/div-class-title-birth-without-intervention-in-women-with-severe-mental-illness-cohort-study-div.pdf; doi:https://doi.org/10.1192/bjo.2022.24; html:https://europepmc.org/articles/PMC8935938; pdf:https://europepmc.org/articles/PMC8935938?pdf=render
 35310465,https://doi.org/10.23889/ijpds.v5i4.1697,"Validating the QCOVID risk prediction algorithm for risk of mortality from COVID-19 in the adult population in Wales, UK.","Lyons J, Nafilyan V, Akbari A, Davies G, Griffiths R, Harrison EM, Hippisley-Cox J, Hollinghurst J, Khunti K, North L, Sheikh A, Torabi F, Lyons RA.",,International journal of population data science,2020,2020-01-01,Y,Risk Prediction Models; Sail Databank; Covid-19 Outcomes; Population Data-Linkage; Qcovid Algorithm,,,"<h4>Introduction</h4>COVID-19 risk prediction algorithms can be used to identify at-risk individuals from short-term serious adverse COVID-19 outcomes such as hospitalisation and death. It is important to validate these algorithms in different and diverse populations to help guide risk management decisions and target vaccination and treatment programs to the most vulnerable individuals in society.<h4>Objectives</h4>To validate externally the QCOVID risk prediction algorithm that predicts mortality outcomes from COVID-19 in the adult population of Wales, UK.<h4>Methods</h4>We conducted a retrospective cohort study using routinely collected individual-level data held in the Secure Anonymised Information Linkage (SAIL) Databank. The cohort included individuals aged between 19 and 100 years, living in Wales on 24<sup>th</sup> January 2020, registered with a SAIL-providing general practice, and followed-up to death or study end (28<sup>th</sup> July 2020). Demographic, primary and secondary healthcare, and dispensing data were used to derive all the predictor variables used to develop the published QCOVID algorithm. Mortality data were used to define time to confirmed or suspected COVID-19 death. Performance metrics, including R<sup>2</sup> values (explained variation), Brier scores, and measures of discrimination and calibration were calculated for two periods (24<sup>th</sup> January-30<sup>th</sup> April 2020 and 1<sup>st</sup> May-28<sup>th</sup> July 2020) to assess algorithm performance.<h4>Results</h4>1,956,760 individuals were included. 1,192 (0.06%) and 610 (0.03%) COVID-19 deaths occurred in the first and second time periods, respectively. The algorithms fitted the Welsh data and population well, explaining 68.8% (95% CI: 66.9-70.4) of the variation in time to death, Harrell's C statistic: 0.929 (95% CI: 0.921-0.937) and D statistic: 3.036 (95% CI: 2.913-3.159) for males in the first period. Similar results were found for females and in the second time period for both sexes.<h4>Conclusions</h4>The QCOVID algorithm developed in England can be used for public health risk management for the adult Welsh population.",,pdf:https://ijpds.org/article/download/1697/3337; doi:https://doi.org/10.23889/ijpds.v5i4.1697; html:https://europepmc.org/articles/PMC8900650; pdf:https://europepmc.org/articles/PMC8900650?pdf=render
 38200587,https://doi.org/10.1093/bioinformatics/btae012,Pitfalls of machine learning models for protein-protein interaction networks.,"Lannelongue L, Inouye M.",,"Bioinformatics (Oxford, England)",2024,2024-02-01,Y,,,,"<h4>Motivation</h4>Protein-protein interactions (PPIs) are essential to understanding biological pathways as well as their roles in development and disease. Computational tools, based on classic machine learning, have been successful at predicting PPIs in silico, but the lack of consistent and reliable frameworks for this task has led to network models that are difficult to compare and discrepancies between algorithms that remain unexplained.<h4>Results</h4>To better understand the underlying inference mechanisms that underpin these models, we designed an open-source framework for benchmarking that accounts for a range of biological and statistical pitfalls while facilitating reproducibility. We use it to shed light on the impact of network topology and how different algorithms deal with highly connected proteins. By studying functional genomics-based and sequence-based models on human PPIs, we show their complementarity as the former performs best on lone proteins while the latter specializes in interactions involving hubs. We also show that algorithm design has little impact on performance with functional genomic data. We replicate our results between both human and S. cerevisiae data and demonstrate that models using functional genomics are better suited to PPI prediction across species. With rapidly increasing amounts of sequence and functional genomics data, our study provides a principled foundation for future construction, comparison, and application of PPI networks.<h4>Availability and implementation</h4>The code and data are available on GitHub: https://github.com/Llannelongue/B4PPI.",,pdf:https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae012/55399607/btae012.pdf; doi:https://doi.org/10.1093/bioinformatics/btae012; html:https://europepmc.org/articles/PMC10868344; pdf:https://europepmc.org/articles/PMC10868344?pdf=render
 37337233,https://doi.org/10.1186/s12916-023-02921-8,Trajectories of cardiac troponin in the decades before cardiovascular death: a longitudinal cohort study.,"Kimenai DM, Anand A, de Bakker M, Shipley M, Fujisawa T, Lyngbakken MN, Hveem K, Omland T, Valencia-Hernández CA, Lindbohm JV, Kivimaki M, Singh-Manoux A, Strachan FE, Shah ASV, Kardys I, Boersma E, Brunner EJ, Mills NL.",,BMC medicine,2023,2023-06-19,Y,cardiac troponin; risk factors; Outcome; General Population,,,"<h4>Background</h4>High-sensitivity cardiac troponin testing is a promising tool for cardiovascular risk prediction, but whether serial testing can dynamically predict risk is uncertain. We evaluated the trajectory of cardiac troponin I in the years prior to a cardiovascular event in the general population, and determine whether serial measurements could track risk within individuals.<h4>Methods</h4>In the Whitehall II cohort, high-sensitivity cardiac troponin I concentrations were measured on three occasions over a 15-year period. Time trajectories of troponin were constructed in those who died from cardiovascular disease compared to those who survived or died from other causes during follow up and these were externally validated in the HUNT Study. A joint model that adjusts for cardiovascular risk factors was used to estimate risk of cardiovascular death using serial troponin measurements.<h4>Results</h4>In 7,293 individuals (mean 58 ± 7 years, 29.4% women) cardiovascular and non-cardiovascular death occurred in 281 (3.9%) and 914 (12.5%) individuals (median follow-up 21.4 years), respectively. Troponin concentrations increased in those dying from cardiovascular disease with a steeper trajectory compared to those surviving or dying from other causes in Whitehall and HUNT (P<sub>interaction</sub> < 0.05 for both). The joint model demonstrated an independent association between temporal evolution of troponin and risk of cardiovascular death (HR per doubling, 1.45, 95% CI,1.33-1.75).<h4>Conclusions</h4>Cardiac troponin I concentrations increased in those dying from cardiovascular disease compared to those surviving or dying from other causes over the preceding decades. Serial cardiac troponin testing in the general population has potential to track future cardiovascular risk.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-023-02921-8; doi:https://doi.org/10.1186/s12916-023-02921-8; html:https://europepmc.org/articles/PMC10280894; pdf:https://europepmc.org/articles/PMC10280894?pdf=render
-38459430,https://doi.org/10.1186/s12859-024-05682-0,Bayesian inference for identifying tumour-specific cancer dependencies through integration of ex-vivo drug response assays and drug-protein profiling.,"Xing H, Yau C.",,BMC bioinformatics,2024,2024-03-08,Y,Gaussian Process; Chemical Perturbation; Spike-and-slab Regression; Tumor-specific Molecular Dependencies,,,"The identification of tumor-specific molecular dependencies is essential for the development of effective cancer therapies. Genetic and chemical perturbations are powerful tools for discovering these dependencies. Even though chemical perturbations can be applied to primary cancer samples at large scale, the interpretation of experiment outcomes is often complicated by the fact that one chemical compound can affect multiple proteins. To overcome this challenge, Batzilla et al. (PLoS Comput Biol 18(8): e1010438, 2022) proposed DepInfeR, a regularized multi-response regression model designed to identify and estimate specific molecular dependencies of individual cancers from their ex-vivo drug sensitivity profiles. Inspired by their work, we propose a Bayesian extension to DepInfeR. Our proposed approach offers several advantages over DepInfeR, including e.g. the ability to handle missing values in both protein-drug affinity and drug sensitivity profiles without the need for data pre-processing steps such as imputation. Moreover, our approach uses Gaussian Processes to capture more complex molecular dependency structures, and provides probabilistic statements about whether a protein in the protein-drug affinity profiles is informative to the drug sensitivity profiles. Simulation studies demonstrate that our proposed approach achieves better prediction accuracy, and is able to discover unreported dependency structures.",,pdf:https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05682-0; doi:https://doi.org/10.1186/s12859-024-05682-0; html:https://europepmc.org/articles/PMC10921766; pdf:https://europepmc.org/articles/PMC10921766?pdf=render
 30474191,https://doi.org/10.1111/dme.13870,Utility of HbA<sub>1c</sub> assessment in people with diabetes awaiting liver transplantation.,"Bhattacharjee D, Vracar S, Round RA, Nightingale PG, Williams JA, Gkoutos GV, Stratton IM, Parker R, Luzio SD, Webber J, Manley SE, Roberts GA, Ghosh S.",,Diabetic medicine : a journal of the British Diabetic Association,2019,2019-04-30,Y,,The Human Phenome,,"<h4>Aims</h4>To investigate the relationship between HbA<sub>1c</sub> and glucose in people with co-existing liver disease and diabetes awaiting transplant, and in those with diabetes but no liver disease.<h4>Methods</h4>HbA<sub>1c</sub> and random plasma glucose data were collected for 125 people with diabetes without liver disease and for 29 people awaiting liver transplant with diabetes and cirrhosis. Cirrhosis was caused by non-alcoholic fatty liver disease, hepatitis C, alcoholic liver disease, hereditary haemochromatosis, polycystic liver/kidneys, cryptogenic/non-cirrhotic portal hypertension and α-1-antitrypsin-related disease.<h4>Results</h4>The median (interquartile range) age of the diabetes with cirrhosis group was 55 (49-63) years compared to 60 (50-71) years (P=0.13) in the group without cirrhosis. In the diabetes with cirrhosis group there were 21 men (72%) compared with 86 men (69%) in the group with diabetes and no cirrhosis (P=0.82). Of the group with diabetes and cirrhosis, 27 people (93%) were of white European ethnicity, two (7%) were South Asian and none was of Afro-Caribbean/other ethnicity compared with 94 (75%), 16 (13%), 10 (8%)/5 (4%), respectively, in the group with diabetes and no cirrhosis (P=0.20). Median (interquartile range) HbA<sub>1c</sub> was 41 (32-56) mmol/mol [5.9 (5.1-7.3)%] vs 61 (52-70) mmol/mol [7.7 (6.9-8.6)%] (P<0.001), respectively, in the diabetes with cirrhosis group vs the diabetes without cirrhosis group. The glucose concentrations were 8.4 (7.0-11.2) mmol/l vs 7.3 (5.2-11.5) mmol/l (P=0.17). HbA<sub>1c</sub> was depressed by 20 mmol/mol (1.8%; P<0.001) in 28 participants with cirrhosis but elevated by 28 mmol/mol (2.6%) in the participant with α-1-antitrypsin disorder. Those with cirrhosis and depressed HbA<sub>1c</sub> had fewer larger erythrocytes, and higher red cell distribution width and reticulocyte count. This was reflected in the positive association of glucose with mean cell volume (r=0.39) and haemoglobin level (r=0.49) and the negative association for HbA<sub>1c</sub> (r=-0.28 and r=-0.26, respectively) in the diabetes group with cirrhosis.<h4>Conclusion</h4>HbA<sub>1c</sub> is not an appropriate test for blood glucose in people with cirrhosis and diabetes awaiting transplant as it reflects altered erythrocyte presentation.","The aim of this article was to investigate the relationship between HbA1c and glucose in patients with diabetes awaiting transplant due to a co-existing liver disease, and in those with diabetes but no liver disease. Statistical analyses results indicated that HbA1c is not an appropriate test for blood glucose in people with cirrhosis and diabetes awaiting transplant, and it might cause misdiagnosis of diabetes and inappropirate clinical care in people with cirrhotic liver disease.",pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/dme.13870; doi:https://doi.org/10.1111/dme.13870; html:https://europepmc.org/articles/PMC6850030; pdf:https://europepmc.org/articles/PMC6850030?pdf=render
 32576605,https://doi.org/10.1136/jech-2020-214051,Efficacy of contact tracing for the containment of the 2019 novel coronavirus (COVID-19).,"Keeling MJ, Hollingsworth TD, Read JM.",,Journal of epidemiology and community health,2020,2020-06-23,Y,epidemiology; Communicable Diseases; Public Health Policy; Disease Modeling,,,"<h4>Objective</h4>Contact tracing is a central public health response to infectious disease outbreaks, especially in the early stages of an outbreak when specific treatments are limited. Importation of novel coronavirus (COVID-19) from China and elsewhere into the UK highlights the need to understand the impact of contact tracing as a control measure.<h4>Design</h4>Detailed survey information on social encounters from over 5800 respondents is coupled to predictive models of contact tracing and control. This is used to investigate the likely efficacy of contact tracing and the distribution of secondary cases that may go untraced.<h4>Results</h4>Taking recent estimates for COVID-19 transmission we predict that under effective contact tracing less than 1 in 6 cases will generate any subsequent untraced infections, although this comes at a high logistical burden with an average of 36 individuals traced per case. Changes to the definition of a close contact can reduce this burden, but with increased risk of untraced cases; we find that tracing using a contact definition requiring more than 4 hours of contact is unlikely to control spread.<h4>Conclusions</h4>The current contact tracing strategy within the UK is likely to identify a sufficient proportion of infected individuals such that subsequent spread could be prevented, although the ultimate success will depend on the rapid detection of cases and isolation of contacts. Given the burden of tracing a large number of contacts to find new cases, there is the potential the system could be overwhelmed if imports of infection occur at a rapid rate.",,pdf:https://jech.bmj.com/content/jech/74/10/861.full.pdf; doi:https://doi.org/10.1136/jech-2020-214051; html:https://europepmc.org/articles/PMC7307459; pdf:https://europepmc.org/articles/PMC7307459?pdf=render
+38459430,https://doi.org/10.1186/s12859-024-05682-0,Bayesian inference for identifying tumour-specific cancer dependencies through integration of ex-vivo drug response assays and drug-protein profiling.,"Xing H, Yau C.",,BMC bioinformatics,2024,2024-03-08,Y,Gaussian Process; Chemical Perturbation; Spike-and-slab Regression; Tumor-specific Molecular Dependencies,,,"The identification of tumor-specific molecular dependencies is essential for the development of effective cancer therapies. Genetic and chemical perturbations are powerful tools for discovering these dependencies. Even though chemical perturbations can be applied to primary cancer samples at large scale, the interpretation of experiment outcomes is often complicated by the fact that one chemical compound can affect multiple proteins. To overcome this challenge, Batzilla et al. (PLoS Comput Biol 18(8): e1010438, 2022) proposed DepInfeR, a regularized multi-response regression model designed to identify and estimate specific molecular dependencies of individual cancers from their ex-vivo drug sensitivity profiles. Inspired by their work, we propose a Bayesian extension to DepInfeR. Our proposed approach offers several advantages over DepInfeR, including e.g. the ability to handle missing values in both protein-drug affinity and drug sensitivity profiles without the need for data pre-processing steps such as imputation. Moreover, our approach uses Gaussian Processes to capture more complex molecular dependency structures, and provides probabilistic statements about whether a protein in the protein-drug affinity profiles is informative to the drug sensitivity profiles. Simulation studies demonstrate that our proposed approach achieves better prediction accuracy, and is able to discover unreported dependency structures.",,pdf:https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05682-0; doi:https://doi.org/10.1186/s12859-024-05682-0; html:https://europepmc.org/articles/PMC10921766; pdf:https://europepmc.org/articles/PMC10921766?pdf=render
 36481043,https://doi.org/10.1016/s2468-1253(22)00389-2,Neutralising antibody potency against SARS-CoV-2 wild-type and omicron BA.1 and BA.4/5 variants in patients with inflammatory bowel disease treated with infliximab and vedolizumab after three doses of COVID-19 vaccine (CLARITY IBD): an analysis of a prospective multicentre cohort study.,"Liu Z, Le K, Zhou X, Alexander JL, Lin S, Bewshea C, Chanchlani N, Nice R, McDonald TJ, Lamb CA, Sebastian S, Kok K, Lees CW, Hart AL, Pollok RC, Boyton RJ, Altmann DM, Pollock KM, Goodhand JR, Kennedy NA, Ahmad T, Powell N, CLARITY study investigators.",,The lancet. Gastroenterology & hepatology,2023,2022-12-05,Y,,,,"<h4>Background</h4>Anti-TNF drugs, such as infliximab, are associated with attenuated antibody responses after SARS-CoV-2 vaccination. We aimed to determine how the anti-TNF drug infliximab and the anti-integrin drug vedolizumab affect vaccine-induced neutralising antibodies against highly transmissible omicron (B.1.1.529) BA.1, and BA.4 and BA.5 (hereafter BA.4/5) SARS-CoV-2 variants, which possess the ability to evade host immunity and, together with emerging sublineages, are now the dominating variants causing current waves of infection.<h4>Methods</h4>CLARITY IBD is a prospective, multicentre, observational cohort study investigating the effect of infliximab and vedolizumab on SARS-CoV-2 infection and vaccination in patients with inflammatory bowel disease (IBD). Patients aged 5 years and older with a diagnosis of IBD and being treated with infliximab or vedolizumab for 6 weeks or longer were recruited from infusion units at 92 hospitals in the UK. In this analysis, we included participants who had received uninterrupted biological therapy since recruitment and without a previous SARS-CoV-2 infection. The primary outcome was neutralising antibody responses against SARS-CoV-2 wild-type and omicron subvariants BA.1 and BA.4/5 after three doses of SARS-CoV-2 vaccine. We constructed Cox proportional hazards models to investigate the risk of breakthrough infection in relation to neutralising antibody titres. The study is registered with the ISRCTN registry, ISRCTN45176516, and is closed to accrual.<h4>Findings</h4>Between Sept 22 and Dec 23, 2020, 7224 patients with IBD were recruited to the CLARITY IBD study, of whom 1288 had no previous SARS-CoV-2 infection after three doses of SARS-CoV-2 vaccine and were established on either infliximab (n=871) or vedolizumab (n=417) and included in this study (median age was 46·1 years [IQR 33·6-58·2], 610 [47·4%] were female, 671 [52·1%] were male, 1209 [93·9%] were White, and 46 [3·6%] were Asian). After three doses of SARS-CoV-2 vaccine, 50% neutralising titres (NT50s) were significantly lower in patients treated with infliximab than in those treated with vedolizumab, against wild-type (geometric mean 2062 [95% CI 1720-2473] vs 3440 [2939-4026]; p<0·0001), BA.1 (107·3 [86·40-133·2] vs 648·9 [523·5-804·5]; p<0·0001), and BA.4/5 (40·63 [31·99-51·60] vs 223·0 [183·1-271·4]; p<0·0001) variants. Breakthrough infection was significantly more frequent in patients treated with infliximab (119 [13·7%; 95% CI 11·5-16·2] of 871) than in those treated with vedolizumab (29 [7·0% [4·8-10·0] of 417; p=0·00040). Cox proportional hazards models of time to breakthrough infection after the third dose of vaccine showed infliximab treatment to be associated with a higher hazard risk than treatment with vedolizumab (hazard ratio [HR] 1·71 [95% CI 1·08-2·71]; p=0·022). Among participants who had a breakthrough infection, we found that higher neutralising antibody titres against BA.4/5 were associated with a lower hazard risk and, hence, a longer time to breakthrough infection (HR 0·87 [0·79-0·95]; p=0·0028).<h4>Interpretation</h4>Our findings underline the importance of continued SARS-CoV-2 vaccination programmes, including second-generation bivalent vaccines, especially in patient subgroups where vaccine immunogenicity and efficacy might be reduced, such as those on anti-TNF therapies.<h4>Funding</h4>Royal Devon University Healthcare NHS Foundation Trust; Hull University Teaching Hospital NHS Trust; NIHR Imperial Biomedical Research Centre; Crohn's and Colitis UK; Guts UK; National Core Studies Immunity Programme, UK Research and Innovation; and unrestricted educational grants from F Hoffmann-La Roche, Biogen, Celltrion Healthcare, Takeda, and Galapagos.",,doi:https://doi.org/10.1016/s2468-1253(22)00389-2; doi:https://doi.org/10.1016/S2468-1253(22)00389-2; html:https://europepmc.org/articles/PMC9757903; pdf:https://europepmc.org/articles/PMC9757903?pdf=render
 35332197,https://doi.org/10.1038/s41598-022-08690-3,Identifying multimorbidity clusters in an unselected population of hospitalised patients.,"Robertson L, Vieira R, Butler J, Johnston M, Sawhney S, Black C.",,Scientific reports,2022,2022-03-24,Y,,,,"Multimorbidity (multiple coexisting chronic health conditions) is common and increasing worldwide, and makes care challenging for both patients and healthcare systems. To ensure care is patient-centred rather than specialty-centred, it is important to know which conditions commonly occur together and identify the corresponding patient profile. To date, no studies have described multimorbidity clusters within an unselected hospital population. Our aim was to identify and characterise multimorbidity clusters, in a large, unselected hospitalised patient population. Linked inpatient hospital episode data were used to identify adults admitted to hospital in Grampian, Scotland in 2014 who had ≥ 2 of 30 chronic conditions diagnosed in the 5 years prior. Cluster analysis (Gower distance and Partitioning around Medoids) was used to identify groups of patients with similar conditions. Clusters of conditions were defined based on clinical review and assessment of prevalence within patient groups and labelled according to the most prevalent condition. Patient profiles for each group were described by age, sex, admission type, deprivation and urban-rural area of residence. 11,389 of 41,545 hospitalised patients (27%) had ≥ 2 conditions. Ten clusters of conditions were identified: hypertension; asthma; alcohol misuse; chronic kidney disease and diabetes; chronic kidney disease; chronic pain; cancer; chronic heart failure; diabetes; hypothyroidism. Age ranged from 51 (alcohol misuse) to 79 (chronic heart failure). Women were a higher proportion in the chronic pain and hypothyroidism clusters. The proportion of patients from the most deprived quintile of the population ranged from 6% (hypertension) to 14% (alcohol misuse). Identifying clusters of conditions in hospital patients is a first step towards identifying opportunities to target patient-centred care towards people with unmet needs, leading to improved outcomes and increased efficiency. Here we have demonstrated the face validity of cluster analysis as an exploratory method for identifying clusters of conditions in hospitalised patients with multimorbidity.",,pdf:https://www.nature.com/articles/s41598-022-08690-3.pdf; doi:https://doi.org/10.1038/s41598-022-08690-3; html:https://europepmc.org/articles/PMC8948299; pdf:https://europepmc.org/articles/PMC8948299?pdf=render
 37311808,https://doi.org/10.1038/s41467-023-39193-y,"Natural history of long-COVID in a nationwide, population cohort study.","Hastie CE, Lowe DJ, McAuley A, Mills NL, Winter AJ, Black C, Scott JT, O'Donnell CA, Blane DN, Browne S, Ibbotson TR, Pell JP.",,Nature communications,2023,2023-06-13,Y,,,,"Previous studies on the natural history of long-COVID have been few and selective. Without comparison groups, disease progression cannot be differentiated from symptoms originating from other causes. The Long-COVID in Scotland Study (Long-CISS) is a Scotland-wide, general population cohort of adults who had laboratory-confirmed SARS-CoV-2 infection matched to PCR-negative adults. Serial, self-completed, online questionnaires collected information on pre-existing health conditions and current health six, 12 and 18 months after index test. Of those with previous symptomatic infection, 35% reported persistent incomplete/no recovery, 12% improvement and 12% deterioration. At six and 12 months, one or more symptom was reported by 71.5% and 70.7% respectively of those previously infected, compared with 53.5% and 56.5% of those never infected. Altered taste, smell and confusion improved over time compared to the never infected group and adjusted for confounders. Conversely, late onset dry and productive cough, and hearing problems were more likely following SARS-CoV-2 infection.",,pdf:https://www.nature.com/articles/s41467-023-39193-y.pdf; doi:https://doi.org/10.1038/s41467-023-39193-y; html:https://europepmc.org/articles/PMC10263377; pdf:https://europepmc.org/articles/PMC10263377?pdf=render
 33243817,https://doi.org/10.1136/bmjopen-2020-042813,COVID-19 in Pregnancy in Scotland (COPS): protocol for an observational study using linked Scottish national data.,"Stock SJ, McAllister D, Vasileiou E, Simpson CR, Stagg HR, Agrawal U, McCowan C, Hopkins L, Donaghy J, Ritchie L, Robertson C, Sheikh A, Wood R.",,BMJ open,2020,2020-11-26,Y,Obstetrics; epidemiology; Neonatology; Perinatology; Covid-19,,,"<h4>Introduction</h4>The effects of SARS-CoV-2 in pregnancy are not fully delineated. We will describe the incidence of COVID-19 in pregnancy at population level in Scotland, in a prospective cohort study using linked data. We will determine associations between COVID-19 and adverse pregnancy, neonatal and maternal outcomes and the proportion of confirmed cases of SARS-CoV-2 infection in neonates associated with maternal COVID-19.<h4>Methods and analysis</h4>Prospective cohort study using national linked data sets. We will include all women in Scotland, UK, who were pregnant on or became pregnant after, 1 March 2020 (the date of the first confirmed case of SARS-CoV-2 infection in Scotland) and all births in Scotland from 1 March 2020 onwards. Individual-level data will be extracted from data sets containing details of all livebirths, stillbirth, terminations of pregnancy and miscarriages and ectopic pregnancies treated in hospital or attending general practice. Records will be linked within the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) platform, which includes primary care records, virology and serology results and details of COVID-19 Community Hubs and Assessment Centre contacts and deaths. We will perform analyses using definitions for confirmed, probable and possible COVID-19 and report serology results (where available). Outcomes will include congenital anomaly, miscarriage, stillbirth, termination of pregnancy, preterm birth, neonatal infection, severe maternal disease and maternal deaths. We will perform descriptive analyses and appropriate modelling, adjusting for demographic and pregnancy characteristics and the presence of comorbidities. The cohort will provide a platform for future studies of the effectiveness and safety of therapeutic interventions and immunisations for COVID-19 and their effects on childhood and developmental outcomes.<h4>Ethics and dissemination</h4>COVID-19 in Pregnancy in Scotland is a substudy of EAVE II(, which has approval from the National Research Ethics Service Committee. Findings will be reported to Scottish Government, Public Health Scotland and published in peer-reviewed journals.",,pdf:https://bmjopen.bmj.com/content/bmjopen/10/11/e042813.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-042813; html:https://europepmc.org/articles/PMC7691999; pdf:https://europepmc.org/articles/PMC7691999?pdf=render
 39250923,https://doi.org/10.1016/s2213-8587(24)00219-5,Sodium-glucose co-transporter-2 inhibitors for hospitalised patients with COVID-19: a prospective meta-analysis of randomised trials.,"Vale C, Godolphin PJ, Fisher D, Horby PW, Kosiborod MN, Hochman JS, Webster K, Higgins JPT, Althouse AD, Berwanger O, Furtado RHM, Gasparyan SB, Haynes R, Koch GG, Landray M, Leifer E, Marshall J, Murthy S, Neal MD, Staplin N, Diaz J, Sterne JAC, Shankar-Hari M, WHO Rapid Evidence Appraisal for COVID-19 Therapies (REACT) Working Group.",,The lancet. Diabetes & endocrinology,2024,2024-09-06,N,,,,"<h4>Background</h4>Sodium-glucose co-transporter-2 (SGLT2) inhibitors have been proposed as a potential treatment for adults hospitalised with COVID-19, due to their potential anti-inflammatory and endothelial protective effects. Published evidence from randomised control trials (RCTs) does not provide evidence of benefit. We aimed to estimate the effect of oral administration of SGLT2 inhibitors compared with usual care or placebo in adults hospitalised with COVID-19.<h4>Methods</h4>Eligible RCTs that estimated the effect of oral administration of SGLT2 inhibitors compared with usual care or placebo on 28-day all-cause mortality (primary outcome) were included in this prospective meta-analysis. The primary safety outcome was ketoacidosis by 28 days. Trials were identified through systematic searches of ClinicalTrials.gov, EudraCT, and the WHO ISRCTN registry between Nov 1, 2022 and Jan 31, 2023. The search terms were ""random*"" AND ""COVID"" AND each SGLT2i, not restricted by trial status or language. Individual searches were then combined. Prespecified summary outcome data, overall and within subgroups of interest, were provided by each trial. The primary analyses were inverse variance weighted meta-analysis of odds ratios (ORs). Risk of bias was assessed using the Cochrane Risk of Bias tool. This study was registered with PROSPERO, CRD42023406442.<h4>Findings</h4>Three eligible trials randomly assigned 6096 participants (3025 to the SGLT2 inhibitor group and 3071 to the usual care or placebo group). 2381 (39%) patients were women and 1547 (25%) had type 2 diabetes at randomisation. By 28 days, there were 351 deaths in the SGLT2 inhibitor group and 382 deaths in the usual care or placebo group (summary OR 0·93 [95% CI 0·79-1·08]; p=0·33, I<sup>2</sup> for inconsistency across trials 0%). The risk of bias was assessed as being low. Ketoacidosis was observed in seven participants in the SGLT2 inhibitor group and two patients in the usual care or placebo group.<h4>Interpretation</h4>Although administration of SGLT2 inhibitor was safe, we found no clear evidence that adding SGLT2 inhibitor therapy improved outcomes in patients hospitalised with COVID-19 compared with usual care or placebo. These data do not support the use of SGLT2 inhibitors as standard treatment in adults hospitalised for COVID-19.<h4>Funding</h4>None.",,doi:https://doi.org/10.1016/S2213-8587(24)00219-5
 32877922,https://doi.org/10.1093/gerona/glaa216,Frailty Is Associated With Neutrophil Dysfunction Which Is Correctable With Phosphoinositol-3-Kinase Inhibitors.,"Wilson D, Drew W, Jasper A, Crisford H, Nightingale P, Newby P, Jackson T, Lord JM, Sapey E.",,"The journals of gerontology. Series A, Biological sciences and medical sciences",2020,2020-11-01,Y,Inflammation; Proteinases; innate immunity; Comorbidity,,,"Neutrophil dysfunction has been described with age, appears exaggerated in infection, with altered phosphoinositol signaling a potential mechanism. However, functional aging is heterogeneous. Frailty is a negative health status and is more common in older adults. We hypothesized that neutrophil migration may be compromised in frailty, associated with the degree of frailty experienced by the older person. We compared measures of frailty, neutrophil function, and systemic inflammation in 40 young and 77 older community-dwelling adults in the United Kingdom. Systemic neutrophils exhibited an age-associated reduction in the accuracy of migration (chemotaxis) which was further blunted with frailty. The degree of migratory inaccuracy correlated with physical (adjusted hand grip strength) and cognitive (Stroop test) markers of frailty. Regression analysis demonstrated that age, Charlson comorbidity index, and frailty index were able to predict neutrophil chemotaxis. Reduced chemotaxis of neutrophils from frail adults could be reversed using selective PI3K inhibitors. Exposure of neutrophils from young adults to plasma from chronically inflamed frail older adults could not recapitulate the migratory deficit in vitro, and there were no relationships with systemic inflammation and neutrophil dysfunction. Frailty exaggerated the neutrophil deficits seen with advanced age but aspects of the frailty-associated deficit in neutrophil function are rescuable and thus potentially form a therapeutic target to improve outcomes from infection in older adults.",,pdf:https://academic.oup.com/biomedgerontology/article-pdf/75/12/2320/34289886/glaa216.pdf; doi:https://doi.org/10.1093/gerona/glaa216; html:https://europepmc.org/articles/PMC7662170; pdf:https://europepmc.org/articles/PMC7662170?pdf=render
-37408471,https://doi.org/10.1093/eurheartj/ehad424,The CODE-EHR global framework: lifting the veil on health record data.,"Asselbergs FW, Kotecha D.",,European heart journal,2023,2023-09-01,N,,,,,,pdf:https://academic.oup.com/eurheartj/advance-article-pdf/doi/10.1093/eurheartj/ehad424/50827856/ehad424.pdf; doi:https://doi.org/10.1093/eurheartj/ehad424
 34722933,https://doi.org/10.12688/wellcomeopenres.16507.1,The international Perinatal Outcomes in the Pandemic (iPOP) study: protocol.,"Stock SJ, Zoega H, Brockway M, Mulholland RH, Miller JE, Been JV, Wood R, Abok II, Alshaikh B, Ayede AI, Bacchini F, Bhutta ZA, Brew BK, Brook J, Calvert C, Campbell-Yeo M, Chan D, Chirombo J, Connor KL, Daly M, Einarsdóttir K, Fantasia I, Franklin M, Fraser A, Håberg SE, Hui L, Huicho L, Magnus MC, Morris AD, Nagy-Bonnard L, Nassar N, Nyadanu SD, Iyabode Olabisi D, Palmer KR, Pedersen LH, Pereira G, Racine-Poon A, Ranger M, Rihs T, Saner C, Sheikh A, Swift EM, Tooke L, Urquia ML, Whitehead C, Yilgwan C, Rodriguez N, Burgner D, Azad MB, iPOP Study Team.",,Wellcome open research,2021,2021-02-02,Y,Stillbirth; Low Birth Weight; Preterm Birth; Global Trends; Perinatal Outcomes; Covid-19; Pandemic Lockdowns,,,"Preterm birth is the leading cause of infant death worldwide, but the causes of preterm birth are largely unknown. During the early COVID-19 lockdowns, dramatic reductions in preterm birth were reported; however, these trends may be offset by increases in stillbirth rates. It is important to study these trends globally as the pandemic continues, and to understand the underlying cause(s). Lockdowns have dramatically impacted maternal workload, access to healthcare, hygiene practices, and air pollution - all of which could impact perinatal outcomes and might affect pregnant women differently in different regions of the world. In the international Perinatal Outcomes in the Pandemic (iPOP) Study, we will seize the unique opportunity offered by the COVID-19 pandemic to answer urgent questions about perinatal health. In the first two study phases, we will use population-based aggregate data and standardized outcome definitions to: 1) Determine rates of preterm birth, low birth weight, and stillbirth and describe changes during lockdowns; and assess if these changes are consistent globally, or differ by region and income setting, 2) Determine if the magnitude of changes in adverse perinatal outcomes during lockdown are modified by regional differences in COVID-19 infection rates, lockdown stringency, adherence to lockdown measures, air quality, or other social and economic markers, obtained from publicly available datasets. We will undertake an interrupted time series analysis covering births from January 2015 through July 2020. The iPOP Study will involve at least 121 researchers in 37 countries, including obstetricians, neonatologists, epidemiologists, public health researchers, environmental scientists, and policymakers. We will leverage the most disruptive and widespread ""natural experiment"" of our lifetime to make rapid discoveries about preterm birth. Whether the COVID-19 pandemic is worsening or unexpectedly improving perinatal outcomes, our research will provide critical new information to shape prenatal care strategies throughout (and well beyond) the pandemic.",,doi:https://doi.org/10.12688/wellcomeopenres.16507.1; html:https://europepmc.org/articles/PMC8524299; pdf:https://europepmc.org/articles/PMC8524299?pdf=render
-37596262,https://doi.org/10.1038/s41467-023-40679-y,A genome-wide association study of blood cell morphology identifies cellular proteins implicated in disease aetiology.,"Akbari P, Vuckovic D, Stefanucci L, Jiang T, Kundu K, Kreuzhuber R, Bao EL, Collins JH, Downes K, Grassi L, Guerrero JA, Kaptoge S, Knight JC, Meacham S, Sambrook J, Seyres D, Stegle O, Verboon JM, Walter K, Watkins NA, Danesh J, Roberts DJ, Di Angelantonio E, Sankaran VG, Frontini M, Burgess S, Kuijpers T, Peters JE, Butterworth AS, Ouwehand WH, Soranzo N, Astle WJ.",,Nature communications,2023,2023-08-18,Y,,,,"Blood cells contain functionally important intracellular structures, such as granules, critical to immunity and thrombosis. Quantitative variation in these structures has not been subjected previously to large-scale genetic analysis. We perform genome-wide association studies of 63 flow-cytometry derived cellular phenotypes-including cell-type specific measures of granularity, nucleic acid content and reactivity-in 41,515 participants in the INTERVAL study. We identify 2172 distinct variant-trait associations, including associations near genes coding for proteins in organelles implicated in inflammatory and thrombotic diseases. By integrating with epigenetic data we show that many intracellular structures are likely to be determined in immature precursor cells. By integrating with proteomic data we identify the transcription factor FOG2 as an early regulator of platelet formation and α-granularity. Finally, we show that colocalisation of our associations with disease risk signals can suggest aetiological cell-types-variants in IL2RA and ITGA4 respectively mirror the known effects of daclizumab in multiple sclerosis and vedolizumab in inflammatory bowel disease.",,doi:https://doi.org/10.1038/s41467-023-40679-y; html:https://europepmc.org/articles/PMC10439125; pdf:https://europepmc.org/articles/PMC10439125?pdf=render
+37408471,https://doi.org/10.1093/eurheartj/ehad424,The CODE-EHR global framework: lifting the veil on health record data.,"Asselbergs FW, Kotecha D.",,European heart journal,2023,2023-09-01,N,,,,,,pdf:https://academic.oup.com/eurheartj/advance-article-pdf/doi/10.1093/eurheartj/ehad424/50827856/ehad424.pdf; doi:https://doi.org/10.1093/eurheartj/ehad424
 37927438,https://doi.org/10.1016/j.lanepe.2023.100741,Comparative effectiveness of nirmatrelvir/ritonavir versus sotrovimab and molnupiravir for preventing severe COVID-19 outcomes in non-hospitalised high-risk patients during Omicron waves: observational cohort study using the OpenSAFELY platform.,"Zheng B, Tazare J, Nab L, Green AC, Curtis HJ, Mahalingasivam V, Herrett EL, Costello RE, Eggo RM, Speed V, Bacon SC, Bates C, Parry J, Cockburn J, Hester F, Harper S, Schaffer AL, Hulme WJ, Mehrkar A, Evans SJ, MacKenna B, Goldacre B, Douglas IJ, Tomlinson LA, OpenSAFELY Collaborative.",,The Lancet regional health. Europe,2023,2023-10-08,Y,Comparative Effectiveness; Real-world Data; Covid-19; Sotrovimab; Paxlovid,,,"<h4>Background</h4>Timely evidence of the comparative effectiveness between COVID-19 therapies in real-world settings is needed to inform clinical care. This study aimed to compare the effectiveness of nirmatrelvir/ritonavir versus sotrovimab and molnupiravir in preventing severe COVID-19 outcomes in non-hospitalised high-risk COVID-19 adult patients during Omicron waves.<h4>Methods</h4>With the approval of NHS England, we conducted a real-world cohort study using the OpenSAFELY-TPP platform. Patient-level primary care data were obtained from 24 million people in England and were securely linked with data on COVID-19 infection and therapeutics, hospital admission, and death, covering a period where both nirmatrelvir/ritonavir and sotrovimab were first-line treatment options in community settings (February 10, 2022-November 27, 2022). Molnupiravir (third-line option) was used as an exploratory comparator to nirmatrelvir/ritonavir, both of which were antivirals. Cox proportional hazards model stratified by area was used to compare the risk of 28-day COVID-19 related hospitalisation/death across treatment groups.<h4>Findings</h4>A total of 9026 eligible patients treated with nirmatrelvir/ritonavir (n = 5704) and sotrovimab (n = 3322) were included in the main analysis. The mean age was 52.7 (SD = 14.9) years and 93% (8436/9026) had three or more COVID-19 vaccinations. Within 28 days after treatment initiation, 55/9026 (0.61%) COVID-19 related hospitalisations/deaths were observed (34/5704 [0.60%] treated with nirmatrelvir/ritonavir and 21/3322 [0.63%] with sotrovimab). After adjusting for demographics, high-risk cohort categories, vaccination status, calendar time, body mass index and other comorbidities, we observed no significant difference in outcome risk between nirmatrelvir/ritonavir and sotrovimab users (HR = 0.89, 95% CI: 0.48-1.63; P = 0.698). Results from propensity score weighted model also showed non-significant difference between treatment groups (HR = 0.82, 95% CI: 0.45-1.52; P = 0.535). The exploratory analysis comparing nirmatrelvir/ritonavir users with 1041 molnupiravir users (13/1041 [1.25%] COVID-19 related hospitalisations/deaths) showed an association in favour of nirmatrelvir/ritonavir (HR = 0.45, 95% CI: 0.22-0.94; P = 0.033).<h4>Interpretation</h4>In routine care of non-hospitalised high-risk adult patients with COVID-19 in England, no substantial difference in the risk of severe COVID-19 outcomes was observed between those who received nirmatrelvir/ritonavir and sotrovimab between February and November 2022, when Omicron subvariants BA.2, BA.5, or BQ.1 were dominant.<h4>Funding</h4>UK Research and Innovation, Wellcome Trust, UK Medical Research Council, National Institute for Health and Care Research, and Health Data Research UK.",,doi:https://doi.org/10.1016/j.lanepe.2023.100741; doi:https://doi.org/10.1016/j.lanepe.2023.100741; html:https://europepmc.org/articles/PMC10624988; pdf:https://europepmc.org/articles/PMC10624988?pdf=render
+37596262,https://doi.org/10.1038/s41467-023-40679-y,A genome-wide association study of blood cell morphology identifies cellular proteins implicated in disease aetiology.,"Akbari P, Vuckovic D, Stefanucci L, Jiang T, Kundu K, Kreuzhuber R, Bao EL, Collins JH, Downes K, Grassi L, Guerrero JA, Kaptoge S, Knight JC, Meacham S, Sambrook J, Seyres D, Stegle O, Verboon JM, Walter K, Watkins NA, Danesh J, Roberts DJ, Di Angelantonio E, Sankaran VG, Frontini M, Burgess S, Kuijpers T, Peters JE, Butterworth AS, Ouwehand WH, Soranzo N, Astle WJ.",,Nature communications,2023,2023-08-18,Y,,,,"Blood cells contain functionally important intracellular structures, such as granules, critical to immunity and thrombosis. Quantitative variation in these structures has not been subjected previously to large-scale genetic analysis. We perform genome-wide association studies of 63 flow-cytometry derived cellular phenotypes-including cell-type specific measures of granularity, nucleic acid content and reactivity-in 41,515 participants in the INTERVAL study. We identify 2172 distinct variant-trait associations, including associations near genes coding for proteins in organelles implicated in inflammatory and thrombotic diseases. By integrating with epigenetic data we show that many intracellular structures are likely to be determined in immature precursor cells. By integrating with proteomic data we identify the transcription factor FOG2 as an early regulator of platelet formation and α-granularity. Finally, we show that colocalisation of our associations with disease risk signals can suggest aetiological cell-types-variants in IL2RA and ITGA4 respectively mirror the known effects of daclizumab in multiple sclerosis and vedolizumab in inflammatory bowel disease.",,doi:https://doi.org/10.1038/s41467-023-40679-y; html:https://europepmc.org/articles/PMC10439125; pdf:https://europepmc.org/articles/PMC10439125?pdf=render
 35677101,https://doi.org/10.23889/ijpds.v5i4.1715,"Impact of COVID-19 pandemic on community medication dispensing: a national cohort analysis in Wales, UK.","Torabi F, Akbari A, Bedston S, Davies G, Abbasizanjani H, Gravenor M, Griffiths R, Harris D, Jenkins N, Lyons J, Morris A, North L, Halcox J, Lyons RA.",,International journal of population data science,2020,2020-01-01,Y,Public Health; Covid-19; Dispensed Medication; Community Dispensing; Interactive Dispensing Dashboard,,,"<h4>Background</h4>Population-level information on dispensed medication provides insight on the distribution of treated morbidities, particularly if linked to other population-scale data at an individual-level.<h4>Objective</h4>To evaluate the impact of COVID-19 on dispensing patterns of medications.<h4>Methods</h4>Retrospective observational study using population-scale, individual-level dispensing records in Wales, UK. Total dispensed drug items for the population between 1 <sup><i>st</i></sup> January 2016 and 31 <sup><i>st</i></sup> December 2019 (3-years, pre-COVID-19) were compared to 2020 with follow up until 27 <sup><i>th</i></sup> July 2021 (COVID-19 period). We compared trends across all years and British National Formulary (BNF) chapters and highlighted the trends in three major chapters for 2019-21: 1-Cardiovascular system (CVD); 2-Central Nervous System (CNS); 3-Immunological & Vaccine. We developed an interactive dashboard to enable monitoring of changes as the pandemic evolves.<h4>Result</h4>Amongst all BNF chapters, 73,410,543 items were dispensed in 2020 compared to 74,121,180 items in 2019 demonstrating -0.96% relative decrease in 2020. Comparison of monthly patterns showed average difference (D) of -59,220 and average Relative Change (RC) of -0.74% between the number of dispensed items in 2020 and 2019. Maximum RC was observed in March 2020 (D = +1,224,909 and RC = +20.62), followed by second peak in June 2020 (D = +257,920, RC = +4.50%). A third peak was observed in September 2020 (D = +264,138, RC = +4.35%). Large increases in March 2020 were observed for CVD and CNS medications across all age groups. The Immunological and Vaccine products dropped to very low levels across all age groups and all months (including the March dispensing peak).<h4>Conclusions</h4>Reconfiguration of routine clinical services during COVID-19 led to substantial changes in community pharmacy drug dispensing. This change may contribute to a long-term burden of COVID-19, raising the importance of a comprehensive and timely monitoring of changes for evaluation of the potential impact on clinical care and outcomes.",,pdf:https://ijpds.org/article/download/1715/3382; doi:https://doi.org/10.23889/ijpds.v5i4.1715; html:https://europepmc.org/articles/PMC9135049; pdf:https://europepmc.org/articles/PMC9135049?pdf=render
 38839194,https://doi.org/10.1016/j.ajcnut.2024.03.018,Waist-to-height ratio and body fat percentage as risk factors for ischemic cardiovascular disease: a prospective cohort study from UK Biobank.,"Feng Q, Bešević J, Conroy M, Omiyale W, Woodward M, Lacey B, Allen N.",,The American journal of clinical nutrition,2024,2024-05-09,Y,Myocardial infarction; Ischemic stroke; Body Fat Percentage; Uk Biobank; Waist-to-height Ratio; Ischemic Cardiovascular Diseases,,,"<h4>Background</h4>The independent effect of waist-to-height ratio (WHtR) and body fat percentage (BF%) on ischemic cardiovascular disease (CVD) remains uncertain.<h4>Objectives</h4>This study aimed to investigate the independent associations of WHtR and BF% with ischemic CVD.<h4>Methods</h4>This prospective cohort study used data from the UK Biobank. BF% was calculated as fat mass divided by body weight, measured by bioimpedance. Cox models estimated hazard ratios (HRs) with 95% confidence intervals (CIs) for overall and sex-specific associations of BF% and WHtR with risks of ischemic CVD and its main subtypes [myocardial infarction (MI) and ischemic stroke (IS)], adjusted for a range of potential confounders, including mutual adjustment for BF% and WHtR.<h4>Results</h4>In total, 468,333 participants without existing CVD were included in the analysis. During 12 y of follow-up, 20,151 ischemic CVD events, 13,604 MIs, and 6681 ISs were recorded. WHtR was linearly associated with ischemic CVD, MI, and IS, with an HR per 5% increase of 1.23 (95% CI: 1.20, 1.25), 1.24 (95% CI: 1.21, 1.27), and 1.22 (95% CI: 1.18, 1.26), respectively, independent of BF%. A stronger association between WHtR and MI was seen in females than in males. The association of BF% with these outcomes was substantially attenuated in both sexes after adjustment for WHtR. For example, in females, the HR (highest compared with lowest fifth) was reduced from 1.94 (95% CI: 1.76, 2.15) to 1.04 (95% CI: 0.90, 1.01) for ischemic CVD, from 2.04 (95% CI: 1.79, 2.32) to 0.97 (95% CI: 0.81, 1.16) for MI, and from 1.81 (95% CI: 1.54, 2.13) to 1.07 (95% CI: 0.85, 1.33) for IS.<h4>Conclusions</h4>WHtR, when used as a proxy measure for central obesity, is linearly associated with ischemic CVD in both sexes, which is independent of BF%. In contrast, the relationship of BF% with these health outcomes is predominantly driven by its correlation with WHtR.",,doi:https://doi.org/10.1016/j.ajcnut.2024.03.018; html:https://europepmc.org/articles/PMC11196863; pdf:https://europepmc.org/articles/PMC11196863?pdf=render
 38191614,https://doi.org/10.1038/s41591-023-02686-w,A common framework for health data governance standards.,"Torabi F, Squires E, Orton C, Heys S, Ford D, Lyons RA, Thompson S.",,Nature medicine,2024,2024-01-01,N,,,,,,doi:https://doi.org/10.1038/s41591-023-02686-w
 35726508,https://doi.org/10.1177/10398562221103117,Improving quantification of anticholinergic burden using the Anticholinergic Effect on Cognition Scale - a healthcare improvement study in a geriatric ward setting.,"Balasundaram B, Ang WST, Stewart R, Bishara D, Ooi CH, Li F, Akram F, Eu Kwek AB.",,Australasian psychiatry : bulletin of Royal Australian and New Zealand College of Psychiatrists,2022,2022-06-21,Y,Dementia; Delirium; Anticholinergic drugs; Anticholinergic Burden Scales; Anticholinergic Effect On Cognition Scale,,,"<h4>Objective</h4>Anticholinergic burden refers to the cumulative effects of taking multiple medications with anticholinergic effects. This study was carried out in a public hospital in Singapore, aimed to improve and achieve a 100% comprehensive identification and review of measured, anticholinergic burden in a geriatric psychiatry liaison service to geriatric wards. We evaluated changes in pre-to post-assessment anticholinergic burden scores and trainee feedback.<h4>Method</h4>Plan Do Study Act methodology was employed, and Anticholinergic Effect on Cognition scale (AEC) was implemented as the study intervention. A survey instrument evaluated trainee feedback.<h4>Results</h4>There was no measured anticholinergic burden in a baseline of 170 assessments. 75 liaison psychiatry assessments were conducted between June and November 2021 in two cycles. 94.7% of pre-assessments (at the time of assessment) and 71.1% of post-assessments (following assessment) had a record of AEC scores in clinical documentation in cycle one, improving in the second cycle to 100%, 94.6%, respectively. A high post-assessment AEC score of 3 and over reduced from 15.8% in cycle one to 5.4% in cycle two. The trainee feedback suggested an enriching educational experience.<h4>Conclusions</h4>Using the AEC scale, the findings support the feasibility of comprehensive identification and review of measured anticholinergic burden in older people with neurocognitive disorders.",,doi:https://doi.org/10.1177/10398562221103117; doi:https://doi.org/10.1177/10398562221103117; html:https://europepmc.org/articles/PMC9379386; pdf:https://europepmc.org/articles/PMC9379386?pdf=render
-34786063,https://doi.org/,Immune infiltration and prognostic and diagnostic use of LGALS4 in colon adenocarcinoma and bladder urothelial carcinoma.,"Acharjee A, Agarwal P, Nash K, Bano S, Rahman T, Gkoutos GV.",,American journal of translational research,2021,2021-10-15,N,Biomarker; Translational Research; Immune Infiltration; Omics Integration; Blca; Lgals4,,,"Colon adenocarcinoma (COAD) is a common tumor of the gastrointestinal tract with a high mortality rate. Current research has identified many genes associated with immune infiltration that play a vital role in the development of COAD. In this study, we analysed the prognostic and diagnostic features of such immune-related genes in the context of colonic adenocarcinoma (COAD). We analysed 17 overlapping gene expression profiles of COAD and healthy samples obtained from TCGA-COAD and public single-cell sequencing resources, to identify potential therapeutic COAD targets. We evaluated the abundance of immune infiltration with those genes using the TIMER (Tumor Immune Estimation Resource) deconvolution method. Subsequently, we developed predictive and survival models to assess the prognostic value of these genes. The LGALS4 (Galectin-4) gene was found to be significantly (P<0.05) downregulated in COAD and bladder urothelial carcinoma (BLCA) compared to healthy samples. We identified LGALS4 as a prognostic and diagnostic marker for multiple cancer types, including COAD and BLCA. Our analysis reveals a series of novel candidate drug targets, as well as candidate molecular markers, that may explain the pathogenesis of COAD and BLCA. LGALS4 gene is associated with multiple cancer types and is a possible prognostic, as well as diagnostic, marker of COAD and BLCA.",,html:https://europepmc.org/articles/PMC8581917; pdf:https://europepmc.org/articles/PMC8581917?pdf=render
-34693751,https://doi.org/10.1177/14799731211053332,The diagnosis of asthma. Can physiological tests of small airways function help?,"Almeshari MA, Stockley J, Sapey E.",,Chronic respiratory disease,2021,2021-01-01,Y,Diagnosis; Asthma; Spirometry; Oscillometry; Small Airways Function,,,"Asthma is a common, chronic, and heterogeneous disease with a global impact and substantial economic costs. It is also associated with significant mortality and morbidity and the burden of undiagnosed asthma is significant. Asthma can be difficult to diagnose as there is no gold standard test and, while spirometry is central in diagnosing asthma, it may not be sufficient to confirm or exclude the diagnosis. The most commonly reported spirometric measures (forced expiratory volume in one second (FEV<sub>1</sub>) and forced vital capacity assess function in the larger airways. However, small airway dysfunction is highly prevalent in asthma and some studies suggest small airway involvement is one of the earliest disease manifestations. Moreover, there are new inhaled therapies with ultrafine particles that are specifically designed to target the small airways. Potentially, tests of small airways may more accurately diagnose early or mild asthma and assess the response to treatment than spirometry. Furthermore, some assessment techniques do not rely on forced ventilatory manoeuvres and may, therefore, be easier for certain groups to perform. This review discusses the current evidence of small airways tests in asthma and future research that may be needed to further assess their utility.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/14799731211053332; doi:https://doi.org/10.1177/14799731211053332; html:https://europepmc.org/articles/PMC8543738; pdf:https://europepmc.org/articles/PMC8543738?pdf=render
 33565992,https://doi.org/10.2196/22164,Identifying Myocardial Infarction Using Hierarchical Template Matching-Based Myocardial Strain: Algorithm Development and Usability Study.,"Bhalodiya JM, Palit A, Giblin G, Tiwari MK, Prasad SK, Bhudia SK, Arvanitis TN, Williams MA.",,JMIR medical informatics,2021,2021-02-10,Y,Myocardium; Strain; Myocardial infarction; Left ventricle,,,"<h4>Background</h4>Myocardial infarction (MI; location and extent of infarction) can be determined by late enhancement cardiac magnetic resonance (CMR) imaging, which requires the injection of a potentially harmful gadolinium-based contrast agent (GBCA). Alternatively, emerging research in the area of myocardial strain has shown potential to identify MI using strain values.<h4>Objective</h4>This study aims to identify the location of MI by developing an applied algorithmic method of circumferential strain (CS) values, which are derived through a novel hierarchical template matching (HTM) method.<h4>Methods</h4>HTM-based CS H-spread from end-diastole to end-systole was used to develop an applied method. Grid-tagging magnetic resonance imaging was used to calculate strain values in the left ventricular (LV) myocardium, followed by the 16-segment American Heart Association model. The data set was used with k-fold cross-validation to estimate the percentage reduction of H-spread among infarcted and noninfarcted LV segments. A total of 43 participants (38 MI and 5 healthy) who underwent CMR imaging were retrospectively selected. Infarcted segments detected by using this method were validated by comparison with late enhancement CMR, and the diagnostic performance of the applied algorithmic method was evaluated with a receiver operating characteristic curve test.<h4>Results</h4>The H-spread of the CS was reduced in infarcted segments compared with noninfarcted segments of the LV. The reductions were 30% in basal segments, 30% in midventricular segments, and 20% in apical LV segments. The diagnostic accuracy of detection, using the reported method, was represented by area under the curve values, which were 0.85, 0.82, and 0.87 for basal, midventricular, and apical slices, respectively, demonstrating good agreement with the late-gadolinium enhancement-based detections.<h4>Conclusions</h4>The proposed applied algorithmic method has the potential to accurately identify the location of infarcted LV segments without the administration of late-gadolinium enhancement. Such an approach adds the potential to safely identify MI, potentially reduce patient scanning time, and extend the utility of CMR in patients who are contraindicated for the use of GBCA.",,pdf:https://medinform.jmir.org/2021/2/e22164/PDF; doi:https://doi.org/10.2196/22164; html:https://europepmc.org/articles/PMC7904396
+34693751,https://doi.org/10.1177/14799731211053332,The diagnosis of asthma. Can physiological tests of small airways function help?,"Almeshari MA, Stockley J, Sapey E.",,Chronic respiratory disease,2021,2021-01-01,Y,Diagnosis; Asthma; Spirometry; Oscillometry; Small Airways Function,,,"Asthma is a common, chronic, and heterogeneous disease with a global impact and substantial economic costs. It is also associated with significant mortality and morbidity and the burden of undiagnosed asthma is significant. Asthma can be difficult to diagnose as there is no gold standard test and, while spirometry is central in diagnosing asthma, it may not be sufficient to confirm or exclude the diagnosis. The most commonly reported spirometric measures (forced expiratory volume in one second (FEV<sub>1</sub>) and forced vital capacity assess function in the larger airways. However, small airway dysfunction is highly prevalent in asthma and some studies suggest small airway involvement is one of the earliest disease manifestations. Moreover, there are new inhaled therapies with ultrafine particles that are specifically designed to target the small airways. Potentially, tests of small airways may more accurately diagnose early or mild asthma and assess the response to treatment than spirometry. Furthermore, some assessment techniques do not rely on forced ventilatory manoeuvres and may, therefore, be easier for certain groups to perform. This review discusses the current evidence of small airways tests in asthma and future research that may be needed to further assess their utility.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/14799731211053332; doi:https://doi.org/10.1177/14799731211053332; html:https://europepmc.org/articles/PMC8543738; pdf:https://europepmc.org/articles/PMC8543738?pdf=render
+34786063,https://doi.org/,Immune infiltration and prognostic and diagnostic use of LGALS4 in colon adenocarcinoma and bladder urothelial carcinoma.,"Acharjee A, Agarwal P, Nash K, Bano S, Rahman T, Gkoutos GV.",,American journal of translational research,2021,2021-10-15,N,Biomarker; Translational Research; Immune Infiltration; Omics Integration; Blca; Lgals4,,,"Colon adenocarcinoma (COAD) is a common tumor of the gastrointestinal tract with a high mortality rate. Current research has identified many genes associated with immune infiltration that play a vital role in the development of COAD. In this study, we analysed the prognostic and diagnostic features of such immune-related genes in the context of colonic adenocarcinoma (COAD). We analysed 17 overlapping gene expression profiles of COAD and healthy samples obtained from TCGA-COAD and public single-cell sequencing resources, to identify potential therapeutic COAD targets. We evaluated the abundance of immune infiltration with those genes using the TIMER (Tumor Immune Estimation Resource) deconvolution method. Subsequently, we developed predictive and survival models to assess the prognostic value of these genes. The LGALS4 (Galectin-4) gene was found to be significantly (P<0.05) downregulated in COAD and bladder urothelial carcinoma (BLCA) compared to healthy samples. We identified LGALS4 as a prognostic and diagnostic marker for multiple cancer types, including COAD and BLCA. Our analysis reveals a series of novel candidate drug targets, as well as candidate molecular markers, that may explain the pathogenesis of COAD and BLCA. LGALS4 gene is associated with multiple cancer types and is a possible prognostic, as well as diagnostic, marker of COAD and BLCA.",,html:https://europepmc.org/articles/PMC8581917; pdf:https://europepmc.org/articles/PMC8581917?pdf=render
 36735963,https://doi.org/10.1080/09553002.2023.2173823,Machine intelligence for radiation science: summary of the Radiation Research Society 67th annual meeting symposium.,"Wilson LJ, Kiffer FC, Berrios DC, Bryce-Atkinson A, Costes SV, Gevaert O, Matarèse BFE, Miller J, Mukherjee P, Peach K, Schofield PN, Slater LT, Langen B.",,International journal of radiation biology,2023,2023-02-06,N,Artificial intelligence; Lung cancer; Radiotherapy; Radiobiology; Ontology; Machine Learning; Voxel-based Analysis,,,"The era of high-throughput techniques created big data in the medical field and research disciplines. Machine intelligence (MI) approaches can overcome critical limitations on how those large-scale data sets are processed, analyzed, and interpreted. The 67<sup>th</sup> Annual Meeting of the Radiation Research Society featured a symposium on MI approaches to highlight recent advancements in the radiation sciences and their clinical applications. This article summarizes three of those presentations regarding recent developments for metadata processing and ontological formalization, data mining for radiation outcomes in pediatric oncology, and imaging in lung cancer.",,doi:https://doi.org/10.1080/09553002.2023.2173823; doi:https://doi.org/10.1080/09553002.2023.2173823
-39311593,https://doi.org/10.1111/trf.17963,The power of arts-based film interventions to encourage Black blood donors.,"Mills R, Okubanjo A, Acheampong N, Croucher M, Eaton N, Kazi A, di Angelantonio E, Wood A, Masser B, Ferguson E.",,Transfusion,2024,2024-09-23,N,Donors | Co‐design | Art‐based | Film Campaigns,,,"<h4>Background</h4>Blood services must consider innovative ways to encourage more Black people to donate to enhance the efficacy of treatments. We evaluate how two innovative arts-based approaches (co-designed and locally produced films and a large-scale Marvel Studios'/NHSBT collaboration) can achieve this by generalizing to a wider audience from their target audiences.<h4>Study design and methods</h4>Four co-designed short community films were produced in the United Kingdom: Comedy, Reciprocity, Donor-Recipient, and Sliding Doors. In Study 1 (N = 44: Black people), these films were evaluated in the target community in which they were produced. In Study 2 (N = 1237: Black = 638, White = 599), the community and Marvel Black Panther/NHSBT films were evaluated in a nontarget general population sample. Evaluations were in terms of campaign behavioral efficacy (e.g., willingness to donate, encourage others to donate) and affect. These analyses were segmented by donor status, age, and gender.<h4>Results</h4>Study 1 shows that the community groups rated the films very positively, with over 90% stating that they would be convinced to donate blood. Study 2 shows the results from the community films generalized to the general population, with the Black Panther film also rated positively in the general population. Three community films and the Black Panther film were rated equally positively. There were notable differences across generations and by donor status.<h4>Discussion</h4>The results highlight the power of arts-based approaches (both locally co-produced community films and franchise collaborations) in encouraging donors within their target audiences and, importantly, on the broader population.",,doi:https://doi.org/10.1111/trf.17963
 36745545,https://doi.org/10.1099/mgen.0.000887,The use of representative community samples to assess SARS-CoV-2 lineage competition: Alpha outcompetes Beta and wild-type in England from January to March 2021.,"Eales O, Page AJ, Tang SN, Walters CE, Wang H, Haw D, Trotter AJ, Le Viet T, Foster-Nyarko E, Prosolek S, Atchison C, Ashby D, Cooke G, Barclay W, Donnelly CA, O'Grady J, Volz E, The Covid-Genomics Uk Cog-Uk Consortium, Darzi A, Ward H, Elliott P, Riley S.",,Microbial genomics,2023,2023-02-01,Y,,,,"Genomic surveillance for SARS-CoV-2 lineages informs our understanding of possible future changes in transmissibility and vaccine efficacy and will be a high priority for public health for the foreseeable future. However, small changes in the frequency of one lineage over another are often difficult to interpret because surveillance samples are obtained using a variety of methods all of which are known to contain biases. As a case study, using an approach which is largely free of biases, we here describe lineage dynamics and phylogenetic relationships of the Alpha and Beta variant in England during the first 3 months of 2021 using sequences obtained from a random community sample who provided a throat and nose swab for rt-PCR as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. Overall, diversity decreased during the first quarter of 2021, with the Alpha variant (first identified in Kent) becoming predominant, driven by a reproduction number 0.3 higher than for the prior wild-type. During January, positive samples were more likely to be Alpha in those aged 18 to 54 years old. Although individuals infected with the Alpha variant were no more likely to report one or more classic COVID-19 symptoms compared to those infected with wild-type, they were more likely to be antibody-positive 6 weeks after infection. Further, viral load was higher in those infected with the Alpha variant as measured by cycle threshold (Ct) values. The presence of infections with non-imported Beta variant (first identified in South Africa) during January, but not during February or March, suggests initial establishment in the community followed by fade-out. However, this occurred during a period of stringent social distancing. These results highlight how sequence data from representative community surveys such as REACT-1 can augment routine genomic surveillance during periods of lineage diversity.",,doi:https://doi.org/10.1099/mgen.0.000887; html:https://europepmc.org/articles/PMC9997751; pdf:https://europepmc.org/articles/PMC9997751?pdf=render
+39311593,https://doi.org/10.1111/trf.17963,The power of arts-based film interventions to encourage Black blood donors.,"Mills R, Okubanjo A, Acheampong N, Croucher M, Eaton N, Kazi A, di Angelantonio E, Wood A, Masser B, Ferguson E.",,Transfusion,2024,2024-09-23,N,Donors | Co‐design | Art‐based | Film Campaigns,,,"<h4>Background</h4>Blood services must consider innovative ways to encourage more Black people to donate to enhance the efficacy of treatments. We evaluate how two innovative arts-based approaches (co-designed and locally produced films and a large-scale Marvel Studios'/NHSBT collaboration) can achieve this by generalizing to a wider audience from their target audiences.<h4>Study design and methods</h4>Four co-designed short community films were produced in the United Kingdom: Comedy, Reciprocity, Donor-Recipient, and Sliding Doors. In Study 1 (N = 44: Black people), these films were evaluated in the target community in which they were produced. In Study 2 (N = 1237: Black = 638, White = 599), the community and Marvel Black Panther/NHSBT films were evaluated in a nontarget general population sample. Evaluations were in terms of campaign behavioral efficacy (e.g., willingness to donate, encourage others to donate) and affect. These analyses were segmented by donor status, age, and gender.<h4>Results</h4>Study 1 shows that the community groups rated the films very positively, with over 90% stating that they would be convinced to donate blood. Study 2 shows the results from the community films generalized to the general population, with the Black Panther film also rated positively in the general population. Three community films and the Black Panther film were rated equally positively. There were notable differences across generations and by donor status.<h4>Discussion</h4>The results highlight the power of arts-based approaches (both locally co-produced community films and franchise collaborations) in encouraging donors within their target audiences and, importantly, on the broader population.",,doi:https://doi.org/10.1111/trf.17963
 34356905,https://doi.org/10.3390/biomedicines9070841,Relationship between Circulating PCSK9 and Markers of Subclinical Atherosclerosis-The IMPROVE Study.,"Coggi D, Frigerio B, Bonomi A, Ruscica M, Ferri N, Sansaro D, Ravani A, Ferrante P, Damigella M, Veglia F, Capra N, Lupo MG, Macchi C, Savonen K, Silveira A, Kurl S, Giral P, Pirro M, Strawbridge RJ, Gigante B, Smit AJ, Tremoli E, Amato M, Baldassarre D, On Behalf Of The Improve Study Group.",,Biomedicines,2021,2021-07-19,Y,Intima-media thickness; carotid artery; Pcsk9; Subclinical Atherosclerosis; Echolucency,,,"(1) Background and purpose: circulating proprotein convertase subtilisin/kexin type 9 (PCSK9) is one of the key regulators of cholesterol metabolism. Despite this, its role as a player in atherosclerosis development is still matter of debate. Here, we investigated the relationships between this protein and several markers of subclinical atherosclerosis. (2) Methods: the IMPROVE study enrolled 3703 European subjects (54-79 years; 48% men; with ≥3 vascular risk factors), asymptomatic for cardiovascular diseases. PCSK9 levels were measured by ELISA. B-mode ultrasound was used to measure markers of carotid subclinical atherosclerosis. (3) Results: in the crude analysis, PCSK9 levels were associated with several baseline measures of carotid intima-media thickness (cIMT) (all <i>p</i> < 0.0001); with cIMT change over time (Fastest-IMTmax-progr) (<i>p</i> = 0.01); with inter-adventitia common carotid artery diameter (ICCAD) (<i>p</i> < 0.0001); and with the echolucency (Grey Scale Median; GSM) of both carotid plaque and plaque-free common carotid IMT (both <i>p</i> < 0.0001). However, after adjustment for age, sex, latitude, and pharmacological treatment, all the afore-mentioned correlations were no longer statistically significant. The lack of correlation was also observed after stratification for sex, latitude, and pharmacological treatments. (4) Conclusions: in subjects who are asymptomatic for cardiovascular diseases, PCSK9 plasma levels do not correlate with vascular damage and/or subclinical atherosclerosis of extracranial carotid arteries.",,pdf:https://www.mdpi.com/2227-9059/9/7/841/pdf?version=1626837519; doi:https://doi.org/10.3390/biomedicines9070841; html:https://europepmc.org/articles/PMC8301759; pdf:https://europepmc.org/articles/PMC8301759?pdf=render
-39033821,https://doi.org/10.1016/j.clinme.2024.100230,Strategies to identify medical patients suitable for management through same-day emergency care services: A systematic review.,"Atkin C, Khosla R, Belsham J, Hegarty H, Hennessy C, Sapey E.",,"Clinical medicine (London, England)",2024,2024-07-19,Y,Scoring; Acute Medicine; Same Day Emergency Care; Admission Pathways,,,"Same-day emergency care (SDEC) in unplanned and emergency care is an NHS England (NHSE) priority. Optimal use of these services requires rapid identification of suitable patients. NHSE suggests the use of one tool for this purpose. This systematic review compares studies that evaluate the performance of selection tools for SDEC pathways. Nine studies met the inclusion criteria. Three scores were evaluated: the Amb score (seven studies), Glasgow Admission Prediction Score (GAPS) (six studies) and Sydney Triage to Admission Risk Tool (START) (two studies). There was heterogeneity in the populations assessed, exclusion criteria used and definitions used for SDEC suitability, with proportions of patients deemed 'suitable' for SDEC ranging from 20 to 80%. Reported score sensitivity and specificity ranged between 18-99% and 10-89%. Score performance could not be compared due to heterogeneity between studies. No studies assessed clinical implementation. The current evidence to support the use of a specific tool for SDEC is limited and requires further evaluation.",,doi:https://doi.org/10.1016/j.clinme.2024.100230; html:https://europepmc.org/articles/PMC11359741; pdf:https://europepmc.org/articles/PMC11359741?pdf=render
 35379238,https://doi.org/10.1186/s12933-022-01482-z,Metformin and high-sensitivity cardiac troponin I and T trajectories in type 2 diabetes patients: a post-hoc analysis of a randomized controlled trial.,"Stultiens JMG, Top WMC, Kimenai DM, Lehert P, Bekers O, Stehouwer CDA, Kooy A, Meex SJR.",,Cardiovascular diabetology,2022,2022-04-04,Y,Troponin; Mechanism; Cardiac; Biomarker; Metformin; Longitudinal; Cardioprotective,,,"<h4>Background</h4>Metformin has favorable effects on cardiovascular outcomes in both newly onset and advanced type 2 diabetes, as previously reported findings from the UK Prospective Diabetes Study and the HOME trial have demonstrated. Patients with type 2 diabetes present with chronically elevated circulating cardiac troponin levels, an established predictor of cardiovascular endpoints and prognostic marker of subclinical myocardial injury. It is unknown whether metformin affects cardiac troponin levels. The study aimed to evaluate cardiac troponin I and T trajectories in patients with diabetes treated either with metformin or placebo.<h4>Methods</h4>This study is a post-hoc analysis of a randomized controlled trial (HOME trial) that included 390 patients with advanced type 2 diabetes randomized to 850 mg metformin or placebo up to three times daily concomitant to continued insulin treatment. Cardiac troponin I and T concentrations were measured at baseline and after 4, 17, 30, 43 and 52 months. We evaluated cardiac troponin trajectories by linear mixed-effects modeling, correcting for age, sex, smoking status and history of cardiovascular disease.<h4>Results</h4>This study enrolled 390 subjects, of which 196 received metformin and 194 received placebo. In the treatment and placebo groups, mean age was 64 and 59 years; with 50% and 58% of subjects of the female sex, respectively. Despite the previously reported reduction of macrovascular disease risk in this cohort by metformin, linear mixed-effects regression modelling did not reveal evidence for an effect on cardiac troponin I and cardiac troponin T levels [- 8.4% (- 18.6, 3.2), p = 0.150, and - 4.6% (- 12, 3.2), p = 0.242, respectively]. A statistically significant time-treatment interaction was found for troponin T [- 1.6% (- 2.9, - 0.2), p = 0.021] but not troponin I concentrations [- 1.5% (- 4.2, 1.2), p = 0.263].<h4>Conclusions</h4>In this post-hoc analysis of a 4.3-year randomized controlled trial, metformin did not exert a clinically relevant effect on cardiac troponin I and cardiac troponin T levels when compared to placebo. Cardioprotective effects of the drug observed in clinical studies are not reflected by a reduction in these biomarkers of subclinical myocardial injury. Trial registration ClinicalTrials.gov identifier NCT00375388.",,pdf:https://cardiab.biomedcentral.com/track/pdf/10.1186/s12933-022-01482-z; doi:https://doi.org/10.1186/s12933-022-01482-z; html:https://europepmc.org/articles/PMC8981770; pdf:https://europepmc.org/articles/PMC8981770?pdf=render
 37143610,https://doi.org/10.1093/ehjopen/oead037,"SAIL study of stroke, systemic embolism and bleeding outcomes with warfarin anticoagulation in non-valvular atrial fibrillation (S<sup>4</sup>-BOW-AF).","Harris DE, Torabi F, Mallory D, Akbari A, Thayer D, Wang T, Grundy S, Gravenor M, Alikhan R, Lister S, Halcox J.",,European heart journal open,2023,2023-04-13,Y,Bleeding; Atrial fibrillation; Stroke; Warfarin; Pharmacotherapy; Inr Control,,,"<h4>Aims</h4>In patients with non-valvular atrial fibrillation (NVAF) prescribed warfarin, the association between guideline defined international normalised ratio (INR) control and adverse outcomes in unknown. We aimed to (i) determine stroke and systemic embolism (SSE) and bleeding events in NVAF patients prescribed warfarin; and (ii) estimate the increased risk of these adverse events associated with poor INR control in this population.<h4>Methods and results</h4>Individual-level population-scale linked patient data were used to investigate the association between INR control and both SSE and bleeding events using (i) the National Institute for Health and Care Excellence (NICE) criteria of poor INR control [time in therapeutic range (TTR) <65%, two INRs <1.5 or two INRs >5 in a 6-month period or any INR >8]. A total of 35 891 patients were included for SSE and 35 035 for bleeding outcome analyses. Mean CHA<sub>2</sub>DS<sub>2</sub>-VASc score was 3.5 (SD = 1.7), and the mean follow up was 4.3 years for both analyses. Mean TTR was 71.9%, with 34% of time spent in poor INR control according to NICE criteria.SSE and bleeding event rates (per 100 patient years) were 1.01 (95%CI 0.95-1.08) and 3.4 (95%CI 3.3-3.5), respectively, during adequate INR control, rising to 1.82 (95%CI 1.70-1.94) and 4.8 (95% CI 4.6-5.0) during poor INR control.Poor INR control was independently associated with increased risk of both SSE [HR = 1.69 (95%CI = 1.54-1.86), <i>P</i> < 0.001] and bleeding [HR = 1.40 (95%CI 1.33-1.48), <i>P</i> < 0.001] in Cox-multivariable models.<h4>Conclusion</h4>Guideline-defined poor INR control is associated with significantly higher SSE and bleeding event rates, independent of recognised risk factors for stroke or bleeding.",,pdf:https://academic.oup.com/ehjopen/advance-article-pdf/doi/10.1093/ehjopen/oead037/49878718/oead037.pdf; doi:https://doi.org/10.1093/ehjopen/oead037; html:https://europepmc.org/articles/PMC10153743; pdf:https://europepmc.org/articles/PMC10153743?pdf=render
 36716318,https://doi.org/10.1371/journal.pmed.1004174,Therapeutic potential of IL6R blockade for the treatment of sepsis and sepsis-related death: A Mendelian randomisation study.,"Hamilton FW, Thomas M, Arnold D, Palmer T, Moran E, Mentzer AJ, Maskell N, Baillie K, Summers C, Hingorani A, MacGowan A, Khandaker GM, Mitchell R, Davey Smith G, Ghazal P, Timpson NJ.",,PLoS medicine,2023,2023-01-30,Y,,,,"<h4>Background</h4>Sepsis is characterised by dysregulated, life-threatening immune responses, which are thought to be driven by cytokines such as interleukin 6 (IL-6). Genetic variants in IL6R known to down-regulate IL-6 signalling are associated with improved Coronavirus Disease 2019 (COVID-19) outcomes, a finding later confirmed in randomised trials of IL-6 receptor antagonists (IL6RAs). We hypothesised that blockade of IL6R could also improve outcomes in sepsis.<h4>Methods and findings</h4>We performed a Mendelian randomisation (MR) analysis using single nucleotide polymorphisms (SNPs) in and near IL6R to evaluate the likely causal effects of IL6R blockade on sepsis (primary outcome), sepsis severity, other infections, and COVID-19 (secondary outcomes). We weighted SNPs by their effect on CRP and combined results across them in inverse variance weighted meta-analysis, proxying the effect of IL6RA. Our outcomes were measured in UK Biobank, FinnGen, the COVID-19 Host Genetics Initiative (HGI), and the GenOSept and GainS consortium. We performed several sensitivity analyses to test assumptions of our methods, including utilising variants around CRP and gp130 in a similar analysis. In the UK Biobank cohort (N = 486,484, including 11,643 with sepsis), IL6R blockade was associated with a decreased risk of our primary outcome, sepsis (odds ratio (OR) = 0.80; 95% confidence interval (CI) 0.66 to 0.96, per unit of natural log-transformed CRP decrease). The size of this effect increased with severity, with larger effects on 28-day sepsis mortality (OR = 0.74; 95% CI 0.47 to 1.15); critical care admission with sepsis (OR = 0.48, 95% CI 0.30 to 0.78) and critical care death with sepsis (OR = 0.37, 95% CI 0.14 to 0.98). Similar associations were seen with severe respiratory infection: OR for pneumonia in critical care 0.69 (95% CI 0.49 to 0.97) and for sepsis survival in critical care (OR = 0.22; 95% CI 0.04 to 1.31) in the GainS and GenOSept consortium, although this result had a large degree of imprecision. We also confirm the previously reported protective effect of IL6R blockade on severe COVID-19 (OR = 0.69, 95% CI 0.57 to 0.84) in the COVID-19 HGI, which was of similar magnitude to that seen in sepsis. Sensitivity analyses did not alter our primary results. These results are subject to the limitations and assumptions of MR, which in this case reflects interpretation of these SNP effects as causally acting through blockade of IL6R, and reflect lifetime exposure to IL6R blockade, rather than the effect of therapeutic IL6R blockade.<h4>Conclusions</h4>IL6R blockade is causally associated with reduced incidence of sepsis. Similar but imprecisely estimated results supported a causal effect also on sepsis related mortality and critical care admission with sepsis. These effects are comparable in size to the effect seen in severe COVID-19, where IL-6 receptor antagonists were shown to improve survival. These data suggest that a randomised trial of IL-6 receptor antagonists in sepsis should be considered.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004174&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004174; html:https://europepmc.org/articles/PMC9925069; pdf:https://europepmc.org/articles/PMC9925069?pdf=render
 35608440,https://doi.org/10.1126/science.abq4411,Twin peaks: The Omicron SARS-CoV-2 BA.1 and BA.2 epidemics in England.,"Elliott P, Eales O, Steyn N, Tang D, Bodinier B, Wang H, Elliott J, Whitaker M, Atchison C, Diggle PJ, Page AJ, Trotter AJ, Ashby D, Barclay W, Taylor G, Ward H, Darzi A, Cooke GS, Donnelly CA, Chadeau-Hyam M.",,"Science (New York, N.Y.)",2022,2022-06-24,Y,,,,"Rapid transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has led to record-breaking incidence rates around the world. The Real-time Assessment of Community Transmission-1 (REACT-1) study has tracked SARS-CoV-2 infection in England using reverse transcription polymerase chain reaction (RT-PCR) results from self-administered throat and nose swabs from randomly selected participants aged 5 years and older approximately monthly from May 2020 to March 2022. Weighted prevalence in March 2022 was the highest recorded in REACT-1 at 6.37% (<i>N</i> = 109,181), with the Omicron BA.2 variant largely replacing the BA.1 variant. Prevalence was increasing overall, with the greatest increase in those aged 65 to 74 years and 75 years and older. This was associated with increased hospitalizations and deaths, but at much lower levels than in previous waves against a backdrop of high levels of vaccination.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9161371; doi:https://doi.org/10.1126/science.abq4411; html:https://europepmc.org/articles/PMC9161371; pdf:https://europepmc.org/articles/PMC9161371?pdf=render
+39033821,https://doi.org/10.1016/j.clinme.2024.100230,Strategies to identify medical patients suitable for management through same-day emergency care services: A systematic review.,"Atkin C, Khosla R, Belsham J, Hegarty H, Hennessy C, Sapey E.",,"Clinical medicine (London, England)",2024,2024-07-19,Y,Scoring; Acute Medicine; Same Day Emergency Care; Admission Pathways,,,"Same-day emergency care (SDEC) in unplanned and emergency care is an NHS England (NHSE) priority. Optimal use of these services requires rapid identification of suitable patients. NHSE suggests the use of one tool for this purpose. This systematic review compares studies that evaluate the performance of selection tools for SDEC pathways. Nine studies met the inclusion criteria. Three scores were evaluated: the Amb score (seven studies), Glasgow Admission Prediction Score (GAPS) (six studies) and Sydney Triage to Admission Risk Tool (START) (two studies). There was heterogeneity in the populations assessed, exclusion criteria used and definitions used for SDEC suitability, with proportions of patients deemed 'suitable' for SDEC ranging from 20 to 80%. Reported score sensitivity and specificity ranged between 18-99% and 10-89%. Score performance could not be compared due to heterogeneity between studies. No studies assessed clinical implementation. The current evidence to support the use of a specific tool for SDEC is limited and requires further evaluation.",,doi:https://doi.org/10.1016/j.clinme.2024.100230; html:https://europepmc.org/articles/PMC11359741; pdf:https://europepmc.org/articles/PMC11359741?pdf=render
 33879450,https://doi.org/10.1136/heartjnl-2021-319118,Sex differences in investigations and outcomes among patients with type 2 myocardial infarction.,"Kimenai DM, Lindahl B, Chapman AR, Baron T, Gard A, Wereski R, Meex SJR, Jernberg T, Mills NL, Eggers KM.",,Heart (British Cardiac Society),2021,2021-04-20,Y,Myocardial infarction; acute coronary syndrome; risk factors,,,"<h4>Objectives</h4>Type 2 myocardial infarction (MI) is a heterogenous condition and whether there are differences between women and men is unknown. We evaluated sex differences in clinical characteristics, investigations and outcomes in patients with type 2 MI.<h4>Methods</h4>In the Swedish Web based system for Enhancement and Development of Evidence based care in Heart disease Evaluated According to Recommended Therapies (SWEDEHEART) registry, we compared patients admitted to coronary care units with a diagnosis of type 1 or type 2 MI. Sex-stratified Cox regression models evaluated the association with all-cause death in men and women separately.<h4>Results</h4>We included 57 264 (median age 73 years, 65% men) and 6485 (median age 78 years, 50% men) patients with type 1 and type 2 MI, respectively. No differences were observed in the proportion of men and women with type 2 MI who underwent echocardiography and coronary angiography, but women were less likely than men to have left ventricular (LV) impairment and obstructive coronary artery disease (CAD). Compared with type 1 MI, patients with type 2 MI had higher risk of death regardless of sex (men: adjusted HR 1.55 (95% CI 1.44 to 1.67); women: adjusted HR 1.34 (95% CI 1.24 to 1.45)). In those with type 2 MI, the risk of death was lower for women than men (adjusted HR 0.85 (95% CI 0.76 to 0.92) (men, reference)).<h4>Conclusions</h4>Type 2 MI occurred in men and women equally and we found no evidence of sex bias in the selection of patients for cardiac investigations. Patients with type 2 MI had worse outcomes, but women were less likely to have obstructive CAD or severe LV impairment and were more likely to survive than men.",,pdf:https://heart.bmj.com/content/heartjnl/107/18/1480.full.pdf; doi:https://doi.org/10.1136/heartjnl-2021-319118; html:https://europepmc.org/articles/PMC8408584; pdf:https://europepmc.org/articles/PMC8408584?pdf=render
-37656609,https://doi.org/10.1093/aje/kwad179,CHALLENGES IN ESTIMATING THE EFFECTIVENESS OF 2 DOSES OF COVID-19 VACCINE BEYOND 6 MONTHS IN ENGLAND.,"Horne EMF, Hulme WJ, Keogh RH, Palmer TM, Williamson EJ, Parker EPK, Walker VM, Knight R, Wei Y, Taylor K, Fisher L, Morley J, Mehrkar A, Dillingham I, Bacon S, Goldacre B, Sterne JAC, OpenSAFELY Collaborative FT.",,American journal of epidemiology,2024,2024-01-01,Y,,,,,,pdf:https://academic.oup.com/aje/advance-article-pdf/doi/10.1093/aje/kwad179/51329819/kwad179.pdf; doi:https://doi.org/10.1093/aje/kwad179; html:https://europepmc.org/articles/PMC10773473; pdf:https://europepmc.org/articles/PMC10773473?pdf=render
-37248229,https://doi.org/10.1038/s41467-023-38756-3,Evidence-driven spatiotemporal COVID-19 hospitalization prediction with Ising dynamics.,"Gao J, Heintz J, Mack C, Glass L, Cross A, Sun J.",,Nature communications,2023,2023-05-29,Y,,,,"In this work, we aim to accurately predict the number of hospitalizations during the COVID-19 pandemic by developing a spatiotemporal prediction model. We propose HOIST, an Ising dynamics-based deep learning model for spatiotemporal COVID-19 hospitalization prediction. By drawing the analogy between locations and lattice sites in statistical mechanics, we use the Ising dynamics to guide the model to extract and utilize spatial relationships across locations and model the complex influence of granular information from real-world clinical evidence. By leveraging rich linked databases, including insurance claims, census information, and hospital resource usage data across the U.S., we evaluate the HOIST model on the large-scale spatiotemporal COVID-19 hospitalization prediction task for 2299 counties in the U.S. In the 4-week hospitalization prediction task, HOIST achieves 368.7 mean absolute error, 0.6 [Formula: see text] and 0.89 concordance correlation coefficient score on average. Our detailed number needed to treat (NNT) and cost analysis suggest that future COVID-19 vaccination efforts may be most impactful in rural areas. This model may serve as a resource for future county and state-level vaccination efforts.",,doi:https://doi.org/10.1038/s41467-023-38756-3; doi:https://doi.org/10.1038/s41467-023-38756-3; html:https://europepmc.org/articles/PMC10226446; pdf:https://europepmc.org/articles/PMC10226446?pdf=render
 38079428,https://doi.org/10.1371/journal.pone.0273596,"Factors associated with low school readiness, a linked health and education data study in Wales, UK.","Bandyopadhyay A, Marchant E, Jones H, Parker M, Evans J, Brophy S.",,PloS one,2023,2023-12-11,Y,,,,"<h4>Background</h4>School readiness is a measure of a child's cognitive, social, and emotional readiness to begin formal schooling. Children with low school readiness need additional support from schools for learning, developing required social and academic skills, and catching-up with their school-ready peers. This study aims to identify the most significant risk factors associated with low school readiness using linked routine data for children in Wales.<h4>Method</h4>This was a longitudinal cohort study using linked data. The cohort comprises of children who completed the Foundation Phase assessment between 2012 and 2018. Individuals were identified by linking Welsh Demographic Service and Pre16 Education Attainment datasets. School readiness was assessed via the binary outcome of the Foundation Phase assessment (achieved/not achieved). This study used multivariable logistic regression model and a decision tree to identify and weight the most important risk factors associated with low school readiness.<h4>Results</h4>In order of importance, logistic regression identified maternal learning difficulties (adjusted odds ratio 5.35(95% confidence interval 3.97-7.22)), childhood epilepsy (2.95(2.39-3.66)), very low birth weight (2.24(1.86-2.70), being a boy (2.11(2.04-2.19)), being on free school meals (1.85(1.78-1.93)), living in the most deprived areas (1.67(1.57-1.77)), maternal death (1.47(1.09-1.98)), and maternal diabetes (1.46(1.23-1.78)) as factors associated with low school readiness. Using a decision tree, eligibility for free school meals, being a boy, absence/low attendance at school, being born late in the academic year, being a low birthweight child, and not being breastfed were factors which were associated with low school readiness.<h4>Conclusion</h4>This work suggests that public health interventions focusing on children who are: boys, living in deprived areas, have poor early years attendance, have parents with learning difficulties, have parents with an illness or have illnesses themselves, would make the most difference to school readiness in the population.",,doi:https://doi.org/10.1371/journal.pone.0273596; html:https://europepmc.org/articles/PMC10712842; pdf:https://europepmc.org/articles/PMC10712842?pdf=render
+37248229,https://doi.org/10.1038/s41467-023-38756-3,Evidence-driven spatiotemporal COVID-19 hospitalization prediction with Ising dynamics.,"Gao J, Heintz J, Mack C, Glass L, Cross A, Sun J.",,Nature communications,2023,2023-05-29,Y,,,,"In this work, we aim to accurately predict the number of hospitalizations during the COVID-19 pandemic by developing a spatiotemporal prediction model. We propose HOIST, an Ising dynamics-based deep learning model for spatiotemporal COVID-19 hospitalization prediction. By drawing the analogy between locations and lattice sites in statistical mechanics, we use the Ising dynamics to guide the model to extract and utilize spatial relationships across locations and model the complex influence of granular information from real-world clinical evidence. By leveraging rich linked databases, including insurance claims, census information, and hospital resource usage data across the U.S., we evaluate the HOIST model on the large-scale spatiotemporal COVID-19 hospitalization prediction task for 2299 counties in the U.S. In the 4-week hospitalization prediction task, HOIST achieves 368.7 mean absolute error, 0.6 [Formula: see text] and 0.89 concordance correlation coefficient score on average. Our detailed number needed to treat (NNT) and cost analysis suggest that future COVID-19 vaccination efforts may be most impactful in rural areas. This model may serve as a resource for future county and state-level vaccination efforts.",,doi:https://doi.org/10.1038/s41467-023-38756-3; doi:https://doi.org/10.1038/s41467-023-38756-3; html:https://europepmc.org/articles/PMC10226446; pdf:https://europepmc.org/articles/PMC10226446?pdf=render
 34966903,https://doi.org/10.3389/fdgth.2021.778305,Development of a Lexicon for Pain.,"Chaturvedi J, Mascio A, Velupillai SU, Roberts A.",,Frontiers in digital health,2021,2021-12-13,Y,Pain; Mental health; Lexicon; Electronic Health Records; Natural Language Processing,,,"Pain has been an area of growing interest in the past decade and is known to be associated with mental health issues. Due to the ambiguous nature of how pain is described in text, it presents a unique natural language processing (NLP) challenge. Understanding how pain is described in text and utilizing this knowledge to improve NLP tasks would be of substantial clinical importance. Not much work has previously been done in this space. For this reason, and in order to develop an English lexicon for use in NLP applications, an exploration of pain concepts within free text was conducted. The exploratory text sources included two hospital databases, a social media platform (Twitter), and an online community (Reddit). This exploration helped select appropriate sources and inform the construction of a pain lexicon. The terms within the final lexicon were derived from three sources-literature, ontologies, and word embedding models. This lexicon was validated by two clinicians as well as compared to an existing 26-term pain sub-ontology and MeSH (Medical Subject Headings) terms. The final validated lexicon consists of 382 terms and will be used in downstream NLP tasks by helping select appropriate pain-related documents from electronic health record (EHR) databases, as well as pre-annotating these words to help in development of an NLP application for classification of mentions of pain within the documents. The lexicon and the code used to generate the embedding models have been made publicly available.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8710455; doi:https://doi.org/10.3389/fdgth.2021.778305; html:https://europepmc.org/articles/PMC8710455; pdf:https://europepmc.org/articles/PMC8710455?pdf=render
-39446320,https://doi.org/10.1001/jamanetworkopen.2024.41166,Pharmacologic Treatments for Dementia and the Risk of Developing Age-Related Macular Degeneration.,"Wang J, Antza C, Lee WH, Coker J, Keane PA, Denniston AK, Nirantharakumar K, Adderley NJ.",,JAMA network open,2024,2024-10-01,N,,,,"<h4>Importance</h4>Age-related macular degeneration (AMD) is the leading cause of blindness among people aged 50 years or older worldwide. There is a need for new strategies for the prevention and treatment of AMD. There is some limited evidence to suggest the possibility of a protective association of dementia medications with the development of some types of AMD, but the evidence is weak.<h4>Objective</h4>To investigate whether the dementia medications memantine and donepezil are associated with the risk of developing AMD.<h4>Design, setting, and participants</h4>Three population-based cohort studies were performed using data from the Clinical Practice Research Datalink GOLD and Aurum databases from May 15, 2002, to June 21, 2022. Participants included individuals with dementia (vascular dementia, nonvascular dementia, or Alzheimer disease) aged 40 years or older. Statistical analysis was carried out between February and November 2023.<h4>Exposures</h4>Exposures were dementia medications. Cohort 1 compared patients prescribed donepezil with those prescribed rivastigmine or galantamine using the new-user design. Cohort 2 compared memantine with donepezil, rivastigmine, or galantamine using the prevalent new-user design. In a sensitivity analysis, cohort 3 compared memantine with rivastigmine or galantamine only.<h4>Main outcomes and measures</h4>New diagnosis of AMD.<h4>Results</h4>There were 132 846 individuals (mean [SD] age, 80.4 [7.6] years; 61.8% women; mean [SD] body mass index [BMI], 25.5 [4.6]) with a diagnosis of dementia included in cohort 1, 159 419 individuals (mean [SD] age, 81.2 [7.6] years; 59.7% women; mean [SD] body mass index [BMI], 25.6 [4.7]) with a diagnosis of dementia included in cohort 2, and 92 328 individuals with a diagnosis of dementia included in cohort 3 (mean [SD] age, 80.9 [7.7] years; 58.5% women; mean [SD] body mass index [BMI], 25.5 [4.7]). The adjusted hazard ratio (HR) for donepezil compared with rivastigmine or galantamine (cohort 1) was 0.95 (95% CI, 0.67-1.35). The adjusted HR for memantine compared with donepezil, rivastigmine, or galantamine (cohort 2) was 1.03 (95% CI, 0.83-1.27). The adjusted HR for memantine vs rivastigmine or galantamine only (cohort 3) was 1.24 (95% CI, 0.83-1.86).<h4>Conclusions and relevance</h4>This cohort study of patients with dementia found no significant associations between memantine or donepezil compared with other dementia medications and the risk of development of AMD. Further research is recommended to examine any possible pathophysiological protective action of memantine and other dementia medications against the development of AMD.",,doi:https://doi.org/10.1001/jamanetworkopen.2024.41166
+37656609,https://doi.org/10.1093/aje/kwad179,CHALLENGES IN ESTIMATING THE EFFECTIVENESS OF 2 DOSES OF COVID-19 VACCINE BEYOND 6 MONTHS IN ENGLAND.,"Horne EMF, Hulme WJ, Keogh RH, Palmer TM, Williamson EJ, Parker EPK, Walker VM, Knight R, Wei Y, Taylor K, Fisher L, Morley J, Mehrkar A, Dillingham I, Bacon S, Goldacre B, Sterne JAC, OpenSAFELY Collaborative FT.",,American journal of epidemiology,2024,2024-01-01,Y,,,,,,pdf:https://academic.oup.com/aje/advance-article-pdf/doi/10.1093/aje/kwad179/51329819/kwad179.pdf; doi:https://doi.org/10.1093/aje/kwad179; html:https://europepmc.org/articles/PMC10773473; pdf:https://europepmc.org/articles/PMC10773473?pdf=render
 34261639,https://doi.org/10.1136/bmj.n1592,Risks of covid-19 hospital admission and death for people with learning disability: population based cohort study using the OpenSAFELY platform.,"Williamson EJ, McDonald HI, Bhaskaran K, Walker AJ, Bacon S, Davy S, Schultze A, Tomlinson L, Bates C, Ramsay M, Curtis HJ, Forbes H, Wing K, Minassian C, Tazare J, Morton CE, Nightingale E, Mehrkar A, Evans D, Inglesby P, MacKenna B, Cockburn J, Rentsch CT, Mathur R, Wong AYS, Eggo RM, Hulme W, Croker R, Parry J, Hester F, Harper S, Douglas IJ, Evans SJW, Smeeth L, Goldacre B, Kuper H.",,BMJ (Clinical research ed.),2021,2021-07-14,Y,,,,"<h4>Objective</h4>To assess the association between learning disability and risk of hospital admission and death from covid-19 in England among adults and children.<h4>Design</h4>Population based cohort study on behalf of NHS England using the OpenSAFELY platform.<h4>Setting</h4>Patient level data were obtained for more than 17 million people registered with a general practice in England that uses TPP software. Electronic health records were linked with death data from the Office for National Statistics and hospital admission data from NHS Secondary Uses Service.<h4>Participants</h4>Adults (aged 16-105 years) and children (<16 years) from two cohorts: wave 1 (registered with a TPP practice as of 1 March 2020 and followed until 31 August 2020); and wave 2 (registered 1 September 2020 and followed until 8 February 2021). The main exposure group consisted of people on a general practice learning disability register; a subgroup was defined as those having profound or severe learning disability. People with Down's syndrome and cerebral palsy were identified (whether or not they were on the learning disability register).<h4>Main outcome measure</h4>Covid-19 related hospital admission and covid-19 related death. Non-covid-19 deaths were also explored.<h4>Results</h4>For wave 1, 14 312 023 adults aged ≥16 years were included, and 90 307 (0.63%) were on the learning disability register. Among adults on the register, 538 (0.6%) had a covid-19 related hospital admission; there were 222 (0.25%) covid-19 related deaths and 602 (0.7%) non-covid deaths. Among adults not on the register, 29 781 (0.2%) had a covid-19 related hospital admission; there were 13 737 (0.1%) covid-19 related deaths and 69 837 (0.5%) non-covid deaths. Wave 1 hazard ratios for adults on the learning disability register (adjusted for age, sex, ethnicity, and geographical location) were 5.3 (95% confidence interval 4.9 to 5.8) for covid-19 related hospital admission and 8.2 (7.2 to 9.4) for covid-19 related death. Wave 2 produced similar estimates. Associations were stronger among those classified as having severe to profound learning disability, and among those in residential care. For both waves, Down's syndrome and cerebral palsy were associated with increased hazards for both events; Down's syndrome to a greater extent. Hazard ratios for non-covid deaths followed similar patterns with weaker associations. Similar patterns of increased relative risk were seen for children, but covid-19 related deaths and hospital admissions were rare, reflecting low event rates among children.<h4>Conclusions</h4>People with learning disability have markedly increased risks of hospital admission and death from covid-19, over and above the risks observed for non-covid causes of death. Prompt access to covid-19 testing and healthcare is warranted for this vulnerable group, and prioritisation for covid-19 vaccination and other targeted preventive measures should be considered.",,pdf:https://www.bmj.com/content/bmj/374/bmj.n1592.full.pdf; doi:https://doi.org/10.1136/bmj.n1592; html:https://europepmc.org/articles/PMC8278652; pdf:https://europepmc.org/articles/PMC8278652?pdf=render
+39446320,https://doi.org/10.1001/jamanetworkopen.2024.41166,Pharmacologic Treatments for Dementia and the Risk of Developing Age-Related Macular Degeneration.,"Wang J, Antza C, Lee WH, Coker J, Keane PA, Denniston AK, Nirantharakumar K, Adderley NJ.",,JAMA network open,2024,2024-10-01,N,,,,"<h4>Importance</h4>Age-related macular degeneration (AMD) is the leading cause of blindness among people aged 50 years or older worldwide. There is a need for new strategies for the prevention and treatment of AMD. There is some limited evidence to suggest the possibility of a protective association of dementia medications with the development of some types of AMD, but the evidence is weak.<h4>Objective</h4>To investigate whether the dementia medications memantine and donepezil are associated with the risk of developing AMD.<h4>Design, setting, and participants</h4>Three population-based cohort studies were performed using data from the Clinical Practice Research Datalink GOLD and Aurum databases from May 15, 2002, to June 21, 2022. Participants included individuals with dementia (vascular dementia, nonvascular dementia, or Alzheimer disease) aged 40 years or older. Statistical analysis was carried out between February and November 2023.<h4>Exposures</h4>Exposures were dementia medications. Cohort 1 compared patients prescribed donepezil with those prescribed rivastigmine or galantamine using the new-user design. Cohort 2 compared memantine with donepezil, rivastigmine, or galantamine using the prevalent new-user design. In a sensitivity analysis, cohort 3 compared memantine with rivastigmine or galantamine only.<h4>Main outcomes and measures</h4>New diagnosis of AMD.<h4>Results</h4>There were 132 846 individuals (mean [SD] age, 80.4 [7.6] years; 61.8% women; mean [SD] body mass index [BMI], 25.5 [4.6]) with a diagnosis of dementia included in cohort 1, 159 419 individuals (mean [SD] age, 81.2 [7.6] years; 59.7% women; mean [SD] body mass index [BMI], 25.6 [4.7]) with a diagnosis of dementia included in cohort 2, and 92 328 individuals with a diagnosis of dementia included in cohort 3 (mean [SD] age, 80.9 [7.7] years; 58.5% women; mean [SD] body mass index [BMI], 25.5 [4.7]). The adjusted hazard ratio (HR) for donepezil compared with rivastigmine or galantamine (cohort 1) was 0.95 (95% CI, 0.67-1.35). The adjusted HR for memantine compared with donepezil, rivastigmine, or galantamine (cohort 2) was 1.03 (95% CI, 0.83-1.27). The adjusted HR for memantine vs rivastigmine or galantamine only (cohort 3) was 1.24 (95% CI, 0.83-1.86).<h4>Conclusions and relevance</h4>This cohort study of patients with dementia found no significant associations between memantine or donepezil compared with other dementia medications and the risk of development of AMD. Further research is recommended to examine any possible pathophysiological protective action of memantine and other dementia medications against the development of AMD.",,doi:https://doi.org/10.1001/jamanetworkopen.2024.41166
 34957254,https://doi.org/10.3389/fcvm.2021.766287,Radiomics Analysis Derived From LGE-MRI Predict Sudden Cardiac Death in Participants With Hypertrophic Cardiomyopathy.,"Wang J, Bravo L, Zhang J, Liu W, Wan K, Sun J, Zhu Y, Han Y, Gkoutos GV, Chen Y.",,Frontiers in cardiovascular medicine,2021,2021-12-10,Y,hypertrophic cardiomyopathy; Sudden Cardiac Death; Machine Learning; Late Gadolinium Enhancement; Radiomics,,,"<b>Objectives:</b> To identify significant radiomics features derived from late gadolinium enhancement (LGE) images in participants with hypertrophic cardiomyopathy (HCM) and assess their prognostic value in predicting sudden cardiac death (SCD) endpoint. <b>Method:</b> The 157 radiomic features of 379 sequential participants with HCM who underwent cardiovascular magnetic resonance imaging (MRI) were extracted. CoxNet (Least Absolute Shrinkage and Selection Operator (LASSO) and Elastic Net) and Random Forest models were applied to optimize feature selection for the SCD risk prediction and cross-validation was performed. <b>Results:</b> During a median follow-up of 29 months (interquartile range, 20-42 months), 27 participants with HCM experienced SCD events. Cox analysis revealed that two selected features, local binary patterns (LBP) (19) (hazard ratio (HR), 1.028, 95% CI: 1.032-1.134; <i>P</i> = 0.001) and Moment (1) (HR, 1.212, 95%CI: 1.032-1.423; <i>P</i> = 0.02) provided significant prognostic value to predict the SCD endpoints after adjustment for the clinical risk predictors and late gadolinium enhancement. Furthermore, the univariately significant risk predictor was improved by the addition of the selected radiomics features, LBP (19) and Moment (1), to predict SCD events (<i>P</i> < 0.05). <b>Conclusion:</b> The radiomics features of LBP (19) and Moment (1) extracted from LGE images, reflecting scar heterogeneity, have independent prognostic value in identifying high SCD risk patients with HCM.",,pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2021.766287/pdf; doi:https://doi.org/10.3389/fcvm.2021.766287; html:https://europepmc.org/articles/PMC8702805; pdf:https://europepmc.org/articles/PMC8702805?pdf=render
 33838587,https://doi.org/10.1016/j.epidem.2021.100460,Competition between RSV and influenza: Limits of modelling inference from surveillance data.,"Waterlow NR, Flasche S, Minter A, Eggo RM.",,Epidemics,2021,2021-03-26,Y,Interaction; Competition; Influenza; Respiratory syncytial virus; Inference,,,"Respiratory Syncytial Virus (RSV) and Influenza cause a large burden of disease. Evidence of their interaction via temporary cross-protection implies that prevention of one could inadvertently lead to an increase in the burden of the other. However, evidence for the public health impact of such interaction is sparse and largely derives from ecological analyses of peak shifts in surveillance data. To test the robustness of estimates of interaction parameters between RSV and Influenza from surveillance data we conducted a simulation and back-inference study. We developed a two-pathogen interaction model, parameterised to simulate RSV and Influenza epidemiology in the UK. Using the infection model in combination with a surveillance-like stochastic observation process we generated a range of possible RSV and Influenza trajectories and then used Markov Chain Monte Carlo (MCMC) methods to back-infer parameters including those describing competition. We find that in most scenarios both the strength and duration of RSV and Influenza interaction could be estimated from the simulated surveillance data reasonably well. However, the robustness of inference declined towards the extremes of the plausible parameter ranges, with misleading results. It was for instance not possible to tell the difference between low/moderate interaction and no interaction. In conclusion, our results illustrate that in a plausible parameter range, the strength of RSV and Influenza interaction can be estimated from a single season of high-quality surveillance data but also highlights the importance to test parameter identifiability a priori in such situations.",,doi:https://doi.org/10.1016/j.epidem.2021.100460; doi:https://doi.org/10.1016/j.epidem.2021.100460; html:https://europepmc.org/articles/PMC8193815
 36158997,https://doi.org/10.3389/fdgth.2022.874237,Evaluating physical urban features in several mental illnesses using electronic health record data.,"Mahabadi Z, Mahabadi M, Velupillai S, Roberts A, McGuire P, Ibrahim Z, Patel R.",,Frontiers in digital health,2022,2022-09-07,Y,Schizophrenia; Bipolar disorder; Psychosis; Machine Learning; Ehr (Electric Heath Record); Geospatial Informatics,,,"<h4>Objectives</h4>Understanding the potential impact of physical characteristics of the urban environment on clinical outcomes on several mental illnesses.<h4>Materials and methods</h4>Physical features of the urban environment were examined as predictors for affective and non-affective several mental illnesses (SMI), the number and length of psychiatric hospital admissions, and the number of short and long-acting injectable antipsychotic prescriptions. In addition, the urban features with the greatest weight in the predicted model were determined. The data included 28 urban features and 6 clinical variables obtained from 30,210 people with SMI receiving care from the South London and Maudsley NHS Foundation Trust (SLaM) using the Clinical Record Interactive Search (CRIS) tool. Five machine learning regression models were evaluated for the highest prediction accuracy followed by the Self-Organising Map (SOM) to represent the results visually.<h4>Results</h4>The prevalence of SMI, number and duration of psychiatric hospital admission, and antipsychotic prescribing were greater in urban areas. However, machine learning analysis was unable to accurately predict clinical outcomes using urban environmental data.<h4>Discussion</h4>The urban environment is associated with an increased prevalence of SMI. However, urban features alone cannot explain the variation observed in psychotic disorder prevalence or clinical outcomes measured through psychiatric hospitalisation or exposure to antipsychotic treatments.<h4>Conclusion</h4>Urban areas are associated with a greater prevalence of SMI but clinical outcomes are likely to depend on a combination of urban and individual patient-level factors. Future mental healthcare service planning should focus on providing appropriate resources to people with SMI in urban environments.",,pdf:https://www.frontiersin.org/articles/10.3389/fdgth.2022.874237/pdf; doi:https://doi.org/10.3389/fdgth.2022.874237; html:https://europepmc.org/articles/PMC9490173; pdf:https://europepmc.org/articles/PMC9490173?pdf=render
-39175920,https://doi.org/10.1136/bmjmed-2023-000633,Age and sex specific thresholds for risk stratification of cardiovascular disease and clinical decision making: prospective open cohort study.,"Xu Z, Usher-Smith J, Pennells L, Chung R, Arnold M, Kim L, Kaptoge S, Sperrin M, Di Angelantonio E, Wood AM.",,BMJ medicine,2024,2024-08-12,Y,Cardiovascular disease; Risk stratification; Risk Prediction; Statin Treatment,,,"<h4>Objective</h4>To quantify the potential advantages of using 10 year risk prediction models for cardiovascular disease, in combination with risk thresholds specific to both age and sex, to identify individuals at high risk of cardiovascular disease for allocation of statin treatment.<h4>Design</h4>Prospective open cohort study.<h4>Setting</h4>Primary care data from the UK Clinical Practice Research Datalink GOLD, linked with hospital admissions from Hospital Episode Statistics and national mortality records from the Office for National Statistics in England, 1 January 2006 to 31 May 2019.<h4>Participants</h4>1 046 736 individuals (aged 40-85 years) with no cardiovascular disease, diabetes, or a history of statin treatment at baseline using data from electronic health records.<h4>Main outcome measures</h4>10 year risk of cardiovascular disease, calculated with version 2 of the QRISK cardiovascular disease risk algorithm (QRISK2), with two main strategies to identify individuals at high risk: in strategy A, estimated risk was a fixed cut-off value of ≥10% (ie, as per the UK National Institute for Health and Care Excellence guidelines); in strategy B, estimated risk was ≥10% or ≥90th centile of age and sex specific risk distributions.<h4>Results</h4>Compared with strategy A, strategy B stratified 20 241 (149.8%) more women aged ≤53 years and 9832 (150.2%) more men aged ≤47 years as having a high risk of cardiovascular disease; for all other ages the strategies were the same. Assuming that treatment with statins would be initiated in those identified as high risk, differences in the estimated gain in cardiovascular disease-free life years from statin treatment for strategy B versus strategy A were 0.14 and 0.16 years for women and men aged 40 years, respectively; among individuals aged 40-49 years, the numbers needed to treat to prevent one cardiovascular disease event for strategy B versus strategy A were 39 versus 21 in women and 19 versus 15 in men, respectively.<h4>Conclusions</h4>This study quantified the potential gains in cardiovascular disease-free life years when implementing prevention strategies based on age and sex specific risk thresholds instead of a fixed risk threshold for allocation of statin treatment. Such gains should be weighed against the costs of treating more younger people with statins for longer.",,doi:https://doi.org/10.1136/bmjmed-2023-000633; html:https://europepmc.org/articles/PMC11340247; pdf:https://europepmc.org/articles/PMC11340247?pdf=render
-35474585,https://doi.org/10.1111/bcp.15366,Angiotensin-converting enzyme inhibitors and risk of age-related macular degeneration in individuals with hypertension.,"Subramanian A, Han D, Braithwaite T, Thayakaran R, Zemedikun DT, Gokhale KM, Lee WH, Coker J, Keane PA, Denniston AK, Nirantharakumar K, Azoulay L, Adderley NJ.",,British journal of clinical pharmacology,2022,2022-05-11,Y,Hypertension; Angiotensin-converting enzyme inhibitors; Age-related macular degeneration,,,"<h4>Aims</h4>Several observational studies have examined the potential protective effect of angiotensin-converting enzyme inhibitor (ACE-I) use on the risk of age-related macular degeneration (AMD) and have reported contradictory results owing to confounding and time-related biases. We aimed to assess the risk of AMD in a base cohort of patients aged 40 years and above with hypertension among new users of ACE-I compared to an active comparator cohort of new users of calcium channel blockers (CCB) using data obtained from IQVIA Medical Research Data, a primary care database in the UK.<h4>Methods</h4>In this study, 53 832 and 43 106 new users of ACE-I and CCB were included between 1995 and 2019, respectively. In an on-treatment analysis, patients were followed up from the time of index drug initiation to the date of AMD diagnosis, loss to follow-up, discontinuation or switch to the comparator drug. A comprehensive range of covariates were used to estimate propensity scores to weight and match new users of ACE-I and CCB. Standardized mortality ratio weighted Cox proportional hazards model was used to estimate hazard ratios of developing AMD.<h4>Results</h4>During a median follow-up of 2 years (interquartile range 1-5 years), the incidence rate of AMD was 2.4 (95% confidence interval 2.2-2.6) and 2.2 (2.0-2.4) per 1000 person-years among the weighted new users of ACE-I and CCB, respectively. There was no association of ACE-I use on the risk of AMD compared to CCB use in either the propensity score weighted or matched, on-treatment analysis (adjusted hazard ratio: 1.07 [95% confidence interval 0.90-1.27] and 0.87 [0.71-1.07], respectively).<h4>Conclusion</h4>We found no evidence that the use of ACE-I is associated with risk of AMD in patients with hypertension.",,doi:https://doi.org/10.1111/bcp.15366; doi:https://doi.org/10.1111/bcp.15366; html:https://europepmc.org/articles/PMC9541840; pdf:https://europepmc.org/articles/PMC9541840?pdf=render
 31591592,https://doi.org/10.1038/s41591-019-0597-x,Avoidable flaws in observational analyses: an application to statins and cancer.,"Dickerman BA, García-Albéniz X, Logan RW, Denaxas S, Hernán MA.",,Nature medicine,2019,2019-10-07,N,,,,"The increasing availability of large healthcare databases is fueling an intense debate on whether real-world data should play a role in the assessment of the benefit-risk of medical treatments. In many observational studies, for example, statin users were found to have a substantially lower risk of cancer than in meta-analyses of randomized trials. Although such discrepancies are often attributed to a lack of randomization in the observational studies, they might be explained by flaws that can be avoided by explicitly emulating a target trial (the randomized trial that would answer the question of interest). Using the electronic health records of 733,804 UK adults, we emulated a target trial of statins and cancer and compared our estimates with those obtained using previously applied analytic approaches. Over the 10-yr follow-up, 28,408 individuals developed cancer. Under the target trial approach, estimated observational analogs of intention-to-treat and per-protocol 10-yr cancer-free survival differences were -0.5% (95% confidence interval (CI) -1.0%, 0.0%) and -0.3% (95% CI -1.5%, 0.5%), respectively. By contrast, previous analytic approaches yielded estimates that appeared to be strongly protective. Our findings highlight the importance of explicitly emulating a target trial to reduce bias in the effect estimates derived from observational analyses.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7076561; doi:https://doi.org/10.1038/s41591-019-0597-x; html:https://europepmc.org/articles/PMC7076561; pdf:https://europepmc.org/articles/PMC7076561?pdf=render; doi:https://doi.org/10.1038/s41591-019-0597-x
-38317644,https://doi.org/10.1177/03331024241229410,How migraine and its associated treatment impact on pregnancy outcomes: Umbrella review with updated systematic review and meta-analysis.,"Phillips K, Clerkin-Oliver C, Nirantharakumar K, Crowe FL, Wakerley BR.",,Cephalalgia : an international journal of headache,2024,2024-02-01,N,Pregnancy; Migraine,,,"<h4>Background</h4>Migraine is common in reproductive aged women. Understanding the impact of migraine and associated treatments on pregnancy outcomes remains very important. An umbrella review of systematic reviews, with or without meta-analyses, examined the link between migraine and pregnancy outcomes.<h4>Methods</h4>We systematically searched Medline, Embase and Cochrane to 27 October 2022. Quality appraisal was carried out using the AMSTAR2 tool. An established framework was used to determine whether included reviews were eligible for update.<h4>Results</h4>Four studies met review criteria. Migraine was reported to be associated with increased odds ratio (OR) of pre-eclampsia, low birth weight and peripartum mental illness (pooled OR = 3.54 (2.24-5.59)). Triptan-exposed women had increased odds of miscarriage compared to women without migraine (pooled OR = 3.54 (2.24-5.59)). In updated meta-analyses, migraine was associated with an increased odds of pre-eclampsia and preterm birth (pooled OR = 2.05 (1.47-2.84) and 1.26 (1.21-1.32) respectively).<h4>Conclusions</h4>Migraine is associated with increased odds of pre-eclampsia, peripartum mental illness and preterm birth. Further investigation of the relationship between migraine and placental abruption, low birth weight and small for gestational age is warranted, as well as the relationship between migraine, triptans and miscarriage risk.<b>Systematic Review Registration:</b> Prospero CRD42022357630.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/03331024241229410; doi:https://doi.org/10.1177/03331024241229410
-32180562,https://doi.org/10.1016/j.molmet.2020.01.009,Genome-wide association study of adipocyte lipolysis in the GENetics of adipocyte lipolysis (GENiAL) cohort.,"Kulyté A, Lundbäck V, Lindgren CM, Luan J, Lotta LA, Langenberg C, Arner P, Strawbridge RJ, Dahlman I.",,Molecular metabolism,2020,2020-01-25,Y,Adipocytes; Gene Expression; Subcutaneous; Genetic Variants; Lipolysis,The Human Phenome,,"<h4>Objectives</h4>Lipolysis, hydrolysis of triglycerides to fatty acids in adipocytes, is tightly regulated, poorly understood, and, if perturbed, can lead to metabolic diseases including obesity and type 2 diabetes. The goal of this study was to identify the genetic regulators of lipolysis and elucidate their molecular mechanisms.<h4>Methods</h4>Adipocytes from abdominal subcutaneous adipose tissue biopsies were isolated and were incubated without (spontaneous lipolysis) or with a catecholamine (stimulated lipolysis) to analyze lipolysis. DNA was extracted and genome-wide genotyping and imputation conducted. After quality control, 939 samples with genetic and lipolysis data were available. Genome-wide association studies of spontaneous and stimulated lipolysis were conducted. Subsequent in vitro gene expression analyses were used to identify candidate genes and explore their regulation of adipose tissue biology.<h4>Results</h4>One locus on chromosome 19 demonstrated genome-wide significance with spontaneous lipolysis. 60 loci showed suggestive associations with spontaneous or stimulated lipolysis, of which many influenced both traits. In the chromosome 19 locus, only HIF3A was expressed in the adipocytes and displayed genotype-dependent gene expression. HIF3A knockdown in vitro increased lipolysis and the expression of key lipolysis-regulating genes.<h4>Conclusions</h4>In conclusion, we identified a genetic regulator of spontaneous lipolysis and provided evidence of HIF3A as a novel key regulator of lipolysis in subcutaneous adipocytes as the mechanism through which the locus influences adipose tissue biology.","How the body breaks down fat is poorly understood, and, if this mechanism does not happen effiently in the body it can lead to metabolic diseases including obesity and type 2 diabetes. The goal of this study was to identify the genetic regulators of how the body break down fat and explain their molecular mechanisms.",doi:https://doi.org/10.1016/j.molmet.2020.01.009; doi:https://doi.org/10.1016/j.molmet.2020.01.009; html:https://europepmc.org/articles/PMC7021539; pdf:https://europepmc.org/articles/PMC7021539?pdf=render
+35474585,https://doi.org/10.1111/bcp.15366,Angiotensin-converting enzyme inhibitors and risk of age-related macular degeneration in individuals with hypertension.,"Subramanian A, Han D, Braithwaite T, Thayakaran R, Zemedikun DT, Gokhale KM, Lee WH, Coker J, Keane PA, Denniston AK, Nirantharakumar K, Azoulay L, Adderley NJ.",,British journal of clinical pharmacology,2022,2022-05-11,Y,Hypertension; Angiotensin-converting enzyme inhibitors; Age-related macular degeneration,,,"<h4>Aims</h4>Several observational studies have examined the potential protective effect of angiotensin-converting enzyme inhibitor (ACE-I) use on the risk of age-related macular degeneration (AMD) and have reported contradictory results owing to confounding and time-related biases. We aimed to assess the risk of AMD in a base cohort of patients aged 40 years and above with hypertension among new users of ACE-I compared to an active comparator cohort of new users of calcium channel blockers (CCB) using data obtained from IQVIA Medical Research Data, a primary care database in the UK.<h4>Methods</h4>In this study, 53 832 and 43 106 new users of ACE-I and CCB were included between 1995 and 2019, respectively. In an on-treatment analysis, patients were followed up from the time of index drug initiation to the date of AMD diagnosis, loss to follow-up, discontinuation or switch to the comparator drug. A comprehensive range of covariates were used to estimate propensity scores to weight and match new users of ACE-I and CCB. Standardized mortality ratio weighted Cox proportional hazards model was used to estimate hazard ratios of developing AMD.<h4>Results</h4>During a median follow-up of 2 years (interquartile range 1-5 years), the incidence rate of AMD was 2.4 (95% confidence interval 2.2-2.6) and 2.2 (2.0-2.4) per 1000 person-years among the weighted new users of ACE-I and CCB, respectively. There was no association of ACE-I use on the risk of AMD compared to CCB use in either the propensity score weighted or matched, on-treatment analysis (adjusted hazard ratio: 1.07 [95% confidence interval 0.90-1.27] and 0.87 [0.71-1.07], respectively).<h4>Conclusion</h4>We found no evidence that the use of ACE-I is associated with risk of AMD in patients with hypertension.",,doi:https://doi.org/10.1111/bcp.15366; doi:https://doi.org/10.1111/bcp.15366; html:https://europepmc.org/articles/PMC9541840; pdf:https://europepmc.org/articles/PMC9541840?pdf=render
 34282121,https://doi.org/10.1038/s41398-021-01522-4,Phenotypic and genetic associations between anhedonia and brain structure in UK Biobank.,"Zhu X, Ward J, Cullen B, Lyall DM, Strawbridge RJ, Lyall LM, Smith DJ.",,Translational psychiatry,2021,2021-07-16,Y,,,,"Anhedonia is a core symptom of multiple psychiatric disorders and has been associated with alterations in brain structure. Genome-wide association studies suggest that anhedonia is heritable, with a polygenic architecture, but few studies have explored the association between genetic loading for anhedonia-indexed by polygenic risk scores for anhedonia (PRS-anhedonia)-and structural brain imaging phenotypes. Here, we investigated how anhedonia and PRS-anhedonia were associated with brain structure within the UK Biobank cohort. Brain measures (including total grey/white matter volumes, subcortical volumes, cortical thickness (CT) and white matter integrity) were analysed using linear mixed models in relation to anhedonia and PRS-anhedonia in 19,592 participants (9225 males; mean age = 62.6 years, SD = 7.44). We found that state anhedonia was significantly associated with reduced total grey matter volume (GMV); increased total white matter volume (WMV); smaller volumes in thalamus and nucleus accumbens; reduced CT within the paracentral cortex, the opercular part of inferior frontal gyrus, precentral cortex, insula and rostral anterior cingulate cortex; and poorer integrity of many white matter tracts. PRS-anhedonia was associated with reduced total GMV; increased total WMV; reduced white matter integrity; and reduced CT within the parahippocampal cortex, superior temporal gyrus and insula. Overall, both state anhedonia and PRS-anhedonia were associated with individual differences in multiple brain structures, including within reward-related circuits. These associations may represent vulnerability markers for psychopathology relevant to a range of psychiatric disorders.",,pdf:https://www.nature.com/articles/s41398-021-01522-4.pdf; doi:https://doi.org/10.1038/s41398-021-01522-4; html:https://europepmc.org/articles/PMC8289859; pdf:https://europepmc.org/articles/PMC8289859?pdf=render
+39175920,https://doi.org/10.1136/bmjmed-2023-000633,Age and sex specific thresholds for risk stratification of cardiovascular disease and clinical decision making: prospective open cohort study.,"Xu Z, Usher-Smith J, Pennells L, Chung R, Arnold M, Kim L, Kaptoge S, Sperrin M, Di Angelantonio E, Wood AM.",,BMJ medicine,2024,2024-08-12,Y,Cardiovascular disease; Risk stratification; Risk Prediction; Statin Treatment,,,"<h4>Objective</h4>To quantify the potential advantages of using 10 year risk prediction models for cardiovascular disease, in combination with risk thresholds specific to both age and sex, to identify individuals at high risk of cardiovascular disease for allocation of statin treatment.<h4>Design</h4>Prospective open cohort study.<h4>Setting</h4>Primary care data from the UK Clinical Practice Research Datalink GOLD, linked with hospital admissions from Hospital Episode Statistics and national mortality records from the Office for National Statistics in England, 1 January 2006 to 31 May 2019.<h4>Participants</h4>1 046 736 individuals (aged 40-85 years) with no cardiovascular disease, diabetes, or a history of statin treatment at baseline using data from electronic health records.<h4>Main outcome measures</h4>10 year risk of cardiovascular disease, calculated with version 2 of the QRISK cardiovascular disease risk algorithm (QRISK2), with two main strategies to identify individuals at high risk: in strategy A, estimated risk was a fixed cut-off value of ≥10% (ie, as per the UK National Institute for Health and Care Excellence guidelines); in strategy B, estimated risk was ≥10% or ≥90th centile of age and sex specific risk distributions.<h4>Results</h4>Compared with strategy A, strategy B stratified 20 241 (149.8%) more women aged ≤53 years and 9832 (150.2%) more men aged ≤47 years as having a high risk of cardiovascular disease; for all other ages the strategies were the same. Assuming that treatment with statins would be initiated in those identified as high risk, differences in the estimated gain in cardiovascular disease-free life years from statin treatment for strategy B versus strategy A were 0.14 and 0.16 years for women and men aged 40 years, respectively; among individuals aged 40-49 years, the numbers needed to treat to prevent one cardiovascular disease event for strategy B versus strategy A were 39 versus 21 in women and 19 versus 15 in men, respectively.<h4>Conclusions</h4>This study quantified the potential gains in cardiovascular disease-free life years when implementing prevention strategies based on age and sex specific risk thresholds instead of a fixed risk threshold for allocation of statin treatment. Such gains should be weighed against the costs of treating more younger people with statins for longer.",,doi:https://doi.org/10.1136/bmjmed-2023-000633; html:https://europepmc.org/articles/PMC11340247; pdf:https://europepmc.org/articles/PMC11340247?pdf=render
+32180562,https://doi.org/10.1016/j.molmet.2020.01.009,Genome-wide association study of adipocyte lipolysis in the GENetics of adipocyte lipolysis (GENiAL) cohort.,"Kulyté A, Lundbäck V, Lindgren CM, Luan J, Lotta LA, Langenberg C, Arner P, Strawbridge RJ, Dahlman I.",,Molecular metabolism,2020,2020-01-25,Y,Adipocytes; Gene Expression; Subcutaneous; Genetic Variants; Lipolysis,The Human Phenome,,"<h4>Objectives</h4>Lipolysis, hydrolysis of triglycerides to fatty acids in adipocytes, is tightly regulated, poorly understood, and, if perturbed, can lead to metabolic diseases including obesity and type 2 diabetes. The goal of this study was to identify the genetic regulators of lipolysis and elucidate their molecular mechanisms.<h4>Methods</h4>Adipocytes from abdominal subcutaneous adipose tissue biopsies were isolated and were incubated without (spontaneous lipolysis) or with a catecholamine (stimulated lipolysis) to analyze lipolysis. DNA was extracted and genome-wide genotyping and imputation conducted. After quality control, 939 samples with genetic and lipolysis data were available. Genome-wide association studies of spontaneous and stimulated lipolysis were conducted. Subsequent in vitro gene expression analyses were used to identify candidate genes and explore their regulation of adipose tissue biology.<h4>Results</h4>One locus on chromosome 19 demonstrated genome-wide significance with spontaneous lipolysis. 60 loci showed suggestive associations with spontaneous or stimulated lipolysis, of which many influenced both traits. In the chromosome 19 locus, only HIF3A was expressed in the adipocytes and displayed genotype-dependent gene expression. HIF3A knockdown in vitro increased lipolysis and the expression of key lipolysis-regulating genes.<h4>Conclusions</h4>In conclusion, we identified a genetic regulator of spontaneous lipolysis and provided evidence of HIF3A as a novel key regulator of lipolysis in subcutaneous adipocytes as the mechanism through which the locus influences adipose tissue biology.","How the body breaks down fat is poorly understood, and, if this mechanism does not happen effiently in the body it can lead to metabolic diseases including obesity and type 2 diabetes. The goal of this study was to identify the genetic regulators of how the body break down fat and explain their molecular mechanisms.",doi:https://doi.org/10.1016/j.molmet.2020.01.009; doi:https://doi.org/10.1016/j.molmet.2020.01.009; html:https://europepmc.org/articles/PMC7021539; pdf:https://europepmc.org/articles/PMC7021539?pdf=render
+38317644,https://doi.org/10.1177/03331024241229410,How migraine and its associated treatment impact on pregnancy outcomes: Umbrella review with updated systematic review and meta-analysis.,"Phillips K, Clerkin-Oliver C, Nirantharakumar K, Crowe FL, Wakerley BR.",,Cephalalgia : an international journal of headache,2024,2024-02-01,N,Pregnancy; Migraine,,,"<h4>Background</h4>Migraine is common in reproductive aged women. Understanding the impact of migraine and associated treatments on pregnancy outcomes remains very important. An umbrella review of systematic reviews, with or without meta-analyses, examined the link between migraine and pregnancy outcomes.<h4>Methods</h4>We systematically searched Medline, Embase and Cochrane to 27 October 2022. Quality appraisal was carried out using the AMSTAR2 tool. An established framework was used to determine whether included reviews were eligible for update.<h4>Results</h4>Four studies met review criteria. Migraine was reported to be associated with increased odds ratio (OR) of pre-eclampsia, low birth weight and peripartum mental illness (pooled OR = 3.54 (2.24-5.59)). Triptan-exposed women had increased odds of miscarriage compared to women without migraine (pooled OR = 3.54 (2.24-5.59)). In updated meta-analyses, migraine was associated with an increased odds of pre-eclampsia and preterm birth (pooled OR = 2.05 (1.47-2.84) and 1.26 (1.21-1.32) respectively).<h4>Conclusions</h4>Migraine is associated with increased odds of pre-eclampsia, peripartum mental illness and preterm birth. Further investigation of the relationship between migraine and placental abruption, low birth weight and small for gestational age is warranted, as well as the relationship between migraine, triptans and miscarriage risk.<b>Systematic Review Registration:</b> Prospero CRD42022357630.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/03331024241229410; doi:https://doi.org/10.1177/03331024241229410
 34782484,https://doi.org/10.1136/thoraxjnl-2021-217580,External validation of the QCovid risk prediction algorithm for risk of COVID-19 hospitalisation and mortality in adults: national validation cohort study in Scotland.,"Simpson CR, Robertson C, Kerr S, Shi T, Vasileiou E, Moore E, McCowan C, Agrawal U, Docherty A, Mulholland R, Murray J, Ritchie LD, McMenamin J, Hippisley-Cox J, Sheikh A.",,Thorax,2022,2021-11-15,Y,Clinical Epidemiology; Covid-19,,,"<h4>Background</h4>The QCovid algorithm is a risk prediction tool that can be used to stratify individuals by risk of COVID-19 hospitalisation and mortality. Version 1 of the algorithm was trained using data covering 10.5 million patients in England in the period 24 January 2020 to 30 April 2020. We carried out an external validation of version 1 of the QCovid algorithm in Scotland.<h4>Methods</h4>We established a national COVID-19 data platform using individual level data for the population of Scotland (5.4 million residents). Primary care data were linked to reverse-transcription PCR (RT-PCR) virology testing, hospitalisation and mortality data. We assessed the performance of the QCovid algorithm in predicting COVID-19 hospitalisations and deaths in our dataset for two time periods matching the original study: 1 March 2020 to 30 April 2020, and 1 May 2020 to 30 June 2020.<h4>Results</h4>Our dataset comprised 5 384 819 individuals, representing 99% of the estimated population (5 463 300) resident in Scotland in 2020. The algorithm showed good calibration in the first period, but systematic overestimation of risk in the second period, prior to temporal recalibration. Harrell's C for deaths in females and males in the first period was 0.95 (95% CI 0.94 to 0.95) and 0.93 (95% CI 0.92 to 0.93), respectively. Harrell's C for hospitalisations in females and males in the first period was 0.81 (95% CI 0.80 to 0.82) and 0.82 (95% CI 0.81 to 0.82), respectively.<h4>Conclusions</h4>Version 1 of the QCovid algorithm showed high levels of discrimination in predicting the risk of COVID-19 hospitalisations and deaths in adults resident in Scotland for the original two time periods studied, but is likely to need ongoing recalibration prospectively.",,pdf:https://thorax.bmj.com/content/thoraxjnl/77/5/497.full.pdf; doi:https://doi.org/10.1136/thoraxjnl-2021-217580; html:https://europepmc.org/articles/PMC8595052; pdf:https://europepmc.org/articles/PMC8595052?pdf=render
 38419826,https://doi.org/10.23889/ijpds.v8i4.2164,Common governance model: a way to avoid data segregation between existing trusted research environment.,"Torabi F, Orton C, Squires E, Heys S, Hier R, Lyons RA, Thompson S.",,International journal of population data science,2023,2023-11-08,Y,Data Protection; Data Governance; Trusted Research Environments,,,"<h4>Background</h4>Trusted Research Environments provide a legitimate basis for data access along with a set of technologies to support implementation of the ""five-safes"" framework for privacy protection. Lack of standard approaches in achieving compliance with the ""five-safes"" framework results in a diversity of approaches across different TREs. Data access and analysis across multiple TREs has a range of benefits including improved precision of analysis due to larger sample sizes and broader availability of out-of-sample records, particularly in the study of rare conditions. Knowledge of governance approaches used across UK-TREs is limited.<h4>Objective</h4>To document key governance features in major UK-TRE contributing to UK wide analysis and to identify elements that would directly facilitate multi TRE collaborations and federated analysis in future.<h4>Method</h4>We summarised three main characteristics across 15 major UK-based TREs: 1) data access environment; 2) data access requests and disclosure control procedures; and 3) governance models. We undertook case studies of collaborative analyses conducted in more than one TRE. We identified an array of TREs operating on an equivalent level of governance. We further identify commonly governed TREs with architectural considerations for achieving an equivalent level of information security management system standards to facilitate multi TRE functionality and federated analytics.<h4>Results</h4>All 15 UK-TREs allow pooling and analysis of aggregated research outputs only when they have passed human-operated disclosure control checks. Data access requests procedures are unique to each TRE. We also observed a variability in disclosure control procedures across various TREs with no or minimal researcher guidance on best practices for file out request procedures. In 2023, six TREs (40.0%) held ISO 20071 accreditation, while 9 TREs (56.2%) participated in four-nation analyses.<h4>Conclusion</h4>Secure analysis of individual-level data from multiple TREs is possible through existing technical solutions but requires development of a well-established governance framework meeting all stakeholder requirements and addressing public and patient concerns. Formation of a standard model could act as the catalyst for evolution of current TREs governance models to a multi TRE ecosystem within the UK and beyond.",,doi:https://doi.org/10.23889/ijpds.v8i4.2164; html:https://europepmc.org/articles/PMC10900179; pdf:https://europepmc.org/articles/PMC10900179?pdf=render
 34632260,https://doi.org/10.1093/rap/rkab042,"Biologic use in psoriatic arthritis and ankylosing spondylitis patients: a descriptive epidemiological study using linked, routine data in Wales, UK.","Cooksey R, Rahman MA, Kennedy J, Brophy S, Choy E.",,Rheumatology advances in practice,2021,2021-06-27,Y,Ankylosing spondylitis; Psoriatic Arthritis; Outcomes; Biologics; Electronic Health Records; Treatment Pathways,,,"<h4>Objectives</h4>PsA and AS are chronic diseases associated with significant morbidities. National and international management guidelines include treatment with biologic therapies to improve outcomes and quality of life. There are limited real-world data on the patients' journey from symptom onset to diagnosis and treatment in the UK. We use real-life, linked health data to explore patient pathways and the impact of biologics on patient outcomes.<h4>Methods</h4>Data from the Secure Anonymised Information Linkage databank in Wales were used to assess diagnosis and treatment of patients ≥18 years of age with at least one International Classification of Diseases, Tenth Revision code present for PsA/AS in rheumatology clinic data and at least one Read code present in primary care records. We investigated the use of biologics while exploring demographics, comorbidities and surgical procedures of 641 AS patients and 1312 PsA patients.<h4>Results</h4>AS patients were significantly younger at diagnosis and were predominantly male. The average time from presenting symptoms to diagnosis of AS and PsA was 7.9 (s.d. 5.5) and 9.3 (s.d. 5.5) years, respectively. The proportion of patients receiving biologic treatment was significantly higher in AS (46%) compared with PsA patients (28.8%); of these, 23.1% of AS and 22.2% of PsA patients stopped/switched a biologic. There was a significant reduction in primary care involvement, sick notes and disability living allowance for both AS and PsA patients following biologic initiation.<h4>Conclusion</h4>This real-world descriptive study confirms that patients treated with biologics have reduced disability and time off work despite being initiated ∼13 years after the first symptoms and 6 years after diagnosis.",,pdf:https://academic.oup.com/rheumap/article-pdf/5/2/rkab042/39307450/rkab042.pdf; doi:https://doi.org/10.1093/rap/rkab042; html:https://europepmc.org/articles/PMC8496109; pdf:https://europepmc.org/articles/PMC8496109?pdf=render
 37634386,https://doi.org/10.1016/j.schres.2023.08.014,Trends in socioeconomic inequalities in incidence of severe mental illness - A population-based linkage study using primary and secondary care routinely collected data between 2000 and 2017.,"Lee SC, DelPozo-Banos M, Lloyd K, Jones I, Walters JTR, John A.",,Schizophrenia research,2023,2023-08-25,N,Deprivation; Severe Mental Illness; Inequality; Recession; Urbanicity; Austerity,,,"<h4>Objective</h4>In 2008, the UK entered a period of economic recession followed by sustained austerity measures. We investigate changes in inequalities by area deprivation and urbanicity in incidence of severe mental illness (SMI, including schizophrenia-related disorders and bipolar disorder) between 2000 and 2017.<h4>Methods</h4>We analysed 4.4 million individuals from primary and secondary care routinely collected datasets (2000-2017) in Wales and estimated the incidence of SMI by deprivation and urbanicity measured by the Welsh Index of Multiple Deprivation (WIMD) and urban/rural indicator respectively. Using linear modelling and joinpoint regression approaches, we examined time trends of the incidence and incidence rate ratios (IRR) of SMI by the WIMD and urban/rural indicator adjusted for available confounders.<h4>Results</h4>We observed a turning point of time trends of incidence of SMI at 2008/2009 where slope changes of time trends were significantly increasing. IRRs by deprivation/urbanicity remained stable or significantly decreased over the study period except for those with bipolar disorder sourced from secondary care settings, with increasing trend of IRRs (increase in IRR by deprivation after 2010: 1.6 % per year, 95 % CI: 1.0 %-2.2 %; increase in IRR by urbanicity 1.0 % per year, 95 % CI: 0.6 %-1.3 %).<h4>Conclusions</h4>There was an association between recession/austerity and an increase in the incidence of SMI over time. There were variations in the effects of deprivation/urbanicity on incidence of SMI associated with short- and long-term socioeconomic change. These findings may support targeted interventions and social protection systems to reduce incidence of SMI.",,pdf:https://orca.cardiff.ac.uk/161774/1/SCHIZR~1.PDF; doi:https://doi.org/10.1016/j.schres.2023.08.014
-33842409,https://doi.org/10.3389/fped.2021.630036,Microtia: A Data Linkage Study of Epidemiology and Implications for Service Delivery.,"Jovic TH, Gibson JAG, Griffiths R, Dobbs TD, Akbari A, Wilson-Jones N, Costello R, Evans P, Cooper M, Key S, Lyons R, Whitaker IS.",,Frontiers in pediatrics,2021,2021-03-26,Y,epidemiology; congenital; Otology; Reconstructive Surgery; Microtia,,,"<b>Introduction:</b> Previous studies of microtia epidemiology globally have demonstrated significant geographical and ethnic variation, cited broadly as affecting 3-5 in 10,000 live births. The aim of this study was to determine the incidence of microtia in a largely homogeneous ethnic population in the United Kingdom (Wales) and to identify factors, such as distance and socioeconomic status, which may influence the access to surgical intervention. <b>Materials and Methods:</b> A retrospective cohort study was conducted using data linkage to identify patients born between 2000 and 2018 with a diagnosis of microtia. Microtia incidence was calculated using annual and geographic birth rates. Surgical operation codes were used to classify patients into those that had no surgery, autologous reconstruction or prosthetic reconstruction. Sociodemographic attributes were compared using descriptive statistics to determine differences in access to each type of surgical intervention. <b>Results:</b> A total of 101 patients were identified, 64.4% were male and the median age was 12 (8-16). The mean annual incidence was 2.13 microtia cases per 10,000 births over the 19-year study period. Both temporal and geographic variation was noted. The majority of patients undergoing surgery opted for autologous reconstruction (72.9%) at a median age of 9 (7-10) compared to 7 (5-8) for prosthetic reconstruction. Autologous reconstruction had a higher median number of surgeries (2, 1-3) than prosthetic (1.5, 1-2) and a higher median socioeconomic status of 3 (2-4) compared to 2 (1-4) for the prosthetic cohort. There were no statistically significant differences in the distance traveled for surgery. <b>Discussion:</b> This study highlights a role for data linkage in epidemiological analyses and provides a revised incidence of microtia in Wales. Although the majority of patients opted for autologous reconstruction, demographic disparities in socioeconomic status warrant further investigation, emphasizing the importance of striving for equity in accessibility to surgical intervention.",,pdf:https://www.frontiersin.org/articles/10.3389/fped.2021.630036/pdf; doi:https://doi.org/10.3389/fped.2021.630036; html:https://europepmc.org/articles/PMC8033003; pdf:https://europepmc.org/articles/PMC8033003?pdf=render
 33182605,https://doi.org/10.3390/genes11111326,"Exploring the Role of Contactins across Psychological, Psychiatric and Cardiometabolic Traits within UK Biobank.","Morris J, Leung SSY, Bailey MES, Cullen B, Ferguson A, Graham N, Johnston KJA, Lyall DM, Lyall LM, Ward J, Smith DJ, Strawbridge RJ.",,Genes,2020,2020-11-10,Y,Hypertension; Genetic variation; Type 2 diabetes; Psychiatric disorders; Single Nucleotide Polymorphisms; Gene Expression; Uk Biobank; Contactins; Cardiometabolic Diseases,,,"Individuals with severe mental illness have an increased risk of cardiometabolic diseases compared to the general population. Shared risk factors and medication effects explain part of this excess risk; however, there is growing evidence to suggest that shared biology (including genetic variation) is likely to contribute to comorbidity between mental and physical illness. Contactins are a family of genes involved in development of the nervous system and implicated, though genome-wide association studies, in a wide range of psychological, psychiatric and cardiometabolic conditions. Contactins are plausible candidates for shared pathology between mental and physical health. We used data from UK Biobank to systematically assess how genetic variation in contactin genes was associated with a wide range of psychological, psychiatric and cardiometabolic conditions. We also investigated whether associations for cardiometabolic and psychological traits represented the same or distinct signals and how the genetic variation might influence the measured traits. We identified: A novel genetic association between variation in <i>CNTN1</i> and current smoking; two independent signals in <i>CNTN4</i> for BMI; and demonstrated that associations between <i>CNTN5</i> and neuroticism were distinct from those between <i>CNTN5</i> and blood pressure/HbA1c. There was no evidence that the contactin genes contributed to shared aetiology between physical and mental illness.",,pdf:https://www.mdpi.com/2073-4425/11/11/1326/pdf?version=1605520057; doi:https://doi.org/10.3390/genes11111326; html:https://europepmc.org/articles/PMC7697406; pdf:https://europepmc.org/articles/PMC7697406?pdf=render
+33842409,https://doi.org/10.3389/fped.2021.630036,Microtia: A Data Linkage Study of Epidemiology and Implications for Service Delivery.,"Jovic TH, Gibson JAG, Griffiths R, Dobbs TD, Akbari A, Wilson-Jones N, Costello R, Evans P, Cooper M, Key S, Lyons R, Whitaker IS.",,Frontiers in pediatrics,2021,2021-03-26,Y,epidemiology; congenital; Otology; Reconstructive Surgery; Microtia,,,"<b>Introduction:</b> Previous studies of microtia epidemiology globally have demonstrated significant geographical and ethnic variation, cited broadly as affecting 3-5 in 10,000 live births. The aim of this study was to determine the incidence of microtia in a largely homogeneous ethnic population in the United Kingdom (Wales) and to identify factors, such as distance and socioeconomic status, which may influence the access to surgical intervention. <b>Materials and Methods:</b> A retrospective cohort study was conducted using data linkage to identify patients born between 2000 and 2018 with a diagnosis of microtia. Microtia incidence was calculated using annual and geographic birth rates. Surgical operation codes were used to classify patients into those that had no surgery, autologous reconstruction or prosthetic reconstruction. Sociodemographic attributes were compared using descriptive statistics to determine differences in access to each type of surgical intervention. <b>Results:</b> A total of 101 patients were identified, 64.4% were male and the median age was 12 (8-16). The mean annual incidence was 2.13 microtia cases per 10,000 births over the 19-year study period. Both temporal and geographic variation was noted. The majority of patients undergoing surgery opted for autologous reconstruction (72.9%) at a median age of 9 (7-10) compared to 7 (5-8) for prosthetic reconstruction. Autologous reconstruction had a higher median number of surgeries (2, 1-3) than prosthetic (1.5, 1-2) and a higher median socioeconomic status of 3 (2-4) compared to 2 (1-4) for the prosthetic cohort. There were no statistically significant differences in the distance traveled for surgery. <b>Discussion:</b> This study highlights a role for data linkage in epidemiological analyses and provides a revised incidence of microtia in Wales. Although the majority of patients opted for autologous reconstruction, demographic disparities in socioeconomic status warrant further investigation, emphasizing the importance of striving for equity in accessibility to surgical intervention.",,pdf:https://www.frontiersin.org/articles/10.3389/fped.2021.630036/pdf; doi:https://doi.org/10.3389/fped.2021.630036; html:https://europepmc.org/articles/PMC8033003; pdf:https://europepmc.org/articles/PMC8033003?pdf=render
 34983063,https://doi.org/10.1093/bioinformatics/btab879,CACONET: a novel classification framework for microbial correlation networks.,"Xu Y, Nash K, Acharjee A, Gkoutos GV.",,"Bioinformatics (Oxford, England)",2022,2022-03-01,Y,,,,"<h4>Motivation</h4>Existing microbiome-based disease prediction relies on the ability of machine learning methods to differentiate disease from healthy subjects based on the observed taxa abundance across samples. Despite numerous microbes have been implicated as potential biomarkers, challenges remain due to not only the statistical nature of microbiome data but also the lack of understanding of microbial interactions which can be indicative of the disease.<h4>Results</h4>We propose CACONET (classification of Compositional-Aware COrrelation NETworks), a computational framework that learns to classify microbial correlation networks and extracts potential signature interactions, taking as input taxa relative abundance across samples and their health status. By using Bayesian compositional-aware correlation inference, a collection of posterior correlation networks can be drawn and used for graph-level classification, thus incorporating uncertainty in the estimates. CACONET then employs a deep learning approach for graph classification, achieving excellent performance metrics by exploiting the correlation structure. We test the framework on both simulated data and a large real-world dataset pertaining to microbiome samples of colorectal cancer (CRC) and healthy subjects, and identify potential network substructure characteristic of CRC microbiota. CACONET is customizable and can be adapted to further improve its utility.<h4>Availability and implementation</h4>CACONET is available at https://github.com/yuanwxu/corr-net-classify.<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online.",,pdf:https://academic.oup.com/bioinformatics/article-pdf/38/6/1639/42744567/btab879.pdf; doi:https://doi.org/10.1093/bioinformatics/btab879; html:https://europepmc.org/articles/PMC8896646; pdf:https://europepmc.org/articles/PMC8896646?pdf=render
-38833617,https://doi.org/10.1093/cvr/cvae123,Sex inequalities in cardiovascular risk prediction.,"Elliott J, Bodinier B, Whitaker M, Wada R, Cooke G, Ward H, Tzoulaki I, Elliott P, Chadeau-Hyam M.",,Cardiovascular research,2024,2024-09-01,Y,Biomarkers; Cvd Risk Prediction; Pooled Cohort Equations; Qrisk3; Sparse Variable Selection,,,"<h4>Aims</h4>Evaluate sex differences in cardiovascular disease (CVD) risk prediction, including use of (i) optimal sex-specific risk predictors and (ii) sex-specific risk thresholds.<h4>Methods and results</h4>Prospective cohort study using UK Biobank, including 121 724 and 182 632 healthy men and women, respectively, aged 38-73 years at baseline. There were 11 899 (men) and 9110 (women) incident CVD cases (hospitalization or mortality) with a median of 12.1 years of follow-up. We used recalibrated pooled cohort equations (PCEs; 7.5% 10-year risk threshold as per US guidelines), QRISK3 (10% 10-year risk threshold as per UK guidelines), and Cox survival models using sparse sex-specific variable sets (via LASSO stability selection) to predict CVD risk separately in men and women. LASSO stability selection included 12 variables in common between men and women, with 3 additional variables selected for men and 1 for women. C-statistics were slightly lower for PCE than QRISK3 and models using stably selected variables, but were similar between men and women: 0.67 (0.66-0.68), 0.70 (0.69-0.71), and 0.71 (0.70-0.72) in men and 0.69 (0.68-0.70), 0.72 (0.71-0.73), and 0.72 (0.71-0.73) in women for PCE, QRISK3, and models using stably selected variables, respectively. At current clinically implemented risk thresholds, test sensitivity was markedly lower in women than men for all models: at 7.5% 10-year risk, sensitivity was 65.1 and 68.2% in men and 24.0 and 33.4% in women for PCE and models using stably selected variables, respectively; at 10% 10-year risk, sensitivity was 53.7 and 52.3% in men and 16.8 and 20.2% in women for QRISK3 and models using stably selected variables, respectively. Specificity was correspondingly higher in women than men. However, the sensitivity in women at 5% 10-year risk threshold increased to 50.1, 58.5, and 55.7% for PCE, QRISK3, and models using stably selected variables, respectively.<h4>Conclusion</h4>Use of sparse sex-specific variables improved CVD risk prediction compared with PCE but not QRISK3. At current risk thresholds, PCE and QRISK3 work less well for women than men, but sensitivity was improved in women using a 5% 10-year risk threshold. Use of sex-specific risk thresholds should be considered in any re-evaluation of CVD risk calculators.",,doi:https://doi.org/10.1093/cvr/cvae123; html:https://europepmc.org/articles/PMC11416056; pdf:https://europepmc.org/articles/PMC11416056?pdf=render
-36936594,https://doi.org/10.1136/bmjmed-2022-000247,Measuring multimorbidity in research: Delphi consensus study.,"Ho ISS, Azcoaga-Lorenzo A, Akbari A, Davies J, Khunti K, Kadam UT, Lyons RA, McCowan C, Mercer SW, Nirantharakumar K, Staniszewska S, Guthrie B.",,BMJ medicine,2022,2022-07-27,Y,Medicine; epidemiology; Primary Health Care; Public Health; Research Design,,,"<h4>Objective</h4>To develop international consensus on the definition and measurement of multimorbidity in research.<h4>Design</h4>Delphi consensus study.<h4>Setting</h4>International consensus; data collected in three online rounds from participants between 30 November 2020 and 18 May 2021.<h4>Participants</h4>Professionals interested in multimorbidity and people with long term conditions were recruited to professional and public panels.<h4>Results</h4>150 professional and 25 public participants completed the first survey round. Response rates for rounds 2/3 were 83%/92% for professionals and 88%/93% in the public panel, respectively. Across both panels, the consensus was that multimorbidity should be defined as two or more long term conditions. Complex multimorbidity was perceived to be a useful concept, but the panels were unable to agree on how to define it. Both panels agreed that conditions should be included in a multimorbidity measure if they were one or more of the following: currently active; permanent in their effects; requiring current treatment, care, or therapy; requiring surveillance; or relapsing-remitting conditions requiring ongoing care. Consensus was reached for 24 conditions to always include in multimorbidity measures, and 35 conditions to usually include unless a good reason not to existed. Simple counts were preferred for estimating prevalence and examining clustering or trajectories, and weighted measures were preferred for risk adjustment and outcome prediction.<h4>Conclusions</h4>Previous multimorbidity research is limited by inconsistent definitions and approaches to measuring multimorbidity. This Delphi study identifies professional and public panel consensus guidance to facilitate consistency of definition and measurement, and to improve study comparability and reproducibility.",,pdf:https://bmjmedicine.bmj.com/content/bmjmed/1/1/e000247.full.pdf; doi:https://doi.org/10.1136/bmjmed-2022-000247; html:https://europepmc.org/articles/PMC9978673; pdf:https://europepmc.org/articles/PMC9978673?pdf=render
-35505353,https://doi.org/10.1186/s12916-022-02349-6,Predictive performance of a competing risk cardiovascular prediction tool CRISK compared to QRISK3 in older people and those with comorbidity: population cohort study.,"Livingstone SJ, Guthrie B, Donnan PT, Thompson A, Morales DR.",,BMC medicine,2022,2022-05-04,Y,Primary Prevention; Cardiovascular Risk; Risk Prediction; Competing Risk; Qrisk3,,,"<h4>Background</h4>Recommended cardiovascular disease (CVD) prediction tools do not account for competing mortality risk and over-predict incident CVD in older and multimorbid people. The aim of this study was to derive and validate a competing risk model (CRISK) to predict incident CVD and compare its performance to that of QRISK3 in UK primary care.<h4>Methods</h4>We used UK linked primary care data from the Clinical Practice Research Datalink (CPRD) GOLD to identify people aged 25-84 years with no previous CVD or statin treatment split into derivation and validation cohorts. In the derivation cohort, we derived models using the same covariates as QRISK3 with Fine-Gray competing risk modelling alone (CRISK) and with Charlson Comorbidity score (CRISK-CCI) as an additional predictor of non-CVD death. In a separate validation cohort, we examined discrimination and calibration compared to QRISK3. Reclassification analysis examined the number of patients recommended for treatment and the estimated number needed to treat (NNT) to prevent a new CVD event.<h4>Results</h4>The derivation and validation cohorts included 989,732 and 494,865 women and 946,784 and 473,392 men respectively. Overall discrimination of CRISK and CRISK-CCI were excellent and similar to QRISK3 (for women, C-statistic = 0.863/0.864/0.863 respectively; for men 0.833/0.819/0.832 respectively). CRISK and CRISK-CCI calibration overall and in younger people was excellent. CRISK over-predicted in older and multimorbid people although performed better than QRISK3, whilst CRISK-CCI performed the best. The proportion of people reclassified by CRISK-CCI varied by QRISK3 risk score category, with 0.7-9.7% of women and 2.8-25.2% of men reclassified as higher risk and 21.0-69.1% of women and 27.1-57.4% of men reclassified as lower risk. Overall, CRISK-CCI recommended fewer people for treatment and had a lower estimated NNT at 10% risk threshold. Patients reclassified as higher risk were younger, had lower SBP and higher BMI, and were more likely to smoke.<h4>Conclusions</h4>CRISK and CRISK-CCI performed better than QRISK3. CRISK-CCI recommends fewer people for treatment and has a lower NNT to prevent a new CVD event compared to QRISK3. Competing risk models should be recommended for CVD primary prevention treatment recommendations.",,pdf:https://bmcmedicine.biomedcentral.com/track/pdf/10.1186/s12916-022-02349-6; doi:https://doi.org/10.1186/s12916-022-02349-6; html:https://europepmc.org/articles/PMC9066924; pdf:https://europepmc.org/articles/PMC9066924?pdf=render
 33965593,https://doi.org/10.1016/j.jaip.2021.04.055,Intolerance to Angiotensin Converting Enzyme Inhibitors in Asthma and the General Population: A UK Population-Based Cohort Study.,"Morales DR, Lipworth BJ, Donnan PT, Wang H.",,The journal of allergy and clinical immunology. In practice,2021,2021-05-06,Y,Hypertension; Angiotensin converting enzyme; Asthma; epidemiology; Cough,,,"<h4>Background</h4>Angiotensin converting enzyme inhibitor (ACEI) intolerance commonly occurs, requiring switching to an angiotensin-II receptor blocker (ARB). Angiotensin converting enzyme inhibitor intolerance may be mediated by bradykinin, potentially affecting airway hyperresponsiveness.<h4>Objective</h4>To assess the risk for switching to ARBs in asthma.<h4>Methods</h4>We conducted a new-user cohort study of ACEI initiators identified from electronic health records from the UK Clinical Practice Research Datalink. The risk for switching to ARBs in people with asthma or chronic obstructive pulmonary disease and the general population was compared. Adjusted hazard ratios (HRs) were calculated using Cox regression, stratified by British Thoracic Society (BTS) treatment step and ACEI type.<h4>Results</h4>Of 642,336 new users of ACEI, 6.4% had active asthma. The hazard of switching to ARB was greater in people with asthma (HR = 1.16; 95% confidence interval [CI], 1.14-1.18; P ≤ .001) and highest in those at BTS step 3 or greater (HR = 1.35, 95% CI, 1.32-1.39; and HR = 1.18, 95% CI, 1.15-1.22, P ≤ .001 for patients aged ≥60 and <60 years, respectively). Hazard was highest with enalapril (HR = 1.25, 95% CI, 1.18-1.34, P ≤ .001; HR = 1.44, 95% CI, 1.32-1.58, P ≤ .001 for BTS step 3 or greater asthma). No increased hazard was observed in chronic obstructive pulmonary disease or those younger than age 60 years at BTS step 1/2. The number needed to treat varied by age, sex, and body mass index (BMI), ranging between 21 and 4, and was lowest in older women with a BMI of 25 or greater.<h4>Conclusions</h4>People with active asthma are more likely to switch to ARBs after commencing ACEI therapy. The number needed to treat varies by age, sex, BMI, and BTS step. Angiotensin-II receptor blocker could potentially be considered first-line in people with asthma and in those with high-risk characteristics.",,pdf:https://europepmc.org/articles/pmc8443840?pdf=render; doi:https://doi.org/10.1016/j.jaip.2021.04.055; html:https://europepmc.org/articles/PMC8443840; pdf:https://europepmc.org/articles/PMC8443840?pdf=render
 34514500,https://doi.org/10.1093/infdis/jiab459,The Impact of Cocirculating Pathogens on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/Coronavirus Disease 2019 Surveillance: How Concurrent Epidemics May Introduce Bias and Decrease the Observed SARS-CoV-2 Percentage Positivity.,"Kovacevic A, Eggo RM, Baguelin M, Domenech de Cellès M, Opatowski L.",,The Journal of infectious diseases,2022,2022-01-01,Y,Mathematical Modeling; Multiplex Testing; Sars-cov-2; Covid-19 Surveillance; Cocirculating Respiratory Viruses,,,"<h4>Background</h4>Circulation of seasonal non-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) respiratory viruses with syndromic overlap during the coronavirus disease 2019 (COVID-19) pandemic may alter the quality of COVID-19 surveillance, with possible consequences for real-time analysis and delay in implementation of control measures.<h4>Methods</h4>Using a multipathogen susceptible-exposed-infectious-recovered (SEIR) transmission model formalizing cocirculation of SARS-CoV-2 and another respiratory virus, we assessed how an outbreak of secondary virus may affect 2 COVID-19 surveillance indicators: testing demand and positivity. Using simulation, we assessed to what extent the use of multiplex polymerase chain reaction tests on a subsample of symptomatic individuals can help correct the observed SARS-CoV-2 percentage positivity and improve surveillance quality.<h4>Results</h4>We find that a non-SARS-CoV-2 epidemic strongly increases SARS-CoV-2 daily testing demand and artificially reduces the observed SARS-CoV-2 percentage positivity for the duration of the outbreak. We estimate that performing 1 multiplex test for every 1000 COVID-19 tests on symptomatic individuals could be sufficient to maintain surveillance of other respiratory viruses in the population and correct the observed SARS-CoV-2 percentage positivity.<h4>Conclusions</h4>This study showed that cocirculating respiratory viruses can distort SARS-CoV-2 surveillance. Correction of the positivity rate can be achieved by using multiplex polymerase chain reaction tests, and a low number of samples is sufficient to avoid bias in SARS-CoV-2 surveillance.",,pdf:https://academic.oup.com/jid/article-pdf/225/2/199/42224165/jiab459.pdf; doi:https://doi.org/10.1093/infdis/jiab459; html:https://europepmc.org/articles/PMC8763960; pdf:https://europepmc.org/articles/PMC8763960?pdf=render
+38833617,https://doi.org/10.1093/cvr/cvae123,Sex inequalities in cardiovascular risk prediction.,"Elliott J, Bodinier B, Whitaker M, Wada R, Cooke G, Ward H, Tzoulaki I, Elliott P, Chadeau-Hyam M.",,Cardiovascular research,2024,2024-09-01,Y,Biomarkers; Cvd Risk Prediction; Pooled Cohort Equations; Qrisk3; Sparse Variable Selection,,,"<h4>Aims</h4>Evaluate sex differences in cardiovascular disease (CVD) risk prediction, including use of (i) optimal sex-specific risk predictors and (ii) sex-specific risk thresholds.<h4>Methods and results</h4>Prospective cohort study using UK Biobank, including 121 724 and 182 632 healthy men and women, respectively, aged 38-73 years at baseline. There were 11 899 (men) and 9110 (women) incident CVD cases (hospitalization or mortality) with a median of 12.1 years of follow-up. We used recalibrated pooled cohort equations (PCEs; 7.5% 10-year risk threshold as per US guidelines), QRISK3 (10% 10-year risk threshold as per UK guidelines), and Cox survival models using sparse sex-specific variable sets (via LASSO stability selection) to predict CVD risk separately in men and women. LASSO stability selection included 12 variables in common between men and women, with 3 additional variables selected for men and 1 for women. C-statistics were slightly lower for PCE than QRISK3 and models using stably selected variables, but were similar between men and women: 0.67 (0.66-0.68), 0.70 (0.69-0.71), and 0.71 (0.70-0.72) in men and 0.69 (0.68-0.70), 0.72 (0.71-0.73), and 0.72 (0.71-0.73) in women for PCE, QRISK3, and models using stably selected variables, respectively. At current clinically implemented risk thresholds, test sensitivity was markedly lower in women than men for all models: at 7.5% 10-year risk, sensitivity was 65.1 and 68.2% in men and 24.0 and 33.4% in women for PCE and models using stably selected variables, respectively; at 10% 10-year risk, sensitivity was 53.7 and 52.3% in men and 16.8 and 20.2% in women for QRISK3 and models using stably selected variables, respectively. Specificity was correspondingly higher in women than men. However, the sensitivity in women at 5% 10-year risk threshold increased to 50.1, 58.5, and 55.7% for PCE, QRISK3, and models using stably selected variables, respectively.<h4>Conclusion</h4>Use of sparse sex-specific variables improved CVD risk prediction compared with PCE but not QRISK3. At current risk thresholds, PCE and QRISK3 work less well for women than men, but sensitivity was improved in women using a 5% 10-year risk threshold. Use of sex-specific risk thresholds should be considered in any re-evaluation of CVD risk calculators.",,doi:https://doi.org/10.1093/cvr/cvae123; html:https://europepmc.org/articles/PMC11416056; pdf:https://europepmc.org/articles/PMC11416056?pdf=render
+35505353,https://doi.org/10.1186/s12916-022-02349-6,Predictive performance of a competing risk cardiovascular prediction tool CRISK compared to QRISK3 in older people and those with comorbidity: population cohort study.,"Livingstone SJ, Guthrie B, Donnan PT, Thompson A, Morales DR.",,BMC medicine,2022,2022-05-04,Y,Primary Prevention; Cardiovascular Risk; Risk Prediction; Competing Risk; Qrisk3,,,"<h4>Background</h4>Recommended cardiovascular disease (CVD) prediction tools do not account for competing mortality risk and over-predict incident CVD in older and multimorbid people. The aim of this study was to derive and validate a competing risk model (CRISK) to predict incident CVD and compare its performance to that of QRISK3 in UK primary care.<h4>Methods</h4>We used UK linked primary care data from the Clinical Practice Research Datalink (CPRD) GOLD to identify people aged 25-84 years with no previous CVD or statin treatment split into derivation and validation cohorts. In the derivation cohort, we derived models using the same covariates as QRISK3 with Fine-Gray competing risk modelling alone (CRISK) and with Charlson Comorbidity score (CRISK-CCI) as an additional predictor of non-CVD death. In a separate validation cohort, we examined discrimination and calibration compared to QRISK3. Reclassification analysis examined the number of patients recommended for treatment and the estimated number needed to treat (NNT) to prevent a new CVD event.<h4>Results</h4>The derivation and validation cohorts included 989,732 and 494,865 women and 946,784 and 473,392 men respectively. Overall discrimination of CRISK and CRISK-CCI were excellent and similar to QRISK3 (for women, C-statistic = 0.863/0.864/0.863 respectively; for men 0.833/0.819/0.832 respectively). CRISK and CRISK-CCI calibration overall and in younger people was excellent. CRISK over-predicted in older and multimorbid people although performed better than QRISK3, whilst CRISK-CCI performed the best. The proportion of people reclassified by CRISK-CCI varied by QRISK3 risk score category, with 0.7-9.7% of women and 2.8-25.2% of men reclassified as higher risk and 21.0-69.1% of women and 27.1-57.4% of men reclassified as lower risk. Overall, CRISK-CCI recommended fewer people for treatment and had a lower estimated NNT at 10% risk threshold. Patients reclassified as higher risk were younger, had lower SBP and higher BMI, and were more likely to smoke.<h4>Conclusions</h4>CRISK and CRISK-CCI performed better than QRISK3. CRISK-CCI recommends fewer people for treatment and has a lower NNT to prevent a new CVD event compared to QRISK3. Competing risk models should be recommended for CVD primary prevention treatment recommendations.",,pdf:https://bmcmedicine.biomedcentral.com/track/pdf/10.1186/s12916-022-02349-6; doi:https://doi.org/10.1186/s12916-022-02349-6; html:https://europepmc.org/articles/PMC9066924; pdf:https://europepmc.org/articles/PMC9066924?pdf=render
+36936594,https://doi.org/10.1136/bmjmed-2022-000247,Measuring multimorbidity in research: Delphi consensus study.,"Ho ISS, Azcoaga-Lorenzo A, Akbari A, Davies J, Khunti K, Kadam UT, Lyons RA, McCowan C, Mercer SW, Nirantharakumar K, Staniszewska S, Guthrie B.",,BMJ medicine,2022,2022-07-27,Y,Medicine; epidemiology; Primary Health Care; Public Health; Research Design,,,"<h4>Objective</h4>To develop international consensus on the definition and measurement of multimorbidity in research.<h4>Design</h4>Delphi consensus study.<h4>Setting</h4>International consensus; data collected in three online rounds from participants between 30 November 2020 and 18 May 2021.<h4>Participants</h4>Professionals interested in multimorbidity and people with long term conditions were recruited to professional and public panels.<h4>Results</h4>150 professional and 25 public participants completed the first survey round. Response rates for rounds 2/3 were 83%/92% for professionals and 88%/93% in the public panel, respectively. Across both panels, the consensus was that multimorbidity should be defined as two or more long term conditions. Complex multimorbidity was perceived to be a useful concept, but the panels were unable to agree on how to define it. Both panels agreed that conditions should be included in a multimorbidity measure if they were one or more of the following: currently active; permanent in their effects; requiring current treatment, care, or therapy; requiring surveillance; or relapsing-remitting conditions requiring ongoing care. Consensus was reached for 24 conditions to always include in multimorbidity measures, and 35 conditions to usually include unless a good reason not to existed. Simple counts were preferred for estimating prevalence and examining clustering or trajectories, and weighted measures were preferred for risk adjustment and outcome prediction.<h4>Conclusions</h4>Previous multimorbidity research is limited by inconsistent definitions and approaches to measuring multimorbidity. This Delphi study identifies professional and public panel consensus guidance to facilitate consistency of definition and measurement, and to improve study comparability and reproducibility.",,pdf:https://bmjmedicine.bmj.com/content/bmjmed/1/1/e000247.full.pdf; doi:https://doi.org/10.1136/bmjmed-2022-000247; html:https://europepmc.org/articles/PMC9978673; pdf:https://europepmc.org/articles/PMC9978673?pdf=render
+36841835,https://doi.org/10.1038/s41541-023-00614-0,Incidence determinants and serological correlates of reactive symptoms following SARS-CoV-2 vaccination.,"Holt H, Jolliffe DA, Talaei M, Faustini S, Vivaldi G, Greenig M, Richter AG, Lyons RA, Griffiths CJ, Kee F, Sheikh A, Davies GA, Shaheen SO, Martineau AR.",,NPJ vaccines,2023,2023-02-25,Y,,,,"Prospective population-based studies investigating associations between reactive symptoms following SARS-CoV-2 vaccination and serologic responses to vaccination are lacking. We therefore conducted a study in 9003 adults from the UK general population receiving SARS-CoV-2 vaccines as part of the national vaccination programme. Titres of combined IgG/IgA/IgM responses to SARS-CoV-2 spike (S) glycoprotein were determined in eluates of dried blood spots collected from all participants before and after vaccination. 4262 (47.3%) participants experienced systemic reactive symptoms after a first vaccine dose. Factors associating with lower risk of such symptoms included older age (aOR per additional 10 years of age 0.85, 95% CI: 0.81-0.90), male vs. female sex (0.59, 0.53-0.65) and receipt of an mRNA vaccine vs. ChAdOx1 nCoV-19 (0.29, 0.26-0.32 for BNT162b2; 0.06, 0.01-0.26 for mRNA-1273). Higher risk of such symptoms was associated with SARS-CoV-2 seropositivity and COVID-19 symptoms prior to vaccination (2.23, 1.78-2.81), but not with SARS-CoV-2 seropositivity in the absence of COVID-19 symptoms (0.94, 0.81-1.09). Presence vs. absence of self-reported anxiety or depression at enrolment associated with higher risk of such symptoms (1.24, 1.12-1.39). Post-vaccination anti-S titres were higher among participants who experienced reactive symptoms after vaccination vs. those who did not (P < 0.001). We conclude that factors influencing risk of systemic symptoms after SARS-CoV-2 vaccination include demographic characteristics, pre-vaccination SARS-CoV-2 serostatus and vaccine type. Participants experiencing reactive symptoms following SARS-CoV-2 vaccination had higher post-vaccination titres of IgG/A/M anti-S antibodies. Improved public understanding of the frequency of reactogenic symptoms and their positive association with vaccine immunogenicity could potentially increase vaccine uptake.",,pdf:https://www.nature.com/articles/s41541-023-00614-0.pdf; doi:https://doi.org/10.1038/s41541-023-00614-0; html:https://europepmc.org/articles/PMC9959934; pdf:https://europepmc.org/articles/PMC9959934?pdf=render
 36224173,https://doi.org/10.1038/s41467-022-33415-5,Outcomes among confirmed cases and a matched comparison group in the Long-COVID in Scotland study.,"Hastie CE, Lowe DJ, McAuley A, Winter AJ, Mills NL, Black C, Scott JT, O'Donnell CA, Blane DN, Browne S, Ibbotson TR, Pell JP.",,Nature communications,2022,2022-10-12,Y,,,,"With increasing numbers infected by SARS-CoV-2, understanding long-COVID is essential to inform health and social care support. A Scottish population cohort of 33,281 laboratory-confirmed SARS-CoV-2 infections and 62,957 never-infected individuals were followed-up via 6, 12 and 18-month questionnaires and linkage to hospitalization and death records. Of the 31,486 symptomatic infections,1,856 (6%) had not recovered and 13,350 (42%) only partially. No recovery was associated with hospitalized infection, age, female sex, deprivation, respiratory disease, depression and multimorbidity. Previous symptomatic infection was associated with poorer quality of life, impairment across all daily activities and 24 persistent symptoms including breathlessness (OR 3.43, 95% CI 3.29-3.58), palpitations (OR 2.51, OR 2.36-2.66), chest pain (OR 2.09, 95% CI 1.96-2.23), and confusion (OR 2.92, 95% CI 2.78-3.07). Asymptomatic infection was not associated with adverse outcomes. Vaccination was associated with reduced risk of seven symptoms. Here we describe the nature of long-COVID and the factors associated with it.",,pdf:https://researchonline.gcu.ac.uk/files/64233779/s41467_022_33415_5.pdf; doi:https://doi.org/10.1038/s41467-022-33415-5; html:https://europepmc.org/articles/PMC9556711; pdf:https://europepmc.org/articles/PMC9556711?pdf=render
 37159441,https://doi.org/10.1371/journal.pdig.0000218,Hospital-wide natural language processing summarising the health data of 1 million patients.,"Bean DM, Kraljevic Z, Shek A, Teo J, Dobson RJB.",,PLOS digital health,2023,2023-05-09,Y,,,,"Electronic health records (EHRs) represent a major repository of real world clinical trajectories, interventions and outcomes. While modern enterprise EHR's try to capture data in structured standardised formats, a significant bulk of the available information captured in the EHR is still recorded only in unstructured text format and can only be transformed into structured codes by manual processes. Recently, Natural Language Processing (NLP) algorithms have reached a level of performance suitable for large scale and accurate information extraction from clinical text. Here we describe the application of open-source named-entity-recognition and linkage (NER+L) methods (CogStack, MedCAT) to the entire text content of a large UK hospital trust (King's College Hospital, London). The resulting dataset contains 157M SNOMED concepts generated from 9.5M documents for 1.07M patients over a period of 9 years. We present a summary of prevalence and disease onset as well as a patient embedding that captures major comorbidity patterns at scale. NLP has the potential to transform the health data lifecycle, through large-scale automation of a traditionally manual task.",,doi:https://doi.org/10.1371/journal.pdig.0000218; doi:https://doi.org/10.1371/journal.pdig.0000218; html:https://europepmc.org/articles/PMC10168555; pdf:https://europepmc.org/articles/PMC10168555?pdf=render
-36841835,https://doi.org/10.1038/s41541-023-00614-0,Incidence determinants and serological correlates of reactive symptoms following SARS-CoV-2 vaccination.,"Holt H, Jolliffe DA, Talaei M, Faustini S, Vivaldi G, Greenig M, Richter AG, Lyons RA, Griffiths CJ, Kee F, Sheikh A, Davies GA, Shaheen SO, Martineau AR.",,NPJ vaccines,2023,2023-02-25,Y,,,,"Prospective population-based studies investigating associations between reactive symptoms following SARS-CoV-2 vaccination and serologic responses to vaccination are lacking. We therefore conducted a study in 9003 adults from the UK general population receiving SARS-CoV-2 vaccines as part of the national vaccination programme. Titres of combined IgG/IgA/IgM responses to SARS-CoV-2 spike (S) glycoprotein were determined in eluates of dried blood spots collected from all participants before and after vaccination. 4262 (47.3%) participants experienced systemic reactive symptoms after a first vaccine dose. Factors associating with lower risk of such symptoms included older age (aOR per additional 10 years of age 0.85, 95% CI: 0.81-0.90), male vs. female sex (0.59, 0.53-0.65) and receipt of an mRNA vaccine vs. ChAdOx1 nCoV-19 (0.29, 0.26-0.32 for BNT162b2; 0.06, 0.01-0.26 for mRNA-1273). Higher risk of such symptoms was associated with SARS-CoV-2 seropositivity and COVID-19 symptoms prior to vaccination (2.23, 1.78-2.81), but not with SARS-CoV-2 seropositivity in the absence of COVID-19 symptoms (0.94, 0.81-1.09). Presence vs. absence of self-reported anxiety or depression at enrolment associated with higher risk of such symptoms (1.24, 1.12-1.39). Post-vaccination anti-S titres were higher among participants who experienced reactive symptoms after vaccination vs. those who did not (P < 0.001). We conclude that factors influencing risk of systemic symptoms after SARS-CoV-2 vaccination include demographic characteristics, pre-vaccination SARS-CoV-2 serostatus and vaccine type. Participants experiencing reactive symptoms following SARS-CoV-2 vaccination had higher post-vaccination titres of IgG/A/M anti-S antibodies. Improved public understanding of the frequency of reactogenic symptoms and their positive association with vaccine immunogenicity could potentially increase vaccine uptake.",,pdf:https://www.nature.com/articles/s41541-023-00614-0.pdf; doi:https://doi.org/10.1038/s41541-023-00614-0; html:https://europepmc.org/articles/PMC9959934; pdf:https://europepmc.org/articles/PMC9959934?pdf=render
 35213664,https://doi.org/10.1371/journal.pone.0264529,Achievement of European Society of Cardiology/European Atherosclerosis Society lipid targets in very high-risk patients: Influence of depression and sex.,"Ellins EA, Harris DE, Lacey A, Akbari A, Torabi F, Smith D, Jenkins G, Obaid D, Chase A, John A, Gravenor MB, Halcox JP.",,PloS one,2022,2022-02-25,Y,,,,"<h4>Aims</h4>To explore differences in the use of lipid lowering therapy and/or achievement of lipid guideline targets in patients with and without prior depression and influence of sex in very high-risk coronary patients.<h4>Methods & findings</h4>A retrospective observational cohort study was conducted using individual-level linked electronic health record data in patients who underwent percutaneous coronary intervention (2012-2017) in Wales. The cohort comprised of 13,781 patients (27.4% female), with 26.1% having prior depression. Lipid levels were recorded in 10,050 patients of whom 25% had depression. History of depression was independently associated with not having lipids checked (OR 0.79 95%CI 0.72-0.87 p<0.001). Patients with prior depression were less likely to achieve targets for low density lipoprotein cholesterol (LDL-C <1.8mmol/l), non-high density lipoprotein cholesterol (non-HDL-C <2.6mmol/l) and triglycerides (<2.3mmol/l) than patients without depression (OR 0.86 95%CI 0.78-0.96 p = 0.007, OR 0.80 95%CI 0.69-0.92 p = 0.003 & OR 0.69 95CI% 0.61-0.79 p<0.001 respectively). Females were less likely to achieve targets for LDL-C and non-HDL-C than males (OR 0.55 95%CI 0.50-0.61 p<0.001 & OR 0.63 95%CI 0.55-0.73 p<0.001). There was an additive effect of depression and sex; females with depression were not only least likely to be tested (OR 0.74 95%CI 0.65-0.84 p<0.001) but also (where levels were known) less likely to achieve LDL-C (OR 0.47 95%CI 0.41-0.55 p<0.001) and non-HDL-C targets (OR 0.50 95%CI 0.41-0.60 p<0.001). It was not possible to look at the influence of medication adherence on achievement of lipid targets due to limitations of the use of anonymised routinely-held clinical care data.<h4>Conclusion</h4>Patients with prior depression were less likely to have their lipids monitored and achieve guideline targets within 1-year. Females with depression are the least likely to be tested and achieve lipid targets, suggesting not only a greater risk of future events, but also an opportunity to improve care.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0264529&type=printable; doi:https://doi.org/10.1371/journal.pone.0264529; html:https://europepmc.org/articles/PMC8880762; pdf:https://europepmc.org/articles/PMC8880762?pdf=render
 29992526,https://doi.org/10.1007/s11906-018-0877-8,An Overview of Metabolic Phenotyping in Blood Pressure Research.,"Tzoulaki I, Iliou A, Mikros E, Elliott P.",,Current hypertension reports,2018,2018-07-10,Y,Hypertension; Blood pressure; Metabolomics; Microbiome; Epidemiological Studies; Metabolic Phenotyping,,,"<h4>Purpose of the review</h4>This review presents the analytical techniques, processing and analytical steps used in metabolomics phenotyping studies, as well as the main results from epidemiological studies on the associations between metabolites and high blood pressure.<h4>Recent findings</h4>A variety of metabolomic approaches have been applied to a range of epidemiological studies to uncover the pathophysiology of high blood pressure. Several pathways have been suggested in relation to blood pressure including the possible role of the gut microflora, inflammatory, oxidative stress, and lipid pathways. Metabolic changes have also been identified associated with blood pressure lowering effects of diets high in fruits and vegetables and low in meat intake. However, the current body of literature on metabolic profiling and blood pressure is still in its infancy, not fully consistent and requires careful interpretation. Metabolic phenotyping is a promising approach to uncover metabolic pathways associated with high blood pressure and throw light into the complex pathophysiology of hypertension.",,pdf:https://link.springer.com/content/pdf/10.1007%2Fs11906-018-0877-8.pdf; doi:https://doi.org/10.1007/s11906-018-0877-8; html:https://europepmc.org/articles/PMC6061189; pdf:https://europepmc.org/articles/PMC6061189?pdf=render
 34644365,https://doi.org/10.1371/journal.pone.0258484,Cohort profile: The UK COVID-19 Public Experiences (COPE) prospective longitudinal mixed-methods study of health and well-being during the SARSCoV2 coronavirus pandemic.,"Phillips R, Taiyari K, Torrens-Burton A, Cannings-John R, Williams D, Peddle S, Campbell S, Hughes K, Gillespie D, Sellars P, Pell B, Ashfield-Watt P, Akbari A, Seage CH, Perham N, Joseph-Williams N, Harrop E, Blaxland J, Wood F, Poortinga W, Wahl-Jorgensen K, James DH, Crone D, Thomas-Jones E, Hallingberg B.",,PloS one,2021,2021-10-13,Y,,,,"Public perceptions of pandemic viral threats and government policies can influence adherence to containment, delay, and mitigation policies such as physical distancing, hygienic practices, use of physical barriers, uptake of testing, contact tracing, and vaccination programs. The UK COVID-19 Public Experiences (COPE) study aims to identify determinants of health behaviour using the Capability, Opportunity, Motivation (COM-B) model using a longitudinal mixed-methods approach. Here, we provide a detailed description of the demographic and self-reported health characteristics of the COPE cohort at baseline assessment, an overview of data collected, and plans for follow-up of the cohort. The COPE baseline survey was completed by 11,113 UK adult residents (18+ years of age). Baseline data collection started on the 13th of March 2020 (10-days before the introduction of the first national COVID-19 lockdown in the UK) and finished on the 13th of April 2020. Participants were recruited via the HealthWise Wales (HWW) research registry and through social media snowballing and advertising (Facebook®, Twitter®, Instagram®). Participants were predominantly female (69%), over 50 years of age (68%), identified as white (98%), and were living with their partner (68%). A large proportion (67%) had a college/university level education, and half reported a pre-existing health condition (50%). Initial follow-up plans for the cohort included in-depth surveys at 3-months and 12-months after the first UK national lockdown to assess short and medium-term effects of the pandemic on health behaviour and subjective health and well-being. Additional consent will be sought from participants at follow-up for data linkage and surveys at 18 and 24-months after the initial UK national lockdown. A large non-random sample was recruited to the COPE cohort during the early stages of the COVID-19 pandemic, which will enable longitudinal analysis of the determinants of health behaviour and changes in subjective health and well-being over the course of the pandemic.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0258484&type=printable; doi:https://doi.org/10.1371/journal.pone.0258484; html:https://europepmc.org/articles/PMC8513913; pdf:https://europepmc.org/articles/PMC8513913?pdf=render
@@ -656,9 +656,9 @@ PMC10910267,https://doi.org/,Development and evaluation of a tool to optimise in
 37587484,https://doi.org/10.1186/s12874-023-02000-9,Implementation of the trial emulation approach in medical research: a scoping review.,"Scola G, Chis Ster A, Bean D, Pareek N, Emsley R, Landau S.",,BMC medical research methodology,2023,2023-08-16,Y,Causal Inference; Observational Data; Target Trial; Trial Emulation,,,"<h4>Background</h4>When conducting randomised controlled trials is impractical, an alternative is to carry out an observational study. However, making valid causal inferences from observational data is challenging because of the risk of several statistical biases. In 2016 Hernán and Robins put forward the 'target trial framework' as a guide to best design and analyse observational studies whilst preventing the most common biases. This framework consists of (1) clearly defining a causal question about an intervention, (2) specifying the protocol of the hypothetical trial, and (3) explaining how the observational data will be used to emulate it.<h4>Methods</h4>The aim of this scoping review was to identify and review all explicit attempts of trial emulation studies across all medical fields. Embase, Medline and Web of Science were searched for trial emulation studies published in English from database inception to February 25, 2021. The following information was extracted from studies that were deemed eligible for review: the subject area, the type of observational data that they leveraged, and the statistical methods they used to address the following biases: (A) confounding bias, (B) immortal time bias, and (C) selection bias.<h4>Results</h4>The search resulted in 617 studies, 38 of which we deemed eligible for review. Of those 38 studies, most focused on cardiology, infectious diseases or oncology and the majority used electronic health records/electronic medical records data and cohort studies data. Different statistical methods were used to address confounding at baseline and selection bias, predominantly conditioning on the confounders (N = 18/49, 37%) and inverse probability of censoring weighting (N = 7/20, 35%) respectively. Different approaches were used to address immortal time bias, assigning individuals to treatment strategies at start of follow-up based on their data available at that specific time (N = 21, 55%), using the sequential trial emulations approach (N = 11, 29%) or the cloning approach (N = 6, 16%).<h4>Conclusion</h4>Different methods can be leveraged to address (A) confounding bias, (B) immortal time bias, and (C) selection bias. When working with observational data, and if possible, the 'target trial' framework should be used as it provides a structured conceptual approach to observational research.",,doi:https://doi.org/10.1186/s12874-023-02000-9; html:https://europepmc.org/articles/PMC10428565; pdf:https://europepmc.org/articles/PMC10428565?pdf=render
 37185201,https://doi.org/10.1136/bmjopen-2022-067337,Prevalence of HIV in mental health service users: a retrospective cohort study.,"Heslin M, Jewell A, Croxford S, Chau C, Smith S, Pittrof R, Covshoff E, Sullivan A, Delpech V, Brown A, King HP, Kakaiya M, Campbell L, Hughes E, Stewart R.",,BMJ open,2023,2023-04-25,Y,Mental health; Hiv & Aids; Sexual Medicine,,,"<h4>Objective</h4>To examine the prevalence of HIV in a cohort of people who have used secondary mental health services in the UK.<h4>Design</h4>Retrospective cohort study.<h4>Setting</h4>Routinely collected clinical data from secondary mental health services in South London, UK available for research through the Clinical Record Interactive Search tool at the National Institute for Health and Care Research Maudsley Biomedical Research Centre were matched with pseudonymised national HIV surveillance data held by the UK Health Security Agency using a deterministic matching algorithm.<h4>Participants</h4>All adults aged 16+ who presented for the first time to mental health services in the South London and Maudsley (SLaM) National Health Service Trust between 1 January 2007 and 31 December 2018 were included.<h4>Primary outcome</h4>Point prevalence of HIV.<h4>Results</h4>There were 181 177 people who had contact with mental health services for the first time between 2007 and 2018 in SLaM. Overall, 2.47% (n=4481) of those had a recorded HIV diagnosis in national HIV surveillance data at any time (before, during or after contact with mental health services), 24.73 people per 1000. HIV point prevalence was highest in people with a diagnosed substance use disorder at 3.77% (n=784). A substantial percentage of the sample did not have a formal mental health diagnosis (27%), but even with those excluded, the point prevalence remained high at 2.31%. Around two-thirds of people had their diagnosis of HIV before contact with mental health services (67%; n=1495).<h4>Conclusions</h4>The prevalence of HIV in people who have had contact with mental health services was approximately 2.5 times higher than the general population in the same geographical area. Future work should investigate risk factors and disparities in HIV outcomes between those with and without mental health service contact.",,pdf:https://bmjopen.bmj.com/content/bmjopen/13/4/e067337.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-067337; html:https://europepmc.org/articles/PMC10186409; pdf:https://europepmc.org/articles/PMC10186409?pdf=render
 39040076,https://doi.org/10.1016/j.isci.2024.110298,Explainable AI-prioritized plasma and fecal metabolites in inflammatory bowel disease and their dietary associations.,"Onwuka S, Bravo-Merodio L, Gkoutos GV, Acharjee A.",,iScience,2024,2024-06-17,Y,Human genetics; Bioinformatics; endocrinology,,,"Fecal metabolites effectively discriminate inflammatory bowel disease (IBD) and show differential associations with diet. Metabolomics and AI-based models, including explainable AI (XAI), play crucial roles in understanding IBD. Using datasets from the UK Biobank and the Human Microbiome Project Phase II IBD Multi'omics Database (HMP2 IBDMDB), this study uses multiple machine learning (ML) classifiers and Shapley additive explanations (SHAP)-based XAI to prioritize plasma and fecal metabolites and analyze their diet correlations. Key findings include the identification of discriminative metabolites like glycoprotein acetyl and albumin in plasma, as well as nicotinic acid metabolites andurobilin in feces. Fecal metabolites provided a more robust disease predictor model (AUC [95%]: 0.93 [0.87-0.99]) compared to plasma metabolites (AUC [95%]: 0.74 [0.69-0.79]), with stronger and more group-differential diet-metabolite associations in feces. The study validates known metabolite associations and highlights the impact of IBD on the interplay between gut microbial metabolites and diet.",,doi:https://doi.org/10.1016/j.isci.2024.110298; doi:https://doi.org/10.1016/j.isci.2024.110298; html:https://europepmc.org/articles/PMC11261406; pdf:https://europepmc.org/articles/PMC11261406?pdf=render
+35003715,https://doi.org/10.7189/jogh.11.05026,"Uptake, effectiveness and safety of COVID-19 vaccines in children and young people in Scotland: Protocol for early pandemic evaluation and enhanced surveillance of COVID-19 (EAVE II).","Adeloye D, Katikireddi SV, Woolford L, Simpson CR, Shah SA, Agrawal U, Richie LD, Swann OV, Stock SJ, Robertson C, Sheikh A, Rudan I.",,Journal of global health,2021,2021-12-25,Y,,,,"<h4>Background</h4>The dynamics of acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and severity of disease among children and young people (CYP) across different settings are of considerable clinical, public health and societal interest. Severe COVID-19 cases, requiring hospitalisations, and deaths have been reported in some CYP suggesting a need to extend vaccinations to these age groups. As part of the ongoing Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) study, we aim to investigate the uptake, effectiveness and safety of COVID-19 vaccines in children and young people (CYP) aged 0 to 17 years in Scotland. Specifically, we will estimate: (i) uptake of vaccines against COVID-19, (ii) vaccine effectiveness (VE) against the outcomes of symptomatic SARS-CoV-2 infection, hospitalisation, intensive care unit (ICU) admissions, and death; (iii) VE for first/second dose timing among different age groups and risk groups; and (iv) the safety of vaccines.<h4>Methods and analysis</h4>We will conduct an open prospective cohort study classifying exposure as time-varying. We will compare outcomes amongst first dose vaccinated and second dose vaccinated CYP to those not yet vaccinated. A Test Negative Design (TND) case control study will be nested within this national cohort to investigate VE against symptomatic infection. The primary outcomes will be (i) uptake of vaccines against COVID-19, (ii) time to COVID-19 infection, hospitalisation, ICU admissions or death, and (iii) adverse events related to vaccines. Vaccination status (unvaccinated, one dose and two doses) will be defined as a time-varying exposure. Data from multiple sources will be linked using a unique identifier. We will conduct descriptive analyses to explore trends in vaccine uptake, and association between different exposure variables and vaccine uptake will be determined using multivariable logistic regression models. VE will be assessed from time-dependent Cox models or Poisson regression models, adjusted for relevant confounders, including age, sex, socioeconomic status, and comorbidities. We will employ self-controlled study designs to determine the risk of adverse events following COVID-19 vaccination.<h4>Ethics and dissemination</h4>Ethics approval was obtained from the National Research Ethics Committee, South East Scotland 02. We will present findings of this study at international conferences, in peer-reviewed journals and to policy-makers.",,doi:https://doi.org/10.7189/jogh.11.05026; doi:https://doi.org/10.7189/jogh.11.05026; html:https://europepmc.org/articles/PMC8709900; pdf:https://europepmc.org/articles/PMC8709900?pdf=render
 32463370,https://doi.org/10.2196/16452,Challenges of Clustering Multimodal Clinical Data: Review of Applications in Asthma Subtyping.,"Horne E, Tibble H, Sheikh A, Tsanas A.",,JMIR medical informatics,2020,2020-05-28,Y,Cluster analysis; Asthma; data mining; Machine Learning; Unsupervised Machine Learning,,,"<h4>Background</h4>In the current era of personalized medicine, there is increasing interest in understanding the heterogeneity in disease populations. Cluster analysis is a method commonly used to identify subtypes in heterogeneous disease populations. The clinical data used in such applications are typically multimodal, which can make the application of traditional cluster analysis methods challenging.<h4>Objective</h4>This study aimed to review the research literature on the application of clustering multimodal clinical data to identify asthma subtypes. We assessed common problems and shortcomings in the application of cluster analysis methods in determining asthma subtypes, such that they can be brought to the attention of the research community and avoided in future studies.<h4>Methods</h4>We searched PubMed and Scopus bibliographic databases with terms related to cluster analysis and asthma to identify studies that applied dissimilarity-based cluster analysis methods. We recorded the analytic methods used in each study at each step of the cluster analysis process.<h4>Results</h4>Our literature search identified 63 studies that applied cluster analysis to multimodal clinical data to identify asthma subtypes. The features fed into the cluster algorithms were of a mixed type in 47 (75%) studies and continuous in 12 (19%), and the feature type was unclear in the remaining 4 (6%) studies. A total of 23 (37%) studies used hierarchical clustering with Ward linkage, and 22 (35%) studies used k-means clustering. Of these 45 studies, 39 had mixed-type features, but only 5 specified dissimilarity measures that could handle mixed-type features. A further 9 (14%) studies used a preclustering step to create small clusters to feed on a hierarchical method. The original sample sizes in these 9 studies ranged from 84 to 349. The remaining studies used hierarchical clustering with other linkages (n=3), medoid-based methods (n=3), spectral clustering (n=1), and multiple kernel k-means clustering (n=1), and in 1 study, the methods were unclear. Of 63 studies, 54 (86%) explained the methods used to determine the number of clusters, 24 (38%) studies tested the quality of their cluster solution, and 11 (17%) studies tested the stability of their solution. Reporting of the cluster analysis was generally poor in terms of the methods employed and their justification.<h4>Conclusions</h4>This review highlights common issues in the application of cluster analysis to multimodal clinical data to identify asthma subtypes. Some of these issues were related to the multimodal nature of the data, but many were more general issues in the application of cluster analysis. Although cluster analysis may be a useful tool for investigating disease subtypes, we recommend that future studies carefully consider the implications of clustering multimodal data, the cluster analysis process itself, and the reporting of methods to facilitate replication and interpretation of findings.",,pdf:https://medinform.jmir.org/2020/5/e16452/PDF; doi:https://doi.org/10.2196/16452; html:https://europepmc.org/articles/PMC7290450
 35291009,https://doi.org/10.1093/ageing/afac072,Intensity of COVID-19 in care homes following hospital discharge in the early stages of the UK epidemic.,"Hollinghurst J, North L, Emmerson C, Akbari A, Torabi F, Williams C, Lyons RA, Hawkes AG, Bennett E, Gravenor MB, Fry R.",,Age and ageing,2022,2022-05-01,Y,Older People; Care Homes; Hospital Discharge; Linked Data; Hawkes Process; Multi-level Model; Covid-19,,,"<h4>Background</h4>defining features of the COVID-19 pandemic in many countries were the tragic extent to which care home residents were affected and the difficulty in preventing the introduction and subsequent spread of infection. Management of risk in care homes requires good evidence on the most important transmission pathways. One hypothesised route at the start of the pandemic, prior to widespread testing, was the transfer of patients from hospitals that were experiencing high levels of nosocomial events.<h4>Methods</h4>we tested the hypothesis that hospital discharge events increased the intensity of care home cases using a national individually linked health record cohort in Wales, UK. We monitored 186,772 hospital discharge events over the period from March to July 2020, tracking individuals to 923 care homes and recording the daily case rate in the homes populated by 15,772 residents. We estimated the risk of an increase in case rates following exposure to a hospital discharge using multi-level hierarchical logistic regression and a novel stochastic Hawkes process outbreak model.<h4>Findings</h4>in regression analysis, after adjusting for care home size, we found no significant association between hospital discharge and subsequent increases in care home case numbers (odds ratio: 0.99, 95% CI: 0.82, 1.90). Risk factors for increased cases included care home size, care home resident density and provision of nursing care. Using our outbreak model, we found a significant effect of hospital discharge on the subsequent intensity of cases. However, the effect was small and considerably less than the effect of care home size, suggesting the highest risk of introduction came from interaction with the community. We estimated that approximately 1.8% of hospital discharged patients may have been infected.<h4>Interpretation</h4>there is growing evidence in the UK that the risk of transfer of COVID-19 from the high-risk hospital setting to the high-risk care home setting during the early stages of the pandemic was relatively small. Although access to testing was limited to initial symptomatic cases in each care home at this time, our results suggest that reduced numbers of discharges, selection of patients and action taken within care homes following transfer all may have contributed to the mitigation. The precise key transmission routes from the community remain to be quantified.",,pdf:https://academic.oup.com/ageing/article-pdf/51/5/afac072/43616755/afac072.pdf; doi:https://doi.org/10.1093/ageing/afac072; html:https://europepmc.org/articles/PMC8992303; pdf:https://europepmc.org/articles/PMC8992303?pdf=render
-35003715,https://doi.org/10.7189/jogh.11.05026,"Uptake, effectiveness and safety of COVID-19 vaccines in children and young people in Scotland: Protocol for early pandemic evaluation and enhanced surveillance of COVID-19 (EAVE II).","Adeloye D, Katikireddi SV, Woolford L, Simpson CR, Shah SA, Agrawal U, Richie LD, Swann OV, Stock SJ, Robertson C, Sheikh A, Rudan I.",,Journal of global health,2021,2021-12-25,Y,,,,"<h4>Background</h4>The dynamics of acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and severity of disease among children and young people (CYP) across different settings are of considerable clinical, public health and societal interest. Severe COVID-19 cases, requiring hospitalisations, and deaths have been reported in some CYP suggesting a need to extend vaccinations to these age groups. As part of the ongoing Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) study, we aim to investigate the uptake, effectiveness and safety of COVID-19 vaccines in children and young people (CYP) aged 0 to 17 years in Scotland. Specifically, we will estimate: (i) uptake of vaccines against COVID-19, (ii) vaccine effectiveness (VE) against the outcomes of symptomatic SARS-CoV-2 infection, hospitalisation, intensive care unit (ICU) admissions, and death; (iii) VE for first/second dose timing among different age groups and risk groups; and (iv) the safety of vaccines.<h4>Methods and analysis</h4>We will conduct an open prospective cohort study classifying exposure as time-varying. We will compare outcomes amongst first dose vaccinated and second dose vaccinated CYP to those not yet vaccinated. A Test Negative Design (TND) case control study will be nested within this national cohort to investigate VE against symptomatic infection. The primary outcomes will be (i) uptake of vaccines against COVID-19, (ii) time to COVID-19 infection, hospitalisation, ICU admissions or death, and (iii) adverse events related to vaccines. Vaccination status (unvaccinated, one dose and two doses) will be defined as a time-varying exposure. Data from multiple sources will be linked using a unique identifier. We will conduct descriptive analyses to explore trends in vaccine uptake, and association between different exposure variables and vaccine uptake will be determined using multivariable logistic regression models. VE will be assessed from time-dependent Cox models or Poisson regression models, adjusted for relevant confounders, including age, sex, socioeconomic status, and comorbidities. We will employ self-controlled study designs to determine the risk of adverse events following COVID-19 vaccination.<h4>Ethics and dissemination</h4>Ethics approval was obtained from the National Research Ethics Committee, South East Scotland 02. We will present findings of this study at international conferences, in peer-reviewed journals and to policy-makers.",,doi:https://doi.org/10.7189/jogh.11.05026; doi:https://doi.org/10.7189/jogh.11.05026; html:https://europepmc.org/articles/PMC8709900; pdf:https://europepmc.org/articles/PMC8709900?pdf=render
 37399490,https://doi.org/10.1182/bloodadvances.2023010562,Polygenic risk of major depressive disorder as a risk factor for venous thromboembolism.,"Ward J, Le NQ, Suryakant S, Brody JA, Amouyel P, Boland A, Bown R, Cullen B, Debette S, Deleuze JF, Emmerich J, Graham N, Germain M, Anderson JJ, Pell JP, Lyall DM, Lyall LM, Smith DJ, Wiggins KL, Soria JM, Souto JC, Morange PE, Smith NL, Trégouët DA, Sabater-Lleal M, Strawbridge RJ.",,Blood advances,2023,2023-09-01,Y,,,,"Major depressive disorder (MDD), bipolar disorder (BD), and schizophrenia (SCZ) are associated with an increased risk of cardiovascular diseases, including venous thromboembolism (VTE). The reasons for this are complex and include obesity, smoking, and use of hormones and psychotropic medications. Genetic studies have increasingly provided evidence of the shared genetic risk of psychiatric and cardiometabolic illnesses. This study aimed to determine whether a genetic predisposition to MDD, BD, or SCZ is associated with an increased risk of VTE. Genetic correlations using the largest genome-wide genetic meta-analyses summary statistics for MDD, BD, and SCZ (Psychiatric Genetics Consortium) and a recent genome-wide genetic meta-analysis of VTE (INVENT Consortium) demonstrated a positive association between VTE and MDD but not BD or SCZ. The same summary statistics were used to construct polygenic risk scores for MDD, BD, and SCZ in UK Biobank participants of self-reported White British ancestry. These were assessed for impact on self-reported VTE risk (10 786 cases, 285 124 controls), using logistic regression, in sex-specific and sex-combined analyses. We identified significant positive associations between polygenic risk for MDD and the risk of VTE in men, women, and sex-combined analyses, independent of the known risk factors. Secondary analyses demonstrated that this association was not driven by those with lifetime experience of mental illness. Meta-analyses of individual data from 6 additional independent cohorts replicated the sex-combined association. This report provides evidence for shared biological mechanisms leading to MDD and VTE and suggests that, in the absence of genetic data, a family history of MDD might be considered when assessing the risk of VTE.",,pdf:https://ashpublications.org/bloodadvances/article-pdf/doi/10.1182/bloodadvances.2023010562/2061976/bloodadvances.2023010562.pdf; doi:https://doi.org/10.1182/bloodadvances.2023010562; html:https://europepmc.org/articles/PMC10506044; pdf:https://europepmc.org/articles/PMC10506044?pdf=render
 32613083,https://doi.org/10.12688/wellcomeopenres.15922.2,"Black, Asian and Minority Ethnic groups in England are at increased risk of death from COVID-19: indirect standardisation of NHS mortality data.","Aldridge RW, Lewer D, Katikireddi SV, Mathur R, Pathak N, Burns R, Fragaszy EB, Johnson AM, Devakumar D, Abubakar I, Hayward A.",,Wellcome open research,2020,2020-06-24,Y,Mortality; Minority Ethnic Groups; Covid-19; Sars-cov-2,,,"<b>Background</b>: International and UK data suggest that Black, Asian and Minority Ethnic (BAME) groups are at increased risk of infection and death from COVID-19. We aimed to explore the risk of death in minority ethnic groups in England using data reported by NHS England. <b>Methods</b>: We used NHS data on patients with a positive COVID-19 test who died in hospitals in England published on 28th April, with deaths by ethnicity available from 1st March 2020 up to 5pm on 21 April 2020. We undertook indirect standardisation of these data (using the whole population of England as the reference) to produce ethnic specific standardised mortality ratios (SMRs) adjusted for age and geographical region. <b>Results</b>: The largest total number of deaths in minority ethnic groups were Indian (492 deaths) and Black Caribbean (460 deaths) groups. Adjusting for region we found a lower risk of death for White Irish (SMR 0.52; 95%CIs 0.45-0.60) and White British ethnic groups (0.88; 95%CIs 0.86-0.0.89), but increased risk of death for Black African (3.24; 95%CIs 2.90-3.62), Black Caribbean (2.21; 95%CIs 2.02-2.41), Pakistani (3.29; 95%CIs 2.96-3.64), Bangladeshi (2.41; 95%CIs 1.98-2.91) and Indian (1.70; 95%CIs 1.56-1.85) minority ethnic groups. <b>Conclusion:</b> Our analysis adds to the evidence that BAME people are at increased risk of death from COVID-19 even after adjusting for geographical region, but was limited by the lack of data on deaths outside of NHS settings and ethnicity denominator data being based on the 2011 census. Despite these limitations, we believe there is an urgent need to take action to reduce the risk of death for BAME groups and better understand why some ethnic groups experience greater risk. Actions that are likely to reduce these inequities include ensuring adequate income protection, reducing occupational risks, reducing barriers in accessing healthcare and providing culturally and linguistically appropriate public health communications.",,doi:https://doi.org/10.12688/wellcomeopenres.15922.2; html:https://europepmc.org/articles/PMC7317462; pdf:https://europepmc.org/articles/PMC7317462?pdf=render
 37080124,https://doi.org/10.1016/j.seizure.2023.04.006,COVID-19 vaccination uptake in people with epilepsy in wales.,"Strafford H, Lacey AS, Hollinghurst J, Akbari A, Watkins A, Paterson J, Jennings D, Lyons RA, Powell HR, Kerr MP, Chin RW, Pickrell WO.",,Seizure,2023,2023-04-06,Y,"Epilepsy; Vaccination; Data Linkage; Electronic Health Records; Pandemic, Covid-19",,,"<h4>Purpose</h4>People with epilepsy (PWE) are at increased risk of severe COVID-19. Assessing COVID-19 vaccine uptake is therefore important. We compared COVID-19 vaccination uptake for PWE in Wales with a matched control cohort.<h4>Methods</h4>We performed a retrospective, population, cohort study using linked, anonymised, Welsh electronic health records within the Secure Anonymised Information Linkage (SAIL) Databank (Welsh population=3.1 million).We identified PWE in Wales between 1st March 2020 and 31st December 2021 and created a control cohort using exact 5:1 matching (sex, age and socioeconomic status). We recorded 1st, 2nd and booster COVID-19 vaccinations.<h4>Results</h4>There were 25,404 adults with epilepsy (127,020 controls). 23,454 (92.3%) had a first vaccination, 22,826 (89.9%) a second, and 17,797 (70.1%) a booster. Comparative figures for controls were: 112,334 (87.8%), 109,057 (85.2%) and 79,980 (62.4%).PWE had higher vaccination rates in all age, sex and socioeconomic subgroups apart from booster uptake in older subgroups. Vaccination rates were higher in older subgroups, women and less deprived areas for both cohorts. People with intellectual disability and epilepsy had higher vaccination rates when compared with controls with intellectual disability.<h4>Conclusions</h4>COVID-19 vaccination uptake for PWE in Wales was higher than that for a matched control group.",,pdf:http://www.seizure-journal.com/article/S1059131123001000/pdf; doi:https://doi.org/10.1016/j.seizure.2023.04.006; html:https://europepmc.org/articles/PMC10076248; pdf:https://europepmc.org/articles/PMC10076248?pdf=render
@@ -666,46 +666,46 @@ PMC10910267,https://doi.org/,Development and evaluation of a tool to optimise in
 31462651,https://doi.org/10.1038/s41598-019-48927-2,Hierarchical Template Matching for 3D Myocardial Tracking and Cardiac Strain Estimation.,"Bhalodiya JM, Palit A, Ferrante E, Tiwari MK, Bhudia SK, Arvanitis TN, Williams MA.",,Scientific reports,2019,2019-08-28,Y,,Applied Analytics,,"Myocardial tracking and strain estimation can non-invasively assess cardiac functioning using subject-specific MRI. As the left-ventricle does not have a uniform shape and functioning from base to apex, the development of 3D MRI has provided opportunities for simultaneous 3D tracking, and 3D strain estimation. We have extended a Local Weighted Mean (LWM) transformation function for 3D, and incorporated in a Hierarchical Template Matching model to solve 3D myocardial tracking and strain estimation problem. The LWM does not need to solve a large system of equations, provides smooth displacement of myocardial points, and adapt local geometric differences in images. Hence, 3D myocardial tracking can be performed with 1.49 mm median error, and without large error outliers. The maximum error of tracking is up to 24% reduced compared to benchmark methods. Moreover, the estimated strain can be insightful to improve 3D imaging protocols, and the computer code of LWM could also be useful for geo-spatial and manufacturing image analysis researchers.",,pdf:https://www.nature.com/articles/s41598-019-48927-2.pdf; doi:https://doi.org/10.1038/s41598-019-48927-2; html:https://europepmc.org/articles/PMC6713749; pdf:https://europepmc.org/articles/PMC6713749?pdf=render
 39441952,https://doi.org/10.2196/51259,Digital Phenotyping of Mental and Physical Conditions: Remote Monitoring of Patients Through RADAR-Base Platform.,"Rashid Z, Folarin AA, Zhang Y, Ranjan Y, Conde P, Sankesara H, Sun S, Stewart C, Laiou P, Dobson RJB.",,JMIR mental health,2024,2024-10-23,N,Mobile phone; Biomarkers; Phenotyping; Data collection; Platform; Real-time monitoring; Smartphone; Internet Of Things; Wearable; Mhealth; Mobile Apps; Iot; Digital Biomarkers; Remote Data Collection; Wearables; Open-source Platform; Radar-base,,,"<h4>Background</h4>The use of digital biomarkers through remote patient monitoring offers valuable and timely insights into a patient's condition, including aspects such as disease progression and treatment response. This serves as a complementary resource to traditional health care settings leveraging mobile technology to improve scale and lower latency, cost, and burden.<h4>Objective</h4>Smartphones with embedded and connected sensors have immense potential for improving health care through various apps and mobile health (mHealth) platforms. This capability could enable the development of reliable digital biomarkers from long-term longitudinal data collected remotely from patients.<h4>Methods</h4>We built an open-source platform, RADAR-base, to support large-scale data collection in remote monitoring studies. RADAR-base is a modern remote data collection platform built around Confluent's Apache Kafka to support scalability, extensibility, security, privacy, and quality of data. It provides support for study design and setup and active (eg, patient-reported outcome measures) and passive (eg, phone sensors, wearable devices, and Internet of Things) remote data collection capabilities with feature generation (eg, behavioral, environmental, and physiological markers). The back end enables secure data transmission and scalable solutions for data storage, management, and data access.<h4>Results</h4>The platform has been used to successfully collect longitudinal data for various cohorts in a number of disease areas including multiple sclerosis, depression, epilepsy, attention-deficit/hyperactivity disorder, Alzheimer disease, autism, and lung diseases. Digital biomarkers developed through collected data are providing useful insights into different diseases.<h4>Conclusions</h4>RADAR-base offers a contemporary, open-source solution driven by the community for remotely monitoring, collecting data, and digitally characterizing both physical and mental health conditions. Clinicians have the ability to enhance their insight through the use of digital biomarkers, enabling improved prevention, personalization, and early intervention in the context of disease management.",,doi:https://doi.org/10.2196/51259
 38177344,https://doi.org/10.1038/s41588-023-01585-7,A compendium of genetic regulatory effects across pig tissues.,"Teng J, Gao Y, Yin H, Bai Z, Liu S, Zeng H, PigGTEx Consortium, Bai L, Cai Z, Zhao B, Li X, Xu Z, Lin Q, Pan Z, Yang W, Yu X, Guan D, Hou Y, Keel BN, Rohrer GA, Lindholm-Perry AK, Oliver WT, Ballester M, Crespo-Piazuelo D, Quintanilla R, Canela-Xandri O, Rawlik K, Xia C, Yao Y, Zhao Q, Yao W, Yang L, Li H, Zhang H, Liao W, Chen T, Karlskov-Mortensen P, Fredholm M, Amills M, Clop A, Giuffra E, Wu J, Cai X, Diao S, Pan X, Wei C, Li J, Cheng H, Wang S, Su G, Sahana G, Lund MS, Dekkers JCM, Kramer L, Tuggle CK, Corbett R, Groenen MAM, Madsen O, Gòdia M, Rocha D, Charles M, Li CJ, Pausch H, Hu X, Frantz L, Luo Y, Lin L, Zhou Z, Zhang Z, Chen Z, Cui L, Xiang R, Shen X, Li P, Huang R, Tang G, Li M, Zhao Y, Yi G, Tang Z, Jiang J, Zhao F, Yuan X, Liu X, Chen Y, Xu X, Zhao S, Zhao P, Haley C, Zhou H, Wang Q, Pan Y, Ding X, Ma L, Li J, Navarro P, Zhang Q, Li B, Tenesa A, Li K, Liu GE, Zhang Z, Fang L.",,Nature genetics,2024,2024-01-04,Y,,,,"The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model.",,pdf:https://www.nature.com/articles/s41588-023-01585-7.pdf; doi:https://doi.org/10.1038/s41588-023-01585-7; html:https://europepmc.org/articles/PMC10786720; pdf:https://europepmc.org/articles/PMC10786720?pdf=render
-37658166,https://doi.org/10.1007/s00392-023-02295-0,Efficacy and safety of intravenous beta-blockers in acute atrial fibrillation and flutter is dependent on beta-1 selectivity: a systematic review and meta-analysis of randomised trials.,"Perrett M, Gohil N, Tica O, Bunting KV, Kotecha D.",,Clinical research in cardiology : official journal of the German Cardiac Society,2024,2023-09-01,Y,Meta-analysis; Atrial fibrillation; Acute; Atrial flutter; Systematic review; Beta-blockers,,,"<h4>Background</h4>Intravenous beta-blockers are commonly used to manage patients with acute atrial fibrillation (AF) and atrial flutter (AFl), but the choice of specific agent is often not evidence-based.<h4>Methods</h4>A prospectively-registered systematic review and meta-analysis of randomised trials (PROSPERO: CRD42020204772) to compare the safety and efficacy of intravenous beta-blockers against alternative pharmacological agents.<h4>Results</h4>Twelve trials comparing beta-blockers with diltiazem, digoxin, verapamil, anti-arrhythmic drugs and placebo were included, with variable risk of bias and 1152 participants. With high heterogeneity (I<sup>2</sup> = 87%; p < 0.001), there was no difference in the primary outcomes of heart rate reduction (standardised mean difference - 0.65 beats/minute compared to control, 95% CI - 1.63 to 0.32; p = 0.19) or the proportion that achieved target heart rate (risk ratio [RR] 0.85, 95% CI 0.36-1.97; p = 0.70). Conventional selective beta-1 blockers were inferior for target heart rate reduction versus control (RR 0.33, 0.17-0.64; p < 0.001), whereas super-selective beta-1 blockers were superior (RR 1.98, 1.54-2.54; p < 0.001). There was no significant difference between beta-blockers and comparators for secondary outcomes of conversion to sinus rhythm (RR 1.15, 0.90-1.46; p = 0.28), hypotension (RR 1.85, 0.87-3.93; p = 0.11), bradycardia (RR 1.29, 0.25-6.82; p = 0.76) or adverse events leading to drug discontinuation (RR 1.03, 0.49-2.17; p = 0.93). The incidence of hypotension and bradycardia were greater with non-selective beta-blockers (p = 0.031 and p < 0.001).<h4>Conclusions</h4>Across all intravenous beta-blockers, there was no difference with other medications for acute heart rate control in atrial fibrillation and flutter. Efficacy and safety may be improved by choosing beta-blockers with higher beta-1 selectivity.",,doi:https://doi.org/10.1007/s00392-023-02295-0; html:https://europepmc.org/articles/PMC11108934; pdf:https://europepmc.org/articles/PMC11108934?pdf=render
 35944928,https://doi.org/10.1136/bmjhci-2021-100488,Software development skills for health data researchers.,"Morton C, Devito N, Morley J, Dillingham I, Schultze A, Bacon S, Inglesby P, Maude S, Goldacre B.",,BMJ health & care informatics,2022,2022-08-01,Y,Documentation; data management; Medical Informatics Computing; Data Science; Programming Languages,,,,,pdf:https://informatics.bmj.com/content/bmjhci/29/1/e100488.full.pdf; doi:https://doi.org/10.1136/bmjhci-2021-100488; html:https://europepmc.org/articles/PMC9367192; pdf:https://europepmc.org/articles/PMC9367192?pdf=render
 33667930,https://doi.org/10.1016/j.ijmedinf.2021.104400,Real-time spatial health surveillance: Mapping the UK COVID-19 epidemic.,"Fry R, Hollinghurst J, Stagg HR, Thompson DA, Fronterre C, Orton C, Lyons RA, Ford DV, Sheikh A, Diggle PJ.",,International journal of medical informatics,2021,2021-01-28,Y,,,,"Introduction The COVID-19 pandemic has highlighted the need for robust data linkage systems and methods for identifying outbreaks of disease in near real-time. Objectives The primary objective of this study was to develop a real-time geospatial surveillance system to monitor the spread of COVID-19 across the UK. Methods Using self-reported app data and the Secure Anonymised Information Linkage (SAIL) Databank, we demonstrate the use of sophisticated spatial modelling for near-real-time prediction of COVID-19 prevalence at small-area resolution to inform strategic government policy areas. Results We demonstrate that using a combination of crowd-sourced app data and sophisticated geo-statistical techniques it is possible to predict hot spots of COVID-19 at fine geographic scales, nationally. We are also able to produce estimates of their precision, which is an important pre-requisite to an effective control strategy to guard against over-reaction to potentially spurious features of 'best guess' predictions. Conclusion In the UK, important emerging risk-factors such as social deprivation or ethnicity vary over small distances, hence risk needs to be modelled at fine spatial resolution to avoid aggregation bias. We demonstrate that existing geospatial statistical methods originally developed for global health applications are well-suited to this task and can be used in an anonymised databank environment, thus preserving the privacy of the individuals who contribute their data.",,doi:https://doi.org/10.1016/j.ijmedinf.2021.104400; doi:https://doi.org/10.1016/j.ijmedinf.2021.104400; html:https://europepmc.org/articles/PMC7843148
-39035417,https://doi.org/10.1093/braincomms/fcae219,Multimodal subtypes identified in Alzheimer's Disease Neuroimaging Initiative participants by missing-data-enabled subtype and stage inference.,"Estarellas M, Oxtoby NP, Schott JM, Alexander DC, Young AL.",,Brain communications,2024,2024-06-25,Y,Heterogeneity; Alzheimer’s disease; Subtyping; Missing Data; Multimodal,,,"Alzheimer's disease is a highly heterogeneous disease in which different biomarkers are dynamic over different windows of the decades-long pathophysiological processes, and potentially have distinct involvement in different subgroups. Subtype and Stage Inference is an unsupervised learning algorithm that disentangles the phenotypic heterogeneity and temporal progression of disease biomarkers, providing disease insight and quantitative estimates of individual subtype and stage. However, a key limitation of Subtype and Stage Inference is that it requires a complete set of biomarkers for each subject, reducing the number of datapoints available for model fitting and limiting applications of Subtype and Stage Inference to modalities that are widely collected, e.g. volumetric biomarkers derived from structural MRI. In this study, we adapted the Subtype and Stage Inference algorithm to handle missing data, enabling the application of Subtype and Stage Inference to multimodal data (magnetic resonance imaging, positron emission tomography, cerebrospinal fluid and cognitive tests) from 789 participants in the Alzheimer's Disease Neuroimaging Initiative. Missing-data Subtype and Stage Inference identified five subtypes having distinct progression patterns, which we describe by the earliest unique abnormality as 'Typical AD with Early Tau', 'Typical AD with Late Tau', 'Cortical', 'Cognitive' and 'Subcortical'. These new multimodal subtypes were differentially associated with age, years of education, Apolipoprotein E (APOE4) status, white matter hyperintensity burden and the rate of conversion from mild cognitive impairment to Alzheimer's disease, with the 'Cognitive' subtype showing the fastest clinical progression, and the 'Subcortical' subtype the slowest. Overall, we demonstrate that missing-data Subtype and Stage Inference reveals a finer landscape of Alzheimer's disease subtypes, each of which are associated with different risk factors. Missing-data Subtype and Stage Inference has broad utility, enabling the prediction of progression in a much wider set of individuals, rather than being restricted to those with complete data.",,pdf:https://academic.oup.com/braincomms/advance-article-pdf/doi/10.1093/braincomms/fcae219/58327048/fcae219.pdf; doi:https://doi.org/10.1093/braincomms/fcae219; html:https://europepmc.org/articles/PMC11259979; pdf:https://europepmc.org/articles/PMC11259979?pdf=render
+37658166,https://doi.org/10.1007/s00392-023-02295-0,Efficacy and safety of intravenous beta-blockers in acute atrial fibrillation and flutter is dependent on beta-1 selectivity: a systematic review and meta-analysis of randomised trials.,"Perrett M, Gohil N, Tica O, Bunting KV, Kotecha D.",,Clinical research in cardiology : official journal of the German Cardiac Society,2024,2023-09-01,Y,Meta-analysis; Atrial fibrillation; Acute; Atrial flutter; Systematic review; Beta-blockers,,,"<h4>Background</h4>Intravenous beta-blockers are commonly used to manage patients with acute atrial fibrillation (AF) and atrial flutter (AFl), but the choice of specific agent is often not evidence-based.<h4>Methods</h4>A prospectively-registered systematic review and meta-analysis of randomised trials (PROSPERO: CRD42020204772) to compare the safety and efficacy of intravenous beta-blockers against alternative pharmacological agents.<h4>Results</h4>Twelve trials comparing beta-blockers with diltiazem, digoxin, verapamil, anti-arrhythmic drugs and placebo were included, with variable risk of bias and 1152 participants. With high heterogeneity (I<sup>2</sup> = 87%; p < 0.001), there was no difference in the primary outcomes of heart rate reduction (standardised mean difference - 0.65 beats/minute compared to control, 95% CI - 1.63 to 0.32; p = 0.19) or the proportion that achieved target heart rate (risk ratio [RR] 0.85, 95% CI 0.36-1.97; p = 0.70). Conventional selective beta-1 blockers were inferior for target heart rate reduction versus control (RR 0.33, 0.17-0.64; p < 0.001), whereas super-selective beta-1 blockers were superior (RR 1.98, 1.54-2.54; p < 0.001). There was no significant difference between beta-blockers and comparators for secondary outcomes of conversion to sinus rhythm (RR 1.15, 0.90-1.46; p = 0.28), hypotension (RR 1.85, 0.87-3.93; p = 0.11), bradycardia (RR 1.29, 0.25-6.82; p = 0.76) or adverse events leading to drug discontinuation (RR 1.03, 0.49-2.17; p = 0.93). The incidence of hypotension and bradycardia were greater with non-selective beta-blockers (p = 0.031 and p < 0.001).<h4>Conclusions</h4>Across all intravenous beta-blockers, there was no difference with other medications for acute heart rate control in atrial fibrillation and flutter. Efficacy and safety may be improved by choosing beta-blockers with higher beta-1 selectivity.",,doi:https://doi.org/10.1007/s00392-023-02295-0; html:https://europepmc.org/articles/PMC11108934; pdf:https://europepmc.org/articles/PMC11108934?pdf=render
 34164795,https://doi.org/10.1007/s40801-021-00256-5,Associations Between Anticholinergic Medication Exposure and Adverse Health Outcomes in Older People with Frailty: A Systematic Review and Meta-analysis.,"Mehdizadeh D, Hale M, Todd O, Zaman H, Marques I, Petty D, Alldred DP, Johnson O, Faisal M, Gardner P, Clegg A.",,Drugs - real world outcomes,2021,2021-06-23,Y,,,,"<h4>Introduction</h4>There are robust associations between use of anticholinergic medicines and adverse effects in older people. However, the nature of these associations for older people living with frailty is yet to be established.<h4>Objectives</h4>The aims were to identify and investigate associations between anticholinergics and adverse outcomes in older people living with frailty and to investigate whether exposure is associated with greater risks according to frailty status.<h4>Methods</h4>MEDLINE, CINAHL, EMBASE, Cochrane Database of Systematic Reviews, Web of Science and PsycINFO were searched to 1 August 2019. Observational studies reporting associations between anticholinergics and outcomes in older adults (average age ≥ 65 years) that reported frailty using validated measures were included. Primary outcomes were physical impairment, cognitive dysfunction, and change in frailty status. Risk of bias was evaluated using the Cochrane Risk of Bias In Non-randomised Studies of Interventions (ROBINS-I) tool. Meta-analysis was undertaken where appropriate.<h4>Results</h4>Thirteen studies (21,516 participants) were included (ten community, one residential aged-care facility and two hospital studies). Observed associations included reduced ability for chair standing, slower gait speeds, poorer physical performance, increased risk of falls and mortality. Conflicting results were reported for grip strength, timed up and go test, cognition and activities of daily living. No associations were observed for transitions between frailty states, psychological wellbeing or benzodiazepine-related adverse reactions. There was no clear evidence of differences in risks according to frailty status.<h4>Conclusions</h4>Anticholinergics are associated with adverse outcomes in older people living with frailty; however, the literature has significant methodological limitations. There is insufficient evidence to suggest greater risks based on frailty, and there is an urgent need to evaluate this further in well-designed studies stratifying by frailty.",,pdf:https://link.springer.com/content/pdf/10.1007/s40801-021-00256-5.pdf; doi:https://doi.org/10.1007/s40801-021-00256-5; html:https://europepmc.org/articles/PMC8605959; pdf:https://europepmc.org/articles/PMC8605959?pdf=render
-33780550,https://doi.org/10.1111/anae.15457,Impact of a physician - critical care practitioner pre-hospital service in Wales on trauma survival: a retrospective analysis of linked registry data.,"Lyons J, Gabbe BJ, Rawlinson D, Lockey D, Fry RJ, Akbari A, Lyons RA.",,Anaesthesia,2021,2021-03-29,Y,Trauma; Survival; Critical Care; Pre-hospital Care,,,"The Emergency Medical Retrieval and Transfer Service for Wales launched in 2015. This service delivers senior pre-hospital doctors and advanced critical care practitioners to the scene of time-critical life- and limb-threatening incidents to provide advanced decision-making and pre-hospital clinical care. The impact of the service on 30-day mortality was evaluated retrospectively using a data linkage system. The study included patients who sustained moderate-to-severe blunt traumatic injuries (injury severity score ≥ 9) between 27 April 2015 and 30 November 2018. The association between pre-hospital management by the Emergency Medical Retrieval and Transfer Service and 30-day mortality was assessed using multivariable logistic regression. In total, data from 4035 patients were analysed, of which 412 (10%) were treated by the Emergency Medical Retrieval and Transfer Service. A greater proportion of patients treated by the Emergency Medical Retrieval and Transfer Service had an injury severity score ≥ 16 and Glasgow coma scale ≤ 12 (288 (70%) vs. 1435 (40%) and 126 (31%) vs. 325 (9%), respectively). The unadjusted 30-day mortality rate was 11.7% for patients managed by the Emergency Medical Retrieval and Transfer Service compared with 9.6% for patients managed by standard pre-hospital care services. However, after adjustment for differences in case-mix, the 30-day mortality rate for patients treated by the Emergency Medical Retrieval and Transfer Service was 37% lower (adjusted odds ratio 0.63 (95%CI 0.41-0.97); p = 0.037). The introduction of an emergency medical retrieval service was associated with a reduction in 30-day mortality for patients with blunt traumatic injury.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa56616/Download/56616__19761__8c6edaf906b846a69c8b19bdb94d015d.pdf; doi:https://doi.org/10.1111/anae.15457; html:https://europepmc.org/articles/PMC11497344; pdf:https://europepmc.org/articles/PMC11497344?pdf=render
+39035417,https://doi.org/10.1093/braincomms/fcae219,Multimodal subtypes identified in Alzheimer's Disease Neuroimaging Initiative participants by missing-data-enabled subtype and stage inference.,"Estarellas M, Oxtoby NP, Schott JM, Alexander DC, Young AL.",,Brain communications,2024,2024-06-25,Y,Heterogeneity; Alzheimer’s disease; Subtyping; Missing Data; Multimodal,,,"Alzheimer's disease is a highly heterogeneous disease in which different biomarkers are dynamic over different windows of the decades-long pathophysiological processes, and potentially have distinct involvement in different subgroups. Subtype and Stage Inference is an unsupervised learning algorithm that disentangles the phenotypic heterogeneity and temporal progression of disease biomarkers, providing disease insight and quantitative estimates of individual subtype and stage. However, a key limitation of Subtype and Stage Inference is that it requires a complete set of biomarkers for each subject, reducing the number of datapoints available for model fitting and limiting applications of Subtype and Stage Inference to modalities that are widely collected, e.g. volumetric biomarkers derived from structural MRI. In this study, we adapted the Subtype and Stage Inference algorithm to handle missing data, enabling the application of Subtype and Stage Inference to multimodal data (magnetic resonance imaging, positron emission tomography, cerebrospinal fluid and cognitive tests) from 789 participants in the Alzheimer's Disease Neuroimaging Initiative. Missing-data Subtype and Stage Inference identified five subtypes having distinct progression patterns, which we describe by the earliest unique abnormality as 'Typical AD with Early Tau', 'Typical AD with Late Tau', 'Cortical', 'Cognitive' and 'Subcortical'. These new multimodal subtypes were differentially associated with age, years of education, Apolipoprotein E (APOE4) status, white matter hyperintensity burden and the rate of conversion from mild cognitive impairment to Alzheimer's disease, with the 'Cognitive' subtype showing the fastest clinical progression, and the 'Subcortical' subtype the slowest. Overall, we demonstrate that missing-data Subtype and Stage Inference reveals a finer landscape of Alzheimer's disease subtypes, each of which are associated with different risk factors. Missing-data Subtype and Stage Inference has broad utility, enabling the prediction of progression in a much wider set of individuals, rather than being restricted to those with complete data.",,pdf:https://academic.oup.com/braincomms/advance-article-pdf/doi/10.1093/braincomms/fcae219/58327048/fcae219.pdf; doi:https://doi.org/10.1093/braincomms/fcae219; html:https://europepmc.org/articles/PMC11259979; pdf:https://europepmc.org/articles/PMC11259979?pdf=render
 33801002,https://doi.org/10.3390/s21062190,A Novel Coupled Reaction-Diffusion System for Explainable Gene Expression Profiling.,"Farouq MW, Boulila W, Hussain Z, Rashid A, Shah M, Hussain S, Ng N, Ng D, Hanif H, Shaikh MG, Sheikh A, Hussain A.",,"Sensors (Basel, Switzerland)",2021,2021-03-21,Y,Non-small cell lung cancer; Gene Expression; Diffusion Equation; Explainable Machine Learning; Coupled Reaction Pde,,,"Machine learning (ML)-based algorithms are playing an important role in cancer diagnosis and are increasingly being used to aid clinical decision-making. However, these commonly operate as 'black boxes' and it is unclear how decisions are derived. Recently, techniques have been applied to help us understand how specific ML models work and explain the rational for outputs. This study aims to determine why a given type of cancer has a certain phenotypic characteristic. Cancer results in cellular dysregulation and a thorough consideration of cancer regulators is required. This would increase our understanding of the nature of the disease and help discover more effective diagnostic, prognostic, and treatment methods for a variety of cancer types and stages. Our study proposes a novel explainable analysis of potential biomarkers denoting tumorigenesis in non-small cell lung cancer. A number of these biomarkers are known to appear following various treatment pathways. An enhanced analysis is enabled through a novel mathematical formulation for the regulators of mRNA, the regulators of ncRNA, and the coupled mRNA-ncRNA regulators. Temporal gene expression profiles are approximated in a two-dimensional spatial domain for the transition states before converging to the stationary state, using a system comprised of coupled-reaction partial differential equations. Simulation experiments demonstrate that the proposed mathematical gene-expression profile represents a best fit for the population abundance of these oncogenes. In future, our proposed solution can lead to the development of alternative interpretable approaches, through the application of ML models to discover unknown dynamics in gene regulatory systems.",,pdf:https://www.mdpi.com/1424-8220/21/6/2190/pdf?version=1616388230; doi:https://doi.org/10.3390/s21062190; html:https://europepmc.org/articles/PMC8003942; pdf:https://europepmc.org/articles/PMC8003942?pdf=render
+33780550,https://doi.org/10.1111/anae.15457,Impact of a physician - critical care practitioner pre-hospital service in Wales on trauma survival: a retrospective analysis of linked registry data.,"Lyons J, Gabbe BJ, Rawlinson D, Lockey D, Fry RJ, Akbari A, Lyons RA.",,Anaesthesia,2021,2021-03-29,Y,Trauma; Survival; Critical Care; Pre-hospital Care,,,"The Emergency Medical Retrieval and Transfer Service for Wales launched in 2015. This service delivers senior pre-hospital doctors and advanced critical care practitioners to the scene of time-critical life- and limb-threatening incidents to provide advanced decision-making and pre-hospital clinical care. The impact of the service on 30-day mortality was evaluated retrospectively using a data linkage system. The study included patients who sustained moderate-to-severe blunt traumatic injuries (injury severity score ≥ 9) between 27 April 2015 and 30 November 2018. The association between pre-hospital management by the Emergency Medical Retrieval and Transfer Service and 30-day mortality was assessed using multivariable logistic regression. In total, data from 4035 patients were analysed, of which 412 (10%) were treated by the Emergency Medical Retrieval and Transfer Service. A greater proportion of patients treated by the Emergency Medical Retrieval and Transfer Service had an injury severity score ≥ 16 and Glasgow coma scale ≤ 12 (288 (70%) vs. 1435 (40%) and 126 (31%) vs. 325 (9%), respectively). The unadjusted 30-day mortality rate was 11.7% for patients managed by the Emergency Medical Retrieval and Transfer Service compared with 9.6% for patients managed by standard pre-hospital care services. However, after adjustment for differences in case-mix, the 30-day mortality rate for patients treated by the Emergency Medical Retrieval and Transfer Service was 37% lower (adjusted odds ratio 0.63 (95%CI 0.41-0.97); p = 0.037). The introduction of an emergency medical retrieval service was associated with a reduction in 30-day mortality for patients with blunt traumatic injury.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa56616/Download/56616__19761__8c6edaf906b846a69c8b19bdb94d015d.pdf; doi:https://doi.org/10.1111/anae.15457; html:https://europepmc.org/articles/PMC11497344; pdf:https://europepmc.org/articles/PMC11497344?pdf=render
 37144149,https://doi.org/10.3389/fped.2023.1148975,The psychosocial impact of microtia and ear reconstruction: A national data-linkage study.,"Jovic TH, Gibson JAG, Jovic M, Dobbs TD, Griffiths R, Akbari A, Whitaker IS.",,Frontiers in pediatrics,2023,2023-04-18,Y,Depression; Anxiety; Education; Microtia; Data Science,,,"<h4>Introduction</h4>Children with visible facial differences are believed to be at increased risk of negative psychosocial behaviours which may manifest as affective disorders. The aim of this study was to determine whether a diagnosis of microtia, and the associated surgical intervention, is associated with psychosocial implications including impaired educational attainment and a diagnosis of an affective disorder.<h4>Methods</h4>A retrospective case-control study was conducted using data linkage to identify patients in Wales with a diagnosis of microtia. Matched controls were sought on the basis of age, gender and socioeconomic deprivation status to yield a total sample size of 709. incidence was calculated using annual and geographic birth rates. Surgical operation codes were used to classify patients into those that had no surgery, autologous reconstruction or prosthetic reconstruction. Educational attainment at 11 years of age, plus a diagnosis of depression or anxiety were used as markers of adverse psychosocial outcomes and the relative risk was attained using logistic regression analyses.<h4>Results</h4>There were no significant associations between a diagnosis of microtia and an increased risk of adverse educational attainment or a risk of an affective disorder diagnosis. Male gender and higher deprivation scores were significantly associated with poorer educational attainment, irrespective of a diagnosis of microtia. Surgical intervention of any nature was also not associated with any increased risk of adverse educational or psychosocial outcomes in microtia patients.<h4>Discussion</h4>Microtia patients in Wales do not appear to be at greater risk of developing affective disorders or impaired academic performance as a result of their diagnosis or associated surgical intervention. Whilst reassuring, the need for appropriate support mechanisms to maintain positive psychosocial wellbeing and academic achievement in this patient cohort is reinforced.",,pdf:https://www.frontiersin.org/articles/10.3389/fped.2023.1148975/pdf; doi:https://doi.org/10.3389/fped.2023.1148975; html:https://europepmc.org/articles/PMC10152550; pdf:https://europepmc.org/articles/PMC10152550?pdf=render
 39327485,https://doi.org/10.1038/s41588-024-01937-x,Enhancing the Polygenic Score Catalog with tools for score calculation and ancestry normalization.,"Lambert SA, Wingfield B, Gibson JT, Gil L, Ramachandran S, Yvon F, Saverimuttu S, Tinsley E, Lewis E, Ritchie SC, Wu J, Cánovas R, McMahon A, Harris LW, Parkinson H, Inouye M.",,Nature genetics,2024,2024-10-01,N,,,,,,doi:https://doi.org/10.1038/s41588-024-01937-x
 38254067,https://doi.org/10.1186/s12916-023-03187-w,NHS Health Check attendance is associated with reduced multiorgan disease risk: a matched cohort study in the UK Biobank.,"McCracken C, Raisi-Estabragh Z, Szabo L, Robson J, Raman B, Topiwala A, Roca-Fernández A, Husain M, Petersen SE, Neubauer S, Nichols TE.",,BMC medicine,2024,2024-01-23,Y,Public Health; Preventive Medicine; Primary Care; General Medicine; Nhs Health Check,,,"<h4>Background</h4>The NHS Health Check is a preventive programme in the UK designed to screen for cardiovascular risk and to aid in primary disease prevention. Despite its widespread implementation, the effectiveness of the NHS Health Check for longer-term disease prevention is unclear. In this study, we measured the rate of new diagnoses in UK Biobank participants who underwent the NHS Health Check compared with those who did not.<h4>Methods</h4>Within the UK Biobank prospective study, 48,602 NHS Health Check recipients were identified from linked primary care records. These participants were then covariate-matched on an extensive range of socio-demographic, lifestyle, and medical factors with 48,602 participants without record of the check. Follow-up diagnoses were ascertained from health records over an average of 9 years (SD 2 years) including hypertension, diabetes, hypercholesterolaemia, stroke, dementia, myocardial infarction, atrial fibrillation, heart failure, fatty liver disease, alcoholic liver disease, liver cirrhosis, liver failure, acute kidney injury, chronic kidney disease (stage 3 +), cardiovascular mortality, and all-cause mortality. Time-varying survival modelling was used to compare adjusted outcome rates between the groups.<h4>Results</h4>In the immediate 2 years after the NHS Health Check, higher diagnosis rates were observed for hypertension, high cholesterol, and chronic kidney disease among health check recipients compared to their matched counterparts. However, in the longer term, NHS Health Check recipients had significantly lower risk across all multiorgan disease outcomes and reduced rates of cardiovascular and all-cause mortality.<h4>Conclusions</h4>The NHS Health Check is linked to reduced incidence of disease across multiple organ systems, which may be attributed to risk modification through earlier detection and treatment of key risk factors such as hypertension and high cholesterol. This work adds important evidence to the growing body of research supporting the effectiveness of preventative interventions in reducing longer-term multimorbidity.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-023-03187-w; doi:https://doi.org/10.1186/s12916-023-03187-w; html:https://europepmc.org/articles/PMC10804500; pdf:https://europepmc.org/articles/PMC10804500?pdf=render
 33737413,https://doi.org/10.1136/bmj.n628,Association between living with children and outcomes from covid-19: OpenSAFELY cohort study of 12 million adults in England.,"Forbes H, Morton CE, Bacon S, McDonald HI, Minassian C, Brown JP, Rentsch CT, Mathur R, Schultze A, DeVito NJ, MacKenna B, Hulme WJ, Croker R, Walker AJ, Williamson EJ, Bates C, Mehrkar A, Curtis HJ, Evans D, Wing K, Inglesby P, Drysdale H, Wong AYS, Cockburn J, McManus R, Parry J, Hester F, Harper S, Douglas IJ, Smeeth L, Evans SJW, Bhaskaran K, Eggo RM, Goldacre B, Tomlinson LA.",,BMJ (Clinical research ed.),2021,2021-03-18,Y,,,,"<h4>Objective</h4>To investigate whether risk of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and outcomes of coronavirus disease 2019 (covid-19) differed between adults living with and without children during the first two waves of the UK pandemic.<h4>Design</h4>Population based cohort study, on behalf of NHS England.<h4>Setting</h4>Primary care data and pseudonymously linked hospital and intensive care admissions and death records from England, during wave 1 (1 February to 31 August 2020) and wave 2 (1 September to 18 December 2020).<h4>Participants</h4>Two cohorts of adults (18 years and over) registered at a general practice on 1 February 2020 and 1 September 2020.<h4>Main outcome measures</h4>Adjusted hazard ratios for SARS-CoV-2 infection, covid-19 related admission to hospital or intensive care, or death from covid-19, by presence of children in the household.<h4>Results</h4>Among 9 334 392adults aged 65 years and under, during wave 1, living with children was not associated with materially increased risks of recorded SARS-CoV-2 infection, covid-19 related hospital or intensive care admission, or death from covid-19. In wave 2, among adults aged 65 years and under, living with children of any age was associated with an increased risk of recorded SARS-CoV-2 infection (hazard ratio 1.06 (95% confidence interval 1.05 to 1.08) for living with children aged 0-11 years; 1.22 (1.20 to 1.24) for living with children aged 12-18 years) and covid-19 related hospital admission (1.18 (1.06 to 1.31) for living with children aged 0-11; 1.26 (1.12 to 1.40) for living with children aged 12-18). Living with children aged 0-11 was associated with reduced risk of death from both covid-19 and non-covid-19 causes in both waves; living with children of any age was also associated with lower risk of dying from non-covid-19 causes. For adults 65 years and under during wave 2, living with children aged 0-11 years was associated with an increased absolute risk of having SARS-CoV-2 infection recorded of 40-60 per 10 000 people, from 810 to between 850 and 870, and an increase in the number of hospital admissions of 1-5 per 10 000 people, from 160 to between 161 and 165. Living with children aged 12-18 years was associated with an increase of 160-190 per 10 000 in the number of SARS-CoV-2 infections and an increase of 2-6 per 10 000 in the number of hospital admissions.<h4>Conclusions</h4>In contrast to wave 1, evidence existed of increased risk of reported SARS-CoV-2 infection and covid-19 outcomes among adults living with children during wave 2. However, this did not translate into a materially increased risk of covid-19 mortality, and absolute increases in risk were small.",,pdf:https://www.bmj.com/content/bmj/372/bmj.n628.full.pdf; doi:https://doi.org/10.1136/bmj.n628; html:https://europepmc.org/articles/PMC7970340; pdf:https://europepmc.org/articles/PMC7970340?pdf=render
 34543508,https://doi.org/10.1111/ene.15114,"Adult-onset idiopathic dystonia: A national data-linkage study to determine epidemiological, social deprivation, and mortality characteristics.","Bailey GA, Rawlings A, Torabi F, Pickrell O, Peall KJ.",,European journal of neurology,2022,2021-10-15,Y,Mortality; Prevalence; Socioeconomic Factors; incidence; Dystonia,,,"<h4>Background and purpose</h4>Accurate epidemiological information is essential for the improved understanding of dystonia syndromes, as well as better provisioning of clinical services and providing context for diagnostic decision-making. Here, we determine epidemiological, social deprivation, and mortality characteristics of adult-onset idiopathic dystonia in the Welsh population.<h4>Methods</h4>A retrospective population-based cohort study using anonymized electronic health care data in Wales was conducted to identify individuals with dystonia between 1 January 1994 and 31 December 2017. We developed a case-ascertainment algorithm to determine dystonia incidence and prevalence, as well as characterization of the dystonia cohort, based on social deprivation and mortality.<h4>Results</h4>The case-ascertainment algorithm (79% sensitivity) identified 54,966 cases; of these cases, 41,660 had adult-onset idiopathic dystonia (≥20 years). Amongst the adult-onset form, the median age at diagnosis was 41 years, with males significantly older at time of diagnosis compared to females. Prevalence rates ranged from 0.02% in 1994 to 1.2% in 2017. The average annual incidence was 87.7/100,000/year, increasing from 49.9/100,000/year (1994) to 96.21/100,000/year (2017). In 2017, people with dystonia had a similar life expectancy to the Welsh population.<h4>Conclusions</h4>We have developed a case-ascertainment algorithm, supported by the introduction of a neurologist-reviewed validation cohort, providing a platform for future population-based dystonia studies. We have established robust population-level prevalence and incidence values for adult-onset idiopathic forms of dystonia, with this reflecting increasing clinical recognition and identification of causal genes. Underlying causes of death mirrored those of the general population, including circulatory disorders, respiratory disorders, cancers, and dementia.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/ene.15114; doi:https://doi.org/10.1111/ene.15114; html:https://europepmc.org/articles/PMC9377012; pdf:https://europepmc.org/articles/PMC9377012?pdf=render
-37996473,https://doi.org/10.1038/s41598-023-47371-7,"Evidence for involvement of the alcohol consumption WDPCP gene in lipid metabolism, and liver cirrhosis.","O'Farrell F, Aleyakpo B, Mustafa R, Jiang X, Pinto RC, Elliott P, Tzoulaki I, Dehghan A, Loh SHY, Barclay JW, Martins LM, Pazoki R.",,Scientific reports,2023,2023-11-23,Y,,,,"Biological pathways between alcohol consumption and alcohol liver disease (ALD) are not fully understood. We selected genes with known effect on (1) alcohol consumption, (2) liver function, and (3) gene expression. Expression of the orthologs of these genes in Caenorhabditis elegans and Drosophila melanogaster was suppressed using mutations and/or RNA interference (RNAi). In humans, association analysis, pathway analysis, and Mendelian randomization analysis were performed to identify metabolic changes due to alcohol consumption. In C. elegans, we found a reduction in locomotion rate after exposure to ethanol for RNAi knockdown of ACTR1B and MAPT. In Drosophila, we observed (1) a change in sedative effect of ethanol for RNAi knockdown of WDPCP, TENM2, GPN1, ARPC1B, and SCN8A, (2) a reduction in ethanol consumption for RNAi knockdown of TENM2, (3) a reduction in triradylglycerols (TAG) levels for RNAi knockdown of WDPCP, TENM2, and GPN1. In human, we observed (1) a link between alcohol consumption and several metabolites including TAG, (2) an enrichment of the candidate (alcohol-associated) metabolites within the linoleic acid (LNA) and alpha-linolenic acid (ALA) metabolism pathways, (3) a causal link between gene expression of WDPCP to liver fibrosis and liver cirrhosis. Our results imply that WDPCP might be involved in ALD.",,pdf:https://www.nature.com/articles/s41598-023-47371-7.pdf; doi:https://doi.org/10.1038/s41598-023-47371-7; html:https://europepmc.org/articles/PMC10667215; pdf:https://europepmc.org/articles/PMC10667215?pdf=render
 30928998,https://doi.org/10.4193/rhin18.237,Risk of mortality and cardiovascular events following macrolide prescription in chronic rhinosinusitis patients: a cohort study using linked primary care electronic health records.,"Williamson E, Denaxas S, Morris S, Clarke CS, Thomas M, Evans H, Direk K, Gonzalez-Izquierdo A, Little P, Lund V, Blackshaw H, Schilder A, Philpott C, Hopkins C, Carpenter J, Programme Team OBOTM.",,Rhinology,2019,2019-08-01,N,,,,"<h4>Background</h4>Macrolide antibiotics have demonstrated important anti-inflammatory and immunomodulatory properties in chronic rhinosinusitis (CRS) patients. However, reports of increased risks of cardiovascular events have led to safety concerns. We investigated the risk of all-cause and cardiac death, and cardiovascular outcomes, associated with macrolide use.<h4>Methodology</h4>Observational cohort (1997-2016) using linked data from the Clinical Practice Research Datalink, Hospital Episodes Statistics, and the Office for National Statistics. Patients aged 16-80 years with CRS prescribed a macrolide antibiotic or penicillin were included, comparing prescriptions for macrolide antibiotics to penicillin. Outcomes were all-cause mortality, cardiac death, myocardial infarction, stroke, diagnosis of peripheral vascular disease, and cardiac arrhythmia.<h4>Results</h4>Analysis included 320,798 prescriptions received by 66,331 patients. There were 3,251 deaths, 815 due to cardiovascular causes, 925 incident myocardial infarctions, 859 strokes, 637 diagnoses of peripheral vascular disease, and 1,436 cardiac arrhythmias. A non-statistically significant trend towards increased risk of myocardial infarction during the first 30 days following macrolide prescription was observed. No statistically significant short- or long-term risks were observed for macrolide prescription. No significant risks were identified for clarithromycin in particular.<h4>Conclusions</h4>Although not statistically significant, our best estimates suggest an increased short-term risk of myocardial infarction in patients with CRS following macrolide prescription, supporting previous observational evidence. However, confounding by indication remains a possible explanation for this apparent increased risk. We found no evidence of longer term increased risks.",,pdf:https://www.rhinologyjournal.com/download.php?id=1882; doi:https://doi.org/10.4193/Rhin18.237
 38849195,https://doi.org/10.1136/archdischild-2023-326756,Utility and acceptability of remote 6-lead electrocardiographic monitoring in children with inherited cardiac conditions.,"Lawley CM, Luczak-Wozniak K, Chung SC, Field E, Barnes A, Starling L, Cervi E, Kaski JP.",,Archives of disease in childhood,2024,2024-08-16,Y,Cardiology; Paediatrics,,,"<h4>Objective</h4>This pilot study sought to investigate the utility and acceptability of the KardiaMobile 6-lead ECG (KM6LECG) as a tool for remote monitoring in children with inherited cardiac conditions.<h4>Design</h4>A single-centre prospective cohort study. Children underwent standard clinical evaluation including a 12-lead ECG and a KM6LECG in the clinic. Participants recorded KM6LECGs monthly at home for 3 months. Families completed a questionnaire on their experience.<h4>Setting</h4>Great Ormond Street Hospital Centre for Inherited Cardiovascular Diseases.<h4>Participants</h4>64 children: 22 with hypertrophic cardiomyopathy (HCM); 22 with long QT syndrome and 20 unaffected siblings (controls).<h4>Main outcome measures</h4>Comparison of data extracted from the clinic 12-lead ECG and supervised KM6LECG, and the supervised and unsupervised KM6LECG recording.<h4>Results</h4>Of 64 children (35% female, mean age 12 years), 58 had a baseline 12-lead ECG and appropriate baseline KM6LECG. In children with HCM, abnormalities in ventricular depolarisation/repolarisation in the limb leads of the 12-lead ECG were reliably reproduced. From the whole cohort, there was a strong positive correlation between the corrected QT interval from the 12-lead ECG and baseline KM6LECG (intraclass correlation coefficient=0.839) and baseline KM6LECG with an unsupervised KM6LECG (intraclass correlation coefficient=0.736). Suspected 'lead' misplacement impacted 18% of unsupervised recordings. Overall, the acceptability of the KM6LECG to families was good.<h4>Conclusions</h4>The KM6LECG provides an accurate tool for assessing some ECG abnormalities associated with paediatric inherited cardiovascular disease and may provide a useful at-home adjunct to face-to-face clinical care of children requiring ECG assessment.",,pdf:https://adc.bmj.com/content/archdischild/early/2024/06/07/archdischild-2023-326756.full.pdf; doi:https://doi.org/10.1136/archdischild-2023-326756; html:https://europepmc.org/articles/PMC11347208; pdf:https://europepmc.org/articles/PMC11347208?pdf=render
+37996473,https://doi.org/10.1038/s41598-023-47371-7,"Evidence for involvement of the alcohol consumption WDPCP gene in lipid metabolism, and liver cirrhosis.","O'Farrell F, Aleyakpo B, Mustafa R, Jiang X, Pinto RC, Elliott P, Tzoulaki I, Dehghan A, Loh SHY, Barclay JW, Martins LM, Pazoki R.",,Scientific reports,2023,2023-11-23,Y,,,,"Biological pathways between alcohol consumption and alcohol liver disease (ALD) are not fully understood. We selected genes with known effect on (1) alcohol consumption, (2) liver function, and (3) gene expression. Expression of the orthologs of these genes in Caenorhabditis elegans and Drosophila melanogaster was suppressed using mutations and/or RNA interference (RNAi). In humans, association analysis, pathway analysis, and Mendelian randomization analysis were performed to identify metabolic changes due to alcohol consumption. In C. elegans, we found a reduction in locomotion rate after exposure to ethanol for RNAi knockdown of ACTR1B and MAPT. In Drosophila, we observed (1) a change in sedative effect of ethanol for RNAi knockdown of WDPCP, TENM2, GPN1, ARPC1B, and SCN8A, (2) a reduction in ethanol consumption for RNAi knockdown of TENM2, (3) a reduction in triradylglycerols (TAG) levels for RNAi knockdown of WDPCP, TENM2, and GPN1. In human, we observed (1) a link between alcohol consumption and several metabolites including TAG, (2) an enrichment of the candidate (alcohol-associated) metabolites within the linoleic acid (LNA) and alpha-linolenic acid (ALA) metabolism pathways, (3) a causal link between gene expression of WDPCP to liver fibrosis and liver cirrhosis. Our results imply that WDPCP might be involved in ALD.",,pdf:https://www.nature.com/articles/s41598-023-47371-7.pdf; doi:https://doi.org/10.1038/s41598-023-47371-7; html:https://europepmc.org/articles/PMC10667215; pdf:https://europepmc.org/articles/PMC10667215?pdf=render
+33495722,https://doi.org/10.1109/access.2021.3050524,Remote Assessment of Parkinson's Disease Symptom Severity Using the Simulated Cellular Mobile Telephone Network.,"Tsanas A, Little MA, Ramig LO.",,"IEEE access : practical innovations, open solutions",2021,2021-01-11,Y,Telemedicine; Parkinson’s Disease; Decision Support Tool; Nonlinear Speech Signal Processing,,,"Telemonitoring of Parkinson's Disease (PD) has attracted considerable research interest because of its potential to make a lasting, positive impact on the life of patients and their carers. Purpose-built devices have been developed that record various signals which can be associated with average PD symptom severity, as quantified on standard clinical metrics such as the Unified Parkinson's Disease Rating Scale (UPDRS). Speech signals are particularly promising in this regard, because they can be easily recorded without the use of expensive, dedicated hardware. Previous studies have demonstrated replication of UPDRS to within less than 2 points of a clinical raters' assessment of symptom severity, using high-quality speech signals collected using dedicated telemonitoring hardware. Here, we investigate the potential of using the standard voice-over-GSM (2G) or UMTS (3G) cellular mobile telephone networks for PD telemonitoring, networks that, together, have greater than 5 billion subscribers worldwide. We test the robustness of this approach using a simulated noisy mobile communication network over which speech signals are transmitted, and approximately 6000 recordings from 42 PD subjects. We show that UPDRS can be estimated to within less than 3.5 points difference from the clinical raters' assessment, which is clinically useful given that the inter-rater variability for UPDRS can be as high as 4-5 UPDRS points. This provides compelling evidence that the existing voice telephone network has potential towards facilitating inexpensive, mass-scale PD symptom telemonitoring applications.",,pdf:https://ieeexplore.ieee.org/ielx7/6287639/9312710/09319241.pdf; doi:https://doi.org/10.1109/ACCESS.2021.3050524; html:https://europepmc.org/articles/PMC7821632; pdf:https://europepmc.org/articles/PMC7821632?pdf=render
 39406990,https://doi.org/10.1038/s42003-024-06984-y,Proteo-genomic analyses in relatively lean Chinese adults identify proteins and pathways that affect general and central adiposity levels.,"Iona A, Yao P, Pozarickij A, Kartsonaki C, Said S, Wright N, Lin K, Millwood I, Fry H, Mazidi M, Wang B, Chen Y, Du H, Yang L, Avery D, Schmidt D, Sun D, Pei P, Lv J, Yu C, Hill M, Chen J, Bragg F, Bennett D, Walters R, Li L, Clarke R, Chen Z, China Kadoorie Biobank Collaborative Group.",,Communications biology,2024,2024-10-15,Y,,,,"Adiposity is an established risk factor for multiple diseases, but the causal relationships of different adiposity types with circulating protein biomarkers have not been systematically investigated. We examine the causal associations of general and central adiposity with 2923 plasma proteins among 3977 Chinese adults (mean BMI = 23.9 kg/m²). Genetically-predicted body mass index (BMI), body fat percentage (BF%), waist circumference (WC), and waist-to-hip ratio (WHR) are significantly (FDR < 0.05) associated with 399, 239, 436, and 283 proteins, respectively, with 80 proteins associated with all four and 275 with only one adiposity trait. WHR is associated with the most proteins (n = 90) after adjusting for other adiposity traits. These associations are largely replicated in Europeans (mean BMI = 27.4 kg/m²). Two-sample Mendelian randomisation (MR) analyses in East Asians using cis-protein quantitative trait locus (cis-pQTLs) identified in GWAS find 30/2 proteins significantly affect levels of BMI/WC, respectively, with 10 showing evidence of colocalisation, and seven (inter-alpha-trypsin inhibitor heavy chain H3, complement factor B, EGF-containing fibulin-like extracellular matrix protein 1, thioredoxin domain-containing protein 15, alpha-2-antiplasmin, fibronectin, mimecan) are replicated in separate MR using different cis-pQTLs identified in Europeans. These findings identified potential novel mechanisms and targets, to our knowledge, for improved treatment and prevention of obesity and associated diseases.",,doi:https://doi.org/10.1038/s42003-024-06984-y; html:https://europepmc.org/articles/PMC11480319; pdf:https://europepmc.org/articles/PMC11480319?pdf=render
 34389694,https://doi.org/10.1158/1535-7163.mct-20-1050,Clinical Positioning of the IAP Antagonist Tolinapant (ASTX660) in Colorectal Cancer.,"Crawford N, Stott KJ, Sessler T, McCann C, McDaid W, Lees A, Latimer C, Fox JP, Munck JM, Smyth T, Shah A, Martins V, Lawler M, Dunne PD, Kerr EM, McDade SS, Coyle VM, Longley DB.",,Molecular cancer therapeutics,2021,2021-08-13,Y,,,,"Inhibitors of apoptosis proteins (IAPs) are intracellular proteins, with important roles in regulating cell death, inflammation, and immunity. Here, we examined the clinical and therapeutic relevance of IAPs in colorectal cancer. We found that elevated expression of cIAP1 and cIAP2 (but not XIAP) significantly correlated with poor prognosis in patients with microsatellite stable (MSS) stage III colorectal cancer treated with 5-fluorouracil (5FU)-based adjuvant chemotherapy, suggesting their involvement in promoting chemoresistance. A novel IAP antagonist tolinapant (ASTX660) potently and rapidly downregulated cIAP1 in colorectal cancer models, demonstrating its robust on-target efficacy. In cells co-cultured with TNFα to mimic an inflammatory tumor microenvironment, tolinapant induced caspase-8-dependent apoptosis in colorectal cancer cell line models; however, the extent of apoptosis was limited because of inhibition by the caspase-8 paralogs FLIP and, unexpectedly, caspase-10. Importantly, tolinapant-induced apoptosis was augmented by FOLFOX in human colorectal cancer and murine organoid models <i>in vitro</i> and <i>in vivo</i>, due (at least in part) to FOLFOX-induced downregulation of class I histone deacetylases (HDAC), leading to acetylation of the FLIP-binding partner Ku70 and downregulation of FLIP. Moreover, the effects of FOLFOX could be phenocopied using the clinically relevant class I HDAC inhibitor, entinostat, which also induced acetylation of Ku70 and FLIP downregulation. Further analyses revealed that caspase-8 knockout RIPK3-positive colorectal cancer models were sensitive to tolinapant-induced necroptosis, an effect that could be exploited in caspase-8-proficient models using the clinically relevant caspase inhibitor emricasan. Our study provides evidence for immediate clinical exploration of tolinapant in combination with FOLFOX in poor prognosis MSS colorectal cancer with elevated cIAP1/2 expression.",,pdf:https://aacrjournals.org/mct/article-pdf/20/9/1627/3076208/1627.pdf; doi:https://doi.org/10.1158/1535-7163.MCT-20-1050; html:https://europepmc.org/articles/PMC7611622; pdf:https://europepmc.org/articles/PMC7611622?pdf=render
-33495722,https://doi.org/10.1109/access.2021.3050524,Remote Assessment of Parkinson's Disease Symptom Severity Using the Simulated Cellular Mobile Telephone Network.,"Tsanas A, Little MA, Ramig LO.",,"IEEE access : practical innovations, open solutions",2021,2021-01-11,Y,Telemedicine; Parkinson’s Disease; Decision Support Tool; Nonlinear Speech Signal Processing,,,"Telemonitoring of Parkinson's Disease (PD) has attracted considerable research interest because of its potential to make a lasting, positive impact on the life of patients and their carers. Purpose-built devices have been developed that record various signals which can be associated with average PD symptom severity, as quantified on standard clinical metrics such as the Unified Parkinson's Disease Rating Scale (UPDRS). Speech signals are particularly promising in this regard, because they can be easily recorded without the use of expensive, dedicated hardware. Previous studies have demonstrated replication of UPDRS to within less than 2 points of a clinical raters' assessment of symptom severity, using high-quality speech signals collected using dedicated telemonitoring hardware. Here, we investigate the potential of using the standard voice-over-GSM (2G) or UMTS (3G) cellular mobile telephone networks for PD telemonitoring, networks that, together, have greater than 5 billion subscribers worldwide. We test the robustness of this approach using a simulated noisy mobile communication network over which speech signals are transmitted, and approximately 6000 recordings from 42 PD subjects. We show that UPDRS can be estimated to within less than 3.5 points difference from the clinical raters' assessment, which is clinically useful given that the inter-rater variability for UPDRS can be as high as 4-5 UPDRS points. This provides compelling evidence that the existing voice telephone network has potential towards facilitating inexpensive, mass-scale PD symptom telemonitoring applications.",,pdf:https://ieeexplore.ieee.org/ielx7/6287639/9312710/09319241.pdf; doi:https://doi.org/10.1109/ACCESS.2021.3050524; html:https://europepmc.org/articles/PMC7821632; pdf:https://europepmc.org/articles/PMC7821632?pdf=render
 36794597,https://doi.org/10.1111/trf.17277,Impact of a post-donation hemoglobin testing strategy on efficiency and safety of whole blood donation in England: A modeling study.,"Kim LG, Bolton T, Sweeting MJ, Bell S, Fahle S, McMahon A, Walker M, Ferguson E, Miflin G, Roberts DJ, Di Angelantonio E, Wood AM.",,Transfusion,2023,2023-02-16,Y,Blood Donation; Simulation Modeling; Low Hemoglobin Deferral; Post-donation Testing,,,"<h4>Background</h4>Deferrals due to low hemoglobin are time-consuming and costly for blood donors and donation services. Furthermore, accepting donations from those with low hemoglobin could represent a significant safety issue. One approach to reduce them is to use hemoglobin concentration alongside donor characteristics to inform personalized inter-donation intervals.<h4>Study design and methods</h4>We used data from 17,308 donors to inform a discrete event simulation model comparing personalized inter-donation intervals using ""post-donation"" testing (i.e., estimating current hemoglobin from that measured by a hematology analyzer at last donation) versus the current approach in England (i.e., pre-donation testing with fixed intervals of 12-weeks for men and 16-weeks for women). We reported the impact on total donations, low hemoglobin deferrals, inappropriate bleeds, and blood service costs. Personalized inter-donation intervals were defined using mixed-effects modeling to estimate hemoglobin trajectories and probability of crossing hemoglobin donation thresholds.<h4>Results</h4>The model had generally good internal validation, with predicted events similar to those observed. Over 1 year, a personalized strategy requiring ≥90% probability of being over the hemoglobin threshold, minimized adverse events (low hemoglobin deferrals and inappropriate bleeds) in both sexes and costs in women. Donations per adverse event improved from 3.4 (95% uncertainty interval 2.8, 3.7) under the current strategy to 14.8 (11.6, 19.2) in women, and from 7.1 (6.1, 8.5) to 26.9 (20.8, 42.6) in men. In comparison, a strategy incorporating early returns for those with high certainty of being over the threshold maximized total donations in both men and women, but was less favorable in terms of adverse events, with 8.4 donations per adverse event in women (7.0, 10,1) and 14.8 (12.1, 21.0) in men.<h4>Discussion</h4>Personalized inter-donation intervals using post-donation testing combined with modeling of hemoglobin trajectories can help reduce deferrals, inappropriate bleeds, and costs.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/trf.17277; doi:https://doi.org/10.1111/trf.17277; html:https://europepmc.org/articles/PMC10952564; pdf:https://europepmc.org/articles/PMC10952564?pdf=render
 33939953,https://doi.org/10.1016/s0140-6736(21)00634-6,"Ethnic differences in SARS-CoV-2 infection and COVID-19-related hospitalisation, intensive care unit admission, and death in 17 million adults in England: an observational cohort study using the OpenSAFELY platform.","Mathur R, Rentsch CT, Morton CE, Hulme WJ, Schultze A, MacKenna B, Eggo RM, Bhaskaran K, Wong AYS, Williamson EJ, Forbes H, Wing K, McDonald HI, Bates C, Bacon S, Walker AJ, Evans D, Inglesby P, Mehrkar A, Curtis HJ, DeVito NJ, Croker R, Drysdale H, Cockburn J, Parry J, Hester F, Harper S, Douglas IJ, Tomlinson L, Evans SJW, Grieve R, Harrison D, Rowan K, Khunti K, Chaturvedi N, Smeeth L, Goldacre B, OpenSAFELY Collaborative.",,"Lancet (London, England)",2021,2021-04-30,Y,,,,"<h4>Background</h4>COVID-19 has disproportionately affected minority ethnic populations in the UK. Our aim was to quantify ethnic differences in SARS-CoV-2 infection and COVID-19 outcomes during the first and second waves of the COVID-19 pandemic in England.<h4>Methods</h4>We conducted an observational cohort study of adults (aged ≥18 years) registered with primary care practices in England for whom electronic health records were available through the OpenSAFELY platform, and who had at least 1 year of continuous registration at the start of each study period (Feb 1 to Aug 3, 2020 [wave 1], and Sept 1 to Dec 31, 2020 [wave 2]). Individual-level primary care data were linked to data from other sources on the outcomes of interest: SARS-CoV-2 testing and positive test results and COVID-19-related hospital admissions, intensive care unit (ICU) admissions, and death. The exposure was self-reported ethnicity as captured on the primary care record, grouped into five high-level census categories (White, South Asian, Black, other, and mixed) and 16 subcategories across these five categories, as well as an unknown ethnicity category. We used multivariable Cox regression to examine ethnic differences in the outcomes of interest. Models were adjusted for age, sex, deprivation, clinical factors and comorbidities, and household size, with stratification by geographical region.<h4>Findings</h4>Of 17 288 532 adults included in the study (excluding care home residents), 10 877 978 (62·9%) were White, 1 025 319 (5·9%) were South Asian, 340 912 (2·0%) were Black, 170 484 (1·0%) were of mixed ethnicity, 320 788 (1·9%) were of other ethnicity, and 4 553 051 (26·3%) were of unknown ethnicity. In wave 1, the likelihood of being tested for SARS-CoV-2 infection was slightly higher in the South Asian group (adjusted hazard ratio 1·08 [95% CI 1·07-1·09]), Black group (1·08 [1·06-1·09]), and mixed ethnicity group (1·04 [1·02-1·05]) and was decreased in the other ethnicity group (0·77 [0·76-0·78]) relative to the White group. The risk of testing positive for SARS-CoV-2 infection was higher in the South Asian group (1·99 [1·94-2·04]), Black group (1·69 [1·62-1·77]), mixed ethnicity group (1·49 [1·39-1·59]), and other ethnicity group (1·20 [1·14-1·28]). Compared with the White group, the four remaining high-level ethnic groups had an increased risk of COVID-19-related hospitalisation (South Asian group 1·48 [1·41-1·55], Black group 1·78 [1·67-1·90], mixed ethnicity group 1·63 [1·45-1·83], other ethnicity group 1·54 [1·41-1·69]), COVID-19-related ICU admission (2·18 [1·92-2·48], 3·12 [2·65-3·67], 2·96 [2·26-3·87], 3·18 [2·58-3·93]), and death (1·26 [1·15-1·37], 1·51 [1·31-1·71], 1·41 [1·11-1·81], 1·22 [1·00-1·48]). In wave 2, the risks of hospitalisation, ICU admission, and death relative to the White group were increased in the South Asian group but attenuated for the Black group compared with these risks in wave 1. Disaggregation into 16 ethnicity groups showed important heterogeneity within the five broader categories.<h4>Interpretation</h4>Some minority ethnic populations in England have excess risks of testing positive for SARS-CoV-2 and of adverse COVID-19 outcomes compared with the White population, even after accounting for differences in sociodemographic, clinical, and household characteristics. Causes are likely to be multifactorial, and delineating the exact mechanisms is crucial. Tackling ethnic inequalities will require action across many fronts, including reducing structural inequalities, addressing barriers to equitable care, and improving uptake of testing and vaccination.<h4>Funding</h4>Medical Research Council.",,pdf:https://researchonline.lshtm.ac.uk/id/eprint/4659476/13/PIIS0140673621006346.pdf; doi:https://doi.org/10.1016/S0140-6736(21)00634-6; html:https://europepmc.org/articles/PMC8087292; pdf:https://europepmc.org/articles/PMC8087292?pdf=render
 33419870,https://doi.org/10.1136/bmjhci-2020-100254,Network graph representation of COVID-19 scientific publications to aid knowledge discovery.,"Cernile G, Heritage T, Sebire NJ, Gordon B, Schwering T, Kazemlou S, Borecki Y.",,BMJ health & care informatics,2021,2021-01-01,Y,Health care; Medical Informatics; Information Science; Bmj Health Informatics,,,"<h4>Introduction</h4>Numerous scientific journal articles related to COVID-19 have been rapidly published, making navigation and understanding of relationships difficult.<h4>Methods</h4>A graph network was constructed from the publicly available COVID-19 Open Research Dataset (CORD-19) of COVID-19-related publications using an engine leveraging medical knowledge bases to identify discrete medical concepts and an open-source tool (Gephi) to visualise the network.<h4>Results</h4>The network shows connections between diseases, medications and procedures identified from the title and abstract of 195 958 COVID-19-related publications (CORD-19 Dataset). Connections between terms with few publications, those unconnected to the main network and those irrelevant were not displayed. Nodes were coloured by knowledge base and the size of the node related to the number of publications containing the term. The data set and visualisations were made publicly accessible via a webtool.<h4>Conclusion</h4>Knowledge management approaches (text mining and graph networks) can effectively allow rapid navigation and exploration of entity inter-relationships to improve understanding of diseases such as COVID-19.",,pdf:https://informatics.bmj.com/content/bmjhci/28/1/e100254.full.pdf; doi:https://doi.org/10.1136/bmjhci-2020-100254; html:https://europepmc.org/articles/PMC7798427; pdf:https://europepmc.org/articles/PMC7798427?pdf=render
-38238056,https://doi.org/10.1136/bmjopen-2023-076711,"Cohort profile: Born in Wales-a birth cohort with maternity, parental and child data linkage for life course research in Wales, UK.","Jones H, Seaborne MJ, Kennedy NL, James M, Dredge S, Bandyopadhyay A, Battaglia A, Davies S, Brophy S.",,BMJ open,2024,2024-01-18,Y,epidemiology; Public Health; Community Child Health; Surveys And Questionnaires,,,"<h4>Purpose</h4>Using Wales's national dataset for maternity and births as a core dataset, we have linked related datasets to create a more complete and comprehensive entire country birth cohort. Data of anonymised identified persons are linked on the individual level to data from health, social care and education data within the Secure Anonymised Information Linkage (SAIL) Databank. Each individual is assigned an encrypted Anonymised Linking Field; this field is used to link anonymised individuals across datasets. We present the descriptive data available in the core dataset, and the future expansion plans for the database beyond its initial development stage.<h4>Participants</h4>Descriptive information from 2011 to 2023 has been gathered from the National Community Child Health Database (NCCHD) in SAIL. This comprehensive dataset comprises over 400 000 child electronic records. Additionally, survey responses about health and well-being from a cross-section of the population including 2500 parents and 30 000 primary school children have been collected for enriched personal responses and linkage to the data spine.<h4>Findings to date</h4>The electronic cohort comprises all children born in Wales since 2011, with follow-up conducted until they finish primary school at age 11. The child cohort is 51%: 49% female: male, and 7.8% are from ethnic minority backgrounds. When considering age distribution, 26.8% of children are under the age of 5, while 63.2% fall within the age range of 5-11.<h4>Future plans</h4>Born in Wales will expand by 30 000 new births annually in Wales (in NCCHD), while including follow-up data of children and parents already in the database. Supplementary datasets complement the existing linkage, including primary care, hospital data, educational attainment and social care. Future research includes exploring the long-term implications of COVID-19 on child health and development, and examining the impact of parental work environment on child health and development.",,pdf:https://bmjopen.bmj.com/content/bmjopen/14/1/e076711.full.pdf; doi:https://doi.org/10.1136/bmjopen-2023-076711; html:https://europepmc.org/articles/PMC10806724; pdf:https://europepmc.org/articles/PMC10806724?pdf=render
 34489241,https://doi.org/10.1136/bjsports-2021-104050,Reallocation of time between device-measured movement behaviours and risk of incident cardiovascular disease.,"Walmsley R, Chan S, Smith-Byrne K, Ramakrishnan R, Woodward M, Rahimi K, Dwyer T, Bennett D, Doherty A.",,British journal of sports medicine,2021,2021-09-06,Y,Cardiovascular diseases; Sleep; Methods; Physical Activity; Sedentary Behavior,,,"<h4>Objective</h4>To improve classification of movement behaviours in free-living accelerometer data using machine-learning methods, and to investigate the association between machine-learned movement behaviours and risk of incident cardiovascular disease (CVD) in adults.<h4>Methods</h4>Using free-living data from 152 participants, we developed a machine-learning model to classify movement behaviours (moderate-to-vigorous physical activity behaviours (MVPA), light physical activity behaviours, sedentary behaviour, sleep) in wrist-worn accelerometer data. Participants in UK Biobank, a prospective cohort, were asked to wear an accelerometer for 7 days, and we applied our machine-learning model to classify their movement behaviours. Using compositional data analysis Cox regression, we investigated how reallocating time between movement behaviours was associated with CVD incidence.<h4>Results</h4>In leave-one-participant-out analysis, our machine-learning method classified free-living movement behaviours with mean accuracy 88% (95% CI 87% to 89%) and Cohen's kappa 0.80 (95% CI 0.79 to 0.82). Among 87 498 UK Biobank participants, there were 4105 incident CVD events. Reallocating time from any behaviour to MVPA, or reallocating time from sedentary behaviour to any behaviour, was associated with lower CVD risk. For an average individual, reallocating 20 min/day to MVPA from all other behaviours proportionally was associated with 9% (95% CI 7% to 10%) lower risk, while reallocating 1 hour/day to sedentary behaviour from all other behaviours proportionally was associated with 5% (95% CI 3% to 7%) higher risk.<h4>Conclusion</h4>Machine-learning methods classified movement behaviours accurately in free-living accelerometer data. Reallocating time from other behaviours to MVPA, and from sedentary behaviour to other behaviours, was associated with lower risk of incident CVD, and should be promoted by interventions and guidelines.",,pdf:https://bjsm.bmj.com/content/bjsports/early/2022/02/15/bjsports-2021-104050.full.pdf; doi:https://doi.org/10.1136/bjsports-2021-104050; html:https://europepmc.org/articles/PMC9484395; pdf:https://europepmc.org/articles/PMC9484395?pdf=render
+38238056,https://doi.org/10.1136/bmjopen-2023-076711,"Cohort profile: Born in Wales-a birth cohort with maternity, parental and child data linkage for life course research in Wales, UK.","Jones H, Seaborne MJ, Kennedy NL, James M, Dredge S, Bandyopadhyay A, Battaglia A, Davies S, Brophy S.",,BMJ open,2024,2024-01-18,Y,epidemiology; Public Health; Community Child Health; Surveys And Questionnaires,,,"<h4>Purpose</h4>Using Wales's national dataset for maternity and births as a core dataset, we have linked related datasets to create a more complete and comprehensive entire country birth cohort. Data of anonymised identified persons are linked on the individual level to data from health, social care and education data within the Secure Anonymised Information Linkage (SAIL) Databank. Each individual is assigned an encrypted Anonymised Linking Field; this field is used to link anonymised individuals across datasets. We present the descriptive data available in the core dataset, and the future expansion plans for the database beyond its initial development stage.<h4>Participants</h4>Descriptive information from 2011 to 2023 has been gathered from the National Community Child Health Database (NCCHD) in SAIL. This comprehensive dataset comprises over 400 000 child electronic records. Additionally, survey responses about health and well-being from a cross-section of the population including 2500 parents and 30 000 primary school children have been collected for enriched personal responses and linkage to the data spine.<h4>Findings to date</h4>The electronic cohort comprises all children born in Wales since 2011, with follow-up conducted until they finish primary school at age 11. The child cohort is 51%: 49% female: male, and 7.8% are from ethnic minority backgrounds. When considering age distribution, 26.8% of children are under the age of 5, while 63.2% fall within the age range of 5-11.<h4>Future plans</h4>Born in Wales will expand by 30 000 new births annually in Wales (in NCCHD), while including follow-up data of children and parents already in the database. Supplementary datasets complement the existing linkage, including primary care, hospital data, educational attainment and social care. Future research includes exploring the long-term implications of COVID-19 on child health and development, and examining the impact of parental work environment on child health and development.",,pdf:https://bmjopen.bmj.com/content/bmjopen/14/1/e076711.full.pdf; doi:https://doi.org/10.1136/bmjopen-2023-076711; html:https://europepmc.org/articles/PMC10806724; pdf:https://europepmc.org/articles/PMC10806724?pdf=render
 35813279,https://doi.org/10.1016/s2666-7568(22)00147-7,"Duration of vaccine effectiveness against SARS-CoV-2 infection, hospitalisation, and death in residents and staff of long-term care facilities in England (VIVALDI): a prospective cohort study.","Shrotri M, Krutikov M, Nacer-Laidi H, Azmi B, Palmer T, Giddings R, Fuller C, Irwin-Singer A, Baynton V, Tut G, Moss P, Hayward A, Copas A, Shallcross L.",,The lancet. Healthy longevity,2022,2022-07-04,Y,,,,"<h4>Background</h4>Residents and staff in long-term care facilities have been prioritised for vaccination against SARS-CoV-2, but data on potential waning of vaccine effectiveness and the effect of booster doses in this vulnerable population are scarce. We aimed to evaluate effectiveness of one, two, and three vaccine doses against infection and severe clinical outcomes in staff and residents of long-term care facilities in England over the first year following vaccine roll-out.<h4>Methods</h4>The VIVALDI study is a prospective cohort study done in 331 long-term care facilities in England. Residents aged 65 years or older and staff aged 18 years or older were eligible for participation. Participants had routine PCR testing throughout the study period between Dec 8, 2020, and Dec 11, 2021. We retrieved all PCR results and cycle threshold values for PCR-positive samples from routine testing in long-term care facilities, and positive PCR results from clinical testing in hospitals through the UK's COVID-19 Datastore. PCR results were linked to participants using pseudo-identifiers based on individuals' unique UK National Health Service (NHS) numbers, which were also used to retrieve vaccination records from the National Immunisation Management Service, hospitalisation records from NHS England, and deaths data from the Office for National Statistics through the COVID-19 Datastore. In a Cox proportional hazards regression, we estimated vaccine effectiveness against SARS-CoV-2 infection, COVID-19-related hospitalisation, and COVID-19-related death after one, two, and three vaccine doses, separately by previous SARS-CoV-2 exposure. This study is registered with the ISRCTN Registry, ISRCTN 14447421.<h4>Findings</h4>80 186 residents and staff of long-term care facilities had records available for the study period, of whom 15 518 eligible residents and 19 515 eligible staff were included in the analysis. For residents without evidence of previous SARS-CoV-2 exposure, vaccine effectiveness decreased from 61·7% (95% CI 35·1 to 77·4) to 22·0% (-14·9 to 47·0) against infection; from 89·0% (70·6 to 95·9) to 56·3% (30·1 to 72·6) against hospitalisation; and from 96·4% (84·3 to 99·2) to 64·4% (36·1 to 80·1) against death, when comparing 14-83 days after dose two and 84 days or more after dose two. For staff without evidence of previous exposure, vaccine effectiveness against infection decreased slightly from 57·9% (43·1 to 68·9) at 14-83 days after dose two to 42·1% (29·9 to 52·2) at 84 days or more after dose two. There were no hospitalisations or deaths among unexposed staff at 14-83 days, but seven hospitalisations (vaccine effectiveness 91·0% [95% CI 74·3 to 96·8]) and one death were observed at 84 days or more after dose two. High vaccine effectiveness was restored following a third vaccine dose, with vaccine effectiveness in unexposed residents of 72·7% (55·8 to 83·1) against infection, 90·1% (80·6 to 95·0) against hospitalisation, and 97·5% (88·1 to 99·5) against death; and vaccine effectiveness in unexposed staff of 78·2% (70·0 to 84·1) against infection and 95·8% (49·9 to 99·6) against hospitalisation. There were no COVID-19-related deaths among unexposed staff after the third vaccine dose.<h4>Interpretation</h4>Our findings showed substantial waning of SARS-CoV-2 vaccine effectiveness against all outcomes in residents of long-term care facilities from 12 weeks after a primary course of ChAdOx1-S or mRNA vaccines. Boosters restored protection, and maximised immunity across all outcomes. These findings show the importance of boosting and the need for ongoing surveillance in this vulnerable cohort.<h4>Funding</h4>UK Government Department of Health and Social Care.",,pdf:http://www.thelancet.com/article/S2666756822001477/pdf; doi:https://doi.org/10.1016/S2666-7568(22)00147-7; html:https://europepmc.org/articles/PMC9252508; pdf:https://europepmc.org/articles/PMC9252508?pdf=render
 37236697,https://doi.org/10.1016/s2589-7500(23)00065-1,"Identifying subtypes of heart failure from three electronic health record sources with machine learning: an external, prognostic, and genetic validation study.","Banerjee A, Dashtban A, Chen S, Pasea L, Thygesen JH, Fatemifar G, Tyl B, Dyszynski T, Asselbergs FW, Lund LH, Lumbers T, Denaxas S, Hemingway H.",,The Lancet. Digital health,2023,2023-06-01,N,,,,"<h4>Background</h4>Machine learning has been used to analyse heart failure subtypes, but not across large, distinct, population-based datasets, across the whole spectrum of causes and presentations, or with clinical and non-clinical validation by different machine learning methods. Using our published framework, we aimed to discover heart failure subtypes and validate them upon population representative data.<h4>Methods</h4>In this external, prognostic, and genetic validation study we analysed individuals aged 30 years or older with incident heart failure from two population-based databases in the UK (Clinical Practice Research Datalink [CPRD] and The Health Improvement Network [THIN]) from 1998 to 2018. Pre-heart failure and post-heart failure factors (n=645) included demographic information, history, examination, blood laboratory values, and medications. We identified subtypes using four unsupervised machine learning methods (K-means, hierarchical, K-Medoids, and mixture model clustering) with 87 of 645 factors in each dataset. We evaluated subtypes for (1) external validity (across datasets); (2) prognostic validity (predictive accuracy for 1-year mortality); and (3) genetic validity (UK Biobank), association with polygenic risk score (PRS) for heart failure-related traits (n=11), and single nucleotide polymorphisms (n=12).<h4>Findings</h4>We included 188 800, 124 262, and 9573 individuals with incident heart failure from CPRD, THIN, and UK Biobank, respectively, between Jan 1, 1998, and Jan 1, 2018. After identifying five clusters, we labelled heart failure subtypes as (1) early onset, (2) late onset, (3) atrial fibrillation related, (4) metabolic, and (5) cardiometabolic. In the external validity analysis, subtypes were similar across datasets (c-statistics: THIN model in CPRD ranged from 0·79 [subtype 3] to 0·94 [subtype 1], and CPRD model in THIN ranged from 0·79 [subtype 1] to 0·92 [subtypes 2 and 5]). In the prognostic validity analysis, 1-year all-cause mortality after heart failure diagnosis (subtype 1 0·20 [95% CI 0·14-0·25], subtype 2 0·46 [0·43-0·49], subtype 3 0·61 [0·57-0·64], subtype 4 0·11 [0·07-0·16], and subtype 5 0·37 [0·32-0·41]) differed across subtypes in CPRD and THIN data, as did risk of non-fatal cardiovascular diseases and all-cause hospitalisation. In the genetic validity analysis the atrial fibrillation-related subtype showed associations with the related PRS. Late onset and cardiometabolic subtypes were the most similar and strongly associated with PRS for hypertension, myocardial infarction, and obesity (p<0·0009). We developed a prototype app for routine clinical use, which could enable evaluation of effectiveness and cost-effectiveness.<h4>Interpretation</h4>Across four methods and three datasets, including genetic data, in the largest study of incident heart failure to date, we identified five machine learning-informed subtypes, which might inform aetiological research, clinical risk prediction, and the design of heart failure trials.<h4>Funding</h4>European Union Innovative Medicines Initiative-2.",,pdf:http://www.thelancet.com/article/S2589750023000651/pdf; doi:https://doi.org/10.1016/S2589-7500(23)00065-1
 38552327,https://doi.org/10.1093/bioinformatics/btae172,shinyExprPortal: a configurable 'shiny' portal for sharing analysis of molecular expression data.,"Henkin R, Goldmann K, Lewis M, Barnes MR.",,"Bioinformatics (Oxford, England)",2024,2024-03-01,Y,,,,"<h4>Motivation</h4>The scale of omics research presents many obstacles to full sharing and access to analysis results. Current publication models impose limits on the number of pages and figures, requiring careful preparation and selection of content. At the same time, depositing data in open repositories significantly shifts the burden of access and reproduction to readers, who may include people who are not programmers or analysts.<h4>Results</h4>We introduce shinyExprPortal, an R package that implements omics web portals with minimal coding effort. The portals allow exploration of transcriptomic or proteomic expression data and phenotypes, showcasing results of various types of analysis including differential expression, co-expression and pathways analysis. The integration with bioinformatics workflows enables researchers to focus on their results and share findings using interactive and publication-quality plots.<h4>Availability and implementation</h4>The shinyExprPortal package is available to download and install from CRAN and https://github.com/C4TB/shinyExprPortal.",,pdf:https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae172/57122310/btae172.pdf; doi:https://doi.org/10.1093/bioinformatics/btae172; html:https://europepmc.org/articles/PMC11021805; pdf:https://europepmc.org/articles/PMC11021805?pdf=render
 38834334,https://doi.org/10.1136/bmjdrc-2024-004191,"Identifying subtypes of type 2 diabetes mellitus with machine learning: development, internal validation, prognostic validation and medication burden in linked electronic health records in 420 448 individuals.","Mizani MA, Dashtban A, Pasea L, Zeng Q, Khunti K, Valabhji J, Mamza JB, Gao H, Morris T, Banerjee A.",,BMJ open diabetes research & care,2024,2024-06-04,N,"Diabetes mellitus, type 2; epidemiology; Informatics; Electronic Health Records",,,"<h4>Introduction</h4>None of the studies of type 2 diabetes (T2D) subtyping to date have used linked population-level data for incident and prevalent T2D, incorporating a diverse set of variables, explainable methods for cluster characterization, or adhered to an established framework. We aimed to develop and validate machine learning (ML)-informed subtypes for type 2 diabetes mellitus (T2D) using nationally representative data.<h4>Research design and methods</h4>In population-based electronic health records (2006-2020; Clinical Practice Research Datalink) in individuals ≥18 years with incident T2D (n=420 448), we included factors (n=3787), including demography, history, examination, biomarkers and medications. Using a published framework, we identified subtypes through nine unsupervised ML methods (K-means, K-means++, K-mode, K-prototype, mini-batch, agglomerative hierarchical clustering, Birch, Gaussian mixture models, and consensus clustering). We characterized clusters using intracluster distributions and explainable artificial intelligence (AI) techniques. We evaluated subtypes for (1) internal validity (within dataset; across methods); (2) prognostic validity (prediction for 5-year all-cause mortality, hospitalization and new chronic diseases); and (3) medication burden.<h4>Results</h4><i>Development</i>: We identified four T2D subtypes: metabolic, early onset, late onset and cardiometabolic. <i>Internal validity</i>: Subtypes were predicted with high accuracy (F1 score >0.98). <i>Prognostic validity</i>: 5-year all-cause mortality, hospitalization, new chronic disease incidence and medication burden differed across T2D subtypes. Compared with the metabolic subtype, 5-year risks of mortality and hospitalization in incident T2D were highest in late-onset subtype (HR 1.95, 1.85-2.05 and 1.66, 1.58-1.75) and lowest in early-onset subtype (1.18, 1.11-1.27 and 0.85, 0.80-0.90). Incidence of chronic diseases was highest in late-onset subtype and lowest in early-onset subtype. <i>Medications</i>: Compared with the metabolic subtype, after adjusting for age, sex, and pre-T2D medications, late-onset subtype (1.31, 1.28-1.35) and early-onset subtype (0.83, 0.81-0.85) were most and least likely, respectively, to be prescribed medications within 5 years following T2D onset.<h4>Conclusions</h4>In the largest study using ML to date in incident T2D, we identified four distinct subtypes, with potential future implications for etiology, therapeutics, and risk prediction.",,doi:https://doi.org/10.1136/bmjdrc-2024-004191; doi:https://doi.org/10.1136/bmjdrc-2024-004191
-35836669,https://doi.org/10.1097/txd.0000000000001188,HLA Alleles Cw12 and DQ4 in Kidney Transplant Recipients Are Independent Risk Factors for the Development of Posttransplantation Diabetes.,"Phagura N, Hussain A, Culliford A, Hodson J, Evison F, Gallier S, Borrows R, Lane HA, Briggs D, Sharif A.",,Transplantation direct,2021,2021-07-23,Y,,,,"The association between specific HLA alleles and risk for posttransplantation diabetes (PTDM) in a contemporary and multiethnic kidney transplant recipient cohort is not clear.<h4>Methods</h4>In this single-center analysis, data were retrospectively analyzed for 1560 nondiabetic kidney transplant recipients at a single center between 2007 and 2018, with median follow-up of 33 mo (interquartile range 8-73). HLA typing methodology was by DNA analysis and reported at the resolution required for the national allocation scheme. Diagnosis of PTDM was aligned with International Consensus recommendations.<h4>Results</h4>PTDM developed in 231 kidney transplant recipients. Exploring 99 HLA alleles, the presence of Cw12, B52, B38, B58, DQ4, A80, and DR13 and the absence of DQ3 and DR04 were associated with significant increases in PTDM risk. In a multivariable Cox regression model, adjusting for other clinical risk factors for PTDM, the presence of Cw12 (hazard ratio [HR], 1.57; 95% CI, 1.08-2.27; <i>P</i> = 0.017) and DQ4 (HR, 1.78; 95% CI, 1.07-2.96; <i>P</i> = 0.026) were found to be independent risk factors for PTDM. There was also evidence that the presence of B58 increases PTDM risk within the subgroup of recipients of White ethnicity (HR, 5.01; 95% CI, 2.20-11.42; <i>P</i> < 0.001).<h4>Conclusion</h4>Our data suggest that specific HLA alleles can be associated with PTDM risk, which can be used pretransplantation for PTDM risk stratification. However, association is not causality, and this work requires replication and further investigation to understand underlying biological mechanisms.",,doi:https://doi.org/10.1097/txd.0000000000001188; doi:https://doi.org/10.1097/TXD.0000000000001188; html:https://europepmc.org/articles/PMC9276282; pdf:https://europepmc.org/articles/PMC9276282?pdf=render
 35997000,https://doi.org/10.1111/ene.15530,Longitudinal analysis of the relationship between motor and psychiatric symptoms in idiopathic dystonia.,"Bailey GA, Rawlings A, Torabi F, Pickrell WO, Peall KJ.",,European journal of neurology,2022,2022-09-11,Y,Psychiatric disorders; Movement Disorders; Dystonia; Neurological Disorders,,,"<h4>Background and purpose</h4>Although psychiatric diagnoses are recognized in idiopathic dystonia, no previous studies have examined the temporal relationship between idiopathic dystonia and psychiatric diagnoses at scale. Here, we determine rates of psychiatric diagnoses and psychiatric medication prescription in those diagnosed with idiopathic dystsuponia compared to matched controls.<h4>Methods</h4>A longitudinal population-based cohort study using anonymized electronic health care data in Wales (UK) was conducted to identify individuals with idiopathic dystonia and comorbid psychiatric diagnoses/prescriptions between 1 January 1994 and 31 December 2017. Psychiatric diagnoses/prescriptions were identified from primary and secondary health care records.<h4>Results</h4>Individuals with idiopathic dystonia (n = 52,589) had higher rates of psychiatric diagnosis and psychiatric medication prescription when compared to controls (n = 216,754, 43% vs. 31%, p &lt; 0.001; 45% vs. 37.9%, p &lt; 0.001, respectively), with depression and anxiety being most common (cases: 31% and 28%). Psychiatric diagnoses predominantly predated dystonia diagnosis, particularly in the 12 months prior to diagnosis (incidence rate ratio [IRR] = 1.98, 95% confidence interval [CI] = 1.9-2.1), with an IRR of 12.4 (95% CI = 11.8-13.1) for anxiety disorders. There was, however, an elevated rate of most psychiatric diagnoses throughout the study period, including the 12 months after dystonia diagnosis (IRR = 1.96, 95% CI = 1.85-2.07).<h4>Conclusions</h4>This study suggests a bidirectional relationship between psychiatric disorders and dystonia, particularly with mood disorders. Psychiatric and motor symptoms in dystonia may have common aetiological mechanisms, with psychiatric disorders potentially forming prodromal symptoms of idiopathic dystonia.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa62203/Download/62203__26254__0c88bfc9ff7e4fe2acaea5e2a2d74058.pdf; doi:https://doi.org/10.1111/ene.15530; html:https://europepmc.org/articles/PMC9826317; pdf:https://europepmc.org/articles/PMC9826317?pdf=render
+35836669,https://doi.org/10.1097/txd.0000000000001188,HLA Alleles Cw12 and DQ4 in Kidney Transplant Recipients Are Independent Risk Factors for the Development of Posttransplantation Diabetes.,"Phagura N, Hussain A, Culliford A, Hodson J, Evison F, Gallier S, Borrows R, Lane HA, Briggs D, Sharif A.",,Transplantation direct,2021,2021-07-23,Y,,,,"The association between specific HLA alleles and risk for posttransplantation diabetes (PTDM) in a contemporary and multiethnic kidney transplant recipient cohort is not clear.<h4>Methods</h4>In this single-center analysis, data were retrospectively analyzed for 1560 nondiabetic kidney transplant recipients at a single center between 2007 and 2018, with median follow-up of 33 mo (interquartile range 8-73). HLA typing methodology was by DNA analysis and reported at the resolution required for the national allocation scheme. Diagnosis of PTDM was aligned with International Consensus recommendations.<h4>Results</h4>PTDM developed in 231 kidney transplant recipients. Exploring 99 HLA alleles, the presence of Cw12, B52, B38, B58, DQ4, A80, and DR13 and the absence of DQ3 and DR04 were associated with significant increases in PTDM risk. In a multivariable Cox regression model, adjusting for other clinical risk factors for PTDM, the presence of Cw12 (hazard ratio [HR], 1.57; 95% CI, 1.08-2.27; <i>P</i> = 0.017) and DQ4 (HR, 1.78; 95% CI, 1.07-2.96; <i>P</i> = 0.026) were found to be independent risk factors for PTDM. There was also evidence that the presence of B58 increases PTDM risk within the subgroup of recipients of White ethnicity (HR, 5.01; 95% CI, 2.20-11.42; <i>P</i> < 0.001).<h4>Conclusion</h4>Our data suggest that specific HLA alleles can be associated with PTDM risk, which can be used pretransplantation for PTDM risk stratification. However, association is not causality, and this work requires replication and further investigation to understand underlying biological mechanisms.",,doi:https://doi.org/10.1097/txd.0000000000001188; doi:https://doi.org/10.1097/TXD.0000000000001188; html:https://europepmc.org/articles/PMC9276282; pdf:https://europepmc.org/articles/PMC9276282?pdf=render
 38842977,https://doi.org/10.1016/j.jacep.2024.04.006,Machine Learning of Cardiac Anatomy and the Risk of New-Onset Atrial Fibrillation After TAVR.,"Brahier MS, Kochi S, Huang J, Piliponis E, Smith A, Johnson A, Poian S, Abdulkareem M, Ma X, Wu C, Piccini JP, Petersen S, Vargas JD.",,JACC. Clinical electrophysiology,2024,2024-06-05,N,Machine Learning; Cardiac Imaging; Tavr; New-onset Atrial Fibrillation,,,"<h4>Background</h4>New-onset atrial fibrillation (NOAF) occurs in 5% to 15% of patients who undergo transfemoral transcatheter aortic valve replacement (TAVR). Cardiac imaging has been underutilized to predict NOAF following TAVR.<h4>Objectives</h4>The objective of this analysis was to compare and assess standard, manual echocardiographic and cardiac computed tomography (cCT) measurements as well as machine learning-derived cCT measurements of left atrial volume index and epicardial adipose tissue as risk factors for NOAF following TAVR.<h4>Methods</h4>The study included 1,385 patients undergoing elective, transfemoral TAVR for severe, symptomatic aortic stenosis. Each patient had standard and machine learning-derived measurements of left atrial volume and epicardial adipose tissue from cardiac computed tomography. The outcome of interest was NOAF within 30 days following TAVR. We used a 2-step statistical model including random forest for variable importance ranking, followed by multivariable logistic regression for predictors of highest importance. Model discrimination was assessed by using the C-statistic to compare the performance of the models with and without imaging.<h4>Results</h4>Forty-seven (5.0%) of 935 patients without pre-existing atrial fibrillation (AF) experienced NOAF. Patients with pre-existing AF had the largest left atrial volume index at 76.3 ± 28.6 cm<sup>3</sup>/m<sup>2</sup> followed by NOAF at 68.1 ± 26.6 cm<sup>3</sup>/m<sup>2</sup> and then no AF at 57.0 ± 21.7 cm<sup>3</sup>/m<sup>2</sup> (P < 0.001). Multivariable regression identified the following risk factors in association with NOAF: left atrial volume index ≥76 cm<sup>2</sup> (OR: 2.538 [95% CI: 1.165-5.531]; P = 0.0191), body mass index <22 kg/m<sup>2</sup> (OR: 4.064 [95% CI: 1.500-11.008]; P = 0.0058), EATv (OR: 1.007 [95% CI: 1.000-1.014]; P = 0.043), aortic annulus area ≥659 mm<sup>2</sup> (OR: 6.621 [95% CI: 1.849-23.708]; P = 0.004), and sinotubular junction diameter ≥35 mm (OR: 3.891 [95% CI: 1.040-14.552]; P = 0.0435). The C-statistic of the model was 0.737, compared with 0.646 in a model that excluded imaging variables.<h4>Conclusions</h4>Underlying cardiac structural differences derived from cardiac imaging may be useful in predicting NOAF following transfemoral TAVR, independent of other clinical risk factors.",,doi:https://doi.org/10.1016/j.jacep.2024.04.006
 34837975,https://doi.org/10.1186/s12885-021-09014-w,Temporality of clinical factors associated with pancreatic cancer: a case-control study using linked electronic health records.,"Dayem Ullah AZM, Stasinos K, Chelala C, Kocher HM.",,BMC cancer,2021,2021-11-27,Y,Risk factor; Pancreatic cancer; Lifestyle; Ethnicity; Comorbidity,,,"<h4>Background</h4>Pancreatic cancer risk is poorly quantified in relation to the temporal presentation of medical comorbidities and lifestyle. This study aimed to examine this aspect, with possible influence of demographics.<h4>Methods</h4>We conducted a retrospective case-control study on the ethnically-diverse population of East London, UK, using linked electronic health records. We evaluated the independent and two-way interaction effects of 19 clinico-demographic factors in patients with pancreatic cancer (N = 965), compared with non-malignant pancreatic conditions (N = 3963) or hernia (control; N = 4355), reported between April 1, 2008 and March 6, 2020. Risks were quantified by odds ratios (ORs) and 95% confidence intervals (CIs) from multivariable logistic regression models.<h4>Results</h4>We observed increased odds of pancreatic cancer incidence associated with recent-onset diabetes occurring within 6 months to 3 years before cancer diagnosis (OR 1.95, 95% CI 1.25-3.03), long-standing diabetes for over 3 years (OR 1.74, 95% CI 1.32-2.29), recent smoking (OR 1.81, 95% CI 1.36-2.4) and drinking (OR 1.76, 95% CI 1.31-2.35), as compared to controls but not non-malignant pancreatic conditions. Pancreatic cancer odds was highest for chronic pancreatic disease patients (recent-onset: OR 4.76, 95% CI 2.19-10.3, long-standing: OR 5.1, 95% CI 2.18-11.9), amplified by comorbidities or harmful lifestyle. Concomitant diagnosis of diabetes, upper gastrointestinal or chronic pancreatic conditions followed by a pancreatic cancer diagnosis within 6 months were common, particularly in South Asians. Long-standing cardiovascular, respiratory and hepatobiliary conditions were associated with lower odds of pancreatic cancer.<h4>Conclusions</h4>Several factors are, independently or via effect modifications, associated with higher incidence of pancreatic cancer, but some established risk factors demonstrate similar magnitude of risk measures of developing non-malignant pancreatic conditions. The findings may inform refined risk-stratification strategies and better surveillance for high-risk individuals, and also provide a means for systematic identification of target population for prospective cohort-based early detection research initiatives.",,pdf:https://bmccancer.biomedcentral.com/counter/pdf/10.1186/s12885-021-09014-w; doi:https://doi.org/10.1186/s12885-021-09014-w; html:https://europepmc.org/articles/PMC8626898; pdf:https://europepmc.org/articles/PMC8626898?pdf=render
 38429012,https://doi.org/10.1016/s2468-2667(24)00025-2,Social and spatial inequalities in premature mortality across Europe.,"Bragg F, Lacey B.",,The Lancet. Public health,2024,2024-03-01,N,,,,,,doi:https://doi.org/10.1016/S2468-2667(24)00025-2
 36036238,https://doi.org/10.1002/clt2.12180,Mixed-methods evaluation of a nurse-led allergy clinic model in primary care: Feasibility trial.,"Hammersley V, Kelman M, Morrice L, Kendall M, Mukerjhee M, Harley S, Schwarze J, Sheikh A.",,Clinical and translational allergy,2022,2022-08-01,Y,Allergy; Quality of life; Primary Care,,,"<h4>Introduction</h4>It is now widely acknowledged that there are serious shortcomings in allergy care provision for patients seen in primary care. We sought to assess the feasibility of delivering and evaluating a new nurse-led allergy service in primary care, measured by recruitment, retention and estimates of the potential impact of the intervention on disease-specific quality of life.<h4>Methods</h4>Mixed-methods evaluation of a nurse-led primary care-based allergy clinic in Edinburgh, UK undertaken during the period 2017-2021 with a focus on suspected food allergy and atopic eczema in young children, allergic rhinitis in children and young people, and suspected anaphylaxis in adults. Prior to March 2020, patients were seen face-to-face (Phase 1). Due to COVID-19 pandemic restrictions, recruitment was halted between March-August 2020, and a remote clinic was restarted in September 2020 (Phase 2). Disease-specific quality of life was measured at baseline and 6-12 weeks post intervention using validated instruments. Quantitative data were descriptively analysed. We undertook interviews with 16 carers/patients and nine healthcare professionals, which were thematically analysed.<h4>Results</h4>During Phase 1, 426/506 (84%) referred patients met the eligibility criteria; 40/46 (87%) of Phase 2 referrals were eligible. Males and females were recruited in approximately equal numbers. The majority (83%) of referrals were for possible food allergy or anaphylaxis. Complete data were available for 338/426 (79%) patients seen in Phase 1 and 30/40 (75%) in Phase 2. Compared with baseline assessments, there were improvements in disease-specific quality of life for most categories of patients. Patients/carers and healthcare professionals reported high levels of satisfaction, this being reinforced by the qualitative interviews in which convenience and speed of access to expert opinion, the quality of the consultation, and patient/care empowerment were particularly emphasised.<h4>Conclusion</h4>This large feasibility trial has demonstrated that it is possible to recruit, deliver and retain individuals into a nurse-led allergy clinic with both face-to-face and remote consultations. Our data indicate that the intervention was considered acceptable to patients/carers and healthcare professionals. The before-after data of disease-specific quality of life suggest that the intervention may prove effective, but this now needs to be confirmed through a formal randomised controlled trial.<h4>Trial registration</h4>ClinicalTrials.gov reference NCT03826953.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9362986; doi:https://doi.org/10.1002/clt2.12180; html:https://europepmc.org/articles/PMC9362986; pdf:https://europepmc.org/articles/PMC9362986?pdf=render
 39227814,https://doi.org/10.1186/s12916-024-03578-7,The association of psychological and trauma-related factors with biological and facial aging acceleration: evidence from the UK Biobank.,"Wang J, Han X, Yang Y, Zeng Y, Qu Y, Yang H, Song J, Qiu C, Song H.",,BMC medicine,2024,2024-09-04,Y,Psychological factors; Trauma Experience; Length Of Telomeres; Biological Aging Acceleration; Facial Aging Acceleration,,,"<h4>Background</h4>Psychological and trauma-related factors are associated with many diseases and mortality. However, a comprehensive assessment of the association between psycho-trauma exposures and aging acceleration is currently lacking.<h4>Methods</h4>Using data from 332,359 UK Biobank participants, we calculated biological aging acceleration, indexed by the presence of leukocyte telomere length (LTL) deviation (i.e., the difference between genetically determined and observed LTL > 0). The acceleration of facial aging (i.e., looking older than the chronological age) was assessed using a self-report question. Then, we estimated the associations of each psycho-trauma factor with biological and facial aging acceleration, using logistic regression models adjusted for multiple important covariates. Furthermore, restricted to 99,180 participants with complete psychological and trauma-related data, we identified clusters of individuals with distinct psycho-trauma patterns using the latent class analysis method and assessed their associations with aging acceleration using similar models.<h4>Results</h4>We observed most of the studied psycho-trauma factors were associated with biological and facial aging acceleration. Compared to the ""Absence of trauma and psychopathology"" cluster, the ""adverse childhood experiences (ACEs) with psychopathology"" cluster showed strong associations with those aging measurements (odds ratio [OR] = 1.13 [1.05 - 1.23] for biological and 1.52 [1.18 - 1.95] for facial aging acceleration), while no such association was observed for the ""ACEs without psychopathology"" cluster (1.04 [0.99 - 1.09] and 1.02 [0.84 - 1.24].<h4>Conclusions</h4>Our study demonstrated significant associations of psycho-trauma factors with both biological and facial aging acceleration. The differential aging consequences observed among ACEs exposed individuals with and without psychopathology prompt interventions aimed to improve individuals' psychological resilience to prevent aging acceleration.",,doi:https://doi.org/10.1186/s12916-024-03578-7; html:https://europepmc.org/articles/PMC11373276; pdf:https://europepmc.org/articles/PMC11373276?pdf=render
 34308125,https://doi.org/10.1136/bmjnph-2020-000225,Effect of ultraprocessed food intake on cardiometabolic risk is mediated by diet quality: a cross-sectional study.,"Griffin J, Albaloul A, Kopytek A, Elliott P, Frost G.",,"BMJ nutrition, prevention & health",2021,2021-04-07,Y,metabolic syndrome; Dietary Patterns,,,"<h4>Objective</h4>To examine the effect of the consumption of ultraprocessed food on diet quality, and cardiometabolic risk (CMR) in an occupational cohort.<h4>Design</h4>Cross-sectional.<h4>Setting</h4>Occupational cohort.<h4>Participants</h4>53 163 British police force employees enrolled (2004-2012) into the Airwave Health Monitoring Study. A total of 28 forces across the UK agreed to participate. 9009 participants with available 7-day diet record data and complete co-variate data are reported in this study.<h4>Main outcome measures</h4>A CMR and Dietary Approaches to Stop Hypertension score were treated as continuous variables and used to generate measures of cardiometabolic health and diet quality. Secondary outcome measures include percentage of energy from fat, saturated fat, carbohydrate, protein and non-milk extrinsic sugars (NMES) and fibre grams per 1000 kcal of energy intake.<h4>Results</h4>In this cohort, 58.3%±11.6 of total energy intake was derived from ultraprocessed (NOVA 4) foods. Ultraprocessed food intake was negatively correlated with diet quality (r=-0.32, p<0.001), fibre (r=-0.20, p<0.001) and protein (r = -0.40, p<0.001) and positively correlated with fat (r=0.18, p<0.001), saturated fat (r=0.14, p<0.001) and nmes (r=0.10, p<0.001) intake. Multivariable analysis suggests a positive association between ultraprocessed food (NOVA 4) consumption and CMR. However, this main effect was no longer observed after adjustment for diet quality (p=0.209). Findings from mediation analysis indicate that the effect of ultraprocessed food (NOVA 4) intake on CMR is mediated by diet quality (p<0.001).<h4>Conclusions</h4>Ultraprocessed food consumption is associated with a deterioration in diet quality and positively associated with CMR, although this association is mediated by and dependent on the quality of the diet. The negative impact of ultraprocessed food consumption on diet quality needs to be addressed and controlled studies are needed to fully comprehend whether the relationship between ultraprocessed food consumption and health is independent to its relationship with poor diet quality.",,pdf:https://nutrition.bmj.com/content/bmjnph/4/1/174.full.pdf; doi:https://doi.org/10.1136/bmjnph-2020-000225; html:https://europepmc.org/articles/PMC8258022; pdf:https://europepmc.org/articles/PMC8258022?pdf=render
+38383048,https://doi.org/10.1093/bioinformatics/btae101,"LAVASET: Latent Variable Stochastic Ensemble of Trees. An ensemble method for correlated datasets with spatial, spectral, and temporal dependencies.","Kasapi M, Xu K, Ebbels TMD, O'Regan DP, Ware JS, Posma JM.",,"Bioinformatics (Oxford, England)",2024,2024-03-01,Y,,,,"<h4>Motivation</h4>Random forests (RFs) can deal with a large number of variables, achieve reasonable prediction scores, and yield highly interpretable feature importance values. As such, RFs are appropriate models for feature selection and further dimension reduction. However, RFs are often not appropriate for correlated datasets due to their mode of selecting individual features for splitting. Addressing correlation relationships in high-dimensional datasets is imperative for reducing the number of variables that are assigned high importance, hence making the dimension reduction most efficient. Here, we propose the LAtent VAriable Stochastic Ensemble of Trees (LAVASET) method that derives latent variables based on the distance characteristics of each feature and aims to incorporate the correlation factor in the splitting step.<h4>Results</h4>Without compromising on performance in the majority of examples, LAVASET outperforms RF by accurately determining feature importance across all correlated variables and ensuring proper distribution of importance values. LAVASET yields mostly non-inferior prediction accuracies to traditional RFs when tested in simulated and real 1D datasets, as well as more complex and high-dimensional 3D datatypes. Unlike traditional RFs, LAVASET is unaffected by single 'important' noisy features (false positives), as it considers the local neighbourhood. LAVASET, therefore, highlights neighbourhoods of features, reflecting real signals that collectively impact the model's predictive ability.<h4>Availability and implementation</h4>LAVASET is freely available as a standalone package from https://github.com/melkasapi/LAVASET.",,pdf:https://academic.oup.com/bioinformatics/article-pdf/40/3/btae101/56904442/btae101.pdf; doi:https://doi.org/10.1093/bioinformatics/btae101; html:https://europepmc.org/articles/PMC11212485; pdf:https://europepmc.org/articles/PMC11212485?pdf=render
+35749561,https://doi.org/10.1371/journal.pcbi.1010234,"Evidence for influenza and RSV interaction from 10 years of enhanced surveillance in Nha Trang, Vietnam, a modelling study.","Waterlow NR, Toizumi M, van Leeuwen E, Thi Nguyen HA, Myint-Yoshida L, Eggo RM, Flasche S.",,PLoS computational biology,2022,2022-06-24,Y,,,,"Influenza and Respiratory Syncytial Virus (RSV) interact within their host posing the concern for impacts on heterologous viruses following vaccination. We aimed to estimate the population level impact of their interaction. We developed a dynamic age-stratified two-pathogen mathematical model that includes pathogen interaction through competition for infection and enhanced severity of dual infections. We used parallel tempering to fit its parameters to 11 years of enhanced hospital-based surveillance for acute respiratory illnesses (ARI) in children under 5 years old in Nha Trang, Vietnam. The data supported either a 41% (95%CrI: 36-54) reduction in susceptibility following infection and for 10.0 days (95%CrI 7.1-12.8) thereafter, or no change in susceptibility following infection. We estimate that co-infection increased the probability for an infection in <2y old children to be reported 7.2 fold (95%CrI 5.0-11.4); or 16.6 fold (95%CrI 14.5-18.4) in the moderate or low interaction scenarios. Absence of either pathogen was not to the detriment of the other. We find stronger evidence for severity enhancing than for acquisition limiting interaction. In this setting vaccination against either pathogen is unlikely to have a major detrimental effect on the burden of disease caused by the other.",,pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010234&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1010234; html:https://europepmc.org/articles/PMC9262224; pdf:https://europepmc.org/articles/PMC9262224?pdf=render
+34518162,https://doi.org/10.1136/bjophthalmol-2021-319383,Predicting the immediate impact of national lockdown on neovascular age-related macular degeneration and associated visual morbidity: an INSIGHT Health Data Research Hub for Eye Health report.,"Mollan SP, Fu DJ, Chuo CY, Gannon JG, Lee WH, Hopkins JJ, Hughes C, Denniston AK, Keane PA, Cantrell R.",,The British journal of ophthalmology,2023,2021-09-13,Y,Clinical Trial; Neovascularisation; Covid-19,,,"<h4>Objective</h4>Predicting the impact of neovascular age-related macular degeneration (nAMD) service disruption on visual outcomes following national lockdown in the UK to contain SARS-CoV-2.<h4>Methods and analysis</h4>This retrospective cohort study includes deidentified data from 2229 UK patients from the INSIGHT Health Data Research digital hub. We forecasted the number of treatment-naïve nAMD patients requiring anti-vascular endothelial growth factor (anti-VEGF) initiation during UK lockdown (16 March 2020 through 31 July 2020) at Moorfields Eye Hospital (MEH) and University Hospitals Birmingham (UHB). Best-measured visual acuity (VA) changes without anti-VEGF therapy were predicted using post hoc analysis of Minimally Classic/Occult Trial of the Anti-VEGF Antibody Ranibizumab in the Treatment of Neovascular AMD trial sham-control arm data (n=238).<h4>Results</h4>At our centres, 376 patients were predicted to require anti-VEGF initiation during lockdown (MEH: 325; UHB: 51). Without treatment, mean VA was projected to decline after 12 months. The proportion of eyes in the MEH cohort predicted to maintain the key positive visual outcome of ≥70 ETDRS letters (Snellen equivalent 6/12) fell from 25.5% at baseline to 5.8% at 12 months (UHB: 9.8%-7.8%). Similarly, eyes with VA <25 ETDRS letters (6/96) were predicted to increase from 4.3% to 14.2% at MEH (UHB: 5.9%-7.8%) after 12 months without treatment.<h4>Conclusions</h4>Here, we demonstrate how combining data from a recently founded national digital health data repository with historical industry-funded clinical trial data can enhance predictive modelling in nAMD. The demonstrated detrimental effects of prolonged treatment delay should incentivise healthcare providers to support nAMD patients accessing care in safe environments.<h4>Trial registration number</h4>NCT00056836.",,pdf:https://discovery.ucl.ac.uk/10164981/1/267.full.pdf; doi:https://doi.org/10.1136/bjophthalmol-2021-319383; html:https://europepmc.org/articles/PMC9887382; pdf:https://europepmc.org/articles/PMC9887382?pdf=render
 33623985,https://doi.org/10.1093/cid/ciab159,Shorter and Longer Courses of Antibiotics for Common Infections and the Association With Reductions of Infection-Related Complications Including Hospital Admissions.,"Palin V, Welfare W, Ashcroft DM, van Staa TP.",,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2021,2021-11-01,Y,Antibiotics; Antimicrobial resistance; Antibiotic Duration; Infection Complication,,,"<h4>Background</h4>Antimicrobial resistance is a serious global health concern that emphasizes completing treatment course. Recently, the effectiveness of short versus longer antibiotic courses has been questioned. This study investigated the duration of prescribed antibiotics, their effectiveness, and associated risk of infection-related complications.<h4>Methods</h4>Clinical Practice Research Datalink identified 4 million acute infection episodes prescribed an antibiotic in primary care between January 2014-June 2014, England. Prescriptions were categorized by duration. Risk of infection-related hospitalizations within 30 days was modelled overall and by infection type. Risk was assessed immediately after or within 30 days follow-up to measure confounders given similar and varying exposure, respectively. An interaction term with follow-up time assessed whether hazard ratios (HRs) remained parallel with different antibiotic durations.<h4>Results</h4>The duration of antibiotic courses increased over the study period (5.2-19.1%); 6-7 days were most common (66.9%). Most infection-related hospitalizations occurred with prescriptions of 8-15 days (0.21%), accompanied by greater risk of infection-related complications compared to patients who received a short prescription (HR: 1.75 [95% CI: 1.54-2.00]). Comparing HRs in the first 5 days versus remaining follow-up showed longer antibiotic courses were no more effective than shorter courses (1.02 [95% CI: 0.90-1.16] and 0.92 [95% CI: 0.75-1.12]). No variation by infection-type was observed.<h4>Conclusions</h4>Equal effectiveness was found between shorter and longer antibiotic courses and the reduction of infection-related hospitalizations. Stewardship programs should recommend shorter courses of antibiotics for acute infections. Further research is required for treating patients with a complex medical history.SummaryPrescribing of longer courses increased over the study period. The majority of hospitalizations occurred for patients receiving longer courses. Risk of developing a complication (immediate vs remaining follow-up) found longer courses were no more effective than shorter courses.",,pdf:https://academic.oup.com/cid/advance-article-pdf/doi/10.1093/cid/ciab159/37414330/ciab159.pdf; doi:https://doi.org/10.1093/cid/ciab159; html:https://europepmc.org/articles/PMC8599204; pdf:https://europepmc.org/articles/PMC8599204?pdf=render
 38316529,https://doi.org/10.1111/dar.13816,Approaches and reporting of alcohol and other drug testing for injured patients in hospital-based studies: A systematic review.,"Lau G, Ang JY, Kim N, Gabbe BJ, Mitra B, Dietze PM, Reeder S, Beck B.",,Drug and alcohol review,2024,2024-02-05,N,Alcohol; Injury; Emergency Department; Illicit Drug; Substance Abuse Detection,,,"<h4>Issue</h4>Hospital alcohol and/or other drug (AOD) testing is important for identifying AOD-related injuries; however, testing methods vary. This systematic review aimed to examine biological AOD testing methods from hospital-based studies of injured patients and quantify what proportion reported key information on those testing methods.<h4>Approach</h4>Observational studies published in English from 2010 onwards involving biological AOD testing for injured patients presenting to hospital were included. Studies examining single injury causes were excluded. Extracted data included concentration thresholds for AOD detection (e.g., lower limits of detection, author-defined cut-offs), test type (e.g., immunoassay, breathalyser) and approach (e.g., routine, clinical discretion), timing of testing, sample type and the proportion of injured cases tested for AODs.<h4>Key findings</h4>Of 83 included studies, 76 measured alcohol and 37 other drugs. Forty-nine studies defined blood alcohol concentration thresholds (ranging from 0 to 0.1 g/100 mL). Seven studies defined concentration thresholds for other drugs. Testing approach was reported in 39/76 alcohol and 18/37 other drug studies. Sample type was commonly reported (alcohol: n = 69/76; other drugs: n = 28/37); alcohol was typically measured using blood (n = 60) and other drugs using urine (n = 20). Studies that reported the proportion of cases tested (alcohol: n = 53/76; other drugs: n = 28/37), reported that between 0% and 89% of cases were not tested for alcohol and 0% and 91% for other drugs. Timing of testing was often unreported (alcohol: n = 61; other drugs: n = 30).<h4>Implications and conclusion</h4>Variation in AOD testing methods alongside incomplete reporting of those methods limits data comparability and interpretation. Standardised reporting of testing methods will assist AOD-related injury surveillance and prevention.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/dar.13816; doi:https://doi.org/10.1111/dar.13816
-34518162,https://doi.org/10.1136/bjophthalmol-2021-319383,Predicting the immediate impact of national lockdown on neovascular age-related macular degeneration and associated visual morbidity: an INSIGHT Health Data Research Hub for Eye Health report.,"Mollan SP, Fu DJ, Chuo CY, Gannon JG, Lee WH, Hopkins JJ, Hughes C, Denniston AK, Keane PA, Cantrell R.",,The British journal of ophthalmology,2023,2021-09-13,Y,Clinical Trial; Neovascularisation; Covid-19,,,"<h4>Objective</h4>Predicting the impact of neovascular age-related macular degeneration (nAMD) service disruption on visual outcomes following national lockdown in the UK to contain SARS-CoV-2.<h4>Methods and analysis</h4>This retrospective cohort study includes deidentified data from 2229 UK patients from the INSIGHT Health Data Research digital hub. We forecasted the number of treatment-naïve nAMD patients requiring anti-vascular endothelial growth factor (anti-VEGF) initiation during UK lockdown (16 March 2020 through 31 July 2020) at Moorfields Eye Hospital (MEH) and University Hospitals Birmingham (UHB). Best-measured visual acuity (VA) changes without anti-VEGF therapy were predicted using post hoc analysis of Minimally Classic/Occult Trial of the Anti-VEGF Antibody Ranibizumab in the Treatment of Neovascular AMD trial sham-control arm data (n=238).<h4>Results</h4>At our centres, 376 patients were predicted to require anti-VEGF initiation during lockdown (MEH: 325; UHB: 51). Without treatment, mean VA was projected to decline after 12 months. The proportion of eyes in the MEH cohort predicted to maintain the key positive visual outcome of ≥70 ETDRS letters (Snellen equivalent 6/12) fell from 25.5% at baseline to 5.8% at 12 months (UHB: 9.8%-7.8%). Similarly, eyes with VA <25 ETDRS letters (6/96) were predicted to increase from 4.3% to 14.2% at MEH (UHB: 5.9%-7.8%) after 12 months without treatment.<h4>Conclusions</h4>Here, we demonstrate how combining data from a recently founded national digital health data repository with historical industry-funded clinical trial data can enhance predictive modelling in nAMD. The demonstrated detrimental effects of prolonged treatment delay should incentivise healthcare providers to support nAMD patients accessing care in safe environments.<h4>Trial registration number</h4>NCT00056836.",,pdf:https://discovery.ucl.ac.uk/10164981/1/267.full.pdf; doi:https://doi.org/10.1136/bjophthalmol-2021-319383; html:https://europepmc.org/articles/PMC9887382; pdf:https://europepmc.org/articles/PMC9887382?pdf=render
-35749561,https://doi.org/10.1371/journal.pcbi.1010234,"Evidence for influenza and RSV interaction from 10 years of enhanced surveillance in Nha Trang, Vietnam, a modelling study.","Waterlow NR, Toizumi M, van Leeuwen E, Thi Nguyen HA, Myint-Yoshida L, Eggo RM, Flasche S.",,PLoS computational biology,2022,2022-06-24,Y,,,,"Influenza and Respiratory Syncytial Virus (RSV) interact within their host posing the concern for impacts on heterologous viruses following vaccination. We aimed to estimate the population level impact of their interaction. We developed a dynamic age-stratified two-pathogen mathematical model that includes pathogen interaction through competition for infection and enhanced severity of dual infections. We used parallel tempering to fit its parameters to 11 years of enhanced hospital-based surveillance for acute respiratory illnesses (ARI) in children under 5 years old in Nha Trang, Vietnam. The data supported either a 41% (95%CrI: 36-54) reduction in susceptibility following infection and for 10.0 days (95%CrI 7.1-12.8) thereafter, or no change in susceptibility following infection. We estimate that co-infection increased the probability for an infection in <2y old children to be reported 7.2 fold (95%CrI 5.0-11.4); or 16.6 fold (95%CrI 14.5-18.4) in the moderate or low interaction scenarios. Absence of either pathogen was not to the detriment of the other. We find stronger evidence for severity enhancing than for acquisition limiting interaction. In this setting vaccination against either pathogen is unlikely to have a major detrimental effect on the burden of disease caused by the other.",,pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010234&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1010234; html:https://europepmc.org/articles/PMC9262224; pdf:https://europepmc.org/articles/PMC9262224?pdf=render
-38383048,https://doi.org/10.1093/bioinformatics/btae101,"LAVASET: Latent Variable Stochastic Ensemble of Trees. An ensemble method for correlated datasets with spatial, spectral, and temporal dependencies.","Kasapi M, Xu K, Ebbels TMD, O'Regan DP, Ware JS, Posma JM.",,"Bioinformatics (Oxford, England)",2024,2024-03-01,Y,,,,"<h4>Motivation</h4>Random forests (RFs) can deal with a large number of variables, achieve reasonable prediction scores, and yield highly interpretable feature importance values. As such, RFs are appropriate models for feature selection and further dimension reduction. However, RFs are often not appropriate for correlated datasets due to their mode of selecting individual features for splitting. Addressing correlation relationships in high-dimensional datasets is imperative for reducing the number of variables that are assigned high importance, hence making the dimension reduction most efficient. Here, we propose the LAtent VAriable Stochastic Ensemble of Trees (LAVASET) method that derives latent variables based on the distance characteristics of each feature and aims to incorporate the correlation factor in the splitting step.<h4>Results</h4>Without compromising on performance in the majority of examples, LAVASET outperforms RF by accurately determining feature importance across all correlated variables and ensuring proper distribution of importance values. LAVASET yields mostly non-inferior prediction accuracies to traditional RFs when tested in simulated and real 1D datasets, as well as more complex and high-dimensional 3D datatypes. Unlike traditional RFs, LAVASET is unaffected by single 'important' noisy features (false positives), as it considers the local neighbourhood. LAVASET, therefore, highlights neighbourhoods of features, reflecting real signals that collectively impact the model's predictive ability.<h4>Availability and implementation</h4>LAVASET is freely available as a standalone package from https://github.com/melkasapi/LAVASET.",,pdf:https://academic.oup.com/bioinformatics/article-pdf/40/3/btae101/56904442/btae101.pdf; doi:https://doi.org/10.1093/bioinformatics/btae101; html:https://europepmc.org/articles/PMC11212485; pdf:https://europepmc.org/articles/PMC11212485?pdf=render
 35067242,https://doi.org/10.1192/bjp.2021.219,Prediction models in first-episode psychosis: systematic review and critical appraisal.,"Lee R, Leighton SP, Thomas L, Gkoutos GV, Wood SJ, Fenton SH, Deligianni F, Cavanagh J, Mallikarjun PK.",,The British journal of psychiatry : the journal of mental science,2022,2022-01-24,N,Prediction; Schizophrenia; Psychotic Disorders; Outcome Studies; Precision Medicine,,,"<h4>Background</h4>People presenting with first-episode psychosis (FEP) have heterogenous outcomes. More than 40% fail to achieve symptomatic remission. Accurate prediction of individual outcome in FEP could facilitate early intervention to change the clinical trajectory and improve prognosis.<h4>Aims</h4>We aim to systematically review evidence for prediction models developed for predicting poor outcome in FEP.<h4>Method</h4>A protocol for this study was published on the International Prospective Register of Systematic Reviews, registration number CRD42019156897. Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidance, we systematically searched six databases from inception to 28 January 2021. We used the Checklist for Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modelling Studies and the Prediction Model Risk of Bias Assessment Tool to extract and appraise the outcome prediction models. We considered study characteristics, methodology and model performance.<h4>Results</h4>Thirteen studies reporting 31 prediction models across a range of clinical outcomes met criteria for inclusion. Eleven studies used logistic regression with clinical and sociodemographic predictor variables. Just two studies were found to be at low risk of bias. Methodological limitations identified included a lack of appropriate validation, small sample sizes, poor handling of missing data and inadequate reporting of calibration and discrimination measures. To date, no model has been applied to clinical practice.<h4>Conclusions</h4>Future prediction studies in psychosis should prioritise methodological rigour and external validation in larger samples. The potential for prediction modelling in FEP is yet to be realised.",,pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/597A326F6B5258801F61CA211322F96F/S0007125021002191a.pdf/div-class-title-prediction-models-in-first-episode-psychosis-systematic-review-and-critical-appraisal-div.pdf; doi:https://doi.org/10.1192/bjp.2021.219; html:https://europepmc.org/articles/PMC7612705; pdf:https://europepmc.org/articles/PMC7612705?pdf=render; doi:https://doi.org/10.1192/bjp.2021.219
 39385593,https://doi.org/10.1093/ije/dyae125,Conventional and genetic associations of BMI with major vascular and non-vascular disease incidence and mortality in a relatively lean Chinese population: U-shaped relationship revisited.,"Iona A, Bragg F, Fairhurst-Hunter Z, Millwood IY, Wright N, Lin K, Yang L, Du H, Chen Y, Pei P, Cheng L, Schmidt D, Avery D, Yu C, Lv J, Clarke R, Walters R, Li L, Parish S, Chen Z, China Kadoorie Biobank Collaborative Group
 .",,International journal of epidemiology,2024,2024-08-01,Y,Cardiovascular disease; Stroke; body mass index; Mendelian Randomization,,,"<h4>Background</h4>Higher body mass index (BMI) is associated with higher incidence of cardiovascular and some non-cardiovascular diseases (CVDs/non-CVDs). However, uncertainty remains about its associations with mortality, particularly at lower BMI levels.<h4>Methods</h4>The prospective China Kadoorie Biobank recruited >512 000 adults aged 30-79 years in 2004-08 and genotyped a random subset of 76 000 participants. In conventional and Mendelian randomization (MR) analyses, Cox regression yielded adjusted hazard ratios (HRs) associating measured and genetically predicted BMI levels with incident risks of major vascular events (MVEs; conventional/MR 68 431/23 621), ischaemic heart disease (IHD; 50 698/12 177), ischaemic stroke (IS; 42 427/11 897) and intracerebral haemorrhage (ICH; 7644/4712), and with mortality risks of CVD (15 427/6781), non-CVD (26 915/4355) and all causes (42 342/6784), recorded during ∼12 years of follow-up.<h4>Results</h4>Overall, the mean BMI was 23.8 (standard deviation: 3.2) kg/m2 and 13% had BMIs of <20 kg/m2. Measured and genetically predicted BMI showed positive log-linear associations with MVE, IHD and IS, but a shallower positive association with ICH in conventional analyses. Adjusted HRs per 5 kg/m2 higher genetically predicted BMI were 1.50 (95% CI 1.41-1.58), 1.49 (1.38-1.61), 1.42 (1.31-1.54) and 1.64 (1.58-1.69) for MVE, IHD, IS and ICH, respectively. These were stronger than associations in conventional analyses [1.21 (1.20-1.23), 1.28 (1.26-1.29), 1.31 (1.29-1.33) and 1.14 (1.10-1.18), respectively]. At BMIs of ≥20 kg/m2, there were stronger positive log-linear associations of BMI with CVD, non-CVD and all-cause mortality in MR than in conventional analyses.<h4>Conclusions</h4>Among relatively lean Chinese adults, higher genetically predicted BMI was associated with higher risks of incident CVDs. Excess mortality risks at lower BMI in conventional analyses are likely not causal and may reflect residual reverse causality.",,doi:https://doi.org/10.1093/ije/dyae125; html:https://europepmc.org/articles/PMC11464668; pdf:https://europepmc.org/articles/PMC11464668?pdf=render
@@ -716,44 +716,44 @@ PMC10910267,https://doi.org/,Development and evaluation of a tool to optimise in
 38755181,https://doi.org/10.1038/s41533-024-00369-8,Tobacco control policies and respiratory conditions among children presenting in primary care.,"Faber T, Coffeng LE, Sheikh A, Reiss IK, Mackenbach JP, Been JV.",,NPJ primary care respiratory medicine,2024,2024-05-16,Y,,,,"Tobacco control policies can protect child health. We hypothesised that the parallel introduction in 2008 of smoke-free restaurants and bars in the Netherlands, a tobacco tax increase and mass media campaign, would be associated with decreases in childhood wheezing/asthma, respiratory tract infections (RTIs), and otitis media with effusion (OME) presenting in primary care. We conducted an interrupted time series study using electronic medical records from the Dutch Integrated Primary Care Information database (2000-2016). We estimated step and slope changes in the incidence of each outcome with negative binomial regression analyses, adjusting for underlying time-trends, seasonality, age, sex, electronic medical record system, urbanisation, and social deprivation. Analysing 1,295,124 person-years among children aged 0-12 years, we found positive step changes immediately after the policies (incidence rate ratio (IRR): 1.07, 95% CI: 1.01-1.14 for wheezing/asthma; IRR: 1.16, 95% CI: 1.13-1.19 for RTIs; and IRR: 1.24, 95% CI: 1.14-1.36 for OME). These were followed by slope decreases for wheezing/asthma (IRR: 0.95/year, 95% CI: 0.93-0.97) and RTIs (IRR: 0.97/year, 95% CI: 0.96-0.98), but a slope increase in OME (IRR: 1.05/year, 95% CI: 1.01-1.09). We found no clear evidence of benefit of changes in tobacco control policies in the Netherlands for the outcomes of interest. Our findings need to be interpreted with caution due to substantial uncertainty in the pre-legislation outcome trends.",,pdf:https://www.nature.com/articles/s41533-024-00369-8.pdf; doi:https://doi.org/10.1038/s41533-024-00369-8; html:https://europepmc.org/articles/PMC11099007; pdf:https://europepmc.org/articles/PMC11099007?pdf=render
 35958702,https://doi.org/10.1007/s40653-021-00433-2,The Secondary Harms of Parental Substance Use on Children's Educational Outcomes: A Review.,Lowthian E.,,Journal of child & adolescent trauma,2022,2022-01-14,Y,Drugs; Review; Alcohol; Education; Parental Substance Use,,,"Parental substance use, that is alcohol and illicit drugs, can have a deleterious impact on child health and wellbeing. An area that can be affected by parental substance use is the educational outcomes of children. Current reviews of the literature in the field of parental substance use and children's educational outcomes have only identified a small number of studies, and most focus on children's educational attainment. To grasp the available literature, the method from Arksey and O'Malley (2005) was used to identify literature. Studies were included if they were empirical, after 1950, and focused on children's school or educational outcomes. From this, 51 empirical studies were identified which examined the relationship between parental alcohol and illicit drug use on children's educational outcomes. Five main themes emerged which included attainment, behavior and adjustment, attendance, school enjoyment and satisfaction, academic self-concept, along with other miscellaneous outcomes. This paper highlights the main findings of the studies, the gaps in the current literature, and the challenges presented. Recommendations are made for further research and interventions in the areas of parental substance use and child educational outcomes specifically, but also for broader areas of adversity and child wellbeing.",,pdf:https://link.springer.com/content/pdf/10.1007/s40653-021-00433-2.pdf; doi:https://doi.org/10.1007/s40653-021-00433-2; html:https://europepmc.org/articles/PMC9360289; pdf:https://europepmc.org/articles/PMC9360289?pdf=render
 33472926,https://doi.org/10.1212/wnl.0000000000011463,"Incidence, Prevalence, and Health Care Outcomes in Idiopathic Intracranial Hypertension: A Population Study.","Miah L, Strafford H, Fonferko-Shadrach B, Hollinghurst J, Sawhney IMS, Hadjikoutis S, Rees MI, Powell R, Lacey A, Pickrell WO.",,Neurology,2021,2021-02-22,Y,,,,"<h4>Objective</h4>To characterize trends in incidence, prevalence, and health care outcomes in the idiopathic intracranial hypertension (IIH) population in Wales using routinely collected health care data.<h4>Methods</h4>We used and validated primary and secondary care IIH diagnosis codes within the Secure Anonymised Information Linkage databank to ascertain IIH cases and controls in a retrospective cohort study between 2003 and 2017. We recorded body mass index (BMI), deprivation quintile, CSF diversion surgery, and unscheduled hospital admissions in case and control cohorts.<h4>Results</h4>We analyzed 35 million patient-years of data. There were 1,765 cases of IIH in 2017 (85% female). The prevalence and incidence of IIH in 2017 was 76/100,000 and 7.8/100,000/y, a significant increase from 2003 (corresponding figures = 12/100,000 and 2.3/100,000/y) (<i>p</i> < 0.001). IIH prevalence is associated with increasing BMI and increasing deprivation. The odds ratio for developing IIH in the least deprived quintile compared to the most deprived quintile, adjusted for sex and BMI, was 0.65 (95% confidence interval 0.55 to 0.76). Nine percent of IIH cases had CSF shunts with less than 0.2% having bariatric surgery. Unscheduled hospital admissions were higher in the IIH cohort compared to controls (rate ratio 5.28, <i>p</i> < 0.001) and in individuals with IIH and CSF shunts compared to those without shunts (rate ratio 2.02, <i>p</i> < 0.01).<h4>Conclusions</h4>IIH incidence and prevalence is increasing considerably, corresponding to population increases in BMI, and is associated with increased deprivation. This has important implications for health care professionals and policy makers given the comorbidities, complications, and increased health care utilization associated with IIH.",,pdf:https://n.neurology.org/content/neurology/96/8/e1251.full.pdf; doi:https://doi.org/10.1212/WNL.0000000000011463; html:https://europepmc.org/articles/PMC8055349; pdf:https://europepmc.org/articles/PMC8055349?pdf=render
-31818272,https://doi.org/10.1186/s12889-019-8015-3,"Drinking beer, wine or spirits - does it matter for inequalities in alcohol-related hospital admission? A record-linked longitudinal study in Wales.","Gartner A, Trefan L, Moore S, Akbari A, Paranjothy S, Farewell D.",,BMC public health,2019,2019-12-09,Y,Alcohol; Inequalities; Deprivation; Hospital Admission; Beverage Type; Record Linked,Improving Public Health,,"<h4>Background</h4>Alcohol-related harm has been found to be higher in disadvantaged groups, despite similar alcohol consumption to advantaged groups. This is known as the alcohol harm paradox. Beverage type is reportedly socioeconomically patterned but has not been included in longitudinal studies investigating record-linked alcohol consumption and harm. We aimed to investigate whether and to what extent consumption by beverage type, BMI, smoking and other factors explain inequalities in alcohol-related harm.<h4>Methods</h4>11,038 respondents to the Welsh Health Survey answered questions on their health and lifestyle. Responses were record-linked to wholly attributable alcohol-related hospital admissions (ARHA) eight years before the survey month and until the end of 2016 within the Secure Anonymised Information Linkage (SAIL) Databank. We used survival analysis, specifically multi-level and multi-failure Cox mixed effects models, to calculate the hazard ratios of ARHA. In adjusted models we included the number of units consumed by beverage type and other factors, censoring for death or moving out of Wales.<h4>Results</h4>People living in more deprived areas had a higher risk of admission (HR 1.75; 95% CI 1.23-2.48) compared to less deprived. Adjustment for the number of units by type of alcohol consumed only reduced the risk of ARHA for more deprived areas by 4% (HR 1.72; 95% CI 1.21-2.44), whilst adding smoking and BMI reduced these inequalities by 35.7% (HR 1.48; 95% CI 1.01-2.17). These social patterns were similar for individual-level social class, employment, housing tenure and highest qualification. Inequalities were further reduced by including either health status (16.6%) or mental health condition (5%). Unit increases of spirits drunk were positively associated with increasing risk of ARHA (HR 1.06; 95% CI 1.01-1.12), higher than for other drink types.<h4>Conclusions</h4>Although consumption by beverage type was socioeconomically patterned, it did not help explain inequalities in alcohol-related harm. Smoking and BMI explained around a third of inequalities, but lower socioeconomic groups had a persistently higher risk of (multiple) ARHA. Comorbidities also explained a further proportion of inequalities and need further investigation, including the contribution of specific conditions. The increased harms from consumption of stronger alcoholic beverages may inform public health policy.","This longitudinal study investigated whether and to what extent consumption by beverage type, BMI, smoking and other factors explained inequalities in alcohol-related hospital admission (ARHA). Using statistical analysis methods, it was found that people living in more deprived areas had a higher risk of ARHA compared to less deprived. Smokers and people currently being treated for mental illness had higher risk of ARHA, while BMI appeared to be slightly protective. ",pdf:https://bmcpublichealth.biomedcentral.com/track/pdf/10.1186/s12889-019-8015-3; doi:https://doi.org/10.1186/s12889-019-8015-3; html:https://europepmc.org/articles/PMC6902530; pdf:https://europepmc.org/articles/PMC6902530?pdf=render
 34431993,https://doi.org/10.1093/eurheartj/ehab581,Risk factors for type 1 and type 2 myocardial infarction.,"Wereski R, Kimenai DM, Bularga A, Taggart C, Lowe DJ, Mills NL, Chapman AR.",,European heart journal,2022,2022-01-01,Y,Myocardial infarction; acute coronary syndrome; type 2; risk factors; Universal Definition,,,"<h4>Aims</h4>Whilst the risk factors for type 1 myocardial infarction due to atherosclerotic plaque rupture and thrombosis are established, our understanding of the factors that predispose to type 2 myocardial infarction during acute illness is still emerging. Our aim was to evaluate and compare the risk factors for type 1 and type 2 myocardial infarction.<h4>Methods and results</h4>We conducted a secondary analysis of a multi-centre randomized trial population of 48 282 consecutive patients attending hospital with suspected acute coronary syndrome. The diagnosis of myocardial infarction during the index presentation and all subsequent reattendances was adjudicated according to the Universal Definition of Myocardial Infarction. Cox regression was used to identify predictors of future type 1 and type 2 myocardial infarction during a 1-year follow-up period. Within 1 year, 1331 patients had a subsequent myocardial infarction, with 924 and 407 adjudicated as type 1 and type 2 myocardial infarction, respectively. Risk factors for type 1 and type 2 myocardial infarction were similar, with age, hyperlipidaemia, diabetes, abnormal renal function, and known coronary disease predictors for both (P < 0.05 for all). Whilst women accounted for a greater proportion of patients with type 2 as compared to type 1 myocardial infarction, after adjustment for other risk factors, sex was not a predictor of type 2 myocardial events [adjusted hazard ratio (aHR) 0.82, 95% confidence interval (CI) 0.66-1.01]. The strongest predictor of type 2 myocardial infarction was a prior history of type 2 events (aHR 6.18, 95% CI 4.70-8.12).<h4>Conclusions</h4>Risk factors for coronary disease that are associated with type 1 myocardial infarction are also important predictors of type 2 events during acute illness. Treatment of these risk factors may reduce future risk of both type 1 and type 2 myocardial infarction.",,pdf:https://academic.oup.com/eurheartj/article-pdf/43/2/127/42182731/ehab581.pdf; doi:https://doi.org/10.1093/eurheartj/ehab581; html:https://europepmc.org/articles/PMC8757580; pdf:https://europepmc.org/articles/PMC8757580?pdf=render
+31818272,https://doi.org/10.1186/s12889-019-8015-3,"Drinking beer, wine or spirits - does it matter for inequalities in alcohol-related hospital admission? A record-linked longitudinal study in Wales.","Gartner A, Trefan L, Moore S, Akbari A, Paranjothy S, Farewell D.",,BMC public health,2019,2019-12-09,Y,Alcohol; Inequalities; Deprivation; Hospital Admission; Beverage Type; Record Linked,Improving Public Health,,"<h4>Background</h4>Alcohol-related harm has been found to be higher in disadvantaged groups, despite similar alcohol consumption to advantaged groups. This is known as the alcohol harm paradox. Beverage type is reportedly socioeconomically patterned but has not been included in longitudinal studies investigating record-linked alcohol consumption and harm. We aimed to investigate whether and to what extent consumption by beverage type, BMI, smoking and other factors explain inequalities in alcohol-related harm.<h4>Methods</h4>11,038 respondents to the Welsh Health Survey answered questions on their health and lifestyle. Responses were record-linked to wholly attributable alcohol-related hospital admissions (ARHA) eight years before the survey month and until the end of 2016 within the Secure Anonymised Information Linkage (SAIL) Databank. We used survival analysis, specifically multi-level and multi-failure Cox mixed effects models, to calculate the hazard ratios of ARHA. In adjusted models we included the number of units consumed by beverage type and other factors, censoring for death or moving out of Wales.<h4>Results</h4>People living in more deprived areas had a higher risk of admission (HR 1.75; 95% CI 1.23-2.48) compared to less deprived. Adjustment for the number of units by type of alcohol consumed only reduced the risk of ARHA for more deprived areas by 4% (HR 1.72; 95% CI 1.21-2.44), whilst adding smoking and BMI reduced these inequalities by 35.7% (HR 1.48; 95% CI 1.01-2.17). These social patterns were similar for individual-level social class, employment, housing tenure and highest qualification. Inequalities were further reduced by including either health status (16.6%) or mental health condition (5%). Unit increases of spirits drunk were positively associated with increasing risk of ARHA (HR 1.06; 95% CI 1.01-1.12), higher than for other drink types.<h4>Conclusions</h4>Although consumption by beverage type was socioeconomically patterned, it did not help explain inequalities in alcohol-related harm. Smoking and BMI explained around a third of inequalities, but lower socioeconomic groups had a persistently higher risk of (multiple) ARHA. Comorbidities also explained a further proportion of inequalities and need further investigation, including the contribution of specific conditions. The increased harms from consumption of stronger alcoholic beverages may inform public health policy.","This longitudinal study investigated whether and to what extent consumption by beverage type, BMI, smoking and other factors explained inequalities in alcohol-related hospital admission (ARHA). Using statistical analysis methods, it was found that people living in more deprived areas had a higher risk of ARHA compared to less deprived. Smokers and people currently being treated for mental illness had higher risk of ARHA, while BMI appeared to be slightly protective. ",pdf:https://bmcpublichealth.biomedcentral.com/track/pdf/10.1186/s12889-019-8015-3; doi:https://doi.org/10.1186/s12889-019-8015-3; html:https://europepmc.org/articles/PMC6902530; pdf:https://europepmc.org/articles/PMC6902530?pdf=render
 37935836,https://doi.org/10.1093/eurheartj/ehad736,Mendelian randomization for cardiovascular diseases: principles and applications.,"Larsson SC, Butterworth AS, Burgess S.",,European heart journal,2023,2023-12-01,Y,Genetics; Cardiovascular disease; Single Nucleotide Polymorphisms; Mendelian Randomization,,,"Large-scale genome-wide association studies conducted over the last decade have uncovered numerous genetic variants associated with cardiometabolic traits and risk factors. These discoveries have enabled the Mendelian randomization (MR) design, which uses genetic variation as a natural experiment to improve causal inferences from observational data. By analogy with the random assignment of treatment in randomized controlled trials, the random segregation of genetic alleles when DNA is transmitted from parents to offspring at gamete formation is expected to reduce confounding in genetic associations. Mendelian randomization analyses make a set of assumptions that must hold for valid results. Provided that the assumptions are well justified for the genetic variants that are employed as instrumental variables, MR studies can inform on whether a putative risk factor likely has a causal effect on the disease or not. Mendelian randomization has been increasingly applied over recent years to predict the efficacy and safety of existing and novel drugs targeting cardiovascular risk factors and to explore the repurposing potential of available drugs. This review article describes the principles of the MR design and some applications in cardiovascular epidemiology.",,pdf:https://academic.oup.com/eurheartj/advance-article-pdf/doi/10.1093/eurheartj/ehad736/52829421/ehad736.pdf; doi:https://doi.org/10.1093/eurheartj/ehad736; html:https://europepmc.org/articles/PMC10719501; pdf:https://europepmc.org/articles/PMC10719501?pdf=render
 38538751,https://doi.org/10.1038/s41598-024-57366-7,"An observational analysis of frailty in combination with loneliness or social isolation and their association with socioeconomic deprivation, hospitalisation and mortality among UK Biobank participants.","Politis M, Crawford L, Jani BD, Nicholl BI, Lewsey J, McAllister DA, Mair FS, Hanlon P.",,Scientific reports,2024,2024-03-27,Y,Mortality; Frailty; Loneliness; Social Isolation; Hospitalisation,,,"Frailty, social isolation, and loneliness have individually been associated with adverse health outcomes. This study examines how frailty in combination with loneliness or social isolation is associated with socioeconomic deprivation and with all-cause mortality and hospitalisation rate in a middle-aged and older population. Baseline data from 461,047 UK Biobank participants (aged 37-73) were used to assess frailty (frailty phenotype), social isolation, and loneliness. Weibull models assessed the association between frailty in combination with loneliness or social isolation and all-cause mortality adjusted for age/sex/smoking/alcohol/socioeconomic-status and number of long-term conditions. Negative binomial regression models assessed hospitalisation rate. Frailty prevalence was 3.38%, loneliness 4.75% and social isolation 9.04%. Frailty was present across all ages and increased with age. Loneliness and social isolation were more common in younger participants compared to older. Co-occurrence of frailty and loneliness or social isolation was most common in participants with high socioeconomic deprivation. Frailty was associated with increased mortality and hospitalisation regardless of social isolation/loneliness. Hazard ratios for mortality were 2.47 (2.27-2.69) with social isolation and 2.17 (2.05-2.29) without social isolation, 2.14 (1.92-2.38) with loneliness and 2.16 (2.05-2.27) without loneliness. Loneliness and social isolation were associated with mortality and hospitalisation in robust participants, but this was attenuated in the context of frailty. Frailty and loneliness/social isolation affect individuals across a wide age spectrum and disproportionately co-occur in areas of high deprivation. All were associated with adverse outcomes, but the association between loneliness and social isolation and adverse outcomes was attenuated in the context of frailty. Future interventions should target people living with frailty or loneliness/social isolation, regardless of age.",,pdf:https://www.nature.com/articles/s41598-024-57366-7.pdf; doi:https://doi.org/10.1038/s41598-024-57366-7; html:https://europepmc.org/articles/PMC10973409; pdf:https://europepmc.org/articles/PMC10973409?pdf=render
 35151397,https://doi.org/10.1016/s0140-6736(22)00163-5,"Casirivimab and imdevimab in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial.",RECOVERY Collaborative Group.,,"Lancet (London, England)",2022,2022-02-01,Y,,,,"<h4>Background</h4>Casirivimab and imdevimab are non-competing monoclonal antibodies that bind to two different sites on the receptor binding domain of the SARS-CoV-2 spike glycoprotein, blocking viral entry into host cells. We aimed to evaluate the efficacy and safety of casirivimab and imdevimab administered in combination in patients admitted to hospital with COVID-19.<h4>Methods</h4>RECOVERY is a randomised, controlled, open-label platform trial comparing several possible treatments with usual care in patients admitted to hospital with COVID-19. 127 UK hospitals took part in the evaluation of casirivimab and imdevimab. Eligible participants were any patients aged at least 12 years admitted to hospital with clinically suspected or laboratory-confirmed SARS-CoV-2 infection. Participants were randomly assigned (1:1) to either usual standard of care alone or usual care plus casirivimab 4 g and imdevimab 4 g administered together in a single intravenous infusion. Investigators and data assessors were masked to analyses of the outcome data during the trial. The primary outcome was 28-day all-cause mortality assessed by intention to treat, first only in patients without detectable antibodies to SARS-CoV-2 infection at randomisation (ie, those who were seronegative) and then in the overall population. Safety was assessed in all participants who received casirivimab and imdevimab. The trial is registered with ISRCTN (50189673) and ClinicalTrials.gov (NCT04381936).<h4>Findings</h4>Between Sept 18, 2020, and May 22, 2021, 9785 patients enrolled in RECOVERY were eligible for casirivimab and imdevimab, of which 4839 were randomly assigned to casirivimab and imdevimab plus usual care and 4946 to usual care alone. 3153 (32%) of 9785 patients were seronegative, 5272 (54%) were seropositive, and 1360 (14%) had unknown baseline antibody status. 812 (8%) patients were known to have received at least one dose of a SARS-CoV-2 vaccine. In the primary efficacy population of seronegative patients, 396 (24%) of 1633 patients allocated to casirivimab and imdevimab versus 452 (30%) of 1520 patients allocated to usual care died within 28 days (rate ratio [RR] 0·79, 95% CI 0·69-0·91; p=0·0009). In an analysis of all randomly assigned patients (regardless of baseline antibody status), 943 (19%) of 4839 patients allocated to casirivimab and imdevimab versus 1029 (21%) of 4946 patients allocated to usual care died within 28 days (RR 0·94, 95% CI 0·86-1·02; p=0·14). The proportional effect of casirivimab and imdevimab on mortality differed significantly between seropositive and seronegative patients (p value for heterogeneity=0·002). There were no deaths attributed to the treatment, or meaningful between-group differences in the pre-specified safety outcomes of cause-specific mortality, cardiac arrhythmia, thrombosis, or major bleeding events. Serious adverse reactions reported in seven (<1%) participants were believed by the local investigator to be related to treatment with casirivimab and imdevimab.<h4>Interpretation</h4>In patients admitted to hospital with COVID-19, the monoclonal antibody combination of casirivimab and imdevimab reduced 28-day mortality in patients who were seronegative (and therefore had not mounted their own humoral immune response) at baseline but not in those who were seropositive at baseline.<h4>Funding</h4>UK Research and Innovation (Medical Research Council) and National Institute of Health Research.",,pdf:https://aura.abdn.ac.uk/bitstream/2164/18986/1/Recovery_etal_TL_Casirivimab_And_Imdevimab_VoR.pdf; doi:https://doi.org/10.1016/S0140-6736(22)00163-5; html:https://europepmc.org/articles/PMC8830904
 35845286,https://doi.org/10.1002/jha2.182,"An open-source, expert-designed decision tree application to support accurate diagnosis of myeloid malignancies.","Coats T, Bean D, Vatopoulou T, Vijayavalli D, El-Bashir R, Panopoulou A, Wood H, Wimalachandra M, Coppell J, Medd P, Furtado M, Tucker D, Kulasakeraraj A, Pawade J, Dobson R, Ireland R.",,EJHaem,2021,2021-03-26,Y,Myeloid Leukaemia; Classifications; Diagnostic Haematology; Clinical Haematology,,,"Accurate, reproducible diagnoses can be difficult to make in haemato-oncology due to multi-parameter clinical data, complex diagnostic criteria and time-pressured environments. We have designed a decision tree application (DTA) that reflects WHO diagnostic criteria to support accurate diagnoses of myeloid malignancies. The DTA returned the correct diagnoses in 94% of clinical cases tested. The DTA maintained a high level of accuracy in a second validation using artificially generated clinical cases. Optimisations have been made to the DTA based on the validations, and the revised version is now publicly available for use at http://bit.do/ADAtool.",,pdf:https://discovery.ucl.ac.uk/10145154/1/Bean_An%20open%20source%2C%20expert%20designed%20decision%20tree%20application%20to%20support%20accurate%20diagnosis%20of%20myeloid%20malignancies_VoR.pdf; doi:https://doi.org/10.1002/jha2.182; html:https://europepmc.org/articles/PMC9175663; pdf:https://europepmc.org/articles/PMC9175663?pdf=render
+37185641,https://doi.org/10.1136/bmjopen-2022-070022,EXAcerbations of COPD and their OutcomeS on CardioVascular diseases (EXACOS-CV) Programme: protocol of multicountry observational cohort studies.,"Nordon C, Rhodes K, Quint JK, Vogelmeier CF, Simons SO, Hawkins NM, Marshall J, Ouwens M, Garbe E, Müllerová H.",,BMJ open,2023,2023-04-26,Y,epidemiology; Cardiology; Vascular Medicine; Chronic Airways Disease,,,"<h4>Introduction</h4>In patients with chronic obstructive pulmonary disease (COPD), the risk of certain cardiovascular (CV) events is increased by threefold to fivefold in the year following acute exacerbation of COPD (AECOPD), compared with a non-exacerbation period. While the effect of severe AECOPD is well established, the relationship of moderate exacerbation or prior exacerbation to elevated risk of CV events is less clear. We will conduct cohort studies in multiple countries to further characterise the association between AECOPD and CV events.<h4>Methods and analysis</h4>Retrospective longitudinal cohort studies will be conducted within routinely collected electronic healthcare records or claims databases. The study cohorts will include patients meeting inclusion criteria for COPD between 1 January 2014 and 31 December 2018. Moderate exacerbation is defined as an outpatient visit and/or medication dispensation/prescription for exacerbation; severe exacerbation is defined as hospitalisation for COPD. The primary outcomes of interest are the time to (1) first hospitalisation for a CV event (including acute coronary syndrome, heart failure, arrhythmias or cerebral ischaemia) since cohort entry or (2) death. Time-dependent Cox proportional hazards models will compare the hazard of a CV event between exposed periods following exacerbation (split into these periods: 1-7, 8-14, 15-30, 31-180 and 181-365 days) and the unexposed reference time period, adjusted on time-fixed and time-varying confounders.<h4>Ethics and dissemination</h4>Studies have been approved in Canada, Japan, the Netherlands, Spain and the UK, where an institutional review board is mandated. For each study, the results will be published in peer-reviewed journals.",,pdf:https://bmjopen.bmj.com/content/bmjopen/13/4/e070022.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-070022; html:https://europepmc.org/articles/PMC10151875; pdf:https://europepmc.org/articles/PMC10151875?pdf=render
 PMC9644982,https://doi.org/,Assessing the impacts of COVID-19 on Care Homes in Wales.,"Fry R, Hollinghurst J, North L, Emmerson C, Long S, Akbari A, Gravenor M, Lyons R.",,International journal of population data science,,2022-11-21,Y,,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9644982/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9644982/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC9644982; pdf:https://europepmc.org/articles/PMC9644982?pdf=render
 36211555,https://doi.org/10.3389/fcvm.2022.983091,Cardiac aging synthesis from cross-sectional data with conditional generative adversarial networks.,"Campello VM, Xia T, Liu X, Sanchez P, Martín-Isla C, Petersen SE, Seguí S, Tsaftaris SA, Lekadir K.",,Frontiers in cardiovascular medicine,2022,2022-09-23,Y,Synthesis; Magnetic Resonance Imaging; Data Augmentation; Aging Heart; Generative Adversarial Network,,,"Age has important implications for health, and understanding how age manifests in the human body is the first step for a potential intervention. This becomes especially important for cardiac health, since age is the main risk factor for development of cardiovascular disease. Data-driven modeling of age progression has been conducted successfully in diverse applications such as face or brain aging. While longitudinal data is the preferred option for training deep learning models, collecting such a dataset is usually very costly, especially in medical imaging. In this work, a conditional generative adversarial network is proposed to synthesize older and younger versions of a heart scan by using only cross-sectional data. We train our model with more than 14,000 different scans from the UK Biobank. The induced modifications focused mainly on the interventricular septum and the aorta, which is consistent with the existing literature in cardiac aging. We evaluate the results by measuring image quality, the mean absolute error for predicted age using a pre-trained regressor, and demonstrate the application of synthetic data for counter-balancing biased datasets. The results suggest that the proposed approach is able to model realistic changes in the heart using only cross-sectional data and that these data can be used to correct age bias in a dataset.",,pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2022.983091/pdf; doi:https://doi.org/10.3389/fcvm.2022.983091; html:https://europepmc.org/articles/PMC9537599; pdf:https://europepmc.org/articles/PMC9537599?pdf=render
-37185641,https://doi.org/10.1136/bmjopen-2022-070022,EXAcerbations of COPD and their OutcomeS on CardioVascular diseases (EXACOS-CV) Programme: protocol of multicountry observational cohort studies.,"Nordon C, Rhodes K, Quint JK, Vogelmeier CF, Simons SO, Hawkins NM, Marshall J, Ouwens M, Garbe E, Müllerová H.",,BMJ open,2023,2023-04-26,Y,epidemiology; Cardiology; Vascular Medicine; Chronic Airways Disease,,,"<h4>Introduction</h4>In patients with chronic obstructive pulmonary disease (COPD), the risk of certain cardiovascular (CV) events is increased by threefold to fivefold in the year following acute exacerbation of COPD (AECOPD), compared with a non-exacerbation period. While the effect of severe AECOPD is well established, the relationship of moderate exacerbation or prior exacerbation to elevated risk of CV events is less clear. We will conduct cohort studies in multiple countries to further characterise the association between AECOPD and CV events.<h4>Methods and analysis</h4>Retrospective longitudinal cohort studies will be conducted within routinely collected electronic healthcare records or claims databases. The study cohorts will include patients meeting inclusion criteria for COPD between 1 January 2014 and 31 December 2018. Moderate exacerbation is defined as an outpatient visit and/or medication dispensation/prescription for exacerbation; severe exacerbation is defined as hospitalisation for COPD. The primary outcomes of interest are the time to (1) first hospitalisation for a CV event (including acute coronary syndrome, heart failure, arrhythmias or cerebral ischaemia) since cohort entry or (2) death. Time-dependent Cox proportional hazards models will compare the hazard of a CV event between exposed periods following exacerbation (split into these periods: 1-7, 8-14, 15-30, 31-180 and 181-365 days) and the unexposed reference time period, adjusted on time-fixed and time-varying confounders.<h4>Ethics and dissemination</h4>Studies have been approved in Canada, Japan, the Netherlands, Spain and the UK, where an institutional review board is mandated. For each study, the results will be published in peer-reviewed journals.",,pdf:https://bmjopen.bmj.com/content/bmjopen/13/4/e070022.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-070022; html:https://europepmc.org/articles/PMC10151875; pdf:https://europepmc.org/articles/PMC10151875?pdf=render
 33739254,https://doi.org/10.2807/1560-7917.es.2021.26.11.2100256,"Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England, 16 November to 5 February.","Grint DJ, Wing K, Williamson E, McDonald HI, Bhaskaran K, Evans D, Evans SJ, Walker AJ, Hickman G, Nightingale E, Schultze A, Rentsch CT, Bates C, Cockburn J, Curtis HJ, Morton CE, Bacon S, Davy S, Wong AY, Mehrkar A, Tomlinson L, Douglas IJ, Mathur R, Blomquist P, MacKenna B, Ingelsby P, Croker R, Parry J, Hester F, Harper S, DeVito NJ, Hulme W, Tazare J, Goldacre B, Smeeth L, Eggo RM.",,Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin,2021,2021-03-01,Y,Mortality; Coronavirus; Cfr; Case Fatality Risk; Covid-19; Sars-cov-2; Variant Of Concern,,,The SARS-CoV-2 B.1.1.7 variant of concern (VOC) is increasing in prevalence across Europe. Accurate estimation of disease severity associated with this VOC is critical for pandemic planning. We found increased risk of death for VOC compared with non-VOC cases in England (hazard ratio: 1.67; 95% confidence interval: 1.34-2.09; p < 0.0001). Absolute risk of death by 28 days increased with age and comorbidities. This VOC has potential to spread faster with higher mortality than the pandemic to date.,,pdf:https://www.eurosurveillance.org/deliver/fulltext/eurosurveillance/26/11/eurosurv-26-11-2.pdf?itemId=%2Fcontent%2F10.2807%2F1560-7917.ES.2021.26.11.2100256&mimeType=pdf&containerItemId=content/eurosurveillance; doi:https://doi.org/10.2807/1560-7917.ES.2021.26.11.2100256; html:https://europepmc.org/articles/PMC7976383; pdf:https://europepmc.org/articles/PMC7976383?pdf=render
 38505485,https://doi.org/10.1093/ehjdh/ztae001,Explainable machine learning using echocardiography to improve risk prediction in patients with chronic coronary syndrome.,"Molenaar MA, Bouma BJ, Asselbergs FW, Verouden NJ, Selder JL, Chamuleau SAJ, Schuuring MJ.",,European heart journal. Digital health,2024,2024-01-22,Y,Artificial intelligence; Mortality; Prognosis; coronary artery disease; risk; Machine Learning,,,"<h4>Aims</h4>The European Society of Cardiology guidelines recommend risk stratification with limited clinical parameters such as left ventricular (LV) function in patients with chronic coronary syndrome (CCS). Machine learning (ML) methods enable an analysis of complex datasets including transthoracic echocardiography (TTE) studies. We aimed to evaluate the accuracy of ML using clinical and TTE data to predict all-cause 5-year mortality in patients with CCS and to compare its performance with traditional risk stratification scores.<h4>Methods and results</h4>Data of consecutive patients with CCS were retrospectively collected if they attended the outpatient clinic of Amsterdam UMC location AMC between 2015 and 2017 and had a TTE assessment of the LV function. An eXtreme Gradient Boosting (XGBoost) model was trained to predict all-cause 5-year mortality. The performance of this ML model was evaluated using data from the Amsterdam UMC location VUmc and compared with the reference standard of traditional risk scores. A total of 1253 patients (775 training set and 478 testing set) were included, of which 176 patients (105 training set and 71 testing set) died during the 5-year follow-up period. The ML model demonstrated a superior performance [area under the receiver operating characteristic curve (AUC) 0.79] compared with traditional risk stratification tools (AUC 0.62-0.76) and showed good external performance. The most important TTE risk predictors included in the ML model were LV dysfunction and significant tricuspid regurgitation.<h4>Conclusion</h4>This study demonstrates that an explainable ML model using TTE and clinical data can accurately identify high-risk CCS patients, with a prognostic value superior to traditional risk scores.",,pdf:https://academic.oup.com/ehjdh/advance-article-pdf/doi/10.1093/ehjdh/ztae001/56332468/ztae001.pdf; doi:https://doi.org/10.1093/ehjdh/ztae001; html:https://europepmc.org/articles/PMC10944683; pdf:https://europepmc.org/articles/PMC10944683?pdf=render
-35868811,https://doi.org/10.1016/s2589-7500(22)00122-4,Data provenance and integrity of health-care systems data for clinical trials.,"Murray ML, Love SB, Carpenter JR, Hartley S, Landray MJ, Mafham M, Parmar MKB, Pinches H, Sydes MR, Healthcare Systems Data for Clinical Trials Collaborative Group.",,The Lancet. Digital health,2022,2022-08-01,Y,,,,,,pdf:http://www.thelancet.com/article/S2589750022001224/pdf; doi:https://doi.org/10.1016/S2589-7500(22)00122-4; html:https://europepmc.org/articles/PMC9296098; pdf:https://europepmc.org/articles/PMC9296098?pdf=render
 38053867,https://doi.org/10.1016/j.heliyon.2023.e21734,Wastewater-based surveillance models for COVID-19: A focused review on spatio-temporal models.,"Torabi F, Li G, Mole C, Nicholson G, Rowlingson B, Smith CR, Jersakova R, Diggle PJ, Blangiardo M.",,Heliyon,2023,2023-11-08,Y,Wastewater-based Epidemiology; Covid-19; Wastewater-Based Surveillance; Spatio-Temporal Statistical Modelling,,,"The evident shedding of the SARS-CoV-2 RNA particles from infected individuals into the wastewater opened up a tantalizing array of possibilities for prediction of COVID-19 prevalence prior to symptomatic case identification through community testing. Many countries have therefore explored the use of wastewater metrics as a surveillance tool, replacing traditional direct measurement of prevalence with cost-effective approaches based on SARS-CoV-2 RNA concentrations in wastewater samples. Two important aspects in building prediction models are: time over which the prediction occurs and space for which the predicted case numbers is shown. In this review, our main focus was on finding mathematical models which take into the account both the time-varying and spatial nature of wastewater-based metrics into account. We used six main characteristics as our assessment criteria: i) modelling approach; ii) temporal coverage; iii) spatial coverage; iv) sample size; v) wastewater sampling method; and vi) covariates included in the modelling. The majority of studies in the early phases of the pandemic recognized the temporal association of SARS-CoV-2 RNA concentration level in wastewater with the number of COVID-19 cases, ignoring their spatial context. We examined 15 studies up to April 2023, focusing on models considering both temporal and spatial aspects of wastewater metrics. Most early studies correlated temporal SARS-CoV-2 RNA levels with COVID-19 cases but overlooked spatial factors. Linear regression and SEIR models were commonly used (n = 10, 66.6 % of studies), along with machine learning (n = 1, 6.6 %) and Bayesian approaches (n = 1, 6.6 %) in some cases. Three studies employed spatio-temporal modelling approach (n = 3, 20.0 %). We conclude that the development, validation and calibration of further spatio-temporally explicit models should be done in parallel with the advancement of wastewater metrics before the potential of wastewater as a surveillance tool can be fully realised.",,doi:https://doi.org/10.1016/j.heliyon.2023.e21734; html:https://europepmc.org/articles/PMC10694161; pdf:https://europepmc.org/articles/PMC10694161?pdf=render
+35868811,https://doi.org/10.1016/s2589-7500(22)00122-4,Data provenance and integrity of health-care systems data for clinical trials.,"Murray ML, Love SB, Carpenter JR, Hartley S, Landray MJ, Mafham M, Parmar MKB, Pinches H, Sydes MR, Healthcare Systems Data for Clinical Trials Collaborative Group.",,The Lancet. Digital health,2022,2022-08-01,Y,,,,,,pdf:http://www.thelancet.com/article/S2589750022001224/pdf; doi:https://doi.org/10.1016/S2589-7500(22)00122-4; html:https://europepmc.org/articles/PMC9296098; pdf:https://europepmc.org/articles/PMC9296098?pdf=render
 36545688,https://doi.org/10.1192/bjb.2022.83,EDIFY (Eating Disorders: Delineating Illness and Recovery Trajectories to Inform Personalised Prevention and Early Intervention in Young People): project outline.,"Hemmings A, Sharpe H, Allen K, Bartel H, Campbell IC, Desrivières S, Dobson RJB, Folarin AA, French T, Kelly J, Micali N, Raman S, Treasure J, Abbas R, Heslop B, Street T, Schmidt U.",,BJPsych bulletin,2023,2023-12-01,Y,Eating Disorders; Risk And Resilience; Prevention And Early Intervention; Youth Engagement; Interdisciplinary Working,,,"EDIFY (Eating Disorders: Delineating Illness and Recovery Trajectories to Inform Personalised Prevention and Early Intervention in Young People) is an ambitious research project aiming to revolutionise how eating disorders are perceived, prevented and treated. Six integrated workstreams will address key questions, including: What are young people's experiences of eating disorders and recovery? What are the unique and shared risk factors in different groups? What helps or hinders recovery? How do the brain and behaviour change from early- to later-stage illness? How can we intervene earlier, quicker and in a more personalised way? This 4-year project, involving over 1000 participants, integrates arts, design and humanities with advanced neurobiological, psychosocial and bioinformatics approaches. Young people with lived experience of eating disorders are at the heart of EDIFY, serving as advisors and co-producers throughout. Ultimately, this work will expand public and professional perceptions of eating disorders, uplift under-represented voices and stimulate much-needed advances in policy and practice.",,pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/C1E5FCC67F1D627908A5495EED02577B/S2056469422000833a.pdf/div-class-title-edify-eating-disorders-delineating-illness-and-recovery-trajectories-to-inform-personalised-prevention-and-early-intervention-in-young-people-project-outline-div.pdf; doi:https://doi.org/10.1192/bjb.2022.83; html:https://europepmc.org/articles/PMC10694679; pdf:https://europepmc.org/articles/PMC10694679?pdf=render
 31789939,https://doi.org/10.1097/ede.0000000000001113,Could Greater Physical Activity Reduce Population Prevalence and Socioeconomic Inequalities in Children's Mental Health Problems? A Policy Simulation.,"Chigogora S, Pearce A, Law C, Viner R, Chittleborough C, Griffiths LJ, Hope S.",,"Epidemiology (Cambridge, Mass.)",2020,2020-01-01,Y,,,,"<h4>Background</h4>One in four children 5-16 years (y) of age shows signs of mental health problems in the United Kingdom; risk is higher in economically disadvantaged groups. Greater physical activity is associated with lower risk of internalizing problems such as depression and anxiety. We simulated the potential impact of population-wide physical activity interventions on overall prevalence of internalizing problems, and by family income. Interventions were based on the World Health Organization (WHO) children's target of 60 minutes (min) of moderate-to-vigorous physical activity per day and trial evidence.<h4>Methods</h4>Data were from the UK Millennium Cohort Study, a population-representative cohort of children born in 2000-2002. Household income (5 y) was the exposure; internalizing problems (outcome) were measured using the Strengths and Difficulties Questionnaire (11 y). Of 18,296 singletons, 6,497 had accelerometer physical activity data (mediator, manipulated to simulate interventions) at 7 y. We predicted probabilities of outcome according to exposure in marginal structural models, weighted for attrition and confounding, and adjusted for observed mediator. We then re-estimated probabilities in different physical activity intervention scenarios, assessing income inequalities in internalizing problems with risk ratios (RRs) and differences (RDs) according to income quintile.<h4>Results</h4>Simulating universal achievement of the WHO target led to little change in prevalence (10% [95% CI = 8%, 12%]) and socioeconomic inequalities in internalizing problems; RR: 2.2 (1.1, 3.4); RD: 8% [5%,13%]). More modest increases in physical activity achieved weaker results.<h4>Conclusions</h4>Our simulations suggest that large increases in moderate-to-vigorous physical activity in the United Kingdom would have little effect on prevalence and inequalities in child mental health problems.","This UK based prospective cohort study looked at the potential impact of physical activity on 'internalizing problems' such as depression in children. They measured physical activity level at 7 years, and looked whether mental health problems existed at 11 years, adjusting approrpiately for confounders (ethnicity, maternal age at birth, neighbourhood safety, childhood illness, etc). They conclude that a small reduction in mental health problems could be observed but not enough to justify the national policy of encouraging 60 min of mod-vigorous exercise a day for all children",html:https://journals.lww.com/epidem/Fulltext/2020/01000/Could_Greater_Physical_Activity_Reduce_Population.13.aspx; doi:https://doi.org/10.1097/EDE.0000000000001113; html:https://europepmc.org/articles/PMC6889907; pdf:https://europepmc.org/articles/PMC6889907?pdf=render
 34828364,https://doi.org/10.3390/genes12111758,The Influence of CYP2D6 and CYP2C19 Genetic Variation on Diabetes Mellitus Risk in People Taking Antidepressants and Antipsychotics.,"Austin-Zimmerman I, Wronska M, Wang B, Irizar H, Thygesen JH, Bhat A, Denaxas S, Fatemifar G, Finan C, Harju-Seppänen J, Giannakopoulou O, Kuchenbaecker K, Zartaloudi E, McQuillin A, Bramon E.",,Genes,2021,2021-11-03,Y,Diabetes; CYP2C19; CYP2D6; Pharmacogenetics; Hba1c; Personalized Medicine; Uk Biobank,,,"CYP2D6 and CYP2C19 enzymes are essential in the metabolism of antidepressants and antipsychotics. Genetic variation in these genes may increase risk of adverse drug reactions. Antidepressants and antipsychotics have previously been associated with risk of diabetes. We examined whether individual genetic differences in <i>CYP2D6</i> and <i>CYP2C19</i> contribute to these effects. We identified 31,579 individuals taking antidepressants and 2699 taking antipsychotics within UK Biobank. Participants were classified as poor, intermediate, or normal metabolizers of CYP2D6, and as poor, intermediate, normal, rapid, or ultra-rapid metabolizers of CYP2C19. Risk of diabetes mellitus represented by HbA1c level was examined in relation to the metabolic phenotypes. CYP2D6 poor metabolizers taking paroxetine had higher Hb1Ac than normal metabolizers (mean difference: 2.29 mmol/mol; <i>p</i> < 0.001). Among participants with diabetes who were taking venlafaxine, CYP2D6 poor metabolizers had higher HbA1c levels compared to normal metabolizers (mean differences: 10.15 mmol/mol; <i>p</i> < 0.001. Among participants with diabetes who were taking fluoxetine, CYP2D6 intermediate metabolizers and decreased HbA1c, compared to normal metabolizers (mean difference -7.74 mmol/mol; <i>p</i> = 0.017). We did not observe any relationship between CYP2D6 or CYP2C19 metabolic status and HbA1c levels in participants taking antipsychotic medication. Our results indicate that the impact of genetic variation in CYP2D6 differs depending on diabetes status. Although our findings support existing clinical guidelines, further research is essential to inform pharmacogenetic testing for people taking antidepressants and antipsychotics.",,pdf:https://www.mdpi.com/2073-4425/12/11/1758/pdf?version=1637118460; doi:https://doi.org/10.3390/genes12111758; html:https://europepmc.org/articles/PMC8620997; pdf:https://europepmc.org/articles/PMC8620997?pdf=render
 35305568,https://doi.org/10.1186/s12882-022-02742-6,Interaction between socioeconomic deprivation and ethnicity for likelihood of receiving living-donor kidney transplantation.,"Khalil K, Brotherton A, Moore S, Evison F, Gallier S, Hodson J, Sharif A.",,BMC nephrology,2022,2022-03-19,Y,Diversity; Kidney transplantation; Ethnicity; Deprivation; Living Kidney Donors,,,"<h4>Background</h4>The interplay between ethnicity and socioeconomic deprivation for living-donor kidney transplantation (LDKT) opportunities is unclear.<h4>Methods</h4>Data for 2040 consecutive kidney-alone transplant recipients receiving an allograft between 1st January 2007 and 30th June 2020 at a single center were retrospectively analyzed. The associations between the proportions of transplants that were LDKT (versus deceased donation) and both ethnicity and socioeconomic deprivation were assessed, with the latter quantified by the Index of Multiple Deprivation (IMD) quintile.<h4>Results</h4>The cohort comprised recipients of White (64.7%), South Asian (21.7%), Black (7.0%) and other (6.6%) ethnic groups. Recipients tended to be from socioeconomically deprived areas, with the most deprived quintile being the most frequently observed (quintile 1: 38.6% of patients); non-White recipients were significantly more likely to live in socioeconomically deprived areas (p < 0.001). Overall, 36.5% of transplants were LDKT, with this proportion declining progressively with socioeconomic deprivation, from 50.4 to 27.6% in the least versus most deprived IMD quintile (p < 0.001). A significant difference across recipient ethnicities was also observed, with the proportion of LDKTs ranging from 43.2% in White recipients to 17.8% in Black recipients (p < 0.001). Both socioeconomic deprivation (p < 0.001) and ethnicity (p = 0.005) remained significant predictors of LDKT on multivariable analysis, with a significant interaction between these factors also being observed (p < 0.001). Further assessment of this interaction effect found that, whilst there was a marked difference in the proportions of transplants that were LDKT between White versus non-White recipients in the most socioeconomically deprived groups (39.5% versus 19.3%), no such difference was seen in the least deprived recipients (48.5% versus 51.9%).<h4>Conclusions</h4>Whilst both socioeconomic deprivation and non-White ethnicity are independent predictors for lower proportions of LDKTs, the significant interaction between the two factors should be appreciated.",,pdf:https://bmcnephrol.biomedcentral.com/track/pdf/10.1186/s12882-022-02742-6; doi:https://doi.org/10.1186/s12882-022-02742-6; html:https://europepmc.org/articles/PMC8934457; pdf:https://europepmc.org/articles/PMC8934457?pdf=render
 33020224,https://doi.org/10.1136/heartjnl-2020-317870,Monitoring indirect impact of COVID-19 pandemic on services for cardiovascular diseases in the UK.,"Ball S, Banerjee A, Berry C, Boyle JR, Bray B, Bradlow W, Chaudhry A, Crawley R, Danesh J, Denniston A, Falter F, Figueroa JD, Hall C, Hemingway H, Jefferson E, Johnson T, King G, Lee KK, McKean P, Mason S, Mills NL, Pearson E, Pirmohamed M, Poon MTC, Priedon R, Shah A, Sofat R, Sterne JAC, Strachan FE, Sudlow CLM, Szarka Z, Whiteley W, Wyatt M, CVD-COVID-UK Consortium.",,Heart (British Cardiac Society),2020,2020-10-05,Y,epidemiology; Heart Disease; Health Care Delivery; Global Health Care Delivery; Aortic And Arterial Disease,,,"<h4>Objective</h4>To monitor hospital activity for presentation, diagnosis and treatment of cardiovascular diseases during the COVID-19) pandemic to inform on indirect effects.<h4>Methods</h4>Retrospective serial cross-sectional study in nine UK hospitals using hospital activity data from 28 October 2019 (pre-COVID-19) to 10 May 2020 (pre-easing of lockdown) and for the same weeks during 2018-2019. We analysed aggregate data for selected cardiovascular diseases before and during the epidemic. We produced an online visualisation tool to enable near real-time monitoring of trends.<h4>Results</h4>Across nine hospitals, total admissions and emergency department (ED) attendances decreased after lockdown (23 March 2020) by 57.9% (57.1%-58.6%) and 52.9% (52.2%-53.5%), respectively, compared with the previous year. Activity for cardiac, cerebrovascular and other vascular conditions started to decline 1-2 weeks before lockdown and fell by 31%-88% after lockdown, with the greatest reductions observed for coronary artery bypass grafts, carotid endarterectomy, aortic aneurysm repair and peripheral arterial disease procedures. Compared with before the first UK COVID-19 (31 January 2020), activity declined across diseases and specialties between the first case and lockdown (total ED attendances relative reduction (RR) 0.94, 0.93-0.95; total hospital admissions RR 0.96, 0.95-0.97) and after lockdown (attendances RR 0.63, 0.62-0.64; admissions RR 0.59, 0.57-0.60). There was limited recovery towards usual levels of some activities from mid-April 2020.<h4>Conclusions</h4>Substantial reductions in total and cardiovascular activities are likely to contribute to a major burden of indirect effects of the pandemic, suggesting they should be monitored and mitigated urgently.",,pdf:https://heart.bmj.com/content/heartjnl/106/24/1890.full.pdf; doi:https://doi.org/10.1136/heartjnl-2020-317870; html:https://europepmc.org/articles/PMC7536637; pdf:https://europepmc.org/articles/PMC7536637?pdf=render
 31612961,https://doi.org/10.1093/nar/gkz895,GWAS Central: a comprehensive resource for the discovery and comparison of genotype and phenotype data from genome-wide association studies.,"Beck T, Shorter T, Brookes AJ.",,Nucleic acids research,2020,2020-01-01,Y,,,,"The GWAS Central resource provides a toolkit for integrative access and visualization of a uniquely extensive collection of genome-wide association study data, while ensuring safe open access to prevent research participant identification. GWAS Central is the world's most comprehensive openly accessible repository of summary-level GWAS association information, providing over 70 million P-values for over 3800 studies investigating over 1400 unique phenotypes. The database content comprises direct submissions received from GWAS authors and consortia, in addition to actively gathered data sets from various public sources. GWAS data are discoverable from the perspective of genetic markers, genes, genome regions or phenotypes, via graphical visualizations and detailed downloadable data reports. Tested genetic markers and relevant genomic features can be visually interrogated across up to sixteen multiple association data sets in a single view using the integrated genome browser. The semantic standardization of phenotype descriptions with Medical Subject Headings and the Human Phenotype Ontology allows the precise identification of genetic variants associated with diseases, phenotypes and traits of interest. Harmonization of the phenotype descriptions used across several GWAS-related resources has extended the phenotype search capabilities to enable cross-database study discovery using a range of ontologies. GWAS Central is updated regularly and available at https://www.gwascentral.org.",,pdf:https://academic.oup.com/nar/article-pdf/48/D1/D933/31697824/gkz895.pdf; doi:https://doi.org/10.1093/nar/gkz895; html:https://europepmc.org/articles/PMC7145571; pdf:https://europepmc.org/articles/PMC7145571?pdf=render
-38378812,https://doi.org/10.1007/s00127-024-02620-6,Understanding social and clinical associations with unemployment for people with schizophrenia and bipolar disorders: large-scale health records study.,"Chilman N, Laporte D, Dorrington S, Hatch SL, Morgan C, Okoroji C, Stewart R, Das-Munshi J.",,Social psychiatry and psychiatric epidemiology,2024,2024-02-20,Y,Schizophrenia; Bipolar disorder; Employment; Ethnicity; Occupation; Natural Language Processing,,,"<h4>Purpose</h4>People with severe mental illness (SMI) experience high levels of unemployment. We aimed to better understand the associations between clinical, social, and demographic inequality indicators and unemployment.<h4>Methods</h4>Data were extracted from de-identified health records of people with SMI in contact with secondary mental health services in south London, UK. A Natural Language Processing text-mining application was applied to extract information on unemployment in the health records. Multivariable logistic regression was used to assess associations with unemployment, in people with SMI.<h4>Results</h4>Records from 19,768 service users were used for analysis, 84.9% (n = 16,778) had experienced unemployment. In fully adjusted models, Black Caribbean and Black African service users were more likely to experience unemployment compared with White British service users (Black Caribbean: aOR 1.62, 95% CI 1.45-1.80; Black African: 1.32, 1.15-1.51). Although men were more likely to have experienced unemployment relative to women in unadjusted models (OR 1.36, 95% CI 1.26-1.47), differences were no longer apparent in the fully adjusted models (aOR 1.05, 95% CI 0.97-1.15). The presence of a non-affective (compared to affective) diagnosis (1.24, 1.13-1.35), comorbid substance use (2.02, 1.76-2.33), previous inpatient admissions (4.18, 3.71-4.70), longer inpatient stays (78 + days: 7.78, 6.34-9.54), and compulsory admissions (3.45, 3.04-3.92) were associated with unemployment, in fully adjusted models.<h4>Conclusion</h4>People with SMI experience high levels of unemployment, and we found that unemployment was associated with several clinical and social factors. Interventions to address low employment may need to also address these broader inequalities.",,pdf:https://link.springer.com/content/pdf/10.1007/s00127-024-02620-6.pdf; doi:https://doi.org/10.1007/s00127-024-02620-6; html:https://europepmc.org/articles/PMC11464607; pdf:https://europepmc.org/articles/PMC11464607?pdf=render
+36472984,https://doi.org/10.1371/journal.pmed.1004124,Association between antidementia medication use and mortality in people diagnosed with dementia with Lewy bodies in the UK: A retrospective cohort study.,"Chen S, Price AC, Cardinal RN, Moylett S, Kershenbaum AD, Fitzgerald J, Mueller C, Stewart R, O'Brien JT.",,PLoS medicine,2022,2022-12-06,Y,,,,"<h4>Background</h4>Dementia with Lewy bodies (DLBs) is a common cause of dementia but has higher mortality than Alzheimer's disease (AD). The reasons for this are unclear, but antidementia drugs (including acetylcholinesterase inhibitors [AChEIs] and memantine) symptomatically benefit people with DLB and might improve outcomes. We investigated whether AChEIs and/or memantine were associated with reduced hospital admissions and mortality.<h4>Methods and findings</h4>We performed a retrospective cohort study of those diagnosed with DLB between 1 January 2005 and 31 December 2019, using data from electronic clinical records of secondary care mental health services in Cambridgeshire and Peterborough NHS Foundation Trust (CPFT), United Kingdom (catchment area population approximately 0.86 million), as well as linked records from national Hospital Episode Statistics (HES) data. Eligible patients were those who started AChEIs or memantine within 3 months of their diagnosis (cases) and those who never used AChEIs or memantine (controls). Outcomes included admission, length of stay, and mortality. Cox proportional hazard and linear regression models were used. Of 592 patients with DLB, 219 never took AChEIs or memantine, 100 took AChEIs only, and 273 took both AChEIs and memantine. The cohorts were followed up for an average of 896 days, 981 days, and 1,004 days, respectively. There were no significant differences in the cohorts' baseline characteristics, except for socioeconomic status that was lower in patients who never took AChEIs or memantine (χ2 = 23.34, P = 0.003). After controlling for confounding by sociodemographic factors (age, sex, marital status, ethnicity, socioeconomic status), antipsychotic use, antidepressant use, cognitive status, physical comorbidity, anticholinergic burden, and global health performance, compared with patients who never took AChEIs or memantine, patients taking AChEIs only or taking both had a significantly lower risk of death (adjusted hazard ratio (HR) = 0.67, 95% CI = 0.48 to 0.93, p = 0.02; adjusted HR = 0.64, 95% CI = 0.50 to 0.83, P = 0.001, respectively). Those taking AChEIs or both AChEIs and memantine had significantly shorter periods of unplanned hospital admission for physical disorders (adjusted coefficient -13.48, 95% CI = [-26.87, -0.09], P = 0.049; adjusted coefficient -14.21, 95% CI = [-24.58, -3.85], P = 0.007, respectively), but no difference in length of stay for planned admissions for physical disorders, or for admissions for mental health disorders. No significant additional associations of memantine on admission, length of stay, and mortality were found (all P > 0.05). The main limitation was that this was a naturalistic study and possible confounds cannot be fully controlled, and there may be selection bias resulting from nonrandom prescription behaviour in clinical practice. However, we mimicked the intention-to-treat design of clinical trials, and the majority of baseline characters were balanced between cohorts. In addition, our series of sensitivity analyses confirmed the consistency of our results.<h4>Conclusion</h4>In this study, we observed that use of AChEIs with or without memantine in DLB was associated with shorter duration of hospital admissions and decreased risk of mortality. Although our study was naturalistic, it supports further the use of AChEIs in DLB.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004124&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004124; html:https://europepmc.org/articles/PMC9725132; pdf:https://europepmc.org/articles/PMC9725132?pdf=render
 36992264,https://doi.org/10.3390/vaccines11030680,"Determinants of Equity in Coverage of Measles-Containing Vaccines in Wales, UK, during the Elimination Era.","Perry M, Cottrell S, Gravenor MB, Griffiths L.",,Vaccines,2023,2023-03-17,Y,"Vaccination; Measles; Socioeconomic Factors; Immunisation; Mmr; Measles, Mumps And Rubella Vaccine",,,"In the context of the WHO's measles and rubella elimination targets and European Immunization Agenda 2030, this large cross-sectional study aimed to identify inequalities in measles vaccination coverage in Wales, UK. The vaccination status of individuals aged 2 to 25 years of age, alive and resident in Wales as of 31 August 2021, was ascertained through linkage of the National Community Child Health Database and primary care data. A series of predictor variables were derived from five national datasets and all analysis was carried out in the Secure Anonymised Information Linkage Databank at Swansea University. In these 648,895 individuals, coverage of the first dose of measles-containing vaccine (due at 12-13 months of age) was 97.1%, and coverage of the second dose (due at 3 years and 4 months) in 4 to 25-year-olds was 93.8%. In multivariable analysis, excluding 0.7% with known refusal, the strongest association with being unvaccinated was birth order (families with six or more children) and being born outside of the UK. Living in a deprived area, being eligible for free school meals, a lower level of maternal education, and having a recorded language other than English or Welsh were also associated with lower coverage. Some of these factors may also be associated with refusal. This knowledge can be used to target future interventions and prioritise areas for catch up in a time of limited resource.",,pdf:https://www.mdpi.com/2076-393X/11/3/680/pdf?version=1679031223; doi:https://doi.org/10.3390/vaccines11030680; html:https://europepmc.org/articles/PMC10057771; pdf:https://europepmc.org/articles/PMC10057771?pdf=render
 36227072,https://doi.org/10.1093/jamia/ocac203,Transforming and evaluating the UK Biobank to the OMOP Common Data Model for COVID-19 research and beyond.,"Papez V, Moinat M, Voss EA, Bazakou S, Van Winzum A, Peviani A, Payralbe S, Kallfelz M, Asselbergs FW, Prieto-Alhambra D, Dobson RJB, Denaxas S.",,Journal of the American Medical Informatics Association : JAMIA,2022,2022-12-01,Y,Phenotyping; Electronic Health Records; Omop; Common Data Model; Medical Ontologies,,,"<h4>Objective</h4>The coronavirus disease 2019 (COVID-19) pandemic has demonstrated the value of real-world data for public health research. International federated analyses are crucial for informing policy makers. Common data models (CDMs) are critical for enabling these studies to be performed efficiently. Our objective was to convert the UK Biobank, a study of 500 000 participants with rich genetic and phenotypic data to the Observational Medical Outcomes Partnership (OMOP) CDM.<h4>Materials and methods</h4>We converted UK Biobank data to OMOP CDM v. 5.3. We transformedparticipant research data on diseases collected at recruitment and electronic health records (EHRs) from primary care, hospitalizations, cancer registrations, and mortality from providers in England, Scotland, and Wales. We performed syntactic and semantic validations and compared comorbidities and risk factors between source and transformed data.<h4>Results</h4>We identified 502 505 participants (3086 with COVID-19) and transformed 690 fields (1 373 239 555 rows) to the OMOP CDM using 8 different controlled clinical terminologies and bespoke mappings. Specifically, we transformed self-reported noncancer illnesses 946 053 (83.91% of all source entries), cancers 37 802 (70.81%), medications 1 218 935 (88.25%), and prescriptions 864 788 (86.96%). In EHR, we transformed 13 028 182 (99.95%) hospital diagnoses, 6 465 399 (89.2%) procedures, 337 896 333 primary care diagnoses (CTV3, SNOMED-CT), 139 966 587 (98.74%) prescriptions (dm+d) and 77 127 (99.95%) deaths (ICD-10). We observed good concordance across demographic, risk factor, and comorbidity factors between source and transformed data.<h4>Discussion and conclusion</h4>Our study demonstrated that the OMOP CDM can be successfully leveraged to harmonize complex large-scale biobanked studies combining rich multimodal phenotypic data. Our study uncovered several challenges when transforming data from questionnaires to the OMOP CDM which require further research. The transformed UK Biobank resource is a valuable tool that can enable federated research, like COVID-19 studies.",,pdf:https://academic.oup.com/jamia/article-pdf/30/1/103/47829607/ocac203.pdf; doi:https://doi.org/10.1093/jamia/ocac203; html:https://europepmc.org/articles/PMC9619789; pdf:https://europepmc.org/articles/PMC9619789?pdf=render
-36472984,https://doi.org/10.1371/journal.pmed.1004124,Association between antidementia medication use and mortality in people diagnosed with dementia with Lewy bodies in the UK: A retrospective cohort study.,"Chen S, Price AC, Cardinal RN, Moylett S, Kershenbaum AD, Fitzgerald J, Mueller C, Stewart R, O'Brien JT.",,PLoS medicine,2022,2022-12-06,Y,,,,"<h4>Background</h4>Dementia with Lewy bodies (DLBs) is a common cause of dementia but has higher mortality than Alzheimer's disease (AD). The reasons for this are unclear, but antidementia drugs (including acetylcholinesterase inhibitors [AChEIs] and memantine) symptomatically benefit people with DLB and might improve outcomes. We investigated whether AChEIs and/or memantine were associated with reduced hospital admissions and mortality.<h4>Methods and findings</h4>We performed a retrospective cohort study of those diagnosed with DLB between 1 January 2005 and 31 December 2019, using data from electronic clinical records of secondary care mental health services in Cambridgeshire and Peterborough NHS Foundation Trust (CPFT), United Kingdom (catchment area population approximately 0.86 million), as well as linked records from national Hospital Episode Statistics (HES) data. Eligible patients were those who started AChEIs or memantine within 3 months of their diagnosis (cases) and those who never used AChEIs or memantine (controls). Outcomes included admission, length of stay, and mortality. Cox proportional hazard and linear regression models were used. Of 592 patients with DLB, 219 never took AChEIs or memantine, 100 took AChEIs only, and 273 took both AChEIs and memantine. The cohorts were followed up for an average of 896 days, 981 days, and 1,004 days, respectively. There were no significant differences in the cohorts' baseline characteristics, except for socioeconomic status that was lower in patients who never took AChEIs or memantine (χ2 = 23.34, P = 0.003). After controlling for confounding by sociodemographic factors (age, sex, marital status, ethnicity, socioeconomic status), antipsychotic use, antidepressant use, cognitive status, physical comorbidity, anticholinergic burden, and global health performance, compared with patients who never took AChEIs or memantine, patients taking AChEIs only or taking both had a significantly lower risk of death (adjusted hazard ratio (HR) = 0.67, 95% CI = 0.48 to 0.93, p = 0.02; adjusted HR = 0.64, 95% CI = 0.50 to 0.83, P = 0.001, respectively). Those taking AChEIs or both AChEIs and memantine had significantly shorter periods of unplanned hospital admission for physical disorders (adjusted coefficient -13.48, 95% CI = [-26.87, -0.09], P = 0.049; adjusted coefficient -14.21, 95% CI = [-24.58, -3.85], P = 0.007, respectively), but no difference in length of stay for planned admissions for physical disorders, or for admissions for mental health disorders. No significant additional associations of memantine on admission, length of stay, and mortality were found (all P > 0.05). The main limitation was that this was a naturalistic study and possible confounds cannot be fully controlled, and there may be selection bias resulting from nonrandom prescription behaviour in clinical practice. However, we mimicked the intention-to-treat design of clinical trials, and the majority of baseline characters were balanced between cohorts. In addition, our series of sensitivity analyses confirmed the consistency of our results.<h4>Conclusion</h4>In this study, we observed that use of AChEIs with or without memantine in DLB was associated with shorter duration of hospital admissions and decreased risk of mortality. Although our study was naturalistic, it supports further the use of AChEIs in DLB.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004124&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004124; html:https://europepmc.org/articles/PMC9725132; pdf:https://europepmc.org/articles/PMC9725132?pdf=render
+38378812,https://doi.org/10.1007/s00127-024-02620-6,Understanding social and clinical associations with unemployment for people with schizophrenia and bipolar disorders: large-scale health records study.,"Chilman N, Laporte D, Dorrington S, Hatch SL, Morgan C, Okoroji C, Stewart R, Das-Munshi J.",,Social psychiatry and psychiatric epidemiology,2024,2024-02-20,Y,Schizophrenia; Bipolar disorder; Employment; Ethnicity; Occupation; Natural Language Processing,,,"<h4>Purpose</h4>People with severe mental illness (SMI) experience high levels of unemployment. We aimed to better understand the associations between clinical, social, and demographic inequality indicators and unemployment.<h4>Methods</h4>Data were extracted from de-identified health records of people with SMI in contact with secondary mental health services in south London, UK. A Natural Language Processing text-mining application was applied to extract information on unemployment in the health records. Multivariable logistic regression was used to assess associations with unemployment, in people with SMI.<h4>Results</h4>Records from 19,768 service users were used for analysis, 84.9% (n = 16,778) had experienced unemployment. In fully adjusted models, Black Caribbean and Black African service users were more likely to experience unemployment compared with White British service users (Black Caribbean: aOR 1.62, 95% CI 1.45-1.80; Black African: 1.32, 1.15-1.51). Although men were more likely to have experienced unemployment relative to women in unadjusted models (OR 1.36, 95% CI 1.26-1.47), differences were no longer apparent in the fully adjusted models (aOR 1.05, 95% CI 0.97-1.15). The presence of a non-affective (compared to affective) diagnosis (1.24, 1.13-1.35), comorbid substance use (2.02, 1.76-2.33), previous inpatient admissions (4.18, 3.71-4.70), longer inpatient stays (78 + days: 7.78, 6.34-9.54), and compulsory admissions (3.45, 3.04-3.92) were associated with unemployment, in fully adjusted models.<h4>Conclusion</h4>People with SMI experience high levels of unemployment, and we found that unemployment was associated with several clinical and social factors. Interventions to address low employment may need to also address these broader inequalities.",,pdf:https://link.springer.com/content/pdf/10.1007/s00127-024-02620-6.pdf; doi:https://doi.org/10.1007/s00127-024-02620-6; html:https://europepmc.org/articles/PMC11464607; pdf:https://europepmc.org/articles/PMC11464607?pdf=render
 37158960,https://doi.org/10.1186/s40168-023-01518-w,Pathobionts in the tumour microbiota predict survival following resection for colorectal cancer.,"Alexander JL, Posma JM, Scott A, Poynter L, Mason SE, Doria ML, Herendi L, Roberts L, McDonald JAK, Cameron S, Hughes DJ, Liska V, Susova S, Soucek P, der Sluis VH, Gomez-Romero M, Lewis MR, Hoyles L, Woolston A, Cunningham D, Darzi A, Gerlinger M, Goldin R, Takats Z, Marchesi JR, Teare J, Kinross J.",,Microbiome,2023,2023-05-08,Y,metabolome; Colorectal Cancer; Gut Microbiota; Metataxonomics,,,"<h4>Background and aims</h4>The gut microbiota is implicated in the pathogenesis of colorectal cancer (CRC). We aimed to map the CRC mucosal microbiota and metabolome and define the influence of the tumoral microbiota on oncological outcomes.<h4>Methods</h4>A multicentre, prospective observational study was conducted of CRC patients undergoing primary surgical resection in the UK (n = 74) and Czech Republic (n = 61). Analysis was performed using metataxonomics, ultra-performance liquid chromatography-mass spectrometry (UPLC-MS), targeted bacterial qPCR and tumour exome sequencing. Hierarchical clustering accounting for clinical and oncological covariates was performed to identify clusters of bacteria and metabolites linked to CRC. Cox proportional hazards regression was used to ascertain clusters associated with disease-free survival over median follow-up of 50 months.<h4>Results</h4>Thirteen mucosal microbiota clusters were identified, of which five were significantly different between tumour and paired normal mucosa. Cluster 7, containing the pathobionts Fusobacterium nucleatum and Granulicatella adiacens, was strongly associated with CRC (P<sub>FDR</sub> = 0.0002). Additionally, tumoral dominance of cluster 7 independently predicted favourable disease-free survival (adjusted p = 0.031). Cluster 1, containing Faecalibacterium prausnitzii and Ruminococcus gnavus, was negatively associated with cancer (P<sub>FDR</sub> = 0.0009), and abundance was independently predictive of worse disease-free survival (adjusted p = 0.0009). UPLC-MS analysis revealed two major metabolic (Met) clusters. Met 1, composed of medium chain (MCFA), long-chain (LCFA) and very long-chain (VLCFA) fatty acid species, ceramides and lysophospholipids, was negatively associated with CRC (P<sub>FDR</sub> = 2.61 × 10<sup>-11</sup>); Met 2, composed of phosphatidylcholine species, nucleosides and amino acids, was strongly associated with CRC (P<sub>FDR</sub> = 1.30 × 10<sup>-12</sup>), but metabolite clusters were not associated with disease-free survival (p = 0.358). An association was identified between Met 1 and DNA mismatch-repair deficiency (p = 0.005). FBXW7 mutations were only found in cancers predominant in microbiota cluster 7.<h4>Conclusions</h4>Networks of pathobionts in the tumour mucosal niche are associated with tumour mutation and metabolic subtypes and predict favourable outcome following CRC resection. Video Abstract.",,pdf:https://microbiomejournal.biomedcentral.com/counter/pdf/10.1186/s40168-023-01518-w; doi:https://doi.org/10.1186/s40168-023-01518-w; html:https://europepmc.org/articles/PMC10165813; pdf:https://europepmc.org/articles/PMC10165813?pdf=render
 32614817,https://doi.org/10.1371/journal.pcbi.1008031,Estimation of country-level basic reproductive ratios for novel Coronavirus (SARS-CoV-2/COVID-19) using synthetic contact matrices.,"Hilton J, Keeling MJ.",,PLoS computational biology,2020,2020-07-02,Y,,,,"The 2019-2020 pandemic of atypical pneumonia (COVID-19) caused by the virus SARS-CoV-2 has spread globally and has the potential to infect large numbers of people in every country. Estimating the country-specific basic reproductive ratio is a vital first step in public-health planning. The basic reproductive ratio (R0) is determined by both the nature of pathogen and the network of human contacts through which the disease can spread, which is itself dependent on population age structure and household composition. Here we introduce a transmission model combining age-stratified contact frequencies with age-dependent susceptibility, probability of clinical symptoms, and transmission from asymptomatic (or mild) cases, which we use to estimate the country-specific basic reproductive ratio of COVID-19 for 152 countries. Using early outbreak data from China and a synthetic contact matrix, we estimate an age-stratified transmission structure which can then be extrapolated to 151 other countries for which synthetic contact matrices also exist. This defines a set of country-specific transmission structures from which we can calculate the basic reproductive ratio for each country. Our predicted R0 is critically sensitive to the intensity of transmission from asymptomatic cases; with low asymptomatic transmission the highest values are predicted across Eastern Europe and Japan and the lowest across Africa, Central America and South-Western Asia. This pattern is largely driven by the ratio of children to older adults in each country and the observed propensity of clinical cases in the elderly. If asymptomatic cases have comparable transmission to detected cases, the pattern is reversed. Our results demonstrate the importance of age-specific heterogeneities going beyond contact structure to the spread of COVID-19. These heterogeneities give COVID-19 the capacity to spread particularly quickly in countries with older populations, and that intensive control measures are likely to be necessary to impede its progress in these countries.",,pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008031&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1008031; html:https://europepmc.org/articles/PMC7363110; pdf:https://europepmc.org/articles/PMC7363110?pdf=render
 33082154,https://doi.org/10.1136/bmj.m3731,Living risk prediction algorithm (QCOVID) for risk of hospital admission and mortality from coronavirus 19 in adults: national derivation and validation cohort study.,"Clift AK, Coupland CAC, Keogh RH, Diaz-Ordaz K, Williamson E, Harrison EM, Hayward A, Hemingway H, Horby P, Mehta N, Benger J, Khunti K, Spiegelhalter D, Sheikh A, Valabhji J, Lyons RA, Robson J, Semple MG, Kee F, Johnson P, Jebb S, Williams T, Hippisley-Cox J.",,BMJ (Clinical research ed.),2020,2020-10-20,Y,,,,"<h4>Objective</h4>To derive and validate a risk prediction algorithm to estimate hospital admission and mortality outcomes from coronavirus disease 2019 (covid-19) in adults.<h4>Design</h4>Population based cohort study.<h4>Setting and participants</h4>QResearch database, comprising 1205 general practices in England with linkage to covid-19 test results, Hospital Episode Statistics, and death registry data. 6.08 million adults aged 19-100 years were included in the derivation dataset and 2.17 million in the validation dataset. The derivation and first validation cohort period was 24 January 2020 to 30 April 2020. The second temporal validation cohort covered the period 1 May 2020 to 30 June 2020.<h4>Main outcome measures</h4>The primary outcome was time to death from covid-19, defined as death due to confirmed or suspected covid-19 as per the death certification or death occurring in a person with confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the period 24 January to 30 April 2020. The secondary outcome was time to hospital admission with confirmed SARS-CoV-2 infection. Models were fitted in the derivation cohort to derive risk equations using a range of predictor variables. Performance, including measures of discrimination and calibration, was evaluated in each validation time period.<h4>Results</h4>4384 deaths from covid-19 occurred in the derivation cohort during follow-up and 1722 in the first validation cohort period and 621 in the second validation cohort period. The final risk algorithms included age, ethnicity, deprivation, body mass index, and a range of comorbidities. The algorithm had good calibration in the first validation cohort. For deaths from covid-19 in men, it explained 73.1% (95% confidence interval 71.9% to 74.3%) of the variation in time to death (R<sup>2</sup>); the D statistic was 3.37 (95% confidence interval 3.27 to 3.47), and Harrell's C was 0.928 (0.919 to 0.938). Similar results were obtained for women, for both outcomes, and in both time periods. In the top 5% of patients with the highest predicted risks of death, the sensitivity for identifying deaths within 97 days was 75.7%. People in the top 20% of predicted risk of death accounted for 94% of all deaths from covid-19.<h4>Conclusion</h4>The QCOVID population based risk algorithm performed well, showing very high levels of discrimination for deaths and hospital admissions due to covid-19. The absolute risks presented, however, will change over time in line with the prevailing SARS-C0V-2 infection rate and the extent of social distancing measures in place, so they should be interpreted with caution. The model can be recalibrated for different time periods, however, and has the potential to be dynamically updated as the pandemic evolves.",,pdf:https://www.bmj.com/content/bmj/371/bmj.m3731.full.pdf; doi:https://doi.org/10.1136/bmj.m3731; html:https://europepmc.org/articles/PMC7574532; pdf:https://europepmc.org/articles/PMC7574532?pdf=render
 38735523,https://doi.org/10.1016/j.ejvs.2024.05.010,Challenges of Using Routinely Collected Healthcare System Data in Randomised Trials.,"Twine CP, Ahmed H, Lugg-Widger FV, Waldron CA, Bown MJ, Sydes MR.",,European journal of vascular and endovascular surgery : the official journal of the European Society for Vascular Surgery,2024,2024-05-10,N,Diseases; Cohort; Analyses; Randomised Clinical Trials; Peripheral Arterial; Clinical Research Methodology,,,,,doi:https://doi.org/10.1016/j.ejvs.2024.05.010
-39132877,https://doi.org/10.1002/ehf2.15011,Risk factors for raised left ventricular filling pressure by cardiovascular magnetic resonance: Prognostic insights.,"Thomson RJ, Grafton-Clarke C, Matthews G, Swoboda PP, Swift AJ, Frangi A, Petersen SE, Aung N, Garg P.",,ESC heart failure,2024,2024-08-12,N,MRI; Cardiovascular Magnetic Resonance; Left Ventricular Filling Pressure; Heart Failure Epidemiology,,,"<h4>Background</h4>Cardiovascular magnetic resonance (CMR) imaging shows promise in estimating pulmonary capillary wedge pressure (PCWP) non-invasively. At the population level, the prognostic role of CMR-modelled PCWP remains unknown. Furthermore, the relationship between CMR-modelled PCWP and established risk factors for cardiovascular disease has not been well characterized.<h4>Objective</h4>The main aim of this study was to investigate the prognostic value of CMR-modelled PCWP at the population level.<h4>Methods</h4>Employing data from the imaging substudy of the UK Biobank, a very large prospective population-based cohort study, CMR-modelled PCWP was calculated using a model incorporating left atrial volume, left ventricular mass and sex. Logistic regression explored the relationships between typical cardiovascular risk factors and raised CMR-modelled PCWP (≥15 mmHg). Cox regression was used to examine the impact of typical risk factors and CMR-modelled PCWP on heart failure (HF) and major adverse cardiovascular events (MACE).<h4>Results</h4>Data from 39 163 participants were included in the study. Median age of all participants was 64 years (inter-quartile range: 58 to 70), and 47% were males. Clinical characteristics independently associated with raised CMR-modelled PCWP included hypertension [odds ratio (OR) 1.57, 95% confidence interval (CI) 1.44-1.70, P < 0.001], body mass index (BMI) [OR 1.57, 95% CI 1.52-1.62, per standard deviation (SD) increment, P < 0.001], male sex (OR 1.37, 95% CI 1.26-1.47, P < 0.001), age (OR 1.33, 95% CI 1.27-1.41, per decade increment, P < 0.001) and regular alcohol consumption (OR 1.10, 95% CI 1.02-1.19, P = 0.012). After adjusting for potential confounders, CMR-modelled PCWP was independently associated with incident HF [hazard ratio (HR) 2.91, 95% CI 2.07-4.07, P < 0.001] and MACE (HR 1.48, 95% CI 1.16-1.89, P = 0.002).<h4>Conclusions</h4>Raised CMR-modelled PCWP is an independent risk factor for incident HF and MACE. CMR-modelled PCWP should be incorporated into routine CMR reports to guide HF diagnosis and further management.",,doi:https://doi.org/10.1002/ehf2.15011; doi:https://doi.org/10.1002/ehf2.15011
 36384890,https://doi.org/10.1136/bmj-2022-071932,Comparative effectiveness of sotrovimab and molnupiravir for prevention of severe covid-19 outcomes in patients in the community: observational cohort study with the OpenSAFELY platform.,"Zheng B, Green ACA, Tazare J, Curtis HJ, Fisher L, Nab L, Schultze A, Mahalingasivam V, Parker EPK, Hulme WJ, Bacon SCJ, DeVito NJ, Bates C, Evans D, Inglesby P, Drysdale H, Davy S, Cockburn J, Morton CE, Hickman G, Ward T, Smith RM, Parry J, Hester F, Harper S, Mehrkar A, Eggo RM, Walker AJ, Evans SJW, Douglas IJ, MacKenna B, Goldacre B, Tomlinson LA.",,BMJ (Clinical research ed.),2022,2022-11-16,Y,,,,"<h4>Objective</h4>To compare the effectiveness of sotrovimab (a neutralising monoclonal antibody) with molnupiravir (an antiviral) in preventing severe outcomes of covid-19 in adult patients infected with SARS-CoV-2 in the community and at high risk of severe outcomes from covid-19.<h4>Design</h4>Observational cohort study with the OpenSAFELY platform.<h4>Setting</h4>With the approval of NHS England, a real world cohort study was conducted with the OpenSAFELY-TPP platform (a secure, transparent, open source software platform for analysis of NHS electronic health records), and patient level electronic health record data were obtained from 24 million people registered with a general practice in England that uses TPP software. The primary care data were securely linked with data on SARS-CoV-2 infection and treatments, hospital admission, and death, over a period when both drug treatments were frequently prescribed in community settings.<h4>Participants</h4>Adult patients with covid-19 in the community at high risk of severe outcomes from covid-19, treated with sotrovimab or molnupiravir from 16 December 2021.<h4>Interventions</h4>Sotrovimab or molnupiravir given in the community by covid-19 medicine delivery units.<h4>Main outcome measures</h4>Admission to hospital with covid-19 (ie, with covid-19 as the primary diagnosis) or death from covid-19 (ie, with covid-19 as the underlying or contributing cause of death) within 28 days of the start of treatment.<h4>Results</h4>Between 16 December 2021 and 10 February 2022, 3331 and 2689 patients were treated with sotrovimab and molnupiravir, respectively, with no substantial differences in baseline characteristics. Mean age of all 6020 patients was 52 (standard deviation 16) years; 59% were women, 89% were white, and 88% had received three or more covid-19 vaccinations. Within 28 days of the start of treatment, 87 (1.4%) patients were admitted to hospital or died of infection from SARS-CoV-2 (32 treated with sotrovimab and 55 with molnupiravir). Cox proportional hazards models stratified by area showed that after adjusting for demographic information, high risk cohort categories, vaccination status, calendar time, body mass index, and other comorbidities, treatment with sotrovimab was associated with a substantially lower risk than treatment with molnupiravir (hazard ratio 0.54, 95% confidence interval 0.33 to 0.88, P=0.01). Consistent results were found from propensity score weighted Cox models (0.50, 0.31 to 0.81, P=0.005) and when restricted to people who were fully vaccinated (0.53, 0.31 to 0.90, P=0.02). No substantial effect modifications by other characteristics were detected (all P values for interaction >0.10). The findings were similar in an exploratory analysis of patients treated between 16 February and 1 May 2022 when omicron BA.2 was the predominant variant in England.<h4>Conclusions</h4>In routine care of adult patients in England with covid-19 in the community, at high risk of severe outcomes from covid-19, those who received sotrovimab were at lower risk of severe outcomes of covid-19 than those treated with molnupiravir.",,pdf:https://www.bmj.com/content/bmj/379/bmj-2022-071932.full.pdf; doi:https://doi.org/10.1136/bmj-2022-071932; html:https://europepmc.org/articles/PMC9667468
-33200120,https://doi.org/10.1016/j.eclinm.2020.100630,Ethnicity and clinical outcomes in COVID-19: A systematic review and meta-analysis.,"Sze S, Pan D, Nevill CR, Gray LJ, Martin CA, Nazareth J, Minhas JS, Divall P, Khunti K, Abrams KR, Nellums LB, Pareek M.",,EClinicalMedicine,2020,2020-11-12,Y,Infection; Transmission; RACE; Death; Ethnicity; Outcome; Asian; Hispanic; Ethnic; Sars-cov-2; Covid-19 Black; Disporportionate; Itu Admission,,,"<h4>Background</h4>Patients from ethnic minority groups are disproportionately affected by Coronavirus disease (COVID-19). We performed a systematic review and meta-analysis to explore the relationship between ethnicity and clinical outcomes in COVID-19.<h4>Methods</h4>Databases (MEDLINE, EMBASE, PROSPERO, Cochrane library and <i>MedRxiv</i>) were searched up to 31st August 2020, for studies reporting COVID-19 data disaggregated by ethnicity. Outcomes were: risk of infection; intensive therapy unit (ITU) admission and death. PROSPERO ID: 180654.<h4>Findings</h4>18,728,893 patients from 50 studies were included; 26 were peer-reviewed; 42 were from the United States of America and 8 from the United Kingdom. Individuals from Black and Asian ethnicities had a higher risk of COVID-19 infection compared to White individuals. This was consistent in both the main analysis (pooled adjusted RR for Black: 2.02, 95% CI 1.67-2.44; pooled adjusted RR for Asian: 1.50, 95% CI 1.24-1.83) and sensitivity analyses examining peer-reviewed studies only (pooled adjusted RR for Black: 1.85, 95%CI: 1.46-2.35; pooled adjusted RR for Asian: 1.51, 95% CI 1.22-1.88). Individuals of Asian ethnicity may also be at higher risk of ITU admission (pooled adjusted RR 1.97 95% CI 1.34-2.89) (but no studies had yet been peer-reviewed) and death (pooled adjusted RR/HR 1.22 [0.99-1.50]).<h4>Interpretation</h4>Individuals of Black and Asian ethnicity are at increased risk of COVID-19 infection compared to White individuals; Asians may be at higher risk of ITU admission and death. These findings are of critical public health importance in informing interventions to reduce morbidity and mortality amongst ethnic minority groups.",,pdf:https://figshare.com/articles/journal_contribution/Ethnicity_and_clinical_outcomes_in_COVID-19_A_Systematic_Review_and_Meta-analysis/13147892/1/files/25502810.pdf; doi:https://doi.org/10.1016/j.eclinm.2020.100630; html:https://europepmc.org/articles/PMC7658622; pdf:https://europepmc.org/articles/PMC7658622?pdf=render
+39132877,https://doi.org/10.1002/ehf2.15011,Risk factors for raised left ventricular filling pressure by cardiovascular magnetic resonance: Prognostic insights.,"Thomson RJ, Grafton-Clarke C, Matthews G, Swoboda PP, Swift AJ, Frangi A, Petersen SE, Aung N, Garg P.",,ESC heart failure,2024,2024-08-12,N,MRI; Cardiovascular Magnetic Resonance; Left Ventricular Filling Pressure; Heart Failure Epidemiology,,,"<h4>Background</h4>Cardiovascular magnetic resonance (CMR) imaging shows promise in estimating pulmonary capillary wedge pressure (PCWP) non-invasively. At the population level, the prognostic role of CMR-modelled PCWP remains unknown. Furthermore, the relationship between CMR-modelled PCWP and established risk factors for cardiovascular disease has not been well characterized.<h4>Objective</h4>The main aim of this study was to investigate the prognostic value of CMR-modelled PCWP at the population level.<h4>Methods</h4>Employing data from the imaging substudy of the UK Biobank, a very large prospective population-based cohort study, CMR-modelled PCWP was calculated using a model incorporating left atrial volume, left ventricular mass and sex. Logistic regression explored the relationships between typical cardiovascular risk factors and raised CMR-modelled PCWP (≥15 mmHg). Cox regression was used to examine the impact of typical risk factors and CMR-modelled PCWP on heart failure (HF) and major adverse cardiovascular events (MACE).<h4>Results</h4>Data from 39 163 participants were included in the study. Median age of all participants was 64 years (inter-quartile range: 58 to 70), and 47% were males. Clinical characteristics independently associated with raised CMR-modelled PCWP included hypertension [odds ratio (OR) 1.57, 95% confidence interval (CI) 1.44-1.70, P < 0.001], body mass index (BMI) [OR 1.57, 95% CI 1.52-1.62, per standard deviation (SD) increment, P < 0.001], male sex (OR 1.37, 95% CI 1.26-1.47, P < 0.001), age (OR 1.33, 95% CI 1.27-1.41, per decade increment, P < 0.001) and regular alcohol consumption (OR 1.10, 95% CI 1.02-1.19, P = 0.012). After adjusting for potential confounders, CMR-modelled PCWP was independently associated with incident HF [hazard ratio (HR) 2.91, 95% CI 2.07-4.07, P < 0.001] and MACE (HR 1.48, 95% CI 1.16-1.89, P = 0.002).<h4>Conclusions</h4>Raised CMR-modelled PCWP is an independent risk factor for incident HF and MACE. CMR-modelled PCWP should be incorporated into routine CMR reports to guide HF diagnosis and further management.",,doi:https://doi.org/10.1002/ehf2.15011; doi:https://doi.org/10.1002/ehf2.15011
 37128667,https://doi.org/10.1111/bjhp.12666,A qualitative process evaluation using the behaviour change wheel approach: Did a whole genome sequence report form (SRF) used to reduce nosocomial SARS-CoV-2 within UK hospitals operate as anticipated?,"Flowers P, Leiser R, Mapp F, McLeod J, Stirrup O, Illingworth CJR, Blackstone J, Breuer J.",,British journal of health psychology,2023,2023-05-01,Y,Hospital; Behaviour Change; Infection Prevention And Control; Behaviour Change Wheel; Covid-19; Sequence Report Form,,,"<h4>Purpose</h4>The aim of this study was to conduct a process evaluation of a whole-genome sequence report form (SRF) used to reduce nosocomial SARS-CoV-2 through changing infection prevention and control (IPC) behaviours within the COVID-19 pandemic.<h4>Methods</h4>We used a three-staged design. Firstly, we described and theorized the purported content of the SRF using the behaviour change wheel (BCW). Secondly, we used inductive thematic analysis of one-to-one interviews (n = 39) to explore contextual accounts of using the SRF. Thirdly, further deductive analysis gauged support for the intervention working as earlier anticipated.<h4>Results</h4>It was possible to theorize the SRF using the BCW approach and visualize it within a simple logic model. Inductive thematic analyses identified the SRF's acceptability, ease of use and perceived effectiveness. However, major challenges to embedding it in routine practice during the unfolding COVID-19 crisis were reported. Notwithstanding this insight, deductive analysis showed support for the putative intervention functions 'Education', 'Persuasion' and 'Enablement'; behaviour change techniques '1.2 Problem solving', '2.6 Biofeedback', '2.7 Feedback on outcomes of behaviour' and '7.1 Prompts and cues'; and theoretical domains framework domains 'Knowledge' and 'Behavioural regulation'.<h4>Conclusions</h4>Our process evaluation of the SRF, using the BCW approach to describe and theorize its content, provided granular support for the SRF working to change IPC behaviours as anticipated. However, our complementary inductive thematic analysis highlighted the importance of the local context in constraining its routine use. For SRFs to reach their full potential in reducing nosocomial infections, further implementation research is needed.",,doi:https://doi.org/10.1111/bjhp.12666; doi:https://doi.org/10.1111/bjhp.12666; html:https://europepmc.org/articles/PMC11497355; pdf:https://europepmc.org/articles/PMC11497355?pdf=render
-PMC9644860,https://doi.org/,Maternal mental health and children’s development: a bi-directional relationship?,"Lowthian E, Bedston S, Akbari A, Katz A, Huxley K, Johnson R, Kristensen S, Owen R, Taylor C, Griffiths L.",,International journal of population data science,,2022-11-21,Y,,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9644860/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9644860/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC9644860; pdf:https://europepmc.org/articles/PMC9644860?pdf=render
+33200120,https://doi.org/10.1016/j.eclinm.2020.100630,Ethnicity and clinical outcomes in COVID-19: A systematic review and meta-analysis.,"Sze S, Pan D, Nevill CR, Gray LJ, Martin CA, Nazareth J, Minhas JS, Divall P, Khunti K, Abrams KR, Nellums LB, Pareek M.",,EClinicalMedicine,2020,2020-11-12,Y,Infection; Transmission; RACE; Death; Ethnicity; Outcome; Asian; Hispanic; Ethnic; Sars-cov-2; Covid-19 Black; Disporportionate; Itu Admission,,,"<h4>Background</h4>Patients from ethnic minority groups are disproportionately affected by Coronavirus disease (COVID-19). We performed a systematic review and meta-analysis to explore the relationship between ethnicity and clinical outcomes in COVID-19.<h4>Methods</h4>Databases (MEDLINE, EMBASE, PROSPERO, Cochrane library and <i>MedRxiv</i>) were searched up to 31st August 2020, for studies reporting COVID-19 data disaggregated by ethnicity. Outcomes were: risk of infection; intensive therapy unit (ITU) admission and death. PROSPERO ID: 180654.<h4>Findings</h4>18,728,893 patients from 50 studies were included; 26 were peer-reviewed; 42 were from the United States of America and 8 from the United Kingdom. Individuals from Black and Asian ethnicities had a higher risk of COVID-19 infection compared to White individuals. This was consistent in both the main analysis (pooled adjusted RR for Black: 2.02, 95% CI 1.67-2.44; pooled adjusted RR for Asian: 1.50, 95% CI 1.24-1.83) and sensitivity analyses examining peer-reviewed studies only (pooled adjusted RR for Black: 1.85, 95%CI: 1.46-2.35; pooled adjusted RR for Asian: 1.51, 95% CI 1.22-1.88). Individuals of Asian ethnicity may also be at higher risk of ITU admission (pooled adjusted RR 1.97 95% CI 1.34-2.89) (but no studies had yet been peer-reviewed) and death (pooled adjusted RR/HR 1.22 [0.99-1.50]).<h4>Interpretation</h4>Individuals of Black and Asian ethnicity are at increased risk of COVID-19 infection compared to White individuals; Asians may be at higher risk of ITU admission and death. These findings are of critical public health importance in informing interventions to reduce morbidity and mortality amongst ethnic minority groups.",,pdf:https://figshare.com/articles/journal_contribution/Ethnicity_and_clinical_outcomes_in_COVID-19_A_Systematic_Review_and_Meta-analysis/13147892/1/files/25502810.pdf; doi:https://doi.org/10.1016/j.eclinm.2020.100630; html:https://europepmc.org/articles/PMC7658622; pdf:https://europepmc.org/articles/PMC7658622?pdf=render
 33185672,https://doi.org/10.1093/jamia/ocaa295,Ensemble learning for poor prognosis predictions: A case study on SARS-CoV-2.,"Wu H, Zhang H, Karwath A, Ibrahim Z, Shi T, Zhang X, Wang K, Sun J, Dhaliwal K, Bean D, Cardoso VR, Li K, Teo JT, Banerjee A, Gao-Smith F, Whitehouse T, Veenith T, Gkoutos GV, Wu X, Dobson R, Guthrie B.",,Journal of the American Medical Informatics Association : JAMIA,2021,2021-03-01,Y,Decision Support; Risk Prediction; Ensemble Learning; Covid-19; Model Synergy,,,"<h4>Objective</h4>Risk prediction models are widely used to inform evidence-based clinical decision making. However, few models developed from single cohorts can perform consistently well at population level where diverse prognoses exist (such as the SARS-CoV-2 [severe acute respiratory syndrome coronavirus 2] pandemic). This study aims at tackling this challenge by synergizing prediction models from the literature using ensemble learning.<h4>Materials and methods</h4>In this study, we selected and reimplemented 7 prediction models for COVID-19 (coronavirus disease 2019) that were derived from diverse cohorts and used different implementation techniques. A novel ensemble learning framework was proposed to synergize them for realizing personalized predictions for individual patients. Four diverse international cohorts (2 from the United Kingdom and 2 from China; N = 5394) were used to validate all 8 models on discrimination, calibration, and clinical usefulness.<h4>Results</h4>Results showed that individual prediction models could perform well on some cohorts while poorly on others. Conversely, the ensemble model achieved the best performances consistently on all metrics quantifying discrimination, calibration, and clinical usefulness. Performance disparities were observed in cohorts from the 2 countries: all models achieved better performances on the China cohorts.<h4>Discussion</h4>When individual models were learned from complementary cohorts, the synergized model had the potential to achieve better performances than any individual model. Results indicate that blood parameters and physiological measurements might have better predictive powers when collected early, which remains to be confirmed by further studies.<h4>Conclusions</h4>Combining a diverse set of individual prediction models, the ensemble method can synergize a robust and well-performing model by choosing the most competent ones for individual patients.",,pdf:https://academic.oup.com/jamia/article-pdf/28/4/791/41182395/ocaa295.pdf; doi:https://doi.org/10.1093/jamia/ocaa295; html:https://europepmc.org/articles/PMC7717299; pdf:https://europepmc.org/articles/PMC7717299?pdf=render
+PMC9644860,https://doi.org/,Maternal mental health and children’s development: a bi-directional relationship?,"Lowthian E, Bedston S, Akbari A, Katz A, Huxley K, Johnson R, Kristensen S, Owen R, Taylor C, Griffiths L.",,International journal of population data science,,2022-11-21,Y,,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9644860/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9644860/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC9644860; pdf:https://europepmc.org/articles/PMC9644860?pdf=render
 35953587,https://doi.org/10.1038/s41588-022-01153-5,A multi-tissue atlas of regulatory variants in cattle.,"Liu S, Gao Y, Canela-Xandri O, Wang S, Yu Y, Cai W, Li B, Xiang R, Chamberlain AJ, Pairo-Castineira E, D'Mellow K, Rawlik K, Xia C, Yao Y, Navarro P, Rocha D, Li X, Yan Z, Li C, Rosen BD, Van Tassell CP, Vanraden PM, Zhang S, Ma L, Cole JB, Liu GE, Tenesa A, Fang L.",,Nature genetics,2022,2022-08-11,Y,,,,"Characterization of genetic regulatory variants acting on livestock gene expression is essential for interpreting the molecular mechanisms underlying traits of economic value and for increasing the rate of genetic gain through artificial selection. Here we build a Cattle Genotype-Tissue Expression atlas (CattleGTEx) as part of the pilot phase of the Farm animal GTEx (FarmGTEx) project for the research community based on 7,180 publicly available RNA-sequencing (RNA-seq) samples. We describe the transcriptomic landscape of more than 100 tissues/cell types and report hundreds of thousands of genetic associations with gene expression and alternative splicing for 23 distinct tissues. We evaluate the tissue-sharing patterns of these genetic regulatory effects, and functionally annotate them using multiomics data. Finally, we link gene expression in different tissues to 43 economically important traits using both transcriptome-wide association and colocalization analyses to decipher the molecular regulatory mechanisms underpinning such agronomic traits in cattle.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7613894; doi:https://doi.org/10.1038/s41588-022-01153-5; html:https://europepmc.org/articles/PMC7613894; pdf:https://europepmc.org/articles/PMC7613894?pdf=render
-38811438,https://doi.org/10.1007/s00586-024-08315-5,Early evaluation of a natural language processing tool to improve access to educational resources for surgical patients.,"Booker J, Penn J, Noor K, Dobson RJB, Funnell JP, Koh CH, Khan DZ, Newall N, Rowland D, Sinha S, Williams SC, Sayal P, Marcus HJ.",,"European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society",2024,2024-05-30,Y,Spine; Education; Machine Learning; Natural Language Processing; automation,,,"<h4>Purpose</h4>Accessible patient information sources are vital in educating patients about the benefits and risks of spinal surgery, which is crucial for obtaining informed consent. We aim to assess the effectiveness of a natural language processing (NLP) pipeline in recognizing surgical procedures from clinic letters and linking this with educational resources.<h4>Methods</h4>Retrospective examination of letters from patients seeking surgery for degenerative spinal disease at a single neurosurgical center. We utilized MedCAT, a named entity recognition and linking NLP, integrated into the electronic health record (EHR), which extracts concepts and links them to systematized nomenclature of medicine-clinical terms (SNOMED-CT). Investigators reviewed clinic letters, identifying words or phrases that described or identified operations and recording the SNOMED-CT terms as ground truth. This was compared to SNOMED-CT terms identified by the model, untrained on our dataset. A pipeline linking clinic letters to patient-specific educational resources was established, and precision, recall, and F1 scores were calculated.<h4>Results</h4>Across 199 letters the model identified 582 surgical procedures, and the overall pipeline after adding rules a total of 784 procedures (precision = 0.94, recall = 0.86, F1 = 0.91). Across 187 letters with identified SNOMED-CT terms the integrated pipeline linking education resources directly to the EHR was successful in 157 (78%) patients (precision = 0.99, recall = 0.87, F1 = 0.92).<h4>Conclusions</h4>NLP accurately identifies surgical procedures in pre-operative clinic letters within an untrained subspecialty. Performance varies among letter authors and depends on the language used by clinicians. The identified procedures can be linked to patient education resources, potentially improving patients' understanding of surgical procedures.",,doi:https://doi.org/10.1007/s00586-024-08315-5; doi:https://doi.org/10.1007/s00586-024-08315-5; html:https://europepmc.org/articles/PMC11269391; pdf:https://europepmc.org/articles/PMC11269391?pdf=render
 31249320,https://doi.org/10.1038/s41598-019-45562-9,"Antenatal exposure to solar radiation and learning disabilities: Population cohort study of 422,512 children.","Hastie CE, Mackay DF, Clemens TL, Cherrie MPC, King A, Dibben C, Pell JP.",,Scientific reports,2019,2019-06-27,Y,,Improving Public Health,,"Learning disability varies by month of conception. The underlying mechanism is unknown but vitamin D, necessary for normal brain development, is commonly deficient over winter in high latitude countries due to insufficient ultraviolet radiation. We linked the 2007-2016 Scottish School Pupil Censuses to Scottish maternity records and to sunshine hours and antenatal ultraviolet A/B radiation exposure derived from weather stations and satellites respectively. Logistic regression analyses were used to explore the associations between solar radiation, then ultraviolet B, and learning disabilities, adjusting for the potential confounding effects of month of conception and sex. Of the 422,512 eligible, singleton schoolchildren born at term in Scotland, 79,616 (18.8%) had a learning disability. Total antenatal sunshine hours (highest quintile; adjusted OR 0.89; 95% CI: 0.86, 0.93; p < 0.001) and ultraviolet B exposure (highest quintile; adjusted OR 0.55; 95% CI: 0.51, 0.60; p < 0.001) were inversely associated with learning disabilities with evidence of a dose-relationship. The latter association was independent of ultraviolet A exposure. Significant associations were demonstrated for exposure in all three trimesters. Low maternal exposure to ultraviolet B radiation may play a role in the seasonal patterning of learning disabilities. Further studies are required to corroborate findings and determine the effectiveness of supplements.",,pdf:https://www.nature.com/articles/s41598-019-45562-9.pdf; doi:https://doi.org/10.1038/s41598-019-45562-9; html:https://europepmc.org/articles/PMC6597711; pdf:https://europepmc.org/articles/PMC6597711?pdf=render
-37800588,https://doi.org/10.1097/js9.0000000000000781,Safety outcomes of bariatric surgery in patients with advanced organ disease: the ONWARD study: a prospective cohort study.,"Singhal R, Cardoso VR, Wiggins T, Rajeev Y, Ludwig C, Gkoutos GV, Hanif W, Mahawar K, ONWARD & GENEVA collaborators.",,"International journal of surgery (London, England)",2024,2024-01-01,Y,,,,"<h4>Introduction</h4>Increasing numbers of patients with advanced organ disease are being considered for bariatric and metabolic surgery (BMS). There is no prospective study on the safety of BMS in these patients. This study aimed to capture outcomes for patients with advanced cardiac, renal, or liver disease undergoing BMS.<h4>Materials and methods</h4>This was a multinational, prospective cohort study on the safety of elective BMS in adults (≥18 years) with advanced disease of the heart, liver, or kidney.<h4>Results</h4>Data on 177 patients with advanced diseases of heart, liver, or kidney were submitted by 75 centres in 33 countries. Mean age and BMI was 48.56±11.23 years and 45.55±7.35 kg/m 2 , respectively. Laparoscopic sleeve gastrectomy was performed in 124 patients (70%). The 30-day morbidity and mortality were 15.9% ( n =28) and 1.1% ( n =2), respectively. Thirty-day morbidity was 16.4%, 11.7%, 20.5%, and 50.0% in patients with advanced heart ( n =11/61), liver ( n =8/68), kidney ( n =9/44), and multi-organ disease ( n =2/4), respectively. Cardiac patients with left ventricular ejection fraction less than or equal to 35% and New York Heart Association classification 3 or 4, liver patients with model for end-stage liver disease score greater than or equal to 12, and patients with advanced renal disease not on dialysis were at increased risk of complications. Comparison with a propensity score-matched cohort found advanced disease of the heart, liver, or kidney to be significantly associated with higher 30-day morbidity.<h4>Conclusion</h4>Patients with advanced organ disease are at increased risk of 30-day morbidity following BMS. This prospective study quantifies that risk and identifies patients at the highest risk.",,html:https://journals.lww.com/international-journal-of-surgery/abstract/9900/safety_outcomes_of_bariatric_surgery_in_patients.696.aspx; doi:https://doi.org/10.1097/JS9.0000000000000781; html:https://europepmc.org/articles/PMC10793784; pdf:https://europepmc.org/articles/PMC10793784?pdf=render
+38811438,https://doi.org/10.1007/s00586-024-08315-5,Early evaluation of a natural language processing tool to improve access to educational resources for surgical patients.,"Booker J, Penn J, Noor K, Dobson RJB, Funnell JP, Koh CH, Khan DZ, Newall N, Rowland D, Sinha S, Williams SC, Sayal P, Marcus HJ.",,"European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society",2024,2024-05-30,Y,Spine; Education; Machine Learning; Natural Language Processing; automation,,,"<h4>Purpose</h4>Accessible patient information sources are vital in educating patients about the benefits and risks of spinal surgery, which is crucial for obtaining informed consent. We aim to assess the effectiveness of a natural language processing (NLP) pipeline in recognizing surgical procedures from clinic letters and linking this with educational resources.<h4>Methods</h4>Retrospective examination of letters from patients seeking surgery for degenerative spinal disease at a single neurosurgical center. We utilized MedCAT, a named entity recognition and linking NLP, integrated into the electronic health record (EHR), which extracts concepts and links them to systematized nomenclature of medicine-clinical terms (SNOMED-CT). Investigators reviewed clinic letters, identifying words or phrases that described or identified operations and recording the SNOMED-CT terms as ground truth. This was compared to SNOMED-CT terms identified by the model, untrained on our dataset. A pipeline linking clinic letters to patient-specific educational resources was established, and precision, recall, and F1 scores were calculated.<h4>Results</h4>Across 199 letters the model identified 582 surgical procedures, and the overall pipeline after adding rules a total of 784 procedures (precision = 0.94, recall = 0.86, F1 = 0.91). Across 187 letters with identified SNOMED-CT terms the integrated pipeline linking education resources directly to the EHR was successful in 157 (78%) patients (precision = 0.99, recall = 0.87, F1 = 0.92).<h4>Conclusions</h4>NLP accurately identifies surgical procedures in pre-operative clinic letters within an untrained subspecialty. Performance varies among letter authors and depends on the language used by clinicians. The identified procedures can be linked to patient education resources, potentially improving patients' understanding of surgical procedures.",,doi:https://doi.org/10.1007/s00586-024-08315-5; doi:https://doi.org/10.1007/s00586-024-08315-5; html:https://europepmc.org/articles/PMC11269391; pdf:https://europepmc.org/articles/PMC11269391?pdf=render
 36434299,https://doi.org/10.1007/s00127-022-02393-w,Adverse outcomes associated with recorded victimization in mental health electronic records during the first UK COVID-19 lockdown.,"Kadra-Scalzo G, Kornblum D, Stewart R, Howard LM.",,Social psychiatry and psychiatric epidemiology,2023,2022-11-24,Y,Mental health; Domestic Violence; Victimisation; Adverse Outcomes; Covid-19,,,"<h4>Purpose</h4>The impact of COVID-19 pandemic policies on vulnerable groups such as people with mental health problems who experience violence remains unknown. This study aimed to investigate the prevalence of victimization recorded in mental healthcare records during the first UK lockdown, and associations with subsequent adverse outcomes.<h4>Methods</h4>Using a large mental healthcare database, we identified all adult patients receiving services between 16.12.2019 and 15.06.2020 and extracted records of victimisation between 16.03.2020 and 15.06.2020 (first UK COVID-19 lockdown). We investigated adverse outcomes including acute care, emergency department referrals and all-cause mortality in the year following the lockdown (16.06.2020- 01.11.2021). Multivariable Cox regressions models were constructed, adjusting for socio-demographic, socioeconomic, clinical, and service use factors.<h4>Results</h4>Of 21,037 adults receiving mental healthcare over the observation period, 3,610 (17.2%) had victimisation mentioned between 16.03.2020 and 15.06.2020 (first UK COVID-19 lockdown). Service users with mentions of victimisation in their records had an elevated risk for all outcomes: acute care (adjusted HR: 2.1; 95%CI 1.9-2.3, p < 0.001), emergency department referrals (aHR: 2.0; 95%CI 1.8-2.2; p < 0.001), and all-cause mortality (aHR: 1.5; 95%CI 1.1-1.9; p = 0.003), when compared to service users with no recorded victimisation. We did not observe a statistically significant interaction with gender; however, after adjusting for possible confounders, men had slightly higher hazard ratios for all-cause mortality and emergency department referrals than women.<h4>Conclusion</h4>Patients with documented victimisation during the first UK lockdown were at increased risk for acute care, emergency department referrals and all-cause mortality. Further research is needed into mediating mechanisms.",,pdf:https://link.springer.com/content/pdf/10.1007/s00127-022-02393-w.pdf; doi:https://doi.org/10.1007/s00127-022-02393-w; html:https://europepmc.org/articles/PMC9702612; pdf:https://europepmc.org/articles/PMC9702612?pdf=render
+37800588,https://doi.org/10.1097/js9.0000000000000781,Safety outcomes of bariatric surgery in patients with advanced organ disease: the ONWARD study: a prospective cohort study.,"Singhal R, Cardoso VR, Wiggins T, Rajeev Y, Ludwig C, Gkoutos GV, Hanif W, Mahawar K, ONWARD & GENEVA collaborators.",,"International journal of surgery (London, England)",2024,2024-01-01,Y,,,,"<h4>Introduction</h4>Increasing numbers of patients with advanced organ disease are being considered for bariatric and metabolic surgery (BMS). There is no prospective study on the safety of BMS in these patients. This study aimed to capture outcomes for patients with advanced cardiac, renal, or liver disease undergoing BMS.<h4>Materials and methods</h4>This was a multinational, prospective cohort study on the safety of elective BMS in adults (≥18 years) with advanced disease of the heart, liver, or kidney.<h4>Results</h4>Data on 177 patients with advanced diseases of heart, liver, or kidney were submitted by 75 centres in 33 countries. Mean age and BMI was 48.56±11.23 years and 45.55±7.35 kg/m 2 , respectively. Laparoscopic sleeve gastrectomy was performed in 124 patients (70%). The 30-day morbidity and mortality were 15.9% ( n =28) and 1.1% ( n =2), respectively. Thirty-day morbidity was 16.4%, 11.7%, 20.5%, and 50.0% in patients with advanced heart ( n =11/61), liver ( n =8/68), kidney ( n =9/44), and multi-organ disease ( n =2/4), respectively. Cardiac patients with left ventricular ejection fraction less than or equal to 35% and New York Heart Association classification 3 or 4, liver patients with model for end-stage liver disease score greater than or equal to 12, and patients with advanced renal disease not on dialysis were at increased risk of complications. Comparison with a propensity score-matched cohort found advanced disease of the heart, liver, or kidney to be significantly associated with higher 30-day morbidity.<h4>Conclusion</h4>Patients with advanced organ disease are at increased risk of 30-day morbidity following BMS. This prospective study quantifies that risk and identifies patients at the highest risk.",,html:https://journals.lww.com/international-journal-of-surgery/abstract/9900/safety_outcomes_of_bariatric_surgery_in_patients.696.aspx; doi:https://doi.org/10.1097/JS9.0000000000000781; html:https://europepmc.org/articles/PMC10793784; pdf:https://europepmc.org/articles/PMC10793784?pdf=render
 32525266,https://doi.org/10.1002/jmri.27209,Radiomic Analysis of Native T<sub>1</sub> Mapping Images Discriminates Between MYH7 and MYBPC3-Related Hypertrophic Cardiomyopathy.,"Wang J, Yang F, Liu W, Sun J, Han Y, Li D, Gkoutos GV, Zhu Y, Chen Y.",,Journal of magnetic resonance imaging : JMRI,2020,2020-06-11,N,"Human genetics; Cardiomyopathy, hypertrophic; Support vector machine; Magnetic Resonance Imaging; Machine Learning",,,"<h4>Background</h4>The phenotype via conventional cardiac MRI analysis of MYH7 (β-myosin heavy chain)- and MYBPC3 (β-myosin-binding protein C)-associated hypertrophic cardiomyopathy (HCM) groups is similar. Few studies exist on the genotypic-phenotypic association as assessed by machine learning in HCM patients.<h4>Purpose</h4>To explore the phenotypic differences based on radiomics analysis of T<sub>1</sub> mapping images between MYH7 and MYBPC3-associated HCM subgroups.<h4>Study type</h4>Prospective observational study.<h4>Subjects</h4>In all, 102 HCM patients with pathogenic, or likely pathogenic mutation, in MYH7 (n = 68) or MYBPC3 (n = 34) genes.<h4>Field strength/sequence</h4>Cardiac MRI was performed at 3.0T with balanced steady-state free precession (bSSFP), phase-sensitive inversion recovery (PSIR) late gadolinium enhancement (LGE), and modified Look-Locker inversion recovery (MOLLI) T<sub>1</sub> mapping sequences.<h4>Assessment</h4>All patients underwent next-generation sequencing and Sanger genetic sequencing. Left ventricular native T<sub>1</sub> and LGE were analyzed. One hundred and fifty-seven radiomic features were extracted and modeled using a support vector machine (SVM) combined with principal component analysis (PCA). Each subgroup was randomly split 4:1 (feature selection / test validation).<h4>Statistical tests</h4>Mann-Whitney U-tests and Student's t-tests were performed to assess differences between subgroups. A receiver operating characteristic (ROC) curve was used to assess the model's ability to stratify patients based on radiomic features.<h4>Results</h4>There were no significant differences between MYH7- and MYBPC3-associated HCM subgroups based on traditional native T<sub>1</sub> values (global, basal, and middle short-axis slice native T<sub>1</sub> ; P = 0.760, 0.914, and 0.178, respectively). However, the SVM model combined with PCA achieved an accuracy and area under the curve (AUC) of 92.0% and 0.968 (95% confidence interval [CI]: 0.968-0.971), respectively. For the test validation dataset, the accuracy and AUC were 85.5% and 0.886 (95% CI: 0.881-0.901), respectively.<h4>Data conclusion</h4>Radiomic analysis of native T<sub>1</sub> mapping images may be able to discriminate between MYH7- and MYBPC3-associated HCM patients, exceeding the performance of conventional native T<sub>1</sub> values.<h4>Level of evidence</h4>3 TECHNICAL EFFICACY STAGE: 2 J. MAGN. RESON. IMAGING 2020;52:1714-1721.",,pdf:http://pure-oai.bham.ac.uk/ws/files/96738891/Manuscript_Clear_No_Blind.pdf; doi:https://doi.org/10.1002/jmri.27209
 31774502,https://doi.org/10.1093/ehjcvp/pvz071,An observational study of international normalized ratio control according to NICE criteria in patients with non-valvular atrial fibrillation: the SAIL Warfarin Out of Range Descriptors Study (SWORDS).,"Harris DE, Thayer D, Wang T, Brooks C, Murley G, Gravenor M, Hill NR, Lister S, Halcox J.",,European heart journal. Cardiovascular pharmacotherapy,2021,2021-01-01,Y,Atrial fibrillation; Warfarin; Pharmacoepidemiology,Improving Public Health,,"<h4>Aims</h4>In patients with non-valvular atrial fibrillation prescribed warfarin, the UK National Institute of Health and Care Excellence (NICE) defines poor anticoagulation as a time in therapeutic range (TTR) of <65%, any two international normalized ratios (INRs) within a 6-month period of ≤1.5 ('low'), two INRs ≥5 within 6 months, or any INR ≥8 ('high'). Our objectives were to (i) quantify the number of patients with poor INR control and (ii) describe the demographic and clinical characteristics associated with poor INR control.<h4>Method and results</h4>Linked anonymized health record data for Wales, UK (2006-2017) was used to evaluate patients prescribed warfarin who had at least 6 months of INR data. 32 380 patients were included. In total, 13 913 (43.0%) patients had at least one of the NICE markers of poor INR control. Importantly, in the 24 123 (74.6%) of the cohort with an acceptable TTR (≥65%), 5676 (23.5%) had either low or high INR readings at some point in their history. In a multivariable regression female gender, age (≥75 years), excess alcohol, diabetes heart failure, ischaemic heart disease, and respiratory disease were independently associated with all markers of poor INR control.<h4>Conclusion</h4>Acceptable INR control according to NICE standards is poor. Of those with an acceptable TTR (>65%), one-quarter still had unacceptably low or high INR levels according to NICE criteria. Thus, only using TTR to assess effectiveness with warfarin has the potential to miss a large number of patients with non-therapeutic INRs who are likely to be at increased risk.","This retrospective observational cohort study aimed to quanitfy the number of patients with non-valvular atrial fibrillation (NVAF) prescribed warfarin who exhibit NICE-defined poor international normalised ratio (INR) control. Another objective was to describe the relationship between demographic and clinical characteristics of these patients and poor INR control. The results from statistical analyses in this study suggest a considerable opportunity to improve both embloc and bleeding risk, eben though the relationship between poor INR control and these clinical outcomes remains to be determined.",pdf:https://academic.oup.com/ehjcvp/advance-article-pdf/doi/10.1093/ehjcvp/pvz071/31700014/pvz071.pdf; doi:https://doi.org/10.1093/ehjcvp/pvz071; html:https://europepmc.org/articles/PMC7811400; pdf:https://europepmc.org/articles/PMC7811400?pdf=render
 33152012,https://doi.org/10.1371/journal.pone.0241800,Effect of long-chain polyunsaturated fatty acids in infant formula on long-term cognitive function in childhood: A systematic review and meta-analysis of randomised controlled trials.,"Verfuerden ML, Dib S, Jerrim J, Fewtrell M, Gilbert RE.",,PloS one,2020,2020-11-05,Y,,,,<h4>Study registration</h4>PROSPERO registration numbers CRD42018105196 and CRD42018088868.,,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0241800&type=printable; doi:https://doi.org/10.1371/journal.pone.0241800; html:https://europepmc.org/articles/PMC7644261; pdf:https://europepmc.org/articles/PMC7644261?pdf=render
@@ -767,17 +767,18 @@ PMC9644860,https://doi.org/,Maternal mental health and children’s development:
 33632765,https://doi.org/10.1136/thoraxjnl-2020-215986,"Neutrophils in asthma: the good, the bad and the bacteria.","Crisford H, Sapey E, Rogers GB, Taylor S, Nagakumar P, Lokwani R, Simpson JL.",,Thorax,2021,2021-02-25,Y,Asthma; Bacterial Infection; Paediatric Asthma; Asthma Mechanisms; Neutrophil Biology,,,"Airway inflammation plays a key role in asthma pathogenesis but is heterogeneous in nature. There has been significant scientific discovery with regard to type 2-driven, eosinophil-dominated asthma, with effective therapies ranging from inhaled corticosteroids to novel biologics. However, studies suggest that approximately 1 in 5 adults with asthma have an increased proportion of neutrophils in their airways. These patients tend to be older, have potentially pathogenic airway bacteria and do not respond well to classical therapies. Currently, there are no specific therapeutic options for these patients, such as neutrophil-targeting biologics.Neutrophils comprise 70% of the total circulatory white cells and play a critical defence role during inflammatory and infective challenges. This makes them a problematic target for therapeutics. Furthermore, neutrophil functions change with age, with reduced microbial killing, increased reactive oxygen species release and reduced production of extracellular traps with advancing age. Therefore, different therapeutic strategies may be required for different age groups of patients.The pathogenesis of neutrophil-dominated airway inflammation in adults with asthma may reflect a counterproductive response to the defective neutrophil microbial killing seen with age, resulting in bystander damage to host airway cells and subsequent mucus hypersecretion and airway remodelling. However, in children with asthma, neutrophils are less associated with adverse features of disease, and it is possible that in children, neutrophils are less pathogenic.In this review, we explore the mechanisms of neutrophil recruitment, changes in cellular function across the life course and the implications this may have for asthma management now and in the future. We also describe the prevalence of neutrophilic asthma globally, with a focus on First Nations people of Australia, New Zealand and North America.",,pdf:https://thorax.bmj.com/content/thoraxjnl/76/8/835.full.pdf; doi:https://doi.org/10.1136/thoraxjnl-2020-215986; html:https://europepmc.org/articles/PMC8311087; pdf:https://europepmc.org/articles/PMC8311087?pdf=render
 36518792,https://doi.org/10.1097/txd.0000000000001398,Range and Consistency of Cardiovascular Outcomes Reported by Clinical Trials in Kidney Transplant Recipients: A Systematic Review.,"Wilson GJ, Van K, O'Lone E, Tong A, Craig JC, Sautenet B, Budde K, Forfang D, Gill J, Herrington WG, Jafar TH, Johnson DW, Krane V, Levin A, Malyszko J, Rossignol P, Sawinski D, Scholes-Robertons N, Strippoli G, Wang A, Winkelmayer WC, Hawley CM, Viecelli AK.",,Transplantation direct,2023,2022-12-07,Y,,,,"Cardiovascular disease is a major cause of morbidity and mortality in kidney transplant recipients. Trial evidence to improve cardiovascular outcomes is limited by inconsistent reporting of outcomes, which may also lack patient-relevance. This study aimed to assess the range and consistency of cardiovascular outcomes reported by contemporary trials in kidney transplant recipients.<h4>Methods</h4>A systematic review of all randomized controlled trials involving adult kidney transplant recipients that reported at least 1 cardiovascular outcome from January 2012 to December 2019 was performed, including Embase, MEDLINE, Cochrane, and ClinicalTrials.gov electronic databases. Trial characteristics were extracted and all levels of specification of the cardiovascular outcome measures reported were analyzed (the measure definition, metric' and method of aggregation). Measures assessing a similar aspect of cardiovascular disease were categorized into outcomes.<h4>Results</h4>From 93 eligible trials involving 27 609 participants, 490 outcome measures were identified. The outcome measures were grouped into 38 outcomes. A cardiovascular composite was the most common outcome reported (40 trials, 43%) followed by cardiovascular mortality (42%) and acute coronary syndrome (31%). Cardiovascular composite was also the most heterogeneous outcome with 77 measures reported followed by cardiovascular mortality (n = 58) and inflammatory biomarkers (n = 51). The most common cardiovascular composite outcome components reported were major cardiovascular events (18 trials), stroke unspecified (11 trials), and myocardial infarction unspecified (10 trials).<h4>Conclusions</h4>There is substantial heterogeneity in cardiovascular outcome reporting in kidney transplant trials.",,doi:https://doi.org/10.1097/txd.0000000000001398; doi:https://doi.org/10.1097/TXD.0000000000001398; html:https://europepmc.org/articles/PMC9742089; pdf:https://europepmc.org/articles/PMC9742089?pdf=render
 35501711,https://doi.org/10.1186/s12864-022-08562-0,Single-cell transcriptomic and chromatin accessibility analyses of dairy cattle peripheral blood mononuclear cells and their responses to lipopolysaccharide.,"Gao Y, Li J, Cai G, Wang Y, Yang W, Li Y, Zhao X, Li R, Gao Y, Tuo W, Baldwin RL, Li CJ, Fang L, Liu GE.",,BMC genomics,2022,2022-04-30,Y,Cattle; Lipopolysaccharide; Peripheral blood mononuclear cell; Single-cell Rna-seq; Single-cell Atac-seq,,,"<h4>Background</h4>Gram-negative bacteria are important pathogens in cattle, causing severe infectious diseases, including mastitis. Lipopolysaccharides (LPS) are components of the outer membrane of Gram-negative bacteria and crucial mediators of chronic inflammation in cattle. LPS modulations of bovine immune responses have been studied before. However, the single-cell transcriptomic and chromatin accessibility analyses of bovine peripheral blood mononuclear cells (PBMCs) and their responses to LPS stimulation were never reported.<h4>Results</h4>We performed single-cell RNA sequencing (scRNA-seq) and single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) in bovine PBMCs before and after LPS treatment and demonstrated that seven major cell types, which included CD4 T cells, CD8 T cells, and B cells, monocytes, natural killer cells, innate lymphoid cells, and dendritic cells. Bioinformatic analyses indicated that LPS could increase PBMC cell cycle progression, cellular differentiation, and chromatin accessibility. Gene analyses further showed significant changes in differential expression, transcription factor binding site, gene ontology, and regulatory interactions during the PBMC responses to LPS. Consistent with the findings of previous studies, LPS induced activation of monocytes and dendritic cells, likely through their upregulated TLR4 receptor. NF-κB was observed to be activated by LPS and an increased transcription of an array of pro-inflammatory cytokines, in agreement that NF-κB is an LPS-responsive regulator of innate immune responses. In addition, by integrating LPS-induced differentially expressed genes (DEGs) with large-scale GWAS of 45 complex traits in Holstein, we detected trait-relevant cell types. We found that selected DEGs were significantly associated with immune-relevant health, milk production, and body conformation traits.<h4>Conclusion</h4>This study provided the first scRNAseq and scATAC-seq data for cattle PBMCs and their responses to the LPS stimulation to the best of our knowledge. These results should also serve as valuable resources for the future study of the bovine immune system and open the door for discoveries about immune cell roles in complex traits like mastitis at single-cell resolution.",,pdf:https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-022-08562-0; doi:https://doi.org/10.1186/s12864-022-08562-0; html:https://europepmc.org/articles/PMC9063233; pdf:https://europepmc.org/articles/PMC9063233?pdf=render
-36713473,https://doi.org/10.1093/ofid/ofac694,Clinical Effectiveness of SARS-CoV-2 Booster Vaccine Against Omicron Infection in Residents and Staff of Long-term Care Facilities: A Prospective Cohort Study (VIVALDI).,"Stirrup O, Shrotri M, Adams NL, Krutikov M, Nacer-Laidi H, Azmi B, Palmer T, Fuller C, Irwin-Singer A, Baynton V, Tut G, Moss P, Hayward A, Copas A, Shallcross L.",,Open forum infectious diseases,2023,2022-12-29,Y,Vaccine Effectiveness; Long-term Care Facilities; Covid-19; Sars-cov-2; Omicron,,,"<h4>Background</h4>Successive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have caused severe disease in long-term care facility (LTCF) residents. Primary vaccination provides strong short-term protection, but data are limited on duration of protection following booster vaccines, particularly against the Omicron variant. We investigated the effectiveness of booster vaccination against infections, hospitalizations, and deaths among LTCF residents and staff in England.<h4>Methods</h4>We included residents and staff of LTCFs within the VIVALDI study (ISRCTN 14447421) who underwent routine, asymptomatic testing (December 12, 2021-March 31, 2022). Cox regression was used to estimate relative hazards of SARS-CoV-2 infection, and associated hospitalization and death at 0-13, 14-48, 49-83, 84-111, 112-139, and 140+ days after dose 3 of SARS-CoV-2 vaccination compared with 2 doses (after 84+ days), stratified by previous SARS-CoV-2 infection and adjusting for age, sex, LTCF capacity, and local SARS-CoV-2 incidence.<h4>Results</h4>A total of 14 175 residents and 19 793 staff were included. In residents without prior SARS-CoV-2 infection, infection risk was reduced 0-111 days after the first booster, but no protection was apparent after 112 days. Additional protection following booster vaccination waned but was still present at 140+ days for COVID-associated hospitalization (adjusted hazard ratio [aHR], 0.20; 95% CI, 0.06-0.63) and death (aHR, 0.50; 95% CI, 0.20-1.27). Most residents (64.4%) had received primary course vaccine of AstraZeneca, but this did not impact pre- or postbooster risk. Staff showed a similar pattern of waning booster effectiveness against infection, with few hospitalizations and no deaths.<h4>Conclusions</h4>Our findings suggest that booster vaccination provided sustained protection against severe outcomes following infection with the Omicron variant, but no protection against infection from 4 months onwards. Ongoing surveillance for SARS-CoV-2 in LTCFs is crucial.",,pdf:https://academic.oup.com/ofid/article-pdf/10/1/ofac694/48846221/ofac694.pdf; doi:https://doi.org/10.1093/ofid/ofac694; html:https://europepmc.org/articles/PMC9874026; pdf:https://europepmc.org/articles/PMC9874026?pdf=render
+39486906,https://doi.org/10.1016/s2468-2667(24)00228-7,Alcohol and mortality in Mexico: prospective study of 150 000 adults.,"Trichia E, Alegre-Díaz J, Aguilar-Ramirez D, Ramirez-Reyes R, Garcilazo-Ávila A, González-Carballo C, Bragg F, Friedrichs LG, Herrington WG, Holland L, Torres J, Wade R, Collins R, Peto R, Berumen J, Tapia-Conyer R, Kuri-Morales P, Emberson JR.",,The Lancet. Public health,2024,2024-11-01,N,,,,"<h4>Background</h4>Alcohol consumption is a leading cause of premature death globally, but there is no large-scale prospective evidence from Mexico.<h4>Methods</h4>The Mexico City Prospective Study recruited 150 000 adults aged 35 years or older between 1998 and 2004. Participants were followed up until Oct 1, 2022 for cause-specific mortality. Cox regression in those with no self-reported chronic disease at entry (adjusted for age, sex, district, education, physical activity, smoking, and diabetes) was used to relate baseline-reported alcohol consumption (never, former, occasional [less than monthly], and regular [at least monthly, split into <70, ≥70 to <140, ≥140 to <210, and ≥210 g/week]) to mortality at ages 35-74 from all causes, and from a pre-specified alcohol-related set of underlying causes. Heavy episodic drinking (normally consuming >5 [men] or >4 [women] drinks on a single occasion) and type of preferred drink were also examined.<h4>Findings</h4>Among 138 413 participants aged 35-74 years at recruitment, 21 136 (15%) were regular alcohol drinkers (14 863 [33%] men, 6273 [7%] women), of whom 13 383 (63%) favoured spirits and 6580 (31%) favoured beer. During follow-up, there were 13 889 deaths at ages 35-74 years, including 3067 deaths from the pre-specified alcohol-related causes. Overall, J-shaped associations with mortality were observed. Compared with occasional drinkers, those with baseline-reported consumption ≥210 g/week had 43% higher all-cause mortality (rate ratio [RR] 1·43 [95% CI 1·30-1·56]) and nearly three times the mortality from the pre-specified alcohol-related causes (2·77 [2·39-3·20]). Death from liver disease was strongly related to alcohol consumption; the RR comparing regular drinkers of ≥140 g/week with occasional drinkers was 4·03 (3·36-4·83). Compared with occasional light drinking, occasional heavy episodic drinking was associated with 20% higher alcohol-related mortality (1·20 [1·06-1·35]), and regular heavy episodic drinking was associated with 89% higher alcohol-related mortality (1·89 [1·67-2·15]). Drinks with alcohol percentages higher than spirits were associated with the greatest increased mortality risk, even after accounting for the total alcohol consumed.<h4>Interpretation</h4>In this Mexican population, higher alcohol consumption, episodic drinking, and very high percentage alcoholic products were all associated with increased mortality.<h4>Funding</h4>Wellcome Trust, the Mexican Health Ministry, the National Council of Science and Technology for Mexico, Cancer Research UK, British Heart Foundation, and the UK Medical Research Council.<h4>Translation</h4>For the Spanish translation of the abstract see Supplementary Materials section.",,doi:https://doi.org/10.1016/S2468-2667(24)00228-7
 36812617,https://doi.org/10.1371/journal.pdig.0000162,Informing antimicrobial stewardship with explainable AI.,"Cavallaro M, Moran E, Collyer B, McCarthy ND, Green C, Keeling MJ.",,PLOS digital health,2023,2023-01-05,Y,,,,"The accuracy and flexibility of artificial intelligence (AI) systems often comes at the cost of a decreased ability to offer an intuitive explanation of their predictions. This hinders trust and discourage adoption of AI in healthcare, exacerbated by concerns over liabilities and risks to patients' health in case of misdiagnosis. Providing an explanation for a model's prediction is possible due to recent advances in the field of interpretable machine learning. We considered a data set of hospital admissions linked to records of antibiotic prescriptions and susceptibilities of bacterial isolates. An appropriately trained gradient boosted decision tree algorithm, supplemented by a Shapley explanation model, predicts the likely antimicrobial drug resistance, with the odds of resistance informed by characteristics of the patient, admission data, and historical drug treatments and culture test results. Applying this AI-based system, we found that it substantially reduces the risk of mismatched treatment compared with the observed prescriptions. The Shapley values provide an intuitive association between observations/data and outcomes; the associations identified are broadly consistent with expectations based on prior knowledge from health specialists. The results, and the ability to attribute confidence and explanations, support the wider adoption of AI in healthcare.",,pdf:https://journals.plos.org/digitalhealth/article/file?id=10.1371/journal.pdig.0000162&type=printable; doi:https://doi.org/10.1371/journal.pdig.0000162; html:https://europepmc.org/articles/PMC9931350; pdf:https://europepmc.org/articles/PMC9931350?pdf=render
-36748660,https://doi.org/10.1111/head.14465,Depression and anxiety in women with idiopathic intracranial hypertension compared to migraine: A matched controlled cohort study.,"Mollan SP, Subramanian A, Perrins M, Nirantharakumar K, Adderley NJ, Sinclair AJ.",,Headache,2023,2023-02-07,Y,Depression; Migraine; Anxiety; epidemiology; Primary Care; Idiopathic Intracranial Hypertension,,,"<h4>Objective</h4>To evaluate mental health burden in women with idiopathic intracranial hypertension (IIH) compared to matched women with migraine and population controls.<h4>Background</h4>Depression and anxiety are recognized comorbid conditions in those with IIH and lead to worse predicted medical outcomes. The mental health burden in IIH has not been previously evaluated in a large, matched cohort study.<h4>Methods</h4>We performed a population-based matched, retrospective cohort study to explore mental health outcomes (depression and anxiety). We used data from IQVIA Medical Research Data, an anonymized, nationally representative primary care electronic medical records database in the United Kingdom, from January 1, 1995, to September 25, 2019. Women aged ≥16 years were eligible for inclusion. Women with IIH (exposure) were matched by age and body mass index with up to 10 control women without IIH but with migraine (migraine controls), and without IIH or migraine (population controls).<h4>Results</h4>A total of 3411 women with IIH, 30,879 migraine controls and 33,495 population controls were included. Of these, 237, 2372 and 1695 women with IIH, migraine controls and population controls, respectively, developed depression during follow-up, and 179, 1826 and 1197, respectively, developed anxiety. There was a greater hazard of depression and anxiety in IIH compared to population controls (adjusted hazard ratio [aHR] 1.38, 95% confidence interval [CI] 1.20-1.58; and aHR 1.40, 95% CI 1.19-1.64, respectively), while hazards were similar to migraine controls (aHR 0.98, 95% CI 0.86-1.13; and aHR 0.98, 95% CI 0.83-1.14, respectively).<h4>Conclusion</h4>Depression and anxiety burden in women with IIH is higher than in the general population, and comparable to that in matched women with migraine. This may indicate that presence of headache is a potential driver for comorbid depression and anxiety in IIH.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/head.14465; doi:https://doi.org/10.1111/head.14465; html:https://europepmc.org/articles/PMC10952318; pdf:https://europepmc.org/articles/PMC10952318?pdf=render
+36713473,https://doi.org/10.1093/ofid/ofac694,Clinical Effectiveness of SARS-CoV-2 Booster Vaccine Against Omicron Infection in Residents and Staff of Long-term Care Facilities: A Prospective Cohort Study (VIVALDI).,"Stirrup O, Shrotri M, Adams NL, Krutikov M, Nacer-Laidi H, Azmi B, Palmer T, Fuller C, Irwin-Singer A, Baynton V, Tut G, Moss P, Hayward A, Copas A, Shallcross L.",,Open forum infectious diseases,2023,2022-12-29,Y,Vaccine Effectiveness; Long-term Care Facilities; Covid-19; Sars-cov-2; Omicron,,,"<h4>Background</h4>Successive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have caused severe disease in long-term care facility (LTCF) residents. Primary vaccination provides strong short-term protection, but data are limited on duration of protection following booster vaccines, particularly against the Omicron variant. We investigated the effectiveness of booster vaccination against infections, hospitalizations, and deaths among LTCF residents and staff in England.<h4>Methods</h4>We included residents and staff of LTCFs within the VIVALDI study (ISRCTN 14447421) who underwent routine, asymptomatic testing (December 12, 2021-March 31, 2022). Cox regression was used to estimate relative hazards of SARS-CoV-2 infection, and associated hospitalization and death at 0-13, 14-48, 49-83, 84-111, 112-139, and 140+ days after dose 3 of SARS-CoV-2 vaccination compared with 2 doses (after 84+ days), stratified by previous SARS-CoV-2 infection and adjusting for age, sex, LTCF capacity, and local SARS-CoV-2 incidence.<h4>Results</h4>A total of 14 175 residents and 19 793 staff were included. In residents without prior SARS-CoV-2 infection, infection risk was reduced 0-111 days after the first booster, but no protection was apparent after 112 days. Additional protection following booster vaccination waned but was still present at 140+ days for COVID-associated hospitalization (adjusted hazard ratio [aHR], 0.20; 95% CI, 0.06-0.63) and death (aHR, 0.50; 95% CI, 0.20-1.27). Most residents (64.4%) had received primary course vaccine of AstraZeneca, but this did not impact pre- or postbooster risk. Staff showed a similar pattern of waning booster effectiveness against infection, with few hospitalizations and no deaths.<h4>Conclusions</h4>Our findings suggest that booster vaccination provided sustained protection against severe outcomes following infection with the Omicron variant, but no protection against infection from 4 months onwards. Ongoing surveillance for SARS-CoV-2 in LTCFs is crucial.",,pdf:https://academic.oup.com/ofid/article-pdf/10/1/ofac694/48846221/ofac694.pdf; doi:https://doi.org/10.1093/ofid/ofac694; html:https://europepmc.org/articles/PMC9874026; pdf:https://europepmc.org/articles/PMC9874026?pdf=render
 31398891,https://doi.org/10.3390/nu11081839,Intakes and Food Sources of Dietary Fibre and Their Associations with Measures of Body Composition and Inflammation in UK Adults: Cross-Sectional Analysis of the Airwave Health Monitoring Study.,"Gibson R, Eriksen R, Chambers E, Gao H, Aresu M, Heard A, Chan Q, Elliott P, Frost G.",,Nutrients,2019,2019-08-08,Y,Body composition; body mass index; Dietary fibre; C-reactive Protein; Waist Circumference; Uk Population; Airwave Health Monitoring Study; Food Sources Fibre,Improving Public Health,,"The purpose of this study was to investigate the associations between intakes of fibre from the main food sources of fibre in the UK diet with body mass index (BMI), percentage body fat (%BF), waist circumference (WC) and C-reactive protein (CRP). Participants enrolled in the Airwave Health Monitoring Study (2007-2012) with 7-day food records (<i>n</i> = 6898; 61% men) were included for cross-sectional analyses. General linear models evaluated associations across fifths of fibre intakes (total, vegetable, fruit, potato, whole grain and non-whole grain cereal) with BMI, %BF, WC and CRP. Fully adjusted analyses showed inverse linear trends across fifths of total fibre and fibre from fruit with all outcome measures (<i>p<sub>trend</sub></i> < 0.0001). Vegetable fibre intake showed an inverse association with WC (<i>p<sub>trend</sub></i> 0.0156) and CRP (<i>p<sub>trend</sub></i> 0.0005). Fibre from whole grain sources showed an inverse association with BMI (<i>p<sub>trend</sub></i> 0.0002), %BF (<i>p<sub>trend</sub></i> 0.0007) and WC (<i>p<sub>trend</sub></i> 0.0004). Non-whole grain cereal fibre showed an inverse association with BMI (<i>P<sub>trend</sub></i> 0.0095). Direct associations observed between potato fibre intake and measures of body composition and inflammation were attenuated in fully adjusted analyses controlling for fried potato intake. Higher fibre intake has a beneficial association on body composition, however, there are differential associations based on the food source.",,pdf:https://www.mdpi.com/2072-6643/11/8/1839/pdf?version=1565745447; doi:https://doi.org/10.3390/nu11081839; html:https://europepmc.org/articles/PMC6722677; pdf:https://europepmc.org/articles/PMC6722677?pdf=render
 39113083,https://doi.org/10.1186/s12916-024-03399-8,History of childhood maltreatment associated with hospitalization or death due to COVID-19: a cohort study.,"Wang Y, Ge F, Aspelund T, Ask H, Hauksdóttir A, Hu K, Jakobsdóttir J, Zoega H, Shen Q, Whalley HC, Pedersen OBV, Lehto K, Andreassen OA, Fang F, Song H, Valdimarsdóttir UA.",,BMC medicine,2024,2024-08-07,Y,Mortality; Psychiatric disorders; Hospitalization; Childhood Maltreatment; Covid-19,,,"<h4>Background</h4>Childhood maltreatment (CM) has been indicated in adverse health outcomes across the lifespan, including severe infection-related outcomes. Yet, data are scarce on the potential role of CM in severe COVID-19-related outcomes as well as on mechanisms underlying this association.<h4>Methods</h4>We included 151,427 individuals in the UK Biobank who responded to questions on the history of CM in 2016 and 2017 and were alive on January 31, 2020. Binomial logistic regression models were performed to estimate the association between a history of CM and severe COVID-19 outcomes (i.e. hospitalization or death due to COVID-19), as well as COVID-19 diagnosis and vaccination as secondary outcomes. We then explored the potential mediating roles of socio-economic status, lifestyle and pre-pandemic comorbidities, and the effect modification by polygenic risk score for severe COVID-19 outcomes.<h4>Results</h4>The mean age of the study population at the start of the pandemic was 67.7 (SD = 7.72) years, and 56.5% were female. We found the number of CM types was associated with the risk of severe COVID-19 outcomes in a graded manner (p<sub>for trend</sub> < 0.01). Compared to individuals with no history of CM, individuals exposed to any CM were more likely to be hospitalized or die due to COVID-19 (odds ratio [OR] = 1.54 [95%CI 1.31-1.81]), particularly after physical neglect (2.04 [1.57-2.62]). Largely comparable risk patterns were observed across groups of high vs. low genetic risks for severe COVID-19 outcomes (p<sub>for difference</sub> > 0.05). Mediation analysis revealed that 50.9% of the association between CM and severe COVID-19 outcomes was explained by suboptimal socio-economic status, lifestyle, and pre-pandemic diagnosis of psychiatric disorders or other chronic medical conditions. In contrast, any CM exposure was only weakly associated with COVID-19 diagnosis (1.06 [1.01-1.12]) while significantly associated with not being vaccinated for COVID-19 (1.21 [1.13-1.29]).<h4>Conclusions</h4>Our results add to the growing knowledge base indicating the role of childhood maltreatment in negative health outcomes across the lifespan, including severe COVID-19-related outcomes. The identified factors underlying this association represent potential intervention targets for mitigating the harmful effects of childhood maltreatment in COVID-19 and similar future pandemics.",,doi:https://doi.org/10.1186/s12916-024-03399-8; html:https://europepmc.org/articles/PMC11304908; pdf:https://europepmc.org/articles/PMC11304908?pdf=render
+36748660,https://doi.org/10.1111/head.14465,Depression and anxiety in women with idiopathic intracranial hypertension compared to migraine: A matched controlled cohort study.,"Mollan SP, Subramanian A, Perrins M, Nirantharakumar K, Adderley NJ, Sinclair AJ.",,Headache,2023,2023-02-07,Y,Depression; Migraine; Anxiety; epidemiology; Primary Care; Idiopathic Intracranial Hypertension,,,"<h4>Objective</h4>To evaluate mental health burden in women with idiopathic intracranial hypertension (IIH) compared to matched women with migraine and population controls.<h4>Background</h4>Depression and anxiety are recognized comorbid conditions in those with IIH and lead to worse predicted medical outcomes. The mental health burden in IIH has not been previously evaluated in a large, matched cohort study.<h4>Methods</h4>We performed a population-based matched, retrospective cohort study to explore mental health outcomes (depression and anxiety). We used data from IQVIA Medical Research Data, an anonymized, nationally representative primary care electronic medical records database in the United Kingdom, from January 1, 1995, to September 25, 2019. Women aged ≥16 years were eligible for inclusion. Women with IIH (exposure) were matched by age and body mass index with up to 10 control women without IIH but with migraine (migraine controls), and without IIH or migraine (population controls).<h4>Results</h4>A total of 3411 women with IIH, 30,879 migraine controls and 33,495 population controls were included. Of these, 237, 2372 and 1695 women with IIH, migraine controls and population controls, respectively, developed depression during follow-up, and 179, 1826 and 1197, respectively, developed anxiety. There was a greater hazard of depression and anxiety in IIH compared to population controls (adjusted hazard ratio [aHR] 1.38, 95% confidence interval [CI] 1.20-1.58; and aHR 1.40, 95% CI 1.19-1.64, respectively), while hazards were similar to migraine controls (aHR 0.98, 95% CI 0.86-1.13; and aHR 0.98, 95% CI 0.83-1.14, respectively).<h4>Conclusion</h4>Depression and anxiety burden in women with IIH is higher than in the general population, and comparable to that in matched women with migraine. This may indicate that presence of headache is a potential driver for comorbid depression and anxiety in IIH.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/head.14465; doi:https://doi.org/10.1111/head.14465; html:https://europepmc.org/articles/PMC10952318; pdf:https://europepmc.org/articles/PMC10952318?pdf=render
 36720882,https://doi.org/10.1038/s41597-023-01949-y,"Quality control and removal of technical variation of NMR metabolic biomarker data in ~120,000 UK Biobank participants.","Ritchie SC, Surendran P, Karthikeyan S, Lambert SA, Bolton T, Pennells L, Danesh J, Di Angelantonio E, Butterworth AS, Inouye M.",,Scientific data,2023,2023-01-31,Y,,,,"Metabolic biomarker data quantified by nuclear magnetic resonance (NMR) spectroscopy in approximately 121,000 UK Biobank participants has recently been released as a community resource, comprising absolute concentrations and ratios of 249 circulating metabolites, lipids, and lipoprotein sub-fractions. Here we identify and characterise additional sources of unwanted technical variation influencing individual biomarkers in the data available to download from UK Biobank. These included sample preparation time, shipping plate well, spectrometer batch effects, drift over time within spectrometer, and outlier shipping plates. We developed a procedure for removing this unwanted technical variation, and demonstrate that it increases signal for genetic and epidemiological studies of the NMR metabolic biomarker data in UK Biobank. We subsequently developed an R package, ukbnmr, which we make available to the wider research community to enhance the utility of the UK Biobank NMR metabolic biomarker data and to facilitate rapid analysis.",,pdf:https://www.nature.com/articles/s41597-023-01949-y.pdf; doi:https://doi.org/10.1038/s41597-023-01949-y; html:https://europepmc.org/articles/PMC9887579; pdf:https://europepmc.org/articles/PMC9887579?pdf=render
 35954935,https://doi.org/10.3390/ijerph19159578,Comparing Peak Burn Injury Times and Characteristics in Australia and New Zealand.,"Hong R, Perkins M, Gabbe BJ, Tracy LM.",,International journal of environmental research and public health,2022,2022-08-04,Y,Burns; Cooking; Registry; scald; Flame,,,"Burns are a leading cause of morbidity and mortality worldwide. Understanding when and how burns occur, as well as the differences between countries, would aid prevention efforts. A review of burn injuries occurring between July 2009 and June 2021 was undertaken using data from the Burns Registry of Australia and New Zealand. Peak injury times were identified on a country-by-country basis. Variations in demographic and injury event profiles between countries were compared using descriptive statistics. There were 26,925 admissions recorded across the two countries (23,323 for Australia; 3602 for New Zealand). The greatest number of injuries occurred between 6 PM to 7 PM in Australia (1871, 8.0%) and between 5 PM to 6 PM in New Zealand (280, 7.8%). In both countries, scalds accounted for the greatest proportion of injuries during peak times (988, 45.8%), but a greater proportion of young children (under three years) sustained burns during New Zealand's peak times. The number of burn injuries associated with the preparation and/or consumption of food offers an opportunity for a targeted prevention program that may yield benefits across the two countries. Age- and mechanism-related differences in the profile of burn-injured patients need to be considered when developing and implementing such a program.",,pdf:https://www.mdpi.com/1660-4601/19/15/9578/pdf?version=1659598966; doi:https://doi.org/10.3390/ijerph19159578; html:https://europepmc.org/articles/PMC9368485; pdf:https://europepmc.org/articles/PMC9368485?pdf=render
 37663407,https://doi.org/10.1093/jamiaopen/ooad072,Identifying factors associated with user retention and outcomes of a digital intervention for substance use disorder: a retrospective analysis of real-world data.,"Günther F, Wong D, Elison-Davies S, Yau C.",,JAMIA open,2023,2023-09-02,Y,Substance Use Disorder; Secondary Use; Digital Health Intervention; Real-World Data Exploration; Real-World Uptake,,,"<h4>Objectives</h4>Successful delivery of digital health interventions is affected by multiple real-world factors. These factors may be identified in routinely collected, ecologically valid data from these interventions. We propose ideas for exploring these data, focusing on interventions targeting complex, comorbid conditions.<h4>Materials and methods</h4>This study retrospectively explores pre-post data collected between 2016 and 2019 from users of digital cognitive behavioral therapy (CBT)-containing psychoeducation and practical exercises-for substance use disorder (SUD) at UK addiction services. To identify factors associated with heterogenous user responses to the technology, we employed multivariable and multivariate regressions and random forest models of user-reported questionnaire data.<h4>Results</h4>The dataset contained information from 14 078 individuals of which 12 529 reported complete data at baseline and 2925 did so again after engagement with the CBT. Ninety-three percent screened positive for dependence on 1 of 43 substances at baseline, and 73% screened positive for anxiety or depression. Despite pre-post improvements independent of user sociodemographics, women reported more frequent and persistent symptoms of SUD, anxiety, and depression. Retention-minimum 2 use events recorded-was associated more with deployment environment than user characteristics. Prediction accuracy of post-engagement outcomes was acceptable (Area Under Curve [AUC]: 0.74-0.79), depending non-trivially on user characteristics.<h4>Discussion</h4>Traditionally, performance of digital health interventions is determined in controlled trials. Our analysis showcases multivariate models with which real-world data from these interventions can be explored and sources of user heterogeneity in retention and symptom reduction uncovered.<h4>Conclusion</h4>Real-world data from digital health interventions contain information on natural user-technology interactions which could enrich results from controlled trials.",,pdf:https://academic.oup.com/jamiaopen/article-pdf/6/3/ooad072/51335405/ooad072.pdf; doi:https://doi.org/10.1093/jamiaopen/ooad072; html:https://europepmc.org/articles/PMC10474970; pdf:https://europepmc.org/articles/PMC10474970?pdf=render
 35131989,https://doi.org/10.1097/mcp.0000000000000863,A clinical review of long-COVID with a focus on the respiratory system.,"Daines L, Zheng B, Pfeffer P, Hurst JR, Sheikh A.",,Current opinion in pulmonary medicine,2022,2022-02-07,N,,,,"<h4>Purpose of review</h4>Persistence of symptoms after acute coronavirus disease 2019 (COVID-19), often described as long- COVID, is common and debilitating. In this article, we review the epidemiology, clinical features, and research priorities for long-COVID focusing on the respiratory system.<h4>Recent findings</h4>Breathlessness, cough and chest pain were the most commonly reported respiratory symptoms associated with long-COVID. In hospitalised patients, abnormalities on lung function testing or chest imaging were observed less commonly at 12 months compared to six months since discharge. Clinical assessment of patients with persisting symptoms after acute COVID-19 requires a comprehensive evaluation to exclude other possible causes for symptoms. With no robust current evidence for interventions to treat long-COVID respiratory symptoms, symptomatic treatment, supported self-management and pulmonary rehabilitation should be considered to help individuals with respiratory symptoms associated with long-COVID.<h4>Summary</h4>Long-COVID is a debilitating syndrome that often includes persisting respiratory symptoms and to a lesser degree, abnormalities in lung physiology or imaging. Respiratory features of long-COVID may reduce over time, yet resolution is not seen in all cases. Future research is needed to understand the natural history of long-COVID, identify factors associated with spontaneous improvement/persistence, investigate mechanisms for persisting symptoms, and test interventions to prevent and treat long-COVID.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7612723; doi:https://doi.org/10.1097/MCP.0000000000000863; html:https://europepmc.org/articles/PMC7612723; pdf:https://europepmc.org/articles/PMC7612723?pdf=render; doi:https://doi.org/10.1097/mcp.0000000000000863
-38662697,https://doi.org/10.1093/cid/ciae108,"Reducing the Antigen Prevalence Target Threshold for Stopping and Restarting Mass Drug Administration for Lymphatic Filariasis Elimination: A Model-Based Cost-effectiveness Simulation in Tanzania, India and Haiti.","Antony Oliver MC, Graham M, Gass KM, Medley GF, Clark J, Davis EL, Reimer LJ, King JD, Pouwels KB, Hollingsworth TD.",,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2024,2024-04-01,Y,Threshold; Modeling; Elimination; Health Economics; Lymphatic Filariasis,,,"<h4>Background</h4>The Global Programme to Eliminate Lymphatic Filariasis (GPELF) aims to reduce and maintain infection levels through mass drug administration (MDA), but there is evidence of ongoing transmission after MDA in areas where Culex mosquitoes are the main transmission vector, suggesting that a more stringent criterion is required for MDA decision making in these settings.<h4>Methods</h4>We use a transmission model to investigate how a lower prevalence threshold (<1% antigenemia [Ag] prevalence compared with <2% Ag prevalence) for MDA decision making would affect the probability of local elimination, health outcomes, the number of MDA rounds, including restarts, and program costs associated with MDA and surveys across different scenarios. To determine the cost-effectiveness of switching to a lower threshold, we simulated 65% and 80% MDA coverage of the total population for different willingness to pay per disability-adjusted life-year averted for India ($446.07), Tanzania ($389.83), and Haiti ($219.84).<h4>Results</h4>Our results suggest that with a lower Ag threshold, there is a small proportion of simulations where extra rounds are required to reach the target, but this also reduces the need to restart MDA later in the program. For 80% coverage, the lower threshold is cost-effective across all baseline prevalences for India, Tanzania, and Haiti. For 65% MDA coverage, the lower threshold is not cost-effective due to additional MDA rounds, although it increases the probability of local elimination. Valuing the benefits of elimination to align with the GPELF goals, we find that a willingness to pay per capita government expenditure of approximately $1000-$4000 for 1% increase in the probability of local elimination would be required to make a lower threshold cost-effective.<h4>Conclusions</h4>Lower Ag thresholds for stopping MDAs generally mean a higher probability of local elimination, reducing long-term costs and health impacts. However, they may also lead to an increased number of MDA rounds required to reach the lower threshold and, therefore, increased short-term costs. Collectively, our analyses highlight that lower target Ag thresholds have the potential to assist programs in achieving lymphatic filariasis goals.",,doi:https://doi.org/10.1093/cid/ciae108; doi:https://doi.org/10.1093/cid/ciae108; html:https://europepmc.org/articles/PMC11045020; pdf:https://europepmc.org/articles/PMC11045020?pdf=render
 34308306,https://doi.org/10.1016/j.eclinm.2021.100888,The BCD Triage Sieve outperforms all existing major incident triage tools: Comparative analysis using the UK national trauma registry population.,"Malik NS, Chernbumroong S, Xu Y, Vassallo J, Lee J, Bowley DM, Hodgetts T, Moran CG, Lord JM, Belli A, Keene D, Foster M, Gkoutos GV.",,EClinicalMedicine,2021,2021-05-15,Y,ramp; Disaster; Start; Military Medicine; Major Incident; Triage; Injury Severity Score; Mass Casualty; Major Trauma; Prehospital Medicine; Life-saving Intervention; Careflight; Jumpstart; Bcd Triage Sieve; Mimms; Mptt-24; Mstart,,,"<h4>Background</h4>Natural disasters, conflict, and terrorism are major global causes of death and disability. Central to the healthcare response is triage, vital to ensure the right care is provided to the right patient at the right time. The ideal triage tool has high sensitivity for the highest priority (P1) patients with acceptably low over-triage. This study compared the performance of major incident triage tools in predicting P1 casualty status in adults in the prospective UK Trauma Audit and Research Network (TARN) registry.<h4>Methods</h4>TARN patients aged 16+ years (January 2008-December 2017) were included. Ten existing triage tools were applied using patients' first recorded pre-hospital physiology. Patients were subsequently assigned triage categories (P1, P2, P3, Expectant or Dead) based on pre-defined, intervention-based criteria. Tool performance was assessed by comparing tool-predicted and intervention-based priority status.<h4>Findings</h4>195,709 patients were included; mortality was 7·0% (n=13,601); median Injury Severity Score (ISS) was 9 (IQR 9-17); 97·1% sustained blunt injuries. 22,144 (11·3%) patients fulfilled intervention-based criteria for P1 status, exhibiting higher mortality (12·8% <i>vs.</i> 5·0%, p<0.001), increased intensive care requirement (52·4% <i>vs</i> 5·0%, p<0.001), and more severe injuries (median ISS 21 <i>vs</i> 9, p<0.001) compared with P2 patients.In 16-64 year olds, the highest performing tool was the Battlefield Casualty Drills (BCD) Triage Sieve (Prediction of P1 status: 70·4% sensitivity, over-triage 70·9%, area under the receiver operating curve (AUC) 0·068 [95%CI 0·676-0·684]). The UK National Ambulance Resilience Unit (NARU) Triage Sieve had sensitivity of 44·9%; over-triage 56·4%; AUC 0·666 (95%CI 0·662-0·670). All tools performed poorly amongst the elderly (65+ years).<h4>Interpretation</h4>The BCD Triage Sieve performed best in this nationally representative population; we recommend it supersede the NARU Triage Sieve as the UK primary major incident triage tool. Validated triage category definitions are recommended for appraising future major incidents.<h4>Funding</h4>This study is funded by the National Institute for Health Research (NIHR) Surgical Reconstruction and Microbiology Research Centre. GVG also acknowledges support from the MRC Heath Data Research UK (HDRUK/CFC/01). The views expressed are those of the authors and not necessarily those of the NIHR, the Department of Health and Social Care, or the Ministry of Defence.",,pdf:http://www.thelancet.com/article/S2589537021001681/pdf; doi:https://doi.org/10.1016/j.eclinm.2021.100888; html:https://europepmc.org/articles/PMC8257989; pdf:https://europepmc.org/articles/PMC8257989?pdf=render
+38662697,https://doi.org/10.1093/cid/ciae108,"Reducing the Antigen Prevalence Target Threshold for Stopping and Restarting Mass Drug Administration for Lymphatic Filariasis Elimination: A Model-Based Cost-effectiveness Simulation in Tanzania, India and Haiti.","Antony Oliver MC, Graham M, Gass KM, Medley GF, Clark J, Davis EL, Reimer LJ, King JD, Pouwels KB, Hollingsworth TD.",,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2024,2024-04-01,Y,Threshold; Modeling; Elimination; Health Economics; Lymphatic Filariasis,,,"<h4>Background</h4>The Global Programme to Eliminate Lymphatic Filariasis (GPELF) aims to reduce and maintain infection levels through mass drug administration (MDA), but there is evidence of ongoing transmission after MDA in areas where Culex mosquitoes are the main transmission vector, suggesting that a more stringent criterion is required for MDA decision making in these settings.<h4>Methods</h4>We use a transmission model to investigate how a lower prevalence threshold (<1% antigenemia [Ag] prevalence compared with <2% Ag prevalence) for MDA decision making would affect the probability of local elimination, health outcomes, the number of MDA rounds, including restarts, and program costs associated with MDA and surveys across different scenarios. To determine the cost-effectiveness of switching to a lower threshold, we simulated 65% and 80% MDA coverage of the total population for different willingness to pay per disability-adjusted life-year averted for India ($446.07), Tanzania ($389.83), and Haiti ($219.84).<h4>Results</h4>Our results suggest that with a lower Ag threshold, there is a small proportion of simulations where extra rounds are required to reach the target, but this also reduces the need to restart MDA later in the program. For 80% coverage, the lower threshold is cost-effective across all baseline prevalences for India, Tanzania, and Haiti. For 65% MDA coverage, the lower threshold is not cost-effective due to additional MDA rounds, although it increases the probability of local elimination. Valuing the benefits of elimination to align with the GPELF goals, we find that a willingness to pay per capita government expenditure of approximately $1000-$4000 for 1% increase in the probability of local elimination would be required to make a lower threshold cost-effective.<h4>Conclusions</h4>Lower Ag thresholds for stopping MDAs generally mean a higher probability of local elimination, reducing long-term costs and health impacts. However, they may also lead to an increased number of MDA rounds required to reach the lower threshold and, therefore, increased short-term costs. Collectively, our analyses highlight that lower target Ag thresholds have the potential to assist programs in achieving lymphatic filariasis goals.",,doi:https://doi.org/10.1093/cid/ciae108; doi:https://doi.org/10.1093/cid/ciae108; html:https://europepmc.org/articles/PMC11045020; pdf:https://europepmc.org/articles/PMC11045020?pdf=render
 39461360,https://doi.org/10.1016/s2213-8587(24)00242-0,Younger-onset compared with later-onset type 2 diabetes: an analysis of the UK Prospective Diabetes Study (UKPDS) with up to 30 years of follow-up (UKPDS 92).,"Lin B, Coleman RL, Bragg F, Maddaloni E, Holman RR, Adler AI.",,The lancet. Diabetes & endocrinology,2024,2024-10-22,N,,,,"<h4>Background</h4>Younger-onset type 2 diabetes is associated with accelerated complications. We assessed whether complications and mortality rates differed for younger age compared with older age at diagnosis over 30 years of follow-up.<h4>Methods</h4>In this study, we used data from the UKPDS, collected between 1977 and 2007, of participants aged 25-65 years with newly diagnosed type 2 diabetes with younger-onset (younger than 40 years) or later-onset (40 years or older), and without diabetes autoantibodies. We analysed standardised mortality ratios (SMR) using UK general population data, and incidence rates of prespecified outcomes by 10-year age intervals at diagnosis.<h4>Findings</h4>Of 4550 participants testing negative to all measured autoantibodies, 429 (9·4%) had younger-onset type 2 diabetes. 2704 (59·4%) were male, and mean HbA<sub>1c</sub> was 76 mmol/mol (SD 24·6). The median follow-up was 17·5 years (IQR 12·7-20·8). SMR for younger-onset type 2 diabetes was higher (3·72 [95% CI 2·98-4·64]) compared with later-onset type 2 diabetes (1·54 [1·47-1·61]). The incidence rate was higher for all outcomes in later-onset type 2 diabetes, except for microvascular disease (younger-onset 14·5 (11·9-17·7) vs later-onset 12·1 (11·3-13·0) per 1000 person-years). However, at any given age, the 5-year incidence of any diabetes-related endpoint, all-cause mortality, microvascular disease, and myocardial infarction was higher with younger age at diagnosis. Annual mean HbA<sub>1c</sub> was higher in the first 20 years in younger-onset compared with later-onset type 2 diabetes. Among participants randomised to intensive versus conventional glycaemic control, we observed no interactions by subgroup of younger-onset versus later-onset type 2 diabetes for any outcome.<h4>Interpretation</h4>The risk of dying relative to the general population is even greater for people diagnosed with type 2 diabetes at younger ages. The increased risk of complications and poorer glycaemic control in younger-onset type 2 diabetes calls for the development of services to identify and manage these individuals.<h4>Funding</h4>National Institute of Health and Care Research's Biomedical Research Centre.",,doi:https://doi.org/10.1016/S2213-8587(24)00242-0
 38383380,https://doi.org/10.1186/s12939-024-02114-6,Rapid systematic review on risks and outcomes of sepsis: the influence of risk factors associated with health inequalities.,"Bladon S, Ashiru-Oredope D, Cunningham N, Pate A, Martin GP, Zhong X, Gilham EL, Brown CS, Mirfenderesky M, Palin V, van Staa TP.",,International journal for equity in health,2024,2024-02-21,Y,Sepsis; Antimicrobial resistance; communities; Socioeconomic status; Ethnicity; Deprivation; Health Inequalities; Maternal,,,"<h4>Background and aims</h4>Sepsis is a serious and life-threatening condition caused by a dysregulated immune response to an infection. Recent guidance issued in the UK gave recommendations around recognition and antibiotic treatment of sepsis, but did not consider factors relating to health inequalities. The aim of this study was to summarise the literature investigating associations between health inequalities and sepsis.<h4>Methods</h4>Searches were conducted in Embase for peer-reviewed articles published since 2010 that included sepsis in combination with one of the following five areas: socioeconomic status, race/ethnicity, community factors, medical needs and pregnancy/maternity.<h4>Results</h4>Five searches identified 1,402 studies, with 50 unique studies included in the review after screening (13 sociodemographic, 14 race/ethnicity, 3 community, 3 care/medical needs and 20 pregnancy/maternity; 3 papers examined multiple health inequalities). Most of the studies were conducted in the USA (31/50), with only four studies using UK data (all pregnancy related). Socioeconomic factors associated with increased sepsis incidence included lower socioeconomic status, unemployment and lower education level, although findings were not consistent across studies. For ethnicity, mixed results were reported. Living in a medically underserved area or being resident in a nursing home increased risk of sepsis. Mortality rates after sepsis were found to be higher in people living in rural areas or in those discharged to skilled nursing facilities while associations with ethnicity were mixed. Complications during delivery, caesarean-section delivery, increased deprivation and black and other ethnic minority race were associated with post-partum sepsis.<h4>Conclusion</h4>There are clear correlations between sepsis morbidity and mortality and the presence of factors associated with health inequalities. To inform local guidance and drive public health measures, there is a need for studies conducted across more diverse setting and countries.",,doi:https://doi.org/10.1186/s12939-024-02114-6; html:https://europepmc.org/articles/PMC10882893; pdf:https://europepmc.org/articles/PMC10882893?pdf=render
 37889180,https://doi.org/10.1161/jaha.123.030661,Genome-Wide Association Study of Pericardial Fat Area in 28 161 UK Biobank Participants.,"Salih A, Ardissino M, Wagen AZ, Bard A, Szabo L, Ryten M, Petersen SE, Altmann A, Raisi-Estabragh Z.",,Journal of the American Heart Association,2023,2023-10-27,Y,Cardiovascular disease; Pericardial Adipose Tissue; Genome‐wide Association Study,,,"BACKGROUND Pericardial adipose tissue (PAT) is the visceral adipose tissue compartment surrounding the heart. Experimental and observational research has suggested that greater PAT deposition might mediate cardiovascular disease, independent of general or subcutaneous adiposity. We characterize the genetic architecture of adiposity-adjusted PAT and identify causal associations between PAT and adverse cardiac magnetic resonance imaging measures of cardiac structure and function in 28 161 UK Biobank participants. METHODS AND RESULTS The PAT phenotype was extracted from cardiac magnetic resonance images using an automated image analysis tool previously developed and validated in this cohort. A genome-wide association study was performed with PAT area set as the phenotype, adjusting for age, sex, and other measures of obesity. Functional mapping and Bayesian colocalization were used to understand the biologic role of identified variants. Mendelian randomization analysis was used to examine potential causal links between genetically determined PAT and cardiac magnetic resonance-derived measures of left ventricular structure and function. We discovered 12 genome-wide significant variants, with 2 independent sentinel variants (rs6428792, <i>P</i>=4.20×10<sup>-9</sup> and rs11992444, <i>P</i>=1.30×10<sup>-12</sup>) at 2 distinct genomic loci, that were mapped to 3 potentially causal genes: T-box transcription factor 15 (<i>TBX15</i>), tryptophanyl tRNA synthetase 2, mitochondrial (<i>WARS2</i>) and early B-cell factor-2 (<i>EBF2</i>) through functional annotation. Bayesian colocalization additionally suggested a role of RP4-712E4.1. Genetically predicted differences in adiposity-adjusted PAT were causally associated with adverse left ventricular remodeling. CONCLUSIONS This study provides insights into the genetic architecture determining differential PAT deposition, identifies causal links with left structural and functional parameters, and provides novel data about the pathophysiological importance of adiposity distribution.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.123.030661; doi:https://doi.org/10.1161/JAHA.123.030661; html:https://europepmc.org/articles/PMC10727393; pdf:https://europepmc.org/articles/PMC10727393?pdf=render
@@ -788,56 +789,56 @@ PMC9644860,https://doi.org/,Maternal mental health and children’s development:
 31594227,https://doi.org/10.3233/jad-190571,Partner Bereavement and Detection of Dementia: A UK-Based Cohort Study Using Routine Health Data.,"Forbes HJ, Wong AYS, Morton C, Bhaskaran K, Smeeth L, Richards M, Schmidt SAJ, Langan SM, Warren-Gash C.",,Journal of Alzheimer's disease : JAD,2019,2019-01-01,Y,Diagnosis; Dementia; epidemiology; Bereavement; Clinical Practice Research Datalink,"Improving Public Health, Understanding the Causes of Disease",,"<h4>Background</h4>In the UK, an estimated one third of people with dementia have not received a diagnosis. Good evidence suggests that dementia risk is increased among widowed individuals; however, it is not clear if they are being diagnosed in routine primary care.<h4>Objective</h4>This study aimed to investigate if bereavement influenced the probability of having received a dementia diagnosis.<h4>Methods</h4>A population-based cohort study using UK electronic health records, between 1997 and 2017, among 247,586 opposite-sex partners. Those experiencing partner bereavement were matched (age, sex, and date of bereavement) to a non-bereaved person living in a partnership. Multivariate cox regression was performed.<h4>Results</h4>Partner bereavement was associated with an increased risk of receiving a diagnosis of dementia in the first three months (hazard ratio (HR) 1.43, 95% CI 1.20-1.71) and first six months (HR 1.24, 95% CI 1.09-1.41), while there was a small reduced risk of getting a dementia diagnosis over all follow-up (HR 0.94, 95% CI 0.89-0.98).<h4>Conclusions</h4>Partner bereavement appears to lead to a short-term increased risk of the surviving partner receiving a diagnosis of dementia, suggesting that bereavement unmasks existing undiagnosed dementia. Over the longer term, however, bereaved individuals are less likely to have a diagnosis of dementia in their health records than non-bereaved individuals.",,pdf:https://europepmc.org/articles/pmc6918907?pdf=render; doi:https://doi.org/10.3233/JAD-190571; html:https://europepmc.org/articles/PMC6918907; pdf:https://europepmc.org/articles/PMC6918907?pdf=render
 37678576,https://doi.org/10.1016/j.jaci.2023.08.025,E-cigarette vapor renders neutrophils dysfunctional due to filamentous actin accumulation.,"Jasper AE, Faniyi AA, Davis LC, Grudzinska FS, Halston R, Hazeldine J, Parekh D, Sapey E, Thickett DR, Scott A.",,The Journal of allergy and clinical immunology,2024,2023-09-05,N,Neutrophils; Phagocytosis; Oxidative burst; Nicotine; Netosis; E-cigarettes,,,"<h4>Background</h4>Electronic cigarette (e-cigarette) use continues to rise despite concerns of long-term effects, especially the risk of developing lung diseases such as chronic obstructive pulmonary disease. Neutrophils are central to the pathogenesis of chronic obstructive pulmonary disease, with changes in phenotype and function implicated in tissue damage.<h4>Objective</h4>We sought to measure the impact of direct exposure to nicotine-containing and nicotine-free e-cigarette vapor on human neutrophil function and phenotype.<h4>Methods</h4>Neutrophils were isolated from the whole blood of self-reported nonsmoking, nonvaping healthy volunteers. Neutrophils were exposed to 40 puffs of e-cigarette vapor generated from e-cigarette devices using flavorless e-cigarette liquids with and without nicotine before functions, deformability, and phenotype were assessed.<h4>Results</h4>Neutrophil surface marker expression was altered, with CD62L and CXCR2 expression significantly reduced in neutrophils treated with e-cigarette vapor containing nicotine. Neutrophil migration to IL-8, phagocytosis of Escherichia coli and Staphylococcus aureus pHrodo bioparticles, oxidative burst response, and phorbol 12-myristate 13-acetate-stimulated neutrophil extracellular trap formation were all significantly reduced by e-cigarette vapor treatments, independent of nicotine content. E-cigarette vapor induced increased levels of baseline polymerized filamentous actin levels in the cytoplasm, compared with untreated controls.<h4>Conclusions</h4>The significant reduction in effector neutrophil functions after exposure to high-power e-cigarette devices, even in the absence of nicotine, is associated with excessive filamentous actin polymerization. This highlights the potentially damaging impact of vaping on respiratory health and reinforces the urgency of research to uncover the long-term health implications of e-cigarettes.",,doi:https://doi.org/10.1016/j.jaci.2023.08.025
 35962974,https://doi.org/10.1093/ije/dyac158,Association between household composition and severe COVID-19 outcomes in older people by ethnicity: an observational cohort study using the OpenSAFELY platform.,"Wing K, Grint DJ, Mathur R, Gibbs HP, Hickman G, Nightingale E, Schultze A, Forbes H, Nafilyan V, Bhaskaran K, Williamson E, House T, Pellis L, Herrett E, Gautam N, Curtis HJ, Rentsch CT, Wong AYS, MacKenna B, Mehrkar A, Bacon S, Douglas IJ, Evans SJW, Tomlinson L, Goldacre B, Eggo RM.",,International journal of epidemiology,2022,2022-12-01,Y,Household; Older People; Ethnicity; Deprivation; Comorbidities; Multigenerational; Population-level; Covid-19; Opensafely,,,"<h4>Background</h4>Ethnic differences in the risk of severe COVID-19 may be linked to household composition. We quantified the association between household composition and risk of severe COVID-19 by ethnicity for older individuals.<h4>Methods</h4>With the approval of NHS England, we analysed ethnic differences in the association between household composition and severe COVID-19 in people aged 67 or over in England. We defined households by number of age-based generations living together, and used multivariable Cox regression stratified by location and wave of the pandemic and accounted for age, sex, comorbidities, smoking, obesity, housing density and deprivation. We included 2 692 223 people over 67 years in Wave 1 (1 February 2020-31 August 2020) and 2 731 427 in Wave 2 (1 September 2020-31 January 2021).<h4>Results</h4>Multigenerational living was associated with increased risk of severe COVID-19 for White and South Asian older people in both waves [e.g. Wave 2, 67+ living with three other generations vs 67+-year-olds only: White hazard ratio (HR) 1.61 95% CI 1.38-1.87, South Asian HR 1.76 95% CI 1.48-2.10], with a trend for increased risks of severe COVID-19 with increasing generations in Wave 2. There was also an increased risk of severe COVID-19 in Wave 1 associated with living alone for White (HR 1.35 95% CI 1.30-1.41), South Asian (HR 1.47 95% CI 1.18-1.84) and Other (HR 1.72 95% CI 0.99-2.97) ethnicities, an effect that persisted for White older people in Wave 2.<h4>Conclusions</h4>Both multigenerational living and living alone were associated with severe COVID-19 in older adults. Older South Asian people are over-represented within multigenerational households in England, especially in the most deprived settings, whereas a substantial proportion of White older people live alone. The number of generations in a household, number of occupants, ethnicity and deprivation status are important considerations in the continued roll-out of COVID-19 vaccination and targeting of interventions for future pandemics.",,pdf:https://academic.oup.com/ije/article-pdf/51/6/1745/47882630/dyac158.pdf; doi:https://doi.org/10.1093/ije/dyac158; html:https://europepmc.org/articles/PMC9384728; pdf:https://europepmc.org/articles/PMC9384728?pdf=render
-33545096,https://doi.org/10.1016/s0140-6736(21)00149-5,"Azithromycin in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial.",RECOVERY Collaborative Group.,,"Lancet (London, England)",2021,2021-02-02,Y,,,,"<h4>Background</h4>Azithromycin has been proposed as a treatment for COVID-19 on the basis of its immunomodulatory actions. We aimed to evaluate the safety and efficacy of azithromycin in patients admitted to hospital with COVID-19.<h4>Methods</h4>In this randomised, controlled, open-label, adaptive platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), several possible treatments were compared with usual care in patients admitted to hospital with COVID-19 in the UK. The trial is underway at 176 hospitals in the UK. Eligible and consenting patients were randomly allocated to either usual standard of care alone or usual standard of care plus azithromycin 500 mg once per day by mouth or intravenously for 10 days or until discharge (or allocation to one of the other RECOVERY treatment groups). Patients were assigned via web-based simple (unstratified) randomisation with allocation concealment and were twice as likely to be randomly assigned to usual care than to any of the active treatment groups. Participants and local study staff were not masked to the allocated treatment, but all others involved in the trial were masked to the outcome data during the trial. The primary outcome was 28-day all-cause mortality, assessed in the intention-to-treat population. The trial is registered with ISRCTN, 50189673, and ClinicalTrials.gov, NCT04381936.<h4>Findings</h4>Between April 7 and Nov 27, 2020, of 16 442 patients enrolled in the RECOVERY trial, 9433 (57%) were eligible and 7763 were included in the assessment of azithromycin. The mean age of these study participants was 65·3 years (SD 15·7) and approximately a third were women (2944 [38%] of 7763). 2582 patients were randomly allocated to receive azithromycin and 5181 patients were randomly allocated to usual care alone. Overall, 561 (22%) patients allocated to azithromycin and 1162 (22%) patients allocated to usual care died within 28 days (rate ratio 0·97, 95% CI 0·87-1·07; p=0·50). No significant difference was seen in duration of hospital stay (median 10 days [IQR 5 to >28] vs 11 days [5 to >28]) or the proportion of patients discharged from hospital alive within 28 days (rate ratio 1·04, 95% CI 0·98-1·10; p=0·19). Among those not on invasive mechanical ventilation at baseline, no significant difference was seen in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (risk ratio 0·95, 95% CI 0·87-1·03; p=0·24).<h4>Interpretation</h4>In patients admitted to hospital with COVID-19, azithromycin did not improve survival or other prespecified clinical outcomes. Azithromycin use in patients admitted to hospital with COVID-19 should be restricted to patients in whom there is a clear antimicrobial indication.<h4>Funding</h4>UK Research and Innovation (Medical Research Council) and National Institute of Health Research.",,pdf:http://www.thelancet.com/article/S0140673621001495/pdf; doi:https://doi.org/10.1016/S0140-6736(21)00149-5; html:https://europepmc.org/articles/PMC7884931; pdf:https://europepmc.org/articles/PMC7884931?pdf=render
 34240125,https://doi.org/10.1093/clinchem/hvab109,Sex Differences in Cardiac Troponin I and T and the Prediction of Cardiovascular Events in the General Population.,"Kimenai DM, Shah ASV, McAllister DA, Lee KK, Tsanas A, Meex SJR, Porteous DJ, Hayward C, Campbell A, Sattar N, Mills NL, Welsh P.",,Clinical chemistry,2021,2021-10-01,Y,Sex; cardiac troponin; Cardiovascular events; risk factors,,,"<h4>Background</h4>Cardiac troponin concentrations differ in women and men, but how this influences risk prediction and whether a sex-specific approach is required is unclear. We evaluated whether sex influences the predictive ability of cardiac troponin I and T for cardiovascular events in the general population.<h4>Methods</h4>High-sensitivity cardiac troponin (hs-cTn) I and T were measured in the Generation Scotland Scottish Family Health Study of randomly selected volunteers drawn from the general population between 2006 and 2011. Cox-regression models evaluated associations between hs-cTnI and hs-cTnT and the primary outcome of cardiovascular death, myocardial infarction, or stroke.<h4>Results</h4>In 19 501 (58% women, mean age 47 years) participants, the primary outcome occurred in 2.7% (306/11 375) of women and 5.1% (411/8126) of men during the median follow-up period of 7.9 (IQR, 7.1-9.2) years. Cardiac troponin I and T concentrations were lower in women than men (P < 0.001 for both), and both were more strongly associated with cardiovascular events in women than men. For example, at a hs-cTnI concentration of 10 ng/L, the hazard ratio relative to the limit of blank was 9.7 (95% CI 7.6-12.4) and 5.6 (95% CI 4.7-6.6) for women and men, respectively. The hazard ratio for hs-cTnT at a concentration of 10 ng/L relative to the limit of blank was 3.7 (95% CI 3.1-4.3) and 2.2 (95% CI 2.0-2.5) for women and men, respectively.<h4>Conclusions</h4>Cardiac troponin concentrations differ in women and men and are stronger predictors of cardiovascular events in women. Sex-specific approaches are required to provide equivalent risk prediction.",,pdf:https://academic.oup.com/clinchem/article-pdf/67/10/1351/40494927/hvab109.pdf; doi:https://doi.org/10.1093/clinchem/hvab109; html:https://europepmc.org/articles/PMC8486023; pdf:https://europepmc.org/articles/PMC8486023?pdf=render
-37934728,https://doi.org/10.1093/jamia/ocad212,Multi-faceted analysis and prediction for the outbreak of pediatric respiratory syncytial virus.,"Yang C, Gao J, Glass L, Cross A, Sun J.",,Journal of the American Medical Informatics Association : JAMIA,2023,2023-12-01,N,Respiratory syncytial virus (RSV); Pediatric Diseases; Deep Learning; Tensor Factorization,,,"<h4>Objectives</h4>Respiratory syncytial virus (RSV) is a significant cause of pediatric hospitalizations. This article aims to utilize multisource data and leverage the tensor methods to uncover distinct RSV geographic clusters and develop an accurate RSV prediction model for future seasons.<h4>Materials and methods</h4>This study utilizes 5-year RSV data from sources, including medical claims, CDC surveillance data, and Google search trends. We conduct spatiotemporal tensor analysis and prediction for pediatric RSV in the United States by designing (i) a nonnegative tensor factorization model for pediatric RSV diseases and location clustering; (ii) and a recurrent neural network tensor regression model for county-level trend prediction using the disease and location features.<h4>Results</h4>We identify a clustering hierarchy of pediatric diseases: Three common geographic clusters of RSV outbreaks were identified from independent sources, showing an annual RSV trend shifting across different US regions, from the South and Southeast regions to the Central and Northeast regions and then to the West and Northwest regions, while precipitation and temperature were found as correlative factors with the coefficient of determination R2≈0.5, respectively. Our regression model accurately predicted the 2022-2023 RSV season at the county level, achieving R2≈0.3 mean absolute error MAE < 0.4 and a Pearson correlation greater than 0.75, which significantly outperforms the baselines with P-values <.05.<h4>Conclusion</h4>Our proposed framework provides a thorough analysis of RSV disease in the United States, which enables healthcare providers to better prepare for potential outbreaks, anticipate increased demand for services and supplies, and save more lives with timely interventions.",,doi:https://doi.org/10.1093/jamia/ocad212
 36929232,https://doi.org/10.1002/jmri.28675,Image-Based Biological Heart Age Estimation Reveals Differential Aging Patterns Across Cardiac Chambers.,"Salih AM, Pujadas ER, Campello VM, McCracken C, Harvey NC, Neubauer S, Lekadir K, Nichols TE, Petersen SE, Raisi-Estabragh Z.",,Journal of magnetic resonance imaging : JMRI,2023,2023-03-16,Y,Aging; Cardiac Imaging; Cardiac Health; Radiomics,,,"<h4>Background</h4>Biological heart age estimation can provide insights into cardiac aging. However, existing studies do not consider differential aging across cardiac regions.<h4>Purpose</h4>To estimate biological age of the left ventricle (LV), right ventricle (RV), myocardium, left atrium, and right atrium using magnetic resonance imaging radiomics phenotypes and to investigate determinants of aging by cardiac region.<h4>Study type</h4>Cross-sectional.<h4>Population</h4>A total of 18,117 healthy UK Biobank participants including 8338 men (mean age = 64.2 ± 7.5) and 9779 women (mean age = 63.0 ± 7.4).<h4>Field strength/sequence</h4>A 1.5 T/balanced steady-state free precession.<h4>Assessment</h4>An automated algorithm was used to segment the five cardiac regions, from which radiomic features were extracted. Bayesian ridge regression was used to estimate biological age of each cardiac region with radiomics features as predictors and chronological age as the output. The ""age gap"" was the difference between biological and chronological age. Linear regression was used to calculate associations of age gap from each cardiac region with socioeconomic, lifestyle, body composition, blood pressure and arterial stiffness, blood biomarkers, mental well-being, multiorgan health, and sex hormone exposures (n = 49).<h4>Statistical test</h4>Multiple testing correction with false discovery method (threshold = 5%).<h4>Results</h4>The largest model error was with RV and the smallest with LV age (mean absolute error in men: 5.26 vs. 4.96 years). There were 172 statistically significant age gap associations. Greater visceral adiposity was the strongest correlate of larger age gaps, for example, myocardial age gap in women (Beta = 0.85, P = 1.69 × 10<sup>-26</sup> ). Poor mental health associated with large age gaps, for example, ""disinterested"" episodes and myocardial age gap in men (Beta = 0.25, P = 0.001), as did a history of dental problems (eg LV in men Beta = 0.19, P = 0.02). Higher bone mineral density was the strongest associate of smaller age gaps, for example, myocardial age gap in men (Beta = -1.52, P = 7.44 × 10<sup>-6</sup> ).<h4>Data conclusion</h4>This work demonstrates image-based heart age estimation as a novel method for understanding cardiac aging.<h4>Evidence level</h4>1.<h4>Technical efficacy</h4>Stage 1.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jmri.28675; doi:https://doi.org/10.1002/jmri.28675; html:https://europepmc.org/articles/PMC10947470; pdf:https://europepmc.org/articles/PMC10947470?pdf=render
+37934728,https://doi.org/10.1093/jamia/ocad212,Multi-faceted analysis and prediction for the outbreak of pediatric respiratory syncytial virus.,"Yang C, Gao J, Glass L, Cross A, Sun J.",,Journal of the American Medical Informatics Association : JAMIA,2023,2023-12-01,N,Respiratory syncytial virus (RSV); Pediatric Diseases; Deep Learning; Tensor Factorization,,,"<h4>Objectives</h4>Respiratory syncytial virus (RSV) is a significant cause of pediatric hospitalizations. This article aims to utilize multisource data and leverage the tensor methods to uncover distinct RSV geographic clusters and develop an accurate RSV prediction model for future seasons.<h4>Materials and methods</h4>This study utilizes 5-year RSV data from sources, including medical claims, CDC surveillance data, and Google search trends. We conduct spatiotemporal tensor analysis and prediction for pediatric RSV in the United States by designing (i) a nonnegative tensor factorization model for pediatric RSV diseases and location clustering; (ii) and a recurrent neural network tensor regression model for county-level trend prediction using the disease and location features.<h4>Results</h4>We identify a clustering hierarchy of pediatric diseases: Three common geographic clusters of RSV outbreaks were identified from independent sources, showing an annual RSV trend shifting across different US regions, from the South and Southeast regions to the Central and Northeast regions and then to the West and Northwest regions, while precipitation and temperature were found as correlative factors with the coefficient of determination R2≈0.5, respectively. Our regression model accurately predicted the 2022-2023 RSV season at the county level, achieving R2≈0.3 mean absolute error MAE < 0.4 and a Pearson correlation greater than 0.75, which significantly outperforms the baselines with P-values <.05.<h4>Conclusion</h4>Our proposed framework provides a thorough analysis of RSV disease in the United States, which enables healthcare providers to better prepare for potential outbreaks, anticipate increased demand for services and supplies, and save more lives with timely interventions.",,doi:https://doi.org/10.1093/jamia/ocad212
+33545096,https://doi.org/10.1016/s0140-6736(21)00149-5,"Azithromycin in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial.",RECOVERY Collaborative Group.,,"Lancet (London, England)",2021,2021-02-02,Y,,,,"<h4>Background</h4>Azithromycin has been proposed as a treatment for COVID-19 on the basis of its immunomodulatory actions. We aimed to evaluate the safety and efficacy of azithromycin in patients admitted to hospital with COVID-19.<h4>Methods</h4>In this randomised, controlled, open-label, adaptive platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), several possible treatments were compared with usual care in patients admitted to hospital with COVID-19 in the UK. The trial is underway at 176 hospitals in the UK. Eligible and consenting patients were randomly allocated to either usual standard of care alone or usual standard of care plus azithromycin 500 mg once per day by mouth or intravenously for 10 days or until discharge (or allocation to one of the other RECOVERY treatment groups). Patients were assigned via web-based simple (unstratified) randomisation with allocation concealment and were twice as likely to be randomly assigned to usual care than to any of the active treatment groups. Participants and local study staff were not masked to the allocated treatment, but all others involved in the trial were masked to the outcome data during the trial. The primary outcome was 28-day all-cause mortality, assessed in the intention-to-treat population. The trial is registered with ISRCTN, 50189673, and ClinicalTrials.gov, NCT04381936.<h4>Findings</h4>Between April 7 and Nov 27, 2020, of 16 442 patients enrolled in the RECOVERY trial, 9433 (57%) were eligible and 7763 were included in the assessment of azithromycin. The mean age of these study participants was 65·3 years (SD 15·7) and approximately a third were women (2944 [38%] of 7763). 2582 patients were randomly allocated to receive azithromycin and 5181 patients were randomly allocated to usual care alone. Overall, 561 (22%) patients allocated to azithromycin and 1162 (22%) patients allocated to usual care died within 28 days (rate ratio 0·97, 95% CI 0·87-1·07; p=0·50). No significant difference was seen in duration of hospital stay (median 10 days [IQR 5 to >28] vs 11 days [5 to >28]) or the proportion of patients discharged from hospital alive within 28 days (rate ratio 1·04, 95% CI 0·98-1·10; p=0·19). Among those not on invasive mechanical ventilation at baseline, no significant difference was seen in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (risk ratio 0·95, 95% CI 0·87-1·03; p=0·24).<h4>Interpretation</h4>In patients admitted to hospital with COVID-19, azithromycin did not improve survival or other prespecified clinical outcomes. Azithromycin use in patients admitted to hospital with COVID-19 should be restricted to patients in whom there is a clear antimicrobial indication.<h4>Funding</h4>UK Research and Innovation (Medical Research Council) and National Institute of Health Research.",,pdf:http://www.thelancet.com/article/S0140673621001495/pdf; doi:https://doi.org/10.1016/S0140-6736(21)00149-5; html:https://europepmc.org/articles/PMC7884931; pdf:https://europepmc.org/articles/PMC7884931?pdf=render
 35443953,https://doi.org/10.1136/bmjopen-2021-056523,Can we accurately forecast non-elective bed occupancy and admissions in the NHS? A time-series MSARIMA analysis of longitudinal data from an NHS Trust.,"Eyles E, Redaniel MT, Jones T, Prat M, Keen T.",,BMJ open,2022,2022-04-20,Y,epidemiology; Statistics & Research Methods; Health Services Administration & Management; Accident & Emergency Medicine,,,"<h4>Objectives</h4>The main objective of the study was to develop more accurate and precise short-term forecasting models for admissions and bed occupancy for an NHS Trust located in Bristol, England. Subforecasts for the medical and surgical specialties, and for different lengths of stay were realised DESIGN: Autoregressive integrated moving average models were specified on a training dataset of daily count data, then tested on a 6-week forecast horizon. Explanatory variables were included in the models: day of the week, holiday days, lagged temperature and precipitation.<h4>Setting</h4>A secondary care hospital in an NHS Trust in South West England.<h4>Participants</h4>Hospital admissions between September 2016 and March 2020, comprising 1291 days.<h4>Primary and secondary outcome measures</h4>The accuracy of the forecasts was assessed through standard measures, as well as compared with the actual data using accuracy thresholds of 10% and 20% of the mean number of admissions or occupied beds.<h4>Results</h4>The overall Autoregressive Integrated Moving Average (ARIMA) admissions forecast was compared with the Trust's forecast, and found to be more accurate, namely, being closer to the actual value 95.6% of the time. Furthermore, it was more precise than the Trust's. The subforecasts, as well as those for bed occupancy, tended to be less accurate compared with the overall forecasts. All of the explanatory variables improved the forecasts.<h4>Conclusions</h4>ARIMA models can forecast non-elective admissions in an NHS Trust accurately on a 6-week horizon, which is an improvement on the current predictive modelling in the Trust. These models can be readily applied to other contexts, improving patient flow.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/4/e056523.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-056523; html:https://europepmc.org/articles/PMC9021768; pdf:https://europepmc.org/articles/PMC9021768?pdf=render
 35383067,https://doi.org/10.1136/bmjopen-2021-055447,Potentially avoidable causes of hospitalisation in people with dementia: contemporaneous associations by stage of dementia in a South London clinical cohort.,"Gungabissoon U, Perera G, Galwey NW, Stewart R.",,BMJ open,2022,2022-04-05,Y,Dementia; epidemiology; Old Age Psychiatry,,,"<h4>Objectives</h4>To estimate the frequency of all-cause and ambulatory care sensitive condition (ACSCs)-related hospitalisations among individuals with dementia. In addition, to investigate differences by stage of dementia based on recorded cognitive function.<h4>Setting</h4>Data from a large London dementia care clinical case register, linked to a national hospitalisation database.<h4>Participants</h4>Individuals aged ≥65 years with a confirmed dementia diagnosis with recorded cognitive function.<h4>Outcome measures</h4>Acute general hospital admissions were evaluated within 6 months of a randomly selected cognitive function score in patients with a clinical diagnosis of dementia. To evaluate associations between ACSC-related hospital admissions (overall and individual ACSCs) and stage of dementia, an ordinal regression was performed, modelling stage of dementia as the dependant variable (to facilitate efficient model selection, with no implication concerning the direction of causality).<h4>Results</h4>Of the 5294 people with dementia, 2993 (56.5%) had at least one hospitalisation during a 12-month period of evaluation, and 1192 (22.5%) had an ACSC-related admission. Proportions with an all-cause or ACSC-related hospitalisation were greater in the groups with more advanced dementia (all-cause 53.9%, 57.1% and 60.9%, p 0.002; ACSC-related 19.5%, 24.0% and 25.3%, p<0.0001 in the mild, moderate and severe groups, respectively). An ACSC-related admission was associated with 1.3-fold (95% CI 1.1 to 1.5) increased odds of more severe dementia after adjusting for demographic factors. Concerning admissions for individual ACSCs, the most common ACSC was urinary tract infection /pyelonephritis (9.8% of hospitalised patients) followed by pneumonia (7.1%); in an adjusted model, these were each associated with 1.4-fold increased odds of more severe dementia (95% CI 1.2 to 1.7 and 1.1 to 1.7, respectively).<h4>Conclusions</h4>Potentially avoidable hospitalisations were common in people with dementia, particularly in those with greater cognitive impairment. Our results call for greater attention to the extent of cognitive status impairment, and not just dementia diagnosis, when evaluating measures to reduce the risk of potentially avoidable hospitalisations.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/4/e055447.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-055447; html:https://europepmc.org/articles/PMC8984034; pdf:https://europepmc.org/articles/PMC8984034?pdf=render
 33199838,https://doi.org/10.1038/s41598-020-76860-2,Path-based extensions of local link prediction methods for complex networks.,"Aziz F, Gul H, Uddin I, Gkoutos GV.",,Scientific reports,2020,2020-11-16,Y,,,,"Link prediction in a complex network is a problem of fundamental interest in network science and has attracted increasing attention in recent years. It aims to predict missing (or future) links between two entities in a complex system that are not already connected. Among existing methods, local similarity indices are most popular that take into account the information of common neighbours to estimate the likelihood of existence of a connection between two nodes. In this paper, we propose global and quasi-local extensions of some commonly used local similarity indices. We have performed extensive numerical simulations on publicly available datasets from diverse domains demonstrating that the proposed extensions not only give superior performance, when compared to their respective local indices, but also outperform some of the current, state-of-the-art, local and global link-prediction methods.",,pdf:https://www.nature.com/articles/s41598-020-76860-2.pdf; doi:https://doi.org/10.1038/s41598-020-76860-2; html:https://europepmc.org/articles/PMC7670409; pdf:https://europepmc.org/articles/PMC7670409?pdf=render
 39221081,https://doi.org/10.1177/20552076241272570,Integrating telemedicine in routine heart failure management: Experiences of healthcare professionals - A qualitative study.,"van Eijk J, Trappenburg J, Asselbergs FW, Jaarsma T.",,Digital health,2024,2024-01-01,Y,Heart Failure; Telemedicine; Qualitative Study; Telemonitoring; Healthcare Professionals; Useability; Professional Expertise; Reflexive Thematic Analysis; Challenges In Implementation,,,"<h4>Objective</h4>To describe the experiences of healthcare professionals with integrating telemedicine in routine heart failure (HF) care.<h4>Methods</h4>Semi-structured interviews were conducted with healthcare professionals (<i>n</i> = 19) in the Netherlands who were involved in decision-making, implementation or routine use of telemedicine in HF management. Using purposive sampling, nurses, cardiologists and managers were selected to be interviewed. Interviews were performed in-person, recorded and transcribed verbatim. Interview data were analysed using a reflexive thematic analysis.<h4>Results</h4>This study identified four themes: (1) Responsibility - the lack of a clear delineation of roles and responsibilities among healthcare professionals, patients and suppliers in telemedicine. (2) Confidence and safety - telemedicine is seen by healthcare professionals as capable of enhancing safety, yet also introduces the risk of fostering a false sense of security among patients. (3) Collaboration - actively involving end-users in the development and implementation of telemedicine promotes the adoption. (4) Processes and mutual agreements - rather than replacing traditional care, telemedicine is perceived as an adjunct to it. Structured care pathways support telemedicine implementation, and personalised telemedicine can empower patients in self-care.<h4>Conclusions</h4>Telemedicine is a promising intervention in the management of HF. However, existing systems and care pathways have resulted in limited adoption. Improvements in the collaboration and establishing clear agreements on responsibilities between professional, patient and supplier can lead to more confidence in adopting telemedicine. Structured care pathways can be supportive. A personalised telemedicine approach can ensure that telemedicine remains manageable for patient and professional.",,doi:https://doi.org/10.1177/20552076241272570; html:https://europepmc.org/articles/PMC11363038; pdf:https://europepmc.org/articles/PMC11363038?pdf=render
-39004446,https://doi.org/10.1136/jmg-2023-109791,Estimating cancer risk in carriers of Lynch syndrome variants in UK Biobank.,"Fummey E, Navarro P, Plazzer JP, Frayling IM, Knott S, Tenesa A.",,Journal of medical genetics,2024,2024-08-29,Y,Neoplasms; Human genetics; Genetic predisposition to disease; Germ-line Mutation; Whole Exome Sequencing,,,"BackgroundLynch syndrome (LS) is an inherited cancer predisposition syndrome caused by genetic variants affecting DNA mismatch repair (MMR) genes <i>MLH1</i>, <i>MSH2</i>, <i>MSH6</i> and <i>PMS2</i> Cancer risk in LS is estimated from cohorts of individuals ascertained by individual or family history of cancer, which may upwardly bias estimates.<h4>Methods</h4>830 carriers of pathogenic or likely pathogenic (<i>path_MMR</i>) MMR gene variants classified by InSiGHT were identified in 454 756 UK Biobank (UKB) participants using whole-exome sequence. Nelson-Aalen survival analysis was used to estimate cumulative incidence of colorectal, endometrial and breast cancer (BC).<h4>Results</h4>Cumulative incidence of colorectal and endometrial cancer (EC) by age 70 years was elevated in <i>path_MMR</i> carriers compared with non-carriers (colorectal: 11.8% (95% confidence interval (CI): 9.5% to 14.6%) vs 1.7% (95% CI: 1.6% to 1.7%), endometrial: 13.4% (95% CI: 10.2% to 17.6%) vs 1.0% (95% CI: 0.9% to 1.0%)), but the magnitude of this increase differed between genes. Cumulative BC incidence by age 70 years was not elevated in <i>path_MMR</i> carriers compared with non-carriers (8.9% (95% CI: 6.3% to 12.4%) vs 7.5% (95% CI: 7.4% to 7.6%)). Cumulative cancer incidence estimates in UKB were similar to estimates from the Prospective Lynch Syndrome Database for all genes and cancers, except there was no evidence for elevated EC risk in carriers of pathogenic <i>PMS2</i> variants in UKB.<h4>Conclusion</h4>These results support offering incidentally identified carriers of any <i>path_MMR</i> surveillance to manage colorectal cancer risk. Incidentally identified carriers of pathogenic variants in <i>MLH1</i>, <i>MSH2</i> and <i>MSH6</i> would also benefit from interventions to reduce EC risk. The results suggest that BC is not an LS-related cancer.",,pdf:https://jmg.bmj.com/content/jmedgenet/early/2024/08/06/jmg-2023-109791.full.pdf; doi:https://doi.org/10.1136/jmg-2023-109791; html:https://europepmc.org/articles/PMC11420727; pdf:https://europepmc.org/articles/PMC11420727?pdf=render
 37650026,https://doi.org/10.23889/ijpds.v7i1.1727,An overview of synthetic administrative data for research.,"Kokosi T, De Stavola B, Mitra R, Frayling L, Doherty A, Dove I, Sonnenberg P, Harron K.",,International journal of population data science,2022,2022-05-23,Y,Data Linkage; Statistical Disclosure Control; Data Utility; Synthetic Data; Data Confidentiality; Administrative Datasets,,,"Use of administrative data for research and for planning services has increased over recent decades due to the value of the large, rich information available. However, concerns about the release of sensitive or personal data and the associated disclosure risk can lead to lengthy approval processes and restricted data access. This can delay or prevent the production of timely evidence. A promising solution to facilitate more efficient data access is to create synthetic versions of the original datasets which are less likely to hold confidential information and can minimise disclosure risk. Such data may be used as an interim solution, allowing researchers to develop their analysis plans on non-disclosive data, whilst waiting for access to the real data. We aim to provide an overview of the background and uses of synthetic data and describe common methods used to generate synthetic data in the context of UK administrative research. We propose a simplified terminology for categories of synthetic data (univariate, multivariate, and complex modality synthetic data) as well as a more comprehensive description of the terminology used in the existing literature and illustrate challenges and future directions for research.",,pdf:https://ijpds.org/article/download/1727/3395; doi:https://doi.org/10.23889/ijpds.v7i1.1727; html:https://europepmc.org/articles/PMC10464868; pdf:https://europepmc.org/articles/PMC10464868?pdf=render
+39004446,https://doi.org/10.1136/jmg-2023-109791,Estimating cancer risk in carriers of Lynch syndrome variants in UK Biobank.,"Fummey E, Navarro P, Plazzer JP, Frayling IM, Knott S, Tenesa A.",,Journal of medical genetics,2024,2024-08-29,Y,Neoplasms; Human genetics; Genetic predisposition to disease; Germ-line Mutation; Whole Exome Sequencing,,,"BackgroundLynch syndrome (LS) is an inherited cancer predisposition syndrome caused by genetic variants affecting DNA mismatch repair (MMR) genes <i>MLH1</i>, <i>MSH2</i>, <i>MSH6</i> and <i>PMS2</i> Cancer risk in LS is estimated from cohorts of individuals ascertained by individual or family history of cancer, which may upwardly bias estimates.<h4>Methods</h4>830 carriers of pathogenic or likely pathogenic (<i>path_MMR</i>) MMR gene variants classified by InSiGHT were identified in 454 756 UK Biobank (UKB) participants using whole-exome sequence. Nelson-Aalen survival analysis was used to estimate cumulative incidence of colorectal, endometrial and breast cancer (BC).<h4>Results</h4>Cumulative incidence of colorectal and endometrial cancer (EC) by age 70 years was elevated in <i>path_MMR</i> carriers compared with non-carriers (colorectal: 11.8% (95% confidence interval (CI): 9.5% to 14.6%) vs 1.7% (95% CI: 1.6% to 1.7%), endometrial: 13.4% (95% CI: 10.2% to 17.6%) vs 1.0% (95% CI: 0.9% to 1.0%)), but the magnitude of this increase differed between genes. Cumulative BC incidence by age 70 years was not elevated in <i>path_MMR</i> carriers compared with non-carriers (8.9% (95% CI: 6.3% to 12.4%) vs 7.5% (95% CI: 7.4% to 7.6%)). Cumulative cancer incidence estimates in UKB were similar to estimates from the Prospective Lynch Syndrome Database for all genes and cancers, except there was no evidence for elevated EC risk in carriers of pathogenic <i>PMS2</i> variants in UKB.<h4>Conclusion</h4>These results support offering incidentally identified carriers of any <i>path_MMR</i> surveillance to manage colorectal cancer risk. Incidentally identified carriers of pathogenic variants in <i>MLH1</i>, <i>MSH2</i> and <i>MSH6</i> would also benefit from interventions to reduce EC risk. The results suggest that BC is not an LS-related cancer.",,pdf:https://jmg.bmj.com/content/jmedgenet/early/2024/08/06/jmg-2023-109791.full.pdf; doi:https://doi.org/10.1136/jmg-2023-109791; html:https://europepmc.org/articles/PMC11420727; pdf:https://europepmc.org/articles/PMC11420727?pdf=render
 38837525,https://doi.org/10.1002/alz.13870,"Mapping the interplay of atrial fibrillation, brain structure, and cognitive dysfunction.","Petersen M, Chevalier C, Naegele FL, Ingwersen T, Omidvarnia A, Hoffstaedter F, Patil K, Eickhoff SB, Schnabel RB, Kirchhof P, Schlemm E, Cheng B, Thomalla G, Jensen M.",,Alzheimer's & dementia : the journal of the Alzheimer's Association,2024,2024-06-05,Y,Atrial fibrillation; Neuropsychological Assessment; Diffusion Magnetic Resonance Imaging; Neuroimaging; Structural Magnetic Resonance Imaging,,,"<h4>Introduction</h4>Atrial fibrillation (AF) is associated with an elevated risk of cognitive impairment and dementia. Understanding the cognitive sequelae and brain structural changes associated with AF is vital for addressing ensuing health care needs.<h4>Methods and results</h4>We examined 1335 stroke-free individuals with AF and 2683 matched controls using neuropsychological assessments and multimodal neuroimaging. The analysis revealed that individuals with AF exhibited deficits in executive function, processing speed, and reasoning, accompanied by reduced cortical thickness, elevated extracellular free-water content, and widespread white matter abnormalities, indicative of small vessel pathology. Notably, brain structural differences statistically mediated the relationship between AF and cognitive performance.<h4>Discussion</h4>Integrating a comprehensive analysis approach with extensive clinical and magnetic resonance imaging data, our study highlights small vessel pathology as a possible unifying link among AF, cognitive decline, and abnormal brain structure. These insights can inform diagnostic approaches and motivate the ongoing implementation of effective therapeutic strategies. Highlights We investigated neuropsychological and multimodal neuroimaging data of 1335 individuals with atrial fibrillation (AF) and 2683 matched controls. Our analysis revealed AF-associated deficits in cognitive domains of attention, executive function, processing speed, and reasoning. Cognitive deficits in the AF group were accompanied by structural brain alterations including reduced cortical thickness and gray matter volume, alongside increased extracellular free-water content as well as widespread differences of white matter integrity. Structural brain changes statistically mediated the link between AF and cognitive performance, emphasizing the potential of structural imaging markers as a diagnostic tool in AF-related cognitive decline.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/alz.13870; doi:https://doi.org/10.1002/alz.13870; html:https://europepmc.org/articles/PMC11247702; pdf:https://europepmc.org/articles/PMC11247702?pdf=render
-36073628,https://doi.org/10.1161/jaha.122.026432,Differential Patterns and Outcomes of 20.6 Million Cardiovascular Emergency Department Encounters for Men and Women in the United States.,"Raisi-Estabragh Z, Kobo O, Elbadawi A, Velagapudi P, Sharma G, Bullock-Palmer RP, Petersen SE, Mehta LS, Ullah W, Roguin A, Sun LY, Mamas MA.",,Journal of the American Heart Association,2022,2022-09-08,Y,Men; Essential hypertension; Atrial fibrillation; Stroke; Women; Sex characteristics; United States,,,"Background We describe sex-differential disease patterns and outcomes of >20.6 million cardiovascular emergency department encounters in the United States. Methods and Results We analyzed primary cardiovascular encounters from the Nationwide Emergency Department Sample between 2016 and 2018. We grouped cardiovascular diagnoses into 15 disease categories. The sample included 48.7% women; median age was 67 (interquartile range, 54-78) years. Men had greater overall baseline comorbidity burden; however, women had higher rates of obesity, hypertension, and cerebrovascular disease. For women, the most common emergency department encounters were essential hypertension (16.0%), hypertensive heart or kidney disease (14.1%), and atrial fibrillation/flutter (10.2%). For men, the most common encounters were hypertensive heart or kidney disease (14.7%), essential hypertension (10.8%), and acute myocardial infarction (10.7%). Women were more likely to present with essential hypertension, hypertensive crisis, atrial fibrillation/flutter, supraventricular tachycardia, pulmonary embolism, or ischemic stroke. Men were more likely to present with acute myocardial infarction or cardiac arrest. In logistic regression models adjusted for baseline covariates, compared with men, women with intracranial hemorrhage had higher risk of hospitalization and death. Women presenting with pulmonary embolism or deep vein thrombosis were less likely to be hospitalized. Women with aortic aneurysm/dissection had higher odds of hospitalization and death. Men were more likely to die following presentations with hypertensive heart or kidney disease, atrial fibrillation/flutter, acute myocardial infarction, or cardiac arrest. Conclusions In this large nationally representative sample of cardiovascular emergency department presentations, we demonstrate significant sex differences in disease distribution, hospitalization, and death.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.122.026432; doi:https://doi.org/10.1161/JAHA.122.026432; html:https://europepmc.org/articles/PMC9673731; pdf:https://europepmc.org/articles/PMC9673731?pdf=render
 37868035,https://doi.org/10.1016/j.xgen.2023.100385,Gene expression and RNA splicing explain large proportions of the heritability for complex traits in cattle.,"Xiang R, Fang L, Liu S, Macleod IM, Liu Z, Breen EJ, Gao Y, Liu GE, Tenesa A, CattleGTEx Consortium, Mason BA, Chamberlain AJ, Wray NR, Goddard ME.",,Cell genomics,2023,2023-08-23,Y,RNA splicing; Heritability; Gene Expression; Complex Traits; Eqtl; Sqtl; Bayesr; Bayesrc,,,"Many quantitative trait loci (QTLs) are in non-coding regions. Therefore, QTLs are assumed to affect gene regulation. Gene expression and RNA splicing are primary steps of transcription, so DNA variants changing gene expression (eVariants) or RNA splicing (sVariants) are expected to significantly affect phenotypes. We quantify the contribution of eVariants and sVariants detected from 16 tissues (n = 4,725) to 37 traits of ∼120,000 cattle (average magnitude of genetic correlation between traits = 0.13). Analyzed in Bayesian mixture models, averaged across 37 traits, <i>cis</i> and <i>trans</i> eVariants and sVariants detected from 16 tissues jointly explain 69.2% (SE = 0.5%) of heritability, 44% more than expected from the same number of random variants. This 69.2% includes an average of 24% from <i>trans</i> e-/sVariants (14% more than expected). Averaged across 56 lipidomic traits, multi-tissue <i>cis</i> and <i>trans</i> e-/sVariants also explain 71.5% (SE = 0.3%) of heritability, demonstrating the essential role of proximal and distal regulatory variants in shaping mammalian phenotypes.",,doi:https://doi.org/10.1016/j.xgen.2023.100385; doi:https://doi.org/10.1016/j.xgen.2023.100385; html:https://europepmc.org/articles/PMC10589627; pdf:https://europepmc.org/articles/PMC10589627?pdf=render
+36073628,https://doi.org/10.1161/jaha.122.026432,Differential Patterns and Outcomes of 20.6 Million Cardiovascular Emergency Department Encounters for Men and Women in the United States.,"Raisi-Estabragh Z, Kobo O, Elbadawi A, Velagapudi P, Sharma G, Bullock-Palmer RP, Petersen SE, Mehta LS, Ullah W, Roguin A, Sun LY, Mamas MA.",,Journal of the American Heart Association,2022,2022-09-08,Y,Men; Essential hypertension; Atrial fibrillation; Stroke; Women; Sex characteristics; United States,,,"Background We describe sex-differential disease patterns and outcomes of >20.6 million cardiovascular emergency department encounters in the United States. Methods and Results We analyzed primary cardiovascular encounters from the Nationwide Emergency Department Sample between 2016 and 2018. We grouped cardiovascular diagnoses into 15 disease categories. The sample included 48.7% women; median age was 67 (interquartile range, 54-78) years. Men had greater overall baseline comorbidity burden; however, women had higher rates of obesity, hypertension, and cerebrovascular disease. For women, the most common emergency department encounters were essential hypertension (16.0%), hypertensive heart or kidney disease (14.1%), and atrial fibrillation/flutter (10.2%). For men, the most common encounters were hypertensive heart or kidney disease (14.7%), essential hypertension (10.8%), and acute myocardial infarction (10.7%). Women were more likely to present with essential hypertension, hypertensive crisis, atrial fibrillation/flutter, supraventricular tachycardia, pulmonary embolism, or ischemic stroke. Men were more likely to present with acute myocardial infarction or cardiac arrest. In logistic regression models adjusted for baseline covariates, compared with men, women with intracranial hemorrhage had higher risk of hospitalization and death. Women presenting with pulmonary embolism or deep vein thrombosis were less likely to be hospitalized. Women with aortic aneurysm/dissection had higher odds of hospitalization and death. Men were more likely to die following presentations with hypertensive heart or kidney disease, atrial fibrillation/flutter, acute myocardial infarction, or cardiac arrest. Conclusions In this large nationally representative sample of cardiovascular emergency department presentations, we demonstrate significant sex differences in disease distribution, hospitalization, and death.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.122.026432; doi:https://doi.org/10.1161/JAHA.122.026432; html:https://europepmc.org/articles/PMC9673731; pdf:https://europepmc.org/articles/PMC9673731?pdf=render
 31256764,https://doi.org/10.1192/bjp.2019.153,"Shining the light on eating disorders, incidence, prognosis and profiling of patients in primary and secondary care: national data linkage study.","Demmler JC, Brophy ST, Marchant A, John A, Tan JOA.",,The British journal of psychiatry : the journal of mental science,2020,2020-02-01,Y,epidemiology; Anorexia Nervosa; incidence; Bulimia Nervosa; Eating Disorder,,,"<h4>Background</h4>Diagnosing eating disorders can be difficult and few people with the disorder receive specialist services despite the associated high morbidity and mortality.<h4>Aims</h4>To examine the burden of eating disorders in the population in terms of incidence, comorbidities and survival.<h4>Method</h4>We used linked electronic health records from general practitioner and hospital admissions in Wales, UK within the Secure Anonymised Information Linkage (SAIL) databank to investigate the incidence of new eating disorder diagnoses. We examined the frequency of comorbid diagnoses and prescribed medications in cases and controls in the 2 years before and 3 years after diagnosis, and performed a survival analysis.<h4>Results</h4>A total of 15 558 people were diagnosed with eating disorders between 1990 and 2017. The incidence peaked at 24 per 100 000 people in 2003/04. People with eating disorders showed higher levels of other mental disorders (odds ratio 4.32, 95% CI 4.01-4.66) and external causes of morbidity and mortality (odds ratio 2.92, 95% CI 2.44-3.50). They had greater prescription of central nervous system drugs (odds ratio 3.15, 95% CI 2.97-3.33), gastrointestinal drugs (odds ratio 2.61, 95% CI 2.45-2.79) and dietetic drugs (odds ratio 2.42, 95% CI 2.24-2.62) before diagnosis. These excess diagnoses and prescriptions remained 3 years after diagnosis. Mortality was raised compared with controls for some eating disorders, particularly in females with anorexia nervosa.<h4>Conclusions</h4>Incidence of diagnosed eating disorders is relatively low in the population but there is a major longer term burden in morbidity and mortality to the individual.",,pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/A00E32E32B0FB324075CF2CF0973687F/S0007125019001533a.pdf/div-class-title-shining-the-light-on-eating-disorders-incidence-prognosis-and-profiling-of-patients-in-primary-and-secondary-care-national-data-linkage-study-div.pdf; doi:https://doi.org/10.1192/bjp.2019.153; html:https://europepmc.org/articles/PMC7557634; pdf:https://europepmc.org/articles/PMC7557634?pdf=render
 35879616,https://doi.org/10.1038/s41591-022-01909-w,Symptoms and risk factors for long COVID in non-hospitalized adults.,"Subramanian A, Nirantharakumar K, Hughes S, Myles P, Williams T, Gokhale KM, Taverner T, Chandan JS, Brown K, Simms-Williams N, Shah AD, Singh M, Kidy F, Okoth K, Hotham R, Bashir N, Cockburn N, Lee SI, Turner GM, Gkoutos GV, Aiyegbusi OL, McMullan C, Denniston AK, Sapey E, Lord JM, Wraith DC, Leggett E, Iles C, Marshall T, Price MJ, Marwaha S, Davies EH, Jackson LJ, Matthews KL, Camaradou J, Calvert M, Haroon S.",,Nature medicine,2022,2022-07-25,Y,,,,"Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is associated with a range of persistent symptoms impacting everyday functioning, known as post-COVID-19 condition or long COVID. We undertook a retrospective matched cohort study using a UK-based primary care database, Clinical Practice Research Datalink Aurum, to determine symptoms that are associated with confirmed SARS-CoV-2 infection beyond 12 weeks in non-hospitalized adults and the risk factors associated with developing persistent symptoms. We selected 486,149 adults with confirmed SARS-CoV-2 infection and 1,944,580 propensity score-matched adults with no recorded evidence of SARS-CoV-2 infection. Outcomes included 115 individual symptoms, as well as long COVID, defined as a composite outcome of 33 symptoms by the World Health Organization clinical case definition. Cox proportional hazards models were used to estimate adjusted hazard ratios (aHRs) for the outcomes. A total of 62 symptoms were significantly associated with SARS-CoV-2 infection after 12 weeks. The largest aHRs were for anosmia (aHR 6.49, 95% CI 5.02-8.39), hair loss (3.99, 3.63-4.39), sneezing (2.77, 1.40-5.50), ejaculation difficulty (2.63, 1.61-4.28) and reduced libido (2.36, 1.61-3.47). Among the cohort of patients infected with SARS-CoV-2, risk factors for long COVID included female sex, belonging to an ethnic minority, socioeconomic deprivation, smoking, obesity and a wide range of comorbidities. The risk of developing long COVID was also found to be increased along a gradient of decreasing age. SARS-CoV-2 infection is associated with a plethora of symptoms that are associated with a range of sociodemographic and clinical risk factors.",,pdf:https://www.nature.com/articles/s41591-022-01909-w.pdf; doi:https://doi.org/10.1038/s41591-022-01909-w; html:https://europepmc.org/articles/PMC9388369; pdf:https://europepmc.org/articles/PMC9388369?pdf=render
 38443076,https://doi.org/10.1136/bmjopen-2023-078788,Impact of inconsistent ethnicity recordings on estimates of inequality in child health and education data: a data linkage study of Child and Adolescent Mental Health Services in South London.,"Wickersham A, Das-Munshi J, Ford T, Jewell A, Stewart R, Downs J.",,BMJ open,2024,2024-03-05,Y,Epidemiologic studies; Mental health; Child & Adolescent Psychiatry; Health Equity,,,"<h4>Objectives</h4>Ethnicity data are critical for identifying inequalities, but previous studies suggest that ethnicity is not consistently recorded between different administrative datasets. With researchers increasingly leveraging cross-domain data linkages, we investigated the completeness and consistency of ethnicity data in two linked health and education datasets.<h4>Design</h4>Cohort study.<h4>Setting</h4>South London and Maudsley NHS Foundation Trust deidentified electronic health records, accessed via Clinical Record Interactive Search (CRIS) and the National Pupil Database (NPD) (2007-2013).<h4>Participants</h4>N=30 426 children and adolescents referred to local Child and Adolescent Mental Health Services.<h4>Primary and secondary outcome measures</h4>Ethnicity data were compared between CRIS and the NPD. Associations between ethnicity as recorded from each source and key educational and clinical outcomes were explored with risk ratios.<h4>Results</h4>Ethnicity data were available for 79.3% from the NPD, 87.0% from CRIS, 97.3% from either source and 69.0% from both sources. Among those who had ethnicity data from both, the two data sources agreed on 87.0% of aggregate ethnicity categorisations overall, but with high levels of disagreement in Mixed and Other ethnic groups. Strengths of associations between ethnicity, educational attainment and neurodevelopmental disorder varied according to which data source was used to code ethnicity. For example, as compared with White pupils, a significantly higher proportion of Asian pupils achieved expected educational attainment thresholds only if ethnicity was coded from the NPD (RR=1.46, 95% CI 1.29 to 1.64), not if ethnicity was coded from CRIS (RR=1.11, 0.98 to 1.26).<h4>Conclusions</h4>Data linkage has the potential to minimise missing ethnicity data, and overlap in ethnicity categorisations between CRIS and the NPD was generally high. However, choosing which data source to primarily code ethnicity from can have implications for analyses of ethnicity, mental health and educational outcomes. Users of linked data should exercise caution in combining and comparing ethnicity between different data sources.",,pdf:https://bmjopen.bmj.com/content/bmjopen/14/3/e078788.full.pdf; doi:https://doi.org/10.1136/bmjopen-2023-078788; html:https://europepmc.org/articles/PMC10916132; pdf:https://europepmc.org/articles/PMC10916132?pdf=render
 35308936,https://doi.org/,Mapping the Read2/CTV3 controlled clinical terminologies to Phecodes in UK Biobank primary care electronic health records: implementation and evaluation.,"Denaxas S, Liu G, Feng Q, Fatemifar G, Bastarache L, Kerchberger EV, Hingorani AD, Lumbers T, Peterson JF, Wei WQ, Hemingway H.",,AMIA ... Annual Symposium proceedings. AMIA Symposium,2021,2021-01-01,N,,,,"<b>Objective:</b> To establish and validate mappings between primary care clinical terminologies (Read Version 2, Clinical Terms Version 3) and Phecodes. <b>Methods:</b> We processed 123,662,421 primary care events from 230,096 UK Biobank (UKB) participants. We assessed the validity of the primary care-derived Phecodes by conducting PheWAS analyses for seven pre-selected SNPs in the UKB and compared with estimates from BioVU. <b>Results:</b> We mapped 92% of Read2 (n=10,834) and 91% of CTV3 (n=21,988) to 1,449 and 1,490 Phecodes. UKB PheWAS using Phecodes from primary care EHR and hospitalizations replicated all (n=22) previously-reported genotype-phenotype associations. When limiting Phecodes to primary care EHR, replication was 81% (n=18). <b>Conclusion:</b> We introduced a first version of mappings from Read2/CTV3 to Phecodes. The reference list of diseases provided by Phecodes can be extended, enabling researchers to leverage primary care EHR for high-throughput discovery research.",,html:https://europepmc.org/articles/PMC8861677; pdf:https://europepmc.org/articles/PMC8861677?pdf=render
-39074912,https://doi.org/10.1136/bmjhci-2023-100963,Communicating exploratory unsupervised machine learning analysis in age clustering for paediatric disease.,"Spear JW, Pissaridou E, Bowyer S, Bryant WA, Key D, Booth J, Spiridou A, Denaxas S, Pope R, Taylor AM, Hemingway H, Sebire NJ.",,BMJ health & care informatics,2024,2024-07-29,Y,Data Visualization; Machine Learning; Electronic Health Records; Data Science,,,"<h4>Background</h4>Despite the increasing availability of electronic healthcare record (EHR) data and wide availability of plug-and-play machine learning (ML) Application Programming Interfaces, the adoption of data-driven decision-making within routine hospital workflows thus far, has remained limited. Through the lens of deriving clusters of diagnoses by age, this study investigated the type of ML analysis that can be performed using EHR data and how results could be communicated to lay stakeholders.<h4>Methods</h4>Observational EHR data from a tertiary paediatric hospital, containing 61 522 unique patients and 3315 unique ICD-10 diagnosis codes was used, after preprocessing. K-means clustering was applied to identify age distributions of patient diagnoses. The final model was selected using quantitative metrics and expert assessment of the clinical validity of the clusters. Additionally, uncertainty over preprocessing decisions was analysed.<h4>Findings</h4>Four age clusters of diseases were identified, broadly aligning to ages between: 0 and 1; 1 and 5; 5 and 13; 13 and 18. Diagnoses, within the clusters, aligned to existing knowledge regarding the propensity of presentation at different ages, and sequential clusters presented known disease progressions. The results validated similar methodologies within the literature. The impact of uncertainty induced by preprocessing decisions was large at the individual diagnoses but not at a population level. Strategies for mitigating, or communicating, this uncertainty were successfully demonstrated.<h4>Conclusion</h4>Unsupervised ML applied to EHR data identifies clinically relevant age distributions of diagnoses which can augment existing decision making. However, biases within healthcare datasets dramatically impact results if not appropriately mitigated or communicated.",,doi:https://doi.org/10.1136/bmjhci-2023-100963; html:https://europepmc.org/articles/PMC11288139; pdf:https://europepmc.org/articles/PMC11288139?pdf=render
 36680646,https://doi.org/10.1007/s10654-022-00962-6,Characterising patterns of COVID-19 and long COVID symptoms: evidence from nine UK longitudinal studies.,"Bowyer RCE, Huggins C, Toms R, Shaw RJ, Hou B, Thompson EJ, Kwong ASF, Williams DM, Kibble M, Ploubidis GB, Timpson NJ, Sterne JAC, Chaturvedi N, Steves CJ, Tilling K, Silverwood RJ, CONVALESCENCE Study.",,European journal of epidemiology,2023,2023-01-21,Y,Clustering; Longitudinal Studies; Symptom Patterns; Covid-19; Long Covid,,,"Multiple studies across global populations have established the primary symptoms characterising Coronavirus Disease 2019 (COVID-19) and long COVID. However, as symptoms may also occur in the absence of COVID-19, a lack of appropriate controls has often meant that specificity of symptoms to acute COVID-19 or long COVID, and the extent and length of time for which they are elevated after COVID-19, could not be examined. We analysed individual symptom prevalences and characterised patterns of COVID-19 and long COVID symptoms across nine UK longitudinal studies, totalling over 42,000 participants. Conducting latent class analyses separately in three groups ('no COVID-19', 'COVID-19 in last 12 weeks', 'COVID-19 > 12 weeks ago'), the data did not support the presence of more than two distinct symptom patterns, representing high and low symptom burden, in each group. Comparing the high symptom burden classes between the 'COVID-19 in last 12 weeks' and 'no COVID-19' groups we identified symptoms characteristic of acute COVID-19, including loss of taste and smell, fatigue, cough, shortness of breath and muscle pains or aches. Comparing the high symptom burden classes between the 'COVID-19 > 12 weeks ago' and 'no COVID-19' groups we identified symptoms characteristic of long COVID, including fatigue, shortness of breath, muscle pain or aches, difficulty concentrating and chest tightness. The identified symptom patterns among individuals with COVID-19 > 12 weeks ago were strongly associated with self-reported length of time unable to function as normal due to COVID-19 symptoms, suggesting that the symptom pattern identified corresponds to long COVID. Building the evidence base regarding typical long COVID symptoms will improve diagnosis of this condition and the ability to elicit underlying biological mechanisms, leading to better patient access to treatment and services.",,pdf:https://link.springer.com/content/pdf/10.1007/s10654-022-00962-6.pdf; doi:https://doi.org/10.1007/s10654-022-00962-6; html:https://europepmc.org/articles/PMC9860244; pdf:https://europepmc.org/articles/PMC9860244?pdf=render
+39074912,https://doi.org/10.1136/bmjhci-2023-100963,Communicating exploratory unsupervised machine learning analysis in age clustering for paediatric disease.,"Spear JW, Pissaridou E, Bowyer S, Bryant WA, Key D, Booth J, Spiridou A, Denaxas S, Pope R, Taylor AM, Hemingway H, Sebire NJ.",,BMJ health & care informatics,2024,2024-07-29,Y,Data Visualization; Machine Learning; Electronic Health Records; Data Science,,,"<h4>Background</h4>Despite the increasing availability of electronic healthcare record (EHR) data and wide availability of plug-and-play machine learning (ML) Application Programming Interfaces, the adoption of data-driven decision-making within routine hospital workflows thus far, has remained limited. Through the lens of deriving clusters of diagnoses by age, this study investigated the type of ML analysis that can be performed using EHR data and how results could be communicated to lay stakeholders.<h4>Methods</h4>Observational EHR data from a tertiary paediatric hospital, containing 61 522 unique patients and 3315 unique ICD-10 diagnosis codes was used, after preprocessing. K-means clustering was applied to identify age distributions of patient diagnoses. The final model was selected using quantitative metrics and expert assessment of the clinical validity of the clusters. Additionally, uncertainty over preprocessing decisions was analysed.<h4>Findings</h4>Four age clusters of diseases were identified, broadly aligning to ages between: 0 and 1; 1 and 5; 5 and 13; 13 and 18. Diagnoses, within the clusters, aligned to existing knowledge regarding the propensity of presentation at different ages, and sequential clusters presented known disease progressions. The results validated similar methodologies within the literature. The impact of uncertainty induced by preprocessing decisions was large at the individual diagnoses but not at a population level. Strategies for mitigating, or communicating, this uncertainty were successfully demonstrated.<h4>Conclusion</h4>Unsupervised ML applied to EHR data identifies clinically relevant age distributions of diagnoses which can augment existing decision making. However, biases within healthcare datasets dramatically impact results if not appropriately mitigated or communicated.",,doi:https://doi.org/10.1136/bmjhci-2023-100963; html:https://europepmc.org/articles/PMC11288139; pdf:https://europepmc.org/articles/PMC11288139?pdf=render
 37550086,https://doi.org/10.1136/bmjment-2023-300762,Associations between air pollution and mental health service use in dementia: a retrospective cohort study.,"Ronaldson A, Stewart R, Mueller C, Das-Munshi J, Newbury JB, Mudway IS, Broadbent M, Fisher HL, Beevers S, Dajnak D, Hotopf M, Hatch SL, Bakolis I.",,BMJ mental health,2023,2023-07-01,Y,Psychiatry; Adult Psychiatry; Delirium & Cognitive Disorders,,,"<h4>Background</h4>Little is known about the role of air pollution in how people with dementia use mental health services.<h4>Objective</h4>We examined longitudinal associations between air pollution exposure and mental health service use in people with dementia.<h4>Methods</h4>In 5024 people aged 65 years or older with dementia in South London, high resolution estimates of nitrogen dioxide (NO<sub>2</sub>) and particulate matter (PM<sub>2.5</sub> and PM<sub>10</sub>) levels in ambient air were linked to residential addresses. Associations between air pollution and Community Mental Health Team (CMHT) events (recorded over 9 years) were examined using negative binomial regression models. Cognitive function was measured using the Mini Mental State Examination (MMSE) and health and social functioning was measured using the Health of the Nation Outcomes Scale (HoNOS65+). Associations between air pollution and both MMSE and HoNOS65+ scores were assessed using linear regression models.<h4>Findings</h4>In the first year of follow-up, increased exposure to all air pollutants was associated with an increase in the use of CMHTs in a dose-response manner. These associations were strongest when we compared the highest air pollution quartile (quartile 4: Q4) with the lowest quartile (Q1) (eg, NO<sub>2</sub>: adjusted incidence rate ratio (aIRR) 1.27, 95% CI 1.11 to 1.45, p<0.001). Dose-response patterns between PM<sub>2.5</sub> and CMHT events remained at 5 and 9 years. Associations were strongest for patients with vascular dementia. NO<sub>2</sub> levels were linked with poor functional status, but not cognitive function.<h4>Conclusions</h4>Residential air pollution exposure is associated with increased CMHT usage among people with dementia.<h4>Clinical implications</h4>Efforts to reduce pollutant exposures in urban settings might reduce the use of mental health services in people with dementia, freeing up resources in already considerably stretched psychiatric services.",,doi:https://doi.org/10.1136/bmjment-2023-300762; html:https://europepmc.org/articles/PMC10577765; pdf:https://europepmc.org/articles/PMC10577765?pdf=render
-39272070,https://doi.org/10.1186/s12889-024-19999-1,"Prevalence of undiagnosed hypertension and associated factors in Ndera sector, Gasabo district of Rwanda: a cross-sectional study.","Okesina AA, Habineza JC, Mbazumutima R, Mignonne U, Mahirwe C, Hakizimana S, Gbadamosi MA, Uppal A, Wabwire FP.",,BMC public health,2024,2024-09-13,Y,Hypertension; risk factors; Rwanda; Low- And Middle-income Countries; Healthcare Services; Undiagnosed Hypertension,,,"<h4>Background</h4>Hypertension remains a major global health challenge, including in low- and middle-income countries. In Rwanda, a lack of adequate information and healthcare services impacts healthcare-seeking behaviors, contributing to undiagnosed hypertension in rural areas. Therefore, the need to determine its prevalence and associated factors.<h4>Methods</h4>A cross-sectional study was conducted with 393 adults in the Ndera Sector, of Rwanda's Gasabo District, through a multistage sampling technique. Data was gathered using the WHO STEP-wise approach to non-communicable disease risk factor surveillance (STEPS) questionnaire; physical examination was done to determine blood pressure and body-mass index (BMI), after which the data collected was analyzed using SPSS. Newly diagnosed hypertension was determined when on two different intervals, systolic blood pressure readings was > 140 mmHg, and/or the diastolic blood pressure readings was > 90 mmHg, in the absence of previous hypertension diagnosis.<h4>Results</h4>The overall prevalence of hypertension among patients at Ndera sector was 15%, all of which were newly diagnosed. The mean (SD) age of the participants was 37 (13.7) years and half (53%) were women. The mean systolic blood pressure for men was 124.3 mmHg compared to 120.9 mmHg for women (p = 0.043, 95%CI: 0.12-6.74). Women had a significantly higher mean BMI (26.0) compared to men (22.8) (p < 0.001, 95%CI: -4.18 - -2.31). Age (χ² = 37.400, p < 0.001), residence (χ² = 10.200, p < 0.001), BMI (χ² = 22.1, p < 0.001), and lack of knowledge about hypertension (χ² = 25.1, p < 0.001) were the factors with significantly undiagnosed hypertension.<h4>Conclusions</h4>The high prevalence of undiagnosed hypertension in Ndera Sector is linked to gender, older age, higher BMI, location, and lack of hypertension knowledge. These findings call for multifaceted approaches, combining educational initiatives, geographical targeting, lifestyle modifications, and policy implementations, all aimed at mitigating the burden of undiagnosed hypertension and enhancing community health within the Ndera Sector.",,doi:https://doi.org/10.1186/s12889-024-19999-1; html:https://europepmc.org/articles/PMC11397070; pdf:https://europepmc.org/articles/PMC11397070?pdf=render
 37004203,https://doi.org/10.1093/qjmed/hcad050,Classifying the unclassifiable-a Delphi study to reach consensus on the fibrotic nature of diseases.,"Massen GM, Allen RJ, Leavy OC, Selby NM, Aithal GP, Oliver N, Parfrey H, Wain LV, Jenkins G, Stewart I, Quint JK.",,QJM : monthly journal of the Association of Physicians,2023,2023-06-01,Y,,,,"<h4>Background</h4>Traditionally, clinical research has focused on individual fibrotic diseases or fibrosis in a particular organ. However, it is possible for people to have multiple fibrotic diseases. While multi-organ fibrosis may suggest shared pathogenic mechanisms, yet there is no consensus on what constitutes a fibrotic disease and therefore fibrotic multimorbidity.<h4>Aim</h4>A Delphi study was performed to reach consensus on which diseases may be described as fibrotic.<h4>Methods</h4>Participants were asked to rate a list of diseases, sub-grouped according to eight body regions, as 'fibrotic manifestation always present', 'can develop fibrotic manifestations', 'associated with fibrotic manifestations' or 'not fibrotic nor associated'. Classifications of 'fibrotic manifestation always present' and 'can develop fibrotic manifestations' were merged and termed 'fibrotic'. Clinical consensus was defined according to the interquartile range, having met a minimum number of responses. Clinical agreement was used for classification where diseases did not meet the minimum number of responses (required for consensus measure), were only classified if there was 100% consensus on disease classification.<h4>Results</h4>After consulting experts, searching the literature and coding dictionaries, a total of 323 non-overlapping diseases which might be considered fibrotic were identified; 92 clinical specialists responded to the first round of the survey. Over three survey rounds, 240 diseases were categorized as fibrotic via clinical consensus and 25 additional diseases through clinical agreement.<h4>Conclusion</h4>Using a robust methodology, an extensive list of diseases was classified. The findings lay the foundations for studies estimating the burden of fibrotic multimorbidity, as well as investigating shared mechanisms and therapies.",,pdf:https://academic.oup.com/qjmed/advance-article-pdf/doi/10.1093/qjmed/hcad050/50051055/hcad050.pdf; doi:https://doi.org/10.1093/qjmed/hcad050; html:https://europepmc.org/articles/PMC10250078; pdf:https://europepmc.org/articles/PMC10250078?pdf=render
+39272070,https://doi.org/10.1186/s12889-024-19999-1,"Prevalence of undiagnosed hypertension and associated factors in Ndera sector, Gasabo district of Rwanda: a cross-sectional study.","Okesina AA, Habineza JC, Mbazumutima R, Mignonne U, Mahirwe C, Hakizimana S, Gbadamosi MA, Uppal A, Wabwire FP.",,BMC public health,2024,2024-09-13,Y,Hypertension; risk factors; Rwanda; Low- And Middle-income Countries; Healthcare Services; Undiagnosed Hypertension,,,"<h4>Background</h4>Hypertension remains a major global health challenge, including in low- and middle-income countries. In Rwanda, a lack of adequate information and healthcare services impacts healthcare-seeking behaviors, contributing to undiagnosed hypertension in rural areas. Therefore, the need to determine its prevalence and associated factors.<h4>Methods</h4>A cross-sectional study was conducted with 393 adults in the Ndera Sector, of Rwanda's Gasabo District, through a multistage sampling technique. Data was gathered using the WHO STEP-wise approach to non-communicable disease risk factor surveillance (STEPS) questionnaire; physical examination was done to determine blood pressure and body-mass index (BMI), after which the data collected was analyzed using SPSS. Newly diagnosed hypertension was determined when on two different intervals, systolic blood pressure readings was > 140 mmHg, and/or the diastolic blood pressure readings was > 90 mmHg, in the absence of previous hypertension diagnosis.<h4>Results</h4>The overall prevalence of hypertension among patients at Ndera sector was 15%, all of which were newly diagnosed. The mean (SD) age of the participants was 37 (13.7) years and half (53%) were women. The mean systolic blood pressure for men was 124.3 mmHg compared to 120.9 mmHg for women (p = 0.043, 95%CI: 0.12-6.74). Women had a significantly higher mean BMI (26.0) compared to men (22.8) (p < 0.001, 95%CI: -4.18 - -2.31). Age (χ² = 37.400, p < 0.001), residence (χ² = 10.200, p < 0.001), BMI (χ² = 22.1, p < 0.001), and lack of knowledge about hypertension (χ² = 25.1, p < 0.001) were the factors with significantly undiagnosed hypertension.<h4>Conclusions</h4>The high prevalence of undiagnosed hypertension in Ndera Sector is linked to gender, older age, higher BMI, location, and lack of hypertension knowledge. These findings call for multifaceted approaches, combining educational initiatives, geographical targeting, lifestyle modifications, and policy implementations, all aimed at mitigating the burden of undiagnosed hypertension and enhancing community health within the Ndera Sector.",,doi:https://doi.org/10.1186/s12889-024-19999-1; html:https://europepmc.org/articles/PMC11397070; pdf:https://europepmc.org/articles/PMC11397070?pdf=render
 36329425,https://doi.org/10.1186/s12890-022-02189-3,Derivation of asthma severity from electronic prescription records using British thoracic society treatment steps.,"Tibble H, Sheikh A, Tsanas A.",,BMC pulmonary medicine,2022,2022-11-03,Y,Asthma; Pharmacotherapy; Severity; Pharmacoepidemiology; Electronic Health Records; Treatment Guidelines,,,"<h4>Background</h4>Asthma severity is typically assessed through a retrospective assessment of the treatment required to control symptoms and to prevent exacerbations. The joint British Thoracic Society and Scottish Intercollegiate Guidelines Network (BTS/SIGN) guidelines encourage a stepwise approach to pharmacotherapy, and as such, current treatment step can be considered as a severity categorisation proxy. Briefly, the steps for adults can be summarised as: no controller therapy (Step 0), low-strength Inhaled Corticosteroids (ICS; Step 1), ICS plus Long-Acting Beta-2 Agonist (LABA; Step 2), medium-dose ICS + LABA (Step 3), and finally either an increase in strength or additional therapies (Step 4). This study aimed to investigate how BTS/SIGN Steps can be estimated from across a large cohort using electronic prescription records, and to describe the incidence of each BTS/SIGN Step in a general population.<h4>Methods</h4>There were 41,433,707 prescriptions, for 671,304 individuals, in the Asthma Learning Health System Scottish cohort, between 1/2009 and 3/2017. Days on which an individual had a prescription for at least one asthma controller (preventer) medication were labelled prescription events. A rule-based algorithm was developed for extracting the strength and volume of medication instructed to be taken daily from free-text data fields. Asthma treatment regimens were categorised by the combination of medications prescribed in the 120 days preceding any prescription event and categorised into BTS/SIGN treatment steps.<h4>Results</h4>Almost 4.5 million ALHS prescriptions were for asthma controllers. 26% of prescription events had no inhaled corticosteroid prescriptions in the preceding 120 days (Step 0), 16% were assigned to BTS/SIGN Step 1, 7% to Step 2, 21% to Step 3, and 30% to Step 4. The median days spent on a treatment step before a step-down in treatment was 297 days, whereas a step-up only took a median of 134 days.<h4>Conclusion</h4>We developed a reproducible methodology enabling researchers to estimate BTS/SIGN asthma treatment steps in population health studies, providing valuable insights into population and patient-specific trajectories, towards improving the management of asthma.",,pdf:https://bmcpulmmed.biomedcentral.com/counter/pdf/10.1186/s12890-022-02189-3; doi:https://doi.org/10.1186/s12890-022-02189-3; html:https://europepmc.org/articles/PMC9635147; pdf:https://europepmc.org/articles/PMC9635147?pdf=render
 38360481,https://doi.org/10.1016/j.ebiom.2024.105000,Phenome-wide analysis reveals epistatic associations between APOL1 variants and chronic kidney disease and multiple other disorders.,"Adamson WE, Noyes H, Johnson P, Cooper A, Monckton DG, Ogunsola J, Beckett-Hill G, Sullivan M, Mark P, Parekh RS, MacLeod A.",,EBioMedicine,2024,2024-02-14,Y,Chronic Kidney Disease; Phenome; Apol1; Uk Biobank; Covid-19,,,"<h4>Background</h4>APOL1 variants G1 and G2 are common in populations with recent African ancestry. They are associated with protection from African sleeping sickness, however homozygosity or compound heterozygosity for these variants is associated with chronic kidney disease (CKD) and related conditions. What is not clear is the extent of associations with non-kidney-related disorders, and whether there are clusters of diseases associated with individual APOL1 genotypes.<h4>Methods</h4>Using a cohort of 7462 UK Biobank participants with recent African ancestry, we conducted a phenome-wide association study investigating associations between individual APOL1 genotypes and conditions identified by the International Classification of Disease phenotypes.<h4>Findings</h4>We identified 27 potential associations between individual APOL1 genotypes and a diverse range of conditions. G1/G2 compound heterozygotes were specifically associated with 26 of these conditions (all deleteriously), with an over-representation of infectious diseases (including hospitalisation and death resulting from COVID-19). The analysis also exposed complexities in the relationship between APOL1 and CKD that are not evident when risk variants are grouped together: G1 homozygosity, G2 homozygosity, and G1/G2 compound heterozygosity were each shown to be associated with distinct CKD phenotypes. The multi-locus nature of the G1/G2 genotype means that its associations would go undetected in a standard genome-wide association study.<h4>Interpretation</h4>Our findings have implications for understanding health risks and better-targeted detection, intervention, and therapeutic strategies, particularly in populations where APOL1 G1 and G2 are common such as in sub-Saharan Africa and its diaspora.<h4>Funding</h4>This study was funded by the Wellcome Trust (209511/Z/17/Z) and H3Africa (H3A/18/004).",,doi:https://doi.org/10.1016/j.ebiom.2024.105000; html:https://europepmc.org/articles/PMC10944146; pdf:https://europepmc.org/articles/PMC10944146?pdf=render
 36997954,https://doi.org/10.1186/s13063-023-07251-x,A DELPHI study priority setting the remaining challenges for the use of routinely collected data in trials: COMORANT-UK.,"Williams ADN, Davies G, Farrin AJ, Mafham M, Robling M, Sydes MR, Lugg-Widger FV.",,Trials,2023,2023-03-30,Y,Priority Setting; Consensus; Routinely Collected Data; Trials Methodology,,,"<h4>Background</h4>Researchers are increasingly seeking to use routinely collected data to support clinical trials. This approach has the potential to transform the way clinical trials are conducted in the future. The availability of routinely collected data for research, whether healthcare or administrative, has increased, and infrastructure funding has enabled much of this. However, challenges remain at all stages of a trial life cycle. This study, COMORANT-UK, aimed to systematically identify, with key stakeholders across the UK, the ongoing challenges related to trials that seek to use routinely collected data.<h4>Methods</h4>This three-step Delphi method consisted of two rounds of anonymous web-based surveys and a virtual consensus meeting. Stakeholders included trialists, data infrastructures, funders of trials, regulators, data providers and the public. Stakeholders identified research questions or challenges that they considered were of particular importance and then selected their top 10 in the second survey. The ranked questions were taken forward to the consensus meeting for discussion with representatives invited from the stakeholder groups.<h4>Results</h4>In the first survey, 66 respondents yielded over 260 questions or challenges. These were thematically grouped and merged into a list of 40 unique questions. Eighty-eight stakeholders then ranked their top ten from the 40 questions in the second survey. The most common 14 questions were brought to the virtual consensus meeting in which stakeholders agreed a top list of seven questions. We report these seven questions which are within the following domains: trial design, Patient and Public Involvement, trial set-up, trial open and trial data. These questions address both evidence gaps (requiring further methodological research) and implementation gaps (requiring training and/or service re-organisation).<h4>Conclusion</h4>This prioritised list of seven questions should inform the direction of future research in this area and should direct efforts to ensure that the benefits in major infrastructure for routinely collected data are achieved and translated. Without this and future work to address these questions, the potential societal benefits of using routinely collected data to help answer important clinical questions will not be realised.",,pdf:https://trialsjournal.biomedcentral.com/counter/pdf/10.1186/s13063-023-07251-x; doi:https://doi.org/10.1186/s13063-023-07251-x; html:https://europepmc.org/articles/PMC10064573; pdf:https://europepmc.org/articles/PMC10064573?pdf=render
 38670744,https://doi.org/10.1016/s2589-7500(24)00028-1,Data challenges for international health emergencies: lessons learned from ten international COVID-19 driver projects.,"Boylan S, Arsenault C, Barreto M, Bozza FA, Fonseca A, Forde E, Hookham L, Humphreys GS, Ichihara MY, Le Doare K, Liu XF, McNamara E, Mugunga JC, Oliveira JF, Ouma J, Postlethwaite N, Retford M, Reyes LF, Morris AD, Wozencraft A.",,The Lancet. Digital health,2024,2024-05-01,N,,,,"The COVID-19 pandemic highlighted the importance of international data sharing and access to improve health outcomes for all. The International COVID-19 Data Alliance (ICODA) programme enabled 12 exemplar or driver projects to use existing health-related data to address major research questions relating to the pandemic, and developed data science approaches that helped each research team to overcome challenges, accelerate the data research cycle, and produce rapid insights and outputs. These approaches also sought to address inequity in data access and use, test approaches to ethical health data use, and make summary datasets and outputs accessible to a wider group of researchers. This Health Policy paper focuses on the challenges and lessons learned from ten of the ICODA driver projects, involving researchers from 19 countries and a range of health-related datasets. The ICODA programme reviewed the time taken for each project to complete stages of the health data research cycle and identified common challenges in areas such as data sharing agreements and data curation. Solutions included provision of standard data sharing templates, additional data curation expertise at an early stage, and a trusted research environment that facilitated data sharing across national boundaries and reduced risk. These approaches enabled the driver projects to rapidly produce research outputs, including publications, shared code, dashboards, and innovative resources, which can all be accessed and used by other research teams to address global health challenges.",,doi:https://doi.org/10.1016/s2589-7500(24)00028-1; doi:https://doi.org/10.1016/S2589-7500(24)00028-1
 39364338,https://doi.org/10.12688/wellcomeopenres.20278.2,"VIVALDI Cohort Profile: Using linked, routinely collected data and longitudinal blood sampling to characterise COVID-19 infections, vaccinations, and related outcomes in care home staff and residents in England.","Krutikov M, Bone D, Stirrup O, Bruton R, Azmi B, Fuller C, Lau M, Low J, Rastogi S, Monakhov I, Tut G, Fink D, Moss P, Hayward A, Copas A, Shallcross L.",,Wellcome open research,2023,2023-01-01,Y,Infection; Data Linkage; Care Homes; Older Adults; Covid-19,,,"VIVALDI (ISRCTN14447421) is a government-funded longitudinal open observational cohort study of staff and residents in care homes for older people in England. The study aimed to describe epidemiology (including seroprevalence) and immune responses to COVID-19 in a subset of care homes, in the context of extremely high mortality in this setting, in the first 12-18 months of the pandemic. Data linkage to routine health data was undertaken for all staff and residents and a subset of individuals who consented to sequential blood sampling to investigate SARS-CoV-2 immunity. This paper aims to describe the samples stored within the VIVALDI biobank and associated linked data, available for use by researchers. Over 70,000 individuals from 346 care homes were included in the data linkage cohort (1 <sup>st</sup> March 2020-31 <sup>st</sup> March 2023). 4971 samples from 2264 individuals (1415 staff, 827 residents) collected between 29 <sup>th</sup> October 2020 and 10 <sup>th</sup> March 2023 are stored. Amongst these samples, there was a maximum of seven per participant however, 217 (26.2%) residents and 551 (38.9%) staff participated in one round only. Key study findings include high COVID-19 seroprevalence among surviving residents, exceeding rates in community-dwelling peers. COVID-19 vaccinations generated robust immune responses in staff and residents which waned, supporting the need for booster vaccination, particularly in response to new variants. Prior infection significantly improved vaccine-induced immune responses, however protection from infection declined following Omicron variant emergence. This is a unique cohort of pre- and post-infection samples linked to data on COVID-19 infections, vaccinations, and outcomes. The cohort spans host immune response evolution to infection and vaccination in this rarely sampled population of frail older care home residents who are especially vulnerable to infection and severe outcomes. These samples can be used to investigate biological mechanisms behind disparate infection responses in older people and make a valuable contribution to research into ageing.",,doi:https://doi.org/10.12688/wellcomeopenres.20278.2; html:https://europepmc.org/articles/PMC11447437; pdf:https://europepmc.org/articles/PMC11447437?pdf=render
-38909207,https://doi.org/10.1186/s12887-024-04848-2,"Educational outcomes among children with congenital heart disease compared to peers: a Scotland-wide record-linkage study of 715,850 schoolchildren.","Fleming M, Athanasopoulos P, Mackay DF, Pell JP.",,BMC pediatrics,2024,2024-06-22,Y,Congenital heart disease; Population Study; Educational Outcomes; Record Linkage,,,"<h4>Background</h4>Nine in every thousand children born in the United Kingdom have congenital heart disease, and 250,000 adults are living with the condition. This study aims to investigate the associations between congenital heart disease and educational outcomes among school-aged children in Scotland.<h4>Methods</h4>Routine health and education databases were linked to produce a cohort of all singleton children born in Scotland and attending a local authority run primary, secondary, or special school in Scotland at some point between 2009 and 2013. Children with congenital heart disease within this cohort were compared with children unaffected by congenital conditions. Outcomes investigated were special educational need (SEN), absenteeism, exclusion, academic attainment, and unemployment. All analyses were adjusted for sociodemographic and maternity confounders. Absenteeism was investigated as a mediating factor in the associations with attainment and unemployment.<h4>Results</h4>Of the 715,850 children, 6,295 (0.9%) had congenital heart disease and 4,412 (6.1%) had isolated congenital heart disease. Congenital heart disease and isolated congenital heart disease were both significantly associated with subsequent special educational need (OR 3.45, 95% CI 3.26-3.65, p < 0.001 and OR 1.98, 95% CI 1.84-2.13, p < 0.001 respectively), absenteeism (IRR 1.13, 95% CI 1.10-1.16, p < 0.001 and IRR 1.10, 95% CI 1.06-1.13, p < 0.001 respectively), and low academic attainment (OR 1.69, 95% CI 1.39-2.07, p < 0.001 and OR 1.35, 95% CI 1.07-1.69, p = 0.011 respectively). Neither congenital heart disease nor isolated congenital heart disease were associated with school exclusion. Only congenital heart disease (OR 1.21, 95% CI 1.03-1.42, p = 0.022) but not isolated congenital heart disease was associated with unemployment. When days absent were included in the analyses investigating attainment and unemployment, the conclusions were not altered.<h4>Conclusion</h4>Children with congenital heart disease have greater special educational need, lower school attendance, attain lower examination grades and have greater unemployment compared to peers. In addition to healthcare support, affected children need educational support to avoid additional impact on their long-term wellbeing.",,pdf:https://bmcpediatr.biomedcentral.com/counter/pdf/10.1186/s12887-024-04848-2; doi:https://doi.org/10.1186/s12887-024-04848-2; html:https://europepmc.org/articles/PMC11193247; pdf:https://europepmc.org/articles/PMC11193247?pdf=render
 34842128,https://doi.org/10.1192/j.eurpsy.2021.2255,Investigating the association between physical health comorbidities and disability in individuals with severe mental illness.,"Mirza L, Das-Munshi J, Chaturvedi J, Wu H, Kraljevic Z, Searle T, Shaari S, Mascio A, Skiada N, Roberts A, Bean D, Stewart R, Dobson R, Bendayan R.",,European psychiatry : the journal of the Association of European Psychiatrists,2021,2021-11-29,Y,Schizophrenia; Bipolar disorder; Electronic Health Records; Multimorbidity; Health Of Nations Outcome Scale,,,"<h4>Background</h4>Research suggests that an increased risk of physical comorbidities might have a key role in the association between severe mental illness (SMI) and disability. We examined the association between physical multimorbidity and disability in individuals with SMI.<h4>Methods</h4>Data were extracted from the clinical record interactive search system at South London and Maudsley Biomedical Research Centre. Our sample (n = 13,933) consisted of individuals who had received a primary or secondary SMI diagnosis between 2007 and 2018 and had available data for Health of Nations Outcome Scale (HoNOS) as disability measure. Physical comorbidities were defined using Chapters II-XIV of the International Classification of Diagnoses (ICD-10).<h4>Results</h4>More than 60 % of the sample had complex multimorbidity. The most common organ system affected were neurological (34.7%), dermatological (15.4%), and circulatory (14.8%). All specific comorbidities (ICD-10 Chapters) were associated with higher levels of disability, HoNOS total scores. Individuals with musculoskeletal, skin/dermatological, respiratory, endocrine, neurological, hematological, or circulatory disorders were found to be associated with significant difficulties associated with more than five HoNOS domains while others had a lower number of domains affected.<h4>Conclusions</h4>Individuals with SMI and musculoskeletal, skin/dermatological, respiratory, endocrine, neurological, hematological, or circulatory disorders are at higher risk of disability compared to those who do not have those comorbidities. Individuals with SMI and physical comorbidities are at greater risk of reporting difficulties associated with activities of daily living, hallucinations, and cognitive functioning. Therefore, these should be targeted for prevention and intervention programs.",,pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/F22DF5FD826B1626B9873013DBAFF82B/S0924933821022550a.pdf/div-class-title-investigating-the-association-between-physical-health-comorbidities-and-disability-in-individuals-with-severe-mental-illness-div.pdf; doi:https://doi.org/10.1192/j.eurpsy.2021.2255; html:https://europepmc.org/articles/PMC8727716; pdf:https://europepmc.org/articles/PMC8727716?pdf=render
 34082702,https://doi.org/10.1186/s12874-021-01301-1,Incorporating single-arm studies in meta-analysis of randomised controlled trials: a simulation study.,"Singh J, Abrams KR, Bujkiewicz S.",,BMC medical research methodology,2021,2021-06-03,Y,Meta-analysis; Evidence Synthesis; Real World Data; Arm-Based Methods; Bayesian Hierarchical Methods; Single-Arm Studies,,,"<h4>Background</h4>Use of real world data (RWD) from non-randomised studies (e.g. single-arm studies) is increasingly being explored to overcome issues associated with data from randomised controlled trials (RCTs). We aimed to compare methods for pairwise meta-analysis of RCTs and single-arm studies using aggregate data, via a simulation study and application to an illustrative example.<h4>Methods</h4>We considered contrast-based methods proposed by Begg & Pilote (1991) and arm-based methods by Zhang et al (2019). We performed a simulation study with scenarios varying (i) the proportion of RCTs and single-arm studies in the synthesis (ii) the magnitude of bias, and (iii) between-study heterogeneity. We also applied methods to data from a published health technology assessment (HTA), including three RCTs and 11 single-arm studies.<h4>Results</h4>Our simulation study showed that the hierarchical power and commensurate prior methods by Zhang et al provided a consistent reduction in uncertainty, whilst maintaining over-coverage and small error in scenarios where there was limited RCT data, bias and differences in between-study heterogeneity between the two sets of data. The contrast-based methods provided a reduction in uncertainty, but performed worse in terms of coverage and error, unless there was no marked difference in heterogeneity between the two sets of data.<h4>Conclusions</h4>The hierarchical power and commensurate prior methods provide the most robust approach to synthesising aggregate data from RCTs and single-arm studies, balancing the need to account for bias and differences in between-study heterogeneity, whilst reducing uncertainty in estimates. This work was restricted to considering a pairwise meta-analysis using aggregate data.",,pdf:https://bmcmedresmethodol.biomedcentral.com/track/pdf/10.1186/s12874-021-01301-1; doi:https://doi.org/10.1186/s12874-021-01301-1; html:https://europepmc.org/articles/PMC8176581; pdf:https://europepmc.org/articles/PMC8176581?pdf=render
 34894331,https://doi.org/10.1007/s10461-021-03551-y,Influence of Material Deprivation on Clinical Outcomes Among People Living with HIV in High-Income Countries: A Systematic Review and Meta-analysis.,"Papageorgiou V, Davies B, Cooper E, Singer A, Ward H.",,AIDS and behavior,2022,2021-12-11,Y,HIV; Meta-analysis; Systematic review; Antiretroviral therapy; Socioeconomic Factors; Viral Suppression; Social Determinants Of Health,,,"Despite developments in HIV treatment and care, disparities persist with some not fully benefiting from improvements in the HIV care continuum. We conducted a systematic review to explore associations between social determinants and HIV treatment outcomes (viral suppression and treatment adherence) in high-income countries. A random effects meta-analysis was performed where there were consistent measurements of exposures. We identified 83 observational studies eligible for inclusion. Social determinants linked to material deprivation were identified as education, employment, food security, housing, income, poverty/deprivation, socioeconomic status/position, and social class; however, their measurement and definition varied across studies. Our review suggests a social gradient of health persists in the HIV care continuum; people living with HIV who reported material deprivation were less likely to be virologically suppressed or adherent to antiretrovirals. Future research should use an ecosocial approach to explore these interactions across the lifecourse to help propose a causal pathway.",,pdf:https://link.springer.com/content/pdf/10.1007/s10461-021-03551-y.pdf; doi:https://doi.org/10.1007/s10461-021-03551-y; html:https://europepmc.org/articles/PMC9046343; pdf:https://europepmc.org/articles/PMC9046343?pdf=render
-33577558,https://doi.org/10.1371/journal.pmed.1003497,"Association of socioeconomic deprivation with asthma care, outcomes, and deaths in Wales: A 5-year national linked primary and secondary care cohort study.","Alsallakh MA, Rodgers SE, Lyons RA, Sheikh A, Davies GA.",,PLoS medicine,2021,2021-02-12,Y,,,,"<h4>Background</h4>Socioeconomic deprivation is known to be associated with worse outcomes in asthma, but there is a lack of population-based evidence of its impact across all stages of patient care. We investigated the association of socioeconomic deprivation with asthma-related care and outcomes across primary and secondary care and with asthma-related death in Wales.<h4>Methods and findings</h4>We constructed a national cohort, identified from 76% (2.4 million) of the Welsh population, of continuously treated asthma patients between 2013 and 2017 using anonymised, person-level, linked, routinely collected primary and secondary care data in the Secure Anonymised Information Linkage (SAIL) Databank. We investigated the association between asthma-related health service utilisation, prescribing, and deaths with the 2011 Welsh Index of Multiple Deprivation (WIMD) and its domains. We studied 106,926 patients (534,630 person-years), 56.3% were female, with mean age of 47.5 years (SD = 20.3). Compared to the least deprived patients, the most deprived patients had slightly fewer total asthma-related primary care consultations per patient (incidence rate ratio [IRR] = 0.98, 95% CI 0.97-0.99, p-value < 0.001), slightly fewer routine asthma reviews (IRR = 0.98, 0.97-0.99, p-value < 0.001), lower controller-to-total asthma medication ratios (AMRs; 0.50 versus 0.56, p-value < 0.001), more asthma-related accident and emergency (A&E) attendances (IRR = 1.27, 1.10-1.46, p-value = 0.001), more asthma emergency admissions (IRR = 1.56, 1.39-1.76, p-value < 0.001), longer asthma-related hospital stay (IRR = 1.64, 1.39-1.94, p-value < 0.001), and were at higher risk of asthma-related death (risk ratio of deaths with any mention of asthma 1.56, 1.18-2.07, p-value = 0.002). Study limitations include the deprivation index being area based and the potential for residual confounders and mediators.<h4>Conclusions</h4>In this study, we observed that the most deprived asthma patients in Wales had different prescribing patterns, more A&E attendances, more emergency hospital admissions, and substantially higher risk of death. Interventions specifically designed to improve treatment and outcomes for these disadvantaged groups are urgently needed.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003497&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003497; html:https://europepmc.org/articles/PMC7880491; pdf:https://europepmc.org/articles/PMC7880491?pdf=render
+38909207,https://doi.org/10.1186/s12887-024-04848-2,"Educational outcomes among children with congenital heart disease compared to peers: a Scotland-wide record-linkage study of 715,850 schoolchildren.","Fleming M, Athanasopoulos P, Mackay DF, Pell JP.",,BMC pediatrics,2024,2024-06-22,Y,Congenital heart disease; Population Study; Educational Outcomes; Record Linkage,,,"<h4>Background</h4>Nine in every thousand children born in the United Kingdom have congenital heart disease, and 250,000 adults are living with the condition. This study aims to investigate the associations between congenital heart disease and educational outcomes among school-aged children in Scotland.<h4>Methods</h4>Routine health and education databases were linked to produce a cohort of all singleton children born in Scotland and attending a local authority run primary, secondary, or special school in Scotland at some point between 2009 and 2013. Children with congenital heart disease within this cohort were compared with children unaffected by congenital conditions. Outcomes investigated were special educational need (SEN), absenteeism, exclusion, academic attainment, and unemployment. All analyses were adjusted for sociodemographic and maternity confounders. Absenteeism was investigated as a mediating factor in the associations with attainment and unemployment.<h4>Results</h4>Of the 715,850 children, 6,295 (0.9%) had congenital heart disease and 4,412 (6.1%) had isolated congenital heart disease. Congenital heart disease and isolated congenital heart disease were both significantly associated with subsequent special educational need (OR 3.45, 95% CI 3.26-3.65, p < 0.001 and OR 1.98, 95% CI 1.84-2.13, p < 0.001 respectively), absenteeism (IRR 1.13, 95% CI 1.10-1.16, p < 0.001 and IRR 1.10, 95% CI 1.06-1.13, p < 0.001 respectively), and low academic attainment (OR 1.69, 95% CI 1.39-2.07, p < 0.001 and OR 1.35, 95% CI 1.07-1.69, p = 0.011 respectively). Neither congenital heart disease nor isolated congenital heart disease were associated with school exclusion. Only congenital heart disease (OR 1.21, 95% CI 1.03-1.42, p = 0.022) but not isolated congenital heart disease was associated with unemployment. When days absent were included in the analyses investigating attainment and unemployment, the conclusions were not altered.<h4>Conclusion</h4>Children with congenital heart disease have greater special educational need, lower school attendance, attain lower examination grades and have greater unemployment compared to peers. In addition to healthcare support, affected children need educational support to avoid additional impact on their long-term wellbeing.",,pdf:https://bmcpediatr.biomedcentral.com/counter/pdf/10.1186/s12887-024-04848-2; doi:https://doi.org/10.1186/s12887-024-04848-2; html:https://europepmc.org/articles/PMC11193247; pdf:https://europepmc.org/articles/PMC11193247?pdf=render
 31857590,https://doi.org/10.1038/s41597-019-0337-6,Machine learning for the detection of early immunological markers as predictors of multi-organ dysfunction.,"Bravo-Merodio L, Acharjee A, Hazeldine J, Bentley C, Foster M, Gkoutos GV, Lord JM.",,Scientific data,2019,2019-12-19,Y,,,,"The immune response to major trauma has been analysed mainly within post-hospital admission settings where the inflammatory response is already underway and the early drivers of clinical outcome cannot be readily determined. Thus, there is a need to better understand the immediate immune response to injury and how this might influence important patient outcomes such as multi-organ dysfunction syndrome (MODS). In this study, we have assessed the immune response to trauma in 61 patients at three different post-injury time points (ultra-early (<=1 h), 4-12 h, 48-72 h) and analysed relationships with the development of MODS. We developed a pipeline using Absolute Shrinkage and Selection Operator and Elastic Net feature selection methods that were able to identify 3 physiological features (decrease in neutrophil CD62L and CD63 expression and monocyte CD63 expression and frequency) as possible biomarkers for MODS development. After univariate and multivariate analysis for each feature alongside a stability analysis, the addition of these 3 markers to standard clinical trauma injury severity scores yields a Generalized Liner Model (GLM) with an average Area Under the Curve value of 0.92 ± 0.06. This performance provides an 8% improvement over the Probability of Survival (PS14) outcome measure and a 13% improvement over the New Injury Severity Score (NISS) for identifying patients at risk of MODS.",,pdf:https://www.nature.com/articles/s41597-019-0337-6.pdf; doi:https://doi.org/10.1038/s41597-019-0337-6; html:https://europepmc.org/articles/PMC6923383; pdf:https://europepmc.org/articles/PMC6923383?pdf=render
+33577558,https://doi.org/10.1371/journal.pmed.1003497,"Association of socioeconomic deprivation with asthma care, outcomes, and deaths in Wales: A 5-year national linked primary and secondary care cohort study.","Alsallakh MA, Rodgers SE, Lyons RA, Sheikh A, Davies GA.",,PLoS medicine,2021,2021-02-12,Y,,,,"<h4>Background</h4>Socioeconomic deprivation is known to be associated with worse outcomes in asthma, but there is a lack of population-based evidence of its impact across all stages of patient care. We investigated the association of socioeconomic deprivation with asthma-related care and outcomes across primary and secondary care and with asthma-related death in Wales.<h4>Methods and findings</h4>We constructed a national cohort, identified from 76% (2.4 million) of the Welsh population, of continuously treated asthma patients between 2013 and 2017 using anonymised, person-level, linked, routinely collected primary and secondary care data in the Secure Anonymised Information Linkage (SAIL) Databank. We investigated the association between asthma-related health service utilisation, prescribing, and deaths with the 2011 Welsh Index of Multiple Deprivation (WIMD) and its domains. We studied 106,926 patients (534,630 person-years), 56.3% were female, with mean age of 47.5 years (SD = 20.3). Compared to the least deprived patients, the most deprived patients had slightly fewer total asthma-related primary care consultations per patient (incidence rate ratio [IRR] = 0.98, 95% CI 0.97-0.99, p-value < 0.001), slightly fewer routine asthma reviews (IRR = 0.98, 0.97-0.99, p-value < 0.001), lower controller-to-total asthma medication ratios (AMRs; 0.50 versus 0.56, p-value < 0.001), more asthma-related accident and emergency (A&E) attendances (IRR = 1.27, 1.10-1.46, p-value = 0.001), more asthma emergency admissions (IRR = 1.56, 1.39-1.76, p-value < 0.001), longer asthma-related hospital stay (IRR = 1.64, 1.39-1.94, p-value < 0.001), and were at higher risk of asthma-related death (risk ratio of deaths with any mention of asthma 1.56, 1.18-2.07, p-value = 0.002). Study limitations include the deprivation index being area based and the potential for residual confounders and mediators.<h4>Conclusions</h4>In this study, we observed that the most deprived asthma patients in Wales had different prescribing patterns, more A&E attendances, more emergency hospital admissions, and substantially higher risk of death. Interventions specifically designed to improve treatment and outcomes for these disadvantaged groups are urgently needed.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003497&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003497; html:https://europepmc.org/articles/PMC7880491; pdf:https://europepmc.org/articles/PMC7880491?pdf=render
 37736873,https://doi.org/10.1002/ehf2.14527,Genetically predicted androgenic profiles and adverse cardiac markers: a sex-specific Mendelian randomization study.,"Chen JY, Ardissino M, Reddy RK, Mason AM, Raisi-Estabragh Z, Di Angelantonio E, Burgess S, Ng FS.",,ESC heart failure,2023,2023-09-22,Y,Sex hormones; Testosterone; Heart Failure; Cmr; Mendelian Randomization; Shbg,,,"<h4>Aims</h4>Observational evidence suggests associations between sex hormone levels and heart failure (HF). We used sex-specific genetic variants associated with androgenic sex hormone profiles to investigate the causal relevance of androgenic sex hormone profiles on cardiac structure and function and HF using Mendelian randomization (MR).<h4>Methods and results</h4>Sex-specific uncorrelated genome-wide significant (P < 5 × 10<sup>-8</sup> ) variants predicting sex hormone-binding globulin (SHBG), total testosterone, and bioavailable testosterone were extracted from summary statistics of genome-wide association study (GWAS) on 425 097 participants in the UK Biobank. Sex-specific gene-outcome association estimates were computed for left ventricular ejection fraction (LVEF), left ventricular end-diastolic and end-systolic volumes (LVEDV and LVESV, respectively), left ventricular stroke volume (LVSV), cardiac index, and cardiac output in 11 528 female and 14 356 male UK Biobank Imaging Study participants and for incident or prevalent HF in an external cohort of 47 309 cases and 930 014 controls. Inverse-variance weighted MR was the primary analysis method. In females, higher genetically predicted bioavailable testosterone was associated with lower LVEDV [β per nmol/L = -0.11 (-0.19 to -0.03), P = 0.006], lower LVESV [β = -0.09 (-0.17 to -0.01), P = 0.022], lower LVSV [β = -0.11 (-0.18 to -0.03), P = 0.005], lower cardiac output [β = -0.08 (-0.16 to 0.00), P = 0.046], and lower cardiac index [β = -0.08 (-0.16 to -0.01), P = 0.034] and a higher risk of HF [odds ratio 1.10 (1.01-1.19), P = 0.026] on external validation analysis in larger scale, sex-adjusted GWAS data. Higher genetically predicted SHBG was associated with higher LVEDV [β per nmol/L = 0.17 (0.08-0.25), P = 2 × 10<sup>-4</sup> ], higher LVESV [β = 0.13 (0.05-0.22), P = 0.003], and higher LVSV [β = 0.18 (0.08-0.28), P = 2 × 10<sup>-4</sup> ]. In males, higher genetically predicted total and bioavailable testosterone was associated with lower LVESV [β = -0.07 (-0.12 to -0.02), P = 0.007] and LVEF [β = -0.11 (-0.18 to -0.04), P = 0.003], respectively.<h4>Conclusions</h4>This study supports a causal effect of pro-androgenic sex hormone profiles in females on adverse markers of left ventricular structure and function typically associated with HF with preserved ejection fraction and with HF. There was weaker evidence of association in males.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ehf2.14527; doi:https://doi.org/10.1002/ehf2.14527; html:https://europepmc.org/articles/PMC10682908; pdf:https://europepmc.org/articles/PMC10682908?pdf=render
 34430954,https://doi.org/10.1016/s2666-7568(21)00168-9,Profile of humoral and cellular immune responses to single doses of BNT162b2 or ChAdOx1 nCoV-19 vaccines in residents and staff within residential care homes (VIVALDI): an observational study.,"Tut G, Lancaster T, Krutikov M, Sylla P, Bone D, Kaur N, Spalkova E, Bentley C, Amin U, Jadir AT, Hulme S, Butler MS, Ayodele M, Bruton R, Shrotri M, Azmi B, Fuller C, Irwin-Singer A, Hayward A, Copas A, Shallcross L, Moss P.",,The lancet. Healthy longevity,2021,2021-08-19,Y,,,,"<h4>Background</h4>Residents of long-term care facilities (LTCFs) have been prioritised for COVID-19 vaccination because of the high COVID-19 mortality in this population. Several countries have implemented an extended interval of up to 12 weeks between the first and second vaccine doses to increase population coverage of single-dose vaccination. We aimed to assess the magnitude and quality of adaptive immune responses following a single dose of COVID-19 vaccine in LTCF residents and staff.<h4>Methods</h4>From the LTCFs participating in the ongoing VIVALDI study (ISRCTN14447421), staff and residents who had received a first dose of COVID-19 vaccine (BNT162b2 [tozinameran] or ChAdOx1 nCoV-19), had pre-vaccination and post-vaccination blood samples (collected between Dec 11, 2020, and Feb 16, 2021), and could be linked to a pseudoidentifier in the COVID-19 Data Store were included in our cohort. Past infection with SARS-CoV-2 was defined on the basis of nucleocapsid-specific IgG antibodies being detected through a semiquantitative immunoassay, and participants who tested positive on this assay after but not before vaccination were excluded from the study. Processed blood samples were assessed for spike-specific immune responses, including spike-specific IgG antibody titres, T-cell responses to spike protein peptide mixes, and inhibition of ACE2 binding by spike protein from four variants of SARS-CoV-2 (the original strain as well as the B.1.1.7, B.1.351, and P.1 variants). Responses before and after vaccination were compared on the basis of age, previous infection status, role (staff or resident), and time since vaccination.<h4>Findings</h4>Our cohort comprised 124 participants from 14 LTCFs: 89 (72%) staff (median age 48 years [IQR 35·5-56]) and 35 (28%) residents (87 years [77-90]). Blood samples were collected a median 40 days (IQR 25-47; range 6-52) after vaccination. 30 (24%) participants (18 [20%] staff and 12 [34%] residents) had serological evidence of previous SARS-CoV-2 infection. All participants with previous infection had high antibody titres following vaccination that were independent of age (<i>r</i> <sub>s</sub>=0·076, p=0·70). In participants without evidence of previous infection, titres were negatively correlated with age (<i>r</i> <sub>s</sub>=-0·434, p<0·0001) and were 8·2-times lower in residents than in staff. This effect appeared to result from a kinetic delay antibody generation in older infection-naive participants, with the negative age correlation disappearing only in samples taken more than 42 days post-vaccination (<i>r</i> <sub>s</sub>=-0·207, p=0·20; n=40), in contrast to samples taken after 0-21 days (<i>r</i> <sub>s</sub>=-0·774, p=0·0043; n=12) or 22-42 days (<i>r</i> <sub>s</sub>=-0·437, p=0·0034; n=43). Spike-specific cellular responses were similar between older and younger participants. In infection-naive participants, antibody inhibition of ACE2 binding by spike protein from the original SARS-CoV-2 strain was negatively correlated with age (<i>r</i> <sub>s</sub>=-0·439, p<0·0001), and was significantly lower against spike protein from the B.1.351 variant (median inhibition 31% [14-100], p=0·010) and the P.1 variant (23% [14-97], p<0·0001) than against the original strain (58% [27-100]). By contrast, a single dose of vaccine resulted in around 100% inhibition of the spike-ACE2 interaction against all variants in people with a history of infection.<h4>Interpretation</h4>History of SARS-CoV-2 infection impacts the magnitude and quality of antibody response after a single dose of COVID-19 vaccine in LTCF residents. Residents who are infection-naive have delayed antibody responses to the first dose of vaccine and should be considered for an early second dose where possible.<h4>Funding</h4>UK Government Department of Health and Social Care.",,pdf:https://discovery.ucl.ac.uk/10133388/1/1-s2.0-S2666756821001689-main.pdf; doi:https://doi.org/10.1016/S2666-7568(21)00168-9; html:https://europepmc.org/articles/PMC8376213
 36753492,https://doi.org/10.1371/journal.pone.0281466,Combinations of medicines in patients with polypharmacy aged 65-100 in primary care: Large variability in risks of adverse drug related and emergency hospital admissions.,"Fahmi A, Wong D, Walker L, Buchan I, Pirmohamed M, Sharma A, Cant H, Ashcroft DM, van Staa TP.",,PloS one,2023,2023-02-08,Y,,,,"<h4>Background</h4>Polypharmacy can be a consequence of overprescribing that is prevalent in older adults with multimorbidity. Polypharmacy can cause adverse reactions and result in hospital admission. This study predicted risks of adverse drug reaction (ADR)-related and emergency hospital admissions by medicine classes.<h4>Methods</h4>We used electronic health record data from general practices of Clinical Practice Research Datalink (CPRD GOLD) and Aurum. Older patients who received at least five medicines were included. Medicines were classified using the British National Formulary sections. Hospital admission cases were propensity-matched to controls by age, sex, and propensity for specific diseases. The matched data were used to develop and validate random forest (RF) models to predict the risk of ADR-related and emergency hospital admissions. Shapley Additive eXplanation (SHAP) values were calculated to explain the predictions.<h4>Results</h4>In total, 89,235 cases with polypharmacy and hospitalised with an ADR-related admission were matched to 443,497 controls. There were over 112,000 different combinations of the 50 medicine classes most implicated in ADR-related hospital admission in the RF models, with the most important medicine classes being loop diuretics, domperidone and/or metoclopramide, medicines for iron-deficiency anaemias and for hypoplastic/haemolytic/renal anaemias, and sulfonamides and/or trimethoprim. The RF models strongly predicted risks of ADR-related and emergency hospital admission. The observed Odds Ratio in the highest RF decile was 7.16 (95% CI 6.65-7.72) in the validation dataset. The C-statistics for ADR-related hospital admissions were 0.58 for age and sex and 0.66 for RF probabilities.<h4>Conclusions</h4>Polypharmacy involves a very large number of different combinations of medicines, with substantial differences in risks of ADR-related and emergency hospital admissions. Although the medicines may not be causally related to increased risks, RF model predictions may be useful in prioritising medication reviews. Simple tools based on few medicine classes may not be effective in identifying high risk patients.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0281466&type=printable; doi:https://doi.org/10.1371/journal.pone.0281466; html:https://europepmc.org/articles/PMC9907844; pdf:https://europepmc.org/articles/PMC9907844?pdf=render
 33952557,https://doi.org/10.1136/bmjopen-2021-049964,Study protocol of the Edinburgh and Lothian Virus Intervention Study in Kids: a randomised controlled trial of hypertonic saline nose drops in children with upper respiratory tract infections (ELVIS Kids).,"Ramalingam S, Graham C, Oatey K, Rayson P, Stoddart A, Sheikh A, Cunningham S, ELVIS Kids Trial Investigators.",,BMJ open,2021,2021-05-05,Y,Virology; Community Child Health; Neonatology; Primary Care; Paediatric Infectious Disease & Immunisation,,,"<h4>Introduction</h4>Edinburgh and Lothians' Viral Intervention Study Kids is a parallel, open-label, randomised controlled trial of hypertonic saline (HS) nose drops (~2.6% sodium chloride) vs standard care in children <7 years of age with symptoms of an upper respiratory tract infection (URTI).<h4>Methods and analysis</h4>Children are recruited prior to URTI or within 48 hours of developing URTI symptoms by advertising in areas such as local schools/nurseries, health centres/hospitals, recreational facilities, public events, workplaces, local/social media. Willing parents/guardians, of children <7 years of age will be asked to contact the research team at their local site. Children will be randomised to either a control arm (standard symptomatic care), or intervention arm (three drops/nostril of HS, at least four times a day, until 24 hours after asymptomatic or a maximum of 28 days). All participants are requested to provide a nasal swab at the start of the study (intervention arm: before HS drops) and then daily for four more days. Parent/guardian complete a validated daily diary, an end of illness diary, a satisfaction questionnaire and a wheeze questionnaire (day 28). The parent/guardian of a child in the intervention arm is taught to prepare HS nose drops. Parent/guardian of children asymptomatic at recruitment are requested to inform the research team within 48 hours of their child developing an URTI and follow the instructions already provided. The day 28 questionnaire determines if the child experienced a wheeze following illness. Participation in the study ends on day 28.<h4>Ethics and dissemination</h4>The study has been approved by the West of Scotland Research Ethics Service (18/WS/0080). It is cosponsored by Academic and Clinical Central Office for Research and Development-a partnership between the University of Edinburgh and National Health Service Lothian Health Board. The findings will be disseminated through peer-reviewed publications, conference presentations and via the study website.<h4>Trial registration number</h4>NCT03463694.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/5/e049964.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-049964; html:https://europepmc.org/articles/PMC8103393; pdf:https://europepmc.org/articles/PMC8103393?pdf=render
+34141852,https://doi.org/10.1016/j.ssmph.2021.100828,Media representations of opposition to the 'junk food advertising ban' on the Transport for London (TfL) network: A thematic content analysis of UK news and trade press.,"Thompson C, Clary C, Er V, Adams J, Boyland E, Burgoine T, Cornelsen L, de Vocht F, Egan M, Lake AA, Lock K, Mytton O, Petticrew M, White M, Yau A, Cummins S.",,SSM - population health,2021,2021-05-27,Y,Regulation; Media; Advertising; Childhood Obesity,,,"<h4>Background</h4>Advertising of less healthy foods and drinks is hypothesised to be associated with obesity in adults and children. In February 2019, Transport for London implemented restrictions on advertisements for foods and beverages high in fat, salt or sugar across its network as part of a city-wide strategy to tackle childhood obesity. The policy was extensively debated in the press. This paper identifies arguments for and against the restrictions. Focusing on arguments against the restrictions, it then goes on to deconstruct the discursive strategies underpinning them.<h4>Methods</h4>A qualitative thematic content analysis of media coverage of the restrictions (the 'ban') in UK newspapers and trade press was followed by a document analysis of arguments against the ban. A search period of March 1, 2018 to May 31, 2019 covered: (i) the launch of the public consultation on the ban in May 2018; (ii) the announcement of the ban in November 2018; and (iii) its implementation in February 2019. A systematic search of printed and online publications in English distributed in the UK or published on UK-specific websites identified 152 articles.<h4>Results</h4>Arguments in favour of the ban focused on inequalities and childhood obesity. Arguments against the ban centred on two claims: that childhood obesity was not the 'right' priority; and that an advertising ban was not an effective way to address childhood obesity. These claims were justified via three discursive approaches: (i) claiming more 'important' priorities for action; (ii) disputing the science behind the ban; (iii) emphasising potential financial costs of the ban.<h4>Conclusion</h4>The discursive tactics used in media sources to argue against the ban draw on frames widely used by unhealthy commodities industries in response to structural public health interventions. Our analyses highlight the need for interventions to be framed in ways that can pre-emptively counter common criticisms.",,doi:https://doi.org/10.1016/j.ssmph.2021.100828; doi:https://doi.org/10.1016/j.ssmph.2021.100828; html:https://europepmc.org/articles/PMC8184652; pdf:https://europepmc.org/articles/PMC8184652?pdf=render
 32856160,https://doi.org/10.1007/s10654-020-00677-6,Data extraction for epidemiological research (DExtER): a novel tool for automated clinical epidemiology studies.,"Gokhale KM, Chandan JS, Toulis K, Gkoutos G, Tino P, Nirantharakumar K.",,European journal of epidemiology,2021,2020-08-27,Y,Extract; Research methods; epidemiology; Transform; Observational Study; Computer Science; Load,,,"The use of primary care electronic health records for research is abundant. The benefits gained from utilising such records lies in their size, longitudinal data collection and data quality. However, the use of such data to undertake high quality epidemiological studies, can lead to significant challenges particularly in dealing with misclassification, variation in coding and the significant effort required to pre-process the data in a meaningful format for statistical analysis. In this paper, we describe a methodology to aid with the extraction and processing of such databases, delivered by a novel software programme; the ""Data extraction for epidemiological research"" (DExtER). The basis of DExtER relies on principles of extract, transform and load processes. The tool initially provides the ability for the healthcare dataset to be extracted, then transformed in a format whereby data is normalised, converted and reformatted. DExtER has a user interface designed to obtain data extracts specific to each research question and observational study design. There are facilities to input the requirements for; eligible study period, definition of exposed and unexposed groups, outcome measures and important baseline covariates. To date the tool has been utilised and validated in a multitude of settings. There have been over 35 peer-reviewed publications using the tool, and DExtER has been implemented as a validated public health surveillance tool for obtaining accurate statistics on epidemiology of key morbidities. Future direction of this work will be the application of the framework to linked as well as international datasets and the development of standardised methods for conducting electronic pre-processing and extraction from datasets for research purposes.",,pdf:https://link.springer.com/content/pdf/10.1007/s10654-020-00677-6.pdf; doi:https://doi.org/10.1007/s10654-020-00677-6; html:https://europepmc.org/articles/PMC7987616; pdf:https://europepmc.org/articles/PMC7987616?pdf=render
 39012930,https://doi.org/10.1161/circep.123.012570,"Distal Ventricular Pacing for Drug-Refractory Mid-Cavity Obstructive Hypertrophic Cardiomyopathy: A Randomized, Placebo-Controlled Trial of Personalized Pacing.","Malcolmson JW, Hughes RK, Husselbury T, Khan K, Learoyd AE, Lees M, Wicks EC, Smith J, Simms AD, Moon JC, Lopes LR, O'Mahony C, Sekhri N, Elliott PM, Petersen SE, Dhinoja MB, Mohiddin SA.",,Circulation. Arrhythmia and electrophysiology,2024,2024-06-19,N,"Hemodynamics; Quality of life; Cardiomyopathy, hypertrophic; Random Allocation; Cross-over Studies",,,"<h4>Background</h4>Patients with refractory, symptomatic left ventricular (LV) mid-cavity obstructive (LVMCO) hypertrophic cardiomyopathy have few therapeutic options. Right ventricular pacing is associated with modest hemodynamic and symptomatic improvement, and LV pacing pilot data suggest therapeutic potential. We hypothesized that site-specific pacing would reduce LVMCO gradients and improve symptoms.<h4>Methods</h4>Patients with symptomatic-drug-refractory LVMCO were recruited for a randomized, blinded trial of personalized prescription of pacing (PPoP). Multiple LV and apical right ventricular pacing sites were assessed during an invasive hemodynamic study of multisite pacing. Patient-specific pacing-site and atrioventricular delays, defining PPoP, were selected on the basis of LVMCO gradient reduction and acceptable pacing parameters. Patients were randomized to 6 months of active PPoP or backup pacing in a crossover design. The primary outcome examined invasive gradient change with best-site pacing. Secondary outcomes assessed quality of life and exercise following randomization to PPoP.<h4>Results</h4>A total of 17 patients were recruited; 16 of whom met primary end points. Baseline New York Heart Association was 3±0.6, despite optimal medical therapy. Hemodynamic effects were assessed during pacing at the right ventricular apex and at a mean of 8 LV sites. The gradients in all 16 patients fell with pacing, with maximum gradient reduction achieved via LV pacing in 14 (88%) patients and right ventricular apex in 2. The mean baseline gradient of 80±29 mm Hg fell to 31±21 mm Hg with best-site pacing, a 60% reduction (<i>P</i><0.0001). One cardiac vein perforation occurred in 1 case, and 15 subjects entered crossover; 2 withdrawals occurred during crossover. Of the 13 completing crossover, 9 (69%) chose active pacing in PPoP configuration as preferred setting. PPoP was associated with improved 6-minute walking test performance (328.5±99.9 versus 285.8±105.5 m; <i>P</i>=0.018); other outcome measures also indicated benefit with PPoP.<h4>Conclusions</h4>In a randomized placebo-controlled trial, PPoP reduces obstruction and improves exercise performance in severely symptomatic patients with LVMCO.<h4>Registration</h4>URL: https://clinicaltrials.gov/study; Unique Identifier: NCT03450252.",,doi:https://doi.org/10.1161/CIRCEP.123.012570
-34141852,https://doi.org/10.1016/j.ssmph.2021.100828,Media representations of opposition to the 'junk food advertising ban' on the Transport for London (TfL) network: A thematic content analysis of UK news and trade press.,"Thompson C, Clary C, Er V, Adams J, Boyland E, Burgoine T, Cornelsen L, de Vocht F, Egan M, Lake AA, Lock K, Mytton O, Petticrew M, White M, Yau A, Cummins S.",,SSM - population health,2021,2021-05-27,Y,Regulation; Media; Advertising; Childhood Obesity,,,"<h4>Background</h4>Advertising of less healthy foods and drinks is hypothesised to be associated with obesity in adults and children. In February 2019, Transport for London implemented restrictions on advertisements for foods and beverages high in fat, salt or sugar across its network as part of a city-wide strategy to tackle childhood obesity. The policy was extensively debated in the press. This paper identifies arguments for and against the restrictions. Focusing on arguments against the restrictions, it then goes on to deconstruct the discursive strategies underpinning them.<h4>Methods</h4>A qualitative thematic content analysis of media coverage of the restrictions (the 'ban') in UK newspapers and trade press was followed by a document analysis of arguments against the ban. A search period of March 1, 2018 to May 31, 2019 covered: (i) the launch of the public consultation on the ban in May 2018; (ii) the announcement of the ban in November 2018; and (iii) its implementation in February 2019. A systematic search of printed and online publications in English distributed in the UK or published on UK-specific websites identified 152 articles.<h4>Results</h4>Arguments in favour of the ban focused on inequalities and childhood obesity. Arguments against the ban centred on two claims: that childhood obesity was not the 'right' priority; and that an advertising ban was not an effective way to address childhood obesity. These claims were justified via three discursive approaches: (i) claiming more 'important' priorities for action; (ii) disputing the science behind the ban; (iii) emphasising potential financial costs of the ban.<h4>Conclusion</h4>The discursive tactics used in media sources to argue against the ban draw on frames widely used by unhealthy commodities industries in response to structural public health interventions. Our analyses highlight the need for interventions to be framed in ways that can pre-emptively counter common criticisms.",,doi:https://doi.org/10.1016/j.ssmph.2021.100828; doi:https://doi.org/10.1016/j.ssmph.2021.100828; html:https://europepmc.org/articles/PMC8184652; pdf:https://europepmc.org/articles/PMC8184652?pdf=render
-35814295,https://doi.org/10.1038/s43856-022-00146-z,Machine learning to support visual auditing of home-based lateral flow immunoassay self-test results for SARS-CoV-2 antibodies.,"Wong NCK, Meshkinfamfard S, Turbé V, Whitaker M, Moshe M, Bardanzellu A, Dai T, Pignatelli E, Barclay W, Darzi A, Elliott P, Ward H, Tanaka RJ, Cooke GS, McKendry RA, Atchison CJ, Bharath AA.",,Communications medicine,2022,2022-07-06,Y,Databases; Public Health,,,"<h4>Background</h4>Lateral flow immunoassays (LFIAs) are being used worldwide for COVID-19 mass testing and antibody prevalence studies. Relatively simple to use and low cost, these tests can be self-administered at home, but rely on subjective interpretation of a test line by eye, risking false positives and false negatives. Here, we report on the development of ALFA (Automated Lateral Flow Analysis) to improve reported sensitivity and specificity.<h4>Methods</h4>Our computational pipeline uses machine learning, computer vision techniques and signal processing algorithms to analyse images of the Fortress LFIA SARS-CoV-2 antibody self-test, and subsequently classify results as invalid, IgG negative and IgG positive. A large image library of 595,339 participant-submitted test photographs was created as part of the REACT-2 community SARS-CoV-2 antibody prevalence study in England, UK. Alongside ALFA, we developed an analysis toolkit which could also detect device blood leakage issues.<h4>Results</h4>Automated analysis showed substantial agreement with human experts (Cohen's kappa 0.90-0.97) and performed consistently better than study participants, particularly for weak positive IgG results. Specificity (98.7-99.4%) and sensitivity (90.1-97.1%) were high compared with visual interpretation by human experts (ranges due to the varying prevalence of weak positive IgG tests in datasets).<h4>Conclusions</h4>Given the potential for LFIAs to be used at scale in the COVID-19 response (for both antibody and antigen testing), even a small improvement in the accuracy of the algorithms could impact the lives of millions of people by reducing the risk of false-positive and false-negative result read-outs by members of the public. Our findings support the use of machine learning-enabled automated reading of at-home antibody lateral flow tests as a tool for improved accuracy for population-level community surveillance.",,pdf:https://www.nature.com/articles/s43856-022-00146-z.pdf; doi:https://doi.org/10.1038/s43856-022-00146-z; html:https://europepmc.org/articles/PMC9259560; pdf:https://europepmc.org/articles/PMC9259560?pdf=render
 34556677,https://doi.org/10.1038/s41598-021-96189-8,Combining multi-site magnetic resonance imaging with machine learning predicts survival in pediatric brain tumors.,"Grist JT, Withey S, Bennett C, Rose HEL, MacPherson L, Oates A, Powell S, Novak J, Abernethy L, Pizer B, Bailey S, Clifford SC, Mitra D, Arvanitis TN, Auer DP, Avula S, Grundy R, Peet AC.",,Scientific reports,2021,2021-09-23,Y,,,,"Brain tumors represent the highest cause of mortality in the pediatric oncological population. Diagnosis is commonly performed with magnetic resonance imaging. Survival biomarkers are challenging to identify due to the relatively low numbers of individual tumor types. 69 children with biopsy-confirmed brain tumors were recruited into this study. All participants had perfusion and diffusion weighted imaging performed at diagnosis. Imaging data were processed using conventional methods, and a Bayesian survival analysis performed. Unsupervised and supervised machine learning were performed with the survival features, to determine novel sub-groups related to survival. Sub-group analysis was undertaken to understand differences in imaging features. Survival analysis showed that a combination of diffusion and perfusion imaging were able to determine two novel sub-groups of brain tumors with different survival characteristics (p < 0.01), which were subsequently classified with high accuracy (98%) by a neural network. Analysis of high-grade tumors showed a marked difference in survival (p = 0.029) between the two clusters with high risk and low risk imaging features. This study has developed a novel model of survival for pediatric brain tumors. Tumor perfusion plays a key role in determining survival and should be considered as a high priority for future imaging protocols.",,pdf:https://www.nature.com/articles/s41598-021-96189-8.pdf; doi:https://doi.org/10.1038/s41598-021-96189-8; html:https://europepmc.org/articles/PMC8460620; pdf:https://europepmc.org/articles/PMC8460620?pdf=render
+35814295,https://doi.org/10.1038/s43856-022-00146-z,Machine learning to support visual auditing of home-based lateral flow immunoassay self-test results for SARS-CoV-2 antibodies.,"Wong NCK, Meshkinfamfard S, Turbé V, Whitaker M, Moshe M, Bardanzellu A, Dai T, Pignatelli E, Barclay W, Darzi A, Elliott P, Ward H, Tanaka RJ, Cooke GS, McKendry RA, Atchison CJ, Bharath AA.",,Communications medicine,2022,2022-07-06,Y,Databases; Public Health,,,"<h4>Background</h4>Lateral flow immunoassays (LFIAs) are being used worldwide for COVID-19 mass testing and antibody prevalence studies. Relatively simple to use and low cost, these tests can be self-administered at home, but rely on subjective interpretation of a test line by eye, risking false positives and false negatives. Here, we report on the development of ALFA (Automated Lateral Flow Analysis) to improve reported sensitivity and specificity.<h4>Methods</h4>Our computational pipeline uses machine learning, computer vision techniques and signal processing algorithms to analyse images of the Fortress LFIA SARS-CoV-2 antibody self-test, and subsequently classify results as invalid, IgG negative and IgG positive. A large image library of 595,339 participant-submitted test photographs was created as part of the REACT-2 community SARS-CoV-2 antibody prevalence study in England, UK. Alongside ALFA, we developed an analysis toolkit which could also detect device blood leakage issues.<h4>Results</h4>Automated analysis showed substantial agreement with human experts (Cohen's kappa 0.90-0.97) and performed consistently better than study participants, particularly for weak positive IgG results. Specificity (98.7-99.4%) and sensitivity (90.1-97.1%) were high compared with visual interpretation by human experts (ranges due to the varying prevalence of weak positive IgG tests in datasets).<h4>Conclusions</h4>Given the potential for LFIAs to be used at scale in the COVID-19 response (for both antibody and antigen testing), even a small improvement in the accuracy of the algorithms could impact the lives of millions of people by reducing the risk of false-positive and false-negative result read-outs by members of the public. Our findings support the use of machine learning-enabled automated reading of at-home antibody lateral flow tests as a tool for improved accuracy for population-level community surveillance.",,pdf:https://www.nature.com/articles/s43856-022-00146-z.pdf; doi:https://doi.org/10.1038/s43856-022-00146-z; html:https://europepmc.org/articles/PMC9259560; pdf:https://europepmc.org/articles/PMC9259560?pdf=render
 33971933,https://doi.org/10.1186/s13063-021-05295-5,Accessing routinely collected health data to improve clinical trials: recent experience of access.,"Macnair A, Love SB, Murray ML, Gilbert DC, Parmar MKB, Denwood T, Carpenter J, Sydes MR, Langley RE, Cafferty FH.",,Trials,2021,2021-05-10,Y,Clinical Trials; Electronic Health Records; Data Accessibility; Routinely Collected Data,,,"<h4>Background</h4>Routinely collected electronic health records (EHRs) have the potential to enhance randomised controlled trials (RCTs) by facilitating recruitment and follow-up. Despite this, current EHR use is minimal in UK RCTs, in part due to ongoing concerns about the utility (reliability, completeness, accuracy) and accessibility of the data. The aim of this manuscript is to document the process, timelines and challenges of the application process to help improve the service both for the applicants and data holders.<h4>Methods</h4>This is a qualitative paper providing a descriptive narrative from one UK clinical trials unit (MRC CTU at UCL) on the experience of two trial teams' application process to access data from three large English national datasets: National Cancer Registration and Analysis Service (NCRAS), National Institute for Cardiovascular Outcomes Research (NICOR) and NHS Digital to establish themes for discussion. The underpinning reason for applying for the data was to compare EHRs with data collected through case report forms in two RCTs, Add-Aspirin (ISRCTN 74358648) and PATCH (ISRCTN 70406718).<h4>Results</h4>The Add-Aspirin trial, which had a pre-planned embedded sub-study to assess EHR, received data from NCRAS 13 months after the first application. In the PATCH trial, the decision to request data was made whilst the trial was recruiting. The study received data after 8 months from NICOR and 15 months for NHS Digital following final application submission. This concluded in May 2020. Prior to application submission, significant time and effort was needed particularly in relation to the PATCH trial where negotiations over consent and data linkage took many years.<h4>Conclusions</h4>Our experience demonstrates that data access can be a prolonged and complex process. This is compounded if multiple data sources are required for the same project. This needs to be factored in when planning to use EHR within RCTs and is best considered prior to conception of the trial. Data holders and researchers are endeavouring to simplify and streamline the application process so that the potential of EHR can be realised for clinical trials.",,pdf:https://trialsjournal.biomedcentral.com/counter/pdf/10.1186/s13063-021-05295-5; doi:https://doi.org/10.1186/s13063-021-05295-5; html:https://europepmc.org/articles/PMC8108438; pdf:https://europepmc.org/articles/PMC8108438?pdf=render
 34527726,https://doi.org/10.1183/23120541.00167-2021,Identifying COPD in routinely collected electronic health records: a systematic scoping review.,"Sivakumaran S, Alsallakh MA, Lyons RA, Quint JK, Davies GA.",,ERJ open research,2021,2021-07-01,Y,,,,"Although routinely collected electronic health records (EHRs) are widely used to examine outcomes related to COPD, consensus regarding the identification of cases from electronic healthcare databases is lacking. We systematically examine and summarise approaches from the recent literature. MEDLINE <i>via</i> EBSCOhost was searched for COPD-related studies using EHRs published from January 1, 2018 to November 30, 2019. Data were extracted relating to the case definition of COPD and determination of COPD severity and phenotypes. From 185 eligible studies, we found widespread variation in the definitions used to identify people with COPD in terms of code sets used (with 20 different code sets in use based on the ICD-10 classification alone) and requirement of additional criteria (relating to age (n=139), medication (n=31), multiplicity of events (n=21), spirometry (n=19) and smoking status (n=9)). Only seven studies used a case definition which had been validated against a reference standard in the same dataset. Various proxies of disease severity were used since spirometry results and patient-reported outcomes were not often available. To enable the research community to draw reliable insights from EHRs and aid comparability between studies, clear reporting and greater consistency of the definitions used to identify COPD and related outcome measures is key.",,pdf:https://openres.ersjournals.com/content/erjor/7/3/00167-2021.full.pdf; doi:https://doi.org/10.1183/23120541.00167-2021; html:https://europepmc.org/articles/PMC8435805; pdf:https://europepmc.org/articles/PMC8435805?pdf=render
 PMC9645061,https://doi.org/,Using population-scale medication data to evaluate the impact of the COVID-19 pandemic on the usage of analgesics by cancer patients.,"Han J, Akbari A, Torabi F, Griffiths R, Lyons J, Rolles M, Arnold C, Huws D, Lawler M, Lyons R.",,International journal of population data science,,2022-11-25,Y,,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9645061/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9645061/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC9645061; pdf:https://europepmc.org/articles/PMC9645061?pdf=render
 33933206,https://doi.org/10.1016/s0140-6736(21)00676-0,"Tocilizumab in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial.",RECOVERY Collaborative Group.,,"Lancet (London, England)",2021,2021-05-01,Y,,,,"<h4>Background</h4>In this study, we aimed to evaluate the effects of tocilizumab in adult patients admitted to hospital with COVID-19 with both hypoxia and systemic inflammation.<h4>Methods</h4>This randomised, controlled, open-label, platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing several possible treatments in patients hospitalised with COVID-19 in the UK. Those trial participants with hypoxia (oxygen saturation <92% on air or requiring oxygen therapy) and evidence of systemic inflammation (C-reactive protein ≥75 mg/L) were eligible for random assignment in a 1:1 ratio to usual standard of care alone versus usual standard of care plus tocilizumab at a dose of 400 mg-800 mg (depending on weight) given intravenously. A second dose could be given 12-24 h later if the patient's condition had not improved. The primary outcome was 28-day mortality, assessed in the intention-to-treat population. The trial is registered with ISRCTN (50189673) and ClinicalTrials.gov (NCT04381936).<h4>Findings</h4>Between April 23, 2020, and Jan 24, 2021, 4116 adults of 21 550 patients enrolled into the RECOVERY trial were included in the assessment of tocilizumab, including 3385 (82%) patients receiving systemic corticosteroids. Overall, 621 (31%) of the 2022 patients allocated tocilizumab and 729 (35%) of the 2094 patients allocated to usual care died within 28 days (rate ratio 0·85; 95% CI 0·76-0·94; p=0·0028). Consistent results were seen in all prespecified subgroups of patients, including those receiving systemic corticosteroids. Patients allocated to tocilizumab were more likely to be discharged from hospital within 28 days (57% vs 50%; rate ratio 1·22; 1·12-1·33; p<0·0001). Among those not receiving invasive mechanical ventilation at baseline, patients allocated tocilizumab were less likely to reach the composite endpoint of invasive mechanical ventilation or death (35% vs 42%; risk ratio 0·84; 95% CI 0·77-0·92; p<0·0001).<h4>Interpretation</h4>In hospitalised COVID-19 patients with hypoxia and systemic inflammation, tocilizumab improved survival and other clinical outcomes. These benefits were seen regardless of the amount of respiratory support and were additional to the benefits of systemic corticosteroids.<h4>Funding</h4>UK Research and Innovation (Medical Research Council) and National Institute of Health Research.",,pdf:https://aura.abdn.ac.uk/bitstream/2164/16630/1/Recovery_etal_TL_Tocilizumab_In_Patients_VoR.pdf; doi:https://doi.org/10.1016/S0140-6736(21)00676-0; html:https://europepmc.org/articles/PMC8084355
+35497059,https://doi.org/10.1016/j.eclinm.2022.101392,Health conditions in adults with HIV compared with the general population: A population-based cross-sectional analysis.,"Morales DR, Moreno-Martos D, Matin N, McGettigan P.",,EClinicalMedicine,2022,2022-04-21,Y,HIV; Comorbidity; Multimorbidity,,,"<h4>Background</h4>Life expectancy in adults with human immunodeficiency virus (HIV) has increased and managing other health conditions is increasingly important for patients and healthcare planning. The aim of this study was to examine the prevalence and association between different health conditions and HIV status.<h4>Methods</h4>We performed a cross-sectional analysis of adult UK Clinical Practice Research Datalink primary care electronic medical records linked to hospital admissions as of Nov 30, 2015. We examined 47 health condition groups and 304 physical and mental health conditions by HIV status, after adjustment for age, sex, social deprivation status using logistic regression.<h4>Findings</h4>There were 964 patients with HIV (61.7% male; 92.8% aged <65 years) and 941,113 non-HIV patients (49.4% male; 75.2% aged <65 years). Condition groups with the greatest prevalence in HIV that were also highly prevalent in adults without HIV included: lipid disorder (41.4% vs 40.2%), and hypertension (19.1% vs 24.6%). Following adjustment, 18 (37.5%) condition groups were more likely in adults with HIV and ten (20.8%) were less likely. Individual conditions that were less likely in adults with HIV included: atrial fibrillation (odds ratio [OR] 0.37 [95% CI 0.20-0.64]) and hypertension (OR_0.78 [0.65-0.94]); rheumatoid arthritis (OR 0.27 [0.05-0.84]); asthma (OR_0.65 (0.53-0.80]); and certain eye diseases such as macular degeneration (OR_0.30 [0.09-0.70]). Meanwhile individual conditions that were more likely included: liver fibrosis, sclerosis, and cirrhosis (OR_3.23 [1.85-5.20]); pulmonary embolism (OR_2.06 [1.15-3.36]); male infertility (OR_2.23 [1.50-3.16]) and female infertility (OR_2.01 [1.34-2.88]); bipolar disorder (OR_2.93 [1.52-5.05]) and depression (OR_1.49 [1.28-1.71]); cervical malignancy (OR_4.64 [1.15-12.15]); and infections.<h4>Interpretation</h4>Comorbidity is common in adults with HIV, with physical and mental health conditions spanning a wide spectrum. HIV management should consider multidisciplinary care models to provide optimal patient care.<h4>Funding</h4>The project was funded by the Bart's Charity; DRM was funded by a Wellcome Trust Clinical Research Career Development Fellowship; DRM and DMM received funding from the HDR-UK Precision therapeutics programme.",,pdf:http://www.thelancet.com/article/S2589537022001225/pdf; doi:https://doi.org/10.1016/j.eclinm.2022.101392; html:https://europepmc.org/articles/PMC9046106; pdf:https://europepmc.org/articles/PMC9046106?pdf=render
 37478175,https://doi.org/10.1126/sciadv.adh8839,Citizen science reveals landscape-scale exposures to multiazole-resistant <i>Aspergillus fumigatus</i> bioaerosols.,"Shelton JMG, Rhodes J, Uzzell CB, Hemmings S, Brackin AP, Sewell TR, Alghamdi A, Dyer PS, Fraser M, Borman AM, Johnson EM, Piel FB, Singer AC, Fisher MC.",,Science advances,2023,2023-07-21,Y,,,,"Using a citizen science approach, we identify a country-wide exposure to aerosolized spores of a human fungal pathogen, <i>Aspergillus fumigatus</i>, that has acquired resistance to the agricultural fungicide tebuconazole and first-line azole clinical antifungal drugs. Genomic analysis shows no distinction between resistant genotypes found in the environment and in patients, indicating that at least 40% of azole-resistant <i>A. fumigatus</i> infections are acquired from environmental exposures. Hotspots and coldspots of aerosolized azole-resistant spores were not stable between seasonal sampling periods. This suggests a high degree of atmospheric mixing resulting in an estimated per capita cumulative annual exposure of 21 days (±2.6). Because of the ubiquity of this measured exposure, it is imperative that we determine sources of azole-resistant <i>A. fumigatus</i> to reduce treatment failure in patients with aspergillosis.",,doi:https://doi.org/10.1126/sciadv.adh8839; html:https://europepmc.org/articles/PMC10361594; pdf:https://europepmc.org/articles/PMC10361594?pdf=render
-38388753,https://doi.org/10.1007/s00125-024-06099-3,Phenotype-based targeted treatment of SGLT2 inhibitors and GLP-1 receptor agonists in type 2 diabetes.,"Cardoso P, Young KG, Nair ATN, Hopkins R, McGovern AP, Haider E, Karunaratne P, Donnelly L, Mateen BA, Sattar N, Holman RR, Bowden J, Hattersley AT, Pearson ER, Jones AG, Shields BM, McKinley TJ, Dennis JM, MASTERMIND consortium.",,Diabetologia,2024,2024-02-22,Y,Type 2 diabetes; Precision Medicine; Sglt2-inhibitors; Heterogeneous Treatment Effects; Glp1-receptor Agonists; Bayesian Non-parametric Modelling,,,"<h4>Aims/hypothesis</h4>A precision medicine approach in type 2 diabetes could enhance targeting specific glucose-lowering therapies to individual patients most likely to benefit. We aimed to use the recently developed Bayesian causal forest (BCF) method to develop and validate an individualised treatment selection algorithm for two major type 2 diabetes drug classes, sodium-glucose cotransporter 2 inhibitors (SGLT2i) and glucagon-like peptide-1 receptor agonists (GLP1-RA).<h4>Methods</h4>We designed a predictive algorithm using BCF to estimate individual-level conditional average treatment effects for 12-month glycaemic outcome (HbA<sub>1c</sub>) between SGLT2i and GLP1-RA, based on routine clinical features of 46,394 people with type 2 diabetes in primary care in England (Clinical Practice Research Datalink; 27,319 for model development, 19,075 for hold-out validation), with additional external validation in 2252 people with type 2 diabetes from Scotland (SCI-Diabetes [Tayside & Fife]). Differences in glycaemic outcome with GLP1-RA by sex seen in clinical data were replicated in clinical trial data (HARMONY programme: liraglutide [n=389] and albiglutide [n=1682]). As secondary outcomes, we evaluated the impacts of targeting therapy based on glycaemic response on weight change, tolerability and longer-term risk of new-onset microvascular complications, macrovascular complications and adverse kidney events.<h4>Results</h4>Model development identified marked heterogeneity in glycaemic response, with 4787 (17.5%) of the development cohort having a predicted HbA<sub>1c</sub> benefit >3 mmol/mol (>0.3%) with SGLT2i over GLP1-RA and 5551 (20.3%) having a predicted HbA<sub>1c</sub> benefit >3 mmol/mol with GLP1-RA over SGLT2i. Calibration was good in hold-back validation, and external validation in an independent Scottish dataset identified clear differences in glycaemic outcomes between those predicted to benefit from each therapy. Sex, with women markedly more responsive to GLP1-RA, was identified as a major treatment effect modifier in both the UK observational datasets and in clinical trial data: HARMONY-7 liraglutide (GLP1-RA): 4.4 mmol/mol (95% credible interval [95% CrI] 2.2, 6.3) (0.4% [95% CrI 0.2, 0.6]) greater response in women than men. Targeting the two therapies based on predicted glycaemic response was also associated with improvements in short-term tolerability and long-term risk of new-onset microvascular complications.<h4>Conclusions/interpretation</h4>Precision medicine approaches can facilitate effective individualised treatment choice between SGLT2i and GLP1-RA therapies, and the use of routinely collected clinical features for treatment selection could support low-cost deployment in many countries.",,doi:https://doi.org/10.1007/s00125-024-06099-3; html:https://europepmc.org/articles/PMC10955037; pdf:https://europepmc.org/articles/PMC10955037?pdf=render
 37398988,https://doi.org/10.1007/s40258-023-00821-9,Correction to: The False Economy of Seeking to Eliminate Delayed Transfers of Care: Some Lessons from Queueing Theory.,"Wood RM, Harper AL, Onen-Dumlu Z, Forte PG, Pitt M, Vasilakis C.",,Applied health economics and health policy,2023,2023-09-01,Y,,,,,,pdf:https://link.springer.com/content/pdf/10.1007/s40258-023-00821-9.pdf; doi:https://doi.org/10.1007/s40258-023-00821-9; html:https://europepmc.org/articles/PMC10403424; pdf:https://europepmc.org/articles/PMC10403424?pdf=render
-35497059,https://doi.org/10.1016/j.eclinm.2022.101392,Health conditions in adults with HIV compared with the general population: A population-based cross-sectional analysis.,"Morales DR, Moreno-Martos D, Matin N, McGettigan P.",,EClinicalMedicine,2022,2022-04-21,Y,HIV; Comorbidity; Multimorbidity,,,"<h4>Background</h4>Life expectancy in adults with human immunodeficiency virus (HIV) has increased and managing other health conditions is increasingly important for patients and healthcare planning. The aim of this study was to examine the prevalence and association between different health conditions and HIV status.<h4>Methods</h4>We performed a cross-sectional analysis of adult UK Clinical Practice Research Datalink primary care electronic medical records linked to hospital admissions as of Nov 30, 2015. We examined 47 health condition groups and 304 physical and mental health conditions by HIV status, after adjustment for age, sex, social deprivation status using logistic regression.<h4>Findings</h4>There were 964 patients with HIV (61.7% male; 92.8% aged <65 years) and 941,113 non-HIV patients (49.4% male; 75.2% aged <65 years). Condition groups with the greatest prevalence in HIV that were also highly prevalent in adults without HIV included: lipid disorder (41.4% vs 40.2%), and hypertension (19.1% vs 24.6%). Following adjustment, 18 (37.5%) condition groups were more likely in adults with HIV and ten (20.8%) were less likely. Individual conditions that were less likely in adults with HIV included: atrial fibrillation (odds ratio [OR] 0.37 [95% CI 0.20-0.64]) and hypertension (OR_0.78 [0.65-0.94]); rheumatoid arthritis (OR 0.27 [0.05-0.84]); asthma (OR_0.65 (0.53-0.80]); and certain eye diseases such as macular degeneration (OR_0.30 [0.09-0.70]). Meanwhile individual conditions that were more likely included: liver fibrosis, sclerosis, and cirrhosis (OR_3.23 [1.85-5.20]); pulmonary embolism (OR_2.06 [1.15-3.36]); male infertility (OR_2.23 [1.50-3.16]) and female infertility (OR_2.01 [1.34-2.88]); bipolar disorder (OR_2.93 [1.52-5.05]) and depression (OR_1.49 [1.28-1.71]); cervical malignancy (OR_4.64 [1.15-12.15]); and infections.<h4>Interpretation</h4>Comorbidity is common in adults with HIV, with physical and mental health conditions spanning a wide spectrum. HIV management should consider multidisciplinary care models to provide optimal patient care.<h4>Funding</h4>The project was funded by the Bart's Charity; DRM was funded by a Wellcome Trust Clinical Research Career Development Fellowship; DRM and DMM received funding from the HDR-UK Precision therapeutics programme.",,pdf:http://www.thelancet.com/article/S2589537022001225/pdf; doi:https://doi.org/10.1016/j.eclinm.2022.101392; html:https://europepmc.org/articles/PMC9046106; pdf:https://europepmc.org/articles/PMC9046106?pdf=render
+38388753,https://doi.org/10.1007/s00125-024-06099-3,Phenotype-based targeted treatment of SGLT2 inhibitors and GLP-1 receptor agonists in type 2 diabetes.,"Cardoso P, Young KG, Nair ATN, Hopkins R, McGovern AP, Haider E, Karunaratne P, Donnelly L, Mateen BA, Sattar N, Holman RR, Bowden J, Hattersley AT, Pearson ER, Jones AG, Shields BM, McKinley TJ, Dennis JM, MASTERMIND consortium.",,Diabetologia,2024,2024-02-22,Y,Type 2 diabetes; Precision Medicine; Sglt2-inhibitors; Heterogeneous Treatment Effects; Glp1-receptor Agonists; Bayesian Non-parametric Modelling,,,"<h4>Aims/hypothesis</h4>A precision medicine approach in type 2 diabetes could enhance targeting specific glucose-lowering therapies to individual patients most likely to benefit. We aimed to use the recently developed Bayesian causal forest (BCF) method to develop and validate an individualised treatment selection algorithm for two major type 2 diabetes drug classes, sodium-glucose cotransporter 2 inhibitors (SGLT2i) and glucagon-like peptide-1 receptor agonists (GLP1-RA).<h4>Methods</h4>We designed a predictive algorithm using BCF to estimate individual-level conditional average treatment effects for 12-month glycaemic outcome (HbA<sub>1c</sub>) between SGLT2i and GLP1-RA, based on routine clinical features of 46,394 people with type 2 diabetes in primary care in England (Clinical Practice Research Datalink; 27,319 for model development, 19,075 for hold-out validation), with additional external validation in 2252 people with type 2 diabetes from Scotland (SCI-Diabetes [Tayside & Fife]). Differences in glycaemic outcome with GLP1-RA by sex seen in clinical data were replicated in clinical trial data (HARMONY programme: liraglutide [n=389] and albiglutide [n=1682]). As secondary outcomes, we evaluated the impacts of targeting therapy based on glycaemic response on weight change, tolerability and longer-term risk of new-onset microvascular complications, macrovascular complications and adverse kidney events.<h4>Results</h4>Model development identified marked heterogeneity in glycaemic response, with 4787 (17.5%) of the development cohort having a predicted HbA<sub>1c</sub> benefit >3 mmol/mol (>0.3%) with SGLT2i over GLP1-RA and 5551 (20.3%) having a predicted HbA<sub>1c</sub> benefit >3 mmol/mol with GLP1-RA over SGLT2i. Calibration was good in hold-back validation, and external validation in an independent Scottish dataset identified clear differences in glycaemic outcomes between those predicted to benefit from each therapy. Sex, with women markedly more responsive to GLP1-RA, was identified as a major treatment effect modifier in both the UK observational datasets and in clinical trial data: HARMONY-7 liraglutide (GLP1-RA): 4.4 mmol/mol (95% credible interval [95% CrI] 2.2, 6.3) (0.4% [95% CrI 0.2, 0.6]) greater response in women than men. Targeting the two therapies based on predicted glycaemic response was also associated with improvements in short-term tolerability and long-term risk of new-onset microvascular complications.<h4>Conclusions/interpretation</h4>Precision medicine approaches can facilitate effective individualised treatment choice between SGLT2i and GLP1-RA therapies, and the use of routinely collected clinical features for treatment selection could support low-cost deployment in many countries.",,doi:https://doi.org/10.1007/s00125-024-06099-3; html:https://europepmc.org/articles/PMC10955037; pdf:https://europepmc.org/articles/PMC10955037?pdf=render
 35176022,https://doi.org/10.1371/journal.pmed.1003915,"Changes in household food and drink purchases following restrictions on the advertisement of high fat, salt, and sugar products across the Transport for London network: A controlled interrupted time series analysis.","Yau A, Berger N, Law C, Cornelsen L, Greener R, Adams J, Boyland EJ, Burgoine T, de Vocht F, Egan M, Er V, Lake AA, Lock K, Mytton O, Petticrew M, Thompson C, White M, Cummins S.",,PLoS medicine,2022,2022-02-17,Y,,,,"<h4>Background</h4>Restricting the advertisement of products with high fat, salt, and sugar (HFSS) content has been recommended as a policy tool to improve diet and tackle obesity, but the impact on HFSS purchasing is unknown. This study aimed to evaluate the impact of HFSS advertising restrictions, implemented across the London (UK) transport network in February 2019, on HFSS purchases.<h4>Methods and findings</h4>Over 5 million take-home food and drink purchases were recorded by 1,970 households (London [intervention], n = 977; North of England [control], n = 993) randomly selected from the Kantar Fast Moving Consumer Goods panel. The intervention and control samples were similar in household characteristics but had small differences in main food shopper sex, socioeconomic position, and body mass index. Using a controlled interrupted time series design, we estimated average weekly household purchases of energy and nutrients from HFSS products in the post-intervention period (44 weeks) compared to a counterfactual constructed from the control and pre-intervention (36 weeks) series. Energy purchased from HFSS products was 6.7% (1,001.0 kcal, 95% CI 456.0 to 1,546.0) lower among intervention households compared to the counterfactual. Relative reductions in purchases of fat (57.9 g, 95% CI 22.1 to 93.7), saturated fat (26.4 g, 95% CI 12.4 to 40.4), and sugar (80.7 g, 95% CI 41.4 to 120.1) from HFSS products were also observed. Energy from chocolate and confectionery purchases was 19.4% (317.9 kcal, 95% CI 200.0 to 435.8) lower among intervention households than for the counterfactual, with corresponding relative reductions in fat (13.1 g, 95% CI 7.5 to 18.8), saturated fat (8.7 g, 95% CI 5.7 to 11.7), sugar (41.4 g, 95% CI 27.4 to 55.4), and salt (0.2 g, 95% CI 0.1 to 0.2) purchased from chocolate and confectionery. Relative reductions are in the context of secular increases in HFSS purchases in both the intervention and control areas, so the policy was associated with attenuated growth of HFSS purchases rather than absolute reduction in HFSS purchases. Study limitations include the lack of out-of-home purchases in our analyses and not being able to assess the sustainability of observed changes beyond 44 weeks.<h4>Conclusions</h4>This study finds an association between the implementation of restrictions on outdoor HFSS advertising and relative reductions in energy, sugar, and fat purchased from HFSS products. These findings provide support for policies that restrict HFSS advertising as a tool to reduce purchases of HFSS products.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003915&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003915; html:https://europepmc.org/articles/PMC8853584; pdf:https://europepmc.org/articles/PMC8853584?pdf=render
 34007896,https://doi.org/10.23889/ijpds.v6i1.1387,"A retrospective epidemiological study of type 1 diabetes mellitus in wales, UK between 2008 and 2018.","Rafferty J, Stephens JW, Atkinson MD, Luzio SD, Akbari A, Gregory JW, Bain S, Owens DR, Thomas RL.",,International journal of population data science,2021,2021-04-15,Y,Diabetes mellitus; epidemiology; Electronic Health Records,,,"<h4>Introduction</h4>Studies of prevalence and the demographic profile of type 1 diabetes are challenging because of the relative rarity of the condition, however, these outcomes can be determined using routine healthcare data repositories. Understanding the epidemiology of type 1 diabetes allows for targeted interventions and care of this life-affecting condition.<h4>Objectives</h4>To describe the prevalence, incidence and demographics of persons with type 1 diabetes diagnosed in Wales, UK, using the Secure Anonymised Information Linkage (SAIL) Databank.<h4>Methods</h4>Data derived from primary and secondary care throughout Wales available in the SAIL Databank were used to identify people with type 1 diabetes to determine the prevalence and incidence of type 1 diabetes over a 10 year period (2008-18) and describe the demographic and clinical characteristics of this population by age, socioeconomic deprivation and settlement type. The seasonal variation in incidence rates was also examined.<h4>Results</h4>The prevalence of type 1 diabetes in 2018 was 0.32% in the whole population, being greater in men compared to women (0.35% vs 0.28% respectively); highest in those aged 15-29 years (0.52%) and living in the most socioeconomically deprived areas (0.38%). The incidence of type 1 diabetes over 10 years was 14.0 cases/100,000 people/year for the whole population of Wales. It was highest in children aged 0-14 years (33.6 cases/100,000 people/year) and areas of high socioeconomic deprivation (16.8 cases/100,000 people/year) and least in those aged 45-60 years (6.5 cases/100,000 people/year) and in areas of low socioeconomic deprivation (11.63 cases/100,000 people/year). A seasonal trend in the diagnoses of type 1 diabetes was observed with higher incidence in winter months.<h4>Conclusion</h4>This nation-wide retrospective epidemiological study using routine data revealed that the incidence of type 1 diabetes in Wales was greatest in those aged 0-14 years with a higher incidence and prevalence in the most deprived areas. These findings illustrate the need for health-related policies targeted at high deprivation areas to include type 1 diabetes in their remit.",,pdf:https://ijpds.org/article/download/1387/3155; doi:https://doi.org/10.23889/ijpds.v6i1.1387; html:https://europepmc.org/articles/PMC8103995; pdf:https://europepmc.org/articles/PMC8103995?pdf=render
 35835543,https://doi.org/10.1136/heartjnl-2022-321196,Eligibility for early rhythm control in patients with atrial fibrillation in the UK Biobank.,"Kany S, Cardoso VR, Bravo L, Williams JA, Schnabel R, Fabritz L, Gkoutos GV, Kirchhof P.",,Heart (British Cardiac Society),2022,2022-11-10,Y,Atrial fibrillation; Stroke; Catheter ablation,,,"<h4>Objective</h4>The Early Treatment of Atrial Fibrillation for Stroke Prevention (EAST-AFNET4) trial showed a clinical benefit of early rhythm-control therapy in patients with recently diagnosed atrial fibrillation (AF). The generalisability of the results in the general population is not known.<h4>Methods</h4>Participants in the population-based UK Biobank were assessed for eligibility based on the EAST-AFNET4 inclusion/exclusion criteria. Treatment of all eligible participants was classified as early rhythm-control (antiarrhythmic drug therapy or AF ablation) or usual care. To assess treatment effects, primary care data and Hospital Episode Statistics were merged with UK Biobank data.Efficacy and safety outcomes were compared between groups in the entire cohort and in a propensity-matched data set.<h4>Results</h4>AF was present in 35 526/502 493 (7.1%) participants, including 8340 (988 with AF <1 year) with AF at enrolment and 27 186 with incident AF during follow-up. Most participants (22 003/27 186; 80.9%) with incident AF were eligible for early rhythm-control.Eligible participants were older (70 years vs 63 years) and more likely to be female (42% vs 21%) compared with ineligible patients. Of 9004 participants with full primary care data, 874 (9.02%) received early rhythm-control. Safety outcomes were not different between patients receiving early rhythm-control and controls. The primary outcome of EAST-AFNET 4, a composite of cardiovascular death, stroke/transient ischaemic attack and hospitalisation for heart failure or acute coronary syndrome occurred less often in participants receiving early rhythm-control compared with controls in the entire cohort (HR 0.82, 95% CI 0.71 to 0.94, p=0.005). In the propensity-score matched analysis, early rhythm-control did not significantly decrease of the primary outcome compared with usual care (HR 0.87, 95% CI 0.72 to 1.04, p=0.124).<h4>Conclusion</h4>Around 80% of participants diagnosed with AF in the UK population are eligible for early rhythm-control. Early rhythm-control therapy was safe in routine care.",,pdf:https://heart.bmj.com/content/heartjnl/early/2022/07/13/heartjnl-2022-321196.full.pdf; doi:https://doi.org/10.1136/heartjnl-2022-321196; html:https://europepmc.org/articles/PMC9664114; pdf:https://europepmc.org/articles/PMC9664114?pdf=render
@@ -845,57 +846,57 @@ PMC9645061,https://doi.org/,Using population-scale medication data to evaluate t
 30950797,https://doi.org/10.2196/12286,Applications of Machine Learning in Real-Life Digital Health Interventions: Review of the Literature.,"Triantafyllidis AK, Tsanas A.",,Journal of medical Internet research,2019,2019-04-05,Y,Artificial intelligence; Review; data mining; Telemedicine; Machine Learning; Digital Health,Applied Analytics,,"<h4>Background</h4>Machine learning has attracted considerable research interest toward developing smart digital health interventions. These interventions have the potential to revolutionize health care and lead to substantial outcomes for patients and medical professionals.<h4>Objective</h4>Our objective was to review the literature on applications of machine learning in real-life digital health interventions, aiming to improve the understanding of researchers, clinicians, engineers, and policy makers in developing robust and impactful data-driven interventions in the health care domain.<h4>Methods</h4>We searched the PubMed and Scopus bibliographic databases with terms related to machine learning, to identify real-life studies of digital health interventions incorporating machine learning algorithms. We grouped those interventions according to their target (ie, target condition), study design, number of enrolled participants, follow-up duration, primary outcome and whether this had been statistically significant, machine learning algorithms used in the intervention, and outcome of the algorithms (eg, prediction).<h4>Results</h4>Our literature search identified 8 interventions incorporating machine learning in a real-life research setting, of which 3 (37%) were evaluated in a randomized controlled trial and 5 (63%) in a pilot or experimental single-group study. The interventions targeted depression prediction and management, speech recognition for people with speech disabilities, self-efficacy for weight loss, detection of changes in biopsychosocial condition of patients with multiple morbidity, stress management, treatment of phantom limb pain, smoking cessation, and personalized nutrition based on glycemic response. The average number of enrolled participants in the studies was 71 (range 8-214), and the average follow-up study duration was 69 days (range 3-180). Of the 8 interventions, 6 (75%) showed statistical significance (at the P=.05 level) in health outcomes.<h4>Conclusions</h4>This review found that digital health interventions incorporating machine learning algorithms in real-life studies can be useful and effective. Given the low number of studies identified in this review and that they did not follow a rigorous machine learning evaluation methodology, we urge the research community to conduct further studies in intervention settings following evaluation principles and demonstrating the potential of machine learning in clinical practice.",,pdf:https://www.jmir.org/2019/4/e12286/PDF; doi:https://doi.org/10.2196/12286; html:https://europepmc.org/articles/PMC6473205
 36446790,https://doi.org/10.1038/s41467-022-35017-7,Genetically personalised organ-specific metabolic models in health and disease.,"Foguet C, Xu Y, Ritchie SC, Lambert SA, Persyn E, Nath AP, Davenport EE, Roberts DJ, Paul DS, Di Angelantonio E, Danesh J, Butterworth AS, Yau C, Inouye M.",,Nature communications,2022,2022-11-29,Y,,,,"Understanding how genetic variants influence disease risk and complex traits (variant-to-function) is one of the major challenges in human genetics. Here we present a model-driven framework to leverage human genome-scale metabolic networks to define how genetic variants affect biochemical reaction fluxes across major human tissues, including skeletal muscle, adipose, liver, brain and heart. As proof of concept, we build personalised organ-specific metabolic flux models for 524,615 individuals of the INTERVAL and UK Biobank cohorts and perform a fluxome-wide association study (FWAS) to identify 4312 associations between personalised flux values and the concentration of metabolites in blood. Furthermore, we apply FWAS to identify 92 metabolic fluxes associated with the risk of developing coronary artery disease, many of which are linked to processes previously described to play in role in the disease. Our work demonstrates that genetically personalised metabolic models can elucidate the downstream effects of genetic variants on biochemical reactions involved in common human diseases.",,pdf:https://www.nature.com/articles/s41467-022-35017-7.pdf; doi:https://doi.org/10.1038/s41467-022-35017-7; html:https://europepmc.org/articles/PMC9708841; pdf:https://europepmc.org/articles/PMC9708841?pdf=render
 33875444,https://doi.org/10.1136/bmjopen-2020-045077,COVID-19 in patients with hepatobiliary and pancreatic diseases: a single-centre cross-sectional study in East London.,"Dayem Ullah AZM, Sivapalan L, Kocher HM, Chelala C.",,BMJ open,2021,2021-04-19,Y,Pancreatic Disease; Hepatobiliary Disease; Covid-19,,,"<h4>Objective</h4>To explore risk factors associated with COVID-19 susceptibility and survival in patients with pre-existing hepato-pancreato-biliary (HPB) conditions.<h4>Design</h4>Cross-sectional study.<h4>Setting</h4>East London Pancreatic Cancer Epidemiology (EL-PaC-Epidem) Study at Barts Health National Health Service Trust, UK. Linked electronic health records were interrogated on a cohort of participants (age ≥18 years), reported with HPB conditions between 1 April 2008 and 6 March 2020.<h4>Participants</h4>EL-PaC-Epidem Study participants, alive on 12 February 2020, and living in East London within the previous 6 months (n=15 440). The cohort represents a multi-ethnic population with 51.7% belonging to the non-White background.<h4>Main outcome measure</h4>COVID-19 incidence and mortality.<h4>Results</h4>Some 226 (1.5%) participants had confirmed COVID-19 diagnosis between 12 February and 12 June 2020, with increased odds for men (OR 1.56; 95% CI 1.2 to 2.04) and Black ethnicity (2.04; 1.39 to 2.95) as well as patients with moderate to severe liver disease (2.2; 1.35 to 3.59). Each additional comorbidity increased the odds of infection by 62%. Substance misusers were at more risk of infection, so were patients on vitamin D treatment. The higher ORs in patients with chronic pancreatic or mild liver conditions, age >70, and a history of smoking or obesity were due to coexisting comorbidities. Increased odds of death were observed for men (3.54; 1.68 to 7.85) and Black ethnicity (3.77; 1.38 to 10.7). Patients having respiratory complications from COVID-19 without a history of chronic respiratory disease also had higher odds of death (5.77; 1.75 to 19).<h4>Conclusions</h4>In this large population-based study of patients with HPB conditions, men, Black ethnicity, pre-existing moderate to severe liver conditions, six common medical multimorbidities, substance misuse and a history of vitamin D treatment independently posed higher odds of acquiring COVID-19 compared with their respective counterparts. The odds of death were significantly high for men and Black people.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/4/e045077.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-045077; html:https://europepmc.org/articles/PMC8057071; pdf:https://europepmc.org/articles/PMC8057071?pdf=render
-39266635,https://doi.org/10.1038/s41598-024-68543-z,Oculomic stratification of COVID-19 patients' intensive therapy unit admission status and mortality by retinal morphological findings.,"Courtie E, Taylor M, Danks D, Acharjee A, Jackson T, Logan A, Veenith T, Blanch RJ.",,Scientific reports,2024,2024-09-12,Y,,,,"To investigate if retinal thickness has predictive utility in COVID-19 outcomes by evaluating the statistical association between retinal thickness using OCT and of COVID-19-related mortality. Secondary outcomes included associations between retinal thickness and length of stay (LoS) in hospital. In this retrospective cohort study, OCT scans from 230 COVID-19 patients admitted to the Intensive Care Unit (ITU) were compared with age and gender-matched patients with pneumonia from before March 2020. Total retinal, GCL + IPL, and RNFL thicknesses were recorded, and analysed with systemic measures collected at the time of admission and mortality outcomes, using linear regression models, Pearson's R correlation, and Principal Component Analysis. Retinal thickness was significantly associated with all-time mortality on follow up in the COVID-19 group (p = 0.015), but not 28-day mortality (p = 0.151). Retinal and GCL + IPL layer thicknesses were both significantly associated with LoS in hospital for COVID-19 patients (p = 0.006 for both), but not for patients with pneumonia (p = 0.706 and 0.989 respectively). RNFL thickness was not associated with LoS in either group (COVID-19 p = 0.097, pneumonia p = 0.692). Retinal thickness associated with LoS in hospital and long-term mortality in COVID-19 patients, suggesting that retinal structure could be a surrogate marker for frailty and predictor of disease severity in this group of patients, but not in patients with pneumonia from other causes.",,doi:https://doi.org/10.1038/s41598-024-68543-z; doi:https://doi.org/10.1038/s41598-024-68543-z; html:https://europepmc.org/articles/PMC11393335; pdf:https://europepmc.org/articles/PMC11393335?pdf=render
 34148732,https://doi.org/10.1016/j.bja.2021.05.001,Surgical activity in England and Wales during the COVID-19 pandemic: a nationwide observational cohort study.,"Dobbs TD, Gibson JAG, Fowler AJ, Abbott TE, Shahid T, Torabi F, Griffiths R, Lyons RA, Pearse RM, Whitaker IS.",,British journal of anaesthesia,2021,2021-06-18,Y,Surgery; Anaesthesia; Public Policy; Waiting List; Surgical Activity; Covid-19,,,"<h4>Background</h4>A significant proportion of healthcare resource has been diverted to the care of those with COVID-19. This study reports the volume of surgical activity and the number of cancelled surgical procedures during the COVID-19 pandemic.<h4>Methods</h4>We used hospital episode statistics for all adult patients undergoing surgery between January 1, 2020 and December 31, 2020 in England and Wales. We identified surgical procedures using a previously published list of procedure codes. Procedures were stratified by urgency of surgery as defined by NHS England. We calculated the deficit of surgical activity by comparing the expected number of procedures from 2016 to 2019 with the actual number of procedures in 2020. Using a linear regression model, we calculated the expected cumulative number of cancelled procedures by December 31, 2021.<h4>Results</h4>The total number of surgical procedures carried out in England and Wales in 2020 was 3 102 674 compared with the predicted number of 4 671 338 (95% confidence interval [CI]: 4 218 740-5 123 932). This represents a 33.6% reduction in the national volume of surgical activity. There were 763 730 emergency surgical procedures (13.4% reduction) compared with 2 338 944 elective surgical procedures (38.6% reduction). The cumulative number of cancelled or postponed procedures was 1 568 664 (95% CI: 1 116 066-2 021 258). We estimate that this will increase to 2 358 420 (95% CI: 1 667 587-3 100 808) up to December 31, 2021.<h4>Conclusions</h4>The volume of surgical activity in England and Wales was reduced by 33.6% in 2020, resulting in more than 1.5 million cancelled operations. This deficit will continue to grow in 2021.",,pdf:http://www.bjanaesthesia.org/article/S0007091221002737/pdf; doi:https://doi.org/10.1016/j.bja.2021.05.001; html:https://europepmc.org/articles/PMC8277602; pdf:https://europepmc.org/articles/PMC8277602?pdf=render
+39266635,https://doi.org/10.1038/s41598-024-68543-z,Oculomic stratification of COVID-19 patients' intensive therapy unit admission status and mortality by retinal morphological findings.,"Courtie E, Taylor M, Danks D, Acharjee A, Jackson T, Logan A, Veenith T, Blanch RJ.",,Scientific reports,2024,2024-09-12,Y,,,,"To investigate if retinal thickness has predictive utility in COVID-19 outcomes by evaluating the statistical association between retinal thickness using OCT and of COVID-19-related mortality. Secondary outcomes included associations between retinal thickness and length of stay (LoS) in hospital. In this retrospective cohort study, OCT scans from 230 COVID-19 patients admitted to the Intensive Care Unit (ITU) were compared with age and gender-matched patients with pneumonia from before March 2020. Total retinal, GCL + IPL, and RNFL thicknesses were recorded, and analysed with systemic measures collected at the time of admission and mortality outcomes, using linear regression models, Pearson's R correlation, and Principal Component Analysis. Retinal thickness was significantly associated with all-time mortality on follow up in the COVID-19 group (p = 0.015), but not 28-day mortality (p = 0.151). Retinal and GCL + IPL layer thicknesses were both significantly associated with LoS in hospital for COVID-19 patients (p = 0.006 for both), but not for patients with pneumonia (p = 0.706 and 0.989 respectively). RNFL thickness was not associated with LoS in either group (COVID-19 p = 0.097, pneumonia p = 0.692). Retinal thickness associated with LoS in hospital and long-term mortality in COVID-19 patients, suggesting that retinal structure could be a surrogate marker for frailty and predictor of disease severity in this group of patients, but not in patients with pneumonia from other causes.",,doi:https://doi.org/10.1038/s41598-024-68543-z; doi:https://doi.org/10.1038/s41598-024-68543-z; html:https://europepmc.org/articles/PMC11393335; pdf:https://europepmc.org/articles/PMC11393335?pdf=render
 36374585,https://doi.org/10.1177/01410768221131897,Using national electronic health records for pandemic preparedness: validation of a parsimonious model for predicting excess deaths among those with COVID-19-a data-driven retrospective cohort study.,"Mizani MA, Dashtban A, Pasea L, Lai AG, Thygesen J, Tomlinson C, Handy A, Mamza JB, Morris T, Khalid S, Zaccardi F, Macleod MJ, Torabi F, Canoy D, Akbari A, Berry C, Bolton T, Nolan J, Khunti K, Denaxas S, Hemingway H, Sudlow C, Banerjee A, CVD-COVID-UK Consortium.",,Journal of the Royal Society of Medicine,2023,2022-11-14,N,Infectious diseases; Clinical; epidemiology; Public Health; Health Informatics,,,"<h4>Objectives</h4>To use national, pre- and post-pandemic electronic health records (EHR) to develop and validate a scenario-based model incorporating baseline mortality risk, infection rate (IR) and relative risk (RR) of death for prediction of excess deaths.<h4>Design</h4>An EHR-based, retrospective cohort study.<h4>Setting</h4>Linked EHR in Clinical Practice Research Datalink (CPRD); and linked EHR and COVID-19 data in England provided in NHS Digital Trusted Research Environment (TRE).<h4>Participants</h4>In the development (CPRD) and validation (TRE) cohorts, we included 3.8 million and 35.1 million individuals aged ≥30 years, respectively.<h4>Main outcome measures</h4>One-year all-cause excess deaths related to COVID-19 from March 2020 to March 2021.<h4>Results</h4>From 1 March 2020 to 1 March 2021, there were 127,020 observed excess deaths. Observed RR was 4.34% (95% CI, 4.31-4.38) and IR was 6.27% (95% CI, 6.26-6.28). In the validation cohort, predicted one-year excess deaths were 100,338 compared with the observed 127,020 deaths with a ratio of predicted to observed excess deaths of 0.79.<h4>Conclusions</h4>We show that a simple, parsimonious model incorporating baseline mortality risk, one-year IR and RR of the pandemic can be used for scenario-based prediction of excess deaths in the early stages of a pandemic. Our analyses show that EHR could inform pandemic planning and surveillance, despite limited use in emergency preparedness to date. Although infection dynamics are important in the prediction of mortality, future models should take greater account of underlying conditions.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/01410768221131897; doi:https://doi.org/10.1177/01410768221131897; html:https://europepmc.org/articles/PMC9909113; pdf:https://europepmc.org/articles/PMC9909113?pdf=render; doi:https://doi.org/10.1177/01410768221131897
 37667866,https://doi.org/10.1111/cen.14966,Genetically predicted plasma cortisol and common chronic diseases: A Mendelian randomization study.,"Lee WH, Larsson SC, Wood A, Di Angelantonio E, Butterworth AS, Burgess S, Allara E.",,Clinical endocrinology,2024,2023-09-05,Y,Hypertension; Cortisol; Osteoporosis; Type 2 diabetes; chronic diseases; Mendelian Randomization; Major Mental Illness,,,"<h4>Objective</h4>Cushing's syndrome is characterized by hypercortisolaemia and is frequently accompanied by comorbidities such as type 2 diabetes, hypertension, osteoporosis, depression and schizophrenia. It is unclear whether moderate but lifelong hypercortisolaemia is causally associated with these diseases in the general population. We aimed to address this research gap using a Mendelian randomization approach.<h4>Methods</h4>We used three cortisol-associated genetic variants in the SERPINA6/SERPINA1 region as genetic instruments in a two-sample, inverse-variance-weighted Mendelian randomization analysis. We obtained summary-level statistics for cortisol and disease outcomes from publicly available genetic consortia, and meta-analysed them as appropriate. We conducted a multivariable Mendelian randomization analysis to assess potential mediating effects.<h4>Results</h4>A 1 standard deviation higher genetically predicted plasma cortisol was associated with greater odds of hypertension (odds ratio: 1.12; 95% confidence interval [CI]: 1.05-1.18) as well as higher systolic blood pressure (mean difference [MD]: 0.03 SD change; 95% CI: 0.01-0.05) and diastolic blood pressure (MD: 0.03 SD change; 95% CI: 0.01-0.04). There was no evidence of association with type 2 diabetes, osteoporosis, depression and schizophrenia. The association with hypertension was attenuated upon adjustment for waist circumference, suggesting potential mediation through central obesity.<h4>Conclusion</h4>There is strong evidence for a causal association between plasma cortisol and greater risk for hypertension, potentially mediated by obesity.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/cen.14966; doi:https://doi.org/10.1111/cen.14966; html:https://europepmc.org/articles/PMC7615603; pdf:https://europepmc.org/articles/PMC7615603?pdf=render
-34265229,https://doi.org/10.1177/01410768211032850,"Symptoms, complications and management of long COVID: a review.","Aiyegbusi OL, Hughes SE, Turner G, Rivera SC, McMullan C, Chandan JS, Haroon S, Price G, Davies EH, Nirantharakumar K, Sapey E, Calvert MJ, TLC Study Group.",,Journal of the Royal Society of Medicine,2021,2021-07-15,Y,Infectious diseases; epidemiology; Public Health; Respiratory Medicine; Health Service Research; Covid-19; Long Covid; Post-Covid-19 Syndrome; Persistent Covid-19 Symptoms,,,"Globally, there are now over 160 million confirmed cases of COVID-19 and more than 3 million deaths. While the majority of infected individuals recover, a significant proportion continue to experience symptoms and complications after their acute illness. Patients with 'long COVID' experience a wide range of physical and mental/psychological symptoms. Pooled prevalence data showed the 10 most prevalent reported symptoms were fatigue, shortness of breath, muscle pain, joint pain, headache, cough, chest pain, altered smell, altered taste and diarrhoea. Other common symptoms were cognitive impairment, memory loss, anxiety and sleep disorders. Beyond symptoms and complications, people with long COVID often reported impaired quality of life, mental health and employment issues. These individuals may require multidisciplinary care involving the long-term monitoring of symptoms, to identify potential complications, physical rehabilitation, mental health and social services support. Resilient healthcare systems are needed to ensure efficient and effective responses to future health challenges.",,doi:https://doi.org/10.1177/01410768211032850; doi:https://doi.org/10.1177/01410768211032850; html:https://europepmc.org/articles/PMC8450986; pdf:https://europepmc.org/articles/PMC8450986?pdf=render
+34265229,https://doi.org/10.1177/01410768211032850,"Symptoms, complications and management of long COVID: a review.","Aiyegbusi OL, Hughes SE, Turner G, Rivera SC, McMullan C, Chandan JS, Haroon S, Price G, Davies EH, Nirantharakumar K, Sapey E, Calvert MJ, TLC Study Group.",,Journal of the Royal Society of Medicine,2021,2021-07-15,Y,Infectious diseases; epidemiology; Public Health; Respiratory Medicine; Health Service Research; Covid-19; Long Covid; Persistent Covid-19 Symptoms; Post-Covid-19 Syndrome,,,"Globally, there are now over 160 million confirmed cases of COVID-19 and more than 3 million deaths. While the majority of infected individuals recover, a significant proportion continue to experience symptoms and complications after their acute illness. Patients with 'long COVID' experience a wide range of physical and mental/psychological symptoms. Pooled prevalence data showed the 10 most prevalent reported symptoms were fatigue, shortness of breath, muscle pain, joint pain, headache, cough, chest pain, altered smell, altered taste and diarrhoea. Other common symptoms were cognitive impairment, memory loss, anxiety and sleep disorders. Beyond symptoms and complications, people with long COVID often reported impaired quality of life, mental health and employment issues. These individuals may require multidisciplinary care involving the long-term monitoring of symptoms, to identify potential complications, physical rehabilitation, mental health and social services support. Resilient healthcare systems are needed to ensure efficient and effective responses to future health challenges.",,doi:https://doi.org/10.1177/01410768211032850; doi:https://doi.org/10.1177/01410768211032850; html:https://europepmc.org/articles/PMC8450986; pdf:https://europepmc.org/articles/PMC8450986?pdf=render
 33716109,https://doi.org/10.1016/j.jinf.2021.03.002,Short durations of corticosteroids for hospitalised COVID-19 patients are associated with a high readmission rate.,"Chaudhry Z, Shawe-Taylor M, Rampling T, Cutfield T, Bidwell G, Chan XHS, Last A, Williams B, Logan S, Marks M, Esmail H.",,The Journal of infection,2021,2021-03-11,Y,Dexamethasone; Corticosteroids; Hospital; Readmissions; Covid-19,,,"<h4>Objective</h4>Our objective was to describe the characteristics of patients admitted, discharged and readmitted, due to COVID-19, to a central London acute-care hospital during the second peak, in particular in relation to corticosteroids use.<h4>Methods</h4>We reviewed patients admitted from the community to University College Hospital (UCH) with COVID-19 as their primary diagnosis between 1st-31st December 2020. Re-attendance and readmission data were collected for patients who re-presented within 10 days following discharge. Data were retrospectively collected.<h4>Results</h4>196 patients were admitted from the community with a diagnosis of COVID-19 and discharged alive in December 2020. Corticosteroids were prescribed in hospital for a median of 5 days (IQR 3-8). 20 patients (10.2%) were readmitted within 10 days. 11/20 received corticosteroids in the first admission of which 10 had received 1-3 days of corticosteroids. Readmission rate in those receiving 1-3 days of corticosteroids was 25%.<h4>Conclusions</h4>Most international guidelines have recommended providing up to 10 days of corticosteroids for severe COVID-19 but stopping on discharge. Our findings show shorter courses of corticosteroids during admission are associated with an increased risk of being readmitted and support continuing the course of corticosteroids after hospital discharge monitored in the virtual ward setting.",,pdf:http://www.journalofinfection.com/article/S0163445321001158/pdf; doi:https://doi.org/10.1016/j.jinf.2021.03.002; html:https://europepmc.org/articles/PMC7948670; pdf:https://europepmc.org/articles/PMC7948670?pdf=render
 35923560,https://doi.org/10.1016/j.lanepe.2022.100475,Equity of access to NHS-funded hip replacements in England and Wales: Trends from 2006 to 2016.,"Wyatt S, Bailey R, Moore P, Revell M.",,The Lancet regional health. Europe,2022,2022-07-29,Y,trends; Equity; Hip Replacements; Socio-economic Deprivation,,,"<h4>Background</h4>Elective hip replacement is a cost-effective means of improving hip function. Previous research has suggested that the supply of hip replacements in the NHS is governed by the inverse care law. We examine whether inequities in supply improved in England and Wales between 2006 and 2016.<h4>Methods</h4>We compare levels of need and supply of NHS funded hip replacements to adults aged 50+ years, across quintiles of deprivation in England and Wales between 2006 and 2016. We use data from routine health records and a large longitudinal study and adjust for age and sex using general additive negative-binomial regression.<h4>Findings</h4>The number of NHS-funded hip replacements per 100,000 population rose substantially from 272.6 and 266.7 in 2002, to 539.7 and 466.3 in 2018 in England and Wales respectively. Having adjusted for age and sex, people living in the most deprived quintile were 2.36 (95% CI, 1.69 to 3.29) times more likely to need a hip replacement in 2006 than those living in quintile 3, whereas those living in the least deprived quintile were 0.45 (95% CI, 0.39 to 0.69) as likely. Despite this, people living in the most deprived quintile were 0.81 (95% CI, 0.78 to 0.83) times as likely in England and 0.93 (95% CI, 0.84 to 1.04) as likely in Wales to receive an NHS-funded hip replacement in 2006 than those living in quintile 3. We found no evidence that these substantial inequities had reduced between 2006 and 2016.<h4>Interpretation</h4>With respect to hip-replacement surgery in England and Wales, policy ambitions to reduce healthcare inequities have not been realised.<h4>Funding</h4>This work was supported by Health Data Research UK.",,doi:https://doi.org/10.1016/j.lanepe.2022.100475; doi:https://doi.org/10.1016/j.lanepe.2022.100475; html:https://europepmc.org/articles/PMC9340533; pdf:https://europepmc.org/articles/PMC9340533?pdf=render
-37080566,https://doi.org/10.1183/13993003.01720-2022,Collaboration between explainable artificial intelligence and pulmonologists improves the accuracy of pulmonary function test interpretation.,"Das N, Happaerts S, Gyselinck I, Staes M, Derom E, Brusselle G, Burgos F, Contoli M, Dinh-Xuan AT, Franssen FME, Gonem S, Greening N, Haenebalcke C, Man WD, Moisés J, Peché R, Poberezhets V, Quint JK, Steiner MC, Vanderhelst E, Abdo M, Topalovic M, Janssens W.",,The European respiratory journal,2023,2023-05-18,Y,,,,"<h4>Background</h4>Few studies have investigated the collaborative potential between artificial intelligence (AI) and pulmonologists for diagnosing pulmonary disease. We hypothesised that the collaboration between a pulmonologist and AI with explanations (explainable AI (XAI)) is superior in diagnostic interpretation of pulmonary function tests (PFTs) than the pulmonologist without support.<h4>Methods</h4>The study was conducted in two phases, a monocentre study (phase 1) and a multicentre intervention study (phase 2). Each phase utilised two different sets of 24 PFT reports of patients with a clinically validated gold standard diagnosis. Each PFT was interpreted without (control) and with XAI's suggestions (intervention). Pulmonologists provided a differential diagnosis consisting of a preferential diagnosis and optionally up to three additional diagnoses. The primary end-point compared accuracy of preferential and additional diagnoses between control and intervention. Secondary end-points were the number of diagnoses in differential diagnosis, diagnostic confidence and inter-rater agreement. We also analysed how XAI influenced pulmonologists' decisions.<h4>Results</h4>In phase 1 (n=16 pulmonologists), mean preferential and differential diagnostic accuracy significantly increased by 10.4% and 9.4%, respectively, between control and intervention (p<0.001). Improvements were somewhat lower but highly significant (p<0.0001) in phase 2 (5.4% and 8.7%, respectively; n=62 pulmonologists). In both phases, the number of diagnoses in the differential diagnosis did not reduce, but diagnostic confidence and inter-rater agreement significantly increased during intervention. Pulmonologists updated their decisions with XAI's feedback and consistently improved their baseline performance if AI provided correct predictions.<h4>Conclusion</h4>A collaboration between a pulmonologist and XAI is better at interpreting PFTs than individual pulmonologists reading without XAI support or XAI alone.",,pdf:https://erj.ersjournals.com/content/erj/early/2023/03/15/13993003.01720-2022.full.pdf; doi:https://doi.org/10.1183/13993003.01720-2022; html:https://europepmc.org/articles/PMC10196345; pdf:https://europepmc.org/articles/PMC10196345?pdf=render
+31315158,https://doi.org/10.1002/cnm.3235,Non-invasive coronary CT angiography-derived fractional flow reserve: A benchmark study comparing the diagnostic performance of four different computational methodologies.,"Carson JM, Pant S, Roobottom C, Alcock R, Javier Blanco P, Alberto Bulant C, Vassilevski Y, Simakov S, Gamilov T, Pryamonosov R, Liang F, Ge X, Liu Y, Nithiarasu P.",,International journal for numerical methods in biomedical engineering,2019,2019-08-16,Y,Fractional Flow Reserve; Benchmark; Haemodynamic Models,,,"Non-invasive coronary computed tomography (CT) angiography-derived fractional flow reserve (cFFR) is an emergent approach to determine the functional relevance of obstructive coronary lesions. Its feasibility and diagnostic performance has been reported in several studies. It is unclear if differences in sensitivity and specificity between these studies are due to study design, population, or ""computational methodology."" We evaluate the diagnostic performance of four different computational workflows for the prediction of cFFR using a limited data set of 10 patients, three based on reduced-order modelling and one based on a 3D rigid-wall model. The results for three of these methodologies yield similar accuracy of 6.5% to 10.5% mean absolute difference between computed and measured FFR. The main aspects of modelling which affected cFFR estimation were choice of inlet and outlet boundary conditions and estimation of flow distribution in the coronary network. One of the reduced-order models showed the lowest overall deviation from the clinical FFR measurements, indicating that reduced-order models are capable of a similar level of accuracy to a 3D model. In addition, this reduced-order model did not include a lumped pressure-drop model for a stenosis, which implies that the additional effort of isolating a stenosis and inserting a pressure-drop element in the spatial mesh may not be required for FFR estimation. The present benchmark study is the first of this kind, in which we attempt to homogenize the data required to compute FFR using mathematical models. The clinical data utilised in the cFFR workflows are made publicly available online.","Retrospective case series of 10 patients having coronary angiogram and invasive fractional flow reserve measurement. The authors used 4 different techniques to estimate coronary vessel flow rate and compared their measurement agreement with clinical FFA measurements and with each other. They found that all 4 methods gave different results, but one approach was more similar with the clinical gold standard. They propose this method with most worthy of further investigaiton.",pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cnm.3235; doi:https://doi.org/10.1002/cnm.3235; html:https://europepmc.org/articles/PMC6851543; pdf:https://europepmc.org/articles/PMC6851543?pdf=render
 36384749,https://doi.org/10.1136/heartjnl-2022-321733,Lower birth weight is linked to poorer cardiovascular health in middle-aged population-based adults.,"Raisi-Estabragh Z, Cooper J, Bethell MS, McCracken C, Lewandowski AJ, Leeson P, Neubauer S, Harvey NC, Petersen SE.",,Heart (British Cardiac Society),2023,2023-03-10,Y,epidemiology; Magnetic Resonance Imaging; risk factors,,,"<h4>Objective</h4>To examine associations of birth weight with clinical and imaging indicators of cardiovascular health and evaluate mechanistic pathways in the UK Biobank.<h4>Methods</h4>Competing risk regression was used to estimate associations of birth weight with incident myocardial infarction (MI) and mortality (all-cause, cardiovascular disease, ischaemic heart disease, MI), over 7-12 years of longitudinal follow-up, adjusting for age, sex, deprivation, maternal smoking/hypertension and maternal/paternal diabetes. Mediation analysis was used to evaluate the role of childhood growth, adulthood obesity, cardiometabolic diseases and blood biomarkers in mediating the birth weight-MI relationship. Linear regression was used to estimate associations of birth weight with left ventricular (LV) mass-to-volume ratio, LV stroke volume, global longitudinal strain, LV global function index and left atrial ejection fraction.<h4>Results</h4>258 787 participants from white ethnicities (61% women, median age 56 (49, 62) years) were studied. Birth weight had a non-linear relationship with incident MI, with a significant inverse association below an optimal threshold of 3.2 kg (subdistribution HR: 1.15 (1.08 to 1.22), p=6.0×10<sup>-5</sup>) and attenuation to the null above this threshold. The birth weight-MI effect was mediated through hypertension (8.4%), glycated haemoglobin (7.0%), C reactive protein (6.4%), high-density lipoprotein (5.2%) and high cholesterol (4.1%). Birth weight-mortality associations were statistically non-significant after Bonferroni correction. In participants with cardiovascular magnetic resonance (n=19 314), lower birth weight was associated with adverse LV remodelling (greater concentricity, poorer function).<h4>Conclusions</h4>Lower birth weight was associated with greater risk of incident MI and unhealthy LV phenotypes; effects were partially mediated through cardiometabolic disease and systemic inflammation. These findings support consideration of birth weight in risk prediction and highlight actionable areas for disease prevention.",,pdf:https://heart.bmj.com/content/heartjnl/early/2022/11/15/heartjnl-2022-321733.full.pdf; doi:https://doi.org/10.1136/heartjnl-2022-321733; html:https://europepmc.org/articles/PMC10086465; pdf:https://europepmc.org/articles/PMC10086465?pdf=render
+37080566,https://doi.org/10.1183/13993003.01720-2022,Collaboration between explainable artificial intelligence and pulmonologists improves the accuracy of pulmonary function test interpretation.,"Das N, Happaerts S, Gyselinck I, Staes M, Derom E, Brusselle G, Burgos F, Contoli M, Dinh-Xuan AT, Franssen FME, Gonem S, Greening N, Haenebalcke C, Man WD, Moisés J, Peché R, Poberezhets V, Quint JK, Steiner MC, Vanderhelst E, Abdo M, Topalovic M, Janssens W.",,The European respiratory journal,2023,2023-05-18,Y,,,,"<h4>Background</h4>Few studies have investigated the collaborative potential between artificial intelligence (AI) and pulmonologists for diagnosing pulmonary disease. We hypothesised that the collaboration between a pulmonologist and AI with explanations (explainable AI (XAI)) is superior in diagnostic interpretation of pulmonary function tests (PFTs) than the pulmonologist without support.<h4>Methods</h4>The study was conducted in two phases, a monocentre study (phase 1) and a multicentre intervention study (phase 2). Each phase utilised two different sets of 24 PFT reports of patients with a clinically validated gold standard diagnosis. Each PFT was interpreted without (control) and with XAI's suggestions (intervention). Pulmonologists provided a differential diagnosis consisting of a preferential diagnosis and optionally up to three additional diagnoses. The primary end-point compared accuracy of preferential and additional diagnoses between control and intervention. Secondary end-points were the number of diagnoses in differential diagnosis, diagnostic confidence and inter-rater agreement. We also analysed how XAI influenced pulmonologists' decisions.<h4>Results</h4>In phase 1 (n=16 pulmonologists), mean preferential and differential diagnostic accuracy significantly increased by 10.4% and 9.4%, respectively, between control and intervention (p<0.001). Improvements were somewhat lower but highly significant (p<0.0001) in phase 2 (5.4% and 8.7%, respectively; n=62 pulmonologists). In both phases, the number of diagnoses in the differential diagnosis did not reduce, but diagnostic confidence and inter-rater agreement significantly increased during intervention. Pulmonologists updated their decisions with XAI's feedback and consistently improved their baseline performance if AI provided correct predictions.<h4>Conclusion</h4>A collaboration between a pulmonologist and XAI is better at interpreting PFTs than individual pulmonologists reading without XAI support or XAI alone.",,pdf:https://erj.ersjournals.com/content/erj/early/2023/03/15/13993003.01720-2022.full.pdf; doi:https://doi.org/10.1183/13993003.01720-2022; html:https://europepmc.org/articles/PMC10196345; pdf:https://europepmc.org/articles/PMC10196345?pdf=render
 37118449,https://doi.org/10.1038/s43587-022-00224-w,Robust SARS-CoV-2-specific and heterologous immune responses in vaccine-naïve residents of long-term care facilities who survive natural infection.,"Tut G, Lancaster T, Butler MS, Sylla P, Spalkova E, Bone D, Kaur N, Bentley C, Amin U, Jadir AT, Hulme S, Ayodel M, Dowell AC, Pearce H, Zuo J, Margielewska-Davies S, Verma K, Nicol S, Begum J, Jinks E, Tut E, Bruton R, Krutikov M, Shrotri M, Giddings R, Azmi B, Fuller C, Irwin-Singer A, Hayward A, Copas A, Shallcross L, Moss P.",,Nature aging,2022,2022-05-30,Y,,,,"We studied humoral and cellular immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 152 long-term care facility staff and 124 residents over a prospective 4-month period shortly after the first wave of infection in England. We show that residents of long-term care facilities developed high and stable levels of antibodies against spike protein and receptor-binding domain. Nucleocapsid-specific responses were also elevated but waned over time. Antibodies showed stable and equivalent levels of functional inhibition against spike-angiotensin-converting enzyme 2 binding in all age groups with comparable activity against viral variants of concern. SARS-CoV-2 seropositive donors showed high levels of antibodies to other beta-coronaviruses but serostatus did not impact humoral immunity to influenza or other respiratory syncytial viruses. SARS-CoV-2-specific cellular responses were similar across all ages but virus-specific populations showed elevated levels of activation in older donors. Thus, survivors of SARS-CoV-2 infection show a robust and stable immunity against the virus that does not negatively impact responses to other seasonal viruses.",,pdf:https://www.nature.com/articles/s43587-022-00224-w.pdf; doi:https://doi.org/10.1038/s43587-022-00224-w; html:https://europepmc.org/articles/PMC10154219; pdf:https://europepmc.org/articles/PMC10154219?pdf=render
 36994768,https://doi.org/10.1002/cphy.c210037,Autonomic Cardiovascular Control in Health and Disease.,"Karim S, Chahal A, Khanji MY, Petersen SE, Somers VK.",,Comprehensive Physiology,2023,2023-03-30,N,,,,"Autonomic neural control of the cardiovascular system is formed of complex and dynamic processes able to adjust rapidly to mitigate perturbations in hemodynamics and maintain homeostasis. Alterations in autonomic control feature in the development or progression of a multitude of diseases with wide-ranging physiological implications given the neural system's responsibility for controlling inotropy, chronotropy, lusitropy, and dromotropy. Imbalances in sympathetic and parasympathetic neural control are also implicated in the development of arrhythmia in several cardiovascular conditions sparking interest in autonomic modulation as a form of treatment. A number of measures of autonomic function have shown prognostic significance in health and in pathological states and have undergone varying degrees of refinement, yet adoption into clinical practice remains extremely limited. The focus of this contemporary narrative review is to summarize the anatomy, physiology, and pathophysiology of the cardiovascular autonomic nervous system and describe the merits and shortfalls of testing modalities available. © 2023 American Physiological Society. Compr Physiol 13:4493-4511, 2023.",,pdf:https://qmro.qmul.ac.uk/xmlui/bitstream/123456789/80022/2/Petersen%20Autonomic%20Cardiovascular%20Control%202022%20Accepted.pdf; doi:https://doi.org/10.1002/cphy.c210037; html:https://europepmc.org/articles/PMC10406398; pdf:https://europepmc.org/articles/PMC10406398?pdf=render; doi:https://doi.org/10.1002/cphy.c210037
-31315158,https://doi.org/10.1002/cnm.3235,Non-invasive coronary CT angiography-derived fractional flow reserve: A benchmark study comparing the diagnostic performance of four different computational methodologies.,"Carson JM, Pant S, Roobottom C, Alcock R, Javier Blanco P, Alberto Bulant C, Vassilevski Y, Simakov S, Gamilov T, Pryamonosov R, Liang F, Ge X, Liu Y, Nithiarasu P.",,International journal for numerical methods in biomedical engineering,2019,2019-08-16,Y,Fractional Flow Reserve; Benchmark; Haemodynamic Models,,,"Non-invasive coronary computed tomography (CT) angiography-derived fractional flow reserve (cFFR) is an emergent approach to determine the functional relevance of obstructive coronary lesions. Its feasibility and diagnostic performance has been reported in several studies. It is unclear if differences in sensitivity and specificity between these studies are due to study design, population, or ""computational methodology."" We evaluate the diagnostic performance of four different computational workflows for the prediction of cFFR using a limited data set of 10 patients, three based on reduced-order modelling and one based on a 3D rigid-wall model. The results for three of these methodologies yield similar accuracy of 6.5% to 10.5% mean absolute difference between computed and measured FFR. The main aspects of modelling which affected cFFR estimation were choice of inlet and outlet boundary conditions and estimation of flow distribution in the coronary network. One of the reduced-order models showed the lowest overall deviation from the clinical FFR measurements, indicating that reduced-order models are capable of a similar level of accuracy to a 3D model. In addition, this reduced-order model did not include a lumped pressure-drop model for a stenosis, which implies that the additional effort of isolating a stenosis and inserting a pressure-drop element in the spatial mesh may not be required for FFR estimation. The present benchmark study is the first of this kind, in which we attempt to homogenize the data required to compute FFR using mathematical models. The clinical data utilised in the cFFR workflows are made publicly available online.","Retrospective case series of 10 patients having coronary angiogram and invasive fractional flow reserve measurement. The authors used 4 different techniques to estimate coronary vessel flow rate and compared their measurement agreement with clinical FFA measurements and with each other. They found that all 4 methods gave different results, but one approach was more similar with the clinical gold standard. They propose this method with most worthy of further investigaiton.",pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cnm.3235; doi:https://doi.org/10.1002/cnm.3235; html:https://europepmc.org/articles/PMC6851543; pdf:https://europepmc.org/articles/PMC6851543?pdf=render
 38022395,https://doi.org/10.1088/2515-7620/acf81b,How to estimate carbon footprint when training deep learning models? A guide and review.,"Bouza L, Bugeau A, Lannelongue L.",,Environmental research communications,2023,2023-11-21,Y,Ai Carbon Footprint; Environmental Impacts Of Deep Learning; Measuring Electrical Consumption Of Ai,,,"Machine learning and deep learning models have become essential in the recent fast development of artificial intelligence in many sectors of the society. It is now widely acknowledge that the development of these models has an environmental cost that has been analyzed in many studies. Several online and software tools have been developed to track energy consumption while training machine learning models. In this paper, we propose a comprehensive introduction and comparison of these tools for AI practitioners wishing to start estimating the environmental impact of their work. We review the specific vocabulary, the technical requirements for each tool. We compare the energy consumption estimated by each tool on two deep neural networks for image processing and on different types of servers. From these experiments, we provide some advice for better choosing the right tool and infrastructure.",,doi:https://doi.org/10.1088/2515-7620/acf81b; html:https://europepmc.org/articles/PMC10661046; pdf:https://europepmc.org/articles/PMC10661046?pdf=render
 33212507,https://doi.org/10.1093/molbev/msaa279,Genomic Analysis Revealed a Convergent Evolution of LINE-1 in Coat Color: A Case Study in Water Buffaloes (Bubalus bubalis).,"Liang D, Zhao P, Si J, Fang L, Pairo-Castineira E, Hu X, Xu Q, Hou Y, Gong Y, Liang Z, Tian B, Mao H, Yindee M, Faruque MO, Kongvongxay S, Khamphoumee S, Liu GE, Wu DD, Barker JSF, Han J, Zhang Y.",,Molecular biology and evolution,2021,2021-03-01,Y,Transposon; Water buffalo; Convergent Evolution; Line-1; Asip Gene; White Coat Color,,,"Visible pigmentation phenotypes can be used to explore the regulation of gene expression and the evolution of coat color patterns in animals. Here, we performed whole-genome and RNA sequencing and applied genome-wide association study, comparative population genomics and biological experiments to show that the 2,809-bp-long LINE-1 insertion in the ASIP (agouti signaling protein) gene is the causative mutation for the white coat phenotype in swamp buffalo (Bubalus bubalis). This LINE-1 insertion (3' truncated and containing only 5' UTR) functions as a strong proximal promoter that leads to a 10-fold increase in the transcription of ASIP in white buffalo skin. The 165 bp of 5' UTR transcribed from the LINE-1 is spliced into the first coding exon of ASIP, resulting in a chimeric transcript. The increased expression of ASIP prevents melanocyte maturation, leading to the absence of pigment in white buffalo skin and hairs. Phylogenetic analyses indicate that the white buffalo-specific ASIP allele originated from a recent genetic transposition event in swamp buffalo. Interestingly, as a similar LINE-1 insertion has been identified in the cattle ASIP gene, we discuss the convergent mechanism of coat color evolution in the Bovini tribe.",,pdf:https://academic.oup.com/mbe/article-pdf/38/3/1122/36533820/msaa279.pdf; doi:https://doi.org/10.1093/molbev/msaa279; html:https://europepmc.org/articles/PMC7947781; pdf:https://europepmc.org/articles/PMC7947781?pdf=render
 34534697,https://doi.org/10.1016/j.jbi.2021.103916,Ranking sets of morbidities using hypergraph centrality.,"Rafferty J, Watkins A, Lyons J, Lyons RA, Akbari A, Peek N, Jalali-Najafabadi F, Ba Dhafari T, Pate A, Martin GP, Bailey R.",,Journal of biomedical informatics,2021,2021-09-15,Y,Network Analysis; Hypergraph; Multi-morbidity,,,"Multi-morbidity, the health state of having two or more concurrent chronic conditions, is becoming more common as populations age, but is poorly understood. Identifying and understanding commonly occurring sets of diseases is important to inform clinical decisions to improve patient services and outcomes. Network analysis has been previously used to investigate multi-morbidity, but a classic application only allows for information on binary sets of diseases to contribute to the graph. We propose the use of hypergraphs, which allows for the incorporation of data on people with any number of conditions, and also allows us to obtain a quantitative understanding of the centrality, a measure of how well connected items in the network are to each other, of both single diseases and sets of conditions. Using this framework we illustrate its application with the set of conditions described in the Charlson morbidity index using data extracted from routinely collected population-scale, patient level electronic health records (EHR) for a cohort of adults in Wales, UK. Stroke and diabetes were found to be the most central single conditions. Sets of diseases featuring diabetes; diabetes with Chronic Pulmonary Disease, Renal Disease, Congestive Heart Failure and Cancer were the most central pairs of diseases. We investigated the differences between results obtained from the hypergraph and a classic binary graph and found that the centrality of diseases such as paraplegia, which are connected strongly to a single other disease is exaggerated in binary graphs compared to hypergraphs. The measure of centrality is derived from the weighting metrics calculated for disease sets and further investigation is needed to better understand the effect of the metric used in identifying the clinical significance and ranked centrality of grouped diseases. These initial results indicate that hypergraphs can be used as a valuable tool for analysing previously poorly understood relationships and information available in EHR data.",,doi:https://doi.org/10.1016/j.jbi.2021.103916; doi:https://doi.org/10.1016/j.jbi.2021.103916; html:https://europepmc.org/articles/PMC8524321
+35256633,https://doi.org/10.1038/s41598-022-07291-4,Shared genetic loci for body fat storage and adipocyte lipolysis in humans.,"Kulyté A, Lundbäck V, Arner P, Strawbridge RJ, Dahlman I.",,Scientific reports,2022,2022-03-07,Y,,,,"Total body fat and central fat distribution are heritable traits and well-established predictors of adverse metabolic outcomes. Lipolysis is the process responsible for the hydrolysis of triacylglycerols stored in adipocytes. To increase our understanding of the genetic regulation of body fat distribution and total body fat, we set out to determine if genetic variants associated with body mass index (BMI) or waist-hip-ratio adjusted for BMI (WHRadjBMI) in genome-wide association studies (GWAS) mediate their effect by influencing adipocyte lipolysis. We utilized data from the recent GWAS of spontaneous and isoprenaline-stimulated lipolysis in the unique GENetics of Adipocyte Lipolysis (GENiAL) cohort. GENiAL consists of 939 participants who have undergone abdominal subcutaneous adipose biopsy for the determination of spontaneous and isoprenaline-stimulated lipolysis in adipocytes. We report 11 BMI and 15 WHRadjBMI loci with SNPs displaying nominal association with lipolysis and allele-dependent gene expression in adipose tissue according to in silico analysis. Functional evaluation of candidate genes in these loci by small interfering RNAs (siRNA)-mediated knock-down in adipose-derived stem cells identified ZNF436 and NUP85 as intrinsic regulators of lipolysis consistent with the associations observed in the clinical cohorts. Furthermore, candidate genes in another BMI-locus (STX17) and two more WHRadjBMI loci (NID2, GGA3, GRB2) control lipolysis alone, or in conjunction with lipid storage, and may hereby be involved in genetic control of body fat. The findings expand our understanding of how genetic variants mediate their impact on the complex traits of fat storage and distribution.",,pdf:https://www.nature.com/articles/s41598-022-07291-4.pdf; doi:https://doi.org/10.1038/s41598-022-07291-4; html:https://europepmc.org/articles/PMC8901764; pdf:https://europepmc.org/articles/PMC8901764?pdf=render
 38689316,https://doi.org/10.1186/s13643-024-02540-1,Correction: Patient‑reported outcome (PRO) instruments used in patients undergoing adoptive cell therapy (ACT) for the treatment of cancer: a systematic review.,"Taylor S, Law K, Coomber-Moore J, Davies M, Thistlethwaite F, Calvert M, Aiyegbusi O, Yorke J.",,Systematic reviews,2024,2024-04-30,Y,,,,,,pdf:https://systematicreviewsjournal.biomedcentral.com/counter/pdf/10.1186/s13643-024-02540-1; doi:https://doi.org/10.1186/s13643-024-02540-1; html:https://europepmc.org/articles/PMC11059719; pdf:https://europepmc.org/articles/PMC11059719?pdf=render
 38718225,https://doi.org/10.1093/bioinformatics/btae296,Chainsaw: protein domain segmentation with fully convolutional neural networks.,"Wells J, Hawkins-Hooker A, Bordin N, Sillitoe I, Paige B, Orengo C.",,"Bioinformatics (Oxford, England)",2024,2024-05-01,Y,,,,"<h4>Motivation</h4>Protein domains are fundamental units of protein structure and play a pivotal role in understanding folding, function, evolution, and design. The advent of accurate structure prediction techniques has resulted in an influx of new structural data, making the partitioning of these structures into domains essential for inferring evolutionary relationships and functional classification.<h4>Results</h4>This article presents Chainsaw, a supervised learning approach to domain parsing that achieves accuracy that surpasses current state-of-the-art methods. Chainsaw uses a fully convolutional neural network which is trained to predict the probability that each pair of residues is in the same domain. Domain predictions are then derived from these pairwise predictions using an algorithm that searches for the most likely assignment of residues to domains given the set of pairwise co-membership probabilities. Chainsaw matches CATH domain annotations in 78% of protein domains versus 72% for the next closest method. When predicting on AlphaFold models, expert human evaluators were twice as likely to prefer Chainsaw's predictions versus the next best method.<h4>Availability and implementation</h4>github.com/JudeWells/Chainsaw.",,doi:https://doi.org/10.1093/bioinformatics/btae296; html:https://europepmc.org/articles/PMC11256964; pdf:https://europepmc.org/articles/PMC11256964?pdf=render
 38772405,https://doi.org/10.1016/s0140-6736(24)00537-3,Post-trial monitoring of a randomised controlled trial of intensive glycaemic control in type 2 diabetes extended from 10 years to 24 years (UKPDS 91).,"Adler AI, Coleman RL, Leal J, Whiteley WN, Clarke P, Holman RR.",,"Lancet (London, England)",2024,2024-05-18,N,,,,"<h4>Background</h4>The 20-year UK Prospective Diabetes Study showed major clinical benefits for people with newly diagnosed type 2 diabetes randomly allocated to intensive glycaemic control with sulfonylurea or insulin therapy or metformin therapy, compared with conventional glycaemic control. 10-year post-trial follow-up identified enduring and emerging glycaemic and metformin legacy treatment effects. We aimed to determine whether these effects would wane by extending follow-up for another 14 years.<h4>Methods</h4>5102 patients enrolled between 1977 and 1991, of whom 4209 (82·5%) participants were originally randomly allocated to receive either intensive glycaemic control (sulfonylurea or insulin, or if overweight, metformin) or conventional glycaemic control (primarily diet). At the end of the 20-year interventional trial, 3277 surviving participants entered a 10-year post-trial monitoring period, which ran until Sept 30, 2007. Eligible participants for this study were all surviving participants at the end of the 10-year post-trial monitoring period. An extended follow-up of these participants was done by linking them to their routinely collected National Health Service (NHS) data for another 14 years. Clinical outcomes were derived from records of deaths, hospital admissions, outpatient visits, and accident and emergency unit attendances. We examined seven prespecified aggregate clinical outcomes (ie, any diabetes-related endpoint, diabetes-related death, death from any cause, myocardial infarction, stroke, peripheral vascular disease, and microvascular disease) by the randomised glycaemic control strategy on an intention-to-treat basis using Kaplan-Meier time-to-event and log-rank analyses. This study is registered with the ISRCTN registry, number ISRCTN75451837.<h4>Findings</h4>Between Oct 1, 2007, and Sept 30, 2021, 1489 (97·6%) of 1525 participants could be linked to routinely collected NHS administrative data. Their mean age at baseline was 50·2 years (SD 8·0), and 41·3% were female. The mean age of those still alive as of Sept 30, 2021, was 79·9 years (SD 8·0). Individual follow-up from baseline ranged from 0 to 42 years, median 17·5 years (IQR 12·3-26·8). Overall follow-up increased by 21%, from 66 972 to 80 724 person-years. For up to 24 years after trial end, the glycaemic and metformin legacy effects showed no sign of waning. Early intensive glycaemic control with sulfonylurea or insulin therapy, compared with conventional glycaemic control, showed overall relative risk reductions of 10% (95% CI 2-17; p=0·015) for death from any cause, 17% (6-26; p=0·002) for myocardial infarction, and 26% (14-36; p<0·0001) for microvascular disease. Corresponding absolute risk reductions were 2·7%, 3·3%, and 3·5%, respectively. Early intensive glycaemic control with metformin therapy, compared with conventional glycaemic control, showed overall relative risk reductions of 20% (95% CI 5-32; p=0·010) for death from any cause and 31% (12-46; p=0·003) for myocardial infarction. Corresponding absolute risk reductions were 4·9% and 6·2%, respectively. No significant risk reductions during or after the trial for stroke or peripheral vascular disease were observed for both intensive glycaemic control groups, and no significant risk reduction for microvascular disease was observed for metformin therapy.<h4>Interpretation</h4>Early intensive glycaemic control with sulfonylurea or insulin, or with metformin, compared with conventional glycaemic control, appears to confer a near-lifelong reduced risk of death and myocardial infarction. Achieving near normoglycaemia immediately following diagnosis might be essential to minimise the lifetime risk of diabetes-related complications to the greatest extent possible.<h4>Funding</h4>University of Oxford Nuffield Department of Population Health Pump Priming.",,doi:https://doi.org/10.1016/S0140-6736(24)00537-3
-35256633,https://doi.org/10.1038/s41598-022-07291-4,Shared genetic loci for body fat storage and adipocyte lipolysis in humans.,"Kulyté A, Lundbäck V, Arner P, Strawbridge RJ, Dahlman I.",,Scientific reports,2022,2022-03-07,Y,,,,"Total body fat and central fat distribution are heritable traits and well-established predictors of adverse metabolic outcomes. Lipolysis is the process responsible for the hydrolysis of triacylglycerols stored in adipocytes. To increase our understanding of the genetic regulation of body fat distribution and total body fat, we set out to determine if genetic variants associated with body mass index (BMI) or waist-hip-ratio adjusted for BMI (WHRadjBMI) in genome-wide association studies (GWAS) mediate their effect by influencing adipocyte lipolysis. We utilized data from the recent GWAS of spontaneous and isoprenaline-stimulated lipolysis in the unique GENetics of Adipocyte Lipolysis (GENiAL) cohort. GENiAL consists of 939 participants who have undergone abdominal subcutaneous adipose biopsy for the determination of spontaneous and isoprenaline-stimulated lipolysis in adipocytes. We report 11 BMI and 15 WHRadjBMI loci with SNPs displaying nominal association with lipolysis and allele-dependent gene expression in adipose tissue according to in silico analysis. Functional evaluation of candidate genes in these loci by small interfering RNAs (siRNA)-mediated knock-down in adipose-derived stem cells identified ZNF436 and NUP85 as intrinsic regulators of lipolysis consistent with the associations observed in the clinical cohorts. Furthermore, candidate genes in another BMI-locus (STX17) and two more WHRadjBMI loci (NID2, GGA3, GRB2) control lipolysis alone, or in conjunction with lipid storage, and may hereby be involved in genetic control of body fat. The findings expand our understanding of how genetic variants mediate their impact on the complex traits of fat storage and distribution.",,pdf:https://www.nature.com/articles/s41598-022-07291-4.pdf; doi:https://doi.org/10.1038/s41598-022-07291-4; html:https://europepmc.org/articles/PMC8901764; pdf:https://europepmc.org/articles/PMC8901764?pdf=render
 37649988,https://doi.org/10.1093/jamiaopen/ooad078,"Determining prescriptions in electronic healthcare record data: methods for development of standardized, reproducible drug codelists.","Graul EL, Stone PW, Massen GM, Hatam S, Adamson A, Denaxas S, Peters NS, Quint JK.",,JAMIA open,2023,2023-08-29,Y,epidemiology; Electronic Medical Records; Misclassification Bias; Value Sets; Health Data Science; Code Sets,,,"<h4>Objective</h4>To develop a standardizable, reproducible method for creating drug codelists that incorporates clinical expertise and is adaptable to other studies and databases.<h4>Materials and methods</h4>We developed methods to generate drug codelists and tested this using the Clinical Practice Research Datalink (CPRD) Aurum database, accounting for missing data in the database. We generated codelists for: (1) cardiovascular disease and (2) inhaled Chronic Obstructive Pulmonary Disease (COPD) therapies, applying them to a sample cohort of 335 931 COPD patients. We compared searching all drug dictionary variables (A) against searching only (B) chemical or (C) ontological variables.<h4>Results</h4>In Search A, we identified 165 150 patients prescribed cardiovascular drugs (49.2% of cohort), and 317 963 prescribed COPD inhalers (94.7% of cohort). Evaluating output per search strategy, Search C missed numerous prescriptions, including vasodilator anti-hypertensives (A and B:19 696 prescriptions; C:1145) and SAMA inhalers (A and B:35 310; C:564).<h4>Discussion</h4>We recommend the full search (A) for comprehensiveness. There are special considerations when generating adaptable and generalizable drug codelists, including fluctuating status, cohort-specific drug indications, underlying hierarchical ontology, and statistical analyses.<h4>Conclusions</h4>Methods must have end-to-end clinical input, and be standardizable, reproducible, and understandable to all researchers across data contexts.",,pdf:https://academic.oup.com/jamiaopen/article-pdf/6/3/ooad078/51279371/ooad078.pdf; doi:https://doi.org/10.1093/jamiaopen/ooad078; html:https://europepmc.org/articles/PMC10463548; pdf:https://europepmc.org/articles/PMC10463548?pdf=render
 36541282,https://doi.org/10.14814/phy2.15546,Reduced oxygen saturation entropy is associated with poor prognosis in critically ill patients with sepsis.,"Gheorghita M, Wikner M, Cawthorn A, Oyelade T, Nemeth K, Rockenschaub P, Gonzalez Hernandez F, Swanepoel N, Lilaonitkul W, Mani AR.",,Physiological reports,2022,2022-12-01,Y,Variability; Survival; Sepsis; Entropy; Oxygen saturation; Spo2,,,"Recent studies have found that oxygen saturation (SpO<sub>2</sub> ) variability analysis has potential for noninvasive assessment of the functional connectivity of cardiorespiratory control systems during hypoxia. Patients with sepsis have suboptimal tissue oxygenation and impaired organ system connectivity. Our objective with this report was to highlight the potential use for SpO<sub>2</sub> variability analysis in predicting intensive care survival in patients with sepsis. MIMIC-III clinical data of 164 adults meeting Sepsis-3 criteria and with 30 min of SpO<sub>2</sub> and respiratory rate data were analyzed. The complexity of SpO<sub>2</sub> signals was measured through various entropy calculations such as sample entropy and multiscale entropy analysis. The sequential organ failure assessment (SOFA) score was calculated to assess the severity of sepsis and multiorgan failure. While the standard deviation of SpO<sub>2</sub> signals was comparable in the non-survivor and survivor groups, non-survivors had significantly lower SpO<sub>2</sub> entropy than those who survived their ICU stay (0.107 ± 0.084 vs. 0.070 ± 0.083, p < 0.05). According to Cox regression analysis, higher SpO<sub>2</sub> entropy was a predictor of survival in patients with sepsis. Multivariate analysis also showed that the prognostic value of SpO<sub>2</sub> entropy was independent of other covariates such as age, SOFA score, mean SpO<sub>2</sub> , and ventilation status. When SpO<sub>2</sub> entropy was combined with mean SpO<sub>2</sub> , the composite had a significantly higher performance in prediction of survival. Analysis of SpO<sub>2</sub> entropy can predict patient outcome, and when combined with SpO<sub>2</sub> mean, can provide improved prognostic information. The prognostic power is on par with the SOFA score. This analysis can easily be incorporated into current ICU practice and has potential for noninvasive assessment of critically ill patients.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.14814/phy2.15546; doi:https://doi.org/10.14814/phy2.15546; html:https://europepmc.org/articles/PMC9768724; pdf:https://europepmc.org/articles/PMC9768724?pdf=render
+35440469,https://doi.org/10.3399/bjgp.2022.0083,"Colchicine for COVID-19 in the community (PRINCIPLE): a randomised, controlled, adaptive platform trial.","Dorward J, Yu LM, Hayward G, Saville BR, Gbinigie O, Van Hecke O, Ogburn E, Evans PH, Thomas NP, Patel MG, Richards D, Berry N, Detry MA, Saunders C, Fitzgerald M, Harris V, Shanyinde M, de Lusignan S, Andersson MI, Butler CC, Hobbs FR, PRINCIPLE Trial Collaborative Group.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2022,2022-06-30,Y,Colchicine; Community; Primary Health Care; Randomised Controlled Trial; Covid-19,,,"<h4>Background</h4>Colchicine has been proposed as a COVID-19 treatment.<h4>Aim</h4>To determine whether colchicine reduces time to recovery and COVID-19-related admissions to hospital and/or deaths among people in the community.<h4>Design and setting</h4>Prospective, multicentre, open-label, multi-arm, randomised, controlled, adaptive platform trial (PRINCIPLE).<h4>Method</h4>Adults aged ≥65 years or ≥18 years with comorbidities or shortness of breath, and unwell for ≤14 days with suspected COVID-19 in the community, were randomised to usual care, usual care plus colchicine (500 µg daily for 14 days), or usual care plus other interventions. The co-primary endpoints were time to first self-reported recovery and admission to hospital/death related to COVID-19, within 28 days, analysed using Bayesian models.<h4>Results</h4>The trial opened on 2 April 2020. Randomisation to colchicine started on 4 March 2021 and stopped on 26 May 2021 because the prespecified time to recovery futility criterion was met. The primary analysis model included 2755 participants who were SARS-CoV-2 positive, randomised to colchicine (<i>n</i> = 156), usual care (<i>n</i> = 1145), and other treatments (<i>n</i> = 1454). Time to first self-reported recovery was similar in the colchicine group compared with usual care with an estimated hazard ratio of 0.92 (95% credible interval (CrI) = 0.72 to 1.16) and an estimated increase of 1.4 days in median time to self-reported recovery for colchicine versus usual care. The probability of meaningful benefit in time to recovery was very low at 1.8%. COVID-19-related admissions to hospital/deaths were similar in the colchicine group versus usual care, with an estimated odds ratio of 0.76 (95% CrI = 0.28 to 1.89) and an estimated difference of -0.4% (95% CrI = -2.7 to 2.4).<h4>Conclusion</h4>Colchicine did not improve time to recovery in people at higher risk of complications with COVID-19 in the community.",,pdf:https://bjgp.org/content/bjgp/72/720/e446.full.pdf; doi:https://doi.org/10.3399/BJGP.2022.0083; html:https://europepmc.org/articles/PMC9037186; pdf:https://europepmc.org/articles/PMC9037186?pdf=render
 38216198,https://doi.org/10.1136/bmjopen-2023-080410,"Rationale and design of the THIRST Alert feasibility study: a pragmatic, single-centre, parallel-group randomised controlled trial of an interruptive alert for oral fluid restriction in patients treated with intravenous furosemide.","Chen Y, Shah A, Jani Y, Higgins D, Saleem N, Chafer K, Sydes MR, Asselbergs FW, Lumbers RT.",,BMJ open,2024,2024-01-11,Y,Randomized controlled trial; Heart Failure; Electronic Health Records; Feasibility Studies,,,"<h4>Introduction</h4>Acute heart failure (HF) is a major cause of unplanned hospitalisation characterised by excess body water. A restriction in oral fluid intake is commonly imposed on patients as an adjunct to pharmacological therapy with loop diuretics, but there is a lack of evidence from traditional randomised controlled trials (RCTs) to support the safety and effectiveness of this intervention in the acute setting.This study aims to explore the feasibility of using computer alerts within the electronic health record (EHR) system to invite clinical care teams to enrol patients into a pragmatic RCT at the time of clinical decision-making. It will additionally assess the effectiveness of using an alert to help address the clinical research question of whether oral fluid restriction is a safe and effective adjunct to pharmacological therapy for patients admitted with fluid overload.<h4>Methods and analysis</h4>THIRST (Randomised Controlled <b>T</b>rial within the electronic <b>H</b>ealth record of an <b>I</b>nterruptive alert displaying a fluid <b>R</b>estriction <b>S</b>uggestion in patients with the treatable <b>T</b>rait of congestion) Alert is a single-centre, parallel-group, open-label pragmatic RCT embedded in the EHR system that will be conducted as a feasibility study at an National Health Service (NHS) hospital in London. The clinical care team will be invited to enrol suitable patients in the study using a point-of-care alert with a target sample size of 50 patients. Enrolled patients will then be randomised to either restricted or unrestricted oral fluid intake. Two primary outcomes will be explored (1) the proportion of eligible patients enrolled in the study and (2) the mean difference in oral fluid intake between randomised groups. A series of secondary outcomes are specified to evaluate the effectiveness of the alert, adherence to the randomised treatment allocation and the quality of data generated from routine care, relevant to the outcomes of interest.<h4>Ethics and dissemination</h4>This study was approved by Riverside Research Ethics Committee (Ref: 22/LO/0889) and will be published on completion.<h4>Trial registration number</h4>NCT05869656.",,pdf:https://bmjopen.bmj.com/content/bmjopen/14/1/e080410.full.pdf; doi:https://doi.org/10.1136/bmjopen-2023-080410; html:https://europepmc.org/articles/PMC10806795; pdf:https://europepmc.org/articles/PMC10806795?pdf=render
 36921925,https://doi.org/10.1136/bmj-2022-072808,Comparative effectiveness of BNT162b2 versus mRNA-1273 covid-19 vaccine boosting in England: matched cohort study in OpenSAFELY-TPP.,"Hulme WJ, Horne EMF, Parker EPK, Keogh RH, Williamson EJ, Walker V, Palmer TM, Curtis HJ, Walker AJ, Andrews CD, Mehrkar A, Morley J, MacKenna B, Bacon SCJ, Goldacre B, Hernán MA, Sterne JAC.",,BMJ (Clinical research ed.),2023,2023-03-15,Y,,,,"<h4>Objective</h4>To compare the effectiveness of the BNT162b2 mRNA (Pfizer-BioNTech) and mRNA-1273 (Moderna) covid-19 vaccines during the booster programme in England.<h4>Design</h4>Matched cohort study, emulating a comparative effectiveness trial.<h4>Setting</h4>Linked primary care, hospital, and covid-19 surveillance records available within the OpenSAFELY-TPP research platform, covering a period when the SARS-CoV-2 delta and omicron variants were dominant.<h4>Participants</h4>3 237 918 adults who received a booster dose of either vaccine between 29 October 2021 and 25 February 2022 as part of the national booster programme in England and who received a primary course of BNT162b2 or ChAdOx1.<h4>Intervention</h4>Vaccination with either BNT162b2 or mRNA-1273 as a booster vaccine dose.<h4>Main outcome measures</h4>Recorded SARS-CoV-2 positive test, covid-19 related hospital admission, covid-19 related death, and non-covid-19 related death at 20 weeks after receipt of the booster dose.<h4>Results</h4>1 618 959 people were matched in each vaccine group, contributing a total 64 546 391 person weeks of follow-up. The 20 week risks per 1000 for a positive SARS-CoV-2 test were 164.2 (95% confidence interval 163.3 to 165.1) for BNT162b2 and 159.9 (159.0 to 160.8) for mRNA-1273; the hazard ratio comparing mRNA-1273 with BNT162b2 was 0.95 (95% confidence interval 0.95 to 0.96). The 20 week risks per 1000 for hospital admission with covid-19 were 0.75 (0.71 to 0.79) for BNT162b2 and 0.65 (0.61 to 0.69) for mRNA-1273; the hazard ratio was 0.89 (0.82 to 0.95). Covid-19 related deaths were rare: the 20 week risks per 1000 were 0.028 (0.021 to 0.037) for BNT162b2 and 0.024 (0.018 to 0.033) for mRNA-1273; hazard ratio 0.83 (0.58 to 1.19). Comparative effectiveness was generally similar within subgroups defined by the primary course vaccine brand, age, previous SARS-CoV-2 infection, and clinical vulnerability. Relative benefit was similar when vaccines were compared separately in the delta and omicron variant eras.<h4>Conclusions</h4>This matched observational study of adults estimated a modest benefit of booster vaccination with mRNA-1273 compared with BNT162b2 in preventing positive SARS-CoV-2 tests and hospital admission with covid-19 20 weeks after vaccination, during a period of delta followed by omicron variant dominance.",,pdf:https://www.bmj.com/content/bmj/380/bmj-2022-072808.full.pdf; doi:https://doi.org/10.1136/bmj-2022-072808; html:https://europepmc.org/articles/PMC10014664; pdf:https://europepmc.org/articles/PMC10014664?pdf=render
-35440469,https://doi.org/10.3399/bjgp.2022.0083,"Colchicine for COVID-19 in the community (PRINCIPLE): a randomised, controlled, adaptive platform trial.","Dorward J, Yu LM, Hayward G, Saville BR, Gbinigie O, Van Hecke O, Ogburn E, Evans PH, Thomas NP, Patel MG, Richards D, Berry N, Detry MA, Saunders C, Fitzgerald M, Harris V, Shanyinde M, de Lusignan S, Andersson MI, Butler CC, Hobbs FR, PRINCIPLE Trial Collaborative Group.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2022,2022-06-30,Y,Colchicine; Community; Primary Health Care; Randomised Controlled Trial; Covid-19,,,"<h4>Background</h4>Colchicine has been proposed as a COVID-19 treatment.<h4>Aim</h4>To determine whether colchicine reduces time to recovery and COVID-19-related admissions to hospital and/or deaths among people in the community.<h4>Design and setting</h4>Prospective, multicentre, open-label, multi-arm, randomised, controlled, adaptive platform trial (PRINCIPLE).<h4>Method</h4>Adults aged ≥65 years or ≥18 years with comorbidities or shortness of breath, and unwell for ≤14 days with suspected COVID-19 in the community, were randomised to usual care, usual care plus colchicine (500 µg daily for 14 days), or usual care plus other interventions. The co-primary endpoints were time to first self-reported recovery and admission to hospital/death related to COVID-19, within 28 days, analysed using Bayesian models.<h4>Results</h4>The trial opened on 2 April 2020. Randomisation to colchicine started on 4 March 2021 and stopped on 26 May 2021 because the prespecified time to recovery futility criterion was met. The primary analysis model included 2755 participants who were SARS-CoV-2 positive, randomised to colchicine (<i>n</i> = 156), usual care (<i>n</i> = 1145), and other treatments (<i>n</i> = 1454). Time to first self-reported recovery was similar in the colchicine group compared with usual care with an estimated hazard ratio of 0.92 (95% credible interval (CrI) = 0.72 to 1.16) and an estimated increase of 1.4 days in median time to self-reported recovery for colchicine versus usual care. The probability of meaningful benefit in time to recovery was very low at 1.8%. COVID-19-related admissions to hospital/deaths were similar in the colchicine group versus usual care, with an estimated odds ratio of 0.76 (95% CrI = 0.28 to 1.89) and an estimated difference of -0.4% (95% CrI = -2.7 to 2.4).<h4>Conclusion</h4>Colchicine did not improve time to recovery in people at higher risk of complications with COVID-19 in the community.",,pdf:https://bjgp.org/content/bjgp/72/720/e446.full.pdf; doi:https://doi.org/10.3399/BJGP.2022.0083; html:https://europepmc.org/articles/PMC9037186; pdf:https://europepmc.org/articles/PMC9037186?pdf=render
 33203640,https://doi.org/10.1136/bmjopen-2020-043828,"Estimated impact of the COVID-19 pandemic on cancer services and excess 1-year mortality in people with cancer and multimorbidity: near real-time data on cancer care, cancer deaths and a population-based cohort study.","Lai AG, Pasea L, Banerjee A, Hall G, Denaxas S, Chang WH, Katsoulis M, Williams B, Pillay D, Noursadeghi M, Linch D, Hughes D, Forster MD, Turnbull C, Fitzpatrick NK, Boyd K, Foster GR, Enver T, Nafilyan V, Humberstone B, Neal RD, Cooper M, Jones M, Pritchard-Jones K, Sullivan R, Davie C, Lawler M, Hemingway H.",,BMJ open,2020,2020-11-17,Y,Oncology; Health Informatics; Covid-19,,,"<h4>Objectives</h4>To estimate the impact of the COVID-19 pandemic on cancer care services and overall (direct and indirect) excess deaths in people with cancer.<h4>Methods</h4>We employed near real-time weekly data on cancer care to determine the adverse effect of the pandemic on cancer services. We also used these data, together with national death registrations until June 2020 to model deaths, in excess of background (pre-COVID-19) mortality, in people with cancer. Background mortality risks for 24 cancers with and without COVID-19-relevant comorbidities were obtained from population-based primary care cohort (Clinical Practice Research Datalink) on 3 862 012 adults in England.<h4>Results</h4>Declines in urgent referrals (median=-70.4%) and chemotherapy attendances (median=-41.5%) to a nadir (lowest point) in the pandemic were observed. By 31 May, these declines have only partially recovered; urgent referrals (median=-44.5%) and chemotherapy attendances (median=-31.2%). There were short-term excess death registrations for cancer (without COVID-19), with peak relative risk (RR) of 1.17 at week ending on 3 April. The peak RR for all-cause deaths was 2.1 from week ending on 17 April. Based on these findings and recent literature, we modelled 40% and 80% of cancer patients being affected by the pandemic in the long-term. At 40% affected, we estimated 1-year total (direct and indirect) excess deaths in people with cancer as between 7165 and 17 910, using RRs of 1.2 and 1.5, respectively, where 78% of excess deaths occured in patients with ≥1 comorbidity.<h4>Conclusions</h4>Dramatic reductions were detected in the demand for, and supply of, cancer services which have not fully recovered with lockdown easing. These may contribute, over a 1-year time horizon, to substantial excess mortality among people with cancer and multimorbidity. It is urgent to understand how the recovery of general practitioner, oncology and other hospital services might best mitigate these long-term excess mortality risks.",,pdf:https://bmjopen.bmj.com/content/bmjopen/10/11/e043828.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-043828; html:https://europepmc.org/articles/PMC7674020; pdf:https://europepmc.org/articles/PMC7674020?pdf=render
-39039249,https://doi.org/10.1038/s41591-024-03142-z,Proteomic signatures improve risk prediction for common and rare diseases.,"Carrasco-Zanini J, Pietzner M, Davitte J, Surendran P, Croteau-Chonka DC, Robins C, Torralbo A, Tomlinson C, Grünschläger F, Fitzpatrick N, Ytsma C, Kanno T, Gade S, Freitag D, Ziebell F, Haas S, Denaxas S, Betts JC, Wareham NJ, Hemingway H, Scott RA, Langenberg C.",,Nature medicine,2024,2024-07-22,Y,,,,"For many diseases there are delays in diagnosis due to a lack of objective biomarkers for disease onset. Here, in 41,931 individuals from the United Kingdom Biobank Pharma Proteomics Project, we integrated measurements of ~3,000 plasma proteins with clinical information to derive sparse prediction models for the 10-year incidence of 218 common and rare diseases (81-6,038 cases). We then compared prediction models developed using proteomic data with models developed using either basic clinical information alone or clinical information combined with data from 37 clinical assays. The predictive performance of sparse models including as few as 5 to 20 proteins was superior to the performance of models developed using basic clinical information for 67 pathologically diverse diseases (median delta C-index = 0.07; range = 0.02-0.31). Sparse protein models further outperformed models developed using basic information combined with clinical assay data for 52 diseases, including multiple myeloma, non-Hodgkin lymphoma, motor neuron disease, pulmonary fibrosis and dilated cardiomyopathy. For multiple myeloma, single-cell RNA sequencing from bone marrow in newly diagnosed patients showed that four of the five predictor proteins were expressed specifically in plasma cells, consistent with the strong predictive power of these proteins. External replication of sparse protein models in the EPIC-Norfolk study showed good generalizability for prediction of the six diseases tested. These findings show that sparse plasma protein signatures, including both disease-specific proteins and protein predictors shared across several diseases, offer clinically useful prediction of common and rare diseases.",,doi:https://doi.org/10.1038/s41591-024-03142-z; html:https://europepmc.org/articles/PMC11405273; pdf:https://europepmc.org/articles/PMC11405273?pdf=render
 34217220,https://doi.org/10.1186/s12872-021-02137-9,Pre-existing cardiovascular disease rather than cardiovascular risk factors drives mortality in COVID-19.,"O'Gallagher K, Shek A, Bean DM, Bendayan R, Papachristidis A, Teo JTH, Dobson RJB, Shah AM, Zakeri R.",,BMC cardiovascular disorders,2021,2021-07-03,Y,Hypertension; Diabetes; Cardiovascular disease; Cardiovascular risk factors; Covid-19,,,"<h4>Background</h4>The relative association between cardiovascular (CV) risk factors, such as diabetes and hypertension, established CV disease (CVD), and susceptibility to CV complications or mortality in COVID-19 remains unclear.<h4>Methods</h4>We conducted a cohort study of consecutive adults hospitalised for severe COVID-19 between 1st March and 30th June 2020. Pre-existing CVD, CV risk factors and associations with mortality and CV complications were ascertained.<h4>Results</h4>Among 1721 patients (median age 71 years, 57% male), 349 (20.3%) had pre-existing CVD (CVD), 888 (51.6%) had CV risk factors without CVD (RF-CVD), 484 (28.1%) had neither. Patients with CVD were older with a higher burden of non-CV comorbidities. During follow-up, 438 (25.5%) patients died: 37% with CVD, 25.7% with RF-CVD and 16.5% with neither. CVD was independently associated with in-hospital mortality among patients < 70 years of age (adjusted HR 2.43 [95% CI 1.16-5.07]), but not in those ≥ 70 years (aHR 1.14 [95% CI 0.77-1.69]). RF-CVD were not independently associated with mortality in either age group (< 70 y aHR 1.21 [95% CI 0.72-2.01], ≥ 70 y aHR 1.07 [95% CI 0.76-1.52]). Most CV complications occurred in patients with CVD (66%) versus RF-CVD (17%) or neither (11%; p < 0.001). 213 [12.4%] patients developed venous thromboembolism (VTE). CVD was not an independent predictor of VTE.<h4>Conclusions</h4>In patients hospitalised with COVID-19, pre-existing established CVD appears to be a more important contributor to mortality than CV risk factors in the absence of CVD. CVD-related hazard may be mediated, in part, by new CV complications. Optimal care and vigilance for destabilised CVD are essential in this patient group. Trial registration n/a.",,pdf:https://bmccardiovascdisord.biomedcentral.com/counter/pdf/10.1186/s12872-021-02137-9; doi:https://doi.org/10.1186/s12872-021-02137-9; html:https://europepmc.org/articles/PMC8254437; pdf:https://europepmc.org/articles/PMC8254437?pdf=render
+39039249,https://doi.org/10.1038/s41591-024-03142-z,Proteomic signatures improve risk prediction for common and rare diseases.,"Carrasco-Zanini J, Pietzner M, Davitte J, Surendran P, Croteau-Chonka DC, Robins C, Torralbo A, Tomlinson C, Grünschläger F, Fitzpatrick N, Ytsma C, Kanno T, Gade S, Freitag D, Ziebell F, Haas S, Denaxas S, Betts JC, Wareham NJ, Hemingway H, Scott RA, Langenberg C.",,Nature medicine,2024,2024-07-22,Y,,,,"For many diseases there are delays in diagnosis due to a lack of objective biomarkers for disease onset. Here, in 41,931 individuals from the United Kingdom Biobank Pharma Proteomics Project, we integrated measurements of ~3,000 plasma proteins with clinical information to derive sparse prediction models for the 10-year incidence of 218 common and rare diseases (81-6,038 cases). We then compared prediction models developed using proteomic data with models developed using either basic clinical information alone or clinical information combined with data from 37 clinical assays. The predictive performance of sparse models including as few as 5 to 20 proteins was superior to the performance of models developed using basic clinical information for 67 pathologically diverse diseases (median delta C-index = 0.07; range = 0.02-0.31). Sparse protein models further outperformed models developed using basic information combined with clinical assay data for 52 diseases, including multiple myeloma, non-Hodgkin lymphoma, motor neuron disease, pulmonary fibrosis and dilated cardiomyopathy. For multiple myeloma, single-cell RNA sequencing from bone marrow in newly diagnosed patients showed that four of the five predictor proteins were expressed specifically in plasma cells, consistent with the strong predictive power of these proteins. External replication of sparse protein models in the EPIC-Norfolk study showed good generalizability for prediction of the six diseases tested. These findings show that sparse plasma protein signatures, including both disease-specific proteins and protein predictors shared across several diseases, offer clinically useful prediction of common and rare diseases.",,doi:https://doi.org/10.1038/s41591-024-03142-z; html:https://europepmc.org/articles/PMC11405273; pdf:https://europepmc.org/articles/PMC11405273?pdf=render
 35172999,https://doi.org/10.1136/bmjopen-2021-052911,Can natural language processing models extract and classify instances of interpersonal violence in mental healthcare electronic records: an applied evaluative study.,"Botelle R, Bhavsar V, Kadra-Scalzo G, Mascio A, Williams MV, Roberts A, Velupillai S, Stewart R.",,BMJ open,2022,2022-02-16,Y,Psychiatry; Mental health; Public Health; Health Informatics,,,"<h4>Objective</h4>This paper evaluates the application of a natural language processing (NLP) model for extracting clinical text referring to interpersonal violence using electronic health records (EHRs) from a large mental healthcare provider.<h4>Design</h4>A multidisciplinary team iteratively developed guidelines for annotating clinical text referring to violence. Keywords were used to generate a dataset which was annotated (ie, classified as affirmed, negated or irrelevant) for: presence of violence, patient status (ie, as perpetrator, witness and/or victim of violence) and violence type (domestic, physical and/or sexual). An NLP approach using a pretrained transformer model, BioBERT (Bidirectional Encoder Representations from Transformers for Biomedical Text Mining) was fine-tuned on the annotated dataset and evaluated using 10-fold cross-validation.<h4>Setting</h4>We used the Clinical Records Interactive Search (CRIS) database, comprising over 500 000 de-identified EHRs of patients within the South London and Maudsley NHS Foundation Trust, a specialist mental healthcare provider serving an urban catchment area.<h4>Participants</h4>Searches of CRIS were carried out based on 17 predefined keywords. Randomly selected text fragments were taken from the results for each keyword, amounting to 3771 text fragments from the records of 2832 patients.<h4>Outcome measures</h4>We estimated precision, recall and F1 score for each NLP model. We examined sociodemographic and clinical variables in patients giving rise to the text data, and frequencies for each annotated violence characteristic.<h4>Results</h4>Binary classification models were developed for six labels (violence presence, perpetrator, victim, domestic, physical and sexual). Among annotations affirmed for the presence of any violence, 78% (1724) referred to physical violence, 61% (1350) referred to patients as perpetrator and 33% (731) to domestic violence. NLP models' precision ranged from 89% (perpetrator) to 98% (sexual); recall ranged from 89% (victim, perpetrator) to 97% (sexual).<h4>Conclusions</h4>State of the art NLP models can extract and classify clinical text on violence from EHRs at acceptable levels of scale, efficiency and accuracy.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/2/e052911.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-052911; html:https://europepmc.org/articles/PMC8852656; pdf:https://europepmc.org/articles/PMC8852656?pdf=render
-38102763,https://doi.org/10.1177/15353702231214253,Explainable hierarchical clustering for patient subtyping and risk prediction.,"Werner E, Clark JN, Hepburn A, Bhamber RS, Ambler M, Bourdeaux CP, McWilliams CJ, Santos-Rodriguez R.",,"Experimental biology and medicine (Maywood, N.J.)",2023,2023-12-15,Y,Clinical evaluation; hierarchical clustering; Mortality Prediction; Early Warning Score; Explainability; Patient Subtypes,,,"We present a pipeline in which machine learning techniques are used to automatically identify and evaluate subtypes of hospital patients admitted between 2017 and 2021 in a large UK teaching hospital. Patient clusters are determined using routinely collected hospital data, such as those used in the UK's National Early Warning Score 2 (NEWS2). An iterative, hierarchical clustering process was used to identify the minimum set of relevant features for cluster separation. With the use of state-of-the-art explainability techniques, the identified subtypes are interpreted and assigned clinical meaning, illustrating their robustness. In parallel, clinicians assessed intracluster similarities and intercluster differences of the identified patient subtypes within the context of their clinical knowledge. For each cluster, outcome prediction models were trained and their forecasting ability was illustrated against the NEWS2 of the unclustered patient cohort. These preliminary results suggest that subtype models can outperform the established NEWS2 method, providing improved prediction of patient deterioration. By considering both the computational outputs and clinician-based explanations in patient subtyping, we aim to highlight the mutual benefit of combining machine learning techniques with clinical expertise.",,doi:https://doi.org/10.1177/15353702231214253; html:https://europepmc.org/articles/PMC10854470; pdf:https://europepmc.org/articles/PMC10854470?pdf=render
-36350656,https://doi.org/10.1093/nar/gkac1010,The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource.,"Sollis E, Mosaku A, Abid A, Buniello A, Cerezo M, Gil L, Groza T, Güneş O, Hall P, Hayhurst J, Ibrahim A, Ji Y, John S, Lewis E, MacArthur JAL, McMahon A, Osumi-Sutherland D, Panoutsopoulou K, Pendlington Z, Ramachandran S, Stefancsik R, Stewart J, Whetzel P, Wilson R, Hindorff L, Cunningham F, Lambert SA, Inouye M, Parkinson H, Harris LW.",,Nucleic acids research,2023,2023-01-01,Y,,,,"The NHGRI-EBI GWAS Catalog (www.ebi.ac.uk/gwas) is a FAIR knowledgebase providing detailed, structured, standardised and interoperable genome-wide association study (GWAS) data to >200 000 users per year from academic research, healthcare and industry. The Catalog contains variant-trait associations and supporting metadata for >45 000 published GWAS across >5000 human traits, and >40 000 full P-value summary statistics datasets. Content is curated from publications or acquired via author submission of prepublication summary statistics through a new submission portal and validation tool. GWAS data volume has vastly increased in recent years. We have updated our software to meet this scaling challenge and to enable rapid release of submitted summary statistics. The scope of the repository has expanded to include additional data types of high interest to the community, including sequencing-based GWAS, gene-based analyses and copy number variation analyses. Community outreach has increased the number of shared datasets from under-represented traits, e.g. cancer, and we continue to contribute to awareness of the lack of population diversity in GWAS. Interoperability of the Catalog has been enhanced through links to other resources including the Polygenic Score Catalog and the International Mouse Phenotyping Consortium, refinements to GWAS trait annotation, and the development of a standard format for GWAS data.",,pdf:https://academic.oup.com/nar/article-pdf/51/D1/D977/48440802/gkac1010.pdf; doi:https://doi.org/10.1093/nar/gkac1010; html:https://europepmc.org/articles/PMC9825413; pdf:https://europepmc.org/articles/PMC9825413?pdf=render
-38434152,https://doi.org/10.5334/gh.1298,Characterization of Non-Ischemic Dilated Cardiomyopathy in a Native Tanzanian Cohort: MOYO Study.,"Fundikira LS, Chillo P, Alimohamed MZ, Mayala H, Kifai E, Aloyce GM, Kamuhabwa A, Kwesigabo G, van Laake LW, Asselbergs FW.",,Global heart,2024,2024-02-29,Y,Echocardiography; Heart Failure; Non-ischemic Dilated Cardiomyopathy,,,"<h4>Background</h4>Non-ischemic dilated cardiomyopathy (NIDCM) is a common cause of heart failure with progressive tendency. The disease occurs in one in every 2,500 individuals in the developed world, with high morbidity and mortality. However, detailed data on the role of NIDCM in heart failure in Tanzania is lacking.<h4>Aim</h4>To characterize NIDCM in a Tanzanian cohort with respect to demographics, clinical profile, imaging findings and management.<h4>Methods</h4>Characterization of non-ischemic dilated cardioMyOpathY in a native Tanzanian cOhort (MOYO) is a prospective cohort study of NIDCM patients seen at the Jakaya Kikwete Cardiac Institute. Patients aged ≥18 years with a clinical diagnosis of heart failure, an ejection fraction of ≤45% on echocardiography and no evidence of ischemia were enrolled. Clinical data, echocardiography, electrocardiography (ECG), coronary angiography and stress ECG information were collected from February 2020 to March 2022.<h4>Results</h4>Of 402 patients, n = 220 (54.7%) were males with a median (IQR) age of 55.0 (41.0, 66.0) years. Causes of NIDCM were presumably hypertensive n = 218 (54.2%), idiopathic n = 116 (28.9%), PPCM n = 45 (11.2%), alcoholic n = 10 (2.5%) and other causes n = 13 (3.2%). The most common presenting symptoms were dyspnea n = 342 (85.1%), with the majority of patients presenting with New York Heart Association (NYHA) Class III n = 195 (48.5%). The mean (SD) left ventricular ejection fraction (LVEF) was 29.4% (±7.7), and severe systolic dysfunction (LVEF <30%) was common n = 208 (51.7%). Compared with other forms of DCM, idiopathic DCM patients were significantly younger, had more advanced NYHA class (p < 0.001) and presented more often with left bundle branch block on ECG (p = 0.0042). There was suboptimal use of novel guidelines recommended medications ARNI n = 10 (2.5%) and SGLT2 2-inhibitors n = 2 (0.5%).<h4>Conclusions</h4>In our Tanzanian cohort, the majority of patients with NIDCM have an identified underlying cause, and they present at late stages of the disease. Patients with idiopathic DCM are younger with more severe disease compared to other forms of NIDCM.",,doi:https://doi.org/10.5334/gh.1298; html:https://europepmc.org/articles/PMC10906337; pdf:https://europepmc.org/articles/PMC10906337?pdf=render
 32206896,https://doi.org/10.1007/s00394-020-02220-5,Alcohol consumption in relation to carotid subclinical atherosclerosis and its progression: results from a European longitudinal multicentre study.,"Laguzzi F, Baldassarre D, Veglia F, Strawbridge RJ, Humphries SE, Rauramaa R, Smit AJ, Giral P, Silveira A, Tremoli E, Hamsten A, de Faire U, Frumento P, Leander K, IMPROVE Study group.",,European journal of nutrition,2021,2020-03-24,Y,Atherosclerosis; epidemiology; Carotid intima-media thickness; Alcohol drinking; Progression,,,"<h4>Background/aim</h4>The association between alcohol consumption and subclinical atherosclerosis is still unclear. Using data from a European multicentre study, we assess subclinical atherosclerosis and its 30-month progression by carotid intima-media thickness (C-IMT) measurements, and correlate this information with self-reported data on alcohol consumption.<h4>Methods</h4>Between 2002-2004, 1772 men and 1931 women aged 54-79 years with at least three risk factors for cardiovascular disease (CVD) were recruited in Italy, France, Netherlands, Sweden, and Finland. Self-reported alcohol consumption, assessed at baseline, was categorized as follows: none (0 g/d), very-low (0 - 5 g/d), low (> 5 to  ≤ 10 g/d), moderate (> 10 to ≤ 20 g/d for women,  > 10 to ≤ 30 g/d for men) and high (> 20 g/d for women, > 30 g/d for men). C-IMT was measured in millimeters at baseline and after 30 months. Measurements consisted of the mean and maximum values of the common carotids (CC), internal carotid artery (ICA), and bifurcations (Bif) and whole carotid tree. We used quantile regression to describe the associations between C-IMT measures and alcohol consumption categories, adjusting for sex, age, physical activity, education, smoking, diet, and latitude.<h4>Results</h4>Adjusted differences between median C-IMT values in different levels of alcohol consumption (vs. very-low) showed that moderate alcohol consumption was associated with lower C-IMT<sub>max</sub>[- 0.17(95%CI - 0.32; - 0.02)], and Bif-IMT<sub>mean</sub>[- 0.07(95%CI - 0.13; - 0.01)] at baseline and decreasing C-IMT<sub>mean</sub>[- 0.006 (95%CI - 0.011; - 0.000)], Bif-IMT<sub>mean</sub>[- 0.016(95%CI - 0.027; - 0.005)], ICA-IMT<sub>mean</sub>[- 0.009(95% - 0.016; - 0.002)] and ICA-IMT<sub>max</sub>[- 0.016(95%: - 0.032; - 0.000)] after 30 months. There was no evidence of departure from linearity in the association between alcohol consumption and C-IMT.<h4>Conclusion</h4>In this European population at high risk of CVD, findings show an inverse relation between moderate alcohol consumption and carotid subclinical atherosclerosis and its 30-month progression, independently of several potential confounders.",,pdf:https://link.springer.com/content/pdf/10.1007/s00394-020-02220-5.pdf; doi:https://doi.org/10.1007/s00394-020-02220-5; html:https://europepmc.org/articles/PMC7867553; pdf:https://europepmc.org/articles/PMC7867553?pdf=render
+36350656,https://doi.org/10.1093/nar/gkac1010,The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource.,"Sollis E, Mosaku A, Abid A, Buniello A, Cerezo M, Gil L, Groza T, Güneş O, Hall P, Hayhurst J, Ibrahim A, Ji Y, John S, Lewis E, MacArthur JAL, McMahon A, Osumi-Sutherland D, Panoutsopoulou K, Pendlington Z, Ramachandran S, Stefancsik R, Stewart J, Whetzel P, Wilson R, Hindorff L, Cunningham F, Lambert SA, Inouye M, Parkinson H, Harris LW.",,Nucleic acids research,2023,2023-01-01,Y,,,,"The NHGRI-EBI GWAS Catalog (www.ebi.ac.uk/gwas) is a FAIR knowledgebase providing detailed, structured, standardised and interoperable genome-wide association study (GWAS) data to >200 000 users per year from academic research, healthcare and industry. The Catalog contains variant-trait associations and supporting metadata for >45 000 published GWAS across >5000 human traits, and >40 000 full P-value summary statistics datasets. Content is curated from publications or acquired via author submission of prepublication summary statistics through a new submission portal and validation tool. GWAS data volume has vastly increased in recent years. We have updated our software to meet this scaling challenge and to enable rapid release of submitted summary statistics. The scope of the repository has expanded to include additional data types of high interest to the community, including sequencing-based GWAS, gene-based analyses and copy number variation analyses. Community outreach has increased the number of shared datasets from under-represented traits, e.g. cancer, and we continue to contribute to awareness of the lack of population diversity in GWAS. Interoperability of the Catalog has been enhanced through links to other resources including the Polygenic Score Catalog and the International Mouse Phenotyping Consortium, refinements to GWAS trait annotation, and the development of a standard format for GWAS data.",,pdf:https://academic.oup.com/nar/article-pdf/51/D1/D977/48440802/gkac1010.pdf; doi:https://doi.org/10.1093/nar/gkac1010; html:https://europepmc.org/articles/PMC9825413; pdf:https://europepmc.org/articles/PMC9825413?pdf=render
+38102763,https://doi.org/10.1177/15353702231214253,Explainable hierarchical clustering for patient subtyping and risk prediction.,"Werner E, Clark JN, Hepburn A, Bhamber RS, Ambler M, Bourdeaux CP, McWilliams CJ, Santos-Rodriguez R.",,"Experimental biology and medicine (Maywood, N.J.)",2023,2023-12-15,Y,Clinical evaluation; hierarchical clustering; Mortality Prediction; Early Warning Score; Explainability; Patient Subtypes,,,"We present a pipeline in which machine learning techniques are used to automatically identify and evaluate subtypes of hospital patients admitted between 2017 and 2021 in a large UK teaching hospital. Patient clusters are determined using routinely collected hospital data, such as those used in the UK's National Early Warning Score 2 (NEWS2). An iterative, hierarchical clustering process was used to identify the minimum set of relevant features for cluster separation. With the use of state-of-the-art explainability techniques, the identified subtypes are interpreted and assigned clinical meaning, illustrating their robustness. In parallel, clinicians assessed intracluster similarities and intercluster differences of the identified patient subtypes within the context of their clinical knowledge. For each cluster, outcome prediction models were trained and their forecasting ability was illustrated against the NEWS2 of the unclustered patient cohort. These preliminary results suggest that subtype models can outperform the established NEWS2 method, providing improved prediction of patient deterioration. By considering both the computational outputs and clinician-based explanations in patient subtyping, we aim to highlight the mutual benefit of combining machine learning techniques with clinical expertise.",,doi:https://doi.org/10.1177/15353702231214253; html:https://europepmc.org/articles/PMC10854470; pdf:https://europepmc.org/articles/PMC10854470?pdf=render
+33587202,https://doi.org/10.1007/s10654-021-00722-y,COVID-19 mortality in the UK Biobank cohort: revisiting and evaluating risk factors.,"Elliott J, Bodinier B, Whitaker M, Delpierre C, Vermeulen R, Tzoulaki I, Elliott P, Chadeau-Hyam M.",,European journal of epidemiology,2021,2021-02-15,Y,Risk factor; Prospective Cohort; Uk Biobank; Sars-cov-2; Covid-19 Mortality,,,"Most studies of severe/fatal COVID-19 risk have used routine/hospitalisation data without detailed pre-morbid characterisation. Using the community-based UK Biobank cohort, we investigate risk factors for COVID-19 mortality in comparison with non-COVID-19 mortality. We investigated demographic, social (education, income, housing, employment), lifestyle (smoking, drinking, body mass index), biological (lipids, cystatin C, vitamin D), medical (comorbidities, medications) and environmental (air pollution) data from UK Biobank (N = 473,550) in relation to 459 COVID-19 and 2626 non-COVID-19 deaths to 21 September 2020. We used univariate, multivariable and penalised regression models. Age (OR = 2.76 [2.18-3.49] per S.D. [8.1 years], p = 2.6 × 10<sup>-17</sup>), male sex (OR = 1.47 [1.26-1.73], p = 1.3 × 10<sup>-6</sup>) and Black versus White ethnicity (OR = 1.21 [1.12-1.29], p = 3.0 × 10<sup>-7</sup>) were independently associated with and jointly explanatory of (area under receiver operating characteristic curve, AUC = 0.79) increased risk of COVID-19 mortality. In multivariable regression, alongside demographic covariates, being a healthcare worker, current smoker, having cardiovascular disease, hypertension, diabetes, autoimmune disease, and oral steroid use at enrolment were independently associated with COVID-19 mortality. Penalised regression models selected income, cardiovascular disease, hypertension, diabetes, cystatin C, and oral steroid use as jointly contributing to COVID-19 mortality risk; Black ethnicity, hypertension and oral steroid use contributed to COVID-19 but not non-COVID-19 mortality. Age, male sex and Black ethnicity, as well as comorbidities and oral steroid use at enrolment were associated with increased risk of COVID-19 death. Our results suggest that previously reported associations of COVID-19 mortality with body mass index, low vitamin D, air pollutants, renin-angiotensin-aldosterone system inhibitors may be explained by the aforementioned factors.",,pdf:https://link.springer.com/content/pdf/10.1007/s10654-021-00722-y.pdf; doi:https://doi.org/10.1007/s10654-021-00722-y; html:https://europepmc.org/articles/PMC7882869; pdf:https://europepmc.org/articles/PMC7882869?pdf=render
 33634312,https://doi.org/10.1093/bib/bbab006,Benchmarking network-based gene prioritization methods for cerebral small vessel disease.,"Zhang H, Ferguson A, Robertson G, Jiang M, Zhang T, Sudlow C, Smith K, Rannikmae K, Wu H.",,Briefings in bioinformatics,2021,2021-09-01,Y,Cerebral Small Vessel Disease; Protein–protein Interaction; Benchmarking; Disease Gene Association; Network-based Gene Prioritization,,,"Network-based gene prioritization algorithms are designed to prioritize disease-associated genes based on known ones using biological networks of protein interactions, gene-disease associations (GDAs) and other relationships between biological entities. Various algorithms have been developed based on different mechanisms, but it is not obvious which algorithm is optimal for a specific disease. To address this issue, we benchmarked multiple algorithms for their application in cerebral small vessel disease (cSVD). We curated protein-gene interactions (PGIs) and GDAs from databases and assembled PGI networks and disease-gene heterogeneous networks. A screening of algorithms resulted in seven representative algorithms to be benchmarked. Performance of algorithms was assessed using both leave-one-out cross-validation (LOOCV) and external validation with MEGASTROKE genome-wide association study (GWAS). We found that random walk with restart on the heterogeneous network (RWRH) showed best LOOCV performance, with median LOOCV rediscovery rank of 185.5 (out of 19 463 genes). The GenePanda algorithm had most GWAS-confirmable genes in top 200 predictions, while RWRH had best ranks for small vessel stroke-associated genes confirmed in GWAS. In conclusion, RWRH has overall better performance for application in cSVD despite its susceptibility to bias caused by degree centrality. Choice of algorithms should be determined before applying to specific disease. Current pure network-based gene prioritization algorithms are unlikely to find novel disease-associated genes that are not associated with known ones. The tools for implementing and benchmarking algorithms have been made available and can be generalized for other diseases.",,pdf:https://www.pure.ed.ac.uk/ws/files/198917679/bbab006.pdf; doi:https://doi.org/10.1093/bib/bbab006; html:https://europepmc.org/articles/PMC8425308; pdf:https://europepmc.org/articles/PMC8425308?pdf=render
-38941600,https://doi.org/10.2196/55302,Longitudinal Assessment of Seasonal Impacts and Depression Associations on Circadian Rhythm Using Multimodal Wearable Sensing: Retrospective Analysis.,"Zhang Y, Folarin AA, Sun S, Cummins N, Ranjan Y, Rashid Z, Stewart C, Conde P, Sankesara H, Laiou P, Matcham F, White KM, Oetzmann C, Lamers F, Siddi S, Simblett S, Vairavan S, Myin-Germeys I, Mohr DC, Wykes T, Haro JM, Annas P, Penninx BW, Narayan VA, Hotopf M, Dobson RJ, RADAR-CNS consortium.",,Journal of medical Internet research,2024,2024-06-28,Y,Circadian rhythm; Monitoring; Mental health; Major Depressive Disorder; Biological Rhythms; Mdd; Wearable; Mhealth; Mobile Health; Digital Health,,,"<h4>Background</h4>Previous mobile health (mHealth) studies have revealed significant links between depression and circadian rhythm features measured via wearables. However, the comprehensive impact of seasonal variations was not fully considered in these studies, potentially biasing interpretations in real-world settings.<h4>Objective</h4>This study aims to explore the associations between depression severity and wearable-measured circadian rhythms while accounting for seasonal impacts.<h4>Methods</h4>Data were sourced from a large longitudinal mHealth study, wherein participants' depression severity was assessed biweekly using the 8-item Patient Health Questionnaire (PHQ-8), and participants' behaviors, including sleep, step count, and heart rate (HR), were tracked via Fitbit devices for up to 2 years. We extracted 12 circadian rhythm features from the 14-day Fitbit data preceding each PHQ-8 assessment, including cosinor variables, such as HR peak timing (HR acrophase), and nonparametric features, such as the onset of the most active continuous 10-hour period (M10 onset). To investigate the association between depression severity and circadian rhythms while also assessing the seasonal impacts, we used three nested linear mixed-effects models for each circadian rhythm feature: (1) incorporating the PHQ-8 score as an independent variable, (2) adding seasonality, and (3) adding an interaction term between season and the PHQ-8 score.<h4>Results</h4>Analyzing 10,018 PHQ-8 records alongside Fitbit data from 543 participants (n=414, 76.2% female; median age 48, IQR 32-58 years), we found that after adjusting for seasonal effects, higher PHQ-8 scores were associated with reduced daily steps (β=-93.61, P<.001), increased sleep variability (β=0.96, P<.001), and delayed circadian rhythms (ie, sleep onset: β=0.55, P=.001; sleep offset: β=1.12, P<.001; M10 onset: β=0.73, P=.003; HR acrophase: β=0.71, P=.001). Notably, the negative association with daily steps was more pronounced in spring (β of PHQ-8 × spring = -31.51, P=.002) and summer (β of PHQ-8 × summer = -42.61, P<.001) compared with winter. Additionally, the significant correlation with delayed M10 onset was observed solely in summer (β of PHQ-8 × summer = 1.06, P=.008). Moreover, compared with winter, participants experienced a shorter sleep duration by 16.6 minutes, an increase in daily steps by 394.5, a delay in M10 onset by 20.5 minutes, and a delay in HR peak time by 67.9 minutes during summer.<h4>Conclusions</h4>Our findings highlight significant seasonal influences on human circadian rhythms and their associations with depression, underscoring the importance of considering seasonal variations in mHealth research for real-world applications. This study also indicates the potential of wearable-measured circadian rhythms as digital biomarkers for depression.",,doi:https://doi.org/10.2196/55302; html:https://europepmc.org/articles/PMC11245656
+38434152,https://doi.org/10.5334/gh.1298,Characterization of Non-Ischemic Dilated Cardiomyopathy in a Native Tanzanian Cohort: MOYO Study.,"Fundikira LS, Chillo P, Alimohamed MZ, Mayala H, Kifai E, Aloyce GM, Kamuhabwa A, Kwesigabo G, van Laake LW, Asselbergs FW.",,Global heart,2024,2024-02-29,Y,Echocardiography; Heart Failure; Non-ischemic Dilated Cardiomyopathy,,,"<h4>Background</h4>Non-ischemic dilated cardiomyopathy (NIDCM) is a common cause of heart failure with progressive tendency. The disease occurs in one in every 2,500 individuals in the developed world, with high morbidity and mortality. However, detailed data on the role of NIDCM in heart failure in Tanzania is lacking.<h4>Aim</h4>To characterize NIDCM in a Tanzanian cohort with respect to demographics, clinical profile, imaging findings and management.<h4>Methods</h4>Characterization of non-ischemic dilated cardioMyOpathY in a native Tanzanian cOhort (MOYO) is a prospective cohort study of NIDCM patients seen at the Jakaya Kikwete Cardiac Institute. Patients aged ≥18 years with a clinical diagnosis of heart failure, an ejection fraction of ≤45% on echocardiography and no evidence of ischemia were enrolled. Clinical data, echocardiography, electrocardiography (ECG), coronary angiography and stress ECG information were collected from February 2020 to March 2022.<h4>Results</h4>Of 402 patients, n = 220 (54.7%) were males with a median (IQR) age of 55.0 (41.0, 66.0) years. Causes of NIDCM were presumably hypertensive n = 218 (54.2%), idiopathic n = 116 (28.9%), PPCM n = 45 (11.2%), alcoholic n = 10 (2.5%) and other causes n = 13 (3.2%). The most common presenting symptoms were dyspnea n = 342 (85.1%), with the majority of patients presenting with New York Heart Association (NYHA) Class III n = 195 (48.5%). The mean (SD) left ventricular ejection fraction (LVEF) was 29.4% (±7.7), and severe systolic dysfunction (LVEF <30%) was common n = 208 (51.7%). Compared with other forms of DCM, idiopathic DCM patients were significantly younger, had more advanced NYHA class (p < 0.001) and presented more often with left bundle branch block on ECG (p = 0.0042). There was suboptimal use of novel guidelines recommended medications ARNI n = 10 (2.5%) and SGLT2 2-inhibitors n = 2 (0.5%).<h4>Conclusions</h4>In our Tanzanian cohort, the majority of patients with NIDCM have an identified underlying cause, and they present at late stages of the disease. Patients with idiopathic DCM are younger with more severe disease compared to other forms of NIDCM.",,doi:https://doi.org/10.5334/gh.1298; html:https://europepmc.org/articles/PMC10906337; pdf:https://europepmc.org/articles/PMC10906337?pdf=render
 35780515,https://doi.org/10.1016/j.epidem.2022.100604,Appropriately smoothing prevalence data to inform estimates of growth rate and reproduction number.,"Eales O, Ainslie KEC, Walters CE, Wang H, Atchison C, Ashby D, Donnelly CA, Cooke G, Barclay W, Ward H, Darzi A, Elliott P, Riley S.",,Epidemics,2022,2022-06-22,Y,Cross-sectional study; Reproduction Number; Covid-19; Sars-cov-2; Bayesian P-Spline,,,"The time-varying reproduction number (R<sub>t</sub>) can change rapidly over the course of a pandemic due to changing restrictions, behaviours, and levels of population immunity. Many methods exist that allow the estimation of R<sub>t</sub> from case data. However, these are not easily adapted to point prevalence data nor can they infer R<sub>t</sub> across periods of missing data. We developed a Bayesian P-spline model suitable for fitting to a wide range of epidemic time-series, including point-prevalence data. We demonstrate the utility of the model by fitting to periodic daily SARS-CoV-2 swab-positivity data in England from the first 7 rounds (May 2020-December 2020) of the REal-time Assessment of Community Transmission-1 (REACT-1) study. Estimates of R<sub>t</sub> over the period of two subsequent rounds (6-8 weeks) and single rounds (2-3 weeks) inferred using the Bayesian P-spline model were broadly consistent with estimates from a simple exponential model, with overlapping credible intervals. However, there were sometimes substantial differences in point estimates. The Bayesian P-spline model was further able to infer changes in R<sub>t</sub> over shorter periods tracking a temporary increase above one during late-May 2020, a gradual increase in R<sub>t</sub> over the summer of 2020 as restrictions were eased, and a reduction in R<sub>t</sub> during England's second national lockdown followed by an increase as the Alpha variant surged. The model is robust against both under-fitting and over-fitting and is able to interpolate between periods of available data; it is a particularly versatile model when growth rate can change over small timescales, as in the current SARS-CoV-2 pandemic. This work highlights the importance of pairing robust methods with representative samples to track pandemics.",,doi:https://doi.org/10.1016/j.epidem.2022.100604; doi:https://doi.org/10.1016/j.epidem.2022.100604; html:https://europepmc.org/articles/PMC9220254; pdf:https://europepmc.org/articles/PMC9220254?pdf=render
+38941600,https://doi.org/10.2196/55302,Longitudinal Assessment of Seasonal Impacts and Depression Associations on Circadian Rhythm Using Multimodal Wearable Sensing: Retrospective Analysis.,"Zhang Y, Folarin AA, Sun S, Cummins N, Ranjan Y, Rashid Z, Stewart C, Conde P, Sankesara H, Laiou P, Matcham F, White KM, Oetzmann C, Lamers F, Siddi S, Simblett S, Vairavan S, Myin-Germeys I, Mohr DC, Wykes T, Haro JM, Annas P, Penninx BW, Narayan VA, Hotopf M, Dobson RJ, RADAR-CNS consortium.",,Journal of medical Internet research,2024,2024-06-28,Y,Circadian rhythm; Monitoring; Mental health; Major Depressive Disorder; Biological Rhythms; Mdd; Wearable; Mhealth; Mobile Health; Digital Health,,,"<h4>Background</h4>Previous mobile health (mHealth) studies have revealed significant links between depression and circadian rhythm features measured via wearables. However, the comprehensive impact of seasonal variations was not fully considered in these studies, potentially biasing interpretations in real-world settings.<h4>Objective</h4>This study aims to explore the associations between depression severity and wearable-measured circadian rhythms while accounting for seasonal impacts.<h4>Methods</h4>Data were sourced from a large longitudinal mHealth study, wherein participants' depression severity was assessed biweekly using the 8-item Patient Health Questionnaire (PHQ-8), and participants' behaviors, including sleep, step count, and heart rate (HR), were tracked via Fitbit devices for up to 2 years. We extracted 12 circadian rhythm features from the 14-day Fitbit data preceding each PHQ-8 assessment, including cosinor variables, such as HR peak timing (HR acrophase), and nonparametric features, such as the onset of the most active continuous 10-hour period (M10 onset). To investigate the association between depression severity and circadian rhythms while also assessing the seasonal impacts, we used three nested linear mixed-effects models for each circadian rhythm feature: (1) incorporating the PHQ-8 score as an independent variable, (2) adding seasonality, and (3) adding an interaction term between season and the PHQ-8 score.<h4>Results</h4>Analyzing 10,018 PHQ-8 records alongside Fitbit data from 543 participants (n=414, 76.2% female; median age 48, IQR 32-58 years), we found that after adjusting for seasonal effects, higher PHQ-8 scores were associated with reduced daily steps (β=-93.61, P<.001), increased sleep variability (β=0.96, P<.001), and delayed circadian rhythms (ie, sleep onset: β=0.55, P=.001; sleep offset: β=1.12, P<.001; M10 onset: β=0.73, P=.003; HR acrophase: β=0.71, P=.001). Notably, the negative association with daily steps was more pronounced in spring (β of PHQ-8 × spring = -31.51, P=.002) and summer (β of PHQ-8 × summer = -42.61, P<.001) compared with winter. Additionally, the significant correlation with delayed M10 onset was observed solely in summer (β of PHQ-8 × summer = 1.06, P=.008). Moreover, compared with winter, participants experienced a shorter sleep duration by 16.6 minutes, an increase in daily steps by 394.5, a delay in M10 onset by 20.5 minutes, and a delay in HR peak time by 67.9 minutes during summer.<h4>Conclusions</h4>Our findings highlight significant seasonal influences on human circadian rhythms and their associations with depression, underscoring the importance of considering seasonal variations in mHealth research for real-world applications. This study also indicates the potential of wearable-measured circadian rhythms as digital biomarkers for depression.",,doi:https://doi.org/10.2196/55302; html:https://europepmc.org/articles/PMC11245656
 33635829,https://doi.org/10.1530/eje-20-1163,Increased COVID-19 infections in women with polycystic ovary syndrome: a population-based study.,"Subramanian A, Anand A, Adderley NJ, Okoth K, Toulis KA, Gokhale K, Sainsbury C, O'Reilly MW, Arlt W, Nirantharakumar K.",,European journal of endocrinology,2021,2021-05-01,Y,,,,"<h4>Objective</h4>Several recent observational studies have linked metabolic comorbidities to an increased risk from COVID-19. Here we investigated whether women with PCOS are at an increased risk of COVID-19 infection.<h4>Design</h4>Population-based closed cohort study between 31 January 2020 and 22 July 2020 in the setting of a UK primary care database (The Health Improvement Network, THIN).<h4>Methods</h4>The main outcome was the incidence of COVID-19 coded as suspected or confirmed by the primary care provider. We used Cox proportional hazards regression model with stepwise inclusion of explanatory variables (age, BMI, impaired glucose regulation, androgen excess, anovulation, vitamin D deficiency, hypertension, and cardiovascular disease) to provide unadjusted and adjusted hazard risks (HR) of COVID-19 infection among women with PCOS compared to women without PCOS.<h4>Results</h4>We identified 21 292 women with a coded diagnosis of PCO/PCOS and randomly selected 78 310 aged and general practice matched control women. The crude COVID-19 incidence was 18.1 and 11.9 per 1000 person-years among women with and without PCOS, respectively. Age-adjusted Cox regression analysis suggested a 51% higher risk of COVID-19 among women with PCOS compared to women without PCOS (HR: 1.51 (95% CI: 1.27-1.80), P < 0.001). After adjusting for age and BMI, HR reduced to 1.36 (1.14-1.63)], P = 0.001. In the fully adjusted model, women with PCOS had a 28% increased risk of COVID-19 (aHR: 1.28 (1.05-1.56), P = 0.015).<h4>Conclusion</h4>Women with PCOS are at an increased risk of COVID-19 infection and should be specifically encouraged to adhere to infection control measures during the COVID-19 pandemic.<h4>Significance statement</h4>Women with polycystic ovary syndrome (PCOS) have an increased risk of cardio-metabolic disease, which have been identified as a risk factor for COVID-19. To investigate whether the increased metabolic risk in PCOS translates into an increased risk of COVID-19 infection, we carried out a population-based closed cohort study in the UK during its first wave of the SARS-CoV-2 pandemic (January to July 2020), including 21 292 women with PCOS and 78 310 controls matched for sex, age and general practice location. Results revealed a 52% increased risk of COVID-19 infection in women with PCOS, which remained increased at 28% above controls after adjustment for age, BMI, impaired glucose regulation and other explanatory variables.",,pdf:https://academic.oup.com/ejendo/article-pdf/184/5/637/45221794/eje-20-1163.pdf; doi:https://doi.org/10.1530/EJE-20-1163; html:https://europepmc.org/articles/PMC8052516; pdf:https://europepmc.org/articles/PMC8052516?pdf=render
-33587202,https://doi.org/10.1007/s10654-021-00722-y,COVID-19 mortality in the UK Biobank cohort: revisiting and evaluating risk factors.,"Elliott J, Bodinier B, Whitaker M, Delpierre C, Vermeulen R, Tzoulaki I, Elliott P, Chadeau-Hyam M.",,European journal of epidemiology,2021,2021-02-15,Y,Risk factor; Prospective Cohort; Uk Biobank; Sars-cov-2; Covid-19 Mortality,,,"Most studies of severe/fatal COVID-19 risk have used routine/hospitalisation data without detailed pre-morbid characterisation. Using the community-based UK Biobank cohort, we investigate risk factors for COVID-19 mortality in comparison with non-COVID-19 mortality. We investigated demographic, social (education, income, housing, employment), lifestyle (smoking, drinking, body mass index), biological (lipids, cystatin C, vitamin D), medical (comorbidities, medications) and environmental (air pollution) data from UK Biobank (N = 473,550) in relation to 459 COVID-19 and 2626 non-COVID-19 deaths to 21 September 2020. We used univariate, multivariable and penalised regression models. Age (OR = 2.76 [2.18-3.49] per S.D. [8.1 years], p = 2.6 × 10<sup>-17</sup>), male sex (OR = 1.47 [1.26-1.73], p = 1.3 × 10<sup>-6</sup>) and Black versus White ethnicity (OR = 1.21 [1.12-1.29], p = 3.0 × 10<sup>-7</sup>) were independently associated with and jointly explanatory of (area under receiver operating characteristic curve, AUC = 0.79) increased risk of COVID-19 mortality. In multivariable regression, alongside demographic covariates, being a healthcare worker, current smoker, having cardiovascular disease, hypertension, diabetes, autoimmune disease, and oral steroid use at enrolment were independently associated with COVID-19 mortality. Penalised regression models selected income, cardiovascular disease, hypertension, diabetes, cystatin C, and oral steroid use as jointly contributing to COVID-19 mortality risk; Black ethnicity, hypertension and oral steroid use contributed to COVID-19 but not non-COVID-19 mortality. Age, male sex and Black ethnicity, as well as comorbidities and oral steroid use at enrolment were associated with increased risk of COVID-19 death. Our results suggest that previously reported associations of COVID-19 mortality with body mass index, low vitamin D, air pollutants, renin-angiotensin-aldosterone system inhibitors may be explained by the aforementioned factors.",,pdf:https://link.springer.com/content/pdf/10.1007/s10654-021-00722-y.pdf; doi:https://doi.org/10.1007/s10654-021-00722-y; html:https://europepmc.org/articles/PMC7882869; pdf:https://europepmc.org/articles/PMC7882869?pdf=render
 38589621,https://doi.org/10.1038/s41590-024-01778-0,Large-scale phenotyping of patients with long COVID post-hospitalization reveals mechanistic subtypes of disease.,"Liew F, Efstathiou C, Fontanella S, Richardson M, Saunders R, Swieboda D, Sidhu JK, Ascough S, Moore SC, Mohamed N, Nunag J, King C, Leavy OC, Elneima O, McAuley HJC, Shikotra A, Singapuri A, Sereno M, Harris VC, Houchen-Wolloff L, Greening NJ, Lone NI, Thorpe M, Thompson AAR, Rowland-Jones SL, Docherty AB, Chalmers JD, Ho LP, Horsley A, Raman B, Poinasamy K, Marks M, Kon OM, Howard LS, Wootton DG, Quint JK, de Silva TI, Ho A, Chiu C, Harrison EM, Greenhalf W, Baillie JK, Semple MG, Turtle L, Evans RA, Wain LV, Brightling C, Thwaites RS, Openshaw PJM, PHOSP-COVID collaborative group, ISARIC investigators.",,Nature immunology,2024,2024-04-08,Y,,,,"One in ten severe acute respiratory syndrome coronavirus 2 infections result in prolonged symptoms termed long coronavirus disease (COVID), yet disease phenotypes and mechanisms are poorly understood<sup>1</sup>. Here we profiled 368 plasma proteins in 657 participants ≥3 months following hospitalization. Of these, 426 had at least one long COVID symptom and 233 had fully recovered. Elevated markers of myeloid inflammation and complement activation were associated with long COVID. IL-1R2, MATN2 and COLEC12 were associated with cardiorespiratory symptoms, fatigue and anxiety/depression; MATN2, CSF3 and C1QA were elevated in gastrointestinal symptoms and C1QA was elevated in cognitive impairment. Additional markers of alterations in nerve tissue repair (SPON-1 and NFASC) were elevated in those with cognitive impairment and SCG3, suggestive of brain-gut axis disturbance, was elevated in gastrointestinal symptoms. Severe acute respiratory syndrome coronavirus 2-specific immunoglobulin G (IgG) was persistently elevated in some individuals with long COVID, but virus was not detected in sputum. Analysis of inflammatory markers in nasal fluids showed no association with symptoms. Our study aimed to understand inflammatory processes that underlie long COVID and was not designed for biomarker discovery. Our findings suggest that specific inflammatory pathways related to tissue damage are implicated in subtypes of long COVID, which might be targeted in future therapeutic trials.",,doi:https://doi.org/10.1038/s41590-024-01778-0; html:https://europepmc.org/articles/PMC11003868; pdf:https://europepmc.org/articles/PMC11003868?pdf=render
 39049868,https://doi.org/10.1016/j.lanepe.2024.100994,"Trends in incidence of pneumothorax in England before, during and after the COVID-19 pandemic (2017-2023): a population-based observational study.","Zhong X, Goldacre R, Morris EJA, Hallifax RJ.",,The Lancet regional health. Europe,2024,2024-07-01,Y,epidemiology; Pneumothorax; incidence; Covid,,,"<h4>Background</h4>COVID-19 is a risk factor for pneumothorax. The pandemic may have influenced healthcare-seeking behaviour for pneumothorax. This study aimed to investigate recent trends in the incidence of pneumothorax in England.<h4>Methods</h4>A population-based epidemiological study was conducted using an English national dataset of hospital admissions (Hospital Episode Statistics) from 2017 to 2023. Record-linkage was used to identify multiple admissions per person and co-morbidity. Pneumothoraces co-occurring with COVID-19 were identified by concurrent COVID-19 diagnostic coding. The pre-pandemic (January 2017-February 2020), pandemic (March-2020-February-2021) and post-pandemic periods (March 2021-March 2023) were compared.<h4>Findings</h4>From 2017 to 2023, there were 72,275 hospital admissions for spontaneous pneumothorax among 59,130 patients. Admissions showed marked variability, peaking in January 2021 when the rate of admissions was about two-thirds higher than that of the pre-pandemic level (Incidence rate ratio [IRR] 1.65, 95% CI: 1.48-1.84). However, when excluding patients with a concurrent COVID-19 diagnosis, the overall trend shifted to a reduction during the pandemic period. Post-pandemic rates were not significantly different from pre-pandemic levels (IRR = 0.96, 95% CI: 0.89-1.04). The incidence of spontaneous pneumothorax was significantly higher in males (rate ratio compared to females: 2.29, 95% CI: 2.19-2.39). However, the trends were consistent in both males and females.<h4>Interpretation</h4>This study highlights a significant peak in COVID-19 related cases but a corresponding trough in non-COVID-related cases (end 2020, early 2021). Despite a previous report of increasing incidence of (non-COVID-related) hospitalised spontaneous pneumothorax over the long-term between 1968 and 2016, we did not observe any continued increase throughout this study period, prompting further investigation into the impact of recent guidelines.<h4>Funding</h4>Authors are supported by the NIHR Oxford BRC, Li Ka Shing and Robertson Foundations, MRC, and HDR UK.",,doi:https://doi.org/10.1016/j.lanepe.2024.100994; html:https://europepmc.org/articles/PMC11267084; pdf:https://europepmc.org/articles/PMC11267084?pdf=render
 39356639,https://doi.org/10.1016/j.xpro.2024.103335,Protocol to process follow-up electronic medical records of peritoneal dialysis patients to train AI models.,"Wang T, Zhu Y, Wang Z, Tang W, Zhao X, Wang T, Wang Y, Gao J, Ma L, Wang L.",,STAR protocols,2024,2024-10-01,Y,Bioinformatics; Health Sciences; Computer Sciences,,,"The absence of standardized protocols for integrating end-stage renal disease patient data into AI models has constrained the potential of AI in enhancing patient care. Here, we present a protocol for processing electronic medical records from 1,336 peritoneal dialysis patients with more than 10,000 follow-up records. We describe steps for environment setup and transforming records into analyzable formats. We then detail procedures for developing a directly usable dataset for training AI models to predict one-year all-cause mortality risk. For complete details on the use and execution of this protocol, please refer to Ma et al.<sup>1</sup>.",,doi:https://doi.org/10.1016/j.xpro.2024.103335; html:https://europepmc.org/articles/PMC11480227; pdf:https://europepmc.org/articles/PMC11480227?pdf=render
 37954687,https://doi.org/10.1177/20552076231211551,"Moving from development to implementation of digital innovations within the NHS: myHealthE, a remote monitoring system for tracking patient outcomes in child and adolescent mental health services.","Morris AC, Ibrahim Z, Moghraby OS, Stringaris A, Grant IM, Zalewski L, McClellan S, Moriarty G, Simonoff E, Dobson RJ, Downs J.",,Digital health,2023,2023-01-01,Y,Health; Medicine; Psychology; Mental health; general; Studies; Paediatrics; Outcomes; Wellbeing; Mixed Methods; Online; Personalised Medicine; Mhealth; Electronic; Digital Health,,,"<h4>Objective</h4>This paper aims to report our experience of developing, implementing, and evaluating myHealthE (MHE), a digital innovation for Child and Adolescents Mental Health Services (CAMHS), which automates the remote collection and reporting of Patient-Reported Outcome Measures (PROMs) into National Health Services (NHS) electronic healthcare records.<h4>Methods</h4>We describe the logistical and governance issues encountered in developing the MHE interface with patient-identifiable information, and the steps taken to overcome these development barriers. We describe the application's architecture and hosting environment to enable its operability within the NHS, as well as the capabilities needed within the technical team to bridge the gap between academic development and NHS operational teams.<h4>Results</h4>We present evidence on the feasibility and acceptability of this system within clinical services and the process of iterative development, highlighting additional functions that were incorporated to increase system utility.<h4>Conclusion</h4>This article provides a framework with which to plan, develop, and implement automated PROM collection from remote devices back to NHS infrastructure. The challenges and solutions described in this paper will be pertinent to other digital health innovation researchers aspiring to deploy interoperable systems within NHS clinical systems.",,doi:https://doi.org/10.1177/20552076231211551; html:https://europepmc.org/articles/PMC10638880; pdf:https://europepmc.org/articles/PMC10638880?pdf=render
-35105585,https://doi.org/10.1136/bmjopen-2021-054376,Development of an algorithm to classify primary care electronic health records of alcohol consumption: experience using data linkage from UK Biobank and primary care electronic health data sources.,"Fraile-Navarro D, Azcoaga-Lorenzo A, Agrawal U, Jani B, Fagbamigbe A, Currie D, Baldacchino A, Sullivan F.",,BMJ open,2022,2022-02-01,Y,Public Health; Primary Care; Health Informatics,,,"<h4>Objectives</h4>Develop a novel algorithm to categorise alcohol consumption using primary care electronic health records (EHRs) and asses its reliability by comparing this classification with self-reported alcohol consumption data obtained from the UK Biobank (UKB) cohort.<h4>Design</h4>Cross-sectional study.<h4>Setting</h4>The UKB, a population-based cohort with participants aged between 40 and 69 years recruited across the UK between 2006 and 2010.<h4>Participants</h4>UKB participants from Scotland with linked primary care data.<h4>Primary and secondary outcome measures</h4>Create a rule-based multiclass algorithm to classify alcohol consumption reported by Scottish UKB participants and compare it with their classification using data present in primary care EHRs based on Read Codes. We evaluated agreement metrics (simple agreement and kappa statistic).<h4>Results</h4>Among the Scottish UKB participants, 18 838 (69%) had at least one Read Code related to alcohol consumption and were used in the classification. The agreement of alcohol consumption categories between UKB and primary care data, including assessments within 5 years was 59.6%, and kappa was 0.23 (95% CI 0.21 to 0.24). Differences in classification between the two sources were statistically significant (p<0.001); More individuals were classified as 'sensible drinkers' and in lower alcohol consumption levels in primary care records compared with the UKB. Agreement improved slightly when using only numerical values (k=0.29; 95% CI 0.27 to 0.31) and decreased when using qualitative descriptors only (k=0.18;95% CI 0.16 to 0.20).<h4>Conclusion</h4>Our algorithm classifies alcohol consumption recorded in Primary Care EHRs into discrete meaningful categories. These results suggest that alcohol consumption may be underestimated in primary care EHRs. Using numerical values (alcohol units) may improve classification when compared with qualitative descriptors.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/2/e054376.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-054376; html:https://europepmc.org/articles/PMC8808438; pdf:https://europepmc.org/articles/PMC8808438?pdf=render
 33469151,https://doi.org/10.1038/s42003-020-01613-w,LRIG proteins regulate lipid metabolism via BMP signaling and affect the risk of type 2 diabetes.,"Herdenberg C, Mutie PM, Billing O, Abdullah A, Strawbridge RJ, Dahlman I, Tuck S, Holmlund C, Arner P, Henriksson R, Franks PW, Hedman H.",,Communications biology,2021,2021-01-19,Y,,,,"Leucine-rich repeats and immunoglobulin-like domains (LRIG) proteins have been implicated as regulators of growth factor signaling; however, the possible redundancy among mammalian LRIG1, LRIG2, and LRIG3 has hindered detailed elucidation of their physiological functions. Here, we show that Lrig-null mouse embryonic fibroblasts (MEFs) are deficient in adipogenesis and bone morphogenetic protein (BMP) signaling. In contrast, transforming growth factor-beta (TGF-β) and receptor tyrosine kinase (RTK) signaling appeared unaltered in Lrig-null cells. The BMP signaling defect was rescued by ectopic expression of LRIG1 or LRIG3 but not by expression of LRIG2. Caenorhabditis elegans with mutant LRIG/sma-10 variants also exhibited a lipid storage defect. Human LRIG1 variants were strongly associated with increased body mass index (BMI) yet protected against type 2 diabetes; these effects were likely mediated by altered adipocyte morphology. These results demonstrate that LRIG proteins function as evolutionarily conserved regulators of lipid metabolism and BMP signaling and have implications for human disease.",,pdf:https://www.nature.com/articles/s42003-020-01613-w.pdf; doi:https://doi.org/10.1038/s42003-020-01613-w; html:https://europepmc.org/articles/PMC7815736; pdf:https://europepmc.org/articles/PMC7815736?pdf=render
 39414270,https://doi.org/10.1136/bmjopen-2024-088600,What is the carbon footprint of academic clinical trials? A study of hotspots in 10 trials.,"Griffiths J, Adshead F, Al-Shahi Salman R, Anderson C, Bedson E, Bliss J, Boshoff A, Chen X, Cranley D, Doran P, Dunne F, Gamble C, Gillies K, Hood K, Kavanagh C, Malone J, McGregor N, McNamara C, Midha E, Moore K, Murphy L, Newman C, O'Reilly S, Perkins AM, Pett S, Sydes MR, Whitty L, You F, Fox L, Williamson PR.",,BMJ open,2024,2024-10-16,Y,Climate change; Randomized controlled trial; Clinical Trial; Statistics & Research Methods,,,"<h4>Background</h4>Clinical trials are fundamental to healthcare, however, they also contribute to anthropogenic climate change. Following previous work to develop and test a method and guidance to calculate the carbon footprint of clinical trials, we have now applied the guidance to 10 further UK and international, academically sponsored clinical trials to continue the identification of hotspots and opportunities for lower carbon trial design.<h4>Methods</h4>10 collaborating clinical trial units (CTUs) self-identified and a trial was selected from their portfolio to represent a variety of designs, health areas and interventions. Trial activity data was collated by trial teams across 10 modules spanning trial setup through to closure, then multiplied by emission factors provided in the guidance to calculate the carbon footprint. Feedback was collected from trial teams on the process, experience and ease of use of the guidance.<h4>Results</h4>We footprinted 10 trials: 6 investigational medicinal product trials, 1 nutritional, 1 surgical, 1 health surveillance and one complex intervention trial. Six of these were completed and four ongoing (two in follow-up and two recruiting). The carbon footprint of the 10 trials ranged from 16 to 765 tonnes CO<sub>2</sub>e. Common hotspots were identified as CTU emissions, trial-specific patient assessments and trial team meetings and travel. Hotspots for specific trial designs were also identified. The time taken to collate activity data and complete carbon calculations ranged from 5 to 60 hours. The draft guidance was updated to include new activities identified from the 10 trials and in response to user feedback.<h4>Discussion</h4>There are opportunities to reduce the impact of trials across all modules, particularly trial-specific meetings and travel, patient assessments and laboratory practice. A trial's carbon footprint should be considered at the design stage, but work is required to make this common place.",,doi:https://doi.org/10.1136/bmjopen-2024-088600; html:https://europepmc.org/articles/PMC11487931; pdf:https://europepmc.org/articles/PMC11487931?pdf=render
-37272361,https://doi.org/10.2340/actadv.v103.5268,Relationship between Eczema and Self-reported Difficulties Keeping up with School Education: A Cross-sectional Study.,"Beckman L, Hagquist C, Svensson Å, Langan SM, Von Kobyletzki L.",,Acta dermato-venereologica,2023,2023-06-05,Y,,,,"Eczema is a common chronic disease that affects both children and adults, and may have an adverse impact on school performance, as it is characteristically pruritic, and hence may lead to poor concentration and inadequate sleep. The aim of this study was to elucidate the relationship between eczema and self-reported difficulties keeping up with school education. The study was based on cross-sectional questionnaire data collected in schools among all 9th graders (15-16 years old) within a Swedish county. Logistic regression analyses were used to assess the association between having eczema and self-reported difficulties keeping up with school education. A total of 2,620 pupils participated (50.1% female). An increased odds ratio (OR) of self-reported difficulties keeping up with school education was found in adolescents with eczema compared with those without eczema after adjustment for sex and  family residence (OR 2.13, 95% confidence interval (95% CI) 1.32-3.44), and with additional adjustment for sleeping problems, attention-deficit hyperactivity disorder, allergy, rhinitis, asthma, and alcohol consumption (adjusted OR 1.78, CI 1.05-3.00). Eczema may be a relevant risk factor for difficulty keeping up with school education in adolescents. However, studies that can assess temporality, based in different settings with objective reports of both eczema and self-reported difficulties at school, are needed to confirm these findings.",,doi:https://doi.org/10.2340/actadv.v103.5268; html:https://europepmc.org/articles/PMC10259463; pdf:https://europepmc.org/articles/PMC10259463?pdf=render
+35105585,https://doi.org/10.1136/bmjopen-2021-054376,Development of an algorithm to classify primary care electronic health records of alcohol consumption: experience using data linkage from UK Biobank and primary care electronic health data sources.,"Fraile-Navarro D, Azcoaga-Lorenzo A, Agrawal U, Jani B, Fagbamigbe A, Currie D, Baldacchino A, Sullivan F.",,BMJ open,2022,2022-02-01,Y,Public Health; Primary Care; Health Informatics,,,"<h4>Objectives</h4>Develop a novel algorithm to categorise alcohol consumption using primary care electronic health records (EHRs) and asses its reliability by comparing this classification with self-reported alcohol consumption data obtained from the UK Biobank (UKB) cohort.<h4>Design</h4>Cross-sectional study.<h4>Setting</h4>The UKB, a population-based cohort with participants aged between 40 and 69 years recruited across the UK between 2006 and 2010.<h4>Participants</h4>UKB participants from Scotland with linked primary care data.<h4>Primary and secondary outcome measures</h4>Create a rule-based multiclass algorithm to classify alcohol consumption reported by Scottish UKB participants and compare it with their classification using data present in primary care EHRs based on Read Codes. We evaluated agreement metrics (simple agreement and kappa statistic).<h4>Results</h4>Among the Scottish UKB participants, 18 838 (69%) had at least one Read Code related to alcohol consumption and were used in the classification. The agreement of alcohol consumption categories between UKB and primary care data, including assessments within 5 years was 59.6%, and kappa was 0.23 (95% CI 0.21 to 0.24). Differences in classification between the two sources were statistically significant (p<0.001); More individuals were classified as 'sensible drinkers' and in lower alcohol consumption levels in primary care records compared with the UKB. Agreement improved slightly when using only numerical values (k=0.29; 95% CI 0.27 to 0.31) and decreased when using qualitative descriptors only (k=0.18;95% CI 0.16 to 0.20).<h4>Conclusion</h4>Our algorithm classifies alcohol consumption recorded in Primary Care EHRs into discrete meaningful categories. These results suggest that alcohol consumption may be underestimated in primary care EHRs. Using numerical values (alcohol units) may improve classification when compared with qualitative descriptors.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/2/e054376.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-054376; html:https://europepmc.org/articles/PMC8808438; pdf:https://europepmc.org/articles/PMC8808438?pdf=render
 32620158,https://doi.org/10.1186/s12915-020-00792-6,Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human.,"Liu S, Yu Y, Zhang S, Cole JB, Tenesa A, Wang T, McDaneld TG, Ma L, Liu GE, Fang L.",,BMC biology,2020,2020-07-03,Y,Comparative Epigenomics; Gwas Enrichment; Human-cattle Comparison; Trait-relevant Tissues,,,"<h4>Background</h4>Lack of comprehensive functional annotations across a wide range of tissues and cell types severely hinders the biological interpretations of phenotypic variation, adaptive evolution, and domestication in livestock. Here we used a combination of comparative epigenomics, genome-wide association study (GWAS), and selection signature analysis, to shed light on potential adaptive evolution in cattle.<h4>Results</h4>We cross-mapped 8 histone marks of 1300 samples from human to cattle, covering 178 unique tissues/cell types. By uniformly analyzing 723 RNA-seq and 40 whole genome bisulfite sequencing (WGBS) datasets in cattle, we validated that cross-mapped histone marks captured tissue-specific expression and methylation, reflecting tissue-relevant biology. Through integrating cross-mapped tissue-specific histone marks with large-scale GWAS and selection signature results, we for the first time detected relevant tissues and cell types for 45 economically important traits and artificial selection in cattle. For instance, immune tissues are significantly associated with health and reproduction traits, multiple tissues for milk production and body conformation traits (reflecting their highly polygenic architecture), and thyroid for the different selection between beef and dairy cattle. Similarly, we detected relevant tissues for 58 complex traits and diseases in humans and observed that immune and fertility traits in humans significantly correlated with those in cattle in terms of relevant tissues, which facilitated the identification of causal genes for such traits. For instance, PIK3CG, a gene highly specifically expressed in mononuclear cells, was significantly associated with both age-at-menopause in human and daughter-still-birth in cattle. ICAM, a T cell-specific gene, was significantly associated with both allergic diseases in human and metritis in cattle.<h4>Conclusion</h4>Collectively, our results highlighted that comparative epigenomics in conjunction with GWAS and selection signature analyses could provide biological insights into the phenotypic variation and adaptive evolution. Cattle may serve as a model for human complex traits, by providing additional information beyond laboratory model organisms, particularly when more novel phenotypes become available in the near future.",,pdf:https://bmcbiol.biomedcentral.com/counter/pdf/10.1186/s12915-020-00792-6; doi:https://doi.org/10.1186/s12915-020-00792-6; html:https://europepmc.org/articles/PMC7334855; pdf:https://europepmc.org/articles/PMC7334855?pdf=render
+37272361,https://doi.org/10.2340/actadv.v103.5268,Relationship between Eczema and Self-reported Difficulties Keeping up with School Education: A Cross-sectional Study.,"Beckman L, Hagquist C, Svensson Å, Langan SM, Von Kobyletzki L.",,Acta dermato-venereologica,2023,2023-06-05,Y,,,,"Eczema is a common chronic disease that affects both children and adults, and may have an adverse impact on school performance, as it is characteristically pruritic, and hence may lead to poor concentration and inadequate sleep. The aim of this study was to elucidate the relationship between eczema and self-reported difficulties keeping up with school education. The study was based on cross-sectional questionnaire data collected in schools among all 9th graders (15-16 years old) within a Swedish county. Logistic regression analyses were used to assess the association between having eczema and self-reported difficulties keeping up with school education. A total of 2,620 pupils participated (50.1% female). An increased odds ratio (OR) of self-reported difficulties keeping up with school education was found in adolescents with eczema compared with those without eczema after adjustment for sex and  family residence (OR 2.13, 95% confidence interval (95% CI) 1.32-3.44), and with additional adjustment for sleeping problems, attention-deficit hyperactivity disorder, allergy, rhinitis, asthma, and alcohol consumption (adjusted OR 1.78, CI 1.05-3.00). Eczema may be a relevant risk factor for difficulty keeping up with school education in adolescents. However, studies that can assess temporality, based in different settings with objective reports of both eczema and self-reported difficulties at school, are needed to confirm these findings.",,doi:https://doi.org/10.2340/actadv.v103.5268; html:https://europepmc.org/articles/PMC10259463; pdf:https://europepmc.org/articles/PMC10259463?pdf=render
 30727941,https://doi.org/10.1186/s12859-019-2633-8,DeepPVP: phenotype-based prioritization of causative variants using deep learning.,"Boudellioua I, Kulmanov M, Schofield PN, Gkoutos GV, Hoehndorf R.",,BMC bioinformatics,2019,2019-02-06,Y,Phenotype; Ontology; Machine Learning; Variant Prioritization,Applied Analytics,,"<h4>Background</h4>Prioritization of variants in personal genomic data is a major challenge. Recently, computational methods that rely on comparing phenotype similarity have shown to be useful to identify causative variants. In these methods, pathogenicity prediction is combined with a semantic similarity measure to prioritize not only variants that are likely to be dysfunctional but those that are likely involved in the pathogenesis of a patient's phenotype.<h4>Results</h4>We have developed DeepPVP, a variant prioritization method that combined automated inference with deep neural networks to identify the likely causative variants in whole exome or whole genome sequence data. We demonstrate that DeepPVP performs significantly better than existing methods, including phenotype-based methods that use similar features. DeepPVP is freely available at https://github.com/bio-ontology-research-group/phenomenet-vp .<h4>Conclusions</h4>DeepPVP further improves on existing variant prioritization methods both in terms of speed as well as accuracy.",,pdf:https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2633-8; doi:https://doi.org/10.1186/s12859-019-2633-8; html:https://europepmc.org/articles/PMC6364462; pdf:https://europepmc.org/articles/PMC6364462?pdf=render
-31845899,https://doi.org/10.2196/14782,Efficient Reuse of Natural Language Processing Models for Phenotype-Mention Identification in Free-text Electronic Medical Records: A Phenotype Embedding Approach.,"Wu H, Hodgson K, Dyson S, Morley KI, Ibrahim ZM, Iqbal E, Stewart R, Dobson RJ, Sudlow C.",,JMIR medical informatics,2019,2019-12-17,Y,Phenotype; Clustering; Machine Learning; Electronic Health Records; Natural Language Processing; Text Mining; Word Embedding; Model Adaptation; Phenotype Embedding,Applied Analytics,,"<h4>Background</h4>Much effort has been put into the use of automated approaches, such as natural language processing (NLP), to mine or extract data from free-text medical records in order to construct comprehensive patient profiles for delivering better health care. Reusing NLP models in new settings, however, remains cumbersome, as it requires validation and retraining on new data iteratively to achieve convergent results.<h4>Objective</h4>The aim of this work is to minimize the effort involved in reusing NLP models on free-text medical records.<h4>Methods</h4>We formally define and analyze the model adaptation problem in phenotype-mention identification tasks. We identify ""duplicate waste"" and ""imbalance waste,"" which collectively impede efficient model reuse. We propose a phenotype embedding-based approach to minimize these sources of waste without the need for labelled data from new settings.<h4>Results</h4>We conduct experiments on data from a large mental health registry to reuse NLP models in four phenotype-mention identification tasks. The proposed approach can choose the best model for a new task, identifying up to 76% waste (duplicate waste), that is, phenotype mentions without the need for validation and model retraining and with very good performance (93%-97% accuracy). It can also provide guidance for validating and retraining the selected model for novel language patterns in new tasks, saving around 80% waste (imbalance waste), that is, the effort required in ""blind"" model-adaptation approaches.<h4>Conclusions</h4>Adapting pretrained NLP models for new tasks can be more efficient and effective if the language pattern landscapes of old settings and new settings can be made explicit and comparable. Our experiments show that the phenotype-mention embedding approach is an effective way to model language patterns for phenotype-mention identification tasks and that its use can guide efficient NLP model reuse.",Wu et el. developed a computer algorithm which can transform clinical letters into databases for research. Their approach in processing information in clinical letters is more flexible compared to those before allowing users to define concepts which they want to find in the letters. ,doi:https://doi.org/10.2196/14782; doi:https://doi.org/10.2196/14782; html:https://europepmc.org/articles/PMC6938594
 34249083,https://doi.org/10.3389/fgene.2021.652878,Polymorphism in <i>INSR</i> Locus Modifies Risk of Atrial Fibrillation in Patients on Thyroid Hormone Replacement Therapy.,"Soto-Pedre E, Siddiqui MK, Maroteau C, Dawed AY, Doney AS, Palmer CNA, Pearson ER, Leese GP.",,Frontiers in genetics,2021,2021-06-23,Y,Genetics; Insulin receptor; Hypothyroidism; Atrial fibrillation; Thyroid Hormone Replacement Therapy,,,"<h4>Aims</h4>Atrial fibrillation (AF) is a risk for patients receiving thyroid hormone replacement therapy. No published work has focused on pharmacogenetics relevant to thyroid dysfunction and AF risk. We aimed to assess the effect of L-thyroxine on AF risk stratified by a variation in a candidate gene.<h4>Methods and results</h4>A retrospective follow-up study was done among European Caucasian patients from the Genetics of Diabetes Audit and Research in Tayside Scotland cohort (Scotland, United Kingdom). Linked data on biochemistry, prescribing, hospital admissions, demographics, and genetic biobank were used to ascertain patients on L-thyroxine and diagnosis of AF. A GWAS-identified insulin receptor-<i>INSR</i> locus (rs4804416) was the candidate gene. Cox survival models and sensitivity analyses by taking competing risk of death into account were used. Replication was performed in additional sample (The Genetics of Scottish Health Research register, GoSHARE), and meta-analyses across the results of the study and replication cohorts were done. We analyzed 962 exposed to L-thyroxine and 5,840 unexposed patients who were rs4804416 genotyped. The rarer G/G genotype was present in 18% of the study population. The total follow-up was up to 20 years, and there was a significant increased AF risk for patients homozygous carriers of the G allele exposed to L-thyroxine (RHR = 2.35, <i>P</i> = 1.6e-02). The adjusted increased risk was highest within the first 3 years of exposure (RHR = 9.10, <i>P</i> = 8.5e-04). Sensitivity analysis yielded similar results. Effects were replicated in GoSHARE (<i>n</i> = 3,190).<h4>Conclusion</h4>Homozygous G/G genotype at the <i>INSR</i> locus (rs4804416) is associated with an increased risk of AF in patients on L-thyroxine, independent of serum of free thyroxine and thyroid-stimulating hormone serum concentrations.",,pdf:https://www.frontiersin.org/articles/10.3389/fgene.2021.652878/pdf; doi:https://doi.org/10.3389/fgene.2021.652878; html:https://europepmc.org/articles/PMC8260687; pdf:https://europepmc.org/articles/PMC8260687?pdf=render
-38419411,https://doi.org/10.1093/bjd/ljae080,Defining disease severity in atopic dermatitis and psoriasis for the application to biomarker research: an interdisciplinary perspective.,"Ramessur R, Dand N, Langan SM, Saklatvala J, Fritzsche MC, Holland S, Arents BWM, McAteer H, Proctor A, McMahon D, Greenwood M, Buyx AM, Messer T, Weiler N, Hicks A, Hecht P, Weidinger S, Ndlovu MN, Chengliang D, Hübenthal M, Egeberg A, Paternoster L, Skov L, De Jong EMGJ, Middelkamp-Hup MA, Mahil SK, Barker JN, Flohr C, Brown SJ, Smith CH.",,The British journal of dermatology,2024,2024-06-01,Y,,,,"More severe atopic dermatitis and psoriasis are associated with a higher cumulative impact on quality of life, multimorbidity and healthcare costs. Proactive, early intervention in those most at risk of severe disease may reduce this cumulative burden and modify the disease trajectory to limit progression. The lack of reliable biomarkers for this at-risk group represents a barrier to such a paradigm shift in practice. To expedite discovery and validation, the BIOMarkers in Atopic Dermatitis and Psoriasis (BIOMAP) consortium (a large-scale European, interdisciplinary research initiative) has curated clinical and molecular data across diverse study designs and sources including cross-sectional and cohort studies (small-scale studies through to large multicentre registries), clinical trials, electronic health records and large-scale population-based biobanks. We map all dataset disease severity instruments and measures to three key domains (symptoms, inflammatory activity and disease course), and describe important codependencies and relationships across variables and domains. We prioritize definitions for more severe disease with reference to international consensus, reference standards and/or expert opinion. Key factors to consider when analysing datasets across these diverse study types include explicit early consideration of biomarker purpose and clinical context, candidate biomarkers associated with disease severity at a particular point in time and over time and how they are related, taking the stage of biomarker development into account when selecting disease severity measures for analyses, and validating biomarker associations with disease severity outcomes using both physician- and patient-reported measures and across domains. The outputs from this exercise will ensure coherence and focus across the BIOMAP consortium so that mechanistic insights and biomarkers are clinically relevant, patient-centric and more generalizable to current and future research efforts.",,pdf:https://academic.oup.com/bjd/advance-article-pdf/doi/10.1093/bjd/ljae080/56794617/ljae080.pdf; doi:https://doi.org/10.1093/bjd/ljae080; html:https://europepmc.org/articles/PMC11188926; pdf:https://europepmc.org/articles/PMC11188926?pdf=render
+31845899,https://doi.org/10.2196/14782,Efficient Reuse of Natural Language Processing Models for Phenotype-Mention Identification in Free-text Electronic Medical Records: A Phenotype Embedding Approach.,"Wu H, Hodgson K, Dyson S, Morley KI, Ibrahim ZM, Iqbal E, Stewart R, Dobson RJ, Sudlow C.",,JMIR medical informatics,2019,2019-12-17,Y,Phenotype; Clustering; Machine Learning; Electronic Health Records; Natural Language Processing; Text Mining; Word Embedding; Model Adaptation; Phenotype Embedding,Applied Analytics,,"<h4>Background</h4>Much effort has been put into the use of automated approaches, such as natural language processing (NLP), to mine or extract data from free-text medical records in order to construct comprehensive patient profiles for delivering better health care. Reusing NLP models in new settings, however, remains cumbersome, as it requires validation and retraining on new data iteratively to achieve convergent results.<h4>Objective</h4>The aim of this work is to minimize the effort involved in reusing NLP models on free-text medical records.<h4>Methods</h4>We formally define and analyze the model adaptation problem in phenotype-mention identification tasks. We identify ""duplicate waste"" and ""imbalance waste,"" which collectively impede efficient model reuse. We propose a phenotype embedding-based approach to minimize these sources of waste without the need for labelled data from new settings.<h4>Results</h4>We conduct experiments on data from a large mental health registry to reuse NLP models in four phenotype-mention identification tasks. The proposed approach can choose the best model for a new task, identifying up to 76% waste (duplicate waste), that is, phenotype mentions without the need for validation and model retraining and with very good performance (93%-97% accuracy). It can also provide guidance for validating and retraining the selected model for novel language patterns in new tasks, saving around 80% waste (imbalance waste), that is, the effort required in ""blind"" model-adaptation approaches.<h4>Conclusions</h4>Adapting pretrained NLP models for new tasks can be more efficient and effective if the language pattern landscapes of old settings and new settings can be made explicit and comparable. Our experiments show that the phenotype-mention embedding approach is an effective way to model language patterns for phenotype-mention identification tasks and that its use can guide efficient NLP model reuse.",Wu et el. developed a computer algorithm which can transform clinical letters into databases for research. Their approach in processing information in clinical letters is more flexible compared to those before allowing users to define concepts which they want to find in the letters. ,doi:https://doi.org/10.2196/14782; doi:https://doi.org/10.2196/14782; html:https://europepmc.org/articles/PMC6938594
 34353320,https://doi.org/10.1186/s12916-021-02045-x,Adverse childhood experiences and child mental health: an electronic birth cohort study.,"Lowthian E, Anthony R, Evans A, Daniel R, Long S, Bandyopadhyay A, John A, Bellis MA, Paranjothy S.",,BMC medicine,2021,2021-08-06,Y,Survival analysis; Cohort; Mental health; Wales; Administrative Data; Adverse Childhood Experiences,,,"<h4>Background</h4>Adverse childhood experiences (ACEs) are negatively associated with a range of child health outcomes. In this study, we explored associations between five individual ACEs and child mental health diagnoses or symptoms. ACEs included living with someone who had an alcohol-related problem, common mental health disorder or serious mental illness, or experienced victimisation or death of a household member.<h4>Methods</h4>We analysed data from a population-level electronic cohort of children in Wales, UK, (N = 191,035) between the years of 1998 and 2012. We used Cox regression with discrete time-varying exposure variables to model time to child mental health diagnosis during the first 15 years of life. Child mental health diagnoses include five categories: (i) externalising symptoms (anti-social behaviour), (ii) internalising symptoms (stress, anxiety, depression), (iii) developmental delay (e.g. learning disability), (iv) other (e.g. eating disorder, personality disorders), and (v) any mental health diagnosis, which was created by combining externalising symptoms, internalising symptoms and other. Our analyses were adjusted for social deprivation and perinatal risk factors.<h4>Results</h4>There were strong univariable associations between the five individual ACEs, sociodemographic and perinatal factors (e.g. gestational weight at birth) and an increased risk of child mental health diagnoses. After adjusting for sociodemographic and perinatal aspects, there was a remaining conditional increased risk of any child mental health diagnosis, associated with victimisation (conditional hazard ratio (cHR) 1.90, CI 95% 1.34-2.69), and living with an adult with a common mental health diagnosis (cHR 1.63, CI 95% 1.52-1.75). Coefficients of product terms between ACEs and deprivation were not statistically significant.<h4>Conclusion</h4>The increased risk of child mental health diagnosis associated with victimisation, or exposure to common mental health diagnoses, and alcohol problems in the household supports the need for policy measures and intervention strategies for children and their families.",,pdf:https://bmcmedicine.biomedcentral.com/track/pdf/10.1186/s12916-021-02045-x; doi:https://doi.org/10.1186/s12916-021-02045-x; html:https://europepmc.org/articles/PMC8344166; pdf:https://europepmc.org/articles/PMC8344166?pdf=render
+38419411,https://doi.org/10.1093/bjd/ljae080,Defining disease severity in atopic dermatitis and psoriasis for the application to biomarker research: an interdisciplinary perspective.,"Ramessur R, Dand N, Langan SM, Saklatvala J, Fritzsche MC, Holland S, Arents BWM, McAteer H, Proctor A, McMahon D, Greenwood M, Buyx AM, Messer T, Weiler N, Hicks A, Hecht P, Weidinger S, Ndlovu MN, Chengliang D, Hübenthal M, Egeberg A, Paternoster L, Skov L, De Jong EMGJ, Middelkamp-Hup MA, Mahil SK, Barker JN, Flohr C, Brown SJ, Smith CH.",,The British journal of dermatology,2024,2024-06-01,Y,,,,"More severe atopic dermatitis and psoriasis are associated with a higher cumulative impact on quality of life, multimorbidity and healthcare costs. Proactive, early intervention in those most at risk of severe disease may reduce this cumulative burden and modify the disease trajectory to limit progression. The lack of reliable biomarkers for this at-risk group represents a barrier to such a paradigm shift in practice. To expedite discovery and validation, the BIOMarkers in Atopic Dermatitis and Psoriasis (BIOMAP) consortium (a large-scale European, interdisciplinary research initiative) has curated clinical and molecular data across diverse study designs and sources including cross-sectional and cohort studies (small-scale studies through to large multicentre registries), clinical trials, electronic health records and large-scale population-based biobanks. We map all dataset disease severity instruments and measures to three key domains (symptoms, inflammatory activity and disease course), and describe important codependencies and relationships across variables and domains. We prioritize definitions for more severe disease with reference to international consensus, reference standards and/or expert opinion. Key factors to consider when analysing datasets across these diverse study types include explicit early consideration of biomarker purpose and clinical context, candidate biomarkers associated with disease severity at a particular point in time and over time and how they are related, taking the stage of biomarker development into account when selecting disease severity measures for analyses, and validating biomarker associations with disease severity outcomes using both physician- and patient-reported measures and across domains. The outputs from this exercise will ensure coherence and focus across the BIOMAP consortium so that mechanistic insights and biomarkers are clinically relevant, patient-centric and more generalizable to current and future research efforts.",,pdf:https://academic.oup.com/bjd/advance-article-pdf/doi/10.1093/bjd/ljae080/56794617/ljae080.pdf; doi:https://doi.org/10.1093/bjd/ljae080; html:https://europepmc.org/articles/PMC11188926; pdf:https://europepmc.org/articles/PMC11188926?pdf=render
 32641105,https://doi.org/10.1186/s12874-020-01025-8,Multivariate network meta-analysis incorporating class effects.,"Owen RK, Bujkiewicz S, Tincello DG, Abrams KR.",,BMC medical research methodology,2020,2020-07-08,Y,Meta-analysis; Multivariate; Class Effect; Network Meta-analysis; Mixed Treatment Comparisons,,,"<h4>Background</h4>Network meta-analysis synthesises data from a number of clinical trials in order to assess the comparative efficacy of multiple healthcare interventions in similar patient populations. In situations where clinical trial data are heterogeneously reported i.e. data are missing for one or more outcomes of interest, synthesising such data can lead to disconnected networks of evidence, increased uncertainty, and potentially biased estimates which can have severe implications for decision-making. To overcome this issue, strength can be borrowed between outcomes of interest in multivariate network meta-analyses. Furthermore, in situations where there are relatively few trials informing each treatment comparison, there is a potential issue with the sparsity of data in the treatment networks, which can lead to substantial parameter uncertainty. A multivariate network meta-analysis approach can be further extended to borrow strength between interventions of the same class using hierarchical models.<h4>Methods</h4>We extend the trivariate network meta-analysis model to incorporate the exchangeability between treatment effects belonging to the same class of intervention to increase precision in treatment effect estimates. We further incorporate a missing data framework to estimate uncertainty in trials that did not report measures of variability in order to maximise the use of all available information for healthcare decision-making. The methods are applied to a motivating dataset in overactive bladder syndrome. The outcomes of interest were mean change from baseline in incontinence, voiding and urgency episodes. All models were fitted using Bayesian Markov Chain Monte Carlo (MCMC) methods in WinBUGS.<h4>Results</h4>All models (univariate, multivariate, and multivariate models incorporating class effects) produced similar point estimates for all treatment effects. Incorporating class effects in multivariate models often increased precision in treatment effect estimates.<h4>Conclusions</h4>Multivariate network meta-analysis incorporating class effects allowed for the comparison of all interventions across all outcome measures to ameliorate the potential impact of outcome reporting bias, and further borrowed strength between interventions belonging to the same class of treatment to increase the precision in treatment effect estimates for healthcare policy and decision-making.",,pdf:https://bmcmedresmethodol.biomedcentral.com/track/pdf/10.1186/s12874-020-01025-8; doi:https://doi.org/10.1186/s12874-020-01025-8; html:https://europepmc.org/articles/PMC7341581; pdf:https://europepmc.org/articles/PMC7341581?pdf=render
 35485805,https://doi.org/10.1017/s003329172200109x,Multimorbidity clusters among people with serious mental illness: a representative primary and secondary data linkage cohort study.,"Ma R, Romano E, Ashworth M, Yadegarfar ME, Dregan A, Ronaldson A, de Oliveira C, Jacobs R, Stewart R, Stubbs B.",,Psychological medicine,2023,2022-04-29,Y,Mortality; Schizophrenia; Psychosis; Physical Health; Multimorbidity,,,"<h4>Background</h4>People with serious mental illness (SMI) experience higher mortality partially attributable to higher long-term condition (LTC) prevalence. However, little is known about multiple LTCs (MLTCs) clustering in this population.<h4>Methods</h4>People from South London with SMI and two or more existing LTCs aged 18+ at diagnosis were included using linked primary and mental healthcare records, 2012-2020. Latent class analysis (LCA) determined MLTC classes and multinominal logistic regression examined associations between demographic/clinical characteristics and latent class membership.<h4>Results</h4>The sample included 1924 patients (mean (s.d.) age 48.2 (17.3) years). Five latent classes were identified: 'substance related' (24.9%), 'atopic' (24.2%), 'pure affective' (30.4%), 'cardiovascular' (14.1%), and 'complex multimorbidity' (6.4%). Patients had on average 7-9 LTCs in each cluster. Males were at increased odds of MLTCs in all four clusters, compared to the 'pure affective'. Compared to the largest cluster ('pure affective'), the 'substance related' and the 'atopic' clusters were younger [odds ratios (OR) per year increase 0.99 (95% CI 0.98-1.00) and 0.96 (0.95-0.97) respectively], and the 'cardiovascular' and 'complex multimorbidity' clusters were older (ORs 1.09 (1.07-1.10) and 1.16 (1.14-1.18) respectively). The 'substance related' cluster was more likely to be White, the 'cardiovascular' cluster more likely to be Black (compared to White; OR 1.75, 95% CI 1.10-2.79), and both more likely to have schizophrenia, compared to other clusters.<h4>Conclusion</h4>The current study identified five latent class MLTC clusters among patients with SMI. An integrated care model for treating MLTCs in this population is recommended to improve multimorbidity care.",,pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/BDE3DC6059EB59B00B2E0CD892963804/S003329172200109Xa.pdf/div-class-title-multimorbidity-clusters-among-people-with-serious-mental-illness-a-representative-primary-and-secondary-data-linkage-cohort-study-div.pdf; doi:https://doi.org/10.1017/S003329172200109X; html:https://europepmc.org/articles/PMC10388332; pdf:https://europepmc.org/articles/PMC10388332?pdf=render
 31532828,https://doi.org/10.1210/clinem/dgz006,Increased Infection Risk in Addison's Disease and Congenital Adrenal Hyperplasia.,"Tresoldi AS, Sumilo D, Perrins M, Toulis KA, Prete A, Reddy N, Wass JAH, Arlt W, Nirantharakumar K.",,The Journal of clinical endocrinology and metabolism,2020,2020-02-01,Y,,,,"<h4>Context</h4>Mortality and infection-related hospital admissions are increased in patients with primary adrenal insufficiency (PAI). However, the risk of primary care-managed infections in patients with PAI is unknown.<h4>Objective</h4>To estimate infection risk in PAI due to Addison's disease (AD) and congenital adrenal hyperplasia (CAH) in a primary care setting.<h4>Design</h4>Retrospective cohort study using UK data collected from 1995 to 2018.<h4>Main outcome measures</h4>Incidence of lower respiratory tract infections (LRTIs), urinary tract infections (UTIs), gastrointestinal infections (GIIs), and prescription counts of antimicrobials in adult PAI patients compared to unexposed controls.<h4>Results</h4>A diagnosis of PAI was established in 1580 AD patients (mean age 51.7 years) and 602 CAH patients (mean age 35.4 years). All AD patients and 42% of CAH patients were prescribed glucocorticoids, most frequently hydrocortisone in AD (82%) and prednisolone in CAH (50%). AD and CAH patients exposed to glucocorticoids, but not CAH patients without glucocorticoid treatment, had a significantly increased risk of LRTIs (adjusted incidence rate ratio AD 2.11 [95% confidence interval (CI) 1.64-2.69], CAH 3.23 [95% CI 1.21-8.61]), UTIs (AD 1.51 [95% CI 1.29-1.77], CAH 2.20 [95% CI 1.43-3.34]), and GIIs (AD 3.80 [95% CI 2.99-4.84], CAH 1.93 [95% CI 1.06-3.52]). This was mirrored by increased prescription of antibiotics (AD 1.73 [95% CI 1.69-1.77], CAH 1.77 [95% CI 1.66-1.89]) and antifungals (AD 1.89 [95% CI 1.74-2.05], CAH 1.91 [95% CI 1.50-2.43]).<h4>Conclusions</h4>There is an increased risk of infections and antimicrobial use in PAI in the primary care setting at least partially linked to glucocorticoid treatment. Future studies will need to address whether more physiological glucocorticoid replacement modes could reduce this risk.",People who suffer with primary adrenal insufficiency are more likely to be admitted to hospital. But the risk to patients catching infections whilst being treated in hospital is unknown. This study found that people with PAI being treated in hospital have a higher risk of catching an infection. Some of this risk is linked with how PAI is treated.,pdf:https://academic.oup.com/jcem/article-pdf/105/2/418/33574680/dgz006.pdf; doi:https://doi.org/10.1210/clinem/dgz006; html:https://europepmc.org/articles/PMC7046014
@@ -907,16 +908,16 @@ PMC9645061,https://doi.org/,Using population-scale medication data to evaluate t
 38938233,https://doi.org/10.1016/j.jacadv.2023.100333,A Machine Learning Model to Aid Detection of Familial Hypercholesterolemia.,"Gratton J, Futema M, Humphries SE, Hingorani AD, Finan C, Schmidt AF.",,JACC. Advances,2023,2023-05-24,N,Prediction; Screening; Polygenic Score; Fh; Uk Biobank,,,"<h4>Background</h4>People with monogenic familial hypercholesterolemia (FH) are at an increased risk of premature coronary heart disease and death. With a prevalence of 1:250, FH is relatively common; but currently there is no population screening strategy in place and most carriers are identified late in life, delaying timely and cost-effective interventions.<h4>Objectives</h4>The purpose of this study was to derive an algorithm to identify people with suspected monogenic FH for subsequent confirmatory genomic testing and cascade screening.<h4>Methods</h4>A least absolute shrinkage and selection operator logistic regression model was used to identify predictors that accurately identified people with FH in 139,779 unrelated participants of the UK Biobank. Candidate predictors included information on medical and family history, anthropometric measures, blood biomarkers, and a low-density lipoprotein cholesterol (LDL-C) polygenic score (PGS). Model derivation and evaluation were performed in independent training and testing data.<h4>Results</h4>A total of 488 FH variant carriers were identified using whole-exome sequencing of the <i>low-density lipoprotein receptor</i>, <i>apolipoprotein B, apolipoprotein E, proprotein convertase subtilisin/kexin type 9</i> genes. A 14-variable algorithm for FH was derived, with an area under the curve of 0.77 (95% CI: 0.71-0.83), where the top 5 most important variables included triglyceride, LDL-C, apolipoprotein A1 concentrations, self-reported statin use, and LDL-C PGS. Excluding the PGS as a candidate feature resulted in a 9-variable model with a comparable area under the curve: 0.76 (95% CI: 0.71-0.82). Both multivariable models (w/wo the PGS) outperformed screening-prioritization based on LDL-C adjusted for statin use.<h4>Conclusions</h4>Detecting individuals with FH can be improved by considering additional predictors. This would reduce the sequencing burden in a 2-stage population screening strategy for FH.",,doi:https://doi.org/10.1016/j.jacadv.2023.100333
 38838327,https://doi.org/10.2196/51323,Data-Driven Identification of Potentially Successful Intervention Implementations Using 5 Years of Opioid Prescribing Data: Retrospective Database Study.,"Hopcroft LE, Curtis HJ, Croker R, Pretis F, Inglesby P, Evans D, Bacon S, Goldacre B, Walker AJ, MacKenna B.",,JMIR public health and surveillance,2024,2024-06-05,Y,Identification; Opioid; intervention; General Practice; Primary Care; Opioid Analgesics; Electronic Health Records; Implementations; Implementation Science; Proof Of Concept; Data-driven; Data Science; Unbiased; Analysis Tool; Prescribing Data,,,"<h4>Background</h4>We have previously demonstrated that opioid prescribing increased by 127% between 1998 and 2016. New policies aimed at tackling this increasing trend have been recommended by public health bodies, and there is some evidence that progress is being made.<h4>Objective</h4>We sought to extend our previous work and develop a data-driven approach to identify general practices and clinical commissioning groups (CCGs) whose prescribing data suggest that interventions to reduce the prescribing of opioids may have been successfully implemented.<h4>Methods</h4>We analyzed 5 years of prescribing data (December 2014 to November 2019) for 3 opioid prescribing measures-total opioid prescribing as oral morphine equivalent per 1000 registered population, the number of high-dose opioids prescribed per 1000 registered population, and the number of high-dose opioids as a percentage of total opioids prescribed. Using a data-driven approach, we applied a modified version of our change detection Python library to identify reductions in these measures over time, which may be consistent with the successful implementation of an intervention to reduce opioid prescribing. This analysis was carried out for general practices and CCGs, and organizations were ranked according to the change in prescribing rate.<h4>Results</h4>We identified a reduction in total opioid prescribing in 94 (49.2%) out of 191 CCGs, with a median reduction of 15.1 (IQR 11.8-18.7; range 9.0-32.8) in total oral morphine equivalence per 1000 patients. We present data for the 3 CCGs and practices demonstrating the biggest reduction in opioid prescribing for each of the 3 opioid prescribing measures. We observed a 40% proportional drop (8.9% absolute reduction) in the regular prescribing of high-dose opioids (measured as a percentage of regular opioids) in the highest-ranked CCG (North Tyneside); a 99% drop in this same measure was found in several practices (44%-95% absolute reduction). Decile plots demonstrate that CCGs exhibiting large reductions in opioid prescribing do so via slow and gradual reductions over a long period of time (typically over a period of 2 years); in contrast, practices exhibiting large reductions do so rapidly over a much shorter period of time.<h4>Conclusions</h4>By applying 1 of our existing analysis tools to a national data set, we were able to identify rapid and maintained changes in opioid prescribing within practices and CCGs and rank organizations by the magnitude of reduction. Highly ranked organizations are candidates for further qualitative research into intervention design and implementation.",,doi:https://doi.org/10.2196/51323; doi:https://doi.org/10.2196/51323; html:https://europepmc.org/articles/PMC11187509
 PMC11198649,https://doi.org/,A Machine Learning Model to Aid Detection of Familial Hypercholesterolemia,"Gratton J, Futema M, Humphries S, Hingorani A, Finan C, Schmidt A.",,JACC. Advances,2023,2023-05-24,Y,Prediction; Screening; Polygenic Score; Fh; Uk Biobank,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11198649/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11198649/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC11198649; pdf:https://europepmc.org/articles/PMC11198649?pdf=render
-37745706,https://doi.org/10.3389/fendo.2023.1266557,"Editorial: Integrative multi-modal, multi-omics analytics for the better understanding of metabolic diseases.","Acharjee A, Agarwal P, Gkoutos GV.",,Frontiers in endocrinology,2023,2023-09-08,Y,Biomarker; Therapeutic; Diagnostic; Metabolic Disease; Omics,,,,,doi:https://doi.org/10.3389/fendo.2023.1266557; html:https://europepmc.org/articles/PMC10516571; pdf:https://europepmc.org/articles/PMC10516571?pdf=render
 35932242,https://doi.org/10.1093/ageing/afac176,"Annual risk of falls resulting in emergency department and hospital attendances for older people: an observational study of 781,081 individuals living in Wales (United Kingdom) including deprivation, frailty and dementia diagnoses between 2010 and 2020.","Hollinghurst R, Williams N, Pedrick-Case R, North L, Long S, Fry R, Hollinghurst J.",,Age and ageing,2022,2022-08-01,Y,Frailty; Dementia; Falls; Older People; Covid-19,,,"<h4>Background</h4>falls are common in older people, but associations between falls, dementia and frailty are relatively unknown. The impact of the COVID-19 pandemic on falls admissions has not been studied.<h4>Aim</h4>to investigate the impact of dementia, frailty, deprivation, previous falls and the differences between years for falls resulting in an emergency department (ED) or hospital admission.<h4>Study design</h4>longitudinal cross-sectional observational study.<h4>Setting</h4>older people (aged 65+) resident in Wales between 1 January 2010 and 31 December 2020.<h4>Methods</h4>we created a binary (yes/no) indicator for a fall resulting in an attendance to an ED, hospital or both, per person, per year. We analysed the outcomes using multilevel logistic and multinomial models.<h4>Results</h4>we analysed a total of 5,141,244 person years of data from 781,081 individuals. Fall admission rates were highest in 2012 (4.27%) and lowest in 2020 (4.27%). We found an increased odds ratio (OR [95% confidence interval]) of a fall admission for age (1.05 [1.05, 1.05] per year of age), people with dementia (2.03 [2.00, 2.06]) and people who had a previous fall (2.55 [2.51, 2.60]). Compared with fit individuals, those with frailty had ORs of 1.60 [1.58, 1.62], 2.24 [2.21, 2.28] and 2.94 [2.89, 3.00] for mild, moderate and severe frailty respectively. Reduced odds were observed for males (0.73 [0.73, 0.74]) and less deprived areas; most deprived compared with least OR 0.75 [0.74, 0.76].<h4>Conclusions</h4>falls prevention should be targeted to those at highest risk, and investigations into the reduction in admissions in 2020 is warranted.",,doi:https://doi.org/10.1093/ageing/afac176; doi:https://doi.org/10.1093/ageing/afac176; html:https://europepmc.org/articles/PMC9356534; pdf:https://europepmc.org/articles/PMC9356534?pdf=render
+37745706,https://doi.org/10.3389/fendo.2023.1266557,"Editorial: Integrative multi-modal, multi-omics analytics for the better understanding of metabolic diseases.","Acharjee A, Agarwal P, Gkoutos GV.",,Frontiers in endocrinology,2023,2023-09-08,Y,Biomarker; Therapeutic; Diagnostic; Metabolic Disease; Omics,,,,,doi:https://doi.org/10.3389/fendo.2023.1266557; html:https://europepmc.org/articles/PMC10516571; pdf:https://europepmc.org/articles/PMC10516571?pdf=render
 35079022,https://doi.org/10.1038/s41467-022-28157-3,Regional excess mortality during the 2020 COVID-19 pandemic in five European countries.,"Konstantinoudis G, Cameletti M, Gómez-Rubio V, Gómez IL, Pirani M, Baio G, Larrauri A, Riou J, Egger M, Vineis P, Blangiardo M.",,Nature communications,2022,2022-01-25,Y,,,,"The impact of the COVID-19 pandemic on excess mortality from all causes in 2020 varied across and within European countries. Using data for 2015-2019, we applied Bayesian spatio-temporal models to quantify the expected weekly deaths at the regional level had the pandemic not occurred in England, Greece, Italy, Spain, and Switzerland. With around 30%, Madrid, Castile-La Mancha, Castile-Leon (Spain) and Lombardia (Italy) were the regions with the highest excess mortality. In England, Greece and Switzerland, the regions most affected were Outer London and the West Midlands (England), Eastern, Western and Central Macedonia (Greece), and Ticino (Switzerland), with 15-20% excess mortality in 2020. Our study highlights the importance of the large transportation hubs for establishing community transmission in the first stages of the pandemic. Here, we show that acting promptly to limit transmission around these hubs is essential to prevent spread to other regions and countries.",,pdf:https://www.nature.com/articles/s41467-022-28157-3.pdf; doi:https://doi.org/10.1038/s41467-022-28157-3; html:https://europepmc.org/articles/PMC8789777; pdf:https://europepmc.org/articles/PMC8789777?pdf=render
 37781298,https://doi.org/10.3389/fcvm.2023.1141026,Radiomics analysis enhances the diagnostic performance of CMR stress perfusion: a proof-of-concept study using the Dan-NICAD dataset.,"Raisi-Estabragh Z, Martin-Isla C, Nissen L, Szabo L, Campello VM, Escalera S, Winther S, Bøttcher M, Lekadir K, Petersen SE.",,Frontiers in cardiovascular medicine,2023,2023-09-15,Y,Machine Learning (Ml); Radiomics; Cmr (Cardiovascular Magnetic Resonance); Stress Perfusion Cardiac Mri; Dan-nicad,,,"<h4>Objectives</h4>To assess the feasibility of extracting radiomics signal intensity based features from the myocardium using cardiovascular magnetic resonance (CMR) imaging stress perfusion sequences. Furthermore, to compare the diagnostic performance of radiomics models against standard-of-care qualitative visual assessment of stress perfusion images, with the ground truth stenosis label being defined by invasive Fractional Flow Reserve (FFR) and quantitative coronary angiography.<h4>Methods</h4>We used the Dan-NICAD 1 dataset, a multi-centre study with coronary computed tomography angiography, 1,5 T CMR stress perfusion, and invasive FFR available for a subset of 148 patients with suspected coronary artery disease. Image segmentation was performed by two independent readers. We used the Pyradiomics platform to extract radiomics first-order (<i>n</i> = 14) and texture (<i>n</i> = 75) features from the LV myocardium (basal, mid, apical) in rest and stress perfusion images.<h4>Results</h4>Overall, 92 patients (mean age 62 years, 56 men) were included in the study, 39 with positive FFR. We double-cross validated the model and, in each inner fold, we trained and validated a per territory model. The conventional analysis results reported sensitivity of 41% and specificity of 84%. Our final radiomics model demonstrated an improvement on these results with an average sensitivity of 53% and specificity of 86%.<h4>Conclusion</h4>In this proof-of-concept study from the Dan-NICAD dataset, we demonstrate the feasibility of radiomics analysis applied to CMR perfusion images with a suggestion of superior diagnostic performance of radiomics models over conventional visual analysis of perfusion images in picking up perfusion defects defined by invasive coronary angiography.",,doi:https://doi.org/10.3389/fcvm.2023.1141026; html:https://europepmc.org/articles/PMC10541220; pdf:https://europepmc.org/articles/PMC10541220?pdf=render
-39374974,https://doi.org/10.1136/bmj-2024-080528,Non-pharmaceutical interventions: evaluating challenges and priorities for future health shocks.,"Majeed A, Quint JK, Bhatt S, Davies F, Islam N.",,BMJ (Clinical research ed.),2024,2024-10-07,Y,,,,,,doi:https://doi.org/10.1136/bmj-2024-080528; html:https://europepmc.org/articles/PMC11450877
 31971603,https://doi.org/10.2340/00015555-3384,Psoriasis and Genetics.,"Dand N, Mahil SK, Capon F, Smith CH, Simpson MA, Barker JN.",,Acta dermato-venereologica,2020,2020-01-30,Y,Genetics; Psoriasis; Treatment outcome; Disease Progression; Precision Medicine,,,"Psoriasis is a common inflammatory skin disease caused by the interplay between multiple genetic and environmental risk factors. This review summarises recent progress in elucidating the genetic basis of psoriasis, particularly through large genome-wide association studies. We illustrate the power of genetic analyses for disease stratification. Psoriasis can be stratified by phenotype (common plaque versus rare pustular variants), or by outcome (prognosis, comorbidities, response to treatment); recent progress has been made in delineating the genetic contribution in each of these areas. We also highlight how genetic data can directly inform the development of effective psoriasis treatments.",,doi:https://doi.org/10.2340/00015555-3384; doi:https://doi.org/10.2340/00015555-3384; html:https://europepmc.org/articles/PMC9128944; pdf:https://europepmc.org/articles/PMC9128944?pdf=render
+39374974,https://doi.org/10.1136/bmj-2024-080528,Non-pharmaceutical interventions: evaluating challenges and priorities for future health shocks.,"Majeed A, Quint JK, Bhatt S, Davies F, Islam N.",,BMJ (Clinical research ed.),2024,2024-10-07,Y,,,,,,doi:https://doi.org/10.1136/bmj-2024-080528; html:https://europepmc.org/articles/PMC11450877
 38727134,https://doi.org/10.1002/epi4.12957,Hospital-acquired infections as a risk factor for post-traumatic epilepsy: A registry-based cohort study.,"Chen Z, Laing J, Li J, O'Brien TJ, Gabbe BJ, Semple BD.",,Epilepsia open,2024,2024-05-10,Y,Epilepsy; Sepsis; Bacterial; Meningitis; Seizure; Nosocomial,,,"<h4>Objective</h4>Hospital-acquired infections are a common complication for patients with moderate or severe traumatic brain injury (TBI), contributing to morbidity and mortality. As infection-mediated immune responses can predispose towards epilepsy, we hypothesized that post-injury hospital-acquired infections increase the risk of post-traumatic epilepsy (PTE).<h4>Methods</h4>A retrospective cohort study of adults with moderate to severe TBI was conducted using data from the Victorian State Trauma Registry in Australia. Infections were identified from the International Statistical Classification of Diseases and Related Health Problems 10th Revision-Australian Modification (ICD-10-AM) codes, and diagnosis of PTE was determined by the Glasgow Outcome Scale - Extended questionnaire regarding epileptic fits at 24 months follow-up.<h4>Results</h4>Of all TBI patients (n = 15 152), 24% had evidence of having had any type of infection, with the most common being pneumonia, urinary tract, and respiratory infections. Of those who responded to the PTE question at 24 months (n = 1361), 11% had developed PTE. Univariable analysis found that the incidence of PTE was higher in patients who had any type of infection compared to patients without an infection (p < 0.001). After adjustment for covariates associated with both development of PTE and risk of infection, multivariable analysis found a solid association between infection and PTE (adjusted RR = 1.59; 95% CI: 1.11-2.28; p = 0.011). Having any type of complicating infection acquired during admission was also associated with poor GOSE outcomes at subsequent follow-ups (adjusted OR = 0.20; 95% CI: 0.11-0.35, p < 0.001).<h4>Significance</h4>These findings suggest that hospital-acquired infections contribute to PTE development after TBI. Future investigation into infections as a modifiable target to reduce poor outcomes after TBI is warranted.<h4>Plain language summary</h4>Hospital-acquired infections are common in patients with traumatic brain injuries. A database study of adults with moderate or severe brain injuries in Australia examined whether these infections are associated with the development of epilepsy after a brain injury. 24% of patients had infections, with pneumonia and urinary tract infections being the most common. Of those surveyed 2 years after the injury, 11% developed post-traumatic epilepsy. Patients with infections had a significantly higher risk of epilepsy, even when accounting for other known risk factors, and infections were also linked to poor outcomes more broadly. The study suggests that preventing hospital-acquired infections could be a crucial target for improving outcomes after traumatic brain injuries.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/epi4.12957; doi:https://doi.org/10.1002/epi4.12957; html:https://europepmc.org/articles/PMC11296124; pdf:https://europepmc.org/articles/PMC11296124?pdf=render
 36933612,https://doi.org/10.1016/j.cct.2023.107162,Healthcare systems data in the context of clinical trials - A comparison of cardiovascular data from a clinical trial dataset with routinely collected data.,"Macnair A, Nankivell M, Murray ML, Rosen SD, Appleyard S, Sydes MR, Forcat S, Welland A, Clarke NW, Mangar S, Kynaston H, Kockelbergh R, Al-Hasso A, Deighan J, Marshall J, Parmar M, Langley RE, Gilbert DC.",,Contemporary clinical trials,2023,2023-03-16,N,Cardiovascular disease; prostate cancer; Clinical Trials; Healthcare Systems Data,,,"<h4>Background</h4>Routinely-collected healthcare systems data (HSD) are proposed to improve the efficiency of clinical trials. A comparison was undertaken between cardiovascular (CVS) data from a clinical trial database with two HSD resources.<h4>Methods</h4>Protocol-defined and clinically reviewed CVS events (heart failure (HF), acute coronary syndrome (ACS), thromboembolic stroke, venous and arterial thromboembolism) were identified within the trial data. Data (using pre-specified codes) was obtained from NHS Hospital Episode Statistics (HES) and National Institute for Cardiovascular Outcomes Research (NICOR) HF and myocardial ischaemia audits for trial participants recruited in England between 2010 and 2018 who had provided consent. The primary comparison was trial data versus HES inpatient (APC) main diagnosis (Box-1). Correlations are presented with descriptive statistics and Venn diagrams. Reasons for non-correlation were explored.<h4>Results</h4>From 1200 eligible participants, 71 protocol-defined clinically reviewed CVS events were recorded in the trial database. 45 resulted in a hospital admission and therefore could have been recorded by either HES APC/ NICOR. Of these, 27/45 (60%) were recorded by HES inpatient (Box-1) with an additional 30 potential events also identified. HF and ACS were potentially recorded in all 3 datasets; trial data recorded 18, HES APC 29 and NICOR 24 events respectively. 12/18 (67%) of the HF/ACS events in the trial dataset were recorded by NICOR.<h4>Conclusion</h4>Concordance between datasets was lower than anticipated and the HSD used could not straightforwardly replace current trial practices, nor directly identify protocol-defined CVS events. Further work is required to improve the quality of HSD and consider event definitions when designing clinical trials incorporating HSD.",,doi:https://doi.org/10.1016/j.cct.2023.107162; doi:https://doi.org/10.1016/j.cct.2023.107162
-35216844,https://doi.org/10.1016/j.vaccine.2022.02.056,Localising vaccination services: Qualitative insights on public health and minority group collaborations to co-deliver coronavirus vaccines.,"Kasstan B, Mounier-Jack S, Letley L, Gaskell KM, Roberts CH, Stone NRH, Lal S, Eggo RM, Marks M, Chantler T.",,Vaccine,2022,2022-02-17,Y,Qualitative Research; Ethnic Minorities; Coronavirus Vaccine; Localising Services; Public Health Collaboration,,,"Ethnic and religious minorities have been disproportionately affected by the SARS-CoV-2 pandemic and are less likely to accept coronavirus vaccinations. Orthodox (Haredi) Jewish neighbourhoods in England experienced high incidences of SARS-CoV-2 in 2020-21 and measles outbreaks (2018-19) due to suboptimal childhood vaccination coverage. The objective of our study was to explore how the coronavirus vaccination programme (CVP) was co-delivered between public health services and an Orthodox Jewish health organisation. Methods included 28 semi-structured interviews conducted virtually with public health professionals, community welfare and religious representatives, and household members. We examined CVP delivery from the perspectives of those involved in organising services and vaccine beneficiaries. Interview data was contextualised within debates of the CVP in Orthodox (Haredi) Jewish print and social media. Thematic analysis generated five considerations: i) Prior immunisation-related collaboration with public health services carved a role for Jewish health organisations to host and promote coronavirus vaccination sessions, distribute appointments, and administer vaccines ii) Public health services maintained responsibility for training, logistics, and maintaining vaccination records; iii) The localised approach to service delivery promoted vaccination in a minority with historically suboptimal levels of coverage; iv) Co-delivery promoted trust in the CVP, though a minority of participants maintained concerns around safety; v) Provision of CVP information and stakeholders' response to situated (context-specific) challenges and concerns. Drawing on this example of CVP co-delivery, we propose that a localised approach to delivering immunisation programmes could address service provision gaps in ways that involve trusted community organisations. Localisation of vaccination services can include communication or implementation strategies, but both approaches involve consideration of investment, engagement and coordination, which are not cost-neutral. Localising vaccination services in collaboration with welfare groups raises opportunities for the on-going CVP and other immunisation programmes, and constitutes an opportunity for ethnic and religious minorities to collaborate in safeguarding community health.",,doi:https://doi.org/10.1016/j.vaccine.2022.02.056; doi:https://doi.org/10.1016/j.vaccine.2022.02.056; html:https://europepmc.org/articles/PMC8849863
 38286672,https://doi.org/10.1136/bmjopen-2023-073582,Improving our understanding of the social determinants of mental health: a data linkage study of mental health records and the 2011 UK census.,"Cybulski L, Chilman N, Jewell A, Dewey M, Hildersley R, Morgan C, Huck R, Hotopf M, Stewart R, Pritchard M, Wuerth M, Das-Munshi J.",,BMJ open,2024,2024-01-29,Y,Psychiatry; Mental health; Schizophrenia & Psychotic Disorders,,,"<h4>Objectives</h4>To address the lack of individual-level socioeconomic information in electronic healthcare records, we linked the 2011 census of England and Wales to patient records from a large mental healthcare provider. This paper describes the linkage process and methods for mitigating bias due to non-matching.<h4>Setting</h4>South London and Maudsley NHS Foundation Trust (SLaM), a mental healthcare provider in Southeast London.<h4>Design</h4>Clinical records from SLaM were supplied to the Office of National Statistics for linkage to the census through a deterministic matching algorithm. We examined clinical (International Classification of Disease-10 diagnosis, history of hospitalisation, frequency of service contact) and socio-demographic (age, gender, ethnicity, deprivation) information recorded in Clinical Record Interactive Search (CRIS) as predictors of linkage success with the 2011 census. To assess and adjust for potential biases caused by non-matching, we evaluated inverse probability weighting for mortality associations.<h4>Participants</h4>Individuals of all ages in contact with SLaM up until December 2019 (N=459 374).<h4>Outcome measures</h4>Likelihood of mental health records' linkage to census.<h4>Results</h4>220 864 (50.4%) records from CRIS linked to the 2011 census. Young adults (prevalence ratio (PR) 0.80, 95% CI 0.80 to 0.81), individuals living in more deprived areas (PR 0.78, 95% CI 0.78 to 0.79) and minority ethnic groups (eg, Black African, PR 0.67, 0.66 to 0.68) were less likely to match to census. After implementing inverse probability weighting, we observed little change in the strength of association between clinical/demographic characteristics and mortality (eg, presence of any psychiatric disorder: unweighted PR 2.66, 95% CI 2.52 to 2.80; weighted PR 2.70, 95% CI 2.56 to 2.84).<h4>Conclusions</h4>Lower response rates to the 2011 census among people with psychiatric disorders may have contributed to lower match rates, a potential concern as the census informs service planning and allocation of resources. Due to its size and unique characteristics, the linked data set will enable novel investigations into the relationship between socioeconomic factors and psychiatric disorders.",,doi:https://doi.org/10.1136/bmjopen-2023-073582; html:https://europepmc.org/articles/PMC10826590; pdf:https://europepmc.org/articles/PMC10826590?pdf=render
+35216844,https://doi.org/10.1016/j.vaccine.2022.02.056,Localising vaccination services: Qualitative insights on public health and minority group collaborations to co-deliver coronavirus vaccines.,"Kasstan B, Mounier-Jack S, Letley L, Gaskell KM, Roberts CH, Stone NRH, Lal S, Eggo RM, Marks M, Chantler T.",,Vaccine,2022,2022-02-17,Y,Qualitative Research; Ethnic Minorities; Coronavirus Vaccine; Localising Services; Public Health Collaboration,,,"Ethnic and religious minorities have been disproportionately affected by the SARS-CoV-2 pandemic and are less likely to accept coronavirus vaccinations. Orthodox (Haredi) Jewish neighbourhoods in England experienced high incidences of SARS-CoV-2 in 2020-21 and measles outbreaks (2018-19) due to suboptimal childhood vaccination coverage. The objective of our study was to explore how the coronavirus vaccination programme (CVP) was co-delivered between public health services and an Orthodox Jewish health organisation. Methods included 28 semi-structured interviews conducted virtually with public health professionals, community welfare and religious representatives, and household members. We examined CVP delivery from the perspectives of those involved in organising services and vaccine beneficiaries. Interview data was contextualised within debates of the CVP in Orthodox (Haredi) Jewish print and social media. Thematic analysis generated five considerations: i) Prior immunisation-related collaboration with public health services carved a role for Jewish health organisations to host and promote coronavirus vaccination sessions, distribute appointments, and administer vaccines ii) Public health services maintained responsibility for training, logistics, and maintaining vaccination records; iii) The localised approach to service delivery promoted vaccination in a minority with historically suboptimal levels of coverage; iv) Co-delivery promoted trust in the CVP, though a minority of participants maintained concerns around safety; v) Provision of CVP information and stakeholders' response to situated (context-specific) challenges and concerns. Drawing on this example of CVP co-delivery, we propose that a localised approach to delivering immunisation programmes could address service provision gaps in ways that involve trusted community organisations. Localisation of vaccination services can include communication or implementation strategies, but both approaches involve consideration of investment, engagement and coordination, which are not cost-neutral. Localising vaccination services in collaboration with welfare groups raises opportunities for the on-going CVP and other immunisation programmes, and constitutes an opportunity for ethnic and religious minorities to collaborate in safeguarding community health.",,doi:https://doi.org/10.1016/j.vaccine.2022.02.056; doi:https://doi.org/10.1016/j.vaccine.2022.02.056; html:https://europepmc.org/articles/PMC8849863
 35074819,https://doi.org/10.1136/bmjopen-2021-054414,Mapping multimorbidity in individuals with schizophrenia and bipolar disorders: evidence from the South London and Maudsley NHS Foundation Trust Biomedical Research Centre (SLAM BRC) case register.,"Bendayan R, Kraljevic Z, Shaari S, Das-Munshi J, Leipold L, Chaturvedi J, Mirza L, Aldelemi S, Searle T, Chance N, Mascio A, Skiada N, Wang T, Roberts A, Stewart R, Bean D, Dobson R.",,BMJ open,2022,2022-01-24,Y,Psychiatry; Mental health; epidemiology; Public Health; Health Informatics,,,"<h4>Objectives</h4>The first aim of this study was to design and develop a valid and replicable strategy to extract physical health conditions from clinical notes which are common in mental health services. Then, we examined the prevalence of these conditions in individuals with severe mental illness (SMI) and compared their individual and combined prevalence in individuals with bipolar (BD) and schizophrenia spectrum disorders (SSD).<h4>Design</h4>Observational study.<h4>Setting</h4>Secondary mental healthcare services from South London PARTICIPANTS: Our maximal sample comprised 17 500 individuals aged 15 years or older who had received a primary or secondary SMI diagnosis (International Classification of Diseases, 10th edition, F20-31) between 2007 and 2018.<h4>Measures</h4>We designed and implemented a data extraction strategy for 21 common physical comorbidities using a natural language processing pipeline, MedCAT. Associations were investigated with sex, age at SMI diagnosis, ethnicity and social deprivation for the whole cohort and the BD and SSD subgroups. Linear regression models were used to examine associations with disability measured by the Health of Nations Outcome Scale.<h4>Results</h4>Physical health data were extracted, achieving precision rates (F1) above 0.90 for all conditions. The 10 most prevalent conditions were diabetes, hypertension, asthma, arthritis, epilepsy, cerebrovascular accident, eczema, migraine, ischaemic heart disease and chronic obstructive pulmonary disease. The most prevalent combination in this population included diabetes, hypertension and asthma, regardless of their SMI diagnoses.<h4>Conclusions</h4>Our data extraction strategy was found to be adequate to extract physical health data from clinical notes, which is essential for future multimorbidity research using text records. We found that around 40% of our cohort had multimorbidity from which 20% had complex multimorbidity (two or more physical conditions besides SMI). Sex, age, ethnicity and social deprivation were found to be key to understand their heterogeneity and their differential contribution to disability levels in this population. These outputs have direct implications for researchers and clinicians.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/1/e054414.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-054414; html:https://europepmc.org/articles/PMC8788233; pdf:https://europepmc.org/articles/PMC8788233?pdf=render
 37190903,https://doi.org/10.1002/ijc.34548,Cancer incidence and mortality in 23 000 patients with type 1 diabetes in the UK: Long-term follow-up.,"Swerdlow AJ, Jones ME, Slater SD, Burden ACF, Botha JL, Waugh NR, Morris AD, Gatling W, Gillespie KM, Patterson CC, Schoemaker MJ.",,International journal of cancer,2023,2023-05-15,Y,Cancer; type 1 diabetes; Cohort,,,"Type 2 diabetes is associated with raised risk of several cancers, but for type 1 diabetes risk data are fewer and inconsistent We assembled a cohort of 23 473 UK patients with insulin-treated diabetes diagnosed at ages <30, almost all of whom will have had type 1 diabetes, and for comparison 5058 diagnosed at ages 30 to 49, of whom we estimate two-thirds will have had type 2, and followed them for an average of 30 years for cancer incidence and mortality compared with general population rates. Patients aged <30 at diabetes diagnosis had significantly raised risks only for ovarian (standardised incidence ratio = 1.58; 95% confidence interval 1.16-2.11; P < .01) and vulval (3.55; 1.94-5.96; P < .001) cancers, with greatest risk when diabetes was diagnosed at ages 10-14. Risks of cancer overall (0.89; 0.84-0.95; P < .001) and sites including lung and larynx were significantly diminished. Patients diagnosed with diabetes at ages 30 to 49 had significantly raised risks of liver (1.76;1.08-2.72) and kidney (1.46;1.03-2.00) cancers, and reduced risk of cancer overall (0.89; 0.84-0.95). The raised ovarian and vulval cancer risks in patients with type 1 diabetes, especially with diabetes diagnosed around pubertal ages, suggest possible susceptibility of these organs at puberty to metabolic disruption at diabetes onset. Reduced risk of cancer overall, particularly smoking and alcohol-related sites, might reflect adoption of a healthy lifestyle.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ijc.34548; doi:https://doi.org/10.1002/ijc.34548; html:https://europepmc.org/articles/PMC10952206; pdf:https://europepmc.org/articles/PMC10952206?pdf=render
 35813280,https://doi.org/10.1016/s2666-7568(22)00118-0,Antibody and cellular immune responses following dual COVID-19 vaccination within infection-naive residents of long-term care facilities: an observational cohort study.,"Tut G, Lancaster T, Sylla P, Butler MS, Kaur N, Spalkova E, Bentley C, Amin U, Jadir A, Hulme S, Ayodele M, Bone D, Tut E, Bruton R, Krutikov M, Giddings R, Shrotri M, Azmi B, Fuller C, Baynton V, Irwin-Singer A, Hayward A, Copas A, Shallcross L, Moss P.",,The lancet. Healthy longevity,2022,2022-07-04,Y,,,,"<h4>Background</h4>Older age and frailty are risk factors for poor clinical outcomes following SARS-CoV-2 infection. As such, COVID-19 vaccination has been prioritised for individuals with these factors, but there is concern that immune responses might be impaired due to age-related immune dysregulation and comorbidity. We aimed to study humoral and cellular responses to COVID-19 vaccines in residents of long-term care facilities (LTCFs).<h4>Methods</h4>In this observational cohort study, we assessed antibody and cellular immune responses following COVID-19 vaccination in members of staff and residents at 74 LTCFs across the UK. Staff and residents were eligible for inclusion if it was possible to link them to a pseudo-identifier in the COVID-19 datastore, if they had received two vaccine doses, and if they had given a blood sample 6 days after vaccination at the earliest. There were no comorbidity exclusion criteria. Participants were stratified by age (<65 years or ≥65 years) and infection status (previous SARS-CoV-2 infection [infection-primed group] or SARS-CoV-2 naive [infection-naive group]). Anticoagulated edetic acid (EDTA) blood samples were assessed and humoral and cellular responses were quantified.<h4>Findings</h4>Between Dec 11, 2020, and June 27, 2021, blood samples were taken from 220 people younger than 65 years (median age 51 years [IQR 39-61]; 103 [47%] had previously had a SARS-CoV-2 infection) and 268 people aged 65 years or older of LTCFs (median age 87 years [80-92]; 144 [43%] had a previous SARS-CoV-2 infection). Samples were taken a median of 82 days (IQR 72-100) after the second vaccination. Antibody responses following dual vaccination were strong and equivalent between participants younger then 65 years and those aged 65 years and older in the infection-primed group (median 125 285 Au/mL [1128 BAU/mL] for <65 year olds <i>vs</i> 157 979 Au/mL [1423 BAU/mL] for ≥65 year olds; p=0·47). The antibody response was reduced by 2·4-times (467 BAU/mL; p≤0·0001) in infection-naive people younger than 65 years and 8·1-times (174 BAU/mL; p≤0·0001) in infection-naive residents compared with their infection-primed counterparts. Antibody response was 2·6-times lower in infection-naive residents than in infection-naive people younger than 65 years (p=0·0006). Impaired neutralisation of delta (1.617.2) variant spike binding was also apparent in infection-naive people younger than 65 years and in those aged 65 years and older. Spike-specific T-cell responses were also significantly enhanced in the infection-primed group. Infection-naive people aged 65 years and older (203 SFU per million [IQR 89-374]) had a 52% lower T-cell response compared with infection-naive people younger than 65 years (85 SFU per million [30-206]; p≤0·0001). Post-vaccine spike-specific CD4 T-cell responses displayed single or dual production of IFN-γ and IL-2 were similar across infection status groups, whereas the infection-primed group had an extended functional profile with TNFα and CXCL10 production.<h4>Interpretation</h4>These data reveal suboptimal post-vaccine immune responses within infection-naive residents of LTCFs, and they suggest the need for optimisation of immune protection through the use of booster vaccination.<h4>Funding</h4>UK Government Department of Health and Social Care.",,pdf:http://pure-oai.bham.ac.uk/ws/files/173553190/1_s2.0_S2666756822001180_main.pdf; doi:https://doi.org/10.1016/S2666-7568(22)00118-0; html:https://europepmc.org/articles/PMC9252532; pdf:https://europepmc.org/articles/PMC9252532?pdf=render
@@ -924,40 +925,40 @@ PMC11198649,https://doi.org/,A Machine Learning Model to Aid Detection of Fami
 37978887,https://doi.org/10.1093/eurheartj/ehad748,Adapting cardiovascular risk prediction models to different populations: the need for recalibration.,"Pennells L, Kaptoge S, Di Angelantonio E.",,European heart journal,2024,2024-01-01,N,,,,,,pdf:https://academic.oup.com/eurheartj/advance-article-pdf/doi/10.1093/eurheartj/ehad748/53515704/ehad748.pdf; doi:https://doi.org/10.1093/eurheartj/ehad748
 35685390,https://doi.org/10.1016/s2666-7568(22)00072-1,"Modifiable traits, healthy behaviours, and leukocyte telomere length: a population-based study in UK Biobank.","Bountziouka V, Musicha C, Allara E, Kaptoge S, Wang Q, Angelantonio ED, Butterworth AS, Thompson JR, Danesh JN, Wood AM, Nelson CP, Codd V, Samani NJ.",,The lancet. Healthy longevity,2022,2022-05-01,Y,,,,"<h4>Background</h4>Telomere length is associated with risk of several age-related diseases and cancers. We aimed to investigate the extent to which telomere length might be modifiable through lifestyle and behaviour, and whether such modification has any clinical consequences.<h4>Methods</h4>In this population-based study, we included participants from UK Biobank who had leukocyte telomere length (LTL) measurement, ethnicity, and white blood cell count data. We investigated associations of LTL with 117 potentially modifiable traits, as well as two indices of healthy behaviours incorporating between them smoking, physical activity, diet, maintenance of a healthy bodyweight, and alcohol intake, using both available and imputed data. To help interpretation, associations were summarised as the number of equivalent years of age-related change in LTL by dividing the trait β coefficients with the age β coefficient. We used mendelian randomisation to test causality of selected associations. We investigated whether the associations of LTL with 22 diseases were modified by the number of healthy behaviours and the extent to which the associations of more healthy behaviours with greater life expectancy and lower risk of coronary artery disease might be mediated through LTL.<h4>Findings</h4>422 797 participants were available for the analysis (227 620 [53·8%] were women and 400 036 [94·6%] were White). 71 traits showed significant (p<4·27 × 10<sup>-4</sup>) associations with LTL but most were modest, equivalent to less than 1 year of age-related change in LTL. In multivariable analyses of 17 traits with stronger associations (equivalent to ≥2 years of age-related change in LTL), oily fish intake, educational attainment, and general health status retained a significant association of this magnitude, with walking pace and current smoking being additionally significant at this level of association in the imputed models. Mendelian randomisation analysis suggested that educational attainment and smoking behaviour causally affect LTL. Both indices of healthy behaviour were positively and linearly associated with LTL, with those with the most healthy behaviours having longer LTL equivalent to about 3·5 years of age-related change in LTL than those with the least heathy behaviours (p<0·001). However, healthy behaviours explained less than 0·2% of the total variation in LTL and did not significantly modify the association of LTL with risk of any of the diseases studied. Neither the association of more healthy behaviours on greater life expectancy or lower risk of coronary artery disease were substantially mediated through LTL.<h4>Interpretation</h4>Although several potentially modifiable traits and healthy behaviours have a quantifiable association with LTL, at least some of which are likely to be causal, these effects are not of a sufficient magnitude to substantially alter the association between LTL and various diseases or life expectancy. Attempts to change telomere length through lifestyle or behavioural changes might not confer substantial clinical benefit.<h4>Funding</h4>UK Medical Research Council, UK Biotechnology and Biological Sciences Research Council, and British Heart Foundation.",,pdf:http://www.thelancet.com/article/S2666756822000721/pdf; doi:https://doi.org/10.1016/S2666-7568(22)00072-1; html:https://europepmc.org/articles/PMC9068584
 35996157,https://doi.org/10.1186/s13059-022-02745-4,Comparative transcriptome in large-scale human and cattle populations.,"Yao Y, Liu S, Xia C, Gao Y, Pan Z, Canela-Xandri O, Khamseh A, Rawlik K, Wang S, Li B, Zhang Y, Pairo-Castineira E, D'Mellow K, Li X, Yan Z, Li CJ, Yu Y, Zhang S, Ma L, Cole JB, Ross PJ, Zhou H, Haley C, Liu GE, Fang L, Tenesa A.",,Genome biology,2022,2022-08-22,Y,Rna-seq; Gene Co-expression; Comparative Transcriptome; Inter-individual Variability; Heritability Enrichment,,,"<h4>Background</h4>Cross-species comparison of transcriptomes is important for elucidating evolutionary molecular mechanisms underpinning phenotypic variation between and within species, yet to date it has been essentially limited to model organisms with relatively small sample sizes.<h4>Results</h4>Here, we systematically analyze and compare 10,830 and 4866 publicly available RNA-seq samples in humans and cattle, respectively, representing 20 common tissues. Focusing on 17,315 orthologous genes, we demonstrate that mean/median gene expression, inter-individual variation of expression, expression quantitative trait loci, and gene co-expression networks are generally conserved between humans and cattle. By examining large-scale genome-wide association studies for 46 human traits (average n = 327,973) and 45 cattle traits (average n = 24,635), we reveal that the heritability of complex traits in both species is significantly more enriched in transcriptionally conserved than diverged genes across tissues.<h4>Conclusions</h4>In summary, our study provides a comprehensive comparison of transcriptomes between humans and cattle, which might help decipher the genetic and evolutionary basis of complex traits in both species.",,pdf:https://genomebiology.biomedcentral.com/counter/pdf/10.1186/s13059-022-02745-4; doi:https://doi.org/10.1186/s13059-022-02745-4; html:https://europepmc.org/articles/PMC9394047; pdf:https://europepmc.org/articles/PMC9394047?pdf=render
-35580876,https://doi.org/10.1136/bmj-2021-069704,Long term impact of prophylactic antibiotic use before incision versus after cord clamping on children born by caesarean section: longitudinal study of UK electronic health records.,"Šumilo D, Nirantharakumar K, Willis BH, Rudge GM, Martin J, Gokhale K, Thayakaran R, Adderley NJ, Chandan JS, Okoth K, Harris IM, Hewston R, Skrybant M, Deeks JJ, Brocklehurst P.",,BMJ (Clinical research ed.),2022,2022-05-17,Y,,,,"<h4>Objective</h4>To investigate the impact on child health up to age 5 years of a policy to use antibiotic prophylaxis for caesarean section before incision compared with after cord clamping.<h4>Design</h4>Observational controlled interrupted time series study.<h4>Setting</h4>UK primary and secondary care.<h4>Participants</h4>515 945 children born in 2006-18 with linked maternal records and registered with general practices contributing to two UK primary care databases (The Health Improvement Network and Clinical Practice Research Datalink), and 7 147 884 children with linked maternal records in the Hospital Episode Statistics database covering England, of which 3 945 351 were linked to hospitals that reported the year of policy change to administer prophylactic antibiotics for caesarean section before incision rather than after cord clamping.<h4>Intervention</h4>Fetal exposure to antibiotics shortly before birth (using pre-incision antibiotic policy as proxy) compared with no exposure.<h4>Main outcome measures</h4>The primary outcomes were incidence rate ratios of asthma and eczema in children born by caesarean section when pre-incision prophylactic antibiotics were recommended compared with those born when antibiotics were administered post-cord clamping, adjusted for temporal changes in the incidence rates in children born vaginally.<h4>Results</h4>Prophylactic antibiotics administered before incision for caesarean section compared with after cord clamping were not associated with a significantly higher risk of asthma (incidence rate ratio 0.91, 95% confidence interval 0.78 to 1.05) or eczema (0.98, 0.94 to 1.03), including asthma and eczema resulting in hospital admission (1.05, 0.99 to 1.11 and 0.96, 0.71 to 1.29, respectively), up to age 5 years.<h4>Conclusions</h4>This study found no evidence of an association between pre-incision prophylactic antibiotic use and risk of asthma and eczema in early childhood in children born by caesarean section.",,pdf:https://www.bmj.com/content/bmj/377/bmj-2021-069704.full.pdf; doi:https://doi.org/10.1136/bmj-2021-069704; html:https://europepmc.org/articles/PMC9112858
 33436761,https://doi.org/10.1038/s41598-020-79964-x,The overlap of genetic susceptibility to schizophrenia and cardiometabolic disease can be used to identify metabolically different groups of individuals.,"Strawbridge RJ, Johnston KJA, Bailey MES, Baldassarre D, Cullen B, Eriksson P, deFaire U, Ferguson A, Gigante B, Giral P, Graham N, Hamsten A, Humphries SE, Kurl S, Lyall DM, Lyall LM, Pell JP, Pirro M, Savonen K, Smit AJ, Tremoli E, Tomainen TP, Veglia F, Ward J, Sennblad B, Smith DJ.",,Scientific reports,2021,2021-01-12,Y,,,,"Understanding why individuals with severe mental illness (Schizophrenia, Bipolar Disorder and Major Depressive Disorder) have increased risk of cardiometabolic disease (including obesity, type 2 diabetes and cardiovascular disease), and identifying those at highest risk of cardiometabolic disease are important priority areas for researchers. For individuals with European ancestry we explored whether genetic variation could identify sub-groups with different metabolic profiles. Loci associated with schizophrenia, bipolar disorder and major depressive disorder from previous genome-wide association studies and loci that were also implicated in cardiometabolic processes and diseases were selected. In the IMPROVE study (a high cardiovascular risk sample) and UK Biobank (general population sample) multidimensional scaling was applied to genetic variants implicated in both psychiatric and cardiometabolic disorders. Visual inspection of the resulting plots used to identify distinct clusters. Differences between these clusters were assessed using chi-squared and Kruskall-Wallis tests. In IMPROVE, genetic loci associated with both schizophrenia and cardiometabolic disease (but not bipolar disorder or major depressive disorder) identified three groups of individuals with distinct metabolic profiles. This grouping was replicated within UK Biobank, with somewhat less distinction between metabolic profiles. This work focused on individuals of European ancestry and is unlikely to apply to more genetically diverse populations. Overall, this study provides proof of concept that common biology underlying mental and physical illness may help to stratify subsets of individuals with different cardiometabolic profiles.",,pdf:https://www.nature.com/articles/s41598-020-79964-x.pdf; doi:https://doi.org/10.1038/s41598-020-79964-x; html:https://europepmc.org/articles/PMC7804422; pdf:https://europepmc.org/articles/PMC7804422?pdf=render
+35580876,https://doi.org/10.1136/bmj-2021-069704,Long term impact of prophylactic antibiotic use before incision versus after cord clamping on children born by caesarean section: longitudinal study of UK electronic health records.,"Šumilo D, Nirantharakumar K, Willis BH, Rudge GM, Martin J, Gokhale K, Thayakaran R, Adderley NJ, Chandan JS, Okoth K, Harris IM, Hewston R, Skrybant M, Deeks JJ, Brocklehurst P.",,BMJ (Clinical research ed.),2022,2022-05-17,Y,,,,"<h4>Objective</h4>To investigate the impact on child health up to age 5 years of a policy to use antibiotic prophylaxis for caesarean section before incision compared with after cord clamping.<h4>Design</h4>Observational controlled interrupted time series study.<h4>Setting</h4>UK primary and secondary care.<h4>Participants</h4>515 945 children born in 2006-18 with linked maternal records and registered with general practices contributing to two UK primary care databases (The Health Improvement Network and Clinical Practice Research Datalink), and 7 147 884 children with linked maternal records in the Hospital Episode Statistics database covering England, of which 3 945 351 were linked to hospitals that reported the year of policy change to administer prophylactic antibiotics for caesarean section before incision rather than after cord clamping.<h4>Intervention</h4>Fetal exposure to antibiotics shortly before birth (using pre-incision antibiotic policy as proxy) compared with no exposure.<h4>Main outcome measures</h4>The primary outcomes were incidence rate ratios of asthma and eczema in children born by caesarean section when pre-incision prophylactic antibiotics were recommended compared with those born when antibiotics were administered post-cord clamping, adjusted for temporal changes in the incidence rates in children born vaginally.<h4>Results</h4>Prophylactic antibiotics administered before incision for caesarean section compared with after cord clamping were not associated with a significantly higher risk of asthma (incidence rate ratio 0.91, 95% confidence interval 0.78 to 1.05) or eczema (0.98, 0.94 to 1.03), including asthma and eczema resulting in hospital admission (1.05, 0.99 to 1.11 and 0.96, 0.71 to 1.29, respectively), up to age 5 years.<h4>Conclusions</h4>This study found no evidence of an association between pre-incision prophylactic antibiotic use and risk of asthma and eczema in early childhood in children born by caesarean section.",,pdf:https://www.bmj.com/content/bmj/377/bmj-2021-069704.full.pdf; doi:https://doi.org/10.1136/bmj-2021-069704; html:https://europepmc.org/articles/PMC9112858
 33711543,https://doi.org/10.1016/j.jbi.2021.103728,Explainable automated coding of clinical notes using hierarchical label-wise attention networks and label embedding initialisation.,"Dong H, Suárez-Paniagua V, Whiteley W, Wu H.",,Journal of biomedical informatics,2021,2021-03-09,N,Natural Language Processing; Multi-label Classification; Deep Learning; Attention Mechanisms; Automated Medical Coding; Explainability; Label Correlation,,,"<h4>Background</h4>Diagnostic or procedural coding of clinical notes aims to derive a coded summary of disease-related information about patients. Such coding is usually done manually in hospitals but could potentially be automated to improve the efficiency and accuracy of medical coding. Recent studies on deep learning for automated medical coding achieved promising performances. However, the explainability of these models is usually poor, preventing them to be used confidently in supporting clinical practice. Another limitation is that these models mostly assume independence among labels, ignoring the complex correlations among medical codes which can potentially be exploited to improve the performance.<h4>Methods</h4>To address the issues of model explainability and label correlations, we propose a Hierarchical Label-wise Attention Network (HLAN), which aimed to interpret the model by quantifying importance (as attention weights) of words and sentences related to each of the labels. Secondly, we propose to enhance the major deep learning models with a label embedding (LE) initialisation approach, which learns a dense, continuous vector representation and then injects the representation into the final layers and the label-wise attention layers in the models. We evaluated the methods using three settings on the MIMIC-III discharge summaries: full codes, top-50 codes, and the UK NHS (National Health Service) COVID-19 (Coronavirus disease 2019) shielding codes. Experiments were conducted to compare the HLAN model and label embedding initialisation to the state-of-the-art neural network based methods, including variants of Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNNs).<h4>Results</h4>HLAN achieved the best Micro-level AUC and F<sub>1</sub> on the top-50 code prediction, 91.9% and 64.1%, respectively; and comparable results on the NHS COVID-19 shielding code prediction to other models: around 97% Micro-level AUC. More importantly, in the analysis of model explanations, by highlighting the most salient words and sentences for each label, HLAN showed more meaningful and comprehensive model interpretation compared to the CNN-based models and its downgraded baselines, HAN and HA-GRU. Label embedding (LE) initialisation significantly boosted the previous state-of-the-art model, CNN with attention mechanisms, on the full code prediction to 52.5% Micro-level F<sub>1</sub>. The analysis of the layers initialised with label embeddings further explains the effect of this initialisation approach. The source code of the implementation and the results are openly available at https://github.com/acadTags/Explainable-Automated-Medical-Coding.<h4>Conclusion</h4>We draw the conclusion from the evaluation results and analyses. First, with hierarchical label-wise attention mechanisms, HLAN can provide better or comparable results for automated coding to the state-of-the-art, CNN-based models. Second, HLAN can provide more comprehensive explanations for each label by highlighting key words and sentences in the discharge summaries, compared to the n-grams in the CNN-based models and the downgraded baselines, HAN and HA-GRU. Third, the performance of deep learning based multi-label classification for automated coding can be consistently boosted by initialising label embeddings that captures the correlations among labels. We further discuss the advantages and drawbacks of the overall method regarding its potential to be deployed to a hospital and suggest areas for future studies.",,doi:https://doi.org/10.1016/j.jbi.2021.103728; doi:https://doi.org/10.1016/j.jbi.2021.103728
-35802764,https://doi.org/10.7189/jogh.12.05025,COVID-19 vaccine effectiveness against symptomatic SARS-CoV-2 infection and severe COVID-19 outcomes from Delta AY.4.2: Cohort and test-negative study of 5.4 million individuals in Scotland.,"Kerr S, Vasileiou E, Robertson C, Sheikh A.",,Journal of global health,2022,2022-07-09,Y,,,,"<h4>Background</h4>In July 2021, a new variant of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in the Delta lineage was detected in the United Kingdom (UK), named AY.4.2 or ""Delta plus"". By October 2021, the AY.4.2 variant accounted for approximately 10-11% of cases in the UK. AY.4.2 was designated as a variant under investigation by the UK Health and Security Agency on 20 October 2021. This study aimed to investigate vaccine effectiveness (VE) against symptomatic COVID-19 (Coronavirus disease 2019) infection and COVID-19 hospitalisation/death for the AY.4.2 variant.<h4>Methods</h4>We used the Scotland-wide Early Pandemic Evaluation and Enhanced Surveillance (EAVE-II) platform to estimate the VE of the ChAdOx1, BNT162b2, and mRNA-1273 vaccines against symptomatic infection and severe COVID-19 outcomes in adults. The study was conducted from June 8 to October 25, 2021. We used a test-negative design (TND) to estimate VE against reverse transcriptase polymerase chain reaction (RT-PCR) confirmed symptomatic SARS-CoV-2 infection while adjusting for sex, socioeconomic status, number of coexisting conditions, and splines in time and age. We also performed a cohort study using a Cox proportional hazards model to estimate VE against a composite outcome of COVID-19 hospital admission or death, with the same adjustments.<h4>Results</h4>We found an overall VE against symptomatic SARS-CoV-2 infection due to AY.4.2 of 73% (95% confidence interval (CI) = 62-81) for >14 days post-second vaccine dose. Good protection against AY.4.2 symptomatic infection was observed for BNT162b2, ChAdOx1, and mRNA-1273. In unvaccinated individuals, the hazard ratio (HR) for COVID-19 hospital admission or death from AY.4.2 among community detected cases was 1.77 (95% CI = 1.02-3.07) relative to unvaccinated individuals who were infected with Delta, after adjusting for multiple potential confounders. VE against AY.4.2 COVID-19 admissions or deaths was 87% (95% CI = 74-93) >28 days post-second vaccination relative to unvaccinated.<h4>Conclusions</h4>We found that AY.4.2 was associated with an increased risk of COVID-19 hospitalisations or deaths in unvaccinated individuals compared with Delta and that vaccination provided substantial protection against symptomatic SARS-CoV-2 and severe COVID-19 outcomes following Delta AY.4.2 infection. High levels of vaccine uptake and protection offered by existing vaccines, as well as the rapid emergence of the Omicron variant may have contributed to the AY.4.2 variant never progressing to a variant of concern.",,pdf:https://jogh.org/wp-content/uploads/2022/07/jogh-12-05025.pdf; doi:https://doi.org/10.7189/jogh.12.05025; html:https://europepmc.org/articles/PMC9269984; pdf:https://europepmc.org/articles/PMC9269984?pdf=render
 34044910,https://doi.org/10.1016/bs.acc.2020.08.002,Translational biomarkers in the era of precision medicine.,"Bravo-Merodio L, Acharjee A, Russ D, Bisht V, Williams JA, Tsaprouni LG, Gkoutos GV.",,Advances in clinical chemistry,2021,2020-10-03,N,Artificial intelligence; Clinical Trials; Omics; Big Data; Translational Biomarkers,,,"In this chapter we discuss the past, present and future of clinical biomarker development. We explore the advent of new technologies, paving the way in which health, medicine and disease is understood. This review includes the identification of physicochemical assays, current regulations, the development and reproducibility of clinical trials, as well as, the revolution of omics technologies and state-of-the-art integration and analysis approaches.",,doi:https://doi.org/10.1016/bs.acc.2020.08.002
+35802764,https://doi.org/10.7189/jogh.12.05025,COVID-19 vaccine effectiveness against symptomatic SARS-CoV-2 infection and severe COVID-19 outcomes from Delta AY.4.2: Cohort and test-negative study of 5.4 million individuals in Scotland.,"Kerr S, Vasileiou E, Robertson C, Sheikh A.",,Journal of global health,2022,2022-07-09,Y,,,,"<h4>Background</h4>In July 2021, a new variant of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in the Delta lineage was detected in the United Kingdom (UK), named AY.4.2 or ""Delta plus"". By October 2021, the AY.4.2 variant accounted for approximately 10-11% of cases in the UK. AY.4.2 was designated as a variant under investigation by the UK Health and Security Agency on 20 October 2021. This study aimed to investigate vaccine effectiveness (VE) against symptomatic COVID-19 (Coronavirus disease 2019) infection and COVID-19 hospitalisation/death for the AY.4.2 variant.<h4>Methods</h4>We used the Scotland-wide Early Pandemic Evaluation and Enhanced Surveillance (EAVE-II) platform to estimate the VE of the ChAdOx1, BNT162b2, and mRNA-1273 vaccines against symptomatic infection and severe COVID-19 outcomes in adults. The study was conducted from June 8 to October 25, 2021. We used a test-negative design (TND) to estimate VE against reverse transcriptase polymerase chain reaction (RT-PCR) confirmed symptomatic SARS-CoV-2 infection while adjusting for sex, socioeconomic status, number of coexisting conditions, and splines in time and age. We also performed a cohort study using a Cox proportional hazards model to estimate VE against a composite outcome of COVID-19 hospital admission or death, with the same adjustments.<h4>Results</h4>We found an overall VE against symptomatic SARS-CoV-2 infection due to AY.4.2 of 73% (95% confidence interval (CI) = 62-81) for >14 days post-second vaccine dose. Good protection against AY.4.2 symptomatic infection was observed for BNT162b2, ChAdOx1, and mRNA-1273. In unvaccinated individuals, the hazard ratio (HR) for COVID-19 hospital admission or death from AY.4.2 among community detected cases was 1.77 (95% CI = 1.02-3.07) relative to unvaccinated individuals who were infected with Delta, after adjusting for multiple potential confounders. VE against AY.4.2 COVID-19 admissions or deaths was 87% (95% CI = 74-93) >28 days post-second vaccination relative to unvaccinated.<h4>Conclusions</h4>We found that AY.4.2 was associated with an increased risk of COVID-19 hospitalisations or deaths in unvaccinated individuals compared with Delta and that vaccination provided substantial protection against symptomatic SARS-CoV-2 and severe COVID-19 outcomes following Delta AY.4.2 infection. High levels of vaccine uptake and protection offered by existing vaccines, as well as the rapid emergence of the Omicron variant may have contributed to the AY.4.2 variant never progressing to a variant of concern.",,pdf:https://jogh.org/wp-content/uploads/2022/07/jogh-12-05025.pdf; doi:https://doi.org/10.7189/jogh.12.05025; html:https://europepmc.org/articles/PMC9269984; pdf:https://europepmc.org/articles/PMC9269984?pdf=render
 33521768,https://doi.org/10.1016/s2666-7568(20)30011-8,Tackling immunosenescence to improve COVID-19 outcomes and vaccine response in older adults.,"Cox LS, Bellantuono I, Lord JM, Sapey E, Mannick JB, Partridge L, Gordon AL, Steves CJ, Witham MD.",,The lancet. Healthy longevity,2020,2020-11-09,Y,,,,,,pdf:https://eprint.ncl.ac.uk/fulltext.aspx?url=271502/147E40FC-6152-4060-81B1-702AE3B1D66A.pdf&pub_id=271502; doi:https://doi.org/10.1016/S2666-7568(20)30011-8; html:https://europepmc.org/articles/PMC7834195; pdf:https://europepmc.org/articles/PMC7834195?pdf=render
-36001371,https://doi.org/10.2196/38122,Deployment of a Free-Text Analytics Platform at a UK National Health Service Research Hospital: CogStack at University College London Hospitals.,"Noor K, Roguski L, Bai X, Handy A, Klapaukh R, Folarin A, Romao L, Matteson J, Lea N, Zhu L, Asselbergs FW, Wong WK, Shah A, Dobson RJ.",,JMIR medical informatics,2022,2022-08-24,Y,Information Retrieval; Natural Language Processing; Text Mining; Electronic Health Record System; Clinical Support,,,"<h4>Background</h4>As more health care organizations transition to using electronic health record (EHR) systems, it is important for these organizations to maximize the secondary use of their data to support service improvement and clinical research. These organizations will find it challenging to have systems capable of harnessing the unstructured data fields in the record (clinical notes, letters, etc) and more practically have such systems interact with all of the hospital data systems (legacy and current).<h4>Objective</h4>We describe the deployment of the EHR interfacing information extraction and retrieval platform CogStack at University College London Hospitals (UCLH).<h4>Methods</h4>At UCLH, we have deployed the CogStack platform, an information retrieval platform with natural language processing capabilities. The platform addresses the problem of data ingestion and harmonization from multiple data sources using the Apache NiFi module for managing complex data flows. The platform also facilitates the extraction of structured data from free-text records through use of the MedCAT natural language processing library. Finally, data science tools are made available to support data scientists and the development of downstream applications dependent upon data ingested and analyzed by CogStack.<h4>Results</h4>The platform has been deployed at the hospital, and in particular, it has facilitated a number of research and service evaluation projects. To date, we have processed over 30 million records, and the insights produced from CogStack have informed a number of clinical research use cases at the hospital.<h4>Conclusions</h4>The CogStack platform can be configured to handle the data ingestion and harmonization challenges faced by a hospital. More importantly, the platform enables the hospital to unlock important clinical information from the unstructured portion of the record using natural language processing technology.",,pdf:https://medinform.jmir.org/2022/8/e38122/PDF; doi:https://doi.org/10.2196/38122; html:https://europepmc.org/articles/PMC9453582
 38837310,https://doi.org/10.1002/ejhf.3306,"A nationwide, population-based study on specialized care for acute heart failure throughout the COVID-19 pandemic.","Cannata A, Mizani MA, Bromage DI, Piper SE, Hardman SMC, Sudlow C, de Belder M, Deanfield J, Gardner RS, Clark AL, Cleland JGF, McDonagh TA,  on behalf of the CVD‐COVID‐UK/COVID‐IMPACT Consortium.",,European journal of heart failure,2024,2024-06-04,N,Heart Failure; Specialist Care; Covid‐19; National Heart Failure Audit,,,"<h4>Aims</h4>The COVID-19 pandemic disrupted the delivery of care for patients with heart failure (HF), leading to fewer HF hospitalizations and increased mortality. However, nationwide data on quality of care and long-term outcomes across the pandemic are scarce.<h4>Methods and results</h4>We used data from the National Heart Failure Audit (NHFA) linked to national records for hospitalization and deaths. We compared pre-COVID (2018-2019), COVID (2020), and late/post-COVID (2021-2022) periods. Data for 227 250 patients admitted to hospital with HF were analysed and grouped according to the admission year and the presence of HF with (HFrEF) or without reduced ejection fraction (non-HFrEF). The median age at admission was 81 years (interquartile range 72-88), 55% were men (n = 125 975), 87% were of white ethnicity (n = 102 805), and 51% had HFrEF (n = 116 990). In-hospital management and specialized cardiology care were maintained throughout the pandemic with an increasing percentage of patients discharged on disease-modifying medications over time (p < 0.001). Long-term outcomes improved over time (hazard ratio [HR] 0.92, 95% confidence interval [CI] 0.90-0.95, p < 0.001), mainly driven by a reduction in cardiovascular death. Receiving specialized cardiology care was associated with better long-term outcomes both for those who had HFrEF (HR 0.79, 95% CI 0.77-0.82, p < 0.001) and for those who had non-HFrEF (HR 0.87, 95% CI 0.85-0.90, p < 0.001).<h4>Conclusions</h4>Despite the disruption of healthcare systems, the clinical characteristics of patients admitted with HF were similar and the overall standard of care was maintained throughout the pandemic. Long-term survival of patients hospitalized with HF continued to improve after COVID-19, especially for HFrEF.",,doi:https://doi.org/10.1002/ejhf.3306; doi:https://doi.org/10.1002/ejhf.3306
+36001371,https://doi.org/10.2196/38122,Deployment of a Free-Text Analytics Platform at a UK National Health Service Research Hospital: CogStack at University College London Hospitals.,"Noor K, Roguski L, Bai X, Handy A, Klapaukh R, Folarin A, Romao L, Matteson J, Lea N, Zhu L, Asselbergs FW, Wong WK, Shah A, Dobson RJ.",,JMIR medical informatics,2022,2022-08-24,Y,Information Retrieval; Natural Language Processing; Text Mining; Electronic Health Record System; Clinical Support,,,"<h4>Background</h4>As more health care organizations transition to using electronic health record (EHR) systems, it is important for these organizations to maximize the secondary use of their data to support service improvement and clinical research. These organizations will find it challenging to have systems capable of harnessing the unstructured data fields in the record (clinical notes, letters, etc) and more practically have such systems interact with all of the hospital data systems (legacy and current).<h4>Objective</h4>We describe the deployment of the EHR interfacing information extraction and retrieval platform CogStack at University College London Hospitals (UCLH).<h4>Methods</h4>At UCLH, we have deployed the CogStack platform, an information retrieval platform with natural language processing capabilities. The platform addresses the problem of data ingestion and harmonization from multiple data sources using the Apache NiFi module for managing complex data flows. The platform also facilitates the extraction of structured data from free-text records through use of the MedCAT natural language processing library. Finally, data science tools are made available to support data scientists and the development of downstream applications dependent upon data ingested and analyzed by CogStack.<h4>Results</h4>The platform has been deployed at the hospital, and in particular, it has facilitated a number of research and service evaluation projects. To date, we have processed over 30 million records, and the insights produced from CogStack have informed a number of clinical research use cases at the hospital.<h4>Conclusions</h4>The CogStack platform can be configured to handle the data ingestion and harmonization challenges faced by a hospital. More importantly, the platform enables the hospital to unlock important clinical information from the unstructured portion of the record using natural language processing technology.",,pdf:https://medinform.jmir.org/2022/8/e38122/PDF; doi:https://doi.org/10.2196/38122; html:https://europepmc.org/articles/PMC9453582
 33446033,https://doi.org/10.1177/1460458220977579,Identifying strategies to overcome roadblocks to utilising near real-time healthcare and administrative data to create a Scotland-wide learning health system.,"Mukherjee M, Cresswell K, Sheikh A.",,Health informatics journal,2021,2021-01-01,N,Qualitative Research; Governance; Electronic Health Records; Health Data; Learning Health System,,,"Creating a learning health system could help reduce variations in quality of care. Success is dependent on timely access to health data. To explore the barriers and facilitators to timely access to patients' data, we conducted in-depth semi-structured interviews with 37 purposively sampled participants from government, the NHS and academia across Scotland. Interviews were analysed using the framework approach. Participants were of the view that Scotland could play a leading role in the exploitation of routine data to drive forward service improvements, but highlighted major impediments: (i) persistence of paper-based records and a variety of information systems; (ii) the need for a proportionate approach to managing information governance; and (iii) the need for support structures to facilitate accrual, processing, linking, analysis and timely use and reuse of data for patient benefit. There is a pressing need to digitise and integrate existing health information infrastructures, guided by a nationwide proportionate information governance approach and the need to enhance technological and human capabilities to support these efforts.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/1460458220977579; doi:https://doi.org/10.1177/1460458220977579
 38991538,https://doi.org/10.1038/s41586-024-07773-7,De novo variants in the RNU4-2 snRNA cause a frequent neurodevelopmental syndrome.,"Chen Y, Dawes R, Kim HC, Ljungdahl A, Stenton SL, Walker S, Lord J, Lemire G, Martin-Geary AC, Ganesh VS, Ma J, Ellingford JM, Delage E, D'Souza EN, Dong S, Adams DR, Allan K, Bakshi M, Baldwin EE, Berger SI, Bernstein JA, Bhatnagar I, Blair E, Brown NJ, Burrage LC, Chapman K, Coman DJ, Compton AG, Cunningham CA, D'Souza P, Danecek P, Délot EC, Dias KR, Elias ER, Elmslie F, Evans CA, Ewans L, Ezell K, Fraser JL, Gallacher L, Genetti CA, Goriely A, Grant CL, Haack T, Higgs JE, Hinch AG, Hurles ME, Kuechler A, Lachlan KL, Lalani SR, Lecoquierre F, Leitão E, Fevre AL, Leventer RJ, Liebelt JE, Lindsay S, Lockhart PJ, Ma AS, Macnamara EF, Mansour S, Maurer TM, Mendez HR, Metcalfe K, Montgomery SB, Moosajee M, Nassogne MC, Neumann S, O'Donoghue M, O'Leary M, Palmer EE, Pattani N, Phillips J, Pitsava G, Pysar R, Rehm HL, Reuter CM, Revencu N, Riess A, Rius R, Rodan L, Roscioli T, Rosenfeld JA, Sachdev R, Shaw-Smith CJ, Simons C, Sisodiya SM, Snell P, St Clair L, Stark Z, Stewart HS, Tan TY, Tan NB, Temple SEL, Thorburn DR, Tifft CJ, Uebergang E, VanNoy GE, Vasudevan P, Vilain E, Viskochil DH, Wedd L, Wheeler MT, White SM, Wojcik M, Wolfe LA, Wolfenson Z, Wright CF, Xiao C, Zocche D, Rubenstein JL, Markenscoff-Papadimitriou E, Fica SM, Baralle D, Depienne C, MacArthur DG, Howson JMM, Sanders SJ, O'Donnell-Luria A, Whiffin N.",,Nature,2024,2024-07-11,Y,,,,"Around 60% of individuals with neurodevelopmental disorders (NDD) remain undiagnosed after comprehensive genetic testing, primarily of protein-coding genes<sup>1</sup>. Large genome-sequenced cohorts are improving our ability to discover new diagnoses in the non-coding genome. Here we identify the non-coding RNA RNU4-2 as a syndromic NDD gene. RNU4-2 encodes the U4 small nuclear RNA (snRNA), which is a critical component of the U4/U6.U5 tri-snRNP complex of the major spliceosome<sup>2</sup>. We identify an 18 base pair region of RNU4-2 mapping to two structural elements in the U4/U6 snRNA duplex (the T-loop and stem III) that is severely depleted of variation in the general population, but in which we identify heterozygous variants in 115 individuals with NDD. Most individuals (77.4%) have the same highly recurrent single base insertion (n.64_65insT). In 54 individuals in whom it could be determined, the de novo variants were all on the maternal allele. We demonstrate that RNU4-2 is highly expressed in the developing human brain, in contrast to RNU4-1 and other U4 homologues. Using RNA sequencing, we show how 5' splice-site use is systematically disrupted in individuals with RNU4-2 variants, consistent with the known role of this region during spliceosome activation. Finally, we estimate that variants in this 18 base pair region explain 0.4% of individuals with NDD. This work underscores the importance of non-coding genes in rare disorders and will provide a diagnosis to thousands of individuals with NDD worldwide.",,doi:https://doi.org/10.1038/s41586-024-07773-7; html:https://europepmc.org/articles/PMC11338827; pdf:https://europepmc.org/articles/PMC11338827?pdf=render
+34649997,https://doi.org/10.2337/dc21-0437,"Polycystic Ovary Syndrome, Combined Oral Contraceptives, and the Risk of Dysglycemia: A Population-Based Cohort Study With a Nested Pharmacoepidemiological Case-Control Study.","Kumarendran B, O'Reilly MW, Subramanian A, Šumilo D, Toulis K, Gokhale KM, Wijeratne CN, Coomarasamy A, Tahrani AA, Azoulay L, Arlt W, Nirantharakumar K.",,Diabetes care,2021,2021-10-14,Y,,,,"<h4>Objective</h4>Irregular menstrual cycles are associated with increased cardiovascular mortality. Polycystic ovary syndrome (PCOS) is characterized by androgen excess and irregular menses; androgens are drivers of increased metabolic risk in women with PCOS. Combined oral contraceptive pills (COCPs) are used in PCOS both for cycle regulation and to reduce the biologically active androgen fraction. We examined COCP use and risk of dysglycemia (prediabetes and type 2 diabetes) in women with PCOS.<h4>Research design and methods</h4>Using a large U.K. primary care database (The Health Improvement Network [THIN]; 3.7 million patients from 787 practices), we carried out a retrospective population-based cohort study to determine dysglycemia risk (64,051 women with PCOS and 123,545 matched control subjects), as well as a nested pharmacoepidemiological case-control study to investigate COCP use in relation to dysglycemia risk (2,407 women with PCOS with [case subjects] and without [control subjects] a diagnosis of dysglycemia during follow-up). Cox models were used to estimate the unadjusted and adjusted hazard ratio, and conditional logistic regression was used to obtain adjusted odds ratios (aORs).<h4>Results</h4>The adjusted hazard ratio for dysglycemia in women with PCOS was 1.87 (95% CI 1.78-1.97, <i>P</i> < 0.001; adjustment for age, social deprivation, BMI, ethnicity, and smoking), with increased rates of dysglycemia in all BMI subgroups. Women with PCOS and COCP use had a reduced dysglycemia risk (aOR 0.72, 95% CI 0.59-0.87).<h4>Conclusions</h4>In this study, limited by its retrospective nature and the use of routinely collected electronic general practice record data, which does not allow for exclusion of the impact of prescription-by-indication bias, women with PCOS exposed to COCPs had a reduced risk of dysglycemia across all BMI subgroups. Future prospective studies should be considered for further understanding of these observations and potential causality.",,pdf:https://diabetesjournals.org/care/article-pdf/44/12/2758/631597/dc210437.pdf; doi:https://doi.org/10.2337/dc21-0437; html:https://europepmc.org/articles/PMC8669537; pdf:https://europepmc.org/articles/PMC8669537?pdf=render
+35301875,https://doi.org/10.1161/jaha.121.023146,Long-Term Cardiovascular Risk and Management of Patients Recorded in Primary Care With Unattributed Chest Pain: An Electronic Health Record Study.,"Jordan KP, Rathod-Mistry T, Bailey J, Chen Y, Clarson L, Denaxas S, Hayward RA, Hemingway H, van der Windt DA, Mamas MA.",,Journal of the American Heart Association,2022,2022-03-18,Y,Cardiovascular disease; Chest pain; Primary Care; Electronic Health Records,,,"Background Most adults presenting with chest pain will not receive a diagnosis and be recorded with unattributed chest pain. The objective was to assess if they have increased risk of cardiovascular disease compared with those with noncoronary chest pain and determine whether investigations and interventions are targeted at those at highest risk. Methods and Results We used records from general practices in England linked to hospitalization and mortality information. The study population included patients aged 18 years or over with a new record of chest pain with a noncoronary cause or unattributed between 2002 and 2018, and no cardiovascular disease recorded up to 6 months (diagnostic window) afterward. We compared risk of a future cardiovascular event by type of chest pain, adjusting for cardiovascular risk factors and alternative explanations for chest pain. We determined prevalence of cardiac diagnostic investigations and preventative medication during the diagnostic window in patients with estimated cardiovascular risk ≥10%. There were 375 240 patients with unattributed chest pain (245 329 noncoronary chest pain). There was an increased risk of cardiovascular events for patients with unattributed chest pain, highest in the first year (hazard ratio, 1.25 [95% CI, 1.21-1.29]), persistent up to 10 years. Patients with unattributed chest pain had consistently increased risk of myocardial infarction over time but no increased risk of stroke. Thirty percent of patients at higher risk were prescribed lipid-lowering medication. Conclusions Patients presenting to primary care with unattributed chest pain are at increased risk of cardiovascular events. Primary prevention to reduce cardiovascular events appears suboptimal in those at higher risk.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.121.023146; doi:https://doi.org/10.1161/JAHA.121.023146; html:https://europepmc.org/articles/PMC9075433; pdf:https://europepmc.org/articles/PMC9075433?pdf=render
 39141307,https://doi.org/10.1007/s12471-024-01886-4,Which heart failure patients benefit most from non-invasive telemedicine? An overview of current evidence and future directions.,"van Eijk J, Luijken K, Trappenburg J, Jaarsma T, Asselbergs FW.",,Netherlands heart journal : monthly journal of the Netherlands Society of Cardiology and the Netherlands Heart Foundation,2024,2024-08-14,Y,Heart Failure; Telemedicine; Subgroups; Telemonitoring; Ehealth; Personalised Medicine,,,"Telemedicine in heart failure (HF) management may positively impact health outcomes, but varied effects in studies hinder guidance in HF guidelines. Evidence on the effectiveness of telemedicine in HF subpopulations is limited. We conducted a scoping review to evaluate and synthesise evidence on the effectiveness of telemedicine across HF subpopulations that could guide telemedicine strategies in routine practice. Meta-analyses concerning randomised controlled trials (RCTs) with subgroup analyses on telemedicine effectives were identified in PubMed. We identified 15 RCTs, encompassing 21 different subgroups based on characteristics of HF patients. Findings varied across studies and no definite evidence was found about which patients benefit most from telemedicine. Subgroup definitions were inconsistent, not always a priori defined and subgroups contained few patients. Some studies found heterogeneous effects of telemedicine on mortality and hospitalisation across subgroups defined by: New York Heart Association (NYHA) classification, previous HF decompensation, implantable device, concurrent depression, time since hospital discharge and duration of HF. Patients represented in the RCTs were mostly male, aged 65-75 years, with HF with reduced ejection fraction and NYHA class II/III. Traditional RCTs have not been able to provide clinicians with guidance; continuous real-world evidence generation could enhance monitoring and identify who benefits from telemedicine.",,doi:https://doi.org/10.1007/s12471-024-01886-4; html:https://europepmc.org/articles/PMC11336005; pdf:https://europepmc.org/articles/PMC11336005?pdf=render
 38879791,https://doi.org/10.1093/ije/dyae079,Cohort Profile: Indian Study of Healthy Ageing (ISHA-Barshi).,"Mhatre SS, Bragg F, Panse N, Judge PK, Manjrekar A, Burrett JA, Patil S, Davey Smith G, Kotkar L, Relton CL, Doibale P, Gadhave B, Chaturvedi P, Sherliker P, Jha P, Lewington S, Dikshit R.",,International journal of epidemiology,2024,2024-06-01,Y,,,,,,pdf:https://academic.oup.com/ije/article-pdf/53/4/dyae079/58242858/dyae079.pdf; doi:https://doi.org/10.1093/ije/dyae079; html:https://europepmc.org/articles/PMC11180225; pdf:https://europepmc.org/articles/PMC11180225?pdf=render
-35301875,https://doi.org/10.1161/jaha.121.023146,Long-Term Cardiovascular Risk and Management of Patients Recorded in Primary Care With Unattributed Chest Pain: An Electronic Health Record Study.,"Jordan KP, Rathod-Mistry T, Bailey J, Chen Y, Clarson L, Denaxas S, Hayward RA, Hemingway H, van der Windt DA, Mamas MA.",,Journal of the American Heart Association,2022,2022-03-18,Y,Cardiovascular disease; Chest pain; Primary Care; Electronic Health Records,,,"Background Most adults presenting with chest pain will not receive a diagnosis and be recorded with unattributed chest pain. The objective was to assess if they have increased risk of cardiovascular disease compared with those with noncoronary chest pain and determine whether investigations and interventions are targeted at those at highest risk. Methods and Results We used records from general practices in England linked to hospitalization and mortality information. The study population included patients aged 18 years or over with a new record of chest pain with a noncoronary cause or unattributed between 2002 and 2018, and no cardiovascular disease recorded up to 6 months (diagnostic window) afterward. We compared risk of a future cardiovascular event by type of chest pain, adjusting for cardiovascular risk factors and alternative explanations for chest pain. We determined prevalence of cardiac diagnostic investigations and preventative medication during the diagnostic window in patients with estimated cardiovascular risk ≥10%. There were 375 240 patients with unattributed chest pain (245 329 noncoronary chest pain). There was an increased risk of cardiovascular events for patients with unattributed chest pain, highest in the first year (hazard ratio, 1.25 [95% CI, 1.21-1.29]), persistent up to 10 years. Patients with unattributed chest pain had consistently increased risk of myocardial infarction over time but no increased risk of stroke. Thirty percent of patients at higher risk were prescribed lipid-lowering medication. Conclusions Patients presenting to primary care with unattributed chest pain are at increased risk of cardiovascular events. Primary prevention to reduce cardiovascular events appears suboptimal in those at higher risk.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.121.023146; doi:https://doi.org/10.1161/JAHA.121.023146; html:https://europepmc.org/articles/PMC9075433; pdf:https://europepmc.org/articles/PMC9075433?pdf=render
 38216884,https://doi.org/10.1186/s12859-024-05642-8,Correction: Completing a genomic characterisation of microscopic tumour samples with copy number.,"Nulsen J, Hussain N, Al-Deka A, Yap J, Uddin K, Yau C, Ahmed AA.",,BMC bioinformatics,2024,2024-01-12,Y,,,,,,pdf:https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05642-8; doi:https://doi.org/10.1186/s12859-024-05642-8; html:https://europepmc.org/articles/PMC10785409; pdf:https://europepmc.org/articles/PMC10785409?pdf=render
 34765951,https://doi.org/10.1016/j.eclinm.2021.101163,Net effects of sodium-glucose co-transporter-2 inhibition in different patient groups: a meta-analysis of large placebo-controlled randomized trials.,"Staplin N, Roddick AJ, Emberson J, Reith C, Riding A, Wonnacott A, Kuverji A, Bhandari S, Baigent C, Haynes R, Herrington WG.",,EClinicalMedicine,2021,2021-10-26,Y,Safety; Heart Failure; Randomized Trials; Ckd; Sodium-glucose Co-transporter 2 Inhibitors,,,"<h4>Background</h4>The net absolute effects of sodium-glucose co-transporter-2 (SGLT-2) inhibitors across different patient groups have not been quantified.<h4>Methods</h4>We performed a meta-analysis of published large (>500 participants/arm) placebo-controlled SGLT-2 inhibitor trials after systematically searching MEDLINE and Embase databases from inception to 28th August 2021 (PROSPERO 2021 CRD42021240468).<h4>Findings</h4>Four heart failure trials (n=15,684 participants), four trials in type 2 diabetes mellitus at high atherosclerotic cardiovascular risk (n=42,568), and three trials in chronic kidney disease (n=19,289) were included. Relative risks (RRs) for all cardiovascular, renal and safety outcomes were broadly similar across these three patient groups, and between people with or without diabetes. Overall, compared to placebo, allocation to SGLT-2 inhibition reduced risk of hospitalization for heart failure or cardiovascular death by 23% (RR=0.77, 95%CI 0.73-0.80; n=6658), cardiovascular death by 14% (0.86, 0.81-0.92; n=3962), major adverse cardiovascular events by 11% (0.89, 0.84-0.94; n=5703), kidney disease progression by 36% (0.64, 0.59-0.70; n=2275), acute kidney injury by 30% (0.70, 0.62-0.79; n=1013 events) and severe hypoglycaemia by 13% (0.87, 0.79-0.97; n=1484). There was no effect of SGLT-2 inhibition on risk of non-cardiovascular death (0.93, 0.86-1.01; n=2226), but a net 12% reduction in all-cause mortality remained evident (0.88, 0.84-0.93; n=6188). However, the risk of ketoacidosis was 2-times higher among those allocated SGLT-2 inhibitors compared to placebo (2.03, 1.41-2.93; n=159; absolute excess in people with diabetes ∼0.3/1000 patient years). A small increased risk of urinary tract infection was evident (1.07, 1.02-1.13; n=5384) alongside a known increased risk of mycotic genital infections. Overall, risk of lower limb amputations was increased by 16% (1.16, 1.02-1.31; n=1074), but this risk was largely driven by a single outlying trial (CANVAS).<h4>Interpretations</h4>The relative effects of SGLT-2 inhibition on key safety and efficacy outcomes are consistent across the different studied groups of patient. Consequently, absolute benefits and harms are determined by the absolute baseline risk of particular outcomes, with absolute benefits on mortality and on non-fatal serious cardiac/renal outcomes substantially exceeding the risks of amputation and ketoacidosis in the main patient groups studied to date.<h4>Funding</h4>MRC-UK & KRUK.",,doi:https://doi.org/10.1016/j.eclinm.2021.101163; doi:https://doi.org/10.1016/j.eclinm.2021.101163; html:https://europepmc.org/articles/PMC8571171; pdf:https://europepmc.org/articles/PMC8571171?pdf=render
-34649997,https://doi.org/10.2337/dc21-0437,"Polycystic Ovary Syndrome, Combined Oral Contraceptives, and the Risk of Dysglycemia: A Population-Based Cohort Study With a Nested Pharmacoepidemiological Case-Control Study.","Kumarendran B, O'Reilly MW, Subramanian A, Šumilo D, Toulis K, Gokhale KM, Wijeratne CN, Coomarasamy A, Tahrani AA, Azoulay L, Arlt W, Nirantharakumar K.",,Diabetes care,2021,2021-10-14,Y,,,,"<h4>Objective</h4>Irregular menstrual cycles are associated with increased cardiovascular mortality. Polycystic ovary syndrome (PCOS) is characterized by androgen excess and irregular menses; androgens are drivers of increased metabolic risk in women with PCOS. Combined oral contraceptive pills (COCPs) are used in PCOS both for cycle regulation and to reduce the biologically active androgen fraction. We examined COCP use and risk of dysglycemia (prediabetes and type 2 diabetes) in women with PCOS.<h4>Research design and methods</h4>Using a large U.K. primary care database (The Health Improvement Network [THIN]; 3.7 million patients from 787 practices), we carried out a retrospective population-based cohort study to determine dysglycemia risk (64,051 women with PCOS and 123,545 matched control subjects), as well as a nested pharmacoepidemiological case-control study to investigate COCP use in relation to dysglycemia risk (2,407 women with PCOS with [case subjects] and without [control subjects] a diagnosis of dysglycemia during follow-up). Cox models were used to estimate the unadjusted and adjusted hazard ratio, and conditional logistic regression was used to obtain adjusted odds ratios (aORs).<h4>Results</h4>The adjusted hazard ratio for dysglycemia in women with PCOS was 1.87 (95% CI 1.78-1.97, <i>P</i> < 0.001; adjustment for age, social deprivation, BMI, ethnicity, and smoking), with increased rates of dysglycemia in all BMI subgroups. Women with PCOS and COCP use had a reduced dysglycemia risk (aOR 0.72, 95% CI 0.59-0.87).<h4>Conclusions</h4>In this study, limited by its retrospective nature and the use of routinely collected electronic general practice record data, which does not allow for exclusion of the impact of prescription-by-indication bias, women with PCOS exposed to COCPs had a reduced risk of dysglycemia across all BMI subgroups. Future prospective studies should be considered for further understanding of these observations and potential causality.",,pdf:https://diabetesjournals.org/care/article-pdf/44/12/2758/631597/dc210437.pdf; doi:https://doi.org/10.2337/dc21-0437; html:https://europepmc.org/articles/PMC8669537; pdf:https://europepmc.org/articles/PMC8669537?pdf=render
 36377225,https://doi.org/10.1177/18333583221135710,Concordance between coding sources of burn size and depth across Australian and New Zealand specialist burn services.,"Perkins M, Cleland H, Gabbe BJ, Tracy LM.",,Health information management : journal of the Health Information Management Association of Australia,2024,2022-11-14,N,Burns; Australia; New Zealand; Registries; Health Information Management; International Classification Of Diseases; Clinical Coding,,,"<h4>Background</h4>The percentage of total body surface area (%TBSA) burned and burn depth provide valuable information on burn injury severity.<h4>Objective</h4>This study investigated the concordance between The International Statistical Classification of Diseases and Related Health Problems, Tenth Revision, Australian Modification (ICD-10-AM) codes and expert burn clinicians in assessing burn injury severity.<h4>Method</h4>We conducted a retrospective population-based review of all patients who sustained a burn injury between July 1, 2009, and June 30, 2019, requiring admission into a specialist burn service across Australia and New Zealand. The %TBSA burned (including the percentage of full thickness burns) recorded by expert burn clinicians within the Burns Registry of Australia and New Zealand (BRANZ) were compared to ICD-10-AM coding.<h4>Results</h4>20,642 cases (71.5%) with ICD-10-AM code data were recorded. Overall, kappa scores (95% confidence interval [CI]) for burn size ranged from 0.64 (95% CI 0.63-0.66) to 0.86 (95% CI 0.78-0.94) indicating substantial to almost perfect agreement across all %TBSA groups. When stratified by depth, the lowest agreement was observed for < 10% TBSA and < 10% full thickness (kappa 0.03; 95% CI 0.02-0.04) and the highest agreement was observed for burns of ≥ 90% TBSA and ≥ 90% full thickness (kappa 0.72; 95% CI 0.58-0.85).<h4>Conclusion</h4>Overall, there was substantial agreement between the BRANZ and ICD-10-AM coded data for %TBSA classification. When %TBSA classification was stratified by burn depth, greater agreement was observed for larger and deeper burns compared with smaller and superficial burns.<h4>Implications</h4>Greater consistency in the classification of burns is needed.",,doi:https://doi.org/10.1177/18333583221135710
 33123364,https://doi.org/10.1093/ckj/sfaa192,Temporal changes in complement activation in haemodialysis patients with COVID-19 as a predictor of disease progression.,"Prendecki M, Clarke C, Medjeral-Thomas N, McAdoo SP, Sandhu E, Peters JE, Thomas DC, Willicombe M, Botto M, Pickering MC.",,Clinical kidney journal,2020,2020-10-02,Y,Complement; Haemodialysis; Covid-19,,,"<h4>Background</h4>Complement activation may play a pathogenic role in patients with severe coronavirus disease 2019 (COVID-19) by contributing to tissue inflammation and microvascular thrombosis.<h4>Methods</h4>Serial samples were collected from patients receiving maintenance haemodialysis (HD). Thirty-nine patients had confirmed COVID-19 and 10 patients had no evidence of COVID-19. Plasma C5a and C3a levels were measured using enzyme-linked immunosorbent assay.<h4>Results</h4>We identified elevated levels of plasma C3a and C5a in HD patients with severe COVID-19 compared with controls. Serial sampling identified that C5a levels were elevated prior to clinical deterioration in patients who developed severe disease. C3a more closely mirrored both clinical and biochemical disease severity.<h4>Conclusions</h4>Our findings suggest that activation of complement plays a role in the pathogenesis of COVID-19, leading to endothelial injury and lung damage. C5a may be an earlier biomarker of disease severity than conventional parameters such as C-reactive protein and this warrants further investigation in dedicated biomarker studies. Our data support the testing of complement inhibition as a therapeutic strategy for patients with severe COVID-19.",,pdf:https://academic.oup.com/ckj/article-pdf/13/5/889/33980535/sfaa192.pdf; doi:https://doi.org/10.1093/ckj/sfaa192; html:https://europepmc.org/articles/PMC7577776; pdf:https://europepmc.org/articles/PMC7577776?pdf=render
 36567336,https://doi.org/10.1186/s12872-022-03005-w,Diagnostic signature for heart failure with preserved ejection fraction (HFpEF): a machine learning approach using multi-modality electronic health record data.,"Farajidavar N, O'Gallagher K, Bean D, Nabeebaccus A, Zakeri R, Bromage D, Kraljevic Z, Teo JTH, Dobson RJ, Shah AM.",,BMC cardiovascular disorders,2022,2022-12-26,Y,Dyspnea; Machine Learning; Hfpef,,,"<h4>Background</h4>Heart failure with preserved ejection fraction (HFpEF) is thought to be highly prevalent yet remains underdiagnosed. Evidence-based treatments are available that increase quality of life and decrease hospitalization. We sought to develop a data-driven diagnostic model to predict from electronic health records (EHR) the likelihood of HFpEF among patients with unexplained dyspnea and preserved left ventricular EF.<h4>Methods and results</h4>The derivation cohort comprised patients with dyspnea and echocardiography results. Structured and unstructured data were extracted using an automated informatics pipeline. Patients were retrospectively diagnosed as HFpEF (cases), non-HF (control cohort I), or HF with reduced EF (HFrEF; control cohort II). The ability of clinical parameters and investigations to discriminate cases from controls was evaluated by extreme gradient boosting. A likelihood scoring system was developed and validated in a separate test cohort. The derivation cohort included 1585 consecutive patients: 133 cases of HFpEF (9%), 194 non-HF cases (Control cohort I) and 1258 HFrEF cases (Control cohort II). Two HFpEF diagnostic signatures were derived, comprising symptoms, diagnoses and investigation results. A final prediction model was generated based on the averaged likelihood scores from these two models. In a validation cohort consisting of 269 consecutive patients [with 66 HFpEF cases (24.5%)], the diagnostic power of detecting HFpEF had an AUROC of 90% (P < 0.001) and average precision of 74%.<h4>Conclusion</h4>This diagnostic signature enables discrimination of HFpEF from non-cardiac dyspnea or HFrEF from EHR and can assist in the diagnostic evaluation in patients with unexplained dyspnea. This approach will enable identification of HFpEF patients who may then benefit from new evidence-based therapies.",,pdf:https://bmccardiovascdisord.biomedcentral.com/counter/pdf/10.1186/s12872-022-03005-w; doi:https://doi.org/10.1186/s12872-022-03005-w; html:https://europepmc.org/articles/PMC9791783; pdf:https://europepmc.org/articles/PMC9791783?pdf=render
 36280346,https://doi.org/10.1136/heartjnl-2022-321492,Cardiovascular disease and mortality sequelae of COVID-19 in the UK Biobank.,"Raisi-Estabragh Z, Cooper J, Salih A, Raman B, Lee AM, Neubauer S, Harvey NC, Petersen SE.",,Heart (British Cardiac Society),2022,2022-12-22,Y,epidemiology; Covid-19,,,"<h4>Objective</h4>To examine association of COVID-19 with incident cardiovascular events in 17 871 UK Biobank cases between March 2020 and 2021.<h4>Methods</h4>COVID-19 cases were defined using health record linkage. Each case was propensity score-matched to two uninfected controls on age, sex, deprivation, body mass index, ethnicity, diabetes, prevalent ischaemic heart disease (IHD), smoking, hypertension and high cholesterol. We included the following incident outcomes: myocardial infarction, stroke, heart failure, atrial fibrillation, venous thromboembolism (VTE), pericarditis, all-cause death, cardiovascular death, IHD death. Cox proportional hazards regression was used to estimate associations of COVID-19 with each outcome over an average of 141 days (range 32-395) of prospective follow-up.<h4>Results</h4>Non-hospitalised cases (n=14 304) had increased risk of incident VTE (HR 2.74 (95% CI 1.38 to 5.45), p=0.004) and death (HR 10.23 (95% CI 7.63 to 13.70), p<0.0001). Individuals with primary COVID-19 hospitalisation (n=2701) had increased risk of all outcomes considered. The largest effect sizes were with VTE (HR 27.6 (95% CI 14.5 to 52.3); p<0.0001), heart failure (HR 21.6 (95% CI 10.9 to 42.9); p<0.0001) and stroke (HR 17.5 (95% CI 5.26 to 57.9); p<0.0001). Those hospitalised with COVID-19 as a secondary diagnosis (n=866) had similarly increased cardiovascular risk. The associated risks were greatest in the first 30 days after infection but remained higher than controls even after this period.<h4>Conclusions</h4>Individuals hospitalised with COVID-19 have increased risk of incident cardiovascular events across a range of disease and mortality outcomes. The risk of most events is highest in the early postinfection period. Individuals not requiring hospitalisation have increased risk of VTE, but not of other cardiovascular-specific outcomes.",,pdf:https://heart.bmj.com/content/heartjnl/109/2/119.full.pdf; doi:https://doi.org/10.1136/heartjnl-2022-321492; html:https://europepmc.org/articles/PMC9811071; pdf:https://europepmc.org/articles/PMC9811071?pdf=render
 39385845,https://doi.org/10.1093/ehjimp/qyae094,"Quality control of cardiac magnetic resonance imaging segmentation, feature tracking, aortic flow, and native T1 analysis using automated batch processing in the UK Biobank study.","Chadalavada S, Rauseo E, Salih A, Naderi H, Khanji M, Vargas JD, Lee AM, Amir-Kalili A, Lockhart L, Graham B, Chirvasa M, Fung K, Paiva J, Sanghvi MM, Slabaugh GG, Jensen MT, Aung N, Petersen SE.",,European heart journal. Imaging methods and practice,2024,2024-07-01,Y,Quality control; Machine Learning; Cardiac Magnetic Resonance Imaging; Automated Image Analysis; Shiny App,,,"<h4>Aims</h4>Automated algorithms are regularly used to analyse cardiac magnetic resonance (CMR) images. Validating data output reliability from this method is crucial for enabling widespread adoption. We outline a visual quality control (VQC) process for image analysis using automated batch processing. We assess the performance of automated analysis and the reliability of replacing visual checks with statistical outlier (SO) removal approach in UK Biobank CMR scans.<h4>Methods and results</h4>We included 1987 CMR scans from the UK Biobank COVID-19 imaging study. We used batch processing software (Circle Cardiovascular Imaging Inc.-CVI42) to automatically extract chamber volumetric data, strain, native T1, and aortic flow data. The automated analysis outputs (∼62 000 videos and 2000 images) were visually checked by six experienced clinicians using a standardized approach and a custom-built R Shiny app. Inter-observer variability was assessed. Data from scans passing VQC were compared with a SO removal QC method in a subset of healthy individuals (<i>n</i> = 1069). Automated segmentation was highly rated, with over 95% of scans passing VQC. Overall inter-observer agreement was very good (Gwet's AC2 0.91; 95% confidence interval 0.84, 0.94). No difference in overall data derived from VQC or SO removal in healthy individuals was observed.<h4>Conclusion</h4>Automated image analysis using CVI42 prototypes for UK Biobank CMR scans demonstrated high quality. Larger UK Biobank data sets analysed using these automated algorithms do not require in-depth VQC. SO removal is sufficient as a QC measure, with operator discretion for visual checks based on population or research objectives.",,doi:https://doi.org/10.1093/ehjimp/qyae094; html:https://europepmc.org/articles/PMC11462446; pdf:https://europepmc.org/articles/PMC11462446?pdf=render
 37577380,https://doi.org/10.1093/braincomms/fcad211,Primary care blood tests show lipid profile changes in pre-symptomatic amyotrophic lateral sclerosis.,"Thompson AG, Marsden R, Talbot K, Turner MR.",,Brain communications,2023,2023-07-28,Y,Cholesterol; Biomarker; Amyotrophic Lateral Sclerosis; Motor Neurone Disease; Pre-symptomatic,,,"Multiple sources of evidence suggest that changes in metabolism may precede the onset of motor symptoms in amyotrophic lateral sclerosis. This study aimed to seek evidence for alterations in the levels of blood indices collected routinely in the primary care setting prior to the onset of motor symptoms in amyotrophic lateral sclerosis. Premorbid data, measured as part of routine health screening, for total cholesterol, high-density and low-density lipoprotein cholesterol, triglyceride, glycated haemoglobin A1c and creatinine were collected retrospectively from (i) a cohort of amyotrophic lateral sclerosis patients attending a specialist clinic (<i>n</i> = 143) and (ii) from primary care-linked data within UK Biobank. Data were fitted using linear mixed effects models with linear b-splines to identify inflection points, controlling for age and sex. In specialist amyotrophic lateral sclerosis clinic cases, models indicated decreasing levels of total and low-density lipoprotein cholesterol prior to an inflection point in the years before symptom onset (total cholesterol 3.25 years, low-density lipoprotein cholesterol 1.25 years), after which they stabilized or rose. A similar pattern was observed in amyotrophic lateral sclerosis cases within UK Biobank, occurring several years prior to diagnosis (total cholesterol 7 years, low-density lipoprotein cholesterol 7.25 years), differing significantly from matched controls. High-density lipoprotein cholesterol followed a similar pattern but was less robust to sensitivity analyses. Levels of triglyceride remained stable throughout. Glycated haemoglobin temporal profiles were not consistent between the clinic and biobank cohorts. Creatinine level trajectories prior to amyotrophic lateral sclerosis did not differ significantly from controls but decreased significantly in the symptomatic period after an inflection point of 0.25 years after symptom onset (clinic cohort) or 0.5 years before diagnosis (UK Biobank). These data provide further evidence for a pre-symptomatic period of dynamic metabolic change in amyotrophic lateral sclerosis, consistently associated with alterations in blood cholesterols. Such changes may ultimately contribute to biomarkers applicable to population screening and for pathways guiding the targeting of preventative therapy.",,pdf:https://academic.oup.com/braincomms/advance-article-pdf/doi/10.1093/braincomms/fcad211/51001698/fcad211.pdf; doi:https://doi.org/10.1093/braincomms/fcad211; html:https://europepmc.org/articles/PMC10412752; pdf:https://europepmc.org/articles/PMC10412752?pdf=render
-29716529,https://doi.org/10.1186/s12883-018-1058-8,Severe localised granulomatosis with polyangiitis (Wegener's granulomatosis) manifesting with extensive cranial nerve palsies and cranial diabetes insipidus: a case report and literature review.,"Peters JE, Gupta V, Saeed IT, Offiah C, Jawad ASM.",,BMC neurology,2018,2018-05-01,Y,Diabetes insipidus; Cyclophosphamide; pituitary; Vasculitis; Rituximab; Anca; Cavernous Sinus Syndrome; Collet-sicard Syndrome; Granulomatosis With Polyangiitis; Wegener’s Granulomatosis,,,"<h4>Background</h4>Granulomatosis with polyangiitis (GPA, formerly Wegener's granulomatosis) is a multisystem vasculitis of small- to medium-sized blood vessels. Cranial involvement can result in cranial nerve palsies and, rarely, pituitary infiltration.<h4>Case presentation</h4>We describe the case of a 32 year-old woman with limited but severe GPA manifesting as progressive cranial nerve palsies and pituitary dysfunction. Our patient initially presented with localised ENT involvement, but despite treatment with methotrexate, she deteriorated. Granulomatous inflammatory tissue around the skull base resulted in cavernous sinus syndrome, facial nerve palsy, palsies of cranial nerves IX-XII (Collet-Sicard syndrome), and the rare complication of cranial diabetes insipidus due to pituitary infiltration. The glossopharyngeal, vagus and accessory nerve palsies resulted in severe dysphagia and she required nasogastric tube feeding. Her neurological deficits substantially improved with treatment including high dose corticosteroid, cyclophosphamide and rituximab.<h4>Conclusions</h4>This case emphasises that serious morbidity can arise from localised cranial Wegener's granulomatosis in the absence of systemic disease. In such cases intensive induction immunosuppression is required. Analysis of previously reported cases of pituitary involvement in GPA reveals that this rare complication predominantly affects female patients.",,pdf:https://bmcneurol.biomedcentral.com/track/pdf/10.1186/s12883-018-1058-8; doi:https://doi.org/10.1186/s12883-018-1058-8; html:https://europepmc.org/articles/PMC5930853; pdf:https://europepmc.org/articles/PMC5930853?pdf=render
 34508578,https://doi.org/10.1093/gigascience/giab059,Desiderata for the development of next-generation electronic health record phenotype libraries.,"Chapman M, Mumtaz S, Rasmussen LV, Karwath A, Gkoutos GV, Gao C, Thayer D, Pacheco JA, Parkinson H, Richesson RL, Jefferson E, Denaxas S, Curcin V.",,GigaScience,2021,2021-09-01,Y,Electronic Health Records; Computable Phenotype; Ehr-based Phenotyping; Phenotype Library,,,"<h4>Background</h4>High-quality phenotype definitions are desirable to enable the extraction of patient cohorts from large electronic health record repositories and are characterized by properties such as portability, reproducibility, and validity. Phenotype libraries, where definitions are stored, have the potential to contribute significantly to the quality of the definitions they host. In this work, we present a set of desiderata for the design of a next-generation phenotype library that is able to ensure the quality of hosted definitions by combining the functionality currently offered by disparate tooling.<h4>Methods</h4>A group of researchers examined work to date on phenotype models, implementation, and validation, as well as contemporary phenotype libraries developed as a part of their own phenomics communities. Existing phenotype frameworks were also examined. This work was translated and refined by all the authors into a set of best practices.<h4>Results</h4>We present 14 library desiderata that promote high-quality phenotype definitions, in the areas of modelling, logging, validation, and sharing and warehousing.<h4>Conclusions</h4>There are a number of choices to be made when constructing phenotype libraries. Our considerations distil the best practices in the field and include pointers towards their further development to support portable, reproducible, and clinically valid phenotype design. The provision of high-quality phenotype definitions enables electronic health record data to be more effectively used in medical domains.",,pdf:https://academic.oup.com/gigascience/article-pdf/10/9/giab059/40348225/giab059.pdf; doi:https://doi.org/10.1093/gigascience/giab059; html:https://europepmc.org/articles/PMC8434766; pdf:https://europepmc.org/articles/PMC8434766?pdf=render
+29716529,https://doi.org/10.1186/s12883-018-1058-8,Severe localised granulomatosis with polyangiitis (Wegener's granulomatosis) manifesting with extensive cranial nerve palsies and cranial diabetes insipidus: a case report and literature review.,"Peters JE, Gupta V, Saeed IT, Offiah C, Jawad ASM.",,BMC neurology,2018,2018-05-01,Y,Diabetes insipidus; Cyclophosphamide; pituitary; Vasculitis; Rituximab; Anca; Cavernous Sinus Syndrome; Collet-sicard Syndrome; Granulomatosis With Polyangiitis; Wegener’s Granulomatosis,,,"<h4>Background</h4>Granulomatosis with polyangiitis (GPA, formerly Wegener's granulomatosis) is a multisystem vasculitis of small- to medium-sized blood vessels. Cranial involvement can result in cranial nerve palsies and, rarely, pituitary infiltration.<h4>Case presentation</h4>We describe the case of a 32 year-old woman with limited but severe GPA manifesting as progressive cranial nerve palsies and pituitary dysfunction. Our patient initially presented with localised ENT involvement, but despite treatment with methotrexate, she deteriorated. Granulomatous inflammatory tissue around the skull base resulted in cavernous sinus syndrome, facial nerve palsy, palsies of cranial nerves IX-XII (Collet-Sicard syndrome), and the rare complication of cranial diabetes insipidus due to pituitary infiltration. The glossopharyngeal, vagus and accessory nerve palsies resulted in severe dysphagia and she required nasogastric tube feeding. Her neurological deficits substantially improved with treatment including high dose corticosteroid, cyclophosphamide and rituximab.<h4>Conclusions</h4>This case emphasises that serious morbidity can arise from localised cranial Wegener's granulomatosis in the absence of systemic disease. In such cases intensive induction immunosuppression is required. Analysis of previously reported cases of pituitary involvement in GPA reveals that this rare complication predominantly affects female patients.",,pdf:https://bmcneurol.biomedcentral.com/track/pdf/10.1186/s12883-018-1058-8; doi:https://doi.org/10.1186/s12883-018-1058-8; html:https://europepmc.org/articles/PMC5930853; pdf:https://europepmc.org/articles/PMC5930853?pdf=render
 37139857,https://doi.org/10.1111/dom.15102,Impact of severe hypoglycaemia requiring hospitalization on mortality in people with type 1 diabetes: A national retrospective observational cohort study.,"Moser O, Rafferty J, Eckstein ML, Aziz F, Bain SC, Bergenstal R, Sourij H, Thomas RL.",,"Diabetes, obesity & metabolism",2023,2023-05-04,N,Mortality; type 1 diabetes; Risk Prediction; Severe Hypoglycaemia,,,"<h4>Aims</h4>To assess if the risk of all-cause mortality increases in people with type 1 diabetes (T1D) with increasing number of severe hypoglycaemia episodes requiring hospitalization.<h4>Materials and methods</h4>We conducted a national retrospective observational cohort study in people with T1D (diagnosed between 2000 and 2018). Clinical, comorbidity and demographic variables were assessed for impact on mortality for people with no, one, two and three or more episodes of severe hypoglycaemia requiring hospitalization. The time to death (all-cause mortality) from the timepoint of the last episode of severe hypoglycaemia was modelled using a parametric survival model.<h4>Results</h4>A total of 8224 people had a T1D diagnosis in Wales during the study period. The mortality rate (95% confidence interval [CI]) was 6.9 (6.1-7.8) deaths/ 1000 person-years (crude) and 15.31 (13.3-17.63) deaths/ 1000 person-years (age-adjusted) for those with no occurrence of severe hypoglycaemia requiring hospitalization. For those with one episode of severe hypoglycaemia requiring hospitalization the mortality rate (95% CI) was 24.9 (21.0-29.6; crude) and 53.8 (44.6-64.7) deaths/ 1000 person-years (age-adjusted), for those with two episodes of severe hypoglycaemia requiring hospitalization it was 28.0 (23.1-34.0; crude) and 72.8 (59.2-89.5) deaths/ 1000 person-years (age-adjusted), and for those with three or more episodes of severe hypoglycaemia requiring hospitalization it was 33.5 (30.0-37.3; crude) and 86.3 (71.7-103.9) deaths/ 1000 person years (age-adjusted; P < 0.001). A parametric survival model showed that having two episodes of severe hypoglycaemia requiring hospitalization was the strongest predictor for time to death (accelerated failure time coefficient 0.073 [95% CI 0.009-0.565]), followed by having one episode of severe hypoglycaemia requiring hospitalization (0.126 [0.036-0.438]) and age at most recent episode of severe hypoglycaemia requiring hospitalization (0.917 [0.885-0.951]).<h4>Conclusions</h4>The strongest predictor for time to death was having two or more episodes of severe hypoglycaemia requiring hospitalization.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/dom.15102; doi:https://doi.org/10.1111/dom.15102
-39469534,https://doi.org/10.1016/j.eclinm.2024.102887,Diagnostic performance of deep learning for infectious keratitis: a systematic review and meta-analysis.,"Ong ZZ, Sadek Y, Qureshi R, Liu SH, Li T, Liu X, Takwoingi Y, Sounderajah V, Ashrafian H, Ting DSW, Mehta JS, Rauz S, Said DG, Dua HS, Burton MJ, Ting DSJ.",,EClinicalMedicine,2024,2024-10-18,Y,Artificial intelligence; Corneal Ulcer; Microbial Keratitis; Infectious Keratitis; Corneal Infection; Deep Learning,,,"<h4>Background</h4>Infectious keratitis (IK) is the leading cause of corneal blindness globally. Deep learning (DL) is an emerging tool for medical diagnosis, though its value in IK is unclear. We aimed to assess the diagnostic accuracy of DL for IK and its comparative accuracy with ophthalmologists.<h4>Methods</h4>In this systematic review and meta-analysis, we searched EMBASE, MEDLINE, and clinical registries for studies related to DL for IK published between 1974 and July 16, 2024. We performed meta-analyses using bivariate models to estimate summary sensitivities and specificities. This systematic review was registered with PROSPERO (CRD42022348596).<h4>Findings</h4>Of 963 studies identified, 35 studies (136,401 corneal images from >56,011 patients) were included. Most studies had low risk of bias (68.6%) and low applicability concern (91.4%) in all domains of QUADAS-2, except the index test domain. Against the reference standard of expert consensus and/or microbiological results (seven external validation studies; 10,675 images), the summary estimates (95% CI) for sensitivity and specificity of DL for IK were 86.2% (71.6-93.9) and 96.3% (91.5-98.5). From 28 internal validation studies (16,059 images), summary estimates for sensitivity and specificity were 91.6% (86.8-94.8) and 90.7% (84.8-94.5). Based on seven studies (4007 images), DL and ophthalmologists had comparable summary sensitivity [89.2% (82.2-93.6) versus 82.2% (71.5-89.5); P = 0.20] and specificity [(93.2% (85.5-97.0) versus 89.6% (78.8-95.2); P = 0.45].<h4>Interpretation</h4>DL models may have good diagnostic accuracy for IK and comparable performance to ophthalmologists. These findings should be interpreted with caution due to the image-based analysis that did not account for potential correlation within individuals, relatively homogeneous population studies, lack of pre-specification of DL thresholds, and limited external validation. Future studies should improve their reporting, data diversity, external validation, transparency, and explainability to increase the reliability and generalisability of DL models for clinical deployment.<h4>Funding</h4>NIH, Wellcome Trust, MRC, Fight for Sight, BHP, and ESCRS.",,doi:https://doi.org/10.1016/j.eclinm.2024.102887; html:https://europepmc.org/articles/PMC11513659; pdf:https://europepmc.org/articles/PMC11513659?pdf=render
 36447757,https://doi.org/10.1136/gpsych-2022-100819,Body mass index and mortality in patients with schizophrenia spectrum disorders: a cohort study in a South London catchment area.,"Chen J, Perera G, Shetty H, Broadbent M, Xu Y, Stewart R.",,General psychiatry,2022,2022-11-04,Y,Schizophrenia; Life style; Mental Health Services,,,"<h4>Background</h4>People with schizophrenia have a high premature mortality risk. Obesity is a key potential underlying risk factor that is relatively unevaluated to date.<h4>Aims</h4>In this study, we investigated the associations of routinely recorded body size with all-cause mortality and deaths from common causes in a large cohort of people with schizophrenia spectrum disorders.<h4>Methods</h4>We assembled a retrospective observational cohort using data from a large mental health service in South London. We followed all patients over the age of 18 years with a clinical diagnosis of schizophrenia spectrum disorders from the date of their first recorded body mass index (BMI) between 1 January 2007 and 31 March 2018.<h4>Results</h4>Of 11 900 patients with a BMI recording, 1566 died. The Cox proportional hazards regression models, after adjusting for sociodemographic, socioeconomic variables and comorbidities, indicated that all-cause mortality was only associated with underweight status compared with healthy weight status (hazard ratio (HR): 1.33, 95% confidence interval (CI): 1.01 to 1.76). Obesity (HR: 1.24, 95% CI: 1.01 to 1.52) and morbid obesity (HR: 1.54, 95% CI: 1.03 to 2.42) were associated with all-cause mortality in the 18-45 years age range, and obesity was associated with lower risk (HR: 0.66, 95% CI: 0.50 to 0.87) in those aged 65+ years. Cancer mortality was raised in underweight individuals (HR: 1.93, 95% CI: 1.03 to 4.10) and respiratory disease mortality raised in those with morbid obesity (HR: 2.17, 95% CI: 1.02 to 5.22).<h4>Conclusions</h4>Overall, being underweight was associated with higher mortality in this disorder group; however, this was potentially accounted for by frailty in older age groups, and obesity was a risk factor for premature mortality in younger ages. The impact of obesity on life expectancy for people with schizophrenia spectrum disorders is clear from our findings. A deeper biological understanding of the relationship between these diseases and schizophrenia will help improve clinical practice.",,pdf:https://gpsych.bmj.com/content/gpsych/35/5/e100819.full.pdf; doi:https://doi.org/10.1136/gpsych-2022-100819; html:https://europepmc.org/articles/PMC9639123; pdf:https://europepmc.org/articles/PMC9639123?pdf=render
 37561116,https://doi.org/10.7554/elife.85332,Healthcare in England was affected by the COVID-19 pandemic across the pancreatic cancer pathway: A cohort study using OpenSAFELY-TPP.,"Lemanska A, Andrews C, Fisher L, Bacon S, Frampton AE, Mehrkar A, Inglesby P, Davy S, Roberts K, Patalay P, Goldacre B, MacKenna B, OpenSAFELY Collaborative, Walker AJ.",,eLife,2023,2023-08-10,Y,Human; Pancreatic cancer; epidemiology; Global Health; Healthcare; Healthcare Crisis; Covid-19; Healthcare Disruption,,,"<h4>Background</h4>Healthcare across all sectors, in the UK and globally, was negatively affected by the COVID-19 pandemic. We analysed healthcare services delivered to people with pancreatic cancer from January 2015 to March 2023 to investigate the effect of the COVID-19 pandemic.<h4>Methods</h4>With the approval of NHS England, and drawing from a nationally representative OpenSAFELY-TPP dataset of 24 million patients (over 40% of the English population), we undertook a cohort study of people diagnosed with pancreatic cancer. We queried electronic healthcare records for information on the provision of healthcare services across the pancreatic cancer pathway. To estimate the effect of the COVID-19 pandemic, we predicted the rates of healthcare services if the pandemic had not happened. We used generalised linear models and the pre-pandemic data from January 2015 to February 2020 to predict rates in March 2020 to March 2023. The 95% confidence intervals of the predicted values were used to estimate the significance of the difference between the predicted and observed rates.<h4>Results</h4>The rate of pancreatic cancer and diabetes diagnoses in the cohort was not affected by the pandemic. There were 26,840 people diagnosed with pancreatic cancer from January 2015 to March 2023. The mean age at diagnosis was 72 (±11 SD), 48% of people were female, 95% were of White ethnicity, and 40% were diagnosed with diabetes. We found a reduction in surgical resections by 25-28% during the pandemic. In addition, 20%, 10%, and 4% fewer people received body mass index, glycated haemoglobin, and liver function tests, respectively, before they were diagnosed with pancreatic cancer. There was no impact of the pandemic on the number of people making contact with primary care, but the number of contacts increased on average by 1-2 per person amongst those who made contact. Reporting of jaundice decreased by 28%, but recovered within 12 months into the pandemic. Emergency department visits, hospital admissions, and deaths were not affected.<h4>Conclusions</h4>The pandemic affected healthcare in England across the pancreatic cancer pathway. Positive lessons could be learnt from the services that were resilient and those that recovered quickly. The reductions in healthcare experienced by people with cancer have the potential to lead to worse outcomes. Current efforts should focus on addressing the unmet needs of people with cancer.<h4>Funding</h4>This work was jointly funded by the Wellcome Trust (222097/Z/20/Z); MRC (MR/V015757/1, MC_PC-20059, MR/W016729/1); NIHR (NIHR135559, COV-LT2-0073), and Health Data Research UK (HDRUK2021.000, 2021.0157). This work was funded by Medical Research Council (MRC) grant reference MR/W021390/1 as part of the postdoctoral fellowship awarded to AL and undertaken at the Bennett Institute, University of Oxford. The views expressed are those of the authors and not necessarily those of the NIHR, NHS England, UK Health Security Agency (UKHSA), or the Department of Health and Social Care. Funders had no role in the study design, collection, analysis, and interpretation of data; in the writing of the report; and in the decision to submit the article for publication.",,doi:https://doi.org/10.7554/eLife.85332; html:https://europepmc.org/articles/PMC10414967; pdf:https://europepmc.org/articles/PMC10414967?pdf=render
-38528230,https://doi.org/10.1038/s43587-024-00590-7,Integration of polygenic and gut metagenomic risk prediction for common diseases.,"Liu Y, Ritchie SC, Teo SM, Ruuskanen MO, Kambur O, Zhu Q, Sanders J, Vázquez-Baeza Y, Verspoor K, Jousilahti P, Lahti L, Niiranen T, Salomaa V, Havulinna AS, Knight R, Méric G, Inouye M.",,Nature aging,2024,2024-03-25,Y,,,,"Multiomics has shown promise in noninvasive risk profiling and early detection of various common diseases. In the present study, in a prospective population-based cohort with ~18 years of e-health record follow-up, we investigated the incremental and combined value of genomic and gut metagenomic risk assessment compared with conventional risk factors for predicting incident coronary artery disease (CAD), type 2 diabetes (T2D), Alzheimer disease and prostate cancer. We found that polygenic risk scores (PRSs) improved prediction over conventional risk factors for all diseases. Gut microbiome scores improved predictive capacity over baseline age for CAD, T2D and prostate cancer. Integrated risk models of PRSs, gut microbiome scores and conventional risk factors achieved the highest predictive performance for all diseases studied compared with models based on conventional risk factors alone. The present study demonstrates that integrated PRSs and gut metagenomic risk models improve the predictive value over conventional risk factors for common chronic diseases.",,pdf:https://www.nature.com/articles/s43587-024-00590-7.pdf; doi:https://doi.org/10.1038/s43587-024-00590-7; html:https://europepmc.org/articles/PMC11031402; pdf:https://europepmc.org/articles/PMC11031402?pdf=render
+39469534,https://doi.org/10.1016/j.eclinm.2024.102887,Diagnostic performance of deep learning for infectious keratitis: a systematic review and meta-analysis.,"Ong ZZ, Sadek Y, Qureshi R, Liu SH, Li T, Liu X, Takwoingi Y, Sounderajah V, Ashrafian H, Ting DSW, Mehta JS, Rauz S, Said DG, Dua HS, Burton MJ, Ting DSJ.",,EClinicalMedicine,2024,2024-10-18,Y,Artificial intelligence; Corneal Ulcer; Microbial Keratitis; Infectious Keratitis; Corneal Infection; Deep Learning,,,"<h4>Background</h4>Infectious keratitis (IK) is the leading cause of corneal blindness globally. Deep learning (DL) is an emerging tool for medical diagnosis, though its value in IK is unclear. We aimed to assess the diagnostic accuracy of DL for IK and its comparative accuracy with ophthalmologists.<h4>Methods</h4>In this systematic review and meta-analysis, we searched EMBASE, MEDLINE, and clinical registries for studies related to DL for IK published between 1974 and July 16, 2024. We performed meta-analyses using bivariate models to estimate summary sensitivities and specificities. This systematic review was registered with PROSPERO (CRD42022348596).<h4>Findings</h4>Of 963 studies identified, 35 studies (136,401 corneal images from >56,011 patients) were included. Most studies had low risk of bias (68.6%) and low applicability concern (91.4%) in all domains of QUADAS-2, except the index test domain. Against the reference standard of expert consensus and/or microbiological results (seven external validation studies; 10,675 images), the summary estimates (95% CI) for sensitivity and specificity of DL for IK were 86.2% (71.6-93.9) and 96.3% (91.5-98.5). From 28 internal validation studies (16,059 images), summary estimates for sensitivity and specificity were 91.6% (86.8-94.8) and 90.7% (84.8-94.5). Based on seven studies (4007 images), DL and ophthalmologists had comparable summary sensitivity [89.2% (82.2-93.6) versus 82.2% (71.5-89.5); P = 0.20] and specificity [(93.2% (85.5-97.0) versus 89.6% (78.8-95.2); P = 0.45].<h4>Interpretation</h4>DL models may have good diagnostic accuracy for IK and comparable performance to ophthalmologists. These findings should be interpreted with caution due to the image-based analysis that did not account for potential correlation within individuals, relatively homogeneous population studies, lack of pre-specification of DL thresholds, and limited external validation. Future studies should improve their reporting, data diversity, external validation, transparency, and explainability to increase the reliability and generalisability of DL models for clinical deployment.<h4>Funding</h4>NIH, Wellcome Trust, MRC, Fight for Sight, BHP, and ESCRS.",,doi:https://doi.org/10.1016/j.eclinm.2024.102887; html:https://europepmc.org/articles/PMC11513659; pdf:https://europepmc.org/articles/PMC11513659?pdf=render
 29938349,https://doi.org/10.1007/s11892-018-1021-5,Shared Genetic Contribution of Type 2 Diabetes and Cardiovascular Disease: Implications for Prognosis and Treatment.,"Strawbridge RJ, van Zuydam NR.",,Current diabetes reports,2018,2018-06-25,Y,Type 2 diabetes; Ischemic stroke; coronary artery disease; risk factors; Peripheral Artery Disease; Genetics; Mendelian Randomisation,,,"<h4>Purpose of review</h4>The increased cardiovascular disease (CVD) risk in subjects with type 2 diabetes (T2D) is well established. This review collates the available evidence and assesses the shared genetic background between T2D and CVD: the causal contribution of common risk factors to T2D and CVD and how genetics can be used to improve drug development and clinical outcomes.<h4>Recent findings</h4>Large-scale genome-wide association studies (GWAS) of T2D and CVD support a shared genetic background but minimal individual locus overlap. Mendelian randomisation (MR) analyses show that T2D is causal for CVD, but GWAS of CVD, T2D and their common risk factors provided limited evidence for individual locus overlap. Distinct but functionally related pathways were enriched for CVD and T2D genetic associations reflecting the lack of locus overlap and providing some explanation for the variable associations of common risk factors with CVD and T2D from MR analyses.",,pdf:https://link.springer.com/content/pdf/10.1007/s11892-018-1021-5.pdf; doi:https://doi.org/10.1007/s11892-018-1021-5; html:https://europepmc.org/articles/PMC6015804; pdf:https://europepmc.org/articles/PMC6015804?pdf=render
+31797917,https://doi.org/10.1038/s41398-019-0635-y,"Novel genome-wide associations for anhedonia, genetic correlation with psychiatric disorders, and polygenic association with brain structure.","Ward J, Lyall LM, Bethlehem RAI, Ferguson A, Strawbridge RJ, Lyall DM, Cullen B, Graham N, Johnston KJA, Bailey MES, Murray GK, Smith DJ.",,Translational psychiatry,2019,2019-12-04,Y,,,,"Anhedonia is a core symptom of several psychiatric disorders but its biological underpinnings are poorly understood. We performed a genome-wide association study of state anhedonia in 375,275 UK Biobank participants and assessed for genetic correlation between anhedonia and neuropsychiatric conditions (major depressive disorder, schizophrenia, bipolar disorder, obsessive compulsive disorder and Parkinson's Disease). We then used a polygenic risk score approach to test for association between genetic loading for anhedonia and both brain structure and brain function. This included: magnetic resonance imaging (MRI) assessments of total grey matter volume, white matter volume, cerebrospinal fluid volume, and 15 cortical/subcortical regions of interest; diffusion tensor imaging (DTI) measures of white matter tract integrity; and functional MRI activity during an emotion processing task. We identified 11 novel loci associated at genome-wide significance with anhedonia, with a SNP heritability estimate (h<sub>2</sub>SNP) of 5.6%. Strong positive genetic correlations were found between anhedonia and major depressive disorder, schizophrenia and bipolar disorder; but not with obsessive compulsive disorder or Parkinson's Disease. Polygenic risk for anhedonia was associated with poorer brain white matter integrity, smaller total grey matter volume, and smaller volumes of brain regions linked to reward and pleasure processing, including orbito-frontal cortex. In summary, the identification of novel anhedonia-associated loci substantially expands our current understanding of the biological basis of state anhedonia and genetic correlations with several psychiatric disorders confirm the utility of this phenotype as a transdiagnostic marker of vulnerability to mental illness. We also provide the first evidence that genetic risk for state anhedonia influences brain structure, including in regions associated with reward and pleasure processing.",This study assessed for genetic correlation between anhedonia and neuropsychiatric conditions. A polygenic risk score approach was applied to test for association between anhedonia and brain structure and brain function. Findings confirm that using anhedonia as a marker of vulnerability to mental illness. Findings also suggest that genetic risk for state anhedonia influences brain structure,pdf:https://www.nature.com/articles/s41398-019-0635-y.pdf; doi:https://doi.org/10.1038/s41398-019-0635-y; html:https://europepmc.org/articles/PMC6892870; pdf:https://europepmc.org/articles/PMC6892870?pdf=render
+38528230,https://doi.org/10.1038/s43587-024-00590-7,Integration of polygenic and gut metagenomic risk prediction for common diseases.,"Liu Y, Ritchie SC, Teo SM, Ruuskanen MO, Kambur O, Zhu Q, Sanders J, Vázquez-Baeza Y, Verspoor K, Jousilahti P, Lahti L, Niiranen T, Salomaa V, Havulinna AS, Knight R, Méric G, Inouye M.",,Nature aging,2024,2024-03-25,Y,,,,"Multiomics has shown promise in noninvasive risk profiling and early detection of various common diseases. In the present study, in a prospective population-based cohort with ~18 years of e-health record follow-up, we investigated the incremental and combined value of genomic and gut metagenomic risk assessment compared with conventional risk factors for predicting incident coronary artery disease (CAD), type 2 diabetes (T2D), Alzheimer disease and prostate cancer. We found that polygenic risk scores (PRSs) improved prediction over conventional risk factors for all diseases. Gut microbiome scores improved predictive capacity over baseline age for CAD, T2D and prostate cancer. Integrated risk models of PRSs, gut microbiome scores and conventional risk factors achieved the highest predictive performance for all diseases studied compared with models based on conventional risk factors alone. The present study demonstrates that integrated PRSs and gut metagenomic risk models improve the predictive value over conventional risk factors for common chronic diseases.",,pdf:https://www.nature.com/articles/s43587-024-00590-7.pdf; doi:https://doi.org/10.1038/s43587-024-00590-7; html:https://europepmc.org/articles/PMC11031402; pdf:https://europepmc.org/articles/PMC11031402?pdf=render
 35365351,https://doi.org/10.1016/j.injury.2022.03.039,Injury severity and increased socioeconomic differences: A population-based cohort study.,"Madsen C, Gabbe BJ, Holvik K, Alver K, Grøholt EK, Lund J, Lyons J, Lyons RA, Ohm E.",,Injury,2022,2022-03-24,N,Injury; Socioeconomic status; Hospitalization; Iciss; Injury-vibes; Risk-adjusted Severity,,,"<h4>Background</h4>Several studies have documented an inverse gradient between socioeconomic status (SES) and injury mortality, but the evidence is less consistent for injury morbidity. The aim of this study was to investigate the association between SES and injury severity for acute hospitalizations in a nationwide population-based cohort.<h4>Methods</h4>We conducted a registry-based cohort study of all individuals aged 25-64 years residing in Norway by 1st of January 2008. This cohort was followed from 2008 through 2014 using inpatient registrations for acute hospitalizations due to all-cause injuries. We derived two measures of severity: threat-to-life using the International Classification of Disease-based Injury Severity Score (ICISS), and threat of disability using long-term disability weights from the Injury-VIBES project. Robust Poisson regression models, with adjustment for age, sex, marital status, immigrant status, municipality population size and healthcare region of residence, were used to calculate incidence rate ratios (IRRs) by SES measured as an index of education, income, and occupation.<h4>Results</h4>We identified 177,663 individuals (7% of the population) hospitalized with at least one acute injury in the observation period. Two percent (n = 4,186) had injuries categorized with high threat-to-life, while one quarter (n = 43,530) had injuries with high threat of disability. The overall adjusted IRR of hospitalization among people with low compared to high SES was 1.57 (95% CI 1.55, 1.60). Comparing low to high SES, injuries with low threat-to-life were associated with an IRR of 1.56 (95% CI 1.54, 1.59), while injuries with high threat-to-life had an IRR of 2.25 (95% CI 2.03, 2.51). Comparing low to high SES, injuries with low, medium, and high threat of disability were associated with IRRs of respectively, 1.15 (95% CI 1.11, 1.19), 1.70 (95% CI 1.66, 1.73) and 1.99 (95% CI 1.92, 2.07).<h4>Discussion</h4>We observed an inverse gradient between SES and injury morbidity, with the steepest gradient for the most severe injuries. This suggests a need for targeted preventive measures to reduce the magnitude and burden of severe injuries for patients with low socioeconomic status.",,pdf:http://www.injuryjournal.com/article/S0020138322002327/pdf; doi:https://doi.org/10.1016/j.injury.2022.03.039
 36895179,https://doi.org/10.1093/eurjpc/zwad055,Determining cardiovascular risk in patients with unattributed chest pain in UK primary care: an electronic health record study.,"Jordan KP, Rathod-Mistry T, van der Windt DA, Bailey J, Chen Y, Clarson L, Denaxas S, Hayward RA, Hemingway H, Kyriacou T, Mamas MA.",,European journal of preventive cardiology,2023,2023-08-01,Y,Cardiovascular disease; Chest pain; epidemiology; Primary Health Care; risk; Electronic Health Records,,,"<h4>Aims</h4>Most adults presenting in primary care with chest pain symptoms will not receive a diagnosis ('unattributed' chest pain) but are at increased risk of cardiovascular events. To assess within patients with unattributed chest pain, risk factors for cardiovascular events and whether those at greatest risk of cardiovascular disease can be ascertained by an existing general population risk prediction model or by development of a new model.<h4>Methods and results</h4>The study used UK primary care electronic health records from the Clinical Practice Research Datalink linked to admitted hospitalizations. Study population was patients aged 18 plus with recorded unattributed chest pain 2002-2018. Cardiovascular risk prediction models were developed with external validation and comparison of performance to QRISK3, a general population risk prediction model. There were 374 917 patients with unattributed chest pain in the development data set. The strongest risk factors for cardiovascular disease included diabetes, atrial fibrillation, and hypertension. Risk was increased in males, patients of Asian ethnicity, those in more deprived areas, obese patients, and smokers. The final developed model had good predictive performance (external validation c-statistic 0.81, calibration slope 1.02). A model using a subset of key risk factors for cardiovascular disease gave nearly identical performance. QRISK3 underestimated cardiovascular risk.<h4>Conclusion</h4>Patients presenting with unattributed chest pain are at increased risk of cardiovascular events. It is feasible to accurately estimate individual risk using routinely recorded information in the primary care record, focusing on a small number of risk factors. Patients at highest risk could be targeted for preventative measures.",,pdf:https://academic.oup.com/eurjpc/advance-article-pdf/doi/10.1093/eurjpc/zwad055/49604587/zwad055.pdf; doi:https://doi.org/10.1093/eurjpc/zwad055; html:https://europepmc.org/articles/PMC10442054; pdf:https://europepmc.org/articles/PMC10442054?pdf=render
 36150783,https://doi.org/10.1016/s2589-7500(22)00147-9,Data capture and sharing in the COVID-19 pandemic: a cause for concern.,"Dron L, Kalatharan V, Gupta A, Haggstrom J, Zariffa N, Morris AD, Arora P, Park J.",,The Lancet. Digital health,2022,2022-10-01,Y,,,,"Routine health care and research have been profoundly influenced by digital-health technologies. These technologies range from primary data collection in electronic health records (EHRs) and administrative claims to web-based artificial-intelligence-driven analyses. There has been increased use of such health technologies during the COVID-19 pandemic, driven in part by the availability of these data. In some cases, this has resulted in profound and potentially long-lasting positive effects on medical research and routine health-care delivery. In other cases, high profile shortcomings have been evident, potentially attenuating the effect of-or representing a decreased appetite for-digital-health transformation. In this Series paper, we provide an overview of how facets of health technologies in routinely collected medical data (including EHRs and digital data sharing) have been used for COVID-19 research and tracking, and how these technologies might influence future pandemics and health-care research. We explore the strengths and weaknesses of digital-health research during the COVID-19 pandemic and discuss how learnings from COVID-19 might translate into new approaches in a post-pandemic era.",,doi:https://doi.org/10.1016/s2589-7500(22)00147-9; doi:https://doi.org/10.1016/S2589-7500(22)00147-9; html:https://europepmc.org/articles/PMC9489064; pdf:https://europepmc.org/articles/PMC9489064?pdf=render
-31797917,https://doi.org/10.1038/s41398-019-0635-y,"Novel genome-wide associations for anhedonia, genetic correlation with psychiatric disorders, and polygenic association with brain structure.","Ward J, Lyall LM, Bethlehem RAI, Ferguson A, Strawbridge RJ, Lyall DM, Cullen B, Graham N, Johnston KJA, Bailey MES, Murray GK, Smith DJ.",,Translational psychiatry,2019,2019-12-04,Y,,,,"Anhedonia is a core symptom of several psychiatric disorders but its biological underpinnings are poorly understood. We performed a genome-wide association study of state anhedonia in 375,275 UK Biobank participants and assessed for genetic correlation between anhedonia and neuropsychiatric conditions (major depressive disorder, schizophrenia, bipolar disorder, obsessive compulsive disorder and Parkinson's Disease). We then used a polygenic risk score approach to test for association between genetic loading for anhedonia and both brain structure and brain function. This included: magnetic resonance imaging (MRI) assessments of total grey matter volume, white matter volume, cerebrospinal fluid volume, and 15 cortical/subcortical regions of interest; diffusion tensor imaging (DTI) measures of white matter tract integrity; and functional MRI activity during an emotion processing task. We identified 11 novel loci associated at genome-wide significance with anhedonia, with a SNP heritability estimate (h<sub>2</sub>SNP) of 5.6%. Strong positive genetic correlations were found between anhedonia and major depressive disorder, schizophrenia and bipolar disorder; but not with obsessive compulsive disorder or Parkinson's Disease. Polygenic risk for anhedonia was associated with poorer brain white matter integrity, smaller total grey matter volume, and smaller volumes of brain regions linked to reward and pleasure processing, including orbito-frontal cortex. In summary, the identification of novel anhedonia-associated loci substantially expands our current understanding of the biological basis of state anhedonia and genetic correlations with several psychiatric disorders confirm the utility of this phenotype as a transdiagnostic marker of vulnerability to mental illness. We also provide the first evidence that genetic risk for state anhedonia influences brain structure, including in regions associated with reward and pleasure processing.",This study assessed for genetic correlation between anhedonia and neuropsychiatric conditions. A polygenic risk score approach was applied to test for association between anhedonia and brain structure and brain function. Findings confirm that using anhedonia as a marker of vulnerability to mental illness. Findings also suggest that genetic risk for state anhedonia influences brain structure,pdf:https://www.nature.com/articles/s41398-019-0635-y.pdf; doi:https://doi.org/10.1038/s41398-019-0635-y; html:https://europepmc.org/articles/PMC6892870; pdf:https://europepmc.org/articles/PMC6892870?pdf=render
 34784292,https://doi.org/10.2196/32587,Investigating the Use of Digital Health Technology to Monitor COVID-19 and Its Effects: Protocol for an Observational Study (Covid Collab Study).,"Stewart C, Ranjan Y, Conde P, Rashid Z, Sankesara H, Bai X, Dobson RJB, Folarin AA.",,JMIR research protocols,2021,2021-12-08,Y,Monitoring; Infectious disease; Recovery; Mobile phone; Feasibility; Surveillance; Data; Mental health; Observational; Smartphone; Wearable; Mobile Health; Wearable Devices; Digital Health; Crowdsourced; Covid-19,,,"<h4>Background</h4>The ubiquity of mobile phones and increasing use of wearable fitness trackers offer a wide-ranging window into people's health and well-being. There are clear advantages in using remote monitoring technologies to gain an insight into health, particularly under the shadow of the COVID-19 pandemic.<h4>Objective</h4>Covid Collab is a crowdsourced study that was set up to investigate the feasibility of identifying, monitoring, and understanding the stratification of SARS-CoV-2 infection and recovery through remote monitoring technologies. Additionally, we will assess the impacts of the COVID-19 pandemic and associated social measures on people's behavior, physical health, and mental well-being.<h4>Methods</h4>Participants will remotely enroll in the study through the Mass Science app to donate historic and prospective mobile phone data, fitness tracking wearable data, and regular COVID-19-related and mental health-related survey data. The data collection period will cover a continuous period (ie, both before and after any reported infections), so that comparisons to a participant's own baseline can be made. We plan to carry out analyses in several areas, which will cover symptomatology; risk factors; the machine learning-based classification of illness; and trajectories of recovery, mental well-being, and activity.<h4>Results</h4>As of June 2021, there are over 17,000 participants-largely from the United Kingdom-and enrollment is ongoing.<h4>Conclusions</h4>This paper introduces a crowdsourced study that will include remotely enrolled participants to record mobile health data throughout the COVID-19 pandemic. The data collected may help researchers investigate a variety of areas, including COVID-19 progression; mental well-being during the pandemic; and the adherence of remote, digitally enrolled participants.<h4>International registered report identifier (irrid)</h4>DERR1-10.2196/32587.",,doi:https://doi.org/10.2196/32587; doi:https://doi.org/10.2196/32587; html:https://europepmc.org/articles/PMC8658240
 35290719,https://doi.org/10.1002/alz.12635,"Incidence, morbidity, mortality and disparities in dementia: A population linked electronic health records study of 4.3 million individuals.","Chung SC, Providencia R, Sofat R, Pujades-Rodriguez M, Torralbo A, Fatemifar G, Fitzpatrick NK, Taylor J, Li K, Dale C, Rossor M, Acosta-Mena D, Whittaker J, Denaxas S.",,Alzheimer's & dementia : the journal of the Alzheimer's Association,2023,2022-03-15,Y,Mortality; Alzheimer's disease; Vascular dementia; Cause of death; Dementia; epidemiology; incidence; United Kingdom; Health Inequality; Comorbidity; Electronic Health Records; Hospitalizations; Health-care Use,,,"<h4>Introduction</h4>We report dementia incidence, comorbidities, reasons for health-care visits, mortality, causes of death, and examined dementia patterns by relative deprivation in the UK.<h4>Method</h4>A longitudinal cohort analysis of linked electronic health records from 4.3 million people in the UK was conducted to investigate dementia incidence and mortality. Reasons for hospitalization and causes of death were compared in individuals with and without dementia.<h4>Results</h4>From 1998 to 2016 we observed 145,319 (3.1%) individuals with incident dementia. Repeated hospitalizations among senior adults for infection, unknown morbidity, and multiple primary care visits for chronic pain were observed prior to dementia diagnosis. Multiple long-term conditions are present in half of the individuals at the time of diagnosis. Individuals living in high deprivation areas had higher dementia incidence and high fatality.<h4>Discussion</h4>There is a considerable disparity of dementia that informs priorities of prevention and provision of patient care.",,pdf:https://discovery.ucl.ac.uk/10145566/1/ChungIncidence%2C%20morbidity%2C%20mortality%20and%20disparities%20in%20dementia_AOP.pdf; doi:https://doi.org/10.1002/alz.12635; html:https://europepmc.org/articles/PMC10078672; pdf:https://europepmc.org/articles/PMC10078672?pdf=render
 34298561,https://doi.org/10.1177/2047487320914115,Achievement of European guideline-recommended lipid levels post-percutaneous coronary intervention: A population-level observational cohort study.,"Harris DE, Lacey A, Akbari A, Torabi F, Smith D, Jenkins G, Obaid D, Chase A, Gravenor M, Halcox J.",,European journal of preventive cardiology,2021,2021-07-01,N,Lipids; Cholesterol; Percutaneous coronary intervention; Secondary Prevention; Pharmacoepidemiology; statins,,,"<h4>Aims</h4>European Society of Cardiology/European Atherosclerosis Society 2019 guidelines recommend more aggressive lipid targets in high- and very high-risk patients and the addition of adjuvant treatments to statins in uncontrolled patients. We aimed to assess (a) achievement of prior and new European Society of Cardiology/European Atherosclerosis Society lipid targets and (b) lipid-lowering therapy prescribing in a nationwide cohort of very high-risk patients.<h4>Methods</h4>We conducted a retrospective observational population study using linked health data in patients undergoing percutaneous coronary intervention (2012-2017). Follow-up was for one-year post-discharge.<h4>Results</h4>Altogether, 10,071 patients had a documented LDL-C level, of whom 48% had low-density lipoprotein cholesterol (LDL-C)<1.8 mmol/l (2016 target) and (23%) <1.4 mmol/l (2019 target). Five thousand three hundred and forty patients had non-high-density lipoprotein cholesterol (non-HDL-C) documented with 57% <2.6 mmol/l (2016) and 37% <2.2 mmol/l (2019). In patients with recurrent vascular events, fewer than 6% of the patients achieved the 2019 LDL-C target of <1.0 mmol/l. A total of 10,592 patients had triglyceride (TG) levels documented, of whom 14% were ≥2.3 mmol/l and 41% ≥1.5 mmol/l (2019). High-intensity statins were prescribed in 56.4% of the cohort, only 3% were prescribed ezetimibe, fibrates or prescription-grade N-3 fatty acids. Prescribing of these agents was lower amongst patients above target LDL-C, non-HDL-C and triglyceride levels. Females were more likely to have LDL-C, non-HDL-C and triglyceride levels above target.<h4>Conclusion</h4>There was a low rate of achievement of the new European Society of Cardiology/European Atherosclerosis Society lipid targets in this large post-percutaneous coronary intervention population and relatively low rates of intensive lipid-lowering therapy prescribing in those with uncontrolled lipids. There is considerable potential to optimise lipid-lowering therapy further through statin intensification and appropriate use of novel lipid-lowering therapy, especially in women.",,pdf:https://academic.oup.com/eurjpc/article-pdf/28/8/854/39301721/zwaa298.pdf; doi:https://doi.org/10.1177/2047487320914115
@@ -968,8 +969,8 @@ PMC10686417,https://doi.org/,The impact of restricted provision of publicly fund
 34824100,https://doi.org/10.1136/openhrt-2021-001769,Implementation of an early rule-out pathway for myocardial infarction using a high-sensitivity cardiac troponin T assay.,"Sandeman D, Syed MBJ, Kimenai DM, Lee KK, Anand A, Joshi SS, Dinnel L, Wenham PR, Campbell K, Jarvie M, Galloway D, Anderson M, Roy B, Andrews JPM, Strachan FE, Ferry AV, Chapman AR, Elsby S, Francis M, Cargill R, Shah ASV, Mills NL.",,Open heart,2021,2021-11-01,Y,Biomarkers; Chest pain; acute coronary syndrome,,,"<h4>Objectives</h4>Patients with suspected acute coronary syndrome and high-sensitivity cardiac troponin (hs-cTn) concentrations below the limit of detection at presentation are low risk. We aim to determine whether implementing this approach facilitates the safe early discharge of patients.<h4>Methods</h4>In a prospective single-centre cohort study, consecutive patients with suspected acute coronary syndrome were included before (standard care) and after (intervention) implementation of an early rule-out pathway. During standard care, myocardial infarction was ruled out if hs-cTnT concentrations were <99th centile (14 ng/L) at presentation and at 6-12 hours after symptom onset. In the intervention, patients were ruled out if hs-cTnT concentrations were <5 ng/L at presentation and symptoms present for ≥3 hours or were ≥5 ng/L and unchanged within the reference range at 3 hours. We compared duration of stay (efficacy) and all-cause death at 1 year (safety) before and after implementation.<h4>Results</h4>We included 10 315 consecutive patients (64±16 years, 46% women) with 6642 (64%) and 3673 (36%) in the standard care and intervention groups, respectively. Duration of stay was reduced from 534 (IQR, 220-2279) to 390 (IQR, 218-1910) min (p<0.001) after implementation. At 1 year, all-cause death occurred in 10.9% (721 of 6642) and 10.4% (381 of 3673) of patients in the standard care group (referent) and intervention group, respectively (adjusted OR 1.02, 95% CI 0.88 to 1.18).<h4>Conclusion</h4>In patients with suspected acute coronary syndrome, implementing an early rule-out pathway using hs-cTnT concentrations <5 ng/L at presentation reduced the duration of stay in hospital without compromising safety.",,pdf:https://openheart.bmj.com/content/openhrt/8/2/e001769.full.pdf; doi:https://doi.org/10.1136/openhrt-2021-001769; html:https://europepmc.org/articles/PMC8627412; pdf:https://europepmc.org/articles/PMC8627412?pdf=render
 36134690,https://doi.org/10.1242/dev.200654,Coupled myovascular expansion directs cardiac growth and regeneration.,"DeBenedittis P, Karpurapu A, Henry A, Thomas MC, McCord TJ, Brezitski K, Prasad A, Baker CE, Kobayashi Y, Shah SH, Kontos CD, Tata PR, Lumbers RT, Karra R.",,"Development (Cambridge, England)",2022,2022-09-22,N,Mouse; Cardiomyocyte proliferation; Heart regeneration; Myovascular,,,"Heart regeneration requires multiple cell types to enable cardiomyocyte (CM) proliferation. How these cells interact to create growth niches is unclear. Here, we profile proliferation kinetics of cardiac endothelial cells (CECs) and CMs in the neonatal mouse heart and find that they are spatiotemporally coupled. We show that coupled myovascular expansion during cardiac growth or regeneration is dependent upon VEGF-VEGFR2 signaling, as genetic deletion of Vegfr2 from CECs or inhibition of VEGFA abrogates both CEC and CM proliferation. Repair of cryoinjury displays poor spatial coupling of CEC and CM proliferation. Boosting CEC density after cryoinjury with virus encoding Vegfa enhances regeneration. Using Mendelian randomization, we demonstrate that circulating VEGFA levels are positively linked with human myocardial mass, suggesting that Vegfa can stimulate human cardiac growth. Our work demonstrates the importance of coupled CEC and CM expansion and reveals a myovascular niche that may be therapeutically targeted for heart regeneration.",,pdf:https://journals.biologists.com/dev/article-pdf/149/18/dev200654/2167548/dev200654.pdf; doi:https://doi.org/10.1242/dev.200654; html:https://europepmc.org/articles/PMC10692274; doi:https://doi.org/10.1242/dev.200654
 35945198,https://doi.org/10.1038/s41467-022-32095-5,Transferability of genetic loci and polygenic scores for cardiometabolic traits in British Pakistani and Bangladeshi individuals.,"Huang QQ, Sallah N, Dunca D, Trivedi B, Hunt KA, Hodgson S, Lambert SA, Arciero E, Wright J, Griffiths C, Trembath RC, Hemingway H, Inouye M, Finer S, van Heel DA, Lumbers RT, Martin HC, Kuchenbaecker K.",,Nature communications,2022,2022-08-09,Y,,,,"Individuals with South Asian ancestry have a higher risk of heart disease than other groups but have been largely excluded from genetic research. Using data from 22,000 British Pakistani and Bangladeshi individuals with linked electronic health records from the Genes & Health cohort, we conducted genome-wide association studies of coronary artery disease and its key risk factors. Using power-adjusted transferability ratios, we found evidence for transferability for the majority of cardiometabolic loci powered to replicate. The performance of polygenic scores was high for lipids and blood pressure, but lower for BMI and coronary artery disease. Adding a polygenic score for coronary artery disease to clinical risk factors showed significant improvement in reclassification. In Mendelian randomisation using transferable loci as instruments, our findings were consistent with results in European-ancestry individuals. Taken together, trait-specific transferability of trait loci between populations is an important consideration with implications for risk prediction and causal inference.",,pdf:https://www.nature.com/articles/s41467-022-32095-5.pdf; doi:https://doi.org/10.1038/s41467-022-32095-5; html:https://europepmc.org/articles/PMC9363492; pdf:https://europepmc.org/articles/PMC9363492?pdf=render
-39053121,https://doi.org/10.1016/j.jdiacomp.2024.108813,The effect of bariatric surgery on diabetes related foot complications among patients with type 2 diabetes: A systematic review.,"Wang Z, Crowe FL, Tahrani AA, Singh P, Wang J, Tan L, Nirantharakumar K, Hazlehurst J.",,Journal of diabetes and its complications,2024,2024-07-14,N,Type 2 diabetes; Bariatric Surgery; Diabetes Related Foot Complications,,,"<h4>Background</h4>Bariatric surgery leads to considerable weight loss and improved glycaemic control and seems to have a favourable impact on diabetes related foot complications (DFC).<h4>Objectives</h4>To assess the effect of bariatric surgery on diabetes related foot complications in patients with type 2 diabetes and determine whether DFC symptoms are improved after bariatric surgery.<h4>Methods</h4>We searched MEDLINE, Embase and Cochrane Central Register of Controlled Trials. The primary outcome was the presence of DFC after bariatric surgery. The secondary outcome was the improvement of DFC after bariatric surgery among patients who already had DFC before surgery.<h4>Results</h4>There were nine studies showing the presence of DFC post bariatric surgery and six detailing the changes in DFC post bariatric surgery. Bariatric surgery was not associated with a lower risk of developing or worsening DFC compared to conventional medical treatment based on 4 randomised control trials (IR 0.87, 95 % CI, 0.26, 2.98), while from observational studies was associated with 51 % lower risk of DFC (IR 0.49, 95 % CI, 0.31, 0.77). Bariatric surgery was associated with improvement in diabetic neuropathy assessment parameters including toe tuning fork score, self-reported neuropathy symptoms, neuropathy symptom score, and neuropathy symptom profile.<h4>Conclusion</h4>Bariatric surgery led to a greater reduction in developing or worsening DFC among patients with type 2 diabetes compared to medical treatment in observational studies, but not among RCTs. Bariatric surgery was associated with improvements in diabetic neuropathy related assessment parameters and symptoms. Bariatric surgery could be a promising treatment for patients with type 2 diabetes who are at high risk of DFC.",,doi:https://doi.org/10.1016/j.jdiacomp.2024.108813
 29925668,https://doi.org/10.1136/jech-2017-210370,Emergency hospital admissions associated with a non-randomised housing intervention meeting national housing quality standards: a longitudinal data linkage study.,"Rodgers SE, Bailey R, Johnson R, Berridge D, Poortinga W, Lannon S, Smith R, Lyons RA.",,Journal of epidemiology and community health,2018,2018-06-20,Y,Morbidity; Health Services; Public Health; Housing; Longitudinal Studies,Improving Public Health,,"<h4>Background</h4>We investigated tenant healthcare utilisation associated with upgrading 8558 council houses to a national quality standard. Homes received multiple internal and external improvements and were analysed using repeated measures of healthcare utilisation.<h4>Methods</h4>The primary outcome was emergency hospital admissions for cardiorespiratory conditions and injuries for residents aged 60 years and over. Secondary outcomes included each of the separate conditions, for tenants aged 60 and over, and for all ages. Council home address and intervention records for eight housing cointerventions were anonymously linked to demographic data, hospital admissions and deaths for individuals in a dynamic cohort. Counts of health events were analysed using multilevel regression models to investigate associations between receipt of each housing improvement, adjusting for potential confounding factors and regional trends.<h4>Results</h4>Residents aged 60 years and over living in homes when improvements were made were associated with up to 39% fewer admissions compared with those living in homes that were not upgraded (incidence rate ratio=0.61, 95% CI 0.53 to 0.72). Reduced admissions were associated with electrical systems, windows and doors, wall insulation, and garden paths. There were small non-significant reductions for the primary outcome associated with upgrading heating, adequate loft insulation, new kitchens and new bathrooms.<h4>Conclusion</h4>Results suggest that hospital admissions can be avoided through improving whole home quality standards. This is the first large-scale longitudinal evaluation of a whole home intervention that has evaluated multiple improvement elements using individual-level objective routine health data.",,pdf:https://jech.bmj.com/content/jech/72/10/896.full.pdf; doi:https://doi.org/10.1136/jech-2017-210370; html:https://europepmc.org/articles/PMC6161658; pdf:https://europepmc.org/articles/PMC6161658?pdf=render
+39053121,https://doi.org/10.1016/j.jdiacomp.2024.108813,The effect of bariatric surgery on diabetes related foot complications among patients with type 2 diabetes: A systematic review.,"Wang Z, Crowe FL, Tahrani AA, Singh P, Wang J, Tan L, Nirantharakumar K, Hazlehurst J.",,Journal of diabetes and its complications,2024,2024-07-14,N,Type 2 diabetes; Bariatric Surgery; Diabetes Related Foot Complications,,,"<h4>Background</h4>Bariatric surgery leads to considerable weight loss and improved glycaemic control and seems to have a favourable impact on diabetes related foot complications (DFC).<h4>Objectives</h4>To assess the effect of bariatric surgery on diabetes related foot complications in patients with type 2 diabetes and determine whether DFC symptoms are improved after bariatric surgery.<h4>Methods</h4>We searched MEDLINE, Embase and Cochrane Central Register of Controlled Trials. The primary outcome was the presence of DFC after bariatric surgery. The secondary outcome was the improvement of DFC after bariatric surgery among patients who already had DFC before surgery.<h4>Results</h4>There were nine studies showing the presence of DFC post bariatric surgery and six detailing the changes in DFC post bariatric surgery. Bariatric surgery was not associated with a lower risk of developing or worsening DFC compared to conventional medical treatment based on 4 randomised control trials (IR 0.87, 95 % CI, 0.26, 2.98), while from observational studies was associated with 51 % lower risk of DFC (IR 0.49, 95 % CI, 0.31, 0.77). Bariatric surgery was associated with improvement in diabetic neuropathy assessment parameters including toe tuning fork score, self-reported neuropathy symptoms, neuropathy symptom score, and neuropathy symptom profile.<h4>Conclusion</h4>Bariatric surgery led to a greater reduction in developing or worsening DFC among patients with type 2 diabetes compared to medical treatment in observational studies, but not among RCTs. Bariatric surgery was associated with improvements in diabetic neuropathy related assessment parameters and symptoms. Bariatric surgery could be a promising treatment for patients with type 2 diabetes who are at high risk of DFC.",,doi:https://doi.org/10.1016/j.jdiacomp.2024.108813
 34514354,https://doi.org/10.1093/jamiaopen/ooab001,Transforming and evaluating electronic health record disease phenotyping algorithms using the OMOP common data model: a case study in heart failure.,"Papez V, Moinat M, Payralbe S, Asselbergs FW, Lumbers RT, Hemingway H, Dobson R, Denaxas S.",,JAMIA open,2021,2021-02-04,Y,Phenotyping; Heart Failure; Algorithms; Ehr; Omop,,,"<h4>Objective</h4>The aim of the study was to transform a resource of linked electronic health records (EHR) to the OMOP common data model (CDM) and evaluate the process in terms of syntactic and semantic consistency and quality when implementing disease and risk factor phenotyping algorithms.<h4>Materials and methods</h4>Using heart failure (HF) as an exemplar, we represented three national EHR sources (Clinical Practice Research Datalink, Hospital Episode Statistics Admitted Patient Care, Office for National Statistics) into the OMOP CDM 5.2. We compared the original and CDM HF patient population by calculating and presenting descriptive statistics of demographics, related comorbidities, and relevant clinical biomarkers.<h4>Results</h4>We identified a cohort of 502 536 patients with the incident and prevalent HF and converted 1 099 195 384 rows of data from 216 581 914 encounters across three EHR sources to the OMOP CDM. The largest percentage (65%) of unmapped events was related to medication prescriptions in primary care. The average coverage of source vocabularies was >98% with the exception of laboratory tests recorded in primary care. The raw and transformed data were similar in terms of demographics and comorbidities with the largest difference observed being 3.78% in the prevalence of chronic obstructive pulmonary disease (COPD).<h4>Conclusion</h4>Our study demonstrated that the OMOP CDM can successfully be applied to convert EHR linked across multiple healthcare settings and represent phenotyping algorithms spanning multiple sources. Similar to previous research, challenges mapping primary care prescriptions and laboratory measurements still persist and require further work. The use of OMOP CDM in national UK EHR is a valuable research tool that can enable large-scale reproducible observational research.",,pdf:https://academic.oup.com/jamiaopen/article-pdf/4/3/ooab001/40325375/ooab001.pdf; doi:https://doi.org/10.1093/jamiaopen/ooab001; html:https://europepmc.org/articles/PMC8423424; pdf:https://europepmc.org/articles/PMC8423424?pdf=render
 39196201,https://doi.org/10.1038/s44161-024-00422-2,Markers of imminent myocardial infarction.,"Gustafsson S, Lampa E, Jensevik Eriksson K, Butterworth AS, Elmståhl S, Engström G, Hveem K, Johansson M, Langhammer A, Lind L, Läll K, Masala G, Metspalu A, Moreno-Iribas C, Nilsson PM, Perola M, Simell B, Sipsma H, Åsvold BO, Ingelsson E, Hammar U, Ganna A, Svennblad B, Fall T, Sundström J.",,Nature cardiovascular research,2024,2024-02-12,Y,,,,"Myocardial infarction is a leading cause of death globally but is notoriously difficult to predict. We aimed to identify biomarkers of an imminent first myocardial infarction and design relevant prediction models. Here, we constructed a new case-cohort consortium of 2,018 persons without prior cardiovascular disease from six European cohorts, among whom 420 developed a first myocardial infarction within 6 months after the baseline blood draw. We analyzed 817 proteins and 1,025 metabolites in biobanked blood and 16 clinical variables. Forty-eight proteins, 43 metabolites, age, sex and systolic blood pressure were associated with the risk of an imminent first myocardial infarction. Brain natriuretic peptide was most consistently associated with the risk of imminent myocardial infarction. Using clinically readily available variables, we devised a prediction model for an imminent first myocardial infarction for clinical use in the general population, with good discriminatory performance and potential for motivating primary prevention efforts.",,doi:https://doi.org/10.1038/s44161-024-00422-2; html:https://europepmc.org/articles/PMC11357982; pdf:https://europepmc.org/articles/PMC11357982?pdf=render
 38578666,https://doi.org/10.2196/49548,Implementation of an Electronic Clinical Decision Support System for the Early Recognition and Management of Dysglycemia in an Inpatient Mental Health Setting Using CogStack: Protocol for a Pilot Hybrid Type 3 Effectiveness-Implementation Randomized Controlled Cluster Trial.,"Patel D, Msosa YJ, Wang T, Williams J, Mustafa OG, Gee S, Arroyo B, Larkin D, Tiedt T, Roberts A, Dobson RJB, Gaughran F.",,JMIR research protocols,2024,2024-04-05,Y,Blood sugar; Diabetes; Diabetic; Implementation; Mental health; Randomized controlled trial; hyperglycemia; Hypoglycemia; Mental Illness; Clinical Decision Support System; Decision Support; Medical Informatics; Rct; Cdss; Metabolic Health; Mental Healthcare; Electronic Clinical Decision Support; Dysglycemia,,,"<h4>Background</h4>Severe mental illnesses (SMIs), including schizophrenia, bipolar affective disorder, and major depressive disorder, are associated with an increased risk of physical health comorbidities and premature mortality from conditions including cardiovascular disease and diabetes. Digital technologies such as electronic clinical decision support systems (eCDSSs) could play a crucial role in improving the clinician-led management of conditions such as dysglycemia (deranged blood sugar levels) and associated conditions such as diabetes in people with a diagnosis of SMI in mental health settings.<h4>Objective</h4>We have developed a real-time eCDSS using CogStack, an information retrieval and extraction platform, to automatically alert clinicians with National Health Service Trust-approved, guideline-based recommendations for dysglycemia monitoring and management in secondary mental health care. This novel system aims to improve the management of dysglycemia and associated conditions, such as diabetes, in SMI. This protocol describes a pilot study to explore the acceptability, feasibility, and evaluation of its implementation in a mental health inpatient setting.<h4>Methods</h4>This will be a pilot hybrid type 3 effectiveness-implementation randomized controlled cluster trial in inpatient mental health wards. A ward will be the unit of recruitment, where it will be randomly allocated to receive either access to the eCDSS plus usual care or usual care alone over a 4-month period. We will measure implementation outcomes, including the feasibility and acceptability of the eCDSS to clinicians, as primary outcomes, alongside secondary outcomes relating to the process of care measures such as dysglycemia screening rates. An evaluation of other implementation outcomes relating to the eCDSS will be conducted, identifying facilitators and barriers based on established implementation science frameworks.<h4>Results</h4>Enrollment of wards began in April 2022, after which clinical staff were recruited to take part in surveys and interviews. The intervention period of the trial began in February 2023, and subsequent data collection was completed in August 2023. Data are currently being analyzed, and results are expected to be available in June 2024.<h4>Conclusions</h4>An eCDSS can have the potential to improve clinician-led management of dysglycemia in inpatient mental health settings. If found to be feasible and acceptable, then, in combination with the results of the implementation evaluation, the system can be refined and improved to support future successful implementation. A larger and more definitive effectiveness trial should then be conducted to assess its impact on clinical outcomes and to inform scalability and application to other conditions in wider mental health care settings.<h4>Trial registration</h4>ClinicalTrials.gov NCT04792268; https://clinicaltrials.gov/study/NCT04792268.<h4>International registered report identifier (irrid)</h4>DERR1-10.2196/49548.",,pdf:https://www.researchprotocols.org/2024/1/e49548/PDF; doi:https://doi.org/10.2196/49548; html:https://europepmc.org/articles/PMC11031689
@@ -979,90 +980,91 @@ PMC10686417,https://doi.org/,The impact of restricted provision of publicly fund
 36808078,https://doi.org/10.1136/pn-2021-003286,Outpatient neurology diagnostic coding: a proposed scheme for standardised implementation.,"Biggin F, Knight J, Dayanandan R, Marson A, Wilson M, Nitkunan A, Rog D, Kipps C, Mummery C, Williams A, Emsley HCA.",,Practical neurology,2023,2023-02-20,Y,Clinical Neurology,,,"Clinical coding uses a classification system to assign standard codes to clinical terms and so facilitates good clinical practice through audit, service design and research. However, despite clinical coding being mandatory for inpatient activity, this is often not so for outpatient services, where most neurological care is delivered. Recent reports by the UK National Neurosciences Advisory Group and NHS England's 'Getting It Right First Time' initiative recommend implementing outpatient coding. The UK currently has no standardised system for outpatient neurology diagnostic coding. However, most new attendances at general neurology clinics appear to be classifiable with a limited number of diagnostic terms. We present the rationale for diagnostic coding and its benefits, and the need for clinical engagement to develop a system that is pragmatic, quick and easy to use. We outline a scheme developed in the UK that could be used elsewhere.",,pdf:https://pn.bmj.com/content/practneurol/early/2023/02/19/pn-2021-003286.full.pdf; doi:https://doi.org/10.1136/pn-2021-003286; html:https://europepmc.org/articles/PMC10423506; pdf:https://europepmc.org/articles/PMC10423506?pdf=render
 38336974,https://doi.org/10.1038/s41598-023-49923-3,VertXNet: an ensemble method for vertebral body segmentation and identification from cervical and lumbar spinal X-rays.,"Chen Y, Mo Y, Readie A, Ligozio G, Mandal I, Jabbar F, Coroller T, Papież BW.",,Scientific reports,2024,2024-02-09,Y,,,,"Accurate annotation of vertebral bodies is crucial for automating the analysis of spinal X-ray images. However, manual annotation of these structures is a laborious and costly process due to their complex nature, including small sizes and varying shapes. To address this challenge and expedite the annotation process, we propose an ensemble pipeline called VertXNet. This pipeline currently combines two segmentation mechanisms, semantic segmentation using U-Net, and instance segmentation using Mask R-CNN, to automatically segment and label vertebral bodies in lateral cervical and lumbar spinal X-ray images. VertXNet enhances its effectiveness by adopting a rule-based strategy (termed the ensemble rule) for effectively combining segmentation outcomes from U-Net and Mask R-CNN. It determines vertebral body labels by recognizing specific reference vertebral instances, such as cervical vertebra 2 ('C2') in cervical spine X-rays and sacral vertebra 1 ('S1') in lumbar spine X-rays. Those references are commonly relatively easy to identify at the edge of the spine. To assess the performance of our proposed pipeline, we conducted evaluations on three spinal X-ray datasets, including two in-house datasets and one publicly available dataset. The ground truth annotations were provided by radiologists for comparison. Our experimental results have shown that the proposed pipeline outperformed two state-of-the-art (SOTA) segmentation models on our test dataset with a mean Dice of 0.90, vs. a mean Dice of 0.73 for Mask R-CNN and 0.72 for U-Net. We also demonstrated that VertXNet is a modular pipeline that enables using other SOTA model, like nnU-Net to further improve its performance. Furthermore, to evaluate the generalization ability of VertXNet on spinal X-rays, we directly tested the pre-trained pipeline on two additional datasets. A consistently strong performance was observed, with mean Dice coefficients of 0.89 and 0.88, respectively. In summary, VertXNet demonstrated significantly improved performance in vertebral body segmentation and labeling for spinal X-ray imaging. Its robustness and generalization were presented through the evaluation of both in-house clinical trial data and publicly available datasets.",,pdf:https://www.nature.com/articles/s41598-023-49923-3.pdf; doi:https://doi.org/10.1038/s41598-023-49923-3; html:https://europepmc.org/articles/PMC10858234; pdf:https://europepmc.org/articles/PMC10858234?pdf=render
 38064420,https://doi.org/10.1371/journal.pgph.0002022,"Using electronic medical records to understand the impact of SARS-CoV-2 lockdown measures on maternal and neonatal outcomes in Kampala, Uganda.","Ouma J, Hookham L, Akera LA, Rukundo G, Kyohere M, Kakande A, Nakyesige R, Musoke P, Le Doare K.",,PLOS global public health,2023,2023-12-08,Y,,,,"Kawempe National Referral Hospital (KNRH) is a tertiary facility with over 21,000 pregnant or postpartum women admitted annually. The hospital, located in Kampala, Uganda, uses an Electronic Medical Records (EMR) system to capture patient data. Used since 2017, this readily available electronic health record (EHR) has the benefit of informing real-time clinical care, especially during pandemics such as COVID-19. We investigated the use of EHR to assess risk factors for adverse pregnancy and infant outcomes that can be incorporated into a data visualization dashboard for real time decision making during pandemics. This study analysed data from the UgandaEMR collected at pre-, during- and post-lockdown timepoints of the COVID-19 pandemic to determine its use in monitoring risk factors for adverse pregnancy and neonatal outcomes. Logistic regression models were used to identify the risk factors for adverse pregnancy and maternal outcomes including prematurity, obstetric complications, still births and neonatal deaths. Pearson chi-square test was used for pair-wise comparison of the outcomes at the various stages of the pandemic. Data analysis was performed in R, within the International COVID-19 Data Alliance (ICODA) workbench. A visualisation dashboard was developed based on the risk factors, to support decision making and improved healthcare delivery. Comparison of pre-and post-lockdown variables showed an increased risk of pre-term birth (adjusted Odds Ratio (aOR = 1.67, 95% confidence interval (CI) 1.38-2.01)); obstetric complications (aOR = 2.77, 95% CI: 2.53-3.03); immediate neonatal death (aOR = 3.89, 95% CI 2.65-5.72) and Caesarean section (aOR = 1.22, 95% CI 1.11-1.34). The significant risk factors for adverse outcomes were younger maternal age and gestational age <32weeks at labour. This study demonstrates the feasibility of using EHR to identify and monitor at-risk subpopulation groups accessing health services in real time. This information is critical for the development of timely and appropriate interventions in outbreaks and pandemic situations.",,doi:https://doi.org/10.1371/journal.pgph.0002022; html:https://europepmc.org/articles/PMC10707482; pdf:https://europepmc.org/articles/PMC10707482?pdf=render
-38045436,https://doi.org/10.1093/ehjdh/ztad062,Monitoring left ventricular assist device parameters to detect flow- and power-impacting complications: a proof of concept.,"Moazeni M, Numan L, Szymanski MK, Van der Kaaij NP, Asselbergs FW, van Laake LW, Aarts E.",,European heart journal. Digital health,2023,2023-10-27,Y,Lvad; Intensive Longitudinal Data; Remote Patient Monitoring; Patient-Specific Monitoring,,,"<h4>Aims</h4>The number of patients on left ventricular assist device (LVAD) support increases due to the growing number of patients with end-stage heart failure and the limited number of donor hearts. Despite improving survival rates, patients frequently suffer from adverse events such as cardiac arrhythmia and major bleeding. Telemonitoring is a potentially powerful tool to early detect deteriorations and may further improve outcome after LVAD implantation. Hence, we developed a personalized algorithm to remotely monitor HeartMate3 (HM3) pump parameters aiming to early detect unscheduled admissions due to cardiac arrhythmia or major bleeding.<h4>Methods and results</h4>The source code of the algorithm is published in an open repository. The algorithm was optimized and tested retrospectively using HeartMate 3 (HM3) power and flow data of 120 patients, including 29 admissions due to cardiac arrhythmia and 14 admissions due to major bleeding. Using a true alarm window of 14 days prior to the admission date, the algorithm detected 59 and 79% of unscheduled admissions due to cardiac arrhythmia and major bleeding, respectively, with a false alarm rate of 2%.<h4>Conclusion</h4>The proposed algorithm showed that the personalized algorithm is a viable approach to early identify cardiac arrhythmia and major bleeding by monitoring HM3 pump parameters. External validation is needed and integration with other clinical parameters could potentially improve the predictive value. In addition, the algorithm can be further enhanced using continuous data.",,pdf:https://academic.oup.com/ehjdh/article-pdf/4/6/488/53897330/ztad062.pdf; doi:https://doi.org/10.1093/ehjdh/ztad062; html:https://europepmc.org/articles/PMC10689906; pdf:https://europepmc.org/articles/PMC10689906?pdf=render
 30423068,https://doi.org/10.1093/bioinformatics/bty605,Ontology-based validation and identification of regulatory phenotypes.,"Kulmanov M, Schofield PN, Gkoutos GV, Hoehndorf R.",,"Bioinformatics (Oxford, England)",2018,2018-09-01,Y,,"Applied Analytics, The Human Phenome",,"<h4>Motivation</h4>Function annotations of gene products, and phenotype annotations of genotypes, provide valuable information about molecular mechanisms that can be utilized by computational methods to identify functional and phenotypic relatedness, improve our understanding of disease and pathobiology, and lead to discovery of drug targets. Identifying functions and phenotypes commonly requires experiments which are time-consuming and expensive to carry out; creating the annotations additionally requires a curator to make an assertion based on reported evidence. Support to validate the mutual consistency of functional and phenotype annotations as well as a computational method to predict phenotypes from function annotations, would greatly improve the utility of function annotations.<h4>Results</h4>We developed a novel ontology-based method to validate the mutual consistency of function and phenotype annotations. We apply our method to mouse and human annotations, and identify several inconsistencies that can be resolved to improve overall annotation quality. We also apply our method to the rule-based prediction of regulatory phenotypes from functions and demonstrate that we can predict these phenotypes with Fmax of up to 0.647.<h4>Availability and implementation</h4>https://github.com/bio-ontology-research-group/phenogocon.",,pdf:https://academic.oup.com/bioinformatics/article-pdf/34/17/i857/25702307/bty605.pdf; doi:https://doi.org/10.1093/bioinformatics/bty605; html:https://europepmc.org/articles/PMC6129279; pdf:https://europepmc.org/articles/PMC6129279?pdf=render
-31616478,https://doi.org/10.3389/fgene.2019.00922,Machine Learning Predicts Accurately <i>Mycobacterium tuberculosis</i> Drug Resistance From Whole Genome Sequencing Data.,"Deelder W, Christakoudi S, Phelan J, Benavente ED, Campino S, McNerney R, Palla L, Clark TG.",,Frontiers in genetics,2019,2019-09-26,Y,Mycobacterium tuberculosis; Drug resistance; Mdr-tb; Xdr-tb; Machine Learning,Applied Analytics,,"<b>Background:</b> Tuberculosis disease, caused by <i>Mycobacterium tuberculosis</i>, is a major public health problem. The emergence of <i>M. tuberculosis</i> strains resistant to existing treatments threatens to derail control efforts. Resistance is mainly conferred by mutations in genes coding for drug targets or converting enzymes, but our knowledge of these mutations is incomplete. Whole genome sequencing (WGS) is an increasingly common approach to rapidly characterize isolates and identify mutations predicting antimicrobial resistance and thereby providing a diagnostic tool to assist clinical decision making. <b>Methods:</b> We applied machine learning approaches to 16,688 <i>M. tuberculosis</i> isolates that have undergone WGS and laboratory drug-susceptibility testing (DST) across 14 antituberculosis drugs, with 22.5% of samples being multidrug resistant and 2.1% being extensively drug resistant. We used non-parametric classification-tree and gradient-boosted-tree models to predict drug resistance and uncover any associated novel putative mutations. We fitted separate models for each drug, with and without ""co-occurrent resistance"" markers known to be causing resistance to drugs other than the one of interest. Predictive performance was measured using sensitivity, specificity, and the area under the receiver operating characteristic curve, assuming DST results as the gold standard. <b>Results:</b> The predictive performance was highest for resistance to first-line drugs, amikacin, kanamycin, ciprofloxacin, moxifloxacin, and multidrug-resistant tuberculosis (area under the receiver operating characteristic curve above 96%), and lowest for third-line drugs such as D-cycloserine and Para-aminosalisylic acid (area under the curve below 85%). The inclusion of co-occurrent resistance markers led to improved performance for some drugs and superior results when compared to similar models in other large-scale studies, which had smaller sample sizes. Overall, the gradient-boosted-tree models performed better than the classification-tree models. The mutation-rank analysis detected no new single nucleotide polymorphisms linked to drug resistance. Discordance between DST and genotypically inferred resistance may be explained by DST errors, novel rare mutations, hetero-resistance, and nongenomic drivers such as efflux-pump upregulation. <b>Conclusion:</b> Our work demonstrates the utility of machine learning as a flexible approach to drug resistance prediction that is able to accommodate a much larger number of predictors and to summarize their predictive ability, thus assisting clinical decision making and single nucleotide polymorphism detection in an era of increasing WGS data generation.",,pdf:https://www.frontiersin.org/articles/10.3389/fgene.2019.00922/pdf; doi:https://doi.org/10.3389/fgene.2019.00922; html:https://europepmc.org/articles/PMC6775242; pdf:https://europepmc.org/articles/PMC6775242?pdf=render
+38045436,https://doi.org/10.1093/ehjdh/ztad062,Monitoring left ventricular assist device parameters to detect flow- and power-impacting complications: a proof of concept.,"Moazeni M, Numan L, Szymanski MK, Van der Kaaij NP, Asselbergs FW, van Laake LW, Aarts E.",,European heart journal. Digital health,2023,2023-10-27,Y,Lvad; Intensive Longitudinal Data; Remote Patient Monitoring; Patient-Specific Monitoring,,,"<h4>Aims</h4>The number of patients on left ventricular assist device (LVAD) support increases due to the growing number of patients with end-stage heart failure and the limited number of donor hearts. Despite improving survival rates, patients frequently suffer from adverse events such as cardiac arrhythmia and major bleeding. Telemonitoring is a potentially powerful tool to early detect deteriorations and may further improve outcome after LVAD implantation. Hence, we developed a personalized algorithm to remotely monitor HeartMate3 (HM3) pump parameters aiming to early detect unscheduled admissions due to cardiac arrhythmia or major bleeding.<h4>Methods and results</h4>The source code of the algorithm is published in an open repository. The algorithm was optimized and tested retrospectively using HeartMate 3 (HM3) power and flow data of 120 patients, including 29 admissions due to cardiac arrhythmia and 14 admissions due to major bleeding. Using a true alarm window of 14 days prior to the admission date, the algorithm detected 59 and 79% of unscheduled admissions due to cardiac arrhythmia and major bleeding, respectively, with a false alarm rate of 2%.<h4>Conclusion</h4>The proposed algorithm showed that the personalized algorithm is a viable approach to early identify cardiac arrhythmia and major bleeding by monitoring HM3 pump parameters. External validation is needed and integration with other clinical parameters could potentially improve the predictive value. In addition, the algorithm can be further enhanced using continuous data.",,pdf:https://academic.oup.com/ehjdh/article-pdf/4/6/488/53897330/ztad062.pdf; doi:https://doi.org/10.1093/ehjdh/ztad062; html:https://europepmc.org/articles/PMC10689906; pdf:https://europepmc.org/articles/PMC10689906?pdf=render
 33827849,https://doi.org/10.1136/bmjopen-2020-048139,"Sociodemographic differences in self-reported exposure to high fat, salt and sugar food and drink advertising: a cross-sectional analysis of 2019 UK panel data.","Yau A, Adams J, Boyland EJ, Burgoine T, Cornelsen L, de Vocht F, Egan M, Er V, Lake AA, Lock K, Mytton O, Petticrew M, Thompson C, White M, Cummins S.",,BMJ open,2021,2021-04-07,Y,Public Health; Social Medicine; Nutrition & Dietetics,,,"<h4>Objectives</h4>To explore sociodemographic differences in exposure to advertising for foods and drinks high in fat, salt and sugar (HFSS) and whether exposure is associated with body mass index (BMI).<h4>Design</h4>Cross-sectional survey.<h4>Setting</h4>UK.<h4>Participants</h4>1552 adults recruited to the Kantar Fast Moving Consumer Goods panel for London and the North of England.<h4>Outcome measures</h4>Self-reported advertising exposure stratified by product/service advertised (processed HFSS foods; sugary drinks; sugary cereals; sweet snacks; fast food or digital food delivery services) and advertising setting (traditional; digital; recreational; functional or transport); BMI and sociodemographic characteristics.<h4>Results</h4>Overall, 84.7% of participants reported exposure to HFSS advertising in the past 7 days. Participants in the middle (vs high) socioeconomic group had higher odds of overall self-reported exposure (OR 1.48; 95% CI 1.06 to 2.07). Participants in the low (vs high) socioeconomic group had higher odds of reporting exposure to advertising for three of five product categories (ORs ranging from 1.41 to 1.67), advertising for digital food delivery services (OR 1.47; 95% CI 1.05 to 2.05), traditional advertising (OR 1.44; 95% CI 1.00 to 2.08) and digital advertising (OR 1.50; 95% CI 1.06 to 2.14). Younger adults (18-34 years vs ≥65 years) had higher odds of reporting exposure to advertising for digital food delivery services (OR 2.08; 95% CI 1.20 to 3.59), digital advertising (OR 3.93; 95% CI 2.18 to 7.08) and advertising across transport networks (OR 1.96; 95% CI 1.11 to 3.48). Exposure to advertising for digital food delivery services (OR 1.40; 95% CI 1.05 to 1.88), digital advertising (OR 1.80; 95% CI 1.33 to 2.44) and advertising in recreational environments (OR 1.46; 95% CI 1.02 to 2.09) was associated with increased odds of obesity.<h4>Conclusions</h4>Exposure to less healthy product advertising was prevalent, with adults in lower socioeconomic groups and younger adults more likely to report exposure. Broader restrictions may be needed to reduce sociodemographic differences in exposure to less healthy product advertising.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/4/e048139.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-048139; html:https://europepmc.org/articles/PMC8031692; pdf:https://europepmc.org/articles/PMC8031692?pdf=render
+31616478,https://doi.org/10.3389/fgene.2019.00922,Machine Learning Predicts Accurately <i>Mycobacterium tuberculosis</i> Drug Resistance From Whole Genome Sequencing Data.,"Deelder W, Christakoudi S, Phelan J, Benavente ED, Campino S, McNerney R, Palla L, Clark TG.",,Frontiers in genetics,2019,2019-09-26,Y,Mycobacterium tuberculosis; Drug resistance; Mdr-tb; Xdr-tb; Machine Learning,Applied Analytics,,"<b>Background:</b> Tuberculosis disease, caused by <i>Mycobacterium tuberculosis</i>, is a major public health problem. The emergence of <i>M. tuberculosis</i> strains resistant to existing treatments threatens to derail control efforts. Resistance is mainly conferred by mutations in genes coding for drug targets or converting enzymes, but our knowledge of these mutations is incomplete. Whole genome sequencing (WGS) is an increasingly common approach to rapidly characterize isolates and identify mutations predicting antimicrobial resistance and thereby providing a diagnostic tool to assist clinical decision making. <b>Methods:</b> We applied machine learning approaches to 16,688 <i>M. tuberculosis</i> isolates that have undergone WGS and laboratory drug-susceptibility testing (DST) across 14 antituberculosis drugs, with 22.5% of samples being multidrug resistant and 2.1% being extensively drug resistant. We used non-parametric classification-tree and gradient-boosted-tree models to predict drug resistance and uncover any associated novel putative mutations. We fitted separate models for each drug, with and without ""co-occurrent resistance"" markers known to be causing resistance to drugs other than the one of interest. Predictive performance was measured using sensitivity, specificity, and the area under the receiver operating characteristic curve, assuming DST results as the gold standard. <b>Results:</b> The predictive performance was highest for resistance to first-line drugs, amikacin, kanamycin, ciprofloxacin, moxifloxacin, and multidrug-resistant tuberculosis (area under the receiver operating characteristic curve above 96%), and lowest for third-line drugs such as D-cycloserine and Para-aminosalisylic acid (area under the curve below 85%). The inclusion of co-occurrent resistance markers led to improved performance for some drugs and superior results when compared to similar models in other large-scale studies, which had smaller sample sizes. Overall, the gradient-boosted-tree models performed better than the classification-tree models. The mutation-rank analysis detected no new single nucleotide polymorphisms linked to drug resistance. Discordance between DST and genotypically inferred resistance may be explained by DST errors, novel rare mutations, hetero-resistance, and nongenomic drivers such as efflux-pump upregulation. <b>Conclusion:</b> Our work demonstrates the utility of machine learning as a flexible approach to drug resistance prediction that is able to accommodate a much larger number of predictors and to summarize their predictive ability, thus assisting clinical decision making and single nucleotide polymorphism detection in an era of increasing WGS data generation.",,pdf:https://www.frontiersin.org/articles/10.3389/fgene.2019.00922/pdf; doi:https://doi.org/10.3389/fgene.2019.00922; html:https://europepmc.org/articles/PMC6775242; pdf:https://europepmc.org/articles/PMC6775242?pdf=render
 32855306,https://doi.org/10.1136/gutjnl-2020-321650,Prioritisation by FIT to mitigate the impact of delays in the 2-week wait colorectal cancer referral pathway during the COVID-19 pandemic: a UK modelling study.,"Loveday C, Sud A, Jones ME, Broggio J, Scott S, Gronthound F, Torr B, Garrett A, Nicol DL, Jhanji S, Boyce SA, Williams M, Barry C, Riboli E, Kipps E, McFerran E, Muller DC, Lyratzopoulos G, Lawler M, Abulafi M, Houlston RS, Turnbull C.",,Gut,2021,2020-08-27,Y,Colonoscopy; Colorectal Cancer; Colorectal Cancer Screening,,,"<h4>Objective</h4>To evaluate the impact of faecal immunochemical testing (FIT) prioritisation to mitigate the impact of delays in the colorectal cancer (CRC) urgent diagnostic (2-week-wait (2WW)) pathway consequent from the COVID-19 pandemic.<h4>Design</h4>We modelled the reduction in CRC survival and life years lost resultant from per-patient delays of 2-6 months in the 2WW pathway. We stratified by age group, individual-level benefit in CRC survival versus age-specific nosocomial COVID-19-related fatality per referred patient undergoing colonoscopy. We modelled mitigation strategies using thresholds of FIT triage of 2, 10 and 150 µg Hb/g to prioritise 2WW referrals for colonoscopy. To construct the underlying models, we employed 10-year net CRC survival for England 2008-2017, 2WW pathway CRC case and referral volumes and per-day-delay HRs generated from observational studies of diagnosis-to-treatment interval.<h4>Results</h4>Delay of 2/4/6 months across all 11 266 patients with CRC diagnosed per typical year via the 2WW pathway were estimated to result in 653/1419/2250 attributable deaths and loss of 9214/20 315/32 799 life years. Risk-benefit from urgent investigatory referral is particularly sensitive to nosocomial COVID-19 rates for patients aged >60. Prioritisation out of delay for the 18% of symptomatic referrals with FIT >10 µg Hb/g would avoid 89% of these deaths attributable to presentational/diagnostic delay while reducing immediate requirement for colonoscopy by >80%.<h4>Conclusions</h4>Delays in the pathway to CRC diagnosis and treatment have potential to cause significant mortality and loss of life years. FIT triage of symptomatic patients in primary care could streamline access to colonoscopy, reduce delays for true-positive CRC cases and reduce nosocomial COVID-19 mortality in older true-negative 2WW referrals. However, this strategy offers benefit only in short-term rationalisation of limited endoscopy services: the appreciable false-negative rate of FIT in symptomatic patients means most colonoscopies will still be required.",,pdf:https://gut.bmj.com/content/gutjnl/70/6/1053.full.pdf; doi:https://doi.org/10.1136/gutjnl-2020-321650; html:https://europepmc.org/articles/PMC7447105; pdf:https://europepmc.org/articles/PMC7447105?pdf=render
 33619467,https://doi.org/10.1093/jamiaopen/ooaa047,A semi-supervised approach for rapidly creating clinical biomarker phenotypes in the UK Biobank using different primary care EHR and clinical terminology systems.,"Denaxas S, Shah AD, Mateen BA, Kuan V, Quint JK, Fitzpatrick N, Torralbo A, Fatemifar G, Hemingway H.",,JAMIA open,2020,2020-12-05,Y,Phenotyping; Medical Informatics; Electronic Health Records; Uk Biobank,,,"<h4>Objectives</h4>The UK Biobank (UKB) is making primary care electronic health records (EHRs) for 500 000 participants available for COVID-19-related research. Data are extracted from four sources, recorded using five clinical terminologies and stored in different schemas. The aims of our research were to: (a) develop a semi-supervised approach for bootstrapping EHR phenotyping algorithms in UKB EHR, and (b) to evaluate our approach by implementing and evaluating phenotypes for 31 common biomarkers.<h4>Materials and methods</h4>We describe an algorithmic approach to phenotyping biomarkers in primary care EHR involving (a) bootstrapping definitions using existing phenotypes, (b) excluding generic, rare, or semantically distant terms, (c) forward-mapping terminology terms, (d) expert review, and (e) data extraction. We evaluated the phenotypes by assessing the ability to reproduce known epidemiological associations with all-cause mortality using Cox proportional hazards models.<h4>Results</h4>We created and evaluated phenotyping algorithms for 31 biomarkers many of which are directly related to COVID-19 complications, for example diabetes, cardiovascular disease, respiratory disease. Our algorithm identified 1651 Read v2 and Clinical Terms Version 3 terms and automatically excluded 1228 terms. Clinical review excluded 103 terms and included 44 terms, resulting in 364 terms for data extraction (sensitivity 0.89, specificity 0.92). We extracted 38 190 682 events and identified 220 978 participants with at least one biomarker measured.<h4>Discussion and conclusion</h4>Bootstrapping phenotyping algorithms from similar EHR can potentially address pre-existing methodological concerns that undermine the outputs of biomarker discovery pipelines and provide research-quality phenotyping algorithms.",,pdf:https://academic.oup.com/jamiaopen/article-pdf/3/4/545/36625793/ooaa047.pdf; doi:https://doi.org/10.1093/jamiaopen/ooaa047; html:https://europepmc.org/articles/PMC7717266; pdf:https://europepmc.org/articles/PMC7717266?pdf=render
 36102151,https://doi.org/10.1210/clinem/dgac527,Identification of 4 New Loci Associated With Primary Hyperparathyroidism (PHPT) and a Polygenic Risk Score for PHPT.,"Soto-Pedre E, Newey PJ, Srinivasan S, Siddiqui MK, Palmer CNA, Leese GP.",,The Journal of clinical endocrinology and metabolism,2022,2022-11-01,Y,Genetics; Genome-wide Association Study; Primary Hyperparathyroidism; Polygenic Risk Score,,,"<h4>Context</h4>A hypothesis-free genetic association analysis has not been reported for patients with primary hyperparathyroidism (PHPT).<h4>Objective</h4>We aimed to investigate genetic associations with PHPT using both genome-wide association study (GWAS) and candidate gene approaches.<h4>Methods</h4>A cross-sectional study was conducted among patients of European White ethnicity recruited in Tayside (Scotland, UK). Electronic medical records were used to identify PHPT cases and controls, and linked to genetic biobank data. Genetic associations were performed by logistic regression models and odds ratios (ORs). The combined effect of the genotypes was researched by genetic risk score (GRS) analysis.<h4>Results</h4>We identified 15 622 individuals for the GWAS that yielded 34 top single-nucleotide variations (formerly single-nucleotide polymorphisms), and LPAR3-rs147672681 reached genome-wide statistical significance (P = 1.2e-08). Using a more restricted PHPT definition, 8722 individuals with data on the GWAS-identified loci were found. Age- and sex-adjusted ORs for the effect alleles of SOX9-rs11656269, SLITRK5-rs185436526, and BCDIN3D-AS1-rs2045094 showed statistically significant increased risks (P < 1.5e-03). GRS analysis of 5482 individuals showed an OR of 2.51 (P = 1.6e-04), 3.78 (P = 4.0e-08), and 7.71 (P = 5.3e-17) for the second, third, and fourth quartiles, respectively, compared to the first, and there was a statistically significant linear trend across quartiles (P < 1.0e-04). Results were similar when stratifying by sex.<h4>Conclusion</h4>Using genetic loci discovered in a GWAS of PHPT carried out in a Scottish population, this study suggests new evidence for the involvement of genetic variants at SOX9, SLITRK5, LPAR3, and BCDIN3D-AS1. It also suggests that male and female carriers of greater numbers of PHPT-risk alleles both have a statistically significant increased risk of PHPT.",,pdf:https://academic.oup.com/jcem/article-pdf/107/12/3302/47260242/dgac527.pdf; doi:https://doi.org/10.1210/clinem/dgac527; html:https://europepmc.org/articles/PMC9693767
 33262478,https://doi.org/10.1038/s41433-020-01326-8,Risk factors for having diabetic retinopathy at first screening in persons with type 1 diabetes diagnosed under 18 years of age.,"Rafferty J, Owens DR, Luzio SD, Watts P, Akbari A, Thomas RL.",,"Eye (London, England)",2021,2020-12-01,N,,,,"<h4>Objective</h4>To determine the risk factors for having diabetic retinopathy (DR) in children and young people (CYP) with type 1 diabetes (T1DM) at first screening.<h4>Methods</h4>Records from the Diabetes Eye Screening Wales (DESW) service for people in Wales, UK, with T1DM diagnosed under age 18 years were combined with other electronic health record (EHR) data in the Secure Anonymised Information Linkage (SAIL) Databank. Data close to the screening date were collected, and risk factors derived from multivariate, multinomial logistic regression modelling.<h4>Results</h4>Data from 4172 persons, with median (lower quartile, upper quartile) age 16.3 (13.0, 22.3) years and duration of diabetes 6.6 (2.3, 12.3) years were analysed. 62.6% (n = 2613) had no DR, 26.7% (n = 1112) background DR, and 10.7% (n = 447) had referable DR (RDR). No RDR was observed under 19 years of age. Factors associated with an increased risk of DR were diabetes duration, elevated HbA<sub>1c</sub>, and diastolic blood pressure. People diagnosed with T1DM at 12 years or older had an additional risk for each year they had diabetes compared to those diagnosed before age 12 controlling for the diabetes duration (odds ratios 1.23 and 1.34, respectively).<h4>Conclusions</h4>This study found that 37.4% of the study cohort had DR at first screening, the risk being greater the longer the duration of diabetes or higher the HbA<sub>1c</sub> and diastolic blood pressure. In addition, people diagnosed at 12 years of age or over were more likely to have DR with each additional year with diabetes.",,pdf:https://www.nature.com/articles/s41433-020-01326-8.pdf; doi:https://doi.org/10.1038/s41433-020-01326-8; html:https://europepmc.org/articles/PMC8452782; pdf:https://europepmc.org/articles/PMC8452782?pdf=render; doi:https://doi.org/10.1038/s41433-020-01326-8
+32737300,https://doi.org/10.1038/s41467-020-17696-2,Distinct genetic architectures and environmental factors associate with host response to the γ2-herpesvirus infections.,"Sallah N, Miley W, Labo N, Carstensen T, Fatumo S, Gurdasani D, Pollard MO, Dilthey AT, Mentzer AJ, Marshall V, Cornejo Castro EM, Pomilla C, Young EH, Asiki G, Hibberd ML, Sandhu M, Kellam P, Newton R, Whitby D, Barroso I.",,Nature communications,2020,2020-07-31,Y,,,,"Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr Virus (EBV) establish life-long infections and are associated with malignancies. Striking geographic variation in incidence and the fact that virus alone is insufficient to cause disease, suggests other co-factors are involved. Here we present epidemiological analysis and genome-wide association study (GWAS) in 4365 individuals from an African population cohort, to assess the influence of host genetic and non-genetic factors on virus antibody responses. EBV/KSHV co-infection (OR = 5.71(1.58-7.12)), HIV positivity (OR = 2.22(1.32-3.73)) and living in a more rural area (OR = 1.38(1.01-1.89)) are strongly associated with immunogenicity. GWAS reveals associations with KSHV antibody response in the HLA-B/C region (p = 6.64 × 10<sup>-09</sup>). For EBV, associations are identified for VCA (rs71542439, p = 1.15 × 10<sup>-12</sup>). Human leucocyte antigen (HLA) and trans-ancestry fine-mapping substantiate that distinct variants in HLA-DQA1 (p = 5.24 × 10<sup>-44</sup>) are driving associations for EBNA-1 in Africa. This study highlights complex interactions between KSHV and EBV, in addition to distinct genetic architectures resulting in important differences in pathogenesis and transmission.",,pdf:https://www.nature.com/articles/s41467-020-17696-2.pdf; doi:https://doi.org/10.1038/s41467-020-17696-2; html:https://europepmc.org/articles/PMC7395761; pdf:https://europepmc.org/articles/PMC7395761?pdf=render
 34135032,https://doi.org/10.1136/bmjopen-2020-043906,Realising the full potential of data-enabled trials in the UK: a call for action.,"Sydes MR, Barbachano Y, Bowman L, Denwood T, Farmer A, Garfield-Birkbeck S, Gibson M, Gulliford MC, Harrison DA, Hewitt C, Logue J, Navaie W, Norrie J, O'Kane M, Quint JK, Rycroft-Malone J, Sheffield J, Smeeth L, Sullivan F, Tizzard J, Walker P, Wilding J, Williamson PR, Landray M, Morris A, Walker RR, Williams HC, Valentine J, Data Enabled Trials Group Workshop Group members.",,BMJ open,2021,2021-06-16,Y,Clinical Trials; Health Informatics; Statistics & Research Methods,,,"<h4>Rationale</h4>Clinical trials are the gold standard for testing interventions. COVID-19 has further raised their public profile and emphasised the need to deliver better, faster, more efficient trials for patient benefit. Considerable overlap exists between data required for trials and data already collected routinely in electronic healthcare records (EHRs). Opportunities exist to use these in innovative ways to decrease duplication of effort and speed trial recruitment, conduct and follow-up.<h4>Approach</h4>The National Institute of Health Research (NIHR), Health Data Research UK and Clinical Practice Research Datalink co-organised a national workshop to accelerate the agenda for 'data-enabled clinical trials'. Showcasing successful examples and imagining future possibilities, the plenary talks, panel discussions, group discussions and case studies covered: design/feasibility; recruitment; conduct/follow-up; collecting benefits/harms; and analysis/interpretation.<h4>Reflection</h4>Some notable studies have successfully accessed and used EHR to identify potential recruits, support randomised trials, deliver interventions and supplement/replace trial-specific follow-up. Some outcome measures are already reliably collected; others, like safety, need detailed work to meet regulatory reporting requirements. There is a clear need for system interoperability and a 'route map' to identify and access the necessary datasets. Researchers running regulatory-facing trials must carefully consider how data quality and integrity would be assessed. An experience-sharing forum could stimulate wider adoption of EHR-based methods in trial design and execution.<h4>Discussion</h4>EHR offer opportunities to better plan clinical trials, assess patients and capture data more efficiently, reducing research waste and increasing focus on each trial's specific challenges. The short-term emphasis should be on facilitating patient recruitment and for postmarketing authorisation trials where research-relevant outcome measures are readily collectable. Sharing of case studies is encouraged. The workshop directly informed NIHR's funding call for ambitious data-enabled trials at scale. There is the opportunity for the UK to build upon existing data science capabilities to identify, recruit and monitor patients in trials at scale.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/6/e043906.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-043906; html:https://europepmc.org/articles/PMC8211043; pdf:https://europepmc.org/articles/PMC8211043?pdf=render
-36806317,https://doi.org/10.1038/s41746-023-00749-3,Long-term participant retention and engagement patterns in an app and wearable-based multinational remote digital depression study.,"Zhang Y, Pratap A, Folarin AA, Sun S, Cummins N, Matcham F, Vairavan S, Dineley J, Ranjan Y, Rashid Z, Conde P, Stewart C, White KM, Oetzmann C, Ivan A, Lamers F, Siddi S, Rambla CH, Simblett S, Nica R, Mohr DC, Myin-Germeys I, Wykes T, Haro JM, Penninx BWJH, Annas P, Narayan VA, Hotopf M, Dobson RJB, RADAR-CNS consortium.",,NPJ digital medicine,2023,2023-02-17,Y,,,,"Recent growth in digital technologies has enabled the recruitment and monitoring of large and diverse populations in remote health studies. However, the generalizability of inference drawn from remotely collected health data could be severely impacted by uneven participant engagement and attrition over the course of the study. We report findings on long-term participant retention and engagement patterns in a large multinational observational digital study for depression containing active (surveys) and passive sensor data collected via Android smartphones, and Fitbit devices from 614 participants for up to 2 years. Majority of participants (67.6%) continued to remain engaged in the study after 43 weeks. Unsupervised clustering of participants' study apps and Fitbit usage data showed 3 distinct engagement subgroups for each data stream. We found: (i) the least engaged group had the highest depression severity (4 PHQ8 points higher) across all data streams; (ii) the least engaged group (completed 4 bi-weekly surveys) took significantly longer to respond to survey notifications (3.8 h more) and were 5 years younger compared to the most engaged group (completed 20 bi-weekly surveys); and (iii) a considerable proportion (44.6%) of the participants who stopped completing surveys after 8 weeks continued to share passive Fitbit data for significantly longer (average 42 weeks). Additionally, multivariate survival models showed participants' age, ownership and brand of smartphones, and recruitment sites to be associated with retention in the study. Together these findings could inform the design of future digital health studies to enable equitable and balanced data collection from diverse populations.",,pdf:https://www.nature.com/articles/s41746-023-00749-3.pdf; doi:https://doi.org/10.1038/s41746-023-00749-3; html:https://europepmc.org/articles/PMC9938183; pdf:https://europepmc.org/articles/PMC9938183?pdf=render
 33845766,https://doi.org/10.1186/s12879-021-05992-1,"Informing the public health response to COVID-19: a systematic review of risk factors for disease, severity, and mortality.","Flook M, Jackson C, Vasileiou E, Simpson CR, Muckian MD, Agrawal U, McCowan C, Jia Y, Murray JLK, Ritchie LD, Robertson C, Stock SJ, Wang X, Woolhouse MEJ, Sheikh A, Stagg HR.",,BMC infectious diseases,2021,2021-04-12,Y,Mortality; Review; Morbidity; Coronavirus; Systematic review; risk factors; Covid-19,,,"<h4>Background</h4>Severe Acute Respiratory Syndrome coronavirus-2 (SARS-CoV-2) has challenged public health agencies globally. In order to effectively target government responses, it is critical to identify the individuals most at risk of coronavirus disease-19 (COVID-19), developing severe clinical signs, and mortality. We undertook a systematic review of the literature to present the current status of scientific knowledge in these areas and describe the need for unified global approaches, moving forwards, as well as lessons learnt for future pandemics.<h4>Methods</h4>Medline, Embase and Global Health were searched to the end of April 2020, as well as the Web of Science. Search terms were specific to the SARS-CoV-2 virus and COVID-19. Comparative studies of risk factors from any setting, population group and in any language were included. Titles, abstracts and full texts were screened by two reviewers and extracted in duplicate into a standardised form. Data were extracted on risk factors for COVID-19 disease, severe disease, or death and were narratively and descriptively synthesised.<h4>Results</h4>One thousand two hundred and thirty-eight papers were identified post-deduplication. Thirty-three met our inclusion criteria, of which 26 were from China. Six assessed the risk of contracting the disease, 20 the risk of having severe disease and ten the risk of dying. Age, gender and co-morbidities were commonly assessed as risk factors. The weight of evidence showed increasing age to be associated with severe disease and mortality, and general comorbidities with mortality. Only seven studies presented multivariable analyses and power was generally limited. A wide range of definitions were used for disease severity.<h4>Conclusions</h4>The volume of literature generated in the short time since the appearance of SARS-CoV-2 has been considerable. Many studies have sought to document the risk factors for COVID-19 disease, disease severity and mortality; age was the only risk factor based on robust studies and with a consistent body of evidence. Mechanistic studies are required to understand why age is such an important risk factor. At the start of pandemics, large, standardised, studies that use multivariable analyses are urgently needed so that the populations most at risk can be rapidly protected.<h4>Registration</h4>This review was registered on PROSPERO as CRD42020177714 .",,pdf:https://bmcinfectdis.biomedcentral.com/counter/pdf/10.1186/s12879-021-05992-1; doi:https://doi.org/10.1186/s12879-021-05992-1; html:https://europepmc.org/articles/PMC8040367; pdf:https://europepmc.org/articles/PMC8040367?pdf=render
-32737300,https://doi.org/10.1038/s41467-020-17696-2,Distinct genetic architectures and environmental factors associate with host response to the γ2-herpesvirus infections.,"Sallah N, Miley W, Labo N, Carstensen T, Fatumo S, Gurdasani D, Pollard MO, Dilthey AT, Mentzer AJ, Marshall V, Cornejo Castro EM, Pomilla C, Young EH, Asiki G, Hibberd ML, Sandhu M, Kellam P, Newton R, Whitby D, Barroso I.",,Nature communications,2020,2020-07-31,Y,,,,"Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr Virus (EBV) establish life-long infections and are associated with malignancies. Striking geographic variation in incidence and the fact that virus alone is insufficient to cause disease, suggests other co-factors are involved. Here we present epidemiological analysis and genome-wide association study (GWAS) in 4365 individuals from an African population cohort, to assess the influence of host genetic and non-genetic factors on virus antibody responses. EBV/KSHV co-infection (OR = 5.71(1.58-7.12)), HIV positivity (OR = 2.22(1.32-3.73)) and living in a more rural area (OR = 1.38(1.01-1.89)) are strongly associated with immunogenicity. GWAS reveals associations with KSHV antibody response in the HLA-B/C region (p = 6.64 × 10<sup>-09</sup>). For EBV, associations are identified for VCA (rs71542439, p = 1.15 × 10<sup>-12</sup>). Human leucocyte antigen (HLA) and trans-ancestry fine-mapping substantiate that distinct variants in HLA-DQA1 (p = 5.24 × 10<sup>-44</sup>) are driving associations for EBNA-1 in Africa. This study highlights complex interactions between KSHV and EBV, in addition to distinct genetic architectures resulting in important differences in pathogenesis and transmission.",,pdf:https://www.nature.com/articles/s41467-020-17696-2.pdf; doi:https://doi.org/10.1038/s41467-020-17696-2; html:https://europepmc.org/articles/PMC7395761; pdf:https://europepmc.org/articles/PMC7395761?pdf=render
+36806317,https://doi.org/10.1038/s41746-023-00749-3,Long-term participant retention and engagement patterns in an app and wearable-based multinational remote digital depression study.,"Zhang Y, Pratap A, Folarin AA, Sun S, Cummins N, Matcham F, Vairavan S, Dineley J, Ranjan Y, Rashid Z, Conde P, Stewart C, White KM, Oetzmann C, Ivan A, Lamers F, Siddi S, Rambla CH, Simblett S, Nica R, Mohr DC, Myin-Germeys I, Wykes T, Haro JM, Penninx BWJH, Annas P, Narayan VA, Hotopf M, Dobson RJB, RADAR-CNS consortium.",,NPJ digital medicine,2023,2023-02-17,Y,,,,"Recent growth in digital technologies has enabled the recruitment and monitoring of large and diverse populations in remote health studies. However, the generalizability of inference drawn from remotely collected health data could be severely impacted by uneven participant engagement and attrition over the course of the study. We report findings on long-term participant retention and engagement patterns in a large multinational observational digital study for depression containing active (surveys) and passive sensor data collected via Android smartphones, and Fitbit devices from 614 participants for up to 2 years. Majority of participants (67.6%) continued to remain engaged in the study after 43 weeks. Unsupervised clustering of participants' study apps and Fitbit usage data showed 3 distinct engagement subgroups for each data stream. We found: (i) the least engaged group had the highest depression severity (4 PHQ8 points higher) across all data streams; (ii) the least engaged group (completed 4 bi-weekly surveys) took significantly longer to respond to survey notifications (3.8 h more) and were 5 years younger compared to the most engaged group (completed 20 bi-weekly surveys); and (iii) a considerable proportion (44.6%) of the participants who stopped completing surveys after 8 weeks continued to share passive Fitbit data for significantly longer (average 42 weeks). Additionally, multivariate survival models showed participants' age, ownership and brand of smartphones, and recruitment sites to be associated with retention in the study. Together these findings could inform the design of future digital health studies to enable equitable and balanced data collection from diverse populations.",,pdf:https://www.nature.com/articles/s41746-023-00749-3.pdf; doi:https://doi.org/10.1038/s41746-023-00749-3; html:https://europepmc.org/articles/PMC9938183; pdf:https://europepmc.org/articles/PMC9938183?pdf=render
 39054034,https://doi.org/10.1016/s2213-8587(24)00159-1,Incidence of diabetes after SARS-CoV-2 infection in England and the implications of COVID-19 vaccination: a retrospective cohort study of 16 million people.,"Taylor K, Eastwood S, Walker V, Cezard G, Knight R, Al Arab M, Wei Y, Horne EMF, Teece L, Forbes H, Walker A, Fisher L, Massey J, Hopcroft LEM, Palmer T, Cuitun Coronado J, Ip S, Davy S, Dillingham I, Morton C, Greaves F, Macleod J, Goldacre B, Wood A, Chaturvedi N, Sterne JAC, Denholm R, Longitudinal Health and Wellbeing and Data and Connectivity UK COVID-19 National Core Studies, CONVALESCENCE study, OpenSAFELY collaborative.",,The lancet. Diabetes & endocrinology,2024,2024-08-01,N,,,,"<h4>Background</h4>Some studies have shown that the incidence of type 2 diabetes increases after a diagnosis of COVID-19, although the evidence is not conclusive. However, the effects of the COVID-19 vaccine on this association, or the effect on other diabetes subtypes, are not clear. We aimed to investigate the association between COVID-19 and incidence of type 2, type 1, gestational and non-specific diabetes, and the effect of COVID- 19 vaccination, up to 52 weeks after diagnosis.<h4>Methods</h4>In this retrospective cohort study, we investigated the diagnoses of incident diabetes following COVID-19 diagnosis in England in a pre-vaccination, vaccinated, and unvaccinated cohort using linked electronic health records. People alive and aged between 18 years and 110 years, registered with a general practitioner for at least 6 months before baseline, and with available data for sex, region, and area deprivation were included. Those with a previous COVID-19 diagnosis were excluded. We estimated adjusted hazard ratios (aHRs) comparing diabetes incidence after COVID-19 diagnosis with diabetes incidence before or in the absence of COVID-19 up to 102 weeks after diagnosis. Results were stratified by COVID-19 severity (categorised as hospitalised or non-hospitalised) and diabetes type.<h4>Findings</h4>16 669 943 people were included in the pre-vaccination cohort (Jan 1, 2020-Dec 14, 2021), 12 279 669 in the vaccinated cohort, and 3 076 953 in the unvaccinated cohort (both June 1-Dec 14, 2021). In the pre-vaccination cohort, aHRs for the incidence of type 2 diabetes after COVID-19 (compared with before or in the absence of diagnosis) declined from 4·30 (95% CI 4·06-4·55) in weeks 1-4 to 1·24 (1·14-1.35) in weeks 53-102. aHRs were higher in unvaccinated people (8·76 [7·49-10·25]) than in vaccinated people (1·66 [1·50-1·84]) in weeks 1-4 and in patients hospitalised with COVID-19 (pre-vaccination cohort 28·3 [26·2-30·5]) in weeks 1-4 declining to 2·04 [1·72-2·42] in weeks 53-102) than in those who were not hospitalised (1·95 [1·78-2·13] in weeks 1-4 declining to 1·11 [1·01-1·22] in weeks 53-102). Type 2 diabetes persisted for 4 months after COVID-19 in around 60% of those diagnosed. Patterns were similar for type 1 diabetes, although excess incidence did not persist beyond 1 year after a COVID-19 diagnosis.<h4>Interpretation</h4>Elevated incidence of type 2 diabetes after COVID-19 is greater, and persists for longer, in people who were hospitalised with COVID-19 than in those who were not, and is markedly less apparent in people who have been vaccinated against COVID-19. Testing for type 2 diabetes after severe COVID-19 and the promotion of vaccination are important tools in addressing this public health problem.<h4>Funding</h4>UK National Institute for Health and Care Research, UK Research and Innovation (UKRI) Medical Research Council, UKRI Engineering and Physical Sciences Research Council, Health Data Research UK, Diabetes UK, British Heart Foundation, and the Stroke Association.",,doi:https://doi.org/10.1016/S2213-8587(24)00159-1
+35976089,https://doi.org/10.1515/cclm-2022-0135,"Reference ranges for GDF-15, and risk factors associated with GDF-15, in a large general population cohort.","Welsh P, Kimenai DM, Marioni RE, Hayward C, Campbell A, Porteous D, Mills NL, O'Rahilly S, Sattar N.",,Clinical chemistry and laboratory medicine,2022,2022-08-18,N,Biochemical markers; Guidelines; Reference Ranges,,,"<h4>Objectives</h4>Growth differentiation factor (GDF)-15 is attracting interest as a biomarker in several areas of medicine. We aimed to evaluate the reference range for GDF-15 in a general population, and to explore demographics, classical cardiovascular disease risk factors, and other cardiac biomarkers associated with GDF-15.<h4>Methods</h4>GDF-15 was measured in serum from 19,462 individuals in the Generation Scotland Scottish Family Health Study. Associations of cardiometabolic risk factors with GDF-15 were tested using adjusted linear regression. Among 18,507 participants with no heart disease, heart failure, or stroke, and not pregnant, reference ranges (median and 97.5th centiles) were derived by decade age bands and sex.<h4>Results</h4>Among males in the reference range population, median (97.5th centile) GDF-15 concentration at age <30 years was 537 (1,135) pg/mL, rising to 931 (2,492) pg/mL at 50-59 years, and 2,152 (5,972) pg/mL at ≥80 years. In females, median GDF-15 at age <30 years was 628 (2,195) pg/mL, 881 (2,323) pg/mL at 50-59 years, and 1847 (6,830) pg/mL at ≥80 years. Among those known to be pregnant, median GDF-15 was 19,311 pg/mL. After adjustment, GDF-15 was higher in participants with adverse cardiovascular risk factors, including current smoking (+26.1%), those with previous heart disease (+12.7%), stroke (+17.1%), heart failure (+25.3%), and particularly diabetes (+60.2%). GDF-15 had positive associations with cardiac biomarkers cardiac troponin I, cardiac troponin T, and N-terminal pro B-type natriuretic peptide (NT-proBNP).<h4>Conclusions</h4>These data define reference ranges for GDF-15 for comparison in future studies, and identify potentially confounding risk factors and mediators to be considered in interpreting GDF-15 concentrations.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9524804; doi:https://doi.org/10.1515/cclm-2022-0135; html:https://europepmc.org/articles/PMC9524804; pdf:https://europepmc.org/articles/PMC9524804?pdf=render; doi:https://doi.org/10.1515/cclm-2022-0135
 34785588,https://doi.org/10.1136/openhrt-2021-001784,OpenSAFELY: impact of national guidance on switching anticoagulant therapy during COVID-19 pandemic.,"OpenSAFELY Collaborative, Curtis HJ, MacKenna B, Walker AJ, Croker R, Mehrkar A, Morton C, Bacon S, Hickman G, Inglesby P, Bates C, Evans D, Ward T, Cockburn J, Davy S, Bhaskaran K, Schultze A, Rentsch CT, Williamson E, Hulme W, Tomlinson L, Mathur R, Drysdale H, Eggo RM, Wong AY, Forbes H, Parry J, Hester F, Harper S, Douglas I, Smeeth L, Goldacre B.",,Open heart,2021,2021-11-01,Y,Stroke; Medication Adherence; Healthcare Economics And Organisations; Covid-19,,,"<h4>Background</h4>Early in the COVID-19 pandemic, the National Health Service (NHS) recommended that appropriate patients anticoagulated with warfarin should be switched to direct-acting oral anticoagulants (DOACs), requiring less frequent blood testing. Subsequently, a national safety alert was issued regarding patients being inappropriately coprescribed two anticoagulants following a medication change and associated monitoring.<h4>Objective</h4>To describe which people were switched from warfarin to DOACs; identify potentially unsafe coprescribing of anticoagulants; and assess whether abnormal clotting results have become more frequent during the pandemic.<h4>Methods</h4>With the approval of NHS England, we conducted a cohort study using routine clinical data from 24 million NHS patients in England.<h4>Results</h4>20 000 of 164 000 warfarin patients (12.2%) switched to DOACs between March and May 2020, most commonly to edoxaban and apixaban. Factors associated with switching included: older age, recent renal function test, higher number of recent INR tests recorded, atrial fibrillation diagnosis and care home residency. There was a sharp rise in coprescribing of warfarin and DOACs from typically 50-100 per month to 246 in April 2020, 0.06% of all people receiving a DOAC or warfarin. International normalised ratio (INR) testing fell by 14% to 506.8 patients tested per 1000 warfarin patients each month. We observed a very small increase in elevated INRs (n=470) during April compared with January (n=420).<h4>Conclusions</h4>Increased switching of anticoagulants from warfarin to DOACs was observed at the outset of the COVID-19 pandemic in England following national guidance. There was a small but substantial number of people coprescribed warfarin and DOACs during this period. Despite a national safety alert on the issue, a widespread rise in elevated INR test results was not found. Primary care has responded rapidly to changes in patient care during the COVID-19 pandemic.",,pdf:https://openheart.bmj.com/content/openhrt/8/2/e001784.full.pdf; doi:https://doi.org/10.1136/openhrt-2021-001784; html:https://europepmc.org/articles/PMC8595296; pdf:https://europepmc.org/articles/PMC8595296?pdf=render
 36112916,https://doi.org/10.1177/09622802211055853,Inferring risks of coronavirus transmission from community household data.,"House T, Riley H, Pellis L, Pouwels KB, Bacon S, Eidukas A, Jahanshahi K, Eggo RM, Sarah Walker A.",,Statistical methods in medical research,2022,2022-09-01,Y,Infection; Model; epidemic; risk factors; Covid-19,,,"The response of many governments to the COVID-19 pandemic has involved measures to control within- and between-household transmission, providing motivation to improve understanding of the absolute and relative risks in these contexts. Here, we perform exploratory, residual-based, and transmission-dynamic household analysis of the Office for National Statistics COVID-19 Infection Survey data from 26 April 2020 to 15 July 2021 in England. This provides evidence for: (i) temporally varying rates of introduction of infection into households broadly following the trajectory of the overall epidemic and vaccination programme; (ii) susceptible-Infectious transmission probabilities of within-household transmission in the 15-35% range; (iii) the emergence of the Alpha and Delta variants, with the former being around 50% more infectious than wildtype and 35% less infectious than Delta within households; (iv) significantly (in the range of 25-300%) more risk of bringing infection into the household for workers in patient-facing roles pre-vaccine; (v) increased risk for secondary school-age children of bringing the infection into the household when schools are open; (vi) increased risk for primary school-age children of bringing the infection into the household when schools were open since the emergence of new variants.",,doi:https://doi.org/10.1177/09622802211055853; doi:https://doi.org/10.1177/09622802211055853; html:https://europepmc.org/articles/PMC9465559; pdf:https://europepmc.org/articles/PMC9465559?pdf=render
-36879385,https://doi.org/10.1097/ta.0000000000003950,Cost-effectiveness of a purpose-built ward environment and new allied health model of care for major trauma.,"Gabbe BJ, Reeder S, Ekegren CL, Mather A, Kimmel L, Cameron PA, Higgins AM.",,The journal of trauma and acute care surgery,2023,2023-03-07,N,,,,"<h4>Background</h4>Targeted rehabilitation within the acute inpatient setting could have a substantial impact on improving outcomes for major trauma patients. The aim of this study was to investigate the cost-effectiveness of the introduction of a purpose-built ward environment, and a new allied health model of care (AHMOC) delivered in the acute inpatient setting, in a major trauma population.<h4>Methods</h4>The statewide trauma registry, the trauma center's data warehouse, and electronic medical record data were used for this observational study. There were three phases: baseline, new ward, and new AHMOC. Cost-effectiveness was measured as cost per quality-adjusted life year using preinjury, hospital discharge, 1-month and 6-month 5-level, EQ-5D utility scores. Total costs included initial acute and inpatient rehabilitation care, as well as outpatient, readmission and ED presentations to 6-months.<h4>Results</h4>Four hundred eleven patients were included. Case-mix was stable between phases. The median (IQR) number of allied health services received by patients was 8 (5-17) at baseline, 10 (5-19) in the new ward phase, and 17 (9-23) in the AHMOC phase. The proportion discharged to rehabilitation was 37% at baseline, 45% with the new ward and 28% with the new AHMOC. Mean (SD) total Australian dollar costs were $69,335 ($141,175) at baseline, $55,943 ($82,706) with the new ward and $37,833 ($49,004) with the AHMOC. The probability of the AHMOC being cost-effective at a willingness-to-pay threshold of $50,000 per quality-adjusted life year was 99.4% compared with baseline and 98% compared with the new ward.<h4>Conclusion</h4>The new allied health model of care was found to be a cost-effective intervention. Uptake of this model of allied health care at other trauma centers has the potential to reduce the cost and burden of major trauma.<h4>Level of evidence</h4>Economic and Value-based Evaluations; Level III.",,doi:https://doi.org/10.1097/TA.0000000000003950
-35976089,https://doi.org/10.1515/cclm-2022-0135,"Reference ranges for GDF-15, and risk factors associated with GDF-15, in a large general population cohort.","Welsh P, Kimenai DM, Marioni RE, Hayward C, Campbell A, Porteous D, Mills NL, O'Rahilly S, Sattar N.",,Clinical chemistry and laboratory medicine,2022,2022-08-18,N,Biochemical markers; Guidelines; Reference Ranges,,,"<h4>Objectives</h4>Growth differentiation factor (GDF)-15 is attracting interest as a biomarker in several areas of medicine. We aimed to evaluate the reference range for GDF-15 in a general population, and to explore demographics, classical cardiovascular disease risk factors, and other cardiac biomarkers associated with GDF-15.<h4>Methods</h4>GDF-15 was measured in serum from 19,462 individuals in the Generation Scotland Scottish Family Health Study. Associations of cardiometabolic risk factors with GDF-15 were tested using adjusted linear regression. Among 18,507 participants with no heart disease, heart failure, or stroke, and not pregnant, reference ranges (median and 97.5th centiles) were derived by decade age bands and sex.<h4>Results</h4>Among males in the reference range population, median (97.5th centile) GDF-15 concentration at age <30 years was 537 (1,135) pg/mL, rising to 931 (2,492) pg/mL at 50-59 years, and 2,152 (5,972) pg/mL at ≥80 years. In females, median GDF-15 at age <30 years was 628 (2,195) pg/mL, 881 (2,323) pg/mL at 50-59 years, and 1847 (6,830) pg/mL at ≥80 years. Among those known to be pregnant, median GDF-15 was 19,311 pg/mL. After adjustment, GDF-15 was higher in participants with adverse cardiovascular risk factors, including current smoking (+26.1%), those with previous heart disease (+12.7%), stroke (+17.1%), heart failure (+25.3%), and particularly diabetes (+60.2%). GDF-15 had positive associations with cardiac biomarkers cardiac troponin I, cardiac troponin T, and N-terminal pro B-type natriuretic peptide (NT-proBNP).<h4>Conclusions</h4>These data define reference ranges for GDF-15 for comparison in future studies, and identify potentially confounding risk factors and mediators to be considered in interpreting GDF-15 concentrations.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9524804; doi:https://doi.org/10.1515/cclm-2022-0135; html:https://europepmc.org/articles/PMC9524804; pdf:https://europepmc.org/articles/PMC9524804?pdf=render; doi:https://doi.org/10.1515/cclm-2022-0135
 32310142,https://doi.org/10.2196/14306,"Objective Characterization of Activity, Sleep, and Circadian Rhythm Patterns Using a Wrist-Worn Actigraphy Sensor: Insights Into Posttraumatic Stress Disorder.","Tsanas A, Woodward E, Ehlers A.",,JMIR mHealth and uHealth,2020,2020-04-20,Y,Sleep; Posttraumatic Stress Disorder; actigraphy; Wearable Technology; Geneactiv,,,"<h4>Background</h4>Wearables have been gaining increasing momentum and have enormous potential to provide insights into daily life behaviors and longitudinal health monitoring. However, to date, there is still a lack of principled algorithmic framework to facilitate the analysis of actigraphy and objectively characterize day-by-day data patterns, particularly in cohorts with sleep problems.<h4>Objective</h4>This study aimed to propose a principled algorithmic framework for the assessment of activity, sleep, and circadian rhythm patterns in people with posttraumatic stress disorder (PTSD), a mental disorder with long-lasting distressing symptoms such as intrusive memories, avoidance behaviors, and sleep disturbance. In clinical practice, these symptoms are typically assessed using retrospective self-reports that are prone to recall bias. The aim of this study was to develop objective measures from patients' everyday lives, which could potentially considerably enhance the understanding of symptoms, behaviors, and treatment effects.<h4>Methods</h4>Using a wrist-worn sensor, we recorded actigraphy, light, and temperature data over 7 consecutive days from three groups: 42 people diagnosed with PTSD, 43 traumatized controls, and 30 nontraumatized controls. The participants also completed a daily sleep diary over 7 days and the standardized Pittsburgh Sleep Quality Index questionnaire. We developed a novel approach to automatically determine sleep onset and offset, which can also capture awakenings that are crucial for assessing sleep quality. Moreover, we introduced a new intuitive methodology facilitating actigraphy exploration and characterize day-by-day data across 49 activity, sleep, and circadian rhythm patterns.<h4>Results</h4>We demonstrate that the new sleep detection algorithm closely matches the sleep onset and offset against the participants' sleep diaries consistently outperforming an existing open-access widely used approach. Participants with PTSD exhibited considerably more fragmented sleep patterns (as indicated by greater nocturnal activity, including awakenings) and greater intraday variability compared with traumatized and nontraumatized control groups, showing statistically significant (P<.05) and strong associations (|R|>0.3).<h4>Conclusions</h4>This study lays the foundation for objective assessment of activity, sleep, and circadian rhythm patterns using passively collected data from a wrist-worn sensor, facilitating large community studies to monitor longitudinally healthy and pathological cohorts under free-living conditions. These findings may be useful in clinical PTSD assessment and could inform therapy and monitoring of treatment effects.",,doi:https://doi.org/10.2196/14306; doi:https://doi.org/10.2196/14306; html:https://europepmc.org/articles/PMC7199134
+36879385,https://doi.org/10.1097/ta.0000000000003950,Cost-effectiveness of a purpose-built ward environment and new allied health model of care for major trauma.,"Gabbe BJ, Reeder S, Ekegren CL, Mather A, Kimmel L, Cameron PA, Higgins AM.",,The journal of trauma and acute care surgery,2023,2023-03-07,N,,,,"<h4>Background</h4>Targeted rehabilitation within the acute inpatient setting could have a substantial impact on improving outcomes for major trauma patients. The aim of this study was to investigate the cost-effectiveness of the introduction of a purpose-built ward environment, and a new allied health model of care (AHMOC) delivered in the acute inpatient setting, in a major trauma population.<h4>Methods</h4>The statewide trauma registry, the trauma center's data warehouse, and electronic medical record data were used for this observational study. There were three phases: baseline, new ward, and new AHMOC. Cost-effectiveness was measured as cost per quality-adjusted life year using preinjury, hospital discharge, 1-month and 6-month 5-level, EQ-5D utility scores. Total costs included initial acute and inpatient rehabilitation care, as well as outpatient, readmission and ED presentations to 6-months.<h4>Results</h4>Four hundred eleven patients were included. Case-mix was stable between phases. The median (IQR) number of allied health services received by patients was 8 (5-17) at baseline, 10 (5-19) in the new ward phase, and 17 (9-23) in the AHMOC phase. The proportion discharged to rehabilitation was 37% at baseline, 45% with the new ward and 28% with the new AHMOC. Mean (SD) total Australian dollar costs were $69,335 ($141,175) at baseline, $55,943 ($82,706) with the new ward and $37,833 ($49,004) with the AHMOC. The probability of the AHMOC being cost-effective at a willingness-to-pay threshold of $50,000 per quality-adjusted life year was 99.4% compared with baseline and 98% compared with the new ward.<h4>Conclusion</h4>The new allied health model of care was found to be a cost-effective intervention. Uptake of this model of allied health care at other trauma centers has the potential to reduce the cost and burden of major trauma.<h4>Level of evidence</h4>Economic and Value-based Evaluations; Level III.",,doi:https://doi.org/10.1097/TA.0000000000003950
 38066209,https://doi.org/10.1038/s41591-023-02665-1,A toolkit for capturing a representative and equitable sample in health research.,"Retzer A, Ciytak B, Khatsuria F, El-Awaisi J, Harris IM, Chapman L, Kelly T, Richards J, Lam E, Newsome PN, Calvert M, NIHR Birmingham Biomedical Research Centre REP-EQUITY Group.",,Nature medicine,2023,2023-12-08,Y,,,,"Research participants often do not represent the general population. Systematic exclusion of particular groups from research limits the generalizability of research findings and perpetuates health inequalities. Groups considered underserved by research include those whose inclusion is lower than expected based on population estimates, those with a high healthcare burden but limited research participation opportunities and those whose healthcare engagement is less than others. The REP-EQUITY toolkit guides representative and equitable inclusion in research. The toolkit was developed through a methodological systematic review and synthesis and finalized in a consensus workshop with 24 participants. The REP-EQUITY toolkit describes seven steps for investigators to consider in facilitating representative and equitable sample selection. This includes clearly defining (1) the relevant underserved groups, (2) the aims relating to equity and representativeness, (3) the sample proportion of individuals with characteristics associated with being underserved by research, (4) the recruitment goals, (5) the strategies by which external factors will be managed, (6) the methods by which representation in the final sample will be evaluated and (7) the legacy of having used the toolkit. Using the REP-EQUITY toolkit could promote trust between communities and research institutions, increase diverse participation in research and improve the generalizability of health research. National Institute for Health and Care Research PROSPERO identifier: CRD42022355391.",,doi:https://doi.org/10.1038/s41591-023-02665-1; html:https://europepmc.org/articles/PMC10719102; pdf:https://europepmc.org/articles/PMC10719102?pdf=render
-38304287,https://doi.org/10.3389/fpsyt.2024.1347358,How will AI make sense of our messy lives and improve our mental health?,"Speechley J, McTernan M.",,Frontiers in psychiatry,2024,2024-01-18,Y,Artificial intelligence; Data; Mental health; TRUST; Patient And Public Engagement,,,,,doi:https://doi.org/10.3389/fpsyt.2024.1347358; html:https://europepmc.org/articles/PMC10832992; pdf:https://europepmc.org/articles/PMC10832992?pdf=render
 36805366,https://doi.org/10.2196/43419,Prediction of Suicidal Behaviors in the Middle-aged Population: Machine Learning Analyses of UK Biobank.,"Wang J, Qiu J, Zhu T, Zeng Y, Yang H, Shang Y, Yin J, Sun Y, Qu Y, Valdimarsdóttir UA, Song H.",,JMIR public health and surveillance,2023,2023-02-20,Y,Sex; Model; Behavior; Genetic susceptibility; Data; Suicide; risk; Machine Learning; Risk Prediction; Cost-effective; Machine Learning Approach; Suicidal Behaviors,,,"<h4>Background</h4>Suicidal behaviors, including suicide deaths and attempts, are major public health concerns. However, previous suicide models required a huge amount of input features, resulting in limited applicability in clinical practice.<h4>Objective</h4>We aimed to construct applicable models (ie, with limited features) for short- and long-term suicidal behavior prediction. We further validated these models among individuals with different genetic risks of suicide.<h4>Methods</h4>Based on the prospective cohort of UK Biobank, we included 223 (0.06%) eligible cases of suicide attempts or deaths, according to hospital inpatient or death register data within 1 year from baseline and randomly selected 4460 (1.18%) controls (1:20) without such records. We similarly identified 833 (0.22%) cases of suicidal behaviors 1 to 6 years from baseline and 16,660 (4.42%) corresponding controls. Based on 143 input features, mainly including sociodemographic, environmental, and psychosocial factors; medical history; and polygenic risk scores (PRS) for suicidality, we applied a bagged balanced light gradient-boosting machine (LightGBM) with stratified 10-fold cross-validation and grid-search to construct the full prediction models for suicide attempts or deaths within 1 year or between 1 and 6 years. The Shapley Additive Explanations (SHAP) approach was used to quantify the importance of input features, and the top 20 features with the highest SHAP values were selected to train the applicable models. The external validity of the established models was assessed among 50,310 individuals who participated in UK Biobank repeated assessments both overall and by the level of PRS for suicidality.<h4>Results</h4>Individuals with suicidal behaviors were on average 56 years old, with equal sex distribution. The application of these full models in the external validation data set demonstrated good model performance, with the area under the receiver operating characteristic (AUROC) curves of 0.919 and 0.892 within 1 year and between 1 and 6 years, respectively. Importantly, the applicable models with the top 20 most important features showed comparable external-validated performance (AUROC curves of 0.901 and 0.885) as the full models, based on which we found that individuals in the top quintile of predicted risk accounted for 91.7% (n=11) and 80.7% (n=25) of all suicidality cases within 1 year and during 1 to 6 years, respectively. We further obtained comparable prediction accuracy when applying these models to subpopulations with different genetic susceptibilities to suicidality. For example, for the 1-year risk prediction, the AUROC curves were 0.907 and 0.885 for the high (>2nd tertile of PRS) and low (<1st) genetic susceptibilities groups, respectively.<h4>Conclusions</h4>We established applicable machine learning-based models for predicting both the short- and long-term risk of suicidality with high accuracy across populations of varying genetic risk for suicide, highlighting a cost-effective method of identifying individuals with a high risk of suicidality.",,pdf:https://publichealth.jmir.org/2023/1/e43419/PDF; doi:https://doi.org/10.2196/43419; html:https://europepmc.org/articles/PMC9989910
+38304287,https://doi.org/10.3389/fpsyt.2024.1347358,How will AI make sense of our messy lives and improve our mental health?,"Speechley J, McTernan M.",,Frontiers in psychiatry,2024,2024-01-18,Y,Artificial intelligence; Data; Mental health; TRUST; Patient And Public Engagement,,,,,doi:https://doi.org/10.3389/fpsyt.2024.1347358; html:https://europepmc.org/articles/PMC10832992; pdf:https://europepmc.org/articles/PMC10832992?pdf=render
 37381004,https://doi.org/10.1186/s12913-023-09545-x,A qualitative descriptive study exploring clinicians' perspectives of the management of older trauma care in rural Australia.,"Ferrah N, Parker C, Ibrahim J, Gabbe B, Cameron P.",,BMC health services research,2023,2023-06-28,Y,Trauma; Rural; Interview; Older Adults,,,"<h4>Background</h4>For older trauma patients who sustain trauma in rural areas, the risk of adverse outcomes associated with advancing age, is compounded by the challenges encountered in rural healthcare such as geographic isolation, lack of resources, and accessibility. Little is known of the experience and challenges faced by rural clinicians who manage trauma in older adults. An understanding of stakeholders' views is paramount to the effective development and implementation of a trauma system inclusive of rural communities. The aim of this descriptive qualitative study was to explore the perspectives of clinicians who provide care to older trauma patients in rural settings.<h4>Method</h4>We conducted semi-structured interviews of health professionals (medical doctors, nurses, paramedics, and allied health professionals) who provide care to older trauma patients in rural Queensland, Australia. A thematic analysis consisting of both inductive and deductive coding approaches, was used to identify and develop themes from interviews.<h4>Results</h4>Fifteen participants took part in the interviews. Three key themes were identified: enablers of trauma care, barriers, and changes to improve trauma care of older people. The resilience of rural residents, and breadth of experience of rural clinicians were strengths identified by participants. The perceived systemic lack of resources, both material and in the workforce, and fragmentation of the health system across the state were barriers to the provision of trauma care to older rural patients. Some changes proposed by participants included tailored education programs that would be taught in rural centres, a dedicated case coordinator for older trauma patients from rural areas, and a centralised system designed to streamline the management of older trauma patients coming from rural regions.<h4>Conclusions</h4>Rural clinicians are important stakeholders who should be included in discussions on adapting trauma guidelines to the rural setting. In this study, participants formulated pertinent and concrete recommendations that should be weighed against the current evidence, and tested in rural centres.",,pdf:https://bmchealthservres.biomedcentral.com/counter/pdf/10.1186/s12913-023-09545-x; doi:https://doi.org/10.1186/s12913-023-09545-x; html:https://europepmc.org/articles/PMC10308762; pdf:https://europepmc.org/articles/PMC10308762?pdf=render
-34189274,https://doi.org/10.23889/ijpds.v5i1.1362,Concept libraries for automatic electronic health record based phenotyping: A review.,"Almowil ZA, Zhou SM, Brophy S.",,International journal of population data science,2021,2021-06-16,Y,Review; Phenotype Algorithms; Linked Electronic Health Records; Concept Libraries,,,"<h4>Introduction</h4>Electronic health records (EHR) are linked together to examine disease history and to undertake research into the causes and outcomes of disease. However, the process of constructing algorithms for phenotyping (e.g., identifying disease characteristics) or health characteristics (e.g., smoker) is very time consuming and resource costly. In addition, results can vary greatly between researchers. Reusing or building on algorithms that others have created is a compelling solution to these problems. However, sharing algorithms is not a common practice and many published studies do not detail the clinical code lists used by the researchers in the disease/characteristic definition. To address these challenges, a number of centres across the world have developed health data portals which contain concept libraries (e.g., algorithms for defining concepts such as disease and characteristics) in order to facilitate disease phenotyping and health studies.<h4>Objectives</h4>This study aims to review the literature of existing concept libraries, examine their utilities, identify the current gaps, and suggest future developments.<h4>Methods</h4>The five-stage framework of Arksey and O'Malley was used for the literature search. This approach included defining the research questions, identifying relevant studies through literature review, selecting eligible studies, charting and extracting data, and summarising and reporting the findings.<h4>Results</h4>This review identified seven publicly accessible Electronic Health data concept libraries which were developed in different countries including UK, USA, and Canada. The concept libraries (n = 7) investigated were either general libraries that hold phenotypes of multiple specialties (n = 4) or specialized libraries that manage only certain specialities such as rare diseases (n = 3). There were some clear differences between the general libraries such as archiving data from different electronic sources, and using a range of different types of coding systems. However, they share some clear similarities such as enabling users to upload their own code lists, and allowing users to use/download the publicly accessible code. In addition, there were some differences between the specialized libraries such as difference in ability to search, and if it was possible to use different searching queries such as simple or complex searches. Conversely, there were some similarities between the specialized libraries such as enabling users to upload their own concepts into the libraries and to show where they were published, which facilitates assessing the validity of the concepts. All the specialized libraries aimed to encourage the reuse of research methods such as lists of clinical code and/or metadata.<h4>Conclusion</h4>The seven libraries identified have been developed independently and appear to replicate similar concepts but in different ways. Collaboration between similar libraries would greatly facilitate the use of these libraries for the user. The process of building code lists takes time and effort. Access to existing code lists increases consistency and accuracy of definitions across studies. Concept library developers should collaborate with each other to raise awareness of their existence and of their various functions, which could increase users' contributions to those libraries and promote their wide-ranging adoption.",,doi:https://doi.org/10.23889/ijpds.v5i1.1362; html:https://europepmc.org/articles/PMC8210840; pdf:https://europepmc.org/articles/PMC8210840?pdf=render
 36773891,https://doi.org/10.1016/j.jinf.2023.02.012,"Real-world effectiveness of molnupiravir, nirmatrelvir-ritonavir, and sotrovimab on preventing hospital admission among higher-risk patients with COVID-19 in Wales: A retrospective cohort study.","Evans A, Qi C, Adebayo JO, Underwood J, Coulson J, Bailey R, Lyons R, Edwards A, Cooper A, John G, Akbari A.",,The Journal of infection,2023,2023-02-10,Y,Health protection; Public Health; Covid-19,,,"<h4>Objective</h4>To compare the effectiveness of molnupiravir, nirmatrelvir-ritonavir, and sotrovimab with no treatment in preventing hospital admission or death in higher-risk patients infected with SARS-CoV-2 in the community.<h4>Design</h4>Retrospective cohort study of non-hospitalized adult patients with COVID-19 using the Secure Anonymised Information Linkage (SAIL) Databank.<h4>Setting</h4>A real-world cohort study was conducted within the SAIL Databank (a secure trusted research environment containing anonymised, individual, population-scale electronic health record (EHR) data) for the population of Wales, UK.<h4>Participants</h4>Adult patients with COVID-19 in the community, at higher risk of hospitalization and death, testing positive for SARS-CoV-2 between 16th December 2021 and 22nd April 2022.<h4>Interventions</h4>Molnupiravir, nirmatrelvir-ritonavir, and sotrovimab given in the community by local health boards and the National Antiviral Service in Wales.<h4>Main outcome measures</h4>All-cause admission to hospital or death within 28 days of a positive test for SARS-CoV-2.<h4>Statistical analysis</h4>Cox proportional hazard model with treatment status (treated/untreated) as a time-dependent covariate and adjusted for age, sex, number of comorbidities, Welsh Index of Multiple Deprivation, and vaccination status. Secondary subgroup analyses were by treatment type, number of comorbidities, and before and on or after 20th February 2022, when omicron BA.1 and omicron BA.2 were the dominant subvariants in Wales.<h4>Results</h4>Between 16th December 2021 and 22nd April 2022, 7013 higher-risk patients were eligible for inclusion in the study. Of these, 2040 received treatment with molnupiravir (359, 17.6%), nirmatrelvir-ritonavir (602, 29.5%), or sotrovimab (1079, 52.9%). Patients in the treatment group were younger (mean age 53 vs 57 years), had fewer comorbidities, and a higher proportion had received four or more doses of the COVID-19 vaccine (36.3% vs 17.6%). Within 28 days of a positive test, 628 (9.0%) patients were admitted to hospital or died (84 treated and 544 untreated). The primary analysis indicated a lower risk of hospitalization or death at any point within 28 days in treated participants compared to those not receiving treatment. The adjusted hazard rate was 35% (95% CI: 18-49%) lower in treated than untreated participants. There was no indication of the superiority of one treatment over another and no evidence of a reduction in risk of hospitalization or death within 28 days for patients with no or only one comorbidity. In patients treated with sotrovimab, the event rates before and on or after 20th February 2022 were similar (5.0% vs 4.9%) with no significant difference in the hazard ratios for sotrovimab between the time periods.<h4>Conclusions</h4>In higher-risk adult patients in the community with COVID-19, those who received treatment with molnupiravir, nirmatrelvir-ritonavir, or sotrovimab were at lower risk of hospitalization or death than those not receiving treatment.",,pdf:http://www.journalofinfection.com/article/S0163445323000828/pdf; doi:https://doi.org/10.1016/j.jinf.2023.02.012; html:https://europepmc.org/articles/PMC9911979; pdf:https://europepmc.org/articles/PMC9911979?pdf=render
+34189274,https://doi.org/10.23889/ijpds.v5i1.1362,Concept libraries for automatic electronic health record based phenotyping: A review.,"Almowil ZA, Zhou SM, Brophy S.",,International journal of population data science,2021,2021-06-16,Y,Review; Phenotype Algorithms; Linked Electronic Health Records; Concept Libraries,,,"<h4>Introduction</h4>Electronic health records (EHR) are linked together to examine disease history and to undertake research into the causes and outcomes of disease. However, the process of constructing algorithms for phenotyping (e.g., identifying disease characteristics) or health characteristics (e.g., smoker) is very time consuming and resource costly. In addition, results can vary greatly between researchers. Reusing or building on algorithms that others have created is a compelling solution to these problems. However, sharing algorithms is not a common practice and many published studies do not detail the clinical code lists used by the researchers in the disease/characteristic definition. To address these challenges, a number of centres across the world have developed health data portals which contain concept libraries (e.g., algorithms for defining concepts such as disease and characteristics) in order to facilitate disease phenotyping and health studies.<h4>Objectives</h4>This study aims to review the literature of existing concept libraries, examine their utilities, identify the current gaps, and suggest future developments.<h4>Methods</h4>The five-stage framework of Arksey and O'Malley was used for the literature search. This approach included defining the research questions, identifying relevant studies through literature review, selecting eligible studies, charting and extracting data, and summarising and reporting the findings.<h4>Results</h4>This review identified seven publicly accessible Electronic Health data concept libraries which were developed in different countries including UK, USA, and Canada. The concept libraries (n = 7) investigated were either general libraries that hold phenotypes of multiple specialties (n = 4) or specialized libraries that manage only certain specialities such as rare diseases (n = 3). There were some clear differences between the general libraries such as archiving data from different electronic sources, and using a range of different types of coding systems. However, they share some clear similarities such as enabling users to upload their own code lists, and allowing users to use/download the publicly accessible code. In addition, there were some differences between the specialized libraries such as difference in ability to search, and if it was possible to use different searching queries such as simple or complex searches. Conversely, there were some similarities between the specialized libraries such as enabling users to upload their own concepts into the libraries and to show where they were published, which facilitates assessing the validity of the concepts. All the specialized libraries aimed to encourage the reuse of research methods such as lists of clinical code and/or metadata.<h4>Conclusion</h4>The seven libraries identified have been developed independently and appear to replicate similar concepts but in different ways. Collaboration between similar libraries would greatly facilitate the use of these libraries for the user. The process of building code lists takes time and effort. Access to existing code lists increases consistency and accuracy of definitions across studies. Concept library developers should collaborate with each other to raise awareness of their existence and of their various functions, which could increase users' contributions to those libraries and promote their wide-ranging adoption.",,doi:https://doi.org/10.23889/ijpds.v5i1.1362; html:https://europepmc.org/articles/PMC8210840; pdf:https://europepmc.org/articles/PMC8210840?pdf=render
 37699069,https://doi.org/10.1093/ehjci/jead218,Phenotyping left ventricular systolic dysfunction in asymptomatic individuals for improved risk stratification.,"Rauseo E, Abdulkareem M, Khan A, Cooper J, Lee AM, Aung N, Slabaugh GG, Petersen SE.",,European heart journal. Cardiovascular Imaging,2023,2023-09-01,Y,Prognosis; Cardiovascular events; Risk stratification; Heart Failure; Cardiovascular Magnetic Resonance; Left Ventricular Systolic Dysfunction,,,"<h4>Aims</h4>Left ventricular systolic dysfunction (LSVD) is a heterogeneous condition with several factors influencing prognosis. Better phenotyping of asymptomatic individuals can inform preventative strategies. This study aims to explore the clinical phenotypes of LVSD in initially asymptomatic subjects and their association with clinical outcomes and cardiovascular abnormalities through multi-dimensional data clustering.<h4>Methods and results</h4>Clustering analysis was performed on 60 clinically available variables from 1563 UK Biobank participants without pre-existing heart failure (HF) and with left ventricular ejection fraction (LVEF) < 50% on cardiovascular magnetic resonance (CMR) assessment. Risks of developing HF, other cardiovascular events, death, and a composite of major adverse cardiovascular events (MACE) associated with clusters were investigated. Cardiovascular imaging characteristics, not included in the clustering analysis, were also evaluated. Three distinct clusters were identified, differing considerably in lifestyle habits, cardiovascular risk factors, electrocardiographic parameters, and cardiometabolic profiles. A stepwise increase in risk profile was observed from Cluster 1 to Cluster 3, independent of traditional risk factors and LVEF. Compared with Cluster 1, the lowest risk subset, the risk of MACE ranged from 1.42 [95% confidence interval (CI): 1.03-1.96; P < 0.05] for Cluster 2 to 1.72 (95% CI: 1.36-2.35; P < 0.001) for Cluster 3. Cluster 3, the highest risk profile, had features of adverse cardiovascular imaging with the greatest LV re-modelling, myocardial dysfunction, and decrease in arterial compliance.<h4>Conclusions</h4>Clustering of clinical variables identified three distinct risk profiles and clinical trajectories of LVSD amongst initially asymptomatic subjects. Improved characterization may facilitate tailored interventions based on the LVSD sub-type and improve clinical outcomes.",,doi:https://doi.org/10.1093/ehjci/jead218; html:https://europepmc.org/articles/PMC10531121; pdf:https://europepmc.org/articles/PMC10531121?pdf=render
 37474315,https://doi.org/10.1093/ehjci/jead174,The added value of abnormal regional myocardial function for risk prediction in arrhythmogenic right ventricular cardiomyopathy.,"Kirkels FP, Rootwelt-Norberg C, Bosman LP, Aabel EW, Muller SA, Castrini AI, Taha K, van Osta N, Lie ØH, Asselbergs FW, Lumens J, Te Riele ASJM, Hasselberg NE, Cramer MJ, Haugaa KH, Teske AJ.",,European heart journal. Cardiovascular Imaging,2023,2023-11-01,Y,Echocardiography; Risk stratification; ventricular arrhythmia; Sudden Cardiac Death; Strain Imaging; Arrhythmogenic Cardiomyopathy,,,"<h4>Aims</h4>A risk calculator for individualized prediction of first-time sustained ventricular arrhythmia (VA) in arrhythmogenic right ventricular cardiomyopathy (ARVC) patients has recently been developed and validated (www.ARVCrisk.com). This study aimed to investigate whether regional functional abnormalities, measured by echocardiographic deformation imaging, can provide additional prognostic value.<h4>Methods and results</h4>From two referral centres, 150 consecutive patients with a definite ARVC diagnosis, no prior sustained VA, and an echocardiogram suitable for deformation analysis were included (aged 41 ± 17 years, 50% female). During a median follow-up of 6.3 (interquartile range 3.1-9.8) years, 37 (25%) experienced a first-time sustained VA. All tested left and right ventricular (LV and RV) deformation parameters were univariate predictors for first-time VA. While LV function did not add predictive value in multivariate analysis, two RV deformation parameters did; RV free wall longitudinal strain and regional RV deformation patterns remained independent predictors after adjusting for the calculator-predicted risk [hazard ratio 1.07 (95% CI 1.02-1.11); P = 0.004 and 4.45 (95% CI 1.07-18.57); P = 0.040, respectively] and improved its discriminative value (from C-statistic 0.78 to 0.82 in both; Akaike information criterion change > 2). Importantly, all patients who experienced VA within 5 years from the echocardiographic assessment had abnormal regional RV deformation patterns at baseline.<h4>Conclusions</h4>This study showed that regional functional abnormalities measured by echocardiographic deformation imaging can further refine personalized arrhythmic risk prediction when added to the ARVC risk calculator. The excellent negative predictive value of normal RV deformation could support clinicians considering the timing of implantable cardioverter defibrillator implantation in patients with intermediate arrhythmic risk.",,pdf:https://academic.oup.com/ehjcimaging/advance-article-pdf/doi/10.1093/ehjci/jead174/50920074/jead174.pdf; doi:https://doi.org/10.1093/ehjci/jead174; html:https://europepmc.org/articles/PMC10667035; pdf:https://europepmc.org/articles/PMC10667035?pdf=render
 33320878,https://doi.org/10.1371/journal.pone.0243843,Developing a national birth cohort for child health research using a hospital admissions database in England: The impact of changes to data collection practices.,"Zylbersztejn A, Gilbert R, Hardelid P.",,PloS one,2020,2020-12-15,Y,,,,"<h4>Background</h4>National birth cohorts derived from administrative health databases constitute unique resources for child health research due to whole country coverage, ongoing follow-up and linkage to other data sources. In England, a national birth cohort can be developed using Hospital Episode Statistics (HES), an administrative database covering details of all publicly funded hospital activity, including 97% of births, with longitudinal follow-up via linkage to hospital and mortality records. We present methods for developing a national birth cohort using HES and assess the impact of changes to data collection over time on coverage and completeness of linked follow-up records for children.<h4>Methods</h4>We developed a national cohort of singleton live births in 1998-2015, with information on key risk factors at birth (birth weight, gestational age, maternal age, ethnicity, area-level deprivation). We identified three changes to data collection, which could affect linkage of births to follow-up records: (1) the introduction of the ""NHS Numbers for Babies (NN4B)"", an on-line system which enabled maternity staff to request a unique healthcare patient identifier (NHS number) immediately at birth rather than at civil registration, in Q4 2002; (2) the introduction of additional data quality checks at civil registration in Q3 2009; and (3) correcting a postcode extraction error for births by the data provider in Q2 2013. We evaluated the impact of these changes on trends in two outcomes in infancy: hospital readmissions after birth (using interrupted time series analyses) and mortality rates (compared to published national statistics).<h4>Results</h4>The cohort covered 10,653,998 babies, accounting for 96% of singleton live births in England in 1998-2015. Overall, 2,077,929 infants (19.5%) had at least one hospital readmission after birth. Readmission rates declined by 0.2% percentage points per annual quarter in Q1 1998 to Q3 2002, shifted up by 6.1% percentage points (compared to the expected value based on the trend before Q4 2002) to 17.7% in Q4 2002 when NN4B was introduced, and increased by 0.1% percentage points per annual quarter thereafter. Infant mortality rates were under-reported by 16% for births in 1998-2002 and similar to published national mortality statistics for births in 2003-2015. The trends in infant readmission were not affected by changes to data collection practices in Q3 2009 and Q2 2013, but the proportion of unlinked mortality records in HES and in ONS further declined after 2009.<h4>Discussion</h4>HES can be used to develop a national birth cohort for child health research with follow-up via linkage to hospital and mortality records for children born from 2003 onwards. Re-linking births before 2003 to their follow-up records would maximise potential benefits of this rich resource, enabling studies of outcomes in adolescents with over 20 years of follow-up.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0243843&type=printable; doi:https://doi.org/10.1371/journal.pone.0243843; html:https://europepmc.org/articles/PMC7737962; pdf:https://europepmc.org/articles/PMC7737962?pdf=render
 34174193,https://doi.org/10.1016/s1473-3099(21)00289-9,Vaccine effectiveness of the first dose of ChAdOx1 nCoV-19 and BNT162b2 against SARS-CoV-2 infection in residents of long-term care facilities in England (VIVALDI): a prospective cohort study.,"Shrotri M, Krutikov M, Palmer T, Giddings R, Azmi B, Subbarao S, Fuller C, Irwin-Singer A, Davies D, Tut G, Lopez Bernal J, Moss P, Hayward A, Copas A, Shallcross L.",,The Lancet. Infectious diseases,2021,2021-06-23,Y,,,,"<h4>Background</h4>The effectiveness of SARS-CoV-2 vaccines in older adults living in long-term care facilities is uncertain. We investigated the protective effect of the first dose of the Oxford-AstraZeneca non-replicating viral-vectored vaccine (ChAdOx1 nCoV-19; AZD1222) and the Pfizer-BioNTech mRNA-based vaccine (BNT162b2) in residents of long-term care facilities in terms of PCR-confirmed SARS-CoV-2 infection over time since vaccination.<h4>Methods</h4>The VIVALDI study is a prospective cohort study that commenced recruitment on June 11, 2020, to investigate SARS-CoV-2 transmission, infection outcomes, and immunity in residents and staff in long-term care facilities in England that provide residential or nursing care for adults aged 65 years and older. In this cohort study, we included long-term care facility residents undergoing routine asymptomatic SARS-CoV-2 testing between Dec 8, 2020 (the date the vaccine was first deployed in a long-term care facility), and March 15, 2021, using national testing data linked within the COVID-19 Datastore. Using Cox proportional hazards regression, we estimated the relative hazard of PCR-positive infection at 0-6 days, 7-13 days, 14-20 days, 21-27 days, 28-34 days, 35-48 days, and 49 days and beyond after vaccination, comparing unvaccinated and vaccinated person-time from the same cohort of residents, adjusting for age, sex, previous infection, local SARS-CoV-2 incidence, long-term care facility bed capacity, and clustering by long-term care facility. We also compared mean PCR cycle threshold (Ct) values for positive swabs obtained before and after vaccination. The study is registered with ISRCTN, number 14447421.<h4>Findings</h4>10 412 care home residents aged 65 years and older from 310 LTCFs were included in this analysis. The median participant age was 86 years (IQR 80-91), 7247 (69·6%) of 10 412 residents were female, and 1155 residents (11·1%) had evidence of previous SARS-CoV-2 infection. 9160 (88·0%) residents received at least one vaccine dose, of whom 6138 (67·0%) received ChAdOx1 and 3022 (33·0%) received BNT162b2. Between Dec 8, 2020, and March 15, 2021, there were 36 352 PCR results in 670 628 person-days, and 1335 PCR-positive infections (713 in unvaccinated residents and 612 in vaccinated residents) were included. Adjusted hazard ratios (HRs) for PCR-positive infection relative to unvaccinated residents declined from 28 days after the first vaccine dose to 0·44 (95% CI 0·24-0·81) at 28-34 days and 0·38 (0·19-0·77) at 35-48 days. Similar effect sizes were seen for ChAdOx1 (adjusted HR 0·32, 95% CI 0·15-0·66) and BNT162b2 (0·35, 0·17-0·71) vaccines at 35-48 days. Mean PCR Ct values were higher for infections that occurred at least 28 days after vaccination than for those occurring before vaccination (31·3 [SD 8·7] in 107 PCR-positive tests vs 26·6 [6·6] in 552 PCR-positive tests; p<0·0001).<h4>Interpretation</h4>Single-dose vaccination with BNT162b2 and ChAdOx1 vaccines provides substantial protection against infection in older adults from 4-7 weeks after vaccination and might reduce SARS-CoV-2 transmission. However, the risk of infection is not eliminated, highlighting the ongoing need for non-pharmaceutical interventions to prevent transmission in long-term care facilities.<h4>Funding</h4>UK Government Department of Health and Social Care.",,pdf:http://www.thelancet.com/article/S1473309921002899/pdf; doi:https://doi.org/10.1016/S1473-3099(21)00289-9; html:https://europepmc.org/articles/PMC8221738
 36543561,https://doi.org/10.3399/bjgp.2022.0156,Anticoagulation in older people with atrial fibrillation moving to care homes: a data linkage study.,"Ritchie LA, Harrison SL, Penson PE, Akbari A, Torabi F, Hollinghurst J, Harris D, Oke OB, Akpan A, Halcox JP, Rodgers SE, Lip GY, Lane DA.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2023,2022-12-21,Y,"Anticoagulants; Atrial fibrillation; Primary Health Care; Nursing Homes; Long-term Care; Practice Patterns, Physicians’",,,"<h4>Background</h4>Treatment decisions about oral anticoagulants (OACs) for atrial fibrillation (AF) are complex in older care home residents.<h4>Aim</h4>To explore factors associated with OAC prescription.<h4>Design and setting</h4>Retrospective cohort study set in care homes in Wales, UK, listed in the Care Inspectorate Wales Registry 2017/18.<h4>Method</h4>Analysis of anonymised individual-level electronic health and administrative data was carried out on people aged ≥65 years entering a care home between 1 January 2003 and 31 December 2018, provisioned from the Secure Anonymised Information Linkage Databank.<h4>Results</h4>Between 2003 and 2018, 14 493 people with AF aged ≥65 years became new residents in care homes in Wales and 7057 (48.7%) were prescribed OACs (32.7% in 2003 compared with 72.7% in 2018) within 6 months before care home entry. Increasing age and prescription of antiplatelet therapy were associated with lower odds of OAC prescription (adjusted odds ratio [aOR] 0.96 per 1-year age increase, 95% confidence interval [CI] = 0.95 to 0.96 and aOR 0.91, 95% CI = 0.84 to 0.98, respectively). Conversely, prior venous thromboembolism (aOR 4.06, 95% CI = 3.17 to 5.20), advancing frailty (mild: aOR 4.61, 95% CI = 3.95 to 5.38; moderate: aOR 6.69, 95% CI = 5.74 to 7.80; and severe: aOR 8.42, 95% CI = 7.16 to 9.90), and year of care home entry from 2011 onwards (aOR 1.91, 95% CI = 1.76 to 2.06) were associated with higher odds of an OAC prescription.<h4>Conclusion</h4>There has been an increase in OAC prescribing in older people newly admitted to care homes with AF. This study provides an insight into the factors influencing OAC prescribing in this population.",,pdf:https://bjgp.org/content/bjgp/73/726/e43.full.pdf; doi:https://doi.org/10.3399/BJGP.2022.0156; html:https://europepmc.org/articles/PMC9799341; pdf:https://europepmc.org/articles/PMC9799341?pdf=render
+34716166,https://doi.org/10.1136/bmjopen-2021-053268,Electronic reminders and rewards to improve adherence to inhaled asthma treatment in adolescents: a non-randomised feasibility study in tertiary care.,"De Simoni A, Fleming L, Holliday L, Horne R, Priebe S, Bush A, Sheikh A, Griffiths C.",,BMJ open,2021,2021-10-29,Y,Asthma; Respiratory Medicine (See Thoracic Medicine); Paediatric Thoracic Medicine,,,"<h4>Objective</h4>To test the feasibility and acceptability of a short-term reminder and incentives intervention in adolescents with low adherence to asthma medications.<h4>Methods</h4>Mixed-methods feasibility study in a tertiary care clinic. Adolescents recruited to a 24-week programme with three 8-weekly visits, receiving electronic reminders to prompt inhaled corticosteroid (ICS) inhalation through a mobile app coupled with electronic monitoring devices (EMD). From the second visit, monetary incentives based on adherence of ICS inhalation: £1 per dose, maximum £2 /day, up to £112/study, collected as gift cards at the third visit. End of study interviews and questionnaires assessing perceptions of asthma and ICS, analysed using the Perceptions and Practicalities Framework.<h4>Participants</h4>Adolescents (11-18 years) with documented low ICS adherence (<80% by EMD), and poor asthma control at the first clinic visit.<h4>Results</h4>10 out of 12 adolescents approached were recruited (7 males, 3 females, 12-16 years). Eight participants provided adherence measures up to the fourth visits and received rewards. Mean study duration was 281 days, with 7/10 participants unable to attend their fourth visit due to COVID-19 lockdown. Only 3/10 participants managed to pair the app/EMD up to the fourth visit, which was associated with improved ICS adherence (from 0.51, SD 0.07 to 0.86, SD 0.05). Adherence did not change in adolescents unable to pair the app/EMD. The intervention was acceptable to participants and parents/guardians. Exit interviews showed that participants welcomed reminders and incentives, though expressed frustration with app/EMD technological difficulties. Participants stated the intervention helped through reminding ICS doses, promoting self-monitoring and increasing motivation to take inhalers.<h4>Conclusions</h4>An intervention using electronic reminders and incentives through an app coupled with an EMD was feasible and acceptable to adolescents with asthma. A pilot randomised controlled trial is warranted to better estimate the effect size on adherence, with improved technical support for the EMD.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/10/e053268.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-053268; html:https://europepmc.org/articles/PMC8559117; pdf:https://europepmc.org/articles/PMC8559117?pdf=render
 34641870,https://doi.org/10.1186/s12911-021-01638-z,An informatics consult approach for generating clinical evidence for treatment decisions.,"Lai AG, Chang WH, Parisinos CA, Katsoulis M, Blackburn RM, Shah AD, Nguyen V, Denaxas S, Davey Smith G, Gaunt TR, Nirantharakumar K, Cox MP, Forde D, Asselbergs FW, Harris S, Richardson S, Sofat R, Dobson RJB, Hingorani A, Patel R, Sterne J, Banerjee A, Denniston AK, Ball S, Sebire NJ, Shah NH, Foster GR, Williams B, Hemingway H.",,BMC medical informatics and decision making,2021,2021-10-12,Y,,,,"<h4>Background</h4>An Informatics Consult has been proposed in which clinicians request novel evidence from large scale health data resources, tailored to the treatment of a specific patient. However, the availability of such consultations is lacking. We seek to provide an Informatics Consult for a situation where a treatment indication and contraindication coexist in the same patient, i.e., anti-coagulation use for stroke prevention in a patient with both atrial fibrillation (AF) and liver cirrhosis.<h4>Methods</h4>We examined four sources of evidence for the effect of warfarin on stroke risk or all-cause mortality from: (1) randomised controlled trials (RCTs), (2) meta-analysis of prior observational studies, (3) trial emulation (using population electronic health records (N = 3,854,710) and (4) genetic evidence (Mendelian randomisation). We developed prototype forms to request an Informatics Consult and return of results in electronic health record systems.<h4>Results</h4>We found 0 RCT reports and 0 trials recruiting for patients with AF and cirrhosis. We found broad concordance across the three new sources of evidence we generated. Meta-analysis of prior observational studies showed that warfarin use was associated with lower stroke risk (hazard ratio [HR] = 0.71, CI 0.39-1.29). In a target trial emulation, warfarin was associated with lower all-cause mortality (HR = 0.61, CI 0.49-0.76) and ischaemic stroke (HR = 0.27, CI 0.08-0.91). Mendelian randomisation served as a drug target validation where we found that lower levels of vitamin K1 (warfarin is a vitamin K1 antagonist) are associated with lower stroke risk. A pilot survey with an independent sample of 34 clinicians revealed that 85% of clinicians found information on prognosis useful and that 79% thought that they should have access to the Informatics Consult as a service within their healthcare systems. We identified candidate steps for automation to scale evidence generation and to accelerate the return of results.<h4>Conclusion</h4>We performed a proof-of-concept Informatics Consult for evidence generation, which may inform treatment decisions in situations where there is dearth of randomised trials. Patients are surprised to know that their clinicians are currently not able to learn in clinic from data on 'patients like me'. We identify the key challenges in offering such an Informatics Consult as a service.",,doi:https://doi.org/10.1186/s12911-021-01638-z; doi:https://doi.org/10.1186/s12911-021-01638-z; html:https://europepmc.org/articles/PMC8506488; pdf:https://europepmc.org/articles/PMC8506488?pdf=render
 38872216,https://doi.org/10.1186/s13643-024-02558-5,The optimal second-line therapy for older adults with type 2 diabetes mellitus: protocol for a systematic review and network meta-analysis using individual participant data (IPD).,"Wang J, Nirantharakumar K, Sainsbury C, Moore DJ, Sinclair A, Thomas GN, Hanif W, Singh M, Tan L, Wang Z, Simms-Williams N, Yao M, Gunathilaka MN, Singh P, Toulis K, Tsapas A, Coomar D, Price MJ.",,Systematic reviews,2024,2024-06-13,N,Insulin; Metformin; RANDOMISED CONTROLLED TRIALS; Biguanide; thiazolidinediones; Dipeptidyl Peptidase-4 Inhibitors; Sulfonylureas; Glucagon-like Peptide-1 Agonists; Sodium-glucose Cotransporter-2 Inhibitors; Glucose-lowering Agents,,,"<h4>Background</h4>Due to increasing life expectancy, almost half of people with type 2 diabetes are aged 65 years or over worldwide. When metformin alone does not control blood sugar, the choice of which second-line therapy to prescribe next is not clear from currently available evidence. The existence of frailty and comorbidities in older adults further increases the complexity of medical decision-making. As only a relatively small proportion of trials report results separately for older adults, the relative efficacy and safety of second-line therapies in older adults with type 2 diabetes mellitus are unknown and require further investigation. This individual participant data (IPD) network meta-analysis evaluates the relative efficacy and safety of second-line therapies on their own or in combination in older adults with type 2 diabetes mellitus.<h4>Methods</h4>All relevant published and unpublished trials will be identified. Studies published prior to 2015 will be identified from two previous comprehensive aggregate data network meta-analyses. Searches will be conducted in CENTRAL, MEDLINE, and EMBASE from 1st January 2015 onwards, and in clinicaltrials.gov from inception. Randomised controlled trials with at least 100 estimated older adults (≥ 65 years) receiving at least 24 weeks of intervention that assess the effects of glucose-lowering drugs on mortality, glycemia, vascular and other comorbidities outcomes, and quality of life will be eligible. The screening and data extraction process will be conducted independently by two researchers. The quality of studies will be assessed using the Cochrane risk of bias tool 2. Anonymised IPD of all eligible trials will be requested via clinical trial portals or by contacting the principal investigators or sponsors. Received data will be reanalysed where necessary to standardise outcome metrics. Network meta-analyses will be performed to determine the relative effectiveness of therapies.<h4>Discussion</h4>With the increasing number of older adults with type 2 diabetes worldwide, an IPD network meta-analysis using data from all eligible trials will provide new insights into the optimal choices of second-line antidiabetic drugs to improve patient management and reduce unnecessary adverse events and the subsequent risk of comorbidities in older adults.<h4>Systematic review registration</h4>PROSPERO CRD42021272686.",,pdf:https://systematicreviewsjournal.biomedcentral.com/counter/pdf/10.1186/s13643-024-02558-5; doi:https://doi.org/10.1186/s13643-024-02558-5
-34716166,https://doi.org/10.1136/bmjopen-2021-053268,Electronic reminders and rewards to improve adherence to inhaled asthma treatment in adolescents: a non-randomised feasibility study in tertiary care.,"De Simoni A, Fleming L, Holliday L, Horne R, Priebe S, Bush A, Sheikh A, Griffiths C.",,BMJ open,2021,2021-10-29,Y,Asthma; Respiratory Medicine (See Thoracic Medicine); Paediatric Thoracic Medicine,,,"<h4>Objective</h4>To test the feasibility and acceptability of a short-term reminder and incentives intervention in adolescents with low adherence to asthma medications.<h4>Methods</h4>Mixed-methods feasibility study in a tertiary care clinic. Adolescents recruited to a 24-week programme with three 8-weekly visits, receiving electronic reminders to prompt inhaled corticosteroid (ICS) inhalation through a mobile app coupled with electronic monitoring devices (EMD). From the second visit, monetary incentives based on adherence of ICS inhalation: £1 per dose, maximum £2 /day, up to £112/study, collected as gift cards at the third visit. End of study interviews and questionnaires assessing perceptions of asthma and ICS, analysed using the Perceptions and Practicalities Framework.<h4>Participants</h4>Adolescents (11-18 years) with documented low ICS adherence (<80% by EMD), and poor asthma control at the first clinic visit.<h4>Results</h4>10 out of 12 adolescents approached were recruited (7 males, 3 females, 12-16 years). Eight participants provided adherence measures up to the fourth visits and received rewards. Mean study duration was 281 days, with 7/10 participants unable to attend their fourth visit due to COVID-19 lockdown. Only 3/10 participants managed to pair the app/EMD up to the fourth visit, which was associated with improved ICS adherence (from 0.51, SD 0.07 to 0.86, SD 0.05). Adherence did not change in adolescents unable to pair the app/EMD. The intervention was acceptable to participants and parents/guardians. Exit interviews showed that participants welcomed reminders and incentives, though expressed frustration with app/EMD technological difficulties. Participants stated the intervention helped through reminding ICS doses, promoting self-monitoring and increasing motivation to take inhalers.<h4>Conclusions</h4>An intervention using electronic reminders and incentives through an app coupled with an EMD was feasible and acceptable to adolescents with asthma. A pilot randomised controlled trial is warranted to better estimate the effect size on adherence, with improved technical support for the EMD.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/10/e053268.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-053268; html:https://europepmc.org/articles/PMC8559117; pdf:https://europepmc.org/articles/PMC8559117?pdf=render
 37526977,https://doi.org/10.5830/cvja-2023-037,Yield of family screening in dilated cardiomyopathy within low-income setting: Tanzanian experience.,"Fundikira LS, Julius J, Chillo P, Mayala H, Kifai E, van Laake LW, Kamuhabwa A, Kwesigabo G, Asselbergs FW.",,Cardiovascular journal of Africa,2023,2023-07-25,N,Screening; Dilated cardiomyopathy; First‐degree Relatives,,,"<h4>Background</h4>Dilated cardiomyopathy (DCM) is often familial and screening of relatives is recommended. However, studies on the yield of screening are scarce in developing countries.<h4>Aim</h4>The aim of the study was to identify and characterise First-degree relatives of patients with DCM in Tanzania.<h4>Methods</h4>We recruited first-degree relatives of 57 DCM patients. DCM in the relatives was diagnosed using the 2016 revised definition by the European Society of Cardiology working group on myocardial and pericardial diseases.<h4>Results</h4>We screened 120 first-degree relatives. All were asymptomatic (100%) with a median age of 39.0 years (29.5-49.0), slightly over a half (53.3%) were females and 17 (14.1%) were found to have previously unknown DCM. The mean (± SD) indexed left ventricular end-diastolic volume was significantly higher in relatives with DCM (71 ± 11.5 ml) compared to relatives without DCM (50 ± 11.5) (<i>p</i> = 0.001).<h4>Conclusion</h4>First-degree relatives of patients with DCM are at risk of developing asymptomatic DCM at a young age.",,doi:https://doi.org/10.5830/CVJA-2023-037
-37468148,https://doi.org/10.1136/bmj-2023-075133,Associations between self-reported healthcare disruption due to covid-19 and avoidable hospital admission: evidence from seven linked longitudinal studies for England.,"Green MA, McKee M, Hamilton OK, Shaw RJ, Macleod J, Boyd A, Katikireddi SV, LH&W NCS Collaborative.",,BMJ (Clinical research ed.),2023,2023-07-19,Y,,,,"<h4>Objectives</h4>To examine whether there is an association between people who experienced disrupted access to healthcare during the covid-19 pandemic and risk of an avoidable hospital admission.<h4>Design</h4>Observational analysis using evidence from seven linked longitudinal cohort studies for England.<h4>Setting</h4>Studies linked to electronic health records from NHS Digital from 1 March 2020 to 25 August 2022. Data were accessed using the UK Longitudinal Linkage Collaboration trusted research environment.<h4>Participants</h4>Individual level records for 29 276 people.<h4>Main outcome measures</h4>Avoidable hospital admissions defined as emergency hospital admissions for ambulatory care sensitive and emergency urgent care sensitive conditions.<h4>Results</h4>9742 participants (weighted percentage 35%, adjusted for sample structure of longitudinal cohorts) self-reported some form of disrupted access to healthcare during the covid-19 pandemic. People with disrupted access were at increased risk of any (odds ratio 1.80, 95% confidence interval 1.39 to 2.34), acute (2.01, 1.39 to 2.92), and chronic (1.80, 1.31 to 2.48) ambulatory care sensitive hospital admissions. For people who experienced disrupted access to appointments (eg, visiting their doctor or an outpatient department) and procedures (eg, surgery, cancer treatment), positive associations were found with measures of avoidable hospital admissions.<h4>Conclusions</h4>Evidence from linked individual level data shows that people whose access to healthcare was disrupted were more likely to have a potentially preventable hospital admission. The findings highlight the need to increase healthcare investment to tackle the short and long term implications of the pandemic, and to protect treatments and procedures during future pandemics.",,doi:https://doi.org/10.1136/bmj-2023-075133; html:https://europepmc.org/articles/PMC10354595; pdf:https://europepmc.org/articles/PMC10354595?pdf=render
 35896970,https://doi.org/10.1186/s12879-022-07628-4,SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2.,"Eales O, Page AJ, de Oliveira Martins L, Wang H, Bodinier B, Haw D, Jonnerby J, Atchison C, COVID-19 Genomics UK (COG-UK) Consortium, Ashby D, Barclay W, Taylor G, Cooke G, Ward H, Darzi A, Riley S, Chadeau-Hyam M, Donnelly CA, Elliott P.",,BMC infectious diseases,2022,2022-07-27,Y,Mutation; Genetic diversity; Transmission Advantage; Covid-19; Sars-cov-2; Delta Variant,,,"<h4>Background</h4>Since the emergence of SARS-CoV-2, evolutionary pressure has driven large increases in the transmissibility of the virus. However, with increasing levels of immunity through vaccination and natural infection the evolutionary pressure will switch towards immune escape. Genomic surveillance in regions of high immunity is crucial in detecting emerging variants that can more successfully navigate the immune landscape.<h4>Methods</h4>We present phylogenetic relationships and lineage dynamics within England (a country with high levels of immunity), as inferred from a random community sample of individuals who provided a self-administered throat and nose swab for rt-PCR testing as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. During round 14 (9 September-27 September 2021) and 15 (19 October-5 November 2021) lineages were determined for 1322 positive individuals, with 27.1% of those which reported their symptom status reporting no symptoms in the previous month.<h4>Results</h4>We identified 44 unique lineages, all of which were Delta or Delta sub-lineages, and found a reduction in their mutation rate over the study period. The proportion of the Delta sub-lineage AY.4.2 was increasing, with a reproduction number 15% (95% CI 8-23%) greater than the most prevalent lineage, AY.4. Further, AY.4.2 was less associated with the most predictive COVID-19 symptoms (p = 0.029) and had a reduced mutation rate (p = 0.050). Both AY.4.2 and AY.4 were found to be geographically clustered in September but this was no longer the case by late October/early November, with only the lineage AY.6 exhibiting clustering towards the South of England.<h4>Conclusions</h4>As SARS-CoV-2 moves towards endemicity and new variants emerge, genomic data obtained from random community samples can augment routine surveillance data without the potential biases introduced due to higher sampling rates of symptomatic individuals.",,pdf:https://bmcinfectdis.biomedcentral.com/counter/pdf/10.1186/s12879-022-07628-4; doi:https://doi.org/10.1186/s12879-022-07628-4; html:https://europepmc.org/articles/PMC9326417; pdf:https://europepmc.org/articles/PMC9326417?pdf=render
+37468148,https://doi.org/10.1136/bmj-2023-075133,Associations between self-reported healthcare disruption due to covid-19 and avoidable hospital admission: evidence from seven linked longitudinal studies for England.,"Green MA, McKee M, Hamilton OK, Shaw RJ, Macleod J, Boyd A, Katikireddi SV, LH&W NCS Collaborative.",,BMJ (Clinical research ed.),2023,2023-07-19,Y,,,,"<h4>Objectives</h4>To examine whether there is an association between people who experienced disrupted access to healthcare during the covid-19 pandemic and risk of an avoidable hospital admission.<h4>Design</h4>Observational analysis using evidence from seven linked longitudinal cohort studies for England.<h4>Setting</h4>Studies linked to electronic health records from NHS Digital from 1 March 2020 to 25 August 2022. Data were accessed using the UK Longitudinal Linkage Collaboration trusted research environment.<h4>Participants</h4>Individual level records for 29 276 people.<h4>Main outcome measures</h4>Avoidable hospital admissions defined as emergency hospital admissions for ambulatory care sensitive and emergency urgent care sensitive conditions.<h4>Results</h4>9742 participants (weighted percentage 35%, adjusted for sample structure of longitudinal cohorts) self-reported some form of disrupted access to healthcare during the covid-19 pandemic. People with disrupted access were at increased risk of any (odds ratio 1.80, 95% confidence interval 1.39 to 2.34), acute (2.01, 1.39 to 2.92), and chronic (1.80, 1.31 to 2.48) ambulatory care sensitive hospital admissions. For people who experienced disrupted access to appointments (eg, visiting their doctor or an outpatient department) and procedures (eg, surgery, cancer treatment), positive associations were found with measures of avoidable hospital admissions.<h4>Conclusions</h4>Evidence from linked individual level data shows that people whose access to healthcare was disrupted were more likely to have a potentially preventable hospital admission. The findings highlight the need to increase healthcare investment to tackle the short and long term implications of the pandemic, and to protect treatments and procedures during future pandemics.",,doi:https://doi.org/10.1136/bmj-2023-075133; html:https://europepmc.org/articles/PMC10354595; pdf:https://europepmc.org/articles/PMC10354595?pdf=render
 37432340,https://doi.org/10.1093/rheumatology/kead346,Trends for opioid prescribing and the impact of the COVID-19 pandemic in patients with rheumatic and musculoskeletal diseases between 2006 and 2021.,"Huang YT, Jenkins DA, Yimer BB, Benitez-Aurioles J, Peek N, Lunt M, Dixon WG, Jani M.",,"Rheumatology (Oxford, England)",2024,2024-04-01,Y,RA; SLE; Trend; PSA; Opioids; Oa; Axial Spondyloarthritis; Fm; Covid-19,,,"<h4>Objective</h4>To investigate opioid prescribing trends and assess the impact of the COVID-19 pandemic on opioid prescribing in rheumatic and musculoskeletal diseases (RMDs).<h4>Methods</h4>Adult patients with RA, PsA, axial spondyloarthritis (AxSpA), SLE, OA and FM with opioid prescriptions between 1 January 2006 and 31 August 2021 without cancer in UK primary care were included. Age- and gender-standardized yearly rates of new and prevalent opioid users were calculated between 2006 and 2021. For prevalent users, monthly measures of mean morphine milligram equivalents (MME)/day were calculated between 2006 and 2021. To assess the impact of the pandemic, we fitted regression models to the monthly number of prevalent opioid users between January 2015 and August 2021. The time coefficient reflects the trend pre-pandemic and the interaction term coefficient represents the change in the trend during the pandemic.<h4>Results</h4>The study included 1 313 519 RMD patients. New opioid users for RA, PsA and FM increased from 2.6, 1.0 and 3.4/10 000 persons in 2006 to 4.5, 1.8 and 8.7, respectively, in 2018 or 2019. This was followed by a fall to 2.4, 1.2 and 5.9, respectively, in 2021. Prevalent opioid users for all RMDs increased from 2006 but plateaued or dropped beyond 2018, with a 4.5-fold increase in FM between 2006 and 2021. In this period, MME/day increased for all RMDs, with the highest for FM (≥35). During COVID-19 lockdowns, RA, PsA and FM showed significant changes in the trend of prevalent opioid users. The trend for FM increased pre-pandemic and started decreasing during the pandemic.<h4>Conclusion</h4>The plateauing or decreasing trend of opioid users for RMDs after 2018 may reflect the efforts to tackle rising opioid prescribing in the UK. The pandemic led to fewer people on opioids for most RMDs, providing reassurance that there was no sudden increase in opioid prescribing during the pandemic.",,pdf:https://academic.oup.com/rheumatology/advance-article-pdf/doi/10.1093/rheumatology/kead346/50930066/kead346.pdf; doi:https://doi.org/10.1093/rheumatology/kead346; html:https://europepmc.org/articles/PMC10986805; pdf:https://europepmc.org/articles/PMC10986805?pdf=render
-37022975,https://doi.org/10.1210/clinem/dgad201,Stable Incidence and Increasing Prevalence of Primary Hyperparathyroidism in a Population-based Study in Scotland.,"Soto-Pedre E, Newey PJ, Leese GP.",,The Journal of clinical endocrinology and metabolism,2023,2023-09-01,Y,Parathyroid gland; Prevalence; epidemiology; incidence; Primary Hyperparathyroidism,,,"<h4>Context</h4>Previous studies, including our own, have demonstrated a highly variable incidence of primary hyperparathyroidism (PHPT) from year to year.<h4>Objective</h4>We planned to provide a current estimate of the incidence and prevalence of PHPT in a community-based study.<h4>Methods</h4>A population-based retrospective follow-up study was conducted in Tayside (Scotland) from 2007 to 2018. Record-linkage technology (demography, biochemistry, prescribing, hospital admissions, radiology, and mortality data) was used to identify all patients. Cases of PHPT were defined as those with at least 2 raised serum corrected calcium concentration CCA (> 2.55 mmol/L) and/or hospital admissions with PHPT diagnoses and/or surgery records with parathyroidectomy during the follow-up period. The number of prevalent and incident cases of PHPT per calendar year by age and sex were estimated.<h4>Results</h4>A total of 2118 people (72.3% female, mean age 65 years) were identified with an incident case of PHPT. The overall prevalence of PHPT over the 12 years of the study was 0.84% (95% CI, 0.68%-1.02%), steadily increasing from 0.71% in 2007 to 1.02% in 2018. From 2008, the incidence of PHPT was relatively stable from 4 to 6 cases per 10 000 person-years, declining from 11.5 per 10 000 person-years in 2007. The incidence varied from 0.59 per 10 000 person-years (95% CI, 0.40%-0.77%) for those aged 20 to 29 years, to 12.4 per 10 000 person-years (95% CI, 11.2%-13.3%) in those aged 70 to 79 years. Incidence of PHPT was 2.5 times higher in women than in men.<h4>Conclusion</h4>This study is the first showing a relatively steady annual incidence of PHPT at 4 to 6 per 10 000 person-years. This population-based study reports a PHPT prevalence of 0.84%.",,pdf:https://academic.oup.com/jcem/advance-article-pdf/doi/10.1210/clinem/dgad201/50034331/dgad201.pdf; doi:https://doi.org/10.1210/clinem/dgad201; html:https://europepmc.org/articles/PMC10505547
 33052324,https://doi.org/10.1016/j.eclinm.2020.100574,A case-control and cohort study to determine the relationship between ethnic background and severe COVID-19.,"Zakeri R, Bendayan R, Ashworth M, Bean DM, Dodhia H, Durbaba S, O'Gallagher K, Palmer C, Curcin V, Aitken E, Bernal W, Barker RD, Norton S, Gulliford M, Teo JTH, Galloway J, Dobson RJB, Shah AM.",,EClinicalMedicine,2020,2020-10-09,Y,Case-control study; Ethnicity; Deprivation; Comorbidities; Covid-19,,,"<h4>Background</h4>People of minority ethnic backgrounds may be disproportionately affected by severe COVID-19. Whether this relates to increased infection risk, more severe disease progression, or worse in-hospital survival is unknown. The contribution of comorbidities or socioeconomic deprivation to ethnic patterning of outcomes is also unclear.<h4>Methods</h4>We conducted a case-control and a cohort study in an inner city primary and secondary care setting to examine whether ethnic background affects the risk of hospital admission with severe COVID-19 and/or in-hospital mortality. Inner city adult residents admitted to hospital with confirmed COVID-19 (<i>n</i> = 872 cases) were compared with 3,488 matched controls randomly sampled from a primary healthcare database comprising 344,083 people residing in the same region. For the cohort study, we studied 1827 adults consecutively admitted with COVID-19. The primary exposure variable was self-defined ethnicity. Analyses were adjusted for socio-demographic and clinical variables.<h4>Findings</h4>The 872 cases comprised 48.1% Black, 33.7% White, 12.6% Mixed/Other and 5.6% Asian patients. In conditional logistic regression analyses, Black and Mixed/Other ethnicity were associated with higher admission risk than white (OR 3.12 [95% CI 2.63-3.71] and 2.97 [2.30-3.85] respectively). Adjustment for comorbidities and deprivation modestly attenuated the association (OR 2.24 [1.83-2.74] for Black, 2.70 [2.03-3.59] for Mixed/Other). Asian ethnicity was not associated with higher admission risk (adjusted OR 1.01 [0.70-1.46]). In the cohort study of 1827 patients, 455 (28.9%) died over a median (IQR) of 8 (4-16) days. Age and male sex, but not Black (adjusted HR 1.06 [0.82-1.37]) or Mixed/Other ethnicity (adjusted HR 0.72 [0.47-1.10]), were associated with in-hospital mortality. Asian ethnicity was associated with higher in-hospital mortality but with a large confidence interval (adjusted HR 1.71 [1.15-2.56]).<h4>Interpretation</h4>Black and Mixed ethnicity are independently associated with greater admission risk with COVID-19 and may be risk factors for development of severe disease, but do not affect in-hospital mortality risk. Comorbidities and socioeconomic factors only partly account for this and additional ethnicity-related factors may play a large role. The impact of COVID-19 may be different in Asians.<h4>Funding</h4>British Heart Foundation; the National Institute for Health Research; Health Data Research UK.",,pdf:http://www.thelancet.com/article/S2589537020303187/pdf; doi:https://doi.org/10.1016/j.eclinm.2020.100574; html:https://europepmc.org/articles/PMC7545271; pdf:https://europepmc.org/articles/PMC7545271?pdf=render
-35032176,https://doi.org/10.1007/s00125-021-05640-y,Cardiovascular risk prediction in type 2 diabetes: a comparison of 22 risk scores in primary care settings.,"Dziopa K, Asselbergs FW, Gratton J, Chaturvedi N, Schmidt AF.",,Diabetologia,2022,2022-01-15,Y,Prediction; Diabetes; Cardiovascular disease; Risk Score,,,"<h4>Aims/hypothesis</h4>We aimed to compare the performance of risk prediction scores for CVD (i.e., coronary heart disease and stroke), and a broader definition of CVD including atrial fibrillation and heart failure (CVD+), in individuals with type 2 diabetes.<h4>Methods</h4>Scores were identified through a literature review and were included irrespective of the type of predicted cardiovascular outcome or the inclusion of individuals with type 2 diabetes. Performance was assessed in a contemporary, representative sample of 168,871 UK-based individuals with type 2 diabetes (age ≥18 years without pre-existing CVD+). Missing observations were addressed using multiple imputation.<h4>Results</h4>We evaluated 22 scores: 13 derived in the general population and nine in individuals with type 2 diabetes. The Systemic Coronary Risk Evaluation (SCORE) CVD rule derived in the general population performed best for both CVD (C statistic 0.67 [95% CI 0.67, 0.67]) and CVD+ (C statistic 0.69 [95% CI 0.69, 0.70]). The C statistic of the remaining scores ranged from 0.62 to 0.67 for CVD, and from 0.64 to 0.69 for CVD+. Calibration slopes (1 indicates perfect calibration) ranged from 0.38 (95% CI 0.37, 0.39) to 0.74 (95% CI 0.72, 0.76) for CVD, and from 0.41 (95% CI 0.40, 0.42) to 0.88 (95% CI 0.86, 0.90) for CVD+. A simple recalibration process considerably improved the performance of the scores, with calibration slopes now ranging between 0.96 and 1.04 for CVD. Scores with more predictors did not outperform scores with fewer predictors: for CVD+, QRISK3 (19 variables) had a C statistic of 0.68 (95% CI 0.68, 0.69), compared with SCORE CVD (six variables) which had a C statistic of 0.69 (95% CI 0.69, 0.70). Scores specific to individuals with diabetes did not discriminate better than scores derived in the general population: the UK Prospective Diabetes Study (UKPDS) scores performed significantly worse than SCORE CVD (p value <0.001).<h4>Conclusions/interpretation</h4>CVD risk prediction scores could not accurately identify individuals with type 2 diabetes who experienced a CVD event in the 10 years of follow-up. All 22 evaluated models had a comparable and modest discriminative ability.",,pdf:https://link.springer.com/content/pdf/10.1007/s00125-021-05640-y.pdf; doi:https://doi.org/10.1007/s00125-021-05640-y; html:https://europepmc.org/articles/PMC8894164; pdf:https://europepmc.org/articles/PMC8894164?pdf=render
+37022975,https://doi.org/10.1210/clinem/dgad201,Stable Incidence and Increasing Prevalence of Primary Hyperparathyroidism in a Population-based Study in Scotland.,"Soto-Pedre E, Newey PJ, Leese GP.",,The Journal of clinical endocrinology and metabolism,2023,2023-09-01,Y,Parathyroid gland; Prevalence; epidemiology; incidence; Primary Hyperparathyroidism,,,"<h4>Context</h4>Previous studies, including our own, have demonstrated a highly variable incidence of primary hyperparathyroidism (PHPT) from year to year.<h4>Objective</h4>We planned to provide a current estimate of the incidence and prevalence of PHPT in a community-based study.<h4>Methods</h4>A population-based retrospective follow-up study was conducted in Tayside (Scotland) from 2007 to 2018. Record-linkage technology (demography, biochemistry, prescribing, hospital admissions, radiology, and mortality data) was used to identify all patients. Cases of PHPT were defined as those with at least 2 raised serum corrected calcium concentration CCA (> 2.55 mmol/L) and/or hospital admissions with PHPT diagnoses and/or surgery records with parathyroidectomy during the follow-up period. The number of prevalent and incident cases of PHPT per calendar year by age and sex were estimated.<h4>Results</h4>A total of 2118 people (72.3% female, mean age 65 years) were identified with an incident case of PHPT. The overall prevalence of PHPT over the 12 years of the study was 0.84% (95% CI, 0.68%-1.02%), steadily increasing from 0.71% in 2007 to 1.02% in 2018. From 2008, the incidence of PHPT was relatively stable from 4 to 6 cases per 10 000 person-years, declining from 11.5 per 10 000 person-years in 2007. The incidence varied from 0.59 per 10 000 person-years (95% CI, 0.40%-0.77%) for those aged 20 to 29 years, to 12.4 per 10 000 person-years (95% CI, 11.2%-13.3%) in those aged 70 to 79 years. Incidence of PHPT was 2.5 times higher in women than in men.<h4>Conclusion</h4>This study is the first showing a relatively steady annual incidence of PHPT at 4 to 6 per 10 000 person-years. This population-based study reports a PHPT prevalence of 0.84%.",,pdf:https://academic.oup.com/jcem/advance-article-pdf/doi/10.1210/clinem/dgad201/50034331/dgad201.pdf; doi:https://doi.org/10.1210/clinem/dgad201; html:https://europepmc.org/articles/PMC10505547
 33112263,https://doi.org/10.1530/eje-20-0296,Pubertal timing in boys and girls born to mothers with gestational diabetes mellitus: a systematic review.,"Subramanian A, Idkowiak J, Toulis KA, Thangaratinam S, Arlt W, Nirantharakumar K.",,European journal of endocrinology,2021,2021-01-01,Y,,,,"<h4>Context</h4>The incidence of gestational diabetes mellitus (GDM) has been on the rise, driven by maternal obesity. In parallel, pubertal tempo has increased in the general population, driven by childhood obesity.<h4>Objective</h4>To evaluate the available evidence on pubertal timing of boys and girls born to mothers with GDM.<h4>Data sources</h4>We searched MEDLINE, EMBASE, CINAHL Plus, Cochrane library and grey literature for observational studies up to October 2019.<h4>Study selection and extraction</h4>Two reviewers independently selected studies, collected data and appraised the studies for risk of bias. Results were tabulated and narratively described as reported in the primary studies.<h4>Results</h4>Seven articles (six for girls and four for boys) were included. Study quality score was mostly moderate (ranging from 4 to 10 out of 11). In girls born to mothers with GDM, estimates suggest earlier timing of pubarche, thelarche and menarche although for each of these outcomes only one study each showed a statistically significant association. In boys, there was some association between maternal GDM and earlier pubarche, but inconsistency in the direction of shift of age at onset of genital and testicular development and first ejaculation. Only a single study analysed growth patterns in children of mothers with GDM, describing a 3-month advancement in the age of attainment of peak height velocity and a slight increase in pubertal tempo.<h4>Conclusions</h4>Pubertal timing may be influenced by the presence of maternal GDM, though current evidence is sparse and of limited quality. Prospective cohort studies should be conducted, ideally coupled with objective biochemical tests.",,pdf:https://eje.bioscientifica.com/downloadpdf/journals/eje/184/1/EJE-20-0296.pdf; doi:https://doi.org/10.1530/EJE-20-0296; html:https://europepmc.org/articles/PMC7707806; pdf:https://europepmc.org/articles/PMC7707806?pdf=render
 34190735,https://doi.org/,The changing characteristics of COVID-19 presentations. A regional comparison of SARS-CoV-2 hospitalised patients during the first and second wave.,"Atkin C, Kamwa V, Reddy-Kolanu V, Parekh D, Evison F, Nightingale P, Gallier S, Ball S, Sapey E.",,Acute medicine,2021,2021-01-01,N,,,,"<h4>Background</h4>This study assesses COVID-19 hospitalised patient demography and outcomes during wave 1 and wave 2, prior to new variants of the virus.<h4>Methods</h4>All patients with a positive SARS-CoV-2 swab between 10th March 2020 and 5th July 2020 (wave 1) and 1st September 2020 and 16th November 2020 (wave 2) admitted to University Hospitals Birmingham NHS Foundation Trust were included (n=4856), followed for 28 days.<h4>Results</h4>Wave 2 patients were younger, more ethnically diverse, had less co-morbidities and disease presentation was milder on presentation. After matching for these factors, mortality was reduced, but without differences in intensive care admissions.<h4>Conclusion</h4>Prior to new SARS-CoV-2 variants, outcomes for hospitalised patients with COVID-19 were improving but with similar intensive care needs.",,
-31960476,https://doi.org/10.1111/ppe.12627,Phenotyping congenital anomalies in administrative hospital records.,"Zylbersztejn A, Verfürden M, Hardelid P, Gilbert R, Wijlaars L.",,Paediatric and perinatal epidemiology,2020,2020-01-01,Y,Phenotyping; Congenital Anomalies; International Comparison; Administrative Data,Improving Public Health,,"<h4>Background</h4>Congenital anomalies are a major cause of co-morbidity in children. Diagnostic code lists are increasingly used to identify congenital anomalies in administrative health records. Evidence is lacking on comparability of these code lists.<h4>Objectives</h4>To compare prevalence of congenital anomalies and prognostic outcomes for children with congenital anomalies identified in administrative health records using three different code lists.<h4>Methods</h4>We developed national cohorts of singleton livebirths in England (n = 7 354 363, 2003-2014) and Scotland (n = 493 556, 2003-2011). Children with congenital anomalies were identified if congenital anomaly diagnosis was recorded at birth, during subsequent hospital admission or as cause of death before 2 years old. We used three code lists: the EUROCAT list for congenital anomaly surveillance in Europe; the Hardelid list developed to identify children with chronic conditions (including congenital anomalies) admitted to hospital in England; and the Feudtner list developed to indicate children with complex chronic conditions (including congenital anomalies) admitted to hospitals in the United States. We compared prevalence, and risks of postnatal hospital readmission and death according to each code list in England and Scotland.<h4>Results</h4>Prevalence of congenital anomalies was highest using the EUROCAT list (4.1% of livebirths in England, 3.7% in Scotland), followed by Hardelid (3.1% and 3.0% of livebirths, respectively) and Feudtner (1.8% and 1.5% of livebirths, respectively). 67.2%-73.3% of children with congenital anomalies in England and 65.2%-77.0% in Scotland had at least one postnatal hospital admission across the three code lists; mortality ranged between 42.6-75.4 and 41.5-88.7 deaths per 1000 births in England Scotland, respectively. The risk of these adverse outcomes was highest using Feudtner and lowest using EUROCAT code lists.<h4>Conclusions</h4>The prevalence of congenital anomalies varied by congenital anomaly code list, over time and between countries, reflecting in part differences in hospital coding practices and admission thresholds. As a minimum, researchers using administrative health data to study congenital anomalies should report sensitivity analyses using different code lists.","This study identifies children born with congenital anomalies from administrative health data. The the prevalence of congenital anomalies and prognostic outcomes for children with congenital anomalies are compared using three different code lists. The study found that the prevalence of congenital anomalies varied by code list, over time and between countries. This reflects differences in hospital coding practices and admission thresholds.",pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/ppe.12627; doi:https://doi.org/10.1111/ppe.12627; html:https://europepmc.org/articles/PMC7003968; pdf:https://europepmc.org/articles/PMC7003968?pdf=render
+35032176,https://doi.org/10.1007/s00125-021-05640-y,Cardiovascular risk prediction in type 2 diabetes: a comparison of 22 risk scores in primary care settings.,"Dziopa K, Asselbergs FW, Gratton J, Chaturvedi N, Schmidt AF.",,Diabetologia,2022,2022-01-15,Y,Prediction; Diabetes; Cardiovascular disease; Risk Score,,,"<h4>Aims/hypothesis</h4>We aimed to compare the performance of risk prediction scores for CVD (i.e., coronary heart disease and stroke), and a broader definition of CVD including atrial fibrillation and heart failure (CVD+), in individuals with type 2 diabetes.<h4>Methods</h4>Scores were identified through a literature review and were included irrespective of the type of predicted cardiovascular outcome or the inclusion of individuals with type 2 diabetes. Performance was assessed in a contemporary, representative sample of 168,871 UK-based individuals with type 2 diabetes (age ≥18 years without pre-existing CVD+). Missing observations were addressed using multiple imputation.<h4>Results</h4>We evaluated 22 scores: 13 derived in the general population and nine in individuals with type 2 diabetes. The Systemic Coronary Risk Evaluation (SCORE) CVD rule derived in the general population performed best for both CVD (C statistic 0.67 [95% CI 0.67, 0.67]) and CVD+ (C statistic 0.69 [95% CI 0.69, 0.70]). The C statistic of the remaining scores ranged from 0.62 to 0.67 for CVD, and from 0.64 to 0.69 for CVD+. Calibration slopes (1 indicates perfect calibration) ranged from 0.38 (95% CI 0.37, 0.39) to 0.74 (95% CI 0.72, 0.76) for CVD, and from 0.41 (95% CI 0.40, 0.42) to 0.88 (95% CI 0.86, 0.90) for CVD+. A simple recalibration process considerably improved the performance of the scores, with calibration slopes now ranging between 0.96 and 1.04 for CVD. Scores with more predictors did not outperform scores with fewer predictors: for CVD+, QRISK3 (19 variables) had a C statistic of 0.68 (95% CI 0.68, 0.69), compared with SCORE CVD (six variables) which had a C statistic of 0.69 (95% CI 0.69, 0.70). Scores specific to individuals with diabetes did not discriminate better than scores derived in the general population: the UK Prospective Diabetes Study (UKPDS) scores performed significantly worse than SCORE CVD (p value <0.001).<h4>Conclusions/interpretation</h4>CVD risk prediction scores could not accurately identify individuals with type 2 diabetes who experienced a CVD event in the 10 years of follow-up. All 22 evaluated models had a comparable and modest discriminative ability.",,pdf:https://link.springer.com/content/pdf/10.1007/s00125-021-05640-y.pdf; doi:https://doi.org/10.1007/s00125-021-05640-y; html:https://europepmc.org/articles/PMC8894164; pdf:https://europepmc.org/articles/PMC8894164?pdf=render
 34161326,https://doi.org/10.1371/journal.pcbi.1009121,Contrasting factors associated with COVID-19-related ICU admission and death outcomes in hospitalised patients by means of Shapley values.,"Cavallaro M, Moiz H, Keeling MJ, McCarthy ND.",,PLoS computational biology,2021,2021-06-23,Y,,,,"Identification of those at greatest risk of death due to the substantial threat of COVID-19 can benefit from novel approaches to epidemiology that leverage large datasets and complex machine-learning models, provide data-driven intelligence, and guide decisions such as intensive-care unit admission (ICUA). The objective of this study is two-fold, one substantive and one methodological: substantively to evaluate the association of demographic and health records with two related, yet different, outcomes of severe COVID-19 (viz., death and ICUA); methodologically to compare interpretations based on logistic regression and on gradient-boosted decision tree (GBDT) predictions interpreted by means of the Shapley impacts of covariates. Very different association of some factors, e.g., obesity and chronic respiratory diseases, with death and ICUA may guide review of practice. Shapley explanation of GBDTs identified varying effects of some factors among patients, thus emphasising the importance of individual patient assessment. The results of this study are also relevant for the evaluation of complex automated clinical decision systems, which should optimise prediction scores whilst remaining interpretable to clinicians and mitigating potential biases.",,pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009121&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1009121; html:https://europepmc.org/articles/PMC8259985; pdf:https://europepmc.org/articles/PMC8259985?pdf=render
-36620207,https://doi.org/10.3389/fphys.2022.1089343,Incorporating structural abnormalities in equivalent dipole layer based ECG simulations.,"Boonstra MJ, Oostendorp TF, Roudijk RW, Kloosterman M, Asselbergs FW, Loh P, Van Dam PM.",,Frontiers in physiology,2022,2022-12-22,Y,Simulation; Myocardial Disease; Electrocardiogram (Ecg); Cardiac Activation; Ecgsim; Equivalent Dipole Layer,,,"<b>Introduction:</b> Electrical activity of the myocardium is recorded with the 12-lead ECG. ECG simulations can improve our understanding of the relation between abnormal ventricular activation in diseased myocardium and body surface potentials (BSP). However, in equivalent dipole layer (EDL)-based ECG simulations, the presence of diseased myocardium breaks the equivalence of the dipole layer. To simulate diseased myocardium, patches with altered electrophysiological characteristics were incorporated within the model. The relation between diseased myocardium and corresponding BSP was investigated in a simulation study. <b>Methods:</b> Activation sequences in normal and diseased myocardium were simulated and corresponding 64-lead BSP were computed in four models with distinct patch locations. QRS-complexes were compared using correlation coefficient (CC). The effect of different types of patch activation was assessed. Of one patient, simulated electrograms were compared to electrograms recorded during invasive electro-anatomical mapping. <b>Results:</b> Hundred-fifty-three abnormal activation sequences were simulated. Median QRS-CC of delayed versus dyssynchronous were significantly different (1.00 vs. 0.97, <i>p</i> < 0.001). Depending on the location of the patch, BSP leads were affected differently. Within diseased regions, fragmentation, low bipolar voltages and late potentials were observed in both recorded and simulated electrograms. <b>Discussion:</b> A novel method to simulate cardiomyopathy in EDL-based ECG simulations was established and evaluated. The new patch-based approach created a realistic relation between ECG waveforms and underlying activation sequences. Findings in the simulated cases were in agreement with clinical observations. With this method, our understanding of disease progression in cardiomyopathies may be further improved and used in advanced inverse ECG procedures.",,pdf:https://www.frontiersin.org/articles/10.3389/fphys.2022.1089343/pdf; doi:https://doi.org/10.3389/fphys.2022.1089343; html:https://europepmc.org/articles/PMC9814485; pdf:https://europepmc.org/articles/PMC9814485?pdf=render
+31960476,https://doi.org/10.1111/ppe.12627,Phenotyping congenital anomalies in administrative hospital records.,"Zylbersztejn A, Verfürden M, Hardelid P, Gilbert R, Wijlaars L.",,Paediatric and perinatal epidemiology,2020,2020-01-01,Y,Phenotyping; Congenital Anomalies; International Comparison; Administrative Data,Improving Public Health,,"<h4>Background</h4>Congenital anomalies are a major cause of co-morbidity in children. Diagnostic code lists are increasingly used to identify congenital anomalies in administrative health records. Evidence is lacking on comparability of these code lists.<h4>Objectives</h4>To compare prevalence of congenital anomalies and prognostic outcomes for children with congenital anomalies identified in administrative health records using three different code lists.<h4>Methods</h4>We developed national cohorts of singleton livebirths in England (n = 7 354 363, 2003-2014) and Scotland (n = 493 556, 2003-2011). Children with congenital anomalies were identified if congenital anomaly diagnosis was recorded at birth, during subsequent hospital admission or as cause of death before 2 years old. We used three code lists: the EUROCAT list for congenital anomaly surveillance in Europe; the Hardelid list developed to identify children with chronic conditions (including congenital anomalies) admitted to hospital in England; and the Feudtner list developed to indicate children with complex chronic conditions (including congenital anomalies) admitted to hospitals in the United States. We compared prevalence, and risks of postnatal hospital readmission and death according to each code list in England and Scotland.<h4>Results</h4>Prevalence of congenital anomalies was highest using the EUROCAT list (4.1% of livebirths in England, 3.7% in Scotland), followed by Hardelid (3.1% and 3.0% of livebirths, respectively) and Feudtner (1.8% and 1.5% of livebirths, respectively). 67.2%-73.3% of children with congenital anomalies in England and 65.2%-77.0% in Scotland had at least one postnatal hospital admission across the three code lists; mortality ranged between 42.6-75.4 and 41.5-88.7 deaths per 1000 births in England Scotland, respectively. The risk of these adverse outcomes was highest using Feudtner and lowest using EUROCAT code lists.<h4>Conclusions</h4>The prevalence of congenital anomalies varied by congenital anomaly code list, over time and between countries, reflecting in part differences in hospital coding practices and admission thresholds. As a minimum, researchers using administrative health data to study congenital anomalies should report sensitivity analyses using different code lists.","This study identifies children born with congenital anomalies from administrative health data. The the prevalence of congenital anomalies and prognostic outcomes for children with congenital anomalies are compared using three different code lists. The study found that the prevalence of congenital anomalies varied by code list, over time and between countries. This reflects differences in hospital coding practices and admission thresholds.",pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/ppe.12627; doi:https://doi.org/10.1111/ppe.12627; html:https://europepmc.org/articles/PMC7003968; pdf:https://europepmc.org/articles/PMC7003968?pdf=render
 35039282,https://doi.org/10.1136/bmjopen-2021-049506,Development and external validation of prognostic models for COVID-19 to support risk stratification in secondary care.,"Adderley NJ, Taverner T, Price MJ, Sainsbury C, Greenwood D, Chandan JS, Takwoingi Y, Haniffa R, Hosier I, Welch C, Parekh D, Gallier S, Gokhale K, Denniston AK, Sapey E, Nirantharakumar K.",,BMJ open,2022,2022-01-17,Y,Public Health; Covid-19,,,"<h4>Objectives</h4>Existing UK prognostic models for patients admitted to the hospital with COVID-19 are limited by reliance on comorbidities, which are under-recorded in secondary care, and lack of imaging data among the candidate predictors. Our aims were to develop and externally validate novel prognostic models for adverse outcomes (death and intensive therapy unit (ITU) admission) in UK secondary care and externally validate the existing 4C score.<h4>Design</h4>Candidate predictors included demographic variables, symptoms, physiological measures, imaging and laboratory tests. Final models used logistic regression with stepwise selection.<h4>Setting</h4>Model development was performed in data from University Hospitals Birmingham (UHB). External validation was performed in the CovidCollab dataset.<h4>Participants</h4>Patients with COVID-19 admitted to UHB January-August 2020 were included.<h4>Main outcome measures</h4>Death and ITU admission within 28 days of admission.<h4>Results</h4>1040 patients with COVID-19 were included in the derivation cohort; 288 (28%) died and 183 (18%) were admitted to ITU within 28 days of admission. Area under the receiver operating characteristic curve (AUROC) for mortality was 0.791 (95% CI 0.761 to 0.822) in UHB and 0.767 (95% CI 0.754 to 0.780) in CovidCollab; AUROC for ITU admission was 0.906 (95% CI 0.883 to 0.929) in UHB and 0.811 (95% CI 0.795 to 0.828) in CovidCollab. Models showed good calibration. Addition of comorbidities to candidate predictors did not improve model performance. AUROC for the International Severe Acute Respiratory and Emerging Infection Consortium 4C score in the UHB dataset was 0.753 (95% CI 0.720 to 0.785).<h4>Conclusions</h4>The novel prognostic models showed good discrimination and calibration in derivation and external validation datasets, and performed at least as well as the existing 4C score using only routinely collected patient information. The models can be integrated into electronic medical records systems to calculate each individual patient's probability of death or ITU admission at the time of hospital admission. Implementation of the models and clinical utility should be evaluated.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/1/e049506.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-049506; html:https://europepmc.org/articles/PMC8764710; pdf:https://europepmc.org/articles/PMC8764710?pdf=render
+36620207,https://doi.org/10.3389/fphys.2022.1089343,Incorporating structural abnormalities in equivalent dipole layer based ECG simulations.,"Boonstra MJ, Oostendorp TF, Roudijk RW, Kloosterman M, Asselbergs FW, Loh P, Van Dam PM.",,Frontiers in physiology,2022,2022-12-22,Y,Simulation; Myocardial Disease; Electrocardiogram (Ecg); Cardiac Activation; Ecgsim; Equivalent Dipole Layer,,,"<b>Introduction:</b> Electrical activity of the myocardium is recorded with the 12-lead ECG. ECG simulations can improve our understanding of the relation between abnormal ventricular activation in diseased myocardium and body surface potentials (BSP). However, in equivalent dipole layer (EDL)-based ECG simulations, the presence of diseased myocardium breaks the equivalence of the dipole layer. To simulate diseased myocardium, patches with altered electrophysiological characteristics were incorporated within the model. The relation between diseased myocardium and corresponding BSP was investigated in a simulation study. <b>Methods:</b> Activation sequences in normal and diseased myocardium were simulated and corresponding 64-lead BSP were computed in four models with distinct patch locations. QRS-complexes were compared using correlation coefficient (CC). The effect of different types of patch activation was assessed. Of one patient, simulated electrograms were compared to electrograms recorded during invasive electro-anatomical mapping. <b>Results:</b> Hundred-fifty-three abnormal activation sequences were simulated. Median QRS-CC of delayed versus dyssynchronous were significantly different (1.00 vs. 0.97, <i>p</i> < 0.001). Depending on the location of the patch, BSP leads were affected differently. Within diseased regions, fragmentation, low bipolar voltages and late potentials were observed in both recorded and simulated electrograms. <b>Discussion:</b> A novel method to simulate cardiomyopathy in EDL-based ECG simulations was established and evaluated. The new patch-based approach created a realistic relation between ECG waveforms and underlying activation sequences. Findings in the simulated cases were in agreement with clinical observations. With this method, our understanding of disease progression in cardiomyopathies may be further improved and used in advanced inverse ECG procedures.",,pdf:https://www.frontiersin.org/articles/10.3389/fphys.2022.1089343/pdf; doi:https://doi.org/10.3389/fphys.2022.1089343; html:https://europepmc.org/articles/PMC9814485; pdf:https://europepmc.org/articles/PMC9814485?pdf=render
 35985824,https://doi.org/10.1212/wnl.0000000000201064,"Headache, Opiate Use, and Prescribing Trends in Women With Idiopathic Intracranial Hypertension: A Population-Based Matched Cohort Study.","Adderley NJ, Subramanian A, Perrins M, Nirantharakumar K, Mollan SP, Sinclair AJ.",,Neurology,2022,2022-10-31,Y,,,,"<h4>Background and objectives</h4>Physician prescribing habits for opiates and headache therapies have not been previously evaluated in a large, matched cohort study in idiopathic intracranial hypertension (IIH). Our objective was to evaluate opiate and headache medication prescribing habits in women with IIH compared with matched women with migraine and population controls. We also investigated the occurrence of new onset headache in IIH compared with population controls.<h4>Methods</h4>We performed a population-based matched, retrospective cohort study to explore headache outcomes. Cross-sectional analyses were used to describe medication prescribing patterns. We used data from IQVIA Medical Research Data, an anonymized, nationally representative primary care electronic medical record database in the United Kingdom, from January 1, 1995, to September 25, 2019. Women aged 16 years and older were eligible for inclusion. Women with IIH (exposure) were matched by age and body mass index with up to 10 control women without IIH but with migraine (migraine controls), and without IIH or migraine (population controls).<h4>Results</h4>A total of 3,411 women with IIH, 13,966 migraine controls, and 33,495 population controls were included. The adjusted hazard ratio for new onset headache in IIH compared with population controls was 3.09 (95% CI 2.78-3.43). In the first year after diagnosis, 58% of women with IIH were prescribed acetazolamide and 20% topiramate. In total, 20% of women with IIH were prescribed opiates within the first year of their diagnosis, reducing to 17% after 6 years, compared with 8% and 11% among those with migraine, respectively. Twice as many women with IIH were prescribed opiates compared with migraine controls, and 3 times as many women with IIH were prescribed opiates compared with population controls. Women with IIH were also prescribed more headache preventative medications compared with migraine controls.<h4>Discussion</h4>Women with IIH were more likely to be prescribed opiate and simple analgesics compared with both migraine and population controls. Women with IIH trialed more preventative medications over their disease course suggesting that headaches in IIH may be more refractory to treatment.",,pdf:https://n.neurology.org/content/neurology/99/18/e1968.full.pdf; doi:https://doi.org/10.1212/WNL.0000000000201064; html:https://europepmc.org/articles/PMC9651462; pdf:https://europepmc.org/articles/PMC9651462?pdf=render
 32226230,https://doi.org/10.1016/j.neucom.2018.04.087,Covariate shift estimation based adaptive ensemble learning for handling non-stationarity in motor imagery related EEG-based brain-computer interface.,"Raza H, Rathee D, Zhou SM, Cecotti H, Prasad G.",,Neurocomputing,2019,2019-05-01,Y,"Electroencephalogram (Eeg); Pca, Principal Component Analysis; Brain-computer Interface (Bci); Ensemble Learning; Lda, Linear Discriminant Analysis; Eeg, Electroencephalography; Ssl, Semi-supervised Learning; Mi, Motor Imagery; Covariate Shift; Non-stationary Learning; Bci, Brain-computer-interface; Cs, Covariate Shift; Csa, Covariate Shift Adaptation; Cse, Covariate Shift Estimation; Cse-uael, Cse-based Unsupervised Adaptive Ensemble Learning; Csp, Common Spatial Pattern; Csv, Covariate Shift Validation; Csw, Covariate Shift Warning; Dwec, Dynamically Weighted Ensemble Classification; Erd, Synchronization; Ers, Desynchronization; Ewma, Exponential Weighted Moving Average; Fb, Frequency Band; Fbcsp, Filter Bank Common Spatial Pattern; Knn, K-nearest-neighbors; Nsl, Non-stationary Learning; Pwknn, Probabilistic Weighted K-nearest Neighbour; Rsm, Random Subspace Method",Applied Analytics,neurological,"The non-stationary nature of electroencephalography (EEG) signals makes an EEG-based brain-computer interface (BCI) a dynamic system, thus improving its performance is a challenging task. In addition, it is well-known that due to non-stationarity based covariate shifts, the input data distributions of EEG-based BCI systems change during inter- and intra-session transitions, which poses great difficulty for developments of online adaptive data-driven systems. Ensemble learning approaches have been used previously to tackle this challenge. However, passive scheme based implementation leads to poor efficiency while increasing high computational cost. This paper presents a novel integration of covariate shift estimation and unsupervised adaptive ensemble learning (CSE-UAEL) to tackle non-stationarity in motor-imagery (MI) related EEG classification. The proposed method first employs an exponentially weighted moving average model to detect the covariate shifts in the common spatial pattern features extracted from MI related brain responses. Then, a classifier ensemble was created and updated over time to account for changes in streaming input data distribution wherein new classifiers are added to the ensemble in accordance with estimated shifts. Furthermore, using two publicly available BCI-related EEG datasets, the proposed method was extensively compared with the state-of-the-art single-classifier based passive scheme, single-classifier based active scheme and ensemble based passive schemes. The experimental results show that the proposed active scheme based ensemble learning algorithm significantly enhances the BCI performance in MI classifications.",,doi:https://doi.org/10.1016/j.neucom.2018.04.087; doi:https://doi.org/10.1016/j.neucom.2018.04.087; html:https://europepmc.org/articles/PMC7086459
 36764720,https://doi.org/10.1136/bmjopen-2022-063836,"Weighting of risk factors for low birth weight: a linked routine data cohort study in Wales, UK.","Bandyopadhyay A, Jones H, Parker M, Marchant E, Evans J, Todd C, Rahman MA, Healy J, Win TL, Rowe B, Moore S, Jones A, Brophy S.",,BMJ open,2023,2023-02-10,Y,epidemiology; Public Health; Statistics & Research Methods,,,"<h4>Objective</h4>Globally, 20 million children are born with a birth weight below 2500 g every year, which is considered as a low birthweight (LBW) baby. This study investigates the contribution of modifiable risk factors in a nationally representative Welsh e-cohort of children and their mothers to inform opportunities to reduce LBW prevalence.<h4>Design</h4>A longitudinal cohort study based on anonymously linked, routinely collected multiple administrative data sets.<h4>Participants</h4>The cohort, (N=693 377) comprising of children born between 1 January 1998 and 31 December 2018 in Wales, was selected from the National Community Child Health Database.<h4>Outcome measures</h4>The risk factors associated with a binary LBW (outcome) variable were investigated with multivariable logistic regression (MLR) and decision tree (DT) models.<h4>Results</h4>The MLR model showed that non-singleton children had the highest risk of LBW (adjusted OR 21.74 (95% CI 21.09 to 22.40)), followed by pregnancy interval less than 1 year (2.92 (95% CI 2.70 to 3.15)), maternal physical and mental health conditions including diabetes (2.03 (1.81 to 2.28)), anaemia (1.26 (95% CI 1.16 to 1.36)), depression (1.58 (95% CI 1.43 to 1.75)), serious mental illness (1.46 (95% CI 1.04 to 2.05)), anxiety (1.22 (95% CI 1.08 to 1.38)) and use of antidepressant medication during pregnancy (1.92 (95% CI 1.20 to 3.07)). Additional maternal risk factors include smoking (1.80 (95% CI 1.76 to 1.84)), alcohol-related hospital admission (1.60 (95% CI 1.30 to 1.97)), substance misuse (1.35 (95% CI 1.29 to 1.41)) and evidence of domestic abuse (1.98 (95% CI 1.39 to 2.81)). Living in less deprived area has lower risk of LBW (0.70 (95% CI 0.67 to 0.72)). The most important risk factors from the DT models include maternal factors such as smoking, maternal weight, substance misuse record, maternal age along with deprivation-Welsh Index of Multiple Deprivation score, pregnancy interval and birth order of the child.<h4>Conclusion</h4>Resources to reduce the prevalence of LBW should focus on improving maternal health, reducing preterm births, increasing awareness of what is a sufficient pregnancy interval, and to provide adequate support for mothers' mental health and well-being.",,pdf:https://bmjopen.bmj.com/content/bmjopen/13/2/e063836.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-063836; html:https://europepmc.org/articles/PMC9923297; pdf:https://europepmc.org/articles/PMC9923297?pdf=render
 35637502,https://doi.org/10.1186/s12889-022-13453-w,Age within schoolyear and attention-deficit hyperactivity disorder in Scotland and Wales.,"Fleming M, Bandyopadhyay A, McLay JS, Clark D, King A, Mackay DF, Lyons RA, Sayal K, Brophy S, Pell JP.",,BMC public health,2022,2022-05-30,Y,Children; Education; Data Linkage; School; Attention-deficit Hyperactivity Disorder; Relative Age,,,"<h4>Background</h4>Previous studies suggest an association between age within schoolyear and attention-deficit hyperactivity disorder (ADHD). Scotland and Wales have different school entry cut-off dates (six months apart) and policies on holding back children. We aim to investigate the association between relative age and treated attention deficit hyperactivity disorder (ADHD) in two countries, accounting for held-back children.<h4>Methods</h4>Routine education and health records of 1,063,256 primary and secondary schoolchildren in Scotland (2009-2013) and Wales (2009-2016) were linked. Logistic regression was used to examine the relationships between age within schoolyear and treated ADHD, adjusting for child, maternity and obstetric confounders.<h4>Results</h4>Amongst children in their expected school year, 8,721 (0.87%) had treated ADHD (Scotland 0.84%; Wales 0.96%). In Wales, ADHD increased with decreasing age (youngest quartile, adjusted OR 1.32, 95% CI 1.19-1.46) but, in Scotland, it did not differ between the youngest and oldest quartiles. Including held-back children in analysis of their expected year, the overall prevalence of treated ADHD was 0.93%, and increased across age quartiles in both countries. More children were held back in Scotland (57,979; 7.66%) than Wales (2,401; 0.78%). Held-back children were more likely to have treated ADHD (Scotland OR 2.18, 95% CI 2.01-2.36; Wales OR 1.70, 95% CI 1.21-2.31) and 81.18% of held-back children would have been in the youngest quartile of their expected year.<h4>Conclusions</h4>Children younger within schoolyear are more likely to be treated for ADHD, suggesting immaturity may influence diagnosis. However, these children are more likely to be held back in countries that permit flexibility, attenuating the relative age effect.",,pdf:https://bmcpublichealth.biomedcentral.com/counter/pdf/10.1186/s12889-022-13453-w; doi:https://doi.org/10.1186/s12889-022-13453-w; html:https://europepmc.org/articles/PMC9150337; pdf:https://europepmc.org/articles/PMC9150337?pdf=render
 37105743,https://doi.org/10.3399/bjgp.2022.0353,Impact of COVID-19 pandemic on incidence of long-term conditions in Wales: a population data linkage study using primary and secondary care health records.,"Qi C, Osborne T, Bailey R, Cooper A, Hollinghurst JP, Akbari A, Crowder R, Peters H, Law RJ, Lewis R, Smith D, Edwards A, Lyons RA.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2023,2023-04-27,Y,Diagnosis; Chronic disease; Anxiety; Primary Health Care; Covid-19,,,"<h4>Background</h4>The COVID-19 pandemic has directly and indirectly had an impact on health service provision owing to surges and sustained pressures on the system. The effects of these pressures on the management of long-term or chronic conditions are not fully understood.<h4>Aim</h4>To explore the effects of COVID-19 on the recorded incidence of 17 long-term conditions.<h4>Design and setting</h4>This was an observational retrospective population data linkage study on the population of Wales using primary and secondary care data within the Secure Anonymised Information Linkage (SAIL) Databank.<h4>Method</h4>Monthly rates of new diagnosis between 2000 and 2021 are presented for each long-term condition. Incidence rates post-2020 were compared with expected rates predicted using time series modelling of pre-2020 trends. The proportion of annual incidence is presented by sociodemographic factors: age, sex, social deprivation, ethnicity, frailty, and learning disability.<h4>Results</h4>A total of 5 476 012 diagnoses from 2 257 992 individuals are included. Incidence rates from 2020 to 2021 were lower than mean expected rates across all conditions. The largest relative deficit in incidence was in chronic obstructive pulmonary disease corresponding to 343 (95% confidence interval = 230 to 456) undiagnosed patients per 100 000 population, followed by depression, type 2 diabetes, hypertension, anxiety disorders, and asthma. A GP practice of 10 000 patients might have over 400 undiagnosed long-term conditions. No notable differences between sociodemographic profiles of post- and pre-2020 incidences were observed.<h4>Conclusion</h4>There is a potential backlog of undiagnosed patients with multiple long-term conditions. Resources are required to tackle anticipated workload as part of COVID-19 recovery, particularly in primary care.",,pdf:https://bjgp.org/content/bjgp/early/2023/03/06/BJGP.2022.0353.full.pdf; doi:https://doi.org/10.3399/BJGP.2022.0353; html:https://europepmc.org/articles/PMC9997656; pdf:https://europepmc.org/articles/PMC9997656?pdf=render
 34626176,https://doi.org/10.1093/brain/awab253,Whole-exome sequencing reveals a role of HTRA1 and EGFL8 in brain white matter hyperintensities.,"Malik R, Beaufort N, Frerich S, Gesierich B, Georgakis MK, Rannikmäe K, Ferguson AC, Haffner C, Traylor M, Ehrmann M, Sudlow CLM, Dichgans M.",,Brain : a journal of neurology,2021,2021-10-01,N,Whole-exome Sequencing; White Matter Hyperintensities; Uk Biobank; Htra1; Burden Test,,,"White matter hyperintensities (WMH) are among the most common radiological abnormalities in the ageing population and an established risk factor for stroke and dementia. While common variant association studies have revealed multiple genetic loci with an influence on their volume, the contribution of rare variants to the WMH burden in the general population remains largely unexplored. We conducted a comprehensive analysis of this burden in the UK Biobank using publicly available whole-exome sequencing data (n up to 17 830) and found a splice-site variant in GBE1, encoding 1,4-alpha-glucan branching enzyme 1, to be associated with lower white matter burden on an exome-wide level [c.691+2T>C, β = -0.74, standard error (SE) = 0.13, P = 9.7 × 10-9]. Applying whole-exome gene-based burden tests, we found damaging missense and loss-of-function variants in HTRA1 (frequency of 1 in 275 in the UK Biobank population) to associate with an increased WMH volume (P = 5.5 × 10-6, false discovery rate = 0.04). HTRA1 encodes a secreted serine protease implicated in familial forms of small vessel disease. Domain-specific burden tests revealed that the association with WMH volume was restricted to rare variants in the protease domain (amino acids 204-364; β = 0.79, SE = 0.14, P = 9.4 × 10-8). The frequency of such variants in the UK Biobank population was 1 in 450. The WMH volume was brought forward by ∼11 years in carriers of a rare protease domain variant. A comparison with the effect size of established risk factors for WMH burden revealed that the presence of a rare variant in the HTRA1 protease domain corresponded to a larger effect than meeting the criteria for hypertension (β = 0.26, SE = 0.02, P = 2.9 × 10-59) or being in the upper 99.8% percentile of the distribution of a polygenic risk score based on common genetic variants (β = 0.44, SE = 0.14, P = 0.002). In biochemical experiments, most (6/9) of the identified protease domain variants resulted in markedly reduced protease activity. We further found EGFL8, which showed suggestive evidence for association with WMH volume (P = 1.5 × 10-4, false discovery rate = 0.22) in gene burden tests, to be a direct substrate of HTRA1 and to be preferentially expressed in cerebral arterioles and arteries. In a phenome-wide association study mapping ICD-10 diagnoses to 741 standardized Phecodes, rare variants in the HTRA1 protease domain were associated with multiple neurological and non-neurological conditions including migraine with aura (odds ratio = 12.24, 95%CI: 2.54-35.25; P = 8.3 × 10-5]. Collectively, these findings highlight an important role of rare genetic variation and the HTRA1 protease in determining WMH burden in the general population.",,pdf:https://academic.oup.com/brain/article-pdf/144/9/2670/40880367/awab253.pdf; doi:https://doi.org/10.1093/brain/awab253; html:https://europepmc.org/articles/PMC8557338; pdf:https://europepmc.org/articles/PMC8557338?pdf=render; doi:https://doi.org/10.1093/brain/awab253
-37042240,https://doi.org/10.1161/circimaging.122.014519,Explainable Artificial Intelligence and Cardiac Imaging: Toward More Interpretable Models.,"Salih A, Boscolo Galazzo I, Gkontra P, Lee AM, Lekadir K, Raisi-Estabragh Z, Petersen SE.",,Circulation. Cardiovascular imaging,2023,2023-04-12,N,Artificial intelligence; Diagnostic Imaging; Machine Learning; Cardiac Imaging Techniques,,,"Artificial intelligence applications have shown success in different medical and health care domains, and cardiac imaging is no exception. However, some machine learning models, especially deep learning, are considered black box as they do not provide an explanation or rationale for model outcomes. Complexity and vagueness in these models necessitate a transition to explainable artificial intelligence (XAI) methods to ensure that model results are both transparent and understandable to end users. In cardiac imaging studies, there are a limited number of papers that use XAI methodologies. This article provides a comprehensive literature review of state-of-the-art works using XAI methods for cardiac imaging. Moreover, it provides simple and comprehensive guidelines on XAI. Finally, open issues and directions for XAI in cardiac imaging are discussed.",,doi:https://doi.org/10.1161/CIRCIMAGING.122.014519
+36098502,https://doi.org/10.7554/elife.78427,"Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study.","Stirrup O, Blackstone J, Mapp F, MacNeil A, Panca M, Holmes A, Machin N, Shin GY, Mahungu T, Saeed K, Saluja T, Taha Y, Mahida N, Pope C, Chawla A, Cutino-Moguel MT, Tamuri A, Williams R, Darby A, Robertson DL, Flaviani F, Nastouli E, Robson S, Smith D, Loose M, Laing K, Monahan I, Kele B, Haldenby S, George R, Bashton M, Witney AA, Byott M, Coll F, Chapman M, Peacock SJ, COG-UK HOCI Investigators, COVID-19 Genomics UK (COG-UK) consortium, Hughes J, Nebbia G, Partridge DG, Parker M, Price JR, Peters C, Roy S, Snell LB, de Silva TI, Thomson E, Flowers P, Copas A, Breuer J.",,eLife,2022,2022-09-13,Y,Human; Microbiology; Infectious disease; Molecular epidemiology; Infection control; epidemiology; Global Health; Hospital-acquired Infection; Infection Prevention; Viral Genomics; Healthcare-associated Infection; Covid-19,,,"<h4>Background</h4>Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings.<h4>Methods</h4>We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data collection period, followed by intervention periods comprising 8 weeks of 'rapid' (<48 hr) and 4 weeks of 'longer-turnaround' (5-10 days) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital-onset COVID-19 infections (HOCIs; detected ≥48 hr from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on the incidence of probable/definite hospital-acquired infections (HAIs), was evaluated.<h4>Results</h4>A total of 2170 HOCI cases were recorded from October 2020 to April 2021, corresponding to a period of extreme strain on the health service, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (incidence rate ratio 1.60, 95% CI 0.85-3.01; p<i>=</i>0.14) or rapid (0.85, 0.48-1.50; p<i>=</i>0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8 and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2 and 11.6% of cases where the report was returned. In a 'per-protocol' sensitivity analysis, there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. Capacity to respond effectively to insights from sequencing was breached in most sites by the volume of cases and limited resources.<h4>Conclusions</h4>While we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days.<h4>Funding</h4>COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) (grant code: MC_PC_19027), and Genome Research Limited, operating as the Wellcome Sanger Institute.<h4>Clinical trial number</h4>NCT04405934.",,doi:https://doi.org/10.7554/elife.78427; doi:https://doi.org/10.7554/eLife.78427; html:https://europepmc.org/articles/PMC9596156; pdf:https://europepmc.org/articles/PMC9596156?pdf=render
 35139069,https://doi.org/10.1371/journal.pcbi.1009806,Known allosteric proteins have central roles in genetic disease.,"Abrusán G, Ascher DB, Inouye M.",,PLoS computational biology,2022,2022-02-09,Y,,,,"Allostery is a form of protein regulation, where ligands that bind sites located apart from the active site can modify the activity of the protein. The molecular mechanisms of allostery have been extensively studied, because allosteric sites are less conserved than active sites, and drugs targeting them are more specific than drugs binding the active sites. Here we quantify the importance of allostery in genetic disease. We show that 1) known allosteric proteins are central in disease networks, contribute to genetic disease and comorbidities much more than non-allosteric proteins, and there is an association between being allosteric and involvement in disease; 2) they are enriched in many major disease types like hematopoietic diseases, cardiovascular diseases, cancers, diabetes, or diseases of the central nervous system; 3) variants from cancer genome-wide association studies are enriched near allosteric proteins, indicating their importance to polygenic traits; and 4) the importance of allosteric proteins in disease is due, at least partly, to their central positions in protein-protein interaction networks, and less due to their dynamical properties.",,doi:https://doi.org/10.1371/journal.pcbi.1009806; doi:https://doi.org/10.1371/journal.pcbi.1009806; html:https://europepmc.org/articles/PMC10138267; pdf:https://europepmc.org/articles/PMC10138267?pdf=render
-36382153,https://doi.org/10.5334/gh.1166,Risk Factors and Prevalence of Dilated Cardiomyopathy in Sub-Saharan Africa: A Systematic Review.,"Fundikira LS, Chillo P, Mutagaywa R, Kamuhabwa A, Kwesigabo G, Asselbergs FW, van Laake LW.",,Global heart,2022,2022-10-21,Y,Dilated cardiomyopathy; Sub-Saharan Africa; Cardiovascular risk factors,,,<b>Highlights</b>  Prevalence of DCM varies widely in SSA.Cardiovascular risk factors are important in patients with DCM.The role of genetics in idiopathic DCM is not studied in major part of SSA.,,pdf:http://globalheartjournal.com/articles/10.5334/gh.1166/galley/1329/download/; doi:https://doi.org/10.5334/gh.1166; html:https://europepmc.org/articles/PMC9585983; pdf:https://europepmc.org/articles/PMC9585983?pdf=render
+37042240,https://doi.org/10.1161/circimaging.122.014519,Explainable Artificial Intelligence and Cardiac Imaging: Toward More Interpretable Models.,"Salih A, Boscolo Galazzo I, Gkontra P, Lee AM, Lekadir K, Raisi-Estabragh Z, Petersen SE.",,Circulation. Cardiovascular imaging,2023,2023-04-12,N,Artificial intelligence; Diagnostic Imaging; Machine Learning; Cardiac Imaging Techniques,,,"Artificial intelligence applications have shown success in different medical and health care domains, and cardiac imaging is no exception. However, some machine learning models, especially deep learning, are considered black box as they do not provide an explanation or rationale for model outcomes. Complexity and vagueness in these models necessitate a transition to explainable artificial intelligence (XAI) methods to ensure that model results are both transparent and understandable to end users. In cardiac imaging studies, there are a limited number of papers that use XAI methodologies. This article provides a comprehensive literature review of state-of-the-art works using XAI methods for cardiac imaging. Moreover, it provides simple and comprehensive guidelines on XAI. Finally, open issues and directions for XAI in cardiac imaging are discussed.",,doi:https://doi.org/10.1161/CIRCIMAGING.122.014519
 30984881,https://doi.org/10.12688/wellcomeopenres.15151.1,Causes of death among homeless people: a population-based cross-sectional study of linked hospitalisation and mortality data in England.,"Aldridge RW, Menezes D, Lewer D, Cornes M, Evans H, Blackburn RM, Byng R, Clark M, Denaxas S, Fuller J, Hewett N, Kilmister A, Luchenski S, Manthorpe J, McKee M, Neale J, Story A, Tinelli M, Whiteford M, Wurie F, Hayward A.",,Wellcome open research,2019,2019-03-11,Y,Mortality; Data Linkage; Hospital Discharge; Amenable Mortality; Homeless Health; Homeless Healthcare,,,"<b>Background</b>: Homelessness has increased by 165% since 2010 in England, with evidence from many settings that those affected experience high levels of mortality. In this paper we examine the contribution of different causes of death to overall mortality in homeless people recently admitted to hospitals in England with specialist integrated homeless health and care (SIHHC) schemes.  <b>Methods</b>: We undertook an analysis of linked hospital admission records and mortality data for people attending any one of 17 SIHHC schemes between 1st November 2013 and 30th November 2016. Our primary outcome was death, which we analysed in subgroups of 10th version international classification of disease (ICD-10) specific deaths; and deaths from amenable causes. We compared our results to a sample of people living in areas of high social deprivation (IMD5 group). <b>Results</b>: We collected data on 3,882 individual homeless hospital admissions that were linked to 600 deaths. The median age of death was 51.6 years (interquartile range 42.7-60.2) for SIHHC and 71.5 for the IMD5 (60.67-79.0).  The top three underlying causes of death by ICD-10 chapter in the SIHHC group were external causes of death (21.7%; 130/600), cancer (19.0%; 114/600) and digestive disease (19.0%; 114/600).  The percentage of deaths due to an amenable cause after age and sex weighting was 30.2% in the homeless SIHHC group (181/600) compared to 23.0% in the IMD5 group (578/2,512). <b>Conclusion</b>: Nearly one in three homeless deaths were due to causes amenable to timely and effective health care. The high burden of amenable deaths highlights the extreme health harms of homelessness and the need for greater emphasis on prevention of homelessness and early healthcare interventions.",,doi:https://doi.org/10.12688/wellcomeopenres.15151.1; html:https://europepmc.org/articles/PMC6449792; pdf:https://europepmc.org/articles/PMC6449792?pdf=render
+36382153,https://doi.org/10.5334/gh.1166,Risk Factors and Prevalence of Dilated Cardiomyopathy in Sub-Saharan Africa: A Systematic Review.,"Fundikira LS, Chillo P, Mutagaywa R, Kamuhabwa A, Kwesigabo G, Asselbergs FW, van Laake LW.",,Global heart,2022,2022-10-21,Y,Dilated cardiomyopathy; Sub-Saharan Africa; Cardiovascular risk factors,,,<b>Highlights</b>  Prevalence of DCM varies widely in SSA.Cardiovascular risk factors are important in patients with DCM.The role of genetics in idiopathic DCM is not studied in major part of SSA.,,pdf:http://globalheartjournal.com/articles/10.5334/gh.1166/galley/1329/download/; doi:https://doi.org/10.5334/gh.1166; html:https://europepmc.org/articles/PMC9585983; pdf:https://europepmc.org/articles/PMC9585983?pdf=render
 36038914,https://doi.org/10.1186/s12916-022-02473-3,Polycystic ovary syndrome and risk of adverse obstetric outcomes: a retrospective population-based matched cohort study in England.,"Subramanian A, Lee SI, Phillips K, Toulis KA, Kempegowda P, O'Reilly MW, Adderley NJ, Thangaratinam S, Arlt W, Nirantharakumar K.",,BMC medicine,2022,2022-08-30,Y,Delivery; Preterm; PCOS; Polycystic ovary syndrome; Stillbirth; Birthweight,,,"<h4>Background</h4>Polycystic ovary syndrome (PCOS) affects up to one in five women of childbearing age. Observational studies assessing the association between maternal PCOS and adverse obstetric outcomes have reported varying results, depending on patient population, diagnostic criteria for PCOS and covariates accounted for in their analyses. We aimed to assess the risk of obstetric outcomes among a population-based representative cohort of women with PCOS compared to an age-matched cohort of women without PCOS.<h4>Methods</h4>A retrospective cohort study was conducted of pregnancies of women in England aged 15-49 years identified from the Clinical Practice Research Datalink (CPRD) GOLD pregnancy register and linked Hospital Episodes Statistic (HES) data between March 1997 and March 2020. Pregnancies from the register that had a linked HES delivery record were included. Linked CPRD primary care data was used to ascertain maternal PCOS exposure prior to pregnancy. To improve detection of PCOS, in addition to PCOS diagnostic codes, codes for (1) polycystic ovaries or (2) hyperandrogenism and anovulation together were also considered. Sensitivity analysis was limited to only pregnant women with a diagnostic code for PCOS. Primary outcomes ascertained from linked HES data were (1) preterm delivery (gestation < 37 weeks), (2) mode of delivery, (3) high (> 4000 g) or low birthweight (< 2500 g) and (4) stillbirth. Secondary outcomes were (1) very preterm delivery (< 32 weeks), (2) extremely preterm delivery (< 28 weeks), (3) small and (4) large for gestational age. Conditional logistic regression models were performed adjusting for age, ethnicity, deprivation, dysglycaemia, hypertension, thyroid disorders, number of babies born at index pregnancy, and pre-gravid BMI. Multiple imputation was performed for missing outcome data.<h4>Results</h4>27,586 deliveries with maternal PCOS were matched for age (± 1 year) to 110,344 deliveries without PCOS. In the fully adjusted models, maternal PCOS was associated with an increased risk of (1) preterm birth [aOR: 1.11 (95% CI 1.06-1.17)], and (2) emergency caesarean, elective caesarean and instrumental vaginal compared to spontaneous delivery [aOR: 1.10 (1.05-1.15), 1.07 (1.03-1.12) and 1.04 (1.00-1.09), respectively]. There was absence of association with low birthweight, high birthweight and stillbirth. In the sensitivity analysis, the association with preterm birth [aOR: 1.31 (95% CI 1.13-1.52)], emergency caesarean [aOR: 1.15 (95% CI 1.02-1.30)], and elective caesarean [aOR: 1.03 (95% CI 1.02-1.03)] remained. While there was no significant association with any of the secondary outcomes in the primary analysis, in the sensitivity analysis maternal PCOS was associated with increased risk of extremely preterm delivery [aOR: 1.86 (95% CI 1.31-2.65)], and lower risk of small for gestational age babies [aOR: 0.74 (95% CI 0.59-0.94)].<h4>Conclusions</h4>Maternal PCOS was associated with increased risk of preterm and caesarean delivery. Association with low birthweight may be largely mediated by lower gestational age at birth.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-022-02473-3; doi:https://doi.org/10.1186/s12916-022-02473-3; html:https://europepmc.org/articles/PMC9425992; pdf:https://europepmc.org/articles/PMC9425992?pdf=render
-36098502,https://doi.org/10.7554/elife.78427,"Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study.","Stirrup O, Blackstone J, Mapp F, MacNeil A, Panca M, Holmes A, Machin N, Shin GY, Mahungu T, Saeed K, Saluja T, Taha Y, Mahida N, Pope C, Chawla A, Cutino-Moguel MT, Tamuri A, Williams R, Darby A, Robertson DL, Flaviani F, Nastouli E, Robson S, Smith D, Loose M, Laing K, Monahan I, Kele B, Haldenby S, George R, Bashton M, Witney AA, Byott M, Coll F, Chapman M, Peacock SJ, COG-UK HOCI Investigators, COVID-19 Genomics UK (COG-UK) consortium, Hughes J, Nebbia G, Partridge DG, Parker M, Price JR, Peters C, Roy S, Snell LB, de Silva TI, Thomson E, Flowers P, Copas A, Breuer J.",,eLife,2022,2022-09-13,Y,Human; Microbiology; Infectious disease; Molecular epidemiology; Infection control; epidemiology; Global Health; Hospital-acquired Infection; Infection Prevention; Viral Genomics; Healthcare-associated Infection; Covid-19,,,"<h4>Background</h4>Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings.<h4>Methods</h4>We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data collection period, followed by intervention periods comprising 8 weeks of 'rapid' (<48 hr) and 4 weeks of 'longer-turnaround' (5-10 days) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital-onset COVID-19 infections (HOCIs; detected ≥48 hr from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on the incidence of probable/definite hospital-acquired infections (HAIs), was evaluated.<h4>Results</h4>A total of 2170 HOCI cases were recorded from October 2020 to April 2021, corresponding to a period of extreme strain on the health service, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (incidence rate ratio 1.60, 95% CI 0.85-3.01; p<i>=</i>0.14) or rapid (0.85, 0.48-1.50; p<i>=</i>0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8 and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2 and 11.6% of cases where the report was returned. In a 'per-protocol' sensitivity analysis, there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. Capacity to respond effectively to insights from sequencing was breached in most sites by the volume of cases and limited resources.<h4>Conclusions</h4>While we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days.<h4>Funding</h4>COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) (grant code: MC_PC_19027), and Genome Research Limited, operating as the Wellcome Sanger Institute.<h4>Clinical trial number</h4>NCT04405934.",,doi:https://doi.org/10.7554/elife.78427; doi:https://doi.org/10.7554/eLife.78427; html:https://europepmc.org/articles/PMC9596156; pdf:https://europepmc.org/articles/PMC9596156?pdf=render
-39293053,https://doi.org/10.2196/57334,Metagenomics in the Diagnosis of Pneumonia: Protocol for a Systematic Review.,"Quarton S, Livesey A, Jeff C, Hatton C, Scott A, Parekh D, Thickett D, McNally A, Sapey E.",,JMIR research protocols,2024,2024-09-18,Y,Diagnosis; Ventilator-associated pneumonia; Pneumonia; HAP; Systematic review; Community-acquired pneumonia; Respiratory tract infection; Cap; Metagenomics; Hospital-acquired Pneumonia; Vap,,,"<h4>Background</h4>Causative pathogens are currently identified in only a minority of pneumonia cases, which affects antimicrobial stewardship. Metagenomic next-generation sequencing (mNGS) has potential to enhance pathogen detection due to its sensitivity and broad applicability. However, while studies have shown improved sensitivity compared with conventional microbiological methods for pneumonia diagnosis, it remains unclear whether this can translate into clinical benefit. Most existing studies focus on patients who are ventilated, readily allowing for analysis of bronchoalveolar lavage fluid (BALF). The impact of sample type on the use of metagenomic analysis remains poorly defined. Similarly, previous studies rarely differentiate between the types of pneumonia involved-community-acquired pneumonia (CAP), hospital-acquired pneumonia (HAP), or ventilator-associated pneumonia (VAP)-which have different clinical profiles.<h4>Objective</h4>This study aims to determine the clinical use of mNGS in CAP, HAP, and VAP, compared with traditional microbiological methods.<h4>Methods</h4>We aim to review all studies (excluding case reports of a series of fewer than 10 people) of adult patients with suspected or confirmed pneumonia that compare metagenomic analysis with traditional microbiology techniques, including culture, antigen-based testing, and polymerase chain reaction-based assays. Relevant studies will be identified through systematic searches of the Embase, MEDLINE, Scopus, and Cochrane CENTRAL databases. Screening of titles, abstracts, and subsequent review of eligible full texts will be done by 2 separate reviewers (SQ and 1 of AL, CJ, or CH), with a third clinician (ES) providing adjudication in case of disagreement. Our focus is on the clinical use of metagenomics for patients with CAP, HAP, and VAP. Data extracted will focus on clinically important outcomes-pathogen positivity rate, laboratory turnaround time, impact on clinical decision-making, length of stay, and 30-day mortality. Subgroup analyses will be performed based on the type of pneumonia (CAP, HAP, or VAP) and sample type used. The risk of bias will be assessed using the QUADAS-2 tool for diagnostic accuracy studies. Outcome data will be combined in a random-effects meta-analysis, and where this is not possible, a narrative synthesis will be undertaken.<h4>Results</h4>The searches were completed with the assistance of a medical librarian on January 13, 2024, returning 5750 records. Screening and data extraction are anticipated to be completed by September 2024.<h4>Conclusions</h4>Despite significant promise, the impact of metagenomic analysis on clinical pathways remains unclear. Furthermore, it is unclear whether the use of this technique will alter depending on whether the pneumonia is a CAP, HAP, or VAP or the sample type that is collected. This systematic review will assess the current evidence base to support the benefit of clinical outcomes for metagenomic analysis, depending on the setting of pneumonia diagnosis or specimen type used. It will identify areas where further research is needed to advance this methodology into routine care.<h4>Trial registration</h4>PROSPERO CRD42023488096; https://tinyurl.com/3suy7cma.<h4>International registered report identifier (irrid)</h4>DERR1-10.2196/57334.",,pdf:https://s3.ca-central-1.amazonaws.com/assets.jmir.org/assets/preprints/preprint-57334-accepted.pdf; doi:https://doi.org/10.2196/57334; html:https://europepmc.org/articles/PMC11447427
 36475361,https://doi.org/10.1302/2633-1462.312.bjo-2022-0130.r1,Variation in timely surgery for severe open tibial fractures by time and place of presentation in England from 2012 to 2019 : a cohort study using data collected nationally by the Trauma Audit and Research Network.,"Shah A, Judge A, Griffin XL.",,Bone & joint open,2022,2022-12-01,Y,Trauma; Sensitivity analysis; Debridement; Logistic regression; Cohort study; Orthopaedics; Injury Severity Score; Health Care Quality; Soft-tissue; Open Fracture; Tarn; Regression Analyses; Open Fractures Of The Tibia,,,"<h4>Aims</h4>Several studies have reported that patients presenting during the evening or weekend have poorer quality healthcare. Our objective was to examine how timely surgery for patients with severe open tibial fracture varies by day and time of presentation and by type of hospital. This cohort study included patients with severe open tibial fractures from the Trauma Audit and Research Network (TARN).<h4>Methods</h4>Provision of prompt surgery (debridement within 12 hours and soft-tissue coverage in 72 hours) was examined, using multivariate logistic regression to derive adjusted risk ratios (RRs). Time was categorized into three eight-hour intervals for each day of the week. The models were adjusted for treatment in a major trauma centre (MTC), sex, age, year of presentation, injury severity score, injury mechanism, and number of operations each patient received.<h4>Results</h4>We studied 8,258 patients from 175 hospitals. Patients presenting during the day (08:00 to 15:59; risk ratio (RR) 1.11, 95% confidence interval (CI) 1.02 to 1.20) were more likely to receive debridement within 12 hours, and patients presenting at night (16:00 to 23:59; RR 0.56, 95% CI 0.51 to 0.62) were less likely to achieve the target; triage to a MTC had no effect. Day of presentation was associated with soft-tissue coverage within 72 hours; patients presenting on a Thursday or Friday being less likely to receive this surgery within 72 hours (Thursday RR 0.88, 95% CI 0.81 to 0.97; Friday RR 0.89, 95% CI 0.81 to 0.98), and the standard less likely to be achieved for those treated in 'non-MTC' hospitals (RR 0.76, 95% CI 0.70 to 0.82).<h4>Conclusion</h4>Variations in care were observed for timely surgery for severe open tibial fractures with debridement surgery affected by time of presentation and soft-tissue coverage affected by day of presentation and type of hospital. The variation is unwarranted and highlights that there are opportunities to substantially improve the delivery and quality of care for patients with severe open tibial fracture.Cite this article: <i>Bone Jt Open</i> 2022;3(12):941-952.",,pdf:https://boneandjoint.org.uk/article/10.1302/2633-1462.312.BJO-2022-0130.R1/pdf; doi:https://doi.org/10.1302/2633-1462.312.BJO-2022-0130.R1; html:https://europepmc.org/articles/PMC9783273; pdf:https://europepmc.org/articles/PMC9783273?pdf=render
 36763324,https://doi.org/10.1007/s12687-023-00635-1,What makes a good life: using theatrical performance to enhance communication about polygenic risk scores research in patient and public involvement.,"Mason AM, Obi I, Ayodele O, Lambert SA, Fahle S.",,Journal of community genetics,2023,2023-02-10,Y,,,,"The aim of this patient and public involvement and engagement (PPIE) work was to explore improvised theatre as a tool for facilitating bi-directional dialogue between researchers and patients/members of the public on the topic of polygenic risk scores (PRS) use within primary or secondary care. PRS are a tool to quantify genetic risk for a heritable disease or trait and may be used to predict future health outcomes. In the United Kingdom (UK), they are often cited as a next-in-line public health tool to be implemented, and their use in consumer genetic testing as well as patient-facing settings is increasing. Despite their potential clinical utility, broader themes about how they might influence an individual's perception of disease risk and decision-making are an active area of research; however, this has mostly been in the setting of return of results to patients. We worked with a youth theatre group and patients involved in a PPIE group to develop two short plays about public perceptions of genetic risk information that could be captured by PRS. These plays were shared in a workshop with patients/members of the public to facilitate discussions about PRS and their perceived benefits, concerns and emotional reactions. Discussions with both performers and patients/public raised three key questions: (1) can the data be trusted?; (2) does knowing genetic risk actually help the patient?; and (3) what makes a life worthwhile? Creating and watching fictional narratives helped all participants explore the potential use of PRS in a clinical setting, informing future research considerations and improving communication between the researchers and lay members of the PPIE group.",,pdf:https://link.springer.com/content/pdf/10.1007/s12687-023-00635-1.pdf; doi:https://doi.org/10.1007/s12687-023-00635-1; html:https://europepmc.org/articles/PMC10576689; pdf:https://europepmc.org/articles/PMC10576689?pdf=render
+39293053,https://doi.org/10.2196/57334,Metagenomics in the Diagnosis of Pneumonia: Protocol for a Systematic Review.,"Quarton S, Livesey A, Jeff C, Hatton C, Scott A, Parekh D, Thickett D, McNally A, Sapey E.",,JMIR research protocols,2024,2024-09-18,Y,Diagnosis; Ventilator-associated pneumonia; Pneumonia; HAP; Systematic review; Community-acquired pneumonia; Respiratory tract infection; Cap; Metagenomics; Hospital-acquired Pneumonia; Vap,,,"<h4>Background</h4>Causative pathogens are currently identified in only a minority of pneumonia cases, which affects antimicrobial stewardship. Metagenomic next-generation sequencing (mNGS) has potential to enhance pathogen detection due to its sensitivity and broad applicability. However, while studies have shown improved sensitivity compared with conventional microbiological methods for pneumonia diagnosis, it remains unclear whether this can translate into clinical benefit. Most existing studies focus on patients who are ventilated, readily allowing for analysis of bronchoalveolar lavage fluid (BALF). The impact of sample type on the use of metagenomic analysis remains poorly defined. Similarly, previous studies rarely differentiate between the types of pneumonia involved-community-acquired pneumonia (CAP), hospital-acquired pneumonia (HAP), or ventilator-associated pneumonia (VAP)-which have different clinical profiles.<h4>Objective</h4>This study aims to determine the clinical use of mNGS in CAP, HAP, and VAP, compared with traditional microbiological methods.<h4>Methods</h4>We aim to review all studies (excluding case reports of a series of fewer than 10 people) of adult patients with suspected or confirmed pneumonia that compare metagenomic analysis with traditional microbiology techniques, including culture, antigen-based testing, and polymerase chain reaction-based assays. Relevant studies will be identified through systematic searches of the Embase, MEDLINE, Scopus, and Cochrane CENTRAL databases. Screening of titles, abstracts, and subsequent review of eligible full texts will be done by 2 separate reviewers (SQ and 1 of AL, CJ, or CH), with a third clinician (ES) providing adjudication in case of disagreement. Our focus is on the clinical use of metagenomics for patients with CAP, HAP, and VAP. Data extracted will focus on clinically important outcomes-pathogen positivity rate, laboratory turnaround time, impact on clinical decision-making, length of stay, and 30-day mortality. Subgroup analyses will be performed based on the type of pneumonia (CAP, HAP, or VAP) and sample type used. The risk of bias will be assessed using the QUADAS-2 tool for diagnostic accuracy studies. Outcome data will be combined in a random-effects meta-analysis, and where this is not possible, a narrative synthesis will be undertaken.<h4>Results</h4>The searches were completed with the assistance of a medical librarian on January 13, 2024, returning 5750 records. Screening and data extraction are anticipated to be completed by September 2024.<h4>Conclusions</h4>Despite significant promise, the impact of metagenomic analysis on clinical pathways remains unclear. Furthermore, it is unclear whether the use of this technique will alter depending on whether the pneumonia is a CAP, HAP, or VAP or the sample type that is collected. This systematic review will assess the current evidence base to support the benefit of clinical outcomes for metagenomic analysis, depending on the setting of pneumonia diagnosis or specimen type used. It will identify areas where further research is needed to advance this methodology into routine care.<h4>Trial registration</h4>PROSPERO CRD42023488096; https://tinyurl.com/3suy7cma.<h4>International registered report identifier (irrid)</h4>DERR1-10.2196/57334.",,pdf:https://s3.ca-central-1.amazonaws.com/assets.jmir.org/assets/preprints/preprint-57334-accepted.pdf; doi:https://doi.org/10.2196/57334; html:https://europepmc.org/articles/PMC11447427
 37657941,https://doi.org/10.1212/wnl.0000000000207777,Exploring the Role of Plasma Lipids and Statin Interventions on Multiple Sclerosis Risk and Severity: A Mendelian Randomization Study.,"Almramhi MM, Finan C, Storm CS, Schmidt AF, Kia DA, Coneys R, Chopade S, Hingorani AD, Wood NW.",,Neurology,2023,2023-09-01,Y,,,,"<h4>Background and objectives</h4>There has been considerable interest in statins because of their pleiotropic effects beyond their lipid-lowering properties. Many of these pleiotropic effects are predominantly ascribed to Rho small guanosine triphosphatases (Rho GTPases) proteins. We aimed to genetically investigate the role of lipids and statin interventions on multiple sclerosis (MS) risk and severity.<h4>Method</h4>We used two-sample Mendelian randomization (MR) to investigate (1) the causal role of genetically mimic both cholesterol-dependent (through low-density lipoprotein cholesterol (LDL-C) and cholesterol biosynthesis pathway) and cholesterol-independent (through Rho GTPases) effects of statins on MS risk and MS severity, (2) the causal link between lipids (high-density lipoprotein cholesterol [HDL-C] and triglycerides [TG]) levels and MS risk and severity, and (3) the reverse causation between lipid fractions and MS risk. We used summary statistics from the Global Lipids Genetics Consortium (GLGC), eQTLGen Consortium, and the International MS Genetics Consortium (IMSGC) for lipids, expression quantitative trait loci, and MS, respectively (GLGC: n = 188,577; eQTLGen: n = 31,684; IMSGC (MS risk): n = 41,505; IMSGC (MS severity): n = 7,069).<h4>Results</h4>The results of MR using the inverse-variance weighted method show that genetically predicted <i>RAC2</i>, a member of cholesterol-independent pathway (OR 0.86 [95% CI 0.78-0.95], <i>p</i>-value 3.80E-03), is implicated causally in reducing MS risk. We found no evidence for the causal role of LDL-C and the member of cholesterol biosynthesis pathway on MS risk. The MR results also show that lifelong higher HDL-C (OR 1.14 [95% CI 1.04-1.26], <i>p</i>-value 7.94E-03) increases MS risk but TG was not. Furthermore, we found no evidence for the causal role of lipids and genetically mimicked statins on MS severity. There is no evidence of reverse causation between MS risk and lipids.<h4>Discussion</h4>Evidence from this study suggests that <i>RAC2</i> is a genetic modifier of MS risk. Because <i>RAC2</i> has been reported to mediate some of the pleiotropic effects of statins, we suggest that statins may reduce MS risk through a cholesterol-independent pathway (that is, RAC2-related mechanism(s)). MR analyses also support a causal effect of HDL-C on MS risk.",,pdf:https://n.neurology.org/content/neurology/early/2023/09/01/WNL.0000000000207777.full.pdf; doi:https://doi.org/10.1212/WNL.0000000000207777; html:https://europepmc.org/articles/PMC10624499; pdf:https://europepmc.org/articles/PMC10624499?pdf=render
 38765656,https://doi.org/10.1016/j.jacasi.2024.01.005,The Prognostic Value of Left Ventricular Entropy From T1 Mapping in Patients With Hypertrophic Cardiomyopathy.,"Wang J, Zhang J, Pu L, Qi W, Xu Y, Wan K, Zhu Y, Gkoutos GV, Han Y, Chen Y.",,JACC. Asia,2024,2024-03-26,Y,Entropy; hypertrophic cardiomyopathy; Sudden Cardiac Death; Cardiac Magnetic Resonance; T1 Mapping,,,"<h4>Background</h4>The prognostic value of left ventricular (LV) entropy in hypertrophic cardiomyopathy (HCM) is unclear.<h4>Objectives</h4>This study aimed to assess the prognostic value of LV entropy from T1 mapping in HCM.<h4>Methods</h4>A total of 748 participants with HCM, who underwent cardiovascular magnetic resonance (CMR), were consecutively enrolled. LV entropy was quantified by native T1 mapping. A competing risk analysis and a Cox proportional hazards regression analysis were performed to identify potential associations of LV entropy with sudden cardiac death (SCD) and cardiovascular death (CVD), respectively.<h4>Results</h4>A total of 40 patients with HCM experienced SCD, and 65 experienced CVD during a median follow-up of 43 months. Participants with increased LV entropy (≥4.06) were more likely to experience SCD and CVD (all <i>P</i> < 0.05) in the entire study cohort or the subgroup with low late gadolinium enhancement (LGE) extent (<15%). After adjustment for the European Society of Cardiology predictors and the presence of high LGE extent (≥15%), LV mean entropy was an independent predictor for SCD (HR: 1.03; all <i>P</i> < 0.05) by the multivariable competing risk analysis and CVD (HR: 1.06; 95% CI: 1.03-1.09; <i>P</i> < 0.001) by multivariable Cox regression analysis.<h4>Conclusions</h4>LV mean entropy derived from native T1 mapping, reflecting myocardial tissue heterogeneity, was an independent predictor of SCD and CVD in participants with HCM. (Cardiac Magnetic Resonance Imaging Clinical Application Registration Study; ChiCTR1900024094).",,doi:https://doi.org/10.1016/j.jacasi.2024.01.005; html:https://europepmc.org/articles/PMC11099820; pdf:https://europepmc.org/articles/PMC11099820?pdf=render
-35429382,https://doi.org/10.1093/infdis/jiac146,Severe Acute Respiratory Syndrome Coronavirus 2 Anti-Spike Antibody Levels Following Second Dose of ChAdOx1 nCov-19 or BNT162b2 Vaccine in Residents of Long-term Care Facilities in England (VIVALDI).,"Stirrup O, Krutikov M, Tut G, Palmer T, Bone D, Bruton R, Fuller C, Azmi B, Lancaster T, Sylla P, Kaur N, Spalkova E, Bentley C, Amin U, Jadir A, Hulme S, Giddings R, Nacer-Laidi H, Baynton V, Irwin-Singer A, Hayward A, Moss P, Copas A, Shallcross L.",,The Journal of infectious diseases,2022,2022-11-01,Y,Antibodies; Vaccination; Waning; Long-term Care Facilities; Covid-19,,,"General population studies have shown strong humoral response following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination with subsequent waning of anti-spike antibody levels. Vaccine-induced immune responses are often attenuated in frail and older populations, but published data are scarce. We measured SARS-CoV-2 anti-spike antibody levels in long-term care facility residents and staff following a second vaccination dose with Oxford-AstraZeneca or Pfizer-BioNTech. Vaccination elicited robust antibody responses in older residents, suggesting comparable levels of vaccine-induced immunity to that in the general population. Antibody levels are higher after Pfizer-BioNTech vaccination but fall more rapidly compared to Oxford-AstraZeneca recipients and are enhanced by prior infection in both groups.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9047242; doi:https://doi.org/10.1093/infdis/jiac146; html:https://europepmc.org/articles/PMC9047242; pdf:https://europepmc.org/articles/PMC9047242?pdf=render
 33413610,https://doi.org/10.1186/s13073-020-00822-6,An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets.,"Ward D, Higgins M, Phelan JE, Hibberd ML, Campino S, Clark TG.",,Genome medicine,2021,2021-01-07,Y,Mutation; Epitopes; Surveillance; cross-reactivity; Immuno-informatics; Sars-cov-2; Covid; Human-coronavirus,,,"During COVID-19, diagnostic serological tools and vaccines have been developed. To inform control activities in a post-vaccine surveillance setting, we have developed an online ""immuno-analytics"" resource that combines epitope, sequence, protein and SARS-CoV-2 mutation analysis. SARS-CoV-2 spike and nucleocapsid proteins are both vaccine and serological diagnostic targets. Using the tool, the nucleocapsid protein appears to be a sub-optimal target for use in serological platforms. Spike D614G (and nsp12 L314P) mutations were most frequent (> 86%), whilst spike A222V/L18F have recently increased. Also, Orf3a proteins may be a suitable target for serology. The tool can accessed from: http://genomics.lshtm.ac.uk/immuno (online); https://github.com/dan-ward-bio/COVID-immunoanalytics (source code).",,pdf:https://genomemedicine.biomedcentral.com/counter/pdf/10.1186/s13073-020-00822-6; doi:https://doi.org/10.1186/s13073-020-00822-6; html:https://europepmc.org/articles/PMC7790334; pdf:https://europepmc.org/articles/PMC7790334?pdf=render
+35429382,https://doi.org/10.1093/infdis/jiac146,Severe Acute Respiratory Syndrome Coronavirus 2 Anti-Spike Antibody Levels Following Second Dose of ChAdOx1 nCov-19 or BNT162b2 Vaccine in Residents of Long-term Care Facilities in England (VIVALDI).,"Stirrup O, Krutikov M, Tut G, Palmer T, Bone D, Bruton R, Fuller C, Azmi B, Lancaster T, Sylla P, Kaur N, Spalkova E, Bentley C, Amin U, Jadir A, Hulme S, Giddings R, Nacer-Laidi H, Baynton V, Irwin-Singer A, Hayward A, Moss P, Copas A, Shallcross L.",,The Journal of infectious diseases,2022,2022-11-01,Y,Antibodies; Vaccination; Waning; Long-term Care Facilities; Covid-19,,,"General population studies have shown strong humoral response following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination with subsequent waning of anti-spike antibody levels. Vaccine-induced immune responses are often attenuated in frail and older populations, but published data are scarce. We measured SARS-CoV-2 anti-spike antibody levels in long-term care facility residents and staff following a second vaccination dose with Oxford-AstraZeneca or Pfizer-BioNTech. Vaccination elicited robust antibody responses in older residents, suggesting comparable levels of vaccine-induced immunity to that in the general population. Antibody levels are higher after Pfizer-BioNTech vaccination but fall more rapidly compared to Oxford-AstraZeneca recipients and are enhanced by prior infection in both groups.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9047242; doi:https://doi.org/10.1093/infdis/jiac146; html:https://europepmc.org/articles/PMC9047242; pdf:https://europepmc.org/articles/PMC9047242?pdf=render
 33307988,https://doi.org/10.1177/0961203320979045,Brain network reorganisation and spatial lesion distribution in systemic lupus erythematosus.,"Valdés Hernández MDC, Smith K, Bastin ME, Nicole Amft E, Ralston SH, Wardlaw JM, Wiseman SJ.",,Lupus,2021,2020-12-13,Y,SLE; Connectome; Network Analysis,,,"<h4>Objective</h4>This work investigates network organisation of brain structural connectivity in systemic lupus erythematosus (SLE) relative to healthy controls and its putative association with lesion distribution and disease indicators.<h4>Methods</h4>White matter hyperintensity (WMH) segmentation and connectomics were performed in 47 patients with SLE and 47 healthy age-matched controls from structural and diffusion MRI data. Network nodes were divided into hierarchical tiers based on numbers of connections. Results were compared between patients and controls to assess for differences in brain network organisation. Voxel-based analyses of the spatial distribution of WMH in relation to network measures and SLE disease indicators were conducted.<h4>Results</h4>Despite inter-individual differences in brain network organization observed across the study sample, the connectome networks of SLE patients had larger proportion of connections in the peripheral nodes. SLE patients had statistically larger numbers of links in their networks with generally larger fractional anisotropy weights (i.e. a measure of white matter integrity) and less tendency to aggregate than those of healthy controls. The voxels exhibiting connectomic differences were coincident with WMH clusters, particularly the left hemisphere's intersection between the anterior limb of the internal and external capsules. Moreover, these voxels also associated more strongly with disease indicators.<h4>Conclusion</h4>Our results indicate network differences reflective of compensatory reorganization of the neural circuits, reflecting adaptive or extended neuroplasticity in SLE.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/0961203320979045; doi:https://doi.org/10.1177/0961203320979045; html:https://europepmc.org/articles/PMC7854491; pdf:https://europepmc.org/articles/PMC7854491?pdf=render
-39426795,https://doi.org/10.1016/j.jpeds.2024.114370,Trends in Pediatric Hospital Admissions Caused or Contributed by SARS-CoV-2 Infection in England.,"Wilde H, Tomlinson C, Mateen BA, Selby D, Kanthimathinathan HK, Denaxas S, Flaxman S, Vollmer S, Pagel C, Brown K, CVD-COVID-UK/COVID-IMPACT Consortium.",,The Journal of pediatrics,2024,2024-10-17,N,,,,"<h4>Objective</h4>To investigate the changing characteristics of SARS-CoV-2 related pediatric hospital admissions over time.<h4>Study design</h4>A national, observational cohort study from 1, July 2020, to August 31, 2023, using English population-linked electronic health records. We identified 45,203 children under 18 years old in whom SARS-CoV-2 either caused or contributed to hospitalization, excluding those admitted with ""incidental"" infection. Studied outcomes were types of hospitalization and severe hospitalizations involving either critical care or PIMS-TS.<h4>Results</h4>There were 45,920 SARS-CoV-2 related hospitalizations in children: 34,870 (75.9%) due to COVID-19; 1,845 (4.0%) due to pediatric inflammatory multisystem syndrome - temporally associated with SARS-CoV-2 (PIMS-TS); 8,330 (18.1%) with SARS-CoV-2 as contributor to admission; and 875 (1.9%) acquired nosocomial SARS-CoV-2 infection. The most notable changes between the first three waves (March 2020 through November 2021) and the omicron era (December 2021 onwards) were: a fall in PIMS-TS from 1,575 of 14,020 (11.2%) to 270 of 31,905 (0.8%); a reduction in critical care use from 1,175 of 14,020 (8.4%) to 1,390 of 31,905 (4.4%); a fall in mortality rate among those hospitalized from 521 per 100,000 to 249 per 100,000; and a drop in the median age of hospitalized children from 4.7 (IQR 0.6,12.3) to 1.1 (IQR 0.3,6.4) years. Of children hospitalized, infants, 10.2% of whom had a recorded underlying health condition, comprised 4,225 of 14,020 (30.1%) admissions 2020 through 2021 and 15,555 of 31,900 (48.8%) since 2022. (p<0.001 for all comparisons).<h4>Conclusions</h4>Infants are now the most affected age group by SARS-CoV2, at least partially related to having the least immunity to the virus, and are most vulnerable to respiratory illnesses.",,doi:https://doi.org/10.1016/j.jpeds.2024.114370
+39486903,https://doi.org/10.1016/s2468-2667(24)00215-9,"Contemporary epidemiology of hospitalised heart failure with reduced versus preserved ejection fraction in England: a retrospective, cohort study of whole-population electronic health records.","Fletcher RA, Rockenschaub P, Neuen BL, Walter IJ, Conrad N, Mizani MA, Bolton T, Lawson CA, Tomlinson C, Logothetis SB, Petitjean C, Brizzi LF, Kaptoge S, Raffetti E, Calvert PA, Di Angelantonio E, Banerjee A, Mamas MA, Squire I, Denaxas S, McDonagh TA, Sudlow C, Petersen SE, Chertow GM, Khunti K, Sundström J, Arnott C, Cleland JGF, Danesh J, McMurray JJV, Vaduganathan M, Wood AM, CVD-COVID-UK/COVID-IMPACT Consortium.",,The Lancet. Public health,2024,2024-11-01,N,,,,"<h4>Background</h4>Heart failure is common, complex, and often associated with coexisting chronic medical conditions and a high mortality. We aimed to assess the epidemiology of people admitted to hospital with heart failure with reduced ejection fraction (HFrEF) and heart failure with preserved ejection fraction (HFpEF), including the period covering the COVID-19 pandemic, which was previously not well characterised.<h4>Methods</h4>In this retrospective, cohort study, we used whole-population electronic health records with 57 million individuals in England to identify patients hospitalised with heart failure as the primary diagnosis in any consultant episode of an in-patient admission to a National Health Service (NHS) hospital. We excluded individuals with less than 1 year of medical history records in primary or secondary care; admissions to NHS hospitals for which less than 10% of heart failure cases were linkable to the National Heart Failure Audit (NHFA); individuals younger than 18 years at the time of the heart failure hospitalisation; and patients who died in hospital during the index heart failure admission. For patients with new onset heart failure, we assessed incidence rates of 30-day and 1-year all-cause and cause-specific (cardiovascular, non-cardiovascular, and heart failure-related) emergency rehospitalisation and mortality after discharge, and dispensed guideline-recommended medical therapy (GRMT). Follow-up occurred from the index admission to the earliest occurrence of the event of interest, death, or end of data coverage. We estimated adjusted hazard ratios (HRs) to compare HFrEF with HFpEF. We computed population-attributable fractions to quantify the percentage of outcomes attributable to coexisting chronic medical conditions.<h4>Findings</h4>Among 233 320 patients identified who survived the index heart failure admission across 335 NHS hospitals between Jan 1, 2019, and Dec 31, 2022, 101 320 (43·4%) had HFrEF, 71 910 (30·8%) had HFpEF, and 60 090 (25·8%) had an unknown classification. In patients with new onset heart failure, there were reductions in all-cause 30-day (-5·2% [95% CI -7·7 to -2·6] in 2019-22) and 1-year rehospitalisation rates (-3·9% [-6·6 to -1·2]). Declining 30-day rehospitalisation rates affected patients with HFpEF (-4·8% [-9·2 to -0·2]) and HFrEF (-6·2% [-10·5 to -1·6]), although 1-year rates were not statistically significant for patients with HFpEF (-2·2% [-6·6 to 2·3] vs -5·7% [-10·6 to -0·5] for HFrEF). There were no temporal trends in incidence rates of 30-day or 1-year mortality after discharge. The rates of all-cause (HR 1·20 [1·18-1·22]) and cause-specific rehospitalisation were uniformly higher in those with HFpEF than those with HFrEF. Patients with HFpEF also had higher rates of 1-year all-cause mortality after discharge (HR 1·07 [1·05-1·09]), driven by excess risk of non-cardiovascular death (HR 1·25 [1·21-1·29]). Rates of rehospitalisation and mortality were highest in patients with coexisting chronic kidney disease, chronic obstructive pulmonary disease, dementia, and liver disease. Chronic kidney disease contributed to 6·5% (5·6-7·4) of rehospitalisations within 1 year for HFrEF and 5·0% (4·1-5·9) of rehospitalisations for HFpEF, double that of any other coexisting condition. There was swift implementation of newer GRMT, but markedly lower dispensing of these medications in patients with coexisting chronic kidney disease.<h4>Interpretation</h4>Rates of rehospitalisation in patients with heart failure in England have decreased during 2019-22. Further population health improvements could be reached through enhanced implementation of GRMT, particularly in patients with coexisting chronic kidney disease, who, despite being at high risk, remain undertreated.<h4>Funding</h4>Wellcome Trust, Health Data Research UK, British Heart Foundation Data Science Centre.",,doi:https://doi.org/10.1016/S2468-2667(24)00215-9
 33710281,https://doi.org/10.1093/ageing/afab060,COVID-19 infection and attributable mortality in UK care homes: cohort study using active surveillance and electronic records (March-June 2020).,"Dutey-Magni PF, Williams H, Jhass A, Rait G, Lorencatto F, Hemingway H, Hayward A, Shallcross L.",,Age and ageing,2021,2021-06-01,Y,Mortality; Morbidity; Older People; Long-term Care; Covid-19; Sars-cov-2,,,"<h4>Background</h4>epidemiological data on COVID-19 infection in care homes are scarce. We analysed data from a large provider of long-term care for older people to investigate infection and mortality during the first wave of the pandemic.<h4>Methods</h4>cohort study of 179 UK care homes with 9,339 residents and 11,604 staff. We used manager-reported daily tallies to estimate the incidence of suspected and confirmed infection and mortality in staff and residents. Individual-level electronic health records from 8,713 residents were used to model risk factors for confirmed infection, mortality and estimate attributable mortality.<h4>Results</h4>2,075/9,339 residents developed COVID-19 symptoms (22.2% [95% confidence interval: 21.4%; 23.1%]), while 951 residents (10.2% [9.6%; 10.8%]) and 585 staff (5.0% [4.7%; 5.5%]) had laboratory-confirmed infections. The incidence of confirmed infection was 152.6 [143.1; 162.6] and 62.3 [57.3; 67.5] per 100,000 person-days in residents and staff, respectively. Sixty-eight percent (121/179) of care homes had at least one COVID-19 infection or COVID-19-related death. Lower staffing ratios and higher occupancy rates were independent risk factors for infection.Out of 607 residents with confirmed infection, 217 died (case fatality rate: 35.7% [31.9%; 39.7%]). Mortality in residents with no direct evidence of infection was twofold higher in care homes with outbreaks versus those without (adjusted hazard ratio: 2.2 [1.8; 2.6]).<h4>Conclusions</h4>findings suggest many deaths occurred in people who were infected with COVID-19, but not tested. Higher occupancy and lower staffing levels were independently associated with risks of infection. Protecting staff and residents from infection requires regular testing for COVID-19 and fundamental changes to staffing and care home occupancy.",,pdf:https://academic.oup.com/ageing/article-pdf/50/4/1019/40971734/afab060.pdf; doi:https://doi.org/10.1093/ageing/afab060; html:https://europepmc.org/articles/PMC7989651; pdf:https://europepmc.org/articles/PMC7989651?pdf=render
-35776101,https://doi.org/10.1093/ije/dyac140,Incremental value of risk factor variability for cardiovascular risk prediction in individuals with type 2 diabetes: results from UK primary care electronic health records.,"Xu Z, Arnold M, Sun L, Stevens D, Chung R, Ip S, Barrett J, Kaptoge S, Pennells L, Di Angelantonio E, Wood AM.",,International journal of epidemiology,2022,2022-12-01,Y,Variability; Cardiovascular disease; Type 2 diabetes; Risk Prediction; Repeated Measurements; Electronic Health Records,,,"<h4>Background</h4>Cardiovascular disease (CVD) risk prediction models for individuals with type 2 diabetes are important tools to guide intensification of interventions for CVD prevention. We aimed to assess the added value of incorporating risk factors variability in CVD risk prediction for people with type 2 diabetes.<h4>Methods</h4>We used electronic health records (EHRs) data from 83 910 adults with type 2 diabetes but without pre-existing CVD from the UK Clinical Practice Research Datalink for 2004-2017. Using a landmark-modelling approach, we developed and validated sex-specific Cox models, incorporating conventional predictors and trajectories plus variability of systolic blood pressure (SBP), total and high-density lipoprotein (HDL) cholesterol, and glycated haemoglobin (HbA1c). Such models were compared against simpler models using single last observed values or means.<h4>Results</h4>The standard deviations (SDs) of SBP, HDL cholesterol and HbA1c were associated with higher CVD risk (P < 0.05). Models incorporating trajectories and variability of continuous predictors demonstrated improvement in risk discrimination (C-index = 0.659, 95% CI: 0.654-0.663) as compared with using last observed values (C-index = 0.651, 95% CI: 0.646-0.656) or means (C-index = 0.650, 95% CI: 0.645-0.655). Inclusion of SDs of SBP yielded the greatest improvement in discrimination (C-index increase = 0.005, 95% CI: 0.004-0.007) in comparison to incorporating SDs of total cholesterol (C-index increase = 0.002, 95% CI: 0.000-0.003), HbA1c (C-index increase = 0.002, 95% CI: 0.000-0.003) or HDL cholesterol (C-index increase= 0.003, 95% CI: 0.002-0.005).<h4>Conclusion</h4>Incorporating variability of predictors from EHRs provides a modest improvement in CVD risk discrimination for individuals with type 2 diabetes. Given that repeat measures are readily available in EHRs especially for regularly monitored patients with diabetes, this improvement could easily be achieved.",,pdf:https://academic.oup.com/ije/advance-article-pdf/doi/10.1093/ije/dyac140/45030523/dyac140.pdf; doi:https://doi.org/10.1093/ije/dyac140; html:https://europepmc.org/articles/PMC9749723; pdf:https://europepmc.org/articles/PMC9749723?pdf=render
+39426795,https://doi.org/10.1016/j.jpeds.2024.114370,Trends in Pediatric Hospital Admissions Caused or Contributed by SARS-CoV-2 Infection in England.,"Wilde H, Tomlinson C, Mateen BA, Selby D, Kanthimathinathan HK, Denaxas S, Flaxman S, Vollmer S, Pagel C, Brown K, CVD-COVID-UK/COVID-IMPACT Consortium.",,The Journal of pediatrics,2024,2024-10-17,N,,,,"<h4>Objective</h4>To investigate the changing characteristics of SARS-CoV-2 related pediatric hospital admissions over time.<h4>Study design</h4>A national, observational cohort study from 1, July 2020, to August 31, 2023, using English population-linked electronic health records. We identified 45,203 children under 18 years old in whom SARS-CoV-2 either caused or contributed to hospitalization, excluding those admitted with ""incidental"" infection. Studied outcomes were types of hospitalization and severe hospitalizations involving either critical care or PIMS-TS.<h4>Results</h4>There were 45,920 SARS-CoV-2 related hospitalizations in children: 34,870 (75.9%) due to COVID-19; 1,845 (4.0%) due to pediatric inflammatory multisystem syndrome - temporally associated with SARS-CoV-2 (PIMS-TS); 8,330 (18.1%) with SARS-CoV-2 as contributor to admission; and 875 (1.9%) acquired nosocomial SARS-CoV-2 infection. The most notable changes between the first three waves (March 2020 through November 2021) and the omicron era (December 2021 onwards) were: a fall in PIMS-TS from 1,575 of 14,020 (11.2%) to 270 of 31,905 (0.8%); a reduction in critical care use from 1,175 of 14,020 (8.4%) to 1,390 of 31,905 (4.4%); a fall in mortality rate among those hospitalized from 521 per 100,000 to 249 per 100,000; and a drop in the median age of hospitalized children from 4.7 (IQR 0.6,12.3) to 1.1 (IQR 0.3,6.4) years. Of children hospitalized, infants, 10.2% of whom had a recorded underlying health condition, comprised 4,225 of 14,020 (30.1%) admissions 2020 through 2021 and 15,555 of 31,900 (48.8%) since 2022. (p<0.001 for all comparisons).<h4>Conclusions</h4>Infants are now the most affected age group by SARS-CoV2, at least partially related to having the least immunity to the virus, and are most vulnerable to respiratory illnesses.",,doi:https://doi.org/10.1016/j.jpeds.2024.114370
 31000744,https://doi.org/10.1038/s41598-019-42036-w,"Measuring social, environmental and health inequalities using deep learning and street imagery.","Suel E, Polak JW, Bennett JE, Ezzati M.",,Scientific reports,2019,2019-04-18,Y,,"Applied Analytics, Improving Public Health",,"Cities are home to an increasing majority of the world's population. Currently, it is difficult to track social, economic, environmental and health outcomes in cities with high spatial and temporal resolution, needed to evaluate policies regarding urban inequalities. We applied a deep learning approach to street images for measuring spatial distributions of income, education, unemployment, housing, living environment, health and crime. Our model predicts different outcomes directly from raw images without extracting intermediate user-defined features. To evaluate the performance of the approach, we first trained neural networks on a subset of images from London using ground truth data at high spatial resolution from official statistics. We then compared how trained networks separated the best-off from worst-off deciles for different outcomes in images not used in training. The best performance was achieved for quality of the living environment and mean income. Allocation was least successful for crime and self-reported health (but not objectively measured health). We also evaluated how networks trained in London predict outcomes three other major cities in the UK: Birmingham, Manchester, and Leeds. The transferability analysis showed that networks trained in London, fine-tuned with only 1% of images in other cities, achieved performances similar to ones from trained on data from target cities themselves. Our findings demonstrate that street imagery has the potential complement traditional survey-based and administrative data sources for high-resolution urban surveillance to measure inequalities and monitor the impacts of policies that aim to address them.",,pdf:https://www.nature.com/articles/s41598-019-42036-w.pdf; doi:https://doi.org/10.1038/s41598-019-42036-w; html:https://europepmc.org/articles/PMC6473002; pdf:https://europepmc.org/articles/PMC6473002?pdf=render
+35776101,https://doi.org/10.1093/ije/dyac140,Incremental value of risk factor variability for cardiovascular risk prediction in individuals with type 2 diabetes: results from UK primary care electronic health records.,"Xu Z, Arnold M, Sun L, Stevens D, Chung R, Ip S, Barrett J, Kaptoge S, Pennells L, Di Angelantonio E, Wood AM.",,International journal of epidemiology,2022,2022-12-01,Y,Variability; Cardiovascular disease; Type 2 diabetes; Risk Prediction; Repeated Measurements; Electronic Health Records,,,"<h4>Background</h4>Cardiovascular disease (CVD) risk prediction models for individuals with type 2 diabetes are important tools to guide intensification of interventions for CVD prevention. We aimed to assess the added value of incorporating risk factors variability in CVD risk prediction for people with type 2 diabetes.<h4>Methods</h4>We used electronic health records (EHRs) data from 83 910 adults with type 2 diabetes but without pre-existing CVD from the UK Clinical Practice Research Datalink for 2004-2017. Using a landmark-modelling approach, we developed and validated sex-specific Cox models, incorporating conventional predictors and trajectories plus variability of systolic blood pressure (SBP), total and high-density lipoprotein (HDL) cholesterol, and glycated haemoglobin (HbA1c). Such models were compared against simpler models using single last observed values or means.<h4>Results</h4>The standard deviations (SDs) of SBP, HDL cholesterol and HbA1c were associated with higher CVD risk (P < 0.05). Models incorporating trajectories and variability of continuous predictors demonstrated improvement in risk discrimination (C-index = 0.659, 95% CI: 0.654-0.663) as compared with using last observed values (C-index = 0.651, 95% CI: 0.646-0.656) or means (C-index = 0.650, 95% CI: 0.645-0.655). Inclusion of SDs of SBP yielded the greatest improvement in discrimination (C-index increase = 0.005, 95% CI: 0.004-0.007) in comparison to incorporating SDs of total cholesterol (C-index increase = 0.002, 95% CI: 0.000-0.003), HbA1c (C-index increase = 0.002, 95% CI: 0.000-0.003) or HDL cholesterol (C-index increase= 0.003, 95% CI: 0.002-0.005).<h4>Conclusion</h4>Incorporating variability of predictors from EHRs provides a modest improvement in CVD risk discrimination for individuals with type 2 diabetes. Given that repeat measures are readily available in EHRs especially for regularly monitored patients with diabetes, this improvement could easily be achieved.",,pdf:https://academic.oup.com/ije/advance-article-pdf/doi/10.1093/ije/dyac140/45030523/dyac140.pdf; doi:https://doi.org/10.1093/ije/dyac140; html:https://europepmc.org/articles/PMC9749723; pdf:https://europepmc.org/articles/PMC9749723?pdf=render
 38035863,https://doi.org/10.1016/j.injury.2023.111200,A scoping review of models of care for the management of older trauma patients.,"Ferrah N, Kennedy B, Beck B, Ibrahim J, Gabbe B, Cameron P.",,Injury,2024,2023-11-14,N,Trauma; co-management; Older Adult; Model Of Care; Geriatric Consultation,,,"<h4>Introduction</h4>The number of older people hospitalised with major trauma is rapidly increasing. New models of care have emerged, such as co-management, and trauma centres dedicated to delivering geriatric trauma care. The aim of this scoping review was to explore in-hospital models of care for older adults who experience physical trauma.<h4>Patients and methods</h4>The search was conducted in accordance with the PRISMA- SC (preferred reporting items for systematic reviews and meta-analyses extension for scoping reviews) reporting guidelines. The National Heart Lung, and Blood Institute (NIH) study quality assessment tool was used to evaluate risk of bias in before and after non-randomised experimental studies.<h4>Results</h4>Of 2127 records returned from the database search, 43 papers were included. We identified five types of care models investigated in the reviewed studies: centralised trauma management, consultation services, co-management, patient care protocols, and alert and triage systems. The majority of patients were admitted under a specialised trauma service, intervention teams were for the most part multidisciplinary, and follow-up of patients post-discharge was seldom reported. Consultation services more often had advanced care and discharge planning as treatment objectives. In contrast, patient care protocol and alert systems commonly had management of anticoagulation as a treatment objective. Overall, the impact of the five models of care on patient outcomes was mixed.<h4>Discussion</h4>Given the variability in patient characteristics and capabilities of health services, models of care need to be matched to the local profile of older trauma patients. However, some standards should be incorporated into a care model, including identifying goals of care, medication review and follow up post-discharge.",,doi:https://doi.org/10.1016/j.injury.2023.111200
 32198138,https://doi.org/10.1136/bmj.l6927,"Machine learning and artificial intelligence research for patient benefit: 20 critical questions on transparency, replicability, ethics, and effectiveness.","Vollmer S, Mateen BA, Bohner G, Király FJ, Ghani R, Jonsson P, Cumbers S, Jonas A, McAllister KSL, Myles P, Granger D, Birse M, Branson R, Moons KGM, Collins GS, Ioannidis JPA, Holmes C, Hemingway H.",,BMJ (Clinical research ed.),2020,2020-03-20,Y,,,,,,pdf:https://www.bmj.com/content/bmj/368/bmj.l6927.full.pdf; doi:https://doi.org/10.1136/bmj.l6927; html:https://europepmc.org/articles/PMC11515850
-37859783,https://doi.org/10.1136/bmjmed-2023-000554,"Performance of polygenic risk scores in screening, prediction, and risk stratification: secondary analysis of data in the Polygenic Score Catalog.","Hingorani AD, Gratton J, Finan C, Schmidt AF, Patel R, Sofat R, Kuan V, Langenberg C, Hemingway H, Morris JK, Wald NJ.",,BMJ medicine,2023,2023-10-17,Y,Public Health; Preventive Medicine,,,"<h4>Objective</h4>To clarify the performance of polygenic risk scores in population screening, individual risk prediction, and population risk stratification.<h4>Design</h4>Secondary analysis of data in the Polygenic Score Catalog.<h4>Setting</h4>Polygenic Score Catalog, April 2022. Secondary analysis of 3915 performance metric estimates for 926 polygenic risk scores for 310 diseases to generate estimates of performance in population screening, individual risk, and population risk stratification.<h4>Participants</h4>Individuals contributing to the published studies in the Polygenic Score Catalog.<h4>Main outcome measures</h4>Detection rate for a 5% false positive rate (DR<sub>5</sub>) and the population odds of becoming affected given a positive result; individual odds of becoming affected for a person with a particular polygenic score; and odds of becoming affected for groups of individuals in different portions of a polygenic risk score distribution. Coronary artery disease and breast cancer were used as illustrative examples.<h4>Results</h4>For performance in population screening, median DR<sub>5</sub> for all polygenic risk scores and all diseases studied was 11% (interquartile range 8-18%). Median DR<sub>5</sub> was 12% (9-19%) for polygenic risk scores for coronary artery disease and 10% (9-12%) for breast cancer. The population odds of becoming affected given a positive results were 1:8 for coronary artery disease and 1:21 for breast cancer, with background 10 year odds of 1:19 and 1:41, respectively, which are typical for these diseases at age 50. For individual risk prediction, the corresponding 10 year odds of becoming affected for individuals aged 50 with a polygenic risk score at the 2.5th, 25th, 75th, and 97.5th centiles were 1:54, 1:29, 1:15, and 1:8 for coronary artery disease and 1:91, 1:56, 1:34, and 1:21 for breast cancer. In terms of population risk stratification, at age 50, the risk of coronary artery disease was divided into five groups, with 10 year odds of 1:41 and 1:11 for the lowest and highest quintile groups, respectively. The 10 year odds was 1:7 for the upper 2.5% of the polygenic risk score distribution for coronary artery disease, a group that contributed 7% of cases. The corresponding estimates for breast cancer were 1:72 and 1:26 for the lowest and highest quintile groups, and 1:19 for the upper 2.5% of the distribution, which contributed 6% of cases.<h4>Conclusion</h4>Polygenic risk scores performed poorly in population screening, individual risk prediction, and population risk stratification. Strong claims about the effect of polygenic risk scores on healthcare seem to be disproportionate to their performance.",,doi:https://doi.org/10.1136/bmjmed-2023-000554; html:https://europepmc.org/articles/PMC10582890; pdf:https://europepmc.org/articles/PMC10582890?pdf=render
 31607513,https://doi.org/10.1016/j.cell.2019.08.051,"Genome-wide Association Studies in Ancestrally Diverse Populations: Opportunities, Methods, Pitfalls, and Recommendations.","Peterson RE, Kuchenbaecker K, Walters RK, Chen CY, Popejoy AB, Periyasamy S, Lam M, Iyegbe C, Strawbridge RJ, Brick L, Carey CE, Martin AR, Meyers JL, Su J, Chen J, Edwards AC, Kalungi A, Koen N, Majara L, Schwarz E, Smoller JW, Stahl EA, Sullivan PF, Vassos E, Mowry B, Prieto ML, Cuellar-Barboza A, Bigdeli TB, Edenberg HJ, Huang H, Duncan LE.",,Cell,2019,2019-10-10,N,Population genetics; Diversity; Psychiatry; complex disease; Gwas; Ancestry; Admixed Populations; Trans-ethnic; Trans-ancestry; Cross-ancestry,,,"Genome-wide association studies (GWASs) have focused primarily on populations of European descent, but it is essential that diverse populations become better represented. Increasing diversity among study participants will advance our understanding of genetic architecture in all populations and ensure that genetic research is broadly applicable. To facilitate and promote research in multi-ancestry and admixed cohorts, we outline key methodological considerations and highlight opportunities, challenges, solutions, and areas in need of development. Despite the perception that analyzing genetic data from diverse populations is difficult, it is scientifically and ethically imperative, and there is an expanding analytical toolbox to do it well.",,pdf:http://www.cell.com/article/S0092867419310025/pdf; doi:https://doi.org/10.1016/j.cell.2019.08.051; html:https://europepmc.org/articles/PMC6939869; pdf:https://europepmc.org/articles/PMC6939869?pdf=render; doi:https://doi.org/10.1016/j.cell.2019.08.051
+37859783,https://doi.org/10.1136/bmjmed-2023-000554,"Performance of polygenic risk scores in screening, prediction, and risk stratification: secondary analysis of data in the Polygenic Score Catalog.","Hingorani AD, Gratton J, Finan C, Schmidt AF, Patel R, Sofat R, Kuan V, Langenberg C, Hemingway H, Morris JK, Wald NJ.",,BMJ medicine,2023,2023-10-17,Y,Public Health; Preventive Medicine,,,"<h4>Objective</h4>To clarify the performance of polygenic risk scores in population screening, individual risk prediction, and population risk stratification.<h4>Design</h4>Secondary analysis of data in the Polygenic Score Catalog.<h4>Setting</h4>Polygenic Score Catalog, April 2022. Secondary analysis of 3915 performance metric estimates for 926 polygenic risk scores for 310 diseases to generate estimates of performance in population screening, individual risk, and population risk stratification.<h4>Participants</h4>Individuals contributing to the published studies in the Polygenic Score Catalog.<h4>Main outcome measures</h4>Detection rate for a 5% false positive rate (DR<sub>5</sub>) and the population odds of becoming affected given a positive result; individual odds of becoming affected for a person with a particular polygenic score; and odds of becoming affected for groups of individuals in different portions of a polygenic risk score distribution. Coronary artery disease and breast cancer were used as illustrative examples.<h4>Results</h4>For performance in population screening, median DR<sub>5</sub> for all polygenic risk scores and all diseases studied was 11% (interquartile range 8-18%). Median DR<sub>5</sub> was 12% (9-19%) for polygenic risk scores for coronary artery disease and 10% (9-12%) for breast cancer. The population odds of becoming affected given a positive results were 1:8 for coronary artery disease and 1:21 for breast cancer, with background 10 year odds of 1:19 and 1:41, respectively, which are typical for these diseases at age 50. For individual risk prediction, the corresponding 10 year odds of becoming affected for individuals aged 50 with a polygenic risk score at the 2.5th, 25th, 75th, and 97.5th centiles were 1:54, 1:29, 1:15, and 1:8 for coronary artery disease and 1:91, 1:56, 1:34, and 1:21 for breast cancer. In terms of population risk stratification, at age 50, the risk of coronary artery disease was divided into five groups, with 10 year odds of 1:41 and 1:11 for the lowest and highest quintile groups, respectively. The 10 year odds was 1:7 for the upper 2.5% of the polygenic risk score distribution for coronary artery disease, a group that contributed 7% of cases. The corresponding estimates for breast cancer were 1:72 and 1:26 for the lowest and highest quintile groups, and 1:19 for the upper 2.5% of the distribution, which contributed 6% of cases.<h4>Conclusion</h4>Polygenic risk scores performed poorly in population screening, individual risk prediction, and population risk stratification. Strong claims about the effect of polygenic risk scores on healthcare seem to be disproportionate to their performance.",,doi:https://doi.org/10.1136/bmjmed-2023-000554; html:https://europepmc.org/articles/PMC10582890; pdf:https://europepmc.org/articles/PMC10582890?pdf=render
+33402395,https://doi.org/10.1136/jech-2020-215204,Hospital readmission among people experiencing homelessness in England: a cohort study of 2772 matched homeless and housed inpatients.,"Lewer D, Menezes D, Cornes M, Blackburn RM, Byng R, Clark M, Denaxas S, Evans H, Fuller J, Hewett N, Kilmister A, Luchenski SA, Manthorpe J, McKee M, Neale J, Story A, Tinelli M, Whiteford M, Wurie F, Yavlinsky A, Hayward A, Aldridge R.",,Journal of epidemiology and community health,2021,2021-01-05,Y,Homelessness; Health Inequalities; Record Linkage; Access To Hlth Care,,,"<h4>Background</h4>Inpatients experiencing homelessness are often discharged to unstable accommodation or the street, which may increase the risk of readmission.<h4>Methods</h4>We conducted a cohort study of 2772 homeless patients discharged after an emergency admission at 78 hospitals across England between November 2013 and November 2016. For each individual, we selected a housed patient who lived in a socioeconomically deprived area, matched on age, sex, hospital, and year of discharge. Counts of emergency readmissions, planned readmissions, and Accident and Emergency (A&E) visits post-discharge were derived from national hospital databases, with a median of 2.8 years of follow-up. We estimated the cumulative incidence of readmission over 12 months, and used negative binomial regression to estimate rate ratios.<h4>Results</h4>After adjusting for health measured at the index admission, homeless patients had 2.49 (95% CI 2.29 to 2.70) times the rate of emergency readmission, 0.60 (95% CI 0.53 to 0.68) times the rate of planned readmission and 2.57 (95% CI 2.41 to 2.73) times the rate of A&E visits compared with housed patients. The 12-month risk of emergency readmission was higher for homeless patients (61%, 95% CI 59% to 64%) than housed patients (33%, 95% CI 30% to 36%); and the risk of planned readmission was lower for homeless patients (17%, 95% CI 14% to 19%) than for housed patients (30%, 95% CI 28% to 32%). While the risk of emergency readmission varied with the reason for admission for housed patients, for example being higher for admissions due to cancers than for those due to accidents, the risk was high across all causes for homeless patients.<h4>Conclusions</h4>Hospital patients experiencing homelessness have high rates of emergency readmission that are not explained by health. This highlights the need for discharge arrangements that address their health, housing and social care needs.",,pdf:https://jech.bmj.com/content/jech/75/7/681.full.pdf; doi:https://doi.org/10.1136/jech-2020-215204; html:https://europepmc.org/articles/PMC8223662; pdf:https://europepmc.org/articles/PMC8223662?pdf=render
 35085490,https://doi.org/10.1016/s2213-2600(21)00542-7,SARS-CoV-2 infection and vaccine effectiveness in England (REACT-1): a series of cross-sectional random community surveys.,"Chadeau-Hyam M, Wang H, Eales O, Haw D, Bodinier B, Whitaker M, Walters CE, Ainslie KEC, Atchison C, Fronterre C, Diggle PJ, Page AJ, Trotter AJ, Ashby D, Barclay W, Taylor G, Cooke G, Ward H, Darzi A, Riley S, Donnelly CA, Elliott P, COVID-19 Genomics UK consortium.",,The Lancet. Respiratory medicine,2022,2022-01-24,Y,,,,"<h4>Background</h4>England has experienced a third wave of the COVID-19 epidemic since the end of May, 2021, coinciding with the rapid spread of the delta (B.1.617.2) variant, despite high levels of vaccination among adults. Vaccination rates (single dose) in England are lower among children aged 16-17 years and 12-15 years, whose vaccination in England commenced in August and September, 2021, respectively. We aimed to analyse the underlying dynamics driving patterns in SARS-CoV-2 prevalence during September, 2021, in England.<h4>Methods</h4>The REal-time Assessment of Community Transmission-1 (REACT-1) study, which commenced data collection in May, 2020, involves a series of random cross-sectional surveys in the general population of England aged 5 years and older. Using RT-PCR swab positivity data from 100 527 participants with valid throat and nose swabs in round 14 of REACT-1 (Sept 9-27, 2021), we estimated community-based prevalence of SARS-CoV-2 and vaccine effectiveness against infection by combining round 14 data with data from round 13 (June 24 to July 12, 2021; n=172 862).<h4>Findings</h4>During September, 2021, we estimated a mean RT-PCR positivity rate of 0·83% (95% CrI 0·76-0·89), with a reproduction number (R) overall of 1·03 (95% CrI 0·94-1·14). Among the 475 (62·2%) of 764 sequenced positive swabs, all were of the delta variant; 22 (4·63%; 95% CI 3·07-6·91) included the Tyr145His mutation in the spike protein associated with the AY.4 sublineage, and there was one Glu484Lys mutation. Age, region, key worker status, and household size jointly contributed to the risk of swab positivity. The highest weighted prevalence was observed among children aged 5-12 years, at 2·32% (95% CrI 1·96-2·73) and those aged 13-17 years, at 2·55% (2·11-3·08). The SARS-CoV-2 epidemic grew in those aged 5-11 years, with an R of 1·42 (95% CrI 1·18-1·68), but declined in those aged 18-54 years, with an R of 0·81 (0·68-0·97). At ages 18-64 years, the adjusted vaccine effectiveness against infection was 62·8% (95% CI 49·3-72·7) after two doses compared to unvaccinated people, for all vaccines combined, 44·8% (22·5-60·7) for the ChAdOx1 nCov-19 (Oxford-AstraZeneca) vaccine, and 71·3% (56·6-81·0) for the BNT162b2 (Pfizer-BioNTech) vaccine. In individuals aged 18 years and older, the weighted prevalence of swab positivity was 0·35% (95% CrI 0·31-0·40) if the second dose was administered up to 3 months before their swab but 0·55% (0·50-0·61) for those who received their second dose 3-6 months before their swab, compared to 1·76% (1·60-1·95) among unvaccinated individuals.<h4>Interpretation</h4>In September, 2021, at the start of the autumn school term in England, infections were increasing exponentially in children aged 5-17 years, at a time when vaccination rates were low in this age group. In adults, compared to those who received their second dose less than 3 months ago, the higher prevalence of swab positivity at 3-6 months following two doses of the COVID-19 vaccine suggests an increased risk of breakthrough infections during this period. The vaccination programme needs to reach children as well as unvaccinated and partially vaccinated adults to reduce SARS-CoV-2 transmission and associated disruptions to work and education.<h4>Funding</h4>Department of Health and Social Care, England.",,pdf:http://www.thelancet.com/article/S2213260021005427/pdf; doi:https://doi.org/10.1016/S2213-2600(21)00542-7; html:https://europepmc.org/articles/PMC8786320
 35786634,https://doi.org/10.2196/37821,Methodological Issues in Using a Common Data Model of COVID-19 Vaccine Uptake and Important Adverse Events of Interest: Feasibility Study of Data and Connectivity COVID-19 Vaccines Pharmacovigilance in the United Kingdom.,"Delanerolle G, Williams R, Stipancic A, Byford R, Forbes A, Tsang RSM, Anand SN, Bradley D, Murphy S, Akbari A, Bedston S, Lyons RA, Owen R, Torabi F, Beggs J, Chuter A, Balharry D, Joy M, Sheikh A, Hobbs FDR, de Lusignan S.",,JMIR formative research,2022,2022-08-22,Y,Clinical outcome; Sinus Thrombosis; Health Information; Pharmacovigilance; anaphylaxis; Vaccine Uptake; Systematized Nomenclature Of Medicine; Data Model; Medical Outcome; Health Database; Vaccine Effect; Covid-19; Covid-19 Vaccines; Clinical Coding System,,,"<h4>Background</h4>The Data and Connectivity COVID-19 Vaccines Pharmacovigilance (DaC-VaP) UK-wide collaboration was created to monitor vaccine uptake and effectiveness and provide pharmacovigilance using routine clinical and administrative data. To monitor these, pooled analyses may be needed. However, variation in terminologies present a barrier as England uses the Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT), while the rest of the United Kingdom uses the Read v2 terminology in primary care. The availability of data sources is not uniform across the United Kingdom.<h4>Objective</h4>This study aims to use the concept mappings in the Observational Medical Outcomes Partnership (OMOP) common data model (CDM) to identify common concepts recorded and to report these in a repeated cross-sectional study. We planned to do this for vaccine coverage and 2 adverse events of interest (AEIs), cerebral venous sinus thrombosis (CVST) and anaphylaxis. We identified concept mappings to SNOMED CT, Read v2, the World Health Organization's International Classification of Disease Tenth Revision (ICD-10) terminology, and the UK Dictionary of Medicines and Devices (dm+d).<h4>Methods</h4>Exposures and outcomes of interest to DaC-VaP for pharmacovigilance studies were selected. Mappings of these variables to different terminologies used across the United Kingdom's devolved nations' health services were identified from the Observational Health Data Sciences and Informatics (OHDSI) Automated Terminology Harmonization, Extraction, and Normalization for Analytics (ATHENA) online browser. Lead analysts from each nation then confirmed or added to the mappings identified. These mappings were then used to report AEIs in a common format. We reported rates for windows of 0-2 and 3-28 days postvaccine every 28 days.<h4>Results</h4>We listed the mappings between Read v2, SNOMED CT, ICD-10, and dm+d. For vaccine exposure, we found clear mapping from OMOP to our clinical terminologies, though dm+d had codes not listed by OMOP at the time of searching. We found a list of CVST and anaphylaxis codes. For CVST, we had to use a broader cerebral venous thrombosis conceptual approach to include Read v2. We identified 56 SNOMED CT codes, of which we selected 47 (84%), and 15 Read v2 codes. For anaphylaxis, our refined search identified 60 SNOMED CT codes and 9 Read v2 codes, of which we selected 10 (17%) and 4 (44%), respectively, to include in our repeated cross-sectional studies.<h4>Conclusions</h4>This approach enables the use of mappings to different terminologies within the OMOP CDM without the need to catalogue an entire database. However, Read v2 has less granular concepts than some terminologies, such as SNOMED CT. Additionally, the OMOP CDM cannot compensate for limitations in the clinical coding system. Neither Read v2 nor ICD-10 is sufficiently granular to enable CVST to be specifically flagged. Hence, any pooled analysis will have to be at the less specific level of cerebrovascular venous thrombosis. Overall, the mappings within this CDM are useful, and our method could be used for rapid collaborations where there are only a limited number of concepts to pool.",,pdf:https://formative.jmir.org/2022/8/e37821/PDF; doi:https://doi.org/10.2196/37821; html:https://europepmc.org/articles/PMC9400842; pdf:https://europepmc.org/articles/PMC9400842?pdf=render
-33402395,https://doi.org/10.1136/jech-2020-215204,Hospital readmission among people experiencing homelessness in England: a cohort study of 2772 matched homeless and housed inpatients.,"Lewer D, Menezes D, Cornes M, Blackburn RM, Byng R, Clark M, Denaxas S, Evans H, Fuller J, Hewett N, Kilmister A, Luchenski SA, Manthorpe J, McKee M, Neale J, Story A, Tinelli M, Whiteford M, Wurie F, Yavlinsky A, Hayward A, Aldridge R.",,Journal of epidemiology and community health,2021,2021-01-05,Y,Homelessness; Health Inequalities; Record Linkage; Access To Hlth Care,,,"<h4>Background</h4>Inpatients experiencing homelessness are often discharged to unstable accommodation or the street, which may increase the risk of readmission.<h4>Methods</h4>We conducted a cohort study of 2772 homeless patients discharged after an emergency admission at 78 hospitals across England between November 2013 and November 2016. For each individual, we selected a housed patient who lived in a socioeconomically deprived area, matched on age, sex, hospital, and year of discharge. Counts of emergency readmissions, planned readmissions, and Accident and Emergency (A&E) visits post-discharge were derived from national hospital databases, with a median of 2.8 years of follow-up. We estimated the cumulative incidence of readmission over 12 months, and used negative binomial regression to estimate rate ratios.<h4>Results</h4>After adjusting for health measured at the index admission, homeless patients had 2.49 (95% CI 2.29 to 2.70) times the rate of emergency readmission, 0.60 (95% CI 0.53 to 0.68) times the rate of planned readmission and 2.57 (95% CI 2.41 to 2.73) times the rate of A&E visits compared with housed patients. The 12-month risk of emergency readmission was higher for homeless patients (61%, 95% CI 59% to 64%) than housed patients (33%, 95% CI 30% to 36%); and the risk of planned readmission was lower for homeless patients (17%, 95% CI 14% to 19%) than for housed patients (30%, 95% CI 28% to 32%). While the risk of emergency readmission varied with the reason for admission for housed patients, for example being higher for admissions due to cancers than for those due to accidents, the risk was high across all causes for homeless patients.<h4>Conclusions</h4>Hospital patients experiencing homelessness have high rates of emergency readmission that are not explained by health. This highlights the need for discharge arrangements that address their health, housing and social care needs.",,pdf:https://jech.bmj.com/content/jech/75/7/681.full.pdf; doi:https://doi.org/10.1136/jech-2020-215204; html:https://europepmc.org/articles/PMC8223662; pdf:https://europepmc.org/articles/PMC8223662?pdf=render
+33356394,https://doi.org/10.1161/hypertensionaha.120.16547,"Urate, Blood Pressure, and Cardiovascular Disease: Evidence From Mendelian Randomization and Meta-Analysis of Clinical Trials.","Gill D, Cameron AC, Burgess S, Li X, Doherty DJ, Karhunen V, Abdul-Rahim AH, Taylor-Rowan M, Zuber V, Tsao PS, Klarin D, VA Million Veteran Program, Evangelou E, Elliott P, Damrauer SM, Quinn TJ, Dehghan A, Theodoratou E, Dawson J, Tzoulaki I.",,"Hypertension (Dallas, Tex. : 1979)",2021,2020-12-28,Y,Cardiovascular diseases; Blood pressure; Uric acid; Systematic review; Odds Ratio,,,"Serum urate has been implicated in hypertension and cardiovascular disease, but it is not known whether it is exerting a causal effect. To investigate this, we performed Mendelian randomization analysis using data from UK Biobank, Million Veterans Program and genome-wide association study consortia, and meta-analysis of randomized controlled trials. The main Mendelian randomization analyses showed that every 1-SD increase in genetically predicted serum urate was associated with an increased risk of coronary heart disease (odds ratio, 1.19 [95% CI, 1.10-1.30]; <i>P</i>=4×10<sup>-5</sup>), peripheral artery disease (1.12 [95% CI, 1.03-1.21]; <i>P</i>=9×10<sup>-3</sup>), and stroke (1.11 [95% CI, 1.05-1.18]; <i>P</i>=2×10<sup>-4</sup>). In Mendelian randomization mediation analyses, elevated blood pressure was estimated to mediate approximately one-third of the effect of urate on cardiovascular disease risk. Systematic review and meta-analysis of randomized controlled trials showed a favorable effect of urate-lowering treatment on systolic blood pressure (mean difference, -2.55 mm Hg [95% CI, -4.06 to -1.05]; <i>P</i>=1×10<sup>-3</sup>) and major adverse cardiovascular events in those with previous cardiovascular disease (odds ratio, 0.40 [95% CI, 0.22-0.73]; <i>P</i>=3×10<sup>-3</sup>) but no significant effect on major adverse cardiovascular events in all individuals (odds ratio, 0.67 [95% CI, 0.44-1.03]; <i>P</i>=0.07). In summary, these Mendelian randomization and clinical trial data support an effect of higher serum urate on increasing blood pressure, which may mediate a consequent effect on cardiovascular disease risk. High-quality trials are necessary to provide definitive evidence on the specific clinical contexts where urate lowering may be of cardiovascular benefit.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/HYPERTENSIONAHA.120.16547; doi:https://doi.org/10.1161/HYPERTENSIONAHA.120.16547; html:https://europepmc.org/articles/PMC7803439; pdf:https://europepmc.org/articles/PMC7803439?pdf=render
 38855982,https://doi.org/10.1080/10408363.2024.2360996,Methods applied to neonatal dried blood spot samples for secondary research purposes: a scoping review.,"Canning J, Strawbridge RJ, Miedzybrodzka Z, Marioni RE, Melbye M, Porteous DJ, Hurles ME, Sattar N, Sudlow CLM, Collins R, Padmanabhan S, Pell JP.",,Critical reviews in clinical laboratory sciences,2024,2024-06-10,N,Residual; Dried Blood Spots; neonatal; Scoping Review; Archived,,,"This scoping review aimed to synthesize the analytical techniques used and methodological limitations encountered when undertaking secondary research using residual neonatal dried blood spot (DBS) samples. Studies that used residual neonatal DBS samples for secondary research (i.e. research not related to newborn screening for inherited genetic and metabolic disorders) were identified from six electronic databases: Cochrane Library, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Embase, Medline, PubMed and Scopus. Inclusion was restricted to studies published from 1973 and written in or translated into English that reported the storage, extraction and testing of neonatal DBS samples. Sixty-seven studies were eligible for inclusion. Included studies were predominantly methodological in nature and measured various analytes, including nucleic acids, proteins, metabolites, environmental pollutants, markers of prenatal substance use and medications. Neonatal DBS samples were stored over a range of temperatures (ambient temperature, cold storage or frozen) and durations (two weeks to 40.5 years), both of which impacted the recovery of some analytes, particularly amino acids, antibodies and environmental pollutants. The size of DBS sample used and potential contamination were also cited as methodological limitations. Residual neonatal DBS samples retained by newborn screening programs are a promising resource for secondary research purposes, with many studies reporting the successful measurement of analytes even from neonatal DBS samples stored for long periods of time in suboptimal temperatures and conditions.",,doi:https://doi.org/10.1080/10408363.2024.2360996
 36715329,https://doi.org/10.1093/bjd/ljac090,"The epidemiology, healthcare and societal burden of basal cell carcinoma in Wales 2000-2018: a retrospective nationwide analysis.","Ibrahim N, Jovic M, Ali S, Williams N, Gibson JAG, Griffiths R, Dobbs TD, Akbari A, Lyons RA, Hutchings HA, Whitaker IS.",,The British journal of dermatology,2023,2023-02-01,N,,,,"<h4>Background</h4>Basal cell carcinoma (BCC) represents the most commonly occurring cancer worldwide within the white population. Reports predict 298 308 cases of BCC in the UK by 2025, at a cost of £265-366 million to the National Health Service (NHS). Despite the morbidity, societal and healthcare pressures brought about by BCC, routinely collected healthcare data and global registration remain limited.<h4>Objectives</h4>To calculate the incidence of BCC in Wales between 2000 and 2018 and to establish the related healthcare utilization and estimated cost of care.<h4>Methods</h4>The Secure Anonymised Information Linkage (SAIL) databank is one of the largest and most robust health and social care data repositories in the UK. Cancer registry data were linked to routinely collected healthcare databases between 2000 and 2018. Pathological data from Swansea Bay University Health Board (SBUHB) were used for internal validation.<h4>Results</h4>A total of 61 404 histologically proven BCCs were identified within the SAIL Databank during the study period. The European age-standardized incidence for BCC in 2018 was 224.6 per 100 000 person-years. Based on validated regional data, a 45% greater incidence was noted within SBUHB pathology vs. matched regions within SAIL between 2016 and 2018. A negative association between deprivation and incidence was noted with a higher incidence in the least socially deprived and rural dwellers. Approximately 2% travelled 25-50 miles for dermatological services compared with 37% for plastic surgery. Estimated NHS costs of surgically managed lesions for 2002-2019 equated to £119.2-164.4 million.<h4>Conclusions</h4>Robust epidemiological data that are internationally comparable and representative are scarce for nonmelanoma skin cancer. The rising global incidence coupled with struggling healthcare systems in the post-COVID-19 recovery period serve to intensify the societal and healthcare impact. This study is the first to demonstrate the incidence of BCC in Wales and is one of a small number in the UK using internally validated large cohort datasets. Furthermore, our findings demonstrate one of the highest published incidences within the UK and Europe.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa62055/Download/62055__26915__ae11794993454389b6ceddbb7f50caaa.pdf; doi:https://doi.org/10.1093/bjd/ljac090
-33356394,https://doi.org/10.1161/hypertensionaha.120.16547,"Urate, Blood Pressure, and Cardiovascular Disease: Evidence From Mendelian Randomization and Meta-Analysis of Clinical Trials.","Gill D, Cameron AC, Burgess S, Li X, Doherty DJ, Karhunen V, Abdul-Rahim AH, Taylor-Rowan M, Zuber V, Tsao PS, Klarin D, VA Million Veteran Program, Evangelou E, Elliott P, Damrauer SM, Quinn TJ, Dehghan A, Theodoratou E, Dawson J, Tzoulaki I.",,"Hypertension (Dallas, Tex. : 1979)",2021,2020-12-28,Y,Cardiovascular diseases; Blood pressure; Uric acid; Systematic review; Odds Ratio,,,"Serum urate has been implicated in hypertension and cardiovascular disease, but it is not known whether it is exerting a causal effect. To investigate this, we performed Mendelian randomization analysis using data from UK Biobank, Million Veterans Program and genome-wide association study consortia, and meta-analysis of randomized controlled trials. The main Mendelian randomization analyses showed that every 1-SD increase in genetically predicted serum urate was associated with an increased risk of coronary heart disease (odds ratio, 1.19 [95% CI, 1.10-1.30]; <i>P</i>=4×10<sup>-5</sup>), peripheral artery disease (1.12 [95% CI, 1.03-1.21]; <i>P</i>=9×10<sup>-3</sup>), and stroke (1.11 [95% CI, 1.05-1.18]; <i>P</i>=2×10<sup>-4</sup>). In Mendelian randomization mediation analyses, elevated blood pressure was estimated to mediate approximately one-third of the effect of urate on cardiovascular disease risk. Systematic review and meta-analysis of randomized controlled trials showed a favorable effect of urate-lowering treatment on systolic blood pressure (mean difference, -2.55 mm Hg [95% CI, -4.06 to -1.05]; <i>P</i>=1×10<sup>-3</sup>) and major adverse cardiovascular events in those with previous cardiovascular disease (odds ratio, 0.40 [95% CI, 0.22-0.73]; <i>P</i>=3×10<sup>-3</sup>) but no significant effect on major adverse cardiovascular events in all individuals (odds ratio, 0.67 [95% CI, 0.44-1.03]; <i>P</i>=0.07). In summary, these Mendelian randomization and clinical trial data support an effect of higher serum urate on increasing blood pressure, which may mediate a consequent effect on cardiovascular disease risk. High-quality trials are necessary to provide definitive evidence on the specific clinical contexts where urate lowering may be of cardiovascular benefit.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/HYPERTENSIONAHA.120.16547; doi:https://doi.org/10.1161/HYPERTENSIONAHA.120.16547; html:https://europepmc.org/articles/PMC7803439; pdf:https://europepmc.org/articles/PMC7803439?pdf=render
 38984466,https://doi.org/10.1002/ehf2.14751,Eligibility of Asian and European registry patients for phase III trials in heart failure with reduced ejection fraction.,"Lim YMF, Asselbergs FW, Bagheri A, Denaxas S, Tay WT, Voors A, Lam CSP, Koudstaal S, Grobbee DE, Vaartjes I.",,ESC heart failure,2024,2024-07-10,N,Heart Failure; Clinical Trials; Generalizability; Disease Registry; Patient Eligibility,,,"<h4>Aims</h4>Traditional approaches to designing clinical trials for heart failure (HF) have historically relied on expertise and past practices. However, the evolving landscape of healthcare, marked by the advent of novel data science applications and increased data availability, offers a compelling opportunity to transition towards a data-driven paradigm in trial design. This research aims to evaluate the scope and determinants of disparities between clinical trials and registries by leveraging natural language processing for the analysis of trial eligibility criteria. The findings contribute to the establishment of a robust design framework for guiding future HF trials.<h4>Methods and results</h4>Interventional phase III trials registered for HF on ClinicalTrials.gov as of the end of 2021 were identified. Natural language processing was used to extract and structure the eligibility criteria for quantitative analysis. The most common criteria for HF with reduced ejection fraction (HFrEF) were applied to estimate patient eligibility as a proportion of registry patients in the ASIAN-HF (N = 4868) and BIOSTAT-CHF registries (N = 2545). Of the 375 phase III trials for HF, 163 HFrEF trials were identified. In these trials, the most frequently encountered inclusion criteria were New York Heart Association (NYHA) functional class (69%), worsening HF (23%), and natriuretic peptides (18%), whereas the most frequent comorbidity-based exclusion criteria were acute coronary syndrome (64%), renal disease (55%), and valvular heart disease (47%). On average, 20% of registry patients were eligible for HFrEF trials. Eligibility distributions did not differ (P = 0.18) between Asian [median eligibility 0.20, interquartile range (IQR) 0.08-0.43] and European registry populations (median 0.17, IQR 0.06-0.39). With time, HFrEF trials became more restrictive, where patient eligibility declined from 0.40 in 1985-2005 to 0.19 in 2016-2022 (P = 0.03). When frequency among trials is taken into consideration, the eligibility criteria that were most restrictive were prior myocardial infarction, NYHA class, age, and prior HF hospitalization.<h4>Conclusions</h4>Based on 14 trial criteria, only one-fifth of registry patients were eligible for phase III HFrEF trials. Overall eligibility rates did not differ between the Asian and European patient cohorts.",,doi:https://doi.org/10.1002/ehf2.14751; doi:https://doi.org/10.1002/ehf2.14751
 33813844,https://doi.org/10.1161/hypertensionaha.120.16534,Relationship Between Blood Pressure and Incident Cardiovascular Disease: Linear and Nonlinear Mendelian Randomization Analyses.,"Malik R, Georgakis MK, Vujkovic M, Damrauer SM, Elliott P, Karhunen V, Giontella A, Fava C, Hellwege JN, Shuey MM, Edwards TL, Rogne T, Åsvold BO, Brumpton BM, Burgess S, Dichgans M, Gill D.",,"Hypertension (Dallas, Tex. : 1979)",2021,2021-04-05,Y,Hypertension; Blood pressure; Stroke; coronary artery disease; Primary Prevention,,,[Figure: see text].,,pdf:https://www.ahajournals.org/doi/pdf/10.1161/HYPERTENSIONAHA.120.16534; doi:https://doi.org/10.1161/HYPERTENSIONAHA.120.16534; html:https://europepmc.org/articles/PMC8115430; pdf:https://europepmc.org/articles/PMC8115430?pdf=render
 38509467,https://doi.org/10.1186/s12874-024-02175-9,Implementation and external validation of the Cambridge Multimorbidity Score in the UK Biobank cohort.,"Harrison H, Ip S, Renzi C, Li Y, Barclay M, Usher-Smith J, Lyratzopoulos G, Wood A, Antoniou AC.",,BMC medical research methodology,2024,2024-03-20,Y,Electronic Health Records; Multimorbidity; Uk Biobank; External Validation; Primary Care Records,,,"<h4>Background</h4>Patients with multiple conditions present a growing challenge for healthcare provision. Measures of multimorbidity may support clinical management, healthcare resource allocation and accounting for the health of participants in purpose-designed cohorts. The recently developed Cambridge Multimorbidity scores (CMS) have the potential to achieve these aims using primary care records, however, they have not yet been validated outside of their development cohort.<h4>Methods</h4>The CMS, developed in the Clinical Research Practice Dataset (CPRD), were validated in UK Biobank participants whose data is not available in CPRD (the cohort used for CMS development) with available primary care records (n = 111,898). This required mapping of the 37 pre-existing conditions used in the CMS to the coding frameworks used by UK Biobank data providers. We used calibration plots and measures of discrimination to validate the CMS for two of the three outcomes used in the development study (death and primary care consultation rate) and explored variation by age and sex. We also examined the predictive ability of the CMS for the outcome of cancer diagnosis. The results were compared to an unweighted count score of the 37 pre-existing conditions.<h4>Results</h4>For all three outcomes considered, the CMS were poorly calibrated in UK Biobank. We observed a similar discriminative ability for the outcome of primary care consultation rate to that reported in the development study (C-index: 0.67 (95%CI:0.66-0.68) for both, 5-year follow-up); however, we report lower discrimination for the outcome of death than the development study (0.69 (0.68-0.70) and 0.89 (0.88-0.90) respectively). Discrimination for cancer diagnosis was adequate (0.64 (0.63-0.65)). The CMS performs favourably to the unweighted count score for death, but not for the outcomes of primary care consultation rate or cancer diagnosis.<h4>Conclusions</h4>In the UK Biobank, CMS discriminates reasonably for the outcomes of death, primary care consultation rate and cancer diagnosis and may be a valuable resource for clinicians, public health professionals and data scientists. However, recalibration will be required to make accurate predictions when cohort composition and risk levels differ substantially from the development cohort. The generated resources (including codelists for the conditions and code for CMS implementation in UK Biobank) are available online.",,pdf:https://bmcmedresmethodol.biomedcentral.com/counter/pdf/10.1186/s12874-024-02175-9; doi:https://doi.org/10.1186/s12874-024-02175-9; html:https://europepmc.org/articles/PMC10953059; pdf:https://europepmc.org/articles/PMC10953059?pdf=render
-36935397,https://doi.org/10.1093/bjs/znad055,Validating a novel natural language processing pathway for automated quality assurance in surgical oncology: incomplete excision rates of 34 955 basal cell carcinomas.,"Ali SR, Dobbs TD, Jovic M, Strafford H, Fonferko-Shadrach B, Lacey AS, Williams N, Pickrell WO, Hutchings HA, Whitaker IS.",,The British journal of surgery,2023,2023-08-01,Y,,,,,,pdf:https://academic.oup.com/bjs/advance-article-pdf/doi/10.1093/bjs/znad055/49561408/znad055.pdf; doi:https://doi.org/10.1093/bjs/znad055; html:https://europepmc.org/articles/PMC10416688; pdf:https://europepmc.org/articles/PMC10416688?pdf=render
 36654802,https://doi.org/10.1002/lrh2.10315,"A framework for understanding, designing, developing and evaluating learning health systems.","Foley T, Vale L.",,Learning health systems,2023,2022-05-20,Y,Quality improvement; Informatics; Implementation Science; Learning Health Systems; Learning Healthcare Systems,,,"<h4>Introduction</h4>A Learning Health System is not a technical project. It is the evolution of an existing health system into one capable of learning from every patient. This paper outlines a recently published framework intended to aid the understanding, design, development and evaluation of Learning Health Systems.<h4>Methods</h4>This work extended an existing repository of Learning Health System evidence, adding five more workshops. The total was subjected to thematic analysis, yielding a framework of elements important to understanding, designing, developing and evaluating Learning Health Systems. Purposeful literature reviews were conducted on each element. The findings were revised following a review by a group of international experts.<h4>Results</h4>The resulting framework was arranged around four questions:What is our rationale for developing a Learning Health System?There can be many reasons for developing a Learning Health System. Understanding these will guide its development.What sources of complexity exist at the system and the intervention level?An understanding of complexity is central to making Learning Health Systems work. The non-adoption, abandonment, scale-up, spread and sustainability framework was utilised to help understand and manage it.What strategic approaches to change do we need to consider?A range of strategic issues must be addressed to enable successful change in a Learning Health System. These include, strategy, organisational structure, culture, workforce, implementation science, behaviour change, co-design and evaluation.What technical building blocks will we need?A Learning Health System must capture data from practice, turn it into knowledge and apply it back into practice. There are many methods to achieve this and a range of platforms to help.<h4>Discussion</h4>The results form a framework for understanding, designing, developing and evaluating Learning Health Systems at any scale.<h4>Conclusion</h4>It is hoped that this framework will evolve with use and feedback.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9835047; doi:https://doi.org/10.1002/lrh2.10315; html:https://europepmc.org/articles/PMC9835047; pdf:https://europepmc.org/articles/PMC9835047?pdf=render
+36935397,https://doi.org/10.1093/bjs/znad055,Validating a novel natural language processing pathway for automated quality assurance in surgical oncology: incomplete excision rates of 34 955 basal cell carcinomas.,"Ali SR, Dobbs TD, Jovic M, Strafford H, Fonferko-Shadrach B, Lacey AS, Williams N, Pickrell WO, Hutchings HA, Whitaker IS.",,The British journal of surgery,2023,2023-08-01,Y,,,,,,pdf:https://academic.oup.com/bjs/advance-article-pdf/doi/10.1093/bjs/znad055/49561408/znad055.pdf; doi:https://doi.org/10.1093/bjs/znad055; html:https://europepmc.org/articles/PMC10416688; pdf:https://europepmc.org/articles/PMC10416688?pdf=render
 32626822,https://doi.org/10.1007/s41109-020-00273-3,Normalised degree variance.,"Smith KM, Escudero J.",,Applied network science,2020,2020-06-22,Y,,,,"Finding graph indices which are unbiased to network size and density is of high importance both within a given field and across fields for enhancing comparability of modern network science studies. The degree variance is an important metric for characterising network degree heterogeneity. Here, we provide an analytically valid normalisation of degree variance to replace previous normalisations which are either invalid or not applicable to all networks. It is shown that this normalisation provides equal values for graphs and their complements; it is maximal in the star graph (and its complement); and its expected value is constant with respect to density for Erdös-Rényi (ER) random graphs of the same size. We strengthen these results with model observations in ER random graphs, random geometric graphs, scale-free networks, random hierarchy networks and resting-state brain networks, showing that the proposed normalisation is generally less affected by both network size and density than previous normalisation attempts. The closed form expression proposed also benefits from high computational efficiency and straightforward mathematical analysis. Analysis of 184 real-world binary networks across different disciplines shows that normalised degree variance is not correlated with average degree and is robust to node and edge subsampling. Comparisons across subdomains of biological networks reveals greater degree heterogeneity among brain connectomes and food webs than in protein interaction networks.",,pdf:https://appliednetsci.springeropen.com/track/pdf/10.1007/s41109-020-00273-3; doi:https://doi.org/10.1007/s41109-020-00273-3; html:https://europepmc.org/articles/PMC7319291; pdf:https://europepmc.org/articles/PMC7319291?pdf=render
 34266851,https://doi.org/10.1136/bmjhci-2021-100356,Development of a core competency framework for clinical informatics.,"Davies A, Mueller J, Hassey A, Moulton G.",,BMJ health & care informatics,2021,2021-07-01,Y,Medical Informatics; Bmj Health Informatics,,,"<h4>Objectives</h4>Until this point there was no national core competency framework for clinical informatics in the UK. We report on the final two iterations of work carried out in the formation of a national core competency framework. This follows an initial systematic literature review of existing skills and competencies and a job listing analysis.MethodsAn iterative approach was applied to framework development. Using a mixed-methods design we carried out semi-structured interviews with participants involved in informatics (n=15). The framework was updated based on the interview findings and was subsequently distributed as part of a bespoke online digital survey for wider participation (n=87). The final version of the framework is based on the findings of the survey.<h4>Results</h4>Over 102 people reviewed the framework as part of the interview or survey process. This led to a final core competency framework containing 6 primary domains with 36 subdomains containing 111 individual competencies.<h4>Conclusions</h4>An iterative mixed-methods approach for competency development involving the target community was appropriate for development of the competency framework. There is some contention around the depth of technical competencies required. Care is also needed to avoid professional burnout, as clinicians and healthcare practitioners already have clinical competencies to maintain. Therefore, how the framework is applied in practice and how practitioners meet the competencies requires careful consideration.",,pdf:https://informatics.bmj.com/content/bmjhci/28/1/e100356.full.pdf; doi:https://doi.org/10.1136/bmjhci-2021-100356; html:https://europepmc.org/articles/PMC8286765; pdf:https://europepmc.org/articles/PMC8286765?pdf=render
 34481555,https://doi.org/10.1016/s2213-8587(21)00207-2,"Identifying adults at high-risk for change in weight and BMI in England: a longitudinal, large-scale, population-based cohort study using electronic health records.","Katsoulis M, Lai AG, Diaz-Ordaz K, Gomes M, Pasea L, Banerjee A, Denaxas S, Tsilidis K, Lagiou P, Misirli G, Bhaskaran K, Wannamethee G, Dobson R, Batterham RL, Kipourou DK, Lumbers RT, Wen L, Wareham N, Langenberg C, Hemingway H.",,The lancet. Diabetes & endocrinology,2021,2021-09-02,Y,,,,"<h4>Background</h4>Targeted obesity prevention policies would benefit from the identification of population groups with the highest risk of weight gain. The relative importance of adult age, sex, ethnicity, geographical region, and degree of social deprivation on weight gain is not known. We aimed to identify high-risk groups for changes in weight and BMI using electronic health records (EHR).<h4>Methods</h4>In this longitudinal, population-based cohort study we used linked EHR data from 400 primary care practices (via the Clinical Practice Research Datalink) in England, accessed via the CALIBER programme. Eligible participants were aged 18-74 years, were registered at a general practice clinic, and had BMI and weight measurements recorded between Jan 1, 1998, and June 30, 2016, during the period when they had eligible linked data with at least 1 year of follow-up time. We calculated longitudinal changes in BMI over 1, 5, and 10 years, and investigated the absolute risk and odds ratios (ORs) of transitioning between BMI categories (underweight, normal weight, overweight, obesity class 1 and 2, and severe obesity [class 3]), as defined by WHO. The associations of demographic factors with BMI transitions were estimated by use of logistic regression analysis, adjusting for baseline BMI, family history of cardiovascular disease, use of diuretics, and prevalent chronic conditions.<h4>Findings</h4>We included 2 092 260 eligible individuals with more than 9 million BMI measurements in our study. Young adult age was the strongest risk factor for weight gain at 1, 5, and 10 years of follow-up. Compared with the oldest age group (65-74 years), adults in the youngest age group (18-24 years) had the highest OR (4·22 [95% CI 3·86-4·62]) and greatest absolute risk (37% vs 24%) of transitioning from normal weight to overweight or obesity at 10 years. Likewise, adults in the youngest age group with overweight or obesity at baseline were also at highest risk to transition to a higher BMI category; OR 4·60 (4·06-5·22) and absolute risk (42% vs 18%) of transitioning from overweight to class 1 and 2 obesity, and OR 5·87 (5·23-6·59) and absolute risk (22% vs 5%) of transitioning from class 1 and 2 obesity to class 3 obesity. Other demographic factors were consistently less strongly associated with these transitions; for example, the OR of transitioning from normal weight to overweight or obesity in people living in the most socially deprived versus least deprived areas was 1·23 (1·18-1·27), for men versus women was 1·12 (1·08-1·16), and for Black individuals versus White individuals was 1·13 (1·04-1·24). We provide an open access online risk calculator, and present high-resolution obesity risk charts over a 1-year, 5-year, and 10-year follow-up period.<h4>Interpretation</h4>A radical shift in policy is required to focus on individuals at the highest risk of weight gain (ie, young adults aged 18-24 years) for individual-level and population-level prevention of obesity and its long-term consequences for health and health care.<h4>Funding</h4>The British Hearth Foundation, Health Data Research UK, the UK Medical Research Council, and the National Institute for Health Research.",,pdf:http://www.thelancet.com/article/S2213858721002072/pdf; doi:https://doi.org/10.1016/S2213-8587(21)00207-2; html:https://europepmc.org/articles/PMC8440227; pdf:https://europepmc.org/articles/PMC8440227?pdf=render
@@ -1086,18 +1088,18 @@ PMC10686417,https://doi.org/,The impact of restricted provision of publicly fund
 33262239,https://doi.org/10.1128/msystems.00677-20,Investigating the Role of Diet and Exercise in Gut Microbe-Host Cometabolism.,"Penney N, Barton W, Posma JM, Darzi A, Frost G, Cotter PD, Holmes E, Shanahan F, O'Sullivan O, Garcia-Perez I.",,mSystems,2020,2020-12-01,Y,Metabolism; Diet; Exercise; Microbiome,,,"We investigated the individual and combined effects of diet and physical exercise on metabolism and the gut microbiome to establish how these lifestyle factors influence host-microbiome cometabolism. Urinary and fecal samples were collected from athletes and less active controls. Individuals were further classified according to an objective dietary assessment score of adherence to healthy dietary habits according to WHO guidelines, calculated from their proton nuclear magnetic resonance (<sup>1</sup>H-NMR) urinary profiles. Subsequent models were generated comparing extremes of dietary habits, exercise, and the combined effect of both. Differences in metabolic phenotypes and gut microbiome profiles between the two groups were assessed. Each of the models pertaining to diet healthiness, physical exercise, or a combination of both displayed a metabolic and functional microbial signature, with a significant proportion of the metabolites identified as discriminating between the various pairwise comparisons resulting from gut microbe-host cometabolism. Microbial diversity was associated with a combination of high adherence to healthy dietary habits and exercise and was correlated with a distinct array of microbially derived metabolites, including markers of proteolytic activity. Improved control of dietary confounders, through the use of an objective dietary assessment score, has uncovered further insights into the complex, multifactorial relationship between diet, exercise, the gut microbiome, and metabolism. Furthermore, the observation of higher proteolytic activity associated with higher microbial diversity indicates that increased microbial diversity may confer deleterious as well as beneficial effects on the host.<b>IMPORTANCE</b> Improved control of dietary confounders, through the use of an objective dietary assessment score, has uncovered further insights into the complex, multifactorial relationship between diet, exercise, the gut microbiome, and metabolism. Each of the models pertaining to diet healthiness, physical exercise, or a combination of both, displayed a distinct metabolic and functional microbial signature. A significant proportion of the metabolites identified as discriminating between the various pairwise comparisons result from gut microbe-host cometabolism, and the identified interactions have expanded current knowledge in this area. Furthermore, although increased microbial diversity has previously been linked with health, our observation of higher microbial diversity being associated with increased proteolytic activity indicates that it may confer deleterious as well as beneficial effects on the host.",,pdf:http://spiral.imperial.ac.uk/bitstream/10044/1/85021/8/mSystems-2020-Penney-e00677-20.full.pdf; doi:https://doi.org/10.1128/mSystems.00677-20; html:https://europepmc.org/articles/PMC7716389; pdf:https://europepmc.org/articles/PMC7716389?pdf=render
 34870259,https://doi.org/10.1016/j.xgen.2021.100005,Sequencing-based genome-wide association studies reporting standards.,"McMahon A, Lewis E, Buniello A, Cerezo M, Hall P, Sollis E, Parkinson H, Hindorff LA, Harris LW, MacArthur JAL.",,Cell genomics,2021,2021-10-01,Y,,,,"Genome sequencing has recently become a viable genotyping technology for use in genome-wide association studies (GWASs), offering the potential to analyze a broader range of genome-wide variation, including rare variants. To survey current standards, we assessed the content and quality of reporting of statistical methods, analyses, results, and datasets in 167 exome- or genome-wide-sequencing-based GWAS publications published from 2014 to 2020; 81% of publications included tests of aggregate association across multiple variants, with multiple test models frequently used. We observed a lack of standardized terms and incomplete reporting of datasets, particularly for variants analyzed in aggregate tests. We also find a lower frequency of sharing of summary statistics compared with array-based GWASs. Reporting standards and increased data sharing are required to ensure sequencing-based association study data are findable, interoperable, accessible, and reusable (FAIR). To support that, we recommend adopting the standard terminology of sequencing-based GWAS (seqGWAS). Further, we recommend that single-variant analyses be reported following the same standards and conventions as standard array-based GWASs and be shared in the GWAS Catalog. We also provide initial recommended standards for aggregate analyses metadata and summary statistics.",,doi:https://doi.org/10.1016/j.xgen.2021.100005; doi:https://doi.org/10.1016/j.xgen.2021.100005; html:https://europepmc.org/articles/PMC8637874; pdf:https://europepmc.org/articles/PMC8637874?pdf=render
 37840686,https://doi.org/10.3389/fdgth.2023.1184919,Understanding the performance and reliability of NLP tools: a comparison of four NLP tools predicting stroke phenotypes in radiology reports.,"Casey A, Davidson E, Grover C, Tobin R, Grivas A, Zhang H, Schrempf P, O'Neil AQ, Lee L, Walsh M, Pellie F, Ferguson K, Cvoro V, Wu H, Whalley H, Mair G, Whiteley W, Alex B.",,Frontiers in digital health,2023,2023-09-28,Y,Electronic Health Records; Natural Language Processing; Stroke Phenotype; Brain Radiology,,,"<h4>Background</h4>Natural language processing (NLP) has the potential to automate the reading of radiology reports, but there is a need to demonstrate that NLP methods are adaptable and reliable for use in real-world clinical applications.<h4>Methods</h4>We tested the F1 score, precision, and recall to compare NLP tools on a cohort from a study on delirium using images and radiology reports from NHS Fife and a population-based cohort (Generation Scotland) that spans multiple National Health Service health boards. We compared four off-the-shelf rule-based and neural NLP tools (namely, EdIE-R, ALARM+, ESPRESSO, and Sem-EHR) and reported on their performance for three cerebrovascular phenotypes, namely, ischaemic stroke, small vessel disease (SVD), and atrophy. Clinical experts from the EdIE-R team defined phenotypes using labelling techniques developed in the development of EdIE-R, in conjunction with an expert researcher who read underlying images.<h4>Results</h4>EdIE-R obtained the highest F1 score in both cohorts for ischaemic stroke, ≥93%, followed by ALARM+, ≥87%. The F1 score of ESPRESSO was ≥74%, whilst that of Sem-EHR is ≥66%, although ESPRESSO had the highest precision in both cohorts, 90% and 98%. For F1 scores for SVD, EdIE-R scored ≥98% and ALARM+ ≥90%. ESPRESSO scored lowest with ≥77% and Sem-EHR ≥81%. In NHS Fife, F1 scores for atrophy by EdIE-R and ALARM+ were 99%, dropping in Generation Scotland to 96% for EdIE-R and 91% for ALARM+. Sem-EHR performed lowest for atrophy at 89% in NHS Fife and 73% in Generation Scotland. When comparing NLP tool output with brain image reads using F1 scores, ALARM+ scored 80%, outperforming EdIE-R at 66% in ischaemic stroke. For SVD, EdIE-R performed best, scoring 84%, with Sem-EHR 82%. For atrophy, EdIE-R and both ALARM+ versions were comparable at 80%.<h4>Conclusions</h4>The four NLP tools show varying F1 (and precision/recall) scores across all three phenotypes, although more apparent for ischaemic stroke. If NLP tools are to be used in clinical settings, this cannot be performed ""out of the box."" It is essential to understand the context of their development to assess whether they are suitable for the task at hand or whether further training, re-training, or modification is required to adapt tools to the target task.",,pdf:https://www.frontiersin.org/articles/10.3389/fdgth.2023.1184919/pdf?isPublishedV2=False; doi:https://doi.org/10.3389/fdgth.2023.1184919; html:https://europepmc.org/articles/PMC10569314; pdf:https://europepmc.org/articles/PMC10569314?pdf=render
+30240446,https://doi.org/10.1371/journal.pone.0203896,Polygenic risk scores for major depressive disorder and neuroticism as predictors of antidepressant response: Meta-analysis of three treatment cohorts.,"Ward J, Graham N, Strawbridge RJ, Ferguson A, Jenkins G, Chen W, Hodgson K, Frye M, Weinshilboum R, Uher R, Lewis CM, Biernacka J, Smith DJ.",,PloS one,2018,2018-09-21,Y,,Better Care,,"There are currently no reliable approaches for correctly identifying which patients with major depressive disorder (MDD) will respond well to antidepressant therapy. However, recent genetic advances suggest that Polygenic Risk Scores (PRS) could allow MDD patients to be stratified for antidepressant response. We used PRS for MDD and PRS for neuroticism as putative predictors of antidepressant response within three treatment cohorts: The Genome-based Therapeutic Drugs for Depression (GENDEP) cohort, and 2 sub-cohorts from the Pharmacogenomics Research Network Antidepressant Medication Pharmacogenomics Study PRGN-AMPS (total patient number = 760). Results across cohorts were combined via meta-analysis within a random effects model. Overall, PRS for MDD and neuroticism did not significantly predict antidepressant response but there was a consistent direction of effect, whereby greater genetic loading for both MDD (best MDD result, p < 5*10-5 MDD-PRS at 4 weeks, β = -0.019, S.E = 0.008, p = 0.01) and neuroticism (best neuroticism result, p < 0.1 neuroticism-PRS at 8 weeks, β = -0.017, S.E = 0.008, p = 0.03) were associated with less favourable response. We conclude that the PRS approach may offer some promise for treatment stratification in MDD and should now be assessed within larger clinical cohorts.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0203896&type=printable; doi:https://doi.org/10.1371/journal.pone.0203896; html:https://europepmc.org/articles/PMC6150505; pdf:https://europepmc.org/articles/PMC6150505?pdf=render
 33280008,https://doi.org/10.1093/cercor/bhaa345,Hierarchical Complexity of the Macro-Scale Neonatal Brain.,"Blesa M, Galdi P, Cox SR, Sullivan G, Stoye DQ, Lamb GJ, Quigley AJ, Thrippleton MJ, Escudero J, Bastin ME, Smith KM, Boardman JP.",,"Cerebral cortex (New York, N.Y. : 1991)",2021,2021-03-01,Y,Newborn; Network Analysis; Developing Brain; Dmri; Structural Connectome; Hierarchical Complexity,,,"The human adult structural connectome has a rich nodal hierarchy, with highly diverse connectivity patterns aligned to the diverse range of functional specializations in the brain. The emergence of this hierarchical complexity in human development is unknown. Here, we substantiate the hierarchical tiers and hierarchical complexity of brain networks in the newborn period, assess correspondences with hierarchical complexity in adulthood, and investigate the effect of preterm birth, a leading cause of atypical brain development and later neurocognitive impairment, on hierarchical complexity. We report that neonatal and adult structural connectomes are both composed of distinct hierarchical tiers and that hierarchical complexity is greater in term born neonates than in preterms. This is due to diversity of connectivity patterns of regions within the intermediate tiers, which consist of regions that underlie sensorimotor processing and its integration with cognitive information. For neonates and adults, the highest tier (hub regions) is ordered, rather than complex, with more homogeneous connectivity patterns in structural hubs. This suggests that the brain develops first a more rigid structure in hub regions allowing for the development of greater and more diverse functional specialization in lower level regions, while connectivity underpinning this diversity is dysmature in infants born preterm.",,pdf:https://academic.oup.com/cercor/article-pdf/31/4/2071/36458400/bhaa345.pdf; doi:https://doi.org/10.1093/cercor/bhaa345; html:https://europepmc.org/articles/PMC7945030; pdf:https://europepmc.org/articles/PMC7945030?pdf=render
-37294923,https://doi.org/10.1093/eurjpc/zwad192,Incidence of 12 common cardiovascular diseases and subsequent mortality risk in the general population.,"Prugger C, Perier MC, Gonzalez-Izquierdo A, Hemingway H, Denaxas S, Empana JP.",,European journal of preventive cardiology,2023,2023-10-01,N,Prevention; Survival analysis; Stroke; epidemiology; Coronary Heart Disease; incidence,,,"<h4>Background</h4>Incident events of cardiovascular diseases (CVDs) are heterogenous and may result in different mortality risks. Such evidence may help inform patient and physician decisions in CVD prevention and risk factor management.<h4>Aims</h4>This study aimed to determine the extent to which incident events of common CVD show heterogeneous associations with subsequent mortality risk in the general population.<h4>Methods and results</h4>Based on England-wide linked electronic health records, we established a cohort of 1 310 518 people ≥30 years of age initially free of CVD and followed up for non-fatal events of 12 common CVD and cause-specific mortality. The 12 CVDs were considered as time-varying exposures in Cox's proportional hazards models to estimate hazard rate ratios (HRRs) with 95% confidence intervals (CIs). Over the median follow-up of 4.2 years (2010-16), 81 516 non-fatal CVD, 10 906 cardiovascular deaths, and 40 843 non-cardiovascular deaths occurred. All 12 CVDs were associated with increased risk of cardiovascular mortality, with HRR (95% CI) ranging from 1.67 (1.47-1.89) for stable angina to 7.85 (6.62-9.31) for haemorrhagic stroke. All 12 CVDs were also associated with increased non-cardiovascular and all-cause mortality risk but to a lesser extent: HRR (95% CI) ranged from 1.10 (1.00-1.22) to 4.55 (4.03-5.13) and from 1.24 (1.13-1.35) to 4.92 (4.44-5.46) for transient ischaemic attack and sudden cardiac arrest, respectively.<h4>Conclusion</h4>Incident events of 12 common CVD show significant adverse and markedly differential associations with subsequent cardiovascular, non-cardiovascular, and all-cause mortality risk in the general population.",,doi:https://doi.org/10.1093/eurjpc/zwad192
 36302124,https://doi.org/10.1080/21645515.2022.2127572,Comparative risk of cerebral venous sinus thrombosis (CVST) following COVID-19 vaccination or infection: A national cohort study using linked electronic health records.,"Ohaeri C, Thomas DR, Salmon J, Cottrell S, Lyons J, Akbari A, Lyons RA, Torabi F, Davies GG, Williams C.",,Human vaccines & immunotherapeutics,2022,2022-10-27,Y,Vaccines; Coronavirus; Cerebral Venous Sinus Thrombosis; Cerebral Venous Thrombosis; Covid19,,,"To inform the public and policy makers, we investigated and compared the risk of cerebral venous sinus thrombosis (CVST) after SARS-Cov-2 vaccination or infection using a national cohort of 2,643,699 individuals aged 17 y and above, alive, and resident in Wales on 1 January 2020 followed up through multiple linked data sources until 28 March 2021. Exposures were first dose of Oxford-ChAdOx1 or Pfizer-BioNTech vaccine or polymerase chain reaction (PCR)-confirmed SARS-Cov-2 infection. The outcome was an incident record of CVST. Hazard ratios (HR) were calculated using multivariable Cox regression, adjusted for confounders. HR from SARS-Cov-2 infection was compared with that for SARS-Cov-2 vaccination. We identified 910,556 (34.4%) records of first SARS-Cov-2 vaccination and 165,862 (6.3%) of SARS-Cov-2 infection. A total of 1,372 CVST events were recorded during the study period, of which 52 (3.8%) and 48 (3.5%) occurred within 28 d after vaccination and infection, respectively. We observed slight non-significant risk of CVST within 28 d of vaccination [aHR: 1.34, 95% CI: 0.95-1.90], which remained after stratifying by vaccine [BNT162b2, aHR: 1.18 (95% CI: 0.63-2.21); ChAdOx1, aHR: 1.40 (95% CI: 0.95-2.05)]. Three times the number of CVST events is observed within 28 d of a positive SARS-Cov-2 test [aHR: 3.02 (95% CI: 2.17-4.21)]. The risk of CVST following SARS-Cov-2 infection is 2.3 times that following SARS-Cov-2 vaccine. This is important information both for those designing COVID-19 vaccination programs and for individuals making their own informed decisions on the risk-benefit of vaccination. This record-linkage approach will be useful in monitoring the safety of future vaccine programs.",,doi:https://doi.org/10.1080/21645515.2022.2127572; doi:https://doi.org/10.1080/21645515.2022.2127572; html:https://europepmc.org/articles/PMC9746546; pdf:https://europepmc.org/articles/PMC9746546?pdf=render
-30240446,https://doi.org/10.1371/journal.pone.0203896,Polygenic risk scores for major depressive disorder and neuroticism as predictors of antidepressant response: Meta-analysis of three treatment cohorts.,"Ward J, Graham N, Strawbridge RJ, Ferguson A, Jenkins G, Chen W, Hodgson K, Frye M, Weinshilboum R, Uher R, Lewis CM, Biernacka J, Smith DJ.",,PloS one,2018,2018-09-21,Y,,Better Care,,"There are currently no reliable approaches for correctly identifying which patients with major depressive disorder (MDD) will respond well to antidepressant therapy. However, recent genetic advances suggest that Polygenic Risk Scores (PRS) could allow MDD patients to be stratified for antidepressant response. We used PRS for MDD and PRS for neuroticism as putative predictors of antidepressant response within three treatment cohorts: The Genome-based Therapeutic Drugs for Depression (GENDEP) cohort, and 2 sub-cohorts from the Pharmacogenomics Research Network Antidepressant Medication Pharmacogenomics Study PRGN-AMPS (total patient number = 760). Results across cohorts were combined via meta-analysis within a random effects model. Overall, PRS for MDD and neuroticism did not significantly predict antidepressant response but there was a consistent direction of effect, whereby greater genetic loading for both MDD (best MDD result, p < 5*10-5 MDD-PRS at 4 weeks, β = -0.019, S.E = 0.008, p = 0.01) and neuroticism (best neuroticism result, p < 0.1 neuroticism-PRS at 8 weeks, β = -0.017, S.E = 0.008, p = 0.03) were associated with less favourable response. We conclude that the PRS approach may offer some promise for treatment stratification in MDD and should now be assessed within larger clinical cohorts.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0203896&type=printable; doi:https://doi.org/10.1371/journal.pone.0203896; html:https://europepmc.org/articles/PMC6150505; pdf:https://europepmc.org/articles/PMC6150505?pdf=render
+37294923,https://doi.org/10.1093/eurjpc/zwad192,Incidence of 12 common cardiovascular diseases and subsequent mortality risk in the general population.,"Prugger C, Perier MC, Gonzalez-Izquierdo A, Hemingway H, Denaxas S, Empana JP.",,European journal of preventive cardiology,2023,2023-10-01,N,Prevention; Survival analysis; Stroke; epidemiology; Coronary Heart Disease; incidence,,,"<h4>Background</h4>Incident events of cardiovascular diseases (CVDs) are heterogenous and may result in different mortality risks. Such evidence may help inform patient and physician decisions in CVD prevention and risk factor management.<h4>Aims</h4>This study aimed to determine the extent to which incident events of common CVD show heterogeneous associations with subsequent mortality risk in the general population.<h4>Methods and results</h4>Based on England-wide linked electronic health records, we established a cohort of 1 310 518 people ≥30 years of age initially free of CVD and followed up for non-fatal events of 12 common CVD and cause-specific mortality. The 12 CVDs were considered as time-varying exposures in Cox's proportional hazards models to estimate hazard rate ratios (HRRs) with 95% confidence intervals (CIs). Over the median follow-up of 4.2 years (2010-16), 81 516 non-fatal CVD, 10 906 cardiovascular deaths, and 40 843 non-cardiovascular deaths occurred. All 12 CVDs were associated with increased risk of cardiovascular mortality, with HRR (95% CI) ranging from 1.67 (1.47-1.89) for stable angina to 7.85 (6.62-9.31) for haemorrhagic stroke. All 12 CVDs were also associated with increased non-cardiovascular and all-cause mortality risk but to a lesser extent: HRR (95% CI) ranged from 1.10 (1.00-1.22) to 4.55 (4.03-5.13) and from 1.24 (1.13-1.35) to 4.92 (4.44-5.46) for transient ischaemic attack and sudden cardiac arrest, respectively.<h4>Conclusion</h4>Incident events of 12 common CVD show significant adverse and markedly differential associations with subsequent cardiovascular, non-cardiovascular, and all-cause mortality risk in the general population.",,doi:https://doi.org/10.1093/eurjpc/zwad192
 38740716,https://doi.org/10.1007/s40266-024-01116-x,Associations Between Midlife Anticholinergic Medication Use and Subsequent Cognitive Decline: A British Birth Cohort Study.,"Rawle MJ, Lau WCY, Gonzalez-Izquierdo A, Patalay P, Richards M, Davis D.",,Drugs & aging,2024,2024-05-13,N,,,,"<h4>Background</h4>Anticholinergic medication use is associated with cognitive decline and incident dementia. Our study, a prospective birth cohort analysis, aimed to determine if repeated exposure to anticholinergic medications was associated with greater decline, and whether decline was reversed with medication reduction.<h4>Methods</h4>From the Medical Research Council (MRC) National Survey of Health and Development, a British birth cohort with all participants born in a single week of March 1946, we quantified anticholinergic exposure between ages 53 and 69 years using the Anticholinergic Cognitive Burden Scale (ACBS). We used multinomial regression to estimate associations with global cognition, quantified by the Addenbrooke's Cognitive Examination, 3<sup>rd</sup> Edition (ACE-III). Longitudinal associations between ACBS and cognitive test results (Verbal memory quantified by the Word Learning Test [WLT], and processing speed quantified by the Timed Letter Search Task [TLST]) at three time points (age 53, 60-64 and 69) were assessed using mixed and fixed effects linear regression models. Analyses were adjusted for sex, childhood cognition, education, chronic disease count and severity, and mental health symptoms.<h4>Results</h4>Anticholinergic exposure was associated cross-sectionally with lower ACE-III scores at age 69, with the greatest effects in those with high exposure at ages 60-64 (mean difference - 2.34, 95% confidence interval [CI] - 3.51 to - 1.17). Longitudinally, both mild-moderate and high ACBS scores were linked to lower WLT scores, again with high exposure showing larger effects (mean difference with contemporaneous exposure - 0.90, 95% CI - 1.63 to - 0.17; mean difference with lagged exposure - 1.53, 95% CI - 2.43 to - 0.64). Associations remained in fixed effects models (mean difference with contemporaneous exposure -1.78, 95% CI -2.85 to - 0.71; mean difference with lagged exposure - 2.23, 95% CI - 3.33 to - 1.13). Associations with TLST were noted only in isolated contemporaneous exposure (mean difference - 13.14, 95% CI - 19.04 to - 7.23; p < 0.01).<h4>Conclusions</h4>Anticholinergic exposure throughout mid and later life was associated with lower cognitive function. Reduced processing speed was associated only with contemporaneous anticholinergic medication use, and not historical use. Associations with lower verbal recall were evident with both historical and contemporaneous use of anticholinergic medication, and associations with historical use persisted in individuals even when their anticholinergic medication use decreased over the course of the study.",,doi:https://doi.org/10.1007/s40266-024-01116-x
 35277405,https://doi.org/10.1136/bmjopen-2021-055070,Predictors of falls and fractures leading to hospitalisation in 36 101 people with affective disorders: a large representative cohort study.,"Ma R, Perera G, Romano E, Vancampfort D, Koyanagi A, Stewart R, Mueller C, Stubbs B.",,BMJ open,2022,2022-03-11,Y,Mental health; Anxiety Disorders; Adult Psychiatry; Depression & Mood Disorders,,,"<h4>Objectives</h4>To investigate predictors of falls and fractures leading to hospitalisation in people with affective disorders.<h4>Design</h4>Cohort study.<h4>Setting</h4>The South London and Maudsley National Health Service (NHS) Foundation Trust (SLaM) Biomedical Research Centre (BRC) Case Register.<h4>Participants</h4>A large cohort of people with affective disorders (International Classification of Diseases- 10th version [ICD-10] codes F30-F34) diagnosed between January 2008 and March 2016 was assembled using data from the SLaM BRC Case Register.<h4>Primary and secondary outcome measures</h4>Falls and fractures leading to hospitalisation were ascertained from linked national hospitalisation data. Multivariable Cox proportional hazards analyses were administrated to identify predictors of first falls and fractures.<h4>Results</h4>Of 36 101 people with affective disorders (mean age 44.4 years, 60.2% female), 816 (incidence rate 9.91 per 1000 person-years) and 1117 (incidence rate 11.92 per 1000 person-years) experienced either a fall or fracture, respectively. In multivariable analyses, older age, analgesic use, increased physical illness burden, previous hospital admission due to certain comorbid physical illnesses and increase in attendances to accident and emergency services following diagnosis were significant risk factors for both falls and fractures. Having a history of falls was a strong risk factor for recurrent falls, and a previous fracture was also associated with future fractures.<h4>Conclusions</h4>Over a mean 5 years' follow-up, approximately 8% of people with affective disorders were hospitalised with a fall or fracture. Several similar factors were found to predict risk of falls and fracture, for example, older age, comorbid physical disorders and analgesic use. Routine screening for bone mineral density and fall prevention programmes should be considered for this clinical group.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/3/e055070.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-055070; html:https://europepmc.org/articles/PMC8919445; pdf:https://europepmc.org/articles/PMC8919445?pdf=render
 38563665,https://doi.org/10.1148/radiol.232455,Left Ventricular Trabeculations at Cardiac MRI: Reference Ranges and Association with Cardiovascular Risk Factors in UK Biobank.,"Aung N, Bartoli A, Rauseo E, Cortaredona S, Sanghvi MM, Fournel J, Ghattas B, Khanji MY, Petersen SE, Jacquier A.",,Radiology,2024,2024-04-01,N,,,,"Background The extent of left ventricular (LV) trabeculation and its relationship with cardiovascular (CV) risk factors is unclear. Purpose To apply automated segmentation to UK Biobank cardiac MRI scans to (<i>a</i>) assess the association between individual characteristics and CV risk factors and trabeculated LV mass (LVM) and (<i>b</i>) establish normal reference ranges in a selected group of healthy UK Biobank participants. Materials and Methods In this cross-sectional secondary analysis, prospectively collected data from the UK Biobank (2006 to 2010) were retrospectively analyzed. Automated segmentation of trabeculations was performed using a deep learning algorithm. After excluding individuals with known CV diseases, White adults without CV risk factors (reference group) and those with preexisting CV risk factors (hypertension, hyperlipidemia, diabetes mellitus, or smoking) (exposed group) were compared. Multivariable regression models, adjusted for potential confounders (age, sex, and height), were fitted to evaluate the associations between individual characteristics and CV risk factors and trabeculated LVM. Results Of 43 038 participants (mean age, 64 years ± 8 [SD]; 22 360 women), 28 672 individuals (mean age, 66 years ± 7; 14 918 men) were included in the exposed group, and 7384 individuals (mean age, 60 years ± 7; 4729 women) were included in the reference group. Higher body mass index (BMI) (β = 0.66 [95% CI: 0.63, 0.68]; <i>P</i> < .001), hypertension (β = 0.42 [95% CI: 0.36, 0.48]; <i>P</i> < .001), and higher physical activity level (β = 0.15 [95% CI: 0.12, 0.17]; <i>P</i> < .001) were associated with higher trabeculated LVM. In the reference group, the median trabeculated LVM was 6.3 g (IQR, 4.7-8.5 g) for men and 4.6 g (IQR, 3.4-6.0 g) for women. Median trabeculated LVM decreased with age for men from 6.5 g (IQR, 4.8-8.7 g) at age 45-50 years to 5.9 g (IQR, 4.3-7.8 g) at age 71-80 years (<i>P</i> = .03). Conclusion Higher trabeculated LVM was observed with hypertension, higher BMI, and higher physical activity level. Age- and sex-specific reference ranges of trabeculated LVM in a healthy middle-aged White population were established. © RSNA, 2024 <i>Supplemental material is available for this article.</i> See also the editorial by Kawel-Boehm in this issue.",,doi:https://doi.org/10.1148/radiol.232455
 37350492,https://doi.org/10.1093/eurheartj/ehad376,Troponin in early presenters to rule out myocardial infarction.,"Lowry MTH, Doudesis D, Boeddinghaus J, Kimenai DM, Bularga A, Taggart C, Wereski R, Ferry AV, Stewart SD, Tuck C, Koechlin L, Nestelberger T, Lopez-Ayala P, Huré G, Lee KK, Chapman AR, Newby DE, Anand A, Collinson PO, Mueller C, Mills NL, High-STEACS Investigators.",,European heart journal,2023,2023-08-01,Y,Myocardial infarction; cardiac troponin; Symptoms,,,"<h4>Aims</h4>Whether a single cardiac troponin measurement can safely rule out myocardial infarction in patients presenting within a few hours of symptom onset is uncertain. The study aim was to assess the performance of troponin in early presenters.<h4>Methods and results</h4>In patients with possible myocardial infarction, the diagnostic performance of a single measurement of high-sensitivity cardiac troponin I at presentation was evaluated and externally validated in those tested ≤3, 4-12, and >12 h from symptom onset. The limit-of-detection (2 ng/L), rule-out (5 ng/L), and sex-specific 99th centile (16 ng/L in women; 34 ng/L in men) thresholds were compared. In 41 103 consecutive patients [60 (17) years, 46% women], 12 595 (31%) presented within 3 h, and 3728 (9%) had myocardial infarction. In those presenting ≤3 h, a threshold of 2 ng/L had greater sensitivity and negative predictive value [99.4% (95% confidence interval 99.2%-99.5%) and 99.7% (99.6%-99.8%)] compared with 5 ng/L [96.5% (96.2%-96.8%) and 99.3% (99.1%-99.4%)]. In those presenting ≥3 h, the sensitivity and negative predictive value were similar for both thresholds. The sensitivity of the 99th centile was low in early and late presenters at 71.4% (70.6%-72.2%) and 92.5% (92.0%-93.0%), respectively. Findings were consistent in an external validation cohort of 7088 patients.<h4>Conclusion</h4>In early presenters, a single measurement of high-sensitivity cardiac troponin I below the limit of detection may facilitate the safe rule out of myocardial infarction. The 99th centile should not be used to rule out myocardial infarction at presentation even in those presenting later following symptom onset.",,pdf:https://academic.oup.com/eurheartj/advance-article-pdf/doi/10.1093/eurheartj/ehad376/50684614/ehad376.pdf; doi:https://doi.org/10.1093/eurheartj/ehad376; html:https://europepmc.org/articles/PMC10406338; pdf:https://europepmc.org/articles/PMC10406338?pdf=render
-35940584,https://doi.org/10.1123/pes.2021-0174,Clusters of Activity-Related Social and Physical Home Environmental Factors and Their Association With Children's Home-Based Physical Activity and Sitting.,"Sheldrick MP, Maitland C, Mackintosh KA, Rosenberg M, Griffiths LJ, Fry R, Stratton G.",,Pediatric exercise science,2023,2022-08-08,N,Families; Physical environment; Social Environment; Sedentary Behavior; Correlates; Screen Time,,,"<h4>Purpose</h4>Understanding which physical activity (PA) and sedentary behavior correlates cluster in children is important, particularly in the home, where children spend significant time. Therefore, this study aimed to assess clustering of physical and social activity-related factors at home, and whether these clusters are related to home-based sitting and PA in children. A secondary aim was to explore whether the clusters were associated with child, parent, and family characteristics.<h4>Methods</h4>Altogether, 235 children (55% girls, mean age = 10.2 [0.7] y) and their parents took part. Physical (eg, PA and electronic media equipment, house and garden size, layout) and social (eg, activity preferences, priorities, parental rules) home environmental factors were obtained via the HomeSPACE-II audit and self-report, respectively. Principal component analysis was used to identify clusters of physical and social environmental factors. Backward regression analysis and partial correlations were used to examine relationships between clusters, children's device-measured home-based activity behaviors, and background characteristics.<h4>Results</h4>The findings show that physical and social environment activity-related factors at home cluster. The clusters were associated with several background characteristics, with socioeconomic factors appearing to be particularly influential. The clusters were also associated with home-based activity behaviors in the hypothesized directions.<h4>Conclusion</h4>Interventions which target clusters of social and physical factors at home, especially among low-socioeconomic status families, are warranted.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa60257/Download/60257__24327__e83f9d0502424e5e9075c668a2672db1.pdf; doi:https://doi.org/10.1123/pes.2021-0174
 32460529,https://doi.org/10.1161/circimaging.119.010389,Novel Approach to Imaging Active Takayasu Arteritis Using Somatostatin Receptor Positron Emission Tomography/Magnetic Resonance Imaging.,"Tarkin JM, Wall C, Gopalan D, Aloj L, Manavaki R, Fryer TD, Aboagye EO, Bennett MR, Peters JE, Rudd JHF, Mason JC.",,Circulation. Cardiovascular imaging,2020,2020-05-28,N,Positron emission tomography; Vasculitis; Aortic Diseases; Molecular Imaging; Takayasu Arteritis,,,,,pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCIMAGING.119.010389; doi:https://doi.org/10.1161/CIRCIMAGING.119.010389; html:https://europepmc.org/articles/PMC7610536; pdf:https://europepmc.org/articles/PMC7610536?pdf=render; doi:https://doi.org/10.1161/circimaging.119.010389
-39002770,https://doi.org/10.1016/j.ijid.2024.107169,"Incidence and mortality rates of 14 site-specific infectious diseases in 10 diverse areas of China: findings from China Kadoorie Biobank, 2006-2018.","Huang R, Kartsonaki C, Turnbull I, Pei P, Chen Y, Liu J, Du H, Sun D, Yang L, Barnard M, Lv J, Yu C, Chen J, Li L, Chen Z, Bragg F.",,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2024,2024-07-11,N,China; Infectious diseases; Mortality; Hospitalization; incidence; Case Fatality,,,"<h4>Background</h4>Infectious diseases remain a major global health concern, including in China, with an estimated >10 million cases of infectious disease in 2019. We describe the burden of site-specific infectious diseases among Chinese adults.<h4>Methods</h4>From 2004 to 2008, the prospective China Kadoorie Biobank enrolled 512,726 adults aged 30-79 years from 10 diverse areas (5 rural, 5 urban) of China. During the 12 years of follow-up, 101,673 participants were hospitalized for any infectious disease. Descriptive analyses examined standardized incidence, mortality and case fatality of infections.<h4>Findings</h4>The incidence of any infectious disease was 1856 per 100,000 person-years; respiratory tract infections (1069) were most common. The infectious disease mortality rate was 31.8 per 100,000 person-years (20.3 and 9.4 for respiratory and non-respiratory infections, respectively) and case fatality was 2.2% (2.6% and 1.6% for respiratory and non-respiratory infections, respectively). Infectious disease incidence and mortality rates were higher at older ages and in rural areas. There were no clear sex differences in infectious disease incidence rates, but mortality and case fatality rates were twice as high in men as in women.<h4>Interpretation</h4>Infectious diseases were common in Chinese adults. The observed burden of, and disparities in, site-specific infections can inform targeted prevention efforts.<h4>Funding</h4>Kadoorie Foundation, Wellcome Trust, MRC, BHF, CR-UK, MoST, NNSF.",,doi:https://doi.org/10.1016/j.ijid.2024.107169
+35940584,https://doi.org/10.1123/pes.2021-0174,Clusters of Activity-Related Social and Physical Home Environmental Factors and Their Association With Children's Home-Based Physical Activity and Sitting.,"Sheldrick MP, Maitland C, Mackintosh KA, Rosenberg M, Griffiths LJ, Fry R, Stratton G.",,Pediatric exercise science,2023,2022-08-08,N,Families; Physical environment; Social Environment; Sedentary Behavior; Correlates; Screen Time,,,"<h4>Purpose</h4>Understanding which physical activity (PA) and sedentary behavior correlates cluster in children is important, particularly in the home, where children spend significant time. Therefore, this study aimed to assess clustering of physical and social activity-related factors at home, and whether these clusters are related to home-based sitting and PA in children. A secondary aim was to explore whether the clusters were associated with child, parent, and family characteristics.<h4>Methods</h4>Altogether, 235 children (55% girls, mean age = 10.2 [0.7] y) and their parents took part. Physical (eg, PA and electronic media equipment, house and garden size, layout) and social (eg, activity preferences, priorities, parental rules) home environmental factors were obtained via the HomeSPACE-II audit and self-report, respectively. Principal component analysis was used to identify clusters of physical and social environmental factors. Backward regression analysis and partial correlations were used to examine relationships between clusters, children's device-measured home-based activity behaviors, and background characteristics.<h4>Results</h4>The findings show that physical and social environment activity-related factors at home cluster. The clusters were associated with several background characteristics, with socioeconomic factors appearing to be particularly influential. The clusters were also associated with home-based activity behaviors in the hypothesized directions.<h4>Conclusion</h4>Interventions which target clusters of social and physical factors at home, especially among low-socioeconomic status families, are warranted.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa60257/Download/60257__24327__e83f9d0502424e5e9075c668a2672db1.pdf; doi:https://doi.org/10.1123/pes.2021-0174
 37367415,https://doi.org/10.3390/jcdd10060250,Risk Factors of Secondary Cardiovascular Events in a Multi-Ethnic Asian Population with Acute Myocardial Infarction: A Retrospective Cohort Study from Malaysia.,"Ismail SR, Mohammad MSF, Butterworth AS, Chowdhury R, Danesh J, Di Angelantonio E, Griffin SJ, Pennells L, Wood AM, Md Noh MF, Shah SA.",,Journal of cardiovascular development and disease,2023,2023-06-09,Y,Myocardial infarction; risk factors; Asian; Cardiovascular Mortality; Major Adverse Cardiovascular Events,,,"This retrospective cohort study investigated the incidence and risk factors of major adverse cardiovascular events (MACE) after 1 year of first-documented myocardial infarctions (MIs) in a multi-ethnic Asian population. Secondary MACE were observed in 231 (14.3%) individuals, including 92 (5.7%) cardiovascular-related deaths. Both histories of hypertension and diabetes were associated with secondary MACE after adjustment for age, sex, and ethnicity (HR 1.60 [95%CI 1.22-2.12] and 1.46 [95%CI 1.09-1.97], respectively). With further adjustments for traditional risk factors, individuals with conduction disturbances demonstrated higher risks of MACE: new left-bundle branch block (HR 2.86 [95%CI 1.15-6.55]), right-bundle branch block (HR 2.09 [95%CI 1.02-4.29]), and second-degree heart block (HR 2.45 [95%CI 0.59-10.16]). These associations were broadly similar across different age, sex, and ethnicity groups, although somewhat greater for history of hypertension and BMI among women versus men, for HbA1c control in individuals aged >50 years, and for LVEF ≤ 40% in those with Indian versus Chinese or Bumiputera ethnicities. Several traditional and cardiac risk factors are associated with a higher risk of secondary major adverse cardiovascular events. In addition to hypertension and diabetes, the identification of conduction disturbances in individuals with first-onset MI may be useful for the risk stratification of high-risk individuals.",,pdf:https://www.mdpi.com/2308-3425/10/6/250/pdf?version=1686288586; doi:https://doi.org/10.3390/jcdd10060250; html:https://europepmc.org/articles/PMC10299045; pdf:https://europepmc.org/articles/PMC10299045?pdf=render
+39002770,https://doi.org/10.1016/j.ijid.2024.107169,"Incidence and mortality rates of 14 site-specific infectious diseases in 10 diverse areas of China: findings from China Kadoorie Biobank, 2006-2018.","Huang R, Kartsonaki C, Turnbull I, Pei P, Chen Y, Liu J, Du H, Sun D, Yang L, Barnard M, Lv J, Yu C, Chen J, Li L, Chen Z, Bragg F.",,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2024,2024-07-11,N,China; Infectious diseases; Mortality; Hospitalization; incidence; Case Fatality,,,"<h4>Background</h4>Infectious diseases remain a major global health concern, including in China, with an estimated >10 million cases of infectious disease in 2019. We describe the burden of site-specific infectious diseases among Chinese adults.<h4>Methods</h4>From 2004 to 2008, the prospective China Kadoorie Biobank enrolled 512,726 adults aged 30-79 years from 10 diverse areas (5 rural, 5 urban) of China. During the 12 years of follow-up, 101,673 participants were hospitalized for any infectious disease. Descriptive analyses examined standardized incidence, mortality and case fatality of infections.<h4>Findings</h4>The incidence of any infectious disease was 1856 per 100,000 person-years; respiratory tract infections (1069) were most common. The infectious disease mortality rate was 31.8 per 100,000 person-years (20.3 and 9.4 for respiratory and non-respiratory infections, respectively) and case fatality was 2.2% (2.6% and 1.6% for respiratory and non-respiratory infections, respectively). Infectious disease incidence and mortality rates were higher at older ages and in rural areas. There were no clear sex differences in infectious disease incidence rates, but mortality and case fatality rates were twice as high in men as in women.<h4>Interpretation</h4>Infectious diseases were common in Chinese adults. The observed burden of, and disparities in, site-specific infections can inform targeted prevention efforts.<h4>Funding</h4>Kadoorie Foundation, Wellcome Trust, MRC, BHF, CR-UK, MoST, NNSF.",,doi:https://doi.org/10.1016/j.ijid.2024.107169
 32398093,https://doi.org/10.1186/s13063-020-04329-8,Access to routinely collected health data for clinical trials - review of successful data requests to UK registries.,"Lensen S, Macnair A, Love SB, Yorke-Edwards V, Noor NM, Martyn M, Blenkinsop A, Diaz-Montana C, Powell G, Williamson E, Carpenter J, Sydes MR.",,Trials,2020,2020-05-12,Y,Systematic review; Rct; Registry; Routinely Collected Health Data,,,"<h4>Background</h4>Clinical trials generally each collect their own data despite routinely collected health data (RCHD) increasing in quality and breadth. Our aim is to quantify UK-based randomised controlled trials (RCTs) accessing RCHD for participant data, characterise how these data are used and thereby recommend how more trials could use RCHD.<h4>Methods</h4>We conducted a systematic review of RCTs accessing RCHD from at least one registry in the UK between 2013 and 2018 for the purposes of informing or supplementing participant data. A list of all registries holding RCHD in the UK was compiled. In cases where registries published release registers, these were searched for RCTs accessing RCHD. Where no release register was available, registries were contacted to request a list of RCTs. For each identified RCT, information was collected from all publicly available sources (release registers, websites, protocol etc.). The search and data extraction were undertaken between January and May 2019.<h4>Results</h4>We identified 160 RCTs accessing RCHD between 2013 and 2018 from a total of 22 registries; this corresponds to only a very small proportion of all UK RCTs (about 3%). RCTs accessing RCHD were generally large (median sample size 1590), commonly evaluating treatments for cancer or cardiovascular disease. Most of the included RCTs accessed RCHD from NHS Digital (68%), and the most frequently accessed datasets were mortality (76%) and hospital visits (55%). RCHD was used to inform the primary trial (82%) and long-term follow-up (57%). There was substantial variation in how RCTs used RCHD to inform participant outcome measures. A limitation was the lack of information and transparency from registries and RCTs with respect to which datasets have been accessed and for what purposes.<h4>Conclusions</h4>In the last five years, only a small minority of UK-based RCTs have accessed RCHD to inform participant data. We ask for improved accessibility, confirmed data quality and joined-up thinking between the registries and the regulatory authorities.<h4>Trial registration</h4>PROSPERO CRD42019123088.",,pdf:https://trialsjournal.biomedcentral.com/track/pdf/10.1186/s13063-020-04329-8; doi:https://doi.org/10.1186/s13063-020-04329-8; html:https://europepmc.org/articles/PMC7218527; pdf:https://europepmc.org/articles/PMC7218527?pdf=render
 35055401,https://doi.org/10.3390/jpm12010086,Predicting Hospital Readmission for Campylobacteriosis from Electronic Health Records: A Machine Learning and Text Mining Perspective.,"Zhou SM, Lyons RA, Rahman MA, Holborow A, Brophy S.",,Journal of personalized medicine,2022,2022-01-10,Y,Hospitalisation; Feature Selection; Machine Learning; Readmission; Electronic Health Records; Text Mining; Campylobacter Infections,,,"(1) Background: This study investigates influential risk factors for predicting 30-day readmission to hospital for Campylobacter infections (CI). (2) Methods: We linked general practitioner and hospital admission records of 13,006 patients with CI in Wales (1990-2015). An approach called TF-zR (term frequency-zRelevance) technique was presented to evaluates how relevant a clinical term is to a patient in a cohort characterized by coded health records. The zR is a supervised term-weighting metric to assign weight to a term based on relative frequencies of the term across different classes. Cost-sensitive classifier with swarm optimization and weighted subset learning was integrated to identify influential clinical signals as predictors and optimal model for readmission prediction. (3) Results: From a pool of up to 17,506 variables, 33 most predictive factors were identified, including age, gender, Townsend deprivation quintiles, comorbidities, medications, and procedures. The predictive model predicted readmission with 73% sensitivity and 54% specificity. Variables associated with readmission included male gender, recurrent tonsillitis, non-healing open wounds, operation for in-gown toenails. Cystitis, paracetamol/codeine use, age (21-25), and heliclear triple pack use, were associated with a lower risk of readmission. (4) Conclusions: This study gives a profile of clustered variables that are predictive of readmission associated with campylobacteriosis.",,pdf:https://www.mdpi.com/2075-4426/12/1/86/pdf?version=1641832520; doi:https://doi.org/10.3390/jpm12010086; html:https://europepmc.org/articles/PMC8779953; pdf:https://europepmc.org/articles/PMC8779953?pdf=render
 36813664,https://doi.org/10.1016/j.injury.2023.02.029,Friction burns in cyclists: An under-recognised problem.,"Tracy LM, Gabbe BJ, Beck B.",,Injury,2023,2023-02-15,N,Cycling; Australia; Burn; New Zealand; Registry; Friction,,,"<h4>Introduction</h4>Cycling-related friction burns, also known as abrasions or ""road rash"", can occur when cyclists are involved in a fall or a collision. However, less is known about this type of injury as they are often overshadowed by concurrent traumatic and/or orthopaedic injuries. The aims of this project were to describe the nature and severity of friction burns in cyclists admitted to hospitals with specialist burn services in Australia and New Zealand.<h4>Methods</h4>A review of cycling-related friction burns recorded by the Burns Registry of Australia and New Zealand was undertaken. Summary statistics described demographic, injury event and severity, and in-hospital management data for this cohort of patients.<h4>Results</h4>Between July 2009 and June 2021, 143 cycling-related friction burn admissions were identified (accounting for 0.4% of all burns admissions during the study period). Seventy-six percent of patients with a cycling-related friction burn were male, and the median (interquartile range) of patients was 14 (5-41) years. The greatest proportion of cycling-related friction burns were attributed to non-collision events, namely falls (44% of all cases) and body parts being caught or coming into contact with the bicycle (27% of all cases). Although 89% of patients had a burn affecting less than five percent of their body, 71% of patients underwent a burn wound management procedure in theatre such as debridement and/or skin grafting.<h4>Conclusions</h4>In summary, friction burns in cyclists admitted to participating services were rare. Despite this, there remains opportunities to better understand these events to inform the development of interventions to reduce burn injury in cyclists.",,doi:https://doi.org/10.1016/j.injury.2023.02.029
@@ -1106,38 +1108,38 @@ PMC10686417,https://doi.org/,The impact of restricted provision of publicly fund
 32103533,https://doi.org/10.1002/sim.8503,Propensity scores using missingness pattern information: a practical guide.,"Blake HA, Leyrat C, Mansfield KE, Seaman S, Tomlinson LA, Carpenter J, Williamson EJ.",,Statistics in medicine,2020,2020-02-27,N,Electronic Health Records; Propensity Score Analysis; Missingness Pattern; Missing Indicator; Missing Confounder Data,,,"Electronic health records are a valuable data source for investigating health-related questions, and propensity score analysis has become an increasingly popular approach to address confounding bias in such investigations. However, because electronic health records are typically routinely recorded as part of standard clinical care, there are often missing values, particularly for potential confounders. In our motivating study-using electronic health records to investigate the effect of renin-angiotensin system blockers on the risk of acute kidney injury-two key confounders, ethnicity and chronic kidney disease stage, have 59% and 53% missing data, respectively. The missingness pattern approach (MPA), a variant of the missing indicator approach, has been proposed as a method for handling partially observed confounders in propensity score analysis. In the MPA, propensity scores are estimated separately for each missingness pattern present in the data. Although the assumptions underlying the validity of the MPA are stated in the literature, it can be difficult in practice to assess their plausibility. In this article, we explore the MPA's underlying assumptions by using causal diagrams to assess their plausibility in a range of simple scenarios, drawing general conclusions about situations in which they are likely to be violated. We present a framework providing practical guidance for assessing whether the MPA's assumptions are plausible in a particular setting and thus deciding when the MPA is appropriate. We apply our framework to our motivating study, showing that the MPA's underlying assumptions appear reasonable, and we demonstrate the application of MPA to this study.",,pdf:https://researchonline.lshtm.ac.uk/id/eprint/4656008/1/manuscript.pdf; doi:https://doi.org/10.1002/sim.8503; html:https://europepmc.org/articles/PMC7612316; pdf:https://europepmc.org/articles/PMC7612316?pdf=render; doi:https://doi.org/10.1002/sim.8503
 36525457,https://doi.org/10.1371/journal.pone.0279250,Undergoing radical treatment for prostate cancer and its impact on wellbeing: A qualitative study exploring men's experiences.,"Vyas N, Brunckhorst O, Fox L, Van Hemelrijck M, Muir G, Stewart R, Dasgupta P, Ahmed K.",,PloS one,2022,2022-12-16,Y,,,,"<h4>Introduction</h4>Quality of life in prostate cancer survivorship is becoming increasingly important, with mental and social wellbeing recognised as key components. However, limited global evaluation of psychosocial challenges experienced after treatment exists. Therefore, we aimed to explore the lived experiences of men who underwent radical treatment, and its psychosocial impact.<h4>Material and methods</h4>This qualitative study was conducted using 19 men who had undergone radical treatment (prostatectomy or radiotherapy) for their cancer. Semi-structured interviews were conducted exploring lived experiences of men after treatment. A Structured thematic analysis of collected data was undertaken, with an inductive co-construction of themes through the lens of the biopsychosocial model. Themes generated were considered within a psychological, social, and physical wellbeing framework.<h4>Results</h4>An initial knowledge gap meant mental wellbeing was strongly impacted initially leading to a 'Diagnostic Blow and the Search for Clarity'. Doubt over individuals' future resulted in 'An Uncertain Future' in many men. Once treatment was completed a 'Reflective journey' began, with men considering their outcomes and decisions made. Social wellbeing was also impacted with many identifying the 'Emotional Repercussions' on their relationships and the impact their diagnosis had on their partner and family. Many subsequently sought to increase their support through 'The Social Network and Advocacy', while physical changes led to an increased need for 'Social Planning'. Finally, physical wellbeing was highlighted by a continual acknowledgement of the 'Natural process of ageing' leading to a reluctancy to seek help, whilst simultaneously attempting to improve existing health via 'The Health Kick'.<h4>Conclusions</h4>Radical treatments have a considerable impact on mental and social wellbeing of individuals. Anxiety after diagnosis and significant uncertainty over individual futures exist, with physical complications of treatment leading to social repercussions. Future research should aim to identify forms of support to improve quality of life of these men.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0279250&type=printable; doi:https://doi.org/10.1371/journal.pone.0279250; html:https://europepmc.org/articles/PMC9757548; pdf:https://europepmc.org/articles/PMC9757548?pdf=render
 35297226,https://doi.org/10.1002/jcsm.12971,Association of shorter leucocyte telomere length with risk of frailty.,"Bountziouka V, Nelson CP, Codd V, Wang Q, Musicha C, Allara E, Kaptoge S, Di Angelantonio E, Butterworth AS, Thompson JR, Curtis EM, Wood AM, Danesh JN, Harvey NC, Cooper C, Samani NJ.",,"Journal of cachexia, sarcopenia and muscle",2022,2022-03-17,Y,Frailty; Biological Age; Uk Biobank; Leucocyte Telomere Length,,,"<h4>Background</h4>Frailty is a multidimensional syndrome of decline that affects multiple systems and predisposes to adverse health outcomes. Although chronological age is the major risk factor, inter-individual variation in risk is not fully understood. Leucocyte telomere length (LTL), a proposed marker of biological age, has been associated with risk of many diseases. We sought to determine whether LTL is associated with risk of frailty.<h4>Methods</h4>We utilized cross-sectional data from 441 781 UK Biobank participants (aged 40-69 years), with complete data on frailty indicators and LTL. Frailty was defined as the presence of at least three of five indicators: weaker grip strength, slower walking pace, weight loss in the past year, lower physical activity, and exhaustion in the past 2 weeks. LTL was measured using a validated qPCR method and reported as a ratio of the telomere repeat number (T) to a single-copy gene (S) (T/S ratio). Association of LTL with frailty was evaluated using adjusted (chronological age, sex, deprivation, smoking, alcohol intake, body mass index, and multimorbidity) multinomial and ordinal regression models, and results are presented as relative risk (RRR) or odds ratios (OR), respectively, alongside the 95% confidence interval (CI). Mendelian randomization (MR), using 131 genetic variants associated with LTL, was used to assess if the association of LTL with frailty was causal.<h4>Results</h4>Frail participants (4.6%) were older (median age difference (95% CI): 3 (2.5; 3.5) years, P = 2.73 × 10<sup>-33</sup> ), more likely to be female (61%, P = 1.97 × 10<sup>-129</sup> ), and had shorter LTL (-0.13SD vs. 0.03SD, P = 5.43 × 10<sup>-111</sup> ) than non-frail. In adjusted analyses, both age and LTL were associated with frailty (RRR = 1.03 (95% CI: 1.02; 1.04) per year of older chronological age, P = 3.99 × 10<sup>-12</sup> ; 1.10 (1.08; 1.11) per SD shorter LTL, P = 1.46 × 10<sup>-30</sup> ). Within each age group (40-49, 50-59, 60-69 years), the prevalence of frailty was about 33% higher in participants with shorter (-2SD) versus longer telomeres (+2SD). MR analysis showed an association of LTL with frailty that was directionally consistent with the observational association, but not statistically significant (MR-Median: OR (95% CI): 1.08 (0.98; 1.19) per SD shorter LTL, P = 0.13).<h4>Conclusions</h4>Inter-individual variation in LTL is associated with the risk of frailty independently of chronological age and other risk factors. Our findings provide evidence for an additional biological determinant of frailty.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jcsm.12971; doi:https://doi.org/10.1002/jcsm.12971; html:https://europepmc.org/articles/PMC9178164; pdf:https://europepmc.org/articles/PMC9178164?pdf=render
-36564466,https://doi.org/10.1038/s41598-022-26141-x,Assessing and removing the effect of unwanted technical variations in microbiome data.,"Fachrul M, Méric G, Inouye M, Pamp SJ, Salim A.",,Scientific reports,2022,2022-12-23,Y,,,,"Varying technologies and experimental approaches used in microbiome studies often lead to irreproducible results due to unwanted technical variations. Such variations, often unaccounted for and of unknown source, may interfere with true biological signals, resulting in misleading biological conclusions. In this work, we aim to characterize the major sources of technical variations in microbiome data and demonstrate how in-silico approaches can minimize their impact. We analyzed 184 pig faecal metagenomes encompassing 21 specific combinations of deliberately introduced factors of technical and biological variations. Using the novel Removing Unwanted Variations-III-Negative Binomial (RUV-III-NB), we identified several known experimental factors, specifically storage conditions and freeze-thaw cycles, as likely major sources of unwanted variation in metagenomes. We also observed that these unwanted technical variations do not affect taxa uniformly, with freezing samples affecting taxa of class Bacteroidia the most, for example. Additionally, we benchmarked the performances of different correction methods, including ComBat, ComBat-seq, RUVg, RUVs, and RUV-III-NB. While RUV-III-NB performed consistently robust across our sensitivity and specificity metrics, most other methods did not remove unwanted variations optimally. Our analyses suggest that a careful consideration of possible technical confounders is critical during experimental design of microbiome studies, and that the inclusion of technical replicates is necessary to efficiently remove unwanted variations computationally.",,pdf:https://www.nature.com/articles/s41598-022-26141-x.pdf; doi:https://doi.org/10.1038/s41598-022-26141-x; html:https://europepmc.org/articles/PMC9789116; pdf:https://europepmc.org/articles/PMC9789116?pdf=render
 38069915,https://doi.org/10.1093/clinchem/hvad205,Multiple Cardiac Biomarkers to Improve Prediction of Cardiovascular Events: Findings from the Generation Scotland Scottish Family Health Study.,"Welsh P, Kimenai DM, Shah ASV, Gadd DA, Marioni RE, Woodward M, Sudlow CLM, Campbell A, Cleland JGF, Pellicori P, Hayward C, Mills NL, Sattar N.",,Clinical chemistry,2024,2024-02-01,N,,,,"<h4>Background</h4>Many studies have investigated whether single cardiac biomarkers improve cardiovascular risk prediction for primary prevention but whether a combined approach could further improve risk prediction is unclear. We aimed to test a sex-specific, combined cardiac biomarker approach for cardiovascular risk prediction.<h4>Methods</h4>In the Generation Scotland Scottish Family Health Study, N-terminal pro-B-type natriuretic peptide (NT-proBNP), growth differentiation factor-15 (GDF-15), cardiac troponin I (cTnI), cardiac troponin T (cTnT), and C-reactive protein (CRP) were measured in stored serum using automated immunoassays. Sex-specific Cox models that included SCORE2 risk factors evaluated addition of single and combined biomarkers for prediction of major adverse cardiovascular events (MACE). Combined biomarker models were compared to a baseline model that included SCORE2 risk factors.<h4>Results</h4>The study population comprised 18 383 individuals (58.9% women, median age of 48 years [25th-75th percentile, 35-58 years]). During the median follow up of 11.6 (25th-75th percentile, 10.8-13.0) years, MACE occurred in 942 (5.1%) individuals. The greatest increase in discrimination with addition of individual biomarkers to the base model was for women GDF-15 and for men NT-proBNP (change in c-index: + 0.010 for women and +0.005 for men). For women, combined biomarker models that included GDF-15 and NT-proBNP (+0.012) or GDF-15 and cTnI (+0.013), but not CRP or cTnT, further improved discrimination. For men, combined biomarker models that included NT-proBNP and GDF-15 (+0.007), NT-proBNP and cTnI (+0.006), or NT-proBNP and CRP (+0.008), but not cTnT, further improved discrimination.<h4>Conclusions</h4>A combined biomarker approach, particularly the use of GDF-15, NT-proBNP and cTnI, further refined cardiovascular risk estimates.",,doi:https://doi.org/10.1093/clinchem/hvad205
+36564466,https://doi.org/10.1038/s41598-022-26141-x,Assessing and removing the effect of unwanted technical variations in microbiome data.,"Fachrul M, Méric G, Inouye M, Pamp SJ, Salim A.",,Scientific reports,2022,2022-12-23,Y,,,,"Varying technologies and experimental approaches used in microbiome studies often lead to irreproducible results due to unwanted technical variations. Such variations, often unaccounted for and of unknown source, may interfere with true biological signals, resulting in misleading biological conclusions. In this work, we aim to characterize the major sources of technical variations in microbiome data and demonstrate how in-silico approaches can minimize their impact. We analyzed 184 pig faecal metagenomes encompassing 21 specific combinations of deliberately introduced factors of technical and biological variations. Using the novel Removing Unwanted Variations-III-Negative Binomial (RUV-III-NB), we identified several known experimental factors, specifically storage conditions and freeze-thaw cycles, as likely major sources of unwanted variation in metagenomes. We also observed that these unwanted technical variations do not affect taxa uniformly, with freezing samples affecting taxa of class Bacteroidia the most, for example. Additionally, we benchmarked the performances of different correction methods, including ComBat, ComBat-seq, RUVg, RUVs, and RUV-III-NB. While RUV-III-NB performed consistently robust across our sensitivity and specificity metrics, most other methods did not remove unwanted variations optimally. Our analyses suggest that a careful consideration of possible technical confounders is critical during experimental design of microbiome studies, and that the inclusion of technical replicates is necessary to efficiently remove unwanted variations computationally.",,pdf:https://www.nature.com/articles/s41598-022-26141-x.pdf; doi:https://doi.org/10.1038/s41598-022-26141-x; html:https://europepmc.org/articles/PMC9789116; pdf:https://europepmc.org/articles/PMC9789116?pdf=render
 32788201,https://doi.org/10.1136/archdischild-2020-319027,Predictive value of indicators for identifying child maltreatment and intimate partner violence in coded electronic health records: a systematic review and meta-analysis.,"Syed S, Ashwick R, Schlosser M, Gonzalez-Izquierdo A, Li L, Gilbert R.",,Archives of disease in childhood,2021,2020-08-11,Y,Data collection; epidemiology; Child Abuse; Health Services Research; Drug Withdrawal,,,"<h4>Objective</h4>Electronic health records (EHRs) are routinely used to identify family violence, yet reliable evidence of their validity remains limited. We conducted a systematic review and meta-analysis to evaluate the positive predictive values (PPVs) of coded indicators in EHRs for identifying intimate partner violence (IPV) and child maltreatment (CM), including prenatal neglect.<h4>Methods</h4>We searched 18 electronic databases between January 1980 and May 2020 for studies comparing any coded indicator of IPV or CM including prenatal neglect defined as neonatal abstinence syndrome (NAS) or fetal alcohol syndrome (FAS), against an independent reference standard. We pooled PPVs for each indicator using random effects meta-analyses.<h4>Results</h4>We included 88 studies (3 875 183 individuals) involving 15 indicators for identifying CM in the prenatal period and childhood (0-18 years) and five indicators for IPV among women of reproductive age (12-50 years). Based on the International Classification of Disease system, the pooled PPV was over 80% for NAS (16 studies) but lower for FAS (<40%; seven studies). For young children, primary diagnoses of CM, specific injury presentations (eg, rib fractures and retinal haemorrhages) and assaults showed a high PPV for CM (pooled PPVs: 55.9%-87.8%). Indicators of IPV in women had a high PPV, with primary diagnoses correctly identifying IPV in >85% of cases.<h4>Conclusions</h4>Coded indicators in EHRs have a high likelihood of correctly classifying types of CM and IPV across the life course, providing a useful tool for assessment, support and monitoring of high-risk groups in health services and research.",,pdf:https://adc.bmj.com/content/archdischild/106/1/44.full.pdf; doi:https://doi.org/10.1136/archdischild-2020-319027; html:https://europepmc.org/articles/PMC7788194; pdf:https://europepmc.org/articles/PMC7788194?pdf=render
-39170762,https://doi.org/10.2196/preprints.42449,Charting a course for smartphones and wearables to transform population health research.,"Dixon WG, van der Veer SN, Ali SM, Laidlaw L, Dobson RJ, Sudlow C, Chico T, MacArthur JA, Doherty A.",,Journal of medical Internet research,2023,2023-02-07,N,,,,"The use of data from smartphones and wearable devices has huge potential for population health research given high device ownership, the range of novel health-relevant data types available from consumer devices, and the frequency and duration over which data are, or could be, collected. Yet the uptake and success of large-scale mobile health research in the last decade has not matched the hyped opportunity. We make the argument that digital person-generated health data is required and necessary to answer many top priority research questions through illustrative examples taken from the James Lind Alliance Priority Setting Partnership. We then summarise the findings from two UK initiatives that considered the challenges and possible solutions for what needs to be done, and in what way, to realise the future opportunities of digital person-generated health data for clinically important population health research. Examples of important areas to be addressed to advance the field include digital inequality and addressing possible selection bias, easy access for researchers to the appropriate data collection tools including how best to harmonise data items, analysis methodology for time series data, methods for patient and public involvement and engagement to optimise recruitment, retention and public trust, and providing greater control of their data to research participants. There is also a major opportunity through the linkage of digital persongenerated health data to routinely-collected data to support novel population health research, bringing together clinician-reported and patient-reported measures. We recognise that well conducted studies need a wide range of diverse challenges to be skilfully addressed in unison: for example, epidemiology, data science and biostatistics, psychometrics, behavioural and social science, software engineering, user interface design, information governance, data management and patient and public involvement and engagement. Consequently, progress would be accelerated by the establishment of a new interdisciplinary community where all relevant and necessary skills are brought together to allow excellence throughout the lifecycle of a research study. This will require a partnership of diverse people, of methods and of technology. Get this right and the synergy has the potential to transform many millions of people's lives for the better.",,doi:https://doi.org/10.2196/preprints.42449
 36571960,https://doi.org/10.1016/j.bjps.2022.11.049,Artificial intelligence in the management and treatment of burns: A systematic review and meta-analyses.,"Taib BG, Karwath A, Wensley K, Minku L, Gkoutos GV, Moiemen N.",,"Journal of plastic, reconstructive & aesthetic surgery : JPRAS",2023,2022-11-23,N,Burns; Systematic review; Machine Learning (Ml); Artificial Intelligence (Ai); Diagnostic Test Meta Analyses,,,"<h4>Introduction and aim</h4>Artificial Intelligence (AI) is already being successfully employed to aid the interpretation of multiple facets of burns care. In the light of the growing influence of AI, this systematic review and diagnostic test accuracy meta-analyses aim to appraise and summarise the current direction of research in this field.<h4>Method</h4>A systematic literature review was conducted of relevant studies published between 1990 and 2021, yielding 35 studies. Twelve studies were suitable for a Diagnostic Test Meta-Analyses.<h4>Results</h4>The studies generally focussed on burn depth (Accuracy 68.9%-95.4%, Sensitivity 90.8% and Specificity 84.4%), burn segmentation (Accuracy 76.0%-99.4%, Sensitivity 97.9% and specificity 97.6%) and burn related mortality (Accuracy >90%-97.5% Sensitivity 92.9% and specificity 93.4%). Neural networks were the most common machine learning (ML) algorithm utilised in 69% of the studies. The QUADAS-2 tool identified significant heterogeneity between studies.<h4>Discussion</h4>The potential application of AI in the management of burns patients is promising, especially given its propitious results across a spectrum of dimensions, including burn depth, size, mortality, related sepsis and acute kidney injuries. The accuracy of the results analysed within this study is comparable to current practices in burns care.<h4>Conclusion</h4>The application of AI in the treatment and management of burns patients, as a series of point of care diagnostic adjuncts, is promising. Whilst AI is a potentially valuable tool, a full evaluation of its current utility and potential is limited by significant variations in research methodology and reporting.",,doi:https://doi.org/10.1016/j.bjps.2022.11.049
+39170762,https://doi.org/10.2196/preprints.42449,Charting a course for smartphones and wearables to transform population health research.,"Dixon WG, van der Veer SN, Ali SM, Laidlaw L, Dobson RJ, Sudlow C, Chico T, MacArthur JA, Doherty A.",,Journal of medical Internet research,2023,2023-02-07,N,,,,"The use of data from smartphones and wearable devices has huge potential for population health research given high device ownership, the range of novel health-relevant data types available from consumer devices, and the frequency and duration over which data are, or could be, collected. Yet the uptake and success of large-scale mobile health research in the last decade has not matched the hyped opportunity. We make the argument that digital person-generated health data is required and necessary to answer many top priority research questions through illustrative examples taken from the James Lind Alliance Priority Setting Partnership. We then summarise the findings from two UK initiatives that considered the challenges and possible solutions for what needs to be done, and in what way, to realise the future opportunities of digital person-generated health data for clinically important population health research. Examples of important areas to be addressed to advance the field include digital inequality and addressing possible selection bias, easy access for researchers to the appropriate data collection tools including how best to harmonise data items, analysis methodology for time series data, methods for patient and public involvement and engagement to optimise recruitment, retention and public trust, and providing greater control of their data to research participants. There is also a major opportunity through the linkage of digital persongenerated health data to routinely-collected data to support novel population health research, bringing together clinician-reported and patient-reported measures. We recognise that well conducted studies need a wide range of diverse challenges to be skilfully addressed in unison: for example, epidemiology, data science and biostatistics, psychometrics, behavioural and social science, software engineering, user interface design, information governance, data management and patient and public involvement and engagement. Consequently, progress would be accelerated by the establishment of a new interdisciplinary community where all relevant and necessary skills are brought together to allow excellence throughout the lifecycle of a research study. This will require a partnership of diverse people, of methods and of technology. Get this right and the synergy has the potential to transform many millions of people's lives for the better.",,doi:https://doi.org/10.2196/preprints.42449
 39053458,https://doi.org/10.1016/j.ajhg.2024.06.017,Misexpression of inactive genes in whole blood is associated with nearby rare structural variants.,"Vanderstichele T, Burnham KL, de Klein N, Tardaguila M, Howell B, Walter K, Kundu K, Koeppel J, Lee W, Tokolyi A, Persyn E, Nath AP, Marten J, Petrovski S, Roberts DJ, Di Angelantonio E, Danesh J, Berton A, Platt A, Butterworth AS, Soranzo N, Parts L, Inouye M, Paul DS, Davenport EE.",,American journal of human genetics,2024,2024-07-24,Y,ectopic expression; Misexpression; Aberrant Expression; Structural Variants; Transcriptional Readthrough; Transcript Fusion; Transcriptomic Outlier,,,"Gene misexpression is the aberrant transcription of a gene in a context where it is usually inactive. Despite its known pathological consequences in specific rare diseases, we have a limited understanding of its wider prevalence and mechanisms in humans. To address this, we analyzed gene misexpression in 4,568 whole-blood bulk RNA sequencing samples from INTERVAL study blood donors. We found that while individual misexpression events occur rarely, in aggregate they were found in almost all samples and a third of inactive protein-coding genes. Using 2,821 paired whole-genome and RNA sequencing samples, we identified that misexpression events are enriched in cis for rare structural variants. We established putative mechanisms through which a subset of SVs lead to gene misexpression, including transcriptional readthrough, transcript fusions, and gene inversion. Overall, we develop misexpression as a type of transcriptomic outlier analysis and extend our understanding of the variety of mechanisms by which genetic variants can influence gene expression.",,doi:https://doi.org/10.1101/2023.11.17.567537; doi:https://doi.org/10.1016/j.ajhg.2024.06.017; html:https://europepmc.org/articles/PMC11339615; pdf:https://europepmc.org/articles/PMC11339615?pdf=render
 34571200,https://doi.org/10.1016/j.jaip.2021.09.026,Atopic Eczema-Associated Fracture Risk and Oral Corticosteroids: A Population-Based Cohort Study.,"Matthewman J, Mansfield KE, Prieto-Alhambra D, Mulick AR, Smeeth L, Lowe KE, Silverwood RJ, Langan SM.",,The journal of allergy and clinical immunology. In practice,2022,2021-09-24,Y,Fracture; Atopic Eczema; Atopic Dermatitis; osteoporotic fracture; Oral Corticosteroids,,,"<h4>Background</h4>Evidence suggests adults with atopic eczema have increased fracture risk. However, it is unclear whether oral corticosteroids explain the association.<h4>Objective</h4>To assess to what extent oral corticosteroids mediate the relationship between atopic eczema and fractures.<h4>Methods</h4>We conducted a cohort study using English primary care (Clinical Practice Research Datalink) and hospital admissions (Hospital Episode Statistics) records (1998-2016) including adults (18 years old and older) with atopic eczema matched (age, sex, and general practice) with up to 5 adults without atopic eczema. We used Cox regression to estimate hazard ratios (HRs) for specific major osteoporotic fractures (hip, spine, pelvis, or wrist) and for any-site fracture comparing individuals with atopic eczema with those without, adjusting for 6 different definitions of time-updated oral corticosteroid use (ever any prescription, ever high-dose, and recent, cumulative, current, or peak dose).<h4>Results</h4>We identified 526,808 individuals with atopic eczema and 2,569,030 without. We saw evidence of an association between atopic eczema and major osteoporotic fractures (eg, spine HR 1.15, 99% CI 1.08-1.22; hip HR 1.11, 99% CI 1.08-1.15) that remained after additionally adjusting for oral corticosteroids (eg, cumulative corticosteroid dose: spine HR 1.09, 99% CI 1.03-1.16; hip HR 1.09, 99% CI 1.06-1.12). Fracture rates were higher in people with severe atopic eczema than in people without even after adjusting for oral corticosteroids (eg, spine HR [99% CI]: confounder-adjusted 2.31 [1.91-2.81]; additionally adjusted for cumulative dose 1.71 [1.40-2.09]).<h4>Conclusions</h4>Our findings suggest that little of the association between atopic eczema and major osteoporotic fractures is explained by oral corticosteroid use.",,pdf:http://www.jaci-inpractice.org/article/S2213219821010187/pdf; doi:https://doi.org/10.1016/j.jaip.2021.09.026; html:https://europepmc.org/articles/PMC7612204; pdf:https://europepmc.org/articles/PMC7612204?pdf=render
 33306026,https://doi.org/10.2196/23369,Engagement With a Behavior Change App for Alcohol Reduction: Data Visualization for Longitudinal Observational Study.,"Bell L, Garnett C, Qian T, Perski O, Williamson E, Potts HW.",,Journal of medical Internet research,2020,2020-12-11,Y,Engagement; Behavior Change; Apps; Mobile Health; Digital Health; Just-in-time Adaptive Interventions; Push Notifications; Micro-randomized Trial; Data Visualizations,,,"<h4>Background</h4>Behavior change apps can develop iteratively, where the app evolves into a complex, dynamic, or personalized intervention through cycles of research, development, and implementation. Understanding how existing users engage with an app (eg, frequency, amount, depth, and duration of use) can help guide further incremental improvements. We aim to explore how simple visualizations can provide a good understanding of temporal patterns of engagement, as usage data are often longitudinal and rich.<h4>Objective</h4>This study aims to visualize behavioral engagement with Drink Less, a behavior change app to help reduce hazardous and harmful alcohol consumption in the general adult population of the United Kingdom.<h4>Methods</h4>We explored behavioral engagement among 19,233 existing users of Drink Less. Users were included in the sample if they were from the United Kingdom; were 18 years or older; were interested in reducing their alcohol consumption; had a baseline Alcohol Use Disorders Identification Test score of 8 or above, indicative of excessive drinking; and had downloaded the app between May 17, 2017, and January 22, 2019 (615 days). Measures of when sessions begin, length of sessions, time to disengagement, and patterns of use were visualized with heat maps, timeline plots, k-modes clustering analyses, and Kaplan-Meier plots.<h4>Results</h4>The daily 11 AM notification is strongly associated with a change in engagement in the following hour; reduction in behavioral engagement over time, with 50.00% (9617/19,233) of users disengaging (defined as no use for 7 or more consecutive days) 22 days after download; identification of 3 distinct trajectories of use, namely engagers (4651/19,233, 24.18% of users), slow disengagers (3679/19,233, 19.13% of users), and fast disengagers (10,903/19,233, 56.68% of users); and limited depth of engagement with 85.076% (7,095,348/8,340,005) of screen views occurring within the Self-monitoring and Feedback module. In addition, a peak of both frequency and amount of time spent per session was observed in the evenings.<h4>Conclusions</h4>Visualizations play an important role in understanding engagement with behavior change apps. Here, we discuss how simple visualizations helped identify important patterns of engagement with Drink Less. Our visualizations of behavioral engagement suggest that the daily notification substantially impacts engagement. Furthermore, the visualizations suggest that a fixed notification policy can be effective for maintaining engagement for some users but ineffective for others. We conclude that optimizing the notification policy to target both effectiveness and engagement is a worthwhile investment. Our future goal is to both understand the causal effect of the notification on engagement and further optimize the notification policy within Drink Less by tailoring to contextual circumstances of individuals over time. Such tailoring will be informed from the findings of our micro-randomized trial (MRT), and these visualizations were useful in both gaining a better understanding of engagement and designing the MRT.",,pdf:https://www.jmir.org/2020/12/e23369/PDF; doi:https://doi.org/10.2196/23369; html:https://europepmc.org/articles/PMC7762688
 31104603,https://doi.org/10.1098/rstb.2018.0276,Outbreak analytics: a developing data science for informing the response to emerging pathogens.,"Polonsky JA, Baidjoe A, Kamvar ZN, Cori A, Durski K, Edmunds WJ, Eggo RM, Funk S, Kaiser L, Keating P, de Waroux OLP, Marks M, Moraga P, Morgan O, Nouvellet P, Ratnayake R, Roberts CH, Whitworth J, Jombart T.",,"Philosophical transactions of the Royal Society of London. Series B, Biological sciences",2019,2019-07-01,Y,Methods; Software; epidemics; Infectious; pipeline; Tools,Applied Analytics,,"Despite continued efforts to improve health systems worldwide, emerging pathogen epidemics remain a major public health concern. Effective response to such outbreaks relies on timely intervention, ideally informed by all available sources of data. The collection, visualization and analysis of outbreak data are becoming increasingly complex, owing to the diversity in types of data, questions and available methods to address them. Recent advances have led to the rise of outbreak analytics, an emerging data science focused on the technological and methodological aspects of the outbreak data pipeline, from collection to analysis, modelling and reporting to inform outbreak response. In this article, we assess the current state of the field. After laying out the context of outbreak response, we critically review the most common analytics components, their inter-dependencies, data requirements and the type of information they can provide to inform operations in real time. We discuss some challenges and opportunities and conclude on the potential role of outbreak analytics for improving our understanding of, and response to outbreaks of emerging pathogens. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'. This theme issue is linked with the earlier issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'.",,pdf:https://royalsocietypublishing.org/doi/pdf/10.1098/rstb.2018.0276; doi:https://doi.org/10.1098/rstb.2018.0276; html:https://europepmc.org/articles/PMC6558557; pdf:https://europepmc.org/articles/PMC6558557?pdf=render
-39453837,https://doi.org/10.1056/nejmoa2409183,Long-Term Effects of Empagliflozin in Patients with Chronic Kidney Disease.,"EMPA-KIDNEY Collaborative Group, Herrington WG, Staplin N, Agrawal N, Wanner C, Green JB, Hauske SJ, Emberson JR, Preiss D, Judge P, Zhu D, Dayanandan R, Arimoto R, Mayne KJ, Ng SYA, Sammons E, Hill M, Stevens W, Wallendszus K, Brenner S, Cheung AK, Liu ZH, Li J, Hooi LS, Liu W, Kadowaki T, Nangaku M, Levin A, Cherney DZI, Maggioni AP, Pontremoli R, Deo R, Goto S, Rossello X, Tuttle KR, Steubl D, Massey D, Brueckmann M, Landray MJ, Baigent C, Haynes R.",,The New England journal of medicine,2024,2024-10-25,Y,,,,"<h4>Background</h4>In the EMPA-KIDNEY trial, empagliflozin, a sodium-glucose cotransporter 2 (SGLT2) inhibitor, had positive cardiorenal effects in patients with chronic kidney disease who were at risk for disease progression. Post-trial follow-up was designed to assess how the effects of empagliflozin would evolve after the discontinuation of the trial drug.<h4>Methods</h4>In the active trial, patients with chronic kidney disease were randomly assigned to receive either empagliflozin (10 mg once daily) or matching placebo and were followed for a median of 2 years. All the patients had an estimated glomerular filtration rate (eGFR) of at least 20 but less than 45 ml per minute per 1.73 m<sup>2</sup> of body-surface area or an eGFR of at least 45 but less than 90 ml per minute per 1.73 m<sup>2</sup> with a urinary albumin-to-creatinine ratio (with albumin measured in milligrams and creatinine measured in grams) of at least 200. Subsequently, surviving patients who consented were observed for 2 additional years. No trial empagliflozin or placebo was administered during the post-trial period, but local practitioners could prescribe open-label SGLT2 inhibitors, including open-label empagliflozin. The primary composite outcome was kidney disease progression or cardiovascular death as assessed from the start of the active-trial period to the end of the post-trial period.<h4>Results</h4>Of the 6609 patients who had undergone randomization in the active trial, 4891 (74%) were enrolled in the post-trial period. During this period, the use of open-label SGLT2 inhibitors was similar in the two groups (43% in the empagliflozin group and 40% in the placebo group). During the combined active- and post-trial periods, a primary-outcome event occurred in 865 of 3304 patients (26.2%) in the empagliflozin group and in 1001 of 3305 patients (30.3%) in the placebo group (hazard ratio, 0.79; 95% confidence interval [CI], 0.72 to 0.87). During the post-trial period only, the hazard ratio for a primary-outcome event was 0.87 (95% CI, 0.76 to 0.99). During the combined periods, the risk of kidney disease progression was 23.5% in the empagliflozin group and 27.1% in the placebo group; the risk of the composite of death or end-stage kidney disease was 16.9% and 19.6%, respectively; and the risk of cardiovascular death was 3.8% and 4.9%, respectively. There was no effect of empagliflozin on death from noncardiovascular causes (5.3% in both groups).<h4>Conclusions</h4>In a broad range of patients with chronic kidney disease at risk for progression, empagliflozin continued to have additional cardiorenal benefits for up to 12 months after it was discontinued. (Funded by Boehringer Ingelheim and others; EMPA-KIDNEY ClinicalTrials.gov number, NCT03594110; EuDRACT number, 2017-002971-24.).",,doi:https://doi.org/10.1056/NEJMoa2409183; html:https://europepmc.org/articles/PMC7616743; pdf:https://europepmc.org/articles/PMC7616743?pdf=render
-35143670,https://doi.org/10.1093/molbev/msac034,The Carbon Footprint of Bioinformatics.,"Grealey J, Lannelongue L, Saw WY, Marten J, Méric G, Ruiz-Carmona S, Inouye M.",,Molecular biology and evolution,2022,2022-03-01,Y,Bioinformatics; Genomics; Carbon Footprint; Green Algorithms,,,"Bioinformatic research relies on large-scale computational infrastructures which have a nonzero carbon footprint but so far, no study has quantified the environmental costs of bioinformatic tools and commonly run analyses. In this work, we estimate the carbon footprint of bioinformatics (in kilograms of CO2 equivalent units, kgCO2e) using the freely available Green Algorithms calculator (www.green-algorithms.org, last accessed 2022). We assessed 1) bioinformatic approaches in genome-wide association studies (GWAS), RNA sequencing, genome assembly, metagenomics, phylogenetics, and molecular simulations, as well as 2) computation strategies, such as parallelization, CPU (central processing unit) versus GPU (graphics processing unit), cloud versus local computing infrastructure, and geography. In particular, we found that biobank-scale GWAS emitted substantial kgCO2e and simple software upgrades could make it greener, for example, upgrading from BOLT-LMM v1 to v2.3 reduced carbon footprint by 73%. Moreover, switching from the average data center to a more efficient one can reduce carbon footprint by approximately 34%. Memory over-allocation can also be a substantial contributor to an algorithm's greenhouse gas emissions. The use of faster processors or greater parallelization reduces running time but can lead to greater carbon footprint. Finally, we provide guidance on how researchers can reduce power consumption and minimize kgCO2e. Overall, this work elucidates the carbon footprint of common analyses in bioinformatics and provides solutions which empower a move toward greener research.",,pdf:https://academic.oup.com/mbe/article-pdf/39/3/msac034/42692776/msac034.pdf; doi:https://doi.org/10.1093/molbev/msac034; html:https://europepmc.org/articles/PMC8892942; pdf:https://europepmc.org/articles/PMC8892942?pdf=render
+36299367,https://doi.org/10.1183/23120541.00211-2022,Mortality associated with metabolic syndrome in people with COPD managed in primary care.,"Karsanji U, Evans RA, Quint JK, Khunti K, Lawson CA, Petherick E, Greening NJ, Singh SJ, Richardson M, Steiner MC.",,ERJ open research,2022,2022-10-24,Y,,,,"<h4>Objective</h4>The prevalence of metabolic syndrome (MetS) has been reported to be higher in selected populations of people with COPD. The impact of MetS on mortality in COPD is unknown. We used routinely collected healthcare data to estimate the prevalence of MetS in people with COPD managed in primary care and determine its impact on 5-year mortality.<h4>Methods</h4>Records from 103 955 patients with COPD from the Clinical Practice Research Datalink (CPRD-GOLD) between 2009 to 2017 were scrutinised. MetS was defined as the presence of three or more of: obesity, hypertension, lowered high-density lipoprotein cholesterol, elevated triglycerides or type 2 diabetes mellitus (T2DM). Univariate and multivariable Cox regression models were constructed to determine the prognostic impact of MetS on 5-year mortality. Similar univariate models were constructed for individual components of the definition of MetS.<h4>Results</h4>The prevalence of MetS in the COPD cohort was 10.1%. Univariate analyses showed the presence of MetS increased mortality (hazard ratio (HR) 1.19, 95% CI: 1.12-1.27, p<0.001), but this risk was substantially attenuated in the multivariable analysis (HR 1.06, 95% CI: 0.99-1.13, p<i>=</i>0.085). The presence of hypertension (HR 1.70, 95% CI: 1.63-1.77, p<0.001) and T2DM (HR 1.41, 95% CI: 1.34-1.48, p<0.001) increased and obesity (HR 0.74, 95% CI: 0.71-0.78, p<0.001) reduced mortality risk.<h4>Conclusion</h4>MetS in patients with COPD is associated with higher 5-year mortality, but this impact was minimal when adjusted for indices of COPD disease severity and other comorbidities. Individual components of the MetS definition exerted differential impacts on mortality suggesting limitation to the use of MetS as a multicomponent condition in predicting outcome in COPD.",,pdf:https://openres.ersjournals.com/content/erjor/8/4/00211-2022.full.pdf; doi:https://doi.org/10.1183/23120541.00211-2022; html:https://europepmc.org/articles/PMC9589337; pdf:https://europepmc.org/articles/PMC9589337?pdf=render
 34543272,https://doi.org/10.1371/journal.pcbi.1009324,Ten simple rules to make your computing more environmentally sustainable.,"Lannelongue L, Grealey J, Bateman A, Inouye M.",,PLoS computational biology,2021,2021-09-20,Y,,,,,,pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009324&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1009324; html:https://europepmc.org/articles/PMC8452068; pdf:https://europepmc.org/articles/PMC8452068?pdf=render
+35143670,https://doi.org/10.1093/molbev/msac034,The Carbon Footprint of Bioinformatics.,"Grealey J, Lannelongue L, Saw WY, Marten J, Méric G, Ruiz-Carmona S, Inouye M.",,Molecular biology and evolution,2022,2022-03-01,Y,Bioinformatics; Genomics; Carbon Footprint; Green Algorithms,,,"Bioinformatic research relies on large-scale computational infrastructures which have a nonzero carbon footprint but so far, no study has quantified the environmental costs of bioinformatic tools and commonly run analyses. In this work, we estimate the carbon footprint of bioinformatics (in kilograms of CO2 equivalent units, kgCO2e) using the freely available Green Algorithms calculator (www.green-algorithms.org, last accessed 2022). We assessed 1) bioinformatic approaches in genome-wide association studies (GWAS), RNA sequencing, genome assembly, metagenomics, phylogenetics, and molecular simulations, as well as 2) computation strategies, such as parallelization, CPU (central processing unit) versus GPU (graphics processing unit), cloud versus local computing infrastructure, and geography. In particular, we found that biobank-scale GWAS emitted substantial kgCO2e and simple software upgrades could make it greener, for example, upgrading from BOLT-LMM v1 to v2.3 reduced carbon footprint by 73%. Moreover, switching from the average data center to a more efficient one can reduce carbon footprint by approximately 34%. Memory over-allocation can also be a substantial contributor to an algorithm's greenhouse gas emissions. The use of faster processors or greater parallelization reduces running time but can lead to greater carbon footprint. Finally, we provide guidance on how researchers can reduce power consumption and minimize kgCO2e. Overall, this work elucidates the carbon footprint of common analyses in bioinformatics and provides solutions which empower a move toward greener research.",,pdf:https://academic.oup.com/mbe/article-pdf/39/3/msac034/42692776/msac034.pdf; doi:https://doi.org/10.1093/molbev/msac034; html:https://europepmc.org/articles/PMC8892942; pdf:https://europepmc.org/articles/PMC8892942?pdf=render
+39453837,https://doi.org/10.1056/nejmoa2409183,Long-Term Effects of Empagliflozin in Patients with Chronic Kidney Disease.,"EMPA-KIDNEY Collaborative Group, Herrington WG, Staplin N, Agrawal N, Wanner C, Green JB, Hauske SJ, Emberson JR, Preiss D, Judge P, Zhu D, Dayanandan R, Arimoto R, Mayne KJ, Ng SYA, Sammons E, Hill M, Stevens W, Wallendszus K, Brenner S, Cheung AK, Liu ZH, Li J, Hooi LS, Liu W, Kadowaki T, Nangaku M, Levin A, Cherney DZI, Maggioni AP, Pontremoli R, Deo R, Goto S, Rossello X, Tuttle KR, Steubl D, Massey D, Brueckmann M, Landray MJ, Baigent C, Haynes R.",,The New England journal of medicine,2024,2024-10-25,Y,,,,"<h4>Background</h4>In the EMPA-KIDNEY trial, empagliflozin, a sodium-glucose cotransporter 2 (SGLT2) inhibitor, had positive cardiorenal effects in patients with chronic kidney disease who were at risk for disease progression. Post-trial follow-up was designed to assess how the effects of empagliflozin would evolve after the discontinuation of the trial drug.<h4>Methods</h4>In the active trial, patients with chronic kidney disease were randomly assigned to receive either empagliflozin (10 mg once daily) or matching placebo and were followed for a median of 2 years. All the patients had an estimated glomerular filtration rate (eGFR) of at least 20 but less than 45 ml per minute per 1.73 m<sup>2</sup> of body-surface area or an eGFR of at least 45 but less than 90 ml per minute per 1.73 m<sup>2</sup> with a urinary albumin-to-creatinine ratio (with albumin measured in milligrams and creatinine measured in grams) of at least 200. Subsequently, surviving patients who consented were observed for 2 additional years. No trial empagliflozin or placebo was administered during the post-trial period, but local practitioners could prescribe open-label SGLT2 inhibitors, including open-label empagliflozin. The primary composite outcome was kidney disease progression or cardiovascular death as assessed from the start of the active-trial period to the end of the post-trial period.<h4>Results</h4>Of the 6609 patients who had undergone randomization in the active trial, 4891 (74%) were enrolled in the post-trial period. During this period, the use of open-label SGLT2 inhibitors was similar in the two groups (43% in the empagliflozin group and 40% in the placebo group). During the combined active- and post-trial periods, a primary-outcome event occurred in 865 of 3304 patients (26.2%) in the empagliflozin group and in 1001 of 3305 patients (30.3%) in the placebo group (hazard ratio, 0.79; 95% confidence interval [CI], 0.72 to 0.87). During the post-trial period only, the hazard ratio for a primary-outcome event was 0.87 (95% CI, 0.76 to 0.99). During the combined periods, the risk of kidney disease progression was 23.5% in the empagliflozin group and 27.1% in the placebo group; the risk of the composite of death or end-stage kidney disease was 16.9% and 19.6%, respectively; and the risk of cardiovascular death was 3.8% and 4.9%, respectively. There was no effect of empagliflozin on death from noncardiovascular causes (5.3% in both groups).<h4>Conclusions</h4>In a broad range of patients with chronic kidney disease at risk for progression, empagliflozin continued to have additional cardiorenal benefits for up to 12 months after it was discontinued. (Funded by Boehringer Ingelheim and others; EMPA-KIDNEY ClinicalTrials.gov number, NCT03594110; EuDRACT number, 2017-002971-24.).",,doi:https://doi.org/10.1056/NEJMoa2409183; html:https://europepmc.org/articles/PMC7616743; pdf:https://europepmc.org/articles/PMC7616743?pdf=render
 37794871,https://doi.org/10.1093/ehjdh/ztad044,An artificial intelligence tool for automated analysis of large-scale unstructured clinical cine cardiac magnetic resonance databases.,"Mariscal-Harana J, Asher C, Vergani V, Rizvi M, Keehn L, Kim RJ, Judd RM, Petersen SE, Razavi R, King AP, Ruijsink B, Puyol-Antón E.",,European heart journal. Digital health,2023,2023-07-13,Y,Artificial intelligence; Quality control; Cardiac function; Cardiac Segmentation; Cardiac Magnetic Resonance,,,"<h4>Aims</h4>Artificial intelligence (AI) techniques have been proposed for automating analysis of short-axis (SAX) cine cardiac magnetic resonance (CMR), but no CMR analysis tool exists to automatically analyse large (unstructured) clinical CMR datasets. We develop and validate a robust AI tool for start-to-end automatic quantification of cardiac function from SAX cine CMR in large clinical databases.<h4>Methods and results</h4>Our pipeline for processing and analysing CMR databases includes automated steps to identify the correct data, robust image pre-processing, an AI algorithm for biventricular segmentation of SAX CMR and estimation of functional biomarkers, and automated post-analysis quality control to detect and correct errors. The segmentation algorithm was trained on 2793 CMR scans from two NHS hospitals and validated on additional cases from this dataset (<i>n</i> = 414) and five external datasets (<i>n</i> = 6888), including scans of patients with a range of diseases acquired at 12 different centres using CMR scanners from all major vendors. Median absolute errors in cardiac biomarkers were within the range of inter-observer variability: <8.4 mL (left ventricle volume), <9.2 mL (right ventricle volume), <13.3 g (left ventricular mass), and <5.9% (ejection fraction) across all datasets. Stratification of cases according to phenotypes of cardiac disease and scanner vendors showed good performance across all groups.<h4>Conclusion</h4>We show that our proposed tool, which combines image pre-processing steps, a domain-generalizable AI algorithm trained on a large-scale multi-domain CMR dataset and quality control steps, allows robust analysis of (clinical or research) databases from multiple centres, vendors, and cardiac diseases. This enables translation of our tool for use in fully automated processing of large multi-centre databases.",,pdf:https://academic.oup.com/ehjdh/advance-article-pdf/doi/10.1093/ehjdh/ztad044/50878931/ztad044.pdf; doi:https://doi.org/10.1093/ehjdh/ztad044; html:https://europepmc.org/articles/PMC10545512; pdf:https://europepmc.org/articles/PMC10545512?pdf=render
-36299367,https://doi.org/10.1183/23120541.00211-2022,Mortality associated with metabolic syndrome in people with COPD managed in primary care.,"Karsanji U, Evans RA, Quint JK, Khunti K, Lawson CA, Petherick E, Greening NJ, Singh SJ, Richardson M, Steiner MC.",,ERJ open research,2022,2022-10-24,Y,,,,"<h4>Objective</h4>The prevalence of metabolic syndrome (MetS) has been reported to be higher in selected populations of people with COPD. The impact of MetS on mortality in COPD is unknown. We used routinely collected healthcare data to estimate the prevalence of MetS in people with COPD managed in primary care and determine its impact on 5-year mortality.<h4>Methods</h4>Records from 103 955 patients with COPD from the Clinical Practice Research Datalink (CPRD-GOLD) between 2009 to 2017 were scrutinised. MetS was defined as the presence of three or more of: obesity, hypertension, lowered high-density lipoprotein cholesterol, elevated triglycerides or type 2 diabetes mellitus (T2DM). Univariate and multivariable Cox regression models were constructed to determine the prognostic impact of MetS on 5-year mortality. Similar univariate models were constructed for individual components of the definition of MetS.<h4>Results</h4>The prevalence of MetS in the COPD cohort was 10.1%. Univariate analyses showed the presence of MetS increased mortality (hazard ratio (HR) 1.19, 95% CI: 1.12-1.27, p<0.001), but this risk was substantially attenuated in the multivariable analysis (HR 1.06, 95% CI: 0.99-1.13, p<i>=</i>0.085). The presence of hypertension (HR 1.70, 95% CI: 1.63-1.77, p<0.001) and T2DM (HR 1.41, 95% CI: 1.34-1.48, p<0.001) increased and obesity (HR 0.74, 95% CI: 0.71-0.78, p<0.001) reduced mortality risk.<h4>Conclusion</h4>MetS in patients with COPD is associated with higher 5-year mortality, but this impact was minimal when adjusted for indices of COPD disease severity and other comorbidities. Individual components of the MetS definition exerted differential impacts on mortality suggesting limitation to the use of MetS as a multicomponent condition in predicting outcome in COPD.",,pdf:https://openres.ersjournals.com/content/erjor/8/4/00211-2022.full.pdf; doi:https://doi.org/10.1183/23120541.00211-2022; html:https://europepmc.org/articles/PMC9589337; pdf:https://europepmc.org/articles/PMC9589337?pdf=render
+35964473,https://doi.org/10.1016/j.socscimed.2022.115237,"""We've all got the virus inside us now"": Disaggregating public health relations and responsibilities for health protection in pandemic London.","Kasstan B, Mounier-Jack S, Gaskell KM, Eggo RM, Marks M, Chantler T.",,Social science & medicine (1982),2022,2022-08-07,Y,Pandemic; Public Health; Judaism; Responsibility; London; Covid-19,,,"The COVID-19 pandemic has disproportionately impacted ethnic minorities in the global north, evidenced by higher rates of transmission, morbidity, and mortality relative to population sizes. Orthodox Jewish neighbourhoods in London had extremely high SARS-CoV-2 seroprevalence rates, reflecting patterns in Israel and the US. The aim of this paper is to examine how responsibilities over health protection are conveyed, and to what extent responsibility is sought by, and shared between, state services, and 'community' stakeholders or representative groups, and families in public health emergencies. The study investigates how public health and statutory services stakeholders, Orthodox Jewish communal custodians and households sought to enact health protection in London during the first year of the pandemic (March 2020-March 2021). Twenty-eight semi-structured interviews were conducted across these cohorts. Findings demonstrate that institutional relations - both their formation and at times fragmentation - were directly shaped by issues surrounding COVID-19 control measures. Exchanges around protective interventions (whether control measures, contact tracing technologies, or vaccines) reveal diverse and diverging attributions of responsibility and authority. The paper develops a framework of public health relations to understand negotiations between statutory services and minority groups over responsiveness and accountability in health protection. Disaggregating public health relations can help social scientists to critique who and what characterises institutional relationships with minority groups, and what ideas of responsibility and responsiveness are projected by differently-positioned stakeholders in health protection.",,doi:https://doi.org/10.1016/j.socscimed.2022.115237; doi:https://doi.org/10.1016/j.socscimed.2022.115237; html:https://europepmc.org/articles/PMC9357441; pdf:https://europepmc.org/articles/PMC9357441?pdf=render
 36962513,https://doi.org/10.1371/journal.pgph.0000502,"Association between mobility, non-pharmaceutical interventions, and COVID-19 transmission in Ghana: A modelling study using mobile phone data.","Gibbs H, Liu Y, Abbott S, Baffoe-Nyarko I, Laryea DO, Akyereko E, Kuma-Aboagye P, Asante IA, Mitjà O, LSHTM CMMID COVID-19 Working Group, Ampofo W, Asiedu-Bekoe F, Marks M, Eggo RM.",,PLOS global public health,2022,2022-09-13,Y,,,,"Governments around the world have implemented non-pharmaceutical interventions to limit the transmission of COVID-19. Here we assess if increasing NPI stringency was associated with a reduction in COVID-19 cases in Ghana. While lockdowns and physical distancing have proven effective for reducing COVID-19 transmission, there is still limited understanding of how NPI measures are reflected in indicators of human mobility. Further, there is a lack of understanding about how findings from high-income settings correspond to low and middle-income contexts. In this study, we assess the relationship between indicators of human mobility, NPIs, and estimates of Rt, a real-time measure of the intensity of COVID-19 transmission. We construct a multilevel generalised linear mixed model, combining local disease surveillance data from subnational districts of Ghana with the timing of NPIs and indicators of human mobility from Google and Vodafone Ghana. We observe a relationship between reductions in human mobility and decreases in Rt during the early stages of the COVID-19 epidemic in Ghana. We find that the strength of this relationship varies through time, decreasing after the most stringent period of interventions in the early epidemic. Our findings demonstrate how the association of NPI and mobility indicators with COVID-19 transmission may vary through time. Further, we demonstrate the utility of combining local disease surveillance data with large scale human mobility data to augment existing surveillance capacity to monitor the impact of NPI policies.",,pdf:https://journals.plos.org/globalpublichealth/article/file?id=10.1371/journal.pgph.0000502&type=printable; doi:https://doi.org/10.1371/journal.pgph.0000502; html:https://europepmc.org/articles/PMC10021296; pdf:https://europepmc.org/articles/PMC10021296?pdf=render
 37773956,https://doi.org/10.1371/journal.pone.0292240,Prioritising cardiovascular disease risk assessment to high risk individuals based on primary care records.,"Chung R, Xu Z, Arnold M, Stevens D, Keogh R, Barrett J, Harrison H, Pennells L, Kim LG, DiAngelantonio E, Paige E, Usher-Smith JA, Wood AM.",,PloS one,2023,2023-09-29,Y,,,,"<h4>Objective</h4>To provide quantitative evidence for systematically prioritising individuals for full formal cardiovascular disease (CVD) risk assessment using primary care records with a novel tool (eHEART) with age- and sex- specific risk thresholds.<h4>Methods and analysis</h4>eHEART was derived using landmark Cox models for incident CVD with repeated measures of conventional CVD risk predictors in 1,642,498 individuals from the Clinical Practice Research Datalink. Using 119,137 individuals from UK Biobank, we modelled the implications of initiating guideline-recommended statin therapy using eHEART with age- and sex-specific prioritisation thresholds corresponding to 5% false negative rates to prioritise adults aged 40-69 years in a population in England for invitation to a formal CVD risk assessment.<h4>Results</h4>Formal CVD risk assessment on all adults would identify 76% and 49% of future CVD events amongst men and women respectively, and 93 (95% CI: 90, 95) men and 279 (95% CI: 259, 297) women would need to be screened (NNS) to prevent one CVD event. In contrast, if eHEART was first used to prioritise individuals for formal CVD risk assessment, we would identify 73% and 47% of future events amongst men and women respectively, and a NNS of 75 (95% CI: 72, 77) men and 162 (95% CI: 150, 172) women. Replacing the age- and sex-specific prioritisation thresholds with a 10% threshold identify around 10% less events.<h4>Conclusions</h4>The use of prioritisation tools with age- and sex-specific thresholds could lead to more efficient CVD assessment programmes with only small reductions in effectiveness at preventing new CVD events.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0292240&type=printable; doi:https://doi.org/10.1371/journal.pone.0292240; html:https://europepmc.org/articles/PMC10540947; pdf:https://europepmc.org/articles/PMC10540947?pdf=render
 35781133,https://doi.org/10.3310/zyzc8514,Long-term impact of pre-incision antibiotics on children born by caesarean section: a longitudinal study based on UK electronic health records.,"Šumilo D, Nirantharakumar K, Willis BH, Rudge GM, Martin J, Gokhale K, Thayakaran R, Adderley NJ, Chandan JS, Okoth K, Harris IM, Hewston R, Skrybant M, Deeks JJ, Brocklehurst P.",,"Health technology assessment (Winchester, England)",2022,2022-06-01,N,Asthma; Caesarean section; Eczema; Child Health; Anti-bacterial Agents; Microbiome; Electronic Health Records; Interrupted Time Series Analysis,,,"<h4>Background</h4>Since changes in the national guidance in 2011, prophylactic antibiotics for women undergoing caesarean section are recommended prior to skin incision, rather than after the baby's umbilical cord has been clamped. Evidence from randomised controlled trials conducted outside the UK has shown that this reduces maternal infectious morbidity; however, the prophylactic antibiotics also cross the placenta, meaning that babies are exposed to them around the time of birth. Antibiotics are known to affect the gut microbiota of the babies, but the long-term effects of exposure to high-dose broad-spectrum antibiotics around the time of birth on allergy and immune-related diseases are unknown.<h4>Objectives</h4>We aimed to examine whether or not in-utero exposure to antibiotics immediately prior to birth compared with no pre-incisional antibiotic exposure increases the risk of (1) asthma and (2) eczema in children born by caesarean section.<h4>Design</h4>This was a controlled interrupted time series study.<h4>Setting</h4>The study took place in primary and secondary care.<h4>Participants</h4>Children born in the UK during 2006-18 delivered by caesarean section were compared with a control cohort delivered vaginally.<h4>Interventions</h4>In-utero exposure to antibiotics immediately prior to birth.<h4>Main outcome measures</h4>Asthma and eczema in children in the first 5 years of life. Additional secondary outcomes, including other allergy-related conditions, autoimmune diseases, infections, other immune system-related diseases and neurodevelopmental conditions, were also assessed.<h4>Data sources</h4>The Health Improvement Network (THIN) and the Clinical Practice Research Datalink (CPRD) primary care databases and the Hospital Episode Statistics (HES) database. Previously published linkage strategies were adapted to link anonymised data on mothers and babies in these databases. Duplicate practices contributing to both THIN and the CPRD databases were removed to create a THIN-CPRD data set.<h4>Results</h4>In the THIN-CPRD and HES data sets, records of 515,945 and 3,945,351 mother-baby pairs were analysed, respectively. The risk of asthma was not significantly higher in children born by caesarean section exposed to pre-incision antibiotics than in children whose mothers received post-cord clamping antibiotics, with an incidence rate ratio of 0.91 (95% confidence interval 0.78 to 1.05) for diagnosis of asthma in primary care and an incidence rate ratio of 1.05 (95% confidence interval 0.99 to 1.11) for asthma resulting in a hospital admission. We also did not find an increased risk of eczema, with an incidence rate ratio of 0.98 (95% confidence interval 0.94 to1.03) and an incidence rate ratio of 0.96 (95% confidence interval 0.71 to 1.29) for diagnosis in primary care and hospital admissions, respectively.<h4>Limitations</h4>It was not possible to ascertain the exposure to pre-incision antibiotics at an individual level. The maximum follow-up of children was 5 years.<h4>Conclusions</h4>There was no evidence that the policy change from post-cord clamping to pre-incision prophylactic antibiotics for caesarean sections during 2006-18 had an impact on the incidence of asthma and eczema in early childhood in the UK.<h4>Future work</h4>There is a need for further research to investigate if pre-incision antibiotics have any impact on developing asthma and other allergy and immune-related conditions in older children.<h4>Study registration</h4>This study is registered as researchregistry3736.<h4>Funding</h4>This project was funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme and will be published in full in <i>Health Technology Assessment</i>; Vol. 26, No. 30. See the NIHR Journals Library website for further project information.",,pdf:https://njl-admin.nihr.ac.uk/document/download/2039937; doi:https://doi.org/10.3310/ZYZC8514
 38655112,https://doi.org/10.1089/neur.2023.0127,The Australian Traumatic Brain Injury Initiative: Review and Recommendations for Outcome Measures for Use With Adults and Children After Moderate-to-Severe Traumatic Brain Injury.,"Ponsford JL, Hicks AJ, Bagg MK, Phyland R, Carrier S, James AC, Lannin NA, Rushworth N, O'Brien TJ, Cameron PA, Cooper DJ, Hill R, Gabbe BJ, Fitzgerald M.",,Neurotrauma reports,2024,2024-04-11,Y,Review; Traumatic brain injury; Outcome Measures; Common Data Elements,,,"The Australian Traumatic Brain Injury Initiative (AUS-TBI) aims to select a set of measures to comprehensively predict and assess outcomes following moderate-to-severe traumatic brain injury (TBI) across Australia. The aim of this article was to report on the implementation and findings of an evidence-based consensus approach to develop AUS-TBI recommendations for outcome measures following adult and pediatric moderate-to-severe TBI. Following consultation with a panel of expert clinicians, Aboriginal and Torres Strait Islander representatives and a Living Experience group, and preliminary literature searches with a broader focus, a decision was made to focus on measures of mortality, everyday functional outcomes, and quality of life. Standardized searches of bibliographic databases were conducted through March 2022. Characteristics of 75 outcome measures were extracted from 1485 primary studies. Consensus meetings among the AUS-TBI Steering Committee, an expert panel of clinicians and researchers and a group of individuals with lived experience of TBI resulted in the production of a final list of 11 core outcome measures: the Functional Independence Measure (FIM); Glasgow Outcome Scale-Extended (GOS-E); Satisfaction With Life Scale (SWLS) (adult); mortality; EuroQol-5 Dimensions (EQ5D); Mayo-Portland Adaptability Inventory (MPAI); Return to Work /Study (adult and pediatric); Functional Independence Measure for Children (WEEFIM); Glasgow Outcome Scale Modified for Children (GOS-E PEDS); Paediatric Quality of Life Scale (PEDS-QL); and Strengths and Difficulties Questionnaire (pediatric). These 11 outcome measures will be included as common data elements in the AUS-TBI data dictionary. Review Registration PROSPERO (CRD42022290954).",,doi:https://doi.org/10.1089/neur.2023.0127; html:https://europepmc.org/articles/PMC11035854; pdf:https://europepmc.org/articles/PMC11035854?pdf=render
-35964473,https://doi.org/10.1016/j.socscimed.2022.115237,"""We've all got the virus inside us now"": Disaggregating public health relations and responsibilities for health protection in pandemic London.","Kasstan B, Mounier-Jack S, Gaskell KM, Eggo RM, Marks M, Chantler T.",,Social science & medicine (1982),2022,2022-08-07,Y,Pandemic; Public Health; Judaism; Responsibility; London; Covid-19,,,"The COVID-19 pandemic has disproportionately impacted ethnic minorities in the global north, evidenced by higher rates of transmission, morbidity, and mortality relative to population sizes. Orthodox Jewish neighbourhoods in London had extremely high SARS-CoV-2 seroprevalence rates, reflecting patterns in Israel and the US. The aim of this paper is to examine how responsibilities over health protection are conveyed, and to what extent responsibility is sought by, and shared between, state services, and 'community' stakeholders or representative groups, and families in public health emergencies. The study investigates how public health and statutory services stakeholders, Orthodox Jewish communal custodians and households sought to enact health protection in London during the first year of the pandemic (March 2020-March 2021). Twenty-eight semi-structured interviews were conducted across these cohorts. Findings demonstrate that institutional relations - both their formation and at times fragmentation - were directly shaped by issues surrounding COVID-19 control measures. Exchanges around protective interventions (whether control measures, contact tracing technologies, or vaccines) reveal diverse and diverging attributions of responsibility and authority. The paper develops a framework of public health relations to understand negotiations between statutory services and minority groups over responsiveness and accountability in health protection. Disaggregating public health relations can help social scientists to critique who and what characterises institutional relationships with minority groups, and what ideas of responsibility and responsiveness are projected by differently-positioned stakeholders in health protection.",,doi:https://doi.org/10.1016/j.socscimed.2022.115237; doi:https://doi.org/10.1016/j.socscimed.2022.115237; html:https://europepmc.org/articles/PMC9357441; pdf:https://europepmc.org/articles/PMC9357441?pdf=render
 37982176,https://doi.org/10.1093/ehjci/jead285,Assessing heterogeneity on cardiovascular magnetic resonance imaging: a novel approach to diagnosis and risk stratification in cardiac diseases.,"Hesse K, Khanji MY, Aung N, Dabbagh GS, Petersen SE, Chahal CAA.",,European heart journal. Cardiovascular Imaging,2024,2024-03-01,Y,Disease; Diagnosis; Cardiovascular Magnetic Resonance Imaging; Prognostication; Heterogeneity Biomarker,,,"Cardiac disease affects the heart non-uniformly. Examples include focal septal or apical hypertrophy with reduced strain in hypertrophic cardiomyopathy, replacement fibrosis with akinesia in an infarct-related coronary artery territory, and a pattern of scarring in dilated cardiomyopathy. The detail and versatility of cardiovascular magnetic resonance (CMR) imaging mean it contains a wealth of information imperceptible to the naked eye and not captured by standard global measures. CMR-derived heterogeneity biomarkers could facilitate early diagnosis, better risk stratification, and a more comprehensive prediction of treatment response. Small cohort and case-control studies demonstrate the feasibility of proof-of-concept structural and functional heterogeneity measures. Detailed radiomic analyses of different CMR sequences using open-source software delineate unique voxel patterns as hallmarks of histopathological changes. Meanwhile, measures of dispersion applied to emerging CMR strain sequences describe variable longitudinal, circumferential, and radial function across the myocardium. Two of the most promising heterogeneity measures are the mean absolute deviation of regional standard deviations on native T1 and T2 and the standard deviation of time to maximum regional radial wall motion, termed the tissue synchronization index in a 16-segment left ventricle model. Real-world limitations include the non-standardization of CMR imaging protocols across different centres and the testing of large numbers of radiomic features in small, inadequately powered patient samples. We, therefore, propose a three-step roadmap to benchmark novel heterogeneity biomarkers, including defining normal reference ranges, statistical modelling against diagnosis and outcomes in large epidemiological studies, and finally, comprehensive internal and external validations.",,pdf:https://academic.oup.com/ehjcimaging/advance-article-pdf/doi/10.1093/ehjci/jead285/53585728/jead285.pdf; doi:https://doi.org/10.1093/ehjci/jead285; html:https://europepmc.org/articles/PMC10966332; pdf:https://europepmc.org/articles/PMC10966332?pdf=render
-36745557,https://doi.org/10.1093/bjd/ljac132,"Factors associated with depression, anxiety and severe mental illness among adults with atopic eczema or psoriasis: a systematic review and meta-analysis.","Adesanya EI, Matthewman J, Schonmann Y, Hayes JF, Henderson A, Mathur R, Mulick AR, Smith CH, Langan SM, Mansfield KE.",,The British journal of dermatology,2023,2023-03-01,N,,,,"<h4>Background</h4>Evidence suggests an association between atopic eczema (AE) or psoriasis and mental illness; however, the factors associated with mental illness are unclear.<h4>Objectives</h4>To synthesize and evaluate all available evidence on factors associated with depression, anxiety and severe mental illness (SMI) among adults with AE or psoriasis.<h4>Methods</h4>We searched electronic databases, grey literature databases and clinical trial registries from inception to February 2022 for studies of adults with AE or psoriasis. Eligible studies included randomized controlled trials (RCTs), cohort, cross-sectional or case-control studies where effect estimates of factors associated with depression, anxiety or SMI were reported. We did not apply language or geographical restrictions. We assessed risk of bias using the Quality in Prognosis Studies tool. We synthesized results narratively, and if at least two studies were sufficiently homogeneous, we pooled effect estimates in a random effects meta-analysis.<h4>Results</h4>We included 21 studies (11 observational, 10 RCTs). No observational studies in AE fulfilled our eligibility criteria. Observational studies in people with psoriasis mostly investigated factors associated with depression or anxiety - one cross-sectional study investigated factors associated with schizophrenia. Pooled effect estimates suggest that female sex and psoriatic arthritis were associated with depression [female sex: odds ratio (OR) 1.62, 95% confidence interval (CI) 1.09-2.40, 95% prediction intervals (PIs) 0.62-4.23, I2 = 24.90%, τ2 = 0.05; psoriatic arthritis: OR 2.26, 95% CI 1.56-3.25, 95% PI 0.21-24.23, I2 = 0.00%, τ2 = 0.00] and anxiety (female sex: OR 2.59, 95% CI 1.32-5.07, 95% PI 0.00-3956.27, I2 = 61.90%, τ2 = 0.22; psoriatic arthritis: OR 1.98, 95% CI 1.33-2.94, I2 = 0.00%, τ2 = 0.00). Moderate/severe psoriasis was associated with anxiety (OR 1.14, 95% CI 1.05-1.25, I2 0.00%, τ2 = 0.00), but not depression. Evidence from RCTs suggested that adults with AE or psoriasis given placebo had higher depression and anxiety scores compared with comparators given targeted treatment (e.g. biologic agents).<h4>Conclusions</h4>Our review highlights limited existing research on factors associated with depression, anxiety and SMI in adults with AE or psoriasis. Observational evidence on factors associated with depression or anxiety in people with psoriasis was conflicting or from single studies, but some identified factors were consistent with those in the general population. Evidence on factors associated with SMIs in people with AE or psoriasis was particularly limited. Evidence from RCTs suggested that AE and psoriasis treated with placebo was associated with higher depression and anxiety scores compared with skin disease treated with targeted therapy; however, follow-up was limited. Therefore, long-term effects on mental health are unclear.",,pdf:https://academic.oup.com/bjd/article-pdf/188/4/460/51790111/ljac132.pdf; doi:https://doi.org/10.1093/bjd/ljac132
 34227657,https://doi.org/10.1093/bjs/znab183,Machine learning risk prediction of mortality for patients undergoing surgery with perioperative SARS-CoV-2: the COVIDSurg mortality score.,"COVIDSurg Collaborative
 .",,The British journal of surgery,2021,2021-11-01,Y,,,,,,pdf:https://academic.oup.com/bjs/article-pdf/108/11/1274/47371055/znab183.pdf; doi:https://doi.org/10.1093/bjs/znab183; html:https://europepmc.org/articles/PMC8344569; pdf:https://europepmc.org/articles/PMC8344569?pdf=render
+36745557,https://doi.org/10.1093/bjd/ljac132,"Factors associated with depression, anxiety and severe mental illness among adults with atopic eczema or psoriasis: a systematic review and meta-analysis.","Adesanya EI, Matthewman J, Schonmann Y, Hayes JF, Henderson A, Mathur R, Mulick AR, Smith CH, Langan SM, Mansfield KE.",,The British journal of dermatology,2023,2023-03-01,N,,,,"<h4>Background</h4>Evidence suggests an association between atopic eczema (AE) or psoriasis and mental illness; however, the factors associated with mental illness are unclear.<h4>Objectives</h4>To synthesize and evaluate all available evidence on factors associated with depression, anxiety and severe mental illness (SMI) among adults with AE or psoriasis.<h4>Methods</h4>We searched electronic databases, grey literature databases and clinical trial registries from inception to February 2022 for studies of adults with AE or psoriasis. Eligible studies included randomized controlled trials (RCTs), cohort, cross-sectional or case-control studies where effect estimates of factors associated with depression, anxiety or SMI were reported. We did not apply language or geographical restrictions. We assessed risk of bias using the Quality in Prognosis Studies tool. We synthesized results narratively, and if at least two studies were sufficiently homogeneous, we pooled effect estimates in a random effects meta-analysis.<h4>Results</h4>We included 21 studies (11 observational, 10 RCTs). No observational studies in AE fulfilled our eligibility criteria. Observational studies in people with psoriasis mostly investigated factors associated with depression or anxiety - one cross-sectional study investigated factors associated with schizophrenia. Pooled effect estimates suggest that female sex and psoriatic arthritis were associated with depression [female sex: odds ratio (OR) 1.62, 95% confidence interval (CI) 1.09-2.40, 95% prediction intervals (PIs) 0.62-4.23, I2 = 24.90%, τ2 = 0.05; psoriatic arthritis: OR 2.26, 95% CI 1.56-3.25, 95% PI 0.21-24.23, I2 = 0.00%, τ2 = 0.00] and anxiety (female sex: OR 2.59, 95% CI 1.32-5.07, 95% PI 0.00-3956.27, I2 = 61.90%, τ2 = 0.22; psoriatic arthritis: OR 1.98, 95% CI 1.33-2.94, I2 = 0.00%, τ2 = 0.00). Moderate/severe psoriasis was associated with anxiety (OR 1.14, 95% CI 1.05-1.25, I2 0.00%, τ2 = 0.00), but not depression. Evidence from RCTs suggested that adults with AE or psoriasis given placebo had higher depression and anxiety scores compared with comparators given targeted treatment (e.g. biologic agents).<h4>Conclusions</h4>Our review highlights limited existing research on factors associated with depression, anxiety and SMI in adults with AE or psoriasis. Observational evidence on factors associated with depression or anxiety in people with psoriasis was conflicting or from single studies, but some identified factors were consistent with those in the general population. Evidence on factors associated with SMIs in people with AE or psoriasis was particularly limited. Evidence from RCTs suggested that AE and psoriasis treated with placebo was associated with higher depression and anxiety scores compared with skin disease treated with targeted therapy; however, follow-up was limited. Therefore, long-term effects on mental health are unclear.",,pdf:https://academic.oup.com/bjd/article-pdf/188/4/460/51790111/ljac132.pdf; doi:https://doi.org/10.1093/bjd/ljac132
 32616677,https://doi.org/10.1212/wnl.0000000000009924,Accuracy of identifying incident stroke cases from linked health care data in UK Biobank.,"Rannikmäe K, Ngoh K, Bush K, Al-Shahi Salman R, Doubal F, Flaig R, Henshall DE, Hutchison A, Nolan J, Osborne S, Samarasekera N, Schnier C, Whiteley W, Wilkinson T, Wilson K, Woodfield R, Zhang Q, Allen N, Sudlow CLM.",,Neurology,2020,2020-07-02,Y,,,,"<h4>Objective</h4>In UK Biobank (UKB), a large population-based prospective study, cases of many diseases are ascertained through linkage to routinely collected, coded national health datasets. We assessed the accuracy of these for identifying incident strokes.<h4>Methods</h4>In a regional UKB subpopulation (n = 17,249), we identified all participants with ≥1 code signifying a first stroke after recruitment (incident stroke-coded cases) in linked hospital admission, primary care, or death record data. Stroke physicians reviewed their full electronic patient records (EPRs) and generated reference standard diagnoses. We evaluated the number and proportion of cases that were true-positives (i.e., positive predictive value [PPV]) for all codes combined and by code source and type.<h4>Results</h4>Of 232 incident stroke-coded cases, 97% had EPR information available. Data sources were 30% hospital admission only, 39% primary care only, 28% hospital and primary care, and 3% death records only. While 42% of cases were coded as unspecified stroke type, review of EPRs enabled a pathologic type to be assigned in >99%. PPVs (95% confidence intervals) were 79% (73%-84%) for any stroke (89% for hospital admission codes, 80% for primary care codes) and 83% (74%-90%) for ischemic stroke. PPVs for small numbers of death record and hemorrhagic stroke codes were low but imprecise.<h4>Conclusions</h4>Stroke and ischemic stroke cases in UKB can be ascertained through linked health datasets with sufficient accuracy for many research studies. Further work is needed to understand the accuracy of death record and hemorrhagic stroke codes and to develop scalable approaches for better identifying stroke types.",,pdf:https://n.neurology.org/content/neurology/95/6/e697.full.pdf; doi:https://doi.org/10.1212/WNL.0000000000009924; html:https://europepmc.org/articles/PMC7455356; pdf:https://europepmc.org/articles/PMC7455356?pdf=render
 37828025,https://doi.org/10.1038/s41467-023-41876-5,ADRA2A and IRX1 are putative risk genes for Raynaud's phenomenon.,"Hartmann S, Yasmeen S, Jacobs BM, Denaxas S, Pirmohamed M, Gamazon ER, Caulfield MJ, Genes & Health Research Team, Hemingway H, Pietzner M, Langenberg C.",,Nature communications,2023,2023-10-12,Y,,,,"Raynaud's phenomenon (RP) is a common vasospastic disorder that causes severe pain and ulcers, but despite its high reported heritability, no causal genes have been robustly identified. We conducted a genome-wide association study including 5,147 RP cases and 439,294 controls, based on diagnoses from electronic health records, and identified three unreported genomic regions associated with the risk of RP (p < 5 × 10<sup>-8</sup>). We prioritized ADRA2A (rs7090046, odds ratio (OR) per allele: 1.26; 95%-CI: 1.20-1.31; p < 9.6 × 10<sup>-27</sup>) and IRX1 (rs12653958, OR: 1.17; 95%-CI: 1.12-1.22, p < 4.8 × 10<sup>-13</sup>) as candidate causal genes through integration of gene expression in disease relevant tissues. We further identified a likely causal detrimental effect of low fasting glucose levels on RP risk (r<sub>G</sub> = -0.21; p-value = 2.3 × 10<sup>-3</sup>), and systematically highlighted drug repurposing opportunities, like the antidepressant mirtazapine. Our results provide the first robust evidence for a strong genetic contribution to RP and highlight a so far underrated role of α<sub>2A</sub>-adrenoreceptor signalling, encoded at ADRA2A, as a possible mechanism for hypersensitivity to catecholamine-induced vasospasms.",,pdf:https://www.nature.com/articles/s41467-023-41876-5.pdf; doi:https://doi.org/10.1038/s41467-023-41876-5; html:https://europepmc.org/articles/PMC10570309; pdf:https://europepmc.org/articles/PMC10570309?pdf=render
 37679419,https://doi.org/10.1038/s41588-023-01462-3,"GWAS of random glucose in 476,326 individuals provide insights into diabetes pathophysiology, complications and treatment stratification.","Lagou V, Jiang L, Ulrich A, Zudina L, González KSG, Balkhiyarova Z, Faggian A, Maina JG, Chen S, Todorov PV, Sharapov S, David A, Marullo L, Mägi R, Rujan RM, Ahlqvist E, Thorleifsson G, Gao Η, Εvangelou Ε, Benyamin B, Scott RA, Isaacs A, Zhao JH, Willems SM, Johnson T, Gieger C, Grallert H, Meisinger C, Müller-Nurasyid M, Strawbridge RJ, Goel A, Rybin D, Albrecht E, Jackson AU, Stringham HM, Corrêa IR, Farber-Eger E, Steinthorsdottir V, Uitterlinden AG, Munroe PB, Brown MJ, Schmidberger J, Holmen O, Thorand B, Hveem K, Wilsgaard T, Mohlke KL, Wang Z, GWA-PA Consortium, Shmeliov A, den Hoed M, Loos RJF, Kratzer W, Haenle M, Koenig W, Boehm BO, Tan TM, Tomas A, Salem V, Barroso I, Tuomilehto J, Boehnke M, Florez JC, Hamsten A, Watkins H, Njølstad I, Wichmann HE, Caulfield MJ, Khaw KT, van Duijn CM, Hofman A, Wareham NJ, Langenberg C, Whitfield JB, Martin NG, Montgomery G, Scapoli C, Tzoulaki I, Elliott P, Thorsteinsdottir U, Stefansson K, Brittain EL, McCarthy MI, Froguel P, Sexton PM, Wootten D, Groop L, Dupuis J, Meigs JB, Deganutti G, Demirkan A, Pers TH, Reynolds CA, Aulchenko YS, Kaakinen MA, Jones B, Prokopenko I, Meta-Analysis of Glucose and Insulin-Related Traits Consortium (MAGIC).",,Nature genetics,2023,2023-09-07,Y,,,,"Conventional measurements of fasting and postprandial blood glucose levels investigated in genome-wide association studies (GWAS) cannot capture the effects of DNA variability on 'around the clock' glucoregulatory processes. Here we show that GWAS meta-analysis of glucose measurements under nonstandardized conditions (random glucose (RG)) in 476,326 individuals of diverse ancestries and without diabetes enables locus discovery and innovative pathophysiological observations. We discovered 120 RG loci represented by 150 distinct signals, including 13 with sex-dimorphic effects, two cross-ancestry and seven rare frequency signals. Of these, 44 loci are new for glycemic traits. Regulatory, glycosylation and metagenomic annotations highlight ileum and colon tissues, indicating an underappreciated role of the gastrointestinal tract in controlling blood glucose. Functional follow-up and molecular dynamics simulations of lower frequency coding variants in glucagon-like peptide-1 receptor (GLP1R), a type 2 diabetes treatment target, reveal that optimal selection of GLP-1R agonist therapy will benefit from tailored genetic stratification. We also provide evidence from Mendelian randomization that lung function is modulated by blood glucose and that pulmonary dysfunction is a diabetes complication. Our investigation yields new insights into the biology of glucose regulation, diabetes complications and pathways for treatment stratification.",,pdf:https://www.nature.com/articles/s41588-023-01462-3.pdf; doi:https://doi.org/10.1038/s41588-023-01462-3; html:https://europepmc.org/articles/PMC10484788; pdf:https://europepmc.org/articles/PMC10484788?pdf=render
 39443624,https://doi.org/10.1038/s41746-024-01250-1,Development and assessment of a machine learning tool for predicting emergency admission in Scotland.,"Liley J, Bohner G, Emerson SR, Mateen BA, Borland K, Carr D, Heald S, Oduro SD, Ireland J, Moffat K, Porteous R, Riddell S, Rogers S, Thoma I, Cunningham N, Holmes C, Payne K, Vollmer SJ, Vallejos CA, Aslett LJM.",,NPJ digital medicine,2024,2024-10-23,Y,,,,"Emergency admissions (EA), where a patient requires urgent in-hospital care, are a major challenge for healthcare systems. The development of risk prediction models can partly alleviate this problem by supporting primary care interventions and public health planning. Here, we introduce SPARRAv4, a predictive score for EA risk that will be deployed nationwide in Scotland. SPARRAv4 was derived using supervised and unsupervised machine-learning methods applied to routinely collected electronic health records from approximately 4.8M Scottish residents (2013-18). We demonstrate improvements in discrimination and calibration with respect to previous scores deployed in Scotland, as well as stability over a 3-year timeframe. Our analysis also provides insights about the epidemiology of EA risk in Scotland, by studying predictive performance across different population sub-groups and reasons for admission, as well as by quantifying the effect of individual input features. Finally, we discuss broader challenges including reproducibility and how to safely update risk prediction models that are already deployed at population level.",,doi:https://doi.org/10.1038/s41746-024-01250-1; html:https://europepmc.org/articles/PMC11499905; pdf:https://europepmc.org/articles/PMC11499905?pdf=render
 34819519,https://doi.org/10.1038/s41467-021-27164-0,Synergistic insights into human health from aptamer- and antibody-based proteomic profiling.,"Pietzner M, Wheeler E, Carrasco-Zanini J, Kerrison ND, Oerton E, Koprulu M, Luan J, Hingorani AD, Williams SA, Wareham NJ, Langenberg C.",,Nature communications,2021,2021-11-24,Y,,,,"Affinity-based proteomics has enabled scalable quantification of thousands of protein targets in blood enhancing biomarker discovery, understanding of disease mechanisms, and genetic evaluation of drug targets in humans through protein quantitative trait loci (pQTLs). Here, we integrate two partly complementary techniques-the aptamer-based SomaScan<sup>®</sup> v4 assay and the antibody-based Olink assays-to systematically assess phenotypic consequences of hundreds of pQTLs discovered for 871 protein targets across both platforms. We create a genetically anchored cross-platform proteome-phenome network comprising 547 protein-phenotype connections, 36.3% of which were only seen with one of the two platforms suggesting that both techniques capture distinct aspects of protein biology. We further highlight discordance of genetically predicted effect directions between assays, such as for PILRA and Alzheimer's disease. Our results showcase the synergistic nature of these technologies to better understand and identify disease mechanisms and provide a benchmark for future cross-platform discoveries.",,pdf:https://www.nature.com/articles/s41467-021-27164-0.pdf; doi:https://doi.org/10.1038/s41467-021-27164-0; html:https://europepmc.org/articles/PMC8613205; pdf:https://europepmc.org/articles/PMC8613205?pdf=render
 33147524,https://doi.org/10.1016/j.puhe.2020.08.027,Adverse childhood experiences during childhood and academic attainment at age 7 and 11 years: an electronic birth cohort study.,"Evans A, Hardcastle K, Bandyopadhyay A, Farewell D, John A, Lyons RA, Long S, Bellis MA, Paranjothy S.",,Public health,2020,2020-11-02,N,Social Inequalities; Adverse Childhood Experiences; Education Outcomes,,,"<h4>Objectives</h4>Adverse childhood experiences (ACEs) have a negative impact on childhood health, but their impact on education outcomes is less well known. We investigated whether or not ACEs were associated with reduced educational attainment at age 7 and 11 years.<h4>Study design</h4>The study design used in the study is a population-based electronic cohort study.<h4>Methods</h4>We analysed data from a total population electronic child cohort in Wales, UK. ACEs (exposures) were living with an adult household member with any of (i) serious mental illness, (ii) common mental disorder (CMD), (iii) an alcohol problem; (iv) child victimisation, (v) death of a household member and (vi) low family income. We used multilevel logistic regression to model exposure to these ACEs and not attaining the expected level at statutory education assessments, Key Stage (KS) 1 and KS2 separately, adjusted for known confounders including perinatal, socio-economic and school factors.<h4>Results</h4>There were 107,479 and 43,648 children included in the analysis, with follow-up to 6-7 years (KS1) and 10-11 years (KS2), respectively. An increased risk of not attaining the expected level at KS1 was associated with living with adult household members with CMD (adjusted odds ratio [aOR]: 1.13 [95% confidence interval [CI]: 1.09-1.17]) or an alcohol problem (adjusted odds ratio [aOR]: 1.16 [95% confidence interval [CI]: 1.10-1.22]), childhood victimisation (adjusted odds ratio [aOR]: 1.58 [95% confidence interval [CI]: 1.37-1.82]), death of a household member (adjusted odds ratio [aOR]: 1.14 [95% confidence interval [CI]: 1.04-1.25]) and low family income (adjusted odds ratio [aOR]: 1.92 [95% confidence interval [CI]: 1.84-2.01]). Similar results were observed for KS2. Children with multiple adversities had substantially increased odds of not attaining the expected level at each educational assessment.<h4>Conclusion</h4>The educational potential of many children may not be achieved due to exposure to adversity in childhood. Affected children who come in to contact with services should have relevant information shared between health and care services, and schools to initiate and facilitate a coordinated approach towards providing additional support and help for them to fulfil their educational potential, and subsequent economic and social participation.",,pdf:https://orca.cardiff.ac.uk/136801/8/ACEs%20academic%20attainment%20at%20age%207%20and%2011%20years_FINALaccepted_v2.pdf; doi:https://doi.org/10.1016/j.puhe.2020.08.027
-37562944,https://doi.org/10.1136/emermed-2023-213186,"Biases in the collection of blood alcohol data for adult major trauma patients in Victoria, Australia.","Lau G, Gabbe B, Mitra B, Dietze P, Reeder S, Cameron P, Read DJ, Symons E, Beck B.",,Emergency medicine journal : EMJ,2023,2023-08-10,N,epidemiology; wounds and injuries; toxicology; Alcohol Abuse,,,"<h4>Background</h4>In-hospital alcohol testing provides an opportunity to implement prevention strategies for patients with high risk of experiencing repeated alcohol-related injuries. However, barriers to alcohol testing in emergency settings can prevent patients from being tested. In this study, we aimed to understand potential biases in current data on the completion of blood alcohol tests for major trauma patients at hospitals in Victoria, Australia.<h4>Methods</h4>Victorian State Trauma Registry data on all adult major trauma patients from 1 January 2018 to 31 December 2021 were used. Characteristics associated with having a blood alcohol test recorded in the registry were assessed using logistic regression models.<h4>Results</h4>This study included 14 221 major trauma patients, of which 4563 (32.1%) had a blood alcohol test recorded. Having a blood alcohol test completed was significantly associated with age, socioeconomic disadvantage level, preferred language, having pre-existing mental health or substance use conditions, smoking status, presenting during times associated with heavy community alcohol consumption, injury cause and intent, and Glasgow Coma Scale scores (p<0.05). Restricting analyses to patients from a trauma centre where blood alcohol testing was part of routine clinical care mitigated most biases. However, relative to patients injured while driving a motor vehicle/motorcycle, lower odds of testing were still observed for patients with injuries from flames/scalds/contact burns (adjusted OR (aOR)=0.33, 95% CI 0.18 to 0.61) and low falls (aOR=0.17, 95% CI 0.12 to 0.25). Higher odds of testing were associated with pre-existing mental health (aOR=1.39, 95% CI 1.02 to 1.89) or substance use conditions (aOR=2.33, 95% CI to 1.47-3.70), and living in a more disadvantaged area (most disadvantaged quintile relative to least disadvantaged quintile: aOR=2.30, 95% CI 1.52 to 3.48).<h4>Conclusion</h4>Biases in the collection of blood alcohol data likely impact the surveillance of alcohol-related injuries. Routine alcohol testing after major trauma is needed to accurately inform epidemiology and the subsequent implementation of strategies for reducing alcohol-related injuries.",,doi:https://doi.org/10.1136/emermed-2023-213186
 31685485,https://doi.org/10.1136/bmjopen-2019-031365,"Diagnosed prevalence of Ehlers-Danlos syndrome and hypermobility spectrum disorder in Wales, UK: a national electronic cohort study and case-control comparison.","Demmler JC, Atkinson MD, Reinhold EJ, Choy E, Lyons RA, Brophy ST.",,BMJ open,2019,2019-11-04,Y,Prevalence; Joint Hypermobility Syndrome; Ehlers-danlos Syndromes; Heritable Disorders Of Connective Tissue; Hypermobility Spectrum Disorder; Health Data Linkage,Improving Public Health,,"<h4>Objectives</h4>To describe the epidemiology of diagnosed hypermobility spectrum disorder (HSD) and Ehlers-Danlos syndromes (EDS) using linked electronic medical records. To examine whether these conditions remain rare and primarily affect the musculoskeletal system.<h4>Design</h4>Nationwide linked electronic cohort and nested case-control study.<h4>Setting</h4>Routinely collected data from primary care and hospital admissions in Wales, UK.<h4>Participants</h4>People within the primary care or hospital data systems with a coded diagnosis of EDS or joint hypermobility syndrome (JHS) between 1 July 1990 and 30 June 2017.<h4>Main outcome measures</h4>Combined prevalence of JHS and EDS in Wales. Additional diagnosis and prescription data in those diagnosed with EDS or JHS compared with matched controls.<h4>Results</h4>We found 6021 individuals (men: 30%, women: 70%) with a diagnostic code of either EDS or JHS. This gives a diagnosed point prevalence of 194.2 per 100 000 in 2016/2017 or roughly 10 cases in a practice of 5000 patients. There was a pronounced gender difference of 8.5 years (95% CI: 7.70 to 9.22) in the mean age at diagnosis. EDS or JHS was not only associated with high odds for other musculoskeletal diagnoses and drug prescriptions but also with significantly higher odds of a diagnosis in other disease categories (eg, mental health, nervous and digestive systems) and higher odds of a prescription in most disease categories (eg, gastrointestinal and cardiovascular drugs) within the 12 months before and after the first recorded diagnosis.<h4>Conclusions</h4>EDS and JHS (since March 2017 classified as EDS or HSD) have historically been considered rare diseases only affecting the musculoskeletal system and soft tissues. These data demonstrate that both these assertions should be reconsidered.","epidemiological study looking at the prevalence of ehlos danlos syndrome and joint hypermobility syndrome, using SAIL database for welsh population. They found a steady increase in the rates of diagnosis for these two diseases, higher odds of being on other medication, and association with other diseases categories.",pdf:https://bmjopen.bmj.com/content/bmjopen/9/11/e031365.full.pdf; doi:https://doi.org/10.1136/bmjopen-2019-031365; html:https://europepmc.org/articles/PMC6858200; pdf:https://europepmc.org/articles/PMC6858200?pdf=render
 31628383,https://doi.org/10.1038/s41598-019-51562-6,Whole genome sequencing of drug resistant Mycobacterium tuberculosis isolates from a high burden tuberculosis region of North West Pakistan.,"Jabbar A, Phelan JE, de Sessions PF, Khan TA, Rahman H, Khan SN, Cantillon DM, Wildner LM, Ali S, Campino S, Waddell SJ, Clark TG.",,Scientific reports,2019,2019-10-18,Y,,,,"Tuberculosis (TB), caused by Mycobacterium tuberculosis bacteria, is a leading infectious cause of mortality worldwide, including in Pakistan. Drug resistant M. tuberculosis is an emerging threat for TB control, making it important to detect the underlying genetic mutations, and thereby inform treatment decision making and prevent transmission. Whole genome sequencing has emerged as the new diagnostic to reliably predict drug resistance within a clinically relevant time frame, and its deployment will have the greatest impact on TB control in highly endemic regions. To evaluate the mutations leading to drug resistance and to assess for evidence of the transmission of resistant strains, 81 M. tuberculosis samples from Khyber Pakhtunkhwa province (North West Pakistan) were subjected to whole genome sequencing and standard drug susceptibility testing for eleven anti-TB drugs. We found the majority of M. tuberculosis isolates were the CAS/Delhi strain-type (lineage 3; n = 57; 70.4%) and multi-drug resistant (MDR; n = 62; 76.5%). The most frequent resistance mutations were observed in the katG and rpoB genes, conferring resistance to isoniazid and rifampicin respectively. Mutations were also observed in genes conferring resistance to other first and second-line drugs, including in pncA (pyrazinamide), embB (ethambutol), gyrA (fluoroquinolones), rrs (aminoglycosides), rpsL, rrs and giB (streptomycin) loci. Whilst the majority of mutations have been reported in global datasets, we describe unreported putative resistance markers in katG, ethA (ethionamide), gyrA and gyrB (fluoroquinolones), and pncA. Analysis of the mutations revealed that acquisition of rifampicin resistance often preceded isoniazid in our isolates. We also observed a high proportion (17.6%) of pre-MDR isolates with fluoroquinolone resistance markers, potentially due to unregulated anti-TB drug use. Our isolates were compared to previously sequenced strains from Pakistan in a combined phylogenetic tree analysis. The presence of lineage 2 was only observed in our isolates. Using a cut-off of less than ten genome-wide mutation differences between isolates, a transmission analysis revealed 18 M. tuberculosis isolates clustering within eight networks, thereby providing evidence of drug-resistant TB transmission in the Khyber Pakhtunkhwa province. Overall, we have demonstrated that drug-resistant TB isolates are circulating and transmitted in North West Pakistan. Further, we have shown the usefulness of whole genome sequencing as a diagnostic tool for characterizing M. tuberculosis isolates, which will assist future epidemiological studies and disease control activities in Pakistan.",,pdf:https://www.nature.com/articles/s41598-019-51562-6.pdf; doi:https://doi.org/10.1038/s41598-019-51562-6; html:https://europepmc.org/articles/PMC6802378; pdf:https://europepmc.org/articles/PMC6802378?pdf=render
+37562944,https://doi.org/10.1136/emermed-2023-213186,"Biases in the collection of blood alcohol data for adult major trauma patients in Victoria, Australia.","Lau G, Gabbe B, Mitra B, Dietze P, Reeder S, Cameron P, Read DJ, Symons E, Beck B.",,Emergency medicine journal : EMJ,2023,2023-08-10,N,epidemiology; wounds and injuries; toxicology; Alcohol Abuse,,,"<h4>Background</h4>In-hospital alcohol testing provides an opportunity to implement prevention strategies for patients with high risk of experiencing repeated alcohol-related injuries. However, barriers to alcohol testing in emergency settings can prevent patients from being tested. In this study, we aimed to understand potential biases in current data on the completion of blood alcohol tests for major trauma patients at hospitals in Victoria, Australia.<h4>Methods</h4>Victorian State Trauma Registry data on all adult major trauma patients from 1 January 2018 to 31 December 2021 were used. Characteristics associated with having a blood alcohol test recorded in the registry were assessed using logistic regression models.<h4>Results</h4>This study included 14 221 major trauma patients, of which 4563 (32.1%) had a blood alcohol test recorded. Having a blood alcohol test completed was significantly associated with age, socioeconomic disadvantage level, preferred language, having pre-existing mental health or substance use conditions, smoking status, presenting during times associated with heavy community alcohol consumption, injury cause and intent, and Glasgow Coma Scale scores (p<0.05). Restricting analyses to patients from a trauma centre where blood alcohol testing was part of routine clinical care mitigated most biases. However, relative to patients injured while driving a motor vehicle/motorcycle, lower odds of testing were still observed for patients with injuries from flames/scalds/contact burns (adjusted OR (aOR)=0.33, 95% CI 0.18 to 0.61) and low falls (aOR=0.17, 95% CI 0.12 to 0.25). Higher odds of testing were associated with pre-existing mental health (aOR=1.39, 95% CI 1.02 to 1.89) or substance use conditions (aOR=2.33, 95% CI to 1.47-3.70), and living in a more disadvantaged area (most disadvantaged quintile relative to least disadvantaged quintile: aOR=2.30, 95% CI 1.52 to 3.48).<h4>Conclusion</h4>Biases in the collection of blood alcohol data likely impact the surveillance of alcohol-related injuries. Routine alcohol testing after major trauma is needed to accurately inform epidemiology and the subsequent implementation of strategies for reducing alcohol-related injuries.",,doi:https://doi.org/10.1136/emermed-2023-213186
 37812323,https://doi.org/10.1186/s41687-023-00634-3,Development and usability testing of an electronic patient-reported outcome (ePRO) solution for patients with inflammatory diseases in an Advanced Therapy Medicinal Product (ATMP) basket trial.,"McMullan C, Retzer A, Hughes SE, Aiyegbusi OL, Bathurst C, Boyd A, Coleman J, Davies EH, Denniston AK, Dunster H, Frost C, Harding R, Hunn A, Kyte D, Malpass R, McNamara G, Mitchell S, Mittal S, Newsome PN, Price G, Rowe A, van Reil W, Walker A, Wilson R, Calvert M.",,Journal of patient-reported outcomes,2023,2023-10-09,Y,Inflammatory Conditions; Usability Testing; Cognitive Interviews; Electronic Patient Reported Outcomes; Early Phase Advanced Therapy Trial,,,"<h4>Background</h4>Electronic patient-reported outcome (ePRO) systems are increasingly used in clinical trials to provide evidence of efficacy and tolerability of treatment from the patient perspective. The aim of this study is twofold: (1) to describe how we developed an electronic platform for patients to report their symptoms, and (2) to develop and undertake usability testing of an ePRO solution for use in a study of cell therapy seeking to provide early evidence of efficacy and tolerability of treatment and test the feasibility of the system for use in later phase studies.<h4>Methods</h4>An ePRO system was designed to be used in a single arm, multi-centre, phase II basket trial investigating the safety and activity of the use of ORBCEL-C™ in the treatment of patients with inflammatory conditions. ORBCEL-C™ is an enriched Mesenchymal Stromal Cells product isolated from human umbilical cord tissue using CD362+ cell selection. Usability testing sessions were conducted using cognitive interviews and the 'Think Aloud' method with patient advisory group members and Research Nurses to assess the usability of the system.<h4>Results</h4>Nine patient partners and seven research nurses took part in one usability testing session. Measures of fatigue and health-related quality of life, the PRO-CTCAE™ and FACT-GP5 global tolerability question were included in the ePRO system. Alert notifications to the clinical team were triggered by PRO-CTCAE™ and FACT-GP5 scores. Patient participants liked the simplicity and responsiveness of the patient-facing app. Two patients were unable to complete the testing session, due to technical issues. Research Nurses suggested minor modifications to improve functionality and the layout of the clinician dashboard and the training materials.<h4>Conclusion</h4>By testing the effectiveness, efficiency, and satisfaction of our novel ePRO system (PROmics<sup>R</sup>), we learnt that most people with an inflammatory condition found it easy to report their symptoms using an app on their own device. Their experiences using the PROmics<sup>R</sup> ePRO system within a trial environment will be further explored in our upcoming feasibility testing. Research nurses were also positive and found the clinical dashboard easy-to-use. Using ePROs in early phase trials is important in order to provide evidence of therapeutic responses and tolerability, increase the evidence based, and inform methodology development.<h4>Trial registration</h4>ISRCTN, ISRCTN80103507. Registered 01 April 2022, https://www.isrctn.com/ISRCTN80103507.",,pdf:https://jpro.springeropen.com/counter/pdf/10.1186/s41687-023-00634-3; doi:https://doi.org/10.1186/s41687-023-00634-3; html:https://europepmc.org/articles/PMC10562321; pdf:https://europepmc.org/articles/PMC10562321?pdf=render
 38193339,https://doi.org/10.1161/jaha.123.029827,Soluble Suppression of Tumorigenicity-2 Predicts Mortality and Right Heart Failure in Patients With a Left Ventricular Assist Device.,"Numan L, Aarts E, Ramjankhan F, Oerlemans MIF, van der Meer MG, de Jonge N, Oppelaar AM, Kemperman H, Asselbergs FW, Van Laake LW.",,Journal of the American Heart Association,2024,2024-01-09,Y,Right Heart Failure; Left Ventricular Assist Device; End‐stage Heart Failure; Soluble Suppression Of Tumorigenicity‐2,,,"<h4>Background</h4>Soluble suppression of tumorigenicity-2 (sST2) predicts mortality in patients with heart failure. The predictive value of sST2 in patients with a left ventricular assist device remains unknown. Therefore, we studied the relationship between sST2 and outcome after left ventricular assist device implantation.<h4>Methods and results</h4>sST2 levels of patients with a left ventricular assist device implanted between January 2015 and December 2022 were included in this observational study. The median follow-up was 25 months, during which 1573 postoperative sST2 levels were measured in 199 patients, with a median of 29 ng/mL. Survival of patients with normal and elevated preoperative levels was compared using Kaplan-Meier analysis, which did not differ significantly (<i>P</i>=0.22) between both groups. The relationship between postoperative sST2, survival, and right heart failure was evaluated using a joint model, which showed a significant relationship between the absolute sST2 level and mortality, with a hazard ratio (HR) of 1.20 (95% CI, 1.10-1.130; <i>P</i><0.01) and an HR of 1.22 (95% CI, 1.07-1.39; <i>P</i>=0.01) for right heart failure, both per 10-unit sST2 increase. The sST2 instantaneous change was not predictive for survival or right heart failure (<i>P</i>=0.99 and <i>P</i>=0.94, respectively). Multivariate joint model analysis showed a significant relationship between sST2 with mortality adjusted for NT-proBNP (N-terminal pro-B-type natriuretic peptide), with an HR of 1.19 (95% CI, 1.00-1.42; <i>P</i>=0.05), whereas the HR of right heart failure was not significant (1.22 [95% CI, 0.94-1.59]; <i>P</i>=0.14), both per 10-unit sST2 increase.<h4>Conclusions</h4>Time-dependent postoperative sST2 predicts all-cause mortality after left ventricular assist device implantation after adjustment for NT-proBNP. Future research is warranted into possible target interventions and the optimal monitoring frequency.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.123.029827; doi:https://doi.org/10.1161/JAHA.123.029827; html:https://europepmc.org/articles/PMC10926819; pdf:https://europepmc.org/articles/PMC10926819?pdf=render
 36529816,https://doi.org/10.1038/s41598-022-26357-x,Novel multimorbidity clusters in people with eczema and asthma: a population-based cluster analysis.,"Mulick AR, Henderson AD, Prieto-Merino D, Mansfield KE, Matthewman J, Quint JK, Lyons RA, Sheikh A, McAllister DA, Nitsch D, Langan SM.",,Scientific reports,2022,2022-12-18,Y,,,,"Eczema and asthma are allergic diseases and two of the commonest chronic conditions in high-income countries. Their co-existence with other allergic conditions is common, but little research exists on wider multimorbidity with these conditions. We set out to identify and compare clusters of multimorbidity in people with eczema or asthma and people without. Using routinely-collected primary care data from the U.K. Clinical Research Practice Datalink GOLD, we identified adults ever having eczema (or asthma), and comparison groups never having eczema (or asthma). We derived clusters of multimorbidity from hierarchical cluster analysis of Jaccard distances between pairs of diagnostic categories estimated from mixed-effects logistic regressions. We analysed 434,422 individuals with eczema (58% female, median age 47 years) and 1,333,281 individuals without (55% female, 47 years), and 517,712 individuals with asthma (53% female, 44 years) and 1,601,210 individuals without (53% female, 45 years). Age at first morbidity, sex and having eczema/asthma affected the scope of multimorbidity, with women, older age and eczema/asthma being associated with larger morbidity clusters. Injuries, digestive, nervous system and mental health disorders were more commonly seen in eczema and asthma than control clusters. People with eczema and asthma of all ages and both sexes may experience greater multimorbidity than people without eczema and asthma, including conditions not previously recognised as contributing to their disease burden. This work highlights areas where there is a critical need for research addressing the burden and drivers of multimorbidity in order to inform strategies to reduce poor health outcomes.",,pdf:https://www.nature.com/articles/s41598-022-26357-x.pdf; doi:https://doi.org/10.1038/s41598-022-26357-x; html:https://europepmc.org/articles/PMC9760185; pdf:https://europepmc.org/articles/PMC9760185?pdf=render
@@ -1147,19 +1149,19 @@ PMC10686417,https://doi.org/,The impact of restricted provision of publicly fund
 32926504,https://doi.org/10.1002/pds.5121,Implementing high-dimensional propensity score principles to improve confounder adjustment in UK electronic health records.,"Tazare J, Smeeth L, Evans SJW, Williamson E, Douglas IJ.",,Pharmacoepidemiology and drug safety,2020,2020-09-14,N,Pharmacoepidemiology; Electronic Health Records; Electronic Medical Records; High-dimensional Propensity Score; Database Research; Confounder Adjustment,,,"<h4>Purpose</h4>Recent evidence from US claims data suggests use of high-dimensional propensity score (hd-PS) methods improve adjustment for confounding in non-randomised studies of interventions. However, it is unclear how best to apply hd-PS principles outside their original setting, given important differences between claims data and electronic health records (EHRs). We aimed to implement the hd-PS in the setting of United Kingdom (UK) EHRs.<h4>Methods</h4>We studied the interaction between clopidogrel and proton pump inhibitors (PPIs). Whilst previous observational studies suggested an interaction (with reduced effect of clopidogrel), case-only, genetic and randomised trial approaches showed no interaction, strongly suggesting the original observational findings were subject to confounding. We derived a cohort of clopidogrel users from the UK Clinical Practice Research Datalink linked with the Myocardial Ischaemia National Audit Project. Analyses estimated the hazard ratio (HR) for myocardial infarction (MI) comparing PPI users with non-users using a Cox model adjusting for confounders. To reflect unique characteristics of UK EHRs, we varied the application of hd-PS principles including the level of grouping within coding systems and adapting the assessment of code recurrence. Results were compared with traditional analyses.<h4>Results</h4>Twenty-four thousand four hundred and seventy-one patients took clopidogrel, of whom 9111 were prescribed a PPI. Traditional PS approaches obtained a HR for the association between PPI use and MI of 1.17 (95% CI: 1.00-1.35). Applying hd-PS modifications resulted in estimates closer to the expected null (HR 1.00; 95% CI: 0.78-1.28).<h4>Conclusions</h4>hd-PS provided improved adjustment for confounding compared with other approaches, suggesting hd-PS can be usefully applied in UK EHRs.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pds.5121; doi:https://doi.org/10.1002/pds.5121
 36769754,https://doi.org/10.3390/jcm12031106,The Causal Association of Irritable Bowel Syndrome with Multiple Disease Outcomes: A Phenome-Wide Mendelian Randomization Study.,"Li C, Chen Y, Chen Y, Ying Z, Hu Y, Kuang Y, Yang H, Song H, Zeng X.",,Journal of clinical medicine,2023,2023-01-31,Y,irritable bowel syndrome; Phenome-wide Association Study; Individual-level Mendelian Randomization; Summary-level Mendelian Randomization,,,"<h4>Background</h4>This study aimed to identify novel associations between irritable bowel syndrome (IBS) and a broad range of outcomes.<h4>Methods</h4>In total, 346,352 white participants in the U.K. Biobank were randomly divided into two halves, in which a genome-wide association study (GWAS) of IBS and a polygenic risk score (PRS) analysis of IBS using GWAS summary statistics were conducted, respectively. A phenome-wide association study (PheWAS) based on the PRS of IBS was performed to identify disease outcomes associated with IBS. Then, the causalities of these associations were tested by both one-sample (individual-level data in U.K. Biobank) and two-sample (publicly available summary statistics) Mendelian randomization (MR). Sex-stratified PheWAS-MR analyses were performed in male and female, separately.<h4>Results</h4>Our PheWAS identified five diseases associated with genetically predicted IBS. Conventional MR confirmed these causal associations between IBS and depression (OR: 1.07, 95%CI: 1.01-1.14, <i>p</i> = 0.02), diverticular diseases of the intestine (OR: 1.13, 95%CI: 1.08-1.19, <i>p</i> = 3.00 × 10<sup>-6</sup>), gastro-esophageal reflux disease (OR: 1.09, 95%CI: 1.05-1.13, <i>p</i> = 3.72 × 10<sup>-5</sup>), dyspepsia (OR: 1.21, 95%CI: 1.13-1.30, <i>p</i> = 9.28 × 10<sup>-8</sup>), and diaphragmatic hernia (OR: 1.10, 95%CI: 1.05-1.15, <i>p</i> = 2.75 × 10<sup>-5</sup>). The causality of these associations was observed in female only, but not men.<h4>Conclusions</h4>Increased risks of IBS is found to cause a series of disease outcomes. Our findings support further investigation on the clinical relevance of increased IBS risks with mental and digestive disorders.",,pdf:https://www.mdpi.com/2077-0383/12/3/1106/pdf?version=1675154986; doi:https://doi.org/10.3390/jcm12031106; html:https://europepmc.org/articles/PMC9918111; pdf:https://europepmc.org/articles/PMC9918111?pdf=render
 31611193,https://doi.org/10.1136/archdischild-2019-317248,"Self-harm presentation across healthcare settings by sex in young people: an e-cohort study using routinely collected linked healthcare data in Wales, UK.","Marchant A, Turner S, Balbuena L, Peters E, Williams D, Lloyd K, Lyons R, John A.",,Archives of disease in childhood,2020,2019-10-14,Y,epidemiology; Child Psychiatry; Accident & Emergency; Adolescent Health; Health Service,,,"<h4>Background</h4>This study used individual-level linked data across general practice, emergency departments (EDs), outpatients and hospital admissions to examine contacts across settings and time by sex for self-harm in individuals aged 10-24 years old in Wales, UK.<h4>Methods</h4>A whole population-based e-cohort study of routinely collected healthcare data was conducted. Rates of self-harm across settings over time by sex were examined. Individuals were categorised based on the service(s) to which they presented.<h4>Results</h4>A total of 937 697 individuals aged 10-24 years contributed 5 369 794 person years of data from 1 January 2003 to 30 September 2015. Self-harm incidence was highest in primary care but remained stable over time (incident rate ratio (IRR)=1.0; 95% CI 0.9 to 1.1). Incidence of ED attendance increased over time (IRR=1.3; 95% CI 1.2 to 1.5) as did hospital admissions (IRR=1.4; 95% CI 1.1 to 1.6). Incidence in the 15-19 years age group was the highest across all settings. The largest increases were seen in the youngest age group. There were increases in ED attendances for both sexes; however, females are more likely than males to be admitted following this. This was most evident in individuals 10-15 years old, where 76% of females were admitted compared with just 49% of males. The majority of associated outpatient appointments were under a mental health specialty.<h4>Conclusions</h4>This is the first study to compare self-harm in people aged 10-24 years across primary care, EDs and hospital settings in the UK. The high rates of self-harm in primary care and for young men in EDs highlight these as important settings for intervention.",,pdf:https://adc.bmj.com/content/archdischild/105/4/347.full.pdf; doi:https://doi.org/10.1136/archdischild-2019-317248; html:https://europepmc.org/articles/PMC7146921; pdf:https://europepmc.org/articles/PMC7146921?pdf=render
+31765395,https://doi.org/10.1371/journal.pone.0225625,Semantic computational analysis of anticoagulation use in atrial fibrillation from real world data.,"Bean DM, Teo J, Wu H, Oliveira R, Patel R, Bendayan R, Shah AM, Dobson RJB, Scott PA.",,PloS one,2019,2019-11-25,Y,,,,"Atrial fibrillation (AF) is the most common arrhythmia and significantly increases stroke risk. This risk is effectively managed by oral anticoagulation. Recent studies using national registry data indicate increased use of anticoagulation resulting from changes in guidelines and the availability of newer drugs. The aim of this study is to develop and validate an open source risk scoring pipeline for free-text electronic health record data using natural language processing. AF patients discharged from 1st January 2011 to 1st October 2017 were identified from discharge summaries (N = 10,030, 64.6% male, average age 75.3 ± 12.3 years). A natural language processing pipeline was developed to identify risk factors in clinical text and calculate risk for ischaemic stroke (CHA2DS2-VASc) and bleeding (HAS-BLED). Scores were validated vs two independent experts for 40 patients. Automatic risk scores were in strong agreement with the two independent experts for CHA2DS2-VASc (average kappa 0.78 vs experts, compared to 0.85 between experts). Agreement was lower for HAS-BLED (average kappa 0.54 vs experts, compared to 0.74 between experts). In high-risk patients (CHA2DS2-VASc ≥2) OAC use has increased significantly over the last 7 years, driven by the availability of DOACs and the transitioning of patients from AP medication alone to OAC. Factors independently associated with OAC use included components of the CHA2DS2-VASc and HAS-BLED scores as well as discharging specialty and frailty. OAC use was highest in patients discharged under cardiology (69%). Electronic health record text can be used for automatic calculation of clinical risk scores at scale. Open source tools are available today for this task but require further validation. Analysis of routinely collected EHR data can replicate findings from large-scale curated registries.","Bean et al. looked at using clinical notes to calculate risk scores: CHADSVASC and HASBLED for 10,030 AF patients from 2011 to October 2017), they’ve validated their natural language processing algorithm with getting clinicians to calculate the risk in conventional manner for 40 of cases, the two scores were in higher agreement for stroke risk compared to HAS-BLED They’ve concluded on usefulness of NLP method in risk calculation at the large scale.",pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0225625&type=printable; doi:https://doi.org/10.1371/journal.pone.0225625; html:https://europepmc.org/articles/PMC6876873; pdf:https://europepmc.org/articles/PMC6876873?pdf=render
 32657853,https://doi.org/10.1097/sap.0000000000002434,"Making the Most of Big Data in Plastic Surgery: Improving Outcomes, Protecting Patients, Informing Service Providers.","Gibson JAG, Dobbs TD, Kouzaris L, Lacey A, Thompson S, Akbari A, Hutchings HA, Lineaweaver WC, Lyons RA, Whitaker IS.",,Annals of plastic surgery,2021,2021-03-01,N,,,,"<h4>Abstract</h4>In medicine, ""big data"" refers to the interdisciplinary analysis of high-volume, diverse clinical and lifestyle information on large patient populations. Recent advancements in data storage and electronic record keeping have enabled the expansion of research in this field. In the United Kingdom, Big data has been highlighted as one of the government's ""8 Great Technologies,"" and the Medical Research Council has invested more than £100 million since 2012 in developing the Health Data Research UK infrastructure. The recent Royal College of Surgeons Commission of the Future of Surgery concluded that analysis of big data is one of the 4 most likely avenues to bring some of the most innovative changes to surgical practice in the 21st century.In this article, we provide an overview of the nascent field of big data analytics in plastic and highlight how it has the potential to improve outcomes, increase safety, and aid service planning.We outline the current resources available, the emerging role of big data within the subspecialties of burns, microsurgery, skin and breast cancer, and how these data can be used. We critically review the limitations and considerations raised with big data, offer suggestions regarding database optimization, and suggest future directions for research in this exciting field.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa53972/Download/53972__17281__0cb520258c2b49cdb0e751a62be92c5d.pdf; doi:https://doi.org/10.1097/SAP.0000000000002434
 35793336,https://doi.org/10.1371/journal.pone.0266521,"Spatiotemporal mapping of major trauma in Victoria, Australia.","Beck B, Zammit-Mangion A, Fry R, Smith K, Gabbe B.",,PloS one,2022,2022-07-06,Y,,,,"<h4>Background</h4>Spatiotemporal modelling techniques allow one to predict injury across time and space. However, such methods have been underutilised in injury studies. This study demonstrates the use of statistical spatiotemporal modelling in identifying areas of significantly high injury risk, and areas witnessing significantly increasing risk over time.<h4>Methods</h4>We performed a retrospective review of hospitalised major trauma patients from the Victorian State Trauma Registry, Australia, between 2007 and 2019. Geographical locations of injury events were mapped to the 79 local government areas (LGAs) in the state. We employed Bayesian spatiotemporal models to quantify spatial and temporal patterns, and analysed the results across a range of geographical remoteness and socioeconomic levels.<h4>Results</h4>There were 31,317 major trauma patients included. For major trauma overall, we observed substantial spatial variation in injury incidence and a significant 2.1% increase in injury incidence per year. Area-specific risk of injury by motor vehicle collision was higher in regional areas relative to metropolitan areas, while risk of injury by low fall was higher in metropolitan areas. Significant temporal increases were observed in injury by low fall, and the greatest increases were observed in the most disadvantaged LGAs.<h4>Conclusions</h4>These findings can be used to inform injury prevention initiatives, which could be designed to target areas with relatively high injury risk and with significantly increasing injury risk over time. Our finding that the greatest year-on-year increases in injury incidence were observed in the most disadvantaged areas highlights the need for a greater emphasis on reducing inequities in injury.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0266521&type=printable; doi:https://doi.org/10.1371/journal.pone.0266521; html:https://europepmc.org/articles/PMC9258853; pdf:https://europepmc.org/articles/PMC9258853?pdf=render
-31765395,https://doi.org/10.1371/journal.pone.0225625,Semantic computational analysis of anticoagulation use in atrial fibrillation from real world data.,"Bean DM, Teo J, Wu H, Oliveira R, Patel R, Bendayan R, Shah AM, Dobson RJB, Scott PA.",,PloS one,2019,2019-11-25,Y,,,,"Atrial fibrillation (AF) is the most common arrhythmia and significantly increases stroke risk. This risk is effectively managed by oral anticoagulation. Recent studies using national registry data indicate increased use of anticoagulation resulting from changes in guidelines and the availability of newer drugs. The aim of this study is to develop and validate an open source risk scoring pipeline for free-text electronic health record data using natural language processing. AF patients discharged from 1st January 2011 to 1st October 2017 were identified from discharge summaries (N = 10,030, 64.6% male, average age 75.3 ± 12.3 years). A natural language processing pipeline was developed to identify risk factors in clinical text and calculate risk for ischaemic stroke (CHA2DS2-VASc) and bleeding (HAS-BLED). Scores were validated vs two independent experts for 40 patients. Automatic risk scores were in strong agreement with the two independent experts for CHA2DS2-VASc (average kappa 0.78 vs experts, compared to 0.85 between experts). Agreement was lower for HAS-BLED (average kappa 0.54 vs experts, compared to 0.74 between experts). In high-risk patients (CHA2DS2-VASc ≥2) OAC use has increased significantly over the last 7 years, driven by the availability of DOACs and the transitioning of patients from AP medication alone to OAC. Factors independently associated with OAC use included components of the CHA2DS2-VASc and HAS-BLED scores as well as discharging specialty and frailty. OAC use was highest in patients discharged under cardiology (69%). Electronic health record text can be used for automatic calculation of clinical risk scores at scale. Open source tools are available today for this task but require further validation. Analysis of routinely collected EHR data can replicate findings from large-scale curated registries.","Bean et al. looked at using clinical notes to calculate risk scores: CHADSVASC and HASBLED for 10,030 AF patients from 2011 to October 2017), they’ve validated their natural language processing algorithm with getting clinicians to calculate the risk in conventional manner for 40 of cases, the two scores were in higher agreement for stroke risk compared to HAS-BLED They’ve concluded on usefulness of NLP method in risk calculation at the large scale.",pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0225625&type=printable; doi:https://doi.org/10.1371/journal.pone.0225625; html:https://europepmc.org/articles/PMC6876873; pdf:https://europepmc.org/articles/PMC6876873?pdf=render
 35459950,https://doi.org/10.1093/intqhc/mzac031,Modelling the effect of COVID-19 mass vaccination on acute hospital admissions.,"Booton RD, Powell AL, Turner KME, Wood RM.",,International journal for quality in health care : journal of the International Society for Quality in Health Care,2022,2022-05-01,N,Vaccination; Coronavirus; Mathematical Modelling; Bed Management; Hospital Capacity; Covid-19,,,"<h4>Background</h4>Managing high levels of acute COVID-19 bed occupancy can affect the quality of care provided to both affected patients and those requiring other hospital services. Mass vaccination has offered a route to reduce societal restrictions while protecting hospitals from being overwhelmed. Yet, early in the mass vaccination effort, the possible impact on future bed pressures remained subject to considerable uncertainty.<h4>Objective</h4>The aim of this study was to model the effect of vaccination on projections of acute and intensive care bed demand within a 1 million resident healthcare system located in South West England.<h4>Methods</h4>An age-structured epidemiological model of the susceptible-exposed-infectious-recovered type was fitted to local data up to the time of the study, in early March 2021. Model parameters and vaccination scenarios were calibrated through a system-wide multidisciplinary working group, comprising public health intelligence specialists, healthcare planners, epidemiologists and academics. Scenarios assumed incremental relaxations to societal restrictions according to the envisaged UK Government timeline, with all restrictions to be removed by 21 June 2021.<h4>Results</h4>Achieving 95% vaccine uptake in adults by 31 July 2021 would not avert the third wave in autumn 2021 but would produce a median peak bed requirement ∼6% (IQR: 1-24%) of that experienced during the second wave (January 2021). A 2-month delay in vaccine rollout would lead to significantly higher peak bed occupancy, at 66% (11-146%) of that of the second wave. If only 75% uptake was achieved (the amount typically associated with vaccination campaigns), then the second wave peak for acute and intensive care beds would be exceeded by 4% and 19%, respectively, an amount which would seriously pressure hospital capacity.<h4>Conclusion</h4>Modelling influenced decision-making among senior managers in setting COVID-19 bed capacity levels, as well as highlighting the importance of public health in promoting high vaccine uptake among the population. Forecast accuracy has since been supported by actual data collected following the analysis, with observed peak bed occupancy falling comfortably within the inter-quartile range of modelled projections.",,pdf:https://academic.oup.com/intqhc/article-pdf/34/2/mzac031/43704475/mzac031.pdf; doi:https://doi.org/10.1093/intqhc/mzac031
-37953241,https://doi.org/10.1186/s12916-023-03153-6,Cardiovascular events and venous thromboembolism after primary malignant or non-malignant brain tumour diagnosis: a population matched cohort study in Wales (United Kingdom).,"Poon MTC, Brennan PM, Jin K, Sudlow CLM, Figueroa JD.",,BMC medicine,2023,2023-11-13,Y,Brain cancer; Cerebrovascular disease; Neuro-oncology; Population-based,,,"<h4>Background</h4>Elevated standardised mortality ratio of cardiovascular diseases (CVD) in patients with brain tumours may result from differences in the CVD incidences and cardiovascular risk factors. We compared the risk of CVD among patients with a primary malignant or non-malignant brain tumour to a matched general population cohort, accounting for other co-morbidities.<h4>Methods</h4>Using data from the Secured Anonymised Information Linkage (SAIL) Databank in Wales (United Kingdom), we identified all adults aged ≥ 18 years in the primary care database with first diagnosis of malignant or non-malignant brain tumour identified in the cancer registry in 2000-2014 and a matched cohort (case-to-control ratio 1:5) by age, sex and primary care provider from the general population without any cancer diagnosis. Outcomes included fatal and non-fatal major vascular events (stroke, ischaemic heart disease, aortic and peripheral vascular diseases) and venous thromboembolism (VTE). We used multivariable Cox models adjusted for clinical risk factors to compare risks, stratified by tumour behaviour (malignant or non-malignant) and follow-up period.<h4>Results</h4>There were 2869 and 3931 people diagnosed with malignant or non-malignant brain tumours, respectively, between 2000 and 2014 in Wales. They were matched to 33,785 controls. Within the first year of tumour diagnosis, malignant tumour was associated with a higher risk of VTE (hazard ratio [HR] 21.58, 95% confidence interval 16.12-28.88) and stroke (HR 3.32, 2.44-4.53). After the first year, the risks of VTE (HR 2.20, 1.52-3.18) and stroke (HR 1.45, 1.00-2.10) remained higher than controls. Patients with non-malignant tumours had higher risks of VTE (HR 3.72, 2.73-5.06), stroke (HR 4.06, 3.35-4.93) and aortic and peripheral arterial disease (HR 2.09, 1.26-3.48) within the first year of diagnosis compared with their controls.<h4>Conclusions</h4>The elevated CVD and VTE risks suggested risk reduction may be a strategy to improve life quality and survival in people with a brain tumour.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-023-03153-6; doi:https://doi.org/10.1186/s12916-023-03153-6; html:https://europepmc.org/articles/PMC10641987; pdf:https://europepmc.org/articles/PMC10641987?pdf=render
 31153319,https://doi.org/10.1121/1.5100272,Developing a large scale population screening tool for the assessment of Parkinson's disease using telephone-quality voice.,"Arora S, Baghai-Ravary L, Tsanas A.",,The Journal of the Acoustical Society of America,2019,2019-05-01,N,,Applied Analytics,neurological,"Recent studies have demonstrated that analysis of laboratory-quality voice recordings can be used to accurately differentiate people diagnosed with Parkinson's disease (PD) from healthy controls (HCs). These findings could help facilitate the development of remote screening and monitoring tools for PD. In this study, 2759 telephone-quality voice recordings from 1483 PD and 15 321 recordings from 8300 HC participants were analyzed. To account for variations in phonetic backgrounds, data were acquired from seven countries. A statistical framework for analyzing voice was developed, whereby 307 dysphonia measures that quantify different properties of voice impairment, such as breathiness, roughness, monopitch, hoarse voice quality, and exaggerated vocal tremor, were computed. Feature selection algorithms were used to identify robust parsimonious feature subsets, which were used in combination with a random forests (RFs) classifier to accurately distinguish PD from HC. The best tenfold cross-validation performance was obtained using Gram-Schmidt orthogonalization and RF, leading to mean sensitivity of 64.90% (standard deviation, SD, 2.90%) and mean specificity of 67.96% (SD 2.90%). This large scale study is a step forward toward assessing the development of a reliable, cost-effective, and practical clinical decision support tool for screening the population at large for PD using telephone-quality voice.",,pdf:https://asa.scitation.org/doi/pdf/10.1121/1.5100272; doi:https://doi.org/10.1121/1.5100272; html:https://europepmc.org/articles/PMC6509044; pdf:https://europepmc.org/articles/PMC6509044?pdf=render; doi:https://doi.org/10.1121/1.5100272
-37327673,https://doi.org/10.1016/j.ebiom.2023.104655,HFrEF subphenotypes based on 4210 repeatedly measured circulating proteins are driven by different biological mechanisms.,"Petersen TB, de Bakker M, Asselbergs FW, Harakalova M, Akkerhuis KM, Brugts JJ, van Ramshorst J, Lumbers RT, Ostroff RM, Katsikis PD, van der Spek PJ, Umans VA, Boersma E, Rizopoulos D, Kardys I.",,EBioMedicine,2023,2023-06-14,Y,Proteomics; Phenotypes; Biomarkers; Heart Failure; Unsupervised Machine Learning,,,"<h4>Background</h4>HFrEF is a heterogenous condition with high mortality. We used serial assessments of 4210 circulating proteins to identify distinct novel protein-based HFrEF subphenotypes and to investigate underlying dynamic biological mechanisms. Herewith we aimed to gain pathophysiological insights and fuel opportunities for personalised treatment.<h4>Methods</h4>In 382 patients, we performed trimonthly blood sampling during a median follow-up of 2.1 [IQR:1.1-2.6] years. We selected all baseline samples and two samples closest to the primary endpoint (PEP; composite of cardiovascular mortality, HF hospitalization, LVAD implantation, and heart transplantation) or censoring, and applied an aptamer-based multiplex proteomic approach. Using unsupervised machine learning methods, we derived clusters from 4210 repeatedly measured proteomic biomarkers. Sets of proteins that drove cluster allocation were analysed via an enrichment analysis. Differences in clinical characteristics and PEP occurrence were evaluated.<h4>Findings</h4>We identified four subphenotypes with different protein profiles, prognosis and clinical characteristics, including age (median [IQR] for subphenotypes 1-4, respectively:70 [64, 76], 68 [60, 79], 57 [47, 65], 59 [56, 66]years), EF (30 [26, 36], 26 [20, 38], 26 [22, 32], 33 [28, 37]%), and chronic renal failure (45%, 65%, 36%, 37%). Subphenotype allocation was driven by subsets of proteins associated with various biological functions, such as oxidative stress, inflammation and extracellular matrix organisation. Clinical characteristics of the subphenotypes were aligned with these associations. Subphenotypes 2 and 3 had the worst prognosis compared to subphenotype 1 (adjHR (95%CI):3.43 (1.76-6.69), and 2.88 (1.37-6.03), respectively).<h4>Interpretation</h4>Four circulating-protein based subphenotypes are present in HFrEF, which are driven by varying combinations of protein subsets, and have different clinical characteristics and prognosis.<h4>Clinical trial registration</h4>ClinicalTrials.gov Identifier: NCT01851538https://clinicaltrials.gov/ct2/show/NCT01851538.<h4>Funding</h4>EU/EFPIA IMI2JU BigData@Heart grant n°116074, Jaap Schouten Foundation and Noordwest Academie.",,pdf:http://www.thelancet.com/article/S2352396423002207/pdf; doi:https://doi.org/10.1016/j.ebiom.2023.104655; html:https://europepmc.org/articles/PMC10279550; pdf:https://europepmc.org/articles/PMC10279550?pdf=render
+37953241,https://doi.org/10.1186/s12916-023-03153-6,Cardiovascular events and venous thromboembolism after primary malignant or non-malignant brain tumour diagnosis: a population matched cohort study in Wales (United Kingdom).,"Poon MTC, Brennan PM, Jin K, Sudlow CLM, Figueroa JD.",,BMC medicine,2023,2023-11-13,Y,Brain cancer; Cerebrovascular disease; Neuro-oncology; Population-based,,,"<h4>Background</h4>Elevated standardised mortality ratio of cardiovascular diseases (CVD) in patients with brain tumours may result from differences in the CVD incidences and cardiovascular risk factors. We compared the risk of CVD among patients with a primary malignant or non-malignant brain tumour to a matched general population cohort, accounting for other co-morbidities.<h4>Methods</h4>Using data from the Secured Anonymised Information Linkage (SAIL) Databank in Wales (United Kingdom), we identified all adults aged ≥ 18 years in the primary care database with first diagnosis of malignant or non-malignant brain tumour identified in the cancer registry in 2000-2014 and a matched cohort (case-to-control ratio 1:5) by age, sex and primary care provider from the general population without any cancer diagnosis. Outcomes included fatal and non-fatal major vascular events (stroke, ischaemic heart disease, aortic and peripheral vascular diseases) and venous thromboembolism (VTE). We used multivariable Cox models adjusted for clinical risk factors to compare risks, stratified by tumour behaviour (malignant or non-malignant) and follow-up period.<h4>Results</h4>There were 2869 and 3931 people diagnosed with malignant or non-malignant brain tumours, respectively, between 2000 and 2014 in Wales. They were matched to 33,785 controls. Within the first year of tumour diagnosis, malignant tumour was associated with a higher risk of VTE (hazard ratio [HR] 21.58, 95% confidence interval 16.12-28.88) and stroke (HR 3.32, 2.44-4.53). After the first year, the risks of VTE (HR 2.20, 1.52-3.18) and stroke (HR 1.45, 1.00-2.10) remained higher than controls. Patients with non-malignant tumours had higher risks of VTE (HR 3.72, 2.73-5.06), stroke (HR 4.06, 3.35-4.93) and aortic and peripheral arterial disease (HR 2.09, 1.26-3.48) within the first year of diagnosis compared with their controls.<h4>Conclusions</h4>The elevated CVD and VTE risks suggested risk reduction may be a strategy to improve life quality and survival in people with a brain tumour.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-023-03153-6; doi:https://doi.org/10.1186/s12916-023-03153-6; html:https://europepmc.org/articles/PMC10641987; pdf:https://europepmc.org/articles/PMC10641987?pdf=render
 32864476,https://doi.org/10.23889/ijpds.v5i1.1157,"Prevalence of Down's Syndrome in England, 1998-2013: Comparison of linked surveillance data and electronic health records.","Doidge JC, Morris JK, Harron KL, Stevens S, Gilbert R.",,International journal of population data science,2020,2020-01-01,Y,Prevalence; Data Linkage; Disease Surveillance; Down’s Syndrome; Electronic Health Records; Linkage Error,,,"<h4>Introduction</h4>Disease registers and electronic health records are valuable resources for disease surveillance and research but can be limited by variation in data quality over time. Quality may be limited in terms of the accuracy of clinical information, of the internal linkage that supports person-based analysis of most administrative datasets, or by errors in linkage between multiple datasets.<h4>Objectives</h4>By linking the National Down Syndrome Cytogenetic Register (NDSCR) to Hospital Episode Statistics for England (HES), we aimed to assess the quality of each and establish a consistent approach for analysis of trends in prevalence of Down's syndrome among live births in England.<h4>Methods</h4>Probabilistic record linkage of NDSCR to HES for the period 1998-2013 was supported by linkage of babies to mothers within HES. Comparison of prevalence estimates in England were made using NDSCR only, HES data only, and linked data. Capture-recapture analysis and quantitative bias analysis were used to account for potential errors, including false positive diagnostic codes, unrecorded diagnoses, and linkage error.<h4>Results</h4>Analyses of single-source data indicated increasing live birth prevalence of Down's Syndrome, particularly in the analysis of HES. Linked data indicated a contrastingly stable prevalence of 12.3 (plausible range: 11.6-12.7) cases per 10 000 live births.<h4>Conclusion</h4>Case ascertainment in NDSCR improved slightly over time, creating a picture of slowly increasing prevalence. The emerging epidemic suggested by HES primarily reflects improving linkage within HES (assignment of unique patient identifiers to hospital episodes). Administrative data are valuable but trends should be interpreted with caution, and with assessment of data quality over time. Data linkage with quantitative bias analysis can provide more robust estimation and, in this case, stronger evidence that prevalence is not increasing. Routine linkage of administrative and register data can enhance the value of each.",,pdf:https://ijpds.org/article/download/1157/2531; doi:https://doi.org/10.23889/ijpds.v5i1.1157; html:https://europepmc.org/articles/PMC7115985; pdf:https://europepmc.org/articles/PMC7115985?pdf=render
-37717234,https://doi.org/10.1111/1742-6723.14312,Prevalence of alcohol and other drug detections in non-transport injury events.,"Lau G, Mitra B, Gabbe BJ, Dietze PM, Reeder S, Cameron PA, Smit V, Schneider HG, Symons E, Koolstra C, Stewart C, Beck B.",,Emergency medicine Australasia : EMA,2024,2023-09-17,Y,Alcoholic Intoxication; Illicit Drug; Blood Alcohol Content; Wounds And Injury; Substance-related Disorder; Substance Use Detection,,,"<h4>Objective</h4>To measure the prevalence of alcohol and/or other drug (AOD) detections in suspected major trauma patients with non-transport injuries who presented to an adult major trauma centre.<h4>Methods</h4>This registry-based cohort study examined the prevalence of AOD detections in patients aged ≥18 years who: (i) sustained non-transport injuries; and (ii) met predefined trauma call-out criteria and were therefore managed by an interdisciplinary trauma team between 1 July 2021 and 31 December 2022. Prevalence was measured using routine in-hospital blood alcohol and urine drug screens.<h4>Results</h4>A total of 1469 cases met the inclusion criteria. Of cases with a valid blood test (n = 1248, 85.0%), alcohol was detected in 313 (25.1%) patients. Of the 733 (49.9%) cases with urine drug screen results, cannabinoids were most commonly detected (n = 103, 14.1%), followed by benzodiazepines (n = 98, 13.4%), amphetamine-type substances (n = 80, 10.9%), opioids (n = 28, 3.8%) and cocaine (n = 17, 2.3%). Alcohol and/or at least one other drug was detected in 37.4% (n = 472) of cases with either a blood alcohol or urine drug test completed (n = 1263, 86.0%). Multiple substances were detected in 16.6% (n = 119) of cases with both blood alcohol and urine drug screens (n = 718, 48.9%). Detections were prevalent in cases of interpersonal violence (n = 123/179, 68.7%) and intentional self-harm (n = 50/106, 47.2%), and in those occurring on Friday and Saturday nights (n = 118/191, 61.8%).<h4>Conclusion</h4>AOD detections were common in trauma patients with non-transport injury causes. Population-level surveillance is needed to inform prevention strategies that address AOD use as a significant risk factor for serious injury.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/1742-6723.14312; doi:https://doi.org/10.1111/1742-6723.14312; html:https://europepmc.org/articles/PMC10952644; pdf:https://europepmc.org/articles/PMC10952644?pdf=render
-31951005,https://doi.org/10.1093/jamia/ocz211,On classifying sepsis heterogeneity in the ICU: insight using machine learning.,"Ibrahim ZM, Wu H, Hamoud A, Stappen L, Dobson RJB, Agarossi A.",,Journal of the American Medical Informatics Association : JAMIA,2020,2020-03-01,Y,Sepsis; Machine Learning; Artificial Intelligence In Medicine; Sepsis Prediction; Sepsis Subtypes,Applied Analytics,,"<h4>Objectives</h4>Current machine learning models aiming to predict sepsis from electronic health records (EHR) do not account 20 for the heterogeneity of the condition despite its emerging importance in prognosis and treatment. This work demonstrates the added value of stratifying the types of organ dysfunction observed in patients who develop sepsis in the intensive care unit (ICU) in improving the ability to recognize patients at risk of sepsis from their EHR data.<h4>Materials and methods</h4>Using an ICU dataset of 13 728 records, we identify clinically significant sepsis subpopulations with distinct organ dysfunction patterns. We perform classification experiments with random forest, gradient boost trees, and support vector machines, using the identified subpopulations to distinguish patients who develop sepsis in the ICU from those who do not.<h4>Results</h4>The classification results show that features selected using sepsis subpopulations as background knowledge yield a superior performance in distinguishing septic from non-septic patients regardless of the classification model used. The improved performance is especially pronounced in specificity, which is a current bottleneck in sepsis prediction machine learning models.<h4>Conclusion</h4>Our findings can steer machine learning efforts toward more personalized models for complex conditions including sepsis.",Ibrahim et al. categorized patients in groups based on the type of organ failure. This categorization helped machine based algorithms to correctly identify those at high risk of sepsis.,pdf:https://academic.oup.com/jamia/article-pdf/27/3/437/34153319/ocz211.pdf; doi:https://doi.org/10.1093/jamia/ocz211; html:https://europepmc.org/articles/PMC7025363; pdf:https://europepmc.org/articles/PMC7025363?pdf=render
+37327673,https://doi.org/10.1016/j.ebiom.2023.104655,HFrEF subphenotypes based on 4210 repeatedly measured circulating proteins are driven by different biological mechanisms.,"Petersen TB, de Bakker M, Asselbergs FW, Harakalova M, Akkerhuis KM, Brugts JJ, van Ramshorst J, Lumbers RT, Ostroff RM, Katsikis PD, van der Spek PJ, Umans VA, Boersma E, Rizopoulos D, Kardys I.",,EBioMedicine,2023,2023-06-14,Y,Proteomics; Phenotypes; Biomarkers; Heart Failure; Unsupervised Machine Learning,,,"<h4>Background</h4>HFrEF is a heterogenous condition with high mortality. We used serial assessments of 4210 circulating proteins to identify distinct novel protein-based HFrEF subphenotypes and to investigate underlying dynamic biological mechanisms. Herewith we aimed to gain pathophysiological insights and fuel opportunities for personalised treatment.<h4>Methods</h4>In 382 patients, we performed trimonthly blood sampling during a median follow-up of 2.1 [IQR:1.1-2.6] years. We selected all baseline samples and two samples closest to the primary endpoint (PEP; composite of cardiovascular mortality, HF hospitalization, LVAD implantation, and heart transplantation) or censoring, and applied an aptamer-based multiplex proteomic approach. Using unsupervised machine learning methods, we derived clusters from 4210 repeatedly measured proteomic biomarkers. Sets of proteins that drove cluster allocation were analysed via an enrichment analysis. Differences in clinical characteristics and PEP occurrence were evaluated.<h4>Findings</h4>We identified four subphenotypes with different protein profiles, prognosis and clinical characteristics, including age (median [IQR] for subphenotypes 1-4, respectively:70 [64, 76], 68 [60, 79], 57 [47, 65], 59 [56, 66]years), EF (30 [26, 36], 26 [20, 38], 26 [22, 32], 33 [28, 37]%), and chronic renal failure (45%, 65%, 36%, 37%). Subphenotype allocation was driven by subsets of proteins associated with various biological functions, such as oxidative stress, inflammation and extracellular matrix organisation. Clinical characteristics of the subphenotypes were aligned with these associations. Subphenotypes 2 and 3 had the worst prognosis compared to subphenotype 1 (adjHR (95%CI):3.43 (1.76-6.69), and 2.88 (1.37-6.03), respectively).<h4>Interpretation</h4>Four circulating-protein based subphenotypes are present in HFrEF, which are driven by varying combinations of protein subsets, and have different clinical characteristics and prognosis.<h4>Clinical trial registration</h4>ClinicalTrials.gov Identifier: NCT01851538https://clinicaltrials.gov/ct2/show/NCT01851538.<h4>Funding</h4>EU/EFPIA IMI2JU BigData@Heart grant n°116074, Jaap Schouten Foundation and Noordwest Academie.",,pdf:http://www.thelancet.com/article/S2352396423002207/pdf; doi:https://doi.org/10.1016/j.ebiom.2023.104655; html:https://europepmc.org/articles/PMC10279550; pdf:https://europepmc.org/articles/PMC10279550?pdf=render
 32790708,https://doi.org/10.1371/journal.pone.0237298,Clinical academic research in the time of Corona: A simulation study in England and a call for action.,"Banerjee A, Katsoulis M, Lai AG, Pasea L, Treibel TA, Manisty C, Denaxas S, Quarta G, Hemingway H, Cavalcante JL, Noursadeghi M, Moon JC.",,PloS one,2020,2020-08-13,Y,,,,"<h4>Objectives</h4>We aimed to model the impact of coronavirus (COVID-19) on the clinical academic response in England, and to provide recommendations for COVID-related research.<h4>Design</h4>A stochastic model to determine clinical academic capacity in England, incorporating the following key factors which affect the ability to conduct research in the COVID-19 climate: (i) infection growth rate and population infection rate (from UK COVID-19 statistics and WHO); (ii) strain on the healthcare system (from published model); and (iii) availability of clinical academic staff with appropriate skillsets affected by frontline clinical activity and sickness (from UK statistics).<h4>Setting</h4>Clinical academics in primary and secondary care in England.<h4>Participants</h4>Equivalent of 3200 full-time clinical academics in England.<h4>Interventions</h4>Four policy approaches to COVID-19 with differing population infection rates: ""Italy model"" (6%), ""mitigation"" (10%), ""relaxed mitigation"" (40%) and ""do-nothing"" (80%) scenarios. Low and high strain on the health system (no clinical academics able to do research at 10% and 5% infection rate, respectively.<h4>Main outcome measures</h4>Number of full-time clinical academics available to conduct clinical research during the pandemic in England.<h4>Results</h4>In the ""Italy model"", ""mitigation"", ""relaxed mitigation"" and ""do-nothing"" scenarios, from 5 March 2020 the duration (days) and peak infection rates (%) are 95(2.4%), 115(2.5%), 240(5.3%) and 240(16.7%) respectively. Near complete attrition of academia (87% reduction, <400 clinical academics) occurs 35 days after pandemic start for 11, 34, 62, 76 days respectively-with no clinical academics at all for 37 days in the ""do-nothing"" scenario. Restoration of normal academic workforce (80% of normal capacity) takes 11, 12, 30 and 26 weeks respectively.<h4>Conclusions</h4>Pandemic COVID-19 crushes the science needed at system level. National policies mitigate, but the academic community needs to adapt. We highlight six key strategies: radical prioritisation (eg 3-4 research ideas per institution), deep resourcing, non-standard leadership (repurposing of key non-frontline teams), rationalisation (profoundly simple approaches), careful site selection (eg protected sites with large academic backup) and complete suspension of academic competition with collaborative approaches.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0237298&type=printable; doi:https://doi.org/10.1371/journal.pone.0237298; html:https://europepmc.org/articles/PMC7425844; pdf:https://europepmc.org/articles/PMC7425844?pdf=render
-36812613,https://doi.org/10.1371/journal.pdig.0000190,Optimizing cardiovascular risk assessment and registration in a developing cardiovascular learning health care system: Women benefit most.,"Groenhof TKJ, Haitjema S, Lely AT, Grobbee DE, Asselbergs FW, Bots ML, UCC-CVRM and UPOD Study groups.",,PLOS digital health,2023,2023-02-08,Y,,,,"Since 2015 we organized a uniform, structured collection of a fixed set of cardiovascular risk factors according the (inter)national guidelines on cardiovascular risk management. We evaluated the current state of a developing cardiovascular towards learning healthcare system-the Utrecht Cardiovascular Cohort Cardiovascular Risk Management (UCC-CVRM)-and its potential effect on guideline adherence in cardiovascular risk management. We conducted a before-after study comparing data from patients included in UCC-CVRM (2015-2018) and patients treated in our center before UCC-CVRM (2013-2015) who would have been eligible for UCC-CVRM using the Utrecht Patient Oriented Database (UPOD). Proportions of cardiovascular risk factor measurement before and after UCC-CVRM initiation were compared, as were proportions of patients that required (change of) blood pressure, lipid, or blood glucose lowering treatment. We estimated the likelihood to miss patients with hypertension, dyslipidemia, and elevated HbA1c before UCC-CVRM for the whole cohort and stratified for sex. In the present study, patients included up to October 2018 (n = 1904) were matched with 7195 UPOD patients with similar age, sex, department of referral and diagnose description. Completeness of risk factor measurement increased, ranging from 0% -77% before to 82%-94% after UCC-CVRM initiation. Before UCC-CVRM, we found more unmeasured risk factors in women compared to men. This sex-gap resolved in UCC-CVRM. The likelihood to miss hypertension, dyslipidemia, and elevated HbA1c was reduced by 67%, 75% and 90%, respectively, after UCC-CVRM initiation. A finding more pronounced in women compared to men. In conclusion, a systematic registration of the cardiovascular risk profile substantially improves guideline adherent assessment and decreases the risk of missing patients with elevated levels with an indication for treatment. The sex-gap disappeared after UCC-CVRM initiation. Thus, an LHS approach contributes to a more inclusive insight into quality of care and prevention of cardiovascular disease (progression).",,pdf:https://journals.plos.org/digitalhealth/article/file?id=10.1371/journal.pdig.0000190&type=printable; doi:https://doi.org/10.1371/journal.pdig.0000190; html:https://europepmc.org/articles/PMC9931327; pdf:https://europepmc.org/articles/PMC9931327?pdf=render
+31951005,https://doi.org/10.1093/jamia/ocz211,On classifying sepsis heterogeneity in the ICU: insight using machine learning.,"Ibrahim ZM, Wu H, Hamoud A, Stappen L, Dobson RJB, Agarossi A.",,Journal of the American Medical Informatics Association : JAMIA,2020,2020-03-01,Y,Sepsis; Machine Learning; Artificial Intelligence In Medicine; Sepsis Prediction; Sepsis Subtypes,Applied Analytics,,"<h4>Objectives</h4>Current machine learning models aiming to predict sepsis from electronic health records (EHR) do not account 20 for the heterogeneity of the condition despite its emerging importance in prognosis and treatment. This work demonstrates the added value of stratifying the types of organ dysfunction observed in patients who develop sepsis in the intensive care unit (ICU) in improving the ability to recognize patients at risk of sepsis from their EHR data.<h4>Materials and methods</h4>Using an ICU dataset of 13 728 records, we identify clinically significant sepsis subpopulations with distinct organ dysfunction patterns. We perform classification experiments with random forest, gradient boost trees, and support vector machines, using the identified subpopulations to distinguish patients who develop sepsis in the ICU from those who do not.<h4>Results</h4>The classification results show that features selected using sepsis subpopulations as background knowledge yield a superior performance in distinguishing septic from non-septic patients regardless of the classification model used. The improved performance is especially pronounced in specificity, which is a current bottleneck in sepsis prediction machine learning models.<h4>Conclusion</h4>Our findings can steer machine learning efforts toward more personalized models for complex conditions including sepsis.",Ibrahim et al. categorized patients in groups based on the type of organ failure. This categorization helped machine based algorithms to correctly identify those at high risk of sepsis.,pdf:https://academic.oup.com/jamia/article-pdf/27/3/437/34153319/ocz211.pdf; doi:https://doi.org/10.1093/jamia/ocz211; html:https://europepmc.org/articles/PMC7025363; pdf:https://europepmc.org/articles/PMC7025363?pdf=render
 31416346,https://doi.org/10.1161/circulationaha.119.041980,Machine Learning to Predict the Likelihood of Acute Myocardial Infarction.,"Than MP, Pickering JW, Sandoval Y, Shah ASV, Tsanas A, Apple FS, Blankenberg S, Cullen L, Mueller C, Neumann JT, Twerenbold R, Westermann D, Beshiri A, Mills NL, MI3 Collaborative.",,Circulation,2019,2019-08-16,Y,Troponin; Myocardial infarction; acute coronary syndrome; Machine Learning,Applied Analytics,,"<h4>Background</h4>Variations in cardiac troponin concentrations by age, sex, and time between samples in patients with suspected myocardial infarction are not currently accounted for in diagnostic approaches. We aimed to combine these variables through machine learning to improve the assessment of risk for individual patients.<h4>Methods</h4>A machine learning algorithm (myocardial-ischemic-injury-index [MI<sup>3</sup>]) incorporating age, sex, and paired high-sensitivity cardiac troponin I concentrations, was trained on 3013 patients and tested on 7998 patients with suspected myocardial infarction. MI<sup>3</sup> uses gradient boosting to compute a value (0-100) reflecting an individual's likelihood of a diagnosis of type 1 myocardial infarction and estimates the sensitivity, negative predictive value, specificity and positive predictive value for that individual. Assessment was by calibration and area under the receiver operating characteristic curve. Secondary analysis evaluated example MI<sup>3</sup> thresholds from the training set that identified patients as low risk (99% sensitivity) and high risk (75% positive predictive value), and performance at these thresholds was compared in the test set to the 99th percentile and European Society of Cardiology rule-out pathways.<h4>Results</h4>Myocardial infarction occurred in 404 (13.4%) patients in the training set and 849 (10.6%) patients in the test set. MI<sup>3</sup> was well calibrated with a very high area under the receiver operating characteristic curve of 0.963 [0.956-0.971] in the test set and similar performance in early and late presenters. Example MI<sup>3</sup> thresholds identifying low- and high-risk patients in the training set were 1.6 and 49.7, respectively. In the test set, MI<sup>3</sup> values were <1.6 in 69.5% with a negative predictive value of 99.7% (99.5-99.8%) and sensitivity of 97.8% (96.7-98.7%), and were ≥49.7 in 10.6% with a positive predictive value of 71.8% (68.9-75.0%) and specificity of 96.7% (96.3-97.1%). Using these thresholds, MI<sup>3</sup> performed better than the European Society of Cardiology 0/3-hour pathway (sensitivity, 82.5% [74.5-88.8%]; specificity, 92.2% [90.7-93.5%]) and the 99th percentile at any time point (sensitivity, 89.6% [87.4-91.6%]); specificity, 89.3% [88.6-90.0%]).<h4>Conclusions</h4>Using machine learning, MI<sup>3</sup> provides an individualized and objective assessment of the likelihood of myocardial infarction, which can be used to identify low- and high-risk patients who may benefit from earlier clinical decisions.<h4>Clinical trial registration</h4>URL: https://www.anzctr.org.au. Unique identifier: ACTRN12616001441404.",,doi:https://doi.org/10.1161/circulationaha.119.041980; doi:https://doi.org/10.1161/CIRCULATIONAHA.119.041980; html:https://europepmc.org/articles/PMC6749969; pdf:https://europepmc.org/articles/PMC6749969?pdf=render
+37717234,https://doi.org/10.1111/1742-6723.14312,Prevalence of alcohol and other drug detections in non-transport injury events.,"Lau G, Mitra B, Gabbe BJ, Dietze PM, Reeder S, Cameron PA, Smit V, Schneider HG, Symons E, Koolstra C, Stewart C, Beck B.",,Emergency medicine Australasia : EMA,2024,2023-09-17,Y,Alcoholic Intoxication; Illicit Drug; Blood Alcohol Content; Wounds And Injury; Substance-related Disorder; Substance Use Detection,,,"<h4>Objective</h4>To measure the prevalence of alcohol and/or other drug (AOD) detections in suspected major trauma patients with non-transport injuries who presented to an adult major trauma centre.<h4>Methods</h4>This registry-based cohort study examined the prevalence of AOD detections in patients aged ≥18 years who: (i) sustained non-transport injuries; and (ii) met predefined trauma call-out criteria and were therefore managed by an interdisciplinary trauma team between 1 July 2021 and 31 December 2022. Prevalence was measured using routine in-hospital blood alcohol and urine drug screens.<h4>Results</h4>A total of 1469 cases met the inclusion criteria. Of cases with a valid blood test (n = 1248, 85.0%), alcohol was detected in 313 (25.1%) patients. Of the 733 (49.9%) cases with urine drug screen results, cannabinoids were most commonly detected (n = 103, 14.1%), followed by benzodiazepines (n = 98, 13.4%), amphetamine-type substances (n = 80, 10.9%), opioids (n = 28, 3.8%) and cocaine (n = 17, 2.3%). Alcohol and/or at least one other drug was detected in 37.4% (n = 472) of cases with either a blood alcohol or urine drug test completed (n = 1263, 86.0%). Multiple substances were detected in 16.6% (n = 119) of cases with both blood alcohol and urine drug screens (n = 718, 48.9%). Detections were prevalent in cases of interpersonal violence (n = 123/179, 68.7%) and intentional self-harm (n = 50/106, 47.2%), and in those occurring on Friday and Saturday nights (n = 118/191, 61.8%).<h4>Conclusion</h4>AOD detections were common in trauma patients with non-transport injury causes. Population-level surveillance is needed to inform prevention strategies that address AOD use as a significant risk factor for serious injury.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/1742-6723.14312; doi:https://doi.org/10.1111/1742-6723.14312; html:https://europepmc.org/articles/PMC10952644; pdf:https://europepmc.org/articles/PMC10952644?pdf=render
+36812613,https://doi.org/10.1371/journal.pdig.0000190,Optimizing cardiovascular risk assessment and registration in a developing cardiovascular learning health care system: Women benefit most.,"Groenhof TKJ, Haitjema S, Lely AT, Grobbee DE, Asselbergs FW, Bots ML, UCC-CVRM and UPOD Study groups.",,PLOS digital health,2023,2023-02-08,Y,,,,"Since 2015 we organized a uniform, structured collection of a fixed set of cardiovascular risk factors according the (inter)national guidelines on cardiovascular risk management. We evaluated the current state of a developing cardiovascular towards learning healthcare system-the Utrecht Cardiovascular Cohort Cardiovascular Risk Management (UCC-CVRM)-and its potential effect on guideline adherence in cardiovascular risk management. We conducted a before-after study comparing data from patients included in UCC-CVRM (2015-2018) and patients treated in our center before UCC-CVRM (2013-2015) who would have been eligible for UCC-CVRM using the Utrecht Patient Oriented Database (UPOD). Proportions of cardiovascular risk factor measurement before and after UCC-CVRM initiation were compared, as were proportions of patients that required (change of) blood pressure, lipid, or blood glucose lowering treatment. We estimated the likelihood to miss patients with hypertension, dyslipidemia, and elevated HbA1c before UCC-CVRM for the whole cohort and stratified for sex. In the present study, patients included up to October 2018 (n = 1904) were matched with 7195 UPOD patients with similar age, sex, department of referral and diagnose description. Completeness of risk factor measurement increased, ranging from 0% -77% before to 82%-94% after UCC-CVRM initiation. Before UCC-CVRM, we found more unmeasured risk factors in women compared to men. This sex-gap resolved in UCC-CVRM. The likelihood to miss hypertension, dyslipidemia, and elevated HbA1c was reduced by 67%, 75% and 90%, respectively, after UCC-CVRM initiation. A finding more pronounced in women compared to men. In conclusion, a systematic registration of the cardiovascular risk profile substantially improves guideline adherent assessment and decreases the risk of missing patients with elevated levels with an indication for treatment. The sex-gap disappeared after UCC-CVRM initiation. Thus, an LHS approach contributes to a more inclusive insight into quality of care and prevention of cardiovascular disease (progression).",,pdf:https://journals.plos.org/digitalhealth/article/file?id=10.1371/journal.pdig.0000190&type=printable; doi:https://doi.org/10.1371/journal.pdig.0000190; html:https://europepmc.org/articles/PMC9931327; pdf:https://europepmc.org/articles/PMC9931327?pdf=render
 36712153,https://doi.org/10.1093/ehjdh/ztac046,Systematic approach to outcome assessment from coded electronic healthcare records in the DaRe2THINK NHS-embedded randomized trial.,"Wang X, Mobley AR, Tica O, Okoth K, Ghosh RE, Myles P, Williams T, Haynes S, Nirantharakumar K, Shukla D, Kotecha D, DaRe2THINK Trial Committees .",,European heart journal. Digital health,2022,2022-09-16,Y,Coding; Anticoagulation; Atrial fibrillation; Randomized controlled trial; Primary Care; Secondary Care; Electronic Healthcare Record,,,"<h4>Aims</h4>Improving the efficiency of clinical trials is key to their continued importance in directing evidence-based patient care. Digital innovations, in particular the use of electronic healthcare records (EHRs), allow for large-scale screening and follow up of participants. However, it is critical these developments are accompanied by robust and transparent methods that can support high-quality and high clinical value research.<h4>Methods and results</h4>The DaRe2THINK trial includes a series of novel processes, including nationwide pseudonymized pre screening of the primary-care EHR across England, digital enrolment, remote e-consent, and 'no-visit' follow up by linking all primary- and secondary-care health data with patient-reported outcomes. DaRe2THINK is a pragmatic, healthcare-embedded randomized trial testing whether earlier use of direct oral anticoagulants in patients with prior or current atrial fibrillation can prevent thromboembolic events and cognitive decline (www.birmingham.ac.uk/dare2think). This study outlines the systematic approach and methodology employed to define patient information and outcome events. This includes transparency on all medical code lists and phenotypes used in the trial across a variety of national data sources, including Clinical Practice Research Datalink Aurum (primary care), Hospital Episode Statistics (secondary care), and the Office for National Statistics (mortality).<h4>Conclusion</h4>Co-designed by a patient and public involvement team, DaRe2THINK presents an opportunity to transform the approach to randomized trials in the setting of routine healthcare, providing high-quality evidence generation in populations representative of the community at risk.",,pdf:https://academic.oup.com/ehjdh/article-pdf/3/3/426/47117043/ztac046.pdf; doi:https://doi.org/10.1093/ehjdh/ztac046; html:https://europepmc.org/articles/PMC9708037; pdf:https://europepmc.org/articles/PMC9708037?pdf=render
 38274035,https://doi.org/10.1136/bmjmed-2023-000738,Availability of results of clinical trials registered on EU Clinical Trials Register: cross sectional audit study.,"DeVito NJ, Morley J, Smith JA, Drysdale H, Goldacre B, Heneghan C.",,BMJ medicine,2024,2024-01-12,Y,"Ethics, Medical; Clinical Governance; Clinical Trial; Health Policy",,,"<h4>Objective</h4>To identify the availability of results for trials registered on the European Union Clinical Trials Register (EUCTR) compared with other dissemination routes to understand its value as a results repository.<h4>Design</h4>Cross sectional audit study.<h4>Setting</h4>EUCTR protocols and results sections, data extracted 1-3 December 2020.<h4>Population</h4>Random sample of 500 trials registered on EUCTR with a completion date of more than two years from the beginning of searches (ie, 1 December 2018).<h4>Main outcome measures</h4>Proportion of trials with results across the examined dissemination routes (EUCTR, ClinicalTrials.gov, ISRCTN registry, and journal publications), and for each dissemination route individually. Prespecified secondary outcomes were number and proportion of unique results, and the timing of results, for each dissemination route.<h4>Results</h4>In the sample of 500 trials, availability of results on EUCTR (53.2%, 95% confidence interval 48.8% to 57.6%) was similar to the peer reviewed literature (58.6%, 54.3% to 62.9%) and exceeded the proportion of results available on other registries with matched records. Among the 383 trials with any results, 55 (14.4%, 10.9% to 17.9%) were only available on EUCTR. Also, after the launch of the EUCTR results database, median time to results was fastest on EUCTR (1142 days, 95% confidence interval 812 to 1492), comparable with journal publications (1226 days, 1074 to 1551), and exceeding ClinicalTrials.gov (3321 days, 1653 to undefined). For 117 trials (23.4%, 19.7% to 27.1%), however, results were published elsewhere but not submitted to the EUCTR registry, and no results were located in any dissemination route for 117 trials (23.4%, 19.7% to 27.1).<h4>Conclusions</h4>EUCTR should be considered in results searches for systematic reviews and can help researchers and the public to access the results of clinical trials, unavailable elsewhere, in a timely way. Reporting requirements, such as the EU's, can help in avoiding research waste by ensuring results are reported. The registry's true value, however, is unrealised because of inadequate compliance with EU guidelines, and problems with data quality that complicate the routine use of the registry. As the EU transitions to a new registry, continuing to emphasise the importance of EUCTR and the provision of timely and complete data is critical. For the future, EUCTR will still hold important information from the past two decades of clinical research in Europe. With increased efforts from sponsors and regulators, the registry can continue to grow as a source of results of clinical trials, many of which might be unavailable from other dissemination routes.",,doi:https://doi.org/10.1136/bmjmed-2023-000738; html:https://europepmc.org/articles/PMC10806997; pdf:https://europepmc.org/articles/PMC10806997?pdf=render
 35308999,https://doi.org/,Axes of Prognosis: Identifying Subtypes of COVID-19 Outcomes.,"Whitfield E, Coffey C, Zhang H, Shi T, Wu X, Li Q, Wu H.",,AMIA ... Annual Symposium proceedings. AMIA Symposium,2021,2021-01-01,N,,,,"COVID-19 is a disease with vast impact, yet much remains unclear about patient outcomes. Most approaches to risk prediction of COVID-19 focus on binary or tertiary severity outcomes, despite the heterogeneity of the disease. In this work, we identify heterogeneous subtypes of COVID-19 outcomes by considering 'axes' of prognosis. We propose two innovative clustering approaches - 'Layered Axes' and 'Prognosis Space' - to apply on patients' outcome data. We then show how these clusters can help predict a patient's deterioration pathway on their hospital admission, using random forest classification. We illustrate this methodology on a cohort from Wuhan in early 2020. We discover interesting subgroups of poor prognosis, particularly within respiratory patients, and predict respiratory subgroup membership with high accuracy. This work could assist clinicians in identifying appropriate treatments at patients' hospital admission. Moreover, our method could be used to explore subtypes of 'long COVID' and other diseases with heterogeneous outcomes.",,html:https://europepmc.org/articles/PMC8861682; pdf:https://europepmc.org/articles/PMC8861682?pdf=render
@@ -1174,8 +1176,8 @@ PMC10686417,https://doi.org/,The impact of restricted provision of publicly fund
 35463778,https://doi.org/10.3389/fcvm.2022.859310,Fairness in Cardiac Magnetic Resonance Imaging: Assessing Sex and Racial Bias in Deep Learning-Based Segmentation.,"Puyol-Antón E, Ruijsink B, Mariscal Harana J, Piechnik SK, Neubauer S, Petersen SE, Razavi R, Chowienczyk P, King AP.",,Frontiers in cardiovascular medicine,2022,2022-04-07,Y,Segmentation; Cardiac Magnetic Resonance; Deep Learning; Fair Ai; Inequality Fairness In Deep Learning-Based Cmr Segmentation,,,"<h4>Background</h4>Artificial intelligence (AI) techniques have been proposed for automation of cine CMR segmentation for functional quantification. However, in other applications AI models have been shown to have potential for sex and/or racial bias. The objective of this paper is to perform the first analysis of sex/racial bias in AI-based cine CMR segmentation using a large-scale database.<h4>Methods</h4>A state-of-the-art deep learning (DL) model was used for automatic segmentation of both ventricles and the myocardium from cine short-axis CMR. The dataset consisted of end-diastole and end-systole short-axis cine CMR images of 5,903 subjects from the UK Biobank database (61.5 ± 7.1 years, 52% male, 81% white). To assess sex and racial bias, we compared Dice scores and errors in measurements of biventricular volumes and function between patients grouped by race and sex. To investigate whether segmentation bias could be explained by potential confounders, a multivariate linear regression and ANCOVA were performed.<h4>Results</h4>Results on the overall population showed an excellent agreement between the manual and automatic segmentations. We found statistically significant differences in Dice scores between races (white ∼94% vs. minority ethnic groups 86-89%) as well as in absolute/relative errors in volumetric and functional measures, showing that the AI model was biased against minority racial groups, even after correction for possible confounders. The results of a multivariate linear regression analysis showed that no covariate could explain the Dice score bias between racial groups. However, for the Mixed and Black race groups, sex showed a weak positive association with the Dice score. The results of an ANCOVA analysis showed that race was the main factor that can explain the overall difference in Dice scores between racial groups.<h4>Conclusion</h4>We have shown that racial bias can exist in DL-based cine CMR segmentation models when training with a database that is sex-balanced but not race-balanced such as the UK Biobank.",,pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2022.859310/pdf; doi:https://doi.org/10.3389/fcvm.2022.859310; html:https://europepmc.org/articles/PMC9021445; pdf:https://europepmc.org/articles/PMC9021445?pdf=render
 38796315,https://doi.org/10.1093/ageing/afae102,Development of the Community-based complex Interventions to sustain Independence in Older People (CII-OP) typology: a qualitative synthesis of interventions in randomised controlled trials.,"Crocker TF, Jordão M, Lam N, Ramiz R, Mirza L, Patel I, Ellwood A, Patetsini E, Ensor J, Forster A, Clegg A, Gladman J, HTA complex interventions review team.",,Age and ageing,2024,2024-05-01,Y,Taxonomy; Classification; Older People; Frail; Rehabilitation Therapy; Primary Health Care Practice,,,"<h4>Introduction</h4>Community-based services to sustain independence for older people have varying configurations. A typology of these interventions would improve service provision and research by providing conceptual clarity and enabling the identification of effective configurations. We aimed to produce such a typology.<h4>Method</h4>We developed our typology by qualitatively synthesising community-based complex interventions to sustain independence in older people, evaluated in randomised controlled trials (RCTs), in four stages: (i) systematically identifying relevant RCTs; (ii) extracting descriptions of interventions (including control) using the Template for Intervention Description and Replication; (iii) generating categories of key intervention features and (iv) grouping the interventions based on these categories. PROSPERO registration: CRD42019162195.<h4>Results</h4>Our search identified 129 RCTs involving 266 intervention arms. The Community-based complex Interventions to sustain Independence in Older People (CII-OP) typology comprises 14 action components and 5 tailoring components. Action components include procedures for treating patients or otherwise intended to directly improve their outcomes; regular examples include formal homecare; physical exercise; health education; activities of daily living training; providing aids and adaptations and nutritional support. Tailoring components involve a process that may result in care planning, with multiple action components being planned, recommended or prescribed. Multifactorial action from care planning was the most common tailoring component. It involves individualised, multidomain assessment and management, as in comprehensive geriatric assessment. Sixty-three different intervention types (combinations) were identified.<h4>Conclusions</h4>Our typology provides an empirical basis for service planning and evidence synthesis. We recommend better reporting about organisational aspects of interventions and usual care.",,pdf:https://academic.oup.com/ageing/article-pdf/53/5/afae102/57908349/afae102.pdf; doi:https://doi.org/10.1093/ageing/afae102; html:https://europepmc.org/articles/PMC11127769; pdf:https://europepmc.org/articles/PMC11127769?pdf=render
 37306981,https://doi.org/10.1001/jamaneurol.2023.1580,Independent Associations of Incident Epilepsy and Enzyme-Inducing and Non-Enzyme-Inducing Antiseizure Medications With the Development of Osteoporosis.,"Josephson CB, Gonzalez-Izquierdo A, Denaxas S, Sajobi TT, Klein KM, Wiebe S.",,JAMA neurology,2023,2023-08-01,N,,,,"<h4>Importance</h4>Both epilepsy and enzyme-inducing antiseizure medications (eiASMs) having varying reports of an association with increased risks for osteoporosis.<h4>Objective</h4>To quantify and model the independent hazards for osteoporosis associated with incident epilepsy and eiASMS and non-eiASMs.<h4>Design, setting, and participants</h4>This open cohort study covered the years 1998 to 2019, with a median (IQR) follow-up of 5 (1.7-11.1) years. Data were collected for 6275 patients enrolled in the Clinical Practice Research Datalink and from hospital electronic health records. No patients who met inclusion criteria (Clinical Practice Research Datalink-acceptable data, aged 18 years or older, follow-up after the Hospital Episode Statistics patient care linkage date of 1998, and free of osteoporosis at baseline) were excluded or declined.<h4>Exposure</h4>Incident adult-onset epilepsy using a 5-year washout and receipt of 4 consecutive ASMs.<h4>Main outcomes and measures</h4>The outcome was incident osteoporosis as determined through Cox proportional hazards or accelerated failure time models where appropriate. Incident epilepsy was treated as a time-varying covariate. Analyses controlled for age, sex, socioeconomic status, cancer, 1 or more years of corticosteroid use, body mass index, bariatric surgery, eating disorders, hyperthyroidism, inflammatory bowel disease, rheumatoid arthritis, smoking status, falls, fragility fractures, and osteoporosis screening tests. Subsequent analyses (1) excluded body mass index, which was missing in 30% of patients; (2) applied propensity score matching for receipt of an eiASM; (3) restricted analyses to only those with incident onset epilepsy; and (4) restricted analyses to patients who developed epilepsy at age 65 years or older. Analyses were performed between July 1 and October 31, 2022, and in February 2023 for revisions.<h4>Results</h4>Of 8 095 441 adults identified, 6275 had incident adult-onset epilepsy (3220 female [51%] and 3055 male [49%]; incidence rate, 62 per 100 000 person-years) with a median (IQR) age of 56 (38-73) years. When controlling for osteoporosis risk factors, incident epilepsy was independently associated with a 41% faster time to incident osteoporosis (time ratio [TR], 0.59; 95% CI, 0.52-0.67; P < .001). Both eiASMs (TR, 0.91; 95% CI, 0.87-0.95; P < .001) and non-eiASMs (TR, 0.77; 95% CI, 0.76-0.78; P < .001) were also associated with significant increased risks independent of epilepsy, accounting for 9% and 23% faster times to development of osteoporosis, respectively. The independent associations among epilepsy, eiASMs, and non-eiASMs remained consistent in propensity score-matched analyses, cohorts restricted to adult-onset epilepsy, and cohorts restricted to late-onset epilepsy.<h4>Conclusions and relevance</h4>These findings suggest that epilepsy is independently associated with a clinically meaningful increase in the risk for osteoporosis, as are both eiASMs and non-eiASMs. Routine screening and prophylaxis should be considered in all people with epilepsy.",,doi:https://doi.org/10.1001/jamaneurol.2023.1580; html:https://europepmc.org/articles/PMC10262059; doi:https://doi.org/10.1001/jamaneurol.2023.1580
-33851963,https://doi.org/10.1001/jamadermatol.2021.0009,Association Between Atopic Dermatitis and Educational Attainment in Denmark.,"Schmidt SAJ, Mailhac A, Darvalics B, Mulick A, Deleuran MS, Sørensen HT, Riis JL, Langan SM.",,JAMA dermatology,2021,2021-04-14,Y,,,,"<h4>Importance</h4>Atopic dermatitis (AD) may affect academic performance through multiple pathways, including poor concentration associated with itching, sleep deprivation, or adverse effects of medications. Because educational attainment is associated with health and well-being, any association with a prevalent condition such as AD is of major importance.<h4>Objective</h4>To examine whether a childhood diagnosis of AD is associated with lower educational attainment.<h4>Design, setting, and participants</h4>This population-based cohort study used linked routine health care data from January 1, 1977, to June 30, 2017 (end of registry follow-up), in Denmark. The study population included all children born in Denmark on June 30, 1987, or earlier with an inpatient or outpatient hospital clinic diagnosis of AD recorded before their 13th birthday (baseline) and a comparison cohort of children from the general population matched by birth year and sex. A secondary analysis included exposure-discordant full siblings as a comparison cohort to account for familial factors. Data were analyzed from September 11, 2019, to January 21, 2021.<h4>Exposures</h4>Hospital-diagnosed AD.<h4>Main outcomes and measures</h4>Estimated probability or risk of not attaining specific educational levels (lower secondary, upper secondary, and higher) by 30 years of age among children with AD compared with children in the matched general population cohort. Corresponding risk ratios (RRs) were computed using Poisson regression that was conditioned on matched sets and adjusted for age. The sibling analysis was conditioned on family and adjusted for sex and age.<h4>Results</h4>The study included a total of 61 153 children, 5927 in the AD cohort (3341 male [56.4%]) and 55 226 from the general population (31 182 male [56.5%]). Compared with matched children from the general population, children with AD were at increased risk of not attaining lower secondary education (150 of 5927 [2.5%] vs 924 of 55 226 [1.7%]; adjusted RR, 1.50; 95% CI, 1.26-1.78) and upper secondary education (1141 of 5777 [19.8%] vs 8690 of 52 899 [16.4%]; RR, 1.16; 95% CI, 1.09-1.24), but not higher education (2406 of 4636 [51.9%] vs 18 785 of 35 408 [53.1%]; RR, 0.95; 95% CI, 0.91-1.00). The absolute differences in probability were less than 3.5%. The comparison of 3259 children with AD and 4046 of their full siblings yielded estimates that were less pronounced than those in the main analysis (adjusted RR for lower secondary education, 1.29 [95% CI, 0.92-1.82]; adjusted RR for upper secondary education, 1.05 [95% CI, 0.93-1.18]; adjusted RR for higher education, 0.94 [95% CI, 0.87-1.02]).<h4>Conclusions and relevance</h4>This population-based cohort study found that hospital-diagnosed AD was associated with reduced educational attainment, but the clinical importance was uncertain owing to small absolute differences and possible confounding by familial factors in this study. Future studies should examine for replicability in other populations and variation by AD phenotype.",,pdf:https://jamanetwork.com/journals/jamadermatology/articlepdf/2778389/jamadermatology_schmidt_2021_oi_210002_1623774349.64965.pdf; doi:https://doi.org/10.1001/jamadermatol.2021.0009; html:https://europepmc.org/articles/PMC8047754
 32954362,https://doi.org/10.1038/s43016-020-0093-y,Nutriome-metabolome relationships provide insights into dietary intake and metabolism.,"Posma JM, Garcia-Perez I, Frost G, Aljuraiban GS, Chan Q, Van Horn L, Daviglus M, Stamler J, Holmes E, Elliott P, Nicholson JK.",,Nature food,2020,2020-06-22,N,,,,"Dietary assessment traditionally relies on self-reported data which are often inaccurate and may result in erroneous diet-disease risk associations. We illustrate how urinary metabolic phenotyping can be used as alternative approach for obtaining information on dietary patterns. We used two multi-pass 24-hr dietary recalls, obtained on two occasions on average three weeks apart, paired with two 24-hr urine collections from 1,848 U.S. individuals; 67 nutrients influenced the urinary metabotype measured with <sup>1</sup>H-NMR spectroscopy characterized by 46 structurally identified metabolites. We investigated the stability of each metabolite over time and showed that the urinary metabolic profile is more stable within individuals than reported dietary patterns. The 46 metabolites accurately predicted healthy and unhealthy dietary patterns in a free-living U.S. cohort and replicated in an independent U.K. cohort. We mapped these metabolites into a host-microbial metabolic network to identify key pathways and functions. These data can be used in future studies to evaluate how this set of diet-derived, stable, measurable bioanalytical markers are associated with disease risk. This knowledge may give new insights into biological pathways that characterize the shift from a healthy to unhealthy metabolic phenotype and hence give entry points for prevention and intervention strategies.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7497842; doi:https://doi.org/10.1038/s43016-020-0093-y; html:https://europepmc.org/articles/PMC7497842; pdf:https://europepmc.org/articles/PMC7497842?pdf=render; doi:https://doi.org/10.1038/s43016-020-0093-y
+33851963,https://doi.org/10.1001/jamadermatol.2021.0009,Association Between Atopic Dermatitis and Educational Attainment in Denmark.,"Schmidt SAJ, Mailhac A, Darvalics B, Mulick A, Deleuran MS, Sørensen HT, Riis JL, Langan SM.",,JAMA dermatology,2021,2021-04-14,Y,,,,"<h4>Importance</h4>Atopic dermatitis (AD) may affect academic performance through multiple pathways, including poor concentration associated with itching, sleep deprivation, or adverse effects of medications. Because educational attainment is associated with health and well-being, any association with a prevalent condition such as AD is of major importance.<h4>Objective</h4>To examine whether a childhood diagnosis of AD is associated with lower educational attainment.<h4>Design, setting, and participants</h4>This population-based cohort study used linked routine health care data from January 1, 1977, to June 30, 2017 (end of registry follow-up), in Denmark. The study population included all children born in Denmark on June 30, 1987, or earlier with an inpatient or outpatient hospital clinic diagnosis of AD recorded before their 13th birthday (baseline) and a comparison cohort of children from the general population matched by birth year and sex. A secondary analysis included exposure-discordant full siblings as a comparison cohort to account for familial factors. Data were analyzed from September 11, 2019, to January 21, 2021.<h4>Exposures</h4>Hospital-diagnosed AD.<h4>Main outcomes and measures</h4>Estimated probability or risk of not attaining specific educational levels (lower secondary, upper secondary, and higher) by 30 years of age among children with AD compared with children in the matched general population cohort. Corresponding risk ratios (RRs) were computed using Poisson regression that was conditioned on matched sets and adjusted for age. The sibling analysis was conditioned on family and adjusted for sex and age.<h4>Results</h4>The study included a total of 61 153 children, 5927 in the AD cohort (3341 male [56.4%]) and 55 226 from the general population (31 182 male [56.5%]). Compared with matched children from the general population, children with AD were at increased risk of not attaining lower secondary education (150 of 5927 [2.5%] vs 924 of 55 226 [1.7%]; adjusted RR, 1.50; 95% CI, 1.26-1.78) and upper secondary education (1141 of 5777 [19.8%] vs 8690 of 52 899 [16.4%]; RR, 1.16; 95% CI, 1.09-1.24), but not higher education (2406 of 4636 [51.9%] vs 18 785 of 35 408 [53.1%]; RR, 0.95; 95% CI, 0.91-1.00). The absolute differences in probability were less than 3.5%. The comparison of 3259 children with AD and 4046 of their full siblings yielded estimates that were less pronounced than those in the main analysis (adjusted RR for lower secondary education, 1.29 [95% CI, 0.92-1.82]; adjusted RR for upper secondary education, 1.05 [95% CI, 0.93-1.18]; adjusted RR for higher education, 0.94 [95% CI, 0.87-1.02]).<h4>Conclusions and relevance</h4>This population-based cohort study found that hospital-diagnosed AD was associated with reduced educational attainment, but the clinical importance was uncertain owing to small absolute differences and possible confounding by familial factors in this study. Future studies should examine for replicability in other populations and variation by AD phenotype.",,pdf:https://jamanetwork.com/journals/jamadermatology/articlepdf/2778389/jamadermatology_schmidt_2021_oi_210002_1623774349.64965.pdf; doi:https://doi.org/10.1001/jamadermatol.2021.0009; html:https://europepmc.org/articles/PMC8047754
 37609702,https://doi.org/10.1002/pds.5681,Adverse drug reactions and hospital admissions: Large case-control study of patients aged 65-100 years using linked English primary care and hospital data.,"van Staa TP, Pirmohamed M, Sharma A, Ashcroft DM, Buchan I.",,Pharmacoepidemiology and drug safety,2024,2023-08-23,N,Adverse drug reactions; Primary Care; Medicines; Pharmacovigilance; Polypharmacy,,,"<h4>Background</h4>Adverse drug reactions (ADRs) are common and a leading cause of injury. However, information on ADR risks of individual medicines is often limited. The aim of this hypothesis-generating study was to assess the relative importance of ADR-related and emergency hospital admission for large group of medication classes.<h4>Methods</h4>This study was a propensity-matched case-control study in English primary care. Data sources were Clinical Practice Research Databank and Aurum with longitudinal, anonymized, patient level electronic health records (EHRs) from English general practices linked to hospital records. Cases aged 65-100 with ADR-related or emergency hospital admission were matched to up to six controls by age, sex, morbidity and propensity scores for hospital admission risk. Medication groups with systemic administration as listed in the British National Formulary (used by prescribers for medication advice). Prescribing in the 84 days before the index date was assessed. Only medication groups with 50+ cases exposed were analysed. The outcomes of interest were ADR-related and emergency hospital admissions. Conditional logistic regression estimated odds ratios (ORs) and 95% confidence intervals (CI).<h4>Results</h4>The overall population included 121 546 cases with an ADR-related and 849 769 cases with emergency hospital admission. The percentage of hospitalizations with an ADR-related code for admission diagnosis was 1.83% and 6.58% with an ADR-related code at any time during hospitalization. A total of 137 medication groups was included in the main ADR analyses. Of these, 13 (9.5%) had statistically non-significant adjusted ORs, 58 (42.3%) statistically significant ORs between 1.0 and 1.5, 37 (27.0%) between 1.5-2.0, 18 (13.1%) between 2.0-3.0 and 11 (8.0%) 3.0 or higher. Several classes of antibiotics (including penicillins) were among medicines with largest ORs. Evaluating the 14 medications most often associated with ADRs, a strong association was found between the number of these medicines and the risk of ADR-related hospital admission (adjusted OR of 7.53 (95% CI 7.15-7.93) for those exposed to 6+ of these medicines).<h4>Conclusions and relevance</h4>There is a need for a regular systematic assessment of the harm-benefit ratio of medicines, harvesting the information in large healthcare databases and combining it with causality assessment of individual case histories.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pds.5681; doi:https://doi.org/10.1002/pds.5681
 35317796,https://doi.org/10.1186/s12916-022-02308-1,"Correction to: Lifetime risk of cardiovascular-renal disease in type 2 diabetes: a population-based study in 473,399 individuals.","Zhang R, Mamza JB, Morris T, Godfrey G, Asselbergs FW, Denaxas S, Hemingway H, Banerjee A.",,BMC medicine,2022,2022-03-23,Y,,,,,,pdf:https://bmcmedicine.biomedcentral.com/track/pdf/10.1186/s12916-022-02308-1; doi:https://doi.org/10.1186/s12916-022-02308-1; html:https://europepmc.org/articles/PMC8941726; pdf:https://europepmc.org/articles/PMC8941726?pdf=render
 38040454,https://doi.org/10.1101/cshperspect.a041473,Environmental Impacts of Machine Learning Applications in Protein Science.,"Lannelongue L, Inouye M.",,Cold Spring Harbor perspectives in biology,2023,2023-12-01,N,,,,"Computing tools and machine learning models play an increasingly important role in biology and are now an essential part of discoveries in protein science. The growing energy needs of modern algorithms have raised concerns in the computational science community in light of the climate emergency. In this work, we summarize the different ways in which protein science can negatively impact the environment and we present the carbon footprint of some popular protein algorithms: molecular simulations, inference of protein-protein interactions, and protein structure prediction. We show that large deep learning models such as AlphaFold and ESMFold can have carbon footprints reaching over 100 tonnes of CO<sub>2</sub>e in some cases. The magnitude of these impacts highlights the importance of monitoring and mitigating them, and we list actions scientists can take to achieve more sustainable protein computational science.",,pdf:http://cshperspectives.cshlp.org/content/15/12/a041473.full.pdf; doi:https://doi.org/10.1101/cshperspect.a041473
@@ -1191,8 +1193,8 @@ PMC10686417,https://doi.org/,The impact of restricted provision of publicly fund
 32908801,https://doi.org/10.1167/tvst.9.9.38,Merging Information From Infrared and Autofluorescence Fundus Images for Monitoring of Chorioretinal Atrophic Lesions.,"Ometto G, Montesano G, Sadeghi Afgeh S, Lazaridis G, Liu X, Keane PA, Crabb DP, Denniston AK.",,Translational vision science & technology,2020,2020-08-25,Y,Autofluorescence; Segmentation; infrared; Uveitis; Multimodal,,,"<h4>Purpose</h4>To develop a method for automated detection and progression analysis of chorioretinal atrophic lesions using the combined information of standard infrared (IR) and autofluorescence (AF) fundus images.<h4>Methods</h4>Eighteen eyes (from 16 subjects) with punctate inner choroidopathy were analyzed. Macular IR and blue AF images were acquired in all eyes with a Spectralis HRA+OCT device (Heidelberg Engineering, Heidelberg, Germany). Two clinical experts manually segmented chorioretinal lesions on the AF image. AF images were aligned to the corresponding IR. Two random forest models were trained to classify pixels of lesions, one based on the AF image only, the other based on the aligned IR-AF. The models were validated using a leave-one-out cross-validation and were tested against the manual segmentation to compare their performance. A time series from one eye was identified and used to evaluate the method based on the IR-AF in a case study.<h4>Results</h4>The method based on the AF images correctly classified 95% of the pixels (i.e., in vs. out of the lesion) with a Dice's coefficient of 0.80. The method based on the combined IR-AF correctly classified 96% of the pixels with a Dice's coefficient of 0.84.<h4>Conclusions</h4>The automated segmentation of chorioretinal lesions using IR and AF shows closer alignment to manual segmentation than the same method based on AF only. Merging information from multimodal images improves the automatic and objective segmentation of chorioretinal lesions even when based on a small dataset.<h4>Translational relevance</h4>Merged information from multimodal images improves segmentation performance of chorioretinal lesions.",,doi:https://doi.org/10.1167/tvst.9.9.38; doi:https://doi.org/10.1167/tvst.9.9.38; html:https://europepmc.org/articles/PMC7453042; pdf:https://europepmc.org/articles/PMC7453042?pdf=render
 36834176,https://doi.org/10.3390/ijerph20043477,"Non-Pharmacological Therapies for Post-Viral Syndromes, Including Long COVID: A Systematic Review.","Chandan JS, Brown KR, Simms-Williams N, Bashir NZ, Camaradou J, Heining D, Turner GM, Rivera SC, Hotham R, Minhas S, Nirantharakumar K, Sivan M, Khunti K, Raindi D, Marwaha S, Hughes SE, McMullan C, Marshall T, Calvert MJ, Haroon S, Aiyegbusi OL, TLC Study.",,International journal of environmental research and public health,2023,2023-02-16,Y,Rehabilitation; Systematic review; Pvs; Non-pharmacological Intervention; Covid-19; Long Covid; Post-covid-19 Condition; Post-acute Sequelae Of Sars-cov-2 Infection (Pasc); Post-Viral Syndromes,,,"<h4>Background</h4>Post-viral syndromes (PVS), including Long COVID, are symptoms sustained from weeks to years following an acute viral infection. Non-pharmacological treatments for these symptoms are poorly understood. This review summarises the evidence for the effectiveness of non-pharmacological treatments for PVS.<h4>Methods</h4>We conducted a systematic review to evaluate the effectiveness of non-pharmacological interventions for PVS, as compared to either standard care, alternative non-pharmacological therapy, or placebo. The outcomes of interest were changes in symptoms, exercise capacity, quality of life (including mental health and wellbeing), and work capability. We searched five databases (Embase, MEDLINE, PsycINFO, CINAHL, MedRxiv) for randomised controlled trials (RCTs) published between 1 January 2001 to 29 October 2021. The relevant outcome data were extracted, the study quality was appraised using the Cochrane risk-of-bias tool, and the findings were synthesised narratively.<h4>Findings</h4>Overall, five studies of five different interventions (Pilates, music therapy, telerehabilitation, resistance exercise, neuromodulation) met the inclusion criteria. Aside from music-based intervention, all other selected interventions demonstrated some support in the management of PVS in some patients.<h4>Interpretation</h4>In this study, we observed a lack of robust evidence evaluating the non-pharmacological treatments for PVS, including Long COVID. Considering the prevalence of prolonged symptoms following acute viral infections, there is an urgent need for clinical trials evaluating the effectiveness and cost-effectiveness of non-pharmacological treatments for patients with PVS.<h4>Registration</h4>The study protocol was registered with PROSPERO [CRD42021282074] in October 2021 and published in BMJ Open in 2022.",,pdf:https://www.mdpi.com/1660-4601/20/4/3477/pdf?version=1677135187; doi:https://doi.org/10.3390/ijerph20043477; html:https://europepmc.org/articles/PMC9967466; pdf:https://europepmc.org/articles/PMC9967466?pdf=render
 37191413,https://doi.org/10.14336/ad.2022.1107,Conceptual Overview of Biological Age Estimation.,"Salih A, Nichols T, Szabo L, Petersen SE, Raisi-Estabragh Z.",,Aging and disease,2023,2023-06-01,Y,,,,"Chronological age is an imperfect measure of the aging process, which is affected by a wide range of genetic and environmental exposures. Biological age estimates may be derived using mathematical modelling with biomarkers set as predictors and chronological age as the output. The difference between biological and chronological age is denoted the ""age gap"" and considered a complementary indicator of aging. The utility of the ""age gap"" metric is assessed through examination of its associations with exposures of interest and the demonstration of additional information provided by this metric over chronological age alone. This paper reviews the key concepts of biological age estimation, the age gap metric, and approaches to assessment of model performance in this context. We further discuss specific challenges for the field, in particular the limited generalisability of effect sizes across studies owing to dependency of the age gap metric on pre-processing and model building methods. The discussion will be centred on brain age estimation, but the concepts are transferable to all biological age estimation.",,pdf:http://www.aginganddisease.org/EN/PDF/10.14336/AD.2022.1107; doi:https://doi.org/10.14336/AD.2022.1107; html:https://europepmc.org/articles/PMC10187689; pdf:https://europepmc.org/articles/PMC10187689?pdf=render
-33704068,https://doi.org/10.7554/elife.64827,Longitudinal proteomic profiling of dialysis patients with COVID-19 reveals markers of severity and predictors of death.,"Gisby J, Clarke CL, Medjeral-Thomas N, Malik TH, Papadaki A, Mortimer PM, Buang NB, Lewis S, Pereira M, Toulza F, Fagnano E, Mawhin MA, Dutton EE, Tapeng L, Richard AC, Kirk PD, Behmoaras J, Sandhu E, McAdoo SP, Prendecki MF, Pickering MC, Botto M, Willicombe M, Thomas DC, Peters JE.",,eLife,2021,2021-03-11,Y,Human; Cytokines; Proteomics; Inflammation; Medicine; Biomarkers; immunology; Longitudinal; End-stage Kidney Disease; Covid-19,,,"End-stage kidney disease (ESKD) patients are at high risk of severe COVID-19. We measured 436 circulating proteins in serial blood samples from hospitalised and non-hospitalised ESKD patients with COVID-19 (n = 256 samples from 55 patients). Comparison to 51 non-infected patients revealed 221 differentially expressed proteins, with consistent results in a separate subcohort of 46 COVID-19 patients. Two hundred and three proteins were associated with clinical severity, including IL6, markers of monocyte recruitment (e.g. CCL2, CCL7), neutrophil activation (e.g. proteinase-3), and epithelial injury (e.g. KRT19). Machine-learning identified predictors of severity including IL18BP, CTSD, GDF15, and KRT19. Survival analysis with joint models revealed 69 predictors of death. Longitudinal modelling with linear mixed models uncovered 32 proteins displaying different temporal profiles in severe versus non-severe disease, including integrins and adhesion molecules. These data implicate epithelial damage, innate immune activation, and leucocyte-endothelial interactions in the pathology of severe COVID-19 and provide a resource for identifying drug targets.",,doi:https://doi.org/10.7554/elife.64827; doi:https://doi.org/10.7554/eLife.64827; html:https://europepmc.org/articles/PMC8064756; pdf:https://europepmc.org/articles/PMC8064756?pdf=render
 34399584,https://doi.org/10.1161/strokeaha.120.032619,Risk Prediction Using Polygenic Risk Scores for Prevention of Stroke and Other Cardiovascular Diseases.,"Abraham G, Rutten-Jacobs L, Inouye M.",,Stroke,2021,2021-08-17,N,Genetics; Myocardial infarction; Cardiovascular disease; Stroke; risk assessment,,,"Early prediction of risk of cardiovascular disease (CVD), including stroke, is a cornerstone of disease prevention. Clinical risk scores have been widely used for predicting CVD risk from known risk factors. Most CVDs have a substantial genetic component, which also has been confirmed for stroke in recent gene discovery efforts. However, the role of genetics in prediction of risk of CVD, including stroke, has been limited to testing for highly penetrant monogenic disorders. In contrast, the importance of polygenic variation, the aggregated effect of many common genetic variants across the genome with individually small effects, has become more apparent in the last 5 to 10 years, and powerful polygenic risk scores for CVD have been developed. Here we review the current state of the field of polygenic risk scores for CVD including stroke, and their potential to improve CVD risk prediction. We present findings and lessons from diseases such as coronary artery disease as these will likely be useful to inform future research in stroke polygenic risk prediction.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/STROKEAHA.120.032619; doi:https://doi.org/10.1161/STROKEAHA.120.032619; html:https://europepmc.org/articles/PMC7611731; pdf:https://europepmc.org/articles/PMC7611731?pdf=render; doi:https://doi.org/10.1161/strokeaha.120.032619
+33704068,https://doi.org/10.7554/elife.64827,Longitudinal proteomic profiling of dialysis patients with COVID-19 reveals markers of severity and predictors of death.,"Gisby J, Clarke CL, Medjeral-Thomas N, Malik TH, Papadaki A, Mortimer PM, Buang NB, Lewis S, Pereira M, Toulza F, Fagnano E, Mawhin MA, Dutton EE, Tapeng L, Richard AC, Kirk PD, Behmoaras J, Sandhu E, McAdoo SP, Prendecki MF, Pickering MC, Botto M, Willicombe M, Thomas DC, Peters JE.",,eLife,2021,2021-03-11,Y,Human; Cytokines; Proteomics; Inflammation; Medicine; Biomarkers; immunology; Longitudinal; End-stage Kidney Disease; Covid-19,,,"End-stage kidney disease (ESKD) patients are at high risk of severe COVID-19. We measured 436 circulating proteins in serial blood samples from hospitalised and non-hospitalised ESKD patients with COVID-19 (n = 256 samples from 55 patients). Comparison to 51 non-infected patients revealed 221 differentially expressed proteins, with consistent results in a separate subcohort of 46 COVID-19 patients. Two hundred and three proteins were associated with clinical severity, including IL6, markers of monocyte recruitment (e.g. CCL2, CCL7), neutrophil activation (e.g. proteinase-3), and epithelial injury (e.g. KRT19). Machine-learning identified predictors of severity including IL18BP, CTSD, GDF15, and KRT19. Survival analysis with joint models revealed 69 predictors of death. Longitudinal modelling with linear mixed models uncovered 32 proteins displaying different temporal profiles in severe versus non-severe disease, including integrins and adhesion molecules. These data implicate epithelial damage, innate immune activation, and leucocyte-endothelial interactions in the pathology of severe COVID-19 and provide a resource for identifying drug targets.",,doi:https://doi.org/10.7554/elife.64827; doi:https://doi.org/10.7554/eLife.64827; html:https://europepmc.org/articles/PMC8064756; pdf:https://europepmc.org/articles/PMC8064756?pdf=render
 35322592,https://doi.org/10.1002/ehf2.13910,Cardiovascular outcomes associated with treatment of type 2 diabetes in patients with ischaemic heart failure.,"Godec TR, Bromage DI, Pujades-Rodriguez M, Cannatà A, Gonzalez-Izquierdo A, Denaxas S, Hemingway H, Shah AM, Yellon DM, McDonagh TA.",,ESC heart failure,2022,2022-03-23,Y,Type 2 diabetes; Metformin; Heart Failure; Outcomes; Ischaemic Cardiomyopathy; Antidiabetic Agents,,,"<h4>Aim</h4>The optimal strategy for diabetes control in patients with heart failure (HF) following myocardial infarction (MI) remains unknown. Metformin, a guideline-recommended therapy for patients with chronic HF and type 2 diabetes mellitus (T2DM), is associated with reduced mortality and HF hospitalizations. However, worse outcomes have been reported when used at the time of MI. We compared outcomes of patients with T2DM and HF of ischaemic aetiology according to antidiabetic treatment.<h4>Methods and results</h4>This study used linked data from primary care, hospital admissions, and death registries for 4.7 million inhabitants in England, as part of the CALIBER resource. The primary endpoint was a composite of cardiovascular mortality and HF hospitalization. The secondary endpoints were the individual components of the primary endpoint and all-cause mortality. To evaluate the effect of temporal changes in diabetes treatment, antidiabetic medication was included as time-dependent covariates in survival analyses. The study included 1172 patients with T2DM and prior MI and incident HF between 3 January 1998 and 26 February 2010. Five hundred and ninety-six patients had the primary outcome over median follow-up of 2.53 (IQR: 0.98-4.92) years. Adjusted analyses showed a reduced hazard of the composite endpoint for exposure to all antidiabetic medication with hazard ratios (HRs) of 0.50 [95% confidence interval (CI): 0.42-0.59], 0.66 (95% CI: 0.55-0.80), and 0.53 (95% CI: 0.43-0.65), respectively. A similar effect was seen for all-cause mortality [HRs of 0.43 (95% CI: 0.35-0.52), 0.57 (95% CI: 0.46-0.70), and 0.34 (95% CI: 0.27-0.43), respectively].<h4>Conclusions</h4>When considering changes in antidiabetic treatment over time, all drug classes were associated with reduced risk of cardiovascular mortality and HF hospitalization.",,pdf:https://kclpure.kcl.ac.uk/ws/files/173598342/ESC_Heart_Failure_2022_Godec_Cardiovascular_outcomes_associated_with_treatment_of_type_2_diabetes_in_patients_with.pdf; doi:https://doi.org/10.1002/ehf2.13910; html:https://europepmc.org/articles/PMC9065866; pdf:https://europepmc.org/articles/PMC9065866?pdf=render
 34286192,https://doi.org/10.7861/fhj.2021-0083,Making trials part of good clinical care: lessons from the RECOVERY trial.,"Pessoa-Amorim G, Campbell M, Fletcher L, Horby P, Landray M, Mafham M, Haynes R.",,Future healthcare journal,2021,2021-07-01,N,Recovery; RANDOMISED CONTROLLED TRIALS; evidence-based medicine; Quality-by-design; Covid-19,,,"When COVID-19 hit the UK in early 2020, there were no known treatments for a condition that results in the death of around one in four patients hospitalised with this disease. Around the world, possible treatments were administered to huge numbers of patients, without any reliable assessments of safety and efficacy. The rapid generation of high-quality evidence was vital. RECOVERY is a streamlined, pragmatic, randomised controlled trial, which was set up in response to this challenge. As of April 2021, over 39,000 patients have been enrolled from 178 hospital sites in the UK. Within 100 days of its initiation, RECOVERY demonstrated that dexamethasone improves survival for patients with severe disease; a result that was rapidly implemented in the UK and internationally saving hundreds of thousands of lives. Importantly, it also showed that other widely used treatments (such as hydroxychloroquine and azithromycin) have no meaningful benefit for hospitalised patients. This was only possible through randomisation of large numbers of patients and the adoption of streamlined and pragmatic procedures focused on quality, together with widespread collaboration focused on a single goal. RECOVERY illustrates how clinical trials and healthcare can be integrated, even in a pandemic. This approach provides new opportunities to generate the evidence needed for high-quality healthcare not only for a pandemic but for the many other conditions that place a burden on patients and the healthcare system.",,pdf:https://www.rcpjournals.org/content/futurehosp/8/2/e243.full.pdf; doi:https://doi.org/10.7861/fhj.2021-0083; html:https://europepmc.org/articles/PMC8285150; pdf:https://europepmc.org/articles/PMC8285150?pdf=render; doi:https://doi.org/10.7861/fhj.2021-0083
 39364876,https://doi.org/10.14309/ajg.0000000000003111,Gallstone Disease Is Associated With an Increased Risk of Inflammatory Bowel Disease: Results From 3 Prospective Cohort Studies.,"Mi N, Yang M, Wei L, Nie P, Zhan S, Nguyen LH, Smith FG, Acharjee A, Liu X, Huang J, Xia B, Yuan J, Meng W.",,The American journal of gastroenterology,2024,2024-10-04,N,,,,"<h4>Introduction</h4>Gallstone diseases affect intestinal inflammation, bile flow, and gut microbiota, which in turn may increase the risk of inflammatory bowel disease (IBD). However, epidemiological studies exploring the associations between gallstone diseases and subsequent IBD risk have been limited.<h4>Methods</h4>This is a combined analysis of 3 prospective cohort studies (Nurses' Health Study, Nurses' Health Study II, and UK Biobank) and replicated in a case-control study (Chinese IBD Etiology Study). We evaluated the hazard ratios (HRs)/odds ratios (ORs) between gallstone diseases with IBD risk by Cox logistic regression or conditional logistic regression, adjusting for demographic characteristics, lifestyles, comorbidities, and medication usage.<h4>Results</h4>We identified 3,480 cases of IBD over 2,127,471 person-years of follow-up in the 3 cohort studies. The participants with gallstone disease had a 38% increase in the risk of IBD (HR 1.38, 95% confidence intervals [CI] 1.21-1.59), 68% increase in Crohn's disease (HR 1.68, 95% CI 1.38-2.06), and 24% increase in ulcerative colitis (HR 1.24, 95% CI 1.03-1.49). In Chinese IBD Etiology Study, we found even larger magnitude of effects between gallstone diseases and IBD risk (IBD: OR 3.03, 95% CI 2.32-3.97; Crohn's disease: OR 5.31; 95% CI 3.71-7.60; ulcerative colitis: OR 1.49; 95% CI 1.07-2.06). There were no major differences in the estimated associations between the presence of unremoved gallstones and prior cholecystectomy with IBD risk.<h4>Discussion</h4>Gallstone disease was linked to an increased risk of IBD and its subtypes, independent of traditional risk factors. Further research is needed to confirm these associations and clarify the underlying biological mechanisms.",,doi:https://doi.org/10.14309/ajg.0000000000003111
@@ -1206,13 +1208,13 @@ PMC10686417,https://doi.org/,The impact of restricted provision of publicly fund
 36593100,https://doi.org/10.1136/heartjnl-2022-322124,Response to: Correspondence on 'Cardiovascular disease and mortality sequelae of COVID-19 in the UK Biobank' by Jolobe.,"Raisi-Estabragh Z, Harvey NC, Petersen SE.",,Heart (British Cardiac Society),2023,2023-01-02,N,epidemiology; acute coronary syndrome; Covid-19,,,,,doi:https://doi.org/10.1136/heartjnl-2022-322124
 31329239,https://doi.org/10.1093/jamia/ocz105,UK phenomics platform for developing and validating electronic health record phenotypes: CALIBER.,"Denaxas S, Gonzalez-Izquierdo A, Direk K, Fitzpatrick NK, Fatemifar G, Banerjee A, Dobson RJB, Howe LJ, Kuan V, Lumbers RT, Pasea L, Patel RS, Shah AD, Hingorani AD, Sudlow C, Hemingway H.",,Journal of the American Medical Informatics Association : JAMIA,2019,2019-12-01,Y,Phenotyping; Medical Informatics; Personalized Medicine; Electronic Health Records,The Human Phenome,,"<h4>Objective</h4>Electronic health records (EHRs) are a rich source of information on human diseases, but the information is variably structured, fragmented, curated using different coding systems, and collected for purposes other than medical research. We describe an approach for developing, validating, and sharing reproducible phenotypes from national structured EHR in the United Kingdom with applications for translational research.<h4>Materials and methods</h4>We implemented a rule-based phenotyping framework, with up to 6 approaches of validation. We applied our framework to a sample of 15 million individuals in a national EHR data source (population-based primary care, all ages) linked to hospitalization and death records in England. Data comprised continuous measurements (for example, blood pressure; medication information; coded diagnoses, symptoms, procedures, and referrals), recorded using 5 controlled clinical terminologies: (1) read (primary care, subset of SNOMED-CT [Systematized Nomenclature of Medicine Clinical Terms]), (2) International Classification of Diseases-Ninth Revision and Tenth Revision (secondary care diagnoses and cause of mortality), (3) Office of Population Censuses and Surveys Classification of Surgical Operations and Procedures, Fourth Revision (hospital surgical procedures), and (4) DM+D prescription codes.<h4>Results</h4>Using the CALIBER phenotyping framework, we created algorithms for 51 diseases, syndromes, biomarkers, and lifestyle risk factors and provide up to 6 validation approaches. The EHR phenotypes are curated in the open-access CALIBER Portal (https://www.caliberresearch.org/portal) and have been used by 40 national and international research groups in 60 peer-reviewed publications.<h4>Conclusions</h4>We describe a UK EHR phenomics approach within the CALIBER EHR data platform with initial evidence of validity and use, as an important step toward international use of UK EHR data for health research.",,doi:https://doi.org/10.1093/jamia/ocz105; doi:https://doi.org/10.1093/jamia/ocz105; html:https://europepmc.org/articles/PMC6857510; pdf:https://europepmc.org/articles/PMC6857510?pdf=render
 32763878,https://doi.org/10.2196/18690,Notifications to Improve Engagement With an Alcohol Reduction App: Protocol for a Micro-Randomized Trial.,"Bell L, Garnett C, Qian T, Perski O, Potts HWW, Williamson E.",,JMIR research protocols,2020,2020-08-07,Y,Alcohol; Engagement; Mhealth; Mobile Health; Excessive Alcohol Consumption; Smartphone App; Push Notifications; Digital Behavior Change; Micro-randomized Trial,,,"<h4>Background</h4>Drink Less is a behavior change app that aims to help users in the general adult population reduce hazardous and harmful alcohol consumption. The app includes a daily push notification, delivered at 11 am, asking users to ""Please complete your mood and drinking diaries."" Previous analysis of Drink Less engagement data suggests the current notification strongly influences how users engage with the app in the subsequent hour. To exploit a potential increase of vulnerability of excess drinking and opportunity to engage with the app in the evenings, we changed the delivery time from 11 am to 8 pm. We now aim to further optimise the content and sequence of notifications, testing 30 new evidence-informed notifications targeting the user's perceived usefulness of the app.<h4>Objective</h4>The primary objective is to assess whether sending a notification at 8 pm increases behavioral engagement (opening the app) in the subsequent hour. Secondary objectives include comparing the effect of the new bank of messages with the standard message and effect moderation over time. We also aim to more generally understand the role notifications have on the overall duration, depth, and frequency of engagement with Drink Less over the first 30 days after download.<h4>Methods</h4>This is a protocol for a micro-randomized trial with two additional parallel arms. Inclusion criteria are Drink Less users who (1) consent to participate in the trial; (2) self-report a baseline Alcohol Use Disorders Identification Test score of 8 or above; (3) reside in the United Kingdom; (4) age ≥18 years and; (5) report interest in drinking less alcohol. In the micro-randomized trial, participants will be randomized daily at 8 pm to receive no notification, a notification with text from the new message bank, or the standard message. The primary outcome is the time-varying, binary outcome of ""Did the user open the app in the hour from 8 pm to 9 pm?"". The primary analysis will estimate the marginal relative risk for the notifications using an estimator developed for micro-randomized trials with binary outcomes. Participants randomized to the parallel arms will receive no notifications (Secondary Arm A), or the standard notification delivered daily at 11 am (Secondary Arm B) over 30 days, allowing the comparison of overall engagement between different notification delivery strategies.<h4>Results</h4>Approval was granted by the University College of London's Departmental Research Ethics Committee (CEHP/2016/556) on October 11, 2019, and The London School of Hygiene and Tropical Medicine Interventions Research Ethics Committee (17929) on November 27, 2019. Recruitment began on January 2, 2020, and is ongoing.<h4>Conclusions</h4>Understanding how push notifications may impact engagement with a behavior change app can lead to further improvements in engagement, and ultimately help users reduce their alcohol consumption. This understanding may also be generalizable to other apps that target a variety of behavior changes.<h4>International registered report identifier (irrid)</h4>DERR1-10.2196/18690.",,pdf:https://www.researchprotocols.org/2020/8/e18690/PDF; doi:https://doi.org/10.2196/18690; html:https://europepmc.org/articles/PMC7442945
-35997594,https://doi.org/10.1099/mic.0.001223,Diagnostic MALDI-TOF MS can differentiate between high and low toxic <i>Staphylococcus aureus</i> bacteraemia isolates as a predictor of patient outcome.,"Brignoli T, Recker M, Lee WWY, Dong T, Bhamber R, Albur M, Williams P, Dowsey AW, Massey RC.",,"Microbiology (Reading, England)",2022,2022-08-01,Y,Toxicity; Staphylococcus aureus; Bacteraemia; agr; Maldi-tof Ms Diagnosis,,,"<i>Staphylococcus aureus</i> bacteraemia (SAB) is a major cause of blood-stream infection (BSI) in both healthcare and community settings. While the underlying comorbidities of a patient significantly contributes to their susceptibility to and outcome following SAB, recent studies show the importance of the level of cytolytic toxin production by the infecting bacterium. In this study we demonstrate that this cytotoxicity can be determined directly from the diagnostic MALDI-TOF mass spectrum generated in a routine diagnostic laboratory. With further development this information could be used to guide the management and improve the outcomes for SAB patients.",,pdf:https://research-information.bris.ac.uk/files/356539118/mic001223.pdf; doi:https://doi.org/10.1099/mic.0.001223; html:https://europepmc.org/articles/PMC10323763; pdf:https://europepmc.org/articles/PMC10323763?pdf=render
 31711534,https://doi.org/10.1186/s13326-019-0216-2,Combining string and phonetic similarity matching to identify misspelt names of drugs in medical records written in Portuguese.,"Tissot H, Dobson R.",,Journal of biomedical semantics,2019,2019-11-12,Y,Similarity Search; Phonetic Similarity; Misspelt Names Of Drugs,,,"<h4>Background</h4>There is an increasing amount of unstructured medical data that can be analysed for different purposes. However, information extraction from free text data may be particularly inefficient in the presence of spelling errors. Existing approaches use string similarity methods to search for valid words within a text, coupled with a supporting dictionary. However, they are not rich enough to encode both typing and phonetic misspellings.<h4>Results</h4>Experimental results showed a joint string and language-dependent phonetic similarity is more accurate than traditional string distance metrics when identifying misspelt names of drugs in a set of medical records written in Portuguese.<h4>Conclusion</h4>We present a hybrid approach to efficiently perform similarity match that overcomes the loss of information inherit from using either exact match search or string based similarity search methods.",,pdf:https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-019-0216-2; doi:https://doi.org/10.1186/s13326-019-0216-2; html:https://europepmc.org/articles/PMC6849162; pdf:https://europepmc.org/articles/PMC6849162?pdf=render
+35997594,https://doi.org/10.1099/mic.0.001223,Diagnostic MALDI-TOF MS can differentiate between high and low toxic <i>Staphylococcus aureus</i> bacteraemia isolates as a predictor of patient outcome.,"Brignoli T, Recker M, Lee WWY, Dong T, Bhamber R, Albur M, Williams P, Dowsey AW, Massey RC.",,"Microbiology (Reading, England)",2022,2022-08-01,Y,Toxicity; Staphylococcus aureus; Bacteraemia; agr; Maldi-tof Ms Diagnosis,,,"<i>Staphylococcus aureus</i> bacteraemia (SAB) is a major cause of blood-stream infection (BSI) in both healthcare and community settings. While the underlying comorbidities of a patient significantly contributes to their susceptibility to and outcome following SAB, recent studies show the importance of the level of cytolytic toxin production by the infecting bacterium. In this study we demonstrate that this cytotoxicity can be determined directly from the diagnostic MALDI-TOF mass spectrum generated in a routine diagnostic laboratory. With further development this information could be used to guide the management and improve the outcomes for SAB patients.",,pdf:https://research-information.bris.ac.uk/files/356539118/mic001223.pdf; doi:https://doi.org/10.1099/mic.0.001223; html:https://europepmc.org/articles/PMC10323763; pdf:https://europepmc.org/articles/PMC10323763?pdf=render
 34673925,https://doi.org/10.1093/ageing/afab201,"Do home adaptation interventions help to reduce emergency fall admissions? A national longitudinal data-linkage study of 657,536 older adults living in Wales (UK) between 2010 and 2017.","Hollinghurst J, Daniels H, Fry R, Akbari A, Rodgers S, Watkins A, Hillcoat-Nallétamby S, Williams N, Nikolova S, Meads D, Clegg A.",,Age and ageing,2022,2022-01-01,Y,Frailty; Falls; Older People; Falls Prevention,,,"<h4>Background</h4>falls are common in older people, but evidence for the effectiveness of preventative home adaptations is limited.<h4>Aim</h4>determine whether a national home adaptation service, Care&Repair Cymru (C&RC), identified individuals at risk of falls occurring at home and reduced the likelihood of falls.<h4>Study design</h4>retrospective longitudinal controlled non-randomised intervention cohort study.<h4>Setting</h4>our cohort consisted of 657,536 individuals aged 60+ living in Wales (UK) between 1 January 2010 and 31 December 2017. About 123,729 individuals received a home adaptation service.<h4>Methods</h4>we created a dataset with up to 41 quarterly observations per person. For each quarter, we observed if a fall occurred at home that resulted in either an emergency department or an emergency hospital admission. We analysed the data using multilevel logistic regression.<h4>Results</h4>compared to the control group, C&RC clients had higher odds of falling, with an odds ratio (OR [95% confidence interval]) of 1.93 [1.87, 2.00]. Falls odds was higher for females (1.44 [1.42, 1.46]), older age (1.07 [1.07, 1.07]), increased frailty (mild 1.57 [1.55, 1.60], moderate 2.31 [2.26, 2.35], severe 3.05 [2.96, 3.13]), and deprivation (most deprived compared to least: 1.16 [1.13, 1.19]). Client fall odds decreased post-intervention; OR 0.97 [0.96, 0.97] per quarter. Regional variation existed for falls (5.8%), with most variation at the individual level (31.3%).<h4>Conclusions</h4>C&RC identified people more likely to have an emergency fall admission occurring at home, and their service reduced the odds of falling post-intervention. Service provisioning should meet the needs of an individual and need varies by personal and regional circumstance.",,pdf:https://academic.oup.com/ageing/article-pdf/51/1/afab201/42083711/afab201.pdf; doi:https://doi.org/10.1093/ageing/afab201; html:https://europepmc.org/articles/PMC8753038; pdf:https://europepmc.org/articles/PMC8753038?pdf=render
 32946551,https://doi.org/10.1093/ageing/afaa158,Do home modifications reduce care home admissions for older people? A matched control evaluation of the Care & Repair Cymru service in Wales.,"Hollinghurst J, Fry R, Akbari A, Watkins A, Williams N, Hillcoat-Nallétamby S, Lyons RA, Clegg A, Rodgers SE.",,Age and ageing,2020,2020-10-01,Y,Frailty; Interventions; Older People; Care Homes; Administrative Data,,,"<h4>Background</h4>home advice and modification interventions aim to promote independent living for those living in the community, but quantitative evidence of their effectiveness is limited.<h4>Aim</h4>assess the risk of care home admissions for people with different frailty levels receiving home advice and modification interventions against a control group who do not.<h4>Study design and setting</h4>matched control evaluation using linked longitudinal data from the Secure Anonymised Information Linkage (SAIL) Databank, comprising people aged 60-95, registered with a SAIL contributing general practice. The intervention group received the Care & Repair Cymru (C & RC) service, a home advice and modification service available to residents in Wales.<h4>Methods</h4>frailty, age and gender were used in propensity score matching to assess the Hazard Ratio (HR) of care home admissions within a 1-, 3- and 5-year period for the intervention group (N = 93,863) compared to a matched control group (N = 93,863). Kaplan-Meier curves were used to investigate time to a care home admission.<h4>Results</h4>the intervention group had an increased risk of a care home admission at 1-, 3- and 5-years [HR (95%CI)] for those classified as fit [1-year: 2.02 (1.73, 2.36), 3-years: 1.87 (1.72, 2.04), 5-years: 1.99 (1.86, 2.13)] and mildly frail [1-year: 1.25 (1.09, 1.42), 3-years: 1.25 (1.17, 1.34), 5-years: 1.30 (1.23, 1.38)], but a reduced risk of care home admission for moderately [1-year: 0.66 (0.58, 0.75), 3-years: 0.75 (0.70, 0.80), 5-years: 0.83 (0.78, 0.88)] and severely frail individuals [1-year: 0.44 (0.37, 0.54), 3-years: 0.54 (0.49, 0.60), 5-years: 0.60(0.55, 0.66)].<h4>Conclusions</h4>HRs indicated that the C & RC service helped to prevent care home admissions for moderately and severely frail individuals. The HRs generally increased with follow-up duration.",,pdf:https://academic.oup.com/ageing/article-pdf/49/6/1056/33993322/afaa158.pdf; doi:https://doi.org/10.1093/ageing/afaa158; html:https://europepmc.org/articles/PMC7583515; pdf:https://europepmc.org/articles/PMC7583515?pdf=render
-36439548,https://doi.org/10.3389/fsurg.2022.870494,Development and validation of an automated basal cell carcinoma histopathology information extraction system using natural language processing.,"Ali SR, Strafford H, Dobbs TD, Fonferko-Shadrach B, Lacey AS, Pickrell WO, Hutchings HA, Whitaker IS.",,Frontiers in surgery,2022,2022-08-24,Y,Electronic Health Records (Ehrs); Natural Language Processing (Nlp); Basal Cell Carcinoma (Bcc); Non-melanoma Skin Cancer (Nmsc); Information Extraction (Ie),,,"<h4>Introduction</h4>Routinely collected healthcare data are a powerful research resource, but often lack detailed disease-specific information that is collected in clinical free text such as histopathology reports. We aim to use natural Language Processing (NLP) techniques to extract detailed clinical and pathological information from histopathology reports to enrich routinely collected data.<h4>Methods</h4>We used the general architecture for text engineering (GATE) framework to build an NLP information extraction system using rule-based techniques. During validation, we deployed our rule-based NLP pipeline on 200 previously unseen, de-identified and pseudonymised basal cell carcinoma (BCC) histopathological reports from Swansea Bay University Health Board, Wales, UK. The results of our algorithm were compared with gold standard human annotation by two independent and blinded expert clinicians involved in skin cancer care.<h4>Results</h4>We identified 11,224 items of information with a mean precision, recall, and F1 score of 86.0% (95% CI: 75.1-96.9), 84.2% (95% CI: 72.8-96.1), and 84.5% (95% CI: 73.0-95.1), respectively. The difference between clinician annotator F1 scores was 7.9% in comparison with 15.5% between the NLP pipeline and the gold standard corpus. Cohen's Kappa score on annotated tokens was 0.85.<h4>Conclusion</h4>Using an NLP rule-based approach for named entity recognition in BCC, we have been able to develop and validate a pipeline with a potential application in improving the quality of cancer registry data, supporting service planning, and enhancing the quality of routinely collected data for research.",,pdf:https://www.frontiersin.org/articles/10.3389/fsurg.2022.870494/pdf; doi:https://doi.org/10.3389/fsurg.2022.870494; html:https://europepmc.org/articles/PMC9683031; pdf:https://europepmc.org/articles/PMC9683031?pdf=render
-34026049,https://doi.org/10.12688/f1000research.25484.2,PUblications Metadata Augmentation (PUMA) pipeline.,"Butters OW, Wilson RC, Garner H, Burton TWY.",,F1000Research,2020,2020-09-04,Y,bibliometrics; Bibliography; Alspac; Longitudinal Birth Cohort,,,"Cohort studies collect, generate and distribute data over long periods of time - often over the lifecourse of their participants. It is common for these studies to host a list of publications (which can number many thousands) on their website to demonstrate the impact of the study and facilitate the search of existing research to which the study data has contributed. The ability to search and explore these publication lists varies greatly between studies. We believe a lack of rich search and exploration functionality of study publications is a barrier to entry for new or prospective users of a study's data, since it may be difficult to find and evaluate previous work in a given area. These lists of publications are also typically manually curated, resulting in a lack of rich metadata to analyse, making bibliometric analysis difficult. We present here a software pipeline that aggregates metadata from a variety of third-party providers to power a web based search and exploration tool for lists of publications. Alongside core publication metadata (i.e. author lists, keywords etc.), we include geocoding of first authors and citation counts in our pipeline. This allows a characterisation of a study as a whole based on common locations of authors, frequency of keywords, citation profile etc. This enriched publications metadata can be useful for generating study impact metrics and web-based graphics for public dissemination. In addition, the pipeline produces a research data set for bibliometric analysis or social studies of science. We use a previously published list of publications from a cohort study as an exemplar input data set to show the output and utility of the pipeline here.",,pdf:https://f1000research.com/articles/9-1095/v2/pdf; doi:https://doi.org/10.12688/f1000research.25484.2; html:https://europepmc.org/articles/PMC8108552; pdf:https://europepmc.org/articles/PMC8108552?pdf=render
 33653161,https://doi.org/10.1177/1740774520976617,Making a distinction between data cleaning and central monitoring in clinical trials.,"Love SB, Yorke-Edwards V, Diaz-Montana C, Murray ML, Masters L, Gabriel M, Joffe N, Sydes MR.",,"Clinical trials (London, England)",2021,2021-03-02,Y,,,,,,pdf:https://journals.sagepub.com/doi/pdf/10.1177/1740774520976617; doi:https://doi.org/10.1177/1740774520976617; html:https://europepmc.org/articles/PMC8174009; pdf:https://europepmc.org/articles/PMC8174009?pdf=render
+34026049,https://doi.org/10.12688/f1000research.25484.2,PUblications Metadata Augmentation (PUMA) pipeline.,"Butters OW, Wilson RC, Garner H, Burton TWY.",,F1000Research,2020,2020-09-04,Y,bibliometrics; Bibliography; Alspac; Longitudinal Birth Cohort,,,"Cohort studies collect, generate and distribute data over long periods of time - often over the lifecourse of their participants. It is common for these studies to host a list of publications (which can number many thousands) on their website to demonstrate the impact of the study and facilitate the search of existing research to which the study data has contributed. The ability to search and explore these publication lists varies greatly between studies. We believe a lack of rich search and exploration functionality of study publications is a barrier to entry for new or prospective users of a study's data, since it may be difficult to find and evaluate previous work in a given area. These lists of publications are also typically manually curated, resulting in a lack of rich metadata to analyse, making bibliometric analysis difficult. We present here a software pipeline that aggregates metadata from a variety of third-party providers to power a web based search and exploration tool for lists of publications. Alongside core publication metadata (i.e. author lists, keywords etc.), we include geocoding of first authors and citation counts in our pipeline. This allows a characterisation of a study as a whole based on common locations of authors, frequency of keywords, citation profile etc. This enriched publications metadata can be useful for generating study impact metrics and web-based graphics for public dissemination. In addition, the pipeline produces a research data set for bibliometric analysis or social studies of science. We use a previously published list of publications from a cohort study as an exemplar input data set to show the output and utility of the pipeline here.",,pdf:https://f1000research.com/articles/9-1095/v2/pdf; doi:https://doi.org/10.12688/f1000research.25484.2; html:https://europepmc.org/articles/PMC8108552; pdf:https://europepmc.org/articles/PMC8108552?pdf=render
+36439548,https://doi.org/10.3389/fsurg.2022.870494,Development and validation of an automated basal cell carcinoma histopathology information extraction system using natural language processing.,"Ali SR, Strafford H, Dobbs TD, Fonferko-Shadrach B, Lacey AS, Pickrell WO, Hutchings HA, Whitaker IS.",,Frontiers in surgery,2022,2022-08-24,Y,Electronic Health Records (Ehrs); Natural Language Processing (Nlp); Basal Cell Carcinoma (Bcc); Non-melanoma Skin Cancer (Nmsc); Information Extraction (Ie),,,"<h4>Introduction</h4>Routinely collected healthcare data are a powerful research resource, but often lack detailed disease-specific information that is collected in clinical free text such as histopathology reports. We aim to use natural Language Processing (NLP) techniques to extract detailed clinical and pathological information from histopathology reports to enrich routinely collected data.<h4>Methods</h4>We used the general architecture for text engineering (GATE) framework to build an NLP information extraction system using rule-based techniques. During validation, we deployed our rule-based NLP pipeline on 200 previously unseen, de-identified and pseudonymised basal cell carcinoma (BCC) histopathological reports from Swansea Bay University Health Board, Wales, UK. The results of our algorithm were compared with gold standard human annotation by two independent and blinded expert clinicians involved in skin cancer care.<h4>Results</h4>We identified 11,224 items of information with a mean precision, recall, and F1 score of 86.0% (95% CI: 75.1-96.9), 84.2% (95% CI: 72.8-96.1), and 84.5% (95% CI: 73.0-95.1), respectively. The difference between clinician annotator F1 scores was 7.9% in comparison with 15.5% between the NLP pipeline and the gold standard corpus. Cohen's Kappa score on annotated tokens was 0.85.<h4>Conclusion</h4>Using an NLP rule-based approach for named entity recognition in BCC, we have been able to develop and validate a pipeline with a potential application in improving the quality of cancer registry data, supporting service planning, and enhancing the quality of routinely collected data for research.",,pdf:https://www.frontiersin.org/articles/10.3389/fsurg.2022.870494/pdf; doi:https://doi.org/10.3389/fsurg.2022.870494; html:https://europepmc.org/articles/PMC9683031; pdf:https://europepmc.org/articles/PMC9683031?pdf=render
 33249608,https://doi.org/10.1111/opo.12765,Authors' Reply.,"Wright DM, O'Reilly D, Azuara-Blanco A, Curran R, McMullan M, Hogg RE.",,Ophthalmic & physiological optics : the journal of the British College of Ophthalmic Opticians (Optometrists),2021,2020-11-29,N,,,,,,doi:https://doi.org/10.1111/opo.12765
 35667411,https://doi.org/10.1016/j.jamda.2022.05.003,Stroke in Older Adults Living in Care Homes: Results From a National Data Linkage Study in Wales.,"Harrison SL, Lip GYH, Akbari A, Torabi F, Ritchie LA, Akpan A, Halcox J, Rodgers S, Hollinghurst J, Harris D, Lane DA.",,Journal of the American Medical Directors Association,2022,2022-06-03,N,Anticoagulants; Cerebrovascular disease; Nursing Homes; Antiplatelets,,,"<h4>Objectives</h4>To determine the proportion of older people moving to care homes with a recent stroke, incidence of stroke after moving to a care home, mortality following stroke, and secondary stroke prevention management in older care home residents.<h4>Design</h4>Retrospective cohort study using population-scale individual-level linked data sources between 2003 and 2018 in the Secure Anonymized Information Linkage (SAIL) Databank.<h4>Setting and participants</h4>People aged ≥65 years residing in long-term care homes in Wales.<h4>Methods</h4>Competing risk models and logistic regression models were used to examine the association between prior stroke, incident stroke, and mortality following stroke.<h4>Results</h4>Of 86,602 individuals, 7.0% (n = 6055) experienced a stroke in the 12 months prior to care home entry. The incidence of stroke within 12 months after entry to a care home was 26.2 per 1000 person-years [95% confidence interval (CI) 25.0, 27.5]. Previous stroke was associated with higher risk of incident stroke after moving to a care home (subdistribution hazard ratio 1.83, 95% CI 1.57, 2.13) and 30-day mortality following stroke (odds ratio 2.18, 95% CI 1.59, 2.98). Severe frailty was not significantly associated with risk of stroke or 30-day mortality following stroke. Secondary stroke prevention included statins (51.0%), antiplatelets (61.2%), anticoagulants (52.4% of those with atrial fibrillation), and antihypertensives (92.1% of those with hypertension).<h4>Conclusions and implications</h4>At the time of care home entry, individuals with history of stroke in the previous 12 months are at a higher risk of incident stroke and mortality following an incident stroke. These individuals are frequently not prescribed medications for secondary stroke prevention. Further evidence is needed to determine the optimal care pathways for older people living in long-term care homes with history of stroke.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa60151/Download/60151__25104__e0e71818d5bd49acba048a3d98682425.pdf; doi:https://doi.org/10.1016/j.jamda.2022.05.003
 34169636,https://doi.org/10.1002/pst.2148,Assessing safety at the end of clinical trials using system organ classes: A case and comparative study.,"Carragher R, Robertson C.",,Pharmaceutical statistics,2021,2021-06-24,N,Safety; False Discovery Rate; Adverse Events; System Organ Class; Bayesian Hierarchy,,,"Recent approaches to the statistical analysis of adverse event (AE) data in clinical trials have proposed the use of groupings of related AEs, such as by system organ class (SOC). These methods have opened up the possibility of scanning large numbers of AEs while controlling for multiple comparisons, making the comparative performance of the different methods in terms of AE detection and error rates of interest to investigators. We apply two Bayesian models and two procedures for controlling the false discovery rate (FDR), which use groupings of AEs, to real clinical trial safety data. We find that while the Bayesian models are appropriate for the full data set, the error controlling methods only give similar results to the Bayesian methods when low incidence AEs are removed. A simulation study is used to compare the relative performances of the methods. We investigate the differences between the methods over full trial data sets, and over data sets with low incidence AEs and SOCs removed. We find that while the removal of low incidence AEs increases the power of the error controlling procedures, the estimated power of the Bayesian methods remains relatively constant over all data sizes. Automatic removal of low-incidence AEs however does have an effect on the error rates of all the methods, and a clinically guided approach to their removal is needed. Overall we found that the Bayesian approaches are particularly useful for scanning the large amounts of AE data gathered.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pst.2148; doi:https://doi.org/10.1002/pst.2148
@@ -1222,17 +1224,17 @@ PMC10686417,https://doi.org/,The impact of restricted provision of publicly fund
 37897346,https://doi.org/10.1093/eurheartj/ehad727,Five critical quality criteria for artificial intelligence-based prediction models.,"van Royen FS, Asselbergs FW, Alfonso F, Vardas P, van Smeden M.",,European heart journal,2023,2023-12-01,Y,Prediction; Artificial intelligence; Diagnosis; Prognosis; Digital Health,,,"To raise the quality of clinical artificial intelligence (AI) prediction modelling studies in the cardiovascular health domain and thereby improve their impact and relevancy, the editors for digital health, innovation, and quality standards of the European Heart Journal propose five minimal quality criteria for AI-based prediction model development and validation studies: complete reporting, carefully defined intended use of the model, rigorous validation, large enough sample size, and openness of code and software.",,doi:https://doi.org/10.1093/eurheartj/ehad727; html:https://europepmc.org/articles/PMC10702458; pdf:https://europepmc.org/articles/PMC10702458?pdf=render
 32665523,https://doi.org/10.1097/hjh.0000000000002579,Association of SBP and BMI with cognitive and structural brain phenotypes in UK Biobank.,"Ferguson AC, Tank R, Lyall LM, Ward J, Welsh P, Celis-Morales C, McQueenie R, Strawbridge RJ, Mackay DF, Pell JP, Smith DJ, Sattar N, Cavanagh J, Lyall DM.",,Journal of hypertension,2020,2020-12-01,N,,,,"<h4>Objective</h4>To test for associations between SBP and BMI, with domain-specific cognitive abilities and examine which brain structural phenotypes mediate those associations.<h4>Methods</h4>Using cross-sectional UK Biobank data (final N = 28 412), we examined SBP/BMI vs. cognitive test scores of pairs-matching, matrix completion, trail making test A/B, digit symbol substitution, verbal-numerical reasoning, tower rearranging and simple reaction time. We adjusted for potential confounders of age, sex, deprivation, medication, apolipoprotein e4 genotype, smoking, population stratification and genotypic array. We tested for mediation via multiple structural brain imaging phenotypes and corrected for multiple testing with false discovery rate.<h4>Results</h4>We found positive associations for higher BMI with worse reaction time, reasoning, tower rearranging and matrix completion tasks by 0.024-0.067 SDs per BMI SD (all P < 0.001). Higher SBP was associated with worse reasoning (0.034 SDs) and matrix completion scores (-0.024 SDs; both P < 0.001). Both BMI and SBP were associated with multiple brain structural metrics including total grey/white matter volumes, frontal lobe volumes, white matter tract integrity and white matter hyperintensity volumes: specific metrics mediated around one-third of the associations with cognition.<h4>Conclusion</h4>Our findings add to the body of evidence that addressing cardiovascular risk factors may also preserve cognitive function, via specific aspects of brain structure.",,html:https://journals.lww.com/jhypertension/Fulltext/2020/12000/Association_of_SBP_and_BMI_with_cognitive_and.22.aspx; doi:https://doi.org/10.1097/HJH.0000000000002579
 37821223,https://doi.org/10.1136/jech-2023-220975,Childhood contact with social services and risk of suicide or sudden death in young adulthood: identifying hidden risk in a population-wide cohort study.,"McKenna S, O'Reilly D, Maguire A.",,Journal of epidemiology and community health,2023,2023-12-08,Y,Mortality; Cohort studies; Suicide; Longitudinal Studies; Record Linkage,,,"<h4>Background</h4>Childhood out-of-home care is associated with premature death in adulthood, in particular death by suicide, accidents and violence. However, little is known about the mortality risk in the much larger population of adults that had contact with social services in childhood but never entered out-of-home care. We determine the association between all tiers of contact with children's social services and risk of suicide and other sudden deaths in young adulthood.<h4>Methods</h4>This population-wide, longitudinal, record-linkage study of adults in Northern Ireland born between 1985 and 1997 (n=437 008) followed each individual from age 18 years to July 2021 (maximum age 36 years). Cox regression models estimated the association between level of contact with social services in childhood (no contact; referred but assessed as not in need (NIN); child in need (CIN) and child in care (CIC)) and risk of death by suicide and sudden death in young adulthood.<h4>Results</h4>Individuals with childhood social care contact (n=51 097) comprised 11.7% of the cohort yet accounted for 35.3% of sudden deaths and 39.7% of suicide deaths. Risk of suicide or sudden death increased stepwise with level of childhood contact and was highest in adults with a history of out-of-home care (suicide HR 8.85 (95% CI 6.83 to 11.4)). Individuals assessed as NIN, and those deemed a CIN, had four times the risk of death by suicide in young adulthood compared with unexposed peers (HR 4.25 (95% CI 3.26 to 5.53) and HR 4.49 (95% CI 3.75 to 5.39), respectively).<h4>Conclusion</h4>Childhood contact with social services is a risk marker for death by suicide and sudden death in young adulthood. Risk is not confined to adults with a history of out-of-home care but extends to the much larger population that had contact with social services but never entered care.",,pdf:https://jech.bmj.com/content/jech/early/2023/10/11/jech-2023-220975.full.pdf; doi:https://doi.org/10.1136/jech-2023-220975; html:https://europepmc.org/articles/PMC10715544; pdf:https://europepmc.org/articles/PMC10715544?pdf=render
-33468531,https://doi.org/10.1136/bmjopen-2020-047101,Protocol for the development of the Wales Multimorbidity e-Cohort (WMC): data sources and methods to construct a population-based research platform to investigate multimorbidity.,"Lyons J, Akbari A, Agrawal U, Harper G, Azcoaga-Lorenzo A, Bailey R, Rafferty J, Watkins A, Fry R, McCowan C, Dezateux C, Robson JP, Peek N, Holmes C, Denaxas S, Owen R, Abrams KR, John A, O'Reilly D, Richardson S, Hall M, Gale CP, Davies J, Davies C, Cross L, Gallacher J, Chess J, Brookes AJ, Lyons RA.",,BMJ open,2021,2021-01-19,Y,epidemiology; Public Health; Primary Care; Geriatric Medicine; Health Policy,,,"<h4>Introduction</h4>Multimorbidity is widely recognised as the presence of two or more concurrent long-term conditions, yet remains a poorly understood global issue despite increasing in prevalence.We have created the Wales Multimorbidity e-Cohort (WMC) to provide an accessible research ready data asset to further the understanding of multimorbidity. Our objectives are to create a platform to support research which would help to understand prevalence, trajectories and determinants in multimorbidity, characterise clusters that lead to highest burden on individuals and healthcare services, and evaluate and provide new multimorbidity phenotypes and algorithms to the National Health Service and research communities to support prevention, healthcare planning and the management of individuals with multimorbidity.<h4>Methods and analysis</h4>The WMC has been created and derived from multisourced demographic, administrative and electronic health record data relating to the Welsh population in the Secure Anonymised Information Linkage (SAIL) Databank. The WMC consists of 2.9 million people alive and living in Wales on the 1 January 2000 with follow-up until 31 December 2019, Welsh residency break or death. Published comorbidity indices and phenotype code lists will be used to measure and conceptualise multimorbidity.Study outcomes will include: (1) a description of multimorbidity using published data phenotype algorithms/ontologies, (2) investigation of the associations between baseline demographic factors and multimorbidity, (3) identification of temporal trajectories of clusters of conditions and multimorbidity and (4) investigation of multimorbidity clusters with poor outcomes such as mortality and high healthcare service utilisation.<h4>Ethics and dissemination</h4>The SAIL Databank independent Information Governance Review Panel has approved this study (SAIL Project: 0911). Study findings will be presented to policy groups, public meetings, national and international conferences, and published in peer-reviewed journals.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/1/e047101.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-047101; html:https://europepmc.org/articles/PMC7817800; pdf:https://europepmc.org/articles/PMC7817800?pdf=render
 37717030,https://doi.org/10.1186/s13756-023-01280-6,The impact of the COVID-19 pandemic on the treatment of common infections in primary care and the change to antibiotic prescribing in England.,"Yang YT, Zhong X, Fahmi A, Watts S, Ashcroft DM, Massey J, Fisher L, MacKenna B, Mehrkar A, Bacon SCJ, Goldacre B, Hand K, van Staa T, Palin V.",,Antimicrobial resistance and infection control,2023,2023-09-16,Y,Infection; Antibiotics; Primary Care; Antibiotic Stewardship; Covid-19 Pandemic,,,"<h4>Background</h4>There is concern that the COVID-19 pandemic altered the management of common infections in primary care. This study aimed to evaluate infection-coded consultation rates and antibiotic use during the pandemic and how any change may have affected clinical outcomes.<h4>Methods</h4>With the approval of NHS England, a retrospective cohort study using the OpenSAFELY platform analysed routinely collected electronic health data from GP practices in England between January 2019 and December 2021. Infection coded consultations and antibiotic prescriptions were used estimate multiple measures over calendar months, including age-sex adjusted prescribing rates, prescribing by infection and antibiotic type, infection consultation rates, coding quality and rate of same-day antibiotic prescribing for COVID-19 infections. Interrupted time series (ITS) estimated the effect of COVID-19 pandemic on infection-coded consultation rates. The impact of the pandemic on non- COVID-19 infection-related hospitalisations was also estimated.<h4>Results</h4>Records from 24 million patients were included. The rate of infection-related consultations fell for all infections (mean reduction of 39% in 2020 compared to 2019 mean rate), except for UTI which remained stable. Modelling infection-related consultation rates highlighted this with an incidence rate ratio of 0.44 (95% CI 0.36-0.53) for incident consultations and 0.43 (95% CI 0.33-0.54) for prevalent consultations. Lower respiratory tract infections (LRTI) saw the largest reduction of 0.11 (95% CI 0.07-0.17). Antibiotic prescribing rates fell with a mean reduction of 118.4 items per 1000 patients in 2020, returning to pre-pandemic rates by summer 2021. Prescribing for LRTI decreased 20% and URTI increased 15.9%. Over 60% of antibiotics were issued without an associated same-day infection code, which increased during the pandemic. Infection-related hospitalisations reduced (by 62%), with the largest reduction observed for pneumonia infections (72.9%). Same-day antibiotic prescribing for COVID-19 infection increased from 1 to 10.5% between the second and third national lockdowns and rose again during 2022.<h4>Conclusions</h4>Changes to consultations and hospital admissions may be driven by reduced transmission of non-COVID-19 infections due to reduced social mixing and lockdowns. Inconsistencies in coding practice emphasises the need for improvement to inform new antibiotic stewardship policies and prevent resistance to novel infections.",,pdf:https://aricjournal.biomedcentral.com/counter/pdf/10.1186/s13756-023-01280-6; doi:https://doi.org/10.1186/s13756-023-01280-6; html:https://europepmc.org/articles/PMC10504725; pdf:https://europepmc.org/articles/PMC10504725?pdf=render
 32182948,https://doi.org/10.3390/cells9030665,"Dysregulated Antibody, Natural Killer Cell and Immune Mediator Profiles in Autoimmune Thyroid Diseases.","Martin TC, Ilieva KM, Visconti A, Beaumont M, Kiddle SJ, Dobson RJB, Mangino M, Lim EM, Pezer M, Steves CJ, Bell JT, Wilson SG, Lauc G, Roederer M, Walsh JP, Spector TD, Karagiannis SN.",,Cells,2020,2020-03-09,Y,Apoptosis; Genetic Variants; Antibody-dependent Cell-mediated Cytotoxicity (Adcc); Multi-omic; Autoimmune Thyroid Diseases (Aitd); Anti-thyroid Peroxidase Antibody (Tpoab),Understanding the Causes of Disease,inflammatory and immune system,"The pathogenesis of autoimmune thyroid diseases (AITD) is poorly understood and the association between different immune features and the germline variants involved in AITD are yet unclear. We previously observed systemic depletion of IgG core fucosylation and antennary α1,2 fucosylation in peripheral blood mononuclear cells in AITD, correlated with anti-thyroid peroxidase antibody (TPOAb) levels. Fucose depletion is known to potentiate strong antibody-mediated NK cell activation and enhanced target antigen-expressing cell killing. In autoimmunity, this may translate to autoantibody-mediated immune cell recruitment and attack of self-antigen expressing normal tissues. Hence, we investigated the crosstalk between immune cell traits, secreted proteins, genetic variants and the glycosylation patterns of serum IgG, in a multi-omic and cross-sectional study of 622 individuals from the TwinsUK cohort, 172 of whom were diagnosed with AITD. We observed associations between two genetic variants (rs505922 and rs687621), AITD status, the secretion of Desmoglein-2 protein, and the profile of two IgG N-glycan traits in AITD, but further studies need to be performed to better understand their crosstalk in AITD. On the other side, enhanced afucosylated IgG was positively associated with activatory CD335<sup>-</sup> CD314<sup>+</sup> CD158b<sup>+</sup> NK cell subsets. Increased levels of the apoptosis and inflammation markers Caspase-2 and Interleukin-1α positively associated with AITD. Two genetic variants associated with AITD, rs1521 and rs3094228, were also associated with altered expression of the thyrocyte-expressed ligands known to recognize the NK cell immunoreceptors CD314 and CD158b. Our analyses reveal a combination of heightened Fc-active IgG antibodies, effector cells, cytokines and apoptotic signals in AITD, and AITD genetic variants associated with altered expression of thyrocyte-expressed ligands to NK cell immunoreceptors. Together, TPOAb responses, dysregulated immune features, germline variants associated with immunoactivity profiles, are consistent with a positive autoreactive antibody-dependent NK cell-mediated immune response likely drawn to the thyroid gland in AITD.",,pdf:https://www.mdpi.com/2073-4409/9/3/665/pdf?version=1584361130; doi:https://doi.org/10.3390/cells9030665; html:https://europepmc.org/articles/PMC7140647; pdf:https://europepmc.org/articles/PMC7140647?pdf=render
+33468531,https://doi.org/10.1136/bmjopen-2020-047101,Protocol for the development of the Wales Multimorbidity e-Cohort (WMC): data sources and methods to construct a population-based research platform to investigate multimorbidity.,"Lyons J, Akbari A, Agrawal U, Harper G, Azcoaga-Lorenzo A, Bailey R, Rafferty J, Watkins A, Fry R, McCowan C, Dezateux C, Robson JP, Peek N, Holmes C, Denaxas S, Owen R, Abrams KR, John A, O'Reilly D, Richardson S, Hall M, Gale CP, Davies J, Davies C, Cross L, Gallacher J, Chess J, Brookes AJ, Lyons RA.",,BMJ open,2021,2021-01-19,Y,epidemiology; Public Health; Primary Care; Geriatric Medicine; Health Policy,,,"<h4>Introduction</h4>Multimorbidity is widely recognised as the presence of two or more concurrent long-term conditions, yet remains a poorly understood global issue despite increasing in prevalence.We have created the Wales Multimorbidity e-Cohort (WMC) to provide an accessible research ready data asset to further the understanding of multimorbidity. Our objectives are to create a platform to support research which would help to understand prevalence, trajectories and determinants in multimorbidity, characterise clusters that lead to highest burden on individuals and healthcare services, and evaluate and provide new multimorbidity phenotypes and algorithms to the National Health Service and research communities to support prevention, healthcare planning and the management of individuals with multimorbidity.<h4>Methods and analysis</h4>The WMC has been created and derived from multisourced demographic, administrative and electronic health record data relating to the Welsh population in the Secure Anonymised Information Linkage (SAIL) Databank. The WMC consists of 2.9 million people alive and living in Wales on the 1 January 2000 with follow-up until 31 December 2019, Welsh residency break or death. Published comorbidity indices and phenotype code lists will be used to measure and conceptualise multimorbidity.Study outcomes will include: (1) a description of multimorbidity using published data phenotype algorithms/ontologies, (2) investigation of the associations between baseline demographic factors and multimorbidity, (3) identification of temporal trajectories of clusters of conditions and multimorbidity and (4) investigation of multimorbidity clusters with poor outcomes such as mortality and high healthcare service utilisation.<h4>Ethics and dissemination</h4>The SAIL Databank independent Information Governance Review Panel has approved this study (SAIL Project: 0911). Study findings will be presented to policy groups, public meetings, national and international conferences, and published in peer-reviewed journals.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/1/e047101.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-047101; html:https://europepmc.org/articles/PMC7817800; pdf:https://europepmc.org/articles/PMC7817800?pdf=render
 37814053,https://doi.org/10.1038/s41588-023-01522-8,Age-dependent topic modeling of comorbidities in UK Biobank identifies disease subtypes with differential genetic risk.,"Jiang X, Zhang MJ, Zhang Y, Durvasula A, Inouye M, Holmes C, Price AL, McVean G.",,Nature genetics,2023,2023-10-09,Y,,,,"The analysis of longitudinal data from electronic health records (EHRs) has the potential to improve clinical diagnoses and enable personalized medicine, motivating efforts to identify disease subtypes from patient comorbidity information. Here we introduce an age-dependent topic modeling (ATM) method that provides a low-rank representation of longitudinal records of hundreds of distinct diseases in large EHR datasets. We applied ATM to 282,957 UK Biobank samples, identifying 52 diseases with heterogeneous comorbidity profiles; analyses of 211,908 All of Us samples produced concordant results. We defined subtypes of the 52 heterogeneous diseases based on their comorbidity profiles and compared genetic risk across disease subtypes using polygenic risk scores (PRSs), identifying 18 disease subtypes whose PRS differed significantly from other subtypes of the same disease. We further identified specific genetic variants with subtype-dependent effects on disease risk. In conclusion, ATM identifies disease subtypes with differential genome-wide and locus-specific genetic risk profiles.",,pdf:https://www.nature.com/articles/s41588-023-01522-8.pdf; doi:https://doi.org/10.1038/s41588-023-01522-8; html:https://europepmc.org/articles/PMC10632146; pdf:https://europepmc.org/articles/PMC10632146?pdf=render
 35634533,https://doi.org/10.12688/wellcomeopenres.17360.1,A comprehensive high cost drugs dataset from the NHS in England - An OpenSAFELY-TPP Short Data Report.,"Rowan A, Bates C, Hulme W, Evans D, Davy S, A Kennedy N, Galloway J, E Mansfield K, Bechman K, Matthewman J, Yates M, Brown J, Schultze A, Norton S, J Walker A, E Morton C, Bhaskaran K, T Rentsch C, Williamson E, Croker R, Bacon S, Hickman G, Ward T, Green A, Fisher L, J Curtis H, Tazare J, M Eggo R, Inglesby P, Cockburn J, I McDonald H, Mathur R, Ys Wong A, Forbes H, Parry J, Hester F, Harper S, J Douglas I, Smeeth L, A Tomlinson L, W Lees C, Evans S, Smith C, M Langan S, Mehkar A, MacKenna B, Goldacre B.",,Wellcome open research,2021,2021-12-22,Y,Medications; Biosimilars; Healthcare Administration; Opensafely,,,"<b>Background:</b> At the outset of the COVID-19 pandemic, there was no routine comprehensive hospital medicines data from the UK available to researchers. These records can be important for many analyses including the effect of certain medicines on the risk of severe COVID-19 outcomes. With the approval of NHS England, we set out to obtain data on one specific group of medicines, ""high-cost drugs"" (HCD) which are typically specialist medicines for the management of long-term conditions, prescribed by hospitals to patients. Additionally, we aimed to make these data available to all approved researchers in OpenSAFELY-TPP. This report is intended to support all studies carried out in OpenSAFELY-TPP, and those elsewhere, working with this dataset or similar data. <b>Methods:</b> Working with the North East Commissioning Support Unit and NHS Digital, we arranged for collation of a single national HCD dataset to help inform responses to the COVID-19 pandemic. The dataset was developed from payment submissions from hospitals to commissioners. <b>Results:</b> In the financial year (FY) 2018/19 there were 2.8 million submissions for 1.1 million unique patient IDs recorded in the HCD. The average number of submissions per patient over the year was 2.6. In FY 2019/20 there were 4.0 million submissions for 1.3 million unique patient IDs. The average number of submissions per patient over the year was 3.1. Of the 21 variables in the dataset, three are now available for analysis in OpenSafely-TPP: Financial year and month of drug being dispensed; drug name; and a description of the drug dispensed. <b>Conclusions:</b> We have described the process for sourcing a national HCD dataset, making these data available for COVID-19-related analysis through OpenSAFELY-TPP and provided information on the variables included in the dataset, data coverage and an initial descriptive analysis.",,doi:https://doi.org/10.12688/wellcomeopenres.17360.1; html:https://europepmc.org/articles/PMC9120928; pdf:https://europepmc.org/articles/PMC9120928?pdf=render
 37705832,https://doi.org/10.5837/bjc.2023.003,SGLT2 inhibitors in CKD and HFpEF: two new large trials and two new meta-analyses.,"Mayne KJ, Preiss D, Herrington WG.",,The British journal of cardiology,2023,2023-02-21,N,Cardiovascular disease; Heart Failure; Chronic Kidney Disease; Sodium-Glucose Co-Transporter 2 (Sglt2) Inhibitor,,,,,doi:https://doi.org/10.5837/bjc.2023.003; html:https://europepmc.org/articles/PMC10495762; pdf:https://europepmc.org/articles/PMC10495762?pdf=render; doi:https://doi.org/10.5837/bjc.2023.003
 34088700,https://doi.org/10.2337/dc20-2518,"Type 2 Diabetes, Metabolic Traits, and Risk of Heart Failure: A Mendelian Randomization Study.","Mordi IR, Lumbers RT, Palmer CNA, Pearson ER, Sattar N, Holmes MV, Lang CC, HERMES Consortium.",,Diabetes care,2021,2021-06-04,Y,,,,"<h4>Objective</h4>The aim of this study was to use Mendelian randomization (MR) techniques to estimate the causal relationships between genetic liability to type 2 diabetes (T2D), glycemic traits, and risk of heart failure (HF).<h4>Research design and methods</h4>Summary-level data were obtained from genome-wide association studies of T2D, insulin resistance (IR), glycated hemoglobin, fasting insulin and glucose, and HF. MR was conducted using the inverse-variance weighted method. Sensitivity analyses included the MR-Egger method, weighted median and mode methods, and multivariable MR conditioning on potential mediators.<h4>Results</h4>Genetic liability to T2D was causally related to higher risk of HF (odds ratio [OR] 1.13 per 1-log unit higher risk of T2D; 95% CI 1.11-1.14; <i>P</i> < 0.001); however, sensitivity analysis revealed evidence of directional pleiotropy. The relationship between T2D and HF was attenuated when adjusted for coronary disease, BMI, LDL cholesterol, and blood pressure in multivariable MR. Genetically instrumented higher IR was associated with higher risk of HF (OR 1.19 per 1-log unit higher risk of IR; 95% CI 1.00-1.41; <i>P</i> = 0.041). There were no notable associations identified between fasting insulin, glucose, or glycated hemoglobin and risk of HF. Genetic liability to HF was causally linked to higher risk of T2D (OR 1.49; 95% CI 1.01-2.19; <i>P</i> = 0.042), although again with evidence of pleiotropy.<h4>Conclusions</h4>These findings suggest a possible causal role of T2D and IR in HF etiology, although the presence of both bidirectional effects and directional pleiotropy highlights potential sources of bias that must be considered.",,pdf:https://diabetesjournals.org/care/article-pdf/44/7/1699/632992/dc202518.pdf; doi:https://doi.org/10.2337/dc20-2518; html:https://europepmc.org/articles/PMC8323186; pdf:https://europepmc.org/articles/PMC8323186?pdf=render
 37032516,https://doi.org/10.1111/aor.14537,Incidence and risk factors of late right heart failure in chronic mechanical circulatory support.,"Felix SEA, Numan L, Oerlemans MIF, Aarts E, Ramjankhan FZ, Gianoli M, Asselbergs FW, De Jonge N, Van Laake LW.",,Artificial organs,2023,2023-04-21,N,Risk factor; Mechanical Circulatory Support; Left Ventricular Assist Device; Late Right Heart Failure,,,"<h4>Background</h4>Late right heart failure (LRHF) is a common complication during long-term left ventricular assist device (LVAD) support. We aimed to identify risk factors for LRHF after LVAD implantation.<h4>Methods</h4>Patients undergoing primary LVAD implantation between 2006 and 2019 and surviving the perioperative period were included for this study (n = 261). Univariate Cox proportional hazards analysis was used to assess the association of clinical covariates and LRHF, stratified for device type. Variables with p < 0.10 entered the multivariable model. In a subset of patients with complete echocardiography or right catheterization data, this multivariable model was extended. Postoperative cardiopulmonary exercise test data were compared in patients with and without LRHF.<h4>Results</h4>Nineteen percentage of patients suffered from LRHF after a median of 12 months, of which 67% required hospitalization. A history of atrial fibrillation (AF) (HR: 2.06 [1.08-3.93], p = 0.029), a higher preoperative body mass index (BMI) (HR: 1.07 [1.01-1.13], p = 0.023), and intensive care unit (ICU) duration (HR: 1.03 [1.00-1.06], p = 0.025) were independent predictors of LHRF in the multivariable model. A significant relation between the severity of tricuspid regurgitation (TR) and LRHF (HR: 1.91 [1.13-3.21], p = 0.016) was found in patients with echocardiographic data. Patients with LRHF demonstrated a lower maximal workload and peak VO2 at 6 months postoperatively.<h4>Conclusion</h4>A history of AF, BMI, and longer ICU stay may help identify patients at high risk for LRHF. Severity of TR was significantly related to LRHF in a subset of patients.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/aor.14537; doi:https://doi.org/10.1111/aor.14537
-37194197,https://doi.org/10.1111/acps.13566,Low risk of some common cancers in women with anorexia nervosa: Evidence from a national record-linkage study.,"Seminog O, Thakrar DB, James AC, Goldacre MJ.",,Acta psychiatrica Scandinavica,2023,2023-05-16,Y,Cancer; Caloric restriction; epidemiology; Anorexia Nervosa; risk,,,"<h4>Background</h4>Some studies report that women with anorexia nervosa (AN) have lower risk than others of breast cancer, but increased risk of cancers of other sites. No work has been done to quantify the risk in the English population.<h4>Methods</h4>Retrospective cohort study using a national linked dataset of Hospital Episode Statistics for 1999-2021. We selected individuals with a hospital admission for AN, and compared their relative risk (RR) of developing site-specific cancers, with that in a reference cohort.<h4>Results</h4>We identified 75 cancers in 15,029 women hospitalised with AN. There was a low RR of all cancers combined at 0.75 (95%CI 0.59-0.94), and, notably, low RR for breast cancer 0.43 (0.20-0.81), cancers of secondary and ill-defined sites 0.52 (0.26-0.93). The RR for parotid gland cancer was 4.4 (1.4-10.6) within a year of first recorded diagnosis of AN. In men, we found 12 cancers in 1413 individuals hospitalised with AN, but no increased risks beyond the first year of diagnosis of AN.<h4>Conclusions</h4>This is the first report on the association between AN and cancers in the all-England population. The study showed low rates of breast cancer, and of all cancers combined, in women hospitalised with AN. It is possible that some of the metabolic or hormonal changes observed in AN could work as a protective factor for breast cancer. More experimental work is needed to identify and explain these factors. The new finding on the higher risk of salivary gland tumours could inform clinicians caring for patients with AN.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/acps.13566; doi:https://doi.org/10.1111/acps.13566; html:https://europepmc.org/articles/PMC10953461; pdf:https://europepmc.org/articles/PMC10953461?pdf=render
 37649471,https://doi.org/10.23889/ijpds.v6i3.1705,Data linkage can reduce the burden and increase the opportunities in the implementation of Value-Based Health Care policy: a study in patients with ulcerative colitis (PROUD-UC Study).,"Walshe J, Akbari A, Hawthorne AB, Laing H.",,International journal of population data science,2021,2021-01-01,Y,"Colitis, ulcerative; Health Policy; Patient Reported Outcome Measure; Routinely Collected Health Data; Data Science; Value-based Health Care",,,"<h4>Introduction</h4>Healthcare systems face rising demand and unsustainable cost pressures. In response, health policymakers are adopting Value-Based Health Care (VBHC), targeting available resources to achieve the best possible patient outcomes at the lowest possible cost and actively disinvesting in care of low-value. This requires the evaluation of longitudinal clinical and patient reported outcome measures (PROMs) at an individual-level and population-scale, which can create significant data challenges. Achieving this through routinely collected electronic health record (EHR) data-linkage could facilitate the implementation of VBHC without an unacceptable data burden on patients or health systems and release time for higher-value activities.<h4>Objectives</h4>Our study tested the ability to report an international, patient-centred outcome dataset (ICHOM-IBD) using only anonymised individual-level population-scale linked electronic health record (EHR) data sources, including clinical and patient-reported outcomes, in a cohort of patients with moderate-to-severe ulcerative colitis (UC), receiving biopharmaceutical therapies (""biologics"") in a single, publicly funded, healthcare system.<h4>Results</h4>We identified a cohort of 17,632 patients with UC in Wales and a cohort from two Health Boards of 447 patients with UC receiving biologics. 112 of these patients had completed 866 condition-specific PROMs during their biologics treatment. 44 out of 59 (74.6%) items in the ICHOM-IBD could be derived from routinely collected data of which a primary care source was essential for eight items and desirable for 21.<h4>Conclusions</h4>We demonstrated that it is possible to report most but not all the ICHOM-IBD outcomes using routinely collected data from multiple sources without additional system burden, potentially supporting Value-Based Health Care implementation with population data science. As digital collection of PROMs and use of condition-specific registries grow, greater utility of this approach can be anticipated. We have identified that the availability of longitudinal primary and secondary care data linked with PROMs is essential for this to be possible.",,pdf:https://ijpds.org/article/download/1705/4121; doi:https://doi.org/10.23889/ijpds.v6i3.1705; html:https://europepmc.org/articles/PMC10464864; pdf:https://europepmc.org/articles/PMC10464864?pdf=render
 35673545,https://doi.org/10.12688/wellcomeopenres.17231.2,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody lateral flow assay for antibody prevalence studies following vaccination: a diagnostic accuracy study.,"Cann A, Clarke C, Brown J, Thomson T, Prendecki M, Moshe M, Badhan A, Simmons B, Klaber B, Elliott P, Darzi A, Riley S, Ashby D, Martin P, Gleeson S, Willicombe M, Kelleher P, Ward H, Barclay WS, Cooke GS.",,Wellcome open research,2021,2021-01-01,Y,Antibodies; Seroprevalence; Lateral Flow; Neutralisation; Lfia; Covid-19; Sars-cov-2,,,"<b>Background:</b> Lateral flow immunoassays (LFIAs) are able to achieve affordable, large scale antibody testing and provide rapid results without the support of central laboratories. As part of the development of the REACT programme extensive evaluation of LFIA performance was undertaken with individuals following natural infection. Here we assess the performance of the selected LFIA to detect antibody responses in individuals who have received at least one dose of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine. <b>Methods:</b> This was a prospective diagnostic accuracy study. Sampling was carried out at renal outpatient clinic and healthcare worker testing sites at Imperial College London NHS Trust. Two cohorts of patients were recruited; the first was a cohort of 108 renal transplant patients attending clinic following two doses of SARS-CoV-2 vaccine, the second cohort comprised 40 healthcare workers attending for first SARS-CoV-2 vaccination and subsequent follow up. During the participants visit, finger-prick blood samples were analysed on LFIA device, while paired venous sampling was sent for serological assessment of antibodies to the spike protein (anti-S) antibodies. Anti-S IgG was detected using the Abbott Architect SARS-CoV-2 IgG Quant II CMIA. A total of 186 paired samples were collected. The accuracy of Fortress LFIA in detecting IgG antibodies to SARS-CoV-2 compared to anti-spike protein detection on Abbott Assay <b>Results:</b> The LFIA had an estimated sensitivity of 92.0% (114/124; 95% confidence interval [CI] 85.7% to 96.1%) and specificity of 93.6% (58/62; 95% CI 84.3% to 98.2%) using the Abbott assay as reference standard (using the threshold for positivity of 7.10 BAU/ml) <b>Conclusions:</b> Fortress LFIA performs well in the detection of antibody responses for intended purpose of population level surveillance but does not meet criteria for individual testing.",,doi:https://doi.org/10.12688/wellcomeopenres.17231.2; html:https://europepmc.org/articles/PMC9152464; pdf:https://europepmc.org/articles/PMC9152464?pdf=render
+37194197,https://doi.org/10.1111/acps.13566,Low risk of some common cancers in women with anorexia nervosa: Evidence from a national record-linkage study.,"Seminog O, Thakrar DB, James AC, Goldacre MJ.",,Acta psychiatrica Scandinavica,2023,2023-05-16,Y,Cancer; Caloric restriction; epidemiology; Anorexia Nervosa; risk,,,"<h4>Background</h4>Some studies report that women with anorexia nervosa (AN) have lower risk than others of breast cancer, but increased risk of cancers of other sites. No work has been done to quantify the risk in the English population.<h4>Methods</h4>Retrospective cohort study using a national linked dataset of Hospital Episode Statistics for 1999-2021. We selected individuals with a hospital admission for AN, and compared their relative risk (RR) of developing site-specific cancers, with that in a reference cohort.<h4>Results</h4>We identified 75 cancers in 15,029 women hospitalised with AN. There was a low RR of all cancers combined at 0.75 (95%CI 0.59-0.94), and, notably, low RR for breast cancer 0.43 (0.20-0.81), cancers of secondary and ill-defined sites 0.52 (0.26-0.93). The RR for parotid gland cancer was 4.4 (1.4-10.6) within a year of first recorded diagnosis of AN. In men, we found 12 cancers in 1413 individuals hospitalised with AN, but no increased risks beyond the first year of diagnosis of AN.<h4>Conclusions</h4>This is the first report on the association between AN and cancers in the all-England population. The study showed low rates of breast cancer, and of all cancers combined, in women hospitalised with AN. It is possible that some of the metabolic or hormonal changes observed in AN could work as a protective factor for breast cancer. More experimental work is needed to identify and explain these factors. The new finding on the higher risk of salivary gland tumours could inform clinicians caring for patients with AN.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/acps.13566; doi:https://doi.org/10.1111/acps.13566; html:https://europepmc.org/articles/PMC10953461; pdf:https://europepmc.org/articles/PMC10953461?pdf=render
 38100737,https://doi.org/10.1371/journal.pdig.0000383,Phenotypes and rates of cancer-relevant symptoms and tests in the year before cancer diagnosis in UK Biobank and CPRD Gold.,"Barclay M, Renzi C, Antoniou A, Denaxas S, Harrison H, Ip S, Pashayan N, Torralbo A, Usher-Smith J, Wood A, Lyratzopoulos G.",,PLOS digital health,2023,2023-12-15,Y,,,,"Early diagnosis of cancer relies on accurate assessment of cancer risk in patients presenting with symptoms, when screening is not appropriate. But recorded symptoms in cancer patients pre-diagnosis may vary between different sources of electronic health records (EHRs), either genuinely or due to differential completeness of symptom recording. To assess possible differences, we analysed primary care EHRs in the year pre-diagnosis of cancer in UK Biobank and Clinical Practice Research Datalink (CPRD) populations linked to cancer registry data. We developed harmonised phenotypes in Read v2 and CTV3 coding systems for 21 symptoms and eight blood tests relevant to cancer diagnosis. Among 22,601 CPRD and 11,594 UK Biobank cancer patients, 54% and 36%, respectively, had at least one consultation for possible cancer symptoms recorded in the year before their diagnosis. Adjusted comparisons between datasets were made using multivariable Poisson models, comparing rates of symptoms/tests in CPRD against expected rates if cancer site-age-sex-deprivation associations were the same as in UK Biobank. UK Biobank cancer patients compared with those in CPRD had lower rates of consultation for possible cancer symptoms [RR: 0.61 (0.59-0.63)], and lower rates for any primary care consultation [RR: 0.86 (95%CI 0.85-0.87)]. Differences were larger for 'non-alarm' symptoms [RR: 0.54 (0.52-0.56)], and smaller for 'alarm' symptoms [RR: 0.80 (0.76-0.84)] and blood tests [RR: 0.93 (0.90-0.95)]. In the CPRD cohort, approximately representative of the UK population, half of cancer patients had recorded symptoms in the year before diagnosis. The frequency of non-specific presenting symptoms recorded in the year pre-diagnosis of cancer was substantially lower among UK Biobank participants. The degree to which results based on highly selected biobank cohorts are generalisable needs to be examined in disease-specific contexts.",,doi:https://doi.org/10.1371/journal.pdig.0000383; html:https://europepmc.org/articles/PMC10723831; pdf:https://europepmc.org/articles/PMC10723831?pdf=render
 34890511,https://doi.org/10.1080/09638288.2021.1992517,"""It's been a long hard road"": challenges faced in the first three years following traumatic brain injury.","Downing MG, Hicks AJ, Braaf S, Myles DB, Gabbe BJ, Ponsford J.",,Disability and rehabilitation,2022,2021-12-10,N,Recovery; Challenges; Traumatic brain injury; Outcome; Qualitative Study,,,"<h4>Purpose</h4>There is limited qualitative research exploring challenges experienced following severe traumatic brain injury (TBI). We investigated challenges to recovery identified by individuals who sustained severe TBI three years earlier or their close others (COs), as well as suggestions for managing these challenges.<h4>Materials and methods</h4>Nine participants with TBI and 16 COs completed semi-structured interviews. Using reflexive thematic analysis, challenges were identified across several timeframes (i.e., at the injury, acute care, inpatient rehabilitation, outpatient rehabilitation, and at home/other location).<h4>Results</h4>Challenges experienced across all timeframes included: lack of information and poor communication, pre-existing conditions, missed injuries, and issues with medical staff, and continuity of care. From acute care onwards, there were TBI-related consequences, issues with coping and emotional adjustment, negative outlook, insufficient treatment, lack of support for COs, and issues with compensation and funding for rehabilitation needs. Some challenges were unique to a specific timeframe (e.g., over-stimulating ward setting during acute care, and limited or unsupportive families once injured individuals went home). Suggestions for managing some of the challenges were provided (e.g., information provision, having peer supports).<h4>Conclusion</h4>Suggestions should be considered to promote successful outcomes following severe TBI.IMPLICATIONS FOR REHABILITATIONRecovery following a severe traumatic brain injury can be hindered by challenges, such as poor communication, limited information provision, injury-related consequences, limited services and emotional support for the injured individual and their Close Others, and a need for education of the broader community about traumatic brain injury.Suggestions for managing these challenges (e.g., peer supports; services closer to home) could be used to inform clinical guidelines that could be used in a rehabilitation context.These suggestions ultimately aim to improve the post-injury experience and outcomes of individuals with traumatic brain injury and their Close Others.",,doi:https://doi.org/10.1080/09638288.2021.1992517
 31398202,https://doi.org/10.1371/journal.pone.0220771,The role of health and social factors in education outcome: A record-linked electronic birth cohort analysis.,"Evans A, Dunstan F, Fone DL, Bandyopadhyay A, Schofield B, Demmler JC, Rahman MA, Lyons RA, Paranjothy S.",,PloS one,2019,2019-08-09,Y,,Improving Public Health,,"<h4>Background and objective</h4>Health status in childhood is correlated with educational outcomes. Emergency hospital admissions during childhood are common but it is not known how these unplanned breaks from schooling impact on education outcomes. We hypothesised that children who had emergency hospital admissions had an increased risk of lower educational attainment, in addition to the increased risks associated with other health, social and school factors.<h4>Methods</h4>This record-linked electronic birth cohort, included children born in Wales between 1 January 1998 and 31 August 2001. We fitted multilevel logistic regression models grouped by schools, to determine whether emergency hospital inpatient admission before age 7 years was associated with the educational outcome of not attaining the expected level in a teacher-based assessment at age 7 years (KS1). We adjusted for pregnancy, perinatal, socio-economic, neighbourhood, pupil mobility and school-level factors.<h4>Results</h4>The cohort comprised 64 934 children. Overall, 4680 (7.2%) did not attain the expected educational level. Emergency admission to hospital was associated with poor educational attainment (OR 1.12 95% Credible Interval (CI) 1.05, 1.20 for all causes during childhood, OR 1.19 95%CI 1.07, 1.32 for injuries and external causes and OR 1.31 95%CI 1.04, 1.22 for admissions during infancy), after adjusting for known determinants of education outcomes such as extreme prematurity, being small for gestational age and socio-economic indicators, such as eligibility for free school meals.<h4>Conclusion</h4>Emergency inpatient hospital admission during childhood, particularly during infancy or for injuries and external causes was associated with an increased risk of lower education attainment at age 7 years, in addition to the effects of pregnancy factors (gestational age, birthweight) and social deprivation. These findings support the need for injury prevention measures and additional support in school for affected children to help them to achieve their potential.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0220771&type=printable; doi:https://doi.org/10.1371/journal.pone.0220771; html:https://europepmc.org/articles/PMC6688802; pdf:https://europepmc.org/articles/PMC6688802?pdf=render
@@ -1241,29 +1243,29 @@ PMC10686417,https://doi.org/,The impact of restricted provision of publicly fund
 39434187,https://doi.org/10.1186/s13073-024-01395-4,Integrating metabolomics and proteomics to identify novel drug targets for heart failure and atrial fibrillation.,"van Vugt M, Finan C, Chopade S, Providencia R, Bezzina CR, Asselbergs FW, van Setten J, Schmidt AF.",,Genome medicine,2024,2024-10-21,Y,Proteomics; Atrial fibrillation; Cardiomyopathy; Metabolomics; Heart Failure; Drug Development; Mendelian Randomisation,,,"<h4>Background</h4>Altered metabolism plays a role in the pathophysiology of cardiac diseases, such as atrial fibrillation (AF) and heart failure (HF). We aimed to identify novel plasma metabolites and proteins associating with cardiac disease.<h4>Methods</h4>Mendelian randomisation (MR) was used to assess the association of 174 metabolites measured in up to 86,507 participants with AF, HF, dilated cardiomyopathy (DCM), and non-ischemic cardiomyopathy (NICM). Subsequently, we sourced data on 1567 plasma proteins and performed cis MR to identify proteins affecting the identified metabolites as well as the cardiac diseases. Proteins were prioritised on cardiac expression and druggability, and mapped to biological pathways.<h4>Results</h4>We identified 35 metabolites associating with cardiac disease. AF was affected by seventeen metabolites, HF by nineteen, DCM by four, and NCIM by taurine. HF was particularly enriched for phosphatidylcholines (p = 0.029) and DCM for acylcarnitines (p = 0.001). Metabolite involvement with AF was more uniform, spanning for example phosphatidylcholines, amino acids, and acylcarnitines. We identified 38 druggable proteins expressed in cardiac tissue, with a directionally concordant effect on metabolites and cardiac disease. We recapitulated known associations, for example between the drug target of digoxin (AT1B2), taurine and NICM risk. Additionally, we identified numerous novel findings, such as higher RET values associating with phosphatidylcholines and decreasing AF and HF. RET is targeted by drugs such as regorafenib which has known cardiotoxic side-effects. Pathway analysis implicated involvement of GDF15 signalling through RET, and ghrelin regulation of energy homeostasis in cardiac pathogenesis.<h4>Conclusions</h4>This study identified 35 plasma metabolites involved with cardiac diseases and linked these to 38 druggable proteins, providing actionable leads for drug development.",,doi:https://doi.org/10.1186/s13073-024-01395-4; html:https://europepmc.org/articles/PMC11492627; pdf:https://europepmc.org/articles/PMC11492627?pdf=render
 37549998,https://doi.org/10.1136/bjsports-2022-106460,Device-based measurement of physical activity in cardiovascular healthcare: possibilities and challenges.,"Chico TJ, Stamatakis E, Ciravegna F, Dunn J, Redwood S, Al-Lamee R, Sofat R, Gill J.",,British journal of sports medicine,2023,2023-08-07,N,Cardiovascular diseases; Health; Physical Activity,,,,,doi:https://doi.org/10.1136/bjsports-2022-106460
 36197964,https://doi.org/10.1126/scitranslmed.abq4810,"Comment on ""A proteomic surrogate for cardiovascular outcomes that is sensitive to multiple mechanisms of change in risk"".","Kivimäki M, Hingorani AD, Lindbohm JV.",,Science translational medicine,2022,2022-10-05,N,,,,"A 27-protein signature has been proposed to predict cardiovascular disease, but its applicability in clinical decision-making remains unclear.",,pdf:https://www.science.org/doi/pdf/10.1126/scitranslmed.abq4810?download=true; doi:https://doi.org/10.1126/scitranslmed.abq4810
-38050140,https://doi.org/10.1136/jnnp-2023-332322,Premorbid brain structure influences risk of amyotrophic lateral sclerosis.,"Thompson AG, Taschler B, Smith SM, Turner MR.",,"Journal of neurology, neurosurgery, and psychiatry",2024,2024-03-13,Y,MRI; ALS,,,"<h4>Background</h4>Amyotrophic lateral sclerosis (ALS) is a disease of the motor network associated with brain structure and functional connectivity alterations that are implicated in disease progression. Whether such changes have a causal role in ALS, fitting with a postulated influence of premorbid cerebral architecture on the phenotypes associated with neurodegenerative disorders is not known.<h4>Methods</h4>This study considered causal effects and shared genetic risk of 2240 structural and functional MRI brain scan imaging-derived phenotypes (IDPs) on ALS using two sample Mendelian randomisation, with putative associations further examined with extensive sensitivity analysis. Shared genetic predisposition between IDPs and ALS was explored using genetic correlation analysis.<h4>Results</h4>Increased white matter volume in the cerebral hemispheres was causally associated with ALS. Weaker causal associations were observed for brain stem grey matter volume, parieto-occipital white matter surface and volume of the left thalamic ventral anterior nucleus. Genetic correlation was observed between ALS and intracellular volume fraction and isotropic free water volume fraction within the posterior limb of the internal capsule.<h4>Conclusions</h4>This study provides evidence that premorbid brain structure, in particular white matter volume, contributes to the risk of ALS.",,doi:https://doi.org/10.1136/jnnp-2023-332322; html:https://europepmc.org/articles/PMC10958375; pdf:https://europepmc.org/articles/PMC10958375?pdf=render
 38374065,https://doi.org/10.1038/s41467-024-45779-x,Genetic influences on circulating retinol and its relationship to human health.,"Reay WR, Kiltschewskij DJ, Di Biase MA, Gerring ZF, Kundu K, Surendran P, Greco LA, Clarke ED, Collins CE, Mondul AM, Albanes D, Cairns MJ.",,Nature communications,2024,2024-02-19,Y,,,,"Retinol is a fat-soluble vitamin that plays an essential role in many biological processes throughout the human lifespan. Here, we perform the largest genome-wide association study (GWAS) of retinol to date in up to 22,274 participants. We identify eight common variant loci associated with retinol, as well as a rare-variant signal. An integrative gene prioritisation pipeline supports novel retinol-associated genes outside of the main retinol transport complex (RBP4:TTR) related to lipid biology, energy homoeostasis, and endocrine signalling. Genetic proxies of circulating retinol were then used to estimate causal relationships with almost 20,000 clinical phenotypes via a phenome-wide Mendelian randomisation study (MR-pheWAS). The MR-pheWAS suggests that retinol may exert causal effects on inflammation, adiposity, ocular measures, the microbiome, and MRI-derived brain phenotypes, amongst several others. Conversely, circulating retinol may be causally influenced by factors including lipids and serum creatinine. Finally, we demonstrate how a retinol polygenic score could identify individuals more likely to fall outside of the normative range of circulating retinol for a given age. In summary, this study provides a comprehensive evaluation of the genetics of circulating retinol, as well as revealing traits which should be prioritised for further investigation with respect to retinol related therapies or nutritional intervention.",,pdf:https://www.nature.com/articles/s41467-024-45779-x.pdf; doi:https://doi.org/10.1038/s41467-024-45779-x; html:https://europepmc.org/articles/PMC10876955; pdf:https://europepmc.org/articles/PMC10876955?pdf=render
 34671274,https://doi.org/10.3389/fphys.2021.730736,Comparing Non-invasive Inverse Electrocardiography With Invasive Endocardial and Epicardial Electroanatomical Mapping During Sinus Rhythm.,"Roudijk RW, Boonstra MJ, Brummel R, Kassenberg W, Blom LJ, Oostendorp TF, Te Riele ASJM, van der Heijden JF, Asselbergs FW, van Dam PM, Loh P.",,Frontiers in physiology,2021,2021-10-04,Y,Cardiac Arrhythmia; Sudden Cardiac Death; Electroanatomical Mapping; Electrocardiographic Imaging (Ecgi); Non-invasive Mapping; Equivalent Dipole Layer; Inverse Problem Of Electrocardiography,,,"This study presents a novel non-invasive equivalent dipole layer (EDL) based inverse electrocardiography (<i>i</i>ECG) technique which estimates both endocardial and epicardial ventricular activation sequences. We aimed to quantitatively compare our <i>i</i>ECG approach with invasive electro-anatomical mapping (EAM) during sinus rhythm with the objective of enabling functional substrate imaging and sudden cardiac death risk stratification in patients with cardiomyopathy. Thirteen patients (77% males, 48 ± 20 years old) referred for endocardial and epicardial EAM underwent 67-electrode body surface potential mapping and CT imaging. The EDL-based <i>i</i>ECG approach was improved by mimicking the effects of the His-Purkinje system on ventricular activation. EAM local activation timing (LAT) maps were compared with <i>i</i>ECG-LAT maps using absolute differences and Pearson's correlation coefficient, reported as mean ± standard deviation [95% confidence interval]. The correlation coefficient between <i>i</i>ECG-LAT maps and EAM was 0.54 ± 0.19 [0.49-0.59] for epicardial activation, 0.50 ± 0.27 [0.41-0.58] for right ventricular endocardial activation and 0.44 ± 0.29 [0.32-0.56] for left ventricular endocardial activation. The absolute difference in timing between <i>i</i>ECG maps and EAM was 17.4 ± 7.2 ms for epicardial maps, 19.5 ± 7.7 ms for right ventricular endocardial maps, 27.9 ± 8.7 ms for left ventricular endocardial maps. The absolute distance between right ventricular endocardial breakthrough sites was 30 ± 16 mm and 31 ± 17 mm for the left ventricle. The absolute distance for latest epicardial activation was median 12.8 [IQR: 2.9-29.3] mm. This first in-human quantitative comparison of <i>i</i>ECG and invasive LAT-maps on both the endocardial and epicardial surface during sinus rhythm showed improved agreement, although with considerable absolute difference and moderate correlation coefficient. Non-invasive <i>i</i>ECG requires further refinements to facilitate clinical implementation and risk stratification.",,pdf:https://www.frontiersin.org/articles/10.3389/fphys.2021.730736/pdf; doi:https://doi.org/10.3389/fphys.2021.730736; html:https://europepmc.org/articles/PMC8521153; pdf:https://europepmc.org/articles/PMC8521153?pdf=render
-32896935,https://doi.org/10.1002/cbm.2166,Are Liaison and Diversion interventions in policing delivering the planned impact: A longitudinal evaluation in two constabularies?,"Kane E, Evans E, Mitsch J, Jilani T.",,Criminal behaviour and mental health : CBMH,2020,2020-09-08,N,Mental health; Outcomes; Offending; Policing; Liaison & Diversion,,,"Liaison and Diversion (L&D) has twin objectives: improving mental health outcomes and reducing re-offending. Early diversion from police custody seems promising, but evidence of benefit is required to sustain such programmes. To test the hypothesis that contact with L&D services while in police custody would lead to improved mental health outcomes and a reduction in type and level of offending, we used a pre-post service use design. National Health Service (NHS) records in two counties were searched for evidence that patients had been involved with L&D services while in police custody during the period July 2009-December 2017. We defined January 2009-July 2014 as the pre-intervention period and any time after contact as the post-intervention period. Data from the Police National Computer were gathered for each period for these individuals, to assess their pre-post L&D contact offending histories. NHS Trust data were similarly gathered to assess their pre-post use of mental health legislation. 4,462 individuals were identified who had used L&D services in police custody. There were statistically significant reductions in the amount of offending following contact with the L&D service (whether one or two contacts), regardless of offence type. Statistically significant reductions were also observed in use of the four most commonly used legislative powers for detaining patients in hospital on mental disorder grounds, regardless of offending status (prolific/non-prolific). Our results indicate positive associations between the L&D interventions and change in offending and use of compulsory hospital detention. Whilst our research does not allow a direct causal relationship to be established in either area, the findings go beyond other impact assessments of L&D which have either been with small samples or relied only on qualitative data or expert opinion.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cbm.2166; doi:https://doi.org/10.1002/cbm.2166
+38050140,https://doi.org/10.1136/jnnp-2023-332322,Premorbid brain structure influences risk of amyotrophic lateral sclerosis.,"Thompson AG, Taschler B, Smith SM, Turner MR.",,"Journal of neurology, neurosurgery, and psychiatry",2024,2024-03-13,Y,MRI; ALS,,,"<h4>Background</h4>Amyotrophic lateral sclerosis (ALS) is a disease of the motor network associated with brain structure and functional connectivity alterations that are implicated in disease progression. Whether such changes have a causal role in ALS, fitting with a postulated influence of premorbid cerebral architecture on the phenotypes associated with neurodegenerative disorders is not known.<h4>Methods</h4>This study considered causal effects and shared genetic risk of 2240 structural and functional MRI brain scan imaging-derived phenotypes (IDPs) on ALS using two sample Mendelian randomisation, with putative associations further examined with extensive sensitivity analysis. Shared genetic predisposition between IDPs and ALS was explored using genetic correlation analysis.<h4>Results</h4>Increased white matter volume in the cerebral hemispheres was causally associated with ALS. Weaker causal associations were observed for brain stem grey matter volume, parieto-occipital white matter surface and volume of the left thalamic ventral anterior nucleus. Genetic correlation was observed between ALS and intracellular volume fraction and isotropic free water volume fraction within the posterior limb of the internal capsule.<h4>Conclusions</h4>This study provides evidence that premorbid brain structure, in particular white matter volume, contributes to the risk of ALS.",,doi:https://doi.org/10.1136/jnnp-2023-332322; html:https://europepmc.org/articles/PMC10958375; pdf:https://europepmc.org/articles/PMC10958375?pdf=render
 36682888,https://doi.org/10.1111/cch.13097,Adversity profiles of children receiving care and support from social services: A latent-class analysis of school-aged children in Wales.,"Anthony R, Scourfield J, Moore G, Paranjothy S, Evans A, Brophy S, Daniel R, Long S.",,"Child: care, health and development",2023,2023-01-31,Y,Care; Child Welfare; Social Services; Latent Class Analysis; Adverse Childhood Experiences,,,"<h4>Background</h4>Children receive care and support from social services due to the risk of harm or impeded development or because of disability. This study aimed to identify typologies of adversity experienced by children receiving care and support from social services and to explore how typologies differ by sociodemographic characteristics.<h4>Methods</h4>This is a cross-sectional study of 'Children Receiving Care and Support' (N = 12 792) during 2017/2018 in Wales, UK. We sought to (1) examine the prevalence of household adversities experienced by children in receipt of care and support from social services; (2) identify typologies of household adversities; and (3) explore how typologies of household adversities differ by family characteristics (demographics, measures of social disadvantage, perinatal and care factors).<h4>Results</h4>We found evidence for multiple risk factor constellations. The four-class solution suggested four distinct classes of adversities: child disability (50.0%), low adversities (20.3%), family poor health (6.7%) and multiple risks (23.0%). Children in the 'multiple risk' class were significantly more likely to be younger, more deprived and 'looked after' by the local authority compared with those in the 'low adversities' class.<h4>Conclusions</h4>Given the presence of different constellations of household adversities, policies and interventions that address multiple risk factors simultaneously may be more effective and have longer-lasting benefits.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/cch.13097; doi:https://doi.org/10.1111/cch.13097; html:https://europepmc.org/articles/PMC10946723; pdf:https://europepmc.org/articles/PMC10946723?pdf=render
-37008054,https://doi.org/10.14336/ad.2022.0829,Identifying Dynamic Patterns of Polypharmacy for Patients with Dementia from Primary Care Electronic Health Records: A Machine Learning Driven Longitudinal Study.,"Longo E, Burnett B, Bauermeister S, Zhou SM.",,Aging and disease,2023,2023-04-01,Y,Diagnosis; Dementia; Patient Safety; Machine Learning; Polypharmacy; Electronic Health Records; Exploratory Factor Analysis,,,"It is unclear how medication use evolved before diagnosis of dementia (DoD). This study aims to identify varied patterns of polypharmacy before DoD, their prevalence and possible complications. We collected primary care e-health records for 33,451 dementia patients in Wales from 1990 to 2015. The medication uses in every 5-year period along with 20-years prior to dementia diagnosis were considered. Exploratory factor analysis was used to identify clusters of medicines for every 5-year period. The prevalence of patients taking three or more medications was 82.16%, 69.7%, 41.1% and 5.5% in the Period 1 (0-5 years before DoD) ~ Period 4 (16-20 years before DoD) respectively. The Period 1 showed 3 clusters of polypharmacy - medicines for respiratory/urinary infections, arthropathies and rheumatism, and cardio-vascular disease (CVD) (66.55%); medicines for infections, arthropathies and rheumatism (AR), cardio-metabolic disease (CMD) and depression (22.02%); and medicines for arthropathies, rheumatism and osteoarthritis (2.6%). The Period 2 showed 4 clusters of polypharmacy - medicines for infections, arthropathies, and CVD (69.7%); medicines for CVD and depression (3%); medicines for CMD and arthropathies (0.3%); and medicines for AR, and CVD (2,5%). The Period 3 showed 6 clusters of polypharmacy - medicines for infections, arthropathies, and CVD (41.1%); medicines for CVD, acute-respiratory-infection (ARI), and arthropathies (1.25%); medicines for AR (1.16%); medicines for depression, anxiety (0.06%); medicines for CMD (1.4%); and medicines for dermatologic disorders (0.9%). The Period 4 showed 3 main clusters of polypharmacy - medicines for infections, arthropathy, and CVD (5.5%); medicines for anxiety, ARI (2.4%); and medicines for ARI and CVD (2.1%). As the development towards dementia progressed, the associative diseases tended to cluster with a larger prevalence in each cluster. Farther away before DoD, the clusters of polypharmacy tended to be clearly distinct between each other, resulting in an increasing number of patterns, but in a smaller prevalence.",,doi:https://doi.org/10.14336/ad.2022.0829; doi:https://doi.org/10.14336/AD.2022.0829; html:https://europepmc.org/articles/PMC10017143; pdf:https://europepmc.org/articles/PMC10017143?pdf=render
+32896935,https://doi.org/10.1002/cbm.2166,Are Liaison and Diversion interventions in policing delivering the planned impact: A longitudinal evaluation in two constabularies?,"Kane E, Evans E, Mitsch J, Jilani T.",,Criminal behaviour and mental health : CBMH,2020,2020-09-08,N,Mental health; Outcomes; Offending; Policing; Liaison & Diversion,,,"Liaison and Diversion (L&D) has twin objectives: improving mental health outcomes and reducing re-offending. Early diversion from police custody seems promising, but evidence of benefit is required to sustain such programmes. To test the hypothesis that contact with L&D services while in police custody would lead to improved mental health outcomes and a reduction in type and level of offending, we used a pre-post service use design. National Health Service (NHS) records in two counties were searched for evidence that patients had been involved with L&D services while in police custody during the period July 2009-December 2017. We defined January 2009-July 2014 as the pre-intervention period and any time after contact as the post-intervention period. Data from the Police National Computer were gathered for each period for these individuals, to assess their pre-post L&D contact offending histories. NHS Trust data were similarly gathered to assess their pre-post use of mental health legislation. 4,462 individuals were identified who had used L&D services in police custody. There were statistically significant reductions in the amount of offending following contact with the L&D service (whether one or two contacts), regardless of offence type. Statistically significant reductions were also observed in use of the four most commonly used legislative powers for detaining patients in hospital on mental disorder grounds, regardless of offending status (prolific/non-prolific). Our results indicate positive associations between the L&D interventions and change in offending and use of compulsory hospital detention. Whilst our research does not allow a direct causal relationship to be established in either area, the findings go beyond other impact assessments of L&D which have either been with small samples or relied only on qualitative data or expert opinion.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cbm.2166; doi:https://doi.org/10.1002/cbm.2166
 35135774,https://doi.org/10.1136/bmjopen-2021-055603,"Observational retrospective study calculating health service costs of patients receiving surgery for chronic rhinosinusitis in England, using linked patient-level primary and secondary care electronic data.","Clarke CS, Williamson E, Denaxas S, Carpenter JR, Thomas M, Blackshaw H, Schilder AGM, Philpott CM, Hopkins C, Morris S, MACRO programme team.",,BMJ open,2022,2022-02-08,Y,Otolaryngology; Clinical Trials; Health Economics,,,"<h4>Objectives</h4>Chronic rhinosinusitis (CRS) symptoms are experienced by an estimated 11% of UK adults, and symptoms have major impacts on quality of life. Data from UK and elsewhere suggest high economic burden of CRS, but detailed cost information and economic analyses regarding surgical pathway are lacking. This paper estimates healthcare costs for patients receiving surgery for CRS in England.<h4>Design</h4>Observational retrospective study examining cost of healthcare of patients receiving CRS surgery.<h4>Setting</h4>Linked electronic health records from the Clinical Practice Research Datalink, Hospital Episode Statistics and Office for National Statistics databases in England.<h4>Participants</h4>A phenotyping algorithm using medical ontology terms identified 'definite' CRS cases who received CRS surgery. Patients were registered with a general practice in England. Data covered the period 1997-2016. A cohort of 13 462 patients had received surgery for CRS, with 9056 (67%) having confirmed nasal polyps.<h4>Outcome measures</h4>Information was extracted on numbers and types of primary care prescriptions and consultations, and inpatient and outpatient hospital investigations and procedures. Resource use was costed using published sources.<h4>Results</h4>Total National Health Service costs in CRS surgery patients were £2173 over 1 year including surgery. Total costs per person-quarter were £1983 in the quarter containing surgery, mostly comprising surgical inpatient care costs (£1902), and around £60 per person-quarter in the 2 years before and after surgery, of which half were outpatient costs. Outpatient and primary care costs were low compared with the peak in inpatient costs at surgery. The highest outpatient expenditure was on CT scans, peaking in the quarter preceding surgery.<h4>Conclusions</h4>We present the first study of costs to the English healthcare system for patients receiving surgery for CRS. The total aggregate costs provide a further impetus for trials to evaluate the relative benefit of surgical intervention.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/2/e055603.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-055603; html:https://europepmc.org/articles/PMC8830221; pdf:https://europepmc.org/articles/PMC8830221?pdf=render
+37008054,https://doi.org/10.14336/ad.2022.0829,Identifying Dynamic Patterns of Polypharmacy for Patients with Dementia from Primary Care Electronic Health Records: A Machine Learning Driven Longitudinal Study.,"Longo E, Burnett B, Bauermeister S, Zhou SM.",,Aging and disease,2023,2023-04-01,Y,Diagnosis; Dementia; Patient Safety; Machine Learning; Polypharmacy; Electronic Health Records; Exploratory Factor Analysis,,,"It is unclear how medication use evolved before diagnosis of dementia (DoD). This study aims to identify varied patterns of polypharmacy before DoD, their prevalence and possible complications. We collected primary care e-health records for 33,451 dementia patients in Wales from 1990 to 2015. The medication uses in every 5-year period along with 20-years prior to dementia diagnosis were considered. Exploratory factor analysis was used to identify clusters of medicines for every 5-year period. The prevalence of patients taking three or more medications was 82.16%, 69.7%, 41.1% and 5.5% in the Period 1 (0-5 years before DoD) ~ Period 4 (16-20 years before DoD) respectively. The Period 1 showed 3 clusters of polypharmacy - medicines for respiratory/urinary infections, arthropathies and rheumatism, and cardio-vascular disease (CVD) (66.55%); medicines for infections, arthropathies and rheumatism (AR), cardio-metabolic disease (CMD) and depression (22.02%); and medicines for arthropathies, rheumatism and osteoarthritis (2.6%). The Period 2 showed 4 clusters of polypharmacy - medicines for infections, arthropathies, and CVD (69.7%); medicines for CVD and depression (3%); medicines for CMD and arthropathies (0.3%); and medicines for AR, and CVD (2,5%). The Period 3 showed 6 clusters of polypharmacy - medicines for infections, arthropathies, and CVD (41.1%); medicines for CVD, acute-respiratory-infection (ARI), and arthropathies (1.25%); medicines for AR (1.16%); medicines for depression, anxiety (0.06%); medicines for CMD (1.4%); and medicines for dermatologic disorders (0.9%). The Period 4 showed 3 main clusters of polypharmacy - medicines for infections, arthropathy, and CVD (5.5%); medicines for anxiety, ARI (2.4%); and medicines for ARI and CVD (2.1%). As the development towards dementia progressed, the associative diseases tended to cluster with a larger prevalence in each cluster. Farther away before DoD, the clusters of polypharmacy tended to be clearly distinct between each other, resulting in an increasing number of patterns, but in a smaller prevalence.",,doi:https://doi.org/10.14336/ad.2022.0829; doi:https://doi.org/10.14336/AD.2022.0829; html:https://europepmc.org/articles/PMC10017143; pdf:https://europepmc.org/articles/PMC10017143?pdf=render
 36050271,https://doi.org/10.1016/s2589-7500(22)00151-0,CODE-EHR best-practice framework for the use of structured electronic health-care records in clinical research.,"Kotecha D, Asselbergs FW, Achenbach S, Anker SD, Atar D, Baigent C, Banerjee A, Beger B, Brobert G, Casadei B, Ceccarelli C, Cowie MR, Crea F, Cronin M, Denaxas S, Derix A, Fitzsimons D, Fredriksson M, Gale CP, Gkoutos GV, Goettsch W, Hemingway H, Ingvar M, Jonas A, Kazmierski R, Løgstrup S, Lumbers RT, Lüscher TF, McGreavy P, Piña IL, Roessig L, Steinbeisser C, Sundgren M, Tyl B, Thiel GV, Bochove KV, Vardas PE, Villanueva T, Vrana M, Weber W, Weidinger F, Windecker S, Wood A, Grobbee DE, Innovative Medicines Initiative BigData@Heart Consortium, European Society of Cardiology, and CODE-EHR International Consensus Group.",,The Lancet. Digital health,2022,2022-08-29,N,,,,"Big data is important to new developments in global clinical science that aim to improve the lives of patients. Technological advances have led to the regular use of structured electronic health-care records with the potential to address key deficits in clinical evidence that could improve patient care. The COVID-19 pandemic has shown this potential in big data and related analytics but has also revealed important limitations. Data verification, data validation, data privacy, and a mandate from the public to conduct research are important challenges to effective use of routine health-care data. The European Society of Cardiology and the BigData@Heart consortium have brought together a range of international stakeholders, including representation from patients, clinicians, scientists, regulators, journal editors, and industry members. In this Review, we propose the CODE-EHR minimum standards framework to be used by researchers and clinicians to improve the design of studies and enhance transparency of study methods. The CODE-EHR framework aims to develop robust and effective utilisation of health-care data for research purposes.",,doi:https://doi.org/10.1016/s2589-7500(22)00151-0; doi:https://doi.org/10.1016/S2589-7500(22)00151-0
-37140153,https://doi.org/10.1093/ehjci/jead093,Determinants of post-operative left ventricular dysfunction in degenerative mitral regurgitation.,"Althunayyan AM, Alborikan S, Badiani S, Wong K, Uppal R, Patel N, Petersen SE, Lloyd G, Bhattacharyya S.",,European heart journal. Cardiovascular Imaging,2023,2023-08-01,N,Surgery; Mitral regurgitation; Mitral Valve Prolapse; Global Longitudinal Strain; Lv Volumes,,,"<h4>Aims</h4>Chronic degenerative mitral regurgitation leads to volume overload causing left ventricular (LV) enlargement and eventually LV impairment. Current guidelines determining thresholds for intervention are based on LV diameters and ejection fraction (LVEF). There are sparse data examining the value of LV volumes and newer markers of LV performance on outcomes of surgery in mitral valve prolapse. The aim of this study is to identify the best marker of LV impairment after mitral valve surgery.<h4>Methods and results</h4>Prospective, observational study of patients with mitral valve prolapse undergoing mitral valve surgery. Pre-operative LV diameters, volumes, LVEF, global longitudinal strain (GLS), and myocardial work measured. Post-operative LV impairment defined as LVEF < 50% at 1 year post-surgery. Eighty-seven patients included. Thirteen percent developed post-operative LV impairment. Patients with post-operative LV dysfunction showed significantly larger indexed LV end-systolic diameters, indexed LV end-systolic volumes (LVESVi), lower LVEF, and more abnormal GLS than patients without post-operative LV dysfunction. In multivariate analysis, LVESVi [odds ratio 1.11 (95% CI 1.01-1.23), P = 0.039] and GLS [odds ratio 1.46 (95% CI 1.00-2.14), P = 0.054] were the only independent predictors of post-operative LV dysfunction. The optimal cut-off of 36.3 mL/m2 for LVESVi had a sensitivity of 82% and specificity of 78% for detection of post-operative LV impairment.<h4>Conclusion</h4>Post-operative LV impairment is common. Indexed LV volumes (36.3 mL/m2) provided the best marker of post-operative LV impairment.",,pdf:https://academic.oup.com/ehjcimaging/advance-article-pdf/doi/10.1093/ehjci/jead093/50200028/jead093.pdf; doi:https://doi.org/10.1093/ehjci/jead093
 36276403,https://doi.org/10.3389/fpubh.2022.875198,The mental health experiences of ethnic minorities in the UK during the Coronavirus pandemic: A qualitative exploration.,"Van Bortel T, Lombardo C, Guo L, Solomon S, Martin S, Hughes K, Weeks L, Crepaz-Keay D, McDaid S, Chantler O, Thorpe L, Morton A, Davidson G, John A, Kousoulis AA.",,Frontiers in public health,2022,2022-10-06,Y,Mental health; United Kingdom; Inequalities; Ethnic Minorities; Covid-19; Coronavirus Pandemic; Bame Ethnicity,,,"<h4>Background</h4>Worldwide, the Coronavirus pandemic has had a major impact on people's health, lives, and livelihoods. However, this impact has not been felt equally across various population groups. People from ethnic minority backgrounds in the UK have been more adversely affected by the pandemic, especially in terms of their physical health. Their mental health, on the other hand, has received less attention. This study aimed to explore the mental health experiences of UK adults from ethnic minorities during the Coronavirus pandemic. This work forms part of our wider long-term UK population study ""Mental Health in the Pandemic.""<h4>Methods</h4>We conducted an exploratory qualitative study with people from ethnic minority communities across the UK. A series of in-depth interviews were conducted with 15 women, 14 men and 1 non-binary person from ethnic minority backgrounds, aged between 18 and 65 years old (mean age = 40). We utilized purposefully selected maximum variation sampling in order to capture as wide a variety of views, perceptions and experiences as possible. Inclusion criteria: adults (18+) from ethnic minorities across the UK; able to provide full consent to participate; able to participate in a video- or phone-call interview. All interviews took place <i>via</i> MS Teams or Zoom. The gathered data were transcribed verbatim and underwent thematic analysis following Braun and Clarke carried out using NVivo 12 software.<h4>Results</h4>The qualitative data analysis yielded seven overarching themes: (1) pandemic-specific mental health and wellbeing experiences; (2) issues relating to the media; (3) coping mechanisms; (4) worries around and attitudes toward vaccination; (5) suggestions for support in moving forward; (6) best and worst experiences during pandemic and lockdowns; (7) biggest areas of change in personal life. Generally, participants' mental health experiences varied with some not being affected by the pandemic in a way related to their ethnicity, some sharing positive experiences and coping strategies (exercising more, spending more time with family, community cohesion), and some expressing negative experiences (eating or drinking more, feeling more isolated, or even racism and abuse, especially toward Asian communities). Concerns were raised around trust issues in relation to the media, the inadequate representation of ethnic minorities, and the spread of fake news especially on social media. Attitudes toward vaccinations varied too, with some people more willing to have the vaccine than others.<h4>Conclusion</h4>This study's findings highlight the diversity in the pandemic mental health experiences of ethnic minorities in the UK and has implications for policy, practice and further research. To enable moving forward beyond the pandemic, our study surfaced the need for culturally appropriate mental health support, financial support (as a key mental health determinant), accurate media representation, and clear communication messaging from the Governments of the UK.",,pdf:https://www.frontiersin.org/articles/10.3389/fpubh.2022.875198/pdf; doi:https://doi.org/10.3389/fpubh.2022.875198; html:https://europepmc.org/articles/PMC9582845; pdf:https://europepmc.org/articles/PMC9582845?pdf=render
+37140153,https://doi.org/10.1093/ehjci/jead093,Determinants of post-operative left ventricular dysfunction in degenerative mitral regurgitation.,"Althunayyan AM, Alborikan S, Badiani S, Wong K, Uppal R, Patel N, Petersen SE, Lloyd G, Bhattacharyya S.",,European heart journal. Cardiovascular Imaging,2023,2023-08-01,N,Surgery; Mitral regurgitation; Mitral Valve Prolapse; Global Longitudinal Strain; Lv Volumes,,,"<h4>Aims</h4>Chronic degenerative mitral regurgitation leads to volume overload causing left ventricular (LV) enlargement and eventually LV impairment. Current guidelines determining thresholds for intervention are based on LV diameters and ejection fraction (LVEF). There are sparse data examining the value of LV volumes and newer markers of LV performance on outcomes of surgery in mitral valve prolapse. The aim of this study is to identify the best marker of LV impairment after mitral valve surgery.<h4>Methods and results</h4>Prospective, observational study of patients with mitral valve prolapse undergoing mitral valve surgery. Pre-operative LV diameters, volumes, LVEF, global longitudinal strain (GLS), and myocardial work measured. Post-operative LV impairment defined as LVEF < 50% at 1 year post-surgery. Eighty-seven patients included. Thirteen percent developed post-operative LV impairment. Patients with post-operative LV dysfunction showed significantly larger indexed LV end-systolic diameters, indexed LV end-systolic volumes (LVESVi), lower LVEF, and more abnormal GLS than patients without post-operative LV dysfunction. In multivariate analysis, LVESVi [odds ratio 1.11 (95% CI 1.01-1.23), P = 0.039] and GLS [odds ratio 1.46 (95% CI 1.00-2.14), P = 0.054] were the only independent predictors of post-operative LV dysfunction. The optimal cut-off of 36.3 mL/m2 for LVESVi had a sensitivity of 82% and specificity of 78% for detection of post-operative LV impairment.<h4>Conclusion</h4>Post-operative LV impairment is common. Indexed LV volumes (36.3 mL/m2) provided the best marker of post-operative LV impairment.",,pdf:https://academic.oup.com/ehjcimaging/advance-article-pdf/doi/10.1093/ehjci/jead093/50200028/jead093.pdf; doi:https://doi.org/10.1093/ehjci/jead093
 30279426,https://doi.org/10.1038/s41598-018-32876-3,OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants.,"Boudellioua I, Kulmanov M, Schofield PN, Gkoutos GV, Hoehndorf R.",,Scientific reports,2018,2018-10-02,Y,,"Applied Analytics, The Human Phenome",,"An increasing number of disorders have been identified for which two or more distinct alleles in two or more genes are required to either cause the disease or to significantly modify its onset, severity or phenotype. It is difficult to discover such interactions using existing approaches. The purpose of our work is to develop and evaluate a system that can identify combinations of alleles underlying digenic and oligogenic diseases in individual whole exome or whole genome sequences. Information that links patient phenotypes to databases of gene-phenotype associations observed in clinical or non-human model organism research can provide useful information and improve variant prioritization for genetic diseases. Additional background knowledge about interactions between genes can be utilized to identify sets of variants in different genes in the same individual which may then contribute to the overall disease phenotype. We have developed OligoPVP, an algorithm that can be used to prioritize causative combinations of variants in digenic and oligogenic diseases, using whole exome or whole genome sequences together with patient phenotypes as input. We demonstrate that OligoPVP has significantly improved performance when compared to state of the art pathogenicity detection methods in the case of digenic diseases. Our results show that OligoPVP can efficiently prioritize sets of variants in digenic diseases using a phenotype-driven approach and identify etiologically important variants in whole genomes. OligoPVP naturally extends to oligogenic disease involving interactions between variants in two or more genes. It can be applied to the identification of multiple interacting candidate variants contributing to phenotype, where the action of modifier genes is suspected from pedigree analysis or failure of traditional causative variant identification.",,pdf:https://www.nature.com/articles/s41598-018-32876-3.pdf; doi:https://doi.org/10.1038/s41598-018-32876-3; html:https://europepmc.org/articles/PMC6168481; pdf:https://europepmc.org/articles/PMC6168481?pdf=render
-37963560,https://doi.org/10.1098/rsif.2023.0410,Spatio-temporal surveillance and early detection of SARS-CoV-2 variants of concern: a retrospective analysis.,"Cavallaro M, Dyson L, Tildesley MJ, Todkill D, Keeling MJ.",,"Journal of the Royal Society, Interface",2023,2023-11-15,Y,Disease Emergence; Anomaly Detection; Early Warning Signals; Sars-cov-2,,,"The SARS-CoV-2 pandemic has been characterized by the repeated emergence of genetically distinct virus variants of increased transmissibility and immune evasion compared to pre-existing lineages. In many countries, their containment required the intervention of public health authorities and the imposition of control measures. While the primary role of testing is to identify infection, target treatment, and limit spread (through isolation and contact tracing), a secondary benefit is in terms of surveillance and the early detection of new variants. Here we study the spatial invasion and early spread of the Alpha, Delta and Omicron (BA.1 and BA.2) variants in England from September 2020 to February 2022 using the random neighbourhood covering (RaNCover) method. This is a statistical technique for the detection of aberrations in spatial point processes, which we tailored here to community PCR (polymerase-chain-reaction) test data where the TaqPath kit provides a proxy measure of the switch between variants. Retrospectively, RaNCover detected the earliest signals associated with the four novel variants that led to large infection waves in England. With suitable data our method therefore has the potential to rapidly detect outbreaks of future SARS-CoV-2 variants, thus helping to inform targeted public health interventions.",,doi:https://doi.org/10.1098/rsif.2023.0410; html:https://europepmc.org/articles/PMC10645511; pdf:https://europepmc.org/articles/PMC10645511?pdf=render
 38195748,https://doi.org/10.1038/s41591-023-02715-8,A federated learning system for precision oncology in Europe: DigiONE.,"Mahon P, Chatzitheofilou I, Dekker A, Fernández X, Hall G, Helland A, Traverso A, Van Marcke C, Vehreschild J, Ciliberto G, Tonon G.",,Nature medicine,2024,2024-02-01,N,,,,,,doi:https://doi.org/10.1038/s41591-023-02715-8
+37963560,https://doi.org/10.1098/rsif.2023.0410,Spatio-temporal surveillance and early detection of SARS-CoV-2 variants of concern: a retrospective analysis.,"Cavallaro M, Dyson L, Tildesley MJ, Todkill D, Keeling MJ.",,"Journal of the Royal Society, Interface",2023,2023-11-15,Y,Disease Emergence; Anomaly Detection; Early Warning Signals; Sars-cov-2,,,"The SARS-CoV-2 pandemic has been characterized by the repeated emergence of genetically distinct virus variants of increased transmissibility and immune evasion compared to pre-existing lineages. In many countries, their containment required the intervention of public health authorities and the imposition of control measures. While the primary role of testing is to identify infection, target treatment, and limit spread (through isolation and contact tracing), a secondary benefit is in terms of surveillance and the early detection of new variants. Here we study the spatial invasion and early spread of the Alpha, Delta and Omicron (BA.1 and BA.2) variants in England from September 2020 to February 2022 using the random neighbourhood covering (RaNCover) method. This is a statistical technique for the detection of aberrations in spatial point processes, which we tailored here to community PCR (polymerase-chain-reaction) test data where the TaqPath kit provides a proxy measure of the switch between variants. Retrospectively, RaNCover detected the earliest signals associated with the four novel variants that led to large infection waves in England. With suitable data our method therefore has the potential to rapidly detect outbreaks of future SARS-CoV-2 variants, thus helping to inform targeted public health interventions.",,doi:https://doi.org/10.1098/rsif.2023.0410; html:https://europepmc.org/articles/PMC10645511; pdf:https://europepmc.org/articles/PMC10645511?pdf=render
 36942567,https://doi.org/10.1161/circep.122.011585,Outcomes of Early Rhythm Control Therapy in Patients With Atrial Fibrillation and a High Comorbidity Burden in Large Real-World Cohorts.,"Dickow J, Kany S, Roth Cardoso V, Ellinor PT, Gkoutos GV, Van Houten HK, Kirchhof P, Metzner A, Noseworthy PA, Yao X, Rillig A.",,Circulation. Arrhythmia and electrophysiology,2023,2023-03-21,N,Atrial fibrillation; Stroke; Catheter ablation; Heart Failure; Comorbidity,,,"<h4>Background</h4>A recent subanalysis of the EAST-AFNET 4 (Early Treatment of Atrial Fibrillation for Stroke Prevention Trial) suggests a stronger benefit of early rhythm control (ERC) in patients with atrial fibrillation and a high comorbidity burden when compared to patients with a lower comorbidity burden.<h4>Methods</h4>We identified 109 739 patients with newly diagnosed atrial fibrillation in a large United States deidentified administrative claims database (OptumLabs) and 11 625 patients in the population-based UKB (UK Biobank). ERC was defined as atrial fibrillation ablation or antiarrhythmic drug therapy within the first year after atrial fibrillation diagnosis. Patients were classified as (1) ERC and high comorbidity burden (CHA<sub>2</sub>DS<sub>2</sub>-VASc score ≥4); (2) ERC and lower comorbidity burden (CHA<sub>2</sub>DS<sub>2</sub>-VASc score 2-3); (3) no ERC and high comorbidity burden; and (4) no ERC and lower comorbidity burden. Patients without an elevated comorbidity burden (CHA<sub>2</sub>DS<sub>2</sub>-VASc score 0-1) were excluded. Propensity score overlap weighting and cox proportional hazards regression were used to balance patients and compare groups for the primary composite outcome of all-cause mortality, stroke, or hospitalization with the diagnoses heart failure or myocardial infarction as well as for a primary composite safety outcome of death, stroke, and serious adverse events related to ERC.<h4>Results</h4>In both cohorts, ERC was associated with a reduced risk for the primary composite outcome in patients with a high comorbidity burden (OptumLabs: hazard ratio, 0.83 [95% CI 0.72-0.95]; <i>P</i>=0.006; UKB: hazard ratio, 0.77 [95% CI, 0.63-0.94]; <i>P</i>=0.009). In patients with a lower comorbidity burden, the difference in outcomes was not significant (OptumLabs: hazard ratio, 0.92 [95% CI, 0.54-1.57]; <i>P</i>=0.767; UKB: hazard ratio, 0.94 [95% CI, 0.83-1.06]; <i>P</i>=0.310). The comorbidity burden interacted with ERC in the UKB (interaction- <i>P</i>=0.027) but not in OptumLabs (interaction-<i>P</i>=0.720). ERC was not associated with an increased risk for the primary safety outcome.<h4>Conclusions</h4>ERC is safe and may be more favorable in a population-based sample of patients with high a comorbidity burden (CHA<sub>2</sub>DS<sub>2</sub>-VASc score ≥4).",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCEP.122.011585; doi:https://doi.org/10.1161/CIRCEP.122.011585; html:https://europepmc.org/articles/PMC10205477; pdf:https://europepmc.org/articles/PMC10205477?pdf=render; doi:https://doi.org/10.1161/circep.122.011585
 36134546,https://doi.org/10.7189/jogh.12.05044,Risk of COVID-19 hospitalizations among school-aged children in Scotland: A national incident cohort study.,"Shi T, Pan J, Moore E, Katikireddi SV, Docherty AB, Fenton L, McCowan C, Agrawal U, Kerr S, Shah SA, Stock SJ, Simpson CR, Robertson C, Sheikh A, Public Health Scotland and the EAVE II Collaborators.",,Journal of global health,2022,2022-09-23,Y,,,,"<h4>Background</h4>There is considerable policy, clinical and public interest about whether children should be vaccinated against SARS-CoV-2 and, if so, which children should be prioritised (particularly if vaccine resources are limited). To inform such deliberations, we sought to identify children and young people at highest risk of hospitalization from COVID-19.<h4>Methods</h4>We used the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) platform to undertake a national incident cohort analysis to investigate the risk of hospitalization among 5-17 years old living in Scotland in risk groups defined by the living risk prediction algorithm (QCOVID). A Cox proportional hazard model was used to derive hazard ratios (HR) and 95% confidence intervals (CIs) for the association between risk groups and COVID-19 hospital admission. Adjustments were made for age, sex, socioeconomic status, co-morbidity, and prior hospitalization.<h4>Results</h4>Between March 1, 2020 and November 22, 2021, there were 146 183 (19.4% of all 752 867 children in Scotland) polymerase chain reaction (PCR) confirmed SARS-CoV-2 infections among 5-17 years old. Of those with confirmed infection, 973 (0.7%) were admitted to hospital with COVID-19. The rate of COVID-19 hospitalization was higher in those within each QCOVID risk group compared to those without the condition. Similar results were found in age stratified analyses (5-11 and 12-17 years old). Risk groups associated with an increased risk of COVID-19 hospital admission, included (adjusted HR, 95% CIs): sickle cell disease 14.35 (8.48-24.28), chronic kidney disease 11.34 (4.61-27.87), blood cancer 6.32 (3.24-12.35), rare pulmonary diseases 5.04 (2.58-9.86), type 2 diabetes 3.04 (1.34-6.92), epilepsy 2.54 (1.69-3.81), type 1 diabetes 2.48 (1.47-4.16), Down syndrome 2.45 (0.96-6.25), cerebral palsy 2.37 (1.26-4.47), severe mental illness 1.43 (0.63-3.24), fracture 1.41 (1.02-1.95), congenital heart disease 1.35 (0.82-2.23), asthma 1.28 (1.06-1.55), and learning disability (excluding Down syndrome) 1.08 (0.82-1.42), when compared to those without these conditions. Although our Cox models were adjusted for a number of potential confounders, residual confounding remains a possibility.<h4>Conclusions</h4>In this national study, we observed an increased risk of COVID-19 hospital admissions among school-aged children with specific underlying long-term health conditions compared with children without these conditions.",,pdf:https://jogh.org/wp-content/uploads/2022/10/jogh-12-05044.pdf; doi:https://doi.org/10.7189/jogh.12.05044; html:https://europepmc.org/articles/PMC9494196; pdf:https://europepmc.org/articles/PMC9494196?pdf=render
-39169209,https://doi.org/10.1038/s43856-024-00590-z,"Predicting 1, 2 and 3 year emergent referable diabetic retinopathy and maculopathy using deep learning.","Nderitu P, Nunez do Rio JM, Webster L, Mann S, Cardoso MJ, Modat M, Hopkins D, Bergeles C, Jackson TL.",,Communications medicine,2024,2024-08-21,Y,,,,"<h4>Background</h4>Predicting diabetic retinopathy (DR) progression could enable individualised screening with prompt referral for high-risk individuals for sight-saving treatment, whilst reducing screening burden for low-risk individuals. We developed and validated deep learning systems (DLS) that predict 1, 2 and 3 year emergent referable DR and maculopathy using risk factor characteristics (tabular DLS), colour fundal photographs (image DLS) or both (multimodal DLS).<h4>Methods</h4>From 162,339 development-set eyes from south-east London (UK) diabetic eye screening programme (DESP), 110,837 had eligible longitudinal data, with the remaining 51,502 used for pretraining. Internal and external (Birmingham DESP, UK) test datasets included 27,996, and 6928 eyes respectively.<h4>Results</h4>Internal multimodal DLS emergent referable DR, maculopathy or either area-under-the receiver operating characteristic (AUROC) were 0.95 (95% CI: 0.92-0.98), 0.84 (0.82-0.86), 0.85 (0.83-0.87) for 1 year, 0.92 (0.87-0.96), 0.84 (0.82-0.87), 0.85 (0.82-0.87) for 2 years, and 0.85 (0.80-0.90), 0.79 (0.76-0.82), 0.79 (0.76-0.82) for 3 years. External multimodal DLS emergent referable DR, maculopathy or either AUROC were 0.93 (0.88-0.97), 0.85 (0.80-0.89), 0.85 (0.76-0.85) for 1 year, 0.93 (0.89-0.97), 0.79 (0.74-0.84), 0.80 (0.76-0.85) for 2 years, and 0.91 (0.84-0.98), 0.79 (0.74-0.83), 0.79 (0.74-0.84) for 3 years.<h4>Conclusions</h4>Multimodal and image DLS performance is significantly better than tabular DLS at all intervals. DLS accurately predict 1, 2 and 3 year emergent referable DR and referable maculopathy using colour fundal photographs, with additional risk factor characteristics conferring improvements in prognostic performance. Proposed DLS are a step towards individualised risk-based screening, whereby AI-assistance allows high-risk individuals to be closely monitored while reducing screening burden for low-risk individuals.",,doi:https://doi.org/10.1038/s43856-024-00590-z; doi:https://doi.org/10.1038/s43856-024-00590-z; html:https://europepmc.org/articles/PMC11339445; pdf:https://europepmc.org/articles/PMC11339445?pdf=render
 37662524,https://doi.org/10.1016/j.eclinm.2023.102172,Tafamidis treatment in patients with transthyretin amyloid cardiomyopathy: a systematic review and meta-analysis.,"Wang J, Chen H, Tang Z, Zhang J, Xu Y, Wan K, Hussain K, Gkoutos GV, Han Y, Chen Y.",,EClinicalMedicine,2023,2023-08-24,Y,Prognosis; Tafamidis; Attr; Transthyretin Amyloid Cardiomyopathy,,,"<h4>Background</h4>Previous studies have reported that tafamidis treatment was associated with better outcomes in patients with transthyretin amyloid cardiomyopathy (ATTR-CM) compared with those without tafamidis treatment. Therefore, we aimed to systematically assess the association of tafamidis treatment with outcomes in patients with ATTR-CM.<h4>Methods</h4>The protocol for this systematic review and meta-analysis was registered in the PROSPERO (CRD42022381985). Pubmed, Ovid Embase, Scopus, Cochrane Library, and Web of Science were interrogated to identify studies that evaluated the impact of tafamidis on prognosis in ATTR-CM, from January 1, 2000 to June 1, 2023. A random-effects model was used to determine the pooled risk ratio (RR) for the adverse endpoints. In addition, the main outcomes included all-cause death or heart transplantation, the composite endpoints included all-cause death, heart transplantation, cardiac-assist device implantation, heart failure exacerbations, and hospitalization.<h4>Findings</h4>Fifteen studies comprising 2765 patients (mean age 75.9 ± 9.3 years; 83.7% male) with a mean follow-up duration of 18.7 ± 17.1 months were included in the meta-analysis. There was a decrease in left ventricular ejection fraction (LVEF) (standard mean differences (SMD: -0.17; 95% confidence interval (CI), -0.31 to -0.03; <i>P</i> = 0.02) but were no significant differences in intraventricular septum (IVS) thickness or global longitudinal strain (GLS) after tafamidis treatment. However, subgroup analysis showed no significant deterioration in LVEF in the patients with wild-type ATTR after tafamidis treatment (SMD: -0.11; 95% CI, -0.34 to 0.12, <i>P</i> = 0.34). In addition, the group with tafamidis treatment had a decreased risk for all-cause death or heart transplantation compared to patients without treatment (the pooled RR, 0.44; 95% CI, 0.31-0.65; <i>P</i> < 0.01). Subgroup analysis showed that there was no significant difference of tafamidis on the outcomes in patients with wild-type or hereditary ATTR (RR, 0.44; 95% CI, 0.27-0.73 <i>versus</i> 0.21, 95% CI, 0.11-0.40, <i>P</i> = 0.08). Furthermore, tafamidis treatment was associated with a lower risk of the composite endpoint (RR, 0.57; 95% CI, 0.42-0.77; <i>P</i> < 0.01).<h4>Interpretation</h4>Our findings suggested that there was no significant deterioration in LVEF in the patients with wild-type ATTR after tafamidis treatment. In addition, tafamidis treatment was associated with a low risk of all-cause death and adverse cardiovascular events.<h4>Funding</h4>This work was supported by grants from the Natural Science Foundation of Sichuan Province [Grant Number: 23NSFSC4589] and the National Natural Science Foundation of China [Grant Number: 82202248].",,doi:https://doi.org/10.1016/j.eclinm.2023.102172; html:https://europepmc.org/articles/PMC10474377; pdf:https://europepmc.org/articles/PMC10474377?pdf=render
+39169209,https://doi.org/10.1038/s43856-024-00590-z,"Predicting 1, 2 and 3 year emergent referable diabetic retinopathy and maculopathy using deep learning.","Nderitu P, Nunez do Rio JM, Webster L, Mann S, Cardoso MJ, Modat M, Hopkins D, Bergeles C, Jackson TL.",,Communications medicine,2024,2024-08-21,Y,,,,"<h4>Background</h4>Predicting diabetic retinopathy (DR) progression could enable individualised screening with prompt referral for high-risk individuals for sight-saving treatment, whilst reducing screening burden for low-risk individuals. We developed and validated deep learning systems (DLS) that predict 1, 2 and 3 year emergent referable DR and maculopathy using risk factor characteristics (tabular DLS), colour fundal photographs (image DLS) or both (multimodal DLS).<h4>Methods</h4>From 162,339 development-set eyes from south-east London (UK) diabetic eye screening programme (DESP), 110,837 had eligible longitudinal data, with the remaining 51,502 used for pretraining. Internal and external (Birmingham DESP, UK) test datasets included 27,996, and 6928 eyes respectively.<h4>Results</h4>Internal multimodal DLS emergent referable DR, maculopathy or either area-under-the receiver operating characteristic (AUROC) were 0.95 (95% CI: 0.92-0.98), 0.84 (0.82-0.86), 0.85 (0.83-0.87) for 1 year, 0.92 (0.87-0.96), 0.84 (0.82-0.87), 0.85 (0.82-0.87) for 2 years, and 0.85 (0.80-0.90), 0.79 (0.76-0.82), 0.79 (0.76-0.82) for 3 years. External multimodal DLS emergent referable DR, maculopathy or either AUROC were 0.93 (0.88-0.97), 0.85 (0.80-0.89), 0.85 (0.76-0.85) for 1 year, 0.93 (0.89-0.97), 0.79 (0.74-0.84), 0.80 (0.76-0.85) for 2 years, and 0.91 (0.84-0.98), 0.79 (0.74-0.83), 0.79 (0.74-0.84) for 3 years.<h4>Conclusions</h4>Multimodal and image DLS performance is significantly better than tabular DLS at all intervals. DLS accurately predict 1, 2 and 3 year emergent referable DR and referable maculopathy using colour fundal photographs, with additional risk factor characteristics conferring improvements in prognostic performance. Proposed DLS are a step towards individualised risk-based screening, whereby AI-assistance allows high-risk individuals to be closely monitored while reducing screening burden for low-risk individuals.",,doi:https://doi.org/10.1038/s43856-024-00590-z; doi:https://doi.org/10.1038/s43856-024-00590-z; html:https://europepmc.org/articles/PMC11339445; pdf:https://europepmc.org/articles/PMC11339445?pdf=render
 34798287,https://doi.org/10.1016/j.jclinepi.2021.11.023,Missing data is poorly handled and reported in prediction model studies using machine learning: a literature review.,"Nijman S, Leeuwenberg AM, Beekers I, Verkouter I, Jacobs J, Bots ML, Asselbergs FW, Moons K, Debray T.",,Journal of clinical epidemiology,2022,2021-11-16,N,Prediction; Literature review; Reporting; Missing Data; Machine Learning,,,"<h4>Objectives</h4>Missing data is a common problem during the development, evaluation, and implementation of prediction models. Although machine learning (ML) methods are often said to be capable of circumventing missing data, it is unclear how these methods are used in medical research. We aim to find out if and how well prediction model studies using machine learning report on their handling of missing data.<h4>Study design and setting</h4>We systematically searched the literature on published papers between 2018 and 2019 about primary studies developing and/or validating clinical prediction models using any supervised ML methodology across medical fields. From the retrieved studies information about the amount and nature (e.g. missing completely at random, potential reasons for missingness) of missing data and the way they were handled were extracted.<h4>Results</h4>We identified 152 machine learning-based clinical prediction model studies. A substantial amount of these 152 papers did not report anything on missing data (n = 56/152). A majority (n = 96/152) reported details on the handling of missing data (e.g., methods used), though many of these (n = 46/96) did not report the amount of the missingness in the data. In these 96 papers the authors only sometimes reported possible reasons for missingness (n = 7/96) and information about missing data mechanisms (n = 8/96). The most common approach for handling missing data was deletion (n = 65/96), mostly via complete-case analysis (CCA) (n = 43/96). Very few studies used multiple imputation (n = 8/96) or built-in mechanisms such as surrogate splits (n = 7/96) that directly address missing data during the development, validation, or implementation of the prediction model.<h4>Conclusion</h4>Though missing values are highly common in any type of medical research and certainly in the research based on routine healthcare data, a majority of the prediction model studies using machine learning does not report sufficient information on the presence and handling of missing data. Strategies in which patient data are simply omitted are unfortunately the most often used methods, even though it is generally advised against and well known that it likely causes bias and loss of analytical power in prediction model development and in the predictive accuracy estimates. Prediction model researchers should be much more aware of alternative methodologies to address missing data.",,pdf:http://www.jclinepi.com/article/S0895435621003759/pdf; doi:https://doi.org/10.1016/j.jclinepi.2021.11.023
 35132056,https://doi.org/10.1038/s41467-022-28252-5,Genome-wide association meta-analysis identifies 29 new acne susceptibility loci.,"Mitchell BL, Saklatvala JR, Dand N, Hagenbeek FA, Li X, Min JL, Thomas L, Bartels M, Jan Hottenga J, Lupton MK, Boomsma DI, Dong X, Hveem K, Løset M, Martin NG, Barker JN, Han J, Smith CH, Rentería ME, Simpson MA.",,Nature communications,2022,2022-02-07,Y,,,,"Acne vulgaris is a highly heritable skin disorder that primarily impacts facial skin. Severely inflamed lesions may leave permanent scars that have been associated with long-term psychosocial consequences. Here, we perform a GWAS meta-analysis comprising 20,165 individuals with acne from nine independent European ancestry cohorts. We identify 29 novel genome-wide significant loci and replicate 14 of the 17 previously identified risk loci, bringing the total number of reported acne risk loci to 46. Using fine-mapping and eQTL colocalisation approaches, we identify putative causal genes at several acne susceptibility loci that have previously been implicated in Mendelian hair and skin disorders, including pustular psoriasis. We identify shared genetic aetiology between acne, hormone levels, hormone-sensitive cancers and psychiatric traits. Finally, we show that a polygenic risk score calculated from our results explains up to 5.6% of the variance in acne liability in an independent cohort.",,pdf:https://www.nature.com/articles/s41467-022-28252-5.pdf; doi:https://doi.org/10.1038/s41467-022-28252-5; html:https://europepmc.org/articles/PMC8821634; pdf:https://europepmc.org/articles/PMC8821634?pdf=render
 38595770,https://doi.org/10.2147/clep.s437937,"A Harmonised Approach to Curating Research-Ready Datasets for Asthma, Chronic Obstructive Pulmonary Disease (COPD) and Interstitial Lung Disease (ILD) in England, Wales and Scotland Using Clinical Practice Research Datalink (CPRD), Secure Anonymised Information Linkage (SAIL) Databank and DataLoch.","Hatam S, Scully ST, Cook S, Evans HT, Hume A, Kallis C, Farr I, Orton C, Sheikh A, Quint JK.",,Clinical epidemiology,2024,2024-04-04,Y,Asthma; COPD; Harmonisation; Data Curation; Her; Ild,,,"<h4>Background</h4>Electronic healthcare records (EHRs) are an important resource for health research that can be used to improve patient outcomes in chronic respiratory diseases. However, consistent approaches in the analysis of these datasets are needed for coherent messaging, and when undertaking comparative studies across different populations.<h4>Methods and results</h4>We developed a harmonised curation approach to generate comparable patient cohorts for asthma, chronic obstructive pulmonary disease (COPD) and interstitial lung disease (ILD) using datasets from within Clinical Practice Research Datalink (CPRD; for England), Secure Anonymised Information Linkage (SAIL; for Wales) and DataLoch (for Scotland) by defining commonly derived variables consistently between the datasets. By working in parallel on the curation methodology used for CPRD, SAIL and DataLoch for asthma, COPD and ILD, we were able to highlight key differences in coding and recording between the databases and identify solutions to enable valid comparisons.<h4>Conclusion</h4>Codelists and metadata generated have been made available to help re-create the asthma, COPD and ILD cohorts in CPRD, SAIL and DataLoch for different time periods, and provide a starting point for the curation of respiratory datasets in other EHR databases, expediting further comparable respiratory research.",,pdf:https://www.dovepress.com/getfile.php?fileID=98087; doi:https://doi.org/10.2147/CLEP.S437937; html:https://europepmc.org/articles/PMC11002787; pdf:https://europepmc.org/articles/PMC11002787?pdf=render
 31477110,https://doi.org/10.1186/s12913-019-4286-8,Weekend admissions and mortality for major acute disorders across England and Wales: record linkage cohort studies.,"Roberts SE, John A, Lewis KE, Brown J, Lyons RA, Williams JG.",,BMC health services research,2019,2019-09-02,Y,Mortality; Weekend Admissions; Acute Disorders,Improving Public Health,,"<h4>Background</h4>To establish which major disorders are susceptible to increased mortality following acute admissions on weekends, compared with week days, and how this may be explained.<h4>Methods</h4>Cohorts based on national administrative inpatient and mortality data for 14,168,443 hospitalised patients in England and 913,068 in Wales who were admitted for 66 disorders that were associated with at least 200 deaths within 30 days of acute admission. The main outcome measure was the weekend mortality effect (defined as the conventional mortality odds ratio for admissions on weekends compared with week days).<h4>Results</h4>There were large, statistically significant weekend mortality effects (> 20%) in England for 22 of the 66 conditions and in both countries for 14. These 14 were 4 of 13 cancers (oesophageal, colorectal, lung and lymphomas); 4 of 13 circulatory disorders (angina, abdominal aortic aneurysm, peripheral vascular disease and arterial embolism & thrombosis); one of 8 respiratory disorders (pleural effusion); 2 of 12 gastrointestinal disorders (alcoholic and other liver disease); 2 of 3 ageing-related disorders (Alzheimer's disease and dementia); none of 7 trauma conditions; and one of 10 other disorders (acute renal failure). Across the disorders, 64% of the variation in weekend mortality effects in England and Wales was explained by reductions in admission rates at weekends and the medical disease category.<h4>Conclusions</h4>The effect of weekend admission on 30 day mortality is seen mainly for cancers, some circulatory disorders, liver disease and a few other conditions which are mainly ageing- or cancer-related. Most of the increased mortality is associated with reduced admission rates at weekends and the medical disease category.",,pdf:https://bmchealthservres.biomedcentral.com/counter/pdf/10.1186/s12913-019-4286-8; doi:https://doi.org/10.1186/s12913-019-4286-8; html:https://europepmc.org/articles/PMC6720086; pdf:https://europepmc.org/articles/PMC6720086?pdf=render
-34847088,https://doi.org/10.1097/ede.0000000000001429,The Authors Respond.,"Katsoulis M, De Stavola B, Lai AG, Gomes M, Diaz-Ordaz K.",,"Epidemiology (Cambridge, Mass.)",2022,2022-01-01,N,,,,,,html:https://journals.lww.com/epidem/Fulltext/2022/01000/The_Authors_Respond.22.aspx; doi:https://doi.org/10.1097/EDE.0000000000001429
 32908284,https://doi.org/10.1038/s41591-020-1037-7,Guidelines for clinical trial protocols for interventions involving artificial intelligence: the SPIRIT-AI extension.,"Cruz Rivera S, Liu X, Chan AW, Denniston AK, Calvert MJ, SPIRIT-AI and CONSORT-AI Working Group, SPIRIT-AI and CONSORT-AI Steering Group, SPIRIT-AI and CONSORT-AI Consensus Group.",,Nature medicine,2020,2020-09-09,Y,,,,"The SPIRIT 2013 statement aims to improve the completeness of clinical trial protocol reporting by providing evidence-based recommendations for the minimum set of items to be addressed. This guidance has been instrumental in promoting transparent evaluation of new interventions. More recently, there has been a growing recognition that interventions involving artificial intelligence (AI) need to undergo rigorous, prospective evaluation to demonstrate their impact on health outcomes. The SPIRIT-AI (Standard Protocol Items: Recommendations for Interventional Trials-Artificial Intelligence) extension is a new reporting guideline for clinical trial protocols evaluating interventions with an AI component. It was developed in parallel with its companion statement for trial reports: CONSORT-AI (Consolidated Standards of Reporting Trials-Artificial Intelligence). Both guidelines were developed through a staged consensus process involving literature review and expert consultation to generate 26 candidate items, which were consulted upon by an international multi-stakeholder group in a two-stage Delphi survey (103 stakeholders), agreed upon in a consensus meeting (31 stakeholders) and refined through a checklist pilot (34 participants). The SPIRIT-AI extension includes 15 new items that were considered sufficiently important for clinical trial protocols of AI interventions. These new items should be routinely reported in addition to the core SPIRIT 2013 items. SPIRIT-AI recommends that investigators provide clear descriptions of the AI intervention, including instructions and skills required for use, the setting in which the AI intervention will be integrated, considerations for the handling of input and output data, the human-AI interaction and analysis of error cases. SPIRIT-AI will help promote transparency and completeness for clinical trial protocols for AI interventions. Its use will assist editors and peer reviewers, as well as the general readership, to understand, interpret and critically appraise the design and risk of bias for a planned clinical trial.",,pdf:https://www.nature.com/articles/s41591-020-1037-7.pdf; doi:https://doi.org/10.1038/s41591-020-1037-7; html:https://europepmc.org/articles/PMC7598944; pdf:https://europepmc.org/articles/PMC7598944?pdf=render
+34847088,https://doi.org/10.1097/ede.0000000000001429,The Authors Respond.,"Katsoulis M, De Stavola B, Lai AG, Gomes M, Diaz-Ordaz K.",,"Epidemiology (Cambridge, Mass.)",2022,2022-01-01,N,,,,,,html:https://journals.lww.com/epidem/Fulltext/2022/01000/The_Authors_Respond.22.aspx; doi:https://doi.org/10.1097/EDE.0000000000001429
 32908283,https://doi.org/10.1038/s41591-020-1034-x,Reporting guidelines for clinical trial reports for interventions involving artificial intelligence: the CONSORT-AI extension.,"Liu X, Cruz Rivera S, Moher D, Calvert MJ, Denniston AK, SPIRIT-AI and CONSORT-AI Working Group.",,Nature medicine,2020,2020-09-09,Y,,,,"The CONSORT 2010 statement provides minimum guidelines for reporting randomized trials. Its widespread use has been instrumental in ensuring transparency in the evaluation of new interventions. More recently, there has been a growing recognition that interventions involving artificial intelligence (AI) need to undergo rigorous, prospective evaluation to demonstrate impact on health outcomes. The CONSORT-AI (Consolidated Standards of Reporting Trials-Artificial Intelligence) extension is a new reporting guideline for clinical trials evaluating interventions with an AI component. It was developed in parallel with its companion statement for clinical trial protocols: SPIRIT-AI (Standard Protocol Items: Recommendations for Interventional Trials-Artificial Intelligence). Both guidelines were developed through a staged consensus process involving literature review and expert consultation to generate 29 candidate items, which were assessed by an international multi-stakeholder group in a two-stage Delphi survey (103 stakeholders), agreed upon in a two-day consensus meeting (31 stakeholders) and refined through a checklist pilot (34 participants). The CONSORT-AI extension includes 14 new items that were considered sufficiently important for AI interventions that they should be routinely reported in addition to the core CONSORT 2010 items. CONSORT-AI recommends that investigators provide clear descriptions of the AI intervention, including instructions and skills required for use, the setting in which the AI intervention is integrated, the handling of inputs and outputs of the AI intervention, the human-AI interaction and provision of an analysis of error cases. CONSORT-AI will help promote transparency and completeness in reporting clinical trials for AI interventions. It will assist editors and peer reviewers, as well as the general readership, to understand, interpret and critically appraise the quality of clinical trial design and risk of bias in the reported outcomes.",,pdf:https://www.nature.com/articles/s41591-020-1034-x.pdf; doi:https://doi.org/10.1038/s41591-020-1034-x; html:https://europepmc.org/articles/PMC7598943; pdf:https://europepmc.org/articles/PMC7598943?pdf=render
 34985035,https://doi.org/10.1097/htr.0000000000000741,Epidemiology and 6- and 12-Month Outcomes of Intimate Partner Violence and Other Violence-Related Traumatic Brain Injury in Major Trauma: A Population-Based Trauma Registry Study.,"Gabbe BJ, Braaf S, Cameron PA, Berecki-Gisolf J.",,The Journal of head trauma rehabilitation,2022,2022-01-01,N,,,,"<h4>Objective</h4>To compare the epidemiology, in-hospital outcomes, and 6-month and 12-month patient-reported, outcomes of major trauma patients with intimate partner violence (IPV)-related traumatic brain injury (TBI) with other interpersonal violence (OV)-related TBI.<h4>Setting</h4>Victoria, Australia.<h4>Participants</h4>Adult (≥18 years) major trauma cases with TBI (concussion, skull fracture, or intracranial injury), injured through IPV or OV, between July 2010 and June 2020, and included on the population-based Victorian State Trauma Registry. There were 133 adult major trauma cases due to IPV and 1796 due to OV. The prevalence of TBI was 39% (n = 52) in the IPV group and 56% (n = 1010) in the OV group.<h4>Design</h4>Registry-based cohort study.<h4>Main measures</h4>Trauma care indicators and 6- and 12-month patient-reported outcomes (self-reported disability, Glasgow Outcome Scale-Extended, EQ-5D-3L, and return to work).<h4>Results</h4>The annual incidence (95% CI) of major trauma involving TBI was 0.11 (0.08-0.14) per 100 000 population for IPV and 2.11 (1.98-2.24) per 100 000 for OV. A higher proportion of IPV-related cases were women (73% vs 5%), had sustained a severe TBI (Glasgow Coma Scale score 3-8; 27% vs 15%), were admitted to intensive care (56% vs 37%), and died in hospital (14% vs 5%). The median (interquartile range) time to definitive care (4.7 hours vs 3.3 hours) and head computed tomographic scan (5.0 hours vs 3.1 hours) was longer in the IPV group. Follow-up rates at 6 and 12 months were 71% and 69%, respectively. The 6- and 12-month outcomes were generally poorer in the IPV-related group.<h4>Conclusion</h4>The incidence of IPV-related major trauma with TBI was low. However, the prevalence of severe TBI, the time to key aspects of clinical care, in-hospital mortality, and longer-term work-related disability were higher. However, power to detect differences was low due to the small number of IPV-related cases compared with the OV group.",,doi:https://doi.org/10.1097/HTR.0000000000000741
 33820530,https://doi.org/10.1186/s12916-021-01940-7,"Machine learning for subtype definition and risk prediction in heart failure, acute coronary syndromes and atrial fibrillation: systematic review of validity and clinical utility.","Banerjee A, Chen S, Fatemifar G, Zeina M, Lumbers RT, Mielke J, Gill S, Kotecha D, Freitag DF, Denaxas S, Hemingway H.",,BMC medicine,2021,2021-04-06,Y,Subtype; Cardiovascular disease; Systematic review; Machine Learning; Informatics; Risk Prediction,,,"<h4>Background</h4>Machine learning (ML) is increasingly used in research for subtype definition and risk prediction, particularly in cardiovascular diseases. No existing ML models are routinely used for cardiovascular disease management, and their phase of clinical utility is unknown, partly due to a lack of clear criteria. We evaluated ML for subtype definition and risk prediction in heart failure (HF), acute coronary syndromes (ACS) and atrial fibrillation (AF).<h4>Methods</h4>For ML studies of subtype definition and risk prediction, we conducted a systematic review in HF, ACS and AF, using PubMed, MEDLINE and Web of Science from January 2000 until December 2019. By adapting published criteria for diagnostic and prognostic studies, we developed a seven-domain, ML-specific checklist.<h4>Results</h4>Of 5918 studies identified, 97 were included. Across studies for subtype definition (n = 40) and risk prediction (n = 57), there was variation in data source, population size (median 606 and median 6769), clinical setting (outpatient, inpatient, different departments), number of covariates (median 19 and median 48) and ML methods. All studies were single disease, most were North American (n = 61/97) and only 14 studies combined definition and risk prediction. Subtype definition and risk prediction studies respectively had limitations in development (e.g. 15.0% and 78.9% of studies related to patient benefit; 15.0% and 15.8% had low patient selection bias), validation (12.5% and 5.3% externally validated) and impact (32.5% and 91.2% improved outcome prediction; no effectiveness or cost-effectiveness evaluations).<h4>Conclusions</h4>Studies of ML in HF, ACS and AF are limited by number and type of included covariates, ML methods, population size, country, clinical setting and focus on single diseases, not overlap or multimorbidity. Clinical utility and implementation rely on improvements in development, validation and impact, facilitated by simple checklists. We provide clear steps prior to safe implementation of machine learning in clinical practice for cardiovascular diseases and other disease areas.",,pdf:https://bmcmedicine.biomedcentral.com/track/pdf/10.1186/s12916-021-01940-7; doi:https://doi.org/10.1186/s12916-021-01940-7; html:https://europepmc.org/articles/PMC8022365; pdf:https://europepmc.org/articles/PMC8022365?pdf=render
@@ -1275,14 +1277,14 @@ PMC10686417,https://doi.org/,The impact of restricted provision of publicly fund
 38041850,https://doi.org/10.1093/ecco-jcc/jjad203,Biologic Therapy for Inflammatory Bowel Disease: Real-World Comparative Effectiveness and Impact of Drug Sequencing in 13 222 Patients within the UK IBD BioResource.,"Kapizioni C, Desoki R, Lam D, Balendran K, Al-Sulais E, Subramanian S, Rimmer JE, De La Revilla Negro J, Pavey H, Pele L, Brooks J, Moran GW, Irving PM, Limdi JK, Lamb CA, UK IBD BioResource Investigators
 , Parkes M, Raine T.",,Journal of Crohn's & colitis,2024,2024-06-01,Y,Sequencing; Ulcerative colitis; Biologic Therapy; Crohn’s Disease; Real-world Effectiveness,,,"<h4>Background and aims</h4>This study compares the effectiveness of different biologic therapies and sequences in patients with inflammatory bowel disease [IBD] using real-world data from a large cohort with long exposure.<h4>Methods</h4>Demographic, disease, treatment, and outcome data were retrieved for patients in the UK IBD BioResource. Effectiveness of treatment was based on persistence free of discontinuation or failure, analysed by Kaplan-Meier survival analysis with inverse probability of treatment weighting to adjust for differences between groups.<h4>Results</h4>In total, 13 222 evaluable patients received at least one biologic. In ulcerative colitis [UC] first-line vedolizumab [VDZ] demonstrated superior effectiveness over 5 years compared to anti-tumour necrosis factor [anti-TNF] agents [p = 0.006]. VDZ was superior to both infliximab [IFX] and adalimumab [ADA] after ADA and IFX failure respectively [p < 0.001 and p < 0.001]. Anti-TNF therapy showed similar effectiveness when used as first-line treatment, or after failure of VDZ. In Crohn's disease [CD] we found significant differences between first-line treatments over 10 years [p = 0.045], with superior effectiveness of IFX compared to ADA in perianal CD. Non-anti-TNF biologics were superior to a second anti-TNF after first-line anti-TNF failure in CD [p = 0.035]. Patients with UC or CD experiencing TNF failure due to delayed loss of response or intolerance had superior outcomes when switching to a non-anti-TNF biologic, rather than a second anti-TNF.<h4>Conclusions</h4>We provide real-world evidence to guide biologic selection and sequencing in a range of common scenarios. Our findings challenge current guidelines regarding drug selection after loss of response to first anti-TNF treatment.",,pdf:https://academic.oup.com/ecco-jcc/advance-article-pdf/doi/10.1093/ecco-jcc/jjad203/53975982/jjad203.pdf; doi:https://doi.org/10.1093/ecco-jcc/jjad203; html:https://europepmc.org/articles/PMC11147798; pdf:https://europepmc.org/articles/PMC11147798?pdf=render
 36538350,https://doi.org/10.2196/41200,Identifying Patterns of Clinical Interest in Clinicians' Treatment Preferences: Hypothesis-free Data Science Approach to Prioritizing Prescribing Outliers for Clinical Review.,"MacKenna B, Curtis HJ, Hopcroft LEM, Walker AJ, Croker R, Macdonald O, Evans SJW, Inglesby P, Evans D, Morley J, Bacon SCJ, Goldacre B.",,JMIR medical informatics,2022,2022-12-20,Y,Prescribing; Clinical Audit; Antipsychotics; Pericyazine; Data Science; Nhs England; Promazine Hydrochloride,,,"<h4>Background</h4>Data analysis is used to identify signals suggestive of variation in treatment choice or clinical outcome. Analyses to date have generally focused on a hypothesis-driven approach.<h4>Objective</h4>This study aimed to develop a hypothesis-free approach to identify unusual prescribing behavior in primary care data. We aimed to apply this methodology to a national data set in a cross-sectional study to identify chemicals with significant variation in use across Clinical Commissioning Groups (CCGs) for further clinical review, thereby demonstrating proof of concept for prioritization approaches.<h4>Methods</h4>Here we report a new data-driven approach to identify unusual prescribing behaviour in primary care data. This approach first applies a set of filtering steps to identify chemicals with prescribing rate distributions likely to contain outliers, then applies two ranking approaches to identify the most extreme outliers amongst those candidates. This methodology has been applied to three months of national prescribing data (June-August 2017).<h4>Results</h4>Our methodology provides rankings for all chemicals by administrative region. We provide illustrative results for 2 antipsychotic drugs of particular clinical interest: promazine hydrochloride and pericyazine, which rank highly by outlier metrics. Specifically, our method identifies that, while promazine hydrochloride and pericyazine are barely used by most clinicians (with national prescribing rates of 11.1 and 6.2 per 1000 antipsychotic prescriptions, respectively), they make up a substantial proportion of antipsychotic prescribing in 2 small geographic regions in England during the study period (with maximum regional prescribing rates of 298.7 and 241.1 per 1000 antipsychotic prescriptions, respectively).<h4>Conclusions</h4>Our hypothesis-free approach is able to identify candidates for audit and review in clinical practice. To illustrate this, we provide 2 examples of 2 very unusual antipsychotics used disproportionately in 2 small geographic areas of England.",,pdf:https://medinform.jmir.org/2022/12/e41200/PDF; doi:https://doi.org/10.2196/41200; html:https://europepmc.org/articles/PMC9812268
-37951941,https://doi.org/10.1186/s12920-023-01710-9,A phenome-wide approach to identify causal risk factors for deep vein thrombosis.,"Constantinescu AE, Bull CJ, Goudswaard LJ, Zheng J, Elsworth B, Timpson NJ, Moore SF, Hers I, Vincent EE.",,BMC medical genomics,2023,2023-11-11,Y,Deep vein thrombosis; Alspac; Genome-wide Association Study; Mendelian Randomization; Protein Quantitative Trait Loci,,,"Deep vein thrombosis (DVT) is the formation of a blood clot in a deep vein. DVT can lead to a venous thromboembolism (VTE), the combined term for DVT and pulmonary embolism, a leading cause of death and disability worldwide. Despite the prevalence and associated morbidity of DVT, the underlying causes are not well understood. Our aim was to leverage publicly available genetic summary association statistics to identify causal risk factors for DVT. We conducted a Mendelian randomization phenome-wide association study (MR-PheWAS) using genetic summary association statistics for 973 exposures and DVT (6,767 cases and 330,392 controls in UK Biobank). There was evidence for a causal effect of 57 exposures on DVT risk, including previously reported risk factors (e.g. body mass index-BMI and height) and novel risk factors (e.g. hyperthyroidism and varicose veins). As the majority of identified risk factors were adiposity-related, we explored the molecular link with DVT by undertaking a two-sample MR mediation analysis of BMI-associated circulating proteins on DVT risk. Our results indicate that circulating neurogenic locus notch homolog protein 1 (NOTCH1), inhibin beta C chain (INHBC) and plasminogen activator inhibitor 1 (PAI-1) influence DVT risk, with PAI-1 mediating the BMI-DVT relationship. Using a phenome-wide approach, we provide putative causal evidence that hyperthyroidism, varicose veins and BMI enhance the risk of DVT. Furthermore, the circulating protein PAI-1 has a causal role in DVT aetiology and is involved in mediating the BMI-DVT relationship.",,pdf:https://bmcmedgenomics.biomedcentral.com/counter/pdf/10.1186/s12920-023-01710-9; doi:https://doi.org/10.1186/s12920-023-01710-9; html:https://europepmc.org/articles/PMC10640748; pdf:https://europepmc.org/articles/PMC10640748?pdf=render
 31442537,https://doi.org/10.1016/j.jaad.2019.08.039,Atopic dermatitis and risk of atrial fibrillation or flutter: A 35-year follow-up study.,"Schmidt SAJ, Olsen M, Schmidt M, Vestergaard C, Langan SM, Deleuran MS, Riis JL.",,Journal of the American Academy of Dermatology,2020,2019-08-20,Y,Validation; Atrial fibrillation; Atrial flutter; Cohort study; risk factors; Atopic Dermatitis,Understanding the Causes of Disease,,"<h4>Background</h4>Atopic dermatitis is characterized by chronic inflammation, which is a risk factor for atrial fibrillation.<h4>Objective</h4>To examine the association between hospital-diagnosed atopic dermatitis and atrial fibrillation.<h4>Methods</h4>Using linked population-based Danish registries, we identified persons with an inpatient or outpatient hospital diagnosis of atopic dermatitis during 1977-2013 and a comparison cohort individually matched to the atopic dermatitis cohort. We followed cohorts until death, emigration, atrial fibrillation diagnosis, or end of study (January 1, 2013). We compared 35-year risk of atrial fibrillation and estimated hazard ratios with 95% confidence intervals using Cox regression, adjusting for birth year and sex. We validated 100 atopic dermatitis diagnoses from a dermatologic department through medical record review.<h4>Results</h4>We included 13,126 persons with atopic dermatitis and 124,211 comparators and followed them for a median of 19.3 years. The 35-year risk of atrial fibrillation was 0.81% and 0.67%, respectively. The positive predictive value of atopic dermatitis diagnoses was 99%. The hazard ratio was 1.2 (95% confidence interval 1.0-1.6) and remained increased after adjusting for various atrial fibrillation risk factors.<h4>Limitations</h4>Analyses were limited to persons with moderate-to-severe atopic dermatitis, and we had no lifestyle data.<h4>Conclusion</h4>Patients with hospital-diagnosed atopic dermatitis have a 20% increased long-term risk of atrial fibrillation, but the absolute risk remains low.",,pdf:http://www.jaad.org/article/S0190962219326143/pdf; doi:https://doi.org/10.1016/j.jaad.2019.08.039; html:https://europepmc.org/articles/PMC7704103; pdf:https://europepmc.org/articles/PMC7704103?pdf=render
-35921096,https://doi.org/10.1001/jamacardio.2022.2333,Joint Genetic Inhibition of PCSK9 and CETP and the Association With Coronary Artery Disease: A Factorial Mendelian Randomization Study.,"Cupido AJ, Reeskamp LF, Hingorani AD, Finan C, Asselbergs FW, Hovingh GK, Schmidt AF.",,JAMA cardiology,2022,2022-09-01,N,,,,"<h4>Importance</h4>Cholesteryl ester transfer protein inhibition (CETP) has been shown to increase levels of high-density lipoprotein cholesterol (HDL-C) and reduce levels of low-density lipoprotein cholesterol (LDL-C). Current LDL-C target attainment is low, and novel phase 3 trials are underway to investigate whether CETP inhibitors result in reduction of cardiovascular disease risk in high-risk patients who may be treated with PCSK9-inhibiting agents.<h4>Objective</h4>To explore the associations of combined reduction of CETP and PCSK9 concentrations with risk of coronary artery disease (CAD) and other clinical and safety outcomes.<h4>Design, setting, and participants</h4>Two-sample 2 × 2 factorial Mendelian randomization study in a general population sample that includes data for UK Biobank participants of European ancestry.<h4>Exposures</h4>Separate genetic scores were constructed for CETP and PCSK9 plasma protein concentrations, which were combined to determine the associations of combined genetically reduced CETP and PCSK9 concentrations with disease.<h4>Main outcomes and measures</h4>Blood lipid and lipoprotein concentrations, blood pressure, CAD, age-related macular degeneration, type 2 diabetes, any stroke and ischemic stroke, Alzheimer disease, vascular dementia, heart failure, atrial fibrillation, chronic kidney disease, asthma, and multiple sclerosis.<h4>Results</h4>Data for 425 354 UKB participants were included; the median (IQR) age was 59 years (51-64), and 229 399 (53.9%) were female. The associations of lower CETP and lower PCSK9 concentrations with CAD are similar when scaled per 10-mg/dL reduction in LDL-C concentrations (CETP: odds ratio [OR], 0.74; 95% CI, 0.67 to 0.81; PCSK9: OR, 0.75; 95% CI, 0.71 to 0.79). Combined exposure to lower CETP and PCSK9 concentrations was associated with an additive magnitude with lipids and all outcomes, and we did not observe any nonadditive interactions, most notably for LDL-C (CETP: effect size, -1.11 mg/dL; 95% CI, -1.40 to -0.82; PCSK9: effect size, -2.13 mg/dL; 95% CI, -2.43 to -1.84; combined: effect size, -3.47 mg/dL; 95% CI, -3.76 to -3.18; P = .34 for interaction) and CAD (CETP: OR, 0.96; 95% CI, 0.94 to 1.00; PCSK9: OR, 0.94; 95% CI, 0.91 to 0.97; combined: OR, 0.90; 95% CI, 0.87 to 0.93; P = .83 for interaction). In addition, when corrected for multiple testing, lower CETP concentrations were associated with increased age-related macular degeneration (OR, 1.11; 95% CI, 1.04 to 1.19).<h4>Conclusions and relevance</h4>Our results suggest that joint inhibition of CETP and PCSK9 has additive effects on lipid traits and disease risk, including a lower risk of CAD. Further research may explore whether a combination of CETP- and PCSK9-related therapeutics can benefit high-risk patients who are unable to reach treatment targets with existing options.",,doi:https://doi.org/10.1001/jamacardio.2022.2333; html:https://europepmc.org/articles/PMC9350849; doi:https://doi.org/10.1001/jamacardio.2022.2333
+37951941,https://doi.org/10.1186/s12920-023-01710-9,A phenome-wide approach to identify causal risk factors for deep vein thrombosis.,"Constantinescu AE, Bull CJ, Goudswaard LJ, Zheng J, Elsworth B, Timpson NJ, Moore SF, Hers I, Vincent EE.",,BMC medical genomics,2023,2023-11-11,Y,Deep vein thrombosis; Alspac; Genome-wide Association Study; Mendelian Randomization; Protein Quantitative Trait Loci,,,"Deep vein thrombosis (DVT) is the formation of a blood clot in a deep vein. DVT can lead to a venous thromboembolism (VTE), the combined term for DVT and pulmonary embolism, a leading cause of death and disability worldwide. Despite the prevalence and associated morbidity of DVT, the underlying causes are not well understood. Our aim was to leverage publicly available genetic summary association statistics to identify causal risk factors for DVT. We conducted a Mendelian randomization phenome-wide association study (MR-PheWAS) using genetic summary association statistics for 973 exposures and DVT (6,767 cases and 330,392 controls in UK Biobank). There was evidence for a causal effect of 57 exposures on DVT risk, including previously reported risk factors (e.g. body mass index-BMI and height) and novel risk factors (e.g. hyperthyroidism and varicose veins). As the majority of identified risk factors were adiposity-related, we explored the molecular link with DVT by undertaking a two-sample MR mediation analysis of BMI-associated circulating proteins on DVT risk. Our results indicate that circulating neurogenic locus notch homolog protein 1 (NOTCH1), inhibin beta C chain (INHBC) and plasminogen activator inhibitor 1 (PAI-1) influence DVT risk, with PAI-1 mediating the BMI-DVT relationship. Using a phenome-wide approach, we provide putative causal evidence that hyperthyroidism, varicose veins and BMI enhance the risk of DVT. Furthermore, the circulating protein PAI-1 has a causal role in DVT aetiology and is involved in mediating the BMI-DVT relationship.",,pdf:https://bmcmedgenomics.biomedcentral.com/counter/pdf/10.1186/s12920-023-01710-9; doi:https://doi.org/10.1186/s12920-023-01710-9; html:https://europepmc.org/articles/PMC10640748; pdf:https://europepmc.org/articles/PMC10640748?pdf=render
 37456658,https://doi.org/10.12688/hrbopenres.13667.1,Qualitative data sharing practices in clinical trials in the UK and Ireland: towards the production of good practice guidance.,"McCarthy M, Gillies K, Rousseau N, Wade J, Gamble C, Toomey E, Matvienko-Sikar K, Sydes M, Dowling M, Bryant V, Biesty L, Houghton C.",,HRB open research,2023,2023-02-06,Y,data sharing; Qualitative; trials; Focus Groups,,,"<b>Background</b>: Data sharing enables researchers to conduct novel research with previously collected datasets, thus maximising scientific findings and cost effectiveness, and reducing research waste. The value of sharing, even de-identified, quantitative data from clinical trials is well recognised with a moderated access approach recommended. While substantial challenges to sharing quantitative data remain, there are additional challenges for sharing qualitative data in trials. Incorporating the necessary information about how qualitative data will be shared into already complex trial recruitment and consent processes proves challenging. The aim of this study was to explore whether and how trial teams share qualitative data collected as part of the design, conduct, analysis, or delivery of clinical trials. <b>Methods: </b>Phase 1 involved semi-structured, in-depth qualitative interviews and focus groups with key trial stakeholder groups including trial managers and clinical trialists (n=3), qualitative researchers in trials (n=9), members of research funding bodies (n=2) and trial participants (n=1). Data were analysed using thematic analysis. In Phase 2, we conducted a content analysis of 16 participant information leaflets (PIL) and consent forms (CF) for trials that collected qualitative data. <b>Results:</b> Three key themes were identified from our Phase 1 findings: ' <i>Understanding and experiences of the potential benefits of sharing qualitative data from trials', 'Concerns about qualitative data sharing'</i>, and ' <i>Future guidance and funding</i>'. In phase 2, the PILs and CFs received revealed that the benefits of data sharing for participants were only explained in two of the study documents. <b>Conclusions:</b> The value of sharing qualitative data was acknowledged, but there are many uncertainties as to how, when, and where to share this data. In addition, there were ethical concerns in relation to the consent process required for qualitative data sharing in trials. This study provides insight into the existing practice of qualitative data sharing in trials.",,pdf:https://hrbopenresearch.org/articles/6-10/pdf; doi:https://doi.org/10.12688/hrbopenres.13667.1; html:https://europepmc.org/articles/PMC10345597; pdf:https://europepmc.org/articles/PMC10345597?pdf=render
+35921096,https://doi.org/10.1001/jamacardio.2022.2333,Joint Genetic Inhibition of PCSK9 and CETP and the Association With Coronary Artery Disease: A Factorial Mendelian Randomization Study.,"Cupido AJ, Reeskamp LF, Hingorani AD, Finan C, Asselbergs FW, Hovingh GK, Schmidt AF.",,JAMA cardiology,2022,2022-09-01,N,,,,"<h4>Importance</h4>Cholesteryl ester transfer protein inhibition (CETP) has been shown to increase levels of high-density lipoprotein cholesterol (HDL-C) and reduce levels of low-density lipoprotein cholesterol (LDL-C). Current LDL-C target attainment is low, and novel phase 3 trials are underway to investigate whether CETP inhibitors result in reduction of cardiovascular disease risk in high-risk patients who may be treated with PCSK9-inhibiting agents.<h4>Objective</h4>To explore the associations of combined reduction of CETP and PCSK9 concentrations with risk of coronary artery disease (CAD) and other clinical and safety outcomes.<h4>Design, setting, and participants</h4>Two-sample 2 × 2 factorial Mendelian randomization study in a general population sample that includes data for UK Biobank participants of European ancestry.<h4>Exposures</h4>Separate genetic scores were constructed for CETP and PCSK9 plasma protein concentrations, which were combined to determine the associations of combined genetically reduced CETP and PCSK9 concentrations with disease.<h4>Main outcomes and measures</h4>Blood lipid and lipoprotein concentrations, blood pressure, CAD, age-related macular degeneration, type 2 diabetes, any stroke and ischemic stroke, Alzheimer disease, vascular dementia, heart failure, atrial fibrillation, chronic kidney disease, asthma, and multiple sclerosis.<h4>Results</h4>Data for 425 354 UKB participants were included; the median (IQR) age was 59 years (51-64), and 229 399 (53.9%) were female. The associations of lower CETP and lower PCSK9 concentrations with CAD are similar when scaled per 10-mg/dL reduction in LDL-C concentrations (CETP: odds ratio [OR], 0.74; 95% CI, 0.67 to 0.81; PCSK9: OR, 0.75; 95% CI, 0.71 to 0.79). Combined exposure to lower CETP and PCSK9 concentrations was associated with an additive magnitude with lipids and all outcomes, and we did not observe any nonadditive interactions, most notably for LDL-C (CETP: effect size, -1.11 mg/dL; 95% CI, -1.40 to -0.82; PCSK9: effect size, -2.13 mg/dL; 95% CI, -2.43 to -1.84; combined: effect size, -3.47 mg/dL; 95% CI, -3.76 to -3.18; P = .34 for interaction) and CAD (CETP: OR, 0.96; 95% CI, 0.94 to 1.00; PCSK9: OR, 0.94; 95% CI, 0.91 to 0.97; combined: OR, 0.90; 95% CI, 0.87 to 0.93; P = .83 for interaction). In addition, when corrected for multiple testing, lower CETP concentrations were associated with increased age-related macular degeneration (OR, 1.11; 95% CI, 1.04 to 1.19).<h4>Conclusions and relevance</h4>Our results suggest that joint inhibition of CETP and PCSK9 has additive effects on lipid traits and disease risk, including a lower risk of CAD. Further research may explore whether a combination of CETP- and PCSK9-related therapeutics can benefit high-risk patients who are unable to reach treatment targets with existing options.",,doi:https://doi.org/10.1001/jamacardio.2022.2333; html:https://europepmc.org/articles/PMC9350849; doi:https://doi.org/10.1001/jamacardio.2022.2333
 33655079,https://doi.org/10.12688/wellcomeopenres.16304.2,Impact of baseline cases of cough and fever on UK COVID-19 diagnostic testing rates: estimates from the Bug Watch community cohort study.,"Eyre MT, Burns R, Kirkby V, Smith C, Denaxas S, Nguyen V, Hayward A, Shallcross L, Fragaszy E, Aldridge RW.",,Wellcome open research,2020,2020-01-01,Y,Fever; Cough; United Kingdom; Diagnostic Testing Capacity; Swab Test; Covid-19,,,"<b>Background:</b> Diagnostic testing forms a major part of the UK's response to the current coronavirus disease 2019 (COVID-19) pandemic with tests offered to anyone with a continuous cough, high temperature or anosmia. Testing capacity must be sufficient during the winter respiratory season when levels of cough and fever are high due to non-COVID-19 causes. This study aims to make predictions about the contribution of baseline cough or fever to future testing demand in the UK. <b>Methods:</b> In this analysis of the Bug Watch community cohort study, we estimated the incidence of cough or fever in England in 2018-2019. We then estimated the COVID-19 diagnostic testing rates required in the UK for baseline cough or fever cases for the period July 2020-June 2021. This was explored for different rates of the population requesting tests, four COVID-19 second wave scenarios and high and low baseline cough or fever incidence scenarios. <b>Results:</b> Under the high baseline cough or fever scenario, incidence in the UK is expected to rise rapidly from 250,708 (95%CI 181,095 - 347,080) cases per day in September to a peak of 444,660 (95%CI 353,084 - 559,988) in December. If 80% of these cases request tests, testing demand would exceed 1.4 million tests per week for five consecutive months. Demand was significantly lower in the low cough or fever incidence scenario, with 129,115 (95%CI 111,596 - 151,679) tests per day in January 2021, compared to 340,921 (95%CI 276,039 - 424,491) tests per day in the higher incidence scenario. <b>Conclusions:</b> Our results show that national COVID-19 testing demand is highly dependent on background cough or fever incidence. This study highlights that the UK's response to the COVID-19 pandemic must ensure that a high proportion of people with symptoms request tests, and that testing capacity is sufficient to meet the high predicted demand.",,doi:https://doi.org/10.12688/wellcomeopenres.16304.2; html:https://europepmc.org/articles/PMC7890379; pdf:https://europepmc.org/articles/PMC7890379?pdf=render
 34629034,https://doi.org/10.1080/02640414.2021.1928409,Are individual and social factors specific to the home associated with children's behaviour and physical environment at home.,"Sheldrick MPR, Maitland C, Mackintosh KA, Rosenberg M, Griffiths LJ, Fry R, Stratton G.",,Journal of sports sciences,2021,2021-10-09,N,Youth; Family; House; Sedentary Time; Moderate-vigorous Physical Activity,,,"This study used linear regression analyses to investigate the influence of parent-reported home-specific social and individual factors on: (i) 235 children's home-based objectively measured overall sitting time, breaks in sitting, and PA, and; (ii) the home physical environment via an audit. Parental importance assigned to active play for children was positively associated with PA equipment (accessibility and availability), as well as light physical activity (LPA) and sitting breaks on both weekdays and weekend days. Parental preference for being active at home and limits on screen-time were associated with less household media equipment and portable media equipment, respectively. Greater parental importance placed on playing electronic games/using computers for fun was associated with less LPA and more sitting on weekdays. Further, children who preferred being sedentary sat more and engaged in less moderate-vigorous physical activity (MVPA) on weekdays. Parental and child preferences and priorities, as well as parental rules for activity at home, were associated with children's home-based sitting and PA, especially on weekdays. Such factors were also associated with the physical environment in the expected directions. The findings suggest interventions need to target social and individual factors, alongside adapting the physical environment to create homes more promotive of physical activity.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa56833/Download/56833__19829__9b0bb77f67e84342b525fbccaba98e67.pdf; doi:https://doi.org/10.1080/02640414.2021.1928409
-38965219,https://doi.org/10.1038/s41398-024-02997-7,"Vitamin D, chronic pain, and depression: linear and non-linear Mendelian randomization analyses.","Bassett E, Gjekmarkaj E, Mason AM, Zhao SS, Burgess S.",,Translational psychiatry,2024,2024-07-04,Y,,,,"Vitamin D deficiency has been linked to various chronic pain conditions. However, randomized trials of vitamin D supplementation have had mixed results. In contrast, systematic reviews of randomized trials indicate a protective effect of vitamin D supplementation on depression. We undertake a Mendelian randomization investigation in UK Biobank, a study of UK residents aged 40-65 at recruitment. We perform linear and non-linear Mendelian randomization analyses for four outcomes: fibromyalgia, clinical fatigue, chronic widespread pain, and probable lifetime major depression. We use genetic variants from four gene regions with known links to vitamin D biology as instruments. In linear analyses, genetically-predicted levels of 25-hydroxyvitamin D [25(OH)D], a clinical marker of vitamin D status, were not associated with fibromyalgia (odds ratio [OR] per 10 nmol/L higher 25(OH)D 1.02, 95% confidence interval [CI] 0.93, 1.12), clinical fatigue (OR 0.99, 95% CI 0.94, 1.05), chronic widespread pain (OR 0.95, 95% CI 0.89, 1.02), or probable lifetime major depression (OR 0.97, 95% CI 0.93, 1.01). In non-linear analyses, an association was observed between genetically-predicted 25(OH)D levels and depression in the quintile of the population with the lowest 25(OH)D levels (OR 0.75, 95% CI 0.59, 0.94); associations were null in other strata. Our findings suggest that population-wide vitamin D supplementation will not substantially reduce pain or depression; however, targeted supplementation of deficient individuals may reduce risk of depression.",,doi:https://doi.org/10.1038/s41398-024-02997-7; html:https://europepmc.org/articles/PMC11224391; pdf:https://europepmc.org/articles/PMC11224391?pdf=render
 36864090,https://doi.org/10.1038/s41598-023-30369-6,Effect of tissue-grouped regulatory variants associated to type 2 diabetes in related secondary outcomes.,"Hemerich D, Smit RAJ, Preuss M, Stalbow L, van der Laan SW, Asselbergs FW, van Setten J, Tragante V.",,Scientific reports,2023,2023-03-02,Y,,,,"Genome-wide association studies have identified over five hundred loci that contribute to variation in type 2 diabetes (T2D), an established risk factor for many diseases. However, the mechanisms and extent through which these loci contribute to subsequent outcomes remain elusive. We hypothesized that combinations of T2D-associated variants acting on tissue-specific regulatory elements might account for greater risk for tissue-specific outcomes, leading to diversity in T2D disease progression. We searched for T2D-associated variants acting on regulatory elements and expression quantitative trait loci (eQTLs) in nine tissues. We used T2D tissue-grouped variant sets as genetic instruments to conduct 2-Sample Mendelian Randomization (MR) in ten related outcomes whose risk is increased by T2D using the FinnGen cohort. We performed PheWAS analysis to investigate whether the T2D tissue-grouped variant sets had specific predicted disease signatures. We identified an average of 176 variants acting in nine tissues implicated in T2D, and an average of 30 variants acting on regulatory elements that are unique to the nine tissues of interest. In 2-Sample MR analyses, all subsets of regulatory variants acting in different tissues were associated with increased risk of the ten secondary outcomes studied on similar levels. No tissue-grouped variant set was associated with an outcome significantly more than other tissue-grouped variant sets. We did not identify different disease progression profiles based on tissue-specific regulatory and transcriptome information. Bigger sample sizes and other layers of regulatory information in critical tissues may help identify subsets of T2D variants that are implicated in certain secondary outcomes, uncovering system-specific disease progression.",,pdf:https://www.nature.com/articles/s41598-023-30369-6.pdf; doi:https://doi.org/10.1038/s41598-023-30369-6; html:https://europepmc.org/articles/PMC9981672; pdf:https://europepmc.org/articles/PMC9981672?pdf=render
+38965219,https://doi.org/10.1038/s41398-024-02997-7,"Vitamin D, chronic pain, and depression: linear and non-linear Mendelian randomization analyses.","Bassett E, Gjekmarkaj E, Mason AM, Zhao SS, Burgess S.",,Translational psychiatry,2024,2024-07-04,Y,,,,"Vitamin D deficiency has been linked to various chronic pain conditions. However, randomized trials of vitamin D supplementation have had mixed results. In contrast, systematic reviews of randomized trials indicate a protective effect of vitamin D supplementation on depression. We undertake a Mendelian randomization investigation in UK Biobank, a study of UK residents aged 40-65 at recruitment. We perform linear and non-linear Mendelian randomization analyses for four outcomes: fibromyalgia, clinical fatigue, chronic widespread pain, and probable lifetime major depression. We use genetic variants from four gene regions with known links to vitamin D biology as instruments. In linear analyses, genetically-predicted levels of 25-hydroxyvitamin D [25(OH)D], a clinical marker of vitamin D status, were not associated with fibromyalgia (odds ratio [OR] per 10 nmol/L higher 25(OH)D 1.02, 95% confidence interval [CI] 0.93, 1.12), clinical fatigue (OR 0.99, 95% CI 0.94, 1.05), chronic widespread pain (OR 0.95, 95% CI 0.89, 1.02), or probable lifetime major depression (OR 0.97, 95% CI 0.93, 1.01). In non-linear analyses, an association was observed between genetically-predicted 25(OH)D levels and depression in the quintile of the population with the lowest 25(OH)D levels (OR 0.75, 95% CI 0.59, 0.94); associations were null in other strata. Our findings suggest that population-wide vitamin D supplementation will not substantially reduce pain or depression; however, targeted supplementation of deficient individuals may reduce risk of depression.",,doi:https://doi.org/10.1038/s41398-024-02997-7; html:https://europepmc.org/articles/PMC11224391; pdf:https://europepmc.org/articles/PMC11224391?pdf=render
 34939031,https://doi.org/10.1093/braincomms/fcab241,Degeneration of basal and limbic networks is a core feature of behavioural variant frontotemporal dementia.,"Vuksanović V, Staff RT, Morson S, Ahearn T, Bracoud L, Murray AD, Bentham P, Kipps CM, Harrington CR, Wischik CM.",,Brain communications,2021,2021-10-21,Y,Neurodegeneration; Brain Networks; Behavioural Variant Frontotemporal Dementia; Rich Club; Anatomical Subtypes,,,"The behavioural variant of frontotemporal dementia is a clinical syndrome characterized by changes in behaviour, cognition and functional ability. Although atrophy in frontal and temporal regions would appear to be a defining feature, neuroimaging studies have identified volumetric differences distributed across large parts of the cortex, giving rise to a classification into distinct neuroanatomical subtypes. Here, we extended these neuroimaging studies to examine how distributed patterns of cortical atrophy map onto brain network hubs. We used baseline structural magnetic resonance imaging data collected from 213 behavioural variant of frontotemporal dementia patients meeting consensus diagnostic criteria and having definite evidence of frontal and/or temporal lobe atrophy from a global clinical trial conducted in 70 sites in Canada, United States of America, Australia, Asia and Europe. These were compared with data from 244 healthy elderly subjects from a well-characterized cohort study. We have used statistical methods of hierarchical agglomerative clustering of 68 regional cortical and subcortical volumes (34 in each hemisphere) to determine the reproducibility of previously described neuroanatomical subtypes in a global study. We have also attempted to link the structural findings to clinical features defined systematically using well-validated clinical scales (Addenbrooke's Cognitive Examination Revised, the Mini-Mental Status Examination, the Frontotemporal Dementia Rating Scale and the Functional Assessment Questionnaire) and subscales derived from them. Whilst we can confirm that the subtypes are robust, they have limited value in explaining the clinical heterogeneity of the syndrome. We have found that a common pattern of degeneration affecting a small number of subcortical, limbic and frontal nodes within highly connected networks (most previously identified as rich club members or functional binding nodes) is shared by all the anatomical subtypes. Degeneration in these core regions is correlated with cognitive and functional impairment, but less so with behavioural impairment. These findings suggest that degeneration in highly connected basal, limbic and frontal networks is a core feature of the behavioural variant of frontotemporal dementia phenotype irrespective of neuroanatomical and clinical heterogeneity, and may underly the impairment of integration in cognition, function and behaviour responsible for the loss of insight that characterizes the syndrome.",,pdf:https://academic.oup.com/braincomms/article-pdf/3/4/fcab241/41829863/fcab241.pdf; doi:https://doi.org/10.1093/braincomms/fcab241; html:https://europepmc.org/articles/PMC8688778; pdf:https://europepmc.org/articles/PMC8688778?pdf=render
 36719715,https://doi.org/10.2196/41248,Patterns in the Use of Heart Failure Telemonitoring: Post Hoc Analysis of the e-Vita Heart Failure Trial.,"Brons M, Ten Klooster I, van Gemert-Pijnen L, Jaarsma T, Asselbergs FW, Oerlemans MIFJ, Koudstaal S, Rutten FH.",,JMIR cardio,2023,2023-01-31,Y,Adherence; Heart Failure; Patient Monitoring; Remote Monitoring; Telemonitoring; Ehealth; Electronic Personal Health Record,,,"<h4>Background</h4>Research on the use of home telemonitoring data and adherence to it can provide new insights into telemonitoring for the daily management of patients with heart failure (HF).<h4>Objective</h4>We described the use of a telemonitoring platform-including remote patient monitoring of blood pressure, pulse, and weight-and the use of the electronic personal health record. Patient characteristics were assessed in both adherent and nonadherent patients to weight transmissions.<h4>Methods</h4>We used the data of the e-Vita HF study, a 3-arm parallel randomized trial performed in stable patients with HF managed in outpatient clinics in the Netherlands. In this study, data were analyzed from the participants in the intervention arm (ie, e-Vita HF platform). Adherence to weight transmissions was defined as transmitting weight ≥3 times per week for at least 42 weeks during a year.<h4>Results</h4>Data from 150 patients (mean age 67, SD 11 years; n=37, 25% female; n=123, 82% self-assessed New York Heart Association class I-II) were analyzed. One-year adherence to weight transmissions was 74% (n=111). Patients adherent to weight transmissions were less often hospitalized for HF in the 6 months before enrollment in the study compared to those who were nonadherent (n=9, 8% vs n=9, 23%; P=.02). The percentage of patients visiting the personal health record dropped steadily over time (n=140, 93% vs n=59, 39% at one year). With univariable analyses, there was no significant correlation between patient characteristics and adherence to weight transmissions.<h4>Conclusions</h4>Adherence to remote patient monitoring was high among stable patients with HF and best for weighing; however, adherence decreased over time. Clinical and demographic variables seem not related to adherence to transmitting weight.<h4>Trial registration</h4>ClinicalTrials.gov NCT01755988; https://clinicaltrials.gov/ct2/show/NCT01755988.",,pdf:https://cardio.jmir.org/2023/1/e41248/PDF; doi:https://doi.org/10.2196/41248; html:https://europepmc.org/articles/PMC9929726; pdf:https://europepmc.org/articles/PMC9929726?pdf=render
 38045433,https://doi.org/10.1093/ehjdh/ztad049,Developing a personalized remote patient monitoring algorithm: a proof-of-concept in heart failure.,"Moazeni M, Numan L, Brons M, Houtgraaf J, Rutten FH, Oberski DL, van Laake LW, Asselbergs FW, Aarts E.",,European heart journal. Digital health,2023,2023-08-23,Y,Heart Failure; dynamic monitoring; Process Monitoring; Intensive Longitudinal Data; Statistical Process Control Chart; Remote Patient Monitoring,,,"<h4>Aims</h4>Non-invasive remote patient monitoring is an increasingly popular technique to aid clinicians in the early detection of worsening heart failure (HF) alongside regular follow-ups. However, previous studies have shown mixed results in the performance of such systems. Therefore, we developed and evaluated a personalized monitoring algorithm aimed at increasing positive-predictive-value (PPV) (i.e. alarm quality) and compared performance with simple rule-of-thumb and moving average convergence-divergence algorithms (MACD).<h4>Methods and results</h4>In this proof-of-concept study, the developed algorithm was applied to retrospective data of daily bodyweight, heart rate, and systolic blood pressure of 74 HF-patients with a median observation period of 327 days (IQR: 183 days), during which 31 patients experienced 64 clinical worsening HF episodes. The algorithm combined information on both the monitored patients and a group of stable HF patients, and is increasingly personalized over time, using linear mixed-effect modelling and statistical process control charts. Optimized on alarm quality, heart rate showed the highest PPV (Personalized: 92%, MACD: 2%, Rule-of-thumb: 7%) with an F1 score of (Personalized: 28%, MACD: 6%, Rule-of-thumb: 8%). Bodyweight demonstrated the lowest PPV (Personalized: 16%, MACD: 0%, Rule-of-thumb: 6%) and F1 score (Personalized: 10%, MACD: 3%, Rule-of-thumb: 7%) overall compared methods.<h4>Conclusion</h4>The personalized algorithm with flexible patient-tailored thresholds led to higher PPV, and performance was more sensitive compared to common simple monitoring methods (rule-of-thumb and MACD). However, many episodes of worsening HF remained undetected. Heart rate and systolic blood pressure monitoring outperformed bodyweight in predicting worsening HF. The algorithm source code is publicly available for future validation and improvement.",,pdf:https://academic.oup.com/ehjdh/advance-article-pdf/doi/10.1093/ehjdh/ztad049/51233223/ztad049.pdf; doi:https://doi.org/10.1093/ehjdh/ztad049; html:https://europepmc.org/articles/PMC10689918; pdf:https://europepmc.org/articles/PMC10689918?pdf=render
@@ -1291,18 +1293,18 @@ PMC10686417,https://doi.org/,The impact of restricted provision of publicly fund
 34610958,https://doi.org/10.1136/emermed-2019-209368,Association between anticoagulants and mortality and functional outcomes in older patients with major trauma.,"Sato N, Cameron P, Mclellan S, Beck B, Gabbe B.",,Emergency medicine journal : EMJ,2021,2021-10-05,N,Research; Trauma; Geriatrics; Major Trauma Management; Death/mortality,,,"<h4>Background</h4>The number of trauma patients taking anticoagulants and antiplatelet agents is increasing as society ages. However, there have been limited and inconsistent reports of the association between anticoagulants and mortality and functional outcomes. This study aimed to quantify the association between anticoagulant/antiplatelet medication at the time of injury and both short-term and longer-term outcomes in older major trauma patients.<h4>Methods</h4>This was a population-based registry study using data from the Victorian State Trauma Registry from July 2017 to June 2018. We included patients with major trauma aged 65 years and older. The outcomes of interest were in-hospital mortality, hospital length of stay, intensive care unit length of stay and the Extended Glasgow Outcome Scale (GOS-E) at 6 months after injury. We examined the association between the outcomes and anticoagulants/antiplatelet agents at the time of injury and used multivariable logistic regression models to account for known confounders.<h4>Results</h4>There were 1323 older adults eligible for inclusion in the study, of which 249 (18.8%) were taking anticoagulants (n=8 were taking both anticoagulants and antiplatelet agents), 380 (28.7%) were taking antiplatelet agents and 694 (52.5%) were not using either. Any anticoagulant use was associated with higher odds of in-hospital mortality (adjusted OR (AOR), 2.38; 95% CI 1.58 to 3.59) compared with not using anticoagulants. No differences were observed in the GOS-E at 6 months after injury between any anticoagulants use, antiplatelet use and no anticoagulant use (anticoagulant AOR, 0.71; 95% CI 0.48 to 1.05, antiplatelet AOR, 1.02; 95% CI 0.73 to 1.42).<h4>Conclusion</h4>Anticoagulant use at the time of injury was associated with higher odds of in-hospital mortality but did not adversely impact functional outcomes at 6 months after injury. These findings demonstrate the importance of seeking an accurate history of anticoagulant use and its indication, as well as the immediate initiation of reversal therapies.",,doi:https://doi.org/10.1136/emermed-2019-209368
 38304411,https://doi.org/10.26633/rpsp.2024.12,[Guidelines for clinical trial protocols for interventions involving artificial intelligence: the SPIRIT-AI extensionDiretrizes para protocolos de ensaios clínicos com intervenções que utilizam inteligência artificial: a extensão SPIRIT-AI].,"Cruz Rivera S, Liu X, Chan AW, Denniston AK, Calvert MJ, Grupo de Trabajo SPIRIT-AI y CONSORT-AI, Grupo Directivo SPIRIT-AI y CONSORT-AI , Grupo de Consenso SPIRIT-AI y CONSORT-AI .",,Revista panamericana de salud publica = Pan American journal of public health,2024,2023-02-01,Y,,,,"The SPIRIT 2013 statement aims to improve the completeness of clinical trial protocol reporting by providing evidence-based recommendations for the minimum set of items to be addressed. This guidance has been instrumental in promoting transparent evaluation of new interventions. More recently, there has been a growing recognition that interventions involving artificial intelligence (AI) need to undergo rigorous, prospective evaluation to demonstrate their impact on health outcomes. The SPIRIT-AI (Standard Protocol Items: Recommendations for Interventional Trials-Artificial Intelligence) extension is a new reporting guideline for clinical trial protocols evaluating interventions with an AI component. It was developed in parallel with its companion statement for trial reports: CONSORT-AI (Consolidated Standards of Reporting Trials-Artificial Intelligence). Both guidelines were developed through a staged consensus process involving literature review and expert consultation to generate 26 candidate items, which were consulted upon by an international multi-stakeholder group in a two-stage Delphi survey (103 stakeholders), agreed upon in a consensus meeting (31 stakeholders) and refined through a checklist pilot (34 participants). The SPIRIT-AI extension includes 15 new items that were considered sufficiently important for clinical trial protocols of AI interventions. These new items should be routinely reported in addition to the core SPIRIT 2013 items. SPIRIT-AI recommends that investigators provide clear descriptions of the AI intervention, including instructions and skills required for use, the setting in which the AI intervention will be integrated, considerations for the handling of input and output data, the human-AI interaction and analysis of error cases. SPIRIT-AI will help promote transparency and completeness for clinical trial protocols for AI interventions. Its use will assist editors and peer reviewers, as well as the general readership, to understand, interpret and critically appraise the design and risk of bias for a planned clinical trial.",,pdf:https://iris.paho.org/bitstream/10665.2/59241/1/v48e122024.pdf; doi:https://doi.org/10.26633/RPSP.2024.12; html:https://europepmc.org/articles/PMC10832304; pdf:https://europepmc.org/articles/PMC10832304?pdf=render
 35896705,https://doi.org/10.1038/s41598-022-16639-9,Estimation of biological heart age using cardiovascular magnetic resonance radiomics.,"Raisi-Estabragh Z, Salih A, Gkontra P, Atehortúa A, Radeva P, Boscolo Galazzo I, Menegaz G, Harvey NC, Lekadir K, Petersen SE.",,Scientific reports,2022,2022-07-27,Y,,,,"We developed a novel interpretable biological heart age estimation model using cardiovascular magnetic resonance radiomics measures of ventricular shape and myocardial character. We included 29,996 UK Biobank participants without cardiovascular disease. Images were segmented using an automated analysis pipeline. We extracted 254 radiomics features from the left ventricle, right ventricle, and myocardium of each study. We then used Bayesian ridge regression with tenfold cross-validation to develop a heart age estimation model using the radiomics features as the model input and chronological age as the model output. We examined associations of radiomics features with heart age in men and women, observing sex-differential patterns. We subtracted actual age from model estimated heart age to calculate a ""heart age delta"", which we considered as a measure of heart aging. We performed a phenome-wide association study of 701 exposures with heart age delta. The strongest correlates of heart aging were measures of obesity, adverse serum lipid markers, hypertension, diabetes, heart rate, income, multimorbidity, musculoskeletal health, and respiratory health. This technique provides a new method for phenotypic assessment relating to cardiovascular aging; further studies are required to assess whether it provides incremental risk information over current approaches.",,pdf:https://www.nature.com/articles/s41598-022-16639-9.pdf; doi:https://doi.org/10.1038/s41598-022-16639-9; html:https://europepmc.org/articles/PMC9329281; pdf:https://europepmc.org/articles/PMC9329281?pdf=render
-34427560,https://doi.org/10.1684/ejd.2021.4108,"The association between immunosuppression and skin cancer in solid organ transplant recipients: a control-matched cohort study of 2,852 patients.","Gibson JAG, Cordaro A, Dobbs TD, Griffiths R, Akbari A, Whitaker S, Hutchings HA, Lyons RA, Whitaker IS.",,European journal of dermatology : EJD,2021,2021-12-01,N,Transplant; Oncology; immunosuppression; Skin Cancer,,,"Skin cancer is more common in transplant recipients, although the quoted incidence is variable. This study investigated the incidence of skin cancer in solid organ transplant recipients (OTRs) in a national cohort and the effect of pharmacotherapeutic agents Transplant patients were identified from Patient Episode Database for Wales (PEDW) using Office of Population Census and Surveys Classifications of Interventions and Procedures-4 (OPCS-4) codes. Controls were matched to cases according to age, sex and socioeconomic status. Skin cancer data were obtained from linkage with other national data sources. Incidence was calculated per 100,000 person-years at risk (PYAR). Negative binomial regression was used to calculate adjusted incidence rate ratios (IRRs) for each organ type. During 2000-2018, 2,852 Welsh patients underwent solid organ transplantation. A total of 13,527 controls were matched from the general population. The incidence of skin cancer within the OTR cohort was 1203.2 per 100,000 PYAR vs 133.9 in the matched control group. Age, male gender and azathioprine use were all associated with an increased risk of skin cancer. Contemporary immunomodulators such as tacrolimus and mycophenolate were associated with a reduction in skin cancer risk when compared to their predecessors, cyclosporin and azathioprine. The highest adjusted IRR was observed in heart transplant recipients (IRR: 10.82; 95% CI: 3.64-32.19) and the lowest in liver transplant recipients (IRR: 2.86; 95% CI: 1.15-7.13). This study highlights the need for long-term routine skin cancer surveillance for all OTRs and the importance of using contemporary immunomodulators, when possible, for risk reduction.",,doi:https://doi.org/10.1684/ejd.2021.4108
 32771960,https://doi.org/10.1016/j.ijmedinf.2020.104237,Core competencies for clinical informaticians: A systematic review.,"Davies A, Mueller J, Moulton G.",,International journal of medical informatics,2020,2020-07-24,N,Bioinformatics; Health; Clinical; Pharmacy; Skills; Informatics; Requirements; Core Competencies; Healthcare Data Science,,,"<h4>Background</h4>Building on initial work carried out by the Faculty of Clinical Informatics (FCI) in the UK, the creation of a national competency framework for Clinical Informatics is required for the definition of clinical informaticians' professional attributes and skills. We aimed to systematically review the academic literature relating to competencies, skills and existing course curricula in the clinical and health related informatics domains.<h4>Methods</h4>Two independent reviewers searched Web of Science, EMBASE, ERIC, PubMed and CINAHL. Publications were included if they reported details of relevant competencies, skills and existing course curricula. We report findings using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) statement.<h4>Results</h4>A total of 82 publications were included. The most frequently used method was surveys (30 %) followed by narrative descriptions (28 %). Most of the publications describe curriculum design (23 %) followed by competency definition (18 %) and skills, qualifications & training (18 %). Core skills surrounding data, information systems and information management appear to be cross-cutting across the various informatics disciplines with Bioinformatics and Pharmacy Informatics expressing the most unique competency requirements.<h4>Conclusion</h4>We identified eight key domains that cut across the different sub-disciplines of health informatics, including data, information management, human factors, project management, research skills/knowledge, leadership and management, systems development and evaluation, and health/healthcare. Some informatics disciplines such as Nursing Informatics appear to be further ahead at achieving widespread competency standardisation. Attempts at standardisation for competencies should be tempered with flexibility to allow for local variation and requirements.",,doi:https://doi.org/10.1016/j.ijmedinf.2020.104237
-34435642,https://doi.org/10.1093/eurheartj/ehab350,Evidence to support magnetic resonance conditional labelling of all pacemaker and defibrillator leads in patients with cardiac implantable electronic devices.,"Bhuva AN, Moralee R, Brunker T, Lascelles K, Cash L, Patel KP, Lowe M, Sekhri N, Alpendurada F, Pennell DJ, Schilling R, Lambiase PD, Chow A, Moon JC, Litt H, Baksi AJ, Manisty CH.",,European heart journal,2022,2022-07-01,Y,Pacemaker; Magnetic Resonance Imaging; Defibrillator,,,"<h4>Aims</h4>Many cardiac pacemakers and defibrillators are not approved by regulators for magnetic resonance imaging (MRI). Even following generator exchange to an approved magnetic resonance (MR)-conditional model, many systems remain classified 'non-MR conditional' due to the leads. This classification makes patient access to MRI challenging, but there is no evidence of increased clinical risk. We compared the effect of MRI on non-MR conditional and MR-conditional pacemaker and defibrillator leads.<h4>Methods and results</h4>Patients undergoing clinical 1.5T MRI with pacemakers and defibrillators in three centres over 5 years were included. Magnetic resonance imaging protocols were similar for MR-conditional and non-MR conditional systems. Devices were interrogated pre- and immediately post-scan, and at follow-up, and adverse clinical events recorded. Lead parameter changes peri-scan were stratified by MR-conditional labelling. A total of 1148 MRI examinations were performed in 970 patients (54% non-MR conditional systems, 39% defibrillators, 15% pacing-dependent) with 2268 leads. There were no lead-related adverse clinical events, and no clinically significant immediate or late lead parameter changes following MRI in either MR-conditional or non-MR conditional leads. Small reductions in atrial and right ventricular sensed amplitudes and impedances were similar between groups, with no difference in the proportion of leads with parameter changes greater than pre-defined thresholds (7.1%, 95% confidence interval: 6.1-8.3).<h4>Conclusions</h4>There was no increased risk of MRI in patients with non-MR conditional pacemaker or defibrillator leads when following recommended protocols. Standardizing MR conditions for all leads would significantly improve access to MRI by enabling patients to be scanned in non-specialist centres, with no discernible incremental risk.",,pdf:https://academic.oup.com/eurheartj/advance-article-pdf/doi/10.1093/eurheartj/ehab350/39932149/ehab350.pdf; doi:https://doi.org/10.1093/eurheartj/ehab350; html:https://europepmc.org/articles/PMC9259370; pdf:https://europepmc.org/articles/PMC9259370?pdf=render
+34427560,https://doi.org/10.1684/ejd.2021.4108,"The association between immunosuppression and skin cancer in solid organ transplant recipients: a control-matched cohort study of 2,852 patients.","Gibson JAG, Cordaro A, Dobbs TD, Griffiths R, Akbari A, Whitaker S, Hutchings HA, Lyons RA, Whitaker IS.",,European journal of dermatology : EJD,2021,2021-12-01,N,Transplant; Oncology; immunosuppression; Skin Cancer,,,"Skin cancer is more common in transplant recipients, although the quoted incidence is variable. This study investigated the incidence of skin cancer in solid organ transplant recipients (OTRs) in a national cohort and the effect of pharmacotherapeutic agents Transplant patients were identified from Patient Episode Database for Wales (PEDW) using Office of Population Census and Surveys Classifications of Interventions and Procedures-4 (OPCS-4) codes. Controls were matched to cases according to age, sex and socioeconomic status. Skin cancer data were obtained from linkage with other national data sources. Incidence was calculated per 100,000 person-years at risk (PYAR). Negative binomial regression was used to calculate adjusted incidence rate ratios (IRRs) for each organ type. During 2000-2018, 2,852 Welsh patients underwent solid organ transplantation. A total of 13,527 controls were matched from the general population. The incidence of skin cancer within the OTR cohort was 1203.2 per 100,000 PYAR vs 133.9 in the matched control group. Age, male gender and azathioprine use were all associated with an increased risk of skin cancer. Contemporary immunomodulators such as tacrolimus and mycophenolate were associated with a reduction in skin cancer risk when compared to their predecessors, cyclosporin and azathioprine. The highest adjusted IRR was observed in heart transplant recipients (IRR: 10.82; 95% CI: 3.64-32.19) and the lowest in liver transplant recipients (IRR: 2.86; 95% CI: 1.15-7.13). This study highlights the need for long-term routine skin cancer surveillance for all OTRs and the importance of using contemporary immunomodulators, when possible, for risk reduction.",,doi:https://doi.org/10.1684/ejd.2021.4108
 35151869,https://doi.org/10.1016/j.jbi.2022.104010,Patient-centric characterization of multimorbidity trajectories in patients with severe mental illnesses: A temporal bipartite network modeling approach.,"Wang T, Bendayan R, Msosa Y, Pritchard M, Roberts A, Stewart R, Dobson R.",,Journal of biomedical informatics,2022,2022-02-11,Y,Network Evolution; Multimorbidity; Severe Mental Illnesses; Disease Trajectories; Ehr Data Linkage; Temporal Bipartite Network,,,"Multimorbidity is a major factor contributing to increased mortality among people with severe mental illnesses (SMI). Previous studies either focus on estimating prevalence of a disease in a population without considering relationships between diseases or ignore heterogeneity of individual patients in examining disease progression by looking merely at aggregates across a whole cohort. Here, we present a temporal bipartite network model to jointly represent detailed information on both individual patients and diseases, which allows us to systematically characterize disease trajectories from both patient and disease centric perspectives. We apply this approach to a large set of longitudinal diagnostic records for patients with SMI collected through a data linkage between electronic health records from a large UK mental health hospital and English national hospital administrative database. We find that the resulting diagnosis networks show disassortative mixing by degree, suggesting that patients affected by a small number of diseases tend to suffer from prevalent diseases. Factors that determine the network structures include an individual's age, gender and ethnicity. Our analysis on network evolution further shows that patients and diseases become more interconnected over the illness duration of SMI, which is largely driven by the process that patients with similar attributes tend to suffer from the same conditions. Our analytic approach provides a guide for future patient-centric research on multimorbidity trajectories and contributes to achieving precision medicine.",,doi:https://doi.org/10.1016/j.jbi.2022.104010; doi:https://doi.org/10.1016/j.jbi.2022.104010; html:https://europepmc.org/articles/PMC8894882
+34435642,https://doi.org/10.1093/eurheartj/ehab350,Evidence to support magnetic resonance conditional labelling of all pacemaker and defibrillator leads in patients with cardiac implantable electronic devices.,"Bhuva AN, Moralee R, Brunker T, Lascelles K, Cash L, Patel KP, Lowe M, Sekhri N, Alpendurada F, Pennell DJ, Schilling R, Lambiase PD, Chow A, Moon JC, Litt H, Baksi AJ, Manisty CH.",,European heart journal,2022,2022-07-01,Y,Pacemaker; Magnetic Resonance Imaging; Defibrillator,,,"<h4>Aims</h4>Many cardiac pacemakers and defibrillators are not approved by regulators for magnetic resonance imaging (MRI). Even following generator exchange to an approved magnetic resonance (MR)-conditional model, many systems remain classified 'non-MR conditional' due to the leads. This classification makes patient access to MRI challenging, but there is no evidence of increased clinical risk. We compared the effect of MRI on non-MR conditional and MR-conditional pacemaker and defibrillator leads.<h4>Methods and results</h4>Patients undergoing clinical 1.5T MRI with pacemakers and defibrillators in three centres over 5 years were included. Magnetic resonance imaging protocols were similar for MR-conditional and non-MR conditional systems. Devices were interrogated pre- and immediately post-scan, and at follow-up, and adverse clinical events recorded. Lead parameter changes peri-scan were stratified by MR-conditional labelling. A total of 1148 MRI examinations were performed in 970 patients (54% non-MR conditional systems, 39% defibrillators, 15% pacing-dependent) with 2268 leads. There were no lead-related adverse clinical events, and no clinically significant immediate or late lead parameter changes following MRI in either MR-conditional or non-MR conditional leads. Small reductions in atrial and right ventricular sensed amplitudes and impedances were similar between groups, with no difference in the proportion of leads with parameter changes greater than pre-defined thresholds (7.1%, 95% confidence interval: 6.1-8.3).<h4>Conclusions</h4>There was no increased risk of MRI in patients with non-MR conditional pacemaker or defibrillator leads when following recommended protocols. Standardizing MR conditions for all leads would significantly improve access to MRI by enabling patients to be scanned in non-specialist centres, with no discernible incremental risk.",,pdf:https://academic.oup.com/eurheartj/advance-article-pdf/doi/10.1093/eurheartj/ehab350/39932149/ehab350.pdf; doi:https://doi.org/10.1093/eurheartj/ehab350; html:https://europepmc.org/articles/PMC9259370; pdf:https://europepmc.org/articles/PMC9259370?pdf=render
 33707775,https://doi.org/10.1038/s41591-021-01266-0,Plasma metabolites to profile pathways in noncommunicable disease multimorbidity.,"Pietzner M, Stewart ID, Raffler J, Khaw KT, Michelotti GA, Kastenmüller G, Wareham NJ, Langenberg C.",,Nature medicine,2021,2021-03-11,N,,,,"Multimorbidity, the simultaneous presence of multiple chronic conditions, is an increasing global health problem and research into its determinants is of high priority. We used baseline untargeted plasma metabolomics profiling covering >1,000 metabolites as a comprehensive readout of human physiology to characterize pathways associated with and across 27 incident noncommunicable diseases (NCDs) assessed using electronic health record hospitalization and cancer registry data from over 11,000 participants (219,415 person years). We identified 420 metabolites shared between at least 2 NCDs, representing 65.5% of all 640 significant metabolite-disease associations. We integrated baseline data on over 50 diverse clinical risk factors and characteristics to identify actionable shared pathways represented by those metabolites. Our study highlights liver and kidney function, lipid and glucose metabolism, low-grade inflammation, surrogates of gut microbial diversity and specific health-related behaviors as antecedents of common NCD multimorbidity with potential for early prevention. We integrated results into an open-access webserver ( https://omicscience.org/apps/mwasdisease/ ) to facilitate future research and meta-analyses.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8127079; doi:https://doi.org/10.1038/s41591-021-01266-0; html:https://europepmc.org/articles/PMC8127079; pdf:https://europepmc.org/articles/PMC8127079?pdf=render; doi:https://doi.org/10.1038/s41591-021-01266-0
-38450564,https://doi.org/10.1089/neu.2023.0462,The Australian Traumatic Brain Injury Initiative: Systematic Review and Consensus Process to Determine the Predictive Value of Pre-existing Health Conditions for People with Moderate-Severe Traumatic Brain Injury.,"Antonic-Baker A, Auvrez C, Tao G, Bagg MK, Gadowski A, McKimmie A, Hicks AJ, Hill R, Romero L, Ponsford JL, Lannin NA, Gabbe BJ, Cameron PA, Cooper DJ, Rushworth N, Fitzgerald M, O'Brien TJ.",,Journal of neurotrauma,2024,2024-04-15,N,"Health care; Mental health; Comorbidity; Common Data Elements; Multiple Chronic Conditions; Brain Injuries, Traumatic; Outcome Assessment, Systematic Review [Publication Type]",,,"The first aim of the Australian Traumatic Brain Injury Initiative (AUS-TBI) encompasses development of a set of measures that comprehensively predict outcomes for people with moderate-severe TBI across Australia. This process engaged diverse stakeholders and information sources across six areas: social, health, and clinical factors; biological markers; treatments; and longer-term outcomes. Here, we report the systematic review of pre-existing health conditions as predictors of outcome for people with moderate-severe TBI. Standardized searches were implemented across databases until March 31, 2022. English-language reports of studies evaluating association between pre-existing health conditions and clinical outcome in at least 10 patients with moderate-severe TBI were included. A predefined algorithm was used to assign a judgement of predictive value to each observed association. The list of identified pre-existing health conditions was then discussed with key stakeholders during a consensus meeting to determine the feasibility of incorporating them into standard care. The searches retrieved 22,217 records, of which 47 articles were included. The process led to identification of 88 unique health predictors (homologized to 21 predictor categories) of 55 outcomes (homologized to 19 outcome categories). Only pre-existing health conditions with high and moderate predictive values were discussed during the consensus meeting. Following the consensus meeting, 5 out of 11 were included (migraine, mental health conditions, ≥4 pre-existing health conditions, osteoporosis, and body mass index [BMI]) as common data elements in the AUS-TBI data dictionary. Upon further discussion, 3 additional pre-existing health conditions were included. These are pre-existing heart disease, frailty score, and previous incidence of TBI.",,doi:https://doi.org/10.1089/neu.2023.0462
 36936265,https://doi.org/10.1136/bmjmed-2022-000276,"Trends, variation, and clinical characteristics of recipients of antiviral drugs and neutralising monoclonal antibodies for covid-19 in community settings: retrospective, descriptive cohort study of 23.4 million people in OpenSAFELY.","Green ACA, Curtis HJ, Higgins R, Nab L, Mahalingasivam V, Smith RM, Mehrkar A, Inglesby P, Drysdale H, DeVito NJ, Croker R, Rentsch CT, Bhaskaran K, Tazare J, Zheng B, Andrews CD, Bacon SCJ, Davy S, Dillingham I, Evans D, Fisher L, Hickman G, Hopcroft LEM, Hulme WJ, Massey J, MacDonald O, Morley J, Morton CE, Park RY, Walker AJ, Ward T, Wiedemann M, Bates C, Cockburn J, Parry J, Hester F, Harper S, Douglas IJ, Evans SJW, Goldacre B, Tomlinson LA, MacKenna B.",,BMJ medicine,2023,2023-01-13,Y,Therapeutics; Community health services; Public Health; Covid-19,,,"<h4>Objective</h4>To ascertain patient eligibility status and describe coverage of antiviral drugs and neutralising monoclonal antibodies (nMAB) as treatment for covid-19 in community settings in England.<h4>Design</h4>Retrospective, descriptive cohort study, approved by NHS England.<h4>Setting</h4>Routine clinical data from 23.4 million people linked to data on covid-19 infection and treatment, within the OpenSAFELY-TPP database.<h4>Participants</h4>Outpatients with covid-19 at high risk of severe outcomes.<h4>Interventions</h4>Nirmatrelvir/ritonavir (paxlovid), sotrovimab, molnupiravir, casirivimab/imdevimab, or remdesivir, used in the community by covid-19 medicine delivery units.<h4>Results</h4>93 870 outpatients with covid-19 were identified between 11 December 2021 and 28 April 2022 to be at high risk of severe outcomes and therefore potentially eligible for antiviral or nMAB treatment (or both). Of these patients, 19 040 (20%) received treatment (sotrovimab, 9660 (51%); molnupiravir, 4620 (24%); paxlovid, 4680 (25%); casirivimab/imdevimab, 50 (<1%); and remdesivir, 30 (<1%)). The proportion of patients treated increased from 9% (190/2220) in the first week of treatment availability to 29% (460/1600) in the latest week. The proportion treated varied by high risk group, being lowest in those with liver disease (16%; 95% confidence interval 15% to 17%); by treatment type, with sotrovimab favoured over molnupiravir and paxlovid in all but three high risk groups (Down's syndrome (35%; 30% to 39%), rare neurological conditions (45%; 43% to 47%), and immune deficiencies (48%; 47% to 50%)); by age, ranging from ≥80 years (13%; 12% to 14%) to 50-59 years (23%; 22% to 23%); by ethnic group, ranging from black (11%; 10% to 12%) to white (21%; 21% to 21%); by NHS region, ranging from 13% (12% to 14%) in Yorkshire and the Humber to 25% (24% to 25%) in the East of England); and by deprivation level, ranging from 15% (14% to 15%) in the most deprived areas to 23% (23% to 24%) in the least deprived areas. Groups that also had lower coverage included unvaccinated patients (7%; 6% to 9%), those with dementia (6%; 5% to 7%), and care home residents (6%; 6% to 7%).<h4>Conclusions</h4>Using the OpenSAFELY platform, we were able to identify patients with covid-19 at high risk of severe outcomes who were potentially eligible to receive treatment and assess the coverage of these new treatments among these patients. In the context of a rapid deployment of a new service, the NHS analytical code used to determine eligibility could have been over-inclusive and some of the eligibility criteria not fully captured in healthcare data. However targeted activity might be needed to resolve apparent lower treatment coverage observed among certain groups, in particular (at present): different NHS regions, ethnic groups, people aged ≥80 years, those living in socioeconomically deprived areas, and care home residents.",,pdf:https://bmjmedicine.bmj.com/content/bmjmed/2/1/e000276.full.pdf; doi:https://doi.org/10.1136/bmjmed-2022-000276; html:https://europepmc.org/articles/PMC9951378; pdf:https://europepmc.org/articles/PMC9951378?pdf=render
+38450564,https://doi.org/10.1089/neu.2023.0462,The Australian Traumatic Brain Injury Initiative: Systematic Review and Consensus Process to Determine the Predictive Value of Pre-existing Health Conditions for People with Moderate-Severe Traumatic Brain Injury.,"Antonic-Baker A, Auvrez C, Tao G, Bagg MK, Gadowski A, McKimmie A, Hicks AJ, Hill R, Romero L, Ponsford JL, Lannin NA, Gabbe BJ, Cameron PA, Cooper DJ, Rushworth N, Fitzgerald M, O'Brien TJ.",,Journal of neurotrauma,2024,2024-04-15,N,"Health care; Mental health; Comorbidity; Common Data Elements; Multiple Chronic Conditions; Brain Injuries, Traumatic; Outcome Assessment, Systematic Review [Publication Type]",,,"The first aim of the Australian Traumatic Brain Injury Initiative (AUS-TBI) encompasses development of a set of measures that comprehensively predict outcomes for people with moderate-severe TBI across Australia. This process engaged diverse stakeholders and information sources across six areas: social, health, and clinical factors; biological markers; treatments; and longer-term outcomes. Here, we report the systematic review of pre-existing health conditions as predictors of outcome for people with moderate-severe TBI. Standardized searches were implemented across databases until March 31, 2022. English-language reports of studies evaluating association between pre-existing health conditions and clinical outcome in at least 10 patients with moderate-severe TBI were included. A predefined algorithm was used to assign a judgement of predictive value to each observed association. The list of identified pre-existing health conditions was then discussed with key stakeholders during a consensus meeting to determine the feasibility of incorporating them into standard care. The searches retrieved 22,217 records, of which 47 articles were included. The process led to identification of 88 unique health predictors (homologized to 21 predictor categories) of 55 outcomes (homologized to 19 outcome categories). Only pre-existing health conditions with high and moderate predictive values were discussed during the consensus meeting. Following the consensus meeting, 5 out of 11 were included (migraine, mental health conditions, ≥4 pre-existing health conditions, osteoporosis, and body mass index [BMI]) as common data elements in the AUS-TBI data dictionary. Upon further discussion, 3 additional pre-existing health conditions were included. These are pre-existing heart disease, frailty score, and previous incidence of TBI.",,doi:https://doi.org/10.1089/neu.2023.0462
 33328049,https://doi.org/10.1016/s2589-7500(20)30219-3,Guidelines for clinical trial protocols for interventions involving artificial intelligence: the SPIRIT-AI extension.,"Cruz Rivera S, Liu X, Chan AW, Denniston AK, Calvert MJ, SPIRIT-AI and CONSORT-AI Working Group.",,The Lancet. Digital health,2020,2020-09-09,Y,,,,"The SPIRIT 2013 statement aims to improve the completeness of clinical trial protocol reporting by providing evidence-based recommendations for the minimum set of items to be addressed. This guidance has been instrumental in promoting transparent evaluation of new interventions. More recently, there has been a growing recognition that interventions involving artificial intelligence (AI) need to undergo rigorous, prospective evaluation to demonstrate their impact on health outcomes. The SPIRIT-AI (Standard Protocol Items: Recommendations for Interventional Trials-Artificial Intelligence) extension is a new reporting guideline for clinical trial protocols evaluating interventions with an AI component. It was developed in parallel with its companion statement for trial reports: CONSORT-AI (Consolidated Standards of Reporting Trials-Artificial Intelligence). Both guidelines were developed through a staged consensus process involving literature review and expert consultation to generate 26 candidate items, which were consulted upon by an international multi-stakeholder group in a two-stage Delphi survey (103 stakeholders), agreed upon in a consensus meeting (31 stakeholders) and refined through a checklist pilot (34 participants). The SPIRIT-AI extension includes 15 new items that were considered sufficiently important for clinical trial protocols of AI interventions. These new items should be routinely reported in addition to the core SPIRIT 2013 items. SPIRIT-AI recommends that investigators provide clear descriptions of the AI intervention, including instructions and skills required for use, the setting in which the AI intervention will be integrated, considerations for the handling of input and output data, the human-AI interaction and analysis of error cases. SPIRIT-AI will help promote transparency and completeness for clinical trial protocols for AI interventions. Its use will assist editors and peer reviewers, as well as the general readership, to understand, interpret, and critically appraise the design and risk of bias for a planned clinical trial.",,pdf:http://www.thelancet.com/article/S2589750020302193/pdf; doi:https://doi.org/10.1016/S2589-7500(20)30219-3; html:https://europepmc.org/articles/PMC8212701; pdf:https://europepmc.org/articles/PMC8212701?pdf=render
 33678589,https://doi.org/10.1016/s2589-7500(20)30317-4,Health data poverty: an assailable barrier to equitable digital health care.,"Ibrahim H, Liu X, Zariffa N, Morris AD, Denniston AK.",,The Lancet. Digital health,2021,2021-03-04,N,,,,"Data-driven digital health technologies have the power to transform health care. If these tools could be sustainably delivered at scale, they might have the potential to provide everyone, everywhere, with equitable access to expert-level care, narrowing the global health and wellbeing gap. Conversely, it is highly possible that these transformative technologies could exacerbate existing health-care inequalities instead. In this Viewpoint, we describe the problem of health data poverty: the inability for individuals, groups, or populations to benefit from a discovery or innovation due to a scarcity of data that are adequately representative. We assert that health data poverty is a threat to global health that could prevent the benefits of data-driven digital health technologies from being more widely realised and might even lead to them causing harm. We argue that the time to act is now to avoid creating a digital health divide that exacerbates existing health-care inequalities and to ensure that no one is left behind in the digital era.",,pdf:http://www.thelancet.com/article/S2589750020303174/pdf; doi:https://doi.org/10.1016/S2589-7500(20)30317-4
+32065794,https://doi.org/10.3233/jad-191163,Working Towards a Blood-Derived Gene Expression Biomarker Specific for Alzheimer's Disease.,"Patel H, Iniesta R, Stahl D, Dobson RJB, Newhouse SJ.",,Journal of Alzheimer's disease : JAD,2020,2020-01-01,Y,Human; Biomarkers; Alzheimer’s disease; Dementia; Gene Expression; Neurodegenerative Disorders; Machine Learning; Microarray Analysis; Age-related Memory Disorders,,,"<h4>Background</h4>The typical approach to identify blood-derived gene expression signatures as a biomarker for Alzheimer's disease (AD) have relied on training classification models using AD and healthy controls only. This may inadvertently result in the identification of markers for general illness rather than being disease-specific.<h4>Objective</h4>Investigate whether incorporating additional related disorders in the classification model development process can lead to the discovery of an AD-specific gene expression signature.<h4>Methods</h4>Two types of XGBoost classification models were developed. The first used 160 AD and 127 healthy controls and the second used the same 160 AD with 6,318 upsampled mixed controls consisting of Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis, bipolar disorder, schizophrenia, coronary artery disease, rheumatoid arthritis, chronic obstructive pulmonary disease, and cognitively healthy subjects. Both classification models were evaluated in an independent cohort consisting of 127 AD and 687 mixed controls.<h4>Results</h4>The AD versus healthy control models resulted in an average 48.7% sensitivity (95% CI = 34.7-64.6), 41.9% specificity (95% CI = 26.8-54.3), 13.6% PPV (95% CI = 9.9-18.5), and 81.1% NPV (95% CI = 73.3-87.7). In contrast, the mixed control models resulted in an average of 40.8% sensitivity (95% CI = 27.5-52.0), 95.3% specificity (95% CI = 93.3-97.1), 61.4% PPV (95% CI = 53.8-69.6), and 89.7% NPV (95% CI = 87.8-91.4).<h4>Conclusions</h4>This early work demonstrates the value of incorporating additional related disorders into the classification model developmental process, which can result in models with improved ability to distinguish AD from a heterogeneous aging population. However, further improvement to the sensitivity of the test is still required.",,pdf:https://content.iospress.com:443/download/journal-of-alzheimers-disease/jad191163?id=journal-of-alzheimers-disease%2Fjad191163; doi:https://doi.org/10.3233/JAD-191163; html:https://europepmc.org/articles/PMC7175937; pdf:https://europepmc.org/articles/PMC7175937?pdf=render
 37440761,https://doi.org/10.1093/ehjci/jead166,Neuroticism personality traits are linked to adverse cardiovascular phenotypes in the UK Biobank.,"Mahmood A, Simon J, Cooper J, Murphy T, McCracken C, Quiroz J, Laranjo L, Aung N, Lee AM, Khanji MY, Neubauer S, Raisi-Estabragh Z, Maurovich-Horvat P, Petersen SE.",,European heart journal. Cardiovascular Imaging,2023,2023-10-01,Y,Cardiac function; Cardiac morphology; Mental health; Cardiovascular Magnetic Resonance; Neuroticism; Cardiovascular Remodelling,,,"<h4>Aims</h4>To evaluate the relationship between neuroticism personality traits and cardiovascular magnetic resonance (CMR) measures of cardiac morphology and function, considering potential differential associations in men and women.<h4>Methods and results</h4>The analysis includes 36 309 UK Biobank participants (average age = 63.9 ± 7.7 years; 47.8% men) with CMR available and neuroticism score assessed by the 12-item Eysenck Personality Questionnaire-Revised Short Form. CMR scans were performed on 1.5 Tesla scanners (MAGNETOM Aera, Siemens Healthcare, Erlangen, Germany) according to pre-defined protocols and analysed using automated pipelines. We considered measures of left ventricular (LV) and right ventricular (RV) structure and function, and indicators of arterial compliance. Multivariable linear regression was used to estimate association of neuroticism score with individual CMR metrics, with adjustment for age, sex, obesity, deprivation, smoking, diabetes, hypertension, hypercholesterolaemia, alcohol use, exercise, and education. Higher neuroticism scores were associated with smaller LV and RV end-diastolic volumes, lower LV mass, greater concentricity (higher LV mass to volume ratio), and higher native T1. Greater neuroticism was also linked to poorer LV and RV function (lower stroke volumes) and greater arterial stiffness. In sex-stratified analyses, the relationships between neuroticism and LV stroke volume, concentricity, and arterial stiffness were attenuated in women. In men, association (with exception of native T1) remained robust.<h4>Conclusion</h4>Greater tendency towards neuroticism personality traits is linked to smaller, poorer functioning ventricles with lower LV mass, higher myocardial fibrosis, and higher arterial stiffness. These relationships are independent of traditional vascular risk factors and are more robust in men than women.",,pdf:https://academic.oup.com/ehjcimaging/advance-article-pdf/doi/10.1093/ehjci/jead166/50880139/jead166.pdf; doi:https://doi.org/10.1093/ehjci/jead166; html:https://europepmc.org/articles/PMC10610755; pdf:https://europepmc.org/articles/PMC10610755?pdf=render
 37739596,https://doi.org/10.1016/j.jtha.2023.07.008,"""C1-inhibitor levels and venous thromboembolism: results from a Mendelian randomization study"": reply.","Cupido AJ, Petersen RS, Schmidt AF, Levi M, Cohn DM, Fijen LM.",,Journal of thrombosis and haemostasis : JTH,2023,2023-10-01,N,,,,,,doi:https://doi.org/10.1016/j.jtha.2023.07.008
-32065794,https://doi.org/10.3233/jad-191163,Working Towards a Blood-Derived Gene Expression Biomarker Specific for Alzheimer's Disease.,"Patel H, Iniesta R, Stahl D, Dobson RJB, Newhouse SJ.",,Journal of Alzheimer's disease : JAD,2020,2020-01-01,Y,Human; Biomarkers; Alzheimer’s disease; Dementia; Gene Expression; Neurodegenerative Disorders; Machine Learning; Microarray Analysis; Age-related Memory Disorders,,,"<h4>Background</h4>The typical approach to identify blood-derived gene expression signatures as a biomarker for Alzheimer's disease (AD) have relied on training classification models using AD and healthy controls only. This may inadvertently result in the identification of markers for general illness rather than being disease-specific.<h4>Objective</h4>Investigate whether incorporating additional related disorders in the classification model development process can lead to the discovery of an AD-specific gene expression signature.<h4>Methods</h4>Two types of XGBoost classification models were developed. The first used 160 AD and 127 healthy controls and the second used the same 160 AD with 6,318 upsampled mixed controls consisting of Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis, bipolar disorder, schizophrenia, coronary artery disease, rheumatoid arthritis, chronic obstructive pulmonary disease, and cognitively healthy subjects. Both classification models were evaluated in an independent cohort consisting of 127 AD and 687 mixed controls.<h4>Results</h4>The AD versus healthy control models resulted in an average 48.7% sensitivity (95% CI = 34.7-64.6), 41.9% specificity (95% CI = 26.8-54.3), 13.6% PPV (95% CI = 9.9-18.5), and 81.1% NPV (95% CI = 73.3-87.7). In contrast, the mixed control models resulted in an average of 40.8% sensitivity (95% CI = 27.5-52.0), 95.3% specificity (95% CI = 93.3-97.1), 61.4% PPV (95% CI = 53.8-69.6), and 89.7% NPV (95% CI = 87.8-91.4).<h4>Conclusions</h4>This early work demonstrates the value of incorporating additional related disorders into the classification model developmental process, which can result in models with improved ability to distinguish AD from a heterogeneous aging population. However, further improvement to the sensitivity of the test is still required.",,pdf:https://content.iospress.com:443/download/journal-of-alzheimers-disease/jad191163?id=journal-of-alzheimers-disease%2Fjad191163; doi:https://doi.org/10.3233/JAD-191163; html:https://europepmc.org/articles/PMC7175937; pdf:https://europepmc.org/articles/PMC7175937?pdf=render
 33085509,https://doi.org/10.7326/m20-4986,COVID-19 Mortality Risk in Down Syndrome: Results From a Cohort Study of 8 Million Adults.,"Clift AK, Coupland CAC, Keogh RH, Hemingway H, Hippisley-Cox J.",,Annals of internal medicine,2021,2020-10-21,Y,,,,,,pdf:https://europepmc.org/articles/pmc7592804?pdf=render; doi:https://doi.org/10.7326/M20-4986; html:https://europepmc.org/articles/PMC7592804; pdf:https://europepmc.org/articles/PMC7592804?pdf=render
 33344049,https://doi.org/10.1167/tvst.9.13.5,Automated Segmentation of Optical Coherence Tomography Angiography Images: Benchmark Data and Clinically Relevant Metrics.,"Giarratano Y, Bianchi E, Gray C, Morris A, MacGillivray T, Dhillon B, Bernabeu MO.",,Translational vision science & technology,2020,2020-12-03,Y,Automated Segmentation; Retinal Vasculature; Optical Coherence Tomography Angiography,,,"<h4>Purpose</h4>To generate the first open dataset of retinal parafoveal optical coherence tomography angiography (OCTA) images with associated ground truth manual segmentations, and to establish a standard for OCTA image segmentation by surveying a broad range of state-of-the-art vessel enhancement and binarization procedures.<h4>Methods</h4>Handcrafted filters and neural network architectures were used to perform vessel enhancement. Thresholding methods and machine learning approaches were applied to obtain the final binarization. Evaluation was performed by using pixelwise metrics and newly proposed topological metrics. Finally, we compare the error in the computation of clinically relevant vascular network metrics (e.g., foveal avascular zone area and vessel density) across segmentation methods.<h4>Results</h4>Our results show that, for the set of images considered, deep learning architectures (U-Net and CS-Net) achieve the best performance (Dice = 0.89). For applications where manually segmented data are not available to retrain these approaches, our findings suggest that optimally oriented flux (OOF) is the best handcrafted filter (Dice = 0.86). Moreover, our results show up to 25% differences in vessel density accuracy depending on the segmentation method used.<h4>Conclusions</h4>In this study, we derive and validate the first open dataset of retinal parafoveal OCTA images with associated ground truth manual segmentations. Our findings should be taken into account when comparing the results of clinical studies and performing meta-analyses. Finally, we release our data and source code to support standardization efforts in OCTA image segmentation.<h4>Translational relevance</h4>This work establishes a standard for OCTA retinal image segmentation and introduces the importance of evaluating segmentation performance in terms of clinically relevant metrics.",,doi:https://doi.org/10.1167/tvst.9.13.5; doi:https://doi.org/10.1167/tvst.9.13.5; html:https://europepmc.org/articles/PMC7718823; pdf:https://europepmc.org/articles/PMC7718823?pdf=render
 38124256,https://doi.org/10.1093/ageing/afad219,New Horizons in artificial intelligence in the healthcare of older people.,"Shiwani T, Relton S, Evans R, Kale A, Heaven A, Clegg A, Ageing Data Research Collaborative (Geridata) AI group, Todd O.",,Age and ageing,2023,2023-12-01,Y,Artificial intelligence; Technology; Ageing; Health; Older People,,,"Artificial intelligence (AI) in healthcare describes algorithm-based computational techniques which manage and analyse large datasets to make inferences and predictions. There are many potential applications of AI in the care of older people, from clinical decision support systems that can support identification of delirium from clinical records to wearable devices that can predict the risk of a fall. We held four meetings of older people, clinicians and AI researchers. Three priority areas were identified for AI application in the care of older people. These included: monitoring and early diagnosis of disease, stratified care and care coordination between healthcare providers. However, the meetings also highlighted concerns that AI may exacerbate health inequity for older people through bias within AI models, lack of external validation amongst older people, infringements on privacy and autonomy, insufficient transparency of AI models and lack of safeguarding for errors. Creating effective interventions for older people requires a person-centred approach to account for the needs of older people, as well as sufficient clinical and technological governance to meet standards of generalisability, transparency and effectiveness. Education of clinicians and patients is also needed to ensure appropriate use of AI technologies, with investment in technological infrastructure required to ensure equity of access.",,doi:https://doi.org/10.1093/ageing/afad219; html:https://europepmc.org/articles/PMC10733173; pdf:https://europepmc.org/articles/PMC10733173?pdf=render
@@ -1329,45 +1331,45 @@ PMC10686417,https://doi.org/,The impact of restricted provision of publicly fund
 34053271,https://doi.org/10.1098/rstb.2020.0266,Real-time monitoring of COVID-19 dynamics using automated trend fitting and anomaly detection.,"Jombart T, Ghozzi S, Schumacher D, Taylor TJ, Leclerc QJ, Jit M, Flasche S, Greaves F, Ward T, Eggo RM, Nightingale E, Meakin S, Brady OJ, Centre for Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Medley GF, Höhle M, Edmunds WJ.",,"Philosophical transactions of the Royal Society of London. Series B, Biological sciences",2021,2021-05-31,Y,Algorithm; Surveillance; outbreak; Machine Learning; Asmodee; Trendbreaker,,,"As several countries gradually release social distancing measures, rapid detection of new localized COVID-19 hotspots and subsequent intervention will be key to avoiding large-scale resurgence of transmission. We introduce ASMODEE (automatic selection of models and outlier detection for epidemics), a new tool for detecting sudden changes in COVID-19 incidence. Our approach relies on automatically selecting the best (fitting or predicting) model from a range of user-defined time series models, excluding the most recent data points, to characterize the main trend in an incidence. We then derive prediction intervals and classify data points outside this interval as outliers, which provides an objective criterion for identifying departures from previous trends. We also provide a method for selecting the optimal breakpoints, used to define how many recent data points are to be excluded from the trend fitting procedure. The analysis of simulated COVID-19 outbreaks suggests ASMODEE compares favourably with a state-of-art outbreak-detection algorithm while being simpler and more flexible. As such, our method could be of wider use for infectious disease surveillance. We illustrate ASMODEE using publicly available data of National Health Service (NHS) Pathways reporting potential COVID-19 cases in England at a fine spatial scale, showing that the method would have enabled the early detection of the flare-ups in Leicester and Blackburn with Darwen, two to three weeks before their respective lockdown. ASMODEE is implemented in the free R package <i>trendbreaker</i>. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.",,pdf:https://royalsocietypublishing.org/doi/pdf/10.1098/rstb.2020.0266; doi:https://doi.org/10.1098/rstb.2020.0266; html:https://europepmc.org/articles/PMC8165581; pdf:https://europepmc.org/articles/PMC8165581?pdf=render
 37067859,https://doi.org/10.1136/bmjmed-2022-000245,Sex differences in cardiovascular complications and mortality in hospital patients with covid-19: registry based observational study.,"Hockham C, Linschoten M, Asselbergs FW, Ghossein C, Woodward M, Peters SAE, CAPACITY-COVID Collaborative Consortium .",,BMJ medicine,2023,2023-02-14,Y,epidemiology; Heart Failure; Cardiology; Covid-19,,,"<h4>Objective</h4>To assess whether the risk of cardiovascular complications of covid-19 differ between the sexes and to determine whether any sex differences in risk are reduced in individuals with pre-existing cardiovascular disease.<h4>Design</h4>Registry based observational study.<h4>Setting</h4>74 hospitals across 13 countries (eight European) participating in CAPACITY-COVID (Cardiac complicAtions in Patients With SARS Corona vIrus 2 regisTrY), from March 2020 to May 2021.<h4>Participants</h4>All adults (aged ≥18 years), predominantly European, admitted to hospital with highly suspected covid-19 disease or covid-19 disease confirmed by positive laboratory test results (n=11 167 patients).<h4>Main outcome measures</h4>Any cardiovascular complication during admission to hospital. Secondary outcomes were in-hospital mortality and individual cardiovascular complications with ≥20 events for each sex. Logistic regression was used to examine sex differences in the risk of cardiovascular outcomes, overall and grouped by pre-existing cardiovascular disease.<h4>Results</h4>Of 11 167 adults (median age 68 years, 40% female participants) included, 3423 (36% of whom were female participants) had pre-existing cardiovascular disease. In both sexes, the most common cardiovascular complications were supraventricular tachycardias (4% of female participants, 6% of male participants), pulmonary embolism (3% and 5%), and heart failure (decompensated or de novo) (2% in both sexes). After adjusting for age, ethnic group, pre-existing cardiovascular disease, and risk factors for cardiovascular disease, female individuals were less likely than male individuals to have a cardiovascular complication (odds ratio 0.72, 95% confidence interval 0.64 to 0.80) or die (0.65, 0.59 to 0.72). Differences between the sexes were not modified by pre-existing cardiovascular disease; for the primary outcome, the female-to-male ratio of the odds ratio in those without, compared with those with, pre-existing cardiovascular disease was 0.84 (0.67 to 1.07).<h4>Conclusions</h4>In patients admitted to hospital for covid-19, female participants were less likely than male participants to have a cardiovascular complication. The differences between the sexes could not be attributed to the lower prevalence of pre-existing cardiovascular disease in female individuals. The reasons for this advantage in female individuals requires further research.",,pdf:https://bmjmedicine.bmj.com/content/bmjmed/2/1/e000245.full.pdf; doi:https://doi.org/10.1136/bmjmed-2022-000245; html:https://europepmc.org/articles/PMC10083523; pdf:https://europepmc.org/articles/PMC10083523?pdf=render
 34859617,https://doi.org/10.1002/edm2.309,The clinical profile and associated mortality in people with and without diabetes with Coronavirus disease 2019 on admission to acute hospital services.,"Gokhale K, Mostafa SA, Wang J, Tahrani AA, Sainsbury CA, Toulis KA, Thomas GN, Hassan-Smith Z, Sapey E, Gallier S, Adderley NJ, Narendran P, Bellary S, Taverner T, Ghosh S, Nirantharakumar K, Hanif W.",,"Endocrinology, diabetes & metabolism",2022,2021-12-03,Y,Diabetes; Complications; Covid-19,,,"<h4>Introduction</h4>To assess if in adults with COVID-19, whether those with diabetes and complications (DM+C) present with a more severe clinical profile and if that relates to increased mortality, compared to those with diabetes with no complications (DM-NC) and those without diabetes.<h4>Methods</h4>Service-level data was used from 996 adults with laboratory confirmed COVID-19 who presented to the Queen Elizabeth Hospital Birmingham, UK, from March to June 2020. All individuals were categorized into DM+C, DM-NC, and non-diabetes groups. Physiological and laboratory measurements in the first 5 days after admission were collated and compared among groups. Cox proportional hazards regression models were used to evaluate associations between diabetes status and the risk of mortality.<h4>Results</h4>Among the 996 individuals, 104 (10.4%) were DM+C, 295 (29.6%) DM-NC and 597 (59.9%) non-diabetes. There were 309 (31.0%) in-hospital deaths documented, 40 (4.0% of total cohort) were DM+C, 99 (9.9%) DM-NC and 170 (17.0%) non-diabetes. Individuals with DM+C were more likely to present with high anion gap/metabolic acidosis, features of renal impairment, and low albumin/lymphocyte count than those with DM-NC or those without diabetes. There was no significant difference in mortality rates among the groups: compared to individuals without diabetes, the adjusted HRs were 1.39 (95% CI 0.95-2.03, p = 0.093) and 1.18 (95% CI 0.90-1.54, p = 0.226) in DM+C and DM-C, respectively.<h4>Conclusions</h4>Those with COVID-19 and DM+C presented with a more severe clinical and biochemical profile, but this did not associate with increased mortality in this study.",,doi:https://doi.org/10.1002/edm2.309; doi:https://doi.org/10.1002/edm2.309; html:https://europepmc.org/articles/PMC8754243; pdf:https://europepmc.org/articles/PMC8754243?pdf=render
-38113090,https://doi.org/10.2196/41540,Association Between Household Online Grocery Delivery Service Use and Food and Drink Purchase Behavior in England: Cross-Sectional Analysis.,"Yau A, Law C, Cornelsen L, Adams J, Boyland E, Burgoine T, de Vocht F, White M, Cummins S.",,JMIR public health and surveillance,2023,2023-12-19,Y,Delivery; Diet; Internet; Public Health; Lifestyle; Consumer Behavior; Inequality; Sociodemographic Factors; Online; Food Preferences; Food Purchase; Supermarkets; Food And Beverages; Online Purchase; Grocery Purchase; Grocery; Online Grocery,,,"<h4>Background</h4>Online grocery delivery services (OGDSs) are a popular way of acquiring food. However, it is unclear whether OGDS use is associated with the healthiness of purchases and whether there are sociodemographic differences in OGDS use. If so, the increased prevalence of OGDS use may have implications for population diet, and differential OGDS use could contribute to diet inequalities.<h4>Objective</h4>This study aimed to examine whether OGDS use varies by sociodemographic characteristics and is associated with the amount and types of groceries purchased.<h4>Methods</h4>Item-level take-home food and drink purchase data (n=3,233,920 items) from households in London and the North of England were available from the 2019 UK Kantar fast-moving consumer goods panel (N=1911). Purchases were categorized as being bought online or in-store. We used logistic regression to estimate the likelihood of an above-median frequency of OGDS use by sociodemographic characteristics. We used Poisson regression to estimate the differences in energy and nutrients purchased by households that had above- and below-median OGDS use and the proportion of energy purchased from products high in fat, salt, and sugar (HFSS) online versus in-store among households that used both shopping methods (n=665).<h4>Results</h4>In total, 668 (35%) households used OGDSs at least once in 2019. Of the households that used OGDSs, the median use was 5 occasions in 2019. Households were more likely to have above-median use in London versus in the North of England (odds ratio 1.29, 95% CI 1.01-1.65) and if they had a higher annual household income (odds ratio 1.56, 95% CI 1.02-2.38 for ≥£50,000 [US $64,000] vs <£20,000 [$25,600]). Households with above-median OGDS use had a higher weekly mean purchase of energy by 1461 (95% CI 1448-1474) kcal per person compared with households with below-median OGDS use. For households that used a combination of in-store and online shopping, HFSS products made up a lower proportion (-10.1%, 95% CI -12% to -8.1%) of energy purchased online compared to in-store.<h4>Conclusions</h4>Differences in grocery purchases between households with above- and below-median OGDS use could have positive or negative consequences. The extra energy purchased among households with above-median OGDS use could lead to overconsumption or food waste, which has negative consequences for population and environmental health. Alternatively, this extra energy may be replacing out-of-home purchasing, which tends to be less healthy, and may be beneficial for the population diet. Households made fewer HFSS purchases when shopping online compared to in-store, which may be due to differences in the shopping environment or experience, such as fewer promotions and advertisements when shopping online or not having to transport and carry purchases home. As higher-income households used OGDS more frequently, the implications of this sociodemographic pattern on dietary inequalities must be explored.",,doi:https://doi.org/10.2196/41540; html:https://europepmc.org/articles/PMC10762614
 36369983,https://doi.org/10.1093/eurheartj/ehac650,Fit for the future: empowering clinical trials with digital technology.,"Kotecha D, DeVore AD, Asselbergs FW.",,European heart journal,2023,2023-01-01,N,,,,,,pdf:https://discovery.ucl.ac.uk/10159909/1/Asselbergs_EHJ%20digital%20viewpoint%202022_final%20accepted.pdf; doi:https://doi.org/10.1093/eurheartj/ehac650
+38113090,https://doi.org/10.2196/41540,Association Between Household Online Grocery Delivery Service Use and Food and Drink Purchase Behavior in England: Cross-Sectional Analysis.,"Yau A, Law C, Cornelsen L, Adams J, Boyland E, Burgoine T, de Vocht F, White M, Cummins S.",,JMIR public health and surveillance,2023,2023-12-19,Y,Delivery; Diet; Internet; Public Health; Lifestyle; Consumer Behavior; Inequality; Sociodemographic Factors; Online; Food Preferences; Food Purchase; Supermarkets; Food And Beverages; Online Purchase; Grocery Purchase; Grocery; Online Grocery,,,"<h4>Background</h4>Online grocery delivery services (OGDSs) are a popular way of acquiring food. However, it is unclear whether OGDS use is associated with the healthiness of purchases and whether there are sociodemographic differences in OGDS use. If so, the increased prevalence of OGDS use may have implications for population diet, and differential OGDS use could contribute to diet inequalities.<h4>Objective</h4>This study aimed to examine whether OGDS use varies by sociodemographic characteristics and is associated with the amount and types of groceries purchased.<h4>Methods</h4>Item-level take-home food and drink purchase data (n=3,233,920 items) from households in London and the North of England were available from the 2019 UK Kantar fast-moving consumer goods panel (N=1911). Purchases were categorized as being bought online or in-store. We used logistic regression to estimate the likelihood of an above-median frequency of OGDS use by sociodemographic characteristics. We used Poisson regression to estimate the differences in energy and nutrients purchased by households that had above- and below-median OGDS use and the proportion of energy purchased from products high in fat, salt, and sugar (HFSS) online versus in-store among households that used both shopping methods (n=665).<h4>Results</h4>In total, 668 (35%) households used OGDSs at least once in 2019. Of the households that used OGDSs, the median use was 5 occasions in 2019. Households were more likely to have above-median use in London versus in the North of England (odds ratio 1.29, 95% CI 1.01-1.65) and if they had a higher annual household income (odds ratio 1.56, 95% CI 1.02-2.38 for ≥£50,000 [US $64,000] vs <£20,000 [$25,600]). Households with above-median OGDS use had a higher weekly mean purchase of energy by 1461 (95% CI 1448-1474) kcal per person compared with households with below-median OGDS use. For households that used a combination of in-store and online shopping, HFSS products made up a lower proportion (-10.1%, 95% CI -12% to -8.1%) of energy purchased online compared to in-store.<h4>Conclusions</h4>Differences in grocery purchases between households with above- and below-median OGDS use could have positive or negative consequences. The extra energy purchased among households with above-median OGDS use could lead to overconsumption or food waste, which has negative consequences for population and environmental health. Alternatively, this extra energy may be replacing out-of-home purchasing, which tends to be less healthy, and may be beneficial for the population diet. Households made fewer HFSS purchases when shopping online compared to in-store, which may be due to differences in the shopping environment or experience, such as fewer promotions and advertisements when shopping online or not having to transport and carry purchases home. As higher-income households used OGDS more frequently, the implications of this sociodemographic pattern on dietary inequalities must be explored.",,doi:https://doi.org/10.2196/41540; html:https://europepmc.org/articles/PMC10762614
 32301135,https://doi.org/10.1111/opo.12685,Delayed attendance at routine eye examinations is associated with increased probability of general practitioner referral: a record linkage study in Northern Ireland.,"Wright DM, O'Reilly D, Azuara-Blanco A, Curran R, McMullan M, Hogg RE.",,Ophthalmic & physiological optics : the journal of the British College of Ophthalmic Opticians (Optometrists),2020,2020-04-16,N,epidemiology; Public Health; Optometry Services,,,"<h4>Purpose</h4>To investigate relationships between health and socio-economic status with delayed attendance at routine eye examinations and risk of subsequent general practitioner (GP) referral in Northern Ireland.<h4>Methods</h4>We constructed a cohort of 132 046 community dwelling individuals aged ≥60 years, drawing contextual information from the 2011 Northern Ireland Census. Using linked administrative records of routine eye examinations between 2009 and 2014, we calculated 311 999 examination intervals. Multinomial models were used to estimate associations between contextual factors and examination interval (classified into three groups: early recall, on-time, delayed attendance). Associations between examination interval and referral risk were estimated using logistic regression.<h4>Results</h4>Delayed attendance was recorded for 129 857 (41.6%) examination intervals, 53 759 (17.2%) delayed by ≥6 months. Female sex, poor general or mental health were each associated with delay, as were longer distances to optometry services among those aged ≥70 years (longest vs shortest: Relative Risk Ratio = 1.21 [1.14, 1.28]). Low income and residence in social housing were associated with reduced delay risk. There were 3347 (3.5%) and 11 401 (5.3%) GP referrals in the 60-69 and ≥70 years age groups respectively. Delayed attendance was associated with increased referral risk in both groups (Odds Ratios: 60-69 years = 1.30 [1.04, 1.61]; ≥70 years = 1.07 [1.01, 1.13]).<h4>Conclusions</h4>Poor health and longer distances to optometry services were associated with delayed attendance at routine eye examinations but low income was not. Delayed attendance was associated with increased GP referral risk, indicative of missed opportunities to detect potentially serious eye conditions.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/opo.12685; doi:https://doi.org/10.1111/opo.12685
 31529485,https://doi.org/10.1111/bjd.18526,"The association of smoking and socioeconomic status on cutaneous melanoma: a population-based, data-linkage, case-control study.","Gibson JAG, Dobbs TD, Griffiths R, Song J, Akbari A, Whitaker S, Watkins A, Langan SM, Hutchings HA, Lyons RA, Whitaker IS.",,The British journal of dermatology,2020,2019-12-01,Y,,Improving Public Health,,"<h4>Background</h4>Previous studies have identified an inverse association between melanoma and smoking; however, data from population-based studies are scarce.<h4>Objectives</h4>To determine the association between smoking and socioeconomic (SES) on the risk of development of melanoma. Furthermore, we sought to determine the implications of smoking and SES on survival.<h4>Methods</h4>We conducted a population-based case-control study. Cases were identified from the Welsh Cancer Intelligence and Surveillance Unit (WCISU) during 2000-2015 and controls from the general population. Smoking and SES were obtained from data linkage with other national databases. The association of smoking status and SES on the incidence of melanoma were assessed using binary logistic regression. Multivariate survival analysis was performed on a melanoma cohort using a Cox proportional hazard model using survival as the outcome.<h4>Results</h4>During 2000-2015, 9636 patients developed melanoma. Smoking data were obtained for 7124 (73·9%) of these patients. There were 26 408 controls identified from the general population. Smoking was inversely associated with melanoma incidence [odds ratio (OR) 0·70, 95% confidence interval (CI) 0·65-0·76]. Smoking was associated with an increased overall mortality [hazard ratio (HR) 1·30, 95% CI 1·09-1·55], but not associated with melanoma-specific mortality. Patients with higher SES had an increased association with melanoma incidence (OR 1·58, 95% CI 1·44-1·73). Higher SES was associated with an increased chance of both overall (HR 0·67, 95% CI 0·56-0·81) and disease-specific survival (HR 0·69, 95% CI 0·53-0·90).<h4>Conclusions</h4>Our study has demonstrated that smoking appeared to be associated with reduced incidence of melanoma. Although smoking increases overall mortality, no association was observed with melanoma-specific mortality. Further work is required to determine if there is a biological mechanism underlying this relationship or an alternative explanation, such as survival bias. What's already known about this topic? Previous studies have been contradictory with both negative and positive associations between smoking and the incidence of melanoma reported. Previous studies have either been limited by publication bias because of selective reporting or underpowered. What does this study add? Our large study identified an inverse association between smoking status and melanoma incidence. Although smoking status was negatively associated with overall disease survival, no significant association was noted in melanoma-specific survival. Socioeconomic status remains closely associated with melanoma. Although higher socioeconomic populations are more likely to develop the disease, patients with lower socioeconomic status continue to have a worse prognosis.","This study investiages whether there is a smoking and socioeconomic status is linked to the risk of developing melanoma (a skin cancer). They used a Welsh database to find data on individuals who had melanoma and linked this data with smoking status and socioeconomic status on other national databases. They found that melanoma was less likely in those who smoked, but was associated with less chance of survival (due to health problems other than melanoma). Those in higher socioeconomic status had overall higher likelihood of survival.",pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/bjd.18526; doi:https://doi.org/10.1111/bjd.18526; html:https://europepmc.org/articles/PMC7383980; pdf:https://europepmc.org/articles/PMC7383980?pdf=render
-38633019,https://doi.org/10.1002/lrh2.10391,ROAD2H: Development and evaluation of an open-source explainable artificial intelligence approach for managing co-morbidity and clinical guidelines.,"Domínguez J, Prociuk D, Marović B, Čyras K, Cocarascu O, Ruiz F, Mi E, Mi E, Ramtale C, Rago A, Darzi A, Toni F, Curcin V, Delaney B.",,Learning health systems,2024,2023-09-12,Y,Clinical Decision Support Systems; Argumentation; Fhir; Cds Hooks; Transition‐based Medical Recommendation Model; Co‐morbidity,,,"<h4>Introduction</h4>Clinical decision support (CDS) systems (CDSSs) that integrate clinical guidelines need to reflect real-world co-morbidity. In patient-specific clinical contexts, transparent recommendations that allow for contraindications and other conflicts arising from co-morbidity are a requirement. In this work, we develop and evaluate a non-proprietary, standards-based approach to the deployment of computable guidelines with explainable argumentation, integrated with a commercial electronic health record (EHR) system in Serbia, a middle-income country in West Balkans.<h4>Methods</h4>We used an ontological framework, the Transition-based Medical Recommendation (TMR) model, to represent, and reason about, guideline concepts, and chose the 2017 International global initiative for chronic obstructive lung disease (GOLD) guideline and a Serbian hospital as the deployment and evaluation site, respectively. To mitigate potential guideline conflicts, we used a TMR-based implementation of the Assumptions-Based Argumentation framework extended with preferences and Goals (ABA+G). Remote EHR integration of computable guidelines was via a microservice architecture based on HL7 FHIR and CDS Hooks. A prototype integration was developed to manage chronic obstructive pulmonary disease (COPD) with comorbid cardiovascular or chronic kidney diseases, and a mixed-methods evaluation was conducted with 20 simulated cases and five pulmonologists.<h4>Results</h4>Pulmonologists agreed 97% of the time with the GOLD-based COPD symptom severity assessment assigned to each patient by the CDSS, and 98% of the time with one of the proposed COPD care plans. Comments were favourable on the principles of explainable argumentation; inclusion of additional co-morbidities was suggested in the future along with customisation of the level of explanation with expertise.<h4>Conclusion</h4>An ontological model provided a flexible means of providing argumentation and explainable artificial intelligence for a long-term condition. Extension to other guidelines and multiple co-morbidities is needed to test the approach further.",,doi:https://doi.org/10.1002/lrh2.10391; html:https://europepmc.org/articles/PMC11019374; pdf:https://europepmc.org/articles/PMC11019374?pdf=render
-37293269,https://doi.org/10.1140/epjds/s13688-023-00394-6,Do poverty and wealth look the same the world over? A comparative study of 12 cities from five high-income countries using street images.,"Suel E, Muller E, Bennett JE, Blakely T, Doyle Y, Lynch J, Mackenbach JD, Middel A, Mizdrak A, Nathvani R, Brauer M, Ezzati M.",,EPJ data science,2023,2023-06-07,Y,Computer vision; Visual Similarity; Urban Inequalities; Street Images,,,"Urbanization and inequalities are two of the major policy themes of our time, intersecting in large cities where social and economic inequalities are particularly pronounced. Large scale street-level images are a source of city-wide visual information and allow for comparative analyses of multiple cities. Computer vision methods based on deep learning applied to street images have been shown to successfully measure inequalities in socioeconomic and environmental features, yet existing work has been within specific geographies and have not looked at how visual environments compare across different cities and countries. In this study, we aim to apply existing methods to understand whether, and to what extent, poor and wealthy groups live in visually similar neighborhoods across cities and countries. We present novel insights on similarity of neighborhoods using street-level images and deep learning methods. We analyzed 7.2 million images from 12 cities in five high-income countries, home to more than 85 million people: Auckland (New Zealand), Sydney (Australia), Toronto and Vancouver (Canada), Atlanta, Boston, Chicago, Los Angeles, New York, San Francisco, and Washington D.C. (United States of America), and London (United Kingdom). Visual features associated with neighborhood disadvantage are more distinct and unique to each city than those associated with affluence. For example, from what is visible from street images, high density poor neighborhoods located near the city center (e.g., in London) are visually distinct from poor suburban neighborhoods characterized by lower density and lower accessibility (e.g., in Atlanta). This suggests that differences between two cities is also driven by historical factors, policies, and local geography. Our results also have implications for image-based measures of inequality in cities especially when trained on data from cities that are visually distinct from target cities. We showed that these are more prone to errors for disadvantaged areas especially when transferring across cities, suggesting more attention needs to be paid to improving methods for capturing heterogeneity in poor environment across cities around the world.<h4>Supplementary information</h4>The online version contains supplementary material available at 10.1140/epjds/s13688-023-00394-6.",,pdf:https://epjdatascience.springeropen.com/counter/pdf/10.1140/epjds/s13688-023-00394-6; doi:https://doi.org/10.1140/epjds/s13688-023-00394-6; html:https://europepmc.org/articles/PMC10245348; pdf:https://europepmc.org/articles/PMC10245348?pdf=render
 39081663,https://doi.org/10.1089/neur.2023.0111,The Australian Traumatic Brain Injury Initiative: Systematic Review of Clinical Factors Associated with Outcomes in People with Moderate-Severe Traumatic Brain Injury.,"McKimmie A, Keeves J, Gadowski A, Bagg MK, Antonic-Baker A, Hicks AJ, Hill R, Clarke N, Holland A, Veitch B, Fatovich D, Reeder S, Romero L, Ponsford JL, Lannin NA, O'Brien TJ, Cooper DJ, Rushworth N, Fitzgerald M, Gabbe BJ, Cameron PA, Australian Traumatic Brain Injury Initiative Investigators**, Australian Traumatic Brain Injury Initiative Investigators.",,Neurotrauma reports,2024,2024-07-04,N,Systematic review; Glasgow coma scale; Physical Examination; Critical Care; Emergency Medical Services; Vital Signs; Trauma Severity Indices; Multiple Trauma; Common Data Elements; Traumatic Brain Injuries; Health Care Outcome Assessment; Mesh Term,,,"The aim of the Australian Traumatic Brain Injury Initiative (AUS-TBI) is to design a data dictionary to inform data collection and facilitate prediction of outcomes for moderate-severe traumatic brain injury (TBI) across Australia. The process has engaged diverse stakeholders across six areas: social, health, clinical, biological, acute interventions, and long-term outcomes. Here, we report the results of the clinical review. Standardized searches were implemented across databases to April 2022. English-language reports of studies evaluating an association between a clinical factor and any clinical outcome in at least 100 patients with moderate-severe TBI were included. Abstracts, and full-text records, were independently screened by at least two reviewers in Covidence. The findings were assessed through a consensus process to determine inclusion in the AUS-TBI data resource. The searches retrieved 22,441 records, of which 1137 were screened at full text and 313 papers were included. The clinical outcomes identified were predominantly measures of survival and disability. The clinical predictors most frequently associated with these outcomes were the Glasgow Coma Scale, pupil reactivity, and blood pressure measures. Following discussion with an expert consensus group, 15 were recommended for inclusion in the data dictionary. This review identified numerous studies evaluating associations between clinical factors and outcomes in patients with moderate-severe TBI. A small number of factors were reported consistently, however, how and when these factors were assessed varied. The findings of this review and the subsequent consensus process have informed the development of an evidence-informed data dictionary for moderate-severe TBI in Australia.",,doi:https://doi.org/10.1089/neur.2023.0111
+38633019,https://doi.org/10.1002/lrh2.10391,ROAD2H: Development and evaluation of an open-source explainable artificial intelligence approach for managing co-morbidity and clinical guidelines.,"Domínguez J, Prociuk D, Marović B, Čyras K, Cocarascu O, Ruiz F, Mi E, Mi E, Ramtale C, Rago A, Darzi A, Toni F, Curcin V, Delaney B.",,Learning health systems,2024,2023-09-12,Y,Clinical Decision Support Systems; Argumentation; Fhir; Cds Hooks; Transition‐based Medical Recommendation Model; Co‐morbidity,,,"<h4>Introduction</h4>Clinical decision support (CDS) systems (CDSSs) that integrate clinical guidelines need to reflect real-world co-morbidity. In patient-specific clinical contexts, transparent recommendations that allow for contraindications and other conflicts arising from co-morbidity are a requirement. In this work, we develop and evaluate a non-proprietary, standards-based approach to the deployment of computable guidelines with explainable argumentation, integrated with a commercial electronic health record (EHR) system in Serbia, a middle-income country in West Balkans.<h4>Methods</h4>We used an ontological framework, the Transition-based Medical Recommendation (TMR) model, to represent, and reason about, guideline concepts, and chose the 2017 International global initiative for chronic obstructive lung disease (GOLD) guideline and a Serbian hospital as the deployment and evaluation site, respectively. To mitigate potential guideline conflicts, we used a TMR-based implementation of the Assumptions-Based Argumentation framework extended with preferences and Goals (ABA+G). Remote EHR integration of computable guidelines was via a microservice architecture based on HL7 FHIR and CDS Hooks. A prototype integration was developed to manage chronic obstructive pulmonary disease (COPD) with comorbid cardiovascular or chronic kidney diseases, and a mixed-methods evaluation was conducted with 20 simulated cases and five pulmonologists.<h4>Results</h4>Pulmonologists agreed 97% of the time with the GOLD-based COPD symptom severity assessment assigned to each patient by the CDSS, and 98% of the time with one of the proposed COPD care plans. Comments were favourable on the principles of explainable argumentation; inclusion of additional co-morbidities was suggested in the future along with customisation of the level of explanation with expertise.<h4>Conclusion</h4>An ontological model provided a flexible means of providing argumentation and explainable artificial intelligence for a long-term condition. Extension to other guidelines and multiple co-morbidities is needed to test the approach further.",,doi:https://doi.org/10.1002/lrh2.10391; html:https://europepmc.org/articles/PMC11019374; pdf:https://europepmc.org/articles/PMC11019374?pdf=render
 33990383,https://doi.org/10.1136/gutjnl-2020-323546,Multicentre derivation and validation of a colitis-associated colorectal cancer risk prediction web tool.,"Curtius K, Kabir M, Al Bakir I, Choi CHR, Hartono JL, Johnson M, East JE, Oxford IBD Cohort Study Investigators, Lindsay JO, Vega R, Thomas-Gibson S, Warusavitarne J, Wilson A, Graham TA, Hart A.",,Gut,2022,2021-05-14,Y,Dysplasia; Ulcerative colitis; Colorectal Cancer; Clinical Decision Making,,,"<h4>Objective</h4>Patients with ulcerative colitis (UC) diagnosed with low-grade dysplasia (LGD) have increased risk of developing advanced neoplasia (AN: high-grade dysplasia or colorectal cancer). We aimed to develop and validate a predictor of AN risk in patients with UC with LGD and create a visual web tool to effectively communicate the risk.<h4>Design</h4>In our retrospective multicentre validated cohort study, adult patients with UC with an index diagnosis of LGD, identified from four UK centres between 2001 and 2019, were followed until progression to AN. In the discovery cohort (n=246), a multivariate risk prediction model was derived from clinicopathological features using Cox regression. Validation used data from three external centres (n=198). The validated model was embedded in a web tool to calculate patient-specific risk.<h4>Results</h4>Four clinicopathological variables were significantly associated with AN progression in the discovery cohort: endoscopically visible LGD >1 cm (HR 2.7; 95% CI 1.2 to 5.9), unresectable or incomplete endoscopic resection (HR 3.4; 95% CI 1.6 to 7.4), moderate/severe histological inflammation within 5 years of LGD diagnosis (HR 3.1; 95% CI 1.5 to 6.7) and multifocality (HR 2.9; 95% CI 1.3 to 6.2). In the validation cohort, this four-variable model accurately predicted future AN cases with overall calibration Observed/Expected=1.01 (95% CI 0.64 to 1.52), and achieved 100% specificity for the lowest risk group over 13 years of available follow-up.<h4>Conclusion</h4>Multicohort validation confirms that patients with large, unresected, multifocal LGD and recent moderate/severe inflammation are at highest risk of developing AN. Personalised risk prediction provided via the Ulcerative Colitis-Cancer Risk Estimator ( <i>www.UC-CaRE.uk</i> ) can support treatment decision-making.",,pdf:https://gut.bmj.com/content/gutjnl/71/4/705.full.pdf; doi:https://doi.org/10.1136/gutjnl-2020-323546; html:https://europepmc.org/articles/PMC8921573; pdf:https://europepmc.org/articles/PMC8921573?pdf=render
+37293269,https://doi.org/10.1140/epjds/s13688-023-00394-6,Do poverty and wealth look the same the world over? A comparative study of 12 cities from five high-income countries using street images.,"Suel E, Muller E, Bennett JE, Blakely T, Doyle Y, Lynch J, Mackenbach JD, Middel A, Mizdrak A, Nathvani R, Brauer M, Ezzati M.",,EPJ data science,2023,2023-06-07,Y,Computer vision; Visual Similarity; Urban Inequalities; Street Images,,,"Urbanization and inequalities are two of the major policy themes of our time, intersecting in large cities where social and economic inequalities are particularly pronounced. Large scale street-level images are a source of city-wide visual information and allow for comparative analyses of multiple cities. Computer vision methods based on deep learning applied to street images have been shown to successfully measure inequalities in socioeconomic and environmental features, yet existing work has been within specific geographies and have not looked at how visual environments compare across different cities and countries. In this study, we aim to apply existing methods to understand whether, and to what extent, poor and wealthy groups live in visually similar neighborhoods across cities and countries. We present novel insights on similarity of neighborhoods using street-level images and deep learning methods. We analyzed 7.2 million images from 12 cities in five high-income countries, home to more than 85 million people: Auckland (New Zealand), Sydney (Australia), Toronto and Vancouver (Canada), Atlanta, Boston, Chicago, Los Angeles, New York, San Francisco, and Washington D.C. (United States of America), and London (United Kingdom). Visual features associated with neighborhood disadvantage are more distinct and unique to each city than those associated with affluence. For example, from what is visible from street images, high density poor neighborhoods located near the city center (e.g., in London) are visually distinct from poor suburban neighborhoods characterized by lower density and lower accessibility (e.g., in Atlanta). This suggests that differences between two cities is also driven by historical factors, policies, and local geography. Our results also have implications for image-based measures of inequality in cities especially when trained on data from cities that are visually distinct from target cities. We showed that these are more prone to errors for disadvantaged areas especially when transferring across cities, suggesting more attention needs to be paid to improving methods for capturing heterogeneity in poor environment across cities around the world.<h4>Supplementary information</h4>The online version contains supplementary material available at 10.1140/epjds/s13688-023-00394-6.",,pdf:https://epjdatascience.springeropen.com/counter/pdf/10.1140/epjds/s13688-023-00394-6; doi:https://doi.org/10.1140/epjds/s13688-023-00394-6; html:https://europepmc.org/articles/PMC10245348; pdf:https://europepmc.org/articles/PMC10245348?pdf=render
 32128788,https://doi.org/10.1111/bjd.18889,The association between partner bereavement and melanoma: cohort studies in the U.K. and Denmark.,"Wong AYS, Frøslev T, Dearing L, Forbes HJ, Mulick A, Mansfield KE, Silverwood RJ, Kjaersgaard A, Sørensen HT, Smeeth L, Lewin A, Schmidt SAJ, Langan SM.",,The British journal of dermatology,2020,2020-03-03,Y,,,,"<h4>Background</h4>Psychological stress is commonly cited as a risk factor for melanoma, but clinical evidence is limited.<h4>Objectives</h4>This study aimed to evaluate the association between partner bereavement and (i) first-time melanoma diagnosis and (ii) mortality in patients with melanoma.<h4>Methods</h4>We conducted two cohort studies using data from the U.K. Clinical Practice Research Datalink (1997-2017) and Danish nationwide registries (1997-2016). In study 1, we compared the risk of first melanoma diagnosis in bereaved vs. matched nonbereaved people using stratified Cox regression. In study 2 we estimated hazard ratios (HRs) for death from melanoma in bereaved compared with nonbereaved individuals with melanoma using Cox regression. We estimated HRs separately for the U.K. and for Denmark, and then pooled the data to perform a random-effects meta-analysis.<h4>Results</h4>In study 1, the pooled adjusted HR for the association between partner bereavement and melanoma diagnosis was 0·88 [95% confidence interval (CI) 0·84-0·92] across the entire follow-up period. In study 2, we observed increased melanoma-specific mortality in people experiencing partner bereavement across the entire follow-up period (HR 1·17, 95% CI 1·06-1·30), with the peak occurring during the first year of follow-up (HR 1·31, 95% CI 1·07-1·60).<h4>Conclusions</h4>We found decreased risk of melanoma diagnosis, but increased mortality associated with partner bereavement. These findings may be partly explained by delayed detection resulting from the loss of a partner who could notice skin changes. Stress may play a role in melanoma progression. Our findings indicate the need for a low threshold for skin examination in individuals whose partners have died. What is already known about this topic? Psychological stress has been proposed as a risk factor for the development and progression of cancer, including melanoma, but evidence is conflicting. Clinical evidence is limited by small sample sizes, potential recall bias associated with self-report, and heterogeneous stress definitions. What does this study add? We found a decreased risk of melanoma diagnosis, but increased mortality associated with partner bereavement. While stress might play a role in the progression of melanoma, an alternative explanation is that bereaved people no longer have a close person to help notice skin changes, leading to delayed melanoma detection. Linked Comment: Talaganis et al. Br J Dermatol 2020; 183:607-608.",,doi:https://doi.org/10.1111/bjd.18889; doi:https://doi.org/10.1111/bjd.18889; html:https://europepmc.org/articles/PMC7587014; pdf:https://europepmc.org/articles/PMC7587014?pdf=render
 37703231,https://doi.org/10.1371/journal.pdig.0000334,A population-based study exploring phenotypic clusters and clinical outcomes in stroke using unsupervised machine learning approach.,"Akyea RK, Ntaios G, Kontopantelis E, Georgiopoulos G, Soria D, Asselbergs FW, Kai J, Weng SF, Qureshi N.",,PLOS digital health,2023,2023-09-13,Y,,,,"Individuals developing stroke have varying clinical characteristics, demographic, and biochemical profiles. This heterogeneity in phenotypic characteristics can impact on cardiovascular disease (CVD) morbidity and mortality outcomes. This study uses a novel clustering approach to stratify individuals with incident stroke into phenotypic clusters and evaluates the differential burden of recurrent stroke and other cardiovascular outcomes. We used linked clinical data from primary care, hospitalisations, and death records in the UK. A data-driven clustering analysis (kamila algorithm) was used in 48,114 patients aged ≥ 18 years with incident stroke, from 1-Jan-1998 to 31-Dec-2017 and no prior history of serious vascular events. Cox proportional hazards regression was used to estimate hazard ratios (HRs) for subsequent adverse outcomes, for each of the generated clusters. Adverse outcomes included coronary heart disease (CHD), recurrent stroke, peripheral vascular disease (PVD), heart failure, CVD-related and all-cause mortality. Four distinct phenotypes with varying underlying clinical characteristics were identified in patients with incident stroke. Compared with cluster 1 (n = 5,201, 10.8%), the risk of composite recurrent stroke and CVD-related mortality was higher in the other 3 clusters (cluster 2 [n = 18,655, 38.8%]: hazard ratio [HR], 1.07; 95% CI, 1.02-1.12; cluster 3 [n = 10,244, 21.3%]: HR, 1.20; 95% CI, 1.14-1.26; and cluster 4 [n = 14,014, 29.1%]: HR, 1.44; 95% CI: 1.37-1.50). Similar trends in risk were observed for composite recurrent stroke and all-cause mortality outcome, and subsequent recurrent stroke outcome. However, results were not consistent for subsequent risk in CHD, PVD, heart failure, CVD-related mortality, and all-cause mortality. In this proof of principle study, we demonstrated how a heterogenous population of patients with incident stroke can be stratified into four relatively homogenous phenotypes with differential risk of recurrent and major cardiovascular outcomes. This offers an opportunity to revisit the stratification of care for patients with incident stroke to improve patient outcomes.",,pdf:https://journals.plos.org/digitalhealth/article/file?id=10.1371/journal.pdig.0000334&type=printable; doi:https://doi.org/10.1371/journal.pdig.0000334; html:https://europepmc.org/articles/PMC10499205; pdf:https://europepmc.org/articles/PMC10499205?pdf=render
 33653753,https://doi.org/10.1136/bmjopen-2020-043290,Temporal trends in heart failure medication prescription in a population-based cohort study.,"Uijl A, Vaartjes I, Denaxas S, Hemingway H, Shah A, Cleland J, Grobbee D, Hoes A, Asselbergs FW, Koudstaal S.",,BMJ open,2021,2021-03-02,Y,Heart Failure; Public Health; Cardiac Epidemiology,,,"<h4>Objective</h4>We examined temporal heart failure (HF) prescription patterns in a large representative sample of real-world patients in the UK, using electronic health records (EHR).<h4>Methods</h4>From primary and secondary care EHR, we identified 85 732 patients with a HF diagnosis between 2002 and 2015. Almost 50% of patients with HF were women and the median age was 79.1 (IQR 70.2-85.7) years, with age at diagnosis increasing over time.<h4>Results</h4>We found several trends in pharmacological HF management, including increased beta blocker prescriptions over time (29% in 2002-2005 and 54% in 2013-2015), which was not observed for mineralocorticoid receptor-antagonists (MR-antagonists) (18% in 2002-2005 and 18% in 2013-2015); higher prescription rates of loop diuretics in women and elderly patients together with lower prescription rates of angiotensin-converting enzyme inhibitors and/or angiotensin II receptor blockers, beta blockers or MR-antagonists in these patients; little change in medication prescription rates occurred after 6 months of HF diagnosis and, finally, patients hospitalised for HF who had no recorded follow-up in primary care had considerably lower prescription rates compared with patients with a HF diagnosis in primary care with or without HF hospitalisation.<h4>Conclusion</h4>In the general population, the use of MR-antagonists for HF remained low and did not change throughout 13 years of follow-up. For most patients, few changes were seen in pharmacological management of HF in the 6 months following diagnosis.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/3/e043290.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-043290; html:https://europepmc.org/articles/PMC7929882; pdf:https://europepmc.org/articles/PMC7929882?pdf=render
+32249120,https://doi.org/10.1016/j.schres.2020.03.044,"Area deprivation, urbanicity, severe mental illness and social drift - A population-based linkage study using routinely collected primary and secondary care data.","Lee SC, DelPozo-Banos M, Lloyd K, Jones I, Walters JTR, Owen MJ, O'Donovan M, John A.",,Schizophrenia research,2020,2020-04-02,N,Schizophrenia; Bipolar disorder; Deprivation; Severe Mental Illness; Urbanicity; Social Drift,Improving Public Health,mental health,"We investigated whether associations between area deprivation, urbanicity and elevated risk of severe mental illnesses (SMIs, including schizophrenia and bipolar disorder) is accounted for by social drift or social causation. We extracted primary and secondary care electronic health records from 2004 to 2015 from a population of 3.9 million. We identified prevalent and incident individuals with SMIs and their level of deprivation and urbanicity using the Welsh Index of Multiple Deprivation (WIMD) and urban/rural indicator. The presence of social drift was determined by whether odds ratios (ORs) from logistic regression is greater than the incidence rate ratios (IRRs) from Poisson regression. Additionally, we performed longitudinal analysis to measure the proportion of change in deprivation level and rural/urban residence 10 years after an incident diagnosis of SMI and compared it to the general population using standardised rate ratios (SRRs). Prevalence and incidence of SMIs were significantly associated with deprivation and urbanicity (all ORs and IRRs significantly >1). ORs and IRRs were similar across all conditions and cohorts (ranging from 1.1 to 1.4). Results from the longitudinal analysis showed individuals with SMIs are more likely to move compared to the general population. However, they did not preferentially move to more deprived or urban areas. There was little evidence of downward social drift over a 10-year period. These findings have implications for the allocation of resources, service configuration and access to services in deprived communities, as well as, for broader public health interventions addressing poverty, and social and environmental contexts.",,doi:https://doi.org/10.1016/j.schres.2020.03.044; doi:https://doi.org/10.1016/j.schres.2020.03.044
 31744503,https://doi.org/10.1186/s12916-019-1438-y,"Bleeding in cardiac patients prescribed antithrombotic drugs: electronic health record phenotyping algorithms, incidence, trends and prognosis.","Pasea L, Chung SC, Pujades-Rodriguez M, Shah AD, Alvarez-Madrazo S, Allan V, Teo JT, Bean D, Sofat R, Dobson R, Banerjee A, Patel RS, Timmis A, Denaxas S, Hemingway H.",,BMC medicine,2019,2019-11-20,Y,Phenotype; Bleeding; Prognosis; Antithrombotic Therapy; Electronic Health Records,The Human Phenome,,"<h4>Background</h4>Clinical guidelines and public health authorities lack recommendations on scalable approaches to defining and monitoring the occurrence and severity of bleeding in populations prescribed antithrombotic therapy.<h4>Methods</h4>We examined linked primary care, hospital admission and death registry electronic health records (CALIBER 1998-2010, England) of patients with newly diagnosed atrial fibrillation, acute myocardial infarction, unstable angina or stable angina with the aim to develop algorithms for bleeding events. Using the developed bleeding phenotypes, Kaplan-Meier plots were used to estimate the incidence of bleeding events and we used Cox regression models to assess the prognosis for all-cause mortality, atherothrombotic events and further bleeding.<h4>Results</h4>We present electronic health record phenotyping algorithms for bleeding based on bleeding diagnosis in primary or hospital care, symptoms, transfusion, surgical procedures and haemoglobin values. In validation of the phenotype, we estimated a positive predictive value of 0.88 (95% CI 0.64, 0.99) for hospitalised bleeding. Amongst 128,815 patients, 27,259 (21.2%) had at least 1 bleeding event, with 5-year risks of bleeding of 29.1%, 21.9%, 25.3% and 23.4% following diagnoses of atrial fibrillation, acute myocardial infarction, unstable angina and stable angina, respectively. Rates of hospitalised bleeding per 1000 patients more than doubled from 1.02 (95% CI 0.83, 1.22) in January 1998 to 2.68 (95% CI 2.49, 2.88) in December 2009 coinciding with the increased rates of antiplatelet and vitamin K antagonist prescribing. Patients with hospitalised bleeding and primary care bleeding, with or without markers of severity, were at increased risk of all-cause mortality and atherothrombotic events compared to those with no bleeding. For example, the hazard ratio for all-cause mortality was 1.98 (95% CI 1.86, 2.11) for primary care bleeding with markers of severity and 1.99 (95% CI 1.92, 2.05) for hospitalised bleeding without markers of severity, compared to patients with no bleeding.<h4>Conclusions</h4>Electronic health record bleeding phenotyping algorithms offer a scalable approach to monitoring bleeding in the population. Incidence of bleeding has doubled in incidence since 1998, affects one in four cardiovascular disease patients, and is associated with poor prognosis. Efforts are required to tackle this iatrogenic epidemic.",A phenotyping algorithm is presented to monitor bleeding in primary and hospital care. Model is well presented in the document and has potential to be scalable and applied to other conditions.,pdf:https://bmcmedicine.biomedcentral.com/track/pdf/10.1186/s12916-019-1438-y; doi:https://doi.org/10.1186/s12916-019-1438-y; html:https://europepmc.org/articles/PMC6864929; pdf:https://europepmc.org/articles/PMC6864929?pdf=render
 35642867,https://doi.org/10.1111/bjhp.12606,"Perceived threat of COVID-19, attitudes towards vaccination, and vaccine hesitancy: A prospective longitudinal study in the UK.","Phillips R, Gillespie D, Hallingberg B, Evans J, Taiyari K, Torrens-Burton A, Cannings-John R, Williams D, Sheils E, Ashfield-Watt P, Akbari A, Hughes K, Thomas-Jones E, James D, Wood F.",,British journal of health psychology,2022,2022-06-01,Y,Risk Perception; Behaviour Change; Vaccine Hesitancy; Covid-19; Sars Cov2,,,"<h4>Objectives</h4>Using the Health Belief Model as a conceptual framework, we investigated the association between attitudes towards COVID-19, COVID-19 vaccinations, and vaccine hesitancy and change in these variables over a 9-month period in a UK cohort.<h4>Methods</h4>The COPE study cohort (n = 11,113) was recruited via an online survey at enrolment in March/April 2020. The study was advertised via the HealthWise Wales research registry and social media. Follow-up data were available for 6942 people at 3 months (June/July 2020) and 5037 at 12 months (March/April 2021) post-enrolment. Measures included demographics, perceived threat of COVID-19, perceived control, intention to accept or decline a COVID-19 vaccination, and attitudes towards vaccination. Logistic regression models were fitted cross-sectionally at 3 and 12 months to assess the association between motivational factors and vaccine hesitancy. Longitudinal changes in motivational variables for vaccine-hesitant and non-hesitant groups were examined using mixed-effect analysis of variance models.<h4>Results</h4>Fear of COVID-19, perceived susceptibility to COVID-19, and perceived personal control over COVID-19 infection transmission decreased between the 3- and 12-month surveys. Vaccine hesitancy at 12 months was independently associated with low fear of the disease and more negative attitudes towards COVID-19 vaccination. Specific barriers to COVID-19 vaccine uptake included concerns about safety and efficacy in light of its rapid development, mistrust of government and pharmaceutical companies, dislike of coercive policies, and perceived lack of relaxation in COVID-19-related restrictions as the vaccination programme progressed.<h4>Conclusions</h4>Decreasing fear of COVID-19, perceived susceptibility to the disease, and perceptions of personal control over reducing infection-transmission may impact future COVID-19 vaccination uptake.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa60128/Download/60128__24479__4d74009536e649b0b17180e2bfd80435.pdf; doi:https://doi.org/10.1111/bjhp.12606; html:https://europepmc.org/articles/PMC9347957; pdf:https://europepmc.org/articles/PMC9347957?pdf=render
-32249120,https://doi.org/10.1016/j.schres.2020.03.044,"Area deprivation, urbanicity, severe mental illness and social drift - A population-based linkage study using routinely collected primary and secondary care data.","Lee SC, DelPozo-Banos M, Lloyd K, Jones I, Walters JTR, Owen MJ, O'Donovan M, John A.",,Schizophrenia research,2020,2020-04-02,N,Schizophrenia; Bipolar disorder; Deprivation; Severe Mental Illness; Urbanicity; Social Drift,Improving Public Health,mental health,"We investigated whether associations between area deprivation, urbanicity and elevated risk of severe mental illnesses (SMIs, including schizophrenia and bipolar disorder) is accounted for by social drift or social causation. We extracted primary and secondary care electronic health records from 2004 to 2015 from a population of 3.9 million. We identified prevalent and incident individuals with SMIs and their level of deprivation and urbanicity using the Welsh Index of Multiple Deprivation (WIMD) and urban/rural indicator. The presence of social drift was determined by whether odds ratios (ORs) from logistic regression is greater than the incidence rate ratios (IRRs) from Poisson regression. Additionally, we performed longitudinal analysis to measure the proportion of change in deprivation level and rural/urban residence 10 years after an incident diagnosis of SMI and compared it to the general population using standardised rate ratios (SRRs). Prevalence and incidence of SMIs were significantly associated with deprivation and urbanicity (all ORs and IRRs significantly >1). ORs and IRRs were similar across all conditions and cohorts (ranging from 1.1 to 1.4). Results from the longitudinal analysis showed individuals with SMIs are more likely to move compared to the general population. However, they did not preferentially move to more deprived or urban areas. There was little evidence of downward social drift over a 10-year period. These findings have implications for the allocation of resources, service configuration and access to services in deprived communities, as well as, for broader public health interventions addressing poverty, and social and environmental contexts.",,doi:https://doi.org/10.1016/j.schres.2020.03.044; doi:https://doi.org/10.1016/j.schres.2020.03.044
 30729733,https://doi.org/10.1111/ijpo.12512,Predictors of objectively measured physical activity in 12-month-old infants: A study of linked birth cohort data with electronic health records.,"Raza H, Zhou SM, Todd C, Christian D, Marchant E, Morgan K, Khanom A, Hill R, Lyons RA, Brophy S.",,Pediatric obesity,2019,2019-02-06,Y,Gestation; Infants; postnatal development; Physical Activity,Improving Public Health,,"<h4>Background</h4>Physical activity (PA) levels are associated with long-term health, and levels of PA when young are predictive of adult activity levels.<h4>Objectives</h4>This study examines factors associated with PA levels in 12-month infants.<h4>Method</h4>One hundred forty-one mother-infant pairs were recruited via a longitudinal birth cohort study (April 2010 to March 2013). The PA level was collected using accelerometers and linked to postnatal notes and electronic medical records via the Secure Anonymised Information Linkage databank. Univariable and multivariable linear regressions were used to examine the factors associated with PA levels.<h4>Results</h4>Using univariable analysis, higher PA was associated with the following (P value less than 0.05): being male, larger infant size, healthy maternal blood pressure levels, full-term gestation period, higher consumption of vegetables (infant), lower consumption of juice (infant), low consumption of adult crisps (infant), longer breastfeeding duration, and more movement during sleep (infant) but fewer night wakings. Combined into a multivariable regression model (R<sup>2</sup>  = 0.654), all factors remained significant, showing lower PA levels were associated with female gender, smaller infant, preterm birth, higher maternal blood pressure, low vegetable consumption, high crisp consumption, and less night movement.<h4>Conclusion</h4>The PA levels of infants were strongly associated with both gestational and postnatal environmental factors. Healthy behaviours appear to cluster, and a healthy diet was associated with a more active infant. Boys were substantially more active than girls, even at age 12 months. These findings can help inform interventions to promote healthier lives for infants and to understand the determinants of their PA levels.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/ijpo.12512; doi:https://doi.org/10.1111/ijpo.12512; html:https://europepmc.org/articles/PMC6563068; pdf:https://europepmc.org/articles/PMC6563068?pdf=render
 39414802,https://doi.org/10.1038/s41597-024-03960-3,CAPTURE-24: A large dataset of wrist-worn activity tracker data collected in the wild for human activity recognition.,"Chan S, Hang Y, Tong C, Acquah A, Schonfeldt A, Gershuny J, Doherty A.",,Scientific data,2024,2024-10-16,Y,,,,"Existing activity tracker datasets for human activity recognition are typically obtained by having participants perform predefined activities in an enclosed environment under supervision. This results in small datasets with a limited number of activities and heterogeneity, lacking the mixed and nuanced movements normally found in free-living scenarios. As such, models trained on laboratory-style datasets may not generalise out of sample. To address this problem, we introduce a new dataset involving wrist-worn accelerometers, wearable cameras, and sleep diaries, enabling data collection for over 24 hours in a free-living setting. The result is CAPTURE-24, a large activity tracker dataset collected in the wild from 151 participants, amounting to 3883 hours of accelerometer data, of which 2562 hours are annotated. CAPTURE-24 is two to three orders of magnitude larger than existing publicly available datasets, which is critical to developing accurate human activity recognition models.",,doi:https://doi.org/10.1038/s41597-024-03960-3; html:https://europepmc.org/articles/PMC11484779; pdf:https://europepmc.org/articles/PMC11484779?pdf=render
 37218687,https://doi.org/10.1093/ehjqcco/qcad029,Sex-based differences in risk factors for incident myocardial infarction and stroke in the UK Biobank.,"Remfry E, Ardissino M, McCracken C, Szabo L, Neubauer S, Harvey NC, Mamas MA, Robson J, Petersen SE, Raisi-Estabragh Z.",,European heart journal. Quality of care & clinical outcomes,2024,2024-03-01,Y,Myocardial infarction; Stroke; Sex differences; risk factors,,,"<h4>Aim</h4>This study examined sex-based differences in associations of vascular risk factors with incident cardiovascular events in the UK Biobank.<h4>Methods</h4>Baseline participant demographic, clinical, laboratory, anthropometric, and imaging characteristics were collected. Multivariable Cox regression was used to estimate independent associations of vascular risk factors with incident myocardial infarction (MI) and ischaemic stroke for men and women. Women-to-men ratios of hazard ratios (RHRs), and related 95% confidence intervals, represent the relative effect-size magnitude by sex.<h4>Results</h4>Among the 363 313 participants (53.5% women), 8470 experienced MI (29.9% women) and 7705 experienced stroke (40.1% women) over 12.66 [11.93, 13.38] years of prospective follow-up. Men had greater risk factor burden and higher arterial stiffness index at baseline. Women had greater age-related decline in aortic distensibility. Older age [RHR: 1.02 (1.01-1.03)], greater deprivation [RHR: 1.02 (1.00-1.03)], hypertension [RHR: 1.14 (1.02-1.27)], and current smoking [RHR: 1.45 (1.27-1.66)] were associated with a greater excess risk of MI in women than men. Low-density lipoprotein cholesterol was associated with excess MI risk in men [RHR: 0.90 (0.84-0.95)] and apolipoprotein A (ApoA) was less protective for MI in women [RHR: 1.65 (1.01-2.71)]. Older age was associated with excess risk of stroke [RHR: 1.01 (1.00-1.02)] and ApoA was less protective for stroke in women [RHR: 2.55 (1.58-4.14)].<h4>Conclusion</h4>Older age, hypertension, and smoking appeared stronger drivers of cardiovascular disease in women, whereas lipid metrics appeared stronger risk determinants for men. These findings highlight the importance of sex-specific preventive strategies and suggest priority targets for intervention in men and women.",,pdf:https://academic.oup.com/ehjqcco/advance-article-pdf/doi/10.1093/ehjqcco/qcad029/50422842/qcad029.pdf; doi:https://doi.org/10.1093/ehjqcco/qcad029; html:https://europepmc.org/articles/PMC10904726; pdf:https://europepmc.org/articles/PMC10904726?pdf=render
 35440465,https://doi.org/10.3399/bjgp.2021.0689,Association between oral anticoagulants and COVID-19-related outcomes: a population-based cohort study.,"Wong AY, Tomlinson L, Brown JP, Elson W, Walker AJ, Schultze A, Morton CE, Evans D, Inglesby P, MacKenna B, Bhaskaran K, Rentsch CT, Powell E, Williamson E, Croker R, Bacon S, Hulme W, Bates C, Curtis HJ, Mehrkar A, Cockburn J, McDonald HI, Mathur R, Wing K, Forbes H, Eggo RM, Evans SJ, Smeeth L, Goldacre B, Douglas IJ, (The OpenSAFELY Collaborative).",,The British journal of general practice : the journal of the Royal College of General Practitioners,2022,2022-06-30,Y,Warfarin; Factor Xa Inhibitors; Dabigatran; Covid-19,,,"<h4>Background</h4>Early evidence has shown that anticoagulant reduces the risk of thrombotic events in those infected with COVID-19. However, evidence of the role of routinely prescribed oral anticoagulants (OACs) in COVID-19 outcomes is limited.<h4>Aim</h4>To investigate the association between OACs and COVID-19 outcomes in those with atrial fibrillation and a CHA<sub>2</sub>DS<sub>2</sub>-VASc score of 2.<h4>Design and setting</h4>On behalf of NHS England, a population-based cohort study was conducted.<h4>Method</h4>The study used primary care data and pseudonymously-linked SARS-CoV-2 antigen testing data, hospital admissions, and death records from England. Cox regression was used to estimate hazard ratios (HRs) for COVID-19 outcomes comparing people with current OAC use versus non-use, accounting for age, sex, comorbidities, other medications, deprivation, and general practice.<h4>Results</h4>Of 71 103 people with atrial fibrillation and a CHA<sub>2</sub>DS<sub>2</sub>-VASc score of 2, there were 52 832 current OAC users and 18 271 non-users. No difference in risk of being tested for SARS-CoV-2 was associated with current use (adjusted HR [aHR] 0.99, 95% confidence interval [CI] = 0.95 to 1.04) versus non-use. A lower risk of testing positive for SARS-CoV-2 (aHR 0.77, 95% CI = 0.63 to 0.95) and a marginally lower risk of COVID-19-related death (aHR, 0.74, 95% CI = 0.53 to 1.04) were associated with current use versus non-use.<h4>Conclusion</h4>Among those at low baseline stroke risk, people receiving OACs had a lower risk of testing positive for SARS-CoV-2 and severe COVID-19 outcomes than non-users; this might be explained by a causal effect of OACs in preventing severe COVID-19 outcomes or unmeasured confounding, including more cautious behaviours leading to reduced infection risk.",,pdf:https://bjgp.org/content/bjgp/early/2022/04/19/BJGP.2021.0689.full.pdf; doi:https://doi.org/10.3399/BJGP.2021.0689; html:https://europepmc.org/articles/PMC9037187; pdf:https://europepmc.org/articles/PMC9037187?pdf=render
 31504435,https://doi.org/10.1093/eurheartj/ehz569,Obesity causes cardiovascular diseases: adding to the weight of evidence.,"Hingorani AD, Finan C, Schmidt AF.",,European heart journal,2020,2020-01-01,N,,,,,,pdf:https://academic.oup.com/eurheartj/article-pdf/41/2/227/31731687/ehz569.pdf; doi:https://doi.org/10.1093/eurheartj/ehz569
-36644660,https://doi.org/10.1177/20552076221128677,Evaluation of prototype risk prediction tools for clinicians and people living with type 2 diabetes in North West London using the think aloud method.,"Gardner C, Wake D, Brodie D, Silverstein A, Young S, Cunningham S, Sainsbury C, Ilia M, Lucas A, Willis T, Halligan J.",,Digital health,2023,2023-01-08,Y,Artificial intelligence; Internet; Diabetes; Qualitative; risk factors; Machine Learning; Health Informatics; Behaviour Change; Personalised Medicine; Digital Health,,,"The prevalence of type 2 diabetes in North West London (NWL) is relatively high compared to other parts of the United Kingdom with outcomes suboptimal. This presents a need for more effective strategies to identify people living with type 2 diabetes who need additional support. An emerging subset of web-based interventions for diabetes self-management and population management has used artificial intelligence and machine learning models to stratify the risk of complications from diabetes and identify patients in need of immediate support. In this study, two prototype risk prediction tools on the MyWay Diabetes and MyWay Clinical platforms were evaluated with six clinicians and six people living with type 2 diabetes in NWL using the think aloud method. The results of the sessions with people living with type 2 diabetes showed that the concept of the tool was intuitive, however, more instruction on how to correctly use the risk prediction tool would be valuable. The feedback from the sessions with clinicians was that the data presented in the tool aligned with the key diabetes targets in NWL, and that this would be useful for identifying and inviting patients to the practice who are overdue for tests and at risk of complications. The findings of the evaluation have been used to support the development of the prototype risk predictions tools. This study demonstrates the value of conducting usability testing on web-based interventions designed to support the targeted management of type 2 diabetes in local communities.",,doi:https://doi.org/10.1177/20552076221128677; doi:https://doi.org/10.1177/20552076221128677; html:https://europepmc.org/articles/PMC9834412; pdf:https://europepmc.org/articles/PMC9834412?pdf=render
 34230034,https://doi.org/10.1136/bmjresp-2021-000967,Increase in recruitment upon integration of trial into a clinical care pathway: an observational study.,"Yip KP, Gompertz S, Snelson C, Willson J, Madathil S, Huq SS, Rauf F, Salmon N, Tengende J, Tracey J, Cooper B, Filby K, Ball S, Parekh D, Dosanjh DPS.",,BMJ open respiratory research,2021,2021-07-01,Y,Covid-19,,,"<h4>Introduction</h4>Many respiratory clinical trials fail to reach their recruitment target and this problem exacerbates existing funding issues. Integration of the clinical trial recruitment process into a clinical care pathway (CCP) may represent an effective way to significantly increase recruitment numbers.<h4>Methods</h4>A respiratory support unit and a CCP for escalation of patients with severe COVID-19 were established on 11 January 2021. The recruitment process for the Randomised Evaluation of COVID-19 Therapy-Respiratory Support trial was integrated into the CCP on the same date. Recruitment data for the trial were collected before and after integration into the CCP.<h4>Results</h4>On integration of the recruitment process into a CCP, there was a significant increase in recruitment numbers. Fifty patients were recruited over 266 days before this process occurred whereas 108 patients were recruited over 49 days after this process. There was a statistically significant increase in both the proportion of recruited patients relative to the number of COVID-19 hospital admissions (change from 2.8% to 9.1%, p<0.0001) and intensive therapy unit admissions (change from 17.8% to 50.2%, p<0.001) over the same period, showing that this increase in recruitment was independent of COVID-19 prevalence.<h4>Discussion</h4>Integrating the trial recruitment process into a CCP can significantly boost recruitment numbers. This represents an innovative model that can be used to maximise recruitment without impacting on the financial and labour costs associated with the running of a respiratory clinical trial.",,pdf:https://bmjopenrespres.bmj.com/content/bmjresp/8/1/e000967.full.pdf; doi:https://doi.org/10.1136/bmjresp-2021-000967; html:https://europepmc.org/articles/PMC8261886; pdf:https://europepmc.org/articles/PMC8261886?pdf=render
+36644660,https://doi.org/10.1177/20552076221128677,Evaluation of prototype risk prediction tools for clinicians and people living with type 2 diabetes in North West London using the think aloud method.,"Gardner C, Wake D, Brodie D, Silverstein A, Young S, Cunningham S, Sainsbury C, Ilia M, Lucas A, Willis T, Halligan J.",,Digital health,2023,2023-01-08,Y,Artificial intelligence; Internet; Diabetes; Qualitative; risk factors; Machine Learning; Health Informatics; Behaviour Change; Personalised Medicine; Digital Health,,,"The prevalence of type 2 diabetes in North West London (NWL) is relatively high compared to other parts of the United Kingdom with outcomes suboptimal. This presents a need for more effective strategies to identify people living with type 2 diabetes who need additional support. An emerging subset of web-based interventions for diabetes self-management and population management has used artificial intelligence and machine learning models to stratify the risk of complications from diabetes and identify patients in need of immediate support. In this study, two prototype risk prediction tools on the MyWay Diabetes and MyWay Clinical platforms were evaluated with six clinicians and six people living with type 2 diabetes in NWL using the think aloud method. The results of the sessions with people living with type 2 diabetes showed that the concept of the tool was intuitive, however, more instruction on how to correctly use the risk prediction tool would be valuable. The feedback from the sessions with clinicians was that the data presented in the tool aligned with the key diabetes targets in NWL, and that this would be useful for identifying and inviting patients to the practice who are overdue for tests and at risk of complications. The findings of the evaluation have been used to support the development of the prototype risk predictions tools. This study demonstrates the value of conducting usability testing on web-based interventions designed to support the targeted management of type 2 diabetes in local communities.",,doi:https://doi.org/10.1177/20552076221128677; doi:https://doi.org/10.1177/20552076221128677; html:https://europepmc.org/articles/PMC9834412; pdf:https://europepmc.org/articles/PMC9834412?pdf=render
 34544691,https://doi.org/10.3399/bjgp.2021.0153,Identifying symptoms associated with diagnosis of pancreatic exocrine and neuroendocrine neoplasms: a nested case-control study of the UK primary care population.,"Liao W, Clift AK, Patone M, Coupland C, González-Izquierdo A, Pereira SP, Hippisley-Cox J.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2021,2021-10-28,Y,Symptom; Early diagnosis; Pancreatic neoplasms; Primary Health Care; Pancreatic Ductal Adenocarcinoma (Pdac); Pancreatic Neuroendocrine Neoplasms (Pnen),,,"<h4>Background</h4>Pancreatic cancer has the worst survival rate among all cancers. Almost 70% of patients in the UK were diagnosed at Stage IV.<h4>Aim</h4>This study aimed to investigate the symptoms associated with the diagnoses of pancreatic ductal adenocarcinoma (PDAC) and pancreatic neuroendocrine neoplasms (PNEN), and comparatively characterise the symptomatology between the two tumour types to inform earlier diagnosis.<h4>Design and setting</h4>A nested case-control study in primary care was conducted using data from the QResearch<sup>®</sup> database. Patients aged ≥25 years and diagnosed with PDAC or PNEN during 2000 to 2019 were included as cases. Up to 10 controls from the same general practice were matched with each case by age, sex, and calendar year using incidence density sampling.<h4>Method</h4>Conditional logistic regression was used to investigate the association between the 42 shortlisted symptoms and the diagnoses of PDAC and (or) PNEN in different timeframes relative to the index date, adjusting for patients' sociodemographic characteristics, lifestyle, and relevant comorbidities.<h4>Results</h4>A total of 23 640 patients were identified as diagnosed with PDAC and 596 with PNEN. Of the symptoms identified, 23 were significantly associated with PDAC, and nine symptoms with PNEN. The two alarm symptoms for both tumours were jaundice and gastrointestinal bleeding. The two newly identified symptoms for PDAC were thirst and dark urine. The risk of unintentional weight loss may be longer than 2 years before the diagnosis of PNEN.<h4>Conclusion</h4>PDAC and PNEN have overlapping symptom profiles. The QCancer<sup>®</sup> (pancreas) risk prediction model could be updated by including the newly identified symptoms and comorbidities, which could help GPs identify high-risk patients for timely investigation in primary care.",,pdf:https://bjgp.org/content/bjgp/71/712/e836.full.pdf; doi:https://doi.org/10.3399/BJGP.2021.0153; html:https://europepmc.org/articles/PMC8463137; pdf:https://europepmc.org/articles/PMC8463137?pdf=render
 36426221,https://doi.org/10.3389/fcvm.2022.1016032,Clinician's guide to trustworthy and responsible artificial intelligence in cardiovascular imaging.,"Szabo L, Raisi-Estabragh Z, Salih A, McCracken C, Ruiz Pujadas E, Gkontra P, Kiss M, Maurovich-Horvath P, Vago H, Merkely B, Lee AM, Lekadir K, Petersen SE.",,Frontiers in cardiovascular medicine,2022,2022-11-08,Y,Artificial intelligence; Trustworthiness; Cardiovascular Imaging; Machine Learning (Ml); Ai Risk,,,"A growing number of artificial intelligence (AI)-based systems are being proposed and developed in cardiology, driven by the increasing need to deal with the vast amount of clinical and imaging data with the ultimate aim of advancing patient care, diagnosis and prognostication. However, there is a critical gap between the development and clinical deployment of AI tools. A key consideration for implementing AI tools into real-life clinical practice is their ""trustworthiness"" by end-users. Namely, we must ensure that AI systems can be trusted and adopted by all parties involved, including clinicians and patients. Here we provide a summary of the concepts involved in developing a ""trustworthy AI system."" We describe the main risks of AI applications and potential mitigation techniques for the wider application of these promising techniques in the context of cardiovascular imaging. Finally, we show why trustworthy AI concepts are important governing forces of AI development.",,pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2022.1016032/pdf; doi:https://doi.org/10.3389/fcvm.2022.1016032; html:https://europepmc.org/articles/PMC9681217; pdf:https://europepmc.org/articles/PMC9681217?pdf=render
-37143831,https://doi.org/10.1183/23120541.00591-2022,Ethnic variation in asthma healthcare utilisation and exacerbation: systematic review and meta-analysis.,"Akin-Imran A, Bajpai A, McCartan D, Heaney LG, Kee F, Redmond C, Busby J.",,ERJ open research,2023,2023-05-02,Y,,,,"<h4>Background</h4>Patients from ethnic minority groups (EMGs) frequently report poorer asthma outcomes; however, a broad synthesis summarising ethnic disparities is yet to be undertaken. What is the magnitude of ethnic disparities in asthma healthcare utilisation, exacerbations and mortality?<h4>Methods</h4>MEDLINE, Embase and Web of Science databases were searched for studies reporting ethnic variation in asthma healthcare outcomes (primary care attendance, exacerbation, emergency department (ED) visits, hospitalisation, hospital readmission, ventilation/intubation and mortality) between White patients and those from EMGs. Estimates were displayed using forest plots and random-effects models were used to calculate pooled estimates. We conducted subgroup analyses to explore heterogeneity, including by specific ethnicity (Black, Hispanic, Asian and other).<h4>Results</h4>65 studies, comprising 699 882 patients, were included. Most studies (92.3%) were conducted in the United States of America (USA). Patients from EMGs had evidence suggestive of lower levels of primary care attendance (OR 0.72, 95% CI 0.48-1.09), but substantially higher ED visits (OR 1.74, 95% CI 1.53-1.98), hospitalisations (OR 1.63, 95% CI 1.48-1.79) and ventilation/intubation (OR 2.67, 95% CI 1.65-4.31) when compared to White patients. In addition, we found evidence suggestive of increased hospital readmissions (OR 1.19, 95% CI 0.90-1.57) and exacerbation rates (OR 1.10, 95% CI 0.94-1.28) among EMGs. No eligible studies explored disparities in mortality. ED visits were much higher among Black and Hispanic patients, while Asian and other ethnicities had similar rates to White patients.<h4>Conclusions</h4>EMGs had higher secondary care utilisation and exacerbations. Despite the global importance of this issue, the majority of studies were performed in the USA. Further research into the causes of these disparities, including whether these vary by specific ethnicity, is required to aid the design of effective interventions.",,pdf:https://openres.ersjournals.com/content/erjor/early/2023/02/16/23120541.00591-2022.full.pdf; doi:https://doi.org/10.1183/23120541.00591-2022; html:https://europepmc.org/articles/PMC10152257; pdf:https://europepmc.org/articles/PMC10152257?pdf=render
 33168126,https://doi.org/10.1192/bjo.2020.42,Impact of schizophrenia genetic liability on the association between schizophrenia and physical illness: data-linkage study.,"Kendall KM, John A, Lee SC, Rees E, Pardiñas AF, Banos MDP, Owen MJ, O'Donovan MC, Kirov G, Lloyd K, Jones I, Legge SE, Walters JTR.",,BJPsych open,2020,2020-11-10,Y,Genetics; Schizophrenia; Physical Health; Psychotic Disorders,,,"<h4>Background</h4>Individuals with schizophrenia are at higher risk of physical illnesses, which are a major contributor to their 20-year reduced life expectancy. It is currently unknown what causes the increased risk of physical illness in schizophrenia.<h4>Aims</h4>To link genetic data from a clinically ascertained sample of individuals with schizophrenia to anonymised National Health Service (NHS) records. To assess (a) rates of physical illness in those with schizophrenia, and (b) whether physical illness in schizophrenia is associated with genetic liability.<h4>Method</h4>We linked genetic data from a clinically ascertained sample of individuals with schizophrenia (Cardiff Cognition in Schizophrenia participants, n = 896) to anonymised NHS records held in the Secure Anonymised Information Linkage (SAIL) databank. Physical illnesses were defined from the General Practice Database and Patient Episode Database for Wales. Genetic liability for schizophrenia was indexed by (a) rare copy number variants (CNVs), and (b) polygenic risk scores.<h4>Results</h4>Individuals with schizophrenia in SAIL had increased rates of epilepsy (standardised rate ratio (SRR) = 5.34), intellectual disability (SRR = 3.11), type 2 diabetes (SRR = 2.45), congenital disorders (SRR = 1.77), ischaemic heart disease (SRR = 1.57) and smoking (SRR = 1.44) in comparison with the general SAIL population. In those with schizophrenia, carrier status for schizophrenia-associated CNVs and neurodevelopmental disorder-associated CNVs was associated with height (P = 0.015-0.017), with carriers being 7.5-7.7 cm shorter than non-carriers. We did not find evidence that the increased rates of poor physical health outcomes in schizophrenia were associated with genetic liability for the disorder.<h4>Conclusions</h4>This study demonstrates the value of and potential for linking genetic data from clinically ascertained research studies to anonymised health records. The increased risk for physical illness in schizophrenia is not caused by genetic liability for the disorder.",,pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/A00360A347FCC91E2E9D0B39FBDCE887/S2056472420000423a.pdf/div-class-title-impact-of-schizophrenia-genetic-liability-on-the-association-between-schizophrenia-and-physical-illness-data-linkage-study-div.pdf; doi:https://doi.org/10.1192/bjo.2020.42; html:https://europepmc.org/articles/PMC7745237; pdf:https://europepmc.org/articles/PMC7745237?pdf=render
-37338108,https://doi.org/10.1093/eurjpc/zwad202,The relevance of competing risk adjustment in cardiovascular risk prediction models for clinical practice.,"Hageman SHJ, Dorresteijn JAN, Pennells L, van Smeden M, Bots ML, Di Angelantonio E, Visseren FLJ.",,European journal of preventive cardiology,2023,2023-11-01,N,Education; Personalized Medicine; Risk Prediction; Competing Risks; Score2,,,"<h4>Background</h4>Many models developed for predicting the risk of cardiovascular disease (CVD) are adjusted for the competing risk of non-CVD mortality, which has been suggested to reduce potential overestimation of cumulative incidence in populations where the risk of competing events is high. The objective was to evaluate and illustrate the clinical impact of competing risk adjustment when deriving a CVD prediction model in a high-risk population.<h4>Methods and results</h4>Individuals with established atherosclerotic CVD were included from the Utrecht Cardiovascular Cohort-Secondary Manifestations of ARTerial disease (UCC-SMART). In 8355 individuals, followed for a median of 8.2 years (IQR 4.2-12.5), two similar prediction models for the estimation of 10-year residual CVD risk were derived: with competing risk adjustment using a Fine and Gray model and without competing risk adjustment using a Cox proportional hazards model. On average, predictions were higher from the Cox model. The Cox model predictions overestimated the cumulative incidence [predicted-observed ratio 1.14 (95% CI 1.09-1.20)], which was most apparent in the highest risk quartiles and in older persons. Discrimination of both models was similar. When determining treatment eligibility on thresholds of predicted risks, more individuals would be treated based on the Cox model predictions. If, for example, individuals with a predicted risk > 20% were considered eligible for treatment, 34% of the population would be treated according to the Fine and Gray model predictions and 44% according to the Cox model predictions.<h4>Interpretation</h4>Individual predictions from the model unadjusted for competing risks were higher, reflecting the different interpretations of both models. For models aiming to accurately predict absolute risks, especially in high-risk populations, competing risk adjustment must be considered.",,doi:https://doi.org/10.1093/eurjpc/zwad202; doi:https://doi.org/10.1093/eurjpc/zwad202
+37143831,https://doi.org/10.1183/23120541.00591-2022,Ethnic variation in asthma healthcare utilisation and exacerbation: systematic review and meta-analysis.,"Akin-Imran A, Bajpai A, McCartan D, Heaney LG, Kee F, Redmond C, Busby J.",,ERJ open research,2023,2023-05-02,Y,,,,"<h4>Background</h4>Patients from ethnic minority groups (EMGs) frequently report poorer asthma outcomes; however, a broad synthesis summarising ethnic disparities is yet to be undertaken. What is the magnitude of ethnic disparities in asthma healthcare utilisation, exacerbations and mortality?<h4>Methods</h4>MEDLINE, Embase and Web of Science databases were searched for studies reporting ethnic variation in asthma healthcare outcomes (primary care attendance, exacerbation, emergency department (ED) visits, hospitalisation, hospital readmission, ventilation/intubation and mortality) between White patients and those from EMGs. Estimates were displayed using forest plots and random-effects models were used to calculate pooled estimates. We conducted subgroup analyses to explore heterogeneity, including by specific ethnicity (Black, Hispanic, Asian and other).<h4>Results</h4>65 studies, comprising 699 882 patients, were included. Most studies (92.3%) were conducted in the United States of America (USA). Patients from EMGs had evidence suggestive of lower levels of primary care attendance (OR 0.72, 95% CI 0.48-1.09), but substantially higher ED visits (OR 1.74, 95% CI 1.53-1.98), hospitalisations (OR 1.63, 95% CI 1.48-1.79) and ventilation/intubation (OR 2.67, 95% CI 1.65-4.31) when compared to White patients. In addition, we found evidence suggestive of increased hospital readmissions (OR 1.19, 95% CI 0.90-1.57) and exacerbation rates (OR 1.10, 95% CI 0.94-1.28) among EMGs. No eligible studies explored disparities in mortality. ED visits were much higher among Black and Hispanic patients, while Asian and other ethnicities had similar rates to White patients.<h4>Conclusions</h4>EMGs had higher secondary care utilisation and exacerbations. Despite the global importance of this issue, the majority of studies were performed in the USA. Further research into the causes of these disparities, including whether these vary by specific ethnicity, is required to aid the design of effective interventions.",,pdf:https://openres.ersjournals.com/content/erjor/early/2023/02/16/23120541.00591-2022.full.pdf; doi:https://doi.org/10.1183/23120541.00591-2022; html:https://europepmc.org/articles/PMC10152257; pdf:https://europepmc.org/articles/PMC10152257?pdf=render
 30969971,https://doi.org/10.1371/journal.pone.0213435,Are active children and young people at increased risk of injuries resulting in hospital admission or accident and emergency department attendance? Analysis of linked cohort and electronic hospital records in Wales and Scotland.,"Griffiths LJ, Cortina-Borja M, Tingay K, Bandyopadhyay A, Akbari A, DeStavola BL, Bedford H, Lyons RA, Dezateux C.",,PloS one,2019,2019-04-10,Y,,Improving Public Health,,"<h4>Introduction</h4>Children and young people (CYP) are encouraged to increase time spent being physically active, especially in moderate and vigorous intensity pursuits. However, there is limited evidence on the prospective association of activity levels with injuries resulting in use of hospital services. We examined the relationship between objectively-measured physical activity (PA) and subsequent injuries resulting in hospital admissions or accident and emergency department (A&E) attendances, using linked electronic hospital records (EHR) from a nationally representative prospective cohort of CYP in Wales and Scotland.<h4>Methods</h4>We analysed accelerometer-based estimates of moderate to vigorous (MVPA) and vigorous PA (VPA) from 1,585 (777 [46%] boys) seven-year-old Millennium Cohort Study members, living in Wales or Scotland, whose parents consented to linkage of cohort records to EHRs up until their 14th birthday. Negative binomial regression models adjusted by potential individual, household and area-level confounders, were fitted to estimate associations between average daily minutes of MVPA, and VPA (in 10-minute increments), and number of injury-related hospital admissions and/or A&E attendances from age nine to 14 years.<h4>Results</h4>CYP spent a median of 59.5 and 18.1 minutes in MVPA and VPA/day respectively, with boys significantly more active than girls; 47.3% of children experienced at least one injury-related admission or A&E attendance during the study period. Rates of injury-related hospital admission and/or A&E attendance were positively associated with MVPA and VPA in boys but not in girls: respective adjusted incidence rate ratios (95% CI) for boys: 1.09 (1.01, 1.17) and 1.16 (1.00, 1.34), and for girls: 0.94 (0.86, 1.03) and 0.85 (0.69, 1.04).<h4>Conclusion</h4>Boys but not girls who engage in more intense PA at age seven years are at higher risk of injury-related hospital admission or A&E attendance when aged nine to 14 years than their less active peers. This may reflect gender differences in the type and associated risks of activities undertaken. EHRs can make a useful contribution to injury surveillance and prevention if routinely augmented with information on context and setting of the injuries sustained. Injury prevention initiatives should not discourage engagement in PA and outdoor play given their over-riding health and social benefits.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0213435&type=printable; doi:https://doi.org/10.1371/journal.pone.0213435; html:https://europepmc.org/articles/PMC6457613; pdf:https://europepmc.org/articles/PMC6457613?pdf=render
+37338108,https://doi.org/10.1093/eurjpc/zwad202,The relevance of competing risk adjustment in cardiovascular risk prediction models for clinical practice.,"Hageman SHJ, Dorresteijn JAN, Pennells L, van Smeden M, Bots ML, Di Angelantonio E, Visseren FLJ.",,European journal of preventive cardiology,2023,2023-11-01,N,Education; Personalized Medicine; Risk Prediction; Competing Risks; Score2,,,"<h4>Background</h4>Many models developed for predicting the risk of cardiovascular disease (CVD) are adjusted for the competing risk of non-CVD mortality, which has been suggested to reduce potential overestimation of cumulative incidence in populations where the risk of competing events is high. The objective was to evaluate and illustrate the clinical impact of competing risk adjustment when deriving a CVD prediction model in a high-risk population.<h4>Methods and results</h4>Individuals with established atherosclerotic CVD were included from the Utrecht Cardiovascular Cohort-Secondary Manifestations of ARTerial disease (UCC-SMART). In 8355 individuals, followed for a median of 8.2 years (IQR 4.2-12.5), two similar prediction models for the estimation of 10-year residual CVD risk were derived: with competing risk adjustment using a Fine and Gray model and without competing risk adjustment using a Cox proportional hazards model. On average, predictions were higher from the Cox model. The Cox model predictions overestimated the cumulative incidence [predicted-observed ratio 1.14 (95% CI 1.09-1.20)], which was most apparent in the highest risk quartiles and in older persons. Discrimination of both models was similar. When determining treatment eligibility on thresholds of predicted risks, more individuals would be treated based on the Cox model predictions. If, for example, individuals with a predicted risk > 20% were considered eligible for treatment, 34% of the population would be treated according to the Fine and Gray model predictions and 44% according to the Cox model predictions.<h4>Interpretation</h4>Individual predictions from the model unadjusted for competing risks were higher, reflecting the different interpretations of both models. For models aiming to accurately predict absolute risks, especially in high-risk populations, competing risk adjustment must be considered.",,doi:https://doi.org/10.1093/eurjpc/zwad202; doi:https://doi.org/10.1093/eurjpc/zwad202
 38784722,https://doi.org/10.1093/jbmrpl/ziae058,"Bone health, cardiovascular disease, and imaging outcomes in UK Biobank: a causal analysis.","Condurache DG, D'Angelo S, Salih AM, Szabo L, McCracken C, Mahmood A, Curtis EM, Altmann A, Petersen SE, Harvey NC, Raisi-Estabragh Z.",,JBMR plus,2024,2024-04-25,Y,Cardiovascular diseases; Osteoporosis; BMD; Bone Health; Cardiovascular Magnetic Resonance; Mendelian Randomization; Cardiovascular Imaging; Heel Ultrasound,,,"This study examined the association of estimated heel bone mineral density (eBMD, derived from quantitative ultrasound) with: (1) prevalent and incident cardiovascular diseases (CVDs: ischemic heart disease (IHD), myocardial infarction (MI), heart failure (HF), non-ischemic cardiomyopathy (NICM), arrhythmia), (2) mortality (all-cause, CVD, IHD), and (3) cardiovascular magnetic resonance (CMR) measures of left ventricular and atrial structure and function and aortic distensibility, in the UK Biobank. Clinical outcomes were ascertained using health record linkage over 12.3 yr of prospective follow-up. Two-sample Mendelian randomization (MR) was conducted to assess causal associations between BMD and CMR metrics using genetic instrumental variables identified from published genome-wide association studies. The analysis included 485 257 participants (55% women, mean age 56.5 <i>±</i> 8.1 yr). Higher heel eBMD was associated with lower odds of all prevalent CVDs considered. The greatest magnitude of effect was seen in association with HF and NICM, where 1-SD increase in eBMD was associated with 15% lower odds of HF and 16% lower odds of NICM. Association between eBMD and incident IHD and MI was non-significant; the strongest relationship was with incident HF (SHR: 0.90 [95% CI, 0.89-0.92]). Higher eBMD was associated with a decreased risk in all-cause, CVD, and IHD mortality, in the fully adjusted model. Higher eBMD was associated with greater aortic distensibility; associations with other CMR metrics were null. Higher heel eBMD is linked to reduced risk of a range of prevalent and incident CVD and mortality outcomes. Although observational analyses suggest associations between higher eBMD and greater aortic compliance, MR analysis did not support a causal relationship between genetically predicted BMD and CMR phenotypes. These findings support the notion that bone-cardiovascular associations reflect shared risk factors/mechanisms rather than direct causal pathways.",,pdf:https://academic.oup.com/jbmrplus/advance-article-pdf/doi/10.1093/jbmrpl/ziae058/57334584/ziae058.pdf; doi:https://doi.org/10.1093/jbmrpl/ziae058; html:https://europepmc.org/articles/PMC11114472; pdf:https://europepmc.org/articles/PMC11114472?pdf=render
+29457906,https://doi.org/10.1021/acs.jproteome.7b00879,Optimized Phenotypic Biomarker Discovery and Confounder Elimination via Covariate-Adjusted Projection to Latent Structures from Metabolic Spectroscopy Data.,"Posma JM, Garcia-Perez I, Ebbels TMD, Lindon JC, Stamler J, Elliott P, Holmes E, Nicholson JK.",,Journal of proteome research,2018,2018-02-27,Y,Chemometrics; multivariate data analysis; Biomarker Discovery; Sampling Bias; Covariate Adjustment; Metabolic Phenotyping; Random Matrix Theory; Reanalysis; Monte Carlo Cross-validation; Confounder Elimination,Applied Analytics,,"Metabolism is altered by genetics, diet, disease status, environment, and many other factors. Modeling either one of these is often done without considering the effects of the other covariates. Attributing differences in metabolic profile to one of these factors needs to be done while controlling for the metabolic influence of the rest. We describe here a data analysis framework and novel confounder-adjustment algorithm for multivariate analysis of metabolic profiling data. Using simulated data, we show that similar numbers of true associations and significantly less false positives are found compared to other commonly used methods. Covariate-adjusted projections to latent structures (CA-PLS) are exemplified here using a large-scale metabolic phenotyping study of two Chinese populations at different risks for cardiovascular disease. Using CA-PLS, we find that some previously reported differences are actually associated with external factors and discover a number of previously unreported biomarkers linked to different metabolic pathways. CA-PLS can be applied to any multivariate data where confounding may be an issue and the confounder-adjustment procedure is translatable to other multivariate regression techniques.",,pdf:https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.7b00879; doi:https://doi.org/10.1021/acs.jproteome.7b00879; html:https://europepmc.org/articles/PMC5891819; pdf:https://europepmc.org/articles/PMC5891819?pdf=render
 35589356,https://doi.org/10.1136/bmjopen-2021-057343,"Linkage of National Congenital Heart Disease Audit data to hospital, critical care and mortality national data sets to enable research focused on quality improvement.","Espuny Pujol F, Pagel C, Brown KL, Doidge JC, Feltbower RG, Franklin RC, Gonzalez-Izquierdo A, Gould DW, Norman LJ, Stickley J, Taylor JA, Crowe S.",,BMJ open,2022,2022-05-19,Y,Congenital heart disease; Audit; Health Informatics; Statistics & Research Methods; Quality In Health Care,,,"<h4>Objectives</h4>To link five national data sets (three registries, two administrative) and create longitudinal healthcare trajectories for patients with congenital heart disease (CHD), describing the quality and the summary statistics of the linked data set.<h4>Design</h4>Bespoke linkage of record-level patient identifiers across five national data sets. Generation of spells of care defined as periods of time-overlapping events across the data sets.<h4>Setting</h4>National Congenital Heart Disease Audit (NCHDA) procedures in public (National Health Service; NHS) hospitals in England and Wales, paediatric and adult intensive care data sets (Paediatric Intensive Care Audit Network; PICANet and the Case Mix Programme from the Intensive Care National Audit & Research Centre; ICNARC-CMP), administrative hospital episodes (hospital episode statistics; HES inpatient, outpatient, accident and emergency; A&E) and mortality registry data.<h4>Participants</h4>Patients with any CHD procedure recorded in NCHDA between April 2000 and March 2017 from public hospitals.<h4>Primary and secondary outcome measures</h4>Primary: number of linked records, number of unique patients and number of generated spells of care. Secondary: quality and completeness of linkage.<h4>Results</h4>There were 143 862 records in NCHDA relating to 96 041 unique patients. We identified 65 797 linked PICANet patient admissions, 4664 linked ICNARC-CMP admissions and over 6 million linked HES episodes of care (1.1M inpatient, 4.7M outpatient). The linked data set had 4 908 153 spells of care after quality checks, with a median (IQR) of 3.4 (1.8-6.3) spells per patient-year. Where linkage was feasible (in terms of year and centre), 95.6% surgical procedure records were linked to a corresponding HES record, 93.9% paediatric (cardiac) surgery procedure records to a corresponding PICANet admission and 76.8% adult surgery procedure records to a corresponding ICNARC-CMP record.<h4>Conclusions</h4>We successfully linked four national data sets to the core data set of all CHD procedures performed between 2000 and 2017. This will enable a much richer analysis of longitudinal patient journeys and outcomes. We hope that our detailed description of the linkage process will be useful to others looking to link national data sets to address important research priorities.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/5/e057343.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-057343; html:https://europepmc.org/articles/PMC9121475; pdf:https://europepmc.org/articles/PMC9121475?pdf=render
 33475522,https://doi.org/10.2196/18229,Risk Factors and Prevalence of Dilated Cardiomyopathy in Sub-Saharan Africa: Protocol for a Systematic Review.,"Fundikira LS, Chillo P, van Laake LW, Mutagaywa RK, Schmidt AF, Kamuhabwa A, Kwesigabo G, Asselbergs FW.",,JMIR research protocols,2021,2021-01-21,Y,Dilated cardiomyopathy; Sub-Saharan Africa; Cardiomyopathy; Cardiovascular risk factors; Heart Failure,,,"<h4>Background</h4>Cardiomyopathies, defined as diseases involving mainly the heart muscles, are linked to an estimated 5.9 of 100,000 deaths globally. In sub-Saharan Africa, cardiomyopathies constitute 21.4% of heart failure cases, with dilated cardiomyopathy (DCM) being the most common form. The etiology of DCM is heterogeneous and is broadly categorized as genetic or nongenetic, as well as a mixed disease in which genetics interact with intrinsic and environmental factors. Factors such as age, gender, family history, and ethnicity are nonmodifiable, whereas modifiable risk factors include poor nutrition, physical inactivity, and excessive alcohol consumption, among others. However, the relative contribution of the different risk factors to the etiology of DCM is not known in sub-Saharan Africa, and the prevalence of DCM among heart failure patients has not been systematically studied in the region.<h4>Objective</h4>The aim of this review is to synthesize available literature from sub-Saharan Africa on the prevalence of DCM among patients with heart failure, as well as the literature on factors associated with DCM. This paper outlines the protocol that will be followed to conduct the systematic review.<h4>Methods</h4>A limited search of the PubMed database will be performed to identify relevant keywords contained in the title, abstract, and subject descriptors using initial search terms ""heart failure,"" ""cardiomyopathy,"" and ""sub-Saharan Africa."" These search terms and their synonyms will then be used in an extensive search in PubMed, and will address the first research question on prevalence. To address the second research question on risk factors, the terms ""heart failure,"" ""cardiomyopathy,"" and ""cardiovascular risk factors"" in ""Sub-Saharan Africa"" will be used, listing them one by one. Articles published from 2000 and in the English language will be included. Indexed articles in PubMed and Embase will be included, as well as the first 300 articles retrieved from a Google Scholar search. Collected data will be organized in Endnote and then uploaded to the Rayyan web app for systematic reviews. Two reviewers will independently select articles against the inclusion criteria. Discrepancies in reviewer selections will be resolved by an arbitrator. PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines for reporting systematic reviews will be applied. A map of sub-Saharan Africa with colors to show disease prevalence in each country will be included. For quantitative data, where possible, odds ratios (for categorical outcome data) or standardized mean differences (for continuous data) and their 95% CIs will be calculated.<h4>Results</h4>The primary outcomes will be the prevalence of DCM among patients with heart failure and cardiovascular risk factors associated with DCM in sub-Saharan Africa. The literature search will begin on January 1, 2021, and data analysis is expected to be completed by April 30, 2021.<h4>Conclusions</h4>This review will provide information on the current status of the prevalence and associated factors of DCM, and possibly identify gaps, including paucity of data or conflicting results that need to be addressed to improve our understanding of DCM in sub-Saharan Africa.<h4>International registered report identifier (irrid)</h4>PRR1-10.2196/18229.",,pdf:https://jmir.org/api/download?alt_name=resprot_v10i1e18229_app1.pdf&filename=7e28e6f3581cda60eb7faa74a1bb7968.pdf; doi:https://doi.org/10.2196/18229; html:https://europepmc.org/articles/PMC7862000
 36991119,https://doi.org/10.1038/s41586-023-05844-9,An atlas of genetic scores to predict multi-omic traits.,"Xu Y, Ritchie SC, Liang Y, Timmers PRHJ, Pietzner M, Lannelongue L, Lambert SA, Tahir UA, May-Wilson S, Foguet C, Johansson Å, Surendran P, Nath AP, Persyn E, Peters JE, Oliver-Williams C, Deng S, Prins B, Luan J, Bomba L, Soranzo N, Di Angelantonio E, Pirastu N, Tai ES, van Dam RM, Parkinson H, Davenport EE, Paul DS, Yau C, Gerszten RE, Mälarstig A, Danesh J, Sim X, Langenberg C, Wilson JF, Butterworth AS, Inouye M.",,Nature,2023,2023-03-29,N,,,,"The use of omic modalities to dissect the molecular underpinnings of common diseases and traits is becoming increasingly common. But multi-omic traits can be genetically predicted, which enables highly cost-effective and powerful analyses for studies that do not have multi-omics<sup>1</sup>. Here we examine a large cohort (the INTERVAL study<sup>2</sup>; n = 50,000 participants) with extensive multi-omic data for plasma proteomics (SomaScan, n = 3,175; Olink, n = 4,822), plasma metabolomics (Metabolon HD4, n = 8,153), serum metabolomics (Nightingale, n = 37,359) and whole-blood Illumina RNA sequencing (n = 4,136), and use machine learning to train genetic scores for 17,227 molecular traits, including 10,521 that reach Bonferroni-adjusted significance. We evaluate the performance of genetic scores through external validation across cohorts of individuals of European, Asian and African American ancestries. In addition, we show the utility of these multi-omic genetic scores by quantifying the genetic control of biological pathways and by generating a synthetic multi-omic dataset of the UK Biobank<sup>3</sup> to identify disease associations using a phenome-wide scan. We highlight a series of biological insights with regard to genetic mechanisms in metabolism and canonical pathway associations with disease; for example, JAK-STAT signalling and coronary atherosclerosis. Finally, we develop a portal ( https://www.omicspred.org/ ) to facilitate public access to all genetic scores and validation results, as well as to serve as a platform for future extensions and enhancements of multi-omic genetic scores.",,pdf:https://www.pure.ed.ac.uk/ws/files/337957796/An_atlas_of_genetic_scores_to_predict_multi_omic_traits_s41586_023_05844_9.pdf; doi:https://doi.org/10.1038/s41586-023-05844-9; html:https://europepmc.org/articles/PMC10323211; pdf:https://europepmc.org/articles/PMC10323211?pdf=render; doi:https://doi.org/10.1038/s41586-023-05844-9
 36744612,https://doi.org/10.1111/ppe.12959,Trends in survival of children with severe congenital heart defects by gestational age at birth: A population-based study using administrative hospital data for England.,"Gimeno L, Brown K, Harron K, Peppa M, Gilbert R, Blackburn R.",,Paediatric and perinatal epidemiology,2023,2023-02-06,Y,Survival analysis; Congenital heart defects; England; trends; Gestational Age; Administrative Data,,,"<h4>Background</h4>Children with congenital heart defects (CHD) are twice as likely as their peers to be born preterm (<37 weeks' gestation), yet descriptions of recent trends in long-term survival by gestational age at birth (GA) are lacking.<h4>Objectives</h4>To quantify changes in survival to age 5 years of children in England with severe CHD by GA.<h4>Methods</h4>We estimated changes in survival to age five of children with severe CHD and all other children born in England between April 2004 and March 2016, overall and by GA-group using linked hospital and mortality records.<h4>Results</h4>Of 5,953,598 livebirths, 5.7% (339,080 of 5,953,598) were born preterm, 0.35% (20,648 of 5,953,598) died before age five and 3.6 per 1000 (21,291 of 5,953,598) had severe CHD. Adjusting for GA, under-five mortality rates fell at a similar rate between 2004-2008 and 2012-2016 for children with severe CHD (adjusted hazard ratio [HR] 0.79, 95% CI 0.71, 0.88) and all other children (HR 0.78, 95% CI 0.76, 0.81). For children with severe CHD, overall survival to age five increased from 87.5% (95% CI 86.6, 88.4) in 2004-2008 to 89.6% (95% CI 88.9, 90.3) in 2012-2016. There was strong evidence for better survival in the ≥39-week group (90.2%, 95% CI 89.1, 91.2 to 93%, 95% CI 92.4, 93.9), weaker evidence at 24-31 and 37-38 weeks and no evidence at 32-36 weeks. We estimate that 51 deaths (95% CI 24, 77) per year in children with severe CHD were averted in 2012-2016 compared to what would have been the case had 2004-2008 mortality rates persisted.<h4>Conclusions</h4>Nine out of 10 children with severe CHD in 2012-2016 survived to age five. The small improvement in survival over the study period was driven by increased survival in term children. Most children with severe CHD are reaching school age and may require additional support by schools and healthcare services.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/ppe.12959; doi:https://doi.org/10.1111/ppe.12959; html:https://europepmc.org/articles/PMC10946523; pdf:https://europepmc.org/articles/PMC10946523?pdf=render
-29457906,https://doi.org/10.1021/acs.jproteome.7b00879,Optimized Phenotypic Biomarker Discovery and Confounder Elimination via Covariate-Adjusted Projection to Latent Structures from Metabolic Spectroscopy Data.,"Posma JM, Garcia-Perez I, Ebbels TMD, Lindon JC, Stamler J, Elliott P, Holmes E, Nicholson JK.",,Journal of proteome research,2018,2018-02-27,Y,Chemometrics; multivariate data analysis; Biomarker Discovery; Sampling Bias; Covariate Adjustment; Metabolic Phenotyping; Random Matrix Theory; Reanalysis; Monte Carlo Cross-validation; Confounder Elimination,Applied Analytics,,"Metabolism is altered by genetics, diet, disease status, environment, and many other factors. Modeling either one of these is often done without considering the effects of the other covariates. Attributing differences in metabolic profile to one of these factors needs to be done while controlling for the metabolic influence of the rest. We describe here a data analysis framework and novel confounder-adjustment algorithm for multivariate analysis of metabolic profiling data. Using simulated data, we show that similar numbers of true associations and significantly less false positives are found compared to other commonly used methods. Covariate-adjusted projections to latent structures (CA-PLS) are exemplified here using a large-scale metabolic phenotyping study of two Chinese populations at different risks for cardiovascular disease. Using CA-PLS, we find that some previously reported differences are actually associated with external factors and discover a number of previously unreported biomarkers linked to different metabolic pathways. CA-PLS can be applied to any multivariate data where confounding may be an issue and the confounder-adjustment procedure is translatable to other multivariate regression techniques.",,pdf:https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.7b00879; doi:https://doi.org/10.1021/acs.jproteome.7b00879; html:https://europepmc.org/articles/PMC5891819; pdf:https://europepmc.org/articles/PMC5891819?pdf=render
-36580444,https://doi.org/10.1371/journal.pmed.1004141,Associations of genetically predicted fatty acid levels across the phenome: A mendelian randomisation study.,"Zagkos L, Dib MJ, Pinto R, Gill D, Koskeridis F, Drenos F, Markozannes G, Elliott P, Zuber V, Tsilidis K, Dehghan A, Tzoulaki I.",,PLoS medicine,2022,2022-12-29,Y,,,,"<h4>Background</h4>Fatty acids are important dietary factors that have been extensively studied for their implication in health and disease. Evidence from epidemiological studies and randomised controlled trials on their role in cardiovascular, inflammatory, and other diseases remains inconsistent. The objective of this study was to assess whether genetically predicted fatty acid concentrations affect the risk of disease across a wide variety of clinical health outcomes.<h4>Methods and findings</h4>The UK Biobank (UKB) is a large study involving over 500,000 participants aged 40 to 69 years at recruitment from 2006 to 2010. We used summary-level data for 117,143 UKB samples (base dataset), to extract genetic associations of fatty acids, and individual-level data for 322,232 UKB participants (target dataset) to conduct our discovery analysis. We studied potentially causal relationships of circulating fatty acids with 845 clinical diagnoses, using mendelian randomisation (MR) approach, within a phenome-wide association study (PheWAS) framework. Regression models in PheWAS were adjusted for sex, age, and the first 10 genetic principal components. External summary statistics were used for replication. When several fatty acids were associated with a health outcome, multivariable MR and MR-Bayesian method averaging (MR-BMA) was applied to disentangle their causal role. Genetic predisposition to higher docosahexaenoic acid (DHA) was associated with cholelithiasis and cholecystitis (odds ratio per mmol/L: 0.76, 95% confidence interval: 0.66 to 0.87). This was supported in replication analysis (FinnGen study) and by the genetically predicted omega-3 fatty acids analyses. Genetically predicted linoleic acid (LA), omega-6, polyunsaturated fatty acids (PUFAs), and total fatty acids (total FAs) showed positive associations with cardiovascular outcomes with support from replication analysis. Finally, higher genetically predicted levels of DHA (0.83, 0.73 to 0.95) and omega-3 (0.83, 0.75 to 0.92) were found to have a protective effect on obesity, which was supported using body mass index (BMI) in the GIANT consortium as replication analysis. Multivariable MR analysis suggested a direct detrimental effect of LA (1.64, 1.07 to 2.50) and omega-6 fatty acids (1.81, 1.06 to 3.09) on coronary heart disease (CHD). MR-BMA prioritised LA and omega-6 fatty acids as the top risk factors for CHD. Although we present a range of sensitivity analyses to the address MR assumptions, horizontal pleiotropy may still bias the reported associations and further evaluation in clinical trials is needed.<h4>Conclusions</h4>Our study suggests potentially protective effects of circulating DHA and omega-3 concentrations on cholelithiasis and cholecystitis and on obesity, highlighting the need to further assess them as prevention treatments in clinical trials. Moreover, our findings do not support the supplementation of unsaturated fatty acids for cardiovascular disease prevention.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004141&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004141; html:https://europepmc.org/articles/PMC9799317; pdf:https://europepmc.org/articles/PMC9799317?pdf=render
 36543768,https://doi.org/10.1038/s41467-022-35321-2,Multi-organ imaging demonstrates the heart-brain-liver axis in UK Biobank participants.,"McCracken C, Raisi-Estabragh Z, Veldsman M, Raman B, Dennis A, Husain M, Nichols TE, Petersen SE, Neubauer S.",,Nature communications,2022,2022-12-21,Y,,,,"Medical imaging provides numerous insights into the subclinical changes that precede serious diseases such as heart disease and dementia. However, most imaging research either describes a single organ system or draws on clinical cohorts with small sample sizes. In this study, we use state-of-the-art multi-organ magnetic resonance imaging phenotypes to investigate cross-sectional relationships across the heart-brain-liver axis in 30,444 UK Biobank participants. Despite controlling for an extensive range of demographic and clinical covariates, we find significant associations between imaging-derived phenotypes of the heart (left ventricular structure, function and aortic distensibility), brain (brain volumes, white matter hyperintensities and white matter microstructure), and liver (liver fat, liver iron and fibroinflammation). Simultaneous three-organ modelling identifies differentially important pathways across the heart-brain-liver axis with evidence of both direct and indirect associations. This study describes a potentially cumulative burden of multiple-organ dysfunction and provides essential insight into multi-organ disease prevention.",,pdf:https://www.nature.com/articles/s41467-022-35321-2.pdf; doi:https://doi.org/10.1038/s41467-022-35321-2; html:https://europepmc.org/articles/PMC9772225; pdf:https://europepmc.org/articles/PMC9772225?pdf=render
 34194954,https://doi.org/10.1002/advs.202100707,Green Algorithms: Quantifying the Carbon Footprint of Computation.,"Lannelongue L, Grealey J, Inouye M.",,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2021,2021-05-02,Y,Climate change; Green Computing; Computational Research,,,"Climate change is profoundly affecting nearly all aspects of life on earth, including human societies, economies, and health. Various human activities are responsible for significant greenhouse gas (GHG) emissions, including data centers and other sources of large-scale computation. Although many important scientific milestones are achieved thanks to the development of high-performance computing, the resultant environmental impact is underappreciated. In this work, a methodological framework to estimate the carbon footprint of any computational task in a standardized and reliable way is presented and metrics to contextualize GHG emissions are defined. A freely available online tool, Green Algorithms (www.green-algorithms.org) is developed, which enables a user to estimate and report the carbon footprint of their computation. The tool easily integrates with computational processes as it requires minimal information and does not interfere with existing code, while also accounting for a broad range of hardware configurations. Finally, the GHG emissions of algorithms used for particle physics simulations, weather forecasts, and natural language processing are quantified. Taken together, this study develops a simple generalizable framework and freely available tool to quantify the carbon footprint of nearly any computation. Combined with recommendations to minimize unnecessary CO<sub>2</sub> emissions, the authors hope to raise awareness and facilitate greener computation.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/advs.202100707; doi:https://doi.org/10.1002/advs.202100707; html:https://europepmc.org/articles/PMC8224424; pdf:https://europepmc.org/articles/PMC8224424?pdf=render
+36580444,https://doi.org/10.1371/journal.pmed.1004141,Associations of genetically predicted fatty acid levels across the phenome: A mendelian randomisation study.,"Zagkos L, Dib MJ, Pinto R, Gill D, Koskeridis F, Drenos F, Markozannes G, Elliott P, Zuber V, Tsilidis K, Dehghan A, Tzoulaki I.",,PLoS medicine,2022,2022-12-29,Y,,,,"<h4>Background</h4>Fatty acids are important dietary factors that have been extensively studied for their implication in health and disease. Evidence from epidemiological studies and randomised controlled trials on their role in cardiovascular, inflammatory, and other diseases remains inconsistent. The objective of this study was to assess whether genetically predicted fatty acid concentrations affect the risk of disease across a wide variety of clinical health outcomes.<h4>Methods and findings</h4>The UK Biobank (UKB) is a large study involving over 500,000 participants aged 40 to 69 years at recruitment from 2006 to 2010. We used summary-level data for 117,143 UKB samples (base dataset), to extract genetic associations of fatty acids, and individual-level data for 322,232 UKB participants (target dataset) to conduct our discovery analysis. We studied potentially causal relationships of circulating fatty acids with 845 clinical diagnoses, using mendelian randomisation (MR) approach, within a phenome-wide association study (PheWAS) framework. Regression models in PheWAS were adjusted for sex, age, and the first 10 genetic principal components. External summary statistics were used for replication. When several fatty acids were associated with a health outcome, multivariable MR and MR-Bayesian method averaging (MR-BMA) was applied to disentangle their causal role. Genetic predisposition to higher docosahexaenoic acid (DHA) was associated with cholelithiasis and cholecystitis (odds ratio per mmol/L: 0.76, 95% confidence interval: 0.66 to 0.87). This was supported in replication analysis (FinnGen study) and by the genetically predicted omega-3 fatty acids analyses. Genetically predicted linoleic acid (LA), omega-6, polyunsaturated fatty acids (PUFAs), and total fatty acids (total FAs) showed positive associations with cardiovascular outcomes with support from replication analysis. Finally, higher genetically predicted levels of DHA (0.83, 0.73 to 0.95) and omega-3 (0.83, 0.75 to 0.92) were found to have a protective effect on obesity, which was supported using body mass index (BMI) in the GIANT consortium as replication analysis. Multivariable MR analysis suggested a direct detrimental effect of LA (1.64, 1.07 to 2.50) and omega-6 fatty acids (1.81, 1.06 to 3.09) on coronary heart disease (CHD). MR-BMA prioritised LA and omega-6 fatty acids as the top risk factors for CHD. Although we present a range of sensitivity analyses to the address MR assumptions, horizontal pleiotropy may still bias the reported associations and further evaluation in clinical trials is needed.<h4>Conclusions</h4>Our study suggests potentially protective effects of circulating DHA and omega-3 concentrations on cholelithiasis and cholecystitis and on obesity, highlighting the need to further assess them as prevention treatments in clinical trials. Moreover, our findings do not support the supplementation of unsaturated fatty acids for cardiovascular disease prevention.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004141&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004141; html:https://europepmc.org/articles/PMC9799317; pdf:https://europepmc.org/articles/PMC9799317?pdf=render
 37395705,https://doi.org/10.1167/tvst.12.7.3,Reliability of Optical Coherence Tomography Angiography Retinal Blood Flow Analyses.,"Courtie EF, Gilani A, Capewell N, Kale AU, Hui BTK, Liu X, Montesano G, Teussink M, Denniston AK, Veenith T, Blanch RJ.",,Translational vision science & technology,2023,2023-07-01,Y,,,,"<h4>Purpose</h4>Investigate the association between the optical coherence tomography angiography (OCTA) metrics derived from different analysis programs to understand the comparability of studies using these different approaches.<h4>Methods</h4>Secondary analysis of a prospective observational study (March 2018-September 2021). Forty-four right eyes and 42 left eyes from 44 patients were included. Patients were either undergoing upper gastrointestinal surgery with a critical care stay planned or were already in the critical care unit with sepsis. OCTA scans were obtained in an ophthalmology department or critical care setting. Fourteen OCTA metrics were compared within and between the programs, and agreement was measured by Pearson's R coefficient and intraclass correlation coefficient.<h4>Results</h4>Correlation was highest between all Heidelberg metrics and Fractalyse (all >0.84), and lowest between Matlab skeletonized or foveal avascular zone metrics and all other measures (e.g., skeletal fractal dimension and vessel density at -0.02). Agreement between eyes was moderate to excellent in all metrics (0.60-0.90).<h4>Conclusions</h4>The significant variability between metrics and programs used for OCTA analysis demonstrates that they are not interchangeable and supports a recommendation for perfusion density metrics to be reported as standard.<h4>Translational relevance</h4>Agreement between different OCTA analyses is variable and not interchangeable. The high agreement between non-skeletonized vessel density metrics suggests that these should be routinely reported.",,doi:https://doi.org/10.1167/tvst.12.7.3; doi:https://doi.org/10.1167/tvst.12.7.3; html:https://europepmc.org/articles/PMC10324418; pdf:https://europepmc.org/articles/PMC10324418?pdf=render
-38091687,https://doi.org/10.1016/j.bjps.2023.10.106,Revisiting basal cell carcinoma clinical margins: Leveraging natural language processing and multivariate analysis with updated Royal College of Pathologists histological reporting standards.,"Ali SR, Dobbs TD, Jovic M, Strafford H, Lacey AS, Williams N, Pickrell WO, Hutchings HA, Whitaker IS.",,"Journal of plastic, reconstructive & aesthetic surgery : JPRAS",2024,2023-10-20,N,multivariate analysis; Royal College Of Pathologists; Basal Cell Carcinoma; Natural Language Processing; Clinical Margins; Histological Reporting Guidelines,,,"<h4>Introduction</h4>Data supporting the current British Association of Dermatologists guidelines for the management of basal cell carcinoma (BCC) are based on historic studies and do not consider the updated Royal College of Pathologists (RCPath) histological reporting standards. The aim of this study was to use natural language processing (NLP)-derived data and undertake a multivariate analysis with updated RCPath standards, providing a contemporary update on the excision margins required to achieve histological clearance in BCC.<h4>Methods</h4>A validated NLP information extraction model was used to perform a rapid multi-centre, pan-specialty, consecutive retrospective analysis of BCCs, managed with surgical excision using a pre-determined clinical margin, over a 17-year period (2004-2021) at Swansea Bay University Health Board. Logistic regression assessed the relationship between the peripheral and deep margins and histological clearance.<h4>Results</h4>We ran our NLP algorithm on 34,955 BCCs. Out of the 1447 BCCs that met the inclusion criteria, the peripheral margin clearance was not influenced by the BCC risk level (p = 0.670). A clinical peripheral margin of 6 mm achieved a 95% histological clearance rate (95% confidence interval [CI], 0.93-0.98). Tumour thickness inversely affected deep-margin histological clearance (OR 0.720, 95% CI, 0.525-0.991, p < 0.05). Depth level 2 had a 97% probability of achieving deep-margin histological clearance across all tumour thicknesses.<h4>Conclusion</h4>Updated RCPath reporting standards minimally impact the peripheral margin histological clearance in BCC. Larger clinical peripheral margins than those indicated by current guidelines may be necessary to achieve excision rates of ≥95%. These findings emphasise the need for continuous reassessment of clinical standards to enhance patient care.",,pdf:http://www.jprasurg.com/article/S1748681523006769/pdf; doi:https://doi.org/10.1016/j.bjps.2023.10.106
 34304048,https://doi.org/10.1016/j.ebiom.2021.103485,Shorter leukocyte telomere length is associated with adverse COVID-19 outcomes: A cohort study in UK Biobank.,"Wang Q, Codd V, Raisi-Estabragh Z, Musicha C, Bountziouka V, Kaptoge S, Allara E, Angelantonio ED, Butterworth AS, Wood AM, Thompson JR, Petersen SE, Harvey NC, Danesh JN, Samani NJ, Nelson CP.",,EBioMedicine,2021,2021-07-23,Y,,,,"Background Older age is the most powerful risk factor for adverse coronavirus disease-19 (COVID-19) outcomes. It is uncertain whether leucocyte telomere length (LTL), previously proposed as a marker of biological age, is also associated with COVID-19 outcomes. Methods We associated LTL values obtained from participants recruited into UK Biobank (UKB) during 2006-2010 with adverse COVID-19 outcomes recorded by 30 November 2020, defined as a composite of any of the following: hospital admission, need for critical care, respiratory support, or mortality. Using information on 130 LTL-associated genetic variants, we conducted exploratory Mendelian randomisation (MR) analyses in UKB to evaluate whether observational associations might reflect cause-and-effect relationships. Findings Of 6775 participants in UKB who tested positive for infection with SARS-CoV-2 in the community, there were 914 (13.5%) with adverse COVID-19 outcomes. The odds ratio (OR) for adverse COVID-19 outcomes was 1·17 (95% CI 1·05-1·30; P = 0·004) per 1-SD shorter usual LTL, after adjustment for age, sex and ethnicity. Similar ORs were observed in analyses that: adjusted for additional risk factors; disaggregated the composite outcome and reduced the scope for selection or collider bias. In MR analyses, the OR for adverse COVID-19 outcomes was directionally concordant but non-significant. Interpretation Shorter LTL is associated with higher risk of adverse COVID-19 outcomes, independent of several major risk factors for COVID-19 including age. Further data are needed to determine whether this association reflects causality. Funding UK Medical Research Council, Biotechnology and Biological Sciences Research Council and British Heart Foundation.",,pdf:http://www.thelancet.com/article/S2352396421002784/pdf; doi:https://doi.org/10.1016/j.ebiom.2021.103485; html:https://europepmc.org/articles/PMC8299112; pdf:https://europepmc.org/articles/PMC8299112?pdf=render
+38091687,https://doi.org/10.1016/j.bjps.2023.10.106,Revisiting basal cell carcinoma clinical margins: Leveraging natural language processing and multivariate analysis with updated Royal College of Pathologists histological reporting standards.,"Ali SR, Dobbs TD, Jovic M, Strafford H, Lacey AS, Williams N, Pickrell WO, Hutchings HA, Whitaker IS.",,"Journal of plastic, reconstructive & aesthetic surgery : JPRAS",2024,2023-10-20,N,multivariate analysis; Royal College Of Pathologists; Basal Cell Carcinoma; Natural Language Processing; Clinical Margins; Histological Reporting Guidelines,,,"<h4>Introduction</h4>Data supporting the current British Association of Dermatologists guidelines for the management of basal cell carcinoma (BCC) are based on historic studies and do not consider the updated Royal College of Pathologists (RCPath) histological reporting standards. The aim of this study was to use natural language processing (NLP)-derived data and undertake a multivariate analysis with updated RCPath standards, providing a contemporary update on the excision margins required to achieve histological clearance in BCC.<h4>Methods</h4>A validated NLP information extraction model was used to perform a rapid multi-centre, pan-specialty, consecutive retrospective analysis of BCCs, managed with surgical excision using a pre-determined clinical margin, over a 17-year period (2004-2021) at Swansea Bay University Health Board. Logistic regression assessed the relationship between the peripheral and deep margins and histological clearance.<h4>Results</h4>We ran our NLP algorithm on 34,955 BCCs. Out of the 1447 BCCs that met the inclusion criteria, the peripheral margin clearance was not influenced by the BCC risk level (p = 0.670). A clinical peripheral margin of 6 mm achieved a 95% histological clearance rate (95% confidence interval [CI], 0.93-0.98). Tumour thickness inversely affected deep-margin histological clearance (OR 0.720, 95% CI, 0.525-0.991, p < 0.05). Depth level 2 had a 97% probability of achieving deep-margin histological clearance across all tumour thicknesses.<h4>Conclusion</h4>Updated RCPath reporting standards minimally impact the peripheral margin histological clearance in BCC. Larger clinical peripheral margins than those indicated by current guidelines may be necessary to achieve excision rates of ≥95%. These findings emphasise the need for continuous reassessment of clinical standards to enhance patient care.",,pdf:http://www.jprasurg.com/article/S1748681523006769/pdf; doi:https://doi.org/10.1016/j.bjps.2023.10.106
 37337639,https://doi.org/10.1002/ctm2.1291,Trans-ethnic polygenic risk scores for body mass index: An international hundred K+ cohorts consortium study.,"Qu HQ, Connolly JJ, Kraft P, Long J, Pereira A, Flatley C, Turman C, Prins B, Mentch F, Lotufo PA, Magnus P, Stampfer MJ, Tamimi R, Eliassen AH, Zheng W, Knudsen GPS, Helgeland O, Butterworth AS, Hakonarson H, Sleiman PM, IHCC consortium.",,Clinical and translational medicine,2023,2023-06-01,Y,Obesity; Population admixture; body mass index; Polygenic Risk Score; Trans-ethnic,,,"<h4>Background</h4>While polygenic risk scores hold significant promise in estimating an individual's risk of developing a complex trait such as obesity, their application in the clinic has, to date, been limited by a lack of data from non-European populations. As a collaboration model of the International Hundred K+ Cohorts Consortium (IHCC), we endeavored to develop a globally applicable trans-ethnic PRS for body mass index (BMI) through this relatively new international effort.<h4>Methods</h4>The polygenic risk score (PRS) model was developed, trained and tested at the Center for Applied Genomics (CAG) of The Children's Hospital of Philadelphia (CHOP) based on a BMI meta-analysis from the GIANT consortium. The validated PRS models were subsequently disseminated to the participating sites. Scores were generated by each site locally on their cohorts and summary statistics returned to CAG for final analysis.<h4>Results</h4>We show that in the absence of a well powered trans-ethnic GWAS from which to derive marker SNPs and effect estimates for PRS, trans-ethnic scores can be generated from European ancestry GWAS using Bayesian approaches such as LDpred, by adjusting the summary statistics using trans-ethnic linkage disequilibrium reference panels. The ported trans-ethnic scores outperform population specific-PRS across all non-European ancestry populations investigated including East Asians and three-way admixed Brazilian cohort.<h4>Conclusions</h4>Here we show that for a truly polygenic trait such as BMI adjusting the summary statistics of a well powered European ancestry study using trans-ethnic LD reference results in a score that is predictive across a range of ancestries including East Asians and three-way admixed Brazilians.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ctm2.1291; doi:https://doi.org/10.1002/ctm2.1291; html:https://europepmc.org/articles/PMC10280047; pdf:https://europepmc.org/articles/PMC10280047?pdf=render
 35271547,https://doi.org/10.1097/ta.0000000000003592,Does patient preference for online or telephone follow-up impact on response rates and data completeness following injury?,"Gabbe BJ, Hart MJ, Brown A, McLellan S, Morgan MJ, Beck B, de Steiger RS, Cameron PA.",,The journal of trauma and acute care surgery,2022,2022-03-08,N,,,,"<h4>Background</h4>Routine collection of patient-reported outcomes is needed to better understand recovery, benchmark between trauma centers and systems, and monitor outcomes over time. A key component of follow-up methodology is the mode of administration of outcome measures with multiple options available. We aimed to quantify patient preference and compare the response rates and data completeness for telephone and online completion in trauma patients.<h4>Methods</h4>A registry-based cohort study of adult (16 years and older) patients registered to the Victorian State Trauma Registry and Victorian Orthopedic Trauma Outcomes Registry from April 2020 to December 2020 was undertaken. Survivors to discharge were contacted by telephone and offered the option of telephone or online completion of 6-month follow-up using the five-level EuroQol five-dimension (EQ-5D-5L) questionnaire and the 12-item World Health Organization Disability Assessment Schedule (WHODAS). The online and telephone groups were compared for differences in characteristics, follow-up rates, and data completeness. Multivariable logistic regression was used to identify predictors of choosing online completion.<h4>Results</h4>Of the 3,886 patients, 51% (n = 1,994) chose online follow-up, and the follow-up rates were lower for online (77%), compared with telephone (89%), follow-up. Younger age, higher socioeconomic status, and preferred language other than English were associated with higher adjusted odds of choosing online completion. Admission to intensive care was associated with lower adjusted odds of choosing online completion. Completion rate for the EQ-5D-5L utility score was 97% for both groups. A valid total 12-WHODAS score could be calculated for 63% of online respondents compared with 86% for the telephone group.<h4>Conclusion</h4>More than half of trauma patients opted for online completion. Completion rates did differ depending on the questionnaire and telephone follow-up rates were higher. Nevertheless, given the wide diversity of the trauma population, the high rate of online uptake, and potential resource constraints, the study findings largely support the use of dual methods for follow-up.<h4>Level of evidence</h4>Prognostic/Epidemiological, Level III.",,doi:https://doi.org/10.1097/TA.0000000000003592
 30999919,https://doi.org/10.1186/s12911-019-0805-0,Identifying clinically important COPD sub-types using data-driven approaches in primary care population based electronic health records.,"Pikoula M, Quint JK, Nissen F, Hemingway H, Smeeth L, Denaxas S.",,BMC medical informatics and decision making,2019,2019-04-18,Y,Cluster analysis; Electronic Health Records; Copd Exacerbations; Copd Epidemiology,The Human Phenome,,"<h4>Background</h4>COPD is a highly heterogeneous disease composed of different phenotypes with different aetiological and prognostic profiles and current classification systems do not fully capture this heterogeneity. In this study we sought to discover, describe and validate COPD subtypes using cluster analysis on data derived from electronic health records.<h4>Methods</h4>We applied two unsupervised learning algorithms (k-means and hierarchical clustering) in 30,961 current and former smokers diagnosed with COPD, using linked national structured electronic health records in England available through the CALIBER resource. We used 15 clinical features, including risk factors and comorbidities and performed dimensionality reduction using multiple correspondence analysis. We compared the association between cluster membership and COPD exacerbations and respiratory and cardiovascular death with 10,736 deaths recorded over 146,466 person-years of follow-up. We also implemented and tested a process to assign unseen patients into clusters using a decision tree classifier.<h4>Results</h4>We identified and characterized five COPD patient clusters with distinct patient characteristics with respect to demographics, comorbidities, risk of death and exacerbations. The four subgroups were associated with 1) anxiety/depression; 2) severe airflow obstruction and frailty; 3) cardiovascular disease and diabetes and 4) obesity/atopy. A fifth cluster was associated with low prevalence of most comorbid conditions.<h4>Conclusions</h4>COPD patients can be sub-classified into groups with differing risk factors, comorbidities, and prognosis, based on data included in their primary care records. The identified clusters confirm findings of previous clustering studies and draw attention to anxiety and depression as important drivers of the disease in young, female patients.",,pdf:https://bmcmedinformdecismak.biomedcentral.com/track/pdf/10.1186/s12911-019-0805-0; doi:https://doi.org/10.1186/s12911-019-0805-0; html:https://europepmc.org/articles/PMC6472089; pdf:https://europepmc.org/articles/PMC6472089?pdf=render
@@ -1382,19 +1384,19 @@ PMC10686417,https://doi.org/,The impact of restricted provision of publicly fund
 37986130,https://doi.org/10.1186/s41512-023-00159-9,An external validation of the Kidney Donor Risk Index in the UK transplant population in the presence of semi-competing events.,"Riley S, Tam K, Tse WY, Connor A, Wei Y.",,Diagnostic and prognostic research,2023,2023-11-21,Y,Survival analysis; Kidney transplantation; Risk Prediction; External Validation; Time-to-event Model; Competing Events,,,"<h4>Background</h4>Transplantation represents the optimal treatment for many patients with end-stage kidney disease. When a donor kidney is available to a waitlisted patient, clinicians responsible for the care of the potential recipient must make the decision to accept or decline the offer based upon complex and variable information about the donor, the recipient and the transplant process. A clinical prediction model may be able to support clinicians in their decision-making. The Kidney Donor Risk Index (KDRI) was developed in the United States to predict graft failure following kidney transplantation. The survival process following transplantation consists of semi-competing events where death precludes graft failure, but not vice-versa.<h4>Methods</h4>We externally validated the KDRI in the UK kidney transplant population and assessed whether validation under a semi-competing risks framework impacted predictive performance. Additionally, we explored whether the KDRI requires updating. We included 20,035 adult recipients of first, deceased donor, single, kidney-only transplants between January 1, 2004, and December 31, 2018, collected by the UK Transplant Registry and held by NHS Blood and Transplant. The outcomes of interest were 1- and 5-year graft failure following transplantation. In light of the semi-competing events, recipient death was handled in two ways: censoring patients at the time of death and modelling death as a competing event. Cox proportional hazard models were used to validate the KDRI when censoring graft failure by death, and cause-specific Cox models were used to account for death as a competing event.<h4>Results</h4>The KDRI underestimated event probabilities for those at higher risk of graft failure. For 5-year graft failure, discrimination was poorer in the semi-competing risks model (0.625, 95% CI 0.611 to 0.640;0.611, 95% CI 0.597 to 0.625), but predictions were more accurate (Brier score 0.117, 95% CI 0.112 to 0.121; 0.114, 95% CI 0.109 to 0.118). Calibration plots were similar regardless of whether the death was modelled as a competing event or not. Updating the KDRI worsened calibration, but marginally improved discrimination.<h4>Conclusions</h4>Predictive performance for 1-year graft failure was similar between death-censored and competing event graft failure, but differences appeared when predicting 5-year graft failure. The updated index did not have superior performance and we conclude that updating the KDRI in the present form is not required.",,doi:https://doi.org/10.1186/s41512-023-00159-9; html:https://europepmc.org/articles/PMC10662562; pdf:https://europepmc.org/articles/PMC10662562?pdf=render
 34781301,https://doi.org/10.1159/000520674,"Identification and Mapping Real-World Data Sources for Heart Failure, Acute Coronary Syndrome, and Atrial Fibrillation.","Studer R, Sartini C, Suzart-Woischnik K, Agrawal R, Natani H, Gill SK, Wirta SB, Asselbergs FW, Dobson R, Denaxas S, Kotecha D.",,Cardiology,2022,2021-11-15,N,Data Sources; cardiovascular; Real-world Data; Real-world Evidence,,,"<h4>Background</h4>Transparent and robust real-world evidence sources are increasingly important for global health, including cardiovascular (CV) diseases. We aimed to identify global real-world data (RWD) sources for heart failure (HF), acute coronary syndrome (ACS), and atrial fibrillation (AF).<h4>Methods</h4>We conducted a systematic review of publications with RWD pertaining to HF, ACS, and AF (2010-2018), generating a list of unique data sources. Metadata were extracted based on the source type (e.g., electronic health records, genomics, and clinical data), study design, population size, clinical characteristics, follow-up duration, outcomes, and assessment of data availability for future studies and linkage.<h4>Results</h4>Overall, 11,889 publications were retrieved for HF, 10,729 for ACS, and 6,262 for AF. From these, 322 (HF), 287 (ACS), and 220 (AF) data sources were selected for detailed review. The majority of data sources had near complete data on demographic variables (HF: 94%, ACS: 99%, and AF: 100%) and considerable data on comorbidities (HF: 77%, ACS: 93%, and AF: 97%). The least reported data categories were drug codes (HF, ACS, and AF: 10%) and caregiver involvement (HF: 6%, ACS: 1%, and AF: 1%). Only a minority of data sources provided information on access to data for other researchers (11%) or whether data could be linked to other data sources to maximize clinical impact (20%). The list and metadata for the RWD sources are publicly available at www.escardio.org/bigdata.<h4>Conclusions</h4>This review has created a comprehensive resource of CV data sources, providing new avenues to improve future real-world research and to achieve better patient outcomes.",,pdf:https://www.karger.com/Article/Pdf/520674; doi:https://doi.org/10.1159/000520674; html:https://europepmc.org/articles/PMC8985014; doi:https://doi.org/10.1159/000520674
 37200150,https://doi.org/10.1210/clinem/dgad276,Preconception Management of Hyperthyroidism and Thyroid Status in Subsequent Pregnancy: A Population-Based Cohort Study.,"Minassian C, Allen LA, Okosieme O, Vaidya B, Taylor P.",,The Journal of clinical endocrinology and metabolism,2023,2023-10-01,Y,Pregnancy; Thyroxine; Hyperthyroidism; Thyroid stimulating hormone; TSH; Thyroid function; Ft3; Ft4; Carbimazole; Tri-iodothyronine; Ptu; Cprd,,,"<h4>Context</h4>Optimal thyroid status in pregnancy is essential in reducing the risk of adverse outcomes. The management of hyperthyroidism in women of reproductive age poses unique challenges and it is unclear how preconception treatment strategies impact on thyroid status in subsequent pregnancy.<h4>Objective</h4>We aimed to determine trends in the management of hyperthyroidism before and during pregnancy and to assess the impact of different preconception treatment strategies on maternal thyroid status.<h4>Methods</h4>We utilized the Clinical Practice Research Datalink database to evaluate all females aged 15-45 years with a clinical diagnosis of hyperthyroidism and a subsequent pregnancy (January 2000 to December 2017). We compared thyroid status in pregnancy according to preconception treatment, namely, (1) antithyroid drugs up to or beyond pregnancy onset, (2) definitive treatment with thyroidectomy or radioiodine before pregnancy, and (3) no treatment at pregnancy onset.<h4>Results</h4>Our study cohort comprised 4712 pregnancies. Thyrotropin (TSH) was measured in only 53.1% of pregnancies, of which 28.1% showed suboptimal thyroid status (TSH >4.0 mU/L or TSH <0.1 mU/L plus FT4 >reference range). Pregnancies with prior definitive treatment were more likely to have suboptimal thyroid status compared with pregnancies starting during antithyroid drug treatment (odds ratio 4.72, 95% CI 3.50-6.36). A steady decline in the use of definitive treatment before pregnancy was observed from 2000 to 2017. One-third (32.6%) of first trimester carbimazole-exposed pregnancies were switched to propylthiouracil while 6.0% of propylthiouracil-exposed pregnancies switched to carbimazole.<h4>Conclusion</h4>The management of women with hyperthyroidism who become pregnant is suboptimal, particularly in those with preconception definitive treatment, and needs urgent improvement. Better thyroid monitoring and prenatal counseling are needed to optimize thyroid status, reduce teratogenic drug exposure, and ultimately reduce the risk of adverse pregnancy outcomes.",,doi:https://doi.org/10.1210/clinem/dgad276; doi:https://doi.org/10.1210/clinem/dgad276; html:https://europepmc.org/articles/PMC10584009
-38528983,https://doi.org/10.3389/fpsyt.2024.1347100,Machine learning in mental health and its relationship with epidemiological practice.,"DelPozo-Banos M, Stewart R, John A.",,Frontiers in psychiatry,2024,2024-03-11,Y,Research methods; Mental health; epidemiology; Machine Learning; Challenges And Opportunities,,,,,pdf:https://www.frontiersin.org/journals/psychiatry/articles/10.3389/fpsyt.2024.1347100/pdf; doi:https://doi.org/10.3389/fpsyt.2024.1347100; html:https://europepmc.org/articles/PMC10961376; pdf:https://europepmc.org/articles/PMC10961376?pdf=render
 34873584,https://doi.org/10.1016/j.eclinm.2021.101212,Disentangling post-vaccination symptoms from early COVID-19.,"Canas LS, Österdahl MF, Deng J, Hu C, Selvachandran S, Polidori L, May A, Molteni E, Murray B, Chen L, Kerfoot E, Klaser K, Antonelli M, Hammers A, Spector T, Ourselin S, Steves C, Sudre CH, Modat M, Duncan EL.",,EClinicalMedicine,2021,2021-12-01,Y,"Vaccination; Side-effects; Early Detection; Mobile Technology; Self-reported Symptoms; Auc, Area Under The Curve; Bmi, Body Mass Index; Ci, Confidence Interval; Roc, Receiver Operating Curve; Lr, Logistic Regression; Iqr, Inter Quartile Range; Rf, Random Forest; Covid-19, Coronavirus Disease 2019; Covid-19 Detection; Rtpcr, Reverse Transcription Polymerase Chain Reaction; Severe Acute Respiratory Syndrome‐Related Coronavirus 2 (Sars-Cov-2); Css, Covid Symptoms Study; Di, Data Invalid; Kcl, King's College London; Lfat, Lateral Flow Antigen Test; Nhs Uk, National Health Service Of The United Kingdom; O-az, Oxford-astrazeneca Adenovirus-vectored Vaccine; Pb, Pfizer-bointech Mrna Vaccine; Sars-cov-2, Severe Acute Respiratory Syndrome-related Coronavirus-2; Uk, United Kingdom Of Great Britain And Nothern Ireland; Bmem, Bayesian Mixed-effect Model",,,"<h4>Background</h4>Identifying and testing individuals likely to have SARS-CoV-2 is critical for infection control, including post-vaccination. Vaccination is a major public health strategy to reduce SARS-CoV-2 infection globally. Some individuals experience systemic symptoms post-vaccination, which overlap with COVID-19 symptoms. This study compared early post-vaccination symptoms in individuals who subsequently tested positive or negative for SARS-CoV-2, using data from the COVID Symptom Study (CSS) app.<h4>Methods</h4>We conducted a prospective observational study in 1,072,313 UK CSS participants who were asymptomatic when vaccinated with Pfizer-BioNTech mRNA vaccine (BNT162b2) or Oxford-AstraZeneca adenovirus-vectored vaccine (ChAdOx1 nCoV-19) between 8 December 2020 and 17 May 2021, who subsequently reported symptoms within seven days (N=362,770) (other than local symptoms at injection site) and were tested for SARS-CoV-2 (N=14,842), aiming to differentiate vaccination side-effects <i>per se</i> from superimposed SARS-CoV-2 infection. The post-vaccination symptoms and SARS-CoV-2 test results were contemporaneously logged by participants. Demographic and clinical information (including comorbidities) were recorded. Symptom profiles in individuals testing positive were compared with a 1:1 matched population testing negative, including using machine learning and multiple models considering UK testing criteria.<h4>Findings</h4>Differentiating post-vaccination side-effects alone from early COVID-19 was challenging, with a sensitivity in identification of individuals testing positive of 0.6 at best. Most of these individuals did not have fever, persistent cough, or anosmia/dysosmia, requisite symptoms for accessing UK testing; and many only had systemic symptoms commonly seen post-vaccination in individuals negative for SARS-CoV-2 (headache, myalgia, and fatigue).<h4>Interpretation</h4>Post-vaccination symptoms <i>per se</i> cannot be differentiated from COVID-19 with clinical robustness, either using symptom profiles or machine-derived models. Individuals presenting with systemic symptoms post-vaccination should be tested for SARS-CoV-2 or quarantining, to prevent community spread.<h4>Funding</h4>UK Government Department of Health and Social Care, Wellcome Trust, UK Engineering and Physical Sciences Research Council, UK National Institute for Health Research, UK Medical Research Council and British Heart Foundation, Chronic Disease Research Foundation, Zoe Limited.",,pdf:https://discovery.ucl.ac.uk/10139946/1/Sudre_PIIS2589537021004934.pdf; doi:https://doi.org/10.1016/j.eclinm.2021.101212; html:https://europepmc.org/articles/PMC8635464; pdf:https://europepmc.org/articles/PMC8635464?pdf=render
-36501061,https://doi.org/10.3390/nu14235031,Associations of Genetically Predicted Vitamin B<sub>12</sub> Status across the Phenome.,"Dib MJ, Ahmadi KR, Zagkos L, Gill D, Morris B, Elliott P, Dehghan A, Tzoulaki I.",,Nutrients,2022,2022-11-26,Y,Vitamin B12; Deficiency; epidemiology; Mendelian Randomisation; Pernicious Anaemia,,,"Variation in vitamin B<sub>12</sub> levels has been associated with a range of diseases across the life-course, the causal nature of which remains elusive. We aimed to interrogate genetically predicted vitamin B<sub>12</sub> status in relation to a plethora of clinical outcomes available in the UK Biobank. Genome-wide association study (GWAS) summary data obtained from a Danish and Icelandic cohort of 45,576 individuals were used to identify 8 genetic variants associated with vitamin B<sub>12</sub> levels, serving as genetic instruments for vitamin B<sub>12</sub> status in subsequent analyses. We conducted a Mendelian randomisation (MR)-phenome-wide association study (PheWAS) of vitamin B<sub>12</sub> status with 945 distinct phenotypes in 439,738 individuals from the UK Biobank using these 8 genetic instruments to proxy alterations in vitamin B<sub>12</sub> status. We used external GWAS summary statistics for replication of significant findings. Correction for multiple testing was taken into consideration using a 5% false discovery rate (FDR) threshold. MR analysis identified an association between higher genetically predicted vitamin B<sub>12</sub> status and lower risk of vitamin B deficiency (including all B vitamin deficiencies), serving as a positive control outcome. We further identified associations between higher genetically predicted vitamin B<sub>12</sub> status and a reduced risk of megaloblastic anaemia (OR = 0.35, 95% CI: 0.20-0.50) and pernicious anaemia (0.29, 0.19-0.45), which was supported in replication analyses. Our study highlights that higher genetically predicted vitamin B<sub>12</sub> status is potentially protective of risk of vitamin B<sub>12</sub> deficiency associated with pernicious anaemia diagnosis, and reduces risk of megaloblastic anaemia. The potential use of genetically predicted vitamin B<sub>12</sub> status in disease diagnosis, progression and management remains to be investigated.",,pdf:https://www.mdpi.com/2072-6643/14/23/5031/pdf?version=1669449806; doi:https://doi.org/10.3390/nu14235031; html:https://europepmc.org/articles/PMC9740080; pdf:https://europepmc.org/articles/PMC9740080?pdf=render
+38528983,https://doi.org/10.3389/fpsyt.2024.1347100,Machine learning in mental health and its relationship with epidemiological practice.,"DelPozo-Banos M, Stewart R, John A.",,Frontiers in psychiatry,2024,2024-03-11,Y,Research methods; Mental health; epidemiology; Machine Learning; Challenges And Opportunities,,,,,pdf:https://www.frontiersin.org/journals/psychiatry/articles/10.3389/fpsyt.2024.1347100/pdf; doi:https://doi.org/10.3389/fpsyt.2024.1347100; html:https://europepmc.org/articles/PMC10961376; pdf:https://europepmc.org/articles/PMC10961376?pdf=render
 36194451,https://doi.org/10.2196/40667,Associations Between Depression Symptom Severity and Daily-Life Gait Characteristics Derived From Long-Term Acceleration Signals in Real-World Settings: Retrospective Analysis.,"Zhang Y, Folarin AA, Sun S, Cummins N, Vairavan S, Qian L, Ranjan Y, Rashid Z, Conde P, Stewart C, Laiou P, Sankesara H, Matcham F, White KM, Oetzmann C, Ivan A, Lamers F, Siddi S, Simblett S, Rintala A, Mohr DC, Myin-Germeys I, Wykes T, Haro JM, Penninx BWJH, Narayan VA, Annas P, Hotopf M, Dobson RJB, RADAR-CNS Consortium.",,JMIR mHealth and uHealth,2022,2022-10-04,Y,Monitoring; Depression; Gait; Mental health; Mobile Phones; Mhealth; Mobile Health; Wearable Devices; Acceleration Signals,,,"<h4>Background</h4>Gait is an essential manifestation of depression. However, the gait characteristics of daily walking and their relationships with depression have yet to be fully explored.<h4>Objective</h4>The aim of this study was to explore associations between depression symptom severity and daily-life gait characteristics derived from acceleration signals in real-world settings.<h4>Methods</h4>We used two ambulatory data sets (N=71 and N=215) with acceleration signals collected by wearable devices and mobile phones, respectively. We extracted 12 daily-life gait features to describe the distribution and variance of gait cadence and force over a long-term period. Spearman coefficients and linear mixed-effects models were used to explore the associations between daily-life gait features and depression symptom severity measured by the 15-item Geriatric Depression Scale (GDS-15) and 8-item Patient Health Questionnaire (PHQ-8) self-reported questionnaires. The likelihood-ratio (LR) test was used to test whether daily-life gait features could provide additional information relative to the laboratory gait features.<h4>Results</h4>Higher depression symptom severity was significantly associated with lower gait cadence of high-performance walking (segments with faster walking speed) over a long-term period in both data sets. The linear regression model with long-term daily-life gait features (R<sup>2</sup>=0.30) fitted depression scores significantly better (LR test P=.001) than the model with only laboratory gait features (R<sup>2</sup>=0.06).<h4>Conclusions</h4>This study indicated that the significant links between daily-life walking characteristics and depression symptom severity could be captured by both wearable devices and mobile phones. The daily-life gait patterns could provide additional information for predicting depression symptom severity relative to laboratory walking. These findings may contribute to developing clinical tools to remotely monitor mental health in real-world settings.",,pdf:https://mhealth.jmir.org/2022/10/e40667/PDF; doi:https://doi.org/10.2196/40667; html:https://europepmc.org/articles/PMC9579931
-36707908,https://doi.org/10.1186/s13643-023-02173-w,A comparison of international modelling methods to evaluate health economics of colorectal cancer screening: a systematic review protocol.,"Adair O, McFerran E, Owen T, McKee C, Lamrock F, Lawler M.",,Systematic reviews,2023,2023-01-27,Y,Screening; Economic evaluation; Colorectal Cancer; Health Economics; Cost-effectiveness Analysis; Quality-adjusted Life Years; Cost-utility; Incremental Cost-effectiveness Ratio; Cost–benefit; Life Years Gained,,,"<h4>Background</h4>Colorectal cancer (CRC) is becoming an increasing health problem worldwide. However, with the help of screening, early diagnosis can reduce incidence and mortality rates. To elevate the economic burden that CRC can cause, cost-effectiveness analysis (CEA) can assist healthcare systems to make screening programmes more cost-effective and prolong survival for early-stage CRC patients. This review aims to identify different CEA modelling methods used internationally to evaluate health economics of CRC screening.<h4>Methods</h4>This review will systematically search electronic databases which include MEDLINE, EMBASE, Web of Science and Scopus. The Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidance recommendations will design the review, and the Consolidated Health Economic Evaluation Reporting Standards (CHEERS) statement will be used to extract relevant data from studies retrieved. Two reviewers will screen through the evidence using the PICOS (Participant, Intervention, Comparators, Outcomes, Study Design) framework, with a third reviewer to settle any disagreements. Once data extraction and quality assessment are complete, the results will be presented qualitatively and tabulated using the CHEERS checklist.<h4>Discussion</h4>The results obtained from the systematic review will highlight how different CRC screening programmes around the world utilise and incorporate health economic modelling methods to be more cost-effective. This information can help modellers develop CEA models which can be adapted to suit the specific screening programmes that they are evaluating.<h4>Systematic review registration</h4>PROSPERO CRD42022296113.",,pdf:https://systematicreviewsjournal.biomedcentral.com/counter/pdf/10.1186/s13643-023-02173-w; doi:https://doi.org/10.1186/s13643-023-02173-w; html:https://europepmc.org/articles/PMC9883863; pdf:https://europepmc.org/articles/PMC9883863?pdf=render
+36501061,https://doi.org/10.3390/nu14235031,Associations of Genetically Predicted Vitamin B<sub>12</sub> Status across the Phenome.,"Dib MJ, Ahmadi KR, Zagkos L, Gill D, Morris B, Elliott P, Dehghan A, Tzoulaki I.",,Nutrients,2022,2022-11-26,Y,Vitamin B12; Deficiency; epidemiology; Mendelian Randomisation; Pernicious Anaemia,,,"Variation in vitamin B<sub>12</sub> levels has been associated with a range of diseases across the life-course, the causal nature of which remains elusive. We aimed to interrogate genetically predicted vitamin B<sub>12</sub> status in relation to a plethora of clinical outcomes available in the UK Biobank. Genome-wide association study (GWAS) summary data obtained from a Danish and Icelandic cohort of 45,576 individuals were used to identify 8 genetic variants associated with vitamin B<sub>12</sub> levels, serving as genetic instruments for vitamin B<sub>12</sub> status in subsequent analyses. We conducted a Mendelian randomisation (MR)-phenome-wide association study (PheWAS) of vitamin B<sub>12</sub> status with 945 distinct phenotypes in 439,738 individuals from the UK Biobank using these 8 genetic instruments to proxy alterations in vitamin B<sub>12</sub> status. We used external GWAS summary statistics for replication of significant findings. Correction for multiple testing was taken into consideration using a 5% false discovery rate (FDR) threshold. MR analysis identified an association between higher genetically predicted vitamin B<sub>12</sub> status and lower risk of vitamin B deficiency (including all B vitamin deficiencies), serving as a positive control outcome. We further identified associations between higher genetically predicted vitamin B<sub>12</sub> status and a reduced risk of megaloblastic anaemia (OR = 0.35, 95% CI: 0.20-0.50) and pernicious anaemia (0.29, 0.19-0.45), which was supported in replication analyses. Our study highlights that higher genetically predicted vitamin B<sub>12</sub> status is potentially protective of risk of vitamin B<sub>12</sub> deficiency associated with pernicious anaemia diagnosis, and reduces risk of megaloblastic anaemia. The potential use of genetically predicted vitamin B<sub>12</sub> status in disease diagnosis, progression and management remains to be investigated.",,pdf:https://www.mdpi.com/2072-6643/14/23/5031/pdf?version=1669449806; doi:https://doi.org/10.3390/nu14235031; html:https://europepmc.org/articles/PMC9740080; pdf:https://europepmc.org/articles/PMC9740080?pdf=render
 34639458,https://doi.org/10.3390/ijerph181910156,Health-Related Quality of Life (HRQoL) Outcomes Following Injury in Childhood and Adolescence Using EuroQol (EQ-5D) Responses with Pooled Longitudinal Data.,"Dipnall JF, Rivara FP, Lyons RA, Ameratunga S, Brussoni M, Lecky FE, Bradley C, Beck B, Lyons J, Schneeberg A, Harrison JE, Gabbe BJ.",,International journal of environmental research and public health,2021,2021-09-27,Y,Trauma; Children; Injury; Pediatric; Adolescents; Disability; Health-related Quality Of Life; Health Outcomes; Eq-5d,,,"<h4>Background</h4>Injury is a leading contributor to the global disease burden in children, affecting their health-related quality of life (HRQoL)-yet valid estimates of burden are absent.<h4>Methods</h4>This study pooled longitudinal data from five cohort studies of pediatric injury survivors (5-17 years) at baseline, 1-, 4-, 6-, 12-, and 24- months (<i>n</i> = 2334). HRQoL post-injury was measured using the 3-level EQ-5D utility score (EQ-5D) and five health states (mobility, self-care, activity, pain, anxiety and depression (anxiety)).<h4>Results</h4>Mean EQ-5D post-injury did not return to baseline level (0.95) by 24 months (0.88) and was lower for females over time (-0.04, 95%CI -0.05, -0.02). A decreased adjusted risk ratio over time (ARR) was observed for intentional injuries (pain: 0.85, 95%CI 0.73,0.98; anxiety: 0.62, 95%CI 0.49,0.78); spinal cord injuries (mobility: 0.61, 95%CI 0.45,0.83), self-care: 0.76, 95%CI 0.63,0.91, activity: 0.64, 95%CI 0.47,0.88); moderate/severe traumatic brain injury (activity: 0.83, 95%CI 0.71,0.96). ARRs were also low for certain fractures, with various health states affected.<h4>Conclusions</h4>HRQoL outcomes over time for children and adolescents post-injury differed across key demographic and injury related attributes. HRQoL did not reach levels consistent with full health by 24 months with recovery plateauing from 6 to 24 months. Tailored interventions are required to respond to the varying post-injury recovery trajectories in this population.",,doi:https://doi.org/10.3390/ijerph181910156; html:https://europepmc.org/articles/PMC8507627; pdf:https://europepmc.org/articles/PMC8507627?pdf=render
 36580301,https://doi.org/10.1161/circgen.121.003542,Sex-Specific Survival Bias and Interaction Modeling in Coronary Artery Disease Risk Prediction.,"Surakka I, Wolford BN, Ritchie SC, Hornsby WE, Sutton NR, Elvenstad Gabrielsen M, Skogholt AH, Thomas L, Inouye M, Hveem K, Willer CJ.",,Circulation. Genomic and precision medicine,2023,2022-12-29,N,Atherosclerosis; Sex; Cardiovascular disease; coronary artery disease; risk,,,"<h4>Background</h4>The 10-year Atherosclerotic Cardiovascular Disease risk score is the standard approach to predict risk of incident cardiovascular events, and recently, addition of coronary artery disease (CAD) polygenic scores has been evaluated. Although age and sex strongly predict the risk of CAD, their interaction with genetic risk prediction has not been systematically examined. This study performed an extensive evaluation of age and sex effects in genetic CAD risk prediction.<h4>Methods</h4>The population-based Norwegian HUNT2 (Trøndelag Health Study 2) cohort of 51 036 individuals was used as the primary dataset. Findings were replicated in the UK Biobank (372 410 individuals). Models for 10-year CAD risk were fitted using Cox proportional hazards, and Harrell concordance index, sensitivity, and specificity were compared.<h4>Results</h4>Inclusion of age and sex interactions of CAD polygenic score to the prediction models increased the C-index and sensitivity by accounting for nonadditive effects of CAD polygenic score and likely countering the observed survival bias in the baseline. The sensitivity for females was lower than males in all models including genetic information. We identified a total of 82.6% of incident CAD cases by using a 2-step approach: (1) Atherosclerotic Cardiovascular Disease risk score (74.1%) and (2) the CAD polygenic score interaction model for those in low clinical risk (additional 8.5%).<h4>Conclusions</h4>These findings highlight the importance and complexity of genetic risk in predicting CAD. There is a need for modeling age- and sex-interaction terms with polygenic scores to optimize detection of individuals at high risk, those who warrant preventive interventions. Sex-specific studies are needed to understand and estimate CAD risk with genetic information.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCGEN.121.003542; doi:https://doi.org/10.1161/CIRCGEN.121.003542; html:https://europepmc.org/articles/PMC10525909; pdf:https://europepmc.org/articles/PMC10525909?pdf=render; doi:https://doi.org/10.1161/circgen.121.003542
+36707908,https://doi.org/10.1186/s13643-023-02173-w,A comparison of international modelling methods to evaluate health economics of colorectal cancer screening: a systematic review protocol.,"Adair O, McFerran E, Owen T, McKee C, Lamrock F, Lawler M.",,Systematic reviews,2023,2023-01-27,Y,Screening; Economic evaluation; Colorectal Cancer; Health Economics; Cost-effectiveness Analysis; Quality-adjusted Life Years; Cost-utility; Incremental Cost-effectiveness Ratio; Cost–benefit; Life Years Gained,,,"<h4>Background</h4>Colorectal cancer (CRC) is becoming an increasing health problem worldwide. However, with the help of screening, early diagnosis can reduce incidence and mortality rates. To elevate the economic burden that CRC can cause, cost-effectiveness analysis (CEA) can assist healthcare systems to make screening programmes more cost-effective and prolong survival for early-stage CRC patients. This review aims to identify different CEA modelling methods used internationally to evaluate health economics of CRC screening.<h4>Methods</h4>This review will systematically search electronic databases which include MEDLINE, EMBASE, Web of Science and Scopus. The Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidance recommendations will design the review, and the Consolidated Health Economic Evaluation Reporting Standards (CHEERS) statement will be used to extract relevant data from studies retrieved. Two reviewers will screen through the evidence using the PICOS (Participant, Intervention, Comparators, Outcomes, Study Design) framework, with a third reviewer to settle any disagreements. Once data extraction and quality assessment are complete, the results will be presented qualitatively and tabulated using the CHEERS checklist.<h4>Discussion</h4>The results obtained from the systematic review will highlight how different CRC screening programmes around the world utilise and incorporate health economic modelling methods to be more cost-effective. This information can help modellers develop CEA models which can be adapted to suit the specific screening programmes that they are evaluating.<h4>Systematic review registration</h4>PROSPERO CRD42022296113.",,pdf:https://systematicreviewsjournal.biomedcentral.com/counter/pdf/10.1186/s13643-023-02173-w; doi:https://doi.org/10.1186/s13643-023-02173-w; html:https://europepmc.org/articles/PMC9883863; pdf:https://europepmc.org/articles/PMC9883863?pdf=render
 39215973,https://doi.org/10.1093/eurheartj/ehae611,Biomarker-based prediction of sinus rhythm in atrial fibrillation patients: the EAST-AFNET 4 biomolecule study.,"Fabritz L, Al-Taie C, Borof K, Breithardt G, Camm AJ, Crijns HJGM, Roth Cardoso V, Chua W, van Elferen S, Eckardt L, Gkoutos G, Goette A, Guasch E, Hatem S, Metzner A, Mont L, Murukutla VA, Obergassel J, Rillig A, Sinner MF, Schnabel RB, Schotten U, Sommerfeld LC, Wienhues-Thelen UH, Zapf A, Zeller T, Kirchhof P.",,European heart journal,2024,2024-08-31,N,Atrial fibrillation; Natriuretic peptides; Risk Score; Rhythm Control; Risk Prediction; Sinus Rhythm; Blood Biomarker; Angiopoietin 2; Bone Morphogenetic Protein 10,,,"<h4>Background and aims</h4>In patients with atrial fibrillation (AF), recurrent AF and sinus rhythm during follow-up are determined by interactions between cardiovascular disease processes and rhythm-control therapy. Predictors of attaining sinus rhythm at follow-up are not well known.<h4>Methods</h4>To quantify the interaction between cardiovascular disease processes and rhythm outcomes, 14 biomarkers reflecting AF-related cardiovascular disease processes in 1586 patients in the EAST-AFNET 4 biomolecule study (71 years old, 46% women) were quantified at baseline. Mixed logistic regression models including clinical features were constructed for each biomarker. Biomarkers were interrogated for interaction with early rhythm control. Outcome was sinus rhythm at 12 months. Results were validated at 24 months and in external datasets.<h4>Results</h4>Higher baseline concentrations of three biomarkers were independently associated with a lower chance of sinus rhythm at 12 months: angiopoietin 2 (ANGPT2) (odds ratio [OR] 0.76 [95% confidence interval 0.65-0.89], p=0.001), bone morphogenetic protein 10 (BMP10) (OR 0.83 [0.71-0.97], p=0.017) and N-terminal pro-B-type natriuretic peptide (NT-proBNP) (OR 0.73 [0.60-0.88], p=0.001). Analysis of rhythm at 24 months confirmed the results. Early rhythm control interacted with the predictive potential of NT-proBNP (pinteraction=0.033). The predictive effect of NT-proBNP was reduced in patients randomized to early rhythm control (usual care: OR 0.64 [0.51-0.80], p<0.001; early rhythm control: OR 0.90 [0.69-1.18], p=0.453). External validation confirmed that low concentrations of ANGPT2, BMP10 and NT-proBNP predict sinus rhythm during follow-up.<h4>Conclusions</h4>Low concentrations of ANGPT2, BMP10 and NT-proBNP identify patients with AF who are likely to attain sinus rhythm during follow-up. The predictive ability of NT-proBNP is attenuated in patients receiving rhythm control.",,doi:https://doi.org/10.1093/eurheartj/ehae611
 33342219,https://doi.org/10.1161/circoutcomes.120.007085,Estimating the Effect of Reduced Attendance at Emergency Departments for Suspected Cardiac Conditions on Cardiac Mortality During the COVID-19 Pandemic.,"Katsoulis M, Gomes M, Lai AG, Henry A, Denaxas S, Lagiou P, Nafilyan V, Humberstone B, Banerjee A, Hemingway H, Lumbers RT.",,Circulation. Cardiovascular quality and outcomes,2021,2020-12-20,Y,"Cardiovascular diseases; Coronavirus; Pandemic; Heart Disease; Death, Sudden, Cardiac",,,,,pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCOUTCOMES.120.007085; doi:https://doi.org/10.1161/CIRCOUTCOMES.120.007085; html:https://europepmc.org/articles/PMC7819531; pdf:https://europepmc.org/articles/PMC7819531?pdf=render
 32979970,https://doi.org/10.1016/s0140-6736(20)31966-8,Models for mortality require tailoring in the context of the COVID-19 pandemic - Authors' reply.,"Banerjee A, Pasea L, Denaxas S, Williams B, Hemingway H.",,"Lancet (London, England)",2020,2020-09-01,Y,,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7515579; doi:https://doi.org/10.1016/S0140-6736(20)31966-8; html:https://europepmc.org/articles/PMC7515579; pdf:https://europepmc.org/articles/PMC7515579?pdf=render
 37740900,https://doi.org/10.1093/ageing/afad176,Interventions for reducing anticholinergic medication burden in older adults-a systematic review and meta-analysis.,"Braithwaite E, Todd OM, Atkin A, Hulatt R, Tadrous R, Alldred DP, Pirmohamed M, Walker L, Lawton R, Clegg A.",,Age and ageing,2023,2023-09-01,Y,Cognition; Meta-analysis; Systematic review; Falls; Older People; Older Adult; Anticholinergic Medication,,,"<h4>Introduction</h4>Anticholinergic medications block the neurotransmitter acetylcholine in the brain and peripheral nervous system. Many medications have anticholinergic properties, and the cumulative effect of these medications is termed anticholinergic burden. Increased anticholinergic burden can have short-term side effects such as dry mouth, blurred vision and urinary retention as well as long-term effects including dementia, worsening physical function and falls.<h4>Methods</h4>We carried out a systematic review (SR) with meta-analysis (MA) looking at randomised controlled trials addressing interventions to reduce anticholinergic burden in older adults.<h4>Results</h4>We identified seven papers suitable for inclusion in our SR and MA. Interventions included multi-disciplinary involvement in medication reviews and deprescribing of AC medications. Pooled data revealed no significant difference in outcomes between control and intervention group for falls (OR = 0.76, 95% CI: 0.52-1.11, n = 647), cognition (mean difference = 1.54, 95% CI: -0.04 to 3.13, n = 405), anticholinergic burden (mean difference = 0.04, 95% CI: -0.11 to 0.18, n = 710) or quality of life (mean difference = 0.04, 95% CI: -0.04 to 0.12, n = 461).<h4>Discussion</h4>Overall, there was no significant difference with interventions to reduce anticholinergic burden. As we did not see a significant change in anticholinergic burden scores following interventions, it is likely other outcomes would not change. Short follow-up time and lack of training and support surrounding successful deprescribing may have contributed.",,pdf:https://academic.oup.com/ageing/article-pdf/52/9/afad176/51729004/afad176.pdf; doi:https://doi.org/10.1093/ageing/afad176; html:https://europepmc.org/articles/PMC10517713; pdf:https://europepmc.org/articles/PMC10517713?pdf=render
-37645022,https://doi.org/10.1183/20734735.0058-2023,The impact of poor housing and indoor air quality on respiratory health in children.,"Holden KA, Lee AR, Hawcutt DB, Sinha IP.",,"Breathe (Sheffield, England)",2023,2023-06-01,Y,,,,"It is becoming increasingly apparent that poor housing quality affects indoor air quality, significantly impacting on respiratory health in children and young people. Exposure to damp and/or mould in the home, cold homes and the presence of pests and pollutants all have a significant detrimental impact on child respiratory health. There is a complex relationship between features of poor-quality housing, such as being in a state of disrepair, poor ventilation, overcrowding and being cold, that favour an environment resulting in poor indoor air quality. Children living in rented (private or public) housing are more likely to come from lower-income backgrounds and are most at risk of living in substandard housing posing a serious threat to respiratory health. Children have the right to safe and adequate housing, and research has shown that either rehousing or making modifications to poor-quality housing to improve indoor air quality results in improved respiratory health. Urgent action is needed to address this threat to health. All stakeholders should understand the relationship between poor-quality housing and respiratory health in children and act, working with families, to redress this modifiable risk factor.<h4>Educational aims</h4>The reader should understand how housing quality and indoor air quality affect respiratory health in children.The reader should understand which children are at most risk of living in poor-quality housing.The reader should understand what policy recommendations have been made and what actions need to be undertaken to improve housing quality and respiratory health in children and young people.",,doi:https://doi.org/10.1183/20734735.0058-2023; html:https://europepmc.org/articles/PMC10461733; pdf:https://europepmc.org/articles/PMC10461733?pdf=render
 37505992,https://doi.org/10.1093/ageing/afad136,The extent of anticholinergic burden across an older Welsh population living with frailty: cross-sectional analysis of general practice records.,"Cheong VL, Mehdizadeh D, Todd OM, Gardner P, Zaman H, Clegg A, Alldred DP, Faisal M.",,Age and ageing,2023,2023-07-01,Y,Frailty; Older People; Older Adults; Routine Data; Anticholinergic Burden; Structured Medication Review,,,"<h4>Background</h4>Anticholinergic medicines are associated with adverse outcomes for older people. However, little is known about their use in frailty. The objectives were to (i) investigate the prevalence of anticholinergic prescribing for older patients, and (ii) examine anticholinergic burden according to frailty status.<h4>Methods</h4>Cross-sectional analysis of Welsh primary care data from the Secure Anonymised Information Linkage databank including patients aged ≥65 at their first GP consultation between 1 January and 31 December 2018. Frailty was identified using the electronic Frailty Index and anticholinergic burden using the Anticholinergic Cognitive Burden (ACB) scale. Descriptive analysis and logistic regression were conducted to (i) describe the type and frequency of anticholinergics prescribed; and (ii) to estimate the association between frailty and cumulative ACB score (ACB-Sum).<h4>Results</h4>In this study of 529,095 patients, 47.4% of patients receiving any prescription medications were prescribed at least one anticholinergic medicine. Adjusted regression analysis showed that patients with increasing frailty had higher odds of having an ACB-Sum of >3 compared with patients who were fit (mild frailty, adj OR 1.062 (95%CI 1.061-1.064), moderate frailty, adj OR 1.134 (95%CI 1.131-1.136), severe frailty, adj OR 1.208 (95%CI 1.203-1.213)).<h4>Conclusions</h4>Anticholinergic prescribing was high in this older population. Older people with advancing frailty are exposed to the highest anticholinergic burden despite being the most vulnerable to the associated adverse effects. Older people with advancing frailty should be considered for medicines review to prevent overaccumulation of anticholinergic medications, given the risks of functional and cognitive decline that frailty presents.",,pdf:https://academic.oup.com/ageing/article-pdf/52/7/afad136/50976589/afad136.pdf; doi:https://doi.org/10.1093/ageing/afad136; html:https://europepmc.org/articles/PMC10378723; pdf:https://europepmc.org/articles/PMC10378723?pdf=render
+37645022,https://doi.org/10.1183/20734735.0058-2023,The impact of poor housing and indoor air quality on respiratory health in children.,"Holden KA, Lee AR, Hawcutt DB, Sinha IP.",,"Breathe (Sheffield, England)",2023,2023-06-01,Y,,,,"It is becoming increasingly apparent that poor housing quality affects indoor air quality, significantly impacting on respiratory health in children and young people. Exposure to damp and/or mould in the home, cold homes and the presence of pests and pollutants all have a significant detrimental impact on child respiratory health. There is a complex relationship between features of poor-quality housing, such as being in a state of disrepair, poor ventilation, overcrowding and being cold, that favour an environment resulting in poor indoor air quality. Children living in rented (private or public) housing are more likely to come from lower-income backgrounds and are most at risk of living in substandard housing posing a serious threat to respiratory health. Children have the right to safe and adequate housing, and research has shown that either rehousing or making modifications to poor-quality housing to improve indoor air quality results in improved respiratory health. Urgent action is needed to address this threat to health. All stakeholders should understand the relationship between poor-quality housing and respiratory health in children and act, working with families, to redress this modifiable risk factor.<h4>Educational aims</h4>The reader should understand how housing quality and indoor air quality affect respiratory health in children.The reader should understand which children are at most risk of living in poor-quality housing.The reader should understand what policy recommendations have been made and what actions need to be undertaken to improve housing quality and respiratory health in children and young people.",,doi:https://doi.org/10.1183/20734735.0058-2023; html:https://europepmc.org/articles/PMC10461733; pdf:https://europepmc.org/articles/PMC10461733?pdf=render
 37532769,https://doi.org/10.1038/s42003-023-05171-9,Direct inference and control of genetic population structure from RNA sequencing data.,"Fachrul M, Karkey A, Shakya M, Judd LM, Harshegyi T, Sim KS, Tonks S, Dongol S, Shrestha R, Salim A, STRATAA study group, Baker S, Pollard AJ, Khor CC, Dolecek C, Basnyat B, Dunstan SJ, Holt KE, Inouye M.",,Communications biology,2023,2023-08-02,Y,,,,"RNAseq data can be used to infer genetic variants, yet its use for estimating genetic population structure remains underexplored. Here, we construct a freely available computational tool (RGStraP) to estimate RNAseq-based genetic principal components (RG-PCs) and assess whether RG-PCs can be used to control for population structure in gene expression analyses. Using whole blood samples from understudied Nepalese populations and the Geuvadis study, we show that RG-PCs had comparable results to paired array-based genotypes, with high genotype concordance and high correlations of genetic principal components, capturing subpopulations within the dataset. In differential gene expression analysis, we found that inclusion of RG-PCs as covariates reduced test statistic inflation. Our paper demonstrates that genetic population structure can be directly inferred and controlled for using RNAseq data, thus facilitating improved retrospective and future analyses of transcriptomic data.",,pdf:https://www.nature.com/articles/s42003-023-05171-9.pdf; doi:https://doi.org/10.1038/s42003-023-05171-9; html:https://europepmc.org/articles/PMC10397182; pdf:https://europepmc.org/articles/PMC10397182?pdf=render
 37997097,https://doi.org/10.1016/s0140-6736(23)02103-7,The impact of risk stratification by polygenic risk and age on breast cancer screening in women aged 40-49 years: a modelling study.,"Huntley C, Torr B, Sud A, Houlston RS, Hingorani AD, Jones ME, Turnbull C.",,"Lancet (London, England)",2023,2023-11-01,N,,,,"<h4>Background</h4>Polygenic Risk Scores (PRSs) have been proposed as a mechanism for risk-stratification of screening, increasing efficiency and enabling extension of existing programmes to improve survival in our aging population. We sought to model the impact of three hypothetical programmes of annual breast cancer screening in women aged 40-49 years: screening the PRS-defined high-risk quintile, screening the oldest quintile, and screening the full population.<h4>Methods</h4>In this UK-based modelling study, we used the published estimate of the area under the curve (AUC) of a currently available breast cancer PRS (0·64) to calculate the proportion of cancers captured by the PRS-defined high-risk quintile. We used population size estimates from the Office for National Statistics alongside age-stratified incidence rates of breast cancer, and age or stage-specific survival data from the National Cancer Registry, to build our model. We used stage-specific route-to-diagnosis data to reassign stage-specific survival for screen-detected cancers. Ethics approval was not required.<h4>Findings</h4>The PRS-defined high-risk quintile, oldest quintile, and full population capture 37% (n=2811), 29% (n=2198), and 100% (n=7533) of breast cancers occurring in women aged 40-49 each year. Annual screening of each group using digital mammography (sensitivity 70%, specificity 92%) would identify 1968, 1538, and 5273 breast cancers per year, respectively. This corresponds to an improvement in survival of 1·4% (102 deaths averted), 1·1% (80 deaths averted) and 3·6% (274 deaths averted) compared with baseline (no screening). Full population screening would require 4 369 703 mammograms and 354 246 confirmatory tests (breast biopsies) every year, while screening the oldest quintile would require 937 850 mammograms and 76 390 biopsies. Screening the PRS-defined high-risk quintile would require 873 941 mammograms and 71 658 biopsies, in addition to a PRS for all women in the age group (4 369 703).<h4>Interpretation</h4>Under favourable assumptions, stratifying screening by PRS rather than age results in modest gains in survival but increases overdiagnoses, logistical complexity, and economic costs. Our study is limited by our modelling parameters (anticipated to maximise survival estimates), including complete uptake of PRS profiling and cancer screening, no interval cancers, and application of screening tools superior to those currently available in the UK. Only with randomised controlled trials, can the uptake, clinical impact, costs, and harms of PRS-stratified screening be definitively assessed.<h4>Funding</h4>The Wellcome Trust.",,doi:https://doi.org/10.1016/S0140-6736(23)02103-7
 37223892,https://doi.org/10.1111/dme.15153,Inequalities in the management of diabetic kidney disease in UK primary care: A cross-sectional analysis of a large primary care database.,"Phillips K, Hazlehurst JM, Sheppard C, Bellary S, Hanif W, Karamat MA, Crowe FL, Stone A, Thomas GN, Peracha J, Fenton A, Sainsbury C, Nirantharakumar K, Dasgupta I.",,Diabetic medicine : a journal of the British Diabetic Association,2024,2023-06-14,N,Diabetes; Ethnicity; Inequality; Dkd,,,"<h4>Aims</h4>To determine differences in the management of diabetic kidney disease (DKD) relevant to patient sex, ethnicity and socio-economic group in UK primary care.<h4>Methods</h4>A cross-sectional analysis as of January 1, 2019 was undertaken using the IQVIA Medical Research Data dataset, to determine the proportion of people with DKD managed in accordance with national guidelines, stratified by demographics. Robust Poisson regression models were used to calculate adjusted risk ratios (aRR) adjusting for age, sex, ethnicity and social deprivation.<h4>Results</h4>Of the 2.3 million participants, 161,278 had type 1 or 2 diabetes, of which 32,905 had DKD. Of people with DKD, 60% had albumin creatinine ratio (ACR) measured, 64% achieved blood pressure (BP, <140/90 mmHg) target, 58% achieved glycosylated haemoglobin (HbA1c, <58 mmol/mol) target, 68% prescribed renin-angiotensin-aldosterone system (RAAS) inhibitor in the previous year. Compared to men, women were less likely to have creatinine: aRR 0.99 (95% CI 0.98-0.99), ACR: aRR 0.94 (0.92-0.96), BP: aRR 0.98 (0.97-0.99), HbA<sub>1c</sub> : aRR 0.99 (0.98-0.99) and serum cholesterol: aRR 0.97 (0.96-0.98) measured; achieve BP: aRR 0.95 (0.94-0.98) or total cholesterol (<5 mmol/L) targets: aRR 0.86 (0.84-0.87); or be prescribed RAAS inhibitors: aRR 0.92 (0.90-0.94) or statins: aRR 0.94 (0.92-0.95). Compared to the least deprived areas, people from the most deprived areas were less likely to have BP measurements: aRR 0.98 (0.96-0.99); achieve BP: aRR 0.91 (0.8-0.95) or HbA<sub>1c</sub> : aRR 0.88 (0.85-0.92) targets, or be prescribed RAAS inhibitors: aRR 0.91 (0.87-0.95). Compared to people of white ethnicity; those of black ethnicity were less likely to be prescribed statins aRR 0.91 (0.85-0.97).<h4>Conclusions</h4>There are unmet needs and inequalities in the management of DKD in the UK. Addressing these could reduce the increasing human and societal cost of managing DKD.",,doi:https://doi.org/10.1111/dme.15153; doi:https://doi.org/10.1111/dme.15153
@@ -1408,18 +1410,18 @@ PMC10686417,https://doi.org/,The impact of restricted provision of publicly fund
 32894757,https://doi.org/10.1093/ageing/afaa138,Short physical performance battery as a practical tool to assess mortality risk in chronic obstructive pulmonary disease.,"Fermont JM, Mohan D, Fisk M, Bolton CE, Macnee W, Cockcroft JR, McEniery C, Fuld J, Cheriyan J, Tal-Singer R, Müllerova H, Wood AM, Wilkinson IB, Polkey MI, ERICA consortium.",,Age and ageing,2021,2021-05-01,Y,Mortality; Skeletal muscle; Biomarkers; Older People; chronic obstructive pulmonary disease,,,"<h4>Rationale</h4>chronic obstructive pulmonary disease (COPD) is a leading cause of mortality and common in older adults. The BODE Index is the most recognised mortality risk score in COPD but includes a 6-minute walk test (6MWT) that is seldom available in practise; the BODE Index may be better adopted if the 6MWT was replaced.<h4>Objectives</h4>we investigated whether a modified BODE Index in which 6MWT was replaced by an alternative measure of physical capacity, specifically the short physical performance battery (SPPB) or components, retained its predictive ability for mortality in individuals with COPD.<h4>Methods</h4>we analysed 630 COPD patients from the ERICA cohort study for whom UK Office for National Statistics verified mortality data were available. Variables tested at baseline included spirometry, 6MWT, SPPB and its components (4-m gait speed test [4MGS], chair stand and balance). Predictive models were developed using stratified multivariable Cox regression, and assessed by C-indices and calibration plots with 10-fold cross-validation and replication.<h4>Results</h4>during median 2 years of follow-up, 60 (10%) individuals died. There was no significant difference between the discriminative ability of BODE6MWT (C-index 0.709, 95% confidence interval [CI], 0.680-0.737), BODESPPB (C-index 0.683, 95% CI, 0.647-0.712), BODE4MGS (C-index 0.676, 95% CI, 0.643-0.700) and BODEBALANCE (C-index 0.686, 95% CI, 0.651-0.713) for predicting mortality.<h4>Conclusions</h4>the SPPB, and its 4MGS and balance components, can potentially be used as an alternative to the 6MWT in the BODE Index without significant loss of predictive ability in all-cause mortality.",,pdf:https://academic.oup.com/ageing/article-pdf/50/3/795/37807880/afaa138.pdf; doi:https://doi.org/10.1093/ageing/afaa138; html:https://europepmc.org/articles/PMC8098797; pdf:https://europepmc.org/articles/PMC8098797?pdf=render
 34974610,https://doi.org/10.1093/eurheartj/ehab874,The year in cardiovascular medicine 2021: digital health and innovation.,"Vardas PE, Asselbergs FW, van Smeden M, Friedman P.",,European heart journal,2022,2022-01-01,N,Cardiovascular Medicine; Machine Learning; Big Data; Digital Health; Ai-ecg; Ai-wearables,,,"This article presents some of the most important developments in the field of digital medicine that have appeared over the last 12 months and are related to cardiovascular medicine. The article consists of three main sections, as follows: (i) artificial intelligence-enabled cardiovascular diagnostic tools, techniques, and methodologies, (ii) big data and prognostic models for cardiovascular risk protection, and (iii) wearable devices in cardiovascular risk assessment, cardiovascular disease prevention, diagnosis, and management. To conclude the article, the authors present a brief further prospective on this new domain, highlighting existing gaps that are specifically related to artificial intelligence technologies, such as explainability, cost-effectiveness, and, of course, the importance of proper regulatory oversight for each clinical implementation.",,pdf:https://academic.oup.com/eurheartj/article-pdf/43/4/271/46630082/ehab874.pdf; doi:https://doi.org/10.1093/eurheartj/ehab874
 37389932,https://doi.org/10.2196/44126,Barriers to and Facilitators of Using Remote Measurement Technology in the Long-Term Monitoring of Individuals With ADHD: Interview Study.,"Denyer H, Deng Q, Adanijo A, Asherson P, Bilbow A, Folarin A, Groom MJ, Hollis C, Wykes T, Dobson RJ, Kuntsi J, Simblett S.",,JMIR formative research,2023,2023-06-30,Y,Mobile phone; ADHD; Qualitative analysis; Engagement; Attention-deficit/hyperactivity Disorder; Barriers And Facilitators; Remote Measurement Technology,,,"<h4>Background</h4>Remote measurement technology (RMT) has the potential to address current research and clinical challenges of attention-deficit/hyperactivity disorder (ADHD) symptoms and its co-occurring mental health problems. Despite research using RMT already being successfully applied to other populations, adherence and attrition are potential obstacles when applying RMT to a disorder such as ADHD. Hypothetical views and attitudes toward using RMT in a population with ADHD have previously been explored; however, to our knowledge, there is no previous research that has used qualitative methods to understand the barriers to and facilitators of using RMT in individuals with ADHD following participation in a remote monitoring period.<h4>Objective</h4>We aimed to evaluate the barriers to and facilitators of using RMT in individuals with ADHD compared with a group of people who did not have a diagnosis of ADHD. We also aimed to explore participants' views on using RMT for 1 or 2 years in future studies.<h4>Methods</h4>In total, 20 individuals with ADHD and 20 individuals without ADHD were followed up for 10 weeks using RMT that involved active (questionnaires and cognitive tasks) and passive (smartphone sensors and wearable devices) monitoring; 10 adolescents and adults with ADHD and 12 individuals in a comparison group completed semistructured qualitative interviews at the end of the study period. The interviews focused on potential barriers to and facilitators of using RMT in adults with ADHD. A framework methodology was used to explore the data qualitatively.<h4>Results</h4>Barriers to and facilitators of using RMT were categorized as health-related, user-related, and technology-related factors across both participant groups. When comparing themes that emerged across the participant groups, both individuals with and without ADHD experienced similar barriers and facilitators in using RMT. The participants agreed that RMT can provide useful objective data. However, slight differences between the participant groups were identified as barriers to RMT across all major themes. Individuals with ADHD described the impact that their ADHD symptoms had on participating (health-related theme), commented on the perceived cost of completing the cognitive tasks (user-related theme), and described more technical challenges (technology-related theme) than individuals without ADHD. Hypothetical views on future studies using RMT in individuals with ADHD for 1 or 2 years were positive.<h4>Conclusions</h4>Individuals with ADHD agreed that RMT, which uses repeated measurements with ongoing active and passive monitoring, can provide useful objective data. Although themes overlapped with previous research on barriers to and facilitators of engagement with RMT (eg, depression and epilepsy) and with a comparison group, there are unique considerations for people with ADHD, for example, understanding the impact that ADHD symptoms may have on engaging with RMT. Researchers need to continue working with people with ADHD to develop future RMT studies for longer periods.",,pdf:https://formative.jmir.org/2023/1/e44126/PDF; doi:https://doi.org/10.2196/44126; html:https://europepmc.org/articles/PMC10365629; pdf:https://europepmc.org/articles/PMC10365629?pdf=render
-34125897,https://doi.org/10.1093/nar/gkab449,DGLinker: flexible knowledge-graph prediction of disease-gene associations.,"Hu J, Lepore R, Dobson RJB, Al-Chalabi A, M Bean D, Iacoangeli A.",,Nucleic acids research,2021,2021-07-01,Y,,,,"As a result of the advent of high-throughput technologies, there has been rapid progress in our understanding of the genetics underlying biological processes. However, despite such advances, the genetic landscape of human diseases has only marginally been disclosed. Exploiting the present availability of large amounts of biological and phenotypic data, we can use our current understanding of disease genetics to train machine learning models to predict novel genetic factors associated with the disease. To this end, we developed DGLinker, a webserver for the prediction of novel candidate genes for human diseases given a set of known disease genes. DGLinker has a user-friendly interface that allows non-expert users to exploit biomedical information from a wide range of biological and phenotypic databases, and/or to upload their own data, to generate a knowledge-graph and use machine learning to predict new disease-associated genes. The webserver includes tools to explore and interpret the results and generates publication-ready figures. DGLinker is available at https://dglinker.rosalind.kcl.ac.uk. The webserver is free and open to all users without the need for registration.",,doi:https://doi.org/10.1093/nar/gkab449; doi:https://doi.org/10.1093/nar/gkab449; html:https://europepmc.org/articles/PMC8262728; pdf:https://europepmc.org/articles/PMC8262728?pdf=render
 33655501,https://doi.org/10.1111/bjd.19885,Four childhood atopic dermatitis subtypes identified from trajectory and severity of disease and internally validated in a large UK birth cohort.,"Mulick AR, Mansfield KE, Silverwood RJ, Budu-Aggrey A, Roberts A, Custovic A, Pearce N, Irvine AD, Smeeth L, Abuabara K, Langan SM.",,The British journal of dermatology,2021,2021-05-09,N,,,,"<h4>Background</h4>Atopic dermatitis (AD) disease activity and severity is highly variable during childhood. Early attempts to identify subtypes based on disease trajectory have assessed AD presence over time without incorporating severity.<h4>Objectives</h4>To identify childhood AD subtypes from symptom severity and trajectories, and determine associations with genetic risk factors, comorbidities and demographic and environmental variables.<h4>Methods</h4>We split data from children in the Avon Longitudinal Study of Parents and Children birth cohort into development and validation sets. To identify subtypes, we ran latent class analyses in the development set on AD symptom reports up to age 14 years. We regressed identified subtypes on nongenetic variables in mutually adjusted, multiply imputed (genetic: unadjusted, complete case) multinomial regression analyses. We repeated analyses in the validation set and report confirmed results.<h4>Results</h4>There were 11 866 children who contributed to analyses. We identified one Unaffected/Rare class (66% of children) and four AD subtypes: Severe-Frequent (4%), Moderate-Frequent (7%), Moderate-Declining (11%) and Mild-Intermittent (12%). Symptom patterns within the first two subtypes appeared more homogeneous than the last two. Filaggrin (FLG) null mutations, an AD polygenic risk score (PRS), being female, parental AD and comorbid asthma were associated with higher risk for some or all subtypes; FLG, AD-PRS and asthma associations were stronger along a subtype gradient arranged by increasing severity and frequency; FLG and AD-PRS further differentiated some phenotypes from each other.<h4>Conclusions</h4>Considering severity and AD trajectories leads to four well-defined and recognizable subtypes. The differential associations of risk factors among and between subtypes is novel and requires further research.",,pdf:https://researchonline.lshtm.ac.uk/id/eprint/4660846/7/Mulick_etal_2021_Four-childhood-atopic-dermatitis-subtypes.pdf; doi:https://doi.org/10.1111/bjd.19885; html:https://europepmc.org/articles/PMC8410876; pdf:https://europepmc.org/articles/PMC8410876?pdf=render; doi:https://doi.org/10.1111/bjd.19885
+34125897,https://doi.org/10.1093/nar/gkab449,DGLinker: flexible knowledge-graph prediction of disease-gene associations.,"Hu J, Lepore R, Dobson RJB, Al-Chalabi A, M Bean D, Iacoangeli A.",,Nucleic acids research,2021,2021-07-01,Y,,,,"As a result of the advent of high-throughput technologies, there has been rapid progress in our understanding of the genetics underlying biological processes. However, despite such advances, the genetic landscape of human diseases has only marginally been disclosed. Exploiting the present availability of large amounts of biological and phenotypic data, we can use our current understanding of disease genetics to train machine learning models to predict novel genetic factors associated with the disease. To this end, we developed DGLinker, a webserver for the prediction of novel candidate genes for human diseases given a set of known disease genes. DGLinker has a user-friendly interface that allows non-expert users to exploit biomedical information from a wide range of biological and phenotypic databases, and/or to upload their own data, to generate a knowledge-graph and use machine learning to predict new disease-associated genes. The webserver includes tools to explore and interpret the results and generates publication-ready figures. DGLinker is available at https://dglinker.rosalind.kcl.ac.uk. The webserver is free and open to all users without the need for registration.",,doi:https://doi.org/10.1093/nar/gkab449; doi:https://doi.org/10.1093/nar/gkab449; html:https://europepmc.org/articles/PMC8262728; pdf:https://europepmc.org/articles/PMC8262728?pdf=render
 38023948,https://doi.org/10.18332/ejm/171802,A qualitative study exploring healthcare workers' lived experiences of the impacts of COVID-19 policies and guidelines on maternal and reproductive healthcare services in the United Kingdom.,"Chaloner J, Qureshi I, Gogoi M, Ekezie WC, Al-Oraibi A, Wobi F, Agbonmwandolor JO, Nellums LB, Pareek M.",,European journal of midwifery,2023,2023-11-08,Y,Healthcare Workers; Vaccine Hesitancy; Redeployment; Infection Controls; Covid-19; Policies And Guidelines,,,"<h4>Introduction</h4>During the COVID-19 pandemic, pregnant women were regarded as vulnerable to poor health outcomes if infected with the SARS-CoV-2 (COVID-19) virus. To protect the United Kingdom's (UK) National Health Service (NHS) and pregnant patients, strict infection control policies and regulations were implemented. This study aimed to understand the impact of the COVID-19 policies and guidelines on maternal and reproductive health services during the pandemic from the experiences of healthcare workers (HCWs) caring for these patients.<h4>Methods</h4>This qualitative study involved HCWs from the United Kingdom Research study into Ethnicity and COVID-19 outcomes in Healthcare workers (UK-REACH) project. Semi-structured interviews and focus groups were conducted online or by telephone with 44 diverse HCWs. Transcripts were thematically analyzed following Braun and Clarke's principles of qualitative analysis.<h4>Results</h4>Three key themes were identified during analysis. First, infection control policies impacted appointment availability, resulting in many cancellations and delays to treatment. Telemedicine was also used extensively to reduce risks from face-to-face consultations, disadvantaging patients from minoritized ethnicities. Secondly, staff shortages and redeployments reduced availability of consultations, appointments, and sonography scans. Finally, staff and patients reported challenges accessing timely, reliable and accurate information and guidance.<h4>Conclusions</h4>COVID-19 demonstrated how a global health crisis can impact maternal and reproductive health services, leading to reduced service quality and surgical delays due to staff redeployment policies. Our findings underscore the implications of policy and future health crises preparedness. This includes tailored infection control policies, addressing elective surgery backlogs early and improved dissemination of relevant vaccine information.",,pdf:https://www.europeanjournalofmidwifery.eu/pdf-171802-96110?filename=A qualitative study.pdf; doi:https://doi.org/10.18332/ejm/171802; html:https://europepmc.org/articles/PMC10630987; pdf:https://europepmc.org/articles/PMC10630987?pdf=render
 33096553,https://doi.org/10.1093/ajcn/nqaa266,"Association between diet and periodontitis: a cross-sectional study of 10,000 NHANES participants.","Wright DM, McKenna G, Nugent A, Winning L, Linden GJ, Woodside JV.",,The American journal of clinical nutrition,2020,2020-12-01,N,Diet; Periodontitis; Nhanes; Robust Regression; Treelet Transformation,,,"<h4>Background</h4>Periodontitis is a major cause of tooth loss globally. Risk factors include age, smoking, and diabetes. Intake of specific nutrients has been associated with periodontitis risk but there has been little research into the influence of overall diet, potentially more relevant when formulating dietary recommendations.<h4>Objectives</h4>We aimed to investigate potential associations between diet and periodontitis using novel statistical techniques for dietary pattern analysis.<h4>Methods</h4>Two 24-h dietary recalls and periodontal examination data from the cross-sectional US NHANES, 2009-2014 (n = 10,010), were used. Dietary patterns were extracted using treelet transformation, a data-driven hierarchical clustering and dimension reduction technique. Associations between each pattern [treelet component (TC)] and extent of periodontitis [proportion of sites with clinical attachment loss (CAL) ≥ 3 mm] were estimated using robust logistic quantile regression, adjusting for age, sex, ethnicity, education level, smoking, BMI, and diabetes.<h4>Results</h4>Eight TCs explained 21% of the variation in diet, 1 of which (TC1) was associated with CAL extent. High TC1 scores represented a diet rich in salad, fruit, vegetables, poultry and seafood, and plain water or tea to drink. There was a substantial negative gradient in CAL extent from the lowest to the highest decile of TC1 (median proportion of sites with CAL ≥ 3 mm: decile 1 = 19.1%, decile 10 = 8.1%; OR, decile 10 compared with decile 1: 0.67; 95% CI: 0.46, 0.99).<h4>Conclusions</h4>Most dietary patterns identified were not associated with periodontitis extent. One pattern, however, rich in salad, fruit, and vegetables and with plain water or tea to drink, was associated with lower CAL extent. Treelet transformation may be a useful approach for calculating dietary patterns in nutrition research.",,pdf:https://academic.oup.com/ajcn/article-pdf/112/6/1485/34844146/nqaa266.pdf; doi:https://doi.org/10.1093/ajcn/nqaa266
-38932357,https://doi.org/10.3390/vaccines12060628,"COVID-19 Vaccine Uptake and Effectiveness by Time since Vaccination in the Western Cape Province, South Africa: An Observational Cohort Study during 2020-2022.","Kassanjee R, Davies MA, Heekes A, Mahomed H, Hawkridge AJ, Morden E, Jacobs T, Cohen C, Moultrie H, Lessells RJ, Van Der Walt N, Arendse JO, Wolter N, Walaza S, Jassat W, von Gottberg A, Hannan PL, Feikin DR, Cloete K, Boulle A.",,Vaccines,2024,2024-06-05,Y,Cohort; South Africa; Vaccine Effectiveness; Observational; Covid-19; Sars-cov-2,,,"There are few data on the real-world effectiveness of COVID-19 vaccines and boosting in Africa, which experienced widespread SARS-CoV-2 infection before vaccine availability. We assessed the association between vaccination and severe COVID-19 in the Western Cape, South Africa, in an observational cohort study of >2 million adults during 2020-2022. We described SARS-CoV-2 testing, COVID-19 outcomes, and vaccine uptake over time. We used multivariable cox models to estimate the association of BNT162b2 and Ad26.COV2.S vaccination with COVID-19-related hospitalization and death, adjusting for demographic characteristics, underlying health conditions, socioeconomic status proxies, and healthcare utilization. We found that by the end of 2022, 41% of surviving adults had completed vaccination and 8% had received a booster dose. Recent vaccination was associated with notable reductions in severe COVID-19 during periods dominated by Delta, and Omicron BA.1/2 and BA.4/5 (sub)lineages. During the latest Omicron BA.4/5 wave, within 3 months of vaccination or boosting, BNT162b2 and Ad26.COV2.S were each 84% effective against death (95% CIs: 57-94 and 49-95, respectively). However, distinct reductions of effectiveness occurred at longer times post completing or boosting vaccination. Results highlight the importance of continued emphasis on COVID-19 vaccination and boosting for those at high risk of severe COVID-19, even in settings with widespread infection-induced immunity.",,doi:https://doi.org/10.3390/vaccines12060628; html:https://europepmc.org/articles/PMC11209070; pdf:https://europepmc.org/articles/PMC11209070?pdf=render
 36648036,https://doi.org/10.1016/j.jcmg.2022.06.011,Incident Clinical and Mortality Associations of Myocardial Native T1 in the UK Biobank.,"Raisi-Estabragh Z, McCracken C, Hann E, Condurache DG, Harvey NC, Munroe PB, Ferreira VM, Neubauer S, Piechnik SK, Petersen SE.",,JACC. Cardiovascular imaging,2023,2022-09-14,Y,Mortality; Cardiovascular disease; Cardiac Magnetic Resonance; Native T1 Mapping; Incident Events,,,"<h4>Background</h4>Cardiac magnetic resonance native T1-mapping provides noninvasive, quantitative, and contrast-free myocardial characterization. However, its predictive value in population cohorts has not been studied.<h4>Objectives</h4>The associations of native T1 with incident events were evaluated in 42,308 UK Biobank participants over 3.17 ± 1.53 years of prospective follow-up.<h4>Methods</h4>Native T1-mapping was performed in 1 midventricular short-axis slice using the Shortened Modified Look-Locker Inversion recovery technique (WIP780B) in 1.5-T scanners (Siemens Healthcare). Global myocardial T1 was calculated using an automated tool. Associations of T1 with: 1) prevalent risk factors (eg, diabetes, hypertension, and high cholesterol); 2) prevalent and incident diseases (eg, any cardiovascular disease [CVD], any brain disease, valvular heart disease, heart failure, nonischemic cardiomyopathies, cardiac arrhythmias, atrial fibrillation [AF], myocardial infarction, ischemic heart disease [IHD], and stroke); and 3) mortality (eg, all-cause, CVD, and IHD) were examined. Results are reported as odds ratios (ORs) or HRs per SD increment of T1 value with 95% CIs and corrected P values, from logistic and Cox proportional hazards regression models.<h4>Results</h4>Higher myocardial T1 was associated with greater odds of a range of prevalent conditions (eg, any CVD, brain disease, heart failure, nonischemic cardiomyopathies, AF, stroke, and diabetes). The strongest relationships were with heart failure (OR: 1.41 [95% CI: 1.26-1.57]; P = 1.60 × 10<sup>-9</sup>) and nonischemic cardiomyopathies (OR: 1.40 [95% CI: 1.16-1.66]; P = 2.42 × 10<sup>-4</sup>). Native T1 was positively associated with incident AF (HR: 1.25 [95% CI: 1.10-1.43]; P = 9.19 × 10<sup>-4</sup>), incident heart failure (HR: 1.47 [95% CI: 1.31-1.65]; P = 4.79 × 10<sup>-11</sup>), all-cause mortality (HR: 1.24 [95% CI: 1.12-1.36]; P = 1.51 × 10<sup>-5</sup>), CVD mortality (HR: 1.40 [95% CI: 1.14-1.73]; P = 0.0014), and IHD mortality (HR: 1.36 [95% CI: 1.03-1.80]; P = 0.0310).<h4>Conclusions</h4>This large population study demonstrates the utility of myocardial native T1-mapping for disease discrimination and outcome prediction.",,doi:https://doi.org/10.1016/j.jcmg.2022.06.011; doi:https://doi.org/10.1016/j.jcmg.2022.06.011; html:https://europepmc.org/articles/PMC10102720; pdf:https://europepmc.org/articles/PMC10102720?pdf=render
+38932357,https://doi.org/10.3390/vaccines12060628,"COVID-19 Vaccine Uptake and Effectiveness by Time since Vaccination in the Western Cape Province, South Africa: An Observational Cohort Study during 2020-2022.","Kassanjee R, Davies MA, Heekes A, Mahomed H, Hawkridge AJ, Morden E, Jacobs T, Cohen C, Moultrie H, Lessells RJ, Van Der Walt N, Arendse JO, Wolter N, Walaza S, Jassat W, von Gottberg A, Hannan PL, Feikin DR, Cloete K, Boulle A.",,Vaccines,2024,2024-06-05,Y,Cohort; South Africa; Vaccine Effectiveness; Observational; Covid-19; Sars-cov-2,,,"There are few data on the real-world effectiveness of COVID-19 vaccines and boosting in Africa, which experienced widespread SARS-CoV-2 infection before vaccine availability. We assessed the association between vaccination and severe COVID-19 in the Western Cape, South Africa, in an observational cohort study of >2 million adults during 2020-2022. We described SARS-CoV-2 testing, COVID-19 outcomes, and vaccine uptake over time. We used multivariable cox models to estimate the association of BNT162b2 and Ad26.COV2.S vaccination with COVID-19-related hospitalization and death, adjusting for demographic characteristics, underlying health conditions, socioeconomic status proxies, and healthcare utilization. We found that by the end of 2022, 41% of surviving adults had completed vaccination and 8% had received a booster dose. Recent vaccination was associated with notable reductions in severe COVID-19 during periods dominated by Delta, and Omicron BA.1/2 and BA.4/5 (sub)lineages. During the latest Omicron BA.4/5 wave, within 3 months of vaccination or boosting, BNT162b2 and Ad26.COV2.S were each 84% effective against death (95% CIs: 57-94 and 49-95, respectively). However, distinct reductions of effectiveness occurred at longer times post completing or boosting vaccination. Results highlight the importance of continued emphasis on COVID-19 vaccination and boosting for those at high risk of severe COVID-19, even in settings with widespread infection-induced immunity.",,doi:https://doi.org/10.3390/vaccines12060628; html:https://europepmc.org/articles/PMC11209070; pdf:https://europepmc.org/articles/PMC11209070?pdf=render
 36357675,https://doi.org/10.1038/s41591-022-02046-0,Rare and common genetic determinants of metabolic individuality and their effects on human health.,"Surendran P, Stewart ID, Au Yeung VPW, Pietzner M, Raffler J, Wörheide MA, Li C, Smith RF, Wittemans LBL, Bomba L, Menni C, Zierer J, Rossi N, Sheridan PA, Watkins NA, Mangino M, Hysi PG, Di Angelantonio E, Falchi M, Spector TD, Soranzo N, Michelotti GA, Arlt W, Lotta LA, Denaxas S, Hemingway H, Gamazon ER, Howson JMM, Wood AM, Danesh J, Wareham NJ, Kastenmüller G, Fauman EB, Suhre K, Butterworth AS, Langenberg C.",,Nature medicine,2022,2022-11-10,Y,,,,"Garrod's concept of 'chemical individuality' has contributed to comprehension of the molecular origins of human diseases. Untargeted high-throughput metabolomic technologies provide an in-depth snapshot of human metabolism at scale. We studied the genetic architecture of the human plasma metabolome using 913 metabolites assayed in 19,994 individuals and identified 2,599 variant-metabolite associations (P < 1.25 × 10<sup>-11</sup>) within 330 genomic regions, with rare variants (minor allele frequency ≤ 1%) explaining 9.4% of associations. Jointly modeling metabolites in each region, we identified 423 regional, co-regulated, variant-metabolite clusters called genetically influenced metabotypes. We assigned causal genes for 62.4% of these genetically influenced metabotypes, providing new insights into fundamental metabolite physiology and clinical relevance, including metabolite-guided discovery of potential adverse drug effects (DPYD and SRD5A2). We show strong enrichment of inborn errors of metabolism-causing genes, with examples of metabolite associations and clinical phenotypes of non-pathogenic variant carriers matching characteristics of the inborn errors of metabolism. Systematic, phenotypic follow-up of metabolite-specific genetic scores revealed multiple potential etiological relationships.",,pdf:https://www.nature.com/articles/s41591-022-02046-0.pdf; doi:https://doi.org/10.1038/s41591-022-02046-0; html:https://europepmc.org/articles/PMC9671801; pdf:https://europepmc.org/articles/PMC9671801?pdf=render
 30181555,https://doi.org/10.1038/s41398-018-0236-1,"Genetics of self-reported risk-taking behaviour, trans-ethnic consistency and relevance to brain gene expression.","Strawbridge RJ, Ward J, Lyall LM, Tunbridge EM, Cullen B, Graham N, Ferguson A, Johnston KJA, Lyall DM, Mackay D, Cavanagh J, Howard DM, Adams MJ, Deary I, Escott-Price V, O'Donovan M, McIntosh AM, Bailey MES, Pell JP, Harrison PJ, Smith DJ.",,Translational psychiatry,2018,2018-09-04,Y,,Understanding the Causes of Disease,,"Risk-taking behaviour is an important component of several psychiatric disorders, including attention-deficit hyperactivity disorder, schizophrenia and bipolar disorder. Previously, two genetic loci have been associated with self-reported risk taking and significant genetic overlap with psychiatric disorders was identified within a subsample of UK Biobank. Using the white British participants of the full UK Biobank cohort (n = 83,677 risk takers versus 244,662 controls) for our primary analysis, we conducted a genome-wide association study of self-reported risk-taking behaviour. In secondary analyses, we assessed sex-specific effects, trans-ethnic heterogeneity and genetic overlap with psychiatric traits. We also investigated the impact of risk-taking-associated SNPs on both gene expression and structural brain imaging. We identified 10 independent loci for risk-taking behaviour, of which eight were novel and two replicated previous findings. In addition, we found two further sex-specific risk-taking loci. There were strong positive genetic correlations between risk-taking and attention-deficit hyperactivity disorder, bipolar disorder and schizophrenia. Index genetic variants demonstrated effects generally consistent with the discovery analysis in individuals of non-British White, South Asian, African-Caribbean or mixed ethnicity. Polygenic risk scores comprising alleles associated with increased risk taking were associated with lower white matter integrity. Genotype-specific expression pattern analyses highlighted DPYSL5, CGREF1 and C15orf59 as plausible candidate genes. Overall, our findings substantially advance our understanding of the biology of risk-taking behaviour, including the possibility of sex-specific contributions, and reveal consistency across ethnicities. We further highlight several putative novel candidate genes, which may mediate these genetic effects.",,pdf:https://www.nature.com/articles/s41398-018-0236-1.pdf; doi:https://doi.org/10.1038/s41398-018-0236-1; html:https://europepmc.org/articles/PMC6123450; pdf:https://europepmc.org/articles/PMC6123450?pdf=render
 35650647,https://doi.org/10.1186/s41512-022-00124-y,A scoping methodological review of simulation studies comparing statistical and machine learning approaches to risk prediction for time-to-event data.,"Smith H, Sweeting M, Morris T, Crowther MJ.",,Diagnostic and prognostic research,2022,2022-06-02,Y,Survival analysis; Machine Learning; Simulation Studies; Clinical Risk Prediction; Prognostic Modelling,,,"<h4>Background</h4>There is substantial interest in the adaptation and application of so-called machine learning approaches to prognostic modelling of censored time-to-event data. These methods must be compared and evaluated against existing methods in a variety of scenarios to determine their predictive performance. A scoping review of how machine learning methods have been compared to traditional survival models is important to identify the comparisons that have been made and issues where they are lacking, biased towards one approach or misleading.<h4>Methods</h4>We conducted a scoping review of research articles published between 1 January 2000 and 2 December 2020 using PubMed. Eligible articles were those that used simulation studies to compare statistical and machine learning methods for risk prediction with a time-to-event outcome in a medical/healthcare setting. We focus on data-generating mechanisms (DGMs), the methods that have been compared, the estimands of the simulation studies, and the performance measures used to evaluate them.<h4>Results</h4>A total of ten articles were identified as eligible for the review. Six of the articles evaluated a method that was developed by the authors, four of which were machine learning methods, and the results almost always stated that this developed method's performance was equivalent to or better than the other methods compared. Comparisons were often biased towards the novel approach, with the majority only comparing against a basic Cox proportional hazards model, and in scenarios where it is clear it would not perform well. In many of the articles reviewed, key information was unclear, such as the number of simulation repetitions and how performance measures were calculated.<h4>Conclusion</h4>It is vital that method comparisons are unbiased and comprehensive, and this should be the goal even if realising it is difficult. Fully assessing how newly developed methods perform and how they compare to a variety of traditional statistical methods for prognostic modelling is imperative as these methods are already being applied in clinical contexts. Evaluations of the performance and usefulness of recently developed methods for risk prediction should be continued and reporting standards improved as these methods become increasingly popular.",,pdf:https://diagnprognres.biomedcentral.com/track/pdf/10.1186/s41512-022-00124-y; doi:https://doi.org/10.1186/s41512-022-00124-y; html:https://europepmc.org/articles/PMC9161606; pdf:https://europepmc.org/articles/PMC9161606?pdf=render
 37118525,https://doi.org/10.1038/s43587-022-00328-3,Strong peak immunogenicity but rapid antibody waning following third vaccine dose in older residents of care homes.,"Tut G, Lancaster T, Krutikov M, Sylla P, Bone D, Spalkova E, Bentley C, Amin U, Jadir A, Hulme S, Kaur N, Tut E, Bruton R, Wu MY, Harvey R, Carr EJ, Crick COVID Immunity Pipeline, Beale R, Stirrup O, Shrotri M, Azmi B, Fuller C, Baynton V, Irwin-Singer A, Hayward A, Copas A, Shallcross L, Moss P.",,Nature aging,2023,2023-01-20,Y,,,,"Third-dose coronavirus disease 2019 vaccines are being deployed widely but their efficacy has not been assessed adequately in vulnerable older people who exhibit suboptimal responses after primary vaccination series. This observational study, which was carried out by the VIVALDI study based in England, looked at spike-specific immune responses in 341 staff and residents in long-term care facilities who received an mRNA vaccine following dual primary series vaccination with BNT162b2 or ChAdOx1. Third-dose vaccination strongly increased antibody responses with preferential relative enhancement in older people and was required to elicit neutralization of Omicron. Cellular immune responses were also enhanced with strong cross-reactive recognition of Omicron. However, antibody titers fell 21-78% within 100 d after vaccine and 27% of participants developed a breakthrough Omicron infection. These findings reveal strong immunogenicity of a third vaccine in one of the most vulnerable population groups and endorse an approach for widespread delivery across this population. Ongoing assessment will be required to determine the stability of immune protection.",,pdf:https://www.nature.com/articles/s43587-022-00328-3.pdf; doi:https://doi.org/10.1038/s43587-022-00328-3; html:https://europepmc.org/articles/PMC10154221; pdf:https://europepmc.org/articles/PMC10154221?pdf=render
-35537476,https://doi.org/10.1177/01410768221095245,Indirect effects of the pandemic: highlighting the need for data-driven policy and preparedness.,"Banerjee A, Sudlow C, Lawler M.",,Journal of the Royal Society of Medicine,2022,2022-05-10,Y,,,,,,pdf:https://journals.sagepub.com/doi/pdf/10.1177/01410768221095245; doi:https://doi.org/10.1177/01410768221095245; html:https://europepmc.org/articles/PMC9234890; pdf:https://europepmc.org/articles/PMC9234890?pdf=render
 31194737,https://doi.org/10.1371/journal.pgen.1008164,Genome-wide association study of multisite chronic pain in UK Biobank.,"Johnston KJA, Adams MJ, Nicholl BI, Ward J, Strawbridge RJ, Ferguson A, McIntosh AM, Bailey MES, Smith DJ.",,PLoS genetics,2019,2019-06-13,Y,,Understanding the Causes of Disease,,"Chronic pain is highly prevalent worldwide and represents a significant socioeconomic and public health burden. Several aspects of chronic pain, for example back pain and a severity-related phenotype 'chronic pain grade', have been shown previously to be complex heritable traits with a polygenic component. Additional pain-related phenotypes capturing aspects of an individual's overall sensitivity to experiencing and reporting chronic pain have also been suggested as a focus for investigation. We made use of a measure of the number of sites of chronic pain in individuals within the UK general population. This measure, termed Multisite Chronic Pain (MCP), is a complex trait and its genetic architecture has not previously been investigated. To address this, we carried out a large-scale genome-wide association study (GWAS) of MCP in ~380,000 UK Biobank participants. Our findings were consistent with MCP having a significant polygenic component, with a Single Nucleotide Polymorphism (SNP) heritability of 10.2%. In total 76 independent lead SNPs at 39 risk loci were associated with MCP. Additional gene-level association analyses identified neurogenesis, synaptic plasticity, nervous system development, cell-cycle progression and apoptosis genes as enriched for genetic association with MCP. Genetic correlations were observed between MCP and a range of psychiatric, autoimmune and anthropometric traits, including major depressive disorder (MDD), asthma and Body Mass Index (BMI). Furthermore, in Mendelian randomisation (MR) analyses a causal effect of MCP on MDD was observed. Additionally, a polygenic risk score (PRS) for MCP was found to significantly predict chronic widespread pain (pain all over the body), indicating the existence of genetic variants contributing to both of these pain phenotypes. Overall, our findings support the proposition that chronic pain involves a strong nervous system component with implications for our understanding of the physiology of chronic pain. These discoveries may also inform the future development of novel treatment approaches.",,pdf:https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1008164&type=printable; doi:https://doi.org/10.1371/journal.pgen.1008164; html:https://europepmc.org/articles/PMC6592570; pdf:https://europepmc.org/articles/PMC6592570?pdf=render
+35537476,https://doi.org/10.1177/01410768221095245,Indirect effects of the pandemic: highlighting the need for data-driven policy and preparedness.,"Banerjee A, Sudlow C, Lawler M.",,Journal of the Royal Society of Medicine,2022,2022-05-10,Y,,,,,,pdf:https://journals.sagepub.com/doi/pdf/10.1177/01410768221095245; doi:https://doi.org/10.1177/01410768221095245; html:https://europepmc.org/articles/PMC9234890; pdf:https://europepmc.org/articles/PMC9234890?pdf=render
 35487738,https://doi.org/10.1136/bmjopen-2021-057017,Variation in the estimated prevalence of multimorbidity: systematic review and meta-analysis of 193 international studies.,"Ho IS, Azcoaga-Lorenzo A, Akbari A, Davies J, Hodgins P, Khunti K, Kadam U, Lyons R, McCowan C, Mercer SW, Nirantharakumar K, Guthrie B.",,BMJ open,2022,2022-04-29,Y,epidemiology; Geriatric Medicine; General Medicine (See Internal Medicine),,,"<h4>Objective</h4>(1) To estimate the pooled prevalence of multimorbidity in all age groups, globally. (2) To examine how measurement of multimorbidity impacted the estimated prevalence.<h4>Methods</h4>In this systematic review and meta-analysis, we conducted searches in nine bibliographic databases (PsycINFO, Embase, Global Health, Medline, Scopus, Web of Science, Cochrane Library, CINAHL and ProQuest Dissertations and Theses Global) for prevalence studies published between database inception and 21 January 2020. Studies reporting the prevalence of multimorbidity (in all age groups and in community, primary care, care home and hospital settings) were included. Studies with an index condition or those that did not include people with no long-term conditions in the denominator were excluded. Retrieved studies were independently reviewed by two reviewers, and relevant data were extracted using predesigned pro forma. We used meta-analysis to pool the estimated prevalence of multimorbidity across studies, and used random-effects meta-regression and subgroup analysis to examine the association of heterogeneous prevalence estimates with study and measure characteristics.<h4>Results</h4>13 807 titles were screened, of which 193 met inclusion criteria for meta-analysis. The pooled prevalence of multimorbidity was 42.4% (95% CI 38.9% to 46.0%) with high heterogeneity (I<sup>2</sup> >99%). In adjusted meta-regression models, participant mean age and the number of conditions included in a measure accounted for 47.8% of heterogeneity in effect sizes. The estimated prevalence of multimorbidity was significantly higher in studies with older adults and those that included larger numbers of conditions. There was no significant difference in estimated prevalence between low-income or middle-income countries (36.8%) and high-income countries (44.3%), or between self-report (40.0%) and administrative/clinical databases (52.7%).<h4>Conclusions</h4>The pooled prevalence of multimorbidity was significantly higher in older populations and when studies included a larger number of baseline conditions. The findings suggest that, to improve study comparability and quality of reporting, future studies should use a common core conditions set for multimorbidity measurement and report multimorbidity prevalence stratified by sociodemographics.<b>PROSPERO registration number</b>CRD42020172409.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/4/e057017.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-057017; html:https://europepmc.org/articles/PMC9058768; pdf:https://europepmc.org/articles/PMC9058768?pdf=render
 37706486,https://doi.org/10.1080/09638288.2023.2254235,Stepped collaborative care for pain and posttraumatic stress disorder after major trauma: a randomized controlled feasibility trial.,"Giummarra MJ, Reeder S, Williams S, Devlin A, Knol R, Ponsford J, Arnold CA, Konstantatos A, Gabbe BJ, Clarke H, Katz J, Mitchell F, Robinson E, Zatzick D.",,Disability and rehabilitation,2024,2023-09-14,Y,Trauma; Injury; Recovery; Pain; Hospitalization; Ptsd; Brief Intervention,,,"<h4>Purpose</h4>To examine feasibility and acceptability of providing stepped collaborative care case management targeting posttraumatic stress disorder (PTSD) and pain symptoms after major traumatic injury.<h4>Materials and methods</h4>Participants were major trauma survivors in Victoria, Australia, at risk of persistent pain or PTSD with high baseline symptoms. Participants were block-randomized, stratified by compensation-status, to the usual care (<i>n</i> = 15) or intervention (<i>n</i> = 17) group (46% of eligible patients). The intervention was adapted from existing stepped collaborative care interventions with input from interdisciplinary experts and people with lived experience in trauma and disability. The proactive case management intervention targeted PTSD and pain management for 6-months using motivational interviewing, cognitive behavioral therapy strategies, and collaborative care. Qualitative interviews explored intervention acceptability.<h4>Results</h4>Intervention participants received a median of 7 h case manager contact and reported that they valued the supportive and non-judgmental listening, and timely access to effective strategies, resources, and treatments post-injury from the case manager. Participants reported few disadvantages from participation, and positive impacts on symptoms and recovery outcomes consistent with the reduction in PTSD and pain symptoms measured at 1-, 3- and 6-months.<h4>Conclusions</h4>Stepped collaborative care was low-cost, feasible, and acceptable to people at risk of PTSD or pain after major trauma.IMPLICATIONS FOR REHABILITATIONAfter hospitalization for injury, people can experience difficulty accessing timely support to manage posttraumatic stress, pain and other concerns.Stepped case management-based interventions that provide individualized support and collaborative care have reduced posttraumatic stress symptom severity for patients admitted to American trauma centers.We showed that this model of care could be adapted to target pain and mental health in the trauma system in Victoria, Australia.The intervention was low cost, acceptable and highly valued by most participants who perceived that it helped them use strategies to better manage post-traumatic symptoms, and to access clinicians and treatments relevant to their needs.",,pdf:https://www.tandfonline.com/doi/pdf/10.1080/09638288.2023.2254235?needAccess=true; doi:https://doi.org/10.1080/09638288.2023.2254235; html:https://europepmc.org/articles/PMC10937328; pdf:https://europepmc.org/articles/PMC10937328?pdf=render
 37394283,https://doi.org/10.1002/ehf2.14444,Survival after HeartMate 3 left ventricular assist device implantation: real-world data from Europe.,"Numan L, Schramm R, Oerlemans MIFJ, van der Kaaij NP, Aarts E, Ramjankhan FZ, Oppelaar AM, Morshuis M, Guenther SPW, Zimpfer D, Riebandt J, Wiedemann D, Asselbergs FW, Van Laake LW.",,ESC heart failure,2023,2023-07-02,Y,,,,,,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ehf2.14444; doi:https://doi.org/10.1002/ehf2.14444; html:https://europepmc.org/articles/PMC10375103; pdf:https://europepmc.org/articles/PMC10375103?pdf=render
@@ -1433,33 +1435,33 @@ PMC10686417,https://doi.org/,The impact of restricted provision of publicly fund
 36713101,https://doi.org/10.1093/ehjdh/ztab082,A data mining-based cross-industry process for predicting major bleeding in mechanical circulatory support.,"Felix SEA, Bagheri A, Ramjankhan FR, Spruit MR, Oberski D, de Jonge N, van Laake LW, Suyker WJL, Asselbergs FW.",,European heart journal. Digital health,2021,2021-10-01,Y,Prediction; Bleeding; data mining; Mechanical Circulatory Support; Cross-Industry Standard Process For Data Mining (Crisp-Dm),,,"<h4>Aims</h4>Over a third of patients, treated with mechanical circulatory support (MCS) for end-stage heart failure, experience major bleeding. Currently, the prediction of a major bleeding in the near future is difficult because of many contributing factors. Predictive analytics using data mining could help calculating the risk of bleeding; however, its application is generally reserved for experienced researchers on this subject. We propose an easily applicable data mining tool to predict major bleeding in MCS patients.<h4>Methods and results</h4>All data of electronic health records of MCS patients in the University Medical Centre Utrecht were included. Based on the cross-industry standard process for data mining (CRISP-DM) methodology, an application named Auto-Crisp was developed. Auto-Crisp was used to evaluate the predictive models for a major bleeding in the next 3, 7, and 30 days after the first 30 days post-operatively following MCS implantation. The performance of the predictive models is investigated by the area under the curve (AUC) evaluation measure. In 25.6% of 273 patients, a total of 142 major bleedings occurred during a median follow-up period of 542 [interquartile range (IQR) 205-1044] days. The best predictive models assessed by Auto-Crisp had AUC values of 0.792, 0.788, and 0.776 for bleedings in the next 3, 7, and 30 days, respectively.<h4>Conclusion</h4>The Auto-Crisp-based predictive model created in this study had an acceptable performance to predict major bleeding in MCS patients in the near future. However, further validation of the application is needed to evaluate Auto-Crisp in other research projects.",,pdf:https://academic.oup.com/ehjdh/article-pdf/2/4/635/41972750/ztab082.pdf; doi:https://doi.org/10.1093/ehjdh/ztab082; html:https://europepmc.org/articles/PMC9707970; pdf:https://europepmc.org/articles/PMC9707970?pdf=render
 35025917,https://doi.org/10.1371/journal.pone.0261142,Inpatient COVID-19 mortality has reduced over time: Results from an observational cohort.,"Bechman K, Yates M, Mann K, Nagra D, Smith LJ, Rutherford AI, Patel A, Periselneris J, Walder D, Dobson RJB, Kraljevic Z, Teo JHT, Bernal W, Barker R, Galloway JB, Norton S.",,PloS one,2022,2022-01-13,Y,,,,"<h4>Background</h4>The Covid-19 pandemic in the United Kingdom has seen two waves; the first starting in March 2020 and the second in late October 2020. It is not known whether outcomes for those admitted with severe Covid were different in the first and second waves.<h4>Methods</h4>The study population comprised all patients admitted to a 1,500-bed London Hospital Trust between March 2020 and March 2021, who tested positive for Covid-19 by PCR within 3-days of admissions. Primary outcome was death within 28-days of admission. Socio-demographics (age, sex, ethnicity), hypertension, diabetes, obesity, baseline physiological observations, CRP, neutrophil, chest x-ray abnormality, remdesivir and dexamethasone were incorporated as co-variates. Proportional subhazards models compared mortality risk between wave 1 and wave 2. Cox-proportional hazard model with propensity score adjustment were used to compare mortality in patients prescribed remdesivir and dexamethasone.<h4>Results</h4>There were 3,949 COVID-19 admissions, 3,195 hospital discharges and 733 deaths. There were notable differences in age, ethnicity, comorbidities, and admission disease severity between wave 1 and wave 2. Twenty-eight-day mortality was higher during wave 1 (26.1% versus 13.1%). Mortality risk adjusted for co-variates was significantly lower in wave 2 compared to wave 1 [adjSHR 0.49 (0.37, 0.65) p<0.001]. Analysis of treatment impact did not show statistically different effects of remdesivir [HR 0.84 (95%CI 0.65, 1.08), p = 0.17] or dexamethasone [HR 0.97 (95%CI 0.70, 1.35) p = 0.87].<h4>Conclusion</h4>There has been substantial improvements in COVID-19 mortality in the second wave, even accounting for demographics, comorbidity, and disease severity. Neither dexamethasone nor remdesivir appeared to be key explanatory factors, although there may be unmeasured confounding present.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0261142&type=printable; doi:https://doi.org/10.1371/journal.pone.0261142; html:https://europepmc.org/articles/PMC8757902; pdf:https://europepmc.org/articles/PMC8757902?pdf=render
 35277454,https://doi.org/10.1136/heartjnl-2021-320417,Smartphone detection of atrial fibrillation using photoplethysmography: a systematic review and meta-analysis.,"Gill S, Bunting KV, Sartini C, Cardoso VR, Ghoreishi N, Uh HW, Williams JA, Suzart-Woischnik K, Banerjee A, Asselbergs FW, Eijkemans M, Gkoutos GV, Kotecha D.",,Heart (British Cardiac Society),2022,2022-09-26,Y,Atrial fibrillation; Photoplethysmography; Smartphone,,,"<h4>Objectives</h4>Timely diagnosis of atrial fibrillation (AF) is essential to reduce complications from this increasingly common condition. We sought to assess the diagnostic accuracy of smartphone camera photoplethysmography (PPG) compared with conventional electrocardiogram (ECG) for AF detection.<h4>Methods</h4>This is a systematic review of MEDLINE, EMBASE and Cochrane (1980-December 2020), including any study or abstract, where smartphone PPG was compared with a reference ECG (1, 3 or 12-lead). Random effects meta-analysis was performed to pool sensitivity/specificity and identify publication bias, with study quality assessed using the QUADAS-2 (Quality Assessment of Diagnostic Accuracy Studies-2) risk of bias tool.<h4>Results</h4>28 studies were included (10 full-text publications and 18 abstracts), providing 31 comparisons of smartphone PPG versus ECG for AF detection. 11 404 participants were included (2950 in AF), with most studies being small and based in secondary care. Sensitivity and specificity for AF detection were high, ranging from 81% to 100%, and from 85% to 100%, respectively. 20 comparisons from 17 studies were meta-analysed, including 6891 participants (2299 with AF); the pooled sensitivity was 94% (95% CI 92% to 95%) and specificity 97% (96%-98%), with substantial heterogeneity (p<0.01). Studies were of poor quality overall and none met all the QUADAS-2 criteria, with particular issues regarding selection bias and the potential for publication bias.<h4>Conclusion</h4>PPG provides a non-invasive, patient-led screening tool for AF. However, current evidence is limited to small, biased, low-quality studies with unrealistically high sensitivity and specificity. Further studies are needed, preferably independent from manufacturers, in order to advise clinicians on the true value of PPG technology for AF detection.",,pdf:https://heart.bmj.com/content/heartjnl/early/2022/03/10/heartjnl-2021-320417.full.pdf; doi:https://doi.org/10.1136/heartjnl-2021-320417; html:https://europepmc.org/articles/PMC9554073; pdf:https://europepmc.org/articles/PMC9554073?pdf=render
-37119604,https://doi.org/10.1016/j.canep.2023.102367,"Whole-population trends in pathology-confirmed cancer incidence in Northern Ireland, Scotland and Wales during the SARS-CoV-2 pandemic: A retrospective observational study.","Greene GJ, Thomson CS, Donnelly D, Chung D, Bhatti L, Gavin AT, Lawler M, Huws DW, Rolles MJ, Bennée F, Morrison DS.",,Cancer epidemiology,2023,2023-04-21,Y,Pandemic; Population-based Incidence; Covid-19; Sars-cov-2; Pathology-Confirmed Cancer,,,"<h4>Introduction</h4>The COVID-19 epidemic interrupted normal cancer diagnosis procedures. Population-based cancer registries report incidence at least 18 months after it happens. Our goal was to make more timely estimates by using pathologically confirmed cancers (PDC) as a proxy for incidence. We compared the 2020 and 2021 PDC with the 2019 pre-pandemic baseline in Scotland, Wales, and Northern Ireland (NI).<h4>Methods</h4>Numbers of female breast (ICD-10 C50), lung (C33-34), colorectal (C18-20), gynaecological (C51-58), prostate (C61), head and neck (C00-C14, C30-32), upper gastro-intestinal (C15-16), urological (C64-68), malignant melanoma (C43), and non-melanoma skin (NMSC) (C44) cancers were counted. Multiple pairwise comparisons generated incidence rate ratios (IRR).<h4>Results</h4>Data were accessible within 5 months of the pathological diagnosis date. Between 2019 and 2020, the number of pathologically confirmed malignancies (excluding NMSC) decreased by 7315 (14.1 %). Scotland experienced early monthly declines of up to 64 % (colorectal cancers, April 2020 versus April 2019). Wales experienced the greatest overall change in 2020, but Northern Ireland experienced the quickest recovery. The pandemic's effects varied by cancer type, with no significant change in lung cancer diagnoses in Wales in 2020 (IRR 0.97 (95 % CI 0.90-1.05)), followed by an increase in 2021 (IRR 1.11 (1.03-1.20).<h4>Conclusion</h4>PDC are useful in reporting cancer incidence quicker than cancer registrations. Temporal and geographical differences between participating countries mirrored differences in responses to the COVID-19 pandemic, indicating face validity and the potential for quick cancer diagnosis assessment. To verify their sensitivity and specificity against the gold standard of cancer registrations, however, additional research is required.",,doi:https://doi.org/10.1016/j.canep.2023.102367; html:https://europepmc.org/articles/PMC10121133; pdf:https://europepmc.org/articles/PMC10121133?pdf=render
 34137744,https://doi.org/10.1097/ta.0000000000003317,Association between type 2 diabetes and long-term outcomes in middle-aged and older trauma patients.,"Daly SL, Gabbe BJ, Climie RE, Ekegren CL.",,The journal of trauma and acute care surgery,2022,2022-01-01,N,,,,"<h4>Background</h4>Diabetes is associated with increased hospital complications and mortality following trauma. However, there is limited research on the longer-term recovery of trauma patients with diabetes. The aim of this study was to explore the association between type 2 diabetes (T2D) and in-hospital and 24-month outcomes in major trauma patients.<h4>Methods</h4>In this cohort study using the Victorian State Trauma Registry, middle-aged and older adults (≥45 years) with major trauma were followed up at 24 months postinjury. Logistic regression (univariable and multivariable) analyses were used to determine the association between diabetes status and 24-month patient-reported outcomes. In-hospital outcomes were compared between groups using χ2 tests.<h4>Results</h4>Of the 11,490 participants who survived to hospital discharge, 8,493 survived to 24 months postinjury and were followed up at that time point: 953 people (11%) with and 7540 (89%) without T2D. People with T2D had a higher in-hospital death rate (19%) compared with people without T2D (16%; p < 0.001). After adjusting for confounders, people with T2D had poorer outcomes 24 months postinjury than people without T2D, with respect to functional recovery (Glasgow Outcome Scale Extended) (adjusted odds ratio [AOR], 0.58; 95% confidence interval [CI], 0.48-0.69) and return to work/study (AOR, 0.51; 95% CI, 0.37-0.71]). People with T2D experienced higher odds of problems with mobility (AOR, 1.92; 95% CI, 1.60-2.30), self-care (AOR, 1.94; 95% CI, 1.64, 2.29), usual activities (AOR, 1.50; 95% CI, 1.26-1.79), pain and discomfort (AOR, 1.75; 95% CI, 1.49-2.07), anxiety and depression (AOR, 1.45; 95% CI, 1.24, 1.70), and self-reported disability (AOR, 1.51; 95% CI, 1.28-1.79) than people without T2D.<h4>Conclusion</h4>Major trauma patients with T2D have a poorer prognosis than patients without T2D, both during their hospital admission and 24 months postinjury. Patients with T2D may need additional health care and support following trauma to reach their recovery potential.<h4>Level of evidence</h4>Prognostic, level III.",,doi:https://doi.org/10.1097/TA.0000000000003317
+37119604,https://doi.org/10.1016/j.canep.2023.102367,"Whole-population trends in pathology-confirmed cancer incidence in Northern Ireland, Scotland and Wales during the SARS-CoV-2 pandemic: A retrospective observational study.","Greene GJ, Thomson CS, Donnelly D, Chung D, Bhatti L, Gavin AT, Lawler M, Huws DW, Rolles MJ, Bennée F, Morrison DS.",,Cancer epidemiology,2023,2023-04-21,Y,Pandemic; Population-based Incidence; Covid-19; Sars-cov-2; Pathology-Confirmed Cancer,,,"<h4>Introduction</h4>The COVID-19 epidemic interrupted normal cancer diagnosis procedures. Population-based cancer registries report incidence at least 18 months after it happens. Our goal was to make more timely estimates by using pathologically confirmed cancers (PDC) as a proxy for incidence. We compared the 2020 and 2021 PDC with the 2019 pre-pandemic baseline in Scotland, Wales, and Northern Ireland (NI).<h4>Methods</h4>Numbers of female breast (ICD-10 C50), lung (C33-34), colorectal (C18-20), gynaecological (C51-58), prostate (C61), head and neck (C00-C14, C30-32), upper gastro-intestinal (C15-16), urological (C64-68), malignant melanoma (C43), and non-melanoma skin (NMSC) (C44) cancers were counted. Multiple pairwise comparisons generated incidence rate ratios (IRR).<h4>Results</h4>Data were accessible within 5 months of the pathological diagnosis date. Between 2019 and 2020, the number of pathologically confirmed malignancies (excluding NMSC) decreased by 7315 (14.1 %). Scotland experienced early monthly declines of up to 64 % (colorectal cancers, April 2020 versus April 2019). Wales experienced the greatest overall change in 2020, but Northern Ireland experienced the quickest recovery. The pandemic's effects varied by cancer type, with no significant change in lung cancer diagnoses in Wales in 2020 (IRR 0.97 (95 % CI 0.90-1.05)), followed by an increase in 2021 (IRR 1.11 (1.03-1.20).<h4>Conclusion</h4>PDC are useful in reporting cancer incidence quicker than cancer registrations. Temporal and geographical differences between participating countries mirrored differences in responses to the COVID-19 pandemic, indicating face validity and the potential for quick cancer diagnosis assessment. To verify their sensitivity and specificity against the gold standard of cancer registrations, however, additional research is required.",,doi:https://doi.org/10.1016/j.canep.2023.102367; html:https://europepmc.org/articles/PMC10121133; pdf:https://europepmc.org/articles/PMC10121133?pdf=render
 33543581,https://doi.org/10.1111/ans.16578,Outcomes of surgical site infections following spinal column trauma.,"Baroun-Agob L, Liew S, Gabbe B.",,ANZ journal of surgery,2021,2021-02-05,N,Spine; Trauma; Surgical Wound Infection; Orthopaedic Surgery; Patient-reported Outcome Measures,,,"<h4>Background</h4>Surgical site infections (SSI) are an undesirable outcome of spinal surgery for both the patient and healthcare system. To date, few studies have investigated the impact of SSI on patient-reported and clinical outcomes. Sepsis and readmission are potential sequelae of SSI, with sepsis potentially being life threatening. This study aimed to assess the association between SSI and patient outcomes in a spinal trauma cohort.<h4>Methods</h4>Adult (16+ years) patients who underwent emergency spinal surgery due to trauma between January 2010 and December 2016 at a major trauma centre in Melbourne, Australia, were identified through the Victorian Orthopaedic Trauma Outcomes Registry. The presence of an SSI was abstracted from the electronic medical record and outcomes were compared between patients with and without an SSI. Clinical outcomes were obtained from the medical record, and patient-reported outcomes at 6 and 12 months were obtained from the Victorian Orthopaedic Trauma Outcomes Registry. Chi-squared tests were used to compare patient outcomes between groups.<h4>Results</h4>Of the 458 included patients, 26 (5.7%) developed an SSI. Patient-reported outcomes at 6 and 12 months were not different between the groups. An SSI was associated with sepsis (χ<sup>2</sup><sub>1</sub> = 24.20, P < 0.01), readmission (χ<sup>2</sup><sub>1</sub> = 215.34, P < 0.01), revision surgery (χ<sup>2</sup><sub>1</sub> = 171.21, P < 0.01) and removal of implants (χ<sup>2</sup><sub>1</sub> = 4.31, P = 0.04) within 12 months of discharge.<h4>Conclusion</h4>These findings indicate that spine trauma SSIs are not associated with patient-reported outcomes and may not have lasting effects on patients. Larger studies are required to assess further follow-up and support our findings and possibly distinguish outcomes between superficial and deep SSI.",,doi:https://doi.org/10.1111/ans.16578
 35595677,https://doi.org/10.1016/s2589-7500(22)00061-9,Identifying adverse childhood experiences with electronic health records of linked mothers and children in England: a multistage development and validation study.,"Syed S, Gonzalez-Izquierdo A, Allister J, Feder G, Li L, Gilbert R.",,The Lancet. Digital health,2022,2022-05-17,N,,,,"<h4>Background</h4>Electronic health records (EHRs) of mothers and children provide an opportunity to identify adverse childhood experiences (ACEs) during crucial periods of childhood development, yet well developed indicators of ACEs remain scarce. We aimed to develop clinically relevant indicators of ACEs for linked EHRs of mothers and children using a multistage prediction model of child maltreatment and maternal intimate partner violence (IPV).<h4>Methods</h4>In this multistage development and validation study, we developed a representative population-based birth cohort of mothers and children in England, followed from up to 2 years before birth to up to 5 years after birth across the Clinical Practice Research Datalink (CPRD) GOLD (primary care), Hospital Episode Statistics (secondary care), and the Office for National Statistics mortality register. We included livebirths in England between July 1, 2004, and June 30, 2016, to mothers aged 16-55 years, who had registered with a general practitioner (GP) that met CPRD quality standards before 21 weeks of gestation. The primary outcome (reference standard) was any child maltreatment or maternal IPV in either the mother's or child's record from 2 years before birth (maternal IPV only) to 5 years after birth. We used seven prediction models, combined with expert ratings, to systematically develop indicators. We validated the final indicators by integrating results from machine learning models, survival analyses, and clustering analyses in the validation cohort.<h4>Findings</h4>We included data collected between July 1, 2002, and June 27, 2018. Of 376 006 eligible births, we included 211 393 mother-child pairs (422 786 patients) from 400 practices, of whom 126 837 mother-child pairs (60·0%; 240 practices) were randomly assigned to a derivation cohort and 84 556 pairs (40·0%; 160 practices) to a validation cohort. We included 63 indicators in six ACE domains: maternal mental health problems, maternal substance misuse, adverse family environments, child maltreatment, maternal IPV, and high-risk presentations of child maltreatment. Excluding the seven indicators in the reference standard, 56 indicators showed high discriminative validity for the reference standard of any child maltreatment or maternal IPV between 2 years before and 5 years after birth (validation cohort, area under the receiver operating characteristic curve 0·85 [95% CI 0·84-0·86]). During the 2 years before birth and 5 years after birth, the overall period prevalence of maternal IPV and child maltreatment (reference standard) was 2·3% (2876 of 126 837 pairs) in the derivation cohort and 2·3% (1916 of 84 556 pairs) in the validation cohort. During the 2 years before and after birth, the period prevalence was 39·1% (95% CI 38·7-39·5; 34 773 pairs) for any of the 63 ACE indicators, 22·2% (21·8-22·5%; 20 122 pairs) for maternal mental health problems, 15·7% (15·4-16·0%; 14 549 pairs) for adverse family environments, 8·1% (7·8-8·3%; 6808 pairs) for high-risk presentations of child maltreatment, 6·9% (6·7-7·2%; 7856 pairs) for maternal substance misuse, and 3·0% (2·9-3·2%; 2540 pairs) for any child maltreatment (2·4% [2·3-5·6%; 2051 pairs]) and maternal IPV (1·0% [0·8-1·0%; 875 pairs]). 62·6% (21 785 of 34 773 pairs) of ACEs were recorded in primary care only, and 72·3% (25 140 cases) were recorded in the maternal record only.<h4>Interpretation</h4>We developed clinically relevant indicators for identifying ACEs using the EHRs of mothers and children presenting to general practices and hospital admissions. Over 70% of ACEs were identified via maternal records and were recorded in primary care by GPs within 2 years of birth, reinforcing the importance of reviewing parental and carer records to inform clinical responses to children. ACE indicators can contribute to longitudinal surveillance informing public health policy and resource allocation. Further evaluation is required to determine how ACE indicators can be used in clinical practice.<h4>Funding</h4>None.",,pdf:http://www.thelancet.com/article/S2589750022000619/pdf; doi:https://doi.org/10.1016/S2589-7500(22)00061-9
 32071531,https://doi.org/10.1016/j.jor.2020.02.001,Predictors of clavicle fixation in multiply injured patients.,"Tinney A, Moaveni AK, Kimmel LA, Gabbe BJ.",,Journal of orthopaedics,2020,2020-02-04,N,Trauma; Operative treatment; Trauma Registry; Clavicle Fracture; Surgical Fixation; Multiply Injured Patient,,,"<h4>Introduction</h4>Clavicle fractures account for approximately 10% of all fractures in multiply injured patients. Our study aims to determine factors associated with surgical fixation of the clavicle fracture in multiply injured patients.<h4>Methods</h4>Major adult trauma patients from 2005 to 2014 with a clavicle fracture were included. Multivariate analysis was undertaken to determine the variables associated with fixation.<h4>Results</h4>1779 patients (median age of 47 and a median Injury Severity Score of 17) were included. 273 (15%) patients underwent clavicle fixation. Factors associated with surgical fixation of the clavicle included: year, younger age, ICU admission, or an associated humerus or scapula fracture.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7016330; doi:https://doi.org/10.1016/j.jor.2020.02.001; html:https://europepmc.org/articles/PMC7016330; pdf:https://europepmc.org/articles/PMC7016330?pdf=render; doi:https://doi.org/10.1016/j.jor.2020.02.001
 33766511,https://doi.org/10.1016/j.jid.2021.02.744,Raising the Bar for Randomized Trials Involving Artificial Intelligence: The SPIRIT-Artificial Intelligence and CONSORT-Artificial Intelligence Guidelines.,"Taylor M, Liu X, Denniston A, Esteva A, Ko J, Daneshjou R, Chan AW, SPIRIT-AI and CONSORT-AI Working Group.",,The Journal of investigative dermatology,2021,2021-03-22,N,,,,"Artificial intelligence (AI)-based applications have the potential to improve the quality and efficiency of patient care in dermatology. Unique challenges in the development and validation of these technologies may limit their generalizability and real-world applicability. Before the widespread adoption of AI interventions, randomized trials should be conducted to evaluate their efficacy, safety, and cost effectiveness in clinical settings. The recent Standard Protocol Items: Recommendations for Interventional Trials-AI extension and Consolidated Standards of Reporting Trials-AI extension guidelines provide recommendations for reporting the methods and results of trials involving AI interventions. High-quality trials will provide gold standard evidence to support the adoption of AI for the benefit of patient care.",,doi:https://doi.org/10.1016/j.jid.2021.02.744
-38660106,https://doi.org/10.1016/j.jacasi.2024.02.003,Depression and Incident Cardiovascular Disease.,"Pennells L, Mascie-Taylor CGN.",,JACC. Asia,2024,2024-04-03,Y,Sex difference; Depression; Cardiovascular disease; epidemiology,,,,,doi:https://doi.org/10.1016/j.jacasi.2024.02.003; html:https://europepmc.org/articles/PMC11035929; pdf:https://europepmc.org/articles/PMC11035929?pdf=render
 33517835,https://doi.org/10.1080/17457300.2021.1876736,Identify the key characteristics of pedestrian collisions through in-depth interviews: a pilot study.,"Perkins M, Casalaz S, Mitra B, Gabbe B, Brown J, Oxley J, Cameron P, Beck B.",,International journal of injury control and safety promotion,2021,2021-01-31,N,Behaviour; Public Health; Pedestrian,,,"This study aimed to assess the feasibility of recruiting injured pedestrians from the emergency department of a major trauma centre, using an in-depth interview shortly post collision. Convenience sampling was used to prospectively recruit injured pedestrians from the Alfred Hospital Emergency and Trauma Centre. Of the 102 injured pedestrians, 39 met eligibility criteria and of these, 30 (77%) consented and completed the questionnaire. Over half of the collisions occurred at an intersection (57%), and of these the most common pre-impact vehicle manoeuvre was a vehicle turning into the street the pedestrian was crossing. In-depth interview during the early post-crash period was a feasible and effective method of collecting detailed data in an accessible sample. However, only 38% of patients met eligibility criteria. To enhance representativeness, supplementing interview data with police-reported crash data, recruiting from hospital wards and crash location assessment is recommended.",,pdf:https://figshare.com/articles/journal_contribution/Identify_the_key_characteristics_of_pedestrian_collisions_through_in-depth_interviews_a_pilot_study/13671482/1/files/26241158.pdf; doi:https://doi.org/10.1080/17457300.2021.1876736
+38660106,https://doi.org/10.1016/j.jacasi.2024.02.003,Depression and Incident Cardiovascular Disease.,"Pennells L, Mascie-Taylor CGN.",,JACC. Asia,2024,2024-04-03,Y,Sex difference; Depression; Cardiovascular disease; epidemiology,,,,,doi:https://doi.org/10.1016/j.jacasi.2024.02.003; html:https://europepmc.org/articles/PMC11035929; pdf:https://europepmc.org/articles/PMC11035929?pdf=render
 36224187,https://doi.org/10.1038/s41467-022-33826-4,Key considerations to reduce or address respondent burden in patient-reported outcome (PRO) data collection.,"Aiyegbusi OL, Roydhouse J, Rivera SC, Kamudoni P, Schache P, Wilson R, Stephens R, Calvert M.",,Nature communications,2022,2022-10-12,Y,,,,"Patient-reported outcomes (PROs) are used in clinical trials to provide evidence of the benefits and risks of interventions from a patient perspective and to inform regulatory decisions and health policy. The collection of PROs in routine practice can facilitate monitoring of patient symptoms; identification of unmet needs; prioritisation and/or tailoring of treatment to the needs of individual patients and inform value-based healthcare initiatives. However, respondent burden needs to be carefully considered and addressed to avoid high rates of missing data and poor reporting of PRO results, which may lead to poor quality data for regulatory decision making and/or clinical care.",,pdf:https://www.nature.com/articles/s41467-022-33826-4.pdf; doi:https://doi.org/10.1038/s41467-022-33826-4; html:https://europepmc.org/articles/PMC9556436; pdf:https://europepmc.org/articles/PMC9556436?pdf=render
 30909231,https://doi.org/10.3233/jad-181085,A Meta-Analysis of Alzheimer's Disease Brain Transcriptomic Data.,"Patel H, Dobson RJB, Newhouse SJ.",,Journal of Alzheimer's disease : JAD,2019,2019-01-01,Y,Human; Meta-analysis; Neuropathology; Mental disorders; Alzheimer’s disease; Gene Expression; Neurodegenerative Disorders; Microarray Analysis,,,"<h4>Background</h4>Microarray technologies have identified imbalances in the expression of specific genes and biological pathways in Alzheimer's disease (AD) brains. However, there is a lack of reproducibility across individual AD studies, and many related neurodegenerative and mental health disorders exhibit similar perturbations.<h4>Objective</h4>Meta-analyze publicly available transcriptomic data from multiple brain-related disorders to identify robust transcriptomic changes specific to AD brains.<h4>Methods</h4>Twenty-two AD, eight schizophrenia, five bipolar disorder, four Huntington's disease, two major depressive disorder, and one Parkinson's disease dataset totaling 2,667 samples and mapping to four different brain regions (temporal lobe, frontal lobe, parietal lobe, and cerebellum) were analyzed. Differential expression analysis was performed independently in each dataset, followed by meta-analysis using a combining p-value method known as Adaptively Weighted with One-sided Correction.<h4>Results</h4>Meta-analysis identified 323, 435, 1,023, and 828 differentially expressed genes specific to the AD temporal lobe, frontal lobe, parietal lobe, and cerebellum brain regions, respectively. Seven of these genes were consistently perturbed across all AD brain regions with SPCS1 gene expression pattern replicating in RNA-Seq data. A further nineteen genes were perturbed specifically in AD brain regions affected by both plaques and tangles, suggesting possible involvement in AD neuropathology. In addition, biological pathways involved in the ""metabolism of proteins"" and viral components were significantly enriched across AD brains.<h4>Conclusion</h4>This study identified transcriptomic changes specific to AD brains, which could make a significant contribution toward the understanding of AD disease mechanisms and may also provide new therapeutic targets.",,pdf:https://content.iospress.com:443/download/journal-of-alzheimers-disease/jad181085?id=journal-of-alzheimers-disease%2Fjad181085; doi:https://doi.org/10.3233/JAD-181085; html:https://europepmc.org/articles/PMC6484273; pdf:https://europepmc.org/articles/PMC6484273?pdf=render
-38526449,https://doi.org/10.1002/clt2.12348,Ethnic differences in depression and anxiety among adults with atopic eczema: Population-based matched cohort studies within UK primary care.,"Adesanya EI, Henderson A, Hayes JF, Lewin A, Mathur R, Mulick A, Morton C, Smith C, Langan SM, Mansfield KE.",,Clinical and translational allergy,2024,2024-03-01,Y,Depression; Anxiety; epidemiology; Atopic Eczema; Ethnicity,,,"<h4>Background</h4>Evidence demonstrates that individuals with atopic eczema (eczema) have increased depression and anxiety; however, the role of ethnicity in these associations is poorly understood. We aimed to investigate whether associations between eczema and depression or anxiety differed between adults from white and minority ethnic groups in the UK.<h4>Methods</h4>We used UK Clinical Practice Research Datalink GOLD to conduct matched cohort studies of adults (≥18 years) with ethnicity recorded in primary care electronic health records (April 2006-January 2020). We matched (age, sex, practice) adults with eczema to up to five adults without. We used stratified Cox regression with an interaction between eczema and ethnicity, to estimate hazard ratios (HRs) for associations between eczema and incident depression and anxiety in individuals from white ethnic groups and a pooled minority ethnic group (adults from Black, South Asian, Mixed and Other groups).<h4>Results</h4>We identified separate cohorts for depression (215,073 with eczema matched to 646,539 without) and anxiety (242,598 with eczema matched to 774,113 without). After adjusting for matching variables and potential confounders (age, sex, practice, deprivation, calendar period), we found strong evidence (p < 0.01) of ethnic differences in associations between eczema and depression (minority ethnic groups: HR = 1.33, 95% CI = 1.22,1.45; white ethnic groups: HR = 1.15, 95% CI = 1.12,1.17) and anxiety (minority ethnic groups: HR = 1.41, 95% CI = 1.28,1.55; white ethnic groups: HR = 1.17, 95% CI = 1.14,1.19).<h4>Conclusions</h4>Adults with eczema from minority ethnic groups appear to be at increased depression and anxiety risk compared with their white counterparts. Culturally adapted mental health promotion and prevention strategies should be considered in individuals with eczema from minority ethnic groups.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/clt2.12348; doi:https://doi.org/10.1002/clt2.12348; html:https://europepmc.org/articles/PMC10962487; pdf:https://europepmc.org/articles/PMC10962487?pdf=render
 35816976,https://doi.org/10.1016/j.jpsychires.2022.06.044,Anticoagulation for atrial fibrillation in people with serious mental illness in the general hospital setting.,"Farran D, Bean D, Wang T, Msosa Y, Casetta C, Dobson R, Teo JT, Scott P, Gaughran F.",,Journal of psychiatric research,2022,2022-06-28,N,Atrial fibrillation; Warfarin; Serious Mental Illness; Oral Anticoagulation; Doacs,,,"<h4>Objective</h4>People with serious mental illnesses (SMI) have an increased risk of stroke compared to the general population. This study aims to evaluate oral anticoagulation prescription trends in atrial fibrillation (AF) patients with and without a comorbid SMI.<h4>Methods</h4>An open-source retrieval system for clinical data (CogStack) was used to identify a cohort of AF patients with SMI who ever had an inpatient admission to King's College Hospital from 2011 to 2020. A Natural Language Processing pipeline was used to calculate CHA2DS2-VASc and HASBLED risk scores from Electronic Health Records free text. Antithrombotic prescriptions of warfarin and Direct acting oral anti-coagulants (DOACs) (apixaban, rivaroxaban, dabigatran, edoxaban) were extracted from discharge summaries.<h4>Results</h4>Among patients included in the study (n = 16 916), 2.7% had a recorded co-morbid SMI diagnosis. Compared to non-SMI patients, those with SMI had significantly higher CHA2DS2-VASc (mean (SD): 5.3 (1.96) vs 4.7 (2.08), p < 0.001) and HASBLED scores (mean (SD): 3.2 (1.27) vs 2.5 (1.29), p < 0.001). Among AF patients having a CHA2DS2-VASc ≥2, those with co-morbid SMI were less likely than non-SMI patients to be prescribed an OAC (44% vs 54%, p < 0.001). However, there was no evidence of a significant difference between the two groups since 2019.<h4>Conclusion</h4>Over recent years, DOAC prescription rates have increased among AF patients with SMI in acute hospitals. More research is needed to confirm whether the introduction of DOACs has reduced OAC treatment gaps in people with serious mental illness and to assess whether the use of DOACs has improved health outcomes in this population.",,doi:https://doi.org/10.1016/j.jpsychires.2022.06.044; doi:https://doi.org/10.1016/j.jpsychires.2022.06.044
+38526449,https://doi.org/10.1002/clt2.12348,Ethnic differences in depression and anxiety among adults with atopic eczema: Population-based matched cohort studies within UK primary care.,"Adesanya EI, Henderson A, Hayes JF, Lewin A, Mathur R, Mulick A, Morton C, Smith C, Langan SM, Mansfield KE.",,Clinical and translational allergy,2024,2024-03-01,Y,Depression; Anxiety; epidemiology; Atopic Eczema; Ethnicity,,,"<h4>Background</h4>Evidence demonstrates that individuals with atopic eczema (eczema) have increased depression and anxiety; however, the role of ethnicity in these associations is poorly understood. We aimed to investigate whether associations between eczema and depression or anxiety differed between adults from white and minority ethnic groups in the UK.<h4>Methods</h4>We used UK Clinical Practice Research Datalink GOLD to conduct matched cohort studies of adults (≥18 years) with ethnicity recorded in primary care electronic health records (April 2006-January 2020). We matched (age, sex, practice) adults with eczema to up to five adults without. We used stratified Cox regression with an interaction between eczema and ethnicity, to estimate hazard ratios (HRs) for associations between eczema and incident depression and anxiety in individuals from white ethnic groups and a pooled minority ethnic group (adults from Black, South Asian, Mixed and Other groups).<h4>Results</h4>We identified separate cohorts for depression (215,073 with eczema matched to 646,539 without) and anxiety (242,598 with eczema matched to 774,113 without). After adjusting for matching variables and potential confounders (age, sex, practice, deprivation, calendar period), we found strong evidence (p < 0.01) of ethnic differences in associations between eczema and depression (minority ethnic groups: HR = 1.33, 95% CI = 1.22,1.45; white ethnic groups: HR = 1.15, 95% CI = 1.12,1.17) and anxiety (minority ethnic groups: HR = 1.41, 95% CI = 1.28,1.55; white ethnic groups: HR = 1.17, 95% CI = 1.14,1.19).<h4>Conclusions</h4>Adults with eczema from minority ethnic groups appear to be at increased depression and anxiety risk compared with their white counterparts. Culturally adapted mental health promotion and prevention strategies should be considered in individuals with eczema from minority ethnic groups.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/clt2.12348; doi:https://doi.org/10.1002/clt2.12348; html:https://europepmc.org/articles/PMC10962487; pdf:https://europepmc.org/articles/PMC10962487?pdf=render
+32946613,https://doi.org/10.1111/cea.13741,Ethnicity-based differences in the incident risk of allergic diseases and autoimmune disorders: A UK-based retrospective cohort study of 4.4 million participants.,"Subramanian A, Adderley NJ, Gkoutos GV, Gokhale KM, Nirantharakumar K, Krishna MT.",,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2021,2020-09-29,N,Asthma; Rheumatoid; SLE; Autoimmunity; Rhinitis; Vitiligo; epidemiology; Ethnicity; Atopic Dermatitis,,,,,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/cea.13741; doi:https://doi.org/10.1111/cea.13741
 39277784,https://doi.org/10.1093/ndt/gfae203,Empagliflozin lowers serum uric acid in chronic kidney disease: exploratory analyses from the EMPA-KIDNEY trial.,"Mayne KJ, Sardell RJ, Staplin N, Judge PK, Zhu D, Sammons E, Cherney DZI, Green JB, Levin A, Pontremoli R, Hauske SJ, Emberson J, Preiss D, Landray MJ, Baigent C, Wanner C, Haynes R, Herrington WG, EMPA-KIDNEY Collaborative Group
 .",,"Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association",2024,2024-09-14,Y,Uric acid; Gout; Sglt2 Inhibitor; Ckd; Empagliflozin,,,"<h4>Background and hypothesis</h4>Hyperuricaemia and gout are common in chronic kidney disease (CKD). We aimed to assess the effects of sodium-glucose co-transporter-2 (SGLT2) inhibition on uric acid (urate) and gout in patients with CKD.<h4>Methods</h4>The EMPA-KIDNEY trial randomised 6609 patients with CKD (estimated glomerular filtration rate [eGFR] ≥20 and <90 mL/min/1.73m2) to receive either empagliflozin 10 mg daily or matching placebo over a median of two years follow-up. Serum uric acid was measured at randomisation then 2 and 18 months of follow-up and the effects of empagliflozin were analysed using a pre-specified mixed model repeated measures approach. Participant-reported gout events were analysed in Cox regression models (first events) with the Andersen-Gill extension (total events). A post-hoc composite outcome included new initiation of uric acid lowering therapy or colchicine. EMPA-KIDNEY primary and kidney disease progression outcomes were also assessed in subgroups of baseline serum uric acid.<h4>Results</h4>Baseline mean ± SD serum uric acid concentration was 431±114 µmol/L. Allocation to empagliflozin resulted in a study-average between-group difference in serum uric acid of -25.6 (95%CI -30.3,-21.0) µmol/L with larger effects in those with higher eGFR (trend P < 0.001) and without diabetes (heterogeneity P < 0.001). Compared to placebo, empagliflozin did not significantly reduce first or total gout events (HR 0.87, 95%CI 0.74-1.02 for the 595 first events, and 0.86, 0.72-1.03 for the 869 total events) with similar hazard ratios for the post-hoc composite and across subgroups, including by diabetes and eGFR. The effect of empagliflozin on the primary outcome and kidney disease progression outcomes were similar irrespective of baseline level of uric acid.<h4>Conclusion</h4>SGLT2 inhibition reduces serum uric acid in patients with CKD with larger effects at higher eGFR and in the absence of diabetes. However, the effect on uric acid is modest and did not translate into reduced risk of gout in EMPA-KIDNEY.",,doi:https://doi.org/10.1093/ndt/gfae203; html:https://europepmc.org/articles/PMC7616479; pdf:https://europepmc.org/articles/PMC7616479?pdf=render
-32946613,https://doi.org/10.1111/cea.13741,Ethnicity-based differences in the incident risk of allergic diseases and autoimmune disorders: A UK-based retrospective cohort study of 4.4 million participants.,"Subramanian A, Adderley NJ, Gkoutos GV, Gokhale KM, Nirantharakumar K, Krishna MT.",,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2021,2020-09-29,N,Asthma; Rheumatoid; SLE; Autoimmunity; Rhinitis; Vitiligo; epidemiology; Ethnicity; Atopic Dermatitis,,,,,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/cea.13741; doi:https://doi.org/10.1111/cea.13741
 32975552,https://doi.org/10.1001/jamapediatrics.2020.4573,Susceptibility to SARS-CoV-2 Infection Among Children and Adolescents Compared With Adults: A Systematic Review and Meta-analysis.,"Viner RM, Mytton OT, Bonell C, Melendez-Torres GJ, Ward J, Hudson L, Waddington C, Thomas J, Russell S, van der Klis F, Koirala A, Ladhani S, Panovska-Griffiths J, Davies NG, Booy R, Eggo RM.",,JAMA pediatrics,2021,2021-02-01,N,,,,"<h4>Importance</h4>The degree to which children and adolescents are infected by and transmit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unclear. The role of children and adolescents in transmission of SARS-CoV-2 is dependent on susceptibility, symptoms, viral load, social contact patterns, and behavior.<h4>Objective</h4>To systematically review the susceptibility to and transmission of SARS-CoV-2 among children and adolescents compared with adults.<h4>Data sources</h4>PubMed and medRxiv were searched from database inception to July 28, 2020, and a total of 13 926 studies were identified, with additional studies identified through hand searching of cited references and professional contacts.<h4>Study selection</h4>Studies that provided data on the prevalence of SARS-CoV-2 in children and adolescents (younger than 20 years) compared with adults (20 years and older) derived from contact tracing or population screening were included. Single-household studies were excluded.<h4>Data extraction and synthesis</h4>PRISMA guidelines for abstracting data were followed, which was performed independently by 2 reviewers. Quality was assessed using a critical appraisal checklist for prevalence studies. Random-effects meta-analysis was undertaken.<h4>Main outcomes and measures</h4>Secondary infection rate (contact-tracing studies) or prevalence or seroprevalence (population screening studies) among children and adolescents compared with adults.<h4>Results</h4>A total of 32 studies comprising 41 640 children and adolescents and 268 945 adults met inclusion criteria, including 18 contact-tracing studies and 14 population screening studies. The pooled odds ratio of being an infected contact in children compared with adults was 0.56 (95% CI, 0.37-0.85), with substantial heterogeneity (I2 = 94.6%). Three school-based contact-tracing studies found minimal transmission from child or teacher index cases. Findings from population screening studies were heterogenous and were not suitable for meta-analysis. Most studies were consistent with lower seroprevalence in children compared with adults, although seroprevalence in adolescents appeared similar to adults.<h4>Conclusions and relevance</h4>In this meta-analysis, there is preliminary evidence that children and adolescents have lower susceptibility to SARS-CoV-2, with an odds ratio of 0.56 for being an infected contact compared with adults. There is weak evidence that children and adolescents play a lesser role than adults in transmission of SARS-CoV-2 at a population level. This study provides no information on the infectivity of children.",,html:https://europepmc.org/articles/pmc7519436; doi:https://doi.org/10.1001/jamapediatrics.2020.4573; html:https://europepmc.org/articles/PMC7519436; doi:https://doi.org/10.1001/jamapediatrics.2020.4573
 38967666,https://doi.org/10.1007/s00125-024-06214-4,Single-cell transcriptomic profiling of human pancreatic islets reveals genes responsive to glucose exposure over 24 h.,"Grenko CM, Taylor HJ, Bonnycastle LL, Xue D, Lee BN, Weiss Z, Yan T, Swift AJ, Mansell EC, Lee A, Robertson CC, Narisu N, Erdos MR, Chen S, Collins FS, Taylor DL.",,Diabetologia,2024,2024-07-05,Y,Genetics; Genomics; Islets; Type 2 diabetes; Transcriptomics; Single-cell; Gsis,,,"<h4>Aims/hypothesis</h4>Disruption of pancreatic islet function and glucose homeostasis can lead to the development of sustained hyperglycaemia, beta cell glucotoxicity and subsequently type 2 diabetes. In this study, we explored the effects of in vitro hyperglycaemic conditions on human pancreatic islet gene expression across 24 h in six pancreatic cell types: alpha; beta; gamma; delta; ductal; and acinar. We hypothesised that genes associated with hyperglycaemic conditions may be relevant to the onset and progression of diabetes.<h4>Methods</h4>We exposed human pancreatic islets from two donors to low (2.8 mmol/l) and high (15.0 mmol/l) glucose concentrations over 24 h in vitro. To assess the transcriptome, we performed single-cell RNA-seq (scRNA-seq) at seven time points. We modelled time as both a discrete and continuous variable to determine momentary and longitudinal changes in transcription associated with islet time in culture or glucose exposure. Additionally, we integrated genomic features and genetic summary statistics to nominate candidate effector genes. For three of these genes, we functionally characterised the effect on insulin production and secretion using CRISPR interference to knock down gene expression in EndoC-βH1 cells, followed by a glucose-stimulated insulin secretion assay.<h4>Results</h4>In the discrete time models, we identified 1344 genes associated with time and 668 genes associated with glucose exposure across all cell types and time points. In the continuous time models, we identified 1311 genes associated with time, 345 genes associated with glucose exposure and 418 genes associated with interaction effects between time and glucose across all cell types. By integrating these expression profiles with summary statistics from genetic association studies, we identified 2449 candidate effector genes for type 2 diabetes, HbA<sub>1c</sub>, random blood glucose and fasting blood glucose. Of these candidate effector genes, we showed that three (ERO1B, HNRNPA2B1 and RHOBTB3) exhibited an effect on glucose-stimulated insulin production and secretion in EndoC-βH1 cells.<h4>Conclusions/interpretation</h4>The findings of our study provide an in-depth characterisation of the 24 h transcriptomic response of human pancreatic islets to glucose exposure at a single-cell resolution. By integrating differentially expressed genes with genetic signals for type 2 diabetes and glucose-related traits, we provide insights into the molecular mechanisms underlying glucose homeostasis. Finally, we provide functional evidence to support the role of three candidate effector genes in insulin secretion and production.<h4>Data availability</h4>The scRNA-seq data from the 24 h glucose exposure experiment performed in this study are available in the database of Genotypes and Phenotypes (dbGap; https://www.ncbi.nlm.nih.gov/gap/ ) with accession no. phs001188.v3.p1. Study metadata and summary statistics for the differential expression, gene set enrichment and candidate effector gene prediction analyses are available in the Zenodo data repository ( https://zenodo.org/ ) under accession number 11123248. The code used in this study is publicly available at https://github.com/CollinsLabBioComp/publication-islet_glucose_timecourse .",,doi:https://doi.org/10.1007/s00125-024-06214-4; doi:https://doi.org/10.1007/s00125-024-06214-4; html:https://europepmc.org/articles/PMC11447040; pdf:https://europepmc.org/articles/PMC11447040?pdf=render
 35508365,https://doi.org/10.1136/injuryprev-2021-044513,Prevalence of alcohol and other drug use in patients presenting to hospital for fall-related injuries: a systematic review.,"Lau G, Ang JY, Kim N, Gabbe BJ, Mitra B, Dietze PM, Reeder S, Beck B.",,Injury prevention : journal of the International Society for Child and Adolescent Injury Prevention,2022,2022-05-04,N,Drugs; Alcohol; Fall; Systematic review; Metanalysis,,,"<h4>Background</h4>Alcohol and other drug (AOD) use is a key preventable risk factor for serious injuries. Prevention strategies to date have largely focused on transport injuries, despite AOD use being a significant risk factor for other injury causes, including falls. This systematic review aimed to report the prevalence of AOD use in patients presenting to hospital for fall-related injuries.<h4>Methods</h4>This systematic review includes studies published in English after the year 2010 that objectively measured the prevalence of AOD use in patients presenting to hospital for a fall-related injury. Screening, data extraction and risk of bias assessments were completed by two independent reviewers. Data were presented using narrative synthesis and, where appropriate, meta-analyses.<h4>Results</h4>A total of 12 707 records were screened. Full texts were retrieved for 2042 records, of which 29 were included. Four studies reported the combined prevalence of any alcohol and/or drug use, generating a pooled prevalence estimate of 37% (95% CI 25% to 49%). Twenty-two records reported on the prevalence of acute alcohol use alone and nine reported specifically on the prevalence of drugs other than alcohol, with prevalence ranging from 2% to 57% and 7% to 46%, respectively. The variation in prevalence estimates likely resulted from differences in toxicology testing methods across studies.<h4>Conclusions</h4>AOD exposure was common in hospitalised fall-related injuries. However, research addressing prevalence across different types of falls and the use of drugs other than alcohol was limited. Future research should address these areas to improve our understanding of which populations should be targeted in AOD and injury prevention strategies .<h4>Prospero registration number</h4>CRD42020188746.",,doi:https://doi.org/10.1136/injuryprev-2021-044513
-38355192,https://doi.org/10.1136/bmjopen-2023-080678,How far back do we need to look to capture diagnoses in electronic health records? A retrospective observational study of hospital electronic health record data.,"Lewis J, Evison F, Doal R, Field J, Gallier S, Harris S, le Roux P, Osman M, Plummer C, Sapey E, Singer M, Sayer AA, Witham MD, ADMISSION Research Collaborative.",,BMJ open,2024,2024-02-13,Y,Hospitals; Electronic Health Records; Information Extraction,,,"<h4>Objectives</h4>Analysis of routinely collected electronic health data is a key tool for long-term condition research and practice for hospitalised patients. This requires accurate and complete ascertainment of a broad range of diagnoses, something not always recorded on an admission document at a single point in time. This study aimed to ascertain how far back in time electronic hospital records need to be interrogated to capture long-term condition diagnoses.<h4>Design</h4>Retrospective observational study of routinely collected hospital electronic health record data.<h4>Setting</h4>Queen Elizabeth Hospital Birmingham (UK)-linked data held by the PIONEER acute care data hub.<h4>Participants</h4>Patients whose first recorded admission for chronic obstructive pulmonary disease (COPD) exacerbation (n=560) or acute stroke (n=2142) was between January and December 2018 and who had a minimum of 10 years of data prior to the index date.<h4>Outcome measures</h4>We identified the most common International Classification of Diseases version 10-coded diagnoses received by patients with COPD and acute stroke separately. For each diagnosis, we derived the number of patients with the diagnosis recorded at least once over the full 10-year lookback period, and then compared this with shorter lookback periods from 1 year to 9 years prior to the index admission.<h4>Results</h4>Seven of the top 10 most common diagnoses in the COPD dataset reached >90% completeness by 6 years of lookback. Atrial fibrillation and diabetes were >90% coded with 2-3 years of lookback, but hypertension and asthma completeness continued to rise all the way out to 10 years of lookback. For stroke, 4 of the top 10 reached 90% completeness by 5 years of lookback; angina pectoris was >90% coded at 7 years and previous transient ischaemic attack completeness continued to rise out to 10 years of lookback.<h4>Conclusion</h4>A 7-year lookback captures most, but not all, common diagnoses. Lookback duration should be tailored to the conditions being studied.",,pdf:https://bmjopen.bmj.com/content/bmjopen/14/2/e080678.full.pdf; doi:https://doi.org/10.1136/bmjopen-2023-080678; html:https://europepmc.org/articles/PMC10868273; pdf:https://europepmc.org/articles/PMC10868273?pdf=render
 37658971,https://doi.org/10.1007/s11897-023-00626-w,Multimorbidity in Heart Failure: Leveraging Cluster Analysis to Guide Tailored Treatment Strategies.,"van de Veerdonk MC, Savarese G, Handoko ML, Beulens JWJ, Asselbergs F, Uijl A.",,Current heart failure reports,2023,2023-09-02,Y,Clustering; Phenotyping; Heart Failure; Machine Learning; Treatment Response; Precision Medicine,,,"<h4>Review purpose</h4>This review summarises key findings on treatment effects within phenotypical clusters of patients with heart failure (HF), making a distinction between patients with preserved ejection fraction (HFpEF) and reduced ejection fraction (HFrEF).<h4>Findings</h4>Treatment response differed among clusters; ACE inhibitors were beneficial in all HFrEF phenotypes, while only some studies show similar beneficial prognostic effects in HFpEF patients. Beta-blockers had favourable effects in all HFrEF patients but not in HFpEF phenotypes and tended to worsen prognosis in older, cardiorenal patients. Mineralocorticoid receptor antagonists had more favourable prognostic effects in young, obese males and metabolic HFpEF patients. While a phenotype-guided approach is a promising solution for individualised treatment strategies, there are several aspects that still require improvements before such an approach could be implemented in clinical practice. Stronger evidence from clinical trials and real-world data may assist in establishing a phenotype-guided treatment approach for patient with HF in the future.",,pdf:https://link.springer.com/content/pdf/10.1007/s11897-023-00626-w.pdf; doi:https://doi.org/10.1007/s11897-023-00626-w; html:https://europepmc.org/articles/PMC10589138; pdf:https://europepmc.org/articles/PMC10589138?pdf=render
 36660920,https://doi.org/10.1093/ehjci/jeac270,The role of obesity-related cardiovascular remodelling in mediating incident cardiovascular outcomes: a population-based observational study.,"Szabo L, McCracken C, Cooper J, Rider OJ, Vago H, Merkely B, Harvey NC, Neubauer S, Petersen SE, Raisi-Estabragh Z.",,European heart journal. Cardiovascular Imaging,2023,2023-06-01,Y,Obesity; body mass index; Mediation; Cardiac Magnetic Resonance Imaging; Cardiovascular Remodelling; Waist-to-hip Ratio; Disease Mechanisms; Incident Cardiovascular Outcomes,,,"<h4>Aims</h4>We examined associations of obesity with incident cardiovascular outcomes and cardiovascular magnetic resonance (CMR) phenotypes, integrating information from body mass index (BMI) and waist-to-hip ratio (WHR). Then, we used multiple mediation to define the role of obesity-related cardiac remodelling in driving obesity-outcome associations, independent of cardiometabolic diseases.<h4>Methods and results</h4>In 491 606 UK Biobank participants, using Cox proportional hazard models, greater obesity (higher WHR, higher BMI) was linked to significantly greater risk of incident ischaemic heart disease, atrial fibrillation (AF), heart failure (HF), all-cause mortality, and cardiovascular disease (CVD) mortality. In combined stratification by BMI and WHR thresholds, elevated WHR was associated with greater risk of adverse outcomes at any BMI level. Individuals with overweight BMI but normal WHR had weaker disease associations. In the subset of participants with CMR (n = 31 107), using linear regression, greater obesity was associated with higher left ventricular (LV) mass, greater LV concentricity, poorer LV systolic function, lower myocardial native T1, larger left atrial (LA) volumes, poorer LA function, and lower aortic distensibility. Of note, higher BMI was linked to higher, whilst greater WHR was linked to lower LV end-diastolic volume (LVEDV). In Cox models, greater LVEDV and LV mass (LVM) were linked to increased risk of CVD, most importantly HF and an increased LA maximal volume was the key predictive measure of new-onset AF. In multiple mediation analyses, hypertension and adverse LV remodelling (higher LVM, greater concentricity) were major independent mediators of the obesity-outcome associations. Atrial remodelling and native T1 were additional mediators in the associations of obesity with AF and HF, respectively.<h4>Conclusions</h4>We demonstrate associations of obesity with adverse cardiovascular phenotypes and their significant independent role in mediating obesity-outcome relationships. In addition, our findings support the integrated use of BMI and WHR to evaluate obesity-related cardiovascular risk.",,pdf:https://academic.oup.com/ehjcimaging/advance-article-pdf/doi/10.1093/ehjci/jeac270/48798234/jeac270.pdf; doi:https://doi.org/10.1093/ehjci/jeac270; html:https://europepmc.org/articles/PMC10284050; pdf:https://europepmc.org/articles/PMC10284050?pdf=render
+38355192,https://doi.org/10.1136/bmjopen-2023-080678,How far back do we need to look to capture diagnoses in electronic health records? A retrospective observational study of hospital electronic health record data.,"Lewis J, Evison F, Doal R, Field J, Gallier S, Harris S, le Roux P, Osman M, Plummer C, Sapey E, Singer M, Sayer AA, Witham MD, ADMISSION Research Collaborative.",,BMJ open,2024,2024-02-13,Y,Hospitals; Electronic Health Records; Information Extraction,,,"<h4>Objectives</h4>Analysis of routinely collected electronic health data is a key tool for long-term condition research and practice for hospitalised patients. This requires accurate and complete ascertainment of a broad range of diagnoses, something not always recorded on an admission document at a single point in time. This study aimed to ascertain how far back in time electronic hospital records need to be interrogated to capture long-term condition diagnoses.<h4>Design</h4>Retrospective observational study of routinely collected hospital electronic health record data.<h4>Setting</h4>Queen Elizabeth Hospital Birmingham (UK)-linked data held by the PIONEER acute care data hub.<h4>Participants</h4>Patients whose first recorded admission for chronic obstructive pulmonary disease (COPD) exacerbation (n=560) or acute stroke (n=2142) was between January and December 2018 and who had a minimum of 10 years of data prior to the index date.<h4>Outcome measures</h4>We identified the most common International Classification of Diseases version 10-coded diagnoses received by patients with COPD and acute stroke separately. For each diagnosis, we derived the number of patients with the diagnosis recorded at least once over the full 10-year lookback period, and then compared this with shorter lookback periods from 1 year to 9 years prior to the index admission.<h4>Results</h4>Seven of the top 10 most common diagnoses in the COPD dataset reached >90% completeness by 6 years of lookback. Atrial fibrillation and diabetes were >90% coded with 2-3 years of lookback, but hypertension and asthma completeness continued to rise all the way out to 10 years of lookback. For stroke, 4 of the top 10 reached 90% completeness by 5 years of lookback; angina pectoris was >90% coded at 7 years and previous transient ischaemic attack completeness continued to rise out to 10 years of lookback.<h4>Conclusion</h4>A 7-year lookback captures most, but not all, common diagnoses. Lookback duration should be tailored to the conditions being studied.",,pdf:https://bmjopen.bmj.com/content/bmjopen/14/2/e080678.full.pdf; doi:https://doi.org/10.1136/bmjopen-2023-080678; html:https://europepmc.org/articles/PMC10868273; pdf:https://europepmc.org/articles/PMC10868273?pdf=render
 37827807,https://doi.org/10.1136/bmjresp-2023-001806,Observational cohort study protocol: neutrophil function and energetics in adults with pneumonia and sepsis - Pneumonia Metabolism in Ageing (PUMA).,"Grudzinska FS, Faniyi AA, Scott A, Sapey E, Thickett DR.",,BMJ open respiratory research,2023,2023-10-01,Y,Pneumonia; innate immunity; Bacterial Infection; respiratory infection; Neutrophil Biology,,,"<h4>Introduction</h4>Community-acquired pneumonia has high mortality and is associated with significant healthcare costs. In older adults with community-acquired pneumonia neutrophil dysfunction has been identified and is associated with poor outcomes for patients. Immunometabolism is a rapidly developing field which links immune cell function to metabolism. This study aims to explore neutrophil metabolism in community-acquired pneumonia.<h4>Methods and analysis</h4>Pneumonia Metabolism in Ageing study is a prospective observational study recruiting older adults hospitalised with community-acquired pneumonia to examine neutrophil function and metabolic status. Controls will be older adults with no acute illness. The primary endpoint is neutrophil chemotaxis.<h4>Ethics and dissemination</h4>The study has ethical approval from the Research Ethics Committee Wales, reference 19/WA/0299. This study involves participants who may lack the capacity to consent to research involvement, in this situation, personal or professional assent will be sought. The results from this study will be submitted for publication in peer-reviewed journals and disseminated at local and international conferences.",,pdf:https://bmjopenrespres.bmj.com/content/bmjresp/10/1/e001806.full.pdf; doi:https://doi.org/10.1136/bmjresp-2023-001806; html:https://europepmc.org/articles/PMC10582892; pdf:https://europepmc.org/articles/PMC10582892?pdf=render
 32485082,https://doi.org/10.1002/ejhf.1924,Angiotensin-converting enzyme inhibitors and angiotensin II receptor blockers are not associated with severe COVID-19 infection in a multi-site UK acute hospital trust.,"Bean DM, Kraljevic Z, Searle T, Bendayan R, Kevin O, Pickles A, Folarin A, Roguski L, Noor K, Shek A, Zakeri R, Shah AM, Teo JTH, Dobson RJB.",,European journal of heart failure,2020,2020-06-01,Y,Hypertension; Angiotensin-converting enzyme inhibitors; Disease Outcome; Covid-19,,,"<h4>Aims</h4>The SARS-CoV-2 virus binds to the angiotensin-converting enzyme 2 (ACE2) receptor for cell entry. It has been suggested that angiotensin-converting enzyme inhibitors (ACEi) and angiotensin II receptor blockers (ARB), which are commonly used in patients with hypertension or diabetes and may raise tissue ACE2 levels, could increase the risk of severe COVID-19 infection.<h4>Methods and results</h4>We evaluated this hypothesis in a consecutive cohort of 1200 acute inpatients with COVID-19 at two hospitals with a multi-ethnic catchment population in London (UK). The mean age was 68 ± 17 years (57% male) and 74% of patients had at least one comorbidity. Overall, 415 patients (34.6%) reached the primary endpoint of death or transfer to a critical care unit for organ support within 21 days of symptom onset. A total of 399 patients (33.3%) were taking ACEi or ARB. Patients on ACEi/ARB were significantly older and had more comorbidities. The odds ratio for the primary endpoint in patients on ACEi and ARB, after adjustment for age, sex and co-morbidities, was 0.63 (95% confidence interval 0.47-0.84, P < 0.01).<h4>Conclusions</h4>There was no evidence for increased severity of COVID-19 in hospitalised patients on chronic treatment with ACEi or ARB. A trend towards a beneficial effect of ACEi/ARB requires further evaluation in larger meta-analyses and randomised clinical trials.","This study aimed to determine whether or not two specific types of medication (ACE inhibitors and angiotensin-2 blockers - ACEi/ARB) used for hypertension or diabetes are associated with increased risk of severe COVID-19 infection in a sample of 1,200 inpatients (one third of whom were taking the medications under investigation) in two London hospitals. The researchers used data from electonic medical notes and electronic health records. The patients who were taking the medication were, on average, older and had more underlying health conditions than patients who were not. After accounting for these differences in patient health the researchers found that the risk of severe COVID infection was not higher for patients taking ACEi/ARB. This finding is important for patients because it suggests that they should continue to take ACEi/ARB that have been presecribed to them.",doi:https://doi.org/10.1002/ejhf.1924; doi:https://doi.org/10.1002/ejhf.1924; html:https://europepmc.org/articles/PMC7301045; pdf:https://europepmc.org/articles/PMC7301045?pdf=render
 36350810,https://doi.org/10.1371/journal.pone.0276781,"Primary hypertension, anti-hypertensive medications and the risk of severe COVID-19 in UK Biobank.","Pavey H, Kulkarni S, Wood A, Ben-Shlomo Y, Sever P, McEniery C, Wilkinson I.",,PloS one,2022,2022-11-09,Y,,,,"Hypertension appears to be one of the commonest comorbidities in COVID-19 patients, although whether hypertensive individuals have a higher risk of severe COVID-19 compared with non-hypertensives is unclear. It is also unclear whether the absolute level of systolic blood pressure, or the type of anti-hypertensive medication is related to this risk. Analyses were conducted using data from the UK Biobank and linked health records. Logistic regression models were fitted to assess the impact of hypertension, systolic blood pressure (SBP) and medications on the risk of severe COVID-19. 16,134 individuals tested positive for severe acute respiratory syndrome-coronavirus, 22% (n = 3,584) developed severe COVID-19 and 40% (n = 6,517) were hypertensive. Hypertension was associated with 22% higher odds of severe COVID-19 (Odds ratio (OR) 1.22; 95% confidence interval (CI) 1.12, 1.33), compared with normotension after adjusting for confounding variables. In those taking anti-hypertensive medications, elevated SBP showed a dose-response relationship with severe COVID-19 (150-159mmHg versus 120-129mmHg (OR 1.91; 95% CI 1.44, 2.53), &gt;180+mmHg versus 120-129mmHg (OR 1.93; 95% CI 1.06, 3.51)). SBP &lt;120mmHg was associated with greater odds of severe COVID-19 (OR 1.40; 95% CI 1.11, 1.78). Angiotensin-converting enzyme inhibitors or angiotensin-II receptor blockers were not associated with altered risk of severe COVID-19. Hypertension is an important risk factor for COVID-19. A better understanding of the underlying mechanisms is warranted in case of more severe strains or other viruses in the future.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0276781&type=printable; doi:https://doi.org/10.1371/journal.pone.0276781; html:https://europepmc.org/articles/PMC9645600; pdf:https://europepmc.org/articles/PMC9645600?pdf=render
 37225263,https://doi.org/10.1136/bmjgast-2023-001139,Delphi consensus survey: the opinions of patients living with refractory ulcerative proctitis and the health care professionals who care for them.,"Kyriacou M, Radford S, Moran GW, Focus group collaborators group.",,BMJ open gastroenterology,2023,2023-05-01,Y,Ulcerative colitis; Inflammatory Bowel Disease; Adjuvant Treatment,,,"<h4>Background</h4>Refractory ulcerative proctitis presents a huge clinical challenge not only for the patients living with this chronic, progressive condition but also for the professionals who care for them. Currently, there is limited research and evidence-based guidance, resulting in many patients living with the symptomatic burden of disease and reduced quality of life. The aim of this study was to establish a consensus on the thoughts and opinions related to refractory proctitis disease burden and best practice for management.<h4>Methods</h4>A three-round Delphi consensus survey was conducted among patients living with refractory proctitis and the healthcare experts with knowledge on this disease from the UK. A brainstorming stage involving a focus group where the participants came up with an initial list of statements was completed. Following this, there were three rounds of Delphi surveys in which the participants were asked to rank the importance of the statements and provide any additional comments or clarifications. Calculation of mean scores, analysis of comments and revisions were performed to produce a final list of statements.<h4>Results</h4>In total, 14 statements were suggested by the focus group at the initial brainstorming stage. Following completion of three Delphi survey rounds, all 14 statements reached consensus following appropriate revision.<h4>Conclusions</h4>We established consensus on the thoughts and opinions related to refractory proctitis from both the experts who manage this disease and the patients living with it. This represents the first step towards developing clinical research data and ultimately the evidence needed for best practice management guidance of this condition.",,pdf:https://bmjopengastro.bmj.com/content/bmjgast/10/1/e001139.full.pdf; doi:https://doi.org/10.1136/bmjgast-2023-001139; html:https://europepmc.org/articles/PMC10230891; pdf:https://europepmc.org/articles/PMC10230891?pdf=render
-37751239,https://doi.org/10.2196/49438,Design and Evaluation of an Intensive Care Unit Dashboard Built in Response to the COVID-19 Pandemic: Semistructured Interview Study.,"Wac M, Craddock I, Chantziara S, Campbell T, Santos-Rodriguez R, Davidson B, McWilliams C.",,JMIR human factors,2023,2023-09-26,Y,Design; Health; ICU; EPR; intensive care unit; Interview; Intensive Care; Critical Care; Electronic Patient Record; Participatory Design; Ehr; Electronic Health Record; Software Engineering; Clinical Information System; Cis; Thematic Analysis; Dashboard; Human-centered Design; Covid-19; Interactive Display,,,"<h4>Background</h4>Dashboards and interactive displays are becoming increasingly prevalent in most health care settings and have the potential to streamline access to information, consolidate disparate data sources and deliver new insights. Our research focuses on intensive care units (ICUs) which are heavily instrumented, critical care environments that generate vast amounts of data and frequently require individualized support for each patient. Consequently, clinicians experience a high cognitive load, which can translate to suboptimal performance. The global COVID-19 pandemic exacerbated this problem by generating a large number of additional hospitalizations, which necessitated a new tool that would help manage ICUs' census. In a previous study, we interviewed clinicians at the University Hospitals Bristol and Weston National Health Service Foundation Trust to capture the requirements for bespoke dashboards that would alleviate this problem.<h4>Objective</h4>This study aims to design, implement, and evaluate an ICU dashboard to allow for monitoring of the high volume of patients in need of critical care, particularly tailored to high-demand situations, such as those seen during the COVID-19 pandemic.<h4>Methods</h4>Building upon the previously gathered requirements, we developed a dashboard, integrated it within the ICU of a National Health Service trust, and allowed all staff to access our tool. For evaluation purposes, participants were recruited and interviewed following a 25-day period during which they were able to use the dashboard clinically. The semistructured interviews followed a topic guide aimed at capturing the usability of the dashboard, supplemented with additional questions asked post hoc to probe themes established during the interview. Interview transcripts were analyzed using a thematic analysis framework that combined inductive and deductive approaches and integrated the Technology Acceptance Model.<h4>Results</h4>A total of 10 participants with 4 different roles in the ICU (6 consultants, 2 junior doctors, 1 nurse, and 1 advanced clinical practitioner) participated in the interviews. Our analysis generated 4 key topics that prevailed across the data: our dashboard met the usability requirements of the participants and was found useful and intuitive; participants perceived that it impacted their delivery of patient care by improving the access to the information and better equipping them to do their job; the tool was used in a variety of ways and for different reasons and tasks; and there were barriers to integration of our dashboard into practice, including familiarity with existing systems, which stifled the adoption of our tool.<h4>Conclusions</h4>Our findings show that the perceived utility of the dashboard had a positive impact on the clinicians' workflows in the ICU. Improving access to information translated into more efficient patient care and transformed some of the existing processes. The introduction of our tool was met with positive reception, but its integration during the COVID-19 pandemic limited its adoption into practice.",,doi:https://doi.org/10.2196/49438; doi:https://doi.org/10.2196/49438; html:https://europepmc.org/articles/PMC10565627
 32895316,https://doi.org/10.1136/thoraxjnl-2020-215566,We need a robust evidence base to unravel the relationship between sex hormones and asthma.,"Sheikh A, Mukherjee M.",,Thorax,2020,2020-09-07,N,Asthma,,,,,pdf:https://thorax.bmj.com/content/thoraxjnl/75/10/826.full.pdf; doi:https://doi.org/10.1136/thoraxjnl-2020-215566
+37751239,https://doi.org/10.2196/49438,Design and Evaluation of an Intensive Care Unit Dashboard Built in Response to the COVID-19 Pandemic: Semistructured Interview Study.,"Wac M, Craddock I, Chantziara S, Campbell T, Santos-Rodriguez R, Davidson B, McWilliams C.",,JMIR human factors,2023,2023-09-26,Y,Design; Health; ICU; EPR; intensive care unit; Interview; Intensive Care; Critical Care; Electronic Patient Record; Participatory Design; Ehr; Electronic Health Record; Software Engineering; Clinical Information System; Cis; Thematic Analysis; Dashboard; Human-centered Design; Covid-19; Interactive Display,,,"<h4>Background</h4>Dashboards and interactive displays are becoming increasingly prevalent in most health care settings and have the potential to streamline access to information, consolidate disparate data sources and deliver new insights. Our research focuses on intensive care units (ICUs) which are heavily instrumented, critical care environments that generate vast amounts of data and frequently require individualized support for each patient. Consequently, clinicians experience a high cognitive load, which can translate to suboptimal performance. The global COVID-19 pandemic exacerbated this problem by generating a large number of additional hospitalizations, which necessitated a new tool that would help manage ICUs' census. In a previous study, we interviewed clinicians at the University Hospitals Bristol and Weston National Health Service Foundation Trust to capture the requirements for bespoke dashboards that would alleviate this problem.<h4>Objective</h4>This study aims to design, implement, and evaluate an ICU dashboard to allow for monitoring of the high volume of patients in need of critical care, particularly tailored to high-demand situations, such as those seen during the COVID-19 pandemic.<h4>Methods</h4>Building upon the previously gathered requirements, we developed a dashboard, integrated it within the ICU of a National Health Service trust, and allowed all staff to access our tool. For evaluation purposes, participants were recruited and interviewed following a 25-day period during which they were able to use the dashboard clinically. The semistructured interviews followed a topic guide aimed at capturing the usability of the dashboard, supplemented with additional questions asked post hoc to probe themes established during the interview. Interview transcripts were analyzed using a thematic analysis framework that combined inductive and deductive approaches and integrated the Technology Acceptance Model.<h4>Results</h4>A total of 10 participants with 4 different roles in the ICU (6 consultants, 2 junior doctors, 1 nurse, and 1 advanced clinical practitioner) participated in the interviews. Our analysis generated 4 key topics that prevailed across the data: our dashboard met the usability requirements of the participants and was found useful and intuitive; participants perceived that it impacted their delivery of patient care by improving the access to the information and better equipping them to do their job; the tool was used in a variety of ways and for different reasons and tasks; and there were barriers to integration of our dashboard into practice, including familiarity with existing systems, which stifled the adoption of our tool.<h4>Conclusions</h4>Our findings show that the perceived utility of the dashboard had a positive impact on the clinicians' workflows in the ICU. Improving access to information translated into more efficient patient care and transformed some of the existing processes. The introduction of our tool was met with positive reception, but its integration during the COVID-19 pandemic limited its adoption into practice.",,doi:https://doi.org/10.2196/49438; doi:https://doi.org/10.2196/49438; html:https://europepmc.org/articles/PMC10565627
 37230417,https://doi.org/10.1016/j.jtha.2023.05.012,C1-inhibitor levels and venous thromboembolism: results from a Mendelian randomization study.,"Cupido AJ, Petersen RS, Schmidt AF, Levi M, Cohn DM, Fijen LM.",,Journal of thrombosis and haemostasis : JTH,2023,2023-05-23,N,,,,,,pdf:http://www.jthjournal.org/article/S1538783623004257/pdf; doi:https://doi.org/10.1016/j.jtha.2023.05.012
 36137640,https://doi.org/10.1136/bmjopen-2022-064586,Myocardial infarction and stroke subsequent to urinary tract infection (MISSOURI): protocol for a self-controlled case series using linked electronic health records.,"Reeve NF, Best V, Gillespie D, Hughes K, Lugg-Widger FV, Cannings-John R, Torabi F, Wootton M, Akbari A, Ahmed H.",,BMJ open,2022,2022-09-22,Y,Myocardial infarction; Stroke; Urinary tract infections,,,"<h4>Introduction</h4>There is increasing interest in the relationship between acute infections and acute cardiovascular events. Most previous research has focused on understanding whether the risk of acute cardiovascular events increases following a respiratory tract infection. The relationship between urinary tract infections (UTIs) and acute cardiovascular events is less well studied. Therefore, the aim of this study is to determine whether there is a causal relationship between UTI and acute myocardial infarction (MI) or stroke.<h4>Methods and analysis</h4>We will undertake a self-controlled case series study using linked anonymised general practice, hospital admission and microbiology data held within the Secure Anonymised Information Linkage (SAIL) Databank. Self-controlled case series is a relatively novel study design where individuals act as their own controls, thereby inherently controlling for time-invariant confounders. Only individuals who experience an exposure and outcome of interest are included.We will identify individuals in the SAIL Databank who have a hospital admission record for acute MI or stroke during the study period of 2010-2020. Individuals will need to be aged 30-100 during the study period and be Welsh residents for inclusion. UTI will be identified using general practice, microbiology and hospital admissions data. We will calculate the incidence of MI and stroke in predefined risk periods following an UTI and in 'baseline' periods (without UTI exposure) and use conditional Poisson regression models to derive incidence rate ratios.<h4>Ethics and dissemination</h4>Data access, research permissions and approvals have been obtained from the SAIL independent Information Governance Review Panel, project number 0972. Findings will be disseminated through conferences, blogs, social media threads and peer-reviewed journals. Results will be of interest internationally to primary and secondary care clinicians who manage UTIs and may inform future clinical trials of preventative therapy.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/9/e064586.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-064586; html:https://europepmc.org/articles/PMC9511592; pdf:https://europepmc.org/articles/PMC9511592?pdf=render
 29944675,https://doi.org/10.1371/journal.pone.0199026,"The diagnosis, burden and prognosis of dementia: A record-linkage cohort study in England.","Pujades-Rodriguez M, Assi V, Gonzalez-Izquierdo A, Wilkinson T, Schnier C, Sudlow C, Hemingway H, Whiteley WN.",,PloS one,2018,2018-06-26,Y,,The Human Phenome,,"<h4>Objectives</h4>Electronic health records (EHR) might be a useful resource to study the risk factors and clinical care of people with dementia. We sought to determine the diagnostic validity of dementia captured in linked EHR.<h4>Methods and findings</h4>A cohort of adults in linked primary care, hospital, disease registry and mortality records in England, [CALIBER (CArdiovascular disease research using LInked Bespoke studies and Electronic health Records)]. The proportion of individuals with dementia, Alzheimer's disease, vascular and rare dementia in each data source was determined. A comparison was made of symptoms and care between people with dementia and age-, sex- and general practice-matched controls, using conditional logistic regression. The lifetime risk and prevalence of dementia and mortality rates in people with and without dementia were estimated with random-effects Poisson models. There were 47,386 people with dementia: 12,633 with Alzheimer's disease, 9540 with vascular and 1539 with rare dementia. Seventy-four percent of cases had corroborating evidence of dementia. People with dementia were more likely to live in a deprived area (conditional OR 1.26;95%CI:1.20-1.31 most vs least deprived), have documented memory impairment (cOR = 11.97;95%CI:11.24-12.75), falls (cOR = 2.36;95%CI:2.31-2.41), depression (cOR = 2.03; 95%CI:1.98-2.09) or anxiety (cOR = 1.27; 95%CI:1.23-1.32). The lifetime risk of dementia at age 65 was 9.2% (95%CI:9.0%-9.4%), in men and 14.9% (95%CI:14.7%-15.1%) in women. The population prevalence of recorded dementia increased from 0.3% in 2000 to 0.7% in 2010. A higher mortality rate was observed in people with than without dementia (IRR = 1.56;95%CI:1.54-1.58).<h4>Conclusions</h4>Most people with a record of dementia in linked UK EHR had some corroborating evidence for diagnosis. The estimated 10-year risk of dementia was higher than published population-based estimations. EHR are therefore a promising source of data for dementia research.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0199026&type=printable; doi:https://doi.org/10.1371/journal.pone.0199026; html:https://europepmc.org/articles/PMC6019102; pdf:https://europepmc.org/articles/PMC6019102?pdf=render
@@ -1468,27 +1470,27 @@ PMC10686417,https://doi.org/,The impact of restricted provision of publicly fund
 37489768,https://doi.org/10.1161/jaha.122.029296,Using Polygenic Risk Scores for Prioritizing Individuals at Greatest Need of a Cardiovascular Disease Risk Assessment.,"Chung R, Xu Z, Arnold M, Ip S, Harrison H, Barrett J, Pennells L, Kim LG, Di Angelantonio E, Paige E, Ritchie SC, Inouye M, Usher-Smith JA, Wood AM.",,Journal of the American Heart Association,2023,2023-07-25,Y,Screening; Genomics; Cardiovascular disease; Electronic Health Records; Primary Care Records,,,"Background The aim of this study was to provide quantitative evidence of the use of polygenic risk scores for systematically identifying individuals for invitation for full formal cardiovascular disease (CVD) risk assessment. Methods and Results A total of 108 685 participants aged 40 to 69 years, with measured biomarkers, linked primary care records, and genetic data in UK Biobank were used for model derivation and population health modeling. Prioritization tools using age, polygenic risk scores for coronary artery disease and stroke, and conventional risk factors for CVD available within longitudinal primary care records were derived using sex-specific Cox models. We modeled the implications of initiating guideline-recommended statin therapy after prioritizing individuals for invitation to a formal CVD risk assessment. If primary care records were used to prioritize individuals for formal risk assessment using age- and sex-specific thresholds corresponding to 5% false-negative rates, then the numbers of men and women needed to be screened to prevent 1 CVD event are 149 and 280, respectively. In contrast, adding polygenic risk scores to both prioritization and formal assessments, and selecting thresholds to capture the same number of events, resulted in a number needed to screen of 116 for men and 180 for women. Conclusions Using both polygenic risk scores and primary care records to prioritize individuals at highest risk of a CVD event for a formal CVD risk assessment can efficiently prioritize those who need interventions the most than using primary care records alone. This could lead to better allocation of resources by reducing the number of risk assessments in primary care while still preventing the same number of CVD events.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.122.029296; doi:https://doi.org/10.1161/JAHA.122.029296; html:https://europepmc.org/articles/PMC7614905; pdf:https://europepmc.org/articles/PMC7614905?pdf=render
 33130851,https://doi.org/10.1093/ije/dyaa216,High-throughput multivariable Mendelian randomization analysis prioritizes apolipoprotein B as key lipid risk factor for coronary artery disease.,"Zuber V, Gill D, Ala-Korpela M, Langenberg C, Butterworth A, Bottolo L, Burgess S.",,International journal of epidemiology,2021,2021-07-01,Y,Lipoproteins; Apolipoprotein B; Metabolomics; blood lipids; coronary artery disease; Mendelian Randomization; Risk Factor Selection,,,"<h4>Background</h4>Genetic variants can be used to prioritize risk factors as potential therapeutic targets via Mendelian randomization (MR). An agnostic statistical framework using Bayesian model averaging (MR-BMA) can disentangle the causal role of correlated risk factors with shared genetic predictors. Here, our objective is to identify lipoprotein measures as mediators between lipid-associated genetic variants and coronary artery disease (CAD) for the purpose of detecting therapeutic targets for CAD.<h4>Methods</h4>As risk factors we consider 30 lipoprotein measures and metabolites derived from a high-throughput metabolomics study including 24 925 participants. We fit multivariable MR models of genetic associations with CAD estimated in 453 595 participants (including 113 937 cases) regressed on genetic associations with the risk factors. MR-BMA assigns to each combination of risk factors a model score quantifying how well the genetic associations with CAD are explained. Risk factors are ranked by their marginal score and selected using false-discovery rate (FDR) criteria. We perform supplementary and sensitivity analyses varying the dataset for genetic associations with CAD.<h4>Results</h4>In the main analysis, the top combination of risk factors ranked by the model score contains apolipoprotein B (ApoB) only. ApoB is also the highest ranked risk factor with respect to the marginal score (FDR <0.005). Additionally, ApoB is selected in all sensitivity analyses. No other measure of cholesterol or triglyceride is consistently selected otherwise.<h4>Conclusions</h4>Our agnostic genetic investigation prioritizes ApoB across all datasets considered, suggesting that ApoB, representing the total number of hepatic-derived lipoprotein particles, is the primary lipid determinant of CAD.",,doi:https://doi.org/10.1093/ije/dyaa216; doi:https://doi.org/10.1093/ije/dyaa216; html:https://europepmc.org/articles/PMC8271202; pdf:https://europepmc.org/articles/PMC8271202?pdf=render
 37001969,https://doi.org/10.1136/archdischild-2022-325219,Identifying opportunities for upstream evaluations relevant to child and maternal health: a UK policy-mapping review.,"Stewart E, Pearce A, Given J, Gilbert R, Brophy S, Cookson R, Hardelid P, Harron KL, Leyland A, Wood R, Dundas R.",,Archives of disease in childhood,2023,2023-03-31,Y,Child Development; Child Health,,,"<h4>Objective</h4>Interventions to tackle the social determinants of health can improve outcomes during pregnancy and early childhood, leading to better health across the life course. Variation in content, timing and implementation of policies across the 4 UK nations allows for evaluation. We conducted a policy-mapping review (1981-2021) to identify relevant UK early years policies across the social determinants of health framework, and determine suitable candidates for evaluation using administrative data.<h4>Methods</h4>We used open keyword and category searches of UK and devolved Government websites, and hand searched policy reviews. Policies were rated and included using five criteria: (1) Potential for policy to affect maternal and child health outcomes; (2) Implementation variation across the UK; (3) Population reach and expected effect size; (4) Ability to identify exposed/eligible group in administrative data; (5) Potential to affect health inequalities. An expert consensus workshop determined a final shortlist.<h4>Results</h4>336 policies and 306 strategy documents were identified. Policies were mainly excluded due to criteria 2-4, leaving 88. The consensus workshop identified three policy areas as suitable candidates for natural experiment evaluation using administrative data: pregnancy grants, early years education and childcare, and Universal Credit.<h4>Conclusion</h4>Our comprehensive policy review identifies valuable opportunities to evaluate sociostructural impacts on mother and child outcomes. However, many potentially impactful policies were excluded. This may lead to the inverse evidence law, where there is least evidence for policies believed to be most effective. This could be ameliorated by better access to administrative data, staged implementation of future policies or alternative evaluation methods.",,pdf:https://adc.bmj.com/content/archdischild/early/2023/03/30/archdischild-2022-325219.full.pdf; doi:https://doi.org/10.1136/archdischild-2022-325219; html:https://europepmc.org/articles/PMC10314013; pdf:https://europepmc.org/articles/PMC10314013?pdf=render
-38491524,https://doi.org/10.1186/s40246-024-00585-w,A genome-wide association study of neutrophil count in individuals associated to an African continental ancestry group facilitates studies of malaria pathogenesis.,"Constantinescu AE, Hughes DA, Bull CJ, Fleming K, Mitchell RE, Zheng J, Kar S, Timpson NJ, Amulic B, Vincent EE.",,Human genomics,2024,2024-03-15,Y,Malaria; Gwas; Mendelian Randomization; Neutrophil Count; African Ancestry,,,"<h4>Background</h4>'Benign ethnic neutropenia' (BEN) is a heritable condition characterized by lower neutrophil counts, predominantly observed in individuals of African ancestry, and the genetic basis of BEN remains a subject of extensive research. In this study, we aimed to dissect the genetic architecture underlying neutrophil count variation through a linear-mixed model genome-wide association study (GWAS) in a population of African ancestry (N = 5976). Malaria caused by P. falciparum imposes a tremendous public health burden on people living in sub-Saharan Africa. Individuals living in malaria endemic regions often have a reduced circulating neutrophil count due to BEN, raising the possibility that reduced neutrophil counts modulate severity of malaria in susceptible populations. As a follow-up, we tested this hypothesis by conducting a Mendelian randomization (MR) analysis of neutrophil counts on severe malaria (MalariaGEN, N = 17,056).<h4>Results</h4>We carried out a GWAS of neutrophil count in individuals associated to an African continental ancestry group within UK Biobank, identifying 73 loci (r<sup>2</sup> = 0.1) and 10 index SNPs (GCTA-COJO loci) associated with neutrophil count, including previously unknown rare loci regulating neutrophil count in a non-European population. BOLT-LMM was reliable when conducted in a non-European population, and additional covariates added to the model did not largely alter the results of the top loci or index SNPs. The two-sample bi-directional MR analysis between neutrophil count and severe malaria showed the greatest evidence for an effect between neutrophil count and severe anaemia, although the confidence intervals crossed the null.<h4>Conclusion</h4>Our GWAS of neutrophil count revealed unique loci present in individuals of African ancestry. We note that a small sample-size reduced our power to identify variants with low allele frequencies and/or low effect sizes in our GWAS. Our work highlights the need for conducting large-scale biobank studies in Africa and for further exploring the link between neutrophils and severe malaria.",,pdf:https://humgenomics.biomedcentral.com/counter/pdf/10.1186/s40246-024-00585-w; doi:https://doi.org/10.1186/s40246-024-00585-w; html:https://europepmc.org/articles/PMC10941368; pdf:https://europepmc.org/articles/PMC10941368?pdf=render
 35038301,https://doi.org/10.2196/30523,Requirements for a Bespoke Intensive Care Unit Dashboard in Response to the COVID-19 Pandemic: Semistructured Interview Study.,"Davidson B, Ferrer Portillo KM, Wac M, McWilliams C, Bourdeaux C, Craddock I.",,JMIR human factors,2022,2022-04-13,Y,Development; Monitoring; Design; Disease monitoring; ICU; Interview; Intensive Care; Critical Care; Ehealth; Dashboard; Human-centered Design; Covid-19,,,"<h4>Background</h4>Intensive care units (ICUs) around the world are in high demand due to patients with COVID-19 requiring hospitalization. As researchers at the University of Bristol, we were approached to develop a bespoke data visualization dashboard to assist two local ICUs during the pandemic that will centralize disparate data sources in the ICU to help reduce the cognitive load on busy ICU staff in the ever-evolving pandemic.<h4>Objective</h4>The aim of this study was to conduct interviews with ICU staff in University Hospitals Bristol and Weston National Health Service Foundation Trust to elicit requirements for a bespoke dashboard to monitor the high volume of patients, particularly during the COVID-19 pandemic.<h4>Methods</h4>We conducted six semistructured interviews with clinical staff to obtain an overview of their requirements for the dashboard and to ensure its ultimate suitability for end users. Interview questions aimed to understand the job roles undertaken in the ICU, potential uses of the dashboard, specific issues associated with managing COVID-19 patients, key data of interest, and any concerns about the introduction of a dashboard into the ICU.<h4>Results</h4>From our interviews, we found the following design requirements: (1) a flexible dashboard, where the functionality can be updated quickly and effectively to respond to emerging information about the management of this new disease; (2) a mobile dashboard, which allows staff to move around on wards with a dashboard, thus potentially replacing paper forms to enable detailed and consistent data entry; (3) a customizable and intuitive dashboard, where individual users would be able to customize the appearance of the dashboard to suit their role; (4) real-time data and trend analysis via informative data visualizations that help busy ICU staff to understand a patient's clinical trajectory; and (5) the ability to manage tasks and staff, tracking both staff and patient movements, handovers, and task monitoring to ensure the highest quality of care.<h4>Conclusions</h4>The findings of this study confirm that digital solutions for ICU use would potentially reduce the cognitive load of ICU staff and reduce clinical errors at a time of notably high demand of intensive health care.",,pdf:https://humanfactors.jmir.org/2022/2/e30523/PDF; doi:https://doi.org/10.2196/30523; html:https://europepmc.org/articles/PMC9009380
+38491524,https://doi.org/10.1186/s40246-024-00585-w,A genome-wide association study of neutrophil count in individuals associated to an African continental ancestry group facilitates studies of malaria pathogenesis.,"Constantinescu AE, Hughes DA, Bull CJ, Fleming K, Mitchell RE, Zheng J, Kar S, Timpson NJ, Amulic B, Vincent EE.",,Human genomics,2024,2024-03-15,Y,Malaria; Gwas; Mendelian Randomization; Neutrophil Count; African Ancestry,,,"<h4>Background</h4>'Benign ethnic neutropenia' (BEN) is a heritable condition characterized by lower neutrophil counts, predominantly observed in individuals of African ancestry, and the genetic basis of BEN remains a subject of extensive research. In this study, we aimed to dissect the genetic architecture underlying neutrophil count variation through a linear-mixed model genome-wide association study (GWAS) in a population of African ancestry (N = 5976). Malaria caused by P. falciparum imposes a tremendous public health burden on people living in sub-Saharan Africa. Individuals living in malaria endemic regions often have a reduced circulating neutrophil count due to BEN, raising the possibility that reduced neutrophil counts modulate severity of malaria in susceptible populations. As a follow-up, we tested this hypothesis by conducting a Mendelian randomization (MR) analysis of neutrophil counts on severe malaria (MalariaGEN, N = 17,056).<h4>Results</h4>We carried out a GWAS of neutrophil count in individuals associated to an African continental ancestry group within UK Biobank, identifying 73 loci (r<sup>2</sup> = 0.1) and 10 index SNPs (GCTA-COJO loci) associated with neutrophil count, including previously unknown rare loci regulating neutrophil count in a non-European population. BOLT-LMM was reliable when conducted in a non-European population, and additional covariates added to the model did not largely alter the results of the top loci or index SNPs. The two-sample bi-directional MR analysis between neutrophil count and severe malaria showed the greatest evidence for an effect between neutrophil count and severe anaemia, although the confidence intervals crossed the null.<h4>Conclusion</h4>Our GWAS of neutrophil count revealed unique loci present in individuals of African ancestry. We note that a small sample-size reduced our power to identify variants with low allele frequencies and/or low effect sizes in our GWAS. Our work highlights the need for conducting large-scale biobank studies in Africa and for further exploring the link between neutrophils and severe malaria.",,pdf:https://humgenomics.biomedcentral.com/counter/pdf/10.1186/s40246-024-00585-w; doi:https://doi.org/10.1186/s40246-024-00585-w; html:https://europepmc.org/articles/PMC10941368; pdf:https://europepmc.org/articles/PMC10941368?pdf=render
 35210898,https://doi.org/10.2147/por.s353400,Deriving a Standardised Recommended Respiratory Disease Codelist Repository for Future Research.,"MacRae C, Whittaker H, Mukherjee M, Daines L, Morgan A, Iwundu C, Alsallakh M, Vasileiou E, O'Rourke E, Williams AT, Stone PW, Sheikh A, Quint JK.",,Pragmatic and observational research,2022,2022-02-16,Y,Asthma; COPD; Respiratory Tract Infections; Electronic Healthcare Records,,,"<h4>Background</h4>Electronic health record (EHR) databases provide rich, longitudinal data on interactions with healthcare providers and can be used to advance research into respiratory conditions. However, since these data are primarily collected to support health care delivery, clinical coding can be inconsistent, resulting in inherent challenges in using these data for research purposes.<h4>Methods</h4>We systematically searched existing international literature and UK code repositories to find respiratory disease codelists for asthma from January 2018, and chronic obstructive pulmonary disease and respiratory tract infections from January 2020, based on prior searches. Medline searches using key terms provided in article lists. Full-text articles, supplementary files, and reference lists were examined for codelists, and codelists repositories were searched. A reproducible methodology for codelists creation was developed with recommended lists for each disease created based on multidisciplinary expert opinion and previously published literature.<h4>Results</h4>Medline searches returned 1126 asthma articles, 70 COPD articles, and 90 respiratory infection articles, with 3%, 22% and 5% including codelists, respectively. Repository searching returned 12 asthma, 23 COPD, and 64 respiratory infection codelists. We have systematically compiled respiratory disease codelists and from these derived recommended lists for use by researchers to find the most up-to-date and relevant respiratory disease codelists that can be tailored to individual research questions.<h4>Conclusion</h4>Few published papers include codelists, and where published diverse codelists were used, even when answering similar research questions. Whilst some advances have been made, greater consistency and transparency across studies using routine data to study respiratory diseases are needed.",,pdf:https://www.dovepress.com/getfile.php?fileID=78337; doi:https://doi.org/10.2147/POR.S353400; html:https://europepmc.org/articles/PMC8859726; pdf:https://europepmc.org/articles/PMC8859726?pdf=render
 35264566,https://doi.org/10.1038/s41467-022-28729-3,Elucidating mechanisms of genetic cross-disease associations at the PROCR vascular disease locus.,"Stacey D, Chen L, Stanczyk PJ, Howson JMM, Mason AM, Burgess S, MacDonald S, Langdown J, McKinney H, Downes K, Farahi N, Peters JE, Basu S, Pankow JS, Tang W, Pankratz N, Sabater-Lleal M, de Vries PS, Smith NL, CHARGE Hemostasis Working Group, Gelinas AD, Schneider DJ, Janjic N, Samani NJ, Ye S, Summers C, Chilvers ER, Danesh J, Paul DS.",,Nature communications,2022,2022-03-09,Y,,,,"Many individual genetic risk loci have been associated with multiple common human diseases. However, the molecular basis of this pleiotropy often remains unclear. We present an integrative approach to reveal the molecular mechanism underlying the PROCR locus, associated with lower coronary artery disease (CAD) risk but higher venous thromboembolism (VTE) risk. We identify PROCR-p.Ser219Gly as the likely causal variant at the locus and protein C as a causal factor. Using genetic analyses, human recall-by-genotype and in vitro experimentation, we demonstrate that PROCR-219Gly increases plasma levels of (activated) protein C through endothelial protein C receptor (EPCR) ectodomain shedding in endothelial cells, attenuating leukocyte-endothelial cell adhesion and vascular inflammation. We also associate PROCR-219Gly with an increased pro-thrombotic state via coagulation factor VII, a ligand of EPCR. Our study, which links PROCR-219Gly to CAD through anti-inflammatory mechanisms and to VTE through pro-thrombotic mechanisms, provides a framework to reveal the mechanisms underlying similar cross-phenotype associations.",,pdf:https://www.nature.com/articles/s41467-022-28729-3.pdf; doi:https://doi.org/10.1038/s41467-022-28729-3; html:https://europepmc.org/articles/PMC8907312; pdf:https://europepmc.org/articles/PMC8907312?pdf=render
-37679551,https://doi.org/10.1038/s41590-023-01635-6,Author Correction: Genetics of circulating inflammatory proteins identifies drivers of immune-mediated disease risk and therapeutic targets.,"Zhao JH, Stacey D, Eriksson N, Macdonald-Dunlop E, Hedman ÅK, Kalnapenkis A, Enroth S, Cozzetto D, Digby-Bell J, Marten J, Folkersen L, Herder C, Jonsson L, Bergen SE, Gieger C, Needham EJ, Surendran P, Estonian Biobank Research Team, Paul DS, Polasek O, Thorand B, Grallert H, Roden M, Võsa U, Esko T, Hayward C, Johansson Å, Gyllensten U, Powell N, Hansson O, Mattsson-Carlgren N, Joshi PK, Danesh J, Padyukov L, Klareskog L, Landén M, Wilson JF, Siegbahn A, Wallentin L, Mälarstig A, Butterworth AS, Peters JE.",,Nature immunology,2023,2023-11-01,Y,,,,,,doi:https://doi.org/10.1038/s41590-023-01635-6; html:https://europepmc.org/articles/PMC10602847; pdf:https://europepmc.org/articles/PMC10602847?pdf=render
 35776955,https://doi.org/10.1093/ehjqcco/qcac039,One step closer to quantifying 'clinical likelihood' in pre-test probability.,"Weir-McCall JR, Williams MC, Wood A.",,European heart journal. Quality of care & clinical outcomes,2022,2022-09-01,N,,,,,,doi:https://doi.org/10.1093/ehjqcco/qcac039; html:https://europepmc.org/articles/PMC9442847; pdf:https://europepmc.org/articles/PMC9442847?pdf=render; doi:https://doi.org/10.1093/ehjqcco/qcac039
-38346686,https://doi.org/10.1093/ageing/afae004,The impact of digital technology in care homes on unplanned secondary care usage and associated costs.,"Garner A, Lewis J, Dixon S, Preston N, Caiado CCS, Hanratty B, Jones M, Knight J, Mason SM.",,Age and ageing,2024,2024-02-01,Y,Older People; Emergency Medicine; Care Homes; Long-term Care; Telehealth; Routinely Collected Data,,,"<h4>Background</h4>A substantial number of Emergency Department (ED) attendances by care home residents are potentially avoidable. Health Call Digital Care Homes is an app-based technology that aims to streamline residents' care by recording their observations such as vital parameters electronically. Observations are triaged by remote clinical staff. This study assessed the effectiveness of the Health Call technology to reduce unplanned secondary care usage and associated costs.<h4>Methods</h4>A retrospective analysis of health outcomes and economic impact based on an intervention. The study involved 118 care homes across the North East of UK from 2018 to 2021. Routinely collected NHS secondary care data from County Durham and Darlington NHS Foundation Trust was linked with data from the Health Call app. Three outcomes were modelled monthly using Generalised Linear Mixed Models: counts of emergency attendances, emergency admissions and length of stay of emergency admissions. A similar approach was taken for costs. The impact of Health Call was tested on each outcome using the models.<h4>Findings</h4>Data from 8,702 residents were used in the analysis. Results show Health Call reduces the number of emergency attendances by 11% [6-15%], emergency admissions by 25% [20-39%] and length of stay by 11% [3-18%] (with an additional month-by-month decrease of 28% [24-34%]). The cost analysis found a cost reduction of £57 per resident in 2018, increasing to £113 in 2021.<h4>Interpretation</h4>The introduction of a digital technology, such as Health Call, could significantly reduce contacts with and costs resulting from unplanned secondary care usage by care home residents.",,pdf:https://academic.oup.com/ageing/article-pdf/53/2/afae004/56661196/afae004.pdf; doi:https://doi.org/10.1093/ageing/afae004; html:https://europepmc.org/articles/PMC10861323; pdf:https://europepmc.org/articles/PMC10861323?pdf=render
+37679551,https://doi.org/10.1038/s41590-023-01635-6,Author Correction: Genetics of circulating inflammatory proteins identifies drivers of immune-mediated disease risk and therapeutic targets.,"Zhao JH, Stacey D, Eriksson N, Macdonald-Dunlop E, Hedman ÅK, Kalnapenkis A, Enroth S, Cozzetto D, Digby-Bell J, Marten J, Folkersen L, Herder C, Jonsson L, Bergen SE, Gieger C, Needham EJ, Surendran P, Estonian Biobank Research Team, Paul DS, Polasek O, Thorand B, Grallert H, Roden M, Võsa U, Esko T, Hayward C, Johansson Å, Gyllensten U, Powell N, Hansson O, Mattsson-Carlgren N, Joshi PK, Danesh J, Padyukov L, Klareskog L, Landén M, Wilson JF, Siegbahn A, Wallentin L, Mälarstig A, Butterworth AS, Peters JE.",,Nature immunology,2023,2023-11-01,Y,,,,,,doi:https://doi.org/10.1038/s41590-023-01635-6; html:https://europepmc.org/articles/PMC10602847; pdf:https://europepmc.org/articles/PMC10602847?pdf=render
 30183734,https://doi.org/10.1371/journal.pone.0202359,Time spent at blood pressure target and the risk of death and cardiovascular diseases.,"Chung SC, Pujades-Rodriguez M, Duyx B, Denaxas SC, Pasea L, Hingorani A, Timmis A, Williams B, Hemingway H.",,PloS one,2018,2018-09-05,Y,,The Human Phenome,,"<h4>Background</h4>The time a patient spends with blood pressure at target level is an intuitive measure of successful BP management, but population studies on its effectiveness are as yet unavailable.<h4>Method</h4>We identified a population-based cohort of 169,082 individuals with newly identified high blood pressure who were free of cardiovascular disease from January 1997 to March 2010. We used 1.64 million clinical blood pressure readings to calculate the TIme at TaRgEt (TITRE) based on current target blood pressure levels.<h4>Result</h4>The median (Inter-quartile range) TITRE among all patients was 2.8 (0.3, 5.6) months per year, only 1077 (0.6%) patients had a TITRE ≥11 months. Compared to people with a 0% TITRE, patients with a TITRE of 3-5.9 months, and 6-8.9 months had 75% and 78% lower odds of the composite of cardiovascular death, myocardial infarction and stroke (adjusted odds ratios, 0.25 (95% confidence interval: 0.21, 0.31) and 0.22 (0.17, 0.27), respectively). These associations were consistent for heart failure and any cardiovascular disease and death (comparing a 3-5.9 month to 0% TITRE, 63% and 60% lower in odds, respectively), among people who did or did not have blood pressure 'controlled' on a single occasion during the first year of follow-up, and across groups defined by number of follow-up BP measure categories.<h4>Conclusion</h4>Based on the current frequency of measurement of blood pressure this study suggests that few newly hypertensive patients sustained a complete, year-round on target blood pressure over time. The inverse associations between a higher TITRE and lower risk of incident cardiovascular diseases were independent of widely-used blood pressure 'control' indicators. Randomized trials are required to evaluate interventions to increase a person's time spent at blood pressure target.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0202359&type=printable; doi:https://doi.org/10.1371/journal.pone.0202359; html:https://europepmc.org/articles/PMC6124703; pdf:https://europepmc.org/articles/PMC6124703?pdf=render
+38346686,https://doi.org/10.1093/ageing/afae004,The impact of digital technology in care homes on unplanned secondary care usage and associated costs.,"Garner A, Lewis J, Dixon S, Preston N, Caiado CCS, Hanratty B, Jones M, Knight J, Mason SM.",,Age and ageing,2024,2024-02-01,Y,Older People; Emergency Medicine; Care Homes; Long-term Care; Telehealth; Routinely Collected Data,,,"<h4>Background</h4>A substantial number of Emergency Department (ED) attendances by care home residents are potentially avoidable. Health Call Digital Care Homes is an app-based technology that aims to streamline residents' care by recording their observations such as vital parameters electronically. Observations are triaged by remote clinical staff. This study assessed the effectiveness of the Health Call technology to reduce unplanned secondary care usage and associated costs.<h4>Methods</h4>A retrospective analysis of health outcomes and economic impact based on an intervention. The study involved 118 care homes across the North East of UK from 2018 to 2021. Routinely collected NHS secondary care data from County Durham and Darlington NHS Foundation Trust was linked with data from the Health Call app. Three outcomes were modelled monthly using Generalised Linear Mixed Models: counts of emergency attendances, emergency admissions and length of stay of emergency admissions. A similar approach was taken for costs. The impact of Health Call was tested on each outcome using the models.<h4>Findings</h4>Data from 8,702 residents were used in the analysis. Results show Health Call reduces the number of emergency attendances by 11% [6-15%], emergency admissions by 25% [20-39%] and length of stay by 11% [3-18%] (with an additional month-by-month decrease of 28% [24-34%]). The cost analysis found a cost reduction of £57 per resident in 2018, increasing to £113 in 2021.<h4>Interpretation</h4>The introduction of a digital technology, such as Health Call, could significantly reduce contacts with and costs resulting from unplanned secondary care usage by care home residents.",,pdf:https://academic.oup.com/ageing/article-pdf/53/2/afae004/56661196/afae004.pdf; doi:https://doi.org/10.1093/ageing/afae004; html:https://europepmc.org/articles/PMC10861323; pdf:https://europepmc.org/articles/PMC10861323?pdf=render
 35699189,https://doi.org/10.1161/jaha.121.024248,Low-Density Lipoprotein Cholesterol Attributable Cardiovascular Disease Risk Is Sex Specific.,"Cupido AJ, Asselbergs FW, Schmidt AF, Hovingh GK.",,Journal of the American Heart Association,2022,2022-06-14,Y,Genetics; Cardiovascular disease; Risk factor; Sex‐differences,,,"Background Epidemiological studies show that women are generally at lower risk for cardiovascular disease than men. Here, we investigated the sex-specific differential effect of genetically increased low-density lipoprotein cholesterol (LDL-C) on cardiovascular disease (CVD) and other lipid-associated diseases. Methods and Results This is a 2-sample Mendelian randomization study that uses individual participant data from 425 043 participants from the UK Biobank, including 229 279 female participants. An 80-variant LDL-C weighted genetic score was generated. Linear and logistic regression models with interactions were used to identify differences between sex-specific LDL-C effects on lipids, carotid-intima media thickness, and multiple cardiovascular outcomes such as CVD, ischemic heart disease, peripheral artery disease, heart failure, aortic valve disease, type 2 diabetes, atrial fibrillation, and aortic aneurysm and dissection. After correction for multiple testing, we observed that the genetically increased LDL-C effect on CVD events was sex specific: per SD genetically increased LDL-C, female participants had a higher LDL-C increase but an attenuated CVD risk increase compared with male participants (LDL-C: female participants 0.71 mmol/L, 95% CI, 0.70-0.72 and male participants 0.57 mmol/L, 95% CI, 0.56-0.59. <i>P</i> for interaction: 5.03×10<sup>-60</sup>; CVD: female participants: odds ratio [OR], 1.32; 95% CI 1.24-1.40 and male participants: OR, 1.52; 95% CI, 1.46-1.58. <i>P</i> for interaction: 9.88×10<sup>-5</sup>). We also observed attenuated risks for ischemic heart disease and (nominally for) heart failure in female participants, and genetically increased LDL-C results in higher risk for aortic valve disease in female participants compared with male participants. Genetically increased LDL-C was also associated with an attenuated carotid-intima media thickness increase in female participants. We did not observe other significant attenuations. Sensitivity analyses with an unweighted genetic score and sex-specific weighted genetic scores showed similar results. Conclusions We found that genetically increased LDL-C has a sex-specific differential effect on the risk for cardiovascular disease, ischemic heart disease, heart failure, and aortic valve stenosis. Our observations provide evidence that LDL-C might be a less important determinant of CVD in women compared with men, suggesting that male patients might benefit more from LDL-C targeted therapies for CVD management than female patients and warranting investigations into the sex-specific relative contribution of risk factors for CVD.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.121.024248; doi:https://doi.org/10.1161/JAHA.121.024248; html:https://europepmc.org/articles/PMC9238661; pdf:https://europepmc.org/articles/PMC9238661?pdf=render
 31529100,https://doi.org/10.1093/pm/pnz209,"Pain, Anxiety, and Depression in the First Two Years Following Transport-Related Major Trauma: A Population-Based, Prospective Registry Cohort Study.","Giummarra MJ, Simpson P, Gabbe BJ.",,"Pain medicine (Malden, Mass.)",2020,2020-02-01,N,Trauma; Injury; Prognostic; Recovery; Motor Vehicle,,,"<h4>Objectives</h4>This study aimed to characterize the population prevalence of pain and mental health problems postinjury and to identify risk factors that could improve service delivery to optimize recovery of at-risk patients.<h4>Methods</h4>This population-based registry cohort study included 5,350 adult survivors of transport-related major trauma injuries from the Victorian State Trauma Registry. Outcome profiles were generated separately for pain and mental health outcomes using the ""pain or discomfort"" and ""anxiety or depression"" items of the EuroQol Five Dimensions Three-Level questionnaire at six, 12, and 24 months postinjury. Profiles were ""resilient"" (no problems at every follow-up), ""recovered"" (problems at six- and/or 12-month follow-up that later resolved), ""worsening"" (problems at 12 and/or 24 months after no problems at six and/or 12 months), and ""persistent"" (problems at every follow-up).<h4>Results</h4>Most participants had persistent (pain/discomfort, N = 2,171, 39.7%; anxiety/depression, N = 1,428, 26.2%) and resilient profiles (pain/discomfort, N = 1,220, 22.3%; anxiety/depression, N = 2,055, 37.7%), followed by recovered (pain/discomfort, N = 1,116, 20.4%; anxiety/depression, N = 1,025, 18.8%) and worsening profiles (pain/discomfort, N = 956, 17.5%; anxiety/depression, N = 948, 17.4%). Adjusted multinomial logistic regressions showed increased risk of problems (persistent, worsening, or resolved) vs no problems (resilient) in relation to female sex, middle age, neighborhood disadvantage, pre-injury unemployment, pre-injury disability, and spinal cord injury. People living in rural areas, motorcyclists, pedal cyclists, and people with head, chest, and abdominal injuries had lower risk of problems.<h4>Discussion</h4>Targeted interventions delivered to people with the risk factors identified may help to attenuate the severity and impact of pain and mental health problems after transport injury.",,pdf:https://academic.oup.com/painmedicine/article-pdf/21/2/291/32739506/pnz209.pdf; doi:https://doi.org/10.1093/pm/pnz209
-38904124,https://doi.org/10.1136/bmjopen-2023-079169,"10-year multimorbidity patterns among people with and without rheumatic and musculoskeletal diseases: an observational cohort study using linked electronic health records from Wales, UK.","Jalali-Najafabadi F, Bailey R, Lyons J, Akbari A, Ba Dhafari T, Azadbakht N, Rafferty J, Watkins A, Martin GP, Bowes J, Lyons RA, Barton A, Peek N.",,BMJ open,2024,2024-06-19,Y,epidemiology; Rheumatology; Electronic Health Records,,,"<h4>Objectives</h4>To compare the patterns of multimorbidity between people with and without rheumatic and musculoskeletal diseases (RMDs) and to describe how these patterns change by age and sex over time, between 2010 and 2019.<h4>Participants</h4>103 426 people with RMDs and 2.9 million comparators registered in 395 Wales general practices (GPs). Each patient with an RMD aged 0-100 years between January 2010 and December 2019 registered in Clinical Practice Research Welsh practices was matched with up to five comparators without an RMD, based on age, gender and GP code.<h4>Primary outcome measures</h4>The prevalence of 29 Elixhauser-defined comorbidities in people with RMDs and comparators categorised by age, gender and GP practices. Conditional logistic regression models were fitted to calculate differences (OR, 95% CI) in associations with comorbidities between cohorts.<h4>Results</h4>The most prevalent comorbidities were cardiovascular risk factors, hypertension and diabetes. Having an RMD diagnosis was associated with a significantly higher odds for many conditions including deficiency anaemia (OR 1.39, 95% CI (1.32 to 1.46)), hypothyroidism (OR 1.34, 95% CI (1.19 to 1.50)), pulmonary circulation disorders (OR 1.39, 95% CI 1.12 to 1.73) diabetes (OR 1.17, 95% CI (1.11 to 1.23)) and fluid and electrolyte disorders (OR 1.27, 95% CI (1.17 to 1.38)). RMDs have a higher proportion of multimorbidity (two or more conditions in addition to the RMD) compared with non-RMD group (81% and 73%, respectively in 2019) and the mean number of comorbidities was higher in women from the age of 25 and 50 in men than in non-RMDs group.<h4>Conclusion</h4>People with RMDs are approximately 1.5 times as likely to have multimorbidity as the general population and provide a high-risk group for targeted intervention studies. The individuals with RMDs experience a greater load of coexisting health conditions, which tend to manifest at earlier ages. This phenomenon is particularly pronounced among women. Additionally, there is an under-reporting of comorbidities in individuals with RMDs.",,doi:https://doi.org/10.1136/bmjopen-2023-079169; doi:https://doi.org/10.1136/bmjopen-2023-079169; html:https://europepmc.org/articles/PMC11191776; pdf:https://europepmc.org/articles/PMC11191776?pdf=render
 36691123,https://doi.org/10.1136/bmjopen-2022-063199,Feasibility of a new electronic patient-reported outcome (ePRO) system for an advanced therapy clinical trial in immune-mediated inflammatory disease (PROmics): protocol for a qualitative feasibility study.,"Hughes SE, McMullan C, Rowe A, Retzer A, Malpass R, Bathurst C, Davies EH, Frost C, McNamara G, Harding R, Price G, Wilson R, Walker A, Newsome PN, Calvert M.",,BMJ open,2022,2022-09-06,Y,information technology; immunology; Hepatology; Inflammatory Bowel Disease; Rheumatology,,,"<h4>Introduction</h4>The use of electronic patient-reported outcome (ePRO) systems to capture PRO data in clinical trials is increasing; however, their feasibility, acceptability and utility in clinical trials of advanced therapy medicinal products (ATMPs) are not yet well understood. This protocol describes a qualitative study that aims to evaluate the feasibility and acceptability of ePRO data capture using a trial-specific ePRO system (the PROmics system) within an advanced therapy trial involving patients with immune-mediated inflammatory disease (rheumatoid arthritis, lupus, primary sclerosing cholangitis (PSC) and Crohn's disease).<h4>Methods and analysis</h4>This protocol for a remote, qualitative, interview-based feasibility study is embedded within the POLARISE trial, a single-arm, phase II, multisite ATMP basket trial in the UK. 10-15 patients enrolled in the POLARISE trial and 10-15 research team members at the trial sites will be recruited. Participants will take part in semistructured interviews which will be transcribed verbatim and analysed thematically according to the framework method. Data collection and analysis will occur concurrently and iteratively. Researcher triangulation will be used to achieve a consensus-based analysis, enhancing rigour and trustworthiness.<h4>Ethics and dissemination</h4>This study was approved by the London-West London and GTAC Research Ethics Committee (Ref: 21/LO/0475). Informed consent will be obtained from all participants prior to data collection. The study findings will be published in peer-review journals and disseminated via conference presentations and other media. Our patient and public involvement and engagement group and ATMP stakeholder networks will be consulted to maximise dissemination and impact.<h4>Trial registration number</h4>ISRCTN80103507.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/9/e063199.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-063199; html:https://europepmc.org/articles/PMC9453996; pdf:https://europepmc.org/articles/PMC9453996?pdf=render
 34261736,https://doi.org/10.1136/heartjnl-2021-319229,Heart failure medication dosage and survival in women and men seen at outpatient clinics.,"Bots SH, Onland-Moret NC, Tulevski II, van der Harst P, Cramer MJM, Asselbergs FW, Somsen GA, den Ruijter HM.",,Heart (British Cardiac Society),2021,2021-07-14,Y,epidemiology; Heart Failure; Electronic Health Records,,,"<h4>Objective</h4>Women with heart failure with reduced ejection fraction (HFrEF) may reach optimal treatment effect at half of the guideline-recommended medication dose. This study investigates prescription practice and its relation with survival of patients with HF in daily care.<h4>Methods</h4>Electronic health record data from 13 Dutch outpatient cardiology clinics were extracted for HF receiving at least one guideline-recommended HF medication. Dose changes over consecutive prescriptions were modelled using natural cubic splines. Inverse probability-weighted Cox regression was used to assess the relationship between dose (reference≥50% target dose) and all-cause mortality.<h4>Results</h4>The study population comprised 561 women (29% HFrEF (ejection fraction (EF)<40%), 49% heart failure with preserved ejection fraction (EF≥50%); HFpEF and 615 men (47% and 25%, respectively). During a median follow-up of 3.7 years, 252 patients died (48% women; 167 HFrEF, 84 HFpEF). Nine hundred thirty-four patients (46% women) received ACE inhibitors (ACEIs) or angiotensin receptor blockers (ARBs), 795 (48% women) beta blockers and 178 (42% women) mineralocorticoid receptor antagonists (MRAs). In both sexes, the mean target dose across prescriptions was 50% for ACEI/ARBs and beta blockers, and 100% for MRAs. ACEI/ARB dose of <50% was associated with lower mortality in women but not in men with HFrEF. This was not seen in patients with HFpEF. Beta-blocker dose was not associated with all-cause mortality.<h4>Conclusion</h4>Patients with HF seen in outpatient cardiology clinics receive half of the guideline-recommended medication dose. Lower ACEI/ARB dose was associated with improved survival in women with HFrEF. These results underscore the importance of (re)defining optimal medical therapy for women with HFrEF.",,pdf:https://heart.bmj.com/content/heartjnl/107/21/1748.full.pdf; doi:https://doi.org/10.1136/heartjnl-2021-319229; html:https://europepmc.org/articles/PMC8522453; pdf:https://europepmc.org/articles/PMC8522453?pdf=render
+38904124,https://doi.org/10.1136/bmjopen-2023-079169,"10-year multimorbidity patterns among people with and without rheumatic and musculoskeletal diseases: an observational cohort study using linked electronic health records from Wales, UK.","Jalali-Najafabadi F, Bailey R, Lyons J, Akbari A, Ba Dhafari T, Azadbakht N, Rafferty J, Watkins A, Martin GP, Bowes J, Lyons RA, Barton A, Peek N.",,BMJ open,2024,2024-06-19,Y,epidemiology; Rheumatology; Electronic Health Records,,,"<h4>Objectives</h4>To compare the patterns of multimorbidity between people with and without rheumatic and musculoskeletal diseases (RMDs) and to describe how these patterns change by age and sex over time, between 2010 and 2019.<h4>Participants</h4>103 426 people with RMDs and 2.9 million comparators registered in 395 Wales general practices (GPs). Each patient with an RMD aged 0-100 years between January 2010 and December 2019 registered in Clinical Practice Research Welsh practices was matched with up to five comparators without an RMD, based on age, gender and GP code.<h4>Primary outcome measures</h4>The prevalence of 29 Elixhauser-defined comorbidities in people with RMDs and comparators categorised by age, gender and GP practices. Conditional logistic regression models were fitted to calculate differences (OR, 95% CI) in associations with comorbidities between cohorts.<h4>Results</h4>The most prevalent comorbidities were cardiovascular risk factors, hypertension and diabetes. Having an RMD diagnosis was associated with a significantly higher odds for many conditions including deficiency anaemia (OR 1.39, 95% CI (1.32 to 1.46)), hypothyroidism (OR 1.34, 95% CI (1.19 to 1.50)), pulmonary circulation disorders (OR 1.39, 95% CI 1.12 to 1.73) diabetes (OR 1.17, 95% CI (1.11 to 1.23)) and fluid and electrolyte disorders (OR 1.27, 95% CI (1.17 to 1.38)). RMDs have a higher proportion of multimorbidity (two or more conditions in addition to the RMD) compared with non-RMD group (81% and 73%, respectively in 2019) and the mean number of comorbidities was higher in women from the age of 25 and 50 in men than in non-RMDs group.<h4>Conclusion</h4>People with RMDs are approximately 1.5 times as likely to have multimorbidity as the general population and provide a high-risk group for targeted intervention studies. The individuals with RMDs experience a greater load of coexisting health conditions, which tend to manifest at earlier ages. This phenomenon is particularly pronounced among women. Additionally, there is an under-reporting of comorbidities in individuals with RMDs.",,doi:https://doi.org/10.1136/bmjopen-2023-079169; doi:https://doi.org/10.1136/bmjopen-2023-079169; html:https://europepmc.org/articles/PMC11191776; pdf:https://europepmc.org/articles/PMC11191776?pdf=render
 31827124,https://doi.org/10.1038/s41598-019-54849-w,Improving the odds of drug development success through human genomics: modelling study.,"Hingorani AD, Kuan V, Finan C, Kruger FA, Gaulton A, Chopade S, Sofat R, MacAllister RJ, Overington JP, Hemingway H, Denaxas S, Prieto D, Casas JP.",,Scientific reports,2019,2019-12-11,Y,,,,"Lack of efficacy in the intended disease indication is the major cause of clinical phase drug development failure. Explanations could include the poor external validity of pre-clinical (cell, tissue, and animal) models of human disease and the high false discovery rate (FDR) in preclinical science. FDR is related to the proportion of true relationships available for discovery (γ), and the type 1 (false-positive) and type 2 (false negative) error rates of the experiments designed to uncover them. We estimated the FDR in preclinical science, its effect on drug development success rates, and improvements expected from use of human genomics rather than preclinical studies as the primary source of evidence for drug target identification. Calculations were based on a sample space defined by all human diseases - the 'disease-ome' - represented as columns; and all protein coding genes - 'the protein-coding genome'- represented as rows, producing a matrix of unique gene- (or protein-) disease pairings. We parameterised the space based on 10,000 diseases, 20,000 protein-coding genes, 100 causal genes per disease and 4000 genes encoding druggable targets, examining the effect of varying the parameters and a range of underlying assumptions, on the inferences drawn. We estimated γ, defined mathematical relationships between preclinical FDR and drug development success rates, and estimated improvements in success rates based on human genomics (rather than orthodox preclinical studies). Around one in every 200 protein-disease pairings was estimated to be causal (γ = 0.005) giving an FDR in preclinical research of 92.6%, which likely makes a major contribution to the reported drug development failure rate of 96%. Observed success rate was only slightly greater than expected for a random pick from the sample space. Values for γ back-calculated from reported preclinical and clinical drug development success rates were also close to the a priori estimates. Substituting genome wide (or druggable genome wide) association studies for preclinical studies as the major information source for drug target identification was estimated to reverse the probability of late stage failure because of the more stringent type 1 error rate employed and the ability to interrogate every potential druggable target in the same experiment. Genetic studies conducted at much larger scale, with greater resolution of disease end-points, e.g. by connecting genomics and electronic health record data within healthcare systems has the potential to produce radical improvement in drug development success rate.","This study investigates the unreliability of target identification leading to low development sucess rates, inefficiency and escalating costs to healthcare users. The more targeted use of genomics couldimprove improved efficency.",pdf:https://www.nature.com/articles/s41598-019-54849-w.pdf; doi:https://doi.org/10.1038/s41598-019-54849-w; html:https://europepmc.org/articles/PMC6906499; pdf:https://europepmc.org/articles/PMC6906499?pdf=render
 36587850,https://doi.org/10.1016/j.jaci.2022.12.810,The gut microbiome is a significant risk factor for future chronic lung disease.,"Liu Y, Teo SM, Méric G, Tang HHF, Zhu Q, Sanders JG, Vázquez-Baeza Y, Verspoor K, Vartiainen VA, Jousilahti P, Lahti L, Niiranen T, Havulinna AS, Knight R, Salomaa V, Inouye M.",,The Journal of allergy and clinical immunology,2023,2022-12-29,Y,Gut; Asthma; COPD; Metagenomics; Microbiome,,,"<h4>Background</h4>The gut-lung axis is generally recognized, but there are few large studies of the gut microbiome and incident respiratory disease in adults.<h4>Objective</h4>We sought to investigate the association and predictive capacity of the gut microbiome for incident asthma and chronic obstructive pulmonary disease (COPD).<h4>Methods</h4>Shallow metagenomic sequencing was performed for stool samples from a prospective, population-based cohort (FINRISK02; N = 7115 adults) with linked national administrative health register-derived classifications for incident asthma and COPD up to 15 years after baseline. Generalized linear models and Cox regressions were used to assess associations of microbial taxa and diversity with disease occurrence. Predictive models were constructed using machine learning with extreme gradient boosting. Models considered taxa abundances individually and in combination with other risk factors, including sex, age, body mass index, and smoking status.<h4>Results</h4>A total of 695 and 392 statistically significant associations were found between baseline taxonomic groups and incident asthma and COPD, respectively. Gradient boosting decision trees of baseline gut microbiome abundance predicted incident asthma and COPD in the validation data sets with mean area under the curves of 0.608 and 0.780, respectively. Cox analysis showed that the baseline gut microbiome achieved higher predictive performance than individual conventional risk factors, with C-indices of 0.623 for asthma and 0.817 for COPD. The integration of the gut microbiome and conventional risk factors further improved prediction capacities.<h4>Conclusions</h4>The gut microbiome is a significant risk factor for incident asthma and incident COPD and is largely independent of conventional risk factors.",,pdf:http://www.jacionline.org/article/S0091674922025775/pdf; doi:https://doi.org/10.1016/j.jaci.2022.12.810; html:https://europepmc.org/articles/PMC10109092; pdf:https://europepmc.org/articles/PMC10109092?pdf=render
-36403308,https://doi.org/10.1016/j.media.2022.102678,DragNet: Learning-based deformable registration for realistic cardiac MR sequence generation from a single frame.,"Zakeri A, Hokmabadi A, Bi N, Wijesinghe I, Nix MG, Petersen SE, Frangi AF, Taylor ZA, Gooya A.",,Medical image analysis,2023,2022-11-02,N,Uncertainty Estimation; Uk Biobank; Deep Learning; Deformable Temporal Image Registration; Sequential Image Data Generation; Variational Recurrent Neural Networks,,,"Deformable image registration (DIR) can be used to track cardiac motion. Conventional DIR algorithms aim to establish a dense and non-linear correspondence between independent pairs of images. They are, nevertheless, computationally intensive and do not consider temporal dependencies to regulate the estimated motion in a cardiac cycle. In this paper, leveraging deep learning methods, we formulate a novel hierarchical probabilistic model, termed DragNet, for fast and reliable spatio-temporal registration in cine cardiac magnetic resonance (CMR) images and for generating synthetic heart motion sequences. DragNet is a variational inference framework, which takes an image from the sequence in combination with the hidden states of a recurrent neural network (RNN) as inputs to an inference network per time step. As part of this framework, we condition the prior probability of the latent variables on the hidden states of the RNN utilised to capture temporal dependencies. We further condition the posterior of the motion field on a latent variable from hierarchy and features from the moving image. Subsequently, the RNN updates the hidden state variables based on the feature maps of the fixed image and the latent variables. Different from traditional methods, DragNet performs registration on unseen sequences in a forward pass, which significantly expedites the registration process. Besides, DragNet enables generating a large number of realistic synthetic image sequences given only one frame, where the corresponding deformations are also retrieved. The probabilistic framework allows for computing spatio-temporal uncertainties in the estimated motion fields. Our results show that DragNet performance is comparable with state-of-the-art methods in terms of registration accuracy, with the advantage of offering analytical pixel-wise motion uncertainty estimation across a cardiac cycle and being a motion generator. We will make our code publicly available.",,doi:https://doi.org/10.1016/j.media.2022.102678; doi:https://doi.org/10.1016/j.media.2022.102678
-34000735,https://doi.org/10.1093/ije/dyab025,Commentary: Obstetric oxytocin exposure and risk of attention-deficit hyperactivity disorder and autism spectrum disorder in offspring-case closed.,"Morales DR, Nordeng HM.",,International journal of epidemiology,2021,2021-05-01,N,,,,,,pdf:https://academic.oup.com/ije/article-pdf/50/2/457/37947593/dyab025.pdf; doi:https://doi.org/10.1093/ije/dyab025
 PMC8855010,https://doi.org/,POS-894 PREDICTING PANDEMIC-RELATED EXCESS-DEATH USING PRE-PANDEMIC RISK OF MORTALITY IN INDIVIDUALS WITH CHRONIC KIDNEY DISEASE,"Dashtban M, Mizani M, Gonazalez-Izquierdo A, Corbett R, Denaxas S, Quint J, Mamza J, Morris T, Hemingway H, Sudlow C, Banerjee A.",,Kidney international reports,2022,2022-02-01,Y,,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8855010/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8855010/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC8855010; pdf:https://europepmc.org/articles/PMC8855010?pdf=render
+34000735,https://doi.org/10.1093/ije/dyab025,Commentary: Obstetric oxytocin exposure and risk of attention-deficit hyperactivity disorder and autism spectrum disorder in offspring-case closed.,"Morales DR, Nordeng HM.",,International journal of epidemiology,2021,2021-05-01,N,,,,,,pdf:https://academic.oup.com/ije/article-pdf/50/2/457/37947593/dyab025.pdf; doi:https://doi.org/10.1093/ije/dyab025
+36403308,https://doi.org/10.1016/j.media.2022.102678,DragNet: Learning-based deformable registration for realistic cardiac MR sequence generation from a single frame.,"Zakeri A, Hokmabadi A, Bi N, Wijesinghe I, Nix MG, Petersen SE, Frangi AF, Taylor ZA, Gooya A.",,Medical image analysis,2023,2022-11-02,N,Uncertainty Estimation; Uk Biobank; Deep Learning; Deformable Temporal Image Registration; Sequential Image Data Generation; Variational Recurrent Neural Networks,,,"Deformable image registration (DIR) can be used to track cardiac motion. Conventional DIR algorithms aim to establish a dense and non-linear correspondence between independent pairs of images. They are, nevertheless, computationally intensive and do not consider temporal dependencies to regulate the estimated motion in a cardiac cycle. In this paper, leveraging deep learning methods, we formulate a novel hierarchical probabilistic model, termed DragNet, for fast and reliable spatio-temporal registration in cine cardiac magnetic resonance (CMR) images and for generating synthetic heart motion sequences. DragNet is a variational inference framework, which takes an image from the sequence in combination with the hidden states of a recurrent neural network (RNN) as inputs to an inference network per time step. As part of this framework, we condition the prior probability of the latent variables on the hidden states of the RNN utilised to capture temporal dependencies. We further condition the posterior of the motion field on a latent variable from hierarchy and features from the moving image. Subsequently, the RNN updates the hidden state variables based on the feature maps of the fixed image and the latent variables. Different from traditional methods, DragNet performs registration on unseen sequences in a forward pass, which significantly expedites the registration process. Besides, DragNet enables generating a large number of realistic synthetic image sequences given only one frame, where the corresponding deformations are also retrieved. The probabilistic framework allows for computing spatio-temporal uncertainties in the estimated motion fields. Our results show that DragNet performance is comparable with state-of-the-art methods in terms of registration accuracy, with the advantage of offering analytical pixel-wise motion uncertainty estimation across a cardiac cycle and being a motion generator. We will make our code publicly available.",,doi:https://doi.org/10.1016/j.media.2022.102678; doi:https://doi.org/10.1016/j.media.2022.102678
 38388919,https://doi.org/10.1186/s12913-024-10716-7,"Spatio-temporal modelling of referrals to outpatient respiratory clinics in the integrated care system of the Morecambe Bay area, England.","Mountain R, Knight J, Heys K, Giorgi E, Gatheral T.",,BMC health services research,2024,2024-02-22,Y,Spatio-temporal; Integrated Care; Chronic Respiratory Disease; Routinely Collected Data; Outpatient Referrals,,,"<h4>Background</h4>Promoting integrated care is a key goal of the NHS Long Term Plan to improve population respiratory health, yet there is limited data-driven evidence of its effectiveness. The Morecambe Bay Respiratory Network is an integrated care initiative operating in the North-West of England since 2017. A key target area has been reducing referrals to outpatient respiratory clinics by upskilling primary care teams. This study aims to explore space-time patterns in referrals from general practice in the Morecambe Bay area to evaluate the impact of the initiative.<h4>Methods</h4>Data on referrals to outpatient clinics and chronic respiratory disease patient counts between 2012-2020 were obtained from the Morecambe Bay Community Data Warehouse, a large store of routinely collected healthcare data. For analysis, the data is aggregated by year and small area geography. The methodology comprises of two parts. The first explores the issues that can arise when using routinely collected primary care data for space-time analysis and applies spatio-temporal conditional autoregressive modelling to adjust for data complexities. The second part models the rate of outpatient referral via a Poisson generalised linear mixed model that adjusts for changes in demographic factors and number of respiratory disease patients.<h4>Results</h4>The first year of the Morecambe Bay Respiratory Network was not associated with a significant difference in referral rate. However, the second and third years saw significant reductions in areas that had received intervention, with full intervention associated with a 31.8% (95% CI 17.0-43.9) and 40.5% (95% CI 27.5-50.9) decrease in referral rate in 2018 and 2019, respectively.<h4>Conclusions</h4>Routinely collected data can be used to robustly evaluate key outcome measures of integrated care. The results demonstrate that effective integrated care has real potential to ease the burden on respiratory outpatient services by reducing the need for an onward referral. This is of great relevance given the current pressure on outpatient services globally, particularly long waiting lists following the COVID-19 pandemic and the need for more innovative models of care.",,doi:https://doi.org/10.1186/s12913-024-10716-7; html:https://europepmc.org/articles/PMC10882730; pdf:https://europepmc.org/articles/PMC10882730?pdf=render
-35487318,https://doi.org/10.1016/j.ijcard.2022.04.067,Implications of elevated troponin on time-to-surgery in non-ST elevation myocardial infarction (NIHR Health Informatics Collaborative: TROP-CABG study).,"Benedetto U, Sinha S, Mulla A, Glampson B, Davies J, Panoulas V, Gautama S, Papadimitriou D, Woods K, Elliott P, Hemingway H, Williams B, Asselbergs FW, Melikian N, Krasopoulos G, Sayeed R, Wendler O, Baig K, Chukwuemeka A, Angelini GD, Sterne JAC, Johnson T, Shah AM, Perera D, Patel RS, Kharbanda R, Channon KM, Mayet J, Kaura A.",,International journal of cardiology,2022,2022-04-27,N,Troponin; Myocardial infarction; Coronary Artery Bypass Grafting; Timing-to-surgery,,,"Implications of elevated troponin on time-to-surgery in non-ST elevation myocardial infarction(NIHR Health Informatics Collaborative:TROP-CABG study). Benedetto et al. BACKGROUND: The optimal timing of coronary artery bypass grafting (CABG) in patients with non-ST elevation myocardial infarction (NSTEMI) and the utility of pre-operative troponin levels in decision-making remains unclear. We investigated (a) the association between peak pre-operative troponin and survival post-CABG in a large cohort of NSTEMI patients and (b) the interaction between troponin and time-to-surgery. METHODS AND RESULTS: Our cohort consisted of 1746 patients (1684 NSTEMI; 62 unstable angina) (mean age 69 ± 11 years,21% female) with recorded troponins that had CABG at five United Kingdom centers between 2010 and 2017. Time-segmented Cox regression was used to investigate the interaction of peak troponin and time-to-surgery on early (within 30 days) and late (beyond 30 days) survival. Average interval from peak troponin to surgery was 9 ± 15 days, with 1466 (84.0%) patients having CABG during the same admission. Sixty patients died within 30-days and another 211 died after a mean follow-up of 4 ± 2 years (30-day survival 0.97 ± 0.004 and 5-year survival 0.83 ± 0.01). Peak troponin was a strong predictor of early survival (adjusted P = 0.002) with a significant interaction with time-to-surgery (P interaction = 0.007). For peak troponin levels <100 times the upper limit of normal, there was no improvement in early survival with longer time-to-surgery. However, in patients with higher troponins, early survival increased progressively with a longer time-to-surgery, till day 10. Peak troponin did not influence survival beyond 30 days (adjusted P = 0.64). CONCLUSIONS: Peak troponin in NSTEMI patients undergoing CABG was a significant predictor of early mortality, strongly influenced the time-to-surgery and may prove to be a clinically useful biomarker in the management of these patients.",,doi:https://doi.org/10.1016/j.ijcard.2022.04.067
 32717063,https://doi.org/10.1093/cvr/cvaa233,Gene expression profiling of hypertrophic cardiomyocytes identifies new players in pathological remodelling.,"Vigil-Garcia M, Demkes CJ, Eding JEC, Versteeg D, de Ruiter H, Perini I, Kooijman L, Gladka MM, Asselbergs FW, Vink A, Harakalova M, Bossu A, van Veen TAB, Boogerd CJ, van Rooij E.",,Cardiovascular research,2021,2021-05-01,Y,Cardiomyocyte; hypertrophy; Heart Failure; Rna Sequencing; Pfkp; Pathological Remodelling,,,"<h4>Aims</h4>Pathological cardiac remodelling is characterized by cardiomyocyte (CM) hypertrophy and fibroblast activation, which can ultimately lead to maladaptive hypertrophy and heart failure (HF). Genome-wide expression analysis on heart tissue has been instrumental for the identification of molecular mechanisms at play. However, these data were based on signals derived from all cardiac cell types. Here, we aimed for a more detailed view on molecular changes driving maladaptive CM hypertrophy to aid in the development of therapies to reverse pathological remodelling.<h4>Methods and results</h4>Utilizing CM-specific reporter mice exposed to pressure overload by transverse aortic banding and CM isolation by flow cytometry, we obtained gene expression profiles of hypertrophic CMs in the more immediate phase after stress, and CMs showing pathological hypertrophy. We identified subsets of genes differentially regulated and specific for either stage. Among the genes specifically up-regulated in the CMs during the maladaptive phase we found known stress markers, such as Nppb and Myh7, but additionally identified a set of genes with unknown roles in pathological hypertrophy, including the platelet isoform of phosphofructokinase (PFKP). Norepinephrine-angiotensin II treatment of cultured human CMs induced the secretion of N-terminal-pro-B-type natriuretic peptide (NT-pro-BNP) and recapitulated the up-regulation of these genes, indicating conservation of the up-regulation in failing CMs. Moreover, several genes induced during pathological hypertrophy were also found to be increased in human HF, with their expression positively correlating to the known stress markers NPPB and MYH7. Mechanistically, suppression of Pfkp in primary CMs attenuated stress-induced gene expression and hypertrophy, indicating that Pfkp is an important novel player in pathological remodelling of CMs.<h4>Conclusion</h4>Using CM-specific transcriptomic analysis, we identified novel genes induced during pathological hypertrophy that are relevant for human HF, and we show that PFKP is a conserved failure-induced gene that can modulate the CM stress response.",,doi:https://doi.org/10.1093/cvr/cvaa233; doi:https://doi.org/10.1093/cvr/cvaa233; html:https://europepmc.org/articles/PMC8152696; pdf:https://europepmc.org/articles/PMC8152696?pdf=render
+35487318,https://doi.org/10.1016/j.ijcard.2022.04.067,Implications of elevated troponin on time-to-surgery in non-ST elevation myocardial infarction (NIHR Health Informatics Collaborative: TROP-CABG study).,"Benedetto U, Sinha S, Mulla A, Glampson B, Davies J, Panoulas V, Gautama S, Papadimitriou D, Woods K, Elliott P, Hemingway H, Williams B, Asselbergs FW, Melikian N, Krasopoulos G, Sayeed R, Wendler O, Baig K, Chukwuemeka A, Angelini GD, Sterne JAC, Johnson T, Shah AM, Perera D, Patel RS, Kharbanda R, Channon KM, Mayet J, Kaura A.",,International journal of cardiology,2022,2022-04-27,N,Troponin; Myocardial infarction; Coronary Artery Bypass Grafting; Timing-to-surgery,,,"Implications of elevated troponin on time-to-surgery in non-ST elevation myocardial infarction(NIHR Health Informatics Collaborative:TROP-CABG study). Benedetto et al. BACKGROUND: The optimal timing of coronary artery bypass grafting (CABG) in patients with non-ST elevation myocardial infarction (NSTEMI) and the utility of pre-operative troponin levels in decision-making remains unclear. We investigated (a) the association between peak pre-operative troponin and survival post-CABG in a large cohort of NSTEMI patients and (b) the interaction between troponin and time-to-surgery. METHODS AND RESULTS: Our cohort consisted of 1746 patients (1684 NSTEMI; 62 unstable angina) (mean age 69 ± 11 years,21% female) with recorded troponins that had CABG at five United Kingdom centers between 2010 and 2017. Time-segmented Cox regression was used to investigate the interaction of peak troponin and time-to-surgery on early (within 30 days) and late (beyond 30 days) survival. Average interval from peak troponin to surgery was 9 ± 15 days, with 1466 (84.0%) patients having CABG during the same admission. Sixty patients died within 30-days and another 211 died after a mean follow-up of 4 ± 2 years (30-day survival 0.97 ± 0.004 and 5-year survival 0.83 ± 0.01). Peak troponin was a strong predictor of early survival (adjusted P = 0.002) with a significant interaction with time-to-surgery (P interaction = 0.007). For peak troponin levels <100 times the upper limit of normal, there was no improvement in early survival with longer time-to-surgery. However, in patients with higher troponins, early survival increased progressively with a longer time-to-surgery, till day 10. Peak troponin did not influence survival beyond 30 days (adjusted P = 0.64). CONCLUSIONS: Peak troponin in NSTEMI patients undergoing CABG was a significant predictor of early mortality, strongly influenced the time-to-surgery and may prove to be a clinically useful biomarker in the management of these patients.",,doi:https://doi.org/10.1016/j.ijcard.2022.04.067
 33652931,https://doi.org/10.3390/jcm10050921,Diagnosis and Risk Prediction of Dilated Cardiomyopathy in the Era of Big Data and Genomics.,"Sammani A, Baas AF, Asselbergs FW, Te Riele ASJM.",,Journal of clinical medicine,2021,2021-02-26,Y,Artificial intelligence; Diagnosis; Prognosis; Genetic; Dilated cardiomyopathy; Big Data; Deep Learning,,,"Dilated cardiomyopathy (DCM) is a leading cause of heart failure and life-threatening ventricular arrhythmias (LTVA). Work-up and risk stratification of DCM is clinically challenging, as there is great heterogeneity in phenotype and genotype. Throughout the last decade, improved genetic testing of patients has identified genotype-phenotype associations and enhanced evaluation of at-risk relatives leading to better patient prognosis. The field is now ripe to explore opportunities to improve personalised risk assessments. Multivariable risk models presented as ""risk calculators"" can incorporate a multitude of clinical variables and predict outcome (such as heart failure hospitalisations or LTVA). In addition, genetic risk scores derived from genome/exome-wide association studies can estimate an individual's lifetime genetic risk of developing DCM. The use of clinically granular investigations, such as late gadolinium enhancement on cardiac magnetic resonance imaging, is warranted in order to increase predictive performance. To this end, constructing big data infrastructures improves accessibility of data by using electronic health records, existing research databases, and disease registries. By applying methods such as machine and deep learning, we can model complex interactions, identify new phenotype clusters, and perform prognostic modelling. This review aims to provide an overview of the evolution of DCM definitions as well as its clinical work-up and considerations in the era of genomics. In addition, we present exciting examples in the field of big data infrastructures, personalised prognostic assessment, and artificial intelligence.",,pdf:https://www.mdpi.com/2077-0383/10/5/921/pdf?version=1615467325; doi:https://doi.org/10.3390/jcm10050921; html:https://europepmc.org/articles/PMC7956169; pdf:https://europepmc.org/articles/PMC7956169?pdf=render
 34356044,https://doi.org/10.3390/genes12071029,A Causal Web between Chronotype and Metabolic Health Traits.,"Williams JA, Russ D, Bravo-Merodio L, Cardoso VR, Pendleton SC, Aziz F, Acharjee A, Gkoutos GV.",,Genes,2021,2021-07-01,Y,Circadian rhythm; Diabetes; Bipolar disorder; Alcohol Intake; Mendelian Randomization; Chronotype,,,"Observational and experimental evidence has linked chronotype to both psychological and cardiometabolic traits. Recent Mendelian randomization (MR) studies have investigated direct links between chronotype and several of these traits, often in isolation of outside potential mediating or moderating traits. We mined the EpiGraphDB MR database for calculated chronotype-trait associations (<i>p</i>-value < 5 × 10<sup>-8</sup>). We then re-analyzed those relevant to metabolic or mental health and investigated for statistical evidence of horizontal pleiotropy. Analyses passing multiple testing correction were then investigated for confounders, colliders, intermediates, and reverse intermediates using the EpiGraphDB database, creating multiple chronotype-trait interactions among each of the the traits studied. We revealed 10 significant chronotype-exposure associations (false discovery rate < 0.05) exposed to 111 potential previously known confounders, 52 intermediates, 18 reverse intermediates, and 31 colliders. Chronotype-lipid causal associations collided with treatment and diabetes effects; chronotype-bipolar associations were mediated by breast cancer; and chronotype-alcohol intake associations were impacted by confounders and intermediate variables including known zeitgebers and molecular traits. We have reported the influence of chronotype on several cardiometabolic and behavioural traits, and identified potential confounding variables not reported on in studies while discovering new associations to drugs and disease.",,pdf:https://www.mdpi.com/2073-4425/12/7/1029/pdf?version=1625724795; doi:https://doi.org/10.3390/genes12071029; html:https://europepmc.org/articles/PMC8303793; pdf:https://europepmc.org/articles/PMC8303793?pdf=render
 33180769,https://doi.org/10.1371/journal.pone.0240902,"Probable PTSD, depression and anxiety in 40,299 UK police officers and staff: Prevalence, risk factors and associations with blood pressure.","Stevelink SAM, Opie E, Pernet D, Gao H, Elliott P, Wessely S, Fear NT, Hotopf M, Greenberg N.",,PloS one,2020,2020-11-12,Y,,,,"<h4>Introduction</h4>Police employees undertake challenging duties which may adversely impact their health. This study explored the prevalence of and risk factors for probable mental disorders amongst a representative sample of UK police employees. The association between mental illness and alterations in blood pressure was also explored.<h4>Methods</h4>Data were used from the Airwave Health Monitoring Study which was established to monitor the possible physical health impacts of a new communication system on police employees. Data included sociodemographic characteristics, lifestyle habits, depression, anxiety, and post-traumatic stress disorder (PTSD) symptoms and blood pressure. Descriptive statistics were used to explore the prevalence of probable mental disorders and associated factors. Stepwise linear regression was conducted, controlling for confounding variables, to examine associations between mental disorders and blood pressure.<h4>Results</h4>The sample included 40,299 police staff, police constable/sergeants and inspectors or above. Probable depression was most frequently reported (9.8%), followed by anxiety (8.5%) and PTSD (3.9%). Groups at risk for probable mental disorders included police staff, and police employees who reported drinking heavily. Police employees exposed to traumatic incidents in the past six months had a doubling in rates of anxiety or depression and a six-fold increase in PTSD compared to those with no recent trauma exposure. Adjusted logistic regression models did not reveal any significant association between probable mental disorders and systolic blood pressure but significantly elevated diastolic blood pressure (≈1mmHg) was found across mental disorders.<h4>Conclusions</h4>These results show lower rates of probable mental disorders, especially PTSD, than reported in other studies focusing on police employees. Although mental ill health was associated with increased diastolic blood pressure, this was unlikely to be clinically significant. These findings highlight the importance of continued health monitoring of members of the UK police forces, focusing on employees recently exposed to traumatic incidents, heavy drinkers and police staff.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0240902&type=printable; doi:https://doi.org/10.1371/journal.pone.0240902; html:https://europepmc.org/articles/PMC7660485; pdf:https://europepmc.org/articles/PMC7660485?pdf=render
@@ -1499,8 +1501,8 @@ PMC8855010,https://doi.org/,POS-894 PREDICTING PANDEMIC-RELATED EXCESS-DEATH USI
 35104366,https://doi.org/10.1111/bjd.21042,Vaccine hesitancy and access to psoriasis care during the COVID-19 pandemic: findings from a global patient-reported cross-sectional survey.,"Bechman K, Cook ES, Dand N, Yiu ZZN, Tsakok T, Meynell F, Coker B, Vincent A, Bachelez H, Barbosa I, Brown MA, Capon F, Contreras CR, De La Cruz C, Meglio PD, Gisondi P, Jullien D, Kelly J, Lambert J, Lancelot C, Langan SM, Mason KJ, McAteer H, Moorhead L, Naldi L, Norton S, Puig L, Spuls PI, Torres T, Urmston D, Vesty A, Warren RB, Waweru H, Weinman J, Griffiths CEM, Barker JN, Smith CH, Galloway JB, Mahil SK, PsoProtect study group.",,The British journal of dermatology,2022,2022-05-03,Y,,,,,,pdf:https://biblio.ugent.be/publication/8757812/file/8757816.pdf; doi:https://doi.org/10.1111/bjd.21042; html:https://europepmc.org/articles/PMC9545500; pdf:https://europepmc.org/articles/PMC9545500?pdf=render
 37285143,https://doi.org/10.1001/jamacardio.2023.1290,Diagnostic and Prognostic Value of Stress Cardiovascular Magnetic Resonance Imaging in Patients With Known or Suspected Coronary Artery Disease: A Systematic Review and Meta-analysis.,"Ricci F, Khanji MY, Bisaccia G, Cipriani A, Di Cesare A, Ceriello L, Mantini C, Zimarino M, Fedorowski A, Gallina S, Petersen SE, Bucciarelli-Ducci C.",,JAMA cardiology,2023,2023-07-01,N,,,,"<h4>Importance</h4>The clinical utility of stress cardiovascular magnetic resonance imaging (CMR) in stable chest pain is still debated, and the low-risk period for adverse cardiovascular (CV) events after a negative test result is unknown.<h4>Objective</h4>To provide contemporary quantitative data synthesis of the diagnostic accuracy and prognostic value of stress CMR in stable chest pain.<h4>Data sources</h4>PubMed and Embase databases, the Cochrane Database of Systematic Reviews, PROSPERO, and the ClinicalTrials.gov registry were searched for potentially relevant articles from January 1, 2000, through December 31, 2021.<h4>Study selection</h4>Selected studies evaluated CMR and reported estimates of diagnostic accuracy and/or raw data of adverse CV events for participants with either positive or negative stress CMR results. Prespecified combinations of keywords related to the diagnostic accuracy and prognostic value of stress CMR were used. A total of 3144 records were evaluated for title and abstract; of those, 235 articles were included in the full-text assessment of eligibility. After exclusions, 64 studies (74 470 total patients) published from October 29, 2002, through October 19, 2021, were included.<h4>Data extraction and synthesis</h4>This systematic review and meta-analysis adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses.<h4>Main outcomes and measures</h4>Diagnostic odds ratios (DORs), sensitivity, specificity, area under the receiver operating characteristic curve (AUROC), odds ratio (OR), and annualized event rate (AER) for all-cause death, CV death, and major adverse cardiovascular events (MACEs) defined as the composite of myocardial infarction and CV death.<h4>Results</h4>A total of 33 diagnostic studies pooling 7814 individuals and 31 prognostic studies pooling 67 080 individuals (mean [SD] follow-up, 3.5 [2.1] years; range, 0.9-8.8 years; 381 357 person-years) were identified. Stress CMR yielded a DOR of 26.4 (95% CI, 10.6-65.9), a sensitivity of 81% (95% CI, 68%-89%), a specificity of 86% (95% CI, 75%-93%), and an AUROC of 0.84 (95% CI, 0.77-0.89) for the detection of functionally obstructive coronary artery disease. In the subgroup analysis, stress CMR yielded higher diagnostic accuracy in the setting of suspected coronary artery disease (DOR, 53.4; 95% CI, 27.7-103.0) or when using 3-T imaging (DOR, 33.2; 95% CI, 19.9-55.4). The presence of stress-inducible ischemia was associated with higher all-cause mortality (OR, 1.97; 95% CI, 1.69-2.31), CV mortality (OR, 6.40; 95% CI, 4.48-9.14), and MACEs (OR, 5.33; 95% CI, 4.04-7.04). The presence of late gadolinium enhancement (LGE) was associated with higher all-cause mortality (OR, 2.22; 95% CI, 1.99-2.47), CV mortality (OR, 6.03; 95% CI, 2.76-13.13), and increased risk of MACEs (OR, 5.42; 95% CI, 3.42-8.60). After a negative test result, pooled AERs for CV death were less than 1.0%.<h4>Conclusion and relevance</h4>In this study, stress CMR yielded high diagnostic accuracy and delivered robust prognostication, particularly when 3-T scanners were used. While inducible myocardial ischemia and LGE were associated with higher mortality and risk of MACEs, normal stress CMR results were associated with a lower risk of MACEs for at least 3.5 years.",,doi:https://doi.org/10.1001/jamacardio.2023.1290; html:https://europepmc.org/articles/PMC10248816; doi:https://doi.org/10.1001/jamacardio.2023.1290
 31349307,https://doi.org/10.3233/shti190058,Phenotyping UK Electronic Health Records from 15 Million Individuals for Precision Medicine: The CALIBER Resource.,"Denaxas S, Gonzalez-Izquierdo A, Fitzpatrick N, Direk K, Hemingway H.",,Studies in health technology and informatics,2019,2019-07-01,N,Prognosis; Phenotyping; Data Linkage; Electronic Health Records; Biomedical Informatics,,,"Electronic health records (EHR) are increasingly being used for observational research at scale. In the UK, we have established the CALIBER research resource which utilizes national primary and hospital EHR data sources and enables researchers to create and validate longitudinal disease phenotypes at scale. In this work, we will describe the core components of the resource and provide results from three exemplar research studies on high-resolution epidemiology, disease risk prediction and subtype discovery which demonstrate both the opportunities and challenges of using EHR for research.",,doi:https://doi.org/10.3233/SHTI190058
-36332947,https://doi.org/10.1136/bmjopen-2022-061843,Numbers and types of neurological emergencies in England and the influence of socioeconomic deprivation: a retrospective analysis of hospital episode statistics data.,"Jackson M, Szczepaniak M, Wall J, Maskery M, Mummery C, Morrish P, Williams A, Knight J, Emsley HCA.",,BMJ open,2022,2022-11-04,Y,Epilepsy; Neurology; Public Health,,,"<h4>Objectives</h4>In this first large-scale analysis of neurological emergency admissions in England, we determine the number and types of emergency admissions with neurological emergency diagnostic codes, how many are under the care of a neurologist or neurosurgeon and how such admissions vary by levels of deprivation.<h4>Design</h4>Retrospective empirical research employing a derived list of neurological emergency diagnostic codes SETTING: This study used the Hospital Episode Statistics data set for the financial year 2019/2020 based on 17 million in-year inpatient admissions in England including 6.5 million (100%) emergency admissions with any diagnosis codes.<h4>Results</h4>There were 1.4 million (21.2%) emergency inpatient admissions with a mention of any neurological code, approx. 248 455 (3.8%) with mention of a specific neurological emergency code from the derived list, and 72 485 (1.1%) included such a code as the primary reason for admission. The highest number of in-year admissions for adults was for epilepsy (145 995), with epilepsy as the primary diagnostic code in 15 945 (10.9%). Acute nerve root/spinal cord syndrome (41 215), head injury (29 235) and subarachnoid haemorrhage (18 505) accounted for the next three highest number of admissions. 3230 (1.4%) in-year emergency hospital admissions with mention of a neurological emergency code were under the care of a neurologist or neurosurgeon, with only 1315 (0.9%) admissions with mention of an epilepsy code under a neurologist. There was significant variation for epilepsy and functional neurological disorders (FNDs) in particular by Index of Multiple Deprivation decile. The association between deprivation and epilepsy and FND was significant with p-values of 2.5e-6 and 1.5e-8, respectively.<h4>Conclusions</h4>This study has identified important findings in relation to the burden of neurological emergency admissions but further work is needed, with greater clinical engagement in diagnostic coding, to better understand the implications for workforce and changes to service delivery needing to be implemented.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/11/e061843.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-061843; html:https://europepmc.org/articles/PMC9639083; pdf:https://europepmc.org/articles/PMC9639083?pdf=render
 32861307,https://doi.org/10.1016/s0140-6736(20)30930-2,Invasive versus non-invasive management of older patients with non-ST elevation myocardial infarction (SENIOR-NSTEMI): a cohort study based on routine clinical data.,"Kaura A, Sterne JAC, Trickey A, Abbott S, Mulla A, Glampson B, Panoulas V, Davies J, Woods K, Omigie J, Shah AD, Channon KM, Weber JN, Thursz MR, Elliott P, Hemingway H, Williams B, Asselbergs FW, O'Sullivan M, Lord GM, Melikian N, Johnson T, Francis DP, Shah AM, Perera D, Kharbanda R, Patel RS, Mayet J.",,"Lancet (London, England)",2020,2020-08-01,Y,,,,"<h4>Background</h4>Previous trials suggest lower long-term risk of mortality after invasive rather than non-invasive management of patients with non-ST elevation myocardial infarction (NSTEMI), but the trials excluded very elderly patients. We aimed to estimate the effect of invasive versus non-invasive management within 3 days of peak troponin concentration on the survival of patients aged 80 years or older with NSTEMI.<h4>Methods</h4>Routine clinical data for this study were obtained from five collaborating hospitals hosting NIHR Biomedical Research Centres in the UK (all tertiary centres with emergency departments). Eligible patients were 80 years old or older when they underwent troponin measurements and were diagnosed with NSTEMI between 2010 (2008 for University College Hospital) and 2017. Propensity scores (patients' estimated probability of receiving invasive management) based on pretreatment variables were derived using logistic regression; patients with high probabilities of non-invasive or invasive management were excluded. Patients who died within 3 days of peak troponin concentration without receiving invasive management were assigned to the invasive or non-invasive management groups based on their propensity scores, to mitigate immortal time bias. We estimated mortality hazard ratios comparing invasive with non-invasive management, and compared the rate of hospital admissions for heart failure.<h4>Findings</h4>Of the 1976 patients with NSTEMI, 101 died within 3 days of their peak troponin concentration and 375 were excluded because of extreme propensity scores. The remaining 1500 patients had a median age of 86 (IQR 82-89) years of whom (845 [56%] received non-invasive management. During median follow-up of 3·0 (IQR 1·2-4·8) years, 613 (41%) patients died. The adjusted cumulative 5-year mortality was 36% in the invasive management group and 55% in the non-invasive management group (adjusted hazard ratio 0·68, 95% CI 0·55-0·84). Invasive management was associated with lower incidence of hospital admissions for heart failure (adjusted rate ratio compared with non-invasive management 0·67, 95% CI 0·48-0·93).<h4>Interpretation</h4>The survival advantage of invasive compared with non-invasive management appears to extend to patients with NSTEMI who are aged 80 years or older.<h4>Funding</h4>NIHR Imperial Biomedical Research Centre, as part of the NIHR Health Informatics Collaborative.",,pdf:http://www.thelancet.com/article/S0140673620309302/pdf; doi:https://doi.org/10.1016/S0140-6736(20)30930-2; html:https://europepmc.org/articles/PMC7456783; pdf:https://europepmc.org/articles/PMC7456783?pdf=render
+36332947,https://doi.org/10.1136/bmjopen-2022-061843,Numbers and types of neurological emergencies in England and the influence of socioeconomic deprivation: a retrospective analysis of hospital episode statistics data.,"Jackson M, Szczepaniak M, Wall J, Maskery M, Mummery C, Morrish P, Williams A, Knight J, Emsley HCA.",,BMJ open,2022,2022-11-04,Y,Epilepsy; Neurology; Public Health,,,"<h4>Objectives</h4>In this first large-scale analysis of neurological emergency admissions in England, we determine the number and types of emergency admissions with neurological emergency diagnostic codes, how many are under the care of a neurologist or neurosurgeon and how such admissions vary by levels of deprivation.<h4>Design</h4>Retrospective empirical research employing a derived list of neurological emergency diagnostic codes SETTING: This study used the Hospital Episode Statistics data set for the financial year 2019/2020 based on 17 million in-year inpatient admissions in England including 6.5 million (100%) emergency admissions with any diagnosis codes.<h4>Results</h4>There were 1.4 million (21.2%) emergency inpatient admissions with a mention of any neurological code, approx. 248 455 (3.8%) with mention of a specific neurological emergency code from the derived list, and 72 485 (1.1%) included such a code as the primary reason for admission. The highest number of in-year admissions for adults was for epilepsy (145 995), with epilepsy as the primary diagnostic code in 15 945 (10.9%). Acute nerve root/spinal cord syndrome (41 215), head injury (29 235) and subarachnoid haemorrhage (18 505) accounted for the next three highest number of admissions. 3230 (1.4%) in-year emergency hospital admissions with mention of a neurological emergency code were under the care of a neurologist or neurosurgeon, with only 1315 (0.9%) admissions with mention of an epilepsy code under a neurologist. There was significant variation for epilepsy and functional neurological disorders (FNDs) in particular by Index of Multiple Deprivation decile. The association between deprivation and epilepsy and FND was significant with p-values of 2.5e-6 and 1.5e-8, respectively.<h4>Conclusions</h4>This study has identified important findings in relation to the burden of neurological emergency admissions but further work is needed, with greater clinical engagement in diagnostic coding, to better understand the implications for workforce and changes to service delivery needing to be implemented.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/11/e061843.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-061843; html:https://europepmc.org/articles/PMC9639083; pdf:https://europepmc.org/articles/PMC9639083?pdf=render
 31558464,https://doi.org/10.1136/bmjopen-2019-033013,Long-term impact of giving antibiotics before skin incision versus after cord clamping on children born by caesarean section: protocol for a longitudinal study based on UK electronic health records.,"Šumilo D, Nirantharakumar K, Willis BH, Rudge G, Martin J, Gokhale K, Thayakaran R, Adderley NJ, Chandan JS, Okoth K, Hewston R, Skrybant M, Deeks JJ, Brocklehurst P.",,BMJ open,2019,2019-09-26,Y,Child; Asthma; Caesarean section; Eczema; Antibiotic Prophylaxis; Immune System Diseases,,,"<h4>Introduction</h4>In the UK, about a quarter of women give birth by caesarean section (CS) and are offered prophylactic broad-spectrum antibiotics to reduce the risk of maternal postpartum infection. In 2011, national guidance was changed from recommending antibiotics after the umbilical cord was cut to giving antibiotics prior to skin incision based on evidence that earlier administration reduces maternal infectious morbidity. Although antibiotics cross the placenta, there are no known short-term harms to the baby. This study aims to address the research gap on longer term impact of these antibiotics on child health.<h4>Methods and analysis</h4>A controlled interrupted time series study will use anonymised mother-baby linked routine electronic health records for children born during 2006-2018 recorded in UK primary care (The Health Improvement Network, THIN and Clinical Practice Research Datalink, CPRD) and secondary care (Hospital Episode Statistics, HES) databases. The primary outcomes of interest are asthma and eczema, two common allergy-related diseases in childhood. In-utero exposure to antibiotics immediately prior to CS will be compared with no exposure when given after cord clamping. The risk of outcomes in children delivered by CS will also be compared with a control cohort delivered vaginally to account for time effects. We will use all available data from THIN, CPRD and HES with estimated power of 80% and 90% to detect relative increase in risk of asthma of 16% and 18%, respectively at the 5% significance level.<h4>Ethics and dissemination</h4>Ethical approval has been obtained from the University of Birmingham Ethical Review Committee with scientific approvals obtained from the independent scientific advisory committees from the Medicines and Healthcare products Regulatory Agency for CPRD and the data provider, IQVIA for THIN. The results will be published in peer-reviewed journals, presented at national and international conferences and disseminated to stakeholders.",,pdf:https://bmjopen.bmj.com/content/bmjopen/9/9/e033013.full.pdf; doi:https://doi.org/10.1136/bmjopen-2019-033013; html:https://europepmc.org/articles/PMC6773283; pdf:https://europepmc.org/articles/PMC6773283?pdf=render
 34598995,https://doi.org/10.1136/bmjopen-2021-055219,"wEight chanGes, caRdio-mEtabolic risks and morTality in patients with hyperthyroidism (EGRET): a protocol for a CPRD-HES linked cohort study.","Torlinska B, Hazlehurst JM, Nirantharakumar K, Thomas GN, Priestley JR, Finnikin SJ, Saunders P, Abrams KR, Boelaert K.",,BMJ open,2021,2021-10-01,Y,Thyroid disease; epidemiology; Cardiac Epidemiology,,,"<h4>Introduction</h4>Hyperthyroidism is a common condition affecting up to 3% of the UK population. Treatment improves symptoms and reduces the risk of atrial fibrillation and stroke that contribute to increased mortality. The most common symptom is weight loss, which is reversed during treatment. However, the weight regain may be excessive, contributing to increased risk of obesity. Current treatment options include antithyroid drugs, radioiodine and thyroidectomy. Whether there are differences in either weight change or the long-term cardiometabolic risk between the three treatments is unclear.<h4>Methods and analysis</h4>The study will establish the natural history of weight change in hyperthyroidism, investigate the risk of obesity and risks of cardiometabolic conditions and death relative to the treatment. The data on patients diagnosed with hyperthyroidism between 1 January 1996 and 31 December 2015 will come from Clinical Practice Research Datalink linked to Hospital Episode Statistics and Office of National Statistics Death Registry. The weight changes will be modelled using a flexible joint modelling, accounting for mortality. Obesity prevalence in the general population will be sourced from Health Survey for England and compared with the post-treatment prevalence of obesity in patients with hyperthyroidism. The incidence and time-to-event of major adverse cardiovascular events, other cardiometabolic outcomes and mortality will be compared between the treatments using the inverse propensity weighting model. Incidence rate ratios of outcomes will be modelled with Poisson regression. Time to event will be analysed using Cox proportional hazards model. A competing risks approach will be adopted to estimate comparative incidences to allow for the impact of mortality.<h4>Ethics and dissemination</h4>The study will bring new knowledge on the risk of developing obesity, cardiometabolic morbidity and mortality following treatment for hyperthyroidism to inform clinical practice and public health policies. The results will be disseminated via open-access peer-reviewed publications and directly to the patients and public groups (Independent Scientific Advisory Committee protocol approval #20_000185).",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/10/e055219.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-055219; html:https://europepmc.org/articles/PMC8488707; pdf:https://europepmc.org/articles/PMC8488707?pdf=render
 32282926,https://doi.org/10.1111/bjd.19122,"Partner bereavement and risk of chronic urticaria, alopecia areata and vitiligo: cohort studies in the UK and Denmark.","Wong AYS, Kjaersgaard A, Frøslev T, Forbes HJ, Mansfield KE, Silverwood RJ, Sørensen HT, Smeeth L, Schmidt SAJ, Langan SM.",,The British journal of dermatology,2020,2020-06-10,N,,,,,,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/bjd.19122; doi:https://doi.org/10.1111/bjd.19122
@@ -1517,8 +1519,8 @@ PMC8855010,https://doi.org/,POS-894 PREDICTING PANDEMIC-RELATED EXCESS-DEATH USI
 37133927,https://doi.org/10.2196/45534,"Understanding Views Around the Creation of a Consented, Donated Databank of Clinical Free Text to Develop and Train Natural Language Processing Models for Research: Focus Group Interviews With Stakeholders.","Fitzpatrick NK, Dobson R, Roberts A, Jones K, Shah AD, Nenadic G, Ford E.",,JMIR medical informatics,2023,2023-05-03,Y,Consent; Governance; Electronic Health Records; Natural Language Processing; Free Text; Databank; Public Involvement; Unstructured Text,,,"<h4>Background</h4>Information stored within electronic health records is often recorded as unstructured text. Special computerized natural language processing (NLP) tools are needed to process this text; however, complex governance arrangements make such data in the National Health Service hard to access, and therefore, it is difficult to use for research in improving NLP methods. The creation of a donated databank of clinical free text could provide an important opportunity for researchers to develop NLP methods and tools and may circumvent delays in accessing the data needed to train the models. However, to date, there has been little or no engagement with stakeholders on the acceptability and design considerations of establishing a free-text databank for this purpose.<h4>Objective</h4>This study aimed to ascertain stakeholder views around the creation of a consented, donated databank of clinical free text to help create, train, and evaluate NLP for clinical research and to inform the potential next steps for adopting a partner-led approach to establish a national, funded databank of free text for use by the research community.<h4>Methods</h4>Web-based in-depth focus group interviews were conducted with 4 stakeholder groups (patients and members of the public, clinicians, information governance leads and research ethics members, and NLP researchers).<h4>Results</h4>All stakeholder groups were strongly in favor of the databank and saw great value in creating an environment where NLP tools can be tested and trained to improve their accuracy. Participants highlighted a range of complex issues for consideration as the databank is developed, including communicating the intended purpose, the approach to access and safeguarding the data, who should have access, and how to fund the databank. Participants recommended that a small-scale, gradual approach be adopted to start to gather donations and encouraged further engagement with stakeholders to develop a road map and set of standards for the databank.<h4>Conclusions</h4>These findings provide a clear mandate to begin developing the databank and a framework for stakeholder expectations, which we would aim to meet with the databank delivery.",,pdf:https://medinform.jmir.org/2023/1/e45534/PDF; doi:https://doi.org/10.2196/45534; html:https://europepmc.org/articles/PMC10193205
 38117144,https://doi.org/10.1089/neu.2023.0467,The Australian Traumatic Brain Injury Initiative: Single Data Dictionary to Predict Outcome for People With Moderate-Severe Traumatic Brain Injury.,"Fitzgerald M, Ponsford JL, Hill R, Rushworth N, Kendall E, Armstrong E, Gilroy J, Bullen J, Keeves J, Bagg MK, Hellewell SC, Lannin NA, O'Brien TJ, Cameron PA, Cooper DJ, Gabbe BJ.",,Journal of neurotrauma,2024,2024-04-03,N,"Common Data Elements; Brain Injuries, Traumatic; Outcome Assessment, Health Care",,,"In this series of eight articles, the Australian Traumatic Brain Injury Initiative (AUS-TBI) consortium describes the Australian approach used to select the common data elements collected acutely that have been shown to predict outcome following moderate-severe traumatic brain injury (TBI) across the lifespan. This article presents the unified single data dictionary, together with additional measures chosen to facilitate comparative effectiveness research and data linkage. Consultations with the AUS-TBI Lived Experience Expert Group provided insights on the merits and considerations regarding data elements for some of the study areas, as well as more general principles to guide the collection of data and the selection of meaningful measures. These are presented as a series of guiding principles and themes. The AUS-TBI Aboriginal and Torres Strait Islander Advisory Group identified a number of key points and considerations for the project approach specific to Aboriginal and Torres Strait Islander peoples, including key issues of data sovereignty and community involvement. These are outlined in the form of principles to guide selection of appropriate methodologies, data management, and governance. Implementation of the AUS-TBI approach aims to maximize ongoing data collection and linkage, to facilitate personalization of care and improved outcomes for people who experience moderate-severe TBI.",,pdf:https://research-repository.griffith.edu.au/bitstreams/20d2aa11-4551-4048-80f3-971b947f8598/download; doi:https://doi.org/10.1089/neu.2023.0467
 33382071,https://doi.org/10.1093/schbul/sbaa176,Corrigendum to: Using Natural Language Processing on Electronic Health Records to Enhance Detection and Prediction of Psychosis Risk.,,,Schizophrenia bulletin,2021,2021-03-01,N,,,,,,pdf:https://academic.oup.com/schizophreniabulletin/article-pdf/47/2/575/36620724/sbaa176.pdf; doi:https://doi.org/10.1093/schbul/sbaa176; html:https://europepmc.org/articles/PMC7965055; pdf:https://europepmc.org/articles/PMC7965055?pdf=render; doi:https://doi.org/10.1093/schbul/sbaa176
-37750555,https://doi.org/10.1161/jaha.123.030766,Impact of New Cardiovascular Events on Quality of Life and Hospital Costs in People With Cardiovascular Disease in the United Kingdom and United States.,"Lui JNM, Williams C, Keng MJ, Hopewell JC, Sammons E, Chen F, Gray A, Bowman L, Landray SMJ, Mihaylova B, REVEAL Collaborative Group.",,Journal of the American Heart Association,2023,2023-09-26,Y,Cardiovascular diseases; Quality of life; United States; United Kingdom; Secondary Prevention; Health Care Costs,,,"<h4>Background</h4>Despite optimized risk factor control, people with prior cardiovascular disease remain at high cardiovascular disease risk. We assess the immediate- and longer-term impacts of new vascular and nonvascular events on quality of life (QoL) and hospital costs among participants in the REVEAL (Randomized Evaluation of the Effects of Anacetrapib Through Lipid Modification) trial in secondary prevention.<h4>Methods and results</h4>Data on demographic and clinical characteristics, health-related quality of life (QoL: EuroQoL 5-Dimension-5-Level), adverse events, and hospital admissions during the 4-year follow-up of the 21 820 participants recruited in Europe and North America informed assessments of the impacts of new adverse events on QoL and hospital costs from the UK and US health systems' perspectives using generalized linear regression models. Reductions in QoL were estimated in the years of event occurrence for nonhemorrhagic stroke (-0.067 [United Kingdom], -0.069 [US]), heart failure admission (-0.072 [United Kingdom], -0.103 [US]), incident cancer (-0.064 [United Kingdom], -0.068 [US]), and noncoronary revascularization (-0.071 [United Kingdom], -0.061 [US]), as well as in subsequent years following these events. Myocardial infarction and coronary revascularization (CRV) procedures were not found to affect QoL. All adverse events were associated with additional hospital costs in the years of events and in subsequent years, with the highest additional costs in the years of noncoronary revascularization (£5830 [United Kingdom], $14 133 [US Medicare]), of myocardial infarction with urgent CRV procedure (£5614, $24722), and of urgent/nonurgent CRV procedure without myocardial infarction (£4674/£4651 and $15 251/$17 539).<h4>Conclusions</h4>Stroke, heart failure, and noncoronary revascularization procedures substantially reduce QoL, and all cardiovascular disease events increase hospital costs. These estimates are useful in informing cost-effectiveness of interventions to reduce cardiovascular disease risk in secondary prevention.<h4>Registration</h4>URL: https://www.clinicaltrials.gov; Unique identifier: NCT01252953; https://www.Isrctn.com. Unique identifier: ISRCTN48678192; https://www.clinicaltrialsregister.eu. Unique identifier: 2010-023467-18.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.123.030766; doi:https://doi.org/10.1161/JAHA.123.030766; html:https://europepmc.org/articles/PMC7615160; pdf:https://europepmc.org/articles/PMC7615160?pdf=render
 32929109,https://doi.org/10.1038/s41598-020-72060-0,A data-driven typology of asthma medication adherence using cluster analysis.,"Tibble H, Chan A, Mitchell EA, Horne E, Doudesis D, Horne R, Mizani MA, Sheikh A, Tsanas A.",,Scientific reports,2020,2020-09-14,Y,,,,"Asthma preventer medication non-adherence is strongly associated with poor asthma control. One-dimensional measures of adherence may ignore clinically important patterns of medication-taking behavior. We sought to construct a data-driven multi-dimensional typology of medication non-adherence in children with asthma. We analyzed data from an intervention study of electronic inhaler monitoring devices, comprising 211 patients yielding 35,161 person-days of data. Five adherence measures were extracted: the percentage of doses taken, the percentage of days on which zero doses were taken, the percentage of days on which both doses were taken, the number of treatment intermissions per 100 study days, and the duration of treatment intermissions per 100 study days. We applied principal component analysis on the measures and subsequently applied k-means to determine cluster membership. Decision trees identified the measure that could predict cluster assignment with the highest accuracy, increasing interpretability and increasing clinical utility. We demonstrate the use of adherence measures towards a three-group categorization of medication non-adherence, which succinctly describes the diversity of patient medication taking patterns in asthma. The percentage of prescribed doses taken during the study contributed to the prediction of cluster assignment most accurately (84% in out-of-sample data).",,pdf:https://www.nature.com/articles/s41598-020-72060-0.pdf; doi:https://doi.org/10.1038/s41598-020-72060-0; html:https://europepmc.org/articles/PMC7490405; pdf:https://europepmc.org/articles/PMC7490405?pdf=render
+37750555,https://doi.org/10.1161/jaha.123.030766,Impact of New Cardiovascular Events on Quality of Life and Hospital Costs in People With Cardiovascular Disease in the United Kingdom and United States.,"Lui JNM, Williams C, Keng MJ, Hopewell JC, Sammons E, Chen F, Gray A, Bowman L, Landray SMJ, Mihaylova B, REVEAL Collaborative Group.",,Journal of the American Heart Association,2023,2023-09-26,Y,Cardiovascular diseases; Quality of life; United States; United Kingdom; Secondary Prevention; Health Care Costs,,,"<h4>Background</h4>Despite optimized risk factor control, people with prior cardiovascular disease remain at high cardiovascular disease risk. We assess the immediate- and longer-term impacts of new vascular and nonvascular events on quality of life (QoL) and hospital costs among participants in the REVEAL (Randomized Evaluation of the Effects of Anacetrapib Through Lipid Modification) trial in secondary prevention.<h4>Methods and results</h4>Data on demographic and clinical characteristics, health-related quality of life (QoL: EuroQoL 5-Dimension-5-Level), adverse events, and hospital admissions during the 4-year follow-up of the 21 820 participants recruited in Europe and North America informed assessments of the impacts of new adverse events on QoL and hospital costs from the UK and US health systems' perspectives using generalized linear regression models. Reductions in QoL were estimated in the years of event occurrence for nonhemorrhagic stroke (-0.067 [United Kingdom], -0.069 [US]), heart failure admission (-0.072 [United Kingdom], -0.103 [US]), incident cancer (-0.064 [United Kingdom], -0.068 [US]), and noncoronary revascularization (-0.071 [United Kingdom], -0.061 [US]), as well as in subsequent years following these events. Myocardial infarction and coronary revascularization (CRV) procedures were not found to affect QoL. All adverse events were associated with additional hospital costs in the years of events and in subsequent years, with the highest additional costs in the years of noncoronary revascularization (£5830 [United Kingdom], $14 133 [US Medicare]), of myocardial infarction with urgent CRV procedure (£5614, $24722), and of urgent/nonurgent CRV procedure without myocardial infarction (£4674/£4651 and $15 251/$17 539).<h4>Conclusions</h4>Stroke, heart failure, and noncoronary revascularization procedures substantially reduce QoL, and all cardiovascular disease events increase hospital costs. These estimates are useful in informing cost-effectiveness of interventions to reduce cardiovascular disease risk in secondary prevention.<h4>Registration</h4>URL: https://www.clinicaltrials.gov; Unique identifier: NCT01252953; https://www.Isrctn.com. Unique identifier: ISRCTN48678192; https://www.clinicaltrialsregister.eu. Unique identifier: 2010-023467-18.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.123.030766; doi:https://doi.org/10.1161/JAHA.123.030766; html:https://europepmc.org/articles/PMC7615160; pdf:https://europepmc.org/articles/PMC7615160?pdf=render
 31302040,https://doi.org/10.1016/j.jchf.2019.03.009,Risk for Heart Failure: The Opportunity for Prevention With the American Heart Association's Life's Simple 7.,"Uijl A, Koudstaal S, Vaartjes I, Boer JMA, Verschuren WMM, van der Schouw YT, Asselbergs FW, Hoes AW, Sluijs I.",,JACC. Heart failure,2019,2019-07-10,N,Heart Failure; Cardiovascular Disease Risk Factors; Healthy Lifestyle; Life’s Simple 7,,,"<h4>Objectives</h4>The aim of this study is to determine whether combinations of specific Life's Simple 7 (LS7) components are associated with reduced risk for heart failure (HF).<h4>Background</h4>The American Heart Association recommends the concept of LS7: healthy behaviors that have been shown to reduce cardiovascular disease.<h4>Methods</h4>A total of 37,803 participants from the EPIC-NL (European Prospective Investigation Into Cancer and Nutrition-Netherlands) cohort were included (mean age: 49.4 ± 11.9 years, 74.7% women). The LS7 score ranged from 0 to 14 and was calculated by assigning 0, 1, or 2 points for smoking, physical activity, body mass index, diet, blood pressure, total cholesterol, and blood glucose. An overall ideal score (11 to 14 points) was present in 23.2% of participants, an intermediate score (9 or 10 points) in 35.3%, and an inadequate score (0 to 8 points) in 41.5%.<h4>Results</h4>Over a median follow-up period of 15.2 years (interquartile range: 14.1 to 16.5 years), 690 participants (1.8%) developed HF. In Cox proportional hazards models, ideal and intermediate LS7 scores were associated with reduced risk for HF compared with the inadequate category (hazard ratio: 0.45 [95% confidence interval (CI): 0.34 to 0.60] and hazard ratio: 0.53 [95% CI: 0.44 to 0.64], respectively). Our analyses show that combinations with specific LS7 components, notably glucose, body mass index, smoking, and blood pressure, are associated with a lower incidence of HF.<h4>Conclusions</h4>A healthy lifestyle, as reflected in an ideal LS7 score, was associated with a 55% lower risk for HF compared with an inadequate LS7 score. Preventive strategies that target combinations of specific LS7 components could have a significant impact on decreasing incident HF in the population at large.",,doi:https://doi.org/10.1016/j.jchf.2019.03.009
 38142238,https://doi.org/10.1093/ije/dyad175,Cohort Profile: The Cardiovascular Research Data Catalogue.,"Reinikainen J, Palosaari T, Canosa-Valls AJ, Schmidt CO, Wissa R, Chadalavada S, Codó L, Gelpí JL, Joseph B, van der Lugt A, Pacella E, Petersen SE, Pujadas ER, Szabo L, Zeller T, Niiranen T, Lekadir K, Kuulasmaa K.",,International journal of epidemiology,2024,2024-02-01,N,,,,,,doi:https://doi.org/10.1093/ije/dyad175
 32991065,https://doi.org/10.1111/dom.14203,Sodium-glucose co-transporter-2 inhibitors and susceptibility to COVID-19: A population-based retrospective cohort study.,"Sainsbury C, Wang J, Gokhale K, Acosta-Mena D, Dhalla S, Byne N, Chandan JS, Anand A, Cooper J, Okoth K, Subramanian A, Bangash MN, Taverner T, Hanif W, Ghosh S, Narendran P, Cheng KK, Marshall T, Gkoutos G, Toulis K, Thomas N, Tahrani A, Adderley NJ, Haroon S, Nirantharakumar K.",,"Diabetes, obesity & metabolism",2021,2020-10-19,Y,Type 2 diabetes; Dpp-4 Inhibitor; Pharmaco-epidemiology; Sglt2 Inhibitor; Antidiabetic Drug,,,"Sodium-glucose co-transporter-2 (SGLT2) inhibitors are widely prescribed in people with type 2 diabetes. We aimed to investigate whether SGLT2 inhibitor prescription is associated with COVID-19, when compared with an active comparator. We performed a propensity-score-matched cohort study with active comparators and a negative control outcome in a large UK-based primary care dataset. Participants prescribed SGLT2 inhibitors (n = 9948) and a comparator group prescribed dipeptidyl peptidase-4 (DPP-4) inhibitors (n = 14 917) were followed up from January 30 to July 27, 2020. The primary outcome was confirmed or clinically suspected COVID-19. The incidence rate of COVID-19 was 19.7/1000 person-years among users of SGLT2 inhibitors and 24.7/1000 person-years among propensity-score-matched users of DPP-4 inhibitors. The adjusted hazard ratio was 0.92 (95% confidence interval 0.66 to 1.29), and there was no evidence of residual confounding in the negative control analysis. We did not observe an increased risk of COVID-19 in primary care amongst those prescribed SGLT2 inhibitors compared to DPP-4 inhibitors, suggesting that clinicians may safely use these agents in the everyday care of people with type 2 diabetes during the COVID-19 pandemic.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/dom.14203; doi:https://doi.org/10.1111/dom.14203; html:https://europepmc.org/articles/PMC7537530; pdf:https://europepmc.org/articles/PMC7537530?pdf=render
@@ -1529,46 +1531,46 @@ PMC8855010,https://doi.org/,POS-894 PREDICTING PANDEMIC-RELATED EXCESS-DEATH USI
 37990330,https://doi.org/10.1186/s13063-023-07763-6,"Correction: Medicines and Healthcare products Regulatory Agency's ""Consultation on proposals for legislative changes for clinical trials"": a response from the Trials Methodology Research Partnership Adaptive Designs Working Group, with a focus on data sharing.","Law M, Couturier DL, Choodari-Oskooei B, Crout P, Gamble C, Jacko P, Pallmann P, Pilling M, Robertson DS, Robling M, Sydes MR, Villar SS, Wason J, Wheeler G, Williamson SF, Yap C, Jaki T.",,Trials,2023,2023-11-21,Y,,,,,,pdf:https://trialsjournal.biomedcentral.com/counter/pdf/10.1186/s13063-023-07763-6; doi:https://doi.org/10.1186/s13063-023-07763-6; html:https://europepmc.org/articles/PMC10664262; pdf:https://europepmc.org/articles/PMC10664262?pdf=render
 37987834,https://doi.org/10.1007/s00330-023-10311-0,Radiomics of pericardial fat: a new frontier in heart failure discrimination and prediction.,"Szabo L, Salih A, Pujadas ER, Bard A, McCracken C, Ardissino M, Antoniades C, Vago H, Maurovich-Horvat P, Merkely B, Neubauer S, Lekadir K, Petersen SE, Raisi-Estabragh Z.",,European radiology,2024,2023-11-21,N,Pericardium; Adipose tissue; Magnetic Resonance Imaging; Machine Learning; Radiomics,,,"<h4>Objectives</h4>To use pericardial adipose tissue (PAT) radiomics phenotyping to differentiate existing and predict future heart failure (HF) cases in the UK Biobank.<h4>Methods</h4>PAT segmentations were derived from cardiovascular magnetic resonance (CMR) studies using an automated quality-controlled model to define the region-of-interest for radiomics analysis. Prevalent (present at time of imaging) and incident (first occurrence after imaging) HF were ascertained using health record linkage. We created balanced cohorts of non-HF individuals for comparison. PyRadiomics was utilised to extract 104 radiomics features, of which 28 were chosen after excluding highly correlated ones (0.8). These features, plus sex and age, served as predictors in binary classification models trained separately to detect (1) prevalent and (2) incident HF. We tested seven modeling methods using tenfold nested cross-validation and examined feature importance with explainability methods.<h4>Results</h4>We studied 1204 participants in total, 297 participants with prevalent (60 ± 7 years, 21% female) and 305 with incident (61 ± 6 years, 32% female) HF, and an equal number of non-HF comparators. We achieved good discriminative performance for both prevalent (voting classifier; AUC: 0.76; F1 score: 0.70) and incident (light gradient boosting machine: AUC: 0.74; F1 score: 0.68) HF. Our radiomics models showed marginally better performance compared to PAT area alone. Increased PAT size (maximum 2D diameter in a given column or slice) and texture heterogeneity (sum entropy) were important features for prevalent and incident HF classification models.<h4>Conclusions</h4>The amount and character of PAT discriminate individuals with prevalent HF and predict incidence of future HF.<h4>Clinical relevance statement</h4>This study presents an innovative application of pericardial adipose tissue (PAT) radiomics phenotyping as a predictive tool for heart failure (HF), a major public health concern. By leveraging advanced machine learning methods, the research uncovers that the quantity and characteristics of PAT can be used to identify existing cases of HF and predict future occurrences. The enhanced performance of these radiomics models over PAT area alone supports the potential for better personalised care through earlier detection and prevention of HF.<h4>Key points</h4>•PAT radiomics applied to CMR was used for the first time to derive binary machine learning classifiers to develop models for discrimination of prevalence and prediction of incident heart failure. •Models using PAT area provided acceptable discrimination between cases of prevalent or incident heart failure and comparator groups. •An increased PAT volume (increased diameter using shape features) and greater texture heterogeneity captured by radiomics texture features (increased sum entropy) can be used as an additional classifier marker for heart failure.",,pdf:https://link.springer.com/content/pdf/10.1007/s00330-023-10311-0.pdf; doi:https://doi.org/10.1007/s00330-023-10311-0
 36285341,https://doi.org/10.1080/17434440.2022.2132147,Data-driven monitoring in patients on left ventricular assist device support.,"Numan L, Moazeni M, Oerlemans MIFJ, Aarts E, Van Der Kaaij NP, Asselbergs FW, Van Laake LW.",,Expert review of medical devices,2022,2022-09-01,N,Prediction; Circadian rhythm; Algorithms; Remote Monitoring; Left Ventricular Assist Device; Lvad,,,"<h4>Introduction</h4>Despite an increasing population of patients supported with a left ventricular assist device (LVAD), it remains a complex therapy, and patients are frequently admitted. Therefore, a strict follow-up including frequent hospital visits, patient self-management and telemonitoring is needed.<h4>Areas covered</h4>The current review describes the principles of LVADs, the possibilities of (tele)monitoring using noninvasive and invasive devices. Furthermore, possibilities, challenges, and future perspectives in this emerging field are discussed.<h4>Expert opinion</h4>Several studies described initial experiences on telemonitoring in LVAD patients, using mobile phone applications to collect clinical data and pump data. This may replace frequent hospital visits in near future. In addition, algorithms were developed aiming to early detect pump thrombosis or driveline infections. Since not all complications are reflected by pump parameters, data from different sources should be combined to detect a broader spectrum of complications in an early stage. We need to focus on the development of sophisticated but understandable algorithms and infrastructure combining different data sources, while addressing essential aspects such as data safety, privacy, and cost-effectiveness.",,doi:https://doi.org/10.1080/17434440.2022.2132147; doi:https://doi.org/10.1080/17434440.2022.2132147
-39054354,https://doi.org/10.1038/s41594-024-01357-9,Structural basis for activity switching in polymerases determining the fate of let-7 pre-miRNAs.,"Yi G, Ye M, Carrique L, El-Sagheer A, Brown T, Norbury CJ, Zhang P, Gilbert RJC.",,Nature structural & molecular biology,2024,2024-07-25,Y,,,,"Tumor-suppressor let-7 pre-microRNAs (miRNAs) are regulated by terminal uridylyltransferases TUT7 and TUT4 that either promote let-7 maturation by adding a single uridine nucleotide to the pre-miRNA 3' end or mark them for degradation by the addition of multiple uridines. Oligo-uridylation is increased in cells by enhanced TUT7/4 expression and especially by the RNA-binding pluripotency factor LIN28A. Using cryogenic electron microscopy, we captured high-resolution structures of active forms of TUT7 alone, of TUT7 plus pre-miRNA and of both TUT7 and TUT4 bound with pre-miRNA and LIN28A. Our structures reveal that pre-miRNAs engage the enzymes in fundamentally different ways depending on the presence of LIN28A, which clamps them onto the TUTs to enable processive 3' oligo-uridylation. This study reveals the molecular basis for mono- versus oligo-uridylation by TUT7/4, as determined by the presence of LIN28A, and thus their mechanism of action in the regulation of cell fate and in cancer.",,doi:https://doi.org/10.1038/s41594-024-01357-9; doi:https://doi.org/10.1038/s41594-024-01357-9; html:https://europepmc.org/articles/PMC11402785; pdf:https://europepmc.org/articles/PMC11402785?pdf=render
 35103964,https://doi.org/10.1007/978-1-0716-2140-0_6,Chromatin Immunoprecipitation Sequencing (ChIP-seq) Protocol for Small Amounts of Frozen Biobanked Cardiac Tissue.,"Pei J, van den Dungen NAM, Asselbergs FW, Mokry M, Harakalova M.",,"Methods in molecular biology (Clifton, N.J.)",2022,2022-01-01,N,Sequencing; Antibody; Promoters; Cardiac Tissues; Chromatin Immunoprecipitation; Enhancers; Small Biopsy,,,"Chromatin immunoprecipitation and sequencing (ChIP-seq) is a well-established method to study the epigenetic profile at the genome-wide scale, including histone modifications and DNA-protein interactions. It provides valuable insights to better understand disease mechanisms. Here we present an optimized ChIP-seq protocol suitable for human cardiac tissues, especially the frozen biobanked small biopsy samples.",,doi:https://doi.org/10.1007/978-1-0716-2140-0_6
 35452565,https://doi.org/10.1002/cpz1.373,The COPILOT Raw Illumina Genotyping QC Protocol.,"Patel H, Lee SH, Breen G, Menzel S, Ojewunmi O, Dobson RJB.",,Current protocols,2022,2022-04-01,N,Genotyping; Gwas; Illumina; Docker; Qc Pipeline,,,"The Illumina genotyping microarrays generate data in image format, which is processed by the platform-specific software GenomeStudio, followed by an array of complex bioinformatics analyses that rely on various software, different programming languages, and numerous dependencies to be installed and configured correctly. The entire process can be time-consuming, can lead to reproducibility errors, and can be a daunting task for bioinformaticians. To address this, we introduce the COPILOT protocol, which has been successfully used to transform raw Illumina genotype intensity data into high-quality analysis-ready data on tens of thousands of human patient samples that have been genotyped on a variety of Illumina genotyping arrays. This includes processing both mainstream and custom content genotyping chips with over 4 million markers per sample. The COPILOT QC protocol consists of two distinct tandem procedures to process raw Illumina genotyping data. The first protocol is an up-to-date process to systematically QC raw Illumina microarray genotyping data using the Illumina-specific GenomeStudio software. The second protocol takes the output from the first protocol and further processes the data through the COPILOT (Containerised wOrkflow for Processing ILlumina genOtyping daTa) containerized QC pipeline, to automate an array of complex bioinformatics analyses to improve data quality through a secondary clustering algorithm and to automatically identify typical Genome-Wide Association Study (GWAS) data issues, including gender discrepancies, heterozygosity outliers, related individuals, and population outliers, through ancestry estimation. The data is returned to the user in analysis-ready PLINK binary format and is accompanied by a comprehensive and interactive HTML summary report file which quickly helps the user understand the data and guides the user for further data analyses. The COPILOT protocol and containerized pipeline are also available at https://khp-informatics.github.io/COPILOT/index.html. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Processing raw Illumina genotyping data using GenomeStudio Basic Protocol 2: COPILOT: A containerised workflow for processing Illumina genotyping data.",,pdf:https://discovery.ucl.ac.uk/10149151/1/Dobson_The%20COPILOT%20Raw%20Illumina%20Genotyping%20QC%20Protocol_VoR.pdf; doi:https://doi.org/10.1002/cpz1.373
+39054354,https://doi.org/10.1038/s41594-024-01357-9,Structural basis for activity switching in polymerases determining the fate of let-7 pre-miRNAs.,"Yi G, Ye M, Carrique L, El-Sagheer A, Brown T, Norbury CJ, Zhang P, Gilbert RJC.",,Nature structural & molecular biology,2024,2024-07-25,Y,,,,"Tumor-suppressor let-7 pre-microRNAs (miRNAs) are regulated by terminal uridylyltransferases TUT7 and TUT4 that either promote let-7 maturation by adding a single uridine nucleotide to the pre-miRNA 3' end or mark them for degradation by the addition of multiple uridines. Oligo-uridylation is increased in cells by enhanced TUT7/4 expression and especially by the RNA-binding pluripotency factor LIN28A. Using cryogenic electron microscopy, we captured high-resolution structures of active forms of TUT7 alone, of TUT7 plus pre-miRNA and of both TUT7 and TUT4 bound with pre-miRNA and LIN28A. Our structures reveal that pre-miRNAs engage the enzymes in fundamentally different ways depending on the presence of LIN28A, which clamps them onto the TUTs to enable processive 3' oligo-uridylation. This study reveals the molecular basis for mono- versus oligo-uridylation by TUT7/4, as determined by the presence of LIN28A, and thus their mechanism of action in the regulation of cell fate and in cancer.",,doi:https://doi.org/10.1038/s41594-024-01357-9; doi:https://doi.org/10.1038/s41594-024-01357-9; html:https://europepmc.org/articles/PMC11402785; pdf:https://europepmc.org/articles/PMC11402785?pdf=render
 36809311,https://doi.org/10.1093/ejendo/lvad024,The ultra-acute steroid response to traumatic injury: a cohort study.,"Bentley C, Hazeldine J, Bravo L, Taylor AE, Gilligan LC, Shaheen F, Acharjee A, Gkoutos G, Foster MA, Arlt W, Lord JM.",,European journal of endocrinology,2023,2023-03-01,N,Steroids; Mass spectrometry; Glucocorticoids; Major Trauma; 11-Oxygenated Androgens,,,"<h4>Objective</h4>Trauma-induced steroid changes have been studied post-hospital admission, resulting in a lack of understanding of the speed and extent of the immediate endocrine response to injury. The Golden Hour study was designed to capture the ultra-acute response to traumatic injury.<h4>Design</h4>We conducted an observational cohort study including adult male trauma patients <60 years, with blood samples drawn ≤1 h of major trauma by pre-hospital emergency responders.<h4>Methods</h4>We recruited 31 adult male trauma patients (mean age 28 [range 19-59] years) with a mean injury severity score (ISS) of 16 (IQR 10-21). The median time to first sample was 35 (range 14-56) min, with follow-up samples collected 4-12 and 48-72 h post-injury. Serum steroids in patients and age- and sex-matched healthy controls (HCs) (n = 34) were analysed by tandem mass spectrometry.<h4>Results</h4>Within 1 h of injury, we observed an increase in glucocorticoid and adrenal androgen biosynthesis. Cortisol and 11-hydroxyandrostendione increased rapidly, whilst cortisone and 11-ketoandrostenedione decreased, reflective of increased cortisol and 11-oxygenated androgen precursor biosynthesis by 11β-hydroxylase and increased cortisol activation by 11β-hydroxysteroid dehydrogenase type 1. Active classic gonadal androgens testosterone and 5α-dihydrotestosterone decreased, whilst the active 11-oxygenated androgen 11-ketotestosterone maintained pre-injury levels.<h4>Conclusions</h4>Changes in steroid biosynthesis and metabolism occur within minutes of traumatic injury. Studies that address whether ultra-early changes in steroid metabolism are associated with patient outcomes are now required.",,pdf:https://academic.oup.com/ejendo/article-pdf/188/3/290/49630912/lvad024.pdf; doi:https://doi.org/10.1093/ejendo/lvad024
-38821540,https://doi.org/10.1038/s41591-024-03085-5,Mutations in the U4 snRNA gene RNU4-2 cause one of the most prevalent monogenic neurodevelopmental disorders.,"Greene D, Thys C, Berry IR, Jarvis J, Ortibus E, Mumford AD, Freson K, Turro E.",,Nature medicine,2024,2024-05-31,Y,,,,"Most people with intellectual disability (ID) do not receive a molecular diagnosis following genetic testing. To identify new etiologies of ID, we performed a genetic association analysis comparing the burden of rare variants in 41,132 noncoding genes between 5,529 unrelated cases and 46,401 unrelated controls. RNU4-2, which encodes U4 small nuclear RNA, a critical component of the spliceosome, was the most strongly associated gene. We implicated de novo variants among 47 cases in two regions of RNU4-2 in the etiology of a syndrome characterized by ID, microcephaly, short stature, hypotonia, seizures and motor delay. We replicated this finding in three collections, bringing the number of unrelated cases to 73. Analysis of national genomic diagnostic data showed RNU4-2 to be a more common etiological gene for neurodevelopmental abnormality than any previously reported autosomal gene. Our findings add to the growing evidence of spliceosome dysfunction in the etiologies of neurological disorders.",,doi:https://doi.org/10.1038/s41591-024-03085-5; html:https://europepmc.org/articles/PMC11333284; pdf:https://europepmc.org/articles/PMC11333284?pdf=render
 35022215,https://doi.org/10.1136/bmj-2021-067519,Indirect effects of the covid-19 pandemic on childhood infection in England: population based observational study.,"Kadambari S, Goldacre R, Morris E, Goldacre MJ, Pollard AJ.",,BMJ (Clinical research ed.),2022,2022-01-12,Y,,,,"<h4>Objective</h4>To assess the impact of the covid-19 pandemic on hospital admission rates and mortality outcomes for childhood respiratory infections, severe invasive infections, and vaccine preventable disease in England.<h4>Design</h4>Population based observational study of 19 common childhood respiratory, severe invasive, and vaccine preventable infections, comparing hospital admission rates and mortality outcomes before and after the onset of the pandemic in England.<h4>Setting</h4>Hospital admission data from every NHS hospital in England from 1 March 2017 to 30 June 2021 with record linkage to national mortality data.<h4>Population</h4>Children aged 0-14 years admitted to an NHS hospital with a selected childhood infection from 1 March 2017 to 30 June 2021.<h4>Main outcome measures</h4>For each infection, numbers of hospital admissions every month from 1 March 2017 to 30 June 2021, percentage changes in the number of hospital admissions before and after 1 March 2020, and adjusted odds ratios to compare 60 day case fatality outcomes before and after 1 March 2020.<h4>Results</h4>After 1 March 2020, substantial and sustained reductions in hospital admissions were found for all but one of the 19 infective conditions studied. Among the respiratory infections, the greatest percentage reductions were for influenza (mean annual number admitted between 1 March 2017 and 29 February 2020 was 5379 and number of children admitted from 1 March 2020 to 28 February 2021 was 304, 94% reduction, 95% confidence interval 89% to 97%), and bronchiolitis (from 51 655 to 9423, 82% reduction, 95% confidence interval 79% to 84%). Among the severe invasive infections, the greatest reduction was for meningitis (50% reduction, 47% to 52%). For the vaccine preventable infections, reductions ranged from 53% (32% to 68%) for mumps to 90% (80% to 95%) for measles. Reductions were seen across all demographic subgroups and in children with underlying comorbidities. Corresponding decreases were also found for the absolute numbers of 60 day case fatalities, although the proportion of children admitted for pneumonia who died within 60 days increased (age-sex adjusted odds ratio 1.71, 95% confidence interval 1.43 to 2.05). More recent data indicate that some respiratory infections increased to higher levels than usual after May 2021.<h4>Conclusions</h4>During the covid-19 pandemic, a range of behavioural changes (adoption of non-pharmacological interventions) and societal strategies (school closures, lockdowns, and restricted travel) were used to reduce transmission of SARS-CoV-2, which also reduced admissions for common and severe childhood infections. Continued monitoring of these infections is required as social restrictions evolve.",,pdf:https://www.bmj.com/content/bmj/376/bmj-2021-067519.full.pdf; doi:https://doi.org/10.1136/bmj-2021-067519; html:https://europepmc.org/articles/PMC8753487; pdf:https://europepmc.org/articles/PMC8753487?pdf=render
-36576811,https://doi.org/10.1001/jamacardio.2022.4466,Predictive Utility of a Coronary Artery Disease Polygenic Risk Score in Primary Prevention.,"Marston NA, Pirruccello JP, Melloni GEM, Koyama S, Kamanu FK, Weng LC, Roselli C, Kamatani Y, Komuro I, Aragam KG, Butterworth AS, Ito K, Lubitz SA, Ellinor PT, Sabatine MS, Ruff CT.",,JAMA cardiology,2023,2023-02-01,N,,,,"<h4>Importance</h4>The clinical utility of polygenic risk scores (PRS) for coronary artery disease (CAD) has not yet been established.<h4>Objective</h4>To investigate the ability of a CAD PRS to potentially guide statin initiation in primary prevention after accounting for age and clinical risk.<h4>Design, setting, and participants</h4>This was a longitudinal cohort study with enrollment starting on January 1, 2006, and ending on December 31, 2010, with data updated to mid-2021, using data from the UK Biobank, a long-term population study of UK citizens. A replication analysis was performed in Biobank Japan. The analysis included all patients without a history of CAD and who were not taking lipid-lowering therapy. Data were analyzed from January 1 to June 30, 2022.<h4>Exposures</h4>Polygenic risk for CAD was defined as low (bottom 20%), intermediate, and high (top 20%) using a CAD PRS including 241 genome-wide significant single-nucleotide variations (SNVs). The pooled cohort equations were used to estimate 10-year atherosclerotic cardiovascular disease (ASCVD) risk and classify individuals as low (<5%), borderline (5-<7.5%), intermediate (7.5-<20%), or high risk (≥20%).<h4>Main outcomes and measures</h4>Myocardial infarction (MI) and ASCVD events (defined as incident clinical CAD [including MI], stroke, or CV death).<h4>Results</h4>A total of 330 201 patients (median [IQR] age, 57 [40-74] years; 189 107 female individuals [57%]) were included from the UK Biobank. Over the 10-year follow-up, 4454 individuals had an MI. The CAD PRS was significantly associated with the risk of MI in all age groups but had significantly stronger risk prediction at younger ages (age <50 years: hazard ratio [HR] per 1 SD of PRS, 1.72; 95% CI, 1.56-1.89; age 50-60 years: HR, 1.46; 95% CI, 1.38-1.53; age >60 years: HR, 1.42; 95% CI, 1.37-1.48; P for interaction <.001). In patients younger than 50 years, those with high PRS had a 3- to 4-fold increased associated risk of MI compared with those in the low PRS category. A significant interaction between CAD PRS and age was replicated in Biobank Japan. When CAD PRS testing was added to the clinical ASCVD risk score in individuals younger than 50 years, 591 of 4373 patients (20%) with borderline risk were risk stratified into intermediate risk, warranting initiation of statin therapy and 3198 of 7477 patients (20%) with both borderline or intermediate risk were stratified as low risk, thus not warranting therapy.<h4>Conclusions and relevance</h4>Results of this cohort study suggest that the predictive ability of a CAD PRS was greater in younger individuals and can be used to better identify patients with borderline and intermediate clinical risk who should initiate statin therapy.",,doi:https://doi.org/10.1001/jamacardio.2022.4466; html:https://europepmc.org/articles/PMC9857431; doi:https://doi.org/10.1001/jamacardio.2022.4466
+38821540,https://doi.org/10.1038/s41591-024-03085-5,Mutations in the U4 snRNA gene RNU4-2 cause one of the most prevalent monogenic neurodevelopmental disorders.,"Greene D, Thys C, Berry IR, Jarvis J, Ortibus E, Mumford AD, Freson K, Turro E.",,Nature medicine,2024,2024-05-31,Y,,,,"Most people with intellectual disability (ID) do not receive a molecular diagnosis following genetic testing. To identify new etiologies of ID, we performed a genetic association analysis comparing the burden of rare variants in 41,132 noncoding genes between 5,529 unrelated cases and 46,401 unrelated controls. RNU4-2, which encodes U4 small nuclear RNA, a critical component of the spliceosome, was the most strongly associated gene. We implicated de novo variants among 47 cases in two regions of RNU4-2 in the etiology of a syndrome characterized by ID, microcephaly, short stature, hypotonia, seizures and motor delay. We replicated this finding in three collections, bringing the number of unrelated cases to 73. Analysis of national genomic diagnostic data showed RNU4-2 to be a more common etiological gene for neurodevelopmental abnormality than any previously reported autosomal gene. Our findings add to the growing evidence of spliceosome dysfunction in the etiologies of neurological disorders.",,doi:https://doi.org/10.1038/s41591-024-03085-5; html:https://europepmc.org/articles/PMC11333284; pdf:https://europepmc.org/articles/PMC11333284?pdf=render
 35242820,https://doi.org/10.3389/fcvm.2021.816985,A Systematic Quality Scoring Analysis to Assess Automated Cardiovascular Magnetic Resonance Segmentation Algorithms.,"Rauseo E, Omer M, Amir-Khalili A, Sojoudi A, Le TT, Cook SA, Hausenloy DJ, Ang B, Toh DF, Bryant J, Chin CWL, Paiva JM, Fung K, Cooper J, Khanji MY, Aung N, Petersen SE.",,Frontiers in cardiovascular medicine,2021,2022-02-15,Y,Quality control; Assessment; Machine Learning; Cardiac Segmentation; Cardiac Magnetic Resonance (Cmr); Automated Contouring,,,"<h4>Background</h4>The quantitative measures used to assess the performance of automated methods often do not reflect the clinical acceptability of contouring. A quality-based assessment of automated cardiac magnetic resonance (CMR) segmentation more relevant to clinical practice is therefore needed.<h4>Objective</h4>We propose a new method for assessing the quality of machine learning (ML) outputs. We evaluate the clinical utility of the proposed method as it is employed to systematically analyse the quality of an automated contouring algorithm.<h4>Methods</h4>A dataset of short-axis (SAX) cine CMR images from a clinically heterogeneous population (<i>n</i> = 217) were manually contoured by a team of experienced investigators. On the same images we derived automated contours using a ML algorithm. A contour quality scoring application randomly presented manual and automated contours to four blinded clinicians, who were asked to assign a quality score from a predefined rubric. Firstly, we analyzed the distribution of quality scores between the two contouring methods across all clinicians. Secondly, we analyzed the interobserver reliability between the raters. Finally, we examined whether there was a variation in scores based on the type of contour, SAX slice level, and underlying disease.<h4>Results</h4>The overall distribution of scores between the two methods was significantly different, with automated contours scoring better than the manual (OR (95% CI) = 1.17 (1.07-1.28), <i>p</i> = 0.001; <i>n</i> = 9401). There was substantial scoring agreement between raters for each contouring method independently, albeit it was significantly better for automated segmentation (automated: AC2 = 0.940, 95% CI, 0.937-0.943 vs manual: AC2 = 0.934, 95% CI, 0.931-0.937; <i>p</i> = 0.006). Next, the analysis of quality scores based on different factors was performed. Our approach helped identify trends patterns of lower segmentation quality as observed for left ventricle epicardial and basal contours with both methods. Similarly, significant differences in quality between the two methods were also found in dilated cardiomyopathy and hypertension.<h4>Conclusions</h4>Our results confirm the ability of our systematic scoring analysis to determine the clinical acceptability of automated contours. This approach focused on the contours' clinical utility could ultimately improve clinicians' confidence in artificial intelligence and its acceptability in the clinical workflow.",,pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2021.816985/pdf; doi:https://doi.org/10.3389/fcvm.2021.816985; html:https://europepmc.org/articles/PMC8886212; pdf:https://europepmc.org/articles/PMC8886212?pdf=render
-37284234,https://doi.org/10.1140/epjds/s13688-023-00391-9,"The shock, the coping, the resilience: smartphone application use reveals Covid-19 lockdown effects on human behaviors.","Liu XF, Wang ZZ, Xu XK, Wu Y, Zhao Z, Deng H, Wang P, Chao N, Huang YC.",,EPJ data science,2023,2023-06-05,Y,Human behaviors; Natural Experiment; Lockdown; Smartphone Apps; Covid-19,,,"Human mobility restriction policies have been widely used to contain the coronavirus disease-19 (COVID-19). However, a critical question is how these policies affect individuals' behavioral and psychological well-being during and after confinement periods. Here, we analyze China's five most stringent city-level lockdowns in 2021, treating them as natural experiments that allow for examining behavioral changes in millions of people through smartphone application use. We made three fundamental observations. First, the use of physical and economic activity-related apps experienced a steep decline, yet apps that provide daily necessities maintained normal usage. Second, apps that fulfilled lower-level human needs, such as working, socializing, information seeking, and entertainment, saw an immediate and substantial increase in screen time. Those that satisfied higher-level needs, such as education, only attracted delayed attention. Third, human behaviors demonstrated resilience as most routines resumed after the lockdowns were lifted. Nonetheless, long-term lifestyle changes were observed, as significant numbers of people chose to continue working and learning online, becoming ""digital residents."" This study also demonstrates the capability of smartphone screen time analytics in the study of human behaviors.<h4>Supplementary information</h4>The online version contains supplementary material available at 10.1140/epjds/s13688-023-00391-9.",,doi:https://doi.org/10.1140/epjds/s13688-023-00391-9; doi:https://doi.org/10.1140/epjds/s13688-023-00391-9; html:https://europepmc.org/articles/PMC10240109; pdf:https://europepmc.org/articles/PMC10240109?pdf=render
+36576811,https://doi.org/10.1001/jamacardio.2022.4466,Predictive Utility of a Coronary Artery Disease Polygenic Risk Score in Primary Prevention.,"Marston NA, Pirruccello JP, Melloni GEM, Koyama S, Kamanu FK, Weng LC, Roselli C, Kamatani Y, Komuro I, Aragam KG, Butterworth AS, Ito K, Lubitz SA, Ellinor PT, Sabatine MS, Ruff CT.",,JAMA cardiology,2023,2023-02-01,N,,,,"<h4>Importance</h4>The clinical utility of polygenic risk scores (PRS) for coronary artery disease (CAD) has not yet been established.<h4>Objective</h4>To investigate the ability of a CAD PRS to potentially guide statin initiation in primary prevention after accounting for age and clinical risk.<h4>Design, setting, and participants</h4>This was a longitudinal cohort study with enrollment starting on January 1, 2006, and ending on December 31, 2010, with data updated to mid-2021, using data from the UK Biobank, a long-term population study of UK citizens. A replication analysis was performed in Biobank Japan. The analysis included all patients without a history of CAD and who were not taking lipid-lowering therapy. Data were analyzed from January 1 to June 30, 2022.<h4>Exposures</h4>Polygenic risk for CAD was defined as low (bottom 20%), intermediate, and high (top 20%) using a CAD PRS including 241 genome-wide significant single-nucleotide variations (SNVs). The pooled cohort equations were used to estimate 10-year atherosclerotic cardiovascular disease (ASCVD) risk and classify individuals as low (<5%), borderline (5-<7.5%), intermediate (7.5-<20%), or high risk (≥20%).<h4>Main outcomes and measures</h4>Myocardial infarction (MI) and ASCVD events (defined as incident clinical CAD [including MI], stroke, or CV death).<h4>Results</h4>A total of 330 201 patients (median [IQR] age, 57 [40-74] years; 189 107 female individuals [57%]) were included from the UK Biobank. Over the 10-year follow-up, 4454 individuals had an MI. The CAD PRS was significantly associated with the risk of MI in all age groups but had significantly stronger risk prediction at younger ages (age <50 years: hazard ratio [HR] per 1 SD of PRS, 1.72; 95% CI, 1.56-1.89; age 50-60 years: HR, 1.46; 95% CI, 1.38-1.53; age >60 years: HR, 1.42; 95% CI, 1.37-1.48; P for interaction <.001). In patients younger than 50 years, those with high PRS had a 3- to 4-fold increased associated risk of MI compared with those in the low PRS category. A significant interaction between CAD PRS and age was replicated in Biobank Japan. When CAD PRS testing was added to the clinical ASCVD risk score in individuals younger than 50 years, 591 of 4373 patients (20%) with borderline risk were risk stratified into intermediate risk, warranting initiation of statin therapy and 3198 of 7477 patients (20%) with both borderline or intermediate risk were stratified as low risk, thus not warranting therapy.<h4>Conclusions and relevance</h4>Results of this cohort study suggest that the predictive ability of a CAD PRS was greater in younger individuals and can be used to better identify patients with borderline and intermediate clinical risk who should initiate statin therapy.",,doi:https://doi.org/10.1001/jamacardio.2022.4466; html:https://europepmc.org/articles/PMC9857431; doi:https://doi.org/10.1001/jamacardio.2022.4466
 37269003,https://doi.org/10.1186/s13643-023-02261-x,Non-adherence and non-persistence to intravitreal anti-vascular endothelial growth factor (anti-VEGF) therapy: a systematic review and meta-analysis.,"Shahzad H, Mahmood S, McGee S, Hubbard J, Haque S, Paudyal V, Denniston AK, Hill LJ, Jalal Z.",,Systematic reviews,2023,2023-06-02,Y,Meta-analysis; Intravitreal; Anti-vegf; Non-adherence; Macular; Non-persistence; Covid-19,,,"<h4>Background</h4>Intravitreal anti-vascular endothelial growth factor (anti-VEGF) injections play a key role in treating a range of macular diseases. The effectiveness of these therapies is dependent on patients' adherence (the extent to which a patient takes their medicines as per agreed recommendations from the healthcare provider) and persistence (continuation of the treatment for the prescribed duration) to their prescribed treatment regimens. The aim of this systematic review was to demonstrate the need for further investigation into the prevalence of, and factors contributing to, patient-led non-adherence and non-persistence, thus facilitating improved clinical outcomes.<h4>Methods</h4>Systematic searches were conducted in Google Scholar, Web of Science, PubMed, MEDLINE, and the Cochrane Library. Studies in English conducted before February 2023 that reported the level of, and/or barriers to, non-adherence or non-persistence to intravitreal anti-VEGF ocular disease therapy were included. Duplicate papers, literature reviews, expert opinion articles, case studies, and case series were excluded following screening by two independent authors.<h4>Results</h4>Data from a total of 409,215 patients across 52 studies were analysed. Treatment regimens included pro re nata, monthly and treat-and-extend protocols; study durations ranged from 4 months to 8 years. Of the 52 studies, 22 included a breakdown of reasons for patient non-adherence/non-persistence. Patient-led non-adherence varied between 17.5 and 35.0% depending on the definition used. Overall pooled prevalence of patient-led treatment non-persistence was 30.0% (P = 0.000). Reasons for non-adherence/non-persistence included dissatisfaction with treatment results (29.9%), financial burden (19%), older age/comorbidities (15.5%), difficulty booking appointments (8.5%), travel distance/social isolation (7.9%), lack of time (5.8%), satisfaction with the perceived improvement in their condition (4.4%), fear of injection (4.0%), loss of motivation (4.0%), apathy towards eyesight (2.5%), dissatisfaction with facilities 2.3%, and discomfort/pain (0.3%). Three studies found non-adherence rates between 51.6 and 68.8% during the COVID-19 pandemic, in part due to fear of exposure to COVID-19 and difficulties travelling during lockdown.<h4>Discussion</h4>Results suggest high levels of patient-led non-adherence/non-persistence to anti-VEGF therapy, mostly due to dissatisfaction with treatment results, a combination of comorbidities, loss of motivation and the burden of travel. This study provides key information on prevalence and factors contributing to non-adherence/non-persistence in anti-VEGF treatment for macular diseases, aiding identification of at-risk individuals to improve real-world visual outcomes. Improvements in the literature can be achieved by establishing uniform definitions and standard timescales for what constitutes non-adherence/non-persistence.<h4>Systematic review registration</h4>PROSPERO CRD42020216205.",,doi:https://doi.org/10.1186/s13643-023-02261-x; doi:https://doi.org/10.1186/s13643-023-02261-x; html:https://europepmc.org/articles/PMC10237080; pdf:https://europepmc.org/articles/PMC10237080?pdf=render
+37284234,https://doi.org/10.1140/epjds/s13688-023-00391-9,"The shock, the coping, the resilience: smartphone application use reveals Covid-19 lockdown effects on human behaviors.","Liu XF, Wang ZZ, Xu XK, Wu Y, Zhao Z, Deng H, Wang P, Chao N, Huang YC.",,EPJ data science,2023,2023-06-05,Y,Human behaviors; Natural Experiment; Lockdown; Smartphone Apps; Covid-19,,,"Human mobility restriction policies have been widely used to contain the coronavirus disease-19 (COVID-19). However, a critical question is how these policies affect individuals' behavioral and psychological well-being during and after confinement periods. Here, we analyze China's five most stringent city-level lockdowns in 2021, treating them as natural experiments that allow for examining behavioral changes in millions of people through smartphone application use. We made three fundamental observations. First, the use of physical and economic activity-related apps experienced a steep decline, yet apps that provide daily necessities maintained normal usage. Second, apps that fulfilled lower-level human needs, such as working, socializing, information seeking, and entertainment, saw an immediate and substantial increase in screen time. Those that satisfied higher-level needs, such as education, only attracted delayed attention. Third, human behaviors demonstrated resilience as most routines resumed after the lockdowns were lifted. Nonetheless, long-term lifestyle changes were observed, as significant numbers of people chose to continue working and learning online, becoming ""digital residents."" This study also demonstrates the capability of smartphone screen time analytics in the study of human behaviors.<h4>Supplementary information</h4>The online version contains supplementary material available at 10.1140/epjds/s13688-023-00391-9.",,doi:https://doi.org/10.1140/epjds/s13688-023-00391-9; doi:https://doi.org/10.1140/epjds/s13688-023-00391-9; html:https://europepmc.org/articles/PMC10240109; pdf:https://europepmc.org/articles/PMC10240109?pdf=render
 37538142,https://doi.org/10.1093/ehjdh/ztad037,Predicting left ventricular hypertrophy from the 12-lead electrocardiogram in the UK Biobank imaging study using machine learning.,"Naderi H, Ramírez J, van Duijvenboden S, Pujadas ER, Aung N, Wang L, Anwar Ahmed Chahal C, Lekadir K, Petersen SE, Munroe PB.",,European heart journal. Digital health,2023,2023-06-01,Y,Electrocardiogram; Left ventricular hypertrophy; Cardiovascular Screening; Machine Learning; Cardiovascular Magnetic Resonance Imaging,,,"<h4>Aims</h4>Left ventricular hypertrophy (LVH) is an established, independent predictor of cardiovascular disease. Indices derived from the electrocardiogram (ECG) have been used to infer the presence of LVH with limited sensitivity. This study aimed to classify LVH defined by cardiovascular magnetic resonance (CMR) imaging using the 12-lead ECG for cost-effective patient stratification.<h4>Methods and results</h4>We extracted ECG biomarkers with a known physiological association with LVH from the 12-lead ECG of 37 534 participants in the UK Biobank imaging study. Classification models integrating ECG biomarkers and clinical variables were built using logistic regression, support vector machine (SVM) and random forest (RF). The dataset was split into 80% training and 20% test sets for performance evaluation. Ten-fold cross validation was applied with further validation testing performed by separating data based on UK Biobank imaging centres. QRS amplitude and blood pressure (<i>P</i> < 0.001) were the features most strongly associated with LVH. Classification with logistic regression had an accuracy of 81% [sensitivity 70%, specificity 81%, Area under the receiver operator curve (AUC) 0.86], SVM 81% accuracy (sensitivity 72%, specificity 81%, AUC 0.85) and RF 72% accuracy (sensitivity 74%, specificity 72%, AUC 0.83). ECG biomarkers enhanced model performance of all classifiers, compared to using clinical variables alone. Validation testing by UK Biobank imaging centres demonstrated robustness of our models.<h4>Conclusion</h4>A combination of ECG biomarkers and clinical variables were able to predict LVH defined by CMR. Our findings provide support for the ECG as an inexpensive screening tool to risk stratify patients with LVH as a prelude to advanced imaging.",,pdf:https://academic.oup.com/ehjdh/advance-article-pdf/doi/10.1093/ehjdh/ztad037/50634764/ztad037.pdf; doi:https://doi.org/10.1093/ehjdh/ztad037; html:https://europepmc.org/articles/PMC10393938; pdf:https://europepmc.org/articles/PMC10393938?pdf=render
 37634573,https://doi.org/10.1016/j.cardfail.2023.08.008,Does Heterogeneity Exist in Treatment Associations With Renin-Angiotensin-System Inhibitors or Beta-blockers According to Phenotype Clusters in Heart Failure with Preserved Ejection Fraction?,"Uijl A, Koudstaal S, Stolfo D, Dahlström U, Vaartjes I, Grobbee RE, Asselbergs FW, Lund LH, Savarese G.",,Journal of cardiac failure,2024,2023-08-25,N,Personalized Medicine; Beta-blockers; Hfpef; Renin–angiotensin System Inhibitors; Phenotype Clusters,,,"<h4>Background</h4>We explored the association between use of renin-angiotensin system inhibitors and beta-blockers, with mortality/morbidity in 5 previously identified clusters of patients with heart failure with preserved ejection fraction (HFpEF).<h4>Methods and results</h4>We analyzed 20,980 patients with HFpEF from the Swedish HF registry, phenotyped into young-low comorbidity burden (12%), atrial fibrillation-hypertensive (32%), older-atrial fibrillation (24%), obese-diabetic (15%), and a cardiorenal cluster (17%). In Cox proportional hazard models with inverse probability weighting, there was no heterogeneity in the association between renin-angiotensin system inhibitor use and cluster membership for any of the outcomes: cardiovascular (CV) mortality, all-cause mortality, HF hospitalisation, CV hospitalisation, or non-CV hospitalisation. In contrast, we found a statistical interaction between beta-blocker use and cluster membership for all-cause mortality (P = .03) and non-CV hospitalisation (P = .001). In the young-low comorbidity burden and atrial fibrillation-hypertensive cluster, beta-blocker use was associated with statistically significant lower all-cause mortality and non-CV hospitalisation and in the obese-diabetic cluster beta-blocker use was only associated with a statistically significant lower non-CV hospitalisation. The interaction between beta-blocker use and cluster membership for all-cause mortality could potentially be driven by patients with improved EF. However, patient numbers were diminished when excluding those with improved EF and the direction of the associations remained similar.<h4>Conclusions</h4>In patients with HFpEF, the association with all-cause mortality and non-CV hospitalisation was heterogeneous across clusters for beta-blockers. It remains to be elucidated how heterogeneity in HFpEF could influence personalized medicine and future clinical trial design.",,pdf:http://www.onlinejcf.com/article/S1071916423003044/pdf; doi:https://doi.org/10.1016/j.cardfail.2023.08.008
 38778017,https://doi.org/10.1038/s41541-024-00878-0,Influence of individuals' determinants including vaccine type on cellular and humoral responses to SARS-CoV-2 vaccination.,"Chambers ES, Cai W, Vivaldi G, Jolliffe DA, Perdek N, Li W, Faustini SE, Gibbons JM, Pade C, Richter AG, Coussens AK, Martineau AR.",,NPJ vaccines,2024,2024-05-22,Y,,,,"Vaccine development targeting SARS-CoV-2 in 2020 was of critical importance in reducing COVID-19 severity and mortality. In the U.K. during the initial roll-out most individuals either received two doses of Pfizer COVID-19 vaccine (BNT162b2) or the adenovirus-based vaccine from Oxford/AstraZeneca (ChAdOx1-nCoV-19). There are conflicting data as to the impact of age, sex and body habitus on cellular and humoral responses to vaccination, and most studies in this area have focused on determinants of mRNA vaccine immunogenicity. Here, we studied a cohort of participants in a population-based longitudinal study (COVIDENCE UK) to determine the influence of age, sex, body mass index (BMI) and pre-vaccination anti-Spike (anti-S) antibody status on vaccine-induced humoral and cellular immune responses to two doses of BNT162b2 or ChAdOx-n-CoV-19 vaccination. Younger age and pre-vaccination anti-S seropositivity were both associated with stronger antibody responses to vaccination. BNT162b2 generated higher neutralising and anti-S antibody titres to vaccination than ChAdOx1-nCoV-19, but cellular responses to the two vaccines were no different. Irrespective of vaccine type, increasing age was also associated with decreased frequency of cytokine double-positive CD4+T cells. Increasing BMI was associated with reduced frequency of SARS-CoV-2-specific TNF+CD8% T cells for both vaccines. Together, our findings demonstrate that increasing age and BMI are associated with attenuated cellular and humoral responses to SARS-CoV-2 vaccination. Whilst both vaccines induced T cell responses, BNT162b2 induced significantly elevated humoral immune response as compared to ChAdOx-n-CoV-19.",,pdf:https://www.nature.com/articles/s41541-024-00878-0.pdf; doi:https://doi.org/10.1038/s41541-024-00878-0; html:https://europepmc.org/articles/PMC11111746; pdf:https://europepmc.org/articles/PMC11111746?pdf=render
 32352158,https://doi.org/10.1002/bjs.11580,Author response to: Comment on: Impact of bariatric surgery on cardiovascular outcomes and mortality: a population-based cohort study.,"Adderley N, Singh P, Tahrani AA, Nirantharakumar K.",,The British journal of surgery,2020,2020-04-30,N,,,,,,pdf:https://academic.oup.com/bjs/article-pdf/107/7/e220/35705126/bjs11580.pdf; doi:https://doi.org/10.1002/bjs.11580
+35440446,https://doi.org/10.1136/bmjopen-2021-052514,Protocol for the COG-UK hospital-onset COVID-19 infection (HOCI) multicentre interventional clinical study: evaluating the efficacy of rapid genome sequencing of SARS-CoV-2 in limiting the spread of COVID-19 in UK NHS hospitals.,"Blackstone J, Stirrup O, Mapp F, Panca M, Copas A, Flowers P, Hockey L, Price J, Partridge D, Peters C, de Silva T, Nebbia G, Snell LB, McComish R, COVID-19 Genomics UK (COG-UK) Consortium, Breuer J.",,BMJ open,2022,2022-04-19,Y,Molecular biology; Infection control; epidemiology; Covid-19,,,"<h4>Objectives</h4>Nosocomial transmission of SARS-CoV-2 has been a significant cause of mortality in National Health Service (NHS) hospitals during the COVID-19 pandemic. The COG-UK Consortium Hospital-Onset COVID-19 Infections (COG-UK HOCI) study aims to evaluate whether the use of rapid whole-genome sequencing of SARS-CoV-2, supported by a novel probabilistic reporting methodology, can inform infection prevention and control (IPC) practice within NHS hospital settings.<h4>Design</h4>Multicentre, prospective, interventional, superiority study.<h4>Setting</h4>14 participating NHS hospitals over winter-spring 2020/2021 in the UK.<h4>Participants</h4>Eligible patients must be admitted to hospital with first-confirmed SARS-CoV-2 PCR-positive test result >48 hour from time of admission, where COVID-19 diagnosis not suspected on admission. The projected sample size is 2380 patients.<h4>Intervention</h4>The intervention is the return of a sequence report, within 48 hours in one phase (rapid local lab processing) and within 5-10 days in a second phase (mimicking central lab), comparing the viral genome from an eligible study participant with others within and outside the hospital site.<h4>Primary and secondary outcome measures</h4>The primary outcomes are incidence of Public Health England (PHE)/IPC-defined SARS-CoV-2 hospital-acquired infection during the baseline and two interventional phases, and proportion of hospital-onset cases with genomic evidence of transmission linkage following implementation of the intervention where such linkage was not suspected by initial IPC investigation. Secondary outcomes include incidence of hospital outbreaks, with and without sequencing data; actual and desirable changes to IPC actions; periods of healthcare worker (HCW) absence. Health economic analysis will be conducted to determine cost benefit of the intervention. A process evaluation using qualitative interviews with HCWs will be conducted alongside the study.<h4>Trial registration number</h4>ISRCTN50212645. Pre-results stage. This manuscript is based on protocol V.6.0. 2 September 2021.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/4/e052514.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-052514; html:https://europepmc.org/articles/PMC9019828; pdf:https://europepmc.org/articles/PMC9019828?pdf=render
 32856398,https://doi.org/10.1111/1742-6723.13604,To intubate or not to intubate? Predictors of inhalation injury in burn-injured patients before arrival at the burn centre.,"Dyson K, Baker P, Garcia N, Braun A, Aung M, Pilcher D, Smith K, Cleland H, Gabbe B.",,Emergency medicine Australasia : EMA,2021,2020-08-27,N,Burn; Pre-hospital; Inhalation Injury; Endotracheal Intubation,,,"<h4>Objective</h4>Inhalation injury occurs in approximately 10-20% of burn patients and is associated with increased mortality. There is no clear method of identifying patients at risk of inhalation injury or requiring intubation in the pre-hospital setting. Our objective was to identify pre-burn centre factors associated with inhalation injury confirmed on bronchoscopy, and to develop a prognostic model for inhalation injury.<h4>Methods</h4>We analysed acute admissions from the Victorian Adult Burns Service and Ambulance Victoria electronic patient care records for 1 July 2009 to 30 June 2016. We defined inhalation injury as an Abbreviated Injury Scale of >1 on bronchoscopy. A multivariable logistic regression prediction model was developed based on pre-burn centre factors.<h4>Results</h4>Emergency medical services transported 1148 patients who were admitted to the burn centre. The median age of patients was 39 years and most patients had <10% total body surface area (%TBSA) burned. The prevalence of confirmed inhalation injury was 11%. Increasing %TBSA burned, flame, enclosed space, face burns, hoarse voice, soot in mouth and shortness of breath were predictive of inhalation injury. The model provided excellent discrimination (area under curve 0.87, 95% confidence interval 0.84-0.91). A lower proportion of patients intubated at a non-burn centre had an inhalation injury (33%) compared to patients intubated by emergency medical services (54%) and in the burn centre (58%).<h4>Conclusions</h4>A model to predict inhalation injury in burn-injured patients was developed with excellent discrimination. This model requires prospective testing but could form an integral part of clinician decision-making.",,doi:https://doi.org/10.1111/1742-6723.13604
 34145643,https://doi.org/10.1111/jdv.17450,Describing the burden of the COVID-19 pandemic in people with psoriasis: findings from a global cross-sectional study.,"Mahil SK, Yates M, Yiu ZZN, Langan SM, Tsakok T, Dand N, Mason KJ, McAteer H, Meynell F, Coker B, Vincent A, Urmston D, Vesty A, Kelly J, Lancelot C, Moorhead L, Bachelez H, Capon F, Contreras CR, De La Cruz C, Di Meglio P, Gisondi P, Jullien D, Lambert J, Naldi L, Norton S, Puig L, Spuls P, Torres T, Warren RB, Waweru H, Weinman J, Brown MA, Galloway JB, Griffiths CM, Barker JN, Smith CH, PsoProtect study group.",,Journal of the European Academy of Dermatology and Venereology : JEADV,2021,2021-08-19,Y,,,,,,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/jdv.17450; doi:https://doi.org/10.1111/jdv.17450; html:https://europepmc.org/articles/PMC8447018; pdf:https://europepmc.org/articles/PMC8447018?pdf=render
-35440446,https://doi.org/10.1136/bmjopen-2021-052514,Protocol for the COG-UK hospital-onset COVID-19 infection (HOCI) multicentre interventional clinical study: evaluating the efficacy of rapid genome sequencing of SARS-CoV-2 in limiting the spread of COVID-19 in UK NHS hospitals.,"Blackstone J, Stirrup O, Mapp F, Panca M, Copas A, Flowers P, Hockey L, Price J, Partridge D, Peters C, de Silva T, Nebbia G, Snell LB, McComish R, COVID-19 Genomics UK (COG-UK) Consortium, Breuer J.",,BMJ open,2022,2022-04-19,Y,Molecular biology; Infection control; epidemiology; Covid-19,,,"<h4>Objectives</h4>Nosocomial transmission of SARS-CoV-2 has been a significant cause of mortality in National Health Service (NHS) hospitals during the COVID-19 pandemic. The COG-UK Consortium Hospital-Onset COVID-19 Infections (COG-UK HOCI) study aims to evaluate whether the use of rapid whole-genome sequencing of SARS-CoV-2, supported by a novel probabilistic reporting methodology, can inform infection prevention and control (IPC) practice within NHS hospital settings.<h4>Design</h4>Multicentre, prospective, interventional, superiority study.<h4>Setting</h4>14 participating NHS hospitals over winter-spring 2020/2021 in the UK.<h4>Participants</h4>Eligible patients must be admitted to hospital with first-confirmed SARS-CoV-2 PCR-positive test result >48 hour from time of admission, where COVID-19 diagnosis not suspected on admission. The projected sample size is 2380 patients.<h4>Intervention</h4>The intervention is the return of a sequence report, within 48 hours in one phase (rapid local lab processing) and within 5-10 days in a second phase (mimicking central lab), comparing the viral genome from an eligible study participant with others within and outside the hospital site.<h4>Primary and secondary outcome measures</h4>The primary outcomes are incidence of Public Health England (PHE)/IPC-defined SARS-CoV-2 hospital-acquired infection during the baseline and two interventional phases, and proportion of hospital-onset cases with genomic evidence of transmission linkage following implementation of the intervention where such linkage was not suspected by initial IPC investigation. Secondary outcomes include incidence of hospital outbreaks, with and without sequencing data; actual and desirable changes to IPC actions; periods of healthcare worker (HCW) absence. Health economic analysis will be conducted to determine cost benefit of the intervention. A process evaluation using qualitative interviews with HCWs will be conducted alongside the study.<h4>Trial registration number</h4>ISRCTN50212645. Pre-results stage. This manuscript is based on protocol V.6.0. 2 September 2021.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/4/e052514.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-052514; html:https://europepmc.org/articles/PMC9019828; pdf:https://europepmc.org/articles/PMC9019828?pdf=render
 34304930,https://doi.org/10.1016/j.burns.2021.06.007,Trends in Victorian burn injuries 2008-2017.,"Cleland H, Fernando DT, Gabbe BJ.",,Burns : journal of the International Society for Burn Injuries,2022,2021-07-07,N,Burns Mortality; Burns Epidemiology; Burns Australia,,,"<h4>Objectives</h4>To describe incidence and characteristics of hospital presentations and deaths due to burn injury in the Australian state of Victoria from 2008 to 2017 and identify trends in incidence and patterns.<h4>Methods</h4>Three population-based datasets were used to ascertain burn-related hospital admissions, emergency department presentations, and deaths. These were the Victorian Admitted Episodes Dataset (VAED), Victorian Emergency Minimum Dataset (VEMD), and the Cause of Death-Unit Record File (COD-URF), respectively. Descriptive statistics on demographics (age and gender), burn injury characteristics (intent, cause, burn size and body region) and hospital burden (length of stay (LOS) and costs) were used to present the profile of patients. Incidence rates by age, gender and intent were calculated. Trend analysis on incidence was carried out using forced Poisson Regression models with the natural logarithm of the annual populations as an offset. Incident rate ratios were used to interpret the models. Risk ratios were used to compare the risk differences between population sub-groups. A negative binomial model was used to test the association between LOS and age and the total body surface area (TBSA) of the burn.<h4>Results</h4>Overall males had higher rates of death, admission and ED presentation. For adults, the elderly had the highest rates of deaths and admissions while for children, the very young had highest rates for admissions and presentations. Exposure to smoke, fire and flames was the most common cause of deaths, and contact with heat and hot substances was most common among ED presentations. The elderly and those with Total Body Surface Area (TBSA) burn ≥20% had a higher risk of longer hospital stay. Rates of severe burns and deaths from burns remained stable during the study period in the setting of an annual 2% increase in population. Paediatric hospital admission rates decreased over time.<h4>Conclusion</h4>The risk of sustaining burn injury, the types of burn and outcomes, varied by age and gender. We found evidence of a limited decrease in burn injury rates in some sub-groups: appropriate and effective targeted prevention strategies for burns are needed to avoid the significant short and long-term suffering experienced.",,doi:https://doi.org/10.1016/j.burns.2021.06.007
+32119825,https://doi.org/10.1016/s2214-109x(20)30074-7,Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts.,"Hellewell J, Abbott S, Gimma A, Bosse NI, Jarvis CI, Russell TW, Munday JD, Kucharski AJ, Edmunds WJ, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Funk S, Eggo RM.",,The Lancet. Global health,2020,2020-02-28,Y,,Improving Public Health,COVID-19,"<h4>Background</h4>Isolation of cases and contact tracing is used to control outbreaks of infectious diseases, and has been used for coronavirus disease 2019 (COVID-19). Whether this strategy will achieve control depends on characteristics of both the pathogen and the response. Here we use a mathematical model to assess if isolation and contact tracing are able to control onwards transmission from imported cases of COVID-19.<h4>Methods</h4>We developed a stochastic transmission model, parameterised to the COVID-19 outbreak. We used the model to quantify the potential effectiveness of contact tracing and isolation of cases at controlling a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-like pathogen. We considered scenarios that varied in the number of initial cases, the basic reproduction number (R<sub>0</sub>), the delay from symptom onset to isolation, the probability that contacts were traced, the proportion of transmission that occurred before symptom onset, and the proportion of subclinical infections. We assumed isolation prevented all further transmission in the model. Outbreaks were deemed controlled if transmission ended within 12 weeks or before 5000 cases in total. We measured the success of controlling outbreaks using isolation and contact tracing, and quantified the weekly maximum number of cases traced to measure feasibility of public health effort.<h4>Findings</h4>Simulated outbreaks starting with five initial cases, an R<sub>0</sub> of 1·5, and 0% transmission before symptom onset could be controlled even with low contact tracing probability; however, the probability of controlling an outbreak decreased with the number of initial cases, when R<sub>0</sub> was 2·5 or 3·5 and with more transmission before symptom onset. Across different initial numbers of cases, the majority of scenarios with an R<sub>0</sub> of 1·5 were controllable with less than 50% of contacts successfully traced. To control the majority of outbreaks, for R<sub>0</sub> of 2·5 more than 70% of contacts had to be traced, and for an R<sub>0</sub> of 3·5 more than 90% of contacts had to be traced. The delay between symptom onset and isolation had the largest role in determining whether an outbreak was controllable when R<sub>0</sub> was 1·5. For R<sub>0</sub> values of 2·5 or 3·5, if there were 40 initial cases, contact tracing and isolation were only potentially feasible when less than 1% of transmission occurred before symptom onset.<h4>Interpretation</h4>In most scenarios, highly effective contact tracing and case isolation is enough to control a new outbreak of COVID-19 within 3 months. The probability of control decreases with long delays from symptom onset to isolation, fewer cases ascertained by contact tracing, and increasing transmission before symptoms. This model can be modified to reflect updated transmission characteristics and more specific definitions of outbreak control to assess the potential success of local response efforts.<h4>Funding</h4>Wellcome Trust, Global Challenges Research Fund, and Health Data Research UK.",,pdf:https://europepmc.org/articles/pmc7097845?pdf=render; doi:https://doi.org/10.1016/S2214-109X(20)30074-7; html:https://europepmc.org/articles/PMC7097845; pdf:https://europepmc.org/articles/PMC7097845?pdf=render
 37964568,https://doi.org/10.1192/bjo.2023.547,"The association of anxiety disorders and depression with facial scarring: population-based, data linkage, matched cohort analysis of 358 158 patients.","Gibson JAG, Dobbs TD, Griffiths R, Song J, Akbari A, Bodger O, Hutchings HA, Lyons RA, John A, Whitaker IS.",,BJPsych open,2023,2023-11-15,Y,epidemiology; risk assessment; Depressive Disorders; Trauma And Stressor-related Disorders; Anxiety Or Fear-related Disorders,,,"<h4>Background</h4>Estimates suggest that 1 in 100 people in the UK live with facial scarring. Despite this incidence, psychological support is limited.<h4>Aims</h4>The aim of this study was to strengthen the case for improving such support by determining the incidence and risk factors for anxiety and depression disorders in patients with facial scarring.<h4>Method</h4>A matched cohort study was performed. Patients were identified via secondary care data sources, using clinical codes for conditions resulting in facial scarring. A diagnosis of anxiety or depression was determined by linkage with the patient's primary care general practice data. Incidence was calculated per 1000 person-years at risk (PYAR). Logistic regression was used to determine risk factors.<h4>Results</h4>Between 2009 and 2018, 179 079 patients met the study criteria and were identified as having a facial scar, and matched to 179 079 controls. The incidence of anxiety in the facial scarring group was 10.05 per 1000 PYAR compared with 7.48 per 1000 PYAR for controls. The incidence of depression in the facial scarring group was 16.28 per 1000 PYAR compared with 9.56 per 1000 PYAR for controls. Age at the time of scarring, previous history of anxiety or depression, female gender, socioeconomic status and classification of scarring increased the risk of both anxiety disorders and depression.<h4>Conclusions</h4>There is a high burden of anxiety disorders and depression in this patient group. Risk of these mental health disorders is very much determined by factors apparent at the time of injury, supporting the need for psychological support.",,pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/269D54BC172655C337E4E02E05E0A4FB/S2056472423005471a.pdf/div-class-title-the-association-of-anxiety-disorders-and-depression-with-facial-scarring-population-based-data-linkage-matched-cohort-analysis-of-358-158-patients-div.pdf; doi:https://doi.org/10.1192/bjo.2023.547; html:https://europepmc.org/articles/PMC10753955; pdf:https://europepmc.org/articles/PMC10753955?pdf=render
 34306597,https://doi.org/10.1155/2021/6663884,Automatic Prediction of Recurrence of Major Cardiovascular Events: A Text Mining Study Using Chest X-Ray Reports.,"Bagheri A, Groenhof TKJ, Asselbergs FW, Haitjema S, Bots ML, Veldhuis WB, de Jong PA, Oberski DL.",,Journal of healthcare engineering,2021,2021-07-09,Y,,,,"<h4>Methods</h4>We used EHR data of patients included in the Second Manifestations of ARTerial disease (SMART) study. We propose a deep learning-based multimodal architecture for our text mining pipeline that integrates neural text representation with preprocessed clinical predictors for the prediction of recurrence of major cardiovascular events in cardiovascular patients. Text preprocessing, including cleaning and stemming, was first applied to filter out the unwanted texts from X-ray radiology reports. Thereafter, text representation methods were used to numerically represent unstructured radiology reports with vectors. Subsequently, these text representation methods were added to prediction models to assess their clinical relevance. In this step, we applied logistic regression, support vector machine (SVM), multilayer perceptron neural network, convolutional neural network, long short-term memory (LSTM), and bidirectional LSTM deep neural network (BiLSTM).<h4>Results</h4>We performed various experiments to evaluate the added value of the text in the prediction of major cardiovascular events. The two main scenarios were the integration of radiology reports (1) with classical clinical predictors and (2) with only age and sex in the case of unavailable clinical predictors. In total, data of 5603 patients were used with 5-fold cross-validation to train the models. In the first scenario, the multimodal BiLSTM (MI-BiLSTM) model achieved an area under the curve (AUC) of 84.7%, misclassification rate of 14.3%, and F1 score of 83.8%. In this scenario, the SVM model, trained on clinical variables and bag-of-words representation, achieved the lowest misclassification rate of 12.2%. In the case of unavailable clinical predictors, the MI-BiLSTM model trained on radiology reports and demographic (age and sex) variables reached an AUC, F1 score, and misclassification rate of 74.5%, 70.8%, and 20.4%, respectively.<h4>Conclusions</h4>Using the case study of routine care chest X-ray radiology reports, we demonstrated the clinical relevance of integrating text features and classical predictors in our text mining pipeline for cardiovascular risk prediction. The MI-BiLSTM model with word embedding representation appeared to have a desirable performance when trained on text data integrated with the clinical variables from the SMART study. Our results mined from chest X-ray reports showed that models using text data in addition to laboratory values outperform those using only known clinical predictors.",,pdf:https://downloads.hindawi.com/journals/jhe/2021/6663884.pdf; doi:https://doi.org/10.1155/2021/6663884; html:https://europepmc.org/articles/PMC8285182; pdf:https://europepmc.org/articles/PMC8285182?pdf=render
-32119825,https://doi.org/10.1016/s2214-109x(20)30074-7,Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts.,"Hellewell J, Abbott S, Gimma A, Bosse NI, Jarvis CI, Russell TW, Munday JD, Kucharski AJ, Edmunds WJ, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Funk S, Eggo RM.",,The Lancet. Global health,2020,2020-02-28,Y,,Improving Public Health,COVID-19,"<h4>Background</h4>Isolation of cases and contact tracing is used to control outbreaks of infectious diseases, and has been used for coronavirus disease 2019 (COVID-19). Whether this strategy will achieve control depends on characteristics of both the pathogen and the response. Here we use a mathematical model to assess if isolation and contact tracing are able to control onwards transmission from imported cases of COVID-19.<h4>Methods</h4>We developed a stochastic transmission model, parameterised to the COVID-19 outbreak. We used the model to quantify the potential effectiveness of contact tracing and isolation of cases at controlling a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-like pathogen. We considered scenarios that varied in the number of initial cases, the basic reproduction number (R<sub>0</sub>), the delay from symptom onset to isolation, the probability that contacts were traced, the proportion of transmission that occurred before symptom onset, and the proportion of subclinical infections. We assumed isolation prevented all further transmission in the model. Outbreaks were deemed controlled if transmission ended within 12 weeks or before 5000 cases in total. We measured the success of controlling outbreaks using isolation and contact tracing, and quantified the weekly maximum number of cases traced to measure feasibility of public health effort.<h4>Findings</h4>Simulated outbreaks starting with five initial cases, an R<sub>0</sub> of 1·5, and 0% transmission before symptom onset could be controlled even with low contact tracing probability; however, the probability of controlling an outbreak decreased with the number of initial cases, when R<sub>0</sub> was 2·5 or 3·5 and with more transmission before symptom onset. Across different initial numbers of cases, the majority of scenarios with an R<sub>0</sub> of 1·5 were controllable with less than 50% of contacts successfully traced. To control the majority of outbreaks, for R<sub>0</sub> of 2·5 more than 70% of contacts had to be traced, and for an R<sub>0</sub> of 3·5 more than 90% of contacts had to be traced. The delay between symptom onset and isolation had the largest role in determining whether an outbreak was controllable when R<sub>0</sub> was 1·5. For R<sub>0</sub> values of 2·5 or 3·5, if there were 40 initial cases, contact tracing and isolation were only potentially feasible when less than 1% of transmission occurred before symptom onset.<h4>Interpretation</h4>In most scenarios, highly effective contact tracing and case isolation is enough to control a new outbreak of COVID-19 within 3 months. The probability of control decreases with long delays from symptom onset to isolation, fewer cases ascertained by contact tracing, and increasing transmission before symptoms. This model can be modified to reflect updated transmission characteristics and more specific definitions of outbreak control to assess the potential success of local response efforts.<h4>Funding</h4>Wellcome Trust, Global Challenges Research Fund, and Health Data Research UK.",,pdf:https://europepmc.org/articles/pmc7097845?pdf=render; doi:https://doi.org/10.1016/S2214-109X(20)30074-7; html:https://europepmc.org/articles/PMC7097845; pdf:https://europepmc.org/articles/PMC7097845?pdf=render
 33240510,https://doi.org/10.15420/aer.2020.26,Big Data and Artificial Intelligence: Opportunities and Threats in Electrophysiology.,"van de Leur RR, Boonstra MJ, Bagheri A, Roudijk RW, Sammani A, Taha K, Doevendans PA, van der Harst P, van Dam PM, Hassink RJ, van Es R, Asselbergs FW.",,Arrhythmia & electrophysiology review,2020,2020-11-01,Y,Artificial intelligence; Electrophysiology; Neural networks; ECG; Cardiology; Big Data; Deep Learning,,,"The combination of big data and artificial intelligence (AI) is having an increasing impact on the field of electrophysiology. Algorithms are created to improve the automated diagnosis of clinical ECGs or ambulatory rhythm devices. Furthermore, the use of AI during invasive electrophysiological studies or combining several diagnostic modalities into AI algorithms to aid diagnostics are being investigated. However, the clinical performance and applicability of created algorithms are yet unknown. In this narrative review, opportunities and threats of AI in the field of electrophysiology are described, mainly focusing on ECGs. Current opportunities are discussed with their potential clinical benefits as well as the challenges. Challenges in data acquisition, model performance, (external) validity, clinical implementation, algorithm interpretation as well as the ethical aspects of AI research are discussed. This article aims to guide clinicians in the evaluation of new AI applications for electrophysiology before their clinical implementation.",,doi:https://doi.org/10.15420/aer.2020.26; doi:https://doi.org/10.15420/aer.2020.26; html:https://europepmc.org/articles/PMC7675143; pdf:https://europepmc.org/articles/PMC7675143?pdf=render
 35202588,https://doi.org/10.1016/s2213-8587(22)00015-8,Dose-response relationships for vitamin D and all-cause mortality - Authors' reply.,"Burgess S, Butterworth AS.",,The lancet. Diabetes & endocrinology,2022,2022-03-01,N,,,,,,pdf:http://www.thelancet.com/article/S2213858722000158/pdf; doi:https://doi.org/10.1016/S2213-8587(22)00015-8
 37101398,https://doi.org/10.1002/ejhf.2868,Sex differences in the generalizability of randomized clinical trials in heart failure with reduced ejection fraction.,"Schroeder M, Lim YMF, Savarese G, Suzart-Woischnik K, Baudier C, Dyszynski T, Vaartjes I, Eijkemans MJC, Uijl A, Herrera R, Vradi E, Brugts JJ, Brunner-La Rocca HP, Blanc-Guillemaud V, Waechter S, Couvelard F, Tyl B, Fatoba S, Hoes AW, Lund LH, Gerlinger C, Asselbergs FW, Grobbee DE, Cronin M, Koudstaal S.",,European journal of heart failure,2023,2023-05-18,N,Heart Failure; Randomized Clinical Trial; Females; Enrichment Strategies; Standardized Mortality Ratios; Real-world Evidence,,,"<h4>Aims</h4>In order to understand how sex differences impact the generalizability of randomized clinical trials (RCTs) in patients with heart failure (HF) and reduced ejection fraction (HFrEF), we sought to compare clinical characteristics and clinical outcomes between RCTs and HF observational registries stratified by sex.<h4>Methods and results</h4>Data from two HF registries and five HFrEF RCTs were used to create three subpopulations: one RCT population (n = 16 917; 21.7% females), registry patients eligible for RCT inclusion (n = 26 104; 31.8% females), and registry patients ineligible for RCT inclusion (n = 20 810; 30.2% females). Clinical endpoints included all-cause mortality, cardiovascular mortality, and first HF hospitalization at 1 year. Males and females were equally eligible for trial enrolment (56.9% of females and 55.1% of males in the registries). One-year mortality rates were 5.6%, 14.0%, and 28.6% for females and 6.9%, 10.7%, and 24.6% for males in the RCT, RCT-eligible, and RCT-ineligible groups, respectively. After adjusting for 11 HF prognostic variables, RCT females showed higher survival compared to RCT-eligible females (standardized mortality ratio [SMR] 0.72; 95% confidence interval [CI] 0.62-0.83), while RCT males showed higher adjusted mortality rates compared to RCT-eligible males (SMR 1.16; 95% CI 1.09-1.24). Similar results were also found for cardiovascular mortality (SMR 0.89; 95% CI 0.76-1.03 for females, SMR 1.43; 95% CI 1.33-1.53 for males).<h4>Conclusion</h4>Generalizability of HFrEF RCTs differed substantially between the sexes, with females having lower trial participation and female trial participants having lower mortality rates compared to similar females in the registries, while males had higher than expected cardiovascular mortality rates in RCTs compared to similar males in registries.",,doi:https://doi.org/10.1002/ejhf.2868; doi:https://doi.org/10.1002/ejhf.2868
+36243582,https://doi.org/10.1016/j.injury.2022.09.052,Older trauma patients with isolated chest injuries have low rates of complications.,"Ferrah N, Beck B, Ibrahim J, Gabbe B, McLellan MS, Cameron P.",,Injury,2022,2022-10-07,N,Geriatric; Complication; Pneumonia; Chest Trauma; Older; Trauma Centre,,,"<h4>Introduction</h4>The number of older adults hospitalised for injury is growing rapidly. The population-adjusted incidence of isolated thoracic injuries in older adults is also growing. While some older adults are at high risk of post-traumatic complications, not all older adults will need treatment in a major trauma service (MTS). The aim of this study was to characterise older patients with isolated chest injuries, determine the rates of post-traumatic complications, including respiratory failure and pneumonia, and the factors associated with the risk of developing these complications.<h4>Patients and methods</h4>This was a retrospective review of patients aged 65 years and over with isolated chest trauma, from January 2007 to June 2017, using data from the Victorian State Trauma Registry. Patient characteristics and rates of complications were compared between patients with 1. isolated rib fractures, and 2. complex chest injury. Multivariable logistic regression was used to identify predictors of respiratory failure, and pneumonia.<h4>Results</h4>The study population comprised 5401 patients aged 65 years or more, with isolated chest injuries. Two-thirds (65%) of all patients had isolated rib fractures, and 58% of patients (n = 3156) were directly admitted to a non-major trauma centre. Complications were uncommon, with 5.45% of all patients (n = 295) having pneumonia and 3.2% (n = 175) having respiratory failure. Factors associated with increased risk of pneumonia and respiratory failure included advancing age, smoking, chronic obstructive pulmonary disease, congestive heart failure, and more severe and complex chest injury. The adjusted odds of complications were lowest amongst patients not classified as major trauma and receiving definitive treatment in non-MTS.<h4>Discussion</h4>Our findings suggest that rates of complications in older patients with isolated chest trauma in this study were low, and that there is a large group of patients with isolated, uncomplicated rib fractures, who may not need to be treated in a major trauma centre. Further work should be undertaken to appropriately risk stratify and manage older adults with isolated chest trauma.",,doi:https://doi.org/10.1016/j.injury.2022.09.052
 34907415,https://doi.org/10.1093/ehjci/jeab266,Left atrial structure and function are associated with cardiovascular outcomes independent of left ventricular measures: a UK Biobank CMR study.,"Raisi-Estabragh Z, McCracken C, Condurache D, Aung N, Vargas JD, Naderi H, Munroe PB, Neubauer S, Harvey NC, Petersen SE.",,European heart journal. Cardiovascular Imaging,2022,2022-08-01,Y,Mortality; Atrial fibrillation; Stroke; Ischaemic Heart Disease; Cardiovascular Magnetic Resonance; Left ventricle; Vascular Risk Factors; Cardiovascular Outcomes; Lef; T Atrium,,,"<h4>Aims</h4>We evaluated the associations of left atrial (LA) structure and function with prevalent and incident cardiovascular disease (CVD), independent of left ventricular (LV) metrics, in 25 896 UK Biobank participants.<h4>Methods and results</h4>We estimated the association of cardiovascular magnetic resonance (CMR) metrics [LA maximum volume (LAV), LA ejection fraction (LAEF), LV mass : LV end-diastolic volume ratio (LVM : LVEDV), global longitudinal strain, and LV global function index (LVGFI)] with vascular risk factors (hypertension, diabetes, high cholesterol, and smoking), prevalent and incident CVDs [atrial fibrillation (AF), stroke, ischaemic heart disease (IHD), myocardial infarction], all-cause mortality, and CVD mortality. We created uncorrelated CMR variables using orthogonal principal component analysis rotation. All five CMR metrics were simultaneously entered into multivariable regression models adjusted for sex, age, ethnicity, deprivation, education, body size, and physical activity. Lower LAEF was associated with diabetes, smoking, and all the prevalent and incident CVDs. Diabetes, smoking, and high cholesterol were associated with smaller LAV. Hypertension, IHD, AF (incident and prevalent), incident stroke, and CVD mortality were associated with larger LAV. LV and LA metrics were both independently informative in associations with prevalent disease, however LAEF showed the most consistent associations with incident CVDs. Lower LVGFI was associated with greater all-cause and CVD mortality. In secondary analyses, compared with LVGFI, LV ejection fraction showed similar but less consistent disease associations.<h4>Conclusion</h4>LA structure and function measures (LAEF and LAV) demonstrate significant associations with key prevalent and incident cardiovascular outcomes, independent of LV metrics. These measures have potential clinical utility for disease discrimination and outcome prediction.",,pdf:https://academic.oup.com/ehjcimaging/advance-article-pdf/doi/10.1093/ehjci/jeab266/41764801/jeab266.pdf; doi:https://doi.org/10.1093/ehjci/jeab266; html:https://europepmc.org/articles/PMC9365306; pdf:https://europepmc.org/articles/PMC9365306?pdf=render
 36752447,https://doi.org/10.1016/j.jcmg.2022.11.012,Prognostic Value of RV Abnormalities on CMR in Patients With Known or Suspected Cardiac Sarcoidosis.,"Wang J, Zhang J, Hosadurg N, Iwanaga Y, Chen Y, Liu W, Wan K, Patel AR, Wicks EC, Gkoutos GV, Han Y, Chen Y.",,JACC. Cardiovascular imaging,2023,2023-01-11,N,Right Ventricle; Sudden Cardiac Death; Cardiac Sarcoidosis; Cardiac Magnetic Resonance; Late Gadolinium Enhancement,,,"<h4>Background</h4>Left ventricular abnormalities in cardiac sarcoidosis (CS) are associated with adverse cardiovascular events, whereas the prognostic value of right ventricular (RV) involvement found on cardiac magnetic resonance is unclear.<h4>Objectives</h4>This study aimed to systematically assess the prognostic value of right ventricular ejection fraction (RVEF) and RV late gadolinium enhancement (LGE) in known or suspected CS.<h4>Methods</h4>This study was prospectively registered in PROSPERO (CRD42022302579). PubMed, Embase, and Web of Science were searched to identify studies that evaluated the association between RVEF or RV LGE on clinical outcomes in CS. A composite endpoint of all-cause death, cardiovascular events, or sudden cardiac death (SCD) was used. A meta-analysis was performed to determine the pooled risk ratio (RR) for these adverse events. The calculated sensitivity, specificity, and area under the curve with 95% CIs were weighted and summarized.<h4>Results</h4>Eight studies including a total of 899 patients with a mean follow-up duration of 3.2 ± 0.7 years were included. The pooled RR of RV systolic dysfunction was 3.1 (95% CI: 1.7-5.5; P < 0.01) for composite events and 3.0 (95% CI: 1.3-7.0; P < 0.01) for SCD events. In addition, CS patients with RV LGE had a significant risk for composite events (RR: 4.8 [95% CI: 2.4-9.6]; P < 0.01) and a higher risk for SCD (RR: 9.5 [95% CI: 4.4-20.5]; P < 0.01) than patients without RV LGE. Furthermore, the pooled area under the curve, sensitivity, and specificity of RV LGE for identifying patients with CS who were at highest SCD risk were 0.8 (95% CI: 0.8-0.9), 69% (95% CI: 50%-84%), and 90% (95% CI: 70%-97%), respectively.<h4>Conclusions</h4>In patients with known or suspected CS, RVEF and RV LGE were both associated with adverse events. Furthermore, RV LGE shows good discrimination in identifying CS patients at high risk of SCD.",,doi:https://doi.org/10.1016/j.jcmg.2022.11.012; doi:https://doi.org/10.1016/j.jcmg.2022.11.012; html:https://europepmc.org/articles/PMC11229671; pdf:https://europepmc.org/articles/PMC11229671?pdf=render; doi:https://doi.org/10.1016/j.jcmg.2022.11.012
-36243582,https://doi.org/10.1016/j.injury.2022.09.052,Older trauma patients with isolated chest injuries have low rates of complications.,"Ferrah N, Beck B, Ibrahim J, Gabbe B, McLellan MS, Cameron P.",,Injury,2022,2022-10-07,N,Geriatric; Complication; Pneumonia; Chest Trauma; Older; Trauma Centre,,,"<h4>Introduction</h4>The number of older adults hospitalised for injury is growing rapidly. The population-adjusted incidence of isolated thoracic injuries in older adults is also growing. While some older adults are at high risk of post-traumatic complications, not all older adults will need treatment in a major trauma service (MTS). The aim of this study was to characterise older patients with isolated chest injuries, determine the rates of post-traumatic complications, including respiratory failure and pneumonia, and the factors associated with the risk of developing these complications.<h4>Patients and methods</h4>This was a retrospective review of patients aged 65 years and over with isolated chest trauma, from January 2007 to June 2017, using data from the Victorian State Trauma Registry. Patient characteristics and rates of complications were compared between patients with 1. isolated rib fractures, and 2. complex chest injury. Multivariable logistic regression was used to identify predictors of respiratory failure, and pneumonia.<h4>Results</h4>The study population comprised 5401 patients aged 65 years or more, with isolated chest injuries. Two-thirds (65%) of all patients had isolated rib fractures, and 58% of patients (n = 3156) were directly admitted to a non-major trauma centre. Complications were uncommon, with 5.45% of all patients (n = 295) having pneumonia and 3.2% (n = 175) having respiratory failure. Factors associated with increased risk of pneumonia and respiratory failure included advancing age, smoking, chronic obstructive pulmonary disease, congestive heart failure, and more severe and complex chest injury. The adjusted odds of complications were lowest amongst patients not classified as major trauma and receiving definitive treatment in non-MTS.<h4>Discussion</h4>Our findings suggest that rates of complications in older patients with isolated chest trauma in this study were low, and that there is a large group of patients with isolated, uncomplicated rib fractures, who may not need to be treated in a major trauma centre. Further work should be undertaken to appropriately risk stratify and manage older adults with isolated chest trauma.",,doi:https://doi.org/10.1016/j.injury.2022.09.052
 32379357,https://doi.org/10.1002/sim.8563,A Bayesian hierarchical approach for multiple outcomes in routinely collected healthcare data.,"Carragher R, Mueller T, Bennie M, Robertson C.",,Statistics in medicine,2020,2020-05-07,N,Observational Study; Multiple Outcomes; Direct Oral Anticoagulants; Safety Outcomes; Bayesian Hierarchy,,,"Clinical trials are the standard approach for evaluating new treatments, but may lack the power to assess rare outcomes. Trial results are also necessarily restricted to the population considered in the study. The availability of routinely collected healthcare data provides a source of information on the performance of treatments beyond that offered by clinical trials, but the analysis of this type of data presents a number of challenges. Hierarchical methods, which take advantage of known relationships between clinical outcomes, while accounting for bias, may be a suitable statistical approach for the analysis of this data. A study of direct oral anticoagulants in Scotland is discussed and used to motivate a modeling approach. A Bayesian hierarchical model, which allows a stratification of the population into clusters with similar characteristics, is proposed and applied to the direct oral anticoagulant study data. A simulation study is used to assess its performance in terms of outcome detection and error rates.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/sim.8563; doi:https://doi.org/10.1002/sim.8563
 37286615,https://doi.org/10.1038/s41598-023-36214-0,Combining machine learning with Cox models to identify predictors for incident post-menopausal breast cancer in the UK Biobank.,"Liu X, Morelli D, Littlejohns TJ, Clifton DA, Clifton L.",,Scientific reports,2023,2023-06-07,Y,,,,"We aimed to identify potential novel predictors for breast cancer among post-menopausal women, with pre-specified interest in the role of polygenic risk scores (PRS) for risk prediction. We utilised an analysis pipeline where machine learning was used for feature selection, prior to risk prediction by classical statistical models. An ""extreme gradient boosting"" (XGBoost) machine with Shapley feature-importance measures were used for feature selection among [Formula: see text] 1.7 k features in 104,313 post-menopausal women from the UK Biobank. We constructed and compared the ""augmented"" Cox model (incorporating the two PRS, known and novel predictors) with a ""baseline"" Cox model (incorporating the two PRS and known predictors) for risk prediction. Both of the two PRS were significant in the augmented Cox model ([Formula: see text]). XGBoost identified 10 novel features, among which five showed significant associations with post-menopausal breast cancer: plasma urea (HR = 0.95, 95% CI 0.92-0.98, [Formula: see text]), plasma phosphate (HR = 0.68, 95% CI 0.53-0.88, [Formula: see text]), basal metabolic rate (HR = 1.17, 95% CI 1.11-1.24, [Formula: see text]), red blood cell count (HR = 1.21, 95% CI 1.08-1.35, [Formula: see text]), and creatinine in urine (HR = 1.05, 95% CI 1.01-1.09, [Formula: see text]). Risk discrimination was maintained in the augmented Cox model, yielding C-index 0.673 vs 0.667 (baseline Cox model) with the training data and 0.665 vs 0.664 with the test data. We identified blood/urine biomarkers as potential novel predictors for post-menopausal breast cancer. Our findings provide new insights to breast cancer risk. Future research should validate novel predictors, investigate using multiple PRS and more precise anthropometry measures for better breast cancer risk prediction.",,pdf:https://www.nature.com/articles/s41598-023-36214-0.pdf; doi:https://doi.org/10.1038/s41598-023-36214-0; html:https://europepmc.org/articles/PMC10247810; pdf:https://europepmc.org/articles/PMC10247810?pdf=render
 36721180,https://doi.org/10.1186/s12961-022-00956-6,Tracking health system performance in times of crisis using routine health data: lessons learned from a multicountry consortium.,"Turcotte-Tremblay AM, Leerapan B, Akweongo P, Amponsah F, Aryal A, Asai D, Awoonor-Williams JK, Ayele W, Bauhoff S, Doubova SV, Gadeka DD, Dulal M, Gage A, Gordon-Strachan G, Haile-Mariam D, Joseph JP, Kaewkamjornchai P, Kapoor NR, Gelaw SK, Kim MK, Kruk ME, Kubota S, Margozzini P, Mehata S, Mthethwa L, Nega A, Oh J, Park SK, Passi-Solar A, Perez Cuevas RE, Reddy T, Rittiphairoj T, Sapag JC, Thermidor R, Tlou B, Arsenault C.",,Health research policy and systems,2023,2023-01-31,Y,Quality Of Care; Health Systems; Routine Health Information Systems; Covid-19,,,"COVID-19 has prompted the use of readily available administrative data to track health system performance in times of crisis and to monitor disruptions in essential healthcare services. In this commentary we describe our experience working with these data and lessons learned across countries. Since April 2020, the Quality Evidence for Health System Transformation (QuEST) network has used administrative data and routine health information systems (RHIS) to assess health system performance during COVID-19 in Chile, Ethiopia, Ghana, Haiti, Lao People's Democratic Republic, Mexico, Nepal, South Africa, Republic of Korea and Thailand. We compiled a large set of indicators related to common health conditions for the purpose of multicountry comparisons. The study compiled 73 indicators. A total of 43% of the indicators compiled pertained to reproductive, maternal, newborn and child health (RMNCH). Only 12% of the indicators were related to hypertension, diabetes or cancer care. We also found few indicators related to mental health services and outcomes within these data systems. Moreover, 72% of the indicators compiled were related to volume of services delivered, 18% to health outcomes and only 10% to the quality of processes of care. While several datasets were complete or near-complete censuses of all health facilities in the country, others excluded some facility types or population groups. In some countries, RHIS did not capture services delivered through non-visit or nonconventional care during COVID-19, such as telemedicine. We propose the following recommendations to improve the analysis of administrative and RHIS data to track health system performance in times of crisis: ensure the scope of health conditions covered is aligned with the burden of disease, increase the number of indicators related to quality of care and health outcomes; incorporate data on nonconventional care such as telehealth; continue improving data quality and expand reporting from private sector facilities; move towards collecting patient-level data through electronic health records to facilitate quality-of-care assessment and equity analyses; implement more resilient and standardized health information technologies; reduce delays and loosen restrictions for researchers to access the data; complement routine data with patient-reported data; and employ mixed methods to better understand the underlying causes of service disruptions.",,pdf:https://health-policy-systems.biomedcentral.com/counter/pdf/10.1186/s12961-022-00956-6; doi:https://doi.org/10.1186/s12961-022-00956-6; html:https://europepmc.org/articles/PMC9888332; pdf:https://europepmc.org/articles/PMC9888332?pdf=render
 33531486,https://doi.org/10.1038/s41467-021-21370-6,Author Correction: Genetic architecture of host proteins involved in SARS-CoV-2 infection.,"Pietzner M, Wheeler E, Carrasco-Zanini J, Raffler J, Kerrison ND, Oerton E, Auyeung VPW, Luan J, Finan C, Casas JP, Ostroff R, Williams SA, Kastenmüller G, Ralser M, Gamazon ER, Wareham NJ, Hingorani AD, Langenberg C.",,Nature communications,2021,2021-02-02,Y,,,,,,pdf:https://www.nature.com/articles/s41467-021-21370-6.pdf; doi:https://doi.org/10.1038/s41467-021-21370-6; html:https://europepmc.org/articles/PMC7854714; pdf:https://europepmc.org/articles/PMC7854714?pdf=render
 33560181,https://doi.org/10.1177/0272989x21994035,The Value of Triage during Periods of Intense COVID-19 Demand: Simulation Modeling Study.,"Wood RM, Pratt AC, Kenward C, McWilliams CJ, Booton RD, Thomas MJ, Bourdeaux CP, Vasilakis C.",,Medical decision making : an international journal of the Society for Medical Decision Making,2021,2021-02-09,N,Computer simulation; Coronavirus; Intensive Care; Critical Care; Triage; Covid-19,,,"<h4>Background</h4>During the COVID-19 pandemic, many intensive care units have been overwhelmed by unprecedented levels of demand. Notwithstanding ethical considerations, the prioritization of patients with better prognoses may support a more effective use of available capacity in maximizing aggregate outcomes. This has prompted various proposed triage criteria, although in none of these has an objective assessment been made in terms of impact on number of lives and life-years saved.<h4>Design</h4>An open-source computer simulation model was constructed for approximating the intensive care admission and discharge dynamics under triage. The model was calibrated from observational data for 9505 patient admissions to UK intensive care units. To explore triage efficacy under various conditions, scenario analysis was performed using a range of demand trajectories corresponding to differing nonpharmaceutical interventions.<h4>Results</h4>Triaging patients at the point of expressed demand had negligible effect on deaths but reduces life-years lost by up to 8.4% (95% confidence interval: 2.6% to 18.7%). Greater value may be possible through ""reverse triage"", that is, promptly discharging any patient not meeting the criteria if admission cannot otherwise be guaranteed for one who does. Under such policy, life-years lost can be reduced by 11.7% (2.8% to 25.8%), which represents 23.0% (5.4% to 50.1%) of what is operationally feasible with no limit on capacity and in the absence of improved clinical treatments.<h4>Conclusions</h4>The effect of simple triage is limited by a tradeoff between reduced deaths within intensive care (due to improved outcomes) and increased deaths resulting from declined admission (due to lower throughput given the longer lengths of stay of survivors). Improvements can be found through reverse triage, at the expense of potentially complex ethical considerations.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/0272989X21994035; doi:https://doi.org/10.1177/0272989X21994035
 35477524,https://doi.org/10.1136/bmj-2022-070230,Development and validation of the symptom burden questionnaire for long covid (SBQ-LC): Rasch analysis.,"Hughes SE, Haroon S, Subramanian A, McMullan C, Aiyegbusi OL, Turner GM, Jackson L, Davies EH, Frost C, McNamara G, Price G, Matthews K, Camaradou J, Ormerod J, Walker A, Calvert MJ.",,BMJ (Clinical research ed.),2022,2022-04-27,Y,,,,"<h4>Objective</h4>To describe the development and validation of a novel patient reported outcome measure for symptom burden from long covid, the symptom burden questionnaire for long covid (SBQ-LC).<h4>Design</h4>Multiphase, prospective mixed methods study.<h4>Setting</h4>Remote data collection and social media channels in the United Kingdom, 14 April to 1 August 2021.<h4>Participants</h4>13 adults (aged ≥18 years) with self-reported long covid and 10 clinicians evaluated content validity. 274 adults with long covid field tested the draft questionnaire.<h4>Main outcome measures</h4>Published systematic reviews informed development of SBQ-LC's conceptual framework and initial item pool. Thematic analysis of transcripts from cognitive debriefing interviews and online clinician surveys established content validity. Consensus discussions with the patient and public involvement group of the Therapies for Long COVID in non-hospitalised individuals: From symptoms, patient reported outcomes and immunology to targeted therapies (TLC Study) confirmed face validity. Rasch analysis of field test data guided item and scale refinement and provided initial evidence of the SBQ-LC's measurement properties.<h4>Results</h4>SBQ-LC (version 1.0) is a modular instrument measuring patient reported outcomes and is composed of 17 independent scales with promising psychometric properties. Respondents rate their symptom burden during the past seven days using a dichotomous response or 4 point rating scale. Each scale provides coverage of a different symptom domain and returns a summed raw score that can be transformed to a linear (0-100) score. Higher scores represent higher symptom burden. After rating scale refinement and item reduction, all scales satisfied the Rasch model requirements for unidimensionality (principal component analysis of residuals: first residual contrast values <2.00 eigenvalue units) and item fit (outfit mean square values within 0.5 -1.5 logits). Rating scale categories were ordered with acceptable category fit statistics (outfit mean square values <2.0 logits). 14 item pairs had evidence of local dependency (residual correlation values >0.4). Across the 17 scales, person reliability ranged from 0.34 to 0.87, person separation ranged from 0.71 to 2.56, item separation ranged from 1.34 to 13.86, and internal consistency reliability (Cronbach's alpha) ranged from 0.56 to 0.91.<h4>Conclusions</h4>SBQ-LC (version 1.0) is a comprehensive patient reported outcome instrument developed using modern psychometric methods. It measures symptoms of long covid important to people with lived experience of the condition and may be used to evaluate the impact of interventions and inform best practice in clinical management.",,pdf:https://www.bmj.com/content/bmj/377/bmj-2022-070230.full.pdf; doi:https://doi.org/10.1136/bmj-2022-070230; html:https://europepmc.org/articles/PMC9043395; pdf:https://europepmc.org/articles/PMC9043395?pdf=render
-39174501,https://doi.org/10.1038/s41467-024-51451-1,Structural insights into Frizzled3 through nanobody modulators.,"Hillier J, Zhao Y, Carrique L, Malinauskas T, Ruza RR, Chang TH, Yi G, Duyvesteyn HME, Yu J, Lu W, Pardon E, Steyaert J, Zhu Y, Ni T, Jones EY.",,Nature communications,2024,2024-08-22,Y,,,,"The Wnt receptor Frizzled3 (FZD3) is important for brain axonal development and cancer progression. We report structures of FZD3 in complex with extracellular and intracellular binding nanobodies (Nb). The crystal structure of Nb8 in complex with the FZD3 cysteine-rich domain (CRD) reveals that the nanobody binds at the base of the lipid-binding groove and can compete with Wnt5a. Nb8 fused with the Dickkopf-1 C-terminal domain behaves as a FZD3-specific Wnt surrogate, activating β-catenin signalling. The cryo-EM structure of FZD3 in complex with Nb9 reveals partially resolved density for the CRD, which exhibits positional flexibility, and a transmembrane conformation that resembles active GPCRs. Nb9 binds to the cytoplasmic region of FZD3 at the putative Dishevelled (DVL) or G protein-binding site, competes with DVL binding, and inhibits GαS coupling. In combination, our FZD3 structures with nanobody modulators map extracellular and intracellular interaction surfaces of functional, and potentially therapeutic, relevance.",,doi:https://doi.org/10.1038/s41467-024-51451-1; html:https://europepmc.org/articles/PMC11341715; pdf:https://europepmc.org/articles/PMC11341715?pdf=render
 35048949,https://doi.org/10.1093/eurjpc/zwac008,Light to moderate coffee consumption is associated with lower risk of death: a UK Biobank study.,"Simon J, Fung K, Raisi-Estabragh Z, Aung N, Khanji MY, Kolossváry M, Merkely B, Munroe PB, Harvey NC, Piechnik SK, Neubauer S, Petersen SE, Maurovich-Horvat P.",,European journal of preventive cardiology,2022,2022-05-01,N,Cardiac Magnetic Resonance; Cardiovascular Health; Coffee Consumption,,,"<h4>Aims</h4>To study the association of daily coffee consumption with all-cause and cardiovascular (CV) mortality and major CV outcomes. In a subgroup of participants who underwent cardiovascular magnetic resonance (CMR) imaging, we evaluated the association between regular coffee intake and cardiac structure and function.<h4>Methods and results</h4>UK Biobank participants without clinically manifested heart disease at the time of recruitment were included. Regular coffee intake was categorized into three groups: zero, light-to-moderate (0.5-3 cups/day), and high (>3 cups/day). In the multivariate analysis, we adjusted for the main CV risk factors. We included 468 629 individuals (56.2 ± 8.1 years, 44.2% male), of whom 22.1% did not consume coffee regularly, 58.4% had 0.5-3 cups per day, and 19.5% had >3 cups per day. Compared to non-coffee drinkers, light-to-moderate (0.5-3 cups per day) coffee drinking was associated with lower risk of all-cause mortality [multivariate hazard ratio (HR) = 0.88, 95% confidence interval (CI): 0.83-0.92; P < 0.001] and CV mortality (multivariate HR = 0.83, 95% CI: 0.74-0.94; P = 0.006), and incident stroke (multivariate HR = 0.79, 95% CI: 0.63-0.99 P = 0.037) after a median follow-up of 11 years. CMR data were available in 30 650 participants. Both light-to-moderate and high coffee consuming categories were associated with dose-dependent increased left and right ventricular end-diastolic, end-systolic and stroke volumes, and greater left ventricular mass.<h4>Conclusion</h4>Coffee consumption of up to three cups per day was associated with favourable CV outcomes. Regular coffee consumption was also associated with a likely healthy pattern of CMR metrics in keeping with the reverse of age-related cardiac alterations.",,pdf:https://academic.oup.com/eurjpc/article-pdf/29/6/982/43589594/zwac008.pdf; doi:https://doi.org/10.1093/eurjpc/zwac008
+39174501,https://doi.org/10.1038/s41467-024-51451-1,Structural insights into Frizzled3 through nanobody modulators.,"Hillier J, Zhao Y, Carrique L, Malinauskas T, Ruza RR, Chang TH, Yi G, Duyvesteyn HME, Yu J, Lu W, Pardon E, Steyaert J, Zhu Y, Ni T, Jones EY.",,Nature communications,2024,2024-08-22,Y,,,,"The Wnt receptor Frizzled3 (FZD3) is important for brain axonal development and cancer progression. We report structures of FZD3 in complex with extracellular and intracellular binding nanobodies (Nb). The crystal structure of Nb8 in complex with the FZD3 cysteine-rich domain (CRD) reveals that the nanobody binds at the base of the lipid-binding groove and can compete with Wnt5a. Nb8 fused with the Dickkopf-1 C-terminal domain behaves as a FZD3-specific Wnt surrogate, activating β-catenin signalling. The cryo-EM structure of FZD3 in complex with Nb9 reveals partially resolved density for the CRD, which exhibits positional flexibility, and a transmembrane conformation that resembles active GPCRs. Nb9 binds to the cytoplasmic region of FZD3 at the putative Dishevelled (DVL) or G protein-binding site, competes with DVL binding, and inhibits GαS coupling. In combination, our FZD3 structures with nanobody modulators map extracellular and intracellular interaction surfaces of functional, and potentially therapeutic, relevance.",,doi:https://doi.org/10.1038/s41467-024-51451-1; html:https://europepmc.org/articles/PMC11341715; pdf:https://europepmc.org/articles/PMC11341715?pdf=render
 35028631,https://doi.org/10.1016/s2666-7568(21)00281-6,The importance of blood pressure thresholds versus predicted cardiovascular risk on subsequent rates of cardiovascular disease: a cohort study in English primary care.,"Herrett E, Strongman H, Gadd S, Tomlinson L, Nitsch D, Bhaskaran K, Williamson E, van Staa T, Sofat R, Timmis A, Wells S, Smeeth L, Jackson R.",,The lancet. Healthy longevity,2022,2022-01-01,Y,,,,"<h4>Background</h4>For five decades, blood pressure lowering treatment has been recommended for patients with hypertension (currently defined as blood pressure of ≥140/90 mm Hg). In the past 20 years, guidelines for treatment began incorporating predicted absolute cardiovascular disease risk (predicted risk) and reducing blood pressure thresholds. The blood pressure threshold at which to start treatment has become a secondary consideration in some countries. We aimed to provide descriptive data to assess the relative importance of blood pressure thresholds versus predicted risk on the subsequent rate of cardiovascular disease to inform treatment decisions.<h4>Methods</h4>In this English population-based cohort study, we used linked data from the Clinical Practice Research Datalink (CPRD) GOLD, Hospital Episode Statistics Admitted Patient Care, and the Office for National Statistics mortality data, and area-based deprivation indices (Townsend scores). Eligible patients were aged 30-79 years on Jan 1, 2011 (cohort entry date) and could be linked to hospital, mortality, and deprivation data. Patients were followed up until death, end of CPRD follow-up, or Nov 31, 2018. We examined three outcomes: cardiovascular disease, markers of potential target organ damage, and incident dementia without a known cause. The rate of each outcome was estimated and stratified by systolic blood pressure and predicted 10-year risk of cardiovascular disease (QRISK2 algorithm).<h4>Findings</h4>Between Jan 1, 2011, and Nov 31, 2018, 1 098 991 patients were included in the cohort and followed up for a median of 4·3 years (IQR 2·6-6·0; total follow-up of 4·6 million person-years). Median age at entry was 52 years (IQR 42-62) and 629 711 (57·3%) patients were female. There were 51 996 cardiovascular disease events and the overall rate of cardiovascular disease was 11·2 per 1000 person-years (95% CI 11·1-11·3). Median QRISK2 10-year predicted risk was 4·6% (IQR 1·4-12·0) and mean systolic blood pressure before cohort entry was 129·1 mm Hg (SD 15·7). Within strata of predicted risk, the effect of increasing systolic blood pressure on outcomes was small. For example, in the group with 10·0-19·9% predicted risk, rates of all cardiovascular disease rose from 20·1 to 23·6 per 1000 person-years between systolic blood pressures less than 110 mm Hg and 180 and higher mm Hg. But among patients with systolic blood pressure 140·0-149·9 mm Hg, rates rose from 6·9 to 52·3 per 1000 person-years between those with less than 10·0% risk and those with 30·0% or higher predicted risk.<h4>Interpretation</h4>For a wide range of blood pressures, the rate of cardiovascular disease and effectiveness of blood pressure drug treatment was mainly determined by predicted risk, with blood pressure thresholds 140/90 mm Hg or 160/100 mm Hg-ubiquitous in most countries-adding little useful information. When medium-term predicted risk is low, there is no urgency to initiate drug treatment, allowing time to attempt non-pharmacological blood pressure reduction.<h4>Funding</h4>National Institute for Health Research.",,pdf:http://www.thelancet.com/article/S2666756821002816/pdf; doi:https://doi.org/10.1016/S2666-7568(21)00281-6; html:https://europepmc.org/articles/PMC8732286
 33289226,https://doi.org/10.1111/ans.16426,Association between gender and outcomes of acute burns patients.,"Perkins M, Abesamis GM, Cleland H, Gabbe BJ, Tracy LM.",,ANZ journal of surgery,2020,2020-12-01,N,Burns; Gender; Outcomes,,,"<h4>Background</h4>Burn injuries are a complex and serious public health concern. Where the total body surface area of the burn exceeds 50%, mortality rates as high as 48% have been reported. While the association between gender and burn injury outcomes has been explored, findings are inconsistent.<h4>Methods</h4>Adult patients (>15 years) admitted between 1 July 2009 and 30 June 2018 to intensive care units of burn centres that provide specialist burn care in Australia and New Zealand were included. Raw mortality rates were examined and a multivariable Cox proportional hazards regression was used to investigate the association between gender and time to in-hospital death.<h4>Results</h4>There were 2227 eligible burn injury admissions. Men comprised the majority (77.6%). The proportion of women who died in hospital was greater than men and the adjusted odds of in-hospital mortality were 34% lower in men (odds ratio 0.66; 95% confidence interval (CI) 0.45-0.98). The unadjusted rate of in-hospital mortality for men was 44% lower than women (hazard ratio 0.56; 95% CI 0.41-0.76). After adjusting for confounders, there was no association between gender and survival time (hazard ratio 0.76; 95% CI 0.54-1.06).<h4>Conclusion</h4>After adjustment for key differences in case-mix between men and women, there was an association between gender and in-hospital mortality and no association between gender and time to death. Our findings indicate that the worse outcomes observed for women are associated with different age and patterns of injury, and provide further information to direct and inform targeted prevention measures for vulnerable populations.",,doi:https://doi.org/10.1111/ans.16426
 34849869,https://doi.org/10.1093/gigascience/giab076,An overview of the National COVID-19 Chest Imaging Database: data quality and cohort analysis.,"Cushnan D, Bennett O, Berka R, Bertolli O, Chopra A, Dorgham S, Favaro A, Ganepola T, Halling-Brown M, Imreh G, Jacob J, Jefferson E, Lemarchand F, Schofield D, Wyatt JC, NCCID Collaborative.",,GigaScience,2021,2021-11-01,Y,Medical imaging; Machine Learning; Thoracic Imaging; Covid-19; Sars-cov2,,,"<h4>Background</h4>The National COVID-19 Chest Imaging Database (NCCID) is a centralized database containing mainly chest X-rays and computed tomography scans from patients across the UK. The objective of the initiative is to support a better understanding of the coronavirus SARS-CoV-2 disease (COVID-19) and the development of machine learning technologies that will improve care for patients hospitalized with a severe COVID-19 infection. This article introduces the training dataset, including a snapshot analysis covering the completeness of clinical data, and availability of image data for the various use-cases (diagnosis, prognosis, longitudinal risk). An additional cohort analysis measures how well the NCCID represents the wider COVID-19-affected UK population in terms of geographic, demographic, and temporal coverage.<h4>Findings</h4>The NCCID offers high-quality DICOM images acquired across a variety of imaging machinery; multiple time points including historical images are available for a subset of patients. This volume and variety make the database well suited to development of diagnostic/prognostic models for COVID-associated respiratory conditions. Historical images and clinical data may aid long-term risk stratification, particularly as availability of comorbidity data increases through linkage to other resources. The cohort analysis revealed good alignment to general UK COVID-19 statistics for some categories, e.g., sex, whilst identifying areas for improvements to data collection methods, particularly geographic coverage.<h4>Conclusion</h4>The NCCID is a growing resource that provides researchers with a large, high-quality database that can be leveraged both to support the response to the COVID-19 pandemic and as a test bed for building clinically viable medical imaging models.",,doi:https://doi.org/10.1093/gigascience/giab076; doi:https://doi.org/10.1093/gigascience/giab076; html:https://europepmc.org/articles/PMC8633457; pdf:https://europepmc.org/articles/PMC8633457?pdf=render
-33728815,https://doi.org/10.1002/art.41709,Epidemiology of Scleritis in the United Kingdom From 1997 to 2018: Population-Based Analysis of 11 Million Patients and Association Between Scleritis and Infectious and Immune-Mediated Inflammatory Disease.,"Braithwaite T, Adderley NJ, Subramanian A, Galloway J, Kempen JH, Gokhale K, Cope AP, Dick AD, Nirantharakumar K, Denniston AK.",,"Arthritis & rheumatology (Hoboken, N.J.)",2021,2021-06-06,N,,,,"<h4>Objective</h4>To estimate 22-year trends in the prevalence and incidence of scleritis, and the associations of scleritis with infectious and immune-mediated inflammatory diseases (I-IMIDs) in the UK.<h4>Methods</h4>The retrospective cross-sectional and population cohort study (1997-2018) included 10,939,823 patients (2,946 incident scleritis cases) in The Health Improvement Network, a nationally representative primary care records database. The case-control and matched cohort study (1995-2019) included 3,005 incident scleritis cases and 12,020 control patients matched by age, sex, region, and Townsend deprivation index. Data were analyzed using multivariable Poisson regression, multivariable logistic regression, and Cox proportional hazards multivariable models adjusted for age, sex, Townsend deprivation index, race/ethnicity, smoking status, nation within the UK, and body mass index. Incidence rate ratios (IRRs) and 95% confidence intervals (95% CIs) were calculated.<h4>Results</h4>Scleritis incidence rates per 100,000 person-years declined from 4.23 (95% CI 2.16-6.31) to 2.79 (95% CI 2.19-3.39) between 1997 and 2018. The prevalence of scleritis per 100,000 person-years was 93.62 (95% CI 90.17-97.07) in 2018 (61,650 UK patients). Among 2,946 patients with incident scleritis, 1,831 (62.2%) were female, the mean ± SD age was 44.9 ± 17.6 years (range 1-93), and 1,257 (88.8%) were White. Higher risk of incident scleritis was associated with female sex (adjusted IRR 1.53 [95% CI 1.43-1.66], P < 0.001), Black race/ethnicity (adjusted IRR 1.52 [95% CI 1.14-2.01], P = 0.004 compared to White race/ethnicity), or South Asian race/ethnicity (adjusted IRR 1.50 [95% CI 1.19-1.90], P < 0.001 compared to White race/ethnicity), and older age (peak adjusted IRR 4.95 [95% CI 3.99-6.14], P < 0.001 for patients ages 51-60 years versus those ages ≤10 years). Compared to controls, scleritis patients had a 2-fold increased risk of a prior I-IMID diagnosis (17 I-IMIDs, P < 0.001) and significantly increased risk of subsequent diagnosis (13 I-IMIDs). The I-IMIDs most strongly associated with scleritis included granulomatosis with polyangiitis, Behçet's disease, and Sjögren's syndrome.<h4>Conclusion</h4>From 1997 through 2018, the UK incidence of scleritis declined from 4.23 to 2.79/100,000 person-years. Incident scleritis was associated with 19 I-IMIDs, providing data for rational investigation and cross-specialty engagement.",,doi:https://doi.org/10.1002/art.41709; doi:https://doi.org/10.1002/art.41709
 31757515,https://doi.org/10.1016/j.jaci.2019.09.015,Atopic eczema and fracture risk in adults: A population-based cohort study.,"Lowe KE, Mansfield KE, Delmestri A, Smeeth L, Roberts A, Abuabara K, Prieto-Alhambra D, Langan SM.",,The Journal of allergy and clinical immunology,2020,2019-11-19,Y,Osteoporosis; Fracture; Atopic Eczema; Severity; Population Based,Understanding the Causes of Disease,,"<h4>Background</h4>Limited evidence suggests increased fracture risk in people with atopic eczema. Any link could have substantial effect; atopic eczema is common, and fractures have associated morbidity and mortality.<h4>Objective</h4>We sought to examine whether atopic eczema is associated with fracture and whether fracture risk varies with eczema severity.<h4>Methods</h4>We performed a matched cohort study set in primary care (Clinical Practice Research Datalink GOLD 1998-2016) and linked hospital admissions data (Hospital Episode Statistics), including adults (≥18 years old) with atopic eczema matched (by age, sex, general practice, and cohort entry date) with up to 5 individuals without eczema. We estimated hazard ratios (HRs) from stratified Cox regression comparing risk of major osteoporotic (hip, pelvis, spine, wrist, and proximal humerus) fractures individually and any fracture in those with and without atopic eczema.<h4>Results</h4>We identified 526,808 people with atopic eczema and 2,569,030 people without atopic eczema. Those with eczema had increased risk of hip (HR, 1.10; 99% CI, 1.06-1.14), pelvic (HR, 1.10; 99% CI, 1.02-1.19), spinal (HR, 1.18; 99% CI, 1.10-1.27), and wrist (HR, 1.07; 99% CI, 1.03,-1.11) fractures. We found no evidence of increased proximal humeral (HR, 1.06; 99% CI, 0.97-1.15) fracture risk. Fracture risk increased with increasing eczema severity, with the strongest associations in people with severe eczema (compared with those without) for spinal (HR, 2.09; 99% CI, 1.66-2.65), pelvic (HR, 1.66; 99% CI, 1.26-2.20), and hip (HR, 1.50; 99% CI, 1.30-1.74) fractures. Associations persisted after oral glucocorticoid adjustment.<h4>Conclusions</h4>People with atopic eczema have increased fracture risk, particularly major osteoporotic fractures.",This population-wide study used datalinkage methods to create a matched cohort study between 1998-2016. The study estimated hazard ratios and compared the risk of major fractures and any fracture in people with and without atopic eczema. Findings suggest that people with atopic eczema have an increased fracture risk.,pdf:http://www.jacionline.org/article/S0091674919312515/pdf; doi:https://doi.org/10.1016/j.jaci.2019.09.015; html:https://europepmc.org/articles/PMC7014587; pdf:https://europepmc.org/articles/PMC7014587?pdf=render
+33728815,https://doi.org/10.1002/art.41709,Epidemiology of Scleritis in the United Kingdom From 1997 to 2018: Population-Based Analysis of 11 Million Patients and Association Between Scleritis and Infectious and Immune-Mediated Inflammatory Disease.,"Braithwaite T, Adderley NJ, Subramanian A, Galloway J, Kempen JH, Gokhale K, Cope AP, Dick AD, Nirantharakumar K, Denniston AK.",,"Arthritis & rheumatology (Hoboken, N.J.)",2021,2021-06-06,N,,,,"<h4>Objective</h4>To estimate 22-year trends in the prevalence and incidence of scleritis, and the associations of scleritis with infectious and immune-mediated inflammatory diseases (I-IMIDs) in the UK.<h4>Methods</h4>The retrospective cross-sectional and population cohort study (1997-2018) included 10,939,823 patients (2,946 incident scleritis cases) in The Health Improvement Network, a nationally representative primary care records database. The case-control and matched cohort study (1995-2019) included 3,005 incident scleritis cases and 12,020 control patients matched by age, sex, region, and Townsend deprivation index. Data were analyzed using multivariable Poisson regression, multivariable logistic regression, and Cox proportional hazards multivariable models adjusted for age, sex, Townsend deprivation index, race/ethnicity, smoking status, nation within the UK, and body mass index. Incidence rate ratios (IRRs) and 95% confidence intervals (95% CIs) were calculated.<h4>Results</h4>Scleritis incidence rates per 100,000 person-years declined from 4.23 (95% CI 2.16-6.31) to 2.79 (95% CI 2.19-3.39) between 1997 and 2018. The prevalence of scleritis per 100,000 person-years was 93.62 (95% CI 90.17-97.07) in 2018 (61,650 UK patients). Among 2,946 patients with incident scleritis, 1,831 (62.2%) were female, the mean ± SD age was 44.9 ± 17.6 years (range 1-93), and 1,257 (88.8%) were White. Higher risk of incident scleritis was associated with female sex (adjusted IRR 1.53 [95% CI 1.43-1.66], P < 0.001), Black race/ethnicity (adjusted IRR 1.52 [95% CI 1.14-2.01], P = 0.004 compared to White race/ethnicity), or South Asian race/ethnicity (adjusted IRR 1.50 [95% CI 1.19-1.90], P < 0.001 compared to White race/ethnicity), and older age (peak adjusted IRR 4.95 [95% CI 3.99-6.14], P < 0.001 for patients ages 51-60 years versus those ages ≤10 years). Compared to controls, scleritis patients had a 2-fold increased risk of a prior I-IMID diagnosis (17 I-IMIDs, P < 0.001) and significantly increased risk of subsequent diagnosis (13 I-IMIDs). The I-IMIDs most strongly associated with scleritis included granulomatosis with polyangiitis, Behçet's disease, and Sjögren's syndrome.<h4>Conclusion</h4>From 1997 through 2018, the UK incidence of scleritis declined from 4.23 to 2.79/100,000 person-years. Incident scleritis was associated with 19 I-IMIDs, providing data for rational investigation and cross-specialty engagement.",,doi:https://doi.org/10.1002/art.41709; doi:https://doi.org/10.1002/art.41709
 34378227,https://doi.org/10.1111/tri.14010,"Health-related quality of life, uncertainty and coping strategies in solid organ transplant recipients during shielding for the COVID-19 pandemic.","McKay SC, Lembach H, Hann A, Okoth K, Anderton J, Nirantharakumar K, Magill L, Torlinska B, Armstrong M, Mascaro J, Inston N, Pinkney T, Ranasinghe A, Borrows R, Ferguson J, Isaac J, Calvert M, Perera MTPR, Hartog H.",,Transplant international : official journal of the European Society for Organ Transplantation,2021,2021-09-16,Y,Isolation; Transplant; Mental health; Health-related Quality Of Life; Shielding; Covid-19,,,"Strict isolation of vulnerable individuals has been a strategy implemented by authorities to protect people from COVID-19. Our objective was to investigate health-related quality of life (HRQoL), uncertainty and coping behaviours in solid organ transplant (SOT) recipients during the COVID-19 pandemic. A cross-sectional survey of adult SOT recipients undergoing follow-up at our institution was performed. Perceived health status, uncertainty and coping strategies were assessed using the EQ-5D-5L, Short-form Mishel Uncertainty in Illness Scale (SF-MUIS) and Brief Cope, respectively. Interactions with COVID-19 risk perception, access to health care, demographic and clinical variables were assessed. The survey was completed by 826 of 3839 (21.5%) invited participants. Overall, low levels of uncertainty in illness were reported, and acceptance was the major coping strategy (92%). Coping by acceptance, feeling protected, self-perceived susceptibility to COVID-19 were associated with lower levels of uncertainty. Health status index scores were significantly lower for those with mental health illness, compromised access to health care, a perceived high risk of severe COVID-19 infection and higher levels of uncertainty. A history of mental health illness, risk perceptions, restricted healthcare access, uncertainty and coping strategies was associated with poorer HRQoL in SOT recipients during strict isolation. These findings may allow identification of strategies to improve HRQoL in SOT recipients during the pandemic.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/tri.14010; doi:https://doi.org/10.1111/tri.14010; html:https://europepmc.org/articles/PMC8420473; pdf:https://europepmc.org/articles/PMC8420473?pdf=render
 32426117,https://doi.org/10.7189/jogh.10.010348,Novel approaches to estimate compliance with lockdown measures in the COVID-19 pandemic.,"Sheikh A, Sheikh Z, Sheikh A.",,Journal of global health,2020,2020-06-01,Y,,,,,This is a summary of new methods for estimating phyiscal distancing and compliance with lockdown. I haven't scored the content because it isn't primary research.,doi:https://doi.org/10.7189/jogh.10.010348; doi:https://doi.org/10.7189/jogh.10.010348; html:https://europepmc.org/articles/PMC7211415; pdf:https://europepmc.org/articles/PMC7211415?pdf=render
 37884627,https://doi.org/10.1038/s41591-023-02608-w,The value of standards for health datasets in artificial intelligence-based applications.,"Arora A, Alderman JE, Palmer J, Ganapathi S, Laws E, McCradden MD, Oakden-Rayner L, Pfohl SR, Ghassemi M, McKay F, Treanor D, Rostamzadeh N, Mateen B, Gath J, Adebajo AO, Kuku S, Matin R, Heller K, Sapey E, Sebire NJ, Cole-Lewis H, Calvert M, Denniston A, Liu X.",,Nature medicine,2023,2023-10-26,Y,,,,"Artificial intelligence as a medical device is increasingly being applied to healthcare for diagnosis, risk stratification and resource allocation. However, a growing body of evidence has highlighted the risk of algorithmic bias, which may perpetuate existing health inequity. This problem arises in part because of systemic inequalities in dataset curation, unequal opportunity to participate in research and inequalities of access. This study aims to explore existing standards, frameworks and best practices for ensuring adequate data diversity in health datasets. Exploring the body of existing literature and expert views is an important step towards the development of consensus-based guidelines. The study comprises two parts: a systematic review of existing standards, frameworks and best practices for healthcare datasets; and a survey and thematic analysis of stakeholder views of bias, health equity and best practices for artificial intelligence as a medical device. We found that the need for dataset diversity was well described in literature, and experts generally favored the development of a robust set of guidelines, but there were mixed views about how these could be implemented practically. The outputs of this study will be used to inform the development of standards for transparency of data diversity in health datasets (the STANDING Together initiative).",,pdf:https://www.nature.com/articles/s41591-023-02608-w.pdf; doi:https://doi.org/10.1038/s41591-023-02608-w; html:https://europepmc.org/articles/PMC10667100; pdf:https://europepmc.org/articles/PMC10667100?pdf=render
@@ -1581,57 +1583,57 @@ PMC8855010,https://doi.org/,POS-894 PREDICTING PANDEMIC-RELATED EXCESS-DEATH USI
 37563721,https://doi.org/10.1186/s13063-023-07473-z,Evaluation of interventions to prevent vasovagal reactions among whole blood donors: rationale and design of a large cluster randomised trial.,"McMahon A, Kaptoge S, Walker M, Mehenny S, Gilchrist PT, Sambrook J, Akhtar N, Sweeting M, Wood AM, Stirrups K, Chung R, Fahle S, Johnson E, Cullen D, Godfrey R, Duthie S, Allen L, Harvey P, Berkson M, Allen E, Watkins NA, Bradley JR, Kingston N, Miflin G, Armitage J, Roberts DJ, Danesh J, Di Angelantonio E.",,Trials,2023,2023-08-10,Y,Cross-over; Blood donors; Blood Donation; Factorial Design; Vasovagal Reactions; Cluster Randomised Trial; Stepped-wedge,,,"<h4>Background</h4>Vasovagal reactions (VVRs) are the most common acute complications of blood donation. Responsible for substantial morbidity, they also reduce the likelihood of repeated donations and are disruptive and costly for blood services. Although blood establishments worldwide have adopted different strategies to prevent VVRs (including water loading and applied muscle tension [AMT]), robust evidence is limited. The Strategies to Improve Donor Experiences (STRIDES) trial aims to reliably assess the impact of four different interventions to prevent VVRs among blood donors.<h4>Methods</h4>STRIDES is a cluster-randomised cross-over/stepped-wedge factorial trial of four interventions to reduce VVRs involving about 1.4 million whole blood donors enrolled from all 73 blood donation sites (mobile teams and donor centres) of National Health Service Blood and Transplant (NHSBT) in England. Each site (""cluster"") has been randomly allocated to receive one or more interventions during a 36-month period, using principles of cross-over, stepped-wedge and factorial trial design to assign the sequence of interventions. Each of the four interventions is compared to NHSBT's current practices: (i) 500-ml isotonic drink before donation (vs current 500-ml plain water); (ii) 3-min rest on donation chair after donation (vs current 2 min); (iii) new modified AMT (vs current practice of AMT); and (iv) psychosocial intervention using preparatory materials (vs current practice of nothing). The primary outcome is the number of in-session VVRs with loss of consciousness (i.e. episodes involving loss of consciousness of any duration, with or without additional complications). Secondary outcomes include all in-session VVRs (i.e. with and without loss of consciousness), all delayed VVRs (i.e. those occurring after leaving the venue) and any in-session non-VVR adverse events or reactions.<h4>Discussion</h4>The STRIDES trial should yield novel information about interventions, singly and in combination, for the prevention of VVRs, with the aim of generating policy-shaping evidence to help inform blood services to improve donor health, donor experience, and service efficiency.<h4>Trial registration</h4>ISRCTN: 10412338. Registration date: October 24, 2019.",,doi:https://doi.org/10.1186/s13063-023-07473-z; html:https://europepmc.org/articles/PMC10413586; pdf:https://europepmc.org/articles/PMC10413586?pdf=render
 32571619,https://doi.org/10.1016/j.schres.2020.05.007,Real-world implementation of precision psychiatry: Transdiagnostic risk calculator for the automatic detection of individuals at-risk of psychosis.,"Oliver D, Spada G, Colling C, Broadbent M, Baldwin H, Patel R, Stewart R, Stahl D, Dobson R, McGuire P, Fusar-Poli P.",,Schizophrenia research,2021,2020-06-19,Y,Feasibility; Implementation; Risk Calculator; Precision Psychiatry; Psychosis;transdiagnostic,,,"<h4>Background</h4>Risk estimation models integrated into Electronic Health Records (EHRs) can deliver innovative approaches in psychiatry, but clinicians' endorsement and their real-world usability are unknown. This study aimed to investigate the real-world feasibility of implementing an individualised, transdiagnostic risk calculator to automatically screen EHRs and detect individuals at-risk for psychosis.<h4>Methods</h4>Feasibility implementation study encompassing an in-vitro phase (March 2018 to May 2018) and in-vivo phase (May 2018 to April 2019). The in-vitro phase addressed implementation barriers and embedded the risk calculator (predictors: age, gender, ethnicity, index cluster diagnosis, age*gender) into the local EHR. The in-vivo phase investigated the real-world feasibility of screening individuals accessing secondary mental healthcare at the South London and Maudsley NHS Trust. The primary outcome was adherence of clinicians to automatic EHR screening, defined by the proportion of clinicians who responded to alerts from the risk calculator, over those contacted.<h4>Results</h4>In-vitro phase: implementation barriers were identified/overcome with clinician and service user engagement, and the calculator was successfully integrated into the local EHR through the CogStack platform. In-vivo phase: 3722 individuals were automatically screened and 115 were detected. Clinician adherence was 74% without outreach and 85% with outreach. One-third of clinicians responded to the first email (37.1%) or phone calls (33.7%). Among those detected, cumulative risk of developing psychosis was 12% at six-month follow-up.<h4>Conclusion</h4>This is the first implementation study suggesting that combining precision psychiatry and EHR methods to improve detection of individuals with emerging psychosis is feasible. Future psychiatric implementation research is urgently needed.",,doi:https://doi.org/10.1016/j.schres.2020.05.007; doi:https://doi.org/10.1016/j.schres.2020.05.007; html:https://europepmc.org/articles/PMC7875179
 39119725,https://doi.org/10.1161/circgen.124.004755,Proteome- and Transcriptome-Wide Genetic Analysis Identifies Biological Pathways and Candidate Drug Targets for Preeclampsia.,"Ardissino M, Truong B, Slob EAW, Schuermans A, Yoshiji S, Morley AP, Burgess S, Ng FS, de Marvao A, Natarajan P, Nicolaides K, Gaziano L, Butterworth A, Honigberg MC.",,Circulation. Genomic and precision medicine,2024,2024-08-09,N,Genes; Proteins; Genetics; Preeclampsia; risk factors,,,"<h4>Background</h4>Preeclampsia is a leading cause of maternal and perinatal morbidity and mortality. However, the current understanding of its underlying biological pathways remains limited.<h4>Methods</h4>In this study, we performed a cross-platform proteome- and transcriptome-wide genetic analysis aimed at evaluating the causal relevance of >2000 circulating proteins with preeclampsia, supported by data on the expression of over 15 000 genes across 36 tissues leveraging large-scale preeclampsia genetic association data from women of European ancestry.<h4>Results</h4>We demonstrate genetic associations of 18 circulating proteins with preeclampsia (SULT1A1 [sulfotransferase 1A1], SH2B3 [SH2B adapter protein 3], SERPINE2 [serpin family E member 2], RGS18 [regulator of G-protein signaling 18], PZP [pregnancy zone protein], NOTUM [notum, palmitoleoyl-protein carboxylesterase], METAP1 [methionyl aminopeptidase 1], MANEA [mannosidase endo-alpha], jun-D [JunD proto-oncogene], GDF15 [growth differentiation factor 15], FGL1 [fibrinogen like 1], FGF5 [fibroblast growth factor 5], FES [FES proto-oncogene], APOBR [apolipoprotein B receptor], ANP [natriuretic peptide A], ALDH-E2 [aldehyde dehydrogenase 2 family member], ADAMTS13 [ADAM metallopeptidase with thrombospondin type 1 motif 13], and 3MG [N-methylpurine DNA glycosylase]), among which 11 were either directly or indirectly supported by gene expression data, 9 were supported by Bayesian colocalization analyses, and 5 (SERPINE2, PZP, FGF5, FES, and ANP) were supported by all lines of evidence examined. Protein interaction mapping identified potential shared biological pathways through natriuretic peptide signaling, blood pressure regulation, immune tolerance, and thrombin activity regulation.<h4>Conclusions</h4>This investigation identified multiple targetable proteins linked to cardiovascular, inflammatory, and coagulation pathways, with SERPINE2, PZP, FGF5, FES, and ANP identified as pivotal proteins with likely causal roles in the development of preeclampsia. The identification of these potential targets may guide the development of targeted therapies for preeclampsia.",,doi:https://doi.org/10.1161/CIRCGEN.124.004755
-37438684,https://doi.org/10.1186/s12874-023-01935-3,Estimating medication adherence from Electronic Health Records: comparing methods for mining and processing asthma treatment prescriptions.,"Tibble H, Sheikh A, Tsanas A.",,BMC medical research methodology,2023,2023-07-12,Y,Adherence; Asthma; Compliance; corticosteroid; Electronic Health Records,,,"<h4>Background</h4>Medication adherence is usually defined as the extent of the agreement between the medication regimen agreed to by patients with their healthcare provider and the real-world implementation. Proactive identification of those with poor adherence may be useful to identify those with poor disease control and offers the opportunity for ameliorative action. Adherence can be estimated from Electronic Health Records (EHRs) by comparing medication dispensing records to the prescribed regimen. Several methods have been developed in the literature to infer adherence from EHRs, however there is no clear consensus on what should be considered the gold standard in each use case. Our objectives were to critically evaluate different measures of medication adherence in a large longitudinal Scottish EHR dataset. We used asthma, a chronic condition with high prevalence and high rates of non-adherence, as a case study.<h4>Methods</h4>Over 1.6 million asthma controllers were prescribed for our cohort of 91,334 individuals, between January 2009 and March 2017. Eight adherence measures were calculated, and different approaches to estimating the amount of medication supply available at any time were compared.<h4>Results</h4>Estimates from different measures of adherence varied substantially. Three of the main drivers of the differences between adherence measures were the expected duration (if taken as in accordance with the dose directions), whether there was overlapping supply between prescriptions, and whether treatment had been discontinued. However, there are also wider, study-related, factors which are crucial to consider when comparing the adherence measures.<h4>Conclusions</h4>We evaluated the limitations of various medication adherence measures, and highlight key considerations about the underlying data, condition, and population to guide researchers choose appropriate adherence measures. This guidance will enable researchers to make more informed decisions about the methodology they employ, ensuring that adherence is captured in the most meaningful way for their particular application needs.",,pdf:https://bmcmedresmethodol.biomedcentral.com/counter/pdf/10.1186/s12874-023-01935-3; doi:https://doi.org/10.1186/s12874-023-01935-3; html:https://europepmc.org/articles/PMC10337150; pdf:https://europepmc.org/articles/PMC10337150?pdf=render
 33830993,https://doi.org/10.1371/journal.pgen.1009428,Sex-stratified genome-wide association study of multisite chronic pain in UK Biobank.,"Johnston KJA, Ward J, Ray PR, Adams MJ, McIntosh AM, Smith BH, Strawbridge RJ, Price TJ, Smith DJ, Nicholl BI, Bailey MES.",,PLoS genetics,2021,2021-04-08,Y,,,,"Chronic pain is highly prevalent worldwide and imparts a significant socioeconomic and public health burden. Factors influencing susceptibility to, and mechanisms of, chronic pain development, are not fully understood, but sex is thought to play a significant role, and chronic pain is more prevalent in women than in men. To investigate sex differences in chronic pain, we carried out a sex-stratified genome-wide association study of Multisite Chronic Pain (MCP), a derived chronic pain phenotype, in UK Biobank on 178,556 men and 209,093 women, as well as investigating sex-specific genetic correlations with a range of psychiatric, autoimmune and anthropometric phenotypes and the relationship between sex-specific polygenic risk scores for MCP and chronic widespread pain. We also assessed whether MCP-associated genes showed expression pattern enrichment across tissues. A total of 123 SNPs at five independent loci were significantly associated with MCP in men. In women, a total of 286 genome-wide significant SNPs at ten independent loci were discovered. Meta-analysis of sex-stratified GWAS outputs revealed a further 87 independent associated SNPs. Gene-level analyses revealed sex-specific MCP associations, with 31 genes significantly associated in females, 37 genes associated in males, and a single gene, DCC, associated in both sexes. We found evidence for sex-specific pleiotropy and risk for MCP was found to be associated with chronic widespread pain in a sex-differential manner. Male and female MCP were highly genetically correlated, but at an rg of significantly less than 1 (0.92). All 37 male MCP-associated genes and all but one of 31 female MCP-associated genes were found to be expressed in the dorsal root ganglion, and there was a degree of enrichment for expression in sex-specific tissues. Overall, the findings indicate that sex differences in chronic pain exist at the SNP, gene and transcript abundance level, and highlight possible sex-specific pleiotropy for MCP. Results support the proposition of a strong central nervous-system component to chronic pain in both sexes, additionally highlighting a potential role for the DRG and nociception.",,pdf:https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1009428&type=printable; doi:https://doi.org/10.1371/journal.pgen.1009428; html:https://europepmc.org/articles/PMC8031124; pdf:https://europepmc.org/articles/PMC8031124?pdf=render
+37438684,https://doi.org/10.1186/s12874-023-01935-3,Estimating medication adherence from Electronic Health Records: comparing methods for mining and processing asthma treatment prescriptions.,"Tibble H, Sheikh A, Tsanas A.",,BMC medical research methodology,2023,2023-07-12,Y,Adherence; Asthma; Compliance; corticosteroid; Electronic Health Records,,,"<h4>Background</h4>Medication adherence is usually defined as the extent of the agreement between the medication regimen agreed to by patients with their healthcare provider and the real-world implementation. Proactive identification of those with poor adherence may be useful to identify those with poor disease control and offers the opportunity for ameliorative action. Adherence can be estimated from Electronic Health Records (EHRs) by comparing medication dispensing records to the prescribed regimen. Several methods have been developed in the literature to infer adherence from EHRs, however there is no clear consensus on what should be considered the gold standard in each use case. Our objectives were to critically evaluate different measures of medication adherence in a large longitudinal Scottish EHR dataset. We used asthma, a chronic condition with high prevalence and high rates of non-adherence, as a case study.<h4>Methods</h4>Over 1.6 million asthma controllers were prescribed for our cohort of 91,334 individuals, between January 2009 and March 2017. Eight adherence measures were calculated, and different approaches to estimating the amount of medication supply available at any time were compared.<h4>Results</h4>Estimates from different measures of adherence varied substantially. Three of the main drivers of the differences between adherence measures were the expected duration (if taken as in accordance with the dose directions), whether there was overlapping supply between prescriptions, and whether treatment had been discontinued. However, there are also wider, study-related, factors which are crucial to consider when comparing the adherence measures.<h4>Conclusions</h4>We evaluated the limitations of various medication adherence measures, and highlight key considerations about the underlying data, condition, and population to guide researchers choose appropriate adherence measures. This guidance will enable researchers to make more informed decisions about the methodology they employ, ensuring that adherence is captured in the most meaningful way for their particular application needs.",,pdf:https://bmcmedresmethodol.biomedcentral.com/counter/pdf/10.1186/s12874-023-01935-3; doi:https://doi.org/10.1186/s12874-023-01935-3; html:https://europepmc.org/articles/PMC10337150; pdf:https://europepmc.org/articles/PMC10337150?pdf=render
 33749694,https://doi.org/,The evidence for assessing frailty and sarcopenia in an acute medical unit: a systematic review.,"Kamwa V, Seccombe A, Sapey E.",,Acute medicine,2021,2021-01-01,N,,,,"<h4>Background/objectives</h4>A systematic review was conducted to assess if frailty and sarcopenia were associated with poorer outcomes in older adults admitted to an acute medical unit (AMU).<h4>Methods</h4>Eligible studies included older adults with an unplanned admission to an AMU and included a measure of frailty or sarcopenia, completed within 72 hours of admission. Risk of bias was assessed.<h4>Results</h4>Of 1659 identified articles, 16 were included (4 on sarcopenia and 12 on frailty). There was significant study heterogeneity. Overall, frailty and sarcopenia were associated with worse outcomes. Targeted interventions appeared to improve outcomes.<h4>Conclusion</h4>Current evidence suggests some benefit in screening older adults admitted to an AMU for frailty and sarcopenia. However, further studies are required before clinical adoption.",,
 37757876,https://doi.org/10.1097/ede.0000000000001649,Comparative Effectiveness of Dynamic Treatment Strategies for Medication Use and Dosage: Emulating a Target Trial Using Observational Data.,"Birnie K, Tomson C, Caskey FJ, Ben-Shlomo Y, Nitsch D, Casula A, Murray EJ, Sterne JAC.",,"Epidemiology (Cambridge, Mass.)",2023,2023-09-26,N,,,,"<h4>Background</h4>Availability of detailed data from electronic health records (EHRs) has increased the potential to examine the comparative effectiveness of dynamic treatment strategies using observational data. Inverse probability (IP) weighting of dynamic marginal structural models can control for time-varying confounders. However, IP weights for continuous treatments may be sensitive to model choice.<h4>Methods</h4>We describe a target trial comparing strategies for treating anemia with darbepoetin in hemodialysis patients using EHR data from the UK Renal Registry 2004 to 2016. Patients received a specified dose (microgram/week) or did not receive darbepoetin. We compared 4 methods for modeling time-varying treatment: (A) logistic regression for zero dose, standard linear regression for log dose; (B) logistic regression for zero dose, heteroscedastic linear regression for log dose; (C) logistic regression for zero dose, heteroscedastic linear regression for log dose, multinomial regression for patients who recently received very low or high doses; and (D) ordinal logistic regression.<h4>Results</h4>For this dataset, method (C) was the only approach that provided a robust estimate of the mortality hazard ratio (HR), with less-extreme weights in a fully weighted analysis and no substantial change of the HR point estimate after weight truncation. After truncating IP weights at the 95th percentile, estimates were similar across the methods.<h4>Conclusions</h4>EHR data can be used to emulate target trials estimating the comparative effectiveness of dynamic strategies adjusting treatment to evolving patient characteristics. However, model checking, monitoring of large weights, and adaptation of model strategies to account for these is essential if an aspect of treatment is continuous.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7615288; doi:https://doi.org/10.1097/EDE.0000000000001649; html:https://europepmc.org/articles/PMC7615288; pdf:https://europepmc.org/articles/PMC7615288?pdf=render; doi:https://doi.org/10.1097/ede.0000000000001649
 35016872,https://doi.org/10.1016/j.apmr.2021.12.014,Chronic Physical Health Conditions After Injury: A Comparison of Prevalence and Risk in People With Orthopedic Major Trauma and Other Types of Injury.,"Gelaw AY, Gabbe BJ, Ekegren CL.",,Archives of physical medicine and rehabilitation,2022,2022-01-10,N,Cardiovascular diseases; Rehabilitation; Chronic disease; wounds and injuries; Multiple Trauma,,,"<h4>Objectives</h4>To determine (1) the prevalence of chronic physical health conditions reported preinjury, at the time of injury, up to 1 year postinjury, and 1 to 5 years postinjury; and (2) the risk of chronic physical health conditions reported 1 to 5 years postinjury in people with orthopedic and other types of major trauma.<h4>Design</h4>Cohort study using linked trauma registry and health administrative datasets.<h4>Setting</h4>This study used linked data from the Victorian State Trauma Registry (VSTR), the Victorian Registry of Births, Deaths and Marriages (BDM), the Victorian Admitted Episodes Dataset (VAED), and the Victorian Emergency Minimum Dataset (VEMD).<h4>Participants</h4>Major trauma patients (N=28,522) aged 18 years and older who were registered by the VSTR, with dates of injury from 2007 to 2016, and who survived to at least 1 year after injury, were included in this study. Major trauma cases were classified into 4 groups: (1) orthopedic injury, (2) severe traumatic brain injury (s-TBI), (3) spinal cord injury, and (4) other major trauma.<h4>Intervention</h4>Not applicable.<h4>Main outcome measure</h4>Prevalence of chronic physical health conditions.<h4>Results</h4>The cumulative prevalence of any chronic physical health condition for all participants was 69.3%. The s-TBI group had the highest cumulative prevalence of conditions. The most common conditions were arthritis and arthropathies, cancer, and cardiovascular diseases. Preinjury chronic conditions were most common in people with s-TBI (19.3%) and were least common in people with other types of major trauma (6.6%). The highest prevalence of new-onset conditions after injury was found in people with s-TBI (21.7%) and orthopedic major trauma (21.4%), whereas the lowest prevalence was found in people with other types of major trauma (9.2%). For the orthopedic injury group, there were no significant differences in the adjusted risk of conditions reported 1 to 5 years postinjury compared with other major trauma groups.<h4>Conclusions</h4>Chronic physical health conditions were common among all injury groups. There was no significant difference in the risk of chronic conditions among injury groups. Rehabilitation practitioners should be aware of the risk of chronic conditions in people with orthopedic and other types of major trauma. Long-term follow-up care after injury should include prevention and treatment of chronic conditions.",,doi:https://doi.org/10.1016/j.apmr.2021.12.014
-31345952,https://doi.org/10.1136/heartjnl-2018-313855,Do beta-blockers and inhibitors of the renin-angiotensin aldosterone system improve outcomes in patients with heart failure and left ventricular ejection fraction >40%?,"Lumbers RT, Martin N, Manoharan K, Thomas J, Davies LC.",,Heart (British Cardiac Society),2019,2019-07-25,N,Pharmacology; Meta-analysis; epidemiology; Heart Failure With Preserved Ejection Fraction; Systemic Review,,,,,doi:https://doi.org/10.1136/heartjnl-2018-313855
 34734970,https://doi.org/10.1001/jamaophthalmol.2021.4601,"Association of Smoking, Alcohol Consumption, Blood Pressure, Body Mass Index, and Glycemic Risk Factors With Age-Related Macular Degeneration: A Mendelian Randomization Study.","Kuan V, Warwick A, Hingorani A, Tufail A, Cipriani V, Burgess S, Sofat R, International AMD Genomics Consortium (IAMDGC).",,JAMA ophthalmology,2021,2021-12-01,Y,,,,"<h4>Importance</h4>Advanced age-related macular degeneration (AMD) is a leading cause of blindness in Western countries. Causal, modifiable risk factors need to be identified to develop preventive measures for advanced AMD.<h4>Objective</h4>To assess whether smoking, alcohol consumption, blood pressure, body mass index, and glycemic traits are associated with increased risk of advanced AMD.<h4>Design, setting, participants</h4>This study used 2-sample mendelian randomization. Genetic instruments composed of variants associated with risk factors at genome-wide significance (P < 5 × 10-8) were obtained from published genome-wide association studies. Summary-level statistics for these instruments were obtained for advanced AMD from the International AMD Genomics Consortium 2016 data set, which consisted of 16 144 individuals with AMD and 17 832 control individuals. Data were analyzed from July 2020 to September 2021.<h4>Exposures</h4>Smoking initiation, smoking cessation, lifetime smoking, age at smoking initiation, alcoholic drinks per week, body mass index, systolic and diastolic blood pressure, type 2 diabetes, glycated hemoglobin, fasting glucose, and fasting insulin.<h4>Main outcomes and measures</h4>Advanced AMD and its subtypes, geographic atrophy (GA), and neovascular AMD.<h4>Results</h4>A 1-SD increase in logodds of genetically predicted smoking initiation was associated with higher risk of advanced AMD (odds ratio [OR], 1.26; 95% CI, 1.13-1.40; P < .001), while a 1-SD increase in logodds of genetically predicted smoking cessation (former vs current smoking) was associated with lower risk of advanced AMD (OR, 0.66; 95% CI, 0.50-0.87; P = .003). Genetically predicted increased lifetime smoking was associated with increased risk of advanced AMD (OR per 1-SD increase in lifetime smoking behavior, 1.32; 95% CI, 1.09-1.59; P = .004). Genetically predicted alcohol consumption was associated with higher risk of GA (OR per 1-SD increase of log-transformed alcoholic drinks per week, 2.70; 95% CI, 1.48-4.94; P = .001). There was insufficient evidence to suggest that genetically predicted blood pressure, body mass index, and glycemic traits were associated with advanced AMD.<h4>Conclusions and relevance</h4>This study provides genetic evidence that increased alcohol intake may be a causal risk factor for GA. As there are currently no known treatments for GA, this finding has important public health implications. These results also support previous observational studies associating smoking behavior with risk of advanced AMD, thus reinforcing existing public health messages regarding the risk of blindness associated with smoking.",,pdf:https://jamanetwork.com/journals/jamaophthalmology/articlepdf/2785704/jamaophthalmology_kuan_2021_oi_210068_1639510445.31311.pdf; doi:https://doi.org/10.1001/jamaophthalmol.2021.4601; html:https://europepmc.org/articles/PMC8569599
-31361079,https://doi.org/10.1111/1742-6723.13361,"Animal-vehicle collisions in Victoria, Australia: An under-recognised cause of road traffic crashes.","Ang JY, Gabbe B, Cameron P, Beck B.",,Emergency medicine Australasia : EMA,2019,2019-07-30,N,Injury; Prevention; Traffic; Motor Vehicle,,,"<h4>Objective</h4>Non-fatal injuries sustained from animal-vehicle collisions are a globally under-recognised road safety issue, with limited data on these crash types. The present study aimed to quantify the number and causes of major trauma events resulting from animal-vehicle collisions.<h4>Methods</h4>The study was a retrospective analysis of major trauma cases occurring in Victoria, Australia, between 2007 and 2016, using data from the population-based Victorian State Trauma Registry. To identify animal-vehicle collisions, Victorian State Trauma Registry injury codes were combined with text-mining of the text description of the injury event.<h4>Results</h4>Over the 10 year period, there were 152 major trauma patients who were admitted to Victorian trauma-receiving hospitals due to vehicle collisions with animals. The crude population-based incidence rate for animal-vehicle collisions increased by 6.7% per year (incidence rate ratio 1.07; 95% confidence interval 1.01-1.13; P = 0.02).<h4>Conclusion</h4>Development of systematic recording methods of animal-vehicle collisions will improve reporting of these crash types to assist future studies in implementing effective countermeasures.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/1742-6723.13361; doi:https://doi.org/10.1111/1742-6723.13361
 33127858,https://doi.org/10.1681/asn.2020050679,Conventional and Genetic Evidence on the Association between Adiposity and CKD.,"Zhu P, Herrington WG, Haynes R, Emberson J, Landray MJ, Sudlow CLM, Woodward M, Baigent C, Lewington S, Staplin N.",,Journal of the American Society of Nephrology : JASN,2021,2020-10-30,N,Obesity; body mass index; Chronic Kidney Disease; Mendelian Randomization; Central Adiposity; Epidemiology And Outcomes,,,"<h4>Background</h4>The size of any causal contribution of central and general adiposity to CKD risk and the underlying mechanism of mediation are unknown.<h4>Methods</h4>Data from 281,228 UK Biobank participants were used to estimate the relevance of waist-to-hip ratio and body mass index (BMI) to CKD prevalence. Conventional approaches used logistic regression. Genetic analyses used Mendelian randomization (MR) and data from 394 waist-to-hip ratio and 773 BMI-associated loci. Models assessed the role of known mediators (diabetes mellitus and BP) by adjusting for measured values (conventional analyses) or genetic associations of the selected loci (multivariable MR).<h4>Results</h4>Evidence of CKD was found in 18,034 (6.4%) participants. Each 0.06 higher measured waist-to-hip ratio and each 5-kg/m<sup>2</sup> increase in BMI were associated with 69% (odds ratio, 1.69; 95% CI, 1.64 to 1.74) and 58% (1.58; 1.55 to 1.62) higher odds of CKD, respectively. In analogous MR analyses, each 0.06-genetically-predicted higher waist-to-hip ratio was associated with a 29% (1.29; 1.20 to 1.38) increased odds of CKD, and each 5-kg/m<sup>2</sup> genetically-predicted higher BMI was associated with a 49% (1.49; 1.39 to 1.59) increased odds. After adjusting for diabetes and measured BP, chi-squared values for associations for waist-to-hip ratio and BMI fell by 56%. In contrast, mediator adjustment using multivariable MR found 83% and 69% reductions in chi-squared values for genetically-predicted waist-to-hip ratio and BMI models, respectively.<h4>Conclusions</h4>Genetic analyses suggest that conventional associations between central and general adiposity with CKD are largely causal. However, conventional approaches underestimate mediating roles of diabetes, BP, and their correlates. Genetic approaches suggest these mediators explain most of adiposity-CKD-associated risk.",,pdf:https://jasn.asnjournals.org/content/jnephrol/32/1/127.full.pdf; doi:https://doi.org/10.1681/ASN.2020050679; html:https://europepmc.org/articles/PMC7894659; doi:https://doi.org/10.1681/asn.2020050679
+31345952,https://doi.org/10.1136/heartjnl-2018-313855,Do beta-blockers and inhibitors of the renin-angiotensin aldosterone system improve outcomes in patients with heart failure and left ventricular ejection fraction >40%?,"Lumbers RT, Martin N, Manoharan K, Thomas J, Davies LC.",,Heart (British Cardiac Society),2019,2019-07-25,N,Pharmacology; Meta-analysis; epidemiology; Heart Failure With Preserved Ejection Fraction; Systemic Review,,,,,doi:https://doi.org/10.1136/heartjnl-2018-313855
+31361079,https://doi.org/10.1111/1742-6723.13361,"Animal-vehicle collisions in Victoria, Australia: An under-recognised cause of road traffic crashes.","Ang JY, Gabbe B, Cameron P, Beck B.",,Emergency medicine Australasia : EMA,2019,2019-07-30,N,Injury; Prevention; Traffic; Motor Vehicle,,,"<h4>Objective</h4>Non-fatal injuries sustained from animal-vehicle collisions are a globally under-recognised road safety issue, with limited data on these crash types. The present study aimed to quantify the number and causes of major trauma events resulting from animal-vehicle collisions.<h4>Methods</h4>The study was a retrospective analysis of major trauma cases occurring in Victoria, Australia, between 2007 and 2016, using data from the population-based Victorian State Trauma Registry. To identify animal-vehicle collisions, Victorian State Trauma Registry injury codes were combined with text-mining of the text description of the injury event.<h4>Results</h4>Over the 10 year period, there were 152 major trauma patients who were admitted to Victorian trauma-receiving hospitals due to vehicle collisions with animals. The crude population-based incidence rate for animal-vehicle collisions increased by 6.7% per year (incidence rate ratio 1.07; 95% confidence interval 1.01-1.13; P = 0.02).<h4>Conclusion</h4>Development of systematic recording methods of animal-vehicle collisions will improve reporting of these crash types to assist future studies in implementing effective countermeasures.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/1742-6723.13361; doi:https://doi.org/10.1111/1742-6723.13361
 30972781,https://doi.org/10.1111/apt.15232,Early and late mortality following unscheduled admissions for severe liver disease across England and Wales.,"Roberts SE, John A, Brown J, Napier DJ, Lyons RA, Williams JG.",,Alimentary pharmacology & therapeutics,2019,2019-04-11,Y,,,,"<h4>Background</h4>There is a known shortfall in hepatology service resources across England and Wales.<h4>Aim</h4>To investigate early and late mortality following unscheduled admissions for severe liver disease, overall and by cause of death, and to determine how mortality is related to admissions to transplant centres, transplant surgery, hospital size, consultant specialty, patient socio-demographics, seasonal and geographical factors.<h4>Methods</h4>Cohorts of people with a first unscheduled admission for severe liver disease across England and Wales from 2004, based on record linkage of national inpatient and mortality data.<h4>Findings</h4>Mortality for alcoholic liver disease and hepatic failure was 23.4% and 35.4% respectively at 60 days and 61.8% and 57.1% at 5 years. Standardised mortality ratios (SMRs) were extremely high at 60 days (184 and 117 respectively) and remained highly increased at 5 years (16.7 and 6.3). Mortality at 5 years was most elevated from liver disease, viral hepatitis and varices. The 60-day mortality was significantly lower for patients seen by consultant hepatologists and gastroenterologists. Both early and late mortality were significantly reduced for patients admitted to transplant centres or larger hospitals, who received a liver transplant, or were resident in London. Early mortality was significantly higher for patients admitted in winter and autumn, while elevated mortality among the most vs least deprived quintile increased with longer follow-up.<h4>Conclusions</h4>The study shows a very poor prognosis for people with unscheduled hospitalisation for severe liver disease. The findings suggest that access to specialist expertise and services improves survival, both in the short and long term.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/apt.15232; doi:https://doi.org/10.1111/apt.15232; html:https://europepmc.org/articles/PMC6519290; pdf:https://europepmc.org/articles/PMC6519290?pdf=render
 32355555,https://doi.org/10.7189/jogh.10.010104,COVID-19 must catalyse key global natural experiments.,"Been JV, Sheikh A.",,Journal of global health,2020,2020-06-01,Y,,,,,"""Been and Sheikh’s editorial about COVID-19, outlines the importance of two natural experiments: a- how different countries responded to the pandemic and its effects and b- impact of improvements in air quality on human and planetary health.""",doi:https://doi.org/10.7189/jogh.10.010104; doi:https://doi.org/10.7189/jogh.10.010104; html:https://europepmc.org/articles/PMC7179980; pdf:https://europepmc.org/articles/PMC7179980?pdf=render
 30648344,https://doi.org/10.1002/cnm.3180,A semi-active human digital twin model for detecting severity of carotid stenoses from head vibration-A coupled computational mechanics and computer vision method.,"Chakshu NK, Carson J, Sazonov I, Nithiarasu P.",,International journal for numerical methods in biomedical engineering,2019,2019-02-20,Y,Computer vision; Blood flow; Systemic Circulation; Carotid Stenoses; Digital Twin; Biomechanical Vibrations; Face Video,Applied Analytics,,"In this work, we propose a methodology to detect the severity of carotid stenosis from a video of a human face with the help of a coupled blood flow and head vibration model. This semi-active digital twin model is an attempt to link noninvasive video of a patient face to the percentage of carotid occlusion. The pulsatile nature of blood flow through the carotid arteries induces a subtle head vibration. This vibration is a potential indicator of carotid stenosis severity, and it is exploited in the present study. A head vibration model has been proposed in the present work that is linked to the forces generated by blood flow with or without occlusion. The model is used to generate a large number of virtual head vibration data for different degrees of occlusion. In order to determine the in vivo head vibration, a computer vision algorithm is adopted to use human face videos. The in vivo vibrations are compared against the virtual vibration data generated from the coupled computational blood flow/vibration model. A comparison of the in vivo vibration is made against the virtual data to find the best fit between in vivo and virtual data. The preliminary results on healthy subjects and a patient clearly indicate that the model is accurate and it possesses the potential for detecting approximate severity of carotid artery stenoses.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cnm.3180; doi:https://doi.org/10.1002/cnm.3180; html:https://europepmc.org/articles/PMC6593817; pdf:https://europepmc.org/articles/PMC6593817?pdf=render
+34642218,https://doi.org/10.1136/bcr-2021-243424,Neurological injury from virtual reality mishap.,"Warner N, Teo JT.",,BMJ case reports,2021,2021-10-12,Y,Cranial nerves; Neurology; Neurological Injury; Trauma Cns /Pns,,,"Consumer virtual reality systems are becoming increasingly popular with the increasing availability of devices and gamified technologies. Self-sustained injury risks exist with the use of this technology in the uncontrolled home environment, however, the public awareness of these risks may not be recognised. We present a case of a low- impact virtual reality fall resulting in spinal cord injury, hypoglossal nerve injury, vertebral artery dissection and traumatic brain injury.",,pdf:https://casereports.bmj.com/content/bmjcr/14/10/e243424.full.pdf; doi:https://doi.org/10.1136/bcr-2021-243424; html:https://europepmc.org/articles/PMC8513217; pdf:https://europepmc.org/articles/PMC8513217?pdf=render
 38894942,https://doi.org/10.1177/20552076241258276,A text-based conversational agent for asthma support: Mixed-methods feasibility study.,"Cook D, Peters D, Moradbakhti L, Su T, Da Re M, Schuller BW, Quint J, Wong E, Calvo RA.",,Digital health,2024,2024-01-01,Y,Asthma; Ehealth; Digital Health; Healthcare Technology; Whatsapp; Chatbots; Conversational Agents,,,"<h4>Objective</h4>Millions of people in the UK have asthma, yet 70% do not access basic care, leading to the largest number of asthma-related deaths in Europe. Chatbots may extend the reach of asthma support and provide a bridge to traditional healthcare. This study evaluates 'Brisa', a chatbot designed to improve asthma patients' self-assessment and self-management.<h4>Methods</h4>We recruited 150 adults with an asthma diagnosis to test our chatbot. Participants were recruited over three waves through social media and a research recruitment platform. Eligible participants had access to 'Brisa' via a WhatsApp or website version for 28 days and completed entry and exit questionnaires to evaluate user experience and asthma control. Weekly symptom tracking, user interaction metrics, satisfaction measures, and qualitative feedback were utilised to evaluate the chatbot's usability and potential effectiveness, focusing on changes in asthma control and self-reported behavioural improvements.<h4>Results</h4>74% of participants engaged with 'Brisa' at least once. High task completion rates were observed: asthma attack risk assessment (86%), voice recording submission (83%) and asthma control tracking (95.5%). Post use, an 8% improvement in asthma control was reported. User satisfaction surveys indicated positive feedback on helpfulness (80%), privacy (87%), trustworthiness (80%) and functionality (84%) but highlighted a need for improved conversational depth and personalisation.<h4>Conclusions</h4>The study indicates that chatbots are effective for asthma support, demonstrated by the high usage of features like risk assessment and control tracking, as well as a statistically significant improvement in asthma control. However, lower satisfaction in conversational flexibility highlights rising expectations for chatbot fluency, influenced by advanced models like ChatGPT. Future health-focused chatbots must balance conversational capability with accuracy and safety to maintain engagement and effectiveness.",,doi:https://doi.org/10.1177/20552076241258276; html:https://europepmc.org/articles/PMC11185032; pdf:https://europepmc.org/articles/PMC11185032?pdf=render
 34143303,https://doi.org/10.1007/s00787-021-01817-3,National record-linkage study of hospital admissions for schizophrenia in childhood and adolescence in England.,"Seminog O, Hoang U, Goldacre M, James A.",,European child & adolescent psychiatry,2022,2021-06-18,Y,Schizophrenia; Children; epidemiology; Electronic Records; Childhood Onset,,,"<h4>Background</h4>There is a lack of information on changes in hospital admission rates for childhood-onset schizophrenia (COS), or on patient characteristics, to inform clinical research and health service provision.<h4>Aims</h4>To report age- and sex-specific incidence rates of hospital admissions and day patient care for schizophrenia (ICD-10 F20) and non-affective psychosis (ICD-10 F20-29), by year of occurrence and age, in childhood and adolescence.<h4>Methods</h4>Population-based study using person-linked data for England (available 2001-2016); time-periods in single years and 4-year groups.<h4>Results</h4>Hospitalised incidence for schizophrenia increased with increasing age, from 0.03 (95% confidence interval (CI) 0.02-0.05) and 0.01 (0-0.01) per 100,000 in, respectively, males and females aged 5-12 years, to 3.67 (3.44-3.91) in males and 1.58 (1.43-1.75) in females aged 13-17 years. There was no gender difference in hospitalised incidence rates in children aged 5-12, but in 13-17 years old, there was a male excess. Rates for schizophrenia were stable over time in 5-12 years old. In ages 13-17, rates for schizophrenia decreased between 2001-2004 and 2013-2016 in males, from 6.65 (6.04-7.31) down to 1.40 (1.13-1.73), and in females from 2.42 (2.05-2.83) to 1.18 (0.92-1.48). The hospitalisation rates for schizophrenia and non-affective psychosis, combined, in 13-17 years old decreased in males from 14.20 (13.30-15.14) in 2001-2004 to 10.77 (9.97-11.60) in 2013-2016, but increased in females from 7.49 (6.83-8.20) to 10.16 (9.38-11.00).<h4>Conclusions</h4>The study confirms that childhood-onset schizophrenia is extremely rare, with only 32 cases identified over a 15-year period in the whole of England. The incidence of schizophrenia and non-affective psychosis increased substantially in adolescence; however, the marked reduction in the proportion of those diagnosed with schizophrenia in this age group suggests a possible change in diagnostic practice.",,pdf:https://link.springer.com/content/pdf/10.1007/s00787-021-01817-3.pdf; doi:https://doi.org/10.1007/s00787-021-01817-3; html:https://europepmc.org/articles/PMC9663394; pdf:https://europepmc.org/articles/PMC9663394?pdf=render
-34642218,https://doi.org/10.1136/bcr-2021-243424,Neurological injury from virtual reality mishap.,"Warner N, Teo JT.",,BMJ case reports,2021,2021-10-12,Y,Cranial nerves; Neurology; Neurological Injury; Trauma Cns /Pns,,,"Consumer virtual reality systems are becoming increasingly popular with the increasing availability of devices and gamified technologies. Self-sustained injury risks exist with the use of this technology in the uncontrolled home environment, however, the public awareness of these risks may not be recognised. We present a case of a low- impact virtual reality fall resulting in spinal cord injury, hypoglossal nerve injury, vertebral artery dissection and traumatic brain injury.",,pdf:https://casereports.bmj.com/content/bmjcr/14/10/e243424.full.pdf; doi:https://doi.org/10.1136/bcr-2021-243424; html:https://europepmc.org/articles/PMC8513217; pdf:https://europepmc.org/articles/PMC8513217?pdf=render
 34409990,https://doi.org/10.1093/dote/doab058,Demographic and lifestyle risk factors for gastroesophageal reflux disease and Barrett's esophagus in Australia.,"Wang SE, Kendall BJ, Hodge AM, Dixon-Suen SC, Dashti SG, Makalic E, Williamson EM, Thomas RJS, Giles GG, English DR.",,Diseases of the esophagus : official journal of the International Society for Diseases of the Esophagus,2022,2022-01-01,N,Risk factor; Barrett’s esophagus; epidemiology; Gastroesophageal Reflux (Gerd),,,"We examined demographic and lifestyle risk factors for incidence of gastroesophageal reflux disease (GERD) and Barrett's esophagus (BE) in an Australian cohort of 20,975 participants aged 40-63 at recruitment (1990-1994). Information on GERD and BE was collected between 2007 and 2010. GERD symptoms were defined as self-reported heartburn or acid regurgitation. BE was defined as endoscopically confirmed columnar-lined esophagus. Risk factors for developing GERD symptoms, BE diagnosis, age at symptom onset, and age at BE diagnosis were quantified using regression. During a mean follow-up of 15.8 years, risk of GERD symptoms was 7.5% (n = 1,318) for daily, 7.5% (n = 1,333) for 2-6 days/week, and 4.3% (n = 751) for 1 day/week. There were 210 (1.0%) endoscopically diagnosed BE cases, of whom 141 had histologically confirmed esophageal intestinal metaplasia. Female sex, younger age, lower socioeconomic position (SEP) and educational attainment, and former smoking were associated with higher GERD risk. Male sex and smoking were associated with earlier GERD symptom onset. Men, older participants, those with higher SEP, and former smokers were at higher BE risk. There was some evidence higher SEP was associated with earlier BE diagnosis. GERD and BE had different demographic risk factors but shared similar lifestyle factors. Earlier GERD symptom onset for men and smokers might have contributed to higher BE risk. The SEP patterns observed for GERD and BE suggest potential inequity in access to care. These findings would be important in the development of clinical risk prediction models for early detection of BE.",,pdf:https://academic.oup.com/dote/article-pdf/35/1/doab058/42098674/doab058.pdf; doi:https://doi.org/10.1093/dote/doab058
-36729586,https://doi.org/10.2196/42965,Assessing the Feasibility of a Text-Based Conversational Agent for Asthma Support: Protocol for a Mixed Methods Observational Study.,"Calvo RA, Peters D, Moradbakhti L, Cook D, Rizos G, Schuller B, Kallis C, Wong E, Quint J.",,JMIR research protocols,2023,2023-02-02,Y,Artificial intelligence; Health; Asthma; Health education; Well-being; Behavior Change; Conversational Agent; Chatbot,,,"<h4>Background</h4>Despite efforts, the UK death rate from asthma is the highest in Europe, and 65% of people with asthma in the United Kingdom do not receive the professional care they are entitled to. Experts have recommended the use of digital innovations to help address the issues of poor outcomes and lack of care access. An automated SMS text messaging-based conversational agent (ie, chatbot) created to provide access to asthma support in a familiar format via a mobile phone has the potential to help people with asthma across demographics and at scale. Such a chatbot could help improve the accuracy of self-assessed risk, improve asthma self-management, increase access to professional care, and ultimately reduce asthma attacks and emergencies.<h4>Objective</h4>The aims of this study are to determine the feasibility and usability of a text-based conversational agent that processes a patient's text responses and short sample voice recordings to calculate an estimate of their risk for an asthma exacerbation and then offers follow-up information for lowering risk and improving asthma control; assess the levels of engagement for different groups of users, particularly those who do not access professional services and those with poor asthma control; and assess the extent to which users of the chatbot perceive it as helpful for improving their understanding and self-management of their condition.<h4>Methods</h4>We will recruit 300 adults through four channels for broad reach: Facebook, YouGov, Asthma + Lung UK social media, and the website Healthily (a health self-management app). Participants will be screened, and those who meet inclusion criteria (adults diagnosed with asthma and who use WhatsApp) will be provided with a link to access the conversational agent through WhatsApp on their mobile phones. Participants will be sent scheduled and randomly timed messages to invite them to engage in dialogue about their asthma risk during the period of study. After a data collection period (28 days), participants will respond to questionnaire items related to the quality of the interaction. A pre- and postquestionnaire will measure asthma control before and after the intervention.<h4>Results</h4>This study was funded in March 2021 and started in January 2022. We developed a prototype conversational agent, which was iteratively improved with feedback from people with asthma, asthma nurses, and specialist doctors. Fortnightly reviews of iterations by the clinical team began in September 2022 and are ongoing. This feasibility study will start recruitment in January 2023. The anticipated completion of the study is July 2023. A future randomized controlled trial will depend on the outcomes of this study and funding.<h4>Conclusions</h4>This feasibility study will inform a follow-up pilot and larger randomized controlled trial to assess the impact of a conversational agent on asthma outcomes, self-management, behavior change, and access to care.<h4>International registered report identifier (irrid)</h4>PRR1-10.2196/42965.",,pdf:https://www.researchprotocols.org/2023/1/e42965/PDF; doi:https://doi.org/10.2196/42965; html:https://europepmc.org/articles/PMC9936366
 37730605,https://doi.org/10.1186/s12889-023-16523-9,Inequalities and mental health during the Coronavirus pandemic in the UK: a mixed-methods exploration.,"Lombardo C, Guo L, Solomon S, Crepaz-Keay D, McDaid S, Thorpe L, Martin S, John A, Morton A, Davidson G, Kousoulis AA, Van Bortel T.",,BMC public health,2023,2023-09-20,Y,Coronavirus; Mental health; Pandemic; United Kingdom; Inequalities; Social Determinants; Inequity; Adult Population; Covid-19,,,"<h4>Background</h4>The World Health Organisation declared the novel Coronavirus disease (COVID-19) a global pandemic on 11th March 2020. Since then, the world has been firmly in its grip. At the time of writing, there were more than 767,972,961 million confirmed cases and over 6,950,655 million deaths. While the main policy focus has been on controlling the virus and ensuring vaccine roll-out and uptake, the population mental health impacts of the pandemic are expected to be long-term, with certain population groups affected more than others.<h4>Methods</h4>The overall objectives of our 'Coronavirus: Mental Health and the Pandemic' study were to explore UK adults' experiences of the Coronavirus pandemic and to gain insights into the mental health impacts, population-level changes over time, current and future mental health needs, and how these can best be addressed. The wider mixed-methods study consisted of repeated cross-sectional surveys and embedded qualitative sub-studies including in-depth interviews and focus group discussions with the wider UK adult population. For this particular inequalities and mental health sub-study, we used mixed methods data from our cross-sectional surveys and we carried out three Focus Group Discussions with a maximum variation sample from across the UK adult population. The discussions covered the broader topic of 'Inequalities and mental health during the Coronavirus pandemic in the UK' and took place online between April and August 2020. Focus Groups transcripts were analysed using thematic analysis in NVIVO. Cross-sectional survey data were analysed using STATA for descriptive statistics.<h4>Results</h4>Three broad main themes emerged, each supporting a number of sub-themes: (1) Impacts of the pandemic; (2) Moving forward: needs and recommendations; (3) Coping mechanisms and resilience. Findings showed that participants described their experiences of the pandemic in relation to its impact on themselves and on different groups of people. Their experiences illustrated how the pandemic and subsequent measures had exacerbated existing inequalities and created new ones, and triggered various emotional responses. Participants also described their coping strategies and what worked and did not work for them, as well as support needs and recommendations for moving forward through, and out of, the pandemic; all of which are valuable learnings to be considered in policy making for improving mental health and for ensuring future preparedness.<h4>Conclusions</h4>The pandemic is taking a long-term toll on the nations' mental health which will continue to have impacts for years to come. It is therefore crucial to learn the vital lessons learned from this pandemic. Specific as well as whole-government policies need to respond to this, address inequalities and the different needs across the life-course and across society, and take a holistic approach to mental health improvement across the UK.",,pdf:https://bmcpublichealth.biomedcentral.com/counter/pdf/10.1186/s12889-023-16523-9; doi:https://doi.org/10.1186/s12889-023-16523-9; html:https://europepmc.org/articles/PMC10510114; pdf:https://europepmc.org/articles/PMC10510114?pdf=render
+36729586,https://doi.org/10.2196/42965,Assessing the Feasibility of a Text-Based Conversational Agent for Asthma Support: Protocol for a Mixed Methods Observational Study.,"Calvo RA, Peters D, Moradbakhti L, Cook D, Rizos G, Schuller B, Kallis C, Wong E, Quint J.",,JMIR research protocols,2023,2023-02-02,Y,Artificial intelligence; Health; Asthma; Health education; Well-being; Behavior Change; Conversational Agent; Chatbot,,,"<h4>Background</h4>Despite efforts, the UK death rate from asthma is the highest in Europe, and 65% of people with asthma in the United Kingdom do not receive the professional care they are entitled to. Experts have recommended the use of digital innovations to help address the issues of poor outcomes and lack of care access. An automated SMS text messaging-based conversational agent (ie, chatbot) created to provide access to asthma support in a familiar format via a mobile phone has the potential to help people with asthma across demographics and at scale. Such a chatbot could help improve the accuracy of self-assessed risk, improve asthma self-management, increase access to professional care, and ultimately reduce asthma attacks and emergencies.<h4>Objective</h4>The aims of this study are to determine the feasibility and usability of a text-based conversational agent that processes a patient's text responses and short sample voice recordings to calculate an estimate of their risk for an asthma exacerbation and then offers follow-up information for lowering risk and improving asthma control; assess the levels of engagement for different groups of users, particularly those who do not access professional services and those with poor asthma control; and assess the extent to which users of the chatbot perceive it as helpful for improving their understanding and self-management of their condition.<h4>Methods</h4>We will recruit 300 adults through four channels for broad reach: Facebook, YouGov, Asthma + Lung UK social media, and the website Healthily (a health self-management app). Participants will be screened, and those who meet inclusion criteria (adults diagnosed with asthma and who use WhatsApp) will be provided with a link to access the conversational agent through WhatsApp on their mobile phones. Participants will be sent scheduled and randomly timed messages to invite them to engage in dialogue about their asthma risk during the period of study. After a data collection period (28 days), participants will respond to questionnaire items related to the quality of the interaction. A pre- and postquestionnaire will measure asthma control before and after the intervention.<h4>Results</h4>This study was funded in March 2021 and started in January 2022. We developed a prototype conversational agent, which was iteratively improved with feedback from people with asthma, asthma nurses, and specialist doctors. Fortnightly reviews of iterations by the clinical team began in September 2022 and are ongoing. This feasibility study will start recruitment in January 2023. The anticipated completion of the study is July 2023. A future randomized controlled trial will depend on the outcomes of this study and funding.<h4>Conclusions</h4>This feasibility study will inform a follow-up pilot and larger randomized controlled trial to assess the impact of a conversational agent on asthma outcomes, self-management, behavior change, and access to care.<h4>International registered report identifier (irrid)</h4>PRR1-10.2196/42965.",,pdf:https://www.researchprotocols.org/2023/1/e42965/PDF; doi:https://doi.org/10.2196/42965; html:https://europepmc.org/articles/PMC9936366
 33632741,https://doi.org/10.2337/db20-0895,"Relationship Between Glycemia and Cognitive Function, Structural Brain Outcomes, and Dementia: A Mendelian Randomization Study in the UK Biobank.","Garfield V, Farmaki AE, Fatemifar G, Eastwood SV, Mathur R, Rentsch CT, Denaxas S, Bhaskaran K, Smeeth L, Chaturvedi N.",,Diabetes,2021,2021-02-25,N,,,,"We investigated the relationship between glycemia and cognitive function, brain structure and incident dementia using bidirectional Mendelian randomization (MR). Data were from the UK Biobank (<i>n</i> = ∼500,000). Our exposures were genetic instruments for type 2 diabetes (157 variants) and HbA<sub>1c</sub> (51 variants) and our outcomes were reaction time (RT), visual memory, hippocampal volume (HV), white matter hyperintensity volume (WMHV), and Alzheimer dementia (AD). We also investigated associations between genetic variants for RT (43 variants) and diabetes and HbA<sub>1c</sub> We used conventional inverse-variance-weighted (IVW) MR alongside MR sensitivity analyses. Using IVW, genetic liability to type 2 diabetes was not associated with RT (exponentiated β [expβ] = 1.00 [95% CI 1.00; 1.00]), visual memory (expβ = 1.00 [95% CI 0.99; 1.00]), WMHV (expβ = 0.99 [95% CI 0.97; 1.01]), HV (β-coefficient mm<sup>3</sup> = -2.30 [95% CI -12.39; 7.78]) or AD (odds ratio [OR] 1.15 [95% CI 0.87; 1.52]). HbA<sub>1c</sub> was not associated with RT (expβ = 1.00 [95% CI 0.99; 1.02]), visual memory (expβ = 0.99 [95% CI 0.96; 1.02]), WMHV (expβ = 1.03 [95% CI 0.88; 1.22]), HV (β = -21.31 [95% CI -82.96; 40.34]), or risk of AD (OR 1.09 [95% CI 0.42; 2.83]). IVW showed that reaction time was not associated with diabetes risk (OR 0.94 [95% CI 0.54; 1.65]), or with HbA<sub>1c</sub> (β-coefficient mmol/mol = -0.88 [95% CI = -1.88; 0.13]) after exclusion of a pleiotropic variant. Overall, we observed little evidence of causal association between genetic instruments for type 2 diabetes or peripheral glycemia and some measures of cognition and brain structure in midlife.",,pdf:https://diabetesjournals.org/diabetes/article-pdf/70/10/2313/628539/db200895.pdf; doi:https://doi.org/10.2337/db20-0895
-31500613,https://doi.org/10.1186/s12911-019-0908-7,A validated natural language processing algorithm for brain imaging phenotypes from radiology reports in UK electronic health records.,"Wheater E, Mair G, Sudlow C, Alex B, Grover C, Whiteley W.",,BMC medical informatics and decision making,2019,2019-09-09,Y,Stroke; Phenotyping; Brain imaging; Radiology; Natural Language Processing; Radiology Reports,"Applied Analytics, Better Care",,"<h4>Background</h4>Manual coding of phenotypes in brain radiology reports is time consuming. We developed a natural language processing (NLP) algorithm to enable automatic identification of brain imaging in radiology reports performed in routine clinical practice in the UK National Health Service (NHS).<h4>Methods</h4>We used anonymized text brain imaging reports from a cohort study of stroke/TIA patients and from a regional hospital to develop and test an NLP algorithm. Two experts marked up text in 1692 reports for 24 cerebrovascular and other neurological phenotypes. We developed and tested a rule-based NLP algorithm first within the cohort study, and further evaluated it in the reports from the regional hospital.<h4>Results</h4>The agreement between expert readers was excellent (Cohen's κ =0.93) in both datasets. In the final test dataset (n = 700) in unseen regional hospital reports, the algorithm had very good performance for a report of any ischaemic stroke [sensitivity 89% (95% CI:81-94); positive predictive value (PPV) 85% (76-90); specificity 100% (95% CI:0.99-1.00)]; any haemorrhagic stroke [sensitivity 96% (95% CI: 80-99), PPV 72% (95% CI:55-84); specificity 100% (95% CI:0.99-1.00)]; brain tumours [sensitivity 96% (CI:87-99); PPV 84% (73-91); specificity: 100% (95% CI:0.99-1.00)] and cerebral small vessel disease and cerebral atrophy (sensitivity, PPV and specificity all > 97%). We obtained few reports of subarachnoid haemorrhage, microbleeds or subdural haematomas. In 110,695 reports from NHS Tayside, atrophy (n = 28,757, 26%), small vessel disease (15,015, 14%) and old, deep ischaemic strokes (10,636, 10%) were the commonest findings.<h4>Conclusions</h4>An NLP algorithm can be developed in UK NHS radiology records to allow identification of cohorts of patients with important brain imaging phenotypes at a scale that would otherwise not be possible.",,pdf:https://bmcmedinformdecismak.biomedcentral.com/track/pdf/10.1186/s12911-019-0908-7; doi:https://doi.org/10.1186/s12911-019-0908-7; html:https://europepmc.org/articles/PMC6734359; pdf:https://europepmc.org/articles/PMC6734359?pdf=render
 37072241,https://doi.org/10.1136/heartjnl-2022-321888,Incident cardiovascular events and imaging phenotypes in UK Biobank participants with past cancer.,"Raisi-Estabragh Z, Cooper J, McCracken C, Crosbie EJ, Walter FM, Manisty CH, Robson J, Mamas MA, Harvey NC, Neubauer S, Petersen SE.",,Heart (British Cardiac Society),2023,2023-06-14,Y,epidemiology; Magnetic Resonance Imaging,,,"<h4>Objectives</h4>To evaluate incident cardiovascular outcomes and imaging phenotypes in UK Biobank participants with previous cancer.<h4>Methods</h4>Cancer and cardiovascular disease (CVD) diagnoses were ascertained using health record linkage. Participants with cancer history (breast, lung, prostate, colorectal, uterus, haematological) were propensity matched on vascular risk factors to non-cancer controls. Competing risk regression was used to calculate subdistribution HRs (SHRs) for associations of cancer history with incident CVD (ischaemic heart disease (IHD), non-ischaemic cardiomyopathy (NICM), heart failure (HF), atrial fibrillation/flutter, stroke, pericarditis, venous thromboembolism (VTE)) and mortality outcomes (any CVD, IHD, HF/NICM, stroke, hypertensive disease) over 11.8±1.7 years of prospective follow-up. Linear regression was used to assess associations of cancer history with left ventricular (LV) and left atrial metrics.<h4>Results</h4>We studied 18 714 participants (67% women, age: 62 (IQR: 57-66) years, 97% white ethnicities) with cancer history, including 1354 individuals with cardiovascular magnetic resonance. Participants with cancer had high burden of vascular risk factors and prevalent CVDs. Haematological cancer was associated with increased risk of all incident CVDs considered (SHRs: 1.92-3.56), larger chamber volumes, lower ejection fractions, and poorer LV strain. Breast cancer was associated with increased risk of selected CVDs (NICM, HF, pericarditis and VTE; SHRs: 1.34-2.03), HF/NICM death, hypertensive disease death, lower LV ejection fraction, and lower LV global function index. Lung cancer was associated with increased risk of pericarditis, HF, and CVD death. Prostate cancer was linked to increased VTE risk.<h4>Conclusions</h4>Cancer history is linked to increased risk of incident CVDs and adverse cardiac remodelling independent of shared vascular risk factors.",,pdf:https://heart.bmj.com/content/heartjnl/early/2023/03/21/heartjnl-2022-321888.full.pdf; doi:https://doi.org/10.1136/heartjnl-2022-321888; html:https://europepmc.org/articles/PMC10314020; pdf:https://europepmc.org/articles/PMC10314020?pdf=render
+31500613,https://doi.org/10.1186/s12911-019-0908-7,A validated natural language processing algorithm for brain imaging phenotypes from radiology reports in UK electronic health records.,"Wheater E, Mair G, Sudlow C, Alex B, Grover C, Whiteley W.",,BMC medical informatics and decision making,2019,2019-09-09,Y,Stroke; Phenotyping; Brain imaging; Radiology; Natural Language Processing; Radiology Reports,"Applied Analytics, Better Care",,"<h4>Background</h4>Manual coding of phenotypes in brain radiology reports is time consuming. We developed a natural language processing (NLP) algorithm to enable automatic identification of brain imaging in radiology reports performed in routine clinical practice in the UK National Health Service (NHS).<h4>Methods</h4>We used anonymized text brain imaging reports from a cohort study of stroke/TIA patients and from a regional hospital to develop and test an NLP algorithm. Two experts marked up text in 1692 reports for 24 cerebrovascular and other neurological phenotypes. We developed and tested a rule-based NLP algorithm first within the cohort study, and further evaluated it in the reports from the regional hospital.<h4>Results</h4>The agreement between expert readers was excellent (Cohen's κ =0.93) in both datasets. In the final test dataset (n = 700) in unseen regional hospital reports, the algorithm had very good performance for a report of any ischaemic stroke [sensitivity 89% (95% CI:81-94); positive predictive value (PPV) 85% (76-90); specificity 100% (95% CI:0.99-1.00)]; any haemorrhagic stroke [sensitivity 96% (95% CI: 80-99), PPV 72% (95% CI:55-84); specificity 100% (95% CI:0.99-1.00)]; brain tumours [sensitivity 96% (CI:87-99); PPV 84% (73-91); specificity: 100% (95% CI:0.99-1.00)] and cerebral small vessel disease and cerebral atrophy (sensitivity, PPV and specificity all > 97%). We obtained few reports of subarachnoid haemorrhage, microbleeds or subdural haematomas. In 110,695 reports from NHS Tayside, atrophy (n = 28,757, 26%), small vessel disease (15,015, 14%) and old, deep ischaemic strokes (10,636, 10%) were the commonest findings.<h4>Conclusions</h4>An NLP algorithm can be developed in UK NHS radiology records to allow identification of cohorts of patients with important brain imaging phenotypes at a scale that would otherwise not be possible.",,pdf:https://bmcmedinformdecismak.biomedcentral.com/track/pdf/10.1186/s12911-019-0908-7; doi:https://doi.org/10.1186/s12911-019-0908-7; html:https://europepmc.org/articles/PMC6734359; pdf:https://europepmc.org/articles/PMC6734359?pdf=render
 37805492,https://doi.org/10.1186/s12864-023-09663-0,Mapping the epigenomic landscape of human monocytes following innate immune activation reveals context-specific mechanisms driving endotoxin tolerance.,"Amarasinghe HE, Zhang P, Whalley JP, Allcock A, Migliorini G, Brown AC, Scozzafava G, Knight JC.",,BMC genomics,2023,2023-10-07,Y,Chromatin Accessibility; Expression Quantitative Trait Loci; Endotoxin Tolerance; Human Monocytes; Enhancer Rna; Context-specificity,,,"<h4>Background</h4>Monocytes are key mediators of innate immunity to infection, undergoing profound and dynamic changes in epigenetic state and immune function which are broadly protective but may be dysregulated in disease. Here, we aimed to advance understanding of epigenetic regulation following innate immune activation, acutely and in endotoxin tolerant states.<h4>Methods</h4>We exposed human primary monocytes from healthy donors (n = 6) to interferon-γ or differing combinations of endotoxin (lipopolysaccharide), including acute response (2 h) and two models of endotoxin tolerance: repeated stimulations (6 + 6 h) and prolonged exposure to endotoxin (24 h). Another subset of monocytes was left untreated (naïve). We identified context-specific regulatory elements based on epigenetic signatures for chromatin accessibility (ATAC-seq) and regulatory non-coding RNAs from total RNA sequencing.<h4>Results</h4>We present an atlas of differential gene expression for endotoxin and interferon response, identifying widespread context specific changes. Across assayed states, only 24-29% of genes showing differential exon usage are also differential at the gene level. Overall, 19.9% (6,884 of 34,616) of repeatedly observed ATAC peaks were differential in at least one condition, the majority upregulated on stimulation and located in distal regions (64.1% vs 45.9% of non-differential peaks) within which sequences were less conserved than non-differential peaks. We identified enhancer-derived RNA signatures specific to different monocyte states that correlated with chromatin accessibility changes. The endotoxin tolerance models showed distinct chromatin accessibility and transcriptomic signatures, with integrated analysis identifying genes and pathways involved in the inflammatory response, detoxification, metabolism and wound healing. We leveraged eQTL mapping for the same monocyte activation states to link potential enhancers with specific genes, identifying 1,946 unique differential ATAC peaks with 1,340 expression associated genes. We further use this to inform understanding of reported GWAS, for example involving FCHO1 and coronary artery disease.<h4>Conclusion</h4>This study reports context-specific regulatory elements based on transcriptomic profiling and epigenetic signatures for enhancer-derived RNAs and chromatin accessibility in immune tolerant monocyte states, and demonstrates the informativeness of linking such elements and eQTL to inform future mechanistic studies aimed at defining therapeutic targets of immunosuppression and diseases.",,doi:https://doi.org/10.1186/s12864-023-09663-0; html:https://europepmc.org/articles/PMC10559536; pdf:https://europepmc.org/articles/PMC10559536?pdf=render
-34761838,https://doi.org/10.1002/biof.1801,Neutrophil to lymphocyte ratio is not related to carotid atherosclerosis progression and cardiovascular events in the primary prevention of cardiovascular disease: Results from the IMPROVE study.,"Mannarino MR, Bianconi V, Gigante B, Strawbridge RJ, Savonen K, Kurl S, Giral P, Smit A, Eriksson P, Tremoli E, Veglia F, Baldassarre D, Pirro M, IMPROVE study group.",,"BioFactors (Oxford, England)",2022,2021-11-11,Y,Lymphocyte; neutrophil; cardiovascular; Carotid; Prospective; Imt; Nlr,,,"Inflammation is a component of the pathogenesis of atherosclerosis and is associated with an increased risk of atherosclerotic cardiovascular disease (ASCVD). The neutrophil to lymphocyte ratio (NLR) is a possible inflammation metric for the detection of ASCVD risk, although results of prospective studies are highly inconsistent on this topic. We investigated the cross-sectional relationship between NLR and carotid intima-media thickness (cIMT) in subjects at moderate-to-high ASCVD risk. The prospective association between NLR, cIMT progression, and incident vascular events (VEs) was also explored. In 3341 subjects from the IMT-Progression as Predictors of VEs (IMPROVE) study, we analyzed the association between NLR, cIMT, and its 15-month progression. The association between NLR and incident VEs was also investigated. NLR was positively associated with cross-sectional measures of cIMT, but not with cIMT progression. The association between NLR and cross-sectional cIMT measures was abolished when adjusted for confounders. No association was found between NRL and incident VEs. Similarly, there were no significant differences in the hazard ratios (HRs) of VEs across NLR quartiles. NLR was neither associated with the presence and progression of carotid atherosclerosis, nor with the risk of VEs. Our findings do not support the role of NLR as a predictor of the risk of atherosclerosis progression and ASCVD events in subjects at moderate-to-high ASCVD risk, in primary prevention. However, the usefulness of NLR for patients at a different level of ASCVD risk cannot be inferred from this study.",,pdf:https://air.unimi.it/bitstream/2434/890337/2/0127%20IMPROVE%20mannarino%20Neutrophil%20to%20lymphocyte%20e%20suppl%20.pdf; doi:https://doi.org/10.1002/biof.1801; html:https://europepmc.org/articles/PMC9299016; pdf:https://europepmc.org/articles/PMC9299016?pdf=render
 34095541,https://doi.org/10.23889/ijpds.v4i2.1134,A Profile of the SAIL Databank on the UK Secure Research Platform.,"Jones KH, Ford DV, Thompson S, Lyons RA.",,International journal of population data science,2019,2019-11-20,Y,,,,"<h4>Background</h4>The Secure Anonymised Information Linkage (SAIL) Databank is a national data safe haven of de identified datasets principally about the population of Wales, made available in anonymised form to researchers across the world. It was established to enable the vast arrays of data collected about individuals in the course of health and other public service delivery to be made available to answer important questions that could not otherwise be addressed without prohibitive effort. The SAIL Databank is the bedrock of other funded centres relying on the data for research.<h4>Approach</h4>SAIL is a data repository surrounded by a suite of physical, technical and procedural control measures embodying a proportionate privacy-by-design governance model, informed by public engagement, to safeguard the data and facilitate data utility. SAIL operates on the UK Secure Research Platform (SeRP), which is a customisable technology and analysis platform. Researchers access anonymised data via this secure research environment, from which results can be released following scrutiny for disclosure risk. SAIL data are being used in multiple research areas to evaluate the impact of health and social exposures and policy interventions.<h4>Discussion</h4>Lessons learned and their applications include: managing evolving legislative and regulatory requirements; employing multiple, tiered security mechanisms; working hard to increase analytical capacity efficiency; and developing a multi-faceted programme of public engagement. Further work includes: incorporating new data types; enabling alternative means of data access; and developing further efficiencies across our operations.<h4>Conclusion</h4>SAIL represents an ongoing programme of work to develop and maintain an extensive, whole population data resource for research. Its privacy-by-design model and UK SeRP technology have received international acclaim, and we continually endeavour to demonstrate trustworthiness to support data provider assurance and public acceptability in data use. We strive for further improvement and continue a mutual learning process with our contemporaries in this rapidly developing field.",,pdf:https://ijpds.org/article/download/1134/2643; doi:https://doi.org/10.23889/ijpds.v4i2.1134; html:https://europepmc.org/articles/PMC8142954; pdf:https://europepmc.org/articles/PMC8142954?pdf=render
-34095527,https://doi.org/10.23889/ijpds.v4i1.581,Electronic Longitudinal Alcohol Study in Communities (ELAStiC) Wales - protocol for platform development.,"Trefan L, Akbari A, Paranjothy S, Farewell DM, Gartner A, Fone D, Greene J, Evans A, Smith A, Adekanmbi V, Kennedy J, Lyons RA, Moore SC.",,International journal of population data science,2019,2019-05-20,Y,,,,"<h4>Introduction</h4>Excessive alcohol consumption has adverse effects on health and there is a recognised need for the longitudinal analysis of population data to improve our understanding of the patterns of alcohol use, harms to consumers and those in their immediate environment. The UK has a number of linkable, longitudinal databases that if assembled properly could support valuable research on this topic.<h4>Aims and objectives</h4>This paper describes the development of a broad set of cross-linked cohorts, e-cohorts, surveys and linked electronic healthcare records (EHRs) to construct an alcohol-specific analytical platform in the United Kingdom using datasets on the population of Wales.The objective of this paper is to provide a description of existing key datasets integrated with existing, routinely collected electronic health data on a secure platform, and relevant derived variables to enable population-based research on alcohol-related harm in Wales. We illustrate our use of these data with some exemplar research questions that are currently under investigation.<h4>Methods</h4>Record-linkage of routine and observational datasets. Routine data includes hospital admissions, general practice, and cohorts specific to children. Two observational studies were included. Routine socioeconomic descriptors and mortality data were also linked.<h4>Conclusion</h4>We described a record-linked, population-based research protocol for alcohol related harm on a secure platform. As the datasets used here are available in many countries, ELAStiC provides a template for setting up similar initiatives in other countries. We have also defined a number of alcohol specific variables using routinely-collected available data that can be used in other epidemiological studies into alcohol related outcomes. With over 10 years of longitudinal data, it will help to understand alcohol-related disease and health trajectories across the lifespan.",,pdf:https://ijpds.org/article/download/581/2923; doi:https://doi.org/10.23889/ijpds.v4i1.581; html:https://europepmc.org/articles/PMC8142962; pdf:https://europepmc.org/articles/PMC8142962?pdf=render
+34761838,https://doi.org/10.1002/biof.1801,Neutrophil to lymphocyte ratio is not related to carotid atherosclerosis progression and cardiovascular events in the primary prevention of cardiovascular disease: Results from the IMPROVE study.,"Mannarino MR, Bianconi V, Gigante B, Strawbridge RJ, Savonen K, Kurl S, Giral P, Smit A, Eriksson P, Tremoli E, Veglia F, Baldassarre D, Pirro M, IMPROVE study group.",,"BioFactors (Oxford, England)",2022,2021-11-11,Y,Lymphocyte; neutrophil; cardiovascular; Carotid; Prospective; Imt; Nlr,,,"Inflammation is a component of the pathogenesis of atherosclerosis and is associated with an increased risk of atherosclerotic cardiovascular disease (ASCVD). The neutrophil to lymphocyte ratio (NLR) is a possible inflammation metric for the detection of ASCVD risk, although results of prospective studies are highly inconsistent on this topic. We investigated the cross-sectional relationship between NLR and carotid intima-media thickness (cIMT) in subjects at moderate-to-high ASCVD risk. The prospective association between NLR, cIMT progression, and incident vascular events (VEs) was also explored. In 3341 subjects from the IMT-Progression as Predictors of VEs (IMPROVE) study, we analyzed the association between NLR, cIMT, and its 15-month progression. The association between NLR and incident VEs was also investigated. NLR was positively associated with cross-sectional measures of cIMT, but not with cIMT progression. The association between NLR and cross-sectional cIMT measures was abolished when adjusted for confounders. No association was found between NRL and incident VEs. Similarly, there were no significant differences in the hazard ratios (HRs) of VEs across NLR quartiles. NLR was neither associated with the presence and progression of carotid atherosclerosis, nor with the risk of VEs. Our findings do not support the role of NLR as a predictor of the risk of atherosclerosis progression and ASCVD events in subjects at moderate-to-high ASCVD risk, in primary prevention. However, the usefulness of NLR for patients at a different level of ASCVD risk cannot be inferred from this study.",,pdf:https://air.unimi.it/bitstream/2434/890337/2/0127%20IMPROVE%20mannarino%20Neutrophil%20to%20lymphocyte%20e%20suppl%20.pdf; doi:https://doi.org/10.1002/biof.1801; html:https://europepmc.org/articles/PMC9299016; pdf:https://europepmc.org/articles/PMC9299016?pdf=render
 33144367,https://doi.org/10.3399/bjgpopen20x101109,Evaluating a cardiovascular disease risk management care continuum within a learning healthcare system: a prospective cohort study.,"Groenhof TKJ, Lely AT, Haitjema S, Nathoe HM, Kortekaas MF, Asselbergs FW, Bots ML, Hollander M, UCC CVRM study group.",,BJGP open,2020,2020-12-15,Y,Cardiovascular diseases; Continuity Of Patient Care; Learning Healthcare System; Cardiovascular Risk Management,,,"<h4>Background</h4>Many patients now present with multimorbidity and chronicity of disease. This means that multidisciplinary management in a care continuum, integrating primary care and hospital care services, is needed to ensure high quality care.<h4>Aim</h4>To evaluate cardiovascular risk management (CVRM) via linkage of health data sources, as an example of a multidisciplinary continuum within a learning healthcare system (LHS).<h4>Design & setting</h4>In this prospective cohort study, data were linked from the Utrecht Cardiovascular Cohort (UCC) to the Julius General Practitioners' Network (JGPN) database. UCC offers structured CVRM at referral to the University Medical Centre (UMC) Utrecht. JGPN consists of electronic health record (EHR) data from referring GPs.<h4>Method</h4>The cardiovascular risk factors were extracted for each patient 13 months before referral (JGPN), at UCC inclusion, and during 12 months follow-up (JGPN). The following areas were assessed: registration of risk factors; detection of risk factor(s) requiring treatment at UCC; communication of risk factors and actionable suggestions from the specialist to the GP; and change of management during follow-up.<h4>Results</h4>In 52% of patients, ≥1 risk factors were registered (that is, extractable from structured fields within routine care health records) before UCC. In 12%-72% of patients, risk factor(s) existed that required (change or start of) treatment at UCC inclusion. Specialist communication included the complete risk profile in 67% of letters, but lacked actionable suggestions in 86%. In 29% of patients, at least one risk factor was registered after UCC. Change in management in GP records was seen in 21%-58% of them.<h4>Conclusion</h4>Evaluation of a multidisciplinary LHS is possible via linkage of health data sources. Efforts have to be made to improve registration in primary care, as well as communication on findings and actionable suggestions for follow-up to bridge the gap in the CVRM continuum.",,pdf:https://bjgpopen.org/content/bjgpoa/4/5/bjgpopen20X101109.full.pdf; doi:https://doi.org/10.3399/bjgpopen20X101109; html:https://europepmc.org/articles/PMC7880177; pdf:https://europepmc.org/articles/PMC7880177?pdf=render
+34095527,https://doi.org/10.23889/ijpds.v4i1.581,Electronic Longitudinal Alcohol Study in Communities (ELAStiC) Wales - protocol for platform development.,"Trefan L, Akbari A, Paranjothy S, Farewell DM, Gartner A, Fone D, Greene J, Evans A, Smith A, Adekanmbi V, Kennedy J, Lyons RA, Moore SC.",,International journal of population data science,2019,2019-05-20,Y,,,,"<h4>Introduction</h4>Excessive alcohol consumption has adverse effects on health and there is a recognised need for the longitudinal analysis of population data to improve our understanding of the patterns of alcohol use, harms to consumers and those in their immediate environment. The UK has a number of linkable, longitudinal databases that if assembled properly could support valuable research on this topic.<h4>Aims and objectives</h4>This paper describes the development of a broad set of cross-linked cohorts, e-cohorts, surveys and linked electronic healthcare records (EHRs) to construct an alcohol-specific analytical platform in the United Kingdom using datasets on the population of Wales.The objective of this paper is to provide a description of existing key datasets integrated with existing, routinely collected electronic health data on a secure platform, and relevant derived variables to enable population-based research on alcohol-related harm in Wales. We illustrate our use of these data with some exemplar research questions that are currently under investigation.<h4>Methods</h4>Record-linkage of routine and observational datasets. Routine data includes hospital admissions, general practice, and cohorts specific to children. Two observational studies were included. Routine socioeconomic descriptors and mortality data were also linked.<h4>Conclusion</h4>We described a record-linked, population-based research protocol for alcohol related harm on a secure platform. As the datasets used here are available in many countries, ELAStiC provides a template for setting up similar initiatives in other countries. We have also defined a number of alcohol specific variables using routinely-collected available data that can be used in other epidemiological studies into alcohol related outcomes. With over 10 years of longitudinal data, it will help to understand alcohol-related disease and health trajectories across the lifespan.",,pdf:https://ijpds.org/article/download/581/2923; doi:https://doi.org/10.23889/ijpds.v4i1.581; html:https://europepmc.org/articles/PMC8142962; pdf:https://europepmc.org/articles/PMC8142962?pdf=render
 35579056,https://doi.org/10.1111/eci.13814,Lifestyle changes and kidney function: A 10-year follow-up study in patients with manifest cardiovascular disease.,"Østergaard HB, Demirhan I, Westerink J, Verhaar MC, Asselbergs FW, de Borst GJ, Kappelle LJ, Visseren FLJ, van der Leeuw J, UCC-SMART studygroup.",,European journal of clinical investigation,2022,2022-05-27,Y,Cardiovascular disease; Lifestyle Factors; Kidney Function Decline,,,"<h4>Background</h4>Patients with cardiovascular disease (CVD) are at higher risk of kidney function decline. The current study aimed to examine the association of lifestyle changes with kidney function decline in patients with manifest CVD.<h4>Methods</h4>A total of 2260 patients from the Utrecht Cardiovascular Cohort-Second Manifestations of ARTerial disease cohort with manifest CVD who returned for a follow-up visit after a median of 9.9 years were included. The relation between change in lifestyle factors (smoking, alcohol consumption, physical activity and obesity) and change in kidney function (eGFR and uACR) was assessed using linear regression models.<h4>Results</h4>An increase in body mass index (β -2.81; 95% CI -3.98; -1.63 per 5 kg/m<sup>2</sup> ) and for men also an increase in waist circumference (β -0.87; 95% CI -1.28; -0.47 per 5 cm) were significantly associated with a steeper decline in eGFR over 10 years. Continuing smoking (β -2.44, 95% CI -4.43; -0.45) and recent smoking cessation during follow-up (β -3.27; 95% CI -5.20; -1.34) were both associated with a steeper eGFR decline compared to patients who remained as non- or previous smokers from baseline. No significant association was observed between physical exercise or alcohol consumption and kidney function decline. No significant relation between any lifestyle factor and change in uACR was observed.<h4>Conclusions</h4>In patients with CVD, continuing smoking, recent smoking cessation and an increase in obesity markers were related to a steeper kidney function decline. Although no definite conclusions from this study can be drawn, the results support the importance of encouraging weight loss and smoking cessation in high-risk patients as a means of slowing down kidney function decline.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/eci.13814; doi:https://doi.org/10.1111/eci.13814; html:https://europepmc.org/articles/PMC9540114; pdf:https://europepmc.org/articles/PMC9540114?pdf=render
-32838035,https://doi.org/10.1002/lrh2.10236,Rapid translation of clinical guidelines into executable knowledge: A case study of COVID-19 and online demonstration.,"Fox J, Khan O, Curtis H, Wright A, Pal C, Cockburn N, Cooper J, Chandan JS, Nirantharakumar K.",,Learning health systems,2021,2020-07-14,Y,Artificial intelligence; Covid‐19; Rapid Learning Systems,,,"<h4>Introduction</h4>We report a pathfinder study of AI/knowledge engineering methods to rapidly formalise COVID-19 guidelines into an executable model of decision making and care pathways. The knowledge source for the study was material published by BMJ Best Practice in March 2020.<h4>Methods</h4>The <i>PROforma</i> guideline modelling language and OpenClinical.net authoring and publishing platform were used to create a data model for care of COVID-19 patients together with executable models of rules, decisions and plans that interpret patient data and give personalised care advice.<h4>Results</h4><i>PROforma</i> and OpenClinical.net proved to be an effective combination for rapidly creating the COVID-19 model; the Pathfinder 1 demonstrator is available for assessment at https://www.openclinical.net/index.php?id=746.<h4>Conclusions</h4>This is believed to be the first use of AI/knowledge engineering methods for disseminating best-practice in COVID-19 care. It demonstrates a novel and promising approach to the rapid translation of clinical guidelines into point of care services, and a foundation for rapid learning systems in many areas of healthcare.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/lrh2.10236; doi:https://doi.org/10.1002/lrh2.10236; html:https://europepmc.org/articles/PMC7323421; pdf:https://europepmc.org/articles/PMC7323421?pdf=render
 34772649,https://doi.org/10.1016/s2589-7500(21)00252-1,Characteristics of publicly available skin cancer image datasets: a systematic review.,"Wen D, Khan SM, Ji Xu A, Ibrahim H, Smith L, Caballero J, Zepeda L, de Blas Perez C, Denniston AK, Liu X, Matin RN.",,The Lancet. Digital health,2022,2021-11-09,N,,,,"Publicly available skin image datasets are increasingly used to develop machine learning algorithms for skin cancer diagnosis. However, the total number of datasets and their respective content is currently unclear. This systematic review aimed to identify and evaluate all publicly available skin image datasets used for skin cancer diagnosis by exploring their characteristics, data access requirements, and associated image metadata. A combined MEDLINE, Google, and Google Dataset search identified 21 open access datasets containing 106 950 skin lesion images, 17 open access atlases, eight regulated access datasets, and three regulated access atlases. Images and accompanying data from open access datasets were evaluated by two independent reviewers. Among the 14 datasets that reported country of origin, most (11 [79%]) originated from Europe, North America, and Oceania exclusively. Most datasets (19 [91%]) contained dermoscopic images or macroscopic photographs only. Clinical information was available regarding age for 81 662 images (76·4%), sex for 82 848 (77·5%), and body site for 79 561 (74·4%). Subject ethnicity data were available for 1415 images (1·3%), and Fitzpatrick skin type data for 2236 (2·1%). There was limited and variable reporting of characteristics and metadata among datasets, with substantial under-representation of darker skin types. This is the first systematic review to characterise publicly available skin image datasets, highlighting limited applicability to real-life clinical settings and restricted population representation, precluding generalisability. Quality standards for characteristics and metadata reporting for skin image datasets are needed.",,pdf:http://www.thelancet.com/article/S2589750021002521/pdf; doi:https://doi.org/10.1016/S2589-7500(21)00252-1
 36828608,https://doi.org/10.1016/s2589-7500(22)00249-7,The role of patient-reported outcome measures in trials of artificial intelligence health technologies: a systematic evaluation of ClinicalTrials.gov records (1997-2022).,"Pearce FJ, Cruz Rivera S, Liu X, Manna E, Denniston AK, Calvert MJ.",,The Lancet. Digital health,2023,2023-03-01,N,,,,"The extent to which patient-reported outcome measures (PROMs) are used in clinical trials for artificial intelligence (AI) technologies is unknown. In this systematic evaluation, we aim to establish how PROMs are being used to assess AI health technologies. We searched ClinicalTrials.gov for interventional trials registered from inception to Sept 20, 2022, and included trials that tested an AI health technology. We excluded observational studies, patient registries, and expanded access reports. We extracted data regarding the form, function, and intended use population of the AI health technology, in addition to the PROMs used and whether PROMs were incorporated as an input or output in the AI model. The search identified 2958 trials, of which 627 were included in the analysis. 152 (24%) of the included trials used one or more PROM, visual analogue scale, patient-reported experience measure, or usability measure as a trial endpoint. The type of AI health technologies used by these trials included AI-enabled smart devices, clinical decision support systems, and chatbots. The number of clinical trials of AI health technologies registered on ClinicalTrials.gov and the proportion of trials that used PROMs increased from registry inception to 2022. The most common clinical areas AI health technologies were designed for were digestive system health for non-PROM trials and musculoskeletal health (followed by mental and behavioural health) for PROM trials, with PROMs commonly used in clinical areas for which assessment of health-related quality of life and symptom burden is particularly important. Additionally, AI-enabled smart devices were the most common applications tested in trials that used at least one PROM. 24 trials tested AI models that captured PROM data as an input for the AI model. PROM use in clinical trials of AI health technologies falls behind PROM use in all clinical trials. Trial records having inadequate detail regarding the PROMs used or the type of AI health technology tested was a limitation of this systematic evaluation and might have contributed to inaccuracies in the data synthesised. Overall, the use of PROMs in the function and assessment of AI health technologies is not only possible, but is a powerful way of showing that, even in the most technologically advanced health-care systems, patients' perspectives remain central.",,doi:https://doi.org/10.1016/s2589-7500(22)00249-7; doi:https://doi.org/10.1016/S2589-7500(22)00249-7
+32838035,https://doi.org/10.1002/lrh2.10236,Rapid translation of clinical guidelines into executable knowledge: A case study of COVID-19 and online demonstration.,"Fox J, Khan O, Curtis H, Wright A, Pal C, Cockburn N, Cooper J, Chandan JS, Nirantharakumar K.",,Learning health systems,2021,2020-07-14,Y,Artificial intelligence; Covid‐19; Rapid Learning Systems,,,"<h4>Introduction</h4>We report a pathfinder study of AI/knowledge engineering methods to rapidly formalise COVID-19 guidelines into an executable model of decision making and care pathways. The knowledge source for the study was material published by BMJ Best Practice in March 2020.<h4>Methods</h4>The <i>PROforma</i> guideline modelling language and OpenClinical.net authoring and publishing platform were used to create a data model for care of COVID-19 patients together with executable models of rules, decisions and plans that interpret patient data and give personalised care advice.<h4>Results</h4><i>PROforma</i> and OpenClinical.net proved to be an effective combination for rapidly creating the COVID-19 model; the Pathfinder 1 demonstrator is available for assessment at https://www.openclinical.net/index.php?id=746.<h4>Conclusions</h4>This is believed to be the first use of AI/knowledge engineering methods for disseminating best-practice in COVID-19 care. It demonstrates a novel and promising approach to the rapid translation of clinical guidelines into point of care services, and a foundation for rapid learning systems in many areas of healthcare.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/lrh2.10236; doi:https://doi.org/10.1002/lrh2.10236; html:https://europepmc.org/articles/PMC7323421; pdf:https://europepmc.org/articles/PMC7323421?pdf=render
 36355406,https://doi.org/10.2196/40707,Effectiveness of a Web-Based Intervention to Prevent Anxiety in the Children of Parents With Anxiety: Protocol for a Randomized Controlled Trial.,"Dunn A, Alvarez J, Arbon A, Bremner S, Elsby-Pearson C, Emsley R, Jones C, Lawrence P, Lester KJ, Majdandžić M, Morson N, Perry N, Simner J, Thomson A, Cartwright-Hatton S.",,JMIR research protocols,2022,2022-11-10,Y,Child; Parent; Youth; Anxiety; Pediatric; Mental health; Randomized controlled trial; Parenting; Rct; Online; Mental Well-being; Online Intervention; Digital Intervention,,,"<h4>Background</h4>Anxiety is the most common childhood mental health condition and is associated with impaired child outcomes, including increased risk of mental health difficulties in adulthood. Anxiety runs in families: when a parent has anxiety, their child has a 50% higher chance of developing it themselves. Environmental factors are predominant in the intergenerational transmission of anxiety and, of these, parenting processes play a major role. Interventions that target parents to support them to limit the impact of any anxiogenic parenting behaviors are associated with reduced anxiety in their children. A brief UK-based group intervention delivered to parents within the UK National Health Service led to a 16% reduction in children meeting the criteria for an anxiety disorder. However, this intervention is not widely accessible. To widen access, a 9-module web-based version of this intervention has been developed. This course comprises psychoeducation and home practice delivered through text, video, animations, and practice tasks.<h4>Objective</h4>This study seeks to evaluate the feasibility of delivering this web-based intervention and assess its effectiveness in reducing child anxiety symptoms.<h4>Methods</h4> This is the protocol for a randomized controlled trial (RCT) of a community sample of 1754 parents with self-identified high levels of anxiety with a child aged 2-11 years. Parents in the intervention arm will receive access to the web-based course, which they undertake at a self-determined rate. The control arm receives no intervention. Follow-up data collection is at months 6 and months 9-21. Intention-to-treat analysis will be conducted on outcomes including child anxiety, child mental health symptoms, and well-being; parental anxiety and well-being; and parenting behaviors.<h4>Results</h4>Funding was received in April 2020, and recruitment started in February 2021 and is projected to end in October 2022. A total of 1350 participants have been recruited as of May 2022.<h4>Conclusions</h4>The results of this RCT will provide evidence on the utility of a web-based course in preventing intergenerational transmission of anxiety and increase the understanding of familial anxiety.<h4>Trial registration</h4>ClinicalTrials.gov NCT04755933; https://clinicaltrials.gov/ct2/show/NCT04755933.<h4>International registered report identifier (irrid)</h4>DERR1-10.2196/40707.",,pdf:https://jmir.org/api/download?alt_name=resprot_v11i11e40707_app2.pdf&filename=4e6914231a45b12439d1932b760a7c34.pdf; doi:https://doi.org/10.2196/40707; html:https://europepmc.org/articles/PMC9693706
 36854461,https://doi.org/10.1136/bmj-2022-073149,Realistic expectations are key to realising the benefits of polygenic scores.,"Sud A, Horton RH, Hingorani AD, Tzoulaki I, Turnbull C, Houlston RS, Lucassen A.",,BMJ (Clinical research ed.),2023,2023-02-28,Y,,,,,,pdf:https://www.bmj.com/content/bmj/380/bmj-2022-073149.full.pdf; doi:https://doi.org/10.1136/bmj-2022-073149; html:https://europepmc.org/articles/PMC9973128
 35623313,https://doi.org/10.1016/j.ejrad.2022.110366,Comparison of state-of-the-art machine and deep learning algorithms to classify proximal humeral fractures using radiology text.,"Dipnall JF, Lu J, Gabbe BJ, Cosic F, Edwards E, Page R, Du L.",,European journal of radiology,2022,2022-05-20,N,Classification; Radiology; Machine Learning; Natural Language Processing; Proximal Humeral Fracture; Deep Learning; Neer; Bert,,,"<h4>Introduction</h4>Proximal humeral fractures account for a significant proportion of all fractures. Detailed accurate classification of the type and severity of the fracture is a key component of clinical decision making, treatment and plays an important role in orthopaedic trauma research. This research aimed to assess the performance of Machine Learning (ML) multiclass classification algorithms to classify proximal humeral fractures using radiology text data.<h4>Materials and methods</h4>Data from adult (16 + years) patients admitted to a major trauma centre for management of their proximal humerus fracture from January 2010 to January 2019 were used (1,324). Six input text datasets were used for classification: X-ray and/or CT scan reports (primary) and concatenation of patient age and/or patient sex. One of seven Neer class labels were classified. Models were evaluated using accuracy, recall, precision, F1, and One-versus-rest scores.<h4>Results</h4>A number of statistical ML algorithms performed acceptably and one of the BERT models, exhibiting good accuracy of 61% and an excellent one-versus-rest score above 0.8. The highest precision, recall and F1 scores were 50%, 39% and 39% respectively, being considered reasonable scores with the sparse text data used and in the context of machine learning.<h4>Conclusion</h4>ML and BERT algorithms based on routine unstructured X-ray and CT text reports, combined with the demographics of the patient, show promise in Neer classification of proximal humeral fractures to aid research. Use of these algorithms shows potential to speed up the classification task and assist radiologist, surgeons and researchers.",,doi:https://doi.org/10.1016/j.ejrad.2022.110366
-35804579,https://doi.org/10.3390/ani12131679,Genetic Basis of Dilated Cardiomyopathy in Dogs and Its Potential as a Bidirectional Model.,"Gaar-Humphreys KR, Spanjersberg TCF, Santarelli G, Grinwis GCM, Szatmári V, Roelen BAJ, Vink A, van Tintelen JP, Asselbergs FW, Fieten H, Harakalova M, van Steenbeek FG.",,Animals : an open access journal from MDPI,2022,2022-06-29,Y,cardiovascular; Human Induced Pluripotent Stem Cells; Fibrofatty Infiltration; Canine Induced Pluripotent Stem Cells; Attenuated Wavy Fibers,,,"Cardiac disease is a leading cause of death for both humans and dogs. Genetic cardiomyopathies, including dilated cardiomyopathy (DCM), account for a proportion of these cases in both species. Patients may suffer from ventricular enlargement and systolic dysfunction resulting in congestive heart failure and ventricular arrhythmias with high risk for sudden cardiac death. Although canine DCM has similar disease progression and subtypes as in humans, only a few candidate genes have been found to be associated with DCM while the genetic background of human DCM has been more thoroughly studied. Additionally, experimental disease models using induced pluripotent stem cells have been widely adopted in the study of human genetic cardiomyopathy but have not yet been fully adapted for the in-depth study of canine genetic cardiomyopathies. The clinical presentation of DCM is extremely heterogeneous for both species with differences occurring based on sex predisposition, age of onset, and the rate of disease progression. Both genetic predisposition and environmental factors play a role in disease development which are identical in dogs and humans in contrast to other experimental animals. Interestingly, different dog breeds have been shown to develop distinct DCM phenotypes, and this presents a unique opportunity for modeling as there are multiple breed-specific models for DCM with less genetic variance than human DCM. A better understanding of DCM in dogs has the potential for improved selection for breeding and could lead to better overall care and treatment for human and canine DCM patients. At the same time, progress in research made for human DCM can have a positive impact on the care given to dogs affected by DCM. Therefore, this review will analyze the feasibility of canines as a naturally occurring bidirectional disease model for DCM in both species. The histopathology of the myocardium in canine DCM will be evaluated in three different breeds compared to control tissue, and the known genetics that contributes to both canine and human DCM will be summarized. Lastly, the prospect of canine iPSCs as a novel method to uncover the contributions of genetic variants to the pathogenesis of canine DCM will be introduced along with the applications for disease modeling and treatment.",,pdf:https://www.mdpi.com/2076-2615/12/13/1679/pdf?version=1656561768; doi:https://doi.org/10.3390/ani12131679; html:https://europepmc.org/articles/PMC9265105; pdf:https://europepmc.org/articles/PMC9265105?pdf=render
 34390586,https://doi.org/10.1111/ejn.15423,Spectral clustering based on structural magnetic resonance imaging and its relationship with major depressive disorder and cognitive ability.,"Yeung HW, Shen X, Stolicyn A, de Nooij L, Harris MA, Romaniuk L, Buchanan CR, Waiter GD, Sandu AL, McNeil CJ, Murray A, Steele JD, Campbell A, Porteous D, Lawrie SM, McIntosh AM, Cox SR, Smith KM, Whalley HC.",,The European journal of neuroscience,2021,2021-09-02,N,Cognition; Clustering; Machine Learning; Major Depressive Disorder; Structural Neuroimaging; Markov Stability,,,"There is increasing interest in using data-driven unsupervised methods to identify structural underpinnings of common mental illnesses, including major depressive disorder (MDD) and associated traits such as cognition. However, studies are often limited to severe clinical cases with small sample sizes and most do not include replication. Here, we examine two relatively large samples with structural magnetic resonance imaging (MRI), measures of lifetime MDD and cognitive variables: Generation Scotland (GS subsample, N = 980) and UK Biobank (UKB, N = 8,900), for discovery and replication, using an exploratory approach. Regional measures of FreeSurfer derived cortical thickness (CT), cortical surface area (CSA), cortical volume (CV) and subcortical volume (subCV) were input into a clustering process, controlling for common covariates. The main analysis steps involved constructing participant K-nearest neighbour graphs and graph partitioning with Markov stability to determine optimal clustering of participants. Resultant clusters were (1) checked whether they were replicated in an independent cohort and (2) tested for associations with depression status and cognitive measures. Participants separated into two clusters based on structural brain measurements in GS subsample, with large Cohen's d effect sizes between clusters in higher order cortical regions, commonly associated with executive function and decision making. Clustering was replicated in the UKB sample, with high correlations of cluster effect sizes for CT, CSA, CV and subCV between cohorts across regions. The identified clusters were not significantly different with respect to MDD case-control status in either cohort (GS subsample: p<sub>FDR</sub>  = .2239-.6585; UKB: p<sub>FDR</sub>  = .2003-.7690). Significant differences in general cognitive ability were, however, found between the clusters for both datasets, for CSA, CV and subCV (GS subsample: d = 0.2529-.3490, p<sub>FDR</sub>  < .005; UKB: d = 0.0868-0.1070, p<sub>FDR</sub>  < .005). Our results suggest that there are replicable natural groupings of participants based on cortical and subcortical brain measures, which may be related to differences in cognitive performance, but not to the MDD case-control status.",,pdf:https://discovery.dundee.ac.uk/files/66344502/ejn.15423.pdf; doi:https://doi.org/10.1111/ejn.15423
+35804579,https://doi.org/10.3390/ani12131679,Genetic Basis of Dilated Cardiomyopathy in Dogs and Its Potential as a Bidirectional Model.,"Gaar-Humphreys KR, Spanjersberg TCF, Santarelli G, Grinwis GCM, Szatmári V, Roelen BAJ, Vink A, van Tintelen JP, Asselbergs FW, Fieten H, Harakalova M, van Steenbeek FG.",,Animals : an open access journal from MDPI,2022,2022-06-29,Y,cardiovascular; Human Induced Pluripotent Stem Cells; Fibrofatty Infiltration; Canine Induced Pluripotent Stem Cells; Attenuated Wavy Fibers,,,"Cardiac disease is a leading cause of death for both humans and dogs. Genetic cardiomyopathies, including dilated cardiomyopathy (DCM), account for a proportion of these cases in both species. Patients may suffer from ventricular enlargement and systolic dysfunction resulting in congestive heart failure and ventricular arrhythmias with high risk for sudden cardiac death. Although canine DCM has similar disease progression and subtypes as in humans, only a few candidate genes have been found to be associated with DCM while the genetic background of human DCM has been more thoroughly studied. Additionally, experimental disease models using induced pluripotent stem cells have been widely adopted in the study of human genetic cardiomyopathy but have not yet been fully adapted for the in-depth study of canine genetic cardiomyopathies. The clinical presentation of DCM is extremely heterogeneous for both species with differences occurring based on sex predisposition, age of onset, and the rate of disease progression. Both genetic predisposition and environmental factors play a role in disease development which are identical in dogs and humans in contrast to other experimental animals. Interestingly, different dog breeds have been shown to develop distinct DCM phenotypes, and this presents a unique opportunity for modeling as there are multiple breed-specific models for DCM with less genetic variance than human DCM. A better understanding of DCM in dogs has the potential for improved selection for breeding and could lead to better overall care and treatment for human and canine DCM patients. At the same time, progress in research made for human DCM can have a positive impact on the care given to dogs affected by DCM. Therefore, this review will analyze the feasibility of canines as a naturally occurring bidirectional disease model for DCM in both species. The histopathology of the myocardium in canine DCM will be evaluated in three different breeds compared to control tissue, and the known genetics that contributes to both canine and human DCM will be summarized. Lastly, the prospect of canine iPSCs as a novel method to uncover the contributions of genetic variants to the pathogenesis of canine DCM will be introduced along with the applications for disease modeling and treatment.",,pdf:https://www.mdpi.com/2076-2615/12/13/1679/pdf?version=1656561768; doi:https://doi.org/10.3390/ani12131679; html:https://europepmc.org/articles/PMC9265105; pdf:https://europepmc.org/articles/PMC9265105?pdf=render
 35435219,https://doi.org/10.1093/ehjqcco/qcac016,Temporal trends in disease-specific causes of cardiovascular mortality amongst patients with cancer in the USA between 1999 and 2019.,"Raisi-Estabragh Z, Kobo O, Freeman P, Petersen SE, Kolman L, Miller RJH, Roguin A, Van Spall HGC, Vuong J, Yang EH, Mamas MA.",,European heart journal. Quality of care & clinical outcomes,2022,2022-12-01,Y,Cancer; Cardiovascular disease; epidemiology; Cardiovascular Mortality; Mortality Trends; Cardio-oncology,,,"<h4>Aims</h4>We report disease-specific cardiovascular causes of mortality among cancer patients in the USA between 1999 and 2019, considering temporal trends by age, sex, and cancer site.<h4>Methods and results</h4>We used the Multiple Cause of Death database, accessed through the Centers for Disease Control and Prevention Wide-Ranging Online Data for Epidemiologic Research resource. We included 629 308 decedents with cardiovascular disease (CVD) recorded as the primary cause of death and active malignancy listed as a contributing cause of death. We created disease-specific CVD categories and grouped cancers by site. We calculated the proportion of CVD deaths attributed to each disease category stratified by sex, age, and cancer site. We also examined disease-specific temporal trends by cancer site. Ischaemic heart disease (IHD) was the most common cardiovascular cause of death across all cancer types (55.6%), being more common in men (59.8%), older ages, and in those with lung (67.8%) and prostate (58.3%) cancers. Cerebrovascular disease (12.9%) and hypertensive diseases (7.6%) were other common causes of death. The proportion of deaths due to heart failure was greatest in haematological (7.7%) and breast (6.3%) cancers. There was a decreasing temporal trend in the proportion of cardiovascular deaths attributed to IHD across all cancer types. The proportion of deaths due to hypertensive diseases showed the greatest percentage increase, with the largest change in breast cancer patients (+191.1%).<h4>Conclusion</h4>We demonstrate differential cardiovascular mortality risk by cancer site and demographics, providing insight into the evolving healthcare needs of this growing high-cardiovascular risk population.",,pdf:https://academic.oup.com/ehjqcco/advance-article-pdf/doi/10.1093/ehjqcco/qcac016/43887262/qcac016.pdf; doi:https://doi.org/10.1093/ehjqcco/qcac016; html:https://europepmc.org/articles/PMC9745666; pdf:https://europepmc.org/articles/PMC9745666?pdf=render
-34275648,https://doi.org/10.1016/j.injury.2021.06.037,Patterns and predictors of personal responsibility attributions after major trauma.,"Lau G, Gabbe BJ, Giummarra MJ.",,Injury,2021,2021-07-06,N,"wounds and injuries; Insurance, Accident; Violence; Guilt; Accidental Injuries; Liability, Legal",,,"<h4>Background</h4>External responsibility attributions after injury are associated with worse recovery. However, there remains limited understanding of who accepts personal responsibilityfor their injury and whether or how responsibility attributions change over time.<h4>Methods</h4>This prospective cohort study included patients who received care from recovery co-ordinators following serious injury and admission to a major trauma centre in Victoria, Australia (n=850). Self-reported personal responsibility attributions (totally, partially, not responsible, or did not know) were collected at three timepoints (admission, discharge, and six months post-injury) and linked to demographic, injury and clinical characteristics from the Victorian State Trauma Registry.<h4>Results</h4>Mixed effects multinomial analyses revealed that female sex (adjusted relative risk ratio, aRRR=3.11-4.66) and compensable injury (aRRR=7.83-15.27) were associated with reporting lower personal responsibility relative to total responsibility. Falls and motorcyclists had decreased risk of reporting lower personal responsibility than non-drivers (motor vehicle/motorcycle passengers, cyclists and pedestrians) (aRRR=0.11-0.19). More than one-third of participants changed their personal responsibility attribution within six months post-injury. Kappa analyses revealed fair to moderate agreement between the three timepoints (kappa=0.38-0.59), and Stuart-Maxwell tests showed unidirectional bias towards reporting lower levels of personal responsibility between admission and discharge (p<0.001). No demographic, health or injury characteristics predicted a change in responsibility attributions in logistic regression analyses.<h4>Conclusions</h4>Personal responsibility attributions often change over time. Therefore, responsibility attributions should not be considered static, and attributions made at different times post-injury should not be used interchangeably in research or clinical settings. Given that external responsibility attributions are associated with worse post-injury outcomes, potential interventions to optimise recovery should be prioritised for patients who predominantly report lower levels of personal responsibility, especially women and people with compensable injuries. Meanwhile, factors associated with high levels of personal responsibility highlight opportunities to implement targeted injury prevention strategies.",,doi:https://doi.org/10.1016/j.injury.2021.06.037
 32142356,https://doi.org/10.1164/rccm.201902-0286oc,"Prenatal, Early-Life, and Childhood Exposure to Air Pollution and Lung Function: The ALSPAC Cohort.","Cai Y, Hansell AL, Granell R, Blangiardo M, Zottoli M, Fecht D, Gulliver J, Henderson AJ, Elliott P.",,American journal of respiratory and critical care medicine,2020,2020-07-01,N,Air pollution; Children; Traffic; Alspac; Respiratory Health,,,"<b>Rationale</b>: Exposure to air pollution during intrauterine development and through childhood may have lasting effects on respiratory health.<b>Objectives</b>: To investigate lung function at ages 8 and 15 years in relation to air pollution exposures during pregnancy, infancy, and childhood in a UK population-based birth cohort.<b>Methods</b>: Individual exposures to source-specific particulate matter ≤10 μm in aerodynamic diameter (PM<sub>10</sub>) during each trimester, 0-6 months, 7-12 months (1990-1993), and up to age 15 years (1991-2008) were examined in relation to FEV<sub>1</sub>% predicted and FVC% predicted at ages 8 (<i>n</i> = 5,276) and 15 (<i>n</i> = 3,446) years using linear regression models adjusted for potential confounders. A profile regression model was used to identify sensitive time periods.<b>Measurements and Main Results</b>: We did not find clear evidence of a sensitive exposure period for PM<sub>10</sub> from road traffic. At age 8 years, 1 μg/m<sup>3</sup> higher exposure during the first trimester was associated with lower FEV<sub>1</sub>% predicted (-0.826; 95% confidence interval [CI], -1.357 to -0.296) and FVC% predicted (-0.817; 95% CI, -1.357 to -0.276), but similar associations were seen for exposures for other trimesters, 0-6 months, 7-12 months, and 0-7 years. Associations were stronger among boys, as well as children whose mother had a lower education level or smoked during pregnancy. For PM<sub>10</sub> from all sources, the third trimester was associated with lower FVC% predicted (-1.312; 95% CI, -2.100 to -0.525). At age 15 years, no adverse associations with lung function were seen.<b>Conclusions</b>: Exposure to road-traffic PM<sub>10</sub> during pregnancy may result in small but significant reductions in lung function at age 8 years.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7328307; doi:https://doi.org/10.1164/rccm.201902-0286OC; html:https://europepmc.org/articles/PMC7328307; pdf:https://europepmc.org/articles/PMC7328307?pdf=render; doi:https://doi.org/10.1164/rccm.201902-0286oc
+34275648,https://doi.org/10.1016/j.injury.2021.06.037,Patterns and predictors of personal responsibility attributions after major trauma.,"Lau G, Gabbe BJ, Giummarra MJ.",,Injury,2021,2021-07-06,N,"wounds and injuries; Insurance, Accident; Violence; Guilt; Accidental Injuries; Liability, Legal",,,"<h4>Background</h4>External responsibility attributions after injury are associated with worse recovery. However, there remains limited understanding of who accepts personal responsibilityfor their injury and whether or how responsibility attributions change over time.<h4>Methods</h4>This prospective cohort study included patients who received care from recovery co-ordinators following serious injury and admission to a major trauma centre in Victoria, Australia (n=850). Self-reported personal responsibility attributions (totally, partially, not responsible, or did not know) were collected at three timepoints (admission, discharge, and six months post-injury) and linked to demographic, injury and clinical characteristics from the Victorian State Trauma Registry.<h4>Results</h4>Mixed effects multinomial analyses revealed that female sex (adjusted relative risk ratio, aRRR=3.11-4.66) and compensable injury (aRRR=7.83-15.27) were associated with reporting lower personal responsibility relative to total responsibility. Falls and motorcyclists had decreased risk of reporting lower personal responsibility than non-drivers (motor vehicle/motorcycle passengers, cyclists and pedestrians) (aRRR=0.11-0.19). More than one-third of participants changed their personal responsibility attribution within six months post-injury. Kappa analyses revealed fair to moderate agreement between the three timepoints (kappa=0.38-0.59), and Stuart-Maxwell tests showed unidirectional bias towards reporting lower levels of personal responsibility between admission and discharge (p<0.001). No demographic, health or injury characteristics predicted a change in responsibility attributions in logistic regression analyses.<h4>Conclusions</h4>Personal responsibility attributions often change over time. Therefore, responsibility attributions should not be considered static, and attributions made at different times post-injury should not be used interchangeably in research or clinical settings. Given that external responsibility attributions are associated with worse post-injury outcomes, potential interventions to optimise recovery should be prioritised for patients who predominantly report lower levels of personal responsibility, especially women and people with compensable injuries. Meanwhile, factors associated with high levels of personal responsibility highlight opportunities to implement targeted injury prevention strategies.",,doi:https://doi.org/10.1016/j.injury.2021.06.037
 35089148,https://doi.org/10.2196/28095,The Association Between Home Stay and Symptom Severity in Major Depressive Disorder: Preliminary Findings From a Multicenter Observational Study Using Geolocation Data From Smartphones.,"Laiou P, Kaliukhovich DA, Folarin AA, Ranjan Y, Rashid Z, Conde P, Stewart C, Sun S, Zhang Y, Matcham F, Ivan A, Lavelle G, Siddi S, Lamers F, Penninx BW, Haro JM, Annas P, Cummins N, Vairavan S, Manyakov NV, Narayan VA, Dobson RJ, Hotopf M, RADAR-CNS.",,JMIR mHealth and uHealth,2022,2022-01-28,Y,GPS; Mobile phone; Major Depressive Disorder; Smartphone; Phq-8; Home Stay,,,"<h4>Background</h4>Most smartphones and wearables are currently equipped with location sensing (using GPS and mobile network information), which enables continuous location tracking of their users. Several studies have reported that various mobility metrics, as well as home stay, that is, the amount of time an individual spends at home in a day, are associated with symptom severity in people with major depressive disorder (MDD). Owing to the use of small and homogeneous cohorts of participants, it is uncertain whether the findings reported in those studies generalize to a broader population of individuals with MDD symptoms.<h4>Objective</h4>The objective of this study is to examine the relationship between the overall severity of depressive symptoms, as assessed by the 8-item Patient Health Questionnaire, and median daily home stay over the 2 weeks preceding the completion of a questionnaire in individuals with MDD.<h4>Methods</h4>We used questionnaire and geolocation data of 164 participants with MDD collected in the observational Remote Assessment of Disease and Relapse-Major Depressive Disorder study. The participants were recruited from three study sites: King's College London in the United Kingdom (109/164, 66.5%); Vrije Universiteit Medisch Centrum in Amsterdam, the Netherlands (17/164, 10.4%); and Centro de Investigación Biomédica en Red in Barcelona, Spain (38/164, 23.2%). We used a linear regression model and a resampling technique (n=100 draws) to investigate the relationship between home stay and the overall severity of MDD symptoms. Participant age at enrollment, gender, occupational status, and geolocation data quality metrics were included in the model as additional explanatory variables. The 95% 2-sided CIs were used to evaluate the significance of model variables.<h4>Results</h4>Participant age and severity of MDD symptoms were found to be significantly related to home stay, with older (95% CI 0.161-0.325) and more severely affected individuals (95% CI 0.015-0.184) spending more time at home. The association between home stay and symptoms severity appeared to be stronger on weekdays (95% CI 0.023-0.178, median 0.098; home stay: 25th-75th percentiles 17.8-22.8, median 20.9 hours a day) than on weekends (95% CI -0.079 to 0.149, median 0.052; home stay: 25th-75th percentiles 19.7-23.5, median 22.3 hours a day). Furthermore, we found a significant modulation of home stay by occupational status, with employment reducing home stay (employed participants: 25th-75th percentiles 16.1-22.1, median 19.7 hours a day; unemployed participants: 25th-75th percentiles 20.4-23.5, median 22.6 hours a day).<h4>Conclusions</h4>Our findings suggest that home stay is associated with symptom severity in MDD and demonstrate the importance of accounting for confounding factors in future studies. In addition, they illustrate that passive sensing of individuals with depression is feasible and could provide clinically relevant information to monitor the course of illness in patients with MDD.",,pdf:https://mhealth.jmir.org/2022/1/e28095/PDF; doi:https://doi.org/10.2196/28095; html:https://europepmc.org/articles/PMC8838593
-33866023,https://doi.org/10.1016/j.oret.2021.04.001,Evolving Treatment Patterns and Outcomes of Neovascular Age-Related Macular Degeneration Over a Decade.,"Schwartz R, Warwick A, Olvera-Barrios A, Pikoula M, Lee AY, Denaxas S, Taylor P, Egan C, Chakravarthy U, Lip PL, Tufail A, of the UK EMR Users Group.",,Ophthalmology. Retina,2021,2021-04-16,N,AMD; Ranibizumab; Anti-vegf; Aflibercept; Electronic Health Records; Etdrs; Early Treatment Diabetic Retinopathy Study,,,"<h4>Purpose</h4>Management of neovascular age-related macular degeneration (nAMD) has evolved over the last decade with several treatment regimens and medications. This study describes the treatment patterns and visual outcomes over 10 years in a large cohort of patients.<h4>Design</h4>Retrospective analysis of electronic health records from 27 National Health Service secondary care healthcare providers in the UK.<h4>Participants</h4>Treatment-naïve patients receiving at least 3 intravitreal anti-vascular endothelial growth factor (VEGF) injections for nAMD in their first 6 months of follow-up were included. Patients with missing data for age or gender and those aged less than 55 years were excluded.<h4>Methods</h4>Eyes with at least 3 years of follow-up were grouped by years of treatment initiation, and 3-year outcomes were compared between the groups. Data were generated during routine clinical care between September 2008 and December 2018.<h4>Main outcome measures</h4>Visual acuity (VA), number of injections, and number of visits.<h4>Results</h4>A total of 15 810 eyes of 13 705 patients receiving 195 104 injections were included. Visual acuity improved from baseline during the first year, but decreased thereafter, resulting in loss of visual gains. This trend remained consistent throughout the past decade. Although an increasing proportion of eyes remained in the driving standard, this was driven by better presenting VA over the decade. The number of injections decreased substantially between the first and subsequent years, from a mean of 6.25 in year 1 to 3 in year 2 and 2.5 in year 3, without improvement over the decade. In a multivariable regression analysis, final VA improved by 0.24 letters for each year since 2008, and younger age and baseline VA were significantly associated with VA at 3 years.<h4>Conclusions</h4>Our findings show that despite improvement in functional VA over the years, primarily driven by improving baseline VA, patients continue to lose vision after the first year of treatment, with only marginal change over the past decade. The data suggest these results may be related to suboptimal treatment patterns, which have not improved over the years. Rethinking treatment strategies may be warranted, possibly on a national level or through the introduction of longer-acting therapies.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9165682; doi:https://doi.org/10.1016/j.oret.2021.04.001; html:https://europepmc.org/articles/PMC9165682; pdf:https://europepmc.org/articles/PMC9165682?pdf=render; doi:https://doi.org/10.1016/j.oret.2021.04.001
 34850874,https://doi.org/10.1093/gigascience/giab083,Erratum to: An overview of the National COVID-19 Chest Imaging Database: data quality and cohort analysis.,"Cushnan D, Bennett O, Berka R, Bertolli O, Chopra A, Dorgham S, Favaro A, Ganepola T, Halling-Brown M, Imreh G, Jacob J, Jefferson E, Lemarchand F, Schofield D, Wyatt JC, Collaborative NCCID.",,GigaScience,2021,2021-12-01,Y,,,,,,pdf:https://academic.oup.com/gigascience/article-pdf/10/12/giab083/41395049/giab083.pdf; doi:https://doi.org/10.1093/gigascience/giab083; html:https://europepmc.org/articles/PMC8634578; pdf:https://europepmc.org/articles/PMC8634578?pdf=render
+33866023,https://doi.org/10.1016/j.oret.2021.04.001,Evolving Treatment Patterns and Outcomes of Neovascular Age-Related Macular Degeneration Over a Decade.,"Schwartz R, Warwick A, Olvera-Barrios A, Pikoula M, Lee AY, Denaxas S, Taylor P, Egan C, Chakravarthy U, Lip PL, Tufail A, of the UK EMR Users Group.",,Ophthalmology. Retina,2021,2021-04-16,N,AMD; Ranibizumab; Anti-vegf; Aflibercept; Electronic Health Records; Etdrs; Early Treatment Diabetic Retinopathy Study,,,"<h4>Purpose</h4>Management of neovascular age-related macular degeneration (nAMD) has evolved over the last decade with several treatment regimens and medications. This study describes the treatment patterns and visual outcomes over 10 years in a large cohort of patients.<h4>Design</h4>Retrospective analysis of electronic health records from 27 National Health Service secondary care healthcare providers in the UK.<h4>Participants</h4>Treatment-naïve patients receiving at least 3 intravitreal anti-vascular endothelial growth factor (VEGF) injections for nAMD in their first 6 months of follow-up were included. Patients with missing data for age or gender and those aged less than 55 years were excluded.<h4>Methods</h4>Eyes with at least 3 years of follow-up were grouped by years of treatment initiation, and 3-year outcomes were compared between the groups. Data were generated during routine clinical care between September 2008 and December 2018.<h4>Main outcome measures</h4>Visual acuity (VA), number of injections, and number of visits.<h4>Results</h4>A total of 15 810 eyes of 13 705 patients receiving 195 104 injections were included. Visual acuity improved from baseline during the first year, but decreased thereafter, resulting in loss of visual gains. This trend remained consistent throughout the past decade. Although an increasing proportion of eyes remained in the driving standard, this was driven by better presenting VA over the decade. The number of injections decreased substantially between the first and subsequent years, from a mean of 6.25 in year 1 to 3 in year 2 and 2.5 in year 3, without improvement over the decade. In a multivariable regression analysis, final VA improved by 0.24 letters for each year since 2008, and younger age and baseline VA were significantly associated with VA at 3 years.<h4>Conclusions</h4>Our findings show that despite improvement in functional VA over the years, primarily driven by improving baseline VA, patients continue to lose vision after the first year of treatment, with only marginal change over the past decade. The data suggest these results may be related to suboptimal treatment patterns, which have not improved over the years. Rethinking treatment strategies may be warranted, possibly on a national level or through the introduction of longer-acting therapies.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9165682; doi:https://doi.org/10.1016/j.oret.2021.04.001; html:https://europepmc.org/articles/PMC9165682; pdf:https://europepmc.org/articles/PMC9165682?pdf=render; doi:https://doi.org/10.1016/j.oret.2021.04.001
 35536740,https://doi.org/10.1136/bmjopen-2021-052884,Gaps in antihypertensive and statin treatments and benefits of optimisation: a modelling study in a 1 million ethnically diverse urban population in UK.,"Wu R, Rison SCG, Raisi-Estabragh Z, Dostal I, Carvalho C, Robson J, Mihaylova B.",,BMJ open,2021,2021-12-30,Y,Hypertension; Preventive Medicine; Ischaemic Heart Disease; Primary Care; Health Policy; Quality In Health Care,,,"<h4>Objectives</h4>To characterise gaps in antihypertensive treatment in people with hypertension and statin treatment in people with cardiovascular diseases (CVD) in a large urban population and quantify the health and economic impacts of their optimisation.<h4>Design</h4>A cross-sectional population study and a long-term CVD decision model.<h4>Setting</h4>Primary care, UK.<h4>Participants</h4>All adults with diagnosed hypertension or CVD in a population of about 1 million people, served by 123 primary care practices in London, UK in 2019.<h4>Interventions</h4>Following UK clinical guidelines, all adults with diagnosed hypertension were categorised into optimal, suboptimal and untreated groups with respect to their antihypertensive treatment, and all adults with diagnosed CVD were categorised in the same manner with respect to their statin treatment.<h4>Outcomes</h4>Proportion of patients suboptimally treated or untreated. Projected cardiovascular events avoided, years and quality-adjusted life years (QALYs) gained and healthcare costs saved with optimised treatments.<h4>Results</h4>21 954 of the 91 828 adults with hypertension (24%; mean age 59 years; 49% women) and 9062 of the 23 723 adults with CVD (38%; mean age 69 years; 43% women) were not optimally treated with antihypertensive or statin treatment, respectively. Per 1000 additional patients optimised over 5 years, hypertension treatment is projected to prevent 25 (95% CI 16 to 32) major vascular events (MVEs) and 7 (3 to 10) vascular deaths, statin treatment, 28 (22 to 33) MVEs and 6 (4 to 7) vascular deaths. Over their lifespan, a patient with uncontrolled hypertension aged 60-69 years is projected to gain 0.64 (95% CI 0.36 to 0.87) QALYs with optimised hypertension treatment, and a similarly aged patient with previous CVD not optimally treated with statin is projected to gain 0.3 (0.24 to 0.37) QALYs with optimised statin treatment. In both cases, the hospital cost savings minus extra medication costs were about £1100 per person over remaining lifespan.<h4>Conclusions</h4>Optimising cardiovascular treatments can cost-effectively reduce cardiovascular risk and improve life expectancy.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/12/e052884.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-052884; html:https://europepmc.org/articles/PMC8719215; pdf:https://europepmc.org/articles/PMC8719215?pdf=render
 36198485,https://doi.org/10.1136/jech-2021-217986,Characteristics of enrolment in an intensive home-visiting programme among eligible first-time adolescent mothers in England: a linked administrative data cohort study.,"Cavallaro FL, Gilbert R, Wijlaars LP, Kennedy E, Howarth E, Kendall S, van der Meulen J, Calin MA, Reed L, Harron K.",,Journal of epidemiology and community health,2022,2022-10-05,Y,Adolescent; Public Health; Child Health,,,"<h4>Background</h4>Intensive home visiting for adolescent mothers may help reduce health disparities. Given limited resources, such interventions need to be effectively targeted. We evaluated which mothers were enrolled in the Family Nurse Partnership (FNP), an intensive home-visiting service for first-time young mothers commissioned in >130 local authorities in England since 2007.<h4>Methods</h4>We created a population-based cohort of first-time mothers aged 13-19 years giving birth in English National Health Service hospitals between 1 April 2010 and 31 March 2017, using administrative hospital data linked with FNP programme, educational and social care data. Mothers living in a local authority with an active FNP site were eligible. We described variation in enrolment rates across sites, and identified maternal and FNP site characteristics associated with enrolment.<h4>Results</h4>Of 110 520 eligible mothers, 25 680 (23.2% (95% CI: 23.0% to 23.5%)) were enrolled. Enrolment rates varied substantially across 122 sites (range: 11%-68%), and areas with greater numbers of first-time adolescent mothers achieved lower enrolment rates. Mothers aged 13-15 years were most likely to be enrolled (52%). However, only 26% of adolescent mothers with markers of vulnerability (including living in the most deprived areas and ever having been looked after as a child) were enrolled.<h4>Conclusion</h4>A substantial proportion of first-time adolescent mothers with vulnerability markers were not enrolled in FNP. Variation in enrolment across sites indicates insufficient commissioning of places that is not proportional to level of need, with mothers in areas with large numbers of other adolescent mothers least likely to receive support.",,pdf:https://jech.bmj.com/content/jech/76/12/991.full.pdf; doi:https://doi.org/10.1136/jech-2021-217986; html:https://europepmc.org/articles/PMC9664100; pdf:https://europepmc.org/articles/PMC9664100?pdf=render
-38383544,https://doi.org/10.1038/s41467-024-45761-7,The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies.,"Lipworth S, Matlock W, Shaw L, Vihta KD, Rodger G, Chau K, Barker L, George S, Kavanagh J, Davies T, Vaughan A, Andersson M, Jeffery K, Oakley S, Morgan M, Hopkins S, Peto T, Crook D, Walker AS, Stoesser N.",,Nature communications,2024,2024-02-22,Y,,,,"Plasmids carry genes conferring antimicrobial resistance and other clinically important traits, and contribute to the rapid dissemination of such genes. Previous studies using complete plasmid assemblies, which are essential for reliable inference, have been small and/or limited to plasmids carrying antimicrobial resistance genes (ARGs). In this study, we sequenced 1,880 complete plasmids from 738 isolates from bloodstream infections in Oxfordshire, UK. The bacteria had been originally isolated in 2009 (194 isolates) and 2018 (368 isolates), plus a stratified selection from intervening years (176 isolates). We demonstrate that plasmids are largely, but not entirely, constrained to a single host species, although there is substantial overlap between species of plasmid gene-repertoire. Most ARGs are carried by a relatively small number of plasmid groups with biological features that are predictable. Plasmids carrying ARGs (including those encoding carbapenemases) share a putative 'backbone' of core genes with those carrying no such genes. These findings suggest that future surveillance should, in addition to tracking plasmids currently associated with clinically important genes, focus on identifying and monitoring the dissemination of high-risk plasmid groups with the potential to rapidly acquire and disseminate these genes.",,doi:https://doi.org/10.1038/s41467-024-45761-7; html:https://europepmc.org/articles/PMC10881496; pdf:https://europepmc.org/articles/PMC10881496?pdf=render
 34038519,https://doi.org/10.1093/ageing/afab084,Developing a UK sarcopenia registry: recruitment and baseline characteristics of the SarcNet pilot.,"Witham MD, Heslop P, Dodds RM, Clegg AP, Hope SV, McDonald C, Smithard D, Storey B, Tan AL, Thornhill A, Sayer AA.",,Age and ageing,2021,2021-09-01,Y,Recruitment; Older People; Registry; Sarcopenia,,,"<h4>Background</h4>sarcopenia registries are a potential method to meet the challenge of recruitment to sarcopenia trials. We tested the feasibility of setting up a UK sarcopenia registry, the feasibility of recruitment methods and sought to characterise the pilot registry population.<h4>Methods</h4>six diverse UK sites took part, with potential participants aged 65 and over approached via mailshots from local primary care practices. Telephone pre-screening using the SARC-F score was followed by in-person screening and baseline visit. Co-morbidities, medications, grip strength, Short Physical Performance Battery, bioimpedance analysis, Geriatric Depression Score, Montreal Cognitive Assessment, Sarcopenia Quality of Life score were performed and permission sought for future recontact. Descriptive statistics for recruitment rates and baseline measures were generated; an embedded randomised trial examined the effect of a University logo on the primary care mailshot on recruitment rates.<h4>Results</h4>sixteen practices contributed a total of 3,508 letters. In total, 428 replies were received (12% response rate); 380 underwent telephone pre-screening of whom 215 (57%) were eligible to attend a screening visit; 150 participants were recruited (40% of those pre-screened) with 147 contributing baseline data. No significant difference was seen in response rates between mailshots with and without the logo (between-group difference 1.1% [95% confidence interval -1.0% to 3.4%], P = 0.31). The mean age of enrollees was 78 years; 72 (49%) were women. In total, 138/147 (94%) had probable sarcopenia on European Working Group on Sarcopenia 2019 criteria and 145/147 (98%) agreed to be recontacted about future studies.<h4>Conclusion</h4>recruitment to a multisite UK sarcopenia registry is feasible, with high levels of consent for recontact.",,pdf:https://academic.oup.com/ageing/article-pdf/50/5/1762/40349116/afab084.pdf; doi:https://doi.org/10.1093/ageing/afab084; html:https://europepmc.org/articles/PMC8437066; pdf:https://europepmc.org/articles/PMC8437066?pdf=render
+38383544,https://doi.org/10.1038/s41467-024-45761-7,The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies.,"Lipworth S, Matlock W, Shaw L, Vihta KD, Rodger G, Chau K, Barker L, George S, Kavanagh J, Davies T, Vaughan A, Andersson M, Jeffery K, Oakley S, Morgan M, Hopkins S, Peto T, Crook D, Walker AS, Stoesser N.",,Nature communications,2024,2024-02-22,Y,,,,"Plasmids carry genes conferring antimicrobial resistance and other clinically important traits, and contribute to the rapid dissemination of such genes. Previous studies using complete plasmid assemblies, which are essential for reliable inference, have been small and/or limited to plasmids carrying antimicrobial resistance genes (ARGs). In this study, we sequenced 1,880 complete plasmids from 738 isolates from bloodstream infections in Oxfordshire, UK. The bacteria had been originally isolated in 2009 (194 isolates) and 2018 (368 isolates), plus a stratified selection from intervening years (176 isolates). We demonstrate that plasmids are largely, but not entirely, constrained to a single host species, although there is substantial overlap between species of plasmid gene-repertoire. Most ARGs are carried by a relatively small number of plasmid groups with biological features that are predictable. Plasmids carrying ARGs (including those encoding carbapenemases) share a putative 'backbone' of core genes with those carrying no such genes. These findings suggest that future surveillance should, in addition to tracking plasmids currently associated with clinically important genes, focus on identifying and monitoring the dissemination of high-risk plasmid groups with the potential to rapidly acquire and disseminate these genes.",,doi:https://doi.org/10.1038/s41467-024-45761-7; html:https://europepmc.org/articles/PMC10881496; pdf:https://europepmc.org/articles/PMC10881496?pdf=render
 31822919,https://doi.org/10.1093/pubmed/fdz172,"Unmet needs of women with GDM: a health needs assessment in Sandwell, West Midlands.","Plant N, Šumilo D, Chapman R, Webber J, Saravanan P, Nirantharakumar K.",,"Journal of public health (Oxford, England)",2020,2020-11-01,N,United Kingdom; Needs Assessment; Gestational Diabetes,,,"<h4>Background</h4>Gestational diabetes mellitus (GDM) affects over 4% of pregnancies in England. We investigated GDM epidemiology within ethnically diverse population and the current offer of services to women with previous GDM to reduce their type 2 diabetes mellitus (T2DM) risk.<h4>Methods</h4>(i) Analysis of routinely collected maternity data examining GDM incidence and risk factors; (ii) local authority self-assessment questionnaire on public health interventions targeting women with previous GDM and (iii) service development discussions regarding the current pathway and areas for improvement.<h4>Results</h4>Of 9390 births between 2014 and 2018, 6.8% had a record of GDM. High body mass index (BMI), maternal age, and ethnicity (South Asian and some mixed ethnic backgrounds) were independent predictors of GDM. There were no public health commissioned services specifically targeting women with previous GDM. Weaknesses in transition from secondary to primary care and areas for improvement when screening for GDM were identified.<h4>Conclusions</h4>GDM burden in this population was high. Awareness should be raised on the importance of regular glucose testing and lifestyle modification to delay or prevent progression to T2DM, particularly within high risk groups. The potential for health visitors to contribute to this should be explored. Commissioners should review evidence to develop a flexible lifestyle services model to meet the specific needs of these women.",,pdf:https://academic.oup.com/jpubhealth/article-pdf/42/4/e516/34469316/fdz172.pdf; doi:https://doi.org/10.1093/pubmed/fdz172
+30745170,https://doi.org/10.1016/j.ebiom.2019.02.005,"Identification of novel genome-wide associations for suicidality in UK Biobank, genetic correlation with psychiatric disorders and polygenic association with completed suicide.","Strawbridge RJ, Ward J, Ferguson A, Graham N, Shaw RJ, Cullen B, Pearsall R, Lyall LM, Johnston KJA, Niedzwiedz CL, Pell JP, Mackay D, Martin JL, Lyall DM, Bailey MES, Smith DJ.",,EBioMedicine,2019,2019-02-08,Y,,Understanding the Causes of Disease,,"<h4>Background</h4>Suicide is a major issue for global public health. Suicidality describes a broad spectrum of thoughts and behaviours, some of which are common in the general population. Although suicide results from a complex interaction of multiple social and psychological factors, predisposition to suicidality is at least partly genetic.<h4>Methods</h4>Ordinal genome-wide association study of suicidality in the UK Biobank cohort comparing: 'no suicidality' controls (N = 83,557); 'thoughts that life was not worth living' (N = 21,063); 'ever contemplated self-harm' (N = 13,038); 'act of deliberate self-harm in the past' (N = 2498); and 'previous suicide attempt' (N = 2666).<h4>Outcomes</h4>We identified three novel genome-wide significant loci for suicidality (on chromosomes nine, 11 and 13) and moderate-to-strong genetic correlations between suicidality and a range of psychiatric disorders, most notably depression (r<sub>g</sub> 0·81).<h4>Interpretation</h4>These findings provide new information about genetic variants relating to increased risk of suicidal thoughts and behaviours. Future work should assess the extent to which polygenic risk scores for suicidality, in combination with non-genetic risk factors, may be useful for stratified approaches to suicide prevention at a population level. FUND: UKRI Innovation-HDR-UK Fellowship (MR/S003061/1). MRC Mental Health Data Pathfinder Award (MC_PC_17217). MRC Doctoral Training Programme Studentship at the University of Glasgow (MR/K501335/1). MRC Doctoral Training Programme Studentship at the Universities of Glasgow and Edinburgh. UKRI Innovation Fellowship (MR/R024774/1).",,pdf:http://www.thelancet.com/article/S2352396419300775/pdf; doi:https://doi.org/10.1016/j.ebiom.2019.02.005; html:https://europepmc.org/articles/PMC6442001; pdf:https://europepmc.org/articles/PMC6442001?pdf=render
 30940752,https://doi.org/10.1136/bmjopen-2018-023232,Using natural language processing to extract structured epilepsy data from unstructured clinic letters: development and validation of the ExECT (extraction of epilepsy clinical text) system.,"Fonferko-Shadrach B, Lacey AS, Roberts A, Akbari A, Thompson S, Ford DV, Lyons RA, Rees MI, Pickrell WO.",,BMJ open,2019,2019-04-01,Y,Epilepsy; Validation; Information Extraction; Natural Language Processing,Applied Analytics,,"<h4>Objective</h4>Routinely collected healthcare data are a powerful research resource but often lack detailed disease-specific information that is collected in clinical free text, for example, clinic letters. We aim to use natural language processing techniques to extract detailed clinical information from epilepsy clinic letters to enrich routinely collected data.<h4>Design</h4>We used the general architecture for text engineering (GATE) framework to build an information extraction system, ExECT (extraction of epilepsy clinical text), combining rule-based and statistical techniques. We extracted nine categories of epilepsy information in addition to clinic date and date of birth across 200 clinic letters. We compared the results of our algorithm with a manual review of the letters by an epilepsy clinician.<h4>Setting</h4>De-identified and pseudonymised epilepsy clinic letters from a Health Board serving half a million residents in Wales, UK.<h4>Results</h4>We identified 1925 items of information with overall precision, recall and F1 score of 91.4%, 81.4% and 86.1%, respectively. Precision and recall for epilepsy-specific categories were: epilepsy diagnosis (88.1%, 89.0%), epilepsy type (89.8%, 79.8%), focal seizures (96.2%, 69.7%), generalised seizures (88.8%, 52.3%), seizure frequency (86.3%-53.6%), medication (96.1%, 94.0%), CT (55.6%, 58.8%), MRI (82.4%, 68.8%) and electroencephalogram (81.5%, 75.3%).<h4>Conclusions</h4>We have built an automated clinical text extraction system that can accurately extract epilepsy information from free text in clinic letters. This can enhance routinely collected data for research in the UK. The information extracted with ExECT such as epilepsy type, seizure frequency and neurological investigations are often missing from routinely collected data. We propose that our algorithm can bridge this data gap enabling further epilepsy research opportunities. While many of the rules in our pipeline were tailored to extract epilepsy specific information, our methods can be applied to other diseases and also can be used in clinical practice to record patient information in a structured manner.",,pdf:https://bmjopen.bmj.com/content/bmjopen/9/4/e023232.full.pdf; doi:https://doi.org/10.1136/bmjopen-2018-023232; html:https://europepmc.org/articles/PMC6500195; pdf:https://europepmc.org/articles/PMC6500195?pdf=render
 32651323,https://doi.org/10.3233/jad-200338,"Alzheimer's Disease Susceptibility Gene Apolipoprotein E (APOE) and Blood Biomarkers in UK Biobank (N = 395,769).","Ferguson AC, Tank R, Lyall LM, Ward J, Celis-Morales C, Strawbridge R, Ho F, Whelan CD, Gill J, Welsh P, Anderson JJ, Mark PB, Mackay DF, Smith DJ, Pell JP, Cavanagh J, Sattar N, Lyall DM.",,Journal of Alzheimer's disease : JAD,2020,2020-01-01,N,Cholesterol; apoE; Alzheimer’s disease; Dementia; Uk Biobank,,,"<h4>Background</h4>Alzheimer's disease (AD) is a neurodegenerative condition where the underlying etiology is still unclear. Investigating the potential influence of apolipoprotein E (APOE), a major genetic risk factor, on common blood biomarkers could provide a greater understanding of the mechanisms of AD and dementia risk.<h4>Objective</h4>Our objective was to conduct the largest (to date) single-protocol investigation of blood biomarkers in the context of APOE genotype, in UK Biobank.<h4>Methods</h4>After quality control and exclusions, data on 395,769 participants of White European ancestry were available for analysis. Linear regressions were used to test potential associations between APOE genotypes and biomarkers.<h4>Results</h4>Several biomarkers significantly associated with APOEɛ4 'risk' and ɛ2 'protective' genotypes (versus neutral ɛ3/ɛ3). Most associations supported previous data: for example, ɛ4 genotype was associated with elevated low-density lipoprotein cholesterol (LDL) (standardized beta [b] = 0.150 standard deviations [SDs] per allele, p < 0.001) and ɛ2 with lower LDL (b = -0.456 SDs, p < 0.001). There were however instances of associations found in unexpected directions: e.g., ɛ4 and increased insulin-like growth factor (IGF-1) (b = 0.017, p < 0.001) where lower levels have been previously suggested as an AD risk factor.<h4>Conclusion</h4>These findings highlight biomarker differences in non-demented people at genetic risk for dementia. The evidence herein supports previous hypotheses of involvement from cardiometabolic and neuroinflammatory pathways.",,pdf:https://eprints.gla.ac.uk/217500/1/217500.pdf; doi:https://doi.org/10.3233/JAD-200338
-37319288,https://doi.org/10.1371/journal.pone.0287264,Evaluation of data processing pipelines on real-world electronic health records data for the purpose of measuring patient similarity.,"Pikoula M, Kallis C, Madjiheurem S, Quint JK, Bafadhel M, Denaxas S.",,PloS one,2023,2023-06-15,Y,,,,"<h4>Background</h4>The ever-growing size, breadth, and availability of patient data allows for a wide variety of clinical features to serve as inputs for phenotype discovery using cluster analysis. Data of mixed types in particular are not straightforward to combine into a single feature vector, and techniques used to address this can be biased towards certain data types in ways that are not immediately obvious or intended. In this context, the process of constructing clinically meaningful patient representations from complex datasets has not been systematically evaluated.<h4>Aims</h4>Our aim was to a) outline and b) implement an analytical framework to evaluate distinct methods of constructing patient representations from routine electronic health record data for the purpose of measuring patient similarity. We applied the analysis on a patient cohort diagnosed with chronic obstructive pulmonary disease.<h4>Methods</h4>Using data from the CALIBER data resource, we extracted clinically relevant features for a cohort of patients diagnosed with chronic obstructive pulmonary disease. We used four different data processing pipelines to construct lower dimensional patient representations from which we calculated patient similarity scores. We described the resulting representations, ranked the influence of each individual feature on patient similarity and evaluated the effect of different pipelines on clustering outcomes. Experts evaluated the resulting representations by rating the clinical relevance of similar patient suggestions with regard to a reference patient.<h4>Results</h4>Each of the four pipelines resulted in similarity scores primarily driven by a unique set of features. It was demonstrated that data transformations according to each pipeline prior to clustering can result in a variation of clustering results of over 40%. The most appropriate pipeline was selected on the basis of feature ranking and clinical expertise. There was moderate agreement between clinicians as measured by Cohen's kappa coefficient.<h4>Conclusions</h4>Data transformation has downstream and unforeseen consequences in cluster analysis. Rather than viewing this process as a black box, we have shown ways to quantitatively and qualitatively evaluate and select the appropriate preprocessing pipeline.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0287264&type=printable; doi:https://doi.org/10.1371/journal.pone.0287264; html:https://europepmc.org/articles/PMC10270623; pdf:https://europepmc.org/articles/PMC10270623?pdf=render
 36855161,https://doi.org/10.1186/s13073-023-01161-y,Refining epigenetic prediction of chronological and biological age.,"Bernabeu E, McCartney DL, Gadd DA, Hillary RF, Lu AT, Murphy L, Wrobel N, Campbell A, Harris SE, Liewald D, Hayward C, Sudlow C, Cox SR, Evans KL, Horvath S, McIntosh AM, Robinson MR, Vallejos CA, Marioni RE.",,Genome medicine,2023,2023-02-28,Y,,,,"<h4>Background</h4>Epigenetic clocks can track both chronological age (cAge) and biological age (bAge). The latter is typically defined by physiological biomarkers and risk of adverse health outcomes, including all-cause mortality. As cohort sample sizes increase, estimates of cAge and bAge become more precise. Here, we aim to develop accurate epigenetic predictors of cAge and bAge, whilst improving our understanding of their epigenomic architecture.<h4>Methods</h4>First, we perform large-scale (N = 18,413) epigenome-wide association studies (EWAS) of chronological age and all-cause mortality. Next, to create a cAge predictor, we use methylation data from 24,674 participants from the Generation Scotland study, the Lothian Birth Cohorts (LBC) of 1921 and 1936, and 8 other cohorts with publicly available data. In addition, we train a predictor of time to all-cause mortality as a proxy for bAge using the Generation Scotland cohort (1214 observed deaths). For this purpose, we use epigenetic surrogates (EpiScores) for 109 plasma proteins and the 8 component parts of GrimAge, one of the current best epigenetic predictors of survival. We test this bAge predictor in four external cohorts (LBC1921, LBC1936, the Framingham Heart Study and the Women's Health Initiative study).<h4>Results</h4>Through the inclusion of linear and non-linear age-CpG associations from the EWAS, feature pre-selection in advance of elastic net regression, and a leave-one-cohort-out (LOCO) cross-validation framework, we obtain cAge prediction with a median absolute error equal to 2.3 years. Our bAge predictor was found to slightly outperform GrimAge in terms of the strength of its association to survival (HR<sub>GrimAge</sub> = 1.47 [1.40, 1.54] with p = 1.08 × 10<sup>-52</sup>, and HR<sub>bAge</sub> = 1.52 [1.44, 1.59] with p = 2.20 × 10<sup>-60</sup>). Finally, we introduce MethylBrowsR, an online tool to visualise epigenome-wide CpG-age associations.<h4>Conclusions</h4>The integration of multiple large datasets, EpiScores, non-linear DNAm effects, and new approaches to feature selection has facilitated improvements to the blood-based epigenetic prediction of biological and chronological age.",,pdf:https://genomemedicine.biomedcentral.com/counter/pdf/10.1186/s13073-023-01161-y; doi:https://doi.org/10.1186/s13073-023-01161-y; html:https://europepmc.org/articles/PMC9976489; pdf:https://europepmc.org/articles/PMC9976489?pdf=render
-30745170,https://doi.org/10.1016/j.ebiom.2019.02.005,"Identification of novel genome-wide associations for suicidality in UK Biobank, genetic correlation with psychiatric disorders and polygenic association with completed suicide.","Strawbridge RJ, Ward J, Ferguson A, Graham N, Shaw RJ, Cullen B, Pearsall R, Lyall LM, Johnston KJA, Niedzwiedz CL, Pell JP, Mackay D, Martin JL, Lyall DM, Bailey MES, Smith DJ.",,EBioMedicine,2019,2019-02-08,Y,,Understanding the Causes of Disease,,"<h4>Background</h4>Suicide is a major issue for global public health. Suicidality describes a broad spectrum of thoughts and behaviours, some of which are common in the general population. Although suicide results from a complex interaction of multiple social and psychological factors, predisposition to suicidality is at least partly genetic.<h4>Methods</h4>Ordinal genome-wide association study of suicidality in the UK Biobank cohort comparing: 'no suicidality' controls (N = 83,557); 'thoughts that life was not worth living' (N = 21,063); 'ever contemplated self-harm' (N = 13,038); 'act of deliberate self-harm in the past' (N = 2498); and 'previous suicide attempt' (N = 2666).<h4>Outcomes</h4>We identified three novel genome-wide significant loci for suicidality (on chromosomes nine, 11 and 13) and moderate-to-strong genetic correlations between suicidality and a range of psychiatric disorders, most notably depression (r<sub>g</sub> 0·81).<h4>Interpretation</h4>These findings provide new information about genetic variants relating to increased risk of suicidal thoughts and behaviours. Future work should assess the extent to which polygenic risk scores for suicidality, in combination with non-genetic risk factors, may be useful for stratified approaches to suicide prevention at a population level. FUND: UKRI Innovation-HDR-UK Fellowship (MR/S003061/1). MRC Mental Health Data Pathfinder Award (MC_PC_17217). MRC Doctoral Training Programme Studentship at the University of Glasgow (MR/K501335/1). MRC Doctoral Training Programme Studentship at the Universities of Glasgow and Edinburgh. UKRI Innovation Fellowship (MR/R024774/1).",,pdf:http://www.thelancet.com/article/S2352396419300775/pdf; doi:https://doi.org/10.1016/j.ebiom.2019.02.005; html:https://europepmc.org/articles/PMC6442001; pdf:https://europepmc.org/articles/PMC6442001?pdf=render
+37319288,https://doi.org/10.1371/journal.pone.0287264,Evaluation of data processing pipelines on real-world electronic health records data for the purpose of measuring patient similarity.,"Pikoula M, Kallis C, Madjiheurem S, Quint JK, Bafadhel M, Denaxas S.",,PloS one,2023,2023-06-15,Y,,,,"<h4>Background</h4>The ever-growing size, breadth, and availability of patient data allows for a wide variety of clinical features to serve as inputs for phenotype discovery using cluster analysis. Data of mixed types in particular are not straightforward to combine into a single feature vector, and techniques used to address this can be biased towards certain data types in ways that are not immediately obvious or intended. In this context, the process of constructing clinically meaningful patient representations from complex datasets has not been systematically evaluated.<h4>Aims</h4>Our aim was to a) outline and b) implement an analytical framework to evaluate distinct methods of constructing patient representations from routine electronic health record data for the purpose of measuring patient similarity. We applied the analysis on a patient cohort diagnosed with chronic obstructive pulmonary disease.<h4>Methods</h4>Using data from the CALIBER data resource, we extracted clinically relevant features for a cohort of patients diagnosed with chronic obstructive pulmonary disease. We used four different data processing pipelines to construct lower dimensional patient representations from which we calculated patient similarity scores. We described the resulting representations, ranked the influence of each individual feature on patient similarity and evaluated the effect of different pipelines on clustering outcomes. Experts evaluated the resulting representations by rating the clinical relevance of similar patient suggestions with regard to a reference patient.<h4>Results</h4>Each of the four pipelines resulted in similarity scores primarily driven by a unique set of features. It was demonstrated that data transformations according to each pipeline prior to clustering can result in a variation of clustering results of over 40%. The most appropriate pipeline was selected on the basis of feature ranking and clinical expertise. There was moderate agreement between clinicians as measured by Cohen's kappa coefficient.<h4>Conclusions</h4>Data transformation has downstream and unforeseen consequences in cluster analysis. Rather than viewing this process as a black box, we have shown ways to quantitatively and qualitatively evaluate and select the appropriate preprocessing pipeline.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0287264&type=printable; doi:https://doi.org/10.1371/journal.pone.0287264; html:https://europepmc.org/articles/PMC10270623; pdf:https://europepmc.org/articles/PMC10270623?pdf=render
 31711543,https://doi.org/10.1186/s13326-019-0214-4,Natural language processing for disease phenotyping in UK primary care records for research: a pilot study in myocardial infarction and death.,"Shah AD, Bailey E, Williams T, Denaxas S, Dobson R, Hemingway H.",,Journal of biomedical semantics,2019,2019-11-12,Y,Myocardial infarction; Chest pain; Primary Care; Natural Language Processing; Free Text,Applied Analytics,,"<h4>Background</h4>Free text in electronic health records (EHR) may contain additional phenotypic information beyond structured (coded) information. For major health events - heart attack and death - there is a lack of studies evaluating the extent to which free text in the primary care record might add information. Our objectives were to describe the contribution of free text in primary care to the recording of information about myocardial infarction (MI), including subtype, left ventricular function, laboratory results and symptoms; and recording of cause of death. We used the CALIBER EHR research platform which contains primary care data from the Clinical Practice Research Datalink (CPRD) linked to hospital admission data, the MINAP registry of acute coronary syndromes and the death registry. In CALIBER we randomly selected 2000 patients with MI and 1800 deaths. We implemented a rule-based natural language engine, the Freetext Matching Algorithm, on site at CPRD to analyse free text in the primary care record without raw data being released to researchers. We analysed text recorded within 90 days before or 90 days after the MI, and on or after the date of death.<h4>Results</h4>We extracted 10,927 diagnoses, 3658 test results, 3313 statements of negation, and 850 suspected diagnoses from the myocardial infarction patients. Inclusion of free text increased the recorded proportion of patients with chest pain in the week prior to MI from 19 to 27%, and differentiated between MI subtypes in a quarter more patients than structured data alone. Cause of death was incompletely recorded in primary care; in 36% the cause was in coded data and in 21% it was in free text. Only 47% of patients had exactly the same cause of death in primary care and the death registry, but this did not differ between coded and free text causes of death.<h4>Conclusions</h4>Among patients who suffer MI or die, unstructured free text in primary care records contains much information that is potentially useful for research such as symptoms, investigation results and specific diagnoses. Access to large scale unstructured data in electronic health records (millions of patients) might yield important insights.", NLP methods were used to analyse free text from hospital records for people with MI. They analysed text recorded within 90 days bfore or 90 days after the MI and found that free text in hospital records contains unformation useful for diagnoses,pdf:https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-019-0214-4; doi:https://doi.org/10.1186/s13326-019-0214-4; html:https://europepmc.org/articles/PMC6849160; pdf:https://europepmc.org/articles/PMC6849160?pdf=render
 31714636,https://doi.org/10.1002/ana.25642,Lipid lowering and Alzheimer disease risk: A mendelian randomization study.,"Williams DM, Finan C, Schmidt AF, Burgess S, Hingorani AD.",,Annals of neurology,2020,2020-01-01,Y,,,,"<h4>Objective</h4>To examine whether genetic variation affecting the expression or function of lipid-lowering drug targets is associated with Alzheimer disease (AD) risk, to evaluate the potential impact of long-term exposure to corresponding therapeutics.<h4>Methods</h4>We conducted Mendelian randomization analyses using variants in genes that encode the protein targets of several approved lipid-lowering drug classes: HMGCR (encoding the target for statins), PCSK9 (encoding the target for PCSK9 inhibitors, eg, evolocumab and alirocumab), NPC1L1 (encoding the target for ezetimibe), and APOB (encoding the target of mipomersen). Variants were weighted by associations with low-density lipoprotein cholesterol (LDL-C) using data from lipid genetics consortia (n up to 295,826). We meta-analyzed Mendelian randomization estimates for regional variants weighted by LDL-C on AD risk from 2 large samples (total n = 24,718 cases, 56,685 controls).<h4>Results</h4>Models for HMGCR, APOB, and NPC1L1 did not suggest that the use of related lipid-lowering drug classes would affect AD risk. In contrast, genetically instrumented exposure to PCSK9 inhibitors was predicted to increase AD risk in both of the AD samples (combined odds ratio per standard deviation lower LDL-C inducible by the drug target = 1.45, 95% confidence interval = 1.23-1.69). This risk increase was opposite to, although more modest than, the degree of protection from coronary artery disease predicted by these same methods for PCSK9 inhibition.<h4>Interpretation</h4>We did not identify genetic support for the repurposing of statins, ezetimibe, or mipomersen for AD prevention. Notwithstanding caveats to this genetic evidence, pharmacovigilance for AD risk among users of PCSK9 inhibitors may be warranted. ANN NEUROL 2020;87:30-39.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ana.25642; doi:https://doi.org/10.1002/ana.25642; html:https://europepmc.org/articles/PMC6944510; pdf:https://europepmc.org/articles/PMC6944510?pdf=render
 36344532,https://doi.org/10.1038/s41598-022-21663-w,Atrial fibrillation prediction by combining ECG markers and CMR radiomics.,"Pujadas ER, Raisi-Estabragh Z, Szabo L, Morcillo CI, Campello VM, Martin-Isla C, Vago H, Merkely B, Harvey NC, Petersen SE, Lekadir K.",,Scientific reports,2022,2022-11-07,Y,,,,"Atrial fibrillation (AF) is the most common cardiac arrhythmia. It is associated with a higher risk of important adverse health outcomes such as stroke and death. AF is linked to distinct electro-anatomic alterations. The main tool for AF diagnosis is the Electrocardiogram (ECG). However, an ECG recorded at a single time point may not detect individuals with paroxysmal AF. In this study, we developed machine learning models for discrimination of prevalent AF using a combination of image-derived radiomics phenotypes and ECG features. Thus, we characterize the phenotypes of prevalent AF in terms of ECG and imaging alterations. Moreover, we explore sex-differential remodelling by building sex-specific models. Our integrative model including radiomics and ECG together resulted in a better performance than ECG alone, particularly in women. ECG had a lower performance in women than men (AUC: 0.77 vs 0.88, p < 0.05) but adding radiomics features, the accuracy of the model was able to improve significantly. The sensitivity also increased considerably in women by adding the radiomics (0.68 vs 0.79, p < 0.05) having a higher detection of AF events. Our findings provide novel insights into AF-related electro-anatomic remodelling and its variations by sex. The integrative radiomics-ECG model also presents a potential novel approach for earlier detection of AF.",,pdf:https://www.nature.com/articles/s41598-022-21663-w.pdf; doi:https://doi.org/10.1038/s41598-022-21663-w; html:https://europepmc.org/articles/PMC9640662; pdf:https://europepmc.org/articles/PMC9640662?pdf=render
@@ -1642,15 +1644,15 @@ PMC8855010,https://doi.org/,POS-894 PREDICTING PANDEMIC-RELATED EXCESS-DEATH USI
 36798028,https://doi.org/10.1002/ehf2.14308,Identifying patients at risk: multi-centre comparison of HeartMate 3 and HeartWare left ventricular assist devices.,"Numan L, Zimpfer D, Zadok OIB, Aarts E, Morshuis M, Guenther SPW, Riebandt J, Wiedemann D, Ramjankhan FZ, Oppelaar AM, Ben-Gal T, Ben-Avraham B, Asselbergs FW, Schramm R, Van Laake LW.",,ESC heart failure,2023,2023-02-16,Y,Mechanical Circulatory Support; Left Ventricular Assist Device; End-stage Heart Failure; Lvad; Centrifugal Continuous Flow Pump,,,"<h4>Aims</h4>Since the withdrawal of HeartWare (HVAD) from the global market, there is an ongoing discussion if and which patients require prophylactically exchange for a HeartMate 3 (HM3). Therefore, it is important to study outcome differences between HVAD and HM3 patients. Because centres differ in patient selection and standard of care, we performed a propensity score (PS)-based study including centres that implanted both devices and aimed to identify which HVAD patients are at highest risk.<h4>Methods and results</h4>We performed an international multi-centre study (n = 1021) including centres that implanted HVAD and HM3. PS-matching was performed using clinical variables and the implanting centre. Survival and complications were compared. As a sensitivity analysis, PS-adjusted Cox regression was performed. Landmark analysis with conditional survival >2 years was conducted to evaluate long-term survival differences. To identify which HVAD patients may benefit from a HM3 upgrade, Cox regression using pre-operative variables and their interaction with device type was performed. Survival was significantly better for HM3 patients (P < 0.01) in 458 matched patients, with a median follow-up of 23 months. Within the matched cohort, HM3 patients had a median age of 58 years, and 83% were male, 80% of the HVAD patients were male, with a median age of 59 years. PS-adjusted Cox regression confirmed a significantly better survival for HM3 patients when compared with HVAD, with a HR of 1.46 (95% confidence interval 1.14-1.85, P < 0.01). Pump thrombosis (P < 0.01) and ischaemic stroke (P < 0.01) occurred less in HM3 patients. No difference was found for haemorrhagic stroke, right heart failure, driveline infection, and major bleeding. Landmark-analysis confirmed a significant difference in conditional survival >2 years after implantation (P = 0.03). None of the pre-operative variable interactions in the Cox regression were significant.<h4>Conclusions</h4>HM3 patients have a significantly better survival and a lower incidence of ischaemic strokes and pump thrombosis than HVAD patients. This survival difference persisted after 2 years of implantation. Additional research using post-operative variables is warranted to identify which HVAD patients need an upgrade to HM3 or expedited transplantation.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ehf2.14308; doi:https://doi.org/10.1002/ehf2.14308; html:https://europepmc.org/articles/PMC10192248; pdf:https://europepmc.org/articles/PMC10192248?pdf=render
 35004880,https://doi.org/10.3389/fcvm.2021.763361,"Cardiac Magnetic Resonance Radiomics Reveal Differential Impact of Sex, Age, and Vascular Risk Factors on Cardiac Structure and Myocardial Tissue.","Raisi-Estabragh Z, Jaggi A, Gkontra P, McCracken C, Aung N, Munroe PB, Neubauer S, Harvey NC, Lekadir K, Petersen SE.",,Frontiers in cardiovascular medicine,2021,2021-12-22,Y,Hypertension; Diabetes; Smoking; Sex differences; High cholesterol; Cardiovascular Magnetic Resonance; Healthy Individuals; Radiomics,,,"<b>Background:</b> Cardiovascular magnetic resonance (CMR) radiomics analysis provides multiple quantifiers of ventricular shape and myocardial texture, which may be used for detailed cardiovascular phenotyping. <b>Objectives:</b> We studied variation in CMR radiomics phenotypes by age and sex in healthy UK Biobank participants. Then, we examined independent associations of classical vascular risk factors (VRFs: smoking, diabetes, hypertension, high cholesterol) with CMR radiomics features, considering potential sex and age differential relationships. <b>Design:</b> Image acquisition was with 1.5 Tesla scanners (MAGNETOM Aera, Siemens). Three regions of interest were segmented from short axis stack images using an automated pipeline: right ventricle, left ventricle, myocardium. We extracted 237 radiomics features from each study using Pyradiomics. In a healthy subset of participants (<i>n</i> = 14,902) without cardiovascular disease or VRFs, we estimated independent associations of age and sex with each radiomics feature using linear regression models adjusted for body size. We then created a sample comprising individuals with at least one VRF matched to an equal number of healthy participants (<i>n</i> = 27,400). We linearly modelled each radiomics feature against age, sex, body size, and all the VRFs. Bonferroni adjustment for multiple testing was applied to all <i>p</i>-values. To aid interpretation, we organised the results into six feature clusters. <b>Results:</b> Amongst the healthy subset, men had larger ventricles with dimmer and less texturally complex myocardium than women. Increasing age was associated with smaller ventricles and greater variation in myocardial intensities. Broadly, all the VRFs were associated with dimmer, less varied signal intensities, greater uniformity of local intensity levels, and greater relative presence of low signal intensity areas within the myocardium. Diabetes and high cholesterol were also associated with smaller ventricular size, this association was of greater magnitude in men than women. The pattern of alteration of radiomics features with the VRFs was broadly consistent in men and women. However, the associations between intensity based radiomics features with both diabetes and hypertension were more prominent in women than men. <b>Conclusions:</b> We demonstrate novel independent associations of sex, age, and major VRFs with CMR radiomics phenotypes. Further studies into the nature and clinical significance of these phenotypes are needed.",,pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2021.763361/pdf; doi:https://doi.org/10.3389/fcvm.2021.763361; html:https://europepmc.org/articles/PMC8727756; pdf:https://europepmc.org/articles/PMC8727756?pdf=render
 32611631,https://doi.org/10.1212/wnl.0000000000009814,"Genetically determined blood pressure, antihypertensive drug classes, and risk of stroke subtypes.","Georgakis MK, Gill D, Webb AJS, Evangelou E, Elliott P, Sudlow CLM, Dehghan A, Malik R, Tzoulaki I, Dichgans M.",,Neurology,2020,2020-07-01,Y,,,,"<h4>Objective</h4>We employed Mendelian randomization to explore whether the effects of blood pressure (BP) and BP-lowering through different antihypertensive drug classes on stroke risk vary by stroke etiology.<h4>Methods</h4>We selected genetic variants associated with systolic and diastolic BP and BP-lowering variants in genes encoding antihypertensive drug targets from genome-wide association studies (GWAS) on 757,601 individuals. Applying 2-sample Mendelian randomization, we examined associations with any stroke (67,162 cases; 454,450 controls), ischemic stroke and its subtypes (large artery, cardioembolic, small vessel stroke), intracerebral hemorrhage (ICH, deep and lobar), and the related small vessel disease phenotype of white matter hyperintensities (WMH).<h4>Results</h4>Genetic predisposition to higher systolic and diastolic BP was associated with higher risk of any stroke, ischemic stroke, and ICH. We found associations between genetically determined BP and all ischemic stroke subtypes with a higher risk of large artery and small vessel stroke compared to cardioembolic stroke, as well as associations with deep, but not lobar ICH. Genetic proxies for calcium channel blockers, but not β-blockers, were associated with lower risk of any stroke and ischemic stroke. Proxies for calcium channel blockers showed particularly strong associations with small vessel stroke and the related radiologic phenotype of WMH.<h4>Conclusions</h4>This study supports a causal role of hypertension in all major stroke subtypes except lobar ICH. We find differences in the effects of BP and BP-lowering through antihypertensive drug classes between stroke subtypes and identify calcium channel blockade as a promising strategy for preventing manifestations of cerebral small vessel disease.",,pdf:https://n.neurology.org/content/neurology/95/4/e353.full.pdf; doi:https://doi.org/10.1212/WNL.0000000000009814; html:https://europepmc.org/articles/PMC7455321; pdf:https://europepmc.org/articles/PMC7455321?pdf=render
+36692937,https://doi.org/10.2196/42866,The Feasibility of Implementing Remote Measurement Technologies in Psychological Treatment for Depression: Mixed Methods Study on Engagement.,"de Angel V, Adeleye F, Zhang Y, Cummins N, Munir S, Lewis S, Laporta Puyal E, Matcham F, Sun S, Folarin AA, Ranjan Y, Conde P, Rashid Z, Dobson R, Hotopf M.",,JMIR mental health,2023,2023-01-24,Y,Depression; Mobile phone; Anxiety; Smartphone; Mhealth; Mobile Health; Wearable Devices; Digital Health; Digital Phenotyping; Passive Sensing,,,"<h4>Background</h4>Remote measurement technologies (RMTs) such as smartphones and wearables can help improve treatment for depression by providing objective, continuous, and ecologically valid insights into mood and behavior. Engagement with RMTs is varied and highly context dependent; however, few studies have investigated their feasibility in the context of treatment.<h4>Objective</h4>A mixed methods design was used to evaluate engagement with active and passive data collection via RMT in people with depression undergoing psychotherapy. We evaluated the effects of treatment on 2 different types of engagement: study attrition (engagement with study protocol) and patterns of missing data (engagement with digital devices), which we termed data availability. Qualitative interviews were conducted to help interpret the differences in engagement.<h4>Methods</h4>A total of 66 people undergoing psychological therapy for depression were followed up for 7 months. Active data were gathered from weekly questionnaires and speech and cognitive tasks, and passive data were gathered from smartphone sensors and a Fitbit (Fitbit Inc) wearable device.<h4>Results</h4>The overall retention rate was 60%. Higher-intensity treatment (χ<sup>2</sup><sub>1</sub>=4.6; P=.03) and higher baseline anxiety (t<sub>56.28</sub>=-2.80, 2-tailed; P=.007) were associated with attrition, but depression severity was not (t<sub>50.4</sub>=-0.18; P=.86). A trend toward significance was found for the association between longer treatments and increased attrition (U=339.5; P=.05). Data availability was higher for active data than for passive data initially but declined at a sharper rate (90%-30% drop in 7 months). As for passive data, wearable data availability fell from a maximum of 80% to 45% at 7 months but showed higher overall data availability than smartphone-based data, which remained stable at the range of 20%-40% throughout. Missing data were more prevalent among GPS location data, followed by among Bluetooth data, then among accelerometry data. As for active data, speech and cognitive tasks had lower completion rates than clinical questionnaires. The participants in treatment provided less Fitbit data but more active data than those on the waiting list.<h4>Conclusions</h4>Different data streams showed varied patterns of missing data, despite being gathered from the same device. Longer and more complex treatments and clinical characteristics such as higher baseline anxiety may reduce long-term engagement with RMTs, and different devices may show opposite patterns of missingness during treatment. This has implications for the scalability and uptake of RMTs in health care settings, the generalizability and accuracy of the data collected by these methods, feature construction, and the appropriateness of RMT use in the long term.",,pdf:https://mental.jmir.org/2023/1/e42866/PDF; doi:https://doi.org/10.2196/42866; html:https://europepmc.org/articles/PMC9906314
 35144240,https://doi.org/10.2196/32543,Artificial Intelligence-Enabled Social Media Analysis for Pharmacovigilance of COVID-19 Vaccinations in the United Kingdom: Observational Study.,"Hussain Z, Sheikh Z, Tahir A, Dashtipour K, Gogate M, Sheikh A, Hussain A.",,JMIR public health and surveillance,2022,2022-05-27,Y,Artificial intelligence; Vaccination; Public Health; Health Informatics; Natural Language Processing; Facebook; Social Media; Twitter; Sentiment Analysis; Infodemiology; Deep Learning; Covid-19,,,"<h4>Background</h4>The rollout of vaccines for COVID-19 in the United Kingdom started in December 2020. Uptake has been high, and there has been a subsequent reduction in infections, hospitalizations, and deaths among vaccinated individuals. However, vaccine hesitancy remains a concern, in particular relating to adverse effects following immunization (AEFIs). Social media analysis has the potential to inform policy makers about AEFIs being discussed by the public as well as public attitudes toward the national immunization campaign.<h4>Objective</h4>We sought to assess the frequency and nature of AEFI-related mentions on social media in the United Kingdom and to provide insights on public sentiments toward COVID-19 vaccines.<h4>Methods</h4>We extracted and analyzed over 121,406 relevant Twitter and Facebook posts, from December 8, 2020, to April 30, 2021. These were thematically filtered using a 2-step approach, initially using COVID-19-related keywords and then using vaccine- and manufacturer-related keywords. We identified AEFI-related keywords and modeled their word frequency to monitor their trends over 2-week periods. We also adapted and utilized our recently developed hybrid ensemble model, which combines state-of-the-art lexicon rule-based and deep learning-based approaches, to analyze sentiment trends relating to the main vaccines available in the United Kingdom.<h4>Results</h4>Our COVID-19 AEFI search strategy identified 46,762 unique Facebook posts by 14,346 users and 74,644 tweets (excluding retweets) by 36,446 users over the 4-month period. We identified an increasing trend in the number of mentions for each AEFI on social media over the study period. The most frequent AEFI mentions were found to be symptoms related to appetite (n=79,132, 14%), allergy (n=53,924, 9%), injection site (n=56,152, 10%), and clots (n=43,907, 8%). We also found some rarely reported AEFIs such as Bell palsy (n=11,909, 2%) and Guillain-Barre syndrome (n=9576, 2%) being discussed as frequently as more well-known side effects like headache (n=10,641, 2%), fever (n=12,707, 2%), and diarrhea (n=16,559, 3%). Overall, we found public sentiment toward vaccines and their manufacturers to be largely positive (58%), with a near equal split between negative (22%) and neutral (19%) sentiments. The sentiment trend was relatively steady over time and had minor variations, likely based on political and regulatory announcements and debates.<h4>Conclusions</h4>The most frequently discussed COVID-19 AEFIs on social media were found to be broadly consistent with those reported in the literature and by government pharmacovigilance. We also detected potential safety signals from our analysis that have been detected elsewhere and are currently being investigated. As such, we believe our findings support the use of social media analysis to provide a complementary data source to conventional knowledge sources being used for pharmacovigilance purposes.",,pdf:https://publichealth.jmir.org/2022/5/e32543/PDF; doi:https://doi.org/10.2196/32543; html:https://europepmc.org/articles/PMC9150729
-38279797,https://doi.org/10.1089/neu.2023.0465,The Australian Traumatic Brain Injury Initiative: Systematic Review of the Effect of Acute Interventions on Outcome for People With Moderate-Severe Traumatic Brain Injury.,"Keeves J, Gadowski A, McKimmie A, Bagg MK, Antonic-Baker A, Hicks AJ, Clarke N, Brown A, McNamara R, Reeder S, Roman C, Jeffcote T, Romero L, Hill R, Ponsford JL, Lannin NA, O'Brien TJ, Cameron PA, Rushworth N, Fitzgerald M, Gabbe BJ, Cooper DJ.",,Journal of neurotrauma,2024,2024-04-08,N,"Common Data Elements; Brain Injuries, Traumatic; Outcome Assessment, Health Care; Systematic Review [Publication Type]; Emergency Medical Services, Critical Care, Early Medical Intervention",,,"The Australian Traumatic Brain Injury Initiative (AUS-TBI) is developing a data resource to enable improved outcome prediction for people with moderate-severe TBI (msTBI) across Australia. Fundamental to this resource is the collaboratively designed data dictionary. This systematic review and consultation aimed to identify acute interventions with potential to modify clinical outcomes for people after msTBI, for inclusion in a data dictionary. Standardized searches were implemented across bibliographic databases from inception through April 2022. English-language reports of randomized controlled trials (RCTs) evaluating any association between any acute intervention and clinical outcome in at least 100 patients with msTBI, were included. A predefined algorithm was used to assign a value to each observed association. Consultation with AUS-TBI clinicians and researchers formed the consensus process for interventions to be included in a single data dictionary. Searches retrieved 14,455 records, of which 124 full-length RCTs were screened, with 35 studies included. These studies evaluated 26 unique acute interventions across 21 unique clinical outcomes. Only 4 interventions were considered to have medium modifying value for any outcome from the review, with an additional 8 interventions agreed upon through the consensus process. The interventions with medium value were tranexamic acid and phenytoin, which had a positive effect on an outcome; and decompressive craniectomy surgery and hypothermia, which negatively affected outcomes. From the systematic review and consensus process, 12 interventions were identified as potential modifiers to be included in the AUS-TBI national data resource.",,doi:https://doi.org/10.1089/neu.2023.0465
 36929968,https://doi.org/10.1016/s0140-6736(22)02235-8,Impact of the temporary suspension of the Bowel Screening Wales programme on inequalities during the COVID-19 pandemic: a retrospective register-based study.,"Bright D, Song J, Hillier S, Huws DW, Greene G, Hodgson K, Akbari A, Griffiths R, Davies AR, Gjini A.",,"Lancet (London, England)",2022,2022-11-24,Y,,,,"<h4>Background</h4>Response to the COVID-19 pandemic resulted in the temporary disruption of routine services in the UK National Health Service, including cancer screening. Following the reintroduction of services, we explored the impact on inequalities in uptake of the Bowel Screening Wales (BSW) programme to identify groups who might benefit from tailored intervention.<h4>Methods</h4>BSW records were linked to electronic health record and administrative data within the Secured Anonymised Information Linkage (SAIL) Databank Trusted Research Environment. We examined uptake in the first 3 months (from August to October, 2020) of invitations following the reintroduction of the BSW programme compared with the same period in the preceding 3 years. We analysed inequalities in uptake by sex, age group, income deprivation quintile, urban and rural location, ethnic group, and uptake between different periods using logistic regression models.<h4>Findings</h4>Overall uptake remained above the 60% Welsh standard during the COVID-19 pandemic period of 2020-21 but declined compared with the pre-pandemic period of 2019-20 (60·4% vs 62·7%; p<0·001). During the COVID-19 pandemic period of 2020-21, uptake declined for most demographic groups, except for older individuals (70-74 years) and those in the most deprived quintile. Variation by sex, age, income deprivation, and ethnic groups was observed in all periods studied. Among low-uptake groups, including males, younger individuals (60-64 years), those living in most deprived areas, and ethnic minorities, uptake remains below the 60% Welsh standard.<h4>Interpretation</h4>Despite the disruption, uptake remained above the Welsh standard and inequalities did not worsen after the programme resumed activities. However, variations associated with sex, age, deprivation, and ethnicity remain. These findings need to be considered in targeting strategies to improve uptake and informed choice in colorectal cancer screening such as co-producing information products with low-uptake groups and upscaling the use of GP-endorsed invitations and reminder letters for bowel screening.<h4>Funding</h4>Health Data Research UK, UK Medical Research Council, Administrative Data Research UK, and Health and Care Research Wales.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9691043; doi:https://doi.org/10.1016/S0140-6736(22)02235-8; html:https://europepmc.org/articles/PMC9691043; pdf:https://europepmc.org/articles/PMC9691043?pdf=render
-36692937,https://doi.org/10.2196/42866,The Feasibility of Implementing Remote Measurement Technologies in Psychological Treatment for Depression: Mixed Methods Study on Engagement.,"de Angel V, Adeleye F, Zhang Y, Cummins N, Munir S, Lewis S, Laporta Puyal E, Matcham F, Sun S, Folarin AA, Ranjan Y, Conde P, Rashid Z, Dobson R, Hotopf M.",,JMIR mental health,2023,2023-01-24,Y,Depression; Mobile phone; Anxiety; Smartphone; Mhealth; Mobile Health; Wearable Devices; Digital Health; Digital Phenotyping; Passive Sensing,,,"<h4>Background</h4>Remote measurement technologies (RMTs) such as smartphones and wearables can help improve treatment for depression by providing objective, continuous, and ecologically valid insights into mood and behavior. Engagement with RMTs is varied and highly context dependent; however, few studies have investigated their feasibility in the context of treatment.<h4>Objective</h4>A mixed methods design was used to evaluate engagement with active and passive data collection via RMT in people with depression undergoing psychotherapy. We evaluated the effects of treatment on 2 different types of engagement: study attrition (engagement with study protocol) and patterns of missing data (engagement with digital devices), which we termed data availability. Qualitative interviews were conducted to help interpret the differences in engagement.<h4>Methods</h4>A total of 66 people undergoing psychological therapy for depression were followed up for 7 months. Active data were gathered from weekly questionnaires and speech and cognitive tasks, and passive data were gathered from smartphone sensors and a Fitbit (Fitbit Inc) wearable device.<h4>Results</h4>The overall retention rate was 60%. Higher-intensity treatment (χ<sup>2</sup><sub>1</sub>=4.6; P=.03) and higher baseline anxiety (t<sub>56.28</sub>=-2.80, 2-tailed; P=.007) were associated with attrition, but depression severity was not (t<sub>50.4</sub>=-0.18; P=.86). A trend toward significance was found for the association between longer treatments and increased attrition (U=339.5; P=.05). Data availability was higher for active data than for passive data initially but declined at a sharper rate (90%-30% drop in 7 months). As for passive data, wearable data availability fell from a maximum of 80% to 45% at 7 months but showed higher overall data availability than smartphone-based data, which remained stable at the range of 20%-40% throughout. Missing data were more prevalent among GPS location data, followed by among Bluetooth data, then among accelerometry data. As for active data, speech and cognitive tasks had lower completion rates than clinical questionnaires. The participants in treatment provided less Fitbit data but more active data than those on the waiting list.<h4>Conclusions</h4>Different data streams showed varied patterns of missing data, despite being gathered from the same device. Longer and more complex treatments and clinical characteristics such as higher baseline anxiety may reduce long-term engagement with RMTs, and different devices may show opposite patterns of missingness during treatment. This has implications for the scalability and uptake of RMTs in health care settings, the generalizability and accuracy of the data collected by these methods, feature construction, and the appropriateness of RMT use in the long term.",,pdf:https://mental.jmir.org/2023/1/e42866/PDF; doi:https://doi.org/10.2196/42866; html:https://europepmc.org/articles/PMC9906314
+38279797,https://doi.org/10.1089/neu.2023.0465,The Australian Traumatic Brain Injury Initiative: Systematic Review of the Effect of Acute Interventions on Outcome for People With Moderate-Severe Traumatic Brain Injury.,"Keeves J, Gadowski A, McKimmie A, Bagg MK, Antonic-Baker A, Hicks AJ, Clarke N, Brown A, McNamara R, Reeder S, Roman C, Jeffcote T, Romero L, Hill R, Ponsford JL, Lannin NA, O'Brien TJ, Cameron PA, Rushworth N, Fitzgerald M, Gabbe BJ, Cooper DJ.",,Journal of neurotrauma,2024,2024-04-08,N,"Common Data Elements; Brain Injuries, Traumatic; Outcome Assessment, Health Care; Systematic Review [Publication Type]; Emergency Medical Services, Critical Care, Early Medical Intervention",,,"The Australian Traumatic Brain Injury Initiative (AUS-TBI) is developing a data resource to enable improved outcome prediction for people with moderate-severe TBI (msTBI) across Australia. Fundamental to this resource is the collaboratively designed data dictionary. This systematic review and consultation aimed to identify acute interventions with potential to modify clinical outcomes for people after msTBI, for inclusion in a data dictionary. Standardized searches were implemented across bibliographic databases from inception through April 2022. English-language reports of randomized controlled trials (RCTs) evaluating any association between any acute intervention and clinical outcome in at least 100 patients with msTBI, were included. A predefined algorithm was used to assign a value to each observed association. Consultation with AUS-TBI clinicians and researchers formed the consensus process for interventions to be included in a single data dictionary. Searches retrieved 14,455 records, of which 124 full-length RCTs were screened, with 35 studies included. These studies evaluated 26 unique acute interventions across 21 unique clinical outcomes. Only 4 interventions were considered to have medium modifying value for any outcome from the review, with an additional 8 interventions agreed upon through the consensus process. The interventions with medium value were tranexamic acid and phenytoin, which had a positive effect on an outcome; and decompressive craniectomy surgery and hypothermia, which negatively affected outcomes. From the systematic review and consensus process, 12 interventions were identified as potential modifiers to be included in the AUS-TBI national data resource.",,doi:https://doi.org/10.1089/neu.2023.0465
 33903145,https://doi.org/10.1136/bjophthalmol-2020-318570,Testing the performance of risk prediction models to determine progression to referable diabetic retinopathy in an Irish type 2 diabetes cohort.,"Smith JJ, Wright DM, Stratton IM, Scanlon PH, Lois N.",,The British journal of ophthalmology,2022,2021-04-26,Y,Retina; Vision; Imaging; Macula; Eye (Globe),,,"<h4>Background /aims</h4>To evaluate the performance of existing prediction models to determine risk of progression to referable diabetic retinopathy (RDR) using data from a prospective Irish cohort of people with type 2 diabetes (T2D).<h4>Methods</h4>A cohort of 939 people with T2D followed prospectively was used to test the performance of risk prediction models developed in Gloucester, UK, and Iceland. Observed risk of progression to RDR in the Irish cohort was compared with that derived from each of the prediction models evaluated. Receiver operating characteristic curves assessed models' performance.<h4>Results</h4>The cohort was followed for a total of 2929 person years during which 2906 screening episodes occurred. Among 939 individuals followed, there were 40 referrals (4%) for diabetic maculopathy, pre-proliferative DR and proliferative DR. The original Gloucester model, which includes results of two consecutive retinal screenings; a model incorporating, in addition, systemic biomarkers (HbA1c and serum cholesterol); and a model including results of one retinopathy screening, HbA1c, total cholesterol and duration of diabetes, had acceptable discriminatory power (area under the curve (AUC) of 0.69, 0.76 and 0.77, respectively). The Icelandic model, which combined retinopathy grading, duration and type of diabetes, HbA1c and systolic blood pressure, performed very similarly (AUC of 0.74).<h4>Conclusion</h4>In an Irish cohort of people with T2D, the prediction models tested had an acceptable performance identifying those at risk of progression to RDR. These risk models would be useful in establishing more personalised screening intervals for people with T2D.",,pdf:https://bjo.bmj.com/content/bjophthalmol/early/2021/04/25/bjophthalmol-2020-318570.full.pdf; doi:https://doi.org/10.1136/bjophthalmol-2020-318570; html:https://europepmc.org/articles/PMC9340042; pdf:https://europepmc.org/articles/PMC9340042?pdf=render
 33328453,https://doi.org/10.1038/s41467-020-19996-z,Genetic architecture of host proteins involved in SARS-CoV-2 infection.,"Pietzner M, Wheeler E, Carrasco-Zanini J, Raffler J, Kerrison ND, Oerton E, Auyeung VPW, Luan J, Finan C, Casas JP, Ostroff R, Williams SA, Kastenmüller G, Ralser M, Gamazon ER, Wareham NJ, Hingorani AD, Langenberg C.",,Nature communications,2020,2020-12-16,Y,,,,"Understanding the genetic architecture of host proteins interacting with SARS-CoV-2 or mediating the maladaptive host response to COVID-19 can help to identify new or repurpose existing drugs targeting those proteins. We present a genetic discovery study of 179 such host proteins among 10,708 individuals using an aptamer-based technique. We identify 220 host DNA sequence variants acting in cis (MAF 0.01-49.9%) and explaining 0.3-70.9% of the variance of 97 of these proteins, including 45 with no previously known protein quantitative trait loci (pQTL) and 38 encoding current drug targets. Systematic characterization of pQTLs across the phenome identified protein-drug-disease links and evidence that putative viral interaction partners such as MARK3 affect immune response. Our results accelerate the evaluation and prioritization of new drug development programmes and repurposing of trials to prevent, treat or reduce adverse outcomes. Rapid sharing and detailed interrogation of results is facilitated through an interactive webserver ( https://omicscience.org/apps/covidpgwas/ ).",,pdf:https://www.nature.com/articles/s41467-020-19996-z.pdf; doi:https://doi.org/10.1038/s41467-020-19996-z; html:https://europepmc.org/articles/PMC7744536; pdf:https://europepmc.org/articles/PMC7744536?pdf=render
 30928915,https://doi.org/10.1136/injuryprev-2018-043085,Comparison of revised Functional Capacity Index scores with Abbreviated Injury Scale 2008 scores in predicting 12-month severe trauma outcomes.,"Palmer CS, Cameron PA, Gabbe BJ.",,Injury prevention : journal of the International Society for Child and Adolescent Injury Prevention,2020,2019-03-30,N,Trauma Registry; Trauma Scoring; Functional Outcomes; Prediction Models; Abbreviated Injury Scale; Major Trauma; Functional Capacity Index; 12-Month Outcomes,,,"<h4>Introduction</h4>Anatomical injury as measured by the AIS often accounts for only a small proportion of variability in outcomes after injury. The predictive Functional Capacity Index (FCI) appended to the 2008 AIS claims to provide a widely available method of predicting 12-month function following injury.<h4>Objectives</h4>To determine the extent to which AIS-based and FCI-based scoring is able to add to a simple predictive model of 12-month function following severe injury.<h4>Methods</h4>Adult trauma patients were drawn from the population-based Victorian State Trauma Registry. Major trauma and severely injured orthopaedic trauma patients were followed up via telephone interview including Glasgow Outcome Scale-Extended, the EQ-5D-3L and return to work status. A battery of AIS-based and FCI-based scores, and a simple count of AIS-coded injuries were added in turn to a base model using age and gender.<h4>Results</h4>A total of 20 813 patients survived to 12 months and had at least one functional outcome recorded, representing 85% follow-up. Predictions using the base model varied substantially across outcome measures. Irrespective of the method used to classify the severity of injury, adding injury severity to the model significantly, but only slightly improved model fit. Across the outcomes evaluated, no method of injury severity assessment consistently outperformed any other.<h4>Conclusions</h4>Anatomical injury is a predictor of trauma outcome. However, injury severity as described by the FCI does not consistently improve discrimination, or even provide the best discrimination compared with AIS-based severity scores or a simple injury count.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa50163/Download/0050163-25062019060819.pdf; doi:https://doi.org/10.1136/injuryprev-2018-043085
-37190768,https://doi.org/10.1017/s2045796023000276,The mental health of all children in contact with social services: a population-wide record-linkage study in Northern Ireland.,"McKenna S, O'Reilly D, Maguire A.",,Epidemiology and psychiatric sciences,2023,2023-05-16,Y,Mental health; Data Linkage; Children’s Social Care,,,"<h4>Aims</h4>Children in contact with social services are at high risk for mental ill health, but it is not known what proportion of the child population has contact with social services or how risk varies within this group compared to unexposed peers. We aim to quantify the extent and nature of contact with social services within the child population in Northern Ireland (NI) and the association with mental ill health. We also examine which social care experiences identify those most at risk.<h4>Methods</h4>This is a population-based record-linkage study of 497,269 children (aged under 18 years) alive and resident in NI in 2015 using routinely collected health and social care data. Exposure was categorized as (1) no contact, (2) referred but assessed as not in need (NIN), (3) child in need (CIN) and (4) child in care (CIC). Multilevel logistic regression analyses estimated odds ratios (ORs) for mental ill health indicated by receipt of psychotropic medication (antidepressants, anxiolytics, antipsychotics and hypnotics), psychiatric hospital admission and hospital-presenting self-harm or ideation.<h4>Results</h4>Over one in six children (17.2%, <i>n</i> = 85,792) were currently or previously in contact with social services, and almost one child in every 20 (4.8%, <i>n</i> = 23,975) had contact in 2015. Likelihood of any mental ill health outcome increased incrementally with the level of contact with social services relative to unexposed peers: NIN (OR 5.90 [95% confidence interval (CI) 5.10-6.83]), CIN (OR 5.99 [95% CI 5.50-6.53]) and CIC (OR 12.60 [95% CI 10.63-14.95]). All tiers of contact, number of referrals, number of care episodes and placement type were strongly associated with the likelihood of mental ill health.<h4>Conclusion</h4>Children who have contact with social services account for a large and disproportionate amount of mental ill health in the child population. Likelihood of poor mental health across indicators is highest in care experienced children but also extends to the much larger population of children in contact with social services but never in care. Findings suggest a need for targeted mental health screening and enhanced support for all children in contact with social services.",,pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/A60E6D761449A937DCE08F3A075B236D/S2045796023000276a.pdf/div-class-title-the-mental-health-of-all-children-in-contact-with-social-services-a-population-wide-record-linkage-study-in-northern-ireland-div.pdf; doi:https://doi.org/10.1017/S2045796023000276; html:https://europepmc.org/articles/PMC10227534; pdf:https://europepmc.org/articles/PMC10227534?pdf=render
 32524641,https://doi.org/10.1002/sim.8556,Selective recruitment designs for improving observational studies using electronic health records.,"Barrett JE, Cakiroglu A, Bunce C, Shah A, Denaxas S.",,Statistics in medicine,2020,2020-06-10,Y,Electronic Health Records; Observational Study; Optimal Experimental Design; Selective Recruitment,,,"Large-scale electronic health records (EHRs) present an opportunity to quickly identify suitable individuals in order to directly invite them to participate in an observational study. EHRs can contain data from millions of individuals, raising the question of how to optimally select a cohort of size n from a larger pool of size N. In this article, we propose a simple selective recruitment protocol that selects a cohort in which covariates of interest tend to have a uniform distribution. We show that selectively recruited cohorts potentially offer greater statistical power and more accurate parameter estimates than randomly selected cohorts. Our protocol can be applied to studies with multiple categorical and continuous covariates. We apply our protocol to a numerically simulated prospective observational study using an EHR database of stable acute coronary disease patients from 82 089 individuals in the U.K. Selective recruitment designs require a smaller sample size, leading to more efficient and cost-effective studies.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/sim.8556; doi:https://doi.org/10.1002/sim.8556; html:https://europepmc.org/articles/PMC8432147; pdf:https://europepmc.org/articles/PMC8432147?pdf=render
+37190768,https://doi.org/10.1017/s2045796023000276,The mental health of all children in contact with social services: a population-wide record-linkage study in Northern Ireland.,"McKenna S, O'Reilly D, Maguire A.",,Epidemiology and psychiatric sciences,2023,2023-05-16,Y,Mental health; Data Linkage; Children’s Social Care,,,"<h4>Aims</h4>Children in contact with social services are at high risk for mental ill health, but it is not known what proportion of the child population has contact with social services or how risk varies within this group compared to unexposed peers. We aim to quantify the extent and nature of contact with social services within the child population in Northern Ireland (NI) and the association with mental ill health. We also examine which social care experiences identify those most at risk.<h4>Methods</h4>This is a population-based record-linkage study of 497,269 children (aged under 18 years) alive and resident in NI in 2015 using routinely collected health and social care data. Exposure was categorized as (1) no contact, (2) referred but assessed as not in need (NIN), (3) child in need (CIN) and (4) child in care (CIC). Multilevel logistic regression analyses estimated odds ratios (ORs) for mental ill health indicated by receipt of psychotropic medication (antidepressants, anxiolytics, antipsychotics and hypnotics), psychiatric hospital admission and hospital-presenting self-harm or ideation.<h4>Results</h4>Over one in six children (17.2%, <i>n</i> = 85,792) were currently or previously in contact with social services, and almost one child in every 20 (4.8%, <i>n</i> = 23,975) had contact in 2015. Likelihood of any mental ill health outcome increased incrementally with the level of contact with social services relative to unexposed peers: NIN (OR 5.90 [95% confidence interval (CI) 5.10-6.83]), CIN (OR 5.99 [95% CI 5.50-6.53]) and CIC (OR 12.60 [95% CI 10.63-14.95]). All tiers of contact, number of referrals, number of care episodes and placement type were strongly associated with the likelihood of mental ill health.<h4>Conclusion</h4>Children who have contact with social services account for a large and disproportionate amount of mental ill health in the child population. Likelihood of poor mental health across indicators is highest in care experienced children but also extends to the much larger population of children in contact with social services but never in care. Findings suggest a need for targeted mental health screening and enhanced support for all children in contact with social services.",,pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/A60E6D761449A937DCE08F3A075B236D/S2045796023000276a.pdf/div-class-title-the-mental-health-of-all-children-in-contact-with-social-services-a-population-wide-record-linkage-study-in-northern-ireland-div.pdf; doi:https://doi.org/10.1017/S2045796023000276; html:https://europepmc.org/articles/PMC10227534; pdf:https://europepmc.org/articles/PMC10227534?pdf=render
 38345865,https://doi.org/10.1113/jp284597,Reduced plakoglobin increases the risk of sodium current defects and atrial conduction abnormalities in response to androgenic anabolic steroid abuse.,"Sommerfeld LC, Holmes AP, Yu TY, O'Shea C, Kavanagh DM, Pike JM, Wright T, Syeda F, Aljehani A, Kew T, Cardoso VR, Kabir SN, Hepburn C, Menon PR, Broadway-Stringer S, O'Reilly M, Witten A, Fortmueller L, Lutz S, Kulle A, Gkoutos GV, Pavlovic D, Arlt W, Lavery GG, Steeds R, Gehmlich K, Stoll M, Kirchhof P, Fabritz L.",,The Journal of physiology,2024,2024-02-12,N,Testosterone; Conduction velocity; Nav1.5; Desmosome; Arrhythmogenic Right Ventricular Cardiomyopathy; Cardiac Atria,,,"Androgenic anabolic steroids (AAS) are commonly abused by young men. Male sex and increased AAS levels are associated with earlier and more severe manifestation of common cardiac conditions, such as atrial fibrillation, and rare ones, such as arrhythmogenic right ventricular cardiomyopathy (ARVC). Clinical observations suggest a potential atrial involvement in ARVC. Arrhythmogenic right ventricular cardiomyopathy is caused by desmosomal gene defects, including reduced plakoglobin expression. Here, we analysed clinical records from 146 ARVC patients to identify that ARVC is more common in males than females. Patients with ARVC also had an increased incidence of atrial arrhythmias and P wave changes. To study desmosomal vulnerability and the effects of AAS on the atria, young adult male mice, heterozygously deficient for plakoglobin (Plako<sup>+/-</sup>), and wild type (WT) littermates were chronically exposed to 5α-dihydrotestosterone (DHT) or placebo. The DHT increased atrial expression of pro-hypertrophic, fibrotic and inflammatory transcripts. In mice with reduced plakoglobin, DHT exaggerated P wave abnormalities, atrial conduction slowing, sodium current depletion, action potential amplitude reduction and the fall in action potential depolarization rate. Super-resolution microscopy revealed a decrease in Na<sub>V</sub>1.5 membrane clustering in Plako<sup>+/-</sup> atrial cardiomyocytes after DHT exposure. In summary, AAS combined with plakoglobin deficiency cause pathological atrial electrical remodelling in young male hearts. Male sex is likely to increase the risk of atrial arrhythmia, particularly in those with desmosomal gene variants. This risk is likely to be exaggerated further by AAS use. KEY POINTS: Androgenic male sex hormones, such as testosterone, might increase the risk of atrial fibrillation in patients with arrhythmogenic right ventricular cardiomyopathy (ARVC), which is often caused by desmosomal gene defects (e.g. reduced plakoglobin expression). In this study, we observed a significantly higher proportion of males who had ARVC compared with females, and atrial arrhythmias and P wave changes represented a common observation in advanced ARVC stages. In mice with reduced plakoglobin expression, chronic administration of 5α-dihydrotestosterone led to P wave abnormalities, atrial conduction slowing, sodium current depletion and a decrease in membrane-localized Na<sub>V</sub>1.5 clusters. 5α-Dihydrotestosterone, therefore, represents a stimulus aggravating the pro-arrhythmic phenotype in carriers of desmosomal mutations and can affect atrial electrical function.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1113/JP284597; doi:https://doi.org/10.1113/JP284597
 32579178,https://doi.org/10.1001/jamadermatol.2020.1948,Association Between Atopic Eczema and Cancer in England and Denmark.,"Mansfield KE, Schmidt SAJ, Darvalics B, Mulick A, Abuabara K, Wong AYS, Sørensen HT, Smeeth L, Bhaskaran K, Dos Santos Silva I, Silverwood RJ, Langan SM.",,JAMA dermatology,2020,2020-10-01,Y,,,,"<h4>Importance</h4>Associations between atopic eczema and cancer are unclear, with competing theories that increased immune surveillance decreases cancer risk and that immune stimulation increases cancer risk. Establishing baseline cancer risk in people with atopic eczema is important before exploring the association between new biologic drugs for atopic eczema and cancer risk.<h4>Objective</h4>To investigate whether atopic eczema is associated with cancer.<h4>Design, setting, and participants</h4>Matched cohort studies were conducted from January 2, 1998, to March 31, 2016, in England and from January 1, 1982, to June 30, 2016, in Denmark. We conducted our analyses between July 2018 and July 2019. The setting was English primary care and nationwide Danish data. Participants with atopic eczema (adults only in England and any age in Denmark) were matched on age, sex, and calendar period (as well as primary care practice in England only) to those without atopic eczema.<h4>Exposure</h4>Atopic eczema.<h4>Main outcomes and measures</h4>Overall cancer risk and risk of specific cancers were compared in people with and without atopic eczema.<h4>Results</h4>In England, matched cohorts included 471 970 individuals with atopic eczema (median [IQR] age, 41.1 [24.9-60.7] years; 276 510 [58.6%] female) and 2 239 775 individuals without atopic eczema (median [IQR] age, 39.8 [25.9-58.4] years; 1 301 074 [58.1%] female). In Denmark, matched cohorts included 44 945 individuals with atopic eczema (median [IQR] age, 13.7 [1.7-21.1] years; 22 826 [50.8%] female) and 445 673 individuals without atopic eczema (median [IQR] age, 13.5 [1.7-20.8] years; 226 323 [50.8%] female). Little evidence was found of associations between atopic eczema and overall cancer (adjusted hazard ratio [HR], 1.04; 99% CI, 1.02-1.06 in England and 1.05; 99% CI, 0.95-1.16 in Denmark) or for most specific cancers. However, noncutaneous lymphoma risk was increased in people with atopic eczema in England (adjusted HR, 1.19; 99% CI, 1.07-1.34 for non-Hodgkin lymphoma [NHL] and 1.48; 99% CI, 1.07-2.04 for Hodgkin lymphoma). Lymphoma risk was increased in people with greater eczema severity vs those without atopic eczema (NHL adjusted HR, 1.06; 99% CI, 0.90-1.25 for mild eczema; 1.24; 99% CI, 1.04-1.48 for moderate eczema; and 2.08; 99% CI, 1.42-3.04 for severe eczema). Danish point estimates also showed increased lymphoma risk in people with moderate to severe eczema compared with those without atopic eczema (minimally adjusted HR, 1.31; 99% CI, 0.76-2.26 for NHL and 1.35; 99% CI, 0.65-2.82 for Hodgkin lymphoma), but the 99% CIs were wide.<h4>Conclusions and relevance</h4>The findings from 2 large population-based studies performed in different settings do not support associations between atopic eczema and most cancers. However, an association was observed between atopic eczema and lymphoma, particularly NHL, that increased with eczema severity. This finding warrants further study as new immunomodulatory systemic therapeutics are brought to market that may alter cancer risk.",,pdf:https://jamanetwork.com/journals/jamadermatology/articlepdf/2767601/jamadermatology_mansfield_2020_oi_200037_1602515656.45058.pdf; doi:https://doi.org/10.1001/jamadermatol.2020.1948; html:https://europepmc.org/articles/PMC7315391
 37408046,https://doi.org/10.1186/s40545-023-00590-9,Delivering the precision oncology paradigm: reduced R&D costs and greater return on investment through a companion diagnostic informed precision oncology medicines approach.,"Henderson RH, French D, Stewart E, Smart D, Idica A, Redmond S, Eckstein M, Clark J, Sullivan R, Keeling P, Lawler M.",,Journal of pharmaceutical policy and practice,2023,2023-07-05,Y,,,,"<h4>Background</h4>Precision oncology medicines represent a paradigm shift compared to non-precision oncology medicines in cancer therapy, in some situations delivering more clinical benefit, and potentially lowering healthcare costs. We determined whether employing a companion diagnostic (CDx) approach during oncology medicines development delivers effective therapies that are within the cost constraints of current health systems. R&D costs of developing a medicine are subject to debate, with average estimates ranging from $765 million (m) to $4.6 billion (b). Our aim was to determine whether precision oncology medicines are cheaper to bring from R&D to market; a secondary goal was to determine whether precision oncology medicines have a greater return on investment (ROI).<h4>Method</h4>Data on oncology medicines approved between 1997 and 2020 by the US Food and Drug Administration (FDA) were analysed from the Securities and Exchange Commission (SEC) filings. Data were compiled from 10-K, 10-Q, and 20-F financial performance filings on medicines' development costs through their R&D lifetime. Clinical trial data were split into clinical trial phases 1-3 and probability of success (POS) of trials was calculated, along with preclinical costs. Cost-of-capital (CoC) approach was applied and, if appropriate, a tax rebate was subtracted from the total.<h4>Results</h4>Data on 42 precision and 29 non-precision oncology medicines from 56 companies listed by the National Cancer Institute which had complete data available were analysed. Estimated mean cost to deliver a new oncology medicine was $4.4b (95% CI, $3.6-5.2b). Costs to bring a precision oncology medicine to market were $1.1b less ($3.5b; 95% CI, $2.7-4.5b) compared to non-precision oncology medicines ($4.6b; 95% CI, $3.5-6.1b). The key driver of costs was POS of clinical trials, accounting for a difference of $591.3 m. Additional data analysis illustrated that there was a 27% increase in return on investment (ROI) of precision oncology medicines over non-precision oncology medicines.<h4>Conclusion</h4>Our results provide an accurate estimate of the R&D spend required to bring an oncology medicine to market. Deployment of a CDx at the earliest stage substantially lowers the cost associated with oncology medicines development, potentially making them available to more patients, while staying within the cost constraints of cancer health systems.",,pdf:https://joppp.biomedcentral.com/counter/pdf/10.1186/s40545-023-00590-9; doi:https://doi.org/10.1186/s40545-023-00590-9; html:https://europepmc.org/articles/PMC10320864; pdf:https://europepmc.org/articles/PMC10320864?pdf=render
@@ -1665,102 +1667,102 @@ PMC8855010,https://doi.org/,POS-894 PREDICTING PANDEMIC-RELATED EXCESS-DEATH USI
 37477803,https://doi.org/10.1007/s11897-023-00615-z,Discovering Distinct Phenotypical Clusters in Heart Failure Across the Ejection Fraction Spectrum: a Systematic Review.,"Meijs C, Handoko ML, Savarese G, Vernooij RWM, Vaartjes I, Banerjee A, Koudstaal S, Brugts JJ, Asselbergs FW, Uijl A.",,Current heart failure reports,2023,2023-07-21,Y,Clustering; Phenotyping; Heart Failure; Machine Learning; Precision Medicine,,,"<h4>Review purpose</h4>This systematic review aims to summarise clustering studies in heart failure (HF) and guide future clinical trial design and implementation in routine clinical practice.<h4>Findings</h4>34 studies were identified (n = 19 in HF with preserved ejection fraction (HFpEF)). There was significant heterogeneity invariables and techniques used. However, 149/165 described clusters could be assigned to one of nine phenotypes: 1) young, low comorbidity burden; 2) metabolic; 3) cardio-renal; 4) atrial fibrillation (AF); 5) elderly female AF; 6) hypertensive-comorbidity; 7) ischaemic-male; 8) valvular disease; and 9) devices. There was room for improvement on important methodological topics for all clustering studies such as external validation and transparency of the modelling process. The large overlap between the phenotypes of the clustering studies shows that clustering is a robust approach for discovering clinically distinct phenotypes. However, future studies should invest in a phenotype model that can be implemented in routine clinical practice and future clinical trial design. HF = heart failure, EF = ejection fraction, HFpEF = heart failure with preserved ejection fraction, HFrEF = heart failure with reduced ejection fraction, CKD = chronic kidney disease, AF = atrial fibrillation, IHD = ischaemic heart disease, CAD = coronary artery disease, ICD = implantable cardioverter-defibrillator, CRT = cardiac resynchronization therapy, NT-proBNP = N-terminal pro b-type natriuretic peptide, BMI = Body Mass Index, COPD = Chronic obstructive pulmonary disease.",,pdf:https://link.springer.com/content/pdf/10.1007/s11897-023-00615-z.pdf; doi:https://doi.org/10.1007/s11897-023-00615-z; html:https://europepmc.org/articles/PMC10589200; pdf:https://europepmc.org/articles/PMC10589200?pdf=render
 36469091,https://doi.org/10.1093/ageing/afac252,Prevalence and outcomes of atrial fibrillation in older people living in care homes in Wales: a routine data linkage study 2003-2018.,"Ritchie LA, Harrison SL, Penson PE, Akbari A, Torabi F, Hollinghurst J, Harris D, Oke OB, Akpan A, Halcox JP, Rodgers SE, Lip GYH, Lane DA.",,Age and ageing,2022,2022-12-01,N,Prevalence; Atrial fibrillation; Stroke; Older People; Care Homes; Health Outcomes,,,"<h4>Objective</h4>To determine atrial fibrillation (AF) prevalence and temporal trends, and examine associations between AF and risk of adverse health outcomes in older care home residents.<h4>Methods</h4>Retrospective cohort study using anonymised linked data from the Secure Anonymised Information Linkage Databank on CARE home residents in Wales with AF (SAIL CARE-AF) between 2003 and 2018. Fine-Gray competing risk models were used to estimate the risk of health outcomes with mortality as a competing risk. Cox regression analyses were used to estimate the risk of mortality.<h4>Results</h4>There were 86,602 older care home residents (median age 86.0 years [interquartile range 80.8-90.6]) who entered a care home between 2003 and 2018. When the pre-care home entry data extraction was standardised, the overall prevalence of AF was 17.4% (95% confidence interval 17.1-17.8) between 2010 and 2018. There was no significant change in the age- and sex-standardised prevalence of AF from 16.8% (15.9-17.9) in 2010 to 17.0% (16.1-18.0) in 2018. Residents with AF had a significantly higher risk of cardiovascular mortality (adjusted hazard ratio [HR] 1.27 [1.17-1.37], P < 0.001), all-cause mortality (adjusted HR 1.14 [1.11-1.17], P < 0.001), ischaemic stroke (adjusted sub-distribution HR 1.55 [1.36-1.76], P < 0.001) and cardiovascular hospitalisation (adjusted sub-distribution HR 1.28 [1.22-1.34], P < 0.001).<h4>Conclusions</h4>Older care home residents with AF have an increased risk of adverse health outcomes, even when higher mortality rates and other confounders are accounted for. This re-iterates the need for appropriate oral anticoagulant prescription and optimal management of cardiovascular co-morbidities, irrespective of frailty status and predicted life expectancy.",,pdf:https://academic.oup.com/ageing/article-pdf/51/12/afac252/47589319/afac252.pdf; doi:https://doi.org/10.1093/ageing/afac252
 38887861,https://doi.org/10.1002/ejhf.3339,Evaluation of the 2021 ESC recommendations for family screening in hereditary transthyretin cardiac amyloidosis.,"Muller SA, Peiró-Aventin B, Biagioni G, Tini G, Saturi G, Kronberger C, Achten A, Dobner S, Te Rijdt WP, Gasperetti A, Te Riele ASJM, Varrà GG, Ponziani A, Hirsch A, Porcari A, van der Meer MG, Zampieri M, van der Harst P, Kammerlander A, Biagini E, van Tintelen JP, Barbato E, Asselbergs FW, Menale S, Gräni C, Merlo M, Michels M, Knackstedt C, Nitsche C, Longhi S, Musumeci B, Cappelli F, Garcia-Pavia P, Oerlemans MIFJ.",,European journal of heart failure,2024,2024-06-17,N,Amyloidosis; Cascade Screening; Repeat Evaluation; Attrv,,,"<h4>Aims</h4>The 2021 European Society of Cardiology (ESC) screening recommendations for individuals carrying a pathogenic transthyretin amyloidosis variant (ATTRv) are based on expert opinion. We aimed to (i) determine the penetrance of ATTRv cardiomyopathy (ATTRv-CM) at baseline; (ii) examine the value of serial evaluation; and (iii) establish the yield of first-line diagnostic tests (i.e. electrocardiogram, echocardiogram, and laboratory tests) as per 2021 ESC position statement.<h4>Methods and results</h4>We included 159 relatives (median age 55.6 [43.2-65.9] years, 52% male) at risk for ATTRv-CM from 10 centres. The primary endpoint, ATTRv-CM diagnosis, was defined as the presence of (i) cardiac tracer uptake in bone scintigraphy; or (ii) transthyretin-positive cardiac biopsy. The secondary endpoint was a composite of heart failure (New York Heart Association class ≥II) and pacemaker-requiring conduction disorders. At baseline, 40/159 (25%) relatives were diagnosed with ATTRv-CM. Of those, 20 (50%) met the secondary endpoint. Indication to screen (≤10 years prior to predicted disease onset and absence of extracardiac amyloidosis) had an excellent negative predictive value (97%). Other pre-screening predictors for ATTRv-CM were infrequently identified variants and male sex. Importantly, 13% of relatives with ATTRv-CM did not show any signs of cardiac involvement on first-line diagnostic tests. The yield of serial evaluation (n = 41 relatives; follow-up 3.1 [2.2-5.2] years) at 3-year interval was 9.4%.<h4>Conclusions</h4>Screening according to the 2021 ESC position statement performs well in daily clinical practice. Clinicians should adhere to repeating bone scintigraphy after 3 years, as progressing to ATTRv-CM without signs of ATTRv-CM on first-line diagnostic tests or symptoms is common.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ejhf.3339; doi:https://doi.org/10.1002/ejhf.3339
-33033797,https://doi.org/10.1016/j.eclinm.2020.100560,Investigating the effects of comprehensive smoke-free legislation on neonatal and infant mortality in Thailand using the synthetic control method.,"Radó MK, van Lenthe FJ, Sheikh A, Been JV.",,EClinicalMedicine,2020,2020-10-02,Y,Thailand; Infant Mortality; Child Health; Smoke-free Legislation; Synthetic Control Method,,,"<h4>Background</h4>Almost all of the evidence on the benefits of smoke-free legislation on child health comes from evaluations in high-income countries. We investigated the effects of Thailand's 2010 comprehensive smoke-free legislation on neonatal and infant mortality.<h4>Methods</h4>To overcome some of the methodological issues inherent to traditional quasi-experimental methods, we applied the novel synthetic control approach. Using 2001-2017 country-level panel data from the World Bank and Penn World datasets, we estimated the effects of smoke-free legislation as the difference between the outcome trends in Thailand versus those in a synthetic control country. The synthetic control country was composed of 'control' middle-income countries without comprehensive smoke-free legislation to recreate trends in Thailand in the 2001-2009 pre-legislation outcomes and covariates. We compared the legislation effects to 'placebo effects' obtained for each control country by fictitiously assuming that comprehensive smoke-free legislation was introduced there in 2010, similar to Thailand.<h4>Findings</h4>Neonatal and infant mortality decreased by 2.9% and 2.8%/year respectively following smoke-free legislation, with an estimated 7463 infant deaths (including 4623 neonatal deaths) having been averted over eight years. The results were robust to different specifications of the control countries. Comparison with placebo effects indicated that the findings were unlikely to be attributable to factors other than the smoke-free legislation.<h4>Interpretation</h4>Expanding comprehensive smoke-free policies to middle-income countries can support national efforts to achieve Sustainable Development Goal 3.2 for reducing preventable early-life deaths.<h4>Funding</h4>Netherlands Lung Foundation, HDRUK, Asthma UK center for Applied Research and NIHR Global Respiratory Health Unit (RESPIRE).",,pdf:http://www.thelancet.com/article/S2589537020303047/pdf; doi:https://doi.org/10.1016/j.eclinm.2020.100560; html:https://europepmc.org/articles/PMC7533363; pdf:https://europepmc.org/articles/PMC7533363?pdf=render
 35259281,https://doi.org/10.1111/acel.13524,Biological mechanisms of aging predict age-related disease co-occurrence in patients.,"Fraser HC, Kuan V, Johnen R, Zwierzyna M, Hingorani AD, Beyer A, Partridge L.",,Aging cell,2022,2022-03-08,Y,Aging; Genetics; Age-related Disease; Multimorbidity; Aging Hallmarks,,,"Genetic, environmental, and pharmacological interventions into the aging process can confer resistance to multiple age-related diseases in laboratory animals, including rhesus monkeys. These findings imply that individual mechanisms of aging might contribute to the co-occurrence of age-related diseases in humans and could be targeted to prevent these conditions simultaneously. To address this question, we text mined 917,645 literature abstracts followed by manual curation and found strong, non-random associations between age-related diseases and aging mechanisms in humans, confirmed by gene set enrichment analysis of GWAS data. Integration of these associations with clinical data from 3.01 million patients showed that age-related diseases associated with each of five aging mechanisms were more likely than chance to be present together in patients. Genetic evidence revealed that innate and adaptive immunity, the intrinsic apoptotic signaling pathway and activity of the ERK1/2 pathway were associated with multiple aging mechanisms and diverse age-related diseases. Mechanisms of aging hence contribute both together and individually to age-related disease co-occurrence in humans and could potentially be targeted accordingly to prevent multimorbidity.",,pdf:https://discovery.ucl.ac.uk/10145565/1/Hignorani_Biological%20mechanisms%20of%20aging%20predict%20age-related%20disease%20co-occurrence%20in%20patients_AOP.pdf; doi:https://doi.org/10.1111/acel.13524; html:https://europepmc.org/articles/PMC9009120; pdf:https://europepmc.org/articles/PMC9009120?pdf=render
-PMC9023380,https://doi.org/,Assessing the spread risk of COVID-19 associated with multi-mode transportation networks in China,"Xu X, Liu X, Wang L, Wu Y, Lu X, Wang X, Pei S.",,Fundamental research,2022,2022-04-22,Y,Complex Network; Spatial Spread; Human Mobility; Transportation Networks; Covid-19,,,"The spatial spread of COVID-19 during early 2020 in China was primarily driven by outbound travelers leaving the epicenter, Wuhan, Hubei province. Existing studies focus on the influence of aggregated out-bound population flows originating from Wuhan; however, the impacts of different modes of transportation and the network structure of transportation systems on the early spread of COVID-19 in China are not well understood. Here, we assess the roles of the road, railway, and air transportation networks in driving the spatial spread of COVID-19 in China. We find that the short-range spread within Hubei province was dominated by ground traffic, notably, the railway transportation. In contrast, long-range spread to cities in other provinces was mediated by multiple factors, including a higher risk of case importation associated with air transportation and a larger outbreak size in hub cities located at the center of transportation networks. We further show that, although the dissemination of SARS-CoV-2 across countries and continents is determined by the worldwide air transportation network, the early geographic dispersal of COVID-19 within China is better predicted by the railway traffic. Given the recent emergence of multiple more transmissible variants of SARS-CoV-2, our findings can support a better assessment of the spread risk of those variants and improve future pandemic preparedness and responses. Graphical abstract Image, graphical abstract.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9023380/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9023380/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC9023380; pdf:https://europepmc.org/articles/PMC9023380?pdf=render
 34873059,https://doi.org/10.1073/pnas.2108395118,How immunity from and interaction with seasonal coronaviruses can shape SARS-CoV-2 epidemiology.,"Waterlow NR, van Leeuwen E, Davies NG, CMMID COVID-19 Working Group, Flasche S, Eggo RM.",,Proceedings of the National Academy of Sciences of the United States of America,2021,2021-12-01,Y,Immunity; Coronaviruses; Cross-protection; Covid-19; Sars-cov-2,,,"We hypothesized that cross-protection from seasonal epidemics of human coronaviruses (HCoVs) could have affected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, including generating reduced susceptibility in children. To determine what the prepandemic distribution of immunity to HCoVs was, we fitted a mathematical model to 6 y of seasonal coronavirus surveillance data from England and Wales. We estimated a duration of immunity to seasonal HCoVs of 7.8 y (95% CI 6.3 to 8.1) and show that, while cross-protection between HCoV and SARS-CoV-2 may contribute to the age distribution, it is insufficient to explain the age pattern of SARS-CoV-2 infections in the first wave of the pandemic in England and Wales. Projections from our model illustrate how different strengths of cross-protection between circulating coronaviruses could determine the frequency and magnitude of SARS-CoV-2 epidemics over the coming decade, as well as the potential impact of cross-protection on future seasonal coronavirus transmission.",,doi:https://doi.org/10.1073/pnas.2108395118; doi:https://doi.org/10.1073/pnas.2108395118; html:https://europepmc.org/articles/PMC8670441; pdf:https://europepmc.org/articles/PMC8670441?pdf=render
+PMC9023380,https://doi.org/,Assessing the spread risk of COVID-19 associated with multi-mode transportation networks in China,"Xu X, Liu X, Wang L, Wu Y, Lu X, Wang X, Pei S.",,Fundamental research,2022,2022-04-22,Y,Complex Network; Spatial Spread; Human Mobility; Transportation Networks; Covid-19,,,"The spatial spread of COVID-19 during early 2020 in China was primarily driven by outbound travelers leaving the epicenter, Wuhan, Hubei province. Existing studies focus on the influence of aggregated out-bound population flows originating from Wuhan; however, the impacts of different modes of transportation and the network structure of transportation systems on the early spread of COVID-19 in China are not well understood. Here, we assess the roles of the road, railway, and air transportation networks in driving the spatial spread of COVID-19 in China. We find that the short-range spread within Hubei province was dominated by ground traffic, notably, the railway transportation. In contrast, long-range spread to cities in other provinces was mediated by multiple factors, including a higher risk of case importation associated with air transportation and a larger outbreak size in hub cities located at the center of transportation networks. We further show that, although the dissemination of SARS-CoV-2 across countries and continents is determined by the worldwide air transportation network, the early geographic dispersal of COVID-19 within China is better predicted by the railway traffic. Given the recent emergence of multiple more transmissible variants of SARS-CoV-2, our findings can support a better assessment of the spread risk of those variants and improve future pandemic preparedness and responses. Graphical abstract Image, graphical abstract.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9023380/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9023380/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC9023380; pdf:https://europepmc.org/articles/PMC9023380?pdf=render
+33033797,https://doi.org/10.1016/j.eclinm.2020.100560,Investigating the effects of comprehensive smoke-free legislation on neonatal and infant mortality in Thailand using the synthetic control method.,"Radó MK, van Lenthe FJ, Sheikh A, Been JV.",,EClinicalMedicine,2020,2020-10-02,Y,Thailand; Infant Mortality; Child Health; Smoke-free Legislation; Synthetic Control Method,,,"<h4>Background</h4>Almost all of the evidence on the benefits of smoke-free legislation on child health comes from evaluations in high-income countries. We investigated the effects of Thailand's 2010 comprehensive smoke-free legislation on neonatal and infant mortality.<h4>Methods</h4>To overcome some of the methodological issues inherent to traditional quasi-experimental methods, we applied the novel synthetic control approach. Using 2001-2017 country-level panel data from the World Bank and Penn World datasets, we estimated the effects of smoke-free legislation as the difference between the outcome trends in Thailand versus those in a synthetic control country. The synthetic control country was composed of 'control' middle-income countries without comprehensive smoke-free legislation to recreate trends in Thailand in the 2001-2009 pre-legislation outcomes and covariates. We compared the legislation effects to 'placebo effects' obtained for each control country by fictitiously assuming that comprehensive smoke-free legislation was introduced there in 2010, similar to Thailand.<h4>Findings</h4>Neonatal and infant mortality decreased by 2.9% and 2.8%/year respectively following smoke-free legislation, with an estimated 7463 infant deaths (including 4623 neonatal deaths) having been averted over eight years. The results were robust to different specifications of the control countries. Comparison with placebo effects indicated that the findings were unlikely to be attributable to factors other than the smoke-free legislation.<h4>Interpretation</h4>Expanding comprehensive smoke-free policies to middle-income countries can support national efforts to achieve Sustainable Development Goal 3.2 for reducing preventable early-life deaths.<h4>Funding</h4>Netherlands Lung Foundation, HDRUK, Asthma UK center for Applied Research and NIHR Global Respiratory Health Unit (RESPIRE).",,pdf:http://www.thelancet.com/article/S2589537020303047/pdf; doi:https://doi.org/10.1016/j.eclinm.2020.100560; html:https://europepmc.org/articles/PMC7533363; pdf:https://europepmc.org/articles/PMC7533363?pdf=render
 32817390,https://doi.org/10.1212/wnl.0000000000010463,"Sleep, major depressive disorder, and Alzheimer disease: A Mendelian randomization study.","Huang J, Zuber V, Matthews PM, Elliott P, Tzoulaki J, Dehghan A.",,Neurology,2020,2020-08-19,Y,,,,"<h4>Objective</h4>To explore the causal relationships between sleep, major depressive disorder (MDD), and Alzheimer disease (AD).<h4>Methods</h4>We conducted bidirectional 2-sample Mendelian randomization analyses. Genetic associations were obtained from the largest genome-wide association studies currently available in UK Biobank (n = 446,118), Psychiatric Genomics Consortium (n = 18,759), and International Genomics of Alzheimer's Project (n = 63,926). We used the inverse variance-weighted Mendelian randomization method to estimate causal effects and weighted median and Mendelian randomization-Egger for sensitivity analyses to test for pleiotropic effects.<h4>Results</h4>We found that higher risk of AD was significantly associated with being a ""morning person"" (odds ratio [OR] 1.01, <i>p</i> = 0.001), shorter sleep duration (self-reported: β = -0.006, <i>p</i> = 1.9 × 10<sup>-4</sup>; accelerometer based: β = -0.015, <i>p</i> = 6.9 × 10<sup>-5</sup>), less likely to report long sleep (β = -0.003, <i>p</i> = 7.3 × 10<sup>-7</sup>), earlier timing of the least active 5 hours (β = -0.024, <i>p</i> = 1.7 × 10<sup>-13</sup>), and a smaller number of sleep episodes (β = -0.025, <i>p</i> = 5.7 × 10<sup>-14</sup>) after adjustment for multiple comparisons. We also found that higher risk of AD was associated with lower risk of insomnia (OR 0.99, <i>p</i> = 7 × 10<sup>-13</sup>). However, we did not find evidence that these abnormal sleep patterns were causally related to AD or for a significant causal relationship between MDD and risk of AD.<h4>Conclusion</h4>We found that AD may causally influence sleep patterns. However, we did not find evidence supporting a causal role of disturbed sleep patterns for AD or evidence for a causal relationship between MDD and AD.",,pdf:https://n.neurology.org/content/neurology/95/14/e1963.full.pdf; doi:https://doi.org/10.1212/WNL.0000000000010463; html:https://europepmc.org/articles/PMC7682841; pdf:https://europepmc.org/articles/PMC7682841?pdf=render
 34364665,https://doi.org/10.1016/j.cardfail.2021.05.012,Empagliflozin in Heart Failure With Predicted Preserved Versus Reduced Ejection Fraction: Data From the EMPA-REG OUTCOME Trial.,"Savarese G, Uijl A, Lund LH, Anker SD, Asselbergs F, Fitchett D, Inzucchi SE, Koudstaal S, Ofstad AP, Schrage B, Vedin O, Wanner C, Zannad F, Zwiener I, Butler J.",,Journal of cardiac failure,2021,2021-08-01,N,Type 2 diabetes mellitus; Heart Failure With Preserved Ejection Fraction; Heart Failure With Reduced Ejection Fraction; Empagliflozin; Empa-reg Outcome; Heart Failure With Mid-range Ejection Fraction; Heart Failure With Mildly Reduced Ejection Fraction,,,"<h4>Background</h4>In the EMPA-REG OUTCOME trial, ejection fraction (EF) data were not collected. In the subpopulation with heart failure (HF), we applied a new predictive model for EF to determine the effects of empagliflozin in HF with predicted reduced (HFrEF) vs preserved (HFpEF) EF vs no HF.<h4>Methods and results</h4>We applied a validated EF predictive model based on patient baseline characteristics and treatments to categorize patients with HF as being likely to have HF with mid-range EF (HFmrEF)/HFrEF (EF <50%) or HFpEF (EF ≥50%). Cox regression was used to assess the effect of empagliflozin vs placebo on cardiovascular death/HF hospitalization (HHF), cardiovascular and all-cause mortality, and HHF in patients with predicted HFpEF, HFmrEF/HFrEF and no HF. Of 7001 EMPA-REG OUTCOME patients with data available for this analysis, 6314 (90%) had no history of HF. Of the 687 with history of HF, 479 (69.7%) were predicted to have HFmrEF/HFrEF and 208 (30.3%) to have HFpEF. Empagliflozin's treatment effect was consistent in predicted HFpEF, HFmrEF/HFrEF and no-HF for each outcome (HR [95% CI] for the primary outcome 0.60 [0.31-1.17], 0.79 [0.51-1.23], and 0.63 [0.50-0.78], respectively; P interaction = 0.62).<h4>Conclusions</h4>In EMPA-REG OUTCOME, one-third of the patients with HF had predicted HFpEF. The benefits of empagliflozin on HF and mortality outcomes were consistent in nonHF, predicted HFpEF and HFmrEF/HFrEF.",,pdf:https://hal.univ-lorraine.fr/hal-03320880/file/1-s2.0-S1071916421002025-main.pdf; doi:https://doi.org/10.1016/j.cardfail.2021.05.012
 36346654,https://doi.org/10.2196/38168,Developing an Automated Assessment of In-session Patient Activation for Psychological Therapy: Codevelopment Approach.,"Malins S, Figueredo G, Jilani T, Long Y, Andrews J, Rawsthorne M, Manolescu C, Clos J, Higton F, Waldram D, Hunt D, Perez Vallejos E, Moghaddam N.",,JMIR medical informatics,2022,2022-11-08,Y,Mental health; Machine Learning; Cognitive Behavioral Therapy; Natural Language Processing; Multimorbidity; Responsible Artificial Intelligence,,,"<h4>Background</h4>Patient activation is defined as a patient's confidence and perceived ability to manage their own health. Patient activation has been a consistent predictor of long-term health and care costs, particularly for people with multiple long-term health conditions. However, there is currently no means of measuring patient activation from what is said in health care consultations. This may be particularly important for psychological therapy because most current methods for evaluating therapy content cannot be used routinely due to time and cost restraints. Natural language processing (NLP) has been used increasingly to classify and evaluate the contents of psychological therapy. This aims to make the routine, systematic evaluation of psychological therapy contents more accessible in terms of time and cost restraints. However, comparatively little attention has been paid to algorithmic trust and interpretability, with few studies in the field involving end users or stakeholders in algorithm development.<h4>Objective</h4>This study applied a responsible design to use NLP in the development of an artificial intelligence model to automate the ratings assigned by a psychological therapy process measure: the consultation interactions coding scheme (CICS). The CICS assesses the level of patient activation observable from turn-by-turn psychological therapy interactions.<h4>Methods</h4>With consent, 128 sessions of remotely delivered cognitive behavioral therapy from 53 participants experiencing multiple physical and mental health problems were anonymously transcribed and rated by trained human CICS coders. Using participatory methodology, a multidisciplinary team proposed candidate language features that they thought would discriminate between high and low patient activation. The team included service-user researchers, psychological therapists, applied linguists, digital research experts, artificial intelligence ethics researchers, and NLP researchers. Identified language features were extracted from the transcripts alongside demographic features, and machine learning was applied using k-nearest neighbors and bagged trees algorithms to assess whether in-session patient activation and interaction types could be accurately classified.<h4>Results</h4>The k-nearest neighbors classifier obtained 73% accuracy (82% precision and 80% recall) in a test data set. The bagged trees classifier obtained 81% accuracy for test data (87% precision and 75% recall) in differentiating between interactions rated high in patient activation and those rated low or neutral.<h4>Conclusions</h4>Coproduced language features identified through a multidisciplinary collaboration can be used to discriminate among psychological therapy session contents based on patient activation among patients experiencing multiple long-term physical and mental health conditions.",,pdf:https://medinform.jmir.org/2022/11/e38168/PDF; doi:https://doi.org/10.2196/38168; html:https://europepmc.org/articles/PMC9682451
 35869974,https://doi.org/10.1093/ndt/gfac224,Care processes and outcomes of deprivation across the clinical course of kidney disease: findings from a high-income country with universal healthcare.,"Sawhney S, Blakeman T, Blana D, Boyers D, Fluck N, Nath M, Methven S, Rzewuska M, Black C.",,"Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association",2023,2023-05-01,Y,Prognosis; epidemiology; Health Inequalities; Ckd; Aki; Care Processes,,,"<h4>Background</h4>No single study contrasts the extent and consequences of inequity of kidney care across the clinical course of kidney disease.<h4>Methods</h4>This population study of Grampian (UK) followed incident presentations of acute kidney injury (AKI) and incident estimated glomerular filtration rate (eGFR) thresholds of <60, <45 and <30 mL/min/1.73 m2 in separate cohorts (2011-2021). The key exposure was area-level deprivation (lowest quintile of the Scottish Index of Multiple Deprivation). Outcomes were care processes (monitoring, prescribing, appointments, unscheduled care), long-term mortality and kidney failure. Modelling involved multivariable logistic regression, negative binomial regression and cause-specific Cox models with and without adjustment of comorbidities.<h4>Results</h4>There were 41 313, 51 190, 32 171 and 17 781 new presentations of AKI and eGFR thresholds <60, <45 and <30  mL/min/1.73 m2. A total of 6.1-7.8% of the population was from deprived areas and (versus all others) presented on average 5 years younger, with more diabetes and pulmonary and liver disease. Those from deprived areas were more likely to present initially in hospital, less likely to receive community monitoring, less likely to attend appointments and more likely to have an unplanned emergency department or hospital admission episode. Deprivation had the greatest association with long-term kidney failure at the eGFR <60 mL/min/1.73 m2 threshold {adjusted hazard ratio [HR] 1.48 [95% confidence interval (CI) 1.17-1.87]} and this association decreased with advancing disease severity [HR 1.09 (95% CI 0.93-1.28) at eGFR <30 mL/min/1.73 m2), with a similar pattern for mortality. Across all analyses the most detrimental associations of deprivation were an eGFR threshold <60 mL/min/1.73 m2, AKI, males and those <65 years of age.<h4>Conclusions</h4>Even in a high-income country with universal healthcare, serious and consistent inequities in kidney care exist. The poorer care and outcomes with area-level deprivation were greater earlier in the disease course.",,pdf:https://academic.oup.com/ndt/advance-article-pdf/doi/10.1093/ndt/gfac224/45505736/gfac224.pdf; doi:https://doi.org/10.1093/ndt/gfac224; html:https://europepmc.org/articles/PMC10157789; pdf:https://europepmc.org/articles/PMC10157789?pdf=render
-35842920,https://doi.org/10.1002/ehf2.14073,Blood-based biomarkers for the prediction of hypertrophic cardiomyopathy prognosis: a systematic review and meta-analysis.,"Jansen M, Algül S, Bosman LP, Michels M, van der Velden J, de Boer RA, van Tintelen JP, Asselbergs FW, Baas AF.",,ESC heart failure,2022,2022-07-17,Y,Prognosis; Biomarker; hypertrophic cardiomyopathy; Systematic review; Heart Failure; Sudden Cardiac Death,,,"<h4>Aims</h4>Hypertrophic cardiomyopathy (HCM) is the most prevalent monogenic heart disease. HCM is an important cause of sudden cardiac death and may also lead to outflow tract obstruction and heart failure. Disease severity is highly variable and risk stratification remains limited. Therefore, we aimed to review current knowledge of prognostic blood-based biomarkers in HCM.<h4>Methods and results</h4>A systematic literature search was performed on PubMed, Embase, and the Cochrane library to identify studies assessing plasma or serum biomarkers for outcomes involving malignant ventricular arrhythmia, outflow tract obstruction, and heart failure. Risk of bias was assessed using the QUIPS tool. Meta-analyses were performed using the random effects method. A total of 26 unique cohort studies assessing 42 biomarkers were identified. Overall risk of bias was moderate. Thirty-two biomarkers were significantly associated to an HCM outcome in at least one study (nine biomarkers in at least two studies). In pooled analyses, cardiovascular mortality was predicted by N-terminal prohormone of brain natriuretic peptide (hazard ratio [HR] 5.38 per log[pg/mL], 95% confidence interval [CI] 2.07-14.03, P < 0.001, I<sup>2</sup>  = 0%) and high-sensitivity C-reactive protein (HR 1.30 per μg/mL, 95% CI 1.00-1.68, P = 0.05, I<sup>2</sup>  = 78%), all-cause mortality by low-density lipoprotein cholesterol (HR 0.63 per μmol/mL, 95% CI 0.49-0.80, P < 0.001, I<sup>2</sup>  = 0%), and a combined congestive heart failure, malignant ventricular arrhythmia, and stroke outcome by high-sensitivity cardiac troponin T (pooled HR 4.19 for ≥0.014 ng/mL, 95% CI 2.22-7.88, P < 0.001, I<sup>2</sup>  = 0%). Quality of evidence was low-moderate.<h4>Conclusions</h4>Several blood-based biomarkers were identified as predictors of HCM outcomes. Additional studies are required to validate their prognostic utility within current risk stratification models.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ehf2.14073; doi:https://doi.org/10.1002/ehf2.14073; html:https://europepmc.org/articles/PMC9715795; pdf:https://europepmc.org/articles/PMC9715795?pdf=render
 36711167,https://doi.org/10.1093/ehjdh/ztaa016,Real-time imputation of missing predictor values in clinical practice.,"Nijman SWJ, Hoogland J, Groenhof TKJ, Brandjes M, Jacobs JJL, Bots ML, Asselbergs FW, Moons KGM, Debray TPA.",,European heart journal. Digital health,2021,2020-12-19,Y,Prediction; Missing Data; Electronic Health Records; Computerized Decision Support System; Real-time Imputation; Joint Modelling Imputation,,,"<h4>Aims</h4>Use of prediction models is widely recommended by clinical guidelines, but usually requires complete information on all predictors, which is not always available in daily practice. We aim to describe two methods for real-time handling of missing predictor values when using prediction models in practice.<h4>Methods and results</h4>We compare the widely used method of mean imputation (M-imp) to a method that personalizes the imputations by taking advantage of the observed patient characteristics. These characteristics may include both prediction model variables and other characteristics (auxiliary variables). The method was implemented using imputation from a joint multivariate normal model of the patient characteristics (joint modelling imputation; JMI). Data from two different cardiovascular cohorts with cardiovascular predictors and outcome were used to evaluate the real-time imputation methods. We quantified the prediction model's overall performance [mean squared error (MSE) of linear predictor], discrimination (c-index), calibration (intercept and slope), and net benefit (decision curve analysis). When compared with mean imputation, JMI substantially improved the MSE (0.10 vs. 0.13), c-index (0.70 vs. 0.68), and calibration (calibration-in-the-large: 0.04 vs. 0.06; calibration slope: 1.01 vs. 0.92), especially when incorporating auxiliary variables. When the imputation method was based on an external cohort, calibration deteriorated, but discrimination remained similar.<h4>Conclusions</h4>We recommend JMI with auxiliary variables for real-time imputation of missing values, and to update imputation models when implementing them in new settings or (sub)populations.",,pdf:https://academic.oup.com/ehjdh/article-pdf/2/1/154/37807088/ztaa016.pdf; doi:https://doi.org/10.1093/ehjdh/ztaa016; html:https://europepmc.org/articles/PMC9707891; pdf:https://europepmc.org/articles/PMC9707891?pdf=render
-32738956,https://doi.org/10.1016/s0140-6736(20)31286-1,Atopic dermatitis.,"Langan SM, Irvine AD, Weidinger S.",,"Lancet (London, England)",2020,2020-08-01,N,,,,"Atopic dermatitis is a common inflammatory skin disorder characterised by recurrent eczematous lesions and intense itch. The disorder affects people of all ages and ethnicities, has a substantial psychosocial impact on patients and relatives, and is the leading cause of the global burden from skin disease. Atopic dermatitis is associated with increased risk of multiple comorbidities, including food allergy, asthma, allergic rhinitis, and mental health disorders. The pathophysiology is complex and involves a strong genetic predisposition, epidermal dysfunction, and T-cell driven inflammation. Although type-2 mechanisms are dominant, there is increasing evidence that the disorder involves multiple immune pathways. Currently, there is no cure, but increasing numbers of innovative and targeted therapies hold promise for achieving disease control, including in patients with recalcitrant disease. We summarise and discuss advances in our understanding of the disease and their implications for prevention, management, and future research.",,doi:https://doi.org/10.1016/S0140-6736(20)31286-1
+35842920,https://doi.org/10.1002/ehf2.14073,Blood-based biomarkers for the prediction of hypertrophic cardiomyopathy prognosis: a systematic review and meta-analysis.,"Jansen M, Algül S, Bosman LP, Michels M, van der Velden J, de Boer RA, van Tintelen JP, Asselbergs FW, Baas AF.",,ESC heart failure,2022,2022-07-17,Y,Prognosis; Biomarker; hypertrophic cardiomyopathy; Systematic review; Heart Failure; Sudden Cardiac Death,,,"<h4>Aims</h4>Hypertrophic cardiomyopathy (HCM) is the most prevalent monogenic heart disease. HCM is an important cause of sudden cardiac death and may also lead to outflow tract obstruction and heart failure. Disease severity is highly variable and risk stratification remains limited. Therefore, we aimed to review current knowledge of prognostic blood-based biomarkers in HCM.<h4>Methods and results</h4>A systematic literature search was performed on PubMed, Embase, and the Cochrane library to identify studies assessing plasma or serum biomarkers for outcomes involving malignant ventricular arrhythmia, outflow tract obstruction, and heart failure. Risk of bias was assessed using the QUIPS tool. Meta-analyses were performed using the random effects method. A total of 26 unique cohort studies assessing 42 biomarkers were identified. Overall risk of bias was moderate. Thirty-two biomarkers were significantly associated to an HCM outcome in at least one study (nine biomarkers in at least two studies). In pooled analyses, cardiovascular mortality was predicted by N-terminal prohormone of brain natriuretic peptide (hazard ratio [HR] 5.38 per log[pg/mL], 95% confidence interval [CI] 2.07-14.03, P < 0.001, I<sup>2</sup>  = 0%) and high-sensitivity C-reactive protein (HR 1.30 per μg/mL, 95% CI 1.00-1.68, P = 0.05, I<sup>2</sup>  = 78%), all-cause mortality by low-density lipoprotein cholesterol (HR 0.63 per μmol/mL, 95% CI 0.49-0.80, P < 0.001, I<sup>2</sup>  = 0%), and a combined congestive heart failure, malignant ventricular arrhythmia, and stroke outcome by high-sensitivity cardiac troponin T (pooled HR 4.19 for ≥0.014 ng/mL, 95% CI 2.22-7.88, P < 0.001, I<sup>2</sup>  = 0%). Quality of evidence was low-moderate.<h4>Conclusions</h4>Several blood-based biomarkers were identified as predictors of HCM outcomes. Additional studies are required to validate their prognostic utility within current risk stratification models.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ehf2.14073; doi:https://doi.org/10.1002/ehf2.14073; html:https://europepmc.org/articles/PMC9715795; pdf:https://europepmc.org/articles/PMC9715795?pdf=render
 34769922,https://doi.org/10.3390/ijerph182111380,"Driver, Collision and Meteorological Characteristics of Motor Vehicle Collisions among Road Trauma Survivors.","Giummarra MJ, Xu R, Guo Y, Dipnall JF, Ponsford J, Cameron PA, Ameratunga S, Gabbe BJ.",,International journal of environmental research and public health,2021,2021-10-29,Y,Trauma; Prevention; Traffic; Motor Vehicle,,,"Road trauma remains a significant public health problem. We aimed to identify sub-groups of motor vehicle collisions in Victoria, Australia, and the association between collision characteristics and outcomes up to 24 months post-injury. Data were extracted from the Victorian State Trauma Registry for injured drivers aged ≥16 years, from 2010 to 2016, with a compensation claim who survived ≥12 months post-injury. People with intentional or severe head injury were excluded, resulting in 2735 cases. Latent class analysis was used to identify collision classes for driver fault and blood alcohol concentration (BAC), day and time of collision, weather conditions, single vs. multi-vehicle and regional vs. metropolitan injury location. Five classes were identified: (1) daytime multi-vehicle collisions, no other at fault; (2) daytime single-vehicle predominantly weekday collisions; (3) evening single-vehicle collisions, no other at fault, 36% with BAC ≥ 0.05; (4) sunrise or sunset weekday collisions; and (5) dusk and evening multi-vehicle in metropolitan areas with BAC < 0.05. Mixed linear and logistic regression analyses examined associations between collision class and return to work, health (EQ-5D-3L summary score) and independent function Glasgow Outcome Scale - Extended at 6, 12 and 24 months. After adjusting for demographic, health and injury characteristics, collision class was not associated with outcomes. Rather, risk of poor outcomes was associated with age, sex and socioeconomic disadvantage, education, pre-injury health and injury severity. People at risk of poor recovery may be identified from factors available during the hospital admission and may benefit from clinical assessment and targeted referrals and treatments.",,pdf:https://www.mdpi.com/1660-4601/18/21/11380/pdf?version=1635513758; doi:https://doi.org/10.3390/ijerph182111380; html:https://europepmc.org/articles/PMC8583338; pdf:https://europepmc.org/articles/PMC8583338?pdf=render
+32738956,https://doi.org/10.1016/s0140-6736(20)31286-1,Atopic dermatitis.,"Langan SM, Irvine AD, Weidinger S.",,"Lancet (London, England)",2020,2020-08-01,N,,,,"Atopic dermatitis is a common inflammatory skin disorder characterised by recurrent eczematous lesions and intense itch. The disorder affects people of all ages and ethnicities, has a substantial psychosocial impact on patients and relatives, and is the leading cause of the global burden from skin disease. Atopic dermatitis is associated with increased risk of multiple comorbidities, including food allergy, asthma, allergic rhinitis, and mental health disorders. The pathophysiology is complex and involves a strong genetic predisposition, epidermal dysfunction, and T-cell driven inflammation. Although type-2 mechanisms are dominant, there is increasing evidence that the disorder involves multiple immune pathways. Currently, there is no cure, but increasing numbers of innovative and targeted therapies hold promise for achieving disease control, including in patients with recalcitrant disease. We summarise and discuss advances in our understanding of the disease and their implications for prevention, management, and future research.",,doi:https://doi.org/10.1016/S0140-6736(20)31286-1
 38170504,https://doi.org/10.1001/jamacardio.2023.4994,Genetic Associations of Circulating Cardiovascular Proteins With Gestational Hypertension and Preeclampsia.,"Schuermans A, Truong B, Ardissino M, Bhukar R, Slob EAW, Nakao T, Dron JS, Small AM, Cho SMJ, Yu Z, Hornsby W, Antoine T, Lannery K, Postupaka D, Gray KJ, Yan Q, Butterworth AS, Burgess S, Wood MJ, Scott NS, Harrington CM, Sarma AA, Lau ES, Roh JD, Januzzi JL, Natarajan P, Honigberg MC.",,JAMA cardiology,2024,2024-03-01,Y,,,,"<h4>Importance</h4>Hypertensive disorders of pregnancy (HDPs), including gestational hypertension and preeclampsia, are important contributors to maternal morbidity and mortality worldwide. In addition, women with HDPs face an elevated long-term risk of cardiovascular disease.<h4>Objective</h4>To identify proteins in the circulation associated with HDPs.<h4>Design, setting, and participants</h4>Two-sample mendelian randomization (MR) tested the associations of genetic instruments for cardiovascular disease-related proteins with gestational hypertension and preeclampsia. In downstream analyses, a systematic review of observational data was conducted to evaluate the identified proteins' dynamics across gestation in hypertensive vs normotensive pregnancies, and phenome-wide MR analyses were performed to identify potential non-HDP-related effects associated with the prioritized proteins. Genetic association data for cardiovascular disease-related proteins were obtained from the Systematic and Combined Analysis of Olink Proteins (SCALLOP) consortium. Genetic association data for the HDPs were obtained from recent European-ancestry genome-wide association study meta-analyses for gestational hypertension and preeclampsia. Study data were analyzed October 2022 to October 2023.<h4>Exposures</h4>Genetic instruments for 90 candidate proteins implicated in cardiovascular diseases, constructed using cis-protein quantitative trait loci (cis-pQTLs).<h4>Main outcomes and measures</h4>Gestational hypertension and preeclampsia.<h4>Results</h4>Genetic association data for cardiovascular disease-related proteins were obtained from 21 758 participants from the SCALLOP consortium. Genetic association data for the HDPs were obtained from 393 238 female individuals (8636 cases and 384 602 controls) for gestational hypertension and 606 903 female individuals (16 032 cases and 590 871 controls) for preeclampsia. Seventy-five of 90 proteins (83.3%) had at least 1 valid cis-pQTL. Of those, 10 proteins (13.3%) were significantly associated with HDPs. Four were robust to sensitivity analyses for gestational hypertension (cluster of differentiation 40, eosinophil cationic protein [ECP], galectin 3, N-terminal pro-brain natriuretic peptide [NT-proBNP]), and 2 were robust for preeclampsia (cystatin B, heat shock protein 27 [HSP27]). Consistent with the MR findings, observational data revealed that lower NT-proBNP (0.76- to 0.88-fold difference vs no HDPs) and higher HSP27 (2.40-fold difference vs no HDPs) levels during the first trimester of pregnancy were associated with increased risk of HDPs, as were higher levels of ECP (1.60-fold difference vs no HDPs). Phenome-wide MR analyses identified 37 unique non-HDP-related protein-disease associations, suggesting potential on-target effects associated with interventions lowering HDP risk through the identified proteins.<h4>Conclusions and relevance</h4>Study findings suggest genetic associations of 4 cardiovascular disease-related proteins with gestational hypertension and 2 associated with preeclampsia. Future studies are required to test the efficacy of targeting the corresponding pathways to reduce HDP risk.",,doi:https://doi.org/10.1001/jamacardio.2023.4994; html:https://europepmc.org/articles/PMC10765315; pdf:https://europepmc.org/articles/PMC10765315?pdf=render
 33372069,https://doi.org/10.1136/bmjopen-2020-038360,Cardiovascular risk prediction using physical performance measures in COPD: results from a multicentre observational study.,"Fermont JM, Fisk M, Bolton CE, MacNee W, Cockcroft JR, Fuld J, Cheriyan J, Mohan D, Mäki-Petäjä KM, Al-Hadithi AB, Tal-Singer R, Müllerova H, Polkey MI, Wood AM, McEniery CM, Wilkinson IB, ERICA consortium.",,BMJ open,2020,2020-12-28,Y,epidemiology; Primary Care; Cardiac Epidemiology; Chronic Airways Disease; Respiratory Medicine (See Thoracic Medicine),,,"<h4>Objectives</h4>Although cardiovascular disease (CVD) is a common comorbidity associated with chronic obstructive pulmonary disease (COPD), it is unknown how to improve prediction of cardiovascular (CV) risk in individuals with COPD. Traditional CV risk scores have been tested in different populations but not uniquely in COPD. The potential of alternative markers to improve CV risk prediction in individuals with COPD is unknown. We aimed to determine the predictive value of conventional CVD risk factors in COPD and to determine if additional markers improve prediction beyond conventional factors.<h4>Design</h4>Data from the Evaluation of the Role of Inflammation in Chronic Airways disease cohort, which enrolled 729 individuals with Global Initiative for Chronic Obstructive Lung Disease (GOLD) stage II-IV COPD were used. Linked hospital episode statistics and survival data were prospectively collected for a median 4.6 years of follow-up.<h4>Setting</h4>Five UK centres interested in COPD.<h4>Participants</h4>Population-based sample including 714 individuals with spirometry-defined COPD, smoked at least 10 pack years and who were clinically stable for >4 weeks.<h4>Interventions</h4>Baseline measurements included aortic pulse wave velocity (aPWV), carotid intima-media thickness (CIMT), C reactive protein (CRP), fibrinogen, spirometry and Body mass index, airflow Obstruction, Dyspnoea and Exercise capacity (BODE) Index, 6 min walk test (6MWT) and 4 m gait speed (4MGS) test.<h4>Primary and secondary outcome measures</h4>New occurrence (first event) of fatal or non-fatal hospitalised CVD, and all-cause and cause-specific mortality.<h4>Results</h4>Out of 714 participants, 192 (27%) had CV hospitalisation and 6 died due to CVD. The overall CV risk model C-statistic was 0.689 (95% CI 0.688 to 0.691). aPWV and CIMT neither had an association with study outcome nor improved model prediction. CRP, fibrinogen, GOLD stage, BODE Index, 4MGS and 6MWT were associated with the outcome, independently of conventional risk factors (p<0.05 for all). However, only 6MWT improved model discrimination (C=0.727, 95% CI 0.726 to 0.728).<h4>Conclusion</h4>Poor physical performance defined by the 6MWT improves prediction of CV hospitalisation in individuals with COPD.<h4>Trial registration number</h4>ID 11101.",,pdf:https://bmjopen.bmj.com/content/bmjopen/10/12/e038360.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-038360; html:https://europepmc.org/articles/PMC7772292; pdf:https://europepmc.org/articles/PMC7772292?pdf=render
 37653496,https://doi.org/10.1186/s12933-023-01963-9,Empagliflozin is associated with lower cardiovascular risk compared with dipeptidyl peptidase-4 inhibitors in adults with and without cardiovascular disease: EMPagliflozin compaRative effectIveness and SafEty (EMPRISE) study results from Europe and Asia.,"Vistisen D, Carstensen B, Elisabetta P, Lanzinger S, Tan EC, Yabe D, Kim DJ, Sheu WH, Melzer-Cohen C, Holl RW, Núñez J, Ha KH, Halvorsen S, Langslet G, Karasik A, Nyström T, Niskanen L, Guleria S, Klement R, Carrasco M, Foersch J, Shay C, Koeneman L, Hoti F, Farsani SF, Khunti K, Zaccardi F, Subramanian A, Nirantharakumar K, EMPRISE EU, East Asia Study Group.",,Cardiovascular diabetology,2023,2023-08-31,Y,Cardiovascular disease; Type 2 diabetes; Heart Failure; Comparative Effectiveness; Dipeptidyl Peptidase-4 Inhibitors; Empagliflozin,,,"<h4>Background</h4>Studies that have reported lower risk for cardiovascular outcomes in users of Sodium-Glucose Cotransporter-2 Inhibitors (SGLT-2i) are limited by residual cofounding and lack of information on prior cardiovascular disease (CVD). This study compared risk of cardiovascular events in patients within routine care settings in Europe and Asia with type 2 diabetes (T2D) initiating empagliflozin compared to dipeptidyl peptidase-4 inhibitors (DPP-4i) stratified by pre-existing CVD and history of heart failure (HF).<h4>Methods and results</h4>Adults initiating empagliflozin and DPP-4i in 2014-2018/19 from 11 countries in Europe and Asia were compared using propensity score matching and Cox proportional hazards regression to assess differences in rates of primary outcomes: hospitalisation for heart failure (HHF), myocardial infarction (MI), stroke; and secondary outcomes: cardiovascular mortality (CVM), coronary revascularisation procedure, composite outcome including HHF or CVM, and 3-point major adverse cardiovascular events (MACE: MI, stroke and CVM). Country-specific results were meta-analysed and pooled hazard ratios (HR) with 95% confidence intervals (CI) from random-effects models are presented. In total, 85,244 empagliflozin/DPP4i PS-matched patient pairs were included with overall mean follow-up of 0.7 years. Among those with pre-existing CVD, lower risk was observed for HHF (HR 0.74; 95% CI 0.64-0.86), CVM (HR 0.55; 95% CI 0.38-0.80), HHF or CVM (HR 0.57; 95% CI 0.48-0.67) and stroke (HR 0.79; 95% CI 0.67-0.94) in patients initiating empagliflozin vs DPP-4i. Similar patterns were observed among patients without pre-existing CVD and those with and without pre-existing HF.<h4>Conclusion</h4>These results from diverse patient populations in routine care settings across Europe and Asia demonstrate that initiation of empagliflozin compared to DPP-4i results in favourable cardioprotective effects regardless of pre-existing CVD or HF status.",,pdf:https://cardiab.biomedcentral.com/counter/pdf/10.1186/s12933-023-01963-9; doi:https://doi.org/10.1186/s12933-023-01963-9; html:https://europepmc.org/articles/PMC10472675; pdf:https://europepmc.org/articles/PMC10472675?pdf=render
 34426417,https://doi.org/10.1136/bmjhci-2021-100385,Review of study reporting guidelines for clinical studies using artificial intelligence in healthcare.,"Shelmerdine SC, Arthurs OJ, Denniston A, Sebire NJ.",,BMJ health & care informatics,2021,2021-08-01,Y,Medical Informatics; Healthcare Sector; Bmj Health Informatics,,,"High-quality research is essential in guiding evidence-based care, and should be reported in a way that is reproducible, transparent and where appropriate, provide sufficient detail for inclusion in future meta-analyses. Reporting guidelines for various study designs have been widely used for clinical (and preclinical) studies, consisting of checklists with a minimum set of points for inclusion. With the recent rise in volume of research using artificial intelligence (AI), additional factors need to be evaluated, which do not neatly conform to traditional reporting guidelines (eg, details relating to technical algorithm development). In this review, reporting guidelines are highlighted to promote awareness of essential content required for studies evaluating AI interventions in healthcare. These include published and in progress extensions to well-known reporting guidelines such as Standard Protocol Items: Recommendations for Interventional Trials-AI (study protocols), Consolidated Standards of Reporting Trials-AI (randomised controlled trials), Standards for Reporting of Diagnostic Accuracy Studies-AI (diagnostic accuracy studies) and Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis-AI (prediction model studies). Additionally there are a number of guidelines that consider AI for health interventions more generally (eg, Checklist for Artificial Intelligence in Medical Imaging (CLAIM), minimum information (MI)-CLAIM, MI for Medical AI Reporting) or address a specific element such as the 'learning curve' (Developmental and Exploratory Clinical Investigation of Decision-AI) . Economic evaluation of AI health interventions is not currently addressed, and may benefit from extension to an existing guideline. In the face of a rapid influx of studies of AI health interventions, reporting guidelines help ensure that investigators and those appraising studies consider both the well-recognised elements of good study design and reporting, while also adequately addressing new challenges posed by AI-specific elements.",,pdf:https://informatics.bmj.com/content/bmjhci/28/1/e100385.full.pdf; doi:https://doi.org/10.1136/bmjhci-2021-100385; html:https://europepmc.org/articles/PMC8383863; pdf:https://europepmc.org/articles/PMC8383863?pdf=render
-38326875,https://doi.org/10.1186/s13059-024-03172-3,"IDHwt glioblastomas can be stratified by their transcriptional response to standard treatment, with implications for targeted therapy.","Tanner G, Barrow R, Ajaib S, Al-Jabri M, Ahmed N, Pollock S, Finetti M, Rippaus N, Bruns AF, Syed K, Poulter JA, Matthews L, Hughes T, Wilson E, Johnson C, Varn FS, Brüning-Richardson A, Hogg C, Droop A, Gusnanto A, Care MA, Cutillo L, Westhead DR, Short SC, Jenkinson MD, Brodbelt A, Chakrabarty A, Ismail A, Verhaak RGW, Stead LF.",,Genome biology,2024,2024-02-07,Y,,,,"<h4>Background</h4>Glioblastoma (GBM) brain tumors lacking IDH1 mutations (IDHwt) have the worst prognosis of all brain neoplasms. Patients receive surgery and chemoradiotherapy but tumors almost always fatally recur.<h4>Results</h4>Using RNA sequencing data from 107 pairs of pre- and post-standard treatment locally recurrent IDHwt GBM tumors, we identify two responder subtypes based on longitudinal changes in gene expression. In two thirds of patients, a specific subset of genes is upregulated from primary to recurrence (Up responders), and in one third, the same genes are downregulated (Down responders), specifically in neoplastic cells. Characterization of the responder subtypes indicates subtype-specific adaptive treatment resistance mechanisms that are associated with distinct changes in the tumor microenvironment. In Up responders, recurrent tumors are enriched in quiescent proneural GBM stem cells and differentiated neoplastic cells, with increased interaction with the surrounding normal brain and neurotransmitter signaling, whereas Down responders commonly undergo mesenchymal transition. ChIP-sequencing data from longitudinal GBM tumors suggests that the observed transcriptional reprogramming could be driven by Polycomb-based chromatin remodeling rather than DNA methylation.<h4>Conclusions</h4>We show that the responder subtype is cancer-cell intrinsic, recapitulated in in vitro GBM cell models, and influenced by the presence of the tumor microenvironment. Stratifying GBM tumors by responder subtype may lead to more effective treatment.",,pdf:https://genomebiology.biomedcentral.com/counter/pdf/10.1186/s13059-024-03172-3; doi:https://doi.org/10.1186/s13059-024-03172-3; html:https://europepmc.org/articles/PMC10848526; pdf:https://europepmc.org/articles/PMC10848526?pdf=render
 34018481,https://doi.org/10.2807/1560-7917.es.2021.26.20.2100428,The potential for vaccination-induced herd immunity against the SARS-CoV-2 B.1.1.7 variant.,"Hodgson D, Flasche S, Jit M, Kucharski AJ, CMMID COVID-19 Working Group, Centre for Mathematical Modelling of Infectious Disease (CMMID) COVID-19 Working Group.",,Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin,2021,2021-05-01,Y,Vaccination; Herd immunity; Seroprevalence; Sars-cov-2,,,"We assess the feasibility of reaching the herd immunity threshold against SARS-CoV-2 through vaccination, considering vaccine effectiveness (VE), transmissibility of the virus and the level of pre-existing immunity in populations, as well as their age structure. If highly transmissible variants of concern become dominant in areas with low levels of naturally-acquired immunity and/or in populations with large proportions of < 15 year-olds, control of infection without non-pharmaceutical interventions may only be possible with a VE ≥ 80%, and coverage extended to children.",,pdf:https://www.eurosurveillance.org/deliver/fulltext/eurosurveillance/26/20/eurosurv-26-20-1.pdf?itemId=%2Fcontent%2F10.2807%2F1560-7917.ES.2021.26.20.2100428&mimeType=pdf&containerItemId=content/eurosurveillance; doi:https://doi.org/10.2807/1560-7917.ES.2021.26.20.2100428; html:https://europepmc.org/articles/PMC8138959; pdf:https://europepmc.org/articles/PMC8138959?pdf=render
-34429368,https://doi.org/10.1136/heartjnl-2021-319566,Sex disparity in subsequent outcomes in survivors of coronary heart disease.,"Akyea RK, Kontopantelis E, Kai J, Weng SF, Patel RS, Asselbergs FW, Qureshi N.",,Heart (British Cardiac Society),2022,2021-08-24,N,Sex difference; Coronary Heart Disease; Secondary Prevention; Competing Risks; Major Adverse Cardiovascular Events,,,"<h4>Objective</h4>Evidence on sex differences in outcomes after developing coronary heart disease (CHD) has focused on recurrent CHD, all-cause mortality or revascularisation. We assessed sex disparities in subsequent major adverse cardiovascular events (MACE) in adults surviving their first-time CHD.<h4>Methods</h4>Using a population-based cohort obtained from the Clinical Practice Research Datalink (CPRD GOLD) linked to hospitalisation and death records in the UK, we identified 143 702 adults (aged ≥18 years) between 1 January 1998 and 31 December 2017 with no prior history of MACE. MACE outcome was a composite of recurrent CHD, stroke, peripheral vascular disease, heart failure and cardiovascular-related mortality. Multivariable models (Cox and competing risks regressions) were used to assess differences between sexes.<h4>Results</h4>There were 143 702 adults with any incident CHD (either angina, myocardial infarction or coronary revascularisation). Women (n=63 078, 43.9%) were older than men (median age, 73 vs 66 years). First subsequent MACE outcome was observed in 91 706 (63.8%). Women had a significantly lower risk of MACE (hazard ratio (HR), 0.68 (95% CI 0.67 to 0.69); sub-hazard ratio (HRsd), 0.71 (0.70 to 0.72), respectively) and recurrent CHD (n=66 543, 46.3%) (HR, 0.60 (0.59 to 0.61); HRsd, 0.62 (0.61 to 0.63)) when compared with men after incident CHD. However, women had a significantly higher risk of stroke (n=5740, 4.0%) (HR, 1.26 (1.19 to 1.33); HRsd, 1.32 (1.25 to 1.39)), heart failure (n=7905, 5.5%) (HR, 1.09 (1.04 to 1.15); HRsd, 1.13 (1.07 to 1.18)) and all-cause mortality (n=29 503, 20.5%) (HR, 1.05 (1.02 to 1.07); HRsd, 1.11 (1.08 to 1.13)).<h4>Conclusions</h4>After incident CHD, women have lower risk of composite MACE and recurrent CHD outcomes but higher risk of stroke, heart failure, and all-cause mortality compared with men.",,pdf:https://heart.bmj.com/content/heartjnl/108/1/37.full.pdf; doi:https://doi.org/10.1136/heartjnl-2021-319566
 35351727,https://doi.org/10.1136/bmjopen-2021-057909,Impact of chronic kidney disease on case ascertainment for hospitalised acute myocardial infarction: an English cohort study.,"Bidulka P, Scott J, Taylor DM, Udayaraj U, Caskey F, Teece L, Sweeting M, Deanfield J, de Belder M, Denaxas S, Weston C, Adlam D, Nitsch D.",,BMJ open,2022,2022-03-28,Y,Myocardial infarction; Cardiology; Nephrology; Audit; Statistics & Research Methods,,,"<h4>Objectives</h4>Acute myocardial infarction (AMI) case ascertainment improves for the UK general population using linked health data sets. Because care pathways for people with chronic kidney disease (CKD) change based on disease severity, AMI case ascertainment for these people may differ compared with the general population. We aimed to determine the association between CKD severity and AMI case ascertainment in two secondary care data sets, and the agreement in estimated glomerular filtration rate (eGFR) between the same data sets.<h4>Methods</h4>We used a cohort study design. Primary care records for people with CKD or risk factors for CKD, identified using the National CKD Audit (2015-2017), were linked to the Myocardial Ischaemia National Audit Project (MINAP, 2007-2017) and Hospital Episode Statistics (HES, 2007-2017) secondary care registries. People with an AMI recorded in either MINAP, HES or both were included in the study cohort. CKD status was defined using eGFR, derived from the most recent serum creatinine value recorded in primary care. Moderate-severe CKD was defined as eGFR <60 mL/min/1.73 m<sup>2</sup>, and mild CKD or at risk of CKD was defined as eGFR ≥60 mL/min/1.73 m<sup>2</sup> or eGFR missing. CKD stages were grouped as (1) At risk of CKD and Stages 1-2 (eGFR missing or ≥60 mL/min/1.73 m<sup>2</sup>), (2) Stage 3a (eGFR 45-59 mL/min/1.73 m<sup>2</sup>), (3) Stage 3b (eGFR 30-44 mL/min/1.73 m<sup>2</sup>) and (4) Stages 4-5 (eGFR <30 mL/min/1.73 m<sup>2</sup>).<h4>Results</h4>We identified 6748 AMIs: 23% were recorded in both MINAP and HES, 66% in HES only and 11% in MINAP only. Compared with people at risk of CKD or with mild CKD, AMIs in people with moderate-severe CKD were more likely to be recorded in both MINAP and HES (42% vs 11%, respectively), or MINAP only (22% vs 5%), and less likely to be recorded in HES only (36% vs 84%). People with AMIs recorded in HES only or MINAP only had increased odds of death during hospitalisation compared with those recorded in both (adjusted OR 1.61, 95% CI 1.32 to 1.96 and OR 1.60, 95% CI 1.26 to 2.04, respectively). Agreement between eGFR at AMI admission (MINAP) and in primary care was poor (kappa (K) 0.42, SE 0.012).<h4>Conclusions</h4>AMI case ascertainment is incomplete in both MINAP and HES, and is associated with CKD severity.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/3/e057909.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-057909; html:https://europepmc.org/articles/PMC8961119; pdf:https://europepmc.org/articles/PMC8961119?pdf=render
-37519214,https://doi.org/10.1177/09622802231188518,Multiple imputation approaches for epoch-level accelerometer data in trials.,"Tackney MS, Williamson E, Cook DG, Limb E, Harris T, Carpenter J.",,Statistical methods in medical research,2023,2023-07-31,Y,Missing Data; Accelerometer; Multiple Imputation; Wearables; Physical Activity Trial,,,"Clinical trials that investigate physical activity interventions often use accelerometers to measure step count at a very granular level, for example in 5-second epochs. Participants typically wear the accelerometer for a week-long period at baseline, and for one or more week-long follow-up periods after the intervention. The data is aggregated to provide daily or weekly step counts for the primary analysis. Missing data are common as participants may not wear the device as per protocol. Approaches to handling missing data in the literature have defined missingness on the day level using a threshold on daily weartime, which leads to loss of information on the time of day when data are missing. We propose an approach to identifying and classifying missingness at the finer epoch-level and present two approaches to handling missingness using multiple imputation. Firstly, we present a parametric approach which accounts for the number of missing epochs per day. Secondly, we describe a non-parametric approach where missing periods during the day are replaced by donor data from the same person where possible, or data from a different person who is matched on demographic and physical activity-related variables. Our simulation studies show that the non-parametric approach leads to estimates of the effect of treatment that are least biased while maintaining small standard errors. We illustrate the application of these different multiple imputation strategies to the analysis of the 2017 PACE-UP trial. The proposed framework is likely to be applicable to other digital health outcomes and to other wearable devices.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/09622802231188518; doi:https://doi.org/10.1177/09622802231188518; html:https://europepmc.org/articles/PMC10563375; pdf:https://europepmc.org/articles/PMC10563375?pdf=render
+34429368,https://doi.org/10.1136/heartjnl-2021-319566,Sex disparity in subsequent outcomes in survivors of coronary heart disease.,"Akyea RK, Kontopantelis E, Kai J, Weng SF, Patel RS, Asselbergs FW, Qureshi N.",,Heart (British Cardiac Society),2022,2021-08-24,N,Sex difference; Coronary Heart Disease; Secondary Prevention; Competing Risks; Major Adverse Cardiovascular Events,,,"<h4>Objective</h4>Evidence on sex differences in outcomes after developing coronary heart disease (CHD) has focused on recurrent CHD, all-cause mortality or revascularisation. We assessed sex disparities in subsequent major adverse cardiovascular events (MACE) in adults surviving their first-time CHD.<h4>Methods</h4>Using a population-based cohort obtained from the Clinical Practice Research Datalink (CPRD GOLD) linked to hospitalisation and death records in the UK, we identified 143 702 adults (aged ≥18 years) between 1 January 1998 and 31 December 2017 with no prior history of MACE. MACE outcome was a composite of recurrent CHD, stroke, peripheral vascular disease, heart failure and cardiovascular-related mortality. Multivariable models (Cox and competing risks regressions) were used to assess differences between sexes.<h4>Results</h4>There were 143 702 adults with any incident CHD (either angina, myocardial infarction or coronary revascularisation). Women (n=63 078, 43.9%) were older than men (median age, 73 vs 66 years). First subsequent MACE outcome was observed in 91 706 (63.8%). Women had a significantly lower risk of MACE (hazard ratio (HR), 0.68 (95% CI 0.67 to 0.69); sub-hazard ratio (HRsd), 0.71 (0.70 to 0.72), respectively) and recurrent CHD (n=66 543, 46.3%) (HR, 0.60 (0.59 to 0.61); HRsd, 0.62 (0.61 to 0.63)) when compared with men after incident CHD. However, women had a significantly higher risk of stroke (n=5740, 4.0%) (HR, 1.26 (1.19 to 1.33); HRsd, 1.32 (1.25 to 1.39)), heart failure (n=7905, 5.5%) (HR, 1.09 (1.04 to 1.15); HRsd, 1.13 (1.07 to 1.18)) and all-cause mortality (n=29 503, 20.5%) (HR, 1.05 (1.02 to 1.07); HRsd, 1.11 (1.08 to 1.13)).<h4>Conclusions</h4>After incident CHD, women have lower risk of composite MACE and recurrent CHD outcomes but higher risk of stroke, heart failure, and all-cause mortality compared with men.",,pdf:https://heart.bmj.com/content/heartjnl/108/1/37.full.pdf; doi:https://doi.org/10.1136/heartjnl-2021-319566
+38326875,https://doi.org/10.1186/s13059-024-03172-3,"IDHwt glioblastomas can be stratified by their transcriptional response to standard treatment, with implications for targeted therapy.","Tanner G, Barrow R, Ajaib S, Al-Jabri M, Ahmed N, Pollock S, Finetti M, Rippaus N, Bruns AF, Syed K, Poulter JA, Matthews L, Hughes T, Wilson E, Johnson C, Varn FS, Brüning-Richardson A, Hogg C, Droop A, Gusnanto A, Care MA, Cutillo L, Westhead DR, Short SC, Jenkinson MD, Brodbelt A, Chakrabarty A, Ismail A, Verhaak RGW, Stead LF.",,Genome biology,2024,2024-02-07,Y,,,,"<h4>Background</h4>Glioblastoma (GBM) brain tumors lacking IDH1 mutations (IDHwt) have the worst prognosis of all brain neoplasms. Patients receive surgery and chemoradiotherapy but tumors almost always fatally recur.<h4>Results</h4>Using RNA sequencing data from 107 pairs of pre- and post-standard treatment locally recurrent IDHwt GBM tumors, we identify two responder subtypes based on longitudinal changes in gene expression. In two thirds of patients, a specific subset of genes is upregulated from primary to recurrence (Up responders), and in one third, the same genes are downregulated (Down responders), specifically in neoplastic cells. Characterization of the responder subtypes indicates subtype-specific adaptive treatment resistance mechanisms that are associated with distinct changes in the tumor microenvironment. In Up responders, recurrent tumors are enriched in quiescent proneural GBM stem cells and differentiated neoplastic cells, with increased interaction with the surrounding normal brain and neurotransmitter signaling, whereas Down responders commonly undergo mesenchymal transition. ChIP-sequencing data from longitudinal GBM tumors suggests that the observed transcriptional reprogramming could be driven by Polycomb-based chromatin remodeling rather than DNA methylation.<h4>Conclusions</h4>We show that the responder subtype is cancer-cell intrinsic, recapitulated in in vitro GBM cell models, and influenced by the presence of the tumor microenvironment. Stratifying GBM tumors by responder subtype may lead to more effective treatment.",,pdf:https://genomebiology.biomedcentral.com/counter/pdf/10.1186/s13059-024-03172-3; doi:https://doi.org/10.1186/s13059-024-03172-3; html:https://europepmc.org/articles/PMC10848526; pdf:https://europepmc.org/articles/PMC10848526?pdf=render
 35504525,https://doi.org/10.1016/j.jclinepi.2022.04.025,How traditional informed consent impairs inclusivity in a learning healthcare system: lessons learned from the Utrecht Cardiovascular Cohort.,"Groenhof TKJ, Mostert M, Lea NC, Haitjema S, de Vries MC, van Dijk WB, Grobbee DE, Asselbergs FW, Bots ML, van der Graaf R.",,Journal of clinical epidemiology,2022,2022-04-30,N,,,,,,pdf:https://discovery.ucl.ac.uk/10160730/1/JCEPI-D-21-01101_R2-2%2022-40.pdf; doi:https://doi.org/10.1016/j.jclinepi.2022.04.025
 38214281,https://doi.org/10.1161/jaha.123.031646,Acute Coronary Syndrome Subphenotypes Based on Repeated Biomarker Measurements in Relation to Long-Term Mortality Risk.,"de Bakker M, Scholte NTB, Oemrawsingh RM, Umans VA, Kietselaer B, Schotborgh C, Ronner E, Lenderink T, Aksoy I, van der Harst P, Asselbergs FW, Maas A, Oude Ophuis AJ, Krenning B, de Winter RJ, The SHK, Wardeh AJ, Hermans W, Cramer GE, van Schaik RH, de Rijke YB, Akkerhuis KM, Kardys I, Boersma E, BIOMArCS Investigators †.",,Journal of the American Heart Association,2024,2024-01-12,Y,Death; Phenotypes; acute coronary syndrome; Repeated Measurements; Cardiovascular Biomarkers,,,"<h4>Background</h4>We aimed to identify patients with subphenotypes of postacute coronary syndrome (ACS) using repeated measurements of high-sensitivity cardiac troponin T, N-terminal pro-B-type natriuretic peptide, high-sensitivity C-reactive protein, and growth differentiation factor 15 in the year after the index admission, and to investigate their association with long-term mortality risk.<h4>Methods and results</h4>BIOMArCS (BIOMarker Study to Identify the Acute Risk of a Coronary Syndrome) was an observational study of patients with ACS, who underwent high-frequency blood sampling for 1 year. Biomarkers were measured in a median of 16 repeated samples per individual. Cluster analysis was performed to identify biomarker-based subphenotypes in 723 patients without a repeat ACS in the first year. Patients with a repeat ACS (N=36) were considered a separate cluster. Differences in all-cause death were evaluated using accelerated failure time models (median follow-up, 9.1 years; 141 deaths). Three biomarker-based clusters were identified: cluster 1 showed low and stable biomarker concentrations, cluster 2 had elevated concentrations that subsequently decreased, and cluster 3 showed persistently elevated concentrations. The temporal biomarker patterns of patients in cluster 3 were similar to those with a repeat ACS during the first year. Clusters 1 and 2 had a similar and favorable long-term mortality risk. Cluster 3 had the highest mortality risk. The adjusted survival time ratio was 0.64 (95% CI, 0.44-0.93; <i>P</i>=0.018) compared with cluster 1, and 0.71 (95% CI, 0.39-1.32; <i>P</i>=0.281) compared with patients with a repeat ACS.<h4>Conclusions</h4>Patients with subphenotypes of post-ACS with different all-cause mortality risks during long-term follow-up can be identified on the basis of repeatedly measured cardiovascular biomarkers. Patients with persistently elevated biomarkers have the worst outcomes, regardless of whether they experienced a repeat ACS in the first year.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.123.031646; doi:https://doi.org/10.1161/JAHA.123.031646; html:https://europepmc.org/articles/PMC10926784; pdf:https://europepmc.org/articles/PMC10926784?pdf=render
+37519214,https://doi.org/10.1177/09622802231188518,Multiple imputation approaches for epoch-level accelerometer data in trials.,"Tackney MS, Williamson E, Cook DG, Limb E, Harris T, Carpenter J.",,Statistical methods in medical research,2023,2023-07-31,Y,Missing Data; Accelerometer; Multiple Imputation; Wearables; Physical Activity Trial,,,"Clinical trials that investigate physical activity interventions often use accelerometers to measure step count at a very granular level, for example in 5-second epochs. Participants typically wear the accelerometer for a week-long period at baseline, and for one or more week-long follow-up periods after the intervention. The data is aggregated to provide daily or weekly step counts for the primary analysis. Missing data are common as participants may not wear the device as per protocol. Approaches to handling missing data in the literature have defined missingness on the day level using a threshold on daily weartime, which leads to loss of information on the time of day when data are missing. We propose an approach to identifying and classifying missingness at the finer epoch-level and present two approaches to handling missingness using multiple imputation. Firstly, we present a parametric approach which accounts for the number of missing epochs per day. Secondly, we describe a non-parametric approach where missing periods during the day are replaced by donor data from the same person where possible, or data from a different person who is matched on demographic and physical activity-related variables. Our simulation studies show that the non-parametric approach leads to estimates of the effect of treatment that are least biased while maintaining small standard errors. We illustrate the application of these different multiple imputation strategies to the analysis of the 2017 PACE-UP trial. The proposed framework is likely to be applicable to other digital health outcomes and to other wearable devices.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/09622802231188518; doi:https://doi.org/10.1177/09622802231188518; html:https://europepmc.org/articles/PMC10563375; pdf:https://europepmc.org/articles/PMC10563375?pdf=render
 35177264,https://doi.org/10.1016/j.injury.2022.02.027,Chronic physical health conditions up to five years after serious orthopaedic injury.,"Gelaw AY, Gabbe BJ, Ekegren CL.",,Injury,2022,2022-02-09,N,Chronic Conditions; Cvd; Major Trauma; Orthopaedic Trauma; Physical Health Conditions; Orthopaedic Injury,,,"<h4>Background</h4>Information about the prevalence of chronic physical health conditions following serious orthopaedic injury is currently lacking in the general population and is essential for quantifying the burden of injury and improving outcomes.<h4>Objectives</h4>To determine the prevalence of chronic physical health conditions recorded within hospitalisations and emergency department presentations and associated factors five years following serious orthopaedic injury.<h4>Methods</h4>We conducted a registry-based cohort study using data from the Victorian State Trauma Registry (2007-2016) linked with hospital admissions and ED presentations for 16,249 adults with serious orthopaedic injuries. We considered that people who were admitted to hospital or presented to an emergency department with a chronic physical health condition one to five years post-injury had ""new-onset"" conditions. We applied Kaplan-Meier failure curves and Cox proportional hazard regression models to determine factors associated with new-onset conditions.<h4>Results</h4>There were 1420 people (11.0%) with at least one new-onset condition. Cancer (6.1%), cardiovascular disease (5.1%) and hypertension (6.2%) were the three most common ""new-onset"" chronic physical health conditions. Older adults, women, smokers, and people with mental health and alcohol and drug-related conditions had a higher risk of hospitalisation or emergency department presentation with new-onset conditions post-injury.<h4>Conclusion</h4>People with serious orthopaedic injuries experienced a significant additional burden of chronic physical health conditions up to five years after serious orthopaedic injury, posing a new challenge to post-trauma care. Early preventive interventions may be required in people with serious orthopaedic injuries to minimise modifiable risk factors such as smoking, excessive consumption of alcohol or drug use.",,doi:https://doi.org/10.1016/j.injury.2022.02.027
 32345651,https://doi.org/10.2337/dc19-2116,"Obstructive Sleep Apnea, a Risk Factor for Cardiovascular and Microvascular Disease in Patients With Type 2 Diabetes: Findings From a Population-Based Cohort Study.","Adderley NJ, Subramanian A, Toulis K, Gokhale K, Taverner T, Hanif W, Haroon S, Thomas GN, Sainsbury C, Tahrani AA, Nirantharakumar K.",,Diabetes care,2020,2020-04-28,N,,,,"<h4>Objective</h4>To determine the risk of cardiovascular disease (CVD), microvascular complications, and mortality in patients with type 2 diabetes who subsequently develop obstructive sleep apnea (OSA) compared with patients with type 2 diabetes without a diagnosis of OSA.<h4>Research design and methods</h4>This age-, sex-, BMI-, and diabetes duration-matched cohort study used data from a U.K. primary care database from 1 January 2005 to 17 January 2018. Participants aged ≥16 years with type 2 diabetes were included. Exposed participants were those who developed OSA after their diabetes diagnosis; unexposed participants were those without diagnosed OSA. Outcomes were composite CVD (ischemic heart disease [IHD], stroke/transient ischemic attack [TIA], heart failure [HF]), peripheral vascular disease (PVD), atrial fibrillation (AF), peripheral neuropathy (PN), diabetes-related foot disease (DFD), referable retinopathy, chronic kidney disease (CKD), and all-cause mortality. The same outcomes were explored in patients with preexisting OSA before a diagnosis of type 2 diabetes versus diabetes without diagnosed OSA.<h4>Results</h4>A total of 3,667 exposed participants and 10,450 matched control participants were included. Adjusted hazard ratios for the outcomes were as follows: composite CVD 1.54 (95% CI 1.32, 1.79), IHD 1.55 (1.26, 1.90), HF 1.67 (1.35, 2.06), stroke/TIA 1.57 (1.27, 1.94), PVD 1.10 (0.91, 1.32), AF 1.53 (1.28, 1.83), PN 1.32 (1.14, 1.51), DFD 1.42 (1.16, 1.74), referable retinopathy 0.99 (0.82, 1.21), CKD (stage 3-5) 1.18 (1.02, 1.36), albuminuria 1.11 (1.01, 1.22), and all-cause mortality 1.24 (1.10, 1.40). In the prevalent OSA cohort, the results were similar, but some associations were not observed.<h4>Conclusions</h4>Patients with type 2 diabetes who develop OSA are at increased risk of CVD, AF, PN, DFD, CKD, and all-cause mortality compared with patients without diagnosed OSA. Patients with type 2 diabetes who develop OSA are a high-risk population, and strategies to detect OSA and prevent cardiovascular and microvascular complications should be implemented.",,pdf:https://care.diabetesjournals.org/content/diacare/43/8/1868.full.pdf; doi:https://doi.org/10.2337/dc19-2116
 30863860,https://doi.org/10.1093/eurheartj/ehz089,Big data analytics in adult congenital heart disease: why coding matters.,"Asselbergs FW, Meijboom FJ.",,European heart journal,2019,2019-04-01,N,,,,,,pdf:https://discovery.ucl.ac.uk/10076628/1/Asselbergs_AAM_Big%20data%20analytics%20in%20adult%20congenital%20heart%20disease.pdf; doi:https://doi.org/10.1093/eurheartj/ehz089
 33053479,https://doi.org/10.1016/j.chiabu.2020.104760,Characterizing newborn and older infant entries into care in England between 2006 and 2014.,"Pearson RJ, Jay MA, O'Donnell M, Wijlaars L, Gilbert R.",,Child abuse & neglect,2020,2020-10-11,Y,Longitudinal data; Infancy; Latent Class Analysis; Entry Into Care; Out-of-court Arrangements,,,"<h4>Background</h4>The risk of entry to state care during infancy is increasing, both here in England and abroad, with most entering within a week of birth ('newborns'). However, little is known about these infants or of their pathways through care over early childhood.<h4>Objective</h4>To characterize infant entries to care in England.<h4>Participants and setting</h4>All children in England who first entered care during infancy, between April 2006 and March 2014 (n = 42,000).<h4>Methods</h4>We compared sociodemographic and care characteristics for infants entering care over the study period by age at first entry (newborn: <1wks, older infant 1-51wks). Among those who entered before April 2010, we further characterized care over follow-up (i.e. 4 years from first entry) and employed latent class analysis to uncover any common pathways through care.<h4>Results</h4>Almost 40 % of infants first entered care as a newborn. Most infants first entered care under s 20 arrangements (i.e. out-of-court, 60 % of newborns vs 47 % of older infants). Among infants entering before April 2010, most were adopted over follow-up (60 % vs 37 %), though many were restored to parental care (20 % vs 32 %) or exited care to live with extended family (13 % vs 19 %). One in six infants (17.7 %) had particularly unstable care trajectories over early childhood, typified by three or more placements or failed reunification.<h4>Conclusions</h4>Evidence-based strengthening of pre-birth social work support is needed to improve preventive interventions before birth, to more effectively target infant placement into care. Linkages between child protection records and information on parents are needed to inform preventive strategies.",,doi:https://doi.org/10.1016/j.chiabu.2020.104760; doi:https://doi.org/10.1016/j.chiabu.2020.104760; html:https://europepmc.org/articles/PMC7718112
 37348153,https://doi.org/10.1016/j.amjcard.2023.05.039,Clinical and Prognostic Implications of Cardiopulmonary Exercise Stress Echocardiography in Asymptomatic Degenerative Mitral Regurgitation.,"Althunayyan A, Alborikan S, Badiani S, Wong K, Uppal R, Patel N, Petersen SE, Lloyd G, Bhattacharyya S.",,The American journal of cardiology,2023,2023-06-20,N,,,,"The current guidelines recommend intervention in severe degenerative mitral regurgitation (MR) in symptomatic patients or asymptomatic patients with left ventricular dilatation or dysfunction. The insidious onset of symptoms may mean that patients do not report their symptoms. The role of systematic exercise testing for symptoms in MR is not clearly defined. A total of 97 patients with moderate to severe asymptomatic MR underwent exercise echocardiography combined with cardiopulmonary exercise testing. The predictors of exercise-induced dyspnea, symptom-free survival, and mitral valve intervention were identified. A total of 18 patients (19%) developed limiting dyspnea on exercise. Spontaneous symptom-free survival at 24 months was significantly higher in those without exercise-induced symptoms than those with exercise-induced symptoms, p <0.0001. The only independent predictors of spontaneous symptoms at 2 years were effective regurgitant orifice area (odds ratio 27.45, 95% confidence interval [CI] 1.43 to 528.40, p = 0.03) and exercise-induced symptoms (odds ratio 11.56, 95% CI 1.71 to 78.09, p = 0.01). The only independent predictor of surgery was indexed left ventricular systolic volumes (odds ratio 1.17, 95% CI 1.04 to 1.30, p = 0.006). Where only the patients who underwent surgery due to symptoms were included, the only independent predictor was exercise-induced symptoms (odds ratio 13.94, 95% CI 1.39 to 140.27, p = 0.025). In conclusion, in patients with primary asymptomatic degenerative MR, 1/5 develop revealed symptoms during exercise. This predicts a subsequent development of spontaneous symptoms and mitral valve intervention due to symptoms.",,doi:https://doi.org/10.1016/j.amjcard.2023.05.039
-37813531,https://doi.org/10.1136/bmjopen-2023-073162,Detection and evaluation of signals associated with exposure to individual and combination of medications in pregnancy: a signal detection study protocol.,"Subramanian A, Lee SI, Hemali Sudasinghe SPB, Wambua S, Phillips K, Singh M, Azcoaga-Lorenzo A, Cockburn N, Wang J, Fagbamigbe A, Usman M, Damase-Michel C, Yau C, Kent L, McCowan C, OReilly D, Santorelli G, Hope H, Kennedy J, Mhereeg M, Abel KM, Eastwood KA, Black M, Loane M, Moss N, Brophy S, Brocklehurst P, Dolk H, Nelson-Piercy C, Nirantharakumar K, MuM-PreDiCT Group.",,BMJ open,2023,2023-10-09,Y,Obstetrics; epidemiology; Maternal Medicine,,,"<h4>Introduction</h4>Considering the high prevalence of polypharmacy in pregnant women and the knowledge gap in the risk-benefit safety profile of their often-complex treatment plan, more research is needed to optimise prescribing. In this study, we aim to detect adverse and protective effect signals of exposure to individual and pairwise combinations of medications during pregnancy.<h4>Methods and analysis</h4>Using a range of real-world data sources from the UK, we aim to conduct a pharmacovigilance study to assess the safety of medications prescribed during the preconception period (3 months prior to conception) and first trimester of pregnancy. Women aged between 15 and 49 years with a record of pregnancy within the Clinical Practice Research Datalink (CPRD) Pregnancy Register, the Welsh Secure Anonymised Information Linkage (SAIL), the Scottish Morbidity Record (SMR) data sets and the Northern Ireland Maternity System (NIMATS) will be included. A series of case control studies will be conducted to estimate measures of disproportionality, detecting signals of association between a range of pregnancy outcomes and exposure to individual and combinations of medications. A multidisciplinary expert team will be invited to a signal detection workshop. By employing a structured framework, signals will be transparently assessed by each member of the team using a questionnaire appraising the signals on aspects of temporality, selection, time and measurement-related biases and confounding by underlying disease or comedications. Through group discussion, the expert team will reach consensus on each of the medication exposure-outcome signal, thereby excluding spurious signals, leaving signals suggestive of causal associations for further evaluation.<h4>Ethics and dissemination</h4>Ethical approval has been obtained from the Independent Scientific Advisory Committee, SAIL Information Governance Review Panel, University of St. Andrews Teaching and Research Ethics Committee and Office for Research Ethics Committees Northern Ireland (ORECNI) for access and use of CPRD, SAIL, SMR and NIMATS data, respectively.",,pdf:https://bmjopen.bmj.com/content/bmjopen/13/10/e073162.full.pdf; doi:https://doi.org/10.1136/bmjopen-2023-073162; html:https://europepmc.org/articles/PMC10565241; pdf:https://europepmc.org/articles/PMC10565241?pdf=render
 33206055,https://doi.org/10.2196/19650,Mobile Clinical Decision Support System for the Management of Diabetic Patients With Kidney Complications in UK Primary Care Settings: Mixed Methods Feasibility Study.,"Alhodaib HI, Antza C, Chandan JS, Hanif W, Sankaranarayanan S, Paul S, Sutcliffe P, Nirantharakumar K.",,JMIR diabetes,2020,2020-11-18,Y,Diabetes mellitus; Chronic Kidney Disease; Feasibility Study; Ehealth; Clinical Decision Support Application,,,"<h4>Background</h4>Attempts to utilize eHealth in diabetes mellitus (DM) management have shown promising outcomes, mostly targeted at patients; however, few solutions have been designed for health care providers.<h4>Objective</h4>The purpose of this study was to conduct a feasibility project developing and evaluating a mobile clinical decision support system (CDSS) tool exclusively for health care providers to manage chronic kidney disease (CKD) in patients with DM.<h4>Methods</h4>The design process was based on the 3 key stages of the user-centered design framework. First, an exploratory qualitative study collected the experiences and views of DM specialist nurses regarding the use of mobile apps in clinical practice. Second, a CDSS tool was developed for the management of patients with DM and CKD. Finally, a randomized controlled trial examined the acceptability and impact of the tool.<h4>Results</h4>We interviewed 15 DM specialist nurses. DM specialist nurses were not currently using eHealth solutions in their clinical practice, while most nurses were not even aware of existing medical apps. However, they appreciated the potential benefits that apps may bring to their clinical practice. Taking into consideration the needs and preferences of end users, a new mobile CDSS app, ""Diabetes & CKD,"" was developed based on guidelines. We recruited 39 junior foundation year 1 doctors (44% male) to evaluate the app. Of them, 44% (17/39) were allocated to the intervention group, and 56% (22/39) were allocated to the control group. There was no significant difference in scores (maximum score=13) assessing the management decisions between the app and paper-based version of the app's algorithm (intervention group: mean 7.24 points, SD 2.46 points; control group: mean 7.39, SD 2.56; t<sub>37</sub>=-0.19, P=.85). However, 82% (14/17) of the participants were satisfied with using the app.<h4>Conclusions</h4>The findings will guide the design of future CDSS apps for the management of DM, aiming to help health care providers with a personalized approach depending on patients' comorbidities, specifically CKD, in accordance with guidelines.",,pdf:https://diabetes.jmir.org/2020/4/e19650/PDF; doi:https://doi.org/10.2196/19650; html:https://europepmc.org/articles/PMC7710444; pdf:https://europepmc.org/articles/PMC7710444?pdf=render
-31984563,https://doi.org/10.1111/jce.14368,Early recurrences of atrial tachyarrhythmias post pulmonary vein isolation.,"von Olshausen G, Uijl A, Jensen-Urstad M, Schwieler J, Drca N, Bastani H, Tapanainen J, Saluveer O, Bourke T, Kennebäck G, Insulander P, Deisenhofer I, Braunschweig F.",,Journal of cardiovascular electrophysiology,2020,2020-01-31,N,Atrial fibrillation; Catheter ablation; Late Recurrence; Early Recurrence; Blanking Period,,,"<h4>Aims</h4>To investigate the significance of early recurrence (ER) of atrial tachyarrhythmias after pulmonary vein isolation (PVI) on the development of late recurrence (LR) and to redefine the blanking period during which an ER is considered nonspecific.<h4>Methods</h4>Data of 713 patients undergoing their first PVI for paroxysmal or persistent atrial fibrillation between January 2012 and December 2017 were included. All patients were followed-up for 12 months according to clinical and outpatient routine and were screened for any atrial tachyarrhythmia lasting >30 seconds occurring during the first 3 months postablation (ER) and after the 3 months blanking period (LR).<h4>Results</h4>Patients with ER compared to those without ER had significantly more LR (74.5% vs 16.5% vs, P < .001). The occurrence of ER during the first, second and third months showed increasing LR rates of 35.2%, 67.9%, and 94.8%, respectively (P < .001). Receiver operator characteristic analysis revealed a blanking period of 46 days with the highest sensitivity (68.1%) and specificity (96.5%). Later timing and longer time span of ER were independent predictors for LR in multivariable analysis.<h4>Conclusion</h4>ER is a strong predictor for LR. Our study advocates a shortening of the post-PVI blanking period followed by a ""gray zone"" up to 3 months where individualized therapeutic decisions based on additional risk factors should be considered. We suggest that the ER time span might serve as such a predictor identifying patients at the highest risk for LR.",,doi:https://doi.org/10.1111/jce.14368
 34019073,https://doi.org/10.1093/ibd/izab059,Ultra-high Magnification Endocytoscopy and Molecular Markers for Defining Endoscopic and Histologic Remission in Ulcerative Colitis-An Exploratory Study to Define Deep Remission.,"Iacucci M, Jeffery L, Acharjee A, Nardone OM, Zardo D, Smith SCL, Bazarova A, Cannatelli R, Shivaji UN, Williams J, Gkoutos G, Ghosh S.",,Inflammatory bowel diseases,2021,2021-10-01,Y,Rna-sequencing; Mucosal Healing; Histological Healing; Noninvasive Markers; Endocytoscope,,,"<h4>Background</h4>Endoscopic and histological remission are both important treatment goals in patients with ulcerative colitis (UC). We aimed to define cellular architecture, expression of molecular markers, and their correlation with endoscopic scores assessed by ultra-high magnification endocytoscopy (ECS) and histological scores.<h4>Methods</h4>Patients with UC (n = 29) were prospectively recruited. The correlation among ECS score (ECSS), Mayo endoscopic score (MES), and histological scores were determined. Area under curve were plotted to determine the best thresholds for ECSS that predicted histological remission by Robarts (RHI) and Nancy Histological Index (NHI).Soluble analytes relevant to inflammation were measured in serum and mucosal culture supernatants using ProcartaPlex Luminex assays and studied by partial least square discriminant analysis and logistic model. Mucosal RNA sequencing and bioinformatics analysis were performed to define differentially expressed genes/pathways.<h4>Results</h4>Endocytoscope scoring system correlated strongly with RHI (r = 0.89; 95% CI, 0.51-0.98) and NHI (r = 0.86; 95% CI, 0.42-0.98) but correlated poorly with MES (r = 0.28; 95% CI, 0.27-0.70). We identified soluble brain-derived neurotrophic factors (BDNF), macrophage inflammatory proteins (MIP-1 α) and soluble vascular cell adhesion molecule 1 (sVCAM-1) predicted histological remission. Mucosal biopsy cultures also identified sVCAM-1 associated with healed mucosa. RNA-seq analysis identified gene expressions shared between ECSS, RHI, or NHI defined healing. A number of gene expressions and pathways were identified including inflammation and metabolic and tumor suppressors that discriminated healed from nonhealed mucosa.<h4>Conclusions</h4>Endocytoscopy represents an interesting tool that may sit between endoscopy and histology-but closer to the latter-identifying gene expression markers and pathways that are also identified by histology.",,pdf:https://academic.oup.com/ibdjournal/article-pdf/27/11/1719/40784408/izab059.pdf; doi:https://doi.org/10.1093/ibd/izab059; html:https://europepmc.org/articles/PMC8528147; pdf:https://europepmc.org/articles/PMC8528147?pdf=render
+31984563,https://doi.org/10.1111/jce.14368,Early recurrences of atrial tachyarrhythmias post pulmonary vein isolation.,"von Olshausen G, Uijl A, Jensen-Urstad M, Schwieler J, Drca N, Bastani H, Tapanainen J, Saluveer O, Bourke T, Kennebäck G, Insulander P, Deisenhofer I, Braunschweig F.",,Journal of cardiovascular electrophysiology,2020,2020-01-31,N,Atrial fibrillation; Catheter ablation; Late Recurrence; Early Recurrence; Blanking Period,,,"<h4>Aims</h4>To investigate the significance of early recurrence (ER) of atrial tachyarrhythmias after pulmonary vein isolation (PVI) on the development of late recurrence (LR) and to redefine the blanking period during which an ER is considered nonspecific.<h4>Methods</h4>Data of 713 patients undergoing their first PVI for paroxysmal or persistent atrial fibrillation between January 2012 and December 2017 were included. All patients were followed-up for 12 months according to clinical and outpatient routine and were screened for any atrial tachyarrhythmia lasting >30 seconds occurring during the first 3 months postablation (ER) and after the 3 months blanking period (LR).<h4>Results</h4>Patients with ER compared to those without ER had significantly more LR (74.5% vs 16.5% vs, P < .001). The occurrence of ER during the first, second and third months showed increasing LR rates of 35.2%, 67.9%, and 94.8%, respectively (P < .001). Receiver operator characteristic analysis revealed a blanking period of 46 days with the highest sensitivity (68.1%) and specificity (96.5%). Later timing and longer time span of ER were independent predictors for LR in multivariable analysis.<h4>Conclusion</h4>ER is a strong predictor for LR. Our study advocates a shortening of the post-PVI blanking period followed by a ""gray zone"" up to 3 months where individualized therapeutic decisions based on additional risk factors should be considered. We suggest that the ER time span might serve as such a predictor identifying patients at the highest risk for LR.",,doi:https://doi.org/10.1111/jce.14368
 32017129,https://doi.org/10.5694/mja2.50485,Discharge destination and patient-reported outcomes after inpatient treatment for isolated lower limb fractures.,"Kimmel LA, Simpson PM, Holland AE, Edwards ER, Cameron PA, de Steiger RS, Page RS, Hau R, Bucknill A, Kasza J, Gabbe BJ.",,The Medical journal of Australia,2020,2020-02-04,N,"Rehabilitation; Treatment outcome; Orthopedic Procedures; Fractures, Bone; Trauma Surgery",,,"<h4>Objectives</h4>To examine the association between discharge destination (home or inpatient rehabilitation) for adult patients treated in hospital for isolated lower limb fractures and patient-reported outcomes.<h4>Design</h4>Review of prospectively collected Victorian Orthopaedic Trauma Outcomes Registry (VOTOR) data.<h4>Setting, participants</h4>Adults (18-64 years old) treated for isolated lower limb fractures at four Melbourne trauma hospitals that contribute data to the VOTOR, 1 March 2007 - 31 March 2016.<h4>Main outcome measures</h4>Return to work and functional recovery (assessed with the extended Glasgow Outcomes Scale, GOS-E); propensity score analysis of association between discharge destination and outcome.<h4>Results</h4>Of 7961 eligible patients, 1432 (18%) were discharged to inpatient rehabilitation, and 6775 (85%) were followed up 12 months after their injuries. After propensity score adjustment, the odds of better functional recovery were 56% lower for patients discharged to inpatient rehabilitation than for those discharged directly home (odds ratio, 0.44; 95% CI, 0.37-0.51); for the 5057 people working before their accident, the odds of return to work were reduced by 66% (odds ratio, 0.34; 95% CI, 0.26-0.46). Propensity score analysis improved matching of the discharge destination groups, but imbalances in funding source remained for both outcome analyses, and for also for site and cause of injury in the GOS-E analysis (standardised differences, 10-16%).<h4>Conclusions</h4>Discharge to inpatient rehabilitation after treatment for isolated lower limb fractures was associated with poorer outcomes than discharge home. Factors that remained unbalanced after propensity score analysis could be assessed in controlled trials.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.5694/mja2.50485; doi:https://doi.org/10.5694/mja2.50485
+37813531,https://doi.org/10.1136/bmjopen-2023-073162,Detection and evaluation of signals associated with exposure to individual and combination of medications in pregnancy: a signal detection study protocol.,"Subramanian A, Lee SI, Hemali Sudasinghe SPB, Wambua S, Phillips K, Singh M, Azcoaga-Lorenzo A, Cockburn N, Wang J, Fagbamigbe A, Usman M, Damase-Michel C, Yau C, Kent L, McCowan C, OReilly D, Santorelli G, Hope H, Kennedy J, Mhereeg M, Abel KM, Eastwood KA, Black M, Loane M, Moss N, Brophy S, Brocklehurst P, Dolk H, Nelson-Piercy C, Nirantharakumar K, MuM-PreDiCT Group.",,BMJ open,2023,2023-10-09,Y,Obstetrics; epidemiology; Maternal Medicine,,,"<h4>Introduction</h4>Considering the high prevalence of polypharmacy in pregnant women and the knowledge gap in the risk-benefit safety profile of their often-complex treatment plan, more research is needed to optimise prescribing. In this study, we aim to detect adverse and protective effect signals of exposure to individual and pairwise combinations of medications during pregnancy.<h4>Methods and analysis</h4>Using a range of real-world data sources from the UK, we aim to conduct a pharmacovigilance study to assess the safety of medications prescribed during the preconception period (3 months prior to conception) and first trimester of pregnancy. Women aged between 15 and 49 years with a record of pregnancy within the Clinical Practice Research Datalink (CPRD) Pregnancy Register, the Welsh Secure Anonymised Information Linkage (SAIL), the Scottish Morbidity Record (SMR) data sets and the Northern Ireland Maternity System (NIMATS) will be included. A series of case control studies will be conducted to estimate measures of disproportionality, detecting signals of association between a range of pregnancy outcomes and exposure to individual and combinations of medications. A multidisciplinary expert team will be invited to a signal detection workshop. By employing a structured framework, signals will be transparently assessed by each member of the team using a questionnaire appraising the signals on aspects of temporality, selection, time and measurement-related biases and confounding by underlying disease or comedications. Through group discussion, the expert team will reach consensus on each of the medication exposure-outcome signal, thereby excluding spurious signals, leaving signals suggestive of causal associations for further evaluation.<h4>Ethics and dissemination</h4>Ethical approval has been obtained from the Independent Scientific Advisory Committee, SAIL Information Governance Review Panel, University of St. Andrews Teaching and Research Ethics Committee and Office for Research Ethics Committees Northern Ireland (ORECNI) for access and use of CPRD, SAIL, SMR and NIMATS data, respectively.",,pdf:https://bmjopen.bmj.com/content/bmjopen/13/10/e073162.full.pdf; doi:https://doi.org/10.1136/bmjopen-2023-073162; html:https://europepmc.org/articles/PMC10565241; pdf:https://europepmc.org/articles/PMC10565241?pdf=render
+35089054,https://doi.org/10.1161/circep.121.010221,Integrating Exercise Into Personalized Ventricular Arrhythmia Risk Prediction in Arrhythmogenic Right Ventricular Cardiomyopathy.,"Bosman LP, Wang W, Lie ØH, van Lint FHM, Rootwelt-Norberg C, Murray B, Tichnell C, Cadrin-Tourigny J, van Tintelen JP, Asselbergs FW, Calkins H, Te Riele ASJM, Haugaa KH, James CA.",,Circulation. Arrhythmia and electrophysiology,2022,2022-01-28,N,Prognosis; Exercise; Arrhythmogenic right ventricular dysplasia,,,"<h4>Background</h4>Exercise is associated with sustained ventricular arrhythmias (VA) in Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC) but is not included in the ARVC risk calculator (arvcrisk.com). The objective of this study is to quantify the influence of exercise at diagnosis on incident VA risk and evaluate whether the risk calculator needs adjustment for exercise.<h4>Methods</h4>We interviewed ARVC patients without sustained VA at diagnosis about their exercise history. The relationship between exercise dose 3 years preceding diagnosis (average METh/wk) and incident VA during follow-up was analyzed with time-to-event analysis. The incremental prognostic value of exercise to the risk calculator was evaluated by Cox models.<h4>Results</h4>We included 176 patients (male, 43.2%; age, 37.6±16.1 years) from 3 ARVC centers, of whom 53 (30.1%) developed sustained VA during 5.4 (2.7-9.7) years of follow-up. Exercise at diagnosis showed a dose-dependent nonlinear relationship with VA, with no significant risk increase <15 to 30 METh/wk. Athlete status, using 3 definitions from literature (>18, >24, and >36 METh/wk), was significantly associated with VA (hazard ratios, 2.53-2.91) but was also correlated with risk factors currently in the risk calculator model. Thus, adding athlete status to the model did not change the C index of 0.77 (0.71-0.84) and showed no significant improvement (Akaike information criterion change, <2).<h4>Conclusions</h4>Exercise at diagnosis was dose dependently associated with risk of sustained VA in ARVC patients but only above 15 to 30 METh/wk. Exercise does not appear to have incremental prognostic value over the risk calculator. The ARVC risk calculator can be used accurately in athletic patients without modification.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCEP.121.010221; doi:https://doi.org/10.1161/CIRCEP.121.010221
 35297548,https://doi.org/10.1002/humu.24369,"Beacon v2 and Beacon networks: A ""lingua franca"" for federated data discovery in biomedical genomics, and beyond.","Rambla J, Baudis M, Ariosa R, Beck T, Fromont LA, Navarro A, Paloots R, Rueda M, Saunders G, Singh B, Spalding JD, Törnroos J, Vasallo C, Veal CD, Brookes AJ.",,Human mutation,2022,2022-04-08,Y,data sharing; Clinical Genomics; Beacon; Data Discovery; Rest Api; Ga4gh,,,"Beacon is a basic data discovery protocol issued by the Global Alliance for Genomics and Health (GA4GH). The main goal addressed by version 1 of the Beacon protocol was to test the feasibility of broadly sharing human genomic data, through providing simple ""yes"" or ""no"" responses to queries about the presence of a given variant in datasets hosted by Beacon providers. The popularity of this concept has fostered the design of a version 2, that better serves real-world requirements and addresses the needs of clinical genomics research and healthcare, as assessed by several contributing projects and organizations. Particularly, rare disease genetics and cancer research will benefit from new case level and genomic variant level requests and the enabling of richer phenotype and clinical queries as well as support for fuzzy searches. Beacon is designed as a ""lingua franca"" to bridge data collections hosted in software solutions with different and rich interfaces. Beacon version 2 works alongside popular standards like Phenopackets, OMOP, or FHIR, allowing implementing consortia to return matches in beacon responses and provide a handover to their preferred data exchange format. The protocol is being explored by other research domains and is being tested in several international projects.",,pdf:http://repositori.upf.edu/bitstream/10230/53310/1/Rambla_2022.pdf; doi:https://doi.org/10.1002/humu.24369; html:https://europepmc.org/articles/PMC9322265; pdf:https://europepmc.org/articles/PMC9322265?pdf=render
 31109684,https://doi.org/10.1016/j.injury.2019.05.004,Agreement between medical record and administrative coding of common comorbidities in orthopaedic trauma patients.,"Daly S, Nguyen TQ, Gabbe BJ, Braaf S, Simpson P, Ekegren CL.",,Injury,2019,2019-05-08,N,Trauma; Comorbidity; Agreement; Orthopaedic; Icd-10-am,,,"<h4>Objective</h4>To i) quantify the agreement between comorbidities documented within medical records and an orthopaedic trauma dataset; and ii) compare agreement between these sources before and after the introduction of new comorbidity coding rules in Australian hospitals.<h4>Study design and setting</h4>A random sample of adult (≥ 16 years) orthopaedic trauma patients (n = 400) were extracted from the Victorian Orthopaedic Trauma Outcomes Registry (VOTOR). Diagnoses of obesity, arthritis, diabetes and cardiac conditions documented within patients' medical records were compared to ICD-10-AM comorbidity codes (provided by hospitals) for the same admission. Agreement was calculated (Cohen's kappa) before and after the introduction of new coding rules.<h4>Results</h4>All comorbidities had the same or higher prevalence in medical record data compared to coded data. Kappa values ranged from <0.001 (poor agreement) for coronary artery disease to 0.94 (excellent agreement) for type 2 diabetes. There was improvement in agreement between sources for most conditions following the introduction of new coding rules.<h4>Conclusion</h4>There has been improvement in the coding of certain comorbidities since the introduction of new coding rules, suggesting that, since 2015, administrative data has improved capacity to capture patients' comorbidity profiles. Consideration must be taken when using the ICD-10-AM data due to its limitations.",,doi:https://doi.org/10.1016/j.injury.2019.05.004
-35089054,https://doi.org/10.1161/circep.121.010221,Integrating Exercise Into Personalized Ventricular Arrhythmia Risk Prediction in Arrhythmogenic Right Ventricular Cardiomyopathy.,"Bosman LP, Wang W, Lie ØH, van Lint FHM, Rootwelt-Norberg C, Murray B, Tichnell C, Cadrin-Tourigny J, van Tintelen JP, Asselbergs FW, Calkins H, Te Riele ASJM, Haugaa KH, James CA.",,Circulation. Arrhythmia and electrophysiology,2022,2022-01-28,N,Prognosis; Exercise; Arrhythmogenic right ventricular dysplasia,,,"<h4>Background</h4>Exercise is associated with sustained ventricular arrhythmias (VA) in Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC) but is not included in the ARVC risk calculator (arvcrisk.com). The objective of this study is to quantify the influence of exercise at diagnosis on incident VA risk and evaluate whether the risk calculator needs adjustment for exercise.<h4>Methods</h4>We interviewed ARVC patients without sustained VA at diagnosis about their exercise history. The relationship between exercise dose 3 years preceding diagnosis (average METh/wk) and incident VA during follow-up was analyzed with time-to-event analysis. The incremental prognostic value of exercise to the risk calculator was evaluated by Cox models.<h4>Results</h4>We included 176 patients (male, 43.2%; age, 37.6±16.1 years) from 3 ARVC centers, of whom 53 (30.1%) developed sustained VA during 5.4 (2.7-9.7) years of follow-up. Exercise at diagnosis showed a dose-dependent nonlinear relationship with VA, with no significant risk increase <15 to 30 METh/wk. Athlete status, using 3 definitions from literature (>18, >24, and >36 METh/wk), was significantly associated with VA (hazard ratios, 2.53-2.91) but was also correlated with risk factors currently in the risk calculator model. Thus, adding athlete status to the model did not change the C index of 0.77 (0.71-0.84) and showed no significant improvement (Akaike information criterion change, <2).<h4>Conclusions</h4>Exercise at diagnosis was dose dependently associated with risk of sustained VA in ARVC patients but only above 15 to 30 METh/wk. Exercise does not appear to have incremental prognostic value over the risk calculator. The ARVC risk calculator can be used accurately in athletic patients without modification.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCEP.121.010221; doi:https://doi.org/10.1161/CIRCEP.121.010221
 35743743,https://doi.org/10.3390/jpm12060958,Immune Cell Networks Uncover Candidate Biomarkers of Melanoma Immunotherapy Response.,"Vo DHT, McGleave G, Overton IM.",,Journal of personalized medicine,2022,2022-06-11,Y,Melanoma; Immunotherapy; Ovarian carcinoma; Biomarker; Network Biology; Systems Immunology; Nivolumab; Systems Medicine; Immune Checkpoint; Precision Oncology,,,"The therapeutic activation of antitumour immunity by immune checkpoint inhibitors (ICIs) is a significant advance in cancer medicine, not least due to the prospect of long-term remission. However, many patients are unresponsive to ICI therapy and may experience serious side effects; companion biomarkers are urgently needed to help inform ICI prescribing decisions. We present the IMMUNETS networks of gene coregulation in five key immune cell types and their application to interrogate control of nivolumab response in advanced melanoma cohorts. The results evidence a role for each of the IMMUNETS cell types in ICI response and in driving tumour clearance with independent cohorts from TCGA. As expected, 'immune hot' status, including T cell proliferation, correlates with response to first-line ICI therapy. Genes regulated in NK, dendritic, and B cells are the most prominent discriminators of nivolumab response in patients that had previously progressed on another ICI. Multivariate analysis controlling for tumour stage and age highlights CIITA and IKZF3 as candidate prognostic biomarkers. IMMUNETS provide a resource for network biology, enabling context-specific analysis of immune components in orthogonal datasets. Overall, our results illuminate the relationship between the tumour microenvironment and clinical trajectories, with potential implications for precision medicine.",,pdf:https://www.mdpi.com/2075-4426/12/6/958/pdf?version=1655284846; doi:https://doi.org/10.3390/jpm12060958; html:https://europepmc.org/articles/PMC9225330; pdf:https://europepmc.org/articles/PMC9225330?pdf=render
-37477360,https://doi.org/10.1097/ypg.0000000000000349,Schizophrenia polygenic risk score and type 2 diabetes onset in older adults with no schizophrenia diagnosis.,"Shamsutdinova D, Ajnakina O, Roberts A, Stahl D.",,Psychiatric genetics,2023,2023-07-04,Y,,,,"<h4>Objectives</h4>An association between type 2 diabetes (T2DM) and schizophrenia has long been observed, and recent research revealed presence of shared genetic factors. However, epidemiological evidence was inconsistent, some reported insignificant contribution of genetic factors to T2DM-schizophrenia comorbidity. Prior works studied people with schizophrenia, particularly, antipsychotic-naive patients, or those during the first psychotic experience to limit schizophrenia-related environmental factors. In contrast, we controlled such factors by utilizing a general population sample of individuals undiagnosed with schizophrenia. We hypothesized that if schizophrenia genetics impact T2DM development and such impact is not fully mediated by schizophrenia-related environment, people with high polygenic schizophrenia risk would exhibit elevated T2DM incidence.<h4>Methods</h4>Using a population-representative sample of adults aged ≥50 from English Longitudinal Study of Ageing ( n  = 5968, 493 T2DM cases, average follow-up 8.7 years), we investigated if schizophrenia polygenic risk score (PGS-SZ) is associated with T2DM onset. A proportional hazards model with interval censoring was adjusted for age and sex (Model 1), and age, sex, BMI, hypertension, cardiovascular diseases, exercise, smoking, depressive symptoms and T2DM polygenic risk score (Model 2). According to the power calculations, hazard rates > 1.14 per standard deviation in PGS-SZ could be detected.<h4>Results</h4>We did not observe a significant association between PGS-SZ and T2DM incidence (hazard ratio 1.04; 95% CI 0.93-1.15; and 1.01, 95% CI 0.94-1.09).<h4>Conclusion</h4>Our results suggest low contribution of the intrinsic biological mechanisms driven by the polygenic risk of schizophrenia on future T2DM onset. Further research is needed.",,html:https://journals.lww.com/psychgenetics/fulltext/9900/schizophrenia_polygenic_risk_score_and_type_2.34.aspx; doi:https://doi.org/10.1097/YPG.0000000000000349; html:https://europepmc.org/articles/PMC10501355; pdf:https://europepmc.org/articles/PMC10501355?pdf=render
 36828609,https://doi.org/10.1016/s2589-7500(22)00252-7,Embedding patient-reported outcomes at the heart of artificial intelligence health-care technologies.,"Cruz Rivera S, Liu X, Hughes SE, Dunster H, Manna E, Denniston AK, Calvert MJ.",,The Lancet. Digital health,2023,2023-03-01,N,,,,"Integration of patient-reported outcome measures (PROMs) in artificial intelligence (AI) studies is a critical part of the humanisation of AI for health. It allows AI technologies to incorporate patients' own views of their symptoms and predict outcomes, reflecting a more holistic picture of health and wellbeing and ultimately helping patients and clinicians to make the best health-care decisions together. By positioning patient-reported outcomes (PROs) as a model input or output we propose a framework to embed PROMs within the function and evaluation of AI health care. However, the integration of PROs in AI systems presents several challenges. These challenges include (1) fragmentation of PRO data collection; (2) validation of AI systems trained and validated against clinician performance, rather than outcome data; (3) scarcity of large-scale PRO datasets; (4) inadequate selection of PROMs for the target population and inadequate infrastructure for collecting PROs; and (5) clinicians might not recognise the value of PROs and therefore not prioritise their adoption; and (6) studies involving PRO or AI frequently present suboptimal design. Notwithstanding these challenges, we propose considerations for the inclusion of PROs in AI health-care technologies to avoid promoting survival at the expense of wellbeing.",,doi:https://doi.org/10.1016/s2589-7500(22)00252-7; doi:https://doi.org/10.1016/S2589-7500(22)00252-7
 PMC8718341,https://doi.org/,"Loneliness, coping, suicidal thoughts and self-harm during the COVID-19 pandemic: a repeat cross-sectional UK population survey","John A, Lee S, Solomon S, Crepaz-Keay D, McDaid S, Morton A, Davidson G, Van Bortel T, Kousoulis A.",,BMJ open,2021,2021-01-01,Y,Mental health; Public Health; Suicide & Self-harm; Covid-19,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8718341/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8718341/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC8718341; pdf:https://europepmc.org/articles/PMC8718341?pdf=render
+37477360,https://doi.org/10.1097/ypg.0000000000000349,Schizophrenia polygenic risk score and type 2 diabetes onset in older adults with no schizophrenia diagnosis.,"Shamsutdinova D, Ajnakina O, Roberts A, Stahl D.",,Psychiatric genetics,2023,2023-07-04,Y,,,,"<h4>Objectives</h4>An association between type 2 diabetes (T2DM) and schizophrenia has long been observed, and recent research revealed presence of shared genetic factors. However, epidemiological evidence was inconsistent, some reported insignificant contribution of genetic factors to T2DM-schizophrenia comorbidity. Prior works studied people with schizophrenia, particularly, antipsychotic-naive patients, or those during the first psychotic experience to limit schizophrenia-related environmental factors. In contrast, we controlled such factors by utilizing a general population sample of individuals undiagnosed with schizophrenia. We hypothesized that if schizophrenia genetics impact T2DM development and such impact is not fully mediated by schizophrenia-related environment, people with high polygenic schizophrenia risk would exhibit elevated T2DM incidence.<h4>Methods</h4>Using a population-representative sample of adults aged ≥50 from English Longitudinal Study of Ageing ( n  = 5968, 493 T2DM cases, average follow-up 8.7 years), we investigated if schizophrenia polygenic risk score (PGS-SZ) is associated with T2DM onset. A proportional hazards model with interval censoring was adjusted for age and sex (Model 1), and age, sex, BMI, hypertension, cardiovascular diseases, exercise, smoking, depressive symptoms and T2DM polygenic risk score (Model 2). According to the power calculations, hazard rates > 1.14 per standard deviation in PGS-SZ could be detected.<h4>Results</h4>We did not observe a significant association between PGS-SZ and T2DM incidence (hazard ratio 1.04; 95% CI 0.93-1.15; and 1.01, 95% CI 0.94-1.09).<h4>Conclusion</h4>Our results suggest low contribution of the intrinsic biological mechanisms driven by the polygenic risk of schizophrenia on future T2DM onset. Further research is needed.",,html:https://journals.lww.com/psychgenetics/fulltext/9900/schizophrenia_polygenic_risk_score_and_type_2.34.aspx; doi:https://doi.org/10.1097/YPG.0000000000000349; html:https://europepmc.org/articles/PMC10501355; pdf:https://europepmc.org/articles/PMC10501355?pdf=render
 35072885,https://doi.org/10.1007/s10439-022-02905-4,Modeling the His-Purkinje Effect in Non-invasive Estimation of Endocardial and Epicardial Ventricular Activation.,"Boonstra MJ, Roudijk RW, Brummel R, Kassenberg W, Blom LJ, Oostendorp TF, Te Riele ASJM, van der Heijden JF, Asselbergs FW, Loh P, van Dam PM.",,Annals of biomedical engineering,2022,2022-01-24,Y,Electrophysiology; Electrocardiography; Cardiovascular Imaging; Electrocardiographic Imaging; Electro-anatomical Mapping; His-purkinje System; Inverse Electrocardiography; Equivalent Dipole Layer; Non-invasive Cardiac Activation Mapping,,,"Inverse electrocardiography (iECG) estimates epi- and endocardial electrical activity from body surface potentials maps (BSPM). In individuals at risk for cardiomyopathy, non-invasive estimation of normal ventricular activation may provide valuable information to aid risk stratification to prevent sudden cardiac death. However, multiple simultaneous activation wavefronts initiated by the His-Purkinje system, severely complicate iECG. To improve the estimation of normal ventricular activation, the iECG method should accurately mimic the effect of the His-Purkinje system, which is not taken into account in the previously published multi-focal iECG. Therefore, we introduce the novel multi-wave iECG method and report on its performance. Multi-wave iECG and multi-focal iECG were tested in four patients undergoing invasive electro-anatomical mapping during normal ventricular activation. In each subject, 67-electrode BSPM were recorded and used as input for both iECG methods. The iECG and invasive local activation timing (LAT) maps were compared. Median epicardial inter-map correlation coefficient (CC) between invasive LAT maps and estimated multi-wave iECG versus multi-focal iECG was 0.61 versus 0.31. Endocardial inter-map CC was 0.54 respectively 0.22. Modeling the His-Purkinje system resulted in a physiologically realistic and robust non-invasive estimation of normal ventricular activation, which might enable the early detection of cardiac disease during normal sinus rhythm.",,pdf:https://link.springer.com/content/pdf/10.1007/s10439-022-02905-4.pdf; doi:https://doi.org/10.1007/s10439-022-02905-4; html:https://europepmc.org/articles/PMC8847268; pdf:https://europepmc.org/articles/PMC8847268?pdf=render
 33824583,https://doi.org/10.2147/copd.s298585,There is No Fast Track to Identify Fast Decliners in Alpha-1 Antitrypsin Deficiency by Spirometry: A Longitudinal Study of Repeated Measurements.,"Stockley JA, Stockley RA, Sapey E.",,International journal of chronic obstructive pulmonary disease,2021,2021-03-29,Y,Lung function; decline; Alpha-1 Antitrypsin Deficiency; Obstructive Airways Disease,,,"<h4>Background</h4>It is known that lung function decline in Alpha-1 Antitrypsin Deficiency (AATD) varies. Those with a rapid decline are at highest risk of poorer outcomes but may benefit most from targeted treatments including augmentation therapy. Current evidence suggests rapid decliners can be identified after 3 years of serial follow-up. It would be advantageous to identify these patients over a shorter time period, especially in mild disease.<h4>Methods</h4>Post-bronchodilator spirometry was performed every 6 months for a total of 18 months (4 measurements) by PiZZ AATD patients (ex- or never-smokers) either without spirometric COPD or with mild COPD. Where possible, retrospective spirometry data were included. Decline was assessed using 2 (baseline and 6 month) or four measurements (including baseline, 6, 12 and 18 months) and compared to retrospective decline rates using annual measurements over 3 years.<h4>Results</h4>Seventy-two PiZZ AATD patients were included, with 27 having at least three years of retrospective, annual spirometry. 18-month progression obtained by linear regression showed variable degrees of change with 29 showing no decline, 8 showing slow decline and 35 showing rapid decline. Bland-Altman plots showed that there was no overall agreement between predicted rate of decline using data obtained over 6 months and that obtained over 18 months. Furthermore, there was no agreement between rate of decline from either 6 or 18 months' data when compared to data collected over 3 years. The positive predictive value for rapid decline with 18 months of data compared to 3 years was only 50.0%.<h4>Conclusion</h4>This study suggests serial lung function over 18 months cannot identify AATD patients who have rapidly declining lung function. There is an urgent need for different biomarkers to help identify these patients at the earliest opportunity.",,pdf:https://www.dovepress.com/getfile.php?fileID=68078; doi:https://doi.org/10.2147/COPD.S298585; html:https://europepmc.org/articles/PMC8018552; pdf:https://europepmc.org/articles/PMC8018552?pdf=render
 33148619,https://doi.org/10.1136/bmj.m3919,Consistency of variety of machine learning and statistical models in predicting clinical risks of individual patients: longitudinal cohort study using cardiovascular disease as exemplar.,"Li Y, Li Y, Sperrin M, Ashcroft DM, van Staa TP.",,BMJ (Clinical research ed.),2020,2020-11-04,Y,,,,"<h4>Objective</h4>To assess the consistency of machine learning and statistical techniques in predicting individual level and population level risks of cardiovascular disease and the effects of censoring on risk predictions.<h4>Design</h4>Longitudinal cohort study from 1 January 1998 to 31 December 2018.<h4>Setting and participants</h4>3.6 million patients from the Clinical Practice Research Datalink registered at 391 general practices in England with linked hospital admission and mortality records.<h4>Main outcome measures</h4>Model performance including discrimination, calibration, and consistency of individual risk prediction for the same patients among models with comparable model performance. 19 different prediction techniques were applied, including 12 families of machine learning models (grid searched for best models), three Cox proportional hazards models (local fitted, QRISK3, and Framingham), three parametric survival models, and one logistic model.<h4>Results</h4>The various models had similar population level performance (C statistics of about 0.87 and similar calibration). However, the predictions for individual risks of cardiovascular disease varied widely between and within different types of machine learning and statistical models, especially in patients with higher risks. A patient with a risk of 9.5-10.5% predicted by QRISK3 had a risk of 2.9-9.2% in a random forest and 2.4-7.2% in a neural network. The differences in predicted risks between QRISK3 and a neural network ranged between -23.2% and 0.1% (95% range). Models that ignored censoring (that is, assumed censored patients to be event free) substantially underestimated risk of cardiovascular disease. Of the 223 815 patients with a cardiovascular disease risk above 7.5% with QRISK3, 57.8% would be reclassified below 7.5% when using another model.<h4>Conclusions</h4>A variety of models predicted risks for the same patients very differently despite similar model performances. The logistic models and commonly used machine learning models should not be directly applied to the prediction of long term risks without considering censoring. Survival models that consider censoring and that are explainable, such as QRISK3, are preferable. The level of consistency within and between models should be routinely assessed before they are used for clinical decision making.",,pdf:https://www.bmj.com/content/bmj/371/bmj.m3919.full.pdf; doi:https://doi.org/10.1136/bmj.m3919; html:https://europepmc.org/articles/PMC7610202
 32478737,https://doi.org/10.3791/60794,Implementation of a Real-Time Psychosis Risk Detection and Alerting System Based on Electronic Health Records using CogStack.,"Wang T, Oliver D, Msosa Y, Colling C, Spada G, Roguski Ł, Folarin A, Stewart R, Roberts A, Dobson RJB, Fusar-Poli P.",,Journal of visualized experiments : JoVE,2020,2020-05-15,N,,,,"Recent studies have shown that an automated, lifespan-inclusive, transdiagnostic, and clinically based, individualized risk calculator provides a powerful system for supporting the early detection of individuals at-risk of psychosis at a large scale, by leveraging electronic health records (EHRs). This risk calculator has been externally validated twice and is undergoing feasibility testing for clinical implementation. Integration of this risk calculator in clinical routine should be facilitated by prospective feasibility studies, which are required to address pragmatic challenges, such as missing data, and the usability of this risk calculator in a real-world and routine clinical setting. Here, we present an approach for a prospective implementation of a real-time psychosis risk detection and alerting service in a real-world EHR system. This method leverages the CogStack platform, which is an open-source, lightweight, and distributed information retrieval and text extraction system. The CogStack platform incorporates a set of services that allow for full-text search of clinical data, lifespan-inclusive, real-time calculation of psychosis risk, early risk-alerting to clinicians, and the visual monitoring of patients over time. Our method includes: 1) ingestion and synchronization of data from multiple sources into the CogStack platform, 2) implementation of a risk calculator, whose algorithm was previously developed and validated, for timely computation of a patient's risk of psychosis, 3) creation of interactive visualizations and dashboards to monitor patients' health status over time, and 4) building automated alerting systems to ensure that clinicians are notified of patients at-risk, so that appropriate actions can be pursued. This is the first ever study that has developed and implemented a similar detection and alerting system in clinical routine for early detection of psychosis.",,pdf:https://www.jove.com/pdf/60794/implementation-real-time-psychosis-risk-detection-alerting-system; doi:https://doi.org/10.3791/60794; html:https://europepmc.org/articles/PMC7272223; pdf:https://europepmc.org/articles/PMC7272223?pdf=render; doi:https://doi.org/10.3791/60794
-35748342,https://doi.org/10.1093/ije/dyac130,Linkage of multiple electronic health record datasets using a 'spine linkage' approach compared with all 'pairwise linkages'.,"Blake HA, Sharples LD, Harron K, van der Meulen JH, Walker K.",,International journal of epidemiology,2023,2023-02-01,Y,Electronic Health Records; Record Linkage; Pairwise Linkage; Spine Linkage Approach,,,"<h4>Background</h4>Methods for linking records between two datasets are well established. However, guidance is needed for linking more than two datasets. Using all 'pairwise linkages'-linking each dataset to every other dataset-is the most inclusive, but resource-intensive, approach. The 'spine' approach links each dataset to a designated 'spine dataset', reducing the number of linkages, but potentially reducing linkage quality.<h4>Methods</h4>We compared the pairwise and spine linkage approaches using real-world data on patients undergoing emergency bowel cancer surgery between 31 October 2013 and 30 April 2018. We linked an administrative hospital dataset (Hospital Episode Statistics; HES) capturing patients admitted to hospitals in England, and two clinical datasets comprising patients diagnosed with bowel cancer and patients undergoing emergency bowel surgery.<h4>Results</h4>The spine linkage approach, with HES as the spine dataset, created an analysis cohort of 15 826 patients, equating to 98.3% of the 16 100 patients identified using the pairwise linkage approach. There were no systematic differences in patient characteristics between these analysis cohorts. Associations of patient and tumour characteristics with mortality, complications and length of stay were not sensitive to the linkage approach. When eligibility criteria were applied before linkage, spine linkage included 14 509 patients (90.0% compared with pairwise linkage).<h4>Conclusion</h4>Spine linkage can be used as an efficient alternative to pairwise linkage if case ascertainment in the spine dataset and data quality of linkage variables are high. These aspects should be systematically evaluated in the nominated spine dataset before spine linkage is used to create the analysis cohort.",,pdf:https://academic.oup.com/ije/advance-article-pdf/doi/10.1093/ije/dyac130/44245961/dyac130.pdf; doi:https://doi.org/10.1093/ije/dyac130; html:https://europepmc.org/articles/PMC9908066; pdf:https://europepmc.org/articles/PMC9908066?pdf=render
 35275087,https://doi.org/10.2196/34898,Longitudinal Relationships Between Depressive Symptom Severity and Phone-Measured Mobility: Dynamic Structural Equation Modeling Study.,"Zhang Y, Folarin AA, Sun S, Cummins N, Vairavan S, Bendayan R, Ranjan Y, Rashid Z, Conde P, Stewart C, Laiou P, Sankesara H, Matcham F, White KM, Oetzmann C, Ivan A, Lamers F, Siddi S, Vilella E, Simblett S, Rintala A, Bruce S, Mohr DC, Myin-Germeys I, Wykes T, Haro JM, Penninx BW, Narayan VA, Annas P, Hotopf M, Dobson RJ, RADAR-CNS consortium.",,JMIR mental health,2022,2022-03-11,Y,Modeling; Mobility; Depression; Mental health; Medical Informatics; Mhealth; Mobile Health; Dynamic Structural Equation Modeling; Location Data,,,"<h4>Background</h4>The mobility of an individual measured by phone-collected location data has been found to be associated with depression; however, the longitudinal relationships (the temporal direction of relationships) between depressive symptom severity and phone-measured mobility have yet to be fully explored.<h4>Objective</h4>We aimed to explore the relationships and the direction of the relationships between depressive symptom severity and phone-measured mobility over time.<h4>Methods</h4>Data used in this paper came from a major EU program, called the Remote Assessment of Disease and Relapse-Major Depressive Disorder, which was conducted in 3 European countries. Depressive symptom severity was measured with the 8-item Patient Health Questionnaire (PHQ-8) through mobile phones every 2 weeks. Participants' location data were recorded by GPS and network sensors in mobile phones every 10 minutes, and 11 mobility features were extracted from location data for the 2 weeks prior to the PHQ-8 assessment. Dynamic structural equation modeling was used to explore the longitudinal relationships between depressive symptom severity and phone-measured mobility.<h4>Results</h4>This study included 2341 PHQ-8 records and corresponding phone-collected location data from 290 participants (age: median 50.0 IQR 34.0, 59.0) years; of whom 215 (74.1%) were female, and 149 (51.4%) were employed. Significant negative correlations were found between depressive symptom severity and phone-measured mobility, and these correlations were more significant at the within-individual level than the between-individual level. For the direction of relationships over time, Homestay (time at home) (φ=0.09, P=.01), Location Entropy (time distribution on different locations) (φ=-0.04, P=.02), and Residential Location Count (reflecting traveling) (φ=0.05, P=.02) were significantly correlated with the subsequent changes in the PHQ-8 score, while changes in the PHQ-8 score significantly affected (φ=-0.07, P<.001) the subsequent periodicity of mobility.<h4>Conclusions</h4>Several phone-derived mobility features have the potential to predict future depression, which may provide support for future clinical applications, relapse prevention, and remote mental health monitoring practices in real-world settings.",,pdf:https://mental.jmir.org/2022/3/e34898/PDF; doi:https://doi.org/10.2196/34898; html:https://europepmc.org/articles/PMC8957008
 35692035,https://doi.org/10.1186/s12916-022-02399-w,"Role of circulating polyunsaturated fatty acids on cardiovascular diseases risk: analysis using Mendelian randomization and fatty acid genetic association data from over 114,000 UK Biobank participants.","Borges MC, Haycock PC, Zheng J, Hemani G, Holmes MV, Davey Smith G, Hingorani AD, Lawlor DA.",,BMC medicine,2022,2022-06-13,Y,Fatty acids; Cardiovascular diseases; Mendelian Randomization,,,"<h4>Background</h4>Despite early interest in the health effects of polyunsaturated fatty acids (PUFA), there is still substantial controversy and uncertainty on the evidence linking PUFA to cardiovascular diseases (CVDs). We investigated the effect of plasma concentration of omega-3 PUFA (i.e. docosahexaenoic acid (DHA) and total omega-3 PUFA) and omega-6 PUFA (i.e. linoleic acid and total omega-6 PUFA) on the risk of CVDs using Mendelian randomization.<h4>Methods</h4>We conducted the largest genome-wide association study (GWAS) of circulating PUFA to date including a sample of 114,999 individuals and incorporated these data in a two-sample Mendelian randomization framework to investigate the involvement of circulating PUFA on a wide range of CVDs in up to 1,153,768 individuals of European ancestry (i.e. coronary artery disease, ischemic stroke, haemorrhagic stroke, heart failure, atrial fibrillation, peripheral arterial disease, aortic aneurysm, venous thromboembolism and aortic valve stenosis).<h4>Results</h4>GWAS identified between 46 and 64 SNPs for the four PUFA traits, explaining 4.8-7.9% of circulating PUFA variance and with mean F statistics >100. Higher genetically predicted DHA (and total omega-3 fatty acids) concentration was related to higher risk of some cardiovascular endpoints; however, these findings did not pass our criteria for multiple testing correction and were attenuated when accounting for LDL-cholesterol through multivariable Mendelian randomization or excluding SNPs in the vicinity of the FADS locus. Estimates for the relation between higher genetically predicted linoleic acid (and total omega-6) concentration were inconsistent across different cardiovascular endpoints and Mendelian randomization methods. There was weak evidence of higher genetically predicted linoleic acid being related to lower risk of ischemic stroke and peripheral artery disease when accounting by LDL-cholesterol.<h4>Conclusions</h4>We have conducted the largest GWAS of circulating PUFA to date and the most comprehensive Mendelian randomization analyses. Overall, our Mendelian randomization findings do not support a protective role of circulating PUFA concentration on the risk of CVDs. However, horizontal pleiotropy via lipoprotein-related traits could be a key source of bias in our analyses.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-022-02399-w; doi:https://doi.org/10.1186/s12916-022-02399-w; html:https://europepmc.org/articles/PMC9190170; pdf:https://europepmc.org/articles/PMC9190170?pdf=render
+35748342,https://doi.org/10.1093/ije/dyac130,Linkage of multiple electronic health record datasets using a 'spine linkage' approach compared with all 'pairwise linkages'.,"Blake HA, Sharples LD, Harron K, van der Meulen JH, Walker K.",,International journal of epidemiology,2023,2023-02-01,Y,Electronic Health Records; Record Linkage; Pairwise Linkage; Spine Linkage Approach,,,"<h4>Background</h4>Methods for linking records between two datasets are well established. However, guidance is needed for linking more than two datasets. Using all 'pairwise linkages'-linking each dataset to every other dataset-is the most inclusive, but resource-intensive, approach. The 'spine' approach links each dataset to a designated 'spine dataset', reducing the number of linkages, but potentially reducing linkage quality.<h4>Methods</h4>We compared the pairwise and spine linkage approaches using real-world data on patients undergoing emergency bowel cancer surgery between 31 October 2013 and 30 April 2018. We linked an administrative hospital dataset (Hospital Episode Statistics; HES) capturing patients admitted to hospitals in England, and two clinical datasets comprising patients diagnosed with bowel cancer and patients undergoing emergency bowel surgery.<h4>Results</h4>The spine linkage approach, with HES as the spine dataset, created an analysis cohort of 15 826 patients, equating to 98.3% of the 16 100 patients identified using the pairwise linkage approach. There were no systematic differences in patient characteristics between these analysis cohorts. Associations of patient and tumour characteristics with mortality, complications and length of stay were not sensitive to the linkage approach. When eligibility criteria were applied before linkage, spine linkage included 14 509 patients (90.0% compared with pairwise linkage).<h4>Conclusion</h4>Spine linkage can be used as an efficient alternative to pairwise linkage if case ascertainment in the spine dataset and data quality of linkage variables are high. These aspects should be systematically evaluated in the nominated spine dataset before spine linkage is used to create the analysis cohort.",,pdf:https://academic.oup.com/ije/advance-article-pdf/doi/10.1093/ije/dyac130/44245961/dyac130.pdf; doi:https://doi.org/10.1093/ije/dyac130; html:https://europepmc.org/articles/PMC9908066; pdf:https://europepmc.org/articles/PMC9908066?pdf=render
 31409800,https://doi.org/10.1038/s41467-019-11451-y,GWAS for urinary sodium and potassium excretion highlights pathways shared with cardiovascular traits.,"Pazoki R, Evangelou E, Mosen-Ansorena D, Pinto RC, Karaman I, Blakeley P, Gill D, Zuber V, Elliott P, Tzoulaki I, Dehghan A.",,Nature communications,2019,2019-08-13,Y,,Understanding the Causes of Disease,,"Urinary sodium and potassium excretion are associated with blood pressure (BP) and cardiovascular disease (CVD). The exact biological link between these traits is yet to be elucidated. Here, we identify 50 loci for sodium and 13 for potassium excretion in a large-scale genome-wide association study (GWAS) on urinary sodium and potassium excretion using data from 446,237 individuals of European descent from the UK Biobank study. We extensively interrogate the results using multiple analyses such as Mendelian randomization, functional assessment, co localization, genetic risk score, and pathway analyses. We identify a shared genetic component between urinary sodium and potassium expression and cardiovascular traits. Ingenuity pathway analysis shows that urinary sodium and potassium excretion loci are over-represented in behavioural response to stimuli. Our study highlights pathways that are shared between urinary sodium and potassium excretion and cardiovascular traits.",,pdf:https://www.nature.com/articles/s41467-019-11451-y.pdf; doi:https://doi.org/10.1038/s41467-019-11451-y; html:https://europepmc.org/articles/PMC6692500; pdf:https://europepmc.org/articles/PMC6692500?pdf=render
-36701266,https://doi.org/10.1371/journal.pmed.1004036,"Gestational age at birth and body size from infancy through adolescence: An individual participant data meta-analysis on 253,810 singletons in 16 birth cohort studies.","Vinther JL, Cadman T, Avraam D, Ekstrøm CT, Sørensen TIA, Elhakeem A, Santos AC, Pinot de Moira A, Heude B, Iñiguez C, Pizzi C, Simons E, Voerman E, Corpeleijn E, Zariouh F, Santorelli G, Inskip HM, Barros H, Carson J, Harris JR, Nader JL, Ronkainen J, Strandberg-Larsen K, Santa-Marina L, Calas L, Cederkvist L, Popovic M, Charles MA, Welten M, Vrijheid M, Azad M, Subbarao P, Burton P, Mandhane PJ, Huang RC, Wilson RC, Haakma S, Fernández-Barrés S, Turvey S, Santos S, Tough SC, Tough SC, Sebert S, Moraes TJ, Salika T, Jaddoe VWV, Lawlor DA, Nybo Andersen AM.",,PLoS medicine,2023,2023-01-26,Y,,,,"<h4>Background</h4>Preterm birth is the leading cause of perinatal morbidity and mortality and is associated with adverse developmental and long-term health outcomes, including several cardiometabolic risk factors and outcomes. However, evidence about the association of preterm birth with later body size derives mainly from studies using birth weight as a proxy of prematurity rather than an actual length of gestation. We investigated the association of gestational age (GA) at birth with body size from infancy through adolescence.<h4>Methods and findings</h4>We conducted a two-stage individual participant data (IPD) meta-analysis using data from 253,810 mother-child dyads from 16 general population-based cohort studies in Europe (Denmark, Finland, France, Italy, Norway, Portugal, Spain, the Netherlands, United Kingdom), North America (Canada), and Australasia (Australia) to estimate the association of GA with body mass index (BMI) and overweight (including obesity) adjusted for the following maternal characteristics as potential confounders: education, height, prepregnancy BMI, ethnic background, parity, smoking during pregnancy, age at child's birth, gestational diabetes and hypertension, and preeclampsia. Pregnancy and birth cohort studies from the LifeCycle and the EUCAN-Connect projects were invited and were eligible for inclusion if they had information on GA and minimum one measurement of BMI between infancy and adolescence. Using a federated analytical tool (DataSHIELD), we fitted linear and logistic regression models in each cohort separately with a complete-case approach and combined the regression estimates and standard errors through random-effects study-level meta-analysis providing an overall effect estimate at early infancy (>0.0 to 0.5 years), late infancy (>0.5 to 2.0 years), early childhood (>2.0 to 5.0 years), mid-childhood (>5.0 to 9.0 years), late childhood (>9.0 to 14.0 years), and adolescence (>14.0 to 19.0 years). GA was positively associated with BMI in the first decade of life, with the greatest increase in mean BMI z-score during early infancy (0.02, 95% confidence interval (CI): 0.00; 0.05, p < 0.05) per week of increase in GA, while in adolescence, preterm individuals reached similar levels of BMI (0.00, 95% CI: -0.01; 0.01, p 0.9) as term counterparts. The association between GA and overweight revealed a similar pattern of association with an increase in odds ratio (OR) of overweight from late infancy through mid-childhood (OR 1.01 to 1.02) per week increase in GA. By adolescence, however, GA was slightly negatively associated with the risk of overweight (OR 0.98 [95% CI: 0.97; 1.00], p 0.1) per week of increase in GA. Although based on only four cohorts (n = 32,089) that reached the age of adolescence, data suggest that individuals born very preterm may be at increased odds of overweight (OR 1.46 [95% CI: 1.03; 2.08], p < 0.05) compared with term counterparts. Findings were consistent across cohorts and sensitivity analyses despite considerable heterogeneity in cohort characteristics. However, residual confounding may be a limitation in this study, while findings may be less generalisable to settings in low- and middle-income countries.<h4>Conclusions</h4>This study based on data from infancy through adolescence from 16 cohort studies found that GA may be important for body size in infancy, but the strength of association attenuates consistently with age. By adolescence, preterm individuals have on average a similar mean BMI to peers born at term.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004036&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004036; html:https://europepmc.org/articles/PMC9879424; pdf:https://europepmc.org/articles/PMC9879424?pdf=render
 34688720,https://doi.org/10.1016/j.ijcard.2021.10.029,Methodological issues in meta-analyses of real-world clinical data to infer causality.,"Uijl A, Lund LH, Asselbergs FW, Savarese G.",,International journal of cardiology,2021,2021-10-22,N,Meta-analysis; Causality; Observational; Sacubitril/valsartan,,,,,doi:https://doi.org/10.1016/j.ijcard.2021.10.029
+32234121,https://doi.org/10.2807/1560-7917.es.2020.25.12.2000256,"Estimating the infection and case fatality ratio for coronavirus disease (COVID-19) using age-adjusted data from the outbreak on the Diamond Princess cruise ship, February 2020.","Russell TW, Hellewell J, Jarvis CI, van Zandvoort K, Abbott S, Ratnayake R, CMMID COVID-19 working group, Flasche S, Eggo RM, Edmunds WJ, Kucharski AJ.",,Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin,2020,2020-03-01,Y,Coronavirus; outbreak; Severity; Asymptomatic; Case Fatality Ratio; Cruise Ship; Covid-19; Infection Fatality Ratio,"COVID-19, Improving Public Health","COVID-19, infection","Adjusting for delay from confirmation to death, we estimated case and infection fatality ratios (CFR, IFR) for coronavirus disease (COVID-19) on the Diamond Princess ship as 2.6% (95% confidence interval (CI): 0.89-6.7) and 1.3% (95% CI: 0.38-3.6), respectively. Comparing deaths on board with expected deaths based on naive CFR estimates from China, we estimated CFR and IFR in China to be 1.2% (95% CI: 0.3-2.7) and 0.6% (95% CI: 0.2-1.3), respectively.",,pdf:https://www.eurosurveillance.org/deliver/fulltext/eurosurveillance/25/12/eurosurv-25-12-3.pdf?itemId=%2Fcontent%2F10.2807%2F1560-7917.ES.2020.25.12.2000256&mimeType=pdf&containerItemId=content/eurosurveillance; doi:https://doi.org/10.2807/1560-7917.ES.2020.25.12.2000256; html:https://europepmc.org/articles/PMC7118348; pdf:https://europepmc.org/articles/PMC7118348?pdf=render
+36701266,https://doi.org/10.1371/journal.pmed.1004036,"Gestational age at birth and body size from infancy through adolescence: An individual participant data meta-analysis on 253,810 singletons in 16 birth cohort studies.","Vinther JL, Cadman T, Avraam D, Ekstrøm CT, Sørensen TIA, Elhakeem A, Santos AC, Pinot de Moira A, Heude B, Iñiguez C, Pizzi C, Simons E, Voerman E, Corpeleijn E, Zariouh F, Santorelli G, Inskip HM, Barros H, Carson J, Harris JR, Nader JL, Ronkainen J, Strandberg-Larsen K, Santa-Marina L, Calas L, Cederkvist L, Popovic M, Charles MA, Welten M, Vrijheid M, Azad M, Subbarao P, Burton P, Mandhane PJ, Huang RC, Wilson RC, Haakma S, Fernández-Barrés S, Turvey S, Santos S, Tough SC, Tough SC, Sebert S, Moraes TJ, Salika T, Jaddoe VWV, Lawlor DA, Nybo Andersen AM.",,PLoS medicine,2023,2023-01-26,Y,,,,"<h4>Background</h4>Preterm birth is the leading cause of perinatal morbidity and mortality and is associated with adverse developmental and long-term health outcomes, including several cardiometabolic risk factors and outcomes. However, evidence about the association of preterm birth with later body size derives mainly from studies using birth weight as a proxy of prematurity rather than an actual length of gestation. We investigated the association of gestational age (GA) at birth with body size from infancy through adolescence.<h4>Methods and findings</h4>We conducted a two-stage individual participant data (IPD) meta-analysis using data from 253,810 mother-child dyads from 16 general population-based cohort studies in Europe (Denmark, Finland, France, Italy, Norway, Portugal, Spain, the Netherlands, United Kingdom), North America (Canada), and Australasia (Australia) to estimate the association of GA with body mass index (BMI) and overweight (including obesity) adjusted for the following maternal characteristics as potential confounders: education, height, prepregnancy BMI, ethnic background, parity, smoking during pregnancy, age at child's birth, gestational diabetes and hypertension, and preeclampsia. Pregnancy and birth cohort studies from the LifeCycle and the EUCAN-Connect projects were invited and were eligible for inclusion if they had information on GA and minimum one measurement of BMI between infancy and adolescence. Using a federated analytical tool (DataSHIELD), we fitted linear and logistic regression models in each cohort separately with a complete-case approach and combined the regression estimates and standard errors through random-effects study-level meta-analysis providing an overall effect estimate at early infancy (>0.0 to 0.5 years), late infancy (>0.5 to 2.0 years), early childhood (>2.0 to 5.0 years), mid-childhood (>5.0 to 9.0 years), late childhood (>9.0 to 14.0 years), and adolescence (>14.0 to 19.0 years). GA was positively associated with BMI in the first decade of life, with the greatest increase in mean BMI z-score during early infancy (0.02, 95% confidence interval (CI): 0.00; 0.05, p < 0.05) per week of increase in GA, while in adolescence, preterm individuals reached similar levels of BMI (0.00, 95% CI: -0.01; 0.01, p 0.9) as term counterparts. The association between GA and overweight revealed a similar pattern of association with an increase in odds ratio (OR) of overweight from late infancy through mid-childhood (OR 1.01 to 1.02) per week increase in GA. By adolescence, however, GA was slightly negatively associated with the risk of overweight (OR 0.98 [95% CI: 0.97; 1.00], p 0.1) per week of increase in GA. Although based on only four cohorts (n = 32,089) that reached the age of adolescence, data suggest that individuals born very preterm may be at increased odds of overweight (OR 1.46 [95% CI: 1.03; 2.08], p < 0.05) compared with term counterparts. Findings were consistent across cohorts and sensitivity analyses despite considerable heterogeneity in cohort characteristics. However, residual confounding may be a limitation in this study, while findings may be less generalisable to settings in low- and middle-income countries.<h4>Conclusions</h4>This study based on data from infancy through adolescence from 16 cohort studies found that GA may be important for body size in infancy, but the strength of association attenuates consistently with age. By adolescence, preterm individuals have on average a similar mean BMI to peers born at term.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004036&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004036; html:https://europepmc.org/articles/PMC9879424; pdf:https://europepmc.org/articles/PMC9879424?pdf=render
 35355205,https://doi.org/10.1007/s11897-022-00544-3,LVEF by Multigated Acquisition Scan Compared to Other Imaging Modalities in Cardio-Oncology: a Systematic Review.,"Printezi MI, Yousif LIE, Kamphuis JAM, van Laake LW, Cramer MJ, Hobbelink MGG, Asselbergs FW, Teske AJ.",,Current heart failure reports,2022,2022-03-30,Y,Cardiotoxicity; Echocardiography; Left ventricular ejection fraction; Cardiac Magnetic Resonance Imaging; Cardio-oncology; Multigated Acquisition Scan,,,"<h4>Purpose of review</h4>The prevalence of cancer therapy-related cardiac dysfunction (CTRCD) is increasing due to improved cancer survival. Serial monitoring of cardiac function is essential to detect CTRCD, guiding timely intervention strategies. Multigated radionuclide angiography (MUGA) has been the main screening tool using left ventricular ejection fraction (LVEF) to monitor cardiac dysfunction. However, transthoracic echocardiography (TTE) and cardiac magnetic resonance imaging (CMR) may be more suitable for serial assessment. We aimed to assess the concordance between different non-radiating imaging modalities with MUGA to determine whether they can be used interchangeably.<h4>Recent findings</h4>In order to identify relevant studies, a PubMed search was performed. We included cross-sectional studies comparing MUGA LVEF to that of 2D TTE, 3D TTE, and CMR. From 470 articles, 22 were selected, comprising 1017 patients in total. Among others, this included three 3D TTE, seven 2D harmonic TTE + contrast (2DHC), and seven CMR comparisons. The correlations and Bland-Altman limits of agreement varied for CMR but were stronger for 3D TTE and 2DHC. Our findings suggest that MUGA and CMR should not be used interchangeably whereas 3D TTE and 2DHC are appropriate alternatives following an initial MUGA scan. We propose a multimodality diagnostic imaging strategy for LVEF monitoring in patients undergoing cancer treatment.",,pdf:https://link.springer.com/content/pdf/10.1007/s11897-022-00544-3.pdf; doi:https://doi.org/10.1007/s11897-022-00544-3; html:https://europepmc.org/articles/PMC9177497; pdf:https://europepmc.org/articles/PMC9177497?pdf=render
-35922433,https://doi.org/10.1038/s41467-022-32219-x,Genome-wide associations of aortic distensibility suggest causality for aortic aneurysms and brain white matter hyperintensities.,"Francis CM, Futschik ME, Huang J, Bai W, Sargurupremraj M, Teumer A, Breteler MMB, Petretto E, Ho ASR, Amouyel P, Engelter ST, Bülow R, Völker U, Völzke H, Dörr M, Imtiaz MA, Aziz NA, Lohner V, Ware JS, Debette S, Elliott P, Dehghan A, Matthews PM.",,Nature communications,2022,2022-08-03,Y,,,,"Aortic dimensions and distensibility are key risk factors for aortic aneurysms and dissections, as well as for other cardiovascular and cerebrovascular diseases. We present genome-wide associations of ascending and descending aortic distensibility and area derived from cardiac magnetic resonance imaging (MRI) data of up to 32,590 Caucasian individuals in UK Biobank. We identify 102 loci (including 27 novel associations) tagging genes related to cardiovascular development, extracellular matrix production, smooth muscle cell contraction and heritable aortic diseases. Functional analyses highlight four signalling pathways associated with aortic distensibility (TGF-β, IGF, VEGF and PDGF). We identify distinct sex-specific associations with aortic traits. We develop co-expression networks associated with aortic traits and apply phenome-wide Mendelian randomization (MR-PheWAS), generating evidence for a causal role for aortic distensibility in development of aortic aneurysms. Multivariable MR suggests a causal relationship between aortic distensibility and cerebral white matter hyperintensities, mechanistically linking aortic traits and brain small vessel disease.",,pdf:https://www.nature.com/articles/s41467-022-32219-x.pdf; doi:https://doi.org/10.1038/s41467-022-32219-x; html:https://europepmc.org/articles/PMC9349177; pdf:https://europepmc.org/articles/PMC9349177?pdf=render
 31446403,https://doi.org/10.1136/bmjopen-2018-026677,Diagnosis and treatment for hyperuricemia and gout: a systematic review of clinical practice guidelines and consensus statements.,"Li Q, Li X, Wang J, Liu H, Kwong JS, Chen H, Li L, Chung SC, Shah A, Chen Y, An Z, Sun X, Hemingway H, Tian H, Li S.",,BMJ open,2019,2019-08-24,Y,Gout; Hyperuricemia; Systematic review; Clinical Practice Guideline,,,"<h4>Objectives</h4>Despite the publication of hundreds of trials on gout and hyperuricemia, management of these conditions remains suboptimal. We aimed to assess the quality and consistency of guidance documents for gout and hyperuricemia.<h4>Design</h4>Systematic review and quality assessment using the appraisal of guidelines for research and evaluation (AGREE) II methodology.<h4>Data sources</h4>PubMed and EMBASE (27 October 2016), two Chinese academic databases, eight guideline databases, and Google and Google scholar (July 2017).<h4>Eligibility criteria</h4>We included the latest version of international and national/regional clinical practice guidelines and consensus statements for diagnosis and/or treatment of hyperuricemia and gout, published in English or Chinese.<h4>Data extraction and synthesis</h4>Two reviewers independently screened searched items and extracted data. Four reviewers independently scored documents using AGREE II. Recommendations from all documents were tabulated and visualised in a coloured grid.<h4>Results</h4>Twenty-four guidance documents (16 clinical practice guidelines and 8 consensus statements) published between 2003 and 2017 were included. Included documents performed well in the domains of scope and purpose (median 85.4%, range 66.7%-100.0%) and clarity of presentation (median 79.2%, range 48.6%-98.6%), but unsatisfactory in applicability (median 10.9%, range 0.0%-66.7%) and editorial independence (median 28.1%, range 0.0%-83.3%). The 2017 British Society of Rheumatology guideline received the highest scores. Recommendations were concordant on the target serum uric acid level for long-term control, on some indications for urate-lowering therapy (ULT), and on the first-line drugs for ULT and for acute attack. Substantially inconsistent recommendations were provided for many items, especially for the timing of initiation of ULT and for treatment for asymptomatic hyperuricemia.<h4>Conclusions</h4>Methodological quality needs improvement in guidance documents on gout and hyperuricemia. Evidence for certain clinical questions is lacking, despite numerous trials in this field. Promoting standard guidance development methods and synthesising high-quality clinical evidence are potential approaches to reduce recommendation inconsistencies.<h4>Prospero registration number</h4>CRD42016046104.",,pdf:https://bmjopen.bmj.com/content/bmjopen/9/8/e026677.full.pdf; doi:https://doi.org/10.1136/bmjopen-2018-026677; html:https://europepmc.org/articles/PMC6720466; pdf:https://europepmc.org/articles/PMC6720466?pdf=render
+35922433,https://doi.org/10.1038/s41467-022-32219-x,Genome-wide associations of aortic distensibility suggest causality for aortic aneurysms and brain white matter hyperintensities.,"Francis CM, Futschik ME, Huang J, Bai W, Sargurupremraj M, Teumer A, Breteler MMB, Petretto E, Ho ASR, Amouyel P, Engelter ST, Bülow R, Völker U, Völzke H, Dörr M, Imtiaz MA, Aziz NA, Lohner V, Ware JS, Debette S, Elliott P, Dehghan A, Matthews PM.",,Nature communications,2022,2022-08-03,Y,,,,"Aortic dimensions and distensibility are key risk factors for aortic aneurysms and dissections, as well as for other cardiovascular and cerebrovascular diseases. We present genome-wide associations of ascending and descending aortic distensibility and area derived from cardiac magnetic resonance imaging (MRI) data of up to 32,590 Caucasian individuals in UK Biobank. We identify 102 loci (including 27 novel associations) tagging genes related to cardiovascular development, extracellular matrix production, smooth muscle cell contraction and heritable aortic diseases. Functional analyses highlight four signalling pathways associated with aortic distensibility (TGF-β, IGF, VEGF and PDGF). We identify distinct sex-specific associations with aortic traits. We develop co-expression networks associated with aortic traits and apply phenome-wide Mendelian randomization (MR-PheWAS), generating evidence for a causal role for aortic distensibility in development of aortic aneurysms. Multivariable MR suggests a causal relationship between aortic distensibility and cerebral white matter hyperintensities, mechanistically linking aortic traits and brain small vessel disease.",,pdf:https://www.nature.com/articles/s41467-022-32219-x.pdf; doi:https://doi.org/10.1038/s41467-022-32219-x; html:https://europepmc.org/articles/PMC9349177; pdf:https://europepmc.org/articles/PMC9349177?pdf=render
 31671849,https://doi.org/10.3390/ijerph16214178,Associations between the Home Physical Environment and Children's Home-Based Physical Activity and Sitting.,"Sheldrick MP, Maitland C, Mackintosh KA, Rosenberg M, Griffiths LJ, Fry R, Stratton G.",,International journal of environmental research and public health,2019,2019-10-29,Y,Families; Youth; Objective; Standing; House; Moderate-to-vigorous Physical Activity; Screen-time,,,"It is important to understand the correlates of children's physical activity (PA) and sitting at home, where children spend significant time. The home social environment has an important influence; however, much less is known about the home physical environment. Therefore, the study aimed to assess relationships between the physical environment and children's sitting and PA at home. In total, 235 child-parent dyads were included in the analyses. Children spent 67% of their time at home sitting. Linear regression analyses examined associations between physical home environmental factors obtained via an audit and children's (55% girl, 10.2 ± 0.7) objective PA and sitting at home. Following adjustment for socio-demographics and social environmental factors, an open plan living area (OPLA), musical instrument accessibility and availability, and perceived house size were negatively and positively associated, whereas media equipment accessibility and availability was positively and negatively associated with sitting and standing, respectively. Additionally, an OPLA was positively associated with total and moderate-to-vigorous PA. Furthermore, sitting breaks were positively associated with objective garden size and negatively associated with digital TV. The physical home environment may have an important influence on children's sitting, standing and PA at home; therefore, interventions that target this environment are needed.",,pdf:https://www.mdpi.com/1660-4601/16/21/4178/pdf?version=1573119054; doi:https://doi.org/10.3390/ijerph16214178; html:https://europepmc.org/articles/PMC6862192; pdf:https://europepmc.org/articles/PMC6862192?pdf=render
-38746859,https://doi.org/10.1183/23120541.00430-2023,"Prevalence, incidence and healthcare burden of eosinophilic granulomatosis with polyangiitis in the UK.","Hwee J, Harper L, Fu Q, Nirantharakumar K, Mu G, Jakes RW.",,ERJ open research,2024,2024-05-13,Y,,,,"<h4>Background</h4>Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare but serious disease characterised by the combination of small-to-medium vessel vasculitis, blood and tissue eosinophilia, and asthma and/or sinonasal disease. This study estimated the prevalence and incidence of diagnosed EGPA in the United Kingdom (UK), and described the demographics, clinical characteristics and healthcare resource utilisation (HCRU) of this population.<h4>Methods</h4>This retrospective longitudinal study of patients with newly diagnosed EGPA (index) (2005-2019) used the Clinical Practice Research Datalink AURUM and Hospital Episode Statistics databases. The primary outcomes were the annual prevalence (2005-2019) and incidence (2006-2019) of EGPA, and secondary outcomes included patient demographics and clinical characteristics, and HCRU in the year pre- and post-index (diagnosis).<h4>Results</h4>Populations of patients with EGPA comprised 940 prevalent cases and 502 incident cases, of which 377 were linked to Hospital Episode Statistics. EGPA prevalence increased from 22.7 to 45.6 cases per 1 000 000 (2005-2019), driven by patients aged ≥18 years. Incidence ranged from 2.3 to 4.0 per 1 000 000 person-years (2006-2019). Pre-index, the most common clinical symptoms were respiratory related, and the most common comorbidities were asthma (80.6%) and nasal polyps (32.1%). Post-index, 19.1% had an EGPA-related inpatient stay (median length of stay 11.0 days) and 38.7% had five or more oral corticosteroid (OCS) prescriptions with a mean OCS possession ratio per patient of 47.0%.<h4>Conclusions</h4>Although EGPA incidence in the UK remains relatively stable, prevalence is increasing, and HCRU and OCS use remain frequent, suggesting considerable healthcare burden for patients with EGPA.",,doi:https://doi.org/10.1183/23120541.00430-2023; html:https://europepmc.org/articles/PMC11089387; pdf:https://europepmc.org/articles/PMC11089387?pdf=render
-32234121,https://doi.org/10.2807/1560-7917.es.2020.25.12.2000256,"Estimating the infection and case fatality ratio for coronavirus disease (COVID-19) using age-adjusted data from the outbreak on the Diamond Princess cruise ship, February 2020.","Russell TW, Hellewell J, Jarvis CI, van Zandvoort K, Abbott S, Ratnayake R, CMMID COVID-19 working group, Flasche S, Eggo RM, Edmunds WJ, Kucharski AJ.",,Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin,2020,2020-03-01,Y,Coronavirus; outbreak; Severity; Asymptomatic; Case Fatality Ratio; Cruise Ship; Covid-19; Infection Fatality Ratio,"COVID-19, Improving Public Health","COVID-19, infection","Adjusting for delay from confirmation to death, we estimated case and infection fatality ratios (CFR, IFR) for coronavirus disease (COVID-19) on the Diamond Princess ship as 2.6% (95% confidence interval (CI): 0.89-6.7) and 1.3% (95% CI: 0.38-3.6), respectively. Comparing deaths on board with expected deaths based on naive CFR estimates from China, we estimated CFR and IFR in China to be 1.2% (95% CI: 0.3-2.7) and 0.6% (95% CI: 0.2-1.3), respectively.",,pdf:https://www.eurosurveillance.org/deliver/fulltext/eurosurveillance/25/12/eurosurv-25-12-3.pdf?itemId=%2Fcontent%2F10.2807%2F1560-7917.ES.2020.25.12.2000256&mimeType=pdf&containerItemId=content/eurosurveillance; doi:https://doi.org/10.2807/1560-7917.ES.2020.25.12.2000256; html:https://europepmc.org/articles/PMC7118348; pdf:https://europepmc.org/articles/PMC7118348?pdf=render
 33905476,https://doi.org/10.1093/cid/ciab192,Model-Based Geostatistical Methods Enable Efficient Design and Analysis of Prevalence Surveys for Soil-Transmitted Helminth Infection and Other Neglected Tropical Diseases.,"Johnson O, Fronterre C, Amoah B, Montresor A, Giorgi E, Midzi N, Mutsaka-Makuvaza MJ, Kargbo-Labor I, Hodges MH, Zhang Y, Okoyo C, Mwandawiro C, Minnery M, Diggle PJ.",,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2021,2021-06-01,Y,Geospatial Analysis; Prevalence Survey; Soil-transmitted Helminth Infection; Model-based Geostatistics; Control Of Neglected Tropical Diseases; Impact Survey,,,"Maps of the geographical variation in prevalence play an important role in large-scale programs for the control of neglected tropical diseases. Precontrol mapping is needed to establish the appropriate control intervention in each area of the country in question. Mapping is also needed postintervention to measure the success of control efforts. In the absence of comprehensive disease registries, mapping efforts can be informed by 2 kinds of data: empirical estimates of local prevalence obtained by testing individuals from a sample of communities within the geographical region of interest, and digital images of environmental factors that are predictive of local prevalence. In this article, we focus on the design and analysis of impact surveys, that is, prevalence surveys that are conducted postintervention with the aim of informing decisions on what further intervention, if any, is needed to achieve elimination of the disease as a public health problem. We show that geospatial statistical methods enable prevalence surveys to be designed and analyzed as efficiently as possible so as to make best use of hard-won field data. We use 3 case studies based on data from soil-transmitted helminth impact surveys in Kenya, Sierra Leone, and Zimbabwe to compare the predictive performance of model-based geostatistics with methods described in current World Health Organization (WHO) guidelines. In all 3 cases, we find that model-based geostatistics substantially outperforms the current WHO guidelines, delivering improved precision for reduced field-sampling effort. We argue from experience that similar improvements will hold for prevalence mapping of other neglected tropical diseases.",,pdf:https://academic.oup.com/cid/article-pdf/72/Supplement_3/S172/38618862/ciab192.pdf; doi:https://doi.org/10.1093/cid/ciab192; html:https://europepmc.org/articles/PMC8201574; pdf:https://europepmc.org/articles/PMC8201574?pdf=render
+38746859,https://doi.org/10.1183/23120541.00430-2023,"Prevalence, incidence and healthcare burden of eosinophilic granulomatosis with polyangiitis in the UK.","Hwee J, Harper L, Fu Q, Nirantharakumar K, Mu G, Jakes RW.",,ERJ open research,2024,2024-05-13,Y,,,,"<h4>Background</h4>Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare but serious disease characterised by the combination of small-to-medium vessel vasculitis, blood and tissue eosinophilia, and asthma and/or sinonasal disease. This study estimated the prevalence and incidence of diagnosed EGPA in the United Kingdom (UK), and described the demographics, clinical characteristics and healthcare resource utilisation (HCRU) of this population.<h4>Methods</h4>This retrospective longitudinal study of patients with newly diagnosed EGPA (index) (2005-2019) used the Clinical Practice Research Datalink AURUM and Hospital Episode Statistics databases. The primary outcomes were the annual prevalence (2005-2019) and incidence (2006-2019) of EGPA, and secondary outcomes included patient demographics and clinical characteristics, and HCRU in the year pre- and post-index (diagnosis).<h4>Results</h4>Populations of patients with EGPA comprised 940 prevalent cases and 502 incident cases, of which 377 were linked to Hospital Episode Statistics. EGPA prevalence increased from 22.7 to 45.6 cases per 1 000 000 (2005-2019), driven by patients aged ≥18 years. Incidence ranged from 2.3 to 4.0 per 1 000 000 person-years (2006-2019). Pre-index, the most common clinical symptoms were respiratory related, and the most common comorbidities were asthma (80.6%) and nasal polyps (32.1%). Post-index, 19.1% had an EGPA-related inpatient stay (median length of stay 11.0 days) and 38.7% had five or more oral corticosteroid (OCS) prescriptions with a mean OCS possession ratio per patient of 47.0%.<h4>Conclusions</h4>Although EGPA incidence in the UK remains relatively stable, prevalence is increasing, and HCRU and OCS use remain frequent, suggesting considerable healthcare burden for patients with EGPA.",,doi:https://doi.org/10.1183/23120541.00430-2023; html:https://europepmc.org/articles/PMC11089387; pdf:https://europepmc.org/articles/PMC11089387?pdf=render
 35802687,https://doi.org/10.1371/journal.pone.0270668,"Association between tocilizumab, sarilumab and all-cause mortality at 28 days in hospitalised patients with COVID-19: A network meta-analysis.","Godolphin PJ, Fisher DJ, Berry LR, Derde LPG, Diaz JV, Gordon AC, Lorenzi E, Marshall JC, Murthy S, Shankar-Hari M, Sterne JAC, Tierney JF, Vale CL.",,PloS one,2022,2022-07-08,Y,,,,"<h4>Background</h4>A recent prospective meta-analysis demonstrated that interleukin-6 antagonists are associated with lower all-cause mortality in hospitalised patients with COVID-19, compared with usual care or placebo. However, emerging evidence suggests that clinicians are favouring the use of tocilizumab over sarilumab. A new randomised comparison of these agents from the REMAP-CAP trial shows similar effects on in-hospital mortality. Therefore, we initiated a network meta-analysis, to estimate pairwise associations between tocilizumab, sarilumab and usual care or placebo with 28-day mortality, in COVID-19 patients receiving concomitant corticosteroids and ventilation, based on all available direct and indirect evidence.<h4>Methods</h4>Eligible trials randomised hospitalised patients with COVID-19 that compared tocilizumab or sarilumab with usual care or placebo in the prospective meta-analysis or that directly compared tocilizumab with sarilumab. Data were restricted to patients receiving corticosteroids and either non-invasive or invasive ventilation at randomisation. Pairwise associations between tocilizumab, sarilumab and usual care or placebo for all-cause mortality 28 days after randomisation were estimated using a frequentist contrast-based network meta-analysis of odds ratios (ORs), implementing multivariate fixed-effects models that assume consistency between the direct and indirect evidence.<h4>Findings</h4>One trial (REMAP-CAP) was identified that directly compared tocilizumab with sarilumab and supplied results on all-cause mortality at 28-days. This network meta-analysis was based on 898 eligible patients (278 deaths) from REMAP-CAP and 3710 eligible patients from 18 trials (1278 deaths) from the prospective meta-analysis. Summary ORs were similar for tocilizumab [0·82 [0·71-0·95, p = 0·008]] and sarilumab [0·80 [0·61-1·04, p = 0·09]] compared with usual care or placebo. The summary OR for 28-day mortality comparing tocilizumab with sarilumab was 1·03 [95%CI 0·81-1·32, p = 0·80]. The p-value for the global test of inconsistency was 0·28.<h4>Conclusions</h4>Administration of either tocilizumab or sarilumab was associated with lower 28-day all-cause mortality compared with usual care or placebo. The association is not dependent on the choice of interleukin-6 receptor antagonist.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0270668&type=printable; doi:https://doi.org/10.1371/journal.pone.0270668; html:https://europepmc.org/articles/PMC9269978; pdf:https://europepmc.org/articles/PMC9269978?pdf=render
 33588321,https://doi.org/10.1016/j.retram.2021.103276,Biological responses to COVID-19: Insights from physiological and blood biomarker profiles.,"Zakeri R, Pickles A, Carr E, Bean DM, O'Gallagher K, Kraljewic Z, Searle T, Shek A, Galloway JB, Teo JTH, Shah AM, Dobson RJB, Bendayan R.",,Current research in translational medicine,2021,2021-02-03,Y,Inflammation; Biomarkers; Classes; Sars-cov-2,,,"<h4>Background</h4>Understanding the spectrum and course of biological responses to coronavirus disease 2019 (COVID-19) may have important therapeutic implications. We sought to characterise biological responses among patients hospitalised with severe COVID-19 based on serial, routinely collected, physiological and blood biomarker values.<h4>Methods and findings</h4>We performed a retrospective cohort study of 1335 patients hospitalised with laboratory-confirmed COVID-19 (median age 70 years, 56 % male), between 1st March and 30th April 2020. Latent profile analysis was performed on serial physiological and blood biomarkers. Patient characteristics, comorbidities and rates of death and admission to intensive care, were compared between the latent classes. A five class solution provided the best fit. Class 1 ""Typical response"" exhibited a moderately elevated and rising C-reactive protein (CRP), stable lymphopaenia, and the lowest rates of 14-day adverse outcomes. Class 2 ""Rapid hyperinflammatory response"" comprised older patients, with higher admission white cell and neutrophil counts, which declined over time, accompanied by a very high and rising CRP and platelet count, and exibited the highest mortality risk. Class 3 ""Progressive inflammatory response"" was similar to the typical response except for a higher and rising CRP, though similar mortality rate. Class 4 ""Inflammatory response with kidney injury"" had prominent lymphopaenia, moderately elevated (and rising) CRP, and severe renal failure. Class 5 ""Hyperinflammatory response with kidney injury"" comprised older patients, with a very high and rising CRP, and severe renal failure that attenuated over time. Physiological measures did not substantially vary between classes at baseline or early admission.<h4>Conclusions and relevance</h4>Our identification of five distinct classes of biomarker profiles provides empirical evidence for heterogeneous biological responses to COVID-19. Early hyperinflammatory responses and kidney injury may signify unique pathophysiology that requires targeted therapy.",,doi:https://doi.org/10.1016/j.retram.2021.103276; doi:https://doi.org/10.1016/j.retram.2021.103276; html:https://europepmc.org/articles/PMC7857048; pdf:https://europepmc.org/articles/PMC7857048?pdf=render
 37538742,https://doi.org/10.1098/rsos.221469,Bayesian inference of polymerase dynamics over the exclusion process.,"Cavallaro M, Wang Y, Hebenstreit D, Dutta R.",,Royal Society open science,2023,2023-08-02,Y,Gene Expression; Bayesian Statistics; Particle Transport; Non-equilbrium Physics,,,"Transcription is a complex phenomenon that permits the conversion of genetic information into phenotype by means of an enzyme called RNA polymerase, which erratically moves along and scans the DNA template. We perform Bayesian inference over a paradigmatic mechanistic model of non-equilibrium statistical physics, i.e. the asymmetric exclusion processes in the hydrodynamic limit, assuming a Gaussian process prior for the polymerase progression rate as a latent variable. Our framework allows us to infer the speed of polymerases during transcription given their spatial distribution, while avoiding the explicit inversion of the system's dynamics. The results, which show processing rates strongly varying with genomic position and minor role of traffic-like congestion, may have strong implications for the understanding of gene expression.",,doi:https://doi.org/10.1098/rsos.221469; doi:https://doi.org/10.1098/rsos.221469; html:https://europepmc.org/articles/PMC10394410; pdf:https://europepmc.org/articles/PMC10394410?pdf=render
 37563195,https://doi.org/10.1038/s41598-023-38880-6,Locational memory of macrovessel vascular cells is transcriptionally imprinted.,"Spanjersberg TCF, Oosterhoff LA, Kruitwagen HS, van den Dungen NAM, Vernooij JCM, Asselbergs FW, Mokry M, Spee B, Harakalova M, van Steenbeek FG.",,Scientific reports,2023,2023-08-10,Y,,,,"Vascular pathologies show locational predisposition throughout the body; further insights into the transcriptomics basis of this vascular heterogeneity are needed. We analyzed transcriptomes from cultured endothelial cells and vascular smooth muscle cells from nine adult canine macrovessels: the aorta, coronary artery, vena cava, portal vein, femoral artery, femoral vein, saphenous vein, pulmonary vein, and pulmonary artery. We observed that organ-specific expression patterns persist in vitro, indicating that these genes are not regulated by blood flow or surrounding cell types but are likely fixed in the epigenetic memory. We further demonstrated the preserved location-specific expression of GATA4 protein in cultured cells and in the primary adult vessel. On a functional level, arterial and venous endothelial cells differed in vascular network morphology as the arterial networks maintained a higher complexity. Our findings prompt the rethinking of the extrapolation of results from single-origin endothelial cell systems.",,pdf:https://www.nature.com/articles/s41598-023-38880-6.pdf; doi:https://doi.org/10.1038/s41598-023-38880-6; html:https://europepmc.org/articles/PMC10415317; pdf:https://europepmc.org/articles/PMC10415317?pdf=render
 38725371,https://doi.org/10.1192/bjo.2024.23,"Contacts with primary and secondary healthcare before suicide by those under the care of mental health services: case-control, whole-population-based study using person-level linked routine data in Wales, UK during 2000-2015.","DelPozo-Banos M, Rodway C, Lee SC, Rouquette OY, Ibrahim S, Lloyd K, Appleby L, Kapur N, John A.",,BJPsych open,2024,2024-05-10,Y,Suicide; Mental Health Services; Primary Care; Secondary Care; Electronic Health Records,,,"<h4>Background</h4>People under the care of mental health services are at increased risk of suicide. Existing studies are small in scale and lack comparisons.<h4>Aims</h4>To identify opportunities for suicide prevention and underpinning data enhancement in people with recent contact with mental health services.<h4>Method</h4>This population-based study includes people who died by suicide in the year following a mental health services contact in Wales, 2001-2015 (cases), paired with similar patients who did not die by suicide (controls). We linked the National Confidential Inquiry into Suicide and Safety in Mental Health and the Suicide Information Database - Cymru with primary and secondary healthcare records. We present results of conditional logistic regression.<h4>Results</h4>We matched 1031 cases with 5155 controls. In the year before their death, 98.3% of cases were in contact with healthcare services, and 28.5% presented with self-harm. Cases had more emergency department contacts (odds ratio 2.4, 95% CI 2.1-2.7) and emergency hospital admissions (odds ratio 1.5, 95% CI 1.4-1.7), but fewer primary care contacts (odds ratio 0.7, 95% CI 0.6-0.9) and out-patient appointments (odds ratio 0.2, 95% CI 0.2-0.3) than controls. Odds ratios were larger in females than males for injury and poisoning (odds ratio: 3.3 (95% CI 2.5-4.5) <i>v.</i> 2.6 (95% CI 2.1-3.1)).<h4>Conclusions</h4>We may be missing existing opportunities to intervene, particularly in emergency departments and hospital admissions with self-harm presentations and with unattributed self-harm, especially in females. Prevention efforts should focus on strengthening routine care contacts, responding to emergency contacts and better self-harm care. There are benefits to enhancing clinical audit systems with routinely collected data.",,pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/4C20CD00C92C75F4F0B4FACD8418B244/S2056472424000231a.pdf/div-class-title-contacts-with-primary-and-secondary-healthcare-before-suicide-by-those-under-the-care-of-mental-health-services-case-control-whole-population-based-study-using-person-level-linked-routine-data-in-wales-uk-during-2000-2015-div.pdf; doi:https://doi.org/10.1192/bjo.2024.23; html:https://europepmc.org/articles/PMC11094447; pdf:https://europepmc.org/articles/PMC11094447?pdf=render
-38951929,https://doi.org/10.1186/s13063-024-08273-9,"Clinical trial results in context: comparison of baseline characteristics and outcomes of 38,510 RECOVERY trial participants versus a reference population of 346,271 people hospitalised with COVID-19 in England.","Pessoa-Amorim G, Goldacre R, Crichton C, Stevens W, Nunn M, King A, Murray D, Welsh R, Pinches H, Rees A, Morris EJA, Landray MJ, Haynes R, Horby P, Wallendszus K, Peto L, Campbell M, Harper C, Mafham M.",,Trials,2024,2024-06-29,Y,Recovery; Randomised Trials; Evidence Translation; Covid-19,,,"<h4>Background</h4>Randomised trials are essential to reliably assess medical interventions. Nevertheless, interpretation of such studies, particularly when considering absolute effects, is enhanced by understanding how the trial population may differ from the populations it aims to represent.<h4>Methods</h4>We compared baseline characteristics and mortality of RECOVERY participants recruited in England (n = 38,510) with a reference population hospitalised with COVID-19 in England (n = 346,271) from March 2020 to November 2021. We used linked hospitalisation and mortality data for both cohorts to extract demographics, comorbidity/frailty scores, and crude and age- and sex-adjusted 28-day all-cause mortality.<h4>Results</h4>Demographics of RECOVERY participants were broadly similar to the reference population, but RECOVERY participants were younger (mean age [standard deviation]: RECOVERY 62.6 [15.3] vs reference 65.7 [18.5] years) and less frequently female (37% vs 45%). Comorbidity and frailty scores were lower in RECOVERY, but differences were attenuated after age stratification. Age- and sex-adjusted 28-day mortality declined over time but was similar between cohorts across the study period (RECOVERY 23.7% [95% confidence interval: 23.3-24.1%]; vs reference 24.8% [24.6-25.0%]), except during the first pandemic wave in the UK (March-May 2020) when adjusted mortality was lower in RECOVERY.<h4>Conclusions</h4>Adjusted 28-day mortality in RECOVERY was similar to a nationwide reference population of patients admitted with COVID-19 in England during the same period but varied substantially over time in both cohorts. Therefore, the absolute effect estimates from RECOVERY were broadly applicable to the target population at the time but should be interpreted in the light of current mortality estimates.<h4>Trial registration</h4>ISRCTN50189673- Feb. 04, 2020, NCT04381936- May 11, 2020.",,doi:https://doi.org/10.1186/s13063-024-08273-9; doi:https://doi.org/10.1186/s13063-024-08273-9; html:https://europepmc.org/articles/PMC11218071; pdf:https://europepmc.org/articles/PMC11218071?pdf=render
 35916366,https://doi.org/10.7554/elife.76272,Integrated analyses of growth differentiation factor-15 concentration and cardiometabolic diseases in humans.,"Lemmelä S, Wigmore EM, Benner C, Havulinna AS, Ong RMY, Kempf T, Wollert KC, Blankenberg S, Zeller T, Peters JE, Salomaa V, Fritsch M, March R, Palotie A, Daly M, Butterworth AS, Kinnunen M, Paul DS, Matakidou A.",,eLife,2022,2022-08-02,Y,Human; Genetics; Obesity; Genomics; BMI; epidemiology; Causality; Global Health; Gdf15; Mendelian Randomisation,,,"Growth differentiation factor-15 (GDF15) is a stress response cytokine that is elevated in several cardiometabolic diseases and has attracted interest as a potential therapeutic target. To further explore the association of GDF15 with human disease, we conducted a broad study into the phenotypic and genetic correlates of GDF15 concentration in up to 14,099 individuals. Assessment of 772 traits across 6610 participants in FINRISK identified associations of GDF15 concentration with a range of phenotypes including all-cause mortality, cardiometabolic disease, respiratory diseases and psychiatric disorders, as well as inflammatory markers. A meta-analysis of genome-wide association studies (GWAS) of GDF15 concentration across three different assay platforms (n=14,099) confirmed significant heterogeneity due to a common missense variant (rs1058587; p.H202D) in <i>GDF15</i>, potentially due to epitope-binding artefacts. After conditioning on rs1058587, statistical fine mapping identified four independent putative causal signals at the locus. Mendelian randomisation (MR) analysis found evidence of a causal relationship between GDF15 concentration and high-density lipoprotein (HDL) but not body mass index (BMI). Using reverse MR, we identified a potential causal association of BMI on GDF15 (IVW p<sub>FDR</sub> = 0.0040). Taken together, our data derived from human population cohorts do not support a role for moderately elevated GDF15 concentrations as a causal factor in human cardiometabolic disease but support its role as a biomarker of metabolic stress.",,doi:https://doi.org/10.7554/elife.76272; doi:https://doi.org/10.7554/eLife.76272; html:https://europepmc.org/articles/PMC9391041; pdf:https://europepmc.org/articles/PMC9391041?pdf=render
-31479767,https://doi.org/10.1016/j.jaip.2019.08.030,Atopic Eczema in Adulthood and Risk of Depression and Anxiety: A Population-Based Cohort Study.,"Schonmann Y, Mansfield KE, Hayes JF, Abuabara K, Roberts A, Smeeth L, Langan SM.",,The journal of allergy and clinical immunology. In practice,2020,2019-08-31,Y,Depression; Anxiety; Atopic Eczema; Atopic Dermatitis; Severity; Population-based,Understanding the Causes of Disease,,"<h4>Background</h4>Atopic eczema is a common and debilitating condition associated with depression and anxiety, but the nature of this association remains unclear.<h4>Objective</h4>To explore the temporal relationship between atopic eczema and new depression/anxiety.<h4>Methods</h4>This matched cohort study used routinely collected data from the UK Clinical Practice Research Datalink, linked to hospital admissions data. We identified adults with atopic eczema (1998-2016) using a validated algorithm, and up to 5 individuals without atopic eczema matched on date of diagnosis, age, sex, and general practice. We estimated the hazard ratio (HR) for new depression/anxiety using stratified Cox regression to account for age, sex, calendar period, Index of Multiple Deprivation, glucocorticoid treatment, obesity, smoking, and harmful alcohol use.<h4>Results</h4>We identified 526,808 adults with atopic eczema who were matched to 2,569,030 without. Atopic eczema was associated with increased incidence of new depression (HR, 1.14; 99% CI, 1.12-1.16) and anxiety (HR, 1.17; 99% CI, 1.14-1.19). We observed a stronger effect of atopic eczema on depression with increasing atopic eczema severity (HR [99% CI] compared with no atopic eczema: mild, 1.10 [1.08-1.13]; moderate, 1.19 [1.15-1.23]; and severe, 1.26 [1.17-1.37]). A dose-response association, however, was less apparent for new anxiety diagnosis (HR [99% CI] compared with no atopic eczema: mild, 1.14 [1.11-1.18]; moderate, 1.21 [1.17-1.26]; and severe, 1.15; [1.05-1.25]).<h4>Conclusions</h4>Adults with atopic eczema are more likely to develop new depression and anxiety. For depression, we observed a dose-response relationship with atopic eczema severity.",,pdf:http://www.jaci-inpractice.org/article/S2213219819307536/pdf; doi:https://doi.org/10.1016/j.jaip.2019.08.030; html:https://europepmc.org/articles/PMC6947493; pdf:https://europepmc.org/articles/PMC6947493?pdf=render
 32685698,https://doi.org/10.12688/wellcomeopenres.15842.3,Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China.,"Endo A, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Abbott S, Kucharski AJ, Funk S.",,Wellcome open research,2020,2020-07-10,Y,Branching Process; Overdispersion; Novel Coronavirus; Covid-19; Sars-cov-2; Superspreading,,,"<b>Background:</b> A novel coronavirus disease (COVID-19) outbreak has now spread to a number of countries worldwide. While sustained transmission chains of human-to-human transmission suggest high basic reproduction number <i>R</i> <sub>0</sub>, variation in the number of secondary transmissions (often characterised by so-called superspreading events) may be large as some countries have observed fewer local transmissions than others. <b>Methods:</b> We quantified individual-level variation in COVID-19 transmission by applying a mathematical model to observed outbreak sizes in affected countries. We extracted the number of imported and local cases in the affected countries from the World Health Organization situation report and applied a branching process model where the number of secondary transmissions was assumed to follow a negative-binomial distribution. <b>Results:</b> Our model suggested a high degree of individual-level variation in the transmission of COVID-19. Within the current consensus range of <i>R</i> <sub>0</sub> (2-3), the overdispersion parameter <i>k</i> of a negative-binomial distribution was estimated to be around 0.1 (median estimate 0.1; 95% CrI: 0.05-0.2 for R0 = 2.5), suggesting that 80% of secondary transmissions may have been caused by a small fraction of infectious individuals (~10%). A joint estimation yielded likely ranges for <i>R</i> <sub>0</sub> and <i>k</i> (95% CrIs: <i>R</i> <sub>0</sub> 1.4-12; <i>k</i> 0.04-0.2); however, the upper bound of <i>R</i> <sub>0</sub> was not well informed by the model and data, which did not notably differ from that of the prior distribution. <b>Conclusions:</b> Our finding of a highly-overdispersed offspring distribution highlights a potential benefit to focusing intervention efforts on superspreading. As most infected individuals do not contribute to the expansion of an epidemic, the effective reproduction number could be drastically reduced by preventing relatively rare superspreading events.",,doi:https://doi.org/10.12688/wellcomeopenres.15842.3; html:https://europepmc.org/articles/PMC7338915; pdf:https://europepmc.org/articles/PMC7338915?pdf=render
+38951929,https://doi.org/10.1186/s13063-024-08273-9,"Clinical trial results in context: comparison of baseline characteristics and outcomes of 38,510 RECOVERY trial participants versus a reference population of 346,271 people hospitalised with COVID-19 in England.","Pessoa-Amorim G, Goldacre R, Crichton C, Stevens W, Nunn M, King A, Murray D, Welsh R, Pinches H, Rees A, Morris EJA, Landray MJ, Haynes R, Horby P, Wallendszus K, Peto L, Campbell M, Harper C, Mafham M.",,Trials,2024,2024-06-29,Y,Recovery; Randomised Trials; Evidence Translation; Covid-19,,,"<h4>Background</h4>Randomised trials are essential to reliably assess medical interventions. Nevertheless, interpretation of such studies, particularly when considering absolute effects, is enhanced by understanding how the trial population may differ from the populations it aims to represent.<h4>Methods</h4>We compared baseline characteristics and mortality of RECOVERY participants recruited in England (n = 38,510) with a reference population hospitalised with COVID-19 in England (n = 346,271) from March 2020 to November 2021. We used linked hospitalisation and mortality data for both cohorts to extract demographics, comorbidity/frailty scores, and crude and age- and sex-adjusted 28-day all-cause mortality.<h4>Results</h4>Demographics of RECOVERY participants were broadly similar to the reference population, but RECOVERY participants were younger (mean age [standard deviation]: RECOVERY 62.6 [15.3] vs reference 65.7 [18.5] years) and less frequently female (37% vs 45%). Comorbidity and frailty scores were lower in RECOVERY, but differences were attenuated after age stratification. Age- and sex-adjusted 28-day mortality declined over time but was similar between cohorts across the study period (RECOVERY 23.7% [95% confidence interval: 23.3-24.1%]; vs reference 24.8% [24.6-25.0%]), except during the first pandemic wave in the UK (March-May 2020) when adjusted mortality was lower in RECOVERY.<h4>Conclusions</h4>Adjusted 28-day mortality in RECOVERY was similar to a nationwide reference population of patients admitted with COVID-19 in England during the same period but varied substantially over time in both cohorts. Therefore, the absolute effect estimates from RECOVERY were broadly applicable to the target population at the time but should be interpreted in the light of current mortality estimates.<h4>Trial registration</h4>ISRCTN50189673- Feb. 04, 2020, NCT04381936- May 11, 2020.",,doi:https://doi.org/10.1186/s13063-024-08273-9; doi:https://doi.org/10.1186/s13063-024-08273-9; html:https://europepmc.org/articles/PMC11218071; pdf:https://europepmc.org/articles/PMC11218071?pdf=render
+31479767,https://doi.org/10.1016/j.jaip.2019.08.030,Atopic Eczema in Adulthood and Risk of Depression and Anxiety: A Population-Based Cohort Study.,"Schonmann Y, Mansfield KE, Hayes JF, Abuabara K, Roberts A, Smeeth L, Langan SM.",,The journal of allergy and clinical immunology. In practice,2020,2019-08-31,Y,Depression; Anxiety; Atopic Eczema; Atopic Dermatitis; Severity; Population-based,Understanding the Causes of Disease,,"<h4>Background</h4>Atopic eczema is a common and debilitating condition associated with depression and anxiety, but the nature of this association remains unclear.<h4>Objective</h4>To explore the temporal relationship between atopic eczema and new depression/anxiety.<h4>Methods</h4>This matched cohort study used routinely collected data from the UK Clinical Practice Research Datalink, linked to hospital admissions data. We identified adults with atopic eczema (1998-2016) using a validated algorithm, and up to 5 individuals without atopic eczema matched on date of diagnosis, age, sex, and general practice. We estimated the hazard ratio (HR) for new depression/anxiety using stratified Cox regression to account for age, sex, calendar period, Index of Multiple Deprivation, glucocorticoid treatment, obesity, smoking, and harmful alcohol use.<h4>Results</h4>We identified 526,808 adults with atopic eczema who were matched to 2,569,030 without. Atopic eczema was associated with increased incidence of new depression (HR, 1.14; 99% CI, 1.12-1.16) and anxiety (HR, 1.17; 99% CI, 1.14-1.19). We observed a stronger effect of atopic eczema on depression with increasing atopic eczema severity (HR [99% CI] compared with no atopic eczema: mild, 1.10 [1.08-1.13]; moderate, 1.19 [1.15-1.23]; and severe, 1.26 [1.17-1.37]). A dose-response association, however, was less apparent for new anxiety diagnosis (HR [99% CI] compared with no atopic eczema: mild, 1.14 [1.11-1.18]; moderate, 1.21 [1.17-1.26]; and severe, 1.15; [1.05-1.25]).<h4>Conclusions</h4>Adults with atopic eczema are more likely to develop new depression and anxiety. For depression, we observed a dose-response relationship with atopic eczema severity.",,pdf:http://www.jaci-inpractice.org/article/S2213219819307536/pdf; doi:https://doi.org/10.1016/j.jaip.2019.08.030; html:https://europepmc.org/articles/PMC6947493; pdf:https://europepmc.org/articles/PMC6947493?pdf=render
 34606520,https://doi.org/10.1371/journal.pmed.1003815,"COVID-19 vaccination in Sindh Province, Pakistan: A modelling study of health impact and cost-effectiveness.","Pearson CAB, Bozzani F, Procter SR, Davies NG, Huda M, Jensen HT, Keogh-Brown M, Khalid M, Sweeney S, Torres-Rueda S, CHiL COVID-19 Working Group, CMMID COVID-19 Working Group, Eggo RM, Vassall A, Jit M.",,PLoS medicine,2021,2021-10-04,Y,,,,"<h4>Background</h4>Multiple Coronavirus Disease 2019 (COVID-19) vaccines appear to be safe and efficacious, but only high-income countries have the resources to procure sufficient vaccine doses for most of their eligible populations. The World Health Organization has published guidelines for vaccine prioritisation, but most vaccine impact projections have focused on high-income countries, and few incorporate economic considerations. To address this evidence gap, we projected the health and economic impact of different vaccination scenarios in Sindh Province, Pakistan (population: 48 million).<h4>Methods and findings</h4>We fitted a compartmental transmission model to COVID-19 cases and deaths in Sindh from 30 April to 15 September 2020. We then projected cases, deaths, and hospitalisation outcomes over 10 years under different vaccine scenarios. Finally, we combined these projections with a detailed economic model to estimate incremental costs (from healthcare and partial societal perspectives), disability-adjusted life years (DALYs), and incremental cost-effectiveness ratio (ICER) for each scenario. We project that 1 year of vaccine distribution, at delivery rates consistent with COVAX projections, using an infection-blocking vaccine at $3/dose with 70% efficacy and 2.5-year duration of protection is likely to avert around 0.9 (95% credible interval (CrI): 0.9, 1.0) million cases, 10.1 (95% CrI: 10.1, 10.3) thousand deaths, and 70.1 (95% CrI: 69.9, 70.6) thousand DALYs, with an ICER of $27.9 per DALY averted from the health system perspective. Under a broad range of alternative scenarios, we find that initially prioritising the older (65+) population generally prevents more deaths. However, unprioritised distribution has almost the same cost-effectiveness when considering all outcomes, and both prioritised and unprioritised programmes can be cost-effective for low per-dose costs. High vaccine prices ($10/dose), however, may not be cost-effective, depending on the specifics of vaccine performance, distribution programme, and future pandemic trends. The principal drivers of the health outcomes are the fitted values for the overall transmission scaling parameter and disease natural history parameters from other studies, particularly age-specific probabilities of infection and symptomatic disease, as well as social contact rates. Other parameters are investigated in sensitivity analyses. This study is limited by model approximations, available data, and future uncertainty. Because the model is a single-population compartmental model, detailed impacts of nonpharmaceutical interventions (NPIs) such as household isolation cannot be practically represented or evaluated in combination with vaccine programmes. Similarly, the model cannot consider prioritising groups like healthcare or other essential workers. The model is only fitted to the reported case and death data, which are incomplete and not disaggregated by, e.g., age. Finally, because the future impact and implementation cost of NPIs are uncertain, how these would interact with vaccination remains an open question.<h4>Conclusions</h4>COVID-19 vaccination can have a considerable health impact and is likely to be cost-effective if more optimistic vaccine scenarios apply. Preventing severe disease is an important contributor to this impact. However, the advantage of prioritising older, high-risk populations is smaller in generally younger populations. This reduction is especially true in populations with more past transmission, and if the vaccine is likely to further impede transmission rather than just disease. Those conditions are typical of many low- and middle-income countries.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003815&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003815; html:https://europepmc.org/articles/PMC8523052; pdf:https://europepmc.org/articles/PMC8523052?pdf=render
-31747863,https://doi.org/10.1161/jaha.119.012551,"UVA and Seasonal Patterning of 56 370 Myocardial Infarctions Across Scotland, 2000-2011.","Mackay DF, Clemens TL, Hastie CE, Cherrie MPC, Dibben C, Pell JP.",,Journal of the American Heart Association,2019,2019-11-21,Y,Environmental factors; UV radiation; Myocardial infarction; epidemiology,"Improving Public Health, Understanding the Causes of Disease",,"Background Myocardial infarction exhibits seasonal patterning, with higher amplitude at increased latitude. Epidemiological evidence suggests that sunlight is protective against cardiovascular disease, independent of ambient temperature, but ultraviolet B-mediated vitamin D production has been discounted as causal. We aimed to determine whether ultraviolet A is associated with the seasonal patterning of myocardial infarction. Methods and Results Routine hospitalization data were used to determine monthly incidence of myocardial infarction in Scotland between 2000 and 2011. Small-area-level aggregated data were obtained on ambient temperature from the Meteorological Office and ultraviolet A and ultraviolet B irradiance from NASA satellites. Autoregressive distributed lag models were run for ultraviolet A and myocardial infarction, including adjustment for ambient temperature and ultraviolet B. Monthly incidence of myocardial infarction displayed winter peaks and summer troughs superimposed on the underlying trend, with a mean amplitude of 0.31 (95% CI: 0.21, 0.41) myocardial infarctions per 100 000 population per month. Ultraviolet A exposure was inversely associated with myocardial infarction independent of ambient temperature (coefficient, -0.05; 95% CI, -0.09, -0.01; <i>P</i>=0.015) and ultraviolet B UVB (coefficient, -0.05; 95% CI, -0.09, -0.02; <i>P</i>=0.004). Conclusions Further research is required to explore whether an ultraviolet-mediated mechanism different to vitamin D, such as nitric oxide-mediated vasodilatation, may play a causal role in the seasonal and geographical patterning of myocardial infarction.",,doi:https://doi.org/10.1161/jaha.119.012551; doi:https://doi.org/10.1161/JAHA.119.012551; html:https://europepmc.org/articles/PMC6912961; pdf:https://europepmc.org/articles/PMC6912961?pdf=render
-37198662,https://doi.org/10.1186/s13293-023-00516-9,Sex-based differences in cardiovascular proteomic profiles and their associations with adverse outcomes in patients with chronic heart failure.,"de Bakker M, Petersen TB, Akkerhuis KM, Harakalova M, Umans VA, Germans T, Caliskan K, Katsikis PD, van der Spek PJ, Suthahar N, de Boer RA, Rizopoulos D, Asselbergs FW, Boersma E, Kardys I.",,Biology of sex differences,2023,2023-05-17,Y,Proteomics; Sex differences; Heart Failure; Hfref,,,"<h4>Background</h4>Studies focusing on sex differences in circulating proteins in patients with heart failure with reduced ejection fraction (HFrEF) are scarce. Insight into sex-specific cardiovascular protein profiles and their associations with the risk of adverse outcomes may contribute to a better understanding of the pathophysiological processes involved in HFrEF. Moreover, it could provide a basis for the use of circulating protein measurements for prognostication in women and men, wherein the most relevant protein measurements are applied in each of the sexes.<h4>Methods</h4>In 382 patients with HFrEF, we performed tri-monthly blood sampling (median follow-up: 25 [13-31] months). We selected all baseline samples and two samples closest to the primary endpoint (PEP: composite of cardiovascular death, heart transplantation, left ventricular assist device implantation, and HF hospitalization) or censoring. We then applied an aptamer-based multiplex proteomic assay identifying 1105 proteins previously associated with cardiovascular disease. We used linear regression models and gene-enrichment analysis to study sex-based differences in baseline levels. We used time-dependent Cox models to study differences in the prognostic value of serially measured proteins. All models were adjusted for the MAGGIC HF mortality risk score and p-values for multiple testing.<h4>Results</h4>In 104 women and 278 men (mean age 62 and 64 years, respectively) cumulative PEP incidence at 30 months was 25% and 35%, respectively. At baseline, 55 (5%) out of the 1105 proteins were significantly different between women and men. The female protein profile was most strongly associated with extracellular matrix organization, while the male profile was dominated by regulation of cell death. The association of endothelin-1 (P<sub>interaction</sub> < 0.001) and somatostatin (P<sub>interaction</sub> = 0.040) with the PEP was modified by sex, independent of clinical characteristics. Endothelin-1 was more strongly associated with the PEP in men (HR 2.62 [95%CI, 1.98, 3.46], p < 0.001) compared to women (1.14 [1.01, 1.29], p = 0.036). Somatostatin was positively associated with the PEP in men (1.23 [1.10, 1.38], p < 0.001), but inversely associated in women (0.33 [0.12, 0.93], p = 0.036).<h4>Conclusion</h4>Baseline cardiovascular protein levels differ between women and men. However, the predictive value of repeatedly measured circulating proteins does not seem to differ except for endothelin-1 and somatostatin.",,pdf:https://bsd.biomedcentral.com/counter/pdf/10.1186/s13293-023-00516-9; doi:https://doi.org/10.1186/s13293-023-00516-9; html:https://europepmc.org/articles/PMC10193800; pdf:https://europepmc.org/articles/PMC10193800?pdf=render
 32814581,https://doi.org/10.1186/s12916-020-01687-7,Seasonal influenza vaccination in Kenya: an economic evaluation using dynamic transmission modelling.,"Dawa J, Emukule GO, Barasa E, Widdowson MA, Anzala O, van Leeuwen E, Baguelin M, Chaves SS, Eggo RM.",,BMC medicine,2020,2020-08-20,Y,Economic evaluation; Influenza vaccine; Cost-effectiveness; Low- And Middle-income Countries; Dynamic Transmission Model; Vaccine Timing; Vaccine Target Group,,,"<h4>Background</h4>There is substantial burden of seasonal influenza in Kenya, which led the government to consider introducing a national influenza vaccination programme. Given the cost implications of a nationwide programme, local economic evaluation data are needed to inform policy on the design and benefits of influenza vaccination. We set out to estimate the cost-effectiveness of seasonal influenza vaccination in Kenya.<h4>Methods</h4>We fitted an age-stratified dynamic transmission model to active surveillance data from patients with influenza from 2010 to 2018. Using a societal perspective, we developed a decision tree cost-effectiveness model and estimated the incremental cost-effectiveness ratio (ICER) per disability-adjusted life year (DALY) averted for three vaccine target groups: children 6-23 months (strategy I), 2-5 years (strategy II) and 6-14 years (strategy III) with either the Southern Hemisphere influenza vaccine (Strategy A) or Northern Hemisphere vaccine (Strategy B) or both (Strategy C: twice yearly vaccination campaigns, or Strategy D: year-round vaccination campaigns). We assessed cost-effectiveness by calculating incremental net monetary benefits (INMB) using a willingness-to-pay (WTP) threshold of 1-51% of the annual gross domestic product per capita ($17-$872).<h4>Results</h4>The mean number of infections across all ages was 2-15 million per year. When vaccination was well timed to influenza activity, the annual mean ICER per DALY averted for vaccinating children 6-23 months ranged between $749 and $1385 for strategy IA, $442 and $1877 for strategy IB, $678 and $4106 for strategy IC and $1147 and $7933 for strategy ID. For children 2-5 years, it ranged between $945 and $1573 for strategy IIA, $563 and $1869 for strategy IIB, $662 and $4085 for strategy IIC, and $1169 and $7897 for strategy IID. For children 6-14 years, it ranged between $923 and $3116 for strategy IIIA, $1005 and $2223 for strategy IIIB, $883 and $4727 for strategy IIIC and $1467 and $6813 for strategy IIID. Overall, no vaccination strategy was cost-effective at the minimum ($17) and median ($445) WTP thresholds. Vaccinating children 6-23 months once a year had the highest mean INMB value at $872 (WTP threshold upper limit); however, this strategy had very low probability of the highest net benefit.<h4>Conclusion</h4>Vaccinating children 6-23 months once a year was the most favourable vaccination option; however, the strategy is unlikely to be cost-effective given the current WTP thresholds.",,pdf:https://bmcmedicine.biomedcentral.com/track/pdf/10.1186/s12916-020-01687-7; doi:https://doi.org/10.1186/s12916-020-01687-7; html:https://europepmc.org/articles/PMC7438179; pdf:https://europepmc.org/articles/PMC7438179?pdf=render
+37198662,https://doi.org/10.1186/s13293-023-00516-9,Sex-based differences in cardiovascular proteomic profiles and their associations with adverse outcomes in patients with chronic heart failure.,"de Bakker M, Petersen TB, Akkerhuis KM, Harakalova M, Umans VA, Germans T, Caliskan K, Katsikis PD, van der Spek PJ, Suthahar N, de Boer RA, Rizopoulos D, Asselbergs FW, Boersma E, Kardys I.",,Biology of sex differences,2023,2023-05-17,Y,Proteomics; Sex differences; Heart Failure; Hfref,,,"<h4>Background</h4>Studies focusing on sex differences in circulating proteins in patients with heart failure with reduced ejection fraction (HFrEF) are scarce. Insight into sex-specific cardiovascular protein profiles and their associations with the risk of adverse outcomes may contribute to a better understanding of the pathophysiological processes involved in HFrEF. Moreover, it could provide a basis for the use of circulating protein measurements for prognostication in women and men, wherein the most relevant protein measurements are applied in each of the sexes.<h4>Methods</h4>In 382 patients with HFrEF, we performed tri-monthly blood sampling (median follow-up: 25 [13-31] months). We selected all baseline samples and two samples closest to the primary endpoint (PEP: composite of cardiovascular death, heart transplantation, left ventricular assist device implantation, and HF hospitalization) or censoring. We then applied an aptamer-based multiplex proteomic assay identifying 1105 proteins previously associated with cardiovascular disease. We used linear regression models and gene-enrichment analysis to study sex-based differences in baseline levels. We used time-dependent Cox models to study differences in the prognostic value of serially measured proteins. All models were adjusted for the MAGGIC HF mortality risk score and p-values for multiple testing.<h4>Results</h4>In 104 women and 278 men (mean age 62 and 64 years, respectively) cumulative PEP incidence at 30 months was 25% and 35%, respectively. At baseline, 55 (5%) out of the 1105 proteins were significantly different between women and men. The female protein profile was most strongly associated with extracellular matrix organization, while the male profile was dominated by regulation of cell death. The association of endothelin-1 (P<sub>interaction</sub> < 0.001) and somatostatin (P<sub>interaction</sub> = 0.040) with the PEP was modified by sex, independent of clinical characteristics. Endothelin-1 was more strongly associated with the PEP in men (HR 2.62 [95%CI, 1.98, 3.46], p < 0.001) compared to women (1.14 [1.01, 1.29], p = 0.036). Somatostatin was positively associated with the PEP in men (1.23 [1.10, 1.38], p < 0.001), but inversely associated in women (0.33 [0.12, 0.93], p = 0.036).<h4>Conclusion</h4>Baseline cardiovascular protein levels differ between women and men. However, the predictive value of repeatedly measured circulating proteins does not seem to differ except for endothelin-1 and somatostatin.",,pdf:https://bsd.biomedcentral.com/counter/pdf/10.1186/s13293-023-00516-9; doi:https://doi.org/10.1186/s13293-023-00516-9; html:https://europepmc.org/articles/PMC10193800; pdf:https://europepmc.org/articles/PMC10193800?pdf=render
+31747863,https://doi.org/10.1161/jaha.119.012551,"UVA and Seasonal Patterning of 56 370 Myocardial Infarctions Across Scotland, 2000-2011.","Mackay DF, Clemens TL, Hastie CE, Cherrie MPC, Dibben C, Pell JP.",,Journal of the American Heart Association,2019,2019-11-21,Y,Environmental factors; UV radiation; Myocardial infarction; epidemiology,"Improving Public Health, Understanding the Causes of Disease",,"Background Myocardial infarction exhibits seasonal patterning, with higher amplitude at increased latitude. Epidemiological evidence suggests that sunlight is protective against cardiovascular disease, independent of ambient temperature, but ultraviolet B-mediated vitamin D production has been discounted as causal. We aimed to determine whether ultraviolet A is associated with the seasonal patterning of myocardial infarction. Methods and Results Routine hospitalization data were used to determine monthly incidence of myocardial infarction in Scotland between 2000 and 2011. Small-area-level aggregated data were obtained on ambient temperature from the Meteorological Office and ultraviolet A and ultraviolet B irradiance from NASA satellites. Autoregressive distributed lag models were run for ultraviolet A and myocardial infarction, including adjustment for ambient temperature and ultraviolet B. Monthly incidence of myocardial infarction displayed winter peaks and summer troughs superimposed on the underlying trend, with a mean amplitude of 0.31 (95% CI: 0.21, 0.41) myocardial infarctions per 100 000 population per month. Ultraviolet A exposure was inversely associated with myocardial infarction independent of ambient temperature (coefficient, -0.05; 95% CI, -0.09, -0.01; <i>P</i>=0.015) and ultraviolet B UVB (coefficient, -0.05; 95% CI, -0.09, -0.02; <i>P</i>=0.004). Conclusions Further research is required to explore whether an ultraviolet-mediated mechanism different to vitamin D, such as nitric oxide-mediated vasodilatation, may play a causal role in the seasonal and geographical patterning of myocardial infarction.",,doi:https://doi.org/10.1161/jaha.119.012551; doi:https://doi.org/10.1161/JAHA.119.012551; html:https://europepmc.org/articles/PMC6912961; pdf:https://europepmc.org/articles/PMC6912961?pdf=render
 PMC11210061,https://doi.org/,Plain language summary of a study looking at the effect of empagliflozin treatment in patients with chronic kidney disease,,,Clinical kidney journal,2024,2024-03-07,Y,,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11210061/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11210061/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC11210061; pdf:https://europepmc.org/articles/PMC11210061?pdf=render
-37993464,https://doi.org/10.1038/s41467-023-43434-5,Structure of the N-RNA/P interface indicates mode of L/P recruitment to the nucleocapsid of human metapneumovirus.,"Whitehead JD, Decool H, Leyrat C, Carrique L, Fix J, Eléouët JF, Galloux M, Renner M.",,Nature communications,2023,2023-11-22,Y,,,,"Human metapneumovirus (HMPV) is a major cause of respiratory illness in young children. The HMPV polymerase (L) binds an obligate cofactor, the phosphoprotein (P). During replication and transcription, the L/P complex traverses the viral RNA genome, which is encapsidated within nucleoproteins (N). An essential interaction between N and a C-terminal region of P tethers the L/P polymerase to the template. This N-P interaction is also involved in the formation of cytoplasmic viral factories in infected cells, called inclusion bodies. To define how the polymerase component P recognizes N-encapsidated RNA (N-RNA) we employed cryogenic electron microscopy (cryo-EM) and molecular dynamics simulations, coupled to activity assays and imaging of inclusion bodies in cells. We report a 2.9 Å resolution structure of a triple-complex between multimeric N, bound to both RNA and the C-terminal region of P. Furthermore, we also present cryo-EM structures of assembled N in different oligomeric states, highlighting the plasticity of N. Combined with our functional assays, these structural data delineate in molecular detail how P attaches to N-RNA whilst retaining substantial conformational dynamics. Moreover, the N-RNA-P triple complex structure provides a molecular blueprint for the design of therapeutics to potentially disrupt the attachment of L/P to its template.",,pdf:https://www.nature.com/articles/s41467-023-43434-5.pdf; doi:https://doi.org/10.1038/s41467-023-43434-5; html:https://europepmc.org/articles/PMC10665349; pdf:https://europepmc.org/articles/PMC10665349?pdf=render
 35410933,https://doi.org/10.1136/bmjopen-2021-057885,"Non-pharmacological therapies for postviral syndromes, including Long COVID: a systematic review and meta-analysis protocol.","Chandan JS, Brown K, Simms-Williams N, Camaradou J, Bashir N, Heining D, Aiyegbusi OL, Turner G, Cruz Rivera S, Hotham R, Nirantharakumar K, Sivan M, Khunti K, Raindi D, Marwaha S, Hughes SE, McMullan C, Calvert M, Haroon S.",,BMJ open,2022,2022-04-11,Y,Infectious diseases; Rehabilitation Medicine; Covid-19,,,"<h4>Introduction</h4>Postviral syndromes (PVS) describe the sustained presence of symptoms following an acute viral infection, for months or even years. Exposure to the SARS-CoV-2 virus and subsequent development of COVID-19 has shown to have similar effects with individuals continuing to exhibit symptoms for greater than 12 weeks. The sustained presence of symptoms is variably referred to as 'post COVID-19 syndrome', 'post-COVID condition' or more commonly 'Long COVID'. Knowledge of the long-term health impacts and treatments for Long COVID are evolving. To minimise overlap with existing work in the field exploring treatments of Long COVID, we have only chosen to focus on non-pharmacological treatments.<h4>Aims</h4>This review aims to summarise the effectiveness of non-pharmacological treatments for PVS, including Long COVID. A secondary aim is to summarise the symptoms and health impacts associated with PVS in individuals recruited to treatment studies.<h4>Methods and analysis</h4>Primary electronic searches will be performed in bibliographic databases including: Embase, MEDLINE, PyscINFO, CINAHL and MedRxiv from 1 January 2001 to 29 October 2021. At least two independent reviewers will screen each study for inclusion and data will be extracted from all eligible studies onto a data extraction form. The quality of all included studies will be assessed using Cochrane risk of bias tools and the Newcastle-Ottawa grading system. Non-pharmacological treatments for PVS and Long COVID will be narratively summarised and effect estimates will be pooled using random effects meta-analysis where there is sufficient methodological homogeneity. The symptoms and health impacts reported in the included studies on non-pharmacological interventions will be extracted and narratively reported.<h4>Ethics and dissemination</h4>This systematic review does not require ethical approval. The findings from this study will be submitted for peer-reviewed publication, shared at conference presentations and disseminated to both clinical and patient groups.<h4>Prospero registration number</h4>The review will adhere to this protocol which has also been registered with PROSPERO (CRD42021282074).",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/4/e057885.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-057885; html:https://europepmc.org/articles/PMC9002258; pdf:https://europepmc.org/articles/PMC9002258?pdf=render
+37993464,https://doi.org/10.1038/s41467-023-43434-5,Structure of the N-RNA/P interface indicates mode of L/P recruitment to the nucleocapsid of human metapneumovirus.,"Whitehead JD, Decool H, Leyrat C, Carrique L, Fix J, Eléouët JF, Galloux M, Renner M.",,Nature communications,2023,2023-11-22,Y,,,,"Human metapneumovirus (HMPV) is a major cause of respiratory illness in young children. The HMPV polymerase (L) binds an obligate cofactor, the phosphoprotein (P). During replication and transcription, the L/P complex traverses the viral RNA genome, which is encapsidated within nucleoproteins (N). An essential interaction between N and a C-terminal region of P tethers the L/P polymerase to the template. This N-P interaction is also involved in the formation of cytoplasmic viral factories in infected cells, called inclusion bodies. To define how the polymerase component P recognizes N-encapsidated RNA (N-RNA) we employed cryogenic electron microscopy (cryo-EM) and molecular dynamics simulations, coupled to activity assays and imaging of inclusion bodies in cells. We report a 2.9 Å resolution structure of a triple-complex between multimeric N, bound to both RNA and the C-terminal region of P. Furthermore, we also present cryo-EM structures of assembled N in different oligomeric states, highlighting the plasticity of N. Combined with our functional assays, these structural data delineate in molecular detail how P attaches to N-RNA whilst retaining substantial conformational dynamics. Moreover, the N-RNA-P triple complex structure provides a molecular blueprint for the design of therapeutics to potentially disrupt the attachment of L/P to its template.",,pdf:https://www.nature.com/articles/s41467-023-43434-5.pdf; doi:https://doi.org/10.1038/s41467-023-43434-5; html:https://europepmc.org/articles/PMC10665349; pdf:https://europepmc.org/articles/PMC10665349?pdf=render
 37180793,https://doi.org/10.3389/fcvm.2023.1136764,Diabetes and heart failure associations in women and men: Results from the MORGAM consortium.,"Chadalavada S, Reinikainen J, Andersson J, Di Castelnuovo A, Iacoviello L, Jousilahti P, Kårhus LL, Linneberg A, Söderberg S, Tunstall-Pedoe H, Lekadir K, Aung N, Jensen MT, Kuulasmaa K, Niiranen TJ, Petersen SE.",,Frontiers in cardiovascular medicine,2023,2023-04-25,Y,Diabetes; Sex differences; epidemiology; Heart Failure; Morgam,,,"<h4>Background</h4>Diabetes and its cardiovascular complications are a growing concern worldwide. Recently, some studies have demonstrated that relative risk of heart failure (HF) is higher in women with type 1 diabetes (T1DM) than in men. This study aims to validate these findings in cohorts representing five countries across Europe.<h4>Methods</h4>This study includes 88,559 (51.8% women) participants, 3,281 (46.3% women) of whom had diabetes at baseline. Survival analysis was performed with the outcomes of interest being death and HF with a follow-up time of 12 years. Sub-group analysis according to sex and type of diabetes was also performed for the HF outcome.<h4>Results</h4>6,460 deaths were recorded, of which 567 were amongst those with diabetes. Additionally, HF was diagnosed in 2,772 individuals (446 with diabetes). A multivariable Cox proportional hazard analysis showed that there was an increased risk of death and HF (hazard ratio (HR) of 1.73 [1.58-1.89] and 2.12 [1.91-2.36], respectively) when comparing those with diabetes and those without. The HR for HF was 6.72 [2.75-16.41] for women with T1DM vs. 5.80 [2.72-12.37] for men with T1DM, but the interaction term for sex differences was insignificant (<i>p</i> for interaction 0.45). There was no significant difference in the relative risk of HF between men and women when both types of diabetes were combined (HR 2.22 [1.93-2.54] vs. 1.99 [1.67-2.38] respectively, <i>p</i> for interaction 0.80).<h4>Conclusion</h4>Diabetes is associated with increased risks of death and heart failure, and there was no difference in relative risk according to sex.",,pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2023.1136764/pdf; doi:https://doi.org/10.3389/fcvm.2023.1136764; html:https://europepmc.org/articles/PMC10167048; pdf:https://europepmc.org/articles/PMC10167048?pdf=render
-36273236,https://doi.org/10.1038/s41746-022-00705-7,"Automated clinical coding: what, why, and where we are?","Dong H, Falis M, Whiteley W, Alex B, Matterson J, Ji S, Chen J, Wu H.",,NPJ digital medicine,2022,2022-10-22,Y,,,,"Clinical coding is the task of transforming medical information in a patient's health records into structured codes so that they can be used for statistical analysis. This is a cognitive and time-consuming task that follows a standard process in order to achieve a high level of consistency. Clinical coding could potentially be supported by an automated system to improve the efficiency and accuracy of the process. We introduce the idea of automated clinical coding and summarise its challenges from the perspective of Artificial Intelligence (AI) and Natural Language Processing (NLP), based on the literature, our project experience over the past two and half years (late 2019-early 2022), and discussions with clinical coding experts in Scotland and the UK. Our research reveals the gaps between the current deep learning-based approach applied to clinical coding and the need for explainability and consistency in real-world practice. Knowledge-based methods that represent and reason the standard, explainable process of a task may need to be incorporated into deep learning-based methods for clinical coding. Automated clinical coding is a promising task for AI, despite the technical and organisational challenges. Coders are needed to be involved in the development process. There is much to achieve to develop and deploy an AI-based automated system to support coding in the next five years and beyond.",,pdf:https://www.nature.com/articles/s41746-022-00705-7.pdf; doi:https://doi.org/10.1038/s41746-022-00705-7; html:https://europepmc.org/articles/PMC9588058; pdf:https://europepmc.org/articles/PMC9588058?pdf=render
 33779119,https://doi.org/10.1002/ejhf.2169,Identification of distinct phenotypic clusters in heart failure with preserved ejection fraction.,"Uijl A, Savarese G, Vaartjes I, Dahlström U, Brugts JJ, Linssen GCM, van Empel V, Brunner-La Rocca HP, Asselbergs FW, Lund LH, Hoes AW, Koudstaal S.",,European journal of heart failure,2021,2021-05-01,Y,Treatment; Phenotyping; Clusters; Latent Class Analysis; Comorbidities; Heart Failure With Preserved Ejection Fraction; External Validation,,,"<h4>Aims</h4>We aimed to derive and validate clinically useful clusters of patients with heart failure with preserved ejection fraction (HFpEF; left ventricular ejection fraction ≥50%).<h4>Methods and results</h4>We derived a cluster model from 6909 HFpEF patients from the Swedish Heart Failure Registry (SwedeHF) and externally validated this in 2153 patients from the Chronic Heart Failure ESC-guideline based Cardiology practice Quality project (CHECK-HF) registry. In SwedeHF, the median age was 80 [interquartile range 72-86] years, 52% of patients were female and most frequent comorbidities were hypertension (82%), atrial fibrillation (68%), and ischaemic heart disease (48%). Latent class analysis identified five distinct clusters: cluster 1 (10% of patients) were young patients with a low comorbidity burden and the highest proportion of implantable devices; cluster 2 (30%) patients had atrial fibrillation, hypertension without diabetes; cluster 3 (25%) patients were the oldest with many cardiovascular comorbidities and hypertension; cluster 4 (15%) patients had obesity, diabetes and hypertension; and cluster 5 (20%) patients were older with ischaemic heart disease, hypertension and renal failure and were most frequently prescribed diuretics. The clusters were reproduced in the CHECK-HF cohort. Patients in cluster 1 had the best prognosis, while patients in clusters 3 and 5 had the worst age- and sex-adjusted prognosis.<h4>Conclusions</h4>Five distinct clusters of HFpEF patients were identified that differed in clinical characteristics, heart failure drug therapy and prognosis. These results confirm the heterogeneity of HFpEF and form a basis for tailoring trial design to individualized drug therapy in HFpEF patients.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ejhf.2169; doi:https://doi.org/10.1002/ejhf.2169; html:https://europepmc.org/articles/PMC8359985; pdf:https://europepmc.org/articles/PMC8359985?pdf=render
+36273236,https://doi.org/10.1038/s41746-022-00705-7,"Automated clinical coding: what, why, and where we are?","Dong H, Falis M, Whiteley W, Alex B, Matterson J, Ji S, Chen J, Wu H.",,NPJ digital medicine,2022,2022-10-22,Y,,,,"Clinical coding is the task of transforming medical information in a patient's health records into structured codes so that they can be used for statistical analysis. This is a cognitive and time-consuming task that follows a standard process in order to achieve a high level of consistency. Clinical coding could potentially be supported by an automated system to improve the efficiency and accuracy of the process. We introduce the idea of automated clinical coding and summarise its challenges from the perspective of Artificial Intelligence (AI) and Natural Language Processing (NLP), based on the literature, our project experience over the past two and half years (late 2019-early 2022), and discussions with clinical coding experts in Scotland and the UK. Our research reveals the gaps between the current deep learning-based approach applied to clinical coding and the need for explainability and consistency in real-world practice. Knowledge-based methods that represent and reason the standard, explainable process of a task may need to be incorporated into deep learning-based methods for clinical coding. Automated clinical coding is a promising task for AI, despite the technical and organisational challenges. Coders are needed to be involved in the development process. There is much to achieve to develop and deploy an AI-based automated system to support coding in the next five years and beyond.",,pdf:https://www.nature.com/articles/s41746-022-00705-7.pdf; doi:https://doi.org/10.1038/s41746-022-00705-7; html:https://europepmc.org/articles/PMC9588058; pdf:https://europepmc.org/articles/PMC9588058?pdf=render
 37735103,https://doi.org/10.1136/bmjresp-2023-001895,"Preterm birth, birth weight, infant weight gain and their associations with childhood asthma and spirometry: a cross-sectional observational study in Nairobi, Kenya.","Meme H, Amukoye E, Bowyer C, Chakaya J, Dobson R, Fuld J, Gray CM, Kiplimo R, Lesosky M, Mortimer K, Ndombi A, Obasi A, Orina F, Quint JK, Semple S, West SE, Zurba L, Devereux G.",,BMJ open respiratory research,2023,2023-09-01,Y,Asthma; Paediatric Lung Disaese; Asthma Epidemiology,,,"<h4>Background</h4>In sub-Saharan Africa, the origins of asthma and high prevalence of abnormal lung function remain unclear. In high-income countries (HICs), associations between birth measurements and childhood asthma and lung function highlight the importance of antenatal and early life factors in the aetiology of asthma and abnormal lung function in children. We present here the first study in sub-Saharan Africa to relate birth characteristics to both childhood respiratory symptoms and lung function.<h4>Methods</h4>Children attending schools in two socioeconomically contrasting but geographically close areas of Nairobi, Kenya, were recruited to a cross-sectional study of childhood asthma and lung function. Questionnaires quantified respiratory symptoms and preterm birth; lung function was measured by spirometry; and parents were invited to bring the child's immunisation booklet containing records of birth weight and serial weights in the first year.<h4>Results</h4>2373 children participated, 52% girls, median age (IQR), 10 years (8-13). Spirometry data were available for 1622. Child immunisation booklets were available for 500 and birth weight and infant weight gain data were available for 323 and 494 children, respectively. In multivariable analyses, preterm birth was associated with the childhood symptoms 'wheeze in the last 12 months'; OR 1.64, (95% CI 1.03 to 2.62), p=0.038; and 'trouble breathing' 3.18 (95% CI 2.27 to 4.45), p<0.001. Birth weight (kg) was associated with forced expiratory volume in 1 s z-score, regression coefficient (β) 0.30 (0.08, 0.52), p=0.008, FVC z-score 0.29 (95% CI 0.08 to 0.51); p=0.008 and restricted spirometry, OR 0.11 (95% CI 0.02 to 0.78), p=0.027.<h4>Conclusion</h4>These associations are in keeping with those in HICs and highlight antenatal factors in the aetiology of asthma and lung function abnormalities in sub-Saharan Africa.",,pdf:https://bmjopenrespres.bmj.com/content/bmjresp/10/1/e001895.full.pdf; doi:https://doi.org/10.1136/bmjresp-2023-001895; html:https://europepmc.org/articles/PMC10514609; pdf:https://europepmc.org/articles/PMC10514609?pdf=render
 33939952,https://doi.org/10.1016/s0140-6736(21)00949-1,COVID-19 and disparities affecting ethnic minorities.,"Morales DR, Ali SN.",,"Lancet (London, England)",2021,2021-04-30,Y,,,,,,pdf:http://www.thelancet.com/article/S0140673621009491/pdf; doi:https://doi.org/10.1016/S0140-6736(21)00949-1; html:https://europepmc.org/articles/PMC9755653; pdf:https://europepmc.org/articles/PMC9755653?pdf=render
 34870256,https://doi.org/10.1016/j.lanepe.2021.100267,Optimising health and economic impacts of COVID-19 vaccine prioritisation strategies in the WHO European Region: a mathematical modelling study.,"Liu Y, Sandmann FG, Barnard RC, Pearson CAB, Pastore R, Pebody R, Flasche S, Jit M.",,The Lancet regional health. Europe,2022,2021-11-30,Y,Europe; Health Economics; Mathematical Modelling; Policy Evaluation; Vaccine Policy; Multicountry Analysis; Covid-19,,,"<h4>Background</h4>Countries in the World Health Organization (WHO) European Region differ in terms of the COVID-19 vaccine supply conditions. We evaluated the health and economic impact of different age-based vaccine prioritisation strategies across this demographically and socio-economically diverse region.<h4>Methods</h4>We fitted age-specific compartmental models to the reported daily COVID-19 mortality in 2020 to inform the immunity level before vaccine roll-out. Models capture country-specific differences in population structures, contact patterns, epidemic history, life expectancy, and GDP per capita.We examined four strategies that prioritise: all adults (V+), younger (20-59 year-olds) followed by older adults (60+) (V20), older followed by younger adults (V60), and the oldest adults (75+) (V75) followed by incrementally younger age groups. We explored four roll-out scenarios (R1-4) - the slowest scenario (R1) reached 30% coverage by December 2022 and the fastest (R4) 80% by December 2021. Five decision-making metrics were summarised over 2021-22: mortality, morbidity, and losses in comorbidity-adjusted life expectancy, comorbidity- and quality-adjusted life years, and human capital. Six vaccine profiles were tested - the highest performing vaccine has 95% efficacy against both infection and disease, and the lowest 50% against diseases and 0% against infection.<h4>Findings</h4>Of the 20 decision-making metrics and roll-out scenario combinations, the same optimal strategy applied to all countries in only one combination; V60 was more or similarly desirable than V75 in 19 combinations. Of the 38 countries with fitted models, 11-37 countries had variable optimal strategies by decision-making metrics or roll-out scenarios. There are greater benefits in prioritising older adults when roll-out is slow and when vaccine profiles are less favourable.<h4>Interpretation</h4>The optimal age-based vaccine prioritisation strategies were sensitive to country characteristics, decision-making metrics, and roll-out speeds. A prioritisation strategy involving more age-based stages (V75) does not necessarily lead to better health and economic outcomes than targeting broad age groups (V60). Countries expecting a slow vaccine roll-out may particularly benefit from prioritising older adults.<h4>Funding</h4>World Health Organization, Bill and Melinda Gates Foundation, the Medical Research Council (United Kingdom), the National Institute of Health Research (United Kingdom), the European Commission, the Foreign, Commonwealth and Development Office (United Kingdom), Wellcome Trust.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8288152; doi:https://doi.org/10.1016/j.lanepe.2021.100267; html:https://europepmc.org/articles/PMC8629724; pdf:https://europepmc.org/articles/PMC8629724?pdf=render
-31994239,https://doi.org/10.1002/bimj.201900041,Estimating treatment effects with partially observed covariates using outcome regression with missing indicators.,"Blake HA, Leyrat C, Mansfield KE, Tomlinson LA, Carpenter J, Williamson EJ.",,Biometrical journal. Biometrische Zeitschrift,2020,2020-01-29,N,Average Treatment Effect; Outcome Regression; Missing Covariate Data; Missing Indicator; Missing Confounder Data,,,"Missing data is a common issue in research using observational studies to investigate the effect of treatments on health outcomes. When missingness occurs only in the covariates, a simple approach is to use missing indicators to handle the partially observed covariates. The missing indicator approach has been criticized for giving biased results in outcome regression. However, recent papers have suggested that the missing indicator approach can provide unbiased results in propensity score analysis under certain assumptions. We consider assumptions under which the missing indicator approach can provide valid inferences, namely, (1) no unmeasured confounding within missingness patterns; either (2a) covariate values of patients with missing data were conditionally independent of treatment or (2b) these values were conditionally independent of outcome; and (3) the outcome model is correctly specified: specifically, the true outcome model does not include interactions between missing indicators and fully observed covariates. We prove that, under the assumptions above, the missing indicator approach with outcome regression can provide unbiased estimates of the average treatment effect. We use a simulation study to investigate the extent of bias in estimates of the treatment effect when the assumptions are violated and we illustrate our findings using data from electronic health records. In conclusion, the missing indicator approach can provide valid inferences for outcome regression, but the plausibility of its assumptions must first be considered carefully.",,pdf:https://researchonline.lshtm.ac.uk/id/eprint/4655332/1/Estimating-treatment-effects-with-partially-observed-covariates-using-outcome-regression-with-missing-indicators.pdf; doi:https://doi.org/10.1002/bimj.201900041
-31282950,https://doi.org/10.1001/jamaneurol.2019.1812,Association Between Idiopathic Intracranial Hypertension and Risk of Cardiovascular Diseases in Women in the United Kingdom.,"Adderley NJ, Subramanian A, Nirantharakumar K, Yiangou A, Gokhale KM, Mollan SP, Sinclair AJ.",,JAMA neurology,2019,2019-09-01,Y,,Understanding the Causes of Disease,,"<h4>Importance</h4>Cardiovascular disease (CVD) risk has not been previously evaluated in a large matched cohort study in idiopathic intracranial hypertension (IIH).<h4>Objectives</h4>To estimate the risk of composite cardiovascular events, heart failure, ischemic heart disease, stroke/transient ischemic attack (TIA), type 2 diabetes, and hypertension in women with idiopathic intracranial hypertension and compare it with the risk in women, matched on body mass index (BMI) and age, without the condition; and to evaluate the prevalence and incidence of IIH.<h4>Design, setting, and participants</h4>This population-based matched controlled cohort study used 28 years of data, from January 1, 1990, to January 17, 2018, from The Health Improvement Network (THIN), an anonymized, nationally representative electronic medical records database in the United Kingdom. All female patients aged 16 years or older were eligible for inclusion. Female patients with IIH (n = 2760) were included and randomly matched with up to 10 control patients (n = 27 125) by BMI and age.<h4>Main outcomes and measures</h4>Adjusted hazard ratios (aHRs) of cardiovascular outcomes were calculated using Cox regression models. The primary outcome was a composite of any CVD (heart failure, ischemic heart disease, and stroke/TIA), and the secondary outcomes were each CVD outcome, type 2 diabetes, and hypertension.<h4>Results</h4>In total, 2760 women with IIH and 27 125 women without IIH were included. Age and BMI were similar between the 2 groups, with a median (interquartile range) age of 32.1 (25.6-42.0) years in the exposed group and 32.1 (25.7-42.1) years in the control group; in the exposed group 1728 women (62.6%) were obese, and in the control group 16514 women (60.9%) were obese. Higher absolute risks for all cardiovascular outcomes were observed in women with IIH compared with control patients. The aHRs were as follows: composite cardiovascular events, 2.10 (95% CI, 1.61-2.74; P < .001); heart failure, 1.97 (95% CI, 1.16-3.37; P = .01); ischemic heart disease, 1.94 (95% CI, 1.27-2.94; P = .002); stroke/TIA, 2.27 (95% CI, 1.61-3.21; P < .001); type 2 diabetes, 1.30 (95% CI, 1.07-1.57; P = .009); and hypertension, 1.55 (95% CI, 1.30-1.84; P < .001). The incidence of IIH in female patients more than tripled between 2005 and 2017, from 2.5 to 9.3 per 100 000 person-years. Similarly, IIH prevalence increased in the same period, from 26 to 79 per 100 000 women. Incidence increased markedly with BMI higher than 30.<h4>Conclusions and relevance</h4>Idiopathic intracranial hypertension in women appeared to be associated with a 2-fold increase in CVD risk; change in patient care to modify risk factors for CVD may reduce long-term morbidity for women with IIH and warrants further evaluation.",,pdf:https://jamanetwork.com/journals/jamaneurology/articlepdf/2737044/jamaneurology_adderley_2019_oi_190046.pdf; doi:https://doi.org/10.1001/jamaneurol.2019.1812; html:https://europepmc.org/articles/PMC6618853
 35381001,https://doi.org/10.1371/journal.pgen.1010093,Analyzing human knockouts to validate GPR151 as a therapeutic target for reduction of body mass index.,"Gurtan A, Dominy J, Khalid S, Vong L, Caplan S, Currie T, Richards S, Lamarche L, Denning D, Shpektor D, Gurinovich A, Rasheed A, Hameed S, Saeed S, Saleem I, Jalal A, Abbas S, Sultana R, Rasheed SZ, Memon FU, Shah N, Ishaq M, Khera AV, Danesh J, Frossard P, Saleheen D.",,PLoS genetics,2022,2022-04-05,Y,,,,"Novel drug targets for sustained reduction in body mass index (BMI) are needed to curb the epidemic of obesity, which affects 650 million individuals worldwide and is a causal driver of cardiovascular and metabolic disease and mortality. Previous studies reported that the Arg95Ter nonsense variant of GPR151, an orphan G protein-coupled receptor, is associated with reduced BMI and reduced risk of Type 2 Diabetes (T2D). Here, we further investigate GPR151 with the Pakistan Genome Resource (PGR), which is one of the largest exome biobanks of human homozygous loss-of-function carriers (knockouts) in the world. Among PGR participants, we identify eleven GPR151 putative loss-of-function (plof) variants, three of which are present at homozygosity (Arg95Ter, Tyr99Ter, and Phe175LeufsTer7), with a cumulative allele frequency of 2.2%. We confirm these alleles in vitro as loss-of-function. We test if GPR151 plof is associated with BMI, T2D, or other metabolic traits and find that GPR151 deficiency in complete human knockouts is not associated with clinically significant differences in these traits. Relative to Gpr151+/+ mice, Gpr151-/- animals exhibit no difference in body weight on normal chow and higher body weight on a high-fat diet. Together, our findings indicate that GPR151 antagonism is not a compelling therapeutic approach to treatment of obesity.",,pdf:https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1010093&type=printable; doi:https://doi.org/10.1371/journal.pgen.1010093; html:https://europepmc.org/articles/PMC9022822; pdf:https://europepmc.org/articles/PMC9022822?pdf=render
+31282950,https://doi.org/10.1001/jamaneurol.2019.1812,Association Between Idiopathic Intracranial Hypertension and Risk of Cardiovascular Diseases in Women in the United Kingdom.,"Adderley NJ, Subramanian A, Nirantharakumar K, Yiangou A, Gokhale KM, Mollan SP, Sinclair AJ.",,JAMA neurology,2019,2019-09-01,Y,,Understanding the Causes of Disease,,"<h4>Importance</h4>Cardiovascular disease (CVD) risk has not been previously evaluated in a large matched cohort study in idiopathic intracranial hypertension (IIH).<h4>Objectives</h4>To estimate the risk of composite cardiovascular events, heart failure, ischemic heart disease, stroke/transient ischemic attack (TIA), type 2 diabetes, and hypertension in women with idiopathic intracranial hypertension and compare it with the risk in women, matched on body mass index (BMI) and age, without the condition; and to evaluate the prevalence and incidence of IIH.<h4>Design, setting, and participants</h4>This population-based matched controlled cohort study used 28 years of data, from January 1, 1990, to January 17, 2018, from The Health Improvement Network (THIN), an anonymized, nationally representative electronic medical records database in the United Kingdom. All female patients aged 16 years or older were eligible for inclusion. Female patients with IIH (n = 2760) were included and randomly matched with up to 10 control patients (n = 27 125) by BMI and age.<h4>Main outcomes and measures</h4>Adjusted hazard ratios (aHRs) of cardiovascular outcomes were calculated using Cox regression models. The primary outcome was a composite of any CVD (heart failure, ischemic heart disease, and stroke/TIA), and the secondary outcomes were each CVD outcome, type 2 diabetes, and hypertension.<h4>Results</h4>In total, 2760 women with IIH and 27 125 women without IIH were included. Age and BMI were similar between the 2 groups, with a median (interquartile range) age of 32.1 (25.6-42.0) years in the exposed group and 32.1 (25.7-42.1) years in the control group; in the exposed group 1728 women (62.6%) were obese, and in the control group 16514 women (60.9%) were obese. Higher absolute risks for all cardiovascular outcomes were observed in women with IIH compared with control patients. The aHRs were as follows: composite cardiovascular events, 2.10 (95% CI, 1.61-2.74; P < .001); heart failure, 1.97 (95% CI, 1.16-3.37; P = .01); ischemic heart disease, 1.94 (95% CI, 1.27-2.94; P = .002); stroke/TIA, 2.27 (95% CI, 1.61-3.21; P < .001); type 2 diabetes, 1.30 (95% CI, 1.07-1.57; P = .009); and hypertension, 1.55 (95% CI, 1.30-1.84; P < .001). The incidence of IIH in female patients more than tripled between 2005 and 2017, from 2.5 to 9.3 per 100 000 person-years. Similarly, IIH prevalence increased in the same period, from 26 to 79 per 100 000 women. Incidence increased markedly with BMI higher than 30.<h4>Conclusions and relevance</h4>Idiopathic intracranial hypertension in women appeared to be associated with a 2-fold increase in CVD risk; change in patient care to modify risk factors for CVD may reduce long-term morbidity for women with IIH and warrants further evaluation.",,pdf:https://jamanetwork.com/journals/jamaneurology/articlepdf/2737044/jamaneurology_adderley_2019_oi_190046.pdf; doi:https://doi.org/10.1001/jamaneurol.2019.1812; html:https://europepmc.org/articles/PMC6618853
+31994239,https://doi.org/10.1002/bimj.201900041,Estimating treatment effects with partially observed covariates using outcome regression with missing indicators.,"Blake HA, Leyrat C, Mansfield KE, Tomlinson LA, Carpenter J, Williamson EJ.",,Biometrical journal. Biometrische Zeitschrift,2020,2020-01-29,N,Average Treatment Effect; Outcome Regression; Missing Covariate Data; Missing Indicator; Missing Confounder Data,,,"Missing data is a common issue in research using observational studies to investigate the effect of treatments on health outcomes. When missingness occurs only in the covariates, a simple approach is to use missing indicators to handle the partially observed covariates. The missing indicator approach has been criticized for giving biased results in outcome regression. However, recent papers have suggested that the missing indicator approach can provide unbiased results in propensity score analysis under certain assumptions. We consider assumptions under which the missing indicator approach can provide valid inferences, namely, (1) no unmeasured confounding within missingness patterns; either (2a) covariate values of patients with missing data were conditionally independent of treatment or (2b) these values were conditionally independent of outcome; and (3) the outcome model is correctly specified: specifically, the true outcome model does not include interactions between missing indicators and fully observed covariates. We prove that, under the assumptions above, the missing indicator approach with outcome regression can provide unbiased estimates of the average treatment effect. We use a simulation study to investigate the extent of bias in estimates of the treatment effect when the assumptions are violated and we illustrate our findings using data from electronic health records. In conclusion, the missing indicator approach can provide valid inferences for outcome regression, but the plausibility of its assumptions must first be considered carefully.",,pdf:https://researchonline.lshtm.ac.uk/id/eprint/4655332/1/Estimating-treatment-effects-with-partially-observed-covariates-using-outcome-regression-with-missing-indicators.pdf; doi:https://doi.org/10.1002/bimj.201900041
 32709646,https://doi.org/10.1136/bmjopen-2019-036099,"Predicting the risk of asthma attacks in children, adolescents and adults: protocol for a machine learning algorithm derived from a primary care-based retrospective cohort.","Hussain Z, Shah SA, Mukherjee M, Sheikh A.",,BMJ open,2020,2020-07-23,Y,Asthma; epidemiology; Public Health; Health Informatics,,,"<h4>Introduction</h4>Most asthma attacks and subsequent deaths are potentially preventable. We aim to develop a prognostic tool for identifying patients at high risk of asthma attacks in primary care by leveraging advances in machine learning.<h4>Methods and analysis</h4>Current prognostic tools use logistic regression to develop a risk scoring model for asthma attacks. We propose to build on this by systematically applying various well-known machine learning techniques to a large longitudinal deidentified primary care database, the Optimum Patient Care Research Database, and comparatively evaluate their performance with the existing logistic regression model and against each other. Machine learning algorithms vary in their predictive abilities based on the dataset and the approach to analysis employed. We will undertake feature selection, classification (both one-class and two-class classifiers) and performance evaluation. Patients who have had actively treated clinician-diagnosed asthma, aged 8-80 years and with 3 years of continuous data, from 2016 to 2018, will be selected. Risk factors will be obtained from the first year, while the next 2 years will form the outcome period, in which the primary endpoint will be the occurrence of an asthma attack.<h4>Ethics and dissemination</h4>We have obtained approval from OPCRD's Anonymous Data Ethics Protocols and Transparency (ADEPT) Committee. We will seek ethics approval from The University of Edinburgh's Research Ethics Group (UREG). We aim to present our findings at scientific conferences and in peer-reviewed journals.",,pdf:https://bmjopen.bmj.com/content/bmjopen/10/7/e036099.full.pdf; doi:https://doi.org/10.1136/bmjopen-2019-036099; html:https://europepmc.org/articles/PMC7380838; pdf:https://europepmc.org/articles/PMC7380838?pdf=render
 31408247,https://doi.org/10.1002/hpja.287,An assessment of program evaluation methods and quality in Australian prevention agencies.,"Schwarzman J, Nau T, Bauman A, Gabbe BJ, Rissel C, Shilton T, Smith BJ.",,Health promotion journal of Australia : official journal of Australian Association of Health Promotion Professionals,2020,2019-08-13,N,Program Evaluation; Government; Primary Prevention; Health Promotion; Evidence-based Practice; Health Equity; Non-government Organisations,,,"<h4>Issue addressed</h4>This study aimed to examine evaluation methods and quality in Australian health promotion agencies and the factors associated with this. The evidence base for prevention strategies is limited, with the evidence generated through program evaluation by health promotion and disease prevention agencies lacking rigour. Despite the need to improve the quality of evaluation, there is limited evidence of what influences evaluation quality in the prevention field.<h4>Methods</h4>Data were collected using the Evaluation Practice Analysis Survey and an audit and appraisal of evaluation reports. Descriptive analysis was used to examine evaluation characteristics and multivariable regression was used to explore the association between evaluation and organisational attributes and evaluation quality.<h4>Results</h4>In total, 392 evaluation reports were reviewed from 78 government and non-government agencies. Process evaluation was conducted most frequently, followed by impact evaluation. Overall evaluation quality was low (median 24.5%). In multivariable regression analysis, only two factors were associated with evaluation quality: health promotion budget (ratio of geometric means 1.53 [95% CI 1.02-2.29]); and, conducting statewide or national prevention programs (1.38 [95% CI 1.05-1.82]).<h4>Conclusions</h4>The findings show that the potential to improve evaluation quality is greatest in smaller organisations that deliver health promotion at a local or regional scale. SO WHAT?: By improving the rigour of existing evaluation, there is opportunity to build the evidence base for prevention strategies, which highlights the importance of embedding the enablers of program learning and evidence generation within health promotion and prevention organisations.",,doi:https://doi.org/10.1002/hpja.287
 33959646,https://doi.org/10.3389/fcvm.2021.658915,"Common Variants Associated With <i>OSMR</i> Expression Contribute to Carotid Plaque Vulnerability, but Not to Cardiovascular Disease in Humans.","van Keulen D, van Koeverden ID, Boltjes A, Princen HMG, van Gool AJ, de Borst GJ, Asselbergs FW, Tempel D, Pasterkamp G, van der Laan SW.",,Frontiers in cardiovascular medicine,2021,2021-04-20,Y,Genetics; Atherosclerosis; Cardiovascular disease; Plaque; Osm; Osmr; Lifr,,,"<b>Background and Aims:</b> Oncostatin M (OSM) signaling is implicated in atherosclerosis, however the mechanism remains unclear. We investigated the impact of common genetic variants in <i>OSM</i> and its receptors, <i>OSMR</i> and <i>LIFR</i>, on overall plaque vulnerability, plaque phenotype, intraplaque <i>OSMR</i> and <i>LIFR</i> expression, coronary artery calcification burden and cardiovascular disease susceptibility. <b>Methods and Results:</b> We queried Genotype-Tissue Expression data and found that rs13168867 (C allele) was associated with decreased <i>OSMR</i> expression and that rs10491509 (A allele) was associated with increased <i>LIFR</i> expression in arterial tissues. No variant was significantly associated with <i>OSM</i> expression. We associated these two variants with plaque characteristics from 1,443 genotyped carotid endarterectomy patients in the Athero-Express Biobank Study. After correction for multiple testing, rs13168867 was significantly associated with an increased overall plaque vulnerability (β = 0.118 ± s.e. = 0.040, <i>p</i> = 3.00 × 10<sup>-3</sup>, C allele). Looking at individual plaque characteristics, rs13168867 showed strongest associations with intraplaque fat (β = 0.248 ± s.e. = 0.088, <i>p</i> = 4.66 × 10<sup>-3</sup>, C allele) and collagen content (β = -0.259 ± s.e. = 0.095, <i>p</i> = 6.22 × 10<sup>-3</sup>, C allele), but these associations were not significant after correction for multiple testing. rs13168867 was not associated with intraplaque <i>OSMR</i> expression. Neither was intraplaque <i>OSMR</i> expression associated with plaque vulnerability and no known <i>OSMR</i> eQTLs were associated with coronary artery calcification burden, or cardiovascular disease susceptibility. No associations were found for rs10491509 in the <i>LIFR</i> locus. <b>Conclusions:</b> Our study suggests that rs1316887 in the OSMR locus is associated with increased plaque vulnerability, but not with coronary calcification or cardiovascular disease risk. It remains unclear through which precise biological mechanisms OSM signaling exerts its effects on plaque morphology. However, the OSM-OSMR/LIFR pathway is unlikely to be causally involved in lifetime cardiovascular disease susceptibility.",,pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2021.658915/pdf; doi:https://doi.org/10.3389/fcvm.2021.658915; html:https://europepmc.org/articles/PMC8093786; pdf:https://europepmc.org/articles/PMC8093786?pdf=render
 32846977,https://doi.org/10.3390/ijerph17176139,Agreement between the International Physical Activity Questionnaire and Accelerometry in Adults with Orthopaedic Injury.,"Veitch WG, Climie RE, Gabbe BJ, Dunstan DW, Owen N, Ekegren CL.",,International journal of environmental research and public health,2020,2020-08-24,Y,Activity; Validation; Sitting; Accelerometer; Sedentary Behaviour; Ipaq,,,"Orthopaedic injury can lead to decreased physical activity. Valid measures for assessing physical activity are therefore needed in this population. The aim of this study was to determine the agreement and concordance between the International Physical Activity Questionnaire-Short Form (IPAQ) and device-measured physical activity and sitting time in orthopaedic injury patients. Adults with isolated upper or lower limb fracture (<i>n</i> = 46; mean age of 40.5 years) wore two activity monitors (ActiGraph wGT3X-BT and activPAL) for 10 days, from 2 weeks post-discharge. The IPAQ was also completed for a concurrent 7-day period. Lin's concordance correlation coefficients and Bland-Altman plots were calculated to compare walking/stepping time, total METmins, and sitting time. The IPAQ overestimated device-derived walking time (mean difference = 2.34 ± 7.33 h/week) and total METmins (mean difference = 767 ± 1659 METmins/week) and underestimated sitting time (mean difference = -2.26 ± 3.87 h/day). There was fair concordance between IPAQ-reported and device-measured walking (ρ = 0.34) and sitting time (ρ = 0.38) and moderate concordance between IPAQ-reported and device-measured METmins (ρ = 0.43). In patients with orthopaedic injury, the IPAQ overestimates physical activity and underestimates sitting time. Higher agreement was observed in the forms of activity (walking, total PA and sitting) commonly performed by this patient group.",,pdf:https://www.mdpi.com/1660-4601/17/17/6139/pdf?version=1598511551; doi:https://doi.org/10.3390/ijerph17176139; html:https://europepmc.org/articles/PMC7504024; pdf:https://europepmc.org/articles/PMC7504024?pdf=render
 33372068,https://doi.org/10.1136/bmjopen-2020-038324,Risk factors for mental illness in adults with atopic eczema or psoriasis: protocol for a systematic review.,"Adesanya EI, Schonmann Y, Hayes JF, Mathur R, Mulick AR, Rayner L, Smeeth L, Smith CH, Langan SM, Mansfield KE.",,BMJ open,2020,2020-12-28,Y,Psoriasis; Mental health; Eczema; Anxiety Disorders; Schizophrenia & Psychotic Disorders; Depression & Mood Disorders,,,"<h4>Introduction</h4>Evidence indicates that people with the common inflammatory skin diseases atopic eczema or psoriasis are at increased risk of mental illness. However, the reasons for the relationship between skin disease and common mental disorders (ie, depression and anxiety) or severe mental illnesses (ie, schizophrenia, bipolar disorder and other psychoses) are unclear. Therefore, we aim to synthesise the available evidence regarding the risk factors for mental illness in adults with atopic eczema or psoriasis.<h4>Methods and analysis</h4>We will conduct a systematic review of randomised controlled trials, cohort, case-control and cross-sectional studies. We will search the following databases from inception to March 2020: Medline, Embase, Global Health, Scopus, the Cochrane Library, Web of Science, Base, PsycInfo, the Global Resource of Eczema Trials, and the grey literature databases Open Grey, PsycExtra and the New York Academy of Medicine Grey Literature Report. We will also search the bibliographies of eligible studies and relevant systematic reviews to identify additional relevant studies. Citation searching of large summary papers will be used to further identify relevant publications. Two reviewers will initially review study titles and abstracts for eligibility, followed by full text screening. We will extract data using a standardised data extraction form. We will assess the risk of bias of included studies using the Quality in Prognosis Studies tool. We will synthesise data narratively, and if studies are sufficiently homogenous, we will consider a meta-analysis. We will assess the quality of the evidence using the Grading of Recommendations, Assessment, Development and Evaluation framework.<h4>Ethics and dissemination</h4>Ethical approval is not required for a systematic review. Results of the review will be published in a peer-reviewed journal and disseminated through conferences.<h4>Prospero registration number</h4>CRD42020163941.",,pdf:https://bmjopen.bmj.com/content/bmjopen/10/12/e038324.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-038324; html:https://europepmc.org/articles/PMC7772326; pdf:https://europepmc.org/articles/PMC7772326?pdf=render
 33956386,https://doi.org/10.1111/ceo.13943,Reporting guidelines for artificial intelligence in healthcare research.,"Ibrahim H, Liu X, Denniston AK.",,Clinical & experimental ophthalmology,2021,2021-05-25,N,Artificial intelligence; Checklist; Research Report; Guidelines; Research Design; Machine Learning,,,"Reporting guidelines are structured tools developed using explicit methodology that specify the minimum information required by researchers when reporting a study. The use of artificial intelligence (AI) reporting guidelines that address potential sources of bias specific to studies involving AI interventions has the potential to improve the quality of AI studies, through improvements in their design and delivery, and the completeness and transparency of their reporting. With a number of guidance documents relating to AI studies emerging from different specialist societies, this Review article provides researchers with some key principles for selecting the most appropriate reporting guidelines for a study involving an AI intervention. As the main determinants of a high-quality study are contained within the methodology of the study design rather than the intervention, researchers are recommended to use reporting guidelines that are specific to the study design, and then supplement them with AI-specific guidance contained within available AI reporting guidelines.",,pdf:http://pure-oai.bham.ac.uk/ws/files/143736502/ceo.13943.pdf; doi:https://doi.org/10.1111/ceo.13943
-35953815,https://doi.org/10.1186/s12931-022-02130-6,Dynamic early warning scores for predicting clinical deterioration in patients with respiratory disease.,"Gonem S, Taylor A, Figueredo G, Forster S, Quinlan P, Garibaldi JM, McKeever TM, Shaw D.",,Respiratory research,2022,2022-08-11,Y,Risk Prediction; Clinical Deterioration; Early Warning Score,,,"<h4>Background</h4>The National Early Warning Score-2 (NEWS-2) is used to detect patient deterioration in UK hospitals but fails to take account of the detailed granularity or temporal trends in clinical observations. We used data-driven methods to develop dynamic early warning scores (DEWS) to address these deficiencies, and tested their accuracy in patients with respiratory disease for predicting (1) death or intensive care unit admission, occurring within 24 h (D/ICU), and (2) clinically significant deterioration requiring urgent intervention, occurring within 4 h (CSD).<h4>Methods</h4>Clinical observations data were extracted from electronic records for 31,590 respiratory in-patient episodes from April 2015 to December 2020 at a large acute NHS Trust. The timing of D/ICU was extracted for all episodes. 1100 in-patient episodes were annotated manually to record the timing of CSD, defined as a specific event requiring a change in treatment. Time series features were entered into logistic regression models to derive DEWS for each of the clinical outcomes. Area under the receiver operating characteristic curve (AUROC) was the primary measure of model accuracy.<h4>Results</h4>AUROC (95% confidence interval) for predicting D/ICU was 0.857 (0.852-0.862) for NEWS-2 and 0.906 (0.899-0.914) for DEWS in the validation data. AUROC for predicting CSD was 0.829 (0.817-0.842) for NEWS-2 and 0.877 (0.862-0.892) for DEWS. NEWS-2 ≥ 5 had sensitivity of 88.2% and specificity of 54.2% for predicting CSD, while DEWS ≥ 0.021 had higher sensitivity of 93.6% and approximately the same specificity of 54.3% for the same outcome. Using these cut-offs, 315 out of 347 (90.8%) CSD events were detected by both NEWS-2 and DEWS, at the time of the event or within the previous 4 h; 12 (3.5%) were detected by DEWS but not by NEWS-2, while 4 (1.2%) were detected by NEWS-2 but not by DEWS; 16 (4.6%) were not detected by either scoring system.<h4>Conclusion</h4>We have developed DEWS that display greater accuracy than NEWS-2 for predicting clinical deterioration events in patients with respiratory disease. Prospective validation studies are required to assess whether DEWS can be used to reduce missed deteriorations and false alarms in real-life clinical settings.",,pdf:https://respiratory-research.biomedcentral.com/counter/pdf/10.1186/s12931-022-02130-6; doi:https://doi.org/10.1186/s12931-022-02130-6; html:https://europepmc.org/articles/PMC9367123; pdf:https://europepmc.org/articles/PMC9367123?pdf=render
 39421942,https://doi.org/10.7189/jogh.14.03042,Barriers to global engagement for African researchers: A position paper from the Alliance for Medical Research in Africa (AMedRA).,"Gaye B, Isiozor NM, Singh G, Gaye ND, Ka MM, Seck D, Gueye K, Kitara DL, Lassale C, Malick A, Diaw M, Seck SM, Sow A, Gaye M, Fall AS, Diongue A, Seck I, Belkhadir J, Wone I, Gueye SM, Sow PS, Kohen JE, Vogelsang D, Mbaye MN, Liyong EA, Kengne AP, Lamptey R, Sougou NM, Sobngwi E, Ba A, Tukakira J, Lorenz T, Kabore EG, Muzumala MG, Olanrewaju A, Jaiteh LE, Delicat-Loembet LM, Alson AOR, Niang K, Maina CW, Mwebaze E, Nabende J, Machuve D, Adie P, Hanne F, Tine R, Sougou M, Koffi KG, Luwanda L, Sattler ELP, Mekonnen D, Ebeid F, Enama JP, Zeba M, Guedou F, Mbelesso P, Carter J, Coulibaly B, Drame ML, Mouanga A, Preux PM, Lacroix P, Diagana M, Ekouevi DK, Houinato D, Faye A, Wambugu V, Kamaté J, Lalika M, Nsoesie E, Ale BM, Fall IS, Samb A, Tshilolo L, Jobe M.",,Journal of global health,2024,2024-10-18,Y,,,,,,doi:https://doi.org/10.7189/jogh.14.03042; html:https://europepmc.org/articles/PMC11487463; pdf:https://europepmc.org/articles/PMC11487463?pdf=render
 34032955,https://doi.org/10.1007/s11136-021-02876-4,"Health status after penetrating major trauma in Victoria, Australia: a registry-based cohort study.","Giummarra MJ, Dipnall JF, Gibson G, Beck B, Gabbe BJ.",,"Quality of life research : an international journal of quality of life aspects of treatment, care and rehabilitation",2021,2021-05-25,N,Recovery; Health Status; Health-related Quality Of Life; Gunshot Wounds; Penetrating Trauma; Stab Wounds,,,"<h4>Purpose</h4>As few studies have examined long-term health after penetrating injury, this population-based registry study sought to assess health outcomes up to 24 months post-injury.<h4>Methods</h4>Major trauma patients with penetrating trauma (2009-2017) were included from the Victorian State Trauma Registry (N = 1,067; 102 died, 208 were lost to follow-up). The EQ-5D-3L was used to measure health status at 6, 12 and 24-months. Mixed linear and logistic regressions were used to examine predictors of summary scores, and problems versus no problems on each health dimension.<h4>Results</h4>Average health status summary scores were 0.70 (sd = 0.26) at 6 and 12 months, and 0.72 (sd = 0.26) at 24 months post-injury. Prevalence of problems was consistent over time: mobility (24-26%), self-care (17-20%), usual activities (47-50%), pain/discomfort (44-49%), and anxiety/depression (54-56%). Lower health status and reporting problems was associated with middle-older age, female sex, unemployment; pre-injury disability, comorbid conditions; and assault and firearm injury versus cutting/piercing.<h4>Conclusion</h4>Problems with usual activities, pain/discomfort and anxiety or depression are common after penetrating major trauma. Risk factor screening in hospital could be used to identify people at risk of poor health outcomes, and to link people at risk with services in hospital or early post-discharge to improve their longer-term health outcomes.",,doi:https://doi.org/10.1007/s11136-021-02876-4
+35953815,https://doi.org/10.1186/s12931-022-02130-6,Dynamic early warning scores for predicting clinical deterioration in patients with respiratory disease.,"Gonem S, Taylor A, Figueredo G, Forster S, Quinlan P, Garibaldi JM, McKeever TM, Shaw D.",,Respiratory research,2022,2022-08-11,Y,Risk Prediction; Clinical Deterioration; Early Warning Score,,,"<h4>Background</h4>The National Early Warning Score-2 (NEWS-2) is used to detect patient deterioration in UK hospitals but fails to take account of the detailed granularity or temporal trends in clinical observations. We used data-driven methods to develop dynamic early warning scores (DEWS) to address these deficiencies, and tested their accuracy in patients with respiratory disease for predicting (1) death or intensive care unit admission, occurring within 24 h (D/ICU), and (2) clinically significant deterioration requiring urgent intervention, occurring within 4 h (CSD).<h4>Methods</h4>Clinical observations data were extracted from electronic records for 31,590 respiratory in-patient episodes from April 2015 to December 2020 at a large acute NHS Trust. The timing of D/ICU was extracted for all episodes. 1100 in-patient episodes were annotated manually to record the timing of CSD, defined as a specific event requiring a change in treatment. Time series features were entered into logistic regression models to derive DEWS for each of the clinical outcomes. Area under the receiver operating characteristic curve (AUROC) was the primary measure of model accuracy.<h4>Results</h4>AUROC (95% confidence interval) for predicting D/ICU was 0.857 (0.852-0.862) for NEWS-2 and 0.906 (0.899-0.914) for DEWS in the validation data. AUROC for predicting CSD was 0.829 (0.817-0.842) for NEWS-2 and 0.877 (0.862-0.892) for DEWS. NEWS-2 ≥ 5 had sensitivity of 88.2% and specificity of 54.2% for predicting CSD, while DEWS ≥ 0.021 had higher sensitivity of 93.6% and approximately the same specificity of 54.3% for the same outcome. Using these cut-offs, 315 out of 347 (90.8%) CSD events were detected by both NEWS-2 and DEWS, at the time of the event or within the previous 4 h; 12 (3.5%) were detected by DEWS but not by NEWS-2, while 4 (1.2%) were detected by NEWS-2 but not by DEWS; 16 (4.6%) were not detected by either scoring system.<h4>Conclusion</h4>We have developed DEWS that display greater accuracy than NEWS-2 for predicting clinical deterioration events in patients with respiratory disease. Prospective validation studies are required to assess whether DEWS can be used to reduce missed deteriorations and false alarms in real-life clinical settings.",,pdf:https://respiratory-research.biomedcentral.com/counter/pdf/10.1186/s12931-022-02130-6; doi:https://doi.org/10.1186/s12931-022-02130-6; html:https://europepmc.org/articles/PMC9367123; pdf:https://europepmc.org/articles/PMC9367123?pdf=render
 34348396,https://doi.org/10.1097/ede.0000000000001393,Weight Change and the Onset of Cardiovascular Diseases: Emulating Trials Using Electronic Health Records.,"Katsoulis M, Stavola BD, Diaz-Ordaz K, Gomes M, Lai A, Lagiou P, Wannamethee G, Tsilidis K, Lumbers RT, Denaxas S, Banerjee A, Parisinos CA, Batterham R, Patel R, Langenberg C, Hemingway H.",,"Epidemiology (Cambridge, Mass.)",2021,2021-09-01,Y,,,,"<h4>Background</h4>Cross-sectional measures of body mass index (BMI) are associated with cardiovascular disease (CVD) incidence, but less is known about whether weight change affects the risk of CVD.<h4>Methods</h4>We estimated the effect of 2-y weight change interventions on 7-y risk of CVD (CVD death, myocardial infarction, stroke, hospitalization from coronary heart disease, and heart failure) by emulating hypothetical interventions using electronic health records. We identified 138,567 individuals with 45-69 years of age without chronic disease in England from 1998 to 2016. We performed pooled logistic regression, using inverse-probability weighting to adjust for baseline and time-varying confounders. We categorized each individual into a weight loss, maintenance, or gain group.<h4>Results</h4>Among those of normal weight, both weight loss [risk difference (RD) vs. weight maintenance = 1.5% (0.3% to 3.0%)] and gain [RD = 1.3% (0.5% to 2.2%)] were associated with increased risk for CVD compared with weight maintenance. Among overweight individuals, we observed moderately higher risk of CVD in both the weight loss [RD = 0.7% (-0.2% to 1.7%)] and the weight gain group [RD = 0.7% (-0.1% to 1.7%)], compared with maintenance. In the obese, those losing weight showed lower risk of coronary heart disease [RD = -1.4% (-2.4% to -0.6%)] but not of stroke. When we assumed that chronic disease occurred 1-3 years before the recorded date, estimates for weight loss and gain were attenuated among overweight individuals; estimates for loss were lower among obese individuals.<h4>Conclusion</h4>Among individuals with obesity, the weight-loss group had a lower risk of coronary heart disease but not of stroke. Weight gain was associated with increased risk of CVD across BMI groups. See video abstract at, http://links.lww.com/EDE/B838.",,html:https://journals.lww.com/epidem/Fulltext/2021/09000/Weight_Change_and_the_Onset_of_Cardiovascular.19.aspx; doi:https://doi.org/10.1097/EDE.0000000000001393; html:https://europepmc.org/articles/PMC8318567; pdf:https://europepmc.org/articles/PMC8318567?pdf=render
 36054463,https://doi.org/10.1111/ans.17985,Examining the patient profile and variance of management and in-hospital outcomes for Australian adult burns patients.,"Tracy LM, Darton A, Gabbe BJ, Heath K, Kurmis R, Lisec C, Lo C, Singer Y, Wood FM, Cleland HJ.",,ANZ journal of surgery,2022,2022-08-22,Y,Adult; Variation; Australia; Burn; Registry,,,"<h4>Background</h4>Burn injuries are a common subtype of trauma. Variation in models of care impacts clinical measures of interest, but a nation-wide examination of these measures has not been undertaken. Using data from the Burns Registry of Australia and New Zealand (BRANZ), we explored variation between Australian adult burn services with respect to treatment and clinical measures of interest.<h4>Methods</h4>Data for admissions July 2016 to June 2020 were extracted. Clinical measures of interest included intensive care admission, skin grafting, in-hospital death, unplanned readmissions, and length of stay (LOS). Estimated probabilities, means, and corresponding 95% confidence intervals (CI) were calculated for each service.<h4>Results</h4>The BRANZ recorded 8365 admissions during the study period. Variation between specialist burn services in admissions, demographics, management, and clinical measures of interest were observed. This variation remained after accounting for covariates. Specifically, the adjusted proportion (95% CI) of in-hospital mortality ranged from 0.15% (0.10-0.21%) to 1.22% (0.9-1.5%). The adjusted mean LOS ranged from 3.8 (3.3-4.3) to 8.2 (6.7-9.7) days.<h4>Conclusions</h4>A decade after its launch, BRANZ data displays variation between Australian specialist burn services. We suspect differences in models of care between services contributes to this variation. Ongoing research has begun to explore reasons underlying how this variation influences clinical measures of interest. Further engagement with services about models of care will enhance understanding of this variation and develop evidence-based guidelines for burn care in Australia.",,doi:https://doi.org/10.1111/ans.17985; doi:https://doi.org/10.1111/ans.17985; html:https://europepmc.org/articles/PMC9804322; pdf:https://europepmc.org/articles/PMC9804322?pdf=render
 35115689,https://doi.org/10.1038/s41588-021-00991-z,Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort.,"Qin Y, Havulinna AS, Liu Y, Jousilahti P, Ritchie SC, Tokolyi A, Sanders JG, Valsta L, Brożyńska M, Zhu Q, Tripathi A, Vázquez-Baeza Y, Loomba R, Cheng S, Jain M, Niiranen T, Lahti L, Knight R, Salomaa V, Inouye M, Méric G.",,Nature genetics,2022,2022-02-03,N,,,,"Human genetic variation affects the gut microbiota through a complex combination of environmental and host factors. Here we characterize genetic variations associated with microbial abundances in a single large-scale population-based cohort of 5,959 genotyped individuals with matched gut microbial metagenomes, and dietary and health records (prevalent and follow-up). We identified 567 independent SNP-taxon associations. Variants at the LCT locus associated with Bifidobacterium and other taxa, but they differed according to dairy intake. Furthermore, levels of Faecalicatena lactaris associated with ABO, and suggested preferential utilization of secreted blood antigens as energy source in the gut. Enterococcus faecalis levels associated with variants in the MED13L locus, which has been linked to colorectal cancer. Mendelian randomization analysis indicated a potential causal effect of Morganella on major depressive disorder, consistent with observational incident disease analysis. Overall, we identify and characterize the intricate nature of host-microbiota interactions and their association with disease.",,pdf:https://www.nature.com/articles/s41588-021-00991-z.pdf; doi:https://doi.org/10.1038/s41588-021-00991-z; html:https://europepmc.org/articles/PMC9883041; pdf:https://europepmc.org/articles/PMC9883041?pdf=render; doi:https://doi.org/10.1038/s41588-021-00991-z
-37419925,https://doi.org/10.1038/s41467-023-38930-7,Optimal strategies for learning multi-ancestry polygenic scores vary across traits.,"Lehmann B, Mackintosh M, McVean G, Holmes C.",,Nature communications,2023,2023-07-07,Y,,,,"Polygenic scores (PGSs) are individual-level measures that aggregate the genome-wide genetic predisposition to a given trait. As PGS have predominantly been developed using European-ancestry samples, trait prediction using such European ancestry-derived PGS is less accurate in non-European ancestry individuals. Although there has been recent progress in combining multiple PGS trained on distinct populations, the problem of how to maximize performance given a multiple-ancestry cohort is largely unexplored. Here, we investigate the effect of sample size and ancestry composition on PGS performance for fifteen traits in UK Biobank. For some traits, PGS estimated using a relatively small African-ancestry training set outperformed, on an African-ancestry test set, PGS estimated using a much larger European-ancestry only training set. We observe similar, but not identical, results when considering other minority-ancestry groups within UK Biobank. Our results emphasise the importance of targeted data collection from underrepresented groups in order to address existing disparities in PGS performance.",,pdf:https://www.nature.com/articles/s41467-023-38930-7.pdf; doi:https://doi.org/10.1038/s41467-023-38930-7; html:https://europepmc.org/articles/PMC10328935; pdf:https://europepmc.org/articles/PMC10328935?pdf=render
 34753797,https://doi.org/10.2337/db21-0320,An Expanded Genome-Wide Association Study of Fructosamine Levels Identifies RCN3 as a Replicating Locus and Implicates FCGRT as the Effector Transcript.,"Riveros-Mckay F, Roberts D, Di Angelantonio E, Yu B, Soranzo N, Danesh J, Selvin E, Butterworth AS, Barroso I.",,Diabetes,2022,2022-02-01,N,,,,"Fructosamine is a measure of short-term glycemic control, which has been suggested as a useful complement to glycated hemoglobin (HbA1c) for the diagnosis and monitoring of diabetes. To date, a single genome-wide association study (GWAS) including 8,951 U.S. White and 2,712 U.S. Black individuals without a diabetes diagnosis has been published. Results in Whites and Blacks yielded different association loci, near RCN3 and CNTN5, respectively. In this study, we performed a GWAS on 20,731 European-ancestry blood donors and meta-analyzed our results with previous data from U.S. White participants from the Atherosclerosis Risk in Communities (ARIC) study (Nmeta = 29,685). We identified a novel association near GCK (rs3757840, βmeta = 0.0062; minor allele frequency [MAF] = 0.49; Pmeta = 3.66 × 10-8) and confirmed the association near RCN3 (rs113886122, βmeta = 0.0134; MAF = 0.17; Pmeta = 5.71 × 10-18). Colocalization analysis with whole-blood expression quantitative trait loci data suggested FCGRT as the effector transcript at the RCN3 locus. We further showed that fructosamine has low heritability (h2 = 7.7%), has no significant genetic correlation with HbA1c and other glycemic traits in individuals without a diabetes diagnosis (P > 0.05), but has evidence of shared genetic etiology with some anthropometric traits (Bonferroni-corrected P < 0.0012). Our results broaden knowledge of the genetic architecture of fructosamine and prioritize FCGRT for downstream functional studies at the established RCN3 locus.",,pdf:https://diabetesjournals.org/diabetes/article-pdf/71/2/359/640867/db210320.pdf; doi:https://doi.org/10.2337/db21-0320; html:https://europepmc.org/articles/PMC8914280; pdf:https://europepmc.org/articles/PMC8914280?pdf=render; doi:https://doi.org/10.2337/db21-0320
+37419925,https://doi.org/10.1038/s41467-023-38930-7,Optimal strategies for learning multi-ancestry polygenic scores vary across traits.,"Lehmann B, Mackintosh M, McVean G, Holmes C.",,Nature communications,2023,2023-07-07,Y,,,,"Polygenic scores (PGSs) are individual-level measures that aggregate the genome-wide genetic predisposition to a given trait. As PGS have predominantly been developed using European-ancestry samples, trait prediction using such European ancestry-derived PGS is less accurate in non-European ancestry individuals. Although there has been recent progress in combining multiple PGS trained on distinct populations, the problem of how to maximize performance given a multiple-ancestry cohort is largely unexplored. Here, we investigate the effect of sample size and ancestry composition on PGS performance for fifteen traits in UK Biobank. For some traits, PGS estimated using a relatively small African-ancestry training set outperformed, on an African-ancestry test set, PGS estimated using a much larger European-ancestry only training set. We observe similar, but not identical, results when considering other minority-ancestry groups within UK Biobank. Our results emphasise the importance of targeted data collection from underrepresented groups in order to address existing disparities in PGS performance.",,pdf:https://www.nature.com/articles/s41467-023-38930-7.pdf; doi:https://doi.org/10.1038/s41467-023-38930-7; html:https://europepmc.org/articles/PMC10328935; pdf:https://europepmc.org/articles/PMC10328935?pdf=render
 39266746,https://doi.org/10.1038/s41591-024-03246-6,The European Health Data Space can be a boost for research beyond borders.,"Ganna A, Carracedo A, Christiansen CF, Di Angelantonio E, Dykstra PA, Dzhambov AM, Eils R, Green S, Schneider KL, Varga TV, Vuorinen AL, Zuccolo L, Rod NH, Hoeyer K.",,Nature medicine,2024,2024-09-12,N,,,,,,doi:https://doi.org/10.1038/s41591-024-03246-6
 36224602,https://doi.org/10.1186/s12916-022-02544-5,Early onset of immune-mediated diseases in minority ethnic groups in the UK.,"Sharma-Oates A, Zemedikun DT, Kumar K, Reynolds JA, Jain A, Raza K, Williams JA, Bravo L, Cardoso VR, Gkoutos G, Nirantharakumar K, Lord JM.",,BMC medicine,2022,2022-10-13,Y,Ageing; Diagnosis; Ethnicity; Rheumatic Diseases; South Asian; African-caribbean; Immune-mediated Diseases; Autoimmune Inflammatory Diseases,,,"<h4>Background</h4>The prevalence of some immune-mediated diseases (IMDs) shows distinct differences between populations of different ethnicities. The aim of this study was to determine if the age at diagnosis of common IMDs also differed between different ethnic groups in the UK, suggestive of distinct influences of ethnicity on disease pathogenesis.<h4>Methods</h4>This was a population-based retrospective primary care study. Linear regression provided unadjusted and adjusted estimates of age at diagnosis for common IMDs within the following ethnic groups: White, South Asian, African-Caribbean and Mixed-race/Other. Potential disease risk confounders in the association between ethnicity and diagnosis age including sex, smoking, body mass index and social deprivation (Townsend quintiles) were adjusted for. The analysis was replicated using data from UK Biobank (UKB).<h4>Results</h4>After adjusting for risk confounders, we observed that individuals from South Asian, African-Caribbean and Mixed-race/Other ethnicities were diagnosed with IMDs at a significantly younger age than their White counterparts for almost all IMDs. The difference in the diagnosis age (ranging from 2 to 30 years earlier) varied for each disease and by ethnicity. For example, rheumatoid arthritis was diagnosed at age 49, 48 and 47 years in individuals of African-Caribbean, South Asian and Mixed-race/Other ethnicities respectively, compared to 56 years in White ethnicities. The earlier diagnosis of most IMDs observed was validated in UKB although with a smaller effect size.<h4>Conclusion</h4>Individuals from non-White ethnic groups in the UK had an earlier age at diagnosis for several IMDs than White adults.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-022-02544-5; doi:https://doi.org/10.1186/s12916-022-02544-5; html:https://europepmc.org/articles/PMC9558944; pdf:https://europepmc.org/articles/PMC9558944?pdf=render
 37393610,https://doi.org/10.1016/j.xpro.2023.102392,Protocol for the automatic extraction of epidemiological information via a pre-trained language model.,"Wang Z, Liu XF, Du Z, Wang L, Wu Y, Holme P, Lachmann M, Lin H, Wang Z, Cao Y, Wong ZSY, Xu XK, Sun Y.",,STAR protocols,2023,2023-07-01,Y,Health Sciences; Clinical Protocol; Computer Sciences,,,"The lack of systems to automatically extract epidemiological fields from open-access COVID-19 cases restricts the timeliness of formulating prevention measures. Here we present a protocol for using CCIE, a COVID-19 Cases Information Extraction system based on the pre-trained language model.<sup>1</sup> We describe steps for preparing supervised training data and executing python scripts for named entity recognition and text category classification. We then detail the use of machine evaluation and manual validation to illustrate the effectiveness of CCIE. For complete details on the use and execution of this protocol, please refer to Wang et al.<sup>2</sup>.",,doi:https://doi.org/10.1016/j.xpro.2023.102392; doi:https://doi.org/10.1016/j.xpro.2023.102392; html:https://europepmc.org/articles/PMC10328978; pdf:https://europepmc.org/articles/PMC10328978?pdf=render
@@ -1769,73 +1771,73 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 35587337,https://doi.org/10.1093/ije/dyac105,"Gestational age at birth, chronic conditions and school outcomes: a population-based data linkage study of children born in England.","Libuy N, Gilbert R, Mc Grath-Lone L, Blackburn R, Etoori D, Harron K.",,International journal of epidemiology,2023,2023-02-01,Y,England; Gestational Age; Chronic Conditions; Academic Performance; Special Educational Needs; Whole-population Cohort,,,"<h4>Introduction</h4>We aimed to generate evidence about child development measured through school attainment and provision of special educational needs (SEN) across the spectrum of gestational age, including for children born early term and >41 weeks of gestation, with and without chronic health conditions.<h4>Methods</h4>We used a national linked dataset of hospital and education records of children born in England between 1 September 2004 and 31 August 2005. We evaluated school attainment at Key Stage 1 (KS1; age 7) and Key Stage 2 (KS2; age 11) and any SEN by age 11. We stratified analyses by chronic health conditions up to age 2, and size-for-gestation, and calculated population attributable fractions (PAF).<h4>Results</h4>Of 306 717 children, 5.8% were born <37 weeks gestation and 7.0% had a chronic condition. The percentage of children not achieving the expected level at KS1 increased from 7.6% at 41 weeks, to 50.0% at 24 weeks of gestation. A similar pattern was seen at KS2. SEN ranged from 29.0% at 41 weeks to 82.6% at 24 weeks. Children born early term (37-38 weeks of gestation) had poorer outcomes than those born at 40 weeks; 3.2% of children with SEN were attributable to having a chronic condition compared with 2.0% attributable to preterm birth.<h4>Conclusions</h4>Children born with early identified chronic conditions contribute more to the burden of poor school outcomes than preterm birth. Evaluation is needed of how early health characteristics can be used to improve preparation for education, before and at entry to school.",,pdf:https://academic.oup.com/ije/article-pdf/52/1/132/49127281/dyac105.pdf; doi:https://doi.org/10.1093/ije/dyac105; html:https://europepmc.org/articles/PMC9908051; pdf:https://europepmc.org/articles/PMC9908051?pdf=render
 37422075,https://doi.org/10.1016/j.jval.2023.06.019,Perspectives on Patient-Reported Outcome Data After Treatment Discontinuation in Cancer Clinical Trials.,"King-Kallimanis BL, Calvert M, Cella D, Cocks K, Coens C, Fairclough D, Howie L, Jonsson P, Mahendraratnam N, Maues J, Sarac S, Shaw J, Stigger N, Trask P, Wieseler B.",,Value in health : the journal of the International Society for Pharmacoeconomics and Outcomes Research,2023,2023-07-06,N,Oncology; Clinical Trials; Patient-reported Outcomes; Multistakeholder Perspective,,,"<h4>Objectives</h4>Patient-reported outcome (PRO) data are critical in understanding treatments from the patient perspective in cancer clinical trials. The potential benefits and methodological approaches to the collection of PRO data after treatment discontinuation (eg, because of progressive disease or unacceptable drug toxicity) are less clear. The purpose of this article is to describe the Food and Drug Administration's Oncology Center of Excellence and the Critical Path Institute cosponsored 2-hour virtual roundtable, held in 2020, to discuss this specific issue.<h4>Methods</h4>We summarize key points from this discussion with 16 stakeholders representing academia, clinical practice, patients, international regulatory agencies, health technology assessment bodies/payers, industry, and PRO instrument development.<h4>Results</h4>Stakeholders recognized that any PRO data collection after treatment discontinuation should have clearly defined objectives to ensure that data can be analyzed and reported.<h4>Conclusions</h4>Data collection after discontinuation without a justification for its use wastes patients' time and effort and is unethical.",,doi:https://doi.org/10.1016/j.jval.2023.06.019
 33836256,https://doi.org/10.1016/j.jclinepi.2021.03.025,Internal-external cross-validation helped to evaluate the generalizability of prediction models in large clustered datasets.,"Takada T, Nijman S, Denaxas S, Snell KIE, Uijl A, Nguyen TL, Asselbergs FW, Debray TPA.",,Journal of clinical epidemiology,2021,2021-04-06,N,Heterogeneity; Discrimination; Validation; Prediction model; calibration; Model Comparison,,,"<h4>Objective</h4>To illustrate how to evaluate the need of complex strategies for developing generalizable prediction models in large clustered datasets.<h4>Study design and setting</h4>We developed eight Cox regression models to estimate the risk of heart failure using a large population-level dataset. These models differed in the number of predictors, the functional form of the predictor effects (non-linear effects and interaction) and the estimation method (maximum likelihood and penalization). Internal-external cross-validation was used to evaluate the models' generalizability across the included general practices.<h4>Results</h4>Among 871,687 individuals from 225 general practices, 43,987 (5.5%) developed heart failure during a median follow-up time of 5.8 years. For discrimination, the simplest prediction model yielded a good concordance statistic, which was not much improved by adopting complex strategies. Between-practice heterogeneity in discrimination was similar in all models. For calibration, the simplest model performed satisfactorily. Although accounting for non-linear effects and interaction slightly improved the calibration slope, it also led to more heterogeneity in the observed/expected ratio. Similar results were found in a second case study involving patients with stroke.<h4>Conclusion</h4>In large clustered datasets, prediction model studies may adopt internal-external cross-validation to evaluate the generalizability of competing models, and to identify promising modelling strategies.",,pdf:http://www.jclinepi.com/article/S0895435621001074/pdf; doi:https://doi.org/10.1016/j.jclinepi.2021.03.025
-35087703,https://doi.org/10.5334/aogh.3465,Household Air Pollution and Respiratory Symptoms a Month Before and During the Stringent COVID-19 Lockdown Levels 5 and 4 in South Africa.,"Wright CY, Kapwata T, Abdelatif N, Batini C, Wernecke B, Kunene Z, Millar DA, Mathee A, Street R, Panchal R, Hansell A, Cordell R, Hey JV.",,Annals of global health,2022,2022-01-10,Y,,,,"<h4>Background</h4>Household air pollution (HAP) is associated with adverse human health impacts. During COVID-19 Lockdown Levels 5 and 4 (the most stringent levels), South Africans remained at home, potentially increasing their exposure to HAP.<h4>Objectives</h4>To investigate changes in fuel use behaviours/patterns of use affecting HAP exposure and associated HAP-related respiratory health outcomes during COVID-19 Lockdown Levels 5 and 4.<h4>Methods</h4>This was a cross-sectional online and telephonic survey of participants from an existing database. Logistic regression and McNemar's test were used to analyse household-level data.<h4>Results</h4>Among 2 505 participants, while electricity was the main energy source for cooking and heating the month before and during Lockdown Levels 5 and 4, some households used less electricity during Lockdown Levels 5 and 4 or switched to ""dirty fuels."" One third of participants reported presence of environmental tobacco smoke in the home, a source of HAP associated with respiratory illnesses. Prevalence of HAP-related respiratory health outcomes were <10% (except dry cough). Majority of households reported cooking more, cleaning more and spending more time indoors during Lockdown Levels 5 and 4 - potentially exposed to HAP.<h4>Conclusion</h4>Should South Africa return to Lockdown Levels 5 or 4, awareness raising about the risks associated with HAP as well as messaging information for prevention of exposure to HAP, including environmental tobacco smoke, and associated adverse health impacts will be necessary.",,pdf:http://www.annalsofglobalhealth.org/articles/10.5334/aogh.3465/galley/3414/download/; doi:https://doi.org/10.5334/aogh.3465; html:https://europepmc.org/articles/PMC8757382; pdf:https://europepmc.org/articles/PMC8757382?pdf=render
 34535484,https://doi.org/10.1136/bmjopen-2021-050647,The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers (UK-REACH): protocol for a prospective longitudinal cohort study of healthcare and ancillary workers in UK healthcare settings.,"Woolf K, Melbourne C, Bryant L, Guyatt AL, McManus IC, Gupta A, Free RC, Nellums L, Carr S, John C, Martin CA, Wain LV, Gray LJ, Garwood C, Modhwadia V, Abrams KR, Tobin MD, Khunti K, Pareek M, UK-REACH Study Collaborative Group+.",,BMJ open,2021,2021-09-17,Y,Mental health; Public Health; Covid-19,,,"<h4>Introduction</h4>The COVID-19 pandemic has resulted in significant morbidity and mortality and devastated economies globally. Among groups at increased risk are healthcare workers (HCWs) and ethnic minority groups. Emerging evidence suggests that HCWs from ethnic minority groups are at increased risk of adverse COVID-19-related outcomes. To date, there has been no large-scale analysis of these risks in UK HCWs or ancillary workers in healthcare settings, stratified by ethnicity or occupation, and adjusted for confounders. This paper reports the protocol for a prospective longitudinal questionnaire study of UK HCWs, as part of the UK-REACH programme (The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers).<h4>Methods and analysis</h4>A baseline questionnaire will be administered to a national cohort of UK HCWs and ancillary workers in healthcare settings, and those registered with UK healthcare regulators, with follow-up questionnaires administered at 4 and 8 months. With consent, questionnaire data will be linked to health records with 25-year follow-up. Univariate associations between ethnicity and clinical COVID-19 outcomes, physical and mental health, and key confounders/explanatory variables will be tested. Multivariable analyses will test for associations between ethnicity and key outcomes adjusted for the confounder/explanatory variables. We will model changes over time by ethnic group, facilitating understanding of absolute and relative risks in different ethnic groups, and generalisability of findings.<h4>Ethics and dissemination</h4>The study is approved by Health Research Authority (reference 20/HRA/4718), and carries minimal risk. We aim to manage the small risk of participant distress about questions on sensitive topics by clearly participant information that the questionnaire covers sensitive topics and there is no obligation to answer these or any other questions, and by providing support organisation links. Results will be disseminated with reports to Government and papers submitted to pre-print servers and peer reviewed journals.<h4>Trial registration number</h4>ISRCTN11811602; Pre-results.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/9/e050647.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-050647; html:https://europepmc.org/articles/PMC8450967; pdf:https://europepmc.org/articles/PMC8450967?pdf=render
-39009924,https://doi.org/10.1007/s10654-024-01141-5,Multi-biobank Mendelian randomization analyses identify opposing pathways in plasma low-density lipoprotein-cholesterol lowering and gallstone disease.,"Yang G, Mason AM, Gill D, Schooling CM, Burgess S.",,European journal of epidemiology,2024,2024-07-15,Y,Gallstone Disease; Ldl-cholesterol; Drug-target Mendelian Randomization; Clustered Mendelian Randomization,,,"Plasma low-density lipoprotein (LDL)-cholesterol is positively associated with coronary artery disease risk while biliary cholesterol promotes gallstone formation. Different plasma LDL-cholesterol lowering pathways may have distinct effects on biliary cholesterol and thereby gallstone disease risk. We conducted a Mendelian randomization (MR) study using data from the UK Biobank (30,547 gallstone disease cases/336,742 controls), FinnGen (34,461 cases/301,383 controls) and Biobank Japan (9,305 cases/168,253 controls). We first performed drug-target MR analyses substantiated by colocalization to investigate the effects of plasma LDL-cholesterol lowering therapies on gallstone disease risk. We then performed clustered MR analyses and pathway analyses to identify distinct mechanisms underlying the association of plasma LDL-cholesterol with gallstone disease risk. For a 1-standard deviation reduction in plasma LDL-cholesterol, genetic mimics of statins were associated with lower gallstone disease risk (odds ratio 0.72 [95% confidence interval 0.62, 0.83]), but genetic mimics of PCSK9 inhibitors and targeting apolipoprotein B were associated with higher risk (1.11 [1.03, 1.19] and 1.23 [1.13, 1.35]). The association for statins was supported by colocalization (posterior probability 98.7%). Clustered MR analyses identified variant clusters showing opposing associations of plasma LDL-cholesterol with gallstone disease risk, with some evidence for ancestry-and sex-specific associations. Among variants lowering plasma LDL-cholesterol, those associated with lower gallstone disease risk were mapped to glycosphingolipid biosynthesis pathway, while those associated with higher risk were mapped to pathways relating to plasma lipoprotein assembly, remodelling, and clearance and ATP-binding cassette transporters. This MR study provides genetic evidence that different plasma LDL-cholesterol lowering pathways have opposing effects on gallstone disease risk.",,doi:https://doi.org/10.1007/s10654-024-01141-5; html:https://europepmc.org/articles/PMC11410903; pdf:https://europepmc.org/articles/PMC11410903?pdf=render
+35087703,https://doi.org/10.5334/aogh.3465,Household Air Pollution and Respiratory Symptoms a Month Before and During the Stringent COVID-19 Lockdown Levels 5 and 4 in South Africa.,"Wright CY, Kapwata T, Abdelatif N, Batini C, Wernecke B, Kunene Z, Millar DA, Mathee A, Street R, Panchal R, Hansell A, Cordell R, Hey JV.",,Annals of global health,2022,2022-01-10,Y,,,,"<h4>Background</h4>Household air pollution (HAP) is associated with adverse human health impacts. During COVID-19 Lockdown Levels 5 and 4 (the most stringent levels), South Africans remained at home, potentially increasing their exposure to HAP.<h4>Objectives</h4>To investigate changes in fuel use behaviours/patterns of use affecting HAP exposure and associated HAP-related respiratory health outcomes during COVID-19 Lockdown Levels 5 and 4.<h4>Methods</h4>This was a cross-sectional online and telephonic survey of participants from an existing database. Logistic regression and McNemar's test were used to analyse household-level data.<h4>Results</h4>Among 2 505 participants, while electricity was the main energy source for cooking and heating the month before and during Lockdown Levels 5 and 4, some households used less electricity during Lockdown Levels 5 and 4 or switched to ""dirty fuels."" One third of participants reported presence of environmental tobacco smoke in the home, a source of HAP associated with respiratory illnesses. Prevalence of HAP-related respiratory health outcomes were <10% (except dry cough). Majority of households reported cooking more, cleaning more and spending more time indoors during Lockdown Levels 5 and 4 - potentially exposed to HAP.<h4>Conclusion</h4>Should South Africa return to Lockdown Levels 5 or 4, awareness raising about the risks associated with HAP as well as messaging information for prevention of exposure to HAP, including environmental tobacco smoke, and associated adverse health impacts will be necessary.",,pdf:http://www.annalsofglobalhealth.org/articles/10.5334/aogh.3465/galley/3414/download/; doi:https://doi.org/10.5334/aogh.3465; html:https://europepmc.org/articles/PMC8757382; pdf:https://europepmc.org/articles/PMC8757382?pdf=render
 33692568,https://doi.org/10.1038/s41588-021-00783-5,The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation.,"Lambert SA, Gil L, Jupp S, Ritchie SC, Xu Y, Buniello A, McMahon A, Abraham G, Chapman M, Parkinson H, Danesh J, MacArthur JAL, Inouye M.",,Nature genetics,2021,2021-04-01,N,,,,,,pdf:https://www.medrxiv.org/content/medrxiv/early/2020/05/23/2020.05.20.20108217.full.pdf; doi:https://doi.org/10.1038/s41588-021-00783-5
+39009924,https://doi.org/10.1007/s10654-024-01141-5,Multi-biobank Mendelian randomization analyses identify opposing pathways in plasma low-density lipoprotein-cholesterol lowering and gallstone disease.,"Yang G, Mason AM, Gill D, Schooling CM, Burgess S.",,European journal of epidemiology,2024,2024-07-15,Y,Gallstone Disease; Ldl-cholesterol; Drug-target Mendelian Randomization; Clustered Mendelian Randomization,,,"Plasma low-density lipoprotein (LDL)-cholesterol is positively associated with coronary artery disease risk while biliary cholesterol promotes gallstone formation. Different plasma LDL-cholesterol lowering pathways may have distinct effects on biliary cholesterol and thereby gallstone disease risk. We conducted a Mendelian randomization (MR) study using data from the UK Biobank (30,547 gallstone disease cases/336,742 controls), FinnGen (34,461 cases/301,383 controls) and Biobank Japan (9,305 cases/168,253 controls). We first performed drug-target MR analyses substantiated by colocalization to investigate the effects of plasma LDL-cholesterol lowering therapies on gallstone disease risk. We then performed clustered MR analyses and pathway analyses to identify distinct mechanisms underlying the association of plasma LDL-cholesterol with gallstone disease risk. For a 1-standard deviation reduction in plasma LDL-cholesterol, genetic mimics of statins were associated with lower gallstone disease risk (odds ratio 0.72 [95% confidence interval 0.62, 0.83]), but genetic mimics of PCSK9 inhibitors and targeting apolipoprotein B were associated with higher risk (1.11 [1.03, 1.19] and 1.23 [1.13, 1.35]). The association for statins was supported by colocalization (posterior probability 98.7%). Clustered MR analyses identified variant clusters showing opposing associations of plasma LDL-cholesterol with gallstone disease risk, with some evidence for ancestry-and sex-specific associations. Among variants lowering plasma LDL-cholesterol, those associated with lower gallstone disease risk were mapped to glycosphingolipid biosynthesis pathway, while those associated with higher risk were mapped to pathways relating to plasma lipoprotein assembly, remodelling, and clearance and ATP-binding cassette transporters. This MR study provides genetic evidence that different plasma LDL-cholesterol lowering pathways have opposing effects on gallstone disease risk.",,doi:https://doi.org/10.1007/s10654-024-01141-5; html:https://europepmc.org/articles/PMC11410903; pdf:https://europepmc.org/articles/PMC11410903?pdf=render
 32743489,https://doi.org/10.1016/j.eclinm.2020.100469,Gender differences in the presentation of fibromyalgia amongst children who have been maltreated.,"Chandan JS, Bandyopadhyay S, Taylor J, Nirantharakumar K.",,EClinicalMedicine,2020,2020-07-23,Y,,,,,,pdf:http://www.thelancet.com/article/S2589537020302133/pdf; doi:https://doi.org/10.1016/j.eclinm.2020.100469; html:https://europepmc.org/articles/PMC7385442; pdf:https://europepmc.org/articles/PMC7385442?pdf=render
-35477354,https://doi.org/10.1186/s12877-022-03077-5,Performance of the SarQoL quality of life tool in a UK population of older people with probable sarcopenia and implications for use in clinical trials: findings from the SarcNet registry.,"Witham MD, Heslop P, Dodds RM, Clegg AP, Hope SV, McDonald C, Smithard D, Storey B, Tan AL, Thornhill A, Sayer AA.",,BMC geriatrics,2022,2022-04-27,Y,Quality of life; Validity; Sarcopenia; Responsiveness; Minimum Clinical Important Difference,,,"<h4>Background</h4>The Sarcopenia Quality of Life (SarQoL) questionnaire is a disease-specific sarcopenia quality of life tool. We aimed to independently assess SarQoL with a particular focus on its suitability as a clinical trial outcome measure.<h4>Methods</h4>We analysed data from the UK Sarcopenia Network and Registry. Measures of physical performance and lean mass were collected at baseline. SarQoL and the Strength, Assistance, Rise, Climb - Falls (SARC-F) questionnaire (to assess functional ability) were collected at both baseline and six-month follow-up. Global changes in fitness and quality of life at 6 months were elicited on seven-point Likert scales. Internal consistency was assessed using Cronbach's alpha. Responsiveness (Cohen's d and Guyatt coefficients) and minimum clinically important differences were calculated for participants reporting slight improvement or worsening in their global scores. Concurrent validity was assessed by correlating baseline SarQoL scores with measures of physical performance and functional ability.<h4>Results</h4>We analysed data from 147 participants, 125 of whom underwent follow up assessment; mean age 78 years; 72 (49%) were women. Internal consistency was good; Cronbach's alpha was 0.944 at baseline and 0.732 at telephone follow-up. Correlation between baseline and follow-up SarQoL was weak (r = 0.27; p = 0.03). The minimum clinically important improvement ranged from 5 to 21 points giving trial sample size estimates of 25-100 participants. SarQoL scores were moderately correlated with handgrip (r = 0.37; p < 0.001), SARC-F (r = - 0.45; p < 0.001), short physical performance battery (r = 0.48; p < 0.001) and 4-m walk speed (r = 0.48; p < 0.001).<h4>Conclusions</h4>SarQoL has acceptable performance in older UK participants with probable sarcopenia and is sufficiently responsive for use in clinical trials for sarcopenia.",,pdf:https://bmcgeriatr.biomedcentral.com/track/pdf/10.1186/s12877-022-03077-5; doi:https://doi.org/10.1186/s12877-022-03077-5; html:https://europepmc.org/articles/PMC9043890; pdf:https://europepmc.org/articles/PMC9043890?pdf=render
 35585575,https://doi.org/10.1186/s12889-022-13219-4,The impact of COVID-19 vaccination in prisons in England and Wales: a metapopulation model.,"McCarthy CV, O'Mara O, van Leeuwen E, CMMID COVID-19 Working Group, Jit M, Sandmann F.",,BMC public health,2022,2022-05-18,Y,Vaccination; mathematical model; Public Health; Prisons; Covid-19,,,"<h4>Background</h4>High incidence of cases and deaths due to coronavirus disease 2019 (COVID-19) have been reported in prisons worldwide. This study aimed to evaluate the impact of different COVID-19 vaccination strategies in epidemiologically semi-enclosed settings such as prisons, where staff interact regularly with those incarcerated and the wider community.<h4>Methods</h4>We used a metapopulation transmission-dynamic model of a local prison in England and Wales. Two-dose vaccination strategies included no vaccination, vaccination of all individuals who are incarcerated and/or staff, and an age-based approach. Outcomes were quantified in terms of COVID-19-related symptomatic cases, losses in quality-adjusted life-years (QALYs), and deaths.<h4>Results</h4>Compared to no vaccination, vaccinating all people living and working in prison reduced cases, QALY loss and deaths over a one-year period by 41%, 32% and 36% respectively. However, if vaccine introduction was delayed until the start of an outbreak, the impact was negligible. Vaccinating individuals who are incarcerated and staff over 50 years old averted one death for every 104 vaccination courses administered. All-staff-only strategies reduced cases by up to 5%. Increasing coverage from 30 to 90% among those who are incarcerated reduced cases by around 30 percentage points.<h4>Conclusions</h4>The impact of vaccination in prison settings was highly dependent on early and rapid vaccine delivery. If administered to both those living and working in prison prior to an outbreak occurring, vaccines could substantially reduce COVID-19-related morbidity and mortality in prison settings.",,pdf:https://bmcpublichealth.biomedcentral.com/track/pdf/10.1186/s12889-022-13219-4; doi:https://doi.org/10.1186/s12889-022-13219-4; html:https://europepmc.org/articles/PMC9115545; pdf:https://europepmc.org/articles/PMC9115545?pdf=render
+35477354,https://doi.org/10.1186/s12877-022-03077-5,Performance of the SarQoL quality of life tool in a UK population of older people with probable sarcopenia and implications for use in clinical trials: findings from the SarcNet registry.,"Witham MD, Heslop P, Dodds RM, Clegg AP, Hope SV, McDonald C, Smithard D, Storey B, Tan AL, Thornhill A, Sayer AA.",,BMC geriatrics,2022,2022-04-27,Y,Quality of life; Validity; Sarcopenia; Responsiveness; Minimum Clinical Important Difference,,,"<h4>Background</h4>The Sarcopenia Quality of Life (SarQoL) questionnaire is a disease-specific sarcopenia quality of life tool. We aimed to independently assess SarQoL with a particular focus on its suitability as a clinical trial outcome measure.<h4>Methods</h4>We analysed data from the UK Sarcopenia Network and Registry. Measures of physical performance and lean mass were collected at baseline. SarQoL and the Strength, Assistance, Rise, Climb - Falls (SARC-F) questionnaire (to assess functional ability) were collected at both baseline and six-month follow-up. Global changes in fitness and quality of life at 6 months were elicited on seven-point Likert scales. Internal consistency was assessed using Cronbach's alpha. Responsiveness (Cohen's d and Guyatt coefficients) and minimum clinically important differences were calculated for participants reporting slight improvement or worsening in their global scores. Concurrent validity was assessed by correlating baseline SarQoL scores with measures of physical performance and functional ability.<h4>Results</h4>We analysed data from 147 participants, 125 of whom underwent follow up assessment; mean age 78 years; 72 (49%) were women. Internal consistency was good; Cronbach's alpha was 0.944 at baseline and 0.732 at telephone follow-up. Correlation between baseline and follow-up SarQoL was weak (r = 0.27; p = 0.03). The minimum clinically important improvement ranged from 5 to 21 points giving trial sample size estimates of 25-100 participants. SarQoL scores were moderately correlated with handgrip (r = 0.37; p < 0.001), SARC-F (r = - 0.45; p < 0.001), short physical performance battery (r = 0.48; p < 0.001) and 4-m walk speed (r = 0.48; p < 0.001).<h4>Conclusions</h4>SarQoL has acceptable performance in older UK participants with probable sarcopenia and is sufficiently responsive for use in clinical trials for sarcopenia.",,pdf:https://bmcgeriatr.biomedcentral.com/track/pdf/10.1186/s12877-022-03077-5; doi:https://doi.org/10.1186/s12877-022-03077-5; html:https://europepmc.org/articles/PMC9043890; pdf:https://europepmc.org/articles/PMC9043890?pdf=render
+30742608,https://doi.org/10.1371/journal.pcbi.1006785,"Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15.","Funk S, Camacho A, Kucharski AJ, Lowe R, Eggo RM, Edmunds WJ.",,PLoS computational biology,2019,2019-02-11,Y,,Applied Analytics,,"Real-time forecasts based on mathematical models can inform critical decision-making during infectious disease outbreaks. Yet, epidemic forecasts are rarely evaluated during or after the event, and there is little guidance on the best metrics for assessment. Here, we propose an evaluation approach that disentangles different components of forecasting ability using metrics that separately assess the calibration, sharpness and bias of forecasts. This makes it possible to assess not just how close a forecast was to reality but also how well uncertainty has been quantified. We used this approach to analyse the performance of weekly forecasts we generated in real time for Western Area, Sierra Leone, during the 2013-16 Ebola epidemic in West Africa. We investigated a range of forecast model variants based on the model fits generated at the time with a semi-mechanistic model, and found that good probabilistic calibration was achievable at short time horizons of one or two weeks ahead but model predictions were increasingly unreliable at longer forecasting horizons. This suggests that forecasts may have been of good enough quality to inform decision making based on predictions a few weeks ahead of time but not longer, reflecting the high level of uncertainty in the processes driving the trajectory of the epidemic. Comparing forecasts based on the semi-mechanistic model to simpler null models showed that the best semi-mechanistic model variant performed better than the null models with respect to probabilistic calibration, and that this would have been identified from the earliest stages of the outbreak. As forecasts become a routine part of the toolkit in public health, standards for evaluation of performance will be important for assessing quality and improving credibility of mathematical models, and for elucidating difficulties and trade-offs when aiming to make the most useful and reliable forecasts.",,pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006785&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1006785; html:https://europepmc.org/articles/PMC6386417; pdf:https://europepmc.org/articles/PMC6386417?pdf=render
 36240828,https://doi.org/10.1016/s2214-109x(22)00358-8,Prediction of upcoming global infection burden of influenza seasons after relaxation of public health and social measures during the COVID-19 pandemic: a modelling study.,"Ali ST, Lau YC, Shan S, Ryu S, Du Z, Wang L, Xu XK, Chen D, Xiong J, Tae J, Tsang TK, Wu P, Lau EHY, Cowling BJ.",,The Lancet. Global health,2022,2022-11-01,Y,,,,"<h4>Background</h4>The transmission dynamics of influenza were affected by public health and social measures (PHSMs) implemented globally since early 2020 to mitigate the COVID-19 pandemic. We aimed to assess the effect of COVID-19 PHSMs on the transmissibility of influenza viruses and to predict upcoming influenza epidemics.<h4>Methods</h4>For this modelling study, we used surveillance data on influenza virus activity for 11 different locations and countries in 2017-22. We implemented a data-driven mechanistic predictive modelling framework to predict future influenza seasons on the basis of pre-COVID-19 dynamics and the effect of PHSMs during the COVID-19 pandemic. We simulated the potential excess burden of upcoming influenza epidemics in terms of fold rise in peak magnitude and epidemic size compared with pre-COVID-19 levels. We also examined how a proactive influenza vaccination programme could mitigate this effect.<h4>Findings</h4>We estimated that COVID-19 PHSMs reduced influenza transmissibility by a maximum of 17·3% (95% CI 13·3-21·4) to 40·6% (35·2-45·9) and attack rate by 5·1% (1·5-7·2) to 24·8% (20·8-27·5) in the 2019-20 influenza season. We estimated a 10-60% increase in the population susceptibility for influenza, which might lead to a maximum of 1-5-fold rise in peak magnitude and 1-4-fold rise in epidemic size for the upcoming 2022-23 influenza season across locations, with a significantly higher fold rise in Singapore and Taiwan. The infection burden could be mitigated by additional proactive one-off influenza vaccination programmes.<h4>Interpretation</h4>Our results suggest the potential for substantial increases in infection burden in upcoming influenza seasons across the globe. Strengthening influenza vaccination programmes is the best preventive measure to reduce the effect of influenza virus infections in the community.<h4>Funding</h4>Health and Medical Research Fund, Hong Kong.",,pdf:https://www.repository.cam.ac.uk/bitstreams/bb5465bd-c08f-4c3d-ab0e-87fee39fc92b/download; doi:https://doi.org/10.1016/S2214-109X(22)00358-8; html:https://europepmc.org/articles/PMC9573849
-36331190,https://doi.org/10.1056/nejmoa2204233,Empagliflozin in Patients with Chronic Kidney Disease.,"The EMPA-KIDNEY Collaborative Group, Herrington WG, Staplin N, Wanner C, Green JB, Hauske SJ, Emberson JR, Preiss D, Judge P, Mayne KJ, Ng SYA, Sammons E, Zhu D, Hill M, Stevens W, Wallendszus K, Brenner S, Cheung AK, Liu ZH, Li J, Hooi LS, Liu W, Kadowaki T, Nangaku M, Levin A, Cherney D, Maggioni AP, Pontremoli R, Deo R, Goto S, Rossello X, Tuttle KR, Steubl D, Petrini M, Massey D, Eilbracht J, Brueckmann M, Landray MJ, Baigent C, Haynes R.",,The New England journal of medicine,2023,2022-11-04,Y,,,,"<h4>Background</h4>The effects of empagliflozin in patients with chronic kidney disease who are at risk for disease progression are not well understood. The EMPA-KIDNEY trial was designed to assess the effects of treatment with empagliflozin in a broad range of such patients.<h4>Methods</h4>We enrolled patients with chronic kidney disease who had an estimated glomerular filtration rate (eGFR) of at least 20 but less than 45 ml per minute per 1.73 m<sup>2</sup> of body-surface area, or who had an eGFR of at least 45 but less than 90 ml per minute per 1.73 m<sup>2</sup> with a urinary albumin-to-creatinine ratio (with albumin measured in milligrams and creatinine measured in grams) of at least 200. Patients were randomly assigned to receive empagliflozin (10 mg once daily) or matching placebo. The primary outcome was a composite of progression of kidney disease (defined as end-stage kidney disease, a sustained decrease in eGFR to <10 ml per minute per 1.73 m<sup>2</sup>, a sustained decrease in eGFR of ≥40% from baseline, or death from renal causes) or death from cardiovascular causes.<h4>Results</h4>A total of 6609 patients underwent randomization. During a median of 2.0 years of follow-up, progression of kidney disease or death from cardiovascular causes occurred in 432 of 3304 patients (13.1%) in the empagliflozin group and in 558 of 3305 patients (16.9%) in the placebo group (hazard ratio, 0.72; 95% confidence interval [CI], 0.64 to 0.82; P<0.001). Results were consistent among patients with or without diabetes and across subgroups defined according to eGFR ranges. The rate of hospitalization from any cause was lower in the empagliflozin group than in the placebo group (hazard ratio, 0.86; 95% CI, 0.78 to 0.95; P = 0.003), but there were no significant between-group differences with respect to the composite outcome of hospitalization for heart failure or death from cardiovascular causes (which occurred in 4.0% in the empagliflozin group and 4.6% in the placebo group) or death from any cause (in 4.5% and 5.1%, respectively). The rates of serious adverse events were similar in the two groups.<h4>Conclusions</h4>Among a wide range of patients with chronic kidney disease who were at risk for disease progression, empagliflozin therapy led to a lower risk of progression of kidney disease or death from cardiovascular causes than placebo. (Funded by Boehringer Ingelheim and others; EMPA-KIDNEY ClinicalTrials.gov number, NCT03594110; EudraCT number, 2017-002971-24.).",,pdf:https://www.nejm.org/doi/pdf/10.1056/NEJMoa2204233?articleTools=true; doi:https://doi.org/10.1056/NEJMoa2204233; html:https://europepmc.org/articles/PMC7614055; pdf:https://europepmc.org/articles/PMC7614055?pdf=render
 35072137,https://doi.org/10.1016/j.xgen.2021.100086,Machine learning optimized polygenic scores for blood cell traits identify sex-specific trajectories and genetic correlations with disease.,"Xu Y, Vuckovic D, Ritchie SC, Akbari P, Jiang T, Grealey J, Butterworth AS, Ouwehand WH, Roberts DJ, Di Angelantonio E, Danesh J, Soranzo N, Inouye M.",,Cell genomics,2022,2022-01-12,Y,Method; Machine Learning; Population Stratification; Polygenic Score; Blood Cell Trait; Disease Assocations,,,"Genetic association studies for blood cell traits, which are key indicators of health and immune function, have identified several hundred associations and defined a complex polygenic architecture. Polygenic scores (PGSs) for blood cell traits have potential clinical utility in disease risk prediction and prevention, but designing PGS remains challenging and the optimal methods are unclear. To address this, we evaluated the relative performance of 6 methods to develop PGS for 26 blood cell traits, including a standard method of pruning and thresholding (P + T) and 5 learning methods: LDpred2, elastic net (EN), Bayesian ridge (BR), multilayer perceptron (MLP) and convolutional neural network (CNN). We evaluated these optimized PGSs on blood cell trait data from UK Biobank and INTERVAL. We find that PGSs designed using common machine learning methods EN and BR show improved prediction of blood cell traits and consistently outperform other methods. Our analyses suggest EN/BR as the top choices for PGS construction, showing improved performance for 25 blood cell traits in the external validation, with correlations with the directly measured traits increasing by 10%-23%. Ten PGSs showed significant statistical interaction with sex, and sex-specific PGS stratification showed that all of them had substantial variation in the trajectories of blood cell traits with age. Genetic correlations between the PGSs for blood cell traits and common human diseases identified well-known as well as new associations. We develop machine learning-optimized PGS for blood cell traits, demonstrate their relationships with sex, age, and disease, and make these publicly available as a resource.",,doi:https://doi.org/10.1016/j.xgen.2021.100086; doi:https://doi.org/10.1016/j.xgen.2021.100086; html:https://europepmc.org/articles/PMC8758502; pdf:https://europepmc.org/articles/PMC8758502?pdf=render
-30742608,https://doi.org/10.1371/journal.pcbi.1006785,"Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15.","Funk S, Camacho A, Kucharski AJ, Lowe R, Eggo RM, Edmunds WJ.",,PLoS computational biology,2019,2019-02-11,Y,,Applied Analytics,,"Real-time forecasts based on mathematical models can inform critical decision-making during infectious disease outbreaks. Yet, epidemic forecasts are rarely evaluated during or after the event, and there is little guidance on the best metrics for assessment. Here, we propose an evaluation approach that disentangles different components of forecasting ability using metrics that separately assess the calibration, sharpness and bias of forecasts. This makes it possible to assess not just how close a forecast was to reality but also how well uncertainty has been quantified. We used this approach to analyse the performance of weekly forecasts we generated in real time for Western Area, Sierra Leone, during the 2013-16 Ebola epidemic in West Africa. We investigated a range of forecast model variants based on the model fits generated at the time with a semi-mechanistic model, and found that good probabilistic calibration was achievable at short time horizons of one or two weeks ahead but model predictions were increasingly unreliable at longer forecasting horizons. This suggests that forecasts may have been of good enough quality to inform decision making based on predictions a few weeks ahead of time but not longer, reflecting the high level of uncertainty in the processes driving the trajectory of the epidemic. Comparing forecasts based on the semi-mechanistic model to simpler null models showed that the best semi-mechanistic model variant performed better than the null models with respect to probabilistic calibration, and that this would have been identified from the earliest stages of the outbreak. As forecasts become a routine part of the toolkit in public health, standards for evaluation of performance will be important for assessing quality and improving credibility of mathematical models, and for elucidating difficulties and trade-offs when aiming to make the most useful and reliable forecasts.",,pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006785&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1006785; html:https://europepmc.org/articles/PMC6386417; pdf:https://europepmc.org/articles/PMC6386417?pdf=render
+36331190,https://doi.org/10.1056/nejmoa2204233,Empagliflozin in Patients with Chronic Kidney Disease.,"The EMPA-KIDNEY Collaborative Group, Herrington WG, Staplin N, Wanner C, Green JB, Hauske SJ, Emberson JR, Preiss D, Judge P, Mayne KJ, Ng SYA, Sammons E, Zhu D, Hill M, Stevens W, Wallendszus K, Brenner S, Cheung AK, Liu ZH, Li J, Hooi LS, Liu W, Kadowaki T, Nangaku M, Levin A, Cherney D, Maggioni AP, Pontremoli R, Deo R, Goto S, Rossello X, Tuttle KR, Steubl D, Petrini M, Massey D, Eilbracht J, Brueckmann M, Landray MJ, Baigent C, Haynes R.",,The New England journal of medicine,2023,2022-11-04,Y,,,,"<h4>Background</h4>The effects of empagliflozin in patients with chronic kidney disease who are at risk for disease progression are not well understood. The EMPA-KIDNEY trial was designed to assess the effects of treatment with empagliflozin in a broad range of such patients.<h4>Methods</h4>We enrolled patients with chronic kidney disease who had an estimated glomerular filtration rate (eGFR) of at least 20 but less than 45 ml per minute per 1.73 m<sup>2</sup> of body-surface area, or who had an eGFR of at least 45 but less than 90 ml per minute per 1.73 m<sup>2</sup> with a urinary albumin-to-creatinine ratio (with albumin measured in milligrams and creatinine measured in grams) of at least 200. Patients were randomly assigned to receive empagliflozin (10 mg once daily) or matching placebo. The primary outcome was a composite of progression of kidney disease (defined as end-stage kidney disease, a sustained decrease in eGFR to <10 ml per minute per 1.73 m<sup>2</sup>, a sustained decrease in eGFR of ≥40% from baseline, or death from renal causes) or death from cardiovascular causes.<h4>Results</h4>A total of 6609 patients underwent randomization. During a median of 2.0 years of follow-up, progression of kidney disease or death from cardiovascular causes occurred in 432 of 3304 patients (13.1%) in the empagliflozin group and in 558 of 3305 patients (16.9%) in the placebo group (hazard ratio, 0.72; 95% confidence interval [CI], 0.64 to 0.82; P<0.001). Results were consistent among patients with or without diabetes and across subgroups defined according to eGFR ranges. The rate of hospitalization from any cause was lower in the empagliflozin group than in the placebo group (hazard ratio, 0.86; 95% CI, 0.78 to 0.95; P = 0.003), but there were no significant between-group differences with respect to the composite outcome of hospitalization for heart failure or death from cardiovascular causes (which occurred in 4.0% in the empagliflozin group and 4.6% in the placebo group) or death from any cause (in 4.5% and 5.1%, respectively). The rates of serious adverse events were similar in the two groups.<h4>Conclusions</h4>Among a wide range of patients with chronic kidney disease who were at risk for disease progression, empagliflozin therapy led to a lower risk of progression of kidney disease or death from cardiovascular causes than placebo. (Funded by Boehringer Ingelheim and others; EMPA-KIDNEY ClinicalTrials.gov number, NCT03594110; EudraCT number, 2017-002971-24.).",,pdf:https://www.nejm.org/doi/pdf/10.1056/NEJMoa2204233?articleTools=true; doi:https://doi.org/10.1056/NEJMoa2204233; html:https://europepmc.org/articles/PMC7614055; pdf:https://europepmc.org/articles/PMC7614055?pdf=render
 37573145,https://doi.org/10.1093/ndt/gfad180,Recovery of kidney function after acute kidney disease-a multi-cohort analysis.,"Sawhney S, Ball W, Bell S, Black C, Christiansen CF, Heide-Jørgensen U, Jensen SK, Lambourg E, Ronksley PE, Tan Z, Tonelli M, James MT.",,"Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association",2024,2024-02-01,Y,Recovery; Prognosis; epidemiology; Ckd; Aki,,,"<h4>Background</h4>There are no consensus definitions for evaluating kidney function recovery after acute kidney injury (AKI) and acute kidney disease (AKD), nor is it clear how recovery varies across populations and clinical subsets. We present a federated analysis of four population-based cohorts from Canada, Denmark and Scotland, 2011-18.<h4>Methods</h4>We identified incident AKD defined by serum creatinine changes within 48 h, 7 days and 90 days based on KDIGO AKI and AKD criteria. Separately, we applied changes up to 365 days to address widely used e-alert implementations that extend beyond the KDIGO AKI and AKD timeframes. Kidney recovery was based on resolution of AKD and a subsequent creatinine measurement below 1.2× baseline. We evaluated transitions between non-recovery, recovery and death up to 1 year; within age, sex and comorbidity subgroups; between subset AKD definitions; and across cohorts.<h4>Results</h4>There were 464 868 incident cases, median age 67-75 years. At 1 year, results were consistent across cohorts, with pooled mortalities for creatinine changes within 48 h, 7 days, 90 days and 365 days (and 95% confidence interval) of 40% (34%-45%), 40% (34%-46%), 37% (31%-42%) and 22% (16%-29%) respectively, and non-recovery of kidney function of 19% (15%-23%), 30% (24%-35%), 25% (21%-29%) and 37% (30%-43%), respectively. Recovery by 14 and 90 days was frequently not sustained at 1 year. Older males and those with heart failure or cancer were more likely to die than to experience sustained non-recovery, whereas the converse was true for younger females and those with diabetes.<h4>Conclusion</h4>Consistently across multiple cohorts, based on 1-year mortality and non-recovery, KDIGO AKD (up to 90 days) is at least prognostically similar to KDIGO AKI (7 days), and covers more people. Outcomes associated with AKD vary by age, sex and comorbidities such that older males are more likely to die, and younger females are less likely to recover.",,pdf:https://academic.oup.com/ndt/advance-article-pdf/doi/10.1093/ndt/gfad180/51104398/gfad180.pdf; doi:https://doi.org/10.1093/ndt/gfad180; html:https://europepmc.org/articles/PMC10899778; pdf:https://europepmc.org/articles/PMC10899778?pdf=render
-37321240,https://doi.org/10.1016/s2215-0366(23)00113-x,Mental health in Europe during the COVID-19 pandemic: a systematic review.,"Ahmed N, Barnett P, Greenburgh A, Pemovska T, Stefanidou T, Lyons N, Ikhtabi S, Talwar S, Francis ER, Harris SM, Shah P, Machin K, Jeffreys S, Mitchell L, Lynch C, Foye U, Schlief M, Appleton R, Saunders KRK, Baldwin H, Allan SM, Sheridan-Rains L, Kharboutly O, Kular A, Goldblatt P, Stewart R, Kirkbride JB, Lloyd-Evans B, Johnson S.",,The lancet. Psychiatry,2023,2023-06-12,Y,,,,"The COVID-19 pandemic caused immediate and far-reaching disruption to society, the economy, and health-care services. We synthesised evidence on the effect of the pandemic on mental health and mental health care in high-income European countries. We included 177 longitudinal and repeated cross-sectional studies comparing prevalence or incidence of mental health problems, mental health symptom severity in people with pre-existing mental health conditions, or mental health service use before versus during the pandemic, or between different timepoints of the pandemic. We found that epidemiological studies reported higher prevalence of some mental health problems during the pandemic compared with before it, but that in most cases this increase reduced over time. Conversely, studies of health records showed reduced incidence of new diagnoses at the start of the pandemic, which further declined during 2020. Mental health service use also declined at the onset of the pandemic but increased later in 2020 and through 2021, although rates of use did not return to pre-pandemic levels for some services. We found mixed patterns of effects of the pandemic on mental health and social outcome for adults already living with mental health conditions.",,pdf:http://www.thelancet.com/article/S221503662300113X/pdf; doi:https://doi.org/10.1016/S2215-0366(23)00113-X; html:https://europepmc.org/articles/PMC10259832; pdf:https://europepmc.org/articles/PMC10259832?pdf=render
 33782427,https://doi.org/10.1038/s41598-021-86266-3,Analysis of temporal trends in potential COVID-19 cases reported through NHS Pathways England.,"Leclerc QJ, Nightingale ES, Abbott S, CMMID COVID-19 Working Group, Jombart T.",,Scientific reports,2021,2021-03-29,Y,,,,"The National Health Service (NHS) Pathways triage system collates data on enquiries to 111 and 999 services in England. Since the 18th of March 2020, these data have been made publically available for potential COVID-19 symptoms self-reported by members of the public. Trends in such reports over time are likely to reflect behaviour of the ongoing epidemic within the wider community, potentially capturing valuable information across a broader severity profile of cases than hospital admission data. We present a fully reproducible analysis of temporal trends in NHS Pathways reports until 14th May 2020, nationally and regionally, and demonstrate that rates of growth/decline and effective reproduction number estimated from these data may be useful in monitoring transmission. This is a particularly pressing issue as lockdown restrictions begin to be lifted and evidence of disease resurgence must be constantly reassessed. We further assess the correlation between NHS Pathways reports and a publicly available NHS dataset of COVID-19-associated deaths in England, finding that enquiries to 111/999 were strongly associated with daily deaths reported 16 days later. Our results highlight the potential of NHS Pathways as the basis of an early warning system. However, this dataset relies on self-reported symptoms, which are at risk of being severely biased. Further detailed work is therefore necessary to investigate potential behavioural issues which might otherwise explain our conclusions.",,pdf:https://www.nature.com/articles/s41598-021-86266-3.pdf; doi:https://doi.org/10.1038/s41598-021-86266-3; html:https://europepmc.org/articles/PMC8007605; pdf:https://europepmc.org/articles/PMC8007605?pdf=render
+37321240,https://doi.org/10.1016/s2215-0366(23)00113-x,Mental health in Europe during the COVID-19 pandemic: a systematic review.,"Ahmed N, Barnett P, Greenburgh A, Pemovska T, Stefanidou T, Lyons N, Ikhtabi S, Talwar S, Francis ER, Harris SM, Shah P, Machin K, Jeffreys S, Mitchell L, Lynch C, Foye U, Schlief M, Appleton R, Saunders KRK, Baldwin H, Allan SM, Sheridan-Rains L, Kharboutly O, Kular A, Goldblatt P, Stewart R, Kirkbride JB, Lloyd-Evans B, Johnson S.",,The lancet. Psychiatry,2023,2023-06-12,Y,,,,"The COVID-19 pandemic caused immediate and far-reaching disruption to society, the economy, and health-care services. We synthesised evidence on the effect of the pandemic on mental health and mental health care in high-income European countries. We included 177 longitudinal and repeated cross-sectional studies comparing prevalence or incidence of mental health problems, mental health symptom severity in people with pre-existing mental health conditions, or mental health service use before versus during the pandemic, or between different timepoints of the pandemic. We found that epidemiological studies reported higher prevalence of some mental health problems during the pandemic compared with before it, but that in most cases this increase reduced over time. Conversely, studies of health records showed reduced incidence of new diagnoses at the start of the pandemic, which further declined during 2020. Mental health service use also declined at the onset of the pandemic but increased later in 2020 and through 2021, although rates of use did not return to pre-pandemic levels for some services. We found mixed patterns of effects of the pandemic on mental health and social outcome for adults already living with mental health conditions.",,pdf:http://www.thelancet.com/article/S221503662300113X/pdf; doi:https://doi.org/10.1016/S2215-0366(23)00113-X; html:https://europepmc.org/articles/PMC10259832; pdf:https://europepmc.org/articles/PMC10259832?pdf=render
 34957541,https://doi.org/10.1111/bjh.18013,A novel algorithmic approach to generate consensus treatment guidelines in adult acute myeloid leukaemia.,"Coats T, Bean D, Basset A, Sirkis T, Brammeld J, Johnson S, Thomas I, Gilkes A, Raj K, Dennis M, Knapper S, Mehta P, Khwaja A, Hunter H, Tauro S, Bowen D, Jones G, Dobson R, Russell N, Dillon R.",,British journal of haematology,2022,2021-12-26,N,Myeloid Leukaemia; Classifications; Diagnostic Haematology; Clinical Haematology,,,"Induction therapy for acute myeloid leukaemia (AML) has changed with the approval of a number of new agents. Clinical guidelines can struggle to keep pace with an evolving treatment and evidence landscape and therefore identifying the most appropriate front-line treatment is challenging for clinicians. Here, we combined drug eligibility criteria and genetic risk stratification into a digital format, allowing the full range of possible treatment eligibility scenarios to be defined. Using exemplar cases representing each of the 22 identified scenarios, we sought to generate consensus on treatment choice from a panel of nine aUK AML experts. We then analysed >2500 real-world cases using the same algorithm, confirming the existence of 21/22 of these scenarios and demonstrating that our novel approach could generate a consensus AML induction treatment in 98% of cases. Our approach, driven by the use of decision trees, is an efficient way to develop consensus guidance rapidly and could be applied to other disease areas. It has the potential to be updated frequently to capture changes in eligibility criteria, novel therapies and emerging trial data. An interactive digital version of the consensus guideline is available.",,pdf:https://discovery.dundee.ac.uk/files/71382229/Br_J_Haematol_2022_Coats_A_novel_algorithmic_approach_to_generate_consensus_treatment_guidelines_in_adult_acute.pdf; doi:https://doi.org/10.1111/bjh.18013
 32023934,https://doi.org/10.3390/ijerph17030892,Identifying Homogeneous Patterns of Injury in Paediatric Trauma Patients to Improve Risk-Adjusted Models of Mortality and Functional Outcomes.,"Dipnall JF, Gabbe BJ, Teague WJ, Beck B.",,International journal of environmental research and public health,2020,2020-01-31,Y,"Trauma; Injury; Paediatric; Latent Class Analysis; Risk Adjustment; Mortality, Koschi, Classes",Improving Public Health,injuries and accidents,"Injury is a leading cause of morbidity and mortality in the paediatric population and exhibits complex injury patterns. This study aimed to identify homogeneous groups of paediatric major trauma patients based on their profile of injury for use in mortality and functional outcomes risk-adjusted models. Data were extracted from the population-based Victorian State Trauma Registry for patients aged 0-15 years, injured 2006-2016. Four Latent Class Analysis (LCA) models with/without covariates of age/sex tested up to six possible latent classes. Five risk-adjusted models of in-hospital mortality and 6-month functional outcomes incorporated a combination of Injury Severity Score (ISS), New ISS (NISS), and LCA classes. LCA models replicated the best log-likelihood and entropy > 0.8 for all models (N = 1281). Four latent injury classes were identified: isolated head; isolated abdominal organ; multi-trauma injuries, and other injuries. The best models, in terms of goodness of fit statistics and model diagnostics, included the LCA classes and NISS. The identification of isolated head, isolated abdominal, multi-trauma and other injuries as key latent paediatric injury classes highlights areas for emphasis in planning prevention initiatives and paediatric trauma system development. Future risk-adjusted paediatric injury models that include these injury classes with the NISS when evaluating mortality and functional outcomes is recommended.",,pdf:https://www.mdpi.com/1660-4601/17/3/892/pdf?version=1580475934; doi:https://doi.org/10.3390/ijerph17030892; html:https://europepmc.org/articles/PMC7037699; pdf:https://europepmc.org/articles/PMC7037699?pdf=render
 31756303,https://doi.org/10.1161/circgen.119.002711,Genetic Determinants of Lipids and Cardiovascular Disease Outcomes: A Wide-Angled Mendelian Randomization Investigation.,"Allara E, Morani G, Carter P, Gkatzionis A, Zuber V, Foley CN, Rees JMB, Mason AM, Bell S, Gill D, Lindström S, Butterworth AS, Di Angelantonio E, Peters J, Burgess S, INVENT consortium.",,Circulation. Genomic and precision medicine,2019,2019-11-22,Y,Lipids; Aortic valve stenosis; epidemiology; Venous Thromboembolism; Mendelian Randomization,,,"<h4>Background</h4>Evidence from randomized trials has shown that therapies that lower LDL (low-density lipoprotein)-cholesterol and triglycerides reduce coronary artery disease (CAD) risk. However, there is still uncertainty about their effects on other cardiovascular outcomes. We therefore performed a systematic investigation of causal relationships between circulating lipids and cardiovascular outcomes using a Mendelian randomization approach.<h4>Methods</h4>In the primary analysis, we performed 2-sample multivariable Mendelian randomization using data from participants of European ancestry. We also conducted univariable analyses using inverse-variance weighted and robust methods, and gene-specific analyses using variants that can be considered as proxies for specific lipid-lowering medications. We obtained associations with lipid fractions from the Global Lipids Genetics Consortium, a meta-analysis of 188 577 participants, and genetic associations with cardiovascular outcomes from 367 703 participants in UK Biobank.<h4>Results</h4>For LDL-cholesterol, in addition to the expected positive associations with CAD risk (odds ratio [OR] per 1 SD increase, 1.45 [95% CI, 1.35-1.57]) and other atheromatous outcomes (ischemic cerebrovascular disease and peripheral vascular disease), we found independent associations of genetically predicted LDL-cholesterol with abdominal aortic aneurysm (OR, 1.75 [95% CI, 1.40-2.17]) and aortic valve stenosis (OR, 1.46 [95% CI, 1.25-1.70]). Genetically predicted triglyceride levels were positively associated with CAD (OR, 1.25 [95% CI, 1.12-1.40]), aortic valve stenosis (OR, 1.29 [95% CI, 1.04-1.61]), and hypertension (OR, 1.17 [95% CI, 1.07-1.27]), but inversely associated with venous thromboembolism (OR, 0.79 [95% CI, 0.67-0.93]) and hemorrhagic stroke (OR, 0.78 [95% CI, 0.62-0.98]). We also found positive associations of genetically predicted LDL-cholesterol and triglycerides with heart failure that appeared to be mediated by CAD.<h4>Conclusions</h4>Lowering LDL-cholesterol is likely to prevent abdominal aortic aneurysm and aortic stenosis, in addition to CAD and other atheromatous cardiovascular outcomes. Lowering triglycerides is likely to prevent CAD and aortic valve stenosis but may increase thromboembolic risk.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCGEN.119.002711; doi:https://doi.org/10.1161/CIRCGEN.119.002711; html:https://europepmc.org/articles/PMC6922071; pdf:https://europepmc.org/articles/PMC6922071?pdf=render
 33615277,https://doi.org/10.1016/j.xpro.2021.100334,Massive expansion and cryopreservation of functional human induced pluripotent stem cell-derived cardiomyocytes.,"Maas RGC, Lee S, Harakalova M, Snijders Blok CJB, Goodyer WR, Hjortnaes J, Doevendans PAFM, Van Laake LW, van der Velden J, Asselbergs FW, Wu JC, Sluijter JPG, Wu SM, Buikema JW.",,STAR protocols,2021,2021-02-09,Y,Cell differentiation; Cell culture; Stem Cells,,,"Since the discovery of human induced pluripotent stem cells (hiPSCs), numerous strategies have been established to efficiently derive cardiomyocytes from hiPSCs (hiPSC-CMs). Here, we describe a cost-effective strategy for the subsequent massive expansion (>250-fold) of high-purity hiPSC-CMs relying on two aspects: removal of cell-cell contacts and small-molecule inhibition with CHIR99021. The protocol maintains CM functionality, allows cryopreservation, and the cells can be used in downstream assays such as disease modeling, drug and toxicity screening, and cell therapy. For complete details on the use and execution of this protocol, please refer to Buikema (2020).",,doi:https://doi.org/10.1016/j.xpro.2021.100334; doi:https://doi.org/10.1016/j.xpro.2021.100334; html:https://europepmc.org/articles/PMC7881265; pdf:https://europepmc.org/articles/PMC7881265?pdf=render
-33521535,https://doi.org/10.1136/bmjnph-2020-000107,Genetic risk of obesity as a modifier of associations between neighbourhood environment and body mass index: an observational study of 335 046 UK Biobank participants.,"Mason KE, Palla L, Pearce N, Phelan J, Cummins S.",,"BMJ nutrition, prevention & health",2020,2020-10-05,Y,Malnutrition; Dietary Patterns,,,"<h4>Background</h4>There is growing recognition that recent global increases in obesity are the product of a complex interplay between genetic and environmental factors. However, in gene-environment studies of obesity, 'environment' usually refers to individual behavioural factors that influence energy balance, whereas more upstream environmental factors are overlooked. We examined gene-environment interactions between genetic risk of obesity and two neighbourhood characteristics likely to be associated with obesity (proximity to takeaway/fast-food outlets and availability of physical activity facilities).<h4>Methods</h4>We used data from 335 046 adults aged 40-70 in the UK Biobank cohort to conduct a population-based cross-sectional study of interactions between neighbourhood characteristics and genetic risk of obesity, in relation to body mass index (BMI). Proximity to a fast-food outlet was defined as distance from home address to nearest takeaway/fast-food outlet, and availability of physical activity facilities as the number of formal physical activity facilities within 1 km of home address. Genetic risk of obesity was operationalised by weighted Genetic Risk Scores of 91 or 69 single nucleotide polymorphisms (SNP), and by six individual SNPs considered separately. Multivariable, mixed-effects models with product terms for the gene-environment interactions were estimated.<h4>Results</h4>After accounting for likely confounding, the association between proximity to takeaway/fast-food outlets and BMI was stronger among those at increased genetic risk of obesity, with evidence of an interaction with polygenic risk scores (p=0.018 and p=0.028 for 69-SNP and 91-SNP scores, respectively) and in particular with a SNP linked to <i>MC4R</i> (p=0.009), a gene known to regulate food intake. We found very little evidence of gene-environment interaction for the availability of physical activity facilities.<h4>Conclusions</h4>Individuals at an increased genetic risk of obesity may be more sensitive to exposure to the local fast-food environment. Ensuring that neighbourhood residential environments are designed to promote a healthy weight may be particularly important for those with greater genetic susceptibility to obesity.",,pdf:https://nutrition.bmj.com/content/bmjnph/3/2/247.full.pdf; doi:https://doi.org/10.1136/bmjnph-2020-000107; html:https://europepmc.org/articles/PMC7841812; pdf:https://europepmc.org/articles/PMC7841812?pdf=render
 36029662,https://doi.org/10.1016/j.bios.2022.114623,Triazole-derivatized near-infrared cyanine dyes enable local functional fluorescent imaging of ocular inflammation.,"Thomas CN, Alfahad N, Capewell N, Cowley J, Hickman E, Fernandez A, Harrison N, Qureshi OS, Bennett N, Barnes NM, Dick AD, Chu CJ, Liu X, Denniston AK, Vendrell M, Hill LJ.",,Biosensors & bioelectronics,2022,2022-08-13,N,Leukocytes; Uveitis; Cyanine; Near-infrared; optical coherence tomography; Fluorophores,,,"Near-infrared (NIR) chemical fluorophores are promising tools for in-vivo imaging in real time but often succumb to rapid photodegradation. Indocyanine green (ICG) is the only NIR dye with regulatory approval for ocular imaging in humans; however, ICG, when employed for applications such as labelling immune cells, has limited sensitivity and does not allow precise detection of specific inflammatory events, for example leukocyte recruitment during uveitic flare-ups. We investigated the potential use of photostable novel triazole NIR cyanine (TNC) dyes for detecting and characterising activated T-cell activity within the eye. Three TNC dyes were evaluated for ocular cytotoxicity in-vitro using a MTT assay and optimised concentrations for intraocular detection within ex-vivo porcine eyes after topical application or intracameral injections of the dyes. TNC labelled T-cell tracking experiments and mechanistic studies were also performed in-vitro. TNC-1 and TNC-2 dyes exhibited greater fluorescence intensity than ICG at 10 μM, whereas TNC-3 was only detectable at 100 μM within the porcine eye. TNC dyes did not demonstrate any ocular cell toxicity at working concentrations of 10 μM. CD4<sup>+</sup>T-cells labelled with TNC-1 or TNC-2 were detected within the porcine eye, with TNC-1 being brighter than TNC-2. Detection of TNC-1 and TNC-2 into CD4<sup>+</sup>T-cells was prevented by prior incubation with dynole 34-2 (50 μM), suggesting active uptake of these dyes via dynamin-dependent processes. The present study provides evidence that TNC dyes are suitable to detect activated CD4<sup>+</sup>T-cells within the eye with potential as a diagnostic marker for ocular inflammatory diseases.",,pdf:https://research-information.bris.ac.uk/files/338519213/1_s2.0_S0956566322006637_main.pdf; doi:https://doi.org/10.1016/j.bios.2022.114623
-36066609,https://doi.org/10.1007/s00392-022-02088-x,Towards automatic classification of cardiovascular magnetic resonance Task Force Criteria for diagnosis of arrhythmogenic right ventricular cardiomyopathy.,"Bourfiss M, Sander J, de Vos BD, Te Riele ASJM, Asselbergs FW, Išgum I, Velthuis BK.",,Clinical research in cardiology : official journal of the German Cardiac Society,2023,2022-09-06,Y,Cardiac Magnetic Resonance Imaging; Arrhythmogenic Right Ventricular Cardiomyopathy; Automatic Segmentation; Deep Learning,,,"<h4>Background</h4>Arrhythmogenic right ventricular cardiomyopathy (ARVC) is diagnosed according to the Task Force Criteria (TFC) in which cardiovascular magnetic resonance (CMR) imaging plays an important role. Our study aims to apply an automatic deep learning-based segmentation for right and left ventricular CMR assessment and evaluate this approach for classification of the CMR TFC.<h4>Methods</h4>We included 227 subjects suspected of ARVC who underwent CMR. Subjects were classified into (1) ARVC patients fulfilling TFC; (2) at-risk family members; and (3) controls. To perform automatic segmentation, a Bayesian Dilated Residual Neural Network was trained and tested. Performance of automatic versus manual segmentation was assessed using Dice-coefficient and Hausdorff distance. Since automatic segmentation is most challenging in basal slices, manual correction of the automatic segmentation in the most basal slice was simulated (automatic<sup>-basal</sup>). CMR TFC calculated using manual and automatic<sup>-basal</sup> segmentation were compared using Cohen's Kappa (κ).<h4>Results</h4>Automatic segmentation was trained on CMRs of 70 subjects (39.6 ± 18.1 years, 47% female) and tested on 157 subjects (36.9 ± 17.6 years, 59% female). Dice-coefficient and Hausdorff distance showed good agreement between manual and automatic segmentations (≥ 0.89 and ≤ 10.6 mm, respectively) which further improved after simulated correction of the most basal slice (≥ 0.92 and ≤ 9.2 mm, p < 0.001). Pearson correlation of volumetric and functional CMR measurements was good to excellent (automatic (r = 0.78-0.99, p < 0.001) and automatic<sup>-basal</sup> (r = 0.88-0.99, p < 0.001) measurements). CMR TFC classification using automatic<sup>-basal</sup> segmentations was comparable to manual segmentations (κ 0.98 ± 0.02) with comparable diagnostic performance.<h4>Conclusions</h4>Combining automatic segmentation of CMRs with correction of the most basal slice results in accurate CMR TFC classification of subjects suspected of ARVC.",,pdf:https://link.springer.com/content/pdf/10.1007/s00392-022-02088-x.pdf; doi:https://doi.org/10.1007/s00392-022-02088-x; html:https://europepmc.org/articles/PMC9998324; pdf:https://europepmc.org/articles/PMC9998324?pdf=render
+33521535,https://doi.org/10.1136/bmjnph-2020-000107,Genetic risk of obesity as a modifier of associations between neighbourhood environment and body mass index: an observational study of 335 046 UK Biobank participants.,"Mason KE, Palla L, Pearce N, Phelan J, Cummins S.",,"BMJ nutrition, prevention & health",2020,2020-10-05,Y,Malnutrition; Dietary Patterns,,,"<h4>Background</h4>There is growing recognition that recent global increases in obesity are the product of a complex interplay between genetic and environmental factors. However, in gene-environment studies of obesity, 'environment' usually refers to individual behavioural factors that influence energy balance, whereas more upstream environmental factors are overlooked. We examined gene-environment interactions between genetic risk of obesity and two neighbourhood characteristics likely to be associated with obesity (proximity to takeaway/fast-food outlets and availability of physical activity facilities).<h4>Methods</h4>We used data from 335 046 adults aged 40-70 in the UK Biobank cohort to conduct a population-based cross-sectional study of interactions between neighbourhood characteristics and genetic risk of obesity, in relation to body mass index (BMI). Proximity to a fast-food outlet was defined as distance from home address to nearest takeaway/fast-food outlet, and availability of physical activity facilities as the number of formal physical activity facilities within 1 km of home address. Genetic risk of obesity was operationalised by weighted Genetic Risk Scores of 91 or 69 single nucleotide polymorphisms (SNP), and by six individual SNPs considered separately. Multivariable, mixed-effects models with product terms for the gene-environment interactions were estimated.<h4>Results</h4>After accounting for likely confounding, the association between proximity to takeaway/fast-food outlets and BMI was stronger among those at increased genetic risk of obesity, with evidence of an interaction with polygenic risk scores (p=0.018 and p=0.028 for 69-SNP and 91-SNP scores, respectively) and in particular with a SNP linked to <i>MC4R</i> (p=0.009), a gene known to regulate food intake. We found very little evidence of gene-environment interaction for the availability of physical activity facilities.<h4>Conclusions</h4>Individuals at an increased genetic risk of obesity may be more sensitive to exposure to the local fast-food environment. Ensuring that neighbourhood residential environments are designed to promote a healthy weight may be particularly important for those with greater genetic susceptibility to obesity.",,pdf:https://nutrition.bmj.com/content/bmjnph/3/2/247.full.pdf; doi:https://doi.org/10.1136/bmjnph-2020-000107; html:https://europepmc.org/articles/PMC7841812; pdf:https://europepmc.org/articles/PMC7841812?pdf=render
 32570434,https://doi.org/10.3233/shti200210,Using Unsupervised Learning to Identify Clinical Subtypes of Alzheimer's Disease in Electronic Health Records.,"Alexander N, Alexander DC, Barkhof F, Denaxas S.",,Studies in health technology and informatics,2020,2020-06-01,N,Phenotyping; Alzheimer’s disease; Machine Learning; Electronic Health Records,,,"Identifying subtypes of Alzheimer's Disease (AD) can lead towards the creation of personalized interventions and potentially improve outcomes. In this study, we use UK primary care electronic health records (EHR) from the CALIBER resource to identify and characterize clinically-meaningful clusters patients using unsupervised learning approaches of MCA and K-means. We discovered and characterized five clusters with different profiles (mental health, non-typical AD, typical AD, CVD and men with cancer). The mental health cluster had faster rate of progression than all the other clusters making it a target for future research and intervention. Our results demonstrate that unsupervised learning approaches can be utilized on EHR to identify subtypes of heterogeneous conditions.",,doi:https://doi.org/10.3233/SHTI200210
+36066609,https://doi.org/10.1007/s00392-022-02088-x,Towards automatic classification of cardiovascular magnetic resonance Task Force Criteria for diagnosis of arrhythmogenic right ventricular cardiomyopathy.,"Bourfiss M, Sander J, de Vos BD, Te Riele ASJM, Asselbergs FW, Išgum I, Velthuis BK.",,Clinical research in cardiology : official journal of the German Cardiac Society,2023,2022-09-06,Y,Cardiac Magnetic Resonance Imaging; Arrhythmogenic Right Ventricular Cardiomyopathy; Automatic Segmentation; Deep Learning,,,"<h4>Background</h4>Arrhythmogenic right ventricular cardiomyopathy (ARVC) is diagnosed according to the Task Force Criteria (TFC) in which cardiovascular magnetic resonance (CMR) imaging plays an important role. Our study aims to apply an automatic deep learning-based segmentation for right and left ventricular CMR assessment and evaluate this approach for classification of the CMR TFC.<h4>Methods</h4>We included 227 subjects suspected of ARVC who underwent CMR. Subjects were classified into (1) ARVC patients fulfilling TFC; (2) at-risk family members; and (3) controls. To perform automatic segmentation, a Bayesian Dilated Residual Neural Network was trained and tested. Performance of automatic versus manual segmentation was assessed using Dice-coefficient and Hausdorff distance. Since automatic segmentation is most challenging in basal slices, manual correction of the automatic segmentation in the most basal slice was simulated (automatic<sup>-basal</sup>). CMR TFC calculated using manual and automatic<sup>-basal</sup> segmentation were compared using Cohen's Kappa (κ).<h4>Results</h4>Automatic segmentation was trained on CMRs of 70 subjects (39.6 ± 18.1 years, 47% female) and tested on 157 subjects (36.9 ± 17.6 years, 59% female). Dice-coefficient and Hausdorff distance showed good agreement between manual and automatic segmentations (≥ 0.89 and ≤ 10.6 mm, respectively) which further improved after simulated correction of the most basal slice (≥ 0.92 and ≤ 9.2 mm, p < 0.001). Pearson correlation of volumetric and functional CMR measurements was good to excellent (automatic (r = 0.78-0.99, p < 0.001) and automatic<sup>-basal</sup> (r = 0.88-0.99, p < 0.001) measurements). CMR TFC classification using automatic<sup>-basal</sup> segmentations was comparable to manual segmentations (κ 0.98 ± 0.02) with comparable diagnostic performance.<h4>Conclusions</h4>Combining automatic segmentation of CMRs with correction of the most basal slice results in accurate CMR TFC classification of subjects suspected of ARVC.",,pdf:https://link.springer.com/content/pdf/10.1007/s00392-022-02088-x.pdf; doi:https://doi.org/10.1007/s00392-022-02088-x; html:https://europepmc.org/articles/PMC9998324; pdf:https://europepmc.org/articles/PMC9998324?pdf=render
 32400358,https://doi.org/10.2807/1560-7917.es.2020.25.18.2000632,"Estimating number of cases and spread of coronavirus disease (COVID-19) using critical care admissions, United Kingdom, February to March 2020.","Jit M, Jombart T, Nightingale ES, Endo A, Abbott S, LSHTM Centre for Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Edmunds WJ.",,Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin,2020,2020-05-01,Y,Surveillance; intensive care unit; mathematical model; Reproduction Number; Sars-cov-2; Coronavirus Disease 2019,,,"An exponential growth model was fitted to critical care admissions from two surveillance databases to determine likely coronavirus disease (COVID-19) case numbers, critical care admissions and epidemic growth in the United Kingdom before the national lockdown. We estimate, on 23 March, a median of 114,000 (95% credible interval (CrI): 78,000-173,000) new cases and 258 (95% CrI: 220-319) new critical care reports, with 527,000 (95% CrI: 362,000-797,000) cumulative cases since 16 February.","The authors of this paper estimate the number of cases and spread of COVID-19 using data on critical care admissions within the UK, from a period of February to March 2020. Their results suggest that the UK had hundreds of thousands of COVID-19 cases by the time the national lockdown was implemented. They highlight the usefulness of surveilling critical care data to better understand the dynamics of the epidemic and better inform the response measures.",pdf:https://www.eurosurveillance.org/deliver/fulltext/eurosurveillance/25/18/eurosurv-25-18-2.pdf?itemId=%2Fcontent%2F10.2807%2F1560-7917.ES.2020.25.18.2000632&mimeType=pdf&containerItemId=content/eurosurveillance; doi:https://doi.org/10.2807/1560-7917.ES.2020.25.18.2000632; html:https://europepmc.org/articles/PMC7219029; pdf:https://europepmc.org/articles/PMC7219029?pdf=render
-37046260,https://doi.org/10.1186/s12913-023-09363-1,Associations between the stringency of COVID-19 containment policies and health service disruptions in 10 countries.,"Reddy T, Kapoor NR, Kubota S, Doubova SV, Asai D, Mariam DH, Ayele W, Mebratie AD, Thermidor R, Sapag JC, Bedregal P, Passi-Solar Á, Gordon-Strachan G, Dulal M, Gadeka DD, Mehata S, Margozzini P, Leerapan B, Rittiphairoj T, Kaewkamjornchai P, Nega A, Awoonor-Williams JK, Kruk ME, Arsenault C.",,BMC health services research,2023,2023-04-12,Y,Health Services; Health Systems; Pandemic Response; Health System Resilience; Covid-19 Restrictions; Health Care Disruptions,,,"<h4>Background</h4>Disruptions in essential health services during the COVID-19 pandemic have been reported in several countries. Yet, patterns in health service disruption according to country responses remain unclear. In this paper, we investigate associations between the stringency of COVID-19 containment policies and disruptions in 31 health services in 10 low- middle- and high-income countries in 2020.<h4>Methods</h4>Using routine health information systems and administrative data from 10 countries (Chile, Ethiopia, Ghana, Haiti, Lao People's Democratic Republic, Mexico, Nepal, South Africa, South Korea, and Thailand) we estimated health service disruptions for the period of April to December 2020 by dividing monthly service provision at national levels by the average service provision in the 15 months pre-COVID (January 2019-March 2020). We used the Oxford COVID-19 Government Response Tracker (OxCGRT) index and multi-level linear regression analyses to assess associations between the stringency of restrictions and health service disruptions over nine months. We extended the analysis by examining associations between 11 individual containment or closure policies and health service disruptions. Models were adjusted for COVID caseload, health service category and country GDP and included robust standard errors.<h4>Findings</h4>Chronic disease care was among the most affected services. Regression analyses revealed that a 10% increase in the mean stringency index was associated with a 3.3 percentage-point (95% CI -3.9, -2.7) reduction in relative service volumes. Among individual policies, curfews, and the presence of a state of emergency, had the largest coefficients and were associated with 14.1 (95% CI -19.6, 8.7) and 10.7 (95% CI -12.7, -8.7) percentage-point lower relative service volumes, respectively. In contrast, number of COVID-19 cases in 2020 was not associated with health service disruptions in any model.<h4>Conclusions</h4>Although containment policies were crucial in reducing COVID-19 mortality in many contexts, it is important to consider the indirect effects of these restrictions. Strategies to improve the resilience of health systems should be designed to ensure that populations can continue accessing essential health care despite the presence of containment policies during future infectious disease outbreaks.",,pdf:https://bmchealthservres.biomedcentral.com/counter/pdf/10.1186/s12913-023-09363-1; doi:https://doi.org/10.1186/s12913-023-09363-1; html:https://europepmc.org/articles/PMC10096103; pdf:https://europepmc.org/articles/PMC10096103?pdf=render
 36253349,https://doi.org/10.1038/s41467-022-33675-1,Systematic Mendelian randomization using the human plasma proteome to discover potential therapeutic targets for stroke.,"Chen L, Peters JE, Prins B, Persyn E, Traylor M, Surendran P, Karthikeyan S, Yonova-Doing E, Di Angelantonio E, Roberts DJ, Watkins NA, Ouwehand WH, Danesh J, Lewis CM, Bronson PG, Markus HS, Burgess S, Butterworth AS, Howson JMM.",,Nature communications,2022,2022-10-17,Y,,,,"Stroke is the second leading cause of death with substantial unmet therapeutic needs. To identify potential stroke therapeutic targets, we estimate the causal effects of 308 plasma proteins on stroke outcomes in a two-sample Mendelian randomization framework and assess mediation effects by stroke risk factors. We find associations between genetically predicted plasma levels of six proteins and stroke (P ≤ 1.62 × 10<sup>-4</sup>). The genetic associations with stroke colocalize (Posterior Probability >0.7) with the genetic associations of four proteins (TFPI, TMPRSS5, CD6, CD40). Mendelian randomization supports atrial fibrillation, body mass index, smoking, blood pressure, white matter hyperintensities and type 2 diabetes as stroke risk factors (P ≤ 0.0071). Body mass index, white matter hyperintensity and atrial fibrillation appear to mediate the TFPI, IL6RA, TMPRSS5 associations with stroke. Furthermore, thirty-six proteins are associated with one or more of these risk factors using Mendelian randomization. Our results highlight causal pathways and potential therapeutic targets for stroke.",,pdf:https://www.nature.com/articles/s41467-022-33675-1.pdf; doi:https://doi.org/10.1038/s41467-022-33675-1; html:https://europepmc.org/articles/PMC9576777; pdf:https://europepmc.org/articles/PMC9576777?pdf=render
-34950917,https://doi.org/10.1016/j.lanepe.2021.100248,"Late effects of cancer in children, teenagers and young adults: Population-based study on the burden of 183 conditions, in-patient and critical care admissions and years of life lost.","Chang WH, Katsoulis M, Tan YY, Mueller SH, Green K, Lai AG.",,The Lancet regional health. Europe,2022,2021-11-14,Y,"Primary Care; Hospitalisation; Cancer Treatment; Years Of Life Lost; Cancer Late Effects; Children, Teenagers And Young Adults",,,"<h4>Background</h4>Children, teenagers and young adults who survived cancer are prone to developing late effects. The burden of late effects across a large number of conditions, in-patient hospitalisation and critical care admissions have not been described using a population-based dataset. We aim to systematically quantify the cumulative burden of late effects across all cancer subtypes, treatment modalities and chemotherapy drug classes.<h4>Methods</h4>We employed primary care records linked to hospitals, the death registry and cancer registry from 1998-2020. CTYA survivors were 25 years or younger at the time of cancer diagnosis had survived ≥5 years post-diagnosis. Year-of-birth and sex-matched community controls were used for comparison. We considered nine treatment types, nine chemotherapy classes and 183 physical and mental health late effects. Cumulative burden was estimated using mean cumulative count, which considers recurring events. Multivariable logistic regression was used to investigate the association between treatment exposures and late effects. Excess years of life lost (YLL) attributable to late effects were estimated.<h4>Findings</h4>Among 4,063 patients diagnosed with cancer, 3,466 survived ≥ 5 years (85%); 13,517 matched controls were identified. The cumulative burden of late effects at age 35 was the highest in survivors of leukaemia (23.52 per individual [95% CI:19.85-29.33]) and lowest in survivors of germ cell tumours (CI:6.04 [5.32-6.91]). In controls, the cumulative burden was 3.99 (CI:3.93-4.08) at age 35 years. When survivors reach age 45, the cumulative burden for immunological conditions and infections was the highest (3.27 [CI:3.01-3.58]), followed by cardiovascular conditions (3.08 [CI:1.98-3.29]). Survivors who received chemotherapy and radiotherapy had the highest disease burden compared to those who received surgery only. These patients also had the highest burden of hospitalisation (by age 45: 10.43 [CI:8.27-11.95]). Survivors who received antimetabolite chemotherapy had the highest disease and hospitalisation burden, while the lowest burden is observed in those receiving antitumour antibiotics. Regression analyses revealed that survivors who received only surgery had lower odds of developing cardiovascular (adjusted odds ratio 0.73 [CI:0.56-0.94]), haematological (aOR 0.51 [CI:0.37-0.70]), immunology and infection (aOR 0.84 [CI:0.71-0.99]) and renal (aOR 0.51 [CI:0.39-0.66]) late effects. By contrast, the opposite trend was observed in survivors who received chemo-radiotherapy. High antimetabolite chemotherapy cumulative dose was associated with increased risks of subsequent cancer (aOR 2.32 [CI:1.06-4.84]), metastatic cancer (aOR 4.44 [CI:1.29-11.66]) and renal (aOR 3.48 [CI:1.36-7.86]) conditions. Patients who received radiation dose of ≥50 Gy experienced higher risks of developing metastatic cancer (aOR 5.51 [CI:2.21-11.86]), cancer (aOR 3.77 [CI:2.22-6.34]), haematological (aOR 3.43 [CI:1.54-6.83]) and neurological (aOR 3.24 [CI:1.78-5.66]) conditions. Similar trends were observed in survivors who received more than three teletherapy fields. Cumulative burden analyses on 183 conditions separately revealed varying dominance of different late effects across cancer types, socioeconomic deprivation and treatment modalities. Late effects are associated with excess YLL (i.e., the difference in YLL between survivors with or without late effects), which was the most pronounced among survivors with haematological comorbidities.<h4>Interpretation</h4>To our knowledge, this is the first study to dissect and quantify the importance of late morbidities on subsequent survival using linked electronic health records from multiple settings. The burden of late effects is heterogeneous, as is the risk of premature mortality associated with late effects. We provide an extensive knowledgebase to help inform treatment decisions at the point of diagnosis, future interventional trials and late-effects screening centred on the holistic needs of this vulnerable population.",,doi:https://doi.org/10.1016/j.lanepe.2021.100248; doi:https://doi.org/10.1016/j.lanepe.2021.100248; html:https://europepmc.org/articles/PMC8672041; pdf:https://europepmc.org/articles/PMC8672041?pdf=render
+37046260,https://doi.org/10.1186/s12913-023-09363-1,Associations between the stringency of COVID-19 containment policies and health service disruptions in 10 countries.,"Reddy T, Kapoor NR, Kubota S, Doubova SV, Asai D, Mariam DH, Ayele W, Mebratie AD, Thermidor R, Sapag JC, Bedregal P, Passi-Solar Á, Gordon-Strachan G, Dulal M, Gadeka DD, Mehata S, Margozzini P, Leerapan B, Rittiphairoj T, Kaewkamjornchai P, Nega A, Awoonor-Williams JK, Kruk ME, Arsenault C.",,BMC health services research,2023,2023-04-12,Y,Health Services; Health Systems; Pandemic Response; Health System Resilience; Covid-19 Restrictions; Health Care Disruptions,,,"<h4>Background</h4>Disruptions in essential health services during the COVID-19 pandemic have been reported in several countries. Yet, patterns in health service disruption according to country responses remain unclear. In this paper, we investigate associations between the stringency of COVID-19 containment policies and disruptions in 31 health services in 10 low- middle- and high-income countries in 2020.<h4>Methods</h4>Using routine health information systems and administrative data from 10 countries (Chile, Ethiopia, Ghana, Haiti, Lao People's Democratic Republic, Mexico, Nepal, South Africa, South Korea, and Thailand) we estimated health service disruptions for the period of April to December 2020 by dividing monthly service provision at national levels by the average service provision in the 15 months pre-COVID (January 2019-March 2020). We used the Oxford COVID-19 Government Response Tracker (OxCGRT) index and multi-level linear regression analyses to assess associations between the stringency of restrictions and health service disruptions over nine months. We extended the analysis by examining associations between 11 individual containment or closure policies and health service disruptions. Models were adjusted for COVID caseload, health service category and country GDP and included robust standard errors.<h4>Findings</h4>Chronic disease care was among the most affected services. Regression analyses revealed that a 10% increase in the mean stringency index was associated with a 3.3 percentage-point (95% CI -3.9, -2.7) reduction in relative service volumes. Among individual policies, curfews, and the presence of a state of emergency, had the largest coefficients and were associated with 14.1 (95% CI -19.6, 8.7) and 10.7 (95% CI -12.7, -8.7) percentage-point lower relative service volumes, respectively. In contrast, number of COVID-19 cases in 2020 was not associated with health service disruptions in any model.<h4>Conclusions</h4>Although containment policies were crucial in reducing COVID-19 mortality in many contexts, it is important to consider the indirect effects of these restrictions. Strategies to improve the resilience of health systems should be designed to ensure that populations can continue accessing essential health care despite the presence of containment policies during future infectious disease outbreaks.",,pdf:https://bmchealthservres.biomedcentral.com/counter/pdf/10.1186/s12913-023-09363-1; doi:https://doi.org/10.1186/s12913-023-09363-1; html:https://europepmc.org/articles/PMC10096103; pdf:https://europepmc.org/articles/PMC10096103?pdf=render
 32735830,https://doi.org/10.1016/s2352-3026(20)30228-3,Cardiovascular adverse events following treatment for non-Hodgkin lymphoma - Authors' reply.,"Linschoten M, Kamphuis JA, Asselbergs FW.",,The Lancet. Haematology,2020,2020-08-01,N,,,,,,doi:https://doi.org/10.1016/S2352-3026(20)30228-3
+34950917,https://doi.org/10.1016/j.lanepe.2021.100248,"Late effects of cancer in children, teenagers and young adults: Population-based study on the burden of 183 conditions, in-patient and critical care admissions and years of life lost.","Chang WH, Katsoulis M, Tan YY, Mueller SH, Green K, Lai AG.",,The Lancet regional health. Europe,2022,2021-11-14,Y,"Primary Care; Hospitalisation; Cancer Treatment; Years Of Life Lost; Cancer Late Effects; Children, Teenagers And Young Adults",,,"<h4>Background</h4>Children, teenagers and young adults who survived cancer are prone to developing late effects. The burden of late effects across a large number of conditions, in-patient hospitalisation and critical care admissions have not been described using a population-based dataset. We aim to systematically quantify the cumulative burden of late effects across all cancer subtypes, treatment modalities and chemotherapy drug classes.<h4>Methods</h4>We employed primary care records linked to hospitals, the death registry and cancer registry from 1998-2020. CTYA survivors were 25 years or younger at the time of cancer diagnosis had survived ≥5 years post-diagnosis. Year-of-birth and sex-matched community controls were used for comparison. We considered nine treatment types, nine chemotherapy classes and 183 physical and mental health late effects. Cumulative burden was estimated using mean cumulative count, which considers recurring events. Multivariable logistic regression was used to investigate the association between treatment exposures and late effects. Excess years of life lost (YLL) attributable to late effects were estimated.<h4>Findings</h4>Among 4,063 patients diagnosed with cancer, 3,466 survived ≥ 5 years (85%); 13,517 matched controls were identified. The cumulative burden of late effects at age 35 was the highest in survivors of leukaemia (23.52 per individual [95% CI:19.85-29.33]) and lowest in survivors of germ cell tumours (CI:6.04 [5.32-6.91]). In controls, the cumulative burden was 3.99 (CI:3.93-4.08) at age 35 years. When survivors reach age 45, the cumulative burden for immunological conditions and infections was the highest (3.27 [CI:3.01-3.58]), followed by cardiovascular conditions (3.08 [CI:1.98-3.29]). Survivors who received chemotherapy and radiotherapy had the highest disease burden compared to those who received surgery only. These patients also had the highest burden of hospitalisation (by age 45: 10.43 [CI:8.27-11.95]). Survivors who received antimetabolite chemotherapy had the highest disease and hospitalisation burden, while the lowest burden is observed in those receiving antitumour antibiotics. Regression analyses revealed that survivors who received only surgery had lower odds of developing cardiovascular (adjusted odds ratio 0.73 [CI:0.56-0.94]), haematological (aOR 0.51 [CI:0.37-0.70]), immunology and infection (aOR 0.84 [CI:0.71-0.99]) and renal (aOR 0.51 [CI:0.39-0.66]) late effects. By contrast, the opposite trend was observed in survivors who received chemo-radiotherapy. High antimetabolite chemotherapy cumulative dose was associated with increased risks of subsequent cancer (aOR 2.32 [CI:1.06-4.84]), metastatic cancer (aOR 4.44 [CI:1.29-11.66]) and renal (aOR 3.48 [CI:1.36-7.86]) conditions. Patients who received radiation dose of ≥50 Gy experienced higher risks of developing metastatic cancer (aOR 5.51 [CI:2.21-11.86]), cancer (aOR 3.77 [CI:2.22-6.34]), haematological (aOR 3.43 [CI:1.54-6.83]) and neurological (aOR 3.24 [CI:1.78-5.66]) conditions. Similar trends were observed in survivors who received more than three teletherapy fields. Cumulative burden analyses on 183 conditions separately revealed varying dominance of different late effects across cancer types, socioeconomic deprivation and treatment modalities. Late effects are associated with excess YLL (i.e., the difference in YLL between survivors with or without late effects), which was the most pronounced among survivors with haematological comorbidities.<h4>Interpretation</h4>To our knowledge, this is the first study to dissect and quantify the importance of late morbidities on subsequent survival using linked electronic health records from multiple settings. The burden of late effects is heterogeneous, as is the risk of premature mortality associated with late effects. We provide an extensive knowledgebase to help inform treatment decisions at the point of diagnosis, future interventional trials and late-effects screening centred on the holistic needs of this vulnerable population.",,doi:https://doi.org/10.1016/j.lanepe.2021.100248; doi:https://doi.org/10.1016/j.lanepe.2021.100248; html:https://europepmc.org/articles/PMC8672041; pdf:https://europepmc.org/articles/PMC8672041?pdf=render
 38479550,https://doi.org/10.1016/j.ajcnut.2024.03.006,Dietary intake of plant- and animal-derived protein and incident cardiovascular diseases: the pan-European EPIC-CVD case-cohort study.,"Zheng JS, Steur M, Imamura F, Freisling H, Johnson L, van der Schouw YT, Tong TY, Weiderpass E, Bajracharya R, Crous-Bou M, Dahm CC, Heath AK, Ibsen DB, Jannasch F, Katzke V, Masala G, Moreno-Iribas C, Sacerdote C, Schulze MB, Sieri S, Wareham NJ, Danesh J, Butterworth AS, Forouhi NG.",,The American journal of clinical nutrition,2024,2024-03-11,Y,Cardiovascular disease; Stroke; ischemic heart disease; Plant-derived Protein; Animal-derived Protein,,,"<h4>Background</h4>Epidemiological evidence suggests that a potential association between dietary protein intake and cardiovascular disease (CVD) may depend on the protein source, that is, plant- or animal-derived, but past research was limited and inconclusive.<h4>Objectives</h4>To evaluate the association of dietary plant- or animal-derived protein consumption with risk of CVD, and its components ischemic heart disease (IHD) and stroke.<h4>Methods</h4>This analysis in the European Prospective Investigation into Cancer and Nutrition (EPIC)-CVD case-cohort study included 16,244 incident CVD cases (10,784 IHD and 6423 stroke cases) and 15,141 subcohort members from 7 European countries. We investigated the association of estimated dietary protein intake with CVD, IHD, and stroke (total, fatal, and nonfatal) using multivariable-adjusted Prentice-weighted Cox regression. We estimated isocaloric substitutions of replacing fats and carbohydrates with plant- or animal-derived protein and replacing food-specific animal protein with plant protein. Multiplicative interactions between dietary protein and prespecified variables were tested.<h4>Results</h4>Neither plant- nor animal-derived protein intake was associated with incident CVD, IHD, or stroke in adjusted analyses without or with macronutrient-specified substitution analyses. Higher plant-derived protein intake was associated with 22% lower total stroke incidence among never smokers [HR 0.78, 95% confidence intervals (CI): 0.62, 0.99], but not among current smokers (HR 1.08, 95% CI: 0.83, 1.40, P-interaction = 0.004). Moreover, higher plant-derived protein (per 3% total energy) when replacing red meat protein (HR 0.52, 95% CI: 0.31, 0.88), processed meat protein (HR 0.39, 95% CI: 0.17, 0.90), and dairy protein (HR 0.54, 95% CI: 0.30, 0.98) was associated with lower incidence of fatal stroke.<h4>Conclusion</h4>Plant- or animal-derived protein intake was not associated with overall CVD. However, the association of plant-derived protein consumption with lower total stroke incidence among nonsmokers, and with lower incidence of fatal stroke highlights the importance of investigating CVD subtypes and potential interactions. These observations warrant further investigation in diverse populations with varying macronutrient intakes and dietary patterns.",,doi:https://doi.org/10.1016/j.ajcnut.2024.03.006; doi:https://doi.org/10.1016/j.ajcnut.2024.03.006; html:https://europepmc.org/articles/PMC11130694; pdf:https://europepmc.org/articles/PMC11130694?pdf=render
 33591280,https://doi.org/10.2196/16348,A Social Media Campaign (#datasaveslives) to Promote the Benefits of Using Health Data for Research Purposes: Mixed Methods Analysis.,"Hassan L, Nenadic G, Tully MP.",,Journal of medical Internet research,2021,2021-02-16,Y,Medical research; Public Engagement; Social Network Analysis; Social Media,,,"<h4>Background</h4>Social media provides the potential to engage a wide audience about scientific research, including the public. However, little empirical research exists to guide health scientists regarding what works and how to optimize impact. We examined the social media campaign #datasaveslives established in 2014 to highlight positive examples of the use and reuse of health data in research.<h4>Objective</h4>This study aims to examine how the #datasaveslives hashtag was used on social media, how often, and by whom; thus, we aim to provide insights into the impact of a major social media campaign in the UK health informatics research community and further afield.<h4>Methods</h4>We analyzed all publicly available posts (tweets) that included the hashtag #datasaveslives (N=13,895) on the microblogging platform Twitter between September 1, 2016, and August 31, 2017. Using a combination of qualitative and quantitative analyses, we determined the frequency and purpose of tweets. Social network analysis was used to analyze and visualize tweet sharing (retweet) networks among hashtag users.<h4>Results</h4>Overall, we found 4175 original posts and 9720 retweets featuring #datasaveslives by 3649 unique Twitter users. In total, 66.01% (2756/4175) of the original posts were retweeted at least once. Higher frequencies of tweets were observed during the weeks of prominent policy publications, popular conferences, and public engagement events. Cluster analysis based on retweet relationships revealed an interconnected series of groups of #datasaveslives users in academia, health services and policy, and charities and patient networks. Thematic analysis of tweets showed that #datasaveslives was used for a broader range of purposes than indexing information, including event reporting, encouraging participation and action, and showing personal support for data sharing.<h4>Conclusions</h4>This study shows that a hashtag-based social media campaign was effective in encouraging a wide audience of stakeholders to disseminate positive examples of health research. Furthermore, the findings suggest that the campaign supported community building and bridging practices within and between the interdisciplinary sectors related to the field of health data science and encouraged individuals to demonstrate personal support for sharing health data.",,pdf:https://www.jmir.org/2021/2/e16348/PDF; doi:https://doi.org/10.2196/16348; html:https://europepmc.org/articles/PMC7925154
 33559289,https://doi.org/10.1002/ejp.1750,The association between exposure to domestic abuse in women and the development of syndromes indicating central nervous system sensitization: A retrospective cohort study using UK primary care records.,"Chandan JS, Keerthy D, Gokhale KM, Bradbury-Jones C, Raza K, Bandyopadhyay S, Taylor J, Nirantharakumar K.",,"European journal of pain (London, England)",2021,2021-03-15,N,,,,"<h4>Background</h4>Domestic abuse is a global public health issue. The association between the development of central sensitivity syndromes (CSS) and previous exposure to domestic abuse has been poorly understood particularly within European populations.<h4>Methods</h4>A retrospective cohort study using the 'The Health Improvement Network,' (UK primary care medical records) between 1st January 1995-31st December 2018. 22,604 adult women exposed to domestic abuse were age matched to 44,671 unexposed women. The average age at cohort entry was 36 years and the median follow-up was 2.5 years. The outcomes of interest were the development of a variety of syndromes which demonstrate central nervous system sensitization. Fibromyalgia, chronic fatigue syndrome and temporomandibular joint disorder outcomes have been reported previously. Outcomes were adjusted for the presence of mental ill health.<h4>Results</h4>During the study period, women exposed to domestic abuse experienced an increased risk of developing chronic lower back pain (adjusted incidence rate ratio [aIRR] 2.28; 95% CI 1.85-2.80), chronic headaches (aIRR 3.15; 95% CI 1.07-9.23), irritable bowel syndrome (aIRR 1.41; 95% CI 1.25-1.60) and restless legs syndrome (aIRR 1.89; 95% CI 1.44-2.48). However, no positive association was seen with the development of interstitial cystitis (aIRR 0.52; 95% CI 0.14-1.93), vulvodynia (aIRR 0.42; 95% CI 0.14-1.25) and myofascial pain syndrome (aIRR 1.01; 95% CI 0.28-3.61).<h4>Conclusion</h4>This study demonstrates the need to consider a past history of domestic abuse in patients presenting with CSS; and also consider preventative approaches in mitigating the risk of developing CSS following exposure to domestic abuse.<h4>Significance</h4>Domestic abuse is a global public health issue, with a poorly understood relationship with the development of complex pain syndromes. Using a large UK primary care database, we were able to conduct the first global cohort study to explore this further. We found a strong pain morbidity burden associated with domestic abuse, suggesting the need for urgent public health intervention to not only prevent domestic abuse but also the associated negative pain consequences.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ejp.1750; doi:https://doi.org/10.1002/ejp.1750
 36828655,https://doi.org/10.1136/bmjopen-2022-068718,Maternal and child outcomes for pregnant women with pre-existing multiple long-term conditions: protocol for an observational study in the UK.,"Lee SI, Hope H, O'Reilly D, Kent L, Santorelli G, Subramanian A, Moss N, Azcoaga-Lorenzo A, Fagbamigbe AF, Nelson-Piercy C, Yau C, McCowan C, Kennedy JI, Phillips K, Singh M, Mhereeg M, Cockburn N, Brocklehurst P, Plachcinski R, Riley RD, Thangaratinam S, Brophy S, Hemali Sudasinghe SPB, Agrawal U, Vowles Z, Abel KM, Nirantharakumar K, Black M, Eastwood KA, MuM-PreDiCT.",,BMJ open,2023,2023-02-24,Y,Obstetrics; epidemiology; Maternal Medicine,,,"<h4>Introduction</h4>One in five pregnant women has multiple pre-existing long-term conditions in the UK. Studies have shown that maternal multiple long-term conditions are associated with adverse outcomes. This observational study aims to compare maternal and child outcomes for pregnant women with multiple long-term conditions to those without multiple long-term conditions (0 or 1 long-term conditions).<h4>Methods and analysis</h4>Pregnant women aged 15-49 years old with a conception date between 2000 and 2019 in the UK will be included with follow-up till 2019. The data source will be routine health records from all four UK nations (Clinical Practice Research Datalink (England), Secure Anonymised Information Linkage (Wales), Scotland routine health records and Northern Ireland Maternity System) and the Born in Bradford birth cohort. The exposure of two or more pre-existing, long-term physical or mental health conditions will be defined from a list of health conditions predetermined by women and clinicians. The association of maternal multiple long-term conditions with (a) antenatal, (b) peripartum, (c) postnatal and long-term and (d) mental health outcomes, for both women and their children will be examined. Outcomes of interest will be guided by a core outcome set. Comparisons will be made between pregnant women with and without multiple long-term conditions using modified Poisson and Cox regression. Generalised estimating equation will account for the clustering effect of women who had more than one pregnancy episode. Where appropriate, multiple imputation with chained equation will be used for missing data. Federated analysis will be conducted for each dataset and results will be pooled using random-effects meta-analyses.<h4>Ethics and dissemination</h4>Approval has been obtained from the respective data sources in each UK nation. Study findings will be submitted for publications in peer-reviewed journals and presented at key conferences.",,pdf:https://bmjopen.bmj.com/content/bmjopen/13/2/e068718.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-068718; html:https://europepmc.org/articles/PMC9972454; pdf:https://europepmc.org/articles/PMC9972454?pdf=render
 36722341,https://doi.org/10.1093/cei/uxad008,Practical challenges for functional validation of STAT1 gain of function genetic variants.,"Albuquerque AS, Maimaris J, McKenna AJ, Lambourne J, Moreira F, Workman S, Megy K, Simeoni I, Lango Allen H, NIHR BioResource-Rare Disease Consortium, Morris EC, Burns SO.",,Clinical and experimental immunology,2023,2023-04-01,Y,Flow cytometry; STAT1; Primary Immunodeficiency; Gain Of Function; Chronic Mucocutaneous Candidiasis; Variants Of Unknown Significance,,,,,pdf:https://academic.oup.com/cei/advance-article-pdf/doi/10.1093/cei/uxad008/49549101/uxad008.pdf; doi:https://doi.org/10.1093/cei/uxad008; html:https://europepmc.org/articles/PMC10128160; pdf:https://europepmc.org/articles/PMC10128160?pdf=render
-39107017,https://doi.org/10.1136/bmjopen-2023-083497,COVID-19 pandemic impact on hypertension management in North East London: an observational cohort study using electronic health records.,"Rison SCG, Redfern OC, Mathur R, Dostal I, Carvalho C, Raisi-Estabragh Z, Robson J.",,BMJ open,2024,2024-08-06,Y,Hypertension; Blood pressure; Cardiovascular disease; Public Health; Primary Care; Health Equity,,,"<h4>Objective</h4>There are established inequities in the monitoring and management of hypertension in England. The COVID-19 pandemic had a major impact on primary care management of long-term conditions such as hypertension. This study investigated the possible disproportionate impact of the pandemic across patient groups.<h4>Design</h4>Open cohort of people with diagnosed hypertension.<h4>Settings</h4>North East London primary care practices from January 2019 to October 2022.<h4>Participants</h4>All 224 329 adults with hypertension registered in 193 primary care practices.<h4>Outcomes</h4>Monitoring and management of hypertension were assessed using two indicators: (i) blood pressure recorded within 1 year of the index date and (ii) blood pressure control to national clinical practice guidelines.<h4>Results</h4>The proportion of patients with a contemporaneous blood pressure recording fell from a 91% pre-pandemic peak to 62% at the end of the pandemic lockdown and improved to 77% by the end of the study. This was paralleled by the proportion of individuals with controlled hypertension which fell from a 73% pre-pandemic peak to 50% at the end of the pandemic lockdown and improved to 60% by the end of the study. However, when excluding patients without a recent blood pressure recording, the proportions of patients with controlled hypertension increased to 81%, 80% and 78% respectively.Throughout the study, in comparison to the White ethnic group, the Black ethnic group was less likely to achieve adequate blood pressure control (ORs 0.81 (95% CI 0.78 to 0.85, p<0.001) to 0.87 (95% CI 0.84 to 0.91, p<0.001)). Conversely, the Asian ethnic group was more likely to have controlled blood pressure (ORs 1.09 (95% CI 1.05 to 1.14, p<0.001) to 1.28 (95% CI 1.23 to 1.32, p<0.001)). Men, younger individuals, more affluent individuals, individuals with unknown or unrecorded ethnicity or those untreated were also less likely to have blood pressure control to target throughout the study.<h4>Conclusion</h4>The COVID-19 pandemic had a greater impact on blood pressure recording than on blood pressure control. Inequities in blood pressure control persisted during the pandemic and remain outstanding.",,doi:https://doi.org/10.1136/bmjopen-2023-083497; html:https://europepmc.org/articles/PMC11308888; pdf:https://europepmc.org/articles/PMC11308888?pdf=render
 33653287,https://doi.org/10.1186/s12875-021-01384-1,"A cross-sectional study reporting concussion exposure, assessment and management in Western Australian general practice.","Thomas E, Chih H, Gabbe B, Fitzgerald M, Cowen G.",,BMC family practice,2021,2021-03-02,Y,,,,"<h4>Background</h4>General Practitioners (GPs) may be called upon to assess patients who have sustained a concussion despite limited information being available at this assessment. Information relating to how concussion is actually being assessed and managed in General Practice is scarce. This study aimed to identify characteristics of current Western Australian (WA) GP exposure to patients with concussion, factors associated with GPs' knowledge of concussion, confidence of GPs in diagnosing and managing patients with concussion, typical referral practices and familiarity of GPs with guidelines.<h4>Methods</h4>In this cross-sectional study, GPs in WA were recruited via the RACGP WA newsletter and shareGP and the consented GPs completed an electronic survey. Associations were performed using Chi-squared tests or Fisher's Exact test.<h4>Results</h4>Sixty-six GPs in WA responded to the survey (response rate = 1.7%). Demographics, usual practice, knowledge, confidence, identification of prolonged recovery as well as guideline and resource awareness of GPs who practised in regional and metropolitan areas were comparable (p > 0.05). Characteristics of GPs were similar between those who identified all symptoms of concussion and distractors correctly and those who did not (p > 0.05). However, 84% of the respondents who had never heard of concussion guidelines were less likely to answer all symptoms and distractors correctly (p = 0.039). Whilst 78% of the GPs who were confident in their diagnoses had heard of guidelines (p = 0.029), confidence in managing concussion was not significantly associated with GPs exposure to guidelines. It should be noted that none of the respondents correctly identified signs of concussion and excluded the distractors.<h4>Conclusions</h4>Knowledge surrounding concussion guidelines, diagnosis and management varied across GPs in WA. Promotion of available concussion guidelines may assist GPs who lack confidence in making a diagnosis. The lack of association between GPs exposure to guidelines and confidence managing concussion highlights that concussion management may be an area where GPs could benefit from additional education and support.",,pdf:https://bmcfampract.biomedcentral.com/track/pdf/10.1186/s12875-021-01384-1; doi:https://doi.org/10.1186/s12875-021-01384-1; html:https://europepmc.org/articles/PMC7927406; pdf:https://europepmc.org/articles/PMC7927406?pdf=render
+39107017,https://doi.org/10.1136/bmjopen-2023-083497,COVID-19 pandemic impact on hypertension management in North East London: an observational cohort study using electronic health records.,"Rison SCG, Redfern OC, Mathur R, Dostal I, Carvalho C, Raisi-Estabragh Z, Robson J.",,BMJ open,2024,2024-08-06,Y,Hypertension; Blood pressure; Cardiovascular disease; Public Health; Primary Care; Health Equity,,,"<h4>Objective</h4>There are established inequities in the monitoring and management of hypertension in England. The COVID-19 pandemic had a major impact on primary care management of long-term conditions such as hypertension. This study investigated the possible disproportionate impact of the pandemic across patient groups.<h4>Design</h4>Open cohort of people with diagnosed hypertension.<h4>Settings</h4>North East London primary care practices from January 2019 to October 2022.<h4>Participants</h4>All 224 329 adults with hypertension registered in 193 primary care practices.<h4>Outcomes</h4>Monitoring and management of hypertension were assessed using two indicators: (i) blood pressure recorded within 1 year of the index date and (ii) blood pressure control to national clinical practice guidelines.<h4>Results</h4>The proportion of patients with a contemporaneous blood pressure recording fell from a 91% pre-pandemic peak to 62% at the end of the pandemic lockdown and improved to 77% by the end of the study. This was paralleled by the proportion of individuals with controlled hypertension which fell from a 73% pre-pandemic peak to 50% at the end of the pandemic lockdown and improved to 60% by the end of the study. However, when excluding patients without a recent blood pressure recording, the proportions of patients with controlled hypertension increased to 81%, 80% and 78% respectively.Throughout the study, in comparison to the White ethnic group, the Black ethnic group was less likely to achieve adequate blood pressure control (ORs 0.81 (95% CI 0.78 to 0.85, p<0.001) to 0.87 (95% CI 0.84 to 0.91, p<0.001)). Conversely, the Asian ethnic group was more likely to have controlled blood pressure (ORs 1.09 (95% CI 1.05 to 1.14, p<0.001) to 1.28 (95% CI 1.23 to 1.32, p<0.001)). Men, younger individuals, more affluent individuals, individuals with unknown or unrecorded ethnicity or those untreated were also less likely to have blood pressure control to target throughout the study.<h4>Conclusion</h4>The COVID-19 pandemic had a greater impact on blood pressure recording than on blood pressure control. Inequities in blood pressure control persisted during the pandemic and remain outstanding.",,doi:https://doi.org/10.1136/bmjopen-2023-083497; html:https://europepmc.org/articles/PMC11308888; pdf:https://europepmc.org/articles/PMC11308888?pdf=render
 36819459,https://doi.org/10.1210/jendso/bvad020,"Polygenic Risk of Prediabetes, Undiagnosed Diabetes, and Incident Type 2 Diabetes Stratified by Diabetes Risk Factors.","Liu X, Collister JA, Clifton L, Hunter DJ, Littlejohns TJ.",,Journal of the Endocrine Society,2023,2023-01-30,Y,BMI; Family History; Polygenic Risk And Diabetes,,,"<h4>Context</h4>Early diagnosis of type 2 diabetes is crucial to reduce severe comorbidities and complications. Current screening recommendations for type 2 diabetes include traditional risk factors, primarily body mass index (BMI) and family history, however genetics also plays a key role in type 2 diabetes risk. It is important to understand whether genetic predisposition to type 2 diabetes modifies the effect of these traditional factors on type 2 diabetes risk.<h4>Objective</h4>This work aimed to investigate whether genetic risk of type 2 diabetes modifies associations between BMI and first-degree family history of diabetes with 1) prevalent prediabetes or undiagnosed diabetes; and 2) incident confirmed type 2 diabetes.<h4>Methods</h4>We included 431 658 individuals aged 40 to 69 years at baseline of multiethnic ancestry from the UK Biobank. We used a multiethnic polygenic risk score for type 2 diabetes (PRS<sub>T2D</sub>) developed by Genomics PLC. Prediabetes or undiagnosed diabetes was defined as baseline glycated hemoglobin greater than or equal to 42 mmol/mol (6.0%), and incident type 2 diabetes was derived from medical records.<h4>Results</h4>At baseline, 43 472 participants had prediabetes or undiagnosed diabetes, and 17 259 developed type 2 diabetes over 15 years follow-up. Dose-response associations were observed for PRS<sub>T2D</sub> with each outcome in each category of BMI or first-degree family history of diabetes. Those in the highest quintile of PRS<sub>T2D</sub> with a normal BMI were at a similar risk as those in the middle quintile who were overweight. Participants who were in the highest quintile of PRS<sub>T2D</sub> and did not have a first-degree family history of diabetes were at a similar risk as those with a family history who were in the middle category of PRS<sub>T2D</sub>.<h4>Conclusion</h4>Genetic risk of type 2 diabetes remains strongly associated with risk of prediabetes, undiagnosed diabetes, and future type 2 diabetes within categories of nongenetic risk factors. This could have important implications for identifying individuals at risk of type 2 diabetes for prevention and early diagnosis programs.",,pdf:https://academic.oup.com/jes/article-pdf/7/4/bvad020/49229172/bvad020.pdf; doi:https://doi.org/10.1210/jendso/bvad020; html:https://europepmc.org/articles/PMC9933896; pdf:https://europepmc.org/articles/PMC9933896?pdf=render
 35152298,https://doi.org/10.1093/ehjci/jeac030,Prognostic value of strain by feature-tracking cardiac magnetic resonance in arrhythmogenic right ventricular cardiomyopathy.,"Bourfiss M, Prakken NHJ, James CA, Planken RN, Boekholdt SM, Ahmetagic D, van den Berg MP, Tichnell C, Van der Heijden JF, Loh P, Murray B, Tandri H, Kamel I, Calkins H, Asselbergs FW, Zimmerman SL, Velthuis BK, Te Riele ASJM.",,European heart journal. Cardiovascular Imaging,2022,2022-12-01,Y,Strain; Arrhythmias; Cardiac Magnetic Resonance Imaging; Arrhythmogenic Right Ventricular Cardiomyopathy; Feature Tracking,,,"<h4>Aims</h4>Arrhythmogenic right ventricular cardiomyopathy (ARVC) is characterized by ventricular dysfunction and ventricular arrhythmias (VA). Adequate arrhythmic risk assessment is important to prevent sudden cardiac death. We aimed to study the incremental value of strain by feature-tracking cardiac magnetic resonance imaging (FT-CMR) in predicting sustained VA in ARVC patients.<h4>Methods and results</h4>CMR images of 132 ARVC patients (43% male, 40.6 ± 16.0 years) without prior VA were analysed for global and regional right and left ventricular (RV, LV) strain. Primary outcome was sustained VA during follow-up. We performed multivariable regression assessing strain, in combination with (i) RV ejection fraction (EF); (ii) LVEF; and (iii) the ARVC risk calculator. False discovery rate adjusted P-values were given to correct for multiple comparisons and c-statistics were calculated for each model. During 4.3 (2.0-7.9) years of follow-up, 19% of patients experienced sustained VA. Compared to patients without VA, those with VA had significantly reduced RV longitudinal (P ≤ 0.03) and LV circumferential (P ≤ 0.04) strain. In addition, patients with VA had significantly reduced biventricular EF (P ≤ 0.02). After correcting for RVEF, LVEF, and the ARVC risk calculator separately in multivariable analysis, both RV and LV strain lost their significance [hazard ratio 1.03-1.18, P > 0.05]. Likewise, while strain improved the c-statistic in combination with RVEF, LVEF, and the ARVC risk calculator separately, this did not reach statistical significance (P ≥ 0.18).<h4>Conclusion</h4>Both RV longitudinal and LV circumferential strain are reduced in ARVC patients with sustained VA during follow-up. However, strain does not have incremental value over RVEF, LVEF, and the ARVC VA risk calculator.",,pdf:https://academic.oup.com/ehjcimaging/advance-article-pdf/doi/10.1093/ehjci/jeac030/42506545/jeac030.pdf; doi:https://doi.org/10.1093/ehjci/jeac030; html:https://europepmc.org/articles/PMC9762936; pdf:https://europepmc.org/articles/PMC9762936?pdf=render
 35115301,https://doi.org/10.1136/bjophthalmol-2021-319641,Metformin and risk of age-related macular degeneration in individuals with type 2 diabetes: a retrospective cohort study.,"Gokhale KM, Adderley NJ, Subramanian A, Lee WH, Han D, Coker J, Braithwaite T, Denniston AK, Keane PA, Nirantharakumar K.",,The British journal of ophthalmology,2023,2022-02-03,N,Degeneration; epidemiology; Macula,,,"<h4>Background</h4>Age-related macular degeneration (AMD) in its late stages is a leading cause of sight loss in developed countries. Some previous studies have suggested that metformin may be associated with a reduced risk of developing AMD, but the evidence is inconclusive.<h4>Aims</h4>To explore the relationship between metformin use and development of AMD among patients with type 2 diabetes in the UK.<h4>Methods</h4>A large, population-based retrospective open cohort study with a time-dependent exposure design was carried out using IQVIA Medical Research Data, 1995-2019. Patients aged ≥40 with diagnosed type 2 diabetes were included.The exposed group was those prescribed metformin (with or without any other antidiabetic medications); the comparator (unexposed) group was those prescribed other antidiabetic medications only. The exposure status was treated as time varying, collected at 3-monthly time intervals.Extended Cox proportional hazards regression was used to calculate the adjusted HRs for development of the outcome, newly diagnosed AMD.<h4>Results</h4>A total of 173 689 patients, 57% men, mean (SD) age 62.8 (11.6) years, with incident type 2 diabetes and a record of one or more antidiabetic medications were included in the study. Median follow-up was 4.8 (IQR 2.3-8.3, range 0.5-23.8) years. 3111 (1.8%) patients developed AMD. The adjusted HR for diagnosis of AMD was 1.02 (95% CI 0.92 to 1.12) in patients prescribed metformin (with or without other antidiabetic medications) compared with those prescribed any other antidiabetic medication only.<h4>Conclusion</h4>We found no evidence that metformin was associated with risk of AMD in primary care patients requiring treatment for type 2 diabetes.",,pdf:https://discovery.ucl.ac.uk/10143945/1/Keane_T2DM%20metformin%20and%20risk%20of%20AMD%20BJO%2020220111%20clean.pdf; doi:https://doi.org/10.1136/bjophthalmol-2021-319641
-36228971,https://doi.org/10.1016/j.jclinepi.2022.10.011,"In simulated data and health records, latent class analysis was the optimum multimorbidity clustering algorithm.","Nichols L, Taverner T, Crowe F, Richardson S, Yau C, Kiddle S, Kirk P, Barrett J, Nirantharakumar K, Griffin S, Edwards D, Marshall T.",,Journal of clinical epidemiology,2022,2022-10-11,Y,Hierarchical cluster analysis; Clustering Methods; Latent Class Analysis; Electronic Medical Records; Multimorbidity; K-means; Multiple Correspondence Analysis,,,"<h4>Background and objectives</h4>To investigate the reproducibility and validity of latent class analysis (LCA) and hierarchical cluster analysis (HCA), multiple correspondence analysis followed by k-means (MCA-kmeans) and k-means (kmeans) for multimorbidity clustering.<h4>Methods</h4>We first investigated clustering algorithms in simulated datasets with 26 diseases of varying prevalence in predetermined clusters, comparing the derived clusters to known clusters using the adjusted Rand Index (aRI). We then them investigated the medical records of male patients, aged 65 to 84 years from 50 UK general practices, with 49 long-term health conditions. We compared within cluster morbidity profiles using the Pearson correlation coefficient and assessed cluster stability using in 400 bootstrap samples.<h4>Results</h4>In the simulated datasets, the closest agreement (largest aRI) to known clusters was with LCA and then MCA-kmeans algorithms. In the medical records dataset, all four algorithms identified one cluster of 20-25% of the dataset with about 82% of the same patients across all four algorithms. LCA and MCA-kmeans both found a second cluster of 7% of the dataset. Other clusters were found by only one algorithm. LCA and MCA-kmeans clustering gave the most similar partitioning (aRI 0.54).<h4>Conclusion</h4>LCA achieved higher aRI than other clustering algorithms.",,doi:https://doi.org/10.1016/j.jclinepi.2022.10.011; doi:https://doi.org/10.1016/j.jclinepi.2022.10.011; html:https://europepmc.org/articles/PMC7613854; pdf:https://europepmc.org/articles/PMC7613854?pdf=render
 34396190,https://doi.org/10.1016/j.jaccao.2019.09.007,Cancer Therapy-Related Cardiac Dysfunction of Nonanthracycline Chemotherapeutics: What Is the Evidence?,"Kamphuis JAM, Linschoten M, Cramer MJ, Gort EH, van Rhenen A, Asselbergs FW, Doevendans PA, Teske AJ.",,JACC. CardioOncology,2019,2019-12-17,Y,"Cardiomyopathy; Heart Failure; Risk Prediction; Fda, Food And Drug Administration; Hf, Heart Failure; Mmc, Mitomycin C; Alkylating Therapy; Ctrcd, Cancer Therapy–Related Cardiac Dysfunction",,,"Cancer therapy-related cardiac dysfunction (CTRCD) is one of the most concerning cardiovascular side effects of cancer treatment. Important reviews within the field of cardio-oncology have described various agents to be associated with a high risk of CTRCD, including mitomycin C, ifosfamide, vincristine, cyclophosphamide, and clofarabine. The aim of this study was to provide insight into the data on which these incidence rates are based. We observed that the reported cardiotoxicity of mitomycin C and ifosfamide is based on studies in which most patients received anthracyclines, complicating the interpretation of their association with CTRCD. The high incidence of vincristine-induced cardiotoxicity is based on an incorrect interpretation of a single study. Incidence rates of clofarabine remain uncertain due to a lack of cardiac screening in clinical trials. The administration of high-dose cyclophosphamide (>1.5 g/m<sup>2</sup>/day) is associated with a high incidence of CTRCD. Based on our findings, a critical re-evaluation of the cardiotoxicity of these agents is warranted.",,doi:https://doi.org/10.1016/j.jaccao.2019.09.007; doi:https://doi.org/10.1016/j.jaccao.2019.09.007; html:https://europepmc.org/articles/PMC8352330; pdf:https://europepmc.org/articles/PMC8352330?pdf=render
+36228971,https://doi.org/10.1016/j.jclinepi.2022.10.011,"In simulated data and health records, latent class analysis was the optimum multimorbidity clustering algorithm.","Nichols L, Taverner T, Crowe F, Richardson S, Yau C, Kiddle S, Kirk P, Barrett J, Nirantharakumar K, Griffin S, Edwards D, Marshall T.",,Journal of clinical epidemiology,2022,2022-10-11,Y,Hierarchical cluster analysis; Clustering Methods; Latent Class Analysis; Electronic Medical Records; Multimorbidity; K-means; Multiple Correspondence Analysis,,,"<h4>Background and objectives</h4>To investigate the reproducibility and validity of latent class analysis (LCA) and hierarchical cluster analysis (HCA), multiple correspondence analysis followed by k-means (MCA-kmeans) and k-means (kmeans) for multimorbidity clustering.<h4>Methods</h4>We first investigated clustering algorithms in simulated datasets with 26 diseases of varying prevalence in predetermined clusters, comparing the derived clusters to known clusters using the adjusted Rand Index (aRI). We then them investigated the medical records of male patients, aged 65 to 84 years from 50 UK general practices, with 49 long-term health conditions. We compared within cluster morbidity profiles using the Pearson correlation coefficient and assessed cluster stability using in 400 bootstrap samples.<h4>Results</h4>In the simulated datasets, the closest agreement (largest aRI) to known clusters was with LCA and then MCA-kmeans algorithms. In the medical records dataset, all four algorithms identified one cluster of 20-25% of the dataset with about 82% of the same patients across all four algorithms. LCA and MCA-kmeans both found a second cluster of 7% of the dataset. Other clusters were found by only one algorithm. LCA and MCA-kmeans clustering gave the most similar partitioning (aRI 0.54).<h4>Conclusion</h4>LCA achieved higher aRI than other clustering algorithms.",,doi:https://doi.org/10.1016/j.jclinepi.2022.10.011; doi:https://doi.org/10.1016/j.jclinepi.2022.10.011; html:https://europepmc.org/articles/PMC7613854; pdf:https://europepmc.org/articles/PMC7613854?pdf=render
 33174528,https://doi.org/10.3310/hta24570,Antimicrobial-impregnated central venous catheters for preventing neonatal bloodstream infection: the PREVAIL RCT.,"Gilbert R, Brown M, Faria R, Fraser C, Donohue C, Rainford N, Grosso A, Sinha AK, Dorling J, Gray J, Muller-Pebody B, Harron K, Moitt T, McGuire W, Bojke L, Gamble C, Oddie SJ.",,"Health technology assessment (Winchester, England)",2020,2020-11-01,Y,Infant; Newborn; Economic analysis; Central Venous Catheter; Bloodstream Infection; Randomised Controlled Trial; Generalisability; Antimicrobial-impregnated Catheter,,,"<h4>Background</h4>Clinical trials show that antimicrobial-impregnated central venous catheters reduce catheter-related bloodstream infection in adults and children receiving intensive care, but there is insufficient evidence for use in newborn babies.<h4>Objectives</h4>The objectives were (1) to determine clinical effectiveness by conducting a randomised controlled trial comparing antimicrobial-impregnated peripherally inserted central venous catheters with standard peripherally inserted central venous catheters for reducing bloodstream or cerebrospinal fluid infections (referred to as bloodstream infections); (2) to conduct an economic evaluation of the costs, cost-effectiveness and value of conducting additional research; and (3) to conduct a generalisability analysis of trial findings to neonatal care in the NHS.<h4>Design</h4>Three separate studies were undertaken, each addressing one of the three objectives. (1) This was a multicentre, open-label, pragmatic randomised controlled trial; (2) an analysis was undertaken of hospital care costs, lifetime cost-effectiveness and value of information from an NHS perspective; and (3) this was a retrospective cohort study of bloodstream infection rates in neonatal units in England.<h4>Setting</h4>The randomised controlled trial was conducted in 18 neonatal intensive care units in England.<h4>Participants</h4>Participants were babies who required a peripherally inserted central venous catheter (of 1 French gauge in size).<h4>Interventions</h4>The interventions were an antimicrobial-impregnated peripherally inserted central venous catheter (coated with rifampicin-miconazole) or a standard peripherally inserted central venous catheter, allocated randomly (1 : 1) using web randomisation.<h4>Main outcome measure</h4>Study 1 - time to first bloodstream infection, sampled between 24 hours after randomisation and 48 hours after peripherally inserted central venous catheter removal. Study 2 - cost-effectiveness of the antimicrobial-impregnated peripherally inserted central venous catheter compared with the standard peripherally inserted central venous catheters. Study 3 - risk-adjusted bloodstream rates in the trial compared with those in neonatal units in England. For study 3, the data used were as follows: (1) case report forms and linked death registrations; (2) case report forms and linked death registrations linked to administrative health records with 6-month follow-up; and (3) neonatal health records linked to infection surveillance data.<h4>Results</h4>Study 1, clinical effectiveness - 861 babies were randomised (antimicrobial-impregnated peripherally inserted central venous catheter, <i>n</i> = 430; standard peripherally inserted central venous catheter, <i>n</i> = 431). Bloodstream infections occurred in 46 babies (10.7%) randomised to antimicrobial-impregnated peripherally inserted central venous catheters and in 44 (10.2%) babies randomised to standard peripherally inserted central venous catheters. No difference in time to bloodstream infection was detected (hazard ratio 1.11, 95% confidence interval 0.73 to 1.67; <i>p</i> = 0.63). Secondary outcomes of rifampicin resistance in positive blood/cerebrospinal fluid cultures, mortality, clinical outcomes at neonatal unit discharge and time to peripherally inserted central venous catheter removal were similar in both groups. Rifampicin resistance in positive peripherally inserted central venous catheter tip cultures was higher in the antimicrobial-impregnated peripherally inserted central venous catheter group (relative risk 3.51, 95% confidence interval 1.16 to 10.57; <i>p</i> = 0.02) than in the standard peripherally inserted central venous catheter group. Adverse events were similar in both groups. Study 2, economic evaluation - the mean cost of babies' hospital care was £83,473. Antimicrobial-impregnated peripherally inserted central venous catheters were not cost-effective. Given the increased price, compared with standard peripherally inserted central venous catheters, the minimum reduction in risk of bloodstream infection for antimicrobial-impregnated peripherally inserted central venous catheters to be cost-effective was 3% and 15% for babies born at 23-27 and 28-32 weeks' gestation, respectively. Study 3, generalisability analysis - risk-adjusted bloodstream infection rates per 1000 peripherally inserted central venous catheter days were similar among babies in the trial and in all neonatal units. Of all bloodstream infections in babies receiving intensive or high-dependency care in neonatal units, 46% occurred during peripherally inserted central venous catheter days.<h4>Limitations</h4>The trial was open label as antimicrobial-impregnated and standard peripherally inserted central venous catheters are different colours. There was insufficient power to determine differences in rifampicin resistance.<h4>Conclusions</h4>No evidence of benefit or harm was found of peripherally inserted central venous catheters impregnated with rifampicin-miconazole during neonatal care. Interventions with small effects on bloodstream infections could be cost-effective over a child's life course. Findings were generalisable to neonatal units in England. Future research should focus on other types of antimicrobial impregnation of peripherally inserted central venous catheters and alternative approaches for preventing bloodstream infections in neonatal care.<h4>Trial registration</h4>Current Controlled Trials ISRCTN81931394.<h4>Funding</h4>This project was funded by the National Institute for Health Research Health Technology Assessment programme and will be published in full in <i>Health Technology Assessment</i>; Vol. 24, No. 57. See the NIHR Journals Library website for further project information.",,pdf:https://njl-admin.nihr.ac.uk/document/download/2034745; html:http://europepmc.org/books/NBK563908; doi:https://doi.org/10.3310/hta24570
 34982094,https://doi.org/10.1167/tvst.11.1.3,OCT Assisted Quantification of Vitreous Inflammation in Uveitis.,"Liu X, Kale AU, Ometto G, Montesano G, Sitch AJ, Capewell N, Radovanovic C, Bucknall N, Beare NAV, Moore DJ, Keane PA, Crabb DP, Denniston AK.",,Translational vision science & technology,2022,2022-01-01,Y,,,,"<h4>Purpose</h4>Vitreous haze (VH) is a key marker of inflammation in uveitis but limited by its subjectivity. Optical coherence tomography (OCT) has potential as an objective, noninvasive method for quantifying VH. We test the hypotheses that OCT can reliably quantify VH and the measurement is associated with slit-lamp based grading of VH.<h4>Methods</h4>In this prospective study, participants underwent three repeated OCT macular scans to evaluate the within-eye reliability of the OCT vitreous intensity (VI). Association between OCT VI and clinical findings (including VH grade, phakic status, visual acuity [VA], anterior chamber cells, and macular thickness) were assessed.<h4>Results</h4>One hundred nineteen participants were included (41 healthy participants, 32 patients with uveitis without VH, and 46 patients with uveitis with VH). Within-eye test reliability of OCT VI was high in healthy eyes and in all grades of VH (intraclass correlation coefficient [ICC] > 0.79). Average OCT VI was significantly different between healthy eyes and uveitic eyes without and uveitic eyes with VH, and was associated with increasing clinical VH grade (P < 0.05). OCT VI was significantly associated with VA, whereas clinical VH grading was not. Cataract was also associated with higher OCT VI (P = 0.03).<h4>Conclusions</h4>OCT VI is a fast, noninvasive, objective, and automated method for measuring vitreous inflammation. It is associated with clinician grading of vitreous inflammation and VA, however, it can be affected by media opacities.<h4>Translational relevance</h4>OCT imaging for quantifying vitreous inflammation shows high within-eye repeatability and is associated with clinical grading of vitreous haze. OCT measurements are also associated with visual acuity but may be affected by structures anterior to the acquisition window, such as lens opacity and other anterior segment changes.",,doi:https://doi.org/10.1167/tvst.11.1.3; doi:https://doi.org/10.1167/tvst.11.1.3; html:https://europepmc.org/articles/PMC8742534; pdf:https://europepmc.org/articles/PMC8742534?pdf=render
+34002035,https://doi.org/10.1038/s41366-021-00807-4,Risk factors mediating the effect of body mass index and waist-to-hip ratio on cardiovascular outcomes: Mendelian randomization analysis.,"Gill D, Zuber V, Dawson J, Pearson-Stuttard J, Carter AR, Sanderson E, Karhunen V, Levin MG, Wootton RE, Klarin D, Tsao PS, Tsilidis KK, Damrauer SM, Burgess S, Elliott P.",,International journal of obesity (2005),2021,2021-05-17,Y,,,,"<h4>Background</h4>Higher body mass index (BMI) and waist-to-hip ratio (WHR) increase the risk of cardiovascular disease, but the extent to which this is mediated by blood pressure, diabetes, lipid traits, and smoking is not fully understood.<h4>Methods</h4>Using consortia and UK Biobank genetic association summary data from 140,595 to 898,130 participants predominantly of European ancestry, Mendelian randomization mediation analysis was performed to investigate the degree to which systolic blood pressure (SBP), diabetes, lipid traits, and smoking mediated an effect of BMI and WHR on the risk of coronary artery disease (CAD), peripheral artery disease (PAD) and stroke.<h4>Results</h4>The odds ratio of CAD per 1-standard deviation increase in genetically predicted BMI was 1.49 (95% CI 1.39 to 1.60). This attenuated to 1.34 (95% CI 1.24 to 1.45) after adjusting for genetically predicted SBP (proportion mediated 27%, 95% CI 3% to 50%), to 1.27 (95% CI 1.17 to 1.37) after adjusting for genetically predicted diabetes (41% mediated, 95% CI 18% to 63%), to 1.47 (95% CI 1.36 to 1.59) after adjusting for genetically predicted lipids (3% mediated, 95% -23% to 29%), and to 1.46 (95% CI 1.34 to 1.58) after adjusting for genetically predicted smoking (6% mediated, 95% CI -20% to 32%). Adjusting for all the mediators together, the estimate attenuated to 1.14 (95% CI 1.04 to 1.26; 66% mediated, 95% CI 42% to 91%). A similar pattern was observed when considering genetically predicted WHR as the exposure, and PAD or stroke as the outcome.<h4>Conclusions</h4>Measures to reduce obesity will lower the risk of cardiovascular disease primarily by impacting downstream metabolic risk factors, particularly diabetes and hypertension. Reduction of obesity prevalence alongside control and management of its mediators is likely to be most effective for minimizing the burden of obesity.",,pdf:https://www.nature.com/articles/s41366-021-00807-4.pdf; doi:https://doi.org/10.1038/s41366-021-00807-4; html:https://europepmc.org/articles/PMC8236409; pdf:https://europepmc.org/articles/PMC8236409?pdf=render
+34425897,https://doi.org/10.1186/s13326-021-00249-x,Linking common human diseases to their phenotypes; development of a resource for human phenomics.,"Kafkas Ş, Althubaiti S, Gkoutos GV, Hoehndorf R, Schofield PN.",,Journal of biomedical semantics,2021,2021-08-23,Y,Ontologies; Text Mining; Uk Biobank; Disease–phenotype Associations,,,"<h4>Background</h4>In recent years a large volume of clinical genomics data has become available due to rapid advances in sequencing technologies. Efficient exploitation of this genomics data requires linkage to patient phenotype profiles. Current resources providing disease-phenotype associations are not comprehensive, and they often do not have broad coverage of the disease terminologies, particularly ICD-10, which is still the primary terminology used in clinical settings.<h4>Methods</h4>We developed two approaches to gather disease-phenotype associations. First, we used a text mining method that utilizes semantic relations in phenotype ontologies, and applies statistical methods to extract associations between diseases in ICD-10 and phenotype ontology classes from the literature. Second, we developed a semi-automatic way to collect ICD-10-phenotype associations from existing resources containing known relationships.<h4>Results</h4>We generated four datasets. Two of them are independent datasets linking diseases to their phenotypes based on text mining and semi-automatic strategies. The remaining two datasets are generated from these datasets and cover a subset of ICD-10 classes of common diseases contained in UK Biobank. We extensively validated our text mined and semi-automatically curated datasets by: comparing them against an expert-curated validation dataset containing disease-phenotype associations, measuring their similarity to disease-phenotype associations found in public databases, and assessing how well they could be used to recover gene-disease associations using phenotype similarity.<h4>Conclusion</h4>We find that our text mining method can produce phenotype annotations of diseases that are correct but often too general to have significant information content, or too specific to accurately reflect the typical manifestations of the sporadic disease. On the other hand, the datasets generated from integrating multiple knowledgebases are more complete (i.e., cover more of the required phenotype annotations for a given disease). We make all data freely available at https://doi.org/10.5281/zenodo.4726713 .",,pdf:https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-021-00249-x; doi:https://doi.org/10.1186/s13326-021-00249-x; html:https://europepmc.org/articles/PMC8383460; pdf:https://europepmc.org/articles/PMC8383460?pdf=render
 33654696,https://doi.org/10.1093/burnst/tkaa044,Venous thromboembolism prophylaxis practice and its association with outcomes in Australia and New Zealand burns patients.,"Tracy LM, Cameron PA, Singer Y, Earnest A, Wood F, Cleland H, Gabbe BJ.",,Burns & trauma,2021,2021-01-01,Y,Australia; New Zealand; Burn injury; Prophylaxis; Venous Thromboembolism,,,"<h4>Background</h4>Patients with burn injuries are considered to have an increased risk of venous thromboembolism (VTE). While untreated VTEs can be fatal, no studies have examined chemoprophylaxis effectiveness. This study aimed to quantify the variation in prevalence of VTE prophylaxis use in patients in Australian and New Zealand burns units and whether prophylaxis use is associated with in-hospital outcomes following burn injury.<h4>Methods</h4>Admission data for adult burns patients (aged ≥16 years) admitted between 1 July 2016 and 31 December 2018 were extracted from the Burns Registry of Australia and New Zealand. Mixed effects logistic regression modelling investigated whether VTE prophylaxis use was associated with the primary outcome of in-hospital mortality.<h4>Results</h4>There were 5066 admissions over the study period. Of these patients, 81% (n = 3799) with a valid response to the VTE prophylaxis data field received some form of VTE prophylaxis. Use of VTE prophylaxis ranged from 48.6% to 94.8% of patients between units. In-hospital death was recorded in <1% of patients (n = 33). After adjusting for confounders, receiving VTE prophylaxis was associated with a decrease in the adjusted odds of in-hospital mortality (adjusted odds ratio = 0.21; 95% CI, 0.07-0.63; <i>p</i> = 0.006).<h4>Conclusions</h4>Variation in the use of VTE prophylaxis was observed between the units, and prophylaxis use was associated with a decrease in the odds of mortality. These findings provide an opportunity to engage with units to further explore differences in prophylaxis use and develop future best practice guidelines.",,pdf:https://academic.oup.com/burnstrauma/article-pdf/doi/10.1093/burnst/tkaa044/37307900/tkaa044.pdf; doi:https://doi.org/10.1093/burnst/tkaa044; html:https://europepmc.org/articles/PMC7901708; pdf:https://europepmc.org/articles/PMC7901708?pdf=render
 33788869,https://doi.org/10.1371/journal.pone.0249258,Using graphic modelling to identify modifiable mediators of the association between area-based deprivation at birth and offspring unemployment.,"Bogie J, Fleming M, Cullen B, Mackay D, Pell JP.",,PloS one,2021,2021-03-31,Y,,,,"<h4>Background</h4>Deprivation can perpetuate across generations; however, the causative pathways are not well understood. Directed acyclic graphs (DAG) with mediation analysis can help elucidate and quantify complex pathways in order to identify modifiable factors at which to target interventions.<h4>Methods and findings</h4>We linked ten Scotland-wide databases (six health and four education) to produce a cohort of 217,226 pupils who attended Scottish schools between 2009 and 2013. The DAG comprised 23 potential mediators of the association between area deprivation at birth and subsequent offspring 'not in education, employment or training' status, covering maternal, antenatal, perinatal and child health, school engagement, and educational factors. Analyses were performed using modified g-computation. Deprivation at birth was associated with a 7.3% increase in offspring 'not in education, employment or training'. The principal mediators of this association were smoking during pregnancy (natural indirect effect of 0·016, 95% CI 0·013, 0·019) and school absences (natural indirect effect of 0·021, 95% CI 0·018, 0·024), explaining 22% and 30% of the total effect respectively. The proportion of the association potentially eliminated by addressing these factors was 19% (controlled direct effect when set to non-smoker 0·058; 95% CI 0·053, 0·063) for smoking during pregnancy and 38% (controlled direct effect when set to no absences 0·043; 95% CI 0·037, 0·049) for school absences.<h4>Conclusions</h4>Combining a DAG with mediation analysis helped disentangle a complex public health problem and quantified the modifiable factors of maternal smoking and school absence that could be targeted for intervention. This study also demonstrates the general utility of DAGs in understanding complex public health problems.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0249258&type=printable; doi:https://doi.org/10.1371/journal.pone.0249258; html:https://europepmc.org/articles/PMC8011734; pdf:https://europepmc.org/articles/PMC8011734?pdf=render
-34425897,https://doi.org/10.1186/s13326-021-00249-x,Linking common human diseases to their phenotypes; development of a resource for human phenomics.,"Kafkas Ş, Althubaiti S, Gkoutos GV, Hoehndorf R, Schofield PN.",,Journal of biomedical semantics,2021,2021-08-23,Y,Ontologies; Text Mining; Uk Biobank; Disease–phenotype Associations,,,"<h4>Background</h4>In recent years a large volume of clinical genomics data has become available due to rapid advances in sequencing technologies. Efficient exploitation of this genomics data requires linkage to patient phenotype profiles. Current resources providing disease-phenotype associations are not comprehensive, and they often do not have broad coverage of the disease terminologies, particularly ICD-10, which is still the primary terminology used in clinical settings.<h4>Methods</h4>We developed two approaches to gather disease-phenotype associations. First, we used a text mining method that utilizes semantic relations in phenotype ontologies, and applies statistical methods to extract associations between diseases in ICD-10 and phenotype ontology classes from the literature. Second, we developed a semi-automatic way to collect ICD-10-phenotype associations from existing resources containing known relationships.<h4>Results</h4>We generated four datasets. Two of them are independent datasets linking diseases to their phenotypes based on text mining and semi-automatic strategies. The remaining two datasets are generated from these datasets and cover a subset of ICD-10 classes of common diseases contained in UK Biobank. We extensively validated our text mined and semi-automatically curated datasets by: comparing them against an expert-curated validation dataset containing disease-phenotype associations, measuring their similarity to disease-phenotype associations found in public databases, and assessing how well they could be used to recover gene-disease associations using phenotype similarity.<h4>Conclusion</h4>We find that our text mining method can produce phenotype annotations of diseases that are correct but often too general to have significant information content, or too specific to accurately reflect the typical manifestations of the sporadic disease. On the other hand, the datasets generated from integrating multiple knowledgebases are more complete (i.e., cover more of the required phenotype annotations for a given disease). We make all data freely available at https://doi.org/10.5281/zenodo.4726713 .",,pdf:https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-021-00249-x; doi:https://doi.org/10.1186/s13326-021-00249-x; html:https://europepmc.org/articles/PMC8383460; pdf:https://europepmc.org/articles/PMC8383460?pdf=render
-34002035,https://doi.org/10.1038/s41366-021-00807-4,Risk factors mediating the effect of body mass index and waist-to-hip ratio on cardiovascular outcomes: Mendelian randomization analysis.,"Gill D, Zuber V, Dawson J, Pearson-Stuttard J, Carter AR, Sanderson E, Karhunen V, Levin MG, Wootton RE, Klarin D, Tsao PS, Tsilidis KK, Damrauer SM, Burgess S, Elliott P.",,International journal of obesity (2005),2021,2021-05-17,Y,,,,"<h4>Background</h4>Higher body mass index (BMI) and waist-to-hip ratio (WHR) increase the risk of cardiovascular disease, but the extent to which this is mediated by blood pressure, diabetes, lipid traits, and smoking is not fully understood.<h4>Methods</h4>Using consortia and UK Biobank genetic association summary data from 140,595 to 898,130 participants predominantly of European ancestry, Mendelian randomization mediation analysis was performed to investigate the degree to which systolic blood pressure (SBP), diabetes, lipid traits, and smoking mediated an effect of BMI and WHR on the risk of coronary artery disease (CAD), peripheral artery disease (PAD) and stroke.<h4>Results</h4>The odds ratio of CAD per 1-standard deviation increase in genetically predicted BMI was 1.49 (95% CI 1.39 to 1.60). This attenuated to 1.34 (95% CI 1.24 to 1.45) after adjusting for genetically predicted SBP (proportion mediated 27%, 95% CI 3% to 50%), to 1.27 (95% CI 1.17 to 1.37) after adjusting for genetically predicted diabetes (41% mediated, 95% CI 18% to 63%), to 1.47 (95% CI 1.36 to 1.59) after adjusting for genetically predicted lipids (3% mediated, 95% -23% to 29%), and to 1.46 (95% CI 1.34 to 1.58) after adjusting for genetically predicted smoking (6% mediated, 95% CI -20% to 32%). Adjusting for all the mediators together, the estimate attenuated to 1.14 (95% CI 1.04 to 1.26; 66% mediated, 95% CI 42% to 91%). A similar pattern was observed when considering genetically predicted WHR as the exposure, and PAD or stroke as the outcome.<h4>Conclusions</h4>Measures to reduce obesity will lower the risk of cardiovascular disease primarily by impacting downstream metabolic risk factors, particularly diabetes and hypertension. Reduction of obesity prevalence alongside control and management of its mediators is likely to be most effective for minimizing the burden of obesity.",,pdf:https://www.nature.com/articles/s41366-021-00807-4.pdf; doi:https://doi.org/10.1038/s41366-021-00807-4; html:https://europepmc.org/articles/PMC8236409; pdf:https://europepmc.org/articles/PMC8236409?pdf=render
 30554166,https://doi.org/10.1136/injuryprev-2018-043019,"Work absence due to compensable RTCs in Victoria, Australia.","Gray SE, Gabbe BJ, Collie A.",,Injury prevention : journal of the International Society for Child and Adolescent Injury Prevention,2020,2018-12-15,N,Functional Outcome; Burden Of Disease; Descriptive Epidemiology; Occupational Injury; Motor Vehicle Occupant,,,"<h4>Introduction</h4>RTC burden is commonly measured using fatality or hospitalisation statistics. However, non-fatal and less severe injuries contribute substantial economic and human costs, including work absence. In Victoria, Australia, two major compensation systems provide income support to employed people injured in RTCs; workers' compensation (if RTC occurred during work) and an RTC-specific compensation system. This study aimed to describe the number and rate of episodes of work absence due to compensable RTC and determine factors associated with work-related RTC resulting in work absence.<h4>Methods</h4>Administrative data for working-age people (15-65 years) with accepted compensation claims between 1 July 2003 and 30 June 2013 were extracted from Victoria's Compensation Research Database and analysed. Injured people receiving at least one day of income support were retained. Rate calculations used Victoria's labour force as the denominator and negative binomial regression determined any time-based trend changes. Multivariable logistic regression was used to determine odds of the RTC being work-related.<h4>Results</h4>There were 40 677 claims made by workers with an RTC injury that consequently missed work, averaging 4068 claims per year at a rate of 12.9 per 100 000 working population. Work-related cases contributed 17.4% (N=7061). Males, older adults and RTCs involving heavy vehicles, buses, trains and trams had higher odds of a work-related RTC resulting in work absence. More severe injuries tended not to be work-related.<h4>Conclusions</h4>Work absence due to RTC injury constitutes a substantial burden, and this measure could provide a valuable addition to conventional RTC statistics.",,doi:https://doi.org/10.1136/injuryprev-2018-043019
-31816119,https://doi.org/10.1002/sim.8443,Dynamic predictive probabilities to monitor rapid cystic fibrosis disease progression.,"Szczesniak RD, Su W, Brokamp C, Keogh RH, Pestian JP, Seid M, Diggle PJ, Clancy JP.",,Statistics in medicine,2020,2019-12-09,Y,Longitudinal Data Analysis; Medical Monitoring; Nonstationary Process; Nowcasting; Predictive Probability Distributions,Understanding the Causes of Disease,,"Cystic fibrosis (CF) is a progressive, genetic disease characterized by frequent, prolonged drops in lung function. Accurately predicting rapid underlying lung-function decline is essential for clinical decision support and timely intervention. Determining whether an individual is experiencing a period of rapid decline is complicated due to its heterogeneous timing and extent, and error component of the measured lung function. We construct individualized predictive probabilities for ""nowcasting"" rapid decline. We assume each patient's true longitudinal lung function, S(t), follows a nonlinear, nonstationary stochastic process, and accommodate between-patient heterogeneity through random effects. Corresponding lung-function decline at time t is defined as the rate of change, S'(t). We predict S'(t) conditional on observed covariate and measurement history by modeling a measured lung function as a noisy version of S(t). The method is applied to data on 30 879 US CF Registry patients. Results are contrasted with a currently employed decision rule using single-center data on 212 individuals. Rapid decline is identified earlier using predictive probabilities than the center's currently employed decision rule (mean difference: 0.65 years; 95% confidence interval (CI): 0.41, 0.89). We constructed a bootstrapping algorithm to obtain CIs for predictive probabilities. We illustrate real-time implementation with R Shiny. Predictive accuracy is investigated using empirical simulations, which suggest this approach more accurately detects peak decline, compared with a uniform threshold of rapid decline. Median area under the ROC curve estimates (Q1-Q3) were 0.817 (0.814-0.822) and 0.745 (0.741-0.747), respectively, implying reasonable accuracy for both. This article demonstrates how individualized rate of change estimates can be coupled with probabilistic predictive inference and implementation for a useful medical-monitoring approach.",The objective of this paper was to construct individualised dynamic predictive probabilities to monitor rapid Cystic Fibrosis (CF) disease progression. The results demonstrated how individualised rate of change estimates can be coupled with probabilitic predictive inference and implementation for a useful medical-monitoring approach.,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/sim.8443; doi:https://doi.org/10.1002/sim.8443; html:https://europepmc.org/articles/PMC7028099; pdf:https://europepmc.org/articles/PMC7028099?pdf=render
 35983770,https://doi.org/10.2807/1560-7917.es.2022.27.33.2100885,"Recording of 'COVID-19 vaccine declined': a cohort study on 57.9 million National Health Service patients' records in situ using OpenSAFELY, England, 8 December 2020 to 25 May 2021.","Curtis HJ, Inglesby P, MacKenna B, Croker R, Hulme WJ, Rentsch CT, Bhaskaran K, Mathur R, Morton CE, Bacon SC, Smith RM, Evans D, Mehrkar A, Tomlinson L, Walker AJ, Bates C, Hickman G, Ward T, Morley J, Cockburn J, Davy S, Williamson EJ, Eggo RM, Parry J, Hester F, Harper S, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Griffiths P, Fowles A, Parkes N, Evans SJ, Douglas IJ, Smeeth L, Goldacre B.",,Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin,2022,2022-08-01,Y,Vaccination; Vaccine Hesitancy; Nhs England; Covid-19; Sars-cov-2,,,"BackgroundPriority patients in England were offered COVID-19 vaccination by mid-April 2021. Codes in clinical record systems can denote the vaccine being declined.AimWe describe records of COVID-19 vaccines being declined, according to clinical and demographic factors.MethodsWith the approval of NHS England, we conducted a retrospective cohort study between 8 December 2020 and 25 May 2021 with primary care records for 57.9 million patients using OpenSAFELY, a secure health analytics platform. COVID-19 vaccination priority patients were those aged ≥ 50 years or ≥ 16 years clinically extremely vulnerable (CEV) or 'at risk'. We describe the proportion recorded as declining vaccination for each group and stratified by clinical and demographic subgroups, subsequent vaccination and distribution of clinical code usage across general practices.ResultsOf 24.5 million priority patients, 663,033 (2.7%) had a decline recorded, while 2,155,076 (8.8%) had neither a vaccine nor decline recorded. Those recorded as declining, who were subsequently vaccinated (n = 125,587; 18.9%) were overrepresented in the South Asian population (32.3% vs 22.8% for other ethnicities aged ≥ 65 years). The proportion of declining unvaccinated patients was highest in CEV (3.3%), varied strongly with ethnicity (black 15.3%, South Asian 5.6%, white 1.5% for ≥ 80 years) and correlated positively with increasing deprivation.ConclusionsClinical codes indicative of COVID-19 vaccinations being declined are commonly used in England, but substantially more common among black and South Asian people, and in more deprived areas. Qualitative research is needed to determine typical reasons for recorded declines, including to what extent they reflect patients actively declining.",,pdf:https://www.eurosurveillance.org/deliver/fulltext/eurosurveillance/27/33/eurosurv-27-33-5.pdf?itemId=%2Fcontent%2F10.2807%2F1560-7917.ES.2022.27.33.2100885&mimeType=pdf&containerItemId=content/eurosurveillance; doi:https://doi.org/10.2807/1560-7917.ES.2022.27.33.2100885; html:https://europepmc.org/articles/PMC9389857
+31816119,https://doi.org/10.1002/sim.8443,Dynamic predictive probabilities to monitor rapid cystic fibrosis disease progression.,"Szczesniak RD, Su W, Brokamp C, Keogh RH, Pestian JP, Seid M, Diggle PJ, Clancy JP.",,Statistics in medicine,2020,2019-12-09,Y,Longitudinal Data Analysis; Medical Monitoring; Nonstationary Process; Nowcasting; Predictive Probability Distributions,Understanding the Causes of Disease,,"Cystic fibrosis (CF) is a progressive, genetic disease characterized by frequent, prolonged drops in lung function. Accurately predicting rapid underlying lung-function decline is essential for clinical decision support and timely intervention. Determining whether an individual is experiencing a period of rapid decline is complicated due to its heterogeneous timing and extent, and error component of the measured lung function. We construct individualized predictive probabilities for ""nowcasting"" rapid decline. We assume each patient's true longitudinal lung function, S(t), follows a nonlinear, nonstationary stochastic process, and accommodate between-patient heterogeneity through random effects. Corresponding lung-function decline at time t is defined as the rate of change, S'(t). We predict S'(t) conditional on observed covariate and measurement history by modeling a measured lung function as a noisy version of S(t). The method is applied to data on 30 879 US CF Registry patients. Results are contrasted with a currently employed decision rule using single-center data on 212 individuals. Rapid decline is identified earlier using predictive probabilities than the center's currently employed decision rule (mean difference: 0.65 years; 95% confidence interval (CI): 0.41, 0.89). We constructed a bootstrapping algorithm to obtain CIs for predictive probabilities. We illustrate real-time implementation with R Shiny. Predictive accuracy is investigated using empirical simulations, which suggest this approach more accurately detects peak decline, compared with a uniform threshold of rapid decline. Median area under the ROC curve estimates (Q1-Q3) were 0.817 (0.814-0.822) and 0.745 (0.741-0.747), respectively, implying reasonable accuracy for both. This article demonstrates how individualized rate of change estimates can be coupled with probabilistic predictive inference and implementation for a useful medical-monitoring approach.",The objective of this paper was to construct individualised dynamic predictive probabilities to monitor rapid Cystic Fibrosis (CF) disease progression. The results demonstrated how individualised rate of change estimates can be coupled with probabilitic predictive inference and implementation for a useful medical-monitoring approach.,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/sim.8443; doi:https://doi.org/10.1002/sim.8443; html:https://europepmc.org/articles/PMC7028099; pdf:https://europepmc.org/articles/PMC7028099?pdf=render
 34931349,https://doi.org/10.1111/bcp.15191,Dissecting the IL-6 pathway in cardiometabolic disease: A Mendelian randomization study on both IL6 and IL6R.,"Cupido AJ, Asselbergs FW, Natarajan P, CHARGE Inflammation Working Group, Ridker PM, Hovingh GK, Schmidt AF.",,British journal of clinical pharmacology,2022,2022-01-28,Y,IL-6; Cardiovascular disease; Trans-signalling; Classical Signalling,,,"<h4>Aims</h4>Chronic inflammation is a risk factor for cardiovascular disease (CVD). IL-6 signalling perturbation through IL-6 or IL-6R blockade may have potential benefit on cardiovascular risk. It is unknown whether targeting either IL-6 or IL-6 receptor may result in similar effects on CVD and adverse events. We compared the anticipated effects of targeting IL-6 and IL-6 receptor on cardiometabolic risk and potential side effects.<h4>Methods</h4>We constructed four instruments: two main instruments with genetic variants in the IL6 and IL6R loci weighted for their association with CRP, and two after firstly filtering variants for their association with IL-6 or IL-6R expression. Analyses were performed for coronary artery disease (CAD), ischemic stroke, atrial fibrillation (AF), heart failure, type 2 diabetes (T2D), rheumatoid arthritis (RA), infection endpoints, and quantitative haematological, metabolic and anthropometric parameters.<h4>Results</h4>A 1 mg/L lower CRP by the IL6 instrument was associated with lower CAD (odds ratio [OR] 0.86, 95% confidence interval [CI] 0.77;0.96), AF and T2D risk. A 1 mg/L lower CRP by the IL6R instrument was associated with lower CAD (OR 0.90, 95% CI 0.86;0.95), any stroke and ischemic stroke, AF, RA risk and higher pneumonia risk. The eQTL-filtered results were in concordance with the main results, but with wider confidence intervals.<h4>Conclusions</h4>IL-6 signalling perturbation by either IL6 or IL6R genetic instruments is associated with a similar risk reduction for multiple cardiometabolic diseases, suggesting that both IL-6 and IL-6R are potential therapeutic targets to lower CVD. Moreover, IL-6 rather than IL-6R inhibition might have a more favourable pneumonia risk.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/bcp.15191; doi:https://doi.org/10.1111/bcp.15191; html:https://europepmc.org/articles/PMC9303316; pdf:https://europepmc.org/articles/PMC9303316?pdf=render
 37264679,https://doi.org/10.1093/eurjpc/zwad187,Improving 10-year cardiovascular risk prediction in apparently healthy people: flexible addition of risk modifiers on top of SCORE2.,"Hageman SHJ, Petitjaen C, Pennells L, Kaptoge S, Pajouheshnia R, Tillmann T, Blaha MJ, McClelland RL, Matsushita K, Nambi V, Klungel OH, Souverein PC, van der Schouw YT, Verschuren WMM, Lehmann N, Erbel R, Jöckel KH, Di Angelantonio E, Visseren FLJ, Dorresteijn JAN.",,European journal of preventive cardiology,2023,2023-10-01,Y,Biomarkers; Risk stratification; Risk Prediction; cardiovascular; Coronary Calcium Score; Score2,,,"<h4>Aims</h4>In clinical practice, factors associated with cardiovascular disease (CVD) like albuminuria, education level, or coronary artery calcium (CAC) are often known, but not incorporated in cardiovascular risk prediction models. The aims of the current study were to evaluate a methodology for the flexible addition of risk modifying characteristics on top of SCORE2 and to quantify the added value of several clinically relevant risk modifying characteristics.<h4>Methods and results</h4>Individuals without previous CVD or DM were included from the UK Biobank; Atherosclerosis Risk in Communities (ARIC); Multi-Ethnic Study of Atherosclerosis (MESA); European Prospective Investigation into Cancer, The Netherlands (EPIC-NL); and Heinz Nixdorf Recall (HNR) studies (n = 409 757) in whom 16 166 CVD events and 19 149 non-cardiovascular deaths were observed over exactly 10.0 years of follow-up. The effect of each possible risk modifying characteristic was derived using competing risk-adjusted Fine and Gray models. The risk modifying characteristics were applied to individual predictions with a flexible method using the population prevalence and the subdistribution hazard ratio (SHR) of the relevant predictor. Risk modifying characteristics that increased discrimination most were CAC percentile with 0.0198 [95% confidence interval (CI) 0.0115; 0.0281] and hs-Troponin-T with 0.0100 (95% CI 0.0063; 0.0137). External validation was performed in the Clinical Practice Research Datalink (CPRD) cohort (UK, n = 518 015, 12 675 CVD events). Adjustment of SCORE2-predicted risks with both single and multiple risk modifiers did not negatively affect calibration and led to a modest increase in discrimination [0.740 (95% CI 0.736-0.745) vs. unimproved SCORE2 risk C-index 0.737 (95% CI 0.732-0.741)].<h4>Conclusion</h4>The current paper presents a method on how to integrate possible risk modifying characteristics that are not included in existing CVD risk models for the prediction of CVD event risk in apparently healthy people. This flexible methodology improves the accuracy of predicted risks and increases applicability of prediction models for individuals with additional risk known modifiers.",,pdf:https://academic.oup.com/eurjpc/advance-article-pdf/doi/10.1093/eurjpc/zwad187/50506335/zwad187.pdf; doi:https://doi.org/10.1093/eurjpc/zwad187; html:https://europepmc.org/articles/PMC10600319; pdf:https://europepmc.org/articles/PMC10600319?pdf=render
 37777287,https://doi.org/10.1016/s2468-2667(23)00178-0,"All-cause hospitalisation among people living with HIV according to gender, mode of HIV acquisition, ethnicity, and geographical origin in Europe and North America: findings from the ART-CC cohort collaboration.","Rein SM, Lampe FC, Ingle SM, Sterne JAC, Trickey A, Gill MJ, Papastamopoulos V, Wittkop L, van der Valk M, Kitchen M, Guest JL, Satre DD, Wandeler G, Galindo P, Castilho J, Crane HM, Smith CJ.",,The Lancet. Public health,2023,2023-10-01,Y,,,,"<h4>Background</h4>Understanding demographic disparities in hospitalisation is crucial for the identification of vulnerable populations, interventions, and resource planning.<h4>Methods</h4>Data were from the Antiretroviral Therapy Cohort Collaboration (ART-CC) on people living with HIV in Europe and North America, followed up between January, 2007 and December, 2020. We investigated differences in all-cause hospitalisation according to gender and mode of HIV acquisition, ethnicity, and combined geographical origin and ethnicity, in people living with HIV on modern combination antiretroviral therapy (cART). Analyses were performed separately for European and North American cohorts. Hospitalisation rates were assessed using negative binomial multilevel regression, adjusted for age, time since cART intitiaion, and calendar year.<h4>Findings</h4>Among 23 594 people living with HIV in Europe and 9612 in North America, hospitalisation rates per 100 person-years were 16·2 (95% CI 16·0-16·4) and 13·1 (12·8-13·5). Compared with gay, bisexual, and other men who have sex with men, rates were higher for heterosexual men and women, and much higher for men and women who acquired HIV through injection drug use (adjusted incidence rate ratios ranged from 1·2 to 2·5 in Europe and from 1·2 to 3·3 in North America). In both regions, individuals with geographical origin other than the region of study generally had lower hospitalisation rates compared with those with geographical origin of the study country. In North America, Indigenous people and Black or African American individuals had higher rates than White individuals (adjusted incidence rate ratios 1·9 and 1·2), whereas Asian and Hispanic people living with HIV had somewhat lower rates. In Europe there was a lower rate in Asian individuals compared with White individuals.<h4>Interpretation</h4>Substantial disparities exist in all-cause hospitalisation between demographic groups of people living with HIV in the current cART era in high-income settings, highlighting the need for targeted support.<h4>Funding</h4>Royal Free Charity and the National Institute on Alcohol Abuse and Alcoholism.",,pdf:http://www.thelancet.com/article/S2468266723001780/pdf; doi:https://doi.org/10.1016/S2468-2667(23)00178-0; html:https://europepmc.org/articles/PMC10851157; pdf:https://europepmc.org/articles/PMC10851157?pdf=render
-35866236,https://doi.org/10.7189/jogh.12.05033,The road to recovery: an interrupted time series analysis of policy intervention to restore essential health services in Mexico during the COVID-19 pandemic.,"Doubova SV, Arsenault C, Contreras-Sánchez SE, Borrayo-Sánchez G, Leslie HH.",,Journal of global health,2022,2022-07-23,Y,,,,"<h4>Background</h4>Recovery of health services disrupted by the COVID-19 pandemic represents a significant challenge in low- and middle-income countries. In April 2021, the Mexican Institute of Social Security (IMSS), which provides health care to 68.5 million people, launched the National Strategy for Health Services Recovery (Recovery policy). The study objective was to evaluate whether the Recovery policy addressed COVID-related declines in maternal, child health, and non-communicable diseases (NCDs) services.<h4>Methods</h4>We analysed the data of 35 IMSS delegations from January 2019 to November 2021 on contraceptive visits, antenatal care consultations, deliveries, caesarean sections, sick children's consultations, child vaccination, breast and cervical cancer screening, diabetes and hypertension consultations, and control. We focused on the period before (April 2020 - March 2021) and during (April 2021 - November 2021) the Recovery policy and used an interrupted time series design and Poisson Generalized Estimating Equation models to estimate the association of this policy with service use and outcomes and change in their trends.<h4>Results</h4>Despite the third wave of the pandemic in 2021, service utilization increased in the Recovery period, reaching (at minimum) 49% of pre-pandemic levels for sick children's consultations and (at maximum) 106% of pre-pandemic levels for breast cancer screenings. Evidence for the Recovery policy role was mixed: the policy was associated with increased facility deliveries (IRR = 1.15, 95%CI = 1.11-1.19) with a growing trend over time (IRR = 1.04, 95%CI = 1.03-1.05); antenatal care and child health services saw strong level effects but decrease over time. Additionally, the Recovery policy was associated with diabetes and hypertension control. Services recovery varied across delegations.<h4>Conclusions</h4>Health service utilization and NCDs control demonstrated important gains in 2021, but evidence suggests the policy had inconsistent effects across services and decreasing impact over time. Further efforts to strengthen essential health services and ensure consistent recovery across delegations are warranted.",,pdf:https://jogh.org/wp-content/uploads/2022/07/jogh-12-05033.pdf; doi:https://doi.org/10.7189/jogh.12.05033; html:https://europepmc.org/articles/PMC9304921; pdf:https://europepmc.org/articles/PMC9304921?pdf=render
 32763829,https://doi.org/10.1016/j.ebiom.2020.102932,Dietary metabolite profiling brings new insight into the relationship between nutrition and metabolic risk: An IMI DIRECT study.,"Eriksen R, Perez IG, Posma JM, Haid M, Sharma S, Prehn C, Thomas LE, Koivula RW, Bizzotto R, Prehn C, Mari A, Giordano GN, Pavo I, Schwenk JM, De Masi F, Tsirigos KD, Brunak S, Viñuela A, Mahajan A, McDonald TJ, Kokkola T, Rutter F, Teare H, Hansen TH, Fernandez J, Jones A, Jennison C, Walker M, McCarthy MI, Pedersen O, Ruetten H, Forgie I, Bell JD, Pearson ER, Franks PW, Adamski J, Holmes E, Frost G.",,EBioMedicine,2020,2020-08-04,Y,Type 2 diabetes; metabolic profiling; Dietary Patterns; Cardiometabolic Health,,,"<h4>Background</h4>Dietary advice remains the cornerstone of prevention and management of type 2 diabetes (T2D). However, understanding the efficacy of dietary interventions is confounded by the challenges inherent in assessing free living diet. Here we profiled dietary metabolites to investigate glycaemic deterioration and cardiometabolic risk in people at risk of or living with T2D.<h4>Methods</h4>We analysed data from plasma collected at baseline and 18-month follow-up in individuals from the Innovative Medicines Initiative (IMI) Diabetes Research on Patient Stratification (DIRECT) cohort 1 n = 403 individuals with normal or impaired glucose regulation (prediabetic) and cohort 2 n = 458 individuals with new onset of T2D. A dietary metabolite profile model (T<sub>pred</sub>) was constructed using multivariable regression of 113 plasma metabolites obtained from targeted metabolomics assays. The continuous T<sub>pred</sub> score was used to explore the relationships between diet, glycaemic deterioration and cardio-metabolic risk via multiple linear regression models.<h4>Findings</h4>A higher T<sub>pred</sub> score was associated with healthier diets high in wholegrain (β=3.36 g, 95% CI 0.31, 6.40 and β=2.82 g, 95% CI 0.06, 5.57) and lower energy intake (β=-75.53 kcal, 95% CI -144.71, -2.35 and β=-122.51 kcal, 95% CI -186.56, -38.46), and saturated fat (β=-0.92 g, 95% CI -1.56, -0.28 and β=-0.98 g, 95% CI -1.53, -0.42 g), respectively for cohort 1 and 2. In both cohorts a higher T<sub>pred</sub> score was also associated with lower total body adiposity and favourable lipid profiles HDL-cholesterol (β=0.07 mmol/L, 95% CI 0.03, 0.1), (β=0.08 mmol/L, 95% CI 0.04, 0.1), and triglycerides (β=-0.1 mmol/L, 95% CI -0.2, -0.03), (β=-0.2 mmol/L, 95% CI -0.3, -0.09), respectively for cohort 1 and 2. In cohort 2, the T<sub>pred</sub> score was negatively associated with liver fat (β=-0.74%, 95% CI -0.67, -0.81), and lower fasting concentrations of HbA1c (β=-0.9 mmol/mol, 95% CI -1.5, -0.1), glucose (β=-0.2 mmol/L, 95% CI -0.4, -0.05) and insulin (β=-11.0 pmol/mol, 95% CI -19.5, -2.6). Longitudinal analysis showed at 18-month follow up a higher T<sub>pred</sub> score was also associated lower total body adiposity in both cohorts and lower fasting glucose (β=-0.2 mmol/L, 95% CI -0.3, -0.01) and insulin (β=-9.2 pmol/mol, 95% CI -17.9, -0.4) concentrations in cohort 2.<h4>Interpretation</h4>Plasma dietary metabolite profiling provides objective measures of diet intake, showing a relationship to glycaemic deterioration and cardiometabolic health.<h4>Funding</h4>This work was supported by the Innovative Medicines Initiative Joint Undertaking under grant agreement no. 115,317 (DIRECT), resources of which are composed of financial contribution from the European Union's Seventh Framework Programme (FP7/2007-2013) and EFPIA companies.",,pdf:http://www.thelancet.com/article/S235239642030308X/pdf; doi:https://doi.org/10.1016/j.ebiom.2020.102932; html:https://europepmc.org/articles/PMC7406914; pdf:https://europepmc.org/articles/PMC7406914?pdf=render
-36082306,https://doi.org/10.1016/j.xgen.2021.100004,Workshop proceedings: GWAS summary statistics standards and sharing.,"MacArthur JAL, Buniello A, Harris LW, Hayhurst J, McMahon A, Sollis E, Cerezo M, Hall P, Lewis E, Whetzel PL, Bahcall OG, Barroso I, Carroll RJ, Inouye M, Manolio TA, Rich SS, Hindorff LA, Wiley K, Parkinson H.",,Cell genomics,2021,2021-10-01,Y,,,,"Genome-wide association studies (GWASs) have enabled robust mapping of complex traits in humans. The open sharing of GWAS summary statistics (SumStats) is essential in facilitating the larger meta-analyses needed for increased power in resolving the genetic basis of disease. However, most GWAS SumStats are not readily accessible because of limited sharing and a lack of defined standards. With the aim of increasing the availability, quality, and utility of GWAS SumStats, the National Human Genome Research Institute-European Bioinformatics Institute (NHGRI-EBI) GWAS Catalog organized a community workshop to address the standards, infrastructure, and incentives required to promote and enable sharing. We evaluated the barriers to SumStats sharing, both technological and sociological, and developed an action plan to address those challenges and ensure that SumStats and study metadata are findable, accessible, interoperable, and reusable (FAIR). We encourage early deposition of datasets in the GWAS Catalog as the recognized central repository. We recommend standard requirements for reporting elements and formats for SumStats and accompanying metadata as guidelines for community standards and a basis for submission to the GWAS Catalog. Finally, we provide recommendations to enable, promote, and incentivize broader data sharing, standards and FAIRness in order to advance genomic medicine.",,doi:https://doi.org/10.1016/j.xgen.2021.100004; doi:https://doi.org/10.1016/j.xgen.2021.100004; html:https://europepmc.org/articles/PMC9451133; pdf:https://europepmc.org/articles/PMC9451133?pdf=render
+35866236,https://doi.org/10.7189/jogh.12.05033,The road to recovery: an interrupted time series analysis of policy intervention to restore essential health services in Mexico during the COVID-19 pandemic.,"Doubova SV, Arsenault C, Contreras-Sánchez SE, Borrayo-Sánchez G, Leslie HH.",,Journal of global health,2022,2022-07-23,Y,,,,"<h4>Background</h4>Recovery of health services disrupted by the COVID-19 pandemic represents a significant challenge in low- and middle-income countries. In April 2021, the Mexican Institute of Social Security (IMSS), which provides health care to 68.5 million people, launched the National Strategy for Health Services Recovery (Recovery policy). The study objective was to evaluate whether the Recovery policy addressed COVID-related declines in maternal, child health, and non-communicable diseases (NCDs) services.<h4>Methods</h4>We analysed the data of 35 IMSS delegations from January 2019 to November 2021 on contraceptive visits, antenatal care consultations, deliveries, caesarean sections, sick children's consultations, child vaccination, breast and cervical cancer screening, diabetes and hypertension consultations, and control. We focused on the period before (April 2020 - March 2021) and during (April 2021 - November 2021) the Recovery policy and used an interrupted time series design and Poisson Generalized Estimating Equation models to estimate the association of this policy with service use and outcomes and change in their trends.<h4>Results</h4>Despite the third wave of the pandemic in 2021, service utilization increased in the Recovery period, reaching (at minimum) 49% of pre-pandemic levels for sick children's consultations and (at maximum) 106% of pre-pandemic levels for breast cancer screenings. Evidence for the Recovery policy role was mixed: the policy was associated with increased facility deliveries (IRR = 1.15, 95%CI = 1.11-1.19) with a growing trend over time (IRR = 1.04, 95%CI = 1.03-1.05); antenatal care and child health services saw strong level effects but decrease over time. Additionally, the Recovery policy was associated with diabetes and hypertension control. Services recovery varied across delegations.<h4>Conclusions</h4>Health service utilization and NCDs control demonstrated important gains in 2021, but evidence suggests the policy had inconsistent effects across services and decreasing impact over time. Further efforts to strengthen essential health services and ensure consistent recovery across delegations are warranted.",,pdf:https://jogh.org/wp-content/uploads/2022/07/jogh-12-05033.pdf; doi:https://doi.org/10.7189/jogh.12.05033; html:https://europepmc.org/articles/PMC9304921; pdf:https://europepmc.org/articles/PMC9304921?pdf=render
 34750571,https://doi.org/10.1038/s42255-021-00478-5,Integrative analysis of the plasma proteome and polygenic risk of cardiometabolic diseases.,"Ritchie SC, Lambert SA, Arnold M, Teo SM, Lim S, Scepanovic P, Marten J, Zahid S, Chaffin M, Liu Y, Abraham G, Ouwehand WH, Roberts DJ, Watkins NA, Drew BG, Calkin AC, Di Angelantonio E, Soranzo N, Burgess S, Chapman M, Kathiresan S, Khera AV, Danesh J, Butterworth AS, Inouye M.",,Nature metabolism,2021,2021-11-08,Y,,,,"Cardiometabolic diseases are frequently polygenic in architecture, comprising a large number of risk alleles with small effects spread across the genome<sup>1-3</sup>. Polygenic scores (PGS) aggregate these into a metric representing an individual's genetic predisposition to disease. PGS have shown promise for early risk prediction<sup>4-7</sup> and there is an open question as to whether PGS can also be used to understand disease biology<sup>8</sup>. Here, we demonstrate that cardiometabolic disease PGS can be used to elucidate the proteins underlying disease pathogenesis. In 3,087 healthy individuals, we found that PGS for coronary artery disease, type 2 diabetes, chronic kidney disease and ischaemic stroke are associated with the levels of 49 plasma proteins. Associations were polygenic in architecture, largely independent of cis and trans protein quantitative trait loci and present for proteins without quantitative trait loci. Over a follow-up of 7.7 years, 28 of these proteins associated with future myocardial infarction or type 2 diabetes events, 16 of which were mediators between polygenic risk and incident disease. Twelve of these were druggable targets with therapeutic potential. Our results demonstrate the potential for PGS to uncover causal disease biology and targets with therapeutic potential, including those that may be missed by approaches utilizing information at a single locus.",,pdf:https://www.nature.com/articles/s42255-021-00478-5.pdf; doi:https://doi.org/10.1038/s42255-021-00478-5; html:https://europepmc.org/articles/PMC8574944; pdf:https://europepmc.org/articles/PMC8574944?pdf=render
+36082306,https://doi.org/10.1016/j.xgen.2021.100004,Workshop proceedings: GWAS summary statistics standards and sharing.,"MacArthur JAL, Buniello A, Harris LW, Hayhurst J, McMahon A, Sollis E, Cerezo M, Hall P, Lewis E, Whetzel PL, Bahcall OG, Barroso I, Carroll RJ, Inouye M, Manolio TA, Rich SS, Hindorff LA, Wiley K, Parkinson H.",,Cell genomics,2021,2021-10-01,Y,,,,"Genome-wide association studies (GWASs) have enabled robust mapping of complex traits in humans. The open sharing of GWAS summary statistics (SumStats) is essential in facilitating the larger meta-analyses needed for increased power in resolving the genetic basis of disease. However, most GWAS SumStats are not readily accessible because of limited sharing and a lack of defined standards. With the aim of increasing the availability, quality, and utility of GWAS SumStats, the National Human Genome Research Institute-European Bioinformatics Institute (NHGRI-EBI) GWAS Catalog organized a community workshop to address the standards, infrastructure, and incentives required to promote and enable sharing. We evaluated the barriers to SumStats sharing, both technological and sociological, and developed an action plan to address those challenges and ensure that SumStats and study metadata are findable, accessible, interoperable, and reusable (FAIR). We encourage early deposition of datasets in the GWAS Catalog as the recognized central repository. We recommend standard requirements for reporting elements and formats for SumStats and accompanying metadata as guidelines for community standards and a basis for submission to the GWAS Catalog. Finally, we provide recommendations to enable, promote, and incentivize broader data sharing, standards and FAIRness in order to advance genomic medicine.",,doi:https://doi.org/10.1016/j.xgen.2021.100004; doi:https://doi.org/10.1016/j.xgen.2021.100004; html:https://europepmc.org/articles/PMC9451133; pdf:https://europepmc.org/articles/PMC9451133?pdf=render
 38180742,https://doi.org/10.1097/qai.0000000000003326,Estimation of Improvements in Mortality in Spectrum Among Adults With HIV Receiving Antiretroviral Therapy in High-Income Countries.,"Trickey A, Glaubius R, Pantazis N, Zangerle R, Wittkop L, Vehreschild J, Grabar S, Cavassini M, Teira R, d'Arminio Monforte A, Casabona J, van Sighem A, Jarrin I, Ingle SM, Sterne JAC, Imai-Eaton JW, Johnson LF.",,Journal of acquired immune deficiency syndromes (1999),2024,2024-01-04,Y,,,,"<h4>Introduction</h4>Mortality rates for people living with HIV (PLHIV) on antiretroviral therapy (ART) in high-income countries continue to decline. We compared mortality rates among PLHIV on ART in Europe for 2016-2020 with Spectrum's estimates.<h4>Methods</h4>The AIDS Impact Module in Spectrum is a compartmental HIV epidemic model coupled with a demographic population projection model. We used national Spectrum projections developed for the 2022 HIV estimates round to calculate mortality rates among PLHIV on ART, adjusting to the age/country distribution of PLHIV starting ART from 1996 to 2020 in the Antiretroviral Therapy Cohort Collaboration (ART-CC)'s European cohorts.<h4>Results</h4>In the ART-CC, 11,504 of 162,835 PLHIV died. Between 1996-1999 and 2016-2020, AIDS-related mortality in the ART-CC decreased from 8.8 (95% CI: 7.6 to 10.1) to 1.0 (0.9-1.2) and from 5.9 (4.4-8.1) to 1.1 (0.9-1.4) deaths per 1000 person-years among men and women, respectively. Non-AIDS-related mortality decreased from 9.1 (7.9-10.5) to 6.1 (5.8-6.5) and from 7.0 (5.2-9.3) to 4.8 (4.3-5.2) deaths per 1000 person-years among men and women, respectively. Adjusted all-cause mortality rates in Spectrum among men were near ART-CC estimates for 2016-2020 (Spectrum: 7.02-7.47 deaths per 1000 person-years) but approximately 20% lower in women (Spectrum: 4.66-4.70). Adjusted excess mortality rates in Spectrum were 2.5-fold higher in women and 3.1-3.4-fold higher in men in comparison to the ART-CC's AIDS-specific mortality rates.<h4>Discussion</h4>Spectrum's all-cause mortality estimates among PLHIV are consistent with age/country-controlled mortality observed in ART-CC, with some underestimation of mortality among women. Comparing results suggest that 60%-70% of excess deaths among PLHIV on ART in Spectrum are from non-AIDS causes.",,html:https://journals.lww.com/jaids/fulltext/2024/01011/estimation_of_improvements_in_mortality_in.10.aspx; doi:https://doi.org/10.1097/QAI.0000000000003326; html:https://europepmc.org/articles/PMC10769170; pdf:https://europepmc.org/articles/PMC10769170?pdf=render
-38190103,https://doi.org/10.1016/j.xgen.2023.100469,Genome-wide classification of epigenetic activity reveals regions of enriched heritability in immune-related traits.,"Stricker M, Zhang W, Cheng WY, Gazal S, Dendrou C, Nahkuri S, Palamara PF.",,Cell genomics,2024,2023-12-28,Y,Immune system; Heritability; Epigenetics; Machine Learning,,,"Epigenetics underpins the regulation of genes known to play a key role in the adaptive and innate immune system (AIIS). We developed a method, EpiNN, that leverages epigenetic data to detect AIIS-relevant genomic regions and used it to detect 2,765 putative AIIS loci. Experimental validation of one of these loci, DNMT1, provided evidence for a novel AIIS-specific transcription start site. We built a genome-wide AIIS annotation and used linkage disequilibrium (LD) score regression to test whether it predicts regional heritability using association statistics for 176 traits. We detected significant heritability effects (average |τ<sup>∗</sup>|=1.65) for 20 out of 26 immune-relevant traits. In a meta-analysis, immune-relevant traits and diseases were 4.45× more enriched for heritability than other traits. The EpiNN annotation was also depleted of trans-ancestry genetic correlation, indicating ancestry-specific effects. These results underscore the effectiveness of leveraging supervised learning algorithms and epigenetic data to detect loci implicated in specific classes of traits and diseases.",,doi:https://doi.org/10.1016/j.xgen.2023.100469; html:https://europepmc.org/articles/PMC10794845; pdf:https://europepmc.org/articles/PMC10794845?pdf=render
 33837377,https://doi.org/10.1038/s41591-021-01310-z,Actionable druggable genome-wide Mendelian randomization identifies repurposing opportunities for COVID-19.,"Gaziano L, Giambartolomei C, Pereira AC, Gaulton A, Posner DC, Swanson SA, Ho YL, Iyengar SK, Kosik NM, Vujkovic M, Gagnon DR, Bento AP, Barrio-Hernandez I, Rönnblom L, Hagberg N, Lundtoft C, Langenberg C, Pietzner M, Valentine D, Gustincich S, Tartaglia GG, Allara E, Surendran P, Burgess S, Zhao JH, Peters JE, Prins BP, Angelantonio ED, Devineni P, Shi Y, Lynch KE, DuVall SL, Garcon H, Thomann LO, Zhou JJ, Gorman BR, Huffman JE, O'Donnell CJ, Tsao PS, Beckham JC, Pyarajan S, Muralidhar S, Huang GD, Ramoni R, Beltrao P, Danesh J, Hung AM, Chang KM, Sun YV, Joseph J, Leach AR, Edwards TL, Cho K, Gaziano JM, Butterworth AS, Casas JP, VA Million Veteran Program COVID-19 Science Initiative.",,Nature medicine,2021,2021-04-09,Y,,,,"Drug repurposing provides a rapid approach to meet the urgent need for therapeutics to address COVID-19. To identify therapeutic targets relevant to COVID-19, we conducted Mendelian randomization analyses, deriving genetic instruments based on transcriptomic and proteomic data for 1,263 actionable proteins that are targeted by approved drugs or in clinical phase of drug development. Using summary statistics from the Host Genetics Initiative and the Million Veteran Program, we studied 7,554 patients hospitalized with COVID-19 and >1 million controls. We found significant Mendelian randomization results for three proteins (ACE2, P = 1.6 × 10<sup>-6</sup>; IFNAR2, P = 9.8 × 10<sup>-11</sup> and IL-10RB, P = 2.3 × 10<sup>-14</sup>) using cis-expression quantitative trait loci genetic instruments that also had strong evidence for colocalization with COVID-19 hospitalization. To disentangle the shared expression quantitative trait loci signal for IL10RB and IFNAR2, we conducted phenome-wide association scans and pathway enrichment analysis, which suggested that IFNAR2 is more likely to play a role in COVID-19 hospitalization. Our findings prioritize trials of drugs targeting IFNAR2 and ACE2 for early management of COVID-19.",,pdf:https://www.nature.com/articles/s41591-021-01310-z.pdf; doi:https://doi.org/10.1038/s41591-021-01310-z; html:https://europepmc.org/articles/PMC7612986; pdf:https://europepmc.org/articles/PMC7612986?pdf=render
 32810544,https://doi.org/10.1016/j.ijcard.2020.08.030,The relation between VLDL-cholesterol and risk of cardiovascular events in patients with manifest cardiovascular disease.,"Heidemann BE, Koopal C, Bots ML, Asselbergs FW, Westerink J, Visseren FLJ.",,International journal of cardiology,2021,2020-08-15,N,Inflammation; Vascular disease; Major Adverse Cardiovascular Events; Non-hdl-c; Vldl-c; Triglyceride Rich Lipoproteins,,,"<h4>Introduction</h4>Apolipoprotein B containing lipoproteins are atherogenic. There is evidence that with low plasma low density lipoprotein cholesterol (LDL-C) levels residual vascular risk might be caused by triglyceride rich lipoproteins such as very-low density lipoproteins (VLDL), chylomicrons and their remnants. We investigated the relationship between VLDL-cholesterol (VLDL-C) and recurrent major adverse cardiovascular events (MACE), major adverse limb events (MALE) and all-cause mortality in a cohort of patients with cardiovascular disease.<h4>Methods</h4>Prospective cohort study in 8057 patients with cardiovascular disease from the UCC-SMART study. The relation between calculated VLDL-C levels and the occurrence of MACE, MALE and all-cause mortality was analyzed with Cox regression models.<h4>Results</h4>Patients mean age was 60 ± 10 years, 74% were male, 4894 (61%) had coronary artery disease, 2445 (30%) stroke, 1425 (18%) peripheral arterial disease and 684 (8%) patients had an abdominal aorta aneurysm at baseline. A total of 1535 MACE, 571 MALE and 1792 deaths were observed during a median follow up of 8.2 years (interquartile range 4.512.2). VLDL-C was not associated with risk of MACE or all-cause mortality. In the highest quartile of VLDL-C the risk was higher for major adverse limb events (MALE) (HR 1.49; 95%CI 1.16-1.93) compared to the lowest quartile, after adjustment for confounders including LDL-C and lipid lowering medication.<h4>Conclusion</h4>In patients with clinically manifest cardiovascular disease plasma VLDL-C confers an increased risk for MALE, but not for MACE and all-cause mortality, independent of established risk factors including LDL-C and lipid-lowering medication.",,pdf:http://www.internationaljournalofcardiology.com/article/S0167527320335579/pdf; doi:https://doi.org/10.1016/j.ijcard.2020.08.030
+38190103,https://doi.org/10.1016/j.xgen.2023.100469,Genome-wide classification of epigenetic activity reveals regions of enriched heritability in immune-related traits.,"Stricker M, Zhang W, Cheng WY, Gazal S, Dendrou C, Nahkuri S, Palamara PF.",,Cell genomics,2024,2023-12-28,Y,Immune system; Heritability; Epigenetics; Machine Learning,,,"Epigenetics underpins the regulation of genes known to play a key role in the adaptive and innate immune system (AIIS). We developed a method, EpiNN, that leverages epigenetic data to detect AIIS-relevant genomic regions and used it to detect 2,765 putative AIIS loci. Experimental validation of one of these loci, DNMT1, provided evidence for a novel AIIS-specific transcription start site. We built a genome-wide AIIS annotation and used linkage disequilibrium (LD) score regression to test whether it predicts regional heritability using association statistics for 176 traits. We detected significant heritability effects (average |τ<sup>∗</sup>|=1.65) for 20 out of 26 immune-relevant traits. In a meta-analysis, immune-relevant traits and diseases were 4.45× more enriched for heritability than other traits. The EpiNN annotation was also depleted of trans-ancestry genetic correlation, indicating ancestry-specific effects. These results underscore the effectiveness of leveraging supervised learning algorithms and epigenetic data to detect loci implicated in specific classes of traits and diseases.",,doi:https://doi.org/10.1016/j.xgen.2023.100469; html:https://europepmc.org/articles/PMC10794845; pdf:https://europepmc.org/articles/PMC10794845?pdf=render
 33072403,https://doi.org/10.1186/s40959-020-00079-3,Early- and late anthracycline-induced cardiac dysfunction: echocardiographic characterization and response to heart failure therapy.,"Kamphuis JAM, Linschoten M, Cramer MJ, Doevendans PA, Asselbergs FW, Teske AJ.",,"Cardio-oncology (London, England)",2020,2020-10-13,Y,Heart Failure; Anthracyclines; Cardiac Dysfunction; Cardiac Effects Of Cancer Treatment,,,"<h4>Background</h4>Anthracycline-induced cardiac dysfunction (ACD) is a notorious side effect of anticancer treatment. It has been described as a phenomenon of a continuous progressive decline of cardiac function, eventually leading to dilated cardiomyopathy (DCM). This progressive nature suggests that patients with a delayed ACD diagnosis have greater compromise of cardiac function and more adverse remodeling, with a poor response to heart failure (HF) treatment. This study aimed to delineate the impact of a delayed ACD diagnosis on echocardiographic characteristics and response to HF treatment.<h4>Methods and results</h4>From the population of our cardio-oncology outpatient clinic, 92 ACD patients were included in this study (age 51.6 ± 16.2 years, median cumulative anthracycline dose 329 [200-329] mg/m<sup>2</sup>), and a median follow-up of 25.0 [9.6-37.2] months after ACD diagnosis. Median time to ACD diagnosis for patients diagnosed early (< 1 year) and late (> 1 year) was 4.0 vs. 47.7 months respectively. There were no echocardiographic differences between patients diagnosed early vs. late (LVEF 43.6 ± 4.9% vs. 43.0 ± 6.2% and iEDV 63.6 vs. 62.9 mL/m<sup>2</sup>). Eighty-three percent of patients presented with mild LV dysfunction and in 79% the LV was not dilated. Patients diagnosed early were more likely to have (partial) recovery of cardiac function upon HF treatment initiation (<i>p</i> = 0.015).<h4>Conclusions</h4>In the setting of a cardio-oncology outpatient clinic, patients with ACD presented with a hypokinetic non-dilated cardiomyopathy, rather than typical DCM. Timing of ACD diagnosis did not impact HF disease severity. However, in patients receiving an early diagnosis, cardiac function was more likely to recover upon HF treatment.",,pdf:https://cardiooncologyjournal.biomedcentral.com/track/pdf/10.1186/s40959-020-00079-3; doi:https://doi.org/10.1186/s40959-020-00079-3; html:https://europepmc.org/articles/PMC7557080; pdf:https://europepmc.org/articles/PMC7557080?pdf=render
-38663408,https://doi.org/10.1016/j.xgen.2024.100541,Characterization of the genetic determinants of context-specific DNA methylation in primary monocytes.,"Gilchrist JJ, Fang H, Danielli S, Tomkova M, Nassiri I, Ng E, Tong O, Taylor C, Muldoon D, Cohen LRZ, Al-Mossawi H, Lau E, Neville M, Schuster-Boeckler B, Knight JC, Fairfax BP.",,Cell genomics,2024,2024-04-24,Y,Genetics; Monocytes; Cancer; LPS; DNA methylation; Innate Immune Activation; Mqtl; Epigenetic Aging,,,"To better understand inter-individual variation in sensitivity of DNA methylation (DNAm) to immune activity, we characterized effects of inflammatory stimuli on primary monocyte DNAm (n = 190). We find that monocyte DNAm is site-dependently sensitive to lipopolysaccharide (LPS), with LPS-induced demethylation occurring following hydroxymethylation. We identify 7,359 high-confidence immune-modulated CpGs (imCpGs) that differ in genomic localization and transcription factor usage according to whether they represent a gain or loss in DNAm. Demethylated imCpGs are profoundly enriched for enhancers and colocalize to genes enriched for disease associations, especially cancer. DNAm is age associated, and we find that 24-h LPS exposure triggers approximately 6 months of gain in epigenetic age, directly linking epigenetic aging with innate immune activity. By integrating LPS-induced changes in DNAm with genetic variation, we identify 234 imCpGs under local genetic control. Exploring shared causal loci between LPS-induced DNAm responses and human disease traits highlights examples of disease-associated loci that modulate imCpG formation.",,pdf:https://ora.ox.ac.uk/objects/uuid:d3672019-795b-477f-a48c-8bcd9d51ecfb/files/sjw827d50r; doi:https://doi.org/10.1016/j.xgen.2024.100541; html:https://europepmc.org/articles/PMC11099345; pdf:https://europepmc.org/articles/PMC11099345?pdf=render
 32247548,https://doi.org/10.1016/j.tips.2020.03.003,Electronic Health Records to Predict Gestational Diabetes Risk.,"Mateen BA, David AL, Denaxas S.",,Trends in pharmacological sciences,2020,2020-04-01,N,Artificial intelligence; Gestational Diabetes Mellitus; Machine Learning; Risk Prediction; Electronic Health Records,,,"Gestational diabetes mellitus is a common pregnancy complication associated with significant adverse health outcomes for both women and infants. Effective screening and early prediction tools as part of routine clinical care are needed to reduce the impact of the disease on the baby and mother. Using large-scale electronic health records, Artzi and colleagues developed and evaluated a machine learning driven tool to identify women at high and low risk of GDM. Their findings showcase how artificial intelligence approaches can potentially be embedded in clinical care to enable accurate and rapid risk stratification.",,pdf:https://discovery.ucl.ac.uk/10097090/3/Denaxas_Electronic%20Health%20Records%20to%20Predict%20Gestational%20Diabetes%20Risk_AAM.pdf; doi:https://doi.org/10.1016/j.tips.2020.03.003
+38663408,https://doi.org/10.1016/j.xgen.2024.100541,Characterization of the genetic determinants of context-specific DNA methylation in primary monocytes.,"Gilchrist JJ, Fang H, Danielli S, Tomkova M, Nassiri I, Ng E, Tong O, Taylor C, Muldoon D, Cohen LRZ, Al-Mossawi H, Lau E, Neville M, Schuster-Boeckler B, Knight JC, Fairfax BP.",,Cell genomics,2024,2024-04-24,Y,Genetics; Monocytes; Cancer; LPS; DNA methylation; Innate Immune Activation; Mqtl; Epigenetic Aging,,,"To better understand inter-individual variation in sensitivity of DNA methylation (DNAm) to immune activity, we characterized effects of inflammatory stimuli on primary monocyte DNAm (n = 190). We find that monocyte DNAm is site-dependently sensitive to lipopolysaccharide (LPS), with LPS-induced demethylation occurring following hydroxymethylation. We identify 7,359 high-confidence immune-modulated CpGs (imCpGs) that differ in genomic localization and transcription factor usage according to whether they represent a gain or loss in DNAm. Demethylated imCpGs are profoundly enriched for enhancers and colocalize to genes enriched for disease associations, especially cancer. DNAm is age associated, and we find that 24-h LPS exposure triggers approximately 6 months of gain in epigenetic age, directly linking epigenetic aging with innate immune activity. By integrating LPS-induced changes in DNAm with genetic variation, we identify 234 imCpGs under local genetic control. Exploring shared causal loci between LPS-induced DNAm responses and human disease traits highlights examples of disease-associated loci that modulate imCpG formation.",,pdf:https://ora.ox.ac.uk/objects/uuid:d3672019-795b-477f-a48c-8bcd9d51ecfb/files/sjw827d50r; doi:https://doi.org/10.1016/j.xgen.2024.100541; html:https://europepmc.org/articles/PMC11099345; pdf:https://europepmc.org/articles/PMC11099345?pdf=render
 37984978,https://doi.org/10.1136/bmj-2023-076754,ROB-ME: a tool for assessing risk of bias due to missing evidence in systematic reviews with meta-analysis.,"Page MJ, Sterne JAC, Boutron I, Hróbjartsson A, Kirkham JJ, Li T, Lundh A, Mayo-Wilson E, McKenzie JE, Stewart LA, Sutton AJ, Bero L, Dunn AG, Dwan K, Elbers RG, Kanukula R, Meerpohl JJ, Turner EH, Higgins JPT.",,BMJ (Clinical research ed.),2023,2023-11-20,N,,,,,,doi:https://doi.org/10.1136/bmj-2023-076754
 31965568,https://doi.org/10.1002/bjs.11433,Impact of bariatric surgery on cardiovascular outcomes and mortality: a population-based cohort study.,"Singh P, Subramanian A, Adderley N, Gokhale K, Singhal R, Bellary S, Nirantharakumar K, Tahrani AA.",,The British journal of surgery,2020,2020-01-21,N,,,,"<h4>Background</h4>Cohort studies have shown that bariatric surgery may reduce the incidence of and mortality from cardiovascular disease (CVD), but studies using real-world data are limited. This study examined the impact of bariatric surgery on incident CVD, hypertension and atrial fibrillation, and all-cause mortality.<h4>Methods</h4>A retrospective, matched, controlled cohort study of The Health Improvement Network primary care database (from 1 January 1990 to 31 January 2018) was performed (approximately 6 per cent of the UK population). Adults with a BMI of 30 kg/m<sup>2</sup> or above who did not have gastric cancer were included as the exposed group. Each exposed patient, who had undergone bariatric surgery, was matched for age, sex, BMI and presence of type 2 diabetes mellitus (T2DM) with two controls who had not had bariatric surgery.<h4>Results</h4>A total of 5170 exposed and 9995 control participants were included; their mean(s.d.) age was 45·3(10·5) years and 21·5 per cent (3265 of 15 165 participants) had T2DM. Median follow-up was 3·9 (i.q.r. 1·8- 6·4) years. Mean(s.d.) percentage weight loss was 20·0(13·2) and 0·8(9·5) per cent in exposed and control groups respectively. Overall, bariatric surgery was not associated with a significantly lower CVD risk (adjusted hazard ratio (HR) 0·80; 95 per cent c.i. 0·62 to 1·02; P = 0·074). Only in the gastric bypass group was a significant impact on CVD observed (HR 0·53, 0·34 to 0·81; P = 0·003). Bariatric surgery was associated with significant reduction in all-cause mortality (adjusted HR 0·70, 0·55 to 0·89; P = 0·004), hypertension (adjusted HR 0·41, 0·34 to 0·50; P < 0·001) and heart failure (adjusted HR 0·57, 0·34 to 0·96; P = 0·033). Outcomes were similar in patients with and those without T2DM (exposed versus controls), except for incident atrial fibrillation, which was reduced in the T2DM group.<h4>Conclusion</h4>Bariatric surgery is associated with a reduced risk of hypertension, heart failure and mortality, compared with routine care. Gastric bypass was associated with reduced risk of CVD compared to routine care.",,pdf:https://academic.oup.com/bjs/article-pdf/107/4/432/36117941/bjs11433.pdf; doi:https://doi.org/10.1002/bjs.11433
 37994361,https://doi.org/10.12688/gatesopenres.13654.1,"Higher mortality associated with the SARS-CoV-2 Delta variant in the Western Cape, South Africa, using RdRp target delay as a proxy: a cross-sectional study.","Hussey H, Davies MA, Heekes A, Williamson C, Valley-Omar Z, Hardie D, Korsman S, Doolabh D, Preiser W, Maponga T, Iranzadeh A, Engelbrecht S, Wasserman S, Schrueder N, Boloko L, Symons G, Raubenheimer P, Viljoen A, Parker A, Cohen C, Jasat W, Lessells R, Wilkinson RJ, Boulle A, Hsiao M.",,Gates open research,2022,2022-08-31,Y,DELTA; South Africa; Clinical Severity; Sars-cov-2; B.1.617.2; Rdrp Target Delay,,,"<b>Background:</b> The SARS-CoV-2 Delta variant (B.1.617.2) has been associated with more severe disease, particularly when compared to the Alpha variant. Most of this data, however, is from high income countries and less is understood about the variant's disease severity in other settings, particularly in an African context, and when compared to the Beta variant. <b>Methods:</b> A novel proxy marker, RNA-dependent RNA polymerase (RdRp) target delay in the Seegene Allplex <sup>TM</sup> 2019-nCoV (polymerase chain reaction) PCR assay, was used to identify suspected Delta variant infection in routine laboratory data. All cases diagnosed on this assay in the public sector in the Western Cape, South Africa, from 1 April to 31 July 2021, were included in the dataset provided by the Western Cape Provincial Health Data Centre (PHDC). The PHDC collates information on all COVID-19 related laboratory tests, hospital admissions and deaths for the province. Odds ratios for the association between the proxy marker and death were calculated, adjusted for prior diagnosed infection and vaccination status. <b>Results:</b> A total of 11,355 cases with 700 deaths were included in this study. RdRp target delay (suspected Delta variant) was associated with higher mortality (adjusted odds ratio [aOR] 1.45; 95% confidence interval [CI]: 1.13-1.86), compared to presumptive Beta infection. Prior diagnosed infection during the previous COVID-19 wave, which was driven by the Beta variant, was protective (aOR 0.32; 95%CI: 0.11-0.92) as was vaccination (aOR [95%CI] 0.15 [0.03-0.62] for complete vaccination [≥28 days post a single dose of Ad26.COV2.S or ≥14 days post second BNT162b2 dose]). <b>Conclusion:</b> RdRp target delay, a proxy for infection with the Delta variant, is associated with an increased risk of mortality amongst those who were tested for COVID-19 in our setting.",,doi:https://doi.org/10.12688/gatesopenres.13654.1; html:https://europepmc.org/articles/PMC10663174; pdf:https://europepmc.org/articles/PMC10663174?pdf=render
-32200692,https://doi.org/10.1080/09602011.2020.1744453,Factors facilitating recovery following severe traumatic brain injury: A qualitative study.,"Downing M, Hicks A, Braaf S, Myles D, Gabbe B, Cameron P, Ameratunga S, Ponsford J.",,Neuropsychological rehabilitation,2021,2020-03-23,N,Recovery; Traumatic brain injury; Qualitative; Outcome; Positive Factors,,,"Given the significant impact of severe traumatic brain injury (TBI), understanding factors influencing recovery is critical to inform prognostication and treatment planning. Previous research has focussed primarily on factors negatively associated with outcome, with less focus on factors facilitating the recovery process. The current qualitative study examined positive factors identified for recovery by individuals who had sustained severe TBI three years earlier. Semi-structured interviews were conducted with nine participants with TBI and 16 close-others. Participants were asked to identify factors about themselves (or the injured individual), those around them, and the care they received that they felt were positive for recovery. Using reflexive thematic analysis, three themes were identified as positive for recovery after a TBI. <i>Having a support network</i> included social supports such as family and friends, and receiving other funded/non-funded assistance towards improving independence and participation. <i>Being positive and engaged</i> included being able to participate, being positive, using compensatory strategies, and becoming fit, healthy and happy. <i>Getting good care</i> included patients perceiving they had a comprehensive and good quality hospital experience, and access to multidisciplinary outpatient services. A focus on enhancing these positive environmental, personal and service factors in service provision may enhance outcomes following severe TBI.",,doi:https://doi.org/10.1080/09602011.2020.1744453
 32238333,https://doi.org/10.2196/16400,Low-Density Lipoprotein Cholesterol Target Attainment in Patients With Established Cardiovascular Disease: Analysis of Routine Care Data.,"Groenhof TKJ, Kofink D, Bots ML, Nathoe HM, Hoefer IE, Van Solinge WW, Lely AT, Asselbergs FW, Haitjema S.",,JMIR medical informatics,2020,2020-04-02,Y,LDL-C; Cardiovascular Risk Management; Learning Health Care System; Routine Clinical Data,Better Care,cardiovascular,"<h4>Background</h4>Direct feedback on quality of care is one of the key features of a learning health care system (LHS), enabling health care professionals to improve upon the routine clinical care of their patients during practice.<h4>Objective</h4>This study aimed to evaluate the potential of routine care data extracted from electronic health records (EHRs) in order to obtain reliable information on low-density lipoprotein cholesterol (LDL-c) management in cardiovascular disease (CVD) patients referred to a tertiary care center.<h4>Methods</h4>We extracted all LDL-c measurements from the EHRs of patients with a history of CVD referred to the University Medical Center Utrecht. We assessed LDL-c target attainment at the time of referral and per year. In patients with multiple measurements, we analyzed LDL-c trajectories, truncated at 6 follow-up measurements. Lastly, we performed a logistic regression analysis to investigate factors associated with improvement of LDL-c at the next measurement.<h4>Results</h4>Between February 2003 and December 2017, 250,749 LDL-c measurements were taken from 95,795 patients, of whom 23,932 had a history of CVD. At the time of referral, 51% of patients had not reached their LDL-c target. A large proportion of patients (55%) had no follow-up LDL-c measurements. Most of the patients with repeated measurements showed no change in LDL-c levels over time: the transition probability to remain in the same category was up to 0.84. Sequence clustering analysis showed more women (odds ratio 1.18, 95% CI 1.07-1.10) in the cluster with both most measurements off target and the most LDL-c measurements furthest from the target. Timing of drug prescription was difficult to determine from our data, limiting the interpretation of results regarding medication management.<h4>Conclusions</h4>Routine care data can be used to provide feedback on quality of care, such as LDL-c target attainment. These routine care data show high off-target prevalence and little change in LDL-c over time. Registrations of diagnosis; follow-up trajectory, including primary and secondary care; and medication use need to be improved in order to enhance usability of the EHR system for adequate feedback.",,pdf:https://medinform.jmir.org/2020/4/e16400/PDF; doi:https://doi.org/10.2196/16400; html:https://europepmc.org/articles/PMC7163416
+32200692,https://doi.org/10.1080/09602011.2020.1744453,Factors facilitating recovery following severe traumatic brain injury: A qualitative study.,"Downing M, Hicks A, Braaf S, Myles D, Gabbe B, Cameron P, Ameratunga S, Ponsford J.",,Neuropsychological rehabilitation,2021,2020-03-23,N,Recovery; Traumatic brain injury; Qualitative; Outcome; Positive Factors,,,"Given the significant impact of severe traumatic brain injury (TBI), understanding factors influencing recovery is critical to inform prognostication and treatment planning. Previous research has focussed primarily on factors negatively associated with outcome, with less focus on factors facilitating the recovery process. The current qualitative study examined positive factors identified for recovery by individuals who had sustained severe TBI three years earlier. Semi-structured interviews were conducted with nine participants with TBI and 16 close-others. Participants were asked to identify factors about themselves (or the injured individual), those around them, and the care they received that they felt were positive for recovery. Using reflexive thematic analysis, three themes were identified as positive for recovery after a TBI. <i>Having a support network</i> included social supports such as family and friends, and receiving other funded/non-funded assistance towards improving independence and participation. <i>Being positive and engaged</i> included being able to participate, being positive, using compensatory strategies, and becoming fit, healthy and happy. <i>Getting good care</i> included patients perceiving they had a comprehensive and good quality hospital experience, and access to multidisciplinary outpatient services. A focus on enhancing these positive environmental, personal and service factors in service provision may enhance outcomes following severe TBI.",,doi:https://doi.org/10.1080/09602011.2020.1744453
 33591566,https://doi.org/10.1007/s43441-021-00263-2,Advancing UK Regulatory Science Strategy in the Context of Global Regulation: a Stakeholder Survey.,"Cruz Rivera S, Torlinska B, Marston E, Denniston AK, Oliver K, Hoare S, Calvert MJ.",,Therapeutic innovation & regulatory science,2021,2021-02-16,Y,Regulatory Science; Health Products; Medicines And Devices,,,"<h4>Background</h4>The UK's transition from the European Union creates both an urgent need and key opportunity for the UK and its global collaborators to consider new approaches to the regulation of emerging technologies, underpinned by regulatory science. This survey aimed to identify the most accurate definition of regulatory science, to define strategic areas of the regulation of healthcare innovation which can be informed through regulatory science and to explore the training and infrastructure needed to advance UK and international regulatory science.<h4>Methods</h4>A survey was distributed to UK healthcare professionals, academics, patients, health technology assessment agencies, ethicists and trade associations, as well as international regulators, pharmaceutical companies and small or medium enterprises which have expertise in regulatory science and in developing or applying regulation in healthcare. Subsequently, a descriptive quantitative analyses of survey results and directed thematic analysis of free-text comments were applied.<h4>Results</h4>Priority areas for UK regulatory science identified by 145 participants included the following: flexibility: the capability of regulations to adapt to novel products and target patient outcomes; co-development: collaboration across sectors, e.g. patients, manufacturers, regulators, and educators working together to develop appropriate training for novel product deployment; responsiveness: the preparation of frameworks which enable timely innovation required by emerging events; speed: the rate at which new products can reach the market; reimbursement: developing effective tools to track and evaluate outcomes for ""pay for performance"" products; and education and professional development.<h4>Conclusions</h4>The UK has a time-critical opportunity to establish its national and international strategy for regulatory science leadership by harnessing broader academic input, developing strategic cross-sector collaborations, incorporating patients' experiences and perspectives, and investing in a skilled workforce.",,pdf:https://link.springer.com/content/pdf/10.1007/s43441-021-00263-2.pdf; doi:https://doi.org/10.1007/s43441-021-00263-2; html:https://europepmc.org/articles/PMC7885762; pdf:https://europepmc.org/articles/PMC7885762?pdf=render
 32639589,https://doi.org/10.1111/bcp.14458,Measuring and reporting treatment adherence: What can we learn by comparing two respiratory conditions?,"Tibble H, Flook M, Sheikh A, Tsanas A, Horne R, Vrijens B, De Geest S, Stagg HR.",,British journal of clinical pharmacology,2021,2020-07-27,N,Tuberculosis; Adherence; Persistence; Asthma; Compliance,,,"Medication non-adherence, defined as any deviation from the regimen recommended by their healthcare provider, can increase morbidity, mortality and side effects, while reducing effectiveness. Through studying two respiratory conditions, asthma and tuberculosis (TB), we thoroughly review the current understanding of the measurement and reporting of medication adherence. In this paper, we identify major methodological issues in the standard ways that adherence has been conceptualised, defined and studied in asthma and TB. Between and within the two diseases there are substantial variations in adherence reporting, linked to differences in dosing intervals and treatment duration. Critically, the communicable nature of TB has resulted in dose-by-dose monitoring becoming a recommended treatment standard. Through the lens of these similarities and contrasts, we highlight contemporary shortcomings in the generalised conceptualisation of medication adherence. Furthermore, we outline elements in which knowledge could be directly transferred from one condition to the other, such as the application of large-scale cost-effective monitoring methods in TB to resource-poor settings in asthma. To develop a more robust evidence-based approach, we recommend the use of standard taxonomies detailed in the ABC taxonomy when measuring and discussing adherence. Regimen and intervention development and use should be based on sufficient evidence of the commonality and type of adherence behaviours displayed by patients with the relevant condition. A systematic approach to the measurement and reporting of adherence could improve the value and generalisability of research across all health conditions.",,pdf:https://bpspubs.onlinelibrary.wiley.com/doi/pdfdirect/10.1111/bcp.14458; doi:https://doi.org/10.1111/bcp.14458
 32907797,https://doi.org/10.1136/bmj.m3210,Guidelines for clinical trial protocols for interventions involving artificial intelligence: the SPIRIT-AI Extension.,"Rivera SC, Liu X, Chan AW, Denniston AK, Calvert MJ, SPIRIT-AI and CONSORT-AI Working Group.",,BMJ (Clinical research ed.),2020,2020-09-09,Y,,,,"The SPIRIT 2013 (The Standard Protocol Items: Recommendations for Interventional Trials) statement aims to improve the completeness of clinical trial protocol reporting, by providing evidence-based recommendations for the minimum set of items to be addressed. This guidance has been instrumental in promoting transparent evaluation of new interventions. More recently, there is a growing recognition that interventions involving artificial intelligence need to undergo rigorous, prospective evaluation to demonstrate their impact on health outcomes.The SPIRIT-AI extension is a new reporting guideline for clinical trials protocols evaluating interventions with an AI component. It was developed in parallel with its companion statement for trial reports: CONSORT-AI. Both guidelines were developed using a staged consensus process, involving a literature review and expert consultation to generate 26 candidate items, which were consulted on by an international multi-stakeholder group in a 2-stage Delphi survey (103 stakeholders), agreed on in a consensus meeting (31 stakeholders) and refined through a checklist pilot (34 participants).The SPIRIT-AI extension includes 15 new items, which were considered sufficiently important for clinical trial protocols of AI interventions. These new items should be routinely reported in addition to the core SPIRIT 2013 items. SPIRIT-AI recommends that investigators provide clear descriptions of the AI intervention, including instructions and skills required for use, the setting in which the AI intervention will be integrated, considerations around the handling of input and output data, the human-AI interaction and analysis of error cases.SPIRIT-AI will help promote transparency and completeness for clinical trial protocols for AI interventions. Its use will assist editors and peer-reviewers, as well as the general readership, to understand, interpret and critically appraise the design and risk of bias for a planned clinical trial.",,pdf:https://www.bmj.com/content/bmj/370/bmj.m3210.full.pdf; doi:https://doi.org/10.1136/bmj.m3210; html:https://europepmc.org/articles/PMC7490785
@@ -1845,32 +1847,32 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 37647652,https://doi.org/10.1182/blood.2023021100,A signature of platelet reactivity in CBC scattergrams reveals genetic predictors of thrombotic disease risk.,"Verdier H, Thomas P, Batista J, Kempster C, McKinney H, Gleadall N, Danesh J, Mumford A, Heemskerk JWM, Ouwehand WH, Downes K, Astle WJ, Turro E.",,Blood,2023,2023-11-01,Y,,,,"Genetic studies of platelet reactivity (PR) phenotypes may identify novel antiplatelet drug targets. However, such studies have been limited by small sample sizes (n < 5000) because of the complexity of measuring PR. We trained a model to predict PR from complete blood count (CBC) scattergrams. A genome-wide association study of this phenotype in 29 806 blood donors identified 21 distinct associations implicating 20 genes, of which 6 have been identified previously. The effect size estimates were significantly correlated with estimates from a study of flow cytometry-measured PR and a study of a phenotype of in vitro thrombus formation. A genetic score of PR built from the 21 variants was associated with the incidence rates of myocardial infarction and pulmonary embolism. Mendelian randomization analyses showed that PR was causally associated with the risks of coronary artery disease, stroke, and venous thromboembolism. Our approach provides a blueprint for using phenotype imputation to study the determinants of hard-to-measure but biologically important hematological traits.",,pdf:https://ashpublications.org/blood/article-pdf/doi/10.1182/blood.2023021100/2076169/blood.2023021100.pdf; doi:https://doi.org/10.1182/blood.2023021100; html:https://europepmc.org/articles/PMC10733829
 36732776,https://doi.org/10.1186/s13040-023-00321-5,LoFTK: a framework for fully automated calculation of predicted Loss-of-Function variants and genes.,"Alasiri A, Karczewski KJ, Cole B, Loza BL, Moore JH, van der Laan SW, Asselbergs FW, Keating BJ, van Setten J.",,BioData mining,2023,2023-02-02,Y,Human Genetic; Loss-of-function Variants; Compound Heterozygotes; Knockout Genes,,,"<h4>Background</h4>Loss-of-Function (LoF) variants in human genes are important due to their impact on clinical phenotypes and frequent occurrence in the genomes of healthy individuals. The association of LoF variants with complex diseases and traits may lead to the discovery and validation of novel therapeutic targets. Current approaches predict high-confidence LoF variants without identifying the specific genes or the number of copies they affect. Moreover, there is a lack of methods for detecting knockout genes caused by compound heterozygous (CH) LoF variants.<h4>Results</h4>We have developed the Loss-of-Function ToolKit (LoFTK), which allows efficient and automated prediction of LoF variants from genotyped, imputed and sequenced genomes. LoFTK enables the identification of genes that are inactive in one or two copies and provides summary statistics for downstream analyses. LoFTK can identify CH LoF variants, which result in LoF genes with two copies lost. Using data from parents and offspring we show that 96% of CH LoF genes predicted by LoFTK in the offspring have the respective alleles donated by each parent.<h4>Conclusions</h4>LoFTK is a command-line based tool that provides a reliable computational workflow for predicting LoF variants from genotyped and sequenced genomes, identifying genes that are inactive in 1 or 2 copies. LoFTK is an open software and is freely available to non-commercial users at https://github.com/CirculatoryHealth/LoFTK .",,pdf:https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-023-00321-5; doi:https://doi.org/10.1186/s13040-023-00321-5; html:https://europepmc.org/articles/PMC9893534; pdf:https://europepmc.org/articles/PMC9893534?pdf=render
 38106559,https://doi.org/10.1016/j.eclinm.2023.102251,Long-term symptom profiles after COVID-19 <i>vs</i> other acute respiratory infections: an analysis of data from the COVIDENCE UK study.,"Vivaldi G, Pfeffer PE, Talaei M, Basera TJ, Shaheen SO, Martineau AR.",,EClinicalMedicine,2023,2023-10-06,Y,Acute respiratory infections; Sars-cov-2; Long Covid; Post-acute Sequelae,,,"<h4>Background</h4>Long COVID is a well recognised, if heterogeneous, entity. Acute respiratory infections (ARIs) due to other pathogens may cause long-term symptoms, but few studies compare post-acute sequelae between SARS-CoV-2 and other ARIs. We aimed to compare symptom profiles between people with previous SARS-CoV-2 infection, people with previous non-COVID-19 ARIs, and contemporaneous controls, and to identify clusters of long-term symptoms.<h4>Methods</h4>COVIDENCE UK is a prospective, population-based UK study of ARIs in adults. We analysed data for 16 potential long COVID symptoms and health-related quality of life (HRQoL), reported between January 21 and February 15, 2021, by participants unvaccinated against SARS-CoV-2. We classified participants as having previous SARS-CoV-2 infection or previous non-COVID-19 ARI (≥4 weeks prior) or no reported ARI. We compared symptoms by infection status using logistic and fractional regression, and identified symptom clusters using latent class analysis (LCA). This study is registered with ClinicalTrials.gov, NCT04330599.<h4>Findings</h4>We included 10,171 participants (1311 [12.9%] with SARS-CoV-2 infection, 472 [4.6%] with non-COVID-19 ARI). Both types of infection were associated with increased prevalence/severity of most symptoms and decreased HRQoL compared with no infection. Participants with SARS-CoV-2 infection had increased odds of problems with taste/smell (odds ratio 19.74, 95% CI 10.53-37.00) and lightheadedness or dizziness (1.74, 1.18-2.56) compared with participants with non-COVID-19 ARIs. Separate LCA models identified three symptom severity groups for each infection type. In the most severe groups (representing 22% of participants for both SARS-CoV-2 and non-COVID-19 ARI), SARS-CoV-2 infection presented with a higher probability of problems with taste/smell (probability 0.41 <i>vs</i> 0.04), hair loss (0.25 <i>vs</i> 0.16), unusual sweating (0.38 <i>vs</i> 0.25), unusual racing of the heart (0.43 <i>vs</i> 0.33), and memory problems (0.70 <i>vs</i> 0.55) than non-COVID-19 ARI.<h4>Interpretation</h4>Both SARS-CoV-2 and non-COVID-19 ARIs are associated with a wide range of symptoms more than 4 weeks after the acute infection. Research on post-acute sequelae of ARIs should extend from SARS-CoV-2 to include other pathogens.<h4>Funding</h4>Barts Charity.",,doi:https://doi.org/10.1016/j.eclinm.2023.102251; html:https://europepmc.org/articles/PMC10721552; pdf:https://europepmc.org/articles/PMC10721552?pdf=render
-38751312,https://doi.org/10.1093/aje/kwae039,Regression calibration of self-reported mobile phone use to optimize quantitative risk estimation in the COSMOS study.,"Reedijk M, Portengen L, Auvinen A, Kojo K, Heinävaara S, Feychting M, Tettamanti G, Hillert L, Elliott P, Toledano MB, Smith RB, Heller J, Schüz J, Deltour I, Poulsen AH, Johansen C, Verheij R, Peeters P, Rookus M, Traini E, Huss A, Kromhout H, Vermeulen R, COSMOS Study Group.",,American journal of epidemiology,2024,2024-10-01,Y,Cohort Analysis; Measurement error; Regression calibration; Health Outcomes; Exposure assessment; Mobile Phone Use,,,"The Cohort Study of Mobile Phone Use and Health (COSMOS) has repeatedly collected self-reported and operator-recorded data on mobile phone use. Assessing health effects using self-reported information is prone to measurement error, but operator data were available prospectively for only part of the study population and did not cover past mobile phone use. To optimize the available data and reduce bias, we evaluated different statistical approaches for constructing mobile phone exposure histories within COSMOS. We evaluated and compared the performance of 4 regression calibration (RC) methods (simple, direct, inverse, and generalized additive model for location, shape, and scale), complete-case analysis, and multiple imputation in a simulation study with a binary health outcome. We used self-reported and operator-recorded mobile phone call data collected at baseline (2007-2012) from participants in Denmark, Finland, the Netherlands, Sweden, and the United Kingdom. Parameter estimates obtained using simple, direct, and inverse RC methods were associated with less bias and lower mean squared error than those obtained with complete-case analysis or multiple imputation. We showed that RC methods resulted in more accurate estimation of the relationship between mobile phone use and health outcomes by combining self-reported data with objective operator-recorded data available for a subset of participants.",,pdf:https://academic.oup.com/aje/advance-article-pdf/doi/10.1093/aje/kwae039/57572723/kwae039.pdf; doi:https://doi.org/10.1093/aje/kwae039; html:https://europepmc.org/articles/PMC11458186; pdf:https://europepmc.org/articles/PMC11458186?pdf=render
 37671353,https://doi.org/10.23889/ijpds.v5i3.2133,Public Involvement & Engagement in health inequalities research on COVID-19 pandemic: a case study of CIDACS/FIOCRUZ BAHIA.,"Dos Anjos Fonseca A, Pimenta DM, de Almeida MRS, Lima RT, Barreto ML, Ichihara MYT.",,International journal of population data science,2020,2020-01-01,Y,Brazil; Pandemic; Policymakers; Social Inequalities; Public Engagement; Community Groups; Public Involvement,,,"<h4>Introduction</h4>Health inequalities in Brazil have deepened on Covid-19 pandemic, and the most vulnerable people were the more affected. A multidisciplinary team from Cidacs/Fiocruz Bahia developed a Social Disparities Index for Covid-19 (IDS-COVID-19) to support the evaluation of effects of health inequalities on the pandemic in Brazil. Public Involvement and Engagement were the pillars of this research because they allowed us to access first hand experiences about the social context in our country.<h4>Objectives</h4>This paper aims to describe our Public Involvement and Engagement experience by analysing our challenges, strategies, activities, results, and lessons learned during the construction of IDS-COVID-19.<h4>Methods</h4>The basis of the IDS-Covid-19 public engagement model was the participation of different social groups through methods and techniques that allow dialogue. Several activities and communication products supported the continuous interactions. Another guideline was the inclusion and the welcoming of participants from the beginning of the project to ensure that the participant's contributions could drive decision-making about the research.<h4>Results</h4>Participants made several contributions to the research as a new layer of information to the Index, and improvements were made to the interactive panel. They also compromised to support the dissemination and use of the product. Eight representatives of community groups and 29 policymakers participated in our engagement activities during the project. More than 500 people were in our open webinars. In addition, more than 140 news items about IDS-Covid-19 were published in national and international media.<h4>Conclusions</h4>We highlight as lessons learned the adaptation of some dissemination formats to the public, and the necessity of being flexible and accessible to participants. We strengthened the relationship with relevant stakeholders by exploring individual conversations by phone, WhatsApp, email, and interviews to produce a documentary that registered this whole experience. Cidacs/Fiocruz Bahia has also embedded public engagement and involvement in the study agenda.",,doi:https://doi.org/10.23889/ijpds.v5i3.2133; html:https://europepmc.org/articles/PMC10476697; pdf:https://europepmc.org/articles/PMC10476697?pdf=render
+38751312,https://doi.org/10.1093/aje/kwae039,Regression calibration of self-reported mobile phone use to optimize quantitative risk estimation in the COSMOS study.,"Reedijk M, Portengen L, Auvinen A, Kojo K, Heinävaara S, Feychting M, Tettamanti G, Hillert L, Elliott P, Toledano MB, Smith RB, Heller J, Schüz J, Deltour I, Poulsen AH, Johansen C, Verheij R, Peeters P, Rookus M, Traini E, Huss A, Kromhout H, Vermeulen R, COSMOS Study Group.",,American journal of epidemiology,2024,2024-10-01,Y,Cohort Analysis; Measurement error; Regression calibration; Health Outcomes; Exposure assessment; Mobile Phone Use,,,"The Cohort Study of Mobile Phone Use and Health (COSMOS) has repeatedly collected self-reported and operator-recorded data on mobile phone use. Assessing health effects using self-reported information is prone to measurement error, but operator data were available prospectively for only part of the study population and did not cover past mobile phone use. To optimize the available data and reduce bias, we evaluated different statistical approaches for constructing mobile phone exposure histories within COSMOS. We evaluated and compared the performance of 4 regression calibration (RC) methods (simple, direct, inverse, and generalized additive model for location, shape, and scale), complete-case analysis, and multiple imputation in a simulation study with a binary health outcome. We used self-reported and operator-recorded mobile phone call data collected at baseline (2007-2012) from participants in Denmark, Finland, the Netherlands, Sweden, and the United Kingdom. Parameter estimates obtained using simple, direct, and inverse RC methods were associated with less bias and lower mean squared error than those obtained with complete-case analysis or multiple imputation. We showed that RC methods resulted in more accurate estimation of the relationship between mobile phone use and health outcomes by combining self-reported data with objective operator-recorded data available for a subset of participants.",,pdf:https://academic.oup.com/aje/advance-article-pdf/doi/10.1093/aje/kwae039/57572723/kwae039.pdf; doi:https://doi.org/10.1093/aje/kwae039; html:https://europepmc.org/articles/PMC11458186; pdf:https://europepmc.org/articles/PMC11458186?pdf=render
 32900377,https://doi.org/10.1186/s12916-020-01754-z,Going on up to the SPIRIT in AI: will new reporting guidelines for clinical trials of AI interventions improve their rigour?,"Wicks P, Liu X, Denniston AK.",,BMC medicine,2020,2020-09-09,Y,Artificial intelligence; Checklist; Clinical Trial; Machine Learning; Reporting Guidelines,,,,,pdf:https://bmcmedicine.biomedcentral.com/track/pdf/10.1186/s12916-020-01754-z; doi:https://doi.org/10.1186/s12916-020-01754-z; html:https://europepmc.org/articles/PMC7487816; pdf:https://europepmc.org/articles/PMC7487816?pdf=render
 34954079,https://doi.org/10.1016/j.jnutbio.2021.108929,Iron-mediated epigenetic activation of NRF2 targets.,"Horniblow RD, Pathak P, Balacco DL, Acharjee A, Lles E, Gkoutos G, Beggs AD, Tselepis C.",,The Journal of nutritional biochemistry,2022,2021-12-23,N,Iron; Diet; Oxidative stress; NRF2; Epigenome; Nutrigenetics; Hypomethylation,,,"The toxic effects of excess dietary iron within the colonic lumen are well documented, particularly in the context of Inflammatory Bowel Disease (IBD) and Colorectal Cancer (CRC). Proposed mechanisms that underpin iron-associated intestinal disease include: (1) the pro-inflammatory and ROS-promoting nature of iron, (2) gene-expression alterations, and (3) intestinal microbial dysbiosis. However, to date no studies have examined the effect of iron on the colonic epigenome. Here we demonstrate that chronic iron exposure of colonocytes leads to significant hypomethylation of the epigenome. Bioinformatic analysis highlights a significant epigenetic effect on NRF2 (nuclear factor erythroid 2-related factor 2) pathway targets (including NAD(P)H Quinone Dehydrogenase 1 [NQO1] and Glutathione peroxidase 2 [GPX2]); this demethylating effect was validated and subsequent gene and protein expression quantified. These epigenetic modifications were not observed upon the diminishment of cellular lipid peroxidation with endogenous glutathione and the subsequent removal of iron. Additionally, the induction of TET1 expression was found post-iron treatment, highlighting the possibility of an oxidative-stress induction of TET1 and subsequent hypomethylation of NRF2 targets. In addition, a strong time dependence on the establishment of iron-orchestrated hypomethylation was found which was concurrent with the increase in the intracellular labile iron pool (LIP) and lipid peroxidation levels. These epigenetic changes were further validated in murine intestinal mucosa in models administered a chronic iron diet, providing evidence for the likelihood of dietary-iron mediated epigenetic alterations in vivo. Furthermore, significant correlations were found between NQO1 and GPX2 demethylation and human intestinal tissue iron-status, thus suggesting that these iron-mediated epigenetic modifications are likely in iron-replete enterocytes. Together, these data describe a novel mechanism by which excess dietary iron is able to alter the intestinal phenotype, which could have implications in iron-mediated intestinal disease and the regulation of ferroptosis.",,doi:https://doi.org/10.1016/j.jnutbio.2021.108929; doi:https://doi.org/10.1016/j.jnutbio.2021.108929
 36958365,https://doi.org/10.1016/s2352-3018(23)00028-0,Life expectancy after 2015 of adults with HIV on long-term antiretroviral therapy in Europe and North America: a collaborative analysis of cohort studies.,"Trickey A, Sabin CA, Burkholder G, Crane H, d'Arminio Monforte A, Egger M, Gill MJ, Grabar S, Guest JL, Jarrin I, Lampe FC, Obel N, Reyes JM, Stephan C, Sterling TR, Teira R, Touloumi G, Wasmuth JC, Wit F, Wittkop L, Zangerle R, Silverberg MJ, Justice A, Sterne JAC.",,The lancet. HIV,2023,2023-03-20,N,,,,"<h4>Background</h4>The life expectancy of people with HIV taking antiretroviral therapy (ART) has increased substantially over the past 25 years. Most previous studies of life expectancy were based on data from the first few years after starting ART, when mortality is highest. However, many people with HIV have been successfully treated with ART for many years, and up-to-date prognosis data are needed. We aimed to estimate life expectancy in adults with HIV on ART for at least 1 year in Europe and North America from 2015 onwards.<h4>Methods</h4>We used data for people with HIV taking ART from the Antiretroviral Therapy Cohort Collaboration and the UK Collaborative HIV Cohort Study. Included participants started ART between 1996 and 2014 and had been on ART for at least 1 year by 2015, or started ART between 2015 and 2019 and survived for at least 1 year; all participants were aged at least 16 years at ART initiation. We used Poisson models to estimate the associations between mortality and demographic and clinical characteristics, including CD4 cell count at the start of follow-up. We also estimated the remaining years of life left for people with HIV aged 40 years who were taking ART, and stratified these estimates by variables associated with mortality. These estimates were compared with estimates for years of life remaining in a corresponding multi-country general population.<h4>Findings</h4>Among 206 891 people with HIV included, 5780 deaths were recorded since 2015. We estimated that women with HIV at age 40 years had 35·8 years (95% CI 35·2-36·4) of life left if they started ART before 2015, and 39·0 years (38·5-39·5) left if they started ART after 2015. For men with HIV, the corresponding estimates were 34·5 years (33·8-35·2) and 37·0 (36·5-37·6). Women with CD4 counts of fewer than 49 cells per μL at the start of follow-up had an estimated 19·4 years (18·2-20·5) of life left at age 40 years if they started ART before 2015 and 24·9 years (23·9-25·9) left if they started ART after 2015. The corresponding estimates for men were 18·2 years (17·1-19·4) and 23·7 years (22·7-24·8). Women with CD4 counts of at least 500 cells per μL at the start of follow-up had an estimated 40·2 years (39·7-40·6) of life left at age 40 years if they started ART before 2015 and 42·0 years (41·7-42·3) left if they started ART after 2015. The corresponding estimates for men were 38·0 years (37·5-38·5) and 39·2 years (38·7-39·7).<h4>Interpretation</h4>For people with HIV on ART and with high CD4 cell counts who survived to 2015 or started ART after 2015, life expectancy was only a few years lower than that in the general population, irrespective of when ART was started. However, for people with low CD4 counts at the start of follow-up, life-expectancy estimates were substantially lower, emphasising the continuing importance of early diagnosis and sustained treatment of HIV.<h4>Funding</h4>US National Institute on Alcohol Abuse and Alcoholism and UK Medical Research Council.",,doi:https://doi.org/10.1016/s2352-3018(23)00028-0; doi:https://doi.org/10.1016/S2352-3018(23)00028-0; html:https://europepmc.org/articles/PMC10288029; pdf:https://europepmc.org/articles/PMC10288029?pdf=render; doi:https://doi.org/10.1016/s2352-3018(23)00028-0
-35241573,https://doi.org/10.1136/bmjqs-2020-012108,Comparing antibiotic prescribing between clinicians in UK primary care: an analysis in a cohort study of eight different measures of antibiotic prescribing.,"Van Staa T, Li Y, Gold N, Chadborn T, Welfare W, Palin V, Ashcroft DM, Bircher J.",,BMJ quality & safety,2022,2022-10-19,Y,General Practice; Antibiotic Management; Healthcare Quality Improvement,,,"<h4>Background</h4>There is a need to reduce antimicrobial uses in humans. Previous studies have found variations in antibiotic (AB) prescribing between practices in primary care. This study assessed variability of AB prescribing between clinicians.<h4>Methods</h4>Clinical Practice Research Datalink, which collects electronic health records in primary care, was used to select anonymised clinicians providing 500+ consultations during 2012-2017. Eight measures of AB prescribing were assessed, such as overall and incidental AB prescribing, repeat AB courses and extent of risk-based prescribing. Poisson regression models with random effect for clinicians were fitted.<h4>Results</h4>6111 clinicians from 466 general practices were included. Considerable variability between individual clinicians was found for most AB measures. For example, the rate of AB prescribing varied between 77.4 and 350.3 per 1000 consultations; percentage of repeat AB courses within 30 days ranged from 13.1% to 34.3%; predicted patient risk of hospital admission for infection-related complications in those prescribed AB ranged from 0.03% to 0.32% (5th and 95th percentiles). The adjusted relative rate between clinicians in rates of AB prescribing was 5.23. Weak correlation coefficients (<0.5) were found between most AB measures. There was considerable variability in case mix seen by clinicians. The largest potential impact to reduce AB prescribing could be around encouraging risk-based prescribing and addressing repeat issues of ABs. Reduction of repeat AB courses to prescribing habit of median clinician would save 21 813 AB prescriptions per 1000 clinicians per year.<h4>Conclusions</h4>The wide variation seen in all measures of AB prescribing and weak correlation between them suggests that a single AB measure, such as prescribing rate, is not sufficient to underpin the optimisation of AB prescribing.",,pdf:https://qualitysafety.bmj.com/content/qhc/early/2022/03/02/bmjqs-2020-012108.full.pdf; doi:https://doi.org/10.1136/bmjqs-2020-012108; html:https://europepmc.org/articles/PMC9606525; pdf:https://europepmc.org/articles/PMC9606525?pdf=render
 34237806,https://doi.org/10.1515/dmdi-2021-0104,Prevalence of <i>CYP2C19*2</i> carriers in Saudi ischemic stroke patients and the suitability of using genotyping to guide antiplatelet therapy in a university hospital setup.,"Al-Rubaish AM, Al-Muhanna FA, Alshehri AM, Alsulaiman AA, Alabdulali MM, Alkhamis F, Alamri AS, Alali RA, Akhtar MS, Cyrus C, Claassens DMF, Asselbergs FW, Al-Ali AK.",,Drug metabolism and personalized therapy,2021,2021-07-08,N,Genotyping; Stroke; aspirin; Clopidogrel; Cyp2c19*2,,,"<h4>Objectives</h4>To mitigate the incidence of recurrent stroke in patients, dual antiplatelet therapy comprising aspirin and clopidogrel is usually administered. Clopidogrel is a prodrug and its bioactivation is catalyzed by cytochrome P450 (CYP)2C19. The main objective of this work was to determine the prevalence of <i>CYP2C19*2</i> carriers in Saudi ischemic stroke patients and assess the suitability of using genotyping to guide antiplatelet therapy in a university hospital setup.<h4>Methods</h4>This prospective (2018-2019) study was conducted on 256 patients (age 61 ± 12.5) clinically diagnosed with ischemic stroke who were genotyped using Spartan RX <i>CYP2C19</i> assay.<h4>Results</h4>From the total patient group (256), upon admission, 210 patients were prescribed either aspirin, clopidogrel or dual antiplatelet therapy. Of the 27 patients with the <i>CYP2C19*2</i> allele who were prescribed clopidogrel (18) or dual antiplatelet therapy (9), only 21 patients could be followed up for a period of six months post stroke event, in addition to 21 age- and sex-matched patients with the normal allele. The <i>CYP2C19*2</i> allele carriers had a statistically significant increased risk of recurrent stroke compared to patients carrying the normal allele.<h4>Conclusions</h4>This study shows the suitability of using genotyping to guide antiplatelet therapy in ischemic stroke patients in a clinical setting.",,pdf:https://discovery.ucl.ac.uk/10135735/1/Asselbergs_10.1515_dmdi-2021-0104.pdf; doi:https://doi.org/10.1515/dmdi-2021-0104
+35241573,https://doi.org/10.1136/bmjqs-2020-012108,Comparing antibiotic prescribing between clinicians in UK primary care: an analysis in a cohort study of eight different measures of antibiotic prescribing.,"Van Staa T, Li Y, Gold N, Chadborn T, Welfare W, Palin V, Ashcroft DM, Bircher J.",,BMJ quality & safety,2022,2022-10-19,Y,General Practice; Antibiotic Management; Healthcare Quality Improvement,,,"<h4>Background</h4>There is a need to reduce antimicrobial uses in humans. Previous studies have found variations in antibiotic (AB) prescribing between practices in primary care. This study assessed variability of AB prescribing between clinicians.<h4>Methods</h4>Clinical Practice Research Datalink, which collects electronic health records in primary care, was used to select anonymised clinicians providing 500+ consultations during 2012-2017. Eight measures of AB prescribing were assessed, such as overall and incidental AB prescribing, repeat AB courses and extent of risk-based prescribing. Poisson regression models with random effect for clinicians were fitted.<h4>Results</h4>6111 clinicians from 466 general practices were included. Considerable variability between individual clinicians was found for most AB measures. For example, the rate of AB prescribing varied between 77.4 and 350.3 per 1000 consultations; percentage of repeat AB courses within 30 days ranged from 13.1% to 34.3%; predicted patient risk of hospital admission for infection-related complications in those prescribed AB ranged from 0.03% to 0.32% (5th and 95th percentiles). The adjusted relative rate between clinicians in rates of AB prescribing was 5.23. Weak correlation coefficients (<0.5) were found between most AB measures. There was considerable variability in case mix seen by clinicians. The largest potential impact to reduce AB prescribing could be around encouraging risk-based prescribing and addressing repeat issues of ABs. Reduction of repeat AB courses to prescribing habit of median clinician would save 21 813 AB prescriptions per 1000 clinicians per year.<h4>Conclusions</h4>The wide variation seen in all measures of AB prescribing and weak correlation between them suggests that a single AB measure, such as prescribing rate, is not sufficient to underpin the optimisation of AB prescribing.",,pdf:https://qualitysafety.bmj.com/content/qhc/early/2022/03/02/bmjqs-2020-012108.full.pdf; doi:https://doi.org/10.1136/bmjqs-2020-012108; html:https://europepmc.org/articles/PMC9606525; pdf:https://europepmc.org/articles/PMC9606525?pdf=render
 35385889,https://doi.org/10.1515/dmpt-2021-0104,Prevalence of <i>CYP2C19*2</i> carriers in Saudi ischemic stroke patients and the suitability of using genotyping to guide antiplatelet therapy in a university hospital setup.,"Al-Rubaish AM, Al-Muhanna FA, Alshehri AM, Alsulaiman AA, Alabdulali MM, Alkhamis F, Alamri AS, Alali RA, Akhtar MS, Cyrus C, Claassens DMF, Asselbergs FW, Al-Ali AK.",,Drug metabolism and personalized therapy,2021,2021-07-08,N,Genotyping; Stroke; aspirin; Clopidogrel; Cyp2c19*2,,,"<h4>Objectives</h4>To mitigate the incidence of recurrent stroke in patients, dual antiplatelet therapy comprising aspirin and clopidogrel is usually administered. Clopidogrel is a prodrug and its bioactivation is catalyzed by cytochrome P450 (CYP)2C19. The main objective of this work was to determine the prevalence of <i>CYP2C19*2</i> carriers in Saudi ischemic stroke patients and assess the suitability of using genotyping to guide antiplatelet therapy in a university hospital setup.<h4>Methods</h4>This prospective (2018-2019) study was conducted on 256 patients (age 61 ± 12.5) clinically diagnosed with ischemic stroke who were genotyped using Spartan RX <i>CYP2C19</i> assay.<h4>Results</h4>From the total patient group (256), upon admission, 210 patients were prescribed either aspirin, clopidogrel or dual antiplatelet therapy. Of the 27 patients with the <i>CYP2C19*2</i> allele who were prescribed clopidogrel (18) or dual antiplatelet therapy (9), only 21 patients could be followed up for a period of six months post stroke event, in addition to 21 age- and sex-matched patients with the normal allele. The <i>CYP2C19*2</i> allele carriers had a statistically significant increased risk of recurrent stroke compared to patients carrying the normal allele.<h4>Conclusions</h4>This study shows the suitability of using genotyping to guide antiplatelet therapy in ischemic stroke patients in a clinical setting.",,pdf:https://discovery.ucl.ac.uk/10135735/1/Asselbergs_10.1515_dmdi-2021-0104.pdf; doi:https://doi.org/10.1515/dmpt-2021-0104
 33354439,https://doi.org/10.1109/jtehm.2020.3040236,Modeling Large Sparse Data for Feature Selection: Hospital Admission Predictions of the Dementia Patients Using Primary Care Electronic Health Records.,"Tsang G, Zhou SM, Xie X.",,IEEE journal of translational engineering in health and medicine,2021,2020-11-24,Y,Dementia; risk factors; Hospitalization; Feature Selection; Machine Learning; Electronic Health Records; Deep Learning; Weight Regularization,,,"A growing elderly population suffering from incurable, chronic conditions such as dementia present a continual strain on medical services due to mental impairment paired with high comorbidity resulting in increased hospitalization risk. The identification of at risk individuals allows for preventative measures to alleviate said strain. Electronic health records provide opportunity for big data analysis to address such applications. Such data however, provides a challenging problem space for traditional statistics and machine learning due to high dimensionality and sparse data elements. This article proposes a novel machine learning methodology: entropy regularization with ensemble deep neural networks (ECNN), which simultaneously provides high predictive performance of hospitalization of patients with dementia whilst enabling an interpretable heuristic analysis of the model architecture, able to identify individual features of importance within a large feature domain space. Experimental results on health records containing 54,647 features were able to identify 10 event indicators within a patient timeline: a collection of diagnostic events, medication prescriptions and procedural events, the highest ranked being essential hypertension. The resulting subset was still able to provide a highly competitive hospitalization prediction (Accuracy: 0.759) as compared to the full feature domain (Accuracy: 0.755) or traditional feature selection techniques (Accuracy: 0.737), a significant reduction in feature size. The discovery and heuristic evidence of correlation provide evidence for further clinical study of said medical events as potential novel indicators. There also remains great potential for adaption of ECNN within other medical big data domains as a data mining tool for novel risk factor identification.",,pdf:https://ieeexplore.ieee.org/ielx7/6221039/9246949/09268962.pdf; doi:https://doi.org/10.1109/JTEHM.2020.3040236; html:https://europepmc.org/articles/PMC7737850; pdf:https://europepmc.org/articles/PMC7737850?pdf=render
+31168069,https://doi.org/10.1038/s41380-019-0439-8,"The genomic basis of mood instability: identification of 46 loci in 363,705 UK Biobank participants, genetic correlation with psychiatric disorders, and association with gene expression and function.","Ward J, Tunbridge EM, Sandor C, Lyall LM, Ferguson A, Strawbridge RJ, Lyall DM, Cullen B, Graham N, Johnston KJA, Webber C, Escott-Price V, O'Donovan M, Pell JP, Bailey MES, Harrison PJ, Smith DJ.",,Molecular psychiatry,2020,2019-06-05,Y,,,,"Genome-wide association studies (GWAS) of psychiatric phenotypes have tended to focus on categorical diagnoses, but to understand the biology of mental illness it may be more useful to study traits which cut across traditional boundaries. Here, we report the results of a GWAS of mood instability as a trait in a large population cohort (UK Biobank, n = 363,705). We also assess the clinical and biological relevance of the findings, including whether genetic associations show enrichment for nervous system pathways. Forty six unique loci associated with mood instability were identified with a SNP heritability estimate of 9%. Linkage Disequilibrium Score Regression (LDSR) analyses identified genetic correlations with Major Depressive Disorder (MDD), Bipolar Disorder (BD), Schizophrenia, anxiety, and Post Traumatic Stress Disorder (PTSD). Gene-level and gene set analyses identified 244 significant genes and 6 enriched gene sets. Tissue expression analysis of the SNP-level data found enrichment in multiple brain regions, and eQTL analyses highlighted an inversion on chromosome 17 plus two brain-specific eQTLs. In addition, we used a Phenotype Linkage Network (PLN) analysis and community analysis to assess for enrichment of nervous system gene sets using mouse orthologue databases. The PLN analysis found enrichment in nervous system PLNs for a community containing serotonin and melatonin receptors. In summary, this work has identified novel loci, tissues and gene sets contributing to mood instability. These findings may be relevant for the identification of novel trans-diagnostic drug targets and could help to inform future stratified medicine innovations in mental health.",,pdf:https://eprints.gla.ac.uk/185493/1/185493.pdf; doi:https://doi.org/10.1038/s41380-019-0439-8; html:https://europepmc.org/articles/PMC7116257; pdf:https://europepmc.org/articles/PMC7116257?pdf=render
 30848519,https://doi.org/10.1111/dme.13945,Impact of glycaemic control on fracture risk in 5368 people with newly diagnosed Type 1 diabetes: a time-dependent analysis.,"Thayakaran R, Perrins M, Gokhale KM, Kumaran S, Narendran P, Price MJ, Nirantharakumar K, Toulis KA.",,Diabetic medicine : a journal of the British Diabetic Association,2019,2019-04-05,N,,,,"<h4>Aims</h4>To assess whether glycaemic control is associated with a lifelong increased risk of fracture in people with newly diagnosed Type 1 diabetes.<h4>Methods</h4>People with newly diagnosed Type 1 diabetes between 1 January 1995 and 10 May 2016 were identified in The Health Improvement Network database. Longitudinal HbA<sub>1c</sub> measurements from diagnosis to fracture or study end or loss to follow-up were collected. A Cox proportional hazards model with HbA<sub>1c</sub> included as a time-dependent variable was fitted to these data.<h4>Results</h4>Some 5368 people with newly diagnosed Type 1 diabetes were included. The estimated adjusted hazard ratio (aHR) for HbA<sub>1c</sub> was statistically significant [aHR 1.007; 95% confidence interval (CI) 1.002-1.011 (mmol/mol) and aHR 1.07; 95% CI 1.03-1.12 (%)]. An incremental higher risk of fracture was observed with increasing levels of HbA<sub>1c</sub> .<h4>Conclusions</h4>In people with newly diagnosed Type 1 diabetes, higher HbA<sub>1c</sub> is associated with an increased risk for fractures.",,doi:https://doi.org/10.1111/dme.13945
-36060542,https://doi.org/10.3389/fdgth.2022.939292,Clinical deployment environments: Five pillars of translational machine learning for health.,"Harris S, Bonnici T, Keen T, Lilaonitkul W, White MJ, Swanepoel N.",,Frontiers in digital health,2022,2022-08-19,Y,Safety; Artificial intelligence; Machine Learning; Health Informatics; Translational Medicine; Ml-ops,,,"Machine Learning for Health (ML4H) has demonstrated efficacy in computer imaging and other self-contained digital workflows, but has failed to substantially impact routine clinical care. This is no longer because of poor adoption of Electronic Health Records Systems (EHRS), but because ML4H needs an infrastructure for development, deployment and evaluation within the healthcare institution. In this paper, we propose a design pattern called a Clinical Deployment Environment (CDE). We sketch the five pillars of the CDE: (1) real world development supported by live data where ML4H teams can iteratively build and test at the bedside (2) an ML-Ops platform that brings the rigour and standards of continuous deployment to ML4H (3) design and supervision by those with expertise in AI safety (4) the methods of implementation science that enable the algorithmic insights to influence the behaviour of clinicians and patients and (5) continuous evaluation that uses randomisation to avoid bias but in an agile manner. The CDE is intended to answer the same requirements that bio-medicine articulated in establishing the translational medicine domain. It envisions a transition from ""real-world"" data to ""real-world"" development.",,pdf:https://www.frontiersin.org/articles/10.3389/fdgth.2022.939292/pdf; doi:https://doi.org/10.3389/fdgth.2022.939292; html:https://europepmc.org/articles/PMC9437594; pdf:https://europepmc.org/articles/PMC9437594?pdf=render
 36814324,https://doi.org/10.1186/s13195-023-01184-y,"Investigating associations between blood metabolites, later life brain imaging measures, and genetic risk for Alzheimer's disease.","Green RE, Lord J, Scelsi MA, Xu J, Wong A, Naomi-James S, Handy A, Gilchrist L, Williams DM, Parker TD, Lane CA, Malone IB, Cash DM, Sudre CH, Coath W, Thomas DL, Keuss S, Dobson R, Legido-Quigley C, Fox NC, Schott JM, Richards M, Proitsi P, Insight 46 study team.",,Alzheimer's research & therapy,2023,2023-02-22,Y,Metabolites; Ageing; Brain imaging; Alzheimer’s disease; Dementia; Birth Cohort; Polygenic Scores; Weighted-gene Coexpression Network Analysis,,,"<h4>Background</h4>Identifying blood-based signatures of brain health and preclinical pathology may offer insights into early disease mechanisms and highlight avenues for intervention. Here, we systematically profiled associations between blood metabolites and whole-brain volume, hippocampal volume, and amyloid-β status among participants of Insight 46-the neuroscience sub-study of the National Survey of Health and Development (NSHD). We additionally explored whether key metabolites were associated with polygenic risk for Alzheimer's disease (AD).<h4>Methods</h4>Following quality control, levels of 1019 metabolites-detected with liquid chromatography-mass spectrometry-were available for 1740 participants at age 60-64. Metabolite data were subsequently clustered into modules of co-expressed metabolites using weighted coexpression network analysis. Accompanying MRI and amyloid-PET imaging data were present for 437 participants (age 69-71). Regression analyses tested relationships between metabolite measures-modules and hub metabolites-and imaging outcomes. Hub metabolites were defined as metabolites that were highly connected within significant (p<sub>FDR</sub> < 0.05) modules or were identified as a hub in a previous analysis on cognitive function in the same cohort. Regression models included adjustments for age, sex, APOE genotype, lipid medication use, childhood cognitive ability, and social factors. Finally, associations were tested between AD polygenic risk scores (PRS), including and excluding the APOE region, and metabolites and modules that significantly associated (p<sub>FDR</sub> < 0.05) with an imaging outcome (N = 1638).<h4>Results</h4>In the fully adjusted model, three lipid modules were associated with a brain volume measure (p<sub>FDR</sub> < 0.05): one enriched in sphingolipids (hippocampal volume: ß = 0.14, 95% CI = [0.055,0.23]), one in several fatty acid pathways (whole-brain volume: ß =  - 0.072, 95%CI = [- 0.12, - 0.026]), and another in diacylglycerols and phosphatidylethanolamines (whole-brain volume: ß =  - 0.066, 95% CI = [- 0.11, - 0.020]). Twenty-two hub metabolites were associated (p<sub>FDR</sub> < 0.05) with an imaging outcome (whole-brain volume: 22; hippocampal volume: 4). Some nominal associations were reported for amyloid-β, and with an AD PRS in our genetic analysis, but none survived multiple testing correction.<h4>Conclusions</h4>Our findings highlight key metabolites, with functions in membrane integrity and cell signalling, that associated with structural brain measures in later life. Future research should focus on replicating this work and interrogating causality.",,pdf:https://alzres.biomedcentral.com/counter/pdf/10.1186/s13195-023-01184-y; doi:https://doi.org/10.1186/s13195-023-01184-y; html:https://europepmc.org/articles/PMC9945600; pdf:https://europepmc.org/articles/PMC9945600?pdf=render
-31168069,https://doi.org/10.1038/s41380-019-0439-8,"The genomic basis of mood instability: identification of 46 loci in 363,705 UK Biobank participants, genetic correlation with psychiatric disorders, and association with gene expression and function.","Ward J, Tunbridge EM, Sandor C, Lyall LM, Ferguson A, Strawbridge RJ, Lyall DM, Cullen B, Graham N, Johnston KJA, Webber C, Escott-Price V, O'Donovan M, Pell JP, Bailey MES, Harrison PJ, Smith DJ.",,Molecular psychiatry,2020,2019-06-05,Y,,,,"Genome-wide association studies (GWAS) of psychiatric phenotypes have tended to focus on categorical diagnoses, but to understand the biology of mental illness it may be more useful to study traits which cut across traditional boundaries. Here, we report the results of a GWAS of mood instability as a trait in a large population cohort (UK Biobank, n = 363,705). We also assess the clinical and biological relevance of the findings, including whether genetic associations show enrichment for nervous system pathways. Forty six unique loci associated with mood instability were identified with a SNP heritability estimate of 9%. Linkage Disequilibrium Score Regression (LDSR) analyses identified genetic correlations with Major Depressive Disorder (MDD), Bipolar Disorder (BD), Schizophrenia, anxiety, and Post Traumatic Stress Disorder (PTSD). Gene-level and gene set analyses identified 244 significant genes and 6 enriched gene sets. Tissue expression analysis of the SNP-level data found enrichment in multiple brain regions, and eQTL analyses highlighted an inversion on chromosome 17 plus two brain-specific eQTLs. In addition, we used a Phenotype Linkage Network (PLN) analysis and community analysis to assess for enrichment of nervous system gene sets using mouse orthologue databases. The PLN analysis found enrichment in nervous system PLNs for a community containing serotonin and melatonin receptors. In summary, this work has identified novel loci, tissues and gene sets contributing to mood instability. These findings may be relevant for the identification of novel trans-diagnostic drug targets and could help to inform future stratified medicine innovations in mental health.",,pdf:https://eprints.gla.ac.uk/185493/1/185493.pdf; doi:https://doi.org/10.1038/s41380-019-0439-8; html:https://europepmc.org/articles/PMC7116257; pdf:https://europepmc.org/articles/PMC7116257?pdf=render
+36060542,https://doi.org/10.3389/fdgth.2022.939292,Clinical deployment environments: Five pillars of translational machine learning for health.,"Harris S, Bonnici T, Keen T, Lilaonitkul W, White MJ, Swanepoel N.",,Frontiers in digital health,2022,2022-08-19,Y,Safety; Artificial intelligence; Machine Learning; Health Informatics; Translational Medicine; Ml-ops,,,"Machine Learning for Health (ML4H) has demonstrated efficacy in computer imaging and other self-contained digital workflows, but has failed to substantially impact routine clinical care. This is no longer because of poor adoption of Electronic Health Records Systems (EHRS), but because ML4H needs an infrastructure for development, deployment and evaluation within the healthcare institution. In this paper, we propose a design pattern called a Clinical Deployment Environment (CDE). We sketch the five pillars of the CDE: (1) real world development supported by live data where ML4H teams can iteratively build and test at the bedside (2) an ML-Ops platform that brings the rigour and standards of continuous deployment to ML4H (3) design and supervision by those with expertise in AI safety (4) the methods of implementation science that enable the algorithmic insights to influence the behaviour of clinicians and patients and (5) continuous evaluation that uses randomisation to avoid bias but in an agile manner. The CDE is intended to answer the same requirements that bio-medicine articulated in establishing the translational medicine domain. It envisions a transition from ""real-world"" data to ""real-world"" development.",,pdf:https://www.frontiersin.org/articles/10.3389/fdgth.2022.939292/pdf; doi:https://doi.org/10.3389/fdgth.2022.939292; html:https://europepmc.org/articles/PMC9437594; pdf:https://europepmc.org/articles/PMC9437594?pdf=render
 32079223,https://doi.org/10.3390/jcm9020545,Quantitative Approach to Fragmented QRS in Arrhythmogenic Cardiomyopathy: From Disease towards Asymptomatic Carriers of Pathogenic Variants.,"Roudijk RW, Bosman LP, van der Heijden JF, de Bakker JMT, Hauer RNW, van Tintelen JP, Asselbergs FW, Te Riele ASJM, Loh P.",,Journal of clinical medicine,2020,2020-02-17,Y,Genetics; Electrocardiography; ventricular arrhythmia; Sudden Cardiac Death; Fragmented Qrs; Fqrs; Arrhythmogenic Cardiomyopathy; Inherited Cardiomyopathies,Understanding the Causes of Disease,cardiovascular,"Fragmented QRS complexes (fQRS) are common in patients with arrhythmogenic cardiomyopathy (ACM). A new method of fQRS quantification may aid early disease detection in pathogenic variant carriers and assessment of prognosis in patients with early stage ACM. Patients with definite ACM (<i>n</i> = 221, 66%), carriers of a pathogenic ACM-associated variant without a definite ACM diagnosis (<i>n</i> = 57, 17%) and control subjects (<i>n</i> = 58, 17%) were included. Quantitative fQRS (Q-fQRS) was defined as the total amount of deflections in the QRS complex in all 12 electrocardiography (ECG) leads. Q-fQRS was scored by a single observer and reproducibility was determined by three independent observers. Q-fQRS count was feasible with acceptable intra- and inter-observer agreement. Q-fQRS count is significantly higher in patients with definite ACM (54 ± 15) and pathogenic variant carriers (55 ± 10) compared to controls (35 ± 5) (<i>p</i> < 0.001). In patients with ACM, Q-fQRS was not associated with sustained ventricular arrhythmia (<i>p</i> = 0.701) at baseline or during follow-up (<i>p</i> = 0.335). Both definite ACM patients and pathogenic variant carriers not fulfilling ACM diagnosis have a higher Q-fQRS than controls. This may indicate that increased Q-fQRS is an early sign of disease penetrance. In concealed and early stages of ACM the role of Q-fQRS for risk stratification is limited.",,pdf:https://www.mdpi.com/2077-0383/9/2/545/pdf?version=1581938622; doi:https://doi.org/10.3390/jcm9020545; html:https://europepmc.org/articles/PMC7073517; pdf:https://europepmc.org/articles/PMC7073517?pdf=render
 34535985,https://doi.org/10.1002/hep4.1805,Genome-Wide Association Study of NAFLD Using Electronic Health Records.,"Fairfield CJ, Drake TM, Pius R, Bretherick AD, Campbell A, Clark DW, Fallowfield JA, Hayward C, Henderson NC, Joshi PK, Mills NL, Porteous DJ, Ramachandran P, Semple RK, Shaw CA, Sudlow CLM, Timmers PRHJ, Wilson JF, Wigmore SJ, Harrison EM, Spiliopoulou A.",,Hepatology communications,2022,2021-09-17,Y,,,,"Genome-wide association studies (GWAS) have identified several risk loci for nonalcoholic fatty liver disease (NAFLD). Previous studies have largely relied on small sample sizes and have assessed quantitative traits. We performed a case-control GWAS in the UK Biobank using recorded diagnosis of NAFLD based on diagnostic codes recommended in recent consensus guidelines. We performed a GWAS of 4,761 cases of NAFLD and 373,227 healthy controls without evidence of NAFLD. Sensitivity analyses were performed excluding other co-existing hepatic pathology, adjusting for body mass index (BMI) and adjusting for alcohol intake. A total of 9,723,654 variants were assessed by logistic regression adjusted for age, sex, genetic principal components, and genotyping batch. We performed a GWAS meta-analysis using available summary association statistics. Six risk loci were identified (P < 5*10<sup>-8</sup> ) (apolipoprotein E [APOE], patatin-like phospholipase domain containing 3 [PNPLA3, transmembrane 6 superfamily member 2 [TM6SF2], glucokinase regulator [GCKR], mitochondrial amidoxime reducing component 1 [MARC1], and tribbles pseudokinase 1 [TRIB1]). All loci retained significance in sensitivity analyses without co-existent hepatic pathology and after adjustment for BMI. PNPLA3 and TM6SF2 remained significant after adjustment for alcohol (alcohol intake was known in only 158,388 individuals), with others demonstrating consistent direction and magnitude of effect. All six loci were significant on meta-analysis. Rs429358 (P = 2.17*10<sup>-11</sup> ) is a missense variant within the APOE gene determining ϵ4 versus ϵ2/ϵ3 alleles. The ϵ4 allele of APOE offered protection against NAFLD (odds ratio for heterozygotes 0.84 [95% confidence interval 0.78-0.90] and homozygotes 0.64 [0.50-0.79]). Conclusion: This GWAS replicates six known NAFLD-susceptibility loci and confirms that the ϵ4 allele of APOE is associated with protection against NAFLD. The results are consistent with published GWAS using histological and radiological measures of NAFLD, confirming that NAFLD identified through diagnostic codes from consensus guidelines is a valid alternative to more invasive and costly approaches.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/hep4.1805; doi:https://doi.org/10.1002/hep4.1805; html:https://europepmc.org/articles/PMC8793997; pdf:https://europepmc.org/articles/PMC8793997?pdf=render
 31312209,https://doi.org/10.3389/fgene.2019.00567,Use of Pharmacogenetic Drugs by the Dutch Population.,"Alshabeeb MA, Deneer VHM, Khan A, Asselbergs FW.",,Frontiers in genetics,2019,2019-07-02,Y,CYP2C19; CYP2D6; Pharmacogenetics; Adrs; Slco1b1; Preemptive Genetic Testing,Better Care,,"<h4>Introduction</h4>The Dutch Pharmacogenetics Working Group (DPWG) indicated a list of actionable genotypes that affect patients' response to more 50 drugs; these drugs which show variable effects based on patients' genetic traits were named as pharmacogenetics (PGX) drugs. Preemptive genetic testing before using these drugs may protect certain patients from serious adverse reactions and could help in avoiding treatment failures. The objectives of this study include identifying the rate of PGX drug usage among Dutch population, estimating the level of users who carry the actionable genotypes and determining the main genes involved in drug's effect variability.<h4>Methods</h4>Usage of PGX drugs over 2011-2017 by the insured population (an average of 11.4 million) in outpatient clinics in Netherlands was obtained from the publically available GIP databank. The data of 45 drugs were analyzed and their interactions with selected pharmacogenes were estimated. Frequency of actionable genotypes of 249 Dutch parents was obtained from the public database: Genome of Netherlands (GoNL), to identify the pattern of genetic characteristics of Dutch population.<h4>Results</h4>Over a 7 year period, 51.3 million exposures of patients to PGX drugs were reported with an average of 5.3 exposures per each drug user. One quarterof the exposures (12.4 million) are predicted to be experienced by individuals with actionable genotypes (risky exposures). Up to 60% of the risky exposures (around 7.5 million) were related to drugs metabolized by CYP2D6. SLCO1B1, and CYP2C19 were also identified among the top genes affecting response of drugs users (involved in about 22 and 12.4% of the risky exposures, respectively). Cardiovascular medications were the top prescribed PGX drug class (43%), followed by gastroenterology (29%) and psychiatry/neurology medications (15%). Women use more PGX drugs than men (55.8 vs. 44.2%, respectively) with the majority (84%) of users in both sexes are above 45 years.<h4>Conclusion</h4>PGX drugs are commonly used in Netherlands. Preemptive panel testing for CYP2D6, SLCO1B1, and CYP2C19 only could be useful to predict 95% of vulnerable patients' exposures to PGX drugs. Future studies to assess the economic impact of preemptive panel testing on patients of older age are suggested.",,pdf:https://www.frontiersin.org/articles/10.3389/fgene.2019.00567/pdf; doi:https://doi.org/10.3389/fgene.2019.00567; html:https://europepmc.org/articles/PMC6614185; pdf:https://europepmc.org/articles/PMC6614185?pdf=render
 36689332,https://doi.org/10.1093/neuonc/noad021,GBMdeconvoluteR accurately infers proportions of neoplastic and immune cell populations from bulk glioblastoma transcriptomics data.,"Ajaib S, Lodha D, Pollock S, Hemmings G, Finetti MA, Gusnanto A, Chakrabarty A, Ismail A, Wilson E, Varn FS, Hunter B, Filby A, Brockman AA, McDonald D, Verhaak RGW, Ihrie RA, Stead LF.",,Neuro-oncology,2023,2023-07-01,Y,Immune; Deconvolution; Glioblastoma; Neoplastic; Transcriptomics,,,"<h4>Background</h4>Characterizing and quantifying cell types within glioblastoma (GBM) tumors at scale will facilitate a better understanding of the association between the cellular landscape and tumor phenotypes or clinical correlates. We aimed to develop a tool that deconvolutes immune and neoplastic cells within the GBM tumor microenvironment from bulk RNA sequencing data.<h4>Methods</h4>We developed an IDH wild-type (IDHwt) GBM-specific single immune cell reference consisting of B cells, T-cells, NK-cells, microglia, tumor associated macrophages, monocytes, mast and DC cells. We used this alongside an existing neoplastic single cell-type reference for astrocyte-like, oligodendrocyte- and neuronal progenitor-like and mesenchymal GBM cancer cells to create both marker and gene signature matrix-based deconvolution tools. We applied single-cell resolution imaging mass cytometry (IMC) to ten IDHwt GBM samples, five paired primary and recurrent tumors, to determine which deconvolution approach performed best.<h4>Results</h4>Marker-based deconvolution using GBM-tissue specific markers was most accurate for both immune cells and cancer cells, so we packaged this approach as GBMdeconvoluteR. We applied GBMdeconvoluteR to bulk GBM RNAseq data from The Cancer Genome Atlas and recapitulated recent findings from multi-omics single cell studies with regards associations between mesenchymal GBM cancer cells and both lymphoid and myeloid cells. Furthermore, we expanded upon this to show that these associations are stronger in patients with worse prognosis.<h4>Conclusions</h4>GBMdeconvoluteR accurately quantifies immune and neoplastic cell proportions in IDHwt GBM bulk RNA sequencing data and is accessible here: https://gbmdeconvoluter.leeds.ac.uk.",,pdf:https://academic.oup.com/neuro-oncology/advance-article-pdf/doi/10.1093/neuonc/noad021/49522012/noad021.pdf; doi:https://doi.org/10.1093/neuonc/noad021; html:https://europepmc.org/articles/PMC10326489; pdf:https://europepmc.org/articles/PMC10326489?pdf=render
 30444743,https://doi.org/10.1097/ccm.0000000000003424,"Risk Factors for 1-Year Mortality and Hospital Utilization Patterns in Critical Care Survivors: A Retrospective, Observational, Population-Based Data Linkage Study.","Szakmany T, Walters AM, Pugh R, Battle C, Berridge DM, Lyons RA.",,Critical care medicine,2019,2019-01-01,N,,,,"<h4>Objectives</h4>Clear understanding of the long-term consequences of critical care survivorship is essential. We investigated the care process and individual factors associated with long-term mortality among ICU survivors and explored hospital use in this group.<h4>Design</h4>Population-based data linkage study using the Secure Anonymised Information Linkage databank.<h4>Setting</h4>All ICUs between 2006 and 2013 in Wales, United Kingdom.<h4>Patients</h4>We identified 40,631 patients discharged alive from Welsh adult ICUs.<h4>Interventions</h4>None.<h4>Measurements and main results</h4>Primary outcome was 365-day survival. The secondary outcomes were 30- and 90-day survival and hospital utilization in the 365 days following ICU discharge. Kaplan-Meier curves were plotted to compare survival rates. Cox proportional hazards regression models were used to determine risk factors of mortality. Seven-thousand eight-hundred eighty-three patients (19.4%) died during the 1-year follow-up period. In the multivariable Cox regression analysis, advanced age and comorbidities were significant determinants of long-term mortality. Expedited discharge due to ICU bed shortage was associated with higher risk. The rate of hospitalization in the year prior to the critical care admission was 28 hospitalized days/1,000 d; post critical care was 88 hospitalized days/1,000 d for those who were still alive; and 57 hospitalized days/1,000 d and 412 hospitalized days/1,000 d for those who died by the end of the study, respectively.<h4>Conclusions</h4>One in five ICU survivors die within 1 year, with advanced age and comorbidity being significant predictors of outcome, leading to high resource use. Care process factors indicating high system stress were associated with increased risk. More detailed understanding is needed on the effects of the potentially modifiable factors to optimize service delivery and improve long-term outcomes of the critically ill.",,pdf:https://europepmc.org/articles/pmc6330072?pdf=render; doi:https://doi.org/10.1097/CCM.0000000000003424; html:https://europepmc.org/articles/PMC6330072; pdf:https://europepmc.org/articles/PMC6330072?pdf=render; doi:https://doi.org/10.1097/ccm.0000000000003424
 36462729,https://doi.org/10.1016/j.neuroimage.2022.119779,Amplitudes of resting-state functional networks - investigation into their correlates and biophysical properties.,"Lee S, Bijsterbosch JD, Almagro FA, Elliott L, McCarthy P, Taschler B, Sala-Llonch R, Beckmann CF, Duff EP, Smith SM, Douaud G.",,NeuroImage,2023,2022-12-01,Y,Dual regression; Gwas; Resting-state Fmri; Uk Biobank; Temporal Synchrony; Network Amplitude,,,"Resting-state fMRI studies have shown that multiple functional networks, which consist of distributed brain regions that share synchronised spontaneous activity, co-exist in the brain. As these resting-state networks (RSNs) have been thought to reflect the brain's intrinsic functional organization, intersubject variability in the networks' spontaneous fluctuations may be associated with individuals' clinical, physiological, cognitive, and genetic traits. Here, we investigated resting-state fMRI data along with extensive clinical, lifestyle, and genetic data collected from 37,842 UK Biobank participants, with the object of elucidating intersubject variability in the fluctuation amplitudes of RSNs. Functional properties of the RSN amplitudes were first examined by analyzing correlations with the well-established between-network functional connectivity. It was found that a network amplitude is highly correlated with the mean strength of the functional connectivity that the network has with the other networks. Intersubject clustering analysis showed the amplitudes are most strongly correlated with age, cardiovascular factors, body composition, blood cell counts, lung function, and sex, with some differences in the correlation strengths between sensory and cognitive RSNs. Genome-wide association studies (GWASs) of RSN amplitudes identified several significant genetic variants reported in previous GWASs for their implications in sleep duration. We provide insight into key factors determining RSN amplitudes and demonstrate that intersubject variability of the amplitudes primarily originates from differences in temporal synchrony between functionally linked brain regions, rather than differences in the magnitude of raw voxelwise BOLD signal changes. This finding additionally revealed intriguing differences between sensory and cognitive RSNs with respect to sex effects on temporal synchrony and provided evidence suggesting that synchronous coactivations of functionally linked brain regions, and magnitudes of BOLD signal changes, may be related to different genetic mechanisms. These results underscore that intersubject variability of the amplitudes in health and disease need to be interpreted largely as a measure of the sum of within-network temporal synchrony and amplitudes of BOLD signals, with a dominant contribution from the former.",,doi:https://doi.org/10.1016/j.neuroimage.2022.119779; doi:https://doi.org/10.1016/j.neuroimage.2022.119779; html:https://europepmc.org/articles/PMC10933815; pdf:https://europepmc.org/articles/PMC10933815?pdf=render
-37705296,https://doi.org/10.1002/sim.9898,Using temporal recalibration to improve the calibration of risk prediction models in competing risk settings when there are trends in survival over time.,"Booth S, Mozumder SI, Archer L, Ensor J, Riley RD, Lambert PC, Rutherford MJ.",,Statistics in medicine,2023,2023-09-13,Y,calibration; Risk Prediction; Competing Risks; Temporal Recalibration; Prognostic Models,,,"We have previously proposed temporal recalibration to account for trends in survival over time to improve the calibration of predictions from prognostic models for new patients. This involves first estimating the predictor effects using data from all individuals (full dataset) and then re-estimating the baseline using a subset of the most recent data whilst constraining the predictor effects to remain the same. In this article, we demonstrate how temporal recalibration can be applied in competing risk settings by recalibrating each cause-specific (or subdistribution) hazard model separately. We illustrate this using an example of colon cancer survival with data from the Surveillance Epidemiology and End Results (SEER) program. Data from patients diagnosed in 1995-2004 were used to fit two models for deaths due to colon cancer and other causes respectively. We discuss considerations that need to be made in order to apply temporal recalibration such as the choice of data used in the recalibration step. We also demonstrate how to assess the calibration of these models in new data for patients diagnosed subsequently in 2005. Comparison was made to a standard analysis (when improvements over time are not taken into account) and a period analysis which is similar to temporal recalibration but differs in the data used to estimate the predictor effects. The 10-year calibration plots demonstrated that using the standard approach over-estimated the risk of death due to colon cancer and the total risk of death and that calibration was improved using temporal recalibration or period analysis.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/sim.9898; doi:https://doi.org/10.1002/sim.9898; html:https://europepmc.org/articles/PMC10946485; pdf:https://europepmc.org/articles/PMC10946485?pdf=render
-31481394,https://doi.org/10.1136/bmj.l4892,"Thyroid replacement therapy, thyroid stimulating hormone concentrations, and long term health outcomes in patients with hypothyroidism: longitudinal study.","Thayakaran R, Adderley NJ, Sainsbury C, Torlinska B, Boelaert K, Šumilo D, Price M, Thomas GN, Toulis KA, Nirantharakumar K.",,BMJ (Clinical research ed.),2019,2019-09-03,Y,,Understanding the Causes of Disease,,"<h4>Objective</h4>To explore whether thyroid stimulating hormone (TSH) concentration in patients with a diagnosis of hypothyroidism is associated with increased all cause mortality and a higher risk of cardiovascular disease and fractures.<h4>Design</h4>Retrospective cohort study.<h4>Setting</h4>The Health Improvement Network (THIN), a database of electronic patient records from UK primary care.<h4>Participants</h4>Adult patients with incident hypothyroidism from 1 January 1995 to 31 December 2017.<h4>Exposure</h4>TSH concentration in patients with hypothyroidism.<h4>Main outcome measures</h4>Ischaemic heart disease, heart failure, stroke/transient ischaemic attack, atrial fibrillation, any fractures, fragility fractures, and mortality. Longitudinal TSH measurements from diagnosis to outcomes, study end, or loss to follow-up were collected. An extended Cox proportional hazards model with TSH considered as a time varying covariate was fitted for each outcome.<h4>Results</h4>162 369 patients with hypothyroidism and 863 072 TSH measurements were included in the analysis. Compared with the reference TSH category (2-2.5 mIU/L), risk of ischaemic heart disease and heart failure increased at high TSH concentrations (>10 mIU/L) (hazard ratio 1.18 (95% confidence interval 1.02 to 1.38; P=0.03) and 1.42 (1.21 to 1.67; P<0.001), respectively). A protective effect for heart failure was seen at low TSH concentrations (hazard ratio 0.79 (0.64 to 0.99; P=0.04) for TSH <0.1 mIU/L and 0.76 (0.62 to 0.92; P=0.006) for 0.1-0.4 mIU/L). Increased mortality was observed in both the lowest and highest TSH categories (hazard ratio 1.18 (1.08 to 1.28; P<0.001), 1.29 (1.22 to 1.36; P<0.001), and 2.21 (2.07 to 2.36; P<0.001) for TSH <0.1 mIU/L, 4-10 mIU/L, and >10 mIU/L. An increase in the risk of fragility fractures was observed in patients in the highest TSH category (>10 mIU/L) (hazard ratio 1.15 (1.01 to 1.31; P=0.03)).<h4>Conclusions</h4>In patients with a diagnosis of hypothyroidism, no evidence was found to suggest a clinically meaningful difference in the pattern of long term health outcomes (all cause mortality, atrial fibrillation, ischaemic heart disease, heart failure, stroke/transient ischaemic attack, fractures) when TSH concentrations were within recommended normal limits. Evidence was found for adverse health outcomes when TSH concentration is outside this range, particularly above the upper reference value.",,pdf:https://www.bmj.com/content/bmj/366/bmj.l4892.full.pdf; doi:https://doi.org/10.1136/bmj.l4892; html:https://europepmc.org/articles/PMC6719286
 31089183,https://doi.org/10.1038/s41598-019-43861-9,Genetic variation in CADM2 as a link between psychological traits and obesity.,"Morris J, Bailey MES, Baldassarre D, Cullen B, de Faire U, Ferguson A, Gigante B, Giral P, Goel A, Graham N, Hamsten A, Humphries SE, Johnston KJA, Lyall DM, Lyall LM, Sennblad B, Silveira A, Smit AJ, Tremoli E, Veglia F, Ward J, Watkins H, Smith DJ, Strawbridge RJ.",,Scientific reports,2019,2019-05-14,Y,,Understanding the Causes of Disease,,"CADM2 has been associated with a range of behavioural and metabolic traits, including physical activity, risk-taking, educational attainment, alcohol and cannabis use and obesity. Here, we set out to determine whether CADM2 contributes to mechanisms shared between mental and physical health disorders. We assessed genetic variants in the CADM2 locus for association with phenotypes in the UK Biobank, IMPROVE, PROCARDIS and SCARFSHEEP studies, before performing meta-analyses. A wide range of metabolic phenotypes were meta-analysed. Psychological phenotypes analysed in UK Biobank only were major depressive disorder, generalised anxiety disorder, bipolar disorder, neuroticism, mood instability and risk-taking behaviour. In UK Biobank, four, 88 and 172 genetic variants were significantly (p < 1 × 10<sup>-5</sup>) associated with neuroticism, mood instability and risk-taking respectively. In meta-analyses of 4 cohorts, we identified 362, 63 and 11 genetic variants significantly (p < 1 × 10<sup>-5</sup>) associated with BMI, SBP and CRP respectively. Genetic effects on BMI, CRP and risk-taking were all positively correlated, and were consistently inversely correlated with genetic effects on SBP, mood instability and neuroticism. Conditional analyses suggested an overlap in the signals for physical and psychological traits. Many significant variants had genotype-specific effects on CADM2 expression levels in adult brain and adipose tissues. CADM2 variants influence a wide range of both psychological and metabolic traits, suggesting common biological mechanisms across phenotypes via regulation of CADM2 expression levels in adipose tissue. Functional studies of CADM2 are required to fully understand mechanisms connecting mental and physical health conditions.",,pdf:https://www.nature.com/articles/s41598-019-43861-9.pdf; doi:https://doi.org/10.1038/s41598-019-43861-9; html:https://europepmc.org/articles/PMC6517397; pdf:https://europepmc.org/articles/PMC6517397?pdf=render
+31481394,https://doi.org/10.1136/bmj.l4892,"Thyroid replacement therapy, thyroid stimulating hormone concentrations, and long term health outcomes in patients with hypothyroidism: longitudinal study.","Thayakaran R, Adderley NJ, Sainsbury C, Torlinska B, Boelaert K, Šumilo D, Price M, Thomas GN, Toulis KA, Nirantharakumar K.",,BMJ (Clinical research ed.),2019,2019-09-03,Y,,Understanding the Causes of Disease,,"<h4>Objective</h4>To explore whether thyroid stimulating hormone (TSH) concentration in patients with a diagnosis of hypothyroidism is associated with increased all cause mortality and a higher risk of cardiovascular disease and fractures.<h4>Design</h4>Retrospective cohort study.<h4>Setting</h4>The Health Improvement Network (THIN), a database of electronic patient records from UK primary care.<h4>Participants</h4>Adult patients with incident hypothyroidism from 1 January 1995 to 31 December 2017.<h4>Exposure</h4>TSH concentration in patients with hypothyroidism.<h4>Main outcome measures</h4>Ischaemic heart disease, heart failure, stroke/transient ischaemic attack, atrial fibrillation, any fractures, fragility fractures, and mortality. Longitudinal TSH measurements from diagnosis to outcomes, study end, or loss to follow-up were collected. An extended Cox proportional hazards model with TSH considered as a time varying covariate was fitted for each outcome.<h4>Results</h4>162 369 patients with hypothyroidism and 863 072 TSH measurements were included in the analysis. Compared with the reference TSH category (2-2.5 mIU/L), risk of ischaemic heart disease and heart failure increased at high TSH concentrations (>10 mIU/L) (hazard ratio 1.18 (95% confidence interval 1.02 to 1.38; P=0.03) and 1.42 (1.21 to 1.67; P<0.001), respectively). A protective effect for heart failure was seen at low TSH concentrations (hazard ratio 0.79 (0.64 to 0.99; P=0.04) for TSH <0.1 mIU/L and 0.76 (0.62 to 0.92; P=0.006) for 0.1-0.4 mIU/L). Increased mortality was observed in both the lowest and highest TSH categories (hazard ratio 1.18 (1.08 to 1.28; P<0.001), 1.29 (1.22 to 1.36; P<0.001), and 2.21 (2.07 to 2.36; P<0.001) for TSH <0.1 mIU/L, 4-10 mIU/L, and >10 mIU/L. An increase in the risk of fragility fractures was observed in patients in the highest TSH category (>10 mIU/L) (hazard ratio 1.15 (1.01 to 1.31; P=0.03)).<h4>Conclusions</h4>In patients with a diagnosis of hypothyroidism, no evidence was found to suggest a clinically meaningful difference in the pattern of long term health outcomes (all cause mortality, atrial fibrillation, ischaemic heart disease, heart failure, stroke/transient ischaemic attack, fractures) when TSH concentrations were within recommended normal limits. Evidence was found for adverse health outcomes when TSH concentration is outside this range, particularly above the upper reference value.",,pdf:https://www.bmj.com/content/bmj/366/bmj.l4892.full.pdf; doi:https://doi.org/10.1136/bmj.l4892; html:https://europepmc.org/articles/PMC6719286
+37705296,https://doi.org/10.1002/sim.9898,Using temporal recalibration to improve the calibration of risk prediction models in competing risk settings when there are trends in survival over time.,"Booth S, Mozumder SI, Archer L, Ensor J, Riley RD, Lambert PC, Rutherford MJ.",,Statistics in medicine,2023,2023-09-13,Y,calibration; Risk Prediction; Competing Risks; Temporal Recalibration; Prognostic Models,,,"We have previously proposed temporal recalibration to account for trends in survival over time to improve the calibration of predictions from prognostic models for new patients. This involves first estimating the predictor effects using data from all individuals (full dataset) and then re-estimating the baseline using a subset of the most recent data whilst constraining the predictor effects to remain the same. In this article, we demonstrate how temporal recalibration can be applied in competing risk settings by recalibrating each cause-specific (or subdistribution) hazard model separately. We illustrate this using an example of colon cancer survival with data from the Surveillance Epidemiology and End Results (SEER) program. Data from patients diagnosed in 1995-2004 were used to fit two models for deaths due to colon cancer and other causes respectively. We discuss considerations that need to be made in order to apply temporal recalibration such as the choice of data used in the recalibration step. We also demonstrate how to assess the calibration of these models in new data for patients diagnosed subsequently in 2005. Comparison was made to a standard analysis (when improvements over time are not taken into account) and a period analysis which is similar to temporal recalibration but differs in the data used to estimate the predictor effects. The 10-year calibration plots demonstrated that using the standard approach over-estimated the risk of death due to colon cancer and the total risk of death and that calibration was improved using temporal recalibration or period analysis.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/sim.9898; doi:https://doi.org/10.1002/sim.9898; html:https://europepmc.org/articles/PMC10946485; pdf:https://europepmc.org/articles/PMC10946485?pdf=render
 33036417,https://doi.org/10.3390/ijerph17197320,"Prognostic Role of Demographic, Injury and Claim Factors in Disabling Pain and Mental Health Conditions 12 Months after Compensable Injury.","Nguyen TL, Baker KS, Ioannou L, Hassani-Mahmooei B, Gibson SJ, Collie A, Ponsford J, Cameron PA, Gabbe BJ, Giummarra MJ.",,International journal of environmental research and public health,2020,2020-10-07,Y,Injury; Pain; Compensation; Mental health; Insurance; Disability; Traumatic Injury,,,"Identifying who might develop disabling pain or poor mental health after injury is a high priority so that healthcare providers can provide targeted preventive interventions. This retrospective cohort study aimed to identify predictors of disabling pain or probable mental health conditions at 12 months post-injury. Participants were recruited 12-months after admission to a major trauma service for a compensable transport or workplace injury (<i>n</i> = 157). Injury, compensation claim, health services and medication information were obtained from the Victorian Orthopaedic Trauma Outcome Registry, Victorian State Trauma Registry and Compensation Research Database. Participants completed questionnaires about pain, and mental health (anxiety, depression, posttraumatic stress disorder) at 12 months post-injury. One third had disabling pain, one third had at least one probable mental health condition and more than one in five had both disabling pain and a mental health condition at 12 months post-injury. Multivariable logistic regression found mental health treatment 3-6 months post-injury, persistent work disability and opioid use at 6-12 months predicted disabling pain at 12 months post-injury. The presence of opioid use at 3-6 months, work disability and psychotropic medications at 6-12 months predicted a mental health condition at 12 months post-injury. These factors could be used to identify at risk of developing disabling pain who could benefit from timely interventions to better manage both pain and mental health post-injury. Implications for healthcare and compensation system are discussed.",,pdf:https://www.mdpi.com/1660-4601/17/19/7320/pdf?version=1602228180; doi:https://doi.org/10.3390/ijerph17197320; html:https://europepmc.org/articles/PMC7579145; pdf:https://europepmc.org/articles/PMC7579145?pdf=render
 33933530,https://doi.org/10.1016/j.jinf.2021.04.027,Early observations on the impact of a healthcare worker COVID-19 vaccination programme at a major UK tertiary centre.,"Garvey MI, Wilkinson MAC, Holden E, Shields A, Robertson A, Richter A, Ball S.",,The Journal of infection,2021,2021-04-29,Y,Vaccination; Healthcare Workers; Lateral Flow; Covid-19,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8081749; doi:https://doi.org/10.1016/j.jinf.2021.04.027; html:https://europepmc.org/articles/PMC8081749; pdf:https://europepmc.org/articles/PMC8081749?pdf=render
-34939832,https://doi.org/10.1308/rcsann.2021.0206,"Projections for primary hip and knee replacement surgery up to the year 2060: an analysis based on data from The National Joint Registry for England, Wales, Northern Ireland and the Isle of Man.","Matharu GS, Culliford DJ, Blom AW, Judge A.",,Annals of the Royal College of Surgeons of England,2022,2021-12-23,N,Total hip replacement; Total Knee Replacement; Demand; Future Numbers,,,"<h4>Introduction</h4>We estimated the number of primary total hip and knee replacements (THR and TKR) that will need to be performed up to the year 2060.<h4>Methods</h4>We used data from The National Joint Registry for England, Wales, Northern Ireland and the Isle of Man on the volume of primary THRs (<i>n</i>=94,936) and TKRs (<i>n</i>=100,547) performed in 2018. We projected future numbers of THR and TKR using a static estimated rate from 2018 applied to population growth forecast data from the UK Office for National Statistics up to 2060.<h4>Results</h4>By 2060, THR and TKR volume would increase from 2018 levels by an estimated 37.7% (<i>n</i>=130,766) and 36.6% (<i>n</i>=137,341), respectively. For both males and females demand for surgery was also higher for patients aged 70 and over, with older patients having the biggest relative increase in volume over time: 70-79 years (44.6% males, 41.2% females); 80-89 years (112.4% males, 85.6% females); 90 years and older (348.0% males, 198.2% females).<h4>Conclusion</h4>By 2060 demand for hip and knee joint replacement is estimated to increase by almost 40%. Demand will be greatest in older patients (70+ years), which will have significant implications for the health service requiring forward planning given that morbidity and resource use is higher in this population. These issues, coupled with two waves of COVID-19, will impact the ability of health services to deliver timely joint replacement to many patients for a number of years, requiring urgent planning.",,doi:https://doi.org/10.1308/rcsann.2021.0206; html:https://europepmc.org/articles/PMC9157920; pdf:https://europepmc.org/articles/PMC9157920?pdf=render; doi:https://doi.org/10.1308/rcsann.2021.0206
 31964672,https://doi.org/10.1136/bmjopen-2019-033318,"Educational differentials in key domains of physical activity by ethnicity, age and sex: a cross-sectional study of over 40 000 participants in the UK household longitudinal study (2013-2015).","Fluharty ME, Pinto Pereira SM, Benzeval M, Hamer M, Jefferis B, Griffiths LJ, Cooper R, Bann D.",,BMJ open,2020,2020-01-20,Y,epidemiology; Physical Activity; Health Disparities,Improving Public Health,,"<h4>Objectives</h4>To assess whether educational differentials in three key physical activity (PA) domains vary by age, sex and ethnicity.<h4>Design</h4>National cross-sectional survey.<h4>Setting</h4>UK.<h4>Participants</h4>Altogether 40 270 participants, aged 20 years and over, from the UK Household Longitudinal Study with information on education, PA and demographics collected in 2013-2015.<h4>Outcome measures</h4>Participation in active travel (AT), occupational activity (OA) and leisure time physical activity (LTPA) at the time of assessment.<h4>Results</h4>Lower educational attainment was associated with higher AT and OA, but lower weekly LTPA activity; these associations were modified by sex, ethnicity and age. Education-related differences in AT were larger for women-the difference in predicted probability of activity between the highest and the lowest education groups was -10% in women (95% CI: -11.9% to 7.9%) and -3% in men (-4.8% to -0.4%). Education-related differences in OA were larger among men -35% (-36.9% to -32.4%) than women -17% (-19.4% to -15.0%). Finally, education-related differences in moderate-to-vigorous LTPA varied by ethnicity; for example, differences were 17% (16.2% to 18.7%) for white individuals compared with 6% (0.6% to 11.6%) for black individuals.<h4>Conclusions</h4>Educational differences in PA vary by domain and are modified by age, sex and ethnicity. A better understanding of physically inactive subgroups may aid development of interventions to both increase activity levels and reduce health inequalities.","This study which includes over 40 thousant adults in the UK, aims to assess whether there are links between different levels of physical activity and educational achievements. It found that lower educational achievement was associated with higher travel and work related physical activity, but not leisure time activity. They found this difference to be larger in men than in women, and also in white compared to black individuals.",pdf:https://bmjopen.bmj.com/content/bmjopen/10/1/e033318.full.pdf; doi:https://doi.org/10.1136/bmjopen-2019-033318; html:https://europepmc.org/articles/PMC7045199; pdf:https://europepmc.org/articles/PMC7045199?pdf=render
+34939832,https://doi.org/10.1308/rcsann.2021.0206,"Projections for primary hip and knee replacement surgery up to the year 2060: an analysis based on data from The National Joint Registry for England, Wales, Northern Ireland and the Isle of Man.","Matharu GS, Culliford DJ, Blom AW, Judge A.",,Annals of the Royal College of Surgeons of England,2022,2021-12-23,N,Total hip replacement; Total Knee Replacement; Demand; Future Numbers,,,"<h4>Introduction</h4>We estimated the number of primary total hip and knee replacements (THR and TKR) that will need to be performed up to the year 2060.<h4>Methods</h4>We used data from The National Joint Registry for England, Wales, Northern Ireland and the Isle of Man on the volume of primary THRs (<i>n</i>=94,936) and TKRs (<i>n</i>=100,547) performed in 2018. We projected future numbers of THR and TKR using a static estimated rate from 2018 applied to population growth forecast data from the UK Office for National Statistics up to 2060.<h4>Results</h4>By 2060, THR and TKR volume would increase from 2018 levels by an estimated 37.7% (<i>n</i>=130,766) and 36.6% (<i>n</i>=137,341), respectively. For both males and females demand for surgery was also higher for patients aged 70 and over, with older patients having the biggest relative increase in volume over time: 70-79 years (44.6% males, 41.2% females); 80-89 years (112.4% males, 85.6% females); 90 years and older (348.0% males, 198.2% females).<h4>Conclusion</h4>By 2060 demand for hip and knee joint replacement is estimated to increase by almost 40%. Demand will be greatest in older patients (70+ years), which will have significant implications for the health service requiring forward planning given that morbidity and resource use is higher in this population. These issues, coupled with two waves of COVID-19, will impact the ability of health services to deliver timely joint replacement to many patients for a number of years, requiring urgent planning.",,doi:https://doi.org/10.1308/rcsann.2021.0206; html:https://europepmc.org/articles/PMC9157920; pdf:https://europepmc.org/articles/PMC9157920?pdf=render; doi:https://doi.org/10.1308/rcsann.2021.0206
 32393804,https://doi.org/10.1038/s41591-020-0916-2,Real-time tracking of self-reported symptoms to predict potential COVID-19.,"Menni C, Valdes AM, Freidin MB, Sudre CH, Nguyen LH, Drew DA, Ganesh S, Varsavsky T, Cardoso MJ, El-Sayed Moustafa JS, Visconti A, Hysi P, Bowyer RCE, Mangino M, Falchi M, Wolf J, Ourselin S, Chan AT, Steves CJ, Spector TD.",,Nature medicine,2020,2020-05-11,N,,,,"A total of 2,618,862 participants reported their potential symptoms of COVID-19 on a smartphone-based app. Among the 18,401 who had undergone a SARS-CoV-2 test, the proportion of participants who reported loss of smell and taste was higher in those with a positive test result (4,668 of 7,178 individuals; 65.03%) than in those with a negative test result (2,436 of 11,223 participants; 21.71%) (odds ratio = 6.74; 95% confidence interval = 6.31-7.21). A model combining symptoms to predict probable infection was applied to the data from all app users who reported symptoms (805,753) and predicted that 140,312 (17.42%) participants are likely to have COVID-19.",,pdf:https://www.nature.com/articles/s41591-020-0916-2.pdf; doi:https://doi.org/10.1038/s41591-020-0916-2; html:https://europepmc.org/articles/PMC7751267; pdf:https://europepmc.org/articles/PMC7751267?pdf=render; doi:https://doi.org/10.1038/s41591-020-0916-2
 33824163,https://doi.org/10.3399/bjgp20x714161,Post-bariatric surgery nutritional follow-up in primary care: a population-based cohort study.,"Parretti HM, Subramanian A, Adderley NJ, Abbott S, Tahrani AA, Nirantharakumar K.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2021,2021-05-27,Y,Nutrition; Followup; Cohort studies; General Practice; Bariatric Surgery; The Health Improvement Network,,,"<h4>Background</h4>Bariatric surgery is the most effective treatment for severe obesity. However, without recommended follow-up it has long-term risks.<h4>Aim</h4>To investigate whether nutritional and weight monitoring in primary care meets current clinical guidance, after patients are discharged from specialist bariatric care.<h4>Design and setting</h4>Retrospective cohort study in primary care practices contributing to IQVIA Medical Research Data in the UK (1 January 2000 to 17 January 2018).<h4>Method</h4>Participants were adults who had had bariatric surgery with a minimum of 3 years' follow-up post-surgery, as this study focused on patients discharged from specialist care (at 2 years post-surgery). Outcomes were the annual proportion of patients from 2 years post-surgery with a record of recommended nutritional screening blood tests, weight measurement, and prescription of nutritional supplements, and the proportions with nutritional deficiencies based on blood tests.<h4>Results</h4>A total of 3137 participants were included in the study, and median follow-up post-surgery was 5.7 (4.2-7.6) years. Between 45% and 59% of these patients had an annual weight measurement. The greatest proportions of patients with a record of annual nutritional blood tests were for tests routinely conducted in primary care, for example, recorded haemoglobin measurement varied between 44.9% (<i>n</i> = 629/1400) and 61.2% (<i>n</i> = 653/1067). Annual proportions of blood tests specific to bariatric surgery were low, for example, recorded copper measurement varied between 1.2% (<i>n</i> = 10/818) and 1.5% (<i>n</i> = 16/1067) where recommended. Results indicated that the most common deficiency was anaemia. Annual proportions of patients with prescriptions for recommended nutritional supplements were low.<h4>Conclusion</h4>This study suggests that patients who have bariatric surgery are not receiving the recommended nutritional monitoring after discharge from specialist care. GPs and patients should be supported to engage with follow-up care. Future research should aim to understand the reasons underpinning these findings.",,pdf:https://bjgp.org/content/bjgp/71/707/e441.full.pdf; doi:https://doi.org/10.3399/bjgp20X714161; html:https://europepmc.org/articles/PMC8041293; pdf:https://europepmc.org/articles/PMC8041293?pdf=render
 37814896,https://doi.org/10.1161/circgen.123.004181,Cardiovascular Disease Knowledge Portal: A Community Resource for Cardiovascular Disease Research.,"Costanzo MC, Roselli C, Brandes M, Duby M, Hoang Q, Jang D, Koesterer R, Kudtarkar P, Moriondo A, Nguyen T, Ruebenacker O, Smadbeck P, Sun Y, Butterworth AS, Aragam KG, Lumbers RT, Khera AV, Lubitz SA, Ellinor PT, Gaulton KJ, Flannick J, Burtt NP.",,Circulation. Genomic and precision medicine,2023,2023-10-10,N,Cardiovascular diseases; Database; Phenotype; Myocardial infarction; Biomarkers; epigenomics,,,,,pdf:https://research.rug.nl/files/909109629/costanzo-et-al-2023-cardiovascular-disease-knowledge-portal-a-community-resource-for-cardiovascular-disease-research.pdf; doi:https://doi.org/10.1161/CIRCGEN.123.004181
@@ -1890,58 +1892,58 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 39145103,https://doi.org/10.3310/nihropenres.13558.1,Planned and unplanned hospital admissions and health-related school absence rates in children with neurodisability: Protocol for a population-based study using linked education and hospital data from England.,"Gimeno L, Zylbersztejn A, Cant A, Harron K, Gilbert R.",,NIHR open research,2024,2024-05-01,Y,Electronic Health Records; Hospital Admissions; Linked Data; School Absence; Neurodisability,,,"<h4>Background</h4>Neurodisability describes a broad set of conditions affecting the brain and nervous system which result in functional limitations. Children with neurodisability have more hospital admissions than their peers without neurodisability and higher rates of school absence. However, longitudinal evidence comparing rates of hospital admission and school absence in children with neurodisability to peers without neurodisability throughout school is limited, as is understanding about whether differences are greatest for planned care (e.g., scheduled appointments) or unplanned care. This study will describe rates of planned and unplanned hospital admissions and school absence due to illness and medical reasons throughout primary school (Reception to Year 6, ages 4 to 11 in England) for children with neurodisability and all other children, using linked individual-level health and education data.<h4>Methods</h4>We will use the ECHILD (Education and Child Insights from Linked Data) database, which links educational and health records across England. We will define a primary school cohort of children who were born in National Health Service-funded hospitals in England between 1 <sup>st</sup> September 2003 and 31 <sup>st</sup> August 2008, and who were enrolled in Reception (age 4/5) at state-funded schools. We will use hospital admissions records to identify children who have recorded indicators of neurodisability from birth up to the end of primary school (Year 6, age 10/11).<h4>Results</h4>We will describe rates of planned and unplanned hospital admissions and health-related school absence for three groups of children: those with a neurodisability indicator first recorded before beginning primary school, those with neurodisability first recorded during primary school, and those without a record of neurodisability before end of primary school.<h4>Conclusions</h4>We will further explore whether differences between these group vary across primary school years and by socioeconomic and demographic characteristics.",,doi:https://doi.org/10.3310/nihropenres.13558.1; html:https://europepmc.org/articles/PMC11319901; pdf:https://europepmc.org/articles/PMC11319901?pdf=render
 36063293,https://doi.org/10.1186/s12348-022-00304-3,Evaluating patient-reported outcome measures (PROMs) for clinical trials and clinical practice in adult patients with uveitis or scleritis: a systematic review.,"O'Donovan C, Panthagani J, Aiyegbusi OL, Liu X, Bayliss S, Calvert M, Pesudovs K, Denniston A, Moore D, Braithwaite T.",,Journal of ophthalmic inflammation and infection,2022,2022-09-05,Y,,,,"Patient reported outcome measures (PROMs) capture impact of disease and treatment on quality of life, and have an emerging role in clinical trial outcome measurement. This study included a systematic review and quality appraisal of PROMs developed or validated for use in adults with uveitis or scleritis. We searched MEDLINE, EMBASE, PsycINFO, CINAHL and grey literature sources, to 5 November 2021. We used established quality criteria to grade each PROM instrument in multiple domains from A (high quality) to C (low quality), and assessed content development, validity, reliability and responsiveness. For instruments developed using classic test theory-based psychometric approaches, we assessed acceptability, item targeting and internal consistency. For instruments developed using Item Response Theory (IRT) (e.g. Rasch analysis), we assessed response categories, dimensionality, measurement precision, item fit statistics, differential item functioning and targeting. We identified and appraised four instruments applicable to certain uveitis types, but none for scleritis. Specifically, the National Eye Institute Visual Function Questionnaire-25 (NEI-VFQ), a 3-part PROM for Birdshot retinochoroiditis (Birdshot Disease & Medication Symptoms Questionnaire [BD&MSQ], the quality of life (QoL) impact of Birdshot Chorioretinopathy [QoL BCR], and the QoL impact of BCR medication [QoL Meds], the Kings Sarcoidosis Questionnaire (KSQ), and a PROM for cytomegalovirus retinitis. These instruments had limited coverage for these heterogeneous conditions, with a focus on very rare subtypes. Psychometric appraisal revealed considerable variability between instruments, limited content development, and only one developed using Item Response Theory. In conclusion, there are few validated PROMs for patients with uveitis and none for scleritis, and existing instruments have suboptimal psychometric performance. We articulate why we do not recommend their inclusion as clinical trial outcome measures for drug licensing purposes, and highlight an unmet need for PROMs applicable to uveitis and scleritis.",,pdf:https://joii-journal.springeropen.com/counter/pdf/10.1186/s12348-022-00304-3; doi:https://doi.org/10.1186/s12348-022-00304-3; html:https://europepmc.org/articles/PMC9443634; pdf:https://europepmc.org/articles/PMC9443634?pdf=render
 39048560,https://doi.org/10.1038/s41467-024-50297-x,"Causal relevance of different blood pressure traits on risk of cardiovascular diseases: GWAS and Mendelian randomisation in 100,000 Chinese adults.","Pozarickij A, Gan W, Lin K, Clarke R, Fairhurst-Hunter Z, Koido M, Kanai M, Okada Y, Kamatani Y, Bennett D, Du H, Chen Y, Yang L, Avery D, Guo Y, Yu M, Yu C, Schmidt Valle D, Lv J, Chen J, Peto R, Collins R, Li L, Chen Z, Millwood IY, Walters RG, China Kadoorie Biobank Collaborative Group.",,Nature communications,2024,2024-07-24,Y,,,,"Elevated blood pressure (BP) is major risk factor for cardiovascular diseases (CVD). Genome-wide association studies (GWAS) conducted predominantly in populations of European ancestry have identified >2,000 BP-associated loci, but other ancestries have been less well-studied. We conducted GWAS of systolic, diastolic, pulse, and mean arterial BP in 100,453 Chinese adults. We identified 128 non-overlapping loci associated with one or more BP traits, including 74 newly-reported associations. Despite strong genetic correlations between populations, we identified appreciably higher heritability and larger variant effect sizes in Chinese compared with European or Japanese ancestry populations. Using instruments derived from these GWAS, multivariable Mendelian randomisation demonstrated that BP traits contribute differently to the causal associations of BP with CVD. In particular, only pulse pressure was independently causally associated with carotid plaque. These findings reinforce the need for studies in diverse populations to understand the genetic determinants of BP traits and their roles in disease risk.",,doi:https://doi.org/10.1038/s41467-024-50297-x; html:https://europepmc.org/articles/PMC11269703; pdf:https://europepmc.org/articles/PMC11269703?pdf=render
-38198570,https://doi.org/10.1126/scitranslmed.adf4428,Prospective study design and data analysis in UK Biobank.,"Allen NE, Lacey B, Lawlor DA, Pell JP, Gallacher J, Smeeth L, Elliott P, Matthews PM, Lyons RA, Whetton AD, Lucassen A, Hurles ME, Chapman M, Roddam AW, Fitzpatrick NK, Hansell AL, Hardy R, Marioni RE, O'Donnell VB, Williams J, Lindgren CM, Effingham M, Sellors J, Danesh J, Collins R.",,Science translational medicine,2024,2024-01-10,N,,,,"Population-based prospective studies, such as UK Biobank, are valuable for generating and testing hypotheses about the potential causes of human disease. We describe how UK Biobank's study design, data access policies, and approaches to statistical analysis can help to minimize error and improve the interpretability of research findings, with implications for other population-based prospective studies being established worldwide.",,pdf:https://www.pure.ed.ac.uk/ws/files/405264227/scitranslmed.adf4428.pdf; doi:https://doi.org/10.1126/scitranslmed.adf4428
 38597854,https://doi.org/10.1016/j.jcmg.2024.03.001,Noninvasive Techniques for Tracking Biological Aging of the Cardiovascular System: JACC Family Series.,"Raisi-Estabragh Z, Szabo L, Schuermans A, Salih AM, Chin CWL, Vágó H, Altmann A, Ng FS, Garg P, Pavanello S, Marwick TH, Petersen SE.",,JACC. Cardiovascular imaging,2024,2024-04-08,N,Molecular markers; Echocardiography; Cardiac Computed Tomography; Healthy Aging; Cardiac Magnetic Resonance; Multimodality Cardiovascular Imaging; Biological Heart Age,,,"Population aging is one of the most important demographic transformations of our time. Increasing the ""health span""-the proportion of life spent in good health-is a global priority. Biological aging comprises molecular and cellular modifications over many years, which culminate in gradual physiological decline across multiple organ systems and predispose to age-related illnesses. Cardiovascular disease is a major cause of ill health and premature death in older people. The rate at which biological aging occurs varies across individuals of the same age and is influenced by a wide range of genetic and environmental exposures. The authors review the hallmarks of biological cardiovascular aging and their capture using imaging and other noninvasive techniques and examine how this information may be used to understand aging trajectories, with the aim of guiding individual- and population-level interventions to promote healthy aging.",,doi:https://doi.org/10.1016/j.jcmg.2024.03.001; doi:https://doi.org/10.1016/j.jcmg.2024.03.001
+38198570,https://doi.org/10.1126/scitranslmed.adf4428,Prospective study design and data analysis in UK Biobank.,"Allen NE, Lacey B, Lawlor DA, Pell JP, Gallacher J, Smeeth L, Elliott P, Matthews PM, Lyons RA, Whetton AD, Lucassen A, Hurles ME, Chapman M, Roddam AW, Fitzpatrick NK, Hansell AL, Hardy R, Marioni RE, O'Donnell VB, Williams J, Lindgren CM, Effingham M, Sellors J, Danesh J, Collins R.",,Science translational medicine,2024,2024-01-10,N,,,,"Population-based prospective studies, such as UK Biobank, are valuable for generating and testing hypotheses about the potential causes of human disease. We describe how UK Biobank's study design, data access policies, and approaches to statistical analysis can help to minimize error and improve the interpretability of research findings, with implications for other population-based prospective studies being established worldwide.",,pdf:https://www.pure.ed.ac.uk/ws/files/405264227/scitranslmed.adf4428.pdf; doi:https://doi.org/10.1126/scitranslmed.adf4428
 33310109,https://doi.org/10.1016/j.ijid.2020.12.006,"Response to ""Early hydroxychloroquine but not chloroquine use reduces ICU admission in COVID-19 patients"".","Linschoten M, Nab L, van der Horst ICC, Tieleman R, Asselbergs FW.",,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2021,2020-12-09,Y,,,,,,pdf:http://www.ijidonline.com/article/S1201971220325297/pdf; doi:https://doi.org/10.1016/j.ijid.2020.12.006; html:https://europepmc.org/articles/PMC7725132; pdf:https://europepmc.org/articles/PMC7725132?pdf=render
 34596018,https://doi.org/10.2807/1560-7917.es.2021.26.39.2001440,"Strategies to reduce the risk of SARS-CoV-2 importation from international travellers: modelling estimations for the United Kingdom, July 2020.","Clifford S, Quilty BJ, Russell TW, Liu Y, Chan YD, Pearson CAB, Eggo RM, Endo A, CMMID COVID-19 Working Group, Flasche S, Edmunds WJ, Centre for Mathematical Modelling of Infectious Diseases (CMMID) COVID-19 Working Group.",,Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin,2021,2021-09-01,Y,Quarantine; Pcr Testing; Travel Screening; Covid-19; Sars-cov-2,,,"BackgroundTo mitigate SARS-CoV-2 transmission risks from international air travellers, many countries implemented a combination of up to 14 days of self-quarantine upon arrival plus PCR testing in the early stages of the COVID-19 pandemic in 2020.AimTo assess the effectiveness of quarantine and testing of international travellers to reduce risk of onward SARS-CoV-2 transmission into a destination country in the pre-COVID-19 vaccination era.MethodsWe used a simulation model of air travellers arriving in the United Kingdom from the European Union or the United States, incorporating timing of infection stages while varying quarantine duration and timing and number of PCR tests.ResultsQuarantine upon arrival with a PCR test on day 7 plus a 1-day delay for results can reduce the number of infectious arriving travellers released into the community by a median 94% (95% uncertainty interval (UI): 89-98) compared with a no quarantine/no test scenario. This reduction is similar to that achieved by a 14-day quarantine period (median > 99%; 95% UI: 98-100). Even shorter quarantine periods can prevent a substantial amount of transmission; all strategies in which travellers spend at least 5 days (mean incubation period) in quarantine and have at least one negative test before release are highly effective (median reduction 89%; 95% UI: 83-95)).ConclusionThe effect of different screening strategies impacts asymptomatic and symptomatic individuals differently. The choice of an optimal quarantine and testing strategy for unvaccinated air travellers may vary based on the number of possible imported infections relative to domestic incidence.",,pdf:https://www.eurosurveillance.org/deliver/fulltext/eurosurveillance/26/39/eurosurv-26-39-5.pdf?itemId=%2Fcontent%2F10.2807%2F1560-7917.ES.2021.26.39.2001440&mimeType=pdf&containerItemId=content/eurosurveillance; doi:https://doi.org/10.2807/1560-7917.ES.2021.26.39.2001440; html:https://europepmc.org/articles/PMC8485583; pdf:https://europepmc.org/articles/PMC8485583?pdf=render
 37201609,https://doi.org/10.1016/j.ijcard.2023.05.024,Identifying distinct clinical clusters in heart failure with mildly reduced ejection fraction.,"Meijs C, Brugts JJ, Lund LH, Linssen GCM, Rocca HB, Dahlström U, Vaartjes I, Koudstaal S, Asselbergs FW, Savarese G, Uijl A.",,International journal of cardiology,2023,2023-05-16,N,Heterogeneity; Clustering; Latent Class Analysis; Heart Failure With Mildly Reduced Ejection Fraction,,,"<h4>Introduction</h4>Heart failure (HF) is a heterogeneous syndrome, and the specific sub-category HF with mildly reduced ejection fraction (EF) range (HFmrEF; 41-49% EF) is only recently recognised as a distinct entity. Cluster analysis can characterise heterogeneous patient populations and could serve as a stratification tool in clinical trials and for prognostication. The aim of this study was to identify clusters in HFmrEF and compare cluster prognosis.<h4>Methods and results</h4>Latent class analysis to cluster HFmrEF patients based on their characteristics was performed in the Swedish HF registry (n = 7316). Identified clusters were validated in a Dutch cross-sectional HF registry-based dataset CHECK-HF (n = 1536). In Sweden, mortality and hospitalisation across the clusters were compared using a Cox proportional hazard model, with a Fine-Gray sub-distribution for competing risks and adjustment for age and sex. Six clusters were discovered with the following prevalence and hazard ratio with 95% confidence intervals (HR [95%CI]) vs. cluster 1: 1) low-comorbidity (17%, reference), 2) ischaemic-male (13%, HR 0.9 [95% CI 0.7-1.1]), 3) atrial fibrillation (20%, HR 1.5 [95% CI 1.2-1.9]), 4) device/wide QRS (9%, HR 2.7 [95% CI 2.2-3.4]), 5) metabolic (19%, HR 3.1 [95% CI 2.5-3.7]) and 6) cardio-renal phenotype (22%, HR 2.8 [95% CI 2.2-3.6]). The cluster model was robust between both datasets.<h4>Conclusion</h4>We found robust clusters with potential clinical meaning and differences in mortality and hospitalisation. Our clustering model could be valuable as a clinical differentiation support and prognostic tool in clinical trial design.",,pdf:http://www.internationaljournalofcardiology.com/article/S0167527323007180/pdf; doi:https://doi.org/10.1016/j.ijcard.2023.05.024
 31242963,https://doi.org/10.1016/j.vaccine.2019.06.019,An online decision tree for vaccine efficacy trial design during infectious disease epidemics: The InterVax-Tool.,"Bellan SE, Eggo RM, Gsell PS, Kucharski AJ, Dean NE, Donohue R, Zook M, Edmunds WJ, Odhiambo F, Longini IM, Brisson M, Mahon BE, Henao-Restrepo AM.",,Vaccine,2019,2019-06-24,Y,Vaccines; Decision support system; epidemics; Outbreaks; Emerging Infectious Diseases; Phase Iii Trial; Scientific Communication; Public Health Emergency; Vaccine Trial Design,"Applied Analytics, Better Care, Better, Faster and More Efficient Clinical Trials",,"<h4>Background</h4>Licensed vaccines are urgently needed for emerging infectious diseases, but the nature of these epidemics causes challenges for the design of phase III trials to evaluate vaccine efficacy. Designing and executing rigorous, fast, and ethical, vaccine efficacy trials is difficult, and the decisions and limitations in the design of these trials encompass epidemiological, logistical, regulatory, statistical, and ethical dimensions.<h4>Results</h4>Trial design decisions are complex and interrelated, but current guidance documents do not lend themselves to efficient decision-making. We created InterVax-Tool (http://vaxeval.com), an online, interactive decision-support tool, to help diverse stakeholders navigate the decisions in the design of phase III vaccine trials. InterVax-Tool offers high-level visual and interactive assistance through a set of four decision trees, guiding users through selection of the: (1) Primary Endpoint, (2) Target Population, (3) Randomization Scheme, and, (4) Comparator. We provide guidance on how key considerations - grouped as Epidemiological, Vaccine-related, Infrastructural, or Sociocultural - inform each decision in the trial design process.<h4>Conclusions</h4>InterVax-Tool facilitates structured, transparent, and collaborative discussion of trial design, while recording the decision-making process. Users can save and share their decisions, which is useful both for comparing proposed trial designs, and for justifying particular design choices. Here, we describe the goals and features of InterVax-Tool as well as its application to the design of a Zika vaccine efficacy trial.",,doi:https://doi.org/10.1016/j.vaccine.2019.06.019; doi:https://doi.org/10.1016/j.vaccine.2019.06.019; html:https://europepmc.org/articles/PMC6620503
 34796724,https://doi.org/10.1161/jaha.120.019814,"Dietary Fatty Acids, Macronutrient Substitutions, Food Sources and Incidence of Coronary Heart Disease: Findings From the EPIC-CVD Case-Cohort Study Across Nine European Countries.","Steur M, Johnson L, Sharp SJ, Imamura F, Sluijs I, Key TJ, Wood A, Chowdhury R, Guevara M, Jakobsen MU, Johansson I, Koulman A, Overvad K, Sánchez MJ, van der Schouw YT, Trichopoulou A, Weiderpass E, Wennberg M, Zheng JS, Boeing H, Boer JMA, Boutron-Ruault MC, Ericson U, Heath AK, Huybrechts I, Imaz L, Kaaks R, Krogh V, Kühn T, Kyrø C, Masala G, Melander O, Moreno-Iribas C, Panico S, Quirós JR, Rodríguez-Barranco M, Sacerdote C, Santiuste C, Skeie G, Tjønneland A, Tumino R, Verschuren WMM, Zamora-Ros R, Dahm CC, Perez-Cornago A, Schulze MB, Tong TYN, Riboli E, Wareham NJ, Danesh J, Butterworth AS, Forouhi NG.",,Journal of the American Heart Association,2021,2021-11-19,Y,Coronary Heart Disease; Primary Prevention; Dietary Guidelines; Nutritional Epidemiology; Saturated Fat,,,"Background There is controversy about associations between total dietary fatty acids, their classes (saturated fatty acids [SFAs], monounsaturated fatty acids, and polyunsaturated fatty acids), and risk of coronary heart disease (CHD). Specifically, the relevance of food sources of SFAs to CHD associations is uncertain. Methods and Results We conducted a case-cohort study involving 10 529 incident CHD cases and a random subcohort of 16 730 adults selected from a cohort of 385 747 participants in 9 countries of the EPIC (European Prospective Investigation into Cancer and Nutrition) study. We estimated multivariable adjusted country-specific hazard ratios (HRs) and 95% CIs per 5% of energy intake from dietary fatty acids, with and without isocaloric macronutrient substitutions, using Prentice-weighted Cox regression models and pooled results using random-effects meta-analysis. We found no evidence for associations of the consumption of total or fatty acid classes with CHD, regardless of macronutrient substitutions. In analyses considering food sources, CHD incidence was lower per 1% higher energy intake of SFAs from yogurt (HR, 0.93 [95% CI, 0.88-0.99]), cheese (HR, 0.98 [95% CI, 0.96-1.00]), and fish (HR, 0.87 [95% CI, 0.75-1.00]), but higher for SFAs from red meat (HR, 1.07 [95% CI, 1.02-1.12]) and butter (HR, 1.02 [95% CI, 1.00-1.04]). Conclusions This observational study found no strong associations of total fatty acids, SFAs, monounsaturated fatty acids, and polyunsaturated fatty acids, with incident CHD. By contrast, we found associations of SFAs with CHD in opposite directions dependent on the food source. These findings should be further confirmed, but support public health recommendations to consider food sources alongside the macronutrients they contain, and suggest the importance of the overall food matrix.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.120.019814; doi:https://doi.org/10.1161/JAHA.120.019814; html:https://europepmc.org/articles/PMC9075396; pdf:https://europepmc.org/articles/PMC9075396?pdf=render
-38115598,https://doi.org/10.1089/neu.2023.0461,"The Australian Traumatic Brain Injury Initiative: Systematic Review and Consensus Process to Determine the Predictive Value of Demographic, Injury Event, and Social Characteristics on Outcomes for People With Moderate-Severe Traumatic Brain Injury.","Gabbe BJ, Keeves J, McKimmie A, Gadowski AM, Holland AJ, Semple BD, Young JT, Crowe L, Ownsworth T, Bagg MK, Antonic-Baker A, Hicks AJ, Hill R, Curtis K, Romero L, Ponsford JL, Lannin NA, O'Brien TJ, Cameron PA, Cooper DJ, Rushworth N, Fitzgerald M.",,Journal of neurotrauma,2024,2024-04-01,N,"Traumatic; Demography; Common Data Elements; Social Factors; Outcome Assessment, Health Care; Systematic Review [Publication Type]; Brain Injuries, Culture",,,"The objective of the Australian Traumatic Brain Injury (AUS-TBI) Initiative is to develop a data dictionary to inform data collection and facilitate prediction of outcomes of people who experience moderate-severe TBI in Australia. The aim of this systematic review was to summarize the evidence of the association between demographic, injury event, and social characteristics with outcomes, in people with moderate-severe TBI, to identify potentially predictive indicators. Standardized searches were implemented across bibliographic databases to March 31, 2022. English-language reports, excluding case series, which evaluated the association between demographic, injury event, and social characteristics, and any clinical outcome in at least 10 patients with moderate-severe TBI were included. Abstracts and full text records were independently screened by at least two reviewers in Covidence. A pre-defined algorithm was used to assign a judgement of predictive value to each observed association. The review findings were discussed with an expert panel to determine the feasibility of incorporation of routine measurement into standard care. The search strategy retrieved 16,685 records; 867 full-length records were screened, and 111 studies included. Twenty-two predictors of 32 different outcomes were identified; 7 were classified as high-level (age, sex, ethnicity, employment, insurance, education, and living situation at the time of injury). After discussion with an expert consensus group, 15 were recommended for inclusion in the data dictionary. This review identified numerous predictors capable of enabling early identification of those at risk for poor outcomes and improved personalization of care through inclusion in routine data collection.",,doi:https://doi.org/10.1089/neu.2023.0461
 34930919,https://doi.org/10.1038/s41467-021-26280-1,Finding genetically-supported drug targets for Parkinson's disease using Mendelian randomization of the druggable genome.,"Storm CS, Kia DA, Almramhi MM, Bandres-Ciga S, Finan C, International Parkinson’s Disease Genomics Consortium (IPDGC), Hingorani AD, Wood NW.",,Nature communications,2021,2021-12-20,Y,,,,"Parkinson's disease is a neurodegenerative movement disorder that currently has no disease-modifying treatment, partly owing to inefficiencies in drug target identification and validation. We use Mendelian randomization to investigate over 3,000 genes that encode druggable proteins and predict their efficacy as drug targets for Parkinson's disease. We use expression and protein quantitative trait loci to mimic exposure to medications, and we examine the causal effect on Parkinson's disease risk (in two large cohorts), age at onset and progression. We propose 23 drug-targeting mechanisms for Parkinson's disease, including four possible drug repurposing opportunities and two drugs which may increase Parkinson's disease risk. Of these, we put forward six drug targets with the strongest Mendelian randomization evidence. There is remarkably little overlap between our drug targets to reduce Parkinson's disease risk versus progression, suggesting different molecular mechanisms. Drugs with genetic support are considerably more likely to succeed in clinical trials, and we provide compelling genetic evidence and an analysis pipeline to prioritise Parkinson's disease drug development.",,pdf:https://www.nature.com/articles/s41467-021-26280-1.pdf; doi:https://doi.org/10.1038/s41467-021-26280-1; html:https://europepmc.org/articles/PMC8688480; pdf:https://europepmc.org/articles/PMC8688480?pdf=render
+38115598,https://doi.org/10.1089/neu.2023.0461,"The Australian Traumatic Brain Injury Initiative: Systematic Review and Consensus Process to Determine the Predictive Value of Demographic, Injury Event, and Social Characteristics on Outcomes for People With Moderate-Severe Traumatic Brain Injury.","Gabbe BJ, Keeves J, McKimmie A, Gadowski AM, Holland AJ, Semple BD, Young JT, Crowe L, Ownsworth T, Bagg MK, Antonic-Baker A, Hicks AJ, Hill R, Curtis K, Romero L, Ponsford JL, Lannin NA, O'Brien TJ, Cameron PA, Cooper DJ, Rushworth N, Fitzgerald M.",,Journal of neurotrauma,2024,2024-04-01,N,"Traumatic; Demography; Common Data Elements; Social Factors; Outcome Assessment, Health Care; Systematic Review [Publication Type]; Brain Injuries, Culture",,,"The objective of the Australian Traumatic Brain Injury (AUS-TBI) Initiative is to develop a data dictionary to inform data collection and facilitate prediction of outcomes of people who experience moderate-severe TBI in Australia. The aim of this systematic review was to summarize the evidence of the association between demographic, injury event, and social characteristics with outcomes, in people with moderate-severe TBI, to identify potentially predictive indicators. Standardized searches were implemented across bibliographic databases to March 31, 2022. English-language reports, excluding case series, which evaluated the association between demographic, injury event, and social characteristics, and any clinical outcome in at least 10 patients with moderate-severe TBI were included. Abstracts and full text records were independently screened by at least two reviewers in Covidence. A pre-defined algorithm was used to assign a judgement of predictive value to each observed association. The review findings were discussed with an expert panel to determine the feasibility of incorporation of routine measurement into standard care. The search strategy retrieved 16,685 records; 867 full-length records were screened, and 111 studies included. Twenty-two predictors of 32 different outcomes were identified; 7 were classified as high-level (age, sex, ethnicity, employment, insurance, education, and living situation at the time of injury). After discussion with an expert consensus group, 15 were recommended for inclusion in the data dictionary. This review identified numerous predictors capable of enabling early identification of those at risk for poor outcomes and improved personalization of care through inclusion in routine data collection.",,doi:https://doi.org/10.1089/neu.2023.0461
+32909959,https://doi.org/10.1136/bmj.m3164,Reporting guidelines for clinical trial reports for interventions involving artificial intelligence: the CONSORT-AI Extension.,"Liu X, Rivera SC, Moher D, Calvert MJ, Denniston AK, SPIRIT-AI and CONSORT-AI Working Group.",,BMJ (Clinical research ed.),2020,2020-09-09,Y,,,,"The CONSORT 2010 (Consolidated Standards of Reporting Trials) statement provides minimum guidelines for reporting randomised trials. Its widespread use has been instrumental in ensuring transparency when evaluating new interventions. More recently, there has been a growing recognition that interventions involving artificial intelligence (AI) need to undergo rigorous, prospective evaluation to demonstrate impact on health outcomes.The CONSORT-AI extension is a new reporting guideline for clinical trials evaluating interventions with an AI component. It was developed in parallel with its companion statement for clinical trial protocols: SPIRIT-AI. Both guidelines were developed through a staged consensus process, involving a literature review and expert consultation to generate 29 candidate items, which were assessed by an international multi-stakeholder group in a two-stage Delphi survey (103 stakeholders), agreed on in a two-day consensus meeting (31 stakeholders) and refined through a checklist pilot (34 participants).The CONSORT-AI extension includes 14 new items, which were considered sufficiently important for AI interventions, that they should be routinely reported in addition to the core CONSORT 2010 items. CONSORT-AI recommends that investigators provide clear descriptions of the AI intervention, including instructions and skills required for use, the setting in which the AI intervention is integrated, the handling of inputs and outputs of the AI intervention, the human-AI interaction and providing analysis of error cases.CONSORT-AI will help promote transparency and completeness in reporting clinical trials for AI interventions. It will assist editors and peer-reviewers, as well as the general readership, to understand, interpret and critically appraise the quality of clinical trial design and risk of bias in the reported outcomes.",,pdf:https://www.bmj.com/content/bmj/370/bmj.m3164.full.pdf; doi:https://doi.org/10.1136/bmj.m3164; html:https://europepmc.org/articles/PMC7490784
 32735547,https://doi.org/10.2196/20169,Can Robots Improve Testing Capacity for SARS-CoV-2?,"Cresswell K, Ramalingam S, Sheikh A.",,Journal of medical Internet research,2020,2020-08-12,Y,Virus; Infectious disease; Testing; Robotics; Pandemic; Covid-19; Sars-cov-2,,,"There is currently increasing interest internationally in deploying robotic applications for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing, as these can help to reduce the risk of transmission of the virus to health care staff and patients. We provide an overview of key recent developments in this area. We argue that, although there is some potential for deploying robots to help with SARS-CoV-2 testing, the potential of patient-facing applications is likely to be limited. This is due to the high costs associated with patient-facing functionality, and risks of potentially adverse impacts on health care staff work practices and patient interactions. In contrast, back-end laboratory-based robots dealing with sample extraction and amplification, that effectively integrate with established processes, software, and interfaces to process samples, are much more likely to result in safety and efficiency gains. Consideration should therefore be given to deploying these at scale.",,pdf:https://www.jmir.org/2020/8/e20169/PDF; doi:https://doi.org/10.2196/20169; html:https://europepmc.org/articles/PMC7450371
 36774358,https://doi.org/10.1038/s41467-023-36439-7,Genomic and microenvironmental heterogeneity shaping epithelial-to-mesenchymal trajectories in cancer.,"Malagoli Tagliazucchi G, Wiecek AJ, Withnell E, Secrier M.",,Nature communications,2023,2023-02-11,Y,,,,"The epithelial to mesenchymal transition (EMT) is a key cellular process underlying cancer progression, with multiple intermediate states whose molecular hallmarks remain poorly characterised. To fill this gap, we present a method to robustly evaluate EMT transformation in individual tumours based on transcriptomic signals. We apply this approach to explore EMT trajectories in 7180 tumours of epithelial origin and identify three macro-states with prognostic and therapeutic value, attributable to epithelial, hybrid E/M and mesenchymal phenotypes. We show that the hybrid state is relatively stable and linked with increased aneuploidy. We further employ spatial transcriptomics and single cell datasets to explore the spatial heterogeneity of EMT transformation and distinct interaction patterns with cytotoxic, NK cells and fibroblasts in the tumour microenvironment. Additionally, we provide a catalogue of genomic events underlying distinct evolutionary constraints on EMT transformation. This study sheds light on the aetiology of distinct stages along the EMT trajectory, and highlights broader genomic and environmental hallmarks shaping the mesenchymal transformation of primary tumours.",,pdf:https://www.nature.com/articles/s41467-023-36439-7.pdf; doi:https://doi.org/10.1038/s41467-023-36439-7; html:https://europepmc.org/articles/PMC9922305; pdf:https://europepmc.org/articles/PMC9922305?pdf=render
-32909959,https://doi.org/10.1136/bmj.m3164,Reporting guidelines for clinical trial reports for interventions involving artificial intelligence: the CONSORT-AI Extension.,"Liu X, Rivera SC, Moher D, Calvert MJ, Denniston AK, SPIRIT-AI and CONSORT-AI Working Group.",,BMJ (Clinical research ed.),2020,2020-09-09,Y,,,,"The CONSORT 2010 (Consolidated Standards of Reporting Trials) statement provides minimum guidelines for reporting randomised trials. Its widespread use has been instrumental in ensuring transparency when evaluating new interventions. More recently, there has been a growing recognition that interventions involving artificial intelligence (AI) need to undergo rigorous, prospective evaluation to demonstrate impact on health outcomes.The CONSORT-AI extension is a new reporting guideline for clinical trials evaluating interventions with an AI component. It was developed in parallel with its companion statement for clinical trial protocols: SPIRIT-AI. Both guidelines were developed through a staged consensus process, involving a literature review and expert consultation to generate 29 candidate items, which were assessed by an international multi-stakeholder group in a two-stage Delphi survey (103 stakeholders), agreed on in a two-day consensus meeting (31 stakeholders) and refined through a checklist pilot (34 participants).The CONSORT-AI extension includes 14 new items, which were considered sufficiently important for AI interventions, that they should be routinely reported in addition to the core CONSORT 2010 items. CONSORT-AI recommends that investigators provide clear descriptions of the AI intervention, including instructions and skills required for use, the setting in which the AI intervention is integrated, the handling of inputs and outputs of the AI intervention, the human-AI interaction and providing analysis of error cases.CONSORT-AI will help promote transparency and completeness in reporting clinical trials for AI interventions. It will assist editors and peer-reviewers, as well as the general readership, to understand, interpret and critically appraise the quality of clinical trial design and risk of bias in the reported outcomes.",,pdf:https://www.bmj.com/content/bmj/370/bmj.m3164.full.pdf; doi:https://doi.org/10.1136/bmj.m3164; html:https://europepmc.org/articles/PMC7490784
+32935062,https://doi.org/10.23889/ijpds.v5i2.1383,Prospective data linkage to facilitate COVID-19 trials - A call to action.,"Paprica PA, Sydes MR, McGrail KM, Morris AD, Schull MJ, Walker R.",,International journal of population data science,2020,2020-08-11,Y,,,,,,pdf:https://ijpds.org/article/download/1383/2566; doi:https://doi.org/10.23889/ijpds.v5i2.1383; html:https://europepmc.org/articles/PMC7473253; pdf:https://europepmc.org/articles/PMC7473253?pdf=render
 38642613,https://doi.org/10.1016/j.clinme.2024.100209,Addressing ethnic disparities in neurological research in the United Kingdom: An example from the prospective multicentre COVID-19 Clinical Neuroscience Study.,"van Wamelen DJ, Rota S, Hartmann M, Martin NH, Alam AM, Thomas RH, Dodd KC, Jenkins T, Smith CJ, Zandi MS, Easton A, Carr G, Benjamin LA, Lilleker JB, Saucer D, Coles AJ, Wood N, Ray Chaudhuri K, Breen G, Michael BD, COVID-CNS consortium.",,"Clinical medicine (London, England)",2024,2024-04-19,Y,Diversity; Recruitment; Neurology; Ethnicity; Covid-19,,,"<h4>Background</h4>Minority ethnic groups have often been underrepresented in research, posing a problem in relation to external validity and extrapolation of findings. Here, we aimed to assess recruitment and retainment strategies in a large observational study assessing neurological complications following SARS-CoV-2 infection.<h4>Methods</h4>Participants were recruited following confirmed infection with SARS-CoV-2 and hospitalisation. Self-reported ethnicity was recorded alongside other demographic data to identify potential barriers to recruitment.<h4>Results</h4>807 participants were recruited to COVID-CNS, and ethnicity data were available for 93.2%. We identified a proportionate representation of self-reported ethnicity categories, and distribution of broad ethnicity categories mirrored individual centres' catchment areas. White ethnicity within individual centres ranged between 44.5% and 89.1%, with highest percentage of participants with non-White ethnicity in London-based centres. Examples are provided how to reach potentially underrepresented minority ethnic groups.<h4>Conclusions</h4>Recruitment barriers in relation to potentially underrepresented ethnic groups may be overcome with strategies identified here.",,doi:https://doi.org/10.1016/j.clinme.2024.100209; doi:https://doi.org/10.1016/j.clinme.2024.100209; html:https://europepmc.org/articles/PMC11091497; pdf:https://europepmc.org/articles/PMC11091497?pdf=render
 37722858,https://doi.org/10.3399/bjgp.2023.0077,Inequities in hypertension management: observational cross-sectional study in North East London using electronic health records.,"Rison S, Redfern O, Dostal I, Carvalho C, Mathur R, Raisi-Estabragh Z, Robson J.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2023,2023-10-26,Y,Hypertension; Cardiovascular diseases; Blood pressure; General Practice; Antihypertensives; Health Inequities,,,"<h4>Background</h4>Hypertension is a key modifiable risk factor for cardiovascular disease - the leading cause of death in the UK. Good blood pressure (BP) control reduces mortality. However, health inequities may lead to variability in hypertension monitoring and control.<h4>Aim</h4>To investigate health inequities related to ethnicity, sex, age, and socioeconomic status in the monitoring, treatment, and control of BP in a large cohort of adult patients with hypertension.<h4>Design and setting</h4>A cross-sectional cohort study of adults with hypertension registered with general practices in North East London on 1 April 2019.<h4>Method</h4>Multivariable logistic regression was used to estimate associations of demographics and treatment intensity for the following hypertension management indicators: a) BP recording in past 12 months; b) BP on age- adjusted target; and c) BP on age-adjusted target and BP recorded in past 12 months.<h4>Results</h4>In total, 156 296 adults were included. The Black ethnicity group was less likely to have controlled BP than the White ethnicity group (odds ratio [OR] 0.87, 95% [confidence interval] CI = 0.84 to 0.91). The Asian ethnicity group was more likely to have controlled BP (OR 1.28, 95% CI = 1.23 to 1.32). Ethnicity differences in control could not be explained by the likelihood of having a recent BP recording, nor by treatment intensity differences. Older adults (aged ≥50 years) were more likely to have controlled hypertension than younger patients.<h4>Conclusion</h4>Individuals of Black ethnicity and younger people are less likely to have controlled hypertension and may warrant targeted interventions. Possible explanations for these findings are presented but further research is needed about reasons for ethnic differences.",,doi:https://doi.org/10.3399/BJGP.2023.0077; html:https://europepmc.org/articles/PMC10523336; pdf:https://europepmc.org/articles/PMC10523336?pdf=render
-32935062,https://doi.org/10.23889/ijpds.v5i2.1383,Prospective data linkage to facilitate COVID-19 trials - A call to action.,"Paprica PA, Sydes MR, McGrail KM, Morris AD, Schull MJ, Walker R.",,International journal of population data science,2020,2020-08-11,Y,,,,,,pdf:https://ijpds.org/article/download/1383/2566; doi:https://doi.org/10.23889/ijpds.v5i2.1383; html:https://europepmc.org/articles/PMC7473253; pdf:https://europepmc.org/articles/PMC7473253?pdf=render
 37494011,https://doi.org/10.1001/jamacardio.2023.2167,"Association of Longer Leukocyte Telomere Length With Cardiac Size, Function, and Heart Failure.","Aung N, Wang Q, van Duijvenboden S, Burns R, Stoma S, Raisi-Estabragh Z, Ahmet S, Allara E, Wood A, Di Angelantonio E, Danesh J, Munroe PB, Young A, Harvey NC, Codd V, Nelson CP, Petersen SE, Samani NJ.",,JAMA cardiology,2023,2023-09-01,Y,,,,"<h4>Importance</h4>Longer leukocyte telomere length (LTL) is associated with a lower risk of adverse cardiovascular outcomes. The extent to which variation in LTL is associated with intermediary cardiovascular phenotypes is unclear.<h4>Objective</h4>To evaluate the associations between LTL and a diverse set of cardiovascular imaging phenotypes.<h4>Design, setting, and participants</h4>This is a population-based cross-sectional study of UK Biobank participants recruited from 2006 to 2010. LTL was measured using a quantitative polymerase chain reaction method. Cardiovascular measurements were derived from cardiovascular magnetic resonance using machine learning. The median (IQR) duration of follow-up was 12.0 (11.3-12.7) years. The associations of LTL with imaging measurements and incident heart failure (HF) were evaluated by multivariable regression models. Genetic associations between LTL and significantly associated traits were investigated by mendelian randomization. Data were analyzed from January to May 2023.<h4>Exposure</h4>LTL.<h4>Main outcomes and measures</h4>Cardiovascular imaging traits and HF.<h4>Results</h4>Of 40 459 included participants, 19 529 (48.3%) were men, and the mean (SD) age was 55.1 (7.6) years. Longer LTL was independently associated with a pattern of positive cardiac remodeling (higher left ventricular mass, larger global ventricular size and volume, and higher ventricular and atrial stroke volumes) and a lower risk of incident HF (LTL fourth quartile vs first quartile: hazard ratio, 0.86; 95% CI, 0.81-0.91; P = 1.8 × 10-6). Mendelian randomization analysis suggested a potential causal association between LTL and left ventricular mass, global ventricular volume, and left ventricular stroke volume.<h4>Conclusions and relevance</h4>In this cross-sectional study, longer LTL was associated with a larger heart with better cardiac function in middle age, which could potentially explain the observed lower risk of incident HF.",,pdf:https://jamanetwork.com/journals/jamacardiology/articlepdf/2807386/jamacardiology_aung_2023_oi_230032_1689092909.06174.pdf; doi:https://doi.org/10.1001/jamacardio.2023.2167; html:https://europepmc.org/articles/PMC10372756
 36175368,https://doi.org/10.1111/imm.13584,The common IL1A single nucleotide polymorphism rs17561 is a hypomorphic mutation that significantly reduces interleukin-1α release from human blood cells.,"Wiggins KA, Pyrillou K, Humphry M, Butterworth AS, Clarke MC.",,Immunology,2023,2022-10-13,Y,Cytokines; Inflammation; Genomics; Inflammasome,,,"Interleukin-1 alpha (IL-1α) is a powerful cytokine that drives inflammation and modulates adaptive immunity. Due to these powerful effects, IL-1α is controlled at multiple levels from transcription to cleavage and release from the cell. Genome-wide association studies can identify loci that drive important diseases, although often the functional effect of the variant on phenotype remains unknown or small, with most risk variants in non-coding regions. We find that the common variant rs17561 changes a conserved amino acid in the central region of IL-1α linking the pro piece to the cytokine domain. Using a recall-by-genotype study and whole blood stimulation, we find that minor allele homozygotes release ~50% less IL-1α than the major allele, with IL-1β release equivalent. IL-1α transcript level was identical between groups, implying a post-transcriptional effect, whilst cleavage of recombinant pro-IL-1α by multiple proteases was also equivalent for both forms. Importantly, transfected macrophages also release less minor allele IL-1α upon inflammasome activation, revealing that reduced secretion is directly caused by the missense amino acid substitution and more minor allele IL-1α was retained within the cell. Thus, rs17561 represents a very common hypomorphic mutation in IL-1α. We believe this novel data will be important for determining the potential contribution of IL-1α to disease and/or physiological processes, for example, by Mendelian randomisation, and may aid patient stratification when considering anti-IL-1 therapies.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/imm.13584; doi:https://doi.org/10.1111/imm.13584; html:https://europepmc.org/articles/PMC11495263; pdf:https://europepmc.org/articles/PMC11495263?pdf=render
 37751444,https://doi.org/10.1371/journal.pone.0290583,Long Covid symptoms and diagnosis in primary care: A cohort study using structured and unstructured data in The Health Improvement Network primary care database.,"Shah AD, Subramanian A, Lewis J, Dhalla S, Ford E, Haroon S, Kuan V, Nirantharakumar K.",,PloS one,2023,2023-09-26,Y,,,,"<h4>Background</h4>Long Covid is a widely recognised consequence of COVID-19 infection, but little is known about the burden of symptoms that patients present with in primary care, as these are typically recorded only in free text clinical notes.<h4>Aims</h4>To compare symptoms in patients with and without a history of COVID-19, and investigate symptoms associated with a Long Covid diagnosis.<h4>Methods</h4>We used primary care electronic health record data until the end of December 2020 from The Health Improvement Network (THIN), a Cegedim database. We included adults registered with participating practices in England, Scotland or Wales. We extracted information about 89 symptoms and 'Long Covid' diagnoses from free text using natural language processing. We calculated hazard ratios (adjusted for age, sex, baseline medical conditions and prior symptoms) for each symptom from 12 weeks after the COVID-19 diagnosis.<h4>Results</h4>We compared 11,015 patients with confirmed COVID-19 and 18,098 unexposed controls. Only 20% of symptom records were coded, with 80% in free text. A wide range of symptoms were associated with COVID-19 at least 12 weeks post-infection, with strongest associations for fatigue (adjusted hazard ratio (aHR) 3.46, 95% confidence interval (CI) 2.87, 4.17), shortness of breath (aHR 2.89, 95% CI 2.48, 3.36), palpitations (aHR 2.59, 95% CI 1.86, 3.60), and phlegm (aHR 2.43, 95% CI 1.65, 3.59). However, a limited subset of symptoms were recorded within 7 days prior to a Long Covid diagnosis in more than 20% of cases: shortness of breath, chest pain, pain, fatigue, cough, and anxiety / depression.<h4>Conclusions</h4>Numerous symptoms are reported to primary care at least 12 weeks after COVID-19 infection, but only a subset are commonly associated with a GP diagnosis of Long Covid.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0290583&type=printable; doi:https://doi.org/10.1371/journal.pone.0290583; html:https://europepmc.org/articles/PMC10521988; pdf:https://europepmc.org/articles/PMC10521988?pdf=render
-38987242,https://doi.org/10.1038/s41467-024-49998-0,Characterising the genetic architecture of changes in adiposity during adulthood using electronic health records.,"Venkatesh SS, Ganjgahi H, Palmer DS, Coley K, Linchangco GV, Hui Q, Wilson P, Ho YL, Cho K, Arumäe K, Million Veteran Program, Estonian Biobank Research Team, Wittemans LBL, Nellåker C, Vainik U, Sun YV, Holmes C, Lindgren CM, Nicholson G.",,Nature communications,2024,2024-07-10,Y,,,,"Obesity is a heritable disease, characterised by excess adiposity that is measured by body mass index (BMI). While over 1,000 genetic loci are associated with BMI, less is known about the genetic contribution to adiposity trajectories over adulthood. We derive adiposity-change phenotypes from 24.5 million primary-care health records in over 740,000 individuals in the UK Biobank, Million Veteran Program USA, and Estonian Biobank, to discover and validate the genetic architecture of adiposity trajectories. Using multiple BMI measurements over time increases power to identify genetic factors affecting baseline BMI by 14%. In the largest reported genome-wide study of adiposity-change in adulthood, we identify novel associations with BMI-change at six independent loci, including rs429358 (APOE missense variant). The SNP-based heritability of BMI-change (1.98%) is 9-fold lower than that of BMI. The modest genetic correlation between BMI-change and BMI (45.2%) indicates that genetic studies of longitudinal trajectories could uncover novel biology of quantitative traits in adulthood.",,doi:https://doi.org/10.1038/s41467-024-49998-0; doi:https://doi.org/10.1038/s41467-024-49998-0; html:https://europepmc.org/articles/PMC11237142; pdf:https://europepmc.org/articles/PMC11237142?pdf=render
 30551632,https://doi.org/10.3390/ijerph15122845,"Incidence, Costs and Predictors of Non-Union, Delayed Union and Mal-Union Following Long Bone Fracture.","Ekegren CL, Edwards ER, de Steiger R, Gabbe BJ.",,International journal of environmental research and public health,2018,2018-12-13,Y,Costs; Bone; Fracture; Data Linkage; Non-union; Mal-union; Delayed Union,Improving Public Health,,"Fracture healing complications are common and result in significant healthcare burden. The aim of this study was to determine the rate, costs and predictors of two-year readmission for surgical management of healing complications (delayed, mal, non-union) following fracture of the humerus, tibia or femur. Humeral, tibial and femoral (excluding proximal) fractures registered by the Victorian Orthopaedic Trauma Outcomes Registry over five years (<i>n</i> = 3962) were linked with population-level hospital admissions data to identify two-year readmissions for delayed, mal or non-union. Study outcomes included hospital length-of-stay (LOS) and inpatient costs. Multivariable logistic regression was used to determine demographic and injury-related factors associated with admission for fracture healing complications. Of the 3886 patients linked, 8.1% were readmitted for healing complications within two years post-fracture, with non-union the most common complication and higher rates for femoral and tibial shaft fractures. Admissions for fracture healing complications incurred total costs of $4.9 million AUD, with a median LOS of two days. After adjusting for confounders, patients had higher odds of developing complications if they were older, receiving compensation or had tibial or femoral shaft fractures. Patients who are older, with tibial and femoral shaft fractures should be targeted for future research aimed at preventing complications.",,pdf:https://www.mdpi.com/1660-4601/15/12/2845/pdf?version=1544701398; doi:https://doi.org/10.3390/ijerph15122845; html:https://europepmc.org/articles/PMC6313538; pdf:https://europepmc.org/articles/PMC6313538?pdf=render
+38987242,https://doi.org/10.1038/s41467-024-49998-0,Characterising the genetic architecture of changes in adiposity during adulthood using electronic health records.,"Venkatesh SS, Ganjgahi H, Palmer DS, Coley K, Linchangco GV, Hui Q, Wilson P, Ho YL, Cho K, Arumäe K, Million Veteran Program, Estonian Biobank Research Team, Wittemans LBL, Nellåker C, Vainik U, Sun YV, Holmes C, Lindgren CM, Nicholson G.",,Nature communications,2024,2024-07-10,Y,,,,"Obesity is a heritable disease, characterised by excess adiposity that is measured by body mass index (BMI). While over 1,000 genetic loci are associated with BMI, less is known about the genetic contribution to adiposity trajectories over adulthood. We derive adiposity-change phenotypes from 24.5 million primary-care health records in over 740,000 individuals in the UK Biobank, Million Veteran Program USA, and Estonian Biobank, to discover and validate the genetic architecture of adiposity trajectories. Using multiple BMI measurements over time increases power to identify genetic factors affecting baseline BMI by 14%. In the largest reported genome-wide study of adiposity-change in adulthood, we identify novel associations with BMI-change at six independent loci, including rs429358 (APOE missense variant). The SNP-based heritability of BMI-change (1.98%) is 9-fold lower than that of BMI. The modest genetic correlation between BMI-change and BMI (45.2%) indicates that genetic studies of longitudinal trajectories could uncover novel biology of quantitative traits in adulthood.",,doi:https://doi.org/10.1038/s41467-024-49998-0; doi:https://doi.org/10.1038/s41467-024-49998-0; html:https://europepmc.org/articles/PMC11237142; pdf:https://europepmc.org/articles/PMC11237142?pdf=render
 32692755,https://doi.org/10.1371/journal.pone.0236193,A genetic model of ivabradine recapitulates results from randomized clinical trials.,"Legault MA, Sandoval J, Provost S, Barhdadi A, Lemieux Perreault LP, Shah S, Lumbers RT, de Denus S, Tyl B, Tardif JC, Dubé MP.",,PloS one,2020,2020-07-21,Y,,,,"<h4>Background</h4>Naturally occurring human genetic variants provide a valuable tool to identify drug targets and guide drug prioritization and clinical trial design. Ivabradine is a heart rate lowering drug with protective effects on heart failure despite increasing the risk of atrial fibrillation. In patients with coronary artery disease without heart failure, the drug does not protect against major cardiovascular adverse events prompting questions about the ability of genetics to have predicted those effects. This study evaluates the effect of a variant in HCN4, ivabradine's drug target, on safety and efficacy endpoints.<h4>Methods</h4>We used genetic association testing and Mendelian randomization to predict the effect of ivabradine and heart rate lowering on cardiovascular outcomes.<h4>Results</h4>Using data from the UK Biobank and large GWAS consortia, we evaluated the effect of a heart rate-reducing genetic variant at the HCN4 locus encoding ivabradine's drug target. These genetic association analyses showed increases in risk for atrial fibrillation (OR 1.09, 95% CI: 1.06-1.13, P = 9.3 ×10-9) in the UK Biobank. In a cause-specific competing risk model to account for the increased risk of atrial fibrillation, the HCN4 variant reduced incident heart failure in participants that did not develop atrial fibrillation (HR 0.90, 95% CI: 0.83-0.98, P = 0.013). In contrast, the same heart rate reducing HCN4 variant did not prevent a composite endpoint of myocardial infarction or cardiovascular death (OR 0.99, 95% CI: 0.93-1.04, P = 0.61).<h4>Conclusion</h4>Genetic modelling of ivabradine recapitulates its benefits in heart failure, promotion of atrial fibrillation, and neutral effect on myocardial infarction.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0236193&type=printable; doi:https://doi.org/10.1371/journal.pone.0236193; html:https://europepmc.org/articles/PMC7373274; pdf:https://europepmc.org/articles/PMC7373274?pdf=render
 36944376,https://doi.org/10.1098/rsob.220373,"The lipid linked oligosaccharide polymerase Wzy and its regulating co-polymerase, Wzz, from enterobacterial common antigen biosynthesis form a complex.","Weckener M, Woodward LS, Clarke BR, Liu H, Ward PN, Le Bas A, Bhella D, Whitfield C, Naismith JH.",,Open biology,2023,2023-03-22,Y,Oligosaccharides; Lipid; Regulating; Polymerase; Wzy,,,"The enterobacterial common antigen (ECA) is a carbohydrate polymer that is associated with the cell envelope in the <i>Enterobacteriaceae</i>. ECA contains a repeating trisaccharide which is polymerized by WzyE, a member of the Wzy membrane protein polymerase superfamily. WzyE activity is regulated by a membrane protein polysaccharide co-polymerase, WzzE. Förster resonance energy transfer experiments demonstrate that WzyE and WzzE from <i>Pectobacterium atrosepticum</i> form a complex <i>in vivo</i>, and immunoblotting and cryo-electron microscopy (cryo-EM) analysis confirm a defined stoichiometry of approximately eight WzzE to one WzyE. Low-resolution cryo-EM reconstructions of the complex, aided by an antibody recognizing the C-terminus of WzyE, reveals WzyE sits in the central membrane lumen formed by the octameric arrangement of the transmembrane helices of WzzE. The pairing of Wzy and Wzz is found in polymerization systems for other bacterial polymers, including lipopolysaccharide O-antigens and capsular polysaccharides. The data provide new structural insight into a conserved mechanism for regulating polysaccharide chain length in bacteria.",,doi:https://doi.org/10.1098/rsob.220373; doi:https://doi.org/10.1098/rsob.220373; html:https://europepmc.org/articles/PMC10030265; pdf:https://europepmc.org/articles/PMC10030265?pdf=render
-30993728,https://doi.org/10.1111/cen.13990,Risk of incident circulatory disease in patients treated for differentiated thyroid carcinoma with no history of cardiovascular disease.,"Toulis KA, Viola D, Gkoutos G, Keerthy D, Boelaert K, Nirantharakumar K.",,Clinical endocrinology,2019,2019-05-17,N,Atrial fibrillation; Cardiovascular events; Thyroid cancer; Differentiated Thyroid Carcinoma,,,"<h4>Context</h4>The incidence of differentiated thyroid cancer (DTC) is increasing, yet the prognosis is favourable and long-term survival is expected. Exogenous TSH suppression has been used for many years to prevent DTC recurrence and may be associated with increased risks of circulatory diseases.<h4>Design</h4>Risks of circulatory disease in patients treated for DTC were compared to randomly matched patients without DTC (controls) up to a 1:5 ratio using age, sex, body mass index (BMI) and smoking as the matching parameters in a population-based, open cohort study using The Health Improvement Network.<h4>Patients</h4>A total of 3009 patients treated for DTC with no pre-existing cardiovascular disease were identified and matched to 11 303 controls, followed up to median of 5 years.<h4>Results</h4>A total of 1259 incident circulatory events were recorded during the observation period. No difference in the risk of ischaemic heart disease (IHD) (adjusted hazards ratio [aHR]: 1.04, 95% CI: 0.80-1.36) or heart failure (HF) (aHR: 1.27, 95% CI: 0.89-1.81) was detected. The risk of atrial fibrillation (AF) and stroke was significantly higher in patients with DTC (aHR: 1.71, 95% CI: 1.36-2.15 and aHR: 1.34, 95% CI: 1.05-1.72, respectively). In a sensitivity analysis limited to newly diagnosed patients with DTC, only the risk of AF was consistently elevated (aHR: 1.86, 95% CI: 1.33-2.60).<h4>Conclusions</h4>The increased risk of AF in patients who have undergone treatment for DTC but without pre-existing CVD may warrant periodic screening for this arrhythmia. Whereas no evidence of increased risk of IHD or HF was observed, the increased risk of stroke/TIA warrants further investigation.",,doi:https://doi.org/10.1111/cen.13990
 34785789,https://doi.org/10.1038/s41591-021-01546-9,Patient-reported outcomes in the regulatory approval of medical devices.,"Cruz Rivera S, Dickens AP, Aiyegbusi OL, Flint R, Fleetcroft C, McPherson D, Collis P, Calvert MJ.",,Nature medicine,2021,2021-12-01,N,,,,,,pdf:http://pure-oai.bham.ac.uk/ws/files/149366889/The_role_of_PROs_MedicalDevices_NatMed_FINAL_Sep_REVISED_CLEANCOPY2.pdf; doi:https://doi.org/10.1038/s41591-021-01546-9
-34970633,https://doi.org/10.23889/ijpds.v6i1.1674,Evaluation of the ASSIGN open-source deterministic address-matching algorithm for allocating unique property reference numbers to general practitioner-recorded patient addresses.,"Harper G, Stables D, Simon P, Ahmed Z, Smith K, Robson J, Dezateux C.",,International journal of population data science,2021,2021-12-08,Y,Quality assurance; Data Linkage; Population Health; Electronic Health Record; Addresses; Address-matching; Place-based Health,,,"<h4>Introduction</h4>Linking places to people is a core element of the UK government's geospatial strategy. Matching patient addresses in electronic health records to their Unique Property Reference Numbers (UPRNs) enables spatial linkage for research, innovation and public benefit. Available algorithms are not transparent or evaluated for use with addresses recorded by health care providers.<h4>Objectives</h4>To describe and quality assure the open-source deterministic ASSIGN address-matching algorithm applied to general practitioner-recorded patient addresses.<h4>Methods</h4>Best practice standards were used to report the ASSIGN algorithm match rate, sensitivity and positive predictive value using gold-standard datasets from London and Wales. We applied the ASSIGN algorithm to the recorded addresses of a sample of 1,757,018 patients registered with all general practices in north east London. We examined bias in match results for the study population using multivariable analyses to estimate the likelihood of an address-matched UPRN by demographic, registration, and organisational variables.<h4>Results</h4>We found a 99.5% and 99.6% match rate with high sensitivity (0.999,0.998) and positive predictive value (0.996,0.998) for the Welsh and London gold standard datasets respectively, and a 98.6% match rate for the study population.The 1.4% of the study population without a UPRN match were more likely to have changed registered address in the last 12 months (match rate: 95.4%), be from a Chinese ethnic background (95.5%), or registered with a general practice using the SystmOne clinical record system (94.4%). Conversely, people registered for more than 6.5 years with their general practitioner were more likely to have a match (99.4%) than those with shorter registration durations.<h4>Conclusions</h4>ASSIGN is a highly accurate open-source address-matching algorithm with a high match rate and minimal biases when evaluated against a large sample of general practice-recorded patient addresses. ASSIGN has potential to be used in other address-based datasets including those with information relevant to the wider determinants of health.",,pdf:https://ijpds.org/article/download/1674/3300; doi:https://doi.org/10.23889/ijpds.v6i1.1674; html:https://europepmc.org/articles/PMC8678979; pdf:https://europepmc.org/articles/PMC8678979?pdf=render
+30993728,https://doi.org/10.1111/cen.13990,Risk of incident circulatory disease in patients treated for differentiated thyroid carcinoma with no history of cardiovascular disease.,"Toulis KA, Viola D, Gkoutos G, Keerthy D, Boelaert K, Nirantharakumar K.",,Clinical endocrinology,2019,2019-05-17,N,Atrial fibrillation; Cardiovascular events; Thyroid cancer; Differentiated Thyroid Carcinoma,,,"<h4>Context</h4>The incidence of differentiated thyroid cancer (DTC) is increasing, yet the prognosis is favourable and long-term survival is expected. Exogenous TSH suppression has been used for many years to prevent DTC recurrence and may be associated with increased risks of circulatory diseases.<h4>Design</h4>Risks of circulatory disease in patients treated for DTC were compared to randomly matched patients without DTC (controls) up to a 1:5 ratio using age, sex, body mass index (BMI) and smoking as the matching parameters in a population-based, open cohort study using The Health Improvement Network.<h4>Patients</h4>A total of 3009 patients treated for DTC with no pre-existing cardiovascular disease were identified and matched to 11 303 controls, followed up to median of 5 years.<h4>Results</h4>A total of 1259 incident circulatory events were recorded during the observation period. No difference in the risk of ischaemic heart disease (IHD) (adjusted hazards ratio [aHR]: 1.04, 95% CI: 0.80-1.36) or heart failure (HF) (aHR: 1.27, 95% CI: 0.89-1.81) was detected. The risk of atrial fibrillation (AF) and stroke was significantly higher in patients with DTC (aHR: 1.71, 95% CI: 1.36-2.15 and aHR: 1.34, 95% CI: 1.05-1.72, respectively). In a sensitivity analysis limited to newly diagnosed patients with DTC, only the risk of AF was consistently elevated (aHR: 1.86, 95% CI: 1.33-2.60).<h4>Conclusions</h4>The increased risk of AF in patients who have undergone treatment for DTC but without pre-existing CVD may warrant periodic screening for this arrhythmia. Whereas no evidence of increased risk of IHD or HF was observed, the increased risk of stroke/TIA warrants further investigation.",,doi:https://doi.org/10.1111/cen.13990
 30120083,https://doi.org/10.1016/j.ebiom.2018.08.004,"Genome-Wide Association Study of Circadian Rhythmicity in 71,500 UK Biobank Participants and Polygenic Association with Mood Instability.","Ferguson A, Lyall LM, Ward J, Strawbridge RJ, Cullen B, Graham N, Niedzwiedz CL, Johnston KJA, MacKay D, Biello SM, Pell JP, Cavanagh J, McIntosh AM, Doherty A, Bailey MES, Lyall DM, Wyse CA, Smith DJ.",,EBioMedicine,2018,2018-08-14,Y,Mood Instability; Gwas; Polygenic Risk Score; Circadian Rhythmicity; Relative Amplitude,Understanding the Causes of Disease,,"<h4>Background</h4>Circadian rhythms are fundamental to health and are particularly important for mental wellbeing. Disrupted rhythms of rest and activity are recognised as risk factors for major depressive disorder and bipolar disorder.<h4>Methods</h4>We conducted a genome-wide association study (GWAS) of low relative amplitude (RA), an objective measure of rest-activity cycles derived from the accelerometer data of 71,500 UK Biobank participants. Polygenic risk scores (PRS) for low RA were used to investigate potential associations with psychiatric phenotypes.<h4>Outcomes</h4>Two independent genetic loci were associated with low RA, within genomic regions for Neurofascin (NFASC) and Solute Carrier Family 25 Member 17 (SLC25A17). A secondary GWAS of RA as a continuous measure identified a locus within Meis Homeobox 1 (MEIS1). There were no significant genetic correlations between low RA and any of the psychiatric phenotypes assessed. However, PRS for low RA was significantly associated with mood instability across multiple PRS thresholds (at PRS threshold 0·05: OR = 1·02, 95% CI = 1·01-1·02, p = 9·6 × 10<sup>-5</sup>), and with major depressive disorder (at PRS threshold 0·1: OR = 1·03, 95% CI = 1·01-1·05, p = 0·025) and neuroticism (at PRS threshold 0·5: Beta = 0·02, 95% CI = 0·007-0·04, p = 0·021).<h4>Interpretation</h4>Overall, our findings contribute new knowledge on the complex genetic architecture of circadian rhythmicity and suggest a putative biological link between disrupted circadian function and mood disorder phenotypes, particularly mood instability, but also major depressive disorder and neuroticism.<h4>Funding</h4>Medical Research Council (MR/K501335/1).",,pdf:http://www.thelancet.com/article/S2352396418302925/pdf; doi:https://doi.org/10.1016/j.ebiom.2018.08.004; html:https://europepmc.org/articles/PMC6154782; pdf:https://europepmc.org/articles/PMC6154782?pdf=render
-36545235,https://doi.org/10.1177/26335565221145493,The DynAIRx Project Protocol: Artificial Intelligence for dynamic prescribing optimisation and care integration in multimorbidity.,"Walker LE, Abuzour AS, Bollegala D, Clegg A, Gabbay M, Griffiths A, Kullu C, Leeming G, Mair FS, Maskell S, Relton S, Ruddle RA, Shantsila E, Sperrin M, Van Staa T, Woodall A, Buchan I.",,Journal of multimorbidity and comorbidity,2022,2022-01-01,Y,Artificial intelligence; Frailty; Mental health; Polypharmacy; Multimorbidity; Medicines Optimisation,,,"<h4>Background</h4>Structured Medication Reviews (SMRs) are intended to help deliver the NHS Long Term Plan for medicines optimisation in people living with multiple long-term conditions and polypharmacy. It is challenging to gather the information needed for these reviews due to poor integration of health records across providers and there is little guidance on how to identify those patients most urgently requiring review.<h4>Objective</h4>To extract information from scattered clinical records on how health and medications change over time, apply interpretable artificial intelligence (AI) approaches to predict risks of poor outcomes and overlay this information on care records to inform SMRs. We will pilot this approach in primary care prescribing audit and feedback systems, and co-design future medicines optimisation decision support systems.<h4>Design</h4>DynAIRx will target potentially problematic polypharmacy in three key multimorbidity groups, namely, people with (a) mental and physical health problems, (b) four or more long-term conditions taking ten or more drugs and (c) older age and frailty. Structured clinical data will be drawn from integrated care records (general practice, hospital, and social care) covering an ∼11m population supplemented with Natural Language Processing (NLP) of unstructured clinical text. AI systems will be trained to identify patterns of conditions, medications, tests, and clinical contacts preceding adverse events in order to identify individuals who might benefit most from an SMR.<h4>Discussion</h4>By implementing and evaluating an AI-augmented visualisation of care records in an existing prescribing audit and feedback system we will create a learning system for medicines optimisation, co-designed throughout with end-users and patients.",,pdf:https://eprints.whiterose.ac.uk/197084/1/26335565221145493.pdf; doi:https://doi.org/10.1177/26335565221145493; html:https://europepmc.org/articles/PMC9761229; pdf:https://europepmc.org/articles/PMC9761229?pdf=render
+34970633,https://doi.org/10.23889/ijpds.v6i1.1674,Evaluation of the ASSIGN open-source deterministic address-matching algorithm for allocating unique property reference numbers to general practitioner-recorded patient addresses.,"Harper G, Stables D, Simon P, Ahmed Z, Smith K, Robson J, Dezateux C.",,International journal of population data science,2021,2021-12-08,Y,Quality assurance; Data Linkage; Population Health; Electronic Health Record; Addresses; Address-matching; Place-based Health,,,"<h4>Introduction</h4>Linking places to people is a core element of the UK government's geospatial strategy. Matching patient addresses in electronic health records to their Unique Property Reference Numbers (UPRNs) enables spatial linkage for research, innovation and public benefit. Available algorithms are not transparent or evaluated for use with addresses recorded by health care providers.<h4>Objectives</h4>To describe and quality assure the open-source deterministic ASSIGN address-matching algorithm applied to general practitioner-recorded patient addresses.<h4>Methods</h4>Best practice standards were used to report the ASSIGN algorithm match rate, sensitivity and positive predictive value using gold-standard datasets from London and Wales. We applied the ASSIGN algorithm to the recorded addresses of a sample of 1,757,018 patients registered with all general practices in north east London. We examined bias in match results for the study population using multivariable analyses to estimate the likelihood of an address-matched UPRN by demographic, registration, and organisational variables.<h4>Results</h4>We found a 99.5% and 99.6% match rate with high sensitivity (0.999,0.998) and positive predictive value (0.996,0.998) for the Welsh and London gold standard datasets respectively, and a 98.6% match rate for the study population.The 1.4% of the study population without a UPRN match were more likely to have changed registered address in the last 12 months (match rate: 95.4%), be from a Chinese ethnic background (95.5%), or registered with a general practice using the SystmOne clinical record system (94.4%). Conversely, people registered for more than 6.5 years with their general practitioner were more likely to have a match (99.4%) than those with shorter registration durations.<h4>Conclusions</h4>ASSIGN is a highly accurate open-source address-matching algorithm with a high match rate and minimal biases when evaluated against a large sample of general practice-recorded patient addresses. ASSIGN has potential to be used in other address-based datasets including those with information relevant to the wider determinants of health.",,pdf:https://ijpds.org/article/download/1674/3300; doi:https://doi.org/10.23889/ijpds.v6i1.1674; html:https://europepmc.org/articles/PMC8678979; pdf:https://europepmc.org/articles/PMC8678979?pdf=render
 35639667,https://doi.org/10.1093/eurheartj/ehac238,Critical appraisal of artificial intelligence-based prediction models for cardiovascular disease.,"van Smeden M, Heinze G, Van Calster B, Asselbergs FW, Vardas PE, Bruining N, de Jaegere P, Moore JH, Denaxas S, Boulesteix AL, Moons KGM.",,European heart journal,2022,2022-08-01,Y,Prediction; Artificial intelligence; Diagnosis; Prognosis; Machine Learning; Digital Health,,,"The medical field has seen a rapid increase in the development of artificial intelligence (AI)-based prediction models. With the introduction of such AI-based prediction model tools and software in cardiovascular patient care, the cardiovascular researcher and healthcare professional are challenged to understand the opportunities as well as the limitations of the AI-based predictions. In this article, we present 12 critical questions for cardiovascular health professionals to ask when confronted with an AI-based prediction model. We aim to support medical professionals to distinguish the AI-based prediction models that can add value to patient care from the AI that does not.",,pdf:https://academic.oup.com/eurheartj/article-pdf/43/31/2921/45333809/ehac238.pdf; doi:https://doi.org/10.1093/eurheartj/ehac238; html:https://europepmc.org/articles/PMC9443991; pdf:https://europepmc.org/articles/PMC9443991?pdf=render
+36545235,https://doi.org/10.1177/26335565221145493,The DynAIRx Project Protocol: Artificial Intelligence for dynamic prescribing optimisation and care integration in multimorbidity.,"Walker LE, Abuzour AS, Bollegala D, Clegg A, Gabbay M, Griffiths A, Kullu C, Leeming G, Mair FS, Maskell S, Relton S, Ruddle RA, Shantsila E, Sperrin M, Van Staa T, Woodall A, Buchan I.",,Journal of multimorbidity and comorbidity,2022,2022-01-01,Y,Artificial intelligence; Frailty; Mental health; Polypharmacy; Multimorbidity; Medicines Optimisation,,,"<h4>Background</h4>Structured Medication Reviews (SMRs) are intended to help deliver the NHS Long Term Plan for medicines optimisation in people living with multiple long-term conditions and polypharmacy. It is challenging to gather the information needed for these reviews due to poor integration of health records across providers and there is little guidance on how to identify those patients most urgently requiring review.<h4>Objective</h4>To extract information from scattered clinical records on how health and medications change over time, apply interpretable artificial intelligence (AI) approaches to predict risks of poor outcomes and overlay this information on care records to inform SMRs. We will pilot this approach in primary care prescribing audit and feedback systems, and co-design future medicines optimisation decision support systems.<h4>Design</h4>DynAIRx will target potentially problematic polypharmacy in three key multimorbidity groups, namely, people with (a) mental and physical health problems, (b) four or more long-term conditions taking ten or more drugs and (c) older age and frailty. Structured clinical data will be drawn from integrated care records (general practice, hospital, and social care) covering an ∼11m population supplemented with Natural Language Processing (NLP) of unstructured clinical text. AI systems will be trained to identify patterns of conditions, medications, tests, and clinical contacts preceding adverse events in order to identify individuals who might benefit most from an SMR.<h4>Discussion</h4>By implementing and evaluating an AI-augmented visualisation of care records in an existing prescribing audit and feedback system we will create a learning system for medicines optimisation, co-designed throughout with end-users and patients.",,pdf:https://eprints.whiterose.ac.uk/197084/1/26335565221145493.pdf; doi:https://doi.org/10.1177/26335565221145493; html:https://europepmc.org/articles/PMC9761229; pdf:https://europepmc.org/articles/PMC9761229?pdf=render
 39195987,https://doi.org/10.1038/s44161-021-00012-6,Depression and genetic susceptibility to cardiometabolic diseases.,"Ritchie SC, Inouye M.",,Nature cardiovascular research,2022,2022-02-01,N,,,,,,doi:https://doi.org/10.1038/s44161-021-00012-6
 32371477,https://doi.org/10.1126/science.abc0473,Rapid implementation of mobile technology for real-time epidemiology of COVID-19.,"Drew DA, Nguyen LH, Steves CJ, Menni C, Freydin M, Varsavsky T, Sudre CH, Cardoso MJ, Ourselin S, Wolf J, Spector TD, Chan AT, COPE Consortium.",,"Science (New York, N.Y.)",2020,2020-05-05,Y,,,,"The rapid pace of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents challenges to the robust collection of population-scale data to address this global health crisis. We established the COronavirus Pandemic Epidemiology (COPE) Consortium to unite scientists with expertise in big data research and epidemiology to develop the COVID Symptom Study, previously known as the COVID Symptom Tracker, mobile application. This application-which offers data on risk factors, predictive symptoms, clinical outcomes, and geographical hotspots-was launched in the United Kingdom on 24 March 2020 and the United States on 29 March 2020 and has garnered more than 2.8 million users as of 2 May 2020. Our initiative offers a proof of concept for the repurposing of existing approaches to enable rapidly scalable epidemiologic data collection and analysis, which is critical for a data-driven response to this public health challenge.","Drew et al. decribe the use of a smart-phone App to track Covid-19 symptoms reported by users to track, in real time, information on newly infected individuals. It has been launched in the UK and US and has 2.8 million users and is used to rapidly identify emerging hot spots for infection.",pdf:https://www.science.org/cms/asset/fb31d61b-4be3-483a-b040-2ee970dfb432/pap.pdf; doi:https://doi.org/10.1126/science.abc0473; html:https://europepmc.org/articles/PMC7200009; pdf:https://europepmc.org/articles/PMC7200009?pdf=render
 37270201,https://doi.org/10.1136/heartjnl-2023-322616,Reliability of major bleeding events in UK routine data versus clinical trial adjudicated follow-up data.,"Harper C, Mafham M, Herrington W, Staplin N, Stevens W, Wallendszus K, Haynes R, Landray MJ, Parish S, Bowman L, Armitage J.",,Heart (British Cardiac Society),2023,2023-09-13,Y,"Atherosclerosis; Research Design; Electronic Health Records; Outcome Assessment, Health Care",,,"<h4>Objective</h4>To assess how reliable UK routine data are for ascertaining major bleeding events compared with adjudicated follow-up.<h4>Methods</h4>The ASCEND (A Study of Cardiovascular Events iN Diabetes) primary prevention trial randomised 15 480 UK people with diabetes to aspirin versus matching placebo. The primary safety outcome was major bleeding (including intracranial haemorrhage, sight-threatening eye bleeding, serious gastrointestinal bleeding and other major bleeding (epistaxis, haemoptysis, haematuria, vaginal and other bleeding)) ascertained by direct-participant mail-based follow-up, with >90% of outcomes undergoing adjudication. Nearly all participants were linked to routinely collected hospitalisation and death data (ie, routine data). An algorithm categorised bleeding events from routine data as major/minor. Kappa statistics were used to assess agreement between data sources, and randomised comparisons were re-run using routine data.<h4>Results</h4>When adjudicated follow-up and routine data were compared, there was agreement for 318 major bleeding events, with routine data identifying 281 additional-potential events, and not identifying 241 participant-reported events (kappa 0.53, 95% CI 0.49 to 0.57). Repeating ASCEND's randomised comparisons using routine data only found estimated relative and absolute effects of allocation to aspirin versus placebo on major bleeding similar to adjudicated follow-up (adjudicated follow-up: aspirin 314 (4.1%) vs placebo 245 (3.2%); rate ratio (RR) 1.29, 95% CI 1.09 to 1.52; absolute excess +6.3/5000 person-years (mean SE±2.1); vs routine data: 327 (4.2%) vs 272 (3.5%); RR 1.21, 95% CI 1.03 to 1.41; absolute excess +5.0/5000 (±2.2)).<h4>Conclusions</h4>Analyses of the ASCEND randomised trial found that major bleeding events ascertained via UK routine data sources provided relative and absolute treatment effects similar to adjudicated follow-up.<h4>Trial registration number</h4>ISRCTN60635500; NCT00135226.",,pdf:https://heart.bmj.com/content/heartjnl/early/2023/06/02/heartjnl-2023-322616.full.pdf; doi:https://doi.org/10.1136/heartjnl-2023-322616; html:https://europepmc.org/articles/PMC10511984; pdf:https://europepmc.org/articles/PMC10511984?pdf=render
 35861678,https://doi.org/10.2196/36989,Developing a Long COVID Phenotype for Postacute COVID-19 in a National Primary Care Sentinel Cohort: Observational Retrospective Database Analysis.,"Mayor N, Meza-Torres B, Okusi C, Delanerolle G, Chapman M, Wang W, Anand S, Feher M, Macartney J, Byford R, Joy M, Gatenby P, Curcin V, Greenhalgh T, Delaney B, de Lusignan S.",,JMIR public health and surveillance,2022,2022-08-11,Y,Phenotype; Surveillance; epidemiology; Public Health; Hospitalization; Social Class; Disease Management; General Practitioners; Ethnicity; Electronic Health Record; Medical Record Systems; Systematized Nomenclature Of Medicine; Computerized; Bioportal; Biomedical Ontologies; Data Accuracy; Digital Tool; Covid-19; Sars-cov-2; Long Covid; Postacute Covid-19 Syndrome; Data Extracts,,,"<h4>Background</h4>Following COVID-19, up to 40% of people have ongoing health problems, referred to as postacute COVID-19 or long COVID (LC). LC varies from a single persisting symptom to a complex multisystem disease. Research has flagged that this condition is underrecorded in primary care records, and seeks to better define its clinical characteristics and management. Phenotypes provide a standard method for case definition and identification from routine data and are usually machine-processable. An LC phenotype can underpin research into this condition.<h4>Objective</h4>This study aims to develop a phenotype for LC to inform the epidemiology and future research into this condition. We compared clinical symptoms in people with LC before and after their index infection, recorded from March 1, 2020, to April 1, 2021. We also compared people recorded as having acute infection with those with LC who were hospitalized and those who were not.<h4>Methods</h4>We used data from the Primary Care Sentinel Cohort (PCSC) of the Oxford Royal College of General Practitioners (RCGP) Research and Surveillance Centre (RSC) database. This network was recruited to be nationally representative of the English population. We developed an LC phenotype using our established 3-step ontological method: (1) ontological step (defining the reasoning process underpinning the phenotype, (2) coding step (exploring what clinical terms are available, and (3) logical extract model (testing performance). We created a version of this phenotype using Protégé in the ontology web language for BioPortal and using PhenoFlow. Next, we used the phenotype to compare people with LC (1) with regard to their symptoms in the year prior to acquiring COVID-19 and (2) with people with acute COVID-19. We also compared hospitalized people with LC with those not hospitalized. We compared sociodemographic details, comorbidities, and Office of National Statistics-defined LC symptoms between groups. We used descriptive statistics and logistic regression.<h4>Results</h4>The long-COVID phenotype differentiated people hospitalized with LC from people who were not and where no index infection was identified. The PCSC (N=7.4 million) includes 428,479 patients with acute COVID-19 diagnosis confirmed by a laboratory test and 10,772 patients with clinically diagnosed COVID-19. A total of 7471 (1.74%, 95% CI 1.70-1.78) people were coded as having LC, 1009 (13.5%, 95% CI 12.7-14.3) had a hospital admission related to acute COVID-19, and 6462 (86.5%, 95% CI 85.7-87.3) were not hospitalized, of whom 2728 (42.2%) had no COVID-19 index date recorded. In addition, 1009 (13.5%, 95% CI 12.73-14.28) people with LC were hospitalized compared to 17,993 (4.5%, 95% CI 4.48-4.61; P<.001) with uncomplicated COVID-19.<h4>Conclusions</h4>Our LC phenotype enables the identification of individuals with the condition in routine data sets, facilitating their comparison with unaffected people through retrospective research. This phenotype and study protocol to explore its face validity contributes to a better understanding of LC.",,pdf:https://publichealth.jmir.org/2022/8/e36989/PDF; doi:https://doi.org/10.2196/36989; html:https://europepmc.org/articles/PMC9374163
 31053412,https://doi.org/10.1016/j.burns.2019.04.006,Severe burns in Australian and New Zealand adults: Epidemiology and burn centre care.,"Toppi J, Cleland H, Gabbe B.",,Burns : journal of the International Society for Burn Injuries,2019,2019-04-30,N,Mortality; Burn; Severe burns; epidemiology,,,"<h4>Introduction</h4>Studies describing the epidemiology of severe burns (>20% total body surface area) in adults are limited despite the extensive associated morbidity and mortality. This study aimed to describe the epidemiology of severe burn injuries admitted to burn centres in Australia and New Zealand.<h4>Materials and methods</h4>Data from the Burns Registry of Australia and New Zealand (BRANZ) were used in this study. Patients were eligible for inclusion if they were admitted between August 2009 and June 2013, were adults (18-years or older), and had burns of 20% total body surface area (TBSA) or greater. Demographics, burn characteristics and in-hospital mortality risk factors were investigated using multivariable Cox proportional hazards analysis.<h4>Results</h4>There were 496 BRANZ registered patients who met the inclusion criteria. Over half of the patients were aged 18-40 years and most were male. The median (IQR) TBSA was 31 (25-47). Most (75%) patients had burns involving <50% TBSA, 58% sustained their burn injury at home, and 86% had sustained flame burns. Leisure activities, working for income and preparing food together accounted for over 48% of the activities undertaken at the time of injury. The in-hospital mortality rate was 17% and the median (IQR) length of stay was 24 (12-44) days. Seventy-two percent were admitted to an intensive care unit (ICU) and 40% of patients had an associated inhalation injury. Alcohol and/or drug involvement was suspected in 25% of cases.<h4>Conclusion</h4>This study describes the demographics, burn injury characteristics and in-hospital outcomes of severe burn injuries in adults whilst also identifying key predictors of inpatient mortality. Key findings included the over-representation of young males, intentional self-harm injuries and flame as a cause of burns and highlights high risk groups to help aid in the development of targeted prevention strategies.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa50368/Download/0050368-25062019091637.pdf; doi:https://doi.org/10.1016/j.burns.2019.04.006
-32401709,https://doi.org/10.1016/s2468-2667(20)30112-2,COVID-19: a public health approach to manage domestic violence is needed.,"Chandan JS, Taylor J, Bradbury-Jones C, Nirantharakumar K, Kane E, Bandyopadhyay S.",,The Lancet. Public health,2020,2020-05-10,Y,,,,,Chandan et al. comment on the effect the covid pandemic may have on domestic violence and propose surveillance for domestic violence is needed. ,pdf:http://www.thelancet.com/article/S2468266720301122/pdf; doi:https://doi.org/10.1016/S2468-2667(20)30112-2; html:https://europepmc.org/articles/PMC7252171; pdf:https://europepmc.org/articles/PMC7252171?pdf=render
 32346541,https://doi.org/10.1093/burnst/tkz004,Predictors of itch and pain in the 12 months following burn injury: results from the Burns Registry of Australia and New Zealand (BRANZ) Long-Term Outcomes Project.,"Tracy LM, Edgar DW, Schrale R, Cleland H, Gabbe BJ, BRANZ Adult Long-Term Outcomes Pilot Project participating sites and working party.",,Burns & trauma,2020,2020-02-27,Y,Australia; Pain; New Zealand; Cohort study; Outcomes; Predictor; Itch; Burn Registry,Better Care,injuries and accidents,"<h4>Background</h4>Itch and pain are common complaints of patients with burn injuries. This study aimed to describe the prevalence and predictors of itch and moderate to severe pain in the first 12 months following a burn injury, and determine the association between itch, moderate to severe pain, work-related outcomes, and health-related quality of life following a burn injury.<h4>Methods</h4>Burn patients aged 18 years and older were recruited from five Australian specialist burn units. Patients completed the 36-item Short Form Health Survey Version 2 (SF-36 V2), the Sickness Impact Profile (SIP) work scale, and a specially developed questionnaire relating to itch at 1, 6, and 12 months post-injury. Moderate to severe pain was defined as a score less than 40 on the bodily pain domain of the SF-36 V2. Multivariate mixed-effects regression models were used to identify patient and burn injury predictors of itch and moderate to severe pain.<h4>Results</h4>Three hundred and twenty-eight patients were included. The prevalence of itch decreased from 50% at 1 month to 27% at 12 months. Similarly, the prevalence of moderate to severe pain decreased from 23% at 1 month to 13% at 12 months. Compared to patients aged 18-34, the adjusted odds of experiencing any itch were 59% (95% CI: 0.20, 0.82) and 55% (95% CI: 0.22, 0.91) lower for patients aged between 35 and 49 and ≥ 50 years, respectively. Compared to patients aged 18-34, the adjusted odds of experiencing moderate to severe pain were 3.12 (95% CI: 1.35, 7.20) and 3.42 (95% CI: 1.47, 7.93) times higher for patients aged 35-49 and ≥ 50 years, respectively.<h4>Conclusions</h4>Less than 15% of patients reported moderate or severe pain at 12 months, while approximately one-quarter of the patients reported itch at the same period. The presence of moderate to severe pain was associated with a greater negative impact on health-related quality of life and work outcomes compared to itch. Further research is needed to improve our ability to identify patients at higher risk of persistent itch and pain who would benefit from targeted review and intervention studies.",,pdf:https://academic.oup.com/burnstrauma/article-pdf/doi/10.1093/burnst/tkz004/33423529/tkz004.pdf; doi:https://doi.org/10.1093/burnst/tkz004; html:https://europepmc.org/articles/PMC7175773; pdf:https://europepmc.org/articles/PMC7175773?pdf=render
-34040552,https://doi.org/10.3389/fpsyt.2021.627996,Optimising a Simple Fully Convolutional Network for Accurate Brain Age Prediction in the PAC 2019 Challenge.,"Gong W, Beckmann CF, Vedaldi A, Smith SM, Peng H.",,Frontiers in psychiatry,2021,2021-05-10,Y,Brain imaging; Predictive Analysis; Big Data; Deep Learning; Convolution Neural Network; Brain Age Prediction,,,"Brain age prediction from brain MRI scans not only helps improve brain ageing modelling generally, but also provides benchmarks for predictive analysis methods. Brain-age delta, which is the difference between a subject's predicted age and true age, has become a meaningful biomarker for the health of the brain. Here, we report the details of our brain age prediction models and results in the Predictive Analysis Challenge 2019. The aim of the challenge was to use T1-weighted brain MRIs to predict a subject's age in multicentre datasets. We apply a lightweight deep convolutional neural network architecture, Simple Fully Convolutional Neural Network (SFCN), and combined several techniques including data augmentation, transfer learning, model ensemble, and bias correction for brain age prediction. The model achieved first place in both of the two objectives in the PAC 2019 brain age prediction challenge: Mean absolute error (MAE) = 2.90 years without bias removal (Second Place = 3.09 yrs; Third Place = 3.33 yrs), and MAE = 2.95 years with bias removal, leading by a large margin (Second Place = 3.80 yrs; Third Place = 3.92 yrs).",,pdf:https://www.frontiersin.org/articles/10.3389/fpsyt.2021.627996/pdf; doi:https://doi.org/10.3389/fpsyt.2021.627996; html:https://europepmc.org/articles/PMC8141616; pdf:https://europepmc.org/articles/PMC8141616?pdf=render
+32401709,https://doi.org/10.1016/s2468-2667(20)30112-2,COVID-19: a public health approach to manage domestic violence is needed.,"Chandan JS, Taylor J, Bradbury-Jones C, Nirantharakumar K, Kane E, Bandyopadhyay S.",,The Lancet. Public health,2020,2020-05-10,Y,,,,,Chandan et al. comment on the effect the covid pandemic may have on domestic violence and propose surveillance for domestic violence is needed. ,pdf:http://www.thelancet.com/article/S2468266720301122/pdf; doi:https://doi.org/10.1016/S2468-2667(20)30112-2; html:https://europepmc.org/articles/PMC7252171; pdf:https://europepmc.org/articles/PMC7252171?pdf=render
 34236053,https://doi.org/10.1172/jci.insight.149446,Combining multiomics and drug perturbation profiles to identify muscle-specific treatments for spinal muscular atrophy.,"Meijboom KE, Volpato V, Monzón-Sandoval J, Hoolachan JM, Hammond SM, Abendroth F, de Jong OG, Hazell G, Ahlskog N, Wood MJ, Webber C, Bowerman M.",,JCI insight,2021,2021-07-08,Y,Bioinformatics; Drug therapy; Neuroscience; Genetic diseases; Muscle Biology,,,"Spinal muscular atrophy (SMA) is a neuromuscular disorder caused by loss of survival motor neuron (SMN) protein. While SMN restoration therapies are beneficial, they are not a cure. We aimed to identify potentially novel treatments to alleviate muscle pathology combining transcriptomics, proteomics, and perturbational data sets. This revealed potential drug candidates for repurposing in SMA. One of the candidates, harmine, was further investigated in cell and animal models, improving multiple disease phenotypes, including lifespan, weight, and key molecular networks in skeletal muscle. Our work highlights the potential of multiple and parallel data-driven approaches for the development of potentially novel treatments for use in combination with SMN restoration therapies.",,pdf:http://insight.jci.org/articles/view/149446/files/pdf; doi:https://doi.org/10.1172/jci.insight.149446; html:https://europepmc.org/articles/PMC8410072; pdf:https://europepmc.org/articles/PMC8410072?pdf=render
+34040552,https://doi.org/10.3389/fpsyt.2021.627996,Optimising a Simple Fully Convolutional Network for Accurate Brain Age Prediction in the PAC 2019 Challenge.,"Gong W, Beckmann CF, Vedaldi A, Smith SM, Peng H.",,Frontiers in psychiatry,2021,2021-05-10,Y,Brain imaging; Predictive Analysis; Big Data; Deep Learning; Convolution Neural Network; Brain Age Prediction,,,"Brain age prediction from brain MRI scans not only helps improve brain ageing modelling generally, but also provides benchmarks for predictive analysis methods. Brain-age delta, which is the difference between a subject's predicted age and true age, has become a meaningful biomarker for the health of the brain. Here, we report the details of our brain age prediction models and results in the Predictive Analysis Challenge 2019. The aim of the challenge was to use T1-weighted brain MRIs to predict a subject's age in multicentre datasets. We apply a lightweight deep convolutional neural network architecture, Simple Fully Convolutional Neural Network (SFCN), and combined several techniques including data augmentation, transfer learning, model ensemble, and bias correction for brain age prediction. The model achieved first place in both of the two objectives in the PAC 2019 brain age prediction challenge: Mean absolute error (MAE) = 2.90 years without bias removal (Second Place = 3.09 yrs; Third Place = 3.33 yrs), and MAE = 2.95 years with bias removal, leading by a large margin (Second Place = 3.80 yrs; Third Place = 3.92 yrs).",,pdf:https://www.frontiersin.org/articles/10.3389/fpsyt.2021.627996/pdf; doi:https://doi.org/10.3389/fpsyt.2021.627996; html:https://europepmc.org/articles/PMC8141616; pdf:https://europepmc.org/articles/PMC8141616?pdf=render
 34112101,https://doi.org/10.1186/s12872-021-02020-7,Routine clinical care data from thirteen cardiac outpatient clinics: design of the Cardiology Centers of the Netherlands (CCN) database.,"Bots SH, Siegersma KR, Onland-Moret NC, Asselbergs FW, Somsen GA, Tulevski II, den Ruijter HM, Hofstra L.",,BMC cardiovascular disorders,2021,2021-06-10,Y,Prevention; Big Data; Cardiovascular Care; Clinical Care Data,,,"<h4>Background</h4>Despite the increasing availability of clinical data due to the digitalisation of healthcare systems, data often remain inaccessible due to the diversity of data collection systems. In the Netherlands, Cardiology Centers of the Netherlands (CCN) introduced ""one-stop shop"" diagnostic clinics for patients suspected of cardiac disease by their general practitioner. All CCN clinics use the same data collection system and standardised protocol, creating a large regular care database. This database can be used to describe referral practices, evaluate risk factors for cardiovascular disease (CVD) in important patient subgroups, and develop prediction models for use in daily care.<h4>Construction and content</h4>The current database contains data on all patients who underwent a cardiac workup in one of the 13 CCN clinics between 2007 and February 2018 (n = 109,151, 51.9% women). Data were pseudonymised and contain information on anthropometrics, cardiac symptoms, risk factors, comorbidities, cardiovascular and family history, standard blood laboratory measurements, transthoracic echocardiography, electrocardiography in rest and during exercise, and medication use. Clinical follow-up is based on medical need and consisted of either a repeat visit at CCN (43.8%) or referral for an external procedure in a hospital (16.5%). Passive follow-up via linkage to national mortality registers is available for 95% of the database.<h4>Utility and discussion</h4>The CCN database provides a strong base for research into historically underrepresented patient groups due to the large number of patients and the lack of in- and exclusion criteria. It also enables the development of artificial intelligence-based decision support tools. Its contemporary nature allows for comparison of daily care with the current guidelines and protocols. Missing data is an inherent limitation, as the cardiologist could deviate from standardised protocols when clinically indicated.<h4>Conclusion</h4>The CCN database offers the opportunity to conduct research in a unique population referred from the general practitioner to the cardiologist for diagnostic workup. This, in combination with its large size, the representation of historically underrepresented patient groups and contemporary nature makes it a valuable tool for expanding our knowledge of cardiovascular diseases.<h4>Trial registration</h4>Not applicable.",,pdf:https://bmccardiovascdisord.biomedcentral.com/counter/pdf/10.1186/s12872-021-02020-7; doi:https://doi.org/10.1186/s12872-021-02020-7; html:https://europepmc.org/articles/PMC8191101; pdf:https://europepmc.org/articles/PMC8191101?pdf=render
-35869125,https://doi.org/10.1038/s41598-022-16375-0,Minimising multi-centre radiomics variability through image normalisation: a pilot study.,"Campello VM, Martín-Isla C, Izquierdo C, Guala A, Palomares JFR, Viladés D, Descalzo ML, Karakas M, Çavuş E, Raisi-Estabragh Z, Petersen SE, Escalera S, Seguí S, Lekadir K.",,Scientific reports,2022,2022-07-22,Y,,,,"Radiomics is an emerging technique for the quantification of imaging data that has recently shown great promise for deeper phenotyping of cardiovascular disease. Thus far, the technique has been mostly applied in single-centre studies. However, one of the main difficulties in multi-centre imaging studies is the inherent variability of image characteristics due to centre differences. In this paper, a comprehensive analysis of radiomics variability under several image- and feature-based normalisation techniques was conducted using a multi-centre cardiovascular magnetic resonance dataset. 218 subjects divided into healthy (n = 112) and hypertrophic cardiomyopathy (n = 106, HCM) groups from five different centres were considered. First and second order texture radiomic features were extracted from three regions of interest, namely the left and right ventricular cavities and the left ventricular myocardium. Two methods were used to assess features' variability. First, feature distributions were compared across centres to obtain a distribution similarity index. Second, two classification tasks were proposed to assess: (1) the amount of centre-related information encoded in normalised features (centre identification) and (2) the generalisation ability for a classification model when trained on these features (healthy versus HCM classification). The results showed that the feature-based harmonisation technique ComBat is able to remove the variability introduced by centre information from radiomic features, at the expense of slightly degrading classification performance. Piecewise linear histogram matching normalisation gave features with greater generalisation ability for classification ( balanced accuracy in between 0.78 ± 0.08 and 0.79 ± 0.09). Models trained with features from images without normalisation showed the worst performance overall ( balanced accuracy in between 0.45 ± 0.28 and 0.60 ± 0.22). In conclusion, centre-related information removal did not imply good generalisation ability for classification.",,pdf:https://www.nature.com/articles/s41598-022-16375-0.pdf; doi:https://doi.org/10.1038/s41598-022-16375-0; html:https://europepmc.org/articles/PMC9307565; pdf:https://europepmc.org/articles/PMC9307565?pdf=render
 32807724,https://doi.org/10.1016/j.auec.2020.07.007,Pain assessment following burn injury in Australia and New Zealand: Variation in practice and its association on in-hospital outcomes.,"Tracy LM, Cleland H, Cameron PA, Gabbe BJ.",,Australasian emergency care,2021,2020-08-15,N,Australia; Burn; Pain; New Zealand; Registry; Pain Assessment,,,"<h4>Background</h4>Pain is common following burn injury. Pain assessments are required to ensure appropriate pain management is provided. This study aimed to describe the prevalence and potential variation in practice of validated and documented pain assessment following burn injury in Australian and New Zealand burn units, identify clinical characteristics of patients who receive a pain assessment, and explore the associations between receiving a pain assessment and in-hospital outcomes.<h4>Methods</h4>Burns Registry of Australia and New Zealand (BRANZ) admissions data were extracted. Responses to the pain assessment field were presented by contributing burns unit using frequencies and percentages. Demographic, injury severity and event, and in-hospital outcomes data were assessed.<h4>Results</h4>There were 3009 admissions over the study period; 2481 of these received an assessment. The rate of pain assessment varied considerably between units. Women and adult patients more commonly received a pain assessment. Receiving a pain assessment was associated with a 53% adjusted increase in LOS.<h4>Conclusions</h4>There are differences in the profile of patients who receive a pain assessment after burn injury. The findings of this study will be reported back to designated burns units to improve pain assessment rates and patient care.",,doi:https://doi.org/10.1016/j.auec.2020.07.007
+35869125,https://doi.org/10.1038/s41598-022-16375-0,Minimising multi-centre radiomics variability through image normalisation: a pilot study.,"Campello VM, Martín-Isla C, Izquierdo C, Guala A, Palomares JFR, Viladés D, Descalzo ML, Karakas M, Çavuş E, Raisi-Estabragh Z, Petersen SE, Escalera S, Seguí S, Lekadir K.",,Scientific reports,2022,2022-07-22,Y,,,,"Radiomics is an emerging technique for the quantification of imaging data that has recently shown great promise for deeper phenotyping of cardiovascular disease. Thus far, the technique has been mostly applied in single-centre studies. However, one of the main difficulties in multi-centre imaging studies is the inherent variability of image characteristics due to centre differences. In this paper, a comprehensive analysis of radiomics variability under several image- and feature-based normalisation techniques was conducted using a multi-centre cardiovascular magnetic resonance dataset. 218 subjects divided into healthy (n = 112) and hypertrophic cardiomyopathy (n = 106, HCM) groups from five different centres were considered. First and second order texture radiomic features were extracted from three regions of interest, namely the left and right ventricular cavities and the left ventricular myocardium. Two methods were used to assess features' variability. First, feature distributions were compared across centres to obtain a distribution similarity index. Second, two classification tasks were proposed to assess: (1) the amount of centre-related information encoded in normalised features (centre identification) and (2) the generalisation ability for a classification model when trained on these features (healthy versus HCM classification). The results showed that the feature-based harmonisation technique ComBat is able to remove the variability introduced by centre information from radiomic features, at the expense of slightly degrading classification performance. Piecewise linear histogram matching normalisation gave features with greater generalisation ability for classification ( balanced accuracy in between 0.78 ± 0.08 and 0.79 ± 0.09). Models trained with features from images without normalisation showed the worst performance overall ( balanced accuracy in between 0.45 ± 0.28 and 0.60 ± 0.22). In conclusion, centre-related information removal did not imply good generalisation ability for classification.",,pdf:https://www.nature.com/articles/s41598-022-16375-0.pdf; doi:https://doi.org/10.1038/s41598-022-16375-0; html:https://europepmc.org/articles/PMC9307565; pdf:https://europepmc.org/articles/PMC9307565?pdf=render
 34980174,https://doi.org/10.1186/s12967-021-03210-9,"Increased burden of cardiovascular disease in people with liver disease: unequal geographical variations, risk factors and excess years of life lost.","Chang WH, Mueller SH, Chung SC, Foster GR, Lai AG.",,Journal of translational medicine,2022,2022-01-03,Y,liver disease; Geographical variations; incidence; Cardiovascular Risk; Electronic Health Records; Years Of Life Lost,,,"<h4>Background</h4>People with liver disease are at increased risk of developing cardiovascular disease (CVD), however, there has yet been an investigation of incidence burden, risk, and premature mortality across a wide range of liver conditions and cardiovascular outcomes.<h4>Methods</h4>We employed population-wide electronic health records (EHRs; from 1998 to 2020) consisting of almost 4 million adults to assess regional variations in disease burden of five liver conditions, alcoholic liver disease (ALD), autoimmune liver disease, chronic hepatitis B infection (HBV), chronic hepatitis C infection (HCV) and NAFLD, in England. We analysed regional differences in incidence rates for 17 manifestations of CVD in people with or without liver disease. The associations between biomarkers and comorbidities and risk of CVD in patients with liver disease were estimated using Cox models. For each liver condition, we estimated excess years of life lost (YLL) attributable to CVD (i.e., difference in YLL between people with or without CVD).<h4>Results</h4>The age-standardised incidence rate for any liver disease was 114.5 per 100,000 person years. The highest incidence was observed in NAFLD (85.5), followed by ALD (24.7), HCV (6.0), HBV (4.1) and autoimmune liver disease (3.7). Regionally, the North West and North East regions consistently exhibited high incidence burden. Age-specific incidence rate analyses revealed that the peak incidence for liver disease of non-viral aetiology is reached in individuals aged 50-59 years. Patients with liver disease had a two-fold higher incidence burden of CVD (2634.6 per 100,000 persons) compared to individuals without liver disease (1339.7 per 100,000 persons). When comparing across liver diseases, atrial fibrillation was the most common initial CVD presentation while hypertrophic cardiomyopathy was the least common. We noted strong positive associations between body mass index and current smoking and risk of CVD. Patients who also had diabetes, hypertension, proteinuric kidney disease, chronic kidney disease, diverticular disease and gastro-oesophageal reflex disorders had a higher risk of CVD, as do patients with low albumin, raised C-reactive protein and raised International Normalized Ratio levels. All types of CVD were associated with shorter life expectancies. When evaluating excess YLLs by age of CVD onset and by liver disease type, differences in YLLs, when comparing across CVD types, were more pronounced at younger ages.<h4>Conclusions</h4>We developed a public online app ( https://lailab.shinyapps.io/cvd_in_liver_disease/ ) to showcase results interactively. We provide a blueprint that revealed previously underappreciated clinical factors related to the risk of CVD, which differed in the magnitude of effects across liver diseases. We found significant geographical variations in the burden of liver disease and CVD, highlighting the need to devise local solutions. Targeted policies and regional initiatives addressing underserved communities might help improve equity of access to CVD screening and treatment.",,pdf:https://translational-medicine.biomedcentral.com/counter/pdf/10.1186/s12967-021-03210-9; doi:https://doi.org/10.1186/s12967-021-03210-9; html:https://europepmc.org/articles/PMC8722174; pdf:https://europepmc.org/articles/PMC8722174?pdf=render
 39075055,https://doi.org/10.1038/s41467-024-49956-w,Author Correction: Concordance of randomised controlled trials for artificial intelligence interventions with the CONSORT-AI reporting guidelines.,"Martindale APL, Llewellyn CD, de Visser RO, Ng B, Ngai V, Kale AU, di Ruffano LF, Golub RM, Collins GS, Moher D, McCradden MD, Oakden-Rayner L, Rivera SC, Calvert M, Kelly CJ, Lee CS, Yau C, Chan AW, Keane PA, Beam AL, Denniston AK, Liu X.",,Nature communications,2024,2024-07-29,Y,,,,,,pdf:https://www.nature.com/articles/s41467-024-49956-w.pdf; doi:https://doi.org/10.1038/s41467-024-49956-w; html:https://europepmc.org/articles/PMC11286847; pdf:https://europepmc.org/articles/PMC11286847?pdf=render
+33472714,https://doi.org/10.1017/s1368980021000197,Diet and risk of gastro-oesophageal reflux disease in the Melbourne Collaborative Cohort Study.,"Wang SE, Hodge AM, Dashti SG, Dixon-Suen SC, Mitchell H, Thomas RJ, Williamson EM, Makalic E, Boussioutas A, Haydon AM, Giles GG, Milne RL, Kendall BJ, English DR.",,Public health nutrition,2021,2021-01-21,N,Fat; Diet; Prospective Cohort Study; Gastro-oesophageal Reflux Disease; Carbonated Beverages,,,"<h4>Objective</h4>To examine associations between diet and risk of developing gastro-oesophageal reflux disease (GERD).<h4>Design</h4>Prospective cohort with a median follow-up of 15·8 years. Baseline diet was measured using a FFQ. GERD was defined as self-reported current or history of daily heartburn or acid regurgitation beginning at least 2 years after baseline. Sex-specific logistic regressions were performed to estimate OR for GERD associated with diet quality scores and intakes of nutrients, food groups and individual foods and beverages. The effect of substituting saturated fat for monounsaturated or polyunsaturated fat on GERD risk was examined.<h4>Setting</h4>Melbourne, Australia.<h4>Participants</h4>A cohort of 20 926 participants (62 % women) aged 40-59 years at recruitment between 1990 and 1994.<h4>Results</h4>For men, total fat intake was associated with increased risk of GERD (OR 1·05 per 5 g/d; 95 % CI 1·01, 1·09; P = 0·016), whereas total carbohydrate (OR 0·89 per 30 g/d; 95 % CI 0·82, 0·98; P = 0·010) and starch intakes (OR 0·84 per 30 g/d; 95 % CI 0·75, 0·94; P = 0·005) were associated with reduced risk. Nutrients were not associated with risk for women. For both sexes, substituting saturated fat for polyunsaturated or monounsaturated fat did not change risk. For both sexes, fish, chicken, cruciferous vegetables and carbonated beverages were associated with increased risk, whereas total fruit and citrus were associated with reduced risk. No association was observed with diet quality scores.<h4>Conclusions</h4>Diet is a possible risk factor for GERD, but food considered as triggers of GERD symptoms might not necessarily contribute to disease development. Potential differential associations for men and women warrant further investigation.",,pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/274F1A424FA99A10625C3447D256A318/S1368980021000197a.pdf/div-class-title-diet-and-risk-of-gastro-oesophageal-reflux-disease-in-the-melbourne-collaborative-cohort-study-div.pdf; doi:https://doi.org/10.1017/S1368980021000197; html:https://europepmc.org/articles/PMC11082811; pdf:https://europepmc.org/articles/PMC11082811?pdf=render; doi:https://doi.org/10.1017/s1368980021000197
 37477760,https://doi.org/10.1007/s10875-023-01547-y,Immunologic and Genetic Contributors to CD46-Dependent Immune Dysregulation.,"Meyer BJ, Kunz N, Seki S, Higgins R, Ghosh A, Hupfer R, Baldrich A, Hirsiger JR, Jauch AJ, Burgener AV, Lötscher J, Aschwanden M, Dickenmann M, Stegert M, Berger CT, Daikeler T, Heijnen I, Navarini AA, Rudin C, Yamamoto H, Kemper C, Hess C, Recher M.",,Journal of clinical immunology,2023,2023-07-21,Y,SLE; systemic lupus erythematosus; Next-generation Sequencing; Penetrance; Atypical Hemolytic Uremic Syndrome; Cd46; Haploinsufficiency; Ahus; Inborn Errors Of Immunity; Primary Immunodeficiency Complement,,,"Mutations in CD46 predispose to atypical hemolytic uremic syndrome (aHUS) with low penetrance. Factors driving immune-dysregulatory disease in individual mutation carriers have remained ill-understood. In addition to its role as a negative regulator of the complement system, CD46 modifies T cell-intrinsic metabolic adaptation and cytokine production. Comparative immunologic analysis of diseased vs. healthy CD46 mutation carriers has not been performed in detail yet. In this study, we comprehensively analyzed clinical, molecular, immune-phenotypic, cytokine secretion, immune-metabolic, and genetic profiles in healthy vs. diseased individuals carrying a rare, heterozygous CD46 mutation identified within a large single family. Five out of six studied individuals carried a CD46 gene splice-site mutation causing an in-frame deletion of 21 base pairs. One child suffered from aHUS and his paternal uncle manifested with adult-onset systemic lupus erythematosus (SLE). Three mutation carriers had no clinical evidence of CD46-related disease to date. CD4<sup>+</sup> T cell-intrinsic CD46 expression was uniformly 50%-reduced but was comparable in diseased vs. healthy mutation carriers. Reconstitution experiments defined the 21-base pair-deleted CD46 variant as intracellularly-but not surface-expressed and haploinsufficient. Both healthy and diseased mutation carriers displayed reduced CD46-dependent T cell mitochondrial adaptation. Diseased mutation carriers had lower peripheral regulatory T cell (Treg) frequencies and carried potentially epistatic, private rare variants in other inborn errors of immunity (IEI)-associated proinflammatory genes, not found in healthy mutation carriers. In conclusion, low Treg and rare non-CD46 immune-gene variants may contribute to clinically manifest CD46 haploinsufficiency-associated immune-dysregulation.",,pdf:https://link.springer.com/content/pdf/10.1007/s10875-023-01547-y.pdf; doi:https://doi.org/10.1007/s10875-023-01547-y; html:https://europepmc.org/articles/PMC10661731; pdf:https://europepmc.org/articles/PMC10661731?pdf=render
 37280096,https://doi.org/10.1136/thorax-2023-220057,"Asthma symptoms, spirometry and air pollution exposure in schoolchildren in an informal settlement and an affluent area of Nairobi, Kenya.","Meme H, Amukoye E, Bowyer C, Chakaya J, Das D, Dobson R, Dragosits U, Fuld J, Gray C, Hahn M, Kiplimo R, Lesosky M, Loh MM, McKendree J, Mortimer K, Ndombi A, Netter L, Obasi A, Orina F, Pearson C, Price H, Quint JK, Semple S, Twigg M, Waelde C, Walnycki A, Warwick M, Wendler J, West SE, Wilson M, Zurba L, Devereux G.",,Thorax,2023,2023-06-06,Y,Asthma; Paediatric Asthma; Asthma Epidemiology,,,"<h4>Background</h4>Although 1 billion people live in informal (slum) settlements, the consequences for respiratory health of living in these settlements remain largely unknown. This study investigated whether children living in an informal settlement in Nairobi, Kenya are at increased risk of asthma symptoms.<h4>Methods</h4>Children attending schools in Mukuru (an informal settlement in Nairobi) and a more affluent area (Buruburu) were compared. Questionnaires quantified respiratory symptoms and environmental exposures; spirometry was performed; personal exposure to particulate matter (PM<sub>2.5</sub>) was estimated.<h4>Results</h4>2373 children participated, 1277 in Mukuru (median age, IQR 11, 9-13 years, 53% girls), and 1096 in Buruburu (10, 8-12 years, 52% girls). Mukuru schoolchildren were from less affluent homes, had greater exposure to pollution sources and PM<sub>2.5</sub>. When compared with Buruburu schoolchildren, Mukuru schoolchildren had a greater prevalence of symptoms, 'current wheeze' (9.5% vs 6.4%, p=0.007) and 'trouble breathing' (16.3% vs 12.6%, p=0.01), and these symptoms were more severe and problematic. Diagnosed asthma was more common in Buruburu (2.8% vs 1.2%, p=0.004). Spirometry did not differ between Mukuru and Buruburu. Regardless of community, significant adverse associations were observed with self-reported exposure to 'vapours, dusts, gases, fumes', mosquito coil burning, adult smoker(s) in the home, refuse burning near homes and residential proximity to roads.<h4>Conclusion</h4>Children living in informal settlements are more likely to develop wheezing symptoms consistent with asthma that are more severe but less likely to be diagnosed as asthma. Self-reported but not objectively measured air pollution exposure was associated with increased risk of asthma symptoms.",,pdf:https://thorax.bmj.com/content/thoraxjnl/early/2023/05/24/thorax-2023-220057.full.pdf; doi:https://doi.org/10.1136/thorax-2023-220057; html:https://europepmc.org/articles/PMC10715514; pdf:https://europepmc.org/articles/PMC10715514?pdf=render
-33472714,https://doi.org/10.1017/s1368980021000197,Diet and risk of gastro-oesophageal reflux disease in the Melbourne Collaborative Cohort Study.,"Wang SE, Hodge AM, Dashti SG, Dixon-Suen SC, Mitchell H, Thomas RJ, Williamson EM, Makalic E, Boussioutas A, Haydon AM, Giles GG, Milne RL, Kendall BJ, English DR.",,Public health nutrition,2021,2021-01-21,N,Fat; Diet; Prospective Cohort Study; Gastro-oesophageal Reflux Disease; Carbonated Beverages,,,"<h4>Objective</h4>To examine associations between diet and risk of developing gastro-oesophageal reflux disease (GERD).<h4>Design</h4>Prospective cohort with a median follow-up of 15·8 years. Baseline diet was measured using a FFQ. GERD was defined as self-reported current or history of daily heartburn or acid regurgitation beginning at least 2 years after baseline. Sex-specific logistic regressions were performed to estimate OR for GERD associated with diet quality scores and intakes of nutrients, food groups and individual foods and beverages. The effect of substituting saturated fat for monounsaturated or polyunsaturated fat on GERD risk was examined.<h4>Setting</h4>Melbourne, Australia.<h4>Participants</h4>A cohort of 20 926 participants (62 % women) aged 40-59 years at recruitment between 1990 and 1994.<h4>Results</h4>For men, total fat intake was associated with increased risk of GERD (OR 1·05 per 5 g/d; 95 % CI 1·01, 1·09; P = 0·016), whereas total carbohydrate (OR 0·89 per 30 g/d; 95 % CI 0·82, 0·98; P = 0·010) and starch intakes (OR 0·84 per 30 g/d; 95 % CI 0·75, 0·94; P = 0·005) were associated with reduced risk. Nutrients were not associated with risk for women. For both sexes, substituting saturated fat for polyunsaturated or monounsaturated fat did not change risk. For both sexes, fish, chicken, cruciferous vegetables and carbonated beverages were associated with increased risk, whereas total fruit and citrus were associated with reduced risk. No association was observed with diet quality scores.<h4>Conclusions</h4>Diet is a possible risk factor for GERD, but food considered as triggers of GERD symptoms might not necessarily contribute to disease development. Potential differential associations for men and women warrant further investigation.",,pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/274F1A424FA99A10625C3447D256A318/S1368980021000197a.pdf/div-class-title-diet-and-risk-of-gastro-oesophageal-reflux-disease-in-the-melbourne-collaborative-cohort-study-div.pdf; doi:https://doi.org/10.1017/S1368980021000197; html:https://europepmc.org/articles/PMC11082811; pdf:https://europepmc.org/articles/PMC11082811?pdf=render; doi:https://doi.org/10.1017/s1368980021000197
 36449515,https://doi.org/10.1371/journal.pcbi.1010726,Cluster detection with random neighbourhood covering: Application to invasive Group A Streptococcal disease.,"Cavallaro M, Coelho J, Ready D, Decraene V, Lamagni T, McCarthy ND, Todkill D, Keeling MJ.",,PLoS computational biology,2022,2022-11-30,Y,,,,"The rapid detection of outbreaks is a key step in the effective control and containment of infectious diseases. In particular, the identification of cases which might be epidemiologically linked is crucial in directing outbreak-containment efforts and shaping the intervention of public health authorities. Often this requires the detection of clusters of cases whose numbers exceed those expected by a background of sporadic cases. Quantifying exceedances rapidly is particularly challenging when only few cases are typically reported in a precise location and time. To address such important public health concerns, we present a general method which can detect spatio-temporal deviations from a Poisson point process and estimate the odds of an isolate being part of a cluster. This method can be applied to diseases where detailed geographical information is available. In addition, we propose an approach to explicitly take account of delays in microbial typing. As a case study, we considered invasive group A Streptococcus infection events as recorded and typed by Public Health England from 2015 to 2020.",,pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010726&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1010726; html:https://europepmc.org/articles/PMC9744322; pdf:https://europepmc.org/articles/PMC9744322?pdf=render
 32704413,https://doi.org/10.1167/tvst.9.2.7,A Clinician's Guide to Artificial Intelligence: How to Critically Appraise Machine Learning Studies.,"Faes L, Liu X, Wagner SK, Fu DJ, Balaskas K, Sim DA, Bachmann LM, Keane PA, Denniston AK.",,Translational vision science & technology,2020,2020-02-12,Y,Artificial intelligence; Critical Appraisal; Machine Learning,,,"In recent years, there has been considerable interest in the prospect of machine learning models demonstrating expert-level diagnosis in multiple disease contexts. However, there is concern that the excitement around this field may be associated with inadequate scrutiny of methodology and insufficient adoption of scientific good practice in the studies involving artificial intelligence in health care. This article aims to empower clinicians and researchers to critically appraise studies of clinical applications of machine learning, through: (1) introducing basic machine learning concepts and nomenclature; (2) outlining key applicable principles of evidence-based medicine; and (3) highlighting some of the potential pitfalls in the design and reporting of these studies.",,pdf:https://tvst.arvojournals.org/arvo/content_public/journal/tvst/938366/i2164-2591-9-2-7_1597165820.03912.pdf; doi:https://doi.org/10.1167/tvst.9.2.7; html:https://europepmc.org/articles/PMC7346877; pdf:https://europepmc.org/articles/PMC7346877?pdf=render
 38115587,https://doi.org/10.1089/neu.2023.0464,The Australian Traumatic Brain Injury Initiative: Systematic Review of Predictive Value of Biological Markers for People With Moderate-Severe Traumatic Brain Injury.,"Bagg MK, Hellewell SC, Keeves J, Antonic-Baker A, McKimmie A, Hicks AJ, Gadowski A, Newcombe VFJ, Barlow KM, Balogh ZJ, Ross JP, Law M, Caeyenberghs K, Parizel PM, Thorne J, Papini M, Gill G, Jefferson A, Ponsford JL, Lannin NA, O'Brien TJ, Cameron PA, Cooper DJ, Rushworth N, Gabbe BJ, Fitzgerald M.",,Journal of neurotrauma,2024,2024-03-08,N,"Tomography, X-ray computed; Tissues; Biomarkers; Magnetic Resonance Imaging; Body Fluids; Common Data Elements; Brain Injuries, Traumatic; Systematic Review [Publication Type]",,,"The Australian Traumatic Brain Injury Initiative (AUS-TBI) aims to co-design a data resource to predict outcomes for people with moderate-severe traumatic brain injury (TBI) across Australia. Fundamental to this resource is the data dictionary, which is an ontology of data items. Here, we report the systematic review and consensus process for inclusion of biological markers in the data dictionary. Standardized database searches were implemented from inception through April 2022. English-language studies evaluating association between a fluid, tissue, or imaging marker and any clinical outcome in at least 10 patients with moderate-severe TBI were included. Records were screened using a prioritization algorithm and saturation threshold in Research Screener. Full-length records were then screened in Covidence. A pre-defined algorithm was used to assign a judgement of predictive value to each observed association, and high-value predictors were discussed in a consensus process. Searches retrieved 106,593 records; 1,417 full-length records were screened, resulting in 546 included records. Two hundred thirty-nine individual markers were extracted, evaluated against 101 outcomes. Forty-one markers were judged to be high-value predictors of 15 outcomes. Fluid markers retained following the consensus process included ubiquitin C-terminal hydrolase L1 (UCH-L1), S100, and glial fibrillary acidic protein (GFAP). Imaging markers included computed tomography (CT) scores (e.g., Marshall scores), pathological observations (e.g., hemorrhage, midline shift), and magnetic resonance imaging (MRI) classification (e.g., diffuse axonal injury). Clinical context and time of sampling of potential predictive indicators are important considerations for utility. This systematic review and consensus process has identified fluid and imaging biomarkers with high predictive value of clinical and long-term outcomes following moderate-severe TBI.",,doi:https://doi.org/10.1089/neu.2023.0464
-36823471,https://doi.org/10.1038/s42255-023-00753-7,Proteogenomic links to human metabolic diseases.,"Koprulu M, Carrasco-Zanini J, Wheeler E, Lockhart S, Kerrison ND, Wareham NJ, Pietzner M, Langenberg C.",,Nature metabolism,2023,2023-02-23,Y,,,,"Studying the plasma proteome as the intermediate layer between the genome and the phenome has the potential to identify new disease processes. Here, we conducted a cis-focused proteogenomic analysis of 2,923 plasma proteins measured in 1,180 individuals using antibody-based assays. We (1) identify 256 unreported protein quantitative trait loci (pQTL); (2) demonstrate shared genetic regulation of 224 cis-pQTLs with 575 specific health outcomes, revealing examples for notable metabolic diseases (such as gastrin-releasing peptide as a potential therapeutic target for type 2 diabetes); (3) improve causal gene assignment at 40% (n = 192) of overlapping risk loci; and (4) observe convergence of phenotypic consequences of cis-pQTLs and rare loss-of-function gene burden for 12 proteins, such as TIMD4 for lipoprotein metabolism. Our findings demonstrate the value of integrating complementary proteomic technologies with genomics even at moderate scale to identify new mediators of metabolic diseases with the potential for therapeutic interventions.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7614946; doi:https://doi.org/10.1038/s42255-023-00753-7; html:https://europepmc.org/articles/PMC7614946; pdf:https://europepmc.org/articles/PMC7614946?pdf=render
-38745010,https://doi.org/10.1038/s41591-024-02960-5,Dynamics of cognitive variability with age and its genetic underpinning in NIHR BioResource Genes and Cognition cohort participants.,"Rahman MS, Harrison E, Biggs H, Seikus C, Elliott P, Breen G, Kingston N, Bradley JR, Hill SM, Tom BDM, Chinnery PF.",,Nature medicine,2024,2024-05-14,Y,,,,"A leading explanation for translational failure in neurodegenerative disease is that new drugs are evaluated late in the disease course when clinical features have become irreversible. Here, to address this gap, we cognitively profiled 21,051 people aged 17-85 years as part of the Genes and Cognition cohort within the National Institute for Health and Care Research BioResource across England. We describe the cohort, present cognitive trajectories and show the potential utility. Surprisingly, when studied at scale, the APOE genotype had negligible impact on cognitive performance. Different cognitive domains had distinct genetic architectures, with one indicating brain region-specific activation of microglia and another with glycogen metabolism. Thus, the molecular and cellular mechanisms underpinning cognition are distinct from dementia risk loci, presenting different targets to slow down age-related cognitive decline. Participants can now be recalled stratified by genotype and cognitive phenotype for natural history and interventional studies of neurodegenerative and other disorders.",,pdf:https://www.nature.com/articles/s41591-024-02960-5.pdf; doi:https://doi.org/10.1038/s41591-024-02960-5; html:https://europepmc.org/articles/PMC11186791; pdf:https://europepmc.org/articles/PMC11186791?pdf=render
-34173614,https://doi.org/10.1016/s2666-7568(20)30012-x,Evolution and effects of COVID-19 outbreaks in care homes: a population analysis in 189 care homes in one geographical region of the UK.,"Burton JK, Bayne G, Evans C, Garbe F, Gorman D, Honhold N, McCormick D, Othieno R, Stevenson JE, Swietlik S, Templeton KE, Tranter M, Willocks L, Guthrie B.",,The lancet. Healthy longevity,2020,2020-10-20,Y,,,,"<h4>Background</h4>COVID-19 has affected care home residents internationally, but detailed information on outbreaks is scarce. We aimed to describe the evolution of outbreaks of COVID-19 in all care homes in one large health region in Scotland.<h4>Methods</h4>We did a population analysis of testing, cases, and deaths in care homes in the National Health Service (NHS) Lothian health region of the UK. We obtained data for COVID-19 testing (PCR testing of nasopharyngeal swabs for severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) and deaths (COVID-19-related and non-COVID-19-related), and we analysed data by several variables including type of care home, number of beds, and locality. Outcome measures were timing of outbreaks, number of confirmed cases of COVID-19 in care home residents, care home characteristics associated with the presence of an outbreak, and deaths of residents in both care homes and hospitals. We calculated excess deaths (both COVID-19-related and non-COVID-19-related), which we defined as the sum of deaths over and above the historical average in the same period over the past 5 years.<h4>Findings</h4>Between March 10 and Aug 2, 2020, residents at 189 care homes (5843 beds) were tested for COVID-19 when symptomatic. A COVID-19 outbreak was confirmed at 69 (37%) care homes, of which 66 (96%) were care homes for older people. The size of care homes for older people was strongly associated with a COVID-19 outbreak (odds ratio per 20-bed increase 3·35, 95% CI 1·99-5·63). 907 confirmed cases of SARS-CoV-2 infection were recorded during the study period, and 432 COVID-19-related deaths. 229 (25%) COVID-19-related cases and 99 (24%) COVID-related deaths occurred in five (3%) of 189 care homes, and 441 (49%) cases and 207 (50%) deaths were in 13 (7%) care homes. 411 (95%) COVID-19-related deaths occurred in the 69 care homes with a confirmed COVID-19 outbreak, 19 (4%) deaths were in hospital, and two (<1%) were in one of the 120 care homes without a confirmed COVID-19 outbreak. At the 69 care homes with a confirmed COVID-19 outbreak, 74 excess non-COVID-19-related deaths were reported, whereas ten non-COVID-19-related excess deaths were observed in the 120 care homes without a confirmed COVID-19 outbreak. 32 fewer non-COVID-19-related deaths than expected were reported among care home residents in hospital.<h4>Interpretation</h4>The effect of COVID-19 on care homes has been substantial but concentrated in care homes with known outbreaks. A key implication from our findings is that, if community incidence of COVID-19 increases again, many care home residents will be susceptible. Shielding care home residents from potential sources of SARS-CoV-2 infection, and ensuring rapid action to minimise outbreak size if infection is introduced, will be important for any second wave.<h4>Funding</h4>None.",,doi:https://doi.org/10.1016/s2666-7568(20)30012-x; doi:https://doi.org/10.1016/S2666-7568(20)30012-X; html:https://europepmc.org/articles/PMC7574931; pdf:https://europepmc.org/articles/PMC7574931?pdf=render
 37348789,https://doi.org/10.1016/j.jhep.2023.05.046,Liver disease is a significant risk factor for cardiovascular outcomes - A UK Biobank study.,"Roca-Fernandez A, Banerjee R, Thomaides-Brears H, Telford A, Sanyal A, Neubauer S, Nichols TE, Raman B, McCracken C, Petersen SE, Ntusi NA, Cuthbertson DJ, Lai M, Dennis A, Banerjee A.",,Journal of hepatology,2023,2023-06-20,N,Cardiac; MRI; Imaging; Hepatic; Heart Failure; liver disease; Cvd; Nafld; Atrial Fibrilliation,,,"<h4>Background & aims</h4>Chronic liver disease (CLD) is associated with increased cardiovascular disease (CVD) risk. We investigated whether early signs of liver disease (measured by iron-corrected T1-mapping [cT1]) were associated with an increased risk of major CVD events.<h4>Methods</h4>Liver disease activity (cT1) and fat (proton density fat fraction [PDFF]) were measured using LiverMultiScan® between January 2016 and February 2020 in the UK Biobank imaging sub-study. Using multivariable Cox regression, we explored associations between liver cT1 (MRI) and primary CVD (coronary artery disease, atrial fibrillation [AF], embolism/vascular events, heart failure [HF] and stroke), and CVD hospitalisation and all-cause mortality. Liver blood biomarkers, general metabolism biomarkers, and demographics were also included. Subgroup analysis was conducted in those without metabolic syndrome (defined as at least three of: a large waist, high triglycerides, low high-density lipoprotein cholesterol, increased systolic blood pressure, or elevated haemoglobin A1c).<h4>Results</h4>A total of 33,616 participants (mean age 65 years, mean BMI 26 kg/m<sup>2</sup>, mean haemoglobin A1c 35 mmol/mol) had complete MRI liver data with linked clinical outcomes (median time to major CVD event onset: 1.4 years [range: 0.002-5.1]; follow-up: 2.5 years [range: 1.1-5.2]). Liver disease activity (cT1), but not liver fat (PDFF), was associated with higher risk of any major CVD event (hazard ratio 1.14; 95% CI 1.03-1.26; p = 0.008), AF (1.30; 1.12-1.51; p <0.001); HF (1.30; 1.09-1.56; p= 0.004); CVD hospitalisation (1.27; 1.18-1.37; p <0.001) and all-cause mortality (1.19; 1.02-1.38; p = 0.026). FIB-4 index was associated with HF (1.06; 1.01-1.10; p = 0.007). Risk of CVD hospitalisation was independently associated with cT1 in individuals without metabolic syndrome (1.26; 1.13-1.4; p <0.001).<h4>Conclusion</h4>Liver disease activity, by cT1, was independently associated with a higher risk of incident CVD and all-cause mortality, independent of pre-existing metabolic syndrome, liver fibrosis or fat.<h4>Impact and implications</h4>Chronic liver disease (CLD) is associated with a twofold greater incidence of cardiovascular disease. Our work shows that early liver disease on iron-corrected T1 mapping was associated with a higher risk of major cardiovascular disease (14%), cardiovascular disease hospitalisation (27%) and all-cause mortality (19%). These findings highlight the prognostic relevance of a comprehensive evaluation of liver health in populations at risk of CVD and/or CLD, even in the absence of clinical manifestations or metabolic syndrome, when there is an opportunity to modify/address risk factors and prevent disease progression. As such, they are relevant to patients, carers, clinicians, and policymakers.",,pdf:http://www.journal-of-hepatology.eu/article/S0168827823004208/pdf; doi:https://doi.org/10.1016/j.jhep.2023.05.046
+34173614,https://doi.org/10.1016/s2666-7568(20)30012-x,Evolution and effects of COVID-19 outbreaks in care homes: a population analysis in 189 care homes in one geographical region of the UK.,"Burton JK, Bayne G, Evans C, Garbe F, Gorman D, Honhold N, McCormick D, Othieno R, Stevenson JE, Swietlik S, Templeton KE, Tranter M, Willocks L, Guthrie B.",,The lancet. Healthy longevity,2020,2020-10-20,Y,,,,"<h4>Background</h4>COVID-19 has affected care home residents internationally, but detailed information on outbreaks is scarce. We aimed to describe the evolution of outbreaks of COVID-19 in all care homes in one large health region in Scotland.<h4>Methods</h4>We did a population analysis of testing, cases, and deaths in care homes in the National Health Service (NHS) Lothian health region of the UK. We obtained data for COVID-19 testing (PCR testing of nasopharyngeal swabs for severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) and deaths (COVID-19-related and non-COVID-19-related), and we analysed data by several variables including type of care home, number of beds, and locality. Outcome measures were timing of outbreaks, number of confirmed cases of COVID-19 in care home residents, care home characteristics associated with the presence of an outbreak, and deaths of residents in both care homes and hospitals. We calculated excess deaths (both COVID-19-related and non-COVID-19-related), which we defined as the sum of deaths over and above the historical average in the same period over the past 5 years.<h4>Findings</h4>Between March 10 and Aug 2, 2020, residents at 189 care homes (5843 beds) were tested for COVID-19 when symptomatic. A COVID-19 outbreak was confirmed at 69 (37%) care homes, of which 66 (96%) were care homes for older people. The size of care homes for older people was strongly associated with a COVID-19 outbreak (odds ratio per 20-bed increase 3·35, 95% CI 1·99-5·63). 907 confirmed cases of SARS-CoV-2 infection were recorded during the study period, and 432 COVID-19-related deaths. 229 (25%) COVID-19-related cases and 99 (24%) COVID-related deaths occurred in five (3%) of 189 care homes, and 441 (49%) cases and 207 (50%) deaths were in 13 (7%) care homes. 411 (95%) COVID-19-related deaths occurred in the 69 care homes with a confirmed COVID-19 outbreak, 19 (4%) deaths were in hospital, and two (<1%) were in one of the 120 care homes without a confirmed COVID-19 outbreak. At the 69 care homes with a confirmed COVID-19 outbreak, 74 excess non-COVID-19-related deaths were reported, whereas ten non-COVID-19-related excess deaths were observed in the 120 care homes without a confirmed COVID-19 outbreak. 32 fewer non-COVID-19-related deaths than expected were reported among care home residents in hospital.<h4>Interpretation</h4>The effect of COVID-19 on care homes has been substantial but concentrated in care homes with known outbreaks. A key implication from our findings is that, if community incidence of COVID-19 increases again, many care home residents will be susceptible. Shielding care home residents from potential sources of SARS-CoV-2 infection, and ensuring rapid action to minimise outbreak size if infection is introduced, will be important for any second wave.<h4>Funding</h4>None.",,doi:https://doi.org/10.1016/s2666-7568(20)30012-x; doi:https://doi.org/10.1016/S2666-7568(20)30012-X; html:https://europepmc.org/articles/PMC7574931; pdf:https://europepmc.org/articles/PMC7574931?pdf=render
+38745010,https://doi.org/10.1038/s41591-024-02960-5,Dynamics of cognitive variability with age and its genetic underpinning in NIHR BioResource Genes and Cognition cohort participants.,"Rahman MS, Harrison E, Biggs H, Seikus C, Elliott P, Breen G, Kingston N, Bradley JR, Hill SM, Tom BDM, Chinnery PF.",,Nature medicine,2024,2024-05-14,Y,,,,"A leading explanation for translational failure in neurodegenerative disease is that new drugs are evaluated late in the disease course when clinical features have become irreversible. Here, to address this gap, we cognitively profiled 21,051 people aged 17-85 years as part of the Genes and Cognition cohort within the National Institute for Health and Care Research BioResource across England. We describe the cohort, present cognitive trajectories and show the potential utility. Surprisingly, when studied at scale, the APOE genotype had negligible impact on cognitive performance. Different cognitive domains had distinct genetic architectures, with one indicating brain region-specific activation of microglia and another with glycogen metabolism. Thus, the molecular and cellular mechanisms underpinning cognition are distinct from dementia risk loci, presenting different targets to slow down age-related cognitive decline. Participants can now be recalled stratified by genotype and cognitive phenotype for natural history and interventional studies of neurodegenerative and other disorders.",,pdf:https://www.nature.com/articles/s41591-024-02960-5.pdf; doi:https://doi.org/10.1038/s41591-024-02960-5; html:https://europepmc.org/articles/PMC11186791; pdf:https://europepmc.org/articles/PMC11186791?pdf=render
+36823471,https://doi.org/10.1038/s42255-023-00753-7,Proteogenomic links to human metabolic diseases.,"Koprulu M, Carrasco-Zanini J, Wheeler E, Lockhart S, Kerrison ND, Wareham NJ, Pietzner M, Langenberg C.",,Nature metabolism,2023,2023-02-23,Y,,,,"Studying the plasma proteome as the intermediate layer between the genome and the phenome has the potential to identify new disease processes. Here, we conducted a cis-focused proteogenomic analysis of 2,923 plasma proteins measured in 1,180 individuals using antibody-based assays. We (1) identify 256 unreported protein quantitative trait loci (pQTL); (2) demonstrate shared genetic regulation of 224 cis-pQTLs with 575 specific health outcomes, revealing examples for notable metabolic diseases (such as gastrin-releasing peptide as a potential therapeutic target for type 2 diabetes); (3) improve causal gene assignment at 40% (n = 192) of overlapping risk loci; and (4) observe convergence of phenotypic consequences of cis-pQTLs and rare loss-of-function gene burden for 12 proteins, such as TIMD4 for lipoprotein metabolism. Our findings demonstrate the value of integrating complementary proteomic technologies with genomics even at moderate scale to identify new mediators of metabolic diseases with the potential for therapeutic interventions.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7614946; doi:https://doi.org/10.1038/s42255-023-00753-7; html:https://europepmc.org/articles/PMC7614946; pdf:https://europepmc.org/articles/PMC7614946?pdf=render
 33496075,https://doi.org/10.1111/ijpo.12772,Completeness and representativeness of body mass index in children's electronic general practice records: Linked cross-sectional study in an ethnically-diverse urban population in the United Kingdom.,"Firman N, Robson J, Ahmed Z, Boomla K, Dezateux C.",,Pediatric obesity,2021,2021-01-25,Y,BMI; Childhood; General Practice; Electronic Health Records,,,"<h4>Objective</h4>To assess completeness and accuracy of children's body mass index (BMI) recorded in general practice electronic health records (GP-EHRs).<h4>Methods</h4>We linked National Child Measurement Programme (NCMP) records from 29 839 5-year-olds and 26 660 11-year-olds attending state schools in inner London to GP-EHRs (95% linked; 49.1% girls). We estimated adjusted odds (aOR) of at least one GP-BMI record by sex, ethnic background, area-level deprivation, weight-status and long-term conditions. We examined within-child BMI differences and compared obesity prevalence from these sources.<h4>Results</h4>10.5% (2964/28330) and 26.0% (6598/25365) of 5- and 11-year-olds respectively had at least one GP-BMI record. Underweight (aOR;95% CI:1.71;1.34,2.19), obesity (1.45;1.27,1.65), South Asian background (1.55;1.38,1.74), presence of a long-term condition (8.15;7.31,9.10), and residence in deprived areas (Wald statistic 38.73; P-value<0.0001) were independently associated with at least one GP-BMI record. NCMP-BMI and GP-BMI differed by +0.45(95% Limits of Agreement -1.60,+2.51) and + 0.16(-2.86,+3.18) in 5- and 11-year-olds, respectively. The prevalence of obesity based on GP-BMI was 18.2%(16.1,20.5) and 35.9%(33.9,38.0) in 5- and 11-year-olds respectively, compared to 12.9%(12.5,13.3) and 26.9%(26.4,27.4) based on NCMP-BMI.<h4>Conclusion</h4>Child BMI is not comprehensively recorded in urban general practice. Linkage to school measurement records is feasible and enables assessment of health outcomes of obesity.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/ijpo.12772; doi:https://doi.org/10.1111/ijpo.12772; html:https://europepmc.org/articles/PMC11497231; pdf:https://europepmc.org/articles/PMC11497231?pdf=render
 32637892,https://doi.org/10.1016/j.eclinm.2020.100392,The association between exposure to childhood maltreatment and the subsequent development of functional somatic and visceral pain syndromes.,"Chandan JS, Keerthy D, Zemedikun DT, Okoth K, Gokhale KM, Raza K, Bandyopadhyay S, Taylor J, Nirantharakumar K.",,EClinicalMedicine,2020,2020-06-06,Y,epidemiology; Primary Care; Childhood Maltreatment; Central Sensitivity Syndromes,,,"<h4>Background</h4>Childhood maltreatment is a global public health issue linked to a vast mortality and morbidity burden. This study builds on current literature to explore the risk of developing central sensitivity syndromes (CSS) (consisting of somatic and visceral pain syndromes) subsequent to childhood maltreatment exposure.<h4>Methods</h4>A retrospective population based open cohort study using the UK primary care database, 'The Health Improvement Network,' between 1st January 1995-31st December 2018. 80,657 adult patients who had experienced childhood maltreatment or maltreatment related concerns (exposed patients) were matched to 161,314 unexposed patients by age and sex. Outcomes of interest were the development of CSS: either somatic (Fibromyalgia, chronic fatigue syndrome, temporomandibular joint disorder, chronic lower back pain, chronic headache, myofascial pain syndrome and restless leg syndrome) or visceral (Interstitial cystitis, vulvodynia, chronic prostatitis and irritable bowel syndrome) in nature. Effect sizes are presented as adjusted incidence rate ratios (aIRR) with confidence intervals (CI). Models were adjusted for the following covariates at cohort entry: age, sex, deprivation, anxiety, depression and serious mental ill health.<h4>Results</h4>The average age at cohort entry was 23.4 years and the median follow was 2.2 years. There was an increased risk of developing fibromyalgia (aIRR 2.06; 95% CI 1.71-2.48), chronic fatigue syndrome (1.47; 1.08-2.00), chronic lower back pain (1.99; 1.68-2.35), restless leg syndrome (1.82; 1.41-2.35) and irritable bowel syndrome (1.15; 1.08-1.22) when compared to the unexposed group, whereas no statistical association was seen with the development of temporomandibular joint disorder (1.00; 0.88-1.13), chronic headache (1.04; 0.59-1.86), interstitial cystitis (1.19; 0.51-2.74), vulvodynia (0.65; 0.34-1.26), chronic prostatitis (0.34; 0.07-1.77) and myofascial pain syndrome (0.88; 0.36-2.14). Outcome numbers were low, most likely, due to the rarity of visceral conditions (aside from irritable bowel syndrome). The association between a history of childhood maltreatment and CSS were mainly observed in somatic CSS.<h4>Interpretation</h4>The debilitating effects of CSS carry a substantial physical, psychological and economic burden to both the individuals who are diagnosed with them and the health services who serve them. Primary prevention approaches targeting childhood maltreatment as well as secondary preventative approaches should be considered to minimise the associated burden of CSS.",,pdf:http://www.thelancet.com/article/S258953702030136X/pdf; doi:https://doi.org/10.1016/j.eclinm.2020.100392; html:https://europepmc.org/articles/PMC7329705; pdf:https://europepmc.org/articles/PMC7329705?pdf=render
 36415305,https://doi.org/10.1093/ehjopen/oeac066,"Identifying unmet antithrombotic therapeutic need, and implications for stroke and systemic embolism in atrial fibrillation patients: a population-scale longitudinal study.","Torabi F, Harris DE, Bodger O, Akbari A, Lyons RA, Gravenor M, Halcox JP.",,European heart journal open,2022,2022-11-21,Y,Anticoagulation; Atrial fibrillation; Electronic Health Records; Stroke And Systemic Embolism,,,"<h4>Aims</h4>Guidelines recommend anticoagulation (AC) in atrial fibrillation (AF) to reduce stroke and systemic embolism (SSE) risk; however, implementation has been slow across many populations. This study aimed to quantify the potential impact of changing prevalence of AF, associated risk, and AC prescribing on SSE hospitalizations and death.<h4>Methods and results</h4>We evaluated temporal trends of AF, CHA<sub>2</sub>DS<sub>2</sub>-VASc, antithrombotic prescriptions, SSE hospitalizations, death, and their associations between 2012 and 2018 in a longitudinal cohort of AF patients in Wales UK. Multi-state Markov models were used to estimate expected SSE rates given the AC coverage, adjusting for CHA<sub>2</sub>DS<sub>2</sub>-VASc scores. SSE rates were modelled for various past and future AC scenarios. A total of 107 137 AF patients were evaluated (mean age = 74 years, 45% female). AF prevalence increased from 1.75 to 2.22% (<i>P</i>-value <0.001). SSE hospitalizations decreased by 18% (2.34-1.92%, <i>P</i>-value <0.001). Increased AC coverage from 50 to 70% was associated with a 37% lower SSE rate, after adjustment for individual time-dependent CHA<sub>2</sub>DS<sub>2</sub>VASc scores. The observed AC increase accounted for approximately 80 fewer SSE hospitalizations per 100 000/year. If 90% AC coverage had been achieved since 2012, an estimated 279 SSE per 100 000/year may have been prevented. Our model also predicts that improving AC coverage to 90% over the next 9 years could reduce annual SSE rates by 9%.<h4>Conclusion</h4>We quantified the relationship between observed AC coverage, estimating the potential impact of variation in the timing of large-scale implementation. These data emphasize the importance of timely implementation and the considerable opportunity to improve clinical outcomes in the Wales-AF population.",,pdf:https://academic.oup.com/ehjopen/article-pdf/2/6/oeac066/48439565/oeac066.pdf; doi:https://doi.org/10.1093/ehjopen/oeac066; html:https://europepmc.org/articles/PMC9678205; pdf:https://europepmc.org/articles/PMC9678205?pdf=render
@@ -1949,29 +1951,29 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 32573463,https://doi.org/10.2196/18185,Superusers' Engagement in Asthma Online Communities: Asynchronous Web-Based Interview Study.,"De Simoni A, Shah AT, Fulton O, Parkinson J, Sheikh A, Panzarasa P, Pagliari C, Coulson NS, Griffiths CJ.",,Journal of medical Internet research,2020,2020-06-23,Y,Asthma; Misinformation; Social Networks; Leadership; Social Support; Self-management; Social Media; Ehealth; Online Health Communities; Superusers; Online Forums; Peer-to-peer Support,,,"<h4>Background</h4>Superusers, defined as the 1% of users who write a large number of posts, play critical roles in online health communities (OHCs), catalyzing engagement and influencing other users' self-care. Their unique online behavior is key to sustaining activity in OHCs and making them flourish. Our previous work showed the presence of 20 to 30 superusers active on a weekly basis among 3345 users in the nationwide Asthma UK OHC and that the community would disintegrate if superusers were removed. Recruiting these highly skilled individuals for research purposes can be challenging, and little is known about superusers.<h4>Objective</h4>This study aimed to explore superusers' motivation to actively engage in OHCs, the difficulties they may face, and their interactions with health care professionals (HCPs).<h4>Methods</h4>An asynchronous web-based structured interview study was conducted. Superusers of the Asthma UK OHC and Facebook groups were recruited through Asthma UK staff to pilot and subsequently complete the questionnaire. Open-ended questions were analyzed using content analysis.<h4>Results</h4>There were 17 superusers recruited for the study (14 patients with asthma and 3 carers); the majority were female (15/17). The age range of participants was 18 to 75 years. They were active in OHCs for 1 to 6 years and spent between 1 and 20 hours per week reading and 1 and 3 hours per week writing posts. Superusers' participation in OHCs was prompted by curiosity about asthma and its medical treatment and by the availability of spare time when they were off work due to asthma exacerbations or retired. Their engagement increased over time as participants furthered their familiarity with the OHCs and their knowledge of asthma and its self-management. Financial or social recognition of the superuser role was not important; their reward came from helping and interacting with others. According to the replies provided, they showed careful judgment to distinguish what can be dealt with through peer advice and what needs input from HCPs. Difficulties were encountered when dealing with misunderstandings about asthma and its treatment, patients not seeking advice from HCPs when needed, and miracle cures or dangerous ideas. Out of 17 participants, only 3 stated that their HCPs were aware of their engagement with OHCs. All superusers thought that HCPs should direct patients to OHCs, provided they are trusted and moderated. In addition, 9 users felt that HCPs themselves should take part in OHCs.<h4>Conclusions</h4>Superusers from a UK-wide online community are highly motivated, altruistic, and mostly female individuals who exhibit judgment about the complexity of coping with asthma and the limits of their advice. Engagement with OHCs satisfies their psychosocial needs. Future research should explore how to address their unmet needs, their interactions with HCPs, and the potential integration of OHCs in traditional healthcare.",,pdf:https://www.jmir.org/2020/6/e18185/PDF; doi:https://doi.org/10.2196/18185; html:https://europepmc.org/articles/PMC7381072
 37817277,https://doi.org/10.1186/s13063-023-07656-8,"e-Consent in UK academic-led clinical trials: current practice, challenges and the need for more evidence.","Mitchell EJ, Appelbe D, Bravery A, Culliford L, Evans H, Farrin AJ, Gillies K, Hood K, Love SB, Sydes MR, Williamson PR, Wakefield N, as part of the e-Consent collaborative group.",,Trials,2023,2023-10-10,Y,Consent; Clinical Trial; E-consent,,,"<h4>Background</h4>During the COVID-19 pandemic, in-person healthcare visits were reduced. Consequently, trial teams needed to consider implementing remote methods for conducting clinical trials, including e-Consent. Although some clinical trials may have implemented e-Consent prior to the pandemic, anecdotes of uptake for this method increased within academic-led trials. When the increased use of this process emerged, representatives from several large academic clinical trial groups within the UK collaborated to discuss ways in which trialists can learn from one another when implementing e-Consent.<h4>Methods</h4>A survey of UKCRC-registered Clinical Trials Units (CTUs) was undertaken in April-June 2021 to understand the implementation of and their views on the use of e-Consent and experiences from the perspectives of systems programmers and quality assurance staff on the use of e-Consent. CTUs not using e-Consent were asked to provide any reasons/barriers (including no suitable trials) and any plans for implementing it in the future. Two events for trialists and patient and public involvement (PPI) representatives were then held to disseminate findings, foster discussion, share experiences and aid in the identification of areas that the academic CTU community felt required more research.<h4>Results</h4>Thirty-four (64%) of 53 CTUs responded to the survey, with good geographical representation across the UK. Twenty-one (62%) of the responding CTUs had implemented e-Consent in at least one of their trials, across different types of trials, including CTIMPs (Clinical Trial of Investigational Medicinal Product), ATIMPs (Advanced Therapy Medicinal Products) and non-CTIMPs. One hundred ninety-seven participants attended the two workshops for wide-ranging discussions.<h4>Conclusion</h4>e-Consent is increasingly used in academic-led trials, yet uncertainties remain amongst trialists, patients and members of the public. Uncertainties include a lack of formal, practical guidance and a lack of evidence to demonstrate optimal or appropriate methods to use. We strongly encourage trialists to continue to share their own experiences of the implementation of e-Consent.",,pdf:https://trialsjournal.biomedcentral.com/counter/pdf/10.1186/s13063-023-07656-8; doi:https://doi.org/10.1186/s13063-023-07656-8; html:https://europepmc.org/articles/PMC10565982; pdf:https://europepmc.org/articles/PMC10565982?pdf=render
 37907686,https://doi.org/10.1038/s41397-023-00317-8,British South Asian ancestry participants views of pharmacogenomics clinical implementation and research: a thematic analysis.,"Magavern EF, Durrani F, Raza M, Lerner R, Islam MR, Genes & Health Research Team, Clinch M, Caulfield MJ.",,The pharmacogenomics journal,2023,2023-11-01,Y,,,,"<h4>Background</h4>South Asian ancestry populations are underrepresented in genomic studies and therapeutics trials. British South Asians suffer from multi-morbidity leading to polypharmacy. Our objective was to elucidate British South Asian ancestry community perspectives on pharmacogenomic implementation and sharing pharmacogenomic clinical data for research.<h4>Methods</h4>Four focus groups were conducted (9-12 participants in each). Two groups were mixed gender, while one group was male only and one was female only. Simultaneous interpretation was available to participants in Urdu and Bengali. Focus groups were recorded and abridged transcription and thematic analysis were undertaken.<h4>Results</h4>There were 42 participants, 64% female. 26% were born in the UK or Europe. 52% were born in Bangladesh and 17% in Pakistan. 36% reported university level education. Implementation of pharmacogenomics was perceived to be beneficial to individuals but pose a risk of overburdening resource limited systems. Pharmacogenomic research was perceived to be beneficial to the community, with concerns about data privacy and misuse. Data sharing was desirable if the researchers did not have a financial stake, and benefits would be shared. Trust was the key condition for the acceptability of both clinical implementation and research. Trust was linked with medication compliance. Education, outreach, and communication facilitate trust.<h4>Conclusions (significance and impact of the study)</h4>Pharmacogenomics implementation with appropriate education and communication has the potential to enhance trust and contribute to increased medication compliance. Trust drives data sharing, which would enable enhanced representation in research. Representation in scientific evidence base could cyclically enhance trust and compliance.",,doi:https://doi.org/10.1038/s41397-023-00317-8; html:https://europepmc.org/articles/PMC10661738; pdf:https://europepmc.org/articles/PMC10661738?pdf=render
-31363735,https://doi.org/10.1093/hmg/ddz187,Towards clinical utility of polygenic risk scores.,"Lambert SA, Abraham G, Inouye M.",,Human molecular genetics,2019,2019-11-01,N,,,,"Prediction of disease risk is an essential part of preventative medicine, often guiding clinical management. Risk prediction typically includes risk factors such as age, sex, family history of disease and lifestyle (e.g. smoking status); however, in recent years, there has been increasing interest to include genomic information into risk models. Polygenic risk scores (PRS) aggregate the effects of many genetic variants across the human genome into a single score and have recently been shown to have predictive value for multiple common diseases. In this review, we summarize the potential use cases for seven common diseases (breast cancer, prostate cancer, coronary artery disease, obesity, type 1 diabetes, type 2 diabetes and Alzheimer's disease) where PRS has or could have clinical utility. PRS analysis for these diseases frequently revolved around (i) risk prediction performance of a PRS alone and in combination with other non-genetic risk factors, (ii) estimation of lifetime risk trajectories, (iii) the independent information of PRS and family history of disease or monogenic mutations and (iv) estimation of the value of adding a PRS to specific clinical risk prediction scenarios. We summarize open questions regarding PRS usability, ancestry bias and transferability, emphasizing the need for the next wave of studies to focus on the implementation and health-economic value of PRS testing. In conclusion, it is becoming clear that PRS have value in disease risk prediction and there are multiple areas where this may have clinical utility.",,pdf:https://academic.oup.com/hmg/article-pdf/28/R2/R133/31081033/ddz187.pdf; doi:https://doi.org/10.1093/hmg/ddz187
 33986429,https://doi.org/10.1038/s41598-021-89743-x,Predicting sex from retinal fundus photographs using automated deep learning.,"Korot E, Pontikos N, Liu X, Wagner SK, Faes L, Huemer J, Balaskas K, Denniston AK, Khawaja A, Keane PA.",,Scientific reports,2021,2021-05-13,Y,,,,"Deep learning may transform health care, but model development has largely been dependent on availability of advanced technical expertise. Herein we present the development of a deep learning model by clinicians without coding, which predicts reported sex from retinal fundus photographs. A model was trained on 84,743 retinal fundus photos from the UK Biobank dataset. External validation was performed on 252 fundus photos from a tertiary ophthalmic referral center. For internal validation, the area under the receiver operating characteristic curve (AUROC) of the code free deep learning (CFDL) model was 0.93. Sensitivity, specificity, positive predictive value (PPV) and accuracy (ACC) were 88.8%, 83.6%, 87.3% and 86.5%, and for external validation were 83.9%, 72.2%, 78.2% and 78.6% respectively. Clinicians are currently unaware of distinct retinal feature variations between males and females, highlighting the importance of model explainability for this task. The model performed significantly worse when foveal pathology was present in the external validation dataset, ACC: 69.4%, compared to 85.4% in healthy eyes, suggesting the fovea is a salient region for model performance OR (95% CI): 0.36 (0.19, 0.70) p = 0.0022. Automated machine learning (AutoML) may enable clinician-driven automated discovery of novel insights and disease biomarkers.",,pdf:https://www.nature.com/articles/s41598-021-89743-x.pdf; doi:https://doi.org/10.1038/s41598-021-89743-x; html:https://europepmc.org/articles/PMC8119673; pdf:https://europepmc.org/articles/PMC8119673?pdf=render
+31363735,https://doi.org/10.1093/hmg/ddz187,Towards clinical utility of polygenic risk scores.,"Lambert SA, Abraham G, Inouye M.",,Human molecular genetics,2019,2019-11-01,N,,,,"Prediction of disease risk is an essential part of preventative medicine, often guiding clinical management. Risk prediction typically includes risk factors such as age, sex, family history of disease and lifestyle (e.g. smoking status); however, in recent years, there has been increasing interest to include genomic information into risk models. Polygenic risk scores (PRS) aggregate the effects of many genetic variants across the human genome into a single score and have recently been shown to have predictive value for multiple common diseases. In this review, we summarize the potential use cases for seven common diseases (breast cancer, prostate cancer, coronary artery disease, obesity, type 1 diabetes, type 2 diabetes and Alzheimer's disease) where PRS has or could have clinical utility. PRS analysis for these diseases frequently revolved around (i) risk prediction performance of a PRS alone and in combination with other non-genetic risk factors, (ii) estimation of lifetime risk trajectories, (iii) the independent information of PRS and family history of disease or monogenic mutations and (iv) estimation of the value of adding a PRS to specific clinical risk prediction scenarios. We summarize open questions regarding PRS usability, ancestry bias and transferability, emphasizing the need for the next wave of studies to focus on the implementation and health-economic value of PRS testing. In conclusion, it is becoming clear that PRS have value in disease risk prediction and there are multiple areas where this may have clinical utility.",,pdf:https://academic.oup.com/hmg/article-pdf/28/R2/R133/31081033/ddz187.pdf; doi:https://doi.org/10.1093/hmg/ddz187
+32781946,https://doi.org/10.1098/rspb.2020.1405,Key questions for modelling COVID-19 exit strategies.,"Thompson RN, Hollingsworth TD, Isham V, Arribas-Bel D, Ashby B, Britton T, Challenor P, Chappell LHK, Clapham H, Cunniffe NJ, Dawid AP, Donnelly CA, Eggo RM, Funk S, Gilbert N, Glendinning P, Gog JR, Hart WS, Heesterbeek H, House T, Keeling M, Kiss IZ, Kretzschmar ME, Lloyd AL, McBryde ES, McCaw JM, McKinley TJ, Miller JC, Morris M, O'Neill PD, Parag KV, Pearson CAB, Pellis L, Pulliam JRC, Ross JV, Tomba GS, Silverman BW, Struchiner CJ, Tildesley MJ, Trapman P, Webb CR, Mollison D, Restif O.",,Proceedings. Biological sciences,2020,2020-08-12,Y,Uncertainty; Mathematical Modelling; Epidemic Control; Exit Strategy; Covid-19; Sars-cov-2,,,"Combinations of intense non-pharmaceutical interventions (lockdowns) were introduced worldwide to reduce SARS-CoV-2 transmission. Many governments have begun to implement exit strategies that relax restrictions while attempting to control the risk of a surge in cases. Mathematical modelling has played a central role in guiding interventions, but the challenge of designing optimal exit strategies in the face of ongoing transmission is unprecedented. Here, we report discussions from the Isaac Newton Institute 'Models for an exit strategy' workshop (11-15 May 2020). A diverse community of modellers who are providing evidence to governments worldwide were asked to identify the main questions that, if answered, would allow for more accurate predictions of the effects of different exit strategies. Based on these questions, we propose a roadmap to facilitate the development of reliable models to guide exit strategies. This roadmap requires a global collaborative effort from the scientific community and policymakers, and has three parts: (i) improve estimation of key epidemiological parameters; (ii) understand sources of heterogeneity in populations; and (iii) focus on requirements for data collection, particularly in low-to-middle-income countries. This will provide important information for planning exit strategies that balance socio-economic benefits with public health.",,doi:https://doi.org/10.1098/rspb.2020.1405; doi:https://doi.org/10.1098/rspb.2020.1405; html:https://europepmc.org/articles/PMC7575516; pdf:https://europepmc.org/articles/PMC7575516?pdf=render
 34611362,https://doi.org/10.1038/s41588-021-00944-6,Polygenic basis and biomedical consequences of telomere length variation.,"Codd V, Wang Q, Allara E, Musicha C, Kaptoge S, Stoma S, Jiang T, Hamby SE, Braund PS, Bountziouka V, Budgeon CA, Denniff M, Swinfield C, Papakonstantinou M, Sheth S, Nanus DE, Warner SC, Wang M, Khera AV, Eales J, Ouwehand WH, Thompson JR, Di Angelantonio E, Wood AM, Butterworth AS, Danesh JN, Nelson CP, Samani NJ.",,Nature genetics,2021,2021-10-05,Y,,,,"Telomeres, the end fragments of chromosomes, play key roles in cellular proliferation and senescence. Here we characterize the genetic architecture of naturally occurring variation in leukocyte telomere length (LTL) and identify causal links between LTL and biomedical phenotypes in 472,174 well-characterized UK Biobank participants. We identified 197 independent sentinel variants associated with LTL at 138 genomic loci (108 new). Genetically determined differences in LTL were associated with multiple biological traits, ranging from height to bone marrow function, as well as several diseases spanning neoplastic, vascular and inflammatory pathologies. Finally, we estimated that, at the age of 40 years, people with an LTL >1 s.d. shorter than the population mean had a 2.5-year-lower life expectancy compared with the group with ≥1 s.d. longer LDL. Overall, we furnish new insights into the genetic regulation of LTL, reveal wide-ranging influences of LTL on physiological traits, diseases and longevity, and provide a powerful resource available to the global research community.",,pdf:https://www.nature.com/articles/s41588-021-00944-6.pdf; doi:https://doi.org/10.1038/s41588-021-00944-6; html:https://europepmc.org/articles/PMC8492471; pdf:https://europepmc.org/articles/PMC8492471?pdf=render
 34226637,https://doi.org/10.1038/s41366-021-00896-1,Effects of adiposity on the human plasma proteome: observational and Mendelian randomisation estimates.,"Goudswaard LJ, Bell JA, Hughes DA, Corbin LJ, Walter K, Davey Smith G, Soranzo N, Danesh J, Di Angelantonio E, Ouwehand WH, Watkins NA, Roberts DJ, Butterworth AS, Hers I, Timpson NJ.",,International journal of obesity (2005),2021,2021-07-05,Y,,,,"<h4>Background</h4>Variation in adiposity is associated with cardiometabolic disease outcomes, but mechanisms leading from this exposure to disease are unclear. This study aimed to estimate effects of body mass index (BMI) on an extensive set of circulating proteins.<h4>Methods</h4>We used SomaLogic proteomic data from up to 2737 healthy participants from the INTERVAL study. Associations between self-reported BMI and 3622 unique plasma proteins were explored using linear regression. These were complemented by Mendelian randomisation (MR) analyses using a genetic risk score (GRS) comprised of 654 BMI-associated polymorphisms from a recent genome-wide association study (GWAS) of adult BMI. A disease enrichment analysis was performed using DAVID Bioinformatics 6.8 for proteins which were altered by BMI.<h4>Results</h4>Observationally, BMI was associated with 1576 proteins (P < 1.4 × 10<sup>-5</sup>), with particularly strong evidence for a positive association with leptin and fatty acid-binding protein-4 (FABP4), and a negative association with sex hormone-binding globulin (SHBG). Observational estimates were likely confounded, but the GRS for BMI did not associate with measured confounders. MR analyses provided evidence for a causal relationship between BMI and eight proteins including leptin (0.63 standard deviation (SD) per SD BMI, 95% CI 0.48-0.79, P = 1.6 × 10<sup>-15</sup>), FABP4 (0.64 SD per SD BMI, 95% CI 0.46-0.83, P = 6.7 × 10<sup>-12</sup>) and SHBG (-0.45 SD per SD BMI, 95% CI -0.65 to -0.25, P = 1.4 × 10<sup>-5</sup>). There was agreement in the magnitude of observational and MR estimates (R<sup>2</sup> = 0.33) and evidence that proteins most strongly altered by BMI were enriched for genes involved in cardiovascular disease.<h4>Conclusions</h4>This study provides evidence for a broad impact of adiposity on the human proteome. Proteins strongly altered by BMI include those involved in regulating appetite, sex hormones and inflammation; such proteins are also enriched for cardiovascular disease-related genes. Altogether, results help focus attention onto new proteomic signatures of obesity-related disease.",,pdf:https://www.nature.com/articles/s41366-021-00896-1.pdf; doi:https://doi.org/10.1038/s41366-021-00896-1; html:https://europepmc.org/articles/PMC8455324; pdf:https://europepmc.org/articles/PMC8455324?pdf=render
-32781946,https://doi.org/10.1098/rspb.2020.1405,Key questions for modelling COVID-19 exit strategies.,"Thompson RN, Hollingsworth TD, Isham V, Arribas-Bel D, Ashby B, Britton T, Challenor P, Chappell LHK, Clapham H, Cunniffe NJ, Dawid AP, Donnelly CA, Eggo RM, Funk S, Gilbert N, Glendinning P, Gog JR, Hart WS, Heesterbeek H, House T, Keeling M, Kiss IZ, Kretzschmar ME, Lloyd AL, McBryde ES, McCaw JM, McKinley TJ, Miller JC, Morris M, O'Neill PD, Parag KV, Pearson CAB, Pellis L, Pulliam JRC, Ross JV, Tomba GS, Silverman BW, Struchiner CJ, Tildesley MJ, Trapman P, Webb CR, Mollison D, Restif O.",,Proceedings. Biological sciences,2020,2020-08-12,Y,Uncertainty; Mathematical Modelling; Epidemic Control; Exit Strategy; Covid-19; Sars-cov-2,,,"Combinations of intense non-pharmaceutical interventions (lockdowns) were introduced worldwide to reduce SARS-CoV-2 transmission. Many governments have begun to implement exit strategies that relax restrictions while attempting to control the risk of a surge in cases. Mathematical modelling has played a central role in guiding interventions, but the challenge of designing optimal exit strategies in the face of ongoing transmission is unprecedented. Here, we report discussions from the Isaac Newton Institute 'Models for an exit strategy' workshop (11-15 May 2020). A diverse community of modellers who are providing evidence to governments worldwide were asked to identify the main questions that, if answered, would allow for more accurate predictions of the effects of different exit strategies. Based on these questions, we propose a roadmap to facilitate the development of reliable models to guide exit strategies. This roadmap requires a global collaborative effort from the scientific community and policymakers, and has three parts: (i) improve estimation of key epidemiological parameters; (ii) understand sources of heterogeneity in populations; and (iii) focus on requirements for data collection, particularly in low-to-middle-income countries. This will provide important information for planning exit strategies that balance socio-economic benefits with public health.",,doi:https://doi.org/10.1098/rspb.2020.1405; doi:https://doi.org/10.1098/rspb.2020.1405; html:https://europepmc.org/articles/PMC7575516; pdf:https://europepmc.org/articles/PMC7575516?pdf=render
 30537243,https://doi.org/10.1002/ejhf.1370,"Can advanced analytics fix modern medicine's problem of uncertainty, imprecision, and inaccuracy?","Ahmad T, Freeman JV, Asselbergs FW.",,European journal of heart failure,2019,2018-12-10,N,,,,,,doi:https://doi.org/10.1002/ejhf.1370
 32170038,https://doi.org/10.1136/heartjnl-2019-316088,Cardiovascular risk factors and the risk of major adverse limb events in patients with symptomatic cardiovascular disease.,"Hageman SHJ, de Borst GJ, Dorresteijn JAN, Bots ML, Westerink J, Asselbergs FW, Visseren FLJ, UCC-SMART Study Group.",,Heart (British Cardiac Society),2020,2020-03-13,N,Hypertension; Smoking Cessation; Peripheral Vascular Disease; Cardiac Risk Factors And Prevention; Lipoproteins And Hyperlipidaemia,,,"<h4>Aim</h4>To determine the relationship between non-high-density lipoprotein cholesterol (non-HDL-c), systolic blood pressure (SBP) and smoking and the risk of major adverse limb events (MALE) and the combination with major adverse cardiovascular events (MALE/MACE) in patients with symptomatic vascular disease.<h4>Methods</h4>Patients with symptomatic vascular disease from the Utrecht Cardiovascular Cohort - Secondary Manifestations of ARTerial disease (1996-2017) study were included. The effects of non-HDL-c, SBP and smoking on the risk of MALE were analysed with Cox proportional hazard models stratified for presence of peripheral artery disease (PAD). MALE was defined as major amputation, peripheral revascularisation or thrombolysis in the lower limb.<h4>Results</h4>In 8139 patients (median follow-up 7.8 years, IQR 4.0-11.8), 577 MALE (8.7 per 1000 person-years) and 1933 MALE/MACE were observed (29.1 per 1000 person-years). In patients with PAD there was no relation between non-HDL-c and MALE, and in patients with coronary artery disease (CAD), cerebrovascular disease (CVD) or abdominal aortic aneurysm (AAA) the risk of MALE was higher per 1 mmol/L non-HDL-c (HR 1.14, 95% CI 1.01 to 1.29). Per 10 mm Hg SBP, the risk of MALE was higher in patients with PAD (HR 1.06, 95% CI 1.01 to 1.12) and in patients with CVD/CAD/AAA (HR 1.15, 95% CI 1.08 to 1.22). The risk of MALE was higher in smokers with PAD (HR 1.45, 95% CI 0.97 to 2.14) and CAD/CVD/AAA (HR 7.08, 95% CI 3.99 to 12.57).<h4>Conclusions</h4>The risk of MALE and MALE/MACE in patients with symptomatic vascular disease differs according to vascular disease location and is associated with non-HDL-c, SBP and smoking. These findings confirm the importance of MALE as an outcome and underline the importance of risk factor management in patients with vascular disease.",,pdf:https://discovery.ucl.ac.uk/10096914/1/Hageman_Manuscript_MALE_20200211_clean.pdf; doi:https://doi.org/10.1136/heartjnl-2019-316088
 32916155,https://doi.org/10.1016/j.molmet.2020.101072,"Corrigendum to ""Genome-wide association study of adipocyte lipolysis in the GENetics of adipocyte lipolysis (GENiAL) cohort"" [Molecular Metabolism 34 (2020) 85-96].","Kulyté A, Lundbäck V, Lindgren CM, Luan J, Lotta LA, Langenberg C, Arner P, Strawbridge RJ, Dahlman I.",,Molecular metabolism,2020,2020-09-08,Y,,,,,,doi:https://doi.org/10.1016/j.molmet.2020.101072; doi:https://doi.org/10.1016/j.molmet.2020.101072; html:https://europepmc.org/articles/PMC7492984; pdf:https://europepmc.org/articles/PMC7492984?pdf=render
 35513530,https://doi.org/10.1038/s41591-022-01781-8,Patient reported outcome assessment must be inclusive and equitable.,"Calvert MJ, Cruz Rivera S, Retzer A, Hughes SE, Campbell L, Molony-Oates B, Aiyegbusi OL, Stover AM, Wilson R, McMullan C, Anderson NE, Turner GM, Davies EH, Verdi R, Velikova G, Kamudoni P, Muslim S, Gheorghe A, O'Connor D, Liu X, Wu AW, Denniston AK.",,Nature medicine,2022,2022-06-01,N,,,,,,pdf:https://www.nature.com/articles/s41591-022-01781-8.pdf; doi:https://doi.org/10.1038/s41591-022-01781-8
-32679111,https://doi.org/10.1016/s0140-6736(20)31356-8,COVID-19 pandemic and admission rates for and management of acute coronary syndromes in England.,"Mafham MM, Spata E, Goldacre R, Gair D, Curnow P, Bray M, Hollings S, Roebuck C, Gale CP, Mamas MA, Deanfield JE, de Belder MA, Luescher TF, Denwood T, Landray MJ, Emberson JR, Collins R, Morris EJA, Casadei B, Baigent C.",,"Lancet (London, England)",2020,2020-07-14,Y,,,,"<h4>Background</h4>Several countries affected by the COVID-19 pandemic have reported a substantial drop in the number of patients attending the emergency department with acute coronary syndromes and a reduced number of cardiac procedures. We aimed to understand the scale, nature, and duration of changes to admissions for different types of acute coronary syndrome in England and to evaluate whether in-hospital management of patients has been affected as a result of the COVID-19 pandemic.<h4>Methods</h4>We analysed data on hospital admissions in England for types of acute coronary syndrome from Jan 1, 2019, to May 24, 2020, that were recorded in the Secondary Uses Service Admitted Patient Care database. Admissions were classified as ST-elevation myocardial infarction (STEMI), non-STEMI (NSTEMI), myocardial infarction of unknown type, or other acute coronary syndromes (including unstable angina). We identified revascularisation procedures undertaken during these admissions (ie, coronary angiography without percutaneous coronary intervention [PCI], PCI, and coronary artery bypass graft surgery). We calculated the numbers of weekly admissions and procedures undertaken; percentage reductions in weekly admissions and across subgroups were also calculated, with 95% CIs.<h4>Findings</h4>Hospital admissions for acute coronary syndrome declined from mid-February, 2020, falling from a 2019 baseline rate of 3017 admissions per week to 1813 per week by the end of March, 2020, a reduction of 40% (95% CI 37-43). This decline was partly reversed during April and May, 2020, such that by the last week of May, 2020, there were 2522 admissions, representing a 16% (95% CI 13-20) reduction from baseline. During the period of declining admissions, there were reductions in the numbers of admissions for all types of acute coronary syndrome, including both STEMI and NSTEMI, but relative and absolute reductions were larger for NSTEMI, with 1267 admissions per week in 2019 and 733 per week by the end of March, 2020, a percent reduction of 42% (95% CI 38-46). In parallel, reductions were recorded in the number of PCI procedures for patients with both STEMI (438 PCI procedures per week in 2019 vs 346 by the end of March, 2020; percent reduction 21%, 95% CI 12-29) and NSTEMI (383 PCI procedures per week in 2019 vs 240 by the end of March, 2020; percent reduction 37%, 29-45). The median length of stay among patients with acute coronary syndrome fell from 4 days (IQR 2-9) in 2019 to 3 days (1-5) by the end of March, 2020.<h4>Interpretation</h4>Compared with the weekly average in 2019, there was a substantial reduction in the weekly numbers of patients with acute coronary syndrome who were admitted to hospital in England by the end of March, 2020, which had been partly reversed by the end of May, 2020. The reduced number of admissions during this period is likely to have resulted in increases in out-of-hospital deaths and long-term complications of myocardial infarction and missed opportunities to offer secondary prevention treatment for patients with coronary heart disease. The full extent of the effect of COVID-19 on the management of patients with acute coronary syndrome will continue to be assessed by updating these analyses.<h4>Funding</h4>UK Medical Research Council, British Heart Foundation, Public Health England, Health Data Research UK, and the National Institute for Health Research Oxford Biomedical Research Centre.",,doi:https://doi.org/10.1016/s0140-6736(20)31356-8; doi:https://doi.org/10.1016/S0140-6736(20)31356-8; html:https://europepmc.org/articles/PMC7429983; pdf:https://europepmc.org/articles/PMC7429983?pdf=render
 31443926,https://doi.org/10.1016/s0140-6736(19)31674-5,Medium and long-term risks of specific cardiovascular diseases in survivors of 20 adult cancers: a population-based cohort study using multiple linked UK electronic health records databases.,"Strongman H, Gadd S, Matthews A, Mansfield KE, Stanway S, Lyon AR, Dos-Santos-Silva I, Smeeth L, Bhaskaran K.",,"Lancet (London, England)",2019,2019-08-20,Y,,Understanding the Causes of Disease,,"<h4>Background</h4>The past few decades have seen substantial improvements in cancer survival, but concerns exist about long-term cardiovascular disease risk in survivors. Evidence is scarce on the risks of specific cardiovascular diseases in survivors of a wide range of cancers to inform prevention and management. In this study, we used large-scale electronic health records data from multiple linked UK databases to address these evidence gaps.<h4>Methods</h4>For this population-based cohort study, we used linked primary care, hospital, and cancer registry data from the UK Clinical Practice Research Datalink to identify cohorts of survivors of the 20 most common cancers who were 18 years or older and alive 12 months after diagnosis and controls without history of cancer, matched for age, sex, and general practice. We compared risks for a range of cardiovascular disease outcomes using crude and adjusted Cox models. We fitted interactions to investigate effect modification, and flexible parametric survival models to estimate absolute excess risks over time.<h4>Findings</h4>Between Jan 1, 1990, and Dec 31, 2015, 126 120 individuals with a diagnosis of a cancer of interest still being followed up at least 1 year later were identified and matched to 630 144 controls. After exclusions, 108 215 cancer survivors and 523 541 controls were included in the main analyses. Venous thromboembolism risk was elevated in survivors of 18 of 20 site-specific cancers compared with that of controls; adjusted hazard ratios (HRs) ranged from 1·72 (95% CI 1·57-1·89) in patients after prostate cancer to 9·72 (5·50-17·18) after pancreatic cancer. HRs decreased over time, but remained elevated more than 5 years after diagnosis. We observed increased risks of heart failure or cardiomyopathy in patients after ten of 20 cancers, including haematological (adjusted HR 1·94, 1·66-2·25, with non-Hodgkin lymphoma; 1·77, 1·50-2·09, with leukaemia; and 3·29, 2·59-4·18, with multiple myeloma), oesophageal (1·96, 1·46-2·64), lung (1·82, 1·52-2·17) kidney (1·73, 1·38-2·17) and ovarian (1·59, 1·19-2·12). Elevated risks of arrhythmia, pericarditis, coronary artery disease, stroke, and valvular heart disease were also observed for multiple cancers, including haematological malignancies. HRs for heart failure or cardiomyopathy and venous thromboembolism were greater in patients without previous cardiovascular disease and in younger patients. However, absolute excess risks were generally greater with increasing age. Increased risks of these outcomes seemed most pronounced in patients who had received chemotherapy.<h4>Interpretation</h4>Survivors of most site-specific cancers had increased medium-term to long-term risk for one or more cardiovascular diseases compared with that for the general population, with substantial variations between cancer sites.<h4>Funding</h4>Wellcome Trust and Royal Society.",,pdf:http://www.thelancet.com/article/S0140673619316745/pdf; doi:https://doi.org/10.1016/S0140-6736(19)31674-5; html:https://europepmc.org/articles/PMC6857444; pdf:https://europepmc.org/articles/PMC6857444?pdf=render
+32679111,https://doi.org/10.1016/s0140-6736(20)31356-8,COVID-19 pandemic and admission rates for and management of acute coronary syndromes in England.,"Mafham MM, Spata E, Goldacre R, Gair D, Curnow P, Bray M, Hollings S, Roebuck C, Gale CP, Mamas MA, Deanfield JE, de Belder MA, Luescher TF, Denwood T, Landray MJ, Emberson JR, Collins R, Morris EJA, Casadei B, Baigent C.",,"Lancet (London, England)",2020,2020-07-14,Y,,,,"<h4>Background</h4>Several countries affected by the COVID-19 pandemic have reported a substantial drop in the number of patients attending the emergency department with acute coronary syndromes and a reduced number of cardiac procedures. We aimed to understand the scale, nature, and duration of changes to admissions for different types of acute coronary syndrome in England and to evaluate whether in-hospital management of patients has been affected as a result of the COVID-19 pandemic.<h4>Methods</h4>We analysed data on hospital admissions in England for types of acute coronary syndrome from Jan 1, 2019, to May 24, 2020, that were recorded in the Secondary Uses Service Admitted Patient Care database. Admissions were classified as ST-elevation myocardial infarction (STEMI), non-STEMI (NSTEMI), myocardial infarction of unknown type, or other acute coronary syndromes (including unstable angina). We identified revascularisation procedures undertaken during these admissions (ie, coronary angiography without percutaneous coronary intervention [PCI], PCI, and coronary artery bypass graft surgery). We calculated the numbers of weekly admissions and procedures undertaken; percentage reductions in weekly admissions and across subgroups were also calculated, with 95% CIs.<h4>Findings</h4>Hospital admissions for acute coronary syndrome declined from mid-February, 2020, falling from a 2019 baseline rate of 3017 admissions per week to 1813 per week by the end of March, 2020, a reduction of 40% (95% CI 37-43). This decline was partly reversed during April and May, 2020, such that by the last week of May, 2020, there were 2522 admissions, representing a 16% (95% CI 13-20) reduction from baseline. During the period of declining admissions, there were reductions in the numbers of admissions for all types of acute coronary syndrome, including both STEMI and NSTEMI, but relative and absolute reductions were larger for NSTEMI, with 1267 admissions per week in 2019 and 733 per week by the end of March, 2020, a percent reduction of 42% (95% CI 38-46). In parallel, reductions were recorded in the number of PCI procedures for patients with both STEMI (438 PCI procedures per week in 2019 vs 346 by the end of March, 2020; percent reduction 21%, 95% CI 12-29) and NSTEMI (383 PCI procedures per week in 2019 vs 240 by the end of March, 2020; percent reduction 37%, 29-45). The median length of stay among patients with acute coronary syndrome fell from 4 days (IQR 2-9) in 2019 to 3 days (1-5) by the end of March, 2020.<h4>Interpretation</h4>Compared with the weekly average in 2019, there was a substantial reduction in the weekly numbers of patients with acute coronary syndrome who were admitted to hospital in England by the end of March, 2020, which had been partly reversed by the end of May, 2020. The reduced number of admissions during this period is likely to have resulted in increases in out-of-hospital deaths and long-term complications of myocardial infarction and missed opportunities to offer secondary prevention treatment for patients with coronary heart disease. The full extent of the effect of COVID-19 on the management of patients with acute coronary syndrome will continue to be assessed by updating these analyses.<h4>Funding</h4>UK Medical Research Council, British Heart Foundation, Public Health England, Health Data Research UK, and the National Institute for Health Research Oxford Biomedical Research Centre.",,doi:https://doi.org/10.1016/s0140-6736(20)31356-8; doi:https://doi.org/10.1016/S0140-6736(20)31356-8; html:https://europepmc.org/articles/PMC7429983; pdf:https://europepmc.org/articles/PMC7429983?pdf=render
 37719788,https://doi.org/10.1093/noajnl/vdad096,Development of a core outcome set for use in adult primary glioma phase III interventional trials: A mixed methods study.,"Retzer A, Baddeley E, Sivell S, Scott H, Nelson A, Bulbeck H, Seddon K, Grant R, Adams R, Watts C, Aiyegbusi OL, Kearns P, Rivera SC, Dirven L, Calvert M, Byrne A.",,Neuro-oncology advances,2023,2023-01-01,Y,trials; Outcomes; Neuro-oncology; Delphi; Primary Glioma,,,"<h4>Background</h4>Glioma interventional studies should collect data aligned with patient priorities, enabling treatment benefit assessment and informed decision-making. This requires effective data synthesis and meta-analyses, underpinned by consistent trial outcome measurement, analysis, and reporting. Development of a core outcome set (COS) may contribute to a solution.<h4>Methods</h4>A 5-stage process was used to develop a COS for glioma trials from the UK perspective. Outcome lists were generated in stages 1: a trial registry review and systematic review of qualitative studies and 2: interviews with glioma patients and caregivers. In stage 3, the outcome lists were de-duplicated with accessible terminology, in stage 4 outcomes were rated via a 2-round Delphi process, and stage 5 comprised a consensus meeting to finalize the COS. Patient-reportable COS outcomes were identified.<h4>Results</h4>In Delphi round 1, 96 participants rated 35 outcomes identified in stages 1 and 2, to which a further 10 were added. Participants (77/96) rated the resulting 45 outcomes in round 2. Of these, 22 outcomes met a priori threshold for inclusion in the COS. After further review, a COS consisting of 19 outcomes grouped into 7 outcome domains (survival, adverse events, activities of daily living, health-related quality of life, seizure activity, cognitive function, and physical function) was finalized by 13 participants at the consensus meeting.<h4>Conclusions</h4>A COS for glioma trials was developed, comprising 7 outcome domains. Additional research will identify appropriate measurement tools and further validate this COS.",,pdf:https://academic.oup.com/noa/advance-article-pdf/doi/10.1093/noajnl/vdad096/51026152/vdad096.pdf; doi:https://doi.org/10.1093/noajnl/vdad096; html:https://europepmc.org/articles/PMC10503650; pdf:https://europepmc.org/articles/PMC10503650?pdf=render
+35410184,https://doi.org/10.1186/s12889-022-13069-0,The local burden of disease during the first wave of the COVID-19 epidemic in England: estimation using different data sources from changing surveillance practices.,"Nightingale ES, Abbott S, Russell TW, CMMID Covid-19 Working Group, Lowe R, Medley GF, Brady OJ.",,BMC public health,2022,2022-04-11,Y,,,,"<h4>Background</h4>The COVID-19 epidemic has differentially impacted communities across England, with regional variation in rates of confirmed cases, hospitalisations and deaths. Measurement of this burden changed substantially over the first months, as surveillance was expanded to accommodate the escalating epidemic. Laboratory confirmation was initially restricted to clinical need (""pillar 1"") before expanding to community-wide symptomatics (""pillar 2""). This study aimed to ascertain whether inconsistent measurement of case data resulting from varying testing coverage could be reconciled by drawing inference from COVID-19-related deaths.<h4>Methods</h4>We fit a Bayesian spatio-temporal model to weekly COVID-19-related deaths per local authority (LTLA) throughout the first wave (1 January 2020-30 June 2020), adjusting for the local epidemic timing and the age, deprivation and ethnic composition of its population. We combined predictions from this model with case data under community-wide, symptomatic testing and infection prevalence estimates from the ONS infection survey, to infer the likely trajectory of infections implied by the deaths in each LTLA.<h4>Results</h4>A model including temporally- and spatially-correlated random effects was found to best accommodate the observed variation in COVID-19-related deaths, after accounting for local population characteristics. Predicted case counts under community-wide symptomatic testing suggest a total of 275,000-420,000 cases over the first wave - a median of over 100,000 additional to the total confirmed in practice under varying testing coverage. This translates to a peak incidence of around 200,000 total infections per week across England. The extent to which estimated total infections are reflected in confirmed case counts was found to vary substantially across LTLAs, ranging from 7% in Leicester to 96% in Gloucester with a median of 23%.<h4>Conclusions</h4>Limitations in testing capacity biased the observed trajectory of COVID-19 infections throughout the first wave. Basing inference on COVID-19-related mortality and higher-coverage testing later in the time period, we could explore the extent of this bias more explicitly. Evidence points towards substantial under-representation of initial growth and peak magnitude of infections nationally, to which different parts of the country contribute unequally.",,pdf:https://bmcpublichealth.biomedcentral.com/track/pdf/10.1186/s12889-022-13069-0; doi:https://doi.org/10.1186/s12889-022-13069-0; html:https://europepmc.org/articles/PMC8996221; pdf:https://europepmc.org/articles/PMC8996221?pdf=render
 36996819,https://doi.org/10.1016/j.chom.2023.03.004,Characterization of the rotavirus assembly pathway in situ using cryoelectron tomography.,"Shah PNM, Gilchrist JB, Forsberg BO, Burt A, Howe A, Mosalaganti S, Wan W, Radecke J, Chaban Y, Sutton G, Stuart DI, Boyce M.",,Cell host & microbe,2023,2023-03-29,Y,Electron microscopy; In situ; Rotavirus; virus assembly; Reoviridae; Virus Structure; Subtomogram Averaging; Cryoelectron Tomography; Dsrna Viruses; Cellular Structural Biology,,,"Rotavirus assembly is a complex process that involves the stepwise acquisition of protein layers in distinct intracellular locations to form the fully assembled particle. Understanding and visualization of the assembly process has been hampered by the inaccessibility of unstable intermediates. We characterize the assembly pathway of group A rotaviruses observed in situ within cryo-preserved infected cells through the use of cryoelectron tomography of cellular lamellae. Our findings demonstrate that the viral polymerase VP1 recruits viral genomes during particle assembly, as revealed by infecting with a conditionally lethal mutant. Additionally, pharmacological inhibition to arrest the transiently enveloped stage uncovered a unique conformation of the VP4 spike. Subtomogram averaging provided atomic models of four intermediate states, including a pre-packaging single-layered intermediate, the double-layered particle, the transiently enveloped double-layered particle, and the fully assembled triple-layered virus particle. In summary, these complementary approaches enable us to elucidate the discrete steps involved in forming an intracellular rotavirus particle.",,doi:https://doi.org/10.1016/j.chom.2023.03.004; doi:https://doi.org/10.1016/j.chom.2023.03.004; html:https://europepmc.org/articles/PMC7615348; pdf:https://europepmc.org/articles/PMC7615348?pdf=render
 36764723,https://doi.org/10.1136/bmjopen-2022-067254,Associations of remote mental healthcare with clinical outcomes: a natural language processing enriched electronic health record data study protocol.,"Ahmed MS, Kornblum D, Oliver D, Fusar-Poli P, Patel R.",,BMJ open,2023,2023-02-10,Y,Psychiatry; epidemiology; Telemedicine; Health Informatics,,,"<h4>Introduction</h4>People often experience significant difficulties in receiving mental healthcare due to insufficient resources, stigma and lack of access to care. Remote care technology has the potential to overcome these barriers by reducing travel time and increasing frequency of contact with patients. However, the safe delivery of remote mental healthcare requires evidence on which aspects of care are suitable for remote delivery and which are better served by in-person care. We aim to investigate clinical and demographic associations with remote mental healthcare in a large electronic health record (EHR) dataset and the degree to which remote care is associated with differences in clinical outcomes using natural language processing (NLP) derived EHR data.<h4>Methods and analysis</h4>Deidentified EHR data, derived from the South London and Maudsley (SLaM) National Health Service Foundation Trust Biomedical Research Centre (BRC) Case Register, will be extracted using the Clinical Record Interactive Search tool for all patients receiving mental healthcare between 1 January 2019 and 31 March 2022. First, data on a retrospective, longitudinal cohort of around 80 000 patients will be analysed using descriptive statistics to investigate clinical and demographic associations with remote mental healthcare and multivariable Cox regression to compare clinical outcomes of remote versus in-person assessments. Second, NLP models that have been previously developed to extract mental health symptom data will be applied to around 5 million documents to analyse the variation in content of remote versus in-person assessments.<h4>Ethics and dissemination</h4>The SLaM BRC Case Register and Clinical Record Interactive Search (CRIS) tool have received ethical approval as a deidentified dataset (including NLP-derived data from unstructured free text documents) for secondary mental health research from Oxfordshire REC C (Ref: 18/SC/0372). The study has received approval from the SLaM CRIS Oversight Committee. Study findings will be disseminated through peer-reviewed, open access journal articles and service user and carer advisory groups.",,pdf:https://bmjopen.bmj.com/content/bmjopen/13/2/e067254.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-067254; html:https://europepmc.org/articles/PMC9923317; pdf:https://europepmc.org/articles/PMC9923317?pdf=render
-35410184,https://doi.org/10.1186/s12889-022-13069-0,The local burden of disease during the first wave of the COVID-19 epidemic in England: estimation using different data sources from changing surveillance practices.,"Nightingale ES, Abbott S, Russell TW, CMMID Covid-19 Working Group, Lowe R, Medley GF, Brady OJ.",,BMC public health,2022,2022-04-11,Y,,,,"<h4>Background</h4>The COVID-19 epidemic has differentially impacted communities across England, with regional variation in rates of confirmed cases, hospitalisations and deaths. Measurement of this burden changed substantially over the first months, as surveillance was expanded to accommodate the escalating epidemic. Laboratory confirmation was initially restricted to clinical need (""pillar 1"") before expanding to community-wide symptomatics (""pillar 2""). This study aimed to ascertain whether inconsistent measurement of case data resulting from varying testing coverage could be reconciled by drawing inference from COVID-19-related deaths.<h4>Methods</h4>We fit a Bayesian spatio-temporal model to weekly COVID-19-related deaths per local authority (LTLA) throughout the first wave (1 January 2020-30 June 2020), adjusting for the local epidemic timing and the age, deprivation and ethnic composition of its population. We combined predictions from this model with case data under community-wide, symptomatic testing and infection prevalence estimates from the ONS infection survey, to infer the likely trajectory of infections implied by the deaths in each LTLA.<h4>Results</h4>A model including temporally- and spatially-correlated random effects was found to best accommodate the observed variation in COVID-19-related deaths, after accounting for local population characteristics. Predicted case counts under community-wide symptomatic testing suggest a total of 275,000-420,000 cases over the first wave - a median of over 100,000 additional to the total confirmed in practice under varying testing coverage. This translates to a peak incidence of around 200,000 total infections per week across England. The extent to which estimated total infections are reflected in confirmed case counts was found to vary substantially across LTLAs, ranging from 7% in Leicester to 96% in Gloucester with a median of 23%.<h4>Conclusions</h4>Limitations in testing capacity biased the observed trajectory of COVID-19 infections throughout the first wave. Basing inference on COVID-19-related mortality and higher-coverage testing later in the time period, we could explore the extent of this bias more explicitly. Evidence points towards substantial under-representation of initial growth and peak magnitude of infections nationally, to which different parts of the country contribute unequally.",,pdf:https://bmcpublichealth.biomedcentral.com/track/pdf/10.1186/s12889-022-13069-0; doi:https://doi.org/10.1186/s12889-022-13069-0; html:https://europepmc.org/articles/PMC8996221; pdf:https://europepmc.org/articles/PMC8996221?pdf=render
 35244709,https://doi.org/10.1093/europace/euac022,Impact of oral anticoagulation on the association between frailty and clinical outcomes in people with atrial fibrillation: nationwide primary care records on treatment analysis.,"Wilkinson C, Wu J, Clegg A, Nadarajah R, Rockwood K, Todd O, Gale CP.",,"Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology",2022,2022-07-01,Y,Bleeding; Atrial fibrillation; Stroke; Frailty; Outcome; Oral Anticoagulation; Oral Anticoagulation Prescription,,,"<h4>Aims</h4>People with atrial fibrillation (AF) frequently live with frailty, which increases the risk of mortality and stroke. This study reports the association between oral anticoagulation (OAC) and outcomes for people with frailty, and whether there is overall net benefit from treatment in people with AF.<h4>Methods and results</h4>Retrospective open cohort electronic records study. Frailty was identified using the electronic frailty index. Primary care electronic health records of 89 996 adults with AF and CHA2DS2-Vasc score of ≥2 were linked with secondary care and mortality data in the Clinical Practice Research Database (CPRD) from 1 January 1998 to 30 November 2018. The primary outcome was a composite of death, stroke, systemic embolism, or major bleeding. Secondary outcomes were stroke, major bleeding, all-cause mortality, transient ischaemic attack, and falls. Of 89 996 participants, 71 256 (79.2%) were living with frailty. The prescription of OAC increased with degree of frailty. For patients not prescribed OAC, rates of the primary outcome increased alongside frailty category. Prescription of OAC was associated with a reduction in the primary outcome for each frailty category [adjusted hazard ratio, 95% confidence interval, no OAC as reference; fit: vitamin K antagonist (VKA) 0.69, 0.64-0.75, direct oral anticoagulant (DOAC) 0.42, 0.33-0.53; mild frailty: VKA 0.52, 0.50-0.54, DOAC 0.57, 0.52-0.63; moderate: VKA 0.54, 0.52-0.56, DOAC 0.57, 0.52-0.63; severe: VKA 0.48, 0.45-0.51, DOAC 0.58, 0.52-0.65], with cumulative incidence function effects greater for DOAC than VKA.<h4>Conclusion</h4>Frailty among people with AF is common. The OAC was associated with a reduction in the primary endpoint across all degrees of frailty.",,doi:https://doi.org/10.1093/europace/euac022; doi:https://doi.org/10.1093/europace/euac022; html:https://europepmc.org/articles/PMC9326851; pdf:https://europepmc.org/articles/PMC9326851?pdf=render
 34328441,https://doi.org/10.2196/29840,Predicting Depressive Symptom Severity Through Individuals' Nearby Bluetooth Device Count Data Collected by Mobile Phones: Preliminary Longitudinal Study.,"Zhang Y, Folarin AA, Sun S, Cummins N, Ranjan Y, Rashid Z, Conde P, Stewart C, Laiou P, Matcham F, Oetzmann C, Lamers F, Siddi S, Simblett S, Rintala A, Mohr DC, Myin-Germeys I, Wykes T, Haro JM, Penninx BWJH, Narayan VA, Annas P, Hotopf M, Dobson RJB.",,JMIR mHealth and uHealth,2021,2021-07-30,Y,Monitoring; Depression; Mental health; Hierarchical Bayesian Model; Bluetooth; Mhealth; Mobile Health; Digital Health; Digital Biomarkers; Digital Phenotyping,,,"<h4>Background</h4>Research in mental health has found associations between depression and individuals' behaviors and statuses, such as social connections and interactions, working status, mobility, and social isolation and loneliness. These behaviors and statuses can be approximated by the nearby Bluetooth device count (NBDC) detected by Bluetooth sensors in mobile phones.<h4>Objective</h4>This study aimed to explore the value of the NBDC data in predicting depressive symptom severity as measured via the 8-item Patient Health Questionnaire (PHQ-8).<h4>Methods</h4>The data used in this paper included 2886 biweekly PHQ-8 records collected from 316 participants recruited from three study sites in the Netherlands, Spain, and the United Kingdom as part of the EU Remote Assessment of Disease and Relapse-Central Nervous System (RADAR-CNS) study. From the NBDC data 2 weeks prior to each PHQ-8 score, we extracted 49 Bluetooth features, including statistical features and nonlinear features for measuring the periodicity and regularity of individuals' life rhythms. Linear mixed-effect models were used to explore associations between Bluetooth features and the PHQ-8 score. We then applied hierarchical Bayesian linear regression models to predict the PHQ-8 score from the extracted Bluetooth features.<h4>Results</h4>A number of significant associations were found between Bluetooth features and depressive symptom severity. Generally speaking, along with depressive symptom worsening, one or more of the following changes were found in the preceding 2 weeks of the NBDC data: (1) the amount decreased, (2) the variance decreased, (3) the periodicity (especially the circadian rhythm) decreased, and (4) the NBDC sequence became more irregular. Compared with commonly used machine learning models, the proposed hierarchical Bayesian linear regression model achieved the best prediction metrics (R<sup>2</sup>=0.526) and a root mean squared error (RMSE) of 3.891. Bluetooth features can explain an extra 18.8% of the variance in the PHQ-8 score relative to the baseline model without Bluetooth features (R<sup>2</sup>=0.338, RMSE=4.547).<h4>Conclusions</h4>Our statistical results indicate that the NBDC data have the potential to reflect changes in individuals' behaviors and statuses concurrent with the changes in the depressive state. The prediction results demonstrate that the NBDC data have a significant value in predicting depressive symptom severity. These findings may have utility for the mental health monitoring practice in real-world settings.",,pdf:https://mhealth.jmir.org/2021/7/e29840/PDF; doi:https://doi.org/10.2196/29840; html:https://europepmc.org/articles/PMC8367113
-36330526,https://doi.org/10.3389/fimmu.2022.1032331,Levels of soluble complement regulators predict severity of COVID-19 symptoms.,"Tierney AL, Alali WM, Scott T, Rees-Unwin KS, CITIID-NIHR BioResource COVID-19 Collaboration, Clark SJ, Unwin RD.",,Frontiers in immunology,2022,2022-10-18,Y,Complement; Mass spectrometry; Biomarkers; Factor H; Factor H-related Proteins; Covid-19; Sars-cov-2,,,"The SARS-CoV-2 virus continues to cause significant morbidity and mortality worldwide from COVID-19. One of the major challenges of patient management is the broad range of symptoms observed. While the majority of individuals experience relatively mild disease, a significant minority of patients require hospitalisation, with COVID-19 still proving fatal for some. As such, there remains a desperate need to better understand what drives this severe disease, both in terms of the underlying biology, but also to potentially predict at diagnosis which patients are likely to require further interventions, thus enabling better outcomes for both patients and healthcare systems. Several lines of evidence have pointed to dysregulation of the complement cascade as a major factor in severe COVID-19 outcomes. How this is underpinned mechanistically is not known. Here, we have focussed on the role of the soluble complement regulators Complement Factor H (FH), its splice variant Factor H-like 1 (FHL-1) and five Factor H-Related proteins (FHR1-5). Using a targeted mass spectrometry approach, we quantified these proteins in a cohort of 188 plasma samples from controls and SARS-CoV-2 patients taken at diagnosis. This analysis revealed significant elevations in all FHR proteins, but not FH, in patients with more severe disease, particularly FHR2 and FHR5 (FHR2: 1.97-fold, p&lt;0.0001; FHR5: 2.4-fold, p&lt;0.0001). Furthermore, for a subset of 77 SARS-CoV-2 +ve patients we also analysed time course samples taken approximately 28 days post-diagnosis. Here, we see complement regulator levels drop in all individuals with asymptomatic or mild disease, but regulators remain high in those with more severe outcomes, with elevations in FHR2 over baseline levels in this group. These data support the hypothesis that elevation of circulating levels of the FHR family of proteins could predict disease severity in COVID-19 patients, and that the duration of elevation (or lack of immune activation resolution) may be partly responsible for driving poor outcomes in COVID-19.",,pdf:https://www.frontiersin.org/articles/10.3389/fimmu.2022.1032331/pdf; doi:https://doi.org/10.3389/fimmu.2022.1032331; html:https://europepmc.org/articles/PMC9624227; pdf:https://europepmc.org/articles/PMC9624227?pdf=render
 31234639,https://doi.org/10.1161/circulationaha.118.038814,Use of Genetic Variants Related to Antihypertensive Drugs to Inform on Efficacy and Side Effects.,"Gill D, Georgakis MK, Koskeridis F, Jiang L, Feng Q, Wei WQ, Theodoratou E, Elliott P, Denny JC, Malik R, Evangelou E, Dehghan A, Dichgans M, Tzoulaki I.",,Circulation,2019,2019-06-25,Y,Antihypertensive drugs; Mendelian Randomization Analysis,"Better Care, The Human Phenome",,"<h4>Background</h4>Drug effects can be investigated through natural variation in the genes for their protein targets. The present study aimed to use this approach to explore the potential side effects and repurposing potential of antihypertensive drugs, which are among the most commonly used medications worldwide.<h4>Methods</h4>Genetic proxies for the effect of antihypertensive drug classes were identified as variants in the genes for the corresponding targets that associated with systolic blood pressure at genome-wide significance. Mendelian randomization estimates for drug effects on coronary heart disease and stroke risk were compared with randomized, controlled trial results. A phenome-wide association study in the UK Biobank was performed to identify potential side effects and repurposing opportunities, with findings investigated in the Vanderbilt University biobank (BioVU) and in observational analysis of the UK Biobank.<h4>Results</h4>Suitable genetic proxies for angiotensin-converting enzyme inhibitors, β-blockers, and calcium channel blockers (CCBs) were identified. Mendelian randomization estimates for their effect on coronary heart disease and stroke risk, respectively, were comparable to results from randomized, controlled trials against placebo. A phenome-wide association study in the UK Biobank identified an association of the CCB standardized genetic risk score with increased risk of diverticulosis (odds ratio, 1.02 per standard deviation increase; 95% CI, 1.01-1.04), with a consistent estimate found in BioVU (odds ratio, 1.01; 95% CI, 1.00-1.02). Cox regression analysis of drug use in the UK Biobank suggested that this association was specific to nondihydropyridine CCBs (hazard ratio 1.49 considering thiazide diuretic agents as a comparator; 95% CI, 1.04-2.14) but not dihydropyridine CCBs (hazard ratio, 1.04; 95% CI, 0.83-1.32).<h4>Conclusions</h4>Genetic variants can be used to explore the efficacy and side effects of antihypertensive medications. The identified potential effect of nondihydropyridine CCBs on diverticulosis risk could have clinical implications and warrants further investigation.",,doi:https://doi.org/10.1161/circulationaha.118.038814; doi:https://doi.org/10.1161/CIRCULATIONAHA.118.038814; html:https://europepmc.org/articles/PMC6687408; pdf:https://europepmc.org/articles/PMC6687408?pdf=render
-33048945,https://doi.org/10.1371/journal.pmed.1003290,Neurodevelopmental multimorbidity and educational outcomes of Scottish schoolchildren: A population-based record linkage cohort study.,"Fleming M, Salim EE, Mackay DF, Henderson A, Kinnear D, Clark D, King A, McLay JS, Cooper SA, Pell JP.",,PLoS medicine,2020,2020-10-13,Y,,,,"<h4>Background</h4>Neurodevelopmental conditions commonly coexist in children, but compared to adults, childhood multimorbidity attracts less attention in research and clinical practice. We previously reported that children treated for attention deficit hyperactivity disorder (ADHD) and depression have more school absences and exclusions, additional support needs, poorer attainment, and increased unemployment. They are also more likely to have coexisting conditions, including autism and intellectual disability. We investigated prevalence of neurodevelopmental multimorbidity (≥2 conditions) among Scottish schoolchildren and their educational outcomes compared to peers.<h4>Methods and findings</h4>We retrospectively linked 6 Scotland-wide databases to analyse 766,244 children (390,290 [50.9%] boys; 375,954 [49.1%] girls) aged 4 to 19 years (mean = 10.9) attending Scottish schools between 2009 and 2013. Children were distributed across all deprivation quintiles (most to least deprived: 22.7%, 20.1%, 19.3%, 19.5%, 18.4%). The majority (96.2%) were white ethnicity. We ascertained autism spectrum disorder (ASD) and intellectual disabilities from records of additional support needs and ADHD and depression through relevant encashed prescriptions. We identified neurodevelopmental multimorbidity (≥2 of these conditions) in 4,789 (0.6%) children, with ASD and intellectual disability the most common combination. On adjusting for sociodemographic (sex, age, ethnicity, deprivation) and maternity (maternal age, maternal smoking, sex-gestation-specific birth weight centile, gestational age, 5-minute Apgar score, mode of delivery, parity) factors, multimorbidity was associated with increased school absenteeism and exclusion, unemployment, and poorer exam attainment. Significant dose relationships were evident between number of conditions (0, 1, ≥2) and the last 3 outcomes. Compared to children with no conditions, children with 1 condition, and children with 2 or more conditions, had more absenteeism (1 condition adjusted incidence rate ratio [IRR] 1.28, 95% CI 1.27-1.30, p < 0.001 and 2 or more conditions adjusted IRR 1.23, 95% CI 1.20-1.28, p < 0.001), greater exclusion (adjusted IRR 2.37, 95% CI 2.25-2.48, p < 0.001 and adjusted IRR 3.04, 95% CI 2.74-3.38, p < 0.001), poorer attainment (adjusted odds ratio [OR] 3.92, 95% CI 3.63-4.23, p < 0.001 and adjusted OR 12.07, 95% CI 9.15-15.94, p < 0.001), and increased unemployment (adjusted OR 1.57, 95% CI 1.49-1.66, p < 0.001 and adjusted OR 2.11, 95% CI 1.83-2.45, p < 0.001). Associations remained after further adjustment for comorbid physical conditions and additional support needs. Coexisting depression was the strongest driver of absenteeism and coexisting ADHD the strongest driver of exclusion. Absence of formal primary care diagnoses was a limitation since ascertaining depression and ADHD from prescriptions omitted affected children receiving alternative or no treatment and some antidepressants can be prescribed for other indications.<h4>Conclusions</h4>Structuring clinical practice and training around single conditions may disadvantage children with neurodevelopmental multimorbidity, who we observed had significantly poorer educational outcomes compared to children with 1 condition and no conditions.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003290&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003290; html:https://europepmc.org/articles/PMC7553326; pdf:https://europepmc.org/articles/PMC7553326?pdf=render
+36330526,https://doi.org/10.3389/fimmu.2022.1032331,Levels of soluble complement regulators predict severity of COVID-19 symptoms.,"Tierney AL, Alali WM, Scott T, Rees-Unwin KS, CITIID-NIHR BioResource COVID-19 Collaboration, Clark SJ, Unwin RD.",,Frontiers in immunology,2022,2022-10-18,Y,Complement; Mass spectrometry; Biomarkers; Factor H; Factor H-related Proteins; Covid-19; Sars-cov-2,,,"The SARS-CoV-2 virus continues to cause significant morbidity and mortality worldwide from COVID-19. One of the major challenges of patient management is the broad range of symptoms observed. While the majority of individuals experience relatively mild disease, a significant minority of patients require hospitalisation, with COVID-19 still proving fatal for some. As such, there remains a desperate need to better understand what drives this severe disease, both in terms of the underlying biology, but also to potentially predict at diagnosis which patients are likely to require further interventions, thus enabling better outcomes for both patients and healthcare systems. Several lines of evidence have pointed to dysregulation of the complement cascade as a major factor in severe COVID-19 outcomes. How this is underpinned mechanistically is not known. Here, we have focussed on the role of the soluble complement regulators Complement Factor H (FH), its splice variant Factor H-like 1 (FHL-1) and five Factor H-Related proteins (FHR1-5). Using a targeted mass spectrometry approach, we quantified these proteins in a cohort of 188 plasma samples from controls and SARS-CoV-2 patients taken at diagnosis. This analysis revealed significant elevations in all FHR proteins, but not FH, in patients with more severe disease, particularly FHR2 and FHR5 (FHR2: 1.97-fold, p&lt;0.0001; FHR5: 2.4-fold, p&lt;0.0001). Furthermore, for a subset of 77 SARS-CoV-2 +ve patients we also analysed time course samples taken approximately 28 days post-diagnosis. Here, we see complement regulator levels drop in all individuals with asymptomatic or mild disease, but regulators remain high in those with more severe outcomes, with elevations in FHR2 over baseline levels in this group. These data support the hypothesis that elevation of circulating levels of the FHR family of proteins could predict disease severity in COVID-19 patients, and that the duration of elevation (or lack of immune activation resolution) may be partly responsible for driving poor outcomes in COVID-19.",,pdf:https://www.frontiersin.org/articles/10.3389/fimmu.2022.1032331/pdf; doi:https://doi.org/10.3389/fimmu.2022.1032331; html:https://europepmc.org/articles/PMC9624227; pdf:https://europepmc.org/articles/PMC9624227?pdf=render
 33482294,https://doi.org/10.1016/j.jclinepi.2021.01.003,Real-time imputation of missing predictor values improved the application of prediction models in daily practice.,"Nijman SWJ, Groenhof TKJ, Hoogland J, Bots ML, Brandjes M, Jacobs JJL, Asselbergs FW, Moons KGM, Debray TPA.",,Journal of clinical epidemiology,2021,2021-01-19,N,Prediction; Missing Data; Electronic Health Records; Multiple Imputations; Computerized Decision Support System; Real-time Imputation,,,"<h4>Objectives</h4>In clinical practice, many prediction models cannot be used when predictor values are missing. We, therefore, propose and evaluate methods for real-time imputation.<h4>Study design and setting</h4>We describe (i) mean imputation (where missing values are replaced by the sample mean), (ii) joint modeling imputation (JMI, where we use a multivariate normal approximation to generate patient-specific imputations), and (iii) conditional modeling imputation (CMI, where a multivariable imputation model is derived for each predictor from a population). We compared these methods in a case study evaluating the root mean squared error (RMSE) and coverage of the 95% confidence intervals (i.e., the proportion of confidence intervals that contain the true predictor value) of imputed predictor values.<h4>Results</h4>-RMSE was lowest when adopting JMI or CMI, although imputation of individual predictors did not always lead to substantial improvements as compared to mean imputation. JMI and CMI appeared particularly useful when the values of multiple predictors of the model were missing. Coverage reached the nominal level (i.e., 95%) for both CMI and JMI.<h4>Conclusion</h4>Multiple imputations using either CMI or JMI is recommended when dealing with missing predictor values in real-time settings.",,pdf:http://www.jclinepi.com/article/S0895435621000056/pdf; doi:https://doi.org/10.1016/j.jclinepi.2021.01.003
-33306713,https://doi.org/10.1371/journal.pone.0243383,"Health, educational and employment outcomes among children treated for a skin disorder: Scotland-wide retrospective record linkage cohort study of 766,244 children.","Fleming M, McLay JS, Clark D, King A, Mackay DF, Pell JP.",,PloS one,2020,2020-12-11,Y,,,,"<h4>Background</h4>To compare health, educational and employment outcomes of schoolchildren receiving medication for a skin disorder with peers.<h4>Methods</h4>This retrospective population cohort study linked eight Scotland-wide databases, covering dispensed prescriptions, hospital admissions, maternity records, death certificates, annual pupil census, school examinations, school absences/exclusions and unemployment to investigate educational (absence, exclusion, special educational need, academic attainment), employment, and health (admissions and mortality) outcomes of 766,244 children attending local authority run primary, secondary and special schools in Scotland between 2009 and 2013.<h4>Results</h4>After adjusting for sociodemographic and maternity confounders the 130,087 (17.0%) children treated for a skin disorder had increased hospitalisation, particularly within one year of commencing treatment (IRR 1.38, 95% CI 1.35-1.41, p<0.001) and mortality (HR 1.50, 95% CI 1.18-1.90, p<0.001). They had greater special educational need (OR 1.19, 95% CI 1.17-1.21, p<0.001) and more frequent absences from school (IRR 1.07, 95% CI 1.06-1.08, p<0.001) but did not exhibit poorer exam attainment or increased post-school unemployment. The associations remained after further adjustment for comorbid chronic conditions.<h4>Conclusions</h4>Despite increased hospitalisation, school absenteeism, and special educational need, children treated for a skin disorder did not have poorer exam attainment or employment outcomes. Whilst findings relating to educational and employment outcomes are reassuring, the association with increased risk of mortality is alarming and merits further investigation.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0243383&type=printable; doi:https://doi.org/10.1371/journal.pone.0243383; html:https://europepmc.org/articles/PMC7732076; pdf:https://europepmc.org/articles/PMC7732076?pdf=render
+33048945,https://doi.org/10.1371/journal.pmed.1003290,Neurodevelopmental multimorbidity and educational outcomes of Scottish schoolchildren: A population-based record linkage cohort study.,"Fleming M, Salim EE, Mackay DF, Henderson A, Kinnear D, Clark D, King A, McLay JS, Cooper SA, Pell JP.",,PLoS medicine,2020,2020-10-13,Y,,,,"<h4>Background</h4>Neurodevelopmental conditions commonly coexist in children, but compared to adults, childhood multimorbidity attracts less attention in research and clinical practice. We previously reported that children treated for attention deficit hyperactivity disorder (ADHD) and depression have more school absences and exclusions, additional support needs, poorer attainment, and increased unemployment. They are also more likely to have coexisting conditions, including autism and intellectual disability. We investigated prevalence of neurodevelopmental multimorbidity (≥2 conditions) among Scottish schoolchildren and their educational outcomes compared to peers.<h4>Methods and findings</h4>We retrospectively linked 6 Scotland-wide databases to analyse 766,244 children (390,290 [50.9%] boys; 375,954 [49.1%] girls) aged 4 to 19 years (mean = 10.9) attending Scottish schools between 2009 and 2013. Children were distributed across all deprivation quintiles (most to least deprived: 22.7%, 20.1%, 19.3%, 19.5%, 18.4%). The majority (96.2%) were white ethnicity. We ascertained autism spectrum disorder (ASD) and intellectual disabilities from records of additional support needs and ADHD and depression through relevant encashed prescriptions. We identified neurodevelopmental multimorbidity (≥2 of these conditions) in 4,789 (0.6%) children, with ASD and intellectual disability the most common combination. On adjusting for sociodemographic (sex, age, ethnicity, deprivation) and maternity (maternal age, maternal smoking, sex-gestation-specific birth weight centile, gestational age, 5-minute Apgar score, mode of delivery, parity) factors, multimorbidity was associated with increased school absenteeism and exclusion, unemployment, and poorer exam attainment. Significant dose relationships were evident between number of conditions (0, 1, ≥2) and the last 3 outcomes. Compared to children with no conditions, children with 1 condition, and children with 2 or more conditions, had more absenteeism (1 condition adjusted incidence rate ratio [IRR] 1.28, 95% CI 1.27-1.30, p < 0.001 and 2 or more conditions adjusted IRR 1.23, 95% CI 1.20-1.28, p < 0.001), greater exclusion (adjusted IRR 2.37, 95% CI 2.25-2.48, p < 0.001 and adjusted IRR 3.04, 95% CI 2.74-3.38, p < 0.001), poorer attainment (adjusted odds ratio [OR] 3.92, 95% CI 3.63-4.23, p < 0.001 and adjusted OR 12.07, 95% CI 9.15-15.94, p < 0.001), and increased unemployment (adjusted OR 1.57, 95% CI 1.49-1.66, p < 0.001 and adjusted OR 2.11, 95% CI 1.83-2.45, p < 0.001). Associations remained after further adjustment for comorbid physical conditions and additional support needs. Coexisting depression was the strongest driver of absenteeism and coexisting ADHD the strongest driver of exclusion. Absence of formal primary care diagnoses was a limitation since ascertaining depression and ADHD from prescriptions omitted affected children receiving alternative or no treatment and some antidepressants can be prescribed for other indications.<h4>Conclusions</h4>Structuring clinical practice and training around single conditions may disadvantage children with neurodevelopmental multimorbidity, who we observed had significantly poorer educational outcomes compared to children with 1 condition and no conditions.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003290&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003290; html:https://europepmc.org/articles/PMC7553326; pdf:https://europepmc.org/articles/PMC7553326?pdf=render
 35165324,https://doi.org/10.1038/s41598-022-06315-3,Improving robustness of automatic cardiac function quantification from cine magnetic resonance imaging using synthetic image data.,"Gheorghiță BA, Itu LM, Sharma P, Suciu C, Wetzl J, Geppert C, Ali MAA, Lee AM, Piechnik SK, Neubauer S, Petersen SE, Schulz-Menger J, Chițiboi T.",,Scientific reports,2022,2022-02-14,Y,,,,"Although having been the subject of intense research over the years, cardiac function quantification from MRI is still not a fully automatic process in the clinical practice. This is partly due to the shortage of training data covering all relevant cardiovascular disease phenotypes. We propose to synthetically generate short axis CINE MRI using a generative adversarial model to expand the available data sets that consist of predominantly healthy subjects to include more cases with reduced ejection fraction. We introduce a deep learning convolutional neural network (CNN) to predict the end-diastolic volume, end-systolic volume, and implicitly the ejection fraction from cardiac MRI without explicit segmentation. The left ventricle volume predictions were compared to the ground truth values, showing superior accuracy compared to state-of-the-art segmentation methods. We show that using synthetic data generated for pre-training a CNN significantly improves the prediction compared to only using the limited amount of available data, when the training set is imbalanced.",,pdf:https://www.nature.com/articles/s41598-022-06315-3.pdf; doi:https://doi.org/10.1038/s41598-022-06315-3; html:https://europepmc.org/articles/PMC8844403; pdf:https://europepmc.org/articles/PMC8844403?pdf=render
+33306713,https://doi.org/10.1371/journal.pone.0243383,"Health, educational and employment outcomes among children treated for a skin disorder: Scotland-wide retrospective record linkage cohort study of 766,244 children.","Fleming M, McLay JS, Clark D, King A, Mackay DF, Pell JP.",,PloS one,2020,2020-12-11,Y,,,,"<h4>Background</h4>To compare health, educational and employment outcomes of schoolchildren receiving medication for a skin disorder with peers.<h4>Methods</h4>This retrospective population cohort study linked eight Scotland-wide databases, covering dispensed prescriptions, hospital admissions, maternity records, death certificates, annual pupil census, school examinations, school absences/exclusions and unemployment to investigate educational (absence, exclusion, special educational need, academic attainment), employment, and health (admissions and mortality) outcomes of 766,244 children attending local authority run primary, secondary and special schools in Scotland between 2009 and 2013.<h4>Results</h4>After adjusting for sociodemographic and maternity confounders the 130,087 (17.0%) children treated for a skin disorder had increased hospitalisation, particularly within one year of commencing treatment (IRR 1.38, 95% CI 1.35-1.41, p<0.001) and mortality (HR 1.50, 95% CI 1.18-1.90, p<0.001). They had greater special educational need (OR 1.19, 95% CI 1.17-1.21, p<0.001) and more frequent absences from school (IRR 1.07, 95% CI 1.06-1.08, p<0.001) but did not exhibit poorer exam attainment or increased post-school unemployment. The associations remained after further adjustment for comorbid chronic conditions.<h4>Conclusions</h4>Despite increased hospitalisation, school absenteeism, and special educational need, children treated for a skin disorder did not have poorer exam attainment or employment outcomes. Whilst findings relating to educational and employment outcomes are reassuring, the association with increased risk of mortality is alarming and merits further investigation.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0243383&type=printable; doi:https://doi.org/10.1371/journal.pone.0243383; html:https://europepmc.org/articles/PMC7732076; pdf:https://europepmc.org/articles/PMC7732076?pdf=render
 33659712,https://doi.org/10.12688/wellcomeopenres.16431.2,Healthcare use by people who use illicit opioids (HUPIO): development of a cohort based on electronic primary care records in England.,"Lewer D, Padmanathan P, Qummer Ul Arfeen M, Denaxas S, Forbes H, Gonzalez-Izquierdo A, Hickman M.",,Wellcome open research,2020,2020-01-01,Y,Drug dependence; Illicit Drugs; Substance Use Disorders; Electronic Health Records; Opioid Agonist Therapy,,,"<b>Background:</b> People who use illicit opioids such as heroin have substantial health needs, but there are few longitudinal studies of general health and healthcare in this population. Most research to date has focused on a narrow set of outcomes, including overdoses and HIV or hepatitis infections. We developed and validated a cohort using UK primary care electronic health records (Clinical Practice Research Datalink GOLD and AURUM databases) to facilitate research into healthcare use by people who use illicit opioid use (HUPIO). <b>Methods:</b> Participants are patients in England with primary care records indicating a history of illicit opioid use. We identified codes including prescriptions of opioid agonist therapies (methadone and buprenorphine) and clinical observations such as 'heroin dependence'. We constructed a cohort of patients with at least one of these codes and aged 18-64 at cohort entry, with follow-up between January 1997 and March 2020. We validated the cohort by comparing patient characteristics and mortality rates to other cohorts of people who use illicit opioids, with different recruitment methods. <b>Results:</b> Up to March 2020, the HUPIO cohort included 138,761 patients with a history of illicit opioid use. Demographic characteristics and all-cause mortality were similar to existing cohorts: 69% were male; the median age at index for patients in CPRD AURUM (the database with more included participants) was 35.3 (interquartile range 29.1-42.6); the average age of new cohort entrants increased over time; 76% had records indicating current tobacco smoking; patients disproportionately lived in deprived neighbourhoods; and all-cause mortality risk was 6.6 (95% CI 6.5-6.7) times the general population of England. <b>Conclusions:</b> Primary care data offer new opportunities to study holistic health outcomes and healthcare of this population. The large sample enables investigation of rare outcomes, whilst the availability of linkage to external datasets allows investigation of hospital use, cancer treatment, and mortality.",,pdf:https://wellcomeopenresearch.org/articles/5-282/v2/pdf; doi:https://doi.org/10.12688/wellcomeopenres.16431.2; html:https://europepmc.org/articles/PMC7901498; pdf:https://europepmc.org/articles/PMC7901498?pdf=render
 33017023,https://doi.org/10.1001/jamaneurol.2020.3502,Trends in Optic Neuritis Incidence and Prevalence in the UK and Association With Systemic and Neurologic Disease.,"Braithwaite T, Subramanian A, Petzold A, Galloway J, Adderley NJ, Mollan SP, Plant GT, Nirantharakumar K, Denniston AK.",,JAMA neurology,2020,2020-12-01,N,,,,"<h4>Importance</h4>Epidemiologic data on optic neuritis (ON) incidence and associations with immune-mediated inflammatory diseases (IMIDs) are sparse.<h4>Objective</h4>To estimate 22-year trends in ON prevalence and incidence and association with IMIDs in the United Kingdom.<h4>Design, setting, and participants</h4>This cohort study analyzed data from The Health Improvement Network from January 1, 1995, to September 1, 2019. The study included 10 937 511 patients 1 year or older with 75.2 million person-years' follow-up. Annual ON incidence rates were estimated yearly (January 1, 1997, to December 31, 2018), and annual ON prevalence was estimated by performing sequential cross-sectional studies on data collected on January 1 each year for the same period. Data for 1995, 1996, and 2019 were excluded as incomplete. Risk factors for ON were explored in a cohort analysis from January 1, 1997, to December 31, 2018. Matched case-control and retrospective cohort studies were performed using data from January 1, 1995, to September 1, 2019, to explore the odds of antecedent diagnosis and hazard of incident diagnosis of 66 IMIDs in patients compared with controls.<h4>Exposures</h4>Optic neuritis.<h4>Main outcomes and measures</h4>Annual point prevalence and incidence rates of ON, adjusted incident rate ratios (IRRs) for risk factors, and adjusted odds ratios (ORs) and adjusted hazard ratios (HRs) for 66 IMIDs.<h4>Results</h4>A total of 10 937 511 patients (median [IQR] age at cohort entry, 32.6 [18.0-50.4] years; 5 571 282 [50.9%] female) were studied. A total of 1962 of 2826 patients (69.4%) with incident ON were female and 1192 of 1290 92.4%) were White, with a mean (SD) age of 35.6 (15.6) years. Overall incidence across 22 years was stable at 3.7 (95% CI, 3.6-3.9) per 100 000 person-years. Annual point prevalence (per 100 000 population) increased with database maturity, from 69.3 (95% CI, 57.2-81.3) in 1997 to 114.8 (95% CI, 111.0-118.6) in 2018. The highest risk of incident ON was associated with female sex, obesity, reproductive age, smoking, and residence at higher latitude, with significantly lower risk in South Asian or mixed race/ethnicity compared with White people. Patients with ON had significantly higher odds of prior multiple sclerosis (MS) (OR, 98.22; 95% CI, 65.40-147.52), syphilis (OR, 5.76; 95% CI, 1.39-23.96), Mycoplasma (OR, 3.90; 95% CI, 1.09-13.93), vasculitis (OR, 3.70; 95% CI, 1.68-8.15), sarcoidosis (OR, 2.50; 95% CI, 1.21-5.18), Epstein-Barr virus (OR, 2.29; 95% CI, 1.80-2.92), Crohn disease (OR, 1.97; 95% CI, 1.13-3.43), and psoriasis (OR, 1.28; 95% CI, 1.03-1.58). Patients with ON had a significantly higher hazard of incident MS (HR, 284.97; 95% CI, 167.85-483.81), Behçet disease (HR, 17.39; 95% CI, 1.55-195.53), sarcoidosis (HR, 14.80; 95% CI, 4.86-45.08), vasculitis (HR, 4.89; 95% CI, 1.82-13.10), Sjögren syndrome (HR, 3.48; 95% CI, 1.38-8.76), and herpetic infection (HR, 1.68; 95% CI, 1.24-2.28).<h4>Conclusions and relevance</h4>The UK incidence of ON is stable. Even though predominantly associated with MS, ON has numerous other associations with IMIDs. Although individually rare, together these associations outnumber MS-associated ON and typically require urgent management to preserve sight.",,pdf:http://pure-oai.bham.ac.uk/ws/files/100688542/NEU20_1602R_Merged_PDF.pdf; doi:https://doi.org/10.1001/jamaneurol.2020.3502; html:https://europepmc.org/articles/PMC7536630; doi:https://doi.org/10.1001/jamaneurol.2020.3502
 35681241,https://doi.org/10.1186/s12933-022-01525-5,Elevated plasma triglyceride concentration and risk of adverse clinical outcomes in 1.5 million people: a CALIBER linked electronic health record study.,"Patel RS, Pasea L, Soran H, Downie P, Jones R, Hingorani AD, Neely D, Denaxas S, Hemingway H.",,Cardiovascular diabetology,2022,2022-06-09,Y,Lipids; Triglycerides; Myocardial infarction; Diabetes; Pancreatitis,,,"<h4>Background</h4>Assessing the spectrum of disease risk associated with hypertriglyceridemia is needed to inform potential benefits from emerging triglyceride lowering treatments. We sought to examine the associations between a full range of plasma triglyceride concentration with five clinical outcomes.<h4>Methods</h4>We used linked data from primary and secondary care for 15 M people, to explore the association between triglyceride concentration and risk of acute pancreatitis, chronic pancreatitis, new onset diabetes, myocardial infarction and all-cause mortality, over a median of 6-7 years follow up.<h4>Results</h4>Triglyceride concentration was available for 1,530,411 individuals (mean age 56·6 ± 15·6 years, 51·4% female), with a median of 1·3 mmol/L (IQR: 0.9.to 1.9). Severe hypertriglyceridemia, defined as > 10 mmol/L, was identified in 3289 (0·21%) individuals including 620 with > 20 mmol/L. In multivariable analyses, a triglyceride concentration > 20 mmol/L was associated with very high risk for acute pancreatitis (Hazard ratio (HR) 13·55 (95% CI 9·15-20·06)); chronic pancreatitis (HR 25·19 (14·91-42·55)); and high risk for diabetes (HR 5·28 (4·51-6·18)) and all-cause mortality (HR 3·62 (2·82-4·65)) when compared to the reference category of ≤ 1·7 mmol/L. An association with myocardial infarction, however, was only observed for more moderate hypertriglyceridaemia between 1.7 and 10 mmol/L. We found a risk interaction with age, with higher risks for all outcomes including mortality among those ≤ 40 years compared to > 40 years.<h4>Conclusions</h4>We highlight an exponential association between severe hypertriglyceridaemia and risk of incident acute and chronic pancreatitis, new diabetes, and mortality, especially at younger ages, but not for myocardial infarction for which only moderate hypertriglyceridemia conferred risk.",,pdf:https://cardiab.biomedcentral.com/counter/pdf/10.1186/s12933-022-01525-5; doi:https://doi.org/10.1186/s12933-022-01525-5; html:https://europepmc.org/articles/PMC9185961; pdf:https://europepmc.org/articles/PMC9185961?pdf=render
@@ -1981,45 +1983,45 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 35641524,https://doi.org/10.1038/s41533-022-00280-0,Development and validation of a multivariable mortality risk prediction model for COPD in primary care.,"Shah SA, Nwaru BI, Sheikh A, Simpson CR, Kotz D.",,NPJ primary care respiratory medicine,2022,2022-05-31,Y,,,,"Risk stratification of chronic obstructive pulmonary disease (COPD) patients is important to enable targeted management. Existing disease severity classification systems, such as GOLD staging, do not take co-morbidities into account despite their high prevalence in COPD patients. We sought to develop and validate a prognostic model to predict 10-year mortality in patients with diagnosed COPD. We constructed a longitudinal cohort of 37,485 COPD patients (149,196 person-years) from a UK-wide primary care database. The risk factors included in the model pertained to demographic and behavioural characteristics, co-morbidities, and COPD severity. The outcome of interest was all-cause mortality. We fitted an extended Cox-regression model to estimate hazard ratios (HR) with 95% confidence intervals (CI), used machine learning-based data modelling approaches including k-fold cross-validation to validate the prognostic model, and assessed model fitting and discrimination. The inter-quartile ranges of the three metrics on the validation set suggested good performance: 0.90-1.06 for model fit, 0.80-0.83 for Harrel's c-index, and 0.40-0.46 for Royston and Saurebrei's [Formula: see text] with a strong overlap of these metrics on the training dataset. According to the validated prognostic model, the two most important risk factors of mortality were heart failure (HR 1.92; 95% CI 1.87-1.96) and current smoking (HR 1.68; 95% CI 1.66-1.71). We have developed and validated a national, population-based prognostic model to predict 10-year mortality of patients diagnosed with COPD. This model could be used to detect high-risk patients and modify risk factors such as optimising heart failure management and offering effective smoking cessation interventions.",,pdf:https://www.nature.com/articles/s41533-022-00280-0.pdf; doi:https://doi.org/10.1038/s41533-022-00280-0; html:https://europepmc.org/articles/PMC9156666; pdf:https://europepmc.org/articles/PMC9156666?pdf=render
 35047182,https://doi.org/10.7189/jogh.11.01010,"The COVID-19 pandemic in children and young people during 2020-2021: Learning about clinical presentation, patterns of spread, viral load, diagnosis and treatment.","Rudan I, Adeloye D, Katikireddi SV, Murray J, Simpson C, Shah SA, Robertson C, Sheikh A, EAVE II collaboration.",,Journal of global health,2021,2021-12-25,Y,,,,,,doi:https://doi.org/10.7189/jogh.11.01010; doi:https://doi.org/10.7189/jogh.11.01010; html:https://europepmc.org/articles/PMC8763336; pdf:https://europepmc.org/articles/PMC8763336?pdf=render
 34210356,https://doi.org/10.1186/s13059-021-02395-y,CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance.,"Nicholls SM, Poplawski R, Bull MJ, Underwood A, Chapman M, Abu-Dahab K, Taylor B, Colquhoun RM, Rowe WPM, Jackson B, Hill V, O'Toole Á, Rey S, Southgate J, Amato R, Livett R, Gonçalves S, Harrison EM, Peacock SJ, Aanensen DM, Rambaut A, Connor TR, Loman NJ, COVID-19 Genomics UK (COG-UK) Consortium.",,Genome biology,2021,2021-07-01,Y,,,,"In response to the ongoing SARS-CoV-2 pandemic in the UK, the COVID-19 Genomics UK (COG-UK) consortium was formed to rapidly sequence SARS-CoV-2 genomes as part of a national-scale genomic surveillance strategy. The network consists of universities, academic institutes, regional sequencing centres and the four UK Public Health Agencies. We describe the development and deployment of CLIMB-COVID, an encompassing digital infrastructure to address the challenge of collecting and integrating both genomic sequencing data and sample-associated metadata produced across the COG-UK network.",,pdf:https://genomebiology.biomedcentral.com/counter/pdf/10.1186/s13059-021-02395-y; doi:https://doi.org/10.1186/s13059-021-02395-y; html:https://europepmc.org/articles/PMC8247108; pdf:https://europepmc.org/articles/PMC8247108?pdf=render
-35047183,https://doi.org/10.7189/jogh.11.01011,The COVID-19 pandemic in children and young people during 2020-2021: A complex discussion on vaccination.,"Rudan I, Adeloye D, Katikireddi V, Murray J, Simpson C, Shah SA, Robertson C, Sheikh A, EAVE II collaboration.",,Journal of global health,2021,2021-12-25,Y,,,,,,doi:https://doi.org/10.7189/jogh.11.01011; doi:https://doi.org/10.7189/jogh.11.01011; html:https://europepmc.org/articles/PMC8763337; pdf:https://europepmc.org/articles/PMC8763337?pdf=render
 37755828,https://doi.org/10.1001/jamanetworkopen.2023.36023,Reporting of Observational Studies Explicitly Aiming to Emulate Randomized Trials: A Systematic Review.,"Hansford HJ, Cashin AG, Jones MD, Swanson SA, Islam N, Douglas SRG, Rizzo RRN, Devonshire JJ, Williams SA, Dahabreh IJ, Dickerman BA, Egger M, Garcia-Albeniz X, Golub RM, Lodi S, Moreno-Betancur M, Pearson SA, Schneeweiss S, Sterne JAC, Sharp MK, Stuart EA, Hernán MA, Lee H, McAuley JH.",,JAMA network open,2023,2023-09-05,Y,,,,"<h4>Importance</h4>Observational (nonexperimental) studies that aim to emulate a randomized trial (ie, the target trial) are increasingly informing medical and policy decision-making, but it is unclear how these studies are reported in the literature. Consistent reporting is essential for quality appraisal, evidence synthesis, and translation of evidence to policy and practice.<h4>Objective</h4>To assess the reporting of observational studies that explicitly aimed to emulate a target trial.<h4>Evidence review</h4>We searched Medline, Embase, PsycINFO, and Web of Science for observational studies published between March 2012 and October 2022 that explicitly aimed to emulate a target trial of a health or medical intervention. Two reviewers double-screened and -extracted data on study characteristics, key predefined components of the target trial protocol and its emulation (eligibility criteria, treatment strategies, treatment assignment, outcome[s], follow-up, causal contrast[s], and analysis plan), and other items related to the target trial emulation.<h4>Findings</h4>A total of 200 studies that explicitly aimed to emulate a target trial were included. These studies included 26 subfields of medicine, and 168 (84%) were published from January 2020 to October 2022. The aim to emulate a target trial was explicit in 70 study titles (35%). Forty-three studies (22%) reported use of a published reporting guideline (eg, Strengthening the Reporting of Observational Studies in Epidemiology). Eighty-five studies (43%) did not describe all key items of how the target trial was emulated and 113 (57%) did not describe the protocol of the target trial and its emulation.<h4>Conclusion and relevance</h4>In this systematic review of 200 studies that explicitly aimed to emulate a target trial, reporting of how the target trial was emulated was inconsistent. A reporting guideline for studies explicitly aiming to emulate a target trial may improve the reporting of the target trial protocols and other aspects of these emulation attempts.",,pdf:https://jamanetwork.com/journals/jamanetworkopen/articlepdf/2809945/hansford_2023_oi_231035_1695236241.69575.pdf; doi:https://doi.org/10.1001/jamanetworkopen.2023.36023; html:https://europepmc.org/articles/PMC10534275
+35047183,https://doi.org/10.7189/jogh.11.01011,The COVID-19 pandemic in children and young people during 2020-2021: A complex discussion on vaccination.,"Rudan I, Adeloye D, Katikireddi V, Murray J, Simpson C, Shah SA, Robertson C, Sheikh A, EAVE II collaboration.",,Journal of global health,2021,2021-12-25,Y,,,,,,doi:https://doi.org/10.7189/jogh.11.01011; doi:https://doi.org/10.7189/jogh.11.01011; html:https://europepmc.org/articles/PMC8763337; pdf:https://europepmc.org/articles/PMC8763337?pdf=render
 30102210,https://doi.org/10.1016/s1470-2045(18)30425-x,A roadmap for restoring trust in Big Data.,"Lawler M, Morris AD, Sullivan R, Birney E, Middleton A, Makaroff L, Knoppers BM, Horgan D, Eggermont A.",,The Lancet. Oncology,2018,2018-08-01,N,,,,,,doi:https://doi.org/10.1016/S1470-2045(18)30425-X
 31650125,https://doi.org/10.1016/s2589-7500(19)30012-3,A chronological map of 308 physical and mental health conditions from 4 million individuals in the English National Health Service.,"Kuan V, Denaxas S, Gonzalez-Izquierdo A, Direk K, Bhatti O, Husain S, Sutaria S, Hingorani M, Nitsch D, Parisinos CA, Lumbers RT, Mathur R, Sofat R, Casas JP, Wong ICK, Hemingway H, Hingorani AD.",,The Lancet. Digital health,2019,2019-05-20,Y,,The Human Phenome,,"<h4>Background</h4>To effectively prevent, detect, and treat health conditions that affect people during their lifecourse, health-care professionals and researchers need to know which sections of the population are susceptible to which health conditions and at which ages. Hence, we aimed to map the course of human health by identifying the 50 most common health conditions in each decade of life and estimating the median age at first diagnosis.<h4>Methods</h4>We developed phenotyping algorithms and codelists for physical and mental health conditions that involve intensive use of health-care resources. Individuals older than 1 year were included in the study if their primary-care and hospital-admission records met research standards set by the Clinical Practice Research Datalink and they had been registered in a general practice in England contributing up-to-standard data for at least 1 year during the study period. We used linked records of individuals from the CALIBER platform to calculate the sex-standardised cumulative incidence for these conditions by 10-year age groups between April 1, 2010, and March 31, 2015. We also derived the median age at diagnosis and prevalence estimates stratified by age, sex, and ethnicity (black, white, south Asian) over the study period from the primary-care and secondary-care records of patients.<h4>Findings</h4>We developed case definitions for 308 disease phenotypes. We used records of 2 784 138 patients for the calculation of cumulative incidence and of 3 872 451 patients for the calculation of period prevalence and median age at diagnosis of these conditions. Conditions that first gained prominence at key stages of life were: atopic conditions and infections that led to hospital admission in children (<10 years); acne and menstrual disorders in the teenage years (10-19 years); mental health conditions, obesity, and migraine in individuals aged 20-29 years; soft-tissue disorders and gastro-oesophageal reflux disease in individuals aged 30-39 years; dyslipidaemia, hypertension, and erectile dysfunction in individuals aged 40-59 years; cancer, osteoarthritis, benign prostatic hyperplasia, cataract, diverticular disease, type 2 diabetes, and deafness in individuals aged 60-79 years; and atrial fibrillation, dementia, acute and chronic kidney disease, heart failure, ischaemic heart disease, anaemia, and osteoporosis in individuals aged 80 years or older. Black or south-Asian individuals were diagnosed earlier than white individuals for 258 (84%) of the 308 conditions. Bone fractures and atopic conditions were recorded earlier in male individuals, whereas female individuals were diagnosed at younger ages with nutritional anaemias, tubulointerstitial nephritis, and urinary disorders.<h4>Interpretation</h4>We have produced the first chronological map of human health with cumulative-incidence and period-prevalence estimates for multiple morbidities in parallel from birth to advanced age. This can guide clinicians, policy makers, and researchers on how to formulate differential diagnoses, allocate resources, and target research priorities on the basis of the knowledge of who gets which diseases when. We have published our phenotyping algorithms on the CALIBER open-access Portal which will facilitate future research by providing a curated list of reusable case definitions.<h4>Funding</h4>Wellcome Trust, National Institute for Health Research, Medical Research Council, Arthritis Research UK, British Heart Foundation, Cancer Research UK, Chief Scientist Office of the Scottish Government Health and Social Care Directorates, Department of Health and Social Care (England), Health and Social Care Research and Development Division (Welsh Government), Public Health Agency (Northern Ireland), Economic and Social Research Council, Engineering and Physical Sciences Research Council, National Institute for Social Care and Health Research, and The Alan Turing Institute.",,doi:https://doi.org/10.1016/s2589-7500(19)30012-3; doi:https://doi.org/10.1016/S2589-7500(19)30012-3; html:https://europepmc.org/articles/PMC6798263; pdf:https://europepmc.org/articles/PMC6798263?pdf=render
+34345870,https://doi.org/10.1016/j.bbih.2021.100286,The effects of genotype on inflammatory response in hippocampal progenitor cells: A computational approach.,"Lee H, Metz A, McDiarmid A, Palmos A, Lee SH, Curtis CJ, Patel H, Newhouse SJ, Thuret S.",,"Brain, behavior, & immunity - health",2021,2021-08-01,Y,Hippocampus; Neurogenesis; Inflammation; Neural stem cells; in vitro model; single nucleotide polymorphisms SNP; Eqtl; Gene Variants,,,"Cell culture models are valuable tools to study biological mechanisms underlying health and disease in a controlled environment. Although their genotype influences their phenotype, subtle genetic variations in cell lines are rarely characterised and taken into account for in vitro studies. To investigate how the genetic makeup of a cell line might affect the cellular response to inflammation, we characterised the single nucleotide variants (SNPs) relevant to inflammation-related genes in an established hippocampal progenitor cell line (HPC0A07/03C) that is frequently used as an in vitro model for hippocampal neurogenesis (HN). SNPs were identified using a genotyping array, and genes associated with chronic inflammatory and neuroinflammatory response gene ontology terms were retrieved using the AmiGO application. SNPs associated with these genes were then extracted from the genotyping dataset, for which a literature search was conducted, yielding relevant research articles for a total of 17 SNPs. Of these variants, 10 were found to potentially affect hippocampal neurogenesis whereby a majority (n=7) is likely to reduce neurogenesis under inflammatory conditions. Taken together, the existing literature seems to suggest that all stages of hippocampal neurogenesis could be negatively affected due to the genetic makeup in HPC0A07/03C cells under inflammation. Additional experiments will be needed to validate these specific findings in a laboratory setting. However, this computational approach already confirms that in vitro studies in general should control for cell lines subtle genetic variations which could mask or exacerbate findings.",,doi:https://doi.org/10.1016/j.bbih.2021.100286; doi:https://doi.org/10.1016/j.bbih.2021.100286; html:https://europepmc.org/articles/PMC8261829; pdf:https://europepmc.org/articles/PMC8261829?pdf=render
 36100927,https://doi.org/10.28920/dhm52.3.164-174,Hyperbaric Oxygen for Lower Limb Trauma (HOLLT): an international multi-centre randomised clinical trial.,"Millar IL, Lind FG, Jansson KÅ, Hájek M, Smart DR, Fernandes TD, McGinnes RA, Williamson OD, Miller RK, Martin CA, Gabbe BJ, Myles PS, Cameron PA, HOLLT investigator group.",,Diving and hyperbaric medicine,2022,2022-09-01,N,Injuries; Wounds; Fractures; Orthopaedics; Outcome; Hyperbaric Oxygen Treatment; Musculo-skeletal,,,"<h4>Introduction</h4>Hyperbaric oxygen treatment (HBOT) is sometimes used in the management of open fractures and severe soft tissue crush injury, aiming to reduce complications and improve outcomes.<h4>Methods</h4>Patients with open tibial fractures were randomly assigned within 48 hours of injury to receive standard trauma care or standard care plus 12 sessions of HBOT. The primary outcome was the incidence of necrosis or infection or both occurring within 14 days of injury.<h4>Results</h4>One-hundred and twenty patients were enrolled. Intention to treat primary outcome occurred in 25/58 HBOT assigned patients and 34/59 controls (43% vs 58%, odds ratio (OR) 0.55, 95% confidence interval (CI) 0.25 to 1.18, P = 0.12). Tissue necrosis occurred in 29% of HBOT patients and 53% of controls (OR 0.35, 95% CI 0.16 to 0.78, P = 0.01). There were fewer late complications in patients receiving HBOT (6/53 vs 18/52, OR 0.22, 95% CI 0.08 to 0.64, P = 0.007) including delayed fracture union (5/53 vs 13/52, OR 0.31, 95% CI 0.10 to 0.95, P = 0.04). Quality of life measures at one and two years were superior in HBOT patients. The mean score difference in short form 36 was 2.90, 95% CI 1.03 to 4.77, P = 0.002, in the short musculoskeletal function assessment (SMFA) was 2.54, 95% CI 0.62 to 4.46, P = 0.01; and in SMFA daily activities was 19.51, 95% CI 0.06 to 21.08, P = 0.05.<h4>Conclusions</h4>In severe lower limb trauma, early HBOT reduces tissue necrosis and the likelihood of long-term complications, and improves functional outcomes. Future research should focus on optimal dosage and whether HBOT has benefits for other injury types.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9536848; doi:https://doi.org/10.28920/dhm52.3.164-174; html:https://europepmc.org/articles/PMC9536848; pdf:https://europepmc.org/articles/PMC9536848?pdf=render; doi:https://doi.org/10.28920/dhm52.3.164-174
+37339333,https://doi.org/10.1002/jia2.26104,"COVID-19 among adults living with HIV: correlates of mortality among public sector healthcare users in Western Cape, South Africa.","Kassanjee R, Davies MA, Ngwenya O, Osei-Yeboah R, Jacobs T, Morden E, Timmerman V, Britz S, Mendelson M, Taljaard J, Riou J, Boulle A, Tiffin N, Zinyakatira N.",,Journal of the International AIDS Society,2023,2023-06-01,Y,Mortality; HIV; South Africa; Cd4 Count; Covid-19; Sars-cov-2,,,"<h4>Introduction</h4>While a large proportion of people with HIV (PWH) have experienced SARS-CoV-2 infections, there is uncertainty about the role of HIV disease severity on COVID-19 outcomes, especially in lower-income settings. We studied the association of mortality with characteristics of HIV severity and management, and vaccination, among adult PWH.<h4>Methods</h4>We analysed observational cohort data on all PWH aged ≥15 years experiencing a diagnosed SARS-CoV-2 infection (until March 2022), who accessed public sector healthcare in the Western Cape province of South Africa. Logistic regression was used to study the association of mortality with evidence of antiretroviral therapy (ART) collection, time since first HIV evidence, CD4 cell count, viral load (among those with evidence of ART collection) and COVID-19 vaccination, adjusting for demographic characteristics, comorbidities, admission pressure, location and time period.<h4>Results</h4>Mortality occurred in 5.7% (95% CI: 5.3,6.0) of 17,831 first-diagnosed infections. Higher mortality was associated with lower recent CD4, no evidence of ART collection, high or unknown recent viral load and recent first HIV evidence, differentially by age. Vaccination was protective. The burden of comorbidities was high, and tuberculosis (especially more recent episodes of tuberculosis), chronic kidney disease, diabetes and hypertension were associated with higher mortality, more strongly in younger adults.<h4>Conclusions</h4>Mortality was strongly associated with suboptimal HIV control, and the prevalence of these risk factors increased in later COVID-19 waves. It remains a public health priority to ensure PWH are on suppressive ART and vaccinated, and manage any disruptions in care that occurred during the pandemic. The diagnosis and management of comorbidities, including for tuberculosis, should be optimized.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jia2.26104; doi:https://doi.org/10.1002/jia2.26104; html:https://europepmc.org/articles/PMC10281639; pdf:https://europepmc.org/articles/PMC10281639?pdf=render
+32212911,https://doi.org/10.1161/jaha.119.013684,Prognostic significance of troponin level in 3121 patients presenting with atrial fibrillation (The NIHR Health Informatics Collaborative TROP-AF study).,"Kaura A, Arnold AD, Panoulas V, Glampson B, Davies J, Mulla A, Woods K, Omigie J, Shah AD, Channon KM, Weber JN, Thursz MR, Elliott P, Hemingway H, Williams B, Asselbergs FW, O'Sullivan M, Lord GM, Melikian N, Lefroy DC, Francis DP, Shah AM, Kharbanda R, Perera D, Patel RS, Mayet J.",,Journal of the American Heart Association,2020,2020-03-26,Y,Troponin; Mortality; Atrial fibrillation; coronary artery disease; angiography,,,"Background Patients presenting with atrial fibrillation (AF) often undergo a blood test to measure troponin, but interpretation of the result is impeded by uncertainty about its clinical importance. We investigated the relationship between troponin level, coronary angiography, and all-cause mortality in real-world patients presenting with AF. Methods and Results We used National Institute of Health Research Health Informatics Collaborative data to identify patients admitted between 2010 and 2017 at 5 tertiary centers in the United Kingdom with a primary diagnosis of AF. Peak troponin results were scaled as multiples of the upper limit of normal. A total of 3121 patients were included in the analysis. Over a median follow-up of 1462 (interquartile range, 929-1975) days, there were 586 deaths (18.8%). The adjusted hazard ratio for mortality associated with a positive troponin (value above upper limit of normal) was 1.20 (95% CI, 1.01-1.43; <i>P</i><0.05). Higher troponin levels were associated with higher risk of mortality, reaching a maximum hazard ratio of 2.6 (95% CI, 1.9-3.4) at ≈250 multiples of the upper limit of normal. There was an exponential relationship between higher troponin levels and increased odds of coronary angiography. The mortality risk was 36% lower in patients undergoing coronary angiography than in those who did not (adjusted hazard ratio, 0.61; 95% CI, 0.42-0.89; <i>P</i>=0.01). Conclusions Increased troponin was associated with increased risk of mortality in patients presenting with AF. The lower hazard ratio in patients undergoing invasive management raises the possibility that the clinical importance of troponin release in AF may be mediated by coronary artery disease, which may be responsive to revascularization.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.119.013684; doi:https://doi.org/10.1161/JAHA.119.013684; html:https://europepmc.org/articles/PMC7428631; pdf:https://europepmc.org/articles/PMC7428631?pdf=render
 39414775,https://doi.org/10.1038/s41467-024-53091-x,Genetic architecture of routinely acquired blood tests in a British South Asian cohort.,"Jacobs BM, Stow D, Hodgson S, Zöllner J, Samuel M, Kanoni S, Bidi S, Genes & Health Research Team, Walter K, Langenberg C, Dobson R, Finer S, Morton C, Siddiqui MK, Martin HC, Pietzner M, Mathur R, van Heel DA.",,Nature communications,2024,2024-10-16,Y,,,,"Understanding the genetic basis of routinely-acquired blood tests can provide insights into several aspects of human physiology. We report a genome-wide association study of 42 quantitative blood test traits defined using Electronic Healthcare Records (EHRs) of ~50,000 British Bangladeshi and British Pakistani adults. We demonstrate a causal variant within the PIEZO1 locus which was associated with alterations in red cell traits and glycated haemoglobin. Conditional analysis and within-ancestry fine mapping confirmed that this signal is driven by a missense variant - chr16-88716656-G-T<sub>T</sub> - which is common in South Asian ancestries (MAF 3.9%) but ultra-rare in other ancestries. Carriers of the T allele had lower mean HbA1c values, lower HbA1c values for a given level of random or fasting glucose, and delayed diagnosis of Type 2 Diabetes Mellitus. Our results shed light on the genetic basis of clinically-relevant traits in an under-represented population, and emphasise the importance of ancestral diversity in genetic studies.",,doi:https://doi.org/10.1038/s41467-024-53091-x; doi:https://doi.org/10.1038/s41467-024-53091-x; html:https://europepmc.org/articles/PMC11484750; pdf:https://europepmc.org/articles/PMC11484750?pdf=render
 38609437,https://doi.org/10.1038/s41746-024-01062-3,"Self-supervised learning for human activity recognition using 700,000 person-days of wearable data.","Yuan H, Chan S, Creagh AP, Tong C, Acquah A, Clifton DA, Doherty A.",,NPJ digital medicine,2024,2024-04-12,Y,,,,"Accurate physical activity monitoring is essential to understand the impact of physical activity on one's physical health and overall well-being. However, advances in human activity recognition algorithms have been constrained by the limited availability of large labelled datasets. This study aims to leverage recent advances in self-supervised learning to exploit the large-scale UK Biobank accelerometer dataset-a 700,000 person-days unlabelled dataset-in order to build models with vastly improved generalisability and accuracy. Our resulting models consistently outperform strong baselines across eight benchmark datasets, with an F1 relative improvement of 2.5-130.9% (median 24.4%). More importantly, in contrast to previous reports, our results generalise across external datasets, cohorts, living environments, and sensor devices. Our open-sourced pre-trained models will be valuable in domains with limited labelled data or where good sampling coverage (across devices, populations, and activities) is hard to achieve.",,pdf:https://www.nature.com/articles/s41746-024-01062-3.pdf; doi:https://doi.org/10.1038/s41746-024-01062-3; html:https://europepmc.org/articles/PMC11015005; pdf:https://europepmc.org/articles/PMC11015005?pdf=render
-34345870,https://doi.org/10.1016/j.bbih.2021.100286,The effects of genotype on inflammatory response in hippocampal progenitor cells: A computational approach.,"Lee H, Metz A, McDiarmid A, Palmos A, Lee SH, Curtis CJ, Patel H, Newhouse SJ, Thuret S.",,"Brain, behavior, & immunity - health",2021,2021-08-01,Y,Hippocampus; Neurogenesis; Inflammation; Neural stem cells; in vitro model; single nucleotide polymorphisms SNP; Eqtl; Gene Variants,,,"Cell culture models are valuable tools to study biological mechanisms underlying health and disease in a controlled environment. Although their genotype influences their phenotype, subtle genetic variations in cell lines are rarely characterised and taken into account for in vitro studies. To investigate how the genetic makeup of a cell line might affect the cellular response to inflammation, we characterised the single nucleotide variants (SNPs) relevant to inflammation-related genes in an established hippocampal progenitor cell line (HPC0A07/03C) that is frequently used as an in vitro model for hippocampal neurogenesis (HN). SNPs were identified using a genotyping array, and genes associated with chronic inflammatory and neuroinflammatory response gene ontology terms were retrieved using the AmiGO application. SNPs associated with these genes were then extracted from the genotyping dataset, for which a literature search was conducted, yielding relevant research articles for a total of 17 SNPs. Of these variants, 10 were found to potentially affect hippocampal neurogenesis whereby a majority (n=7) is likely to reduce neurogenesis under inflammatory conditions. Taken together, the existing literature seems to suggest that all stages of hippocampal neurogenesis could be negatively affected due to the genetic makeup in HPC0A07/03C cells under inflammation. Additional experiments will be needed to validate these specific findings in a laboratory setting. However, this computational approach already confirms that in vitro studies in general should control for cell lines subtle genetic variations which could mask or exacerbate findings.",,doi:https://doi.org/10.1016/j.bbih.2021.100286; doi:https://doi.org/10.1016/j.bbih.2021.100286; html:https://europepmc.org/articles/PMC8261829; pdf:https://europepmc.org/articles/PMC8261829?pdf=render
-37339333,https://doi.org/10.1002/jia2.26104,"COVID-19 among adults living with HIV: correlates of mortality among public sector healthcare users in Western Cape, South Africa.","Kassanjee R, Davies MA, Ngwenya O, Osei-Yeboah R, Jacobs T, Morden E, Timmerman V, Britz S, Mendelson M, Taljaard J, Riou J, Boulle A, Tiffin N, Zinyakatira N.",,Journal of the International AIDS Society,2023,2023-06-01,Y,Mortality; HIV; South Africa; Cd4 Count; Covid-19; Sars-cov-2,,,"<h4>Introduction</h4>While a large proportion of people with HIV (PWH) have experienced SARS-CoV-2 infections, there is uncertainty about the role of HIV disease severity on COVID-19 outcomes, especially in lower-income settings. We studied the association of mortality with characteristics of HIV severity and management, and vaccination, among adult PWH.<h4>Methods</h4>We analysed observational cohort data on all PWH aged ≥15 years experiencing a diagnosed SARS-CoV-2 infection (until March 2022), who accessed public sector healthcare in the Western Cape province of South Africa. Logistic regression was used to study the association of mortality with evidence of antiretroviral therapy (ART) collection, time since first HIV evidence, CD4 cell count, viral load (among those with evidence of ART collection) and COVID-19 vaccination, adjusting for demographic characteristics, comorbidities, admission pressure, location and time period.<h4>Results</h4>Mortality occurred in 5.7% (95% CI: 5.3,6.0) of 17,831 first-diagnosed infections. Higher mortality was associated with lower recent CD4, no evidence of ART collection, high or unknown recent viral load and recent first HIV evidence, differentially by age. Vaccination was protective. The burden of comorbidities was high, and tuberculosis (especially more recent episodes of tuberculosis), chronic kidney disease, diabetes and hypertension were associated with higher mortality, more strongly in younger adults.<h4>Conclusions</h4>Mortality was strongly associated with suboptimal HIV control, and the prevalence of these risk factors increased in later COVID-19 waves. It remains a public health priority to ensure PWH are on suppressive ART and vaccinated, and manage any disruptions in care that occurred during the pandemic. The diagnosis and management of comorbidities, including for tuberculosis, should be optimized.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jia2.26104; doi:https://doi.org/10.1002/jia2.26104; html:https://europepmc.org/articles/PMC10281639; pdf:https://europepmc.org/articles/PMC10281639?pdf=render
 35045937,https://doi.org/10.1016/j.amjcard.2021.12.022,Relation of Iron Status to Prognosis After Acute Coronary Syndrome.,"Gürgöze MT, Kardys I, Akkerhuis KM, Oemrawsingh RM, Groot HE, van der Harst P, Umans VA, Kietselaer B, Ronner E, Lenderink T, Asselbergs FW, Manintveld OC, Boersma E.",,The American journal of cardiology,2022,2022-01-16,N,,,,"Iron deficiency has been extensively researched and is associated with adverse outcomes in heart failure. However, to our knowledge, the temporal evolution of iron status has not been previously investigated in patients with acute coronary syndrome (ACS). Therefore, we aimed to explore the temporal pattern of repeatedly measured iron, ferritin, transferrin, and transferrin saturation (TSAT) in relation to prognosis post-ACS. BIOMArCS (BIOMarker study to identify the Acute risk of a Coronary Syndrome) is a prospective, multicenter, observational cohort study conducted in The Netherlands between 2008 and 2015. A total of 844 patients with post-ACS were enrolled and underwent high-frequency (median 17) blood sampling during 1 year follow-up. Biomarkers of iron status were measured batchwise in a central laboratory. We analyzed 3 patient subsets, including the case-cohort (n = 187). The primary endpoint (PE) was a composite of cardiovascular mortality and repeat nonfatal ACS, including unstable angina pectoris requiring revascularization. The association between iron status and the PE was analyzed using multivariable joint models. Mean age was 63 years; 78% were men, and >50% had iron deficiency at first sample in the case-cohort. After adjustment for a broad range of clinical variables, 1 SD decrease in log-iron was associated with a 2.2-fold greater risk of the PE (hazard ratio 2.19, 95% confidence interval 1.34 to 3.54, p = 0.002). Similarly, 1 SD decrease in log-TSAT was associated with a 78% increased risk of the PE (hazard ratio 1.78, 95% confidence interval 1.17 to 2.65, p = 0.006). Ferritin and transferrin were not associated with the PE. Repeated measurements of iron and TSAT predict risk of adverse outcomes in patients with post-ACS during 1 year follow-up. Trial Registration: The Netherlands Trial Register. Unique identifiers: NTR1698 and NTR1106. Registered at https://www.trialregister.nl/trial/1614 and https://www.trialregister.nl/trial/1073.",,pdf:http://www.ajconline.org/article/S0002914921012418/pdf; doi:https://doi.org/10.1016/j.amjcard.2021.12.022
-32212911,https://doi.org/10.1161/jaha.119.013684,Prognostic significance of troponin level in 3121 patients presenting with atrial fibrillation (The NIHR Health Informatics Collaborative TROP-AF study).,"Kaura A, Arnold AD, Panoulas V, Glampson B, Davies J, Mulla A, Woods K, Omigie J, Shah AD, Channon KM, Weber JN, Thursz MR, Elliott P, Hemingway H, Williams B, Asselbergs FW, O'Sullivan M, Lord GM, Melikian N, Lefroy DC, Francis DP, Shah AM, Kharbanda R, Perera D, Patel RS, Mayet J.",,Journal of the American Heart Association,2020,2020-03-26,Y,Troponin; Mortality; Atrial fibrillation; coronary artery disease; angiography,,,"Background Patients presenting with atrial fibrillation (AF) often undergo a blood test to measure troponin, but interpretation of the result is impeded by uncertainty about its clinical importance. We investigated the relationship between troponin level, coronary angiography, and all-cause mortality in real-world patients presenting with AF. Methods and Results We used National Institute of Health Research Health Informatics Collaborative data to identify patients admitted between 2010 and 2017 at 5 tertiary centers in the United Kingdom with a primary diagnosis of AF. Peak troponin results were scaled as multiples of the upper limit of normal. A total of 3121 patients were included in the analysis. Over a median follow-up of 1462 (interquartile range, 929-1975) days, there were 586 deaths (18.8%). The adjusted hazard ratio for mortality associated with a positive troponin (value above upper limit of normal) was 1.20 (95% CI, 1.01-1.43; <i>P</i><0.05). Higher troponin levels were associated with higher risk of mortality, reaching a maximum hazard ratio of 2.6 (95% CI, 1.9-3.4) at ≈250 multiples of the upper limit of normal. There was an exponential relationship between higher troponin levels and increased odds of coronary angiography. The mortality risk was 36% lower in patients undergoing coronary angiography than in those who did not (adjusted hazard ratio, 0.61; 95% CI, 0.42-0.89; <i>P</i>=0.01). Conclusions Increased troponin was associated with increased risk of mortality in patients presenting with AF. The lower hazard ratio in patients undergoing invasive management raises the possibility that the clinical importance of troponin release in AF may be mediated by coronary artery disease, which may be responsive to revascularization.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.119.013684; doi:https://doi.org/10.1161/JAHA.119.013684; html:https://europepmc.org/articles/PMC7428631; pdf:https://europepmc.org/articles/PMC7428631?pdf=render
-36869930,https://doi.org/10.1007/s00520-023-07633-6,Cost consequences of unscheduled emergency admissions in cancer patients in the last year of life.,"McFerran E, Cairnduff V, Elder R, Gavin A, Lawler M.",,Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer,2023,2023-03-04,Y,Neoplasms; Death; Palliative care; Emergency Care; Cost Consequences,,,"<h4>Objectives</h4>Cancer is a leading cause of death. This paper examines the utilisation of unscheduled emergency end-of-life healthcare and estimates expenditure in this domain. We explore care patterns and quantify the likely benefits from service reconfigurations which may influence rates of hospital admission and deaths.<h4>Methods</h4>Using prevalence-based retrospective data from the Northern Ireland General Registrar's Office linked by cancer diagnosis to Patient Administration episode data for unscheduled emergency care (1st January 2014 to 31st December 2015), we estimate unscheduled-emergency-care costs in the last year of life. We model potential resources released by reductions in length-of-stay for cancer patients. Linear regression examined patient characteristics affecting length of stay.<h4>Results</h4>A total of 3134 cancer patients used 60,746 days of unscheduled emergency care (average 19.5 days). Of these, 48.9% had ≥1 admission during their last 28 days of life. Total estimated cost was £28,684,261, averaging £9200 per person. Lung cancer patients had the highest proportion of admissions (23.2%, mean length of stay = 17.9 days, mean cost=£7224). The highest service use and total cost was in those diagnosed at stage IV (38.4%), who required 22,099 days of care, costing £9,629,014. Palliative care support, identified in 25.5% of patients, contributed £1,322,328. A 3-day reduction in the mean length of stay with a 10% reduction in admissions, could reduce costs by £7.37 million. Regression analyses explained 41% of length-of-stay variability.<h4>Conclusions</h4>The cost burden from unscheduled care use in the last year of life of cancer patients is significant. Opportunities to prioritise service reconfiguration for high-costing users emphasized lung and colorectal cancers as offering the greatest potential to influence outcomes.",,pdf:https://link.springer.com/content/pdf/10.1007/s00520-023-07633-6.pdf; doi:https://doi.org/10.1007/s00520-023-07633-6; html:https://europepmc.org/articles/PMC9985568; pdf:https://europepmc.org/articles/PMC9985568?pdf=render
 33928785,https://doi.org/10.1161/circulationaha.120.049844,Unfolded Protein Response as a Compensatory Mechanism and Potential Therapeutic Target in PLN R14del Cardiomyopathy.,"Feyen DAM, Perea-Gil I, Maas RGC, Harakalova M, Gavidia AA, Arthur Ataam J, Wu TH, Vink A, Pei J, Vadgama N, Suurmeijer AJ, Te Rijdt WP, Vu M, Amatya PL, Prado M, Zhang Y, Dunkenberger L, Sluijter JPG, Sallam K, Asselbergs FW, Mercola M, Karakikes I.",,Circulation,2021,2021-04-30,N,"Unfolded protein response; Models, Biological; Induced Pluripotent Stem Cells; Phospholamban; Cardiomyopathy, Dilated; Sequence Analysis, Rna",,,"<h4>Background</h4>Phospholamban (PLN) is a critical regulator of calcium cycling and contractility in the heart. The loss of arginine at position 14 in PLN (R14del) is associated with dilated cardiomyopathy with a high prevalence of ventricular arrhythmias. How the R14 deletion causes dilated cardiomyopathy is poorly understood, and there are no disease-specific therapies.<h4>Methods</h4>We used single-cell RNA sequencing to uncover PLN R14del disease mechanisms in human induced pluripotent stem cells (hiPSC-CMs). We used both 2-dimensional and 3-dimensional functional contractility assays to evaluate the impact of modulating disease-relevant pathways in PLN R14del hiPSC-CMs.<h4>Results</h4>Modeling of the PLN R14del cardiomyopathy with isogenic pairs of hiPSC-CMs recapitulated the contractile deficit associated with the disease in vitro. Single-cell RNA sequencing revealed the induction of the unfolded protein response (UPR) pathway in PLN R14del compared with isogenic control hiPSC-CMs. The activation of UPR was also evident in the hearts from PLN R14del patients. Silencing of each of the 3 main UPR signaling branches (IRE1, ATF6, or PERK) by siRNA exacerbated the contractile dysfunction of PLN R14del hiPSC-CMs. We explored the therapeutic potential of activating the UPR with a small molecule activator, BiP (binding immunoglobulin protein) inducer X. PLN R14del hiPSC-CMs treated with BiP protein inducer X showed a dose-dependent amelioration of the contractility deficit in both 2-dimensional cultures and 3-dimensional engineered heart tissues without affecting calcium homeostasis.<h4>Conclusions</h4>Together, these findings suggest that the UPR exerts a protective effect in the setting of PLN R14del cardiomyopathy and that modulation of the UPR might be exploited therapeutically.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCULATIONAHA.120.049844; doi:https://doi.org/10.1161/CIRCULATIONAHA.120.049844; html:https://europepmc.org/articles/PMC8667423; pdf:https://europepmc.org/articles/PMC8667423?pdf=render; doi:https://doi.org/10.1161/circulationaha.120.049844
+36869930,https://doi.org/10.1007/s00520-023-07633-6,Cost consequences of unscheduled emergency admissions in cancer patients in the last year of life.,"McFerran E, Cairnduff V, Elder R, Gavin A, Lawler M.",,Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer,2023,2023-03-04,Y,Neoplasms; Death; Palliative care; Emergency Care; Cost Consequences,,,"<h4>Objectives</h4>Cancer is a leading cause of death. This paper examines the utilisation of unscheduled emergency end-of-life healthcare and estimates expenditure in this domain. We explore care patterns and quantify the likely benefits from service reconfigurations which may influence rates of hospital admission and deaths.<h4>Methods</h4>Using prevalence-based retrospective data from the Northern Ireland General Registrar's Office linked by cancer diagnosis to Patient Administration episode data for unscheduled emergency care (1st January 2014 to 31st December 2015), we estimate unscheduled-emergency-care costs in the last year of life. We model potential resources released by reductions in length-of-stay for cancer patients. Linear regression examined patient characteristics affecting length of stay.<h4>Results</h4>A total of 3134 cancer patients used 60,746 days of unscheduled emergency care (average 19.5 days). Of these, 48.9% had ≥1 admission during their last 28 days of life. Total estimated cost was £28,684,261, averaging £9200 per person. Lung cancer patients had the highest proportion of admissions (23.2%, mean length of stay = 17.9 days, mean cost=£7224). The highest service use and total cost was in those diagnosed at stage IV (38.4%), who required 22,099 days of care, costing £9,629,014. Palliative care support, identified in 25.5% of patients, contributed £1,322,328. A 3-day reduction in the mean length of stay with a 10% reduction in admissions, could reduce costs by £7.37 million. Regression analyses explained 41% of length-of-stay variability.<h4>Conclusions</h4>The cost burden from unscheduled care use in the last year of life of cancer patients is significant. Opportunities to prioritise service reconfiguration for high-costing users emphasized lung and colorectal cancers as offering the greatest potential to influence outcomes.",,pdf:https://link.springer.com/content/pdf/10.1007/s00520-023-07633-6.pdf; doi:https://doi.org/10.1007/s00520-023-07633-6; html:https://europepmc.org/articles/PMC9985568; pdf:https://europepmc.org/articles/PMC9985568?pdf=render
 38352035,https://doi.org/10.26633/rpsp.2024.13,[Reporting guidelines for clinical trial reports for interventions involving artificial intelligence: the CONSORT-AI extensionDiretrizes para relatórios de ensaios clínicos com intervenções que utilizam inteligência artificial: a extensão CONSORT-AI].,"Liu X, Cruz Rivera S, Moher D, Calvert MJ, Denniston AK, Grupo de Trabajo SPIRIT-AI y CONSORT-AI, GRUPO DE DIRECCIÓN SPIRIT-AI Y CONSORT-AI , Grupo de Consenso SPIRIT-AI y CONSORT-AI .",,Revista panamericana de salud publica = Pan American journal of public health,2024,2023-02-12,Y,,,,"The CONSORT 2010 statement provides minimum guidelines for reporting randomized trials. Its widespread use has been instrumental in ensuring transparency in the evaluation of new interventions. More recently, there has been a growing recognition that interventions involving artificial intelligence (AI) need to undergo rigorous, prospective evaluation to demonstrate impact on health outcomes. The CONSORT-AI (Consolidated Standards of Reporting Trials-Artificial Intelligence) extension is a new reporting guideline for clinical trials evaluating interventions with an AI component. It was developed in parallel with its companion statement for clinical trial protocols: SPIRIT-AI (Standard Protocol Items: Recommendations for Interventional Trials-Artificial Intelligence). Both guidelines were developed through a staged consensus process involving literature review and expert consultation to generate 29 candidate items, which were assessed by an international multi-stakeholder group in a two-stage Delphi survey (103 stakeholders), agreed upon in a two-day consensus meeting (31 stakeholders) and refined through a checklist pilot (34 participants). The CONSORT-AI extension includes 14 new items that were considered sufficiently important for AI interventions that they should be routinely reported in addition to the core CONSORT 2010 items. CONSORT-AI recommends that investigators provide clear descriptions of the AI intervention, including instructions and skills required for use, the setting in which the AI intervention is integrated, the handling of inputs and outputs of the AI intervention, the human-AI interaction and provision of an analysis of error cases. CONSORT-AI will help promote transparency and completeness in reporting clinical trials for AI interventions. It will assist editors and peer reviewers, as well as the general readership, to understand, interpret and critically appraise the quality of clinical trial design and risk of bias in the reported outcomes.",,pdf:https://iris.paho.org/bitstream/10665.2/59257/5/v48e132024.pdf; doi:https://doi.org/10.26633/RPSP.2024.13; html:https://europepmc.org/articles/PMC10863743; pdf:https://europepmc.org/articles/PMC10863743?pdf=render
 31657946,https://doi.org/10.1164/rccm.201903-0673oc,Long-Term Outcomes after Severe Traumatic Brain Injury in Older Adults. A Registry-based Cohort Study.,"Maiden MJ, Cameron PA, Rosenfeld JV, Cooper DJ, McLellan S, Gabbe BJ.",,American journal of respiratory and critical care medicine,2020,2020-01-01,N,Elderly; Brain trauma; Functional Performance; Critical Care Outcomes,,,"<b>Rationale:</b> Older adults (≥65 yr old) account for an increasing proportion of patients with severe traumatic brain injury (TBI), yet clinical trials and outcome studies contain relatively few of these patients.<b>Objectives:</b> To determine functional status 6 months after severe TBI in older adults, changes in this status over 2 years, and outcome covariates.<b>Methods:</b> This was a registry-based cohort study of older adults who were admitted to hospitals in Victoria, Australia, between 2007 and 2016 with severe TBI. Functional status was assessed with Glasgow Outcome Scale Extended (GOSE) 6, 12, and 24 months after injury. Cohort subgroups were defined by admission to an ICU. Features associated with functional outcome were assessed from the ICU subgroup.<b>Measurements and Main Results:</b> The study included 540 older adults who had been hospitalized with severe TBI over the 10-year period; 428 (79%) patients died in hospital, and 456 (84%) died 6 months after injury. There were 277 patients who had not been admitted to an ICU; at 6 months, 268 (97%) had died, 8 (3%) were dependent (GOSE 2-4), and 1 (0.4%) was functionally independent (GOSE 5-8). There were 263 patients who had been admitted to an ICU; at 6 months, 188 (73%) had died, 39 (15%) were dependent, and 32 (12%) were functionally independent. These proportions did not change over longer follow-up. The only clinical features associated with a lower rate of functional independence were Injury Severity Score ≥25 (adjusted odds ratio, 0.24 [95% confidence interval, 0.09-0.67]; <i>P</i> = 0.007) and older age groups (<i>P</i> = 0.017).<b>Conclusions:</b> Severe TBI in older adults is a condition with very high mortality, and few recover to functional independence.",,doi:https://doi.org/10.1164/rccm.201903-0673OC
 30862657,https://doi.org/10.2337/dc18-2004,Risk of Incident Obstructive Sleep Apnea Among Patients With Type 2 Diabetes.,"Subramanian A, Adderley NJ, Tracy A, Taverner T, Hanif W, Toulis KA, Thomas GN, Tahrani AA, Nirantharakumar K.",,Diabetes care,2019,2019-03-12,N,,,,"<h4>Objective</h4>This study compared the incidence of obstructive sleep apnea (OSA) in patients with and without type 2 diabetes and investigated risk factors for OSA in patients with type 2 diabetes.<h4>Research design and methods</h4>A retrospective cohort study was performed to compare OSA incidence between adult patients with and without type 2 diabetes matched for age, sex, and BMI. Patients with a prevalent OSA diagnosis were excluded. The study cohort was derived from The Health Improvement Network (THIN), a U.K. primary care database, from 1 January 2005 to 31 December 2017.<h4>Results</h4>There were 3,110 (0.88%) and 5,968 (0.46%) incident OSA cases identified in the 360,250 exposed and 1,296,489 unexposed patient cohorts, respectively. Adjusted incidence rate ratio (aIRR) of OSA in patients with type 2 diabetes compared with those without was 1.48 (95% CI 1.42-1.55; <i>P</i> < 0.001). In a multivariate regression analysis of patients with type 2 diabetes, significant predictors of OSA were diabetes-related foot disease (1.23 [1.06-1.42]; <i>P</i> = 0.005), being prescribed insulin in the last 60 days (1.58 [1.42-1.75]; <i>P</i> < 0.001), male sex (2.27 [2.09-2.46]; <i>P</i> < 0.001), being overweight (2.02 [1.54-2.64]; <i>P</i> < 0.001) or obese (8.29 [6.42-10.69]; <i>P</i> < 0.001), heart failure (1.41 [1.18-1.70]; <i>P</i> < 0.001), ischemic heart disease (1.22 [1.11-1.34]; <i>P</i> < 0.001), atrial fibrillation (1.23 [1.04-1.46]; <i>P</i> = 0.015), hypertension (1.32 [1.23-1.43]; <i>P</i> < 0.001), and depression (1.75 [1.61-1.91]; <i>P</i> < 0.001).<h4>Conclusions</h4>When considered alongside previous evidence, this study indicates that the association between type 2 diabetes and OSA is bidirectional. In addition to known predictors of OSA, diabetes-related foot disease and insulin treatment were identified as risk factors in patients with type 2 diabetes.",,pdf:https://care.diabetesjournals.org/content/diacare/42/5/954.full.pdf; doi:https://doi.org/10.2337/dc18-2004
 36215124,https://doi.org/10.1161/circgen.121.003598,Gene Sequencing Identifies Perturbation in Nitric Oxide Signaling as a Nonlipid Molecular Subtype of Coronary Artery Disease.,"Khera AV, Wang M, Chaffin M, Emdin CA, Samani NJ, Schunkert H, Watkins H, McPherson R, Erdmann J, Elosua R, Boerwinkle E, Ardissino D, Butterworth AS, Di Angelantonio E, Naheed A, Danesh J, Chowdhury R, Krumholz HM, Sheu WH, Rich SS, Rotter JI, Chen YI, Gabriel S, Lander ES, Saleheen D, Kathiresan S.",,Circulation. Genomic and precision medicine,2022,2022-10-10,N,Atherosclerosis; coronary artery disease; Genetic Association Studies; Nitric Oxide Synthase Type Iii; Precision Medicine,,,"<h4>Background</h4>A key goal of precision medicine is to disaggregate common, complex diseases into discrete molecular subtypes. Rare coding variants in the low-density lipoprotein receptor gene (<i>LDLR</i>) are identified in 1% to 2% of coronary artery disease (CAD) patients, defining a molecular subtype with risk driven by hypercholesterolemia.<h4>Methods</h4>To search for additional subtypes, we compared the frequency of rare, predicted loss-of-function and damaging missense variants aggregated within a given gene in 41 081 CAD cases versus 217 115 controls.<h4>Results</h4>Rare variants in <i>LDLR</i> were most strongly associated with CAD, present in 1% of cases and associated with 4.4-fold increased CAD risk. A second subtype was characterized by variants in endothelial nitric oxide synthase gene (<i>NOS3</i>), a key enzyme regulating vascular tone, endothelial function, and platelet aggregation. A rare predicted loss-of-function or damaging missense variants in <i>NOS3</i> was present in 0.6% of cases and associated with 2.42-fold increased risk of CAD (95% CI, 1.80-3.26; <i>P</i>=5.50×10<sup>-9</sup>). These variants were associated with higher systolic blood pressure (+3.25 mm Hg; [95% CI, 1.86-4.65]; <i>P</i>=5.00×10<sup>-6</sup>) and increased risk of hypertension (adjusted odds ratio 1.31; [95% CI, 1.14-1.51]; <i>P</i>=2.00×10<sup>-4</sup>) but not circulating cholesterol concentrations, suggesting that, beyond lipid pathways, nitric oxide synthesis is a key nonlipid driver of CAD risk.<h4>Conclusions</h4>Beyond <i>LDLR</i>, we identified an additional nonlipid molecular subtype of CAD characterized by rare variants in the <i>NOS3</i> gene.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCGEN.121.003598; doi:https://doi.org/10.1161/CIRCGEN.121.003598; html:https://europepmc.org/articles/PMC9771961; pdf:https://europepmc.org/articles/PMC9771961?pdf=render; doi:https://doi.org/10.1161/circgen.121.003598
 35210596,https://doi.org/10.1038/s41591-022-01736-z,Modeling comparative cost-effectiveness of SARS-CoV-2 vaccine dose fractionation in India.,"Du Z, Wang L, Pandey A, Lim WW, Chinazzi M, Piontti APY, Lau EHY, Wu P, Malani A, Cobey S, Cowling BJ.",,Nature medicine,2022,2022-02-24,Y,,,,"Given global Coronavirus Disease 2019 (COVID-19) vaccine shortages and inequity of vaccine distributions, fractionation of vaccine doses might be an effective strategy for reducing public health and economic burden, notwithstanding the emergence of new variants of concern. In this study, we developed a multi-scale model incorporating population-level transmission and individual-level vaccination to estimate the costs of hospitalization and vaccination and the economic benefits of reducing COVID-19 deaths due to dose-fractionation strategies in India. We used large-scale survey data of the willingness to pay together with data of vaccine and hospital admission costs to build the model. We found that fractional doses of vaccines could be an economically viable vaccination strategy compared to alternatives of either full-dose vaccination or no vaccination. Dose-sparing strategies could save a large number of lives, even with the emergence of new variants with higher transmissibility.",,pdf:https://www.nature.com/articles/s41591-022-01736-z.pdf; doi:https://doi.org/10.1038/s41591-022-01736-z; html:https://europepmc.org/articles/PMC9117137; pdf:https://europepmc.org/articles/PMC9117137?pdf=render
 34062542,https://doi.org/10.1159/000517521,Structural Endpoints and Outcome Measures in Uveitis.,"Wintergerst MWM, Liu X, Terheyden JH, Pohlmann D, Li JQ, Montesano G, Ometto G, Holz FG, Crabb DP, Pleyer U, Heinz C, Denniston AK, Finger RP.",,Ophthalmologica. Journal international d'ophtalmologie. International journal of ophthalmology. Zeitschrift fur Augenheilkunde,2021,2021-06-01,N,Biomarker; Uveitis; Outcome; Outcome Measure; Endpoint; Imaging Biomarker; Inflammatory Eye Diseases; Instrument-based Measure,,,"Most uveitis entities are rare diseases but, taken together, are responsible for 5-10% of worldwide visual impairment which largely affects persons of working age. As with many rare diseases, there is a lack of high-level evidence regarding its clinical management, partly due to a dearth of reliable and objective quantitative endpoints for clinical trials. This review provides an overview of available structural outcome measures for uveitis disease activity and damage in an anatomical order from the anterior to the posterior segment of the eye. While there is a multitude of available structural outcome measures, not all might qualify as endpoints for clinical uveitis trials, and thorough testing of applicability is warranted. Furthermore, a consensus on endpoint definition, standardization, and ""core outcomes"" is required. As stipulated by regulatory agencies, endpoints should be precisely defined, clinically important, internally consistent, reliable, responsive to treatment, and relevant for the respective subtype of uveitis. Out of all modalities used for assessment of the reviewed structural outcome measures, optical coherence tomography, color fundus photography, fundus autofluorescence, and fluorescein/indocyanine green angiography represent current ""core modalities"" for reliable and objective quantification of uveitis outcome measures, based on their practical availability and the evidence provided so far.",,pdf:https://www.karger.com/Article/Pdf/517521; doi:https://doi.org/10.1159/000517521
-36343994,https://doi.org/10.1136/bmjopen-2022-063159,"Demographic, behavioural and occupational risk factors associated with SARS-CoV-2 infection in UK healthcare workers: a retrospective observational study.","Cooper DJ, Lear S, Sithole N, Shaw A, Stark H, Ferris M, CITIID-NIHR BioResource COVID-19 collaboration consortium, Bradley J, Maxwell P, Goodfellow I, Weekes MP, Seaman S, Baker S.",,BMJ open,2022,2022-11-07,Y,Infection control; epidemiology; Public Health; Covid-19,,,"<h4>Objective</h4>Healthcare workers (HCWs) are at higher risk of SARS-CoV-2 infection than the general population. This group is pivotal to healthcare system resilience during the COVID-19, and future, pandemics. We investigated demographic, social, behavioural and occupational risk factors for SARS-CoV-2 infection among HCWs.<h4>Design/setting/participants</h4>HCWs enrolled in a large-scale sero-epidemiological study at a UK university teaching hospital were sent questionnaires spanning a 5-month period from March to July 2020. In a retrospective observational cohort study, univariate logistic regression was used to assess factors associated with SARS-CoV-2 infection. A Least Absolute Shrinkage Selection Operator regression model was used to identify variables to include in a multivariate logistic regression model.<h4>Results</h4>Among 2258 HCWs, highest ORs associated with SARS-CoV-2 antibody seropositivity on multivariate analysis were having a household member previously testing positive for SARS-CoV-2 antibodies (OR 6.94 (95% CI 4.15 to 11.6); p&lt;0.0001) and being of black ethnicity (6.21 (95% CI 2.69 to 14.3); p&lt;0.0001). Occupational factors associated with a higher risk of seropositivity included working as a physiotherapist (OR 2.78 (95% CI 1.21 to 6.36); p=0.015) and working predominantly in acute medicine (OR 2.72 (95% CI 1.57 to 4.69); p&lt;0.0001) or medical subspecialties (not including infectious diseases) (OR 2.33 (95% CI 1.4 to 3.88); p=0.001). Reporting that adequate personal protective equipment (PPE) was 'rarely' available had an OR of 2.83 (95% CI 1.29 to 6.25; p=0.01). Reporting attending a handover where social distancing was not possible had an OR of 1.39 (95% CI 1.02 to 1.9; p=0.038).<h4>Conclusions</h4>The emergence of SARS-CoV-2 variants and potential vaccine escape continue to threaten stability of healthcare systems worldwide, and sustained vigilance against HCW infection remains a priority. Enhanced risk assessments should be considered for HCWs of black ethnicity, physiotherapists and those working in acute medicine or medical subspecialties. Workplace risk reduction measures include ongoing access to high-quality PPE and effective social distancing measures.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/11/e063159.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-063159; html:https://europepmc.org/articles/PMC9644078; pdf:https://europepmc.org/articles/PMC9644078?pdf=render
 38280393,https://doi.org/10.1016/s2352-3018(23)00272-2,Longitudinal trends in causes of death among adults with HIV on antiretroviral therapy in Europe and North America from 1996 to 2020: a collaboration of cohort studies.,"Trickey A, McGinnis K, Gill MJ, Abgrall S, Berenguer J, Wyen C, Hessamfar M, Reiss P, Kusejko K, Silverberg MJ, Imaz A, Teira R, d'Arminio Monforte A, Zangerle R, Guest JL, Papastamopoulos V, Crane H, Sterling TR, Grabar S, Ingle SM, Sterne JAC.",,The lancet. HIV,2024,2024-01-24,N,,,,"<h4>Background</h4>Mortality rates among people with HIV have fallen since 1996 following the widespread availability of effective antiretroviral therapy (ART). Patterns of cause-specific mortality are evolving as the population with HIV ages. We aimed to investigate longitudinal trends in cause-specific mortality among people with HIV starting ART in Europe and North America.<h4>Methods</h4>In this collaborative observational cohort study, we used data from 17 European and North American HIV cohorts contributing data to the Antiretroviral Therapy Cohort Collaboration. We included data for people with HIV who started ART between 1996 and 2020 at the age of 16 years or older. Causes of death were classified into a single cause by both a clinician and an algorithm if International Classification of Diseases, Ninth Revision or Tenth Revision data were available, or independently by two clinicians. Disagreements were resolved through panel discussion. We used Poisson models to compare cause-specific mortality rates during the calendar periods 1996-99, 2000-03, 2004-07, 2008-11, 2012-15, and 2016-20, adjusted for time-updated age, CD4 count, and whether the individual was ART-naive at the start of each period.<h4>Findings</h4>Among 189 301 people with HIV included in this study, 16 832 (8·9%) deaths were recorded during 1 519 200 person-years of follow-up. 13 180 (78·3%) deaths were classified by cause: the most common causes were AIDS (4203 deaths; 25·0%), non-AIDS non-hepatitis malignancy (2311; 13·7%), and cardiovascular or heart-related (1403; 8·3%) mortality. The proportion of deaths due to AIDS declined from 49% during 1996-99 to 16% during 2016-20. Rates of all-cause mortality per 1000 person-years decreased from 16·8 deaths (95% CI 15·4-18·4) during 1996-99 to 7·9 deaths (7·6-8·2) during 2016-20. Rates of all-cause mortality declined with time: the average adjusted mortality rate ratio per calendar period was 0·85 (95% CI 0·84-0·86). Rates of cause-specific mortality also declined: the most pronounced reduction was for AIDS-related mortality (0·81; 0·79-0·83). There were also reductions in rates of cardiovascular-related (0·83, 0·79-0·87), liver-related (0·88, 0·84-0·93), non-AIDS infection-related (0·91, 0·86-0·96), non-AIDS-non-hepatocellular carcinoma malignancy-related (0·94, 0·90-0·97), and suicide or accident-related mortality (0·89, 0·82-0·95). Mortality rates among people who acquired HIV through injecting drug use increased in women (1·07, 1·00-1·14) and decreased slightly in men (0·96, 0·93-0·99).<h4>Interpretation</h4>Reductions of most major causes of death, particularly AIDS-related deaths among people with HIV on ART, were not seen for all subgroups. Interventions targeted at high-risk groups, substance use, and comorbidities might further increase life expectancy in people with HIV towards that in the general population.<h4>Funding</h4>US National Institute on Alcohol Abuse and Alcoholism.",,doi:https://doi.org/10.1016/S2352-3018(23)00272-2
 31145509,https://doi.org/10.1002/gepi.22215,A comparison of two workflows for regulome and transcriptome-based prioritization of genetic variants associated with myocardial mass.,"Manduchi E, Hemerich D, van Setten J, Tragante V, Harakalova M, Pei J, Williams SM, van der Harst P, Asselbergs FW, Moore JH.",,Genetic epidemiology,2019,2019-05-30,N,Functional genomics; Gwas; left ventricular mass; Snp Preselection,,,"A typical task arising from main effect analyses in a Genome Wide Association Study (GWAS) is to identify single nucleotide polymorphisms (SNPs), in linkage disequilibrium with the observed signals, that are likely causal variants and the affected genes. The affected genes may not be those closest to associating SNPs. Functional genomics data from relevant tissues are believed to be helpful in selecting likely causal SNPs and interpreting implicated biological mechanisms, ultimately facilitating prevention and treatment in the case of a disease trait. These data are typically used post GWAS analyses to fine-map the statistically significant signals identified agnostically by testing all SNPs and applying a multiple testing correction. The number of tested SNPs is typically in the millions, so the multiple testing burden is high. Motivated by this, in this study we investigated an alternative workflow, which consists in utilizing the available functional genomics data as a first step to reduce the number of SNPs tested for association. We analyzed GWAS on electrocardiographic QRS duration using these two workflows. The alternative workflow identified more SNPs, including some residing in loci not discovered with the typical workflow. Moreover, the latter are corroborated by other reports on QRS duration. This indicates the potential value of incorporating functional genomics information at the onset in GWAS analyses.",,pdf:https://pure.rug.nl/ws/files/89611268/Manduchi_et_al_2019_Genetic_Epidemiology.pdf; doi:https://doi.org/10.1002/gepi.22215; html:https://europepmc.org/articles/PMC6687530; pdf:https://europepmc.org/articles/PMC6687530?pdf=render; doi:https://doi.org/10.1002/gepi.22215
+36343994,https://doi.org/10.1136/bmjopen-2022-063159,"Demographic, behavioural and occupational risk factors associated with SARS-CoV-2 infection in UK healthcare workers: a retrospective observational study.","Cooper DJ, Lear S, Sithole N, Shaw A, Stark H, Ferris M, CITIID-NIHR BioResource COVID-19 collaboration consortium, Bradley J, Maxwell P, Goodfellow I, Weekes MP, Seaman S, Baker S.",,BMJ open,2022,2022-11-07,Y,Infection control; epidemiology; Public Health; Covid-19,,,"<h4>Objective</h4>Healthcare workers (HCWs) are at higher risk of SARS-CoV-2 infection than the general population. This group is pivotal to healthcare system resilience during the COVID-19, and future, pandemics. We investigated demographic, social, behavioural and occupational risk factors for SARS-CoV-2 infection among HCWs.<h4>Design/setting/participants</h4>HCWs enrolled in a large-scale sero-epidemiological study at a UK university teaching hospital were sent questionnaires spanning a 5-month period from March to July 2020. In a retrospective observational cohort study, univariate logistic regression was used to assess factors associated with SARS-CoV-2 infection. A Least Absolute Shrinkage Selection Operator regression model was used to identify variables to include in a multivariate logistic regression model.<h4>Results</h4>Among 2258 HCWs, highest ORs associated with SARS-CoV-2 antibody seropositivity on multivariate analysis were having a household member previously testing positive for SARS-CoV-2 antibodies (OR 6.94 (95% CI 4.15 to 11.6); p&lt;0.0001) and being of black ethnicity (6.21 (95% CI 2.69 to 14.3); p&lt;0.0001). Occupational factors associated with a higher risk of seropositivity included working as a physiotherapist (OR 2.78 (95% CI 1.21 to 6.36); p=0.015) and working predominantly in acute medicine (OR 2.72 (95% CI 1.57 to 4.69); p&lt;0.0001) or medical subspecialties (not including infectious diseases) (OR 2.33 (95% CI 1.4 to 3.88); p=0.001). Reporting that adequate personal protective equipment (PPE) was 'rarely' available had an OR of 2.83 (95% CI 1.29 to 6.25; p=0.01). Reporting attending a handover where social distancing was not possible had an OR of 1.39 (95% CI 1.02 to 1.9; p=0.038).<h4>Conclusions</h4>The emergence of SARS-CoV-2 variants and potential vaccine escape continue to threaten stability of healthcare systems worldwide, and sustained vigilance against HCW infection remains a priority. Enhanced risk assessments should be considered for HCWs of black ethnicity, physiotherapists and those working in acute medicine or medical subspecialties. Workplace risk reduction measures include ongoing access to high-quality PPE and effective social distancing measures.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/11/e063159.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-063159; html:https://europepmc.org/articles/PMC9644078; pdf:https://europepmc.org/articles/PMC9644078?pdf=render
 31863937,https://doi.org/10.1016/j.aap.2019.105333,A systematic review of the association between fault or blame-related attributions and procedures after transport injury and health and work-related outcomes.,"Giummarra MJ, Lau G, Grant G, Gabbe BJ.",,Accident; analysis and prevention,2020,2019-12-19,N,Depression; Recovery; Pain; Anxiety; Mental health; Ptsd; Fault; Road Trauma; Transport Injury,,,"Attributions of fault are often associated with worse injury outcomes; however, the consistency and magnitude of these impacts is not known. This review examined the prognostic role of fault on health, mental health, pain and work outcomes after transport injury. A systematic search of five electronic databases (Medline, Embase, CINAHL, PsycINFO, Cochrane Library) yielded 16,324 records published between 2000 and January 2018. Eligibility criteria were: adult transport injury survivors; prospective design; multivariable analysis; fault-related factor analysed; pain, mental health, general health or work-related outcome. Citations (n = 10,558, excluding duplicates) and full text articles (n = 555) were screened manually (Reviewer 1), and using concurrent machine learning and text mining (Reviewer 2; using Abstrackr, WordStat and QDA miner). Data from 55 papers that met all inclusion criteria were extracted, papers were evaluated for risk of bias using the QUIPS tool, and overall level of evidence was assessed using the GRADE tool. There were six main fault-related factors classified as: fault or responsibility, fault-based compensation, lawyer involvement or litigation, blame or guilt, road user or position in vehicle, and impact direction. Overall there were inconsistent associations between fault and transport injury outcomes, and 60% of papers had high risk of bias. There was moderate evidence that fault-based compensation claims were associated with poorer health-related outcomes, and that lawyer involvement was associated with poorer work outcomes beyond 12 months post-injury. However, the evidence of negative associations between fault-based compensation claims and work-related outcomes was limited. Lawyer involvement and fault-based compensation claims were associated with adverse mental health outcomes six months post-injury, but not beyond 12 months. The most consistent associations between fault and negative outcomes were not for fault attributions, per se, but were related to fault-related procedures (e.g., lawyer engagement, fault-based compensation claims).",,doi:https://doi.org/10.1016/j.aap.2019.105333
 36351458,https://doi.org/10.1016/s0140-6736(22)02074-8,Impact of diabetes on the effects of sodium glucose co-transporter-2 inhibitors on kidney outcomes: collaborative meta-analysis of large placebo-controlled trials.,"Nuffield Department of Population Health Renal Studies Group, SGLT2 inhibitor Meta-Analysis Cardio-Renal Trialists' Consortium.",,"Lancet (London, England)",2022,2022-11-06,Y,,,,"<h4>Background</h4>Large trials have shown that sodium glucose co-transporter-2 (SGLT2) inhibitors reduce the risk of adverse kidney and cardiovascular outcomes in patients with heart failure or chronic kidney disease, or with type 2 diabetes and high risk of atherosclerotic cardiovascular disease. None of the trials recruiting patients with and without diabetes were designed to assess outcomes separately in patients without diabetes.<h4>Methods</h4>We did a systematic review and meta-analysis of SGLT2 inhibitor trials. We searched the MEDLINE and Embase databases for trials published from database inception to Sept 5, 2022. SGLT2 inhibitor trials that were double-blind, placebo-controlled, performed in adults (age ≥18 years), large (≥500 participants per group), and at least 6 months in duration were included. Summary-level data used for analysis were extracted from published reports or provided by trial investigators, and inverse-variance-weighted meta-analyses were conducted to estimate treatment effects. The main efficacy outcomes were kidney disease progression (standardised to a definition of a sustained ≥50% decrease in estimated glomerular filtration rate [eGFR] from randomisation, a sustained low eGFR, end-stage kidney disease, or death from kidney failure), acute kidney injury, and a composite of cardiovascular death or hospitalisation for heart failure. Other outcomes were death from cardiovascular and non-cardiovascular disease considered separately, and the main safety outcomes were ketoacidosis and lower limb amputation. This study is registered with PROSPERO, CRD42022351618.<h4>Findings</h4>We identified 13 trials involving 90 413 participants. After exclusion of four participants with uncertain diabetes status, we analysed 90 409 participants (74 804 [82·7%] participants with diabetes [>99% with type 2 diabetes] and 15 605 [17·3%] without diabetes; trial-level mean baseline eGFR range 37-85 mL/min per 1·73 m<sup>2</sup>). Compared with placebo, allocation to an SGLT2 inhibitor reduced the risk of kidney disease progression by 37% (relative risk [RR] 0·63, 95% CI 0·58-0·69) with similar RRs in patients with and without diabetes. In the four chronic kidney disease trials, RRs were similar irrespective of primary kidney diagnosis. SGLT2 inhibitors reduced the risk of acute kidney injury by 23% (0·77, 0·70-0·84) and the risk of cardiovascular death or hospitalisation for heart failure by 23% (0·77, 0·74-0·81), again with similar effects in those with and without diabetes. SGLT2 inhibitors also reduced the risk of cardiovascular death (0·86, 0·81-0·92) but did not significantly reduce the risk of non-cardiovascular death (0·94, 0·88-1·02). For these mortality outcomes, RRs were similar in patients with and without diabetes. For all outcomes, results were broadly similar irrespective of trial mean baseline eGFR. Based on estimates of absolute effects, the absolute benefits of SGLT2 inhibition outweighed any serious hazards of ketoacidosis or amputation.<h4>Interpretation</h4>In addition to the established cardiovascular benefits of SGLT2 inhibitors, the randomised data support their use for modifying risk of kidney disease progression and acute kidney injury, not only in patients with type 2 diabetes at high cardiovascular risk, but also in patients with chronic kidney disease or heart failure irrespective of diabetes status, primary kidney disease, or kidney function.<h4>Funding</h4>UK Medical Research Council and Kidney Research UK.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7613836; doi:https://doi.org/10.1016/S0140-6736(22)02074-8; html:https://europepmc.org/articles/PMC7613836
 33043790,https://doi.org/10.1177/0141076820961776,Advancing UK regulatory science and innovation in healthcare.,"Calvert MJ, Marston E, Samuels M, Rivera SC, Torlinska B, Oliver K, Denniston AK, Hoare S.",,Journal of the Royal Society of Medicine,2021,2020-10-12,Y,,,,,,pdf:https://journals.sagepub.com/doi/pdf/10.1177/0141076820961776; doi:https://doi.org/10.1177/0141076820961776; html:https://europepmc.org/articles/PMC7809339; pdf:https://europepmc.org/articles/PMC7809339?pdf=render
-38351061,https://doi.org/10.1038/s41467-024-45419-4,Structural and mechanistic characterization of bifunctional heparan sulfate N-deacetylase-N-sulfotransferase 1.,"Mycroft-West CJ, Abdelkarim S, Duyvesteyn HME, Gandhi NS, Skidmore MA, Owens RJ, Wu L.",,Nature communications,2024,2024-02-13,Y,,,,"Heparan sulfate (HS) polysaccharides are major constituents of the extracellular matrix, which are involved in myriad structural and signaling processes. Mature HS polysaccharides contain complex, non-templated patterns of sulfation and epimerization, which mediate interactions with diverse protein partners. Complex HS modifications form around initial clusters of glucosamine-N-sulfate (GlcNS) on nascent polysaccharide chains, but the mechanistic basis underpinning incorporation of GlcNS itself into HS remains unclear. Here, we determine cryo-electron microscopy structures of human N-deacetylase-N-sulfotransferase (NDST)1, the bifunctional enzyme primarily responsible for initial GlcNS modification of HS. Our structures reveal the architecture of both NDST1 deacetylase and sulfotransferase catalytic domains, alongside a non-catalytic N-terminal domain. The two catalytic domains of NDST1 adopt a distinct back-to-back topology that limits direct cooperativity. Binding analyses, aided by activity-modulating nanobodies, suggest that anchoring of the substrate at the sulfotransferase domain initiates the NDST1 catalytic cycle, providing a plausible mechanism for cooperativity despite spatial domain separation. Our data shed light on key determinants of NDST1 activity, and describe tools to probe NDST1 function in vitro and in vivo.",,pdf:https://www.nature.com/articles/s41467-024-45419-4.pdf; doi:https://doi.org/10.1038/s41467-024-45419-4; html:https://europepmc.org/articles/PMC10864358; pdf:https://europepmc.org/articles/PMC10864358?pdf=render
 33323251,https://doi.org/10.1016/s2589-7500(19)30123-2,A comparison of deep learning performance against health-care professionals in detecting diseases from medical imaging: a systematic review and meta-analysis.,"Liu X, Faes L, Kale AU, Wagner SK, Fu DJ, Bruynseels A, Mahendiran T, Moraes G, Shamdas M, Kern C, Ledsam JR, Schmid MK, Balaskas K, Topol EJ, Bachmann LM, Keane PA, Denniston AK.",,The Lancet. Digital health,2019,2019-09-25,N,,,,"<h4>Background</h4>Deep learning offers considerable promise for medical diagnostics. We aimed to evaluate the diagnostic accuracy of deep learning algorithms versus health-care professionals in classifying diseases using medical imaging.<h4>Methods</h4>In this systematic review and meta-analysis, we searched Ovid-MEDLINE, Embase, Science Citation Index, and Conference Proceedings Citation Index for studies published from Jan 1, 2012, to June 6, 2019. Studies comparing the diagnostic performance of deep learning models and health-care professionals based on medical imaging, for any disease, were included. We excluded studies that used medical waveform data graphics material or investigated the accuracy of image segmentation rather than disease classification. We extracted binary diagnostic accuracy data and constructed contingency tables to derive the outcomes of interest: sensitivity and specificity. Studies undertaking an out-of-sample external validation were included in a meta-analysis, using a unified hierarchical model. This study is registered with PROSPERO, CRD42018091176.<h4>Findings</h4>Our search identified 31 587 studies, of which 82 (describing 147 patient cohorts) were included. 69 studies provided enough data to construct contingency tables, enabling calculation of test accuracy, with sensitivity ranging from 9·7% to 100·0% (mean 79·1%, SD 0·2) and specificity ranging from 38·9% to 100·0% (mean 88·3%, SD 0·1). An out-of-sample external validation was done in 25 studies, of which 14 made the comparison between deep learning models and health-care professionals in the same sample. Comparison of the performance between health-care professionals in these 14 studies, when restricting the analysis to the contingency table for each study reporting the highest accuracy, found a pooled sensitivity of 87·0% (95% CI 83·0-90·2) for deep learning models and 86·4% (79·9-91·0) for health-care professionals, and a pooled specificity of 92·5% (95% CI 85·1-96·4) for deep learning models and 90·5% (80·6-95·7) for health-care professionals.<h4>Interpretation</h4>Our review found the diagnostic performance of deep learning models to be equivalent to that of health-care professionals. However, a major finding of the review is that few studies presented externally validated results or compared the performance of deep learning models and health-care professionals using the same sample. Additionally, poor reporting is prevalent in deep learning studies, which limits reliable interpretation of the reported diagnostic accuracy. New reporting standards that address specific challenges of deep learning could improve future studies, enabling greater confidence in the results of future evaluations of this promising technology.<h4>Funding</h4>None.",,pdf:http://www.thelancet.com/article/S2589750019301232/pdf; doi:https://doi.org/10.1016/S2589-7500(19)30123-2
-36093379,https://doi.org/10.1016/j.isci.2022.105079,Epidemiologic information discovery from open-access COVID-19 case reports via pretrained language model.,"Wang Z, Liu XF, Du Z, Wang L, Wu Y, Holme P, Lachmann M, Lin H, Wong ZSY, Xu XK, Sun Y.",,iScience,2022,2022-09-05,Y,Artificial intelligence; Virology; Machine Learning; Health Sciences,,,"Although open-access data are increasingly common and useful to epidemiological research, the curation of such datasets is resource-intensive and time-consuming. Despite the existence of a major source of COVID-19 data, the regularly disclosed case reports were often written in natural language with an unstructured format. Here, we propose a computational framework that can automatically extract epidemiological information from open-access COVID-19 case reports. We develop this framework by coupling a language model developed using deep neural networks with training samples compiled using an optimized data annotation strategy. When applied to the COVID-19 case reports collected from mainland China, our framework outperforms all other state-of-the-art deep learning models. The information extracted from our approach is highly consistent with that obtained from the gold-standard manual coding, with a matching rate of 80%. To disseminate our algorithm, we provide an open-access online platform that is able to estimate key epidemiological statistics in real time, with much less effort for data curation.",,pdf:http://www.cell.com/article/S2589004222013517/pdf; doi:https://doi.org/10.1016/j.isci.2022.105079; html:https://europepmc.org/articles/PMC9441477; pdf:https://europepmc.org/articles/PMC9441477?pdf=render
+38351061,https://doi.org/10.1038/s41467-024-45419-4,Structural and mechanistic characterization of bifunctional heparan sulfate N-deacetylase-N-sulfotransferase 1.,"Mycroft-West CJ, Abdelkarim S, Duyvesteyn HME, Gandhi NS, Skidmore MA, Owens RJ, Wu L.",,Nature communications,2024,2024-02-13,Y,,,,"Heparan sulfate (HS) polysaccharides are major constituents of the extracellular matrix, which are involved in myriad structural and signaling processes. Mature HS polysaccharides contain complex, non-templated patterns of sulfation and epimerization, which mediate interactions with diverse protein partners. Complex HS modifications form around initial clusters of glucosamine-N-sulfate (GlcNS) on nascent polysaccharide chains, but the mechanistic basis underpinning incorporation of GlcNS itself into HS remains unclear. Here, we determine cryo-electron microscopy structures of human N-deacetylase-N-sulfotransferase (NDST)1, the bifunctional enzyme primarily responsible for initial GlcNS modification of HS. Our structures reveal the architecture of both NDST1 deacetylase and sulfotransferase catalytic domains, alongside a non-catalytic N-terminal domain. The two catalytic domains of NDST1 adopt a distinct back-to-back topology that limits direct cooperativity. Binding analyses, aided by activity-modulating nanobodies, suggest that anchoring of the substrate at the sulfotransferase domain initiates the NDST1 catalytic cycle, providing a plausible mechanism for cooperativity despite spatial domain separation. Our data shed light on key determinants of NDST1 activity, and describe tools to probe NDST1 function in vitro and in vivo.",,pdf:https://www.nature.com/articles/s41467-024-45419-4.pdf; doi:https://doi.org/10.1038/s41467-024-45419-4; html:https://europepmc.org/articles/PMC10864358; pdf:https://europepmc.org/articles/PMC10864358?pdf=render
 32619549,https://doi.org/10.1016/j.cels.2020.05.012,Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection.,"Messner CB, Demichev V, Wendisch D, Michalick L, White M, Freiwald A, Textoris-Taube K, Vernardis SI, Egger AS, Kreidl M, Ludwig D, Kilian C, Agostini F, Zelezniak A, Thibeault C, Pfeiffer M, Hippenstiel S, Hocke A, von Kalle C, Campbell A, Hayward C, Porteous DJ, Marioni RE, Langenberg C, Lilley KS, Kuebler WM, Mülleder M, Drosten C, Suttorp N, Witzenrath M, Kurth F, Sander LE, Ralser M.",,Cell systems,2020,2020-06-02,Y,Mass spectrometry; High-throughput Proteomics; Swath-ms; Antiviral Immune Response; Clinical Classifiers; Covid-19 Infection,,,"The COVID-19 pandemic is an unprecedented global challenge, and point-of-care diagnostic classifiers are urgently required. Here, we present a platform for ultra-high-throughput serum and plasma proteomics that builds on ISO13485 standardization to facilitate simple implementation in regulated clinical laboratories. Our low-cost workflow handles up to 180 samples per day, enables high precision quantification, and reduces batch effects for large-scale and longitudinal studies. We use our platform on samples collected from a cohort of early hospitalized cases of the SARS-CoV-2 pandemic and identify 27 potential biomarkers that are differentially expressed depending on the WHO severity grade of COVID-19. They include complement factors, the coagulation system, inflammation modulators, and pro-inflammatory factors upstream and downstream of interleukin 6. All protocols and software for implementing our approach are freely available. In total, this work supports the development of routine proteomic assays to aid clinical decision making and generate hypotheses about potential COVID-19 therapeutic targets.",,pdf:http://www.cell.com/article/S2405471220301976/pdf; doi:https://doi.org/10.1016/j.cels.2020.05.012; html:https://europepmc.org/articles/PMC7264033
+36093379,https://doi.org/10.1016/j.isci.2022.105079,Epidemiologic information discovery from open-access COVID-19 case reports via pretrained language model.,"Wang Z, Liu XF, Du Z, Wang L, Wu Y, Holme P, Lachmann M, Lin H, Wong ZSY, Xu XK, Sun Y.",,iScience,2022,2022-09-05,Y,Artificial intelligence; Virology; Machine Learning; Health Sciences,,,"Although open-access data are increasingly common and useful to epidemiological research, the curation of such datasets is resource-intensive and time-consuming. Despite the existence of a major source of COVID-19 data, the regularly disclosed case reports were often written in natural language with an unstructured format. Here, we propose a computational framework that can automatically extract epidemiological information from open-access COVID-19 case reports. We develop this framework by coupling a language model developed using deep neural networks with training samples compiled using an optimized data annotation strategy. When applied to the COVID-19 case reports collected from mainland China, our framework outperforms all other state-of-the-art deep learning models. The information extracted from our approach is highly consistent with that obtained from the gold-standard manual coding, with a matching rate of 80%. To disseminate our algorithm, we provide an open-access online platform that is able to estimate key epidemiological statistics in real time, with much less effort for data curation.",,pdf:http://www.cell.com/article/S2589004222013517/pdf; doi:https://doi.org/10.1016/j.isci.2022.105079; html:https://europepmc.org/articles/PMC9441477; pdf:https://europepmc.org/articles/PMC9441477?pdf=render
+32255392,https://doi.org/10.1080/09273948.2019.1709650,Non-invasive Instrument-Based Tests for Quantifying Anterior Chamber Flare in Uveitis: A Systematic Review.,"Liu X, McNally TW, Beese S, Downie LE, Solebo AL, Faes L, Husain S, Keane PA, Moore DJ, Denniston AK.",,Ocular immunology and inflammation,2021,2020-04-07,N,"Diagnostic test; Systematic review; Uveitis; optical coherence tomography; Laser Flare Photometry; Anterior Chamber Flare; Tyndall Effect; Aqueous Humor, Aqueous Humour; Aqueous Protein Concentration",,,"<b>Purpose</b>: Anterior chamber (AC) flare is a key sign for anterior uveitis. New instrument-based techniques for measuring AC flare can offer automation and objectivity. This review aims to identify objective instrument-based measures for AC flare.<b>Methods</b>: In this systematic review, we identified studies reporting correlation between instrument-based tests versus clinician AC flare grading, and/or aqueous protein concentration, as well as test reliability.<b>Results</b>: Four index tests were identified in 11 studies: laser-flare photometry (LFP), optical coherence tomography, ocular flare analysis meter (OFAM) and the double-pass technique. The correlation between LFP and clinician grading was 0.40-0.93 and 0.87-0.94 for LFP and protein concentration. The double-pass technique showed no correlation with clinician grading and insufficient information was available for OFAM.<b>Conclusion</b>: LFP shows moderate to strong correlation with clinician grading and aqueous protein concentration. LFP could be a superior reference test compared to clinician AC flare grading for validating new index tests.",,pdf:https://discovery.ucl.ac.uk/10097154/3/Solebo_Liu%20AC%20Flare%20SR%20290919.pdf; doi:https://doi.org/10.1080/09273948.2019.1709650
+35434685,https://doi.org/10.1016/j.lanepe.2022.100381,Dosing interval strategies for two-dose COVID-19 vaccination in 13 middle-income countries of Europe: Health impact modelling and benefit-risk analysis.,"Liu Y, Pearson CAB, Sandmann FG, Barnard RC, Kim JH, CMMID COVID-19 Working Group, Flasche S, Jit M, Abbas K.",,The Lancet regional health. Europe,2022,2022-04-11,Y,"Quantitative Methods; Mathematical Modelling; Public Health Intervention; Vaccine Policy; Ve, Vaccine Efficacy; Covid-19; Sars-cov-2; Voc, Variant Of Concern; Aefi, Adverse Events Following Immunisation; Mic, Middle Income Country",,,"<h4>Background</h4>In settings where the COVID-19 vaccine supply is constrained, extending the intervals between the first and second doses of the COVID-19 vaccine may allow more people receive their first doses earlier. Our aim is to estimate the health impact of COVID-19 vaccination alongside benefit-risk assessment of different dosing intervals in 13 middle-income countries (MICs) of Europe.<h4>Methods</h4>We fitted a dynamic transmission model to country-level daily reported COVID-19 mortality in 13 MICs in Europe (Albania, Armenia, Azerbaijan, Belarus, Bosnia and Herzegovina, Bulgaria, Georgia, Republic of Moldova, Russian Federation, Serbia, North Macedonia, Turkey, and Ukraine). A vaccine product with characteristics similar to those of the Oxford/AstraZeneca COVID-19 (AZD1222) vaccine was used in the base case scenario and was complemented by sensitivity analyses around efficacies similar to other COVID-19 vaccines. Both fixed dosing intervals at 4, 8, 12, 16, and 20 weeks and dose-specific intervals that prioritise specific doses for certain age groups were tested. Optimal intervals minimise COVID-19 mortality between March 2021 and December 2022. We incorporated the emergence of variants of concern (VOCs) into the model and conducted a benefit-risk assessment to quantify the tradeoff between health benefits versus adverse events following immunisation.<h4>Findings</h4>In all countries modelled, optimal strategies are those that prioritise the first doses among older adults (60+ years) or adults (20+ years), which lead to dosing intervals longer than six months. In comparison, a four-week fixed dosing interval may incur 10.1% [range: 4.3% - 19.0%; n = 13 (countries)] more deaths. The rapid waning of the immunity induced by the first dose (i.e. with means ranging 60-120 days as opposed to 360 days in the base case) resulted in shorter optimal dosing intervals of 8-20 weeks. Benefit-risk ratios were the highest for fixed dosing intervals of 8-12 weeks.<h4>Interpretation</h4>We infer that longer dosing intervals of over six months could reduce COVID-19 mortality in MICs of Europe. Certain parameters, such as rapid waning of first-dose induced immunity and increased immune escape through the emergence of VOCs, could significantly shorten the optimal dosing intervals.<h4>Funding</h4>World Health Organization.",,doi:https://doi.org/10.1016/j.lanepe.2022.100381; doi:https://doi.org/10.1016/j.lanepe.2022.100381; html:https://europepmc.org/articles/PMC8996067; pdf:https://europepmc.org/articles/PMC8996067?pdf=render
 38082486,https://doi.org/10.1681/asn.0000000000000271,"Effects of Empagliflozin on Fluid Overload, Weight, and Blood Pressure in CKD.","Mayne KJ, Staplin N, Keane DF, Wanner C, Brenner S, Cejka V, Stegbauer J, Judge PK, Preiss D, Emberson J, Trinca D, Dayanandan R, Lee R, Nolan J, Omata A, Green JB, Cherney DZI, Hooi LS, Pontremoli R, Tuttle KR, Lees JS, Mark PB, Davies SJ, Hauske SJ, Steubl D, Brückmann M, Landray MJ, Baigent C, Haynes R, Herrington WG, EMPA-KIDNEY Collaborative Group.",,Journal of the American Society of Nephrology : JASN,2024,2023-12-12,Y,,,,"<h4>Significance statement</h4>SGLT2 inhibitors reduce risk of kidney progression, AKI, and cardiovascular disease, but the mechanisms of benefit are incompletely understood. Bioimpedance spectroscopy can estimate body water and fat mass. One quarter of the EMPA-KIDNEY bioimpedance substudy CKD population had clinically significant levels of bioimpedance-derived ""Fluid Overload"" at recruitment. Empagliflozin induced a prompt and sustained reduction in ""Fluid Overload,"" irrespective of sex, diabetes, and baseline N-terminal pro B-type natriuretic peptide or eGFR. No significant effect on bioimpedance-derived fat mass was observed. The effects of SGLT2 inhibitors on body water may be one of the contributing mechanisms by which they mediate effects on cardiovascular risk.<h4>Background</h4>CKD is associated with fluid excess that can be estimated by bioimpedance spectroscopy. We aimed to assess effects of sodium glucose co-transporter 2 inhibition on bioimpedance-derived ""Fluid Overload"" and adiposity in a CKD population.<h4>Methods</h4>EMPA-KIDNEY was a double-blind placebo-controlled trial of empagliflozin 10 mg once daily in patients with CKD at risk of progression. In a substudy, bioimpedance measurements were added to the main trial procedures at randomization and at 2- and 18-month follow-up visits. The substudy's primary outcome was the study-average difference in absolute ""Fluid Overload"" (an estimate of excess extracellular water) analyzed using a mixed model repeated measures approach.<h4>Results</h4>The 660 substudy participants were broadly representative of the 6609-participant trial population. Substudy mean baseline absolute ""Fluid Overload"" was 0.4±1.7 L. Compared with placebo, the overall mean absolute ""Fluid Overload"" difference among those allocated empagliflozin was -0.24 L (95% confidence interval [CI], -0.38 to -0.11), with similar sized differences at 2 and 18 months, and in prespecified subgroups. Total body water differences comprised between-group differences in extracellular water of -0.49 L (95% CI, -0.69 to -0.30, including the -0.24 L ""Fluid Overload"" difference) and a -0.30 L (95% CI, -0.57 to -0.03) difference in intracellular water. There was no significant effect of empagliflozin on bioimpedance-derived adipose tissue mass (-0.28 kg [95% CI, -1.41 to 0.85]). The between-group difference in weight was -0.7 kg (95% CI, -1.3 to -0.1).<h4>Conclusions</h4>In a broad range of patients with CKD, empagliflozin resulted in a sustained reduction in a bioimpedance-derived estimate of fluid overload, with no statistically significant effect on fat mass.<h4>Trial registration</h4>Clinicaltrials.gov: NCT03594110 ; EuDRACT: 2017-002971-24 ( https://eudract.ema.europa.eu/ ).",,doi:https://doi.org/10.1681/ASN.0000000000000271; html:https://europepmc.org/articles/PMC7615589; pdf:https://europepmc.org/articles/PMC7615589?pdf=render
 36947103,https://doi.org/10.1093/molbev/msad070,An Assessment of Quaternary Structure Functionality in Homomer Protein Complexes.,"Abrusán G, Foguet C.",,Molecular biology and evolution,2023,2023-04-01,Y,Protein complexes; Coevolution; Neutral evolution; Ligand binding; Homomers,,,"It has been recently suggested that a significant fraction of homomer protein-protein interfaces evolve neutrally, without contributing to function, due to a hydrophobic bias in missense mutations. However, the fraction of such gratuitous complexes is currently unknown. Here, we quantified the fraction of homodimers where multimerization is unlikely to contribute to their biochemical function. We show that: 1) ligand binding-site structure predicts whether a homomer is functional or not; the vast majority of homodimers with multichain binding-sites (MBS) are likely to be functional, while in homodimers with single-chain binding-sites (SBS) and small to medium interfaces, quaternary structure is unlikely to be functional in a significant fraction-35%, even up to 42%-of complexes; 2) the hydrophobicity of interfaces changes little with the strength of selection, and the amino acid composition of interfaces is shaped by the ""hydrophobic ratchet"" in both types, but they are not in a strict equilibrium with mutations; particularly cysteines are much more abundant in mutations than in interfaces or surfaces; 3) in MBS homomers, the interfaces are conserved, while in a high fraction of SBS homomers, the interface is not more conserved than the solvent-accessible surface; and 4) MBS homomer interfaces coevolve more strongly with ligand binding sites than the interfaces of SBS homomers, and MBS complexes have higher capacity to transfer information from ligands across the interfaces than SBS homomers, explaining the enrichment of allostery in the former.",,pdf:https://academic.oup.com/mbe/advance-article-pdf/doi/10.1093/molbev/msad070/49594873/msad070.pdf; doi:https://doi.org/10.1093/molbev/msad070; html:https://europepmc.org/articles/PMC10118308; pdf:https://europepmc.org/articles/PMC10118308?pdf=render
-32255392,https://doi.org/10.1080/09273948.2019.1709650,Non-invasive Instrument-Based Tests for Quantifying Anterior Chamber Flare in Uveitis: A Systematic Review.,"Liu X, McNally TW, Beese S, Downie LE, Solebo AL, Faes L, Husain S, Keane PA, Moore DJ, Denniston AK.",,Ocular immunology and inflammation,2021,2020-04-07,N,"Diagnostic test; Systematic review; Uveitis; optical coherence tomography; Laser Flare Photometry; Anterior Chamber Flare; Tyndall Effect; Aqueous Humor, Aqueous Humour; Aqueous Protein Concentration",,,"<b>Purpose</b>: Anterior chamber (AC) flare is a key sign for anterior uveitis. New instrument-based techniques for measuring AC flare can offer automation and objectivity. This review aims to identify objective instrument-based measures for AC flare.<b>Methods</b>: In this systematic review, we identified studies reporting correlation between instrument-based tests versus clinician AC flare grading, and/or aqueous protein concentration, as well as test reliability.<b>Results</b>: Four index tests were identified in 11 studies: laser-flare photometry (LFP), optical coherence tomography, ocular flare analysis meter (OFAM) and the double-pass technique. The correlation between LFP and clinician grading was 0.40-0.93 and 0.87-0.94 for LFP and protein concentration. The double-pass technique showed no correlation with clinician grading and insufficient information was available for OFAM.<b>Conclusion</b>: LFP shows moderate to strong correlation with clinician grading and aqueous protein concentration. LFP could be a superior reference test compared to clinician AC flare grading for validating new index tests.",,pdf:https://discovery.ucl.ac.uk/10097154/3/Solebo_Liu%20AC%20Flare%20SR%20290919.pdf; doi:https://doi.org/10.1080/09273948.2019.1709650
-35568032,https://doi.org/10.1016/j.ajhg.2022.04.009,Whole-exome sequencing identifies rare genetic variants associated with human plasma metabolites.,"Bomba L, Walter K, Guo Q, Surendran P, Kundu K, Nongmaithem S, Karim MA, Stewart ID, Langenberg C, Danesh J, Di Angelantonio E, Roberts DJ, Ouwehand WH, INTERVAL study, Dunham I, Butterworth AS, Soranzo N.",,American journal of human genetics,2022,2022-05-13,Y,Sequencing; Proteomics; drug targets; Metabolomics; Endophenotypes; Loss-of-function; Metabolon; Wgs; Wes; Rare Genetic Variant,,,"Metabolite levels measured in the human population are endophenotypes for biological processes. We combined sequencing data for 3,924 (whole-exome sequencing, WES, discovery) and 2,805 (whole-genome sequencing, WGS, replication) donors from a prospective cohort of blood donors in England. We used multiple approaches to select and aggregate rare genetic variants (minor allele frequency [MAF] < 0.1%) in protein-coding regions and tested their associations with 995 metabolites measured in plasma by using ultra-high-performance liquid chromatography-tandem mass spectrometry. We identified 40 novel associations implicating rare coding variants (27 genes and 38 metabolites), of which 28 (15 genes and 28 metabolites) were replicated. We developed algorithms to prioritize putative driver variants at each locus and used mediation and Mendelian randomization analyses to test directionality at associations of metabolite and protein levels at the ACY1 locus. Overall, 66% of reported associations implicate gene targets of approved drugs or bioactive drug-like compounds, contributing to drug targets' validating efforts.",,pdf:https://www.repository.cam.ac.uk/bitstreams/ce3ed268-a258-488b-b08c-4948d71b7460/download; doi:https://doi.org/10.1016/j.ajhg.2022.04.009; html:https://europepmc.org/articles/PMC9247822; pdf:https://europepmc.org/articles/PMC9247822?pdf=render
 33184391,https://doi.org/10.1038/s41598-020-76816-6,Prediction of vascular aging based on smartphone acquired PPG signals.,"Dall'Olio L, Curti N, Remondini D, Safi Harb Y, Asselbergs FW, Castellani G, Uh HW.",,Scientific reports,2020,2020-11-12,Y,,,,"Photoplethysmography (PPG) measured by smartphone has the potential for a large scale, non-invasive, and easy-to-use screening tool. Vascular aging is linked to increased arterial stiffness, which can be measured by PPG. We investigate the feasibility of using PPG to predict healthy vascular aging (HVA) based on two approaches: machine learning (ML) and deep learning (DL). We performed data preprocessing, including detrending, demodulating, and denoising on the raw PPG signals. For ML, ridge penalized regression has been applied to 38 features extracted from PPG, whereas for DL several convolutional neural networks (CNNs) have been applied to the whole PPG signals as input. The analysis has been conducted using the crowd-sourced Heart for Heart data. The prediction performance of ML using two features (AUC of 94.7%) - the a wave of the second derivative PPG and tpr, including four covariates, sex, height, weight, and smoking - was similar to that of the best performing CNN, 12-layer ResNet (AUC of 95.3%). Without having the heavy computational cost of DL, ML might be advantageous in finding potential biomarkers for HVA prediction. The whole workflow of the procedure is clearly described, and open software has been made available to facilitate replication of the results.",,pdf:https://www.nature.com/articles/s41598-020-76816-6.pdf; doi:https://doi.org/10.1038/s41598-020-76816-6; html:https://europepmc.org/articles/PMC7661535; pdf:https://europepmc.org/articles/PMC7661535?pdf=render
-35434685,https://doi.org/10.1016/j.lanepe.2022.100381,Dosing interval strategies for two-dose COVID-19 vaccination in 13 middle-income countries of Europe: Health impact modelling and benefit-risk analysis.,"Liu Y, Pearson CAB, Sandmann FG, Barnard RC, Kim JH, CMMID COVID-19 Working Group, Flasche S, Jit M, Abbas K.",,The Lancet regional health. Europe,2022,2022-04-11,Y,"Quantitative Methods; Mathematical Modelling; Public Health Intervention; Vaccine Policy; Ve, Vaccine Efficacy; Covid-19; Sars-cov-2; Voc, Variant Of Concern; Aefi, Adverse Events Following Immunisation; Mic, Middle Income Country",,,"<h4>Background</h4>In settings where the COVID-19 vaccine supply is constrained, extending the intervals between the first and second doses of the COVID-19 vaccine may allow more people receive their first doses earlier. Our aim is to estimate the health impact of COVID-19 vaccination alongside benefit-risk assessment of different dosing intervals in 13 middle-income countries (MICs) of Europe.<h4>Methods</h4>We fitted a dynamic transmission model to country-level daily reported COVID-19 mortality in 13 MICs in Europe (Albania, Armenia, Azerbaijan, Belarus, Bosnia and Herzegovina, Bulgaria, Georgia, Republic of Moldova, Russian Federation, Serbia, North Macedonia, Turkey, and Ukraine). A vaccine product with characteristics similar to those of the Oxford/AstraZeneca COVID-19 (AZD1222) vaccine was used in the base case scenario and was complemented by sensitivity analyses around efficacies similar to other COVID-19 vaccines. Both fixed dosing intervals at 4, 8, 12, 16, and 20 weeks and dose-specific intervals that prioritise specific doses for certain age groups were tested. Optimal intervals minimise COVID-19 mortality between March 2021 and December 2022. We incorporated the emergence of variants of concern (VOCs) into the model and conducted a benefit-risk assessment to quantify the tradeoff between health benefits versus adverse events following immunisation.<h4>Findings</h4>In all countries modelled, optimal strategies are those that prioritise the first doses among older adults (60+ years) or adults (20+ years), which lead to dosing intervals longer than six months. In comparison, a four-week fixed dosing interval may incur 10.1% [range: 4.3% - 19.0%; n = 13 (countries)] more deaths. The rapid waning of the immunity induced by the first dose (i.e. with means ranging 60-120 days as opposed to 360 days in the base case) resulted in shorter optimal dosing intervals of 8-20 weeks. Benefit-risk ratios were the highest for fixed dosing intervals of 8-12 weeks.<h4>Interpretation</h4>We infer that longer dosing intervals of over six months could reduce COVID-19 mortality in MICs of Europe. Certain parameters, such as rapid waning of first-dose induced immunity and increased immune escape through the emergence of VOCs, could significantly shorten the optimal dosing intervals.<h4>Funding</h4>World Health Organization.",,doi:https://doi.org/10.1016/j.lanepe.2022.100381; doi:https://doi.org/10.1016/j.lanepe.2022.100381; html:https://europepmc.org/articles/PMC8996067; pdf:https://europepmc.org/articles/PMC8996067?pdf=render
+35568032,https://doi.org/10.1016/j.ajhg.2022.04.009,Whole-exome sequencing identifies rare genetic variants associated with human plasma metabolites.,"Bomba L, Walter K, Guo Q, Surendran P, Kundu K, Nongmaithem S, Karim MA, Stewart ID, Langenberg C, Danesh J, Di Angelantonio E, Roberts DJ, Ouwehand WH, INTERVAL study, Dunham I, Butterworth AS, Soranzo N.",,American journal of human genetics,2022,2022-05-13,Y,Sequencing; Proteomics; drug targets; Metabolomics; Endophenotypes; Loss-of-function; Metabolon; Wgs; Wes; Rare Genetic Variant,,,"Metabolite levels measured in the human population are endophenotypes for biological processes. We combined sequencing data for 3,924 (whole-exome sequencing, WES, discovery) and 2,805 (whole-genome sequencing, WGS, replication) donors from a prospective cohort of blood donors in England. We used multiple approaches to select and aggregate rare genetic variants (minor allele frequency [MAF] < 0.1%) in protein-coding regions and tested their associations with 995 metabolites measured in plasma by using ultra-high-performance liquid chromatography-tandem mass spectrometry. We identified 40 novel associations implicating rare coding variants (27 genes and 38 metabolites), of which 28 (15 genes and 28 metabolites) were replicated. We developed algorithms to prioritize putative driver variants at each locus and used mediation and Mendelian randomization analyses to test directionality at associations of metabolite and protein levels at the ACY1 locus. Overall, 66% of reported associations implicate gene targets of approved drugs or bioactive drug-like compounds, contributing to drug targets' validating efforts.",,pdf:https://www.repository.cam.ac.uk/bitstreams/ce3ed268-a258-488b-b08c-4948d71b7460/download; doi:https://doi.org/10.1016/j.ajhg.2022.04.009; html:https://europepmc.org/articles/PMC9247822; pdf:https://europepmc.org/articles/PMC9247822?pdf=render
 31055854,https://doi.org/10.5694/mja2.50143,"Traumatic spinal cord injury in Victoria, 2007-2016.","Beck B, Cameron PA, Braaf S, Nunn A, Fitzgerald MC, Judson RT, Teague WJ, Lennox A, Middleton JW, Harrison JE, Gabbe BJ.",,The Medical journal of Australia,2019,2019-05-01,N,"Spinal cord injuries; epidemiology; Traumatology; Trauma, Nervous System",,,"<h4>Objective</h4>To investigate trends in the incidence and causes of traumatic spinal cord injury (TSCI) in Victoria over a 10-year period.<h4>Design, setting, participants</h4>Retrospective cohort study: analysis of Victorian State Trauma Registry (VSTR) data for people who sustained TSCIs during 2007-2016.<h4>Main outcomes and measures</h4>Temporal trends in population-based incidence rates of TSCI (injury to the spinal cord with an Abbreviated Injury Scale [AIS] score of 4 or more).<h4>Results</h4>There were 706 cases of TSCI, most the result of transport events (269 cases, 38%) or low falls (197 cases, 28%). The overall crude incidence of TSCI was 1.26 cases per 100 000 population (95% CI, 1.17-1.36 per 100 000 population), and did not change over the study period (incidence rate ratio [IRR], 1.01; 95% CI, 0.99-1.04). However, the incidence of TSCI resulting from low falls increased by 9% per year (95% CI, 4-15%). The proportion of TSCI cases classified as incomplete tetraplegia increased from 41% in 2007 to 55% in 2016 (P < 0.001). Overall in-hospital mortality was 15% (104 deaths), and was highest among people aged 65 years or more (31%, 70 deaths).<h4>Conclusions</h4>Given the devastating consequences of TSCI, improved primary prevention strategies are needed, particularly as the incidence of TSCI did not decline over the study period. The epidemiologic profile of TSCI has shifted, with an increasing number of TSCI events in older adults. This change has implications for prevention, acute and post-discharge care, and support.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.5694/mja2.50143; doi:https://doi.org/10.5694/mja2.50143
 33542327,https://doi.org/10.1038/s41598-021-82214-3,Classification of paediatric brain tumours by diffusion weighted imaging and machine learning.,"Novak J, Zarinabad N, Rose H, Arvanitis T, MacPherson L, Pinkey B, Oates A, Hales P, Grundy R, Auer D, Gutierrez DR, Jaspan T, Avula S, Abernethy L, Kaur R, Hargrave D, Mitra D, Bailey S, Davies N, Clark C, Peet A.",,Scientific reports,2021,2021-02-04,Y,,,,"To determine if apparent diffusion coefficients (ADC) can discriminate between posterior fossa brain tumours on a multicentre basis. A total of 124 paediatric patients with posterior fossa tumours (including 55 Medulloblastomas, 36 Pilocytic Astrocytomas and 26 Ependymomas) were scanned using diffusion weighted imaging across 12 different hospitals using a total of 18 different scanners. Apparent diffusion coefficient maps were produced and histogram data was extracted from tumour regions of interest. Total histograms and histogram metrics (mean, variance, skew, kurtosis and 10th, 20th and 50th quantiles) were used as data input for classifiers with accuracy determined by tenfold cross validation. Mean ADC values from the tumour regions of interest differed between tumour types, (ANOVA P < 0.001). A cut off value for mean ADC between Ependymomas and Medulloblastomas was found to be of 0.984 × 10<sup>-3</sup> mm<sup>2</sup> s<sup>-1</sup> with sensitivity 80.8% and specificity 80.0%. Overall classification for the ADC histogram metrics were 85% using Naïve Bayes and 84% for Random Forest classifiers. The most commonly occurring posterior fossa paediatric brain tumours can be classified using Apparent Diffusion Coefficient histogram values to a high accuracy on a multicentre basis.",,pdf:https://www.nature.com/articles/s41598-021-82214-3.pdf; doi:https://doi.org/10.1038/s41598-021-82214-3; html:https://europepmc.org/articles/PMC7862387; pdf:https://europepmc.org/articles/PMC7862387?pdf=render
-34903266,https://doi.org/10.1186/s13059-021-02561-2,CIDER: an interpretable meta-clustering framework for single-cell RNA-seq data integration and evaluation.,"Hu Z, Ahmed AA, Yau C.",,Genome biology,2021,2021-12-13,Y,Clustering; Confounding Factors; Single-cell Rna-seq,,,"Clustering of joint single-cell RNA-Seq (scRNA-Seq) data is often challenged by confounding factors, such as batch effects and biologically relevant variability. Existing batch effect removal methods typically require strong assumptions on the composition of cell populations being near identical across samples. Here, we present CIDER, a meta-clustering workflow based on inter-group similarity measures. We demonstrate that CIDER outperforms other scRNA-Seq clustering methods and integration approaches in both simulated and real datasets. Moreover, we show that CIDER can be used to assess the biological correctness of integration in real datasets, while it does not require the existence of prior cellular annotations.",,pdf:https://genomebiology.biomedcentral.com/counter/pdf/10.1186/s13059-021-02561-2; doi:https://doi.org/10.1186/s13059-021-02561-2; html:https://europepmc.org/articles/PMC8667531; pdf:https://europepmc.org/articles/PMC8667531?pdf=render
 33560344,https://doi.org/10.1210/clinem/dgab067,Association of Metformin with Susceptibility to COVID-19 in People with Type 2 Diabetes.,"Wang J, Cooper JM, Gokhale K, Acosta-Mena D, Dhalla S, Byne N, Chandan JS, Anand A, Okoth K, Subramanian A, Bangash MN, Jackson T, Zemedikun D, Taverner T, Hanif W, Ghosh S, Narendran P, Toulis KA, Tahrani AA, Surenthirakumaran R, Adderley NJ, Haroon S, Khunti K, Sainsbury C, Thomas GN, Nirantharakumar K.",,The Journal of clinical endocrinology and metabolism,2021,2021-04-01,Y,Type 2 diabetes mellitus; Metformin; Covid-19; Sars-cov-2 Infection,,,"<h4>Objective</h4>Diabetes has emerged as an important risk factor for mortality from COVID-19. Metformin, the most commonly prescribed glucose-lowering agent, has been proposed to influence susceptibility to and outcomes of COVID-19 via multiple mechanisms. We investigated whether, in patients with diabetes, metformin is associated with susceptibility to COVID-19 and its outcomes.<h4>Research design and methods</h4>We performed a propensity score-matched cohort study with active comparators using a large UK primary care dataset. Adults with type 2 diabetes patients and a current prescription for metformin and other glucose-lowering agents (MF+) were compared to those with a current prescription for glucose-lowering agents that did not include metformin (MF-). Outcomes were confirmed COVID-19, suspected/confirmed COVID-19, and associated mortality. A negative control outcome analysis (back pain) was also performed.<h4>Results</h4>There were 29 558 and 10 271 patients in the MF+ and MF- groups, respectively, who met the inclusion criteria. In the propensity score-matched analysis, the adjusted hazard ratios for suspected/confirmed COVID-19, confirmed COVID-19, and COVID-19-related mortality were 0.85 (95% CI 0.67, 1.08), 0.80 (95% CI 0.49, 1.30), and 0.87 (95% CI 0.34, 2.20) respectively. The negative outcome control analysis did not suggest unobserved confounding.<h4>Conclusion</h4>Current prescription of metformin was not associated with the risk of COVID-19 or COVID-19-related mortality. It is safe to continue prescribing metformin to improve glycemic control in patients with.",,pdf:https://academic.oup.com/jcem/article-pdf/106/5/1255/41848481/dgab067.pdf; doi:https://doi.org/10.1210/clinem/dgab067; html:https://europepmc.org/articles/PMC7928949
+34903266,https://doi.org/10.1186/s13059-021-02561-2,CIDER: an interpretable meta-clustering framework for single-cell RNA-seq data integration and evaluation.,"Hu Z, Ahmed AA, Yau C.",,Genome biology,2021,2021-12-13,Y,Clustering; Confounding Factors; Single-cell Rna-seq,,,"Clustering of joint single-cell RNA-Seq (scRNA-Seq) data is often challenged by confounding factors, such as batch effects and biologically relevant variability. Existing batch effect removal methods typically require strong assumptions on the composition of cell populations being near identical across samples. Here, we present CIDER, a meta-clustering workflow based on inter-group similarity measures. We demonstrate that CIDER outperforms other scRNA-Seq clustering methods and integration approaches in both simulated and real datasets. Moreover, we show that CIDER can be used to assess the biological correctness of integration in real datasets, while it does not require the existence of prior cellular annotations.",,pdf:https://genomebiology.biomedcentral.com/counter/pdf/10.1186/s13059-021-02561-2; doi:https://doi.org/10.1186/s13059-021-02561-2; html:https://europepmc.org/articles/PMC8667531; pdf:https://europepmc.org/articles/PMC8667531?pdf=render
 32702311,https://doi.org/10.1016/s1470-2045(20)30392-2,Effect of delays in the 2-week-wait cancer referral pathway during the COVID-19 pandemic on cancer survival in the UK: a modelling study.,"Sud A, Torr B, Jones ME, Broggio J, Scott S, Loveday C, Garrett A, Gronthoud F, Nicol DL, Jhanji S, Boyce SA, Williams M, Riboli E, Muller DC, Kipps E, Larkin J, Navani N, Swanton C, Lyratzopoulos G, McFerran E, Lawler M, Houlston R, Turnbull C.",,The Lancet. Oncology,2020,2020-07-20,Y,,,,"<h4>Background</h4>During the COVID-19 lockdown, referrals via the 2-week-wait urgent pathway for suspected cancer in England, UK, are reported to have decreased by up to 84%. We aimed to examine the impact of different scenarios of lockdown-accumulated backlog in cancer referrals on cancer survival, and the impact on survival per referred patient due to delayed referral versus risk of death from nosocomial infection with severe acute respiratory syndrome coronavirus 2.<h4>Methods</h4>In this modelling study, we used age-stratified and stage-stratified 10-year cancer survival estimates for patients in England, UK, for 20 common tumour types diagnosed in 2008-17 at age 30 years and older from Public Health England. We also used data for cancer diagnoses made via the 2-week-wait referral pathway in 2013-16 from the Cancer Waiting Times system from NHS Digital. We applied per-day hazard ratios (HRs) for cancer progression that we generated from observational studies of delay to treatment. We quantified the annual numbers of cancers at stage I-III diagnosed via the 2-week-wait pathway using 2-week-wait age-specific and stage-specific breakdowns. From these numbers, we estimated the aggregate number of lives and life-years lost in England for per-patient delays of 1-6 months in presentation, diagnosis, or cancer treatment, or a combination of these. We assessed three scenarios of a 3-month period of lockdown during which 25%, 50%, and 75% of the normal monthly volumes of symptomatic patients delayed their presentation until after lockdown. Using referral-to-diagnosis conversion rates and COVID-19 case-fatality rates, we also estimated the survival increment per patient referred.<h4>Findings</h4>Across England in 2013-16, an average of 6281 patients with stage I-III cancer were diagnosed via the 2-week-wait pathway per month, of whom 1691 (27%) would be predicted to die within 10 years from their disease. Delays in presentation via the 2-week-wait pathway over a 3-month lockdown period (with an average presentational delay of 2 months per patient) would result in 181 additional lives and 3316 life-years lost as a result of a backlog of referrals of 25%, 361 additional lives and 6632 life-years lost for a 50% backlog of referrals, and 542 additional lives and 9948 life-years lost for a 75% backlog in referrals. Compared with all diagnostics for the backlog being done in month 1 after lockdown, additional capacity across months 1-3 would result in 90 additional lives and 1662 live-years lost due to diagnostic delays for the 25% backlog scenario, 183 additional lives and 3362 life-years lost under the 50% backlog scenario, and 276 additional lives and 5075 life-years lost under the 75% backlog scenario. However, a delay in additional diagnostic capacity with provision spread across months 3-8 after lockdown would result in 401 additional lives and 7332 life-years lost due to diagnostic delays under the 25% backlog scenario, 811 additional lives and 14 873 life-years lost under the 50% backlog scenario, and 1231 additional lives and 22 635 life-years lost under the 75% backlog scenario. A 2-month delay in 2-week-wait investigatory referrals results in an estimated loss of between 0·0 and 0·7 life-years per referred patient, depending on age and tumour type.<h4>Interpretation</h4>Prompt provision of additional capacity to address the backlog of diagnostics will minimise deaths as a result of diagnostic delays that could add to those predicted due to expected presentational delays. Prioritisation of patient groups for whom delay would result in most life-years lost warrants consideration as an option for mitigating the aggregate burden of mortality in patients with cancer.<h4>Funding</h4>None.",,pdf:http://www.thelancet.com/article/S1470204520303922/pdf; doi:https://doi.org/10.1016/S1470-2045(20)30392-2; html:https://europepmc.org/articles/PMC7116538; pdf:https://europepmc.org/articles/PMC7116538?pdf=render
 34859219,https://doi.org/10.1093/braincomms/fcab275,Maternal immune activation downregulates schizophrenia genes in the foetal mouse brain.,"Handunnetthi L, Saatci D, Hamley JC, Knight JC.",,Brain communications,2021,2021-11-15,Y,Infection; Genetics; Schizophrenia; Immune; Maternal,,,"Susceptibility to schizophrenia is mediated by genetic and environmental risk factors. Maternal immune activation by infections during pregnancy is hypothesized to be a key environmental risk factor. However, little is known about how maternal immune activation contributes to schizophrenia pathogenesis. In this study, we investigated if maternal immune activation influences the expression of genes associated with schizophrenia in foetal mouse brains. We found that two sets of schizophrenia genes were downregulated more than expected by chance in the foetal mouse brain following maternal immune activation, namely those genes associated with schizophrenia through genome-wide association study (fold change = 1.93, false discovery rate = 4 × 10<sup>-4</sup>) and downregulated genes in adult schizophrenia brains (fold change = 1.51, false discovery rate = 4 × 10<sup>-10</sup>). We found that these genes mapped to key biological processes, such as neuronal cell adhesion. We also identified cortical excitatory neurons and inhibitory interneurons as the most vulnerable cell types to the deleterious effects of this interaction. Subsequently, we used gene expression information from herpes simplex virus 1 infection of neuronal precursor cells as orthogonal evidence to support our findings and to demonstrate that schizophrenia-associated cell adhesion genes, <i>PCDHA2, PCDHA3</i> and <i>PCDHA5</i>, were downregulated following herpes simplex virus 1 infection. Collectively, our results provide novel evidence for a link between genetic and environmental risk factors in schizophrenia pathogenesis. These findings carry important implications for early preventative strategies in schizophrenia.",,pdf:https://academic.oup.com/braincomms/article-pdf/3/4/fcab275/41365065/fcab275.pdf; doi:https://doi.org/10.1093/braincomms/fcab275; html:https://europepmc.org/articles/PMC8633770; pdf:https://europepmc.org/articles/PMC8633770?pdf=render
 32623924,https://doi.org/10.1161/hypertensionaha.119.14302,Estimated 24-Hour Urinary Sodium Excretion and Incident Cardiovascular Disease and Mortality Among 398 628 Individuals in UK Biobank.,"Elliott P, Muller DC, Schneider-Luftman D, Pazoki R, Evangelou E, Dehghan A, Neal B, Tzoulaki I.",,"Hypertension (Dallas, Tex. : 1979)",2020,2020-07-06,N,Cardiovascular diseases; Mortality; Blood pressure; risk,,,"We report on an analysis to explore the association between estimated 24-hour urinary sodium excretion (surrogate for sodium intake) and incident cardiovascular disease (CVD) and mortality. Data were obtained from 398 628 UK Biobank prospective cohort study participants (40-69 years) recruited between 2006 and 2010, with no history of CVD, renal disease, diabetes mellitus or cancer, and cardiovascular events and mortality recorded during follow-up. Hazard ratios between 24-hour sodium excretion were estimated from spot urinary sodium concentrations across incident CVD and its components and all-cause and cause-specific mortality. In restricted cubic splines analyses, there was little evidence for an association between estimated 24-hour sodium excretion and CVD, coronary heart disease, or stroke; hazard ratios for CVD (95% CIs) for the 15th and 85th percentiles (2.5 and 4.2 g/day, respectively) compared with the 50th percentile of estimated sodium excretion (3.2 g/day) were 1.05 (1.01-1.10) and 0.96 (0.92-1.00), respectively. An inverse association was observed with heart failure, but that was no longer apparent in sensitivity analysis. A J-shaped association was observed between estimated sodium excretion and mortality. Our findings do not support a J-shaped association of estimated sodium excretion with CVD, although such an association was apparent for all-cause and cause-specific mortality across a wide range of diseases. Reasons for these differences are unclear; methodological limitations, including the use of estimating equations based on spot urinary data, need to be considered in interpreting our findings.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/HYPERTENSIONAHA.119.14302; doi:https://doi.org/10.1161/HYPERTENSIONAHA.119.14302
@@ -2027,8 +2029,8 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 31492797,https://doi.org/10.1136/bmjopen-2019-032165,Evaluation of the impact of the GRACE risk score on the management and outcome of patients hospitalised with non-ST elevation acute coronary syndrome in the UK: protocol of the UKGRIS cluster-randomised registry-based trial.,"Everett CC, Fox KA, Reynolds C, Fernandez C, Sharples L, Stocken DD, Carruthers K, Hemingway H, Yan AT, Goodman SG, Brieger D, Chew DP, Gale CP.",,BMJ open,2019,2019-09-05,Y,Risk stratification; acute coronary syndrome; Grace; Nsteacs; Cluster Randomised Trial; Guideline-indicated Treatment,"Better, Faster and More Efficient Clinical Trials",,"<h4>Introduction</h4>For non-ST-segment elevation acute coronary syndrome (NSTEACS) there is a gap between the use of class I guideline recommended therapies and clinical practice. The Global Registry of Acute Coronary Events (GRACE) risk score is recommended in international guidelines for the risk stratification of NSTEACS, but its impact on adherence to guideline-indicated treatments and reducing adverse clinical outcomes is unknown. The objective of the UK GRACE Risk Score Intervention Study (UKGRIS) trial is to assess the effectiveness of the GRACE risk score tool and associated treatment recommendations on the use of guideline-indicated care and clinical outcomes.<h4>Methods and analysis</h4>The UKGRIS, a parallel-group cluster randomised registry-based controlled trial, will allocate hospitals in a 1:1 ratio to manage NSTEACS by standard care or according to the GRACE risk score and associated international guidelines. UKGRIS will recruit a minimum of 3000 patients from at least 30 English National Health Service hospitals and collect healthcare data from national electronic health records. The co-primary endpoints are the use of guideline-indicated therapies, and the composite of cardiovascular death, non-fatal myocardial infarction, new onset heart failure hospitalisation or cardiovascular readmission at 12 months. Secondary endpoints include duration of inpatient hospital stay over 12 months, EQ-5D-5L responses and utilities, unscheduled revascularisation and the components of the composite endpoint over 12 months follow-up.<h4>Ethics and dissemination</h4>The study has ethical approval (North East - Tyne & Wear South Research Ethics Committee reference: 14/NE/1180). Findings will be announced at relevant conferences and published in peer-reviewed journals in line with the funder's open access policy.<h4>Trial registration number</h4>ISRCTN29731761; Pre-results.",,pdf:https://bmjopen.bmj.com/content/bmjopen/9/9/e032165.full.pdf; doi:https://doi.org/10.1136/bmjopen-2019-032165; html:https://europepmc.org/articles/PMC6731819; pdf:https://europepmc.org/articles/PMC6731819?pdf=render
 38555664,https://doi.org/10.1016/j.envint.2024.108602,A tool to assess risk of bias in non-randomized follow-up studies of exposure effects (ROBINS-E).,"Higgins JPT, Morgan RL, Rooney AA, Taylor KW, Thayer KA, Silva RA, Lemeris C, Akl EA, Bateson TF, Berkman ND, Glenn BS, Hróbjartsson A, LaKind JS, McAleenan A, Meerpohl JJ, Nachman RM, Obbagy JE, O'Connor A, Radke EG, Savović J, Schünemann HJ, Shea B, Tilling K, Verbeek J, Viswanathan M, Sterne JAC.",,Environment international,2024,2024-03-24,N,Exposure; Environmental; epidemiology; Selection Bias; Confounding; Risk Of Bias; Misclassification/measurement Bias,,,"<h4>Background</h4>Observational epidemiologic studies provide critical data for the evaluation of the potential effects of environmental, occupational and behavioural exposures on human health. Systematic reviews of these studies play a key role in informing policy and practice. Systematic reviews should incorporate assessments of the risk of bias in results of the included studies.<h4>Objective</h4>To develop a new tool, Risk Of Bias In Non-randomized Studies - of Exposures (ROBINS-E) to assess risk of bias in estimates from cohort studies of the causal effect of an exposure on an outcome.<h4>Methods and results</h4>ROBINS-E was developed by a large group of researchers from diverse research and public health disciplines through a series of working groups, in-person meetings and pilot testing phases. The tool aims to assess the risk of bias in a specific result (exposure effect estimate) from an individual observational study that examines the effect of an exposure on an outcome. A series of preliminary considerations informs the core ROBINS-E assessment, including details of the result being assessed and the causal effect being estimated. The assessment addresses bias within seven domains, through a series of 'signalling questions'. Domain-level judgements about risk of bias are derived from the answers to these questions, then combined to produce an overall risk of bias judgement for the result, together with judgements about the direction of bias.<h4>Conclusion</h4>ROBINS-E provides a standardized framework for examining potential biases in results from cohort studies. Future work will produce variants of the tool for other epidemiologic study designs (e.g. case-control studies). We believe that ROBINS-E represents an important development in the integration of exposure assessment, evidence synthesis and causal inference.",,doi:https://doi.org/10.1016/j.envint.2024.108602
 31702773,https://doi.org/10.1093/bioinformatics/btz796,Model selection for metabolomics: predicting diagnosis of coronary artery disease using automated machine learning.,"Orlenko A, Kofink D, Lyytikäinen LP, Nikus K, Mishra P, Kuukasjärvi P, Karhunen PJ, Kähönen M, Laurikka JO, Lehtimäki T, Asselbergs FW, Moore JH.",,"Bioinformatics (Oxford, England)",2020,2020-03-01,Y,,,,"<h4>Motivation</h4>Selecting the optimal machine learning (ML) model for a given dataset is often challenging. Automated ML (AutoML) has emerged as a powerful tool for enabling the automatic selection of ML methods and parameter settings for the prediction of biomedical endpoints. Here, we apply the tree-based pipeline optimization tool (TPOT) to predict angiographic diagnoses of coronary artery disease (CAD). With TPOT, ML models are represented as expression trees and optimal pipelines discovered using a stochastic search method called genetic programing. We provide some guidelines for TPOT-based ML pipeline selection and optimization-based on various clinical phenotypes and high-throughput metabolic profiles in the Angiography and Genes Study (ANGES).<h4>Results</h4>We analyzed nuclear magnetic resonance-derived lipoprotein and metabolite profiles in the ANGES cohort with a goal to identify the role of non-obstructive CAD patients in CAD diagnostics. We performed a comparative analysis of TPOT-generated ML pipelines with selected ML classifiers, optimized with a grid search approach, applied to two phenotypic CAD profiles. As a result, TPOT-generated ML pipelines that outperformed grid search optimized models across multiple performance metrics including balanced accuracy and area under the precision-recall curve. With the selected models, we demonstrated that the phenotypic profile that distinguishes non-obstructive CAD patients from no CAD patients is associated with higher precision, suggesting a discrepancy in the underlying processes between these phenotypes.<h4>Availability and implementation</h4>TPOT is freely available via http://epistasislab.github.io/tpot/.<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online.",,pdf:https://academic.oup.com/bioinformatics/article-pdf/36/6/1772/36089203/btz796.pdf; doi:https://doi.org/10.1093/bioinformatics/btz796; html:https://europepmc.org/articles/PMC7703753; pdf:https://europepmc.org/articles/PMC7703753?pdf=render
-35861818,https://doi.org/10.1161/jaha.121.025473,Interatrial Block Predicts Life-Threatening Arrhythmias in Dilated Cardiomyopathy.,"Henkens MTHM, López Martínez H, Weerts J, Sammani A, Raafs AG, Verdonschot JAJ, van de Leur RR, Sikking MA, Stroeks S, van Empel VPM, Brunner-La Rocca HP, van Stipdonk AMW, Farmakis D, Hazebroek MR, Vernooy K, Bayés-de-Luna A, Asselbergs FW, Bayés-Genís A, Heymans SRB.",,Journal of the American Heart Association,2022,2022-07-15,Y,Electrocardiography; Dilated cardiomyopathy; Sudden Cardiac Death; Interatrial Block; Non‐ischemic Cardiomyopathy; Life‐threatening Arrhythmias,,,"Background Interatrial block (IAB) has been associated with supraventricular arrhythmias and stroke, and even with sudden cardiac death in the general population. Whether IAB is associated with life-threatening arrhythmias (LTA) and sudden cardiac death in dilated cardiomyopathy (DCM) remains unknown. This study aimed to determine the association between IAB and LTA in ambulant patients with DCM. Methods and Results A derivation cohort (Maastricht Dilated Cardiomyopathy Registry; N=469) and an external validation cohort (Utrecht Cardiomyopathy Cohort; N=321) were used for this study. The presence of IAB (P-wave duration>120 milliseconds) or atrial fibrillation (AF) was determined using digital calipers by physicians blinded to the study data. In the derivation cohort, IAB and AF were present in 291 (62%) and 70 (15%) patients with DCM, respectively. LTA (defined as sudden cardiac death, justified shock from implantable cardioverter-defibrillator or anti-tachypacing, or hemodynamic unstable ventricular fibrillation/tachycardia) occurred in 49 patients (3 with no IAB, 35 with IAB, and 11 patients with AF, respectively; median follow-up, 4.4 years [2.1; 7.4]). The LTA-free survival distribution significantly differed between IAB or AF versus no IAB (both <i>P</i><0.01), but not between IAB versus AF (<i>P</i>=0.999). This association remained statistically significant in the multivariable model (IAB: HR, 4.8 (1.4-16.1), <i>P</i>=0.013; AF: HR, 6.4 (1.7-24.0), <i>P</i>=0.007). In the external validation cohort, the survival distribution was also significantly worse for IAB or AF versus no IAB (<i>P</i>=0.037; <i>P</i>=0.005), but not for IAB versus AF (<i>P</i>=0.836). Conclusions IAB is an easy to assess, widely applicable marker associated with LTA in DCM. IAB and AF seem to confer similar risk of LTA. Further research on IAB in DCM, and on the management of IAB in DCM is warranted.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.121.025473; doi:https://doi.org/10.1161/JAHA.121.025473; html:https://europepmc.org/articles/PMC9707810; pdf:https://europepmc.org/articles/PMC9707810?pdf=render
 31653530,https://doi.org/10.1016/j.echo.2019.08.015,A Practical Guide to Assess the Reproducibility of Echocardiographic Measurements.,"Bunting KV, Steeds RP, Slater K, Rogers JK, Gkoutos GV, Kotecha D.",,Journal of the American Society of Echocardiography : official publication of the American Society of Echocardiography,2019,2019-10-22,N,Reproducibility; Echocardiography; Repeatability; reliability,,,"Echocardiography plays an essential role in the diagnosis and assessment of cardiovascular disease. Measurements derived from echocardiography are also used to determine the severity of disease, its progression over time, and to aid in the choice of optimal therapy. It is therefore clinically important that echocardiographic measurements be reproducible, repeatable, and reliable. There are a variety of statistical tests available to assess these parameters, and in this article the authors summarize those available for use by echocardiographers to improve their clinical practice. Correlation coefficients, linear regression, Bland-Altman plots, and the coefficient of variation are explored, along with their limitations. The authors also provide an online tool for the easy calculation of these statistics in the clinical environment (www.birmingham.ac.uk/echo). Quantifying and enhancing the reproducibility of echocardiography has important potential to improve the value of echocardiography as the basis for good clinical decision-making.",,pdf:http://www.onlinejase.com/article/S0894731719309460/pdf; doi:https://doi.org/10.1016/j.echo.2019.08.015
+35861818,https://doi.org/10.1161/jaha.121.025473,Interatrial Block Predicts Life-Threatening Arrhythmias in Dilated Cardiomyopathy.,"Henkens MTHM, López Martínez H, Weerts J, Sammani A, Raafs AG, Verdonschot JAJ, van de Leur RR, Sikking MA, Stroeks S, van Empel VPM, Brunner-La Rocca HP, van Stipdonk AMW, Farmakis D, Hazebroek MR, Vernooy K, Bayés-de-Luna A, Asselbergs FW, Bayés-Genís A, Heymans SRB.",,Journal of the American Heart Association,2022,2022-07-15,Y,Electrocardiography; Dilated cardiomyopathy; Sudden Cardiac Death; Interatrial Block; Non‐ischemic Cardiomyopathy; Life‐threatening Arrhythmias,,,"Background Interatrial block (IAB) has been associated with supraventricular arrhythmias and stroke, and even with sudden cardiac death in the general population. Whether IAB is associated with life-threatening arrhythmias (LTA) and sudden cardiac death in dilated cardiomyopathy (DCM) remains unknown. This study aimed to determine the association between IAB and LTA in ambulant patients with DCM. Methods and Results A derivation cohort (Maastricht Dilated Cardiomyopathy Registry; N=469) and an external validation cohort (Utrecht Cardiomyopathy Cohort; N=321) were used for this study. The presence of IAB (P-wave duration>120 milliseconds) or atrial fibrillation (AF) was determined using digital calipers by physicians blinded to the study data. In the derivation cohort, IAB and AF were present in 291 (62%) and 70 (15%) patients with DCM, respectively. LTA (defined as sudden cardiac death, justified shock from implantable cardioverter-defibrillator or anti-tachypacing, or hemodynamic unstable ventricular fibrillation/tachycardia) occurred in 49 patients (3 with no IAB, 35 with IAB, and 11 patients with AF, respectively; median follow-up, 4.4 years [2.1; 7.4]). The LTA-free survival distribution significantly differed between IAB or AF versus no IAB (both <i>P</i><0.01), but not between IAB versus AF (<i>P</i>=0.999). This association remained statistically significant in the multivariable model (IAB: HR, 4.8 (1.4-16.1), <i>P</i>=0.013; AF: HR, 6.4 (1.7-24.0), <i>P</i>=0.007). In the external validation cohort, the survival distribution was also significantly worse for IAB or AF versus no IAB (<i>P</i>=0.037; <i>P</i>=0.005), but not for IAB versus AF (<i>P</i>=0.836). Conclusions IAB is an easy to assess, widely applicable marker associated with LTA in DCM. IAB and AF seem to confer similar risk of LTA. Further research on IAB in DCM, and on the management of IAB in DCM is warranted.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.121.025473; doi:https://doi.org/10.1161/JAHA.121.025473; html:https://europepmc.org/articles/PMC9707810; pdf:https://europepmc.org/articles/PMC9707810?pdf=render
 34396248,https://doi.org/10.1016/j.jaccao.2020.07.001,Prediction of Lifetime and 10-Year Risk of Cancer in Individual Patients With Established Cardiovascular Disease.,"van 't Klooster CC, Ridker PM, Cook NR, Aerts JGJV, Westerink J, Asselbergs FW, van der Graaf Y, Visseren FLJ, UCC-SMART Study Group.",,JACC. CardioOncology,2020,2020-08-28,Y,"Lung cancer; Colorectal Cancer; Risk Prediction; Crp, C-reactive Protein; Sd, Standard Deviation; Cvd, Cardiovascular Disease; Ci, Confidence Interval; Aic, Akaike’s Information Criterion",,,"<h4>Background</h4>Cardiovascular disease (CVD) and cancer share many common risk factors; patients with CVD also may be at risk of developing cancer.<h4>Objectives</h4>The aim of this study was to derive and externally validate prediction models for the estimation of lifetime and 10-year risk for total, colorectal, and lung cancer in patients with established CVD.<h4>Methods</h4>Data from patients with established CVD from the UCC-SMART cohort (N = 7,280) were used for model development, and from the CANTOS trial (N = 9,322) for model validation. Predictors were selected based on previously published cancer risk scores, clinical availability, and presence in the derivation dataset. Fine and Gray competing risk-adjusted lifetime models were developed for the outcomes total, colorectal, and lung cancer.<h4>Results</h4>Selected predictors were age, sex, smoking, weight, height, alcohol use, antiplatelet use, diabetes, and C-reactive protein. External calibration for the 4-year risk of lung, colorectal, and total cancer was reasonable in our models, as was discrimination with C-statistics of 0.74, 0.64, and 0.63, respectively. Median predicted lifetime and 10-year risks in CANTOS were 26% (range 1% to 52%) and 13% (range 1% to 31%) for total cancer; 4% (range 0% to 13%) and 2% (range 0% to 6%) for colorectal cancer; and 5% (range 0% to 37%) and 2% (range 0% to 24%) for lung cancer.<h4>Conclusions</h4>Lifetime and 10-year risk of total, colorectal, and lung cancer can be estimated reasonably well in patients with established CVD with readily available clinical predictors. With additional study, these tools could be used in clinical practice to further aid in the emphasis of healthy lifestyle changes and to guide thresholds for targeted diagnostics and screening.",,doi:https://doi.org/10.1016/j.jaccao.2020.07.001; doi:https://doi.org/10.1016/j.jaccao.2020.07.001; html:https://europepmc.org/articles/PMC8352343; pdf:https://europepmc.org/articles/PMC8352343?pdf=render
 33021418,https://doi.org/10.1080/09273948.2020.1799038,Noninvasive Instrument-based Tests for Detecting and Measuring Vitreous Inflammation in Uveitis: A Systematic Review.,"Liu X, Hui BT, Way C, Beese S, Adriano A, Keane PA, Moore DJ, Denniston AK.",,Ocular immunology and inflammation,2022,2020-10-06,Y,Imaging; Diagnostic test; Systematic review; Vitreous; ultrasound; Uveitis; optical coherence tomography; Vitritis; Retinal Photography; Vitreous Inflammation,,,"<h4>Purpose</h4>This systematic review aims to identify instrument-based tests for quantifying vitreous inflammation in uveitis, report the test reliability and the level of correlation with clinician grading.<h4>Methods</h4>Studies describing instrument-based tests for detecting vitreous inflammation were identified by searching bibliographic databases and trials registers. Test reliability measures and level of correlation with clinician vitreous haze grading are extracted.<h4>Results</h4>Twelve studies describing ultrasound, optical coherence tomography (OCT), and retinal photography for detecting vitreous inflammation were included: Ultrasound was used for detection of disease features, whereas OCT and retinal photography provided quantifiable measurements. Correlation with clinician grading for OCT was 0.53-0.60 (three studies) and for retinal photography was 0.51 (1 study). Both instruments showed high inter- and intra-observer reliability (>0.70 intraclass correlation and Cohen's kappa), where reported in four studies.<h4>Conclusion</h4>Retinal photography and OCT are able to detect and measure vitreous inflammation. Both techniques are reliable, automatable, and warrant further evaluation.",,pdf:https://www.tandfonline.com/doi/pdf/10.1080/09273948.2020.1799038?needAccess=true; doi:https://doi.org/10.1080/09273948.2020.1799038; html:https://europepmc.org/articles/PMC8935946; pdf:https://europepmc.org/articles/PMC8935946?pdf=render
 34347787,https://doi.org/10.1371/journal.pone.0253809,Developing a Natural Language Processing tool to identify perinatal self-harm in electronic healthcare records.,"Ayre K, Bittar A, Kam J, Verma S, Howard LM, Dutta R.",,PloS one,2021,2021-08-04,Y,,,,"<h4>Background</h4>Self-harm occurring within pregnancy and the postnatal year (""perinatal self-harm"") is a clinically important yet under-researched topic. Current research likely under-estimates prevalence due to methodological limitations. Electronic healthcare records (EHRs) provide a source of clinically rich data on perinatal self-harm.<h4>Aims</h4>(1) To create a Natural Language Processing (NLP) tool that can, with acceptable precision and recall, identify mentions of acts of perinatal self-harm within EHRs. (2) To use this tool to identify service-users who have self-harmed perinatally, based on their EHRs.<h4>Methods</h4>We used the Clinical Record Interactive Search system to extract de-identified EHRs of secondary mental healthcare service-users at South London and Maudsley NHS Foundation Trust. We developed a tool that applied several layers of linguistic processing based on the spaCy NLP library for Python. We evaluated mention-level performance in the following domains: span, status, temporality and polarity. Evaluation was done against a manually coded reference standard. Mention-level performance was reported as precision, recall, F-score and Cohen's kappa for each domain. Performance was also assessed at 'service-user' level and explored whether a heuristic rule improved this. We report per-class statistics for service-user performance, as well as likelihood ratios and post-test probabilities.<h4>Results</h4>Mention-level performance: micro-averaged F-score, precision and recall for span, polarity and temporality >0.8. Kappa for status 0.68, temporality 0.62, polarity 0.91. Service-user level performance with heuristic: F-score, precision, recall of minority class 0.69, macro-averaged F-score 0.81, positive LR 9.4 (4.8-19), post-test probability 69.0% (53-82%). Considering the task difficulty, the tool performs well, although temporality was the attribute with the lowest level of annotator agreement.<h4>Conclusions</h4>It is feasible to develop an NLP tool that identifies, with acceptable validity, mentions of perinatal self-harm within EHRs, although with limitations regarding temporality. Using a heuristic rule, it can also function at a service-user-level.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0253809&type=printable; doi:https://doi.org/10.1371/journal.pone.0253809; html:https://europepmc.org/articles/PMC8336818; pdf:https://europepmc.org/articles/PMC8336818?pdf=render
@@ -2037,12 +2039,12 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 32685697,https://doi.org/10.12688/wellcomeopenres.15788.1,The contribution of pre-symptomatic infection to the transmission dynamics of COVID-2019.,"Liu Y, Centre for Mathematical Modelling of Infectious Diseases nCoV Working Group, Funk S, Flasche S.",,Wellcome open research,2020,2020-04-01,Y,Incubation period; Serial Interval; Covid-19; Pre-symptomatic Transmission,,,"<b>Background:</b> Pre-symptomatic transmission can be a key determinant of the effectiveness of containment and mitigation strategies for infectious diseases, particularly if interventions rely on syndromic case finding. For COVID-19, infections in the absence of apparent symptoms have been reported frequently alongside circumstantial evidence for asymptomatic or pre-symptomatic transmission. We estimated the potential contribution of pre-symptomatic cases to COVID-19 transmission. <b>Methods:</b> Using the probability for symptom onset on a given day inferred from the incubation period, we attributed the serial interval reported from Shenzen, China, into likely pre-symptomatic and symptomatic transmission. We used the serial interval derived for cases isolated more than 6 days after symptom onset as the no active case finding scenario and the unrestricted serial interval as the active case finding scenario. We reported the estimate assuming no correlation between the incubation period and the serial interval alongside a range indicating alternative assumptions of positive and negative correlation. <b>Results:</b> We estimated that 23% (range accounting for correlation: 12 - 28%) of transmissions in Shenzen may have originated from pre-symptomatic infections. Through accelerated case isolation following symptom onset, this percentage increased to 46% (21 - 46%), implying that about 35% of secondary infections among symptomatic cases have been prevented. These results were robust to using reported incubation periods and serial intervals from other settings. <b>Conclusions:</b> Pre-symptomatic transmission may be essential to consider for containment and mitigation strategies for COVID-19.",,doi:https://doi.org/10.12688/wellcomeopenres.15788.1; html:https://europepmc.org/articles/PMC7324944; pdf:https://europepmc.org/articles/PMC7324944?pdf=render
 33453763,https://doi.org/10.1016/s2468-1253(21)00005-4,Impact of the COVID-19 pandemic on the detection and management of colorectal cancer in England: a population-based study.,"Morris EJA, Goldacre R, Spata E, Mafham M, Finan PJ, Shelton J, Richards M, Spencer K, Emberson J, Hollings S, Curnow P, Gair D, Sebag-Montefiore D, Cunningham C, Rutter MD, Nicholson BD, Rashbass J, Landray M, Collins R, Casadei B, Baigent C.",,The lancet. Gastroenterology & hepatology,2021,2021-01-15,Y,,,,"<h4>Background</h4>There are concerns that the COVID-19 pandemic has had a negative effect on cancer care but there is little direct evidence to quantify any effect. This study aims to investigate the impact of the COVID-19 pandemic on the detection and management of colorectal cancer in England.<h4>Methods</h4>Data were extracted from four population-based datasets spanning NHS England (the National Cancer Cancer Waiting Time Monitoring, Monthly Diagnostic, Secondary Uses Service Admitted Patient Care and the National Radiotherapy datasets) for all referrals, colonoscopies, surgical procedures, and courses of rectal radiotherapy from Jan 1, 2019, to Oct 31, 2020, related to colorectal cancer in England. Differences in patterns of care were investigated between 2019 and 2020. Percentage reductions in monthly numbers and proportions were calculated.<h4>Findings</h4>As compared to the monthly average in 2019, in April, 2020, there was a 63% (95% CI 53-71) reduction (from 36 274 to 13 440) in the monthly number of 2-week referrals for suspected cancer and a 92% (95% CI 89-95) reduction in the number of colonoscopies (from 46 441 to 3484). Numbers had just recovered by October, 2020. This resulted in a 22% (95% CI 8-34) relative reduction in the number of cases referred for treatment (from a monthly average of 2781 in 2019 to 2158 referrals in April, 2020). By October, 2020, the monthly rate had returned to 2019 levels but did not exceed it, suggesting that, from April to October, 2020, over 3500 fewer people had been diagnosed and treated for colorectal cancer in England than would have been expected. There was also a 31% (95% CI 19-42) relative reduction in the numbers receiving surgery in April, 2020, and a lower proportion of laparoscopic and a greater proportion of stoma-forming procedures, relative to the monthly average in 2019. By October, 2020, laparoscopic surgery and stoma rates were similar to 2019 levels. For rectal cancer, there was a 44% (95% CI 17-76) relative increase in the use of neoadjuvant radiotherapy in April, 2020, relative to the monthly average in 2019, due to greater use of short-course regimens. Although in June, 2020, there was a drop in the use of short-course regimens, rates remained above 2019 levels until October, 2020.<h4>Interpretation</h4>The COVID-19 pandemic has led to a sustained reduction in the number of people referred, diagnosed, and treated for colorectal cancer. By October, 2020, achievement of care pathway targets had returned to 2019 levels, albeit with smaller volumes of patients and with modifications to usual practice. As pressure grows in the NHS due to the second wave of COVID-19, urgent action is needed to address the growing burden of undetected and untreated colorectal cancer in England.<h4>Funding</h4>Cancer Research UK, the Medical Research Council, Public Health England, Health Data Research UK, NHS Digital, and the National Institute for Health Research Oxford Biomedical Research Centre.",,pdf:https://eprint.ncl.ac.uk/fulltext.aspx?url=273130/2B902152-4D86-41C6-A6F0-0A8D85C82361.pdf&pub_id=273130; doi:https://doi.org/10.1016/S2468-1253(21)00005-4; html:https://europepmc.org/articles/PMC7808901; pdf:https://europepmc.org/articles/PMC7808901?pdf=render
 37210036,https://doi.org/10.1016/j.jacc.2023.05.005,Individualized Family Screening for Arrhythmogenic Right Ventricular Cardiomyopathy.,"Muller SA, Gasperetti A, Bosman LP, Schmidt AF, Baas AF, Amin AS, Houweling AC, Wilde AAM, Compagnucci P, Targetti M, Casella M, Calò L, Tondo C, van der Harst P, Asselbergs FW, van Tintelen JP, Oerlemans MIFJ, Te Riele ASJM.",,Journal of the American College of Cardiology,2023,2023-05-18,N,ventricular arrhythmia; Predictors; Screening Interval; Arvc; Family Screening,,,"<h4>Background</h4>Clinical guidelines recommend regular screening for arrhythmogenic right ventricular cardiomyopathy (ARVC) to monitor at-risk relatives, resulting in a significant burden on clinical resources. Prioritizing relatives on their probability of developing definite ARVC may provide more efficient patient care.<h4>Objectives</h4>The aim of this study was to determine the predictors and probability of ARVC development over time among at-risk relatives.<h4>Methods</h4>A total of 136 relatives (46% men, median age 25.5 years [IQR: 15.8-44.4 years]) from the Netherlands Arrhythmogenic Cardiomyopathy Registry without definite ARVC by 2010 task force criteria were included. Phenotype was ascertained using electrocardiography, Holter monitoring, and cardiac imaging. Subjects were divided into groups with ""possible ARVC"" (only genetic or familial predisposition) and ""borderline ARVC"" (1 minor task force criterion plus genetic or familial predisposition). Cox regression was performed to determine predictors and multistate modeling to assess the probability of ARVC development. Results were replicated in an unrelated Italian cohort (57% men, median age 37.0 years [IQR: 25.4-50.4 years]).<h4>Results</h4>At baseline, 93 subjects (68%) had possible ARVC, and 43 (32%) had borderline ARVC. Follow-up was available for 123 relatives (90%). After 8.1 years (IQR: 4.2-11.4 years), 41 (33%) had developed definite ARVC. Independent of baseline phenotype, symptomatic subjects (P = 0.014) and those 20 to 30 years of age (P = 0.002) had a higher hazard of developing definite ARVC. Furthermore, patients with borderline ARVC had a higher probability of developing definite ARVC compared with those with possible ARVC (1-year probability 13% vs 0.6%, 3-year probability 35% vs 5%; P < 0.01). External replication showed comparable results (P > 0.05).<h4>Conclusions</h4>Symptomatic relatives, those 20 to 30 years of age, and those with borderline ARVC have a higher probability of developing definite ARVC. These patients may benefit from more frequent follow-up, while others may be monitored less often.",,doi:https://doi.org/10.1016/j.jacc.2023.05.005
+37474660,https://doi.org/10.1038/s41591-023-02445-x,Considerations for patient and public involvement and engagement in health research.,"Aiyegbusi OL, McMullan C, Hughes SE, Turner GM, Subramanian A, Hotham R, Davies EH, Frost C, Alder Y, Agyen L, Buckland L, Camaradou J, Chong A, Jeyes F, Kumar S, Matthews KL, Moore P, Ormerod J, Price G, Saint-Cricq M, Stanton D, Walker A, Haroon S, Denniston AK, Calvert MJ, TLC Study Group.",,Nature medicine,2023,2023-07-20,N,,,,"Patient and public involvement and engagement (PPIE) can provide valuable insights into the experiences of those living with and affected by a disease or health condition. Inclusive collaboration between patients, the public and researchers can lead to productive relationships, ensuring that health research addresses patient needs. Guidelines are available to support effective PPIE; however, evaluation of the impact of PPIE strategies in health research is limited. In this Review, we evaluate the impact of PPIE in the 'Therapies for Long COVID in non-hospitalised individuals' (TLC) Study, using a combination of group discussions and interviews with patient partners and researchers. We identify areas of good practice and reflect on areas for improvement. Using these insights and the results of a survey, we synthesize two checklists of considerations for PPIE, and we propose that research teams use these checklists to optimize the impact of PPIE for both patients and researchers in future studies.",,doi:https://doi.org/10.1038/s41591-023-02445-x
 38429458,https://doi.org/10.1038/s41590-024-01754-8,Iron dysregulation and inflammatory stress erythropoiesis associates with long-term outcome of COVID-19.,"Hanson AL, Mulè MP, Ruffieux H, Mescia F, Bergamaschi L, Pelly VS, Turner L, Kotagiri P, Cambridge Institute of Therapeutic Immunology and Infectious Disease–National Institute for Health Research (CITIID–NIHR) COVID BioResource Collaboration, Göttgens B, Hess C, Gleadall N, Bradley JR, Nathan JA, Lyons PA, Drakesmith H, Smith KGC.",,Nature immunology,2024,2024-03-01,Y,,,,"Persistent symptoms following SARS-CoV-2 infection are increasingly reported, although the drivers of post-acute sequelae (PASC) of COVID-19 are unclear. Here we assessed 214 individuals infected with SARS-CoV-2, with varying disease severity, for one year from COVID-19 symptom onset to determine the early correlates of PASC. A multivariate signature detected beyond two weeks of disease, encompassing unresolving inflammation, anemia, low serum iron, altered iron-homeostasis gene expression and emerging stress erythropoiesis; differentiated those who reported PASC months later, irrespective of COVID-19 severity. A whole-blood heme-metabolism signature, enriched in hospitalized patients at month 1-3 post onset, coincided with pronounced iron-deficient reticulocytosis. Lymphopenia and low numbers of dendritic cells persisted in those with PASC, and single-cell analysis reported iron maldistribution, suggesting monocyte iron loading and increased iron demand in proliferating lymphocytes. Thus, defects in iron homeostasis, dysregulated erythropoiesis and immune dysfunction due to COVID-19 possibly contribute to inefficient oxygen transport, inflammatory disequilibrium and persisting symptomatology, and may be therapeutically tractable.",,doi:https://doi.org/10.1038/s41590-024-01754-8; doi:https://doi.org/10.1038/s41590-024-01754-8; html:https://europepmc.org/articles/PMC10907301; pdf:https://europepmc.org/articles/PMC10907301?pdf=render
 36936592,https://doi.org/10.1136/bmjmed-2022-000151,Covid-19 variants of concern and pregnancy.,"Stock SJ, Harmer C, Calvert C.",,BMJ medicine,2022,2022-03-02,Y,Pregnancy complications; Covid-19,,,,,pdf:https://bmjmedicine.bmj.com/content/bmjmed/1/1/e000151.full.pdf; doi:https://doi.org/10.1136/bmjmed-2022-000151; html:https://europepmc.org/articles/PMC9951363; pdf:https://europepmc.org/articles/PMC9951363?pdf=render
-37474660,https://doi.org/10.1038/s41591-023-02445-x,Considerations for patient and public involvement and engagement in health research.,"Aiyegbusi OL, McMullan C, Hughes SE, Turner GM, Subramanian A, Hotham R, Davies EH, Frost C, Alder Y, Agyen L, Buckland L, Camaradou J, Chong A, Jeyes F, Kumar S, Matthews KL, Moore P, Ormerod J, Price G, Saint-Cricq M, Stanton D, Walker A, Haroon S, Denniston AK, Calvert MJ, TLC Study Group.",,Nature medicine,2023,2023-07-20,N,,,,"Patient and public involvement and engagement (PPIE) can provide valuable insights into the experiences of those living with and affected by a disease or health condition. Inclusive collaboration between patients, the public and researchers can lead to productive relationships, ensuring that health research addresses patient needs. Guidelines are available to support effective PPIE; however, evaluation of the impact of PPIE strategies in health research is limited. In this Review, we evaluate the impact of PPIE in the 'Therapies for Long COVID in non-hospitalised individuals' (TLC) Study, using a combination of group discussions and interviews with patient partners and researchers. We identify areas of good practice and reflect on areas for improvement. Using these insights and the results of a survey, we synthesize two checklists of considerations for PPIE, and we propose that research teams use these checklists to optimize the impact of PPIE for both patients and researchers in future studies.",,doi:https://doi.org/10.1038/s41591-023-02445-x
 36048760,https://doi.org/10.1371/journal.pgen.1010294,Neurocognitive trajectory and proteomic signature of inherited risk for Alzheimer's disease.,"Paranjpe MD, Chaffin M, Zahid S, Ritchie S, Rotter JI, Rich SS, Gerszten R, Guo X, Heckbert S, Tracy R, Danesh J, Lander ES, Inouye M, Kathiresan S, Butterworth AS, Khera AV.",,PLoS genetics,2022,2022-09-01,Y,,,,"For Alzheimer's disease-a leading cause of dementia and global morbidity-improved identification of presymptomatic high-risk individuals and identification of new circulating biomarkers are key public health needs. Here, we tested the hypothesis that a polygenic predictor of risk for Alzheimer's disease would identify a subset of the population with increased risk of clinically diagnosed dementia, subclinical neurocognitive dysfunction, and a differing circulating proteomic profile. Using summary association statistics from a recent genome-wide association study, we first developed a polygenic predictor of Alzheimer's disease comprised of 7.1 million common DNA variants. We noted a 7.3-fold (95% CI 4.8 to 11.0; p < 0.001) gradient in risk across deciles of the score among 288,289 middle-aged participants of the UK Biobank study. In cross-sectional analyses stratified by age, minimal differences in risk of Alzheimer's disease and performance on a digit recall test were present according to polygenic score decile at age 50 years, but significant gradients emerged by age 65. Similarly, among 30,541 participants of the Mass General Brigham Biobank, we again noted no significant differences in Alzheimer's disease diagnosis at younger ages across deciles of the score, but for those over 65 years we noted an odds ratio of 2.0 (95% CI 1.3 to 3.2; p = 0.002) in the top versus bottom decile of the polygenic score. To understand the proteomic signature of inherited risk, we performed aptamer-based profiling in 636 blood donors (mean age 43 years) with very high or low polygenic scores. In addition to the well-known apolipoprotein E biomarker, this analysis identified 27 additional proteins, several of which have known roles related to disease pathogenesis. Differences in protein concentrations were consistent even among the youngest subset of blood donors (mean age 33 years). Of these 28 proteins, 7 of the 8 proteins with concentrations available were similarly associated with the polygenic score in participants of the Multi-Ethnic Study of Atherosclerosis. These data highlight the potential for a DNA-based score to identify high-risk individuals during the prolonged presymptomatic phase of Alzheimer's disease and to enable biomarker discovery based on profiling of young individuals in the extremes of the score distribution.",,pdf:https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1010294&type=printable; doi:https://doi.org/10.1371/journal.pgen.1010294; html:https://europepmc.org/articles/PMC9436054; pdf:https://europepmc.org/articles/PMC9436054?pdf=render
-34791170,https://doi.org/10.1093/eurheartj/ehab759,A sex-specific prediction model is not enough to achieve equality for women in preventative cardiovascular medicine.,"Kimenai DM, Shah ASV, Mills NL.",,European heart journal,2022,2022-01-01,Y,,,,,,pdf:https://academic.oup.com/eurheartj/article-pdf/43/3/239/42296399/ehab759.pdf; doi:https://doi.org/10.1093/eurheartj/ehab759; html:https://europepmc.org/articles/PMC8790764; pdf:https://europepmc.org/articles/PMC8790764?pdf=render
 30082368,https://doi.org/10.1136/bmjopen-2018-024755,Validating injury burden estimates using population birth cohorts and longitudinal cohort studies of injury outcomes: the VIBES-Junior study protocol.,"Gabbe BJ, Dipnall JF, Lynch JW, Rivara FP, Lyons RA, Ameratunga S, Brussoni M, Lecky FE, Bradley C, Simpson PM, Beck B, Demmler JC, Lyons J, Schneeberg A, Harrison JE.",,BMJ open,2018,2018-08-05,Y,epidemiology; Public Health; Paediatrics; Trauma Management,"Improving Public Health, The Human Phenome",,"<h4>Introduction</h4>Traumatic injury is a leading contributor to the global disease burden in children and adolescents, but methods used to estimate burden do not account for differences in patterns of injury and recovery between children and adults. A lack of empirical data on postinjury disability in children has limited capacity to derive valid disability weights and describe the long-term individual and societal impacts of injury in the early part of life. The aim of this study is to establish valid estimates of the burden of non-fatal injury in children and adolescents.<h4>Methods and analysis</h4>Five longitudinal studies of paediatric injury survivors <18 years at the time of injury (Australia, Canada, UK and USA) and two whole-of-population linked administrative data paediatric studies (Australia and Wales) will be analysed over a 3-year period commencing 2018. Meta-analysis of deidentified patient-level data (n≈2,600) from five injury-specific longitudinal studies (Victorian State Trauma Registry; Victorian Orthopaedic Trauma Outcomes Registry; UK Burden of Injury; British Columbia Children's Hospital Longitudinal Injury Outcomes; Children's Health After Injury) and >1 million children from two whole-of-population cohorts (South Australian Early Childhood Data Project and Wales Electronic Cohort for Children). Systematic analysis of pooled injury-specific cohort data using a variety of statistical techniques, and parallel analysis of whole-of-population cohorts, will be used to develop estimated disability weights for years lost due to disability, establish appropriate injury classifications and explore factors influencing recovery.<h4>Ethics and dissemination</h4>The project was approved by the Monash University Human Research Ethics Committee project number 12 311. Results of this study will be submitted for publication in internationally peer-reviewed journals. The findings from this project have the capacity to improve the validity of paediatric injury burden measurements in future local and global burden of disease studies.",,pdf:https://bmjopen.bmj.com/content/bmjopen/8/8/e024755.full.pdf; doi:https://doi.org/10.1136/bmjopen-2018-024755; html:https://europepmc.org/articles/PMC6078268; pdf:https://europepmc.org/articles/PMC6078268?pdf=render
+34791170,https://doi.org/10.1093/eurheartj/ehab759,A sex-specific prediction model is not enough to achieve equality for women in preventative cardiovascular medicine.,"Kimenai DM, Shah ASV, Mills NL.",,European heart journal,2022,2022-01-01,Y,,,,,,pdf:https://academic.oup.com/eurheartj/article-pdf/43/3/239/42296399/ehab759.pdf; doi:https://doi.org/10.1093/eurheartj/ehab759; html:https://europepmc.org/articles/PMC8790764; pdf:https://europepmc.org/articles/PMC8790764?pdf=render
 36719157,https://doi.org/10.2215/cjn.05080422,Fibroblast Growth Factor-23 and Risk of Cardiovascular Diseases: A Mendelian Randomization Study.,"Donovan K, Herrington WG, Paré G, Pigeyre M, Haynes R, Sardell R, Butterworth AS, Folkersen L, Gustafsson S, Wang Q, Baigent C, Mälarstig A, Holmes MV, Staplin N, 
                                 on behalf of the SCALLOP Consortium
                                 .",,Clinical journal of the American Society of Nephrology : CJASN,2023,2023-01-01,Y,,,,"<h4>Background</h4>Fibroblast growth factor-23 (FGF-23) is associated with a range of cardiovascular and noncardiovascular diseases in conventional epidemiological studies, but substantial residual confounding may exist. Mendelian randomization approaches can help control for such confounding.<h4>Methods</h4>SCALLOP Consortium data of 19,195 participants were used to generate an FGF-23 genetic score. Data from 337,448 UK Biobank participants were used to estimate associations between higher genetically predicted FGF-23 concentration and the odds of any atherosclerotic cardiovascular disease (n=26,266 events), nonatherosclerotic cardiovascular disease (n=12,652), and noncardiovascular diseases previously linked to FGF-23. Measurements of carotid intima-media thickness and left ventricular mass were available in a subset. Associations with cardiovascular outcomes were also tested in three large case-control consortia: CARDIOGRAMplusC4D (coronary artery disease, n=181,249 cases), MEGASTROKE (stroke, n=34,217), and HERMES (heart failure, n=47,309).<h4>Results</h4>We identified 34 independent variants for circulating FGF-23, which formed a validated genetic score. There were no associations between genetically predicted FGF-23 and any of the cardiovascular or noncardiovascular outcomes. In UK Biobank, the odds ratio (OR) for any atherosclerotic cardiovascular disease per 1-SD higher genetically predicted logFGF-23 was 1.03 (95% confidence interval [95% CI], 0.98 to 1.08), and for any nonatherosclerotic cardiovascular disease, it was 1.01 (95% CI, 0.94 to 1.09). The ORs in the case-control consortia were 1.00 (95% CI, 0.97 to 1.03) for coronary artery disease, 1.01 (95% CI, 0.95 to 1.07) for stroke, and 1.00 (95% CI, 0.95 to 1.05) for heart failure. In those with imaging, logFGF-23 was not associated with carotid or cardiac abnormalities.<h4>Conclusions</h4>Genetically predicted FGF-23 levels are not associated with atherosclerotic and nonatherosclerotic cardiovascular diseases, suggesting no important causal link.<h4>Podcast</h4>This article contains a podcast at https://dts.podtrac.com/redirect.mp3/www.asn-online.org/media/podcast/CJASN/2023_01_10_CJN05080422.mp3.",,pdf:http://uu.diva-portal.org/smash/get/diva2:1745425/FULLTEXT01; doi:https://doi.org/10.2215/CJN.05080422; html:https://europepmc.org/articles/PMC7614195
@@ -2051,30 +2053,30 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 34337345,https://doi.org/10.1123/jmpb.2020-0038,Validation of Wearable Camera Still Images to Assess Posture in Free-Living Conditions.,"Martinez J, Decker A, Cho CC, Doherty A, Swartz AM, Staudenmayer JW, Strath SJ.",,Journal for the measurement of physical behaviour,2021,2021-02-24,N,Activpal; Autographer; Objective Measuring,,,"<h4>Purpose</h4>To assess the convergent validity of body worn wearable camera (WC) still-images (IMGs) for determining posture compared with activPAL (AP) classifications.<h4>Methods</h4>Participants (n=16, mean age 46.7±23.8yrs, 9F) wore an Autographer WC above the xyphoid process and an AP during three, 2hr free-living visits. IMGs were captured on average 8.47 seconds apart and were annotated with output consisting of events, transitory states, unknown and gaps. Events were annotations that matched AP classifications (sit, stand and move) consisting of at least 3 IMGs, transitory states were posture annotations fewer than 3 IMGs, unknown were IMGs that could not be accurately classified, and gaps were time between annotations. For analyses, annotation and AP output were converted to one-sec epochs and matched second-by-second. Total and average length of visits and events are reported in minutes. Bias and 95% CIs for event posture times from IMGs to AP posture times were calculated to determine accuracy and precision. Confusion matrices using total AP posture times were computed to determine misclassification.<h4>Results</h4>43 visits were analyzed with a total visit and event time of 5027.73 and 4237.23 minutes and average visit and event lengths being 116.92 and 98.54 minutes, respectively. Bias was not statistically significant for sitting but significant for standing and movement (0.84, -6.87 and 6.04 minutes). From confusion matrices, IMGs correctly classified sitting, standing and movement 85.69%, 54.87%, and 69.41% of total AP time, respectively.<h4>Conclusion</h4>WC IMGs provide a good estimation of overall sitting time but underestimate standing and overestimate movement time. Future work is warranted to improve posture classifications and examine IMG accuracy and precision in assessing activity type behaviors.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8320753; doi:https://doi.org/10.1123/jmpb.2020-0038; html:https://europepmc.org/articles/PMC8320753; pdf:https://europepmc.org/articles/PMC8320753?pdf=render; doi:https://doi.org/10.1123/jmpb.2020-0038
 36560629,https://doi.org/10.3390/v14122625,Switching of Receptor Binding Poses between Closely Related Enteroviruses.,"Zhou D, Qin L, Duyvesteyn HME, Zhao Y, Lin TY, Fry EE, Ren J, Huang KA, Stuart DI.",,Viruses,2022,2022-11-24,Y,Evolution; Complex; Virus receptor; Glycan; Daf; Binding Pose; Echovirus E11; Enterovirus Structure,,,"Echoviruses, for which there are currently no approved vaccines or drugs, are responsible for a range of human diseases, for example echovirus 11 (E11) is a major cause of serious neonatal morbidity and mortality. Decay-accelerating factor (DAF, also known as CD55) is an attachment receptor for E11. Here, we report the structure of the complex of E11 and the full-length ectodomain of DAF (short consensus repeats, SCRs, 1-4) at 3.1 Å determined by cryo-electron microscopy (cryo-EM). SCRs 3 and 4 of DAF interact with E11 at the southern rim of the canyon via the VP2 EF and VP3 BC loops. We also observe an unexpected interaction between the N-linked glycan (residue 95 of DAF) and the VP2 BC loop of E11. DAF is a receptor for at least 20 enteroviruses and we classify its binding patterns from reported DAF/virus complexes into two distinct positions and orientations, named as E6 and E11 poses. Whilst 60 DAF molecules can attach to the virion in the E6 pose, no more than 30 can attach to E11 due to steric restrictions. Analysis of the distinct modes of interaction and structure and sequence-based phylogenies suggests that the two modes evolved independently, with the E6 mode likely found earlier.",,pdf:https://www.mdpi.com/1999-4915/14/12/2625/pdf?version=1669703629; doi:https://doi.org/10.3390/v14122625; html:https://europepmc.org/articles/PMC9781616; pdf:https://europepmc.org/articles/PMC9781616?pdf=render
 32222069,https://doi.org/10.1111/bjd.19052,Risk of hospitalization and death due to infection in people with psoriasis: a population-based cohort study using the Clinical Practice Research Datalink.,"Yiu ZZN, Parisi R, Lunt M, Warren RB, Griffiths CEM, Langan SM, Ashcroft DM.",,The British journal of dermatology,2021,2020-05-12,N,,,,"<h4>Background</h4>Psoriasis is associated with risk factors for serious infections, but the independent relationship between psoriasis and serious infection is as yet unclear.<h4>Objectives</h4>To determine whether people with psoriasis have a higher risk of hospitalization due to any infection, respiratory infections, soft-tissue and skin infections, or a higher risk of death due to infection.<h4>Methods</h4>We conducted a cohort study of people (≥ 18 years) with psoriasis using the UK Clinical Practice Research Datalink (CPRD GOLD) linked to Hospital Episode Statistics (HES) and Office for National Statistics (ONS) mortality records between 1 April 2003 and 31 December 2016, and matched with up to six comparators on age, sex and general practice. Hospitalization was ascertained from HES records; death was ascertained from ONS mortality records. Stratified Cox proportional hazard models were estimated, with stepwise adjustment in different models for potential confounders or mediators between psoriasis and serious infection.<h4>Results</h4>There were 69 315 people with psoriasis and 338 620 comparators who were followed up for a median (interquartile range) of 4·9 (5·9) and 5·1 (6·3) years, respectively. People with psoriasis had a higher incidence rate of serious infection [20·5 per 1000 person-years, 95% confidence interval (CI) 20·0-21·0, n = 7631] compared with those without psoriasis (16·1 per 1000 person-years, 95% CI 15·9-16·3, n = 30 761). The fully adjusted hazard ratio for the association between psoriasis and serious infection was 1·36 (95% CI 1·31-1·40), with similar results across the other outcomes.<h4>Conclusions</h4>Psoriasis is associated with a small increase in the risk of serious infection. Further research is needed to understand how psoriasis predisposes to a higher risk of infection.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/bjd.19052; doi:https://doi.org/10.1111/bjd.19052
-38594327,https://doi.org/10.1038/s41698-024-00580-3,Image-based consensus molecular subtyping in rectal cancer biopsies and response to neoadjuvant chemoradiotherapy.,"Lafarge MW, Domingo E, Sirinukunwattana K, Wood R, Samuel L, Murray G, Richman SD, Blake A, Sebag-Montefiore D, Gollins S, Klieser E, Neureiter D, Huemer F, Greil R, Dunne P, Quirke P, Weiss L, Rittscher J, Maughan T, Koelzer VH.",,NPJ precision oncology,2024,2024-04-09,Y,,,,"The development of deep learning (DL) models to predict the consensus molecular subtypes (CMS) from histopathology images (imCMS) is a promising and cost-effective strategy to support patient stratification. Here, we investigate whether imCMS calls generated from whole slide histopathology images (WSIs) of rectal cancer (RC) pre-treatment biopsies are associated with pathological complete response (pCR) to neoadjuvant long course chemoradiotherapy (LCRT) with single agent fluoropyrimidine. DL models were trained to classify WSIs of colorectal cancers stained with hematoxylin and eosin into one of the four CMS classes using a multi-centric dataset of resection and biopsy specimens (n = 1057 WSIs) with paired transcriptional data. Classifiers were tested on a held out RC biopsy cohort (ARISTOTLE) and correlated with pCR to LCRT in an independent dataset merging two RC cohorts (ARISTOTLE, n = 114 and SALZBURG, n = 55 patients). DL models predicted CMS with high classification performance in multiple comparative analyses. In the independent cohorts (ARISTOTLE, SALZBURG), cases with WSIs classified as imCMS1 had a significantly higher likelihood of achieving pCR (OR = 2.69, 95% CI 1.01-7.17, p = 0.048). Conversely, imCMS4 was associated with lack of pCR (OR = 0.25, 95% CI 0.07-0.88, p = 0.031). Classification maps demonstrated pathologist-interpretable associations with high stromal content in imCMS4 cases, associated with poor outcome. No significant association was found in imCMS2 or imCMS3. imCMS classification of pre-treatment biopsies is a fast and inexpensive solution to identify patient groups that could benefit from neoadjuvant LCRT. The significant associations between imCMS1/imCMS4 with pCR suggest the existence of predictive morphological features that could enhance standard pathological assessment.",,pdf:https://www.nature.com/articles/s41698-024-00580-3.pdf; doi:https://doi.org/10.1038/s41698-024-00580-3; html:https://europepmc.org/articles/PMC11003957; pdf:https://europepmc.org/articles/PMC11003957?pdf=render
 33090454,https://doi.org/10.1111/bjd.19597,Atopic eczema and obesity: a population-based study.,"Ascott A, Mansfield KE, Schonmann Y, Mulick A, Abuabara K, Roberts A, Smeeth L, Langan SM.",,The British journal of dermatology,2021,2020-12-01,N,,,,"<h4>Background</h4>Atopic eczema is a common chronic inflammatory skin disease. Research suggests an association between atopic eczema and obesity, with inconsistent evidence from European populations.<h4>Objectives</h4>To explore the association between diagnosed atopic eczema and being overweight or obese, and whether increased atopic eczema severity was associated with higher body mass index.<h4>Methods</h4>We undertook a cross-sectional analysis within a cohort of adults (matched by age, sex and general practice) with and without a diagnosis of atopic eczema. We used primary care (Clinical Practice Research Datalink Gold) and linked hospital admissions data (1998-2016). We used conditional logistic regression to compare the odds of being overweight or obese (adjusting for confounders and potential mediators) in those with atopic eczema (mild, moderate and severe, and all eczema) vs. those without.<h4>Results</h4>We identified 441 746 people with atopic eczema, matched to 1 849 722 without. People with atopic eczema had slightly higher odds of being overweight or obese vs. those without [odds ratio (OR) 1·08, 95% confidence interval (CI) 1·07-1·09] after adjusting for age, asthma and socioeconomic deprivation. Adjusting for potential mediators (high-dose glucocorticoids, harmful alcohol use, anxiety, depression, smoking) had a minimal impact on effect estimates (OR 1·07, 95% CI 1·06-1·08). We saw no evidence that odds of being overweight or obese increased with increasing atopic eczema severity, and there was no association in people with severe eczema.<h4>Conclusions</h4>We found evidence of a small overall association between atopic eczema and being overweight or obese. However, there was no association with obesity among those with the most severe eczema. Our findings are largely reassuring for this prevalent patient group who may already have an increased risk of cardiovascular disease.",,pdf:https://researchonline.lshtm.ac.uk/id/eprint/4658151/1/Ascott-etal-2020_Atopic_eczema_and-obesity.pdf; doi:https://doi.org/10.1111/bjd.19597
+38594327,https://doi.org/10.1038/s41698-024-00580-3,Image-based consensus molecular subtyping in rectal cancer biopsies and response to neoadjuvant chemoradiotherapy.,"Lafarge MW, Domingo E, Sirinukunwattana K, Wood R, Samuel L, Murray G, Richman SD, Blake A, Sebag-Montefiore D, Gollins S, Klieser E, Neureiter D, Huemer F, Greil R, Dunne P, Quirke P, Weiss L, Rittscher J, Maughan T, Koelzer VH.",,NPJ precision oncology,2024,2024-04-09,Y,,,,"The development of deep learning (DL) models to predict the consensus molecular subtypes (CMS) from histopathology images (imCMS) is a promising and cost-effective strategy to support patient stratification. Here, we investigate whether imCMS calls generated from whole slide histopathology images (WSIs) of rectal cancer (RC) pre-treatment biopsies are associated with pathological complete response (pCR) to neoadjuvant long course chemoradiotherapy (LCRT) with single agent fluoropyrimidine. DL models were trained to classify WSIs of colorectal cancers stained with hematoxylin and eosin into one of the four CMS classes using a multi-centric dataset of resection and biopsy specimens (n = 1057 WSIs) with paired transcriptional data. Classifiers were tested on a held out RC biopsy cohort (ARISTOTLE) and correlated with pCR to LCRT in an independent dataset merging two RC cohorts (ARISTOTLE, n = 114 and SALZBURG, n = 55 patients). DL models predicted CMS with high classification performance in multiple comparative analyses. In the independent cohorts (ARISTOTLE, SALZBURG), cases with WSIs classified as imCMS1 had a significantly higher likelihood of achieving pCR (OR = 2.69, 95% CI 1.01-7.17, p = 0.048). Conversely, imCMS4 was associated with lack of pCR (OR = 0.25, 95% CI 0.07-0.88, p = 0.031). Classification maps demonstrated pathologist-interpretable associations with high stromal content in imCMS4 cases, associated with poor outcome. No significant association was found in imCMS2 or imCMS3. imCMS classification of pre-treatment biopsies is a fast and inexpensive solution to identify patient groups that could benefit from neoadjuvant LCRT. The significant associations between imCMS1/imCMS4 with pCR suggest the existence of predictive morphological features that could enhance standard pathological assessment.",,pdf:https://www.nature.com/articles/s41698-024-00580-3.pdf; doi:https://doi.org/10.1038/s41698-024-00580-3; html:https://europepmc.org/articles/PMC11003957; pdf:https://europepmc.org/articles/PMC11003957?pdf=render
 37748493,https://doi.org/10.1016/s2213-2600(23)00262-x,"Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study.",C-MORE/PHOSP-COVID Collaborative Group.,,The Lancet. Respiratory medicine,2023,2023-09-22,Y,,,,"<h4>Introduction</h4>The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures.<h4>Methods</h4>In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025.<h4>Findings</h4>Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2-6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p<0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5-5·8]; p<sub>adjusted</sub>=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p<0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4-10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p<0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32-4·82]; p<sub>adjusted</sub>=0·0059), and more likely to have a more severe acute infection (acute CRP >5mg/L, OR 3·55 [1·23-11·88]; p<sub>adjusted</sub>=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation.<h4>Interpretation</h4>After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification.<h4>Funding</h4>UK Research and Innovation and National Institute for Health Research.",,pdf:http://www.thelancet.com/article/S221326002300262X/pdf; doi:https://doi.org/10.1016/S2213-2600(23)00262-X; html:https://europepmc.org/articles/PMC7615263; pdf:https://europepmc.org/articles/PMC7615263?pdf=render
-35386996,https://doi.org/10.3389/falgy.2021.677677,Purinergic Receptors in the Airways: Potential Therapeutic Targets for Asthma?,"Thompson RJ, Sayers I, Kuokkanen K, Hall IP.",,Frontiers in allergy,2021,2021-05-31,Y,Lung; Bioinformatics; Asthma; airway; Gene Expression; purinergic receptor; Purinergic Signaling,,,"Extracellular ATP functions as a signaling messenger through its actions on purinergic receptors, and is known to be involved in numerous physiological and pathophysiological processes throughout the body, including in the lungs and airways. Consequently, purinergic receptors are considered to be promising therapeutic targets for many respiratory diseases, including asthma. This review explores how online bioinformatics resources combined with recently generated datasets can be utilized to investigate purinergic receptor gene expression in tissues and cell types of interest in respiratory disease to identify potential therapeutic targets, which can then be investigated further. These approaches show that different purinergic receptors are expressed at different levels in lung tissue, and that purinergic receptors tend to be expressed at higher levels in immune cells and at more moderate levels in airway structural cells. Notably, P2RX1, P2RX4, P2RX7, P2RY1, P2RY11, and P2RY14 were revealed as the most highly expressed purinergic receptors in lung tissue, therefore suggesting that these receptors have good potential as therapeutic targets for asthma and other respiratory diseases.",,pdf:https://www.frontiersin.org/articles/10.3389/falgy.2021.677677/pdf; doi:https://doi.org/10.3389/falgy.2021.677677; html:https://europepmc.org/articles/PMC8974712; pdf:https://europepmc.org/articles/PMC8974712?pdf=render
 33635119,https://doi.org/10.1161/circgen.120.002963,Life-Time Covariation of Major Cardiovascular Diseases: A 40-Year Longitudinal Study and Genetic Studies.,"Lind L, Sundström J, Ärnlöv J, Ingelsson M, Henry A, Lumbers RT, Lampa E.",,Circulation. Genomic and precision medicine,2021,2021-02-26,N,Adult; Myocardial infarction; Atrial fibrillation; Stroke; Heart Failure,,,"<h4>Background</h4>It is known that certain cardiovascular diseases (CVD) are associated, like atrial fibrillation and stroke. However, for other CVDs, the links and temporal trends are less studied. In this longitudinal study, we have investigated temporal epidemiological and genetic associations between different CVDs.<h4>Methods</h4>The ULSAM (Uppsala Longitudinal Study of Adult Men; 2322 men aged 50 years) has been followed for 40 years regarding 4 major CVDs (incident myocardial infarction, ischemic stroke, heart failure, and atrial fibrillation). For the genetic analyses, publicly available data were used.<h4>Results</h4>Using multistate modeling, significant relationships were seen between pairs of all of the 4 investigated CVDs. However, the risk of obtaining one additional CVD differed substantially both between different CVDs and between their temporal order. The relationship between heart failure and atrial fibrillation showed a high risk ratio (risk ratios, 24-26) regardless of the temporal order. A consistent association was seen also for myocardial infarction and atrial fibrillation but with a lower relative risk (risk ratios, 4-5). In contrast, the risk of receiving a diagnosis of heart failure following a myocardial infarction was almost twice as high as for the reverse temporal order (risk ratios, 16 versus 9). Genetic loci linked to traditional risk factors could partly explain the observed associations between the CVDs, but pathway analyses disclosed also other pathophysiological links.<h4>Conclusions</h4>During 40 years, all of the 4 investigated CVDs were pairwise associated with each other regardless of the temporal order of occurrence, but the risk magnitude differed between different CVDs and their temporal order. Genetic analyses disclosed new pathophysiological links between CVDs.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCGEN.120.002963; doi:https://doi.org/10.1161/CIRCGEN.120.002963; html:https://europepmc.org/articles/PMC8284356; pdf:https://europepmc.org/articles/PMC8284356?pdf=render; doi:https://doi.org/10.1161/circgen.120.002963
+35386996,https://doi.org/10.3389/falgy.2021.677677,Purinergic Receptors in the Airways: Potential Therapeutic Targets for Asthma?,"Thompson RJ, Sayers I, Kuokkanen K, Hall IP.",,Frontiers in allergy,2021,2021-05-31,Y,Lung; Bioinformatics; Asthma; airway; Gene Expression; purinergic receptor; Purinergic Signaling,,,"Extracellular ATP functions as a signaling messenger through its actions on purinergic receptors, and is known to be involved in numerous physiological and pathophysiological processes throughout the body, including in the lungs and airways. Consequently, purinergic receptors are considered to be promising therapeutic targets for many respiratory diseases, including asthma. This review explores how online bioinformatics resources combined with recently generated datasets can be utilized to investigate purinergic receptor gene expression in tissues and cell types of interest in respiratory disease to identify potential therapeutic targets, which can then be investigated further. These approaches show that different purinergic receptors are expressed at different levels in lung tissue, and that purinergic receptors tend to be expressed at higher levels in immune cells and at more moderate levels in airway structural cells. Notably, P2RX1, P2RX4, P2RX7, P2RY1, P2RY11, and P2RY14 were revealed as the most highly expressed purinergic receptors in lung tissue, therefore suggesting that these receptors have good potential as therapeutic targets for asthma and other respiratory diseases.",,pdf:https://www.frontiersin.org/articles/10.3389/falgy.2021.677677/pdf; doi:https://doi.org/10.3389/falgy.2021.677677; html:https://europepmc.org/articles/PMC8974712; pdf:https://europepmc.org/articles/PMC8974712?pdf=render
 33246414,https://doi.org/10.1186/s12874-020-01163-z,Patient-specific record linkage between emergency department and hospital admission data for a cohort of people who inject drugs: methodological considerations for frequent presenters.,"Di Rico R, Nambiar D, Gabbe B, Stoové M, Dietze P.",,BMC medical research methodology,2020,2020-11-27,Y,Methods; Australia; Data Linkage; Record Linkage; Administrative Data; People Who Inject Drugs; Patient Pathways; Frequent Presenters; Vaed; Vemd,,,"<h4>Background</h4>People who inject drugs (PWID) have been identified as frequent users of emergency department (ED) and hospital inpatient services. The specific challenges of record linkage in cohorts with numerous administrative health records occurring in close proximity are not well understood. Here, we present a method for patient-specific record linkage of ED and hospital admission data for a cohort of PWID.<h4>Methods</h4>Data from 688 PWID were linked to two state-wide administrative health databases identifying all ED visits and hospital admissions for the cohort between January 2008 and June 2013. We linked patient-specific ED and hospital admissions data, using administrative date-time timestamps and pre-specified linkage criteria, to identify hospital admissions stemming from ED presentations for a given individual. The ability of standalone databases to identify linked ED visits or hospital admissions was examined.<h4>Results</h4>There were 3459 ED visits and 1877 hospital admissions identified during the study period. Thirty-four percent of ED visits were linked to hospital admissions. Most links had hospital admission timestamps in-between or identical to their ED visit timestamps (n = 1035, 87%). Allowing 24-h between ED visits and hospital admissions captured more linked records, but increased manual inspection requirements. In linked records (n = 1190), the ED 'departure status' variable correctly reflected subsequent hospital admission in only 68% of cases. The hospital 'admission type' variable was non-specific in identifying if a preceding ED visit had occurred.<h4>Conclusions</h4>Linking ED visits with subsequent hospital admissions in PWID requires access to date and time variables for accurate temporal sorting, especially for same-day presentations. Selecting time-windows to capture linked records requires discretion. Researchers risk under-ascertainment of hospital admissions if using ED data alone.",,pdf:https://bmcmedresmethodol.biomedcentral.com/track/pdf/10.1186/s12874-020-01163-z; doi:https://doi.org/10.1186/s12874-020-01163-z; html:https://europepmc.org/articles/PMC7694355; pdf:https://europepmc.org/articles/PMC7694355?pdf=render
 36058413,https://doi.org/10.1016/j.jinf.2022.08.030,A prospective study of risk factors associated with seroprevalence of SARS-CoV-2 antibodies in healthcare workers at a large UK teaching hospital.,"Cooper DJ, Lear S, Watson L, Shaw A, Ferris M, Doffinger R, Bousfield R, Sharrocks K, Weekes MP, Warne B, Sparkes D, Jones NK, Rivett L, Routledge M, Chaudhry A, Dempsey K, Matson M, Lakha A, Gathercole G, O'Connor O, Wilson E, Shahzad O, Toms K, Thompson R, Halsall I, Halsall D, Houghton S, Papadia S, Kingston N, Stirrups KE, Graves B, Townsend P, Walker N, Stark H, CITIID-NIHR BioResource COVID-19 Collaboration, De Angelis D, Seaman S, Dougan G, Bradley JR, Török ME, Goodfellow I, Baker S.",,The Journal of infection,2022,2022-09-02,Y,Healthcare Workers; Sero-epidemiology; Risk Factor Analysis; Covid-19; Sars-cov-2,,,"<h4>Objectives</h4>To describe the risk factors for SARS-CoV-2 infection in UK healthcare workers (HCWs).<h4>Methods</h4>We conducted a prospective sero-epidemiological study of HCWs at a major UK teaching hospital using a SARS-CoV-2 immunoassay. Risk factors for seropositivity were analysed using multivariate logistic regression.<h4>Results</h4>410/5,698 (7·2%) staff tested positive for SARS-CoV-2 antibodies. Seroprevalence was higher in those working in designated COVID-19 areas compared with other areas (9·47% versus 6·16%) Healthcare assistants (aOR 2·06 [95%CI 1·14-3·71]; p=0·016) and domestic and portering staff (aOR 3·45 [95% CI 1·07-11·42]; p=0·039) had significantly higher seroprevalence than other staff groups after adjusting for age, sex, ethnicity and COVID-19 working location. Staff working in acute medicine and medical sub-specialities were also at higher risk (aOR 2·07 [95% CI 1·31-3·25]; p<0·002). Staff from Black, Asian and minority ethnic (BAME) backgrounds had an aOR of 1·65 (95% CI 1·32 - 2·07; p<0·001) compared to white staff; this increased risk was independent of COVID-19 area working. The only symptoms significantly associated with seropositivity in a multivariable model were loss of sense of taste or smell, fever, and myalgia; 31% of staff testing positive reported no prior symptoms.<h4>Conclusions</h4>Risk of SARS-CoV-2 infection amongst HCWs is highly heterogeneous and influenced by COVID-19 working location, role, age and ethnicity. Increased risk amongst BAME staff cannot be accounted for solely by occupational factors.",,pdf:https://www.repository.cam.ac.uk/bitstream/1810/341240/2/1-s2.0-S016344532200514X-main.pdf; doi:https://doi.org/10.1016/j.jinf.2022.08.030; html:https://europepmc.org/articles/PMC9436870; pdf:https://europepmc.org/articles/PMC9436870?pdf=render
 35803473,https://doi.org/10.1016/j.neuroimage.2022.119452,Identifying microstructural changes in diffusion MRI; How to circumvent parameter degeneracy.,"Rafipoor H, Zheng YQ, Griffanti L, Jbabdi S, Cottaar M.",,NeuroImage,2022,2022-07-05,Y,,,,"Biophysical models that attempt to infer real-world quantities from data usually have many free parameters. This over-parameterisation can result in degeneracies in model inversion and render parameter estimation ill-posed. However, in many applications, we are not interested in quantifying the parameters per se, but rather in identifying changes in parameters between experimental conditions (e.g. patients vs controls). Here we present a Bayesian framework to make inference on changes in the parameters of biophysical models even when model inversion is degenerate, which we refer to as Bayesian EstimatioN of CHange (BENCH). We infer the parameter changes in two steps; First, we train models that can estimate the pattern of change in the measurements given any hypothetical direction of change in the parameters using simulations. Next, for any pair of real data sets, we use these pre-trained models to estimate the probability that an observed difference in the data can be explained by each model of change. BENCH is applicable to any type of data and models and particularly useful for biophysical models with parameter degeneracies, where we can assume the change is sparse. In this paper, we apply the approach in the context of microstructural modelling of diffusion MRI data, where the models are usually over-parameterised and not invertible without injecting strong assumptions. Using simulations, we show that in the context of the standard model of white matter our approach is able to identify changes in microstructural parameters from conventional multi-shell diffusion MRI data. We also apply our approach to a subset of subjects from the UK-Biobank Imaging to identify the dominant standard model parameter change in areas of white matter hyperintensities under the assumption that the standard model holds in white matter hyperintensities.",,doi:https://doi.org/10.1016/j.neuroimage.2022.119452; doi:https://doi.org/10.1016/j.neuroimage.2022.119452; html:https://europepmc.org/articles/PMC10933779; pdf:https://europepmc.org/articles/PMC10933779?pdf=render
-38424462,https://doi.org/10.1038/s41588-024-01693-y,Author Correction: Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort.,"Qin Y, Havulinna AS, Liu Y, Jousilahti P, Ritchie SC, Tokolyi A, Sanders JG, Valsta L, Brożyńska M, Zhu Q, Tripathi A, Vázquez-Baeza Y, Loomba R, Cheng S, Jain M, Niiranen T, Lahti L, Knight R, Salomaa V, Inouye M, Méric G.",,Nature genetics,2024,2024-03-01,N,,,,,,pdf:https://www.nature.com/articles/s41588-024-01693-y.pdf; doi:https://doi.org/10.1038/s41588-024-01693-y
 35880304,https://doi.org/10.1002/jbmr.4664,Telomere Length and Risk of Incident Fracture and Arthroplasty: Findings From UK Biobank.,"Curtis EM, Codd V, Nelson C, D'Angelo S, Wang Q, Allara E, Kaptoge S, Matthews PM, Tobias JH, Danesh J, Cooper C, Samani NJ, Harvey NC.",,Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research,2022,2022-09-13,Y,Aging; Osteoporosis; Osteoarthritis; epidemiology; Leucocyte Telomere Length,,,"We investigated independent associations between telomere length and risk of fracture and arthroplasty in UK Biobank participants. Leukocyte telomere length (LTL) was measured in baseline samples using a validated polymerase chain reaction (PCR) method. We used, in men and women separately, Cox proportional hazards models to calculate the hazard ratio (HR) for incident fracture (any, osteoporotic) or arthroplasty (hip or knee) over 1,186,410 person-years of follow-up. Covariates included age, white cell count, ethnicity, smoking, alcohol, physical activity, and menopause (women). In further analyses we adjusted for either estimated bone mineral density (eBMD) from heel quantitative ultrasound, handgrip strength, gait speed, total fat mass (bioimpedance), or blood biomarkers, all measured at baseline (2006-2010). We studied 59,500 women and 51,895 men, mean ± standard deviation (SD) age 56.4 ± 8.0 and 57.0 ± 8.3 years, respectively. During follow-up there were 5619 fractures; 5285 hip and 4261 knee arthroplasties. In confounder-adjusted models, longer LTL was associated with reduced risk of incident knee arthroplasty in both men (HR/SD 0.93; 95% confidence interval [CI], 0.88-0.97) and women (0.92; 95% CI, 0.88-0.96), and hip arthroplasty in men (0.91; 95% CI, 0.87-0.95), but not women (0.98; 95% CI, 0.94-1.01). Longer LTL was weakly associated with reduced risk of any incident fracture in women (HR/SD 0.96; 95% CI, 0.93-1.00) with less evidence in men (0.98; 95% CI, 0.93-1.02). Associations with incident outcomes were not materially altered by adjustment for heel eBMD, grip strength, gait speed, fat mass, or blood biomarker measures. In this, the largest study to date, longer LTL was associated with lower risk of incident knee or hip arthroplasty, but only weakly associated with lower risk of fracture. The relative risks were low at a population level, but our findings suggest that common factors acting on the myeloid and musculoskeletal systems might influence later life musculoskeletal outcomes. © 2022 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).",,pdf:https://research-information.bris.ac.uk/files/341783442/J_of_Bone_Mineral_Res_2022_Curtis_Telomere_Length_and_Risk_of_Incident_Fracture_and_Arthroplasty_Findings_From_UK_1_.pdf; doi:https://doi.org/10.1002/jbmr.4664; html:https://europepmc.org/articles/PMC9826022; pdf:https://europepmc.org/articles/PMC9826022?pdf=render
+38424462,https://doi.org/10.1038/s41588-024-01693-y,Author Correction: Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort.,"Qin Y, Havulinna AS, Liu Y, Jousilahti P, Ritchie SC, Tokolyi A, Sanders JG, Valsta L, Brożyńska M, Zhu Q, Tripathi A, Vázquez-Baeza Y, Loomba R, Cheng S, Jain M, Niiranen T, Lahti L, Knight R, Salomaa V, Inouye M, Méric G.",,Nature genetics,2024,2024-03-01,N,,,,,,pdf:https://www.nature.com/articles/s41588-024-01693-y.pdf; doi:https://doi.org/10.1038/s41588-024-01693-y
 33637859,https://doi.org/10.1038/s41746-021-00404-9,Automatic multilabel detection of ICD10 codes in Dutch cardiology discharge letters using neural networks.,"Sammani A, Bagheri A, van der Heijden PGM, Te Riele ASJM, Baas AF, Oosters CAJ, Oberski D, Asselbergs FW.",,NPJ digital medicine,2021,2021-02-26,Y,,,,"Standard reference terminology of diagnoses and risk factors is crucial for billing, epidemiological studies, and inter/intranational comparisons of diseases. The International Classification of Disease (ICD) is a standardized and widely used method, but the manual classification is an enormously time-consuming endeavor. Natural language processing together with machine learning allows automated structuring of diagnoses using ICD-10 codes, but the limited performance of machine learning models, the necessity of gigantic datasets, and poor reliability of terminal parts of these codes restricted clinical usability. We aimed to create a high performing pipeline for automated classification of reliable ICD-10 codes in the free medical text in cardiology. We focussed on frequently used and well-defined three- and four-digit ICD-10 codes that still have enough granularity to be clinically relevant such as atrial fibrillation (I48), acute myocardial infarction (I21), or dilated cardiomyopathy (I42.0). Our pipeline uses a deep neural network known as a Bidirectional Gated Recurrent Unit Neural Network and was trained and tested with 5548 discharge letters and validated in 5089 discharge and procedural letters. As in clinical practice discharge letters may be labeled with more than one code, we assessed the single- and multilabel performance of main diagnoses and cardiovascular risk factors. We investigated using both the entire body of text and only the summary paragraph, supplemented by age and sex. Given the privacy-sensitive information included in discharge letters, we added a de-identification step. The performance was high, with F1 scores of 0.76-0.99 for three-character and 0.87-0.98 for four-character ICD-10 codes, and was best when using complete discharge letters. Adding variables age/sex did not affect results. For model interpretability, word coefficients were provided and qualitative assessment of classification was manually performed. Because of its high performance, this pipeline can be useful to decrease the administrative burden of classifying discharge diagnoses and may serve as a scaffold for reimbursement and research applications.",,pdf:https://www.nature.com/articles/s41746-021-00404-9.pdf; doi:https://doi.org/10.1038/s41746-021-00404-9; html:https://europepmc.org/articles/PMC7910461; pdf:https://europepmc.org/articles/PMC7910461?pdf=render
 32150548,https://doi.org/10.1371/journal.pgen.1008605,The influence of rare variants in circulating metabolic biomarkers.,"Riveros-Mckay F, Oliver-Williams C, Karthikeyan S, Walter K, Kundu K, Ouwehand WH, Roberts D, Di Angelantonio E, Soranzo N, Danesh J, INTERVAL Study, Wheeler E, Zeggini E, Butterworth AS, Barroso I.",,PLoS genetics,2020,2020-03-09,Y,,Understanding the Causes of Disease,cardiovascular,"Circulating metabolite levels are biomarkers for cardiovascular disease (CVD). Here we studied, association of rare variants and 226 serum lipoproteins, lipids and amino acids in 7,142 (discovery plus follow-up) healthy participants. We leveraged the information from multiple metabolite measurements on the same participants to improve discovery in rare variant association analyses for gene-based and gene-set tests by incorporating correlated metabolites as covariates in the validation stage. Gene-based analysis corrected for the effective number of tests performed, confirmed established associations at APOB, APOC3, PAH, HAL and PCSK (p<1.32x10-7) and identified novel gene-trait associations at a lower stringency threshold with ACSL1, MYCN, FBXO36 and B4GALNT3 (p<2.5x10-6). Regulation of the pyruvate dehydrogenase (PDH) complex was associated for the first time, in gene-set analyses also corrected for effective number of tests, with IDL and LDL parameters, as well as circulating cholesterol (pMETASKAT<2.41x10-6). In conclusion, using an approach that leverages metabolite measurements obtained in the same participants, we identified novel loci and pathways involved in the regulation of these important metabolic biomarkers. As large-scale biobanks continue to amass sequencing and phenotypic information, analytical approaches such as ours will be useful to fully exploit the copious amounts of biological data generated in these efforts.",,pdf:https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1008605&type=printable; doi:https://doi.org/10.1371/journal.pgen.1008605; html:https://europepmc.org/articles/PMC7108731; pdf:https://europepmc.org/articles/PMC7108731?pdf=render
 33724919,https://doi.org/10.2196/26627,Artificial Intelligence-Enabled Analysis of Public Attitudes on Facebook and Twitter Toward COVID-19 Vaccines in the United Kingdom and the United States: Observational Study.,"Hussain A, Tahir A, Hussain Z, Sheikh Z, Gogate M, Dashtipour K, Ali A, Sheikh A.",,Journal of medical Internet research,2021,2021-04-05,Y,Artificial intelligence; Vaccination; Public Health; Health Informatics; Natural Language Processing; Facebook; Social Media; Twitter; Sentiment Analysis; Infodemiology; Deep Learning; Covid-19,,,"<h4>Background</h4>Global efforts toward the development and deployment of a vaccine for COVID-19 are rapidly advancing. To achieve herd immunity, widespread administration of vaccines is required, which necessitates significant cooperation from the general public. As such, it is crucial that governments and public health agencies understand public sentiments toward vaccines, which can help guide educational campaigns and other targeted policy interventions.<h4>Objective</h4>The aim of this study was to develop and apply an artificial intelligence-based approach to analyze public sentiments on social media in the United Kingdom and the United States toward COVID-19 vaccines to better understand the public attitude and concerns regarding COVID-19 vaccines.<h4>Methods</h4>Over 300,000 social media posts related to COVID-19 vaccines were extracted, including 23,571 Facebook posts from the United Kingdom and 144,864 from the United States, along with 40,268 tweets from the United Kingdom and 98,385 from the United States from March 1 to November 22, 2020. We used natural language processing and deep learning-based techniques to predict average sentiments, sentiment trends, and topics of discussion. These factors were analyzed longitudinally and geospatially, and manual reading of randomly selected posts on points of interest helped identify underlying themes and validated insights from the analysis.<h4>Results</h4>Overall averaged positive, negative, and neutral sentiments were at 58%, 22%, and 17% in the United Kingdom, compared to 56%, 24%, and 18% in the United States, respectively. Public optimism over vaccine development, effectiveness, and trials as well as concerns over their safety, economic viability, and corporation control were identified. We compared our findings to those of nationwide surveys in both countries and found them to correlate broadly.<h4>Conclusions</h4>Artificial intelligence-enabled social media analysis should be considered for adoption by institutions and governments alongside surveys and other conventional methods of assessing public attitude. Such analyses could enable real-time assessment, at scale, of public confidence and trust in COVID-19 vaccines, help address the concerns of vaccine sceptics, and help develop more effective policies and communication strategies to maximize uptake.",,pdf:https://www.jmir.org/2021/4/e26627/PDF; doi:https://doi.org/10.2196/26627; html:https://europepmc.org/articles/PMC8023383
 37338017,https://doi.org/10.1111/jvh.13863,Contribution of alcohol use in HIV/hepatitis C virus co-infection to all-cause and cause-specific mortality: A collaboration of cohort studies.,"Trickey A, Ingle SM, Boyd A, Gill MJ, Grabar S, Jarrin I, Obel N, Touloumi G, Zangerle R, Rauch A, Rentsch CT, Satre DD, Silverberg MJ, Bonnet F, Guest J, Burkholder G, Crane H, Teira R, Berenguer J, Wyen C, Abgrall S, Hessamfar M, Reiss P, d'Arminio Monforte A, McGinnis KA, Sterne JAC, Wittkop L, Antiretroviral Therapy Cohort Collaboration.",,Journal of viral hepatitis,2023,2023-06-20,Y,Mortality; Alcohol; Hepatitis C virus; HIV; Cohort; Cause-specific,,,"Among persons with HIV (PWH), higher alcohol use and having hepatitis C virus (HCV) are separately associated with increased morbidity and mortality. We investigated whether the association between alcohol use and mortality among PWH is modified by HCV. Data were combined from European and North American cohorts of adult PWH who started antiretroviral therapy (ART). Self-reported alcohol use data, collected in diverse ways between cohorts, were converted to grams/day. Eligible PWH started ART during 2001-2017 and were followed from ART initiation for mortality. Interactions between the associations of baseline alcohol use (0, 0.1-20.0, >20.0 g/day) and HCV status were assessed using multivariable Cox models. Of 58,769 PWH, 29,711 (51%), 23,974 (41%) and 5084 (9%) self-reported alcohol use of 0 g/day, 0.1-20.0 g/day, and > 20.0 g/day, respectively, and 4799 (8%) had HCV at baseline. There were 844 deaths in 37,729 person-years and 2755 deaths in 443,121 person-years among those with and without HCV, respectively. Among PWH without HCV, adjusted hazard ratios (aHRs) for mortality were 1.18 (95% CI: 1.08-1.29) for 0.0 g/day and 1.84 (1.62-2.09) for >20.0 g/day compared with 0.1-20.0 g/day. This J-shaped pattern was absent among those with HCV: aHRs were 1.00 (0.86-1.17) for 0.0 g/day and 1.64 (1.33-2.02) for >20.0 g/day compared with 0.1-20.0 g/day (interaction p < .001). Among PWH without HCV, mortality was higher in both non-drinkers and heavy drinkers compared with moderate alcohol drinkers. Among those with HCV, mortality was higher in heavy drinkers but not non-drinkers, potentially due to differing reasons for not drinking (e.g. illness) between those with and without HCV.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/jvh.13863; doi:https://doi.org/10.1111/jvh.13863; html:https://europepmc.org/articles/PMC10526649; pdf:https://europepmc.org/articles/PMC10526649?pdf=render
-36335192,https://doi.org/10.1038/s41598-022-22218-9,"Genetic insights into smoking behaviours in 10,558 men of African ancestry from continental Africa and the UK.","Piga NN, Boua PR, Soremekun C, Shrine N, Coley K, Brandenburg JT, Tobin MD, Ramsay M, Fatumo S, Choudhury A, Batini C.",,Scientific reports,2022,2022-11-05,Y,,,,"Smoking is a leading risk factor for many of the top ten causes of death worldwide. Of the 1.3 billion smokers globally, 80% live in low- and middle-income countries, where the number of deaths due to tobacco use is expected to double in the next decade according to the World Health Organization. Genetic studies have helped to identify biological pathways for smoking behaviours, but have mostly focussed on individuals of European ancestry or living in either North America or Europe. We performed a genome-wide association study of two smoking behaviour traits in 10,558 men of African ancestry living in five African countries and the UK. Eight independent variants were associated with either smoking initiation or cessation at P-value < 5 × 10<sup>-6</sup>, four being monomorphic or rare in European populations. Gene prioritisation strategy highlighted five genes, including SEMA6D, previously described as associated with several smoking behaviour traits. These results confirm the importance of analysing underrepresented populations in genetic epidemiology, and the urgent need for larger genomic studies to boost discovery power to better understand smoking behaviours, as well as many other traits.",,pdf:https://www.nature.com/articles/s41598-022-22218-9.pdf; doi:https://doi.org/10.1038/s41598-022-22218-9; html:https://europepmc.org/articles/PMC9637114; pdf:https://europepmc.org/articles/PMC9637114?pdf=render
 31699727,https://doi.org/10.1136/bmjopen-2019-030882,Optical coherence tomography (OCT) in unconscious and systemically unwell patients using a mobile OCT device: a pilot study.,"Liu X, Kale AU, Capewell N, Talbot N, Ahmed S, Keane PA, Mollan S, Belli A, Blanch RJ, Veenith T, Denniston AK.",,BMJ open,2019,2019-11-07,Y,optical coherence tomography; Optical Coherence Tomography Angiography; Adult Intensive & Critical Care,,,"<h4>Objective</h4>This study aims to evaluate the feasibility of retinal imaging in critical care using a novel mobile optical coherence tomography (OCT) device. The Heidelberg SPECTRALIS FLEX module (Heidelberg Engineering, Heidelberg, Germany) is an OCT unit with a boom arm, enabling ocular OCT assessment in less mobile patients.<h4>Design</h4>We undertook an evaluation of the feasibility of using the SPECTRALIS FLEX for undertaking ocular OCT images in unconscious and critically ill patients.<h4>Setting</h4>This study was conducted in the critical care unit of a large tertiary referral unit in the United Kingdom.<h4>Participants</h4>13 systemically unwell patients admitted to the critical care unit were purposively sampled to enable evaluation in patients with a range of clinical states.<h4>Outcome measures</h4>The primary outcome was the feasibility of acquiring clinically interpretable OCT scans on a consecutive series of patients. The standardised scanning protocol included macula-focused OCT, OCT optic nerve head (ONH), OCT angiography (OCTA) of the macula and ONH OCTA.<h4>Results</h4>OCT images from 13 patients were attempted. The success rates of each scan type are 84% for OCT macula, 76% for OCT ONH, 56% for OCTA macula and 36% for OCTA ONH. The overall mean success rate of scans per patient was 64% (95% CI 46% to 81%). Clinicians reported clinical value in 100% scans which were successfully obtained, including both ruling in and ruling out relevant ocular complications such as corneal thinning, macular oedema and optic disc swelling. The most common causes of failure to achieve clinically interpretable scans were inadequately sustained OCT alignment in delirious patients and a compromised ocular surface due to corneal exposure.<h4>Conclusions</h4>This prospective evaluation indicates the feasibility and potential clinical value of the SPECTRALIS FLEX OCT system on the critical care unit. Portable OCT systems have the potential to bring instrument-based ophthalmic assessment to critically ill patients, enabling detection and micron-level monitoring of ocular complications.",,pdf:https://bmjopen.bmj.com/content/bmjopen/9/11/e030882.full.pdf; doi:https://doi.org/10.1136/bmjopen-2019-030882; html:https://europepmc.org/articles/PMC6858135; pdf:https://europepmc.org/articles/PMC6858135?pdf=render
+36335192,https://doi.org/10.1038/s41598-022-22218-9,"Genetic insights into smoking behaviours in 10,558 men of African ancestry from continental Africa and the UK.","Piga NN, Boua PR, Soremekun C, Shrine N, Coley K, Brandenburg JT, Tobin MD, Ramsay M, Fatumo S, Choudhury A, Batini C.",,Scientific reports,2022,2022-11-05,Y,,,,"Smoking is a leading risk factor for many of the top ten causes of death worldwide. Of the 1.3 billion smokers globally, 80% live in low- and middle-income countries, where the number of deaths due to tobacco use is expected to double in the next decade according to the World Health Organization. Genetic studies have helped to identify biological pathways for smoking behaviours, but have mostly focussed on individuals of European ancestry or living in either North America or Europe. We performed a genome-wide association study of two smoking behaviour traits in 10,558 men of African ancestry living in five African countries and the UK. Eight independent variants were associated with either smoking initiation or cessation at P-value < 5 × 10<sup>-6</sup>, four being monomorphic or rare in European populations. Gene prioritisation strategy highlighted five genes, including SEMA6D, previously described as associated with several smoking behaviour traits. These results confirm the importance of analysing underrepresented populations in genetic epidemiology, and the urgent need for larger genomic studies to boost discovery power to better understand smoking behaviours, as well as many other traits.",,pdf:https://www.nature.com/articles/s41598-022-22218-9.pdf; doi:https://doi.org/10.1038/s41598-022-22218-9; html:https://europepmc.org/articles/PMC9637114; pdf:https://europepmc.org/articles/PMC9637114?pdf=render
 37391266,https://doi.org/10.1016/s2589-7500(23)00087-0,Wearable technology and the cardiovascular system: the future of patient assessment.,"Williams GJ, Al-Baraikan A, Rademakers FE, Ciravegna F, van de Vosse FN, Lawrie A, Rothman A, Ashley EA, Wilkins MR, Lawford PV, Omholt SW, Wisløff U, Hose DR, Chico TJA, Gunn JP, Morris PD.",,The Lancet. Digital health,2023,2023-07-01,N,,,,"The past decade has seen a dramatic rise in consumer technologies able to monitor a variety of cardiovascular parameters. Such devices initially recorded markers of exercise, but now include physiological and health-care focused measurements. The public are keen to adopt these devices in the belief that they are useful to identify and monitor cardiovascular disease. Clinicians are therefore often presented with health app data accompanied by a diverse range of concerns and queries. Herein, we assess whether these devices are accurate, their outputs validated, and whether they are suitable for professionals to make management decisions. We review underpinning methods and technologies and explore the evidence supporting the use of these devices as diagnostic and monitoring tools in hypertension, arrhythmia, heart failure, coronary artery disease, pulmonary hypertension, and valvular heart disease. Used correctly, they might improve health care and support research.",,pdf:http://www.thelancet.com/article/S2589750023000870/pdf; doi:https://doi.org/10.1016/S2589-7500(23)00087-0
 37096818,https://doi.org/10.1093/ehjacc/zuad042,"Serially measured high-sensitivity cardiac troponin T, N-terminal-pro-B-type natriuretic peptide, high-sensitivity C-reactive protein, and growth differentiation factor 15 for risk assessment after acute coronary syndrome: the BIOMArCS cohort.","Gürgöze MT, Akkerhuis KM, Oemrawsingh RM, Umans VAWM, Kietselaer B, Schotborgh CE, Ronner E, Lenderink T, Aksoy I, van der Harst P, Asselbergs FW, Maas AC, Oude Ophuis AJ, Krenning B, de Winter RJ, The SHK, Wardeh AJ, Hermans WRM, Cramer GE, van Gorp I, de Rijke YB, van Schaik RHN, Boersma E.",,European heart journal. Acute cardiovascular care,2023,2023-07-01,Y,Prognosis; Biomarkers; acute coronary syndrome; risk assessment; Repeated Measurements,,,"<h4>Aims</h4>Evidence regarding the role of serial measurements of biomarkers for risk assessment in post-acute coronary syndrome (ACS) patients is limited. The aim was to explore the prognostic value of four, serially measured biomarkers in a large, real-world cohort of post-ACS patients.<h4>Methods and results</h4>BIOMArCS is a prospective, multi-centre, observational study in 844 post-ACS patients in whom 12 218 blood samples (median 17 per patient) were obtained during 1-year follow-up. The longitudinal patterns of high-sensitivity cardiac troponin T (hs-cTnT), N-terminal-pro-B-type natriuretic peptide (NT-proBNP), high-sensitivity C-reactive protein (hs-CRP), and growth differentiation factor 15 (GDF-15) were analysed in relation to the primary endpoint (PE) of cardiovascular mortality and recurrent ACS using multivariable joint models. Median age was 63 years, 78% were men and the PE was reached by 45 patients. The average biomarker levels were systematically higher in PE compared with PE-free patients. After adjustment for 6-month post-discharge Global Registry of Acute Coronary Events score, 1 standard deviation increase in log[hs-cTnT] was associated with a 61% increased risk of the PE [hazard ratio (HR) 1.61, 95% confidence interval (CI) 1.02-2.44, P = 0.045], while for log[GDF-15] this was 81% (HR 1.81, 95% CI 1.28-2.70, P = 0.001). These associations remained significant after multivariable adjustment, while NT-proBNP and hs-CRP were not. Furthermore, GDF-15 level showed an increasing trend prior to the PE (Structured Graphical Abstract).<h4>Conclusion</h4>Longitudinally measured hs-cTnT and GDF-15 concentrations provide prognostic value in the risk assessment of clinically stabilized patients post-ACS.<h4>Clinical trial registration</h4>The Netherlands Trial Register. Currently available at URL https://trialsearch.who.int/; Unique Identifiers: NTR1698 and NTR1106.",,pdf:https://academic.oup.com/ehjacc/advance-article-pdf/doi/10.1093/ehjacc/zuad042/50087609/zuad042.pdf; doi:https://doi.org/10.1093/ehjacc/zuad042; html:https://europepmc.org/articles/PMC10328437; pdf:https://europepmc.org/articles/PMC10328437?pdf=render
 35193912,https://doi.org/10.1136/bmjopen-2021-053884,"Variation in health visiting contacts for children in England: cross-sectional analysis of the 2-2½ year review using administrative data (Community Services Dataset, CSDS).","Fraser C, Harron K, Barlow J, Bennett S, Woods G, Shand J, Kendall S, Woodman J.",,BMJ open,2022,2022-02-22,Y,Public Health; Community Child Health; Child Protection; Organisation Of Health Services,,,"<h4>Objective</h4>The 2-2½ year universal health visiting review in England is a key time point for assessing child development and promoting school readiness. We aimed to ascertain which children were least likely to receive their 2-2½ year review and whether there were additional non-mandated contacts for children who missed this review.<h4>Design, setting, participants</h4>Cross-sectional analysis of the 2-2½ year review and additional health visiting contacts for 181 130 children aged 2 in England 2018/2019, stratified by ethnicity, deprivation, safeguarding vulnerability indicator and Looked After Child status.<h4>Analysis</h4>We used data from 33 local authorities submitting highly complete data on health visiting contacts to the Community Services Dataset. We calculated the percentage of children with a recorded 2-2½ year review and/or any additional health visiting contacts and average number of contacts, by child characteristic.<h4>Results</h4>The most deprived children were slightly less likely to receive a 2-2½ year review than the least deprived children (72% vs 78%) and Looked After Children much less likely, compared with other children (44% vs 69%). When all additional contacts were included, the pattern was reversed (deprivation) or disappeared (Looked After children). A substantial proportion of all children (24%), children with a 'safeguarding vulnerability' (22%) and Looked After children (29%) did not have a record of either a 2-2½ year review or any other face-to-face contact in the year.<h4>Conclusions</h4>A substantial minority of children aged 2 with known vulnerabilities did not see the health visiting team at all in the year. Some higher need children (eg, deprived and Looked After) appeared to be seeing the health visiting team but not receiving their mandated health review. Further work is needed to establish the reasons for this, and potential solutions. There is an urgent need to improve the quality of national health visiting data.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/2/e053884.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-053884; html:https://europepmc.org/articles/PMC8867374; pdf:https://europepmc.org/articles/PMC8867374?pdf=render
 33782080,https://doi.org/10.1136/thoraxjnl-2020-216512,Impact of COVID-19 national lockdown on asthma exacerbations: interrupted time-series analysis of English primary care data.,"Shah SA, Quint JK, Nwaru BI, Sheikh A.",,Thorax,2021,2021-03-29,Y,Asthma; Asthma Epidemiology; Covid-19,,,"<h4>Background</h4>The impact of COVID-19 and ensuing national lockdown on asthma exacerbations is unclear.<h4>Methods</h4>We conducted an interrupted time-series (lockdown on 23 March 2020 as point of interruption) analysis in asthma cohort identified using a validated algorithm from a national-level primary care database, the Optimum Patient Care Database. We derived asthma exacerbation rates for every week and compared exacerbation rates in the period: January to August 2020 with a pre-COVID-19 period and January to August 2016-2019. Exacerbations were defined as asthma-related hospital attendance/admission (including accident and emergency visit), or an acute course of oral corticosteroids with evidence of respiratory review, as recorded in primary care. We used a generalised least squares modelling approach and stratified the analyses by age, sex, English region and healthcare setting.<h4>Results</h4>From a database of 9 949 387 patients, there were 100 165 patients with asthma who experienced at least one exacerbation during 2016-2020. Of 278 996 exacerbation episodes, 49 938 (17.9%) required hospital visit. Comparing pre-lockdown to post-lockdown period, we observed a statistically significant reduction in the level (-0.196 episodes per person-year; p<0.001; almost 20 episodes for every 100 patients with asthma per year) of exacerbation rates across all patients. The reductions in level in stratified analyses were: 0.005-0.244 (healthcare setting, only those without hospital attendance/admission were significant), 0.210-0.277 (sex), 0.159-0.367 (age), 0.068-0.590 (region).<h4>Conclusions</h4>There has been a significant reduction in attendance to primary care for asthma exacerbations during the pandemic. This reduction was observed in all age groups, both sexes and across most regions in England.",,pdf:https://thorax.bmj.com/content/thoraxjnl/76/9/860.full.pdf; doi:https://doi.org/10.1136/thoraxjnl-2020-216512; html:https://europepmc.org/articles/PMC8011425; pdf:https://europepmc.org/articles/PMC8011425?pdf=render
 33825703,https://doi.org/10.1107/s2059798321000826,Vagabond: bond-based parametrization reduces overfitting for refinement of proteins.,Ginn HM.,,"Acta crystallographica. Section D, Structural biology",2021,2021-03-30,Y,Models; X-ray diffraction; Protein Flexibility; Bonds; Refinement Software,,,"Structural biology methods have delivered over 150 000 high-resolution structures of macromolecules, which have fundamentally altered our understanding of biology and our approach to developing new medicines. However, the description of molecular flexibility is instrinsically flawed and in almost all cases, regardless of the experimental method used for structure determination, there remains a strong overfitting bias during molecular model building and refinement. In the worst case this can lead to wholly incorrect structures and thus incorrect biological interpretations. Here, by reparametrizing the description of these complex structures in terms of bonds rather than atomic positions, and by modelling flexibility using a deterministic ensemble of structures, it is demonstrated that structures can be described using fewer parameters than in conventional refinement. The current implementation, applied to X-ray diffraction data, significantly reduces the extent of overfitting, allowing the experimental data to reveal more biological information in electron-density maps.",,pdf:https://journals.iucr.org/d/issues/2021/04/00/qj5007/qj5007.pdf; doi:https://doi.org/10.1107/S2059798321000826; html:https://europepmc.org/articles/PMC8025884; pdf:https://europepmc.org/articles/PMC8025884?pdf=render
 36962407,https://doi.org/10.1371/journal.pgph.0000292,Health worker experiences of implementing TB infection prevention and control: A qualitative evidence synthesis to inform implementation recommendations.,"van der Westhuizen HM, Dorward J, Roberts N, Greenhalgh T, Ehrlich R, Butler CC, Tonkin-Crine S.",,PLOS global public health,2022,2022-07-07,Y,,,,"Implementation of TB infection prevention and control (IPC) measures in health facilities is frequently inadequate, despite nosocomial TB transmission to patients and health workers causing harm. We aimed to review qualitative evidence of the complexity associated with implementing TB IPC, to help guide the development of TB IPC implementation plans. We undertook a qualitative evidence synthesis of studies that used qualitative methods to explore the experiences of health workers implementing TB IPC in health facilities. We searched eight databases in November 2021, complemented by citation tracking. Two reviewers screened titles and abstracts and reviewed full texts of potentially eligible papers. We used the Critical Appraisals Skills Programme checklist for quality appraisal, thematic synthesis to identify key findings and the GRADE-CERQual method to appraise the certainty of review findings. The review protocol was pre-registered on PROSPERO, ID CRD42020165314. We screened 1062 titles and abstracts and reviewed 102 full texts, with 37 studies included in the synthesis. We developed 10 key findings, five of which we had high confidence in. We describe several components of TB IPC as a complex intervention. Health workers were influenced by their personal occupational TB risk perceptions when deciding whether to implement TB IPC and neglected the contribution of TB IPC to patient safety. Health workers and researchers expressed multiple uncertainties (for example the duration of infectiousness of people with TB), assumptions and misconceptions about what constitutes effective TB IPC, including focussing TB IPC on patients known with TB on treatment who pose a small risk of transmission. Instead, TB IPC resources should target high risk areas for transmission (crowded, poorly ventilated spaces). Furthermore, TB IPC implementation plans should support health workers to translate TB IPC guidelines to local contexts, including how to navigate unintended stigma caused by IPC, and using limited IPC resources effectively.",,pdf:https://journals.plos.org/globalpublichealth/article/file?id=10.1371/journal.pgph.0000292&type=printable; doi:https://doi.org/10.1371/journal.pgph.0000292; html:https://europepmc.org/articles/PMC10021216; pdf:https://europepmc.org/articles/PMC10021216?pdf=render
-38371671,https://doi.org/10.1016/j.jdin.2023.09.007,Fasting blood glucose and insulin are not associated with atopic dermatitis in a pediatric population: A longitudinal cohort study from the Avon Longitudinal Study of Parents and Children.,"Shan J, Ye M, Ku E, McCulloch CE, Langan SM, Abuabara K.",,JAAD international,2024,2023-10-23,N,Diabetes mellitus; Biomarkers; Clinical research; epidemiology; endocrinology; Atopic Dermatitis; Alspac; Pediatric Dermatology,,,,,doi:https://doi.org/10.1016/j.jdin.2023.09.007; html:https://europepmc.org/articles/PMC10869312; pdf:https://europepmc.org/articles/PMC10869312?pdf=render; doi:https://doi.org/10.1016/j.jdin.2023.09.007
 35099396,https://doi.org/10.2196/21341,"Collaborative Research and Development of a Novel, Patient-Centered Digital Platform (MyEyeSite) for Rare Inherited Retinal Disease Data: Acceptability and Feasibility Study.","Gilbert RM, Sumodhee D, Pontikos N, Hollyhead C, Patrick A, Scarles S, Van Der Smissen S, Young RM, Nettleton N, Webster AR, Cammack J.",,JMIR formative research,2022,2022-01-31,Y,Genetics; Mobile phone; Ophthalmology; Rare Diseases; Digital Health; Gdpr; Eye Data; Inherited Retinal Diseases (Ird); Myeyesite; Subject Access Request (Sar),,,"<h4>Background</h4>Inherited retinal diseases (IRDs) are a leading cause of blindness in children and working age adults in the United Kingdom and other countries, with an appreciable socioeconomic impact. However, by definition, IRD data are individually rare, and as a result, this patient group has been underserved by research. Researchers need larger amounts of these rare data to make progress in this field, for example, through the development of gene therapies. The challenge has been how to find and make these data available to researchers in the most productive way. MyEyeSite is a research collaboration aiming to design and develop a digital platform (the MyEyeSite platform) for people with rare IRDs that will enable patients, doctors, and researchers to aggregate and share specialist eye health data. A crucial component of this platform is the MyEyeSite patient application, which will provide the means for patients with IRD to interact with the system and, in particular, to collate, manage, and share their personal specialist IRD data both for research and their own health care.<h4>Objective</h4>This study aims to test the acceptability and feasibility of the MyEyeSite platform in the target IRD population through a collaborative patient-centered study.<h4>Methods</h4>Qualitative data were generated through focus groups and workshops, and quantitative data were obtained through a survey of patients with IRD. Participants were recruited through clinics at Moorfields Eye Hospital National Health Service (NHS) Foundation Trust and the National Institute for Health Research (NIHR) Moorfields Biomedical Research Centre through their patient and public involvement databases.<h4>Results</h4>Our IRD focus group sample (n=50) highlighted the following themes: frustration with the current system regarding data sharing within the United Kingdom's NHS; positive expectations of the potential benefits of the MyEyeSite patient application, resulting from increased access to this specialized data; and concerns regarding data security, including potentially unethical use of the data outside the NHS. Of the surveyed 80 participants, 68 (85%) were motivated to have a more active role in their eye care and share their data for research purposes using a secure technology, such as a web application or mobile app.<h4>Conclusions</h4>This study demonstrates that patients with IRD are highly motivated to be actively involved in managing their own data for research and their own eye care. It demonstrates the feasibility of involving patients with IRD in the detailed design of the MyEyeSite platform exemplar, with input from the patient with IRD workshops playing a key role in determining both the functionality and accessibility of the designs and prototypes. The development of a user-centered technological solution to the problem of rare health data has the potential to benefit not only the patient with IRD community but also others with rare diseases.",,pdf:https://formative.jmir.org/2022/1/e21341/PDF; doi:https://doi.org/10.2196/21341; html:https://europepmc.org/articles/PMC8845013; pdf:https://europepmc.org/articles/PMC8845013?pdf=render
+38371671,https://doi.org/10.1016/j.jdin.2023.09.007,Fasting blood glucose and insulin are not associated with atopic dermatitis in a pediatric population: A longitudinal cohort study from the Avon Longitudinal Study of Parents and Children.,"Shan J, Ye M, Ku E, McCulloch CE, Langan SM, Abuabara K.",,JAAD international,2024,2023-10-23,N,Diabetes mellitus; Biomarkers; Clinical research; epidemiology; endocrinology; Atopic Dermatitis; Alspac; Pediatric Dermatology,,,,,doi:https://doi.org/10.1016/j.jdin.2023.09.007; html:https://europepmc.org/articles/PMC10869312; pdf:https://europepmc.org/articles/PMC10869312?pdf=render; doi:https://doi.org/10.1016/j.jdin.2023.09.007
 29966429,https://doi.org/10.1177/2047487318785228,"Clinically recorded heart rate and incidence of 12 coronary, cardiac, cerebrovascular and peripheral arterial diseases in 233,970 men and women: A linked electronic health record study.","Archangelidi O, Pujades-Rodriguez M, Timmis A, Jouven X, Denaxas S, Hemingway H.",,European journal of preventive cardiology,2018,2018-07-02,N,Heart rate; Sudden death; Heart Failure; cardiovascular; Linked Electronic Health Records,,,"Background In healthy population cohorts, resting heart rate above 90 bpm is associated with mortality from coronary heart disease, but it is not clear whether associations are present at lower heart rates or whether these associations differ between women. Methods The CALIBER resource of linked electronic health records from primary care, hospitalisations, myocardial infarction registry and cause-specific mortality in the UK was used to assess associations between resting heart rate and 12 fatal and non-fatal coronary, cardiac, cerebral and peripheral vascular cardiovascular diseases and death using Cox proportional hazard models. Results Among 233,970 patients, 29,690 fatal and non-fatal events occurred. Fully adjusted models showed that resting heart rate was not associated in men or women with cerebrovascular events. In men a resting heart rate of 70-79 bpm (29.1% of all men) versus less than 60 bpm was associated with an increased risk of heart failure (hazard ratio (HR) 1.65, 95% confidence interval (CI) 1.26-2.16), unheralded coronary death (HR 1.65, 95% CI 1.13-2.41), total cardiovascular events (HR 1.22, 95% CI 1.15-1.28) and all-cause mortality (HR 1.39, 95% CI 1.22-1.58). Women with a higher resting heart rate level of 80-89 bpm versus 60 bpm had a higher risk of total cardiovascular disease events (HR 1.17, 95% CI 1.07-1.24) and all-cause mortality (HR 1.21, 95% CI 1.07-1.35) compared to a resting heart rate less than 60 bpm. The risk was also present at higher heart rates (>90 bpm) for heart failure and sudden cardiac death. Conclusions A resting heart rate that clinicians currently consider as 'normal' in the general population is specifically associated with the incidence of certain major cardiovascular diseases and death, with the risk starting at lower resting heart rate levels in men compared to women. Further research is required to evaluate whether interventions to lower resting heart rate are warranted to prevent disease. The study is registered at: clinicaltrials.gov (ID: NCT01947361).",,pdf:http://eprints.whiterose.ac.uk/134568/7/OArchangelidi_EJPC_accepted.pdf; doi:https://doi.org/10.1177/2047487318785228
 35144751,https://doi.org/10.1016/j.jacc.2021.11.045,Echocardiographic Deformation Imaging for Early Detection of Genetic Cardiomyopathies: JACC Review Topic of the Week.,"Taha K, Kirkels FP, Teske AJ, Asselbergs FW, van Tintelen JP, Doevendans PA, Kutty S, Haugaa KH, Cramer MJ.",,Journal of the American College of Cardiology,2022,2022-02-01,N,Early Detection; Speckle Tracking; Family Screening; Deformation Imaging; Genetic Cardiomyopathy,,,"Clinical screening of the relatives of patients with genetic cardiomyopathies is challenging, as they often lack detectable cardiac abnormalities at presentation. Life-threatening adverse events can already occur in these early stages of disease, so sensitive tools to reveal the earliest signs of disease are needed. The utility of echocardiographic deformation imaging for early detection has been explored for this population in multiple studies but has not been broadly implemented in clinical practice. The authors discuss contemporary evidence on the utility of deformation imaging in relatives of patients with genetic cardiomyopathies. The available body of data shows that deformation imaging reveals early disease-specific abnormalities in dilated cardiomyopathy, hypertrophic cardiomyopathy, and arrhythmogenic cardiomyopathy. Deformation imaging seems promising to enhance the screening and follow-up protocols in relatives, and the authors propose measures to accelerate its implementation in clinical care.",,doi:https://doi.org/10.1016/j.jacc.2021.11.045; doi:https://doi.org/10.1016/j.jacc.2021.11.045
 34468736,https://doi.org/10.1093/europace/euab162,Comparing clinical performance of current implantable cardioverter-defibrillator implantation recommendations in arrhythmogenic right ventricular cardiomyopathy.,"Bosman LP, Bosman LP, Nielsen Gerlach CL, Cadrin-Tourigny J, Orgeron G, Tichnell C, Murray B, Bourfiss M, van der Heijden JF, Yap SC, Zeppenfeld K, van den Berg MP, Wilde AAM, Asselbergs FW, Tandri H, Calkins H, van Tintelen JP, James CA, Te Riele ASJM.",,"Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology",2022,2022-02-01,Y,Prognosis; Risk stratification; Ventricular Arrhythmias; Implantable Cardioverter-defibrillator; Arrhythmogenic Right Ventricular Cardiomyopathy,,,"<h4>Aims</h4>Arrhythmogenic right ventricular cardiomyopathy (ARVC) patients have an increased risk of ventricular arrhythmias (VA). Four implantable cardioverter-defibrillator (ICD) recommendation algorithms are available The International Task Force Consensus ('ITFC'), an ITFC modification by Orgeron et al. ('mITFC'), the AHA/HRS/ACC guideline for VA management ('AHA'), and the HRS expert consensus statement ('HRS'). This study aims to validate and compare the performance of these algorithms in ARVC.<h4>Methods and results</h4>We classified 617 definite ARVC patients (38.5 ± 15.1 years, 52.4% male, 39.2% prior sustained VA) according to four algorithms. Clinical performance was evaluated by sensitivity, specificity, ROC-analysis, and decision curve analysis for any sustained VA and for fast VA (>250 b.p.m.). During 6.4 [2.8-11.5] years follow-up, 282 (45.7%) patients experienced any sustained VA, and 63 (10.2%) fast VA. For any sustained VA, ITFC and mITFC provide higher sensitivity than AHA and HRS (94.0-97.8% vs. 76.7-83.5%), but lower specificity (15.9-32.0% vs. 42.7%-60.1%). Similarly, for fast VA, ITFC and mITFC provide higher sensitivity than AHA and HRS (95.2-97.1% vs. 76.7-78.4%) but lower specificity (42.7-43.1 vs. 76.7-78.4%). Decision curve analysis showed ITFC and mITFC to be superior for a 5-year sustained VA risk ICD indication threshold between 5-25% or 2-9% for fast VA.<h4>Conclusion</h4>The ITFC and mITFC provide the highest protection rates, whereas AHA and HRS decrease unnecessary ICD placements. ITFC or mITFC should be used if we consider the 5-year threshold for ICD indication to lie within 5-25% for sustained VA or 2-9% for fast VA. These data will inform decision-making for ICD placement in ARVC.",,pdf:https://academic.oup.com/europace/article-pdf/24/2/296/42370389/euab162.pdf; doi:https://doi.org/10.1093/europace/euab162; html:https://europepmc.org/articles/PMC8824519; pdf:https://europepmc.org/articles/PMC8824519?pdf=render
@@ -2093,32 +2095,32 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 34661196,https://doi.org/10.1093/ehjopen/oeab019,Pericoronary and periaortic adipose tissue density are associated with inflammatory disease activity in Takayasu arteritis and atherosclerosis.,"Wall C, Huang Y, Le EPV, Ćorović A, Uy CP, Gopalan D, Ma C, Manavaki R, Fryer TD, Aloj L, Graves MJ, Tombetti E, Ariff B, Bambrough P, Hoole SP, Rusk RA, Jayne DR, Dweck MR, Newby D, Fayad ZA, Bennett MR, Peters JE, Slomka P, Dey D, Mason JC, Rudd JHF, Tarkin JM.",,European heart journal open,2021,2021-08-06,Y,coronary artery disease; Takayasu Arteritis; Pericoronary Adipose Tissue Density,,,"<h4>Aims</h4>To examine pericoronary adipose tissue (PCAT) and periaortic adipose tissue (PAAT) density on coronary computed tomography angiography for assessing arterial inflammation in Takayasu arteritis (TAK) and atherosclerosis.<h4>Methods and results</h4>PCAT and PAAT density was measured in coronary (<i>n</i> = 1016) and aortic (<i>n</i> = 108) segments from 108 subjects [TAK + coronary artery disease (CAD), <i>n</i> = 36; TAK, <i>n</i> = 18; atherosclerotic CAD, <i>n</i> = 32; matched controls, <i>n</i> = 22]. Median PCAT and PAAT densities varied between groups (mPCAT: <i>P</i> < 0.0001; PAAT: <i>P</i> = 0.0002). PCAT density was 7.01 ± standard error of the mean (SEM) 1.78 Hounsfield Unit (HU) higher in coronary segments from TAK + CAD patients than stable CAD patients (<i>P</i> = 0.0002), and 8.20 ± SEM 2.04 HU higher in TAK patients without CAD than controls (<i>P</i> = 0.0001). mPCAT density was correlated with Indian Takayasu Clinical Activity Score (<i>r</i> = 0.43, <i>P</i> = 0.001) and C-reactive protein (<i>r</i> = 0.41, <i>P</i> < 0.0001) and was higher in active vs. inactive TAK (<i>P</i> = 0.002). mPCAT density above -74 HU had 100% sensitivity and 95% specificity for differentiating active TAK from controls [area under the curve = 0.99 (95% confidence interval 0.97-1)]. The association of PCAT density and coronary arterial inflammation measured by <sup>68</sup>Ga-DOTATATE positron emission tomography (PET) equated to an increase of 2.44 ± SEM 0.77 HU in PCAT density for each unit increase in <sup>68</sup>Ga-DOTATATE maximum tissue-to-blood ratio (<i>P</i> = 0.002). These findings remained in multivariable sensitivity analyses adjusted for potential confounders.<h4>Conclusions</h4>PCAT and PAAT density are higher in TAK than atherosclerotic CAD or controls and are associated with clinical, biochemical, and PET markers of inflammation. Owing to excellent diagnostic accuracy, PCAT density could be useful as a clinical adjunct for assessing disease activity in TAK.",,pdf:https://academic.oup.com/ehjopen/article-pdf/1/2/oeab019/41727950/oeab019.pdf; doi:https://doi.org/10.1093/ehjopen/oeab019; html:https://europepmc.org/articles/PMC8508012; pdf:https://europepmc.org/articles/PMC8508012?pdf=render
 33434193,https://doi.org/10.1371/journal.pmed.1003487,Accelerometer measured physical activity and the incidence of cardiovascular disease: Evidence from the UK Biobank cohort study.,"Ramakrishnan R, Doherty A, Smith-Byrne K, Rahimi K, Bennett D, Woodward M, Walmsley R, Dwyer T.",,PLoS medicine,2021,2021-01-12,Y,,,,"<h4>Background</h4>Higher levels of physical activity (PA) are associated with a lower risk of cardiovascular disease (CVD). However, uncertainty exists on whether the inverse relationship between PA and incidence of CVD is greater at the highest levels of PA. Past studies have mostly relied on self-reported evidence from questionnaire-based PA, which is crude and cannot capture all PA undertaken. We investigated the association between accelerometer-measured moderate, vigorous, and total PA and incident CVD.<h4>Methods and findings</h4>We obtained accelerometer-measured moderate-intensity and vigorous-intensity physical activities and total volume of PA, over a 7-day period in 2013-2015, for 90,211 participants without prior or concurrent CVD in the UK Biobank cohort. Participants in the lowest category of total PA smoked more, had higher body mass index and C-reactive protein, and were diagnosed with hypertension. PA was associated with 3,617 incident CVD cases during 440,004 person-years of follow-up (median (interquartile range [IQR]): 5.2 (1.2) years) using Cox regression models. We found a linear dose-response relationship for PA, whether measured as moderate-intensity, vigorous-intensity, or as total volume, with risk of incident of CVD. Hazard ratios (HRs) and 95% confidence intervals for increasing quarters of the PA distribution relative to the lowest fourth were for moderate-intensity PA: 0.71 (0.65, 0.77), 0.59 (0.54, 0.65), and 0.46 (0.41, 0.51); for vigorous-intensity PA: 0.70 (0.64, 0.77), 0.54 (0.49,0.59), and 0.41 (0.37,0.46); and for total volume of PA: 0.73 (0.67, 0.79), 0.63 (0.57, 0.69), and 0.47 (0.43, 0.52). We took account of potential confounders but unmeasured confounding remains a possibility, and while removal of early deaths did not affect the estimated HRs, we cannot completely dismiss the likelihood that reverse causality has contributed to the findings. Another possible limitation of this work is the quantification of PA intensity-levels based on methods validated in relatively small studies.<h4>Conclusions</h4>In this study, we found no evidence of a threshold for the inverse association between objectively measured moderate, vigorous, and total PA with CVD. Our findings suggest that PA is not only associated with lower risk for of CVD, but the greatest benefit is seen for those who are active at the highest level.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003487&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003487; html:https://europepmc.org/articles/PMC7802951; pdf:https://europepmc.org/articles/PMC7802951?pdf=render
 31815634,https://doi.org/10.1186/s12933-019-0972-4,Metformin use and cardiovascular outcomes after acute myocardial infarction in patients with type 2 diabetes: a cohort study.,"Bromage DI, Godec TR, Pujades-Rodriguez M, Gonzalez-Izquierdo A, Denaxas S, Hemingway H, Yellon DM.",,Cardiovascular diabetology,2019,2019-12-09,Y,Acute myocardial infarction; Type 2 diabetes; Cohort studies; Metformin; cardioprotection; Outcomes,,,"<h4>Background</h4>The use of metformin after acute myocardial infarction (AMI) has been associated with reduced mortality in people with type 2 diabetes mellitus (T2DM). However, it is not known if it is acutely cardioprotective in patients taking metformin at the time of AMI. We compared patient outcomes according to metformin status at the time of admission for fatal and non-fatal AMI in a large cohort of patients in England.<h4>Methods</h4>This study used linked data from primary care, hospital admissions and death registry from 4.7 million inhabitants in England, as part of the CALIBER resource. The primary endpoint was a composite of acute myocardial infarction requiring hospitalisation, stroke and cardiovascular death. The secondary endpoints were heart failure (HF) hospitalisation and all-cause mortality.<h4>Results</h4>4,030 patients with T2DM and incident AMI recorded between January 1998 and October 2010 were included. At AMI admission, 63.9% of patients were receiving metformin and 36.1% another oral hypoglycaemic drug. Median follow-up was 343 (IQR: 1-1436) days. Adjusted analyses showed an increased hazard of the composite endpoint in metformin users compared to non-users (HR 1.09 [1.01-1.19]), but not of the secondary endpoints. The higher risk of the composite endpoint in metformin users was only observed in people taking metformin at AMI admission, whereas metformin use post-AMI was associated with a reduction in risk of all-cause mortality (0.76 [0.62-0.93], P = 0.009).<h4>Conclusions</h4>Our study suggests that metformin use at the time of first AMI is associated with increased risk of cardiovascular disease and death in patients with T2DM, while its use post-AMI might be beneficial. Further investigation in well-designed randomised controlled trials is indicated, especially in view of emerging evidence of cardioprotection from sodium-glucose co-transporter-2 (SGLT2) inhibitors.",,pdf:https://cardiab.biomedcentral.com/track/pdf/10.1186/s12933-019-0972-4; doi:https://doi.org/10.1186/s12933-019-0972-4; html:https://europepmc.org/articles/PMC6900858; pdf:https://europepmc.org/articles/PMC6900858?pdf=render
-35279265,https://doi.org/10.1016/s2213-2600(21)00511-7,"Global, regional, and national prevalence of, and risk factors for, chronic obstructive pulmonary disease (COPD) in 2019: a systematic review and modelling analysis.","Adeloye D, Song P, Zhu Y, Campbell H, Sheikh A, Rudan I, NIHR RESPIRE Global Respiratory Health Unit.",,The Lancet. Respiratory medicine,2022,2022-03-10,Y,,,,"<h4>Background</h4>Chronic obstructive pulmonary disease (COPD) is an increasingly important cause of morbidity, disability, and mortality worldwide. We aimed to estimate global, regional, and national COPD prevalence and risk factors to guide policy and population interventions.<h4>Methods</h4>For this systematic review and modelling study, we searched MEDLINE, Embase, Global Health, and CINAHL, for population-based studies on COPD prevalence published between Jan 1, 1990, and Dec 31, 2019. We included data reported using the two main case definitions: the Global Initiative for Chronic Obstructive Lung Disease fixed ratio (GOLD; FEV<sub>1</sub>/FVC<0·7) and the lower limit of normal (LLN; FEV<sub>1</sub>/FVC<LLN). We employed a multilevel multivariable mixed-effects meta-regression approach to generate the age-specific and sex-specific prevalence of COPD in 2019 for high-income countries (HICs) and low-income and middle-income countries (LMICs) according to the World Bank definition. Common risk factors for GOLD-COPD were evaluated using a random-effects meta-analysis.<h4>Findings</h4>We identified 162 articles reporting population-based studies conducted across 260 sites in 65 countries. In 2019, the global prevalence of COPD among people aged 30-79 years was 10·3% (95% CI 8·2-12·8) using the GOLD case definition, which translates to 391·9 million people (95% CI 312·6-487·9), and 7·6% (5·8-10·1) using the LLN definition, which translates to 292·0 million people (219·8-385·6). Using the GOLD definition, we estimated that 391·9 million (95% CI 312·6-487·9) people aged 30-79 years had COPD worldwide in 2019, with most (315·5 million [246·7-399·6]; 80·5%) living in LMICs. The overall prevalence of GOLD-COPD among people aged 30-79 years was the highest in the Western Pacific region (11·7% [95% CI 9·3-14·6]) and lowest in the region of the Americas (6·8% [95% CI 5·6-8·2]). Globally, male sex (OR 2·1 [95% CI 1·8-2·3]), smoking (current smoker 3·2 [2·5-4·0]; ever smoker 2·3 [2·0-2·5]), body-mass index of less than 18·5 kg/m<sup>2</sup> (2·2 [1·7-2·7]), biomass exposure (1·4 [1·2-1·7]), and occupational exposure to dust or smoke (1·4 [1·3-1·6]) were all substantial risk factors for COPD.<h4>Interpretation</h4>With more than three-quarters of global COPD cases in LMICs, tackling this chronic condition is a major and increasing challenge for health systems in these settings. In the absence of targeted population-wide efforts and health system reforms in these settings, many of which are under-resourced, achieving a substantial reduction in the burden of COPD globally might remain a difficult task.<h4>Funding</h4>National Institute for Health Research and Health Data Research UK.",,doi:https://doi.org/10.1016/s2213-2600(21)00511-7; doi:https://doi.org/10.1016/S2213-2600(21)00511-7; html:https://europepmc.org/articles/PMC9050565
 37104291,https://doi.org/10.1371/journal.pmed.1004221,A nutritional biomarker score of the Mediterranean diet and incident type 2 diabetes: Integrated analysis of data from the MedLey randomised controlled trial and the EPIC-InterAct case-cohort study.,"Sobiecki JG, Imamura F, Davis CR, Sharp SJ, Koulman A, Hodgson JM, Guevara M, Schulze MB, Zheng JS, Agnoli C, Bonet C, Colorado-Yohar SM, Fagherazzi G, Franks PW, Gundersen TE, Jannasch F, Kaaks R, Katzke V, Molina-Montes E, Nilsson PM, Palli D, Panico S, Papier K, Rolandsson O, Sacerdote C, Tjønneland A, Tong TYN, van der Schouw YT, Danesh J, Butterworth AS, Riboli E, Murphy KJ, Wareham NJ, Forouhi NG.",,PLoS medicine,2023,2023-04-27,Y,,,,"<h4>Background</h4>Self-reported adherence to the Mediterranean diet has been modestly inversely associated with incidence of type 2 diabetes (T2D) in cohort studies. There is uncertainty about the validity and magnitude of this association due to subjective reporting of diet. The association has not been evaluated using an objectively measured biomarker of the Mediterranean diet.<h4>Methods and findings</h4>We derived a biomarker score based on 5 circulating carotenoids and 24 fatty acids that discriminated between the Mediterranean or habitual diet arms of a parallel design, 6-month partial-feeding randomised controlled trial (RCT) conducted between 2013 and 2014, the MedLey trial (128 participants out of 166 randomised). We applied this biomarker score in an observational study, the European Prospective Investigation into Cancer and Nutrition (EPIC)-InterAct case-cohort study, to assess the association of the score with T2D incidence over an average of 9.7 years of follow-up since the baseline (1991 to 1998). We included 22,202 participants, of whom 9,453 were T2D cases, with relevant biomarkers from an original case-cohort of 27,779 participants sampled from a cohort of 340,234 people. As a secondary measure of the Mediterranean diet, we used a score estimated from dietary-self report. Within the trial, the biomarker score discriminated well between the 2 arms; the cross-validated C-statistic was 0.88 (95% confidence interval (CI) 0.82 to 0.94). The score was inversely associated with incident T2D in EPIC-InterAct: the hazard ratio (HR) per standard deviation of the score was 0.71 (95% CI: 0.65 to 0.77) following adjustment for sociodemographic, lifestyle and medical factors, and adiposity. In comparison, the HR per standard deviation of the self-reported Mediterranean diet was 0.90 (95% CI: 0.86 to 0.95). Assuming the score was causally associated with T2D, higher adherence to the Mediterranean diet in Western European adults by 10 percentiles of the score was estimated to reduce the incidence of T2D by 11% (95% CI: 7% to 14%). The study limitations included potential measurement error in nutritional biomarkers, unclear specificity of the biomarker score to the Mediterranean diet, and possible residual confounding.<h4>Conclusions</h4>These findings suggest that objectively assessed adherence to the Mediterranean diet is associated with lower risk of T2D and that even modestly higher adherence may have the potential to reduce the population burden of T2D meaningfully.<h4>Trial registration</h4>Australian New Zealand Clinical Trials Registry (ANZCTR) ACTRN12613000602729 https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=363860.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004221&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004221; html:https://europepmc.org/articles/PMC10138823; pdf:https://europepmc.org/articles/PMC10138823?pdf=render
+35279265,https://doi.org/10.1016/s2213-2600(21)00511-7,"Global, regional, and national prevalence of, and risk factors for, chronic obstructive pulmonary disease (COPD) in 2019: a systematic review and modelling analysis.","Adeloye D, Song P, Zhu Y, Campbell H, Sheikh A, Rudan I, NIHR RESPIRE Global Respiratory Health Unit.",,The Lancet. Respiratory medicine,2022,2022-03-10,Y,,,,"<h4>Background</h4>Chronic obstructive pulmonary disease (COPD) is an increasingly important cause of morbidity, disability, and mortality worldwide. We aimed to estimate global, regional, and national COPD prevalence and risk factors to guide policy and population interventions.<h4>Methods</h4>For this systematic review and modelling study, we searched MEDLINE, Embase, Global Health, and CINAHL, for population-based studies on COPD prevalence published between Jan 1, 1990, and Dec 31, 2019. We included data reported using the two main case definitions: the Global Initiative for Chronic Obstructive Lung Disease fixed ratio (GOLD; FEV<sub>1</sub>/FVC<0·7) and the lower limit of normal (LLN; FEV<sub>1</sub>/FVC<LLN). We employed a multilevel multivariable mixed-effects meta-regression approach to generate the age-specific and sex-specific prevalence of COPD in 2019 for high-income countries (HICs) and low-income and middle-income countries (LMICs) according to the World Bank definition. Common risk factors for GOLD-COPD were evaluated using a random-effects meta-analysis.<h4>Findings</h4>We identified 162 articles reporting population-based studies conducted across 260 sites in 65 countries. In 2019, the global prevalence of COPD among people aged 30-79 years was 10·3% (95% CI 8·2-12·8) using the GOLD case definition, which translates to 391·9 million people (95% CI 312·6-487·9), and 7·6% (5·8-10·1) using the LLN definition, which translates to 292·0 million people (219·8-385·6). Using the GOLD definition, we estimated that 391·9 million (95% CI 312·6-487·9) people aged 30-79 years had COPD worldwide in 2019, with most (315·5 million [246·7-399·6]; 80·5%) living in LMICs. The overall prevalence of GOLD-COPD among people aged 30-79 years was the highest in the Western Pacific region (11·7% [95% CI 9·3-14·6]) and lowest in the region of the Americas (6·8% [95% CI 5·6-8·2]). Globally, male sex (OR 2·1 [95% CI 1·8-2·3]), smoking (current smoker 3·2 [2·5-4·0]; ever smoker 2·3 [2·0-2·5]), body-mass index of less than 18·5 kg/m<sup>2</sup> (2·2 [1·7-2·7]), biomass exposure (1·4 [1·2-1·7]), and occupational exposure to dust or smoke (1·4 [1·3-1·6]) were all substantial risk factors for COPD.<h4>Interpretation</h4>With more than three-quarters of global COPD cases in LMICs, tackling this chronic condition is a major and increasing challenge for health systems in these settings. In the absence of targeted population-wide efforts and health system reforms in these settings, many of which are under-resourced, achieving a substantial reduction in the burden of COPD globally might remain a difficult task.<h4>Funding</h4>National Institute for Health Research and Health Data Research UK.",,doi:https://doi.org/10.1016/s2213-2600(21)00511-7; doi:https://doi.org/10.1016/S2213-2600(21)00511-7; html:https://europepmc.org/articles/PMC9050565
 33062309,https://doi.org/10.1177/2059513120952336,Epidemiology of burn injury in older adults: An Australian and New Zealand perspective.,"Tracy LM, Singer Y, Schrale R, Gong J, Darton A, Wood F, Kurmis R, Edgar D, Cleland H, Gabbe BJ.",,"Scars, burns & healing",2020,2020-01-01,Y,Burns; Australia; New Zealand; Older Adults; scald; Burn Database,,,"<h4>Introduction</h4>The ageing global population presents a novel set of challenges for trauma systems. Less research has focused on the older adult population with burns and how they differ compared to younger patients. This study aimed to describe, and compare with younger peers, the number, causes and surgical management of older adults with burn injuries in Australia and New Zealand.<h4>Methods</h4>The Burns Registry of Australia and New Zealand was used to identify patients with burn injuries between 1 July 2009 and 31 December 2018. Temporal trends in incidence rates were evaluated and categorised by age at injury. Patient demographics, injury severity and event characteristics, surgical intervention and in-hospital outcomes were investigated.<h4>Results</h4>There were 2394 burn-injured older adults admitted during the study period, accounting for 13.4% of adult admissions. Scalds were the most common cause of burn injury in older adults. The incidence of older adult burns increased by 2.96% each year (incidence rate ratio = 1.030, 95% confidence interval = 1.013-1.046, <i>P</i> < 0.001). Compared to their younger peers, a smaller proportion of older adult patients were taken to theatre for a surgical procedure, though a larger proportion of older adults received a skin graft.<h4>Discussion</h4>Differences in patient and injury characteristics, surgical management and in-hospital outcomes were observed for older adults. These findings provide the Australian and New Zealand burn care community with a greater understanding of burn injury and their treatments in a unique group of patients who are at risk of poorer outcomes than younger people.<h4>Lay summary</h4>The number and proportion of older persons in every country of the world is growing. This may create challenges for healthcare systems. While burn injuries are a unique subset of trauma that affect individuals of all ages, less is known about burns in older adults and how they differ from younger patients.We wanted to look at the number, type, management, and outcomes of burns in older adults in Australia and New Zealand. To do this, we used data from the Burns Registry of Australia and New Zealand, or BRANZ. The BRANZ is a database that collects information on patients that present to Australian and New Zealand hospitals that have a specialist burns unit.Our research found that one in eight adult burns patients was over the age of 65, and that the rate of burn injuries in older adults has increased over the last decade. Older adult burns patients were most commonly affected by scalds after coming in contact with wet heat such as boiling liquids or steam. Fewer older adults went to theatre for an operation or surgical procedure compared to their younger counterparts. However, a larger proportion of older adults that went to theatre had a skin graft (where skin is removed from an uninjured part of the body and placed over the injured part).This research provides important information about a unique and growing group of patients to the local burn care community. It also highlights potential avenues for injury prevention initiatives.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/2059513120952336; doi:https://doi.org/10.1177/2059513120952336; html:https://europepmc.org/articles/PMC7534068; pdf:https://europepmc.org/articles/PMC7534068?pdf=render
 34632432,https://doi.org/10.1016/s2666-5247(21)00128-2,Epidemiology of <i>Mycobacterium abscessus</i> in England: an observational study.,"Lipworth S, Hough N, Weston N, Muller-Pebody B, Phin N, Myers R, Chapman S, Flight W, Alexander E, Smith EG, Robinson E, Peto TEA, Crook DW, Walker AS, Hopkins S, Eyre DW, Walker TM.",,The Lancet. Microbe,2021,2021-10-01,Y,,,,"<h4>Background</h4><i>Mycobacterium abscessus</i> has emerged as a significant clinical concern following reports that it is readily transmissible in health-care settings between patients with cystic fibrosis. We linked routinely collected whole-genome sequencing and health-care usage data with the aim of investigating the extent to which such transmission explains acquisition in patients with and without cystic fibrosis in England.<h4>Methods</h4>In this retrospective observational study, we analysed consecutive <i>M abscessus</i> whole-genome sequencing data from England (beginning of February, 2015, to Nov 14, 2019) to identify genomically similar isolates. Linkage to a national health-care usage database was used to investigate possible contacts between patients. Multivariable regression analysis was done to investigate factors associated with acquisition of a genomically clustered strain (genomic distance <25 single nucleotide polymorphisms [SNPs]).<h4>Findings</h4>2297 isolates from 906 patients underwent whole-genome sequencing as part of the routine Public Health England diagnostic service. Of 14 genomic clusters containing isolates from ten or more patients, all but one contained patients with cystic fibrosis and patients without cystic fibrosis. Patients with cystic fibrosis were equally likely to have clustered isolates (258 [60%] of 431 patients) as those without cystic fibrosis (322 [63%] of 513 patients; p=0·38). High-density phylogenetic clusters were randomly distributed over a wide geographical area. Most isolates with a closest genetic neighbour consistent with potential transmission had no identifiable relevant epidemiological contacts. Having a clustered isolate was independently associated with increasing age (adjusted odds ratio 1·14 per 10 years, 95% CI 1·04-1·26), but not time spent as an hospital inpatient or outpatient. We identified two sibling pairs with cystic fibrosis with genetically highly divergent isolates and one pair with closely related isolates, and 25 uninfected presumed household contacts with cystic fibrosis.<h4>Interpretation</h4>Previously identified widely disseminated dominant clones of <i>M abscessus</i> are not restricted to patients with cystic fibrosis and occur in other chronic respiratory diseases. Although our analysis showed a small number of cases where person-to-person transmission could not be excluded, it did not support this being a major mechanism for <i>M abscessus</i> dissemination at a national level in England. Overall, these data should reassure patients and clinicians that the risk of acquisition from other patients in health-care settings is relatively low and motivate future research efforts to focus on identifying routes of acquisition outside of the cystic fibrosis health-care-associated niche.<h4>Funding</h4>The National Institute for Health Research, Health Data Research UK, The Wellcome Trust, The Medical Research Council, and Public Health England.",,pdf:http://www.thelancet.com/article/S2666524721001282/pdf; doi:https://doi.org/10.1016/S2666-5247(21)00128-2; html:https://europepmc.org/articles/PMC8481905
 36357634,https://doi.org/10.1007/s00467-022-05789-7,Shared genetic risk across different presentations of gene test-negative idiopathic nephrotic syndrome.,"Downie ML, Gupta S, Chan MMY, Sadeghi-Alavijeh O, Cao J, Parekh RS, Diz CB, Bierzynska A, Levine AP, Pepper RJ, Stanescu H, Saleem MA, Kleta R, Bockenhauer D, Koziell AB, Gale DP.",,"Pediatric nephrology (Berlin, Germany)",2023,2022-11-10,Y,Paediatrics; Minimal Change Disease; Focal Segmental Glomerulosclerosis; Monogenic; Genetic Risk Score; Steroid-resistant Nephrotic Syndrome; Steroid-sensitive Nephrotic Syndrome,,,"<h4>Background</h4>Idiop athic nephrotic syndrome (INS) is classified in children according to response to initial corticosteroid therapy into steroid-sensitive (SSNS) and steroid-resistant nephrotic syndrome (SRNS), and in adults according to histology into minimal change disease (MCD) and focal segmental glomerulosclerosis (FSGS). However, there is well-recognised phenotypic overlap between these entities. Genome-wide association studies (GWAS) have shown a strong association between SSNS and variation at HLA, suggesting an underlying immunological basis. We sought to determine whether a risk score generated from genetic variants associated with SSNS could be used to gain insight into the pathophysiology of INS presenting in other ways.<h4>Methods</h4>We developed an SSNS genetic risk score (SSNS-GRS) from the five variants independently associated with childhood SSNS in a previous European GWAS. We quantified SSNS-GRS in independent cohorts of European individuals with childhood SSNS, non-monogenic SRNS, MCD, and FSGS, and contrasted them with SSNS-GRS quantified in individuals with monogenic SRNS, membranous nephropathy (a different immune-mediated disease-causing nephrotic syndrome), and healthy controls.<h4>Results</h4>The SSNS-GRS was significantly elevated in cohorts with SSNS, non-monogenic SRNS, MCD, and FSGS compared to healthy participants and those with membranous nephropathy. The SSNS-GRS in all cohorts with non-monogenic INS were also significantly elevated compared to those with monogenic SRNS.<h4>Conclusions</h4>The shared genetic risk factors among patients with different presentations of INS strongly suggests a shared autoimmune pathogenesis when monogenic causes are excluded. Use of the SSNS-GRS, in addition to testing for monogenic causes, may help to classify patients presenting with INS. A higher resolution version of the Graphical abstract is available as Supplementary information.",,pdf:https://link.springer.com/content/pdf/10.1007/s00467-022-05789-7.pdf; doi:https://doi.org/10.1007/s00467-022-05789-7; html:https://europepmc.org/articles/PMC10154254; pdf:https://europepmc.org/articles/PMC10154254?pdf=render
 32075790,https://doi.org/10.1136/bmj.m331,Associations between macrolide antibiotics prescribing during pregnancy and adverse child outcomes in the UK: population based cohort study.,"Fan H, Gilbert R, O'Callaghan F, Li L.",,BMJ (Clinical research ed.),2020,2020-02-19,Y,,,,"<h4>Objective</h4>To assess the association between macrolide antibiotics prescribing during pregnancy and major malformations, cerebral palsy, epilepsy, attention deficit hyperactivity disorder, and autism spectrum disorder in children.<h4>Design</h4>Population based cohort study.<h4>Setting</h4>The UK Clinical Practice Research Datalink.<h4>Participants</h4>The study cohort included 104 605 children born from 1990 to 2016 whose mothers were prescribed one macrolide monotherapy (erythromycin, clarithromycin, or azithromycin) or one penicillin monotherapy from the fourth gestational week to delivery. Two negative control cohorts consisted of 82 314 children whose mothers were prescribed macrolides or penicillins before conception, and 53 735 children who were siblings of the children in the study cohort.<h4>Main outcome measures</h4>Risks of any major malformations and system specific major malformations (nervous, cardiovascular, gastrointestinal, genital, and urinary) after macrolide or penicillin prescribing during the first trimester (four to 13 gestational weeks), second to third trimester (14 gestational weeks to birth), or any trimester of pregnancy. Additionally, risks of cerebral palsy, epilepsy, attention deficit hyperactivity disorder, and autism spectrum disorder.<h4>Results</h4>Major malformations were recorded in 186 of 8632 children (21.55 per 1000) whose mothers were prescribed macrolides and 1666 of 95 973 children (17.36 per 1000) whose mothers were prescribed penicillins during pregnancy. Macrolide prescribing during the first trimester was associated with an increased risk of any major malformation compared with penicillin (27.65 <i>v</i> 17.65 per 1000, adjusted risk ratio 1.55, 95% confidence interval 1.19 to 2.03) and specifically cardiovascular malformations (10.60 <i>v</i> 6.61 per 1000, 1.62, 1.05 to 2.51). Macrolide prescribing in any trimester was associated with an increased risk of genital malformations (4.75 <i>v</i> 3.07 per 1000, 1.58, 1.14 to 2.19, mainly hypospadias). Erythromycin in the first trimester was associated with an increased risk of any major malformation (27.39 <i>v</i> 17.65 per 1000, 1.50, 1.13 to 1.99). No statistically significant associations were found for other system specific malformations or for neurodevelopmental disorders. Findings were robust to sensitivity analyses.<h4>Conclusions</h4>Prescribing macrolide antibiotics during the first trimester of pregnancy was associated with an increased risk of any major malformation and specifically cardiovascular malformations compared with penicillin antibiotics. Macrolide prescribing in any trimester was associated with an increased risk of genital malformations. These findings show that macrolides should be used with caution during pregnancy and if feasible alternative antibiotics should be prescribed until further research is available.<h4>Trial registration</h4>ClinicalTrials.gov NCT03948620.",,pdf:https://www.bmj.com/content/bmj/368/bmj.m331.full.pdf; doi:https://doi.org/10.1136/bmj.m331; html:https://europepmc.org/articles/PMC7190043
-35835762,https://doi.org/10.1038/s41467-022-31626-4,"Natural Killer cells demonstrate distinct eQTL and transcriptome-wide disease associations, highlighting their role in autoimmunity.","Gilchrist JJ, Makino S, Naranbhai V, Sharma PK, Koturan S, Tong O, Taylor CA, Watson RA, de Los Aires AV, Cooper R, Lau E, Danielli S, Hameiri-Bowen D, Lee W, Ng E, Whalley J, Knight JC, Fairfax BP.",,Nature communications,2022,2022-07-14,Y,,,,"Natural Killer cells are innate lymphocytes with central roles in immunosurveillance and are implicated in autoimmune pathogenesis. The degree to which regulatory variants affect Natural Killer cell gene expression is poorly understood. Here we perform expression quantitative trait locus mapping of negatively selected Natural Killer cells from a population of healthy Europeans (n = 245). We find a significant subset of genes demonstrate expression quantitative trait loci specific to Natural Killer cells and these are highly informative of human disease, in particular autoimmunity. A Natural Killer cell transcriptome-wide association study across five common autoimmune diseases identifies further novel associations at 27 genes. In addition to these cis observations, we find novel master-regulatory regions impacting expression of trans gene networks at regions including 19q13.4, the Killer cell Immunoglobulin-like Receptor region, GNLY, MC1R and UVSSA. Our findings provide new insights into the unique biology of Natural Killer cells, demonstrating markedly different expression quantitative trait loci from other immune cells, with implications for disease mechanisms.",,pdf:https://www.nature.com/articles/s41467-022-31626-4.pdf; doi:https://doi.org/10.1038/s41467-022-31626-4; html:https://europepmc.org/articles/PMC9283523; pdf:https://europepmc.org/articles/PMC9283523?pdf=render
 33713332,https://doi.org/10.1007/s40620-021-00996-1,End-stage kidney disease in patients with clinically manifest vascular disease; incidence and risk factors: results from the UCC-SMART cohort study.,"Østergaard HB, Westerink J, Verhaar MC, Bots ML, Asselbergs FW, de Borst GJ, Kappelle LJ, Visseren FLJ, van der Leeuw J, UCC-SMART studygroup.",,Journal of nephrology,2021,2021-03-13,Y,Cardiovascular disease; incidence; End-stage Kidney Disease; Modifiable Risk Factors,,,"<h4>Background</h4>Patients with cardiovascular disease (CVD) are at increased risk of end-stage kidney disease (ESKD). Insights into the incidence and role of modifiable risk factors for end-stage kidney disease may provide means for prevention in patients with cardiovascular disease.<h4>Methods</h4>We included 8402 patients with stable cardiovascular disease. Incidence rates (IRs) for end-stage kidney disease were determined stratified according to vascular disease location. Cox proportional hazard models were used to assess the risk of end-stage kidney disease for the different determinants.<h4>Results</h4>Sixty-five events were observed with a median follow-up of 8.6 years. The overall incidence rate of end-stage kidney disease was 0.9/1000 person-years. Patients with polyvascular disease had the highest incidence rate (1.8/1000 person-years). Smoking (Hazard ratio (HR) 1.87; 95% CI 1.10-3.19), type 2 diabetes (HR 1.81; 95% CI 1.05-3.14), higher systolic blood pressure (HR 1.37; 95% CI 1.24-1.52/10 mmHg), lower estimated glomerular filtration rate (eGFR) (HR 2.86; 95% CI 2.44-3.23/10 mL/min/1.73 m<sup>2</sup>) and higher urine albumin/creatinine ratio (uACR) (HR 1.19; 95% CI 1.15-1.23/10 mg/mmol) were independently associated with elevated risk of end-stage kidney disease. Body mass index (BMI), waist circumference, non-HDL-cholesterol and exercise were not independently associated with risk of end-stage kidney disease.<h4>Conclusions</h4>Incidence of end-stage kidney disease in patients with cardiovascular disease varies according to vascular disease location. Several modifiable risk factors for end-stage kidney disease were identified in patients with cardiovascular disease. These findings highlight the potential of risk factor management in patients with manifest cardiovascular disease.",,pdf:https://link.springer.com/content/pdf/10.1007/s40620-021-00996-1.pdf; doi:https://doi.org/10.1007/s40620-021-00996-1; html:https://europepmc.org/articles/PMC8494654; pdf:https://europepmc.org/articles/PMC8494654?pdf=render
-38438269,https://doi.org/10.3399/bjgp.2023.0214,Post-hospitalisation asthma management in primary care: a retrospective cohort study.,"Punyadasa D, Simms-Williams N, Adderley NJ, Thayakaran R, Mansur AH, Nirantharakumar K, Nagakumar P, Haroon S.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2024,2024-05-30,Y,Management; Asthma; Cohort studies; Primary Health Care; Ethnic And Racial Minorities; Post-hospitalisation,,,"<h4>Background</h4>Clinical guidelines recommend that patients admitted to hospital for asthma attacks are reviewed in primary care following hospital discharge.<h4>Aim</h4>To evaluate asthma management in primary care following a hospital admission for asthma and its associations with patient characteristics.<h4>Design and setting</h4>A retrospective cohort study using English primary care data from the Clinical Practice Research Datalink Aurum database and linked Hospital Episode Statistics Admitted Patient Care data.<h4>Method</h4>Patients with asthma aged ≥5 years who had at least one asthma-related hospital admission from 1 January 2017 to 31 December 2019 were included. The primary outcome was a composite of any of the following delivered in primary care within 28 days from hospital discharge: asthma review, asthma management plan, asthma medication prescriptions, demonstration of inhaler technique, or smoking cessation counselling. The association between patient characteristics and delivery of clinical care was assessed using logistic regression.<h4>Results</h4>The study included 17 457 patients. A total of 10 515 (60.2%) patients received the primary outcome within 28 days of hospital discharge. There were 2311 (13.2%) who received an asthma review, 1459 (8.4%) an asthma management plan, 9996 (57.3%) an asthma medication, 1500 (8.6%) a demonstration of inhaler technique, and 52 (1.2% of smokers) had smoking cessation counselling. Patients from Black ethnic minority groups received less of this care (27%-54% lower odds, depending on age). However, short-acting bronchodilator prescriptions in the previous year were associated with an increased likelihood of the primary outcome.<h4>Conclusion</h4>A significant proportion of patients do not receive timely follow-up in primary care following asthma-related admissions to hospital, particularly among Black ethnic minority groups.",,doi:https://doi.org/10.3399/BJGP.2023.0214; html:https://europepmc.org/articles/PMC10947362; pdf:https://europepmc.org/articles/PMC10947362?pdf=render
-35538704,https://doi.org/10.1177/1357633x221093434,"The development, validation and application of remote blood sample collection in telehealth programmes.","Koulman A, Rennie KL, Parkington D, Tyrrell CS, Catt M, Gkrania-Klotsas E, Wareham NJ.",,Journal of telemedicine and telecare,2024,2022-05-10,Y,Pathology; Self-care; Telehealth; Blood Sampling; Home Telecare,,,"<h4>Introduction</h4>The ability to collect blood samples remotely without the involvement of healthcare professionals is a key element of future telehealth applications. We developed and validated the application of the Drawbridge OneDraw device for use at home for blood sample collection. The device was then applied in a large population-based remote monitoring study to assess changes in SARS-CoV-2 IgG antibody levels.<h4>Methods</h4>We tested: (1) feasibility of participants using the device at home without a healthcare professional on the upper arm and thigh sites (2) stability of the dried blood sample collected remotely (3) participant acceptability of the device compared with finger-prick and venous blood samples and the validity of SARS-CoV-2 virus antibody measurement versus venous blood sample (4) application to the Fenland COVID-19 study in which 4023 participants at 3 timepoints across 6 months.<h4>Results</h4>Participant acceptability was high, with a significantly lower median perceived pain score and 76% of participants preferring the OneDraw device over the other blood collection methods. There was high level of agreement in SARS-CoV-2 virus antibody results with venous blood samples in 120 participants (Cohen's kappa 0.68 (95% CI 0.56, 0.83). In the Fenland COVID-19 study, 92% of participants returned a sample at baseline (3702/4023), 89% at 3 months (3492/3918) and 93% at 6 months (3453/3731), with almost all samples received successfully processed (99.9%).<h4>Discussion</h4>The OneDraw device enables a standardised blood sample collection at home by participants themselves. Due to its ease-of-use and acceptability the OneDraw device is particularly useful in telehealth approaches where multiple samples need to be collected.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/1357633X221093434; doi:https://doi.org/10.1177/1357633X221093434; html:https://europepmc.org/articles/PMC11027437; pdf:https://europepmc.org/articles/PMC11027437?pdf=render
+35835762,https://doi.org/10.1038/s41467-022-31626-4,"Natural Killer cells demonstrate distinct eQTL and transcriptome-wide disease associations, highlighting their role in autoimmunity.","Gilchrist JJ, Makino S, Naranbhai V, Sharma PK, Koturan S, Tong O, Taylor CA, Watson RA, de Los Aires AV, Cooper R, Lau E, Danielli S, Hameiri-Bowen D, Lee W, Ng E, Whalley J, Knight JC, Fairfax BP.",,Nature communications,2022,2022-07-14,Y,,,,"Natural Killer cells are innate lymphocytes with central roles in immunosurveillance and are implicated in autoimmune pathogenesis. The degree to which regulatory variants affect Natural Killer cell gene expression is poorly understood. Here we perform expression quantitative trait locus mapping of negatively selected Natural Killer cells from a population of healthy Europeans (n = 245). We find a significant subset of genes demonstrate expression quantitative trait loci specific to Natural Killer cells and these are highly informative of human disease, in particular autoimmunity. A Natural Killer cell transcriptome-wide association study across five common autoimmune diseases identifies further novel associations at 27 genes. In addition to these cis observations, we find novel master-regulatory regions impacting expression of trans gene networks at regions including 19q13.4, the Killer cell Immunoglobulin-like Receptor region, GNLY, MC1R and UVSSA. Our findings provide new insights into the unique biology of Natural Killer cells, demonstrating markedly different expression quantitative trait loci from other immune cells, with implications for disease mechanisms.",,pdf:https://www.nature.com/articles/s41467-022-31626-4.pdf; doi:https://doi.org/10.1038/s41467-022-31626-4; html:https://europepmc.org/articles/PMC9283523; pdf:https://europepmc.org/articles/PMC9283523?pdf=render
 33947203,https://doi.org/10.1161/circulationaha.120.053033,Evidence-Based Assessment of Genes in Dilated Cardiomyopathy.,"Jordan E, Peterson L, Ai T, Asatryan B, Bronicki L, Brown E, Celeghin R, Edwards M, Fan J, Ingles J, James CA, Jarinova O, Johnson R, Judge DP, Lahrouchi N, Lekanne Deprez RH, Lumbers RT, Mazzarotto F, Medeiros Domingo A, Miller RL, Morales A, Murray B, Peters S, Pilichou K, Protonotarios A, Semsarian C, Shah P, Syrris P, Thaxton C, van Tintelen JP, Walsh R, Wang J, Ware J, Hershberger RE.",,Circulation,2021,2021-05-05,Y,Genetics; Cardiomyopathy,,,"<h4>Background</h4>Each of the cardiomyopathies, classically categorized as hypertrophic cardiomyopathy, dilated cardiomyopathy (DCM), and arrhythmogenic right ventricular cardiomyopathy, has a signature genetic theme. Hypertrophic cardiomyopathy and arrhythmogenic right ventricular cardiomyopathy are largely understood as genetic diseases of sarcomere or desmosome proteins, respectively. In contrast, >250 genes spanning >10 gene ontologies have been implicated in DCM, representing a complex and diverse genetic architecture. To clarify this, a systematic curation of evidence to establish the relationship of genes with DCM was conducted.<h4>Methods</h4>An international panel with clinical and scientific expertise in DCM genetics evaluated evidence supporting monogenic relationships of genes with idiopathic DCM. The panel used the Clinical Genome Resource semiquantitative gene-disease clinical validity classification framework with modifications for DCM genetics to classify genes into categories on the basis of the strength of currently available evidence. Representation of DCM genes on clinically available genetic testing panels was evaluated.<h4>Results</h4>Fifty-one genes with human genetic evidence were curated. Twelve genes (23%) from 8 gene ontologies were classified as having definitive (<i>BAG3</i>, <i>DES</i>, <i>FLNC</i>, <i>LMNA</i>, <i>MYH7</i>, <i>PLN</i>, <i>RBM20</i>, <i>SCN5A</i>, <i>TNNC1</i>, <i>TNNT2</i>, <i>TTN</i>) or strong (<i>DSP</i>) evidence. Seven genes (14%; <i>ACTC1</i>, <i>ACTN2</i>, <i>JPH2</i>, <i>NEXN</i>, <i>TNNI3</i>, <i>TPM1</i>, <i>VCL</i>) including 2 additional ontologies were classified as moderate evidence; these genes are likely to emerge as strong or definitive with additional evidence. Of these 19 genes, 6 were similarly classified for hypertrophic cardiomyopathy and 3 for arrhythmogenic right ventricular cardiomyopathy. Of the remaining 32 genes (63%), 25 (49%) had limited evidence, 4 (8%) were disputed, 2 (4%) had no disease relationship, and 1 (2%) was supported by animal model data only. Of the 16 evaluated clinical genetic testing panels, most definitive genes were included, but panels also included numerous genes with minimal human evidence.<h4>Conclusions</h4>In the curation of 51 genes, 19 had high evidence (12 definitive/strong, 7 moderate). It is notable that these 19 genes explain only a minority of cases, leaving the remainder of DCM genetic architecture incompletely addressed. Clinical genetic testing panels include most high-evidence genes; however, genes lacking robust evidence are also commonly included. We recommend that high-evidence DCM genes be used for clinical practice and that caution be exercised in the interpretation of variants in variable-evidence DCM genes.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCULATIONAHA.120.053033; doi:https://doi.org/10.1161/CIRCULATIONAHA.120.053033; html:https://europepmc.org/articles/PMC8247549; pdf:https://europepmc.org/articles/PMC8247549?pdf=render
+35538704,https://doi.org/10.1177/1357633x221093434,"The development, validation and application of remote blood sample collection in telehealth programmes.","Koulman A, Rennie KL, Parkington D, Tyrrell CS, Catt M, Gkrania-Klotsas E, Wareham NJ.",,Journal of telemedicine and telecare,2024,2022-05-10,Y,Pathology; Self-care; Telehealth; Blood Sampling; Home Telecare,,,"<h4>Introduction</h4>The ability to collect blood samples remotely without the involvement of healthcare professionals is a key element of future telehealth applications. We developed and validated the application of the Drawbridge OneDraw device for use at home for blood sample collection. The device was then applied in a large population-based remote monitoring study to assess changes in SARS-CoV-2 IgG antibody levels.<h4>Methods</h4>We tested: (1) feasibility of participants using the device at home without a healthcare professional on the upper arm and thigh sites (2) stability of the dried blood sample collected remotely (3) participant acceptability of the device compared with finger-prick and venous blood samples and the validity of SARS-CoV-2 virus antibody measurement versus venous blood sample (4) application to the Fenland COVID-19 study in which 4023 participants at 3 timepoints across 6 months.<h4>Results</h4>Participant acceptability was high, with a significantly lower median perceived pain score and 76% of participants preferring the OneDraw device over the other blood collection methods. There was high level of agreement in SARS-CoV-2 virus antibody results with venous blood samples in 120 participants (Cohen's kappa 0.68 (95% CI 0.56, 0.83). In the Fenland COVID-19 study, 92% of participants returned a sample at baseline (3702/4023), 89% at 3 months (3492/3918) and 93% at 6 months (3453/3731), with almost all samples received successfully processed (99.9%).<h4>Discussion</h4>The OneDraw device enables a standardised blood sample collection at home by participants themselves. Due to its ease-of-use and acceptability the OneDraw device is particularly useful in telehealth approaches where multiple samples need to be collected.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/1357633X221093434; doi:https://doi.org/10.1177/1357633X221093434; html:https://europepmc.org/articles/PMC11027437; pdf:https://europepmc.org/articles/PMC11027437?pdf=render
+38438269,https://doi.org/10.3399/bjgp.2023.0214,Post-hospitalisation asthma management in primary care: a retrospective cohort study.,"Punyadasa D, Simms-Williams N, Adderley NJ, Thayakaran R, Mansur AH, Nirantharakumar K, Nagakumar P, Haroon S.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2024,2024-05-30,Y,Management; Asthma; Cohort studies; Primary Health Care; Ethnic And Racial Minorities; Post-hospitalisation,,,"<h4>Background</h4>Clinical guidelines recommend that patients admitted to hospital for asthma attacks are reviewed in primary care following hospital discharge.<h4>Aim</h4>To evaluate asthma management in primary care following a hospital admission for asthma and its associations with patient characteristics.<h4>Design and setting</h4>A retrospective cohort study using English primary care data from the Clinical Practice Research Datalink Aurum database and linked Hospital Episode Statistics Admitted Patient Care data.<h4>Method</h4>Patients with asthma aged ≥5 years who had at least one asthma-related hospital admission from 1 January 2017 to 31 December 2019 were included. The primary outcome was a composite of any of the following delivered in primary care within 28 days from hospital discharge: asthma review, asthma management plan, asthma medication prescriptions, demonstration of inhaler technique, or smoking cessation counselling. The association between patient characteristics and delivery of clinical care was assessed using logistic regression.<h4>Results</h4>The study included 17 457 patients. A total of 10 515 (60.2%) patients received the primary outcome within 28 days of hospital discharge. There were 2311 (13.2%) who received an asthma review, 1459 (8.4%) an asthma management plan, 9996 (57.3%) an asthma medication, 1500 (8.6%) a demonstration of inhaler technique, and 52 (1.2% of smokers) had smoking cessation counselling. Patients from Black ethnic minority groups received less of this care (27%-54% lower odds, depending on age). However, short-acting bronchodilator prescriptions in the previous year were associated with an increased likelihood of the primary outcome.<h4>Conclusion</h4>A significant proportion of patients do not receive timely follow-up in primary care following asthma-related admissions to hospital, particularly among Black ethnic minority groups.",,doi:https://doi.org/10.3399/BJGP.2023.0214; html:https://europepmc.org/articles/PMC10947362; pdf:https://europepmc.org/articles/PMC10947362?pdf=render
 31820220,https://doi.org/10.1007/s10926-019-09867-w,The Association Between Fault Attribution and Work Participation After Road Traffic Injury: A Registry-Based Observational Study.,"Lau G, Gabbe BJ, Collie A, Ponsford J, Ameratunga S, Cameron PA, Harrison JE, Giummarra MJ.",,Journal of occupational rehabilitation,2020,2020-06-01,N,Trauma; Injury; Recovery; Traffic; Accidents; Return To Work,,,"Purpose To characterise associations between fault attribution and work participation and capacity after road traffic injury. Methods People aged 15-65 years, working pre-injury, without serious brain injury, who survived to 12 months after road traffic injury were included from two Victorian trauma registries (n = 2942). Fault profiles from linked compensation claims were defined as no other at fault, another at fault, denied another at fault, claimed another at fault, and unknown. Claimant reports in the denied and claimed another at fault groups contradicted police reports. Patients reported work capacity (Glasgow outcome scale-extended) and return to work (RTW) at 6, 12 and 24 months post-injury (early and sustained RTW, delayed RTW (≥ 12 months), failed RTW attempts, no RTW attempts). Analyses adjusted for demographic, clinical and injury covariates. Results The risk of not returning to work was higher if another was at fault [adjusted relative risk ratio (aRRR) = 1.67, 95% confidence interval (CI) 1.29, 2.17] or was claimed to be at fault (aRRR = 1.58, 95% CI 1.04, 2.41), and lower for those who denied that another was at fault (aRRR = 0.51, 95% CI 0.29, 0.91), compared to cases with no other at fault. Similarly, people had higher odds of work capacity limitations if another was at fault (12m: AOR = 1.49, 95% CI 1.24, 1.80; 24m: 1.63, 95% CI 1.35, 1.97) or was claimed to be at fault (12m: AOR = 1.54, 95% CI 1.16, 2.05; 24m: AOR = 1.80, 95% CI 1.34, 2.41), and lower odds if they denied another was at fault (6m: AOR = 0.67, 95% CI 0.48, 0.95), compared to cases with no other at fault. Conclusion Targeted interventions are needed to support work participation in people at risk of poor RTW post-injury. While interventions targeting fault and justice-related attributions are currently lacking, these may be beneficial for people who believe that another caused their injury.",,doi:https://doi.org/10.1007/s10926-019-09867-w
-39444499,https://doi.org/10.1002/lrh2.10461,Creating a learning health system to include environmental determinants of health: The GroundsWell experience.,"Rodgers SE, Geary RS, Villegas-Diaz R, Buchan IE, Burnett H, Clemens T, Crook R, Duckworth H, Green MA, King E, Zhang W, Butters O.",,Learning health systems,2024,2024-10-10,Y,Public Health Research; Data Privacy; Household Record Linkage; Public Health Learning System; Record Linkage Complex Systems,,,"<h4>Introduction</h4>Policies aiming to prevent ill health and reduce health inequalities need to consider the full complexity of health systems, including environmental determinants. A learning health system that incorporates environmental factors needs healthcare, social care and non-health data linkage at individual and small-area levels. Our objective was to establish privacy-preserving household record linkage for England to ensure person-level data remain secure and private when linked with data from households or the wider environment.<h4>Methods</h4>A stakeholder workshop with participants from our regional health board, together with the regional data processor, and the national data provider. The workshop discussed the risks and benefits of household linkages. This group then co-designed actionable dataflows between national and local data controllers and processors.<h4>Results</h4>A process was defined whereby the Personal Demographics Service, which includes the addresses of all patients of the National Health Service (NHS) in England, was used to match patients to a home identifier, for the time they are recorded as living at that address. Discussions with NHS England resulted in secure and quality-assured data linkages and a plan to flow these pseudonymised data onwards into regional health boards. Methods were established, including the generation of matching algorithms, transfer processes and information governance approvals. Our collaboration accelerated the development of a new data governance application, facilitating future public health intervention evaluations.<h4>Conclusion</h4>These activities have established a secure method for protecting the privacy of NHS patients in England, while allowing linkage of wider environmental data. This enables local health systems to learn from their data and improve health by optimizing non-health factors. Proportionate governance of health and linked non-health data is practical in England for incorporating key environmental factors into a learning health system.",,doi:https://doi.org/10.1002/lrh2.10461; html:https://europepmc.org/articles/PMC11493545; pdf:https://europepmc.org/articles/PMC11493545?pdf=render
 35728939,https://doi.org/10.1136/archdischild-2021-323681,Reductions in hospital care among clinically vulnerable children aged 0-4 years during the COVID-19 pandemic.,"Etoori D, Harron KL, Mc Grath-Lone L, Verfürden ML, Gilbert R, Blackburn R.",,Archives of disease in childhood,2022,2022-09-20,Y,Child Health; Health Services Research; Healthcare Disparities; Covid-19,,,"<h4>Objective</h4>To quantify reductions in hospital care for clinically vulnerable children during the COVID-19 pandemic.<h4>Design</h4>Birth cohort.<h4>Setting</h4>National Health Service hospitals in England.<h4>Study population</h4>All children aged <5 years with a birth recorded in hospital administrative data (January 2010-March 2021).<h4>Main exposure</h4>Clinical vulnerability defined by a chronic health condition, preterm birth (<37 weeks' gestation) or low birth weight (<2500 g).<h4>Main outcomes</h4>Reductions in care defined by predicted hospital contact rates for 2020, estimated from 2015 to 2019, minus observed rates per 1000 child years during the first year of the pandemic (March 2020-2021).<h4>Results</h4>Of 3 813 465 children, 17.7% (one in six) were clinically vulnerable (9.5% born preterm or low birth weight, 10.3% had a chronic condition). Reductions in hospital care during the pandemic were much higher for clinically vulnerable children than peers: respectively, outpatient attendances (314 vs 73 per 1000 child years), planned admissions (55 vs 10) and unplanned admissions (105 vs 79). Clinically vulnerable children accounted for 50.1% of the reduction in outpatient attendances, 55.0% in planned admissions and 32.8% in unplanned hospital admissions. During the pandemic, weekly rates of planned care returned to prepandemic levels for infants with chronic conditions but not older children. Reductions in care differed by ethnic group and level of deprivation. Virtual outpatient attendances increased from 3.2% to 24.8% during the pandemic.<h4>Conclusion</h4>One in six clinically vulnerable children accounted for one-third to one half of the reduction in hospital care during the pandemic.",,pdf:https://adc.bmj.com/content/archdischild/107/10/e31.full.pdf; doi:https://doi.org/10.1136/archdischild-2021-323681; html:https://europepmc.org/articles/PMC9271837; pdf:https://europepmc.org/articles/PMC9271837?pdf=render
 39092423,https://doi.org/10.12688/wellcomeopenres.19470.2,Estimating disease burden using national linked electronic health records: a study using an English population-based cohort.,"Aldridge RW, Evans HER, Yavlinsky A, Moayyeri A, Bhaskaran K, Mathur R, Jordan KP, Croft P, Denaxas S, Shah AD, Blackburn RM, Moller H, Ng ESW, Hughes A, Fox S, Flowers J, Schmidt J, Hayward A, Gilbert R, Smeeth L, Hemingway H.",,Wellcome open research,2023,2023-01-01,Y,Electronic Health Records; Burden Of Disease,,,"<h4>Background</h4>Electronic health records (EHRs) have the potential to be used to produce detailed disease burden estimates. In this study we created disease estimates using national EHR for three high burden conditions, compared estimates between linked and unlinked datasets and produced stratified estimates by age, sex, ethnicity, socio-economic deprivation and geographical region.<h4>Methods</h4>EHRs containing primary care (Clinical Practice Research Datalink), secondary care (Hospital Episode Statistics) and mortality records (Office for National Statistics) were used. We used existing disease phenotyping algorithms to identify cases of cancer (breast, lung, colorectal and prostate), type 1 and 2 diabetes, and lower back pain. We calculated age-standardised incidence of first cancer, point prevalence for diabetes, and primary care consultation prevalence for low back pain.<h4>Results</h4>7.2 million people contributing 45.3 million person-years of active follow-up between 2000-2014 were included. CPRD-HES combined and CPRD-HES-ONS combined lung and bowel cancer incidence estimates by sex were similar to cancer registry estimates. Linked CPRD-HES estimates for combined Type 1 and Type 2 diabetes were consistently higher than those of CPRD alone, with the difference steadily increasing over time from 0.26% (2.99% for CPRD-HES vs. 2.73 for CPRD) in 2002 to 0.58% (6.17% vs. 5.59) in 2013. Low back pain prevalence was highest in the most deprived quintile and when compared to the least deprived quintile the difference in prevalence increased over time between 2000 and 2013, with the largest difference of 27% (558.70 per 10,000 people vs 438.20) in 2013.<h4>Conclusions</h4>We use national EHRs to produce estimates of burden of disease to produce detailed estimates by deprivation, ethnicity and geographical region. National EHRs have the potential to improve disease burden estimates at a local and global level and may serve as more automated, timely and precise inputs for policy making and global burden of disease estimation.",,doi:https://doi.org/10.12688/wellcomeopenres.19470.2; html:https://europepmc.org/articles/PMC11292189; pdf:https://europepmc.org/articles/PMC11292189?pdf=render
+39444499,https://doi.org/10.1002/lrh2.10461,Creating a learning health system to include environmental determinants of health: The GroundsWell experience.,"Rodgers SE, Geary RS, Villegas-Diaz R, Buchan IE, Burnett H, Clemens T, Crook R, Duckworth H, Green MA, King E, Zhang W, Butters O.",,Learning health systems,2024,2024-10-10,Y,Public Health Research; Data Privacy; Household Record Linkage; Public Health Learning System; Record Linkage Complex Systems,,,"<h4>Introduction</h4>Policies aiming to prevent ill health and reduce health inequalities need to consider the full complexity of health systems, including environmental determinants. A learning health system that incorporates environmental factors needs healthcare, social care and non-health data linkage at individual and small-area levels. Our objective was to establish privacy-preserving household record linkage for England to ensure person-level data remain secure and private when linked with data from households or the wider environment.<h4>Methods</h4>A stakeholder workshop with participants from our regional health board, together with the regional data processor, and the national data provider. The workshop discussed the risks and benefits of household linkages. This group then co-designed actionable dataflows between national and local data controllers and processors.<h4>Results</h4>A process was defined whereby the Personal Demographics Service, which includes the addresses of all patients of the National Health Service (NHS) in England, was used to match patients to a home identifier, for the time they are recorded as living at that address. Discussions with NHS England resulted in secure and quality-assured data linkages and a plan to flow these pseudonymised data onwards into regional health boards. Methods were established, including the generation of matching algorithms, transfer processes and information governance approvals. Our collaboration accelerated the development of a new data governance application, facilitating future public health intervention evaluations.<h4>Conclusion</h4>These activities have established a secure method for protecting the privacy of NHS patients in England, while allowing linkage of wider environmental data. This enables local health systems to learn from their data and improve health by optimizing non-health factors. Proportionate governance of health and linked non-health data is practical in England for incorporating key environmental factors into a learning health system.",,doi:https://doi.org/10.1002/lrh2.10461; html:https://europepmc.org/articles/PMC11493545; pdf:https://europepmc.org/articles/PMC11493545?pdf=render
 34647377,https://doi.org/10.1002/nbm.4630,Added value of magnetic resonance spectroscopy for diagnosing childhood cerebellar tumours.,"Davies NP, Rose HEL, Manias KA, Natarajan K, Abernethy LJ, Oates A, Janjua U, Davies P, MacPherson L, Arvanitis TN, Peet AC.",,NMR in biomedicine,2022,2021-10-13,Y,Metabolites; Classification; Paediatric; Brain Tumours; 1H-magnetic Resonance Spectroscopy,,,"<sup>1</sup> H-magnetic resonance spectroscopy (MRS) provides noninvasive metabolite profiles with the potential to aid the diagnosis of brain tumours. Prospective studies of diagnostic accuracy and comparisons with conventional MRI are lacking. The aim of the current study was to evaluate, prospectively, the diagnostic accuracy of a previously established classifier for diagnosing the three major childhood cerebellar tumours, and to determine added value compared with standard reporting of conventional imaging. Single-voxel MRS (1.5 T, PRESS, TE 30 ms, TR 1500 ms, spectral resolution 1 Hz/point) was acquired prospectively on 39 consecutive cerebellar tumours with histopathological diagnoses of pilocytic astrocytoma, ependymoma or medulloblastoma. Spectra were analysed with LCModel and predefined quality control criteria were applied, leaving 33 cases in the analysis. The MRS diagnostic classifier was applied to this dataset. A retrospective analysis was subsequently undertaken by three radiologists, blind to histopathological diagnosis, to determine the change in diagnostic certainty when sequentially viewing conventional imaging, MRS and a decision support tool, based on the classifier. The overall classifier accuracy, evaluated prospectively, was 91%. Incorrectly classified cases, two anaplastic ependymomas, and a rare histological variant of medulloblastoma, were not well represented in the original training set. On retrospective review of conventional MRI, MRS and the classifier result, all radiologists showed a significant increase (Wilcoxon signed rank test, p < 0.001) in their certainty of the correct diagnosis, between viewing the conventional imaging and MRS with the decision support system. It was concluded that MRS can aid the noninvasive diagnosis of posterior fossa tumours in children, and that a decision support classifier helps in MRS interpretation.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/nbm.4630; doi:https://doi.org/10.1002/nbm.4630; html:https://europepmc.org/articles/PMC11478925; pdf:https://europepmc.org/articles/PMC11478925?pdf=render
 34737870,https://doi.org/10.7189/jogh.11.15003,Research priorities to address the global burden of chronic obstructive pulmonary disease (COPD) in the next decade.,"Adeloye D, Agarwal D, Barnes PJ, Bonay M, van Boven JF, Bryant J, Caramori G, Dockrell D, D'Urzo A, Ekström M, Erhabor G, Esteban C, Greene CM, Hurst J, Juvekar S, Khoo EM, Ko FW, Lipworth B, López-Campos JL, Maddocks M, Mannino DM, Martinez FJ, Martinez-Garcia MA, McNamara RJ, Miravitlles M, Pinnock H, Pooler A, Quint JK, Schwarz P, Slavich GM, Song P, Tai A, Watz H, Wedzicha JA, Williams MC, Campbell H, Sheikh A, Rudan I.",,Journal of global health,2021,2021-10-09,Y,,,,"<h4>Background</h4>The global prevalence of chronic obstructive pulmonary disease (COPD) has increased markedly in recent decades. Given the scarcity of resources available to address global health challenges and respiratory medicine being relatively under-invested in, it is important to define research priorities for COPD globally. In this paper, we aim to identify a ranked set of COPD research priorities that need to be addressed in the next 10 years to substantially reduce the global impact of COPD.<h4>Methods</h4>We adapted the Child Health and Nutrition Research Initiative (CHNRI) methodology to identify global COPD research priorities.<h4>Results</h4>62 experts contributed 230 research ideas, which were scored by 34 researchers according to six pre-defined criteria: answerability, effectiveness, feasibility, deliverability, burden reduction, and equity. The top-ranked research priority was the need for new effective strategies to support smoking cessation. Of the top 20 overall research priorities, six were focused on feasible and cost-effective pulmonary rehabilitation delivery and access, particularly in primary/community care and low-resource settings. Three of the top 10 overall priorities called for research on improved screening and accurate diagnostic methods for COPD in low-resource primary care settings. Further ideas that drew support involved a better understanding of risk factors for COPD, development of effective training programmes for health workers and physicians in low resource settings, and evaluation of novel interventions to encourage physical activity.<h4>Conclusions</h4>The experts agreed that the most pressing feasible research questions to address in the next decade for COPD reduction were on prevention, diagnosis and rehabilitation of COPD, especially in low resource settings. The largest gains should be expected in low- and middle-income countries (LMIC) settings, as the large majority of COPD deaths occur in those settings. Research priorities identified by this systematic international process should inform and motivate policymakers, funders, and researchers to support and conduct research to reduce the global burden of COPD.",,doi:https://doi.org/10.7189/jogh.11.15003; doi:https://doi.org/10.7189/jogh.11.15003; html:https://europepmc.org/articles/PMC8542376; pdf:https://europepmc.org/articles/PMC8542376?pdf=render
 33493433,https://doi.org/10.1016/s1470-2045(20)30743-9,"The impact of the COVID-19 pandemic on radiotherapy services in England, UK: a population-based study.","Spencer K, Jones CM, Girdler R, Roe C, Sharpe M, Lawton S, Miller L, Lewis P, Evans M, Sebag-Montefiore D, Roques T, Smittenaar R, Morris E.",,The Lancet. Oncology,2021,2021-01-22,Y,,,,"<h4>Background</h4>The indirect impact of the COVID-19 pandemic on cancer outcomes is of increasing concern. However, the extent to which key treatment modalities have been affected is unclear. We aimed to assess the impact of the pandemic on radiotherapy activity in England.<h4>Methods</h4>In this population-based study, data relating to all radiotherapy delivered for cancer in the English NHS, between Feb 4, 2019, and June 28, 2020, were extracted from the National Radiotherapy Dataset. Changes in mean weekly radiotherapy courses, attendances (reflecting fractions), and fractionation patterns following the start of the UK lockdown were compared with corresponding months in 2019 overall, for specific diagnoses, and across age groups. The significance of changes in radiotherapy activity during lockdown was examined using interrupted time-series (ITS) analysis.<h4>Findings</h4>In 2020, mean weekly radiotherapy courses fell by 19·9% in April, 6·2% in May, and 11·6% in June compared with corresponding months in 2019. A relatively greater fall was observed for attendances (29·1% in April, 31·4% in May, and 31·5% in June). These changes were significant on ITS analysis (p<0·0001). A greater reduction in treatment courses between 2019 and 2020 was seen for patients aged 70 years or older compared with those aged younger than 70 years (34·4% vs 7·3% in April). By diagnosis, the largest reduction from 2019 to 2020 in treatment courses was for prostate cancer (77·0% in April) and non-melanoma skin cancer (72·4% in April). Conversely, radiotherapy courses in April, 2020, compared with April, 2019, increased by 41·2% in oesophageal cancer, 64·2% in bladder cancer, and 36·3% in rectal cancer. Increased use of ultra-hypofractionated (26 Gy in five fractions) breast radiotherapy as a percentage of all courses (0·2% in April, 2019, to 60·6% in April, 2020; ITS p<0·0001) contributed to the substantial reduction in attendances.<h4>Interpretation</h4>Radiotherapy activity fell significantly, but use of hypofractionated regimens rapidly increased in the English NHS during the first peak of the COVID-19 pandemic. An increase in treatments for some cancers suggests that radiotherapy compensated for reduced surgical activity. These data will assist health-care providers in understanding the indirect consequences of the pandemic and the role of radiotherapy services in minimising these consequences.<h4>Funding</h4>None.",,pdf:https://eprints.whiterose.ac.uk/171109/2/Supplementary%20material_v3.pdf; doi:https://doi.org/10.1016/S1470-2045(20)30743-9; html:https://europepmc.org/articles/PMC7825861; pdf:https://europepmc.org/articles/PMC7825861?pdf=render
 35189884,https://doi.org/10.1186/s12913-022-07607-0,Factors influencing follow-up care post-TIA and minor stroke: a qualitative study using the theoretical domains framework.,"Turner GM, Aquino MRJV, Atkins L, Foy R, Mant J, Calvert M.",,BMC health services research,2022,2022-02-21,Y,Follow-up; Transient Ischaemic Attack; Tia; Minor Stroke; Theoretical Domains Framework,,,"<h4>Background</h4>Follow-up care after transient ischaemic attack (TIA) and minor stroke has been found to be sub-optimal, with individuals often feeling abandoned. We aimed to explore factors influencing holistic follow-up care after TIA and minor stroke.<h4>Methods</h4>Qualitative semi-structured interviews with 24 healthcare providers (HCPs): 5 stroke doctors, 4 nurses, 9 allied health professionals and 6 general practitioners. Participants were recruited from three TIA clinics, seven general practices and one community care trust in the West Midlands, England. Interview transcripts were deductively coded using the Theoretical Domains Framework and themes were generated from coded data.<h4>Results</h4>There was no clear pathway for supporting people with TIA or minor stroke after rapid specialist review in hospital; consequently, these patients had limited access to HCPs from all settings ('Environmental context and resources'). There was lack of understanding of potential needs post-TIA/minor stroke, in particular residual problems such as anxiety/fatigue ('Knowledge'). Identification and management of needs was largely influenced by HCPs' perceived role, professional training ('Social professional role and identity') and time constraints ('Environmental context and resources'). Follow-up was often passive - with onerous on patients to seek support - and predominantly focused on acute medical management ('Intentions'/'Goal').<h4>Conclusions</h4>Follow-up care post-TIA/minor stroke is currently sub-optimal. Through identifying factors which influence follow-up, we can inform guidelines and practical strategies to improve holistic healthcare.",,pdf:https://bmchealthservres.biomedcentral.com/track/pdf/10.1186/s12913-022-07607-0; doi:https://doi.org/10.1186/s12913-022-07607-0; html:https://europepmc.org/articles/PMC8859903; pdf:https://europepmc.org/articles/PMC8859903?pdf=render
 33941991,https://doi.org/10.1016/j.rse.2021.112339,"Multimodal deep learning from satellite and street-level imagery for measuring income, overcrowding, and environmental deprivation in urban areas.","Suel E, Bhatt S, Brauer M, Flaxman S, Ezzati M.",,Remote sensing of environment,2021,2021-05-01,Y,Segmentation; Satellite Images; Convolutional Neural Networks; Street-Level Images; Urban Measurements,,,"Data collected at large scale and low cost (e.g. satellite and street level imagery) have the potential to substantially improve resolution, spatial coverage, and temporal frequency of measurement of urban inequalities. Multiple types of data from different sources are often available for a given geographic area. Yet, most studies utilize a single type of input data when making measurements due to methodological difficulties in their joint use. We propose two deep learning-based methods for jointly utilizing satellite and street level imagery for measuring urban inequalities. We use London as a case study for three selected outputs, each measured in decile classes: income, overcrowding, and environmental deprivation. We compare the performances of our proposed multimodal models to corresponding unimodal ones using mean absolute error (MAE). First, satellite tiles are appended to street level imagery to enhance predictions at locations where street images are available leading to improvements in accuracy by 20, 10, and 9% in units of decile classes for income, overcrowding, and living environment. The second approach, novel to the best of our knowledge, uses a U-Net architecture to make predictions for all grid cells in a city at high spatial resolution (e.g. for 3 m × 3 m pixels in London in our experiments). It can utilize city wide availability of satellite images as well as more sparse information from street-level images where they are available leading to improvements in accuracy by 6, 10, and 11%. We also show examples of prediction maps from both approaches to visually highlight performance differences.",,doi:https://doi.org/10.1016/j.rse.2021.112339; doi:https://doi.org/10.1016/j.rse.2021.112339; html:https://europepmc.org/articles/PMC7985619; pdf:https://europepmc.org/articles/PMC7985619?pdf=render
-37730620,https://doi.org/10.1186/s13643-023-02333-y,What is known about what works in community-involved decision-making relating to urban green and blue spaces? A realist review protocol.,"Rahtz E, Bell SL, Nurse A, Wheeler BW, Guell C, Elliott LR, Thompson CW, McDougall CW, Lovell R.",,Systematic reviews,2023,2023-09-20,Y,,,,"<h4>Background</h4>There is now a relatively well-established evidence base suggesting that greener living environments and time spent in urban green and blue spaces (UGBS) can be beneficial for human health and wellbeing. However, benefits are not universal and there remain widespread social inequalities in access to such resources and experiences, particularly along axes of class, race, ethnicity, age and disability, and in relation to efforts to increase the availability and accessibility of such spaces. These injustices often relate to distributive, procedural and recognition-based processes. There is growing interest in how to ensure that efforts to increase access to or use of UGBS (whether through infrastructural or social programmes) result in equitable outcomes whilst minimising potential for exacerbating existing inequalities and injustices. Community engagement is considered an important step towards more inclusive UGBS decision-making, from planning and design to management and maintenance processes. It is thought to contribute to better and more widely trusted decisions, enhanced democracy, community satisfaction, civic interest and feelings of green space ownership, and greater longevity of UGBS projects. However, uneven representation and barriers to participation can create imbalances and undermine these benefits.<h4>Methods</h4>An iterative, multi-stage realist-inspired review will be conducted to ask what works, in what context and in what ways relating to the meaningful involvement of communities in UGBS decision-making, focusing on the skills, capacities and capabilities of different stakeholders and the role of contexts and processes. 'Effectiveness' (or what works) will be understood as a multifaceted outcome, encompassing both the processes and results of community engagement efforts. Following a scoping stage to identify initial programme theory, inclusion/exclusion criteria and derive search terms, relevant databases and grey literature will be searched to identify interdisciplinary literature in two phases. The first phase will be used to further develop programme theories, which will be articulated as 'if then' statements. The second phase searches will be used to identify sources to further explore and evidence the programme and formal theory. We will assess all includable evidence for conceptual richness, prioritising more conceptually rich sources if needed.<h4>Discussion</h4>The realist synthesis will explore the key context, mechanism and outcome configurations that appear to explain if and how different approaches to community-involved UGBS decision-making are or are not effective. We will consider factors such as different conceptualisations of community, and if and how they have been involved in UGBS decision-making; the types of tools and approaches used; and the socio-cultural and political or governance structures within which decision-making takes place.",,pdf:https://systematicreviewsjournal.biomedcentral.com/counter/pdf/10.1186/s13643-023-02333-y; doi:https://doi.org/10.1186/s13643-023-02333-y; html:https://europepmc.org/articles/PMC10512649; pdf:https://europepmc.org/articles/PMC10512649?pdf=render
-35193920,https://doi.org/10.1136/bmjopen-2021-055773,Investigating the optimal handling of uncertain pregnancy episodes in the CPRD GOLD Pregnancy Register: a methodological study using UK primary care data.,"Campbell J, Bhaskaran K, Thomas S, Williams R, McDonald HI, Minassian C.",,BMJ open,2022,2022-02-22,Y,epidemiology; Public Health; Maternal Medicine,,,"<h4>Objectives</h4>To investigate why episodes of pregnancy identified from electronic health records may be incomplete or conflicting (overlapping), and provide guidance on how to handle them.<h4>Setting</h4>Pregnancy Register generated from the Clinical Practice Research Datalink (CPRD) GOLD UK primary care database.<h4>Participants</h4>Female patients with at least one pregnancy episode in the Register (01 January 1937-31 December 2017) which had no recorded outcome or conflicted with another episode.<h4>Design</h4>We identified multiple scenarios potentially explaining why uncertain episodes occur. Criteria were established and systematically applied to determine whether episodes had evidence of each scenario. Linked Hospital Episode Statistics were used to identify pregnancy events not captured in primary care.<h4>Results</h4>Of 5.8 million pregnancy episodes in the Register, 932 604 (16%) had no recorded outcome, and 478 341 (8.5%) conflicted with another episode (251 026 distinct conflicting pairs of episodes among 210 593 women). 826 146 (89%) of the episodes without outcome recorded in primary care and 215 577 (86%) of the conflicting pairs were consistent with one or more of our proposed scenarios. For 689 737 (74%) episodes with recorded outcome missing and 215 544 (86%) of the conflicting pairs (at least one episode), supportive evidence (eg, antenatal records, linked hospital records) suggested they were true and current pregnancies. Furthermore, 516 818 (55 %) and 160 936 (64%), respectively, were during research quality follow-up time. For a sizeable proportion of uncertain episode, there is evidence to suggest that historical outcomes being recorded by the general practitioner during an ongoing pregnancy may offer explanation (73 208 (29.2%) and 349 874 (37.5%)).<h4>Conclusions</h4>This work provides insight to users of the CPRD Pregnancy Register on why uncertain pregnancy episodes exist and indicates that most of these episodes are likely to be real pregnancies. Guidance is given to help researchers consider whether to include/exclude uncertain pregnancies from their studies, and how to tailor approaches to minimise underestimation and bias.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/2/e055773.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-055773; html:https://europepmc.org/articles/PMC8867343; pdf:https://europepmc.org/articles/PMC8867343?pdf=render
 37117689,https://doi.org/10.1038/s43016-021-00309-6,Author Correction: Nutriome-metabolome relationships provide insights into dietary intake and metabolism.,"Posma JM, Garcia-Perez I, Frost G, Aljuraiban GS, Chan Q, Van Horn L, Daviglus M, Stamler J, Holmes E, Elliott P, Nicholson JK.",,Nature food,2021,2021-07-01,N,,,,,,pdf:https://www.nature.com/articles/s43016-021-00309-6.pdf; doi:https://doi.org/10.1038/s43016-021-00309-6
+35193920,https://doi.org/10.1136/bmjopen-2021-055773,Investigating the optimal handling of uncertain pregnancy episodes in the CPRD GOLD Pregnancy Register: a methodological study using UK primary care data.,"Campbell J, Bhaskaran K, Thomas S, Williams R, McDonald HI, Minassian C.",,BMJ open,2022,2022-02-22,Y,epidemiology; Public Health; Maternal Medicine,,,"<h4>Objectives</h4>To investigate why episodes of pregnancy identified from electronic health records may be incomplete or conflicting (overlapping), and provide guidance on how to handle them.<h4>Setting</h4>Pregnancy Register generated from the Clinical Practice Research Datalink (CPRD) GOLD UK primary care database.<h4>Participants</h4>Female patients with at least one pregnancy episode in the Register (01 January 1937-31 December 2017) which had no recorded outcome or conflicted with another episode.<h4>Design</h4>We identified multiple scenarios potentially explaining why uncertain episodes occur. Criteria were established and systematically applied to determine whether episodes had evidence of each scenario. Linked Hospital Episode Statistics were used to identify pregnancy events not captured in primary care.<h4>Results</h4>Of 5.8 million pregnancy episodes in the Register, 932 604 (16%) had no recorded outcome, and 478 341 (8.5%) conflicted with another episode (251 026 distinct conflicting pairs of episodes among 210 593 women). 826 146 (89%) of the episodes without outcome recorded in primary care and 215 577 (86%) of the conflicting pairs were consistent with one or more of our proposed scenarios. For 689 737 (74%) episodes with recorded outcome missing and 215 544 (86%) of the conflicting pairs (at least one episode), supportive evidence (eg, antenatal records, linked hospital records) suggested they were true and current pregnancies. Furthermore, 516 818 (55 %) and 160 936 (64%), respectively, were during research quality follow-up time. For a sizeable proportion of uncertain episode, there is evidence to suggest that historical outcomes being recorded by the general practitioner during an ongoing pregnancy may offer explanation (73 208 (29.2%) and 349 874 (37.5%)).<h4>Conclusions</h4>This work provides insight to users of the CPRD Pregnancy Register on why uncertain pregnancy episodes exist and indicates that most of these episodes are likely to be real pregnancies. Guidance is given to help researchers consider whether to include/exclude uncertain pregnancies from their studies, and how to tailor approaches to minimise underestimation and bias.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/2/e055773.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-055773; html:https://europepmc.org/articles/PMC8867343; pdf:https://europepmc.org/articles/PMC8867343?pdf=render
+37730620,https://doi.org/10.1186/s13643-023-02333-y,What is known about what works in community-involved decision-making relating to urban green and blue spaces? A realist review protocol.,"Rahtz E, Bell SL, Nurse A, Wheeler BW, Guell C, Elliott LR, Thompson CW, McDougall CW, Lovell R.",,Systematic reviews,2023,2023-09-20,Y,,,,"<h4>Background</h4>There is now a relatively well-established evidence base suggesting that greener living environments and time spent in urban green and blue spaces (UGBS) can be beneficial for human health and wellbeing. However, benefits are not universal and there remain widespread social inequalities in access to such resources and experiences, particularly along axes of class, race, ethnicity, age and disability, and in relation to efforts to increase the availability and accessibility of such spaces. These injustices often relate to distributive, procedural and recognition-based processes. There is growing interest in how to ensure that efforts to increase access to or use of UGBS (whether through infrastructural or social programmes) result in equitable outcomes whilst minimising potential for exacerbating existing inequalities and injustices. Community engagement is considered an important step towards more inclusive UGBS decision-making, from planning and design to management and maintenance processes. It is thought to contribute to better and more widely trusted decisions, enhanced democracy, community satisfaction, civic interest and feelings of green space ownership, and greater longevity of UGBS projects. However, uneven representation and barriers to participation can create imbalances and undermine these benefits.<h4>Methods</h4>An iterative, multi-stage realist-inspired review will be conducted to ask what works, in what context and in what ways relating to the meaningful involvement of communities in UGBS decision-making, focusing on the skills, capacities and capabilities of different stakeholders and the role of contexts and processes. 'Effectiveness' (or what works) will be understood as a multifaceted outcome, encompassing both the processes and results of community engagement efforts. Following a scoping stage to identify initial programme theory, inclusion/exclusion criteria and derive search terms, relevant databases and grey literature will be searched to identify interdisciplinary literature in two phases. The first phase will be used to further develop programme theories, which will be articulated as 'if then' statements. The second phase searches will be used to identify sources to further explore and evidence the programme and formal theory. We will assess all includable evidence for conceptual richness, prioritising more conceptually rich sources if needed.<h4>Discussion</h4>The realist synthesis will explore the key context, mechanism and outcome configurations that appear to explain if and how different approaches to community-involved UGBS decision-making are or are not effective. We will consider factors such as different conceptualisations of community, and if and how they have been involved in UGBS decision-making; the types of tools and approaches used; and the socio-cultural and political or governance structures within which decision-making takes place.",,pdf:https://systematicreviewsjournal.biomedcentral.com/counter/pdf/10.1186/s13643-023-02333-y; doi:https://doi.org/10.1186/s13643-023-02333-y; html:https://europepmc.org/articles/PMC10512649; pdf:https://europepmc.org/articles/PMC10512649?pdf=render
 39117403,https://doi.org/10.1136/bmjopen-2023-082413,Causal evidence of the association between green and blue spaces (GBS) and maternal and neonatal health: a systematic review and meta-analysis protocol.,"Khalaf RKS, Akaraci S, Baldwin FD, Geary RS, Kolamunnage-Dona R, Hunter RF, Rodgers SE.",,BMJ open,2024,2024-08-07,Y,Pregnancy; Systematic review; Public Health; Neonatology; Maternal Medicine,,,"<h4>Introduction</h4>Previous systematic reviews investigating the effects of green and blue space (GBS) on maternal and neonatal health have mainly focused on cross-sectional evidence, limiting potential causal inferences. The last review on the topic was published in January 2024. This review focused on residential greenness effects and neonatal health only but did not include other green/blue space measures, or maternal health outcomes. This review also only included papers published up to June 2023; discounting the 15 studies that have been published since. Thus, this study will capture the growing number of studies that generate causal evidence and aims to investigate the association between GBS and maternal and/or neonatal health.<h4>Methods and analysis</h4>The study protocol was developed with reference to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. This review will include study designs such as experiments, quasi-experiments, longitudinal studies and more. The study independent variable must be a GBS, green space and/or blue space measure. Eligible maternal health outcomes are those reported during pregnancy and up to 1 year after pregnancy. Neonatal health outcomes are limited to neonates no older than 28 days. A total of seven online databases will be searched: Medline, Scopus, Web of Science, PsycInfo, Embase, Environment Complete, and Maternity and Infant Care Database. Abstract and full-text screenings will be undertaken by three reviewers. Risk of bias assessment will be conducted based on the Risk of Bias in Non-randomized Studies-of Exposure framework.A narrative synthesis will be undertaken. If sufficiently comparable studies are identified, meta-analyses using random effects models will be conducted. We will explore heterogeneity using the I<sup>2</sup> test.<h4>Ethics and dissemination</h4>Ethical approval is not required as all the data will be derived from published primary studies that have already obtained ethical permissions. The findings will be disseminated through relevant conferences and peer-reviewed publications.<h4>Prospero registration number</h4>CRD42023396372.",,doi:https://doi.org/10.1136/bmjopen-2023-082413; html:https://europepmc.org/articles/PMC11331951; pdf:https://europepmc.org/articles/PMC11331951?pdf=render
-35251129,https://doi.org/10.3389/fgene.2022.818574,Calculating Polygenic Risk Scores (PRS) in UK Biobank: A Practical Guide for Epidemiologists.,"Collister JA, Liu X, Clifton L.",,Frontiers in genetics,2022,2022-02-18,Y,Polygenic Score; Genetic Risk Score; Uk Biobank; Polygenic Risk Score; Worked Example,,,"A polygenic risk score estimates the genetic risk of an individual for some disease or trait, calculated by aggregating the effect of many common variants associated with the condition. With the increasing availability of genetic data in large cohort studies such as the UK Biobank, inclusion of this genetic risk as a covariate in statistical analyses is becoming more widespread. Previously this required specialist knowledge, but as tooling and data availability have improved it has become more feasible for statisticians and epidemiologists to calculate existing scores themselves for use in analyses. While tutorial resources exist for conducting genome-wide association studies and generating of new polygenic risk scores, fewer guides exist for the simple calculation and application of existing genetic scores. This guide outlines the key steps of this process: selection of suitable polygenic risk scores from the literature, extraction of relevant genetic variants and verification of their quality, calculation of the risk score and key considerations of its inclusion in statistical models, using the UK Biobank imputed data as a model data set. Many of the techniques in this guide will generalize to other datasets, however we also focus on some of the specific techniques required for using data in the formats UK Biobank have selected. This includes some of the challenges faced when working with large numbers of variants, where the computation time required by some tools is impractical. While we have focused on only a couple of tools, which may not be the best ones for every given aspect of the process, one barrier to working with genetic data is the sheer volume of tools available, and the difficulty for a novice to assess their viability. By discussing in depth a couple of tools that are adequate for the calculation even at large scale, we hope to make polygenic risk scores more accessible to a wider range of researchers.",,pdf:https://www.frontiersin.org/articles/10.3389/fgene.2022.818574/pdf; doi:https://doi.org/10.3389/fgene.2022.818574; html:https://europepmc.org/articles/PMC8894758; pdf:https://europepmc.org/articles/PMC8894758?pdf=render
 34648354,https://doi.org/10.1126/science.abj1541,Mapping the proteo-genomic convergence of human diseases.,"Pietzner M, Wheeler E, Carrasco-Zanini J, Cortes A, Koprulu M, Wörheide MA, Oerton E, Cook J, Stewart ID, Kerrison ND, Luan J, Raffler J, Arnold M, Arlt W, O'Rahilly S, Kastenmüller G, Gamazon ER, Hingorani AD, Scott RA, Wareham NJ, Langenberg C.",,"Science (New York, N.Y.)",2021,2021-11-12,N,,,,"Characterization of the genetic regulation of proteins is essential for understanding disease etiology and developing therapies. We identified 10,674 genetic associations for 3892 plasma proteins to create a cis-anchored gene-protein-disease map of 1859 connections that highlights strong cross-disease biological convergence. This proteo-genomic map provides a framework to connect etiologically related diseases, to provide biological context for new or emerging disorders, and to integrate different biological domains to establish mechanisms for known gene-disease links. Our results identify proteo-genomic connections within and between diseases and establish the value of cis-protein variants for annotation of likely causal disease genes at loci identified in genome-wide association studies, thereby addressing a major barrier to experimental validation and clinical translation of genetic discoveries.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9904207; doi:https://doi.org/10.1126/science.abj1541; html:https://europepmc.org/articles/PMC9904207; pdf:https://europepmc.org/articles/PMC9904207?pdf=render; doi:https://doi.org/10.1126/science.abj1541
+35251129,https://doi.org/10.3389/fgene.2022.818574,Calculating Polygenic Risk Scores (PRS) in UK Biobank: A Practical Guide for Epidemiologists.,"Collister JA, Liu X, Clifton L.",,Frontiers in genetics,2022,2022-02-18,Y,Polygenic Score; Genetic Risk Score; Uk Biobank; Polygenic Risk Score; Worked Example,,,"A polygenic risk score estimates the genetic risk of an individual for some disease or trait, calculated by aggregating the effect of many common variants associated with the condition. With the increasing availability of genetic data in large cohort studies such as the UK Biobank, inclusion of this genetic risk as a covariate in statistical analyses is becoming more widespread. Previously this required specialist knowledge, but as tooling and data availability have improved it has become more feasible for statisticians and epidemiologists to calculate existing scores themselves for use in analyses. While tutorial resources exist for conducting genome-wide association studies and generating of new polygenic risk scores, fewer guides exist for the simple calculation and application of existing genetic scores. This guide outlines the key steps of this process: selection of suitable polygenic risk scores from the literature, extraction of relevant genetic variants and verification of their quality, calculation of the risk score and key considerations of its inclusion in statistical models, using the UK Biobank imputed data as a model data set. Many of the techniques in this guide will generalize to other datasets, however we also focus on some of the specific techniques required for using data in the formats UK Biobank have selected. This includes some of the challenges faced when working with large numbers of variants, where the computation time required by some tools is impractical. While we have focused on only a couple of tools, which may not be the best ones for every given aspect of the process, one barrier to working with genetic data is the sheer volume of tools available, and the difficulty for a novice to assess their viability. By discussing in depth a couple of tools that are adequate for the calculation even at large scale, we hope to make polygenic risk scores more accessible to a wider range of researchers.",,pdf:https://www.frontiersin.org/articles/10.3389/fgene.2022.818574/pdf; doi:https://doi.org/10.3389/fgene.2022.818574; html:https://europepmc.org/articles/PMC8894758; pdf:https://europepmc.org/articles/PMC8894758?pdf=render
 31564467,https://doi.org/10.1016/s2215-0366(19)30369-4,"The burden of mental ill health associated with childhood maltreatment in the UK, using The Health Improvement Network database: a population-based retrospective cohort study.","Chandan JS, Thomas T, Gokhale KM, Bandyopadhyay S, Taylor J, Nirantharakumar K.",,The lancet. Psychiatry,2019,2019-09-26,N,,,,"<h4>Background</h4>Childhood maltreatment is a global public health, human rights, and moral issue that is associated with a substantial mental health burden. We aimed to assess the association between childhood maltreatment and the development of mental ill health and the initiation of new prescriptions for mental ill health.<h4>Methods</h4>In this population-based, retrospective, open cohort study, we used a dataset from individuals in The Health Improvement Network (THIN) database. THIN database comprises UK electronic medical records taken from 787 general practices throughout the UK. We used read codes in these records to identify exposed patients (those with a read code identifying officially confirmed childhood maltreatment or a maltreatment-related concern) and up to two unexposed patients (those without such read codes) from the same general practice, who were matched by age and sex. We evaluated the risk of developing depression, anxiety, or serious mental illness (a composite mental ill health outcome) or initiation of a prescription drug used to treat mental ill health, and the odds ratio of these events at baseline, in the exposed versus unexposed patients.<h4>Findings</h4>The first possible date for cohort entry (the study start date) was Jan 1, 1995, and patients could enter the cohort until the study end date, Dec 31, 2018. During the study period, 11 831 850 patients were eligible to participate. Of these patients, we identified 217 758 (1·8%) patients with any recorded childhood maltreatment. These patients were matched to 423 410 unexposed control patients with no recorded exposure to childhood maltreatment. The exposed group were followed up for a median of 1·8 years (IQR 0·6-4·3) versus 3·2 years (1·3-6·1) in the unexposed group. During the study period, 11 665 (5·9%) new diagnoses of mental ill health were made in the exposed group, giving an incidence rate of 16·8 events per 1000 person-years versus 15 301 (3·7%) new recorded diagnoses at an incidence rate of 8·3 events per 1000 person-years in the unexposed cohort, giving an adjusted IRR of 2·14 (95% CI 2·08-2·19). 30 911 (14·8%) patients in the exposed group received a new prescription for any type of mental ill health (incidence rate 46·5 events per 1000 person-years) versus 36 390 (8·9%) patients in the unexposed group (20·5 per 1000 person-years) resulting in an adjusted IRR of 2·44 (95% CI 2·40-2·48).<h4>Interpretation</h4>Childhood maltreatment is thought to affect one in three children globally; therefore, a doubled risk of developing mental ill health among these individuals represents a substantial contribution to the mental ill health burden in the UK. It is imperative that public health approaches, including those aimed at preventing and detecting childhood maltreatment and its associated negative consequences, are implemented to prevent mental ill health.<h4>Funding</h4>None.",,pdf:http://pure-oai.bham.ac.uk/ws/files/77236664/Chandan_et_al_The_burden_of_mental_ill_health_associated_with_childhood_maltreatment_in_the_UK_using_The_Health_Improvement_Network_database_The_Lancet_Psychiatry_2019.pdf; doi:https://doi.org/10.1016/S2215-0366(19)30369-4
 35762393,https://doi.org/10.1093/oncolo/oyac117,Using Patient-Reported Outcomes in Dose-Finding Oncology Trials: Surveys of Key Stakeholders and the National Cancer Research Institute Consumer Forum.,"Lai-Kwon J, Vanderbeek AM, Minchom A, Lee Aiyegbusi O, Ogunleye D, Stephens R, Calvert M, Yap C.",,The oncologist,2022,2022-09-01,Y,Cancer; Quality of life; Clinical Trials; Drug Development; Adverse Events; Patient-reported Outcomes,,,"<h4>Background</h4>Patient-reported adverse events may be a useful adjunct for assessing a drug's tolerability in dose-finding oncology trials (DFOT). We conducted surveys of international stakeholders and the National Cancer Research Institute (NCRI) Consumer Forum to understand attitudes about patient-reported outcome (PRO) use in DFOT.<h4>Methods</h4>A 35-question survey of clinicians, trial managers, statisticians, funders, and regulators of DFOT was distributed via professional bodies examining experience using PROs, benefits/barriers, and their potential role in defining tolerable doses. An 8-question survey of the NCRI Consumer Forum explored similar themes.<h4>Results</h4>International survey: 112 responses from 15 September-30 November 2020; 103 trialists [48 clinicians (42.9%), 38 statisticians (34.0%), 17 trial managers (15.2%)], 7 regulators (6.3%), 2 funders (1.8%)]. Most trialists had no experience designing (73, 70.9%), conducting (52, 50.5%), or reporting (88, 85.4%) PROs in DFOT. Most agreed that PROs could identify new toxicities (75, 67.0%) and provide data on the frequency (86, 76.8%) and duration (81, 72.3%) of toxicities. The top 3 barriers were lack of guidance regarding PRO selection (73/103, 70.9%), missing PRO data (71/103, 68.9%), and overburdening staff (68/103, 66.0%). NCRI survey: 57 responses on 21 March 2021. A total of 28 (49.1%) were willing to spend &lt;15 min/day completing PROs. Most (55, 96.5%) preferred to complete PROs online. 61 (54.5%) trialists and 57 (100%) consumers agreed that patient-reported adverse events should be used to inform dose-escalation decisions.<h4>Conclusion</h4>Stakeholders reported minimal experience using PROs in DFOT but broadly supported their use. Guidelines are needed to standardize PRO selection, analysis, and reporting in DFOT.",,pdf:https://academic.oup.com/oncolo/article-pdf/27/9/768/45667678/oyac117.pdf; doi:https://doi.org/10.1093/oncolo/oyac117; html:https://europepmc.org/articles/PMC9438918; pdf:https://europepmc.org/articles/PMC9438918?pdf=render
 37872160,https://doi.org/10.1038/s41467-023-42284-5,"Genome-wide association study of thyroid-stimulating hormone highlights new genes, pathways and associations with thyroid disease.","Williams AT, Chen J, Coley K, Batini C, Izquierdo A, Packer R, Abner E, Kanoni S, Shepherd DJ, Free RC, Hollox EJ, Brunskill NJ, Ntalla I, Reeve N, Brightling CE, Venn L, Adams E, Bee C, Wallace SE, Pareek M, Hansell AL, Esko T, Estonian Biobank Research Team, Stow D, Jacobs BM, van Heel DA, Genes & Health Research Team, Hennah W, Rao BS, Dudbridge F, Wain LV, Shrine N, Tobin MD, John C.",,Nature communications,2023,2023-10-23,Y,,,,"Thyroid hormones play a critical role in regulation of multiple physiological functions and thyroid dysfunction is associated with substantial morbidity. Here, we use electronic health records to undertake a genome-wide association study of thyroid-stimulating hormone (TSH) levels, with a total sample size of 247,107. We identify 158 novel genetic associations, more than doubling the number of known associations with TSH, and implicate 112 putative causal genes, of which 76 are not previously implicated. A polygenic score for TSH is associated with TSH levels in African, South Asian, East Asian, Middle Eastern and admixed American ancestries, and associated with hypothyroidism and other thyroid disease in South Asians. In Europeans, the TSH polygenic score is associated with thyroid disease, including thyroid cancer and age-of-onset of hypothyroidism and hyperthyroidism. We develop pathway-specific genetic risk scores for TSH levels and use these in phenome-wide association studies to identify potential consequences of pathway perturbation. Together, these findings demonstrate the potential utility of genetic associations to inform future therapeutics and risk prediction for thyroid diseases.",,pdf:https://www.nature.com/articles/s41467-023-42284-5.pdf; doi:https://doi.org/10.1038/s41467-023-42284-5; html:https://europepmc.org/articles/PMC10593800; pdf:https://europepmc.org/articles/PMC10593800?pdf=render
@@ -2130,14 +2132,14 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 35913736,https://doi.org/10.1093/ehjqcco/qcac045,Impact of cancer diagnosis on distribution and trends of cardiovascular hospitalizations in the USA between 2004 and 2017.,"Kobo O, Raisi-Estabragh Z, Gevaert S, Rana JS, Van Spall HGC, Roguin A, Petersen SE, Ky B, Mamas MA.",,European heart journal. Quality of care & clinical outcomes,2022,2022-10-01,N,Prognosis; trends; Cardio- Oncology,,,"<h4>Background and aims</h4>There is limited data on temporal trends of cardiovascular hospitalizations and outcomes amongst cancer patients. We describe the distribution, trends of admissions, and in-hospital mortality associated with key cardiovascular diseases among cancer patients in the USA between 2004 and 2017.<h4>Methods</h4>Using the Nationwide Inpatient Sample we, identified admissions with five cardiovascular diseases of interest: acute myocardial infarction (AMI), pulmonary embolism (PE), ischaemic stroke, heart failure, atrial fibrillation (AF) or atrial flutter, and intracranial haemorrhage. Patients were stratified by cancer status and type. We estimated crude annual rates of hospitalizations and annual in-hospital all-cause mortality rates.<h4>Results</h4>From &gt;42.5 million hospitalizations with a primary cardiovascular diagnosis, 1.9 million (4.5%) had a concurrent record of cancer. Between 2004 and 2017, cardiovascular admission rates increased by 23.2% in patients with cancer, whilst decreasing by 10.9% in patients without cancer. The admission rate increased among cancer patients across all admission causes and cancer types except prostate cancer. Patients with haematological (9.7-13.5), lung (7.4-8.9), and GI cancer (4.6-6.3) had the highest crude rates of cardiovascular hospitalizations per 100 000 US population. Heart failure was the most common reason for cardiovascular admission in patients across all cancer types, except GI cancer (crude admission rates of 13.6-16.6 per 100 000 US population for patients with cancer).<h4>Conclusions</h4>In contrast to declining trends in patients without cancer, primary cardiovascular admissions in patients with cancer is increasing. The highest admission rates are in patients with haematological cancer, and the most common cause of admission is heart failure.",,pdf:https://biblio.ugent.be/publication/01GTEZMFA3PQ4FR2HWVVMJE1PP/file/01GTEZP5YQ68PC7TFPP52TS6QR.pdf; doi:https://doi.org/10.1093/ehjqcco/qcac045; html:https://europepmc.org/articles/PMC9603542; pdf:https://europepmc.org/articles/PMC9603542?pdf=render; doi:https://doi.org/10.1093/ehjqcco/qcac045
 31912232,https://doi.org/10.1007/s00394-019-02170-7,Adherence to the Dutch dietary guidelines and 15-year incidence of heart failure in the EPIC-NL cohort.,"Harbers MC, de Kroon AM, Boer JMA, Asselbergs FW, Geleijnse JM, Verschuren WMM, van der Schouw YT, Sluijs I.",,European journal of nutrition,2020,2020-01-07,N,Heart Failure; Dietary Patterns; Dutch Healthy Diet 2015 Index; Dutch Dietary Guidelines,,,"<h4>Purpose</h4>A healthy diet may contribute to the primary prevention of heart failure (HF), but evidence is still inconclusive. We aimed to study the association between adherence to the Dutch dietary guidelines and incidence of HF.<h4>Methods</h4>We studied 37,468 participants aged 20-70 years and free of HF at baseline from the EPIC-NL cohort. At baseline (1993-1997), data were collected on demographics, lifestyle, and presence of chronic diseases. Dietary intake was assessed using a 178-item validated food frequency questionnaire. Dietary intake data were used to calculate scores on the Dutch Healthy Diet 2015 Index (DHD15-index) measuring adherence to the Dutch dietary guidelines. The DHD15-index is based on the average daily intake of 14 food groups resulting in a total score ranging between 0 and 140, with higher scores indicating better adherence. HF morbidity and mortality during follow-up were ascertained through linkage with national registries. Cox proportional hazards analysis was used to estimate hazard ratios (HRs) and 95% confidence intervals (95% CIs) for the association between DHD15 adherence and HF risk, adjusting for sociodemographic and lifestyle characteristics.<h4>Results</h4>The average score on the DHD15-index was 71 (SD = 15). During a median follow-up of 15.2 years (IQR 14.1-16.5), 674 HF events occurred. After adjustment for demographic and lifestyle characteristics, higher scores on the DHD15-index were associated with lower risk of HF (HR<sub>Q4vsQ1</sub> 0.73; 95% CI 0.58-0.93; P<sub>trend</sub> 0.001).<h4>Conclusion</h4>In a large Dutch population of middle-aged adults, higher adherence to the Dutch dietary guidelines was associated with lower risk of HF.",,pdf:https://discovery.ucl.ac.uk/id/eprint/10104999/1/Harbers%20et%20al.%202019%20Adh%20do%20Dutch%20dietary%20guidelines%20and%20HF.pdf; doi:https://doi.org/10.1007/s00394-019-02170-7
 36446465,https://doi.org/10.1136/bmjopen-2022-065142,"Prevalence, pathophysiology, prediction and health-related quality of life of long COVID: study protocol of the longitudinal multiple cohort CORona Follow Up (CORFU) study.","Ghossein-Doha C, Wintjens MSJN, Janssen EBNJ, Klein D, Heemskerk SCM, Asselbergs FW, Birnie E, Bonsel GJ, van Bussel BCT, Cals JWL, Ten Cate H, Haagsma J, Hemmen B, van der Horst ICC, Kietselaer BLJH, Klok FA, de Kruif MD, Linschoten M, van Santen S, Vernooy K, Willems LH, Westerborg R, Warle M, van Kuijk SMJ.",,BMJ open,2022,2022-11-29,Y,epidemiology; Public Health; Protocols & Guidelines; Covid-19,,,"<h4>Introduction</h4>The variety, time patterns and long-term prognosis of persistent COVID-19 symptoms (long COVID-19) in patients who suffered from mild to severe acute COVID-19 are incompletely understood. Cohort studies will be combined to describe the prevalence of long COVID-19 symptoms, and to explore the pathophysiological mechanisms and impact on health-related quality of life. A prediction model for long COVID-19 will be developed and internally validated to guide care in future patients.<h4>Methods and analysis</h4>Data from seven COVID-19 cohorts will be aggregated in the longitudinal multiple cohort CORona Follow Up (CORFU) study. CORFU includes Dutch patients who suffered from COVID-19 at home, were hospitalised without or with intensive care unit treatment, needed inpatient or outpatient rehabilitation and controls who did not suffer from COVID-19. Individual cohort study designs were aligned and follow-up has been synchronised. Cohort participants will be followed up for a maximum of 24 months after acute infection. Next to the clinical characteristics measured in individual cohorts, the CORFU questionnaire on long COVID-19 outcomes and determinants will be administered digitally at 3, 6, 12, 18 and 24 months after the infection. The primary outcome is the prevalence of long COVID-19 symptoms up to 2 years after acute infection. Secondary outcomes are health-related quality of life (eg, EQ-5D), physical functioning, and the prevalence of thromboembolic complications, respiratory complications, cardiovascular diseases and endothelial dysfunction. A prediction model and a patient platform prototype will be developed.<h4>Ethics and dissemination</h4>Approval was obtained from the medical research ethics committee of Maastricht University Medical Center+ and Maastricht University (METC 2021-2990) and local committees of the participating cohorts. The project is supported by ZonMW and EuroQol Research Foundation. Results will be published in open access peer-reviewed scientific journals and presented at (inter)national conferences.<h4>Trial registration number</h4>NCT05240742.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/11/e065142.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-065142; html:https://europepmc.org/articles/PMC9709810; pdf:https://europepmc.org/articles/PMC9709810?pdf=render
-33888728,https://doi.org/10.1038/s41598-021-86331-x,A multidimensional measure of polypharmacy for older adults using the Health and Retirement Study.,"Carr E, Federman A, Dzahini O, Dobson RJ, Bendayan R.",,Scientific reports,2021,2021-04-22,Y,,,,"Polypharmacy is commonly defined based on the number of medications taken concurrently using standard cut-offs, but several studies have highlighted the need for a multidimensional assessment. We developed a multidimensional measure of polypharmacy and compared with standard cut-offs. Data were extracted for 2141 respondents of the 2007 Prescription Drug Survey, a sub-study of the Health Retirement Study. Latent classes were identified based on multiple indicators of polypharmacy, including quantity, temporality and risk profile. A four-class model was selected based on fit statistics and clinical interpretability: 'High risk, long-term' (Class 1), 'Low risk, long-term' (Class 2), 'High risk, short-term' (Class 3), and 'High risk for drug interactions, medium-term, regular' (Class 4). Classes differed regarding sex, cohabitation, disability and multimorbidity. Participants in the 'low risk' class tended to be male, cohabitating, and reported fewer health conditions, compared to 'high risk' classes. Polypharmacy classes were compared to standard cut-offs (5+ or 9+ medications) in terms of overlap and mortality risk. The three 'high risk' classes overlapped with the groups concurrently taking 5+ and 9+ medications per month. However, the multidimensional measure further differentiated individuals in terms of risk profile and temporality of medication taking, thus offering a richer assessment of polypharmacy.",,pdf:https://www.nature.com/articles/s41598-021-86331-x.pdf; doi:https://doi.org/10.1038/s41598-021-86331-x; html:https://europepmc.org/articles/PMC8062687; pdf:https://europepmc.org/articles/PMC8062687?pdf=render
 34053260,https://doi.org/10.1098/rstb.2020.0283,Exploring surveillance data biases when estimating the reproduction number: with insights into subpopulation transmission of COVID-19 in England.,"Sherratt K, Abbott S, Meakin SR, Hellewell J, Munday JD, Bosse N, CMMID COVID-19 Working Group, Jit M, Funk S.",,"Philosophical transactions of the Royal Society of London. Series B, Biological sciences",2021,2021-05-31,Y,Transmission; Surveillance; Bias; Covid-19; Sars-cov-2; Time-varying Reproduction Number,,,"The time-varying reproduction number (<i>R<sub>t</sub></i>: the average number of secondary infections caused by each infected person) may be used to assess changes in transmission potential during an epidemic. While new infections are not usually observed directly, they can be estimated from data. However, data may be delayed and potentially biased. We investigated the sensitivity of <i>R<sub>t</sub></i> estimates to different data sources representing COVID-19 in England, and we explored how this sensitivity could track epidemic dynamics in population sub-groups. We sourced public data on test-positive cases, hospital admissions and deaths with confirmed COVID-19 in seven regions of England over March through August 2020. We estimated <i>R<sub>t</sub></i> using a model that mapped unobserved infections to each data source. We then compared differences in <i>R<sub>t</sub></i> with the demographic and social context of surveillance data over time. Our estimates of transmission potential varied for each data source, with the relative inconsistency of estimates varying across regions and over time. <i>R<sub>t</sub></i> estimates based on hospital admissions and deaths were more spatio-temporally synchronous than when compared to estimates from all test positives. We found these differences may be linked to biased representations of subpopulations in each data source. These included spatially clustered testing, and where outbreaks in hospitals, care homes, and young age groups reflected the link between age and severity of the disease. We highlight that policy makers could better target interventions by considering the source populations of <i>R<sub>t</sub></i> estimates. Further work should clarify the best way to combine and interpret <i>R<sub>t</sub></i> estimates from different data sources based on the desired use. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.",,pdf:https://royalsocietypublishing.org/doi/pdf/10.1098/rstb.2020.0283; doi:https://doi.org/10.1098/rstb.2020.0283; html:https://europepmc.org/articles/PMC8165604; pdf:https://europepmc.org/articles/PMC8165604?pdf=render
+33888728,https://doi.org/10.1038/s41598-021-86331-x,A multidimensional measure of polypharmacy for older adults using the Health and Retirement Study.,"Carr E, Federman A, Dzahini O, Dobson RJ, Bendayan R.",,Scientific reports,2021,2021-04-22,Y,,,,"Polypharmacy is commonly defined based on the number of medications taken concurrently using standard cut-offs, but several studies have highlighted the need for a multidimensional assessment. We developed a multidimensional measure of polypharmacy and compared with standard cut-offs. Data were extracted for 2141 respondents of the 2007 Prescription Drug Survey, a sub-study of the Health Retirement Study. Latent classes were identified based on multiple indicators of polypharmacy, including quantity, temporality and risk profile. A four-class model was selected based on fit statistics and clinical interpretability: 'High risk, long-term' (Class 1), 'Low risk, long-term' (Class 2), 'High risk, short-term' (Class 3), and 'High risk for drug interactions, medium-term, regular' (Class 4). Classes differed regarding sex, cohabitation, disability and multimorbidity. Participants in the 'low risk' class tended to be male, cohabitating, and reported fewer health conditions, compared to 'high risk' classes. Polypharmacy classes were compared to standard cut-offs (5+ or 9+ medications) in terms of overlap and mortality risk. The three 'high risk' classes overlapped with the groups concurrently taking 5+ and 9+ medications per month. However, the multidimensional measure further differentiated individuals in terms of risk profile and temporality of medication taking, thus offering a richer assessment of polypharmacy.",,pdf:https://www.nature.com/articles/s41598-021-86331-x.pdf; doi:https://doi.org/10.1038/s41598-021-86331-x; html:https://europepmc.org/articles/PMC8062687; pdf:https://europepmc.org/articles/PMC8062687?pdf=render
 32285648,https://doi.org/10.1002/ehf2.12689,Predicting sustained ventricular arrhythmias in dilated cardiomyopathy: a meta-analysis and systematic review.,"Sammani A, Kayvanpour E, Bosman LP, Sedaghat-Hamedani F, Proctor T, Gi WT, Broezel A, Jensen K, Katus HA, Te Riele ASJM, Meder B, Asselbergs FW.",,ESC heart failure,2020,2020-04-14,Y,Prognosis; Dilated cardiomyopathy; risk; Sudden Cardiac Death; Implantable Cardiac-defibrillator,,,"<h4>Aims</h4>Patients with non-ischaemic dilated cardiomyopathy (DCM) are at increased risk of sudden cardiac death. Identification of patients that may benefit from implantable cardioverter-defibrillator implantation remains challenging. In this study, we aimed to determine predictors of sustained ventricular arrhythmias in patients with DCM.<h4>Methods and results</h4>We searched MEDLINE/Embase for studies describing predictors of sustained ventricular arrhythmias in patients with DCM. Quality and bias were assessed using the Quality in Prognostic Studies tool, articles with high risk of bias in ≥2 areas were excluded. Unadjusted hazard ratios (HRs) of uniformly defined predictors were pooled, while all other predictors were evaluated in a systematic review. We included 55 studies (11 451 patients and 3.7 ± 2.3 years follow-up). Crude annual event rate was 4.5%. Younger age [HR 0.82; 95% CI (0.74-1.00)], hypertension [HR 1.95; 95% CI (1.26-3.00)], prior sustained ventricular arrhythmia [HR 4.15; 95% CI (1.32-13.02)], left ventricular ejection fraction on ultrasound [HR 1.45; 95% CI (1.19-1.78)], left ventricular dilatation (HR 1.10), and presence of late gadolinium enhancement [HR 5.55; 95% CI (4.02-7.67)] were associated with arrhythmic outcome in pooled analyses. Prior non-sustained ventricular arrhythmia and several genotypes [mutations in Phospholamban (PLN), Lamin A/C (LMNA), and Filamin-C (FLNC)] were associated with arrhythmic outcome in non-pooled analyses. Quality of evidence was moderate, and heterogeneity among studies was moderate to high.<h4>Conclusions</h4>In patients with DCM, the annual event rate of sustained ventricular arrhythmias is approximately 4.5%. This risk is considerably higher in younger patients with hypertension, prior (non-)sustained ventricular arrhythmia, decreased left ventricular ejection fraction, left ventricular dilatation, late gadolinium enhancement, and genetic mutations (PLN, LMNA, and FLNC). These results may help determine appropriate candidates for implantable cardioverter-defibrillator implantation.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ehf2.12689; doi:https://doi.org/10.1002/ehf2.12689; html:https://europepmc.org/articles/PMC7373946; pdf:https://europepmc.org/articles/PMC7373946?pdf=render
 33493066,https://doi.org/10.1161/strokeaha.120.031659,"Sex, Age, and Socioeconomic Differences in Nonfatal Stroke Incidence and Subsequent Major Adverse Outcomes.","Akyea RK, Vinogradova Y, Qureshi N, Patel RS, Kontopantelis E, Ntaios G, Asselbergs FW, Kai J, Weng SF.",,Stroke,2021,2021-01-25,Y,Population; Cardiovascular diseases; epidemiology; incidence; Secondary Prevention,,,"<h4>Background and purpose</h4>Data about variations in stroke incidence and subsequent major adverse outcomes are essential to inform secondary prevention and prioritizing resources to those at the greatest risk of major adverse end points. We aimed to describe the age, sex, and socioeconomic differences in the rates of first nonfatal stroke and subsequent major adverse outcomes.<h4>Methods</h4>The cohort study used linked Clinical Practice Research Datalink and Hospital Episode Statistics data from the United Kingdom. The incidence rate (IR) ratio of first nonfatal stroke and subsequent major adverse outcomes (composite major adverse cardiovascular events, recurrent stroke, cardiovascular disease-related, and all-cause mortality) were calculated and presented by year, sex, age group, and socioeconomic status based on an individual's location of residence, in adults with incident nonfatal stroke diagnosis between 1998 and 2017.<h4>Results</h4>A total of 82 774 first nonfatal stroke events were recorded in either primary care or hospital data-an IR of 109.20 per 100 000 person-years (95% CI, 108.46-109.95). Incidence was significantly higher in women compared with men (IR ratio, 1.13 [95% CI, 1.12-1.15]; <i>P</i><0.001). Rates adjusted for age and sex were higher in the lowest compared with the highest socioeconomic status group (IR ratio, 1.10 [95% CI, 1.08-1.13]; <i>P</i><0.001). For subsequent major adverse outcomes, the overall incidence for major adverse cardiovascular event was 38.05 per 100 person-years (95% CI, 37.71-38.39) with a slightly higher incidence in women compared with men (38.42 versus 37.62; IR ratio, 1.02 [95% CI, 1.00-1.04]; <i>P</i>=0.0229). Age and socioeconomic status largely accounted for the observed higher incidence of adverse outcomes in women.<h4>Conclusions</h4>In the United Kingdom, incidence of initial stroke and subsequent major adverse outcomes are higher in women, older populations, and people living in socially deprived areas.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/STROKEAHA.120.031659; doi:https://doi.org/10.1161/STROKEAHA.120.031659; html:https://europepmc.org/articles/PMC7834661; pdf:https://europepmc.org/articles/PMC7834661?pdf=render
 32951912,https://doi.org/10.1016/j.jhep.2020.08.030,"Corrigendum to: ""Genome-wide and Mendelian randomisation studies of liver MRI yield insights into the pathogenesis of steatohepatitis"" [J Hepatol (2020) 241-251].","Parisinos CA, Wilman HR, Thomas EL, Kelly M, Nicholls RC, McGonigle J, Neubauer S, Hingorani AD, Patel RS, Hemingway H, Bell JD, Banerjee R, Yaghootkar H.",,Journal of hepatology,2020,2020-09-18,Y,,,,,,pdf:http://www.journal-of-hepatology.eu/article/S0168827820336035/pdf; doi:https://doi.org/10.1016/j.jhep.2020.08.030; html:https://europepmc.org/articles/PMC8055539; pdf:https://europepmc.org/articles/PMC8055539?pdf=render
 33325834,https://doi.org/10.2196/23530,Cystic Fibrosis Point of Personalized Detection (CFPOPD): An Interactive Web Application.,"Wolfe C, Pestian T, Gecili E, Su W, Keogh RH, Pestian JP, Seid M, Diggle PJ, Ziady A, Clancy JP, Grossoehme DH, Szczesniak RD, Brokamp C.",,JMIR medical informatics,2020,2020-12-16,Y,Chronic disease; Clinical Decision Support; Medical Monitoring; Clinical Decision Rules; Application Programming Interface,,,"<h4>Background</h4>Despite steady gains in life expectancy, individuals with cystic fibrosis (CF) lung disease still experience rapid pulmonary decline throughout their clinical course, which can ultimately end in respiratory failure. Point-of-care tools for accurate and timely information regarding the risk of rapid decline is essential for clinical decision support.<h4>Objective</h4>This study aims to translate a novel algorithm for earlier, more accurate prediction of rapid lung function decline in patients with CF into an interactive web-based application that can be integrated within electronic health record systems, via collaborative development with clinicians.<h4>Methods</h4>Longitudinal clinical history, lung function measurements, and time-invariant characteristics were obtained for 30,879 patients with CF who were followed in the US Cystic Fibrosis Foundation Patient Registry (2003-2015). We iteratively developed the application using the R Shiny framework and by conducting a qualitative study with care provider focus groups (N=17).<h4>Results</h4>A clinical conceptual model and 4 themes were identified through coded feedback from application users: (1) ambiguity in rapid decline, (2) clinical utility, (3) clinical significance, and (4) specific suggested revisions. These themes were used to revise our application to the currently released version, available online for exploration. This study has advanced the application's potential prognostic utility for monitoring individuals with CF lung disease. Further application development will incorporate additional clinical characteristics requested by the users and also a more modular layout that can be useful for care provider and family interactions.<h4>Conclusions</h4>Our framework for creating an interactive and visual analytics platform enables generalized development of applications to synthesize, model, and translate electronic health data, thereby enhancing clinical decision support and improving care and health outcomes for chronic diseases and disorders. A prospective implementation study is necessary to evaluate this tool's effectiveness regarding increased communication, enhanced shared decision-making, and improved clinical outcomes for patients with CF.",,pdf:https://medinform.jmir.org/2020/12/e23530/PDF; doi:https://doi.org/10.2196/23530; html:https://europepmc.org/articles/PMC7773511
-38553074,https://doi.org/10.1136/bmjopen-2024-085392,Protocol for a mixed-methods study to develop and feasibility test a digital system for the capture of patient-reported outcomes (PROs) in patients receiving chimeric antigen receptor T-cell (CAR-T) therapies (the PRO-CAR-T study).,"Hughes SE, McMullan C, Aiyegbusi OL, Shaw K, Kinsella F, Ferguson P, Khatsuria F, Burns D, Pyatt L, Ansell J, Chakera E, Richardson-Abraham J, Denniston AK, Davies EH, Craddock C, Calvert M.",,BMJ open,2024,2024-03-29,Y,Gene therapy; Quality of life; Haematology; Patient-centered Care; Ehealth; Patient Reported Outcome Measures,,,"<h4>Introduction</h4>Chimeric antigen receptor (CAR) T-cell therapies are novel, potentially curative therapies for haematological malignancies. CAR T-cell therapies are associated with severe toxicities, meaning patients require monitoring during acute and postacute treatment phases. Electronic patient-reported outcomes (ePROs), self-reports of health status provided via online questionnaires, can complement clinician observation with potential to improve patient outcomes. This study will develop and evaluate feasibility of a new ePRO system for CAR-T patients in routine care.<h4>Methods and analysis</h4>Multiphase, mixed-methods study involving multiple stakeholder groups (patients, family members, carers, clinicians, academics/researchers and policy-makers). The intervention development phase comprises a Delphi study to select PRO measures for the digital system, a codesign workshop and consensus meetings to establish thresholds for notifications to the clinical team if a patient reports severe symptoms or side effects. Usability testing will evaluate how users interact with the digital system and, lastly, we will evaluate ePRO system feasibility with 30 CAR-T patients (adults aged 18+ years) when used in addition to usual care. Feasibility study participants will use the ePRO system to submit self-reports of symptoms, treatment tolerability and quality of life at specific time points. The CAR-T clinical team will respond to system notifications triggered by patients' submitted responses with actions in line with standard clinical practice. Feasibility measures will be collected at prespecified time points following CAR T-cell infusion. A qualitative substudy involving patients and clinical team members will explore acceptability of the ePRO system.<h4>Ethics and dissemination</h4>Favourable ethical opinion was granted by the Health and Social Care Research Ethics Committee B(HSC REC B) (ref: 23/NI/0104) on 28 September 2023. Findings will be submitted for publication in high-quality, peer-reviewed journals. Summaries of results, codeveloped with the Blood and Transplant Research Unit Patient and Public Involvement and Engagement group, will be disseminated to all interested groups.<h4>Trial registration number</h4>ISCTRN11232653.",,pdf:https://bmjopen.bmj.com/content/bmjopen/14/3/e085392.full.pdf; doi:https://doi.org/10.1136/bmjopen-2024-085392; html:https://europepmc.org/articles/PMC10982800; pdf:https://europepmc.org/articles/PMC10982800?pdf=render
 35247983,https://doi.org/10.1186/s12877-021-02673-1,"Age is the main determinant of COVID-19 related in-hospital mortality with minimal impact of pre-existing comorbidities, a retrospective cohort study.","Henkens MTHM, Raafs AG, Verdonschot JAJ, Linschoten M, van Smeden M, Wang P, van der Hooft BHM, Tieleman R, Janssen MLF, Ter Bekke RMA, Hazebroek MR, van der Horst ICC, Asselbergs FW, Magdelijns FJH, Heymans SRB, CAPACITY-COVID collaborative consortium.",,BMC geriatrics,2022,2022-03-05,Y,Mortality; Hospitalization; Netherlands; Mediation Analysis; Covid-19,,,"<h4>Background</h4>Age and comorbidities increase COVID-19 related in-hospital mortality risk, but the extent by which comorbidities mediate the impact of age remains unknown.<h4>Methods</h4>In this multicenter retrospective cohort study with data from 45 Dutch hospitals, 4806 proven COVID-19 patients hospitalized in Dutch hospitals (between February and July 2020) from the CAPACITY-COVID registry were included (age 69[58-77]years, 64% men). The primary outcome was defined as a combination of in-hospital mortality or discharge with palliative care. Logistic regression analysis was performed to analyze the associations between sex, age, and comorbidities with the primary outcome. The effect of comorbidities on the relation of age with the primary outcome was evaluated using mediation analysis.<h4>Results</h4>In-hospital COVID-19 related mortality occurred in 1108 (23%) patients, 836 (76%) were aged ≥70 years (70+). Both age 70+ and female sex were univariably associated with outcome (odds ratio [OR]4.68, 95%confidence interval [4.02-5.45], OR0.68[0.59-0.79], respectively;both p<  0.001). All comorbidities were univariably associated with outcome (p<0.001), and all but dyslipidemia remained significant after adjustment for age70+ and sex. The impact of comorbidities was attenuated after age-spline adjustment, only leaving female sex, diabetes mellitus (DM), chronic kidney disease (CKD), and chronic pulmonary obstructive disease (COPD) significantly associated (female OR0.65[0.55-0.75], DM OR1.47[1.26-1.72], CKD OR1.61[1.32-1.97], COPD OR1.30[1.07-1.59]). Pre-existing comorbidities in older patients negligibly (<6% in all comorbidities) mediated the association between higher age and outcome.<h4>Conclusions</h4>Age is the main determinant of COVID-19 related in-hospital mortality, with negligible mediation effect of pre-existing comorbidities.<h4>Trial registration</h4>CAPACITY-COVID ( NCT04325412 ).",,doi:https://doi.org/10.1186/s12877-021-02673-1; doi:https://doi.org/10.1186/s12877-021-02673-1; html:https://europepmc.org/articles/PMC8897728; pdf:https://europepmc.org/articles/PMC8897728?pdf=render
+38553074,https://doi.org/10.1136/bmjopen-2024-085392,Protocol for a mixed-methods study to develop and feasibility test a digital system for the capture of patient-reported outcomes (PROs) in patients receiving chimeric antigen receptor T-cell (CAR-T) therapies (the PRO-CAR-T study).,"Hughes SE, McMullan C, Aiyegbusi OL, Shaw K, Kinsella F, Ferguson P, Khatsuria F, Burns D, Pyatt L, Ansell J, Chakera E, Richardson-Abraham J, Denniston AK, Davies EH, Craddock C, Calvert M.",,BMJ open,2024,2024-03-29,Y,Gene therapy; Quality of life; Haematology; Patient-centered Care; Ehealth; Patient Reported Outcome Measures,,,"<h4>Introduction</h4>Chimeric antigen receptor (CAR) T-cell therapies are novel, potentially curative therapies for haematological malignancies. CAR T-cell therapies are associated with severe toxicities, meaning patients require monitoring during acute and postacute treatment phases. Electronic patient-reported outcomes (ePROs), self-reports of health status provided via online questionnaires, can complement clinician observation with potential to improve patient outcomes. This study will develop and evaluate feasibility of a new ePRO system for CAR-T patients in routine care.<h4>Methods and analysis</h4>Multiphase, mixed-methods study involving multiple stakeholder groups (patients, family members, carers, clinicians, academics/researchers and policy-makers). The intervention development phase comprises a Delphi study to select PRO measures for the digital system, a codesign workshop and consensus meetings to establish thresholds for notifications to the clinical team if a patient reports severe symptoms or side effects. Usability testing will evaluate how users interact with the digital system and, lastly, we will evaluate ePRO system feasibility with 30 CAR-T patients (adults aged 18+ years) when used in addition to usual care. Feasibility study participants will use the ePRO system to submit self-reports of symptoms, treatment tolerability and quality of life at specific time points. The CAR-T clinical team will respond to system notifications triggered by patients' submitted responses with actions in line with standard clinical practice. Feasibility measures will be collected at prespecified time points following CAR T-cell infusion. A qualitative substudy involving patients and clinical team members will explore acceptability of the ePRO system.<h4>Ethics and dissemination</h4>Favourable ethical opinion was granted by the Health and Social Care Research Ethics Committee B(HSC REC B) (ref: 23/NI/0104) on 28 September 2023. Findings will be submitted for publication in high-quality, peer-reviewed journals. Summaries of results, codeveloped with the Blood and Transplant Research Unit Patient and Public Involvement and Engagement group, will be disseminated to all interested groups.<h4>Trial registration number</h4>ISCTRN11232653.",,pdf:https://bmjopen.bmj.com/content/bmjopen/14/3/e085392.full.pdf; doi:https://doi.org/10.1136/bmjopen-2024-085392; html:https://europepmc.org/articles/PMC10982800; pdf:https://europepmc.org/articles/PMC10982800?pdf=render
 34581777,https://doi.org/10.1182/bloodadvances.2021005453,G protein-coupled receptor kinase 5 regulates thrombin signaling in platelets via PAR-1.,"Downes K, Zhao X, Gleadall NS, McKinney H, Kempster C, Batista J, Thomas PL, Cooper M, Michael JV, Kreuzhuber R, Wedderburn K, Waller K, Varney B, Verdier H, Kriek N, Ashford SE, Stirrups KE, Dunster JL, McKenzie SE, Ouwehand WH, Gibbins JM, Yang J, Astle WJ, Ma P.",,Blood advances,2022,2022-04-01,Y,,,,"The interindividual variation in the functional response of platelets to activation by agonists is heritable. Genome-wide association studies (GWASs) of quantitative measures of platelet function have identified fewer than 20 distinctly associated variants, some with unknown mechanisms. Here, we report GWASs of pathway-specific functional responses to agonism by adenosine 5'-diphosphate, a glycoprotein VI-specific collagen mimetic, and thrombin receptor-agonist peptides, each specific to 1 of the G protein-coupled receptors PAR-1 and PAR-4, in subsets of 1562 individuals. We identified an association (P = 2.75 × 10-40) between a common intronic variant, rs10886430, in the G protein-coupled receptor kinase 5 gene (GRK5) and the sensitivity of platelets to activate through PAR-1. The variant resides in a megakaryocyte-specific enhancer that is bound by the transcription factors GATA1 and MEIS1. The minor allele (G) is associated with fewer GRK5 transcripts in platelets and the greater sensitivity of platelets to activate through PAR-1. We show that thrombin-mediated activation of human platelets causes binding of GRK5 to PAR-1 and that deletion of the mouse homolog Grk5 enhances thrombin-induced platelet activation sensitivity and increases platelet accumulation at the site of vascular injury. This corroborates evidence that the human G allele of rs10886430 is associated with a greater risk for cardiovascular disease. In summary, by combining the results of pathway-specific GWASs and expression quantitative trait locus studies in humans with the results from platelet function studies in Grk5-/- mice, we obtain evidence that GRK5 regulates the human platelet response to thrombin via the PAR-1 pathway.",,pdf:https://ashpublications.org/bloodadvances/article-pdf/6/7/2319/1886257/advancesadv2021005453.pdf; doi:https://doi.org/10.1182/bloodadvances.2021005453; html:https://europepmc.org/articles/PMC9006276; pdf:https://europepmc.org/articles/PMC9006276?pdf=render
 36688706,https://doi.org/10.1093/rheumatology/kead038,Classification of patients with osteoarthritis through clusters of comorbidities using 633 330 individuals from Spain.,"Pineda-Moncusí M, Dernie F, Dell'Isola A, Kamps A, Runhaar J, Swain S, Zhang W, Englund M, Pitsillidou I, Strauss VY, Robinson DE, Prieto-Alhambra D, Khalid S.",,"Rheumatology (Oxford, England)",2023,2023-11-01,Y,Clustering; epidemiology; Comorbidities; Oa,,,"<h4>Objectives</h4>To explore clustering of comorbidities among patients with a new diagnosis of OA and estimate the 10-year mortality risk for each identified cluster.<h4>Methods</h4>This is a population-based cohort study of individuals with first incident diagnosis of OA of the hip, knee, ankle/foot, wrist/hand or 'unspecified' site between 2006 and 2020, using SIDIAP (a primary care database representative of Catalonia, Spain). At the time of OA diagnosis, conditions associated with OA in the literature that were found in ≥1% of the individuals (n = 35) were fitted into two cluster algorithms, k-means and latent class analysis. Models were assessed using a range of internal and external evaluation procedures. Mortality risk of the obtained clusters was assessed by survival analysis using Cox proportional hazards.<h4>Results</h4>We identified 633 330 patients with a diagnosis of OA. Our proposed best solution used latent class analysis to identify four clusters: 'low-morbidity' (relatively low number of comorbidities), 'back/neck pain plus mental health', 'metabolic syndrome' and 'multimorbidity' (higher prevalence of all studied comorbidities). Compared with the 'low-morbidity' cluster, the 'multimorbidity' cluster had the highest risk of 10-year mortality (adjusted hazard ratio [HR]: 2.19 [95% CI: 2.15, 2.23]), followed by the 'metabolic syndrome' cluster (adjusted HR: 1.24 [95% CI: 1.22, 1.27]) and the 'back/neck pain plus mental health' cluster (adjusted HR: 1.12 [95% CI: 1.09, 1.15]).<h4>Conclusion</h4>Patients with a new diagnosis of OA can be clustered into groups based on their comorbidity profile, with significant differences in 10-year mortality risk. Further research is required to understand the interplay between OA and particular comorbidity groups, and the clinical significance of such results.",,pdf:https://academic.oup.com/rheumatology/advance-article-pdf/doi/10.1093/rheumatology/kead038/49101708/kead038.pdf; doi:https://doi.org/10.1093/rheumatology/kead038; html:https://europepmc.org/articles/PMC10629784; pdf:https://europepmc.org/articles/PMC10629784?pdf=render
 30887727,https://doi.org/10.1002/ppul.24314,Physical activity among children with asthma: Cross-sectional analysis in the UK millennium cohort.,"Pike KC, Griffiths LJ, Dezateux C, Pearce A.",,Pediatric pulmonology,2019,2019-03-18,Y,Children; Cohort study; epidemiology; Physical Activity; Asthma And Early Wheeze,Improving Public Health,,"<h4>Background</h4>Although beneficial for health and well-being, most children do not achieve recommended levels of physical activity. Evidence for children with asthma is mixed, with symptom severity rarely considered. This paper aimed to address this gap.<h4>Methods</h4>We analyzed cross-sectional associations between physical activity and parent-reported asthma symptoms and severity for 6497 UK Millennium Cohort Study 7-year-old participants (3321, [49%] girls). Primary outcomes were daily moderate-to-vigorous physical activity (MVPA, minutes) and proportion of children achieving recommended minimum daily levels of 60 minutes of MVPA. Daily steps, sedentary time, and total activity counts per minute (cpm) were recorded, as were parent-reported asthma symptoms, medications, and recent hospital admissions. Associations were investigated using quantile (continuous outcomes) and Poisson (binary outcomes) regression, adjusting for demographic, socioeconomic, health, and environmental factors.<h4>Results</h4>Neither asthma status nor severity was associated with MVPA; children recently hospitalized for asthma were less likely to achieve recommended daily MVPA (risk ratio [95% confidence interval [CI]]: 0.67 [0.44, 1.03]). Recent wheeze, current asthma, and severe asthma symptoms were associated with fewer sedentary hours (difference in medians [95% CI]: -0.18 [-0.27, -0.08]; -0.14 [-0.24, -0.05]; -0.15, [-0.28, -0.02], respectively) and hospital admission with lower total activity (-48 cpm [-68, -28]).<h4>Conclusion</h4>Children with asthma are as physically active as their asthma-free counterparts, while those recently hospitalized for asthma are less active. Qualitative studies are needed to understand the perceptions of children and families about physical activity following hospital admission and to inform support and advice needed to maintain active lifestyles for children with asthma.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ppul.24314; doi:https://doi.org/10.1002/ppul.24314; html:https://europepmc.org/articles/PMC6617805; pdf:https://europepmc.org/articles/PMC6617805?pdf=render
@@ -2151,30 +2153,30 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 33222494,https://doi.org/10.1177/2048872620974605,Cardiac complications in patients hospitalised with COVID-19.,"Linschoten M, Peters S, van Smeden M, Jewbali LS, Schaap J, Siebelink HM, Smits PC, Tieleman RG, van der Harst P, van Gilst WH, Asselbergs FW, CAPACITY-COVID collaborative consortium.",,European heart journal. Acute cardiovascular care,2020,2020-11-21,Y,Pulmonary embolism; Cohorts; Cardiac Complications; Patient Registry; Covid-19/coronavirus,,,"<h4>Aims</h4>To determine the frequency and pattern of cardiac complications in patients hospitalised with coronavirus disease (COVID-19).<h4>Methods and results</h4>CAPACITY-COVID is an international patient registry established to determine the role of cardiovascular disease in the COVID-19 pandemic. In this registry, data generated during routine clinical practice are collected in a standardised manner for patients with a (highly suspected) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection requiring hospitalisation. For the current analysis, consecutive patients with laboratory confirmed COVID-19 registered between 28 March and 3 July 2020 were included. Patients were followed for the occurrence of cardiac complications and pulmonary embolism from admission to discharge. In total, 3011 patients were included, of which 1890 (62.8%) were men. The median age was 67 years (interquartile range 56-76); 937 (31.0%) patients had a history of cardiac disease, with pre-existent coronary artery disease being most common (<i>n</i>=463, 15.4%). During hospitalisation, 595 (19.8%) patients died, including 16 patients (2.7%) with cardiac causes. Cardiac complications were diagnosed in 349 (11.6%) patients, with atrial fibrillation (<i>n</i>=142, 4.7%) being most common. The incidence of other cardiac complications was 1.8% for heart failure (<i>n</i>=55), 0.5% for acute coronary syndrome (<i>n</i>=15), 0.5% for ventricular arrhythmia (<i>n</i>=14), 0.1% for bacterial endocarditis (<i>n</i>=4) and myocarditis (<i>n</i>=3), respectively, and 0.03% for pericarditis (<i>n</i>=1). Pulmonary embolism was diagnosed in 198 (6.6%) patients.<h4>Conclusion</h4>This large study among 3011 hospitalised patients with COVID-19 shows that the incidence of cardiac complications during hospital admission is low, despite a frequent history of cardiovascular disease. Long-term cardiac outcomes and the role of pre-existing cardiovascular disease in COVID-19 outcome warrants further investigation.",,pdf:https://academic.oup.com/ehjacc/article-pdf/9/8/817/49790126/ehjacc0817.pdf; doi:https://doi.org/10.1177/2048872620974605; html:https://europepmc.org/articles/PMC7734244; pdf:https://europepmc.org/articles/PMC7734244?pdf=render
 37981722,https://doi.org/10.1093/aje/kwad232,Inconsistency in UK Biobank Event Definitions From Different Data Sources and Its Impact on Bias and Generalizability: A Case Study of Venous Thromboembolism.,"Bassett E, Broadbent J, Gill D, Burgess S, Mason AM.",,American journal of epidemiology,2024,2024-05-01,Y,Pulmonary embolism; Bias; Deep vein thrombosis; Venous Thromboembolism; Generalizability; Uk Biobank; Sociodemographic Characteristics; Representativeness; Event Definition,,,"The UK Biobank study contains several sources of diagnostic data, including hospital inpatient data and data on self-reported conditions for approximately 500,000 participants and primary-care data for approximately 177,000 participants (35%). Epidemiologic investigations require a primary disease definition, but whether to combine data sources to maximize statistical power or focus on only 1 source to ensure a consistent outcome is not clear. The consistency of disease definitions was investigated for venous thromboembolism (VTE) by evaluating overlap when defining cases from 3 sources: hospital inpatient data, primary-care reports, and self-reported questionnaires. VTE cases showed little overlap between data sources, with only 6% of reported events for persons with primary-care data being identified by all 3 sources (hospital, primary-care, and self-reports), while 71% appeared in only 1 source. Deep vein thrombosis-only events represented 68% of self-reported VTE cases and 36% of hospital-reported VTE cases, while pulmonary embolism-only events represented 20% of self-reported VTE cases and 50% of hospital-reported VTE cases. Additionally, different distributions of sociodemographic characteristics were observed; for example, patients in 46% of hospital-reported VTE cases were female, compared with 58% of self-reported VTE cases. These results illustrate how seemingly neutral decisions taken to improve data quality can affect the representativeness of a data set.",,pdf:https://academic.oup.com/aje/advance-article-pdf/doi/10.1093/aje/kwad232/53485177/kwad232.pdf; doi:https://doi.org/10.1093/aje/kwad232; html:https://europepmc.org/articles/PMC11074710; pdf:https://europepmc.org/articles/PMC11074710?pdf=render
 33437953,https://doi.org/10.1016/j.eclinm.2020.100658,"Education, biological ageing, all-cause and cause-specific mortality and morbidity: UK biobank cohort study.","Chadeau-Hyam M, Bodinier B, Vermeulen R, Karimi M, Zuber V, Castagné R, Elliott J, Muller D, Petrovic D, Whitaker M, Stringhini S, Tzoulaki I, Kivimäki M, Vineis P, Elliott P, Kelly-Irving M, Delpierre C.",,EClinicalMedicine,2020,2020-11-19,Y,Biomarkers; Prospective Cohort; Uk Biobank; Mendelian Randomisation; Biological Ageing; Social Embedding; Allostatic Load Mortality; Incidentpathologies,,,"<h4>Background</h4>Socioeconomic position as measured by education may be embodied and affect the functioning of key physiological systems. Links between social disadvantage, its biological imprint, and cause-specific mortality and morbidity have not been investigated in large populations, and yet may point towards areas for public health interventions beyond targeting individual behaviours.<h4>Methods</h4>Using data from 366,748 UK Biobank participants with 13 biomarker measurements, we calculated a Biological Health Score (BHS, ranging from 0 to 1) capturing the level of functioning of five physiological systems. Associations between BHS and incidence of cardiovascular disease (CVD) and cancer, and mortality from all, CVD, cancer, and external causes were examined. We explored the role of education in these associations. Mendelian randomisation using genetic evidence was used to triangulate these findings.<h4>Findings</h4>An increase in BHS of 0.1 was associated with all-cause (HR = 1.14 [1.12-1.16] and 1.09 [1.07-1.12] in men and women respectively), cancer (HR = 1.11 [1.09-1.14] and 1.07 [1.04-1.10]) and CVD (HR = 1.25 [1.20-1.31] and 1.21 [1.11-1.31]) mortality, CVD incidence (HR = 1.15 [1.13-1.16] and 1.17 [1.15-1.19]). These associations survived adjustment for education, lifestyle-behaviours, body mass index (BMI), co-morbidities and medical treatments. Mendelian randomisation further supported the link between the BHS and CVD incidence (HR = 1.31 [1.21-1.42]). The BHS contributed to CVD incidence prediction (age-adjusted C-statistic = 0.58), other than through education and health behaviours.<h4>Interpretation</h4>The BHS captures features of the embodiment of education, health behaviours, and more proximal unknown factors which all complementarily contribute to all-cause, cancer and CVD morbidity and premature death.",,pdf:http://www.thelancet.com/article/S2589537020304028/pdf; doi:https://doi.org/10.1016/j.eclinm.2020.100658; html:https://europepmc.org/articles/PMC7788440; pdf:https://europepmc.org/articles/PMC7788440?pdf=render
-38296965,https://doi.org/10.1038/s41467-023-43644-x,"Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial.","RECOVERY Collaborative Group, Horby PW, Peto L, Staplin N, Campbell M, Pessoa-Amorim G, Mafham M, Emberson JR, Stewart R, Prudon B, Uriel A, Green CA, Dhasmana DJ, Malein F, Majumdar J, Collini P, Shurmer J, Yates B, Baillie JK, Buch MH, Day J, Faust SN, Jaki T, Jeffery K, Juszczak E, Knight M, Lim WS, Montgomery A, Mumford A, Rowan K, Thwaites G, Haynes R, Landray MJ.",,Nature communications,2024,2024-01-31,Y,,,,"Dimethyl fumarate (DMF) inhibits inflammasome-mediated inflammation and has been proposed as a treatment for patients hospitalised with COVID-19. This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple treatments in patients hospitalised for COVID-19 (NCT04381936, ISRCTN50189673). In this assessment of DMF performed at 27 UK hospitals, adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. Between 2 March 2021 and 18 November 2021, 713 patients were enroled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients received corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.86-1.47; p = 0.40). There was no significant effect of DMF on any secondary outcome.",,pdf:https://www.nature.com/articles/s41467-023-43644-x.pdf; doi:https://doi.org/10.1038/s41467-023-43644-x; html:https://europepmc.org/articles/PMC10831058; pdf:https://europepmc.org/articles/PMC10831058?pdf=render
 33185016,https://doi.org/10.1002/art.41593,Nonsteroidal Antiinflammatory Drugs and Susceptibility to COVID-19.,"Chandan JS, Zemedikun DT, Thayakaran R, Byne N, Dhalla S, Acosta-Mena D, Gokhale KM, Thomas T, Sainsbury C, Subramanian A, Cooper J, Anand A, Okoth KO, Wang J, Adderley NJ, Taverner T, Denniston AK, Lord J, Thomas GN, Buckley CD, Raza K, Bhala N, Nirantharakumar K, Haroon S.",,"Arthritis & rheumatology (Hoboken, N.J.)",2021,2021-05-01,Y,,,,"<h4>Objective</h4>To identify whether active use of nonsteroidal antiinflammatory drugs (NSAIDs) increases susceptibility to developing suspected or confirmed coronavirus disease 2019 (COVID-19) compared to the use of other common analgesics.<h4>Methods</h4>We performed a propensity score-matched cohort study with active comparators, using a large UK primary care data set. The cohort consisted of adult patients age ≥18 years with osteoarthritis (OA) who were followed up from January 30 to July 31, 2020. Patients prescribed an NSAID (excluding topical preparations) were compared to those prescribed either co-codamol (paracetamol and codeine) or co-dydramol (paracetamol and dihydrocodeine). A total of 13,202 patients prescribed NSAIDs were identified, compared to 12,457 patients prescribed the comparator drugs. The primary outcome measure was the documentation of suspected or confirmed COVID-19, and the secondary outcome measure was all-cause mortality.<h4>Results</h4>During follow-up, the incidence rates of suspected/confirmed COVID-19 were 15.4 and 19.9 per 1,000 person-years in the NSAID-exposed group and comparator group, respectively. Adjusted hazard ratios for suspected or confirmed COVID-19 among the unmatched and propensity score-matched OA cohorts, using data from clinical consultations in primary care settings, were 0.82 (95% confidence interval [95% CI] 0.62-1.10) and 0.79 (95% CI 0.57-1.11), respectively, and adjusted hazard ratios for the risk of all-cause mortality were 0.97 (95% CI 0.75-1.27) and 0.85 (95% CI 0.61-1.20), respectively. There was no effect modification by age or sex.<h4>Conclusion</h4>No increase in the risk of suspected or confirmed COVID-19 or mortality was observed among patients with OA in a primary care setting who were prescribed NSAIDs as compared to those who received comparator drugs. These results are reassuring and suggest that in the absence of acute illness, NSAIDs can be safely prescribed during the ongoing pandemic.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/art.41593; doi:https://doi.org/10.1002/art.41593; html:https://europepmc.org/articles/PMC8252419; pdf:https://europepmc.org/articles/PMC8252419?pdf=render
+38296965,https://doi.org/10.1038/s41467-023-43644-x,"Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial.","RECOVERY Collaborative Group, Horby PW, Peto L, Staplin N, Campbell M, Pessoa-Amorim G, Mafham M, Emberson JR, Stewart R, Prudon B, Uriel A, Green CA, Dhasmana DJ, Malein F, Majumdar J, Collini P, Shurmer J, Yates B, Baillie JK, Buch MH, Day J, Faust SN, Jaki T, Jeffery K, Juszczak E, Knight M, Lim WS, Montgomery A, Mumford A, Rowan K, Thwaites G, Haynes R, Landray MJ.",,Nature communications,2024,2024-01-31,Y,,,,"Dimethyl fumarate (DMF) inhibits inflammasome-mediated inflammation and has been proposed as a treatment for patients hospitalised with COVID-19. This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple treatments in patients hospitalised for COVID-19 (NCT04381936, ISRCTN50189673). In this assessment of DMF performed at 27 UK hospitals, adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. Between 2 March 2021 and 18 November 2021, 713 patients were enroled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients received corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.86-1.47; p = 0.40). There was no significant effect of DMF on any secondary outcome.",,pdf:https://www.nature.com/articles/s41467-023-43644-x.pdf; doi:https://doi.org/10.1038/s41467-023-43644-x; html:https://europepmc.org/articles/PMC10831058; pdf:https://europepmc.org/articles/PMC10831058?pdf=render
 35354069,https://doi.org/10.1016/j.cmet.2022.03.002,Early prediction of incident liver disease using conventional risk factors and gut-microbiome-augmented gradient boosting.,"Liu Y, Méric G, Havulinna AS, Teo SM, Åberg F, Ruuskanen M, Sanders J, Zhu Q, Tripathi A, Verspoor K, Cheng S, Jain M, Jousilahti P, Vázquez-Baeza Y, Loomba R, Lahti L, Niiranen T, Salomaa V, Knight R, Inouye M.",,Cell metabolism,2022,2022-03-29,Y,Prediction; Gut; Disease; Microbiota; liver disease; Metagenomics; Microbiome,,,"The gut microbiome has shown promise as a predictive biomarker for various diseases. However, the potential of gut microbiota for prospective risk prediction of liver disease has not been assessed. Here, we utilized shallow shotgun metagenomic sequencing of a large population-based cohort (N > 7,000) with ∼15 years of follow-up in combination with machine learning to investigate the predictive capacity of gut microbial predictors individually and in conjunction with conventional risk factors for incident liver disease. Separately, conventional and microbial factors showed comparable predictive capacity. However, microbiome augmentation of conventional risk factors using machine learning significantly improved the performance. Similarly, disease-free survival analysis showed significantly improved stratification using microbiome-augmented models. Investigation of predictive microbial signatures revealed previously unknown taxa for liver disease, as well as those previously associated with hepatic function and disease. This study supports the potential clinical validity of gut metagenomic sequencing to complement conventional risk factors for prediction of liver diseases.",,pdf:http://www.cell.com/article/S1550413122000900/pdf; doi:https://doi.org/10.1016/j.cmet.2022.03.002; html:https://europepmc.org/articles/PMC9097589
 31233103,https://doi.org/10.1093/bioinformatics/btz469,PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations.,"Kamat MA, Blackshaw JA, Young R, Surendran P, Burgess S, Danesh J, Butterworth AS, Staley JR.",,"Bioinformatics (Oxford, England)",2019,2019-11-01,Y,,Applied Analytics,,"<h4>Summary</h4>PhenoScanner is a curated database of publicly available results from large-scale genetic association studies in humans. This online tool facilitates 'phenome scans', where genetic variants are cross-referenced for association with many phenotypes of different types. Here we present a major update of PhenoScanner ('PhenoScanner V2'), including over 150 million genetic variants and more than 65 billion associations (compared to 350 million associations in PhenoScanner V1) with diseases and traits, gene expression, metabolite and protein levels, and epigenetic markers. The query options have been extended to include searches by genes, genomic regions and phenotypes, as well as for genetic variants. All variants are positionally annotated using the Variant Effect Predictor and the phenotypes are mapped to Experimental Factor Ontology terms. Linkage disequilibrium statistics from the 1000 Genomes project can be used to search for phenotype associations with proxy variants.<h4>Availability and implementation</h4>PhenoScanner V2 is available at www.phenoscanner.medschl.cam.ac.uk.",Kamat et al. developed an improved version of phenoscanner which is a publicly available large-scale genetic dataset for evaluation of genetic associations.,pdf:https://academic.oup.com/bioinformatics/article-pdf/35/22/4851/30706861/btz469.pdf; doi:https://doi.org/10.1093/bioinformatics/btz469; html:https://europepmc.org/articles/PMC6853652; pdf:https://europepmc.org/articles/PMC6853652?pdf=render
 35103484,https://doi.org/10.1161/circgen.121.003553,Genetically Predicted Neutrophil-to-Lymphocyte Ratio and Coronary Artery Disease: Evidence From Mendelian Randomization.,"Cupido AJ, Kraaijenhof JM, Burgess S, Asselbergs FW, Hovingh GK, Gill D.",,Circulation. Genomic and precision medicine,2022,2022-02-01,Y,Neutrophils; Cardiovascular diseases; Inflammation; Causality; Linear Models,,,,,pdf:https://discovery.ucl.ac.uk/10145750/1/CIRCGEN.121.003553.pdf; doi:https://doi.org/10.1161/CIRCGEN.121.003553; html:https://europepmc.org/articles/PMC7612391; pdf:https://europepmc.org/articles/PMC7612391?pdf=render
 33678251,https://doi.org/10.1016/j.jaci.2020.08.026,"The intersect of genetics, environment, and microbiota in asthma-perspectives and challenges.","Tang HHF, Teo SM, Sly PD, Holt PG, Inouye M.",,The Journal of allergy and clinical immunology,2021,2021-03-01,N,Environment; Genomics; Asthma; Microbiota; systems biology; Gene-environment Interaction; Allergy And Immunology,,,"In asthma, a significant portion of the interaction between genetics and environment occurs through microbiota. The proposed mechanisms behind this interaction are complex and at times contradictory. This review covers recent developments in our understanding of this interaction: the ""microbial hypothesis"" and the ""farm effect""; the role of endotoxin and genetic variation in pattern recognition systems; the interaction with allergen exposure; the additional involvement of host gut and airway microbiota; the role of viral respiratory infections in interaction with the 17q21 and CDHR3 genetic loci; and the importance of in utero and early-life timing of exposures. We propose a unified framework for understanding how all these phenomena interact to drive asthma pathogenesis. Finally, we point out some future challenges for continued research in this field, in particular the need for multiomic integration, as well as the potential utility of asthma endotyping.",,doi:https://doi.org/10.1016/j.jaci.2020.08.026
 33692554,https://doi.org/10.1038/s41586-021-03243-6,Improving reporting standards for polygenic scores in risk prediction studies.,"Wand H, Lambert SA, Tamburro C, Iacocca MA, O'Sullivan JW, Sillari C, Kullo IJ, Rowley R, Dron JS, Brockman D, Venner E, McCarthy MI, Antoniou AC, Easton DF, Hegele RA, Khera AV, Chatterjee N, Kooperberg C, Edwards K, Vlessis K, Kinnear K, Danesh JN, Parkinson H, Ramos EM, Roberts MC, Ormond KE, Khoury MJ, Janssens ACJW, Goddard KAB, Kraft P, MacArthur JAL, Inouye M, Wojcik GL.",,Nature,2021,2021-03-10,N,,,,"Polygenic risk scores (PRSs), which often aggregate results from genome-wide association studies, can bridge the gap between initial discovery efforts and clinical applications for the estimation of disease risk using genetics. However, there is notable heterogeneity in the application and reporting of these risk scores, which hinders the translation of PRSs into clinical care. Here, in a collaboration between the Clinical Genome Resource (ClinGen) Complex Disease Working Group and the Polygenic Score (PGS) Catalog, we present the Polygenic Risk Score Reporting Standards (PRS-RS), in which we update the Genetic Risk Prediction Studies (GRIPS) Statement to reflect the present state of the field. Drawing on the input of experts in epidemiology, statistics, disease-specific applications, implementation and policy, this comprehensive reporting framework defines the minimal information that is needed to interpret and evaluate PRSs, especially with respect to downstream clinical applications. Items span detailed descriptions of study populations, statistical methods for the development and validation of PRSs and considerations for the potential limitations of these scores. In addition, we emphasize the need for data availability and transparency, and we encourage researchers to deposit and share PRSs through the PGS Catalog to facilitate reproducibility and comparative benchmarking. By providing these criteria in a structured format that builds on existing standards and ontologies, the use of this framework in publishing PRSs will facilitate translation into clinical care and progress towards defining best practice.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8609771; doi:https://doi.org/10.1038/s41586-021-03243-6; html:https://europepmc.org/articles/PMC8609771; pdf:https://europepmc.org/articles/PMC8609771?pdf=render; doi:https://doi.org/10.1038/s41586-021-03243-6
-38964793,https://doi.org/10.1136/bmjopen-2023-072314,Impact of the first year of COVID-19 vaccination strategy in Brazil: an ecological study.,"Aguilar S, Bastos LSL, Maçaira P, Baião F, Simões P, Cerbino-Neto J, Ranzani O, Hamacher S, Bozza FA.",,BMJ open,2024,2024-07-04,Y,epidemiology; Public Health; Covid-19,,,"<h4>Objectives</h4>No consensus exists about the best COVID-19 vaccination strategy to be adopted by low-income and middle-income countries. Brazil adopted an age-based calendar strategy to reduce mortality and the burden on the healthcare system. This study evaluates the impact of the vaccination campaign in Brazil on the progression of the reported COVID-19 deaths.<h4>Methods</h4>This ecological study analyses the dynamic of vaccination coverage and COVID-19 deaths in hospitalised adults (≥20 years) during the first year of the COVID-19 vaccination roll-out (January to December 2021) using nationwide data (DATASUS). We stratified the adult population into 20-49, 50-59, 60-69 and 70+ years. The dynamic effect of the vaccination campaign on mortality rates was estimated by applying a negative binomial regression. The prevented and possible preventable deaths (observed deaths higher than expected) and potential years of life lost (PYLL) for each age group were obtained in a counterfactual analysis.<h4>Results</h4>During the first year of COVID-19 vaccination, 266 153 517 doses were administered, achieving 91% first-dose coverage. A total of 380 594 deaths were reported, 154 091 (40%) in 70+ years and 136 804 (36%) from 50-59 or 20-49 years. The mortality rates of 70+ decreased by 52% (rate ratio [95% CI]: 0.48 [0.43-0.53]) in 6 months, whereas rates for 20-49 were still increasing due to low coverage (52%). The vaccination roll-out strategy prevented 59 618 deaths, 53 088 (89%) from those aged 70+ years. However, the strategy did not prevent 54 797 deaths, 85% from those under 60 years, being 26 344 (45%) only in 20-49, corresponding to 1 589 271 PYLL, being 1 080 104 PYLL (68%) from those aged 20-49 years.<h4>Conclusion</h4>The adopted aged-based calendar vaccination strategy initially reduced mortality in the oldest but did not prevent the deaths of the youngest as effectively as compared with the older age group. Countries with a high burden, limited vaccine supply and young populations should consider other factors beyond the age to prioritise who should be vaccinated first.",,doi:https://doi.org/10.1136/bmjopen-2023-072314; html:https://europepmc.org/articles/PMC11227766; pdf:https://europepmc.org/articles/PMC11227766?pdf=render
 33769566,https://doi.org/10.1111/bph.15459,Emerging therapies and their delivery for treating age-related macular degeneration.,"Thomas CN, Sim DA, Lee WH, Alfahad N, Dick AD, Denniston AK, Hill LJ.",,British journal of pharmacology,2022,2021-05-12,N,Retina; Complement; Immunotherapy; Age-related macular degeneration; Drug Delivery; Anti-vegf; Ocular Disease,,,"Age-related macular degeneration (AMD) is the most common cause of blindness in the Western world and is characterised in its latter stages by retinal cell death and neovascularisation and earlier stages with the loss of parainflammatory homeostasis. Patients with neovascular AMD (nAMD) are treated with frequent intraocular injections of anti-vascular endothelial growth factor (VEGF) therapies, which are not only unpopular with patients but carry risks of sight-threatening complications. A minority of patients are unresponsive with no alternative treatment available, and some patients who respond initially eventually develop a tolerance to treatment. New therapeutics with improved delivery methods and sustainability of clinical effects are required, in particular for non-neovascular AMD (90% of cases and no current approved treatments). There are age-related and disease-related changes that occur which can affect ocular drug delivery. Here, we review the latest emerging therapies for AMD, their delivery routes and implications for translating to clinical practice. LINKED ARTICLES: This article is part of a themed issue on Inflammation, Repair and Ageing. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v179.9/issuetoc.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/bph.15459; doi:https://doi.org/10.1111/bph.15459
+38964793,https://doi.org/10.1136/bmjopen-2023-072314,Impact of the first year of COVID-19 vaccination strategy in Brazil: an ecological study.,"Aguilar S, Bastos LSL, Maçaira P, Baião F, Simões P, Cerbino-Neto J, Ranzani O, Hamacher S, Bozza FA.",,BMJ open,2024,2024-07-04,Y,epidemiology; Public Health; Covid-19,,,"<h4>Objectives</h4>No consensus exists about the best COVID-19 vaccination strategy to be adopted by low-income and middle-income countries. Brazil adopted an age-based calendar strategy to reduce mortality and the burden on the healthcare system. This study evaluates the impact of the vaccination campaign in Brazil on the progression of the reported COVID-19 deaths.<h4>Methods</h4>This ecological study analyses the dynamic of vaccination coverage and COVID-19 deaths in hospitalised adults (≥20 years) during the first year of the COVID-19 vaccination roll-out (January to December 2021) using nationwide data (DATASUS). We stratified the adult population into 20-49, 50-59, 60-69 and 70+ years. The dynamic effect of the vaccination campaign on mortality rates was estimated by applying a negative binomial regression. The prevented and possible preventable deaths (observed deaths higher than expected) and potential years of life lost (PYLL) for each age group were obtained in a counterfactual analysis.<h4>Results</h4>During the first year of COVID-19 vaccination, 266 153 517 doses were administered, achieving 91% first-dose coverage. A total of 380 594 deaths were reported, 154 091 (40%) in 70+ years and 136 804 (36%) from 50-59 or 20-49 years. The mortality rates of 70+ decreased by 52% (rate ratio [95% CI]: 0.48 [0.43-0.53]) in 6 months, whereas rates for 20-49 were still increasing due to low coverage (52%). The vaccination roll-out strategy prevented 59 618 deaths, 53 088 (89%) from those aged 70+ years. However, the strategy did not prevent 54 797 deaths, 85% from those under 60 years, being 26 344 (45%) only in 20-49, corresponding to 1 589 271 PYLL, being 1 080 104 PYLL (68%) from those aged 20-49 years.<h4>Conclusion</h4>The adopted aged-based calendar vaccination strategy initially reduced mortality in the oldest but did not prevent the deaths of the youngest as effectively as compared with the older age group. Countries with a high burden, limited vaccine supply and young populations should consider other factors beyond the age to prioritise who should be vaccinated first.",,doi:https://doi.org/10.1136/bmjopen-2023-072314; html:https://europepmc.org/articles/PMC11227766; pdf:https://europepmc.org/articles/PMC11227766?pdf=render
 35068290,https://doi.org/10.1080/09537104.2021.2003317,Higher body mass index raises immature platelet count: potential contribution to obesity-related thrombosis.,"Goudswaard LJ, Corbin LJ, Burley KL, Mumford A, Akbari P, Soranzo N, Butterworth AS, Watkins NA, Pournaras DJ, Harris J, Timpson NJ, Hers I.",,Platelets,2022,2022-01-24,N,Obesity; Aggregation; epidemiology; Mendelian Randomization; Immature Platelets,,,"Higher body mass index (BMI) is a risk factor for thrombosis. Platelets are essential for hemostasis but contribute to thrombosis when activated pathologically. We hypothesized that higher BMI leads to changes in platelet characteristics, thereby increasing thrombotic risk. The effect of BMI on platelet traits (measured by Sysmex) was explored in 33 388 UK blood donors (INTERVAL study). Linear regression showed that higher BMI was positively associated with greater plateletcrit (PCT), platelet count (PLT), immature platelet count (IPC), and side fluorescence (SFL, a measure of mRNA content used to derive IPC). Mendelian randomization (MR), applied to estimate a causal effect with BMI proxied by a genetic risk score, provided causal estimates for a positive effect of BMI on both SFL and IPC, but there was little evidence for a causal effect of BMI on PCT or PLT. Follow-up analyses explored the functional relevance of platelet characteristics in a pre-operative cardiac cohort (COPTIC). Linear regression provided observational evidence for a positive association between IPC and agonist-induced whole blood platelet aggregation. Results indicate that higher BMI raises the number of immature platelets, which is associated with greater whole blood platelet aggregation in a cardiac cohort. Higher IPC could therefore contribute to obesity-related thrombosis.",,doi:https://doi.org/10.1080/09537104.2021.2003317; doi:https://doi.org/10.1080/09537104.2021.2003317
 38040695,https://doi.org/10.1038/s41467-023-43522-6,Haplotype-based inference of recent effective population size in modern and ancient DNA samples.,"Fournier R, Tsangalidou Z, Reich D, Palamara PF.",,Nature communications,2023,2023-12-01,Y,,,,"Individuals sharing recent ancestors are likely to co-inherit large identical-by-descent (IBD) genomic regions. The distribution of these IBD segments in a population may be used to reconstruct past demographic events such as effective population size variation, but accurate IBD detection is difficult in ancient DNA data and in underrepresented populations with limited reference data. In this work, we introduce an accurate method for inferring effective population size variation during the past ~2000 years in both modern and ancient DNA data, called HapNe. HapNe infers recent population size fluctuations using either IBD sharing (HapNe-IBD) or linkage disequilibrium (HapNe-LD), which does not require phasing and can be computed in low coverage data, including data sets with heterogeneous sampling times. HapNe shows improved accuracy in a range of simulated demographic scenarios compared to currently available methods for IBD-based and LD-based inference of recent effective population size, while requiring fewer computational resources. We apply HapNe to several modern populations from the 1,000 Genomes Project, the UK Biobank, the Allen Ancient DNA Resource, and recently published samples from Iron Age Britain, detecting multiple instances of recent effective population size variation across these groups.",,pdf:https://www.nature.com/articles/s41467-023-43522-6.pdf; doi:https://doi.org/10.1038/s41467-023-43522-6; html:https://europepmc.org/articles/PMC10692198; pdf:https://europepmc.org/articles/PMC10692198?pdf=render
-35751107,https://doi.org/10.1186/s13059-022-02702-1,Epigenomic analysis reveals a dynamic and context-specific macrophage enhancer landscape associated with innate immune activation and tolerance.,"Zhang P, Amarasinghe HE, Whalley JP, Tay C, Fang H, Migliorini G, Brown AC, Allcock A, Scozzafava G, Rath P, Davies B, Knight JC.",,Genome biology,2022,2022-06-24,Y,,,,"<h4>Background</h4>Chromatin states and enhancers associate gene expression, cell identity and disease. Here, we systematically delineate the acute innate immune response to endotoxin in terms of human macrophage enhancer activity and contrast with endotoxin tolerance, profiling the coding and non-coding transcriptome, chromatin accessibility and epigenetic modifications.<h4>Results</h4>We describe the spectrum of enhancers under acute and tolerance conditions and the regulatory networks between these enhancers and biological processes including gene expression, splicing regulation, transcription factor binding and enhancer RNA signatures. We demonstrate that the vast majority of differentially regulated enhancers on acute stimulation are subject to tolerance and that expression quantitative trait loci, disease-risk variants and eRNAs are enriched in these regulatory regions and related to context-specific gene expression. We find enrichment for context-specific eQTL involving endotoxin response and specific infections and delineate specific differential regions informative for GWAS variants in inflammatory bowel disease and multiple sclerosis, together with a context-specific enhancer involving a bacterial infection eQTL for KLF4. We show enrichment in differential enhancers for tolerance involving transcription factors NFκB-p65, STATs and IRFs and prioritize putative causal genes directly linking genetic variants and disease risk enhancers. We further delineate similarities and differences in epigenetic landscape between stem cell-derived macrophages and primary cells and characterize the context-specific enhancer activities for key innate immune response genes KLF4, SLAMF1 and IL2RA.<h4>Conclusions</h4>Our study demonstrates the importance of context-specific macrophage enhancers in gene regulation and utility for interpreting disease associations, providing a roadmap to link genetic variants with molecular and cellular functions.",,pdf:https://genomebiology.biomedcentral.com/counter/pdf/10.1186/s13059-022-02702-1; doi:https://doi.org/10.1186/s13059-022-02702-1; html:https://europepmc.org/articles/PMC9229144; pdf:https://europepmc.org/articles/PMC9229144?pdf=render
-35520099,https://doi.org/10.23889/ijpds.v6i1.1718,"What makes administrative data ""research-ready""? A systematic review and thematic analysis of published literature.","Grath-Lone LM, Jay MA, Blackburn R, Gordon E, Zylbersztejn A, Wiljaars L, Gilbert R.",,International journal of population data science,2022,2022-04-27,Y,Systematic review; Administrative Data; Thematic Analysis; Research-ready,,,"<h4>Introduction</h4>Administrative data are a valuable research resource, but are under-utilised in the UK due to governance, technical and other barriers (e.g., the time and effort taken to gain secure data access). In recent years, there has been considerable government investment in making administrative data ""research-ready"", but there is no definition of what this term means. A common understanding of what constitutes research-ready administrative data is needed to establish clear principles and frameworks for their development and the realisation of their full research potential.<h4>Objective</h4>To define the characteristics of research-ready administrative data based on a systematic review and synthesis of existing literature.<h4>Methods</h4>On 29<sup>th</sup> June 2021, we systematically searched seven electronic databases for (1) peer-reviewed literature (2) related to research-ready administrative data (3) written in the English language. Following supplementary searches and snowball screening, we conducted a thematic analysis of the identified relevant literature.<h4>Results</h4>Overall, we screened 2,375 records and identified 38 relevant studies published between 2012 and 2021. Most related to administrative data from the UK and US and particularly to health data. The term research-ready was used inconsistently in the literature and there was some conflation with the concept of data being ready for statistical analysis. From the thematic analysis, we identified five defining characteristics of research-ready administrative data: (a) accessible, (b) broad, (c) curated, (d) documented and (e) enhanced for research purposes.<h4>Conclusions</h4>Our proposed characteristics of research-ready administrative data could act as a starting point to help data owners and researchers develop common principles and standards. In the more immediate term, the proposed characteristics are a useful framework for cataloguing existing research-ready administrative databases and relevant resources that can support their development.",,doi:https://doi.org/10.23889/ijpds.v6i1.1718; html:https://europepmc.org/articles/PMC9052961; pdf:https://europepmc.org/articles/PMC9052961?pdf=render
 34593247,https://doi.org/10.1016/j.injury.2021.09.027,An evaluation of the association between fault attribution and healthcare costs and trajectories in the first three years after transport injury.,"Melita J G, Joanna F D, Alex C, Jennie P, Shanthi A, Belinda J G.",,Injury,2021,2021-09-20,N,Trauma; Compensation; Insurance; Biopsychosocial; Health Service Use,,,"<h4>Background</h4>People with complex medical and psychosocial issues have high healthcare needs. This registry-based cohort study sought to quantify the association between external fault attribution, recorded during compensation claim lodgement, and the cost and patterns of healthcare utilisation.<h4>Methods</h4>6,144 survivors of transport-related major trauma between 1 July 2010 and 30 June 2016 were extracted from the Victorian State Trauma Registry (VSTR) and linked to treatment payments from the Transport Accident Commission (TAC). Associations between fault and healthcare costs were examined with Generalised Linear Regression. Healthcare trajectories were identified using Group-Based Multi-Trajectory Modelling and included medical treatments from a physician, or pain, mental health and physical therapy treatments for the first three years post-injury. Trajectories were validated against the EQ-5D-3L health status summary score using mixed linear regression.<h4>Results</h4>While injury severity had the strongest association with healthcare use, people who attributed fault to another had 9% higher healthcare costs. Six multi-trajectory groups were identified: 36% had low treatments over time; 25% had a rapid decline from high medical and physical therapy by 12-months; 12% had moderate to high medical and physical therapy that declined by 2-3 years; 11% had a gradual decline in medical treatment, an early increase in physical therapy but low pain and mental health treatment; 8% had high or increasing medical and physical therapy, moderate mental health therapy and low pain treatment; and 7% had moderate-high treatment across all domains. All groups had poorer health status compared with the group with low treatment levels, and people who attributed fault to another had higher risk of following trajectories with higher levels of treatment versus the low treatment group (beta=0.34, SE=0.12, p=0.01).<h4>Conclusion</h4>These findings highlight the need to provide pro-active multidisciplinary care coordination for people with complex needs after injury to better optimise recovery.",,doi:https://doi.org/10.1016/j.injury.2021.09.027
-31588514,https://doi.org/10.1093/ptj/pzz151,Physical Activity and Sedentary Behavior 6 Months After Musculoskeletal Trauma: What Factors Predict Recovery?,"Ekegren CL, Climie RE, Simpson PM, Owen N, Dunstan DW, Veitch W, Gabbe BJ.",,Physical therapy,2020,2020-02-01,N,,,,"<h4>Background</h4>Physical activity is increasingly recognized as an important marker of functional recovery following fracture.<h4>Objective</h4>The objectives of this study were to measure sedentary behavior and physical activity 2 weeks and 6 months following fracture and to determine associated demographic and injury factors.<h4>Design</h4>This was an observational study.<h4>Methods</h4>Two weeks and 6 months following fracture, 83 adults who were 18 to 69 years old and had upper limb (UL) or lower limb (LL) fractures wore an accelerometer and an inclinometer for 10 days. We calculated sitting time, steps, moderate-intensity physical activity (MPA), and vigorous-intensity physical activity and conducted linear mixed-effects multivariable regression analyses to determine factors associated with temporal changes in activity.<h4>Results</h4>At 6 months versus 2 weeks after fracture, participants sat less, took more steps, and engaged in more MPA. Participants with LL fractures sat 2 hours more, took 66% fewer steps, and engaged in 77% less MPA than participants with UL fractures. Greater reductions in sitting time were observed for participants in the youngest age group and with LL fractures, participants with high preinjury activity, and participants who were overweight or obese. For steps, greater improvement was observed for participants in the youngest and middle-aged groups and those with LL fractures. For MPA, greater improvement was observed for middle-aged participants and those with LL fractures.<h4>Limitations</h4>Although this study was sufficiently powered for the analysis of major categories, a convenience sample that may not be representative of all people with musculoskeletal trauma was used.<h4>Conclusions</h4>Working-age adults with LL fractures had lower levels of physical activity 6 months after fracture than those with UL fractures. Older adults showed less improvement over time, suggesting that they are an important target group for interventions aimed at regaining preinjury activity levels.",,pdf:https://academic.oup.com/ptj/article-pdf/100/2/332/32901113/pzz151.pdf; doi:https://doi.org/10.1093/ptj/pzz151
+35520099,https://doi.org/10.23889/ijpds.v6i1.1718,"What makes administrative data ""research-ready""? A systematic review and thematic analysis of published literature.","Grath-Lone LM, Jay MA, Blackburn R, Gordon E, Zylbersztejn A, Wiljaars L, Gilbert R.",,International journal of population data science,2022,2022-04-27,Y,Systematic review; Administrative Data; Thematic Analysis; Research-ready,,,"<h4>Introduction</h4>Administrative data are a valuable research resource, but are under-utilised in the UK due to governance, technical and other barriers (e.g., the time and effort taken to gain secure data access). In recent years, there has been considerable government investment in making administrative data ""research-ready"", but there is no definition of what this term means. A common understanding of what constitutes research-ready administrative data is needed to establish clear principles and frameworks for their development and the realisation of their full research potential.<h4>Objective</h4>To define the characteristics of research-ready administrative data based on a systematic review and synthesis of existing literature.<h4>Methods</h4>On 29<sup>th</sup> June 2021, we systematically searched seven electronic databases for (1) peer-reviewed literature (2) related to research-ready administrative data (3) written in the English language. Following supplementary searches and snowball screening, we conducted a thematic analysis of the identified relevant literature.<h4>Results</h4>Overall, we screened 2,375 records and identified 38 relevant studies published between 2012 and 2021. Most related to administrative data from the UK and US and particularly to health data. The term research-ready was used inconsistently in the literature and there was some conflation with the concept of data being ready for statistical analysis. From the thematic analysis, we identified five defining characteristics of research-ready administrative data: (a) accessible, (b) broad, (c) curated, (d) documented and (e) enhanced for research purposes.<h4>Conclusions</h4>Our proposed characteristics of research-ready administrative data could act as a starting point to help data owners and researchers develop common principles and standards. In the more immediate term, the proposed characteristics are a useful framework for cataloguing existing research-ready administrative databases and relevant resources that can support their development.",,doi:https://doi.org/10.23889/ijpds.v6i1.1718; html:https://europepmc.org/articles/PMC9052961; pdf:https://europepmc.org/articles/PMC9052961?pdf=render
+35751107,https://doi.org/10.1186/s13059-022-02702-1,Epigenomic analysis reveals a dynamic and context-specific macrophage enhancer landscape associated with innate immune activation and tolerance.,"Zhang P, Amarasinghe HE, Whalley JP, Tay C, Fang H, Migliorini G, Brown AC, Allcock A, Scozzafava G, Rath P, Davies B, Knight JC.",,Genome biology,2022,2022-06-24,Y,,,,"<h4>Background</h4>Chromatin states and enhancers associate gene expression, cell identity and disease. Here, we systematically delineate the acute innate immune response to endotoxin in terms of human macrophage enhancer activity and contrast with endotoxin tolerance, profiling the coding and non-coding transcriptome, chromatin accessibility and epigenetic modifications.<h4>Results</h4>We describe the spectrum of enhancers under acute and tolerance conditions and the regulatory networks between these enhancers and biological processes including gene expression, splicing regulation, transcription factor binding and enhancer RNA signatures. We demonstrate that the vast majority of differentially regulated enhancers on acute stimulation are subject to tolerance and that expression quantitative trait loci, disease-risk variants and eRNAs are enriched in these regulatory regions and related to context-specific gene expression. We find enrichment for context-specific eQTL involving endotoxin response and specific infections and delineate specific differential regions informative for GWAS variants in inflammatory bowel disease and multiple sclerosis, together with a context-specific enhancer involving a bacterial infection eQTL for KLF4. We show enrichment in differential enhancers for tolerance involving transcription factors NFκB-p65, STATs and IRFs and prioritize putative causal genes directly linking genetic variants and disease risk enhancers. We further delineate similarities and differences in epigenetic landscape between stem cell-derived macrophages and primary cells and characterize the context-specific enhancer activities for key innate immune response genes KLF4, SLAMF1 and IL2RA.<h4>Conclusions</h4>Our study demonstrates the importance of context-specific macrophage enhancers in gene regulation and utility for interpreting disease associations, providing a roadmap to link genetic variants with molecular and cellular functions.",,pdf:https://genomebiology.biomedcentral.com/counter/pdf/10.1186/s13059-022-02702-1; doi:https://doi.org/10.1186/s13059-022-02702-1; html:https://europepmc.org/articles/PMC9229144; pdf:https://europepmc.org/articles/PMC9229144?pdf=render
 34432797,https://doi.org/10.1371/journal.pone.0255748,Regional performance variation in external validation of four prediction models for severity of COVID-19 at hospital admission: An observational multi-centre cohort study.,"Wickstrøm KE, Vitelli V, Carr E, Holten AR, Bendayan R, Reiner AH, Bean D, Searle T, Shek A, Kraljevic Z, Teo J, Dobson R, Tonby K, Köhn-Luque A, Amundsen EK.",,PloS one,2021,2021-08-25,Y,,,,"<h4>Background</h4>Prediction models should be externally validated to assess their performance before implementation. Several prediction models for coronavirus disease-19 (COVID-19) have been published. This observational cohort study aimed to validate published models of severity for hospitalized patients with COVID-19 using clinical and laboratory predictors.<h4>Methods</h4>Prediction models fitting relevant inclusion criteria were chosen for validation. The outcome was either mortality or a composite outcome of mortality and ICU admission (severe disease). 1295 patients admitted with symptoms of COVID-19 at Kings Cross Hospital (KCH) in London, United Kingdom, and 307 patients at Oslo University Hospital (OUH) in Oslo, Norway were included. The performance of the models was assessed in terms of discrimination and calibration.<h4>Results</h4>We identified two models for prediction of mortality (referred to as Xie and Zhang1) and two models for prediction of severe disease (Allenbach and Zhang2). The performance of the models was variable. For prediction of mortality Xie had good discrimination at OUH with an area under the receiver-operating characteristic (AUROC) 0.87 [95% confidence interval (CI) 0.79-0.95] and acceptable discrimination at KCH, AUROC 0.79 [0.76-0.82]. In prediction of severe disease, Allenbach had acceptable discrimination (OUH AUROC 0.81 [0.74-0.88] and KCH AUROC 0.72 [0.68-0.75]). The Zhang models had moderate to poor discrimination. Initial calibration was poor for all models but improved with recalibration.<h4>Conclusions</h4>The performance of the four prediction models was variable. The Xie model had the best discrimination for mortality, while the Allenbach model had acceptable results for prediction of severe disease.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0255748&type=printable; doi:https://doi.org/10.1371/journal.pone.0255748; html:https://europepmc.org/articles/PMC8386866; pdf:https://europepmc.org/articles/PMC8386866?pdf=render
+31588514,https://doi.org/10.1093/ptj/pzz151,Physical Activity and Sedentary Behavior 6 Months After Musculoskeletal Trauma: What Factors Predict Recovery?,"Ekegren CL, Climie RE, Simpson PM, Owen N, Dunstan DW, Veitch W, Gabbe BJ.",,Physical therapy,2020,2020-02-01,N,,,,"<h4>Background</h4>Physical activity is increasingly recognized as an important marker of functional recovery following fracture.<h4>Objective</h4>The objectives of this study were to measure sedentary behavior and physical activity 2 weeks and 6 months following fracture and to determine associated demographic and injury factors.<h4>Design</h4>This was an observational study.<h4>Methods</h4>Two weeks and 6 months following fracture, 83 adults who were 18 to 69 years old and had upper limb (UL) or lower limb (LL) fractures wore an accelerometer and an inclinometer for 10 days. We calculated sitting time, steps, moderate-intensity physical activity (MPA), and vigorous-intensity physical activity and conducted linear mixed-effects multivariable regression analyses to determine factors associated with temporal changes in activity.<h4>Results</h4>At 6 months versus 2 weeks after fracture, participants sat less, took more steps, and engaged in more MPA. Participants with LL fractures sat 2 hours more, took 66% fewer steps, and engaged in 77% less MPA than participants with UL fractures. Greater reductions in sitting time were observed for participants in the youngest age group and with LL fractures, participants with high preinjury activity, and participants who were overweight or obese. For steps, greater improvement was observed for participants in the youngest and middle-aged groups and those with LL fractures. For MPA, greater improvement was observed for middle-aged participants and those with LL fractures.<h4>Limitations</h4>Although this study was sufficiently powered for the analysis of major categories, a convenience sample that may not be representative of all people with musculoskeletal trauma was used.<h4>Conclusions</h4>Working-age adults with LL fractures had lower levels of physical activity 6 months after fracture than those with UL fractures. Older adults showed less improvement over time, suggesting that they are an important target group for interventions aimed at regaining preinjury activity levels.",,pdf:https://academic.oup.com/ptj/article-pdf/100/2/332/32901113/pzz151.pdf; doi:https://doi.org/10.1093/ptj/pzz151
 37075078,https://doi.org/10.1371/journal.pmed.1004223,The association between antihypertensive treatment and serious adverse events by age and frailty: A cohort study.,"Sheppard JP, Koshiaris C, Stevens R, Lay-Flurrie S, Banerjee A, Bellows BK, Clegg A, Hobbs FDR, Payne RA, Swain S, Usher-Smith JA, McManus RJ.",,PLoS medicine,2023,2023-04-19,Y,,,,"<h4>Background</h4>Antihypertensives are effective at reducing the risk of cardiovascular disease, but limited data exist quantifying their association with serious adverse events, particularly in older people with frailty. This study aimed to examine this association using nationally representative electronic health record data.<h4>Methods and findings</h4>This was a retrospective cohort study utilising linked data from 1,256 general practices across England held within the Clinical Practice Research Datalink between 1998 and 2018. Included patients were aged 40+ years, with a systolic blood pressure reading between 130 and 179 mm Hg, and not previously prescribed antihypertensive treatment. The main exposure was defined as a first prescription of antihypertensive treatment. The primary outcome was hospitalisation or death within 10 years from falls. Secondary outcomes were hypotension, syncope, fractures, acute kidney injury, electrolyte abnormalities, and primary care attendance with gout. The association between treatment and these serious adverse events was examined by Cox regression adjusted for propensity score. This propensity score was generated from a multivariable logistic regression model with patient characteristics, medical history and medication prescriptions as covariates, and new antihypertensive treatment as the outcome. Subgroup analyses were undertaken by age and frailty. Of 3,834,056 patients followed for a median of 7.1 years, 484,187 (12.6%) were prescribed new antihypertensive treatment in the 12 months before the index date (baseline). Antihypertensives were associated with an increased risk of hospitalisation or death from falls (adjusted hazard ratio [aHR] 1.23, 95% confidence interval (CI) 1.21 to 1.26), hypotension (aHR 1.32, 95% CI 1.29 to 1.35), syncope (aHR 1.20, 95% CI 1.17 to 1.22), acute kidney injury (aHR 1.44, 95% CI 1.41 to 1.47), electrolyte abnormalities (aHR 1.45, 95% CI 1.43 to 1.48), and primary care attendance with gout (aHR 1.35, 95% CI 1.32 to 1.37). The absolute risk of serious adverse events with treatment was very low, with 6 fall events per 10,000 patients treated per year. In older patients (80 to 89 years) and those with severe frailty, this absolute risk was increased, with 61 and 84 fall events per 10,000 patients treated per year (respectively). Findings were consistent in sensitivity analyses using different approaches to address confounding and taking into account the competing risk of death. A strength of this analysis is that it provides evidence regarding the association between antihypertensive treatment and serious adverse events, in a population of patients more representative than those enrolled in previous randomised controlled trials. Although treatment effect estimates fell within the 95% CIs of those from such trials, these analyses were observational in nature and so bias from unmeasured confounding cannot be ruled out.<h4>Conclusions</h4>Antihypertensive treatment was associated with serious adverse events. Overall, the absolute risk of this harm was low, with the exception of older patients and those with moderate to severe frailty, where the risks were similar to the likelihood of benefit from treatment. In these populations, physicians may want to consider alternative approaches to management of blood pressure and refrain from prescribing new treatment.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004223&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004223; html:https://europepmc.org/articles/PMC10155987; pdf:https://europepmc.org/articles/PMC10155987?pdf=render
 35834561,https://doi.org/10.1371/journal.pmed.1004039,"Associations between moderate alcohol consumption, brain iron, and cognition in UK Biobank participants: Observational and mendelian randomization analyses.","Topiwala A, Wang C, Ebmeier KP, Burgess S, Bell S, Levey DF, Zhou H, McCracken C, Roca-Fernández A, Petersen SE, Raman B, Husain M, Gelernter J, Miller KL, Smith SM, Nichols TE.",,PLoS medicine,2022,2022-07-14,Y,,,,"<h4>Background</h4>Brain iron deposition has been linked to several neurodegenerative conditions and reported in alcohol dependence. Whether iron accumulation occurs in moderate drinkers is unknown. Our objectives were to investigate evidence in support of causal relationships between alcohol consumption and brain iron levels and to examine whether higher brain iron represents a potential pathway to alcohol-related cognitive deficits.<h4>Methods and findings</h4>Observational associations between brain iron markers and alcohol consumption (n = 20,729 UK Biobank participants) were compared with associations with genetically predicted alcohol intake and alcohol use disorder from 2-sample mendelian randomization (MR). Alcohol intake was self-reported via a touchscreen questionnaire at baseline (2006 to 2010). Participants with complete data were included. Multiorgan susceptibility-weighted magnetic resonance imaging (9.60 ± 1.10 years after baseline) was used to ascertain iron content of each brain region (quantitative susceptibility mapping (QSM) and T2*) and liver tissues (T2*), a marker of systemic iron. Main outcomes were susceptibility (χ) and T2*, measures used as indices of iron deposition. Brain regions of interest included putamen, caudate, hippocampi, thalami, and substantia nigra. Potential pathways to alcohol-related iron brain accumulation through elevated systemic iron stores (liver) were explored in causal mediation analysis. Cognition was assessed at the scan and in online follow-up (5.82 ± 0.86 years after baseline). Executive function was assessed with the trail-making test, fluid intelligence with puzzle tasks, and reaction time by a task based on the ""Snap"" card game. Mean age was 54.8 ± 7.4 years and 48.6% were female. Weekly alcohol consumption was 17.7 ± 15.9 units and never drinkers comprised 2.7% of the sample. Alcohol consumption was associated with markers of higher iron (χ) in putamen (β = 0.08 standard deviation (SD) [95% confidence interval (CI) 0.06 to 0.09], p < 0.001), caudate (β = 0.05 [0.04 to 0.07], p < 0.001), and substantia nigra (β = 0.03 [0.02 to 0.05], p < 0.001) and lower iron in the thalami (β = -0.06 [-0.07 to -0.04], p < 0.001). Quintile-based analyses found these associations in those consuming >7 units (56 g) alcohol weekly. MR analyses provided weak evidence these relationships are causal. Genetically predicted alcoholic drinks weekly positively associated with putamen and hippocampus susceptibility; however, these associations did not survive multiple testing corrections. Weak evidence for a causal relationship between genetically predicted alcohol use disorder and higher putamen susceptibility was observed; however, this was not robust to multiple comparisons correction. Genetically predicted alcohol use disorder was associated with serum iron and transferrin saturation. Elevated liver iron was observed at just >11 units (88 g) alcohol weekly c.f. <7 units (56 g). Systemic iron levels partially mediated associations of alcohol intake with brain iron. Markers of higher basal ganglia iron associated with slower executive function, lower fluid intelligence, and slower reaction times. The main limitations of the study include that χ and T2* can reflect changes in myelin as well as iron, alcohol use was self-reported, and MR estimates can be influenced by genetic pleiotropy.<h4>Conclusions</h4>To the best of our knowledge, this study represents the largest investigation of moderate alcohol consumption and iron homeostasis to date. Alcohol consumption above 7 units weekly associated with higher brain iron. Iron accumulation represents a potential mechanism for alcohol-related cognitive decline.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004039&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004039; html:https://europepmc.org/articles/PMC9282660; pdf:https://europepmc.org/articles/PMC9282660?pdf=render
 32542387,https://doi.org/10.1093/jac/dkaa222,Towards personalized guidelines: using machine-learning algorithms to guide antimicrobial selection.,"Moran E, Robinson E, Green C, Keeling M, Collyer B.",,The Journal of antimicrobial chemotherapy,2020,2020-09-01,N,,,,"<h4>Background</h4>Electronic decision support systems could reduce the use of inappropriate or ineffective empirical antibiotics. We assessed the accuracy of an open-source machine-learning algorithm trained in predicting antibiotic resistance for three Gram-negative bacterial species isolated from patients' blood and urine within 48 h of hospital admission.<h4>Methods</h4>This retrospective, observational study used routine clinical information collected between January 2010 and October 2016 in Birmingham, UK. Patients from whose blood or urine cultures Escherichia coli, Klebsiella pneumoniae or Pseudomonas aeruginosa was isolated were identified. Their demographic, microbiology and prescribing data were used to train an open-source machine-learning algorithm-XGBoost-in predicting resistance to co-amoxiclav and piperacillin/tazobactam. Multivariate analysis was performed to identify predictors of resistance and create a point-scoring tool. The performance of both methods was compared with that of the original prescribers.<h4>Results</h4>There were 15 695 admissions. The AUC of the receiver operating characteristic curve for the point-scoring tools ranged from 0.61 to 0.67, and performed no better than medical staff in the selection of appropriate antibiotics. The machine-learning system performed statistically but marginally better (AUC 0.70) and could have reduced the use of unnecessary broad-spectrum antibiotics by as much as 40% among those given co-amoxiclav, piperacillin/tazobactam or carbapenems. A validation study is required.<h4>Conclusions</h4>Machine-learning algorithms have the potential to help clinicians predict antimicrobial resistance in patients found to have a Gram-negative infection of blood or urine. Prospective studies are required to assess performance in an unselected patient cohort, understand the acceptability of such systems to clinicians and patients, and assess the impact on patient outcome.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7443728; doi:https://doi.org/10.1093/jac/dkaa222; html:https://europepmc.org/articles/PMC7443728; pdf:https://europepmc.org/articles/PMC7443728?pdf=render; doi:https://doi.org/10.1093/jac/dkaa222
 35388009,https://doi.org/10.1038/s41467-022-29641-6,Publisher Correction: Elucidating mechanisms of genetic cross-disease associations at the PROCR vascular disease locus.,"Stacey D, Chen L, Stanczyk PJ, Howson JMM, Mason AM, Burgess S, MacDonald S, Langdown J, McKinney H, Downes K, Farahi N, Peters JE, Basu S, Pankow JS, Tang W, Pankratz N, Sabater-Lleal M, de Vries PS, Smith NL, CHARGE Hemostasis Working Group, Gelinas AD, Schneider DJ, Janjic N, Samani NJ, Ye S, Summers C, Chilvers ER, Danesh J, Paul DS.",,Nature communications,2022,2022-04-06,Y,,,,,,pdf:https://www.nature.com/articles/s41467-022-29641-6.pdf; doi:https://doi.org/10.1038/s41467-022-29641-6; html:https://europepmc.org/articles/PMC8986867; pdf:https://europepmc.org/articles/PMC8986867?pdf=render
-34645794,https://doi.org/10.1038/s41467-021-25914-8,A cross-sectional analysis of meteorological factors and SARS-CoV-2 transmission in 409 cities across 26 countries.,"Sera F, Armstrong B, Abbott S, Meakin S, O'Reilly K, von Borries R, Schneider R, Royé D, Hashizume M, Pascal M, Tobias A, Vicedo-Cabrera AM, MCC Collaborative Research Network, CMMID COVID-19 Working Group, Gasparrini A, Lowe R.",,Nature communications,2021,2021-10-13,Y,,,,"There is conflicting evidence on the influence of weather on COVID-19 transmission. Our aim is to estimate weather-dependent signatures in the early phase of the pandemic, while controlling for socio-economic factors and non-pharmaceutical interventions. We identify a modest non-linear association between mean temperature and the effective reproduction number (R<sub>e</sub>) in 409 cities in 26 countries, with a decrease of 0.087 (95% CI: 0.025; 0.148) for a 10 °C increase. Early interventions have a greater effect on R<sub>e</sub> with a decrease of 0.285 (95% CI 0.223; 0.347) for a 5th - 95th percentile increase in the government response index. The variation in the effective reproduction number explained by government interventions is 6 times greater than for mean temperature. We find little evidence of meteorological conditions having influenced the early stages of local epidemics and conclude that population behaviour and government interventions are more important drivers of transmission.",,doi:https://doi.org/10.1038/s41467-021-25914-8; doi:https://doi.org/10.1038/s41467-021-25914-8; html:https://europepmc.org/articles/PMC8514574; pdf:https://europepmc.org/articles/PMC8514574?pdf=render
 29780001,https://doi.org/10.1016/s2352-3026(18)30053-x,Automated typing of red blood cell and platelet antigens: a whole-genome sequencing study.,"Lane WJ, Westhoff CM, Gleadall NS, Aguad M, Smeland-Wagman R, Vege S, Simmons DP, Mah HH, Lebo MS, Walter K, Soranzo N, Di Angelantonio E, Danesh J, Roberts DJ, Watkins NA, Ouwehand WH, Butterworth AS, Kaufman RM, Rehm HL, Silberstein LE, Green RC, MedSeq Project.",,The Lancet. Haematology,2018,2018-05-17,N,,The Human Phenome,,"<h4>Background</h4>There are more than 300 known red blood cell (RBC) antigens and 33 platelet antigens that differ between individuals. Sensitisation to antigens is a serious complication that can occur in prenatal medicine and after blood transfusion, particularly for patients who require multiple transfusions. Although pre-transfusion compatibility testing largely relies on serological methods, reagents are not available for many antigens. Methods based on single-nucleotide polymorphism (SNP) arrays have been used, but typing for ABO and Rh-the most important blood groups-cannot be done with SNP typing alone. We aimed to develop a novel method based on whole-genome sequencing to identify RBC and platelet antigens.<h4>Methods</h4>This whole-genome sequencing study is a subanalysis of data from patients in the whole-genome sequencing arm of the MedSeq Project randomised controlled trial (NCT01736566) with no measured patient outcomes. We created a database of molecular changes in RBC and platelet antigens and developed an automated antigen-typing algorithm based on whole-genome sequencing (bloodTyper). This algorithm was iteratively improved to address cis-trans haplotype ambiguities and homologous gene alignments. Whole-genome sequencing data from 110 MedSeq participants (30 × depth) were used to initially validate bloodTyper through comparison with conventional serology and SNP methods for typing of 38 RBC antigens in 12 blood-group systems and 22 human platelet antigens. bloodTyper was further validated with whole-genome sequencing data from 200 INTERVAL trial participants (15 × depth) with serological comparisons.<h4>Findings</h4>We iteratively improved bloodTyper by comparing its typing results with conventional serological and SNP typing in three rounds of testing. The initial whole-genome sequencing typing algorithm was 99·5% concordant across the first 20 MedSeq genomes. Addressing discordances led to development of an improved algorithm that was 99·8% concordant for the remaining 90 MedSeq genomes. Additional modifications led to the final algorithm, which was 99·2% concordant across 200 INTERVAL genomes (or 99·9% after adjustment for the lower depth of coverage).<h4>Interpretation</h4>By enabling more precise antigen-matching of patients with blood donors, antigen typing based on whole-genome sequencing provides a novel approach to improve transfusion outcomes with the potential to transform the practice of transfusion medicine.<h4>Funding</h4>National Human Genome Research Institute, Doris Duke Charitable Foundation, National Health Service Blood and Transplant, National Institute for Health Research, and Wellcome Trust.",,pdf:http://www.thelancet.com/article/S235230261830053X/pdf; doi:https://doi.org/10.1016/S2352-3026(18)30053-X; html:https://europepmc.org/articles/PMC6438177; pdf:https://europepmc.org/articles/PMC6438177?pdf=render; doi:https://doi.org/10.1016/s2352-3026(18)30053-x
-34888366,https://doi.org/10.3389/fcvm.2021.768245,MOCOnet: Robust Motion Correction of Cardiovascular Magnetic Resonance T1 Mapping Using Convolutional Neural Networks.,"Gonzales RA, Zhang Q, Papież BW, Werys K, Lukaschuk E, Popescu IA, Burrage MK, Shanmuganathan M, Ferreira VM, Piechnik SK.",,Frontiers in cardiovascular medicine,2021,2021-11-23,Y,image registration; Cardiovascular Magnetic Resonance; T1 Mapping; Deep Learning; Shmolli,,,"<b>Background:</b> Quantitative cardiovascular magnetic resonance (CMR) T1 mapping has shown promise for advanced tissue characterisation in routine clinical practise. However, T1 mapping is prone to motion artefacts, which affects its robustness and clinical interpretation. Current methods for motion correction on T1 mapping are model-driven with no guarantee on generalisability, limiting its widespread use. In contrast, emerging data-driven deep learning approaches have shown good performance in general image registration tasks. We propose MOCOnet, a convolutional neural network solution, for generalisable motion artefact correction in T1 maps. <b>Methods:</b> The network architecture employs U-Net for producing distance vector fields and utilises warping layers to apply deformation to the feature maps in a coarse-to-fine manner. Using the UK Biobank imaging dataset scanned at 1.5T, MOCOnet was trained on 1,536 mid-ventricular T1 maps (acquired using the ShMOLLI method) with motion artefacts, generated by a customised deformation procedure, and tested on a different set of 200 samples with a diverse range of motion. MOCOnet was compared to a well-validated baseline multi-modal image registration method. Motion reduction was visually assessed by 3 human experts, with motion scores ranging from 0% (strictly no motion) to 100% (very severe motion). <b>Results:</b> MOCOnet achieved fast image registration (<1 second per T1 map) and successfully suppressed a wide range of motion artefacts. MOCOnet significantly reduced motion scores from 37.1±21.5 to 13.3±10.5 (<i>p</i> < 0.001), whereas the baseline method reduced it to 15.8±15.6 (<i>p</i> < 0.001). MOCOnet was significantly better than the baseline method in suppressing motion artefacts and more consistently (<i>p</i> = 0.007). <b>Conclusion:</b> MOCOnet demonstrated significantly better motion correction performance compared to a traditional image registration approach. Salvaging data affected by motion with robustness and in a time-efficient manner may enable better image quality and reliable images for immediate clinical interpretation.",,pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2021.768245/pdf; doi:https://doi.org/10.3389/fcvm.2021.768245; html:https://europepmc.org/articles/PMC8649951; pdf:https://europepmc.org/articles/PMC8649951?pdf=render
+34645794,https://doi.org/10.1038/s41467-021-25914-8,A cross-sectional analysis of meteorological factors and SARS-CoV-2 transmission in 409 cities across 26 countries.,"Sera F, Armstrong B, Abbott S, Meakin S, O'Reilly K, von Borries R, Schneider R, Royé D, Hashizume M, Pascal M, Tobias A, Vicedo-Cabrera AM, MCC Collaborative Research Network, CMMID COVID-19 Working Group, Gasparrini A, Lowe R.",,Nature communications,2021,2021-10-13,Y,,,,"There is conflicting evidence on the influence of weather on COVID-19 transmission. Our aim is to estimate weather-dependent signatures in the early phase of the pandemic, while controlling for socio-economic factors and non-pharmaceutical interventions. We identify a modest non-linear association between mean temperature and the effective reproduction number (R<sub>e</sub>) in 409 cities in 26 countries, with a decrease of 0.087 (95% CI: 0.025; 0.148) for a 10 °C increase. Early interventions have a greater effect on R<sub>e</sub> with a decrease of 0.285 (95% CI 0.223; 0.347) for a 5th - 95th percentile increase in the government response index. The variation in the effective reproduction number explained by government interventions is 6 times greater than for mean temperature. We find little evidence of meteorological conditions having influenced the early stages of local epidemics and conclude that population behaviour and government interventions are more important drivers of transmission.",,doi:https://doi.org/10.1038/s41467-021-25914-8; doi:https://doi.org/10.1038/s41467-021-25914-8; html:https://europepmc.org/articles/PMC8514574; pdf:https://europepmc.org/articles/PMC8514574?pdf=render
 35000827,https://doi.org/10.1016/j.clon.2021.12.017,Can Real-world Data and Rapid Learning Drive Improvements in Lung Cancer Survival? The RAPID-RT Study.,"Price G, Devaney S, French DP, Holley R, Holm S, Kontopantelis E, McWilliam A, Payne K, Proudlove N, Sanders C, Willans R, van Staa T, Hamrang L, Turner B, Parsons S, Faivre-Finn C.",,Clinical oncology (Royal College of Radiologists (Great Britain)),2022,2022-01-06,N,,,,,,pdf:http://www.clinicaloncologyonline.net/article/S0936655521005161/pdf; doi:https://doi.org/10.1016/j.clon.2021.12.017
+34888366,https://doi.org/10.3389/fcvm.2021.768245,MOCOnet: Robust Motion Correction of Cardiovascular Magnetic Resonance T1 Mapping Using Convolutional Neural Networks.,"Gonzales RA, Zhang Q, Papież BW, Werys K, Lukaschuk E, Popescu IA, Burrage MK, Shanmuganathan M, Ferreira VM, Piechnik SK.",,Frontiers in cardiovascular medicine,2021,2021-11-23,Y,image registration; Cardiovascular Magnetic Resonance; T1 Mapping; Deep Learning; Shmolli,,,"<b>Background:</b> Quantitative cardiovascular magnetic resonance (CMR) T1 mapping has shown promise for advanced tissue characterisation in routine clinical practise. However, T1 mapping is prone to motion artefacts, which affects its robustness and clinical interpretation. Current methods for motion correction on T1 mapping are model-driven with no guarantee on generalisability, limiting its widespread use. In contrast, emerging data-driven deep learning approaches have shown good performance in general image registration tasks. We propose MOCOnet, a convolutional neural network solution, for generalisable motion artefact correction in T1 maps. <b>Methods:</b> The network architecture employs U-Net for producing distance vector fields and utilises warping layers to apply deformation to the feature maps in a coarse-to-fine manner. Using the UK Biobank imaging dataset scanned at 1.5T, MOCOnet was trained on 1,536 mid-ventricular T1 maps (acquired using the ShMOLLI method) with motion artefacts, generated by a customised deformation procedure, and tested on a different set of 200 samples with a diverse range of motion. MOCOnet was compared to a well-validated baseline multi-modal image registration method. Motion reduction was visually assessed by 3 human experts, with motion scores ranging from 0% (strictly no motion) to 100% (very severe motion). <b>Results:</b> MOCOnet achieved fast image registration (<1 second per T1 map) and successfully suppressed a wide range of motion artefacts. MOCOnet significantly reduced motion scores from 37.1±21.5 to 13.3±10.5 (<i>p</i> < 0.001), whereas the baseline method reduced it to 15.8±15.6 (<i>p</i> < 0.001). MOCOnet was significantly better than the baseline method in suppressing motion artefacts and more consistently (<i>p</i> = 0.007). <b>Conclusion:</b> MOCOnet demonstrated significantly better motion correction performance compared to a traditional image registration approach. Salvaging data affected by motion with robustness and in a time-efficient manner may enable better image quality and reliable images for immediate clinical interpretation.",,pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2021.768245/pdf; doi:https://doi.org/10.3389/fcvm.2021.768245; html:https://europepmc.org/articles/PMC8649951; pdf:https://europepmc.org/articles/PMC8649951?pdf=render
 33821553,https://doi.org/10.1002/jia2.25697,The impact of disruptions due to COVID-19 on HIV transmission and control among men who have sex with men in China.,"Booton RD, Fu G, MacGregor L, Li J, Ong JJ, Tucker JD, Turner KM, Tang W, Vickerman P, Mitchell KM.",,Journal of the International AIDS Society,2021,2021-04-01,Y,Modelling; Hiv Transmission; Men Who Have Sex With Men; People’s Republic Of China; Key And Vulnerable Populations; Covid-19 Pandemic,,,"<h4>Introduction</h4>The COVID-19 pandemic is impacting HIV care globally, with gaps in HIV treatment expected to increase HIV transmission and HIV-related mortality. We estimated how COVID-19-related disruptions could impact HIV transmission and mortality among men who have sex with men (MSM) in four cities in China, over a one- and five-year time horizon.<h4>Methods</h4>Regional data from China indicated that the number of MSM undergoing facility-based HIV testing reduced by 59% during the COVID-19 pandemic, alongside reductions in ART initiation (34%), numbers of all sexual partners (62%) and consistency of condom use (25%), but initial data indicated no change in viral suppression. A mathematical model of HIV transmission/treatment among MSM was used to estimate the impact of disruptions on HIV infections/HIV-related deaths. Disruption scenarios were assessed for their individual and combined impact over one and five years for 3/4/6-month disruption periods, starting from 1 January 2020.<h4>Results</h4>Our model predicted new HIV infections and HIV-related deaths would be increased most by disruptions to viral suppression, with 25% reductions (25% virally suppressed MSM stop taking ART) for a three-month period increasing HIV infections by 5% to 14% over one year and deaths by 7% to 12%. Observed reductions in condom use increased HIV infections by 5% to 14% but had minimal impact (<1%) on deaths. Smaller impacts on infections and deaths (<3%) were seen for disruptions to facility HIV testing and ART initiation, but reduced partner numbers resulted in 11% to 23% fewer infections and 0.4% to 1.0% fewer deaths. Longer disruption periods (4/6 months) amplified the impact of disruption scenarios. When realistic disruptions were modelled simultaneously, an overall decrease in new HIV infections occurred over one year (3% to 17%), but not for five years (1% increase to 4% decrease), whereas deaths mostly increased over one year (1% to 2%) and five years (1.2 increase to 0.3 decrease).<h4>Conclusions</h4>The overall impact of COVID-19 on new HIV infections and HIV-related deaths is dependent on the nature, scale and length of the various disruptions. Resources should be directed to ensuring levels of viral suppression and condom use are maintained to mitigate any adverse effects of COVID-19-related disruption on HIV transmission and control among MSM in China.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jia2.25697; doi:https://doi.org/10.1002/jia2.25697; html:https://europepmc.org/articles/PMC8022092; pdf:https://europepmc.org/articles/PMC8022092?pdf=render
 30649175,https://doi.org/10.1001/jamacardio.2018.4537,Cardiovascular Risk Factors Associated With Venous Thromboembolism.,"Gregson J, Kaptoge S, Bolton T, Pennells L, Willeit P, Burgess S, Bell S, Sweeting M, Rimm EB, Kabrhel C, Zöller B, Assmann G, Gudnason V, Folsom AR, Arndt V, Fletcher A, Norman PE, Nordestgaard BG, Kitamura A, Mahmoodi BK, Whincup PH, Knuiman M, Salomaa V, Meisinger C, Koenig W, Kavousi M, Völzke H, Cooper JA, Ninomiya T, Casiglia E, Rodriguez B, Ben-Shlomo Y, Després JP, Simons L, Barrett-Connor E, Björkelund C, Notdurfter M, Kromhout D, Price J, Sutherland SE, Sundström J, Kauhanen J, Gallacher J, Beulens JWJ, Dankner R, Cooper C, Giampaoli S, Deen JF, Gómez de la Cámara A, Kuller LH, Rosengren A, Svensson PJ, Nagel D, Crespo CJ, Brenner H, Albertorio-Diaz JR, Atkins R, Brunner EJ, Shipley M, Njølstad I, Lawlor DA, van der Schouw YT, Selmer RM, Trevisan M, Verschuren WMM, Greenland P, Wassertheil-Smoller S, Lowe GDO, Wood AM, Butterworth AS, Thompson SG, Danesh J, Di Angelantonio E, Meade T, Emerging Risk Factors Collaboration.",,JAMA cardiology,2019,2019-02-01,Y,,Understanding the Causes of Disease,,"<h4>Importance</h4>It is uncertain to what extent established cardiovascular risk factors are associated with venous thromboembolism (VTE).<h4>Objective</h4>To estimate the associations of major cardiovascular risk factors with VTE, ie, deep vein thrombosis and pulmonary embolism.<h4>Design, setting, and participants</h4>This study included individual participant data mostly from essentially population-based cohort studies from the Emerging Risk Factors Collaboration (ERFC; 731 728 participants; 75 cohorts; years of baseline surveys, February 1960 to June 2008; latest date of follow-up, December 2015) and the UK Biobank (421 537 participants; years of baseline surveys, March 2006 to September 2010; latest date of follow-up, February 2016). Participants without cardiovascular disease at baseline were included. Data were analyzed from June 2017 to September 2018.<h4>Exposures</h4>A panel of several established cardiovascular risk factors.<h4>Main outcomes and measures</h4>Hazard ratios (HRs) per 1-SD higher usual risk factor levels (or presence/absence). Incident fatal outcomes in ERFC (VTE, 1041; coronary heart disease [CHD], 25 131) and incident fatal/nonfatal outcomes in UK Biobank (VTE, 2321; CHD, 3385). Hazard ratios were adjusted for age, sex, smoking status, diabetes, and body mass index (BMI).<h4>Results</h4>Of the 731 728 participants from the ERFC, 403 396 (55.1%) were female, and the mean (SD) age at the time of the survey was 51.9 (9.0) years; of the 421 537 participants from the UK Biobank, 233 699 (55.4%) were female, and the mean (SD) age at the time of the survey was 56.4 (8.1) years. Risk factors for VTE included older age (ERFC: HR per decade, 2.67; 95% CI, 2.45-2.91; UK Biobank: HR, 1.81; 95% CI, 1.71-1.92), current smoking (ERFC: HR, 1.38; 95% CI, 1.20-1.58; UK Biobank: HR, 1.23; 95% CI, 1.08-1.40), and BMI (ERFC: HR per 1-SD higher BMI, 1.43; 95% CI, 1.35-1.50; UK Biobank: HR, 1.37; 95% CI, 1.32-1.41). For these factors, there were similar HRs for pulmonary embolism and deep vein thrombosis in UK Biobank (except adiposity was more strongly associated with pulmonary embolism) and similar HRs for unprovoked vs provoked VTE. Apart from adiposity, these risk factors were less strongly associated with VTE than CHD. There were inconsistent associations of VTEs with diabetes and blood pressure across ERFC and UK Biobank, and there was limited ability to study lipid and inflammation markers.<h4>Conclusions and relevance</h4>Older age, smoking, and adiposity were consistently associated with higher VTE risk.",,pdf:https://pdxscholar.library.pdx.edu/cgi/viewcontent.cgi?article=1451&context=sph_facpub; doi:https://doi.org/10.1001/jamacardio.2018.4537; html:https://europepmc.org/articles/PMC6386140
 33367483,https://doi.org/10.1093/bioinformatics/btaa1079,A non-linear regression method for estimation of gene-environment heritability.,"Kerin M, Marchini J.",,"Bioinformatics (Oxford, England)",2021,2021-04-01,Y,,,,"<h4>Motivation</h4>Gene-environment (GxE) interactions are one of the least studied aspects of the genetic architecture of human traits and diseases. The environment of an individual is inherently high dimensional, evolves through time and can be expensive and time consuming to measure. The UK Biobank study, with all 500 000 participants having undergone an extensive baseline questionnaire, represents a unique opportunity to assess GxE heritability for many traits and diseases in a well powered setting.<h4>Results</h4>We have developed a randomized Haseman-Elston non-linear regression method applicable when many environmental variables have been measured on each individual. The method (GPLEMMA) simultaneously estimates a linear environmental score (ES) and its GxE heritability. We compare the method via simulation to a whole-genome regression approach (LEMMA) for estimating GxE heritability. We show that GPLEMMA is more computationally efficient than LEMMA on large datasets, and produces results highly correlated with those from LEMMA when applied to simulated data and real data from the UK Biobank.<h4>Availability and implementation</h4>Software implementing the GPLEMMA method is available from https://jmarchini.org/gplemma/.<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online.",,pdf:https://academic.oup.com/bioinformatics/article-pdf/36/24/5632/36899551/btaa1079.pdf; doi:https://doi.org/10.1093/bioinformatics/btaa1079; html:https://europepmc.org/articles/PMC8023682; pdf:https://europepmc.org/articles/PMC8023682?pdf=render
@@ -2190,15 +2192,15 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 32402553,https://doi.org/10.1016/j.ophtha.2020.03.029,"Visual Field Outcomes from the Multicenter, Randomized Controlled Laser in Glaucoma and Ocular Hypertension Trial (LiGHT).","Wright DM, Konstantakopoulou E, Montesano G, Nathwani N, Garg A, Garway-Heath D, Crabb DP, Gazzard G, Laser in Glaucoma and Ocular Hypertension Trial (LiGHT) Study Group, Adeleke M, Ambler G, Barton K, Bourne R, Broadway D, Bunce C, Buszewicz M, Crabb D, Davis A, Garg A, Garway-Heath D, Gazzard G, Hornan D, Hunter R, Jayaram H, Jiang Y, Konstantakopoulou E, Lim S, Liput J, Manners T, Montesano G, Morris S, Nathwani N, Ometto G, Rubin G, Strouthidis N, Vickerstaff V, Wilson S, Wormald R, Wright D, Zhu H.",,Ophthalmology,2020,2020-04-03,N,,,,"<h4>Purpose</h4>To compare visual field outcomes of ocular hypertensive and glaucoma patients treated first with medical therapy with those treated first with selective laser trabeculoplasty (SLT).<h4>Design</h4>Secondary analysis of patients from the Laser in Glaucoma and Ocular Hypertension study, a multicenter randomized controlled trial.<h4>Participants</h4>Three hundred forty-four patients (588 eyes) treated first with medical therapy and 344 patients (590 eyes) treated first with SLT.<h4>Methods</h4>Visual fields (VFs) were measured using standard automated perimetry and arranged in series (median length and duration, 9 VFs over 48 months). Hierarchical linear models were used to estimate pointwise VF progression rates, which were then averaged to produce a global progression estimate for each eye. Proportions of points and patients in each treatment group with fast (<-1 dB/year) or moderate (<-0.5 dB/year) progression were compared using log-binomial regression.<h4>Main outcome measures</h4>Pointwise and global progression rates of total deviation (TD) and pattern deviation (PD).<h4>Results</h4>A greater proportion of eyes underwent moderate or fast TD progression in the medical therapy group compared with the SLT group (26.2% vs. 16.9%; risk ratio [RR], 1.55; 95% confidence interval [CI], 1.23-1.93; P < 0.001). A similar pattern was observed for pointwise rates (medical therapy, 26.1% vs. SLT, 19.0%; RR, 1.37; 95% CI, 1.33-1.42; P < 0.001). A greater proportion of pointwise PD rates were categorized as moderate or fast in the medical therapy group (medical therapy, 11.5% vs. SLT, 8.3%; RR, 1.39; 95% CI, 1.32-1.46; P < 0.001). No statistical difference was found in the proportion of eyes that underwent moderate or fast PD progression (medical therapy, 9.9% vs. SLT, 7.1%; RR, 1.39; 95% CI, 0.95, 2.03; P = 0.0928).<h4>Conclusions</h4>A slightly larger proportion of ocular hypertensive and glaucoma patients treated first with medical therapy underwent rapid VF progression compared with those treated first with SLT.",,pdf:https://openaccess.city.ac.uk/id/eprint/24492/1/Wright%20Crabb%20et%20al%20Ophthalmology%202020.pdf; doi:https://doi.org/10.1016/j.ophtha.2020.03.029
 38613554,https://doi.org/10.1016/j.jcmg.2024.01.009,Cardiovascular Magnetic Resonance Reference Ranges From the Healthy Hearts Consortium.,"Raisi-Estabragh Z, Szabo L, McCracken C, Bülow R, Aquaro GD, Andre F, Le TT, Suchá D, Condurache DG, Salih AM, Chadalavada S, Aung N, Lee AM, Harvey NC, Leiner T, Chin CWL, Friedrich MG, Barison A, Dörr M, Petersen SE.",,JACC. Cardiovascular imaging,2024,2024-04-10,N,Artificial intelligence; Automated analysis; Sex differences; Ethnicity; Cardiovascular Magnetic Resonance; Healthy Reference Ranges,,,"<h4>Background</h4>The absence of population-stratified cardiovascular magnetic resonance (CMR) reference ranges from large cohorts is a major shortcoming for clinical care.<h4>Objectives</h4>This paper provides age-, sex-, and ethnicity-specific CMR reference ranges for atrial and ventricular metrics from the Healthy Hearts Consortium, an international collaborative comprising 9,088 CMR studies from verified healthy individuals, covering the complete adult age spectrum across both sexes, and with the highest ethnic diversity reported to date.<h4>Methods</h4>CMR studies were analyzed using certified software with batch processing capability (cvi42, version 5.14 prototype, Circle Cardiovascular Imaging) by 2 expert readers. Three segmentation methods (smooth, papillary, anatomic) were used to contour the endocardial and epicardial borders of the ventricles and atria from long- and short-axis cine series. Clinically established ventricular and atrial metrics were extracted and stratified by age, sex, and ethnicity. Variations by segmentation method, scanner vendor, and magnet strength were examined. Reference ranges are reported as 95% prediction intervals.<h4>Results</h4>The sample included 4,452 (49.0%) men and 4,636 (51.0%) women with average age of 61.1 ± 12.9 years (range: 18-83 years). Among these, 7,424 (81.7%) were from White, 510 (5.6%) South Asian, 478 (5.3%) mixed/other, 341 (3.7%) Black, and 335 (3.7%) Chinese ethnicities. Images were acquired using 1.5-T (n = 8,779; 96.6%) and 3.0-T (n = 309; 3.4%) scanners from Siemens (n = 8,299; 91.3%), Philips (n = 498; 5.5%), and GE (n = 291, 3.2%).<h4>Conclusions</h4>This work represents a resource with healthy CMR-derived volumetric reference ranges ready for clinical implementation.",,doi:https://doi.org/10.1016/j.jcmg.2024.01.009
 33025017,https://doi.org/10.1093/schbul/sbaa126,Using Natural Language Processing on Electronic Health Records to Enhance Detection and Prediction of Psychosis Risk.,"Irving J, Patel R, Oliver D, Colling C, Pritchard M, Broadbent M, Baldwin H, Stahl D, Stewart R, Fusar-Poli P.",,Schizophrenia bulletin,2021,2021-03-01,N,Prediction; Prevention; Psychosis; Machine Learning; Electronic Health Records; Natural Language Processing,,,"<h4>Background</h4>Using novel data mining methods such as natural language processing (NLP) on electronic health records (EHRs) for screening and detecting individuals at risk for psychosis.<h4>Method</h4>The study included all patients receiving a first index diagnosis of nonorganic and nonpsychotic mental disorder within the South London and Maudsley (SLaM) NHS Foundation Trust between January 1, 2008, and July 28, 2018. Least Absolute Shrinkage and Selection Operator (LASSO)-regularized Cox regression was used to refine and externally validate a refined version of a five-item individualized, transdiagnostic, clinically based risk calculator previously developed (Harrell's C = 0.79) and piloted for implementation. The refined version included 14 additional NLP-predictors: tearfulness, poor appetite, weight loss, insomnia, cannabis, cocaine, guilt, irritability, delusions, hopelessness, disturbed sleep, poor insight, agitation, and paranoia.<h4>Results</h4>A total of 92 151 patients with a first index diagnosis of nonorganic and nonpsychotic mental disorder within the SLaM Trust were included in the derivation (n = 28 297) or external validation (n = 63 854) data sets. Mean age was 33.6 years, 50.7% were women, and 67.0% were of white race/ethnicity. Mean follow-up was 1590 days. The overall 6-year risk of psychosis in secondary mental health care was 3.4 (95% CI, 3.3-3.6). External validation indicated strong performance on unseen data (Harrell's C 0.85, 95% CI 0.84-0.86), an increase of 0.06 from the original model.<h4>Conclusions</h4>Using NLP on EHRs can considerably enhance the prognostic accuracy of psychosis risk calculators. This can help identify patients at risk of psychosis who require assessment and specialized care, facilitating earlier detection and potentially improving patient outcomes.",,pdf:https://academic.oup.com/schizophreniabulletin/article-pdf/47/2/405/36620462/sbaa126.pdf; doi:https://doi.org/10.1093/schbul/sbaa126; html:https://europepmc.org/articles/PMC7965059; pdf:https://europepmc.org/articles/PMC7965059?pdf=render; doi:https://doi.org/10.1093/schbul/sbaa126
-34437535,https://doi.org/10.1371/journal.pgen.1009723,The impact of age on genetic risk for common diseases.,"Jiang X, Holmes C, McVean G.",,PLoS genetics,2021,2021-08-26,Y,,,,"Inherited genetic variation contributes to individual risk for many complex diseases and is increasingly being used for predictive patient stratification. Previous work has shown that genetic factors are not equally relevant to human traits across age and other contexts, though the reasons for such variation are not clear. Here, we introduce methods to infer the form of the longitudinal relationship between genetic relative risk for disease and age and to test whether all genetic risk factors behave similarly. We use a proportional hazards model within an interval-based censoring methodology to estimate age-varying individual variant contributions to genetic relative risk for 24 common diseases within the British ancestry subset of UK Biobank, applying a Bayesian clustering approach to group variants by their relative risk profile over age and permutation tests for age dependency and multiplicity of profiles. We find evidence for age-varying relative risk profiles in nine diseases, including hypertension, skin cancer, atherosclerotic heart disease, hypothyroidism and calculus of gallbladder, several of which show evidence, albeit weak, for multiple distinct profiles of genetic relative risk. The predominant pattern shows genetic risk factors having the greatest relative impact on risk of early disease, with a monotonic decrease over time, at least for the majority of variants, although the magnitude and form of the decrease varies among diseases. As a consequence, for diseases where genetic relative risk decreases over age, genetic risk factors have stronger explanatory power among younger populations, compared to older ones. We show that these patterns cannot be explained by a simple model involving the presence of unobserved covariates such as environmental factors. We discuss possible models that can explain our observations and the implications for genetic risk prediction.",,pdf:https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1009723&type=printable; doi:https://doi.org/10.1371/journal.pgen.1009723; html:https://europepmc.org/articles/PMC8389405; pdf:https://europepmc.org/articles/PMC8389405?pdf=render
 31848017,https://doi.org/10.1016/j.injury.2019.12.016,Pre-injury health status of major trauma patients with orthopaedic injuries.,"Gelaw AY, Gabbe BJ, Simpson PM, Ekegren CL.",,Injury,2020,2019-12-10,N,Trauma; Injury; Quality of life; Health Status; Orthopaedic; Pre-injury,,,"<h4>Background</h4>Pre-injury health status is an important determining factor of long-term outcomes after orthopaedic major trauma. Determining pre-injury health status of major trauma patients with orthopaedic injuries is also important for evaluating the change from pre to post-injury health status.<h4>Objectives</h4>Describe pre-injury health statuses reported at three different time points (6, 12 and 24 months) after injury and compare these with Australian normative values; determine the agreement between pre-injury health status collected at multiple time points post-injury; and identify factors associated with reporting better pre-injury health status.<h4>Materials and methods</h4>A registry-based cohort study was conducted. Major trauma patients with orthopaedic injuries captured by the Victorian State Trauma Registry with a date of injury from January 2009 to December 2016 were included. Pre-injury health status (measured using the EuroQol-Visual Analogue Scale (EQ-VAS)), reported 6, 12 and 24 months post-injury, was compared against Australian population normative values. The Bland-Altman method of comparison was used to determine the agreement between pre-injury EQ-VAS scores reported 6 to 12 and 6 to 24 months post-injury. Mixed effects ordinal logistic regression was used to determine factors associated with reporting better pre-injury health status.<h4>Results</h4>A total of 3,371 patients were eligible for the study. The median (IQR) pre-injury EQ-VAS score reported 6, 12 and 24 months post-injury was 90 (85-100) out of 100. Participants' pre-injury EQ-VAS scores reported 6, 12 and 24 months post-injury were significantly higher than Australian population normative values. Pre-injury EQ-VAS scores reported 6 months post-injury agreed with pre-injury EQ-VAS scores reported 12 and 24 months post-injury. A significant association exists between pre-injury health status and age, comorbidities, injury characteristics, socioeconomic status and pre-injury work status.<h4>Conclusions</h4>People with orthopaedic major trauma have better pre-injury health compared to the general Australian population. Therefore, population-specific values should be used as baseline measures to evaluate orthopaedic trauma outcomes. Pre-injury health status values reported at three different post-injury time points were comparable. If conducting a retrospective pre-injury health evaluation, researchers need be aware of factors that influence self-reporting of pre-injury health status and the response shift that may happen due to encountering injury.",,doi:https://doi.org/10.1016/j.injury.2019.12.016
+34437535,https://doi.org/10.1371/journal.pgen.1009723,The impact of age on genetic risk for common diseases.,"Jiang X, Holmes C, McVean G.",,PLoS genetics,2021,2021-08-26,Y,,,,"Inherited genetic variation contributes to individual risk for many complex diseases and is increasingly being used for predictive patient stratification. Previous work has shown that genetic factors are not equally relevant to human traits across age and other contexts, though the reasons for such variation are not clear. Here, we introduce methods to infer the form of the longitudinal relationship between genetic relative risk for disease and age and to test whether all genetic risk factors behave similarly. We use a proportional hazards model within an interval-based censoring methodology to estimate age-varying individual variant contributions to genetic relative risk for 24 common diseases within the British ancestry subset of UK Biobank, applying a Bayesian clustering approach to group variants by their relative risk profile over age and permutation tests for age dependency and multiplicity of profiles. We find evidence for age-varying relative risk profiles in nine diseases, including hypertension, skin cancer, atherosclerotic heart disease, hypothyroidism and calculus of gallbladder, several of which show evidence, albeit weak, for multiple distinct profiles of genetic relative risk. The predominant pattern shows genetic risk factors having the greatest relative impact on risk of early disease, with a monotonic decrease over time, at least for the majority of variants, although the magnitude and form of the decrease varies among diseases. As a consequence, for diseases where genetic relative risk decreases over age, genetic risk factors have stronger explanatory power among younger populations, compared to older ones. We show that these patterns cannot be explained by a simple model involving the presence of unobserved covariates such as environmental factors. We discuss possible models that can explain our observations and the implications for genetic risk prediction.",,pdf:https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1009723&type=printable; doi:https://doi.org/10.1371/journal.pgen.1009723; html:https://europepmc.org/articles/PMC8389405; pdf:https://europepmc.org/articles/PMC8389405?pdf=render
 34991479,https://doi.org/10.1186/s12877-021-02684-y,The dynamics of frailty development and progression in older adults in primary care in England (2006-2017): a retrospective cohort profile.,"Fogg C, Fraser SDS, Roderick P, de Lusignan S, Clegg A, Brailsford S, Barkham A, Patel HP, Windle V, Harris S, Zhu S, England T, Evenden D, Lambert F, Walsh B, Frailty Dynamics study team.",,BMC geriatrics,2022,2022-01-06,Y,Adults; Frailty; Cohort study; Primary Care; Service Use; Electronic Health Records; Trajectories; Computer Simulation Modelling,,,"<h4>Background</h4>Frailty is a common condition in older adults and has a major impact on patient outcomes and service use. Information on the prevalence in middle-aged adults and the patterns of progression of frailty at an individual and population level is scarce. To address this, a cohort was defined from a large primary care database in England to describe the epidemiology of frailty and understand the dynamics of frailty within individuals and across the population. This article describes the structure of the dataset, cohort characteristics and planned analyses.<h4>Methods</h4>Retrospective cohort study using electronic health records. Participants were aged ≥50 years registered in practices contributing to the Oxford Royal College of General Practitioners Research and Surveillance Centre between 2006 to 2017. Data include GP practice details, patient sociodemographic and clinical characteristics, twice-yearly electronic Frailty Index (eFI), deaths, medication use and primary and secondary care health service use. Participants in each cohort year by age group, GP and patient characteristics at cohort entry are described.<h4>Results</h4>The cohort includes 2,177,656 patients, contributing 15,552,946 person-years, registered at 419 primary care practices in England. The mean age was 61 years, 52.1% of the cohort was female, and 77.6% lived in urban environments. Frailty increased with age, affecting 10% of adults aged 50-64 and 43.7% of adults aged ≥65. The prevalence of long-term conditions and specific frailty deficits increased with age, as did the eFI and the severity of frailty categories.<h4>Conclusion</h4>A comprehensive understanding of frailty dynamics will inform predictions of current and future care needs to facilitate timely planning of appropriate interventions, service configurations and workforce requirements. Analysis of this large, nationally representative cohort including participants aged ≥50 will capture earlier transitions to frailty and enable a detailed understanding of progression and impact. These results will inform novel simulation models which predict future health and service needs of older people living with frailty.<h4>Study registration</h4>Registered on www.clinicaltrials.gov October 25th 2019, NCT04139278 .",,pdf:https://bmcgeriatr.biomedcentral.com/counter/pdf/10.1186/s12877-021-02684-y; doi:https://doi.org/10.1186/s12877-021-02684-y; html:https://europepmc.org/articles/PMC8740419; pdf:https://europepmc.org/articles/PMC8740419?pdf=render
 38135686,https://doi.org/10.1038/s41467-023-42320-4,Para-infectious brain injury in COVID-19 persists at follow-up despite attenuated cytokine and autoantibody responses.,"Michael BD, Dunai C, Needham EJ, Tharmaratnam K, Williams R, Huang Y, Boardman SA, Clark JJ, Sharma P, Subramaniam K, Wood GK, Collie C, Digby R, Ren A, Norton E, Leibowitz M, Ebrahimi S, Fower A, Fox H, Tato E, Ellul MA, Sunderland G, Held M, Hetherington C, Egbe FN, Palmos A, Stirrups K, Grundmann A, Chiollaz AC, Sanchez JC, Stewart JP, Griffiths M, Solomon T, Breen G, Coles AJ, Kingston N, Bradley JR, Chinnery PF, Cavanagh J, Irani SR, Vincent A, Baillie JK, Openshaw PJ, Semple MG, ISARIC4C Investigators, COVID-CNS Consortium, Taams LS, Menon DK.",,Nature communications,2023,2023-12-22,Y,,,,"To understand neurological complications of COVID-19 better both acutely and for recovery, we measured markers of brain injury, inflammatory mediators, and autoantibodies in 203 hospitalised participants; 111 with acute sera (1-11 days post-admission) and 92 convalescent sera (56 with COVID-19-associated neurological diagnoses). Here we show that compared to 60 uninfected controls, tTau, GFAP, NfL, and UCH-L1 are increased with COVID-19 infection at acute timepoints and NfL and GFAP are significantly higher in participants with neurological complications. Inflammatory mediators (IL-6, IL-12p40, HGF, M-CSF, CCL2, and IL-1RA) are associated with both altered consciousness and markers of brain injury. Autoantibodies are more common in COVID-19 than controls and some (including against MYL7, UCH-L1, and GRIN3B) are more frequent with altered consciousness. Additionally, convalescent participants with neurological complications show elevated GFAP and NfL, unrelated to attenuated systemic inflammatory mediators and to autoantibody responses. Overall, neurological complications of COVID-19 are associated with evidence of neuroglial injury in both acute and late disease and these correlate with dysregulated innate and adaptive immune responses acutely.",,pdf:https://www.nature.com/articles/s41467-023-42320-4.pdf; doi:https://doi.org/10.1038/s41467-023-42320-4; html:https://europepmc.org/articles/PMC10746705; pdf:https://europepmc.org/articles/PMC10746705?pdf=render
 37808344,https://doi.org/10.1016/j.jacadv.2023.100573,<i>CYP2C19</i> Genotype Prevalence and Association With Recurrent Myocardial Infarction in British-South Asians Treated With Clopidogrel.,"Magavern EF, Jacobs B, Warren H, Finocchiaro G, Finer S, van Heel DA, Genes & Health Research Team, Smedley D, Caulfield MJ.",,JACC. Advances,2023,2023-09-01,Y,Pharmacogenomics; ischemic heart disease; Pharmacotherapy; Preventive Cardiology,,,"<h4>Background</h4>Cytochrome P450 family 2 subfamily C member 19 (CYP2C19) is a hepatic enzyme involved in the metabolism of clopidogrel from a prodrug to its active metabolite. Prior studies of genetic polymorphisms in <i>CYP2C19</i> and their relationship with clinical efficacy have not included South Asian populations.<h4>Objectives</h4>The objective of this study was to assess prevalence of common <i>CYP2C19</i> genotype polymorphisms in a British-South Asian population and correlate these with recurrent myocardial infarction risk in participants prescribed clopidogrel.<h4>Methods</h4>The Genes & Health cohort of British Bangladeshi and Pakistani ancestry participants were studied. <i>CYP2C19</i> diplotypes were assessed using array data. Multivariable logistic regression was used to test for association between genetically inferred CYP2C19 metabolizer status and recurrent myocardial infarction, controlling for known cardiovascular disease risk factors, percutaneous coronary intervention, age, sex, and population stratification.<h4>Results</h4>Genes & Health cohort participants (N = 44,396) have a high prevalence (57%) of intermediate or poor CYP2C19 metabolizers, with at least 1 loss-of-function <i>CYP2C19</i> allele. The prevalence of poor metabolizers carrying 2 <i>CYP2C19</i> loss-of-function alleles is 13%, which is higher than that in previously studied European (2.4%) and Central/South Asian populations (8.2%). Sixty-nine percent of the cohort who were diagnosed with an acute myocardial infarction were prescribed clopidogrel. Poor metabolizers were significantly more likely to have a recurrent myocardial infarction (OR: 3.1; <i>P</i> = 0.019).<h4>Conclusions</h4>A pharmacogenomic-driven approach to clopidogrel prescribing has the potential to impact significantly on clinical management and outcomes in individuals of Bangladeshi and Pakistani ancestry.",,doi:https://doi.org/10.1016/j.jacadv.2023.100573; html:https://europepmc.org/articles/PMC10550831; pdf:https://europepmc.org/articles/PMC10550831?pdf=render
 34965929,https://doi.org/10.1136/bmj-2021-065834,GP consultation rates for sequelae after acute covid-19 in patients managed in the community or hospital in the UK: population based study.,"Whittaker HR, Gulea C, Koteci A, Kallis C, Morgan AD, Iwundu C, Weeks M, Gupta R, Quint JK.",,BMJ (Clinical research ed.),2021,2021-12-29,Y,,,,"<h4>Objectives</h4>To describe the rates for consulting a general practitioner (GP) for sequelae after acute covid-19 in patients admitted to hospital with covid-19 and those managed in the community, and to determine how the rates change over time for patients in the community and after vaccination for covid-19.<h4>Design</h4>Population based study.<h4>Setting</h4>1392 general practices in England contributing to the Clinical Practice Research Datalink Aurum database.<h4>Participants</h4>456 002 patients with a diagnosis of covid-19 between 1 August 2020 and 14 February 2021 (44.7% men; median age 61 years), admitted to hospital within two weeks of diagnosis or managed in the community, and followed-up for a maximum of 9.2 months. A negative control group included individuals without covid-19 (n=38 511) and patients with influenza before the pandemic (n=21 803).<h4>Main outcome measures</h4>Comparison of rates for consulting a GP for new symptoms, diseases, prescriptions, and healthcare use in individuals admitted to hospital and those managed in the community, separately, before and after covid-19 infection, using Cox regression and negative binomial regression for healthcare use. The analysis was repeated for the negative control and influenza cohorts. In individuals in the community, outcomes were also described over time after a diagnosis of covid-19, and compared before and after vaccination for individuals who were symptomatic after covid-19 infection, using negative binomial regression.<h4>Results</h4>Relative to the negative control and influenza cohorts, patients in the community (n=437 943) had significantly higher GP consultation rates for multiple sequelae, and the most common were loss of smell or taste, or both (adjusted hazard ratio 5.28, 95% confidence interval 3.89 to 7.17, P<0.001); venous thromboembolism (3.35, 2.87 to 3.91, P<0.001); lung fibrosis (2.41, 1.37 to 4.25, P=0.002), and muscle pain (1.89, 1.63 to 2.20, P<0.001); and also for healthcare use after a diagnosis of covid-19 compared with 12 months before infection. For absolute proportions, the most common outcomes ≥4 weeks after a covid-19 diagnosis in patients in the community were joint pain (2.5%), anxiety (1.2%), and prescriptions for non-steroidal anti-inflammatory drugs (1.2%). Patients admitted to hospital (n=18 059) also had significantly higher GP consultation rates for multiple sequelae, most commonly for venous thromboembolism (16.21, 11.28 to 23.31, P<0.001), nausea (4.64, 2.24 to 9.21, P<0.001), prescriptions for paracetamol (3.68, 2.86 to 4.74, P<0.001), renal failure (3.42, 2.67 to 4.38, P<0.001), and healthcare use after a covid-19 diagnosis compared with 12 months before infection. For absolute proportions, the most common outcomes ≥4 weeks after a covid-19 diagnosis in patients admitted to hospital were venous thromboembolism (3.5%), joint pain (2.7%), and breathlessness (2.8%). In patients in the community, anxiety and depression, abdominal pain, diarrhoea, general pain, nausea, chest tightness, and tinnitus persisted throughout follow-up. GP consultation rates were reduced for all symptoms, prescriptions, and healthcare use, except for neuropathic pain, cognitive impairment, strong opiates, and paracetamol use in patients in the community after the first vaccination dose for covid-19 relative to before vaccination. GP consultation rates were also reduced for ischaemic heart disease, asthma, and gastro-oesophageal disease.<h4>Conclusions</h4>GP consultation rates for sequelae after acute covid-19 infection differed between patients with covid-19 who were admitted to hospital and those managed in the community. For individuals in the community, rates of some sequelae decreased over time but those for others, such as anxiety and depression, persisted. Rates of some outcomes decreased after vaccination in this group.",,pdf:https://www.bmj.com/content/bmj/375/bmj-2021-065834.full.pdf; doi:https://doi.org/10.1136/bmj-2021-065834; html:https://europepmc.org/articles/PMC8715128; pdf:https://europepmc.org/articles/PMC8715128?pdf=render
 37060915,https://doi.org/10.1016/s0140-6736(23)00510-x,"Higher dose corticosteroids in patients admitted to hospital with COVID-19 who are hypoxic but not requiring ventilatory support (RECOVERY): a randomised, controlled, open-label, platform trial.","RECOVERY Collaborative Group. Electronic address: recoverytrial@ndph.ox.ac.uk, RECOVERY Collaborative Group.",,"Lancet (London, England)",2023,2023-04-13,Y,,,,"<h4>Background</h4>Low-dose corticosteroids have been shown to reduce mortality for patients with COVID-19 requiring oxygen or ventilatory support (non-invasive mechanical ventilation, invasive mechanical ventilation, or extracorporeal membrane oxygenation). We evaluated the use of a higher dose of corticosteroids in this patient group.<h4>Methods</h4>This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]) is assessing multiple possible treatments in patients hospitalised for COVID-19. Eligible and consenting adult patients with clinical evidence of hypoxia (ie, receiving oxygen or with oxygen saturation <92% on room air) were randomly allocated (1:1) to either usual care with higher dose corticosteroids (dexamethasone 20 mg once daily for 5 days followed by 10 mg dexamethasone once daily for 5 days or until discharge if sooner) or usual standard of care alone (which included dexamethasone 6 mg once daily for 10 days or until discharge if sooner). The primary outcome was 28-day mortality among all randomised participants. On May 11, 2022, the independent data monitoring committee recommended stopping recruitment of patients receiving no oxygen or simple oxygen only due to safety concerns. We report the results for these participants only. Recruitment of patients receiving ventilatory support is ongoing. The RECOVERY trial is registered with ISRCTN (50189673) and ClinicalTrials.gov (NCT04381936).<h4>Findings</h4>Between May 25, 2021, and May 13, 2022, 1272 patients with COVID-19 and hypoxia receiving no oxygen (eight [1%]) or simple oxygen only (1264 [99%]) were randomly allocated to receive usual care plus higher dose corticosteroids (659 patients) versus usual care alone (613 patients, of whom 87% received low-dose corticosteroids during the follow-up period). Of those randomly assigned, 745 (59%) were in Asia, 512 (40%) in the UK, and 15 (1%) in Africa. 248 (19%) had diabetes and 769 (60%) were male. Overall, 123 (19%) of 659 patients allocated to higher dose corticosteroids versus 75 (12%) of 613 patients allocated to usual care died within 28 days (rate ratio 1·59 [95% CI 1·20-2·10]; p=0·0012). There was also an excess of pneumonia reported to be due to non-COVID infection (64 cases [10%] vs 37 cases [6%]; absolute difference 3·7% [95% CI 0·7-6·6]) and an increase in hyperglycaemia requiring increased insulin dose (142 [22%] vs 87 [14%]; absolute difference 7·4% [95% CI 3·2-11·5]).<h4>Interpretation</h4>In patients hospitalised for COVID-19 with clinical hypoxia who required either no oxygen or simple oxygen only, higher dose corticosteroids significantly increased the risk of death compared with usual care, which included low-dose corticosteroids. The RECOVERY trial continues to assess the effects of higher dose corticosteroids in patients hospitalised with COVID-19 who require non-invasive ventilation, invasive mechanical ventilation, or extracorporeal membrane oxygenation.<h4>Funding</h4>UK Research and Innovation (Medical Research Council), National Institute of Health and Care Research, and Wellcome Trust.",,doi:https://doi.org/10.1016/s0140-6736(23)00510-x; doi:https://doi.org/10.1016/S0140-6736(23)00510-X; html:https://europepmc.org/articles/PMC10156147; pdf:https://europepmc.org/articles/PMC10156147?pdf=render
-35717168,https://doi.org/10.1186/s12879-022-07490-4,The contribution of hospital-acquired infections to the COVID-19 epidemic in England in the first half of 2020.,"Knight GM, Pham TM, Stimson J, Funk S, Jafari Y, Pople D, Evans S, Yin M, Brown CS, Bhattacharya A, Hope R, Semple MG, ISARIC4C Investigators, CMMID COVID-19 Working Group, Read JM, Cooper BS, Robotham JV.",,BMC infectious diseases,2022,2022-06-18,Y,Mathematical Modelling; Nosocomial Transmission; Covid-19; Sars-cov-2,,,"<h4>Background</h4>SARS-CoV-2 is known to transmit in hospital settings, but the contribution of infections acquired in hospitals to the epidemic at a national scale is unknown.<h4>Methods</h4>We used comprehensive national English datasets to determine the number of COVID-19 patients with identified hospital-acquired infections (with symptom onset > 7 days after admission and before discharge) in acute English hospitals up to August 2020. As patients may leave the hospital prior to detection of infection or have rapid symptom onset, we combined measures of the length of stay and the incubation period distribution to estimate how many hospital-acquired infections may have been missed. We used simulations to estimate the total number (identified and unidentified) of symptomatic hospital-acquired infections, as well as infections due to onward community transmission from missed hospital-acquired infections, to 31st July 2020.<h4>Results</h4>In our dataset of hospitalised COVID-19 patients in acute English hospitals with a recorded symptom onset date (n = 65,028), 7% were classified as hospital-acquired. We estimated that only 30% (range across weeks and 200 simulations: 20-41%) of symptomatic hospital-acquired infections would be identified, with up to 15% (mean, 95% range over 200 simulations: 14.1-15.8%) of cases currently classified as community-acquired COVID-19 potentially linked to hospital transmission. We estimated that 26,600 (25,900 to 27,700) individuals acquired a symptomatic SARS-CoV-2 infection in an acute Trust in England before 31st July 2020, resulting in 15,900 (15,200-16,400) or 20.1% (19.2-20.7%) of all identified hospitalised COVID-19 cases.<h4>Conclusions</h4>Transmission of SARS-CoV-2 to hospitalised patients likely caused approximately a fifth of identified cases of hospitalised COVID-19 in the ""first wave"" in England, but less than 1% of all infections in England. Using time to symptom onset from admission for inpatients as a detection method likely misses a substantial proportion (> 60%) of hospital-acquired infections.",,pdf:https://bmcinfectdis.biomedcentral.com/counter/pdf/10.1186/s12879-022-07490-4; doi:https://doi.org/10.1186/s12879-022-07490-4; html:https://europepmc.org/articles/PMC9206097; pdf:https://europepmc.org/articles/PMC9206097?pdf=render
 33737684,https://doi.org/10.1038/s41598-021-85877-0,"Proteomic blood profiling in mild, severe and critical COVID-19 patients.","Patel H, Ashton NJ, Dobson RJB, Andersson LM, Yilmaz A, Blennow K, Gisslen M, Zetterberg H.",,Scientific reports,2021,2021-03-18,Y,,,,"The recent SARS-CoV-2 pandemic manifests itself as a mild respiratory tract infection in most individuals, leading to COVID-19 disease. However, in some infected individuals, this can progress to severe pneumonia and acute respiratory distress syndrome (ARDS), leading to multi-organ failure and death. This study explores the proteomic differences between mild, severe, and critical COVID-19 positive patients to further understand the disease progression, identify proteins associated with disease severity, and identify potential therapeutic targets. Blood protein profiling was performed on 59 COVID-19 mild (n = 26), severe (n = 9) or critical (n = 24) cases and 28 controls using the OLINK inflammation, autoimmune, cardiovascular and neurology panels. Differential expression analysis was performed within and between disease groups to generate nine different analyses. From the 368 proteins measured per individual, more than 75% were observed to be significantly perturbed in COVID-19 cases. Six proteins (IL6, CKAP4, Gal-9, IL-1ra, LILRB4 and PD-L1) were identified to be associated with disease severity. The results have been made readily available through an interactive web-based application for instant data exploration and visualization, and can be accessed at https://phidatalab-shiny.rosalind.kcl.ac.uk/COVID19/ . Our results demonstrate that dynamic changes in blood proteins associated with disease severity can potentially be used as early biomarkers to monitor disease severity in COVID-19 and serve as potential therapeutic targets.",,pdf:https://www.nature.com/articles/s41598-021-85877-0.pdf; doi:https://doi.org/10.1038/s41598-021-85877-0; html:https://europepmc.org/articles/PMC7973581; pdf:https://europepmc.org/articles/PMC7973581?pdf=render
+35717168,https://doi.org/10.1186/s12879-022-07490-4,The contribution of hospital-acquired infections to the COVID-19 epidemic in England in the first half of 2020.,"Knight GM, Pham TM, Stimson J, Funk S, Jafari Y, Pople D, Evans S, Yin M, Brown CS, Bhattacharya A, Hope R, Semple MG, ISARIC4C Investigators, CMMID COVID-19 Working Group, Read JM, Cooper BS, Robotham JV.",,BMC infectious diseases,2022,2022-06-18,Y,Mathematical Modelling; Nosocomial Transmission; Covid-19; Sars-cov-2,,,"<h4>Background</h4>SARS-CoV-2 is known to transmit in hospital settings, but the contribution of infections acquired in hospitals to the epidemic at a national scale is unknown.<h4>Methods</h4>We used comprehensive national English datasets to determine the number of COVID-19 patients with identified hospital-acquired infections (with symptom onset > 7 days after admission and before discharge) in acute English hospitals up to August 2020. As patients may leave the hospital prior to detection of infection or have rapid symptom onset, we combined measures of the length of stay and the incubation period distribution to estimate how many hospital-acquired infections may have been missed. We used simulations to estimate the total number (identified and unidentified) of symptomatic hospital-acquired infections, as well as infections due to onward community transmission from missed hospital-acquired infections, to 31st July 2020.<h4>Results</h4>In our dataset of hospitalised COVID-19 patients in acute English hospitals with a recorded symptom onset date (n = 65,028), 7% were classified as hospital-acquired. We estimated that only 30% (range across weeks and 200 simulations: 20-41%) of symptomatic hospital-acquired infections would be identified, with up to 15% (mean, 95% range over 200 simulations: 14.1-15.8%) of cases currently classified as community-acquired COVID-19 potentially linked to hospital transmission. We estimated that 26,600 (25,900 to 27,700) individuals acquired a symptomatic SARS-CoV-2 infection in an acute Trust in England before 31st July 2020, resulting in 15,900 (15,200-16,400) or 20.1% (19.2-20.7%) of all identified hospitalised COVID-19 cases.<h4>Conclusions</h4>Transmission of SARS-CoV-2 to hospitalised patients likely caused approximately a fifth of identified cases of hospitalised COVID-19 in the ""first wave"" in England, but less than 1% of all infections in England. Using time to symptom onset from admission for inpatients as a detection method likely misses a substantial proportion (> 60%) of hospital-acquired infections.",,pdf:https://bmcinfectdis.biomedcentral.com/counter/pdf/10.1186/s12879-022-07490-4; doi:https://doi.org/10.1186/s12879-022-07490-4; html:https://europepmc.org/articles/PMC9206097; pdf:https://europepmc.org/articles/PMC9206097?pdf=render
 35188939,https://doi.org/10.1097/pts.0000000000000867,Optimizing Hospital Electronic Prescribing Systems: A Systematic Scoping Review.,"Williams J, Malden S, Heeney C, Bouamrane M, Holder M, Perera U, Bates DW, Sheikh A.",,Journal of patient safety,2022,2022-03-01,Y,,,,"<h4>Objective</h4>Considerable international investment in hospital electronic prescribing (ePrescribing) systems has been made, but despite this, it is proving difficult for most organizations to realize safety, quality, and efficiency gains in prescribing. The objective of this work was to develop policy-relevant insights into the optimization of hospital ePrescribing systems to maximize the benefits and minimize the risks of these expensive digital health infrastructures.<h4>Methods</h4>We undertook a systematic scoping review of the literature by searching MEDLINE, Embase, and CINAHL databases. We searched for primary studies reporting on ePrescribing optimization strategies and independently screened and abstracted data until saturation was achieved. Findings were theoretically and thematically synthesized taking a medicine life-cycle perspective, incorporating consultative phases with domain experts.<h4>Results</h4>We identified 23,609 potentially eligible studies from which 1367 satisfied our inclusion criteria. Thematic synthesis was conducted on a data set of 76 studies, of which 48 were based in the United States. Key approaches to optimization included the following: stakeholder engagement, system or process redesign, technological innovations, and education and training packages. Single-component interventions (n = 26) described technological optimization strategies focusing on a single, specific step in the prescribing process. Multicomponent interventions (n = 50) used a combination of optimization strategies, typically targeting multiple steps in the medicines management process.<h4>Discussion</h4>We identified numerous optimization strategies for enhancing the performance of ePrescribing systems. Key considerations for ePrescribing optimization include meaningful stakeholder engagement to reconceptualize the service delivery model and implementing technological innovations with supporting training packages to simultaneously impact on different facets of the medicines management process.",,html:https://journals.lww.com/journalpatientsafety/Fulltext/2022/03000/Optimizing_Hospital_Electronic_Prescribing.36.aspx; doi:https://doi.org/10.1097/PTS.0000000000000867; html:https://europepmc.org/articles/PMC8855945; pdf:https://europepmc.org/articles/PMC8855945?pdf=render
 31101093,https://doi.org/10.1186/s12889-019-6888-9,Educational and health outcomes of children and adolescents receiving antiepileptic medication: Scotland-wide record linkage study of 766 244 schoolchildren.,"Fleming M, Fitton CA, Steiner MFC, McLay JS, Clark D, King A, Mackay DF, Pell JP.",,BMC public health,2019,2019-05-17,Y,Epilepsy; Health; Prescribing; Educational Outcomes; Record Linkage; Population Cohort,Improving Public Health,,"<h4>Background</h4>Childhood epilepsy can adversely affect education and employment in addition to health. Previous studies are small or highly selective producing conflicting results. This retrospective cohort study aims to compare educational and health outcomes of children receiving antiepileptic medication versus peers.<h4>Methods</h4>Record linkage of Scotland-wide databases covering dispensed prescriptions, acute and psychiatric hospitalisations, maternity records, deaths, annual pupil census, school absences/exclusions, special educational needs, school examinations, and (un)employment provided data on 766,244 children attending Scottish schools between 2009 and 2013. Outcomes were adjusted for sociodemographic and maternity confounders and comorbid conditions.<h4>Results</h4>Compared with peers, children on antiepileptic medication were more likely to experience school absence (Incidence Rate Ratio [IRR] 1.43, 95% CI: 1.38, 1.48), special educational needs (Odds ratio [OR] 9.60, 95% CI: 9.02, 10.23), achieve the lowest level of attainment (OR 3.43, 95% CI: 2.74, 4.29) be unemployed (OR 1.82, 95% CI: 1.60, 2.07), be admitted to hospital (Hazard Ratio [HR] 3.56, 95% CI: 3.42, 3.70), and die (HR 22.02, 95% CI: 17.00, 28.53). Absenteeism partly explained poorer attainment and higher unemployment. Girls and younger children on antiepileptic medication had higher risk of poor outcomes.<h4>Conclusions</h4>Children on antiepileptic medication fare worse than peers across educational and health outcomes. In order to reduce school absenteeism and mitigate its effects, children with epilepsy should receive integrated care from a multidisciplinary team that spans education and healthcare.",,pdf:https://bmcpublichealth.biomedcentral.com/track/pdf/10.1186/s12889-019-6888-9; doi:https://doi.org/10.1186/s12889-019-6888-9; html:https://europepmc.org/articles/PMC6525436; pdf:https://europepmc.org/articles/PMC6525436?pdf=render
 34192199,https://doi.org/10.1136/bmjpo-2021-001049,Staff-pupil SARS-CoV-2 infection pathways in schools in Wales: a population-level linked data approach.,"Thompson DA, Abbasizanjani H, Fry R, Marchant E, Griffiths L, Akbari A, Hollinghurst J, North L, Lyons J, Torabi F, Davies G, Gravenor MB, Lyons RA.",,BMJ paediatrics open,2021,2021-05-10,Y,Disease transmission; Schools; Public Health; Sars-cov-2,,,"<h4>Background</h4>Better understanding of the role that children and school staff play in the transmission of SARS-CoV-2 is essential to guide policy development on controlling infection while minimising disruption to children's education and well-being.<h4>Methods</h4>Our national e-cohort (n=464531) study used anonymised linked data for pupils, staff and associated households linked via educational settings in Wales. We estimated the odds of testing positive for SARS-CoV-2 infection for staff and pupils over the period August- December 2020, dependent on measures of recent exposure to known cases linked to their educational settings.<h4>Results</h4>The total number of cases in a school was not associated with a subsequent increase in the odds of testing positive (staff OR per case: 0.92, 95% CI 0.85 to 1.00; pupil OR per case: 0.98, 95% CI 0.93 to 1.02). Among pupils, the number of recent cases within the same year group was significantly associated with subsequent increased odds of testing positive (OR per case: 1.12, 95% CI 1.08 to 1.15). These effects were adjusted for a range of demographic covariates, and in particular any known cases within the same household, which had the strongest association with testing positive (staff OR: 39.86, 95% CI 35.01 to 45.38; pupil OR: 9.39, 95% CI 8.94 to 9.88).<h4>Conclusions</h4>In a national school cohort, the odds of staff testing positive for SARS-CoV-2 infection were not significantly increased in the 14-day period after case detection in the school. However, pupils were found to be at increased odds, following cases appearing within their own year group, where most of their contacts occur. Strong mitigation measures over the whole of the study period may have reduced wider spread within the school environment.",,pdf:https://bmjpaedsopen.bmj.com/content/bmjpo/5/1/e001049.full.pdf; doi:https://doi.org/10.1136/bmjpo-2021-001049; html:https://europepmc.org/articles/PMC8111870; pdf:https://europepmc.org/articles/PMC8111870?pdf=render
@@ -2206,8 +2208,8 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 37647632,https://doi.org/10.1182/blood.2023020118,The effects of pathogenic and likely pathogenic variants for inherited hemostasis disorders in 140 214 UK Biobank participants.,"Stefanucci L, Collins J, Sims MC, Barrio-Hernandez I, Sun L, Burren OS, Perfetto L, Bender I, Callahan TJ, Fleming K, Guerrero JA, Hermjakob H, Martin MJ, Stephenson J, Paneerselvam K, Petrovski S, Porras P, Robinson PN, Wang Q, Watkins X, Frontini M, Laskowski RA, Beltrao P, Di Angelantonio E, Gomez K, Laffan M, Ouwehand WH, Mumford AD, Freson K, Carss K, Downes K, Gleadall N, Megy K, Bruford E, Vuckovic D.",,Blood,2023,2023-12-01,Y,,,,"Rare genetic diseases affect millions, and identifying causal DNA variants is essential for patient care. Therefore, it is imperative to estimate the effect of each independent variant and improve their pathogenicity classification. Our study of 140 214 unrelated UK Biobank (UKB) participants found that each of them carries a median of 7 variants previously reported as pathogenic or likely pathogenic. We focused on 967 diagnostic-grade gene (DGG) variants for rare bleeding, thrombotic, and platelet disorders (BTPDs) observed in 12 367 UKB participants. By association analysis, for a subset of these variants, we estimated effect sizes for platelet count and volume, and odds ratios for bleeding and thrombosis. Variants causal of some autosomal recessive platelet disorders revealed phenotypic consequences in carriers. Loss-of-function variants in MPL, which cause chronic amegakaryocytic thrombocytopenia if biallelic, were unexpectedly associated with increased platelet counts in carriers. We also demonstrated that common variants identified by genome-wide association studies (GWAS) for platelet count or thrombosis risk may influence the penetrance of rare variants in BTPD DGGs on their associated hemostasis disorders. Network-propagation analysis applied to an interactome of 18 410 nodes and 571 917 edges showed that GWAS variants with large effect sizes are enriched in DGGs and their first-order interactors. Finally, we illustrate the modifying effect of polygenic scores for platelet count and thrombosis risk on disease severity in participants carrying rare variants in TUBB1 or PROC and PROS1, respectively. Our findings demonstrate the power of association analyses using large population datasets in improving pathogenicity classifications of rare variants.",,doi:https://doi.org/10.1182/blood.2023020118; html:https://europepmc.org/articles/PMC10733830
 30382236,https://doi.org/10.1038/s41433-018-0229-6,The diagnostic accuracy of OCT angiography in naive and treated neovascular age-related macular degeneration: a review.,"Perrott-Reynolds R, Cann R, Cronbach N, Neo YN, Ho V, McNally O, Madi HA, Cochran C, Chakravarthy U.",,"Eye (London, England)",2019,2018-10-31,N,,,,"Optical coherence tomography angiography (OCTA) is a non-invasive retinal imaging innovation that has been gaining popularity for the evaluation of the retinal vasculature. Of clinical importance is its current use either as an alternative or in conjunction with conventional dye-based angiography in neovascular age-related macular degeneration. OCTA is not without limitations and these include image artefact, a relatively small field of view and failure of the segmentation algorithms, which can confound the interpretation of findings. While there are numerous publications on OCTA in neovascular AMD, few have examined the diagnostic accuracy of this new technology compared with the accepted gold standard of fundus fluorescein angiography (FFA). In this review, we summarise the literature on the clinical application of OCTA in nAMD. In particular, we have reviewed the published articles that have reported the sensitivity and specificity of OCTA in the diagnosis of nAMD, and those that have described and or correlated the morphological findings and compared them to dye-based angiography.",Perrott et al. reviewed strengths and limitations of an eye (retinal) imagining method for diagnosis of a condition affecting the central part of the retina (the macula). This degenerative condition may result in loss of central vision in older adults. Perrott et al. concluded that diagnostic accuracy depends on both method and equipment. ,pdf:https://www.nature.com/articles/s41433-018-0229-6.pdf; doi:https://doi.org/10.1038/s41433-018-0229-6; html:https://europepmc.org/articles/PMC6367454; pdf:https://europepmc.org/articles/PMC6367454?pdf=render; doi:https://doi.org/10.1038/s41433-018-0229-6
 33299071,https://doi.org/10.1038/s41746-020-00357-5,Belief of having had unconfirmed Covid-19 infection reduces willingness to participate in app-based contact tracing.,"Bachtiger P, Adamson A, Quint JK, Peters NS.",,NPJ digital medicine,2020,2020-11-06,Y,,,,"Contact tracing and lockdown are health policies being used worldwide to combat the coronavirus (COVID-19). The UK National Health Service (NHS) Track and Trace Service has plans for a nationwide app that notifies the need for self-isolation to those in contact with a person testing positive for COVID-19. To be successful, such an app will require high uptake, the determinants and willingness for which are unclear but essential to understand for effective public health benefit. The objective of this study was to measure the determinants of willingness to participate in an NHS app-based contact-tracing programme using a questionnaire within the Care Information Exchange (CIE)-the largest patient-facing electronic health record in the NHS. Among 47,708 registered NHS users of the CIE, 27% completed a questionnaire asking about willingness to participate in app-based contact tracing, understanding of government advice, mental and physical wellbeing and their healthcare utilisation-related or not to COVID-19. Descriptive statistics are reported alongside univariate and multivariable logistic regression models, with positive or negative responses to a question on app-based contact tracing as the dependent variable. 26.1% of all CIE participants were included in the analysis (N = 12,434, 43.0% male, mean age 55.2). 60.3% of respondents were willing to participate in app-based contact tracing. Out of those who responded 'no', 67.2% stated that this was due to privacy concerns. In univariate analysis, worsening mood, fear and anxiety in relation to changes in government rules around lockdown were associated with lower willingness to participate. Multivariable analysis showed that difficulty understanding government rules was associated with a decreased inclination to download the app, with those scoring 1-2 and 3-4 in their understanding of the new government rules being 45% and 27% less inclined to download the contact-tracing app, respectively; when compared to those who rated their understanding as 5-6/10 (OR for 1-2/10 = 0.57 [CI 0.48-0.67]; OR for 3-4/10 = 0.744 [CI 0.64-0.87]), whereas scores of 7-8 and 9-10 showed a 43% and 31% respective increase. Those reporting an unconfirmed belief of having previously had and recovered from COVID-19 were 27% less likely to be willing to download the app; belief of previous recovery from COVID-19 infection OR 0.727 [0.585-0.908]). In this large UK-wide questionnaire of wellbeing in lockdown, a willingness for app-based contact tracing over an appropriate age range is 60%-close to the estimated 56% population uptake, and substantially less than the smartphone-user uptake considered necessary for an app-based contact tracing to be an effective intervention to help suppress an epidemic. Difficulty comprehending government advice and uncertainty of diagnosis, based on a public health policy of not testing to confirm self-reported COVID-19 infection during lockdown, therefore reduce willingness to adopt a government contact-tracing app to a level below the threshold for effectiveness as a tool to suppress an epidemic.",,pdf:https://www.nature.com/articles/s41746-020-00357-5.pdf; doi:https://doi.org/10.1038/s41746-020-00357-5; html:https://europepmc.org/articles/PMC7648058; pdf:https://europepmc.org/articles/PMC7648058?pdf=render
-35849350,https://doi.org/10.1093/nar/gkac612,Whole-genome long-read TAPS deciphers DNA methylation patterns at base resolution using PacBio SMRT sequencing technology.,"Chen J, Cheng J, Chen X, Inoue M, Liu Y, Song CX.",,Nucleic acids research,2022,2022-10-01,Y,,,,"Long-read sequencing provides valuable information on difficult-to-map genomic regions, which can complement short-read sequencing to improve genome assembly, yet limited methods are available to accurately detect DNA methylation over long distances at a whole-genome scale. By combining our recently developed TET-assisted pyridine borane sequencing (TAPS) method, which enables direct detection of 5-methylcytosine and 5-hydroxymethylcytosine, with PacBio single-molecule real-time sequencing, we present here whole-genome long-read TAPS (wglrTAPS). To evaluate the performance of wglrTAPS, we applied it to mouse embryonic stem cells as a proof of concept, and an N50 read length of 3.5 kb is achieved. By sequencing wglrTAPS to 8.2× depth, we discovered a significant proportion of CpG sites that were not covered in previous 27.5× short-read TAPS. Our results demonstrate that wglrTAPS facilitates methylation profiling on problematic genomic regions with repetitive elements or structural variations, and also in an allelic manner, all of which are extremely difficult for short-read sequencing methods to resolve. This method therefore enhances applications of third-generation sequencing technologies for DNA epigenetics.",,pdf:https://academic.oup.com/nar/article-pdf/50/18/e104/46501243/gkac612.pdf; doi:https://doi.org/10.1093/nar/gkac612; html:https://europepmc.org/articles/PMC9561279; pdf:https://europepmc.org/articles/PMC9561279?pdf=render
 34173574,https://doi.org/10.1016/j.puhip.2020.100039,Schools and COVID-19: Reopening Pandora's box?,"Ziauddeen N, Woods-Townsend K, Saxena S, Gilbert R, Alwan NA.",,"Public health in practice (Oxford, England)",2020,2020-11-01,Y,Safety; Covid-19; School Re-Opening,,,"Schools in countries across the world are reopening as lockdown to slow progression of COVID-19 is eased. The UK government ordered school closures in England from March 20, 2020, later than the rest of Europe. A temporary and limited return for some year groups was trialled from June 2020. Teachers, school governors, the public and doctors have openly challenged the decision. The UK government has struggled to provide enough detailed information to convince the public, teachers and health practitioners, that effective systems for protection, including test, trace and isolate, are in place to prevent and manage outbreaks in schools. Risks of infection on reopening to children, staff and families must be weighed against the harms of closure to children's education and social development. The potential consequences, if the re-opening of schools is managed badly, is subsequent waves of COVID-19 infection leading to more deaths, further school closures and prolonged restrictions, losing any ground gained thus far. This article weighs the evidence for risks and benefits of reopening schools during the pandemic.",,doi:https://doi.org/10.1016/j.puhip.2020.100039; doi:https://doi.org/10.1016/j.puhip.2020.100039; html:https://europepmc.org/articles/PMC7486860; pdf:https://europepmc.org/articles/PMC7486860?pdf=render
+35849350,https://doi.org/10.1093/nar/gkac612,Whole-genome long-read TAPS deciphers DNA methylation patterns at base resolution using PacBio SMRT sequencing technology.,"Chen J, Cheng J, Chen X, Inoue M, Liu Y, Song CX.",,Nucleic acids research,2022,2022-10-01,Y,,,,"Long-read sequencing provides valuable information on difficult-to-map genomic regions, which can complement short-read sequencing to improve genome assembly, yet limited methods are available to accurately detect DNA methylation over long distances at a whole-genome scale. By combining our recently developed TET-assisted pyridine borane sequencing (TAPS) method, which enables direct detection of 5-methylcytosine and 5-hydroxymethylcytosine, with PacBio single-molecule real-time sequencing, we present here whole-genome long-read TAPS (wglrTAPS). To evaluate the performance of wglrTAPS, we applied it to mouse embryonic stem cells as a proof of concept, and an N50 read length of 3.5 kb is achieved. By sequencing wglrTAPS to 8.2× depth, we discovered a significant proportion of CpG sites that were not covered in previous 27.5× short-read TAPS. Our results demonstrate that wglrTAPS facilitates methylation profiling on problematic genomic regions with repetitive elements or structural variations, and also in an allelic manner, all of which are extremely difficult for short-read sequencing methods to resolve. This method therefore enhances applications of third-generation sequencing technologies for DNA epigenetics.",,pdf:https://academic.oup.com/nar/article-pdf/50/18/e104/46501243/gkac612.pdf; doi:https://doi.org/10.1093/nar/gkac612; html:https://europepmc.org/articles/PMC9561279; pdf:https://europepmc.org/articles/PMC9561279?pdf=render
 33407780,https://doi.org/10.1186/s13063-020-04951-6,Reporting guidelines for clinical trials of artificial intelligence interventions: the SPIRIT-AI and CONSORT-AI guidelines.,"Ibrahim H, Liu X, Rivera SC, Moher D, Chan AW, Sydes MR, Calvert MJ, Denniston AK.",,Trials,2021,2021-01-06,Y,Artificial intelligence; Checklist; RANDOMISED CONTROLLED TRIALS; Research Report; Clinical Trials; Guidelines; Research Design; Machine Learning,,,"<h4>Background</h4>The application of artificial intelligence (AI) in healthcare is an area of immense interest. The high profile of 'AI in health' means that there are unusually strong drivers to accelerate the introduction and implementation of innovative AI interventions, which may not be supported by the available evidence, and for which the usual systems of appraisal may not yet be sufficient.<h4>Main text</h4>We are beginning to see the emergence of randomised clinical trials evaluating AI interventions in real-world settings. It is imperative that these studies are conducted and reported to the highest standards to enable effective evaluation because they will potentially be a key part of the evidence that is used when deciding whether an AI intervention is sufficiently safe and effective to be approved and commissioned. Minimum reporting guidelines for clinical trial protocols and reports have been instrumental in improving the quality of clinical trials and promoting completeness and transparency of reporting for the evaluation of new health interventions. The current guidelines-SPIRIT and CONSORT-are suited to traditional health interventions but research has revealed that they do not adequately address potential sources of bias specific to AI systems. Examples of elements that require specific reporting include algorithm version and the procedure for acquiring input data. In response, the SPIRIT-AI and CONSORT-AI guidelines were developed by a multidisciplinary group of international experts using a consensus building methodological process. The extensions include a number of new items that should be reported in addition to the core items. Each item, where possible, was informed by challenges identified in existing studies of AI systems in health settings.<h4>Conclusion</h4>The SPIRIT-AI and CONSORT-AI guidelines provide the first international standards for clinical trials of AI systems. The guidelines are designed to ensure complete and transparent reporting of clinical trial protocols and reports involving AI interventions and have the potential to improve the quality of these clinical trials through improvements in their design and delivery. Their use will help to efficiently identify the safest and most effective AI interventions and commission them with confidence for the benefit of patients and the public.",,pdf:https://trialsjournal.biomedcentral.com/track/pdf/10.1186/s13063-020-04951-6; doi:https://doi.org/10.1186/s13063-020-04951-6; html:https://europepmc.org/articles/PMC7788716; pdf:https://europepmc.org/articles/PMC7788716?pdf=render
 37006331,https://doi.org/10.1093/braincomms/fcad041,Polygenic risk score prediction of multiple sclerosis in individuals of South Asian ancestry.,"Breedon JR, Marshall CR, Giovannoni G, van Heel DA, Genes & Health Research Team , Dobson R, Jacobs BM.",,Brain communications,2023,2023-02-22,Y,Genetics; Multiple sclerosis; Ethnicity,,,"Polygenic risk scores aggregate an individual's burden of risk alleles to estimate the overall genetic risk for a specific trait or disease. Polygenic risk scores derived from genome-wide association studies of European populations perform poorly for other ancestral groups. Given the potential for future clinical utility, underperformance of polygenic risk scores in South Asian populations has the potential to reinforce health inequalities. To determine whether European-derived polygenic risk scores underperform at multiple sclerosis prediction in a South Asian-ancestry population compared with a European-ancestry cohort, we used data from two longitudinal genetic cohort studies: Genes & Health (2015-present), a study of ∼50 000 British-Bangladeshi and British-Pakistani individuals, and UK Biobank (2006-present), which is comprised of ∼500 000 predominantly White British individuals. We compared individuals with and without multiple sclerosis in both studies (Genes & Health: <i>N</i> <sub>Cases</sub> = 42, <i>N</i> <sub>Control</sub> = 40 490; UK Biobank: <i>N</i> <sub>Cases</sub> = 2091, <i>N</i> <sub>Control</sub> = 374 866). Polygenic risk scores were calculated using clumping and thresholding with risk allele effect sizes obtained from the largest multiple sclerosis genome-wide association study to date. Scores were calculated with and without the major histocompatibility complex region, the most influential locus in determining multiple sclerosis risk. Polygenic risk score prediction was evaluated using Nagelkerke's pseudo-<i>R</i> <sup>2</sup> metric adjusted for case ascertainment, age, sex and the first four genetic principal components. We found that, as expected, European-derived polygenic risk scores perform poorly in the Genes & Health cohort, explaining 1.1% (including the major histocompatibility complex) and 1.5% (excluding the major histocompatibility complex) of disease risk. In contrast, multiple sclerosis polygenic risk scores explained 4.8% (including the major histocompatibility complex) and 2.8% (excluding the major histocompatibility complex) of disease risk in European-ancestry UK Biobank participants. These findings suggest that polygenic risk score prediction of multiple sclerosis based on European genome-wide association study results is less accurate in a South Asian population. Genetic studies of ancestrally diverse populations are required to ensure that polygenic risk scores can be useful across ancestries.",,pdf:https://academic.oup.com/braincomms/article-pdf/5/2/fcad041/49521070/fcad041.pdf; doi:https://doi.org/10.1093/braincomms/fcad041; html:https://europepmc.org/articles/PMC10053643; pdf:https://europepmc.org/articles/PMC10053643?pdf=render
 33905882,https://doi.org/10.1016/j.media.2021.102050,Phenotype discovery from population brain imaging.,"Gong W, Beckmann CF, Smith SM.",,Medical image analysis,2021,2021-03-31,Y,Neuroimaging; Uk Biobank; Behaviour Prediction; Multimodal Independent Component Analysis; Phenotype Discovery,,,"Neuroimaging allows for the non-invasive study of the brain in rich detail. Data-driven discovery of patterns of population variability in the brain has the potential to be extremely valuable for early disease diagnosis and understanding the brain. The resulting patterns can be used as imaging-derived phenotypes (IDPs), and may complement existing expert-curated IDPs. However, population datasets, comprising many different structural and functional imaging modalities from thousands of subjects, provide a computational challenge not previously addressed. Here, for the first time, a multimodal independent component analysis approach is presented that is scalable for data fusion of voxel-level neuroimaging data in the full UK Biobank (UKB) dataset, that will soon reach 100,000 imaged subjects. This new computational approach can estimate modes of population variability that enhance the ability to predict thousands of phenotypic and behavioural variables using data from UKB and the Human Connectome Project. A high-dimensional decomposition achieved improved predictive power compared with widely-used analysis strategies, single-modality decompositions and existing IDPs. In UKB data (14,503 subjects with 47 different data modalities), many interpretable associations with non-imaging phenotypes were identified, including multimodal spatial maps related to fluid intelligence, handedness and disease, in some cases where IDP-based approaches failed.",,doi:https://doi.org/10.1016/j.media.2021.102050; doi:https://doi.org/10.1016/j.media.2021.102050; html:https://europepmc.org/articles/PMC8850869; pdf:https://europepmc.org/articles/PMC8850869?pdf=render
@@ -2219,37 +2221,37 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 30351417,https://doi.org/10.1093/bioinformatics/bty837,pJRES Binning Algorithm (JBA): a new method to facilitate the recovery of metabolic information from pJRES 1H NMR spectra.,"Rodriguez-Martinez A, Ayala R, Posma JM, Harvey N, Jiménez B, Sonomura K, Sato TA, Matsuda F, Zalloua P, Gauguier D, Nicholson JK, Dumas ME.",,"Bioinformatics (Oxford, England)",2019,2019-06-01,Y,,Applied Analytics,,"<h4>Motivation</h4>Data processing is a key bottleneck for 1H NMR-based metabolic profiling of complex biological mixtures, such as biofluids. These spectra typically contain several thousands of signals, corresponding to possibly few hundreds of metabolites. A number of binning-based methods have been proposed to reduce the dimensionality of 1 D 1H NMR datasets, including statistical recoupling of variables (SRV). Here, we introduce a new binning method, named JBA (""pJRES Binning Algorithm""), which aims to extend the applicability of SRV to pJRES spectra.<h4>Results</h4>The performance of JBA is comprehensively evaluated using 617 plasma 1H NMR spectra from the FGENTCARD cohort. The results presented here show that JBA exhibits higher sensitivity than SRV to detect peaks from low-abundance metabolites. In addition, JBA allows a more efficient removal of spectral variables corresponding to pure electronic noise, and this has a positive impact on multivariate model building.<h4>Availability and implementation</h4>The algorithm is implemented using the MWASTools R/Bioconductor package.<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online.",,pdf:https://academic.oup.com/bioinformatics/article-pdf/35/11/1916/28759353/bty837.pdf; doi:https://doi.org/10.1093/bioinformatics/bty837; html:https://europepmc.org/articles/PMC6546129; pdf:https://europepmc.org/articles/PMC6546129?pdf=render
 34095526,https://doi.org/10.23889/ijpds.v4i1.579,Record linkage to enhance consented cohort and routinely collected health data from a UK birth cohort.,"Tingay KS, Bandyopadhyay A, Griffiths L, Akbari A, Brophy S, Bedford H, Cortina-Borja M, Setakis E, Walton S, Fitzsimons E, Dezateux C, Lyons RA.",,International journal of population data science,2019,2019-04-02,Y,,,,"<h4>Background</h4>In longitudinal health research, combining the richness of cohort data to the extensiveness of routine data opens up new possibilities, providing information not available from one data source alone. In this study, we set out to extend information from a longitudinal birth cohort study by linking to the cohort child's routine primary and secondary health care data. The resulting linked datasets will be used to examine health outcomes and patterns of health service utilisation for a set of common childhood health problems. We describe the experiences and challenges of acquiring and linking electronic health records for participants in a national longitudinal study, the UK Millennium Cohort Study (MCS).<h4>Method</h4>Written parental consent to link routine health data to survey responses of the MCS cohort member, mother and her partner was obtained for 90.7% of respondents when interviews took place at age seven years in the MCS. Probabilistic and deterministic linkage was used to link MCS cohort members to multiple routinely-collected health data sources in Wales and Scotland.<h4>Results</h4>Overall linkage rates for the consented population using country-specific health service data sources were 97.6% for Scotland and 99.9% for Wales. Linkage rates between different health data sources ranged from 65.3% to 99.6%. Issues relating to acquisition and linkage of data sources are discussed.<h4>Conclusions</h4>Linking longitudinal cohort participants with routine data sources is becoming increasingly popular in population data research. Our results suggest that this is a valid method to enhance information held in both sources of data.",,doi:https://doi.org/10.23889/ijpds.v4i1.579; doi:https://doi.org/10.23889/ijpds.v4i1.579; html:https://europepmc.org/articles/PMC8142967; pdf:https://europepmc.org/articles/PMC8142967?pdf=render
 34910136,https://doi.org/10.1093/eurheartj/ehab863,Long-term safety and efficacy of anacetrapib in patients with atherosclerotic vascular disease.,"HPS3/TIMI55-REVEAL Collaborative Group, Writing Committee, Sammons E, Hopewell JC, Chen F, Stevens W, Wallendszus K, Valdes-Marquez E, Dayanandan R, Knott C, Murphy K, Wincott E, Baxter A, Goodenough R, Lay M, Hill M, Macdonnell S, Fabbri G, Lucci D, Fajardo-Moser M, Brenner S, Hao D, Zhang H, Liu J, Wuhan B, Mosegaard S, Herrington W, Wanner C, Angermann C, Ertl G, Maggioni A, Barter P, Mihaylova B, Mitchel Y, Blaustein R, Goto S, Tobert J, DeLucca P, Chen Y, Chen Z, Gray A, Haynes R, Armitage J, Baigent C, Wiviott S, Cannon C, Braunwald E, Collins R, Bowman L, Landray M, REVEAL Collaborative Group.",,European heart journal,2022,2022-04-01,Y,Randomized Trial; Cetp Inhibitor Therapy,,,"<h4>Aims</h4>REVEAL was the first randomized controlled trial to demonstrate that adding cholesteryl ester transfer protein inhibitor therapy to intensive statin therapy reduced the risk of major coronary events. We now report results from extended follow-up beyond the scheduled study treatment period.<h4>Methods and results</h4>A total of 30 449 adults with prior atherosclerotic vascular disease were randomly allocated to anacetrapib 100 mg daily or matching placebo, in addition to open-label atorvastatin therapy. After stopping the randomly allocated treatment, 26 129 survivors entered a post-trial follow-up period, blind to their original treatment allocation. The primary outcome was first post-randomization major coronary event (i.e. coronary death, myocardial infarction, or coronary revascularization) during the in-trial and post-trial treatment periods, with analysis by intention-to-treat. Allocation to anacetrapib conferred a 9% [95% confidence interval (CI) 3-15%; P = 0.004] proportional reduction in the incidence of major coronary events during the study treatment period (median 4.1 years). During extended follow-up (median 2.2 years), there was a further 20% (95% CI 10-29%; P < 0.001) reduction. Overall, there was a 12% (95% CI 7-17%, P < 0.001) proportional reduction in major coronary events during the overall follow-up period (median 6.3 years), corresponding to a 1.8% (95% CI 1.0-2.6%) absolute reduction. There were no significant effects on non-vascular mortality, site-specific cancer, or other serious adverse events. Morbidity follow-up was obtained for 25 784 (99%) participants.<h4>Conclusion</h4>The beneficial effects of anacetrapib on major coronary events increased with longer follow-up, and no adverse effects emerged on non-vascular mortality or morbidity. These findings illustrate the importance of sufficiently long treatment and follow-up duration in randomized trials of lipid-modifying agents to assess their full benefits and potential harms.<h4>Trial registration</h4>International Standard Randomized Controlled Trial Number (ISRCTN) 48678192; ClinicalTrials.gov No. NCT01252953; EudraCT No. 2010-023467-18.",,pdf:https://academic.oup.com/eurheartj/article-pdf/43/14/1416/43292041/ehab863.pdf; doi:https://doi.org/10.1093/eurheartj/ehab863; html:https://europepmc.org/articles/PMC8986460; pdf:https://europepmc.org/articles/PMC8986460?pdf=render
-39365172,https://doi.org/10.1093/eurjpc/zwae315,Association of circulating fatty acids with cardiovascular disease risk: Analysis of individual-level data in three large prospective cohorts and updated meta-analysis.,"Shi F, Chowdhury R, Sofianopoulou E, Koulman A, Sun L, Steur M, Aleksandrova K, Dahm CC, Schulze MB, van der Schouw YT, Agnoli C, Amiano P, Boer JMA, Bork CS, Cabrera-Castro N, Eichelmann F, Elbaz A, Farràs M, Heath AK, Kaaks R, Katzke V, Keski-Rahkonen P, Masala G, Moreno-Iribas C, Panico S, Papier K, Petrova D, Quirós JR, Ricceri F, Severi G, Tjønneland A, Tong TYN, Tumino R, Wareham N, Weiderpass E, Di Angelantonio E, Forouhi N, Danesh J, Butterworth AS, Kaptoge S.",,European journal of preventive cardiology,2024,2024-10-04,N,,,,"<h4>Background</h4>Associations of saturated and unsaturated fatty acids (FAs) with cardiovascular disease (CVD) remain controversial. We therefore aimed to investigate the prospective associations of objectively measured FAs with CVD, including incident coronary heart disease (CHD) and stroke, as well as CVD mortality.<h4>Methods</h4>Circulating FA concentrations expressed as the percentage of total FAs were assayed in 172,891 participants without prior vascular disease at baseline from the European Prospective Investigation into Cancer and Nutrition-CVD (EPIC-CVD) (7,343 CHD; 6,499 stroke), UK Biobank (1,825; 1,474), and INTERVAL (285; 209) cohort studies. Hazard ratio (HR) per 1-standard deviation (SD) higher FA concentrations was estimated using Cox regression models and pooled by random-effects meta-analysis. Systematic reviews with meta-analysis published by 6 May 2023 on associations between FAs and CVDs were systematically searched and updated meta-analyses using random-effects model were conducted. Evidence from randomized controlled trials (RCTs) was also summarized.<h4>Results</h4>Higher concentrations of total saturated FAs (SFAs) were associated with higher cardiovascular risks in the combined analysis, with differential findings noted for SFA subtypes in further analysis restricted to EPIC-CVD: positive associations for even-chain SFA [HR for CHD 1.24 (95% CI: 1.18-1.32); stroke 1.23 (1.10-1.38)] and negative associations for odd-chain [0.82 (0.76-0.87); 0.73 (0.67-0.78)] and longer-chain [0.95 (0.80-1.12); 0.84 (0.72-0.99)] SFA. In the combined analysis, total n-3 polyunsaturated FA (PUFA) [0.91 (0.85-0.97)], including docosahexaenoic acid (DHA) [0.91 (0.84-0.98)], was negatively associated with incident CHD risk. Similarly, total n-6 PUFA [0.94 (0.91-0.98)], including linoleic acid (LA) [0.89 (0.83-0.95)], was negatively associated with incident stroke risk. By contrast, more detailed analyses in EPIC-CVD revealed that several downstream n-6 PUFAs of LA were positively associated with CHD risk. Updated meta-analyses of 37 FAs including 49 non-overlapping studies, involving between 7,787 to 22,802 CHD and 6,499 to 14,221 stroke cases, showed broadly similar results as our combined empirical analysis and further suggested significant inverse associations of individual long-chain n-3 PUFAs and LA on both CHD and stroke. The findings of long-chain n-3 PUFAs were consistent with those from published RCTs on CHD despite insufficient evidence in monotherapy, while RCT evidence remained unclear for the rest of the explored FAs.<h4>Conclusions</h4>Our study provides an overview of the most recent evidence on the associations between objectively measured FAs and CVD outcomes. Collectively, the data reveals notable differences in associations by SFA subtypes and calls for further studies, especially RCTs, to explore these links.",,doi:https://doi.org/10.1093/eurjpc/zwae315
 34555069,https://doi.org/10.1371/journal.pone.0257361,Predicting fracture outcomes from clinical registry data using artificial intelligence supplemented models for evidence-informed treatment (PRAISE) study protocol.,"Dipnall JF, Page R, Du L, Costa M, Lyons RA, Cameron P, de Steiger R, Hau R, Bucknill A, Oppy A, Edwards E, Varma D, Jung MC, Gabbe BJ.",,PloS one,2021,2021-09-23,Y,,,,"<h4>Background</h4>Distal radius (wrist) fractures are the second most common fracture admitted to hospital. The anatomical pattern of these types of injuries is diverse, with variation in clinical management, guidelines for management remain inconclusive, and the uptake of findings from clinical trials into routine practice limited. Robust predictive modelling, which considers both the characteristics of the fracture and patient, provides the best opportunity to reduce variation in care and improve patient outcomes. This type of data is housed in unstructured data sources with no particular format or schema. The ""Predicting fracture outcomes from clinical Registry data using Artificial Intelligence (AI) Supplemented models for Evidence-informed treatment (PRAISE)"" study aims to use AI methods on unstructured data to describe the fracture characteristics and test if using this information improves identification of key fracture characteristics and prediction of patient-reported outcome measures and clinical outcomes following wrist fractures compared to prediction models based on standard registry data.<h4>Methods and design</h4>Adult (16+ years) patients presenting to the emergency department, treated in a short stay unit, or admitted to hospital for >24h for management of a wrist fracture in four Victorian hospitals will be included in this study. The study will use routine registry data from the Victorian Orthopaedic Trauma Outcomes Registry (VOTOR), and electronic medical record (EMR) information (e.g. X-rays, surgical reports, radiology reports, images). A multimodal deep learning fracture reasoning system (DLFRS) will be developed that reasons on EMR information. Machine learning prediction models will test the performance with/without output from the DLFRS.<h4>Discussion</h4>The PRAISE study will establish the use of AI techniques to provide enhanced information about fracture characteristics in people with wrist fractures. Prediction models using AI derived characteristics are expected to provide better prediction of clinical and patient-reported outcomes following distal radius fracture.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0257361&type=printable; doi:https://doi.org/10.1371/journal.pone.0257361; html:https://europepmc.org/articles/PMC8460020; pdf:https://europepmc.org/articles/PMC8460020?pdf=render
+39365172,https://doi.org/10.1093/eurjpc/zwae315,Association of circulating fatty acids with cardiovascular disease risk: Analysis of individual-level data in three large prospective cohorts and updated meta-analysis.,"Shi F, Chowdhury R, Sofianopoulou E, Koulman A, Sun L, Steur M, Aleksandrova K, Dahm CC, Schulze MB, van der Schouw YT, Agnoli C, Amiano P, Boer JMA, Bork CS, Cabrera-Castro N, Eichelmann F, Elbaz A, Farràs M, Heath AK, Kaaks R, Katzke V, Keski-Rahkonen P, Masala G, Moreno-Iribas C, Panico S, Papier K, Petrova D, Quirós JR, Ricceri F, Severi G, Tjønneland A, Tong TYN, Tumino R, Wareham N, Weiderpass E, Di Angelantonio E, Forouhi N, Danesh J, Butterworth AS, Kaptoge S.",,European journal of preventive cardiology,2024,2024-10-04,N,,,,"<h4>Background</h4>Associations of saturated and unsaturated fatty acids (FAs) with cardiovascular disease (CVD) remain controversial. We therefore aimed to investigate the prospective associations of objectively measured FAs with CVD, including incident coronary heart disease (CHD) and stroke, as well as CVD mortality.<h4>Methods</h4>Circulating FA concentrations expressed as the percentage of total FAs were assayed in 172,891 participants without prior vascular disease at baseline from the European Prospective Investigation into Cancer and Nutrition-CVD (EPIC-CVD) (7,343 CHD; 6,499 stroke), UK Biobank (1,825; 1,474), and INTERVAL (285; 209) cohort studies. Hazard ratio (HR) per 1-standard deviation (SD) higher FA concentrations was estimated using Cox regression models and pooled by random-effects meta-analysis. Systematic reviews with meta-analysis published by 6 May 2023 on associations between FAs and CVDs were systematically searched and updated meta-analyses using random-effects model were conducted. Evidence from randomized controlled trials (RCTs) was also summarized.<h4>Results</h4>Higher concentrations of total saturated FAs (SFAs) were associated with higher cardiovascular risks in the combined analysis, with differential findings noted for SFA subtypes in further analysis restricted to EPIC-CVD: positive associations for even-chain SFA [HR for CHD 1.24 (95% CI: 1.18-1.32); stroke 1.23 (1.10-1.38)] and negative associations for odd-chain [0.82 (0.76-0.87); 0.73 (0.67-0.78)] and longer-chain [0.95 (0.80-1.12); 0.84 (0.72-0.99)] SFA. In the combined analysis, total n-3 polyunsaturated FA (PUFA) [0.91 (0.85-0.97)], including docosahexaenoic acid (DHA) [0.91 (0.84-0.98)], was negatively associated with incident CHD risk. Similarly, total n-6 PUFA [0.94 (0.91-0.98)], including linoleic acid (LA) [0.89 (0.83-0.95)], was negatively associated with incident stroke risk. By contrast, more detailed analyses in EPIC-CVD revealed that several downstream n-6 PUFAs of LA were positively associated with CHD risk. Updated meta-analyses of 37 FAs including 49 non-overlapping studies, involving between 7,787 to 22,802 CHD and 6,499 to 14,221 stroke cases, showed broadly similar results as our combined empirical analysis and further suggested significant inverse associations of individual long-chain n-3 PUFAs and LA on both CHD and stroke. The findings of long-chain n-3 PUFAs were consistent with those from published RCTs on CHD despite insufficient evidence in monotherapy, while RCT evidence remained unclear for the rest of the explored FAs.<h4>Conclusions</h4>Our study provides an overview of the most recent evidence on the associations between objectively measured FAs and CVD outcomes. Collectively, the data reveals notable differences in associations by SFA subtypes and calls for further studies, especially RCTs, to explore these links.",,doi:https://doi.org/10.1093/eurjpc/zwae315
 35380004,https://doi.org/10.1042/bcj20220105,Development of a colorimetric assay for the detection of SARS-CoV-2 3CLpro activity.,"Garland GD, Harvey RF, Mulroney TE, Monti M, Fuller S, Haigh R, Gerber PP, Barer MR, Matheson NJ, Willis AE.",,The Biochemical journal,2022,2022-04-01,Y,Coronavirus; Assay Development; Covid 19,,,"Diagnostic testing continues to be an integral component of the strategy to contain the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) global pandemic, the causative agent of Coronavirus Disease 2019 (COVID-19). The SARS-CoV-2 genome encodes the 3C-like protease (3CLpro) which is essential for coronavirus replication. This study adapts an in vitro colorimetric gold nanoparticle (AuNP) based protease assay to specifically detect the activity of SARS-CoV-2 3CLpro as a purified recombinant protein and as a cellular protein exogenously expressed in HEK293T human cells. We also demonstrate that the specific sensitivity of the assay for SARS-CoV-2 3CLpro can be improved by use of an optimised peptide substrate and through hybrid dimerisation with inactive 3CLpro mutant monomers. These findings highlight the potential for further development of the AuNP protease assay to detect SARS-CoV-2 3CLpro activity as a novel, accessible and cost-effective diagnostic test for SARS-CoV-2 infection at the point-of-care. Importantly, this versatile assay could also be easily adapted to detect specific protease activity associated with other viruses or diseases conditions.",,pdf:https://portlandpress.com/biochemj/article-pdf/479/8/901/932114/bcj-2022-0105.pdf; doi:https://doi.org/10.1042/BCJ20220105; html:https://europepmc.org/articles/PMC9162461; pdf:https://europepmc.org/articles/PMC9162461?pdf=render
 34767555,https://doi.org/10.1371/journal.pmed.1003832,Educational and health outcomes of schoolchildren in local authority care in Scotland: A retrospective record linkage study.,"Fleming M, McLay JS, Clark D, King A, Mackay DF, Minnis H, Pell JP.",,PLoS medicine,2021,2021-11-12,Y,,,,"<h4>Background</h4>Looked after children are defined as children who are in the care of their local authority. Previous studies have reported that looked after children have poorer mental and physical health, increased behavioural problems, and increased self-harm and mortality compared to peers. They also experience poorer educational outcomes, yet population-wide research into the latter is lacking, particularly in the United Kingdom. Education and health share a bidirectional relationship; therefore, it is important to dually investigate both outcomes. Our study aimed to compare educational and health outcomes for looked after children with peers, adjusting for sociodemographic, maternity, and comorbidity confounders.<h4>Methods and findings</h4>Linkage of 9 Scotland-wide databases, covering dispensed prescriptions, hospital admissions, maternity records, death certificates, annual pupil census, examinations, school absences/exclusions, unemployment, and looked after children provided retrospective data on 715,111 children attending Scottish schools between 2009 and 2012 (13,898 [1.9%] looked after). Compared to peers, 13,898 (1.9%) looked after children were more likely to be absent (adjusted incidence rate ratio [AIRR] 1.27, 95% confidence interval [CI] 1.24 to 1.30) and excluded (AIRR 4.09, 95% CI 3.86 to 4.33) from school, have special educational need (SEN; adjusted odds ratio [AOR] 3.48, 95% CI 3.35 to 3.62) and neurodevelopmental multimorbidity (AOR 2.45, 95% CI 2.34 to 2.57), achieve the lowest level of academic attainment (AOR 5.92, 95% CI 5.17 to 6.78), and be unemployed after leaving school (AOR 2.12, 95% CI 1.96 to 2.29). They were more likely to require treatment for epilepsy (AOR 1.50, 95% CI 1.27 to 1.78), attention deficit hyperactivity disorder (ADHD; AOR 3.01, 95% CI 2.76 to 3.27), and depression (AOR 1.90, 95% CI 1.62 to 2.22), be hospitalised overall (adjusted hazard ratio [AHR] 1.23, 95% CI 1.19 to 1.28) for injury (AHR 1.80, 95% CI 1.69 to 1.91) and self-harm (AHR 5.19, 95% CI 4.66 to 5.78), and die prematurely (AHR 3.21, 95% CI 2.16 to 4.77). Compared to children looked after at home, children looked after away from home had less absenteeism (AIRR 0.35, 95% CI 0.33 to 0.36), less exclusion (AIRR 0.63, 95% CI 0.56 to 0.71), less unemployment (AOR 0.53, 95% CI 0.46 to 0.62), and better attainment (AIRR 0.31, 95% CI 0.23 to 0.40). Therefore, among those in care, being cared for away from home appeared to be a protective factor resulting in better educational outcomes. The main limitations of this study were lack of data on local authority care preschool or before 2009, total time spent in care, and age of first contact with social care.<h4>Conclusions</h4>Looked after children had poorer health and educational outcomes than peers independent of increased neurodevelopmental conditions and SEN. Further work is required to understand whether poorer outcomes relate to reasons for entering care, including maltreatment and adverse childhood events, neurodevelopmental vulnerabilities, or characteristics of the care system.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003832&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003832; html:https://europepmc.org/articles/PMC8589203; pdf:https://europepmc.org/articles/PMC8589203?pdf=render
 36998408,https://doi.org/10.3389/fmicb.2023.1070340,A longitudinal study reveals persistence of antimicrobial resistance on livestock farms is not due to antimicrobial usage alone.,"Smith RP, May HE, AbuOun M, Stubberfield E, Gilson D, Chau KK, Crook DW, Shaw LP, Read DS, Stoesser N, Vilar MJ, Anjum MF.",,Frontiers in microbiology,2023,2023-03-14,Y,Sheep; Cattle; Pigs; Antimicrobial resistance; Longitudinal; Antimicrobial Usage,,,"<h4>Introduction</h4>There are concerns that antimicrobial usage (AMU) is driving an increase in multi-drug resistant (MDR) bacteria so treatment of microbial infections is becoming harder in humans and animals. The aim of this study was to evaluate factors, including usage, that affect antimicrobial resistance (AMR) on farm over time.<h4>Methods</h4>A population of 14 cattle, sheep and pig farms within a defined area of England were sampled three times over a year to collect data on AMR in faecal Enterobacterales flora; AMU; and husbandry or management practices. Ten pooled samples were collected at each visit, with each comprising of 10 pinches of fresh faeces. Up to 14 isolates per visit were whole genome sequenced to determine presence of AMR genes.<h4>Results</h4>Sheep farms had very low AMU in comparison to the other species and very few sheep isolates were genotypically resistant at any time point. AMR genes were detected persistently across pig farms at all visits, even on farms with low AMU, whereas AMR bacteria was consistently lower on cattle farms than pigs, even for those with comparably high AMU. MDR bacteria was also more commonly detected on pig farms than any other livestock species.<h4>Discussion</h4>The results may be explained by a complex combination of factors on pig farms including historic AMU; co-selection of AMR bacteria; variation in amounts of antimicrobials used between visits; potential persistence in environmental reservoirs of AMR bacteria; or importation of pigs with AMR microbiota from supplying farms. Pig farms may also be at increased risk of AMR due to the greater use of oral routes of group antimicrobial treatment, which were less targeted than cattle treatments; the latter mostly administered to individual animals. Also, farms which exhibited either increasing or decreasing trends of AMR across the study did not have corresponding trends in their AMU. Therefore, our results suggest that factors other than AMU on individual farms are important for persistence of AMR bacteria on farms, which may be operating at the farm and livestock species level.",,pdf:https://www.frontiersin.org/articles/10.3389/fmicb.2023.1070340/pdf; doi:https://doi.org/10.3389/fmicb.2023.1070340; html:https://europepmc.org/articles/PMC10043416; pdf:https://europepmc.org/articles/PMC10043416?pdf=render
 33782396,https://doi.org/10.1038/s41467-021-22213-0,Implications of the school-household network structure on SARS-CoV-2 transmission under school reopening strategies in England.,"Munday JD, Sherratt K, Meakin S, Endo A, Pearson CAB, Hellewell J, Abbott S, Bosse NI, CMMID COVID-19 Working Group, Atkins KE, Wallinga J, Edmunds WJ, van Hoek AJ, Funk S.",,Nature communications,2021,2021-03-29,Y,,,,"In early 2020 many countries closed schools to mitigate the spread of SARS-CoV-2. Since then, governments have sought to relax the closures, engendering a need to understand associated risks. Using address records, we construct a network of schools in England connected through pupils who share households. We evaluate the risk of transmission between schools under different reopening scenarios. We show that whilst reopening select year-groups causes low risk of large-scale transmission, reopening secondary schools could result in outbreaks affecting up to 2.5 million households if unmitigated, highlighting the importance of careful monitoring and within-school infection control to avoid further school closures or other restrictions.",,pdf:https://www.nature.com/articles/s41467-021-22213-0.pdf; doi:https://doi.org/10.1038/s41467-021-22213-0; html:https://europepmc.org/articles/PMC8007691; pdf:https://europepmc.org/articles/PMC8007691?pdf=render
+33829489,https://doi.org/10.1111/bjd.20140,Defining trajectories of response in patients with psoriasis treated with biologic therapies.,"Geifman N, Azadbakht N, Zeng J, Wilkinson T, Dand N, Buchan I, Stocken D, Di Meglio P, Warren RB, Barker JN, Reynolds NJ, Barnes MR, Smith CH, Griffiths CEM, Peek N, BADBIR Study Group, on behalf of the PSORT Consortium.",,The British journal of dermatology,2021,2021-06-04,N,,,,"<h4>Background</h4>The effectiveness and cost-effectiveness of biologic therapies for psoriasis are significantly compromised by variable treatment responses. Thus, more precise management of psoriasis is needed.<h4>Objectives</h4>To identify subgroups of patients with psoriasis treated with biologic therapies, based on changes in their disease activity over time, that may better inform patient management.<h4>Methods</h4>We applied latent class mixed modelling to identify trajectory-based patient subgroups from longitudinal, routine clinical data on disease severity, as measured by the Psoriasis Area and Severity Index (PASI), from 3546 patients in the British Association of Dermatologists Biologics and Immunomodulators Register, as well as in an independent cohort of 2889 patients pooled across four clinical trials.<h4>Results</h4>We discovered four discrete classes of global response trajectories, each characterized in terms of time to response, size of effect and relapse. Each class was associated with differing clinical characteristics, e.g. body mass index, baseline PASI and prevalence of different manifestations. The results were verified in a second cohort of clinical trial participants, where similar trajectories following the initiation of biologic therapy were identified. Further, we found differential associations of the genetic marker HLA-C*06:02 between our registry-identified trajectories.<h4>Conclusions</h4>These subgroups, defined by change in disease over time, may be indicative of distinct endotypes driven by different biological mechanisms and may help inform the management of patients with psoriasis. Future work will aim to further delineate these mechanisms by extensively characterizing the subgroups with additional molecular and pharmacological data.",,doi:https://doi.org/10.1111/bjd.20140
 38381822,https://doi.org/10.1126/sciadv.adi9379,"Spontaneous, persistent, T cell-dependent IFN-γ release in patients who progress to Long Covid.","Krishna BA, Lim EY, Metaxaki M, Jackson S, Mactavous L, NIHR BioResource, Lyons PA, Doffinger R, Bradley JR, Smith KGC, Sinclair J, Matheson NJ, Lehner PJ, Sithole N, Wills MR.",,Science advances,2024,2024-02-21,Y,,,,"After acute infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a proportion of patients experience persistent symptoms beyond 12 weeks, termed Long Covid. Understanding the mechanisms that cause this debilitating disease and identifying biomarkers for diagnostic, therapeutic, and monitoring purposes are urgently required. We detected persistently high levels of interferon-γ (IFN-γ) from peripheral blood mononuclear cells of patients with Long Covid using highly sensitive FluoroSpot assays. This IFN-γ release was seen in the absence of ex vivo peptide stimulation and remains persistently elevated in patients with Long Covid, unlike the resolution seen in patients recovering from acute SARS-CoV-2 infection. The IFN-γ release was CD8<sup>+</sup> T cell-mediated and dependent on antigen presentation by CD14<sup>+</sup> cells. Longitudinal follow-up of our study cohort showed that symptom improvement and resolution correlated with a decrease in IFN-γ production to baseline levels. Our study highlights a potential mechanism underlying Long Covid, enabling the search for biomarkers and therapeutics in patients with Long Covid.",,pdf:https://www.science.org/doi/pdf/10.1126/sciadv.adi9379?download=true; doi:https://doi.org/10.1126/sciadv.adi9379; html:https://europepmc.org/articles/PMC10881041; pdf:https://europepmc.org/articles/PMC10881041?pdf=render
 36962800,https://doi.org/10.1371/journal.pgph.0000843,Effect of the COVID-19 pandemic on health service utilization across regions of Ethiopia: An interrupted time series analysis of health information system data from 2019-2020.,"Mebratie AD, Nega A, Gage A, Mariam DH, Eshetu MK, Arsenault C.",,PLOS global public health,2022,2022-09-12,Y,,,,"The spread of COVID-19 and associated deaths have remained low in Ethiopia. However, the pandemic could pose a public health crisis indirectly through disruptions in essential health services. The aim of this study was to examine disruptions in health service utilization during the first nine months of the COVID-19 pandemic across 10 regions in Ethiopia. We analyzed utilization of 21 different health services across all of Ethiopia (except the Tigray region) for the period of January 2019 to December 2020. Data were extracted from the Ethiopian district health information system (DHIS2). Monthly visits in 2020 were graphed relative to the same months in 2019. Interrupted time series analysis was used to estimate the effect of the pandemic on service utilization in each region. We found that disruptions in health services were generally higher in urban regions which were most affected by COVID. Outpatient visits declined by 52%, 54%, and 58%, specifically in Dire Dawa, Addis Ababa and Harari, the three urban regions. Similarly, there was a 47% reduction in inpatient admissions in Addis Ababa. In agrarian regions, the pandemic caused an 11% to 17% reduction in outpatient visits and a 10% to 27% decline in inpatient admissions. Visits for children with diarrhea, pneumonia and malnutrition also declined substantially while maternal health services were less affected. Our study indicates that disruptions in health services were more pronounced in areas that were relatively harder hit by the pandemic. Our results show that the Ethiopian health system has a limited capacity to absorb shocks. During future waves of COVID or future pandemics, the Ethiopian health system must be better prepared to maintain essential services and mitigate the indirect impact of the pandemic on public health, particularly in urban areas.",,pdf:https://journals.plos.org/globalpublichealth/article/file?id=10.1371/journal.pgph.0000843&type=printable; doi:https://doi.org/10.1371/journal.pgph.0000843; html:https://europepmc.org/articles/PMC10021875; pdf:https://europepmc.org/articles/PMC10021875?pdf=render
-33829489,https://doi.org/10.1111/bjd.20140,Defining trajectories of response in patients with psoriasis treated with biologic therapies.,"Geifman N, Azadbakht N, Zeng J, Wilkinson T, Dand N, Buchan I, Stocken D, Di Meglio P, Warren RB, Barker JN, Reynolds NJ, Barnes MR, Smith CH, Griffiths CEM, Peek N, BADBIR Study Group, on behalf of the PSORT Consortium.",,The British journal of dermatology,2021,2021-06-04,N,,,,"<h4>Background</h4>The effectiveness and cost-effectiveness of biologic therapies for psoriasis are significantly compromised by variable treatment responses. Thus, more precise management of psoriasis is needed.<h4>Objectives</h4>To identify subgroups of patients with psoriasis treated with biologic therapies, based on changes in their disease activity over time, that may better inform patient management.<h4>Methods</h4>We applied latent class mixed modelling to identify trajectory-based patient subgroups from longitudinal, routine clinical data on disease severity, as measured by the Psoriasis Area and Severity Index (PASI), from 3546 patients in the British Association of Dermatologists Biologics and Immunomodulators Register, as well as in an independent cohort of 2889 patients pooled across four clinical trials.<h4>Results</h4>We discovered four discrete classes of global response trajectories, each characterized in terms of time to response, size of effect and relapse. Each class was associated with differing clinical characteristics, e.g. body mass index, baseline PASI and prevalence of different manifestations. The results were verified in a second cohort of clinical trial participants, where similar trajectories following the initiation of biologic therapy were identified. Further, we found differential associations of the genetic marker HLA-C*06:02 between our registry-identified trajectories.<h4>Conclusions</h4>These subgroups, defined by change in disease over time, may be indicative of distinct endotypes driven by different biological mechanisms and may help inform the management of patients with psoriasis. Future work will aim to further delineate these mechanisms by extensively characterizing the subgroups with additional molecular and pharmacological data.",,doi:https://doi.org/10.1111/bjd.20140
 35094586,https://doi.org/10.1177/17407745221077691,The PROTEUS-Trials Consortium: Optimizing the use of patient-reported outcomes in clinical trials.,"Snyder C, Crossnohere N, King M, Reeve BB, Bottomley A, Calvert M, Thorner E, Wu AW, Brundage M, PROTEUS-Trials Consortium.",,"Clinical trials (London, England)",2022,2022-01-31,Y,Clinical Trials; Protocols; Data Visualization; Patient-reported Outcomes; Reporting Methods; Measure Selection,,,"<h4>Background</h4>The assessment of patient-reported outcomes in clinical trials has enormous potential to promote patient-centred care, but for this potential to be realized, the patient-reported outcomes must be captured effectively and communicated clearly. Over the past decade, methodologic tools have been developed to inform the design, analysis, reporting, and interpretation of patient-reported outcome data from clinical trials. We formed the PROTEUS-Trials Consortium (Patient-Reported Outcomes Tools: Engaging Users and Stakeholders) to disseminate and implement these methodologic tools.<h4>Methods</h4>PROTEUS-Trials are engaging with patient, clinician, research, and regulatory stakeholders from 27 organizations in the United States, Canada, Australia, the United Kingdom, and Europe to develop both organization-specific and cross-cutting strategies for implementing and disseminating the methodologic tools. Guided by the Knowledge-to-Action framework, we conducted consortium-wide webinars and meetings, as well as individual calls with participating organizations, to develop a workplan, which we are currently executing.<h4>Results</h4>Six methodologic tools serve as the foundation for PROTEUS-Trials dissemination and implementation efforts: the Standard Protocol Items: Recommendations for Interventional Trials-patient-reported outcome extension for writing protocols with patient-reported outcomes, the International Society for Quality of Life Research Minimum Standards for selecting a patient-reported outcome measure, Setting International Standards in Analysing Patient-Reported Outcomes and Quality of Life Endpoints Data Consortium recommendations for patient-reported outcome data analysis, the Consolidated Standards for Reporting of Trials-patient-reported outcome extension for reporting clinical trials with patient-reported outcomes, recommendations for the graphic display of patient-reported outcome data, and a Clinician's Checklist for reading and using an article about patient-reported outcomes. The PROTEUS-Trials website (www.TheProteusConsortium.org) serves as a central repository for the methodologic tools and associated resources. To date, we have developed (1) a roadmap to visually display where each of the six methodologic tools applies along the clinical trial trajectory, (2) web tutorials that provide guidance on the methodologic tools at different levels of detail, (3) checklists to provide brief summaries of each tool's recommendations, (4) a handbook to provide a self-guided approach to learning about the tools and recommendations, and (5) publications that address key topics related to patient-reported outcomes in clinical trials. We are also conducting organization-specific activities, including meetings, presentations, workshops, and webinars to publicize the existence of the methodologic tools and the PROTEUS-Trials resources. Work to develop communications strategies to ensure that PROTEUS-Trials reach key audiences with relevant information about patient-reported outcomes in clinical trials and PROTEUS-Trials is ongoing.<h4>Discussion</h4>The PROTEUS-Trials Consortium aims to help researchers generate patient-reported outcome data from clinical trials to (1) enable investigators, regulators, and policy-makers to take the patient perspective into account when conducting research and making decisions; (2) help patients understand treatment options and make treatment decisions; and (3) inform clinicians' discussions with patients regarding treatment options. In these ways, the PROTEUS Consortium promotes patient-centred research and care.",,pdf:http://pure-oai.bham.ac.uk/ws/files/160459757/17407745221077691.pdf; doi:https://doi.org/10.1177/17407745221077691; html:https://europepmc.org/articles/PMC9203669; pdf:https://europepmc.org/articles/PMC9203669?pdf=render
-37208429,https://doi.org/10.1038/s41598-023-33391-w,Rare variant contribution to cholestatic liver disease in a South Asian population in the United Kingdom.,"Zöllner J, Finer S, Linton KJ, Genes and Health Research Team, van Heel DA, Williamson C, Dixon PH.",,Scientific reports,2023,2023-05-19,Y,,,,"This study assessed the contribution of five genes previously known to be involved in cholestatic liver disease in British Bangladeshi and Pakistani people. Five genes (ABCB4, ABCB11, ATP8B1, NR1H4, TJP2) were interrogated by exome sequencing data of 5236 volunteers. Included were non-synonymous or loss of function (LoF) variants with a minor allele frequency < 5%. Variants were filtered, and annotated to perform rare variant burden analysis, protein structure, and modelling analysis in-silico. Out of 314 non-synonymous variants, 180 fulfilled the inclusion criteria and were mostly heterozygous unless specified. 90 were novel and of those variants, 22 were considered likely pathogenic and 9 pathogenic. We identified variants in volunteers with gallstone disease (n = 31), intrahepatic cholestasis of pregnancy (ICP, n = 16), cholangiocarcinoma and cirrhosis (n = 2). Fourteen novel LoF variants were identified: 7 frameshift, 5 introduction of premature stop codon and 2 splice acceptor variants. The rare variant burden was significantly increased in ABCB11. Protein modelling demonstrated variants that appeared to likely cause significant structural alterations. This study highlights the significant genetic burden contributing to cholestatic liver disease. Novel likely pathogenic and pathogenic variants were identified addressing the underrepresentation of diverse ancestry groups in genomic research.",,doi:https://doi.org/10.1038/s41598-023-33391-w; doi:https://doi.org/10.1038/s41598-023-33391-w; html:https://europepmc.org/articles/PMC10199085; pdf:https://europepmc.org/articles/PMC10199085?pdf=render
-34091032,https://doi.org/10.1016/j.neuroimage.2021.118235,Subspace-constrained approaches to low-rank fMRI acceleration.,"Mason HT, Graedel NN, Miller KL, Chiew M.",,NeuroImage,2021,2021-06-03,Y,fMRI; Tikhonov regularization; Acceleration; temporal resolution; Low Rank; Temporal Smoothing; K-t Faster; Low Resolution Priors,,,"Acceleration methods in fMRI aim to reconstruct high fidelity images from under-sampled k-space, allowing fMRI datasets to achieve higher temporal resolution, reduced physiological noise aliasing, and increased statistical degrees of freedom. While low levels of acceleration are typically part of standard fMRI protocols through parallel imaging, there exists the potential for approaches that allow much greater acceleration. One such existing approach is k-t FASTER, which exploits the inherent low-rank nature of fMRI. In this paper, we present a reformulated version of k-t FASTER which includes additional L2 constraints within a low-rank framework. We evaluated the effect of three different constraints against existing low-rank approaches to fMRI reconstruction: Tikhonov constraints, low-resolution priors, and temporal subspace smoothness. The different approaches are separately tested for robustness to under-sampling and thermal noise levels, in both retrospectively and prospectively-undersampled finger-tapping task fMRI data. Reconstruction quality is evaluated by accurate reconstruction of low-rank subspaces and activation maps. The use of L2 constraints was found to achieve consistently improved results, producing high fidelity reconstructions of statistical parameter maps at higher acceleration factors and lower SNR values than existing methods, but at a cost of longer computation time. In particular, the Tikhonov constraint proved very robust across all tested datasets, and the temporal subspace smoothness constraint provided the best reconstruction scores in the prospectively-undersampled dataset. These results demonstrate that regularized low-rank reconstruction of fMRI data can recover functional information at high acceleration factors without the use of any model-based spatial constraints.",,doi:https://doi.org/10.1016/j.neuroimage.2021.118235; doi:https://doi.org/10.1016/j.neuroimage.2021.118235; html:https://europepmc.org/articles/PMC7611820; pdf:https://europepmc.org/articles/PMC7611820?pdf=render
 30949070,https://doi.org/10.3389/fpsyt.2019.00109,Real World Implementation of a Transdiagnostic Risk Calculator for the Automatic Detection of Individuals at Risk of Psychosis in Clinical Routine: Study Protocol.,"Fusar-Poli P, Oliver D, Spada G, Patel R, Stewart R, Dobson R, McGuire P.",,Frontiers in psychiatry,2019,2019-03-13,Y,Schizophrenia; Prevention; risk; Psychosis; Transdiagnostic,"Applied Analytics, Better Care",,"<b>Background:</b> Primary indicated prevention in individuals at-risk for psychosis has the potential to improve the outcomes of this disorder. The ability to detect the majority of at-risk individuals is the main barrier toward extending benefits for the lives of many adolescents and young adults. Current detection strategies are highly inefficient. Only 5% (standalone specialized early detection services) to 12% (youth mental health services) of individuals who will develop a first psychotic disorder can be detected at the time of their at-risk stage. To overcome these challenges a pragmatic, clinically-based, individualized, transdiagnostic risk calculator has been developed to detect individuals at-risk of psychosis in secondary mental health care at scale. This calculator has been externally validated and has demonstrated good prognostic performance. However, it is not known whether it can be used in the real world clinical routine. For example, clinicians may not be willing to adhere to the recommendations made by the transdiagnostic risk calculator. Implementation studies are needed to address pragmatic challenges relating to the real world use of the transdiagnostic risk calculator. The aim of the current study is to provide <i>in-vitro</i> and <i>in-vivo</i> feasibility data to support the implementation of the transdiagnostic risk calculator in clinical routine. <b>Method:</b> This is a study which comprises of two subsequent phases: an <i>in-vitro</i> phase of 1 month and an <i>in-vivo</i> phase of 11 months. The <i>in-vitro</i> phase aims at developing and integrating the transdiagnostic risk calculator in the local electronic health register (primary outcome). The <i>in-vivo</i> phase aims at addressing the clinicians' adherence to the recommendations made by the transdiagnostic risk calculator (primary outcome) and other secondary feasibility parameters that are necessary to estimate the resources needed for its implementation. <b>Discussion:</b> This is the first implementation study for risk prediction models in individuals at-risk for psychosis. Ultimately, successful implementation is the true measure of a prediction model's utility. Therefore, the overall translational deliverable of the current study would be to extend the benefits of primary indicated prevention and improve outcomes of first episode psychosis. This may produce significant social benefits for many adolescents and young adults and their families.",,pdf:https://www.frontiersin.org/articles/10.3389/fpsyt.2019.00109/pdf; doi:https://doi.org/10.3389/fpsyt.2019.00109; html:https://europepmc.org/articles/PMC6436079; pdf:https://europepmc.org/articles/PMC6436079?pdf=render
+34091032,https://doi.org/10.1016/j.neuroimage.2021.118235,Subspace-constrained approaches to low-rank fMRI acceleration.,"Mason HT, Graedel NN, Miller KL, Chiew M.",,NeuroImage,2021,2021-06-03,Y,fMRI; Tikhonov regularization; Acceleration; temporal resolution; Low Rank; Temporal Smoothing; K-t Faster; Low Resolution Priors,,,"Acceleration methods in fMRI aim to reconstruct high fidelity images from under-sampled k-space, allowing fMRI datasets to achieve higher temporal resolution, reduced physiological noise aliasing, and increased statistical degrees of freedom. While low levels of acceleration are typically part of standard fMRI protocols through parallel imaging, there exists the potential for approaches that allow much greater acceleration. One such existing approach is k-t FASTER, which exploits the inherent low-rank nature of fMRI. In this paper, we present a reformulated version of k-t FASTER which includes additional L2 constraints within a low-rank framework. We evaluated the effect of three different constraints against existing low-rank approaches to fMRI reconstruction: Tikhonov constraints, low-resolution priors, and temporal subspace smoothness. The different approaches are separately tested for robustness to under-sampling and thermal noise levels, in both retrospectively and prospectively-undersampled finger-tapping task fMRI data. Reconstruction quality is evaluated by accurate reconstruction of low-rank subspaces and activation maps. The use of L2 constraints was found to achieve consistently improved results, producing high fidelity reconstructions of statistical parameter maps at higher acceleration factors and lower SNR values than existing methods, but at a cost of longer computation time. In particular, the Tikhonov constraint proved very robust across all tested datasets, and the temporal subspace smoothness constraint provided the best reconstruction scores in the prospectively-undersampled dataset. These results demonstrate that regularized low-rank reconstruction of fMRI data can recover functional information at high acceleration factors without the use of any model-based spatial constraints.",,doi:https://doi.org/10.1016/j.neuroimage.2021.118235; doi:https://doi.org/10.1016/j.neuroimage.2021.118235; html:https://europepmc.org/articles/PMC7611820; pdf:https://europepmc.org/articles/PMC7611820?pdf=render
+37208429,https://doi.org/10.1038/s41598-023-33391-w,Rare variant contribution to cholestatic liver disease in a South Asian population in the United Kingdom.,"Zöllner J, Finer S, Linton KJ, Genes and Health Research Team, van Heel DA, Williamson C, Dixon PH.",,Scientific reports,2023,2023-05-19,Y,,,,"This study assessed the contribution of five genes previously known to be involved in cholestatic liver disease in British Bangladeshi and Pakistani people. Five genes (ABCB4, ABCB11, ATP8B1, NR1H4, TJP2) were interrogated by exome sequencing data of 5236 volunteers. Included were non-synonymous or loss of function (LoF) variants with a minor allele frequency < 5%. Variants were filtered, and annotated to perform rare variant burden analysis, protein structure, and modelling analysis in-silico. Out of 314 non-synonymous variants, 180 fulfilled the inclusion criteria and were mostly heterozygous unless specified. 90 were novel and of those variants, 22 were considered likely pathogenic and 9 pathogenic. We identified variants in volunteers with gallstone disease (n = 31), intrahepatic cholestasis of pregnancy (ICP, n = 16), cholangiocarcinoma and cirrhosis (n = 2). Fourteen novel LoF variants were identified: 7 frameshift, 5 introduction of premature stop codon and 2 splice acceptor variants. The rare variant burden was significantly increased in ABCB11. Protein modelling demonstrated variants that appeared to likely cause significant structural alterations. This study highlights the significant genetic burden contributing to cholestatic liver disease. Novel likely pathogenic and pathogenic variants were identified addressing the underrepresentation of diverse ancestry groups in genomic research.",,doi:https://doi.org/10.1038/s41598-023-33391-w; doi:https://doi.org/10.1038/s41598-023-33391-w; html:https://europepmc.org/articles/PMC10199085; pdf:https://europepmc.org/articles/PMC10199085?pdf=render
 35073907,https://doi.org/10.1186/s12916-021-02218-8,Association between hypertensive disorders of pregnancy and later risk of cardiovascular outcomes.,"Oliver-Williams C, Stevens D, Payne RA, Wilkinson IB, Smith GCS, Wood A.",,BMC medicine,2022,2022-01-25,Y,Pregnancy; Cardiovascular disease; Pre-eclampsia; Women; Gestational Hypertension,,,"<h4>Background</h4>Hypertensive disorders of pregnancy are common pregnancy complications that are associated with greater cardiovascular disease risk for mothers. However, risk of cardiovascular disease subtypes associated with gestational hypertension or pre-eclampsia is unclear. The present study aims to compare the risk of cardiovascular disease outcomes for women with and without a history of gestational hypertension and pre-eclampsia using national hospital admissions data.<h4>Methods</h4>This was a retrospective cohort study of national medical records from all National Health Service hospitals in England. Women who had one or more singleton live births in England between 1997 and 2015 were included in the analysis. Risk of total cardiovascular disease and 19 pre-specified cardiovascular disease subtypes, including stroke, coronary heart disease, cardiomyopathy and peripheral arterial disease, was calculated separately for women with a history of gestational hypertension and pre-eclampsia compared to normotensive pregnancies.<h4>Results</h4>Amongst 2,359,386 first live births, there were 85,277 and 74,542 hospital admissions with a diagnosis of gestational hypertension and pre-eclampsia, respectively. During 18 years (16,309,386 person-years) of follow-up, the number and incidence of total CVD for normotensive women, women with prior gestational hypertension and women with prior pre-eclampsia were n = 8668, 57.1 (95% CI: 55.9-58.3) per 100,000 person-years; n = 521, 85.8 (78.6-93.5) per 100,000 person-years; and n = 518, 99.3 (90.9-108.2) per 100,000 person-years, respectively. Adjusted HRs (aHR) for total CVD were aHR (95% CI) = 1.45 (1.33-1.59) for women with prior gestational hypertension and aHR = 1.62 (1.48-1.78) for women with prior pre-eclampsia. Gestational hypertension was strongly associated with dilated cardiomyopathy, aHR = 2.85 (1.67-4.86), and unstable angina, aHR = 1.92 (1.33-2.77). Pre-eclampsia was strongly associated with hypertrophic cardiomyopathy, aHR = 3.27 (1.49-7.19), and acute myocardial infarction, aHR = 2.46 (1.72-3.53). Associations were broadly homogenous across cardiovascular disease subtypes and increased with a greater number of affected pregnancies.<h4>Conclusions</h4>Women with either previous gestational hypertension or pre-eclampsia are at greater risk of a range of cardiovascular outcomes. These women may benefit from clinical risk assessment or early interventions to mitigate their greater risk of various cardiovascular outcomes.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-021-02218-8; doi:https://doi.org/10.1186/s12916-021-02218-8; html:https://europepmc.org/articles/PMC8787919; pdf:https://europepmc.org/articles/PMC8787919?pdf=render
-35482474,https://doi.org/10.1111/bjd.21627,Biomarkers of disease progression in people with psoriasis: a scoping review.,"Ramessur R, Corbett M, Marshall D, Acencio ML, Barbosa IA, Dand N, Di Meglio P, Haddad S, Jensen AHM, Koopmann W, Mahil SK, Ostaszewski M, Rahmatulla S, Rastrick J, Saklatvala J, Weidinger S, Wright K, Eyerich K, Ndlovu M, Barker JN, Skov L, Conrad C, Smith CH, BIOMAP consortium.",,The British journal of dermatology,2022,2022-07-11,Y,,,,"<h4>Background</h4>Identification of those at risk of more severe psoriasis and/or associated morbidities offers opportunity for early intervention, reduced disease burden and more cost-effective healthcare. Prognostic biomarkers of disease progression have thus been the focus of intense research, but none are part of routine practice.<h4>Objectives</h4>To identify and catalogue candidate biomarkers of disease progression in psoriasis for the translational research community.<h4>Methods</h4>A systematic search of CENTRAL, Embase, LILACS and MEDLINE was performed for relevant articles published between 1990 and December 2021. Eligibility criteria were studies involving patients with psoriasis (any age, n ≥ 50) reporting biomarkers associated with disease progression. The main outcomes were any measure of skin severity or any prespecified psoriasis comorbidity. Data were extracted by one reviewer and checked by a second; studies meeting minimal quality criteria (longitudinal design and/or use of methods to control for confounding) were formally assessed for bias. Candidate biomarkers were identified by an expert multistakeholder group using a majority voting consensus exercise, and mapped to relevant cellular and molecular pathways.<h4>Results</h4>Of 181 included studies, most investigated genomic or proteomic biomarkers associated with disease severity (n = 145) or psoriatic arthritis (n = 30). Methodological and reporting limitations compromised interpretation of findings, most notably a lack of longitudinal studies, and inadequate control for key prognostic factors. The following candidate biomarkers with future potential utility were identified for predicting disease severity: LCE3D, interleukin (IL)23R, IL23A, NFKBIL1 loci, HLA-C*06:02 (genomic), IL-17A, IgG aHDL, GlycA, I-FABP and kallikrein 8 (proteomic), tyramine (metabolomic); psoriatic arthritis: HLA-C*06:02, HLA-B*27, HLA-B*38, HLA-B*08, and variation at the IL23R and IL13 loci (genomic); IL-17A, CXCL10, Mac-2 binding protein, integrin b5, matrix metalloproteinase-3 and macrophage-colony stimulating factor (proteomic) and tyramine and mucic acid (metabolomic); and type 2 diabetes mellitus: variation in IL12B and IL23R loci (genomic). No biomarkers were supported by sufficient evidence for clinical use without further validation.<h4>Conclusions</h4>This review provides a comprehensive catalogue of investigated biomarkers of disease progression in psoriasis. Future studies must address the common methodological limitations identified herein to expedite discovery and validation of biomarkers for clinical use. What is already known about this topic? The current treatment paradigm in psoriasis is reactive. There is a need to develop effective risk-stratified management approaches that can proactively attenuate the substantial burden of disease. Prognostic biomarkers of disease progression have therefore been the focus of intense research. What does this study add? This review is the first to scope, collate and catalogue research investigating biomarkers of disease progression in psoriasis. The review identifies potentially promising candidate biomarkers for further investigation and highlights common important limitations that should be considered when designing and conducting future studies in this area.",,pdf:https://kclpure.kcl.ac.uk/ws/files/177671246/Br_J_Dermatol_2022_Ramessur_Biomarkers_of_disease_progression_in_people_with_psoriasis_a_scoping_review.pdf; doi:https://doi.org/10.1111/bjd.21627; html:https://europepmc.org/articles/PMC9796834; pdf:https://europepmc.org/articles/PMC9796834?pdf=render
 31040096,https://doi.org/10.1016/s2352-4642(19)30114-2,"Antimicrobial-impregnated central venous catheters for prevention of neonatal bloodstream infection (PREVAIL): an open-label, parallel-group, pragmatic, randomised controlled trial.","Gilbert R, Brown M, Rainford N, Donohue C, Fraser C, Sinha A, Dorling J, Gray J, McGuire W, Gamble C, Oddie SJ, PREVAIL trial team.",,The Lancet. Child & adolescent health,2019,2019-04-27,N,,"Better, Faster and More Efficient Clinical Trials",,"<h4>Background</h4>Bloodstream infection is associated with high mortality and serious morbidity in preterm babies. Evidence from clinical trials shows that antimicrobial-impregnated central venous catheters (CVCs) reduce catheter-related bloodstream infection in adults and children receiving intensive care, but there is a paucity of similar evidence for babies receiving neonatal intensive care.<h4>Methods</h4>This open-label, parallel-group, pragmatic, randomised controlled trial was done in 18 neonatal intensive care units in England. Newborn babies who needed a peripherally inserted CVC (PICC) were allocated randomly (1:1) to receive either a PICC impregnated with miconazole and rifampicin or a standard (non-antimicrobial-impregnated) PICC. Random allocation was done with a web-based program, which was centrally controlled to ensure allocation concealment. Randomisation sequences were computer-generated in random blocks of two and four, and stratified by site. Masking of clinicians to PICC allocation was impractical because rifampicin caused brown staining of the antimicrobial-impregnated PICC. However, participant inclusion in analyses and occurrence of outcome events were determined following an analysis plan that was specified before individuals saw the unblinded data. The primary outcome was the time from random allocation to first microbiologically confirmed bloodstream or cerebrospinal fluid (CSF) infection between 24 h after randomisation and 48 h after PICC removal or death. We analysed outcome data according to the intention-to-treat principle. We excluded babies for whom a PICC was not inserted from safety analyses, as these analyses were done with groups defined by the PICC used. This trial is registered with ISRCTN, number 81931394.<h4>Findings</h4>Between Aug 12, 2015, and Jan 11, 2017, we randomly assigned 861 babies (754 [88%] born before 32 weeks of gestation) to receive an antimicrobial-impregnated PICC (430 babies) or standard PICC (431 babies). The median time to PICC removal was 8·20 days (IQR 4·77-12·13) in the antimicrobial-impregnated PICC group versus 7·86 days (5·00-12·53) days in the standard PICC group (hazard ratio [HR] 1·03, 95% CI 0·89-1·18, p=0·73), with 46 (11%) of 430 babies versus 44 (10%) of 431 babies having a microbiologically confirmed bloodstream or CSF infection. The time from random allocation to first bloodstream or CSF infection was similar between the two groups (HR 1·11, 95% CI 0·73-1·67, p=0·63). Secondary outcomes relating to infection, rifampicin resistance in positive blood or CSF cultures, mortality, clinical outcomes at neonatal unit discharge, and time to PICC removal were similar between the two groups, although rifampicin resistance in positive cultures of PICC tips was higher in the antimicrobial-impregnated PICC group (relative risk 3·51, 95% CI 1·16-10·57, p=0·018). 60 adverse events were reported from 49 (13%) patients in the antimicrobial-impregnated PICC group and 50 events from 45 (10%) babies in the standard PICC group.<h4>Interpretation</h4>We found no evidence of benefit or harm associated with miconazole and rifampicin-impregnated PICCs compared with standard PICCs for newborn babies. Future research should focus on other types of antimicrobial impregnation of PICCs and alternative approaches for preventing infection.<h4>Funding</h4>UK National Institute for Health Research Health Technology Assessment programme.",,pdf:http://www.thelancet.com/article/S2352464219301142/pdf; doi:https://doi.org/10.1016/S2352-4642(19)30114-2
 31134468,https://doi.org/10.1007/s12471-019-1288-4,UNRAVEL: big data analytics research data platform to improve care of patients with cardiomyopathies using routine electronic health records and standardised biobanking.,"Sammani A, Jansen M, Linschoten M, Bagheri A, de Jonge N, Kirkels H, van Laake LW, Vink A, van Tintelen JP, Dooijes D, Te Riele ASJM, Harakalova M, Baas AF, Asselbergs FW.",,Netherlands heart journal : monthly journal of the Netherlands Society of Cardiology and the Netherlands Heart Foundation,2019,2019-09-01,Y,Cardiomyopathy; Electronic Health Record; Biobanking; Big Data Analytics; Machine learning; Research Data Platform,,,"<h4>Introduction</h4>Despite major advances in our understanding of genetic cardiomyopathies, they remain the leading cause of premature sudden cardiac death and end-stage heart failure in persons under the age of 60 years. Integrated research databases based on a large number of patients may provide a scaffold for future research. Using routine electronic health records and standardised biobanking, big data analysis on a larger number of patients and investigations are possible. In this article, we describe the UNRAVEL research data platform embedded in routine practice to facilitate research in genetic cardiomyopathies.<h4>Design</h4>Eligible participants with proven or suspected cardiac disease and their relatives are asked for permission to use their data and to draw blood for biobanking. Routinely collected clinical data are included in a research database by weekly extraction. A text-mining tool has been developed to enrich UNRAVEL with unstructured data in clinical notes.<h4>Preliminary results</h4>Thus far, 828 individuals with a median age of 57 years have been included, 58% of whom are male. All data are captured in a temporal sequence amounting to a total of 18,565 electrocardiograms, 3619 echocardiograms, data from over 20,000 radiological examinations and 650,000 individual laboratory measurements.<h4>Conclusion</h4>Integration of routine electronic health care in a research data platform allows efficient data collection, including all investigations in chronological sequence. Trials embedded in the electronic health record are now possible, providing cost-effective ways to answer clinical questions. We explicitly welcome national and international collaboration and have provided our protocols and other materials on www.unravelrdp.nl .",,pdf:https://link.springer.com/content/pdf/10.1007/s12471-019-1288-4.pdf; doi:https://doi.org/10.1007/s12471-019-1288-4; html:https://europepmc.org/articles/PMC6712144; pdf:https://europepmc.org/articles/PMC6712144?pdf=render
+35482474,https://doi.org/10.1111/bjd.21627,Biomarkers of disease progression in people with psoriasis: a scoping review.,"Ramessur R, Corbett M, Marshall D, Acencio ML, Barbosa IA, Dand N, Di Meglio P, Haddad S, Jensen AHM, Koopmann W, Mahil SK, Ostaszewski M, Rahmatulla S, Rastrick J, Saklatvala J, Weidinger S, Wright K, Eyerich K, Ndlovu M, Barker JN, Skov L, Conrad C, Smith CH, BIOMAP consortium.",,The British journal of dermatology,2022,2022-07-11,Y,,,,"<h4>Background</h4>Identification of those at risk of more severe psoriasis and/or associated morbidities offers opportunity for early intervention, reduced disease burden and more cost-effective healthcare. Prognostic biomarkers of disease progression have thus been the focus of intense research, but none are part of routine practice.<h4>Objectives</h4>To identify and catalogue candidate biomarkers of disease progression in psoriasis for the translational research community.<h4>Methods</h4>A systematic search of CENTRAL, Embase, LILACS and MEDLINE was performed for relevant articles published between 1990 and December 2021. Eligibility criteria were studies involving patients with psoriasis (any age, n ≥ 50) reporting biomarkers associated with disease progression. The main outcomes were any measure of skin severity or any prespecified psoriasis comorbidity. Data were extracted by one reviewer and checked by a second; studies meeting minimal quality criteria (longitudinal design and/or use of methods to control for confounding) were formally assessed for bias. Candidate biomarkers were identified by an expert multistakeholder group using a majority voting consensus exercise, and mapped to relevant cellular and molecular pathways.<h4>Results</h4>Of 181 included studies, most investigated genomic or proteomic biomarkers associated with disease severity (n = 145) or psoriatic arthritis (n = 30). Methodological and reporting limitations compromised interpretation of findings, most notably a lack of longitudinal studies, and inadequate control for key prognostic factors. The following candidate biomarkers with future potential utility were identified for predicting disease severity: LCE3D, interleukin (IL)23R, IL23A, NFKBIL1 loci, HLA-C*06:02 (genomic), IL-17A, IgG aHDL, GlycA, I-FABP and kallikrein 8 (proteomic), tyramine (metabolomic); psoriatic arthritis: HLA-C*06:02, HLA-B*27, HLA-B*38, HLA-B*08, and variation at the IL23R and IL13 loci (genomic); IL-17A, CXCL10, Mac-2 binding protein, integrin b5, matrix metalloproteinase-3 and macrophage-colony stimulating factor (proteomic) and tyramine and mucic acid (metabolomic); and type 2 diabetes mellitus: variation in IL12B and IL23R loci (genomic). No biomarkers were supported by sufficient evidence for clinical use without further validation.<h4>Conclusions</h4>This review provides a comprehensive catalogue of investigated biomarkers of disease progression in psoriasis. Future studies must address the common methodological limitations identified herein to expedite discovery and validation of biomarkers for clinical use. What is already known about this topic? The current treatment paradigm in psoriasis is reactive. There is a need to develop effective risk-stratified management approaches that can proactively attenuate the substantial burden of disease. Prognostic biomarkers of disease progression have therefore been the focus of intense research. What does this study add? This review is the first to scope, collate and catalogue research investigating biomarkers of disease progression in psoriasis. The review identifies potentially promising candidate biomarkers for further investigation and highlights common important limitations that should be considered when designing and conducting future studies in this area.",,pdf:https://kclpure.kcl.ac.uk/ws/files/177671246/Br_J_Dermatol_2022_Ramessur_Biomarkers_of_disease_progression_in_people_with_psoriasis_a_scoping_review.pdf; doi:https://doi.org/10.1111/bjd.21627; html:https://europepmc.org/articles/PMC9796834; pdf:https://europepmc.org/articles/PMC9796834?pdf=render
 32479194,https://doi.org/10.1161/circulationaha.120.045826,"Lipoprotein(a) in Alzheimer, Atherosclerotic, Cerebrovascular, Thrombotic, and Valvular Disease: Mendelian Randomization Investigation.","Larsson SC, Gill D, Mason AM, Jiang T, Bäck M, Butterworth AS, Burgess S.",,Circulation,2020,2020-06-01,N,Atherosclerosis; Lipoprotein(a); Alzheimer disease; Stroke; Heart valve diseases; Mendelian Randomization Analysis,,,,,pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCULATIONAHA.120.045826; doi:https://doi.org/10.1161/CIRCULATIONAHA.120.045826; html:https://europepmc.org/articles/PMC7614586; pdf:https://europepmc.org/articles/PMC7614586?pdf=render; doi:https://doi.org/10.1161/circulationaha.120.045826
 33939619,https://doi.org/10.2196/29072,Predicting Risk of Hospital Admission in Patients With Suspected COVID-19 in a Community Setting: Protocol for Development and Validation of a Multivariate Risk Prediction Tool.,"Espinosa-Gonzalez AB, Neves AL, Fiorentino F, Prociuk D, Husain L, Ramtale SC, Mi E, Mi E, Macartney J, Anand SN, Sherlock J, Saravanakumar K, Mayer E, de Lusignan S, Greenhalgh T, Delaney BC.",,JMIR research protocols,2021,2021-05-25,Y,Primary Care; Hospital Admission; Electronic Health Records; Early Warning Score; Risk Prediction Tool; Covid-19 Severity,,,"<h4>Background</h4>During the pandemic, remote consultations have become the norm for assessing patients with signs and symptoms of COVID-19 to decrease the risk of transmission. This has intensified the clinical uncertainty already experienced by primary care clinicians when assessing patients with suspected COVID-19 and has prompted the use of risk prediction scores, such as the National Early Warning Score (NEWS2), to assess severity and guide treatment. However, the risk prediction tools available have not been validated in a community setting and are not designed to capture the idiosyncrasies of COVID-19 infection.<h4>Objective</h4>The objective of this study is to produce a multivariate risk prediction tool, RECAP-V1 (Remote COVID-19 Assessment in Primary Care), to support primary care clinicians in the identification of those patients with COVID-19 that are at higher risk of deterioration and facilitate the early escalation of their treatment with the aim of improving patient outcomes.<h4>Methods</h4>The study follows a prospective cohort observational design, whereby patients presenting in primary care with signs and symptoms suggestive of COVID-19 will be followed and their data linked to hospital outcomes (hospital admission and death). Data collection will be carried out by primary care clinicians in four arms: North West London Clinical Commissioning Groups (NWL CCGs), Oxford-Royal College of General Practitioners (RCGP) Research and Surveillance Centre (RSC), Covid Clinical Assessment Service (CCAS), and South East London CCGs (Doctaly platform). The study involves the use of an electronic template that incorporates a list of items (known as RECAP-V0) thought to be associated with disease outcome according to previous qualitative work. Data collected will be linked to patient outcomes in highly secure environments. We will then use multivariate logistic regression analyses for model development and validation.<h4>Results</h4>Recruitment of participants started in October 2020. Initially, only the NWL CCGs and RCGP RSC arms were active. As of March 24, 2021, we have recruited a combined sample of 3827 participants in these two arms. CCAS and Doctaly joined the study in February 2021, with CCAS starting the recruitment process on March 15, 2021. The first part of the analysis (RECAP-V1 model development) is planned to start in April 2021 using the first half of the NWL CCGs and RCGP RSC combined data set. Posteriorly, the model will be validated with the rest of the NWL CCGs and RCGP RSC data as well as the CCAS and Doctaly data sets. The study was approved by the Research Ethics Committee on May 27, 2020 (Integrated Research Application System number: 283024, Research Ethics Committee reference number: 20/NW/0266) and badged as National Institute of Health Research Urgent Public Health Study on October 14, 2020.<h4>Conclusions</h4>We believe the validated RECAP-V1 early warning score will be a valuable tool for the assessment of severity in patients with suspected COVID-19 in the community, either in face-to-face or remote consultations, and will facilitate the timely escalation of treatment with the potential to improve patient outcomes.<h4>Trial registration</h4>ISRCTN registry ISRCTN13953727; https://www.isrctn.com/ISRCTN13953727.<h4>International registered report identifier (irrid)</h4>DERR1-10.2196/29072.",,pdf:https://jmir.org/api/download?alt_name=resprot_v10i5e29072_app1.pdf&filename=e079f888f9036dd40808005eb7b49b6f.pdf; doi:https://doi.org/10.2196/29072; html:https://europepmc.org/articles/PMC8153031
 34139154,https://doi.org/10.1016/j.cels.2021.05.005,A time-resolved proteomic and prognostic map of COVID-19.,"Demichev V, Tober-Lau P, Lemke O, Nazarenko T, Thibeault C, Whitwell H, Röhl A, Freiwald A, Szyrwiel L, Ludwig D, Correia-Melo C, Aulakh SK, Helbig ET, Stubbemann P, Lippert LJ, Grüning NM, Blyuss O, Vernardis S, White M, Messner CB, Joannidis M, Sonnweber T, Klein SJ, Pizzini A, Wohlfarter Y, Sahanic S, Hilbe R, Schaefer B, Wagner S, Mittermaier M, Machleidt F, Garcia C, Ruwwe-Glösenkamp C, Lingscheid T, Bosquillon de Jarcy L, Stegemann MS, Pfeiffer M, Jürgens L, Denker S, Zickler D, Enghard P, Zelezniak A, Campbell A, Hayward C, Porteous DJ, Marioni RE, Uhrig A, Müller-Redetzky H, Zoller H, Löffler-Ragg J, Keller MA, Tancevski I, Timms JF, Zaikin A, Hippenstiel S, Ramharter M, Witzenrath M, Suttorp N, Lilley K, Mülleder M, Sander LE, PA-COVID-19 Study group, Ralser M, Kurth F.",,Cell systems,2021,2021-06-14,Y,Proteomics; Biomarkers; Physiological parameters; Machine Learning; Disease Prognosis; Clinical Disease Progression; Patient Trajectories; Longitudinal Profiling; Covid-19,,,"COVID-19 is highly variable in its clinical presentation, ranging from asymptomatic infection to severe organ damage and death. We characterized the time-dependent progression of the disease in 139 COVID-19 inpatients by measuring 86 accredited diagnostic parameters, such as blood cell counts and enzyme activities, as well as untargeted plasma proteomes at 687 sampling points. We report an initial spike in a systemic inflammatory response, which is gradually alleviated and followed by a protein signature indicative of tissue repair, metabolic reconstitution, and immunomodulation. We identify prognostic marker signatures for devising risk-adapted treatment strategies and use machine learning to classify therapeutic needs. We show that the machine learning models based on the proteome are transferable to an independent cohort. Our study presents a map linking routinely used clinical diagnostic parameters to plasma proteomes and their dynamics in an infectious disease.",,doi:https://doi.org/10.1016/j.cels.2021.05.005; doi:https://doi.org/10.1016/j.cels.2021.05.005; html:https://europepmc.org/articles/PMC8201874
-37118290,https://doi.org/10.1038/s43587-022-00293-x,Immune system-wide Mendelian randomization and triangulation analyses support autoimmunity as a modifiable component in dementia-causing diseases.,"Lindbohm JV, Mars N, Sipilä PN, Singh-Manoux A, Runz H, FinnGen, Livingston G, Seshadri S, Xavier R, Hingorani AD, Ripatti S, Kivimäki M.",,Nature aging,2022,2022-10-14,Y,,,,"Immune system and blood-brain barrier dysfunction are implicated in the development of Alzheimer's and other dementia-causing diseases, but their causal role remains unknown. We performed Mendelian randomization for 1,827 immune system- and blood-brain barrier-related biomarkers and identified 127 potential causal risk factors for dementia-causing diseases. Pathway analyses linked these biomarkers to amyloid-β, tau and α-synuclein pathways and to autoimmunity-related processes. A phenome-wide analysis using Mendelian randomization-based polygenic risk score in the FinnGen study (n = 339,233) for the biomarkers indicated shared genetic background for dementias and autoimmune diseases. This association was further supported by human leukocyte antigen analyses. In inverse-probability-weighted analyses that simulate randomized controlled drug trials in observational data, anti-inflammatory methotrexate treatment reduced the incidence of Alzheimer's disease in high-risk individuals (hazard ratio compared with no treatment, 0.64, 95% confidence interval 0.49-0.88, P = 0.005). These converging results from different lines of human research suggest that autoimmunity is a modifiable component in dementia-causing diseases.",,pdf:https://www.nature.com/articles/s43587-022-00293-x.pdf; doi:https://doi.org/10.1038/s43587-022-00293-x; html:https://europepmc.org/articles/PMC10154235; pdf:https://europepmc.org/articles/PMC10154235?pdf=render
 37770476,https://doi.org/10.1038/s41467-023-41249-y,Genome-wide association studies and cross-population meta-analyses investigating short and long sleep duration.,"Austin-Zimmerman I, Levey DF, Giannakopoulou O, Deak JD, Galimberti M, Adhikari K, Zhou H, Denaxas S, Irizar H, Kuchenbaecker K, McQuillin A, Million Veteran Program, Concato J, Buysse DJ, Gaziano JM, Gottlieb DJ, Polimanti R, Stein MB, Bramon E, Gelernter J.",,Nature communications,2023,2023-09-28,Y,,,,"Sleep duration has been linked to a wide range of negative health outcomes and to reduced life expectancy. We present genome-wide association studies of short ( ≤ 5 h) and long ( ≥ 10 h) sleep duration in adults of European (N = 445,966), African (N = 27,785), East Asian (N = 3141), and admixed-American (N = 16,250) ancestry from UK Biobank and the Million Veteran Programme. In a cross-population meta-analysis, we identify 84 independent loci for short sleep and 1 for long sleep. We estimate SNP-based heritability for both sleep traits in each ancestry based on population derived linkage disequilibrium (LD) scores using cov-LDSC. We identify positive genetic correlation between short and long sleep traits (r<sub>g</sub> = 0.16 ± 0.04; p = 0.0002), as well as similar patterns of genetic correlation with other psychiatric and cardiometabolic phenotypes. Mendelian randomisation reveals a directional causal relationship between short sleep and depression, and a bidirectional causal relationship between long sleep and depression.",,pdf:https://www.nature.com/articles/s41467-023-41249-y.pdf; doi:https://doi.org/10.1038/s41467-023-41249-y; html:https://europepmc.org/articles/PMC10539313; pdf:https://europepmc.org/articles/PMC10539313?pdf=render
+37118290,https://doi.org/10.1038/s43587-022-00293-x,Immune system-wide Mendelian randomization and triangulation analyses support autoimmunity as a modifiable component in dementia-causing diseases.,"Lindbohm JV, Mars N, Sipilä PN, Singh-Manoux A, Runz H, FinnGen, Livingston G, Seshadri S, Xavier R, Hingorani AD, Ripatti S, Kivimäki M.",,Nature aging,2022,2022-10-14,Y,,,,"Immune system and blood-brain barrier dysfunction are implicated in the development of Alzheimer's and other dementia-causing diseases, but their causal role remains unknown. We performed Mendelian randomization for 1,827 immune system- and blood-brain barrier-related biomarkers and identified 127 potential causal risk factors for dementia-causing diseases. Pathway analyses linked these biomarkers to amyloid-β, tau and α-synuclein pathways and to autoimmunity-related processes. A phenome-wide analysis using Mendelian randomization-based polygenic risk score in the FinnGen study (n = 339,233) for the biomarkers indicated shared genetic background for dementias and autoimmune diseases. This association was further supported by human leukocyte antigen analyses. In inverse-probability-weighted analyses that simulate randomized controlled drug trials in observational data, anti-inflammatory methotrexate treatment reduced the incidence of Alzheimer's disease in high-risk individuals (hazard ratio compared with no treatment, 0.64, 95% confidence interval 0.49-0.88, P = 0.005). These converging results from different lines of human research suggest that autoimmunity is a modifiable component in dementia-causing diseases.",,pdf:https://www.nature.com/articles/s43587-022-00293-x.pdf; doi:https://doi.org/10.1038/s43587-022-00293-x; html:https://europepmc.org/articles/PMC10154235; pdf:https://europepmc.org/articles/PMC10154235?pdf=render
 30014898,https://doi.org/10.1016/j.envres.2018.07.015,Estimation of TETRA radio use in the Airwave Health Monitoring Study of the British police forces.,"Vergnaud AC, Aresu M, Kongsgård HW, McRobie D, Singh D, Spear J, Heard A, Gao H, Carpenter JR, Elliott P.",,Environmental research,2018,2018-07-09,N,Tetra; Occupational Exposure; Occupational Cohort; Radiofrequency Electromagnetic Fields,Improving Public Health,,"<h4>Background</h4>The Airwave Health Monitoring Study aims to investigate the possible long-term health effects of Terrestrial Trunked Radio (TETRA) use among the police forces in Great Britain. Here, we investigate whether objective data from the network operator could be used to correct for misreporting in self-reported data and expand the radio usage availability in our cohort.<h4>Methods</h4>We estimated average monthly usage of personal radio in the 12 months prior to enrolment from a missing value imputation model and evaluated its performance against objective and self-reported data. Factors associated with TETRA radio usage variables were investigated using Chi-square tests and analysis of variance.<h4>Results</h4>The imputed data were better correlated with objective than self-reported usage (Spearman correlation coefficient = 0.72 vs. 0. 52 and kappa 0.56 [95% confidence interval 0.55, 0.56] vs. 0.46 [0.45, 0.47]), although the imputation model tended to under-estimate use for higher users. Participants with higher personal radio usage were more likely to be younger, men vs. women and officer vs. staff. The median average monthly usage level for the entire cohort was estimated to be 29.3 min (95% CI: [7.2, 66.6]).<h4>Conclusion</h4>The availability of objective personal radio records for a large proportion of users allowed us to develop a robust imputation model and hence obtain personal radio usage estimates for ~50,000 participants. This substantially reduced exposure misclassification compared to using self-reported data and will allow us to carry out analyses of TETRA usage for the entire cohort in future work.",,pdf:https://researchonline.lshtm.ac.uk/id/eprint/4648566/1/Estimation%20of%20TETRA%20radio_GREEN%20AAM.pdf; doi:https://doi.org/10.1016/j.envres.2018.07.015
-33550229,https://doi.org/10.1136/bmjopen-2020-040167,Assessing public support for extending smoke-free policies beyond enclosed public places and workplaces: protocol for a systematic review and meta-analysis.,"Boderie NW, Mölenberg FJ, Sheikh A, Bramer WM, Burdorf A, van Lenthe FJ, Been JV.",,BMJ open,2021,2021-02-05,Y,Tobacco smoke pollution; Attitude; Smoke-free Policy,,,"<h4>Introduction</h4>Smoke-free enclosed public environments are effective in reducing exposure to secondhand smoke and yield major public health benefits. Building on this, many countries are now implementing smoke-free policies regulating smoking beyond enclosed public places and workplaces. In order to successfully implement such 'novel smoke-free policies', public support is essential. We aim to provide the first comprehensive systematic review and meta-analysis assessing levels and determinants of public support for novel smoke-free policies.<h4>Methods and analysis</h4>The primary objective of this review is to summarise the level of public support for novel smoke-free policies. Eight online databases (Embase.com, Medline ALL Ovid, Web of Science Core Collection, WHO Library Database, Latin American and Caribbean Health Sciences Literature, Scientific Online Library Online, PsychINFO and Google Scholar) will be searched from 1 January 2004 by two independent researchers with no language restrictions. The initial search was performed on 15 April 2020 and will be updated prior to finalisation of the report. Studies are eligible if assessing support for novel smoke-free policies in the general population (age ≥16 years) and have a sample size of n≥400. Studies funded by the tobacco industry or evaluating support among groups with vested interest are excluded. The primary outcome is proportion of public support for smoke-free policies, subdivided according to the spaces covered: (1) indoor private spaces (eg, cars) (2) indoor semiprivate spaces (eg, multi-unit housing) (3) outdoor (semi)private spaces (eg, courtyards) (4) non-hospitality outdoor public spaces (eg, parks, hospital grounds, playgrounds) and (5) hospitality outdoor public spaces (eg, restaurant terraces). The secondary objective is to identify determinants associated with public support on three levels: (1) within-study determinants (eg, smoking status) (2) between-study determinants (eg, survey year) and (3) context-specific determinants (eg, social norms). Risk of bias will be assessed using the Mixed Methods Appraisal Tool and a sensitivity analysis will be performed excluding studies at high risk of bias.<h4>Ethics and dissemination</h4>No formal ethical approval is required. Findings will be disseminated to academics, policymakers and the general public.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/2/e040167.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-040167; html:https://europepmc.org/articles/PMC7925902; pdf:https://europepmc.org/articles/PMC7925902?pdf=render
 34708157,https://doi.org/10.12688/wellcomeopenres.16701.3,Estimating the duration of seropositivity of human seasonal coronaviruses using seroprevalence studies.,"Rees EM, Waterlow NR, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Lowe R, Kucharski AJ.",,Wellcome open research,2021,2021-12-21,Y,Catalytic model; Seroprevalence; Waning Immunity; Seasonal Coronavirus,,,"<b>Background:</b> The duration of immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still uncertain, but it is of key clinical and epidemiological importance. Seasonal human coronaviruses (HCoV) have been circulating for longer and, therefore, may offer insights into the long-term dynamics of reinfection for such viruses. <b>Methods:</b> Combining historical seroprevalence data from five studies covering the four circulating HCoVs with an age-structured reverse catalytic model, we estimated the likely duration of seropositivity following seroconversion. <b>Results:</b> We estimated that antibody persistence lasted between 0.9 (95% Credible interval: 0.6 - 1.6) and 3.8 (95% CrI: 2.0 - 7.4) years. Furthermore, we found the force of infection in older children and adults (those over 8.5 [95% CrI: 7.5 - 9.9] years) to be higher compared with young children in the majority of studies. <b>Conclusions:</b> These estimates of endemic HCoV dynamics could provide an indication of the future long-term infection and reinfection patterns of SARS-CoV-2.",,doi:https://doi.org/10.12688/wellcomeopenres.16701.3; html:https://europepmc.org/articles/PMC8517721; pdf:https://europepmc.org/articles/PMC8517721?pdf=render
+33550229,https://doi.org/10.1136/bmjopen-2020-040167,Assessing public support for extending smoke-free policies beyond enclosed public places and workplaces: protocol for a systematic review and meta-analysis.,"Boderie NW, Mölenberg FJ, Sheikh A, Bramer WM, Burdorf A, van Lenthe FJ, Been JV.",,BMJ open,2021,2021-02-05,Y,Tobacco smoke pollution; Attitude; Smoke-free Policy,,,"<h4>Introduction</h4>Smoke-free enclosed public environments are effective in reducing exposure to secondhand smoke and yield major public health benefits. Building on this, many countries are now implementing smoke-free policies regulating smoking beyond enclosed public places and workplaces. In order to successfully implement such 'novel smoke-free policies', public support is essential. We aim to provide the first comprehensive systematic review and meta-analysis assessing levels and determinants of public support for novel smoke-free policies.<h4>Methods and analysis</h4>The primary objective of this review is to summarise the level of public support for novel smoke-free policies. Eight online databases (Embase.com, Medline ALL Ovid, Web of Science Core Collection, WHO Library Database, Latin American and Caribbean Health Sciences Literature, Scientific Online Library Online, PsychINFO and Google Scholar) will be searched from 1 January 2004 by two independent researchers with no language restrictions. The initial search was performed on 15 April 2020 and will be updated prior to finalisation of the report. Studies are eligible if assessing support for novel smoke-free policies in the general population (age ≥16 years) and have a sample size of n≥400. Studies funded by the tobacco industry or evaluating support among groups with vested interest are excluded. The primary outcome is proportion of public support for smoke-free policies, subdivided according to the spaces covered: (1) indoor private spaces (eg, cars) (2) indoor semiprivate spaces (eg, multi-unit housing) (3) outdoor (semi)private spaces (eg, courtyards) (4) non-hospitality outdoor public spaces (eg, parks, hospital grounds, playgrounds) and (5) hospitality outdoor public spaces (eg, restaurant terraces). The secondary objective is to identify determinants associated with public support on three levels: (1) within-study determinants (eg, smoking status) (2) between-study determinants (eg, survey year) and (3) context-specific determinants (eg, social norms). Risk of bias will be assessed using the Mixed Methods Appraisal Tool and a sensitivity analysis will be performed excluding studies at high risk of bias.<h4>Ethics and dissemination</h4>No formal ethical approval is required. Findings will be disseminated to academics, policymakers and the general public.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/2/e040167.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-040167; html:https://europepmc.org/articles/PMC7925902; pdf:https://europepmc.org/articles/PMC7925902?pdf=render
 35991675,https://doi.org/10.1016/j.lana.2022.100335,Primary healthcare protects vulnerable populations from inequity in COVID-19 vaccination: An ecological analysis of nationwide data from Brazil.,"Bastos LSL, Aguilar S, Rache B, Maçaira P, Baião F, Cerbino-Neto J, Rocha R, Hamacher S, Ranzani OT, Bozza FA.",,Lancet regional health. Americas,2022,2022-08-17,Y,Vaccine; Socioeconomic Factors; Human Development; Primary Healthcare; Low-and-middle-income Countries; Covid19,,,"<h4>Background</h4>There is limited information on the inequity of access to vaccination in low-and-middle-income countries during the COVID-19 pandemic. Here, we described the progression of the Brazilian immunisation program for COVID-19, and the association of socioeconomic development with vaccination rates, considering the potential protective effect of primary health care coverage.<h4>Methods</h4>We performed an ecological analysis of COVID-19 immunisation data from the Brazilian National Immunization Program from January 17 to August 31, 2021. We analysed the dynamics of vaccine coverage in the adult population of 5,570 Brazilian municipalities. We estimated the association of human development index (HDI) levels (low, medium, and high) with age-sex standardised first dose coverage using a multivariable negative binomial regression model. We evaluated the interaction between the HDI and primary health care coverage. Finally, we compared the adjusted monthly progression of vaccination rates, hospital admission and in-hospital death rates among HDI levels.<h4>Findings</h4>From January 17 to August 31, 2021, 202,427,355 COVID-19 vaccine doses were administered in Brazil. By the end of the period, 64·2% of adults had first and 31·4% second doses, with more than 90% of those aged ≥60 years with primary scheme completed. Four distinct vaccine platforms were used in the country, ChAdOx1-S/nCoV-19, Sinovac-CoronaVac, BNT162b2, Ad26.COV2.S, composing 44·8%, 33·2%, 19·6%, and 2·4% of total doses, respectively. First dose coverage differed between municipalities with high, medium, and low HDI (Median [interquartile range] 72 [66, 79], 68 [61, 75] and 63 [55, 70] doses per 100 people, respectively). Municipalities with low (Rate Ratio [RR, 95% confidence interval]: 0·87 [0·85-0·88]) and medium (RR [95% CI]: 0·94 [0·93-0·95]) development were independently associated with lower vaccination rates compared to those with high HDI. Primary health care coverage modified the association of HDI and vaccination rate, improving vaccination rates in those municipalities of low HDI and high primary health care coverage. Low HDI municipalities presented a delayed decrease in adjusted in-hospital death rates by first dose coverage compared to high HDI locations.<h4>Interpretation</h4>In Brazil, socioeconomic disparities negatively impacted the first dose vaccination rate. However, the primary health care mitigated these disparities, suggesting that the primary health care coverage guarantees more equitable access to vaccines in vulnerable locations.<h4>Funding</h4>This work is part of the Grand Challenges ICODA pilot initiative, delivered by Health Data Research UK and funded by the Bill & Melinda Gates Foundation and the Minderoo Foundation. This study was supported by the National Council for Scientific and Technological Development (CNPq), the Coordination for the Improvement of Higher Education Personnel (CAPES) - Finance Code 001, Carlos Chagas Filho Foundation for Research Support of the State of Rio de Janeiro (FAPERJ) and the Pontifical Catholic University of Rio de Janeiro.",,doi:https://doi.org/10.1016/j.lana.2022.100335; doi:https://doi.org/10.1016/j.lana.2022.100335; html:https://europepmc.org/articles/PMC9381845; pdf:https://europepmc.org/articles/PMC9381845?pdf=render
 38388497,https://doi.org/10.1038/s41467-024-45355-3,Concordance of randomised controlled trials for artificial intelligence interventions with the CONSORT-AI reporting guidelines.,"Martindale APL, Llewellyn CD, de Visser RO, Ng B, Ngai V, Kale AU, di Ruffano LF, Golub RM, Collins GS, Moher D, McCradden MD, Oakden-Rayner L, Rivera SC, Calvert M, Kelly CJ, Lee CS, Yau C, Chan AW, Keane PA, Beam AL, Denniston AK, Liu X.",,Nature communications,2024,2024-02-22,Y,,,,"The Consolidated Standards of Reporting Trials extension for Artificial Intelligence interventions (CONSORT-AI) was published in September 2020. Since its publication, several randomised controlled trials (RCTs) of AI interventions have been published but their completeness and transparency of reporting is unknown. This systematic review assesses the completeness of reporting of AI RCTs following publication of CONSORT-AI and provides a comprehensive summary of RCTs published in recent years. 65 RCTs were identified, mostly conducted in China (37%) and USA (18%). Median concordance with CONSORT-AI reporting was 90% (IQR 77-94%), although only 10 RCTs explicitly reported its use. Several items were consistently under-reported, including algorithm version, accessibility of the AI intervention or code, and references to a study protocol. Only 3 of 52 included journals explicitly endorsed or mandated CONSORT-AI. Despite a generally high concordance amongst recent AI RCTs, some AI-specific considerations remain systematically poorly reported. Further encouragement of CONSORT-AI adoption by journals and funders may enable more complete adoption of the full CONSORT-AI guidelines.",,pdf:https://www.nature.com/articles/s41467-024-45355-3.pdf; doi:https://doi.org/10.1038/s41467-024-45355-3; html:https://europepmc.org/articles/PMC10883966; pdf:https://europepmc.org/articles/PMC10883966?pdf=render
 32548911,https://doi.org/10.1002/ehf2.12779,A registry-based algorithm to predict ejection fraction in patients with heart failure.,"Uijl A, Lund LH, Vaartjes I, Brugts JJ, Linssen GC, Asselbergs FW, Hoes AW, Dahlström U, Koudstaal S, Savarese G.",,ESC heart failure,2020,2020-06-17,Y,Prediction; Ejection fraction; Heart Failure; Electronic Health Records; Hfpef; Hfref; Hfmref,,,"<h4>Aims</h4>Left ventricular ejection fraction (EF) is required to categorize heart failure (HF) [i.e. HF with preserved (HFpEF), mid-range (HFmrEF), and reduced (HFrEF) EF] but is often not captured in population-based cohorts or non-HF registries. The aim was to create an algorithm that identifies EF subphenotypes for research purposes.<h4>Methods and results</h4>We included 42 061 HF patients from the Swedish Heart Failure Registry. As primary analysis, we performed two logistic regression models including 22 variables to predict (i) EF≥ vs. <50% and (ii) EF≥ vs. <40%. In the secondary analysis, we performed a multivariable multinomial analysis with 22 variables to create a model for all three separate EF subphenotypes: HFrEF vs. HFmrEF vs. HFpEF. The models were validated in the database from the CHECK-HF study, a cross-sectional survey of 10 627 patients from the Netherlands. The C-statistic (discrimination) was 0.78 [95% confidence interval (CI) 0.77-0.78] for EF ≥50% and 0.76 (95% CI 0.75-0.76) for EF ≥40%. Similar results were achieved for HFrEF and HFpEF in the multinomial model, but the C-statistic for HFmrEF was lower: 0.63 (95% CI 0.63-0.64). The external validation showed similar discriminative ability to the development cohort.<h4>Conclusions</h4>Routine clinical characteristics could potentially be used to identify different EF subphenotypes in databases where EF is not readily available. Accuracy was good for the prediction of HFpEF and HFrEF but lower for HFmrEF. The proposed algorithm enables more effective research on HF in the big data setting.",,doi:https://doi.org/10.1002/ehf2.12779; doi:https://doi.org/10.1002/ehf2.12779; html:https://europepmc.org/articles/PMC7524089; pdf:https://europepmc.org/articles/PMC7524089?pdf=render
 37128097,https://doi.org/10.1038/s43016-020-0092-z,RETRACTED ARTICLE: Dietary metabotype modelling predicts individual responses to dietary interventions.,"Garcia-Perez I, Posma JM, Chambers ES, Mathers JC, Draper J, Beckmann M, Nicholson JK, Holmes E, Frost G.",,Nature food,2020,2020-06-17,N,,,,"Habitual consumption of poor quality diets is linked directly to risk factors for many non-communicable diseases. This has resulted in the vast majority of countries and the World Health Organization developing policies for healthy eating to reduce the prevalence of non-communicable diseases in the population. However, there is mounting evidence of variability in individual metabolic responses to any dietary intervention. We have developed a method for applying a pipeline for understanding interindividual differences in response to diet, based on coupling data from highly controlled dietary studies with deep metabolic phenotyping. In this feasibility study, we create an individual Dietary Metabotype Score (DMS) that embodies interindividual variability in dietary response and captures consequent dynamic changes in concentrations of urinary metabolites. We find an inverse relationship between the DMS and blood glucose concentration. There is also a relationship between the DMS and urinary metabolic energy loss. Furthermore, we use a metabolic entropy approach to visualize individual and collective responses to dietary interventions. Potentially, the DMS offers a method to target and to enhance dietary response at the individual level, thereby reducing the burden of non-communicable diseases at the population level.",,html:http://hdl.handle.net/10044/1/80100; doi:https://doi.org/10.1038/s43016-020-0092-z
-37723491,https://doi.org/10.1186/s13073-023-01221-3,Identification of novel genetic risk factors of dilated cardiomyopathy: from canine to human.,"Niskanen JE, Ohlsson Å, Ljungvall I, Drögemüller M, Ernst RF, Dooijes D, van Deutekom HWM, van Tintelen JP, Snijders Blok CJB, van Vugt M, van Setten J, Asselbergs FW, Petrič AD, Salonen M, Hundi S, Hörtenhuber M, DoGA consortium, Kere J, Pyle WG, Donner J, Postma AV, Leeb T, Andersson G, Hytönen MK, Häggström J, Wiberg M, Friederich J, Eberhard J, Harakalova M, van Steenbeek FG, Wess G, Lohi H.",,Genome medicine,2023,2023-09-18,Y,Genetics; Cardiac; Arrhythmia; Cardiology; Gwas; Transcriptomics; Complex Trait; Companion Animal,,,"<h4>Background</h4>Dilated cardiomyopathy (DCM) is a life-threatening heart disease and a common cause of heart failure due to systolic dysfunction and subsequent left or biventricular dilatation. A significant number of cases have a genetic etiology; however, as a complex disease, the exact genetic risk factors are largely unknown, and many patients remain without a molecular diagnosis.<h4>Methods</h4>We performed GWAS followed by whole-genome, transcriptome, and immunohistochemical analyses in a spontaneously occurring canine model of DCM. Canine gene discovery was followed up in three human DCM cohorts.<h4>Results</h4>Our results revealed two independent additive loci associated with the typical DCM phenotype comprising left ventricular systolic dysfunction and dilatation. We highlight two novel candidate genes, RNF207 and PRKAA2, known for their involvement in cardiac action potentials, energy homeostasis, and morphology. We further illustrate the distinct genetic etiologies underlying the typical DCM phenotype and ventricular premature contractions. Finally, we followed up on the canine discoveries in human DCM patients and discovered candidate variants in our two novel genes.<h4>Conclusions</h4>Collectively, our study yields insight into the molecular pathophysiology of DCM and provides a large animal model for preclinical studies.",,pdf:https://genomemedicine.biomedcentral.com/counter/pdf/10.1186/s13073-023-01221-3; doi:https://doi.org/10.1186/s13073-023-01221-3; html:https://europepmc.org/articles/PMC10506233; pdf:https://europepmc.org/articles/PMC10506233?pdf=render
 35416614,https://doi.org/10.1007/s43441-022-00394-0,Opportunities and Risks of UK Medical Device Reform.,"Han JED, Ibrahim H, Aiyegbusi OL, Liu X, Marston E, Denniston AK, Calvert MJ.",,Therapeutic innovation & regulatory science,2022,2022-04-13,Y,Regulations; Medical devices; In Vitro Diagnostics; Ce Mark; Ukca,,,"<h4>Objectives</h4>To identify the potential opportunities and risks around future UK regulatory reform of medical devices.<h4>Design</h4>A mixed methods approach, comprising a rapid literature review, one-to-one, semi-structured interviews with key stakeholders, a multidisciplinary stakeholder workshop, and a post-workshop survey.<h4>Setting</h4>United Kingdom.<h4>Participants</h4>32 key stakeholders across the medical device sector were identified both from the public and private sectors.<h4>Results</h4>Opportunities relating to regulatory independence were identified, including the potential to create and implement a regulatory framework that ensures availability of medical devices; innovation and investment potential; and safety to the citizens of the UK. The most significant risks identified included threats to the safety of individual patients and the wider health system arising from the delay in awaiting regulatory approval due to the shortage of approved bodies; and reduced competitiveness of UK market and device manufacturers. Recommendations were identified to mitigate risks, centred on harnessing broader cross-sector collaborations, promoting patient and public partnership, and maximizing international engagement.<h4>Conclusions</h4>The UK's medical device sector is at a time-critical juncture to construct a regulatory framework to navigate its exit of Europe and respond to Europe's transition to new medical device regulations whilst also addressing the ongoing demand for rapid approval for new devices in response to the global pandemic. Investment, capacity-building, and international engagement will play a central role in mitigating risks and maximizing opportunities for medical device regulation.",,pdf:https://link.springer.com/content/pdf/10.1007/s43441-022-00394-0.pdf; doi:https://doi.org/10.1007/s43441-022-00394-0; html:https://europepmc.org/articles/PMC9007047; pdf:https://europepmc.org/articles/PMC9007047?pdf=render
+37723491,https://doi.org/10.1186/s13073-023-01221-3,Identification of novel genetic risk factors of dilated cardiomyopathy: from canine to human.,"Niskanen JE, Ohlsson Å, Ljungvall I, Drögemüller M, Ernst RF, Dooijes D, van Deutekom HWM, van Tintelen JP, Snijders Blok CJB, van Vugt M, van Setten J, Asselbergs FW, Petrič AD, Salonen M, Hundi S, Hörtenhuber M, DoGA consortium, Kere J, Pyle WG, Donner J, Postma AV, Leeb T, Andersson G, Hytönen MK, Häggström J, Wiberg M, Friederich J, Eberhard J, Harakalova M, van Steenbeek FG, Wess G, Lohi H.",,Genome medicine,2023,2023-09-18,Y,Genetics; Cardiac; Arrhythmia; Cardiology; Gwas; Transcriptomics; Complex Trait; Companion Animal,,,"<h4>Background</h4>Dilated cardiomyopathy (DCM) is a life-threatening heart disease and a common cause of heart failure due to systolic dysfunction and subsequent left or biventricular dilatation. A significant number of cases have a genetic etiology; however, as a complex disease, the exact genetic risk factors are largely unknown, and many patients remain without a molecular diagnosis.<h4>Methods</h4>We performed GWAS followed by whole-genome, transcriptome, and immunohistochemical analyses in a spontaneously occurring canine model of DCM. Canine gene discovery was followed up in three human DCM cohorts.<h4>Results</h4>Our results revealed two independent additive loci associated with the typical DCM phenotype comprising left ventricular systolic dysfunction and dilatation. We highlight two novel candidate genes, RNF207 and PRKAA2, known for their involvement in cardiac action potentials, energy homeostasis, and morphology. We further illustrate the distinct genetic etiologies underlying the typical DCM phenotype and ventricular premature contractions. Finally, we followed up on the canine discoveries in human DCM patients and discovered candidate variants in our two novel genes.<h4>Conclusions</h4>Collectively, our study yields insight into the molecular pathophysiology of DCM and provides a large animal model for preclinical studies.",,pdf:https://genomemedicine.biomedcentral.com/counter/pdf/10.1186/s13073-023-01221-3; doi:https://doi.org/10.1186/s13073-023-01221-3; html:https://europepmc.org/articles/PMC10506233; pdf:https://europepmc.org/articles/PMC10506233?pdf=render
 31810636,https://doi.org/10.1016/j.injury.2019.11.034,Twelve month mortality rates and independent living in people aged 65 years or older after isolated hip fracture: A prospective registry-based study.,"Giummarra MJ, Ekegren CL, Gong J, Simpson P, Cameron PA, Edwards E, Gabbe BJ.",,Injury,2020,2019-11-23,N,Function; Mortality; Recovery; epidemiology; Falls,,,"<h4>Introduction</h4>This study investigated which patient and injury characteristics are associated with 12-month mortality rates and living independently after isolated hip fracture.<h4>Methods</h4>Older adults aged ≥65 years were included if they had an isolated hip fracture, were admitted to hospital between July 2009 and June 2016, inclusive, and were registered to the Victorian Orthopaedic Trauma Outcomes Registry. Mortality up to 12 months (365 days) post-injury, and functional outcomes (Glasgow Outcome Scale-Extended; GOS-E) at 12 months post-injury were examined. Multivariable Cox proportional hazards regression was used to estimate adjusted hazard ratios (aHRs), and multivariable logistic regression was used to identify predictors of living independently compared with severe disability or death on the GOS-E.<h4>Results</h4>4,912 patients were included, of whom 28% died, 46% had moderate-severe disability, and 26% were living independently 12 months post-injury. Mortality rates were lower in women (aHR=0.56, 95%CI: 0.50, 0.63), and in people injured in a high fall vs low fall (aHR=0.47, 95%CI: 0.31, 0.72). Mortality rates were higher in people in the older age groups (75-84 years: aHR=1.53, 95%CI: 1.21, 1.93; 95+ years: aHR=3.58, 95%CI: 2.68, 4.77), living in areas with the highest level of socioeconomic disadvantage (aHR=1.25, 95%CI: 1.01, 1.55), with a Charlson Comorbidity Index weighting of one (aHR=1.60, 95%CI: 1.36, 1.88) or more than one (aHR=2.21, 95%CI: 1.94, 2.53), whose injury occurred in a residential institution versus at home (aHR=2.63, 95%CI: 1.97, 3.52), that resulted in intensive care unit admission (aHR=1.68, 95%CI: 1.21, 2.32), and in people who did not have surgery versus people who had internal fixation (aHR=1.65, 95%CI: 1.33, 2.04). Independent living was inversely associated with most of the same characteristics; however, people also had lower odds of living independently if they were from metropolitan residential areas versus rural areas (aOR=0.77, 95%CI: 0.62, 0.96), or had mild to moderate (aOR=0.33, 95%CI: 0.27, 0.39) or marked to severe (aOR=0.13, 95%CI: 0.09, 0.20) preinjury disability vs no preinjury disability.<h4>Conclusions</h4>Characteristics that are associated with social disadvantage, frailty, poor health and reduced independence before injury were associated with increased rates of death and reduced odds of living independently 12 months after isolated hip fracture.",,doi:https://doi.org/10.1016/j.injury.2019.11.034
 32845538,https://doi.org/10.1634/theoncologist.2020-0572,Cancer and Risk of COVID-19 Through a General Community Survey.,"Lee KA, Ma W, Sikavi DR, Drew DA, Nguyen LH, Bowyer RCE, Cardoso MJ, Fall T, Freidin MB, Gomez M, Graham M, Guo CG, Joshi AD, Kwon S, Lo CH, Lochlainn MN, Menni C, Murray B, Mehta R, Song M, Sudre CH, Bataille V, Varsavsky T, Visconti A, Franks PW, Wolf J, Steves CJ, Ourselin S, Spector TD, Chan AT, COPE consortium.",,The oncologist,2021,2020-09-07,Y,,,,"Individuals with cancer may be at high risk for coronavirus disease 2019 (COVID-19) and adverse outcomes. However, evidence from large population-based studies examining whether cancer and cancer-related therapy exacerbates the risk of COVID-19 infection is still limited. Data were collected from the COVID Symptom Study smartphone application since March 29 through May 8, 2020. Among 23,266 participants with cancer and 1,784,293 without cancer, we documented 10,404 reports of a positive COVID-19 test. Compared with participants without cancer, those living with cancer had a 60% increased risk of a positive COVID-19 test. Among patients with cancer, current treatment with chemotherapy or immunotherapy was associated with a 2.2-fold increased risk of a positive test. The association between cancer and COVID-19 infection was stronger among participants >65 years and males. Future studies are needed to identify subgroups by tumor types and treatment regimens who are particularly at risk for COVID-19 infection and adverse outcomes.",,pdf:https://academic.oup.com/oncolo/article-pdf/26/1/e182/41923952/oncolo_26_1_n_a.pdf; doi:https://doi.org/10.1634/theoncologist.2020-0572; html:https://europepmc.org/articles/PMC7460944; pdf:https://europepmc.org/articles/PMC7460944?pdf=render
 32878619,https://doi.org/10.1186/s12916-020-01726-3,COVID-19 length of hospital stay: a systematic review and data synthesis.,"Rees EM, Nightingale ES, Jafari Y, Waterlow NR, Clifford S, B Pearson CA, Group CW, Jombart T, Procter SR, Knight GM.",,BMC medicine,2020,2020-09-03,Y,Length Of Stay; Hospitalisation; Icu Capacity; Covid-19; Sars-cov-2; Bed Demand,,,"<h4>Background</h4>The COVID-19 pandemic has placed an unprecedented strain on health systems, with rapidly increasing demand for healthcare in hospitals and intensive care units (ICUs) worldwide. As the pandemic escalates, determining the resulting needs for healthcare resources (beds, staff, equipment) has become a key priority for many countries. Projecting future demand requires estimates of how long patients with COVID-19 need different levels of hospital care.<h4>Methods</h4>We performed a systematic review of early evidence on length of stay (LoS) of patients with COVID-19 in hospital and in ICU. We subsequently developed a method to generate LoS distributions which combines summary statistics reported in multiple studies, accounting for differences in sample sizes. Applying this approach, we provide distributions for total hospital and ICU LoS from studies in China and elsewhere, for use by the community.<h4>Results</h4>We identified 52 studies, the majority from China (46/52). Median hospital LoS ranged from 4 to 53 days within China, and 4 to 21 days outside of China, across 45 studies. ICU LoS was reported by eight studies-four each within and outside China-with median values ranging from 6 to 12 and 4 to 19 days, respectively. Our summary distributions have a median hospital LoS of 14 (IQR 10-19) days for China, compared with 5 (IQR 3-9) days outside of China. For ICU, the summary distributions are more similar (median (IQR) of 8 (5-13) days for China and 7 (4-11) days outside of China). There was a visible difference by discharge status, with patients who were discharged alive having longer LoS than those who died during their admission, but no trend associated with study date.<h4>Conclusion</h4>Patients with COVID-19 in China appeared to remain in hospital for longer than elsewhere. This may be explained by differences in criteria for admission and discharge between countries, and different timing within the pandemic. In the absence of local data, the combined summary LoS distributions provided here can be used to model bed demands for contingency planning and then updated, with the novel method presented here, as more studies with aggregated statistics emerge outside China.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-020-01726-3; doi:https://doi.org/10.1186/s12916-020-01726-3; html:https://europepmc.org/articles/PMC7467845; pdf:https://europepmc.org/articles/PMC7467845?pdf=render
@@ -2257,8 +2259,8 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 31950165,https://doi.org/10.1093/pubmed/fdz188,Is child weight status correctly reported to parents? Cross-sectional analysis of National Child Measurement Programme data using ethnic-specific BMI adjustments.,"Firman N, Boomla K, Hudda MT, Robson J, Whincup P, Dezateux C.",,"Journal of public health (Oxford, England)",2020,2020-11-01,Y,Obesity; Children; Ethnicity,,,"<h4>Background</h4>BMI underestimates and overestimates body fat in children from South Asian and Black ethnic groups, respectively.<h4>Methods</h4>We used cross-sectional NCMP data (2015-17) for 38 270 children in three inner-London local authorities: City & Hackney, Newham and Tower Hamlets (41% South Asian, 18.8% Black): 20 439 4-5 year-olds (48.9% girls) and 17 831 10-11 year-olds (49.1% girls). We estimated the proportion of parents who would have received different information about their child's weight status, and the area-level prevalence of obesity-defined as ≥98th centile-had ethnic-specific BMI adjustments been employed in the English National Child Measurement Programme (NCMP).<h4>Results</h4>Had ethnic-specific adjustment been employed, 19.7% (3112/15 830) of parents of children from South Asian backgrounds would have been informed that their child was in a heavier weight category, and 19.1% (1381/7217) of parents of children from Black backgrounds would have been informed that their child was in a lighter weight category. Ethnic-specific adjustment increased obesity prevalence from 7.9% (95% CI: 7.6, 8.3) to 9.1% (8.7, 9.5) amongst 4-5 year-olds and from 17.5% (16.9, 18.1) to 18.8% (18.2, 19.4) amongst 10-11 year-olds.<h4>Conclusions</h4>Ethnic-specific adjustment in the NCMP would ensure equitable categorization of weight status, provide correct information to parents and support local service provision for families.",,pdf:https://academic.oup.com/jpubhealth/article-pdf/42/4/e541/34469388/fdz188.pdf; doi:https://doi.org/10.1093/pubmed/fdz188; html:https://europepmc.org/articles/PMC7685848; pdf:https://europepmc.org/articles/PMC7685848?pdf=render
 33910683,https://doi.org/10.1016/j.injury.2021.04.033,"Characteristics, management and outcomes of patients with severe traumatic brain injury in Victoria, Australia compared to United Kingdom and Europe: A comparison between two harmonised prospective cohort studies.","Wiegers EJA, Trapani T, Gabbe BJ, Gantner D, Lecky F, Maas AIR, Menon DK, Murray L, Rosenfeld JV, Vallance S, Lingsma HF, Steyerberg EW, Cooper DJ, CENTER-TBI and OzENTER-TBI investigators and participants12, Collaboration groups: CENTER-TBI and OzENTER-TBI investigators and participants.",,Injury,2021,2021-04-20,N,Traumatic brain injury; Intensive Care; Comparative Effectiveness Research; Trauma Systems; Outcome Comparison,,,"<h4>Objective</h4>The aim of this manuscript is to compare characteristics, management, and outcomes of patients with severe Traumatic Brain Injury (TBI) between Australia, the United Kingdom (UK) and Europe.<h4>Methods</h4>We enrolled patients with severe TBI in Victoria, Australia (OzENTER-TBI), in the UK and Europe (CENTER-TBI) from 2015 to 2017. Main outcome measures were mortality and unfavourable outcome (Glasgow Outcome Scale Extended <5) 6 months after injury. Expected outcomes were compared according to the IMPACT-CT prognostic model, with observed to expected (O/E) ratios and 95% confidence intervals.<h4>Results</h4>We included 107 patients from Australia, 171 from UK, and 596 from Europe. Compared to the UK and Europe, patients in Australia were younger (median 32 vs 44 vs 44 years), a larger proportion had secondary brain insults including hypotension (30% vs 17% vs 21%) and a larger proportion received ICP monitoring (75% vs 74% vs 58%). Hospital length of stay was shorter in Australia than in the UK (median: 17 vs 23 vs 16 days), and a higher proportion of patients were discharged to a rehabilitation unit in Australia than in the UK and Europe (64% vs 26% vs 28%). Mortality overall was lower than expected (27% vs 35%, O/E ratio 0.77 [95% CI: 0.64 - 0.87]. O/E ratios were comparable between regions for mortality in Australia 0.86 [95% CI: 0.49-1.23] vs UK 0.82 [0.51-1.15] vs Europe 0.76 [0.60-0.87]). Unfavourable outcome rates overall were in line with historic expectations (O/E ratio 1.32 [0.96-1.68] vs 1.13 [0.84-1.42] vs 0.96 [0.85-1.09]).<h4>Conclusions</h4>There are major differences in case-mix between Australia, UK, and Europe; Australian patients are younger and have a higher rate of secondary brain insults. Despite some differences in management and discharge policies, mortality was less than expected overall, and did not differ between regions. Functional outcomes were similar between regions, but worse than expected, emphasizing the need to improve treatment for patients with severe TBI.",,pdf:http://www.injuryjournal.com/article/S0020138321003429/pdf; doi:https://doi.org/10.1016/j.injury.2021.04.033
 32835195,https://doi.org/10.1016/s2589-7500(20)30134-5,The effects of physical distancing on population mobility during the COVID-19 pandemic in the UK.,"Drake TM, Docherty AB, Weiser TG, Yule S, Sheikh A, Harrison EM.",,The Lancet. Digital health,2020,2020-06-12,Y,,,,,,doi:https://doi.org/10.1016/s2589-7500(20)30134-5; doi:https://doi.org/10.1016/S2589-7500(20)30134-5; html:https://europepmc.org/articles/PMC7292602; pdf:https://europepmc.org/articles/PMC7292602?pdf=render
-34547359,https://doi.org/10.1016/j.jaad.2021.09.018,Mixed evidence on the relationship between socioeconomic position and atopic dermatitis: A systematic review.,"Bajwa H, Baghchechi M, Mujahid M, Kang Dufour MS, Langan SM, Abuabara K.",,Journal of the American Academy of Dermatology,2022,2021-09-20,N,dermatitis; Socioeconomic status; Eczema; Atopic; Socioeconomic Position,,,"<h4>Background</h4>Lower socioeconomic position usually portends worse health outcomes, but multiple studies have found that atopic dermatitis is associated with higher socioeconomic position. The nature of this relationship remains unclear.<h4>Objective</h4>To systematically review the literature on socioeconomic position and atopic dermatitis and determine whether the association varies by patient or study characteristics.<h4>Methods</h4>A literature search was conducted in the PubMed and Embase databases. Individual-level studies addressing the association between all measures of socioeconomic position and the prevalence or incidence of atopic dermatitis were eligible for inclusion. Two independent reviewers screened all texts and extracted all data for qualitative synthesis.<h4>Results</h4>Eighty-eight studies met the inclusion criteria. Of the 88 studies, 42% (37) found a positive association between atopic dermatitis and socioeconomic position, 15% (13) found a negative association, and 43% (38) found a null or inconsistent association. Studies conducted in Europe, among children, and based on self-report of eczema were more likely to find a positive association with socioeconomic position.<h4>Limitations</h4>Studies varied both in terms of the measurement of socioeconomic position and the definition of atopic dermatitis, limiting quantitative synthesis.<h4>Conclusion</h4>The evidence of a positive association between atopic dermatitis and socioeconomic position is not consistent.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8810617; doi:https://doi.org/10.1016/j.jaad.2021.09.018; html:https://europepmc.org/articles/PMC8810617; pdf:https://europepmc.org/articles/PMC8810617?pdf=render; doi:https://doi.org/10.1016/j.jaad.2021.09.018
 32724101,https://doi.org/10.1038/s41467-020-17477-x,Neonatal genetics of gene expression reveal potential origins of autoimmune and allergic disease risk.,"Huang QQ, Tang HHF, Teo SM, Mok D, Ritchie SC, Nath AP, Brozynska M, Salim A, Bakshi A, Holt BJ, Khor CC, Sly PD, Holt PG, Holt KE, Inouye M.",,Nature communications,2020,2020-07-28,Y,,,,"Chronic immune-mediated diseases of adulthood often originate in early childhood. To investigate genetic associations between neonatal immunity and disease, we map expression quantitative trait loci (eQTLs) in resting myeloid cells and CD4<sup>+</sup> T cells from cord blood samples, as well as in response to lipopolysaccharide (LPS) or phytohemagglutinin (PHA) stimulation, respectively. Cis-eQTLs are largely specific to cell type or stimulation, and 31% and 52% of genes with cis-eQTLs have response eQTLs (reQTLs) in myeloid cells and T cells, respectively. We identified cis regulatory factors acting as mediators of trans effects. There is extensive colocalisation between condition-specific neonatal cis-eQTLs and variants associated with immune-mediated diseases, in particular CTSH had widespread colocalisation across diseases. Mendelian randomisation shows causal neonatal gene expression effects on disease risk for BTN3A2, HLA-C and others. Our study elucidates the genetics of gene expression in neonatal immune cells, and aetiological origins of autoimmune and allergic diseases.",,pdf:https://www.nature.com/articles/s41467-020-17477-x.pdf; doi:https://doi.org/10.1038/s41467-020-17477-x; html:https://europepmc.org/articles/PMC7387553; pdf:https://europepmc.org/articles/PMC7387553?pdf=render
+34547359,https://doi.org/10.1016/j.jaad.2021.09.018,Mixed evidence on the relationship between socioeconomic position and atopic dermatitis: A systematic review.,"Bajwa H, Baghchechi M, Mujahid M, Kang Dufour MS, Langan SM, Abuabara K.",,Journal of the American Academy of Dermatology,2022,2021-09-20,N,dermatitis; Socioeconomic status; Eczema; Atopic; Socioeconomic Position,,,"<h4>Background</h4>Lower socioeconomic position usually portends worse health outcomes, but multiple studies have found that atopic dermatitis is associated with higher socioeconomic position. The nature of this relationship remains unclear.<h4>Objective</h4>To systematically review the literature on socioeconomic position and atopic dermatitis and determine whether the association varies by patient or study characteristics.<h4>Methods</h4>A literature search was conducted in the PubMed and Embase databases. Individual-level studies addressing the association between all measures of socioeconomic position and the prevalence or incidence of atopic dermatitis were eligible for inclusion. Two independent reviewers screened all texts and extracted all data for qualitative synthesis.<h4>Results</h4>Eighty-eight studies met the inclusion criteria. Of the 88 studies, 42% (37) found a positive association between atopic dermatitis and socioeconomic position, 15% (13) found a negative association, and 43% (38) found a null or inconsistent association. Studies conducted in Europe, among children, and based on self-report of eczema were more likely to find a positive association with socioeconomic position.<h4>Limitations</h4>Studies varied both in terms of the measurement of socioeconomic position and the definition of atopic dermatitis, limiting quantitative synthesis.<h4>Conclusion</h4>The evidence of a positive association between atopic dermatitis and socioeconomic position is not consistent.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8810617; doi:https://doi.org/10.1016/j.jaad.2021.09.018; html:https://europepmc.org/articles/PMC8810617; pdf:https://europepmc.org/articles/PMC8810617?pdf=render; doi:https://doi.org/10.1016/j.jaad.2021.09.018
 33201485,https://doi.org/10.1007/s12471-020-01517-8,ONCOR: design of the Dutch cardio-oncology registry.,"Kamphuis JAM, Linschoten M, Cramer MJ, Alsemgeest F, van Kessel DJW, Urgel K, Post MC, Manintveld OC, Hassing HC, Liesting C, Wardeh AJ, Olde Bijvank EGM, Schaap J, Stevense-den Boer AM, Doevendans PA, Asselbergs FW, Teske AJ.",,Netherlands heart journal : monthly journal of the Netherlands Society of Cardiology and the Netherlands Heart Foundation,2021,2020-11-17,Y,Research Design; Registries; Cardio-oncology,,,"<h4>Background</h4>The relative new subspecialty 'cardio-oncology' was established to meet the growing demand for an interdisciplinary approach to the management of cancer therapy-related cardiovascular adverse events. In recent years, specialised cardio-oncology services have been implemented worldwide, which all strive to improve the cardiovascular health of cancer patients. However, limited data are currently available on the outcomes and experiences of these specialised services, and optimal strategies for cardio-oncological care have not been established.<h4>Aim</h4>The ONCOR registry has been created for prospective data collection and evaluation of cardio-oncological care in daily practice.<h4>Methods</h4>Dutch hospitals using a standardised cardio-oncology care pathway are included in this national, multicentre, observational cohort study. All patients visiting these cardio-oncology services are eligible for study inclusion. Data collection at baseline consists of the (planned) cancer treatment and the cardiovascular risk profile, which are used to estimate the cardiotoxic risk. Information regarding invasive and noninvasive tests is collected during the time patients receive cardio-oncological care. Outcome data consist of the incidence of cardiovascular complications and major adverse cardiac events, and the impact of these events on the oncological treatment.<h4>Discussion</h4>Outcomes of the ONCOR registry may aid in gaining more insight into the incidence of cancer therapy-related cardiovascular complications. The registry facilitates research on mechanisms of cardiovascular complications and on diagnostic, prognostic and therapeutic strategies. In addition, it provides a platform for future (interventional) studies. Centres with cardio-oncology services that are interested in contributing to the ONCOR registry are hereby invited to participate.",,pdf:https://link.springer.com/content/pdf/10.1007/s12471-020-01517-8.pdf; doi:https://doi.org/10.1007/s12471-020-01517-8; html:https://europepmc.org/articles/PMC8062648; pdf:https://europepmc.org/articles/PMC8062648?pdf=render
 31358974,https://doi.org/10.1038/s41562-019-0653-z,New alcohol-related genes suggest shared genetic mechanisms with neuropsychiatric disorders.,"Evangelou E, Gao H, Chu C, Ntritsos G, Blakeley P, Butts AR, Pazoki R, Suzuki H, Koskeridis F, Yiorkas AM, Karaman I, Elliott J, Luo Q, Aeschbacher S, Bartz TM, Baumeister SE, Braund PS, Brown MR, Brody JA, Clarke TK, Dimou N, Faul JD, Homuth G, Jackson AU, Kentistou KA, Joshi PK, Lemaitre RN, Lind PA, Lyytikäinen LP, Mangino M, Milaneschi Y, Nelson CP, Nolte IM, Perälä MM, Polasek O, Porteous D, Ratliff SM, Smith JA, Stančáková A, Teumer A, Tuominen S, Thériault S, Vangipurapu J, Whitfield JB, Wood A, Yao J, Yu B, Zhao W, Arking DE, Auvinen J, Liu C, Männikkö M, Risch L, Rotter JI, Snieder H, Veijola J, Blakemore AI, Boehnke M, Campbell H, Conen D, Eriksson JG, Grabe HJ, Guo X, van der Harst P, Hartman CA, Hayward C, Heath AC, Jarvelin MR, Kähönen M, Kardia SLR, Kühne M, Kuusisto J, Laakso M, Lahti J, Lehtimäki T, McIntosh AM, Mohlke KL, Morrison AC, Martin NG, Oldehinkel AJ, Penninx BWJH, Psaty BM, Raitakari OT, Rudan I, Samani NJ, Scott LJ, Spector TD, Verweij N, Weir DR, Wilson JF, Levy D, Tzoulaki I, Bell JD, Matthews PM, Rothenfluh A, Desrivières S, Schumann G, Elliott P.",,Nature human behaviour,2019,2019-07-29,N,,,,"Excessive alcohol consumption is one of the main causes of death and disability worldwide. Alcohol consumption is a heritable complex trait. Here we conducted a meta-analysis of genome-wide association studies of alcohol consumption (g d<sup>-1</sup>) from the UK Biobank, the Alcohol Genome-Wide Consortium and the Cohorts for Heart and Aging Research in Genomic Epidemiology Plus consortia, collecting data from 480,842 people of European descent to decipher the genetic architecture of alcohol intake. We identified 46 new common loci and investigated their potential functional importance using magnetic resonance imaging data and gene expression studies. We identify genetic pathways associated with alcohol consumption and suggest genetic mechanisms that are shared with neuropsychiatric disorders such as schizophrenia.",,pdf:https://boris.unibe.ch/174991/1/nihms-1649425.pdf; doi:https://doi.org/10.1038/s41562-019-0653-z; html:https://europepmc.org/articles/PMC7711277; pdf:https://europepmc.org/articles/PMC7711277?pdf=render; doi:https://doi.org/10.1038/s41562-019-0653-z
 34568585,https://doi.org/10.23889/ijpds.v6i1.1671,Linking education and hospital data in England: linkage process and quality.,"Libuy N, Harron K, Gilbert R, Caulton R, Cameron E, Blackburn R.",,International journal of population data science,2021,2021-09-16,Y,Bias; Data Linkage; Record Linkage; Administrative Data; Hospital Records; Linkage Error; Educational Records,,,"<h4>Introduction</h4>Linkage of administrative data for universal state education and National Health Service (NHS) hospital care would enable research into the inter-relationships between education and health for all children in England.<h4>Objectives</h4>We aim to describe the linkage process and evaluate the quality of linkage of four one-year birth cohorts within the National Pupil Database (NPD) and Hospital Episode Statistics (HES).<h4>Methods</h4>We used multi-step deterministic linkage algorithms to link longitudinal records from state schools to the chronology of records in the NHS Personal Demographics Service (PDS; linkage stage 1), and HES (linkage stage 2). We calculated linkage rates and compared pupil characteristics in linked and unlinked samples for each stage of linkage and each cohort (1990/91, 1996/97, 1999/00, and 2004/05).<h4>Results</h4>Of the 2,287,671 pupil records, 2,174,601 (95%) linked to HES. Linkage rates improved over time (92% in 1990/91 to 99% in 2004/05). Ethnic minority pupils and those living in more deprived areas were less likely to be matched to hospital records, but differences in pupil characteristics between linked and unlinked samples were moderate to small.<h4>Conclusion</h4>We linked nearly all pupils to at least one hospital record. The high coverage of the linkage represents a unique opportunity for wide-scale analyses across the domains of health and education. However, missed links disproportionately affected ethnic minorities or those living in the poorest neighbourhoods: selection bias could be mitigated by increasing the quality and completeness of identifiers recorded in administrative data or the application of statistical methods that account for missed links.<h4>Highlights</h4>Longitudinal administrative records for all children attending state school and acute hospital services in England have been used for research for more than two decades, but lack of a shared unique identifier has limited scope for linkage between these databases.We applied multi-step deterministic linkage algorithms to 4 one-year cohorts of children born 1 September-31 August in 1990/91, 1996/97, 1999/00 and 2004/05. In stage 1, full names, date of birth, and postcode histories from education data in the National Pupil Database were linked to the NHS Personal Demographic Service. In stage 2, NHS number, postcode, date of birth and sex were linked to hospital records in Hospital Episode Statistics.Between 92% and 99% of school pupils linked to at least one hospital record. Ethnic minority pupils and pupils who were living in the most deprived areas were least likely to link. Ethnic minority pupils were less likely than white children to link at the first step in both algorithms.Bias due to linkage errors could lead to an underestimate of the health needs in disadvantaged groups. Improved data quality, more sensitive linkage algorithms, and/or statistical methods that account for missed links in analyses, should be considered to reduce linkage bias.",,pdf:https://ijpds.org/article/download/1671/3248; doi:https://doi.org/10.23889/ijpds.v6i1.1671; html:https://europepmc.org/articles/PMC8445153; pdf:https://europepmc.org/articles/PMC8445153?pdf=render
@@ -2267,14 +2269,14 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 32750130,https://doi.org/10.1182/bloodadvances.2020001894,Development and validation of a universal blood donor genotyping platform: a multinational prospective study.,"Gleadall NS, Veldhuisen B, Gollub J, Butterworth AS, Ord J, Penkett CJ, Timmer TC, Sauer CM, van der Bolt N, Brown C, Brugger K, Dilthey AT, Duarte D, Grimsley S, van den Hurk K, Jongerius JM, Luken J, Megy K, Miflin G, Nelson CS, Prinsze FJ, Sambrook J, Simeoni I, Sweeting M, Thornton N, Trompeter S, Tuna S, Varma R, Walker MR, NIHR BioResource, Danesh J, Roberts DJ, Ouwehand WH, Stirrups KE, Rendon A, Westhoff CM, Di Angelantonio E, van der Schoot CE, Astle WJ, Watkins NA, Lane WJ.",,Blood advances,2020,2020-08-01,N,,,,"Each year, blood transfusions save millions of lives. However, under current blood-matching practices, sensitization to non-self-antigens is an unavoidable adverse side effect of transfusion. We describe a universal donor typing platform that could be adopted by blood services worldwide to facilitate a universal extended blood-matching policy and reduce sensitization rates. This DNA-based test is capable of simultaneously typing most clinically relevant red blood cell (RBC), human platelet (HPA), and human leukocyte (HLA) antigens. Validation was performed, using samples from 7927 European, 27 South Asian, 21 East Asian, and 9 African blood donors enrolled in 2 national biobanks. We illustrated the usefulness of the platform by analyzing antibody data from patients sensitized with multiple RBC alloantibodies. Genotyping results demonstrated concordance of 99.91%, 99.97%, and 99.03% with RBC, HPA, and HLA clinically validated typing results in 89 371, 3016, and 9289 comparisons, respectively. Genotyping increased the total number of antigen typing results available from 110 980 to >1 200 000. Dense donor typing allowed identification of 2 to 6 times more compatible donors to serve 3146 patients with multiple RBC alloantibodies, providing at least 1 match for 176 individuals for whom previously no blood could be found among the same donors. This genotyping technology is already being used to type thousands of donors taking part in national genotyping studies. Extraction of dense antigen-typing data from these cohorts provides blood supply organizations with the opportunity to implement a policy of genomics-based precision matching of blood.",,pdf:https://ashpublications.org/bloodadvances/article-pdf/4/15/3495/1751450/advancesadv2020001894.pdf; doi:https://doi.org/10.1182/bloodadvances.2020001894; html:https://europepmc.org/articles/PMC7422129; pdf:https://europepmc.org/articles/PMC7422129?pdf=render; doi:https://doi.org/10.1182/bloodadvances.2020001894
 35606928,https://doi.org/10.1111/bjd.21677,Biomarkers of systemic treatment response in people with psoriasis: a scoping review.,"Corbett M, Ramessur R, Marshall D, Acencio ML, Ostaszewski M, Barbosa IA, Dand N, Di Meglio P, Haddad S, Jensen AHM, Koopmann W, Mahil SK, Rahmatulla S, Rastrick J, Saklatvala J, Weidinger S, Wright K, Eyerich K, Barker JN, Ndlovu M, Conrad C, Skov L, Smith CH, BIOMAP consortium.",,The British journal of dermatology,2022,2022-07-20,Y,,,,"<h4>Background</h4>Responses to the systemic treatments commonly used to treat psoriasis vary. Biomarkers that accurately predict effectiveness and safety would enable targeted treatment selection, improved patient outcomes and more cost-effective healthcare.<h4>Objectives</h4>To perform a scoping review to identify and catalogue candidate biomarkers of systemic treatment response in psoriasis for the translational research community.<h4>Methods</h4>A systematic search of CENTRAL, Embase, LILACS and MEDLINE was performed for relevant articles published between 1990 and December 2021. Eligibility criteria were studies involving patients with psoriasis (any age, n ≥ 50) reporting biomarkers associated with systemic treatment response. The main outcomes were any measure of systemic treatment efficacy or safety. Data were extracted by one reviewer and checked by a second; studies meeting minimal quality criteria (use of methods to control for confounding) were formally assessed for bias. Candidate biomarkers were identified by an expert multistakeholder group using a majority voting consensus exercise and mapped to relevant cellular and molecular pathways.<h4>Results</h4>Of 71 included studies (67 studying effectiveness outcomes and eight safety outcomes; four studied both), most reported genomic or proteomic biomarkers associated with response to biologics (48 studies). Methodological or reporting limitations frequently compromised the interpretation of findings, including inadequate control for key covariates, lack of adjustment for multiple testing, and selective outcome reporting. We identified candidate biomarkers of efficacy to tumour necrosis factor inhibitors [variation in CARD14, CDKAL1, IL1B, IL12B and IL17RA loci, and lipopolysaccharide-induced phosphorylation of nuclear factor (NF)-κB in type 2 dendritic cells] and ustekinumab (HLA-C*06:02 and variation in an IL1B locus). None were supported by sufficient evidence for clinical use without further validation studies. Candidate biomarkers were found to be involved in the immune cellular crosstalk implicated in psoriasis pathogenesis, most notably antigen presentation, T helper (Th)17 cell differentiation, positive regulation of NF-κB, and Th17 cell activation.<h4>Conclusions</h4>This comprehensive catalogue provides a key resource for researchers and reveals a diverse range of biomarker types and outcomes in the included studies. The candidate biomarkers identified require further evaluation in methodologically robust studies to establish potential clinical utility. Future studies should aim to address the common methodological limitations highlighted in this review to expedite discovery and validation of biomarkers for clinical use. What is already known about this topic? Responses to the systemic treatments commonly used to treat psoriasis vary. Biomarkers that accurately predict effectiveness and safety would enable targeted treatment selection, improved patient outcomes and more cost-effective healthcare. What does this study add? This review provides a comprehensive catalogue of investigated biomarkers of systemic treatment response in psoriasis. A diverse range of biomarker types and outcomes was found in the included studies, serving as a key resource for the translational research community.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9796396; doi:https://doi.org/10.1111/bjd.21677; html:https://europepmc.org/articles/PMC9796396; pdf:https://europepmc.org/articles/PMC9796396?pdf=render
 35301688,https://doi.org/10.1007/s12471-022-01670-2,Electrocardiogram-based mortality prediction in patients with COVID-19 using machine learning.,"van de Leur RR, Bleijendaal H, Taha K, Mast T, Gho JMIH, Linschoten M, van Rees B, Henkens MTHM, Heymans S, Sturkenboom N, Tio RA, Offerhaus JA, Bor WL, Maarse M, Haerkens-Arends HE, Kolk MZH, van der Lingen ACJ, Selder JJ, Wierda EE, van Bergen PFMM, Winter MM, Zwinderman AH, Doevendans PA, van der Harst P, Pinto YM, Asselbergs FW, van Es R, Tjong FVY, CAPACITY-COVID collaborative consortium.",,Netherlands heart journal : monthly journal of the Netherlands Society of Cardiology and the Netherlands Heart Foundation,2022,2022-03-17,Y,Mortality; Electrocardiogram; Arrhythmia; Machine Learning; Deep Learning; Covid-19,,,"<h4>Background and purpose</h4>The electrocardiogram (ECG) is frequently obtained in the work-up of COVID-19 patients. So far, no study has evaluated whether ECG-based machine learning models have added value to predict in-hospital mortality specifically in COVID-19 patients.<h4>Methods</h4>Using data from the CAPACITY-COVID registry, we studied 882 patients admitted with COVID-19 across seven hospitals in the Netherlands. Raw format 12-lead ECGs recorded within 72 h of admission were studied. With data from five hospitals (n = 634), three models were developed: (a) a logistic regression baseline model using age and sex, (b) a least absolute shrinkage and selection operator (LASSO) model using age, sex and human annotated ECG features, and (c) a pre-trained deep neural network (DNN) using age, sex and the raw ECG waveforms. Data from two hospitals (n = 248) was used for external validation.<h4>Results</h4>Performances for models a, b and c were comparable with an area under the receiver operating curve of 0.73 (95% confidence interval [CI] 0.65-0.79), 0.76 (95% CI 0.68-0.82) and 0.77 (95% CI 0.70-0.83) respectively. Predictors of mortality in the LASSO model were age, low QRS voltage, ST depression, premature atrial complexes, sex, increased ventricular rate, and right bundle branch block.<h4>Conclusion</h4>This study shows that the ECG-based prediction models could be helpful for the initial risk stratification of patients diagnosed with COVID-19, and that several ECG abnormalities are associated with in-hospital all-cause mortality of COVID-19 patients. Moreover, this proof-of-principle study shows that the use of pre-trained DNNs for ECG analysis does not underperform compared with time-consuming manual annotation of ECG features.",,pdf:https://link.springer.com/content/pdf/10.1007/s12471-022-01670-2.pdf; doi:https://doi.org/10.1007/s12471-022-01670-2; html:https://europepmc.org/articles/PMC8929464; pdf:https://europepmc.org/articles/PMC8929464?pdf=render
-32678323,https://doi.org/10.1038/s41366-020-0642-3,"Cross-sectional associations between central and general adiposity with albuminuria: observations from 400,000 people in UK Biobank.","Zhu P, Lewington S, Haynes R, Emberson J, Landray MJ, Cherney D, Woodward M, Baigent C, Herrington WG, Staplin N.",,International journal of obesity (2005),2020,2020-07-16,Y,,,,"<h4>Background</h4>Whether measures of central adiposity are more or less strongly associated with risk of albuminuria than body mass index (BMI), and by how much diabetes/levels of glycosylated haemoglobin (HbA1c) explain or modify these associations, is uncertain.<h4>Methods</h4>Ordinal logistic regression was used to estimate associations between values of central adiposity (waist-to-hip ratio) and, separately, general adiposity (BMI) with categories of urinary albumin-to-creatinine ratio (uACR) in 408,527 UK Biobank participants. Separate central and general adiposity-based models were initially adjusted for potential confounders and measurement error, then sequentially, models were mutually adjusted (e.g. waist-to-hip ratio adjusted for BMI, and vice versa), and finally they were adjusted for potential mediators.<h4>Results</h4>Levels of albuminuria were generally low: 20,425 (5%) had a uACR ≥3 mg/mmol. After adjustment for confounders and measurement error, each 0.06 higher waist-to-hip ratio was associated with a 55% (95%CI 53-57%) increase in the odds of being in a higher uACR category. After adjustment for baseline BMI, this association was reduced to 32% (30-34%). Each 5 kg/m<sup>2</sup> higher BMI was associated with a 47% (46-49%) increase in the odds of being in a higher uACR category. Adjustment for baseline waist-to-hip ratio reduced this association to 35% (33-37%). Those with higher HbA1c were at progressively higher odds of albuminuria, but positive associations between both waist-to-hip ratio and BMI were apparent irrespective of HbA1c. Altogether, about 40% of central adiposity associations appeared to be mediated by diabetes, vascular disease and blood pressure.<h4>Conclusions</h4>Conventional epidemiological approaches suggest that higher waist-to-hip ratio and BMI are independently positively associated with albuminuria. Adiposity-albuminuria associations appear strong among people with normal HbA1c, as well as people with pre-diabetes or diabetes.",,pdf:https://www.nature.com/articles/s41366-020-0642-3.pdf; doi:https://doi.org/10.1038/s41366-020-0642-3; html:https://europepmc.org/articles/PMC7577847; pdf:https://europepmc.org/articles/PMC7577847?pdf=render
 31204027,https://doi.org/10.1016/j.injury.2019.06.012,"Comparing the outcomes of isolated, serious traumatic brain injury in older adults managed at major trauma centres and neurosurgical services: A registry-based cohort study.","Dunn MS, Beck B, Simpson PM, Cameron PA, Kennedy M, Maiden M, Judson R, Gabbe BJ.",,Injury,2019,2019-06-10,N,Traumatic brain injury; Functional Outcome; Older Adult; Tbi; Trauma Systems,,,"<h4>Background</h4>The incidence of older adult traumatic brain injury (TBI) is increasing in both high and middle to low-income countries. It is unknown whether older adults with isolated, serious TBI can be safely managed outside of major trauma centres. This registry based cohort study aimed to compare mortality and functional outcomes of older adults with isolated, serious TBI who were managed at specialised Major Trauma Services (MTS) and Metropolitan Neurosurgical Services (MNS).<h4>Method</h4>Older adults (65 years and over) who sustained an isolated, serious TBI following a low fall (from standing or ≤ 1 m) were extracted from the Victorian State Trauma Registry from 2007 to 2016. Multivariable models were fitted to assess the association between hospital designation (MTS vs. MNS) and the two outcomes of interest: in-hospital mortality and functional outcome, adjusting for potential confounders. Functional outcomes were measured using the Glasgow Outcome Scale Extended at six months post-injury.<h4>Results</h4>From 2007-2016, there were 1904 older adults who sustained an isolated, serious TBI from a low fall who received definitive care at an MTS (n = 1124) or an MNS (n = 780). After adjusting for confounders, there was no mortality benefit for patients managed at an MTS over an MNS (OR = 0.84; 95% CI: 0.65, 1.08; P = 0.17) or improvement in functional outcome six months post-injury (OR = 1.13; 95% CI: 0.94, 1.36; P = 0.21).<h4>Conclusion</h4>For older adults with isolated, serious TBI following a low fall, there was no difference in mortality or functional outcome based on definitive management at an MTS or an MNS. This confirms that MNS without the added designation of a major trauma centre are a suitable destination for the management of isolated, serious TBI in older adults.",,doi:https://doi.org/10.1016/j.injury.2019.06.012
+32678323,https://doi.org/10.1038/s41366-020-0642-3,"Cross-sectional associations between central and general adiposity with albuminuria: observations from 400,000 people in UK Biobank.","Zhu P, Lewington S, Haynes R, Emberson J, Landray MJ, Cherney D, Woodward M, Baigent C, Herrington WG, Staplin N.",,International journal of obesity (2005),2020,2020-07-16,Y,,,,"<h4>Background</h4>Whether measures of central adiposity are more or less strongly associated with risk of albuminuria than body mass index (BMI), and by how much diabetes/levels of glycosylated haemoglobin (HbA1c) explain or modify these associations, is uncertain.<h4>Methods</h4>Ordinal logistic regression was used to estimate associations between values of central adiposity (waist-to-hip ratio) and, separately, general adiposity (BMI) with categories of urinary albumin-to-creatinine ratio (uACR) in 408,527 UK Biobank participants. Separate central and general adiposity-based models were initially adjusted for potential confounders and measurement error, then sequentially, models were mutually adjusted (e.g. waist-to-hip ratio adjusted for BMI, and vice versa), and finally they were adjusted for potential mediators.<h4>Results</h4>Levels of albuminuria were generally low: 20,425 (5%) had a uACR ≥3 mg/mmol. After adjustment for confounders and measurement error, each 0.06 higher waist-to-hip ratio was associated with a 55% (95%CI 53-57%) increase in the odds of being in a higher uACR category. After adjustment for baseline BMI, this association was reduced to 32% (30-34%). Each 5 kg/m<sup>2</sup> higher BMI was associated with a 47% (46-49%) increase in the odds of being in a higher uACR category. Adjustment for baseline waist-to-hip ratio reduced this association to 35% (33-37%). Those with higher HbA1c were at progressively higher odds of albuminuria, but positive associations between both waist-to-hip ratio and BMI were apparent irrespective of HbA1c. Altogether, about 40% of central adiposity associations appeared to be mediated by diabetes, vascular disease and blood pressure.<h4>Conclusions</h4>Conventional epidemiological approaches suggest that higher waist-to-hip ratio and BMI are independently positively associated with albuminuria. Adiposity-albuminuria associations appear strong among people with normal HbA1c, as well as people with pre-diabetes or diabetes.",,pdf:https://www.nature.com/articles/s41366-020-0642-3.pdf; doi:https://doi.org/10.1038/s41366-020-0642-3; html:https://europepmc.org/articles/PMC7577847; pdf:https://europepmc.org/articles/PMC7577847?pdf=render
 32888427,https://doi.org/10.1016/j.ajhg.2020.08.009,Inferring Gene-by-Environment Interactions with a Bayesian Whole-Genome Regression Model.,"Kerin M, Marchini J.",,American journal of human genetics,2020,2020-09-03,Y,Linear Mixed Model; Gxe Interactions; Whole-genome Regression; Gxe Heritability,,,"The contribution of gene-by-environment (GxE) interactions for many human traits and diseases is poorly characterized. We propose a Bayesian whole-genome regression model for joint modeling of main genetic effects and GxE interactions in large-scale datasets, such as the UK Biobank, where many environmental variables have been measured. The method is called LEMMA (Linear Environment Mixed Model Analysis) and estimates a linear combination of environmental variables, called an environmental score (ES), that interacts with genetic markers throughout the genome. The ES provides a readily interpretable way to examine the combined effect of many environmental variables. The ES can be used both to estimate the proportion of phenotypic variance attributable to GxE effects and to test for GxE effects at genetic variants across the genome. GxE effects can induce heteroskedasticity in quantitative traits, and LEMMA accounts for this by using robust standard error estimates when testing for GxE effects. When applied to body mass index, systolic blood pressure, diastolic blood pressure, and pulse pressure in the UK Biobank, we estimate that 9.3%, 3.9%, 1.6%, and 12.5%, respectively, of phenotypic variance is explained by GxE interactions and that low-frequency variants explain most of this variance. We also identify three loci that interact with the estimated environmental scores (-log<sub>10</sub>p>7.3).",,pdf:http://www.cell.com/article/S0002929720302779/pdf; doi:https://doi.org/10.1016/j.ajhg.2020.08.009; html:https://europepmc.org/articles/PMC7536582; pdf:https://europepmc.org/articles/PMC7536582?pdf=render
 33742045,https://doi.org/10.1038/s41598-021-85354-8,Short and long-read genome sequencing methodologies for somatic variant detection; genomic analysis of a patient with diffuse large B-cell lymphoma.,"Roberts HE, Lopopolo M, Pagnamenta AT, Sharma E, Parkes D, Lonie L, Freeman C, Knight SJL, Lunter G, Dreau H, Lockstone H, Taylor JC, Schuh A, Bowden R, Buck D.",,Scientific reports,2021,2021-03-19,Y,,,,"Recent advances in throughput and accuracy mean that the Oxford Nanopore Technologies PromethION platform is a now a viable solution for genome sequencing. Much of the validation of bioinformatic tools for this long-read data has focussed on calling germline variants (including structural variants). Somatic variants are outnumbered many-fold by germline variants and their detection is further complicated by the effects of tumour purity/subclonality. Here, we evaluate the extent to which Nanopore sequencing enables detection and analysis of somatic variation. We do this through sequencing tumour and germline genomes for a patient with diffuse B-cell lymphoma and comparing results with 150 bp short-read sequencing of the same samples. Calling germline single nucleotide variants (SNVs) from specific chromosomes of the long-read data achieved good specificity and sensitivity. However, results of somatic SNV calling highlight the need for the development of specialised joint calling algorithms. We find the comparative genome-wide performance of different tools varies significantly between structural variant types, and suggest long reads are especially advantageous for calling large somatic deletions and duplications. Finally, we highlight the utility of long reads for phasing clinically relevant variants, confirming that a somatic 1.6 Mb deletion and a p.(Arg249Met) mutation involving TP53 are oriented in trans.",,pdf:https://www.nature.com/articles/s41598-021-85354-8.pdf; doi:https://doi.org/10.1038/s41598-021-85354-8; html:https://europepmc.org/articles/PMC7979876; pdf:https://europepmc.org/articles/PMC7979876?pdf=render
 32327693,https://doi.org/10.1038/s42003-020-0921-5,Predicted loss and gain of function mutations in ACO1 are associated with erythropoiesis.,"Oskarsson GR, Oddsson A, Magnusson MK, Kristjansson RP, Halldorsson GH, Ferkingstad E, Zink F, Helgadottir A, Ivarsdottir EV, Arnadottir GA, Jensson BO, Katrinardottir H, Sveinbjornsson G, Kristinsdottir AM, Lee AL, Saemundsdottir J, Stefansdottir L, Sigurdsson JK, Davidsson OB, Benonisdottir S, Jonasdottir A, Jonasdottir A, Jonsson S, Gudmundsson RL, Asselbergs FW, Tragante V, Gunnarsson B, Masson G, Thorleifsson G, Rafnar T, Holm H, Olafsson I, Onundarson PT, Gudbjartsson DF, Norddahl GL, Thorsteinsdottir U, Sulem P, Stefansson K.",,Communications biology,2020,2020-04-23,Y,,,,"Hemoglobin is the essential oxygen-carrying molecule in humans and is regulated by cellular iron and oxygen sensing mechanisms. To search for novel variants associated with hemoglobin concentration, we performed genome-wide association studies of hemoglobin concentration using a combined set of 684,122 individuals from Iceland and the UK. Notably, we found seven novel variants, six rare coding and one common, at the ACO1 locus associating with either decreased or increased hemoglobin concentration. Of these variants, the missense Cys506Ser and the stop-gained Lys334Ter mutations are specific to eight and ten generation pedigrees, respectively, and have the two largest effects in the study (Effect<sub>Cys506Ser</sub> = -1.61 SD, CI<sub>95</sub> = [-1.98, -1.35]; Effect<sub>Lys334Ter</sub> = 0.63 SD, CI<sub>95</sub> = [0.36, 0.91]). We also find Cys506Ser to associate with increased risk of persistent anemia (OR = 17.1, P = 2 × 10<sup>-14</sup>). The strong bidirectional effects seen in this study implicate ACO1, a known iron sensing molecule, as a major homeostatic regulator of hemoglobin concentration.",,pdf:https://www.nature.com/articles/s42003-020-0921-5.pdf; doi:https://doi.org/10.1038/s42003-020-0921-5; html:https://europepmc.org/articles/PMC7181819; pdf:https://europepmc.org/articles/PMC7181819?pdf=render
 38839884,https://doi.org/10.1038/s41588-024-01763-1,"Genome-wide meta-analyses of restless legs syndrome yield insights into genetic architecture, disease biology and risk prediction.","Schormair B, Zhao C, Bell S, Didriksen M, Nawaz MS, Schandra N, Stefani A, Högl B, Dauvilliers Y, Bachmann CG, Kemlink D, Sonka K, Paulus W, Trenkwalder C, Oertel WH, Hornyak M, Teder-Laving M, Metspalu A, Hadjigeorgiou GM, Polo O, Fietze I, Ross OA, Wszolek ZK, Ibrahim A, Bergmann M, Kittke V, Harrer P, Dowsett J, Chenini S, Ostrowski SR, Sørensen E, Erikstrup C, Pedersen OB, Topholm Bruun M, Nielsen KR, Butterworth AS, Soranzo N, Ouwehand WH, Roberts DJ, Danesh J, Burchell B, Furlotte NA, Nandakumar P, 23andMe Research Team, D.E.S.I.R. study group, Earley CJ, Ondo WG, Xiong L, Desautels A, Perola M, Vodicka P, Dina C, Stoll M, Franke A, Lieb W, Stewart AFR, Shah SH, Gieger C, Peters A, Rye DB, Rouleau GA, Berger K, Stefansson H, Ullum H, Stefansson K, Hinds DA, Di Angelantonio E, Oexle K, Winkelmann J.",,Nature genetics,2024,2024-06-05,Y,,,,"Restless legs syndrome (RLS) affects up to 10% of older adults. Their healthcare is impeded by delayed diagnosis and insufficient treatment. To advance disease prediction and find new entry points for therapy, we performed meta-analyses of genome-wide association studies in 116,647 individuals with RLS (cases) and 1,546,466 controls of European ancestry. The pooled analysis increased the number of risk loci eightfold to 164, including three on chromosome X. Sex-specific meta-analyses revealed largely overlapping genetic predispositions of the sexes (r<sub>g</sub> = 0.96). Locus annotation prioritized druggable genes such as glutamate receptors 1 and 4, and Mendelian randomization indicated RLS as a causal risk factor for diabetes. Machine learning approaches combining genetic and nongenetic information performed best in risk prediction (area under the curve (AUC) = 0.82-0.91). In summary, we identified targets for drug development and repurposing, prioritized potential causal relationships between RLS and relevant comorbidities and risk factors for follow-up and provided evidence that nonlinear interactions are likely relevant to RLS risk prediction.",,pdf:https://www.nature.com/articles/s41588-024-01763-1.pdf; doi:https://doi.org/10.1038/s41588-024-01763-1; html:https://europepmc.org/articles/PMC11176086; pdf:https://europepmc.org/articles/PMC11176086?pdf=render
-37575973,https://doi.org/10.2147/clep.s417176,Anxiety and Depression in People with Eczema or Psoriasis: A Comparison of Associations in UK Biobank and Linked Primary Care Data.,"Matthewman J, Mansfield KE, Hayes JF, Adesanya EI, Smith CH, Roberts A, Langan SM, Henderson AD.",,Clinical epidemiology,2023,2023-08-07,Y,Depression; Psoriasis; Anxiety; Eczema; Cross-sectional study; Data Linkage; Electronic Health Records; Ascertainment; Uk Biobank,,,"<h4>Introduction</h4>Previous research has shown associations between eczema and psoriasis and anxiety and depression. We investigated whether associations are consistent across different settings of ascertainment for depression and anxiety, including interview and survey responses from UK Biobank (a large longitudinal cohort recruiting individuals aged 40-69 years between 2006-2010), and linked primary care data, with the aim of drawing more reliable conclusions through triangulation.<h4>Methods</h4>In cross-sectional studies, we estimated associations between eczema or psoriasis and anxiety or depression, defining anxiety or depression as 1) self-reported previous diagnosis at UK Biobank recruitment interview; 2) PHQ-9/GAD-7 score indicating depression or anxiety from a UK Biobank mental health follow-up survey in 2016; and 3) diagnosis in linked primary care electronic health record data.<h4>Results</h4>We analysed 230,047 people with linked Biobank and primary care data. We found poor agreement between the data sources for eczema, psoriasis, anxiety, and depression. Eg, 9474 had a previous eczema diagnosis in primary care data, 4069 self-reported previous eczema diagnosis at the UK biobank interview, and 1536 had eczema in both data sources (for depression 40,455; 13,320; and 9588 respectively). Having eczema or psoriasis (recorded in primary care or baseline interview) was associated with higher odds of anxiety and depression. Eg, the adjusted odds ratio for depression comparing those with eczema to those without was greater than 1 when defining the outcome from 1) the recruitment interview (1.36, 95% confidence interval 1.27-1.45); 2) the follow-up survey (1.24, 1.09-1.39), and 3) primary care records (1.56, 1.50-1.62).<h4>Discussion</h4>Our findings support increased prevalence of mental illness in people with psoriasis and eczema across multiple data sources, which should be considered in planning of mental health services. However, we found poor agreement in disease ascertainment between settings, with implications for data interpretation in electronic health records.",,pdf:https://www.dovepress.com/getfile.php?fileID=91773; doi:https://doi.org/10.2147/CLEP.S417176; html:https://europepmc.org/articles/PMC10421744; pdf:https://europepmc.org/articles/PMC10421744?pdf=render
 35288697,https://doi.org/10.1038/s41591-022-01750-1,COVID-19 and resilience of healthcare systems in ten countries.,"Arsenault C, Gage A, Kim MK, Kapoor NR, Akweongo P, Amponsah F, Aryal A, Asai D, Awoonor-Williams JK, Ayele W, Bedregal P, Doubova SV, Dulal M, Gadeka DD, Gordon-Strachan G, Mariam DH, Hensman D, Joseph JP, Kaewkamjornchai P, Eshetu MK, Gelaw SK, Kubota S, Leerapan B, Margozzini P, Mebratie AD, Mehata S, Moshabela M, Mthethwa L, Nega A, Oh J, Park S, Passi-Solar Á, Pérez-Cuevas R, Phengsavanh A, Reddy T, Rittiphairoj T, Sapag JC, Thermidor R, Tlou B, Valenzuela Guiñez F, Bauhoff S, Kruk ME.",,Nature medicine,2022,2022-03-14,Y,,,,"Declines in health service use during the Coronavirus Disease 2019 (COVID-19) pandemic could have important effects on population health. In this study, we used an interrupted time series design to assess the immediate effect of the pandemic on 31 health services in two low-income (Ethiopia and Haiti), six middle-income (Ghana, Lao People's Democratic Republic, Mexico, Nepal, South Africa and Thailand) and high-income (Chile and South Korea) countries. Despite efforts to maintain health services, disruptions of varying magnitude and duration were found in every country, with no clear patterns by country income group or pandemic intensity. Disruptions in health services often preceded COVID-19 waves. Cancer screenings, TB screening and detection and HIV testing were most affected (26-96% declines). Total outpatient visits declined by 9-40% at national levels and remained lower than predicted by the end of 2020. Maternal health services were disrupted in approximately half of the countries, with declines ranging from 5% to 33%. Child vaccinations were disrupted for shorter periods, but we estimate that catch-up campaigns might not have reached all children missed. By contrast, provision of antiretrovirals for HIV was not affected. By the end of 2020, substantial disruptions remained in half of the countries. Preliminary data for 2021 indicate that disruptions likely persisted. Although a portion of the declines observed might result from decreased needs during lockdowns (from fewer infectious illnesses or injuries), a larger share likely reflects a shortfall of health system resilience. Countries must plan to compensate for missed healthcare during the current pandemic and invest in strategies for better health system resilience for future emergencies.",,pdf:https://www.nature.com/articles/s41591-022-01750-1.pdf; doi:https://doi.org/10.1038/s41591-022-01750-1; html:https://europepmc.org/articles/PMC9205770; pdf:https://europepmc.org/articles/PMC9205770?pdf=render
+37575973,https://doi.org/10.2147/clep.s417176,Anxiety and Depression in People with Eczema or Psoriasis: A Comparison of Associations in UK Biobank and Linked Primary Care Data.,"Matthewman J, Mansfield KE, Hayes JF, Adesanya EI, Smith CH, Roberts A, Langan SM, Henderson AD.",,Clinical epidemiology,2023,2023-08-07,Y,Depression; Psoriasis; Anxiety; Eczema; Cross-sectional study; Data Linkage; Electronic Health Records; Ascertainment; Uk Biobank,,,"<h4>Introduction</h4>Previous research has shown associations between eczema and psoriasis and anxiety and depression. We investigated whether associations are consistent across different settings of ascertainment for depression and anxiety, including interview and survey responses from UK Biobank (a large longitudinal cohort recruiting individuals aged 40-69 years between 2006-2010), and linked primary care data, with the aim of drawing more reliable conclusions through triangulation.<h4>Methods</h4>In cross-sectional studies, we estimated associations between eczema or psoriasis and anxiety or depression, defining anxiety or depression as 1) self-reported previous diagnosis at UK Biobank recruitment interview; 2) PHQ-9/GAD-7 score indicating depression or anxiety from a UK Biobank mental health follow-up survey in 2016; and 3) diagnosis in linked primary care electronic health record data.<h4>Results</h4>We analysed 230,047 people with linked Biobank and primary care data. We found poor agreement between the data sources for eczema, psoriasis, anxiety, and depression. Eg, 9474 had a previous eczema diagnosis in primary care data, 4069 self-reported previous eczema diagnosis at the UK biobank interview, and 1536 had eczema in both data sources (for depression 40,455; 13,320; and 9588 respectively). Having eczema or psoriasis (recorded in primary care or baseline interview) was associated with higher odds of anxiety and depression. Eg, the adjusted odds ratio for depression comparing those with eczema to those without was greater than 1 when defining the outcome from 1) the recruitment interview (1.36, 95% confidence interval 1.27-1.45); 2) the follow-up survey (1.24, 1.09-1.39), and 3) primary care records (1.56, 1.50-1.62).<h4>Discussion</h4>Our findings support increased prevalence of mental illness in people with psoriasis and eczema across multiple data sources, which should be considered in planning of mental health services. However, we found poor agreement in disease ascertainment between settings, with implications for data interpretation in electronic health records.",,pdf:https://www.dovepress.com/getfile.php?fileID=91773; doi:https://doi.org/10.2147/CLEP.S417176; html:https://europepmc.org/articles/PMC10421744; pdf:https://europepmc.org/articles/PMC10421744?pdf=render
 32714939,https://doi.org/10.3389/fnut.2020.00080,Future Directions for Integrative Objective Assessment of Eating Using Wearable Sensing Technology.,"Skinner A, Toumpakari Z, Stone C, Johnson L.",,Frontiers in nutrition,2020,2020-07-02,Y,Technology; Assessment; Eating; Objective; Wearable,,,"Established methods for nutritional assessment suffer from a number of important limitations. Diaries are burdensome to complete, food frequency questionnaires only capture average food intake, and both suffer from difficulties in self estimation of portion size and biases resulting from misreporting. Online and app versions of these methods have been developed, but issues with misreporting and portion size estimation remain. New methods utilizing passive data capture are required that address reporting bias, extend timescales for data collection, and transform what is possible for measuring habitual intakes. Digital and sensing technologies are enabling the development of innovative and transformative new methods in this area that will provide a better understanding of eating behavior and associations with health. In this article we describe how wrist-worn wearables, on-body cameras, and body-mounted biosensors can be used to capture data about when, what, and how much people eat and drink. We illustrate how these new techniques can be integrated to provide complete solutions for the passive, objective assessment of a wide range of traditional dietary factors, as well as novel measures of eating architecture, within person variation in intakes, and food/nutrient combinations within meals. We also discuss some of the challenges these new approaches will bring.",,pdf:https://www.frontiersin.org/articles/10.3389/fnut.2020.00080/pdf; doi:https://doi.org/10.3389/fnut.2020.00080; html:https://europepmc.org/articles/PMC7343846; pdf:https://europepmc.org/articles/PMC7343846?pdf=render
 37789377,https://doi.org/10.1186/s12943-023-01863-2,Spatial transcriptomic analysis of virtual prostate biopsy reveals confounding effect of tissue heterogeneity on genomic signatures.,"Figiel S, Yin W, Doultsinos D, Erickson A, Poulose N, Singh R, Magnussen A, Anbarasan T, Teague R, He M, Lundeberg J, Loda M, Verrill C, Colling R, Gill PS, Bryant RJ, Hamdy FC, Woodcock DJ, Mills IG, Cussenot O, Lamb AD.",,Molecular cancer,2023,2023-10-03,Y,prostate cancer; Virtual Biopsy; Spatial Transcriptomics; Prognostic Genetic Signatures,,,"Genetic signatures have added a molecular dimension to prognostics and therapeutic decision-making. However, tumour heterogeneity in prostate cancer and current sampling methods could confound accurate assessment. Based on previously published spatial transcriptomic data from multifocal prostate cancer, we created virtual biopsy models that mimic conventional biopsy placement and core size. We then analysed the gene expression of different prognostic signatures (OncotypeDx®, Decipher®, Prostadiag®) using a step-wise approach with increasing resolution from pseudo-bulk analysis of the whole biopsy, to differentiation by tissue subtype (benign, stroma, tumour), followed by distinct tumour grade and finally clonal resolution. The gene expression profile of virtual tumour biopsies revealed clear differences between grade groups and tumour clones, compared to a benign control, which were not reflected in bulk analyses. This suggests that bulk analyses of whole biopsies or tumour-only areas, as used in clinical practice, may provide an inaccurate assessment of gene profiles. The type of tissue, the grade of the tumour and the clonal composition all influence the gene expression in a biopsy. Clinical decision making based on biopsy genomics should be made with caution while we await more precise targeting and cost-effective spatial analyses.",,pdf:https://molecular-cancer.biomedcentral.com/counter/pdf/10.1186/s12943-023-01863-2; doi:https://doi.org/10.1186/s12943-023-01863-2; html:https://europepmc.org/articles/PMC10546768; pdf:https://europepmc.org/articles/PMC10546768?pdf=render
 37542272,https://doi.org/10.1186/s12916-023-02948-x,Common mental health disorders in adults with inflammatory skin conditions: nationwide population-based matched cohort studies in the UK.,"Henderson AD, Adesanya E, Mulick A, Matthewman J, Vu N, Davies F, Smith CH, Hayes J, Mansfield KE, Langan SM.",,BMC medicine,2023,2023-08-04,Y,Depression; Anxiety; Skin Disease; Electronic Health Records,,,"<h4>Background</h4>Psoriasis and atopic eczema are common inflammatory skin diseases. Existing research has identified increased risks of common mental disorders (anxiety, depression) in people with eczema and psoriasis; however, explanations for the associations remain unclear. We aimed to establish the risk factors for mental illness in those with eczema or psoriasis and identify the population groups most at risk.<h4>Methods</h4>We used routinely collected data from the UK Clinical Practice Research Datalink (CPRD) GOLD. Adults registered with a general practice in CPRD (1997-2019) were eligible for inclusion. Individuals with eczema/psoriasis were matched (age, sex, practice) to up to five adults without eczema/psoriasis. We used Cox regression to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for hazards of anxiety or depression in people with eczema/psoriasis compared to people without. We adjusted for known confounders (deprivation, asthma [eczema], psoriatic arthritis [psoriasis], Charlson comorbidity index, calendar period) and potential mediators (harmful alcohol use, body mass index [BMI], smoking status, and, in eczema only, sleep quality [insomnia diagnoses, specific sleep problem medications] and high-dose oral glucocorticoids).<h4>Results</h4>We identified two cohorts with and without eczema (1,032,782, matched to 4,990,125 without), and with and without psoriasis (366,884, matched to 1,834,330 without). Sleep quality was imbalanced in the eczema cohorts, twice as many people with eczema had evidence of poor sleep at baseline than those without eczema, including over 20% of those with severe eczema. After adjusting for potential confounders and mediators, eczema and psoriasis were associated with anxiety (adjusted HR [95% CI]: eczema 1.14 [1.13-1.16], psoriasis 1.17 [1.15-1.19]) and depression (adjusted HR [95% CI]: eczema 1.11 [1.1-1.12], psoriasis 1.21 [1.19-1.22]). However, we found evidence that these increased hazards are unlikely to be constant over time and were especially high 1-year after study entry.<h4>Conclusions</h4>Atopic eczema and psoriasis are associated with increased incidence of anxiety and depression in adults. These associations may be mediated through known modifiable risk factors, especially sleep quality in people with eczema. Our findings highlight potential opportunities for the prevention of anxiety and depression in people with eczema/psoriasis through treatment of modifiable risk factors and enhanced eczema/psoriasis management.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-023-02948-x; doi:https://doi.org/10.1186/s12916-023-02948-x; html:https://europepmc.org/articles/PMC10403838; pdf:https://europepmc.org/articles/PMC10403838?pdf=render
@@ -2284,23 +2286,23 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 36562446,https://doi.org/10.1136/bmj-2021-069048,CODE-EHR best practice framework for the use of structured electronic healthcare records in clinical research.,"Kotecha D, Asselbergs FW, Achenbach S, Anker SD, Atar D, Baigent C, Banerjee A, Beger B, Brobert G, Casadei B, Ceccarelli C, Cowie MR, Crea F, Cronin M, Denaxas S, Derix A, Fitzsimons D, Fredriksson M, Gale CP, Gkoutos GV, Goettsch W, Hemingway H, Ingvar M, Jonas A, Kazmierski R, Løgstrup S, Lumbers RT, Lüscher TF, McGreavy P, Piña IL, Roessig L, Steinbeisser C, Sundgren M, Tyl B, van Thiel G, van Bochove K, Vardas PE, Villanueva T, Vrana M, Weber W, Weidinger F, Windecker S, Wood A, Grobbee DE, Innovative Medicines Initiative BigData@Heart Consortium, European Society of Cardiology, CODE-EHR international consensus group.",,BMJ (Clinical research ed.),2022,2022-08-29,Y,,,,,,pdf:https://www.bmj.com/content/bmj/378/bmj-2021-069048.full.pdf; doi:https://doi.org/10.1136/bmj-2021-069048; html:https://europepmc.org/articles/PMC9403753
 33341984,https://doi.org/10.1111/tme.12750,Comparison of four methods to measure haemoglobin concentrations in whole blood donors (COMPARE): A diagnostic accuracy study.,"Bell S, Sweeting M, Ramond A, Chung R, Kaptoge S, Walker M, Bolton T, Sambrook J, Moore C, McMahon A, Fahle S, Cullen D, Mehenny S, Wood AM, Armitage J, Ouwehand WH, Miflin G, Roberts DJ, Danesh J, Di Angelantonio E, COMPARE Study Group.",,"Transfusion medicine (Oxford, England)",2021,2020-12-20,Y,Hemocue; Gravimetry; Whole Blood Donor; Non-invasive Haemoglobin Measurement; Haemoglobin Screening; Inappropriate Bleeding; Inappropriate Deferral,,,"<h4>Objective</h4>To compare four haemoglobin measurement methods in whole blood donors.<h4>Background</h4>To safeguard donors, blood services measure haemoglobin concentration in advance of each donation. NHS Blood and Transplant's (NHSBT) customary method have been capillary gravimetry (copper sulphate), followed by venous spectrophotometry (HemoCue) for donors failing gravimetry. However, NHSBT's customary method results in 10% of donors being inappropriately bled (ie, with haemoglobin values below the regulatory threshold).<h4>Methods</h4>We compared the following four methods in 21 840 blood donors (aged ≥18 years) recruited from 10 NHSBT centres in England, with the Sysmex XN-2000 haematology analyser, the reference standard: (1) NHSBT's customary method; (2) ""post donation"" approach, that is, estimating current haemoglobin concentration from that measured by a haematology analyser at a donor's most recent prior donation; (3) ""portable haemoglobinometry"" (using capillary HemoCue); (4) non-invasive spectrometry (using MBR Haemospect or Orsense NMB200). We assessed sensitivity; specificity; proportion who would have been inappropriately bled, or rejected from donation (""deferred"") incorrectly; and test preference.<h4>Results</h4>Compared with the reference standard, the methods ranged in test sensitivity from 17.0% (MBR Haemospect) to 79.0% (portable haemoglobinometry) in men, and from 19.0% (MBR Haemospect) to 82.8% (portable haemoglobinometry) in women. For specificity, the methods ranged from 87.2% (MBR Haemospect) to 99.9% (NHSBT's customary method) in men, and from 74.1% (Orsense NMB200) to 99.8% (NHSBT's customary method) in women. The proportion of donors who would have been inappropriately bled ranged from 2.2% in men for portable haemoglobinometry to 18.9% in women for MBR Haemospect. The proportion of donors who would have been deferred incorrectly with haemoglobin concentration above the minimum threshold ranged from 0.1% in men for NHSBT's customary method to 20.3% in women for OrSense. Most donors preferred non-invasive spectrometry.<h4>Conclusion</h4>In the largest study reporting head-to-head comparisons of four methods to measure haemoglobin prior to blood donation, our results support replacement of NHSBT's customary method with portable haemoglobinometry.",,pdf:https://www.repository.cam.ac.uk/bitstream/1810/315673/1/tme.12750.pdf; doi:https://doi.org/10.1111/tme.12750; html:https://europepmc.org/articles/PMC8048787; pdf:https://europepmc.org/articles/PMC8048787?pdf=render
 38548763,https://doi.org/10.1038/s41467-024-46982-6,The SARS-CoV-2 neutralizing antibody response to SD1 and its evasion by BA.2.86.,"Zhou D, Supasa P, Liu C, Dijokaite-Guraliuc A, Duyvesteyn HME, Selvaraj M, Mentzer AJ, Das R, Dejnirattisai W, Temperton N, Klenerman P, Dunachie SJ, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR.",,Nature communications,2024,2024-03-28,Y,,,,"Under pressure from neutralising antibodies induced by vaccination or infection the SARS-CoV-2 spike gene has become a hotspot for evolutionary change, leading to the failure of all mAbs developed for clinical use. Most potent antibodies bind to the receptor binding domain which has become heavily mutated. Here we study responses to a conserved epitope in sub-domain-1 (SD1) of spike which have become more prominent because of mutational escape from antibodies directed to the receptor binding domain. Some SD1 reactive mAbs show potent and broad neutralization of SARS-CoV-2 variants. We structurally map the dominant SD1 epitope and provide a mechanism of action by blocking interaction with ACE2. Mutations in SD1 have not been sustained to date, but one, E554K, leads to escape from mAbs. This mutation has now emerged in several sublineages including BA.2.86, reflecting selection pressure on the virus exerted by the increasing prominence of the anti-SD1 response.",,pdf:https://www.nature.com/articles/s41467-024-46982-6.pdf; doi:https://doi.org/10.1038/s41467-024-46982-6; html:https://europepmc.org/articles/PMC10978878; pdf:https://europepmc.org/articles/PMC10978878?pdf=render
-33480434,https://doi.org/10.1093/pubmed/fdaa267,"Complex differences in infection rates between ethnic groups in Scotland: a retrospective, national census-linked cohort study of 1.65 million cases.","Gruer LD, Cézard GI, Wallace LA, Hutchinson SJ, Douglas AF, Buchanan D, Katikireddi SV, Millard AD, Goldberg DJ, Sheikh A, Bhopal RS.",,"Journal of public health (Oxford, England)",2022,2022-03-01,Y,Infectious disease; epidemiology; Ethnicity,,,"<h4>Background</h4>Ethnicity can influence susceptibility to infection, as COVID-19 has shown. Few countries have systematically investigated ethnic variations in infection.<h4>Methods</h4>We linked the Scotland 2001 Census, including ethnic group, to national databases of hospitalizations/deaths and serological diagnoses of bloodborne viruses for 2001-2013. We calculated age-adjusted rate ratios (RRs) in 12 ethnic groups for all infections combined, 15 infection categories, and human immunodeficiency virus (HIV), hepatitis B (HBV) and hepatitis C (HCV) viruses.<h4>Results</h4>We analysed over 1.65 million infection-related hospitalisations/deaths. Compared with White Scottish, RRs for all infections combined were 0.8 or lower for Other White British, Other White and Chinese males and females, and 1.2-1.4 for Pakistani and African males and females. Adjustment for socioeconomic status or birthplace had little effect. RRs for specific infection categories followed similar patterns with striking exceptions. For HIV, RRs were 136 in African females and 14 in males; for HBV, 125 in Chinese females and 59 in males, 55 in African females and 24 in males; and for HCV, 2.3-3.1 in Pakistanis and Africans.<h4>Conclusions</h4>Ethnic differences were found in overall rates and many infection categories, suggesting multiple causative pathways. We recommend census linkage as a powerful method for studying the disproportionate impact of COVID-19.",,pdf:https://academic.oup.com/jpubhealth/advance-article-pdf/doi/10.1093/pubmed/fdaa267/36684631/fdaa267.pdf; doi:https://doi.org/10.1093/pubmed/fdaa267; html:https://europepmc.org/articles/PMC7928762; pdf:https://europepmc.org/articles/PMC7928762?pdf=render
 31372838,https://doi.org/10.1007/s12471-019-01308-w,"A computerised decision support system for cardiovascular risk management 'live' in the electronic health record environment: development, validation and implementation-the Utrecht Cardiovascular Cohort Initiative.","Groenhof TKJ, Rittersma ZH, Bots ML, Brandjes M, Jacobs JJL, Grobbee DE, van Solinge WW, Visseren FLJ, Haitjema S, Asselbergs FW, Members of the UCC-CVRM Study Group.",,Netherlands heart journal : monthly journal of the Netherlands Society of Cardiology and the Netherlands Heart Foundation,2019,2019-09-01,Y,Adherence; Health Information Technology; Big Data; Real-world Data; Cardiovascular Risk Management; Computerised Decision Support System,,,"<h4>Purpose</h4>We set out to develop a real-time computerised decision support system (CDSS) embedded in the electronic health record (EHR) with information on risk factors, estimated risk, and guideline-based advice on treatment strategy in order to improve adherence to cardiovascular risk management (CVRM) guidelines with the ultimate aim of improving patient healthcare.<h4>Methods</h4>We defined a project plan including the scope and requirements, infrastructure and interface, data quality and study population, validation and evaluation of the CDSS.<h4>Results</h4>In collaboration with clinicians, data scientists, epidemiologists, ICT architects, and user experience and interface designers we developed a CDSS that provides 'live' information on CVRM within the environment of the EHR. The CDSS provides information on cardiovascular risk factors (age, sex, medical and family history, smoking, blood pressure, lipids, kidney function, and glucose intolerance measurements), estimated 10-year cardiovascular risk, guideline-compliant suggestions for both pharmacological and non-pharmacological treatment to optimise risk factors, and an estimate on the change in 10-year risk of cardiovascular disease if treatment goals are adhered to. Our pilot study identified a number of issues that needed to be addressed, such as missing data, rules and regulations, privacy, and patient participation.<h4>Conclusion</h4>Development of a CDSS is complex and requires a multidisciplinary approach. We identified opportunities and challenges in our project developing a CDSS aimed at improving adherence to CVRM guidelines. The regulatory environment, including guidance on scientific evaluation, legislation, and privacy issues needs to evolve within this emerging field of eHealth.",,pdf:https://link.springer.com/content/pdf/10.1007/s12471-019-01308-w.pdf; doi:https://doi.org/10.1007/s12471-019-01308-w; html:https://europepmc.org/articles/PMC6712110; pdf:https://europepmc.org/articles/PMC6712110?pdf=render
+33480434,https://doi.org/10.1093/pubmed/fdaa267,"Complex differences in infection rates between ethnic groups in Scotland: a retrospective, national census-linked cohort study of 1.65 million cases.","Gruer LD, Cézard GI, Wallace LA, Hutchinson SJ, Douglas AF, Buchanan D, Katikireddi SV, Millard AD, Goldberg DJ, Sheikh A, Bhopal RS.",,"Journal of public health (Oxford, England)",2022,2022-03-01,Y,Infectious disease; epidemiology; Ethnicity,,,"<h4>Background</h4>Ethnicity can influence susceptibility to infection, as COVID-19 has shown. Few countries have systematically investigated ethnic variations in infection.<h4>Methods</h4>We linked the Scotland 2001 Census, including ethnic group, to national databases of hospitalizations/deaths and serological diagnoses of bloodborne viruses for 2001-2013. We calculated age-adjusted rate ratios (RRs) in 12 ethnic groups for all infections combined, 15 infection categories, and human immunodeficiency virus (HIV), hepatitis B (HBV) and hepatitis C (HCV) viruses.<h4>Results</h4>We analysed over 1.65 million infection-related hospitalisations/deaths. Compared with White Scottish, RRs for all infections combined were 0.8 or lower for Other White British, Other White and Chinese males and females, and 1.2-1.4 for Pakistani and African males and females. Adjustment for socioeconomic status or birthplace had little effect. RRs for specific infection categories followed similar patterns with striking exceptions. For HIV, RRs were 136 in African females and 14 in males; for HBV, 125 in Chinese females and 59 in males, 55 in African females and 24 in males; and for HCV, 2.3-3.1 in Pakistanis and Africans.<h4>Conclusions</h4>Ethnic differences were found in overall rates and many infection categories, suggesting multiple causative pathways. We recommend census linkage as a powerful method for studying the disproportionate impact of COVID-19.",,pdf:https://academic.oup.com/jpubhealth/advance-article-pdf/doi/10.1093/pubmed/fdaa267/36684631/fdaa267.pdf; doi:https://doi.org/10.1093/pubmed/fdaa267; html:https://europepmc.org/articles/PMC7928762; pdf:https://europepmc.org/articles/PMC7928762?pdf=render
 35505938,https://doi.org/10.1016/j.eclinm.2022.101417,Multivariate profile and acute-phase correlates of cognitive deficits in a COVID-19 hospitalised cohort.,"Hampshire A, Chatfield DA, MPhil AM, Jolly A, Trender W, Hellyer PJ, Giovane MD, Newcombe VFJ, Outtrim JG, Warne B, Bhatti J, Pointon L, Elmer A, Sithole N, Bradley J, Kingston N, Sawcer SJ, Bullmore ET, Rowe JB, Menon DK, Cambridge NeuroCOVID Group, the NIHR COVID-19 BioResource, and Cambridge NIHR Clinical Research Facility.",,EClinicalMedicine,2022,2022-04-28,Y,Memory; Cognition; Attention; Planning; Cognitive Assessment; Reasoning; Covid-19,,,"<h4>Background</h4>Preliminary evidence has highlighted a possible association between severe COVID-19 and persistent cognitive deficits. Further research is required to confirm this association, determine whether cognitive deficits relate to clinical features from the acute phase or to mental health status at the point of assessment, and quantify rate of recovery.<h4>Methods</h4>46 individuals who received critical care for COVID-19 at Addenbrooke's hospital between 10th March 2020 and 31st July 2020 (16 mechanically ventilated) underwent detailed computerised cognitive assessment alongside scales measuring anxiety, depression and post-traumatic stress disorder under supervised conditions at a mean follow up of 6.0 (± 2.1) months following acute illness. Patient and matched control (<i>N</i> = 460) performances were transformed into standard deviation from expected scores, accounting for age and demographic factors using <i>N</i> = 66,008 normative datasets. Global accuracy and response time composites were calculated (G_SScore & G_RT). Linear modelling predicted composite score deficits from acute severity, mental-health status at assessment, and time from hospital admission. The pattern of deficits across tasks was qualitatively compared with normal age-related decline, and early-stage dementia.<h4>Findings</h4>COVID-19 survivors were less accurate (G_SScore=-0.53SDs) and slower (G_RT=+0.89SDs) in their responses than expected compared to their matched controls. Acute illness, but not chronic mental health, significantly predicted cognitive deviation from expected scores (G_SScore (<i>p</i>=​​0.0037) and G_RT (<i>p</i> = 0.0366)). The most prominent task associations with COVID-19 were for higher cognition and processing speed, which was qualitatively distinct from the profiles of normal ageing and dementia and similar in magnitude to the effects of ageing between 50 and 70 years of age. A trend towards reduced deficits with time from illness (r∼=0.15) did not reach statistical significance.<h4>Interpretation</h4>Cognitive deficits after severe COVID-19 relate most strongly to acute illness severity, persist long into the chronic phase, and recover slowly if at all, with a characteristic profile highlighting higher cognitive functions and processing speed.<h4>Funding</h4>This work was funded by the National Institute for Health Research (NIHR) Cambridge Biomedical Research Centre (BRC), NIHR Cambridge Clinical Research Facility (BRC-1215-20014), the Addenbrooke's Charities Trust and NIHR COVID-19 BioResource RG9402. AH is funded by the UK Dementia Research Institute Care Research and Technology Centre and Imperial College London Biomedical Research Centre. ETB and DKM are supported by NIHR Senior Investigator awards. JBR is supported by the Wellcome Trust (220258) and Medical Research Council (SUAG/051 G101400). VFJN is funded by an Academy of Medical Sciences/ The Health Foundation Clinician Scientist Fellowship. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health and Social Care.",,pdf:http://www.thelancet.com/article/S258953702200147X/pdf; doi:https://doi.org/10.1016/j.eclinm.2022.101417; html:https://europepmc.org/articles/PMC9048584; pdf:https://europepmc.org/articles/PMC9048584?pdf=render
 33541353,https://doi.org/10.1186/s12916-020-01872-8,The impact of non-pharmaceutical interventions on SARS-CoV-2 transmission across 130 countries and territories.,"Liu Y, Morgenstern C, Kelly J, Lowe R, CMMID COVID-19 Working Group, Jit M.",,BMC medicine,2021,2021-02-05,Y,Quantitative; Pandemic; Health Impact Assessment; Public Health Intervention; Longitudinal Analysis; Policy Evaluation; Non-pharmaceutical Interventions; Covid-19; Sars-cov-2,,,"<h4>Background</h4>Non-pharmaceutical interventions (NPIs) are used to reduce transmission of SARS coronavirus 2 (SARS-CoV-2) that causes coronavirus disease 2019 (COVID-19). However, empirical evidence of the effectiveness of specific NPIs has been inconsistent. We assessed the effectiveness of NPIs around internal containment and closure, international travel restrictions, economic measures, and health system actions on SARS-CoV-2 transmission in 130 countries and territories.<h4>Methods</h4>We used panel (longitudinal) regression to estimate the effectiveness of 13 categories of NPIs in reducing SARS-CoV-2 transmission using data from January to June 2020. First, we examined the temporal association between NPIs using hierarchical cluster analyses. We then regressed the time-varying reproduction number (R<sub>t</sub>) of COVID-19 against different NPIs. We examined different model specifications to account for the temporal lag between NPIs and changes in R<sub>t</sub>, levels of NPI intensity, time-varying changes in NPI effect, and variable selection criteria. Results were interpreted taking into account both the range of model specifications and temporal clustering of NPIs.<h4>Results</h4>There was strong evidence for an association between two NPIs (school closure, internal movement restrictions) and reduced R<sub>t</sub>. Another three NPIs (workplace closure, income support, and debt/contract relief) had strong evidence of effectiveness when ignoring their level of intensity, while two NPIs (public events cancellation, restriction on gatherings) had strong evidence of their effectiveness only when evaluating their implementation at maximum capacity (e.g. restrictions on 1000+ people gathering were not effective, restrictions on < 10 people gathering were). Evidence about the effectiveness of the remaining NPIs (stay-at-home requirements, public information campaigns, public transport closure, international travel controls, testing, contact tracing) was inconsistent and inconclusive. We found temporal clustering between many of the NPIs. Effect sizes varied depending on whether or not we included data after peak NPI intensity.<h4>Conclusion</h4>Understanding the impact that specific NPIs have had on SARS-CoV-2 transmission is complicated by temporal clustering, time-dependent variation in effects, and differences in NPI intensity. However, the effectiveness of school closure and internal movement restrictions appears robust across different model specifications, with some evidence that other NPIs may also be effective under particular conditions. This provides empirical evidence for the potential effectiveness of many, although not all, actions policy-makers are taking to respond to the COVID-19 pandemic.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-020-01872-8; doi:https://doi.org/10.1186/s12916-020-01872-8; html:https://europepmc.org/articles/PMC7861967; pdf:https://europepmc.org/articles/PMC7861967?pdf=render
+33725121,https://doi.org/10.1093/rheumatology/keab250,COVID-19 in patients with autoimmune diseases: characteristics and outcomes in a multinational network of cohorts across three countries.,"Tan EH, Sena AG, Prats-Uribe A, You SC, Ahmed WU, Kostka K, Reich C, Duvall SL, Lynch KE, Matheny ME, Duarte-Salles T, Bertolin SF, Hripcsak G, Natarajan K, Falconer T, Spotnitz M, Ostropolets A, Blacketer C, Alshammari TM, Alghoul H, Alser O, Lane JCE, Dawoud DM, Shah K, Yang Y, Zhang L, Areia C, Golozar A, Recalde M, Casajust P, Jonnagaddala J, Subbian V, Vizcaya D, Lai LYH, Nyberg F, Morales DR, Posada JD, Shah NH, Gong M, Vivekanantham A, Abend A, Minty EP, Suchard M, Rijnbeek P, Ryan PB, Prieto-Alhambra D.",,"Rheumatology (Oxford, England)",2021,2021-10-01,Y,Mortality; Hospitalization; Open Science; Autoimmune Condition; Observational Health Data Sciences And Informatics (Ohdsi); Observational Medical Outcomes Partnership (Omop); Covid-19,,,"<h4>Objective</h4>Patients with autoimmune diseases were advised to shield to avoid coronavirus disease 2019 (COVID-19), but information on their prognosis is lacking. We characterized 30-day outcomes and mortality after hospitalization with COVID-19 among patients with prevalent autoimmune diseases, and compared outcomes after hospital admissions among similar patients with seasonal influenza.<h4>Methods</h4>A multinational network cohort study was conducted using electronic health records data from Columbia University Irving Medical Center [USA, Optum (USA), Department of Veterans Affairs (USA), Information System for Research in Primary Care-Hospitalization Linked Data (Spain) and claims data from IQVIA Open Claims (USA) and Health Insurance and Review Assessment (South Korea). All patients with prevalent autoimmune diseases, diagnosed and/or hospitalized between January and June 2020 with COVID-19, and similar patients hospitalized with influenza in 2017-18 were included. Outcomes were death and complications within 30 days of hospitalization.<h4>Results</h4>We studied 133 589 patients diagnosed and 48 418 hospitalized with COVID-19 with prevalent autoimmune diseases. Most patients were female, aged ≥50 years with previous comorbidities. The prevalence of hypertension (45.5-93.2%), chronic kidney disease (14.0-52.7%) and heart disease (29.0-83.8%) was higher in hospitalized vs diagnosed patients with COVID-19. Compared with 70 660 hospitalized with influenza, those admitted with COVID-19 had more respiratory complications including pneumonia and acute respiratory distress syndrome, and higher 30-day mortality (2.2-4.3% vs 6.32-24.6%).<h4>Conclusion</h4>Compared with influenza, COVID-19 is a more severe disease, leading to more complications and higher mortality.",,pdf:https://academic.oup.com/rheumatology/article-pdf/60/SI/SI37/40544680/keab250.pdf; doi:https://doi.org/10.1093/rheumatology/keab250; html:https://europepmc.org/articles/PMC7989171; pdf:https://europepmc.org/articles/PMC7989171?pdf=render
 33664499,https://doi.org/10.1038/s41431-021-00835-8,Colocalization analysis of polycystic ovary syndrome to identify potential disease-mediating genes and proteins.,"Censin JC, Bovijn J, Holmes MV, Lindgren CM.",,European journal of human genetics : EJHG,2021,2021-03-04,Y,,,,"Polycystic ovary syndrome (PCOS) is a common complex disease in women with a strong genetic component and downstream consequences for reproductive, metabolic and psychological health. There are currently 19 known PCOS risk loci, primarily identified in women of Han Chinese or European ancestry, and 14 of these risk loci were identified or replicated in a genome-wide association study of PCOS performed in up to 10,074 cases and 103,164 controls of European descent. However, for most of these loci the gene responsible for the association is unknown. We therefore use a Bayesian colocalization approach (Coloc) to highlight genes in PCOS-associated regions that may have a role in mediating the disease risk. We evaluated the posterior probabilities of evidence consistent with shared causal variants between 14 PCOS genetic risk loci and intermediate cellular phenotypes in one protein (N = 3301) and two expression quantitative trait locus datasets (N = 31,684 and N = 80-491). Through these analyses, we identified seven proteins or genes with evidence of a possibly shared causal variant for almost 30% of known PCOS signals, including follicle stimulating hormone and ERBB3, IKZF4, RPS26, SUOX, ZFP36L2, and C8orf49. Several of these potential effector proteins and genes have been implicated in the hypothalamic-pituitary-gonadal signalling pathway and provide an avenue for functional follow-up in order to demonstrate a causal role in PCOS pathophysiology.",,pdf:https://www.nature.com/articles/s41431-021-00835-8.pdf; doi:https://doi.org/10.1038/s41431-021-00835-8; html:https://europepmc.org/articles/PMC8440598; pdf:https://europepmc.org/articles/PMC8440598?pdf=render
 32719032,https://doi.org/10.1128/jcm.00670-20,DNA Thermo-Protection Facilitates Whole-Genome Sequencing of Mycobacteria Direct from Clinical Samples.,"George S, Xu Y, Rodger G, Morgan M, Sanderson ND, Hoosdally SJ, Thulborn S, Robinson E, Rathod P, Walker AS, Peto TEA, Crook DW, Dingle KE.",,Journal of clinical microbiology,2020,2020-09-22,Y,DNA sequencing; Mycobacterium tuberculosis; Mycobacteria; Clinical Diagnostics; Nanopore Dna Sequencing; Direct-from-sample Sequencing,,,"<i>Mycobacterium tuberculosis</i> is the leading cause of death from bacterial infection. Improved rapid diagnosis and antimicrobial resistance determination, such as by whole-genome sequencing, are required. Our aim was to develop a simple, low-cost method of preparing DNA for sequencing direct from <i>M. tuberculosis</i>-positive clinical samples (without culture). Simultaneous sputum liquefaction, bacteria heat inactivation (99°C/30 min), and enrichment for mycobacteria DNA were achieved using an equal volume of thermo-protection buffer (4 M KCl, 0.05 M HEPES buffer, pH 7.5, 0.1% dithiothreitol [DTT]). The buffer emulated intracellular conditions found in hyperthermophiles, thus protecting DNA from rapid thermodegradation, which renders it a poor template for sequencing. Initial validation experiments employed mycobacteria DNA, either extracted or intracellular. Next, mock clinical samples (infection-negative human sputum spiked with 0 to 10<sup>5</sup><i>Mycobacterium bovis</i> BCG cells/ml) underwent liquefaction in thermo-protection buffer and heat inactivation. DNA was extracted and sequenced. Human DNA degraded faster than mycobacteria DNA, resulting in target enrichment. Four replicate experiments achieved <i>M. tuberculosis</i> detection at 10<sup>1</sup> BCG cells/ml, with 31 to 59 <i>M. tuberculosis</i> complex reads. Maximal genome coverage (>97% at 5× depth) occurred at 10<sup>4</sup> BCG cells/ml; >91% coverage (1× depth) occurred at 10<sup>3</sup> BCG cells/ml. Final validation employed <i>M. tuberculosis</i>-positive clinical samples (<i>n</i> = 20), revealing that initial sample volumes of ≥1 ml typically yielded higher mean depths of <i>M. tuberculosis</i> genome coverage, with an overall range of 0.55 to 81.02. A mean depth of 3 gave >96% 1-fold tuberculosis (TB) genome coverage (in 15/20 clinical samples). A mean depth of 15 achieved >99% 5-fold genome coverage (in 9/20 clinical samples). In summary, direct-from-sample sequencing of <i>M. tuberculosis</i> genomes was facilitated by a low-cost thermo-protection buffer.",,doi:https://doi.org/10.1128/jcm.00670-20; doi:https://doi.org/10.1128/JCM.00670-20; html:https://europepmc.org/articles/PMC7512152; pdf:https://europepmc.org/articles/PMC7512152?pdf=render
-33725121,https://doi.org/10.1093/rheumatology/keab250,COVID-19 in patients with autoimmune diseases: characteristics and outcomes in a multinational network of cohorts across three countries.,"Tan EH, Sena AG, Prats-Uribe A, You SC, Ahmed WU, Kostka K, Reich C, Duvall SL, Lynch KE, Matheny ME, Duarte-Salles T, Bertolin SF, Hripcsak G, Natarajan K, Falconer T, Spotnitz M, Ostropolets A, Blacketer C, Alshammari TM, Alghoul H, Alser O, Lane JCE, Dawoud DM, Shah K, Yang Y, Zhang L, Areia C, Golozar A, Recalde M, Casajust P, Jonnagaddala J, Subbian V, Vizcaya D, Lai LYH, Nyberg F, Morales DR, Posada JD, Shah NH, Gong M, Vivekanantham A, Abend A, Minty EP, Suchard M, Rijnbeek P, Ryan PB, Prieto-Alhambra D.",,"Rheumatology (Oxford, England)",2021,2021-10-01,Y,Mortality; Hospitalization; Open Science; Autoimmune Condition; Observational Health Data Sciences And Informatics (Ohdsi); Observational Medical Outcomes Partnership (Omop); Covid-19,,,"<h4>Objective</h4>Patients with autoimmune diseases were advised to shield to avoid coronavirus disease 2019 (COVID-19), but information on their prognosis is lacking. We characterized 30-day outcomes and mortality after hospitalization with COVID-19 among patients with prevalent autoimmune diseases, and compared outcomes after hospital admissions among similar patients with seasonal influenza.<h4>Methods</h4>A multinational network cohort study was conducted using electronic health records data from Columbia University Irving Medical Center [USA, Optum (USA), Department of Veterans Affairs (USA), Information System for Research in Primary Care-Hospitalization Linked Data (Spain) and claims data from IQVIA Open Claims (USA) and Health Insurance and Review Assessment (South Korea). All patients with prevalent autoimmune diseases, diagnosed and/or hospitalized between January and June 2020 with COVID-19, and similar patients hospitalized with influenza in 2017-18 were included. Outcomes were death and complications within 30 days of hospitalization.<h4>Results</h4>We studied 133 589 patients diagnosed and 48 418 hospitalized with COVID-19 with prevalent autoimmune diseases. Most patients were female, aged ≥50 years with previous comorbidities. The prevalence of hypertension (45.5-93.2%), chronic kidney disease (14.0-52.7%) and heart disease (29.0-83.8%) was higher in hospitalized vs diagnosed patients with COVID-19. Compared with 70 660 hospitalized with influenza, those admitted with COVID-19 had more respiratory complications including pneumonia and acute respiratory distress syndrome, and higher 30-day mortality (2.2-4.3% vs 6.32-24.6%).<h4>Conclusion</h4>Compared with influenza, COVID-19 is a more severe disease, leading to more complications and higher mortality.",,pdf:https://academic.oup.com/rheumatology/article-pdf/60/SI/SI37/40544680/keab250.pdf; doi:https://doi.org/10.1093/rheumatology/keab250; html:https://europepmc.org/articles/PMC7989171; pdf:https://europepmc.org/articles/PMC7989171?pdf=render
+31782492,https://doi.org/10.1093/ajcn/nqz293,The association of fish consumption and its urinary metabolites with cardiovascular risk factors: the International Study of Macro-/Micronutrients and Blood Pressure (INTERMAP).,"Gibson R, Lau CE, Loo RL, Ebbels TMD, Chekmeneva E, Dyer AR, Miura K, Ueshima H, Zhao L, Daviglus ML, Stamler J, Van Horn L, Elliott P, Holmes E, Chan Q.",,The American journal of clinical nutrition,2020,2020-02-01,Y,Hypertension; Blood pressure; FISH; Shellfish; Biomarkers; body mass index; Seafood; Metabonomics; Homarine; Intermap Metabolomics,Improving Public Health,,"<h4>Background</h4>Results from observational studies regarding associations between fish (including shellfish) intake and cardiovascular disease risk factors, including blood pressure (BP) and BMI, are inconsistent.<h4>Objective</h4>To investigate associations of fish consumption and associated urinary metabolites with BP and BMI in free-living populations.<h4>Methods</h4>We used cross-sectional data from the International Study of Macro-/Micronutrients and Blood Pressure (INTERMAP), including 4680 men and women (40-59 y) from Japan, China, the United Kingdom, and United States. Dietary intakes were assessed by four 24-h dietary recalls and BP from 8 measurements. Urinary metabolites (2 timed 24-h urinary samples) associated with fish intake acquired from NMR spectroscopy were identified. Linear models were used to estimate BP and BMI differences across categories of intake and per 2 SD higher intake of fish and its biomarkers.<h4>Results</h4>No significant associations were observed between fish intake and BP. There was a direct association with fish intake and BMI in the Japanese population sample (P trend = 0.03; fully adjusted model). In Japan, trimethylamine-N-oxide (TMAO) and taurine, respectively, demonstrated area under the receiver operating characteristic curve (AUC) values of 0.81 and 0.78 in discriminating high against low fish intake, whereas homarine (a metabolite found in shellfish muscle) demonstrated an AUC of 0.80 for high/nonshellfish intake. Direct associations were observed between urinary TMAO and BMI for all regions except Japan (P < 0.0001) and in Western populations between TMAO and BP (diastolic blood pressure: mean difference 1.28; 95% CI: 0.55, 2.02 mmHg; P = 0.0006, systolic blood pressure: mean difference 1.67; 95% CI: 0.60, 2.73 mmHg; P = 0.002).<h4>Conclusions</h4>Urinary TMAO showed a stronger association with fish intake in the Japanese compared with the Western population sample. Urinary TMAO was directly associated with BP in the Western but not the Japanese population sample. Associations between fish intake and its biomarkers and downstream associations with BP/BMI appear to be context specific. INTERMAP is registered at www.clinicaltrials.gov as NCT00005271.",Gibson et al.’s study investigates whether having fish in diet will have an effect on urinary metabolism. They’ve assessed dietary and BP measurement across Asian and Westerns and shown that the relationship was stronger in Japanese population compared to Western population and is highly context dependant. ,doi:https://doi.org/10.1093/ajcn/nqz293; doi:https://doi.org/10.1093/ajcn/nqz293; html:https://europepmc.org/articles/PMC6997096; pdf:https://europepmc.org/articles/PMC6997096?pdf=render
 34653419,https://doi.org/10.1016/s2468-2667(21)00205-x,Life expectancy and risk of death in 6791 communities in England from 2002 to 2019: high-resolution spatiotemporal analysis of civil registration data.,"Rashid T, Bennett JE, Paciorek CJ, Doyle Y, Pearson-Stuttard J, Flaxman S, Fecht D, Toledano MB, Li G, Daby HI, Johnson E, Davies B, Ezzati M.",,The Lancet. Public health,2021,2021-10-13,Y,,,,"<h4>Background</h4>High-resolution data for how mortality and longevity have changed in England, UK are scarce. We aimed to estimate trends from 2002 to 2019 in life expectancy and probabilities of death at different ages for all 6791 middle-layer super output areas (MSOAs) in England.<h4>Methods</h4>We performed a high-resolution spatiotemporal analysis of civil registration data from the UK Small Area Health Statistics Unit research database using de-identified data for all deaths in England from 2002 to 2019, with information on age, sex, and MSOA of residence, and population counts by age, sex, and MSOA. We used a Bayesian hierarchical model to obtain estimates of age-specific death rates by sharing information across age groups, MSOAs, and years. We used life table methods to calculate life expectancy at birth and probabilities of death in different ages by sex and MSOA.<h4>Findings</h4>In 2002-06 and 2006-10, all but a few (0-1%) MSOAs had a life expectancy increase for female and male sexes. In 2010-14, female life expectancy decreased in 351 (5·2%) of 6791 MSOAs. By 2014-19, the number of MSOAs with declining life expectancy was 1270 (18·7%) for women and 784 (11·5%) for men. The life expectancy increase from 2002 to 2019 was smaller in MSOAs where life expectancy had been lower in 2002 (mostly northern urban MSOAs), and larger in MSOAs where life expectancy had been higher in 2002 (mostly MSOAs in and around London). As a result of these trends, the gap between the first and 99th percentiles of MSOA life expectancy for women increased from 10·7 years (95% credible interval 10·4-10·9) in 2002 to reach 14·2 years (13·9-14·5) in 2019, and for men increased from 11·5 years (11·3-11·7) in 2002 to 13·6 years (13·4-13·9) in 2019.<h4>Interpretation</h4>In the decade before the COVID-19 pandemic, life expectancy declined in increasing numbers of communities in England. To ensure that this trend does not continue or worsen, there is a need for pro-equity economic and social policies, and greater investment in public health and health care throughout the entire country.<h4>Funding</h4>Wellcome Trust, Imperial College London, Medical Research Council, Health Data Research UK, and National Institutes of Health Research.",,pdf:http://www.thelancet.com/article/S246826672100205X/pdf; doi:https://doi.org/10.1016/S2468-2667(21)00205-X; html:https://europepmc.org/articles/PMC8554392
 34935001,https://doi.org/10.1016/s2666-7568(21)00282-8,Prevalence and duration of detectable SARS-CoV-2 nucleocapsid antibodies in staff and residents of long-term care facilities over the first year of the pandemic (VIVALDI study): prospective cohort study in England.,"Krutikov M, Palmer T, Tut G, Fuller C, Azmi B, Giddings R, Shrotri M, Kaur N, Sylla P, Lancaster T, Irwin-Singer A, Hayward A, Moss P, Copas A, Shallcross L.",,The lancet. Healthy longevity,2022,2021-12-16,Y,,,,"<h4>Background</h4>Long-term care facilities (LTCFs) have reported high SARS-CoV-2 infection rates and related mortality, but the proportion of infected people among those who have survived, and duration of the antibody response to natural infection, is unknown. We determined the prevalence and stability of nucleocapsid antibodies (the standard assay for detection of previous infection) in staff and residents in LTCFs in England.<h4>Methods</h4>This was a prospective cohort study of residents 65 years or older and of staff 65 years or younger in 201 LTCFs in England between March 1, 2020, and May 7, 2021. Participants were linked to a unique pseudo-identifier based on their UK National Health Service identification number. Serial blood samples were tested for IgG antibodies against SARS-CoV-2 nucleocapsid protein using the Abbott ARCHITECT i-system (Abbott, Maidenhead, UK) immunoassay. Primary endpoints were prevalence and cumulative incidence of antibody positivity, which were weighted to the LTCF population. Incidence rate of loss of antibodies (seroreversion) was estimated from Kaplan-Meier curves.<h4>Findings</h4>9488 samples were included, 8636 (91·0%) of which could be individually linked to 1434 residents and 3288 staff members. The cumulative incidence of nucleocapsid seropositivity was 34·6% (29·6-40·0) in residents and 26·1% (23·0-29·5) in staff over 11 months. 239 (38·6%) residents and 503 women (81·3%) were included in the antibody-waning analysis, and median follow-up was 149 days (IQR 107-169). The incidence rate of seroreversion was 2·1 per 1000 person-days at risk, and median time to reversion was 242·5 days.<h4>Interpretation</h4>At least a quarter of staff and a third of surviving residents were infected with SAR-CoV-2 during the first two waves of the pandemic in England. Nucleocapsid-specific antibodies often become undetectable within the first year following infection, which is likely to lead to marked underestimation of the true proportion of people with previous infection. Given that natural infection might act to boost vaccine responses, better assays to identify natural infection should be developed.<h4>Funding</h4>UK Government Department of Health and Social Care.",,pdf:http://www.thelancet.com/article/S2666756821002828/pdf; doi:https://doi.org/10.1016/S2666-7568(21)00282-8; html:https://europepmc.org/articles/PMC8676418
-31782492,https://doi.org/10.1093/ajcn/nqz293,The association of fish consumption and its urinary metabolites with cardiovascular risk factors: the International Study of Macro-/Micronutrients and Blood Pressure (INTERMAP).,"Gibson R, Lau CE, Loo RL, Ebbels TMD, Chekmeneva E, Dyer AR, Miura K, Ueshima H, Zhao L, Daviglus ML, Stamler J, Van Horn L, Elliott P, Holmes E, Chan Q.",,The American journal of clinical nutrition,2020,2020-02-01,Y,Hypertension; Blood pressure; FISH; Shellfish; Biomarkers; body mass index; Seafood; Metabonomics; Homarine; Intermap Metabolomics,Improving Public Health,,"<h4>Background</h4>Results from observational studies regarding associations between fish (including shellfish) intake and cardiovascular disease risk factors, including blood pressure (BP) and BMI, are inconsistent.<h4>Objective</h4>To investigate associations of fish consumption and associated urinary metabolites with BP and BMI in free-living populations.<h4>Methods</h4>We used cross-sectional data from the International Study of Macro-/Micronutrients and Blood Pressure (INTERMAP), including 4680 men and women (40-59 y) from Japan, China, the United Kingdom, and United States. Dietary intakes were assessed by four 24-h dietary recalls and BP from 8 measurements. Urinary metabolites (2 timed 24-h urinary samples) associated with fish intake acquired from NMR spectroscopy were identified. Linear models were used to estimate BP and BMI differences across categories of intake and per 2 SD higher intake of fish and its biomarkers.<h4>Results</h4>No significant associations were observed between fish intake and BP. There was a direct association with fish intake and BMI in the Japanese population sample (P trend = 0.03; fully adjusted model). In Japan, trimethylamine-N-oxide (TMAO) and taurine, respectively, demonstrated area under the receiver operating characteristic curve (AUC) values of 0.81 and 0.78 in discriminating high against low fish intake, whereas homarine (a metabolite found in shellfish muscle) demonstrated an AUC of 0.80 for high/nonshellfish intake. Direct associations were observed between urinary TMAO and BMI for all regions except Japan (P < 0.0001) and in Western populations between TMAO and BP (diastolic blood pressure: mean difference 1.28; 95% CI: 0.55, 2.02 mmHg; P = 0.0006, systolic blood pressure: mean difference 1.67; 95% CI: 0.60, 2.73 mmHg; P = 0.002).<h4>Conclusions</h4>Urinary TMAO showed a stronger association with fish intake in the Japanese compared with the Western population sample. Urinary TMAO was directly associated with BP in the Western but not the Japanese population sample. Associations between fish intake and its biomarkers and downstream associations with BP/BMI appear to be context specific. INTERMAP is registered at www.clinicaltrials.gov as NCT00005271.",Gibson et al.’s study investigates whether having fish in diet will have an effect on urinary metabolism. They’ve assessed dietary and BP measurement across Asian and Westerns and shown that the relationship was stronger in Japanese population compared to Western population and is highly context dependant. ,doi:https://doi.org/10.1093/ajcn/nqz293; doi:https://doi.org/10.1093/ajcn/nqz293; html:https://europepmc.org/articles/PMC6997096; pdf:https://europepmc.org/articles/PMC6997096?pdf=render
-35710247,https://doi.org/10.1136/bmjopen-2021-060280,Structured follow-up pathway to support people after transient ischaemic attack and minor stroke (SUPPORT TIA): protocol for a feasibility study and process evaluation.,"Turner GM, Jones R, Collis P, Patel S, Jowett S, Tearne S, Foy R, Atkins L, Mant J, Calvert M.",,BMJ open,2022,2022-06-16,Y,Qualitative Research; Rehabilitation Medicine; Stroke Medicine; Protocols & Guidelines; Organisation Of Health Services; Depression & Mood Disorders,,,"<h4>Introduction</h4>People who experience transient ischaemic attack (TIA) and minor stroke have limited follow-up despite rapid specialist review in hospital. This means they often have unmet needs and feel abandoned following discharge. Care needs after TIA/minor stroke include information provision (diagnosis and stroke risk), stroke prevention (medication and lifestyle change) and holistic care (residual problems and return to work or usual activities). This protocol describes a feasibility study and process evaluation of an intervention to support people after TIA/minor stroke. The study aims to assess the feasibility and acceptability of (1) the intervention and (2) the trial procedures for a future randomised controlled trial of this intervention.<h4>Methods and analysis</h4>This is a multicentre, randomised (1:1) feasibility study with a mixed-methods process evaluation. Sixty participants will be recruited from TIA clinics or stroke wards at three hospital sites (England). Intervention arm participants will be offered a nurse or allied health professional-led follow-up appointment 4 weeks after TIA/minor stroke. The multifaceted intervention includes: a needs checklist, action plan, resources to support management of needs, a general practitioner letter and training to deliver the intervention. Control arm participants will receive usual care. Follow-up will be self-completed questionnaires (12 weeks and 24 weeks) and a clinic appointment (24 weeks). Follow-up questionnaires will measure anxiety, depression, fatigue, health related quality of life, self-efficacy and medication adherence. The clinic appointment will collect body mass index, blood pressure, cholesterol and medication. Assessment of feasibility and acceptability will include quantitative process variables (such as recruitment and questionnaire response rates), structured observations of study processes, and interviews with a subsample of participants and clinical staff.<h4>Ethics and dissemination</h4>Favourable ethical opinion was gained from the Wales Research Ethics Committee (REC) 1 (23 February 2021, REC reference: 21/WA/0036). Study results will be published in peer-reviewed journals and presented at conferences. A lay summary and dissemination strategy will be codesigned with consumers. The lay summary and journal publication will be distributed on social media.<h4>Trial registration number</h4>ISRCTN39864003.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/6/e060280.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-060280; html:https://europepmc.org/articles/PMC9207897; pdf:https://europepmc.org/articles/PMC9207897?pdf=render
 36208161,https://doi.org/10.1093/eurheartj/ehac426,CODE-EHR best practice framework for the use of structured electronic healthcare records in clinical research.,"Kotecha D, Asselbergs FW, Achenbach S, Anker SD, Atar D, Baigent C, Banerjee A, Beger B, Brobert G, Casadei B, Ceccarelli C, Cowie MR, Crea F, Cronin M, Denaxas S, Derix A, Fitzsimons D, Fredriksson M, Gale CP, Gkoutos GV, Goettsch W, Hemingway H, Ingvar M, Jonas A, Kazmierski R, Løgstrup S, Thomas Lumbers R, Lüscher TF, McGreavy P, Piña IL, Roessig L, Steinbeisser C, Sundgren M, Tyl B, van Thiel G, van Bochove K, Vardas PE, Villanueva T, Vrana M, Weber W, Weidinger F, Windecker S, Wood A, Grobbee DE, Innovative Medicines Initiative BigData@Heart Consortium, European Society of Cardiology, CODE-EHR international consensus group.",,European heart journal,2022,2022-10-01,Y,,,,"Big data is central to new developments in global clinical science aiming to improve the lives of patients. Technological advances have led to the routine use of structured electronic healthcare records with the potential to address key gaps in clinical evidence. The covid-19 pandemic has demonstrated the potential of big data and related analytics, but also important pitfalls. Verification, validation, and data privacy, as well as the social mandate to undertake research are key challenges. The European Society of Cardiology and the BigData@Heart consortium have brought together a range of international stakeholders, including patient representatives, clinicians, scientists, regulators, journal editors and industry. We propose the CODE-EHR Minimum Standards Framework as a means to improve the design of studies, enhance transparency and develop a roadmap towards more robust and effective utilisation of healthcare data for research purposes.",,pdf:https://academic.oup.com/eurheartj/article-pdf/43/37/3578/46535456/ehac426.pdf; doi:https://doi.org/10.1093/eurheartj/ehac426; html:https://europepmc.org/articles/PMC9452067; pdf:https://europepmc.org/articles/PMC9452067?pdf=render
+35710247,https://doi.org/10.1136/bmjopen-2021-060280,Structured follow-up pathway to support people after transient ischaemic attack and minor stroke (SUPPORT TIA): protocol for a feasibility study and process evaluation.,"Turner GM, Jones R, Collis P, Patel S, Jowett S, Tearne S, Foy R, Atkins L, Mant J, Calvert M.",,BMJ open,2022,2022-06-16,Y,Qualitative Research; Rehabilitation Medicine; Stroke Medicine; Protocols & Guidelines; Organisation Of Health Services; Depression & Mood Disorders,,,"<h4>Introduction</h4>People who experience transient ischaemic attack (TIA) and minor stroke have limited follow-up despite rapid specialist review in hospital. This means they often have unmet needs and feel abandoned following discharge. Care needs after TIA/minor stroke include information provision (diagnosis and stroke risk), stroke prevention (medication and lifestyle change) and holistic care (residual problems and return to work or usual activities). This protocol describes a feasibility study and process evaluation of an intervention to support people after TIA/minor stroke. The study aims to assess the feasibility and acceptability of (1) the intervention and (2) the trial procedures for a future randomised controlled trial of this intervention.<h4>Methods and analysis</h4>This is a multicentre, randomised (1:1) feasibility study with a mixed-methods process evaluation. Sixty participants will be recruited from TIA clinics or stroke wards at three hospital sites (England). Intervention arm participants will be offered a nurse or allied health professional-led follow-up appointment 4 weeks after TIA/minor stroke. The multifaceted intervention includes: a needs checklist, action plan, resources to support management of needs, a general practitioner letter and training to deliver the intervention. Control arm participants will receive usual care. Follow-up will be self-completed questionnaires (12 weeks and 24 weeks) and a clinic appointment (24 weeks). Follow-up questionnaires will measure anxiety, depression, fatigue, health related quality of life, self-efficacy and medication adherence. The clinic appointment will collect body mass index, blood pressure, cholesterol and medication. Assessment of feasibility and acceptability will include quantitative process variables (such as recruitment and questionnaire response rates), structured observations of study processes, and interviews with a subsample of participants and clinical staff.<h4>Ethics and dissemination</h4>Favourable ethical opinion was gained from the Wales Research Ethics Committee (REC) 1 (23 February 2021, REC reference: 21/WA/0036). Study results will be published in peer-reviewed journals and presented at conferences. A lay summary and dissemination strategy will be codesigned with consumers. The lay summary and journal publication will be distributed on social media.<h4>Trial registration number</h4>ISRCTN39864003.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/6/e060280.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-060280; html:https://europepmc.org/articles/PMC9207897; pdf:https://europepmc.org/articles/PMC9207897?pdf=render
 36539756,https://doi.org/10.1186/s12888-022-04429-6,ADHD Remote Technology study of cardiometabolic risk factors and medication adherence (ART-CARMA): a multi-centre prospective cohort study protocol.,"Denyer H, Ramos-Quiroga JA, Folarin A, Ramos C, Nemeth P, Bilbow A, Woodward E, Whitwell S, Müller-Sedgwick U, Larsson H, Dobson RJ, Kuntsi J.",,BMC psychiatry,2022,2022-12-20,Y,ADHD; Cardiovascular disease; Attention Deficit Hyperactivity Disorder; Medication Adherence; Remote Monitoring; Mhealth; Digital Phenotyping; Remote Measurement Technology,,,"<h4>Background</h4>Emerging evidence points at substantial comorbidity between adult attention deficit hyperactivity disorder (ADHD) and cardiometabolic diseases, but our understanding of the comorbidity and how to manage cardiometabolic disease in adults with ADHD is limited. The ADHD Remote Technology study of cardiometabolic risk factors and medication adherence (ART-CARMA) project uses remote measurement technology to obtain real-world data from daily life to assess the extent to which ADHD medication treatment and physical activity, individually and jointly, may influence cardiometabolic risks in adults with ADHD. Our second main aim is to obtain valuable real-world data on adherence to pharmacological treatment and its predictors and correlates during daily life from adults with ADHD.<h4>Methods</h4>ART-CARMA is a multi-site prospective cohort study within the EU-funded collaboration 'TIMESPAN' (Management of chronic cardiometabolic disease and treatment discontinuity in adult ADHD patients) that will recruit 300 adults from adult ADHD waiting lists. The participants will be monitored remotely over a period of 12 months that starts from pre-treatment initiation. Passive monitoring, which involves the participants wearing a wrist-worn device (EmbracePlus) and downloading the RADAR-base Passive App and the Empatica Care App on their smartphone, provides ongoing data collection on a wide range of variables, such as physical activity, sleep, pulse rate (PR) and pulse rate variability (PRV), systolic peaks, electrodermal activity (EDA), oxygen saturation (SpO2), peripheral temperature, smartphone usage including social connectivity, and the environment (e.g. ambient noise, light levels, relative location). By combining data across these variables measured, processes such as physical activity, sleep, autonomic arousal, and indicators of cardiovascular health can be captured. Active remote monitoring involves the participant completing tasks using a smartphone app (such as completing clinical questionnaires or speech tasks), measuring their blood pressure and weight, or using a PC/laptop (cognitive tasks). The ART system is built on the RADAR-base mobile-health platform.<h4>Discussion</h4>The long-term goal is to use these data to improve the management of cardiometabolic disease in adults with ADHD, and to improve ADHD medication treatment adherence and the personalisation of treatment.",,pdf:https://bmcpsychiatry.biomedcentral.com/counter/pdf/10.1186/s12888-022-04429-6; doi:https://doi.org/10.1186/s12888-022-04429-6; html:https://europepmc.org/articles/PMC9764531; pdf:https://europepmc.org/articles/PMC9764531?pdf=render
-33528799,https://doi.org/10.1007/s12471-021-01542-1,Risk stratification and subclinical phenotyping of dilated and/or arrhythmogenic cardiomyopathy mutation-positive relatives: CVON eDETECT consortium.,"Roudijk RW, Taha K, Bourfiss M, Loh P, van den Heuvel L, Boonstra MJ, van Lint F, van der Voorn SM, Te Riele ASJM, Bosman LP, Christiaans I, van Veen TAB, Remme CA, van den Berg MP, van Tintelen JP, Asselbergs FW.",,Netherlands heart journal : monthly journal of the Netherlands Society of Cardiology and the Netherlands Heart Foundation,2021,2021-02-02,Y,Dilated cardiomyopathy; Phospholamban; Arrhythmogenic Cardiomyopathy; Pathogenic Variants; Cascade Screening; Plakophilin‑2,,,"In relatives of index patients with dilated cardiomyopathy and arrhythmogenic cardiomyopathy, early detection of disease onset is essential to prevent sudden cardiac death and facilitate early treatment of heart failure. However, the optimal screening interval and combination of diagnostic techniques are unknown. The clinical course of disease in index patients and their relatives is variable due to incomplete and age-dependent penetrance. Several biomarkers, electrocardiographic and imaging (echocardiographic deformation imaging and cardiac magnetic resonance imaging) techniques are promising non-invasive methods for detection of subclinical cardiomyopathy. However, these techniques need optimisation and integration into clinical practice. Furthermore, determining the optimal interval and intensity of cascade screening may require a personalised approach. To address this, the CVON-eDETECT (early detection of disease in cardiomyopathy mutation carriers) consortium aims to integrate electronic health record data from long-term follow-up, diagnostic data sets, tissue and plasma samples in a multidisciplinary biobank environment to provide personalised risk stratification for heart failure and sudden cardiac death. Adequate risk stratification may lead to personalised screening, treatment and optimal timing of implantable cardioverter defibrillator implantation. In this article, we describe non-invasive diagnostic techniques used for detection of subclinical disease in relatives of index patients with dilated cardiomyopathy and arrhythmogenic cardiomyopathy.",,pdf:https://link.springer.com/content/pdf/10.1007/s12471-021-01542-1.pdf; doi:https://doi.org/10.1007/s12471-021-01542-1; html:https://europepmc.org/articles/PMC8160055; pdf:https://europepmc.org/articles/PMC8160055?pdf=render
 35498042,https://doi.org/10.3389/fcvm.2022.768972,Unravelling the Difference Between Men and Women in Post-CABG Survival.,"Schmidt AF, Haitjema S, Sartipy U, Holzmann MJ, Malenka DJ, Ross CS, van Gilst W, Rouleau JL, Meeder AM, Baker RA, Shiomi H, Kimura T, Tran L, Smith JA, Reid CM, Asselbergs FW, den Ruijter HM.",,Frontiers in cardiovascular medicine,2022,2022-04-13,Y,Atherosclerosis; Sex; Gender; Prognosis; Cabg; Outcome,,,"<h4>Objectives</h4>Women have a worse prognosis after coronary artery bypass grafting (CABG) surgery compared to men. We sought to quantify to what extent this difference in post-CABG survival could be attributed to sex itself, or whether this was mediated by difference between men and women at the time of intervention. Additionally, we explored to what extent these effects were homogenous across patient subgroups.<h4>Methods</h4>Time to all-cause mortality was available for 102,263 CABG patients, including 20,988 (21%) women, sourced through an individual participant data meta-analysis of five cohort studies. Difference between men and women in survival duration was assessed using Kaplan-Meier estimates, and Cox's proportional hazards model.<h4>Results</h4>During a median follow-up of 5 years, 13,598 (13%) patients died, with women more likely to die than men: female HR 1.20 (95%CI 1.16; 1.25). We found that differences in patient characteristics at the time of CABG procedure mediated this sex effect, and accounting for these resulted in a neutral female HR 0.98 (95%CI 0.94; 1.02). Next we performed <i>a priori</i> defined subgroup analyses of the five most prominent mediators: age, creatinine, peripheral vascular disease, type 2 diabetes, and heart failure. We found that women without peripheral vascular disease (PVD) or women aged 70+, survived longer than men (interaction <i>p</i>-values 0.04 and 6 × 10<sup>-5</sup>, respectively), with an effect reversal in younger women.<h4>Conclusion</h4>Sex differences in post-CABG survival were readily explained by difference in patient characteristics and comorbidities. Pre-planned analyses revealed patient subgroups (aged 70+, or without PVD) of women that survived longer than men, and a subgroup of younger women with comparatively poorer survival.",,pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2022.768972/pdf; doi:https://doi.org/10.3389/fcvm.2022.768972; html:https://europepmc.org/articles/PMC9043514; pdf:https://europepmc.org/articles/PMC9043514?pdf=render
-31950891,https://doi.org/10.1192/bjo.2019.96,Predicting high-cost care in a mental health setting.,"Colling C, Khondoker M, Patel R, Fok M, Harland R, Broadbent M, McCrone P, Stewart R.",,BJPsych open,2020,2020-01-17,Y,Prediction; Natural Language Processing; Mental Health Service; Digital Health Records,,,"<h4>Background</h4>The density of information in digital health records offers new potential opportunities for automated prediction of cost-relevant outcomes.<h4>Aims</h4>We investigated the extent to which routinely recorded data held in the electronic health record (EHR) predict priority service outcomes and whether natural language processing tools enhance the predictions. We evaluated three high priority outcomes: in-patient duration, readmission following in-patient care and high service cost after first presentation.<h4>Method</h4>We used data obtained from a clinical database derived from the EHR of a large mental healthcare provider within the UK. We combined structured data with text-derived data relating to diagnosis statements, medication and psychiatric symptomatology. Predictors of the three different clinical outcomes were modelled using logistic regression with performance evaluated against a validation set to derive areas under receiver operating characteristic curves.<h4>Results</h4>In validation samples, the full models (using all available data) achieved areas under receiver operating characteristic curves between 0.59 and 0.85 (in-patient duration 0.63, readmission 0.59, high service use 0.85). Adding natural language processing-derived data to the models increased the variance explained across all clinical scenarios (observed increase in r2 = 12-46%).<h4>Conclusions</h4>EHR data offer the potential to improve routine clinical predictions by utilising previously inaccessible data. Of our scenarios, prediction of high service use after initial presentation achieved the highest performance.","This study uses data from a mental healthcare provider to predict 3 things: 1) extended duration of stay in a hospital, 2) the likelihood of needing to be admitted to hospital again after discharge, and 3) likehood of needing 'high intesity service' (high cost services). The authors developed a natural language processing model (a computer system than aims to interpret text and draw out useful information) to review the text, diagnoses, medications and the patient symptoms to work out which patients would fall within those 3 categories. They conclude that their model could be used to improve services through predicting users who will require the most intense and costly care.",pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/6EF9FC74DC5A744C9D841DD649992ABE/S2056472419000966a.pdf/div-class-title-predicting-high-cost-care-in-a-mental-health-setting-div.pdf; doi:https://doi.org/10.1192/bjo.2019.96; html:https://europepmc.org/articles/PMC7001466; pdf:https://europepmc.org/articles/PMC7001466?pdf=render
+33528799,https://doi.org/10.1007/s12471-021-01542-1,Risk stratification and subclinical phenotyping of dilated and/or arrhythmogenic cardiomyopathy mutation-positive relatives: CVON eDETECT consortium.,"Roudijk RW, Taha K, Bourfiss M, Loh P, van den Heuvel L, Boonstra MJ, van Lint F, van der Voorn SM, Te Riele ASJM, Bosman LP, Christiaans I, van Veen TAB, Remme CA, van den Berg MP, van Tintelen JP, Asselbergs FW.",,Netherlands heart journal : monthly journal of the Netherlands Society of Cardiology and the Netherlands Heart Foundation,2021,2021-02-02,Y,Dilated cardiomyopathy; Phospholamban; Arrhythmogenic Cardiomyopathy; Pathogenic Variants; Cascade Screening; Plakophilin‑2,,,"In relatives of index patients with dilated cardiomyopathy and arrhythmogenic cardiomyopathy, early detection of disease onset is essential to prevent sudden cardiac death and facilitate early treatment of heart failure. However, the optimal screening interval and combination of diagnostic techniques are unknown. The clinical course of disease in index patients and their relatives is variable due to incomplete and age-dependent penetrance. Several biomarkers, electrocardiographic and imaging (echocardiographic deformation imaging and cardiac magnetic resonance imaging) techniques are promising non-invasive methods for detection of subclinical cardiomyopathy. However, these techniques need optimisation and integration into clinical practice. Furthermore, determining the optimal interval and intensity of cascade screening may require a personalised approach. To address this, the CVON-eDETECT (early detection of disease in cardiomyopathy mutation carriers) consortium aims to integrate electronic health record data from long-term follow-up, diagnostic data sets, tissue and plasma samples in a multidisciplinary biobank environment to provide personalised risk stratification for heart failure and sudden cardiac death. Adequate risk stratification may lead to personalised screening, treatment and optimal timing of implantable cardioverter defibrillator implantation. In this article, we describe non-invasive diagnostic techniques used for detection of subclinical disease in relatives of index patients with dilated cardiomyopathy and arrhythmogenic cardiomyopathy.",,pdf:https://link.springer.com/content/pdf/10.1007/s12471-021-01542-1.pdf; doi:https://doi.org/10.1007/s12471-021-01542-1; html:https://europepmc.org/articles/PMC8160055; pdf:https://europepmc.org/articles/PMC8160055?pdf=render
 33532905,https://doi.org/10.1007/s12471-021-01539-w,BIO FOr CARE: biomarkers of hypertrophic cardiomyopathy development and progression in carriers of Dutch founder truncating MYBPC3 variants-design and status.,"Jansen M, Christiaans I, van der Crabben SN, Michels M, Huurman R, Hoedemaekers YM, Dooijes D, Jongbloed JDH, Boven LG, Lekanne Deprez RH, Wilde AAM, Jans JJM, van der Velden J, de Boer RA, van Tintelen JP, Asselbergs FW, Baas AF.",,Netherlands heart journal : monthly journal of the Netherlands Society of Cardiology and the Netherlands Heart Foundation,2021,2021-02-02,Y,Prognosis; Biomarkers; hypertrophic cardiomyopathy; Mybpc3,,,"<h4>Background</h4>Hypertrophic cardiomyopathy (HCM) is the most prevalent monogenic heart disease, commonly caused by truncating variants in the MYBPC3 gene. HCM is an important cause of sudden cardiac death; however, overall prognosis is good and penetrance in genotype-positive individuals is incomplete. The underlying mechanisms are poorly understood and risk stratification remains limited.<h4>Aim</h4>To create a nationwide cohort of carriers of truncating MYBPC3 variants for identification of predictive biomarkers for HCM development and progression.<h4>Methods</h4>In the multicentre, observational BIO FOr CARe (Identification of BIOmarkers of hypertrophic cardiomyopathy development and progression in Dutch MYBPC3 FOunder variant CARriers) cohort, carriers of the c.2373dupG, c.2827C > T, c.2864_2865delCT and c.3776delA MYBPC3 variants are included and prospectively undergo longitudinal blood collection. Clinical data are collected from first presentation onwards. The primary outcome constitutes a composite endpoint of HCM progression (maximum wall thickness ≥ 20 mm, septal reduction therapy, heart failure occurrence, sustained ventricular arrhythmia and sudden cardiac death).<h4>Results</h4>So far, 250 subjects (median age 54.9 years (interquartile range 43.3, 66.6), 54.8% male) have been included. HCM was diagnosed in 169 subjects and dilated cardiomyopathy in 4. The primary outcome was met in 115 subjects. Blood samples were collected from 131 subjects.<h4>Conclusion</h4>BIO FOr CARe is a genetically homogeneous, phenotypically heterogeneous cohort incorporating a clinical data registry and longitudinal blood collection. This provides a unique opportunity to study biomarkers for HCM development and prognosis. The established infrastructure can be extended to study other genetic variants. Other centres are invited to join our consortium.",,pdf:https://link.springer.com/content/pdf/10.1007/s12471-021-01539-w.pdf; doi:https://doi.org/10.1007/s12471-021-01539-w; html:https://europepmc.org/articles/PMC8160056; pdf:https://europepmc.org/articles/PMC8160056?pdf=render
+31950891,https://doi.org/10.1192/bjo.2019.96,Predicting high-cost care in a mental health setting.,"Colling C, Khondoker M, Patel R, Fok M, Harland R, Broadbent M, McCrone P, Stewart R.",,BJPsych open,2020,2020-01-17,Y,Prediction; Natural Language Processing; Mental Health Service; Digital Health Records,,,"<h4>Background</h4>The density of information in digital health records offers new potential opportunities for automated prediction of cost-relevant outcomes.<h4>Aims</h4>We investigated the extent to which routinely recorded data held in the electronic health record (EHR) predict priority service outcomes and whether natural language processing tools enhance the predictions. We evaluated three high priority outcomes: in-patient duration, readmission following in-patient care and high service cost after first presentation.<h4>Method</h4>We used data obtained from a clinical database derived from the EHR of a large mental healthcare provider within the UK. We combined structured data with text-derived data relating to diagnosis statements, medication and psychiatric symptomatology. Predictors of the three different clinical outcomes were modelled using logistic regression with performance evaluated against a validation set to derive areas under receiver operating characteristic curves.<h4>Results</h4>In validation samples, the full models (using all available data) achieved areas under receiver operating characteristic curves between 0.59 and 0.85 (in-patient duration 0.63, readmission 0.59, high service use 0.85). Adding natural language processing-derived data to the models increased the variance explained across all clinical scenarios (observed increase in r2 = 12-46%).<h4>Conclusions</h4>EHR data offer the potential to improve routine clinical predictions by utilising previously inaccessible data. Of our scenarios, prediction of high service use after initial presentation achieved the highest performance.","This study uses data from a mental healthcare provider to predict 3 things: 1) extended duration of stay in a hospital, 2) the likelihood of needing to be admitted to hospital again after discharge, and 3) likehood of needing 'high intesity service' (high cost services). The authors developed a natural language processing model (a computer system than aims to interpret text and draw out useful information) to review the text, diagnoses, medications and the patient symptoms to work out which patients would fall within those 3 categories. They conclude that their model could be used to improve services through predicting users who will require the most intense and costly care.",pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/6EF9FC74DC5A744C9D841DD649992ABE/S2056472419000966a.pdf/div-class-title-predicting-high-cost-care-in-a-mental-health-setting-div.pdf; doi:https://doi.org/10.1192/bjo.2019.96; html:https://europepmc.org/articles/PMC7001466; pdf:https://europepmc.org/articles/PMC7001466?pdf=render
 30984759,https://doi.org/10.3389/fmed.2019.00048,"Direct-to-Consumer Genetic Testing's Red Herring: ""Genetic Ancestry"" and Personalized Medicine.","Blell M, Hunter MA.",,Frontiers in medicine,2019,2019-03-29,Y,RACE; Ethics; Ethnicity; Genetic Testing; Personalized Medicine,Understanding the Causes of Disease,,"The growth in the direct-to-consumer genetic testing industry poses a number of challenges for healthcare practice, among a number of other areas of concern. Several companies providing this service send their customers reports including information variously referred to as genetic ethnicity, genetic heritage, biogeographic ancestry, and genetic ancestry. In this article, we argue that such information should not be used in healthcare consultations or to assess health risks. Far from representing a move toward personalized medicine, use of this information poses risks both to patients as individuals and to racialized ethnic groups because of the way it misrepresents human genetic diversity.",,pdf:https://www.frontiersin.org/articles/10.3389/fmed.2019.00048/pdf; doi:https://doi.org/10.3389/fmed.2019.00048; html:https://europepmc.org/articles/PMC6449432; pdf:https://europepmc.org/articles/PMC6449432?pdf=render
 30928767,https://doi.org/10.1016/j.evalprogplan.2019.03.002,Understanding the factors that influence health promotion evaluation: The development and validation of the evaluation practice analysis survey.,"Schwarzman J, Bauman A, Gabbe BJ, Rissel C, Shilton T, Smith BJ.",,Evaluation and program planning,2019,2019-03-22,N,Measurement; Validity; reliability; Health Promotion; Evaluation Capacity Building; Evaluation Practice,,,"The demand for improved quality of health promotion evaluation and greater capacity to undertake evaluation is growing, yet evidence of the challenges and facilitators to evaluation practice within the health promotion field is lacking. A limited number of evaluation capacity measurement instruments have been validated in government or non-government organisations (NGO), however there is no instrument designed for health promotion organisations. This study aimed to develop and validate an Evaluation Practice Analysis Survey (EPAS) to examine evaluation practices in health promotion organisations. Qualitative interviews, existing frameworks and instruments informed the survey development. Health promotion practitioners from government agencies and NGOs completed the survey (n = 169). Principal components analysis was used to determine scale structure and Cronbach's α used to estimate internal reliability. Logistic regression was conducted to assess predictive validity of selected EPAS scale. The final survey instrument included 25 scales (125 items). The EPAS demonstrated good internal reliability (α > 0.7) for 23 scales. Dedicated resources and time for evaluation, leadership, organisational culture and internal support for evaluation showed promising predictive validity. The EPAS can be used to describe elements of evaluation capacity at the individual, organisational and system levels and to guide initiatives to improve evaluation practice in health promotion organisations.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa49960/Download/0049960-14052019134527.pdf; doi:https://doi.org/10.1016/j.evalprogplan.2019.03.002
 36470992,https://doi.org/10.1038/s41375-022-01773-0,Continuous Indexing of Fibrosis (CIF): improving the assessment and classification of MPN patients.,"Ryou H, Sirinukunwattana K, Aberdeen A, Grindstaff G, Stolz BJ, Byrne H, Harrington HA, Sousos N, Godfrey AL, Harrison CN, Psaila B, Mead AJ, Rees G, Turner GDH, Rittscher J, Royston D.",,Leukemia,2023,2022-12-05,Y,,,,"The grading of fibrosis in myeloproliferative neoplasms (MPN) is an important component of disease classification, prognostication and monitoring. However, current fibrosis grading systems are only semi-quantitative and fail to fully capture sample heterogeneity. To improve the quantitation of reticulin fibrosis, we developed a machine learning approach using bone marrow trephine (BMT) samples (n = 107) from patients diagnosed with MPN or a reactive marrow. The resulting Continuous Indexing of Fibrosis (CIF) enhances the detection and monitoring of fibrosis within BMTs, and aids MPN subtyping. When combined with megakaryocyte feature analysis, CIF discriminates between the frequently challenging differential diagnosis of essential thrombocythemia (ET) and pre-fibrotic myelofibrosis with high predictive accuracy [area under the curve = 0.94]. CIF also shows promise in the identification of MPN patients at risk of disease progression; analysis of samples from 35 patients diagnosed with ET and enrolled in the Primary Thrombocythemia-1 trial identified features predictive of post-ET myelofibrosis (area under the curve = 0.77). In addition to these clinical applications, automated analysis of fibrosis has clear potential to further refine disease classification boundaries and inform future studies of the micro-environmental factors driving disease initiation and progression in MPN and other stem cell disorders.",,pdf:https://www.nature.com/articles/s41375-022-01773-0.pdf; doi:https://doi.org/10.1038/s41375-022-01773-0; html:https://europepmc.org/articles/PMC9898027; pdf:https://europepmc.org/articles/PMC9898027?pdf=render
@@ -2317,12 +2319,12 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 34937765,https://doi.org/10.1136/injuryprev-2021-044309,Predictors of health-related quality of life following injury in childhood and adolescence: a pooled analysis.,"Dipnall JF, Rivara FP, Lyons RA, Ameratunga S, Brussoni M, Lecky FE, Bradley C, Beck B, Lyons J, Schneeberg A, Harrison JE, Gabbe BJ.",,Injury prevention : journal of the International Society for Child and Adolescent Injury Prevention,2022,2021-12-22,N,Public Health; Disability; Longitudinal,,,"<h4>Background</h4>Injury is a leading contributor to the global disease burden in children and places children at risk for adverse and lasting impacts on their health-related quality of life (HRQoL) and development. This study aimed to identify key predictors of HRQoL following injury in childhood and adolescence.<h4>Methods</h4>Data from 2259 injury survivors (<18 years when injured) were pooled from four longitudinal cohort studies (Australia, Canada, UK, USA) from the paediatric Validating Injury Burden Estimates Study (VIBES-Junior). Outcomes were the Paediatric Quality of Life Inventory (PedsQL) total, physical, psychosocial functioning scores at 1, 3-4, 6, 12, 24 months postinjury.<h4>Results</h4>Mean PedsQL total score increased with higher socioeconomic status and decreased with increasing age. It was lower for transport-related incidents, ≥1 comorbidities, intentional injuries, spinal cord injury, vertebral column fracture, moderate/severe traumatic brain injury and fracture of patella/tibia/fibula/ankle. Mean PedsQL physical score was lower for females, fracture of femur, fracture of pelvis and burns. Mean PedsQL psychosocial score was lower for asphyxiation/non-fatal submersion and muscle/tendon/dislocation injuries.<h4>Conclusions</h4>Postinjury HRQoL was associated with survivors' socioeconomic status, intent, mechanism of injury and comorbidity status. Patterns of physical and psychosocial functioning postinjury differed according to sex and nature of injury sustained. The findings improve understanding of the long-term individual and societal impacts of injury in the early part of life and guide the prioritisation of prevention efforts, inform health and social service planning to help reduce injury burden, and help guide future Global Burden of Disease estimates.",,doi:https://doi.org/10.1136/injuryprev-2021-044309
 35265823,https://doi.org/10.1016/j.eclinm.2022.101317,Variation in global COVID-19 symptoms by geography and by chronic disease: A global survey using the COVID-19 Symptom Mapper.,"Kadirvelu B, Burcea G, Quint JK, Costelloe CE, Faisal AA.",,EClinicalMedicine,2022,2022-03-06,Y,"Comorbidities; Pcr, Polymerase Chain Reaction; Covid-19; Covid-19 Symptoms; Covid Symptom Profile; Covid Symptoms Mapper; Covid Symptoms Survey; Covid-19, The Coronavirus Disease That First Appeared In 2019 Caused By The Sars-cov-2 Coronavirus.; Who, World Health Organization, A Specialized Agency Of The United Nations Responsible For International Public Health.",,,"<h4>Background</h4>COVID-19 is typically characterised by a triad of symptoms: cough, fever and loss of taste and smell, however, this varies globally. This study examines variations in COVID-19 symptom profiles based on underlying chronic disease and geographical location.<h4>Methods</h4>Using a global online symptom survey of 78,299 responders in 190 countries between 09/04/2020 and 22/09/2020, we conducted an exploratory study to examine symptom profiles associated with a positive COVID-19 test result by country and underlying chronic disease (single, co- or multi-morbidities) using statistical and machine learning methods.<h4>Findings</h4>From the results of 7980 COVID-19 tested positive responders, we find that symptom patterns differ by country. For example, India reported a lower proportion of headache (22.8% vs 47.8%, p<1e-13) and itchy eyes (7.3% vs. 16.5%, p=2e-8) than other countries. As with geographic location, we find people differed in their reported symptoms if they suffered from specific chronic diseases. For example, COVID-19 positive responders with asthma (25.3% vs. 13.7%, p=7e-6) were more likely to report shortness of breath compared to those with no underlying chronic disease.<h4>Interpretation</h4>We have identified variation in COVID-19 symptom profiles depending on geographic location and underlying chronic disease. Failure to reflect this symptom variation in public health messaging may contribute to asymptomatic COVID-19 spread and put patients with chronic diseases at a greater risk of infection. Future work should focus on symptom profile variation in the emerging variants of the SARS-CoV-2 virus. This is crucial to speed up clinical diagnosis, predict prognostic outcomes and target treatment.<h4>Funding</h4>We acknowledge funding to AAF by a UKRI Turing AI Fellowship and to CEC by a personal NIHR Career Development Fellowship (grant number NIHR-2016-090-015). JKQ has received grants from The Health Foundation, MRC, GSK, Bayer, BI, Asthma UK-British Lung Foundation, IQVIA, Chiesi AZ, and Insmed. This work is supported by BREATHE - The Health Data Research Hub for Respiratory Health [MC_PC_19004]. BREATHE is funded through the UK Research and Innovation Industrial Strategy Challenge Fund and delivered through Health Data Research UK. Imperial College London is grateful for the support from the Northwest London NIHR Applied Research Collaboration. The views expressed in this publication are those of the authors and not necessarily those of the NIHR or the Department of Health and Social Care.",,pdf:http://www.thelancet.com/article/S2589537022000475/pdf; doi:https://doi.org/10.1016/j.eclinm.2022.101317; html:https://europepmc.org/articles/PMC8898170; pdf:https://europepmc.org/articles/PMC8898170?pdf=render
 35246709,https://doi.org/10.1007/s00127-022-02257-3,Ethnic inequalities in clozapine use among people with treatment-resistant schizophrenia: a retrospective cohort study using data from electronic clinical records.,"de Freitas DF, Patel I, Kadra-Scalzo G, Pritchard M, Shetty H, Broadbent M, Patel R, Downs J, Segev A, Khondoker M, MacCabe JH, Bhui K, Hayes RD.",,Social psychiatry and psychiatric epidemiology,2022,2022-03-04,Y,Clozapine; Health Inequalities; Benign Ethnic Neutropenia; Black British; Refractory Psychosis; Asian British,,,"<h4>Purpose</h4>Clozapine is the most effective intervention for treatment-resistant schizophrenia (TRS). Several studies report ethnic disparities in clozapine treatment. However, few studies restrict analyses to TRS cohorts alone or address confounding by benign ethnic neutropenia. This study investigates ethnic equity in access to clozapine treatment for people with treatment-resistant schizophrenia spectrum disorder.<h4>Methods</h4>A retrospective cohort study, using information from 11 years of clinical records (2007-2017) from the South London and Maudsley NHS Trust. We identified a cohort of service-users with TRS using a validated algorithm. We investigated associations between ethnicity and clozapine treatment, adjusting for sociodemographic factors, psychiatric multi-morbidity, substance misuse, neutropenia, and service-use.<h4>Results</h4>Among 2239 cases of TRS, Black service-users were less likely to be receive clozapine compared with White British service-users after adjusting for confounders (Black African aOR = 0.49, 95% CI [0.33, 0.74], p = 0.001; Black Caribbean aOR = 0.64, 95% CI [0.43, 0.93], p = 0.019; Black British aOR = 0.61, 95% CI [0.41, 0.91], p = 0.016). It was additionally observed that neutropenia was not related to treatment with clozapine. Also, a detention under the Mental Health Act was negatively associated clozapine receipt, suggesting people with TRS who were detained are less likely to be treated with clozapine.<h4>Conclusion</h4>Black service-users with TRS were less likely to receive clozapine than White British service-users. Considering the protective effect of treatment with clozapine, these inequities may place Black service-users at higher risk for hospital admissions and mortality.",,pdf:https://link.springer.com/content/pdf/10.1007/s00127-022-02257-3.pdf; doi:https://doi.org/10.1007/s00127-022-02257-3; html:https://europepmc.org/articles/PMC9246775; pdf:https://europepmc.org/articles/PMC9246775?pdf=render
-34442458,https://doi.org/10.3390/jpm11080814,Reduced MIP-1β as a Trait Marker and Reduced IL-7 and IL-12 as State Markers of Anorexia Nervosa.,"Keeler JL, Patsalos O, Chung R, Schmidt U, Breen G, Treasure J, Himmerich H, Dalton B.",,Journal of personalized medicine,2021,2021-08-20,Y,Cytokines; Chemokines; Brain-derived neurotrophic factor; Anorexia Nervosa; cross-sectional; Inflammatory Markers,,,"Alterations in certain inflammatory markers have been found in individuals with anorexia nervosa (AN). However, their relation to clinical characteristics has not been extensively explored, nor is it clear whether they are trait or state features of the disorder. This cross-sectional study measured serum concentrations of 36 inflammatory markers in people with acute AN (<i>n</i> = 56), recovered AN (rec-AN; <i>n</i> = 24) and healthy controls (HC; <i>n</i> = 51). The relationship between body mass index (BMI), eating disorder psychopathology, depression symptoms and inflammatory markers was assessed. Statistical models controlled for variables known to influence cytokine concentrations (i.e., age, ethnicity, smoking status and medication usage). Overall, most inflammatory markers including pro-inflammatory cytokines were unchanged in AN and rec-AN. However, in AN and rec-AN, concentrations of macrophage inflammatory protein (MIP)-1β were lower than HCs. Interleukin (IL)-7 and IL-12/IL-23p40 were reduced in AN, and concentrations of macrophage-derived chemokine, MIP-1α and tumor necrosis factor-α were reduced in rec-AN compared to HC. In conclusion, a reduction in MIP-1β may be a trait marker of the illness, whereas reductions in IL-7 and IL-12/IL-23p40 may be state markers. The absence of increased pro-inflammatory cytokines in AN is contradictory to the wider literature, although the inclusion of covariates may explain our differing findings.",,pdf:https://www.mdpi.com/2075-4426/11/8/814/pdf?version=1629458822; doi:https://doi.org/10.3390/jpm11080814; html:https://europepmc.org/articles/PMC8399452; pdf:https://europepmc.org/articles/PMC8399452?pdf=render
 32891970,https://doi.org/10.1016/j.chiabu.2020.104689,Exploring placement stability for children in out-of-home care in England: a sequence analysis of longitudinal administrative data.,"Mc Grath-Lone L, Harron K, Dearden L, Gilbert R.",,Child abuse & neglect,2020,2020-09-03,N,Sequence analysis; Administrative Data; Longitudinal Care Histories,,,"<h4>Background</h4>To monitor stability of care, the proportion of children in England who have experienced three or more placements in the preceding 12-month period is published in government statistics. However, these annual snapshots cannot capture the complexity and heterogeneity of children's longitudinal care histories.<h4>Objective</h4>To describe the stability of care histories from birth to age 18 for children in England using a national administrative social care dataset, the Children Looked After return (CLA).<h4>Participants and setting</h4>We analyzed CLA data for a large, representative sample of children born between 1992 and 1994 (N = 16,000).<h4>Methods</h4>Using sequence analysis methods, we identified distinct patterns of stability, based on the number, duration, and timing of care placements throughout childhood.<h4>Results</h4>Although care histories were varied, six distinct patterns of stability were evident including; adolescent 1<sup>st</sup> entries (17.6%), long-term complex care (13.1%) and early intervention (6.9%). Overall, most children (58.4%) had a care history that we classified as shorter term care with an average of 276 days and 2.48 placements in care throughout childhood. Few children (4.0%) had a care history that could be described as long-term stable care.<h4>Conclusions</h4>Longitudinal analyses of administrative data can refine our understanding of how out-of-home care is used as a social care intervention. Sequence analysis is a particularly useful tool for exploring heterogeneous and complex care histories. Considering out-of-home care histories from a life course perspective over the entire childhood period could enable service providers to better understand and address the needs of looked after children.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7613165; doi:https://doi.org/10.1016/j.chiabu.2020.104689; html:https://europepmc.org/articles/PMC7613165; pdf:https://europepmc.org/articles/PMC7613165?pdf=render; doi:https://doi.org/10.1016/j.chiabu.2020.104689
+34442458,https://doi.org/10.3390/jpm11080814,Reduced MIP-1β as a Trait Marker and Reduced IL-7 and IL-12 as State Markers of Anorexia Nervosa.,"Keeler JL, Patsalos O, Chung R, Schmidt U, Breen G, Treasure J, Himmerich H, Dalton B.",,Journal of personalized medicine,2021,2021-08-20,Y,Cytokines; Chemokines; Brain-derived neurotrophic factor; Anorexia Nervosa; cross-sectional; Inflammatory Markers,,,"Alterations in certain inflammatory markers have been found in individuals with anorexia nervosa (AN). However, their relation to clinical characteristics has not been extensively explored, nor is it clear whether they are trait or state features of the disorder. This cross-sectional study measured serum concentrations of 36 inflammatory markers in people with acute AN (<i>n</i> = 56), recovered AN (rec-AN; <i>n</i> = 24) and healthy controls (HC; <i>n</i> = 51). The relationship between body mass index (BMI), eating disorder psychopathology, depression symptoms and inflammatory markers was assessed. Statistical models controlled for variables known to influence cytokine concentrations (i.e., age, ethnicity, smoking status and medication usage). Overall, most inflammatory markers including pro-inflammatory cytokines were unchanged in AN and rec-AN. However, in AN and rec-AN, concentrations of macrophage inflammatory protein (MIP)-1β were lower than HCs. Interleukin (IL)-7 and IL-12/IL-23p40 were reduced in AN, and concentrations of macrophage-derived chemokine, MIP-1α and tumor necrosis factor-α were reduced in rec-AN compared to HC. In conclusion, a reduction in MIP-1β may be a trait marker of the illness, whereas reductions in IL-7 and IL-12/IL-23p40 may be state markers. The absence of increased pro-inflammatory cytokines in AN is contradictory to the wider literature, although the inclusion of covariates may explain our differing findings.",,pdf:https://www.mdpi.com/2075-4426/11/8/814/pdf?version=1629458822; doi:https://doi.org/10.3390/jpm11080814; html:https://europepmc.org/articles/PMC8399452; pdf:https://europepmc.org/articles/PMC8399452?pdf=render
 34167318,https://doi.org/10.1161/circulationaha.121.054302,Cardiac Troponin Thresholds and Kinetics to Differentiate Myocardial Injury and Myocardial Infarction.,"Wereski R, Kimenai DM, Taggart C, Doudesis D, Lee KK, Lowry MTH, Bularga A, Lowe DJ, Fujisawa T, Apple FS, Collinson PO, Anand A, Chapman AR, Mills NL.",,Circulation,2021,2021-06-25,Y,Kinetics; Troponin; Myocardial infarction; Predictive Value Of Tests,,,"<h4>Background</h4>Although the 99th percentile is the recommended diagnostic threshold for myocardial infarction, some guidelines also advocate the use of higher troponin thresholds to rule in myocardial infarction at presentation. It is unclear whether the magnitude or change in troponin concentration can differentiate causes of myocardial injury and infarction in practice.<h4>Methods</h4>In a secondary analysis of a multicenter randomized controlled trial, we identified 46 092 consecutive patients presenting with suspected acute coronary syndrome without ST-segment-elevation myocardial infarction. High-sensitivity cardiac troponin I concentrations at presentation and on serial testing were compared between patients with myocardial injury and infarction. The positive predictive value and specificity were determined at the sex-specific 99th percentile upper reference limit and rule-in thresholds of 64 ng/L and 5-fold of the upper reference limit for a diagnosis of type 1 myocardial infarction.<h4>Results</h4>Troponin was above the 99th percentile in 8188 patients (18%). The diagnosis was type 1 or type 2 myocardial infarction in 50% and 14% and acute or chronic myocardial injury in 20% and 16%, respectively. Troponin concentrations were similar at presentation in type 1 (median [25th-75th percentile] 91 [30-493] ng/L) and type 2 (50 [22-147] ng/L) myocardial infarction and in acute (50 [26-134] ng/L) and chronic (51 [31-130] ng/L) myocardial injury. The 99th percentile and rule-in thresholds of 64 ng/L and 5-fold upper reference limit gave a positive predictive value of 57% (95% CI, 56%-58%), 59% (58%-61%), and 62% (60%-64%) and a specificity of 96% (96%-96%), 96% (96%-96%), and 98% (97%-98%), respectively. The absolute, relative, and rate of change in troponin concentration were highest in patients with type 1 myocardial infarction (<i>P</i><0.001 for all). Discrimination improved when troponin concentration and change in troponin were combined compared with troponin concentration at presentation alone (area under the curve, 0.661 [0.642-0.680] versus 0.613 [0.594-0.633]).<h4>Conclusions</h4>Although we observed important differences in the kinetics, cardiac troponin concentrations at presentation are insufficient to distinguish type 1 myocardial infarction from other causes of myocardial injury or infarction in practice and should not guide management decisions in isolation. Registration: URL: https://www.clinicaltrials.gov; Unique identifier: NCT01852123.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCULATIONAHA.121.054302; doi:https://doi.org/10.1161/CIRCULATIONAHA.121.054302; html:https://europepmc.org/articles/PMC8360674; pdf:https://europepmc.org/articles/PMC8360674?pdf=render
 31748235,https://doi.org/10.1136/bmj.l6055,Association of troponin level and age with mortality in 250 000 patients: cohort study across five UK acute care centres.,"Kaura A, Panoulas V, Glampson B, Davies J, Mulla A, Woods K, Omigie J, Shah AD, Channon KM, Weber JN, Thursz MR, Elliott P, Hemingway H, Williams B, Asselbergs FW, O'Sullivan M, Kharbanda R, Lord GM, Melikian N, Patel RS, Perera D, Shah AM, Francis DP, Mayet J.",,BMJ (Clinical research ed.),2019,2019-11-20,Y,,,,"<h4>Objective</h4>To determine the relation between age and troponin level and its prognostic implication.<h4>Design</h4>Retrospective cohort study.<h4>Setting</h4>Five cardiovascular centres in the UK National Institute for Health Research Health Informatics Collaborative (UK-NIHR HIC).<h4>Participants</h4>257 948 consecutive patients undergoing troponin testing for any clinical reason between 2010 and 2017.<h4>Main outcome measure</h4>All cause mortality.<h4>Results</h4>257 948 patients had troponin measured during the study period. Analyses on troponin were performed using the peak troponin level, which was the highest troponin level measured during the patient's hospital stay. Troponin levels were standardised as a multiple of each laboratory's 99th centile of the upper limit of normal (ULN). During a median follow-up of 1198 days (interquartile range 514-1866 days), 55 850 (21.7%) deaths occurred. A positive troponin result (that is, higher than the upper limit of normal) signified a 3.2 higher mortality hazard (95% confidence interval 3.1 to 3.2) over three years. Mortality varied noticeably with age, with a hazard ratio of 10.6 (8.5 to 13.3) in 18-29 year olds and 1.5 (1.4 to 1.6) in those older than 90. A positive troponin result was associated with an approximately 15 percentage points higher absolute three year mortality across all age groups. The excess mortality with a positive troponin result was heavily concentrated in the first few weeks. Results were analysed using multivariable adjusted restricted cubic spline Cox regression. A direct relation was seen between troponin level and mortality in patients without acute coronary syndrome (ACS, n=120 049), whereas an inverted U shaped relation was found in patients with ACS (n=14 468), with a paradoxical decline in mortality at peak troponin levels >70×ULN. In the group with ACS, the inverted U shaped relation persisted after multivariable adjustment in those who were managed invasively; however, a direct positive relation was found between troponin level and mortality in patients managed non-invasively.<h4>Conclusions</h4>A positive troponin result was associated with a clinically important increased mortality, regardless of age, even if the level was only slightly above normal. The excess mortality with a raised troponin was heavily concentrated in the first few weeks.<h4>Study registration</h4>ClinicalTrials.gov NCT03507309.",Kaura et al. used a large database of about a quarter of a million patients who had toponin measurements and concluded that there was an association between positive troponin results and mortality regardless of age ,pdf:https://www.bmj.com/content/bmj/367/bmj.l6055.full.pdf; doi:https://doi.org/10.1136/bmj.l6055; html:https://europepmc.org/articles/PMC6865859
-33628949,https://doi.org/10.12688/wellcomeopenres.16020.2,The Avon Longitudinal Study of Parents and Children - A resource for COVID-19 research: Questionnaire data capture April-May 2020.,"Northstone K, Howarth S, Smith D, Bowring C, Wells N, Timpson NJ.",,Wellcome open research,2020,2020-11-20,Y,Coronavirus; Mental health; Alspac; Birth Cohort Study; Online Questionnaire; Children Of The 90S; Covid-19,,,"The Avon Longitudinal Study of Parents and Children (ALSPAC) is a prospective population-based cohort study which recruited pregnant women in 1990-1992. The resource provides an informative and efficient setting for collecting data on the current coronavirus 2019 (COVID-19) pandemic. In early March 2020, a questionnaire was developed in collaboration with other longitudinal population studies to ensure cross-cohort comparability. It targeted retrospective and current COVID-19 infection information (exposure assessment, symptom tracking and reported clinical outcomes) and the impact of both disease and mitigating measures implemented to manage the COVID-19 crisis more broadly. Data were collected on symptoms of COVID-19 and seasonal flu, travel prior to the pandemic, mental health and social, behavioural and lifestyle factors. The online questionnaire was deployed across parent (G0) and offspring (G1) generations between 9 <sup>th</sup> April and 15 <sup>th</sup> May 2020. 6807 participants completed the questionnaire (2706 original mothers, 1014 original fathers/partners, 2973 offspring (mean age ~28 years) and 114 offspring partners). Eight (0.01%) participants (4 G0 and 4 G1) reported a positive test for COVID-19, 77 (1.13%; 28 G0 and 49 G1) reported that they had been told by a doctor they likely had COVID-19 and 865 (12.7%; 426 G0 and 439 G1) suspected that they have had COVID-19.  Using algorithmically defined cases, we estimate that the predicted proportion of COVID-19 cases ranged from 1.03% - 4.19% depending on timing during the period of reporting (October 2019-March 2020). Data from this first questionnaire will be complemented with at least two more follow-up questionnaires, linkage to health records and results of biological testing as they become available. Data has been released as: 1) a standard dataset containing <i>all</i> participant responses with key sociodemographic factors and 2) as a composite release coordinating data from the existing resource, thus enabling bespoke research across all areas supported by the study.",,doi:https://doi.org/10.12688/wellcomeopenres.16020.2; html:https://europepmc.org/articles/PMC7883314; pdf:https://europepmc.org/articles/PMC7883314?pdf=render
 35477539,https://doi.org/10.1136/gutjnl-2021-326183,Activation of innate-adaptive immune machinery by poly(I:C) exposes a therapeutic vulnerability to prevent relapse in stroma-rich colon cancer.,"Corry SM, McCorry AM, Lannagan TR, Leonard NA, Fisher NC, Byrne RM, Tsantoulis P, Cortes-Lavaud X, Amirkhah R, Redmond KL, McCooey AJ, Malla SB, Rogan E, Sakhnevych S, Gillespie MA, White M, Richman SD, Jackstadt RF, Campbell AD, Maguire S, S:CORT and ACRCelerate consortia, McDade SS, Longley DB, Loughrey MB, Coleman HG, Kerr EM, Tejpar S, Maughan T, Leedham SJ, Small DM, Ryan AE, Sansom OJ, Lawler M, Dunne PD.",,Gut,2022,2022-04-27,Y,Cancer; Colorectal Cancer; Adjuvant Treatment; Colon Carcinogenesis,,,"<h4>Objective</h4>Stroma-rich tumours represent a poor prognostic subtype in stage II/III colon cancer (CC), with high relapse rates and limited response to standard adjuvant chemotherapy.<h4>Design</h4>To address the lack of efficacious therapeutic options for patients with stroma-rich CC, we stratified our human tumour cohorts according to stromal content, enabling identification of the biology underpinning relapse and potential therapeutic vulnerabilities specifically within stroma-rich tumours that could be exploited clinically. Following human tumour-based discovery and independent clinical validation, we use a series of <i>in vitro</i> and stroma-rich <i>in vivo</i> models to test and validate the therapeutic potential of elevating the biology associated with reduced relapse in human tumours.<h4>Results</h4>By performing our analyses specifically within the stroma-rich/high-fibroblast (HiFi) subtype of CC, we identify and validate the clinical value of a HiFi-specific prognostic signature (HPS), which stratifies tumours based on STAT1-related signalling (High-HPS v Low-HPS=HR 0.093, CI 0.019 to 0.466). Using <i>in silico, in vitro</i> and <i>in vivo</i> models, we demonstrate that the HPS is associated with antigen processing and presentation within discrete immune lineages in stroma-rich CC, downstream of double-stranded RNA and viral response signalling. Treatment with the TLR3 agonist poly(I:C) elevated the HPS signalling and antigen processing phenotype across <i>in vitro</i> and <i>in vivo</i> models. In an <i>in vivo</i> model of stroma-rich CC, poly(I:C) treatment significantly increased systemic cytotoxic T cell activity (p<0.05) and reduced liver metastases (p<0.0002).<h4>Conclusion</h4>This study reveals new biological insight that offers a novel therapeutic option to reduce relapse rates in patients with the worst prognosis CC.",,pdf:https://gut.bmj.com/content/gutjnl/early/2022/04/10/gutjnl-2021-326183.full.pdf; doi:https://doi.org/10.1136/gutjnl-2021-326183; html:https://europepmc.org/articles/PMC9664095; pdf:https://europepmc.org/articles/PMC9664095?pdf=render
+33628949,https://doi.org/10.12688/wellcomeopenres.16020.2,The Avon Longitudinal Study of Parents and Children - A resource for COVID-19 research: Questionnaire data capture April-May 2020.,"Northstone K, Howarth S, Smith D, Bowring C, Wells N, Timpson NJ.",,Wellcome open research,2020,2020-11-20,Y,Coronavirus; Mental health; Alspac; Birth Cohort Study; Online Questionnaire; Children Of The 90S; Covid-19,,,"The Avon Longitudinal Study of Parents and Children (ALSPAC) is a prospective population-based cohort study which recruited pregnant women in 1990-1992. The resource provides an informative and efficient setting for collecting data on the current coronavirus 2019 (COVID-19) pandemic. In early March 2020, a questionnaire was developed in collaboration with other longitudinal population studies to ensure cross-cohort comparability. It targeted retrospective and current COVID-19 infection information (exposure assessment, symptom tracking and reported clinical outcomes) and the impact of both disease and mitigating measures implemented to manage the COVID-19 crisis more broadly. Data were collected on symptoms of COVID-19 and seasonal flu, travel prior to the pandemic, mental health and social, behavioural and lifestyle factors. The online questionnaire was deployed across parent (G0) and offspring (G1) generations between 9 <sup>th</sup> April and 15 <sup>th</sup> May 2020. 6807 participants completed the questionnaire (2706 original mothers, 1014 original fathers/partners, 2973 offspring (mean age ~28 years) and 114 offspring partners). Eight (0.01%) participants (4 G0 and 4 G1) reported a positive test for COVID-19, 77 (1.13%; 28 G0 and 49 G1) reported that they had been told by a doctor they likely had COVID-19 and 865 (12.7%; 426 G0 and 439 G1) suspected that they have had COVID-19.  Using algorithmically defined cases, we estimate that the predicted proportion of COVID-19 cases ranged from 1.03% - 4.19% depending on timing during the period of reporting (October 2019-March 2020). Data from this first questionnaire will be complemented with at least two more follow-up questionnaires, linkage to health records and results of biological testing as they become available. Data has been released as: 1) a standard dataset containing <i>all</i> participant responses with key sociodemographic factors and 2) as a composite release coordinating data from the existing resource, thus enabling bespoke research across all areas supported by the study.",,doi:https://doi.org/10.12688/wellcomeopenres.16020.2; html:https://europepmc.org/articles/PMC7883314; pdf:https://europepmc.org/articles/PMC7883314?pdf=render
 33627748,https://doi.org/10.1038/s41746-021-00406-7,Real-time clinician text feeds from electronic health records.,"Teo JTH, Dinu V, Bernal W, Davidson P, Oliynyk V, Breen C, Barker RD, Dobson RJB.",,NPJ digital medicine,2021,2021-02-24,Y,,,,"Analyses of search engine and social media feeds have been attempted for infectious disease outbreaks, but have been found to be susceptible to artefactual distortions from health scares or keyword spamming in social media or the public internet. We describe an approach using real-time aggregation of keywords and phrases of freetext from real-time clinician-generated documentation in electronic health records to produce a customisable real-time viral pneumonia signal providing up to 4 days warning for secondary care capacity planning. This low-cost approach is open-source, is locally customisable, is not dependent on any specific electronic health record system and can provide an ensemble of signals if deployed at multiple organisational scales.",,pdf:https://www.nature.com/articles/s41746-021-00406-7.pdf; doi:https://doi.org/10.1038/s41746-021-00406-7; html:https://europepmc.org/articles/PMC7904856; pdf:https://europepmc.org/articles/PMC7904856?pdf=render
 34346861,https://doi.org/10.1099/mgen.0.000615,Generalizable characteristics of false-positive bacterial variant calls.,Bush SJ.,,Microbial genomics,2021,2021-08-01,Y,Best Practice; False Positive; Benchmarking; Variant Calling,,,"Minimizing false positives is a critical issue when variant calling as no method is without error. It is common practice to post-process a variant-call file (VCF) using hard filter criteria intended to discriminate true-positive (TP) from false-positive (FP) calls. These are applied on the simple principle that certain characteristics are disproportionately represented among the set of FP calls and that a user-chosen threshold can maximize the number detected. To provide guidance on this issue, this study empirically characterized all false SNP and indel calls made using real Illumina sequencing data from six disparate species and 166 variant-calling pipelines (the combination of 14 read aligners with up to 13 different variant callers, plus four 'all-in-one' pipelines). We did not seek to optimize filter thresholds but instead to draw attention to those filters of greatest efficacy and the pipelines to which they may most usefully be applied. In this respect, this study acts as a coda to our previous benchmarking evaluation of bacterial variant callers, and provides general recommendations for effective practice. The results suggest that, of the pipelines analysed in this study, the most straightforward way of minimizing false positives would simply be to use Snippy. We also find that a disproportionate number of false calls, irrespective of the variant-calling pipeline, are located in the vicinity of indels, and highlight this as an issue for future development.",,doi:https://doi.org/10.1099/mgen.0.000615; doi:https://doi.org/10.1099/mgen.0.000615; html:https://europepmc.org/articles/PMC8549357; pdf:https://europepmc.org/articles/PMC8549357?pdf=render
 36706770,https://doi.org/10.1016/s2214-109x(23)00007-4,Global investments in pandemic preparedness and COVID-19: development assistance and domestic spending on health between 1990 and 2026.,Global Burden of Disease 2021 Health Financing Collaborator Network.,,The Lancet. Global health,2023,2023-01-24,Y,,,,"<h4>Background</h4>The COVID-19 pandemic highlighted gaps in health surveillance systems, disease prevention, and treatment globally. Among the many factors that might have led to these gaps is the issue of the financing of national health systems, especially in low-income and middle-income countries (LMICs), as well as a robust global system for pandemic preparedness. We aimed to provide a comparative assessment of global health spending at the onset of the pandemic; characterise the amount of development assistance for pandemic preparedness and response disbursed in the first 2 years of the COVID-19 pandemic; and examine expectations for future health spending and put into context the expected need for investment in pandemic preparedness.<h4>Methods</h4>In this analysis of global health spending between 1990 and 2021, and prediction from 2021 to 2026, we estimated four sources of health spending: development assistance for health (DAH), government spending, out-of-pocket spending, and prepaid private spending across 204 countries and territories. We used the Organisation for Economic Co-operation and Development (OECD)'s Creditor Reporting System (CRS) and the WHO Global Health Expenditure Database (GHED) to estimate spending. We estimated development assistance for general health, COVID-19 response, and pandemic preparedness and response using a keyword search. Health spending estimates were combined with estimates of resources needed for pandemic prevention and preparedness to analyse future health spending patterns, relative to need.<h4>Findings</h4>In 2019, at the onset of the COVID-19 pandemic, US$9·2 trillion (95% uncertainty interval [UI] 9·1-9·3) was spent on health worldwide. We found great disparities in the amount of resources devoted to health, with high-income countries spending $7·3 trillion (95% UI 7·2-7·4) in 2019; 293·7 times the $24·8 billion (95% UI 24·3-25·3) spent by low-income countries in 2019. That same year, $43·1 billion in development assistance was provided to maintain or improve health. The pandemic led to an unprecedented increase in development assistance targeted towards health; in 2020 and 2021, $1·8 billion in DAH contributions was provided towards pandemic preparedness in LMICs, and $37·8 billion was provided for the health-related COVID-19 response. Although the support for pandemic preparedness is 12·2% of the recommended target by the High-Level Independent Panel (HLIP), the support provided for the health-related COVID-19 response is 252·2% of the recommended target. Additionally, projected spending estimates suggest that between 2022 and 2026, governments in 17 (95% UI 11-21) of the 137 LMICs will observe an increase in national government health spending equivalent to an addition of 1% of GDP, as recommended by the HLIP.<h4>Interpretation</h4>There was an unprecedented scale-up in DAH in 2020 and 2021. We have a unique opportunity at this time to sustain funding for crucial global health functions, including pandemic preparedness. However, historical patterns of underfunding of pandemic preparedness suggest that deliberate effort must be made to ensure funding is maintained.<h4>Funding</h4>Bill & Melinda Gates Foundation.",,pdf:http://www.thelancet.com/article/S2214109X23000074/pdf; doi:https://doi.org/10.1016/S2214-109X(23)00007-4; html:https://europepmc.org/articles/PMC9998276
@@ -2337,11 +2339,11 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 33664493,https://doi.org/10.1038/s41591-021-01275-z,The need for ethical guidance for the use of patient-reported outcomes in research and clinical practice.,"Cruz Rivera S, Mercieca-Bebber R, Aiyegbusi OL, Scott J, Hunn A, Fernandez C, Ives J, Ells C, Price G, Draper H, Calvert MJ.",,Nature medicine,2021,2021-04-01,N,,,,,,pdf:https://www.nature.com/articles/s41591-021-01275-z.pdf; doi:https://doi.org/10.1038/s41591-021-01275-z
 37920851,https://doi.org/10.1038/s44161-022-00171-0,Transcriptomic-based clustering of human atherosclerotic plaques identifies subgroups with different underlying biology and clinical presentation.,"Mokry M, Boltjes A, Slenders L, Bel-Bordes G, Cui K, Brouwer E, Mekke JM, Depuydt MAC, Timmerman N, Waissi F, Verwer MC, Turner AW, Khan MD, Hodonsky CJ, Benavente ED, Hartman RJG, van den Dungen NAM, Lansu N, Nagyova E, Prange KHM, Kovacic JC, Björkegren JLM, Pavlos E, Andreakos E, Schunkert H, Owens GK, Monaco C, Finn AV, Virmani R, Leeper NJ, de Winther MPJ, Kuiper J, de Borst GJ, Stroes ESG, Civelek M, de Kleijn DPV, den Ruijter HM, Asselbergs FW, van der Laan SW, Miller CL, Pasterkamp G.",,Nature cardiovascular research,2022,2022-12-12,N,,,,"Histopathological studies have revealed key processes of atherosclerotic plaque thrombosis. However, the diversity and complexity of lesion types highlight the need for improved sub-phenotyping. Here we analyze the gene expression profiles of 654 advanced human carotid plaques. The unsupervised, transcriptome-driven clustering revealed five dominant plaque types. These plaque phenotypes were associated with clinical presentation and showed differences in cellular compositions. Validation in coronary segments showed that the molecular signature of these plaques was linked to coronary ischemia. One of the plaque types with the most severe clinical symptoms pointed to both inflammatory and fibrotic cell lineages. Further, we did a preliminary analysis of potential circulating biomarkers that mark the different plaques phenotypes. In conclusion, the definition of the plaque at risk for a thrombotic event can be fine-tuned by in-depth transcriptomic-based phenotyping. These differential plaque phenotypes prove clinically relevant for both carotid and coronary artery plaques and point to distinct underlying biology of symptomatic lesions.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10621615; doi:https://doi.org/10.1038/s44161-022-00171-0; html:https://europepmc.org/articles/PMC10621615; pdf:https://europepmc.org/articles/PMC10621615?pdf=render; doi:https://doi.org/10.1038/s44161-022-00171-0
 32514173,https://doi.org/10.1038/s41591-020-0941-1,Developing specific reporting guidelines for diagnostic accuracy studies assessing AI interventions: The STARD-AI Steering Group.,"Sounderajah V, Ashrafian H, Aggarwal R, De Fauw J, Denniston AK, Greaves F, Karthikesalingam A, King D, Liu X, Markar SR, McInnes MDF, Panch T, Pearson-Stuttard J, Ting DSW, Golub RM, Moher D, Bossuyt PM, Darzi A.",,Nature medicine,2020,2020-06-01,N,,,,,,html:http://hdl.handle.net/10044/1/85586; doi:https://doi.org/10.1038/s41591-020-0941-1
-30981377,https://doi.org/10.1016/j.aap.2019.03.007,How much space do drivers provide when passing cyclists? Understanding the impact of motor vehicle and infrastructure characteristics on passing distance.,"Beck B, Chong D, Olivier J, Perkins M, Tsay A, Rushford A, Li L, Cameron P, Fry R, Johnson M.",,Accident; analysis and prevention,2019,2019-04-10,N,Road Infrastructure; Overtaking; Cyclist Safety; Passing Distance,,,"<h4>Background</h4>Understanding factors that influence the distance that drivers provide when passing cyclists is critical to reducing subjective risk and improving cycling participation. This study aimed to quantify passing distance and assess the impact of motor vehicle and road infrastructure characteristics on passing distance.<h4>Methods</h4>An on-road observational study was conducted in Victoria, Australia. Participants had a custom device installed on their bicycle and rode as per their usual cycling for one to two weeks. A hierarchical linear model was used to investigate the relationship between motor vehicle and infrastructure characteristics (location, presence of on-road marked bicycle lane and the presence of parked cars on the kerbside) and passing distance (defined as the lateral distance between the end of the bicycle handlebars and the passing motor vehicle).<h4>Results</h4>Sixty cyclists recorded 18,527 passing events over 422 trips. The median passing distance was 173 cm (Q1: 137 cm, Q3: 224 cm) and 1085 (5.9%) passing events were less than 100 cm. Relative to sedans, 4WDs had a reduced mean passing distance of 15 cm (Q1: 12 cm, Q3: 17 cm) and buses had a reduced mean passing distance of 28 cm (Q1: 16 cm, Q3: 40 cm). Relative to passing events that occurred on roads without a marked bicycle lane and without parked cars, passing events on roads with a bike lane with no parked cars had a reduced mean passing distance of 27 cm (Q1: 25 cm, Q3: 29 cm), and passing events on roads with a bike lane and parked cars had a mean lower passing distance of 40 cm (Q1: 37 cm, Q3: 43 cm).<h4>Conclusions</h4>One in every 17 passing events was a close (<100 cm) passing event. We identified that on-road bicycle lanes and parked cars reduced passing distance. These data can be used to inform the selection and design of cycling-related infrastructure and road use with the aim of improving safety for cyclists.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa50030/Download/0050030-20052019102229.pdf; doi:https://doi.org/10.1016/j.aap.2019.03.007
 35353173,https://doi.org/10.1001/jamapsychiatry.2022.0407,Inflammation and Brain Structure in Schizophrenia and Other Neuropsychiatric Disorders: A Mendelian Randomization Study.,"Williams JA, Burgess S, Suckling J, Lalousis PA, Batool F, Griffiths SL, Palmer E, Karwath A, Barsky A, Gkoutos GV, Wood S, Barnes NM, David AS, Donohoe G, Neill JC, Deakin B, Khandaker GM, Upthegrove R, PIMS Collaboration.",,JAMA psychiatry,2022,2022-05-01,Y,,,,"<h4>Importance</h4>Previous in vitro and postmortem research suggests that inflammation may lead to structural brain changes via activation of microglia and/or astrocytic dysfunction in a range of neuropsychiatric disorders.<h4>Objective</h4>To investigate the relationship between inflammation and changes in brain structures in vivo and to explore a transcriptome-driven functional basis with relevance to mental illness.<h4>Design, setting, and participants</h4>This study used multistage linked analyses, including mendelian randomization (MR), gene expression correlation, and connectivity analyses. A total of 20 688 participants in the UK Biobank, which includes clinical, genomic, and neuroimaging data, and 6 postmortem brains from neurotypical individuals in the Allen Human Brain Atlas (AHBA), including RNA microarray data. Data were extracted in February 2021 and analyzed between March and October 2021.<h4>Exposures</h4>Genetic variants regulating levels and activity of circulating interleukin 1 (IL-1), IL-2, IL-6, C-reactive protein (CRP), and brain-derived neurotrophic factor (BDNF) were used as exposures in MR analyses.<h4>Main outcomes and measures</h4>Brain imaging measures, including gray matter volume (GMV) and cortical thickness (CT), were used as outcomes. Associations were considered significant at a multiple testing-corrected threshold of P < 1.1 × 10-4. Differential gene expression in AHBA data was modeled in brain regions mapped to areas significant in MR analyses; genes were tested for biological and disease overrepresentation in annotation databases and for connectivity in protein-protein interaction networks.<h4>Results</h4>Of 20 688 participants in the UK Biobank sample, 10 828 (52.3%) were female, and the mean (SD) age was 55.5 (7.5) years. In the UK Biobank sample, genetically predicted levels of IL-6 were associated with GMV in the middle temporal cortex (z score, 5.76; P = 8.39 × 10-9), inferior temporal (z score, 3.38; P = 7.20 × 10-5), fusiform (z score, 4.70; P = 2.60 × 10-7), and frontal (z score, -3.59; P = 3.30 × 10-5) cortex together with CT in the superior frontal region (z score, -5.11; P = 3.22 × 10-7). No significant associations were found for IL-1, IL-2, CRP, or BDNF after correction for multiple comparison. In the AHBA sample, 5 of 6 participants (83%) were male, and the mean (SD) age was 42.5 (13.4) years. Brain-wide coexpression analysis showed a highly interconnected network of genes preferentially expressed in the middle temporal gyrus (MTG), which further formed a highly connected protein-protein interaction network with IL-6 (enrichment test of expected vs observed network given the prevalence and degree of interactions in the STRING database: 43 nodes/30 edges observed vs 8 edges expected; mean node degree, 1.4; genome-wide significance, P = 4.54 × 10-9). MTG differentially expressed genes that were functionally enriched for biological processes in schizophrenia, autism spectrum disorder, and epilepsy.<h4>Conclusions and relevance</h4>In this study, genetically determined IL-6 was associated with brain structure and potentially affects areas implicated in developmental neuropsychiatric disorders, including schizophrenia and autism.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8968718; doi:https://doi.org/10.1001/jamapsychiatry.2022.0407; html:https://europepmc.org/articles/PMC8968718
+30981377,https://doi.org/10.1016/j.aap.2019.03.007,How much space do drivers provide when passing cyclists? Understanding the impact of motor vehicle and infrastructure characteristics on passing distance.,"Beck B, Chong D, Olivier J, Perkins M, Tsay A, Rushford A, Li L, Cameron P, Fry R, Johnson M.",,Accident; analysis and prevention,2019,2019-04-10,N,Road Infrastructure; Overtaking; Cyclist Safety; Passing Distance,,,"<h4>Background</h4>Understanding factors that influence the distance that drivers provide when passing cyclists is critical to reducing subjective risk and improving cycling participation. This study aimed to quantify passing distance and assess the impact of motor vehicle and road infrastructure characteristics on passing distance.<h4>Methods</h4>An on-road observational study was conducted in Victoria, Australia. Participants had a custom device installed on their bicycle and rode as per their usual cycling for one to two weeks. A hierarchical linear model was used to investigate the relationship between motor vehicle and infrastructure characteristics (location, presence of on-road marked bicycle lane and the presence of parked cars on the kerbside) and passing distance (defined as the lateral distance between the end of the bicycle handlebars and the passing motor vehicle).<h4>Results</h4>Sixty cyclists recorded 18,527 passing events over 422 trips. The median passing distance was 173 cm (Q1: 137 cm, Q3: 224 cm) and 1085 (5.9%) passing events were less than 100 cm. Relative to sedans, 4WDs had a reduced mean passing distance of 15 cm (Q1: 12 cm, Q3: 17 cm) and buses had a reduced mean passing distance of 28 cm (Q1: 16 cm, Q3: 40 cm). Relative to passing events that occurred on roads without a marked bicycle lane and without parked cars, passing events on roads with a bike lane with no parked cars had a reduced mean passing distance of 27 cm (Q1: 25 cm, Q3: 29 cm), and passing events on roads with a bike lane and parked cars had a mean lower passing distance of 40 cm (Q1: 37 cm, Q3: 43 cm).<h4>Conclusions</h4>One in every 17 passing events was a close (<100 cm) passing event. We identified that on-road bicycle lanes and parked cars reduced passing distance. These data can be used to inform the selection and design of cycling-related infrastructure and road use with the aim of improving safety for cyclists.",,pdf:https://cronfa.swan.ac.uk/Record/cronfa50030/Download/0050030-20052019102229.pdf; doi:https://doi.org/10.1016/j.aap.2019.03.007
 39422666,https://doi.org/10.1099/jgv.0.002032,A broadly reactive ultralong bovine antibody that can determine the integrity of foot-and-mouth disease virus capsids.,"Clarke JD, Duyvesteyn HME, Perez-Martin E, Latišenko U, Porta C, Humphreys KV, Hay AL, Ren J, Fry EE, van den Born E, Charleston B, Bonnet-Di Placido M, Owens RJ, Stuart DI, Hammond JA.",,The Journal of general virology,2024,2024-10-01,Y,FMDV; Single particle analysis; Pan-specific; Ultralong Cdr Antibody; Vaccine Quality Assurance,,,"Foot-and-mouth disease vaccination using inactivated virus is suboptimal, as the icosahedral viral capsids often disassemble into antigenically distinct pentameric units during long-term storage, or exposure to elevated temperature or lowered pH, and thus raise a response that is no longer protective. Furthermore, as foot-and-mouth disease virus (FMDV)'s seven serotypes are antigenically diverse, cross-protection from a single serotype vaccine is limited, and most existing mouse and bovine antibodies and camelid single-domain heavy chain-only antibodies are serotype-specific. For quality control purposes, there is a real need for pan-serotype antibodies that clearly distinguish between pentamer (12S) and protective intact FMDV capsid. To date, few cross-serotype bovine-derived antibodies have been reported in the literature. We identify a bovine antibody with an ultralong CDR-H3, Ab117, whose structural analysis reveals that it binds to a deep, hydrophobic pocket on the interior surface of the capsid via the CDR-H3. Main-chain and hydrophobic interactions provide broad serotype specificity. ELISA analysis confirms that Ab117 is a novel pan-serotype and conformational epitope-specific 12S reagent, suitable for assessing capsid integrity.",,doi:https://doi.org/10.1099/jgv.0.002032; html:https://europepmc.org/articles/PMC11488517; pdf:https://europepmc.org/articles/PMC11488517?pdf=render
-34732073,https://doi.org/10.1161/strokeaha.121.034787,"Risk, Clinical Course, and Outcome of Ischemic Stroke in Patients Hospitalized With COVID-19: A Multicenter Cohort Study.","Sluis WM, Linschoten M, Buijs JE, Biesbroek JM, den Hertog HM, Ribbers T, Nieuwkamp DJ, van Houwelingen RC, Dias A, van Uden IWM, Kerklaan JP, Bienfait HP, Vermeer SE, de Jong SW, Ali M, Wermer MJH, de Graaf MT, Brouwers PJAM, Asselbergs FW, Kappelle LJ, van der Worp HB, Algra AM, CAPACITY-COVID Collaborative Consortium*.",,Stroke,2021,2021-11-04,N,Intensive care units; Pulmonary embolism; incidence; Hospital Mortality; Patient Discharge; Covid-19,,,"<h4>Background and purpose</h4>The frequency of ischemic stroke in patients with coronavirus disease 2019 (COVID-19) varies in the current literature, and risk factors are unknown. We assessed the incidence, risk factors, and outcomes of acute ischemic stroke in hospitalized patients with COVID-19.<h4>Methods</h4>We included patients with a laboratory-confirmed SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) infection admitted in 16 Dutch hospitals participating in the international CAPACITY-COVID registry between March 1 and August 1, 2020. Patients were screened for the occurrence of acute ischemic stroke. We calculated the cumulative incidence of ischemic stroke and compared risk factors, cardiovascular complications, and in-hospital mortality in patients with and without ischemic stroke.<h4>Results</h4>We included 2147 patients with COVID-19, of whom 586 (27.3%) needed treatment at an intensive care unit. Thirty-eight patients (1.8%) had an ischemic stroke. Patients with stroke were older but did not differ in sex or cardiovascular risk factors. Median time between the onset of COVID-19 symptoms and diagnosis of stroke was 2 weeks. The incidence of ischemic stroke was higher among patients who were treated at an intensive care unit (16/586; 2.7% versus nonintensive care unit, 22/1561; 1.4%; <i>P</i>=0.039). Pulmonary embolism was more common in patients with (8/38; 21.1%) than in those without stroke (160/2109; 7.6%; adjusted risk ratio, 2.08 [95% CI, 1.52-2.84]). Twenty-seven patients with ischemic stroke (71.1%) died during admission or were functionally dependent at discharge. Patients with ischemic stroke were at a higher risk of in-hospital mortality (adjusted risk ratio, 1.56 [95% CI, 1.13-2.15]) than patients without stroke.<h4>Conclusions</h4>In this multicenter cohort study, the cumulative incidence of acute ischemic stroke in hospitalized patients with COVID-19 was ≈2%, with a higher risk in patients treated at an intensive care unit. The majority of stroke patients had a poor outcome. The association between ischemic stroke and pulmonary embolism warrants further investigation.",,pdf:https://europepmc.org/articles/pmc8607920?pdf=render; doi:https://doi.org/10.1161/STROKEAHA.121.034787; html:https://europepmc.org/articles/PMC8607920; pdf:https://europepmc.org/articles/PMC8607920?pdf=render; doi:https://doi.org/10.1161/strokeaha.121.034787
 33012285,https://doi.org/10.1186/s12916-020-01779-4,The impact of COVID-19 control measures on social contacts and transmission in Kenyan informal settlements.,"Quaife M, van Zandvoort K, Gimma A, Shah K, McCreesh N, Prem K, Barasa E, Mwanga D, Kangwana B, Pinchoff J, CMMID COVID-19 Working Group, Edmunds WJ, Jarvis CI, Austrian K.",,BMC medicine,2020,2020-10-05,Y,Social Contacts; Covid-19; Sars-cov-2; Physical Distancing,,,"<h4>Background</h4>Many low- and middle-income countries have implemented control measures against coronavirus disease 2019 (COVID-19). However, it is not clear to what extent these measures explain the low numbers of recorded COVID-19 cases and deaths in Africa. One of the main aims of control measures is to reduce respiratory pathogen transmission through direct contact with others. In this study, we collect contact data from residents of informal settlements around Nairobi, Kenya, to assess if control measures have changed contact patterns, and estimate the impact of changes on the basic reproduction number (R<sub>0</sub>).<h4>Methods</h4>We conducted a social contact survey with 213 residents of five informal settlements around Nairobi in early May 2020, 4 weeks after the Kenyan government introduced enhanced physical distancing measures and a curfew between 7 pm and 5 am. Respondents were asked to report all direct physical and non-physical contacts made the previous day, alongside a questionnaire asking about the social and economic impact of COVID-19 and control measures. We examined contact patterns by demographic factors, including socioeconomic status. We described the impact of COVID-19 and control measures on income and food security. We compared contact patterns during control measures to patterns from non-pandemic periods to estimate the change in R<sub>0</sub>.<h4>Results</h4>We estimate that control measures reduced physical contacts by 62% and non-physical contacts by either 63% or 67%, depending on the pre-COVID-19 comparison matrix used. Masks were worn by at least one person in 92% of contacts. Respondents in the poorest socioeconomic quintile reported 1.5 times more contacts than those in the richest. Eighty-six percent of respondents reported a total or partial loss of income due to COVID-19, and 74% reported eating less or skipping meals due to having too little money for food.<h4>Conclusion</h4>COVID-19 control measures have had a large impact on direct contacts and therefore transmission, but have also caused considerable economic and food insecurity. Reductions in R<sub>0</sub> are consistent with the comparatively low epidemic growth in Kenya and other sub-Saharan African countries that implemented similar, early control measures. However, negative and inequitable impacts on economic and food security may mean control measures are not sustainable in the longer term.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-020-01779-4; doi:https://doi.org/10.1186/s12916-020-01779-4; html:https://europepmc.org/articles/PMC7533154; pdf:https://europepmc.org/articles/PMC7533154?pdf=render
+34732073,https://doi.org/10.1161/strokeaha.121.034787,"Risk, Clinical Course, and Outcome of Ischemic Stroke in Patients Hospitalized With COVID-19: A Multicenter Cohort Study.","Sluis WM, Linschoten M, Buijs JE, Biesbroek JM, den Hertog HM, Ribbers T, Nieuwkamp DJ, van Houwelingen RC, Dias A, van Uden IWM, Kerklaan JP, Bienfait HP, Vermeer SE, de Jong SW, Ali M, Wermer MJH, de Graaf MT, Brouwers PJAM, Asselbergs FW, Kappelle LJ, van der Worp HB, Algra AM, CAPACITY-COVID Collaborative Consortium*.",,Stroke,2021,2021-11-04,N,Intensive care units; Pulmonary embolism; incidence; Hospital Mortality; Patient Discharge; Covid-19,,,"<h4>Background and purpose</h4>The frequency of ischemic stroke in patients with coronavirus disease 2019 (COVID-19) varies in the current literature, and risk factors are unknown. We assessed the incidence, risk factors, and outcomes of acute ischemic stroke in hospitalized patients with COVID-19.<h4>Methods</h4>We included patients with a laboratory-confirmed SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) infection admitted in 16 Dutch hospitals participating in the international CAPACITY-COVID registry between March 1 and August 1, 2020. Patients were screened for the occurrence of acute ischemic stroke. We calculated the cumulative incidence of ischemic stroke and compared risk factors, cardiovascular complications, and in-hospital mortality in patients with and without ischemic stroke.<h4>Results</h4>We included 2147 patients with COVID-19, of whom 586 (27.3%) needed treatment at an intensive care unit. Thirty-eight patients (1.8%) had an ischemic stroke. Patients with stroke were older but did not differ in sex or cardiovascular risk factors. Median time between the onset of COVID-19 symptoms and diagnosis of stroke was 2 weeks. The incidence of ischemic stroke was higher among patients who were treated at an intensive care unit (16/586; 2.7% versus nonintensive care unit, 22/1561; 1.4%; <i>P</i>=0.039). Pulmonary embolism was more common in patients with (8/38; 21.1%) than in those without stroke (160/2109; 7.6%; adjusted risk ratio, 2.08 [95% CI, 1.52-2.84]). Twenty-seven patients with ischemic stroke (71.1%) died during admission or were functionally dependent at discharge. Patients with ischemic stroke were at a higher risk of in-hospital mortality (adjusted risk ratio, 1.56 [95% CI, 1.13-2.15]) than patients without stroke.<h4>Conclusions</h4>In this multicenter cohort study, the cumulative incidence of acute ischemic stroke in hospitalized patients with COVID-19 was ≈2%, with a higher risk in patients treated at an intensive care unit. The majority of stroke patients had a poor outcome. The association between ischemic stroke and pulmonary embolism warrants further investigation.",,pdf:https://europepmc.org/articles/pmc8607920?pdf=render; doi:https://doi.org/10.1161/STROKEAHA.121.034787; html:https://europepmc.org/articles/PMC8607920; pdf:https://europepmc.org/articles/PMC8607920?pdf=render; doi:https://doi.org/10.1161/strokeaha.121.034787
 32656368,https://doi.org/10.12688/wellcomeopenres.15889.2,What settings have been linked to SARS-CoV-2 transmission clusters?,"Leclerc QJ, Fuller NM, Knight LE, CMMID COVID-19 Working Group, Funk S, Knight GM.",,Wellcome open research,2020,2020-06-05,Y,Transmission; Cluster; Coronavirus; Settings; Lockdown; Covid-19; Sars-cov-2,,,"<b>Background</b>: Concern about the health impact of novel coronavirus SARS-CoV-2 has resulted in widespread enforced reductions in people's movement (""lockdowns""). However, there are increasing concerns about the severe economic and wider societal consequences of these measures. Some countries have begun to lift some of the rules on physical distancing in a stepwise manner, with differences in what these ""exit strategies"" entail and their timeframes. The aim of this work was to inform such exit strategies by exploring the types of indoor and outdoor settings where transmission of SARS-CoV-2 has been reported to occur and result in clusters of cases. Identifying potential settings that result in transmission clusters allows these to be kept under close surveillance and/or to remain closed as part of strategies that aim to avoid a resurgence in transmission following the lifting of lockdown measures. <b>Methods</b>: We performed a systematic review of available literature and media reports to find settings reported in peer reviewed articles and media with these characteristics. These sources are curated and made available in an editable online database. <b>Results</b>: We found many examples of SARS-CoV-2 clusters linked to a wide range of mostly indoor settings. Few reports came from schools, many from households, and an increasing number were reported in hospitals and elderly care settings across Europe. <b>Conclusions:</b> We identified possible places that are linked to clusters of COVID-19 cases and could be closely monitored and/or remain closed in the first instance following the progressive removal of lockdown restrictions. However, in part due to the limits in surveillance capacities in many settings, the gathering of information such as cluster sizes and attack rates is limited in several ways: inherent recall bias, biased media reporting and missing data.",,doi:https://doi.org/10.12688/wellcomeopenres.15889.2; html:https://europepmc.org/articles/PMC7327724; pdf:https://europepmc.org/articles/PMC7327724?pdf=render
 36541441,https://doi.org/10.1002/hbm.26182,"Predicting sex, age, general cognition and mental health with machine learning on brain structural connectomes.","Yeung HW, Stolicyn A, Buchanan CR, Tucker-Drob EM, Bastin ME, Luz S, McIntosh AM, Whalley HC, Cox SR, Smith K.",,Human brain mapping,2023,2022-12-21,Y,Cognition; Diffusion Tensor Imaging; General Psychopathology; Deep Learning; Structural Connectomes,,,"There is an increasing expectation that advanced, computationally expensive machine learning (ML) techniques, when applied to large population-wide neuroimaging datasets, will help to uncover key differences in the human brain in health and disease. We take a comprehensive approach to explore how multiple aspects of brain structural connectivity can predict sex, age, general cognitive function and general psychopathology, testing different ML algorithms from deep learning (DL) model (BrainNetCNN) to classical ML methods. We modelled N = 8183 structural connectomes from UK Biobank using six different structural network weightings obtained from diffusion MRI. Streamline count generally provided the highest prediction accuracies in all prediction tasks. DL did not improve on prediction accuracies from simpler linear models. Further, high correlations between gradient attribution coefficients from DL and model coefficients from linear models suggested the models ranked the importance of features in similar ways, which indirectly suggested the similarity in models' strategies for making predictive decision to some extent. This highlights that model complexity is unlikely to improve detection of associations between structural connectomes and complex phenotypes with the current sample size.",,doi:https://doi.org/10.1002/hbm.26182; doi:https://doi.org/10.1002/hbm.26182; html:https://europepmc.org/articles/PMC9980898; pdf:https://europepmc.org/articles/PMC9980898?pdf=render
 37719470,https://doi.org/10.3390/rs14143429,What you see is what you breathe? Estimating air pollution spatial variation using street level imagery.,"Suel E, Sorek-Hamer M, Moise I, von Pohle M, Sahasrabhojanee A, Asanjan AA, Arku RE, Alli AS, Barratt B, Clark SN, Middel A, Deardorff E, Lingenfelter V, Oza N, Yadav N, Ezzati M, Brauer M.",,Remote sensing,2022,2022-07-01,Y,Air pollution; Computer vision; Urban pollution; transferability; Deep Learning; Data Science; Street Images,,,"High spatial resolution information on urban air pollution levels is unavailable in many areas globally, partially due to high input data needs of existing estimation approaches. Here we introduce a computer vision method to estimate annual means for air pollution levels from street level images. We used annual mean estimates of NO<sub>2</sub> and PM<sub>2.5</sub> concentrations from locally calibrated models as labels from London, New York, and Vancouver to allow for compilation of a sufficiently large dataset (~250k images for each city). Our experimental setup is designed to quantify intra and intercity transferability of image-based model estimates. Performances were high and comparable to traditional land-use regression (LUR) and dispersion models when training and testing on images from the same city (R<sup>2</sup> values between 0.51 and 0.95 when validated on data from ground monitoring stations). Like LUR models, transferability of models between cities in different geographies is more difficult. Specifically, transferability between the three cities i.e., London, New York, and Vancouver, which have similar pollution source profiles were moderately successful (R<sup>2</sup> values between zero and 0.67). Comparatively, performances when transferring models trained on these cities with very different source profiles i.e., Accra in Ghana and Hong Kong were lower (R<sup>2</sup> between zero and 0.21) suggesting the need for local calibration with local calibration using additional measurement data from cities that share similar source profiles.",,pdf:https://www.mdpi.com/2072-4292/14/14/3429/pdf?version=1658213065; doi:https://doi.org/10.3390/rs14143429; html:https://europepmc.org/articles/PMC7615101; pdf:https://europepmc.org/articles/PMC7615101?pdf=render
@@ -2351,8 +2353,8 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 35255491,https://doi.org/10.1038/s41586-022-04569-5,SARS-CoV-2 is associated with changes in brain structure in UK Biobank.,"Douaud G, Lee S, Alfaro-Almagro F, Arthofer C, Wang C, McCarthy P, Lange F, Andersson JLR, Griffanti L, Duff E, Jbabdi S, Taschler B, Keating P, Winkler AM, Collins R, Matthews PM, Allen N, Miller KL, Nichols TE, Smith SM.",,Nature,2022,2022-03-07,Y,,,,"There is strong evidence of brain-related abnormalities in COVID-19<sup>1-13</sup>. However, it remains unknown whether the impact of SARS-CoV-2 infection can be detected in milder cases, and whether this can reveal possible mechanisms contributing to brain pathology. Here we investigated brain changes in 785 participants of UK Biobank (aged 51-81 years) who were imaged twice using magnetic resonance imaging, including 401 cases who tested positive for infection with SARS-CoV-2 between their two scans-with 141 days on average separating their diagnosis and the second scan-as well as 384 controls. The availability of pre-infection imaging data reduces the likelihood of pre-existing risk factors being misinterpreted as disease effects. We identified significant longitudinal effects when comparing the two groups, including (1) a greater reduction in grey matter thickness and tissue contrast in the orbitofrontal cortex and parahippocampal gyrus; (2) greater changes in markers of tissue damage in regions that are functionally connected to the primary olfactory cortex; and (3) a greater reduction in global brain size in the SARS-CoV-2 cases. The participants who were infected with SARS-CoV-2 also showed on average a greater cognitive decline between the two time points. Importantly, these imaging and cognitive longitudinal effects were still observed after excluding the 15 patients who had been hospitalised. These mainly limbic brain imaging results may be the in vivo hallmarks of a degenerative spread of the disease through olfactory pathways, of neuroinflammatory events, or of the loss of sensory input due to anosmia. Whether this deleterious effect can be partially reversed, or whether these effects will persist in the long term, remains to be investigated with additional follow-up.",,pdf:https://www.nature.com/articles/s41586-022-04569-5.pdf; doi:https://doi.org/10.1038/s41586-022-04569-5; html:https://europepmc.org/articles/PMC9046077; pdf:https://europepmc.org/articles/PMC9046077?pdf=render
 35509371,https://doi.org/10.12688/wellcomeopenres.16883.2,Single-cell multi-omics analysis reveals IFN-driven alterations in T lymphocytes and natural killer cells in systemic lupus erythematosus.,"Trzupek D, Lee M, Hamey F, Wicker LS, Todd JA, Ferreira RC.",,Wellcome open research,2021,2021-01-01,Y,Biomarker; Systemic Lupus Erythematosus (Sle); Type I Interferon (Ifn); Multi-omics; Single-cell Rna-sequencing (Scrna-seq); Abseq; Bd Rhapsody; Cytotoxic Cd4+ T Cells (Ctls),,,"<b>Background:</b> The characterisation of the peripheral immune system in the autoimmune disease systemic lupus erythematosus (SLE) at the single-cell level has been limited by the reduced sensitivity of current whole-transcriptomic technologies. Here we employ a targeted single-cell multi-omics approach, combining protein and mRNA quantification, to generate a high-resolution map of the T lymphocyte and natural killer (NK) cell populations in blood from SLE patients. <b>Methods:</b> We designed a custom panel to quantify the transcription of 534 genes in parallel with the expression of 51 surface protein targets using the BD Rhapsody AbSeq single-cell system. We applied this technology to profile 20,656 T and NK cells isolated from peripheral blood from an SLE patient with a type I interferon (IFN)-induced gene expression signature (IFN <sup>hi</sup>), and an age- and sex- matched IFN <sup>low</sup> SLE patient and healthy donor. <b>Results:</b> We confirmed the presence of a rare cytotoxic CD4 <sup>+</sup> T cell (CTL) subset, which was exclusively present in the IFN <sup>hi</sup> patient. Furthermore, we identified additional alterations consistent with increased immune activation in this patient, most notably a shift towards terminally differentiated CD57 <sup>+</sup> CD8 <sup>+</sup> T cell and CD16 <sup>+</sup> NK <sup>dim</sup> phenotypes, and the presence of a subset of recently-activated naïve CD4 <sup>+</sup> T cells. <b>Conclusions:</b> Our results identify IFN-driven changes in the composition and phenotype of T and NK cells that are consistent with a systemic immune activation within the IFN <sup>hi</sup> patient, and underscore the added resolving power of this multi-omics approach to identify rare immune subsets. Consequently, we were able to find evidence for novel cellular peripheral biomarkers of SLE disease activity, including a subpopulation of CD57 <sup>+</sup> CD4 <sup>+</sup> CTLs.",,pdf:https://wellcomeopenresearch.org/articles/6-149/v2/pdf; doi:https://doi.org/10.12688/wellcomeopenres.16883.2; html:https://europepmc.org/articles/PMC9046903; pdf:https://europepmc.org/articles/PMC9046903?pdf=render
 34740937,https://doi.org/10.1136/bmjopen-2021-056601,Analysis of mental and physical disorders associated with COVID-19 in online health forums: a natural language processing study.,"Patel R, Smeraldi F, Abdollahyan M, Irving J, Bessant C.",,BMJ open,2021,2021-11-05,Y,information technology; Health Informatics; Covid-19,,,"<h4>Objectives</h4>Online health forums provide rich and untapped real-time data on population health. Through novel data extraction and natural language processing (NLP) techniques, we characterise the evolution of mental and physical health concerns relating to the COVID-19 pandemic among online health forum users.<h4>Setting and design</h4>We obtained data from three leading online health forums: HealthBoards, Inspire and HealthUnlocked, from the period 1 January 2020 to 31 May 2020. Using NLP, we analysed the content of posts related to COVID-19.<h4>Primary outcome measures</h4>(1) Proportion of forum posts containing COVID-19 keywords; (2) proportion of forum users making their very first post about COVID-19; (3) proportion of COVID-19-related posts containing content related to physical and mental health comorbidities.<h4>Results</h4>Data from 739 434 posts created by 53 134 unique users were analysed. A total of 35 581 posts (4.8%) contained a COVID-19 keyword. Posts discussing COVID-19 and related comorbid disorders spiked in early March to mid-March around the time of global implementation of lockdowns prompting a large number of users to post on online health forums for the first time. Over a quarter of COVID-19-related thread titles mentioned a physical or mental health comorbidity.<h4>Conclusions</h4>We demonstrate that it is feasible to characterise the content of online health forum user posts regarding COVID-19 and measure changes over time. The pandemic and corresponding public response has had a significant impact on posters' queries regarding mental health. Social media data sources such as online health forums can be harnessed to strengthen population-level mental health surveillance.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/11/e056601.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-056601; html:https://europepmc.org/articles/PMC8573296; pdf:https://europepmc.org/articles/PMC8573296?pdf=render
-34732839,https://doi.org/10.1038/s41379-021-00953-0,Stratification of chemotherapy-treated stage III colorectal cancer patients using multiplexed imaging and single-cell analysis of T-cell populations.,"Stachtea X, Loughrey MB, Salvucci M, Lindner AU, Cho S, McDonough E, Sood A, Graf J, Santamaria-Pang A, Corwin A, Laurent-Puig P, Dasgupta S, Shia J, Owens JR, Abate S, Van Schaeybroeck S, Lawler M, Prehn JHM, Ginty F, Longley DB.",,"Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc",2022,2021-11-03,Y,,,,"Colorectal cancer (CRC) has one of the highest cancer incidences and mortality rates. In stage III, postoperative chemotherapy benefits <20% of patients, while more than 50% will develop distant metastases. Biomarkers for identification of patients at increased risk of disease recurrence following adjuvant chemotherapy are currently lacking. In this study, we assessed immune signatures in the tumor and tumor microenvironment (TME) using an in situ multiplexed immunofluorescence imaging and single-cell analysis technology (Cell DIVE<sup>TM</sup>) and evaluated their correlations with patient outcomes. Tissue microarrays (TMAs) with up to three 1 mm diameter cores per patient were prepared from 117 stage III CRC patients treated with adjuvant fluoropyrimidine/oxaliplatin (FOLFOX) chemotherapy. Single sections underwent multiplexed immunofluorescence staining for immune cell markers (CD45, CD3, CD4, CD8, FOXP3, PD1) and tumor/cell segmentation markers (DAPI, pan-cytokeratin, AE1, NaKATPase, and S6). We used annotations and a probabilistic classification algorithm to build statistical models of immune cell types. Images were also qualitatively assessed independently by a Pathologist as 'high', 'moderate' or 'low', for stromal and total immune cell content. Excellent agreement was found between manual assessment and total automated scores (p < 0.0001). Moreover, compared to single markers, a multi-marker classification of regulatory T cells (Tregs: CD3+/CD4+FOXP3+/PD1-) was significantly associated with disease-free survival (DFS) and overall survival (OS) (p = 0.049 and 0.032) of FOLFOX-treated patients. Our results also showed that PD1- Tregs rather than PD1+ Tregs were associated with improved survival. These findings were supported by results from an independent FOLFOX-treated cohort of 191 stage III CRC patients, where higher PD1- Tregs were associated with an increase overall survival (p = 0.015) for CD3+/CD4+/FOXP3+/PD1-. Overall, compared to single markers, multi-marker classification provided more accurate quantitation of immune cell types with stronger correlations with outcomes.",,pdf:https://www.nature.com/articles/s41379-021-00953-0.pdf; doi:https://doi.org/10.1038/s41379-021-00953-0; html:https://europepmc.org/articles/PMC8964416; pdf:https://europepmc.org/articles/PMC8964416?pdf=render
 31675503,https://doi.org/10.1016/j.cell.2019.10.004,Uganda Genome Resource Enables Insights into Population History and Genomic Discovery in Africa.,"Gurdasani D, Carstensen T, Fatumo S, Chen G, Franklin CS, Prado-Martinez J, Bouman H, Abascal F, Haber M, Tachmazidou I, Mathieson I, Ekoru K, DeGorter MK, Nsubuga RN, Finan C, Wheeler E, Chen L, Cooper DN, Schiffels S, Chen Y, Ritchie GRS, Pollard MO, Fortune MD, Mentzer AJ, Garrison E, Bergström A, Hatzikotoulas K, Adeyemo A, Doumatey A, Elding H, Wain LV, Ehret G, Auer PL, Kooperberg CL, Reiner AP, Franceschini N, Maher D, Montgomery SB, Kadie C, Widmer C, Xue Y, Seeley J, Asiki G, Kamali A, Young EH, Pomilla C, Soranzo N, Zeggini E, Pirie F, Morris AP, Heckerman D, Tyler-Smith C, Motala AA, Rotimi C, Kaleebu P, Barroso I, Sandhu MS.",,Cell,2019,2019-10-01,N,,,,"Genomic studies in African populations provide unique opportunities to understand disease etiology, human diversity, and population history. In the largest study of its kind, comprising genome-wide data from 6,400 individuals and whole-genome sequences from 1,978 individuals from rural Uganda, we find evidence of geographically correlated fine-scale population substructure. Historically, the ancestry of modern Ugandans was best represented by a mixture of ancient East African pastoralists. We demonstrate the value of the largest sequence panel from Africa to date as an imputation resource. Examining 34 cardiometabolic traits, we show systematic differences in trait heritability between European and African populations, probably reflecting the differential impact of genes and environment. In a multi-trait pan-African GWAS of up to 14,126 individuals, we identify novel loci associated with anthropometric, hematological, lipid, and glycemic traits. We find that several functionally important signals are driven by Africa-specific variants, highlighting the value of studying diverse populations across the region.",,pdf:http://www.cell.com/article/S0092867419311201/pdf; doi:https://doi.org/10.1016/j.cell.2019.10.004; html:https://europepmc.org/articles/PMC7202134; pdf:https://europepmc.org/articles/PMC7202134?pdf=render; doi:https://doi.org/10.1016/j.cell.2019.10.004
+34732839,https://doi.org/10.1038/s41379-021-00953-0,Stratification of chemotherapy-treated stage III colorectal cancer patients using multiplexed imaging and single-cell analysis of T-cell populations.,"Stachtea X, Loughrey MB, Salvucci M, Lindner AU, Cho S, McDonough E, Sood A, Graf J, Santamaria-Pang A, Corwin A, Laurent-Puig P, Dasgupta S, Shia J, Owens JR, Abate S, Van Schaeybroeck S, Lawler M, Prehn JHM, Ginty F, Longley DB.",,"Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc",2022,2021-11-03,Y,,,,"Colorectal cancer (CRC) has one of the highest cancer incidences and mortality rates. In stage III, postoperative chemotherapy benefits <20% of patients, while more than 50% will develop distant metastases. Biomarkers for identification of patients at increased risk of disease recurrence following adjuvant chemotherapy are currently lacking. In this study, we assessed immune signatures in the tumor and tumor microenvironment (TME) using an in situ multiplexed immunofluorescence imaging and single-cell analysis technology (Cell DIVE<sup>TM</sup>) and evaluated their correlations with patient outcomes. Tissue microarrays (TMAs) with up to three 1 mm diameter cores per patient were prepared from 117 stage III CRC patients treated with adjuvant fluoropyrimidine/oxaliplatin (FOLFOX) chemotherapy. Single sections underwent multiplexed immunofluorescence staining for immune cell markers (CD45, CD3, CD4, CD8, FOXP3, PD1) and tumor/cell segmentation markers (DAPI, pan-cytokeratin, AE1, NaKATPase, and S6). We used annotations and a probabilistic classification algorithm to build statistical models of immune cell types. Images were also qualitatively assessed independently by a Pathologist as 'high', 'moderate' or 'low', for stromal and total immune cell content. Excellent agreement was found between manual assessment and total automated scores (p < 0.0001). Moreover, compared to single markers, a multi-marker classification of regulatory T cells (Tregs: CD3+/CD4+FOXP3+/PD1-) was significantly associated with disease-free survival (DFS) and overall survival (OS) (p = 0.049 and 0.032) of FOLFOX-treated patients. Our results also showed that PD1- Tregs rather than PD1+ Tregs were associated with improved survival. These findings were supported by results from an independent FOLFOX-treated cohort of 191 stage III CRC patients, where higher PD1- Tregs were associated with an increase overall survival (p = 0.015) for CD3+/CD4+/FOXP3+/PD1-. Overall, compared to single markers, multi-marker classification provided more accurate quantitation of immune cell types with stronger correlations with outcomes.",,pdf:https://www.nature.com/articles/s41379-021-00953-0.pdf; doi:https://doi.org/10.1038/s41379-021-00953-0; html:https://europepmc.org/articles/PMC8964416; pdf:https://europepmc.org/articles/PMC8964416?pdf=render
 35386118,https://doi.org/10.3389/fnagi.2022.840651,Genome-Wide Association Study of Alzheimer's Disease Brain Imaging Biomarkers and Neuropsychological Phenotypes in the European Medical Information Framework for Alzheimer's Disease Multimodal Biomarker Discovery Dataset.,"Homann J, Osburg T, Ohlei O, Dobricic V, Deecke L, Bos I, Vandenberghe R, Gabel S, Scheltens P, Teunissen CE, Engelborghs S, Frisoni G, Blin O, Richardson JC, Bordet R, Lleó A, Alcolea D, Popp J, Clark C, Peyratout G, Martinez-Lage P, Tainta M, Dobson RJB, Legido-Quigley C, Sleegers K, Van Broeckhoven C, Wittig M, Franke A, Lill CM, Blennow K, Zetterberg H, Lovestone S, Streffer J, Ten Kate M, Vos SJB, Barkhof F, Visser PJ, Bertram L.",,Frontiers in aging neuroscience,2022,2022-03-21,Y,X chromosome; MRI; Imaging; Cognitive function; Genome-wide Association Study; Gwas; Alzheimer’s Disease (Ad),,,"Alzheimer's disease (AD) is the most frequent neurodegenerative disease with an increasing prevalence in industrialized, aging populations. AD susceptibility has an established genetic basis which has been the focus of a large number of genome-wide association studies (GWAS) published over the last decade. Most of these GWAS used dichotomized clinical diagnostic status, i.e., case vs. control classification, as outcome phenotypes, without the use of biomarkers. An alternative and potentially more powerful study design is afforded by using quantitative AD-related phenotypes as GWAS outcome traits, an analysis paradigm that we followed in this work. Specifically, we utilized genotype and phenotype data from <i>n</i> = 931 individuals collected under the auspices of the European Medical Information Framework for Alzheimer's Disease Multimodal Biomarker Discovery (EMIF-AD MBD) study to perform a total of 19 separate GWAS analyses. As outcomes we used five magnetic resonance imaging (MRI) traits and seven cognitive performance traits. For the latter, longitudinal data from at least two timepoints were available in addition to cross-sectional assessments at baseline. Our GWAS analyses revealed several genome-wide significant associations for the neuropsychological performance measures, in particular those assayed longitudinally. Among the most noteworthy signals were associations in or near <i>EHBP1</i> (EH domain binding protein 1; on chromosome 2p15) and <i>CEP112</i> (centrosomal protein 112; 17q24.1) with delayed recall as well as <i>SMOC2</i> (SPARC related modular calcium binding 2; 6p27) with immediate recall in a memory performance test. On the X chromosome, which is often excluded in other GWAS, we identified a genome-wide significant signal near <i>IL1RAPL1</i> (interleukin 1 receptor accessory protein like 1; Xp21.3). While polygenic score (PGS) analyses showed the expected strong associations with SNPs highlighted in relevant previous GWAS on hippocampal volume and cognitive function, they did not show noteworthy associations with recent AD risk GWAS findings. In summary, our study highlights the power of using quantitative endophenotypes as outcome traits in AD-related GWAS analyses and nominates several new loci not previously implicated in cognitive decline.",,pdf:https://www.frontiersin.org/articles/10.3389/fnagi.2022.840651/pdf; doi:https://doi.org/10.3389/fnagi.2022.840651; html:https://europepmc.org/articles/PMC8979334; pdf:https://europepmc.org/articles/PMC8979334?pdf=render
 33444378,https://doi.org/10.1371/journal.pcbi.1008417,Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differences in transmission.,"Eyre DW, Laager M, Walker AS, Cooper BS, Wilson DJ, CDC Modeling Infectious Diseases in Healthcare Program (MInD-Healthcare).",,PLoS computational biology,2021,2021-01-14,Y,,,,"Fitting stochastic transmission models to electronic patient data can offer detailed insights into the transmission of healthcare-associated infections and improve infection control. Pathogen whole-genome sequencing may improve the precision of model inferences, but computational constraints have limited modelling applications predominantly to small datasets and specific outbreaks, whereas large-scale sequencing studies have mostly relied on simple rules for identifying/excluding plausible transmission. We present a novel approach for integrating detailed epidemiological data on patient contact networks in hospitals with large-scale pathogen sequencing data. We apply our approach to study Clostridioides difficile transmission using a dataset of 1223 infections in Oxfordshire, UK, 2007-2011. 262 (21% [95% credibility interval 20-22%]) infections were estimated to have been acquired from another known case. There was heterogeneity by sequence type (ST) in the proportion of cases acquired from another case with the highest rates in ST1 (ribotype-027), ST42 (ribotype-106) and ST3 (ribotype-001). These same STs also had higher rates of transmission mediated via environmental contamination/spores persisting after patient discharge/recovery; for ST1 these persisted longer than for most other STs except ST3 and ST42. We also identified variation in transmission between hospitals, medical specialties and over time; by 2011 nearly all transmission from known cases had ceased in our hospitals. Our findings support previous work suggesting only a minority of C. difficile infections are acquired from known cases but highlight a greater role for environmental contamination than previously thought. Our approach is applicable to other healthcare-associated infections. Our findings have important implications for effective control of C. difficile.",,pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008417&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1008417; html:https://europepmc.org/articles/PMC7840057; pdf:https://europepmc.org/articles/PMC7840057?pdf=render
 32987048,https://doi.org/10.1016/j.ijcard.2020.09.053,Predicting 10-year risk of recurrent cardiovascular events andcardiovascular interventions in patients with established cardiovascular disease: results from UCC-SMART and REACH.,"Klooster CCV', Bhatt DL, Steg PG, Massaro JM, Dorresteijn JAN, Westerink J, Ruigrok YM, de Borst GJ, Asselbergs FW, van der Graaf Y, Visseren FLJ, UCC-SMART study group.",,International journal of cardiology,2021,2020-09-25,N,Risk Prediction; Cardiovascular Interventions; Major Cardiovascular Events; Patients With Established Cardiovascular Disease,,,"<h4>Background</h4>Existing cardiovascular risk scores for patients with established cardiovascular disease (CVD) estimate residual risk of recurrent major cardiovascular events (MACE). The aim of the current study is to develop and externally validate a prediction model to estimate the 10-year combined risk of recurrent MACE and cardiovascular interventions (MACE+) in patients with established CVD.<h4>Methods</h4>Data of patients with established CVD from the UCC-SMART cohort (N = 8421) were used for model development, and patient data from REACH Western Europe (N = 14,528) and REACH North America (N = 19,495) for model validation. Predictors were selected based on the existing SMART risk score. A Fine and Gray competing risk-adjusted 10-year risk model was developed for the combined outcome MACE+. The model was validated in all patients and in strata of coronary heart disease (CHD), cerebrovascular disease (CeVD), peripheral artery disease (PAD).<h4>Results</h4>External calibration for 2-year risk in REACH Western Europe and REACH North America was good, c-statistics were moderate: 0.60 and 0.58, respectively. In strata of CVD at baseline good external calibration was observed in patients with CHD and CeVD, however, poor calibration was seen in patients with PAD. C-statistics for patients with CHD were 0.60 and 0.57, for patients with CeVD 0.62 and 0.61, and for patients with PAD 0.53 and 0.54 in REACH Western Europe and REACH North America, respectively.<h4>Conclusions</h4>The 10-year combined risk of recurrent MACE and cardiovascular interventions can be estimated in patients with established CHD or CeVD. However, cardiovascular interventions in patients with PAD could not be predicted reliably.",,pdf:http://www.internationaljournalofcardiology.com/article/S0167527320338341/pdf; doi:https://doi.org/10.1016/j.ijcard.2020.09.053
@@ -2366,9 +2368,9 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 31073125,https://doi.org/10.1038/s41533-019-0132-z,Systematic review of clinical prediction models to support the diagnosis of asthma in primary care.,"Daines L, McLean S, Buelo A, Lewis S, Sheikh A, Pinnock H.",,NPJ primary care respiratory medicine,2019,2019-05-09,Y,,The Human Phenome,,"Diagnosing asthma is challenging. Misdiagnosis can lead to untreated symptoms, incorrect treatment and avoidable deaths. The best combination of clinical features and tests to achieve a diagnosis of asthma is unclear. As asthma is usually diagnosed in non-specialist settings, a clinical prediction model to aid the assessment of the probability of asthma in primary care may improve diagnostic accuracy. We aimed to identify and describe existing prediction models to support the diagnosis of asthma in children and adults in primary care. We searched Medline, Embase, CINAHL, TRIP and US National Guidelines Clearinghouse databases from 1 January 1990 to 23 November 17. We included prediction models designed for use in primary care or equivalent settings to aid the diagnostic decision-making of clinicians assessing patients with symptoms suggesting asthma. Two reviewers independently screened titles, abstracts and full texts for eligibility, extracted data and assessed risk of bias. From 13,798 records, 53 full-text articles were reviewed. We included seven modelling studies; all were at high risk of bias. Model performance varied, and the area under the receiving operating characteristic curve ranged from 0.61 to 0.82. Patient-reported wheeze, symptom variability and history of allergy or allergic rhinitis were associated with asthma. In conclusion, clinical prediction models may support the diagnosis of asthma in primary care, but existing models are at high risk of bias and thus unreliable for informing practice. Future studies should adhere to recognised standards, conduct model validation and include a broader range of clinical data to derive a prediction model of value for clinicians.",,pdf:https://www.nature.com/articles/s41533-019-0132-z.pdf; doi:https://doi.org/10.1038/s41533-019-0132-z; html:https://europepmc.org/articles/PMC6509212; pdf:https://europepmc.org/articles/PMC6509212?pdf=render
 36647047,https://doi.org/10.1186/s12916-022-02722-5,"Polypharmacy during pregnancy and associated risk factors: a retrospective analysis of 577 medication exposures among 1.5 million pregnancies in the UK, 2000-2019.","Subramanian A, Azcoaga-Lorenzo A, Anand A, Phillips K, Lee SI, Cockburn N, Fagbamigbe AF, Damase-Michel C, Yau C, McCowan C, O'Reilly D, Santorelli G, Hope H, Kennedy JI, Abel KM, Eastwood KA, Locock L, Black M, Loane M, Moss N, Plachcinski R, Thangaratinam S, Brophy S, Agrawal U, Vowles Z, Brocklehurst P, Dolk H, Nelson-Piercy C, Nirantharakumar K, MuM-PreDiCT Group.",,BMC medicine,2023,2023-01-16,Y,Pregnancy; Prescriptions; Polypharmacy; Medications; Multimorbidity; Multiple Medications; Multiple Long-term Conditions,,,"<h4>Background</h4>The number of medications prescribed during pregnancy has increased over the past few decades. Few studies have described the prevalence of multiple medication use among pregnant women. This study aims to describe the overall prevalence over the last two decades among all pregnant women and those with multimorbidity and to identify risk factors for polypharmacy in pregnancy.<h4>Methods</h4>A retrospective cohort study was conducted between 2000 and 2019 using the Clinical Practice Research Datalink (CPRD) pregnancy register. Prescription records for 577 medication categories were obtained. Prevalence estimates for polypharmacy (ranging from 2+ to 11+ medications) were presented along with the medications commonly prescribed individually and in pairs during the first trimester and the entire pregnancy period. Logistic regression models were performed to identify risk factors for polypharmacy.<h4>Results</h4>During the first trimester (812,354 pregnancies), the prevalence of polypharmacy ranged from 24.6% (2+ medications) to 0.1% (11+ medications). During the entire pregnancy period (774,247 pregnancies), the prevalence ranged from 58.7 to 1.4%. Broad-spectrum penicillin (6.6%), compound analgesics (4.5%) and treatment of candidiasis (4.3%) were commonly prescribed. Pairs of medication prescribed to manage different long-term conditions commonly included selective beta 2 agonists or selective serotonin re-uptake inhibitors (SSRIs). Risk factors for being prescribed 2+ medications during the first trimester of pregnancy include being overweight or obese [aOR: 1.16 (1.14-1.18) and 1.55 (1.53-1.57)], belonging to an ethnic minority group [aOR: 2.40 (2.33-2.47), 1.71 (1.65-1.76), 1.41 (1.35-1.47) and 1.39 (1.30-1.49) among women from South Asian, Black, other and mixed ethnicities compared to white women] and smoking or previously smoking [aOR: 1.19 (1.18-1.20) and 1.05 (1.03-1.06)]. Higher and lower age, higher gravidity, increasing number of comorbidities and increasing level of deprivation were also associated with increased odds of polypharmacy.<h4>Conclusions</h4>The prevalence of polypharmacy during pregnancy has increased over the past two decades and is particularly high in younger and older women; women with high BMI, smokers and ex-smokers; and women with multimorbidity, higher gravidity and higher levels of deprivation. Well-conducted pharmaco-epidemiological research is needed to understand the effects of multiple medication use on the developing foetus.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-022-02722-5; doi:https://doi.org/10.1186/s12916-022-02722-5; html:https://europepmc.org/articles/PMC9843951; pdf:https://europepmc.org/articles/PMC9843951?pdf=render
 36084617,https://doi.org/10.1016/j.ebiom.2022.104243,Machine learning integration of multimodal data identifies key features of blood pressure regulation.,"Louca P, Tran TQB, Toit CD, Christofidou P, Spector TD, Mangino M, Suhre K, Padmanabhan S, Menni C.",,EBioMedicine,2022,2022-09-06,Y,Diet; Blood pressure; Genomics; Metabolomics; Machine Learning,,,"<h4>Background</h4>Association studies have identified several biomarkers for blood pressure and hypertension, but a thorough understanding of their mutual dependencies is lacking. By integrating two different high-throughput datasets, biochemical and dietary data, we aim to understand the multifactorial contributors of blood pressure (BP).<h4>Methods</h4>We included 4,863 participants from TwinsUK with concurrent BP, metabolomics, genomics, biochemical measures, and dietary data. We used 5-fold cross-validation with the machine learning XGBoost algorithm to identify features of importance in context of one another in TwinsUK (80% training, 20% test). The features tested in TwinsUK were then probed using the same algorithm in an independent dataset of 2,807 individuals from the Qatari Biobank (QBB).<h4>Findings</h4>Our model explained 39·2% [4·5%, MAE:11·32 mmHg (95%CI, +/- 0·65)] of the variance in systolic BP (SBP) in TwinsUK. Of the top 50 features, the most influential non-demographic variables were dihomo-linolenate, cis-4-decenoyl carnitine, lactate, chloride, urate, and creatinine along with dietary intakes of total, trans and saturated fat. We also highlight the incremental value of each included dimension. Furthermore, we replicated our model in the QBB [SBP variance explained = 45·2% (13·39%)] cohort and 30 of the top 50 features overlapped between cohorts.<h4>Interpretation</h4>We show that an integrated analysis of omics, biochemical and dietary data improves our understanding of their in-between relationships and expands the range of potential biomarkers for blood pressure. Our results point to potentially key biological pathways to be prioritised for mechanistic studies.<h4>Funding</h4>Chronic Disease Research Foundation, Medical Research Council, Wellcome Trust, Qatar Foundation.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9463529; doi:https://doi.org/10.1016/j.ebiom.2022.104243; html:https://europepmc.org/articles/PMC9463529; pdf:https://europepmc.org/articles/PMC9463529?pdf=render
+33024096,https://doi.org/10.1038/s41467-020-18783-0,Changing travel patterns in China during the early stages of the COVID-19 pandemic.,"Gibbs H, Liu Y, Pearson CAB, Jarvis CI, Grundy C, Quilty BJ, Diamond C, LSHTM CMMID COVID-19 working group, Eggo RM.",,Nature communications,2020,2020-10-06,Y,,,,"Understanding changes in human mobility in the early stages of the COVID-19 pandemic is crucial for assessing the impacts of travel restrictions designed to reduce disease spread. Here, relying on data from mainland China, we investigate the spatio-temporal characteristics of human mobility between 1st January and 1st March 2020, and discuss their public health implications. An outbound travel surge from Wuhan before travel restrictions were implemented was also observed across China due to the Lunar New Year, indicating that holiday travel may have played a larger role in mobility changes compared to impending travel restrictions. Holiday travel also shifted healthcare pressure related to COVID-19 towards locations with lower healthcare capacity. Network analyses showed no sign of major changes in the transportation network after Lunar New Year. Changes observed were temporary and did not lead to structural reorganisation of the transportation network during the study period.",,pdf:https://www.nature.com/articles/s41467-020-18783-0.pdf; doi:https://doi.org/10.1038/s41467-020-18783-0; html:https://europepmc.org/articles/PMC7538915; pdf:https://europepmc.org/articles/PMC7538915?pdf=render
 37315048,https://doi.org/10.1371/journal.pone.0287091,LMIC-PRIEST: Derivation and validation of a clinical severity score for acutely ill adults with suspected COVID-19 in a middle-income setting.,"Marincowitz C, Hodkinson P, McAlpine D, Fuller G, Goodacre S, Bath PA, Bath PA, Sbaffi L, Hasan M, Omer Y, Wallis L.",,PloS one,2023,2023-06-14,Y,,,,"<h4>Background</h4>Uneven vaccination and less resilient health care systems mean hospitals in LMICs are at risk of being overwhelmed during periods of increased COVID-19 infection. Risk-scores proposed for rapid triage of need for admission from the emergency department (ED) have been developed in higher-income settings during initial waves of the pandemic.<h4>Methods</h4>Routinely collected data for public hospitals in the Western Cape, South Africa from the 27th August 2020 to 11th March 2022 were used to derive a cohort of 446,084 ED patients with suspected COVID-19. The primary outcome was death or ICU admission at 30 days. The cohort was divided into derivation and Omicron variant validation sets. We developed the LMIC-PRIEST score based on the coefficients from multivariable analysis in the derivation cohort and existing triage practices. We externally validated accuracy in the Omicron period and a UK cohort.<h4>Results</h4>We analysed 305,564 derivation, 140,520 Omicron and 12,610 UK validation cases. Over 100 events per predictor parameter were modelled. Multivariable analyses identified eight predictor variables retained across models. We used these findings and clinical judgement to develop a score based on South African Triage Early Warning Scores and also included age, sex, oxygen saturation, inspired oxygen, diabetes and heart disease. The LMIC-PRIEST score achieved C-statistics: 0.82 (95% CI: 0.82 to 0.83) development cohort; 0.79 (95% CI: 0.78 to 0.80) Omicron cohort; and 0.79 (95% CI: 0.79 to 0.80) UK cohort. Differences in prevalence of outcomes led to imperfect calibration in external validation. However, use of the score at thresholds of three or less would allow identification of very low-risk patients (NPV ≥0.99) who could be rapidly discharged using information collected at initial assessment.<h4>Conclusion</h4>The LMIC-PRIEST score shows good discrimination and high sensitivity at lower thresholds and can be used to rapidly identify low-risk patients in LMIC ED settings.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0287091&type=printable; doi:https://doi.org/10.1371/journal.pone.0287091; html:https://europepmc.org/articles/PMC10266677; pdf:https://europepmc.org/articles/PMC10266677?pdf=render
 31062032,https://doi.org/10.1093/ije/dyz073,"Cohort Profile: Extended Cohort for E-health, Environment and DNA (EXCEED).","John C, Reeve NF, Free RC, Williams AT, Ntalla I, Farmaki AE, Bethea J, Barton LM, Shrine N, Batini C, Packer R, Terry S, Hargadon B, Wang Q, Melbourne CA, Adams EL, Bee CE, Harrington K, Miola J, Brunskill NJ, Brightling CE, Barwell J, Wallace SE, Hsu R, Shepherd DJ, Hollox EJ, Wain LV, Tobin MD.",,International journal of epidemiology,2019,2019-06-01,Y,,,,,,pdf:https://academic.oup.com/ije/article-pdf/48/3/678/29005217/dyz073.pdf; doi:https://doi.org/10.1093/ije/dyz073; html:https://europepmc.org/articles/PMC6659362; pdf:https://europepmc.org/articles/PMC6659362?pdf=render
-33024096,https://doi.org/10.1038/s41467-020-18783-0,Changing travel patterns in China during the early stages of the COVID-19 pandemic.,"Gibbs H, Liu Y, Pearson CAB, Jarvis CI, Grundy C, Quilty BJ, Diamond C, LSHTM CMMID COVID-19 working group, Eggo RM.",,Nature communications,2020,2020-10-06,Y,,,,"Understanding changes in human mobility in the early stages of the COVID-19 pandemic is crucial for assessing the impacts of travel restrictions designed to reduce disease spread. Here, relying on data from mainland China, we investigate the spatio-temporal characteristics of human mobility between 1st January and 1st March 2020, and discuss their public health implications. An outbound travel surge from Wuhan before travel restrictions were implemented was also observed across China due to the Lunar New Year, indicating that holiday travel may have played a larger role in mobility changes compared to impending travel restrictions. Holiday travel also shifted healthcare pressure related to COVID-19 towards locations with lower healthcare capacity. Network analyses showed no sign of major changes in the transportation network after Lunar New Year. Changes observed were temporary and did not lead to structural reorganisation of the transportation network during the study period.",,pdf:https://www.nature.com/articles/s41467-020-18783-0.pdf; doi:https://doi.org/10.1038/s41467-020-18783-0; html:https://europepmc.org/articles/PMC7538915; pdf:https://europepmc.org/articles/PMC7538915?pdf=render
 34110679,https://doi.org/10.1002/1878-0261.13038,Cost-effectiveness of precision diagnostic testing for precision medicine approaches against non-small-cell lung cancer: A systematic review.,"Henderson R, Keeling P, French D, Smart D, Sullivan R, Lawler M.",,Molecular oncology,2021,2021-07-19,Y,Biomarker; Economic evaluation; non-small-cell lung cancer; Cost-effectiveness Analysis; Precision Medicine; Precision Diagnostic Test,,,"Precision diagnostic testing (PDT) employs appropriate biomarkers to identify cancer patients that may optimally respond to precision medicine (PM) approaches, such as treatments with targeted agents and immuno-oncology drugs. To date, there are no published systematic appraisals evaluating the cost-effectiveness of PDT in non-small-cell lung cancer (NSCLC). To address this gap, we conducted Preferred Reporting Items for Systematic Reviews and Meta-Analyses searches for the years 2009-2019. Consolidated Health Economic Evaluation Reporting Standards were employed to screen, assess and extract data. Employing base costs, life years gained or quality-adjusted life years, as well as willingness-to-pay (WTP) threshold for each country, net monetary benefit was calculated to determine cost-effectiveness of each intervention. Thirty-seven studies (50%) were included for analysis; a further 37 (50%) were excluded, having failed population-, intervention-, comparator-, outcomes- and study-design criteria. Within the 37 studies included, we defined 64 scenarios. Eleven scenarios compared PDT-guided PM with non-guided therapy [epidermal growth factor receptor (EGFR), n = 5; programmed death-ligand 1 (PD-L1), n = 6]. Twenty-eight scenarios compared PDT-guided PM with chemotherapy alone (anaplastic lymphoma kinase, n = 3; EGFR, n = 17; PD-L1, n = 8). Twenty-five scenarios compared PDT-guided PM with chemotherapy alone, while varying the PDT approach. Thirty-four scenarios (53%) were cost-effective, 28 (44%) were not cost-effective, and two were marginal, dependent on their country's WTP threshold. When PDT-guided therapy was compared with a therapy-for-all patients approach, all scenarios (100%) proved cost-effective. Seven of 37 studies had been structured appropriately to assess PDT-PM cost-effectiveness. Within these seven studies, all evaluated scenarios were cost-effective. However, 81% of studies had been poorly designed. Our systematic analysis implies that more robust health economic evaluation could help identify additional approaches towards PDT cost-effectiveness, underpinning value-based care and enhanced outcomes for patients with NSCLC.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/1878-0261.13038; doi:https://doi.org/10.1002/1878-0261.13038; html:https://europepmc.org/articles/PMC8486593; pdf:https://europepmc.org/articles/PMC8486593?pdf=render
 34371093,https://doi.org/10.1016/j.jaad.2021.07.066,The impact of psoriasis and sexual orientation on mental and physical health among adults in the United States.,"Mansh MD, Mulick A, Langan SM.",,Journal of the American Academy of Dermatology,2022,2021-08-08,Y,,,,,,doi:https://doi.org/10.1016/j.jaad.2021.07.066; doi:https://doi.org/10.1016/j.jaad.2021.07.066; html:https://europepmc.org/articles/PMC7612892; pdf:https://europepmc.org/articles/PMC7612892?pdf=render
 34857859,https://doi.org/10.1038/s42003-021-02867-8,A computational exploration of resilience and evolvability of protein-protein interaction networks.,"Klein B, Holmér L, Smith KM, Johnson MM, Swain A, Stolp L, Teufel AI, Kleppe AS.",,Communications biology,2021,2021-12-02,Y,,,,"Protein-protein interaction (PPI) networks represent complex intra-cellular protein interactions, and the presence or absence of such interactions can lead to biological changes in an organism. Recent network-based approaches have shown that a phenotype's PPI network's resilience to environmental perturbations is related to its placement in the tree of life; though we still do not know how or why certain intra-cellular factors can bring about this resilience. Here, we explore the influence of gene expression and network properties on PPI networks' resilience. We use publicly available data of PPIs for E. coli, S. cerevisiae, and H. sapiens, where we compute changes in network resilience as new nodes (proteins) are added to the networks under three node addition mechanisms-random, degree-based, and gene-expression-based attachments. By calculating the resilience of the resulting networks, we estimate the effectiveness of these node addition mechanisms. We demonstrate that adding nodes with gene-expression-based preferential attachment (as opposed to random or degree-based) preserves and can increase the original resilience of PPI network in all three species, regardless of gene expression distribution or network structure. These findings introduce a general notion of prospective resilience, which highlights the key role of network structures in understanding the evolvability of phenotypic traits.",,pdf:https://www.nature.com/articles/s42003-021-02867-8.pdf; doi:https://doi.org/10.1038/s42003-021-02867-8; html:https://europepmc.org/articles/PMC8639913; pdf:https://europepmc.org/articles/PMC8639913?pdf=render
@@ -2376,24 +2378,24 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 33430602,https://doi.org/10.1161/circheartfailure.120.007022,Proteomic and Functional Studies Reveal Detyrosinated Tubulin as Treatment Target in Sarcomere Mutation-Induced Hypertrophic Cardiomyopathy.,"Schuldt M, Pei J, Harakalova M, Dorsch LM, Schlossarek S, Mokry M, Knol JC, Pham TV, Schelfhorst T, Piersma SR, Dos Remedios C, Dalinghaus M, Michels M, Asselbergs FW, Moutin MJ, Carrier L, Jimenez CR, van der Velden J, Kuster DWD.",,Circulation. Heart failure,2021,2021-01-12,Y,Mutation; Genotype; Tubulin; Heart diseases; Proteomics; Treatment; Cardiomyopathies,,,"<h4>Background</h4>Hypertrophic cardiomyopathy (HCM) is the most common genetic heart disease. While ≈50% of patients with HCM carry a sarcomere gene mutation (sarcomere mutation-positive, HCM<sub>SMP</sub>), the genetic background is unknown in the other half of the patients (sarcomere mutation-negative, HCM<sub>SMN</sub>). Genotype-specific differences have been reported in cardiac function. Moreover, HCM<sub>SMN</sub> patients have later disease onset and a better prognosis than HCM<sub>SMP</sub> patients. To define if genotype-specific derailments at the protein level may explain the heterogeneity in disease development, we performed a proteomic analysis in cardiac tissue from a clinically well-phenotyped HCM patient group.<h4>Methods</h4>A proteomics screen was performed in cardiac tissue from 39 HCM<sub>SMP</sub> patients, 11HCM<sub>SMN</sub> patients, and 8 nonfailing controls. Patients with HCM had obstructive cardiomyopathy with left ventricular outflow tract obstruction and diastolic dysfunction. A novel <i>MYBPC3</i><sub>2373insG</sub> mouse model was used to confirm functional relevance of our proteomic findings.<h4>Results</h4>In all HCM patient samples, we found lower levels of metabolic pathway proteins and higher levels of extracellular matrix proteins. Levels of total and detyrosinated α-tubulin were markedly higher in HCM<sub>SMP</sub> than in HCM<sub>SMN</sub> and controls. Higher tubulin detyrosination was also found in 2 unrelated <i>MYBPC3</i> mouse models and its inhibition with parthenolide normalized contraction and relaxation time of isolated cardiomyocytes.<h4>Conclusions</h4>Our findings indicate that microtubules and especially its detyrosination contribute to the pathomechanism of patients with HCM<sub>SMP</sub>. This is of clinical importance since it represents a potential treatment target to improve cardiac function in patients with HCM<sub>SMP</sub>, whereas a beneficial effect may be limited in patients with HCM<sub>SMN</sub>.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCHEARTFAILURE.120.007022; doi:https://doi.org/10.1161/CIRCHEARTFAILURE.120.007022; html:https://europepmc.org/articles/PMC7819533; pdf:https://europepmc.org/articles/PMC7819533?pdf=render
 32784218,https://doi.org/10.3399/bjgp20x712313,Suboptimal prescribing behaviour associated with clinical software design features: a retrospective cohort study in English NHS primary care.,"MacKenna B, Curtis HJ, Walker AJ, Bacon S, Croker R, Goldacre B.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2020,2020-08-27,N,Cohort studies; Primary Care; Clinical Software; Drugs Prescribing; Ghost-branded Generics,,,"<h4>Background</h4>Electronic health record (EHR) systems are used by clinicians to record patients' medical information, and support clinical activities such as prescribing. In England, healthcare professionals are advised to 'prescribe generically' because generic drugs are usually cheaper than branded alternatives, and have fixed reimbursement costs. 'Ghost-branded generics' are a new category of medicines savings, caused by prescribers specifying a manufacturer for a generic product, often resulting in a higher reimbursement price compared with the true generic.<h4>Aim</h4>To describe time trends and practice factors associated with excess medication costs from ghost-branded generic prescribing.<h4>Design and setting</h4>Retrospective cohort study of English GP prescribing data and EHR deployment data.<h4>Method</h4>A retrospective cohort study was conducted, based on data from the OpenPrescribing.net database from May 2013 to May 2019. Total spending on ghost-branded generics across England was calculated, and excess spend on ghost-branded generics calculated as a percentage of all spending on generics for every CCG and general practice in England, for every month in the study period.<h4>Results</h4>There were 31.8 million ghost-branded generic items and £9.5 million excess cost in 2018, compared with 7.45 million ghost-branded generic items and £1.3 million excess cost in 2014. Most excess costs were associated with one EHR, SystmOne, and it was identified that SystmOne offered ghost-branded generic options as the default. After informing the vendor, the authors monitored for subsequent change in costs, and report a rapid decrease in ghost-branded generic expenditure.<h4>Conclusion</h4>A design choice in a commonly used EHR has led to £9.5 million in avoidable excess prescribing costs for the NHS in 1 year. Notifying the vendor led to a change in user interface and a rapid, substantial spend reduction. This finding illustrates that EHR user interface design has a substantial impact on the quality, safety, and cost-effectiveness of clinical practice; this should be a priority for quantitative research.",,pdf:https://bjgp.org/content/bjgp/70/698/e636.full.pdf; doi:https://doi.org/10.3399/bjgp20X712313; html:https://europepmc.org/articles/PMC7425205; pdf:https://europepmc.org/articles/PMC7425205?pdf=render; doi:https://doi.org/10.3399/bjgp20x712313
 32430455,https://doi.org/10.1136/bmjopen-2020-038530,Evaluating the real-world implementation of the Family Nurse Partnership in England: protocol for a data linkage study.,"Cavallaro FL, Gilbert R, Wijlaars L, Kennedy E, Swarbrick A, van der Meulen J, Harron K.",,BMJ open,2020,2020-05-18,Y,Public Health; Community Child Health; Child Protection; Health Informatics,,,"<h4>Introduction</h4>Almost 20 000 babies are born to teenage mothers each year in England, with poorer outcomes for mothers and babies than among older mothers. A nurse home visitation programme in the USA was found to improve a wide range of outcomes for young mothers and their children. However, a randomised controlled trial in England found no effect on short-term primary outcomes, although cognitive development up to age 2 showed improvement. Our study will use linked routinely collected health, education and social care data to evaluate the real-world effects of the Family Nurse Partnership (FNP) on child outcomes up to age 7, with a focus on identifying whether the FNP works better for particular groups of families, thereby informing programme targeting and resource allocation.<h4>Methods and analysis</h4>We will construct a retrospective cohort of all women aged 13-24 years giving birth in English NHS hospitals between 2010 and 2017, linking information on mothers and children from FNP programme data, Hospital Episodes Statistics and the National Pupil Database. To assess the effectiveness of FNP, we will compare outcomes for eligible mothers ever and never enrolled in FNP, and their children, using two analysis strategies to adjust for measured confounding: propensity score matching and analyses adjusting for maternal characteristics up to enrolment/28 weeks gestation. Outcomes of interest include early childhood development, childhood unplanned hospital admissions for injury or maltreatment-related diagnoses and children in care. Subgroup analyses will determine whether the effect of FNP varied according to maternal characteristics (eg, age and education).<h4>Ethics and dissemination</h4>The Nottingham Research Ethics Committee approved this study. Mothers participating in FNP were supportive of our planned research. Results will inform policy-makers for targeting home visiting programmes. Methodological findings on the accuracy and reliability of cross-sectoral data linkage will be of interest to researchers.",,pdf:https://bmjopen.bmj.com/content/bmjopen/10/5/e038530.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-038530; html:https://europepmc.org/articles/PMC7239518; pdf:https://europepmc.org/articles/PMC7239518?pdf=render
-34244281,https://doi.org/10.1136/bmjopen-2021-049611,"Ethnicity and COVID-19 outcomes among healthcare workers in the UK: UK-REACH ethico-legal research, qualitative research on healthcare workers' experiences and stakeholder engagement protocol.","Gogoi M, Reed-Berendt R, Al-Oraibi A, Hassan O, Wobi F, Gupta A, Abubakar I, Dove E, Nellums LB, Pareek M, UK-REACH Collaborative Group.",,BMJ open,2021,2021-07-09,Y,Medical Ethics; Qualitative Research; Medical Law; Covid-19,,,"<h4>Introduction</h4>As the world continues to grapple with the COVID-19 pandemic, emerging evidence suggests that individuals from ethnic minority backgrounds may be disproportionately affected. The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers (UK-REACH) project has been initiated to generate rapid evidence on whether and why ethnicity affects COVID-19 diagnosis and clinical outcomes in healthcare workers (HCWs) in the UK, through five interlinked work packages/work streams, three of which form the basis of this protocol. The ethico-legal work (Work Package 3) aims to understand and address legal, ethical and acceptability issues around big data research; the HCWs' experiences study (Work Package 4) explores their work and personal experiences, perceptions of risk, support and coping mechanisms; the stakeholder engagement work (Work Package 5) aims to provide feedback and support with the formulation and dissemination of the project recommendations.<h4>Methods and analysis</h4>Work Package 3 has two different research strands: (A) desk-based doctrinal research; and (B) empirical qualitative research with key opinion leaders. For the empirical research, in-depth interviews will be conducted digitally and recorded with participants' permission. Recordings will be transcribed, coded and analysed using thematic analysis. In Work Package 4, online in-depth interviews and focus groups will be conducted with approximately 150 HCWs, from across the UK, and these will be recorded with participants' consent. The recordings will be transcribed and coded and data will be analysed using thematic analysis. Work Package 5 will achieve its objectives through regular group meetings and in-group discussions.<h4>Ethics and dissemination</h4>Ethical approval has been received from the London-Brighton & Sussex Research Ethics Committee of the Health Research Authority (Ref No 20/HRA/4718). Results of the study will be published in open-access journals, and disseminated through conference presentations, project website, stakeholder organisations, media and scientific advisory groups.<h4>Trial registration number</h4>ISRCTN11811602.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/7/e049611.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-049611; html:https://europepmc.org/articles/PMC8275361; pdf:https://europepmc.org/articles/PMC8275361?pdf=render
+39210026,https://doi.org/10.1038/s41562-024-01963-z,The genetic landscape of neuro-related proteins in human plasma.,"Repetto L, Chen J, Yang Z, Zhai R, Timmers PRHJ, Feng X, Li T, Yao Y, Maslov D, Timoshchuk A, Tu F, Twait EL, May-Wilson S, Muckian MD, Prins BP, Png G, Kooperberg C, Johansson Å, Hillary RF, Wheeler E, Pan L, He Y, Klasson S, Ahmad S, Peters JE, Gilly A, Karaleftheri M, Tsafantakis E, Haessler J, Gyllensten U, Harris SE, Wareham NJ, Göteson A, Lagging C, Ikram MA, van Duijn CM, Jern C, Landén M, Langenberg C, Deary IJ, Marioni RE, Enroth S, Reiner AP, Dedoussis G, Zeggini E, Sharapov S, Aulchenko YS, Butterworth AS, Mälarstig A, Wilson JF, Navarro P, Shen X.",,Nature human behaviour,2024,2024-08-29,N,,,,"Understanding the genetic basis of neuro-related proteins is essential for dissecting the molecular basis of human behavioural traits and the disease aetiology of neuropsychiatric disorders. Here the SCALLOP Consortium conducted a genome-wide association meta-analysis of over 12,000 individuals for 184 neuro-related proteins in human plasma. The analysis identified 125 cis-regulatory protein quantitative trait loci (cis-pQTL) and 164 trans-pQTL. The mapped pQTL capture on average 50% of each protein's heritability. At the cis-pQTL, multiple proteins shared a genetic basis with human behavioural traits such as alcohol and food intake, smoking and educational attainment, as well as neurological conditions and psychiatric disorders such as pain, neuroticism and schizophrenia. Integrating with established drug information, the causal inference analysis validated 52 out of 66 matched combinations of protein targets and diseases or side effects with available drugs while suggesting hundreds of repurposing and new therapeutic targets.",,doi:https://doi.org/10.1038/s41562-024-01963-z
 31196905,https://doi.org/10.1136/bmjopen-2019-028929,Recorded poor insight as a predictor of service use outcomes: cohort study of patients with first-episode psychosis in a large mental healthcare database.,"Ramu N, Kolliakou A, Sanyal J, Patel R, Stewart R.",,BMJ open,2019,2019-06-12,Y,Insight; Psychosis; Natural Language Processing; Mental Health Outcomes; Cris; Service Use Outcomes,Applied Analytics,,"<h4>Objectives</h4>To investigate recorded poor insight in relation to mental health and service use outcomes in a cohort with first-episode psychosis.<h4>Design</h4>We developed a natural language processing algorithm to ascertain statements of poor or diminished insight and tested this in a cohort of patients with first-episode psychosis.<h4>Setting</h4>The clinical record text at the South London and Maudsley National Health Service Trust in the UK was used.<h4>Participants</h4>We applied the algorithm to characterise a cohort of 2026 patients with first-episode psychosis attending an early intervention service.<h4>Primary and secondary outcome measures</h4>Recorded poor insight within 1 month of registration was investigated in relation to (1) incidence of psychiatric hospitalisation, (2) odds of legally enforced hospitalisation, (3) number of days spent as a mental health inpatient and (4) number of different antipsychotic agents prescribed; outcomes were measured over varying follow-up periods from 12 months to 60 months, adjusting for a range of sociodemographic and clinical covariates.<h4>Results</h4>Recorded poor insight, present in 48.9% of the sample, was positively associated with youngest and oldest age groups, unemployment and schizophrenia (compared with bipolar disorder) and was negatively associated with Asian ethnicity, married status, home ownership and recorded cannabis use. It was significantly associated with higher levels of all four outcomes over the succeeding 12 months. Associations with hospitalisation incidence and number of antipsychotics remained independently significant when measured over 60 and 48 months, respectively.<h4>Conclusions</h4>Recorded poor insight in people with recent onset psychosis predicted higher subsequent inpatient mental healthcare use. Improving insight might benefit patients' course of illness as well as reduce mental health service use.",,pdf:https://bmjopen.bmj.com/content/bmjopen/9/6/e028929.full.pdf; doi:https://doi.org/10.1136/bmjopen-2019-028929; html:https://europepmc.org/articles/PMC6577359; pdf:https://europepmc.org/articles/PMC6577359?pdf=render
+34244281,https://doi.org/10.1136/bmjopen-2021-049611,"Ethnicity and COVID-19 outcomes among healthcare workers in the UK: UK-REACH ethico-legal research, qualitative research on healthcare workers' experiences and stakeholder engagement protocol.","Gogoi M, Reed-Berendt R, Al-Oraibi A, Hassan O, Wobi F, Gupta A, Abubakar I, Dove E, Nellums LB, Pareek M, UK-REACH Collaborative Group.",,BMJ open,2021,2021-07-09,Y,Medical Ethics; Qualitative Research; Medical Law; Covid-19,,,"<h4>Introduction</h4>As the world continues to grapple with the COVID-19 pandemic, emerging evidence suggests that individuals from ethnic minority backgrounds may be disproportionately affected. The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers (UK-REACH) project has been initiated to generate rapid evidence on whether and why ethnicity affects COVID-19 diagnosis and clinical outcomes in healthcare workers (HCWs) in the UK, through five interlinked work packages/work streams, three of which form the basis of this protocol. The ethico-legal work (Work Package 3) aims to understand and address legal, ethical and acceptability issues around big data research; the HCWs' experiences study (Work Package 4) explores their work and personal experiences, perceptions of risk, support and coping mechanisms; the stakeholder engagement work (Work Package 5) aims to provide feedback and support with the formulation and dissemination of the project recommendations.<h4>Methods and analysis</h4>Work Package 3 has two different research strands: (A) desk-based doctrinal research; and (B) empirical qualitative research with key opinion leaders. For the empirical research, in-depth interviews will be conducted digitally and recorded with participants' permission. Recordings will be transcribed, coded and analysed using thematic analysis. In Work Package 4, online in-depth interviews and focus groups will be conducted with approximately 150 HCWs, from across the UK, and these will be recorded with participants' consent. The recordings will be transcribed and coded and data will be analysed using thematic analysis. Work Package 5 will achieve its objectives through regular group meetings and in-group discussions.<h4>Ethics and dissemination</h4>Ethical approval has been received from the London-Brighton & Sussex Research Ethics Committee of the Health Research Authority (Ref No 20/HRA/4718). Results of the study will be published in open-access journals, and disseminated through conference presentations, project website, stakeholder organisations, media and scientific advisory groups.<h4>Trial registration number</h4>ISRCTN11811602.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/7/e049611.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-049611; html:https://europepmc.org/articles/PMC8275361; pdf:https://europepmc.org/articles/PMC8275361?pdf=render
 35584845,https://doi.org/10.1136/bmj-2022-070904,Reporting guideline for the early stage clinical evaluation of decision support systems driven by artificial intelligence: DECIDE-AI.,"Vasey B, Nagendran M, Campbell B, Clifton DA, Collins GS, Denaxas S, Denniston AK, Faes L, Geerts B, Ibrahim M, Liu X, Mateen BA, Mathur P, McCradden MD, Morgan L, Ordish J, Rogers C, Saria S, Ting DSW, Watkinson P, Weber W, Wheatstone P, McCulloch P, DECIDE-AI expert group.",,BMJ (Clinical research ed.),2022,2022-05-18,Y,,,,,,pdf:https://www.bmj.com/content/bmj/377/bmj-2022-070904.full.pdf; doi:https://doi.org/10.1136/bmj-2022-070904; html:https://europepmc.org/articles/PMC9116198
-39210026,https://doi.org/10.1038/s41562-024-01963-z,The genetic landscape of neuro-related proteins in human plasma.,"Repetto L, Chen J, Yang Z, Zhai R, Timmers PRHJ, Feng X, Li T, Yao Y, Maslov D, Timoshchuk A, Tu F, Twait EL, May-Wilson S, Muckian MD, Prins BP, Png G, Kooperberg C, Johansson Å, Hillary RF, Wheeler E, Pan L, He Y, Klasson S, Ahmad S, Peters JE, Gilly A, Karaleftheri M, Tsafantakis E, Haessler J, Gyllensten U, Harris SE, Wareham NJ, Göteson A, Lagging C, Ikram MA, van Duijn CM, Jern C, Landén M, Langenberg C, Deary IJ, Marioni RE, Enroth S, Reiner AP, Dedoussis G, Zeggini E, Sharapov S, Aulchenko YS, Butterworth AS, Mälarstig A, Wilson JF, Navarro P, Shen X.",,Nature human behaviour,2024,2024-08-29,N,,,,"Understanding the genetic basis of neuro-related proteins is essential for dissecting the molecular basis of human behavioural traits and the disease aetiology of neuropsychiatric disorders. Here the SCALLOP Consortium conducted a genome-wide association meta-analysis of over 12,000 individuals for 184 neuro-related proteins in human plasma. The analysis identified 125 cis-regulatory protein quantitative trait loci (cis-pQTL) and 164 trans-pQTL. The mapped pQTL capture on average 50% of each protein's heritability. At the cis-pQTL, multiple proteins shared a genetic basis with human behavioural traits such as alcohol and food intake, smoking and educational attainment, as well as neurological conditions and psychiatric disorders such as pain, neuroticism and schizophrenia. Integrating with established drug information, the causal inference analysis validated 52 out of 66 matched combinations of protein targets and diseases or side effects with available drugs while suggesting hundreds of repurposing and new therapeutic targets.",,doi:https://doi.org/10.1038/s41562-024-01963-z
 34568827,https://doi.org/10.1093/schizbullopen/sgab041,Development and Validation of a Nonremission Risk Prediction Model in First-Episode Psychosis: An Analysis of 2 Longitudinal Studies.,"Leighton SP, Krishnadas R, Upthegrove R, Marwaha S, Steyerberg EW, Gkoutos GV, Broome MR, Liddle PF, Everard L, Singh SP, Freemantle N, Fowler D, Jones PB, Sharma V, Murray R, Wykes T, Drake RJ, Buchan I, Rogers S, Cavanagh J, Lewis SW, Birchwood M, Mallikarjun PK.",,Schizophrenia bulletin open,2021,2021-01-01,Y,Schizophrenia; Prognosis; Logistic regression; early intervention; Psychotic Disorders; Precision Medicine,,,"Psychosis is a major mental illness with first onset in young adults. The prognosis is poor in around half of the people affected, and difficult to predict. The few tools available to predict prognosis have major weaknesses which limit their use in clinical practice. We aimed to develop and validate a risk prediction model of symptom nonremission in first-episode psychosis. Our development cohort consisted of 1027 patients with first-episode psychosis recruited between 2005 and 2010 from 14 early intervention services across the National Health Service in England. Our validation cohort consisted of 399 patients with first-episode psychosis recruited between 2006 and 2009 from a further 11 English early intervention services. The one-year nonremission rate was 52% and 54% in the development and validation cohorts, respectively. Multivariable logistic regression was used to develop a risk prediction model for nonremission, which was externally validated. The prediction model showed good discrimination C-statistic of 0.73 (0.71, 0.75) and adequate calibration with intercept alpha of 0.12 (0.02, 0.22) and slope beta of 0.98 (0.85, 1.11). Our model improved the net-benefit by 15% at a risk threshold of 50% compared to the strategy of treating all, equivalent to 15 more detected nonremitted first-episode psychosis individuals per 100 without incorrectly classifying remitted cases. Once prospectively validated, our first episode psychosis prediction model could help identify patients at increased risk of nonremission at initial clinical contact.",,pdf:https://academic.oup.com/schizbullopen/article-pdf/2/1/sgab041/40430058/sgab041.pdf; doi:https://doi.org/10.1093/schizbullopen/sgab041; html:https://europepmc.org/articles/PMC8458108; pdf:https://europepmc.org/articles/PMC8458108?pdf=render
 35051442,https://doi.org/10.1016/j.jviromet.2022.114471,Reduced amplification efficiency of the RNA-dependent-RNA-polymerase target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests.,"Valley-Omar Z, Marais G, Iranzadeh A, Naidoo M, Korsman S, Maponga T, Hussey H, Davies MA, Boulle A, Doolabh D, Laubscher M, Wojno J, Deetlefs JD, Maritz J, Scott L, Msomi N, Naicker C, Tegally H, de Oliveira T, Bhiman J, Williamson C, Preiser W, Hardie D, Hsiao NY.",,Journal of virological methods,2022,2022-01-18,Y,Surveillance; Diagnostic test; South Africa; Covid-19; Sars-cov-2; Delta Variant,,,"Routine SARS-CoV-2 surveillance in the Western Cape region of South Africa (January-August 2021) found a reduced RT-PCR amplification efficiency of the RdRp-gene target of the Seegene, Allplex 2019-nCoV diagnostic assay from June 2021 when detecting the Delta variant. We investigated whether the reduced amplification efficiency denoted by an increased RT-PCR cycle threshold value (RΔE) can be used as an indirect measure of SARS-CoV-2 Delta variant prevalence. We found a significant increase in the median RΔE for patient samples tested from June 2021, which coincided with the emergence of the SARS-CoV-2 Delta variant within our sample set. Whole genome sequencing on a subset of patient samples identified a highly conserved G15451A, non-synonymous mutation exclusively within the RdRp gene of Delta variants, which may cause reduced RT-PCR amplification efficiency. While whole genome sequencing plays an important in identifying novel SARS-CoV-2 variants, monitoring RΔE value can serve as a useful surrogate for rapid tracking of Delta variant prevalence.",,doi:https://doi.org/10.1016/j.jviromet.2022.114471; doi:https://doi.org/10.1016/j.jviromet.2022.114471; html:https://europepmc.org/articles/PMC8763409; pdf:https://europepmc.org/articles/PMC8763409?pdf=render
 34216337,https://doi.org/10.1007/s10552-021-01466-6,"Physical activity in relation to circulating hormone concentrations in 117,100 men in UK Biobank.","Watts EL, Perez-Cornago A, Doherty A, Allen NE, Fensom GK, Tin Tin S, Key TJ, Travis RC.",,Cancer causes & control : CCC,2021,2021-07-03,Y,Testosterone; IGF-I; Physical Activity; Accelerometer; Shbg; Uk Biobank,,,"<h4>Purpose</h4>Physical activity may reduce the risk of some types of cancer in men. Biological mechanisms may involve changes in hormone concentrations; however, this relationship is not well established. Therefore, we aimed to investigate the associations of physical activity with circulating insulin-like growth factor-I (IGF-I), sex hormone-binding globulin (SHBG, which modifies sex hormone activity), and total and free testosterone concentrations, and the extent these associations might be mediated by body mass index (BMI).<h4>Methods</h4>Circulating concentrations of these hormones and anthropometric measurements and self-reported physical activity data were available for 117,100 healthy male UK Biobank participants at recruitment. Objectively measured accelerometer physical activity levels were also collected on average 5.7 years after recruitment in 28,000 men. Geometric means of hormone concentrations were estimated using multivariable-adjusted analysis of variance, with and without adjustment for BMI.<h4>Results</h4>The associations between physical activity and hormones were modest and similar for objectively measured (accelerometer) and self-reported physical activity. Compared to men with the lowest objectively measured physical activity, men with high physical activity levels had 14% and 8% higher concentrations of SHBG and total testosterone, respectively, and these differences were attenuated to 6% and 3% following adjustment for BMI.<h4>Conclusion</h4>Our results suggest that the associations of physical activity with the hormones investigated are, at most, modest; and following adjustment for BMI, the small associations with SHBG and total testosterone were largely attenuated. Therefore, it is unlikely that changes in these circulating hormones explain the associations of physical activity with risk of cancer either independently or via BMI.",,pdf:https://link.springer.com/content/pdf/10.1007/s10552-021-01466-6.pdf; doi:https://doi.org/10.1007/s10552-021-01466-6; html:https://europepmc.org/articles/PMC8492588; pdf:https://europepmc.org/articles/PMC8492588?pdf=render
 32032817,https://doi.org/10.1016/j.nicl.2020.102172,Distinguishing between paediatric brain tumour types using multi-parametric magnetic resonance imaging and machine learning: A multi-site study.,"Grist JT, Withey S, MacPherson L, Oates A, Powell S, Novak J, Abernethy L, Pizer B, Grundy R, Bailey S, Mitra D, Arvanitis TN, Auer DP, Avula S, Peet AC.",,NeuroImage. Clinical,2020,2020-01-23,Y,Diffusion; Perfusion; Machine Learning,Understanding the Causes of Disease,cancer and neoplasms,"The imaging and subsequent accurate diagnosis of paediatric brain tumours presents a radiological challenge, with magnetic resonance imaging playing a key role in providing tumour specific imaging information. Diffusion weighted and perfusion imaging are commonly used to aid the non-invasive diagnosis of children's brain tumours, but are usually evaluated by expert qualitative review. Quantitative studies are mainly single centre and single modality. The aim of this work was to combine multi-centre diffusion and perfusion imaging, with machine learning, to develop machine learning based classifiers to discriminate between three common paediatric tumour types. The results show that diffusion and perfusion weighted imaging of both the tumour and whole brain provide significant features which differ between tumour types, and that combining these features gives the optimal machine learning classifier with >80% predictive precision. This work represents a step forward to aid in the non-invasive diagnosis of paediatric brain tumours, using advanced clinical imaging.",Grist et al. team trained computers to analyse brain images from children for identification of tumours. They’ve shown that applying analytical methods to enable machine distinguishes between the entire brain area and the tumour area in the images more than 80% improves how machine analyses the image to identify exact tumour area. ,doi:https://doi.org/10.1016/j.nicl.2020.102172; doi:https://doi.org/10.1016/j.nicl.2020.102172; html:https://europepmc.org/articles/PMC7005468; pdf:https://europepmc.org/articles/PMC7005468?pdf=render
-33602244,https://doi.org/10.1186/s12916-021-01924-7,The impact of local and national restrictions in response to COVID-19 on social contacts in England: a longitudinal natural experiment.,"Jarvis CI, Gimma A, van Zandvoort K, Wong KLM, CMMID COVID-19 working group, Edmunds WJ.",,BMC medicine,2021,2021-02-19,Y,Pandemic; England; United Kingdom; Disease Outbreak; Non-pharmaceutical Interventions; Covid-19; Contact Survey; Lockdowns,,,"<h4>Background</h4>England's COVID-19 response transitioned from a national lockdown to localised interventions. In response to rising cases, these were supplemented by national restrictions on contacts (the Rule of Six), then 10 pm closing for bars and restaurants, and encouragement to work from home. These were quickly followed by a 3-tier system applying different restrictions in different localities. As cases continued to rise, a second national lockdown was declared. We used a national survey to quantify the impact of these restrictions on epidemiologically relevant contacts.<h4>Methods</h4>We compared paired measures on setting-specific contacts before and after each restriction started and tested for differences using paired permutation tests on the mean change in contacts and the proportion of individuals decreasing their contacts.<h4>Results</h4>Following the imposition of each measure, individuals tended to report fewer contacts than they had before. However, the magnitude of the changes was relatively small and variable. For instance, although early closure of bars and restaurants appeared to have no measurable effect on contacts, the work from home directive reduced mean daily work contacts by 0.99 (95% confidence interval CI] 0.03-1.94), and the Rule of Six reduced non-work and school contacts by a mean of 0.25 (0.01-0.5) per day. Whilst Tier 3 appeared to also reduce non-work and school contacts, the evidence for an effect of the lesser restrictions (Tiers 1 and 2) was much weaker. There may also have been some evidence of saturation of effects, with those who were in Tier 1 (least restrictive) reducing their contacts markedly when they entered lockdown, which was not reflected in similar changes in those who were already under tighter restrictions (Tiers 2 and 3).<h4>Conclusions</h4>The imposition of various local and national measures in England during the summer and autumn of 2020 has gradually reduced contacts. However, these changes are smaller than the initial lockdown in March. This may partly be because many individuals were already starting from a lower number of contacts.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-021-01924-7; doi:https://doi.org/10.1186/s12916-021-01924-7; html:https://europepmc.org/articles/PMC7892289; pdf:https://europepmc.org/articles/PMC7892289?pdf=render
 33879569,https://doi.org/10.1073/pnas.2009808118,Mendelian randomization identifies blood metabolites previously linked to midlife cognition as causal candidates in Alzheimer's disease.,"Lord J, Jermy B, Green R, Wong A, Xu J, Legido-Quigley C, Dobson R, Richards M, Proitsi P.",,Proceedings of the National Academy of Sciences of the United States of America,2021,2021-04-01,Y,Biomarkers; Alzheimer’s disease; Metabolomics; Causality; Mendelian Randomization,,,"There are currently no disease-modifying treatments for Alzheimer's disease (AD), and an understanding of preclinical causal biomarkers to help target disease pathogenesis in the earliest phases remains elusive. Here, we investigated whether 19 metabolites previously associated with midlife cognition-a preclinical predictor of AD-translate to later clinical risk, using Mendelian randomization (MR) to tease out AD-specific causal relationships. Summary statistics from the largest genome-wide association studies (GWASs) for AD and metabolites were used to perform bidirectional univariable MR. Bayesian model averaging (BMA) was additionally performed to address high correlation between metabolites and identify metabolite combinations that may be on the AD causal pathway. Univariable MR indicated four extra-large high-density lipoproteins (XL.HDL) on the causal pathway to AD: free cholesterol (XL.HDL.FC: 95% CI = 0.78 to 0.94), total lipids (XL.HDL.L: 95% CI = 0.80 to 0.97), phospholipids (XL.HDL.PL: 95% CI = 0.81 to 0.97), and concentration of XL.HDL particles (95% CI = 0.79 to 0.96), significant at an adjusted <i>P</i> < 0.009. MR-BMA corroborated XL.HDL.FC to be among the top three causal metabolites, in addition to total cholesterol in XL.HDL (XL.HDL.C) and glycoprotein acetyls (GP). Both XL.HDL.C and GP demonstrated suggestive univariable evidence of causality (<i>P</i> < 0.05), and GP successfully replicated within an independent dataset. This study offers insight into the causal relationship between metabolites demonstrating association with midlife cognition and AD. It highlights GP in addition to several XL.HDLs-particularly XL.HDL.FC-as causal candidates warranting further investigation. As AD pathology is thought to develop decades prior to symptom onset, expanding on these findings could inform risk reduction strategies.",,doi:https://doi.org/10.1073/pnas.2009808118; doi:https://doi.org/10.1073/pnas.2009808118; html:https://europepmc.org/articles/PMC8072203; pdf:https://europepmc.org/articles/PMC8072203?pdf=render
+33602244,https://doi.org/10.1186/s12916-021-01924-7,The impact of local and national restrictions in response to COVID-19 on social contacts in England: a longitudinal natural experiment.,"Jarvis CI, Gimma A, van Zandvoort K, Wong KLM, CMMID COVID-19 working group, Edmunds WJ.",,BMC medicine,2021,2021-02-19,Y,Pandemic; England; United Kingdom; Disease Outbreak; Non-pharmaceutical Interventions; Covid-19; Contact Survey; Lockdowns,,,"<h4>Background</h4>England's COVID-19 response transitioned from a national lockdown to localised interventions. In response to rising cases, these were supplemented by national restrictions on contacts (the Rule of Six), then 10 pm closing for bars and restaurants, and encouragement to work from home. These were quickly followed by a 3-tier system applying different restrictions in different localities. As cases continued to rise, a second national lockdown was declared. We used a national survey to quantify the impact of these restrictions on epidemiologically relevant contacts.<h4>Methods</h4>We compared paired measures on setting-specific contacts before and after each restriction started and tested for differences using paired permutation tests on the mean change in contacts and the proportion of individuals decreasing their contacts.<h4>Results</h4>Following the imposition of each measure, individuals tended to report fewer contacts than they had before. However, the magnitude of the changes was relatively small and variable. For instance, although early closure of bars and restaurants appeared to have no measurable effect on contacts, the work from home directive reduced mean daily work contacts by 0.99 (95% confidence interval CI] 0.03-1.94), and the Rule of Six reduced non-work and school contacts by a mean of 0.25 (0.01-0.5) per day. Whilst Tier 3 appeared to also reduce non-work and school contacts, the evidence for an effect of the lesser restrictions (Tiers 1 and 2) was much weaker. There may also have been some evidence of saturation of effects, with those who were in Tier 1 (least restrictive) reducing their contacts markedly when they entered lockdown, which was not reflected in similar changes in those who were already under tighter restrictions (Tiers 2 and 3).<h4>Conclusions</h4>The imposition of various local and national measures in England during the summer and autumn of 2020 has gradually reduced contacts. However, these changes are smaller than the initial lockdown in March. This may partly be because many individuals were already starting from a lower number of contacts.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-021-01924-7; doi:https://doi.org/10.1186/s12916-021-01924-7; html:https://europepmc.org/articles/PMC7892289; pdf:https://europepmc.org/articles/PMC7892289?pdf=render
 35477868,https://doi.org/10.1136/bmjopen-2021-057579,Public opinion on sharing data from health services for clinical and research purposes without explicit consent: an anonymous online survey in the UK.,"Jones LA, Nelder JR, Fryer JM, Alsop PH, Geary MR, Prince M, Cardinal RN.",,BMJ open,2022,2022-04-27,Y,Information management; Mental health; Health Policy; Health Informatics,,,"<h4>Objectives</h4>UK National Health Service/Health and Social Care (NHS/HSC) data are variably shared between healthcare organisations for direct care, and increasingly de-identified for research. Few large-scale studies have examined public opinion on sharing, including of mental health (MH) versus physical health (PH) data. We measured data sharing preferences.<h4>Design/setting/interventions/outcomes</h4>Pre-registered anonymous online survey, measuring expressed preferences, recruiting February to September 2020. Participants were randomised to one of three framing statements regarding MH versus PH data.<h4>Participants</h4>Open to all UK residents. Participants numbered 29 275; 40% had experienced an MH condition.<h4>Results</h4>Most (76%) supported identifiable data sharing for direct clinical care without explicit consent, but 20% opposed this. Preference for clinical/identifiable sharing decreased with geographical distance and was slightly less for MH than PH data, with small framing effects. Preference for research/de-identified data sharing without explicit consent showed the same small PH/MH and framing effects, plus greater preference for sharing structured data than de-identified free text. There was net support for research sharing to the NHS, academic institutions, and national research charities, net ambivalence about sharing to profit-making companies researching treatments, and net opposition to sharing to other companies (similar to sharing publicly). De-identified linkage to non-health data was generally supported, except to data held by private companies. We report demographic influences on preference. A majority (89%) supported a single NHS mechanism to choose uses of their data. Support for data sharing increased during COVID-19.<h4>Conclusions</h4>Support for healthcare data sharing for direct care without explicit consent is broad but not universal. There is net support for the sharing of de-identified data for research to the NHS, academia, and the charitable sector, but not the commercial sector. A single national NHS-hosted system for patients to control the use of their NHS data for clinical purposes and for research would have broad support.<h4>Trial registration number</h4>ISRCTN37444142.",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/4/e057579.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-057579; html:https://europepmc.org/articles/PMC9058801; pdf:https://europepmc.org/articles/PMC9058801?pdf=render
 31862893,https://doi.org/10.1038/s41467-019-13848-1,Genomic risk score offers predictive performance comparable to clinical risk factors for ischaemic stroke.,"Abraham G, Malik R, Yonova-Doing E, Salim A, Wang T, Danesh J, Butterworth AS, Howson JMM, Inouye M, Dichgans M.",,Nature communications,2019,2019-12-20,Y,,,,"Recent genome-wide association studies in stroke have enabled the generation of genomic risk scores (GRS) but their predictive power has been modest compared to established stroke risk factors. Here, using a meta-scoring approach, we develop a metaGRS for ischaemic stroke (IS) and analyse this score in the UK Biobank (n = 395,393; 3075 IS events by age 75). The metaGRS hazard ratio for IS (1.26, 95% CI 1.22-1.31 per metaGRS standard deviation) doubles that of a previous GRS, identifying a subset of individuals at monogenic levels of risk: the top 0.25% of metaGRS have three-fold risk of IS. The metaGRS is similarly or more predictive compared to several risk factors, such as family history, blood pressure, body mass index, and smoking. We estimate the reductions needed in modifiable risk factors for individuals with different levels of genomic risk and suggest that, for individuals with high metaGRS, achieving risk factor levels recommended by current guidelines may be insufficient to mitigate risk.",,pdf:https://www.nature.com/articles/s41467-019-13848-1.pdf; doi:https://doi.org/10.1038/s41467-019-13848-1; html:https://europepmc.org/articles/PMC6925280; pdf:https://europepmc.org/articles/PMC6925280?pdf=render
 33436814,https://doi.org/10.1038/s41598-020-80457-0,A natural language processing approach for identifying temporal disease onset information from mental healthcare text.,"Viani N, Botelle R, Kerwin J, Yin L, Patel R, Stewart R, Velupillai S.",,Scientific reports,2021,2021-01-12,Y,,,,"Receiving timely and appropriate treatment is crucial for better health outcomes, and research on the contribution of specific variables is essential. In the mental health domain, an important research variable is the date of psychosis symptom onset, as longer delays in treatment are associated with worse intervention outcomes. The growing adoption of electronic health records (EHRs) within mental health services provides an invaluable opportunity to study this problem at scale retrospectively. However, disease onset information is often only available in open text fields, requiring natural language processing (NLP) techniques for automated analyses. Since this variable can be documented at different points during a patient's care, NLP methods that model clinical and temporal associations are needed. We address the identification of psychosis onset by: 1) manually annotating a corpus of mental health EHRs with disease onset mentions, 2) modelling the underlying NLP problem as a paragraph classification approach, and 3) combining multiple onset paragraphs at the patient level to generate a ranked list of likely disease onset dates. For 22/31 test patients (71%) the correct onset date was found among the top-3 NLP predictions. The proposed approach was also applied at scale, allowing an onset date to be estimated for 2483 patients.",,pdf:https://www.nature.com/articles/s41598-020-80457-0.pdf; doi:https://doi.org/10.1038/s41598-020-80457-0; html:https://europepmc.org/articles/PMC7804184; pdf:https://europepmc.org/articles/PMC7804184?pdf=render
 34212120,https://doi.org/10.1136/bmjpo-2021-001112,"Incorporating parent, former patient and clinician perspectives in the design of a national UK double-cluster, randomised controlled trial addressing uncertainties in preterm nutrition.","Lammons W, Moss B, Battersby C, Cornelius V, Babalis D, Modi N.",,BMJ paediatrics open,2021,2021-06-15,Y,Neonatology; Qualitative Research; Health Services Research,,,"<h4>Background</h4>Comparative effectiveness randomised controlled trials are powerful tools to resolve uncertainties in existing treatments and care processes. We sought parent and patient perspectives on the design of a planned national, double-cluster randomised controlled trial (COLLABORATE) to resolve two longstanding uncertainties in preterm nutrition.<h4>Methods</h4>We used qualitative focus groups and interviews with parents, former patients and clinicians. We followed the Consolidated Criteria for Reporting Qualitative Research checklist and conducted framework analysis, a specific methodology within thematic analysis.<h4>Results</h4>We identified support for the trial's methodology and vision, and elicited themes illustrating parents' emotional needs in relation to clinical research. These were: relieving the pressure on mothers to breastfeed; opt-out consent as reducing parent stress; the desire for research to be a partnership between clinicians, parents and researchers; the value of presenting trial information in a collaborative tone; and in a format that allows assimilation by parents at their own pace. We identified anxiety and cognitive dissonance among some clinicians in which they recognised the uncertainties that justify the trial but felt unable to participate because of their strongly held views.<h4>Conclusions</h4>The early involvement of parents and former patients identified the centrality of parents' emotional needs in the design of comparative effectiveness research. These insights have been incorporated into trial enrolment processes and information provided to participants. Specific outputs were a two-sided leaflet providing very brief as well as more detailed information, and use of language that parents perceive as inclusive and participatory. Further work is warranted to support clinicians to address personal biases that inhibit trial participation.",,pdf:https://bmjpaedsopen.bmj.com/content/bmjpo/5/1/e001112.full.pdf; doi:https://doi.org/10.1136/bmjpo-2021-001112; html:https://europepmc.org/articles/PMC8208018; pdf:https://europepmc.org/articles/PMC8208018?pdf=render
 34750105,https://doi.org/10.3399/bjgp.2021.0380,OpenSAFELY NHS Service Restoration Observatory 1: primary care clinical activity in England during the first wave of COVID-19.,"Curtis HJ, MacKenna B, Croker R, Inglesby P, Walker AJ, Morley J, Mehrkar A, Morton CE, Bacon S, Hickman G, Bates C, Evans D, Ward T, Cockburn J, Davy S, Bhaskaran K, Schultze A, Rentsch CT, Williamson EJ, Hulme WJ, McDonald HI, Tomlinson L, Mathur R, Drysdale H, Eggo RM, Wing K, Wong AY, Forbes H, Parry J, Hester F, Harper S, Evans SJ, Douglas IJ, Smeeth L, Goldacre B, (The OpenSAFELY Collaborative).",,The British journal of general practice : the journal of the Royal College of General Practitioners,2022,2021-12-31,Y,Primary Health Care; General Practice; Electronic Health Records; Covid-19,,,"<h4>Background</h4>The COVID-19 pandemic has disrupted healthcare activity. The NHS stopped non-urgent work in March 2020, later recommending services be restored to near-normal levels before winter where possible.<h4>Aim</h4>To describe the volume and variation of coded clinical activity in general practice, taking respiratory disease and laboratory procedures as examples.<h4>Design and setting</h4>Working on behalf of NHS England, a cohort study was conducted of 23.8 million patient records in general practice, <i>in situ</i> using OpenSAFELY.<h4>Method</h4>Activity using Clinical Terms Version 3 codes and keyword searches from January 2019 to September 2020 are described.<h4>Results</h4>Activity recorded in general practice declined during the pandemic, but largely recovered by September. There was a large drop in coded activity for laboratory tests, with broad recovery to pre-pandemic levels by September. One exception was the international normalised ratio test, with a smaller reduction (median tests per 1000 patients in 2020: February 8.0; April 6.2; September 6.9). The pattern of recording for respiratory symptoms was less affected, following an expected seasonal pattern and classified as 'no change'. Respiratory infections exhibited a sustained drop, not returning to pre-pandemic levels by September. Asthma reviews experienced a small drop but recovered, whereas chronic obstructive pulmonary disease reviews remained below baseline.<h4>Conclusion</h4>An open-source software framework was delivered to describe trends and variation in clinical activity across an unprecedented scale of primary care data. The COVD-19 pandemic led to a substantial change in healthcare activity. Most laboratory tests showed substantial reduction, largely recovering to near-normal levels by September, with some important tests less affected and recording of respiratory disease codes was mixed.",,doi:https://doi.org/10.3399/bjgp.2021.0380; doi:https://doi.org/10.3399/BJGP.2021.0380; html:https://europepmc.org/articles/PMC8589464; pdf:https://europepmc.org/articles/PMC8589464?pdf=render
+32546850,https://doi.org/10.1038/s41598-020-66737-9,Genetic aetiology of self-harm ideation and behaviour.,"Campos AI, Verweij KJH, Statham DJ, Madden PAF, Maciejewski DF, Davis KAS, John A, Hotopf M, Heath AC, Martin NG, Rentería ME.",,Scientific reports,2020,2020-06-16,Y,,,,"Family studies have identified a heritable component to self-harm that is partially independent from comorbid psychiatric disorders. However, the genetic aetiology of broad sense (non-suicidal and suicidal) self-harm has not been characterised on the molecular level. In addition, controversy exists about the degree to which suicidal and non-suicidal self-harm share a common genetic aetiology. In the present study, we conduct genome-wide association studies (GWAS) on lifetime self-harm ideation and self-harm behaviour (i.e. any lifetime self-harm act regardless of suicidal intent) using data from the UK Biobank (n > 156,000). We also perform genome wide gene-based tests and characterize the SNP heritability and genetic correlations between these traits. Finally, we test whether polygenic risk scores (PRS) for self-harm ideation and self-harm behaviour predict suicide attempt, suicide thoughts and non-suicidal self-harm (NSSH) in an independent target sample of 8,703 Australian adults. Our GWAS results identified one genome-wide significant locus associated with each of the two phenotypes. SNP heritability (h<sub>snp</sub><sup>2</sup>) estimates were ~10%, and both traits were highly genetically correlated (LDSC r<sub>g</sub> > 0.8). Gene-based tests identified seven genes associated with self-harm ideation and four with self-harm behaviour. Furthermore, in the target sample, PRS for self-harm ideation were significantly associated with suicide thoughts and NSSH, and PRS for self-harm behaviour predicted suicide thoughts and suicide attempt. Follow up regressions identified a shared genetic aetiology between NSSH and suicide thoughts, and between suicide thoughts and suicide attempt. Evidence for shared genetic aetiology between NSSH and suicide attempt was not statistically significant.",,pdf:https://www.nature.com/articles/s41598-020-66737-9.pdf; doi:https://doi.org/10.1038/s41598-020-66737-9; html:https://europepmc.org/articles/PMC7297971; pdf:https://europepmc.org/articles/PMC7297971?pdf=render
 34503493,https://doi.org/10.1186/s12916-021-02107-0,"Estimating the impact of reopening schools on the reproduction number of SARS-CoV-2 in England, using weekly contact survey data.","Munday JD, Jarvis CI, Gimma A, Wong KLM, van Zandvoort K, CMMID COVID-19 Working Group, Funk S, Edmunds WJ.",,BMC medicine,2021,2021-09-10,Y,School Closure; Reproduction Number; Social Contacts; Covid-19; Sars-cov-2; Comix,,,"<h4>Background</h4>Schools were closed in England on 4 January 2021 as part of increased national restrictions to curb transmission of SARS-CoV-2. The UK government reopened schools on 8 March. Although there was evidence of lower individual-level transmission risk amongst children compared to adults, the combined effects of this with increased contact rates in school settings and the resulting impact on the overall transmission rate in the population were not clear.<h4>Methods</h4>We measured social contacts of > 5000 participants weekly from March 2020, including periods when schools were both open and closed, amongst other restrictions. We combined these data with estimates of the susceptibility and infectiousness of children compared with adults to estimate the impact of reopening schools on the reproduction number.<h4>Results</h4>Our analysis indicates that reopening all schools under the same measures as previous periods that combined lockdown with face-to-face schooling would be likely to increase the reproduction number substantially. Assuming a baseline of 0.8, we estimated a likely increase to between 1.0 and 1.5 with the reopening of all schools or to between 0.9 and 1.2 reopening primary or secondary schools alone.<h4>Conclusion</h4>Our results suggest that reopening schools would likely halt the fall in cases observed between January and March 2021 and would risk a return to rising infections, but these estimates relied heavily on the latest estimates or reproduction number and the validity of the susceptibility and infectiousness profiles we used at the time of reopening.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-021-02107-0; doi:https://doi.org/10.1186/s12916-021-02107-0; html:https://europepmc.org/articles/PMC8428960; pdf:https://europepmc.org/articles/PMC8428960?pdf=render
 37221222,https://doi.org/10.1038/s41397-023-00307-w,SLCO1B1*5 is protective against non-senile cataracts in cohort prescribed statins: analysis in a British-South Asian cohort.,"Magavern EF, van Heel DA, Genes & Health Research Team, Smedley D, Caulfield MJ.",,The pharmacogenomics journal,2023,2023-05-23,Y,,,,"<h4>Background</h4>Reported association between statin use and cataract risk is controversial. The SLCO1B1 gene encodes a transport protein responsible for statin clearance. The aim of this study was to investigate a possible association between the SLCO1B1*5 reduced function variant and cataract risk in statin users of South Asian ethnicity.<h4>Methods</h4>The Genes & Health cohort consists of British-Bangladeshi and British-Pakistani participants from East London, Manchester and Bradford, UK. SLCO1B1*5 genotype was assessed with the Illumina GSAMD-24v3-0-EA chip. Medication data from primary care health record linkage was used to compare those who had regularly used statins compared to those who had not. Multivariable logistic regression was used to test for association between statin use and cataracts, adjusting for population characteristics and potential confounders in 36,513 participants. Multivariable logistic regression was used to test association between SLCO1B1*5 heterozygotes or homozygotes and cataracts, in subgroups having been regularly prescribed statins versus not.<h4>Results</h4>Statins were prescribed to 35% (12,704) of participants (average age 41 years old, 45% male). Non-senile cataract was diagnosed in 5% (1686) of participants. An apparent association between statins and non-senile cataract (12% in statin users and 0.8% in non-statin users) was negated by inclusion of confounders. In those prescribed a statin, presence of the SLCO1B1*5 genotype was independently associated with a decreased risk of non-senile cataract (OR 0.7 (CI 0.5-0.9, p 0.007)).<h4>Conclusions</h4>Our findings suggest that there is no independent association between statin use and non-senile cataract risk after adjusting for confounders. Among statin users, the SLCO1B1*5 genotype is associated with a 30% risk reduction of non-senile cataracts. Stratification of on-drug cohorts by validated pharmacogenomic variants is a useful tool to support or repudiate adverse drug events in observational cohorts.",,pdf:https://www.nature.com/articles/s41397-023-00307-w.pdf; doi:https://doi.org/10.1038/s41397-023-00307-w; html:https://europepmc.org/articles/PMC10506906; pdf:https://europepmc.org/articles/PMC10506906?pdf=render
-32546850,https://doi.org/10.1038/s41598-020-66737-9,Genetic aetiology of self-harm ideation and behaviour.,"Campos AI, Verweij KJH, Statham DJ, Madden PAF, Maciejewski DF, Davis KAS, John A, Hotopf M, Heath AC, Martin NG, Rentería ME.",,Scientific reports,2020,2020-06-16,Y,,,,"Family studies have identified a heritable component to self-harm that is partially independent from comorbid psychiatric disorders. However, the genetic aetiology of broad sense (non-suicidal and suicidal) self-harm has not been characterised on the molecular level. In addition, controversy exists about the degree to which suicidal and non-suicidal self-harm share a common genetic aetiology. In the present study, we conduct genome-wide association studies (GWAS) on lifetime self-harm ideation and self-harm behaviour (i.e. any lifetime self-harm act regardless of suicidal intent) using data from the UK Biobank (n > 156,000). We also perform genome wide gene-based tests and characterize the SNP heritability and genetic correlations between these traits. Finally, we test whether polygenic risk scores (PRS) for self-harm ideation and self-harm behaviour predict suicide attempt, suicide thoughts and non-suicidal self-harm (NSSH) in an independent target sample of 8,703 Australian adults. Our GWAS results identified one genome-wide significant locus associated with each of the two phenotypes. SNP heritability (h<sub>snp</sub><sup>2</sup>) estimates were ~10%, and both traits were highly genetically correlated (LDSC r<sub>g</sub> > 0.8). Gene-based tests identified seven genes associated with self-harm ideation and four with self-harm behaviour. Furthermore, in the target sample, PRS for self-harm ideation were significantly associated with suicide thoughts and NSSH, and PRS for self-harm behaviour predicted suicide thoughts and suicide attempt. Follow up regressions identified a shared genetic aetiology between NSSH and suicide thoughts, and between suicide thoughts and suicide attempt. Evidence for shared genetic aetiology between NSSH and suicide attempt was not statistically significant.",,pdf:https://www.nature.com/articles/s41598-020-66737-9.pdf; doi:https://doi.org/10.1038/s41598-020-66737-9; html:https://europepmc.org/articles/PMC7297971; pdf:https://europepmc.org/articles/PMC7297971?pdf=render
 36245269,https://doi.org/10.15252/embj.2022111857,Cryo-EM structures of perforin-2 in isolation and assembled on a membrane suggest a mechanism for pore formation.,"Yu X, Ni T, Munson G, Zhang P, Gilbert RJC.",,The EMBO journal,2022,2022-10-17,Y,Cryo-electron Tomography; Cryo-em; Subtomogram Averaging; Pore-forming Protein; Perforin-2,,,"Perforin-2 (PFN2, MPEG1) is a key pore-forming protein in mammalian innate immunity restricting intracellular bacteria proliferation. It forms a membrane-bound pre-pore complex that converts to a pore-forming structure upon acidification; but its mechanism of conformational transition has been debated. Here we used cryo-electron microscopy, tomography and subtomogram averaging to determine structures of PFN2 in pre-pore and pore conformations in isolation and bound to liposomes. In isolation and upon acidification, the pre-assembled complete pre-pore rings convert to pores in both flat ring and twisted conformations. On membranes, in situ assembled PFN2 pre-pores display various degrees of completeness; whereas PFN2 pores are mainly incomplete arc structures that follow the same subunit packing arrangements as found in isolation. Both assemblies on membranes use their P2 β-hairpin for binding to the lipid membrane surface. Overall, these structural snapshots suggest a molecular mechanism for PFN2 pre-pore to pore transition on a targeted membrane, potentially using the twisted pore as an intermediate or alternative state to the flat conformation, with the capacity to cause bilayer distortion during membrane insertion.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.15252/embj.2022111857; doi:https://doi.org/10.15252/embj.2022111857; html:https://europepmc.org/articles/PMC9713709; pdf:https://europepmc.org/articles/PMC9713709?pdf=render
 32591531,https://doi.org/10.1038/s41467-020-16969-0,Genetic drug target validation using Mendelian randomisation.,"Schmidt AF, Finan C, Gordillo-Marañón M, Asselbergs FW, Freitag DF, Patel RS, Tyl B, Chopade S, Faraway R, Zwierzyna M, Hingorani AD.",,Nature communications,2020,2020-06-26,Y,,,,"Mendelian randomisation (MR) analysis is an important tool to elucidate the causal relevance of environmental and biological risk factors for disease. However, causal inference is undermined if genetic variants used to instrument a risk factor also influence alternative disease-pathways (horizontal pleiotropy). Here we report how the 'no horizontal pleiotropy assumption' is strengthened when proteins are the risk factors of interest. Proteins are typically the proximal effectors of biological processes encoded in the genome. Moreover, proteins are the targets of most medicines, so MR studies of drug targets are becoming a fundamental tool in drug development. To enable such studies, we introduce a mathematical framework that contrasts MR analysis of proteins with that of risk factors located more distally in the causal chain from gene to disease. We illustrate key model decisions and introduce an analytical framework for maximising power and evaluating the robustness of analyses.",,pdf:https://www.nature.com/articles/s41467-020-16969-0.pdf; doi:https://doi.org/10.1038/s41467-020-16969-0; html:https://europepmc.org/articles/PMC7320010; pdf:https://europepmc.org/articles/PMC7320010?pdf=render
 33617936,https://doi.org/10.1016/j.jhin.2021.02.012,Global and national estimates of the number of healthcare workers at high risk of SARS-CoV-2 infection.,"McCarthy CV, Sandmann FG, CMMID COVID-19 Working Group, Jit M.",,The Journal of hospital infection,2021,2021-02-20,Y,,,,,,pdf:http://www.journalofhospitalinfection.com/article/S0195670121000712/pdf; doi:https://doi.org/10.1016/j.jhin.2021.02.012; html:https://europepmc.org/articles/PMC7896121; pdf:https://europepmc.org/articles/PMC7896121?pdf=render
@@ -2405,16 +2407,16 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 31113941,https://doi.org/10.1038/s41467-019-10417-4,Author Correction: Towards a data-integrated cell.,"Malod-Dognin N, Petschnigg J, Windels SFL, Povh J, Hemingway H, Ketteler R, Pržulj N.",,Nature communications,2019,2019-05-21,Y,,,,"The original version of this Article contained an error in the spelling of the author Harry Hemingway, which was incorrectly given as Harry Hemmingway. This has been corrected in both the PDF and HTML versions of the Article.",,pdf:https://www.nature.com/articles/s41467-019-10417-4.pdf; doi:https://doi.org/10.1038/s41467-019-10417-4; html:https://europepmc.org/articles/PMC6529418; pdf:https://europepmc.org/articles/PMC6529418?pdf=render
 35764313,https://doi.org/10.1055/s-0042-1749345,Long-Read Sequencing Identifies the First Retrotransposon Insertion and Resolves Structural Variants Causing Antithrombin Deficiency.,"de la Morena-Barrio B, Stephens J, de la Morena-Barrio ME, Stefanucci L, Padilla J, Miñano A, Gleadall N, García JL, López-Fernández MF, Morange PE, Puurunen M, Undas A, Vidal F, Raymond FL, Vicente V, Ouwehand WH, Corral J, Sanchis-Juan A, NIHR BioResource.",,Thrombosis and haemostasis,2022,2022-06-28,Y,,,,"The identification of inherited antithrombin deficiency (ATD) is critical to prevent potentially life-threatening thrombotic events. Causal variants in <i>SERPINC1</i> are identified for up to 70% of cases, the majority being single-nucleotide variants and indels. The detection and characterization of structural variants (SVs) in ATD remain challenging due to the high number of repetitive elements in <i>SERPINC1</i>. Here, we performed long-read whole-genome sequencing on 10 familial and 9 singleton cases with type I ATD proven by functional and antigen assays, who were selected from a cohort of 340 patients with this rare disorder because genetic analyses were either negative, ambiguous, or not fully characterized. We developed an analysis workflow to identify disease-associated SVs. This approach resolved, independently of its size or type, all eight SVs detected by multiple ligation-dependent probe amplification, and identified for the first time a complex rearrangement previously misclassified as a deletion. Remarkably, we identified the mechanism explaining ATD in 2 out of 11 cases with previous unknown defect: the insertion of a novel 2.4 kb SINE-VNTR-Alu retroelement, which was characterized by de novo assembly and verified by specific polymerase chain reaction amplification and sequencing in the probands and affected relatives. The nucleotide-level resolution achieved for all SVs allowed breakpoint analysis, which revealed repetitive elements and microhomologies supporting a common replication-based mechanism for all the SVs. Our study underscores the utility of long-read sequencing technology as a complementary method to identify, characterize, and unveil the molecular mechanism of disease-causing SVs involved in ATD, and enlarges the catalogue of genetic disorders caused by retrotransposon insertions.",,pdf:http://www.thieme-connect.de/products/ejournals/pdf/10.1055/s-0042-1749345.pdf; doi:https://doi.org/10.1055/s-0042-1749345; html:https://europepmc.org/articles/PMC9393088; pdf:https://europepmc.org/articles/PMC9393088?pdf=render
 37253531,https://doi.org/10.1136/bmjgh-2022-009997,Effectiveness of a multicomponent intervention to face the COVID-19 pandemic in Rio de Janeiro's favelas: difference-in-differences analysis.,"Batista-da-Silva AA, Moraes CB, Bozza HR, Bastos LDSL, Ranzani OT, Hamacher S, Bozza FA, Comitê Gestor Conexão Saúde.",,BMJ global health,2023,2023-05-01,Y,"Control strategies; Public Health; Intervention Study; Infections, Diseases, Disorders, Injuries; Covid-19",,,"<h4>Introduction</h4>Few community-based interventions addressing the transmission control and clinical management of COVID-19 cases have been reported, especially in poor urban communities from low-income and middle-income countries. Here, we analyse the impact of a multicomponent intervention that combines community engagement, mobile surveillance, massive testing and telehealth on COVID-19 cases detection and mortality rates in a large vulnerable community (<i>Complexo da Maré</i>) in Rio de Janeiro, Brazil.<h4>Methods</h4>We performed a difference-in-differences (DID) analysis to estimate the impact of the multicomponent intervention in <i>Maré,</i> before (March-August 2020) and after the intervention (September 2020 to April 2021), compared with equivalent local vulnerable communities. We applied a negative binomial regression model to estimate the intervention effect in weekly cases and mortality rates in <i>Maré</i>.<h4>Results</h4>Before the intervention, <i>Maré</i> presented lower rates of reported COVID-19 cases compared with the control group (1373 vs 1579 cases/100 000 population), comparable mortality rates (309 vs 287 deaths/100 000 population) and higher case fatality rates (13.7% vs 12.2%). After the intervention, <i>Maré</i> displayed a 154% (95% CI 138.6% to 170.4%) relative increase in reported case rates. Relative changes in reported death rates were -60% (95% CI -69.0% to -47.9%) in Maré and -28% (95% CI -42.0% to -9.8%) in the control group. The case fatality rate was reduced by 77% (95% CI -93.1% to -21.1%) in <i>Maré</i> and 52% (95% CI -81.8% to -29.4%) in the control group. The DID showed a reduction of 46% (95% CI 17% to 65%) of weekly reported deaths and an increased 23% (95% CI 5% to 44%) of reported cases in <i>Maré</i> after intervention onset.<h4>Conclusion</h4>An integrated intervention combining communication, surveillance and telehealth, with a strong community engagement component, could reduce COVID-19 mortality and increase case detection in a large vulnerable community in Rio de Janeiro. These findings show that investment in community-based interventions may reduce mortality and improve pandemic control in poor communities from low-income and middle-income countries.",,doi:https://doi.org/10.1136/bmjgh-2022-009997; doi:https://doi.org/10.1136/bmjgh-2022-009997; html:https://europepmc.org/articles/PMC10230340; pdf:https://europepmc.org/articles/PMC10230340?pdf=render
-35322056,https://doi.org/10.1038/s41598-022-08351-5,Automated quality assessment of large digitised histology cohorts by artificial intelligence.,"Haghighat M, Browning L, Sirinukunwattana K, Malacrino S, Khalid Alham N, Colling R, Cui Y, Rakha E, Hamdy FC, Verrill C, Rittscher J.",,Scientific reports,2022,2022-03-23,Y,,,,"Research using whole slide images (WSIs) of histopathology slides has increased exponentially over recent years. Glass slides from retrospective cohorts, some with patient follow-up data are digitised for the development and validation of artificial intelligence (AI) tools. Such resources, therefore, become very important, with the need to ensure that their quality is of the standard necessary for downstream AI development. However, manual quality control of large cohorts of WSIs by visual assessment is unfeasible, and whilst quality control AI algorithms exist, these focus on bespoke aspects of image quality, e.g. focus, or use traditional machine-learning methods, which are unable to classify the range of potential image artefacts that should be considered. In this study, we have trained and validated a multi-task deep neural network to automate the process of quality control of a large retrospective cohort of prostate cases from which glass slides have been scanned several years after production, to determine both the usability of the images at the diagnostic level (considered in this study to be the minimal standard for research) and the common image artefacts present. Using a two-layer approach, quality overlays of WSIs were generated from a quality assessment (QA) undertaken at patch-level at [Formula: see text] magnification. From these quality overlays the slide-level quality scores were predicted and then compared to those generated by three specialist urological pathologists, with a Pearson correlation of 0.89 for overall 'usability' (at a diagnostic level), and 0.87 and 0.82 for focus and H&E staining quality scores respectively. To demonstrate its wider potential utility, we subsequently applied our QA pipeline to the TCGA prostate cancer cohort and to a colorectal cancer cohort, for comparison. Our model, designated as PathProfiler, indicates comparable predicted usability of images from the cohorts assessed (86-90% of WSIs predicted to be usable), and perhaps more significantly is able to predict WSIs that could benefit from an intervention such as re-scanning or re-staining for quality improvement. We have shown in this study that AI can be used to automate the process of quality control of large retrospective WSI cohorts to maximise their utility for research.",,pdf:https://www.nature.com/articles/s41598-022-08351-5.pdf; doi:https://doi.org/10.1038/s41598-022-08351-5; html:https://europepmc.org/articles/PMC8943120; pdf:https://europepmc.org/articles/PMC8943120?pdf=render
 31792462,https://doi.org/10.1038/s41591-019-0665-2,Plasma protein patterns as comprehensive indicators of health.,"Williams SA, Kivimaki M, Langenberg C, Hingorani AD, Casas JP, Bouchard C, Jonasson C, Sarzynski MA, Shipley MJ, Alexander L, Ash J, Bauer T, Chadwick J, Datta G, DeLisle RK, Hagar Y, Hinterberg M, Ostroff R, Weiss S, Ganz P, Wareham NJ.",,Nature medicine,2019,2019-12-02,N,,,,"Proteins are effector molecules that mediate the functions of genes<sup>1,2</sup> and modulate comorbidities<sup>3-10</sup>, behaviors and drug treatments<sup>11</sup>. They represent an enormous potential resource for personalized, systemic and data-driven diagnosis, prevention, monitoring and treatment. However, the concept of using plasma proteins for individualized health assessment across many health conditions simultaneously has not been tested. Here, we show that plasma protein expression patterns strongly encode for multiple different health states, future disease risks and lifestyle behaviors. We developed and validated protein-phenotype models for 11 different health indicators: liver fat, kidney filtration, percentage body fat, visceral fat mass, lean body mass, cardiopulmonary fitness, physical activity, alcohol consumption, cigarette smoking, diabetes risk and primary cardiovascular event risk. The analyses were prospectively planned, documented and executed at scale on archived samples and clinical data, with a total of ~85 million protein measurements in 16,894 participants. Our proof-of-concept study demonstrates that protein expression patterns reliably encode for many different health issues, and that large-scale protein scanning<sup>12-16</sup> coupled with machine learning is viable for the development and future simultaneous delivery of multiple measures of health. We anticipate that, with further validation and the addition of more protein-phenotype models, this approach could enable a single-source, individualized so-called liquid health check.",,pdf:https://europepmc.org/articles/pmc6922049?pdf=render; doi:https://doi.org/10.1038/s41591-019-0665-2; html:https://europepmc.org/articles/PMC6922049; pdf:https://europepmc.org/articles/PMC6922049?pdf=render; doi:https://doi.org/10.1038/s41591-019-0665-2
+35322056,https://doi.org/10.1038/s41598-022-08351-5,Automated quality assessment of large digitised histology cohorts by artificial intelligence.,"Haghighat M, Browning L, Sirinukunwattana K, Malacrino S, Khalid Alham N, Colling R, Cui Y, Rakha E, Hamdy FC, Verrill C, Rittscher J.",,Scientific reports,2022,2022-03-23,Y,,,,"Research using whole slide images (WSIs) of histopathology slides has increased exponentially over recent years. Glass slides from retrospective cohorts, some with patient follow-up data are digitised for the development and validation of artificial intelligence (AI) tools. Such resources, therefore, become very important, with the need to ensure that their quality is of the standard necessary for downstream AI development. However, manual quality control of large cohorts of WSIs by visual assessment is unfeasible, and whilst quality control AI algorithms exist, these focus on bespoke aspects of image quality, e.g. focus, or use traditional machine-learning methods, which are unable to classify the range of potential image artefacts that should be considered. In this study, we have trained and validated a multi-task deep neural network to automate the process of quality control of a large retrospective cohort of prostate cases from which glass slides have been scanned several years after production, to determine both the usability of the images at the diagnostic level (considered in this study to be the minimal standard for research) and the common image artefacts present. Using a two-layer approach, quality overlays of WSIs were generated from a quality assessment (QA) undertaken at patch-level at [Formula: see text] magnification. From these quality overlays the slide-level quality scores were predicted and then compared to those generated by three specialist urological pathologists, with a Pearson correlation of 0.89 for overall 'usability' (at a diagnostic level), and 0.87 and 0.82 for focus and H&E staining quality scores respectively. To demonstrate its wider potential utility, we subsequently applied our QA pipeline to the TCGA prostate cancer cohort and to a colorectal cancer cohort, for comparison. Our model, designated as PathProfiler, indicates comparable predicted usability of images from the cohorts assessed (86-90% of WSIs predicted to be usable), and perhaps more significantly is able to predict WSIs that could benefit from an intervention such as re-scanning or re-staining for quality improvement. We have shown in this study that AI can be used to automate the process of quality control of large retrospective WSI cohorts to maximise their utility for research.",,pdf:https://www.nature.com/articles/s41598-022-08351-5.pdf; doi:https://doi.org/10.1038/s41598-022-08351-5; html:https://europepmc.org/articles/PMC8943120; pdf:https://europepmc.org/articles/PMC8943120?pdf=render
 36474045,https://doi.org/10.1038/s41588-022-01233-6,Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants.,"Aragam KG, Jiang T, Goel A, Kanoni S, Wolford BN, Atri DS, Weeks EM, Wang M, Hindy G, Zhou W, Grace C, Roselli C, Marston NA, Kamanu FK, Surakka I, Venegas LM, Sherliker P, Koyama S, Ishigaki K, Åsvold BO, Brown MR, Brumpton B, de Vries PS, Giannakopoulou O, Giardoglou P, Gudbjartsson DF, Güldener U, Haider SMI, Helgadottir A, Ibrahim M, Kastrati A, Kessler T, Kyriakou T, Konopka T, Li L, Ma L, Meitinger T, Mucha S, Munz M, Murgia F, Nielsen JB, Nöthen MM, Pang S, Reinberger T, Schnitzler G, Smedley D, Thorleifsson G, von Scheidt M, Ulirsch JC, Biobank Japan, EPIC-CVD, Arnar DO, Burtt NP, Costanzo MC, Flannick J, Ito K, Jang DK, Kamatani Y, Khera AV, Komuro I, Kullo IJ, Lotta LA, Nelson CP, Roberts R, Thorgeirsson G, Thorsteinsdottir U, Webb TR, Baras A, Björkegren JLM, Boerwinkle E, Dedoussis G, Holm H, Hveem K, Melander O, Morrison AC, Orho-Melander M, Rallidis LS, Ruusalepp A, Sabatine MS, Stefansson K, Zalloua P, Ellinor PT, Farrall M, Danesh J, Ruff CT, Finucane HK, Hopewell JC, Clarke R, Gupta RM, Erdmann J, Samani NJ, Schunkert H, Watkins H, Willer CJ, Deloukas P, Kathiresan S, Butterworth AS, CARDIoGRAMplusC4D Consortium.",,Nature genetics,2022,2022-12-06,Y,,,,"The discovery of genetic loci associated with complex diseases has outpaced the elucidation of mechanisms of disease pathogenesis. Here we conducted a genome-wide association study (GWAS) for coronary artery disease (CAD) comprising 181,522 cases among 1,165,690 participants of predominantly European ancestry. We detected 241 associations, including 30 new loci. Cross-ancestry meta-analysis with a Japanese GWAS yielded 38 additional new loci. We prioritized likely causal variants using functionally informed fine-mapping, yielding 42 associations with less than five variants in the 95% credible set. Similarity-based clustering suggested roles for early developmental processes, cell cycle signaling and vascular cell migration and proliferation in the pathogenesis of CAD. We prioritized 220 candidate causal genes, combining eight complementary approaches, including 123 supported by three or more approaches. Using CRISPR-Cas9, we experimentally validated the effect of an enhancer in MYO9B, which appears to mediate CAD risk by regulating vascular cell motility. Our analysis identifies and systematically characterizes >250 risk loci for CAD to inform experimental interrogation of putative causal mechanisms for CAD.",,pdf:https://www.nature.com/articles/s41588-022-01233-6.pdf; doi:https://doi.org/10.1038/s41588-022-01233-6; html:https://europepmc.org/articles/PMC9729111; pdf:https://europepmc.org/articles/PMC9729111?pdf=render
+33531015,https://doi.org/10.1186/s12916-021-01906-9,The importance of supplementary immunisation activities to prevent measles outbreaks during the COVID-19 pandemic in Kenya.,"Mburu CN, Ojal J, Chebet R, Akech D, Karia B, Tuju J, Sigilai A, Abbas K, Jit M, Funk S, Smits G, van Gageldonk PGM, van der Klis FRM, Tabu C, Nokes DJ, LSHTM CMMID COVID-19 Working Group, Scott J, Flasche S, Adetifa I.",,BMC medicine,2021,2021-02-03,Y,outbreak; Measles; Vaccination Coverage; Supplementary Immunisation Activities; Covid-19,,,"<h4>Background</h4>The COVID-19 pandemic has disrupted routine measles immunisation and supplementary immunisation activities (SIAs) in most countries including Kenya. We assessed the risk of measles outbreaks during the pandemic in Kenya as a case study for the African Region.<h4>Methods</h4>Combining measles serological data, local contact patterns, and vaccination coverage into a cohort model, we predicted the age-adjusted population immunity in Kenya and estimated the probability of outbreaks when contact-reducing COVID-19 interventions are lifted. We considered various scenarios for reduced measles vaccination coverage from April 2020.<h4>Results</h4>In February 2020, when a scheduled SIA was postponed, population immunity was close to the herd immunity threshold and the probability of a large outbreak was 34% (8-54). As the COVID-19 contact restrictions are nearly fully eased, from December 2020, the probability of a large measles outbreak will increase to 38% (19-54), 46% (30-59), and 54% (43-64) assuming a 15%, 50%, and 100% reduction in measles vaccination coverage. By December 2021, this risk increases further to 43% (25-56), 54% (43-63), and 67% (59-72) for the same coverage scenarios respectively. However, the increased risk of a measles outbreak following the lifting of all restrictions can be overcome by conducting a SIA with ≥ 95% coverage in under-fives.<h4>Conclusion</h4>While contact restrictions sufficient for SAR-CoV-2 control temporarily reduce measles transmissibility and the risk of an outbreak from a measles immunity gap, this risk rises rapidly once these restrictions are lifted. Implementing delayed SIAs will be critical for prevention of measles outbreaks given the roll-back of contact restrictions in Kenya.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-021-01906-9; doi:https://doi.org/10.1186/s12916-021-01906-9; html:https://europepmc.org/articles/PMC7854026; pdf:https://europepmc.org/articles/PMC7854026?pdf=render
 30609404,https://doi.org/10.1016/j.ajhg.2018.11.014,Integrating Genomics into Healthcare: A Global Responsibility.,"Stark Z, Dolman L, Manolio TA, Ozenberger B, Hill SL, Caulfied MJ, Levy Y, Glazer D, Wilson J, Lawler M, Boughtwood T, Braithwaite J, Goodhand P, Birney E, North KN.",,American journal of human genetics,2019,2019-01-01,N,,Understanding the Causes of Disease,,"Genomic sequencing is rapidly transitioning into clinical practice, and implementation into healthcare systems has been supported by substantial government investment, totaling over US$4 billion, in at least 14 countries. These national genomic-medicine initiatives are driving transformative change under real-life conditions while simultaneously addressing barriers to implementation and gathering evidence for wider adoption. We review the diversity of approaches and current progress made by national genomic-medicine initiatives in the UK, France, Australia, and US and provide a roadmap for sharing strategies, standards, and data internationally to accelerate implementation.",,pdf:http://www.cell.com/article/S0002929718304221/pdf; doi:https://doi.org/10.1016/j.ajhg.2018.11.014; html:https://europepmc.org/articles/PMC6323624; pdf:https://europepmc.org/articles/PMC6323624?pdf=render; doi:https://doi.org/10.1016/j.ajhg.2018.11.014
 33714592,https://doi.org/10.1016/j.mayocp.2021.02.007,"Place and Underlying Cause of Death During the COVID-19 Pandemic: Retrospective Cohort Study of 3.5 Million Deaths in England and Wales, 2014 to 2020.","Wu J, Mafham M, Mamas MA, Rashid M, Kontopantelis E, Deanfield JE, de Belder MA, Gale CP.",,Mayo Clinic proceedings,2021,2021-02-16,Y,,,,"<h4>Objective</h4>To describe the place and cause of death during the coronavirus disease 2019 (COVID-19) pandemic to assess its impact on excess mortality.<h4>Methods</h4>This national death registry included all adult (aged ≥18 years) deaths in England and Wales between January 1, 2014, and June 30, 2020. Daily deaths during the COVID-19 pandemic were compared against the expected daily deaths, estimated with use of the Farrington surveillance algorithm for daily historical data between 2014 and 2020 by place and cause of death.<h4>Results</h4>Between March 2 and June 30, 2020, there was an excess mortality of 57,860 (a proportional increase of 35%) compared with the expected deaths, of which 50,603 (87%) were COVID-19 related. At home, only 14% (2267) of the 16,190 excess deaths were related to COVID-19, with 5963 deaths due to cancer and 2485 deaths due to cardiac disease, few of which involved COVID-19. In care homes or hospices, 61% (15,623) of the 25,611 excess deaths were related to COVID-19, 5539 of which were due to respiratory disease, and most of these (4315 deaths) involved COVID-19. In the hospital, there were 16,174 fewer deaths than expected that did not involve COVID-19, with 4088 fewer deaths due to cancer and 1398 fewer deaths due to cardiac disease than expected.<h4>Conclusion</h4>The COVID-19 pandemic has resulted in a large excess of deaths in care homes that were poorly characterized and likely to be the result of undiagnosed COVID-19. There was a smaller but important and ongoing excess in deaths at home, particularly from cancer and cardiac disease, suggesting public avoidance of hospital care for non-COVID-19 conditions.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7885692; doi:https://doi.org/10.1016/j.mayocp.2021.02.007; html:https://europepmc.org/articles/PMC7885692; pdf:https://europepmc.org/articles/PMC7885692?pdf=render
-33531015,https://doi.org/10.1186/s12916-021-01906-9,The importance of supplementary immunisation activities to prevent measles outbreaks during the COVID-19 pandemic in Kenya.,"Mburu CN, Ojal J, Chebet R, Akech D, Karia B, Tuju J, Sigilai A, Abbas K, Jit M, Funk S, Smits G, van Gageldonk PGM, van der Klis FRM, Tabu C, Nokes DJ, LSHTM CMMID COVID-19 Working Group, Scott J, Flasche S, Adetifa I.",,BMC medicine,2021,2021-02-03,Y,outbreak; Measles; Vaccination Coverage; Supplementary Immunisation Activities; Covid-19,,,"<h4>Background</h4>The COVID-19 pandemic has disrupted routine measles immunisation and supplementary immunisation activities (SIAs) in most countries including Kenya. We assessed the risk of measles outbreaks during the pandemic in Kenya as a case study for the African Region.<h4>Methods</h4>Combining measles serological data, local contact patterns, and vaccination coverage into a cohort model, we predicted the age-adjusted population immunity in Kenya and estimated the probability of outbreaks when contact-reducing COVID-19 interventions are lifted. We considered various scenarios for reduced measles vaccination coverage from April 2020.<h4>Results</h4>In February 2020, when a scheduled SIA was postponed, population immunity was close to the herd immunity threshold and the probability of a large outbreak was 34% (8-54). As the COVID-19 contact restrictions are nearly fully eased, from December 2020, the probability of a large measles outbreak will increase to 38% (19-54), 46% (30-59), and 54% (43-64) assuming a 15%, 50%, and 100% reduction in measles vaccination coverage. By December 2021, this risk increases further to 43% (25-56), 54% (43-63), and 67% (59-72) for the same coverage scenarios respectively. However, the increased risk of a measles outbreak following the lifting of all restrictions can be overcome by conducting a SIA with ≥ 95% coverage in under-fives.<h4>Conclusion</h4>While contact restrictions sufficient for SAR-CoV-2 control temporarily reduce measles transmissibility and the risk of an outbreak from a measles immunity gap, this risk rises rapidly once these restrictions are lifted. Implementing delayed SIAs will be critical for prevention of measles outbreaks given the roll-back of contact restrictions in Kenya.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-021-01906-9; doi:https://doi.org/10.1186/s12916-021-01906-9; html:https://europepmc.org/articles/PMC7854026; pdf:https://europepmc.org/articles/PMC7854026?pdf=render
 38361499,https://doi.org/10.26633/rpsp.2023.149,[Guidelines for clinical trial protocols for interventions involving artificial intelligence: the SPIRIT-AI extensionDiretrizes para protocolos de ensaios clínicos com intervenções que utilizam inteligência artificial: a extensão SPIRIT-AI].,"Cruz Rivera S, Liu X, Chan AW, Denniston AK, Calvert MJ, Grupo de Trabajo SPIRIT-AI y CONSORT-AI, Grupo Directivo SPIRIT-AI y CONSORT-AI , Grupo de Consenso SPIRIT-AI y CONSORT-AI .",,Revista panamericana de salud publica = Pan American journal of public health,2023,2023-12-08,Y,,,,"The SPIRIT 2013 statement aims to improve the completeness of clinical trial protocol reporting by providing evidence-based recommendations for the minimum set of items to be addressed. This guidance has been instrumental in promoting transparent evaluation of new interventions. More recently, there has been a growing recognition that interventions involving artificial intelligence (AI) need to undergo rigorous, prospective evaluation to demonstrate their impact on health outcomes. The SPIRIT-AI (Standard Protocol Items: Recommendations for Interventional Trials-Artificial Intelligence) extension is a new reporting guideline for clinical trial protocols evaluating interventions with an AI component. It was developed in parallel with its companion statement for trial reports: CONSORT-AI (Consolidated Standards of Reporting Trials-Artificial Intelligence). Both guidelines were developed through a staged consensus process involving literature review and expert consultation to generate 26 candidate items, which were consulted upon by an international multi-stakeholder group in a two-stage Delphi survey (103 stakeholders), agreed upon in a consensus meeting (31 stakeholders) and refined through a checklist pilot (34 participants). The SPIRIT-AI extension includes 15 new items that were considered sufficiently important for clinical trial protocols of AI interventions. These new items should be routinely reported in addition to the core SPIRIT 2013 items. SPIRIT-AI recommends that investigators provide clear descriptions of the AI intervention, including instructions and skills required for use, the setting in which the AI intervention will be integrated, considerations for the handling of input and output data, the human-AI interaction and analysis of error cases. SPIRIT-AI will help promote transparency and completeness for clinical trial protocols for AI interventions. Its use will assist editors and peer reviewers, as well as the general readership, to understand, interpret and critically appraise the design and risk of bias for a planned clinical trial.",,doi:https://doi.org/10.26633/RPSP.2023.149; html:https://europepmc.org/articles/PMC10868409; pdf:https://europepmc.org/articles/PMC10868409?pdf=render
 34788413,https://doi.org/10.1093/ije/dyab149,Data Resource Profile: The Education and Child Health Insights from Linked Data (ECHILD) Database.,"Mc Grath-Lone L, Libuy N, Harron K, Jay MA, Wijlaars L, Etoori D, Lilliman M, Gilbert R, Blackburn R.",,International journal of epidemiology,2022,2022-02-01,Y,Education; Social Care; Adolescent Health; Administrative Data; Linked Data; Key Words: Child Health,,,,,pdf:https://academic.oup.com/ije/article-pdf/51/1/17/42555483/dyab149.pdf; doi:https://doi.org/10.1093/ije/dyab149; html:https://europepmc.org/articles/PMC8856003; pdf:https://europepmc.org/articles/PMC8856003?pdf=render
-38296292,https://doi.org/10.1136/bmjopen-2023-078135,"Risk factor associations for severe COVID-19, influenza and pneumonia in people with diabetes to inform future pandemic preparations: UK population-based cohort study.","Hopkins R, Young KG, Thomas NJ, Godwin J, Raja D, Mateen BA, Challen RJ, Vollmer SJ, Shields BM, McGovern AP, Dennis JM.",,BMJ open,2024,2024-01-31,Y,risk factors; Electronic Health Records; Diabetes & Endocrinology; Covid-19,,,"<h4>Objective</h4>This study aimed to compare clinical and sociodemographic risk factors for severe COVID-19, influenza and pneumonia, in people with diabetes.<h4>Design</h4>Population-based cohort study.<h4>Setting</h4>UK primary care records (Clinical Practice Research Datalink) linked to mortality and hospital records.<h4>Participants</h4>Individuals with type 1 and type 2 diabetes (COVID-19 cohort: n=43 033 type 1 diabetes and n=584 854 type 2 diabetes, influenza and pneumonia cohort: n=42 488 type 1 diabetes and n=585 289 type 2 diabetes).<h4>Primary and secondary outcome measures</h4>COVID-19 hospitalisation from 1 February 2020 to 31 October 2020 (pre-COVID-19 vaccination roll-out), and influenza and pneumonia hospitalisation from 1 September 2016 to 31 May 2019 (pre-COVID-19 pandemic). Secondary outcomes were COVID-19 and pneumonia mortality. Associations between clinical and sociodemographic risk factors and each outcome were assessed using multivariable Cox proportional hazards models. In people with type 2 diabetes, we explored modifying effects of glycated haemoglobin (HbA1c) and body mass index (BMI) by age, sex and ethnicity.<h4>Results</h4>In type 2 diabetes, poor glycaemic control and severe obesity were consistently associated with increased risk of hospitalisation for COVID-19, influenza and pneumonia. The highest HbA1c and BMI-associated relative risks were observed in people aged under 70 years. Sociodemographic-associated risk differed markedly by respiratory infection, particularly for ethnicity. Compared with people of white ethnicity, black and south Asian groups had a greater risk of COVID-19 hospitalisation, but a lesser risk of pneumonia hospitalisation. Risk factor associations for type 1 diabetes and for type 2 diabetes mortality were broadly consistent with the primary analysis.<h4>Conclusions</h4>Clinical risk factors of high HbA1c and severe obesity are consistently associated with severe outcomes from COVID-19, influenza and pneumonia, especially in younger people. In contrast, associations with sociodemographic risk factors differed by type of respiratory infection. This emphasises that risk stratification should be specific to individual respiratory infections.",,pdf:https://bmjopen.bmj.com/content/bmjopen/14/1/e078135.full.pdf; doi:https://doi.org/10.1136/bmjopen-2023-078135; html:https://europepmc.org/articles/PMC10831438; pdf:https://europepmc.org/articles/PMC10831438?pdf=render
 33777379,https://doi.org/10.1093/ckj/sfaa045,Accelerometer-measured physical activity and functional behaviours among people on dialysis.,"Nawab KA, Storey BC, Staplin N, Walmsley R, Haynes R, Sutherland S, Crosbie S, Pugh CW, Harper CHS, Landray MJ, Doherty A, Herrington WG.",,Clinical kidney journal,2021,2020-08-31,Y,Age; Haemodialysis; epidemiology; Physical Activity; cardiovascular,,,"<h4>Background</h4>The feasibility of wrist-worn accelerometers, and the patterns and determinants of physical activity, among people on dialysis are uncertain.<h4>Methods</h4>People on maintenance dialysis were fitted with a wrist-worn AxivityAX3 accelerometer. Subsets also wore a 14-day electrocardiograph patch (Zio<sup>®</sup>PatchXT) and wearable cameras. Age-, sex- and season-matched UK Biobank control groups were derived for comparison.<h4>Results</h4>Median (interquartile range) accelerometer wear time for the 101 recruits was 12.5 (10.4-13.5) days, of which 73 participants (mean age 66.5 years) had excellent wear on both dialysis and non-dialysis days. Mean (standard error) overall physical activity levels were 15.5 (0.7) milligravity units (m<i>g</i>), 14.8 (0.7) m<i>g</i> on dialysis days versus 16.2 (0.8) m<i>g</i> on non-dialysis days. This compared with 28.1 (0.5) m<i>g</i> for apparently healthy controls, 23.4 (0.4) m<i>g</i> for controls with prior cardiovascular disease (CVD) and/or diabetes mellitus and 22.9 (0.6) m<i>g</i> for heart failure controls. Each day, we estimated that those on dialysis spent an average of about 1 hour (h/day) walking, 0.6 h/day engaging in moderate-intensity activity, 0.7 h/day on light tasks, 13.2 h/day sedentary and 8.6 h/day asleep. Older age and self-reported leg weakness were associated with decreased levels of physical activity, but the presence of prior CVD, arrhythmias and listing for transplantation were not.<h4>Conclusions</h4>Wrist-worn accelerometers are an acceptable and reliable method to measure physical activity in people on dialysis and may also be used to estimate functional behaviours. Among people on dialysis, who are broadly half as active as general population controls, age and leg weakness appear to be more important determinants of low activity levels than CVD.",,pdf:https://academic.oup.com/ckj/article-pdf/14/3/950/36670473/sfaa045.pdf; doi:https://doi.org/10.1093/ckj/sfaa045; html:https://europepmc.org/articles/PMC7986362; pdf:https://europepmc.org/articles/PMC7986362?pdf=render
+38296292,https://doi.org/10.1136/bmjopen-2023-078135,"Risk factor associations for severe COVID-19, influenza and pneumonia in people with diabetes to inform future pandemic preparations: UK population-based cohort study.","Hopkins R, Young KG, Thomas NJ, Godwin J, Raja D, Mateen BA, Challen RJ, Vollmer SJ, Shields BM, McGovern AP, Dennis JM.",,BMJ open,2024,2024-01-31,Y,risk factors; Electronic Health Records; Diabetes & Endocrinology; Covid-19,,,"<h4>Objective</h4>This study aimed to compare clinical and sociodemographic risk factors for severe COVID-19, influenza and pneumonia, in people with diabetes.<h4>Design</h4>Population-based cohort study.<h4>Setting</h4>UK primary care records (Clinical Practice Research Datalink) linked to mortality and hospital records.<h4>Participants</h4>Individuals with type 1 and type 2 diabetes (COVID-19 cohort: n=43 033 type 1 diabetes and n=584 854 type 2 diabetes, influenza and pneumonia cohort: n=42 488 type 1 diabetes and n=585 289 type 2 diabetes).<h4>Primary and secondary outcome measures</h4>COVID-19 hospitalisation from 1 February 2020 to 31 October 2020 (pre-COVID-19 vaccination roll-out), and influenza and pneumonia hospitalisation from 1 September 2016 to 31 May 2019 (pre-COVID-19 pandemic). Secondary outcomes were COVID-19 and pneumonia mortality. Associations between clinical and sociodemographic risk factors and each outcome were assessed using multivariable Cox proportional hazards models. In people with type 2 diabetes, we explored modifying effects of glycated haemoglobin (HbA1c) and body mass index (BMI) by age, sex and ethnicity.<h4>Results</h4>In type 2 diabetes, poor glycaemic control and severe obesity were consistently associated with increased risk of hospitalisation for COVID-19, influenza and pneumonia. The highest HbA1c and BMI-associated relative risks were observed in people aged under 70 years. Sociodemographic-associated risk differed markedly by respiratory infection, particularly for ethnicity. Compared with people of white ethnicity, black and south Asian groups had a greater risk of COVID-19 hospitalisation, but a lesser risk of pneumonia hospitalisation. Risk factor associations for type 1 diabetes and for type 2 diabetes mortality were broadly consistent with the primary analysis.<h4>Conclusions</h4>Clinical risk factors of high HbA1c and severe obesity are consistently associated with severe outcomes from COVID-19, influenza and pneumonia, especially in younger people. In contrast, associations with sociodemographic risk factors differed by type of respiratory infection. This emphasises that risk stratification should be specific to individual respiratory infections.",,pdf:https://bmjopen.bmj.com/content/bmjopen/14/1/e078135.full.pdf; doi:https://doi.org/10.1136/bmjopen-2023-078135; html:https://europepmc.org/articles/PMC10831438; pdf:https://europepmc.org/articles/PMC10831438?pdf=render
 34172543,https://doi.org/10.1136/bmjopen-2020-042893,Developing a model to predict individualised treatment for gonorrhoea: a modelling study.,"Findlater L, Mohammed H, Gobin M, Fifer H, Ross J, Geffen Obregon O, Turner KME.",,BMJ open,2021,2021-06-25,Y,epidemiology; Public Health; Genitourinary Medicine; Sexual Medicine,,,"<h4>Objective</h4>To develop a tool predicting individualised treatment for gonorrhoea, enabling treatment with previously recommended antibiotics, to reduce use of last-line treatment ceftriaxone.<h4>Design</h4>A modelling study.<h4>Setting</h4>England and Wales.<h4>Participants</h4>Individuals accessing sentinel health services.<h4>Intervention</h4>Developing an Excel model which uses participants' demographic, behavioural and clinical characteristics to predict susceptibility to legacy antibiotics. Model parameters were calculated using data for 2015-2017 from the Gonococcal Resistance to Antimicrobials Surveillance Programme.<h4>Main outcome measures</h4>Estimated number of doses of ceftriaxone saved, and number of people delayed effective treatment, by model use in clinical practice. Model outputs are the predicted risk of resistance to ciprofloxacin, azithromycin, penicillin and cefixime, in groups of individuals with different combinations of characteristics (gender, sexual orientation, number of recent sexual partners, age, ethnicity), and a treatment recommendation.<h4>Results</h4>Between 2015 and 2017, 8013 isolates were collected: 64% from men who have sex with men, 18% from heterosexual men and 18% from women. Across participant subgroups, stratified by all predictors, resistance prevalence was high for ciprofloxacin (range: 11%-51%) and penicillin (range: 6%-33%). Resistance prevalence for azithromycin and cefixime ranged from 0% to 13% and for ceftriaxone it was 0%. Simulating model use, 88% of individuals could be given cefixime and 10% azithromycin, saving 97% of ceftriaxone doses, with 1% of individuals delayed effective treatment.<h4>Conclusions</h4>Using demographic and behavioural characteristics, we could not reliably identify a participant subset in which ciprofloxacin or penicillin would be effective. Cefixime resistance was almost universally low; however, substituting ceftriaxone for near-uniform treatment with cefixime risks re-emergence of resistance to cefixime and ceftriaxone. Several subgroups had low azithromycin resistance, but widespread azithromycin monotherapy risks resistance at population level. However, this dataset had limitations; further exploration of individual characteristics to predict resistance to a wider range of legacy antibiotics may still be appropriate.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/6/e042893.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-042893; html:https://europepmc.org/articles/PMC8237724; pdf:https://europepmc.org/articles/PMC8237724?pdf=render
 31969318,https://doi.org/10.1136/bmj.l6987,Risk of herpes zoster after exposure to varicella to explore the exogenous boosting hypothesis: self controlled case series study using UK electronic healthcare data.,"Forbes H, Douglas I, Finn A, Breuer J, Bhaskaran K, Smeeth L, Packer S, Langan SM, Mansfield KE, Marlow R, Whitaker H, Warren-Gash C.",,BMJ (Clinical research ed.),2020,2020-01-22,Y,,,,"<h4>Objective</h4>To assess the magnitude and duration of any hypothesised protective effect of household exposure to a child with varicella on the relative incidence of herpes zoster in adults.<h4>Design</h4>Self controlled case series.<h4>Setting</h4>UK general practices contributing to Clinical Practice Research Datalink.<h4>Participants</h4>9604 adults (≥18 years) with a diagnosis of herpes zoster (in primary care or hospital records) between 1997 and 2018, who during their observation period lived with a child (<18 years) with a diagnosis of varicella.<h4>Main outcome measures</h4>Relative incidence of herpes zoster in the 20 years after exposure to a child with varicella in the household compared with baseline time (all other time, excluding the 60 days before exposure).<h4>Results</h4>6584 of the 9604 adults with herpes zoster (68.6%) were women. Median age of exposure to a child with varicella was 38.3 years (interquartile range 32.3-48.8 years) and median observation period was 14.7 (11.1-17.7) years. 4116 adults developed zoster in the baseline period, 433 in the 60 days before exposure and 5055 in the risk period. After adjustment for age, calendar time, and season, strong evidence suggested that in the two years after household exposure to a child with varicella, adults were 33% less likely to develop zoster (incidence ratio 0.67, 95% confidence interval 0.62 to 0.73) compared with baseline time. In the 10-20 years after exposure, adults were 27% less likely to develop herpes zoster (0.73, 0.62 to 0.87) compared with baseline time. A stronger boosting effect was observed among men than among women after exposure to varicella.<h4>Conclusions</h4>The relative incidence of zoster was lower in the periods after exposure to a household contact with varicella, with modest but long lasting protective effects observed. This study suggests that exogenous boosting provides some protection from the risk of herpes zoster, but not complete immunity, as assumed by previous cost effectiveness estimates of varicella immunisation.",,pdf:https://www.bmj.com/content/bmj/368/bmj.l6987.full.pdf; doi:https://doi.org/10.1136/bmj.l6987; html:https://europepmc.org/articles/PMC7190015
 31478583,https://doi.org/10.1002/ejhf.1615,Association between beta-blocker use and mortality/morbidity in older patients with heart failure with reduced ejection fraction. A propensity score-matched analysis from the Swedish Heart Failure Registry.,"Stolfo D, Uijl A, Benson L, Schrage B, Fudim M, Asselbergs FW, Koudstaal S, Sinagra G, Dahlström U, Rosano G, Savarese G.",,European journal of heart failure,2020,2019-10-23,N,Elderly; Heart Failure; Beta-blocker; Registry; Swedehf,Improving Public Health,cardiovascular,"<h4>Background</h4>Beta-blockers reduce mortality and morbidity in heart failure (HF) with reduced ejection fraction (HFrEF). However, patients older than 80 years are poorly represented in randomized controlled trials. We assessed the association between beta-blocker use and outcomes in HFrEF patients aged ≥80 years.<h4>Methods and results</h4>We included patients with an ejection fraction <40% and aged ≥80 years from the Swedish HF Registry. The association between beta-blocker use, all-cause mortality and cardiovascular (CV) mortality/HF hospitalization was assessed by Cox proportional hazard models in a 1:1 propensity score-matched cohort. To assess consistency, the same analyses were performed in a positive control cohort with age <80 years. A negative control outcome analysis was run using hospitalization for cancer as endpoint. Of 6562 patients aged ≥80 years, 5640 (86%) received beta-blockers. In the matched cohort including 1732 patients, beta-blocker use was associated with a significant reduction in the risk of all-cause mortality [hazard ratio (HR) 0.89, 95% confidence interval (CI) 0.79-0.99]. Reduction in CV mortality/HF hospitalization was not significant (HR 0.94, 95% CI 0.85-1.05) due to the lack of association with HF hospitalization, whereas CV death was significantly reduced. After adjustment rather than matching for the propensity score in the overall cohort, beta-blocker use was associated with reduced risk of all outcomes. In patients aged <80 years, use of beta-blockers was associated with reduced risk of all-cause death (HR 0.79, 95% CI 0.68-0.92) and of the composite outcome (HR 0.88, 95% CI 0.77-0.99).<h4>Conclusions</h4>In HFrEF patients ≥80 years of age, use of beta-blockers was high and was associated with improved all-cause and CV survival.",This study looked at 6562 people with severe heart failure and whether there was an association between taking beta-blockers (a drug to control heart rate) and heart disease. They used a national Swedish registry of patients with heart failure and compared those who were taking beta blockers (866 patients) to those not taking beta blockers (866 patients). The study found that patients who were taking beta blockers tended also to have lower risk of heart complications and were more likely to survive.,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ejhf.1615; doi:https://doi.org/10.1002/ejhf.1615
@@ -2422,17 +2424,17 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 32289242,https://doi.org/10.1098/rsob.190297,"Why is cancer not more common? A changing microenvironment may help to explain why, and suggests strategies for anti-cancer therapy.","Jiang X, Tomlinson IPM.",,Open biology,2020,2020-04-15,Y,Cancer Genetics; Evolutionary Biology; Mathematical Modelling,,,"One of the great unsolved puzzles in cancer biology is not why cancers occur, but rather explaining why so few cancers occur compared with the theoretical number that could occur, given the number of progenitor cells in the body and the normal mutation rate. We hypothesized that a contributory explanation is that the tumour microenvironment (TME) is not fixed due to factors such as immune cell infiltration, and that this could impair the ability of neoplastic cells to retain a high enough fitness to become a cancer. The TME has implicitly been assumed to be static in most cancer evolution models, and we therefore developed a mathematical model of spatial cancer evolution assuming that the TME, and thus the optimum cancer phenotype, changes over time. Based on simulations, we show how cancer cell populations adapt to diverse changing TME conditions and fitness landscapes. Compared with static TMEs, which generate neutral dynamics, changing TMEs lead to complex adaptations with characteristic spatio-temporal heterogeneity involving variable fitness effects of driver mutations, subclonal mixing, subclonal competition and phylogeny patterns. In many cases, cancer cell populations fail to grow or undergo spontaneous regression, and even extinction. Our analyses predict that cancer evolution in a changing TME is challenging, and can help to explain why cancer is neither inevitable nor as common as expected. Should cancer driver mutations with effects dependent of the TME exist, they are likely to be selected. Anti-cancer prevention and treatment strategies based on changing the TME are feasible and potentially effective.",,pdf:https://royalsocietypublishing.org/doi/pdf/10.1098/rsob.190297; doi:https://doi.org/10.1098/rsob.190297; html:https://europepmc.org/articles/PMC7241076; pdf:https://europepmc.org/articles/PMC7241076?pdf=render
 31666364,https://doi.org/10.1128/jcm.00963-19,Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples.,"Lewandowski K, Xu Y, Pullan ST, Lumley SF, Foster D, Sanderson N, Vaughan A, Morgan M, Bright N, Kavanagh J, Vipond R, Carroll M, Marriott AC, Gooch KE, Andersson M, Jeffery K, Peto TEA, Crook DW, Walker AS, Matthews PC.",,Journal of clinical microbiology,2019,2019-12-23,Y,DNA sequencing; Sequencing; Influenza; Diagnosis; Molecular epidemiology; epidemiology; Diagnostics; Metagenomics; Nanopore; Metagenomic,Understanding the Causes of Disease,,"Influenza is a major global public health threat as a result of its highly pathogenic variants, large zoonotic reservoir, and pandemic potential. Metagenomic viral sequencing offers the potential for a diagnostic test for influenza virus which also provides insights on transmission, evolution, and drug resistance and simultaneously detects other viruses. We therefore set out to apply the Oxford Nanopore Technologies sequencing method to metagenomic sequencing of respiratory samples. We generated influenza virus reads down to a limit of detection of 10<sup>2</sup> to 10<sup>3</sup> genome copies/ml in pooled samples, observing a strong relationship between the viral titer and the proportion of influenza virus reads (<i>P</i> = 4.7 × 10<sup>-5</sup>). Applying our methods to clinical throat swabs, we generated influenza virus reads for 27/27 samples with mid-to-high viral titers (cycle threshold [<i>C<sub>T</sub></i> ] values, <30) and 6/13 samples with low viral titers (<i>C<sub>T</sub></i> values, 30 to 40). No false-positive reads were generated from 10 influenza virus-negative samples. Thus, Nanopore sequencing operated with 83% sensitivity (95% confidence interval [CI], 67 to 93%) and 100% specificity (95% CI, 69 to 100%) compared to the current diagnostic standard. Coverage of full-length virus was dependent on sample composition, being negatively influenced by increased host and bacterial reads. However, at high influenza virus titers, we were able to reconstruct >99% complete sequences for all eight gene segments. We also detected a human coronavirus coinfection in one clinical sample. While further optimization is required to improve sensitivity, this approach shows promise for the Nanopore platform to be used in the diagnosis and genetic analysis of influenza virus and other respiratory viruses.",,doi:https://doi.org/10.1128/jcm.00963-19; doi:https://doi.org/10.1128/JCM.00963-19; html:https://europepmc.org/articles/PMC6935926; pdf:https://europepmc.org/articles/PMC6935926?pdf=render
 33985965,https://doi.org/10.3399/bjgpo.2021.0020,Trends and variation in antidepressant prescribing in English primary care: a retrospective longitudinal study.,"Bogowicz P, Curtis HJ, Walker AJ, Cowen P, Geddes J, Goldacre B.",,BJGP open,2021,2021-08-24,Y,Antidepressive agents; Primary Health Care; Quality Of Health Care,,,"<h4>Background</h4>Antidepressants are commonly prescribed. There are clear national guidelines in relation to treatment sequencing. This study examines trends and variation in antidepressant prescribing across English primary care.<h4>Aim</h4>To examine trends and variation in antidepressant prescribing in England, with a focus on: monoamine oxidase inhibitors (MAOIs); paroxetine; and dosulepin and trimipramine. DESIGN & SETTIN: <u>g</u>Retrospective longitudinal study using national and practice-level data on antidepressant items prescribed per year (1998-2018) and per month (2010-2019).<h4>Method</h4>Class- and drug-specific proportions were calculated at national and practice levels. Descriptive statistics were generated, percentile charts and maps were plotted, and logistic regression analysis was conducted.<h4>Results</h4>Antidepressant prescriptions more than tripled between 1998 and 2018, from 377 items per 1000 population to 1266 per 1000. MAOI prescribing fell substantially, from 0.7% of all antidepressant items in 1998 to 0.1% in 2018. There was marked variation between practices in past year prescribing of paroxetine (median practice proportion [MPP] = 1.7%, interdecile range [IDR] = 2.6%) and dosulepin (MPP = 0.7%, IDR = 1.8%), but less for trimipramine (MPP = 0%, IDR = 0.2%).<h4>Conclusion</h4>Rapid growth and substantial variation in antidepressant prescribing behaviour was found between practices. The causes could be explored using mixed-methods research. Interventions to reduce prescribing of specific antidepressants, such as dosulepin, could include review prompts, alerts at the time of prescribing, and clinician feedback through tools like OpenPrescribing.net.",,pdf:https://bjgpopen.org/content/bjgpoa/5/4/BJGPO.2021.0020.full.pdf; doi:https://doi.org/10.3399/BJGPO.2021.0020; html:https://europepmc.org/articles/PMC8450889; pdf:https://europepmc.org/articles/PMC8450889?pdf=render
-37918923,https://doi.org/10.1136/bmjopen-2023-072531,Evaluation of variation in special educational needs provision and its impact on health and education using administrative records for England: umbrella protocol for a mixed-methods research programme.,"Zylbersztejn A, Lewis K, Nguyen V, Matthews J, Winterburn I, Karwatowska L, Barnes S, Lilliman M, Saxton J, Stone A, Boddy K, Downs J, Logan S, Rahi J, Black-Hawkins K, Dearden L, Ford T, Harron K, De Stavola B, Gilbert R.",,BMJ open,2023,2023-11-02,Y,epidemiology; Public Health; Qualitative Research; Health Informatics; Statistics & Research Methods; Health Equity,,,"<h4>Introduction</h4>One-third of children in England have special educational needs (SEN) provision recorded during their school career. The proportion of children with SEN provision varies between schools and demographic groups, which may reflect variation in need, inequitable provision and/or systemic factors. There is scant evidence on whether SEN provision improves health and education outcomes.<h4>Methods</h4>The Health Outcomes of young People in Education (HOPE) research programme uses administrative data from the Education and Child Health Insights from Linked Data-ECHILD-which contains data from all state schools, and contacts with National Health Service hospitals in England, to explore variation in SEN provision and its impact on health and education outcomes. This umbrella protocol sets out analyses across four work packages (WP). WP1 defined a range of 'health phenotypes', that is health conditions expected to need SEN provision in primary school. Next, we describe health and education outcomes (WP1) and individual, school-level and area-level factors affecting variation in SEN provision across different phenotypes (WP2). WP3 assesses the impact of SEN provision on health and education outcomes for specific health phenotypes using a range of causal inference methods to account for confounding factors and possible selection bias. In WP4 we review local policies and synthesise findings from surveys, interviews and focus groups of service users and providers to understand factors associated with variation in and experiences of identification, assessment and provision for SEN. Triangulation of findings on outcomes, variation and impact of SEN provision for different health phenotypes in ECHILD, with experiences of SEN provision will inform interpretation of findings for policy, practice and families and methods for future evaluation.<h4>Ethics and dissemination</h4>Research ethics committees have approved the use of the ECHILD database and, separately, the survey, interviews and focus groups of young people, parents and service providers. These stakeholders will contribute to the design, interpretation and communication of findings.",,doi:https://doi.org/10.1136/bmjopen-2023-072531; html:https://europepmc.org/articles/PMC10626865; pdf:https://europepmc.org/articles/PMC10626865?pdf=render
 30681347,https://doi.org/10.1161/circgen.118.002328,Integrative Functional Annotation of 52 Genetic Loci Influencing Myocardial Mass Identifies Candidate Regulatory Variants and Target Genes.,"Hemerich D, Pei J, Harakalova M, van Setten J, Boymans S, Boukens BJ, Efimov IR, Michels M, van der Velden J, Vink A, Cheng C, van der Harst P, Moore JH, Mokry M, Tragante V, Asselbergs FW.",,Circulation. Genomic and precision medicine,2019,2019-02-01,N,Genetics; Electrocardiography; Acetylation; Heart Failure; Cardiomyopathies,The Human Phenome,,"<h4>Background</h4>Regulatory elements may be involved in the mechanisms by which 52 loci influence myocardial mass, reflected by abnormal amplitude and duration of the QRS complex on the ECG. Functional annotation thus far did not take into account how these elements are affected in disease context.<h4>Methods</h4>We generated maps of regulatory elements on hypertrophic cardiomyopathy patients (ChIP-seq N=14 and RNA-seq N=11) and nondiseased hearts (ChIP-seq N=4 and RNA-seq N=11). We tested enrichment of QRS-associated loci on elements differentially acetylated and directly regulating differentially expressed genes between hypertrophic cardiomyopathy patients and controls. We further performed functional annotation on QRS-associated loci using these maps of differentially active regulatory elements.<h4>Results</h4>Regions differentially affected in disease showed a stronger enrichment ( P=8.6×10<sup>-5</sup>) for QRS-associated variants than those not showing differential activity ( P=0.01). Promoters of genes differentially regulated between hypertrophic cardiomyopathy patients and controls showed more enrichment ( P=0.001) than differentially acetylated enhancers ( P=0.8) and super-enhancers ( P=0.025). We also identified 74 potential causal variants overlapping these differential regulatory elements. Eighteen of the genes mapped confirmed previous findings, now also pinpointing the potentially affected regulatory elements and candidate causal variants. Fourteen new genes were also mapped.<h4>Conclusions</h4>Our results suggest differentially active regulatory elements between hypertrophic cardiomyopathy patients and controls can offer more insights into the mechanisms of QRS-associated loci than elements not affected by disease.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCGEN.118.002328; doi:https://doi.org/10.1161/CIRCGEN.118.002328; html:https://europepmc.org/articles/PMC6380958; pdf:https://europepmc.org/articles/PMC6380958?pdf=render; doi:https://doi.org/10.1161/circgen.118.002328
+37918923,https://doi.org/10.1136/bmjopen-2023-072531,Evaluation of variation in special educational needs provision and its impact on health and education using administrative records for England: umbrella protocol for a mixed-methods research programme.,"Zylbersztejn A, Lewis K, Nguyen V, Matthews J, Winterburn I, Karwatowska L, Barnes S, Lilliman M, Saxton J, Stone A, Boddy K, Downs J, Logan S, Rahi J, Black-Hawkins K, Dearden L, Ford T, Harron K, De Stavola B, Gilbert R.",,BMJ open,2023,2023-11-02,Y,epidemiology; Public Health; Qualitative Research; Health Informatics; Statistics & Research Methods; Health Equity,,,"<h4>Introduction</h4>One-third of children in England have special educational needs (SEN) provision recorded during their school career. The proportion of children with SEN provision varies between schools and demographic groups, which may reflect variation in need, inequitable provision and/or systemic factors. There is scant evidence on whether SEN provision improves health and education outcomes.<h4>Methods</h4>The Health Outcomes of young People in Education (HOPE) research programme uses administrative data from the Education and Child Health Insights from Linked Data-ECHILD-which contains data from all state schools, and contacts with National Health Service hospitals in England, to explore variation in SEN provision and its impact on health and education outcomes. This umbrella protocol sets out analyses across four work packages (WP). WP1 defined a range of 'health phenotypes', that is health conditions expected to need SEN provision in primary school. Next, we describe health and education outcomes (WP1) and individual, school-level and area-level factors affecting variation in SEN provision across different phenotypes (WP2). WP3 assesses the impact of SEN provision on health and education outcomes for specific health phenotypes using a range of causal inference methods to account for confounding factors and possible selection bias. In WP4 we review local policies and synthesise findings from surveys, interviews and focus groups of service users and providers to understand factors associated with variation in and experiences of identification, assessment and provision for SEN. Triangulation of findings on outcomes, variation and impact of SEN provision for different health phenotypes in ECHILD, with experiences of SEN provision will inform interpretation of findings for policy, practice and families and methods for future evaluation.<h4>Ethics and dissemination</h4>Research ethics committees have approved the use of the ECHILD database and, separately, the survey, interviews and focus groups of young people, parents and service providers. These stakeholders will contribute to the design, interpretation and communication of findings.",,doi:https://doi.org/10.1136/bmjopen-2023-072531; html:https://europepmc.org/articles/PMC10626865; pdf:https://europepmc.org/articles/PMC10626865?pdf=render
 34810237,https://doi.org/10.1136/thoraxjnl-2021-217629,Prospective validation of the 4C prognostic models for adults hospitalised with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol.,"Knight SR, Gupta RK, Ho A, Pius R, Buchan I, Carson G, Drake TM, Dunning J, Fairfield CJ, Gamble C, Green CA, Halpin S, Hardwick HE, Holden KA, Horby PW, Jackson C, Mclean KA, Merson L, Nguyen-Van-Tam JS, Norman L, Olliaro PL, Pritchard MG, Russell CD, Shaw CA, Sheikh A, Solomon T, Sudlow C, Swann OV, Turtle LCW, Openshaw PJM, Baillie JK, Docherty A, Semple MG, Noursadeghi M, Harrison EM, ISARIC Coronavirus Clinical Characterisation Consortium (ISARIC4C) Investigators, ISARIC4C investigators.",,Thorax,2022,2021-11-22,Y,Covid-19,,,"<h4>Purpose</h4>To prospectively validate two risk scores to predict mortality (4C Mortality) and in-hospital deterioration (4C Deterioration) among adults hospitalised with COVID-19.<h4>Methods</h4>Prospective observational cohort study of adults (age ≥18 years) with confirmed or highly suspected COVID-19 recruited into the International Severe Acute Respiratory and emerging Infections Consortium (ISARIC) WHO Clinical Characterisation Protocol UK (CCP-UK) study in 306 hospitals across England, Scotland and Wales. Patients were recruited between 27 August 2020 and 17 February 2021, with at least 4 weeks follow-up before final data extraction. The main outcome measures were discrimination and calibration of models for in-hospital deterioration (defined as any requirement of ventilatory support or critical care, or death) and mortality, incorporating predefined subgroups.<h4>Results</h4>76 588 participants were included, of whom 27 352 (37.4%) deteriorated and 12 581 (17.4%) died. Both the 4C Mortality (0.78 (0.77 to 0.78)) and 4C Deterioration scores (pooled C-statistic 0.76 (95% CI 0.75 to 0.77)) demonstrated consistent discrimination across all nine National Health Service regions, with similar performance metrics to the original validation cohorts. Calibration remained stable (4C Mortality: pooled slope 1.09, pooled calibration-in-the-large 0.12; 4C Deterioration: 1.00, -0.04), with no need for temporal recalibration during the second UK pandemic wave of hospital admissions.<h4>Conclusion</h4>Both 4C risk stratification models demonstrate consistent performance to predict clinical deterioration and mortality in a large prospective second wave validation cohort of UK patients. Despite recent advances in the treatment and management of adults hospitalised with COVID-19, both scores can continue to inform clinical decision making.<h4>Trial registration number</h4>ISRCTN66726260.",,pdf:https://thorax.bmj.com/content/thoraxjnl/77/6/606.full.pdf; doi:https://doi.org/10.1136/thoraxjnl-2021-217629; html:https://europepmc.org/articles/PMC8610617; pdf:https://europepmc.org/articles/PMC8610617?pdf=render
 33415961,https://doi.org/10.19191/ep20.5-6.s1.p179.088,Initial plans for a large-scale investigation into the chronic health effects of earthquakes in Italy: building on Barbara Pacelli's legacy.,"Allara E, Ripoll Gallardo A, Fabiani L, Barone Adesi F, Sofianopoulou E, Ragazzoni L, Wood A, Faggiano F, Della Corte F.",,Epidemiologia e prevenzione,2020,2020-09-01,N,,,,"Barbara Pacelli, a young Italian epidemiologist, passed away unexpectedly in September 2019. During her prolific professional life, she gave several scientific contributions to natural disaster epidemiology, particularly in relation to the medium and long-term health effects of earthquakes. In this opinion paper, we reflect on Barbara's legacy and outline potential actions that could arise from her work. Particularly, availability of electronic health records would enable a systematic and large-scale investigation into the long-term health effects of earthquakes in Italy, a country with high seismic risk. This effort would have high societal value as it would likely enable mitigation of substantial morbidity and mortality in areas affected by earthquakes. In this paper, we define scope, objectives, potential data sources, and analysis methods that could be used to systematically assess the chronic health effects of recent earthquakes in Italy. Keywords: earthquakes; chronic diseases; electronic health records; retrospective cohort; case crossover study.",,doi:https://doi.org/10.19191/EP20.5-6.S1.P179.088
 34645462,https://doi.org/10.1186/s12974-021-02287-9,T lymphocyte senescence is attenuated in Parkinson's disease.,"Kouli A, Jensen M, Papastavrou V, Scott KM, Kolenda C, Parker C, Solim IH, Camacho M, Martin-Ruiz C, Williams-Gray CH.",,Journal of neuroinflammation,2021,2021-10-13,Y,T lymphocytes; Immunosenescence; Parkinson’s Disease; Ageing Markers,,,"<h4>Background</h4>Immune involvement is well-described in Parkinson's disease (PD), including an adaptive T lymphocyte response. Given the increasing prevalence of Parkinson's disease in older age, age-related dysregulation of T lymphocytes may be relevant in this disorder, and we have previously observed changes in age-associated CD8<sup>+</sup> T cell subsets in mid-stage PD. This study aimed to further characterise T cell immunosenescence in newly diagnosed PD patients, including shifts in CD4<sup>+</sup> and CD8<sup>+</sup> subpopulations, and changes in markers of cellular ageing in CD8<sup>+</sup> T lymphocytes.<h4>Methods</h4>Peripheral blood mononuclear cells were extracted from the blood of 61 newly diagnosed PD patients and 63 age- and sex-matched controls. Flow cytometric analysis was used for immunophenotyping of CD8<sup>+</sup> and CD4<sup>+</sup> lymphocyte subsets, and analysis of recent thymic emigrant cells. Telomere length within CD8<sup>+</sup> T lymphocytes was assessed, as well as the expression of the telomerase reverse transcriptase enzyme (hTERT), and the cell-ageing markers p16<sup>INK4a</sup> and p21<sup>CIP1/Waf1</sup>.<h4>Results</h4>The number of CD8<sup>+</sup> TEMRA T cells was found to be significantly reduced in PD patients compared to controls. The expression of p16<sup>INK4a</sup> in CD8<sup>+</sup> lymphocytes was also lower in patients versus controls. Chronic latent CMV infection was associated with increased senescent CD8<sup>+</sup> lymphocytes in healthy controls, but this shift was less apparent in PD patients.<h4>Conclusions</h4>Taken together, our data demonstrate a reduction in CD8<sup>+</sup> T cell replicative senescence which is present at the earliest stages of Parkinson's disease.",,pdf:https://jneuroinflammation.biomedcentral.com/track/pdf/10.1186/s12974-021-02287-9; doi:https://doi.org/10.1186/s12974-021-02287-9; html:https://europepmc.org/articles/PMC8513368; pdf:https://europepmc.org/articles/PMC8513368?pdf=render
 35605170,https://doi.org/10.2196/37668,Differences in Clinical Presentation With Long COVID After Community and Hospital Infection and Associations With All-Cause Mortality: English Sentinel Network Database Study.,"Meza-Torres B, Delanerolle G, Okusi C, Mayor N, Anand S, Macartney J, Gatenby P, Glampson B, Chapman M, Curcin V, Mayer E, Joy M, Greenhalgh T, Delaney B, de Lusignan S.",,JMIR public health and surveillance,2022,2022-08-16,Y,Phenotype; Hospitalization; Social Class; General Practitioners; Ethnicity; Medical Record Systems; Systematized Nomenclature Of Medicine; Computerized; Biomedical Ontologies; Data Accuracy; Covid-19; Sars-cov-2; Long Covid; Post–covid-19 Syndrome; Post–acute Covid-19 Syndrome; Data Extracts,,,"<h4>Background</h4>Most studies of long COVID (symptoms of COVID-19 infection beyond 4 weeks) have focused on people hospitalized in their initial illness. Long COVID is thought to be underrecorded in UK primary care electronic records.<h4>Objective</h4>We sought to determine which symptoms people present to primary care after COVID-19 infection and whether presentation differs in people who were not hospitalized, as well as post-long COVID mortality rates.<h4>Methods</h4>We used routine data from the nationally representative primary care sentinel cohort of the Oxford-Royal College of General Practitioners Research and Surveillance Centre (N=7,396,702), applying a predefined long COVID phenotype and grouped by whether the index infection occurred in hospital or in the community. We included COVID-19 infection cases from March 1, 2020, to April 1, 2021. We conducted a before-and-after analysis of long COVID symptoms prespecified by the Office of National Statistics, comparing symptoms presented between 1 and 6 months after the index infection matched with the same months 1 year previously. We conducted logistic regression analysis, quoting odds ratios (ORs) with 95% CIs.<h4>Results</h4>In total, 5.63% (416,505/7,396,702) and 1.83% (7623/416,505) of the patients had received a coded diagnosis of COVID-19 infection and diagnosis of, or referral for, long COVID, respectively. People with diagnosis or referral of long COVID had higher odds of presenting the prespecified symptoms after versus before COVID-19 infection (OR 2.66, 95% CI 2.46-2.88, for those with index community infection and OR 2.42, 95% CI 2.03-2.89, for those hospitalized). After an index community infection, patients were more likely to present with nonspecific symptoms (OR 3.44, 95% CI 3.00-3.95; P<.001) compared with after a hospital admission (OR 2.09, 95% CI 1.56-2.80; P<.001). Mental health sequelae were more strongly associated with index hospital infections (OR 2.21, 95% CI 1.64-2.96) than with index community infections (OR 1.36, 95% CI 1.21-1.53; P<.001). People presenting to primary care after hospital infection were more likely to be men (OR 1.43, 95% CI 1.25-1.64; P<.001), more socioeconomically deprived (OR 1.42, 95% CI 1.24-1.63; P<.001), and with higher multimorbidity scores (OR 1.41, 95% CI 1.26-1.57; P<.001) than those presenting after an index community infection. All-cause mortality in people with long COVID was associated with increasing age, male sex (OR 3.32, 95% CI 1.34-9.24; P=.01), and higher multimorbidity score (OR 2.11, 95% CI 1.34-3.29; P<.001). Vaccination was associated with reduced odds of mortality (OR 0.10, 95% CI 0.03-0.35; P<.001).<h4>Conclusions</h4>The low percentage of people recorded as having long COVID after COVID-19 infection reflects either low prevalence or underrecording. The characteristics and comorbidities of those presenting with long COVID after a community infection are different from those hospitalized. This study provides insights into the presentation of long COVID in primary care and implications for workload.",,pdf:https://publichealth.jmir.org/2022/8/e37668/PDF; doi:https://doi.org/10.2196/37668; html:https://europepmc.org/articles/PMC9384859
 33623826,https://doi.org/10.12688/wellcomeopenres.16164.2,"The effectiveness of social bubbles as part of a Covid-19 lockdown exit strategy, a modelling study.","Leng T, White C, Hilton J, Kucharski A, Pellis L, Stage H, Davies NG, Centre for Mathematical Modelling of Infectious Disease 2019 nCoV Working Group, Keeling MJ, Flasche S.",,Wellcome open research,2020,2020-01-01,Y,Exit Strategy; Covid-19; Contact Clustering; Social Bubble,,,"<b>Background:</b> <i>​</i> During the coronavirus disease 2019 (COVID-19) lockdown, contact clustering in social bubbles may allow extending contacts beyond the household at minimal additional risk and hence has been considered as part of modified lockdown policy or a gradual lockdown exit strategy. We estimated the impact of such strategies on epidemic and mortality risk using the UK as a case study. <b>Methods:</b> <i>​</i> We used an individual based model for a synthetic population similar to the UK, stratified into transmission risks from the community, within the household and from other households in the same social bubble. The base case considers a situation where non-essential shops and schools are closed, the secondary household attack rate is 20% and the initial reproduction number is 0.8. We simulate social bubble strategies (where two households form an exclusive pair) for households including children, for single occupancy households, and for all households. We test the sensitivity of results to a range of alternative model assumptions and parameters. <b>Results:</b>  Clustering contacts outside the household into exclusive bubbles is an effective strategy of increasing contacts while limiting the associated increase in epidemic risk. In the base case, social bubbles reduced fatalities by 42% compared to an unclustered increase of contacts. We find that if all households were to form social bubbles the reproduction number would likely increase to above the epidemic threshold of R=1. Strategies allowing households with young children or single occupancy households to form social bubbles increased the reproduction number by less than 11%. The corresponding increase in mortality is proportional to the increase in the epidemic risk but is focussed in older adults irrespective of inclusion in social bubbles. <b>Conclusions: ​</b> If managed appropriately, social bubbles can be an effective way of extending contacts beyond the household while limiting the increase in epidemic risk.",,doi:https://doi.org/10.12688/wellcomeopenres.16164.2; html:https://europepmc.org/articles/PMC7871360; pdf:https://europepmc.org/articles/PMC7871360?pdf=render
 35142634,https://doi.org/10.2196/31885,Investigating Genetic and Other Determinants of First-Onset Myocardial Infarction in Malaysia: Protocol for the Malaysian Acute Vascular Events Risk Study.,"Chowdhury R, Noh MFM, Ismail SR, van Daalen KR, Kamaruddin PSNM, Zulkiply SH, Azizul NH, Khalid NM, Ali A, Idris IM, Mei YS, Abdullah SR, Faridus N, Yusof NAM, Yusoff NNFM, Jamal R, Rahim AAA, Ghapar AKA, Radhakrishnan AK, Fong AYY, Ismail O, Krishinan S, Lee CY, Bang LH, Mageswaren E, Mahendran K, Amin NHM, Muthusamy G, Jin AOH, Ramli AW, Ross NT, Ruhani AI, Yahya M, Yusoff Y, Abidin SKZ, Amado L, Bolton T, Weston S, Crawte J, Ovenden N, Michielsen A, Monower MM, Mahiyuddin WRW, Wood A, Di Angelantonio E, Sulaiman NS, Danesh J, Butterworth AS.",,JMIR research protocols,2022,2022-02-10,Y,Myocardial infarction; Malaysia; Cardiovascular disease; Case-control study,,,"<h4>Background</h4>Although the burden of premature myocardial infarction (MI) is high in Malaysia, direct evidence on the determinants of MI in this multi-ethnic population remains sparse.<h4>Objective</h4>The Malaysian Acute Vascular Events Risk (MAVERIK) study is a retrospective case-control study established to investigate the genomic, lipid-related, and other determinants of acute MI in Malaysia. In this paper, we report the study protocol and early results.<h4>Methods</h4>By June 2019, we had enrolled approximately 2500 patients with their first MI and 2500 controls without cardiovascular disease, who were frequency-matched by age, sex, and ethnicity, from 17 hospitals in Malaysia. For each participant, serum and whole blood have been collected and stored. Clinical, demographic, and behavioral information has been obtained using a 200-item questionnaire.<h4>Results</h4>Tobacco consumption, a history of diabetes, hypertension, markers of visceral adiposity, indicators of lower socioeconomic status, and a family history of coronary disease were more prevalent in cases than in controls. Adjusted (age and sex) logistic regression models for traditional risk factors indicated that current smoking (odds ratio [OR] 4.11, 95% CI 3.56-4.75; P<.001), previous smoking (OR 1.34, 95% CI 1.12-1.60; P=.001), a history of high blood pressure (OR 2.13, 95% CI 1.86-2.44; P<.001), a history of diabetes mellitus (OR 2.72, 95% CI 2.34-3.17; P<.001), a family history of coronary heart disease (OR 1.28, 95% CI 1.07-1.55; P=.009), and obesity (BMI >30 kg/m<sup>2</sup>; OR 1.19, 95% CI 1.05-1.34; P=.009) were associated with MI in age- and sex-adjusted models.<h4>Conclusions</h4>The MAVERIK study can serve as a useful platform to investigate genetic and other risk factors for MI in an understudied Southeast Asian population. It should help to hasten the discovery of disease-causing pathways and inform regionally appropriate strategies that optimize public health action.<h4>International registered report identifier (irrid)</h4>RR1-10.2196/31885.",,pdf:https://www.researchprotocols.org/2022/2/e31885/PDF; doi:https://doi.org/10.2196/31885; html:https://europepmc.org/articles/PMC8874931
-35545669,https://doi.org/10.1038/s41586-022-04712-2,Genetic and chemotherapeutic influences on germline hypermutation.,"Kaplanis J, Ide B, Sanghvi R, Neville M, Danecek P, Coorens T, Prigmore E, Short P, Gallone G, McRae J, Genomics England Research Consortium, Carmichael J, Barnicoat A, Firth H, O'Brien P, Rahbari R, Hurles M.",,Nature,2022,2022-05-11,Y,,,,"Mutations in the germline generates all evolutionary genetic variation and is a cause of genetic disease. Parental age is the primary determinant of the number of new germline mutations in an individual's genome<sup>1,2</sup>. Here we analysed the genome-wide sequences of 21,879 families with rare genetic diseases and identified 12 individuals with a hypermutated genome with between two and seven times more de novo single-nucleotide variants than expected. In most families (9 out of 12), the excess mutations came from the father. Two families had genetic drivers of germline hypermutation, with fathers carrying damaging genetic variation in DNA-repair genes. For five of the families, paternal exposure to chemotherapeutic agents before conception was probably a key driver of hypermutation. Our results suggest that the germline is well protected from mutagenic effects, hypermutation is rare, the number of excess mutations is relatively modest and most individuals with a hypermutated genome will not have a genetic disease.",,pdf:https://www.nature.com/articles/s41586-022-04712-2.pdf; doi:https://doi.org/10.1038/s41586-022-04712-2; html:https://europepmc.org/articles/PMC9117138; pdf:https://europepmc.org/articles/PMC9117138?pdf=render
-31794059,https://doi.org/10.1111/bjd.18778,What is the evidence for interactions between filaggrin null mutations and environmental exposures in the aetiology of atopic dermatitis? A systematic review.,"Blakeway H, Van-de-Velde V, Allen VB, Kravvas G, Palla L, Page MJ, Flohr C, Weller RB, Irvine AD, McPherson T, Roberts A, Williams HC, Reynolds N, Brown SJ, Paternoster L, Langan SM, (on behalf of UK TREND Eczema Network).",,The British journal of dermatology,2020,2020-02-11,Y,,,,"<h4>Background</h4>Epidemiological studies indicate that gene-environment interactions play a role in atopic dermatitis (AD).<h4>Objectives</h4>To review the evidence for gene-environment interactions in AD aetiology, focusing on filaggrin (FLG) loss-of-function mutations.<h4>Methods</h4>A systematic search from inception to September 2018 in Embase, MEDLINE and BIOSIS was performed. Search terms included all synonyms for AD and filaggrin/FLG; any genetic or epidemiological study design using any statistical methods were included. Quality assessment using criteria modified from guidance (ROBINS-I and Human Genome Epidemiology Network) for nonrandomized and genetic studies was completed, including consideration of power. Heterogeneity of study design and analyses precluded the use of meta-analysis.<h4>Results</h4>Of 1817 papers identified, 12 studies fulfilled the inclusion criteria required and performed formal interaction testing. There was some evidence for FLG-environment interactions in six of the studies (P-value for interaction ≤ 0·05), including early-life cat ownership, older siblings, water hardness, phthalate exposure, higher urinary phthalate metabolite levels (which all increased AD risk additional to FLG null genotype) and prolonged breastfeeding (which decreased AD risk in the context of FLG null genotype). Major limitations of published studies were the low numbers of individuals (ranging from five to 94) with AD and FLG loss-of-function mutations and exposure to specific environmental factors, and variation in exposure definitions.<h4>Conclusions</h4>Evidence on FLG-environment interactions in AD aetiology is limited. However, many of the studies lacked large enough sample sizes to assess these interactions fully. Further research is needed with larger sample sizes and clearly defined exposure assessment. Linked Comment: Park and Seo. Br J Dermatol 2020; 183:411.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/bjd.18778; doi:https://doi.org/10.1111/bjd.18778; html:https://europepmc.org/articles/PMC7496176; pdf:https://europepmc.org/articles/PMC7496176?pdf=render
 32184442,https://doi.org/10.1038/s42003-020-0857-9,Genome-wide association identifies seven loci for pelvic organ prolapse in Iceland and the UK Biobank.,"Olafsdottir T, Thorleifsson G, Sulem P, Stefansson OA, Medek H, Olafsson K, Ingthorsson O, Gudmundsson V, Jonsdottir I, Halldorsson GH, Kristjansson RP, Frigge ML, Stefansdottir L, Sigurdsson JK, Oddsson A, Sigurdsson A, Eggertsson HP, Melsted P, Halldorsson BV, Lund SH, Styrkarsdottir U, Steinthorsdottir V, Gudmundsson J, Holm H, Tragante V, Asselbergs FW, Thorsteinsdottir U, Gudbjartsson DF, Jonsdottir K, Rafnar T, Stefansson K.",,Communications biology,2020,2020-03-17,Y,,,,"Pelvic organ prolapse (POP) is a downward descent of one or more of the pelvic organs, resulting in a protrusion of the vaginal wall and/or uterus. We performed a genome-wide association study of POP using data from Iceland and the UK Biobank, a total of 15,010 cases with hospital-based diagnosis code and 340,734 female controls, and found eight sequence variants at seven loci associating with POP (P < 5 × 10<sup>-8</sup>); seven common (minor allele frequency >5%) and one with minor allele frequency of 4.87%. Some of the variants associating with POP also associated with traits of similar pathophysiology. Of these, rs3820282, which may alter the estrogen-based regulation of WNT4, also associates with leiomyoma of uterus, gestational duration and endometriosis. Rs3791675 at EFEMP1, a gene involved in connective tissue homeostasis, also associates with hernias and carpal tunnel syndrome. Our results highlight the role of connective tissue metabolism and estrogen exposure in the etiology of POP.",,pdf:https://www.nature.com/articles/s42003-020-0857-9.pdf; doi:https://doi.org/10.1038/s42003-020-0857-9; html:https://europepmc.org/articles/PMC7078216; pdf:https://europepmc.org/articles/PMC7078216?pdf=render
+31794059,https://doi.org/10.1111/bjd.18778,What is the evidence for interactions between filaggrin null mutations and environmental exposures in the aetiology of atopic dermatitis? A systematic review.,"Blakeway H, Van-de-Velde V, Allen VB, Kravvas G, Palla L, Page MJ, Flohr C, Weller RB, Irvine AD, McPherson T, Roberts A, Williams HC, Reynolds N, Brown SJ, Paternoster L, Langan SM, (on behalf of UK TREND Eczema Network).",,The British journal of dermatology,2020,2020-02-11,Y,,,,"<h4>Background</h4>Epidemiological studies indicate that gene-environment interactions play a role in atopic dermatitis (AD).<h4>Objectives</h4>To review the evidence for gene-environment interactions in AD aetiology, focusing on filaggrin (FLG) loss-of-function mutations.<h4>Methods</h4>A systematic search from inception to September 2018 in Embase, MEDLINE and BIOSIS was performed. Search terms included all synonyms for AD and filaggrin/FLG; any genetic or epidemiological study design using any statistical methods were included. Quality assessment using criteria modified from guidance (ROBINS-I and Human Genome Epidemiology Network) for nonrandomized and genetic studies was completed, including consideration of power. Heterogeneity of study design and analyses precluded the use of meta-analysis.<h4>Results</h4>Of 1817 papers identified, 12 studies fulfilled the inclusion criteria required and performed formal interaction testing. There was some evidence for FLG-environment interactions in six of the studies (P-value for interaction ≤ 0·05), including early-life cat ownership, older siblings, water hardness, phthalate exposure, higher urinary phthalate metabolite levels (which all increased AD risk additional to FLG null genotype) and prolonged breastfeeding (which decreased AD risk in the context of FLG null genotype). Major limitations of published studies were the low numbers of individuals (ranging from five to 94) with AD and FLG loss-of-function mutations and exposure to specific environmental factors, and variation in exposure definitions.<h4>Conclusions</h4>Evidence on FLG-environment interactions in AD aetiology is limited. However, many of the studies lacked large enough sample sizes to assess these interactions fully. Further research is needed with larger sample sizes and clearly defined exposure assessment. Linked Comment: Park and Seo. Br J Dermatol 2020; 183:411.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/bjd.18778; doi:https://doi.org/10.1111/bjd.18778; html:https://europepmc.org/articles/PMC7496176; pdf:https://europepmc.org/articles/PMC7496176?pdf=render
+35545669,https://doi.org/10.1038/s41586-022-04712-2,Genetic and chemotherapeutic influences on germline hypermutation.,"Kaplanis J, Ide B, Sanghvi R, Neville M, Danecek P, Coorens T, Prigmore E, Short P, Gallone G, McRae J, Genomics England Research Consortium, Carmichael J, Barnicoat A, Firth H, O'Brien P, Rahbari R, Hurles M.",,Nature,2022,2022-05-11,Y,,,,"Mutations in the germline generates all evolutionary genetic variation and is a cause of genetic disease. Parental age is the primary determinant of the number of new germline mutations in an individual's genome<sup>1,2</sup>. Here we analysed the genome-wide sequences of 21,879 families with rare genetic diseases and identified 12 individuals with a hypermutated genome with between two and seven times more de novo single-nucleotide variants than expected. In most families (9 out of 12), the excess mutations came from the father. Two families had genetic drivers of germline hypermutation, with fathers carrying damaging genetic variation in DNA-repair genes. For five of the families, paternal exposure to chemotherapeutic agents before conception was probably a key driver of hypermutation. Our results suggest that the germline is well protected from mutagenic effects, hypermutation is rare, the number of excess mutations is relatively modest and most individuals with a hypermutated genome will not have a genetic disease.",,pdf:https://www.nature.com/articles/s41586-022-04712-2.pdf; doi:https://doi.org/10.1038/s41586-022-04712-2; html:https://europepmc.org/articles/PMC9117138; pdf:https://europepmc.org/articles/PMC9117138?pdf=render
 35962208,https://doi.org/10.1038/s41591-022-01951-8,Publisher Correction: Reporting guideline for the early-stage clinical evaluation of decision support systems driven by artificial intelligence: DECIDE-AI.,"Vasey B, Nagendran M, Campbell B, Clifton DA, Collins GS, Denaxas S, Denniston AK, Faes L, Geerts B, Ibrahim M, Liu X, Mateen BA, Mathur P, McCradden MD, Morgan L, Ordish J, Rogers C, Saria S, Ting DSW, Watkinson P, Weber W, Wheatstone P, McCulloch P, DECIDE-AI expert group.",,Nature medicine,2022,2022-10-01,N,,,,,,pdf:https://www.nature.com/articles/s41591-022-01951-8.pdf; doi:https://doi.org/10.1038/s41591-022-01951-8
 34468322,https://doi.org/10.2196/30083,An Early Warning Risk Prediction Tool (RECAP-V1) for Patients Diagnosed With COVID-19: Protocol for a Statistical Analysis Plan.,"Fiorentino F, Prociuk D, Espinosa Gonzalez AB, Neves AL, Husain L, Ramtale SC, Mi E, Mi E, Macartney J, Anand SN, Sherlock J, Saravanakumar K, Mayer E, de Lusignan S, Greenhalgh T, Delaney BC.",,JMIR research protocols,2021,2021-10-05,Y,Modeling; Early warning; Risk Score; Remote Assessment; Covid-19,,,"<h4>Background</h4>Since the start of the COVID-19 pandemic, efforts have been made to develop early warning risk scores to help clinicians decide which patient is likely to deteriorate and require hospitalization. The RECAP (Remote COVID-19 Assessment in Primary Care) study investigates the predictive risk of hospitalization, deterioration, and death of patients with confirmed COVID-19, based on a set of parameters chosen through a Delphi process performed by clinicians. We aim to use rich data collected remotely through the use of electronic data templates integrated in the electronic health systems of several general practices across the United Kingdom to construct accurate predictive models. The models will be based on preexisting conditions and monitoring data of a patient's clinical parameters (eg, blood oxygen saturation) to make reliable predictions as to the patient's risk of hospital admission, deterioration, and death.<h4>Objective</h4>This statistical analysis plan outlines the statistical methods to build the prediction model to be used in the prioritization of patients in the primary care setting. The statistical analysis plan for the RECAP study includes the development and validation of the RECAP-V1 prediction model as a primary outcome. This prediction model will be adapted as a three-category risk score split into red (high risk), amber (medium risk), and green (low risk) for any patient with suspected COVID-19. The model will predict the risk of deterioration and hospitalization.<h4>Methods</h4>After the data have been collected, we will assess the degree of missingness and use a combination of traditional data imputation using multiple imputation by chained equations, as well as more novel machine-learning approaches to impute the missing data for the final analysis. For predictive model development, we will use multiple logistic regression analyses to construct the model. We aim to recruit a minimum of 1317 patients for model development and validation. We will then externally validate the model on an independent dataset of 1400 patients. The model will also be applied for multiple different datasets to assess both its performance in different patient groups and its applicability for different methods of data collection.<h4>Results</h4>As of May 10, 2021, we have recruited 3732 patients. A further 2088 patients have been recruited through the National Health Service Clinical Assessment Service, and approximately 5000 patients have been recruited through the DoctalyHealth platform.<h4>Conclusions</h4>The methodology for the development of the RECAP-V1 prediction model as well as the risk score will provide clinicians with a statistically robust tool to help prioritize COVID-19 patients.<h4>Trial registration</h4>ClinicalTrials.gov NCT04435041; https://clinicaltrials.gov/ct2/show/NCT04435041.<h4>International registered report identifier (irrid)</h4>DERR1-10.2196/30083.",,doi:https://doi.org/10.2196/30083; doi:https://doi.org/10.2196/30083; html:https://europepmc.org/articles/PMC8494068
 31382511,https://doi.org/10.3390/toxins11080454,Indoxyl Sulfate Stimulates Angiogenesis by Regulating Reactive Oxygen Species Production via CYP1B1.,"Pei J, Juni R, Harakalova M, Duncker DJ, Asselbergs FW, Koolwijk P, Hinsbergh VV, Verhaar MC, Mokry M, Cheng C.",,Toxins,2019,2019-08-02,Y,Reactive oxygen species; Angiogenesis; Chronic Kidney Disease; Cyp1b1; Indoxyl Sulfate,Understanding the Causes of Disease,,"Indoxyl sulfate (IS) is an accumulative protein-bound uremic toxin found in patients with kidney disease. It is reported that IS impairs the vascular endothelium, but a comprehensive overview of all mechanisms active in IS-injury currently remains lacking. Here we performed RNA sequencing in human umbilical vein endothelial cells (HUVECs) after IS or control medium treatment and identified 1293 genes that were affected in a IS-induced response. Gene enrichment analysis highlighted pathways involved in altered vascular formation and cell metabolism. We confirmed these transcriptome profiles at the functional level by demonstrating decreased viability and increased cell senescence in response to IS treatment. In line with the additional pathways highlighted by the transcriptome analysis, we further could demonstrate that IS exposure of HUVECs promoted tubule formation as shown by the increase in total tubule length in a 3D HUVECs/pericytes co-culture assay. Notably, the pro-angiogenic response of IS and increased ROS production were abolished when <i>CYP1B1</i>, one of the main target genes that was highly upregulated by IS, was silenced. This observation indicates IS-induced ROS in endothelial cells is <i>CYP1B1</i>-dependent. Taken together, our findings demonstrate that IS promotes angiogenesis and <i>CYP1B1</i> is an important factor in IS-activated angiogenic response.",,pdf:https://www.mdpi.com/2072-6651/11/8/454/pdf?version=1565690179; doi:https://doi.org/10.3390/toxins11080454; html:https://europepmc.org/articles/PMC6723868; pdf:https://europepmc.org/articles/PMC6723868?pdf=render
@@ -2441,8 +2443,8 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 34600625,https://doi.org/10.1016/s0140-6736(21)01609-3,"Fatal police violence by race and state in the USA, 1980-2019: a network meta-regression.",GBD 2019 Police Violence US Subnational Collaborators.,,"Lancet (London, England)",2021,2021-10-01,Y,,,,"<h4>Background</h4>The burden of fatal police violence is an urgent public health crisis in the USA. Mounting evidence shows that deaths at the hands of the police disproportionately impact people of certain races and ethnicities, pointing to systemic racism in policing. Recent high-profile killings by police in the USA have prompted calls for more extensive and public data reporting on police violence. This study examines the presence and extent of under-reporting of police violence in US Government-run vital registration data, offers a method for correcting under-reporting in these datasets, and presents revised estimates of deaths due to police violence in the USA.<h4>Methods</h4>We compared data from the USA National Vital Statistics System (NVSS) to three non-governmental, open-source databases on police violence: Fatal Encounters, Mapping Police Violence, and The Counted. We extracted and standardised the age, sex, US state of death registration, year of death, and race and ethnicity (non-Hispanic White, non-Hispanic Black, non-Hispanic of other races, and Hispanic of any race) of each decedent for all data sources and used a network meta-regression to quantify the rate of under-reporting within the NVSS. Using these rates to inform correction factors, we provide adjusted estimates of deaths due to police violence for all states, ages, sexes, and racial and ethnic groups from 1980 to 2019 across the USA.<h4>Findings</h4>Across all races and states in the USA, we estimate 30 800 deaths (95% uncertainty interval [UI] 30 300-31 300) from police violence between 1980 and 2018; this represents 17 100 more deaths (16 600-17 600) than reported by the NVSS. Over this time period, the age-standardised mortality rate due to police violence was highest in non-Hispanic Black people (0·69 [95% UI 0·67-0·71] per 100 000), followed by Hispanic people of any race (0·35 [0·34-0·36]), non-Hispanic White people (0·20 [0·19-0·20]), and non-Hispanic people of other races (0·15 [0·14- 0·16]). This variation is further affected by the decedent's sex and shows large discrepancies between states. Between 1980 and 2018, the NVSS did not report 55·5% (54·8-56·2) of all deaths attributable to police violence. When aggregating all races, the age-standardised mortality rate due to police violence was 0·25 (0·24-0·26) per 100 000 in the 1980s and 0·34 (0·34-0·35) per 100 000 in the 2010s, an increase of 38·4% (32·4-45·1) over the period of study.<h4>Interpretation</h4>We found that more than half of all deaths due to police violence that we estimated in the USA from 1980 to 2018 were unreported in the NVSS. Compounding this, we found substantial differences in the age-standardised mortality rate due to police violence over time and by racial and ethnic groups within the USA. Proven public health intervention strategies are needed to address these systematic biases. State-level estimates allow for appropriate targeting of these strategies to address police violence and improve its reporting.<h4>Funding</h4>Bill & Melinda Gates Foundation, National Institute on Minority Health and Health Disparities, and National Heart, Lung, and Blood Institute.",,pdf:http://www.thelancet.com/article/S0140673621016093/pdf; doi:https://doi.org/10.1016/S0140-6736(21)01609-3; html:https://europepmc.org/articles/PMC8485022; pdf:https://europepmc.org/articles/PMC8485022?pdf=render
 38448586,https://doi.org/10.1038/s41586-024-07148-y,Genome-wide characterization of circulating metabolic biomarkers.,"Karjalainen MK, Karthikeyan S, Oliver-Williams C, Sliz E, Allara E, Fung WT, Surendran P, Zhang W, Jousilahti P, Kristiansson K, Salomaa V, Goodwin M, Hughes DA, Boehnke M, Fernandes Silva L, Yin X, Mahajan A, Neville MJ, van Zuydam NR, de Mutsert R, Li-Gao R, Mook-Kanamori DO, Demirkan A, Liu J, Noordam R, Trompet S, Chen Z, Kartsonaki C, Li L, Lin K, Hagenbeek FA, Hottenga JJ, Pool R, Ikram MA, van Meurs J, Haller T, Milaneschi Y, Kähönen M, Mishra PP, Joshi PK, Macdonald-Dunlop E, Mangino M, Zierer J, Acar IE, Hoyng CB, Lechanteur YTE, Franke L, Kurilshikov A, Zhernakova A, Beekman M, van den Akker EB, Kolcic I, Polasek O, Rudan I, Gieger C, Waldenberger M, Asselbergs FW, China Kadoorie Biobank Collaborative Group, Estonian Biobank Research Team, FinnGen, Hayward C, Fu J, den Hollander AI, Menni C, Spector TD, Wilson JF, Lehtimäki T, Raitakari OT, Penninx BWJH, Esko T, Walters RG, Jukema JW, Sattar N, Ghanbari M, Willems van Dijk K, Karpe F, McCarthy MI, Laakso M, Järvelin MR, Timpson NJ, Perola M, Kooner JS, Chambers JC, van Duijn C, Slagboom PE, Boomsma DI, Danesh J, Ala-Korpela M, Butterworth AS, Kettunen J.",,Nature,2024,2024-03-06,Y,,,,"Genome-wide association analyses using high-throughput metabolomics platforms have led to novel insights into the biology of human metabolism<sup>1-7</sup>. This detailed knowledge of the genetic determinants of systemic metabolism has been pivotal for uncovering how genetic pathways influence biological mechanisms and complex diseases<sup>8-11</sup>. Here we present a genome-wide association study for 233 circulating metabolic traits quantified by nuclear magnetic resonance spectroscopy in up to 136,016 participants from 33 cohorts. We identify more than 400 independent loci and assign probable causal genes at two-thirds of these using manual curation of plausible biological candidates. We highlight the importance of sample and participant characteristics that can have significant effects on genetic associations. We use detailed metabolic profiling of lipoprotein- and lipid-associated variants to better characterize how known lipid loci and novel loci affect lipoprotein metabolism at a granular level. We demonstrate the translational utility of comprehensively phenotyped molecular data, characterizing the metabolic associations of intrahepatic cholestasis of pregnancy. Finally, we observe substantial genetic pleiotropy for multiple metabolic pathways and illustrate the importance of careful instrument selection in Mendelian randomization analysis, revealing a putative causal relationship between acetone and hypertension. Our publicly available results provide a foundational resource for the community to examine the role of metabolism across diverse diseases.",,pdf:https://www.nature.com/articles/s41586-024-07148-y.pdf; doi:https://doi.org/10.1038/s41586-024-07148-y; html:https://europepmc.org/articles/PMC10990933; pdf:https://europepmc.org/articles/PMC10990933?pdf=render
 37178379,https://doi.org/10.1002/ajmg.b.32938,Genetic examination of the Mood Disorder Questionnaire and its relationship with bipolar disorder.,"Mundy J, Hübel C, Adey BN, Davies HL, Davies MR, Coleman JRI, Hotopf M, Kalsi G, Lee SH, McIntosh AM, Rogers HC, Eley TC, Murray RM, Vassos E, Breen G.",,"American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics",2023,2023-05-13,Y,Factor analysis; Genetic correlation; Bipolar disorder; Mania; Hypomania; Genome-wide Association Study,,,"The Mood Disorder Questionnaire (MDQ) is a common screening tool for bipolar disorder that assesses manic symptoms. Its utility for genetic studies of mania or bipolar traits has not been fully examined. We psychometrically compared the MDQ to self-reported bipolar disorder in participants from the United Kingdom National Institute of Health and Care Research Mental Health BioResource. We conducted genome-wide association studies of manic symptom quantitative traits and symptom subgroups, derived from the MDQ items (N = 11,568-19,859). We calculated genetic correlations with bipolar disorder and other psychiatric and behavioral traits. The MDQ screener showed low positive predictive value (0.29) for self-reported bipolar disorder. Neither concurrent nor lifetime manic symptoms were genetically correlated with bipolar disorder. Lifetime manic symptoms had a highest genetic correlation (r<sub>g</sub>  = 1.0) with posttraumatic stress disorder although this was not confirmed by within-cohort phenotypic correlations (r<sub>p</sub>  = 0.41). Other significant genetic correlations included attention deficit hyperactivity disorder (r<sub>g</sub>  = 0.69), insomnia (r<sub>g</sub>  = 0.55), and major depressive disorder (r<sub>g</sub>  = 0.42). Our study adds to existing literature questioning the MDQ's validity and suggests it may capture symptoms of general distress or psychopathology, rather than hypomania/mania specifically, in at-risk populations.",,doi:https://doi.org/10.1002/ajmg.b.32938; html:https://europepmc.org/articles/PMC10952822; pdf:https://europepmc.org/articles/PMC10952822?pdf=render
-35879886,https://doi.org/10.1017/s0033291722002501,"Depression, anxiety and PTSD symptoms before and during the COVID-19 pandemic in the UK.","Young KS, Purves KL, Hübel C, Davies MR, Thompson KN, Bristow S, Krebs G, Danese A, Hirsch C, Parsons CE, Vassos E, Adey BN, Bright S, Hegemann L, Lee YT, Kalsi G, Monssen D, Mundy J, Peel AJ, Rayner C, Rogers HC, Ter Kuile A, Ward C, York K, Lin Y, Palmos AB, Schmidt U, Veale D, Nicholson TR, Pollak TA, Stevelink SAM, Moukhtarian T, Martineau AR, Holt H, Maughan B, Al-Chalabi A, Chaudhuri KR, Richardson MP, Bradley JR, Chinnery PF, Kingston N, Papadia S, Stirrups KE, Linger R, Hotopf M, Eley TC, Breen G.",,Psychological medicine,2023,2022-07-26,Y,Depression; Anxiety; Ptsd; Covid-19,,,"<h4>Background</h4>The impact of the coronavirus disease 2019 (COVID-19) pandemic on mental health is still being unravelled. It is important to identify which individuals are at greatest risk of worsening symptoms. This study aimed to examine changes in depression, anxiety and post-traumatic stress disorder (PTSD) symptoms using prospective and retrospective symptom change assessments, and to find and examine the effect of key risk factors.<h4>Method</h4>Online questionnaires were administered to 34 465 individuals (aged 16 years or above) in April/May 2020 in the UK, recruited from existing cohorts or via social media. Around one-third (<i>n</i> = 12 718) of included participants had prior diagnoses of depression or anxiety and had completed pre-pandemic mental health assessments (between September 2018 and February 2020), allowing prospective investigation of symptom change.<h4>Results</h4>Prospective symptom analyses showed small decreases in depression (PHQ-9: -0.43 points) and anxiety [generalised anxiety disorder scale - 7 items (GAD)-7: -0.33 points] and increases in PTSD (PCL-6: 0.22 points). Conversely, retrospective symptom analyses demonstrated significant large increases (PHQ-9: 2.40; GAD-7 = 1.97), with 55% reported worsening mental health since the beginning of the pandemic on a global change rating. Across both prospective and retrospective measures of symptom change, worsening depression, anxiety and PTSD symptoms were associated with prior mental health diagnoses, female gender, young age and unemployed/student status.<h4>Conclusions</h4>We highlight the effect of prior mental health diagnoses on worsening mental health during the pandemic and confirm previously reported sociodemographic risk factors. Discrepancies between prospective and retrospective measures of changes in mental health may be related to recall bias-related underestimation of prior symptom severity.",,pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/8C3760ED596F1ED8B80F729AC5E47B9B/S0033291722002501a.pdf/div-class-title-depression-anxiety-and-ptsd-symptoms-before-and-during-the-covid-19-pandemic-in-the-uk-div.pdf; doi:https://doi.org/10.1017/S0033291722002501; html:https://europepmc.org/articles/PMC10482709; pdf:https://europepmc.org/articles/PMC10482709?pdf=render
 32862087,https://doi.org/10.1016/j.atherosclerosis.2020.07.014,Sex-specific predictors of PCSK9 levels in a European population: The IMPROVE study.,"Ferri N, Ruscica M, Coggi D, Bonomi A, Amato M, Frigerio B, Sansaro D, Ravani A, Veglia F, Capra N, Lupo MG, Macchi C, Castelnuovo S, Savonen K, Silveira A, Kurl S, Giral P, Pirro M, Strawbridge RJ, Gigante B, Smit AJ, Tremoli E, Colombo GI, Baldassarre D, IMPROVE study group.",,Atherosclerosis,2020,2020-07-30,N,Atherosclerosis; Cardiovascular risk factors; Sex differences; Pcsk9 Predictors,,,"<h4>Background and aims</h4>Proprotein convertase subtilisin/kexin type 9 (PCSK9) is one of the key regulators of low-density lipoprotein cholesterol plasma levels. Circulating PCSK9, which differs between genders, represents a valid pharmacological target for preventing cardiovascular (CV) events. We aimed to investigate sex-related associations between PCSK9 plasma levels and biochemical and anthropomorphic factors, and familial and personal morbidities, in a large European cohort (n = 3673) of men (47.9%) and women (52.1%).<h4>Methods</h4>Individuals (aged 54-79 years) free of CV diseases were enrolled in seven centers of five European countries: Finland, France, Italy, the Netherlands, and Sweden. PCSK9 plasma levels were measured by ELISA.<h4>Results</h4>PCSK9 was higher in women than in men. Multiple linear regression analysis showed that latitude, sex, and treatments with statins and fibrates were the strongest predictors of PCSK9 in the whole group. These variables, together with triglycerides and high-density lipoprotein cholesterol, were also associated with PCSK9 in men or women. Mean corpuscular hemoglobin concentration and pack-years were PCSK9 independent predictors in women, whereas hypercholesterolemia and physical activity were independent predictors in men. The associations between PCSK9 and latitude, uric acid, diabetes, hypercholesterolemia and physical activity were significantly different in men and women (p<sub>interaction</sub> <0.05 for all).<h4>Conclusions</h4>Besides confirming the association with lipids in the whole group, our study revealed previously unknown differences in PCSK9 predictors in men and women. These might be taken into account when defining individual risk for CV events and/or for refining PCSK9 lowering treatments.",,pdf:http://www.atherosclerosis-journal.com/article/S0021915020303816/pdf; doi:https://doi.org/10.1016/j.atherosclerosis.2020.07.014
+35879886,https://doi.org/10.1017/s0033291722002501,"Depression, anxiety and PTSD symptoms before and during the COVID-19 pandemic in the UK.","Young KS, Purves KL, Hübel C, Davies MR, Thompson KN, Bristow S, Krebs G, Danese A, Hirsch C, Parsons CE, Vassos E, Adey BN, Bright S, Hegemann L, Lee YT, Kalsi G, Monssen D, Mundy J, Peel AJ, Rayner C, Rogers HC, Ter Kuile A, Ward C, York K, Lin Y, Palmos AB, Schmidt U, Veale D, Nicholson TR, Pollak TA, Stevelink SAM, Moukhtarian T, Martineau AR, Holt H, Maughan B, Al-Chalabi A, Chaudhuri KR, Richardson MP, Bradley JR, Chinnery PF, Kingston N, Papadia S, Stirrups KE, Linger R, Hotopf M, Eley TC, Breen G.",,Psychological medicine,2023,2022-07-26,Y,Depression; Anxiety; Ptsd; Covid-19,,,"<h4>Background</h4>The impact of the coronavirus disease 2019 (COVID-19) pandemic on mental health is still being unravelled. It is important to identify which individuals are at greatest risk of worsening symptoms. This study aimed to examine changes in depression, anxiety and post-traumatic stress disorder (PTSD) symptoms using prospective and retrospective symptom change assessments, and to find and examine the effect of key risk factors.<h4>Method</h4>Online questionnaires were administered to 34 465 individuals (aged 16 years or above) in April/May 2020 in the UK, recruited from existing cohorts or via social media. Around one-third (<i>n</i> = 12 718) of included participants had prior diagnoses of depression or anxiety and had completed pre-pandemic mental health assessments (between September 2018 and February 2020), allowing prospective investigation of symptom change.<h4>Results</h4>Prospective symptom analyses showed small decreases in depression (PHQ-9: -0.43 points) and anxiety [generalised anxiety disorder scale - 7 items (GAD)-7: -0.33 points] and increases in PTSD (PCL-6: 0.22 points). Conversely, retrospective symptom analyses demonstrated significant large increases (PHQ-9: 2.40; GAD-7 = 1.97), with 55% reported worsening mental health since the beginning of the pandemic on a global change rating. Across both prospective and retrospective measures of symptom change, worsening depression, anxiety and PTSD symptoms were associated with prior mental health diagnoses, female gender, young age and unemployed/student status.<h4>Conclusions</h4>We highlight the effect of prior mental health diagnoses on worsening mental health during the pandemic and confirm previously reported sociodemographic risk factors. Discrepancies between prospective and retrospective measures of changes in mental health may be related to recall bias-related underestimation of prior symptom severity.",,pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/8C3760ED596F1ED8B80F729AC5E47B9B/S0033291722002501a.pdf/div-class-title-depression-anxiety-and-ptsd-symptoms-before-and-during-the-covid-19-pandemic-in-the-uk-div.pdf; doi:https://doi.org/10.1017/S0033291722002501; html:https://europepmc.org/articles/PMC10482709; pdf:https://europepmc.org/articles/PMC10482709?pdf=render
 32505923,https://doi.org/10.1016/j.ebiom.2020.102818,"Children first, or last?",Modi N.,,EBioMedicine,2020,2020-06-04,Y,,,,,,pdf:http://www.thelancet.com/article/S2352396420301936/pdf; doi:https://doi.org/10.1016/j.ebiom.2020.102818; html:https://europepmc.org/articles/PMC7276509; pdf:https://europepmc.org/articles/PMC7276509?pdf=render
 34515361,https://doi.org/10.15252/embj.2021108610,Porin threading drives receptor disengagement and establishes active colicin transport through Escherichia coli OmpF.,"Francis MR, Webby MN, Housden NG, Kaminska R, Elliston E, Chinthammit B, Lukoyanova N, Kleanthous C.",,The EMBO journal,2021,2021-09-13,Y,Cryo-electron microscopy; Outer membrane; Bacteriocins; Gram-negative Bacteria; fluorescent microscopy,,,"Bacteria deploy weapons to kill their neighbours during competition for resources and to aid survival within microbiomes. Colicins were the first such antibacterial system identified, yet how these bacteriocins cross the outer membrane (OM) of Escherichia coli is unknown. Here, by solving the structures of translocation intermediates via cryo-EM and by imaging toxin import, we uncover the mechanism by which the Tol-dependent nuclease colicin E9 (ColE9) crosses the bacterial OM. We show that threading of ColE9's disordered N-terminal domain through two pores of the trimeric porin OmpF causes the colicin to disengage from its primary receptor, BtuB, and reorganises the translocon either side of the membrane. Subsequent import of ColE9 through the lumen of a single OmpF subunit is driven by the proton-motive force, which is delivered by the TolQ-TolR-TolA-TolB assembly. Our study answers longstanding questions, such as why OmpF is a better translocator than OmpC, and reconciles the mechanisms by which both Tol- and Ton-dependent bacteriocins cross the bacterial outer membrane.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.15252/embj.2021108610; doi:https://doi.org/10.15252/embj.2021108610; html:https://europepmc.org/articles/PMC8561637; pdf:https://europepmc.org/articles/PMC8561637?pdf=render
 35017564,https://doi.org/10.1038/s41467-021-27950-w,Mapping inhibitory sites on the RNA polymerase of the 1918 pandemic influenza virus using nanobodies.,"Keown JR, Zhu Z, Carrique L, Fan H, Walker AP, Serna Martin I, Pardon E, Steyaert J, Fodor E, Grimes JM.",,Nature communications,2022,2022-01-11,Y,,,,"Influenza A viruses cause seasonal epidemics and global pandemics, representing a considerable burden to healthcare systems. Central to the replication cycle of influenza viruses is the viral RNA-dependent RNA polymerase which transcribes and replicates the viral RNA genome. The polymerase undergoes conformational rearrangements and interacts with viral and host proteins to perform these functions. Here we determine the structure of the 1918 influenza virus polymerase in transcriptase and replicase conformations using cryo-electron microscopy (cryo-EM). We then structurally and functionally characterise the binding of single-domain nanobodies to the polymerase of the 1918 pandemic influenza virus. Combining these functional and structural data we identify five sites on the polymerase which are sensitive to inhibition by nanobodies. We propose that the binding of nanobodies at these sites either prevents the polymerase from assuming particular functional conformations or interactions with viral or host factors. The polymerase is highly conserved across the influenza A subtypes, suggesting these sites as effective targets for potential influenza antiviral development.",,pdf:https://www.nature.com/articles/s41467-021-27950-w.pdf; doi:https://doi.org/10.1038/s41467-021-27950-w; html:https://europepmc.org/articles/PMC8752864; pdf:https://europepmc.org/articles/PMC8752864?pdf=render
@@ -2452,8 +2454,8 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 35231023,https://doi.org/10.1371/journal.pmed.1003907,Changes in social contacts in England during the COVID-19 pandemic between March 2020 and March 2021 as measured by the CoMix survey: A repeated cross-sectional study.,"Gimma A, Munday JD, Wong KLM, Coletti P, van Zandvoort K, Prem K, CMMID COVID-19 working group, Klepac P, Rubin GJ, Funk S, Edmunds WJ, Jarvis CI.",,PLoS medicine,2022,2022-03-01,Y,,,,"<h4>Background</h4>During the Coronavirus Disease 2019 (COVID-19) pandemic, the United Kingdom government imposed public health policies in England to reduce social contacts in hopes of curbing virus transmission. We conducted a repeated cross-sectional study to measure contact patterns weekly from March 2020 to March 2021 to estimate the impact of these policies, covering 3 national lockdowns interspersed by periods of less restrictive policies.<h4>Methods and findings</h4>The repeated cross-sectional survey data were collected using online surveys of representative samples of the UK population by age and gender. Survey participants were recruited by the online market research company Ipsos MORI through internet-based banner and social media ads and email campaigns. The participant data used for this analysis are restricted to those who reported living in England. We calculated the mean daily contacts reported using a (clustered) bootstrap and fitted a censored negative binomial model to estimate age-stratified contact matrices and estimate proportional changes to the basic reproduction number under controlled conditions using the change in contacts as a scaling factor. To put the findings in perspective, we discuss contact rates recorded throughout the year in terms of previously recorded rates from the POLYMOD study social contact study. The survey recorded 101,350 observations from 19,914 participants who reported 466,710 contacts over 53 weeks. We observed changes in social contact patterns in England over time and by participants' age, personal risk factors, and perception of risk. The mean reported contacts for adults 18 to 59 years old ranged between 2.39 (95% confidence interval [CI] 2.20 to 2.60) contacts and 4.93 (95% CI 4.65 to 5.19) contacts during the study period. The mean contacts for school-age children (5 to 17 years old) ranged from 3.07 (95% CI 2.89 to 3.27) to 15.11 (95% CI 13.87 to 16.41). This demonstrates a sustained decrease in social contacts compared to a mean of 11.08 (95% CI 10.54 to 11.57) contacts per participant in all age groups combined as measured by the POLYMOD social contact study in 2005 to 2006. Contacts measured during periods of lockdowns were lower than in periods of eased social restrictions. The use of face coverings outside the home has remained high since the government mandated use in some settings in July 2020. The main limitations of this analysis are the potential for selection bias, as participants are recruited through internet-based campaigns, and recall bias, in which participants may under- or overreport the number of contacts they have made.<h4>Conclusions</h4>In this study, we observed that recorded contacts reduced dramatically compared to prepandemic levels (as measured in the POLYMOD study), with changes in reported contacts correlated with government interventions throughout the pandemic. Despite easing of restrictions in the summer of 2020, the mean number of reported contacts only returned to about half of that observed prepandemic at its highest recorded level. The CoMix survey provides a unique repeated cross-sectional data set for a full year in England, from the first day of the first lockdown, for use in statistical analyses and mathematical modelling of COVID-19 and other diseases.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003907&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003907; html:https://europepmc.org/articles/PMC8887739; pdf:https://europepmc.org/articles/PMC8887739?pdf=render
 33087179,https://doi.org/10.1186/s12916-020-01790-9,Reconstructing the early global dynamics of under-ascertained COVID-19 cases and infections.,"Russell TW, Golding N, Hellewell J, Abbott S, Wright L, Pearson CAB, van Zandvoort K, Jarvis CI, Gibbs H, Liu Y, Eggo RM, Edmunds WJ, Kucharski AJ, CMMID COVID-19 working group.",,BMC medicine,2020,2020-10-22,Y,Surveillance; Situational Awareness; Under-reporting; Case Ascertainment; Outbreak Analysis; Covid-19; Sars-cov-2,,,"<h4>Background</h4>Asymptomatic or subclinical SARS-CoV-2 infections are often unreported, which means that confirmed case counts may not accurately reflect underlying epidemic dynamics. Understanding the level of ascertainment (the ratio of confirmed symptomatic cases to the true number of symptomatic individuals) and undetected epidemic progression is crucial to informing COVID-19 response planning, including the introduction and relaxation of control measures. Estimating case ascertainment over time allows for accurate estimates of specific outcomes such as seroprevalence, which is essential for planning control measures.<h4>Methods</h4>Using reported data on COVID-19 cases and fatalities globally, we estimated the proportion of symptomatic cases (i.e. any person with any of fever ≥ 37.5 °C, cough, shortness of breath, sudden onset of anosmia, ageusia or dysgeusia illness) that were reported in 210 countries and territories, given those countries had experienced more than ten deaths. We used published estimates of the baseline case fatality ratio (CFR), which was adjusted for delays and under-ascertainment, then calculated the ratio of this baseline CFR to an estimated local delay-adjusted CFR to estimate the level of under-ascertainment in a particular location. We then fit a Bayesian Gaussian process model to estimate the temporal pattern of under-ascertainment.<h4>Results</h4>Based on reported cases and deaths, we estimated that, during March 2020, the median percentage of symptomatic cases detected across the 84 countries which experienced more than ten deaths ranged from 2.4% (Bangladesh) to 100% (Chile). Across the ten countries with the highest number of total confirmed cases as of 6 July 2020, we estimated that the peak number of symptomatic cases ranged from 1.4 times (Chile) to 18 times (France) larger than reported. Comparing our model with national and regional seroprevalence data where available, we find that our estimates are consistent with observed values. Finally, we estimated seroprevalence for each country. As of 7 June, our seroprevalence estimates range from 0% (many countries) to 13% (95% CrI 5.6-24%) (Belgium).<h4>Conclusions</h4>We found substantial under-ascertainment of symptomatic cases, particularly at the peak of the first wave of the SARS-CoV-2 pandemic, in many countries. Reported case counts will therefore likely underestimate the rate of outbreak growth initially and underestimate the decline in the later stages of an epidemic. Although there was considerable under-reporting in many locations, our estimates were consistent with emerging serological data, suggesting that the proportion of each country's population infected with SARS-CoV-2 worldwide is generally low.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-020-01790-9; doi:https://doi.org/10.1186/s12916-020-01790-9; html:https://europepmc.org/articles/PMC7577796; pdf:https://europepmc.org/articles/PMC7577796?pdf=render
 34321180,https://doi.org/10.1016/j.aucc.2021.05.013,The impact of distance on post-ICU disability.,"D'Arcy J, Haines K, Paul E, Doherty Z, Goodwin A, Bailey M, Barrett J, Bellomo R, Bucknall T, Gabbe BJ, Higgins AM, Iwashyna TJ, Murray LJ, Myles PS, Ponsford J, Pilcher D, Udy AA, Walker C, Young M, Cooper DJJ, Hodgson CL, ICU-Recovery Investigators.",,Australian critical care : official journal of the Confederation of Australian Critical Care Nurses,2022,2021-07-25,N,Quality of life; Mechanical ventilation; Distance; Disability; Intensive Care,,,"<h4>Background</h4>Nonurban residential living is associated with adverse outcomes for a number of chronic health conditions. However, it is unclear what effect it has amongst survivors of critical illness.<h4>Objectives</h4>The purpose of this study is to determine whether patients living greater than 50 km from the treating intensive care unit (ICU) have disability outcomes at 6 months that differ from people living within 50 km.<h4>Methods</h4>This was a multicentre, prospective cohort study conducted in five metropolitan ICUs. Participants were adults admitted to the ICU, who received >24 h of mechanical ventilation and survived to hospital discharge. In a secondary analysis of these data, the cohort was dichotomised based on residential distance from the treating ICU: <50 km and ≥50 km. The primary outcome was patient-reported disability using the 12-item World Health Organization's Disability Assessment Schedule (WHODAS 2.0). This was recorded at 6 months after ICU admission by telephone interview. Secondary outcomes included health status as measured by EQ-5D-5L return to work and psychological function as measured by the Hospital Anxiety and Depression Scale (HADS). Multivariable logistic regression was used to assess the association between distance from the ICU and moderate to severe disability, adjusted for potential confounders. Variables included in the multivariable model were deemed to be clinically relevant and had baseline imbalance between groups (p < 0.10). These included marital status and hours of mechanical ventilation. Sensitivity analysis was also conducted using distance in kilometres as a continuous variable.<h4>Results</h4>A total of 262 patients were enrolled, and 169 (65%) lived within 50 km of the treating ICU and 93 (35%) lived ≥50 km from the treating ICU (interquartile range [IQR] 10-664 km). There was no difference in patient-reported disability at 6 months between patients living <50 km and those living ≥50 km (WHODAS total disability % [IQR] 10.4 [2.08-25] v 14.6 [2.08-20.8], P = 0.74). There was also no difference between groups for the six major life domains of the WHODAS. There was no difference in rates of anxiety or depression as measured by HADS score (HADS anxiety median [IQR] 4 [1-7] v 3 [1-7], P = 0.60) (HADS depression median [IQR] 3 [1-6] v 3 [1-6], P = 0.62); health status as measured by EQ-5D (mean [SD] 66.7 [20] v 69.8 [22.2], P = 0.24); or health-related unemployment (% (N) 39 [26] v 25 [29.1], P = 0.61). After adjusting for confounders, living ≥50 km from the treating ICU was not associated with increased disability (odds ratio 0.61, 95% confidence interval: 0.33-1.16; P = 0.13) CONCLUSIONS: Survivors of intensive care in Victoria, Australia, who live at least 50 km from the treating ICU did not have greater disability than people living less than 50 km at 6 months after discharge. Living 50 km or more from the treating ICU was not associated with disability, nor was it associated with anxiety or depression, health status, or unemployment due to health.",,doi:https://doi.org/10.1016/j.aucc.2021.05.013
-36608816,https://doi.org/10.1016/j.diabet.2022.101418,Empagliflozin cardiovascular and renal effectiveness and safety compared to dipeptidyl peptidase-4 inhibitors across 11 countries in Europe and Asia: Results from the EMPagliflozin compaRative effectIveness and SafEty (EMPRISE) study.,"Karasik A, Lanzinger S, Chia-Hui Tan E, Yabe D, Kim DJ, Sheu WH, Melzer-Cohen C, Holl RW, Ha KH, Khunti K, Zaccardi F, Subramanian A, Nirantharakumar K, Nyström T, Niskanen L, Linnemann Jensen M, Hoti F, Klement R, Déruaz-Luyet A, Kyaw MH, Koeneman L, Vistisen D, Carstensen B, Halvorsen S, Langslet G, Fazeli Farsani S, Patorno E, Núñez J, EMPRISE Europe and Asia Study Group.",,Diabetes & metabolism,2023,2023-01-03,N,Cardiovascular diseases; Meta-analysis; Heart Failure; All-cause Mortality; Pharmacoepidemiology; Observational Study; Comparative Effectiveness; Dipeptidyl Peptidase-4 Inhibitors; Empagliflozin; Sodium-glucose Transporter 2 Inhibitors,,,"<h4>Background</h4>Continued expansion of indications for sodium-glucose cotransporter-2 inhibitors increases importance of evaluating cardiovascular and kidney efficacy and safety of empagliflozin in patients with type 2 diabetes compared to similar therapies.<h4>Methods</h4>The EMPRISE Europe and Asia study is a non-interventional cohort study using data from 2014-2019 in seven European (Denmark, Finland, Germany, Norway, Spain, Sweden, United Kingdom) and four Asian (Israel, Japan, South Korea, Taiwan) countries. Patients with type 2 diabetes initiating empagliflozin were 1:1 propensity score matched to patients initiating dipeptidyl peptidase-4 inhibitors. Primary endpoints included hospitalization for heart failure, all-cause mortality, myocardial infarction and stroke. Other cardiovascular, renal, and safety outcomes were examined.<h4>Findings</h4>Among 83,946 matched patient pairs, (0·7 years overall mean follow-up time), initiation of empagliflozin was associated with lower risk of hospitalization for heart failure compared to dipeptidyl peptidase-4 inhibitors (Hazard Ratio 0·70; 95% CI 0.60 to 0.83). Risks of all-cause mortality (0·55; 0·48 to 0·63), stroke (0·82; 0·71 to 0·96), and end-stage renal disease (0·43; 0·30 to 0·63) were lower and risk for myocardial infarction, bone fracture, severe hypoglycemia, and lower-limb amputation were similar between initiators of empagliflozin and dipeptidyl peptidase-4 inhibitors. Initiation of empagliflozin was associated with higher risk for diabetic ketoacidosis (1·97; 1·28 to 3·03) compared to dipeptidyl peptidase-4 inhibitors. Results were consistent across continents and regions.<h4>Interpretation</h4>Results from this EMPRISE Europe and Asia study complements previous clinical trials and real-world studies by providing further evidence of the beneficial cardiorenal effects and overall safety of empagliflozin compared to dipeptidyl peptidase-4 inhibitors.",,doi:https://doi.org/10.1016/j.diabet.2022.101418; doi:https://doi.org/10.1016/j.diabet.2022.101418
 32681152,https://doi.org/10.1038/s41596-020-0343-3,Identifying unknown metabolites using NMR-based metabolic profiling techniques.,"Garcia-Perez I, Posma JM, Serrano-Contreras JI, Boulangé CL, Chan Q, Frost G, Stamler J, Elliott P, Lindon JC, Holmes E, Nicholson JK.",,Nature protocols,2020,2020-07-17,N,,,,"Metabolic profiling of biological samples provides important insights into multiple physiological and pathological processes but is hindered by a lack of automated annotation and standardized methods for structure elucidation of candidate disease biomarkers. Here we describe a system for identifying molecular species derived from nuclear magnetic resonance (NMR) spectroscopy-based metabolic phenotyping studies, with detailed information on sample preparation, data acquisition and data modeling. We provide eight different modular workflows to be followed in a recommended sequential order according to their level of difficulty. This multi-platform system involves the use of statistical spectroscopic tools such as Statistical Total Correlation Spectroscopy (STOCSY), Subset Optimization by Reference Matching (STORM) and Resolution-Enhanced (RED)-STORM to identify other signals in the NMR spectra relating to the same molecule. It also uses two-dimensional NMR spectroscopic analysis, separation and pre-concentration techniques, multiple hyphenated analytical platforms and data extraction from existing databases. The complete system, using all eight workflows, would take up to a month, as it includes multi-dimensional NMR experiments that require prolonged experiment times. However, easier identification cases using fewer steps would take 2 or 3 days. This approach to biomarker discovery is efficient and cost-effective and offers increased chemical space coverage of the metabolome, resulting in faster and more accurate assignment of NMR-generated biomarkers arising from metabolic phenotyping studies. It requires a basic understanding of MATLAB to use the statistical spectroscopic tools and analytical skills to perform solid phase extraction (SPE), liquid chromatography (LC) fraction collection, LC-NMR-mass spectroscopy and one-dimensional and two-dimensional NMR experiments.",,doi:https://doi.org/10.1038/s41596-020-0343-3
+36608816,https://doi.org/10.1016/j.diabet.2022.101418,Empagliflozin cardiovascular and renal effectiveness and safety compared to dipeptidyl peptidase-4 inhibitors across 11 countries in Europe and Asia: Results from the EMPagliflozin compaRative effectIveness and SafEty (EMPRISE) study.,"Karasik A, Lanzinger S, Chia-Hui Tan E, Yabe D, Kim DJ, Sheu WH, Melzer-Cohen C, Holl RW, Ha KH, Khunti K, Zaccardi F, Subramanian A, Nirantharakumar K, Nyström T, Niskanen L, Linnemann Jensen M, Hoti F, Klement R, Déruaz-Luyet A, Kyaw MH, Koeneman L, Vistisen D, Carstensen B, Halvorsen S, Langslet G, Fazeli Farsani S, Patorno E, Núñez J, EMPRISE Europe and Asia Study Group.",,Diabetes & metabolism,2023,2023-01-03,N,Cardiovascular diseases; Meta-analysis; Heart Failure; All-cause Mortality; Pharmacoepidemiology; Observational Study; Comparative Effectiveness; Dipeptidyl Peptidase-4 Inhibitors; Empagliflozin; Sodium-glucose Transporter 2 Inhibitors,,,"<h4>Background</h4>Continued expansion of indications for sodium-glucose cotransporter-2 inhibitors increases importance of evaluating cardiovascular and kidney efficacy and safety of empagliflozin in patients with type 2 diabetes compared to similar therapies.<h4>Methods</h4>The EMPRISE Europe and Asia study is a non-interventional cohort study using data from 2014-2019 in seven European (Denmark, Finland, Germany, Norway, Spain, Sweden, United Kingdom) and four Asian (Israel, Japan, South Korea, Taiwan) countries. Patients with type 2 diabetes initiating empagliflozin were 1:1 propensity score matched to patients initiating dipeptidyl peptidase-4 inhibitors. Primary endpoints included hospitalization for heart failure, all-cause mortality, myocardial infarction and stroke. Other cardiovascular, renal, and safety outcomes were examined.<h4>Findings</h4>Among 83,946 matched patient pairs, (0·7 years overall mean follow-up time), initiation of empagliflozin was associated with lower risk of hospitalization for heart failure compared to dipeptidyl peptidase-4 inhibitors (Hazard Ratio 0·70; 95% CI 0.60 to 0.83). Risks of all-cause mortality (0·55; 0·48 to 0·63), stroke (0·82; 0·71 to 0·96), and end-stage renal disease (0·43; 0·30 to 0·63) were lower and risk for myocardial infarction, bone fracture, severe hypoglycemia, and lower-limb amputation were similar between initiators of empagliflozin and dipeptidyl peptidase-4 inhibitors. Initiation of empagliflozin was associated with higher risk for diabetic ketoacidosis (1·97; 1·28 to 3·03) compared to dipeptidyl peptidase-4 inhibitors. Results were consistent across continents and regions.<h4>Interpretation</h4>Results from this EMPRISE Europe and Asia study complements previous clinical trials and real-world studies by providing further evidence of the beneficial cardiorenal effects and overall safety of empagliflozin compared to dipeptidyl peptidase-4 inhibitors.",,doi:https://doi.org/10.1016/j.diabet.2022.101418; doi:https://doi.org/10.1016/j.diabet.2022.101418
 32935027,https://doi.org/10.23889/ijpds.v4i1.1093,Health Data Linkage for UK Public Interest Research: Key Obstacles and Solutions.,"Mourby MJ, Doidge J, Jones KH, Aidinlis S, Smith H, Bell J, Gilbert R, Dutey-Magni P, Kaye J.",,International journal of population data science,2019,2019-04-02,Y,,,,"<h4>Introduction</h4>Analysis of linked health data can generate important, even life-saving, insights into population health. Yet obstacles both legal and organisational in nature can impede this work.<h4>Approach</h4>We focus on three UK infrastructures set up to link and share data for research: the Administrative Data Research Network, NHS Digital, and the Secure Anonymised Information Linkage Databank. Bringing an interdisciplinary perspective, we identify key issues underpinning their challenges and successes in linking health data for research.<h4>Results</h4>We identify examples of uncertainty surrounding legal powers to share and link data, and around data protection obligations, as well as systemic delays and historic public backlash. These issues require updated official guidance on the relevant law, approaches to linkage which are planned for impact and ongoing utility, greater transparency between data providers and researchers, and engagement with the patient population which is both high-profile and carefully considered.<h4>Conclusions</h4>Health data linkage for research presents varied challenges, to which there can be no single solution. Our recommendations would require action from a number of data providers and regulators to be meaningfully advanced. This illustrates the scale and complexity of the challenge of health data linkage, in the UK and beyond: a challenge which our case studies suggest no single organisation can combat alone. Planned programmes of linkage are critical because they allow time for organisations to address these challenges without adversely affecting the feasibility of individual research projects.",,pdf:https://ijpds.org/article/download/1093/1035; doi:https://doi.org/10.23889/ijpds.v4i1.1093; html:https://europepmc.org/articles/PMC7482514; pdf:https://europepmc.org/articles/PMC7482514?pdf=render
 34458849,https://doi.org/10.1093/oxfimm/iqab014,Protease inhibitor plasma concentrations associate with COVID-19 infection.,"Medjeral-Thomas NR, Troldborg A, Hansen AG, Pihl R, Clarke CL, Peters JE, Thomas DC, Willicombe M, Palarasah Y, Botto M, Pickering MC, Thiel S.",,Oxford open immunology,2021,2021-07-07,Y,Coronavirus; Protease inhibitors; innate immunity; Covid-19,,,"Protease inhibitors influence a range of innate immunity and inflammatory pathways. We quantified plasma concentrations of key anti-inflammatory protease inhibitors in chronic haemodialysis patients with coronavirus disease 2019 (COVID-19). The samples were collected early in the disease course to determine whether plasma protease inhibitor levels associated with the presence and severity of COVID-19. We used antibody-based immunoassays to measure plasma concentrations of C1 esterase inhibitor, alpha2-macroglobulin, antithrombin and inter-alpha-inhibitor heavy chain 4 (ITIH4) in 100 serial samples from 27 haemodialysis patients with COVID-19. ITIH4 was tested in two assays, one measuring intact ITIH4 and another also detecting any fragmented ITIH4 (total ITIH4). Control cohorts were 32 haemodialysis patients without COVID-19 and 32 healthy controls. We compared protease inhibitor concentration based on current and future COVID-19 severity and with C-reactive protein. Results were adjusted for repeated measures and multiple comparisons. Analysis of all available samples demonstrated lower plasma C1 esterase inhibitor and α2M and higher total ITIH4 in COVID-19 compared with dialysis controls. These differences were also seen in the first sample collected after COVID-19 diagnosis, a median of 4 days from diagnostic swab. Plasma ITIH4 levels were higher in severe than the non-severe COVID-19. Serum C-reactive protein correlated positively with plasma levels of antithrombin, intact ITIH4 and total ITIH4. In conclusion, plasma protease inhibitor concentrations are altered in COVID-19.",,pdf:https://academic.oup.com/ooim/article-pdf/2/1/iqab014/48744499/iqab014.pdf; doi:https://doi.org/10.1093/oxfimm/iqab014; html:https://europepmc.org/articles/PMC8371939; pdf:https://europepmc.org/articles/PMC8371939?pdf=render
 33203906,https://doi.org/10.1038/s41598-020-76518-z,Accelerated MRI-predicted brain ageing and its associations with cardiometabolic and brain disorders.,"Kolbeinsson A, Filippi S, Panagakis Y, Matthews PM, Elliott P, Dehghan A, Tzoulaki I.",,Scientific reports,2020,2020-11-17,Y,,,,"Brain structure in later life reflects both influences of intrinsic aging and those of lifestyle, environment and disease. We developed a deep neural network model trained on brain MRI scans of healthy people to predict ""healthy"" brain age. Brain regions most informative for the prediction included the cerebellum, hippocampus, amygdala and insular cortex. We then applied this model to data from an independent group of people not stratified for health. A phenome-wide association analysis of over 1,410 traits in the UK Biobank with differences between the predicted and chronological ages for the second group identified significant associations with over 40 traits including diseases (e.g., type I and type II diabetes), disease risk factors (e.g., increased diastolic blood pressure and body mass index), and poorer cognitive function. These observations highlight relationships between brain and systemic health and have implications for understanding contributions of the latter to late life dementia risk.",,pdf:https://www.nature.com/articles/s41598-020-76518-z.pdf; doi:https://doi.org/10.1038/s41598-020-76518-z; html:https://europepmc.org/articles/PMC7672070; pdf:https://europepmc.org/articles/PMC7672070?pdf=render
@@ -2461,22 +2463,22 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 34411511,https://doi.org/10.1016/s2213-2600(21)00164-8,"Global, regional, and national burden of respiratory tract cancers and associated risk factors from 1990 to 2019: a systematic analysis for the Global Burden of Disease Study 2019.",GBD 2019 Respiratory Tract Cancers Collaborators.,,The Lancet. Respiratory medicine,2021,2021-08-16,Y,,,,"<h4>Background</h4>Prevention, control, and treatment of respiratory tract cancers are important steps towards achieving target 3.4 of the UN Sustainable Development Goals (SDGs)-a one-third reduction in premature mortality due to non-communicable diseases by 2030. We aimed to provide global, regional, and national estimates of the burden of tracheal, bronchus, and lung cancer and larynx cancer and their attributable risks from 1990 to 2019.<h4>Methods</h4>Based on the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019 methodology, we evaluated the incidence, mortality, years lived with disability, years of life lost, and disability-adjusted life-years (DALYs) of respiratory tract cancers (ie, tracheal, bronchus, and lung cancer and larynx cancer). Deaths from tracheal, bronchus, and lung cancer and larynx cancer attributable to each risk factor were estimated on the basis of risk exposure, relative risks, and the theoretical minimum risk exposure level input from 204 countries and territories, stratified by sex and Socio-demographic Index (SDI). Trends were estimated from 1990 to 2019, with an emphasis on the 2010-19 period.<h4>Findings</h4>Globally, there were 2·26 million (95% uncertainty interval 2·07 to 2·45) new cases of tracheal, bronchus, and lung cancer, and 2·04 million (1·88 to 2·19) deaths and 45·9 million (42·3 to 49·3) DALYs due to tracheal, bronchus, and lung cancer in 2019. There were 209 000 (194 000 to 225 000) new cases of larynx cancer, and 123 000 (115 000 to 133 000) deaths and 3·26 million (3·03 to 3·51) DALYs due to larynx cancer globally in 2019. From 2010 to 2019, the number of new tracheal, bronchus, and lung cancer cases increased by 23·3% (12·9 to 33·6) globally and the number of larynx cancer cases increased by 24·7% (16·0 to 34·1) globally. Global age-standardised incidence rates of tracheal, bronchus, and lung cancer decreased by 7·4% (-16·8 to 1·6) and age-standardised incidence rates of larynx cancer decreased by 3·0% (-10·5 to 5·0) in males over the past decade; however, during the same period, age-standardised incidence rates in females increased by 0·9% (-8·2 to 10·2) for tracheal, bronchus, and lung cancer and decreased by 0·5% (-8·4 to 8·1) for larynx cancer. Furthermore, although age-standardised incidence and death rates declined in both sexes combined from 2010 to 2019 at the global level for tracheal, bronchus, lung and larynx cancers, some locations had rising rates, particularly those on the lower end of the SDI range. Smoking contributed to an estimated 64·2% (61·9-66·4) of all deaths from tracheal, bronchus, and lung cancer and 63·4% (56·3-69·3) of all deaths from larynx cancer in 2019. For males and for both sexes combined, smoking was the leading specific risk factor for age-standardised deaths from tracheal, bronchus, and lung cancer per 100 000 in all SDI quintiles and GBD regions in 2019. However, among females, household air pollution from solid fuels was the leading specific risk factor in the low SDI quintile and in three GBD regions (central, eastern, and western sub-Saharan Africa) in 2019.<h4>Interpretation</h4>The numbers of incident cases and deaths from tracheal, bronchus, and lung cancer and larynx cancer increased globally during the past decade. Even more concerning, age-standardised incidence and death rates due to tracheal, bronchus, lung cancer and larynx cancer increased in some populations-namely, in the lower SDI quintiles and among females. Preventive measures such as smoking control interventions, air quality management programmes focused on major air pollution sources, and widespread access to clean energy should be prioritised in these settings.<h4>Funding</h4>Bill & Melinda Gates Foundation.",,pdf:http://www.thelancet.com/article/S2213260021001648/pdf; doi:https://doi.org/10.1016/S2213-2600(21)00164-8; html:https://europepmc.org/articles/PMC8410610
 36865374,https://doi.org/10.12688/wellcomeopenres.18175.1,GroundsWell: Community-engaged and data-informed systems transformation of Urban Green and Blue Space for population health - a new initiative.,"Hunter RF, Rodgers SE, Hilton J, Clarke M, Garcia L, Ward Thompson C, Geary R, Green MA, O'Neill C, Longo A, Lovell R, Nurse A, Wheeler BW, Clement S, Porroche-Escudero A, Mitchell R, Barr B, Barry J, Bell S, Bryan D, Buchan I, Butters O, Clemens T, Clewley N, Corcoran R, Elliott L, Ellis G, Guell C, Jurek-Loughrey A, Kee F, Maguire A, Maskell S, Murtagh B, Smith G, Taylor T, Jepson R, GroundsWell Consortium.",,Wellcome open research,2022,2022-09-20,Y,Public Health; Non-Communicable Disease; Green And Blue Space; Complex Systems; Data Science; Citizen Science; Interdisciplinary; Health Inequalities,,,"Natural environments, such as parks, woodlands and lakes, have positive impacts on health and wellbeing. Urban Green and Blue Spaces (UGBS), and the activities that take place in them, can significantly influence the health outcomes of all communities, and reduce health inequalities. Improving access and quality of UGBS needs understanding of the range of systems (e.g. planning, transport, environment, community) in which UGBS are located. UGBS offers an ideal exemplar for testing systems innovations as it reflects place-based and <i>whole society</i> processes <i>,</i> with potential to reduce non-communicable disease (NCD) risk and associated social inequalities in health. UGBS can impact multiple behavioural and environmental aetiological pathways. However, the systems which desire, design, develop, and deliver UGBS are fragmented and siloed, with ineffective mechanisms for data generation, knowledge exchange and mobilisation. Further, UGBS need to be co-designed with and by those whose health could benefit most from them, so they are appropriate, accessible, valued and used well. This paper describes a major new prevention research programme and partnership, <i>GroundsWell</i>, which aims to transform UGBS-related systems by improving how we plan, design, evaluate and manage UGBS so that it benefits all communities, especially those who are in poorest health. We use a broad definition of health to include physical, mental, social wellbeing and quality of life. Our objectives are to transform systems so that UGBS are planned, developed, implemented, maintained and evaluated with our communities and data systems to enhance health and reduce inequalities. GroundsWell will use interdisciplinary, problem-solving approaches to accelerate and optimise community collaborations among citizens, users, implementers, policymakers and researchers to impact research, policy, practice and active citizenship. GroundsWell will be shaped and developed in three pioneer cities (Belfast, Edinburgh, Liverpool) and their regional contexts, with embedded translational mechanisms to ensure that outputs and impact have UK-wide and international application.",,doi:https://doi.org/10.12688/wellcomeopenres.18175.1; html:https://europepmc.org/articles/PMC9971655; pdf:https://europepmc.org/articles/PMC9971655?pdf=render
 30772400,https://doi.org/10.1016/j.neuroimage.2019.02.028,Hierarchical complexity of the adult human structural connectome.,"Smith K, Bastin ME, Cox SR, Valdés Hernández MC, Wiseman S, Escudero J, Sudlow C.",,NeuroImage,2019,2019-02-14,Y,MRI; Brain Networks; Hierarchical Complexity; Human Structural Connectome,The Human Phenome,,"The structural network of the human brain has a rich topology which many have sought to characterise using standard network science measures and concepts. However, this characterisation remains incomplete and the non-obvious features of this topology have largely confounded attempts towards comprehensive constructive modelling. This calls for new perspectives. Hierarchical complexity is an emerging paradigm of complex network topology based on the observation that complex systems are composed of hierarchies within which the roles of hierarchically equivalent nodes display highly variable connectivity patterns. Here we test the hierarchical complexity of the human structural connectomes of a group of seventy-nine healthy adults. Binary connectomes are found to be more hierarchically complex than three benchmark random network models. This provides a new key description of brain structure, revealing a rich diversity of connectivity patterns within hierarchically equivalent nodes. Dividing the connectomes into four tiers based on degree magnitudes indicates that the most complex nodes are neither those with the highest nor lowest degrees but are instead found in the middle tiers. Spatial mapping of the brain regions in each hierarchical tier reveals consistency with the current anatomical, functional and neuropsychological knowledge of the human brain. The most complex tier (Tier 3) involves regions believed to bridge high-order cognitive (Tier 1) and low-order sensorimotor processing (Tier 2). We then show that such diversity of connectivity patterns aligns with the diversity of functional roles played out across the brain, demonstrating that hierarchical complexity can characterise functional diversity strictly from the network topology.",,doi:https://doi.org/10.1016/j.neuroimage.2019.02.028; doi:https://doi.org/10.1016/j.neuroimage.2019.02.028; html:https://europepmc.org/articles/PMC6503942
-32097451,https://doi.org/10.1093/ije/dyaa015,Commentary: Using human genetics to guide the repurposing of medicines.,"Bovijn J, Censin JC, Lindgren CM, Holmes MV.",,International journal of epidemiology,2020,2020-08-01,N,,,,,,pdf:https://academic.oup.com/ije/article-pdf/49/4/1140/34275903/dyaa015.pdf; doi:https://doi.org/10.1093/ije/dyaa015; html:https://europepmc.org/articles/PMC7660148; pdf:https://europepmc.org/articles/PMC7660148?pdf=render; doi:https://doi.org/10.1093/ije/dyaa015
 31063847,https://doi.org/10.1016/j.bbi.2019.05.009,Transcriptomic analysis of probable asymptomatic and symptomatic alzheimer brains.,"Patel H, Hodges AK, Curtis C, Lee SH, Troakes C, Dobson RJB, Newhouse SJ.",,"Brain, behavior, and immunity",2019,2019-05-04,N,Human; Mitochondria; Brain; Frontal lobe; Astrocytes; Neuropathology; Alzheimer’s disease; Gene Expression; Microarray Analysis; Gene Regulatory Networks,,,"Individuals with intact cognition and neuropathology consistent with Alzheimer's disease (AD) are referred to as asymptomatic AD (AsymAD). These individuals are highly likely to develop AD, yet transcriptomic changes in the brain which might reveal mechanisms for their AD vulnerability are currently unknown. Entorhinal cortex, frontal cortex, temporal cortex and cerebellum tissue from 27 control, 33 AsymAD and 52 AD human brains were microarray expression profiled. Differential expression analysis identified a significant increase of transcriptomic activity in the frontal cortex of AsymAD subjects, suggesting fundamental changes in AD may initially begin within the frontal cortex region prior to AD diagnosis. Co-expression analysis identified an overactivation of the brain ""glutamate-glutamine cycle"", and disturbances in the brain energy pathways in both AsymAD and AD subjects, while the connectivity of key hub genes in this network indicates a shift from an already increased cell proliferation in AsymAD subjects to stress response and removal of amyloidogenic proteins in AD subjects. This study provides new insight into the earliest biological changes occurring in the brain prior to the manifestation of clinical AD symptoms and provides new potential therapeutic targets for early disease intervention.",,doi:https://doi.org/10.1016/j.bbi.2019.05.009; doi:https://doi.org/10.1016/j.bbi.2019.05.009
+32097451,https://doi.org/10.1093/ije/dyaa015,Commentary: Using human genetics to guide the repurposing of medicines.,"Bovijn J, Censin JC, Lindgren CM, Holmes MV.",,International journal of epidemiology,2020,2020-08-01,N,,,,,,pdf:https://academic.oup.com/ije/article-pdf/49/4/1140/34275903/dyaa015.pdf; doi:https://doi.org/10.1093/ije/dyaa015; html:https://europepmc.org/articles/PMC7660148; pdf:https://europepmc.org/articles/PMC7660148?pdf=render; doi:https://doi.org/10.1093/ije/dyaa015
 34039579,https://doi.org/10.1136/bmjopen-2021-049721,Changes in daily mental health service use and mortality at the commencement and lifting of COVID-19 'lockdown' policy in 10 UK sites: a regression discontinuity in time design.,"Bakolis I, Stewart R, Baldwin D, Beenstock J, Bibby P, Broadbent M, Cardinal R, Chen S, Chinnasamy K, Cipriani A, Douglas S, Horner P, Jackson CA, John A, Joyce DW, Lee SC, Lewis J, McIntosh A, Nixon N, Osborn D, Phiri P, Rathod S, Smith T, Sokal R, Waller R, Landau S.",,BMJ open,2021,2021-05-26,Y,Mental health; Adult Psychiatry; Old Age Psychiatry; Organisation Of Health Services; Covid-19,,,"<h4>Objectives</h4>To investigate changes in daily mental health (MH) service use and mortality in response to the introduction and the lifting of the COVID-19 'lockdown' policy in Spring 2020.<h4>Design</h4>A regression discontinuity in time (RDiT) analysis of daily service-level activity.<h4>Setting and participants</h4>Mental healthcare data were extracted from 10 UK providers.<h4>Outcome measures</h4>Daily (weekly for one site) deaths from all causes, referrals and discharges, inpatient care (admissions, discharges, caseloads) and community services (face-to-face (f2f)/non-f2f contacts, caseloads): Adult, older adult and child/adolescent mental health; early intervention in psychosis; home treatment teams and liaison/Accident and Emergency (A&E). Data were extracted from 1 Jan 2019 to 31 May 2020 for all sites, supplemented to 31 July 2020 for four sites. Changes around the commencement and lifting of COVID-19 'lockdown' policy (23 March and 10 May, respectively) were estimated using a RDiT design with a difference-in-difference approach generating incidence rate ratios (IRRs), meta-analysed across sites.<h4>Results</h4>Pooled estimates for the lockdown transition showed increased daily deaths (IRR 2.31, 95% CI 1.86 to 2.87), reduced referrals (IRR 0.62, 95% CI 0.55 to 0.70) and reduced inpatient admissions (IRR 0.75, 95% CI 0.67 to 0.83) and caseloads (IRR 0.85, 95% CI 0.79 to 0.91) compared with the pre lockdown period. All community services saw shifts from f2f to non-f2f contacts, but varied in caseload changes. Lift of lockdown was associated with reduced deaths (IRR 0.42, 95% CI 0.27 to 0.66), increased referrals (IRR 1.36, 95% CI 1.15 to 1.60) and increased inpatient admissions (IRR 1.21, 95% CI 1.04 to 1.42) and caseloads (IRR 1.06, 95% CI 1.00 to 1.12) compared with the lockdown period. Site-wide activity, inpatient care and community services did not return to pre lockdown levels after lift of lockdown, while number of deaths did. Between-site heterogeneity most often indicated variation in size rather than direction of effect.<h4>Conclusions</h4>MH service delivery underwent sizeable changes during the first national lockdown, with as-yet unknown and unevaluated consequences.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/5/e049721.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-049721; html:https://europepmc.org/articles/PMC8159668; pdf:https://europepmc.org/articles/PMC8159668?pdf=render
 34330923,https://doi.org/10.1038/s41467-021-24930-y,Toxin import through the antibiotic efflux channel TolC.,"Housden NG, Webby MN, Lowe ED, El-Baba TJ, Kaminska R, Redfield C, Robinson CV, Kleanthous C.",,Nature communications,2021,2021-07-30,Y,,,,"Bacteria often secrete diffusible protein toxins (bacteriocins) to kill bystander cells during interbacterial competition. Here, we use biochemical, biophysical and structural analyses to show how a bacteriocin exploits TolC, a major outer-membrane antibiotic efflux channel in Gram-negative bacteria, to transport itself across the outer membrane of target cells. Klebicin C (KlebC), a rRNase toxin produced by Klebsiella pneumoniae, binds TolC of a related species (K. quasipneumoniae) with high affinity through an N-terminal, elongated helical hairpin domain common amongst bacteriocins. The KlebC helical hairpin opens like a switchblade to bind TolC. A cryo-EM structure of this partially translocated state, at 3.1 Å resolution, reveals that KlebC associates along the length of the TolC channel. Thereafter, the unstructured N-terminus of KlebC protrudes beyond the TolC iris, presenting a TonB-box sequence to the periplasm. Association with proton-motive force-linked TonB in the inner membrane drives toxin import through the channel. Finally, we demonstrate that KlebC binding to TolC blocks drug efflux from bacteria. Our results indicate that TolC, in addition to its known role in antibiotic export, can function as a protein import channel for bacteriocins.",,pdf:https://www.nature.com/articles/s41467-021-24930-y.pdf; doi:https://doi.org/10.1038/s41467-021-24930-y; html:https://europepmc.org/articles/PMC8324772; pdf:https://europepmc.org/articles/PMC8324772?pdf=render
 32706893,https://doi.org/10.1182/bloodadvances.2020002230,Artificial intelligence-based morphological fingerprinting of megakaryocytes: a new tool for assessing disease in MPN patients.,"Sirinukunwattana K, Aberdeen A, Theissen H, Sousos N, Psaila B, Mead AJ, Turner GDH, Rees G, Rittscher J, Royston D.",,Blood advances,2020,2020-07-01,N,,,,"Accurate diagnosis and classification of myeloproliferative neoplasms (MPNs) requires integration of clinical, morphological, and genetic findings. Despite major advances in our understanding of the molecular and genetic basis of MPNs, the morphological assessment of bone marrow trephines (BMT) is critical in differentiating MPN subtypes and their reactive mimics. However, morphological assessment is heavily constrained by a reliance on subjective, qualitative, and poorly reproducible criteria. To improve the morphological assessment of MPNs, we have developed a machine learning approach for the automated identification, quantitative analysis, and abstract representation of megakaryocyte features using reactive/nonneoplastic BMT samples (n = 43) and those from patients with established diagnoses of essential thrombocythemia (n = 45), polycythemia vera (n = 18), or myelofibrosis (n = 25). We describe the application of an automated workflow for the identification and delineation of relevant histological features from routinely prepared BMTs. Subsequent analysis enabled the tissue diagnosis of MPN with a high predictive accuracy (area under the curve = 0.95) and revealed clear evidence of the potential to discriminate between important MPN subtypes. Our method of visually representing abstracted megakaryocyte features in the context of analyzed patient cohorts facilitates the interpretation and monitoring of samples in a manner that is beyond conventional approaches. The automated BMT phenotyping approach described here has significant potential as an adjunct to standard genetic and molecular testing in established or suspected MPN patients, either as part of the routine diagnostic pathway or in the assessment of disease progression/response to treatment.",,pdf:https://ashpublications.org/bloodadvances/article-pdf/4/14/3284/1749738/advancesadv2020002230.pdf; doi:https://doi.org/10.1182/bloodadvances.2020002230; html:https://europepmc.org/articles/PMC7391156; pdf:https://europepmc.org/articles/PMC7391156?pdf=render; doi:https://doi.org/10.1182/bloodadvances.2020002230
 30778056,https://doi.org/10.1038/s41467-019-08797-8,Towards a data-integrated cell.,"Malod-Dognin N, Petschnigg J, Windels SFL, Povh J, Hemingway H, Ketteler R, Pržulj N.",,Nature communications,2019,2019-02-18,Y,,Applied Analytics,,"We are increasingly accumulating molecular data about a cell. The challenge is how to integrate them within a unified conceptual and computational framework enabling new discoveries. Hence, we propose a novel, data-driven concept of an integrated cell, iCell. Also, we introduce a computational prototype of an iCell, which integrates three omics, tissue-specific molecular interaction network types. We construct iCells of four cancers and the corresponding tissue controls and identify the most rewired genes in cancer. Many of them are of unknown function and cannot be identified as different in cancer in any specific molecular network. We biologically validate that they have a role in cancer by knockdown experiments followed by cell viability assays. We find additional support through Kaplan-Meier survival curves of thousands of patients. Finally, we extend this analysis to uncover pan-cancer genes. Our methodology is universal and enables integrative comparisons of diverse omics data over cells and tissues.",,pdf:https://www.nature.com/articles/s41467-019-08797-8.pdf; doi:https://doi.org/10.1038/s41467-019-08797-8; html:https://europepmc.org/articles/PMC6379402; pdf:https://europepmc.org/articles/PMC6379402?pdf=render
 35235826,https://doi.org/10.1016/j.ijid.2022.02.051,"Assessing the clinical severity of the Omicron variant in the Western Cape Province, South Africa, using the diagnostic PCR proxy marker of RdRp target delay to distinguish between Omicron and Delta infections - a survival analysis.","Hussey H, Davies MA, Heekes A, Williamson C, Valley-Omar Z, Hardie D, Korsman S, Doolabh D, Preiser W, Maponga T, Iranzadeh A, Wasserman S, Boloko L, Symons G, Raubenheimer P, Parker A, Schrueder N, Solomon W, Rousseau P, Wolter N, Jassat W, Cohen C, Lessells R, Wilkinson RJ, Boulle A, Hsiao NY.",,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2022,2022-02-27,Y,South Africa; Clinical Severity; Sars-cov-2; Omicron Variant; Rdrp Target Delay,,,"<h4>Background</h4>At present, it is unclear whether the extent of reduced risk of severe disease seen with SARS-Cov-2 Omicron variant infection is caused by a decrease in variant virulence or by higher levels of population immunity.<h4>Methods</h4>RdRp target delay (RTD) in the Seegene Allplex<sup>TM</sup> 2019-nCoV PCR assay is a proxy marker for the Delta variant. The absence of this proxy marker in the transition period was used to identify suspected Omicron infections. Cox regression was performed for the outcome of hospital admission in those who tested positive for SARS-CoV-2 on the Seegene Allplex<sup>TM</sup> assay from November 1 to December 14, 2021 in the Western Cape Province, South Africa, in the public sector. Adjustments were made for vaccination status and prior diagnosis of infection.<h4>Results</h4>A total of 150 cases with RTD and 1486 cases without RTD were included. Cases without RTD had a lower hazard of admission (adjusted hazard ratio [aHR], 0.56; 95% confidence interval [CI], 0.34-0.91). Complete vaccination was protective against admission, with an aHR of 0.45 (95% CI, 0.26-0.77).<h4>Conclusion</h4>Omicron has resulted in a lower risk of hospital admission compared with contemporaneous Delta infection, when using the proxy marker of RTD. Under-ascertainment of reinfections with an immune escape variant remains a challenge to accurately assessing variant virulence.",,pdf:http://spiral.imperial.ac.uk/bitstream/10044/1/95846/7/1-s2.0-S1201971222001291-main.pdf; doi:https://doi.org/10.1016/j.ijid.2022.02.051; html:https://europepmc.org/articles/PMC8882068; pdf:https://europepmc.org/articles/PMC8882068?pdf=render
-34796246,https://doi.org/10.1093/ofid/ofab496,"Acceptability, Usability, and Performance of Lateral Flow Immunoassay Tests for Severe Acute Respiratory Syndrome Coronavirus 2 Antibodies: REACT-2 Study of Self-Testing in Nonhealthcare Key Workers.","Davies B, Araghi M, Moshe M, Gao H, Bennet K, Jenkins J, Atchison C, Darzi A, Ashby D, Riley S, Barclay W, Elliott P, Ward H, Cooke G.",,Open forum infectious diseases,2021,2021-10-04,Y,Sensitivity and specificity; Antibody testing; Sars-cov-2; Covid-19 Diagnostic Testing,,,"<h4>Background</h4>Seroprevalence studies are essential to understand the epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Various technologies, including laboratory assays and point-of-care self-tests, are available for antibody testing. The interpretation of seroprevalence studies requires comparative data on the performance of antibody tests.<h4>Methods</h4>In June 2020, current and former members of the United Kingdom police forces and fire service performed a self-test lateral flow immunoassay (LFIA), had a nurse-performed LFIA, and provided a venous blood sample for enzyme-linked immunosorbent assay (ELISA). We present the prevalence of antibodies to SARS-CoV-2 and the acceptability and usability of self-test LFIAs, and we determine the sensitivity and specificity of LFIAs compared with laboratory ELISA.<h4>Results</h4>In this cohort of 5189 current and former members of the police service and 263 members of the fire service, 7.4% (396 of 5348; 95% confidence interval [CI], 6.7-8.1) were antibody positive. Seroprevalence was 8.9% (95% CI, 6.9-11.4) in those under 40 years, 11.5% (95% CI, 8.8-15.0) in those of nonwhite ethnicity, and 7.8% (95% CI, 7.1-8.7) in those currently working. Self-test LFIA had an acceptability of 97.7% and a usability of 90.0%. There was substantial agreement between within-participant LFIA results (kappa 0.80; 95% CI, 0.77-0.83). The LFIAs had a similar performance: compared with ELISA, sensitivity was 82.1% (95% CI, 77.7-86.0) self-test and 76.4% (95% CI, 71.9-80.5) nurse-performed with specificity of 97.8% (95% CI, 97.3-98.2) and 98.5% (95% CI, 98.1-98.8), respectively.<h4>Conclusions</h4>A greater proportion of this nonhealthcare key worker cohort showed evidence of previous infection with SARS-CoV-2 than the general population at 6.0% (95% CI, 5.8-6.1) after the first wave in England. The high acceptability and usability reported by participants and similar performance of self-test and nurse-performed LFIAs indicate that the self-test LFIA is fit for purpose for home testing in occupational and community prevalence studies.",,pdf:https://academic.oup.com/ofid/article-pdf/8/11/ofab496/41174715/ofab496.pdf; doi:https://doi.org/10.1093/ofid/ofab496; html:https://europepmc.org/articles/PMC8522420; pdf:https://europepmc.org/articles/PMC8522420?pdf=render
 31013802,https://doi.org/10.3390/ijerph16081325,Using Patient-Reported Outcomes to Predict Revision Arthroplasty Following Femoral Neck Fracture: Enhancing the Value of Clinical Registries through Data Linkage.,"Ekegren CL, de Steiger R, Edwards ER, Page RS, Hau R, Liew S, Oppy A, Gabbe BJ.",,International journal of environmental research and public health,2019,2019-04-12,Y,Pain; Femoral neck fractures; Arthroplasty; Registries; Patient Reported Outcome Measures,Improving Public Health,,"The aim of this study was to determine the association between patient-reported outcome measures (PROMs) six months following femoral neck fracture after a low fall and future arthroplasty, and the factors associated with this. Six-month post-fracture PROMs were collected from the Victorian Orthopaedic Trauma Outcomes Registry (VOTOR) for patients aged >55 years who were admitted for a femoral neck fracture after a low fall between March 2007 and June 2015. These cases were linked with those registered by Australian Orthopaedic Association National Joint Replacement Registry (AOANJRR) up to October 2016. Multivariable analysis was performed using a Cox proportional hazards model to determine factors associated with future arthroplasty, including six-month PROMs. Of the 7077 hip fracture patients registered by VOTOR during the study period, 2325 met the inclusion criteria. Internal fixation being used for the initial hip fracture surgery, being younger and having no pre-injury disability were all independently associated with future revision or conversion to arthroplasty. Out of all PROMs, reporting pain and discomfort six months post-fracture was associated with a 9.5-fold increase in the risk of future arthroplasty (95% CI: 3.81, 23.67). The value of clinical registries can be enhanced via data linkage, in this case by using PROMs to predict arthroplasty following femoral neck fracture.",,pdf:https://www.mdpi.com/1660-4601/16/8/1325/pdf?version=1555077276; doi:https://doi.org/10.3390/ijerph16081325; html:https://europepmc.org/articles/PMC6517898; pdf:https://europepmc.org/articles/PMC6517898?pdf=render
+34796246,https://doi.org/10.1093/ofid/ofab496,"Acceptability, Usability, and Performance of Lateral Flow Immunoassay Tests for Severe Acute Respiratory Syndrome Coronavirus 2 Antibodies: REACT-2 Study of Self-Testing in Nonhealthcare Key Workers.","Davies B, Araghi M, Moshe M, Gao H, Bennet K, Jenkins J, Atchison C, Darzi A, Ashby D, Riley S, Barclay W, Elliott P, Ward H, Cooke G.",,Open forum infectious diseases,2021,2021-10-04,Y,Sensitivity and specificity; Antibody testing; Sars-cov-2; Covid-19 Diagnostic Testing,,,"<h4>Background</h4>Seroprevalence studies are essential to understand the epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Various technologies, including laboratory assays and point-of-care self-tests, are available for antibody testing. The interpretation of seroprevalence studies requires comparative data on the performance of antibody tests.<h4>Methods</h4>In June 2020, current and former members of the United Kingdom police forces and fire service performed a self-test lateral flow immunoassay (LFIA), had a nurse-performed LFIA, and provided a venous blood sample for enzyme-linked immunosorbent assay (ELISA). We present the prevalence of antibodies to SARS-CoV-2 and the acceptability and usability of self-test LFIAs, and we determine the sensitivity and specificity of LFIAs compared with laboratory ELISA.<h4>Results</h4>In this cohort of 5189 current and former members of the police service and 263 members of the fire service, 7.4% (396 of 5348; 95% confidence interval [CI], 6.7-8.1) were antibody positive. Seroprevalence was 8.9% (95% CI, 6.9-11.4) in those under 40 years, 11.5% (95% CI, 8.8-15.0) in those of nonwhite ethnicity, and 7.8% (95% CI, 7.1-8.7) in those currently working. Self-test LFIA had an acceptability of 97.7% and a usability of 90.0%. There was substantial agreement between within-participant LFIA results (kappa 0.80; 95% CI, 0.77-0.83). The LFIAs had a similar performance: compared with ELISA, sensitivity was 82.1% (95% CI, 77.7-86.0) self-test and 76.4% (95% CI, 71.9-80.5) nurse-performed with specificity of 97.8% (95% CI, 97.3-98.2) and 98.5% (95% CI, 98.1-98.8), respectively.<h4>Conclusions</h4>A greater proportion of this nonhealthcare key worker cohort showed evidence of previous infection with SARS-CoV-2 than the general population at 6.0% (95% CI, 5.8-6.1) after the first wave in England. The high acceptability and usability reported by participants and similar performance of self-test and nurse-performed LFIAs indicate that the self-test LFIA is fit for purpose for home testing in occupational and community prevalence studies.",,pdf:https://academic.oup.com/ofid/article-pdf/8/11/ofab496/41174715/ofab496.pdf; doi:https://doi.org/10.1093/ofid/ofab496; html:https://europepmc.org/articles/PMC8522420; pdf:https://europepmc.org/articles/PMC8522420?pdf=render
 37188768,https://doi.org/10.1038/s42003-023-04836-9,Fine-mapping of retinal vascular complexity loci identifies Notch regulation as a shared mechanism with myocardial infarction outcomes.,"Villaplana-Velasco A, Pigeyre M, Engelmann J, Rawlik K, Canela-Xandri O, Tochel C, Lona-Durazo F, Mookiah MRK, Doney A, Parra EJ, Trucco E, MacGillivray T, Rannikmae K, Tenesa A, Pairo-Castineira E, Bernabeu MO.",,Communications biology,2023,2023-05-15,Y,,,,"There is increasing evidence that the complexity of the retinal vasculature measured as fractal dimension, D<sub>f</sub>, might offer earlier insights into the progression of coronary artery disease (CAD) before traditional biomarkers can be detected. This association could be partly explained by a common genetic basis; however, the genetic component of D<sub>f</sub> is poorly understood. We present a genome-wide association study (GWAS) of 38,000 individuals with white British ancestry from the UK Biobank aimed to comprehensively study the genetic component of D<sub>f</sub> and analyse its relationship with CAD. We replicated 5 D<sub>f</sub> loci and found 4 additional loci with suggestive significance (P < 1e-05) to contribute to D<sub>f</sub> variation, which previously were reported in retinal tortuosity and complexity, hypertension, and CAD studies. Significant negative genetic correlation estimates support the inverse relationship between D<sub>f</sub> and CAD, and between D<sub>f</sub> and myocardial infarction (MI), one of CAD's fatal outcomes. Fine-mapping of D<sub>f</sub> loci revealed Notch signalling regulatory variants supporting a shared mechanism with MI outcomes. We developed a predictive model for MI incident cases, recorded over a 10-year period following clinical and ophthalmic evaluation, combining clinical information, D<sub>f</sub>, and a CAD polygenic risk score. Internal cross-validation demonstrated a considerable improvement in the area under the curve (AUC) of our predictive model (AUC = 0.770 ± 0.001) when comparing with an established risk model, SCORE, (AUC = 0.741 ± 0.002) and extensions thereof leveraging the PRS (AUC = 0.728 ± 0.001). This evidences that D<sub>f</sub> provides risk information beyond demographic, lifestyle, and genetic risk factors. Our findings shed new light on the genetic basis of D<sub>f</sub>, unveiling a common control with MI, and highlighting the benefits of its application in individualised MI risk prediction.",,doi:https://doi.org/10.1038/s42003-023-04836-9; html:https://europepmc.org/articles/PMC10185685; pdf:https://europepmc.org/articles/PMC10185685?pdf=render
 37538507,https://doi.org/10.1016/j.rpth.2023.100175,<i>PIK3R3</i> is a candidate regulator of platelet count in people of Bangladeshi ancestry.,"Burley K, Fitzgibbon L, van Heel D, Genes & Health Research Team@EastLondonGenes, Vuckovic D, Mumford AD, Genes & Health Research Team.",,Research and practice in thrombosis and haemostasis,2023,2023-05-14,Y,Blood platelets; Cardiovascular diseases; Bangladesh; Genome-wide Association Study; Phosphatidylinositol 3-Kinases,,,"<h4>Background</h4>Blood platelets are mediators of atherothrombotic disease and are regulated by complex sets of genes. Association studies in European ancestry populations have already detected informative platelet regulatory loci. Studies in other ancestries can potentially reveal new associations because of different allele frequencies, linkage structures, and variant effects.<h4>Objectives</h4>To reveal new regulatory genes for platelet count (PLT).<h4>Methods</h4>Genome-wide association studies (GWAS) were performed in 20,218 Bangladeshi and 9198 Pakistani individuals from the Genes & Health study. Loci significantly associated with PLT underwent fine-mapping to identify candidate genes.<h4>Results</h4>Of 1588 significantly associated variants (<i>P</i> < 5 × 10<sup>-8</sup>) at 20 loci in the Bangladeshi analysis, most replicated findings in prior transancestry GWAS and in the Pakistani analysis. However, the Bangladeshi locus defined by rs946528 (chr1:46019890) did not associate with PLT in the Pakistani analysis but was in the same linkage disequilibrium block (<i>r</i><sup>2</sup> ≥ 0.5) as PLT-associated variants in prior East Asian GWAS. The single independent association signal was refined to a 95% credible set of 343 variants spanning 8 coding genes. Functional annotation, mapping to megakaryocyte regulatory regions, and colocalization with blood expression quantitative trait loci identified the likely mediator of the PLT phenotype to be <i>PIK3R3</i> encoding a regulator of phosphoinositol 3-kinase (PI3K).<h4>Conclusion</h4>Abnormal PI3K activity in the vessel wall is already implicated in the pathogenesis of atherothrombosis. Our identification of a new association between <i>PIK3R3</i> and PLT provides further mechanistic insights into the contribution of the PI3K pathway to platelet biology.",,doi:https://doi.org/10.1016/j.rpth.2023.100175; html:https://europepmc.org/articles/PMC10394561; pdf:https://europepmc.org/articles/PMC10394561?pdf=render
 31806382,https://doi.org/10.1016/j.injury.2019.11.023,Variation in documented inhalation injury rates following burn injury in Australia and New Zealand.,"Tracy LM, Dyson K, Mercier LL, Cleland H, McInnes JA, Cameron PA, Singer Y, Edgar DW, Darton A, Gabbe BJ.",,Injury,2020,2019-11-17,N,Variation; Australia; New Zealand; Inhalation Injury; Burn Registry,,,"<h4>Introduction</h4>The negative impact of inhalation injuries on in-hospital outcomes for burn patients is well known, but the burns community is yet to form a consensus on diagnostic criteria and clinical definitions. The diagnosis of inhalation injuries is consequently highly subjective. This study aimed to assess the variation in the rate of documented inhalation injury for adult patients in Australian and New Zealand burn units.<h4>Methods</h4>Data for sequential admissions collected from eight adult burn centres across Australia and New Zealand between July 2009 and June 2016 were extracted from the Burns Registry of Australia and New Zealand (BRANZ). Inhalation injury was classified in two ways: (i) a field in the BRANZ data dictionary, and (ii) through a series of International Classification of Disease 10th Revision Australian Modification (ICD-10-AM) codes. Variation in inhalation injury prevalence was assessed using descriptive statistics, funnel plots, logistic regression, and predicted probabilities.<h4>Results</h4>There were 11,206 admissions to BRANZ sites over the study period. Inhalation injury prevalence was the highest at Site D (13.1% for the BRANZ field and 11.8% for the ICD-10-AM codes), but there was significant variation between the contributing sites and the inhalation injury classification methods.<h4>Conclusion</h4>There is significant variation in the prevalence of documented inhalation injury among Australian and New Zealand burns units. The variation in the prevalence of documented inhalation injury across Australian and New Zealand sites reinforces the need for a consensus definition in the diagnosis of these injuries. Further work is required to improve data quality and reconcile the differences between clinical and ICD-10-AM coding prevalence before changes in clinical practice can be recommended from these data.",,doi:https://doi.org/10.1016/j.injury.2019.11.023
 33905495,https://doi.org/10.1093/nar/gkab291,Endonuclease enrichment TAPS for cost-effective genome-wide base-resolution DNA methylation detection.,"Cheng J, Siejka-Zielińska P, Liu Y, Chandran A, Kriaucionis S, Song CX.",,Nucleic acids research,2021,2021-07-01,Y,,,,"Whole genome base-resolution methylome sequencing allows for the most comprehensive analysis of DNA methylation, however, the considerable sequencing cost often limits its applications. While reduced representation sequencing can be an affordable alternative, over 80% of CpGs in the genome are not covered. Building on our recently developed TET-assisted pyridine borane sequencing (TAPS) method, we here described endonuclease enrichment TAPS (eeTAPS), which utilizes dihydrouracil (DHU)-cleaving endonuclease digestion of TAPS-converted DNA to enrich methylated CpG sites (mCpGs). eeTAPS can accurately detect 87% of mCpGs in the mouse genome with a sequencing depth equivalent to 4× whole genome sequencing. In comparison, reduced representation TAPS (rrTAPS) detected less than 4% of mCpGs with 2.5× sequencing depth. Our results demonstrate eeTAPS to be a new strategy for cost-effective genome-wide methylation analysis at single-CpG resolution that can fill the gap between whole-genome and reduced representation sequencing.",,pdf:https://ora.ox.ac.uk/objects/uuid:3e48f9e0-d3c3-41ec-99ff-cc64d141d6cf/files/rcz30pt21m; doi:https://doi.org/10.1093/nar/gkab291; html:https://europepmc.org/articles/PMC8287915; pdf:https://europepmc.org/articles/PMC8287915?pdf=render
 37034358,https://doi.org/10.1016/j.eclinm.2023.101932,Contextualising adverse events of special interest to characterise the baseline incidence rates in 24 million patients with COVID-19 across 26 databases: a multinational retrospective cohort study.,"Voss EA, Shoaibi A, Yin Hui Lai L, Blacketer C, Alshammari T, Makadia R, Haynes K, Sena AG, Rao G, van Sandijk S, Fraboulet C, Boyer L, Le Carrour T, Horban S, Morales DR, Martínez Roldán J, Ramírez-Anguita JM, Mayer MA, de Wilde M, John LH, Duarte-Salles T, Roel E, Pistillo A, Kolde R, Maljković F, Denaxas S, Papez V, Kahn MG, Natarajan K, Reich C, Secora A, Minty EP, Shah NH, Posada JD, Garcia Morales MT, Bosca D, Cadenas Juanino H, Diaz Holgado A, Pedrera Jiménez M, Serrano Balazote P, García Barrio N, Şen S, Üresin AY, Erdogan B, Belmans L, Byttebier G, Malbrain MLNG, Dedman DJ, Cuccu Z, Vashisht R, Butte AJ, Patel A, Dahm L, Han C, Bu F, Arshad F, Ostropolets A, Nyberg F, Hripcsak G, Suchard MA, Prieto-Alhambra D, Rijnbeek PR, Schuemie MJ, Ryan PB.",,EClinicalMedicine,2023,2023-04-04,Y,Observational Research; Omop Cdm; Covid-19; Adverse Events Of Special Interest,,,"<h4>Background</h4>Adverse events of special interest (AESIs) were pre-specified to be monitored for the COVID-19 vaccines. Some AESIs are not only associated with the vaccines, but with COVID-19. Our aim was to characterise the incidence rates of AESIs following SARS-CoV-2 infection in patients and compare these to historical rates in the general population.<h4>Methods</h4>A multi-national cohort study with data from primary care, electronic health records, and insurance claims mapped to a common data model. This study's evidence was collected between Jan 1, 2017 and the conclusion of each database (which ranged from Jul 2020 to May 2022). The 16 pre-specified prevalent AESIs were: acute myocardial infarction, anaphylaxis, appendicitis, Bell's palsy, deep vein thrombosis, disseminated intravascular coagulation, encephalomyelitis, Guillain- Barré syndrome, haemorrhagic stroke, non-haemorrhagic stroke, immune thrombocytopenia, myocarditis/pericarditis, narcolepsy, pulmonary embolism, transverse myelitis, and thrombosis with thrombocytopenia. Age-sex standardised incidence rate ratios (SIR) were estimated to compare post-COVID-19 to pre-pandemic rates in each of the databases.<h4>Findings</h4>Substantial heterogeneity by age was seen for AESI rates, with some clearly increasing with age but others following the opposite trend. Similarly, differences were also observed across databases for same health outcome and age-sex strata. All studied AESIs appeared consistently more common in the post-COVID-19 compared to the historical cohorts, with related meta-analytic SIRs ranging from 1.32 (1.05 to 1.66) for narcolepsy to 11.70 (10.10 to 13.70) for pulmonary embolism.<h4>Interpretation</h4>Our findings suggest all AESIs are more common after COVID-19 than in the general population. Thromboembolic events were particularly common, and over 10-fold more so. More research is needed to contextualise post-COVID-19 complications in the longer term.<h4>Funding</h4>None.",,doi:https://doi.org/10.1016/j.eclinm.2023.101932; doi:https://doi.org/10.1016/j.eclinm.2023.101932; html:https://europepmc.org/articles/PMC10072853; pdf:https://europepmc.org/articles/PMC10072853?pdf=render
-38575161,https://doi.org/10.1183/13993003.01853-2023,Symptoms before and after COVID-19: a population and case-control study using prospective data.,"Sudre CH, Antonelli M, Cheetham NJ, Molteni E, Canas LS, Bowyer V, Murray B, Rjoob K, Modat M, Capdevila Pujol J, Hu C, Wolf J, Spector TD, Hammers A, Steves CJ, Ourselin S, Duncan EL.",,The European respiratory journal,2024,2024-07-18,Y,,,,"<h4>Background</h4>Some individuals experience prolonged illness after acute coronavirus disease 2019 (COVID-19). We assessed whether pre-infection symptoms affected post-acute COVID illness duration.<h4>Methods</h4>Survival analysis was performed in adults (n=23 452) with community-managed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection prospectively self-logging data through the ZOE COVID Symptom Study app, at least weekly, from 8 weeks before to 12 weeks after COVID-19 onset, conditioned on presence <i>versus</i> absence of baseline symptoms (4-8 weeks before COVID-19). A case-control study was performed in 1350 individuals with long illness (≥8 weeks, including 906 individuals (67.1%) with illness ≥12 weeks), matched 1:1 (for age, sex, body mass index, testing week, prior infection, vaccination, smoking, index of multiple deprivation) with 1350 individuals with short illness (<4 weeks). Baseline symptoms were compared between the two groups, and against post-COVID symptoms.<h4>Results</h4>Individuals reporting baseline symptoms had longer COVID-related symptom duration (median 15 days <i>versus</i> 10 days for individuals without baseline symptoms) with baseline fatigue nearly doubling duration. Two-thirds (910 (67.4%) of 1350) of individuals with long illness were asymptomatic beforehand. However, 440 (32.6%) had baseline symptoms, <i>versus</i> 255 (18.9%) of 1350 individuals with short illness (p<0.0001). Baseline symptoms doubled the odds ratio for long illness (2.14, 95% CI 1.78-2.57). Prior comorbidities were more common in individuals with long <i>versus</i> short illness. In individuals with long illness, baseline symptomatic (<i>versus</i> asymptomatic) individuals were more likely to be female, younger, and have prior comorbidities; and baseline and post-acute symptoms, and symptom burden, correlated strongly.<h4>Conclusions</h4>Individuals experiencing symptoms before COVID-19 had longer illness duration and increased odds of long illness. However, many individuals with long illness were well before SARS-CoV-2 infection.",,pdf:https://erj.ersjournals.com/content/erj/early/2024/03/21/13993003.01853-2023.full.pdf; doi:https://doi.org/10.1183/13993003.01853-2023; html:https://europepmc.org/articles/PMC11255388; pdf:https://europepmc.org/articles/PMC11255388?pdf=render
 31666709,https://doi.org/10.1038/s41433-019-0657-y,Comment on: 'Quantification of anterior chamber reaction after intravitreal injections of conbercept and ranibizumab: a pilot study'.,"Minocha A, Liu X, Denniston AK, Petrushkin H, Solebo AL.",,"Eye (London, England)",2020,2019-10-30,N,,,,,,pdf:https://www.nature.com/articles/s41433-019-0657-y.pdf; doi:https://doi.org/10.1038/s41433-019-0657-y; html:https://europepmc.org/articles/PMC7376231; pdf:https://europepmc.org/articles/PMC7376231?pdf=render; doi:https://doi.org/10.1038/s41433-019-0657-y
+38575161,https://doi.org/10.1183/13993003.01853-2023,Symptoms before and after COVID-19: a population and case-control study using prospective data.,"Sudre CH, Antonelli M, Cheetham NJ, Molteni E, Canas LS, Bowyer V, Murray B, Rjoob K, Modat M, Capdevila Pujol J, Hu C, Wolf J, Spector TD, Hammers A, Steves CJ, Ourselin S, Duncan EL.",,The European respiratory journal,2024,2024-07-18,Y,,,,"<h4>Background</h4>Some individuals experience prolonged illness after acute coronavirus disease 2019 (COVID-19). We assessed whether pre-infection symptoms affected post-acute COVID illness duration.<h4>Methods</h4>Survival analysis was performed in adults (n=23 452) with community-managed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection prospectively self-logging data through the ZOE COVID Symptom Study app, at least weekly, from 8 weeks before to 12 weeks after COVID-19 onset, conditioned on presence <i>versus</i> absence of baseline symptoms (4-8 weeks before COVID-19). A case-control study was performed in 1350 individuals with long illness (≥8 weeks, including 906 individuals (67.1%) with illness ≥12 weeks), matched 1:1 (for age, sex, body mass index, testing week, prior infection, vaccination, smoking, index of multiple deprivation) with 1350 individuals with short illness (<4 weeks). Baseline symptoms were compared between the two groups, and against post-COVID symptoms.<h4>Results</h4>Individuals reporting baseline symptoms had longer COVID-related symptom duration (median 15 days <i>versus</i> 10 days for individuals without baseline symptoms) with baseline fatigue nearly doubling duration. Two-thirds (910 (67.4%) of 1350) of individuals with long illness were asymptomatic beforehand. However, 440 (32.6%) had baseline symptoms, <i>versus</i> 255 (18.9%) of 1350 individuals with short illness (p<0.0001). Baseline symptoms doubled the odds ratio for long illness (2.14, 95% CI 1.78-2.57). Prior comorbidities were more common in individuals with long <i>versus</i> short illness. In individuals with long illness, baseline symptomatic (<i>versus</i> asymptomatic) individuals were more likely to be female, younger, and have prior comorbidities; and baseline and post-acute symptoms, and symptom burden, correlated strongly.<h4>Conclusions</h4>Individuals experiencing symptoms before COVID-19 had longer illness duration and increased odds of long illness. However, many individuals with long illness were well before SARS-CoV-2 infection.",,pdf:https://erj.ersjournals.com/content/erj/early/2024/03/21/13993003.01853-2023.full.pdf; doi:https://doi.org/10.1183/13993003.01853-2023; html:https://europepmc.org/articles/PMC11255388; pdf:https://europepmc.org/articles/PMC11255388?pdf=render
 38230350,https://doi.org/10.1016/j.gimo.2023.100811,Biallelic variants in the calpain regulatory subunit <i>CAPNS1</i> cause pulmonary arterial hypertension.,"Postma AV, Rapp CK, Knoflach K, Volk AE, Lemke JR, Ackermann M, Regamey N, Latzin P, Celant L, Jansen SMA, Bogaard HJ, Ilgun A, Alders M, van Spaendonck-Zwarts KY, Jonigk D, Klein C, Gräf S, Kubisch C, Houweling AC, Griese M.",,Genetics in medicine open,2023,2023-01-01,Y,Angiogenesis; Calpain; Pulmonary Arterial Hypertension; Capns1,,,"<h4>Purpose</h4>The aim of this study was to identify the monogenic cause of pulmonary arterial hypertension (PAH), a multifactorial and often fatal disease, in 2 unrelated consanguine families.<h4>Methods</h4>We performed exome sequencing and validated variant pathogenicity by whole-blood RNA and protein expression analysis in both families. Further RNA sequencing of preserved lung tissue was performed to investigate the consequences on selected genes that are involved in angiogenesis, proliferation, and apoptosis.<h4>Results</h4>We identified 2 rare biallelic variants in <i>CAPNS1</i>, encoding the regulatory subunit of calpain. The variants cosegregated with PAH in the families. Both variants lead to loss of function (LoF), which is demonstrated by aberrant splicing resulting in the complete absence of the CAPNS1 protein in affected patients. No other LoF <i>CAPNS1</i> variant was identified in the genome data of more than 1000 patients with unresolved PAH.<h4>Conclusion</h4>The calpain holoenzyme was previously linked to pulmonary vascular development and progression of PAH in patients. We demonstrated that biallelic LoF variants in <i>CAPNS1</i> can cause idiopathic PAH by the complete absence of CAPNS1 protein. Screening of this gene in patients who are affected by PAH, especially with suspected autosomal recessive inheritance, should be considered.",,pdf:https://boris.unibe.ch/191728/1/1-s2.0-S2949774423008208-main.pdf; doi:https://doi.org/10.1016/j.gimo.2023.100811; html:https://europepmc.org/articles/PMC10790724
 35103486,https://doi.org/10.1128/msystems.01132-21,Using Community Ecology Theory and Computational Microbiome Methods To Study Human Milk as a Biological System.,"Shenhav L, Azad MB.",,mSystems,2022,2022-02-01,Y,Lactation; Human Milk; Breastfeeding; Chronobiology; Computational Methods; System Biology; Human Microbiome; Community Ecology Theory,,,"Human milk is a complex and dynamic biological system that has evolved to optimally nourish and protect human infants. Yet, according to a recent priority-setting review, ""our current understanding of human milk composition and its individual components and their functions fails to fully recognize the importance of the chronobiology and systems biology of human milk in the context of milk synthesis, optimal timing and duration of feeding, and period of lactation"" (P. Christian et al., Am J Clin Nutr 113:1063-1072, 2021, https://doi.org/10.1093/ajcn/nqab075). We attribute this critical knowledge gap to three major reasons as follows. (i) Studies have typically examined each subsystem of the mother-milk-infant ""triad"" in isolation and often focus on a single element or component (e.g., maternal lactation physiology or milk microbiome or milk oligosaccharides or infant microbiome or infant gut physiology). This undermines our ability to develop comprehensive representations of the interactions between these elements and study their response to external perturbations. (ii) Multiomics studies are often cross-sectional, presenting a snapshot of milk composition, largely ignoring the temporal variability during lactation. The lack of temporal resolution precludes the characterization and inference of robust interactions between the dynamic subsystems of the triad. (iii) We lack computational methods to represent and decipher the complex ecosystem of the mother-milk-infant triad and its environment. In this review, we advocate for longitudinal multiomics data collection and demonstrate how incorporating knowledge gleaned from microbial community ecology and computational methods developed for microbiome research can serve as an anchor to advance the study of human milk and its many components as a ""system within a system.""",,doi:https://doi.org/10.1128/msystems.01132-21; doi:https://doi.org/10.1128/msystems.01132-21; html:https://europepmc.org/articles/PMC8805635; pdf:https://europepmc.org/articles/PMC8805635?pdf=render
 37565978,https://doi.org/10.1016/j.jchf.2023.07.007,Penetrance and Prognosis of MYH7 Variant-Associated Cardiomyopathies: Results From a Dutch Multicenter Cohort Study.,"Jansen M, de Brouwer R, Hassanzada F, Schoemaker AE, Schmidt AF, Kooijman-Reumerman MD, Bracun V, Slieker MG, Dooijes D, Vermeer AMC, Wilde AAM, Amin AS, Lekanne Deprez RH, Herkert JC, Christiaans I, de Boer RA, Jongbloed JDH, van Tintelen JP, Asselbergs FW, Baas AF.",,JACC. Heart failure,2024,2023-08-09,N,Myosin; Screening; Prognosis; Cardiomyopathy; Penetrance; Myh7,,,"<h4>Background</h4>MYH7 variants cause hypertrophic cardiomyopathy (HCM), noncompaction cardiomyopathy (NCCM), and dilated cardiomyopathy (DCM). Screening of relatives of patients with genetic cardiomyopathy is recommended from 10 to 12 years of age onward, irrespective of the affected gene.<h4>Objectives</h4>This study sought to study the penetrance and prognosis of MYH7 variant-associated cardiomyopathies.<h4>Methods</h4>In this multicenter cohort study, penetrance and major cardiomyopathy-related events (MCEs) were assessed in carriers of (likely) pathogenic MYH7 variants by using Kaplan-Meier curves and log-rank tests. Prognostic factors were evaluated using Cox regression with time-dependent coefficients.<h4>Results</h4>In total, 581 subjects (30.1% index patients, 48.4% male, median age 37.0 years [IQR: 19.5-50.2 years]) were included. HCM was diagnosed in 226 subjects, NCCM in 70, and DCM in 55. Early penetrance and MCEs (age <12 years) were common among NCCM-associated variant carriers (21.2% and 12.0%, respectively) and DCM-associated variant carriers (15.3% and 10.0%, respectively), compared with HCM-associated variant carriers (2.9% and 2.1%, respectively). Penetrance was significantly increased in carriers of converter region variants (adjusted HR: 1.87; 95% CI: 1.15-3.04; P = 0.012) and at age ≤1 year in NCCM-associated or DCM-associated variant carriers (adjusted HR: 21.17; 95% CI: 4.81-93.20; P < 0.001) and subjects with a family history of early MCEs (adjusted HR: 2.45; 95% CI: 1.09-5.50; P = 0.030). The risk of MCE was increased in subjects with a family history of early MCEs (adjusted HR: 1.82; 95% CI: 1.15-2.87; P = 0.010) and at age ≤5 years in NCCM-associated or DCM-associated variant carriers (adjusted HR: 38.82; 95% CI: 5.16-291.88; P < 0.001).<h4>Conclusions</h4>MYH7 variants can cause cardiomyopathies and MCEs at a young age. Screening at younger ages may be warranted, particularly in carriers of NCCM- or DCM-associated variants and/or with a family history of MCEs at <12 years.",,doi:https://doi.org/10.1016/j.jchf.2023.07.007
@@ -2489,26 +2491,26 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 34252085,https://doi.org/10.1371/journal.pcbi.1009162,Detecting behavioural changes in human movement to inform the spatial scale of interventions against COVID-19.,"Gibbs H, Nightingale E, Liu Y, Cheshire J, Danon L, Smeeth L, Pearson CAB, Grundy C, LSHTM CMMID COVID-19 working group, Kucharski AJ, Eggo RM.",,PLoS computational biology,2021,2021-07-12,Y,,,,"On March 23 2020, the UK enacted an intensive, nationwide lockdown to mitigate transmission of COVID-19. As restrictions began to ease, more localized interventions were used to target resurgences in transmission. Understanding the spatial scale of networks of human interaction, and how these networks change over time, is critical to targeting interventions at the most at-risk areas without unnecessarily restricting areas at low risk of resurgence. We use detailed human mobility data aggregated from Facebook users to determine how the spatially-explicit network of movements changed before and during the lockdown period, in response to the easing of restrictions, and to the introduction of locally-targeted interventions. We also apply community detection techniques to the weighted, directed network of movements to identify geographically-explicit movement communities and measure the evolution of these community structures through time. We found that the mobility network became more sparse and the number of mobility communities decreased under the national lockdown, a change that disproportionately affected long distance connections central to the mobility network. We also found that the community structure of areas in which locally-targeted interventions were implemented following epidemic resurgence did not show reorganization of community structure but did show small decreases in indicators of travel outside of local areas. We propose that communities detected using Facebook or other mobility data be used to assess the impact of spatially-targeted restrictions and may inform policymakers about the spatial extent of human movement patterns in the UK. These data are available in near real-time, allowing quantification of changes in the distribution of the population across the UK, as well as changes in travel patterns to inform our understanding of the impact of geographically-targeted interventions.",,pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009162&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1009162; html:https://europepmc.org/articles/PMC8297940; pdf:https://europepmc.org/articles/PMC8297940?pdf=render
 37130615,https://doi.org/10.3399/bjgp.2022.0389,Predicting the risk of acute kidney injury in primary care: derivation and validation of STRATIFY-AKI.,"Koshiaris C, Archer L, Lay-Flurrie S, Snell KI, Riley RD, Stevens R, Banerjee A, Usher-Smith JA, Clegg A, Payne RA, Ogden M, Hobbs FR, McManus RJ, Sheppard JP.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2023,2023-07-27,Y,Blood pressure; Vascular diseases; epidemiology; Primary Health Care; Electronic Health Records; Drug-related Side Effects And Adverse Reactions,,,"<h4>Background</h4>Antihypertensives reduce the risk of cardiovascular disease but are also associated with harms including acute kidney injury (AKI). Few data exist to guide clinical decision making regarding these risks.<h4>Aim</h4>To develop a prediction model estimating the risk of AKI in people potentially indicated for antihypertensive treatment.<h4>Design and setting</h4>Observational cohort study using routine primary care data from the Clinical Practice Research Datalink (CPRD) in England.<h4>Method</h4>People aged ≥40 years, with at least one blood pressure measurement between 130 mmHg and 179 mmHg were included. Outcomes were admission to hospital or death with AKI within 1, 5, and 10 years. The model was derived with data from CPRD GOLD (<i>n</i> = 1 772 618), using a Fine-Gray competing risks approach, with subsequent recalibration using pseudo-values. External validation used data from CPRD Aurum (<i>n</i> = 3 805 322).<h4>Results</h4>The mean age of participants was 59.4 years and 52% were female. The final model consisted of 27 predictors and showed good discrimination at 1, 5, and 10 years (C-statistic for 10-year risk 0.821, 95% confidence interval [CI] = 0.818 to 0.823). There was some overprediction at the highest predicted probabilities (ratio of observed to expected event probability for 10-year risk 0.633, 95% CI = 0.621 to 0.645), affecting patients with the highest risk. Most patients (>95%) had a low 1- to 5-year risk of AKI, and at 10 years only 0.1% of the population had a high AKI and low CVD risk.<h4>Conclusion</h4>This clinical prediction model enables GPs to accurately identify patients at high risk of AKI, which will aid treatment decisions. As the vast majority of patients were at low risk, such a model may provide useful reassurance that most antihypertensive treatment is safe and appropriate while flagging the few for whom this is not the case.",,pdf:https://bjgp.org/content/bjgp/early/2023/01/31/BJGP.2022.0389.full.pdf; doi:https://doi.org/10.3399/BJGP.2022.0389; html:https://europepmc.org/articles/PMC10170524; pdf:https://europepmc.org/articles/PMC10170524?pdf=render
 30819382,https://doi.org/10.1016/j.jchf.2019.01.009,Adverse Drug Reactions to Guideline-Recommended Heart Failure Drugs in Women: A Systematic Review of the Literature.,"Bots SH, Groepenhoff F, Eikendal ALM, Tannenbaum C, Rochon PA, Regitz-Zagrosek V, Miller VM, Day D, Asselbergs FW, den Ruijter HM.",,JACC. Heart failure,2019,2019-03-01,N,Women; Sex differences; Heart Failure; Adverse drug reactions; Sex-specific Reporting,The Human Phenome,,"<h4>Objectives</h4>This study sought to summarize all available evidence on sex differences in adverse drug reactions (ADRs) to heart failure (HF) medication.<h4>Background</h4>Women are more likely to experience ADRs than men, and these reactions may negatively affect women's immediate and long-term health. HF in particular is associated with increased ADR risk because of the high number of comorbidities and older age. However, little is known about ADRs in women with HF who are treated with guideline-recommended drugs.<h4>Methods</h4>A systematic search of PubMed and EMBASE was performed to collect all available information on ADRs to angiotensin-converting enzyme inhibitors, β-blockers, angiotensin II receptor blockers, mineralocorticoid receptor antagonists, ivabradine, and digoxin in both women and men with HF.<h4>Results</h4>The search identified 155 eligible records, of which only 11 (7%) reported ADR data for women and men separately. Sex-stratified reporting of ADRs did not increase over the last decades. Six of the 11 studies did not report sex differences. Three studies reported a higher risk of angiotensin-converting enzyme inhibitor-related ADRs in women, 1 study showed higher digoxin-related mortality risk for women, and 1 study reported a higher risk of mineralocorticoid receptor antagonist-related ADRs in men. No sex differences in ADRs were reported for angiotensin II receptor blockers and β-blockers. Sex-stratified data were not available for ivabradine.<h4>Conclusions</h4>These results underline the scarcity of ADR data stratified by sex. The study investigators call for a change in standard scientific practice toward reporting of ADR data for women and men separately.",,doi:https://doi.org/10.1016/j.jchf.2019.01.009; doi:https://doi.org/10.1016/j.jchf.2019.01.009
-34036180,https://doi.org/10.23889/ijpds.v5i2.1385,Linking data on women in public family law court proceedings concerning their children to mental health service records in South London.,"Pearson RJ, Jewell A, Wijlaars L, Bedston S, Finch E, Broadhurst K, Downs J, Gilbert R.",,International journal of population data science,2021,2021-02-24,Y,,,,"<h4>Introduction</h4>Maternal mental health problems and substance misuse are key risk factors for child neglect or abuse and court-mandated placement into care. Linkage between mental health records and family court data could raise awareness about parent mental health needs and inform approaches to address them.<h4>Objectives</h4>To evaluate data linkage between administrative family court data and electronic mental health records for a population-based mental health service for 1.3 million people in South London.<h4>Methods</h4>We deterministically linked administrative family court data for women (n=5463) involved in care proceedings in South London with service user records from the South London and Maudsley NHS Mental Health Trust (SLaM). We restricted the cohort to women involved in proceedings between 2007 and 2019, in local authorities where SLaM solely provides secondary/tertiary mental health services and the Improving Access to Psychological Therapies (IAPT) (n=3226). We analysed the associations between match status and sociodemographic/case characteristics using multivariable logistic regression.<h4>Results</h4>Two-thirds (2317/3226; 66%) of women linked to a SLaM service user record at some point; most (91%) who linked accessed secondary/tertiary mental health services, indicating serious mental illness. Accounting for possible missed matches, we estimated that 70-83% of women accessed SLaM services at some point. Older women at index proceedings (>35yrs OR: 0.69, 95%CI: 0.54-0.88vs <25yrs) and Black women or women from other ethnic groups (Black ethnic groups 0.65, 0.50-0.83; other ethnicity 0.59, 0.43-0.81 vs White ethnic groups) had lower odds of linking. Odds of linking were higher for women with an infant in proceedings (1.42, 1.18-1.71), or with curtailed/terminated parental responsibility (1.44, 1.20-1.73).<h4>Conclusion</h4>Our linkage supports growing evidence of a high burden of mental health problems and substance misuse among women whose children enter care in England, compared to the general population. Research using this linkage should inform strategies to address the considerable mental health needs of vulnerable women and their children.",,doi:https://doi.org/10.23889/ijpds.v5i2.1385; html:https://europepmc.org/articles/PMC8133060; pdf:https://europepmc.org/articles/PMC8133060?pdf=render
 37286573,https://doi.org/10.1038/s41467-023-38383-y,Elevated plasma complement factor H related 5 protein is associated with venous thromboembolism.,"Iglesias MJ, Sanchez-Rivera L, Ibrahim-Kosta M, Naudin C, Munsch G, Goumidi L, Farm M, Smith PM, Thibord F, Kral-Pointner JB, Hong MG, Suchon P, Germain M, Schrottmaier W, Dusart P, Boland A, Kotol D, Edfors F, Koprulu M, Pietzner M, Langenberg C, Damrauer SM, Johnson AD, Klarin DM, Smith NL, Smadja DM, Holmström M, Magnusson M, Silveira A, Uhlén M, Renné T, Martinez-Perez A, Emmerich J, Deleuze JF, Antovic J, Soria Fernandez JM, Assinger A, Schwenk JM, Souto Andres JC, Morange PE, Butler LM, Trégouët DA, Odeberg J.",,Nature communications,2023,2023-06-07,Y,,,,"Venous thromboembolism (VTE) is a common, multi-causal disease with potentially serious short- and long-term complications. In clinical practice, there is a need for improved plasma biomarker-based tools for VTE diagnosis and risk prediction. Here we show, using proteomics profiling to screen plasma from patients with suspected acute VTE, and several case-control studies for VTE, how Complement Factor H Related 5 protein (CFHR5), a regulator of the alternative pathway of complement activation, is a VTE-associated plasma biomarker. In plasma, higher CFHR5 levels are associated with increased thrombin generation potential and recombinant CFHR5 enhanced platelet activation in vitro. GWAS analysis of ~52,000 participants identifies six loci associated with CFHR5 plasma levels, but Mendelian randomization do not demonstrate causality between CFHR5 and VTE. Our results indicate an important role for the regulation of the alternative pathway of complement activation in VTE and that CFHR5 represents a potential diagnostic and/or risk predictive plasma biomarker.",,pdf:https://www.nature.com/articles/s41467-023-38383-y.pdf; doi:https://doi.org/10.1038/s41467-023-38383-y; html:https://europepmc.org/articles/PMC10247781; pdf:https://europepmc.org/articles/PMC10247781?pdf=render
+34036180,https://doi.org/10.23889/ijpds.v5i2.1385,Linking data on women in public family law court proceedings concerning their children to mental health service records in South London.,"Pearson RJ, Jewell A, Wijlaars L, Bedston S, Finch E, Broadhurst K, Downs J, Gilbert R.",,International journal of population data science,2021,2021-02-24,Y,,,,"<h4>Introduction</h4>Maternal mental health problems and substance misuse are key risk factors for child neglect or abuse and court-mandated placement into care. Linkage between mental health records and family court data could raise awareness about parent mental health needs and inform approaches to address them.<h4>Objectives</h4>To evaluate data linkage between administrative family court data and electronic mental health records for a population-based mental health service for 1.3 million people in South London.<h4>Methods</h4>We deterministically linked administrative family court data for women (n=5463) involved in care proceedings in South London with service user records from the South London and Maudsley NHS Mental Health Trust (SLaM). We restricted the cohort to women involved in proceedings between 2007 and 2019, in local authorities where SLaM solely provides secondary/tertiary mental health services and the Improving Access to Psychological Therapies (IAPT) (n=3226). We analysed the associations between match status and sociodemographic/case characteristics using multivariable logistic regression.<h4>Results</h4>Two-thirds (2317/3226; 66%) of women linked to a SLaM service user record at some point; most (91%) who linked accessed secondary/tertiary mental health services, indicating serious mental illness. Accounting for possible missed matches, we estimated that 70-83% of women accessed SLaM services at some point. Older women at index proceedings (>35yrs OR: 0.69, 95%CI: 0.54-0.88vs <25yrs) and Black women or women from other ethnic groups (Black ethnic groups 0.65, 0.50-0.83; other ethnicity 0.59, 0.43-0.81 vs White ethnic groups) had lower odds of linking. Odds of linking were higher for women with an infant in proceedings (1.42, 1.18-1.71), or with curtailed/terminated parental responsibility (1.44, 1.20-1.73).<h4>Conclusion</h4>Our linkage supports growing evidence of a high burden of mental health problems and substance misuse among women whose children enter care in England, compared to the general population. Research using this linkage should inform strategies to address the considerable mental health needs of vulnerable women and their children.",,doi:https://doi.org/10.23889/ijpds.v5i2.1385; html:https://europepmc.org/articles/PMC8133060; pdf:https://europepmc.org/articles/PMC8133060?pdf=render
 35188868,https://doi.org/10.1080/19490976.2022.2038863,The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma.,"Bosch S, Acharjee A, Quraishi MN, Rojas P, Bakkali A, Jansen EE, Brizzio Brentar M, Kuijvenhoven J, Stokkers P, Struys E, Beggs AD, Gkoutos GV, de Meij TG, de Boer NK.",,Gut microbes,2022,2022-01-01,Y,Biomarker; Surveillance; Adenoma; Colorectal Cancer; Omics,,,"The risk of recurrent dysplastic colonic lesions is increased following polypectomy. Yield of endoscopic surveillance after adenoma removal is low, while interval colorectal cancers occur. To longitudinally assess the dynamics of fecal microbiota and amino acids in the presence of adenomatous lesions and after their endoscopic removal. In this longitudinal case-control study, patients collected fecal samples prior to bowel preparation before scheduled colonoscopy and 3 months after this intervention. Based on colonoscopy outcomes, patients with advanced adenomas and nonadvanced adenomas (0.5-1.0 cm) who underwent polypectomy during endoscopy (<i>n</i> = 19) were strictly matched on age, body-mass index, and smoking habits to controls without endoscopic abnormalities (<i>n</i> = 19). Microbial taxa were measured by 16S RNA sequencing, and amino acids (AA) were measured by high-performance liquid chromatography (HPLC). Adenoma patients were discriminated from controls based on AA and microbial composition. Levels of proline (<i>p</i> = .001), ornithine (<i>p</i> = .02) and serine (<i>p</i> = .02) were increased in adenoma patients compared to controls but decreased to resemble those of controls after adenoma removal. These AAs were combined as a potential adenoma-specific panel (AUC 0.79(0.64-0.94)). For bacterial taxa, differences between patients with adenomas and controls were found (<i>Bifidobacterium</i> spp.↓, <i>Anaerostipes</i> spp.↓, <i>Butyricimonas</i> spp.↑, <i>Faecalitalea</i> spp.↑ <i>and Catenibacterium</i> spp.↑), but no alterations in relative abundance were observed after polypectomy. Furthermore, <i>Faecalitalea</i> spp. and <i>Butyricimonas</i> spp. were significantly correlated with adenoma-specific amino acids. We selected an amino acid panel specifically increased in the presence of adenomas and a microbial signature present in adenoma patients, irrespective of polypectomy. Upon validation, these panels may improve the effectiveness of the surveillance program by detection of high-risk individuals and determination of surveillance endoscopy timing, leading to less unnecessary endoscopies and less interval cancer.",,pdf:https://www.tandfonline.com/doi/pdf/10.1080/19490976.2022.2038863?needAccess=true; doi:https://doi.org/10.1080/19490976.2022.2038863; html:https://europepmc.org/articles/PMC8865277; pdf:https://europepmc.org/articles/PMC8865277?pdf=render
 33293538,https://doi.org/10.1038/s41467-020-20096-1,Patient and public perspectives on cell and gene therapies: a systematic review.,"Aiyegbusi OL, Macpherson K, Elston L, Myles S, Washington J, Sungum N, Briggs M, Newsome PN, Calvert MJ.",,Nature communications,2020,2020-12-08,Y,,,,"Cell and gene therapies offer opportunities for treating disease with potential to restore function, and cure disease. However, they are not without risk and pose complex logistical, economic, ethical and social challenges for health systems. Here we report our systematic review of the current evidence on patient and public knowledge and perspectives of cell and gene therapies, to inform future research, education and awareness raising activities. We screened 10,735 titles and abstracts, and evaluated the full texts of 151 publications. The final selection was 35 publications. Four themes were generated from the narrative synthesis of the study findings namely: (1) Knowledge and understanding of cell and gene therapies, (2) Acceptance of cell and gene therapies (3) Understanding of risk and benefits of therapy, and (4) Information needs and current sources of information. As potential funders or future recipients, it is important that the public and patients are aware of these therapies, understand the issues involved, and can contribute to the debate. This review highlights the need for appropriate patient and public education on the various aspects of cell and gene therapies. High quality studies exploring patient and public opinions and experiences of cell and gene therapy are required. Patient and public perceptions of these therapies, alongside evidence of clinical and cost-effectiveness, will be central to their uptake and use.",,pdf:https://www.nature.com/articles/s41467-020-20096-1.pdf; doi:https://doi.org/10.1038/s41467-020-20096-1; html:https://europepmc.org/articles/PMC7722871; pdf:https://europepmc.org/articles/PMC7722871?pdf=render
 31847828,https://doi.org/10.1186/s12875-019-1057-x,TIA and minor stroke: a qualitative study of long-term impact and experiences of follow-up care.,"Turner GM, McMullan C, Atkins L, Foy R, Mant J, Calvert M.",,BMC family practice,2019,2019-12-17,Y,Rehabilitation; Quality of life; Qualitative; Transient Ischemic Attack; Minor Stroke,,,"<h4>Background</h4>Transient ischaemic attack (TIA) and minor stroke are often considered transient events; however, many patients experience residual problems and reduced quality of life. Current follow-up healthcare focuses on stroke prevention and care for other long-term problems is not routinely provided. We aimed to explore patient and healthcare provider (HCP) experiences of residual problems post-TIA/minor stroke, the impact of TIA/minor stroke on patients' lives, and current follow-up care and sources of support.<h4>Methods</h4>This qualitative study recruited participants from three TIA clinics, seven general practices and one community care trust in the West Midlands, England. Semi-structured interviews were conducted with 12 TIA/minor stroke patients and 24 HCPs from primary, secondary and community care. Data was analysed using framework analysis.<h4>Results</h4>A diverse range of residual problems were reported post-TIA/minor stroke, including psychological, cognitive and physical impairments. Consultants and general practitioners generally lacked awareness of these long-term problems; however, there was better recognition among nurses and allied HCPs. Residual problems significantly affected patients' lives, including return to work, social activities, and relationships with family and friends. Follow-up care was variable and medically focused. While HCPs prioritised medical investigations and stroke prevention medication, patients emphasised the importance of understanding their diagnosis, individualised support regarding stroke risk, and addressing residual problems.<h4>Conclusion</h4>HCPs could better communicate information about TIA/minor stroke diagnosis and secondary stroke prevention using lay language, and improve their identification of and response to important residual impairments affecting patients.",,pdf:https://bmcfampract.biomedcentral.com/track/pdf/10.1186/s12875-019-1057-x; doi:https://doi.org/10.1186/s12875-019-1057-x; html:https://europepmc.org/articles/PMC6918619; pdf:https://europepmc.org/articles/PMC6918619?pdf=render
 33995410,https://doi.org/10.3389/fimmu.2021.671052,Plasma Lectin Pathway Complement Proteins in Patients With COVID-19 and Renal Disease.,"Medjeral-Thomas NR, Troldborg A, Hansen AG, Gisby J, Clarke CL, Prendecki M, McAdoo SP, Sandhu E, Lightstone L, Thomas DC, Willicombe M, Botto M, Peters JE, Pickering MC, Thiel S.",,Frontiers in immunology,2021,2021-04-29,Y,Complement; Lectin; Coronavirus; Chronic Kidney Disease; Covid-19,,,"We do not understand why non-white ethnicity and chronic kidney disease increase susceptibility to COVID-19. The lectin pathway of complement activation is a key contributor to innate immunity and inflammation. Concentrations of plasma lectin pathway proteins influence pathway activity and vary with ethnicity. We measured circulating lectin proteins in a multi-ethnic cohort of chronic kidney disease patients with and without COVID19 infection to determine if lectin pathway activation was contributing to COVID19 severity. We measured 11 lectin proteins in serial samples from a cohort of 33 patients with chronic kidney impairment and COVID19. Controls were single plasma samples from 32 patients on dialysis and 32 healthy individuals. We demonstrated multiple associations between recognition molecules and associated proteases of the lectin pathway and COVID-19, including COVID-19 severity. Some of these associations were unique to patients of Asian and White ethnicity. Our novel findings demonstrate that COVID19 infection alters the concentration of plasma lectin proteins and some of these changes were linked to ethnicity. This suggests a role for the lectin pathway in the host response to COVID-19 and suggest that variability within this pathway may contribute to ethnicity-associated differences in susceptibility to severe COVID-19.",,pdf:https://www.frontiersin.org/articles/10.3389/fimmu.2021.671052/pdf; doi:https://doi.org/10.3389/fimmu.2021.671052; html:https://europepmc.org/articles/PMC8118695; pdf:https://europepmc.org/articles/PMC8118695?pdf=render
 33932483,https://doi.org/10.1016/j.jclinepi.2021.04.015,Probabilistic linkage without personal information successfully linked national clinical datasets.,"Blake HA, Sharples LD, Harron K, van der Meulen JH, Walker K.",,Journal of clinical epidemiology,2021,2021-04-28,Y,Electronic Health Records; Record Linkage; Personal Information; Probabilistic Linkage; National Clinical Datasets; Patient Identifiers,,,"<h4>Background</h4>Probabilistic linkage can link patients from different clinical databases without the need for personal information. If accurate linkage can be achieved, it would accelerate the use of linked datasets to address important clinical and public health questions.<h4>Objective</h4>We developed a step-by-step process for probabilistic linkage of national clinical and administrative datasets without personal information, and validated it against deterministic linkage using patient identifiers.<h4>Study design and setting</h4>We used electronic health records from the National Bowel Cancer Audit and Hospital Episode Statistics databases for 10,566 bowel cancer patients undergoing emergency surgery in the English National Health Service.<h4>Results</h4>Probabilistic linkage linked 81.4% of National Bowel Cancer Audit records to Hospital Episode Statistics, vs. 82.8% using deterministic linkage. No systematic differences were seen between patients that were and were not linked, and regression models for mortality and length of hospital stay according to patient and tumour characteristics were not sensitive to the linkage approach.<h4>Conclusion</h4>Probabilistic linkage was successful in linking national clinical and administrative datasets for patients undergoing a major surgical procedure. It allows analysts outside highly secure data environments to undertake linkage while minimizing costs and delays, protecting data security, and maintaining linkage quality.",,pdf:http://www.jclinepi.com/article/S0895435621001384/pdf; doi:https://doi.org/10.1016/j.jclinepi.2021.04.015; html:https://europepmc.org/articles/PMC8443839
 35585198,https://doi.org/10.1038/s41591-022-01772-9,Reporting guideline for the early-stage clinical evaluation of decision support systems driven by artificial intelligence: DECIDE-AI.,"Vasey B, Nagendran M, Campbell B, Clifton DA, Collins GS, Denaxas S, Denniston AK, Faes L, Geerts B, Ibrahim M, Liu X, Mateen BA, Mathur P, McCradden MD, Morgan L, Ordish J, Rogers C, Saria S, Ting DSW, Watkinson P, Weber W, Wheatstone P, McCulloch P, DECIDE-AI expert group.",,Nature medicine,2022,2022-05-18,N,,,,"A growing number of artificial intelligence (AI)-based clinical decision support systems are showing promising performance in preclinical, in silico evaluation, but few have yet demonstrated real benefit to patient care. Early-stage clinical evaluation is important to assess an AI system's actual clinical performance at small scale, ensure its safety, evaluate the human factors surrounding its use and pave the way to further large-scale trials. However, the reporting of these early studies remains inadequate. The present statement provides a multi-stakeholder, consensus-based reporting guideline for the Developmental and Exploratory Clinical Investigations of DEcision support systems driven by Artificial Intelligence (DECIDE-AI). We conducted a two-round, modified Delphi process to collect and analyze expert opinion on the reporting of early clinical evaluation of AI systems. Experts were recruited from 20 pre-defined stakeholder categories. The final composition and wording of the guideline was determined at a virtual consensus meeting. The checklist and the Explanation & Elaboration (E&E) sections were refined based on feedback from a qualitative evaluation process. In total, 123 experts participated in the first round of Delphi, 138 in the second round, 16 in the consensus meeting and 16 in the qualitative evaluation. The DECIDE-AI reporting guideline comprises 17 AI-specific reporting items (made of 28 subitems) and ten generic reporting items, with an E&E paragraph provided for each. Through consultation and consensus with a range of stakeholders, we developed a guideline comprising key items that should be reported in early-stage clinical studies of AI-based decision support systems in healthcare. By providing an actionable checklist of minimal reporting items, the DECIDE-AI guideline will facilitate the appraisal of these studies and replicability of their findings.",,pdf:https://www.nature.com/articles/s41591-022-01772-9.pdf; doi:https://doi.org/10.1038/s41591-022-01772-9
-30921401,https://doi.org/10.1371/journal.pone.0214607,Effect of impregnated central venous catheters on thrombosis in paediatric intensive care: Post-hoc analyses of the CATCH trial.,"Wu Y, Fraser C, Gilbert R, Mok Q.",,PloS one,2019,2019-03-28,Y,,"Better, Faster and More Efficient Clinical Trials",,"<h4>Purpose</h4>The CATheter infections in CHildren (CATCH) trial reported reduced risks of bloodstream infection with antibiotic impregnated compared with heparin-bonded or standard central venous catheters (CVC) in paediatric intensive care. CVC impregnation did not increase the risk of thrombosis which was recorded in 24% of participants. This post-hoc analysis determines the effect of CVC impregnation on the risk of thrombosis leading to CVC removal or swollen limb.<h4>Methods</h4>We analysed patients in the CATCH trial, blind to CVC allocation, to define clinically relevant thrombosis based on the clinical sign most frequently recorded in patients where the CVC was removed because of concerns regarding thrombosis. In post-hoc, three-way comparisons of antibiotic, heparin and standard CVCs, we determined the effect of CVC type on time to clinically relevant thrombosis, using Cox proportional hazards regression.<h4>Results</h4>Of 1409 participants with a successful CVC insertion, the sign most frequently resulting in CVC removal was swollen limb (37.6%; 41/109), with lower rates of removal of CVC following 2 episodes of difficulty withdrawing blood or of flushing to unblock the CVC. In intention to treat analyses (n = 1485), clinically relevant thrombosis, defined by 1 or more record of swollen limb or CVC removal due to concerns about thrombosis, was recorded in 11.9% (58/486) of antibiotic CVCs, 12.1% (60/497) of heparin CVCs, and 10.2% (51/502) of standard CVCs. We found no differences in time to clinically relevant thrombosis according to type of CVC.<h4>Conclusions</h4>We found no evidence for an increased risk of clinically relevant thrombosis in antibiotic impregnated compared to heparin-bonded or standard CVCs in children receiving intensive care.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0214607&type=printable; doi:https://doi.org/10.1371/journal.pone.0214607; html:https://europepmc.org/articles/PMC6438638; pdf:https://europepmc.org/articles/PMC6438638?pdf=render
 31844048,https://doi.org/10.1038/s41467-019-13585-5,Genome-wide analysis identifies molecular systems and 149 genetic loci associated with income.,"Hill WD, Davies NM, Ritchie SJ, Skene NG, Bryois J, Bell S, Di Angelantonio E, Roberts DJ, Xueyi S, Davies G, Liewald DCM, Porteous DJ, Hayward C, Butterworth AS, McIntosh AM, Gale CR, Deary IJ.",,Nature communications,2019,2019-12-16,Y,,Understanding the Causes of Disease,,"Socioeconomic position (SEP) is a multi-dimensional construct reflecting (and influencing) multiple socio-cultural, physical, and environmental factors. In a sample of 286,301 participants from UK Biobank, we identify 30 (29 previously unreported) independent-loci associated with income. Using a method to meta-analyze data from genetically-correlated traits, we identify an additional 120 income-associated loci. These loci show clear evidence of functionality, with transcriptional differences identified across multiple cortical tissues, and links to GABAergic and serotonergic neurotransmission. By combining our genome wide association study on income with data from eQTL studies and chromatin interactions, 24 genes are prioritized for follow up, 18 of which were previously associated with intelligence. We identify intelligence as one of the likely causal, partly-heritable phenotypes that might bridge the gap between molecular genetic inheritance and phenotypic consequence in terms of income differences. These results indicate that, in modern era Great Britain, genetic effects contribute towards some of the observed socioeconomic inequalities.","This study linked genetic sequencing data and information on household income to identify parts of the genome that are more common in people who live in more affluent households. The authors identified 150 parts of the genome that were associated with income, and found that these genetic regions were more commonly expressed in the brain and testes. The results indicate that intelligence and income are causally linked, and suggest that genetics partly explain a small amount of variation (~2%) in household income in the UK.",pdf:https://www.nature.com/articles/s41467-019-13585-5.pdf; doi:https://doi.org/10.1038/s41467-019-13585-5; html:https://europepmc.org/articles/PMC6915786; pdf:https://europepmc.org/articles/PMC6915786?pdf=render
+30921401,https://doi.org/10.1371/journal.pone.0214607,Effect of impregnated central venous catheters on thrombosis in paediatric intensive care: Post-hoc analyses of the CATCH trial.,"Wu Y, Fraser C, Gilbert R, Mok Q.",,PloS one,2019,2019-03-28,Y,,"Better, Faster and More Efficient Clinical Trials",,"<h4>Purpose</h4>The CATheter infections in CHildren (CATCH) trial reported reduced risks of bloodstream infection with antibiotic impregnated compared with heparin-bonded or standard central venous catheters (CVC) in paediatric intensive care. CVC impregnation did not increase the risk of thrombosis which was recorded in 24% of participants. This post-hoc analysis determines the effect of CVC impregnation on the risk of thrombosis leading to CVC removal or swollen limb.<h4>Methods</h4>We analysed patients in the CATCH trial, blind to CVC allocation, to define clinically relevant thrombosis based on the clinical sign most frequently recorded in patients where the CVC was removed because of concerns regarding thrombosis. In post-hoc, three-way comparisons of antibiotic, heparin and standard CVCs, we determined the effect of CVC type on time to clinically relevant thrombosis, using Cox proportional hazards regression.<h4>Results</h4>Of 1409 participants with a successful CVC insertion, the sign most frequently resulting in CVC removal was swollen limb (37.6%; 41/109), with lower rates of removal of CVC following 2 episodes of difficulty withdrawing blood or of flushing to unblock the CVC. In intention to treat analyses (n = 1485), clinically relevant thrombosis, defined by 1 or more record of swollen limb or CVC removal due to concerns about thrombosis, was recorded in 11.9% (58/486) of antibiotic CVCs, 12.1% (60/497) of heparin CVCs, and 10.2% (51/502) of standard CVCs. We found no differences in time to clinically relevant thrombosis according to type of CVC.<h4>Conclusions</h4>We found no evidence for an increased risk of clinically relevant thrombosis in antibiotic impregnated compared to heparin-bonded or standard CVCs in children receiving intensive care.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0214607&type=printable; doi:https://doi.org/10.1371/journal.pone.0214607; html:https://europepmc.org/articles/PMC6438638; pdf:https://europepmc.org/articles/PMC6438638?pdf=render
+32423943,https://doi.org/10.1136/bmjopen-2020-038974,Study protocol for a multicentre longitudinal mixed methods study to explore the Outcomes of ChildrEn and fAmilies in the first year after paediatric Intensive Care: the OCEANIC study.,"Manning JC, Latour JM, Curley MAQ, Draper ES, Jilani T, Quinlan PR, Watson RS, Rennick JE, Colville G, Pinto N, Latif A, Popejoy E, Coad J, OCEANIC Study Investigators.",,BMJ open,2020,2020-05-17,Y,Qualitative Research; Statistics & Research Methods; Paediatric Intensive & Critical Care,,,"<h4>Introduction</h4>Annually in the UK, 20 000 children become very ill or injured and need specialist care within a paediatric intensive care unit (PICU). Most children survive. However, some children and their families may experience problems after they have left the PICU including physical, functional and/or emotional problems. It is unknown which children and families experience such problems, when these occur or what causes them. The aim of this mixed-method longitudinal cohort study is to understand the physical, functional, emotional and social impact of children surviving PICU (aged: 1 month-17 years), their parents and siblings, during the first year after a PICU admission.<h4>Methods and analysis</h4>A quantitative study involving 300 child survivors of PICU; 300 parents; and 150-300 siblings will collect data (using self-completion questionnaires) at baseline, PICU discharge, 1, 3, 6 and 12 months post-PICU discharge. Questionnaires will comprise validated and reliable instruments. Demographic data, PICU admission and treatment data, health-related quality of life, functional status, strengths and difficulties behaviour and post-traumatic stress symptoms will be collected from the child. Parent and sibling data will be collected on the impact of paediatric health conditions on the family's functioning capabilities, levels of anxiety and social impact of the child's PICU admission. Data will be analysed using descriptive and inferential statistics. Concurrently, an embedded qualitative study involving semistructured interviews with 24 enrolled families at 3 months and 9 months post-PICU discharge will be undertaken. Framework analysis will be used to analyse the qualitative data.<h4>Ethics and dissemination</h4>The study has received ethical approval from the National Health Services Research Ethics Committee (Ref: 19/WM/0290) and full governance clearance. This will be the first UK study to comprehensively investigate physical, functional, emotional and social consequences of PICU survival in the first-year postdischarge.Clinical Trials Registration Number: ISRCTN28072812 [Pre-results].",,pdf:https://bmjopen.bmj.com/content/bmjopen/10/5/e038974.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-038974; html:https://europepmc.org/articles/PMC7239532; pdf:https://europepmc.org/articles/PMC7239532?pdf=render
 33186544,https://doi.org/10.1016/j.ajhg.2020.10.009,A Multi-omic Integrative Scheme Characterizes Tissues of Action at Loci Associated with Type 2 Diabetes.,"Torres JM, Abdalla M, Payne A, Fernandez-Tajes J, Thurner M, Nylander V, Gloyn AL, Mahajan A, McCarthy MI.",,American journal of human genetics,2020,2020-11-12,Y,Type 2 diabetes; chromatin; Gene Expression; Gwas; Complex Traits; Eqtl; Fine-mapping; Tactical; Multi-omic; Molecular Epigenomics,,,"Resolving the molecular processes that mediate genetic risk remains a challenge because most disease-associated variants are non-coding and functional characterization of these signals requires knowledge of the specific tissues and cell-types in which they operate. To address this challenge, we developed a framework for integrating tissue-specific gene expression and epigenomic maps to obtain ""tissue-of-action"" (TOA) scores for each association signal by systematically partitioning posterior probabilities from Bayesian fine-mapping. We applied this scheme to credible set variants for 380 association signals from a recent GWAS meta-analysis of type 2 diabetes (T2D) in Europeans. The resulting tissue profiles underscored a predominant role for pancreatic islets and, to a lesser extent, adipose and liver, particularly among signals with greater fine-mapping resolution. We incorporated resulting TOA scores into a rule-based classifier and validated the tissue assignments through comparison with data from cis-eQTL enrichment, functional fine-mapping, RNA co-expression, and patterns of physiological association. In addition to implicating signals with a single TOA, we found evidence for signals with shared effects in multiple tissues as well as distinct tissue profiles between independent signals within heterogeneous loci. Lastly, we demonstrated that TOA scores can be directly coupled with eQTL colocalization to further resolve effector transcripts at T2D signals. This framework guides mechanistic inference by directing functional validation studies to the most relevant tissues and can gain power as fine-mapping resolution and cell-specific annotations become richer. This method is generalizable to all complex traits with relevant annotation data and is made available as an R package.",,pdf:http://www.cell.com/article/S0002929720303670/pdf; doi:https://doi.org/10.1016/j.ajhg.2020.10.009; html:https://europepmc.org/articles/PMC7820628; pdf:https://europepmc.org/articles/PMC7820628?pdf=render
 33516292,https://doi.org/10.1016/s2468-2667(20)30210-3,Associations between pre-pregnancy psychosocial risk factors and infant outcomes: a population-based cohort study in England.,"Harron K, Gilbert R, Fagg J, Guttmann A, van der Meulen J.",,The Lancet. Public health,2021,2021-02-01,Y,,,,"<h4>Background</h4>Existing studies evaluating the association between maternal risk factors and specific infant outcomes such as birthweight, injury admissions, and mortality have mostly focused on single risk factors. We aimed to identify routinely recorded psychosocial characteristics of pregnant women most at risk of adverse infant outcomes to inform targeting of early intervention.<h4>Methods</h4>We created a cohort using administrative hospital data (Hospital Episode Statistics) for all births to mothers aged 15-44 years in England, UK, who gave birth on or after April 1, 2010, and who were discharged before or on March 31, 2015. We used generalised linear models to evaluate associations between psychosocial risk factors recorded in hospital records in the 2 years before the 20th week of pregnancy (ie, teenage motherhood, deprivation, pre-pregnancy hospital admissions for mental health or behavioural conditions, and pre-pregnancy hospital admissions for adversity, including drug or alcohol abuse, violence, and self-harm) and infant outcomes (ie, birthweight, unplanned admission for injury, or death from any cause, within 12 months from postnatal discharge).<h4>Findings</h4>Of 2 520 501 births initially assessed, 2 137 103 were eligible and were included in the birth outcome analysis. Among the eligible births, 93 279 (4·4%) were births to teenage mothers (age <20 years), 168 186 (7·9%) were births to previous teenage mothers, 51 312 (2·4%) were births to mothers who had a history of hospital admissions for mental health or behavioural conditions, 58 107 (2·7%) were births to mothers who had a history of hospital admissions for adversity, and 580 631 (27·2%) were births to mothers living in areas of high deprivation. 1 377 706 (64·5%) of births were to mothers with none of the above risk factors. Infants born to mothers with any of these risk factors had poorer outcomes than those born to mothers without these risk factors. Those born to mothers with a history of mental health or behavioural conditions were 124 g lighter (95% CI 114-134 g) than those born to mothers without these conditions. For teenage mothers compared with older mothers, 3·6% (95% CI 3·3-3·9%) more infants had an unplanned admission for injury, and there were 10·2 (95% CI 7·5-12·9) more deaths per 10 000 infants.<h4>Interpretation</h4>Health-care services should respond proactively to pre-pregnancy psychosocial risk factors. Our study demonstrates a need for effective interventions before, during, and after pregnancy to reduce the downstream burden on health services and prevent long-term adverse effects for children.<h4>Funding</h4>Wellcome Trust.",,pdf:http://www.thelancet.com/article/S2468266720302103/pdf; doi:https://doi.org/10.1016/S2468-2667(20)30210-3; html:https://europepmc.org/articles/PMC7848754; pdf:https://europepmc.org/articles/PMC7848754?pdf=render
-32423943,https://doi.org/10.1136/bmjopen-2020-038974,Study protocol for a multicentre longitudinal mixed methods study to explore the Outcomes of ChildrEn and fAmilies in the first year after paediatric Intensive Care: the OCEANIC study.,"Manning JC, Latour JM, Curley MAQ, Draper ES, Jilani T, Quinlan PR, Watson RS, Rennick JE, Colville G, Pinto N, Latif A, Popejoy E, Coad J, OCEANIC Study Investigators.",,BMJ open,2020,2020-05-17,Y,Qualitative Research; Statistics & Research Methods; Paediatric Intensive & Critical Care,,,"<h4>Introduction</h4>Annually in the UK, 20 000 children become very ill or injured and need specialist care within a paediatric intensive care unit (PICU). Most children survive. However, some children and their families may experience problems after they have left the PICU including physical, functional and/or emotional problems. It is unknown which children and families experience such problems, when these occur or what causes them. The aim of this mixed-method longitudinal cohort study is to understand the physical, functional, emotional and social impact of children surviving PICU (aged: 1 month-17 years), their parents and siblings, during the first year after a PICU admission.<h4>Methods and analysis</h4>A quantitative study involving 300 child survivors of PICU; 300 parents; and 150-300 siblings will collect data (using self-completion questionnaires) at baseline, PICU discharge, 1, 3, 6 and 12 months post-PICU discharge. Questionnaires will comprise validated and reliable instruments. Demographic data, PICU admission and treatment data, health-related quality of life, functional status, strengths and difficulties behaviour and post-traumatic stress symptoms will be collected from the child. Parent and sibling data will be collected on the impact of paediatric health conditions on the family's functioning capabilities, levels of anxiety and social impact of the child's PICU admission. Data will be analysed using descriptive and inferential statistics. Concurrently, an embedded qualitative study involving semistructured interviews with 24 enrolled families at 3 months and 9 months post-PICU discharge will be undertaken. Framework analysis will be used to analyse the qualitative data.<h4>Ethics and dissemination</h4>The study has received ethical approval from the National Health Services Research Ethics Committee (Ref: 19/WM/0290) and full governance clearance. This will be the first UK study to comprehensively investigate physical, functional, emotional and social consequences of PICU survival in the first-year postdischarge.Clinical Trials Registration Number: ISRCTN28072812 [Pre-results].",,pdf:https://bmjopen.bmj.com/content/bmjopen/10/5/e038974.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-038974; html:https://europepmc.org/articles/PMC7239532; pdf:https://europepmc.org/articles/PMC7239532?pdf=render
 33705244,https://doi.org/10.1177/17474930211004277,Stroke risk following traumatic brain injury: Systematic review and meta-analysis.,"Turner GM, McMullan C, Aiyegbusi OL, Bem D, Marshall T, Calvert M, Mant J, Belli A.",,International journal of stroke : official journal of the International Stroke Society,2021,2021-04-04,Y,Meta-analysis; Traumatic brain injury; Stroke; Systematic review; risk,,,"<h4>Background</h4>Traumatic brain injury is a global health problem; worldwide, >60 million people experience a traumatic brain injury each year and incidence is rising. Traumatic brain injury has been proposed as an independent risk factor for stroke.<h4>Aims</h4>To investigate the association between traumatic brain injury and stroke risk.<h4>Summary of review</h4>We undertook a systematic review of MEDLINE, EMBASE, CINAHL, and The Cochrane Library from inception to 4 December 2020. We used random-effects meta-analysis to pool hazard ratios for studies which reported stroke risk post-traumatic brain injury compared to controls. Searches identified 10,501 records; 58 full texts were assessed for eligibility and 18 met the inclusion criteria. The review included a large sample size of 2,606,379 participants from four countries. Six studies included a non-traumatic brain injury control group, all found traumatic brain injury patients had significantly increased risk of stroke compared to controls (pooled hazard ratio 1.86; 95% confidence interval 1.46-2.37). Findings suggest stroke risk may be highest in the first four months post-traumatic brain injury, but remains significant up to five years post-traumatic brain injury. Traumatic brain injury appears to be associated with increased stroke risk regardless of severity or subtype of traumatic brain injury. There was some evidence to suggest an association between reduced stroke risk post-traumatic brain injury and Vitamin K antagonists and statins, but increased stroke risk with certain classes of antidepressants.<h4>Conclusion</h4>Traumatic brain injury is an independent risk factor for stroke, regardless of traumatic brain injury severity or type. Post-traumatic brain injury review and management of risk factors for stroke may be warranted.",,pdf:https://journals.sagepub.com/doi/pdf/10.1177/17474930211004277; doi:https://doi.org/10.1177/17474930211004277; html:https://europepmc.org/articles/PMC8193616; pdf:https://europepmc.org/articles/PMC8193616?pdf=render
 37247330,https://doi.org/10.1093/eurheartj/ehad260,SCORE2-Diabetes: 10-year cardiovascular risk estimation in type 2 diabetes in Europe.,SCORE2-Diabetes Working Group and the ESC Cardiovascular Risk Collaboration.,,European heart journal,2023,2023-07-01,Y,Cardiovascular diseases; Prediction model; Diabetes,,,"<h4>Aims</h4>To develop and validate a recalibrated prediction model (SCORE2-Diabetes) to estimate the 10-year risk of cardiovascular disease (CVD) in individuals with type 2 diabetes in Europe.<h4>Methods and results</h4>SCORE2-Diabetes was developed by extending SCORE2 algorithms using individual-participant data from four large-scale datasets comprising 229 460 participants (43 706 CVD events) with type 2 diabetes and without previous CVD. Sex-specific competing risk-adjusted models were used including conventional risk factors (i.e. age, smoking, systolic blood pressure, total, and HDL-cholesterol), as well as diabetes-related variables (i.e. age at diabetes diagnosis, glycated haemoglobin [HbA1c] and creatinine-based estimated glomerular filtration rate [eGFR]). Models were recalibrated to CVD incidence in four European risk regions. External validation included 217 036 further individuals (38 602 CVD events), and showed good discrimination, and improvement over SCORE2 (C-index change from 0.009 to 0.031). Regional calibration was satisfactory. SCORE2-Diabetes risk predictions varied several-fold, depending on individuals' levels of diabetes-related factors. For example, in the moderate-risk region, the estimated 10-year CVD risk was 11% for a 60-year-old man, non-smoker, with type 2 diabetes, average conventional risk factors, HbA1c of 50 mmol/mol, eGFR of 90 mL/min/1.73 m2, and age at diabetes diagnosis of 60 years. By contrast, the estimated risk was 17% in a similar man, with HbA1c of 70 mmol/mol, eGFR of 60 mL/min/1.73 m2, and age at diabetes diagnosis of 50 years. For a woman with the same characteristics, the risk was 8% and 13%, respectively.<h4>Conclusion</h4>SCORE2-Diabetes, a new algorithm developed, calibrated, and validated to predict 10-year risk of CVD in individuals with type 2 diabetes, enhances identification of individuals at higher risk of developing CVD across Europe.",,pdf:https://academic.oup.com/eurheartj/advance-article-pdf/doi/10.1093/eurheartj/ehad260/50482240/ehad260.pdf; doi:https://doi.org/10.1093/eurheartj/ehad260; html:https://europepmc.org/articles/PMC10361012; pdf:https://europepmc.org/articles/PMC10361012?pdf=render
 34490590,https://doi.org/10.1007/s40256-021-00496-4,Cost Effectiveness of a CYP2C19 Genotype-Guided Strategy in Patients with Acute Myocardial Infarction: Results from the POPular Genetics Trial.,"Claassens DMF, van Dorst PWM, Vos GJA, Bergmeijer TO, Hermanides RS, van 't Hof AWJ, van der Harst P, Barbato E, Morisco C, Tjon Joe Gin RM, Asselbergs FW, Mosterd A, Herrman JR, Dewilde WJM, Postma MJ, Deneer VHM, Ten Berg JM, Boersma C.",,"American journal of cardiovascular drugs : drugs, devices, and other interventions",2022,2021-09-07,N,,,,"<h4>Introduction</h4>The POPular Genetics trial demonstrated that a CYP2C19 genotype-guided P2Y<sub>12</sub> inhibitor strategy reduced bleeding rates compared with standard treatment with ticagrelor or prasugrel without increasing thrombotic event rates after primary percutaneous coronary intervention (PCI).<h4>Objective</h4>In this analysis, we aimed to evaluate the cost effectiveness of a genotype-guided strategy compared with standard treatment with ticagrelor or prasugrel.<h4>Methods</h4>A 1-year decision tree based on the POPular Genetics trial in combination with a lifelong Markov model was developed to compare costs and quality-adjusted life-years (QALYs) between a genotype-guided and a standard P2Y<sub>12</sub> inhibitor strategy in patients with myocardial infarction undergoing primary PCI. The cost-effectiveness analysis was conducted from a Dutch healthcare system perspective. Within-trial survival and utility data were combined with lifetime projections to evaluate lifetime cost effectiveness for a cohort of 1000 patients. Costs and utilities were discounted at 4 and 1.5%, respectively, according to Dutch guidelines for health economic studies. Besides deterministic and probabilistic sensitivity analyses, several scenario analyses were also conducted (different time horizons, different discount rates, equal prices for P2Y<sub>12</sub> inhibitors, and equal distribution of thrombotic events between the two strategies).<h4>Results</h4>Base-case analysis with a hypothetical cohort of 1000 subjects demonstrated 8.98 QALYs gained and €725,550.69 in cost savings for the genotype-guided strategy (dominant). The deterministic and probabilistic sensitivity analysis confirmed the robustness of the model and the cost-effectiveness results. In scenario analyses, the genotype-guided strategy remained dominant.<h4>Conclusion</h4>In patients undergoing primary PCI, a CYP2C19 genotype-guided strategy compared with standard treatment with ticagrelor or prasugrel resulted in QALYs gained and cost savings.<h4>Trial registration</h4>Clinicaltrials.gov number: NCT01761786, Netherlands trial register number: NL2872.",,pdf:https://pure.rug.nl/ws/files/223545267/Cost_Effectiveness_of_a_CYP2C19_Genotype_Guided_Strategy_in_Patients_with_Acute_Myocardial_Infarction_Results_from_the_POPular_Genetics_Trial.pdf; doi:https://doi.org/10.1007/s40256-021-00496-4
 33075408,https://doi.org/10.1016/j.jaci.2020.10.007,Factors associated with adverse COVID-19 outcomes in patients with psoriasis-insights from a global registry-based study.,"Mahil SK, Dand N, Mason KJ, Yiu ZZN, Tsakok T, Meynell F, Coker B, McAteer H, Moorhead L, Mackenzie T, Rossi MT, Rivera R, Mahe E, Carugno A, Magnano M, Rech G, Balogh EA, Feldman SR, De La Cruz C, Choon SE, Naldi L, Lambert J, Spuls P, Jullien D, Bachelez H, McMahon DE, Freeman EE, Gisondi P, Puig L, Warren RB, Di Meglio P, Langan SM, Capon F, Griffiths CEM, Barker JN, Smith CH, PsoProtect study group.",,The Journal of allergy and clinical immunology,2021,2020-10-16,Y,Psoriasis; Immunosuppressants; risk factors; Hospitalization; Biologics; Covid-19,,,"<h4>Background</h4>The multimorbid burden and use of systemic immunosuppressants in people with psoriasis may confer greater risk of adverse outcomes of coronavirus disease 2019 (COVID-19), but the data are limited.<h4>Objective</h4>Our aim was to characterize the course of COVID-19 in patients with psoriasis and identify factors associated with hospitalization.<h4>Methods</h4>Clinicians reported patients with psoriasis with confirmed/suspected COVID-19 via an international registry, Psoriasis Patient Registry for Outcomes, Therapy and Epidemiology of COVID-19 Infection. Multiple logistic regression was used to assess the association between clinical and/or demographic characteristics and hospitalization. A separate patient-facing registry characterized risk-mitigating behaviors.<h4>Results</h4>Of 374 clinician-reported patients from 25 countries, 71% were receiving a biologic, 18% were receiving a nonbiologic, and 10% were not receiving any systemic treatment for psoriasis. In all, 348 patients (93%) were fully recovered from COVID-19, 77 (21%) were hospitalized, and 9 (2%) died. Increased hospitalization risk was associated with older age (multivariable-adjusted odds ratio [OR] = 1.59 per 10 years; 95% CI = 1.19-2.13), male sex (OR = 2.51; 95% CI = 1.23-5.12), nonwhite ethnicity (OR = 3.15; 95% CI = 1.24-8.03), and comorbid chronic lung disease (OR = 3.87; 95% CI = 1.52-9.83). Hospitalization was more frequent in patients using nonbiologic systemic therapy than in those using biologics (OR = 2.84; 95% CI = 1.31-6.18). No significant differences were found between classes of biologics. Independent patient-reported data (n = 1626 across 48 countries) suggested lower levels of social isolation in individuals receiving nonbiologic systemic therapy than in those receiving biologics (OR = 0.68; 95% CI = 0.50-0.94).<h4>Conclusion</h4>In this international case series of patients with moderate-to-severe psoriasis, biologic use was associated with lower risk of COVID-19-related hospitalization than with use of nonbiologic systemic therapies; however, further investigation is warranted on account of potential selection bias and unmeasured confounding. Established risk factors (being older, being male, being of nonwhite ethnicity, and having comorbidities) were associated with higher hospitalization rates.",,pdf:https://researchonline.lshtm.ac.uk/id/eprint/4659367/1/Factors%20associated%20with%20adverse%20COVID-19%20outcomes%20in%20patients%20with%20psoriasis-insights%20from%20a%20global%20registry-based%20study.pdf; doi:https://doi.org/10.1016/j.jaci.2020.10.007; html:https://europepmc.org/articles/PMC7566694; pdf:https://europepmc.org/articles/PMC7566694?pdf=render
 36721385,https://doi.org/10.1002/pul2.12192,Reduced circulating BMP9 and pBMP10 in hospitalized COVID-19 patients.,"Dunmore BJ, Upton PD, Auckland K, Samanta RJ, CITIID‐NIHR BioResource COVID‐19 Collaboration, EpiCov Database, Lyons PA, Smith KGC, Gräf S, Summers C, Morrell NW.",,Pulmonary circulation,2023,2023-01-01,Y,Endothelial Cell Dysfunction; Bmps; Viral Infections And Pathogenesis,,,"Similar to other causes of acute respiratory distress syndrome, coronavirus disease 2019 (COVID-19) is characterized by the aberrant expression of vascular injury biomarkers. We present the first report that circulating plasma bone morphogenetic proteins (BMPs), BMP9 and pBMP10, involved in vascular protection, are reduced in hospitalized patients with COVID-19.",,pdf:https://www.repository.cam.ac.uk/bitstream/1810/345820/2/pul2.12192.pdf; doi:https://doi.org/10.1002/pul2.12192; html:https://europepmc.org/articles/PMC9881210; pdf:https://europepmc.org/articles/PMC9881210?pdf=render
-35189575,https://doi.org/10.1016/j.ebiom.2022.103878,The impact of hypoxia on B cells in COVID-19.,"Kotagiri P, Mescia F, Hanson AL, Turner L, Bergamaschi L, Peñalver A, Richoz N, Moore SD, Ortmann BM, Dunmore BJ, Morgan MD, Tuong ZK, Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID BioResource Collaboration, Göttgens B, Toshner M, Hess C, Maxwell PH, Clatworthy MR, Nathan JA, Bradley JR, Lyons PA, Burrows N, Smith KGC.",,EBioMedicine,2022,2022-02-19,Y,Hypoxia; B cells; Lymphopenia; Covid-19,,,"<h4>Background</h4>Prominent early features of COVID-19 include severe, often clinically silent, hypoxia and a pronounced reduction in B cells, the latter important in defence against SARS-CoV-2. This presentation resembles the phenotype of mice with VHL-deficient B cells, in which Hypoxia-Inducible Factors are constitutively active, suggesting hypoxia might drive B cell abnormalities in COVID-19.<h4>Methods</h4>Detailed B cell phenotyping was undertaken by flow-cytometry on longitudinal samples from patients with COVID-19 across a range of severities (NIHR Cambridge BioResource). The impact of hypoxia on the transcriptome was assessed by single-cell and whole blood RNA sequencing analysis. The direct effect of hypoxia on B cells was determined through immunisation studies in genetically modified and hypoxia-exposed mice.<h4>Findings</h4>We demonstrate the breadth of early and persistent defects in B cell subsets in moderate/severe COVID-19, including reduced marginal zone-like, memory and transitional B cells, changes also observed in B cell VHL-deficient mice. These findings were associated with hypoxia-related transcriptional changes in COVID-19 patient B cells, and similar B cell abnormalities were seen in mice kept in hypoxic conditions.<h4>Interpretation</h4>Hypoxia may contribute to the pronounced and persistent B cell pathology observed in acute COVID-19 pneumonia. Assessment of the impact of early oxygen therapy on these immune defects should be considered, as their correction could contribute to improved outcomes.<h4>Funding</h4>Evelyn Trust, Addenbrooke's Charitable Trust, UKRI/NIHR, Wellcome Trust.",,pdf:http://www.thelancet.com/article/S2352396422000627/pdf; doi:https://doi.org/10.1016/j.ebiom.2022.103878; html:https://europepmc.org/articles/PMC8856886; pdf:https://europepmc.org/articles/PMC8856886?pdf=render
 31171806,https://doi.org/10.1038/s41598-019-44907-8,On neighbourhood degree sequences of complex networks.,Smith KM.,,Scientific reports,2019,2019-06-06,Y,,Applied Analytics,,"Network topology is a fundamental aspect of network science that allows us to gather insights into the complicated relational architectures of the world we inhabit. We provide a first specific study of neighbourhood degree sequences in complex networks. We consider how to explicitly characterise important physical concepts such as similarity, heterogeneity and organization in these sequences, as well as updating the notion of hierarchical complexity to reflect previously unnoticed organizational principles. We also point out that neighbourhood degree sequences are related to a powerful subtree kernel for unlabeled graph classification. We study these newly defined sequence properties in a comprehensive array of graph models and over 200 real-world networks. We find that these indices are neither highly correlated with each other nor with classical network indices. Importantly, the sequences of a wide variety of real world networks are found to have greater similarity and organisation than is expected for networks of their given degree distributions. Notably, while biological, social and technological networks all showed consistently large neighbourhood similarity and organisation, hierarchical complexity was not a consistent feature of real world networks. Neighbourhood degree sequences are an interesting tool for describing unique and important characteristics of complex networks.",,pdf:https://www.nature.com/articles/s41598-019-44907-8.pdf; doi:https://doi.org/10.1038/s41598-019-44907-8; html:https://europepmc.org/articles/PMC6554413; pdf:https://europepmc.org/articles/PMC6554413?pdf=render
+35189575,https://doi.org/10.1016/j.ebiom.2022.103878,The impact of hypoxia on B cells in COVID-19.,"Kotagiri P, Mescia F, Hanson AL, Turner L, Bergamaschi L, Peñalver A, Richoz N, Moore SD, Ortmann BM, Dunmore BJ, Morgan MD, Tuong ZK, Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID BioResource Collaboration, Göttgens B, Toshner M, Hess C, Maxwell PH, Clatworthy MR, Nathan JA, Bradley JR, Lyons PA, Burrows N, Smith KGC.",,EBioMedicine,2022,2022-02-19,Y,Hypoxia; B cells; Lymphopenia; Covid-19,,,"<h4>Background</h4>Prominent early features of COVID-19 include severe, often clinically silent, hypoxia and a pronounced reduction in B cells, the latter important in defence against SARS-CoV-2. This presentation resembles the phenotype of mice with VHL-deficient B cells, in which Hypoxia-Inducible Factors are constitutively active, suggesting hypoxia might drive B cell abnormalities in COVID-19.<h4>Methods</h4>Detailed B cell phenotyping was undertaken by flow-cytometry on longitudinal samples from patients with COVID-19 across a range of severities (NIHR Cambridge BioResource). The impact of hypoxia on the transcriptome was assessed by single-cell and whole blood RNA sequencing analysis. The direct effect of hypoxia on B cells was determined through immunisation studies in genetically modified and hypoxia-exposed mice.<h4>Findings</h4>We demonstrate the breadth of early and persistent defects in B cell subsets in moderate/severe COVID-19, including reduced marginal zone-like, memory and transitional B cells, changes also observed in B cell VHL-deficient mice. These findings were associated with hypoxia-related transcriptional changes in COVID-19 patient B cells, and similar B cell abnormalities were seen in mice kept in hypoxic conditions.<h4>Interpretation</h4>Hypoxia may contribute to the pronounced and persistent B cell pathology observed in acute COVID-19 pneumonia. Assessment of the impact of early oxygen therapy on these immune defects should be considered, as their correction could contribute to improved outcomes.<h4>Funding</h4>Evelyn Trust, Addenbrooke's Charitable Trust, UKRI/NIHR, Wellcome Trust.",,pdf:http://www.thelancet.com/article/S2352396422000627/pdf; doi:https://doi.org/10.1016/j.ebiom.2022.103878; html:https://europepmc.org/articles/PMC8856886; pdf:https://europepmc.org/articles/PMC8856886?pdf=render
 33226834,https://doi.org/10.1164/rccm.202008-3211le,Proportion of Idiopathic Pulmonary Fibrosis Risk Explained by Known Common Genetic Loci in European Populations.,"Leavy OC, Ma SF, Molyneaux PL, Maher TM, Oldham JM, Flores C, Noth I, Jenkins RG, Dudbridge F, Wain LV, Allen RJ.",,American journal of respiratory and critical care medicine,2021,2021-03-01,Y,,,,,,pdf:https://europepmc.org/articles/pmc7958523?pdf=render; doi:https://doi.org/10.1164/rccm.202008-3211LE; html:https://europepmc.org/articles/PMC7958523; pdf:https://europepmc.org/articles/PMC7958523?pdf=render
 32724858,https://doi.org/10.1136/bmjophth-2020-000481,Outcomes important to patients with non-infectious posterior segment-involving uveitis: a qualitative study.,"Tallouzi MO, Moore DJ, Bucknall N, Murray PI, Calvert MJ, Denniston AK, Mathers JM.",,BMJ open ophthalmology,2020,2020-07-21,Y,Inflammation; Public Health; Treatment Other,,,"<h4>Objective</h4>Uveitis, a group of disorders characterised by intraocular inflammation, causes 10%-15% of total blindness in the developed world. The most sight-threatening forms of non-infectious uveitis are those affecting the posterior segment of the eye, collectively known as posterior segment-involving uveitis (PSIU). Numerous different clinical outcomes have been used in trials evaluating treatments for PSIU, but these may not represent patients' and carers' concerns. Therefore, the aims of this study were to understand the impact of PSIU on adult patients' and carers' lives and to explore what outcomes of treatment are important to them.<h4>Methods and analysis</h4>Four focus group discussions were undertaken to understand the perspectives of adult patients (=18) and carers (10) with PSIU. Participants were grouped according to whether or not their uveitis was complicated by the sight-threatening condition uveitic macular oedema. Discussions were audio-recorded, transcribed and analysed using the framework analytical approach. Outcomes were identified and grouped into outcome domains.<h4>Results</h4>Eleven core domains were identified as important to patients and carers undergoing treatment for PSIU, comprising (1) visual function, (2) symptoms, (3) functional ability, (4) impact on relationships, (5) financial impact, (6) psychological morbidity and emotional well-being, (7) psychosocial adjustment to uveitis, (8) doctor/patient/interprofessional relationships and access to healthcare, (9) treatment burden, (10) treatment side effects, and (11) disease control.<h4>Conclusion</h4>The domains identified represent patients' and carers' experience and perspectives and can be used to reflect on outcomes assessed in PSIU. They will directly inform the development of a core outcome set for PSIU clinical trials.",,pdf:https://bmjophth.bmj.com/content/bmjophth/5/1/e000481.full.pdf; doi:https://doi.org/10.1136/bmjophth-2020-000481; html:https://europepmc.org/articles/PMC7375431; pdf:https://europepmc.org/articles/PMC7375431?pdf=render
 37308319,https://doi.org/10.1111/bdi.13355,The network structure of mania symptoms differs between people with and without binge eating.,"Davies HL, Peel AJ, Mundy J, Monssen D, Kakar S, Davies MR, Adey BN, Armour C, Kalsi G, Lin Y, Marsh I, Rogers HC, Walters JTR, Herle M, Glen K, Malouf CM, Kelly EJ, Eley TC, Treasure J, Breen G, Hübel C.",,Bipolar disorders,2023,2023-06-12,Y,Diagnosis; Bipolar disorder; Signs And Symptoms; Anorexia Nervosa; Bulimia Nervosa; Network Analysis; Binge-eating Disorder,,,"<h4>Objectives</h4>People with bipolar disorder who also report binge eating have increased psychopathology and greater impairment than those without binge eating. Whether this co-occurrence is related to binge eating as a symptom or presents differently across full-syndrome eating disorders with binge eating is unclear.<h4>Methods</h4>We first compared networks of 13 lifetime mania symptoms in 34,226 participants from the United Kingdom's National Institute for Health and Care Research BioResource with (n = 12,104) and without (n = 22,122) lifetime binge eating. Second, in the subsample with binge eating, we compared networks of mania symptoms in participants with lifetime anorexia nervosa binge-eating/purging (n = 825), bulimia nervosa (n = 3737), and binge-eating disorder (n = 3648).<h4>Results</h4>People with binge eating endorsed every mania symptom significantly more often than those without binge eating. Within the subsample, people with bulimia nervosa most often had the highest endorsement rate of each mania symptom. We found significant differences in network parameter statistics, including network structure (M = 0.25, p = 0.001) and global strength (S = 1.84, p = 0.002) when comparing the binge eating with no binge-eating participants. However, network structure differences were sensitive to reductions in sample size and the greater density of the latter network was explained by the large proportion of participants (34%) without mania symptoms. The structure of the anorexia nervosa binge-eating/purging network differed from the bulimia nervosa network (M = 0.66, p = 0.001), but the result was unstable.<h4>Conclusions</h4>Our results suggest that the presence and structure of mania symptoms may be more associated with binge eating as a symptom rather than any specific binge-type eating disorder. Further research with larger sample sizes is required to confirm our findings.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/bdi.13355; doi:https://doi.org/10.1111/bdi.13355; html:https://europepmc.org/articles/PMC10768381; pdf:https://europepmc.org/articles/PMC10768381?pdf=render
@@ -2526,22 +2528,22 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 33199917,https://doi.org/10.1038/s41588-020-00725-7,Genome-wide association study of intracranial aneurysms identifies 17 risk loci and genetic overlap with clinical risk factors.,"Bakker MK, van der Spek RAA, van Rheenen W, Morel S, Bourcier R, Hostettler IC, Alg VS, van Eijk KR, Koido M, Akiyama M, Terao C, Matsuda K, Walters RG, Lin K, Li L, Millwood IY, Chen Z, Rouleau GA, Zhou S, Rannikmäe K, Sudlow CLM, Houlden H, van den Berg LH, Dina C, Naggara O, Gentric JC, Shotar E, Eugène F, Desal H, Winsvold BS, Børte S, Johnsen MB, Brumpton BM, Sandvei MS, Willer CJ, Hveem K, Zwart JA, Verschuren WMM, Friedrich CM, Hirsch S, Schilling S, Dauvillier J, Martin O, HUNT All-In Stroke, China Kadoorie Biobank Collaborative Group, BioBank Japan Project Consortium, ICAN Study Group, CADISP Group, Genetics and Observational Subarachnoid Haemorrhage (GOSH) Study investigators, International Stroke Genetics Consortium (ISGC), Jones GT, Bown MJ, Ko NU, Kim H, Coleman JRI, Breen G, Zaroff JG, Klijn CJM, Malik R, Dichgans M, Sargurupremraj M, Tatlisumak T, Amouyel P, Debette S, Rinkel GJE, Worrall BB, Pera J, Slowik A, Gaál-Paavola EI, Niemelä M, Jääskeläinen JE, von Und Zu Fraunberg M, Lindgren A, Broderick JP, Werring DJ, Woo D, Redon R, Bijlenga P, Kamatani Y, Veldink JH, Ruigrok YM.",,Nature genetics,2020,2020-11-16,N,,,,"Rupture of an intracranial aneurysm leads to subarachnoid hemorrhage, a severe type of stroke. To discover new risk loci and the genetic architecture of intracranial aneurysms, we performed a cross-ancestry, genome-wide association study in 10,754 cases and 306,882 controls of European and East Asian ancestry. We discovered 17 risk loci, 11 of which are new. We reveal a polygenic architecture and explain over half of the disease heritability. We show a high genetic correlation between ruptured and unruptured intracranial aneurysms. We also find a suggestive role for endothelial cells by using gene mapping and heritability enrichment. Drug-target enrichment shows pleiotropy between intracranial aneurysms and antiepileptic and sex hormone drugs, providing insights into intracranial aneurysm pathophysiology. Finally, genetic risks for smoking and high blood pressure, the two main clinical risk factors, play important roles in intracranial aneurysm risk, and drive most of the genetic correlation between intracranial aneurysms and other cerebrovascular traits.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7116530; doi:https://doi.org/10.1038/s41588-020-00725-7; html:https://europepmc.org/articles/PMC7116530; pdf:https://europepmc.org/articles/PMC7116530?pdf=render; doi:https://doi.org/10.1038/s41588-020-00725-7
 36434067,https://doi.org/10.1038/s42003-022-04252-5,A conserved glutathione binding site in poliovirus is a target for antivirals and vaccine stabilisation.,"Bahar MW, Nasta V, Fox H, Sherry L, Grehan K, Porta C, Macadam AJ, Stonehouse NJ, Rowlands DJ, Fry EE, Stuart DI.",,Communications biology,2022,2022-11-25,Y,,,,"Strategies to prevent the recurrence of poliovirus (PV) after eradication may utilise non-infectious, recombinant virus-like particle (VLP) vaccines. Despite clear advantages over inactivated or attenuated virus vaccines, instability of VLPs can compromise their immunogenicity. Glutathione (GSH), an important cellular reducing agent, is a crucial co-factor for the morphogenesis of enteroviruses, including PV. We report cryo-EM structures of GSH bound to PV serotype 3 VLPs showing that it can enhance particle stability. GSH binds the positively charged pocket at the interprotomer interface shown recently to bind GSH in enterovirus F3 and putative antiviral benzene sulphonamide compounds in other enteroviruses. We show, using high-resolution cryo-EM, the binding of a benzene sulphonamide compound with a PV serotype 2 VLP, consistent with antiviral activity through over-stabilizing the interprotomer pocket, preventing the capsid rearrangements necessary for viral infection. Collectively, these results suggest GSH or an analogous tight-binding antiviral offers the potential for stabilizing VLP vaccines.",,pdf:https://www.nature.com/articles/s42003-022-04252-5.pdf; doi:https://doi.org/10.1038/s42003-022-04252-5; html:https://europepmc.org/articles/PMC9700776; pdf:https://europepmc.org/articles/PMC9700776?pdf=render
 34593009,https://doi.org/10.1186/s13058-021-01465-0,Genomic risk prediction of coronary artery disease in women with breast cancer: a prospective cohort study.,"Liou L, Kaptoge S, Dennis J, Shah M, Tyrer J, Inouye M, Easton DF, Pharoah PDP.",,Breast cancer research : BCR,2021,2021-09-30,Y,Breast cancer; Cardiovascular disease; coronary artery disease; Coronary Heart Disease; Search; Polygenic Risk Score,,,"<h4>Background</h4>Advancements in cancer therapeutics have resulted in increases in cancer-related survival; however, there is a growing clinical dilemma. The current balancing of survival benefits and future cardiotoxic harms of oncotherapies has resulted in an increased burden of cardiovascular disease in breast cancer survivors. Risk stratification may help address this clinical dilemma. This study is the first to assess the association between a coronary artery disease-specific polygenic risk score and incident coronary artery events in female breast cancer survivors.<h4>Methods</h4>We utilized the Studies in Epidemiology and Research in Cancer Heredity prospective cohort involving 12,413 women with breast cancer with genotype information and without a baseline history of cardiovascular disease. Cause-specific hazard ratios for association of the polygenic risk score and incident coronary artery disease (CAD) were obtained using left-truncated Cox regression adjusting for age, genotype array, conventional risk factors such as smoking and body mass index, as well as other sociodemographic, lifestyle, and medical variables.<h4>Results</h4>Over a median follow-up of 10.3 years (IQR: 16.8) years, 750 incident fatal or non-fatal coronary artery events were recorded. A 1 standard deviation higher polygenic risk score was associated with an adjusted hazard ratio of 1.33 (95% CI 1.20, 1.47) for incident CAD.<h4>Conclusions</h4>This study provides evidence that a coronary artery disease-specific polygenic risk score can risk-stratify breast cancer survivors independently of other established cardiovascular risk factors.",,pdf:https://breast-cancer-research.biomedcentral.com/track/pdf/10.1186/s13058-021-01465-0; doi:https://doi.org/10.1186/s13058-021-01465-0; html:https://europepmc.org/articles/PMC8482562; pdf:https://europepmc.org/articles/PMC8482562?pdf=render
-36436752,https://doi.org/10.1016/j.ijid.2022.11.024,"Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa.","Davies MA, Morden E, Rousseau P, Arendse J, Bam JL, Boloko L, Cloete K, Cohen C, Chetty N, Dane P, Heekes A, Hsiao NY, Hunter M, Hussey H, Jacobs T, Jassat W, Kariem S, Kassanjee R, Laenen I, Roux SL, Lessells R, Mahomed H, Maughan D, Meintjes G, Mendelson M, Mnguni A, Moodley M, Murie K, Naude J, Ntusi NAB, Paleker M, Parker A, Pienaar D, Preiser W, Prozesky H, Raubenheimer P, Rossouw L, Schrueder N, Smith B, Smith M, Solomon W, Symons G, Taljaard J, Wasserman S, Wilkinson RJ, Wolmarans M, Wolter N, Boulle A.",,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2023,2022-11-24,Y,"Covid-19; Omicron; Ba.4; Ba.5; Death, Severe Hospitalization",,,"<h4>Objectives</h4>We aimed to compare the clinical severity of Omicron BA.4/BA.5 infection with BA.1 and earlier variant infections among laboratory-confirmed SARS-CoV-2 cases in the Western Cape, South Africa, using timing of infection to infer the lineage/variant causing infection.<h4>Methods</h4>We included public sector patients aged ≥20 years with laboratory-confirmed COVID-19 between May 01-May 21, 2022 (BA.4/BA.5 wave) and equivalent previous wave periods. We compared the risk between waves of (i) death and (ii) severe hospitalization/death (all within 21 days of diagnosis) using Cox regression adjusted for demographics, comorbidities, admission pressure, vaccination, and previous infection.<h4>Results</h4>Among 3793 patients from the BA.4/BA.5 wave and 190,836 patients from previous waves, the risk of severe hospitalization/death was similar in the BA.4/BA.5 and BA.1 waves (adjusted hazard ratio [aHR] 1.12; 95% confidence interval [CI] 0.93; 1.34). Both Omicron waves had a lower risk of severe outcomes than previous waves. Previous infection (aHR 0.29, 95% CI 0.24; 0.36) and vaccination (aHR 0.17; 95% CI 0.07; 0.40 for at least three doses vs no vaccine) were protective.<h4>Conclusion</h4>Disease severity was similar among diagnosed COVID-19 cases in the BA.4/BA.5 and BA.1 periods in the context of growing immunity against SARS-CoV-2 due to previous infection and vaccination, both of which were strongly protective.",,doi:https://doi.org/10.1016/j.ijid.2022.11.024; doi:https://doi.org/10.1016/j.ijid.2022.11.024; html:https://europepmc.org/articles/PMC9686046; pdf:https://europepmc.org/articles/PMC9686046?pdf=render
 33248277,https://doi.org/10.1016/j.jclinepi.2020.11.014,Text-mining in electronic healthcare records can be used as efficient tool for screening and data collection in cardiovascular trials: a multicenter validation study.,"van Dijk WB, Fiolet ATL, Schuit E, Sammani A, Groenhof TKJ, van der Graaf R, de Vries MC, Alings M, Schaap J, Asselbergs FW, Grobbee DE, Groenwold RHH, Mosterd A.",,Journal of clinical epidemiology,2021,2020-11-25,N,Screening; Recruitment; trials; Multicenter; cardiovascular; Text-mining; Data-mining; Electronic Medical Records (Emrs); Data-collections; Electronic Healthcare Records (Ehrs); Lodoco2,,,"<h4>Objective</h4>This study aimed to validate trial patient eligibility screening and baseline data collection using text-mining in electronic healthcare records (EHRs), comparing the results to those of an international trial.<h4>Study design and setting</h4>In three medical centers with different EHR vendors, EHR-based text-mining was used to automatically screen patients for trial eligibility and extract baseline data on nineteen characteristics. First, the yield of screening with automated EHR text-mining search was compared with manual screening by research personnel. Second, the accuracy of extracted baseline data by EHR text mining was compared to manual data entry by research personnel.<h4>Results</h4>Of the 92,466 patients visiting the out-patient cardiology departments, 568 (0.6%) were enrolled in the trial during its recruitment period using manual screening methods. Automated EHR data screening of all patients showed that the number of patients needed to screen could be reduced by 73,863 (79.9%). The remaining 18,603 (20.1%) contained 458 of the actual participants (82.4% of participants). In trial participants, automated EHR text-mining missed a median of 2.8% (Interquartile range [IQR] across all variables 0.4-8.5%) of all data points compared to manually collected data. The overall accuracy of automatically extracted data was 88.0% (IQR 84.7-92.8%).<h4>Conclusion</h4>Automatically extracting data from EHRs using text-mining can be used to identify trial participants and to collect baseline information.",,pdf:http://www.jclinepi.com/article/S0895435620311859/pdf; doi:https://doi.org/10.1016/j.jclinepi.2020.11.014
+36436752,https://doi.org/10.1016/j.ijid.2022.11.024,"Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa.","Davies MA, Morden E, Rousseau P, Arendse J, Bam JL, Boloko L, Cloete K, Cohen C, Chetty N, Dane P, Heekes A, Hsiao NY, Hunter M, Hussey H, Jacobs T, Jassat W, Kariem S, Kassanjee R, Laenen I, Roux SL, Lessells R, Mahomed H, Maughan D, Meintjes G, Mendelson M, Mnguni A, Moodley M, Murie K, Naude J, Ntusi NAB, Paleker M, Parker A, Pienaar D, Preiser W, Prozesky H, Raubenheimer P, Rossouw L, Schrueder N, Smith B, Smith M, Solomon W, Symons G, Taljaard J, Wasserman S, Wilkinson RJ, Wolmarans M, Wolter N, Boulle A.",,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2023,2022-11-24,Y,"Covid-19; Omicron; Ba.4; Ba.5; Death, Severe Hospitalization",,,"<h4>Objectives</h4>We aimed to compare the clinical severity of Omicron BA.4/BA.5 infection with BA.1 and earlier variant infections among laboratory-confirmed SARS-CoV-2 cases in the Western Cape, South Africa, using timing of infection to infer the lineage/variant causing infection.<h4>Methods</h4>We included public sector patients aged ≥20 years with laboratory-confirmed COVID-19 between May 01-May 21, 2022 (BA.4/BA.5 wave) and equivalent previous wave periods. We compared the risk between waves of (i) death and (ii) severe hospitalization/death (all within 21 days of diagnosis) using Cox regression adjusted for demographics, comorbidities, admission pressure, vaccination, and previous infection.<h4>Results</h4>Among 3793 patients from the BA.4/BA.5 wave and 190,836 patients from previous waves, the risk of severe hospitalization/death was similar in the BA.4/BA.5 and BA.1 waves (adjusted hazard ratio [aHR] 1.12; 95% confidence interval [CI] 0.93; 1.34). Both Omicron waves had a lower risk of severe outcomes than previous waves. Previous infection (aHR 0.29, 95% CI 0.24; 0.36) and vaccination (aHR 0.17; 95% CI 0.07; 0.40 for at least three doses vs no vaccine) were protective.<h4>Conclusion</h4>Disease severity was similar among diagnosed COVID-19 cases in the BA.4/BA.5 and BA.1 periods in the context of growing immunity against SARS-CoV-2 due to previous infection and vaccination, both of which were strongly protective.",,doi:https://doi.org/10.1016/j.ijid.2022.11.024; doi:https://doi.org/10.1016/j.ijid.2022.11.024; html:https://europepmc.org/articles/PMC9686046; pdf:https://europepmc.org/articles/PMC9686046?pdf=render
 31331193,https://doi.org/10.1161/circulationaha.119.041546,Impact of <i>ADCY9</i> Genotype on Response to Anacetrapib.,"Hopewell JC, Ibrahim M, Hill M, Shaw PM, Braunwald E, Blaustein RO, Bowman L, Landray MJ, Sabatine MS, Collins R, HPS3/TIMI55–REVEAL Collaborative Group.",,Circulation,2019,2019-07-23,Y,Randomized controlled trial; Pharmacogenetics; Anacetrapib; Cholesterol Ester Transfer Protein; Adenylate Cyclase 9,"Better, Faster and More Efficient Clinical Trials",,"<h4>Background</h4>Exploratory analyses of previous randomized trials generated a hypothesis that the clinical response to cholesteryl ester transfer protein (CETP) inhibitor therapy differs by <i>ADCY9</i> genotype, prompting the ongoing dal-GenE trial in individuals with a particular genetic profile. The randomized placebo-controlled REVEAL trial (Randomized Evaluation of the Effects of Anacetrapib through Lipid-Modification) demonstrated the clinical efficacy of the CETP inhibitor anacetrapib among patients with preexisting atherosclerotic vascular disease. In the present study, we examined the impact of <i>ADCY9</i> genotype on response to anacetrapib in the REVEAL trial.<h4>Methods</h4>Individuals with stable atherosclerotic vascular disease who were treated with intensive atorvastatin therapy received either anacetrapib 100 mg daily or matching placebo. Cox proportional hazards models, adjusted for the first 5 principal components of ancestry, were used to estimate the effects of allocation to anacetrapib on major vascular events (a composite of coronary death, myocardial infarction, coronary revascularization, or presumed ischemic stroke) and the interaction with <i>ADCY9</i> rs1967309 genotype.<h4>Results</h4>Among 19 210 genotyped individuals of European ancestry, 2504 (13.0%) had a first major vascular event during 4 years median follow-up: 1216 (12.6%) among anacetrapib-allocated participants and 1288 (13.4%) among placebo-allocated participants. Proportional reductions in the risk of major vascular events with anacetrapib did not differ significantly by <i>ADCY9</i> genotype: hazard ratio (HR) = 0.92 (95% CI, 0.81-1.05) for GG; HR = 0.94 (95% CI, 0.84-1.06) for AG; and HR = 0.93 (95% CI, 0.76-1.13) for AA genotype carriers, respectively; genotypic <i>P</i> for interaction = 0.96. Furthermore, there were no associations between <i>ADCY9</i> genotype and the proportional reductions in the separate components of major vascular events or meaningful differences in lipid response to anacetrapib.<h4>Conclusions</h4>The REVEAL trial is the single largest study to date evaluating the <i>ADCY9</i> pharmacogenetic interaction. It provides no support for the hypothesis that <i>ADCY9</i> genotype is materially relevant to the clinical effects of the CETP inhibitor anacetrapib. The ongoing dal-GenE study will provide direct evidence as to whether there is any specific pharmacogenetic interaction with dalcetrapib.<h4>Clinical trial registration</h4>URL: https://www.<h4>Clinicaltrials</h4>gov. Unique identifier: NCT01252953. URL: http://www.isrctn.com. Unique identifier: ISRCTN48678192. URL: https://www.clinicaltrialsregister.eu. Unique identifier: 2010-023467-18.",,doi:https://doi.org/10.1161/circulationaha.119.041546; doi:https://doi.org/10.1161/CIRCULATIONAHA.119.041546; html:https://europepmc.org/articles/PMC6749971; pdf:https://europepmc.org/articles/PMC6749971?pdf=render
 31711539,https://doi.org/10.1186/s13326-019-0211-7,Text mining brain imaging reports.,"Alex B, Grover C, Tobin R, Sudlow C, Mair G, Whiteley W.",,Journal of biomedical semantics,2019,2019-11-12,Y,Stroke Classification; Text Mining; Electronic Healthcare Records; Neuroimaging Reports,,,"<h4>Background</h4>With the improvements to text mining technology and the availability of large unstructured Electronic Healthcare Records (EHR) datasets, it is now possible to extract structured information from raw text contained within EHR at reasonably high accuracy. We describe a text mining system for classifying radiologists' reports of CT and MRI brain scans, assigning labels indicating occurrence and type of stroke, as well as other observations. Our system, the Edinburgh Information Extraction for Radiology reports (EdIE-R) system, which we describe here, was developed and tested on a collection of radiology reports.The work reported in this paper is based on 1168 radiology reports from the Edinburgh Stroke Study (ESS), a hospital-based register of stroke and transient ischaemic attack patients. We manually created annotations for this data in parallel with developing the rule-based EdIE-R system to identify phenotype information related to stroke in radiology reports. This process was iterative and domain expert feedback was considered at each iteration to adapt and tune the EdIE-R text mining system which identifies entities, negation and relations between entities in each report and determines report-level labels (phenotypes).<h4>Results</h4>The inter-annotator agreement (IAA) for all types of annotations is high at 96.96 for entities, 96.46 for negation, 95.84 for relations and 94.02 for labels. The equivalent system scores on the blind test set are equally high at 95.49 for entities, 94.41 for negation, 98.27 for relations and 96.39 for labels for the first annotator and 96.86, 96.01, 96.53 and 92.61, respectively for the second annotator.<h4>Conclusion</h4>Automated reading of such EHR data at such high levels of accuracies opens up avenues for population health monitoring and audit, and can provide a resource for epidemiological studies. We are in the process of validating EdIE-R in separate larger cohorts in NHS England and Scotland. The manually annotated ESS corpus will be available for research purposes on application.",,pdf:https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-019-0211-7; doi:https://doi.org/10.1186/s13326-019-0211-7; html:https://europepmc.org/articles/PMC6849161; pdf:https://europepmc.org/articles/PMC6849161?pdf=render
 35587468,https://doi.org/10.1371/journal.pmed.1003981,Integrating polygenic risk scores in the prediction of type 2 diabetes risk and subtypes in British Pakistanis and Bangladeshis: A population-based cohort study.,"Hodgson S, Huang QQ, Sallah N, Genes & Health Research Team, Griffiths CJ, Newman WG, Trembath RC, Wright J, Lumbers RT, Kuchenbaecker K, van Heel DA, Mathur R, Martin HC, Finer S.",,PLoS medicine,2022,2022-05-19,Y,,,,"<h4>Background</h4>Type 2 diabetes (T2D) is highly prevalent in British South Asians, yet they are underrepresented in research. Genes & Health (G&H) is a large, population study of British Pakistanis and Bangladeshis (BPB) comprising genomic and routine health data. We assessed the extent to which genetic risk for T2D is shared between BPB and European populations (EUR). We then investigated whether the integration of a polygenic risk score (PRS) for T2D with an existing risk tool (QDiabetes) could improve prediction of incident disease and the characterisation of disease subtypes.<h4>Methods and findings</h4>In this observational cohort study, we assessed whether common genetic loci associated with T2D in EUR individuals were replicated in 22,490 BPB individuals in G&H. We replicated fewer loci in G&H (n = 76/338, 22%) than would be expected given power if all EUR-ascertained loci were transferable (n = 101, 30%; p = 0.001). Of the 27 transferable loci that were powered to interrogate this, only 9 showed evidence of shared causal variants. We constructed a T2D PRS and combined it with a clinical risk instrument (QDiabetes) in a novel, integrated risk tool (IRT) to assess risk of incident diabetes. To assess model performance, we compared categorical net reclassification index (NRI) versus QDiabetes alone. In 13,648 patients free from T2D followed up for 10 years, NRI was 3.2% for IRT versus QDiabetes (95% confidence interval (CI): 2.0% to 4.4%). IRT performed best in reclassification of individuals aged less than 40 years deemed low risk by QDiabetes alone (NRI 5.6%, 95% CI 3.6% to 7.6%), who tended to be free from comorbidities and slim. After adjustment for QDiabetes score, PRS was independently associated with progression to T2D after gestational diabetes (hazard ratio (HR) per SD of PRS 1.23, 95% CI 1.05 to 1.42, p = 0.028). Using cluster analysis of clinical features at diabetes diagnosis, we replicated previously reported disease subgroups, including Mild Age-Related, Mild Obesity-related, and Insulin-Resistant Diabetes, and showed that PRS distribution differs between subgroups (p = 0.002). Integrating PRS in this cluster analysis revealed a Probable Severe Insulin Deficient Diabetes (pSIDD) subgroup, despite the absence of clinical measures of insulin secretion or resistance. We also observed differences in rates of progression to micro- and macrovascular complications between subgroups after adjustment for confounders. Study limitations include the absence of an external replication cohort and the potential biases arising from missing or incorrect routine health data.<h4>Conclusions</h4>Our analysis of the transferability of T2D loci between EUR and BPB indicates the need for larger, multiancestry studies to better characterise the genetic contribution to disease and its varied aetiology. We show that a T2D PRS optimised for this high-risk BPB population has potential clinical application in BPB, improving the identification of T2D risk (especially in the young) on top of an established clinical risk algorithm and aiding identification of subgroups at diagnosis, which may help future efforts to stratify care and treatment of the disease.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003981&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003981; html:https://europepmc.org/articles/PMC9119501; pdf:https://europepmc.org/articles/PMC9119501?pdf=render
 33323250,https://doi.org/10.1016/s2589-7500(19)30121-9,"Development and validation of multivariable prediction models of remission, recovery, and quality of life outcomes in people with first episode psychosis: a machine learning approach.","Leighton SP, Upthegrove R, Krishnadas R, Benros ME, Broome MR, Gkoutos GV, Liddle PF, Singh SP, Everard L, Jones PB, Fowler D, Sharma V, Freemantle N, Christensen RHB, Albert N, Nordentoft M, Schwannauer M, Cavanagh J, Gumley AI, Birchwood M, Mallikarjun PK.",,The Lancet. Digital health,2019,2019-09-12,N,,,,"<h4>Background</h4>Outcomes for people with first-episode psychosis are highly heterogeneous. Few reliable validated methods are available to predict the outcome for individual patients in the first clinical contact. In this study, we aimed to build multivariable prediction models of 1-year remission and recovery outcomes using baseline clinical variables in people with first-episode psychosis.<h4>Methods</h4>In this machine learning approach, we applied supervised machine learning, using regularised regression and nested leave-one-site-out cross-validation, to baseline clinical data from the English Evaluating the Development and Impact of Early Intervention Services (EDEN) study (n=1027), to develop and internally validate prediction models at 1-year follow-up. We assessed four binary outcomes that were recorded at 1 year: symptom remission, social recovery, vocational recovery, and quality of life (QoL). We externally validated the prediction models by selecting from the top predictor variables identified in the internal validation models the variables shared with the external validation datasets comprised of two Scottish longitudinal cohort studies (n=162) and the OPUS trial, a randomised controlled trial of specialised assertive intervention versus standard treatment (n=578).<h4>Findings</h4>The performance of prediction models was robust for the four 1-year outcomes of symptom remission (area under the receiver operating characteristic curve [AUC] 0·703, 95% CI 0·664-0·742), social recovery (0·731, 0·697-0·765), vocational recovery (0·736, 0·702-0·771), and QoL (0·704, 0·667-0·742; p<0·0001 for all outcomes), on internal validation. We externally validated the outcomes of symptom remission (AUC 0·680, 95% CI 0·587-0·773), vocational recovery (0·867, 0·805-0·930), and QoL (0·679, 0·522-0·836) in the Scottish datasets, and symptom remission (0·616, 0·553-0·679), social recovery (0·573, 0·504-0·643), vocational recovery (0·660, 0·610-0·710), and QoL (0·556, 0·481-0·631) in the OPUS dataset.<h4>Interpretation</h4>In our machine learning analysis, we showed that prediction models can reliably and prospectively identify poor remission and recovery outcomes at 1 year for patients with first-episode psychosis using baseline clinical variables at first clinical contact.<h4>Funding</h4>Lundbeck Foundation.",,pdf:http://www.thelancet.com/article/S2589750019301219/pdf; doi:https://doi.org/10.1016/S2589-7500(19)30121-9
 37132645,https://doi.org/10.1017/s0033291721002257,"Life expectancy, mortality risks and cause of death in patients with serious mental illness in South East London: a comparison between 2008-2012 and 2013-2017.","Chang CK, Chesney E, Teng WN, Hollandt S, Pritchard M, Shetty H, Stewart R, McGuire P, Patel R.",,Psychological medicine,2023,2021-09-07,Y,Mortality; Schizophrenia; Life expectancy; Cause of death; Bipolar disorder; Standardised Mortality Ratio,,,"<h4>Background</h4>People with serious mental illness (SMI) have a significantly shorter life expectancy than the general population. This study investigates whether the mortality rate in this group has changed over the last decade.<h4>Methods</h4>Using Clinical Record Interactive Search software, we extracted data from a large electronic database of patients in South East London. All patients with schizophrenia, schizoaffective disorder or bipolar disorder from 2008 to 2012 and/or 2013 to 2017 were included. Estimates of life expectancy at birth, standardised mortality ratios and causes of death were obtained for each cohort according to diagnosis and gender. Comparisons were made between cohorts and with the general population using data obtained from the UK Office of National Statistics.<h4>Results</h4>In total, 26 005 patients were included. In men, life expectancy was greater in 2013-2017 (64.9 years; 95% CI 63.6-66.3) than in 2008-2012 (63.2 years; 95% CI 61.5-64.9). Similarly, in women, life expectancy was greater in 2013-2017 (69.1 years; 95% CI 67.5-70.7) than in 2008-2012 (68.1 years; 95% CI 66.2-69.9). The difference with general population life expectancy fell by 0.9 years between cohorts in men, and 0.5 years in women. In the 2013-2017 cohorts, cancer accounted for a similar proportion of deaths as cardiovascular disease.<h4>Conclusions</h4>Relative to the general population, life expectancy for people with SMI is still much worse, though it appears to be improving. The increased cancer-related mortality suggests that physical health monitoring should consider including cancer as well.",,pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/F28CB69D452C5EFDAFF77D0FE59FC094/S0033291721002257a.pdf/div-class-title-life-expectancy-mortality-risks-and-cause-of-death-in-patients-with-serious-mental-illness-in-south-east-london-a-comparison-between-2008-2012-and-2013-2017-div.pdf; doi:https://doi.org/10.1017/S0033291721002257; html:https://europepmc.org/articles/PMC9975985; pdf:https://europepmc.org/articles/PMC9975985?pdf=render
 37418234,https://doi.org/10.1007/s12265-023-10403-8,A Systematic Analysis of the Clinical Outcome Associated with Multiple Reclassified Desmosomal Gene Variants in Arrhythmogenic Right Ventricular Cardiomyopathy Patients.,"Nagyova E, Hoorntje ET, Te Rijdt WP, Bosman LP, Syrris P, Protonotarios A, Elliott PM, Tsatsopoulou A, Mestroni L, Taylor MRG, Sinagra G, Merlo M, Wada Y, Horie M, Mogensen J, Christensen AH, Gerull B, Song L, Yao Y, Fan S, Saguner AM, Duru F, Koskenvuo JW, Cruz Marino T, Tichnell C, Judge DP, Dooijes D, Lekanne Deprez RH, Basso C, Pilichou K, Bauce B, Wilde AAM, Charron P, Fressart V, van der Heijden JF, van den Berg MP, Asselbergs FW, James CA, Jongbloed JDH, Harakalova M, van Tintelen JP.",,Journal of cardiovascular translational research,2023,2023-07-07,Y,Genetics; Arrhythmia; Arvc; Composite Endpoint; Multiple Variants; Desmosomal Genes,,,"The presence of multiple pathogenic variants in desmosomal genes (DSC2, DSG2, DSP, JUP, and PKP2) in patients with arrhythmogenic right ventricular cardiomyopathy (ARVC) has been linked to a severe phenotype. However, the pathogenicity of variants is reclassified frequently, which may result in a changed clinical risk prediction. Here, we present the collection, reclassification, and clinical outcome correlation for the largest series of ARVC patients carrying multiple desmosomal pathogenic variants to date (n = 331). After reclassification, only 29% of patients remained carriers of two (likely) pathogenic variants. They reached the composite endpoint (ventricular arrhythmias, heart failure, and death) significantly earlier than patients with one or no remaining reclassified variant (hazard ratios of 1.9 and 1.8, respectively). Periodic reclassification of variants contributes to more accurate risk stratification and subsequent clinical management strategy. Graphical Abstract.",,pdf:https://link.springer.com/content/pdf/10.1007/s12265-023-10403-8.pdf; doi:https://doi.org/10.1007/s12265-023-10403-8; html:https://europepmc.org/articles/PMC10721666; pdf:https://europepmc.org/articles/PMC10721666?pdf=render
-36697134,https://doi.org/10.1016/j.jacc.2022.10.034,Somatostatin Receptor PET/MR Imaging of Inflammation in Patients With Large Vessel Vasculitis and Atherosclerosis.,"Ćorović A, Wall C, Nus M, Gopalan D, Huang Y, Imaz M, Zulcinski M, Peverelli M, Uryga A, Lambert J, Bressan D, Maughan RT, Pericleous C, Dubash S, Jordan N, Jayne DR, Hoole SP, Calvert PA, Dean AF, Rassl D, Barwick T, Iles M, Frontini M, Hannon G, Manavaki R, Fryer TD, Aloj L, Graves MJ, Gilbert FJ, Dweck MR, Newby DE, Fayad ZA, Reynolds G, Morgan AW, Aboagye EO, Davenport AP, Jørgensen HF, Mallat Z, Bennett MR, Peters JE, Rudd JHF, Mason JC, Tarkin JM.",,Journal of the American College of Cardiology,2023,2023-01-01,Y,Atherosclerosis; Inflammation; Molecular Imaging; Giant Cell Arteritis; Takayasu Arteritis; Somatostatin Receptor,,,"<h4>Background</h4>Assessing inflammatory disease activity in large vessel vasculitis (LVV) can be challenging by conventional measures.<h4>Objectives</h4>We aimed to investigate somatostatin receptor 2 (SST<sub>2</sub>) as a novel inflammation-specific molecular imaging target in LVV.<h4>Methods</h4>In a prospective, observational cohort study, in vivo arterial SST<sub>2</sub> expression was assessed by positron emission tomography/magnetic resonance imaging (PET/MRI) using <sup>68</sup>Ga-DOTATATE and <sup>18</sup>F-FET-βAG-TOCA. Ex vivo mapping of the imaging target was performed using immunofluorescence microscopy; imaging mass cytometry; and bulk, single-cell, and single-nucleus RNA sequencing.<h4>Results</h4>Sixty-one participants (LVV: n = 27; recent atherosclerotic myocardial infarction of ≤2 weeks: n = 25; control subjects with an oncologic indication for imaging: n = 9) were included. Index vessel SST<sub>2</sub> maximum tissue-to-blood ratio was 61.8% (P < 0.0001) higher in active/grumbling LVV than inactive LVV and 34.6% (P = 0.0002) higher than myocardial infarction, with good diagnostic accuracy (area under the curve: ≥0.86; P < 0.001 for both). Arterial SST<sub>2</sub> signal was not elevated in any of the control subjects. SST<sub>2</sub> PET/MRI was generally consistent with <sup>18</sup>F-fluorodeoxyglucose PET/computed tomography imaging in LVV patients with contemporaneous clinical scans but with very low background signal in the brain and heart, allowing for unimpeded assessment of nearby coronary, myocardial, and intracranial artery involvement. Clinically effective treatment for LVV was associated with a 0.49 ± 0.24 (standard error of the mean [SEM]) (P = 0.04; 22.3%) reduction in the SST<sub>2</sub> maximum tissue-to-blood ratio after 9.3 ± 3.2 months. SST<sub>2</sub> expression was localized to macrophages, pericytes, and perivascular adipocytes in vasculitis specimens, with specific receptor binding confirmed by autoradiography. SSTR2-expressing macrophages coexpressed proinflammatory markers.<h4>Conclusions</h4>SST<sub>2</sub> PET/MRI holds major promise for diagnosis and therapeutic monitoring in LVV. (PET Imaging of Giant Cell and Takayasu Arteritis [PITA], NCT04071691; Residual Inflammation and Plaque Progression Long-Term Evaluation [RIPPLE], NCT04073810).",,doi:https://doi.org/10.1016/j.jacc.2022.10.034; doi:https://doi.org/10.1016/j.jacc.2022.10.034; html:https://europepmc.org/articles/PMC9883634; pdf:https://europepmc.org/articles/PMC9883634?pdf=render
 33328634,https://doi.org/10.1038/s41586-020-03043-4,Mapping routine measles vaccination in low- and middle-income countries.,Local Burden of Disease Vaccine Coverage Collaborators.,,Nature,2021,2020-12-16,Y,,,,"The safe, highly effective measles vaccine has been recommended globally since 1974, yet in 2017 there were more than 17 million cases of measles and 83,400 deaths in children under 5 years old, and more than 99% of both occurred in low- and middle-income countries (LMICs)<sup>1-4</sup>. Globally comparable, annual, local estimates of routine first-dose measles-containing vaccine (MCV1) coverage are critical for understanding geographically precise immunity patterns, progress towards the targets of the Global Vaccine Action Plan (GVAP), and high-risk areas amid disruptions to vaccination programmes caused by coronavirus disease 2019 (COVID-19)<sup>5-8</sup>. Here we generated annual estimates of routine childhood MCV1 coverage at 5 × 5-km<sup>2</sup> pixel and second administrative levels from 2000 to 2019 in 101 LMICs, quantified geographical inequality and assessed vaccination status by geographical remoteness. After widespread MCV1 gains from 2000 to 2010, coverage regressed in more than half of the districts between 2010 and 2019, leaving many LMICs far from the GVAP goal of 80% coverage in all districts by 2019. MCV1 coverage was lower in rural than in urban locations, although a larger proportion of unvaccinated children overall lived in urban locations; strategies to provide essential vaccination services should address both geographical contexts. These results provide a tool for decision-makers to strengthen routine MCV1 immunization programmes and provide equitable disease protection for all children.",,pdf:https://www.nature.com/articles/s41586-020-03043-4.pdf; doi:https://doi.org/10.1038/s41586-020-03043-4; html:https://europepmc.org/articles/PMC7739806; pdf:https://europepmc.org/articles/PMC7739806?pdf=render
+36697134,https://doi.org/10.1016/j.jacc.2022.10.034,Somatostatin Receptor PET/MR Imaging of Inflammation in Patients With Large Vessel Vasculitis and Atherosclerosis.,"Ćorović A, Wall C, Nus M, Gopalan D, Huang Y, Imaz M, Zulcinski M, Peverelli M, Uryga A, Lambert J, Bressan D, Maughan RT, Pericleous C, Dubash S, Jordan N, Jayne DR, Hoole SP, Calvert PA, Dean AF, Rassl D, Barwick T, Iles M, Frontini M, Hannon G, Manavaki R, Fryer TD, Aloj L, Graves MJ, Gilbert FJ, Dweck MR, Newby DE, Fayad ZA, Reynolds G, Morgan AW, Aboagye EO, Davenport AP, Jørgensen HF, Mallat Z, Bennett MR, Peters JE, Rudd JHF, Mason JC, Tarkin JM.",,Journal of the American College of Cardiology,2023,2023-01-01,Y,Atherosclerosis; Inflammation; Molecular Imaging; Giant Cell Arteritis; Takayasu Arteritis; Somatostatin Receptor,,,"<h4>Background</h4>Assessing inflammatory disease activity in large vessel vasculitis (LVV) can be challenging by conventional measures.<h4>Objectives</h4>We aimed to investigate somatostatin receptor 2 (SST<sub>2</sub>) as a novel inflammation-specific molecular imaging target in LVV.<h4>Methods</h4>In a prospective, observational cohort study, in vivo arterial SST<sub>2</sub> expression was assessed by positron emission tomography/magnetic resonance imaging (PET/MRI) using <sup>68</sup>Ga-DOTATATE and <sup>18</sup>F-FET-βAG-TOCA. Ex vivo mapping of the imaging target was performed using immunofluorescence microscopy; imaging mass cytometry; and bulk, single-cell, and single-nucleus RNA sequencing.<h4>Results</h4>Sixty-one participants (LVV: n = 27; recent atherosclerotic myocardial infarction of ≤2 weeks: n = 25; control subjects with an oncologic indication for imaging: n = 9) were included. Index vessel SST<sub>2</sub> maximum tissue-to-blood ratio was 61.8% (P < 0.0001) higher in active/grumbling LVV than inactive LVV and 34.6% (P = 0.0002) higher than myocardial infarction, with good diagnostic accuracy (area under the curve: ≥0.86; P < 0.001 for both). Arterial SST<sub>2</sub> signal was not elevated in any of the control subjects. SST<sub>2</sub> PET/MRI was generally consistent with <sup>18</sup>F-fluorodeoxyglucose PET/computed tomography imaging in LVV patients with contemporaneous clinical scans but with very low background signal in the brain and heart, allowing for unimpeded assessment of nearby coronary, myocardial, and intracranial artery involvement. Clinically effective treatment for LVV was associated with a 0.49 ± 0.24 (standard error of the mean [SEM]) (P = 0.04; 22.3%) reduction in the SST<sub>2</sub> maximum tissue-to-blood ratio after 9.3 ± 3.2 months. SST<sub>2</sub> expression was localized to macrophages, pericytes, and perivascular adipocytes in vasculitis specimens, with specific receptor binding confirmed by autoradiography. SSTR2-expressing macrophages coexpressed proinflammatory markers.<h4>Conclusions</h4>SST<sub>2</sub> PET/MRI holds major promise for diagnosis and therapeutic monitoring in LVV. (PET Imaging of Giant Cell and Takayasu Arteritis [PITA], NCT04071691; Residual Inflammation and Plaque Progression Long-Term Evaluation [RIPPLE], NCT04073810).",,doi:https://doi.org/10.1016/j.jacc.2022.10.034; doi:https://doi.org/10.1016/j.jacc.2022.10.034; html:https://europepmc.org/articles/PMC9883634; pdf:https://europepmc.org/articles/PMC9883634?pdf=render
 33245137,https://doi.org/10.1093/ije/dyaa155,"Plant foods, dietary fibre and risk of ischaemic heart disease in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort.","Perez-Cornago A, Crowe FL, Appleby PN, Bradbury KE, Wood AM, Jakobsen MU, Johnson L, Sacerdote C, Steur M, Weiderpass E, Würtz AML, Kühn T, Katzke V, Trichopoulou A, Karakatsani A, La Vecchia C, Masala G, Tumino R, Panico S, Sluijs I, Skeie G, Imaz L, Petrova D, Quirós JR, Yohar SMC, Jakszyn P, Melander O, Sonestedt E, Andersson J, Wennberg M, Aune D, Riboli E, Schulze MB, di Angelantonio E, Wareham NJ, Danesh J, Forouhi NG, Butterworth AS, Key TJ.",,International journal of epidemiology,2021,2021-03-01,Y,Seeds; Fruit; Legumes; vegetables; Coronary Heart Disease; Nuts,,,"<h4>Background</h4>Epidemiological evidence indicates that diets rich in plant foods are associated with a lower risk of ischaemic heart disease (IHD), but there is sparse information on fruit and vegetable subtypes and sources of dietary fibre. This study examined the associations of major plant foods, their subtypes and dietary fibre with risk of IHD in the European Prospective Investigation into Cancer and Nutrition (EPIC).<h4>Methods</h4>We conducted a prospective analysis of 490 311 men and women without a history of myocardial infarction or stroke at recruitment (12.6 years of follow-up, n cases = 8504), in 10 European countries. Dietary intake was assessed using validated questionnaires, calibrated with 24-h recalls. Multivariable Cox regressions were used to estimate hazard ratios (HR) of IHD.<h4>Results</h4>There was a lower risk of IHD with a higher intake of fruit and vegetables combined [HR per 200 g/day higher intake 0.94, 95% confidence interval (CI): 0.90-0.99, P-trend = 0.009], and with total fruits (per 100 g/day 0.97, 0.95-1.00, P-trend = 0.021). There was no evidence for a reduced risk for fruit subtypes, except for bananas. Risk was lower with higher intakes of nuts and seeds (per 10 g/day 0.90, 0.82-0.98, P-trend = 0.020), total fibre (per 10 g/day 0.91, 0.85-0.98, P-trend = 0.015), fruit and vegetable fibre (per 4 g/day 0.95, 0.91-0.99, P-trend = 0.022) and fruit fibre (per 2 g/day 0.97, 0.95-1.00, P-trend = 0.045). No associations were observed between vegetables, vegetables subtypes, legumes, cereals and IHD risk.<h4>Conclusions</h4>In this large prospective study, we found some small inverse associations between plant foods and IHD risk, with fruit and vegetables combined being the most strongly inversely associated with risk. Whether these small associations are causal remains unclear.",,pdf:https://academic.oup.com/ije/article-pdf/50/1/212/36449032/dyaa155.pdf; doi:https://doi.org/10.1093/ije/dyaa155; html:https://europepmc.org/articles/PMC7938513; pdf:https://europepmc.org/articles/PMC7938513?pdf=render
 31992634,https://doi.org/10.1136/bmjhci-2019-100117,Optimising electronic prescribing in hospitals: a scoping review protocol.,"Williams J, Bates DW, Sheikh A.",,BMJ health & care informatics,2020,2020-01-01,Y,Health care; Patient Care; Medical Informatics; Information Systems; Record Systems,,,"<h4>Introduction</h4>Electronic prescribing (ePrescribing) systems can improve the quality of prescribing decisions and substantially reduce the risk of serious medication errors in hospitals. However, realising these benefits depends on ensuring that relevant sociotechnical considerations are addressed. Optimising ePrescribing systems is essential to maximise the associated benefits and minimise the accompanying risks of these large-scale and expensive health informatics infrastructures.<h4>Methods</h4>We will undertake a systematic scoping review of the literature to identify strategies to achieve optimisation of ePrescribing systems. We will search Medline, Embase and CINAHL for the period 1 January 2010 to 1 June 2019 and the grey literature by using Google Scholar. Independent reviewers will screen the results using predefined inclusion and exclusion criteria and will extract data for narrative and thematic synthesis.<h4>Discussion</h4>This work will be published in a peer-reviewed journal and we will ensure that the findings are both accessible and interpretable to the public, academics, policymakers and National Health Service leaders.",,pdf:https://informatics.bmj.com/content/bmjhci/27/1/e100117.full.pdf; doi:https://doi.org/10.1136/bmjhci-2019-100117; html:https://europepmc.org/articles/PMC7062357; pdf:https://europepmc.org/articles/PMC7062357?pdf=render
-31922447,https://doi.org/10.1177/0141076819890551,Moving beyond project-specific patient and public involvement in research.,"Turner G, Aiyegbusi OL, Price G, Skrybant M, Calvert M.",,Journal of the Royal Society of Medicine,2020,2020-01-01,N,,,,,,pdf:https://journals.sagepub.com/doi/pdf/10.1177/0141076819890551; doi:https://doi.org/10.1177/0141076819890551; html:https://europepmc.org/articles/PMC6961168; pdf:https://europepmc.org/articles/PMC6961168?pdf=render; doi:https://doi.org/10.1177/0141076819890551
 38752762,https://doi.org/10.1093/eurjpc/zwae174,Prediction of individual lifetime cardiovascular risk and potential treatment benefit: development and recalibration of the LIFE-CVD2 model to four European risk regions.,"Hageman SHJ, Kaptoge S, de Vries TI, Lu W, Kist JM, van Os HJA, Numans ME, Läll K, Bobak M, Pikhart H, Kubinova R, Malyutina S, Pająk A, Tamosiunas A, Erbel R, Stang A, Schmidt B, Schramm S, Bolton TR, Spackman S, Bakker SJL, Blaha M, Boer JMA, Bonnefond A, Brenner H, Brunner EJ, Cook NR, Davidson K, Dennison E, Donfrancesco C, Dörr M, Floyd JS, Ford I, Fu M, Gansevoort RT, Giampaoli S, Gillum RF, Gómez-de-la-Cámara A, Håheim LL, Hansson PO, Harms P, Humphries SE, Ikram MK, Jukema JW, Kavousi M, Kiechl S, Kucharska-Newton A, Pablos DL, Matsushita K, Meyer HE, Moons KGM, Mortensen MB, Muilwijk M, Nordestgaard BG, Packard C, Pamieri L, Panagiotakos D, Peters A, Potier L, Providencia R, Psaty BM, Ridker PM, Rodriguez B, Rosengren A, Sattar N, Schöttker B, Schwartz JE, Shea S, Shipley MJ, Sofat R, Thorand B, Verschuren WMM, Völzke H, Wareham NJ, Westbury L, Willeit P, Zhou B, Danesh J, Visseren FLJ, Di Angelantonio E, Pennells L, Dorresteijn JAN.",,European journal of preventive cardiology,2024,2024-10-01,Y,Prevention; Cardiovascular disease; lifetime; Primary Prevention; Risk Prediction,,,"<h4>Aims</h4>The 2021 European Society of Cardiology prevention guidelines recommend the use of (lifetime) risk prediction models to aid decisions regarding initiation of prevention. We aimed to update and systematically recalibrate the LIFEtime-perspective CardioVascular Disease (LIFE-CVD) model to four European risk regions for the estimation of lifetime CVD risk for apparently healthy individuals.<h4>Methods and results</h4>The updated LIFE-CVD (i.e. LIFE-CVD2) models were derived using individual participant data from 44 cohorts in 13 countries (687 135 individuals without established CVD, 30 939 CVD events in median 10.7 years of follow-up). LIFE-CVD2 uses sex-specific functions to estimate the lifetime risk of fatal and non-fatal CVD events with adjustment for the competing risk of non-CVD death and is systematically recalibrated to four distinct European risk regions. The updated models showed good discrimination in external validation among 1 657 707 individuals (61 311 CVD events) from eight additional European cohorts in seven countries, with a pooled C-index of 0.795 (95% confidence interval 0.767-0.822). Predicted and observed CVD event risks were well calibrated in population-wide electronic health records data in the UK (Clinical Practice Research Datalink) and the Netherlands (Extramural LUMC Academic Network). When using LIFE-CVD2 to estimate potential gain in CVD-free life expectancy from preventive therapy, projections varied by risk region reflecting important regional differences in absolute lifetime risk. For example, a 50-year-old smoking woman with a systolic blood pressure (SBP) of 140 mmHg was estimated to gain 0.9 years in the low-risk region vs. 1.6 years in the very high-risk region from lifelong 10 mmHg SBP reduction. The benefit of smoking cessation for this individual ranged from 3.6 years in the low-risk region to 4.8 years in the very high-risk region.<h4>Conclusion</h4>By taking into account geographical differences in CVD incidence using contemporary representative data sources, the recalibrated LIFE-CVD2 model provides a more accurate tool for the prediction of lifetime risk and CVD-free life expectancy for individuals without previous CVD, facilitating shared decision-making for cardiovascular prevention as recommended by 2021 European guidelines.",,doi:https://doi.org/10.1093/eurjpc/zwae174; html:https://europepmc.org/articles/PMC11464100; pdf:https://europepmc.org/articles/PMC11464100?pdf=render
-36820079,https://doi.org/10.1183/23120541.00274-2022,Characteristics and risk factors for post-COVID-19 breathlessness after hospitalisation for COVID-19.,"Daines L, Zheng B, Elneima O, Harrison E, Lone NI, Hurst JR, Brown JS, Sapey E, Chalmers JD, Quint JK, Pfeffer P, Siddiqui S, Walker S, Poinasamy K, McAuley H, Sereno M, Shikotra A, Singapuri A, Docherty AB, Marks M, Toshner M, Howard LS, Horsley A, Jenkins G, Porter JC, Ho LP, Raman B, Wain LV, Brightling CE, Evans RA, Heaney LG, De Soyza A, Sheikh A.",,ERJ open research,2023,2023-01-01,Y,,,,"<h4>Background</h4>Persistence of respiratory symptoms, particularly breathlessness, after acute coronavirus disease 2019 (COVID-19) infection has emerged as a significant clinical problem. We aimed to characterise and identify risk factors for patients with persistent breathlessness following COVID-19 hospitalisation.<h4>Methods</h4>PHOSP-COVID is a multicentre prospective cohort study of UK adults hospitalised for COVID-19. Clinical data were collected during hospitalisation and at a follow-up visit. Breathlessness was measured by a numeric rating scale of 0-10. We defined post-COVID-19 breathlessness as an increase in score of ≥1 compared to the pre-COVID-19 level. Multivariable logistic regression was used to identify risk factors and to develop a prediction model for post-COVID-19 breathlessness.<h4>Results</h4>We included 1226 participants (37% female, median age 59 years, 22% mechanically ventilated). At a median 5 months after discharge, 50% reported post-COVID-19 breathlessness. Risk factors for post-COVID-19 breathlessness were socioeconomic deprivation (adjusted OR 1.67, 95% CI 1.14-2.44), pre-existing depression/anxiety (adjusted OR 1.58, 95% CI 1.06-2.35), female sex (adjusted OR 1.56, 95% CI 1.21-2.00) and admission duration (adjusted OR 1.01, 95% CI 1.00-1.02). Black ethnicity (adjusted OR 0.56, 95% CI 0.35-0.89) and older age groups (adjusted OR 0.31, 95% CI 0.14-0.66) were less likely to report post-COVID-19 breathlessness. Post-COVID-19 breathlessness was associated with worse performance on the shuttle walk test and forced vital capacity, but not with obstructive airflow limitation. The prediction model had fair discrimination (concordance statistic 0.66, 95% CI 0.63-0.69) and good calibration (calibration slope 1.00, 95% CI 0.80-1.21).<h4>Conclusions</h4>Post-COVID-19 breathlessness was commonly reported in this national cohort of patients hospitalised for COVID-19 and is likely to be a multifactorial problem with physical and emotional components.",,pdf:https://openres.ersjournals.com/content/erjor/early/2023/01/26/23120541.00274-2022.full.pdf; doi:https://doi.org/10.1183/23120541.00274-2022; html:https://europepmc.org/articles/PMC9790090; pdf:https://europepmc.org/articles/PMC9790090?pdf=render
+31922447,https://doi.org/10.1177/0141076819890551,Moving beyond project-specific patient and public involvement in research.,"Turner G, Aiyegbusi OL, Price G, Skrybant M, Calvert M.",,Journal of the Royal Society of Medicine,2020,2020-01-01,N,,,,,,pdf:https://journals.sagepub.com/doi/pdf/10.1177/0141076819890551; doi:https://doi.org/10.1177/0141076819890551; html:https://europepmc.org/articles/PMC6961168; pdf:https://europepmc.org/articles/PMC6961168?pdf=render; doi:https://doi.org/10.1177/0141076819890551
 31197928,https://doi.org/10.1002/pds.4811,Methods to generate and validate a Pregnancy Register in the UK Clinical Practice Research Datalink primary care database.,"Minassian C, Williams R, Meeraus WH, Smeeth L, Campbell OMR, Thomas SL.",,Pharmacoepidemiology and drug safety,2019,2019-06-13,Y,Pregnancy; United Kingdom; Pregnancy Outcome; Pharmacoepidemiology; Electronic Health Records; Pregnancy Trimesters,"Applied Analytics, The Human Phenome",,"<h4>Purpose</h4>Primary care databases are increasingly used for researching pregnancy, eg, the effects of maternal drug exposures. However, ascertaining pregnancies, their timing, and outcomes in these data is challenging. While individual studies have adopted different methods, no systematic approach to characterise all pregnancies in a primary care database has yet been published. Therefore, we developed a new algorithm to establish a Pregnancy Register in the UK Clinical Practice Research Datalink (CPRD) GOLD primary care database.<h4>Methods</h4>We compiled over 4000 read and entity codes to identify pregnancy-related records among women aged 11 to 49 years in CPRD GOLD. Codes were categorised by the stage or outcome of pregnancy to facilitate delineation of pregnancy episodes. We constructed hierarchical rule systems to handle information from multiple sources. We assessed the validity of the Register to identify pregnancy outcomes by comparing our results to linked hospitalisation records and Office for National Statistics population rates.<h4>Results</h4>Our algorithm identified 5.8 million pregnancies among 2.4 million women (January 1987-February 2018). We observed close agreement with hospitalisation data regarding completeness of pregnancy outcomes (91% sensitivity for deliveries and 77% for pregnancy losses) and their timing (median 0 days difference, interquartile range 0-2 days). Miscarriage and prematurity rates were consistent with population figures, although termination and, to a lesser extent, live birth rates were underestimated in the Register.<h4>Conclusions</h4>The Pregnancy Register offers huge research potential because of its large size, high completeness, and availability. Further validation work is underway to enhance this data resource and identify optimal approaches for its use.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pds.4811; doi:https://doi.org/10.1002/pds.4811; html:https://europepmc.org/articles/PMC6618019; pdf:https://europepmc.org/articles/PMC6618019?pdf=render
+36820079,https://doi.org/10.1183/23120541.00274-2022,Characteristics and risk factors for post-COVID-19 breathlessness after hospitalisation for COVID-19.,"Daines L, Zheng B, Elneima O, Harrison E, Lone NI, Hurst JR, Brown JS, Sapey E, Chalmers JD, Quint JK, Pfeffer P, Siddiqui S, Walker S, Poinasamy K, McAuley H, Sereno M, Shikotra A, Singapuri A, Docherty AB, Marks M, Toshner M, Howard LS, Horsley A, Jenkins G, Porter JC, Ho LP, Raman B, Wain LV, Brightling CE, Evans RA, Heaney LG, De Soyza A, Sheikh A.",,ERJ open research,2023,2023-01-01,Y,,,,"<h4>Background</h4>Persistence of respiratory symptoms, particularly breathlessness, after acute coronavirus disease 2019 (COVID-19) infection has emerged as a significant clinical problem. We aimed to characterise and identify risk factors for patients with persistent breathlessness following COVID-19 hospitalisation.<h4>Methods</h4>PHOSP-COVID is a multicentre prospective cohort study of UK adults hospitalised for COVID-19. Clinical data were collected during hospitalisation and at a follow-up visit. Breathlessness was measured by a numeric rating scale of 0-10. We defined post-COVID-19 breathlessness as an increase in score of ≥1 compared to the pre-COVID-19 level. Multivariable logistic regression was used to identify risk factors and to develop a prediction model for post-COVID-19 breathlessness.<h4>Results</h4>We included 1226 participants (37% female, median age 59 years, 22% mechanically ventilated). At a median 5 months after discharge, 50% reported post-COVID-19 breathlessness. Risk factors for post-COVID-19 breathlessness were socioeconomic deprivation (adjusted OR 1.67, 95% CI 1.14-2.44), pre-existing depression/anxiety (adjusted OR 1.58, 95% CI 1.06-2.35), female sex (adjusted OR 1.56, 95% CI 1.21-2.00) and admission duration (adjusted OR 1.01, 95% CI 1.00-1.02). Black ethnicity (adjusted OR 0.56, 95% CI 0.35-0.89) and older age groups (adjusted OR 0.31, 95% CI 0.14-0.66) were less likely to report post-COVID-19 breathlessness. Post-COVID-19 breathlessness was associated with worse performance on the shuttle walk test and forced vital capacity, but not with obstructive airflow limitation. The prediction model had fair discrimination (concordance statistic 0.66, 95% CI 0.63-0.69) and good calibration (calibration slope 1.00, 95% CI 0.80-1.21).<h4>Conclusions</h4>Post-COVID-19 breathlessness was commonly reported in this national cohort of patients hospitalised for COVID-19 and is likely to be a multifactorial problem with physical and emotional components.",,pdf:https://openres.ersjournals.com/content/erjor/early/2023/01/26/23120541.00274-2022.full.pdf; doi:https://doi.org/10.1183/23120541.00274-2022; html:https://europepmc.org/articles/PMC9790090; pdf:https://europepmc.org/articles/PMC9790090?pdf=render
 33879482,https://doi.org/10.1136/bmjopen-2020-042949,"Gender differences in clinical presentation and illicit substance use during first episode psychosis: a natural language processing, electronic case register study.","Irving J, Colling C, Shetty H, Pritchard M, Stewart R, Fusar-Poli P, McGuire P, Patel R.",,BMJ open,2021,2021-04-20,Y,Substance Misuse; Health Informatics; Schizophrenia & Psychotic Disorders,,,"<h4>Objective</h4>To determine whether gender differences in symptom presentation at first episode psychosis (FEP) remain even when controlling for substance use, age and ethnicity, using natural language processing applied to electronic health records (EHRs).<h4>Design, setting and participants</h4>Data were extracted from EHRs of 3350 people (62% male patients) who had presented to the South London and Maudsley NHS Trust with a FEP between 1 April 2007 and 31 March 2017. Logistic regression was used to examine gender differences in the presentation of positive, negative, depressive, mania and disorganisation symptoms.<h4>Exposures for observational studies</h4>Gender (male vs female).<h4>Main outcomes and measures</h4>Presence of positive, negative, depressive, mania and disorganisation symptoms at initial clinical presentation.<h4>Results</h4>Eight symptoms were significantly more prevalent in men (poverty of thought, negative symptoms, social withdrawal, poverty of speech, aggression, grandiosity, paranoia and agitation). Conversely, tearfulness, low energy, reduced appetite, low mood, pressured speech, mood instability, flight of ideas, guilt, mutism, insomnia, poor concentration, tangentiality and elation were more prevalent in women than men. Negative symptoms were more common among men (OR 1.85, 95% CI 1.33 to 2.62) and depressive and manic symptoms more common among women (OR 0.30, 95% CI 0.26 to 0.35). After adjustment for illicit substance use, the strength of associations between gender and negative, manic and depression symptoms increased, whereas gender differences in aggression, agitation, paranoia and grandiosity became insignificant.<h4>Conclusions</h4>There are clear gender differences in the clinical presentation of FEP. Our findings suggest that gender can have a substantial influence on the nature of clinical presentation in people with psychosis, and that this is only partly explained by exposure to illicit substance use.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/4/e042949.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-042949; html:https://europepmc.org/articles/PMC8061860; pdf:https://europepmc.org/articles/PMC8061860?pdf=render
 36269859,https://doi.org/10.1073/pnas.2206083119,Metabolome-wide association study on <i>ABCA7</i> indicates a role of ceramide metabolism in Alzheimer's disease.,"Dehghan A, Pinto RC, Karaman I, Huang J, Durainayagam BR, Ghanbari M, Nazeer A, Zhong Q, Liggi S, Whiley L, Mustafa R, Kivipelto M, Solomon A, Ngandu T, Kanekiyo T, Aikawa T, Radulescu CI, Barnes SJ, Graça G, Chekmeneva E, Camuzeaux S, Lewis MR, Kaluarachchi MR, Ikram MA, Holmes E, Tzoulaki I, Matthews PM, Griffin JL, Elliott P.",,Proceedings of the National Academy of Sciences of the United States of America,2022,2022-10-21,Y,Ceramide; Alzheimer’s disease; Metabolomics; Genome-wide Association Study; Abca7,,,"Genome-wide association studies (GWASs) have identified genetic loci associated with the risk of Alzheimer's disease (AD), but the molecular mechanisms by which they confer risk are largely unknown. We conducted a metabolome-wide association study (MWAS) of AD-associated loci from GWASs using untargeted metabolic profiling (metabolomics) by ultraperformance liquid chromatography-mass spectrometry (UPLC-MS). We identified an association of lactosylceramides (LacCer) with AD-related single-nucleotide polymorphisms (SNPs) in <i>ABCA7</i> (<i>P</i> = 5.0 × 10<sup>-5</sup> to 1.3 × 10<sup>-44</sup>). We showed that plasma LacCer concentrations are associated with cognitive performance and genetically modified levels of LacCer are associated with AD risk. We then showed that concentrations of sphingomyelins, ceramides, and hexosylceramides were altered in brain tissue from <i>Abca7</i> knockout mice, compared with wild type (WT) (<i>P</i> = 0.049-1.4 × 10<sup>-5</sup>), but not in a mouse model of amyloidosis. Furthermore, activation of microglia increases intracellular concentrations of hexosylceramides in part through induction in the expression of sphingosine kinase, an enzyme with a high control coefficient for sphingolipid and ceramide synthesis. Our work suggests that the risk for AD arising from functional variations in <i>ABCA7</i> is mediated at least in part through ceramides. Modulation of their metabolism or downstream signaling may offer new therapeutic opportunities for AD.",,doi:https://doi.org/10.1073/pnas.2206083119; doi:https://doi.org/10.1073/pnas.2206083119; html:https://europepmc.org/articles/PMC9618092; pdf:https://europepmc.org/articles/PMC9618092?pdf=render
 35617980,https://doi.org/10.1016/s0140-6736(22)00532-3,Measuring the availability of human resources for health and its relationship to universal health coverage for 204 countries and territories from 1990 to 2019: a systematic analysis for the Global Burden of Disease Study 2019.,GBD 2019 Human Resources for Health Collaborators.,,"Lancet (London, England)",2022,2022-05-23,Y,,,,"<h4>Background</h4>Human resources for health (HRH) include a range of occupations that aim to promote or improve human health. The UN Sustainable Development Goals (SDGs) and the WHO Health Workforce 2030 strategy have drawn attention to the importance of HRH for achieving policy priorities such as universal health coverage (UHC). Although previous research has found substantial global disparities in HRH, the absence of comparable cross-national estimates of existing workforces has hindered efforts to quantify workforce requirements to meet health system goals. We aimed to use comparable and standardised data sources to estimate HRH densities globally, and to examine the relationship between a subset of HRH cadres and UHC effective coverage performance.<h4>Methods</h4>Through the International Labour Organization and Global Health Data Exchange databases, we identified 1404 country-years of data from labour force surveys and 69 country-years of census data, with detailed microdata on health-related employment. From the WHO National Health Workforce Accounts, we identified 2950 country-years of data. We mapped data from all occupational coding systems to the International Standard Classification of Occupations 1988 (ISCO-88), allowing for standardised estimation of densities for 16 categories of health workers across the full time series. Using data from 1990 to 2019 for 196 of 204 countries and territories, covering seven Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) super-regions and 21 regions, we applied spatiotemporal Gaussian process regression (ST-GPR) to model HRH densities from 1990 to 2019 for all countries and territories. We used stochastic frontier meta-regression to model the relationship between the UHC effective coverage index and densities for the four categories of health workers enumerated in SDG indicator 3.c.1 pertaining to HRH: physicians, nurses and midwives, dentistry personnel, and pharmaceutical personnel. We identified minimum workforce density thresholds required to meet a specified target of 80 out of 100 on the UHC effective coverage index, and quantified national shortages with respect to those minimum thresholds.<h4>Findings</h4>We estimated that, in 2019, the world had 104·0 million (95% uncertainty interval 83·5-128·0) health workers, including 12·8 million (9·7-16·6) physicians, 29·8 million (23·3-37·7) nurses and midwives, 4·6 million (3·6-6·0) dentistry personnel, and 5·2 million (4·0-6·7) pharmaceutical personnel. We calculated a global physician density of 16·7 (12·6-21·6) per 10 000 population, and a nurse and midwife density of 38·6 (30·1-48·8) per 10 000 population. We found the GBD super-regions of sub-Saharan Africa, south Asia, and north Africa and the Middle East had the lowest HRH densities. To reach 80 out of 100 on the UHC effective coverage index, we estimated that, per 10 000 population, at least 20·7 physicians, 70·6 nurses and midwives, 8·2 dentistry personnel, and 9·4 pharmaceutical personnel would be needed. In total, the 2019 national health workforces fell short of these minimum thresholds by 6·4 million physicians, 30·6 million nurses and midwives, 3·3 million dentistry personnel, and 2·9 million pharmaceutical personnel.<h4>Interpretation</h4>Considerable expansion of the world's health workforce is needed to achieve high levels of UHC effective coverage. The largest shortages are in low-income settings, highlighting the need for increased financing and coordination to train, employ, and retain human resources in the health sector. Actual HRH shortages might be larger than estimated because minimum thresholds for each cadre of health workers are benchmarked on health systems that most efficiently translate human resources into UHC attainment.<h4>Funding</h4>Bill & Melinda Gates Foundation.",,pdf:http://www.thelancet.com/article/S0140673622005323/pdf; doi:https://doi.org/10.1016/S0140-6736(22)00532-3; html:https://europepmc.org/articles/PMC9168805
@@ -2549,8 +2551,8 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 33847595,https://doi.org/10.2196/22397,Using General-purpose Sentiment Lexicons for Suicide Risk Assessment in Electronic Health Records: Corpus-Based Analysis.,"Bittar A, Velupillai S, Roberts A, Dutta R.",,JMIR medical informatics,2021,2021-04-13,Y,"Psychiatry; risk assessment; Suicide; Electronic Health Records; Natural Language Processing; Suicide, Attempted; Sentiment Analysis; Corpus Linguistics",,,"<h4>Background</h4>Suicide is a serious public health issue, accounting for 1.4% of all deaths worldwide. Current risk assessment tools are reported as performing little better than chance in predicting suicide. New methods for studying dynamic features in electronic health records (EHRs) are being increasingly explored. One avenue of research involves using sentiment analysis to examine clinicians' subjective judgments when reporting on patients. Several recent studies have used general-purpose sentiment analysis tools to automatically identify negative and positive words within EHRs to test correlations between sentiment extracted from the texts and specific medical outcomes (eg, risk of suicide or in-hospital mortality). However, little attention has been paid to analyzing the specific words identified by general-purpose sentiment lexicons when applied to EHR corpora.<h4>Objective</h4>This study aims to quantitatively and qualitatively evaluate the coverage of six general-purpose sentiment lexicons against a corpus of EHR texts to ascertain the extent to which such lexical resources are fit for use in suicide risk assessment.<h4>Methods</h4>The data for this study were a corpus of 198,451 EHR texts made up of two subcorpora drawn from a 1:4 case-control study comparing clinical notes written over the period leading up to a suicide attempt (cases, n=2913) with those not preceding such an attempt (controls, n=14,727). We calculated word frequency distributions within each subcorpus to identify representative keywords for both the case and control subcorpora. We quantified the relative coverage of the 6 lexicons with respect to this list of representative keywords in terms of weighted precision, recall, and F score.<h4>Results</h4>The six lexicons achieved reasonable precision (0.53-0.68) but very low recall (0.04-0.36). Many of the most representative keywords in the suicide-related (case) subcorpus were not identified by any of the lexicons. The sentiment-bearing status of these keywords for this use case is thus doubtful.<h4>Conclusions</h4>Our findings indicate that these 6 sentiment lexicons are not optimal for use in suicide risk assessment. We propose a set of guidelines for the creation of more suitable lexical resources for distinguishing suicide-related from non-suicide-related EHR texts.",,pdf:https://medinform.jmir.org/2021/4/e22397/PDF; doi:https://doi.org/10.2196/22397; html:https://europepmc.org/articles/PMC8080148
 37067557,https://doi.org/10.1007/s00134-023-07039-2,Variants of concern and clinical outcomes in critically ill COVID-19 patients.,DP-EFFECT-BRAZIL investigators.,,Intensive care medicine,2023,2023-04-17,Y,,,,,,pdf:https://link.springer.com/content/pdf/10.1007/s00134-023-07039-2.pdf; doi:https://doi.org/10.1007/s00134-023-07039-2; html:https://europepmc.org/articles/PMC10108805; pdf:https://europepmc.org/articles/PMC10108805?pdf=render
 36527096,https://doi.org/10.1186/s12910-022-00875-9,"""Data makes the story come to life:"" understanding the ethical and legal implications of Big Data research involving ethnic minority healthcare workers in the United Kingdom-a qualitative study.","Dove ES, Reed-Berendt R, Pareek M, UK-REACH Study Collaborative Group.",,BMC medical ethics,2022,2022-12-16,Y,Ethics; Public Health; United Kingdom; Healthcare Workers; Ethnic Minorities; Big Data; Covid-19,,,"The aim of UK-REACH (""The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers"") is to understand if, how, and why healthcare workers (HCWs) in the United Kingdom (UK) from ethnic minority groups are at increased risk of poor outcomes from COVID-19. In this article, we present findings from the ethical and legal stream of the study, which undertook qualitative research seeking to understand and address legal, ethical, and social acceptability issues around data protection, privacy, and information governance associated with the linkage of HCWs' registration data and healthcare data. We interviewed 22 key opinion leaders in healthcare and health research from across the UK in two-to-one semi-structured interviews. Transcripts were coded using qualitative thematic analysis. Participants told us that a significant aspect of Big Data research in public health is varying drivers of mistrust-of the research itself, research staff and funders, and broader concerns of mistrust within participant communities, particularly in the context of COVID-19 and those situated in more marginalised community settings. However, despite the challenges, participants also identified ways in which legally compliant and ethically informed approaches to research can be crafted to mitigate or overcome mistrust and establish greater confidence in Big Data public health research. Overall, our research indicates that a ""Big Data Ethics by Design"" approach to research in this area can help assure (1) that meaningful community and participant engagement is taking place and that extant challenges are addressed, and (2) that any new challenges or hitherto unknown unknowns can be rapidly and properly considered to ensure potential (but material) harms are identified and minimised where necessary. Our findings indicate such an approach, in turn, will help drive better scientific breakthroughs that translate into medical innovations and effective public health interventions, which benefit the publics studied, including those who are often marginalised in research.",,pdf:https://bmcmedethics.biomedcentral.com/counter/pdf/10.1186/s12910-022-00875-9; doi:https://doi.org/10.1186/s12910-022-00875-9; html:https://europepmc.org/articles/PMC9756740; pdf:https://europepmc.org/articles/PMC9756740?pdf=render
-36522333,https://doi.org/10.1038/s41467-022-35454-4,Multi-omics identify falling LRRC15 as a COVID-19 severity marker and persistent pro-thrombotic signals in convalescence.,"Gisby JS, Buang NB, Papadaki A, Clarke CL, Malik TH, Medjeral-Thomas N, Pinheiro D, Mortimer PM, Lewis S, Sandhu E, McAdoo SP, Prendecki MF, Willicombe M, Pickering MC, Botto M, Thomas DC, Peters JE.",,Nature communications,2022,2022-12-15,Y,,,,"Patients with end-stage kidney disease (ESKD) are at high risk of severe COVID-19. Here, we perform longitudinal blood sampling of ESKD haemodialysis patients with COVID-19, collecting samples pre-infection, serially during infection, and after clinical recovery. Using plasma proteomics, and RNA-sequencing and flow cytometry of immune cells, we identify transcriptomic and proteomic signatures of COVID-19 severity, and find distinct temporal molecular profiles in patients with severe disease. Supervised learning reveals that the plasma proteome is a superior indicator of clinical severity than the PBMC transcriptome. We show that a decreasing trajectory of plasma LRRC15, a proposed co-receptor for SARS-CoV-2, is associated with a more severe clinical course. We observe that two months after the acute infection, patients still display dysregulated gene expression related to vascular, platelet and coagulation pathways, including PF4 (platelet factor 4), which may explain the prolonged thrombotic risk following COVID-19.",,pdf:https://www.nature.com/articles/s41467-022-35454-4.pdf; doi:https://doi.org/10.1038/s41467-022-35454-4; html:https://europepmc.org/articles/PMC9753891; pdf:https://europepmc.org/articles/PMC9753891?pdf=render
 31350032,https://doi.org/10.1016/j.burns.2019.07.003,"Epidemiology of burn-related fatalities in Australia and New Zealand, 2009-2015.","McInnes JA, Cleland HJ, Cameron PA, Darton A, Tracy LM, Wood FM, Singer Y, Gabbe BJ.",,Burns : journal of the International Society for Burn Injuries,2019,2019-07-24,N,Burns; Mortality; Australia; New Zealand; epidemiology; Fatality,,,"<h4>Background</h4>Knowledge of the epidemiology of burn-related fatalities is limited, with most previous studies based on hospital and burn centre data only.<h4>Aims</h4>To describe the epidemiological characteristics of all burn-related fatalities in Australia and New Zealand, and to identify any trends in burn-related fatality incidence over the study period.<h4>Methods</h4>Data from the National Coronial Information System, including data for pre-hospital and in-hospital burn-related fatality cases, was used to examine the characteristics of burn-related fatalities occurring in Australia and New Zealand from 2009 to 2015. Burn-related fatality rates per 100,000 population were estimated, and incidence trends assessed using Poisson regression analysis.<h4>Results</h4>Of the 310 burn-related fatalities that occurred in Australia and New Zealand, 2009-2015, 41% occurred in a pre-hospital setting. Overall, most burn-related fatality cases were fire related, occurred at home, and were of people aged 41-80 years. One quarter of all burn-related fatalities were a result of intentional self-harm. The population incidence of all burn-related fatalities combined, and for NSW, decreased over the study period.<h4>Conclusions</h4>This study has identified the importance of examining all burn-related fatalities. If this is not done, vulnerable population subgroups will be missed and prevention efforts poorly targeted.",,doi:https://doi.org/10.1016/j.burns.2019.07.003
+36522333,https://doi.org/10.1038/s41467-022-35454-4,Multi-omics identify falling LRRC15 as a COVID-19 severity marker and persistent pro-thrombotic signals in convalescence.,"Gisby JS, Buang NB, Papadaki A, Clarke CL, Malik TH, Medjeral-Thomas N, Pinheiro D, Mortimer PM, Lewis S, Sandhu E, McAdoo SP, Prendecki MF, Willicombe M, Pickering MC, Botto M, Thomas DC, Peters JE.",,Nature communications,2022,2022-12-15,Y,,,,"Patients with end-stage kidney disease (ESKD) are at high risk of severe COVID-19. Here, we perform longitudinal blood sampling of ESKD haemodialysis patients with COVID-19, collecting samples pre-infection, serially during infection, and after clinical recovery. Using plasma proteomics, and RNA-sequencing and flow cytometry of immune cells, we identify transcriptomic and proteomic signatures of COVID-19 severity, and find distinct temporal molecular profiles in patients with severe disease. Supervised learning reveals that the plasma proteome is a superior indicator of clinical severity than the PBMC transcriptome. We show that a decreasing trajectory of plasma LRRC15, a proposed co-receptor for SARS-CoV-2, is associated with a more severe clinical course. We observe that two months after the acute infection, patients still display dysregulated gene expression related to vascular, platelet and coagulation pathways, including PF4 (platelet factor 4), which may explain the prolonged thrombotic risk following COVID-19.",,pdf:https://www.nature.com/articles/s41467-022-35454-4.pdf; doi:https://doi.org/10.1038/s41467-022-35454-4; html:https://europepmc.org/articles/PMC9753891; pdf:https://europepmc.org/articles/PMC9753891?pdf=render
 37923486,https://doi.org/10.1016/s2352-3018(23)00233-3,Integrase strand-transfer inhibitor use and cardiovascular events in adults with HIV: an emulation of target trials in the HIV-CAUSAL Collaboration and the Antiretroviral Therapy Cohort Collaboration.,"Rein SM, Lodi S, Logan RW, Touloumi G, Antoniadou A, Wittkop L, Bonnet F, van Sighem A, van der Valk M, Reiss P, Klein MB, Young J, Jarrin I, d'Arminio Monforte A, Tavelli A, Meyer L, Tran L, Gill MJ, Lang R, Surial B, Haas AD, Justice AC, Rentsch CT, Phillips A, Sabin CA, Miro JM, Trickey A, Ingle SM, Sterne JAC, Hernán MA, Antiretroviral Therapy Cohort Collaboration and the HIV-CAUSAL Collaboration.",,The lancet. HIV,2023,2023-11-01,N,,,,"<h4>Background</h4>A recent observational study suggested that the risk of cardiovascular events could be higher among antiretroviral therapy (ART)-naive individuals with HIV who receive integrase strand-transfer inhibitor (INSTI)-based ART than among those who receive other ART regimens. We aimed to emulate target trials separately in ART-naive and ART-experienced individuals with HIV to examine the effect of using INSTI-based regimens versus other ART regimens on the 4-year risk of cardiovascular events.<h4>Methods</h4>We used routinely recorded clinical data from 12 cohorts that collected information on cardiovascular events, BMI, and blood pressure from two international consortia of cohorts of people with HIV from Europe and North America. For the target trial in individuals who had previously never used ART (ie, ART-naive), eligibility criteria were aged 18 years or older, a detectable HIV-RNA measurement while ART-naive (>50 copies per mL), and no history of a cardiovascular event or cancer. Eligibility criteria for the target trial in those with previous use of non-INSTI-based ART (ie, ART-experienced) were the same except that individuals had to have been on at least one non-INSTI-based ART regimen and be virally suppressed (≤50 copies per mL). We assessed eligibility for both trials for each person-month between January, 2013, and January, 2023, and assigned individuals to the treatment strategy that was compatible with their data. We estimated the standardised 4-year risks of cardiovascular events (myocardial infarction, stroke, or invasive cardiovascular procedure) via pooled logistic regression models adjusting for time and baseline covariates. In per-protocol analyses, we censored individuals if they deviated from their assigned treatment strategy for more than 2 months and weighted uncensored individuals by the inverse of their time-varying probability of remaining uncensored. The denominator of the weight was estimated via a pooled logistic model that included baseline and time-varying covariates.<h4>Findings</h4>The analysis in ART-naive individuals included 10 767 INSTI initiators and 8292 non-initiators of INSTI. There were 43 cardiovascular events in INSTI initiators (median follow-up of 29 months; IQR 15-45) and 52 in non-initiators (39 months; 18-47): standardised 4-year risks were 0·76% (95% CI 0·51 to 1·04) in INSTI initiators and 0·75% (0·54 to 0·98) in non-INSTI initiators; risk ratio 1·01 (0·57 to 1·57); risk difference 0·0089% (-0·43 to 0·36). The analysis in ART-experienced individuals included 7875 INSTI initiators and 373 965 non-initiators. There were 56 events in INSTI initiators (median follow-up 18 months; IQR 9-29) and 3103 events (808 unique) in non-INSTI initiators (26 months; 15-37) in non-initiators: standardised 4-year risks 1·41% (95% CI 0·88 to 2·03) in INSTI initiators and 1·48% (1·28 to 1·71) in non-initiators; risk ratio 0·95 (0·60 to 1·36); risk difference -0·068% (-0·60 to 0·52).<h4>Interpretation</h4>We estimated that INSTI use did not result in a clinically meaningful increase of cardiovascular events in ART-naive and ART-experienced individuals with HIV.<h4>Funding</h4>National Institute of Allergy and Infectious Diseases and National Institute on Alcohol Abuse and Alcoholism.",,pdf:https://research-information.bris.ac.uk/files/382068016/Rev2_clean_InstiCVD.pdf; doi:https://doi.org/10.1016/S2352-3018(23)00233-3
 32156302,https://doi.org/10.1186/s13326-020-00220-2,Temporal information extraction from mental health records to identify duration of untreated psychosis.,"Viani N, Kam J, Yin L, Bittar A, Dutta R, Patel R, Stewart R, Velupillai S.",,Journal of biomedical semantics,2020,2020-03-10,Y,Schizophrenia; Mental health; Electronic Health Records; Natural Language Processing; Temporal Information Extraction,,,"<h4>Background</h4>Duration of untreated psychosis (DUP) is an important clinical construct in the field of mental health, as longer DUP can be associated with worse intervention outcomes. DUP estimation requires knowledge about when psychosis symptoms first started (symptom onset), and when psychosis treatment was initiated. Electronic health records (EHRs) represent a useful resource for retrospective clinical studies on DUP, but the core information underlying this construct is most likely to lie in free text, meaning it is not readily available for clinical research. Natural Language Processing (NLP) is a means to addressing this problem by automatically extracting relevant information in a structured form. As a first step, it is important to identify appropriate documents, i.e., those that are likely to include the information of interest. Next, temporal information extraction methods are needed to identify time references for early psychosis symptoms. This NLP challenge requires solving three different tasks: time expression extraction, symptom extraction, and temporal ""linking"". In this study, we focus on the first step, using two relevant EHR datasets.<h4>Results</h4>We applied a rule-based NLP system for time expression extraction that we had previously adapted to a corpus of mental health EHRs from patients with a diagnosis of schizophrenia (first referrals). We extended this work by applying this NLP system to a larger set of documents and patients, to identify additional texts that would be relevant for our long-term goal, and developed a new corpus from a subset of these new texts (early intervention services). Furthermore, we added normalized value annotations (""2011-05"") to the annotated time expressions (""May 2011"") in both corpora. The finalized corpora were used for further NLP development and evaluation, with promising results (normalization accuracy 71-86%). To highlight the specificities of our annotation task, we also applied the final adapted NLP system to a different temporally annotated clinical corpus.<h4>Conclusions</h4>Developing domain-specific methods is crucial to address complex NLP tasks such as symptom onset extraction and retrospective calculation of duration of a preclinical syndrome. To the best of our knowledge, this is the first clinical text resource annotated for temporal entities in the mental health domain.",,pdf:https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-020-00220-2; doi:https://doi.org/10.1186/s13326-020-00220-2; html:https://europepmc.org/articles/PMC7063705; pdf:https://europepmc.org/articles/PMC7063705?pdf=render
 37173061,https://doi.org/10.1016/j.ajcnut.2022.12.021,"Evidence for human milk as a biological system and recommendations for study design-a report from ""Breastmilk Ecology: Genesis of Infant Nutrition (BEGIN)"" Working Group 4.","Donovan SM, Aghaeepour N, Andres A, Azad MB, Becker M, Carlson SE, Järvinen KM, Lin W, Lönnerdal B, Slupsky CM, Steiber AL, Raiten DJ.",,The American journal of clinical nutrition,2023,2023-04-01,Y,Immune; systems biology; Human Milk; Microbiome; Infant Development,,,"Human milk contains all of the essential nutrients required by the infant within a complex matrix that enhances the bioavailability of many of those nutrients. In addition, human milk is a source of bioactive components, living cells and microbes that facilitate the transition to life outside the womb. Our ability to fully appreciate the importance of this matrix relies on the recognition of short- and long-term health benefits and, as highlighted in previous sections of this supplement, its ecology (i.e., interactions among the lactating parent and breastfed infant as well as within the context of the human milk matrix itself). Designing and interpreting studies to address this complexity depends on the availability of new tools and technologies that account for such complexity. Past efforts have often compared human milk to infant formula, which has provided some insight into the bioactivity of human milk, as a whole, or of individual milk components supplemented with formula. However, this experimental approach cannot capture the contributions of the individual components to the human milk ecology, the interaction between these components within the human milk matrix, or the significance of the matrix itself to enhance human milk bioactivity on outcomes of interest. This paper presents approaches to explore human milk as a biological system and the functional implications of that system and its components. Specifically, we discuss study design and data collection considerations and how emerging analytical technologies, bioinformatics, and systems biology approaches could be applied to advance our understanding of this critical aspect of human biology.",,doi:https://doi.org/10.1016/j.ajcnut.2022.12.021; html:https://europepmc.org/articles/PMC10356565; pdf:https://europepmc.org/articles/PMC10356565?pdf=render
@@ -2566,23 +2568,23 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 32283057,https://doi.org/10.1016/j.jid.2020.03.957,"Clinical Impact of Antibodies against Ustekinumab in Psoriasis: An Observational, Cross-Sectional, Multicenter Study.","Loeff FC, Tsakok T, Dijk L, Hart MH, Duckworth M, Baudry D, Russell A, Dand N, van Leeuwen A, Griffiths CEM, Reynolds NJ, Barker J, Burden AD, Warren RB, de Vries A, Bloem K, Wolbink GJ, Smith CH, Rispens T, BADBIR, BSTOP Study Groups, PSORT consortium.",,The Journal of investigative dermatology,2020,2020-04-10,N,,,,"Ustekinumab is an effective treatment for psoriasis, but response varies between patients. The formation of anti-drug antibodies (ADAs) may explain part of this variation by reducing the free ustekinumab level. Currently, published analyses of the clinical impact of ADAs are incomplete. In this observational cross-sectional multicenter study of 340 patients, we evaluated the impact of ADAs on ustekinumab level and clinical response as assessed by the PASI. Circulating ADA levels were measured using two assays: a drug-sensitive radioimmunoassay and a drug-tolerant ELISA. Circulating ustekinumab levels were measured using an ELISA. ADAs were detected in 3.8% (95% confidence interval [CI] = 3.2-4.2) and in 10.6% (95% CI = 7.9-13.9) of patients using the radioimmunoassay and drug-tolerant ELISA, respectively. At least 85% of the ADAs were neutralizing. Compared with patients negative for ADAs, ADA positivity in the radioimmunoassay and drug-tolerant ELISA were associated with lower median ustekinumab levels (-0.62 μg/ml [95% CI = -1.190 to -0.30] and -0.74 μg/ml [95% CI = -1.09 to -0.47], respectively) and higher absolute PASI (6.6 [95% CI = 3.0-9.9] and 1.9 [95% CI = 0.4-4.0], respectively). Absence of detectable ustekinumab regardless of ADA status correlated with poor clinical outcome (median sample PASI 10.1, 6.5 [95% CI = 3.9-8.8] compared with patients positive for ustekinumab). In conclusion, substantially reduced drug exposure resulting from ADAs formation is associated with impaired clinical response.",,doi:https://doi.org/10.1016/j.jid.2020.03.957; doi:https://doi.org/10.1016/j.jid.2020.03.957
 36914875,https://doi.org/10.1038/s41588-023-01314-0,Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk.,"Shrine N, Izquierdo AG, Chen J, Packer R, Hall RJ, Guyatt AL, Batini C, Thompson RJ, Pavuluri C, Malik V, Hobbs BD, Moll M, Kim W, Tal-Singer R, Bakke P, Fawcett KA, John C, Coley K, Piga NN, Pozarickij A, Lin K, Millwood IY, Chen Z, Li L, China Kadoorie Biobank Collaborative Group, Wijnant SRA, Lahousse L, Brusselle G, Uitterlinden AG, Manichaikul A, Oelsner EC, Rich SS, Barr RG, Kerr SM, Vitart V, Brown MR, Wielscher M, Imboden M, Jeong A, Bartz TM, Gharib SA, Flexeder C, Karrasch S, Gieger C, Peters A, Stubbe B, Hu X, Ortega VE, Meyers DA, Bleecker ER, Gabriel SB, Gupta N, Smith AV, Luan J, Zhao JH, Hansen AF, Langhammer A, Willer C, Bhatta L, Porteous D, Smith BH, Campbell A, Sofer T, Lee J, Daviglus ML, Yu B, Lim E, Xu H, O'Connor GT, Thareja G, Albagha OME, Qatar Genome Program Research (QGPR) Consortium, Suhre K, Granell R, Faquih TO, Hiemstra PS, Slats AM, Mullin BH, Hui J, James A, Beilby J, Patasova K, Hysi P, Koskela JT, Wyss AB, Jin J, Sikdar S, Lee M, May-Wilson S, Pirastu N, Kentistou KA, Joshi PK, Timmers PRHJ, Williams AT, Free RC, Wang X, Morrison JL, Gilliland FD, Chen Z, Wang CA, Foong RE, Harris SE, Taylor A, Redmond P, Cook JP, Mahajan A, Lind L, Palviainen T, Lehtimäki T, Raitakari OT, Kaprio J, Rantanen T, Pietiläinen KH, Cox SR, Pennell CE, Hall GL, Gauderman WJ, Brightling C, Wilson JF, Vasankari T, Laitinen T, Salomaa V, Mook-Kanamori DO, Timpson NJ, Zeggini E, Dupuis J, Hayward C, Brumpton B, Langenberg C, Weiss S, Homuth G, Schmidt CO, Probst-Hensch N, Jarvelin MR, Morrison AC, Polasek O, Rudan I, Lee JH, Sayers I, Rawlins EL, Dudbridge F, Silverman EK, Strachan DP, Walters RG, Morris AP, London SJ, Cho MH, Wain LV, Hall IP, Tobin MD.",,Nature genetics,2023,2023-03-13,Y,,,,"Lung-function impairment underlies chronic obstructive pulmonary disease (COPD) and predicts mortality. In the largest multi-ancestry genome-wide association meta-analysis of lung function to date, comprising 580,869 participants, we identified 1,020 independent association signals implicating 559 genes supported by ≥2 criteria from a systematic variant-to-gene mapping framework. These genes were enriched in 29 pathways. Individual variants showed heterogeneity across ancestries, age and smoking groups, and collectively as a genetic risk score showed strong association with COPD across ancestry groups. We undertook phenome-wide association studies for selected associated variants as well as trait and pathway-specific genetic risk scores to infer possible consequences of intervening in pathways underlying lung function. We highlight new putative causal variants, genes, proteins and pathways, including those targeted by existing drugs. These findings bring us closer to understanding the mechanisms underlying lung function and COPD, and should inform functional genomics experiments and potentially future COPD therapies.",,pdf:https://www.nature.com/articles/s41588-023-01314-0.pdf; doi:https://doi.org/10.1038/s41588-023-01314-0; html:https://europepmc.org/articles/PMC10011137; pdf:https://europepmc.org/articles/PMC10011137?pdf=render
 37263751,https://doi.org/10.1183/13993003.01667-2022,Genome-wide association study of chronic sputum production implicates loci involved in mucus production and infection.,"Packer RJ, Shrine N, Hall R, Melbourne CA, Thompson R, Williams AT, Paynton ML, Guyatt AL, Allen RJ, Lee PH, John C, Campbell A, Hayward C, de Vries M, Vonk JM, Davitte J, Hessel E, Michalovich D, Betts JC, Sayers I, Yeo A, Hall IP, Tobin MD, Wain LV.",,The European respiratory journal,2023,2023-06-15,Y,,,,"<h4>Background</h4>Chronic sputum production impacts on quality of life and is a feature of many respiratory diseases. Identification of the genetic variants associated with chronic sputum production in a disease agnostic sample could improve understanding of its causes and identify new molecular targets for treatment.<h4>Methods</h4>We conducted a genome-wide association study (GWAS) of chronic sputum production in UK Biobank. Signals meeting genome-wide significance (p<5×10<sup>-8</sup>) were investigated in additional independent studies, were fine-mapped and putative causal genes identified by gene expression analysis. GWASs of respiratory traits were interrogated to identify whether the signals were driven by existing respiratory disease among the cases and variants were further investigated for wider pleiotropic effects using phenome-wide association studies (PheWASs).<h4>Results</h4>From a GWAS of 9714 cases and 48 471 controls, we identified six novel genome-wide significant signals for chronic sputum production including signals in the human leukocyte antigen (HLA) locus, chromosome 11 mucin locus (containing <i>MUC2</i>, <i>MUC5AC</i> and <i>MUC5B</i>) and <i>FUT2</i> locus. The four common variant associations were supported by independent studies with a combined sample size of up to 2203 cases and 17 627 controls. The mucin locus signal had previously been reported for association with moderate-to-severe asthma. The HLA signal was fine-mapped to an amino acid change of threonine to arginine (frequency 36.8%) in HLA-DRB1 (<i>HLA-DRB1*03:147</i>). The signal near <i>FUT2</i> was associated with expression of several genes including <i>FUT2</i>, for which the direction of effect was tissue dependent. Our PheWAS identified a wide range of associations including blood cell traits, liver biomarkers, infections, gastrointestinal and thyroid-associated diseases, and respiratory disease.<h4>Conclusions</h4>Novel signals at the <i>FUT2</i> and mucin loci suggest that mucin fucosylation may be a driver of chronic sputum production even in the absence of diagnosed respiratory disease and provide genetic support for this pathway as a target for therapeutic intervention.",,pdf:https://erj.ersjournals.com/content/erj/61/6/2201667.full.pdf; doi:https://doi.org/10.1183/13993003.01667-2022; html:https://europepmc.org/articles/PMC10284065; pdf:https://europepmc.org/articles/PMC10284065?pdf=render
-36451358,https://doi.org/10.1016/j.nicl.2022.103253,Hospitalisation for COVID-19 predicts long lasting cerebrovascular impairment: A prospective observational cohort study.,"Tsvetanov KA, Spindler LRB, Stamatakis EA, Newcombe VFJ, Lupson VC, Chatfield DA, Manktelow AE, Outtrim JG, Elmer A, Kingston N, Bradley JR, Bullmore ET, Rowe JB, Menon DK, Cambridge NeuroCOVID Group, NIHR COVID-19 BioResource, Cambridge NIHR Clinical Research Facility, CITIID-NIHR BioResource COVID-19 Collaboration.",,NeuroImage. Clinical,2022,2022-11-07,Y,Cerebrovascular; Microvascular; Neurology; Cardiorespiratory; Covid-19; Sars-cov-2,,,"Human coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has multiple neurological consequences, but its long-term effect on brain health is still uncertain. The cerebrovascular consequences of COVID-19 may also affect brain health. We studied the chronic effect of COVID-19 on cerebrovascular health, in relation to acute severity, adverse clinical outcomes and in contrast to control group data. Here we assess cerebrovascular health in 45 patients six months after hospitalisation for acute COVID-19 using the resting state fluctuation amplitudes (RSFA) from functional magnetic resonance imaging, in relation to disease severity and in contrast with 42 controls. Acute COVID-19 severity was indexed by COVID-19 WHO Progression Scale, inflammatory and coagulatory biomarkers. Chronic widespread changes in frontoparietal RSFA were related to the severity of the acute COVID-19 episode. This relationship was not explained by chronic cardiorespiratory dysfunction, age, or sex. The level of cerebrovascular dysfunction was associated with cognitive, mental, and physical health at follow-up. The principal findings were consistent across univariate and multivariate approaches. The results indicate chronic cerebrovascular impairment following severe acute COVID-19, with the potential for long-term consequences on cognitive function and mental wellbeing.",,doi:https://doi.org/10.1016/j.nicl.2022.103253; doi:https://doi.org/10.1016/j.nicl.2022.103253; html:https://europepmc.org/articles/PMC9639388; pdf:https://europepmc.org/articles/PMC9639388?pdf=render
 35875883,https://doi.org/10.1093/cvr/cvac115,Long COVID and the cardiovascular system-elucidating causes and cellular mechanisms in order to develop targeted diagnostic and therapeutic strategies: a joint Scientific Statement of the ESC Working Groups on Cellular Biology of the Heart and Myocardial and Pericardial Diseases.,"Gyöngyösi M, Alcaide P, Asselbergs FW, Brundel BJJM, Camici GG, Martins PDC, Ferdinandy P, Fontana M, Girao H, Gnecchi M, Gollmann-Tepeköylü C, Kleinbongard P, Krieg T, Madonna R, Paillard M, Pantazis A, Perrino C, Pesce M, Schiattarella GG, Sluijter JPG, Steffens S, Tschöpe C, Van Linthout S, Davidson SM.",,Cardiovascular research,2023,2023-03-01,Y,Cardiac; cardiovascular; Covid-19; Long Covid; Post Covid,,,"Long COVID has become a world-wide, non-communicable epidemic, caused by long-lasting multiorgan symptoms that endure for weeks or months after SARS-CoV-2 infection has already subsided. This scientific document aims to provide insight into the possible causes and therapeutic options available for the cardiovascular manifestations of long COVID. In addition to chronic fatigue, which is a common symptom of long COVID, patients may present with chest pain, ECG abnormalities, postural orthostatic tachycardia, or newly developed supraventricular or ventricular arrhythmias. Imaging of the heart and vessels has provided evidence of chronic, post-infectious perimyocarditis with consequent left or right ventricular failure, arterial wall inflammation, or microthrombosis in certain patient populations. Better understanding of the underlying cellular and molecular mechanisms of long COVID will aid in the development of effective treatment strategies for its cardiovascular manifestations. A number of mechanisms have been proposed, including those involving direct effects on the myocardium, microthrombotic damage to vessels or endothelium, or persistent inflammation. Unfortunately, existing circulating biomarkers, coagulation, and inflammatory markers, are not highly predictive for either the presence or outcome of long COVID when measured 3 months after SARS-CoV-2 infection. Further studies are needed to understand underlying mechanisms, identify specific biomarkers, and guide future preventive strategies or treatments to address long COVID and its cardiovascular sequelae.",,pdf:https://academic.oup.com/cardiovascres/advance-article-pdf/doi/10.1093/cvr/cvac115/46855438/cvac115.pdf; doi:https://doi.org/10.1093/cvr/cvac115; html:https://europepmc.org/articles/PMC9384470; pdf:https://europepmc.org/articles/PMC9384470?pdf=render
-34972825,https://doi.org/10.1038/s41564-021-01029-0,Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework.,"Nicholson G, Lehmann B, Padellini T, Pouwels KB, Jersakova R, Lomax J, King RE, Mallon AM, Diggle PJ, Richardson S, Blangiardo M, Holmes C.",,Nature microbiology,2022,2021-12-31,Y,,,,"Global and national surveillance of SARS-CoV-2 epidemiology is mostly based on targeted schemes focused on testing individuals with symptoms. These tested groups are often unrepresentative of the wider population and exhibit test positivity rates that are biased upwards compared with the true population prevalence. Such data are routinely used to infer infection prevalence and the effective reproduction number, R<sub>t</sub>, which affects public health policy. Here, we describe a causal framework that provides debiased fine-scale spatiotemporal estimates by combining targeted test counts with data from a randomized surveillance study in the United Kingdom called REACT. Our probabilistic model includes a bias parameter that captures the increased probability of an infected individual being tested, relative to a non-infected individual, and transforms observed test counts to debiased estimates of the true underlying local prevalence and R<sub>t</sub>. We validated our approach on held-out REACT data over a 7-month period. Furthermore, our local estimates of R<sub>t</sub> are indicative of 1-week- and 2-week-ahead changes in SARS-CoV-2-positive case numbers. We also observed increases in estimated local prevalence and R<sub>t</sub> that reflect the spread of the Alpha and Delta variants. Our results illustrate how randomized surveys can augment targeted testing to improve statistical accuracy in monitoring the spread of emerging and ongoing infectious disease.",,pdf:https://www.nature.com/articles/s41564-021-01029-0.pdf; doi:https://doi.org/10.1038/s41564-021-01029-0; html:https://europepmc.org/articles/PMC8727294; pdf:https://europepmc.org/articles/PMC8727294?pdf=render
+36451358,https://doi.org/10.1016/j.nicl.2022.103253,Hospitalisation for COVID-19 predicts long lasting cerebrovascular impairment: A prospective observational cohort study.,"Tsvetanov KA, Spindler LRB, Stamatakis EA, Newcombe VFJ, Lupson VC, Chatfield DA, Manktelow AE, Outtrim JG, Elmer A, Kingston N, Bradley JR, Bullmore ET, Rowe JB, Menon DK, Cambridge NeuroCOVID Group, NIHR COVID-19 BioResource, Cambridge NIHR Clinical Research Facility, CITIID-NIHR BioResource COVID-19 Collaboration.",,NeuroImage. Clinical,2022,2022-11-07,Y,Cerebrovascular; Microvascular; Neurology; Cardiorespiratory; Covid-19; Sars-cov-2,,,"Human coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has multiple neurological consequences, but its long-term effect on brain health is still uncertain. The cerebrovascular consequences of COVID-19 may also affect brain health. We studied the chronic effect of COVID-19 on cerebrovascular health, in relation to acute severity, adverse clinical outcomes and in contrast to control group data. Here we assess cerebrovascular health in 45 patients six months after hospitalisation for acute COVID-19 using the resting state fluctuation amplitudes (RSFA) from functional magnetic resonance imaging, in relation to disease severity and in contrast with 42 controls. Acute COVID-19 severity was indexed by COVID-19 WHO Progression Scale, inflammatory and coagulatory biomarkers. Chronic widespread changes in frontoparietal RSFA were related to the severity of the acute COVID-19 episode. This relationship was not explained by chronic cardiorespiratory dysfunction, age, or sex. The level of cerebrovascular dysfunction was associated with cognitive, mental, and physical health at follow-up. The principal findings were consistent across univariate and multivariate approaches. The results indicate chronic cerebrovascular impairment following severe acute COVID-19, with the potential for long-term consequences on cognitive function and mental wellbeing.",,doi:https://doi.org/10.1016/j.nicl.2022.103253; doi:https://doi.org/10.1016/j.nicl.2022.103253; html:https://europepmc.org/articles/PMC9639388; pdf:https://europepmc.org/articles/PMC9639388?pdf=render
 31995663,https://doi.org/10.1111/cts.12725,Using Real-World Data to Guide Ustekinumab Dosing Strategies for Psoriasis: A Prospective Pharmacokinetic-Pharmacodynamic Study.,"Pan S, Tsakok T, Dand N, Lonsdale DO, Loeff FC, Bloem K, de Vries A, Baudry D, Duckworth M, Mahil S, Pushpa-Rajah A, Russell A, Alsharqi A, Becher G, Murphy R, Wahie S, Wright A, Griffiths CEM, Reynolds NJ, Barker J, Warren RB, David Burden A, Rispens T, Standing JF, Smith CH, BADBIR Study Group, the BSTOP Study Group, the PSORT Consortium.",,Clinical and translational science,2020,2020-01-29,Y,,,skin,"Variation in response to biologic therapy for inflammatory diseases, such as psoriasis, is partly driven by variation in drug exposure. Real-world psoriasis data were used to develop a pharmacokinetic/pharmacodynamic (PK/PD) model for the first-line therapeutic antibody ustekinumab. The impact of differing dosing strategies on response was explored. Data were collected from a UK prospective multicenter observational cohort (491 patients on ustekinumab monotherapy, drug levels, and anti-drug antibody measurements on 797 serum samples, 1,590 measurements of Psoriasis Area Severity Index (PASI)). Ustekinumab PKs were described with a linear one-compartment model. A maximum effect (E<sub>max</sub> ) model inhibited progression of psoriatic skin lesions in the turnover PD mechanism describing PASI evolution while on treatment. A mixture model on half-maximal effective concentration identified a potential nonresponder group, with simulations suggesting that, in future, the model could be incorporated into a Bayesian therapeutic drug monitoring ""dashboard"" to individualize dosing and improve treatment outcomes.",,pdf:https://ascpt.onlinelibrary.wiley.com/doi/pdfdirect/10.1111/cts.12725; doi:https://doi.org/10.1111/cts.12725; html:https://europepmc.org/articles/PMC7070790; pdf:https://europepmc.org/articles/PMC7070790?pdf=render
-34151270,https://doi.org/10.1136/bmjno-2021-000133,"Variation in waiting times by diagnostic category: an observational study of 1,951 referrals to a neurology outpatient clinic.","Biggin F, Howcroft T, Davies Q, Knight J, Emsley HCA.",,BMJ neurology open,2021,2021-06-03,Y,Neurology; Outpatient; Observational Study; Waiting Times; Routinely Collected Data,,,"<h4>Objective</h4>To investigate the frequency of diagnoses seen among new referrals to neurology outpatient services; to understand how these services are used through exploratory analysis of diagnostic tests and follow-up appointments; and to examine the waiting times between referral and appointment.<h4>Methods</h4>Routine data from new National Health Service appointments at a single consultant-delivered clinic between September 2016 and January 2019 were collected. These clinical data were then linked to hospital administrative data. The combined data were assigned diagnostic categories based on working diagnoses to allow further analysis using descriptive statistics.<h4>Results</h4>Five diagnostic categories accounted for 62% of all patients seen within the study period, the most common of which was headache disorders. Following a first appointment, 50% of all patients were offered at least one diagnostic test, and 35% were offered a follow-up appointment, with variation in both measures by diagnostic category. Waiting times from referral to appointment also varied by diagnostic category. 65% of patients with a seizure/epilepsy disorder were seen within the 18-week referral to treatment target, compared with 38% of patients with a movement disorder.<h4>Conclusions</h4>A small number of diagnostic categories account for a large proportion of new patients. This information could be used in policy decision-making to describe a minimum subset of categories for diagnostic coding. We found significant differences in waiting times by diagnostic category, as well as tests ordered, and follow-up offered; further investigation could address causes of variation.",,pdf:https://neurologyopen.bmj.com/content/bmjno/3/1/e000133.full.pdf; doi:https://doi.org/10.1136/bmjno-2021-000133; html:https://europepmc.org/articles/PMC8183200; pdf:https://europepmc.org/articles/PMC8183200?pdf=render
+34972825,https://doi.org/10.1038/s41564-021-01029-0,Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework.,"Nicholson G, Lehmann B, Padellini T, Pouwels KB, Jersakova R, Lomax J, King RE, Mallon AM, Diggle PJ, Richardson S, Blangiardo M, Holmes C.",,Nature microbiology,2022,2021-12-31,Y,,,,"Global and national surveillance of SARS-CoV-2 epidemiology is mostly based on targeted schemes focused on testing individuals with symptoms. These tested groups are often unrepresentative of the wider population and exhibit test positivity rates that are biased upwards compared with the true population prevalence. Such data are routinely used to infer infection prevalence and the effective reproduction number, R<sub>t</sub>, which affects public health policy. Here, we describe a causal framework that provides debiased fine-scale spatiotemporal estimates by combining targeted test counts with data from a randomized surveillance study in the United Kingdom called REACT. Our probabilistic model includes a bias parameter that captures the increased probability of an infected individual being tested, relative to a non-infected individual, and transforms observed test counts to debiased estimates of the true underlying local prevalence and R<sub>t</sub>. We validated our approach on held-out REACT data over a 7-month period. Furthermore, our local estimates of R<sub>t</sub> are indicative of 1-week- and 2-week-ahead changes in SARS-CoV-2-positive case numbers. We also observed increases in estimated local prevalence and R<sub>t</sub> that reflect the spread of the Alpha and Delta variants. Our results illustrate how randomized surveys can augment targeted testing to improve statistical accuracy in monitoring the spread of emerging and ongoing infectious disease.",,pdf:https://www.nature.com/articles/s41564-021-01029-0.pdf; doi:https://doi.org/10.1038/s41564-021-01029-0; html:https://europepmc.org/articles/PMC8727294; pdf:https://europepmc.org/articles/PMC8727294?pdf=render
 31641117,https://doi.org/10.1038/s41467-019-12682-9,Sequence variants with large effects on cardiac electrophysiology and disease.,"Norland K, Sveinbjornsson G, Thorolfsdottir RB, Davidsson OB, Tragante V, Rajamani S, Helgadottir A, Gretarsdottir S, van Setten J, Asselbergs FW, Sverrisson JT, Stephensen SS, Oskarsson G, Sigurdsson EL, Andersen K, Danielsen R, Thorgeirsson G, Thorsteinsdottir U, Arnar DO, Sulem P, Holm H, Gudbjartsson DF, Stefansson K.",,Nature communications,2019,2019-10-22,Y,,,,"Features of the QRS complex of the electrocardiogram, reflecting ventricular depolarisation, associate with various physiologic functions and several pathologic conditions. We test 32.5 million variants for association with ten measures of the QRS complex in 12 leads, using 405,732 electrocardiograms from 81,192 Icelanders. We identify 190 associations at 130 loci, the majority of which have not been reported before, including associations with 21 rare or low-frequency coding variants. Assessment of genes expressed in the heart yields an additional 13 rare QRS coding variants at 12 loci. We find 51 unreported associations between the QRS variants and echocardiographic traits and cardiovascular diseases, including atrial fibrillation, complete AV block, heart failure and supraventricular tachycardia. We demonstrate the advantage of in-depth analysis of the QRS complex in conjunction with other cardiovascular phenotypes to enhance our understanding of the genetic basis of myocardial mass, cardiac conduction and disease.",,pdf:https://www.nature.com/articles/s41467-019-12682-9.pdf; doi:https://doi.org/10.1038/s41467-019-12682-9; html:https://europepmc.org/articles/PMC6805929; pdf:https://europepmc.org/articles/PMC6805929?pdf=render
+34151270,https://doi.org/10.1136/bmjno-2021-000133,"Variation in waiting times by diagnostic category: an observational study of 1,951 referrals to a neurology outpatient clinic.","Biggin F, Howcroft T, Davies Q, Knight J, Emsley HCA.",,BMJ neurology open,2021,2021-06-03,Y,Neurology; Outpatient; Observational Study; Waiting Times; Routinely Collected Data,,,"<h4>Objective</h4>To investigate the frequency of diagnoses seen among new referrals to neurology outpatient services; to understand how these services are used through exploratory analysis of diagnostic tests and follow-up appointments; and to examine the waiting times between referral and appointment.<h4>Methods</h4>Routine data from new National Health Service appointments at a single consultant-delivered clinic between September 2016 and January 2019 were collected. These clinical data were then linked to hospital administrative data. The combined data were assigned diagnostic categories based on working diagnoses to allow further analysis using descriptive statistics.<h4>Results</h4>Five diagnostic categories accounted for 62% of all patients seen within the study period, the most common of which was headache disorders. Following a first appointment, 50% of all patients were offered at least one diagnostic test, and 35% were offered a follow-up appointment, with variation in both measures by diagnostic category. Waiting times from referral to appointment also varied by diagnostic category. 65% of patients with a seizure/epilepsy disorder were seen within the 18-week referral to treatment target, compared with 38% of patients with a movement disorder.<h4>Conclusions</h4>A small number of diagnostic categories account for a large proportion of new patients. This information could be used in policy decision-making to describe a minimum subset of categories for diagnostic coding. We found significant differences in waiting times by diagnostic category, as well as tests ordered, and follow-up offered; further investigation could address causes of variation.",,pdf:https://neurologyopen.bmj.com/content/bmjno/3/1/e000133.full.pdf; doi:https://doi.org/10.1136/bmjno-2021-000133; html:https://europepmc.org/articles/PMC8183200; pdf:https://europepmc.org/articles/PMC8183200?pdf=render
 31647808,https://doi.org/10.1371/journal.pgen.1008405,Causal relationships between obesity and the leading causes of death in women and men.,"Censin JC, Peters SAE, Bovijn J, Ferreira T, Pulit SL, Mägi R, Mahajan A, Holmes MV, Lindgren CM.",,PLoS genetics,2019,2019-10-24,Y,,Understanding the Causes of Disease,,"Obesity traits are causally implicated with risk of cardiometabolic diseases. It remains unclear whether there are similar causal effects of obesity traits on other non-communicable diseases. Also, it is largely unexplored whether there are any sex-specific differences in the causal effects of obesity traits on cardiometabolic diseases and other leading causes of death. We constructed sex-specific genetic risk scores (GRS) for three obesity traits; body mass index (BMI), waist-hip ratio (WHR), and WHR adjusted for BMI, including 565, 324, and 337 genetic variants, respectively. These GRSs were then used as instrumental variables to assess associations between the obesity traits and leading causes of mortality in the UK Biobank using Mendelian randomization. We also investigated associations with potential mediators, including smoking, glycemic and blood pressure traits. Sex-differences were subsequently assessed by Cochran's Q-test (Phet). A Mendelian randomization analysis of 228,466 women and 195,041 men showed that obesity causes coronary artery disease, stroke (particularly ischemic), chronic obstructive pulmonary disease, lung cancer, type 2 and 1 diabetes mellitus, non-alcoholic fatty liver disease, chronic liver disease, and acute and chronic renal failure. Higher BMI led to higher risk of type 2 diabetes in women than in men (Phet = 1.4×10-5). Waist-hip-ratio led to a higher risk of chronic obstructive pulmonary disease (Phet = 3.7×10-6) and higher risk of chronic renal failure (Phet = 1.0×10-4) in men than women. Obesity traits have an etiological role in the majority of the leading global causes of death. Sex differences exist in the effects of obesity traits on risk of type 2 diabetes, chronic obstructive pulmonary disease, and renal failure, which may have downstream implications for public health.","This study aimed to quantify (as genetic risk scores) the causal effects of obesity on leading causes of death, separately, in men and women. Analysis of genetic data for 228,466 women and 195,041 men showed that obesity causes coronary artery disease, stroke, chronic obstructive pulmonary disease, lung cancer, type 2 and 1 diabetes mellitus, non-alcoholic fatty liver disease, chronic liver disease, and acute and chronic renal failure. The authors identified some important differences in these causal effects for men and women.",pdf:https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1008405&type=printable; doi:https://doi.org/10.1371/journal.pgen.1008405; html:https://europepmc.org/articles/PMC6812754; pdf:https://europepmc.org/articles/PMC6812754?pdf=render
 32553019,https://doi.org/10.1099/mgen.0.000391,Genomic surveillance of <i>Escherichia coli</i> and <i>Klebsiella</i> spp. in hospital sink drains and patients.,"Constantinides B, Chau KK, Quan TP, Rodger G, Andersson MI, Jeffery K, Lipworth S, Gweon HS, Peniket A, Pike G, Millo J, Byukusenge M, Holdaway M, Gibbons C, Mathers AJ, Crook DW, Peto TEA, Walker AS, Stoesser N.",,Microbial genomics,2020,2020-07-01,Y,Wastewater; Antibiotic Resistance; Resistome; Sinks; Enterobacterales,,,"<i>Escherichia coli</i> and <i>Klebsiella</i> spp. are important human pathogens that cause a wide spectrum of clinical disease. In healthcare settings, sinks and other wastewater sites have been shown to be reservoirs of antimicrobial-resistant <i>E. coli</i> and <i>Klebsiella</i> spp., particularly in the context of outbreaks of resistant strains amongst patients. Without focusing exclusively on resistance markers or a clinical outbreak, we demonstrate that many hospital sink drains are abundantly and persistently colonized with diverse populations of <i>E. coli</i>, <i>Klebsiella pneumoniae</i> and <i>Klebsiella oxytoca</i>, including both antimicrobial-resistant and susceptible strains. Using whole-genome sequencing of 439 isolates, we show that environmental bacterial populations are largely structured by ward and sink, with only a handful of lineages, such as <i>E. coli</i> ST635, being widely distributed, suggesting different prevailing ecologies, which may vary as a result of different inputs and selection pressures. Whole-genome sequencing of 46 contemporaneous patient isolates identified one (2 %; 95 % CI 0.05-11 %) <i>E. coli</i> urine infection-associated isolate with high similarity to a prior sink isolate, suggesting that sinks may contribute to up to 10 % of infections caused by these organisms in patients on the ward over the same timeframe. Using metagenomics from 20 sink-timepoints, we show that sinks also harbour many clinically relevant antimicrobial resistance genes including <i>bla</i><sub>CTX-M</sub>, <i>bla</i><sub>SHV</sub> and <i>mcr</i>, and may act as niches for the exchange and amplification of these genes. Our study reinforces the potential role of sinks in contributing to Enterobacterales infection and antimicrobial resistance in hospital patients, something that could be amenable to intervention. This article contains data hosted by Microreact.",,doi:https://doi.org/10.1099/mgen.0.000391; doi:https://doi.org/10.1099/mgen.0.000391; html:https://europepmc.org/articles/PMC7478627; pdf:https://europepmc.org/articles/PMC7478627?pdf=render
-38508198,https://doi.org/10.1016/j.xgen.2024.100523,Integrative polygenic risk score improves the prediction accuracy of complex traits and diseases.,"Truong B, Hull LE, Ruan Y, Huang QQ, Hornsby W, Martin H, van Heel DA, Wang Y, Martin AR, Lee SH, Natarajan P.",,Cell genomics,2024,2024-03-19,Y,Combination; Clinical Utility; South Asian; Integrative; Prs; Cross Ancestry,,,"Polygenic risk scores (PRSs) are an emerging tool to predict the clinical phenotypes and outcomes of individuals. We propose PRSmix, a framework that leverages the PRS corpus of a target trait to improve prediction accuracy, and PRSmix+, which incorporates genetically correlated traits to better capture the human genetic architecture for 47 and 32 diseases/traits in European and South Asian ancestries, respectively. PRSmix demonstrated a mean prediction accuracy improvement of 1.20-fold (95% confidence interval [CI], [1.10; 1.3]; p = 9.17 × 10<sup>-5</sup>) and 1.19-fold (95% CI, [1.11; 1.27]; p = 1.92 × 10<sup>-6</sup>), and PRSmix+ improved the prediction accuracy by 1.72-fold (95% CI, [1.40; 2.04]; p = 7.58 × 10<sup>-6</sup>) and 1.42-fold (95% CI, [1.25; 1.59]; p = 8.01 × 10<sup>-7</sup>) in European and South Asian ancestries, respectively. Compared to the previously cross-trait-combination methods with scores from pre-defined correlated traits, we demonstrated that our method improved prediction accuracy for coronary artery disease up to 3.27-fold (95% CI, [2.1; 4.44]; p value after false discovery rate (FDR) correction = 2.6 × 10<sup>-4</sup>). Our method provides a comprehensive framework to benchmark and leverage the combined power of PRS for maximal performance in a desired target population.",,doi:https://doi.org/10.1016/j.xgen.2024.100523; html:https://europepmc.org/articles/PMC11019356; pdf:https://europepmc.org/articles/PMC11019356?pdf=render
+33185739,https://doi.org/10.1007/s00395-020-00828-6,Functional investigation of the coronary artery disease gene SVEP1.,"Winkler MJ, Müller P, Sharifi AM, Wobst J, Winter H, Mokry M, Ma L, van der Laan SW, Pang S, Miritsch B, Hinterdobler J, Werner J, Stiller B, Güldener U, Webb TR, Asselbergs FW, Björkegren JLM, Maegdefessel L, Schunkert H, Sager HB, Kessler T.",,Basic research in cardiology,2020,2020-11-13,Y,Genetics; Atherosclerosis; coronary artery disease; Svep1,,,"A missense variant of the sushi, von Willebrand factor type A, EGF and pentraxin domain containing protein 1 (SVEP1) is genome-wide significantly associated with coronary artery disease. The mechanisms how SVEP1 impacts atherosclerosis are not known. We found endothelial cells (EC) and vascular smooth muscle cells to represent the major cellular source of SVEP1 in plaques. Plaques were larger in atherosclerosis-prone Svep1 haploinsufficient (ApoE<sup>-/-</sup>Svep1<sup>+/-</sup>) compared to Svep1 wild-type mice (ApoE<sup>-/-</sup>Svep1<sup>+/+</sup>) and ApoE<sup>-/-</sup>Svep1<sup>+/-</sup> mice displayed elevated plaque neutrophil, Ly6C<sup>high</sup> monocyte, and macrophage numbers. We assessed how leukocytes accumulated more inside plaques in ApoE<sup>-/-</sup>Svep1<sup>+/-</sup> mice and found enhanced leukocyte recruitment from blood into plaques. In vitro, we examined how SVEP1 deficiency promotes leukocyte recruitment and found elevated expression of the leukocyte attractant chemokine (C-X-C motif) ligand 1 (CXCL1) in EC after incubation with missense compared to wild-type SVEP1. Increasing wild-type SVEP1 levels silenced endothelial CXCL1 release. In line, plasma Cxcl1 levels were elevated in ApoE<sup>-/-</sup>Svep1<sup>+/-</sup> mice. Our studies reveal an atheroprotective role of SVEP1. Deficiency of wild-type Svep1 increased endothelial CXCL1 expression leading to enhanced recruitment of proinflammatory leukocytes from blood to plaque. Consequently, elevated vascular inflammation resulted in enhanced plaque progression in Svep1 deficiency.",,pdf:https://link.springer.com/content/pdf/10.1007/s00395-020-00828-6.pdf; doi:https://doi.org/10.1007/s00395-020-00828-6; html:https://europepmc.org/articles/PMC7666586; pdf:https://europepmc.org/articles/PMC7666586?pdf=render
 35189842,https://doi.org/10.1186/s12888-022-03753-1,"Remote Assessment of Disease and Relapse in Major Depressive Disorder (RADAR-MDD): recruitment, retention, and data availability in a longitudinal remote measurement study.","Matcham F, Leightley D, Siddi S, Lamers F, White KM, Annas P, de Girolamo G, Difrancesco S, Haro JM, Horsfall M, Ivan A, Lavelle G, Li Q, Lombardini F, Mohr DC, Narayan VA, Oetzmann C, Penninx BWJH, Bruce S, Nica R, Simblett SK, Wykes T, Brasen JC, Myin-Germeys I, Rintala A, Conde P, Dobson RJB, Folarin AA, Stewart C, Ranjan Y, Rashid Z, Cummins N, Manyakov NV, Vairavan S, Hotopf M, RADAR-CNS consortium.",,BMC psychiatry,2022,2022-02-21,Y,Cohort study; Longitudinal; Major Depressive Disorder; Multicentre; Remote Measurement Technologies,,,"<h4>Background</h4>Major Depressive Disorder (MDD) is prevalent, often chronic, and requires ongoing monitoring of symptoms to track response to treatment and identify early indicators of relapse. Remote Measurement Technologies (RMT) provide an opportunity to transform the measurement and management of MDD, via data collected from inbuilt smartphone sensors and wearable devices alongside app-based questionnaires and tasks. A key question for the field is the extent to which participants can adhere to research protocols and the completeness of data collected. We aimed to describe drop out and data completeness in a naturalistic multimodal longitudinal RMT study, in people with a history of recurrent MDD. We further aimed to determine whether those experiencing a depressive relapse at baseline contributed less complete data.<h4>Methods</h4>Remote Assessment of Disease and Relapse - Major Depressive Disorder (RADAR-MDD) is a multi-centre, prospective observational cohort study conducted as part of the Remote Assessment of Disease and Relapse - Central Nervous System (RADAR-CNS) program. People with a history of MDD were provided with a wrist-worn wearable device, and smartphone apps designed to: a) collect data from smartphone sensors; and b) deliver questionnaires, speech tasks, and cognitive assessments. Participants were followed-up for a minimum of 11 months and maximum of 24 months.<h4>Results</h4>Individuals with a history of MDD (n = 623) were enrolled in the study,. We report 80% completion rates for primary outcome assessments across all follow-up timepoints. 79.8% of people participated for the maximum amount of time available and 20.2% withdrew prematurely. We found no evidence of an association between the severity of depression symptoms at baseline and the availability of data. In total, 110 participants had > 50% data available across all data types.<h4>Conclusions</h4>RADAR-MDD is the largest multimodal RMT study in the field of mental health. Here, we have shown that collecting RMT data from a clinical population is feasible. We found comparable levels of data availability in active and passive forms of data collection, demonstrating that both are feasible in this patient group.",,pdf:https://bmcpsychiatry.biomedcentral.com/track/pdf/10.1186/s12888-022-03753-1; doi:https://doi.org/10.1186/s12888-022-03753-1; html:https://europepmc.org/articles/PMC8860359; pdf:https://europepmc.org/articles/PMC8860359?pdf=render
+38508198,https://doi.org/10.1016/j.xgen.2024.100523,Integrative polygenic risk score improves the prediction accuracy of complex traits and diseases.,"Truong B, Hull LE, Ruan Y, Huang QQ, Hornsby W, Martin H, van Heel DA, Wang Y, Martin AR, Lee SH, Natarajan P.",,Cell genomics,2024,2024-03-19,Y,Combination; Clinical Utility; South Asian; Integrative; Prs; Cross Ancestry,,,"Polygenic risk scores (PRSs) are an emerging tool to predict the clinical phenotypes and outcomes of individuals. We propose PRSmix, a framework that leverages the PRS corpus of a target trait to improve prediction accuracy, and PRSmix+, which incorporates genetically correlated traits to better capture the human genetic architecture for 47 and 32 diseases/traits in European and South Asian ancestries, respectively. PRSmix demonstrated a mean prediction accuracy improvement of 1.20-fold (95% confidence interval [CI], [1.10; 1.3]; p = 9.17 × 10<sup>-5</sup>) and 1.19-fold (95% CI, [1.11; 1.27]; p = 1.92 × 10<sup>-6</sup>), and PRSmix+ improved the prediction accuracy by 1.72-fold (95% CI, [1.40; 2.04]; p = 7.58 × 10<sup>-6</sup>) and 1.42-fold (95% CI, [1.25; 1.59]; p = 8.01 × 10<sup>-7</sup>) in European and South Asian ancestries, respectively. Compared to the previously cross-trait-combination methods with scores from pre-defined correlated traits, we demonstrated that our method improved prediction accuracy for coronary artery disease up to 3.27-fold (95% CI, [2.1; 4.44]; p value after false discovery rate (FDR) correction = 2.6 × 10<sup>-4</sup>). Our method provides a comprehensive framework to benchmark and leverage the combined power of PRS for maximal performance in a desired target population.",,doi:https://doi.org/10.1016/j.xgen.2024.100523; html:https://europepmc.org/articles/PMC11019356; pdf:https://europepmc.org/articles/PMC11019356?pdf=render
 35347521,https://doi.org/10.1007/s11136-022-03119-w,Knowledge translation concerns for the CONSORT-PRO extension reporting guidance: a review of reviews.,"Mercieca-Bebber R, Aiyegbusi OL, King MT, Brundage M, Snyder C, Calvert M.",,"Quality of life research : an international journal of quality of life aspects of treatment, care and rehabilitation",2022,2022-03-26,Y,Quality of life; research methodology; Reporting; Patient-reported Outcomes; Research Waste; Consort-pro,,,"This review of reviews aimed to appraise the use of the CONSORT-PRO Extension as an evaluation tool for assessing the reporting of patient-reported outcome (PROs) in publications, and to describe the reporting of PRO research across reviews. We also outlined how variation in such evaluations impacts knowledge translation and may lead to potential misuse of the CONSORT-PRO Extension. We systematically searched Medline, Pubmed and CINAHL from 2013 to 2025 March 2021 for reviews of the completeness of reporting of PRO endpoints according to CONSORT-PRO criteria. Two reviewers extracted details of each review, the percentage of included studies that addressed each CONSORT-PRO item, and key recommendations from each review. Fourteen reviews met inclusion criteria, and only six of these used the full CONSORT-PRO checklist with minimal justified modifications. The remaining eight studies made significant or unjustified adjustments to the CONSORT-PRO Extension. Review studies also varied in how they scored multi-component CONSORT-PRO items. CONSORT-PRO items were often unreported in trial reports, and certain CONSORT-PRO items were reported less often than others. The reporting of statistical approaches to dealing with missing PRO data were poor in RCTs included in all 14 review articles. Studies reviewing PRO publications often omitted recommended CONSORT-PRO items from their evaluations, which may cause confusion among readers regarding how best to report their PRO research according to the CONSORT-PRO extension. Many trials published since CONSORT-PRO's release did not report recommended CONSORT-PRO items, which may lead to misinterpretation and consequently to research waste.",,pdf:https://link.springer.com/content/pdf/10.1007/s11136-022-03119-w.pdf; doi:https://doi.org/10.1007/s11136-022-03119-w; html:https://europepmc.org/articles/PMC9470606; pdf:https://europepmc.org/articles/PMC9470606?pdf=render
-33185739,https://doi.org/10.1007/s00395-020-00828-6,Functional investigation of the coronary artery disease gene SVEP1.,"Winkler MJ, Müller P, Sharifi AM, Wobst J, Winter H, Mokry M, Ma L, van der Laan SW, Pang S, Miritsch B, Hinterdobler J, Werner J, Stiller B, Güldener U, Webb TR, Asselbergs FW, Björkegren JLM, Maegdefessel L, Schunkert H, Sager HB, Kessler T.",,Basic research in cardiology,2020,2020-11-13,Y,Genetics; Atherosclerosis; coronary artery disease; Svep1,,,"A missense variant of the sushi, von Willebrand factor type A, EGF and pentraxin domain containing protein 1 (SVEP1) is genome-wide significantly associated with coronary artery disease. The mechanisms how SVEP1 impacts atherosclerosis are not known. We found endothelial cells (EC) and vascular smooth muscle cells to represent the major cellular source of SVEP1 in plaques. Plaques were larger in atherosclerosis-prone Svep1 haploinsufficient (ApoE<sup>-/-</sup>Svep1<sup>+/-</sup>) compared to Svep1 wild-type mice (ApoE<sup>-/-</sup>Svep1<sup>+/+</sup>) and ApoE<sup>-/-</sup>Svep1<sup>+/-</sup> mice displayed elevated plaque neutrophil, Ly6C<sup>high</sup> monocyte, and macrophage numbers. We assessed how leukocytes accumulated more inside plaques in ApoE<sup>-/-</sup>Svep1<sup>+/-</sup> mice and found enhanced leukocyte recruitment from blood into plaques. In vitro, we examined how SVEP1 deficiency promotes leukocyte recruitment and found elevated expression of the leukocyte attractant chemokine (C-X-C motif) ligand 1 (CXCL1) in EC after incubation with missense compared to wild-type SVEP1. Increasing wild-type SVEP1 levels silenced endothelial CXCL1 release. In line, plasma Cxcl1 levels were elevated in ApoE<sup>-/-</sup>Svep1<sup>+/-</sup> mice. Our studies reveal an atheroprotective role of SVEP1. Deficiency of wild-type Svep1 increased endothelial CXCL1 expression leading to enhanced recruitment of proinflammatory leukocytes from blood to plaque. Consequently, elevated vascular inflammation resulted in enhanced plaque progression in Svep1 deficiency.",,pdf:https://link.springer.com/content/pdf/10.1007/s00395-020-00828-6.pdf; doi:https://doi.org/10.1007/s00395-020-00828-6; html:https://europepmc.org/articles/PMC7666586; pdf:https://europepmc.org/articles/PMC7666586?pdf=render
 38514079,https://doi.org/10.1136/bmj-2023-077764,Community based complex interventions to sustain independence in older people: systematic review and network meta-analysis.,"Crocker TF, Ensor J, Lam N, Jordão M, Bajpai R, Bond M, Forster A, Riley RD, Andre D, Brundle C, Ellwood A, Green J, Hale M, Mirza L, Morgan J, Patel I, Patetsini E, Prescott M, Ramiz R, Todd O, Walford R, Gladman J, Clegg A.",,BMJ (Clinical research ed.),2024,2024-03-21,Y,,,,"<h4>Objective</h4>To synthesise evidence of the effectiveness of community based complex interventions, grouped according to their intervention components, to sustain independence for older people.<h4>Design</h4>Systematic review and network meta-analysis.<h4>Data sources</h4>Medline, Embase, CINAHL, PsycINFO, CENTRAL, clinicaltrials.gov, and International Clinical Trials Registry Platform from inception to 9 August 2021 and reference lists of included studies.<h4>Eligibility criteria</h4>Randomised controlled trials or cluster randomised controlled trials with ≥24 weeks' follow-up studying community based complex interventions for sustaining independence in older people (mean age ≥65 years) living at home, with usual care, placebo, or another complex intervention as comparators.<h4>Main outcomes</h4>Living at home, activities of daily living (personal/instrumental), care home placement, and service/economic outcomes at 12 months.<h4>Data synthesis</h4>Interventions were grouped according to a specifically developed typology. Random effects network meta-analysis estimated comparative effects; Cochrane's revised tool (RoB 2) structured risk of bias assessment. Grading of recommendations assessment, development and evaluation (GRADE) network meta-analysis structured certainty assessment.<h4>Results</h4>The review included 129 studies (74 946 participants). Nineteen intervention components, including ""multifactorial action from individualised care planning"" (a process of multidomain assessment and management leading to tailored actions), were identified in 63 combinations. For living at home, compared with no intervention/placebo, evidence favoured multifactorial action from individualised care planning including medication review and regular follow-ups (routine review) (odds ratio 1.22, 95% confidence interval 0.93 to 1.59; moderate certainty); multifactorial action from individualised care planning including medication review without regular follow-ups (2.55, 0.61 to 10.60; low certainty); combined cognitive training, medication review, nutritional support, and exercise (1.93, 0.79 to 4.77; low certainty); and combined activities of daily living training, nutritional support, and exercise (1.79, 0.67 to 4.76; low certainty). Risk screening or the addition of education and self-management strategies to multifactorial action from individualised care planning and routine review with medication review may reduce odds of living at home. For instrumental activities of daily living, evidence favoured multifactorial action from individualised care planning and routine review with medication review (standardised mean difference 0.11, 95% confidence interval 0.00 to 0.21; moderate certainty). Two interventions may reduce instrumental activities of daily living: combined activities of daily living training, aids, and exercise; and combined activities of daily living training, aids, education, exercise, and multifactorial action from individualised care planning and routine review with medication review and self-management strategies. For personal activities of daily living, evidence favoured combined exercise, multifactorial action from individualised care planning, and routine review with medication review and self-management strategies (0.16, -0.51 to 0.82; low certainty). For homecare recipients, evidence favoured addition of multifactorial action from individualised care planning and routine review with medication review (0.60, 0.32 to 0.88; low certainty). High risk of bias and imprecise estimates meant that most evidence was low or very low certainty. Few studies contributed to each comparison, impeding evaluation of inconsistency and frailty.<h4>Conclusions</h4>The intervention most likely to sustain independence is individualised care planning including medicines optimisation and regular follow-up reviews resulting in multifactorial action. Homecare recipients may particularly benefit from this intervention. Unexpectedly, some combinations may reduce independence. Further research is needed to investigate which combinations of interventions work best for different participants and contexts.<h4>Registration</h4>PROSPERO CRD42019162195.",,doi:https://doi.org/10.1136/bmj-2023-077764; html:https://europepmc.org/articles/PMC10955723
 31539079,https://doi.org/10.1001/jamanetworkopen.2019.11970,Association of Untargeted Urinary Metabolomics and Lung Cancer Risk Among Never-Smoking Women in China.,"Seow WJ, Shu XO, Nicholson JK, Holmes E, Walker DI, Hu W, Cai Q, Gao YT, Xiang YB, Moore SC, Bassig BA, Wong JYY, Zhang J, Ji BT, Boulangé CL, Kaluarachchi M, Wijeyesekera A, Zheng W, Elliott P, Rothman N, Lan Q.",,JAMA network open,2019,2019-09-04,Y,,Understanding the Causes of Disease,,"<h4>Importance</h4>Chinese women have the highest rate of lung cancer among female never-smokers in the world, and the etiology is poorly understood.<h4>Objective</h4>To assess the association between metabolomics and lung cancer risk among never-smoking women.<h4>Design, setting, and participants</h4>This nested case-control study included 275 never-smoking female patients with lung cancer and 289 never-smoking cancer-free control participants from the prospective Shanghai Women's Health Study recruited from December 28, 1996, to May 23, 2000. Validated food frequency questionnaires were used for the collection of dietary information. Metabolomic analysis was conducted from November 13, 2015, to January 6, 2016. Data analysis was conducted from January 6, 2016, to November 29, 2018.<h4>Exposures</h4>Untargeted ultra-high-performance liquid chromatography-tandem mass spectrometry and nuclear magnetic resonance metabolomic profiles were characterized using prediagnosis urine samples. A total of 39 416 metabolites were measured.<h4>Main outcomes and measures</h4>Incident lung cancer.<h4>Results</h4>Among the 564 women, those who developed lung cancer (275 participants; median [interquartile range] age, 61.0 [52-65] years) and those who did not develop lung cancer (289 participants; median [interquartile range] age, 62.0 [53-66] years) at follow-up (median [interquartile range] follow-up, 10.9 [9.0-11.7] years) were similar in terms of their secondhand smoke exposure, history of respiratory diseases, and body mass index. A peak metabolite, identified as 5-methyl-2-furoic acid, was significantly associated with lower lung cancer risk (odds ratio, 0.57 [95% CI, 0.46-0.72]; P < .001; false discovery rate = 0.039). Furthermore, this peak was weakly correlated with self-reported dietary soy intake (ρ = 0.21; P < .001). Increasing tertiles of this metabolite were associated with lower lung cancer risk (in comparison with first tertile, odds ratio for second tertile, 0.52 [95% CI, 0.34-0.80]; and odds ratio for third tertile, 0.46 [95% CI, 0.30-0.70]), and the association was consistent across different histological subtypes and follow-up times. Additionally, metabolic pathway analysis found several systemic biological alterations that were associated with lung cancer risk, including 1-carbon metabolism, nucleotide metabolism, oxidative stress, and inflammation.<h4>Conclusions and relevance</h4>This prospective study of the untargeted urinary metabolome and lung cancer among never-smoking women in China provides support for the hypothesis that soy-based metabolites are associated with lower lung cancer risk in never-smoking women and suggests that biological processes linked to air pollution may be associated with higher lung cancer risk in this population.",,pdf:https://jamanetwork.com/journals/jamanetworkopen/articlepdf/2751559/seow_2019_oi_190459.pdf; doi:https://doi.org/10.1001/jamanetworkopen.2019.11970; html:https://europepmc.org/articles/PMC6755532
-36895957,https://doi.org/10.1093/braincomms/fcad037,Investigating genotype-phenotype relationship of extreme neuropathic pain disorders in a UK national cohort.,"Themistocleous AC, Baskozos G, Blesneac I, Comini M, Megy K, Chong S, Deevi SVV, Ginsberg L, Gosal D, Hadden RDM, Horvath R, Mahdi-Rogers M, Manzur A, Mapeta R, Marshall A, Matthews E, McCarthy MI, Reilly MM, Renton T, Rice ASC, Vale TA, van Zuydam N, Walker SM, Woods CG, Bennett DLH.",,Brain communications,2023,2023-02-20,Y,Sodium channels; Neuropathic pain; Peripheral Neuropathy; Whole Genome Sequencing,,,"The aims of our study were to use whole genome sequencing in a cross-sectional cohort of patients to identify new variants in genes implicated in neuropathic pain, to determine the prevalence of known pathogenic variants and to understand the relationship between pathogenic variants and clinical presentation. Patients with extreme neuropathic pain phenotypes (both sensory loss and gain) were recruited from secondary care clinics in the UK and underwent whole genome sequencing as part of the National Institute for Health and Care Research Bioresource Rare Diseases project. A multidisciplinary team assessed the pathogenicity of rare variants in genes previously known to cause neuropathic pain disorders and exploratory analysis of research candidate genes was completed. Association testing for genes carrying rare variants was completed using the gene-wise approach of the combined burden and variance-component test SKAT-O. Patch clamp analysis was performed on transfected HEK293T cells for research candidate variants of genes encoding ion channels. The results include the following: (i) Medically actionable variants were found in 12% of study participants (205 recruited), including known pathogenic variants: <i>SCN9A(ENST00000409672.1):</i> c.2544T>C, p.Ile848Thr that causes inherited erythromelalgia, and <i>SPTLC1(ENST00000262554.2):</i>c.340T>G, p.Cys133Tr variant that causes hereditary sensory neuropathy type-1. (ii) Clinically relevant variants were most common in voltage-gated sodium channels (Na<sub>v</sub>). (iii) <i>SCN9A(ENST00000409672.1):</i>c.554G>A, pArg185His variant was more common in non-freezing cold injury participants than controls and causes a gain of function of Na<sub>V</sub>1.7 after cooling (the environmental trigger for non-freezing cold injury). (iv) Rare variant association testing showed a significant difference in distribution for genes NGF, <i>KIF1A</i>, <i>SCN8A</i>, <i>TRPM8</i>, <i>KIF1A</i>, <i>TRPA1</i> and the regulatory regions of genes <i>SCN11A</i>, <i>FLVCR1</i>, <i>KIF1A</i> and <i>SCN9A</i> between European participants with neuropathic pain and controls. (v) The <i>TRPA1(ENST00000262209.4):c.515C>T,</i> p.Ala172Val variant identified in participants with episodic somatic pain disorder demonstrated gain-of-channel function to agonist stimulation. Whole genome sequencing identified clinically relevant variants in over 10% of participants with extreme neuropathic pain phenotypes. The majority of these variants were found in ion channels. Combining genetic analysis with functional validation can lead to a better understanding as to how rare variants in ion channels lead to sensory neuron hyper-excitability, and how cold, as an environmental trigger, interacts with the gain-of-function Na<sub>V</sub>1.7 p.Arg185His variant. Our findings highlight the role of ion channel variants in the pathogenesis of extreme neuropathic pain disorders, likely mediated through changes in sensory neuron excitability and interaction with environmental triggers.",,pdf:https://academic.oup.com/braincomms/article-pdf/5/2/fcad037/49446967/fcad037.pdf; doi:https://doi.org/10.1093/braincomms/fcad037; html:https://europepmc.org/articles/PMC9991512; pdf:https://europepmc.org/articles/PMC9991512?pdf=render
-35294976,https://doi.org/10.1007/s00127-022-02221-1,Mental health service use among mothers involved in public family law proceedings: linked data cohort study in South London 2007-2019.,"Pearson RJ, Grant C, Wijlaars L, Finch E, Bedston S, Broadhurst K, Gilbert R.",,Social psychiatry and psychiatric epidemiology,2022,2022-03-16,Y,Substance Misuse; Child Protection; Record Linkage; Maternal Mental Health; Family Court,,,"<h4>Purpose</h4>Mental health problems and substance misuse are common among the mothers of children who experience court-mandated placement into care in England, yet there is limited research characterising these health needs to inform evidence-based policy. In this descriptive study, we aimed to generate evidence about the type, severity, and timing of mental health and substance misuse needs among women involved in public family law proceedings concerning child placement into care ('care proceedings').<h4>Methods</h4>This is a retrospective, matched cohort study using linked family court and mental health service records for 2137 (66%) of the 3226 women involved in care proceedings between 2007 and 2019 in the South London and Maudsley NHS Mental Health Trust (SLaM) catchment area. We compared mental health service use and risk of dying with 17,096 female-matched controls who accessed SLaM between 2007 and 2019, aged 16-55 years, and were not involved in care proceedings.<h4>Results</h4>Most women (79%) were known to SLaM before care proceedings began. Women had higher rates of schizophrenia spectrum disorders (19% vs 11% matched controls), personality disorders (21% vs 11%), and substance misuse (33% vs 12%). They were more likely to have a SLaM inpatient admission (27% vs 14%) or to be sectioned (19% vs 8%). Women had a 2.15 (95% CI 1.68-2.74) times greater hazard of dying, compared to matched controls, adjusted for age.<h4>Conclusion</h4>Women involved in care proceedings experience a particularly high burden of severe and complex mental health and substance misuse need. Women's increased risk of mortality following proceedings highlights that interventions responding to maternal mental health and substance misuse within family courts should offer continued, long-term support.",,pdf:https://link.springer.com/content/pdf/10.1007/s00127-022-02221-1.pdf; doi:https://doi.org/10.1007/s00127-022-02221-1; html:https://europepmc.org/articles/PMC9477900; pdf:https://europepmc.org/articles/PMC9477900?pdf=render
 38689001,https://doi.org/10.1038/s41588-024-01714-w,Genome-wide analysis in over 1 million individuals of European ancestry yields improved polygenic risk scores for blood pressure traits.,"Keaton JM, Kamali Z, Xie T, Vaez A, Williams A, Goleva SB, Ani A, Evangelou E, Hellwege JN, Yengo L, Young WJ, Traylor M, Giri A, Zheng Z, Zeng J, Chasman DI, Morris AP, Caulfield MJ, Hwang SJ, Kooner JS, Conen D, Attia JR, Morrison AC, Loos RJF, Kristiansson K, Schmidt R, Hicks AA, Pramstaller PP, Nelson CP, Samani NJ, Risch L, Gyllensten U, Melander O, Riese H, Wilson JF, Campbell H, Rich SS, Psaty BM, Lu Y, Rotter JI, Guo X, Rice KM, Vollenweider P, Sundström J, Langenberg C, Tobin MD, Giedraitis V, Luan J, Tuomilehto J, Kutalik Z, Ripatti S, Salomaa V, Girotto G, Trompet S, Jukema JW, van der Harst P, Ridker PM, Giulianini F, Vitart V, Goel A, Watkins H, Harris SE, Deary IJ, van der Most PJ, Oldehinkel AJ, Keavney BD, Hayward C, Campbell A, Boehnke M, Scott LJ, Boutin T, Mamasoula C, Järvelin MR, Peters A, Gieger C, Lakatta EG, Cucca F, Hui J, Knekt P, Enroth S, De Borst MH, Polašek O, Concas MP, Catamo E, Cocca M, Li-Gao R, Hofer E, Schmidt H, Spedicati B, Waldenberger M, Strachan DP, Laan M, Teumer A, Dörr M, Gudnason V, Cook JP, Ruggiero D, Kolcic I, Boerwinkle E, Traglia M, Lehtimäki T, Raitakari OT, Johnson AD, Newton-Cheh C, Brown MJ, Dominiczak AF, Sever PJ, Poulter N, Chambers JC, Elosua R, Siscovick D, Esko T, Metspalu A, Strawbridge RJ, Laakso M, Hamsten A, Hottenga JJ, de Geus E, Morris AD, Palmer CNA, Nolte IM, Milaneschi Y, Marten J, Wright A, Zeggini E, Howson JMM, O'Donnell CJ, Spector T, Nalls MA, Simonsick EM, Liu Y, van Duijn CM, Butterworth AS, Danesh JN, Menni C, Wareham NJ, Khaw KT, Sun YV, Wilson PWF, Cho K, Visscher PM, Denny JC, Million Veteran Program, Lifelines Cohort Study, CHARGE consortium, ICBP Consortium, Levy D, Edwards TL, Munroe PB, Snieder H, Warren HR.",,Nature genetics,2024,2024-04-30,Y,,,,"Hypertension affects more than one billion people worldwide. Here we identify 113 novel loci, reporting a total of 2,103 independent genetic signals (P < 5 × 10<sup>-8</sup>) from the largest single-stage blood pressure (BP) genome-wide association study to date (n = 1,028,980 European individuals). These associations explain more than 60% of single nucleotide polymorphism-based BP heritability. Comparing top versus bottom deciles of polygenic risk scores (PRSs) reveals clinically meaningful differences in BP (16.9 mmHg systolic BP, 95% CI, 15.5-18.2 mmHg, P = 2.22 × 10<sup>-126</sup>) and more than a sevenfold higher odds of hypertension risk (odds ratio, 7.33; 95% CI, 5.54-9.70; P = 4.13 × 10<sup>-44</sup>) in an independent dataset. Adding PRS into hypertension-prediction models increased the area under the receiver operating characteristic curve (AUROC) from 0.791 (95% CI, 0.781-0.801) to 0.826 (95% CI, 0.817-0.836, ∆AUROC, 0.035, P = 1.98 × 10<sup>-34</sup>). We compare the 2,103 loci results in non-European ancestries and show significant PRS associations in a large African-American sample. Secondary analyses implicate 500 genes previously unreported for BP. Our study highlights the role of increasingly large genomic studies for precision health research.",,doi:https://doi.org/10.1038/s41588-024-01714-w; html:https://europepmc.org/articles/PMC11096100; pdf:https://europepmc.org/articles/PMC11096100?pdf=render
+35294976,https://doi.org/10.1007/s00127-022-02221-1,Mental health service use among mothers involved in public family law proceedings: linked data cohort study in South London 2007-2019.,"Pearson RJ, Grant C, Wijlaars L, Finch E, Bedston S, Broadhurst K, Gilbert R.",,Social psychiatry and psychiatric epidemiology,2022,2022-03-16,Y,Substance Misuse; Child Protection; Record Linkage; Maternal Mental Health; Family Court,,,"<h4>Purpose</h4>Mental health problems and substance misuse are common among the mothers of children who experience court-mandated placement into care in England, yet there is limited research characterising these health needs to inform evidence-based policy. In this descriptive study, we aimed to generate evidence about the type, severity, and timing of mental health and substance misuse needs among women involved in public family law proceedings concerning child placement into care ('care proceedings').<h4>Methods</h4>This is a retrospective, matched cohort study using linked family court and mental health service records for 2137 (66%) of the 3226 women involved in care proceedings between 2007 and 2019 in the South London and Maudsley NHS Mental Health Trust (SLaM) catchment area. We compared mental health service use and risk of dying with 17,096 female-matched controls who accessed SLaM between 2007 and 2019, aged 16-55 years, and were not involved in care proceedings.<h4>Results</h4>Most women (79%) were known to SLaM before care proceedings began. Women had higher rates of schizophrenia spectrum disorders (19% vs 11% matched controls), personality disorders (21% vs 11%), and substance misuse (33% vs 12%). They were more likely to have a SLaM inpatient admission (27% vs 14%) or to be sectioned (19% vs 8%). Women had a 2.15 (95% CI 1.68-2.74) times greater hazard of dying, compared to matched controls, adjusted for age.<h4>Conclusion</h4>Women involved in care proceedings experience a particularly high burden of severe and complex mental health and substance misuse need. Women's increased risk of mortality following proceedings highlights that interventions responding to maternal mental health and substance misuse within family courts should offer continued, long-term support.",,pdf:https://link.springer.com/content/pdf/10.1007/s00127-022-02221-1.pdf; doi:https://doi.org/10.1007/s00127-022-02221-1; html:https://europepmc.org/articles/PMC9477900; pdf:https://europepmc.org/articles/PMC9477900?pdf=render
+36895957,https://doi.org/10.1093/braincomms/fcad037,Investigating genotype-phenotype relationship of extreme neuropathic pain disorders in a UK national cohort.,"Themistocleous AC, Baskozos G, Blesneac I, Comini M, Megy K, Chong S, Deevi SVV, Ginsberg L, Gosal D, Hadden RDM, Horvath R, Mahdi-Rogers M, Manzur A, Mapeta R, Marshall A, Matthews E, McCarthy MI, Reilly MM, Renton T, Rice ASC, Vale TA, van Zuydam N, Walker SM, Woods CG, Bennett DLH.",,Brain communications,2023,2023-02-20,Y,Sodium channels; Neuropathic pain; Peripheral Neuropathy; Whole Genome Sequencing,,,"The aims of our study were to use whole genome sequencing in a cross-sectional cohort of patients to identify new variants in genes implicated in neuropathic pain, to determine the prevalence of known pathogenic variants and to understand the relationship between pathogenic variants and clinical presentation. Patients with extreme neuropathic pain phenotypes (both sensory loss and gain) were recruited from secondary care clinics in the UK and underwent whole genome sequencing as part of the National Institute for Health and Care Research Bioresource Rare Diseases project. A multidisciplinary team assessed the pathogenicity of rare variants in genes previously known to cause neuropathic pain disorders and exploratory analysis of research candidate genes was completed. Association testing for genes carrying rare variants was completed using the gene-wise approach of the combined burden and variance-component test SKAT-O. Patch clamp analysis was performed on transfected HEK293T cells for research candidate variants of genes encoding ion channels. The results include the following: (i) Medically actionable variants were found in 12% of study participants (205 recruited), including known pathogenic variants: <i>SCN9A(ENST00000409672.1):</i> c.2544T>C, p.Ile848Thr that causes inherited erythromelalgia, and <i>SPTLC1(ENST00000262554.2):</i>c.340T>G, p.Cys133Tr variant that causes hereditary sensory neuropathy type-1. (ii) Clinically relevant variants were most common in voltage-gated sodium channels (Na<sub>v</sub>). (iii) <i>SCN9A(ENST00000409672.1):</i>c.554G>A, pArg185His variant was more common in non-freezing cold injury participants than controls and causes a gain of function of Na<sub>V</sub>1.7 after cooling (the environmental trigger for non-freezing cold injury). (iv) Rare variant association testing showed a significant difference in distribution for genes NGF, <i>KIF1A</i>, <i>SCN8A</i>, <i>TRPM8</i>, <i>KIF1A</i>, <i>TRPA1</i> and the regulatory regions of genes <i>SCN11A</i>, <i>FLVCR1</i>, <i>KIF1A</i> and <i>SCN9A</i> between European participants with neuropathic pain and controls. (v) The <i>TRPA1(ENST00000262209.4):c.515C>T,</i> p.Ala172Val variant identified in participants with episodic somatic pain disorder demonstrated gain-of-channel function to agonist stimulation. Whole genome sequencing identified clinically relevant variants in over 10% of participants with extreme neuropathic pain phenotypes. The majority of these variants were found in ion channels. Combining genetic analysis with functional validation can lead to a better understanding as to how rare variants in ion channels lead to sensory neuron hyper-excitability, and how cold, as an environmental trigger, interacts with the gain-of-function Na<sub>V</sub>1.7 p.Arg185His variant. Our findings highlight the role of ion channel variants in the pathogenesis of extreme neuropathic pain disorders, likely mediated through changes in sensory neuron excitability and interaction with environmental triggers.",,pdf:https://academic.oup.com/braincomms/article-pdf/5/2/fcad037/49446967/fcad037.pdf; doi:https://doi.org/10.1093/braincomms/fcad037; html:https://europepmc.org/articles/PMC9991512; pdf:https://europepmc.org/articles/PMC9991512?pdf=render
 32095773,https://doi.org/10.1159/000503957,Advancing the Use of Mobile Technologies in Clinical Trials: Recommendations from the Clinical Trials Transformation Initiative.,"Coran P, Goldsack JC, Grandinetti CA, Bakker JP, Bolognese M, Dorsey ER, Vasisht K, Amdur A, Dell C, Helfgott J, Kirchoff M, Miller CJ, Narayan A, Patel D, Peterson B, Ramirez E, Schiller D, Switzer T, Wing L, Forrest A, Doherty A.",,Digital biomarkers,2019,2019-09-01,N,Clinical Trials; Regulatory Approval; Wearable Sensors; Mobile Technologies,"Better, Faster and More Efficient Clinical Trials",,"Mobile technologies offer the potential to reduce the costs of conducting clinical trials by collecting high-quality information on health outcomes in real-world settings that are relevant to patients and clinicians. However, widespread use of mobile technologies in clinical trials has been impeded by their perceived challenges. To advance solutions to these challenges, the Clinical Trials Transformation Initiative (CTTI) has issued best practices and realistic approaches that clinical trial sponsors can now use. These include CTTI recommendations on technology selection; data collection, analysis, and interpretation; data management; protocol design and execution; and US Food and Drug Administration submission and inspection. The scientific principles underpinning the clinical trials enterprise continue to apply to studies using mobile technologies. These recommendations provide a framework for including mobile technologies in clinical trials that can lead to more efficient assessment of new therapies for patients.","The authors of this publication have developed a set of guidelines for planning, running and writing up research that uses mobile technologies in clinical trials. The guidelines they have put together should make it easer for patient experience to be recorded in clinical trials.",pdf:https://www.karger.com/Article/Pdf/503957; doi:https://doi.org/10.1159/000503957; html:https://europepmc.org/articles/PMC7011727; pdf:https://europepmc.org/articles/PMC7011727?pdf=render; doi:https://doi.org/10.1159/000503957
 32792438,https://doi.org/10.1136/bmjopen-2019-036564,Association between health indicators of maternal adversity and the rate of infant entry to local authority care in England: a longitudinal ecological study.,"Pearson RJ, Jay MA, Wijlaars LPMM, De Stavola B, Syed S, Bedston SJ, Gilbert R.",,BMJ open,2020,2020-08-13,Y,epidemiology; Public Health; Child Protection,,,"<h4>Objective</h4>Infants enter care at varying rates across local authorities (LAs) in England, but evidence is lacking on what is driving these differences. With this ecological study, we aimed to explore the extent to which adversity indicated within women's hospitalisation histories, predelivery, explained the rate of infant entry into care.<h4>Methods</h4>We used two longitudinal person-level data sets on hospitalisations and entries to care to create annual measures for 131 English LAs, between 2006/2007 and 2013/2014 (April-March). We combined these measures by LA and financial year, along with other publicly available data on LA characteristics. We used linear mixed-effects models to analyse the relationship between the outcome-LA-specific rate of infant entry into care (per 10 000 infants in the LA population) - and LA-specific percentage of live births with maternal history of adversity-related hospital admissions (ie, substance misuse, mental health problems or violence-related admissions in the 3 years before delivery), adjusted for other predictors of entry into care.<h4>Results</h4>Rate of infant entry into care (mean: 85.16 per 10 000, SD: 41.07) and percentage of live births with maternal history of adversity-related hospital admissions (4.62%, 2.44%) varied greatly by LA. The prevalence of maternal adversity accounted for 24% of the variation in rate of entry (95% CI 14% to 35%). After adjustment, a percentage point increase in prevalence of maternal adversity-both within and between LAs-was associated with an estimated 2.56 (per 10 000) more infants entering care (1.31-3.82).<h4>Conclusions</h4>The prevalence of maternal adversity before birth helped to explain the variation in LA rates of infant entry into care. Preventive interventions are needed to improve maternal well-being before and during pregnancy, and potentially reduce risk of child maltreatment and therefore entries to care. Evidence on who to target and data to evaluate change require linkage between parent-child healthcare data and administrative data from children's social care.",,pdf:https://bmjopen.bmj.com/content/bmjopen/10/8/e036564.full.pdf; doi:https://doi.org/10.1136/bmjopen-2019-036564; html:https://europepmc.org/articles/PMC7430489; pdf:https://europepmc.org/articles/PMC7430489?pdf=render
 37302069,https://doi.org/10.1016/j.celrep.2023.112613,Proteomic analysis of circulating immune cells identifies cellular phenotypes associated with COVID-19 severity.,"Potts M, Fletcher-Etherington A, Nightingale K, Mescia F, Bergamaschi L, Calero-Nieto FJ, Antrobus R, Williamson J, Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID BioResource Collaboration, Parsons H, Huttlin EL, Kingston N, Göttgens B, Bradley JR, Lehner PJ, Matheson NJ, Smith KGC, Wills MR, Lyons PA, Weekes MP.",,Cell reports,2023,2023-05-29,Y,Cp: Immunology,,,"Certain serum proteins, including C-reactive protein (CRP) and D-dimer, have prognostic value in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Nonetheless, these factors are non-specific, providing limited mechanistic insight into the peripheral blood mononuclear cell (PBMC) populations that drive the pathogenesis of severe COVID-19. To identify cellular phenotypes associated with disease, we performed a comprehensive, unbiased analysis of total and plasma-membrane PBMC proteomes from 40 unvaccinated individuals with SARS-CoV-2, spanning the whole disease spectrum. Combined with RNA sequencing (RNA-seq) and flow cytometry from the same donors, we define a comprehensive multi-omic profile for each severity level, revealing that immune-cell dysregulation progresses with increasing disease. The cell-surface proteins CEACAMs1, 6, and 8, CD177, CD63, and CD89 are strongly associated with severe COVID-19, corresponding to the emergence of atypical CD3<sup>+</sup>CD4<sup>+</sup>CEACAM1/6/8<sup>+</sup>CD177<sup>+</sup>CD63<sup>+</sup>CD89<sup>+</sup> and CD16<sup>+</sup>CEACAM1/6/8<sup>+</sup> mononuclear cells. Utilization of these markers may facilitate real-time patient assessment by flow cytometry and identify immune populations that could be targeted to ameliorate immunopathology.",,pdf:http://www.cell.com/article/S2211124723006241/pdf; doi:https://doi.org/10.1016/j.celrep.2023.112613; html:https://europepmc.org/articles/PMC10243220; pdf:https://europepmc.org/articles/PMC10243220?pdf=render
@@ -2607,10 +2609,10 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 37601966,https://doi.org/10.1016/j.xgen.2023.100361,Genotyping and population characteristics of the China Kadoorie Biobank.,"Walters RG, Millwood IY, Lin K, Schmidt Valle D, McDonnell P, Hacker A, Avery D, Edris A, Fry H, Cai N, Kretzschmar WW, Ansari MA, Lyons PA, Collins R, Donnelly P, Hill M, Peto R, Shen H, Jin X, Nie C, Xu X, Guo Y, Yu C, Lv J, Clarke RJ, Li L, Chen Z, China Kadoorie Biobank Collaborative Group.",,Cell genomics,2023,2023-07-20,Y,Genetics; Genetic epidemiology; Genotyping; complex disease; Gwas; Genetic Association Studies; Biobank; Omics; Prospective; Cardiovascular Health,,,"The China Kadoorie Biobank (CKB) is a population-based prospective cohort of >512,000 adults recruited from 2004 to 2008 from 10 geographically diverse regions across China. Detailed data from questionnaires and physical measurements were collected at baseline, with additional measurements at three resurveys involving ∼5% of surviving participants. Analyses of genome-wide genotyping, for >100,000 participants using custom-designed Axiom arrays, reveal extensive relatedness, recent consanguinity, and signatures reflecting large-scale population movements from recent Chinese history. Systematic genome-wide association studies of incident disease, captured through electronic linkage to death and disease registries and to the national health insurance system, replicate established disease loci and identify 14 novel disease associations. Together with studies of candidate drug targets and disease risk factors and contributions to international genetics consortia, these demonstrate the breadth, depth, and quality of the CKB data. Ongoing high-throughput omics assays of collected biosamples and planned whole-genome sequencing will further enhance the scientific value of this biobank.",,doi:https://doi.org/10.1016/j.xgen.2023.100361; doi:https://doi.org/10.1016/j.xgen.2023.100361; html:https://europepmc.org/articles/PMC10435379; pdf:https://europepmc.org/articles/PMC10435379?pdf=render
 34319235,https://doi.org/10.2196/28873,Remote Assessment of Lung Disease and Impact on Physical and Mental Health (RALPMH): Protocol for a Prospective Observational Study.,"Ranjan Y, Althobiani M, Jacob J, Orini M, Dobson RJ, Porter J, Hurst J, Folarin AA.",,JMIR research protocols,2021,2021-10-07,Y,Lung diseases; Mental health; Remote Monitoring; Respiratory Health; Internet Of Things; Mhealth; Mobile Health; Wearables; Cardiopulmonary Diseases; Covid-19,,,"<h4>Background</h4>Chronic lung disorders like chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are characterized by exacerbations. They are unpleasant for patients and sometimes severe enough to cause hospital admission and death. Moreover, due to the COVID-19 pandemic, vulnerable populations with these disorders are at high risk, and their routine care cannot be done properly. Remote monitoring offers a low cost and safe solution for gaining visibility into the health of people in their daily lives, making it useful for vulnerable populations.<h4>Objective</h4>The primary objective is to assess the feasibility and acceptability of remote monitoring using wearables and mobile phones in patients with pulmonary diseases. The secondary objective is to provide power calculations for future studies centered around understanding the number of exacerbations according to sample size and duration.<h4>Methods</h4>Twenty participants will be recruited in each of three cohorts (COPD, IPF, and posthospitalization COVID). Data collection will be done remotely using the RADAR-Base (Remote Assessment of Disease And Relapse) mobile health (mHealth) platform for different devices, including Garmin wearable devices and smart spirometers, mobile app questionnaires, surveys, and finger pulse oximeters. Passive data include wearable-derived continuous heart rate, oxygen saturation, respiration rate, activity, and sleep. Active data include disease-specific patient-reported outcome measures, mental health questionnaires, and symptom tracking to track disease trajectory. Analyses will assess the feasibility of lung disorder remote monitoring (including data quality, data completeness, system usability, and system acceptability). We will attempt to explore disease trajectory, patient stratification, and identification of acute clinical events such as exacerbations. A key aspect is understanding the potential of real-time data collection. We will simulate an intervention to acquire responses at the time of the event to assess model performance for exacerbation identification.<h4>Results</h4>The Remote Assessment of Lung Disease and Impact on Physical and Mental Health (RALPMH) study provides a unique opportunity to assess the use of remote monitoring in the evaluation of lung disorders. The study started in the middle of June 2021. The data collection apparatus, questionnaires, and wearable integrations were setup and tested by the clinical teams prior to the start of recruitment. While recruitment is ongoing, real-time exacerbation identification models are currently being constructed. The models will be pretrained daily on data of previous days, but the inference will be run in real time.<h4>Conclusions</h4>The RALPMH study will provide a reference infrastructure for remote monitoring of lung diseases. It specifically involves information regarding the feasibility and acceptability of remote monitoring and the potential of real-time data collection and analysis in the context of chronic lung disorders. It will help plan and inform decisions in future studies in the area of respiratory health.<h4>Trial registration</h4>ISRCTN Registry ISRCTN16275601; https://www.isrctn.com/ISRCTN16275601.<h4>International registered report identifier (irrid)</h4>PRR1-10.2196/28873.",,pdf:https://jmir.org/api/download?alt_name=resprot_v10i10e28873_app2.pdf&filename=4dda9f18456291d5d5d6facee1b77a71.pdf; doi:https://doi.org/10.2196/28873; html:https://europepmc.org/articles/PMC8500349
 31822727,https://doi.org/10.1038/s41598-019-55098-7,Co-incidence of RCC-susceptibility polymorphisms with HIF cis-acting sequences supports a pathway tuning model of cancer.,"Schmid V, Lafleur VN, Lombardi O, Li R, Salama R, Colli L, Choudhry H, Chanock S, Ratcliffe PJ, Mole DR.",,Scientific reports,2019,2019-12-10,Y,,Understanding the Causes of Disease,,"Emerging evidence suggests that dysregulation of oncogenic pathways requires precise tuning in order for cancer to develop. To test this, we examined the overlap between cis-acting elements of the hypoxia-inducible factor (HIF) pathway and cancer-susceptibility polymorphisms as defined in genome-wide association studies (GWAS). In renal cancer, where HIF is constitutively and un-physiologically activated by mutation of the von Hippel-Lindau tumour suppressor, we observed marked excess overlap, which extended to potential susceptibility polymorphisms that are below the conventional threshold applied in GWAS. In contrast, in other cancers where HIF is upregulated by different mechanisms, including micro-environmental hypoxia, we observed no excess in overlap. Our findings support a 'pathway tuning' model of cancer, whereby precise modulation of multiple outputs of specific, activated pathways is important in oncogenesis. This implies that selective pressures to modulate such pathways operate during cancer development and should focus attempts to identify their nature and consequences.",This study investigated the association between proteins responsible for DNA replication the susceptibility to cancer using GWAS. ,pdf:https://www.nature.com/articles/s41598-019-55098-7.pdf; doi:https://doi.org/10.1038/s41598-019-55098-7; html:https://europepmc.org/articles/PMC6904466; pdf:https://europepmc.org/articles/PMC6904466?pdf=render
-35112706,https://doi.org/10.1242/dmm.049257,Molecular Subtyping Resource: a user-friendly tool for rapid biological discovery from transcriptional data.,"Ahmaderaghi B, Amirkhah R, Jackson J, Lannagan TRM, Gilroy K, Malla SB, Redmond KL, Quinn G, McDade SS, ACRCelerate Consortium, Maughan T, Leedham S, Campbell ASD, Sansom OJ, Lawler M, Dunne PD.",,Disease models & mechanisms,2022,2022-03-30,Y,Bioinformatics; Rna-seq; Data Analytics,,,"Generation of transcriptional data has dramatically increased in the past decade, driving the development of analytical algorithms that enable interrogation of the biology underpinning the profiled samples. However, these resources require users to have expertise in data wrangling and analytics, reducing opportunities for biological discovery by 'wet-lab' users with a limited programming skillset. Although commercial solutions exist, costs for software access can be prohibitive for academic research groups. To address these challenges, we have developed an open source and user-friendly data analysis platform for on-the-fly bioinformatic interrogation of transcriptional data derived from human or mouse tissue, called Molecular Subtyping Resource (MouSR). This internet-accessible analytical tool, https://mousr.qub.ac.uk/, enables users to easily interrogate their data using an intuitive 'point-and-click' interface, which includes a suite of molecular characterisation options including quality control, differential gene expression, gene set enrichment and microenvironmental cell population analyses from RNA sequencing. The MouSR online tool provides a unique freely available option for users to perform rapid transcriptomic analyses and comprehensive interrogation of the signalling underpinning transcriptional datasets, which alleviates a major bottleneck for biological discovery. This article has an associated First Person interview with the first author of the paper.",,doi:https://doi.org/10.1242/dmm.049257; doi:https://doi.org/10.1242/dmm.049257; html:https://europepmc.org/articles/PMC8990914
+36812516,https://doi.org/10.1371/journal.pdig.0000007,A proteomic survival predictor for COVID-19 patients in intensive care.,"Demichev V, Tober-Lau P, Nazarenko T, Lemke O, Kaur Aulakh S, Whitwell HJ, Röhl A, Freiwald A, Mittermaier M, Szyrwiel L, Ludwig D, Correia-Melo C, Lippert LJ, Helbig ET, Stubbemann P, Olk N, Thibeault C, Grüning NM, Blyuss O, Vernardis S, White M, Messner CB, Joannidis M, Sonnweber T, Klein SJ, Pizzini A, Wohlfarter Y, Sahanic S, Hilbe R, Schaefer B, Wagner S, Machleidt F, Garcia C, Ruwwe-Glösenkamp C, Lingscheid T, Bosquillon de Jarcy L, Stegemann MS, Pfeiffer M, Jürgens L, Denker S, Zickler D, Spies C, Edel A, Müller NB, Enghard P, Zelezniak A, Bellmann-Weiler R, Weiss G, Campbell A, Hayward C, Porteous DJ, Marioni RE, Uhrig A, Zoller H, Löffler-Ragg J, Keller MA, Tancevski I, Timms JF, Zaikin A, Hippenstiel S, Ramharter M, Müller-Redetzky H, Witzenrath M, Suttorp N, Lilley K, Mülleder M, Sander LE, PA-COVID-19 Study group, Kurth F, Ralser M.",,PLOS digital health,2022,2022-01-18,Y,,,,"Global healthcare systems are challenged by the COVID-19 pandemic. There is a need to optimize allocation of treatment and resources in intensive care, as clinically established risk assessments such as SOFA and APACHE II scores show only limited performance for predicting the survival of severely ill COVID-19 patients. Additional tools are also needed to monitor treatment, including experimental therapies in clinical trials. Comprehensively capturing human physiology, we speculated that proteomics in combination with new data-driven analysis strategies could produce a new generation of prognostic discriminators. We studied two independent cohorts of patients with severe COVID-19 who required intensive care and invasive mechanical ventilation. SOFA score, Charlson comorbidity index, and APACHE II score showed limited performance in predicting the COVID-19 outcome. Instead, the quantification of 321 plasma protein groups at 349 timepoints in 50 critically ill patients receiving invasive mechanical ventilation revealed 14 proteins that showed trajectories different between survivors and non-survivors. A predictor trained on proteomic measurements obtained at the first time point at maximum treatment level (i.e. WHO grade 7), which was weeks before the outcome, achieved accurate classification of survivors (AUROC 0.81). We tested the established predictor on an independent validation cohort (AUROC 1.0). The majority of proteins with high relevance in the prediction model belong to the coagulation system and complement cascade. Our study demonstrates that plasma proteomics can give rise to prognostic predictors substantially outperforming current prognostic markers in intensive care.",,pdf:https://journals.plos.org/digitalhealth/article/file?id=10.1371/journal.pdig.0000007&type=printable; doi:https://doi.org/10.1371/journal.pdig.0000007; html:https://europepmc.org/articles/PMC9931303; pdf:https://europepmc.org/articles/PMC9931303?pdf=render
 32936291,https://doi.org/10.1001/jamadermatol.2020.3275,Association of Clinical and Demographic Factors With the Severity of Palmoplantar Pustulosis.,"Benzian-Olsson N, Dand N, Chaloner C, Bata-Csorgo Z, Borroni R, Burden AD, Cooper HL, Cornelius V, Cro S, Dasandi T, Griffiths CEM, Kingo K, Koks S, Lachmann H, McAteer H, Meynell F, Mrowietz U, Parslew R, Patel P, Pink AE, Reynolds NJ, Tanew A, Torz K, Trattner H, Wahie S, Warren RB, Wright A, Barker JN, Navarini AA, Smith CH, Capon F, ERASPEN consortium and the APRICOT and PLUM study team.",,JAMA dermatology,2020,2020-11-01,Y,,,,"<h4>Importance</h4>Although palmoplantar pustulosis (PPP) can significantly impact quality of life, the factors underlying disease severity have not been studied.<h4>Objective</h4>To examine the factors associated with PPP severity.<h4>Design, setting, and participants</h4>An observational, cross-sectional study of 2 cohorts was conducted. A UK data set including 203 patients was obtained through the Anakinra in Pustular Psoriasis, Response in a Controlled Trial (2016-2019) and its sister research study Pustular Psoriasis, Elucidating Underlying Mechanisms (2016-2020). A Northern European cohort including 193 patients was independently ascertained by the European Rare and Severe Psoriasis Expert Network (2014-2017). Patients had been recruited in secondary or tertiary dermatology referral centers. All patients were of European descent. The PPP diagnosis was established by dermatologists, based on clinical examination and/or published consensus criteria. The present study was conducted from October 1, 2014, to March 15, 2020.<h4>Main outcomes and measures</h4>Demographic characteristics, comorbidities, smoking status, Palmoplantar Pustulosis Psoriasis Area Severity Index (PPPASI), measuring severity from 0 (no sign of disease) to 72 (very severe disease), or Physician Global Assessment (PGA), measuring severity as 0 (clear), 1 (almost clear), 2 (mild), 3 (moderate), and 4 (severe).<h4>Results</h4>Among the 203 UK patients (43 men [21%], 160 women [79%]; median age at onset, 48 [interquartile range (IQR), 38-59] years), the PPPASI was inversely correlated with age of onset (r = -0.18, P = .01). Similarly, in the 159 Northern European patients who were eligible for inclusion in this analysis (25 men [16%], 134 women [84%]; median age at onset, 45 [IQR, 34-53.3] years), the median age at onset was lower in individuals with a moderate to severe PGA score (41 years [IQR, 30.5-52 years]) compared with those with a clear to mild PGA score (46.5 years [IQR, 35-55 years]) (P = .04). In the UK sample, the median PPPASI score was higher in women (9.6 [IQR, 3.0-16.2]) vs men (4.0 [IQR, 1.0-11.7]) (P = .01). Likewise, moderate to severe PPP was more prevalent among Northern European women (57 of 134 [43%]) compared with men (5 of 25 [20%]) (P = .03). In the UK cohort, the median PPPASI score was increased in current smokers (10.7 [IQR, 4.2-17.5]) compared with former smokers (7 [IQR, 2.0-14.4]) and nonsmokers (2.2 [IQR, 1-6]) (P = .003). Comparable differences were observed in the Northern European data set, as the prevalence of moderate to severe PPP was higher in former and current smokers (51 of 130 [39%]) compared with nonsmokers (6 of 24 [25%]) (P = .14).<h4>Conclusions and relevance</h4>The findings of this study suggest that PPP severity is associated with early-onset disease, female sex, and smoking status. Thus, smoking cessation intervention might be beneficial.",,pdf:https://jamanetwork.com/journals/jamadermatology/articlepdf/2770779/jamadermatology_benzianolsson_2020_oi_200054_1604610894.93046.pdf; doi:https://doi.org/10.1001/jamadermatol.2020.3275; html:https://europepmc.org/articles/PMC7495329
+35112706,https://doi.org/10.1242/dmm.049257,Molecular Subtyping Resource: a user-friendly tool for rapid biological discovery from transcriptional data.,"Ahmaderaghi B, Amirkhah R, Jackson J, Lannagan TRM, Gilroy K, Malla SB, Redmond KL, Quinn G, McDade SS, ACRCelerate Consortium, Maughan T, Leedham S, Campbell ASD, Sansom OJ, Lawler M, Dunne PD.",,Disease models & mechanisms,2022,2022-03-30,Y,Bioinformatics; Rna-seq; Data Analytics,,,"Generation of transcriptional data has dramatically increased in the past decade, driving the development of analytical algorithms that enable interrogation of the biology underpinning the profiled samples. However, these resources require users to have expertise in data wrangling and analytics, reducing opportunities for biological discovery by 'wet-lab' users with a limited programming skillset. Although commercial solutions exist, costs for software access can be prohibitive for academic research groups. To address these challenges, we have developed an open source and user-friendly data analysis platform for on-the-fly bioinformatic interrogation of transcriptional data derived from human or mouse tissue, called Molecular Subtyping Resource (MouSR). This internet-accessible analytical tool, https://mousr.qub.ac.uk/, enables users to easily interrogate their data using an intuitive 'point-and-click' interface, which includes a suite of molecular characterisation options including quality control, differential gene expression, gene set enrichment and microenvironmental cell population analyses from RNA sequencing. The MouSR online tool provides a unique freely available option for users to perform rapid transcriptomic analyses and comprehensive interrogation of the signalling underpinning transcriptional datasets, which alleviates a major bottleneck for biological discovery. This article has an associated First Person interview with the first author of the paper.",,doi:https://doi.org/10.1242/dmm.049257; doi:https://doi.org/10.1242/dmm.049257; html:https://europepmc.org/articles/PMC8990914
 35337642,https://doi.org/10.1016/s2589-7500(22)00018-8,"Implementation of corticosteroids in treatment of COVID-19 in the ISARIC WHO Clinical Characterisation Protocol UK: prospective, cohort study.","Närhi F, Moonesinghe SR, Shenkin SD, Drake TM, Mulholland RH, Donegan C, Dunning J, Fairfield CJ, Girvan M, Hardwick HE, Ho A, Leeming G, Nguyen-Van-Tam JS, Pius R, Russell CD, Shaw CA, Spencer RG, Turtle L, Openshaw PJM, Baillie JK, Harrison EM, Semple MG, Docherty AB, ISARIC4C investigators.",,The Lancet. Digital health,2022,2022-04-01,Y,,,,"<h4>Background</h4>Dexamethasone was the first intervention proven to reduce mortality in patients with COVID-19 being treated in hospital. We aimed to evaluate the adoption of corticosteroids in the treatment of COVID-19 in the UK after the RECOVERY trial publication on June 16, 2020, and to identify discrepancies in care.<h4>Methods</h4>We did an audit of clinical implementation of corticosteroids in a prospective, observational, cohort study in 237 UK acute care hospitals between March 16, 2020, and April 14, 2021, restricted to patients aged 18 years or older with proven or high likelihood of COVID-19, who received supplementary oxygen. The primary outcome was administration of dexamethasone, prednisolone, hydrocortisone, or methylprednisolone. This study is registered with ISRCTN, ISRCTN66726260.<h4>Findings</h4>Between June 17, 2020, and April 14, 2021, 47 795 (75·2%) of 63 525 of patients on supplementary oxygen received corticosteroids, higher among patients requiring critical care than in those who received ward care (11 185 [86·6%] of 12 909 vs 36 415 [72·4%] of 50 278). Patients 50 years or older were significantly less likely to receive corticosteroids than those younger than 50 years (adjusted odds ratio 0·79 [95% CI 0·70-0·89], p=0·0001, for 70-79 years; 0·52 [0·46-0·58], p<0·0001, for >80 years), independent of patient demographics and illness severity. 84 (54·2%) of 155 pregnant women received corticosteroids. Rates of corticosteroid administration increased from 27·5% in the week before June 16, 2020, to 75-80% in January, 2021.<h4>Interpretation</h4>Implementation of corticosteroids into clinical practice in the UK for patients with COVID-19 has been successful, but not universal. Patients older than 70 years, independent of illness severity, chronic neurological disease, and dementia, were less likely to receive corticosteroids than those who were younger, as were pregnant women. This could reflect appropriate clinical decision making, but the possibility of inequitable access to life-saving care should be considered.<h4>Funding</h4>UK National Institute for Health Research and UK Medical Research Council.",,pdf:http://www.thelancet.com/article/S2589750022000188/pdf; doi:https://doi.org/10.1016/S2589-7500(22)00018-8; html:https://europepmc.org/articles/PMC8940185
-36812516,https://doi.org/10.1371/journal.pdig.0000007,A proteomic survival predictor for COVID-19 patients in intensive care.,"Demichev V, Tober-Lau P, Nazarenko T, Lemke O, Kaur Aulakh S, Whitwell HJ, Röhl A, Freiwald A, Mittermaier M, Szyrwiel L, Ludwig D, Correia-Melo C, Lippert LJ, Helbig ET, Stubbemann P, Olk N, Thibeault C, Grüning NM, Blyuss O, Vernardis S, White M, Messner CB, Joannidis M, Sonnweber T, Klein SJ, Pizzini A, Wohlfarter Y, Sahanic S, Hilbe R, Schaefer B, Wagner S, Machleidt F, Garcia C, Ruwwe-Glösenkamp C, Lingscheid T, Bosquillon de Jarcy L, Stegemann MS, Pfeiffer M, Jürgens L, Denker S, Zickler D, Spies C, Edel A, Müller NB, Enghard P, Zelezniak A, Bellmann-Weiler R, Weiss G, Campbell A, Hayward C, Porteous DJ, Marioni RE, Uhrig A, Zoller H, Löffler-Ragg J, Keller MA, Tancevski I, Timms JF, Zaikin A, Hippenstiel S, Ramharter M, Müller-Redetzky H, Witzenrath M, Suttorp N, Lilley K, Mülleder M, Sander LE, PA-COVID-19 Study group, Kurth F, Ralser M.",,PLOS digital health,2022,2022-01-18,Y,,,,"Global healthcare systems are challenged by the COVID-19 pandemic. There is a need to optimize allocation of treatment and resources in intensive care, as clinically established risk assessments such as SOFA and APACHE II scores show only limited performance for predicting the survival of severely ill COVID-19 patients. Additional tools are also needed to monitor treatment, including experimental therapies in clinical trials. Comprehensively capturing human physiology, we speculated that proteomics in combination with new data-driven analysis strategies could produce a new generation of prognostic discriminators. We studied two independent cohorts of patients with severe COVID-19 who required intensive care and invasive mechanical ventilation. SOFA score, Charlson comorbidity index, and APACHE II score showed limited performance in predicting the COVID-19 outcome. Instead, the quantification of 321 plasma protein groups at 349 timepoints in 50 critically ill patients receiving invasive mechanical ventilation revealed 14 proteins that showed trajectories different between survivors and non-survivors. A predictor trained on proteomic measurements obtained at the first time point at maximum treatment level (i.e. WHO grade 7), which was weeks before the outcome, achieved accurate classification of survivors (AUROC 0.81). We tested the established predictor on an independent validation cohort (AUROC 1.0). The majority of proteins with high relevance in the prediction model belong to the coagulation system and complement cascade. Our study demonstrates that plasma proteomics can give rise to prognostic predictors substantially outperforming current prognostic markers in intensive care.",,pdf:https://journals.plos.org/digitalhealth/article/file?id=10.1371/journal.pdig.0000007&type=printable; doi:https://doi.org/10.1371/journal.pdig.0000007; html:https://europepmc.org/articles/PMC9931303; pdf:https://europepmc.org/articles/PMC9931303?pdf=render
 31477933,https://doi.org/10.1038/s41588-019-0484-x,A method for genome-wide genealogy estimation for thousands of samples.,"Speidel L, Forest M, Shi S, Myers SR.",,Nature genetics,2019,2019-09-02,N,,,,"Knowledge of genome-wide genealogies for thousands of individuals would simplify most evolutionary analyses for humans and other species, but has remained computationally infeasible. We have developed a method, Relate, scaling to >10,000 sequences while simultaneously estimating branch lengths, mutational ages and variable historical population sizes, as well as allowing for data errors. Application to 1,000 Genomes Project haplotypes produces joint genealogical histories for 26 human populations. Highly diverged lineages are present in all groups, but most frequent in Africa. Outside Africa, these mainly reflect ancient introgression from groups related to Neanderthals and Denisovans, while African signals instead reflect unknown events unique to that continent. Our approach allows more powerful inferences of natural selection than has previously been possible. We identify multiple regions under strong positive selection, and multi-allelic traits including hair color, body mass index and blood pressure, showing strong evidence of directional selection, varying among human groups.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7610517; doi:https://doi.org/10.1038/s41588-019-0484-x; html:https://europepmc.org/articles/PMC7610517; pdf:https://europepmc.org/articles/PMC7610517?pdf=render; doi:https://doi.org/10.1038/s41588-019-0484-x
 35977952,https://doi.org/10.1038/s41467-022-29931-z,GWAS meta-analysis of intrahepatic cholestasis of pregnancy implicates multiple hepatic genes and regulatory elements.,"Dixon PH, Levine AP, Cebola I, Chan MMY, Amin AS, Aich A, Mozere M, Maude H, Mitchell AL, Zhang J, NIHR BioResource, Genomics England Research Consortium Collaborators, Chambers J, Syngelaki A, Donnelly J, Cooley S, Geary M, Nicolaides K, Thorsell M, Hague WM, Estiu MC, Marschall HU, Gale DP, Williamson C.",,Nature communications,2022,2022-08-17,Y,,,,"Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disorder affecting 0.5-2% of pregnancies. The majority of cases present in the third trimester with pruritus, elevated serum bile acids and abnormal serum liver tests. ICP is associated with an increased risk of adverse outcomes, including spontaneous preterm birth and stillbirth. Whilst rare mutations affecting hepatobiliary transporters contribute to the aetiology of ICP, the role of common genetic variation in ICP has not been systematically characterised to date. Here, we perform genome-wide association studies (GWAS) and meta-analyses for ICP across three studies including 1138 cases and 153,642 controls. Eleven loci achieve genome-wide significance and have been further investigated and fine-mapped using functional genomics approaches. Our results pinpoint common sequence variation in liver-enriched genes and liver-specific cis-regulatory elements as contributing mechanisms to ICP susceptibility.",,pdf:https://www.nature.com/articles/s41467-022-29931-z.pdf; doi:https://doi.org/10.1038/s41467-022-29931-z; html:https://europepmc.org/articles/PMC9385867; pdf:https://europepmc.org/articles/PMC9385867?pdf=render
 36845321,https://doi.org/10.12688/wellcomeopenres.17403.2,"Characteristics and outcomes of COVID-19 patients with COPD from the United States, South Korea, and Europe.","Moreno-Martos D, Verhamme K, Ostropolets A, Kostka K, Duarte-Sales T, Prieto-Alhambra D, Alshammari TM, Alghoul H, Ahmed WU, Blacketer C, DuVall S, Lai L, Matheny M, Nyberg F, Posada J, Rijnbeek P, Spotnitz M, Sena A, Shah N, Suchard M, Chan You S, Hripcsak G, Ryan P, Morales D.",,Wellcome open research,2022,2022-03-24,Y,COPD; Coronavirus; Epidemiology.; Sars-cov-2; Covid,,,"<b>Background</b>: Characterization studies of COVID-19 patients with chronic obstructive pulmonary disease (COPD) are limited in size and scope. The aim of the study is to provide a large-scale characterization of COVID-19 patients with COPD. <b>Methods</b>: We included thirteen databases contributing data from January-June 2020 from North America (US), Europe and Asia. We defined two cohorts of patients with COVID-19 namely a 'diagnosed' and 'hospitalized' cohort. We followed patients from COVID-19 index date to 30 days or death. We performed descriptive analysis and reported the frequency of characteristics and outcomes among COPD patients with COVID-19. <b>Results</b>: The study included 934,778 patients in the diagnosed COVID-19 cohort and 177,201 in the hospitalized COVID-19 cohort. Observed COPD prevalence in the diagnosed cohort ranged from 3.8% (95%CI 3.5-4.1%) in French data to 22.7% (95%CI 22.4-23.0) in US data, and from 1.9% (95%CI 1.6-2.2) in South Korean to 44.0% (95%CI 43.1-45.0) in US data, in the hospitalized cohorts. COPD patients in the hospitalized cohort had greater comorbidity than those in the diagnosed cohort, including hypertension, heart disease, diabetes and obesity. Mortality was higher in COPD patients in the hospitalized cohort and ranged from 7.6% (95%CI 6.9-8.4) to 32.2% (95%CI 28.0-36.7) across databases. ARDS, acute renal failure, cardiac arrhythmia and sepsis were the most common outcomes among hospitalized COPD patients.   <b>Conclusion</b>: COPD patients with COVID-19 have high levels of COVID-19-associated comorbidities and poor COVID-19 outcomes. Further research is required to identify patients with COPD at high risk of worse outcomes.",,doi:https://doi.org/10.12688/wellcomeopenres.17403.2; html:https://europepmc.org/articles/PMC9951545; pdf:https://europepmc.org/articles/PMC9951545?pdf=render
@@ -2622,15 +2624,15 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 34022072,https://doi.org/10.1002/14651858.cd012721.pub3,Beta-blockers and inhibitors of the renin-angiotensin aldosterone system for chronic heart failure with preserved ejection fraction.,"Martin N, Manoharan K, Davies C, Lumbers RT.",,The Cochrane database of systematic reviews,2021,2021-05-22,N,,,,"<h4>Background</h4>Beta-blockers and inhibitors of the renin-angiotensin-aldosterone system improve survival and reduce morbidity in people with heart failure with reduced left ventricular ejection fraction (LVEF); a review of the evidence is required to determine whether these treatments are beneficial for people with heart failure with preserved ejection fraction (HFpEF).<h4>Objectives</h4>To assess the effects of beta-blockers, angiotensin-converting enzyme inhibitors, angiotensin receptor blockers, angiotensin receptor neprilysin inhibitors, and mineralocorticoid receptor antagonists in people with HFpEF.<h4>Search methods</h4>We updated searches of CENTRAL, MEDLINE, Embase, and one clinical trial register on 14 May 2020 to identify eligible studies, with no language or date restrictions. We checked references from trial reports and review articles for additional studies.  SELECTION CRITERIA: We included randomised controlled trials with a parallel group design, enrolling adults with HFpEF, defined by LVEF greater than 40%.<h4>Data collection and analysis</h4>We used standard methodological procedures expected by Cochrane.<h4>Main results</h4>We included 41 randomised controlled trials (231 reports), totalling 23,492 participants across all comparisons. The risk of bias was frequently unclear and only five studies had a low risk of bias in all domains. Beta-blockers (BBs) We included 10 studies (3087 participants) investigating BBs. Five studies used a placebo comparator and in five the comparator was usual care. The mean age of participants ranged from 30 years to 81 years. A possible reduction in cardiovascular mortality was observed (risk ratio (RR) 0.78, 95% confidence interval (CI) 0.62 to 0.99; number needed to treat for an additional benefit (NNTB) 25; 1046 participants; three studies), however, the certainty of evidence was low. There may be little to no effect on all-cause mortality (RR 0.82, 95% CI 0.67 to 1.00; 1105 participants; four studies; low-certainty evidence). The effects on heart failure hospitalisation, hyperkalaemia, and quality of life remain uncertain. Mineralocorticoid receptor antagonists (MRAs) We included 13 studies (4459 participants) investigating MRA. Eight studies used a placebo comparator and in five the comparator was usual care. The mean age of participants ranged from 54.5 to 80 years. Pooled analysis indicated that MRA treatment probably reduces heart failure hospitalisation (RR 0.82, 95% CI 0.69 to 0.98; NNTB = 41; 3714 participants; three studies; moderate-certainty evidence). However, MRA treatment probably has little or no effect on all-cause mortality (RR 0.91, 95% CI 0.78 to 1.06; 4207 participants; five studies; moderate-certainty evidence) and cardiovascular mortality (RR 0.90, 95% CI 0.74 to 1.11; 4070 participants; three studies; moderate-certainty evidence). MRA treatment may have little or no effect on quality of life measures (mean difference (MD) 0.84, 95% CI -2.30 to 3.98; 511 participants; three studies; low-certainty evidence). MRA treatment was associated with a higher risk of hyperkalaemia (RR 2.11, 95% CI 1.77 to 2.51; number needed to treat for an additional harmful outcome (NNTH) = 11; 4291 participants; six studies; high-certainty evidence). Angiotensin-converting enzyme inhibitors (ACEIs) We included eight studies (2061 participants) investigating ACEIs. Three studies used a placebo comparator and in five the comparator was usual care. The mean age of participants ranged from 70 to 82 years. Pooled analyses with moderate-certainty evidence suggest that ACEI treatment likely has little or no effect on cardiovascular mortality (RR 0.93, 95% CI 0.61 to 1.42; 945 participants; two studies), all-cause mortality (RR 1.04, 95% CI 0.75 to 1.45; 1187 participants; five studies) and heart failure hospitalisation (RR 0.86, 95% CI 0.64 to 1.15; 1019 participants; three studies), and may result in little or no effect on the quality of life (MD -0.09, 95% CI -3.66 to 3.48; 154 participants; two studies; low-certainty evidence). The effects on hyperkalaemia remain uncertain. Angiotensin receptor blockers (ARBs) Eight studies (8755 participants) investigating ARBs were included. Five studies used a placebo comparator and in three the comparator was usual care. The mean age of participants ranged from 61 to 75 years. Pooled analyses with high certainty of evidence suggest that ARB treatment has little or no effect on cardiovascular mortality (RR 1.02, 95% 0.90 to 1.14; 7254 participants; three studies), all-cause mortality (RR 1.01, 95% CI 0.92 to 1.11; 7964 participants; four studies), heart failure hospitalisation (RR 0.92, 95% CI 0.83 to 1.02; 7254 participants; three studies), and quality of life (MD 0.41, 95% CI -0.86 to 1.67; 3117 participants; three studies). ARB was associated with a higher risk of hyperkalaemia (RR 1.88, 95% CI 1.07 to 3.33; 7148 participants; two studies; high-certainty evidence). Angiotensin receptor neprilysin inhibitors (ARNIs) Three studies (7702 participants) investigating ARNIs were included. Two studies used ARBs as the comparator and one used standardised medical therapy, based on participants' established treatments at enrolment. The mean age of participants ranged from 71 to 73 years. Results suggest that ARNIs may have little or no effect on cardiovascular mortality (RR 0.96, 95% CI 0.79 to 1.15; 4796 participants; one study; moderate-certainty evidence), all-cause mortality (RR 0.97, 95% CI 0.84 to 1.11; 7663 participants; three studies; high-certainty evidence), or quality of life (high-certainty evidence). However, ARNI treatment may result in a slight reduction in heart failure hospitalisation, compared to usual care (RR 0.89, 95% CI 0.80 to 1.00; 7362 participants; two studies; moderate-certainty evidence). ARNI treatment was associated with a reduced risk of hyperkalaemia compared with valsartan (RR 0.88, 95% CI 0.77 to 1.01; 5054 participants; two studies; moderate-certainty evidence).<h4>Authors' conclusions</h4>There is evidence that MRA and ARNI treatment in HFpEF probably reduces heart failure hospitalisation but probably has little or no effect on cardiovascular mortality and quality of life. BB treatment may reduce the risk of cardiovascular mortality, however, further trials are needed. The current evidence for BBs, ACEIs, and ARBs is limited and does not support their use in HFpEF in the absence of an alternative indication. Although MRAs and ARNIs are probably effective at reducing the risk of heart failure hospitalisation, the treatment effect sizes are modest. There is a need for improved approaches to patient stratification to identify the subgroup of patients who are most likely to benefit from MRAs and ARNIs, as well as for an improved understanding of disease biology, and for new therapeutic approaches.",,pdf:https://discovery.ucl.ac.uk/10044558/1/Lumbers_et_al-2017-.pdf; doi:https://doi.org/10.1002/14651858.CD012721.pub3; html:https://europepmc.org/articles/PMC8140651; pdf:https://europepmc.org/articles/PMC8140651?pdf=render; doi:https://doi.org/10.1002/14651858.cd012721.pub3
 36053624,https://doi.org/10.1136/bmjpo-2022-001543,Use of parenteral nutrition in the first postnatal week in England and Wales: an observational study using real-world data.,"Webbe J, Battersby C, Longford N, Oughham K, Uthaya S, Modi N, Gale C.",,BMJ paediatrics open,2022,2022-08-01,Y,epidemiology; Neonatology,,,"<h4>Background</h4>Parenteral nutrition (PN) is used to provide supplemental support to neonates while enteral feeding is being established. PN is a high-cost intervention with beneficial and harmful effects. Internationally, there is substantial variation in how PN is used, and there are limited contemporary data describing use across Great Britain.<h4>Objective</h4>To describe PN use in the first postnatal week in infants born and admitted to neonatal care in England, Scotland and Wales.<h4>Method</h4>Data describing neonates admitted to National Health Service neonatal units between 1 January 2012 and 31 December 2017, extracted from routinely recorded data held the National Neonatal Research Database (NNRD); the denominator was live births, from Office for National Statistics.<h4>Results</h4>Over the study period 62 145 neonates were given PN in the first postnatal week (1.4% of all live births); use was higher in more preterm neonates (76% of livebirths at <28 weeks, 0.2% of term livebirths) and in neonates with lower birth weight. 15% (9181/62145) of neonates given PN in the first postnatal week were born at term. There was geographic variation in PN administration: the proportion of live births given PN within neonatal regional networks ranged from 1.0% (95% CIs 1.0 to 1.0) to 2.8% (95% CI 2.7 to 2.9).<h4>Conclusions and relevance</h4>Significant variation exists in neonatal PN use; it is unlikely this reflects optimal use of an expensive intervention. Research is needed to identify which babies will benefit most and which are at risk of harm from early PN.<h4>Trial registration number</h4>ClinicalTrials.gov: NCT03767634; registration date: 6 December 2018.",,pdf:https://bmjpaedsopen.bmj.com/content/bmjpo/6/1/e001543.full.pdf; doi:https://doi.org/10.1136/bmjpo-2022-001543; html:https://europepmc.org/articles/PMC9422803; pdf:https://europepmc.org/articles/PMC9422803?pdf=render
 35876425,https://doi.org/10.1002/mds.29147,"MED27, SLC6A7, and MPPE1 Variants in a Complex Neurodevelopmental Disorder with Severe Dystonia.","Reid KM, Spaull R, Salian S, Barwick K, Meyer E, Zhen J, Hirata H, Sheipouri D, Benkerroum H, Gorman KM, Papandreou A, Simpson MA, Hirano Y, Farabella I, Topf M, Grozeva D, Carss K, Smith M, Pall H, Lunt P, De Gressi S, Kamsteeg EJ, Haack TB, Carr L, Guerreiro R, Bras J, Maher ER, Scott RH, Vandenberg RJ, Raymond FL, Chong WK, Sudhakar S, Mankad K, Reith ME, Campeau PM, Harvey RJ, Kurian MA.",,Movement disorders : official journal of the Movement Disorder Society,2022,2022-07-25,Y,Dystonia; Status Dystonicus; Med27; Mppe1; Slc6a7,,,"<h4>Background</h4>Despite advances in next generation sequencing technologies, the identification of variants of uncertain significance (VUS) can often hinder definitive diagnosis in patients with complex neurodevelopmental disorders.<h4>Objective</h4>The objective of this study was to identify and characterize the underlying cause of disease in a family with two children with severe developmental delay associated with generalized dystonia and episodic status dystonicus, chorea, epilepsy, and cataracts.<h4>Methods</h4>Candidate genes identified by autozygosity mapping and whole-exome sequencing were characterized using cellular and vertebrate model systems.<h4>Results</h4>Homozygous variants were found in three candidate genes: MED27, SLC6A7, and MPPE1. Although the patients had features of MED27-related disorder, the SLC6A7 and MPPE1 variants were functionally investigated. SLC6A7 variant in vitro overexpression caused decreased proline transport as a result of reduced cell-surface expression, and zebrafish knockdown of slc6a7 exhibited developmental delay and fragile motor neuron morphology that could not be rescued by L-proline transporter-G396S RNA. Lastly, patient fibroblasts displayed reduced cell-surface expression of glycophosphatidylinositol-anchored proteins linked to MPPE1 dysfunction.<h4>Conclusions</h4>We report a family harboring a homozygous MED27 variant with additional loss-of-function SLC6A7 and MPPE1 gene variants, which potentially contribute to a blended phenotype caused by multilocus pathogenic variants. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.",,pdf:https://research-information.bris.ac.uk/ws/files/338319463/Movement_Disorders_2022_Reid_MED27_SLC6A7_and_MPPE1_Variants_in_a_Complex_Neurodevelopmental_Disorder_with_Severe.pdf; doi:https://doi.org/10.1002/mds.29147; html:https://europepmc.org/articles/PMC9796674; pdf:https://europepmc.org/articles/PMC9796674?pdf=render
+32907855,https://doi.org/10.1136/bmj.m3339,Risk stratification of patients admitted to hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: development and validation of the 4C Mortality Score.,"Knight SR, Ho A, Pius R, Buchan I, Carson G, Drake TM, Dunning J, Fairfield CJ, Gamble C, Green CA, Gupta R, Halpin S, Hardwick HE, Holden KA, Horby PW, Jackson C, Mclean KA, Merson L, Nguyen-Van-Tam JS, Norman L, Noursadeghi M, Olliaro PL, Pritchard MG, Russell CD, Shaw CA, Sheikh A, Solomon T, Sudlow C, Swann OV, Turtle LC, Openshaw PJ, Baillie JK, Semple MG, Docherty AB, Harrison EM, ISARIC4C investigators.",,BMJ (Clinical research ed.),2020,2020-09-09,Y,,,,"<h4>Objective</h4>To develop and validate a pragmatic risk score to predict mortality in patients admitted to hospital with coronavirus disease 2019 (covid-19).<h4>Design</h4>Prospective observational cohort study.<h4>Setting</h4>International Severe Acute Respiratory and emerging Infections Consortium (ISARIC) World Health Organization (WHO) Clinical Characterisation Protocol UK (CCP-UK) study (performed by the ISARIC Coronavirus Clinical Characterisation Consortium-ISARIC-4C) in 260 hospitals across England, Scotland, and Wales. Model training was performed on a cohort of patients recruited between 6 February and 20 May 2020, with validation conducted on a second cohort of patients recruited after model development between 21 May and 29 June 2020<i>.</i> PARTICIPANTS: Adults (age ≥18 years) admitted to hospital with covid-19 at least four weeks before final data extraction.<h4>Main outcome measure</h4>In-hospital mortality.<h4>Results</h4>35 463 patients were included in the derivation dataset (mortality rate 32.2%) and 22 361 in the validation dataset (mortality rate 30.1%). The final 4C Mortality Score included eight variables readily available at initial hospital assessment: age, sex, number of comorbidities, respiratory rate, peripheral oxygen saturation, level of consciousness, urea level, and C reactive protein (score range 0-21 points). The 4C Score showed high discrimination for mortality (derivation cohort: area under the receiver operating characteristic curve 0.79, 95% confidence interval 0.78 to 0.79; validation cohort: 0.77, 0.76 to 0.77) with excellent calibration (validation: calibration-in-the-large=0, slope=1.0). Patients with a score of at least 15 (n=4158, 19%) had a 62% mortality (positive predictive value 62%) compared with 1% mortality for those with a score of 3 or less (n=1650, 7%; negative predictive value 99%). Discriminatory performance was higher than 15 pre-existing risk stratification scores (area under the receiver operating characteristic curve range 0.61-0.76), with scores developed in other covid-19 cohorts often performing poorly (range 0.63-0.73).<h4>Conclusions</h4>An easy-to-use risk stratification score has been developed and validated based on commonly available parameters at hospital presentation. The 4C Mortality Score outperformed existing scores, showed utility to directly inform clinical decision making, and can be used to stratify patients admitted to hospital with covid-19 into different management groups. The score should be further validated to determine its applicability in other populations.<h4>Study registration</h4>ISRCTN66726260.",,pdf:https://www.bmj.com/content/bmj/370/bmj.m3339.full.pdf; doi:https://doi.org/10.1136/bmj.m3339; html:https://europepmc.org/articles/PMC7116472; pdf:https://europepmc.org/articles/PMC7116472?pdf=render
 35411997,https://doi.org/10.1111/tmi.13752,"Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa.","Davies MA, Kassanjee R, Rousseau P, Morden E, Johnson L, Solomon W, Hsiao NY, Hussey H, Meintjes G, Paleker M, Jacobs T, Raubenheimer P, Heekes A, Dane P, Bam JL, Smith M, Preiser W, Pienaar D, Mendelson M, Naude J, Schrueder N, Mnguni A, Le Roux S, Murie K, Prozesky H, Mahomed H, Rossouw L, Wasserman S, Maughan D, Boloko L, Smith B, Taljaard J, Symons G, Ntusi NAB, Parker A, Wolter N, Jassat W, Cohen C, Lessells R, Wilkinson RJ, Arendse J, Kariem S, Moodley M, Wolmarans M, Cloete K, Boulle A, Western Cape and South African National Departments of Health in collaboration with the National Institute for Communicable Diseases in South Africa Affiliations.",,Tropical medicine & international health : TM & IH,2022,2022-05-10,Y,Vaccination; Immunity; DELTA; Sub-Saharan Africa; Covid-19; Prior Infection; Omicron,,,"<h4>Objectives</h4>The objective was to compare COVID-19 outcomes in the Omicron-driven fourth wave with prior waves in the Western Cape, assess the contribution of undiagnosed prior infection to differences in outcomes in a context of high seroprevalence due to prior infection and determine whether protection against severe disease conferred by prior infection and/or vaccination was maintained.<h4>Methods</h4>In this cohort study, we included public sector patients aged ≥20 years with a laboratory-confirmed COVID-19 diagnosis between 14 November and 11 December 2021 (wave four) and equivalent prior wave periods. We compared the risk between waves of the following outcomes using Cox regression: death, severe hospitalisation or death and any hospitalisation or death (all ≤14 days after diagnosis) adjusted for age, sex, comorbidities, geography, vaccination and prior infection.<h4>Results</h4>We included 5144 patients from wave four and 11,609 from prior waves. The risk of all outcomes was lower in wave four compared to the Delta-driven wave three (adjusted hazard ratio (aHR) [95% confidence interval (CI)] for death 0.27 [0.19; 0.38]. Risk reduction was lower when adjusting for vaccination and prior diagnosed infection (aHR: 0.41, 95% CI: 0.29; 0.59) and reduced further when accounting for unascertained prior infections (aHR: 0.72). Vaccine protection was maintained in wave four (aHR for outcome of death: 0.24; 95% CI: 0.10; 0.58).<h4>Conclusions</h4>In the Omicron-driven wave, severe COVID-19 outcomes were reduced mostly due to protection conferred by prior infection and/or vaccination, but intrinsically reduced virulence may account for a modest reduction in risk of severe hospitalisation or death compared to the Delta-driven wave.",,pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/tmi.13752; doi:https://doi.org/10.1111/tmi.13752; html:https://europepmc.org/articles/PMC9115442; pdf:https://europepmc.org/articles/PMC9115442?pdf=render
 36442657,https://doi.org/10.1016/j.jad.2022.11.051,Factors associated with anxiety disorder comorbidity.,"Davies MR, Glen K, Mundy J, Ter Kuile AR, Adey BN, Armour C, Assary E, Coleman JRI, Goldsmith KA, Hirsch CR, Hotopf M, Hübel C, Jones IR, Kalsi G, Krebs G, McIntosh AM, Morneau-Vaillancourt G, Peel AJ, Purves KL, Lee SH, Skelton M, Smith DJ, Veale D, Walters JTR, Young KS, Zvrskovec J, Breen G, Eley TC.",,Journal of affective disorders,2023,2022-11-26,Y,Affective Disorders; Comorbidity; Anxiety Disorders; Depressive Disorders; Polygenic Risk Score,,,"<h4>Background</h4>Anxiety and depressive disorders often co-occur and the order of their emergence may be associated with different clinical outcomes. However, minimal research has been conducted on anxiety-anxiety comorbidity. This study examined factors associated with anxiety comorbidity and anxiety-MDD temporal sequence.<h4>Methods</h4>Online, self-report data were collected from the UK-based GLAD and COPING NBR cohorts (N = 38,775). Logistic regression analyses compared differences in sociodemographic, trauma, and clinical factors between single anxiety, anxiety-anxiety comorbidity, anxiety-MDD (major depressive disorder) comorbidity, and MDD-only. Additionally, anxiety-first and MDD-first anxiety-MDD were compared. Differences in familial risk were assessed in those participants with self-reported family history or genotype data.<h4>Results</h4>Anxiety-anxiety and anxiety-MDD had higher rates of self-reported anxiety or depressive disorder diagnoses, younger age of onset, and higher recurrence than single anxiety. Anxiety-MDD displayed greater clinical severity/complexity than MDD only. Anxiety-anxiety had more severe current anxiety symptoms, less severe current depressive symptoms, and reduced likelihood of self-reporting an anxiety/depressive disorder diagnosis than anxiety-MDD. Anxiety-first anxiety-MDD had a younger age of onset, more severe anxiety symptoms, and less likelihood of self-reporting a diagnosis than MDD-first. Minimal differences in familial risk were found.<h4>Limitations</h4>Self-report, retrospective measures may introduce recall bias. The familial risk analyses were likely underpowered.<h4>Conclusions</h4>Anxiety-anxiety comorbidity displayed a similarly severe and complex profile of symptoms as anxiety-MDD but distinct features. For anxiety-MDD, first-onset anxiety had an earlier age of onset and greater severity than MDD-first. Anxiety disorders and comorbidity warrant further investigation and attention in research and practice.",,doi:https://doi.org/10.1016/j.jad.2022.11.051; doi:https://doi.org/10.1016/j.jad.2022.11.051; html:https://europepmc.org/articles/PMC10202820
-32907855,https://doi.org/10.1136/bmj.m3339,Risk stratification of patients admitted to hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: development and validation of the 4C Mortality Score.,"Knight SR, Ho A, Pius R, Buchan I, Carson G, Drake TM, Dunning J, Fairfield CJ, Gamble C, Green CA, Gupta R, Halpin S, Hardwick HE, Holden KA, Horby PW, Jackson C, Mclean KA, Merson L, Nguyen-Van-Tam JS, Norman L, Noursadeghi M, Olliaro PL, Pritchard MG, Russell CD, Shaw CA, Sheikh A, Solomon T, Sudlow C, Swann OV, Turtle LC, Openshaw PJ, Baillie JK, Semple MG, Docherty AB, Harrison EM, ISARIC4C investigators.",,BMJ (Clinical research ed.),2020,2020-09-09,Y,,,,"<h4>Objective</h4>To develop and validate a pragmatic risk score to predict mortality in patients admitted to hospital with coronavirus disease 2019 (covid-19).<h4>Design</h4>Prospective observational cohort study.<h4>Setting</h4>International Severe Acute Respiratory and emerging Infections Consortium (ISARIC) World Health Organization (WHO) Clinical Characterisation Protocol UK (CCP-UK) study (performed by the ISARIC Coronavirus Clinical Characterisation Consortium-ISARIC-4C) in 260 hospitals across England, Scotland, and Wales. Model training was performed on a cohort of patients recruited between 6 February and 20 May 2020, with validation conducted on a second cohort of patients recruited after model development between 21 May and 29 June 2020<i>.</i> PARTICIPANTS: Adults (age ≥18 years) admitted to hospital with covid-19 at least four weeks before final data extraction.<h4>Main outcome measure</h4>In-hospital mortality.<h4>Results</h4>35 463 patients were included in the derivation dataset (mortality rate 32.2%) and 22 361 in the validation dataset (mortality rate 30.1%). The final 4C Mortality Score included eight variables readily available at initial hospital assessment: age, sex, number of comorbidities, respiratory rate, peripheral oxygen saturation, level of consciousness, urea level, and C reactive protein (score range 0-21 points). The 4C Score showed high discrimination for mortality (derivation cohort: area under the receiver operating characteristic curve 0.79, 95% confidence interval 0.78 to 0.79; validation cohort: 0.77, 0.76 to 0.77) with excellent calibration (validation: calibration-in-the-large=0, slope=1.0). Patients with a score of at least 15 (n=4158, 19%) had a 62% mortality (positive predictive value 62%) compared with 1% mortality for those with a score of 3 or less (n=1650, 7%; negative predictive value 99%). Discriminatory performance was higher than 15 pre-existing risk stratification scores (area under the receiver operating characteristic curve range 0.61-0.76), with scores developed in other covid-19 cohorts often performing poorly (range 0.63-0.73).<h4>Conclusions</h4>An easy-to-use risk stratification score has been developed and validated based on commonly available parameters at hospital presentation. The 4C Mortality Score outperformed existing scores, showed utility to directly inform clinical decision making, and can be used to stratify patients admitted to hospital with covid-19 into different management groups. The score should be further validated to determine its applicability in other populations.<h4>Study registration</h4>ISRCTN66726260.",,pdf:https://www.bmj.com/content/bmj/370/bmj.m3339.full.pdf; doi:https://doi.org/10.1136/bmj.m3339; html:https://europepmc.org/articles/PMC7116472; pdf:https://europepmc.org/articles/PMC7116472?pdf=render
 31479209,https://doi.org/10.1056/nejmoa1907096,A Genotype-Guided Strategy for Oral P2Y<sub>12</sub> Inhibitors in Primary PCI.,"Claassens DMF, Vos GJA, Bergmeijer TO, Hermanides RS, van 't Hof AWJ, van der Harst P, Barbato E, Morisco C, Tjon Joe Gin RM, Asselbergs FW, Mosterd A, Herrman JR, Dewilde WJM, Janssen PWA, Kelder JC, Postma MJ, de Boer A, Boersma C, Deneer VHM, Ten Berg JM.",,The New England journal of medicine,2019,2019-09-03,N,,Better Care,cardiovascular,"<h4>Background</h4>It is unknown whether patients undergoing primary percutaneous coronary intervention (PCI) benefit from genotype-guided selection of oral P2Y<sub>12</sub> inhibitors.<h4>Methods</h4>We conducted a randomized, open-label, assessor-blinded trial in which patients undergoing primary PCI with stent implantation were assigned in a 1:1 ratio to receive either a P2Y<sub>12</sub> inhibitor on the basis of early <i>CYP2C19</i> genetic testing (genotype-guided group) or standard treatment with either ticagrelor or prasugrel (standard-treatment group) for 12 months. In the genotype-guided group, carriers of <i>CYP2C19</i>*2 or <i>CYP2C19</i>*3 loss-of-function alleles received ticagrelor or prasugrel, and noncarriers received clopidogrel. The two primary outcomes were net adverse clinical events - defined as death from any cause, myocardial infarction, definite stent thrombosis, stroke, or major bleeding defined according to Platelet Inhibition and Patient Outcomes (PLATO) criteria - at 12 months (primary combined outcome; tested for noninferiority, with a noninferiority margin of 2 percentage points for the absolute difference) and PLATO major or minor bleeding at 12 months (primary bleeding outcome).<h4>Results</h4>For the primary analysis, 2488 patients were included: 1242 in the genotype-guided group and 1246 in the standard-treatment group. The primary combined outcome occurred in 63 patients (5.1%) in the genotype-guided group and in 73 patients (5.9%) in the standard-treatment group (absolute difference, -0.7 percentage points; 95% confidence interval [CI], -2.0 to 0.7; P<0.001 for noninferiority). The primary bleeding outcome occurred in 122 patients (9.8%) in the genotype-guided group and in 156 patients (12.5%) in the standard-treatment group (hazard ratio, 0.78; 95% CI, 0.61 to 0.98; P = 0.04).<h4>Conclusions</h4>In patients undergoing primary PCI, a <i>CYP2C19</i> genotype-guided strategy for selection of oral P2Y<sub>12</sub> inhibitor therapy was noninferior to standard treatment with ticagrelor or prasugrel at 12 months with respect to thrombotic events and resulted in a lower incidence of bleeding. (Funded by the Netherlands Organization for Health Research and Development; POPular Genetics ClinicalTrials.gov number, NCT01761786; Netherlands Trial Register number, NL2872.).",,pdf:https://pure.rug.nl/ws/files/99703867/A_Genotype_Guided_Strategy_for_Oral_P2Y12_Inhibitors_in_Primary_PCI.pdf; doi:https://doi.org/10.1056/NEJMoa1907096
 36347531,https://doi.org/10.1136/bmj-2022-070918,Development and external validation of a risk prediction model for falls in patients with an indication for antihypertensive treatment: retrospective cohort study.,"Archer L, Koshiaris C, Lay-Flurrie S, Snell KIE, Riley RD, Stevens R, Banerjee A, Usher-Smith JA, Clegg A, Payne RA, Hobbs FDR, McManus RJ, Sheppard JP, STRAtifying Treatments In the multi-morbid Frail elderlY (STRATIFY) investigators.",,BMJ (Clinical research ed.),2022,2022-11-08,Y,,,,"<h4>Objective</h4>To develop and externally validate the STRAtifying Treatments In the multi-morbid Frail elderlY (STRATIFY)-Falls clinical prediction model to identify the risk of hospital admission or death from a fall in patients with an indication for antihypertensive treatment.<h4>Design</h4>Retrospective cohort study.<h4>Setting</h4>Primary care data from electronic health records contained within the UK Clinical Practice Research Datalink (CPRD).<h4>Participants</h4>Patients aged 40 years or older with at least one blood pressure measurement between 130 mm Hg and 179 mm Hg.<h4>Main outcome measure</h4>First serious fall, defined as hospital admission or death with a primary diagnosis of a fall within 10 years of the index date (12 months after cohort entry). Model development was conducted using a Fine-Gray approach in data from CPRD GOLD, accounting for the competing risk of death from other causes, with subsequent recalibration at one, five, and 10 years using pseudo values. External validation was conducted using data from CPRD Aurum, with performance assessed through calibration curves and the observed to expected ratio, C statistic, and D statistic, pooled across general practices, and clinical utility using decision curve analysis at thresholds around 10%.<h4>Results</h4>Analysis included 1 772 600 patients (experiencing 62 691 serious falls) from CPRD GOLD used in model development, and 3 805 366 (experiencing 206 956 serious falls) from CPRD Aurum in the external validation. The final model consisted of 24 predictors, including age, sex, ethnicity, alcohol consumption, living in an area of high social deprivation, a history of falls, multiple sclerosis, and prescriptions of antihypertensives, antidepressants, hypnotics, and anxiolytics. Upon external validation, the recalibrated model showed good discrimination, with pooled C statistics of 0.833 (95% confidence interval 0.831 to 0.835) and 0.843 (0.841 to 0.844) at five and 10 years, respectively. Original model calibration was poor on visual inspection and although this was improved with recalibration, under-prediction of risk remained (observed to expected ratio at 10 years 1.839, 95% confidence interval 1.811 to 1.865). Nevertheless, decision curve analysis suggests potential clinical utility, with net benefit larger than other strategies.<h4>Conclusions</h4>This prediction model uses commonly recorded clinical characteristics and distinguishes well between patients at high and low risk of falls in the next 1-10 years. Although miscalibration was evident on external validation, the model still had potential clinical utility around risk thresholds of 10% and so could be useful in routine clinical practice to help identify those at high risk of falls who might benefit from closer monitoring or early intervention to prevent future falls. Further studies are needed to explore the appropriate thresholds that maximise the model's clinical utility and cost effectiveness.",,pdf:https://www.bmj.com/content/bmj/379/bmj-2022-070918.full.pdf; doi:https://doi.org/10.1136/bmj-2022-070918; html:https://europepmc.org/articles/PMC9641577
 38432242,https://doi.org/10.1016/s2352-3026(24)00030-9,Haemoglobin thresholds to define anaemia from age 6 months to 65 years: estimates from international data sources.,"Braat S, Fielding KL, Han J, Jackson VE, Zaloumis S, Xu JXH, Moir-Meyer G, Blaauwendraad SM, Jaddoe VWV, Gaillard R, Parkin PC, Borkhoff CM, Keown-Stoneman CDG, Birken CS, Maguire JL, Genes & Health Research Team, Bahlo M, Davidson EM, Pasricha SR.",,The Lancet. Haematology,2024,2024-02-29,Y,,,,"<h4>Background</h4>Detection of anaemia is crucial for clinical medicine and public health. Current WHO anaemia definitions are based on statistical thresholds (fifth centiles) set more than 50 years ago. We sought to establish evidence for the statistical haemoglobin thresholds for anaemia that can be applied globally and inform WHO and clinical guidelines.<h4>Methods</h4>In this analysis we identified international data sources from populations in the USA, England, Australia, China, the Netherlands, Canada, Ecuador, and Bangladesh with sufficient clinical and laboratory information collected between 1998 and 2020 to obtain a healthy reference sample. Individuals with clinical or biochemical evidence of a condition that could reduce haemoglobin concentrations were excluded. We estimated haemoglobin thresholds (ie, 5th centiles) for children aged 6-23 months, 24-59 months, 5-11 years, and 12-17 years, and adults aged 18-65 years (including during pregnancy) for individual datasets and pooled across data sources. We also collated findings from three large-scale genetic studies to summarise genetic variants affecting haemoglobin concentrations in different ancestral populations.<h4>Findings</h4>We identified eight data sources comprising 18 individual datasets that were eligible for inclusion in the analysis. In pooled analyses, the haemoglobin fifth centile was 104·4 g/L (90% CI 103·5-105·3) in 924 children aged 6-23 months, 110·2 g/L (109·5-110·9) in 1874 children aged 24-59 months, and 114·4 g/L (113·6-115·2) in 1839 children aged 5-11 years. Values diverged by sex in adolescents and adults. In pooled analyses, the fifth centile was 122·2 g/L (90% CI 121·3-123·1) in 1741 female adolescents aged 12-17 years and 128·2 g/L (126·4-130·0) in 1103 male adolescents aged 12-17 years. In pooled analyses of adults aged 18-65 years, the fifth centile was 119·7 g/L (90% CI 119·1-120·3) in 3640 non-pregnant females and 134·9 g/L (134·2-135·6) in 2377 males. Fifth centiles in pregnancy were 110·3 g/L (90% CI 109·5-111·0) in the first trimester (n=772) and 105·9 g/L (104·0-107·7) in the second trimester (n=111), with insufficient data for analysis in the third trimester. There were insufficient data for adults older than 65 years. We did not identify ancestry-specific high prevalence of non-clinically relevant genetic variants that influence haemoglobin concentrations.<h4>Interpretation</h4>Our results enable global harmonisation of clinical and public health haemoglobin thresholds for diagnosis of anaemia. Haemoglobin thresholds are similar between sexes until adolescence, after which males have higher thresholds than females. We did not find any evidence that thresholds should differ between people of differering ancestries.<h4>Funding</h4>World Health Organization and the Bill & Melinda Gates Foundation.",,doi:https://doi.org/10.1016/S2352-3026(24)00030-9; html:https://europepmc.org/articles/PMC10983828; pdf:https://europepmc.org/articles/PMC10983828?pdf=render
+31801372,https://doi.org/10.1161/atvbaha.119.313226,"Carotid Intima-Media Thickness: Novel Loci, Sex-Specific Effects, and Genetic Correlations With Obesity and Glucometabolic Traits in UK Biobank.","Strawbridge RJ, Ward J, Bailey MES, Cullen B, Ferguson A, Graham N, Johnston KJA, Lyall LM, Pearsall R, Pell J, Shaw RJ, Tank R, Lyall DM, Smith DJ.",,"Arteriosclerosis, thrombosis, and vascular biology",2020,2019-12-05,Y,"Atherosclerosis; Obesity; Intima-media thickness; coronary artery disease; carotid artery; Genetics, Association Studies; Diabetes, Type 2",Understanding the Causes of Disease,,"<h4>Objective</h4>Atherosclerosis is the underlying cause of most cardiovascular disease, but mechanisms underlying atherosclerosis are incompletely understood. Ultrasound measurement of the carotid intima-media thickness (cIMT) can be used to measure vascular remodeling, which is indicative of atherosclerosis. Genome-wide association studies have identified many genetic loci associated with cIMT, but heterogeneity of measurements collected by many small cohorts have been a major limitation in these efforts. Here, we conducted genome-wide association analyses in UKB (UK Biobank; N=22 179), the largest single study with consistent cIMT measurements. Approach and Results: We used BOLT-LMM software to run linear regression of cIMT in UKB, adjusted for age, sex, and genotyping chip. In white British participants, we identified 5 novel loci associated with cIMT and replicated most previously reported loci. In the first sex-specific analyses of cIMT, we identified a locus on chromosome 5, associated with cIMT in women only and highlight <i>VCAN</i> as a good candidate gene at this locus. Genetic correlations with body mass index and glucometabolic traits were also observed. Two loci influenced risk of ischemic heart disease.<h4>Conclusions</h4>These findings replicate previously reported associations, highlight novel biology, and provide new directions for investigating the sex differences observed in cardiovascular disease presentation and progression.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/ATVBAHA.119.313226; doi:https://doi.org/10.1161/ATVBAHA.119.313226; html:https://europepmc.org/articles/PMC6975521; pdf:https://europepmc.org/articles/PMC6975521?pdf=render
 32601055,https://doi.org/10.3399/bjgp20x710873,Prescription of suboptimal statin treatment regimens: a retrospective cohort study of trends and variation in English primary care.,"Curtis HJ, Walker AJ, MacKenna B, Croker R, Goldacre B.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2020,2020-07-30,Y,Lipids; Cardiovascular diseases; Retrospective studies; Primary Health Care; statins,,,"<h4>Background</h4>Since 2014 English national guidance recommends 'high-intensity' statins, reducing low-density lipoprotein (LDL) cholesterol by ≥40%.<h4>Aim</h4>To describe trends and variation in low-/medium-intensity statin prescribing and assess the feasibility of rapid prescribing behaviour change.<h4>Design and setting</h4>A retrospective cohort study using OpenPrescribing data from all 8142 standard NHS general practices in England from August 2010 to March 2019.<h4>Method</h4>Statins were categorised as high- or low-/medium-intensity using two different thresholds, and the proportion prescribed below these thresholds was calculated. The authors plotted trends and geographical variation, carried out mixed-effects logistic regression to identify practice characteristics associated with breaching of guidance, and used indicator saturation to identify sudden prescribing changes.<h4>Results</h4>The proportion of statins prescribed below the recommended 40% LDL-lowering threshold has decreased gradually from 80% in 2011/2012 to 45% in 2019; the proportion below a pragmatic 37% threshold decreased from 30% to 18% in 2019. Guidance from 2014 had minimal impact on trends. Wide variation was found between practices (interdecile ranges 20% to 85% and 10% to 30% respectively in 2018). Regression identified no strong associations with breaching of guidance. Indicator saturation identified several practices exhibiting sudden changes towards greater guideline compliance.<h4>Conclusion</h4>Breaches of guidance on choice of statin remain common, with substantial variation between practices. Some have implemented rapid change, indicating the feasibility of rapid prescribing behaviour change. This article discusses the potential for a national strategic approach, using data and evidence to optimise care, including targeted education alongside audit and feedback to outliers through services such as OpenPrescribing.",,pdf:https://bjgp.org/content/bjgp/70/697/e525.full.pdf; doi:https://doi.org/10.3399/bjgp20X710873; html:https://europepmc.org/articles/PMC7357867; pdf:https://europepmc.org/articles/PMC7357867?pdf=render
 36810190,https://doi.org/10.1136/bmjebm-2023-112253,Digitally enabled decentralised research: opportunities to improve the efficiency of clinical trials and observational studies.,"Aiyegbusi OL, Davies EH, Myles P, Williams T, Frost C, Haroon S, Hughes SE, Wilson R, McMullan C, Subramanian A, Nirantharakumar K, Calvert MJ.",,BMJ evidence-based medicine,2023,2023-02-21,Y,information technology; drug discovery; Drug Development; Covid-19,,,,,pdf:https://ebm.bmj.com/content/ebmed/early/2023/02/20/bmjebm-2023-112253.full.pdf; doi:https://doi.org/10.1136/bmjebm-2023-112253; html:https://europepmc.org/articles/PMC10579468; pdf:https://europepmc.org/articles/PMC10579468?pdf=render
-31801372,https://doi.org/10.1161/atvbaha.119.313226,"Carotid Intima-Media Thickness: Novel Loci, Sex-Specific Effects, and Genetic Correlations With Obesity and Glucometabolic Traits in UK Biobank.","Strawbridge RJ, Ward J, Bailey MES, Cullen B, Ferguson A, Graham N, Johnston KJA, Lyall LM, Pearsall R, Pell J, Shaw RJ, Tank R, Lyall DM, Smith DJ.",,"Arteriosclerosis, thrombosis, and vascular biology",2020,2019-12-05,Y,"Atherosclerosis; Obesity; Intima-media thickness; coronary artery disease; carotid artery; Genetics, Association Studies; Diabetes, Type 2",Understanding the Causes of Disease,,"<h4>Objective</h4>Atherosclerosis is the underlying cause of most cardiovascular disease, but mechanisms underlying atherosclerosis are incompletely understood. Ultrasound measurement of the carotid intima-media thickness (cIMT) can be used to measure vascular remodeling, which is indicative of atherosclerosis. Genome-wide association studies have identified many genetic loci associated with cIMT, but heterogeneity of measurements collected by many small cohorts have been a major limitation in these efforts. Here, we conducted genome-wide association analyses in UKB (UK Biobank; N=22 179), the largest single study with consistent cIMT measurements. Approach and Results: We used BOLT-LMM software to run linear regression of cIMT in UKB, adjusted for age, sex, and genotyping chip. In white British participants, we identified 5 novel loci associated with cIMT and replicated most previously reported loci. In the first sex-specific analyses of cIMT, we identified a locus on chromosome 5, associated with cIMT in women only and highlight <i>VCAN</i> as a good candidate gene at this locus. Genetic correlations with body mass index and glucometabolic traits were also observed. Two loci influenced risk of ischemic heart disease.<h4>Conclusions</h4>These findings replicate previously reported associations, highlight novel biology, and provide new directions for investigating the sex differences observed in cardiovascular disease presentation and progression.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/ATVBAHA.119.313226; doi:https://doi.org/10.1161/ATVBAHA.119.313226; html:https://europepmc.org/articles/PMC6975521; pdf:https://europepmc.org/articles/PMC6975521?pdf=render
 30842207,https://doi.org/10.1136/heartjnl-2019-314763,Proprotein convertase subtilisin/kexin 9 inhibitors in reducing cardiovascular outcomes: a systematic review and meta-analysis.,"Du H, Li X, Su N, Li L, Hao X, Gao H, Kwong JS, Vandvik PO, Yang X, Nemeth I, Mordi IR, Li Q, Zhang L, Rao L, Lang CC, Li J, Tian H, Li S.",,Heart (British Cardiac Society),2019,2019-03-06,N,Cardiovascular disease; Systematic review; Lipid-lowering Drugs; Low-density Lipoprotein Cholesterol; Proprotein Convertase Subtilisin/kexin Type 9 Inhibitors,,,"<h4>Background</h4>To evaluate the effects of proprotein convertase subtilisin/kexin 9 (PCSK9) inhibitors on major adverse cardiovascular events (MACE).<h4>Methods</h4>Our systematic review included randomised controlled trials if they studied PCSK9 inhibitors in patients for primary and/or secondary prevention of cardiovascular diseases or with hypercholesterolaemia/hyperlipidaemia. Dichotomous variables from individual studies were pooled by relative risks (RR) and their 95% CIs using the random-effect model. Risk difference (RD) in the 10-year frame was also estimated using the pooled RR and the estimated baseline risk using the control group. Grading of Recommendation Assessment, Development and Evaluation was used to assess the quality of evidence.<h4>Results</h4>We included 54 trials with 97 910 patients in the analysis. Compared with controls, PCSK9 inhibitors significantly reduced the risk of MACE by 16% (RR, 0.84; 95% CI 0.79 to 0.89; RD: 47 fewer per 1000 vs 286 as the baseline risk; 95% CI 32 to 59 fewer), non-fatal myocardial infarction (MI) by 17% (RR, 0.83; 95% CI 0.74 to 0.93; RD, 35 fewer per 1000 vs 207 as the baseline; 95% CI 13 to 53 fewer) and any stroke by 25% (RR, 0.75; 95% CI 0.65 to 0.85; RD, 16 fewer per 1000 vs 61 as the baseline; 95% CI 9 to 21 fewer) with moderate quality evidence. No significant differences were found between PCSK9 inhibitors and control groups in all-cause mortality, cardiovascular death, heart failure or unstable angina with low-quality evidence.<h4>Conclusions</h4>This study demonstrated that PCSK9 inhibitors could significantly reduce the risk of MACE, non-fatal MI and stroke.<h4>Trial registration</h4>PROSPERO; CRD42017073904.",,pdf:https://discovery.dundee.ac.uk/ws/files/30348534/Author_Accepted_Manuscript.pdf; doi:https://doi.org/10.1136/heartjnl-2019-314763
 35151371,https://doi.org/10.1016/j.immuni.2022.01.017,Immuno-proteomic profiling reveals aberrant immune cell regulation in the airways of individuals with ongoing post-COVID-19 respiratory disease.,"Vijayakumar B, Boustani K, Ogger PP, Papadaki A, Tonkin J, Orton CM, Ghai P, Suveizdyte K, Hewitt RJ, Desai SR, Devaraj A, Snelgrove RJ, Molyneaux PL, Garner JL, Peters JE, Shah PL, Lloyd CM, Harker JA.",,Immunity,2022,2022-01-26,Y,T cells; Proteomics; Respiratory Tract; Airways; Respiratory Viral Infection; Tissue-resident Memory; Covid-19; Sars-cov-2; Long Covid,,,"Some patients hospitalized with acute COVID-19 suffer respiratory symptoms that persist for many months. We delineated the immune-proteomic landscape in the airways and peripheral blood of healthy controls and post-COVID-19 patients 3 to 6 months after hospital discharge. Post-COVID-19 patients showed abnormal airway (but not plasma) proteomes, with an elevated concentration of proteins associated with apoptosis, tissue repair, and epithelial injury versus healthy individuals. Increased numbers of cytotoxic lymphocytes were observed in individuals with greater airway dysfunction, while increased B cell numbers and altered monocyte subsets were associated with more widespread lung abnormalities. A one-year follow-up of some post-COVID-19 patients indicated that these abnormalities resolved over time. In summary, COVID-19 causes a prolonged change to the airway immune landscape in those with persistent lung disease, with evidence of cell death and tissue repair linked to the ongoing activation of cytotoxic T cells.",,pdf:http://www.cell.com/article/S1074761322000462/pdf; doi:https://doi.org/10.1016/j.immuni.2022.01.017; html:https://europepmc.org/articles/PMC8789571; pdf:https://europepmc.org/articles/PMC8789571?pdf=render
 34812717,https://doi.org/10.1099/mgen.0.000700,Antimicrobial resistance determinants are associated with <i>Staphylococcus aureus</i> bacteraemia and adaptation to the healthcare environment: a bacterial genome-wide association study.,"Young BC, Wu CH, Charlesworth J, Earle S, Price JR, Gordon NC, Cole K, Dunn L, Liu E, Oakley S, Godwin H, Fung R, Miller R, Knox K, Votintseva A, Quan TP, Tilley R, Scarborough M, Crook DW, Peto TE, Walker AS, Llewelyn MJ, Wilson DJ.",,Microbial genomics,2021,2021-11-01,Y,Nosocomial infection; Bacterial Pathogens; Bacteraemia; Microbial Genomics; Microbial Epidemiology,,,"<i>Staphylococcus aureus</i> is a major bacterial pathogen in humans, and a dominant cause of severe bloodstream infections. Globally, antimicrobial resistance (AMR) in <i>S. aureus</i> remains challenging. While human risk factors for infection have been defined, contradictory evidence exists for the role of bacterial genomic variation in <i>S. aureus</i> disease. To investigate the contribution of bacterial lineage and genomic variation to the development of bloodstream infection, we undertook a genome-wide association study comparing bacteria from 1017 individuals with bacteraemia to 984 adults with asymptomatic <i>S. aureus</i> nasal carriage. Within 984 carriage isolates, we also compared healthcare-associated (HA) carriage with community-associated (CA) carriage. All major global lineages were represented in both bacteraemia and carriage, with no evidence for different infection rates. However, kmers tagging trimethoprim resistance-conferring mutation F99Y in <i>dfrB</i> were significantly associated with bacteraemia-vs-carriage (<i>P=</i>10<sup>-8.9</sup>-10<sup>-9.3</sup>). Pooling variation within genes, bacteraemia-vs-carriage was associated with the presence of <i>mecA</i> (HMP=10<sup>-5.3</sup>) as well as the presence of SCCmec (HMP=10<sup>-4.4</sup>). Among <i>S. aureus</i> carriers, no lineages were associated with HA-vs-CA carriage. However, we found a novel signal of HA-vs-CA carriage in the foldase protein <i>prsA</i>, where kmers representing conserved sequence allele were associated with CA carriage (<i>P=</i>10<sup>-7.1</sup>-10<sup>-19.4</sup>), while in <i>gyrA</i>, a ciprofloxacin resistance-conferring mutation, L84S, was associated with HA carriage (<i>P=</i>10<sup>-7.2</sup>). In an extensive study of <i>S. aureus</i> bacteraemia and nasal carriage in the UK, we found strong evidence that all <i>S. aureus</i> lineages are equally capable of causing bloodstream infection, and of being carried in the healthcare environment. Genomic variation in the foldase protein <i>prsA</i> is a novel genomic marker of healthcare origin in <i>S. aureus</i> but was not associated with bacteraemia. AMR determinants were associated with both bacteraemia and healthcare-associated carriage, suggesting that AMR increases the propensity not only to survive in healthcare environments, but also to cause invasive disease.",,doi:https://doi.org/10.1099/mgen.0.000700; doi:https://doi.org/10.1099/mgen.0.000700; html:https://europepmc.org/articles/PMC8743558; pdf:https://europepmc.org/articles/PMC8743558?pdf=render
@@ -2643,8 +2645,8 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 31851298,https://doi.org/10.1093/ajcn/nqz301,A prospective cohort analysis of gut microbial co-metabolism in Alaska Native and rural African people at high and low risk of colorectal cancer.,"Ocvirk S, Wilson AS, Posma JM, Li JV, Koller KR, Day GM, Flanagan CA, Otto JE, Sacco PE, Sacco FD, Sapp FR, Wilson AS, Newton K, Brouard F, DeLany JP, Behnning M, Appolonia CN, Soni D, Bhatti F, Methé B, Fitch A, Morris A, Gaskins HR, Kinross J, Nicholson JK, Thomas TK, O'Keefe SJD.",,The American journal of clinical nutrition,2020,2020-02-01,N,Butyrate; Deoxycholic acid; dietary fiber; Bile acids; Colorectal Cancer; Gut Microbiota; Short-chain Fatty Acids; Alaska Native People; Rural African People,,,"<h4>Background</h4>Alaska Native (AN) people have the world's highest recorded incidence of sporadic colorectal cancer (CRC) (∼91:100,000), whereas rural African (RA) people have the lowest risk (<5:100,000). Previous data supported the hypothesis that diet affected CRC risk through its effects on the colonic microbiota that produce tumor-suppressive or -promoting metabolites.<h4>Objectives</h4>We investigated whether differences in these metabolites may contribute to the high risk of CRC in AN people.<h4>Methods</h4>A cross-sectional observational study assessed dietary intake from 32 AN and 21 RA healthy middle-aged volunteers before screening colonoscopy. Analysis of fecal microbiota composition by 16S ribosomal RNA gene sequencing and fecal/urinary metabolites by 1H-NMR spectroscopy was complemented with targeted quantification of fecal SCFAs, bile acids, and functional microbial genes.<h4>Results</h4>Adenomatous polyps were detected in 16 of 32 AN participants, but not found in RA participants. The AN diet contained higher proportions of fat and animal protein and less fiber. AN fecal microbiota showed a compositional predominance of Blautia and Lachnoclostridium, higher microbial capacity for bile acid conversion, and low abundance of some species involved in saccharolytic fermentation (e.g., Prevotellaceae, Ruminococcaceae), but no significant lack of butyrogenic bacteria. Significantly lower concentrations of tumor-suppressive butyrate (22.5 ± 3.1 compared with 47.2 ± 7.3 SEM µmol/g) coincided with significantly higher concentrations of tumor-promoting deoxycholic acid (26.7 ± 4.2 compared with 11 ± 1.9 µmol/g) in AN fecal samples. AN participants had lower quantities of fecal/urinary metabolites than RA participants and metabolite profiles correlated with the abundance of distinct microbial genera in feces. The main microbial and metabolic CRC-associated markers were not significantly altered in AN participants with adenomatous polyps.<h4>Conclusions</h4>The low-fiber, high-fat diet of AN people and exposure to carcinogens derived from diet or environment are associated with a tumor-promoting colonic milieu as reflected by the high rates of adenomatous polyps in AN participants.",,pdf:https://academic.oup.com/ajcn/article-pdf/111/2/406/32447385/nqz301.pdf; doi:https://doi.org/10.1093/ajcn/nqz301; html:https://europepmc.org/articles/PMC6997097; pdf:https://europepmc.org/articles/PMC6997097?pdf=render; doi:https://doi.org/10.1093/ajcn/nqz301
 31980021,https://doi.org/10.1186/s12875-019-1077-6,General practitioners' views on use of patient reported outcome measures in primary care: a cross-sectional survey and qualitative study.,"Turner GM, Litchfield I, Finnikin S, Aiyegbusi OL, Calvert M.",,BMC family practice,2020,2020-01-24,Y,Survey; Qualitative; General Practitioners; Primary Care; Patient Reported Outcome Measures (Proms),,,"<h4>Background</h4>Patient reported outcome measures (PROMs) are increasingly used to assess impact of disease and treatment on quality of life and symptoms; however, their use in primary care is fragmented. We aimed to understand how PROMs are currently being used in primary care, the barriers and facilitators of this use and if appropriate how it might be optimised.<h4>Methods</h4>Cross-sectional survey and semi-structured interviews among general practitioners (GPs) in England. GPs' opinions were explored using an electronic, self-completed questionnaire disseminated to 100 GPs via an online doctors' community and semi-structured qualitative interviews with 25 GPs.<h4>Results</h4>Most GPs surveyed (77/100; 77%) reported using one or more PROM, primarily to aid clinical management (n = 66) or as screening/diagnostic tools (n = 62). Qualitative interviews highlighted challenges in identifying and selecting PROMs; however, some GPs valued PROMs for shared decision making and to direct patient discussions. The interviews identified key barriers to PROM use including: time constraints; insufficient knowledge; lack of integration into clinical systems; and PROMs being mandated without consultation or explanation. Evidence of the benefit of PROMs is required to promote uptake and use of PROMs in primary care.<h4>Conclusion</h4>Implementation of PROMs in primary care requires integration with clinical systems, a bottom-up approach to PROM selection and system design involving meaningful consultation with patients and primary care clinicians and training/support for use.",,pdf:https://bmcfampract.biomedcentral.com/track/pdf/10.1186/s12875-019-1077-6; doi:https://doi.org/10.1186/s12875-019-1077-6; html:https://europepmc.org/articles/PMC6979354; pdf:https://europepmc.org/articles/PMC6979354?pdf=render
 33067802,https://doi.org/10.1111/acer.14481,Health System-Based Unhealthy Alcohol Use Screening and Treatment Comparing Demographically Matched Participants With and Without HIV.,"Silverberg MJ, Levine-Hall T, Hood N, Anderson AN, Alexeeff SE, Lam JO, Slome SB, Flamm JA, Hare CB, Ross T, Justice AC, Sterne JAC, Williams AE, Bryant KJ, Weisner CM, Horberg MA, Sterling SA, Satre DD.",,"Alcoholism, clinical and experimental research",2020,2020-11-10,N,HIV; epidemiology; Primary Care; Substance Abuse; Alcohol Use,,,"<h4>Background</h4>Unhealthy alcohol use among persons living with HIV (PLWH) is linked to significant morbidity, and use of alcohol services may differ by HIV status. Our objective was to compare unhealthy alcohol use screening and treatment by HIV status in primary care.<h4>Methods</h4>Cohort study of adult (≥18 years) PLWH and HIV-uninfected participants frequency matched 20:1 to PLWH by age, sex, and race/ethnicity who were enrolled in a large integrated healthcare system in the United States, with information ascertained from an electronic health record. Outcomes included unhealthy alcohol screening, prevalence, provider-delivered brief interventions, and addiction specialty care visits. Other predictors included age, sex, race/ethnicity, neighborhood deprivation index, depression, smoking, substance use disorders, Charlson comorbidity index, prior outpatient visits, insurance type, and medical facility. Cox proportional hazards models were used to compute hazard ratios (HR) for the outcomes of time to unhealthy alcohol use screening and time to first addiction specialty visit. Poisson regression with robust standard errors was used to compute prevalence ratios (PR) for other outcomes.<h4>Results</h4>11,235 PLWH and 227,320 HIV-uninfected participants were included. By 4.5 years after baseline, most participants were screened for unhealthy alcohol use (85% of PLWH and 93% of HIV-uninfected), but with a lower rate among PLWH (adjusted HR 0.84, 95% CI 0.82 to 0.85). PLWH were less likely, compared with HIV-uninfected participants, to report unhealthy drinking among those screened (adjusted PR 0.74, 95% CI 0.69 to 0.79), and among those who screened positive, less likely to receive brief interventions (adjusted PR 0.82, 95% CI 0.75 to 0.90), but more likely (adjusted HR 1.7, 95% CI 1.2 to 2.4) to have an addiction specialty visit within 1 year.<h4>Conclusions</h4>Unhealthy alcohol use was lower in PLWH, but the treatment approach by HIV status differed. PLWH reporting unhealthy alcohol use received less brief interventions and more addiction specialty care than HIV-uninfected participants.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7725961; doi:https://doi.org/10.1111/acer.14481; html:https://europepmc.org/articles/PMC7725961; pdf:https://europepmc.org/articles/PMC7725961?pdf=render; doi:https://doi.org/10.1111/acer.14481
-34552082,https://doi.org/10.1038/s41467-021-25833-8,Modelling the persistence and control of Rift Valley fever virus in a spatially heterogeneous landscape.,"Tennant WSD, Cardinale E, Cêtre-Sossah C, Moutroifi Y, Le Godais G, Colombi D, Spencer SEF, Tildesley MJ, Keeling MJ, Charafouddine O, Colizza V, Edmunds WJ, Métras R.",,Nature communications,2021,2021-09-22,Y,,,,"The persistence mechanisms of Rift Valley fever (RVF), a zoonotic arboviral haemorrhagic fever, at both local and broader geographical scales have yet to be fully understood and rigorously quantified. We developed a mathematical metapopulation model describing RVF virus transmission in livestock across the four islands of the Comoros archipelago, accounting for island-specific environments and inter-island animal movements. By fitting our model in a Bayesian framework to 2004-2015 surveillance data, we estimated the importance of environmental drivers and animal movements on disease persistence, and tested the impact of different control scenarios on reducing disease burden throughout the archipelago. Here we report that (i) the archipelago network was able to sustain viral transmission in the absence of explicit disease introduction events after early 2007, (ii) repeated outbreaks during 2004-2020 may have gone under-detected by local surveillance, and (iii) co-ordinated within-island control measures are more effective than between-island animal movement restrictions.",,pdf:https://www.nature.com/articles/s41467-021-25833-8.pdf; doi:https://doi.org/10.1038/s41467-021-25833-8; html:https://europepmc.org/articles/PMC8458460; pdf:https://europepmc.org/articles/PMC8458460?pdf=render
 31730918,https://doi.org/10.1016/j.jclinepi.2019.11.006,Data mining information from electronic health records produced high yield and accuracy for current smoking status.,"Groenhof TKJ, Koers LR, Blasse E, de Groot M, Grobbee DE, Bots ML, Asselbergs FW, Lely AT, Haitjema S, UPOD, UCC-CVRM Study Groups.",,Journal of clinical epidemiology,2020,2019-11-12,N,data mining; Data Quality; Electronic Health Records; Text Mining; Learning Healthcare System; Routine Clinical Data,The Human Phenome,,"<h4>Objectives</h4>Researchers are increasingly using routine clinical data for care evaluations and feedback to patients and clinicians. The quality of these evaluations depends on the quality and completeness of the input data.<h4>Study design and setting</h4>We assessed the performance of an electronic health record (EHR)-based data mining algorithm, using the example of the smoking status in a cardiovascular population. As a reference standard, we used the questionnaire from the Utrecht Cardiovascular Cohort (UCC). To assess diagnostic accuracy, we calculated sensitivity, specificity, negative predictive value (NPV), and positive predictive value (PPV).<h4>Results</h4>We analyzed 1,661 patients included in the UCC to January 18, 2019. Of those, 14% (n = 238) had missing information on smoking status in the UCC questionnaire. Data mining provided information on smoking status in 99% of the 1,661 participants. Diagnostic accuracy for current smoking was sensitivity 88%, specificity 92%, NPV 98%, and PPV 63%. From false positives, 85% reported they had quit smoking at the time of the UCC.<h4>Conclusion</h4>Data mining showed great potential in retrieving information on smoking (a near complete yield). Its diagnostic performance is good for negative smoking statuses. The implications of misclassification with data mining are dependent on the application of the data.",Utilises data mining and routine data to identify a patients smoking status. Does not account for long term smoking behaviour and is limited by the smaller size the dataset.,pdf:http://www.jclinepi.com/article/S0895435619304846/pdf; doi:https://doi.org/10.1016/j.jclinepi.2019.11.006
+34552082,https://doi.org/10.1038/s41467-021-25833-8,Modelling the persistence and control of Rift Valley fever virus in a spatially heterogeneous landscape.,"Tennant WSD, Cardinale E, Cêtre-Sossah C, Moutroifi Y, Le Godais G, Colombi D, Spencer SEF, Tildesley MJ, Keeling MJ, Charafouddine O, Colizza V, Edmunds WJ, Métras R.",,Nature communications,2021,2021-09-22,Y,,,,"The persistence mechanisms of Rift Valley fever (RVF), a zoonotic arboviral haemorrhagic fever, at both local and broader geographical scales have yet to be fully understood and rigorously quantified. We developed a mathematical metapopulation model describing RVF virus transmission in livestock across the four islands of the Comoros archipelago, accounting for island-specific environments and inter-island animal movements. By fitting our model in a Bayesian framework to 2004-2015 surveillance data, we estimated the importance of environmental drivers and animal movements on disease persistence, and tested the impact of different control scenarios on reducing disease burden throughout the archipelago. Here we report that (i) the archipelago network was able to sustain viral transmission in the absence of explicit disease introduction events after early 2007, (ii) repeated outbreaks during 2004-2020 may have gone under-detected by local surveillance, and (iii) co-ordinated within-island control measures are more effective than between-island animal movement restrictions.",,pdf:https://www.nature.com/articles/s41467-021-25833-8.pdf; doi:https://doi.org/10.1038/s41467-021-25833-8; html:https://europepmc.org/articles/PMC8458460; pdf:https://europepmc.org/articles/PMC8458460?pdf=render
 34155378,https://doi.org/10.1038/s41588-021-00887-y,The HIF complex recruits the histone methyltransferase SET1B to activate specific hypoxia-inducible genes.,"Ortmann BM, Burrows N, Lobb IT, Arnaiz E, Wit N, Bailey PSJ, Jordon LH, Lombardi O, Peñalver A, McCaffrey J, Seear R, Mole DR, Ratcliffe PJ, Maxwell PH, Nathan JA.",,Nature genetics,2021,2021-06-21,Y,,,,"Hypoxia-inducible transcription factors (HIFs) are fundamental to cellular adaptation to low oxygen levels, but it is unclear how they interact with chromatin and activate their target genes. Here, we use genome-wide mutagenesis to identify genes involved in HIF transcriptional activity, and define a requirement for the histone H3 lysine 4 (H3K4) methyltransferase SET1B. SET1B loss leads to a selective reduction in transcriptional activation of HIF target genes, resulting in impaired cell growth, angiogenesis and tumor establishment in SET1B-deficient xenografts. Mechanistically, we show that SET1B accumulates on chromatin in hypoxia, and is recruited to HIF target genes by the HIF complex. The selective induction of H3K4 trimethylation at HIF target loci is both HIF- and SET1B-dependent and, when impaired, correlates with decreased promoter acetylation and gene expression. Together, these findings show SET1B as a determinant of site-specific histone methylation and provide insight into how HIF target genes are differentially regulated.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7611696; doi:https://doi.org/10.1038/s41588-021-00887-y; html:https://europepmc.org/articles/PMC7611696; pdf:https://europepmc.org/articles/PMC7611696?pdf=render
 33623019,https://doi.org/10.1038/s41467-021-21505-9,Flavivirus maturation leads to the formation of an occupied lipid pocket in the surface glycoproteins.,"Renner M, Dejnirattisai W, Carrique L, Martin IS, Karia D, Ilca SL, Ho SF, Kotecha A, Keown JR, Mongkolsapaya J, Screaton GR, Grimes JM.",,Nature communications,2021,2021-02-23,Y,,,,"Flaviviruses such as Dengue (DENV) or Zika virus (ZIKV) assemble into an immature form within the endoplasmatic reticulum (ER), and are then processed by furin protease in the trans-Golgi. To better grasp maturation, we carry out cryo-EM reconstructions of immature Spondweni virus (SPOV), a human flavivirus of the same serogroup as ZIKV. By employing asymmetric localised reconstruction we push the resolution to 3.8 Å, enabling us to refine an atomic model which includes the crucial furin protease recognition site and a conserved Histidine pH-sensor. For direct comparison, we also solve structures of the mature forms of SPONV and DENV to 2.6 Å and 3.1 Å, respectively. We identify an ordered lipid that is present in only the mature forms of ZIKV, SPOV, and DENV and can bind as a consequence of rearranging amphipathic stem-helices of E during maturation. We propose a structural role for the pocket and suggest it stabilizes mature E.",,pdf:https://www.nature.com/articles/s41467-021-21505-9.pdf; doi:https://doi.org/10.1038/s41467-021-21505-9; html:https://europepmc.org/articles/PMC7902656; pdf:https://europepmc.org/articles/PMC7902656?pdf=render
 33197716,https://doi.org/10.1016/j.media.2020.101871,Accurate brain age prediction with lightweight deep neural networks.,"Peng H, Gong W, Beckmann CF, Vedaldi A, Smith SM.",,Medical image analysis,2021,2020-10-19,Y,Neuroimaging; Predictive Analysis; Brain Age Prediction; Convolutional Neuralnetworks,,,"Deep learning has huge potential for accurate disease prediction with neuroimaging data, but the prediction performance is often limited by training-dataset size and computing memory requirements. To address this, we propose a deep convolutional neural network model, Simple Fully Convolutional Network (SFCN), for accurate prediction of brain age using T1-weighted structural MRI data. Compared with other popular deep network architectures, SFCN has fewer parameters, so is more compatible with small dataset size and 3D volume data. The network architecture was combined with several techniques for boosting performance, including data augmentation, pre-training, model regularization, model ensemble and prediction bias correction. We compared our overall SFCN approach with several widely-used machine learning models. It achieved state-of-the-art performance in UK Biobank data (N = 14,503), with mean absolute error (MAE) = 2.14y in brain age prediction and 99.5% in sex classification. SFCN also won (both parts of) the 2019 Predictive Analysis Challenge for brain age prediction, involving 79 competing teams (N = 2,638, MAE = 2.90y). We describe here the details of our approach, and its optimisation and validation. Our approach can easily be generalised to other tasks using different image modalities, and is released on GitHub.",,doi:https://doi.org/10.1016/j.media.2020.101871; doi:https://doi.org/10.1016/j.media.2020.101871; html:https://europepmc.org/articles/PMC7610710; pdf:https://europepmc.org/articles/PMC7610710?pdf=render
@@ -2654,8 +2656,8 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 33887342,https://doi.org/10.1016/j.ijcard.2021.04.029,Clopidogrel in noncarriers of CYP2C19 loss-of-function alleles versus ticagrelor in elderly patients with acute coronary syndrome: A pre-specified sub analysis from the POPular Genetics and POPular Age trials CYP2C19 alleles in elderly patients.,"Claassens DMF, Gimbel ME, Bergmeijer TO, Vos GJA, Hermanides RS, van der Harst P, Barbato E, Morisco C, Tjon Joe Gin RM, de Vrey EA, Heestermans TACM, Jukema JW, von Birgelen C, Waalewijn RA, Hofma SH, den Hartog FR, Voskuil M, Van't Hof AWJ, Asselbergs FW, Mosterd A, Herrman JR, Dewilde W, Mahmoodi BK, Deneer VHM, Ten Berg JM.",,International journal of cardiology,2021,2021-04-20,N,Genotyping; Myocardial infarction; CYP2C19; Pharmacogenetics; Older; P2y12,,,"<h4>Background</h4>Patients with acute coronary syndrome (ACS) who are carrying CYP2C19 loss-of-function alleles derive less benefit from clopidogrel treatment. Despite this, in elderly patients, clopidogrel might be preferred over more potent P2Y<sub>12</sub> inhibitors due to a lower bleeding risk. Whether CYP2C19 genotype-guided antiplatelet treatment in the elderly could be of benefit has not been studied specifically.<h4>Methods</h4>Patients aged 70 years and older with known CYP2C19*2 and *3 genotype were identified from the POPular Genetics and POPular Age trials. Noncarriers of loss-of-function alleles treated with clopidogrel were compared to patients, irrespective of CYP2C19 genotype, treated with ticagrelor and to clopidogrel treated carriers of loss-of-function alleles. We assessed net clinical benefit (all-cause death, myocardial infarction, stroke and Platelet Inhibition and Patient Outcomes (PLATO) major bleeding), atherothrombotic outcomes (cardiovascular death, myocardial infarction, stroke) and bleeding outcomes (PLATO major and minor bleeding).<h4>Results</h4>A total of 991 patients were assessed. There was no significant difference in net clinical benefit (17.2% vs. 15.1%, adjusted hazard ratio (adjHR) 1.05, 95% confidence interval (CI) 0.77-1.44), atherothrombotic outcomes (9.7% vs. 9.2%, adjHR 1.00, 95%CI 0.66-1.50), and bleeding outcomes (17.7% vs. 19.8%, adjHR 0.80, 95%CI 0.62-1.12) between clopidogrel in noncarriers of loss-of-function alleles and ticagrelor respectively.<h4>Conclusion</h4>In ACS patients aged 70 years and older, there was no significant difference in net clinical benefit and atherothrombotic outcomes between noncarriers of a loss-of-function allele treated with clopidogrel and patients treated with ticagrelor. The bleeding rate was numerically; though not statistically significant, lower in patients using clopidogrel.",,pdf:https://dspace.library.uu.nl/bitstream/handle/1874/415888/1_s2.0_S0167527321006653_main.pdf?sequence=1&isAllowed=y; doi:https://doi.org/10.1016/j.ijcard.2021.04.029
 34543281,https://doi.org/10.1371/journal.pmed.1003786,The blood metabolome of incident kidney cancer: A case-control study nested within the MetKid consortium.,"Guida F, Tan VY, Corbin LJ, Smith-Byrne K, Alcala K, Langenberg C, Stewart ID, Butterworth AS, Surendran P, Achaintre D, Adamski J, Amiano P, Bergmann MM, Bull CJ, Dahm CC, Gicquiau A, Giles GG, Gunter MJ, Haller T, Langhammer A, Larose TL, Ljungberg B, Metspalu A, Milne RL, Muller DC, Nøst TH, Pettersen Sørgjerd E, Prehn C, Riboli E, Rinaldi S, Rothwell JA, Scalbert A, Schmidt JA, Severi G, Sieri S, Vermeulen R, Vincent EE, Waldenberger M, Timpson NJ, Johansson M.",,PLoS medicine,2021,2021-09-20,Y,,,,"<h4>Background</h4>Excess bodyweight and related metabolic perturbations have been implicated in kidney cancer aetiology, but the specific molecular mechanisms underlying these relationships are poorly understood. In this study, we sought to identify circulating metabolites that predispose kidney cancer and to evaluate the extent to which they are influenced by body mass index (BMI).<h4>Methods and findings</h4>We assessed the association between circulating levels of 1,416 metabolites and incident kidney cancer using pre-diagnostic blood samples from up to 1,305 kidney cancer case-control pairs from 5 prospective cohort studies. Cases were diagnosed on average 8 years after blood collection. We found 25 metabolites robustly associated with kidney cancer risk. In particular, 14 glycerophospholipids (GPLs) were inversely associated with risk, including 8 phosphatidylcholines (PCs) and 2 plasmalogens. The PC with the strongest association was PC ae C34:3 with an odds ratio (OR) for 1 standard deviation (SD) increment of 0.75 (95% confidence interval [CI]: 0.68 to 0.83, p = 2.6 × 10-8). In contrast, 4 amino acids, including glutamate (OR for 1 SD = 1.39, 95% CI: 1.20 to 1.60, p = 1.6 × 10-5), were positively associated with risk. Adjusting for BMI partly attenuated the risk association for some-but not all-metabolites, whereas other known risk factors of kidney cancer, such as smoking and alcohol consumption, had minimal impact on the observed associations. A mendelian randomisation (MR) analysis of the influence of BMI on the blood metabolome highlighted that some metabolites associated with kidney cancer risk are influenced by BMI. Specifically, elevated BMI appeared to decrease levels of several GPLs that were also found inversely associated with kidney cancer risk (e.g., -0.17 SD change [ßBMI] in 1-(1-enyl-palmitoyl)-2-linoleoyl-GPC (P-16:0/18:2) levels per SD change in BMI, p = 3.4 × 10-5). BMI was also associated with increased levels of glutamate (ßBMI: 0.12, p = 1.5 × 10-3). While our results were robust across the participating studies, they were limited to study participants of European descent, and it will, therefore, be important to evaluate if our findings can be generalised to populations with different genetic backgrounds.<h4>Conclusions</h4>This study suggests a potentially important role of the blood metabolome in kidney cancer aetiology by highlighting a wide range of metabolites associated with the risk of developing kidney cancer and the extent to which changes in levels of these metabolites are driven by BMI-the principal modifiable risk factor of kidney cancer.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003786&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003786; html:https://europepmc.org/articles/PMC8496779; pdf:https://europepmc.org/articles/PMC8496779?pdf=render
 35577541,https://doi.org/10.1136/archdischild-2021-323616,Changes in adolescents' planned hospital care during the COVID-19 pandemic: analysis of linked administrative data.,"Mc Grath-Lone L, Etoori D, Gilbert R, Harron KL, Woodman J, Blackburn R.",,Archives of disease in childhood,2022,2022-09-20,Y,Social Work; Child Health Services; Adolescent Health; Covid-19,,,"<h4>Objective</h4>To describe changes in planned hospital care during the pandemic for vulnerable adolescents receiving children's social care (CSC) services or special educational needs (SEN) support, relative to their peers.<h4>Design</h4>Observational cohort in the Education and Child Health Insights from Linked Data database (linked de-identified administrative health, education and social care records of all children in England).<h4>Study population</h4>All secondary school pupils in years 7-11 in academic year 2019/2020 (N=3 030 235).<h4>Main exposure</h4>Receiving SEN support or CSC services.<h4>Main outcomes</h4>Changes in outpatient attendances and planned hospital admissions during the first 9 months of the pandemic (23 March-31 December 2020), estimated by comparing predicted with observed numbers and rates per 1000 child-years.<h4>Results</h4>A fifth of pupils (20.5%) received some form of statutory support: 14.2% received SEN support only, 3.6% received CSC services only and 2.7% received both. Decreases in planned hospital care were greater for these vulnerable adolescents than their peers: -290 vs -225 per 1000 child-years for outpatient attendances and -36 vs -16 per 1000 child-years for planned admissions. Overall, 21% of adolescents who were vulnerable disproportionately bore 25% of the decrease in outpatient attendances and 37% of the decrease in planned hospital admissions. Vulnerable adolescents were less likely than their peers to have face-to-face outpatient care.<h4>Conclusion</h4>These findings indicate that socially vulnerable groups of children have high health needs, which may need to be prioritised to ensure equitable provision, including for catch-up of planned care postpandemic.",,pdf:https://adc.bmj.com/content/archdischild/107/10/e29.full.pdf; doi:https://doi.org/10.1136/archdischild-2021-323616; html:https://europepmc.org/articles/PMC9157329; pdf:https://europepmc.org/articles/PMC9157329?pdf=render
-37414900,https://doi.org/10.1038/s41591-023-02429-x,A multi-ancestry polygenic risk score improves risk prediction for coronary artery disease.,"Patel AP, Wang M, Ruan Y, Koyama S, Clarke SL, Yang X, Tcheandjieu C, Agrawal S, Fahed AC, Ellinor PT, Genes & Health Research Team; the Million Veteran Program, Tsao PS, Sun YV, Cho K, Wilson PWF, Assimes TL, van Heel DA, Butterworth AS, Aragam KG, Natarajan P, Khera AV.",,Nature medicine,2023,2023-07-06,Y,,,,"Identification of individuals at highest risk of coronary artery disease (CAD)-ideally before onset-remains an important public health need. Prior studies have developed genome-wide polygenic scores to enable risk stratification, reflecting the substantial inherited component to CAD risk. Here we develop a new and significantly improved polygenic score for CAD, termed GPS<sub>Mult</sub>, that incorporates genome-wide association data across five ancestries for CAD (>269,000 cases and >1,178,000 controls) and ten CAD risk factors. GPS<sub>Mult</sub> strongly associated with prevalent CAD (odds ratio per standard deviation 2.14, 95% confidence interval 2.10-2.19, P < 0.001) in UK Biobank participants of European ancestry, identifying 20.0% of the population with 3-fold increased risk and conversely 13.9% with 3-fold decreased risk as compared with those in the middle quintile. GPS<sub>Mult</sub> was also associated with incident CAD events (hazard ratio per standard deviation 1.73, 95% confidence interval 1.70-1.76, P < 0.001), identifying 3% of healthy individuals with risk of future CAD events equivalent to those with existing disease and significantly improving risk discrimination and reclassification. Across multiethnic, external validation datasets inclusive of 33,096, 124,467, 16,433 and 16,874 participants of African, European, Hispanic and South Asian ancestry, respectively, GPS<sub>Mult</sub> demonstrated increased strength of associations across all ancestries and outperformed all available previously published CAD polygenic scores. These data contribute a new GPS<sub>Mult</sub> for CAD to the field and provide a generalizable framework for how large-scale integration of genetic association data for CAD and related traits from diverse populations can meaningfully improve polygenic risk prediction.",,pdf:https://www.nature.com/articles/s41591-023-02429-x.pdf; doi:https://doi.org/10.1038/s41591-023-02429-x; html:https://europepmc.org/articles/PMC10353935; pdf:https://europepmc.org/articles/PMC10353935?pdf=render
 35820692,https://doi.org/10.1136/bmj-2021-069881,Clinical prediction models for mortality in patients with covid-19: external validation and individual participant data meta-analysis.,"de Jong VMT, Rousset RZ, Antonio-Villa NE, Buenen AG, Van Calster B, Bello-Chavolla OY, Brunskill NJ, Curcin V, Damen JAA, Fermín-Martínez CA, Fernández-Chirino L, Ferrari D, Free RC, Gupta RK, Haldar P, Hedberg P, Korang SK, Kurstjens S, Kusters R, Major RW, Maxwell L, Nair R, Naucler P, Nguyen TL, Noursadeghi M, Rosa R, Soares F, Takada T, van Royen FS, van Smeden M, Wynants L, Modrák M, CovidRetro collaboration, Asselbergs FW, Linschoten M, CAPACITY-COVID consortium, Moons KGM, Debray TPA.",,BMJ (Clinical research ed.),2022,2022-07-12,Y,,,,"<h4>Objective</h4>To externally validate various prognostic models and scoring rules for predicting short term mortality in patients admitted to hospital for covid-19.<h4>Design</h4>Two stage individual participant data meta-analysis.<h4>Setting</h4>Secondary and tertiary care.<h4>Participants</h4>46 914 patients across 18 countries, admitted to a hospital with polymerase chain reaction confirmed covid-19 from November 2019 to April 2021.<h4>Data sources</h4>Multiple (clustered) cohorts in Brazil, Belgium, China, Czech Republic, Egypt, France, Iran, Israel, Italy, Mexico, Netherlands, Portugal, Russia, Saudi Arabia, Spain, Sweden, United Kingdom, and United States previously identified by a living systematic review of covid-19 prediction models published in <i>The BMJ</i>, and through PROSPERO, reference checking, and expert knowledge.<h4>Model selection and eligibility criteria</h4>Prognostic models identified by the living systematic review and through contacting experts. A priori models were excluded that had a high risk of bias in the participant domain of PROBAST (prediction model study risk of bias assessment tool) or for which the applicability was deemed poor.<h4>Methods</h4>Eight prognostic models with diverse predictors were identified and validated. A two stage individual participant data meta-analysis was performed of the estimated model concordance (C) statistic, calibration slope, calibration-in-the-large, and observed to expected ratio (O:E) across the included clusters.<h4>Main outcome measures</h4>30 day mortality or in-hospital mortality.<h4>Results</h4>Datasets included 27 clusters from 18 different countries and contained data on 46 914patients. The pooled estimates ranged from 0.67 to 0.80 (C statistic), 0.22 to 1.22 (calibration slope), and 0.18 to 2.59 (O:E ratio) and were prone to substantial between study heterogeneity. The 4C Mortality Score by Knight et al (pooled C statistic 0.80, 95% confidence interval 0.75 to 0.84, 95% prediction interval 0.72 to 0.86) and clinical model by Wang et al (0.77, 0.73 to 0.80, 0.63 to 0.87) had the highest discriminative ability. On average, 29% fewer deaths were observed than predicted by the 4C Mortality Score (pooled O:E 0.71, 95% confidence interval 0.45 to 1.11, 95% prediction interval 0.21 to 2.39), 35% fewer than predicted by the Wang clinical model (0.65, 0.52 to 0.82, 0.23 to 1.89), and 4% fewer than predicted by Xie et al's model (0.96, 0.59 to 1.55, 0.21 to 4.28).<h4>Conclusion</h4>The prognostic value of the included models varied greatly between the data sources. Although the Knight 4C Mortality Score and Wang clinical model appeared most promising, recalibration (intercept and slope updates) is needed before implementation in routine care.",,pdf:https://www.bmj.com/content/bmj/378/bmj-2021-069881.full.pdf; doi:https://doi.org/10.1136/bmj-2021-069881; html:https://europepmc.org/articles/PMC9273913; pdf:https://europepmc.org/articles/PMC9273913?pdf=render
+37414900,https://doi.org/10.1038/s41591-023-02429-x,A multi-ancestry polygenic risk score improves risk prediction for coronary artery disease.,"Patel AP, Wang M, Ruan Y, Koyama S, Clarke SL, Yang X, Tcheandjieu C, Agrawal S, Fahed AC, Ellinor PT, Genes & Health Research Team; the Million Veteran Program, Tsao PS, Sun YV, Cho K, Wilson PWF, Assimes TL, van Heel DA, Butterworth AS, Aragam KG, Natarajan P, Khera AV.",,Nature medicine,2023,2023-07-06,Y,,,,"Identification of individuals at highest risk of coronary artery disease (CAD)-ideally before onset-remains an important public health need. Prior studies have developed genome-wide polygenic scores to enable risk stratification, reflecting the substantial inherited component to CAD risk. Here we develop a new and significantly improved polygenic score for CAD, termed GPS<sub>Mult</sub>, that incorporates genome-wide association data across five ancestries for CAD (>269,000 cases and >1,178,000 controls) and ten CAD risk factors. GPS<sub>Mult</sub> strongly associated with prevalent CAD (odds ratio per standard deviation 2.14, 95% confidence interval 2.10-2.19, P < 0.001) in UK Biobank participants of European ancestry, identifying 20.0% of the population with 3-fold increased risk and conversely 13.9% with 3-fold decreased risk as compared with those in the middle quintile. GPS<sub>Mult</sub> was also associated with incident CAD events (hazard ratio per standard deviation 1.73, 95% confidence interval 1.70-1.76, P < 0.001), identifying 3% of healthy individuals with risk of future CAD events equivalent to those with existing disease and significantly improving risk discrimination and reclassification. Across multiethnic, external validation datasets inclusive of 33,096, 124,467, 16,433 and 16,874 participants of African, European, Hispanic and South Asian ancestry, respectively, GPS<sub>Mult</sub> demonstrated increased strength of associations across all ancestries and outperformed all available previously published CAD polygenic scores. These data contribute a new GPS<sub>Mult</sub> for CAD to the field and provide a generalizable framework for how large-scale integration of genetic association data for CAD and related traits from diverse populations can meaningfully improve polygenic risk prediction.",,pdf:https://www.nature.com/articles/s41591-023-02429-x.pdf; doi:https://doi.org/10.1038/s41591-023-02429-x; html:https://europepmc.org/articles/PMC10353935; pdf:https://europepmc.org/articles/PMC10353935?pdf=render
 34820659,https://doi.org/10.1016/j.xgen.2021.100028,The Data Use Ontology to streamline responsible access to human biomedical datasets.,"Lawson J, Cabili MN, Kerry G, Boughtwood T, Thorogood A, Alper P, Bowers SR, Boyles RR, Brookes AJ, Brush M, Burdett T, Clissold H, Donnelly S, Dyke SOM, Freeberg MA, Haendel MA, Hata C, Holub P, Jeanson F, Jene A, Kawashima M, Kawashima S, Konopko M, Kyomugisha I, Li H, Linden M, Rodriguez LL, Morita M, Mulder N, Muller J, Nagaie S, Nasir J, Ogishima S, Ota Wang V, Paglione LD, Pandya RN, Parkinson H, Philippakis AA, Prasser F, Rambla J, Reinold K, Rushton GA, Saltzman A, Saunders G, Sofia HJ, Spalding JD, Swertz MA, Tulchinsky I, van Enckevort EJ, Varma S, Voisin C, Yamamoto N, Yamasaki C, Zass L, Guidry Auvil JM, Nyrönen TH, Courtot M.",,Cell genomics,2021,2021-11-10,Y,Standard; Consent; Ontology; Data Access; Fair; Secondary Data Use; Ga4gh; Controlled Access; Automated Data Access; Data Restrictions,,,"Human biomedical datasets that are critical for research and clinical studies to benefit human health also often contain sensitive or potentially identifying information of individual participants. Thus, care must be taken when they are processed and made available to comply with ethical and regulatory frameworks and informed consent data conditions. To enable and streamline data access for these biomedical datasets, the Global Alliance for Genomics and Health (GA4GH) Data Use and Researcher Identities (DURI) work stream developed and approved the Data Use Ontology (DUO) standard. DUO is a hierarchical vocabulary of human and machine-readable data use terms that consistently and unambiguously represents a dataset's allowable data uses. DUO has been implemented by major international stakeholders such as the Broad and Sanger Institutes and is currently used in annotation of over 200,000 datasets worldwide. Using DUO in data management and access facilitates researchers' discovery and access of relevant datasets. DUO annotations increase the FAIRness of datasets and support data linkages using common data use profiles when integrating the data for secondary analyses. DUO is implemented in the Web Ontology Language (OWL) and, to increase community awareness and engagement, hosted in an open, centralized GitHub repository. DUO, together with the GA4GH Passport standard, offers a new, efficient, and streamlined data authorization and access framework that has enabled increased sharing of biomedical datasets worldwide.",,doi:https://doi.org/10.1016/j.xgen.2021.100028; doi:https://doi.org/10.1016/j.xgen.2021.100028; html:https://europepmc.org/articles/PMC8591903; pdf:https://europepmc.org/articles/PMC8591903?pdf=render
 31775616,https://doi.org/10.1186/s12859-019-3201-y,Manhattan++: displaying genome-wide association summary statistics with multiple annotation layers.,"Grace C, Farrall M, Watkins H, Goel A.",,BMC bioinformatics,2019,2019-11-27,Y,Software; Meta-analysis; Gwas; R; Cran; Manhattan Plot,,,"<h4>Background</h4>Over the last 10 years, there have been over 3300 genome-wide association studies (GWAS). Almost every GWAS study provides a Manhattan plot either as a main figure or in the supplement. Several software packages can generate a Manhattan plot, but they are all limited in the extent to which they can annotate gene-names, allele frequencies, and variants having high impact on gene function or provide any other added information or flexibility. Furthermore, in a conventional Manhattan plot, there is no way of distinguishing a locus identified due to a single variant with very significant p-value from a locus with multiple variants which appear to be in a haplotype block having very similar p-values.<h4>Results</h4>Here we present a software tool written in R, which generates a transposed Manhattan plot along with additional features like variant consequence and minor allele frequency to annotate the plot and addresses these limitations. The software also gives flexibility on how and where the user wants to display the annotations. The software can be downloaded from CRAN repository and also from the GitHub project page.<h4>Conclusions</h4>We present a major step up to the existing conventional Manhattan plot generation tools. We hope this form of display along with the added annotations will bring more insight to the reader from this new Manhattan++ plot.",,pdf:https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3201-y; doi:https://doi.org/10.1186/s12859-019-3201-y; html:https://europepmc.org/articles/PMC6882345; pdf:https://europepmc.org/articles/PMC6882345?pdf=render
 35484151,https://doi.org/10.1038/s41467-022-29932-y,Childhood body size directly increases type 1 diabetes risk based on a lifecourse Mendelian randomization approach.,"Richardson TG, Crouch DJM, Power GM, Morales-Berstein F, Hazelwood E, Fang S, Cho Y, Inshaw JRJ, Robertson CC, Sidore C, Cucca F, Rich SS, Todd JA, Davey Smith G.",,Nature communications,2022,2022-04-28,Y,,,,"The rising prevalence of childhood obesity has been postulated as an explanation for the increasing rate of individuals diagnosed with type 1 diabetes (T1D). In this study, we use Mendelian randomization (MR) to provide evidence that childhood body size has an effect on T1D risk (OR = 2.05 per change in body size category, 95% CI = 1.20 to 3.50, P = 0.008), which remains after accounting for body size at birth and during adulthood using multivariable MR (OR = 2.32, 95% CI = 1.21 to 4.42, P = 0.013). We validate this direct effect of childhood body size using data from a large-scale T1D meta-analysis based on n = 15,573 cases and n = 158,408 controls (OR = 1.94, 95% CI = 1.21 to 3.12, P = 0.006). We also provide evidence that childhood body size influences risk of asthma, eczema and hypothyroidism, although multivariable MR suggested that these effects are mediated by body size in later life. Our findings support a causal role for higher childhood body size on risk of being diagnosed with T1D, whereas its influence on the other immune-associated diseases is likely explained by a long-term effect of remaining overweight for many years over the lifecourse.",,pdf:https://www.nature.com/articles/s41467-022-29932-y.pdf; doi:https://doi.org/10.1038/s41467-022-29932-y; html:https://europepmc.org/articles/PMC9051135; pdf:https://europepmc.org/articles/PMC9051135?pdf=render
@@ -2669,8 +2671,8 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 35460409,https://doi.org/10.1093/ageing/afac090,New horizons in evidence-based care for older people: individual participant data meta-analysis.,"Clegg A, Bandeen-Roche K, Farrin A, Forster A, Gill TM, Gladman J, Kerse N, Lindley R, McManus RJ, Melis R, Mujica-Mota R, Raina P, Rockwood K, Teh R, van der Windt D, Witham M.",,Age and ageing,2022,2022-04-01,Y,Ageing; Meta-analysis; Frailty; Older People; Stratified Care; Individual Participant Data,,,"Evidence-based decisions on clinical and cost-effectiveness of interventions are ideally informed by meta-analyses of intervention trial data. However, when undertaken, such meta-analyses in ageing research have typically been conducted using standard methods whereby summary (aggregate) data are extracted from published trial reports. Although meta-analysis of aggregate data can provide useful insights into the average effect of interventions within a selected trial population, it has limitations regarding robust conclusions on which subgroups of people stand to gain the greatest benefit from an intervention or are at risk of experiencing harm. Future evidence synthesis using individual participant data from ageing research trials for meta-analysis could transform understanding of the effectiveness of interventions for older people, supporting evidence-based and sustainable commissioning. A major advantage of individual participant data meta-analysis (IPDMA) is that it enables examination of characteristics that predict treatment effects, such as frailty, disability, cognitive impairment, ethnicity, gender and other wider determinants of health. Key challenges of IPDMA relate to the complexity and resources needed for obtaining, managing and preparing datasets, requiring a meticulous approach involving experienced researchers, frequently with expertise in designing and analysing clinical trials. In anticipation of future IPDMA work in ageing research, we are establishing an international Ageing Research Trialists collective, to bring together trialists with a common focus on transforming care for older people as a shared ambition across nations.",,pdf:https://academic.oup.com/ageing/article-pdf/51/4/afac090/43408856/afac090.pdf; doi:https://doi.org/10.1093/ageing/afac090; html:https://europepmc.org/articles/PMC9034697; pdf:https://europepmc.org/articles/PMC9034697?pdf=render
 34672950,https://doi.org/10.1016/s2213-2600(21)00435-5,"Colchicine in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial.",RECOVERY Collaborative Group.,,The Lancet. Respiratory medicine,2021,2021-10-18,Y,,,,"<h4>Background</h4>Colchicine has been proposed as a treatment for COVID-19 based on its anti-inflammatory actions. We aimed to evaluate the efficacy and safety of colchicine in patients admitted to hospital with COVID-19.<h4>Methods</h4>In this streamlined, randomised, controlled, open-label trial, underway at 177 hospitals in the UK, two hospitals in Indonesia, and two hospitals in Nepal, several possible treatments were compared with usual care in patients hospitalised with COVID-19. Patients were eligible for inclusion in the study if they were admitted to hospital with clinically suspected or laboratory confirmed SARS-CoV-2 infection and had no medical history that might, in the opinion of the attending clinician, put the patient at significant risk if they were to participate in the trial. Eligible and consenting adults were randomly assigned (1:1) to receive either usual standard of care alone (usual care group) or usual standard of care plus colchicine (colchicine group) using web-based simple (unstratified) randomisation with allocation concealment. Participants received colchicine 1 mg after randomisation followed by 500 μg 12 h later and then 500 μg twice a day by mouth or nasogastric tube for 10 days in total or until discharge. Dose frequency was halved for patients receiving a moderate CYP3A4 inhibitor (eg, diltiazem), patients with an estimated glomerular filtration rate of less than 30 mL/min per 1·73m<sup>2</sup>, and those with an estimated bodyweight of less than 70 kg. The primary outcome was 28-day mortality, secondary endpoints included time to discharge, the proportion of patients discharged from hospital within 28 days, and, in patients not on invasive mechanical ventilation at randomisation, a composite endpoint of invasive mechanical ventilation or death. All analyses were by intention-to-treat. The trial is registered with ISRCTN, 50189673, and ClinicalTrials.gov, NCT04381936.<h4>Findings</h4>Between Nov 27, 2020, and March 4, 2021, 11 340 (58%) of 19 423 patients enrolled into the RECOVERY trial were eligible to receive colchicine; 5610 (49%) patients were randomly assigned to the colchicine group and 5730 (51%) to the usual care group. Overall, 1173 (21%) patients in the colchicine group and 1190 (21%) patients in the usual care group died within 28 days (rate ratio 1·01 [95% CI 0·93 to 1·10]; p=0·77). Consistent results were seen in all prespecified subgroups of patients. Median time to discharge alive (10 days [IQR 5 to >28]) was the same in both groups, and there was no significant difference in the proportion of patients discharged from hospital alive within 28 days (3901 [70%] patients in the colchicine group and 4032 [70%] usual care group; rate ratio 0·98 [95% CI 0·94 to 1·03]; p=0·44). In those not on invasive mechanical ventilation at baseline, there was no significant difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (1344 [25%] in the colchicine group vs 1343 [25%] patients in the usual care group; risk ratio 1·02 [95% CI 0·96 to 1·09]; p=0·47).<h4>Interpretation</h4>In adults hospitalised with COVID-19, colchicine was not associated with reductions in 28-day mortality, duration of hospital stay, or risk of progressing to invasive mechanical ventilation or death.<h4>Funding</h4>UK Research and Innovation (Medical Research Council), National Institute of Health Research, and Wellcome Trust.",,pdf:http://www.thelancet.com/article/S2213260021004355/pdf; doi:https://doi.org/10.1016/S2213-2600(21)00435-5; html:https://europepmc.org/articles/PMC8523117
 30768153,https://doi.org/10.1093/cvr/cvz015,Association of the coronary artery disease risk gene GUCY1A3 with ischaemic events after coronary intervention.,"Kessler T, Wolf B, Eriksson N, Kofink D, Mahmoodi BK, Rai H, Tragante V, Åkerblom A, Becker RC, Bernlochner I, Bopp R, James S, Katus HA, Mayer K, Munz M, Nordio F, O'Donoghue ML, Sager HB, Sibbing D, Solakov L, Storey RF, Wobst J, Asselbergs FW, Byrne RA, Erdmann J, Koenig W, Laugwitz KL, Ten Berg JM, Wallentin L, Kastrati A, Schunkert H.",,Cardiovascular research,2019,2019-08-01,N,Platelet aggregation; Genetic variation; Genome-wide Association Studies; Stent Thrombosis; On-aspirin Platelet Reactivity,,,"<h4>Aim</h4>A common genetic variant at the GUCY1A3 coronary artery disease locus has been shown to influence platelet aggregation. The risk of ischaemic events including stent thrombosis varies with the efficacy of aspirin to inhibit platelet reactivity. This study sought to investigate whether homozygous GUCY1A3 (rs7692387) risk allele carriers display higher on-aspirin platelet reactivity and risk of ischaemic events early after coronary intervention.<h4>Methods and results</h4>The association of GUCY1A3 genotype and on-aspirin platelet reactivity was analysed in the genetics substudy of the ISAR-ASPI registry (n = 1678) using impedance aggregometry. The clinical outcome cardiovascular death or stent thrombosis within 30 days after stenting was investigated in a meta-analysis of substudies of the ISAR-ASPI registry, the PLATO trial (n = 3236), and the Utrecht Coronary Biobank (n = 1003) comprising a total 5917 patients. Homozygous GUCY1A3 risk allele carriers (GG) displayed increased on-aspirin platelet reactivity compared with non-risk allele (AA/AG) carriers [150 (interquartile range 91-209) vs. 134 (85-194) AU⋅min, P < 0.01]. More homozygous risk allele carriers, compared with non-risk allele carriers, were assigned to the high-risk group for ischaemic events (>203 AU⋅min; 29.5 vs. 24.2%, P = 0.02). Homozygous risk allele carriers were also at higher risk for cardiovascular death or stent thrombosis (hazard ratio 1.70, 95% confidence interval 1.08-2.68; P = 0.02). Bleeding risk was not altered.<h4>Conclusion</h4>We conclude that homozygous GUCY1A3 risk allele carriers are at increased risk of cardiovascular death or stent thrombosis within 30 days after coronary stenting, likely due to higher on-aspirin platelet reactivity. Whether GUCY1A3 genotype helps to tailor antiplatelet treatment remains to be investigated.",,pdf:https://academic.oup.com/cardiovascres/article-pdf/115/10/1512/28981341/cvz015.pdf; doi:https://doi.org/10.1093/cvr/cvz015
-36870556,https://doi.org/10.1016/j.jid.2023.02.010,Genetic Validation of Psoriasis Phenotyping in UK Biobank Supports the Utility of Self-Reported Data and Composite Definitions for Large Genetic and Epidemiological Studies.,"Saklatvala JR, Hanscombe KB, Mahil SK, Tsoi LC, Elder JT, Barker JN, Simpson MA, Smith CH, Dand N.",,The Journal of investigative dermatology,2023,2023-03-03,Y,,,,,,pdf:http://www.jidonline.org/article/S0022202X23001069/pdf; doi:https://doi.org/10.1016/j.jid.2023.02.010; html:https://europepmc.org/articles/PMC10689249; pdf:https://europepmc.org/articles/PMC10689249?pdf=render
 33785494,https://doi.org/10.1136/bmjopen-2020-046365,Impact of the COVID-19 pandemic on remote mental healthcare and prescribing in psychiatry: an electronic health record study.,"Patel R, Irving J, Brinn A, Broadbent M, Shetty H, Pritchard M, Downs J, Stewart R, Harland R, McGuire P.",,BMJ open,2021,2021-03-30,Y,Psychiatry; Mental health; epidemiology; Telemedicine; Health Informatics,,,"<h4>Objectives</h4>The recent COVID-19 pandemic has disrupted mental healthcare delivery, with many services shifting from in-person to remote patient contact. We investigated the impact of the pandemic on the use of remote consultation and on the prescribing of psychiatric medications.<h4>Design and setting</h4>The Clinical Record Interactive Search tool was used to examine deidentified electronic health records of people receiving mental healthcare from the South London and Maudsley (SLaM) NHS Foundation Trust. Data from the period before and after the onset of the pandemic were analysed using linear regression, and visualised using locally estimated scatterplot smoothing.<h4>Participants</h4>All patients receiving care from SLaM between 7 January 2019 and 20 September 2020 (around 37 500 patients per week).<h4>Outcome measures</h4>(i) The number of clinical contacts (in-person, remote or non-attended) with mental healthcare professionals per week.(ii) Prescribing of antipsychotic and mood stabiliser medications per week.<h4>Results</h4>Following the onset of the pandemic, the frequency of in-person contacts was significantly reduced compared with that in the previous year (β coefficient: -5829.6 contacts, 95% CI -6919.5 to -4739.6, p<0.001), while the frequency of remote contacts significantly increased (β coefficient: 3338.5 contacts, 95% CI 3074.4 to 3602.7, p<0.001). Rates of remote consultation were lower in older adults than in working age adults, children and adolescents. Despite this change in the type of patient contact, antipsychotic and mood stabiliser prescribing remained at similar levels.<h4>Conclusions</h4>The COVID-19 pandemic has been associated with a marked increase in remote consultation, particularly among younger patients. However, there was no evidence that this has led to changes in psychiatric prescribing. Nevertheless, further work is needed to ensure that older patients are able to access mental healthcare remotely.",,pdf:https://bmjopen.bmj.com/content/bmjopen/11/3/e046365.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-046365; html:https://europepmc.org/articles/PMC8728386; pdf:https://europepmc.org/articles/PMC8728386?pdf=render
+36870556,https://doi.org/10.1016/j.jid.2023.02.010,Genetic Validation of Psoriasis Phenotyping in UK Biobank Supports the Utility of Self-Reported Data and Composite Definitions for Large Genetic and Epidemiological Studies.,"Saklatvala JR, Hanscombe KB, Mahil SK, Tsoi LC, Elder JT, Barker JN, Simpson MA, Smith CH, Dand N.",,The Journal of investigative dermatology,2023,2023-03-03,Y,,,,,,pdf:http://www.jidonline.org/article/S0022202X23001069/pdf; doi:https://doi.org/10.1016/j.jid.2023.02.010; html:https://europepmc.org/articles/PMC10689249; pdf:https://europepmc.org/articles/PMC10689249?pdf=render
 34600575,https://doi.org/10.1186/s13104-021-05789-0,"Application of ensemble clustering and survival tree analysis for identifying prognostic clinicogenomic features in patients with colorectal cancer from the 100,000 Genomes Project.","Wei Y, Papachristou N, Mueller S, Genomics England Research Consortium, Chang WH, Lai AG.",,BMC research notes,2021,2021-10-02,Y,,,,"<h4>Objective</h4>The objective of this study was to employ ensemble clustering and tree-based risk model approaches to identify interactions between clinicogenomic features for colorectal cancer using the 100,000 Genomes Project.<h4>Results</h4>Among the 2211 patients with colorectal cancer (mean age of diagnosis: 67.7; 59.7% male), 16.3%, 36.3%, 39.0% and 8.4% had stage 1, 2, 3 and 4 cancers, respectively. Almost every patient had surgery (99.7%), 47.4% had chemotherapy, 7.6% had radiotherapy and 1.4% had immunotherapy. On average, tumour mutational burden (TMB) was 18 mutations/Mb and 34.4%, 31.3% and 25.7% of patients had structural or copy number mutations in KRAS, BRAF and NRAS, respectively. In the fully adjusted Cox model, patients with advanced cancer [stage 3 hazard ratio (HR)  =  3.2; p  <  0.001; stage 4 HR  =  10.2; p  <  0.001] and those who had immunotherapy (HR  =  1.8; p  <  0.04) or radiotherapy (HR  =  1.5; p  <  0.02) treatment had a higher risk of dying. The ensemble clustering approach generated four distinct clusters where patients in cluster 2 had the best survival outcomes (1-year: 98.7%; 2-year: 96.7%; 3-year: 93.0%) while patients in cluster 3 (1-year: 87.9; 2-year: 70.0%; 3-year: 53.1%) had the worst outcomes. Kaplan-Meier analysis and log rank test revealed that the clusters were separated into distinct prognostic groups (p  <  0.0001). Survival tree or recursive partitioning analyses were performed to further explore risk groups within each cluster. Among patients in cluster 2, for example, interactions between cancer stage, grade, radiotherapy, TMB, BRAF mutation status were identified. Patients with stage 4 cancer and TMB  ≥  1.6 mutations/Mb had 4 times higher risk of dying relative to the baseline hazard in that cluster.",,pdf:https://bmcresnotes.biomedcentral.com/track/pdf/10.1186/s13104-021-05789-0; doi:https://doi.org/10.1186/s13104-021-05789-0; html:https://europepmc.org/articles/PMC8487486; pdf:https://europepmc.org/articles/PMC8487486?pdf=render
 34748544,https://doi.org/10.1371/journal.pbio.3001255,Predicting novel candidate human obesity genes and their site of action by systematic functional screening in Drosophila.,"Agrawal N, Lawler K, Davidson CM, Keogh JM, Legg R, INTERVAL, Barroso I, Farooqi IS, Brand AH.",,PLoS biology,2021,2021-11-08,Y,,,,"The discovery of human obesity-associated genes can reveal new mechanisms to target for weight loss therapy. Genetic studies of obese individuals and the analysis of rare genetic variants can identify novel obesity-associated genes. However, establishing a functional relationship between these candidate genes and adiposity remains a significant challenge. We uncovered a large number of rare homozygous gene variants by exome sequencing of severely obese children, including those from consanguineous families. By assessing the function of these genes in vivo in Drosophila, we identified 4 genes, not previously linked to human obesity, that regulate adiposity (itpr, dachsous, calpA, and sdk). Dachsous is a transmembrane protein upstream of the Hippo signalling pathway. We found that 3 further members of the Hippo pathway, fat, four-jointed, and hippo, also regulate adiposity and that they act in neurons, rather than in adipose tissue (fat body). Screening Hippo pathway genes in larger human cohorts revealed rare variants in TAOK2 associated with human obesity. Knockdown of Drosophila tao increased adiposity in vivo demonstrating the strength of our approach in predicting novel human obesity genes and signalling pathways and their site of action.",,pdf:https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.3001255&type=printable; doi:https://doi.org/10.1371/journal.pbio.3001255; html:https://europepmc.org/articles/PMC8575313; pdf:https://europepmc.org/articles/PMC8575313?pdf=render
 34876579,https://doi.org/10.1038/s41467-021-27326-0,Biological heterogeneity in idiopathic pulmonary arterial hypertension identified through unsupervised transcriptomic profiling of whole blood.,"Kariotis S, Jammeh E, Swietlik EM, Pickworth JA, Rhodes CJ, Otero P, Wharton J, Iremonger J, Dunning MJ, Pandya D, Mascarenhas TS, Errington N, Thompson AAR, Romanoski CE, Rischard F, Garcia JGN, Yuan JX, An TS, Desai AA, Coghlan G, Lordan J, Corris PA, Howard LS, Condliffe R, Kiely DG, Church C, Pepke-Zaba J, Toshner M, Wort S, Gräf S, Morrell NW, Wilkins MR, Lawrie A, Wang D, UK National PAH Cohort Study Consortium.",,Nature communications,2021,2021-12-07,Y,,,,"Idiopathic pulmonary arterial hypertension (IPAH) is a rare but fatal disease diagnosed by right heart catheterisation and the exclusion of other forms of pulmonary arterial hypertension, producing a heterogeneous population with varied treatment response. Here we show unsupervised machine learning identification of three major patient subgroups that account for 92% of the cohort, each with unique whole blood transcriptomic and clinical feature signatures. These subgroups are associated with poor, moderate, and good prognosis. The poor prognosis subgroup is associated with upregulation of the ALAS2 and downregulation of several immunoglobulin genes, while the good prognosis subgroup is defined by upregulation of the bone morphogenetic protein signalling regulator NOG, and the C/C variant of HLA-DPA1/DPB1 (independently associated with survival). These findings independently validated provide evidence for the existence of 3 major subgroups (endophenotypes) within the IPAH classification, could improve risk stratification and provide molecular insights into the pathogenesis of IPAH.",,pdf:https://www.nature.com/articles/s41467-021-27326-0.pdf; doi:https://doi.org/10.1038/s41467-021-27326-0; html:https://europepmc.org/articles/PMC8651638; pdf:https://europepmc.org/articles/PMC8651638?pdf=render
@@ -2693,8 +2695,8 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 32220655,https://doi.org/10.1016/s2468-2667(20)30073-6,"The effect of control strategies to reduce social mixing on outcomes of the COVID-19 epidemic in Wuhan, China: a modelling study.","Prem K, Liu Y, Russell TW, Kucharski AJ, Eggo RM, Davies N, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Jit M, Klepac P.",,The Lancet. Public health,2020,2020-03-25,Y,,,,"<h4>Background</h4>In December, 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus, emerged in Wuhan, China. Since then, the city of Wuhan has taken unprecedented measures in response to the outbreak, including extended school and workplace closures. We aimed to estimate the effects of physical distancing measures on the progression of the COVID-19 epidemic, hoping to provide some insights for the rest of the world.<h4>Methods</h4>To examine how changes in population mixing have affected outbreak progression in Wuhan, we used synthetic location-specific contact patterns in Wuhan and adapted these in the presence of school closures, extended workplace closures, and a reduction in mixing in the general community. Using these matrices and the latest estimates of the epidemiological parameters of the Wuhan outbreak, we simulated the ongoing trajectory of an outbreak in Wuhan using an age-structured susceptible-exposed-infected-removed (SEIR) model for several physical distancing measures. We fitted the latest estimates of epidemic parameters from a transmission model to data on local and internationally exported cases from Wuhan in an age-structured epidemic framework and investigated the age distribution of cases. We also simulated lifting of the control measures by allowing people to return to work in a phased-in way and looked at the effects of returning to work at different stages of the underlying outbreak (at the beginning of March or April).<h4>Findings</h4>Our projections show that physical distancing measures were most effective if the staggered return to work was at the beginning of April; this reduced the median number of infections by more than 92% (IQR 66-97) and 24% (13-90) in mid-2020 and end-2020, respectively. There are benefits to sustaining these measures until April in terms of delaying and reducing the height of the peak, median epidemic size at end-2020, and affording health-care systems more time to expand and respond. However, the modelled effects of physical distancing measures vary by the duration of infectiousness and the role school children have in the epidemic.<h4>Interpretation</h4>Restrictions on activities in Wuhan, if maintained until April, would probably help to delay the epidemic peak. Our projections suggest that premature and sudden lifting of interventions could lead to an earlier secondary peak, which could be flattened by relaxing the interventions gradually. However, there are limitations to our analysis, including large uncertainties around estimates of R<sub>0</sub> and the duration of infectiousness.<h4>Funding</h4>Bill & Melinda Gates Foundation, National Institute for Health Research, Wellcome Trust, and Health Data Research UK.",,pdf:https://repository.publisso.de/resource/frl:6420088/data; doi:https://doi.org/10.1016/S2468-2667(20)30073-6; html:https://europepmc.org/articles/PMC7158905
 35048991,https://doi.org/10.1093/jnci/djac011,Associations Between Glycemic Traits and Colorectal Cancer: A Mendelian Randomization Analysis.,"Murphy N, Song M, Papadimitriou N, Carreras-Torres R, Langenberg C, Martin RM, Tsilidis KK, Barroso I, Chen J, Frayling TM, Bull CJ, Vincent EE, Cotterchio M, Gruber SB, Pai RK, Newcomb PA, Perez-Cornago A, van Duijnhoven FJB, Van Guelpen B, Vodicka P, Wolk A, Wu AH, Peters U, Chan AT, Gunter MJ.",,Journal of the National Cancer Institute,2022,2022-05-01,Y,,,,"<h4>Background</h4>Glycemic traits-such as hyperinsulinemia, hyperglycemia, and type 2 diabetes-have been associated with higher colorectal cancer risk in observational studies; however, causality of these associations is uncertain. We used Mendelian randomization (MR) to estimate the causal effects of fasting insulin, 2-hour glucose, fasting glucose, glycated hemoglobin (HbA1c), and type 2 diabetes with colorectal cancer.<h4>Methods</h4>Genome-wide association study summary data were used to identify genetic variants associated with circulating levels of fasting insulin (n = 34), 2-hour glucose (n = 13), fasting glucose (n = 70), HbA1c (n = 221), and type 2 diabetes (n = 268). Using 2-sample MR, we examined these variants in relation to colorectal cancer risk (48 214 case patient and 64 159 control patients).<h4>Results</h4>In inverse-variance models, higher fasting insulin levels increased colorectal cancer risk (odds ratio [OR] per 1-SD = 1.65, 95% confidence interval [CI] = 1.15 to 2.36). We found no evidence of any effect of 2-hour glucose (OR per 1-SD = 1.02, 95% CI = 0.86 to 1.21) or fasting glucose (OR per 1-SD = 1.04, 95% CI = 0.88 to 1.23) concentrations on colorectal cancer risk. Genetic liability to type 2 diabetes (OR per 1-unit increase in log odds = 1.04, 95% CI = 1.01 to 1.07) and higher HbA1c levels (OR per 1-SD = 1.09, 95% CI = 1.00 to 1.19) increased colorectal cancer risk, although these findings may have been biased by pleiotropy. Higher HbA1c concentrations increased rectal cancer risk in men (OR per 1-SD = 1.21, 95% CI = 1.05 to 1.40), but not in women.<h4>Conclusions</h4>Our results support a causal effect of higher fasting insulin, but not glucose traits or type 2 diabetes, on increased colorectal cancer risk. This suggests that pharmacological or lifestyle interventions that lower circulating insulin levels may be beneficial in preventing colorectal tumorigenesis.",,pdf:https://academic.oup.com/jnci/article-pdf/114/5/740/43623241/djac011.pdf; doi:https://doi.org/10.1093/jnci/djac011; html:https://europepmc.org/articles/PMC9086764; pdf:https://europepmc.org/articles/PMC9086764?pdf=render
 29899974,https://doi.org/10.12688/f1000research.13830.2,Knowledge discovery for Deep Phenotyping serious mental illness from Electronic Mental Health records.,"Jackson R, Patel R, Velupillai S, Gkotsis G, Hoyle D, Stewart R.",,F1000Research,2018,2018-02-21,Y,Schizophrenia; Serious Mental Illness; Electronic Health Records; Natural Language Processing; Word2vec,,,"<b>Background:</b> Deep Phenotyping is the precise and comprehensive analysis of phenotypic features in which the individual components of the phenotype are observed and described. In UK mental health clinical practice, most clinically relevant information is recorded as free text in the Electronic Health Record, and offers a granularity of information beyond what is expressed in most medical knowledge bases. The SNOMED CT nomenclature potentially offers the means to model such information at scale, yet given a sufficiently large body of clinical text collected over many years, it is difficult to identify the language that clinicians favour to express concepts. <b>Methods:</b> By utilising a large corpus of healthcare data, we sought to make use of semantic modelling and clustering techniques to represent the relationship between the clinical vocabulary of internationally recognised SMI symptoms and the preferred language used by clinicians within a care setting. We explore how such models can be used for discovering novel vocabulary relevant to the task of phenotyping Serious Mental Illness (SMI) with only a small amount of prior knowledge.  <b>Results:</b> 20 403 terms were derived and curated via a two stage methodology. The list was reduced to 557 putative concepts based on eliminating redundant information content. These were then organised into 9 distinct categories pertaining to different aspects of psychiatric assessment. 235 concepts were found to be expressions of putative clinical significance. Of these, 53 were identified having novel synonymy with existing SNOMED CT concepts. 106 had no mapping to SNOMED CT. <b>Conclusions:</b> We demonstrate a scalable approach to discovering new concepts of SMI symptomatology based on real-world clinical observation. Such approaches may offer the opportunity to consider broader manifestations of SMI symptomatology than is typically assessed via current diagnostic frameworks, and create the potential for enhancing nomenclatures such as SNOMED CT based on real-world expressions.",,pdf:https://f1000research.com/articles/7-210/v2/pdf; doi:https://doi.org/10.12688/f1000research.13830.2; html:https://europepmc.org/articles/PMC5968362; pdf:https://europepmc.org/articles/PMC5968362?pdf=render
-32735845,https://doi.org/10.1016/j.immuni.2020.07.003,Differential IRF8 Transcription Factor Requirement Defines Two Pathways of Dendritic Cell Development in Humans.,"Cytlak U, Resteu A, Pagan S, Green K, Milne P, Maisuria S, McDonald D, Hulme G, Filby A, Carpenter B, Queen R, Hambleton S, Hague R, Lango Allen H, Thaventhiran JED, Doody G, Collin M, Bigley V.",,Immunity,2020,2020-07-30,Y,Transcription factor; Immunity; Hematopoiesis; Dendritic Cell; Primary Immunodeficiency; Irf8; Cytof; Single-cell Rna Sequencing,,,"The formation of mammalian dendritic cells (DCs) is controlled by multiple hematopoietic transcription factors, including IRF8. Loss of IRF8 exerts a differential effect on DC subsets, including plasmacytoid DCs (pDCs) and the classical DC lineages cDC1 and cDC2. In humans, cDC2-related subsets have been described including AXL<sup>+</sup>SIGLEC6<sup>+</sup> pre-DC, DC2 and DC3. The origin of this heterogeneity is unknown. Using high-dimensional analysis, in vitro differentiation, and an allelic series of human IRF8 deficiency, we demonstrated that cDC2 (CD1c<sup>+</sup>DC) heterogeneity originates from two distinct pathways of development. The lymphoid-primed IRF8<sup>hi</sup> pathway, marked by CD123 and BTLA, carried pDC, cDC1, and DC2 trajectories, while the common myeloid IRF8<sup>lo</sup> pathway, expressing SIRPA, formed DC3s and monocytes. We traced distinct trajectories through the granulocyte-macrophage progenitor (GMP) compartment showing that AXL<sup>+</sup>SIGLEC6<sup>+</sup> pre-DCs mapped exclusively to the DC2 pathway. In keeping with their lower requirement for IRF8, DC3s expand to replace DC2s in human partial IRF8 deficiency.",,pdf:http://www.cell.com/article/S1074761320302831/pdf; doi:https://doi.org/10.1016/j.immuni.2020.07.003; html:https://europepmc.org/articles/PMC7447982
 37248441,https://doi.org/10.1038/s41588-023-01410-1,Genome-wide association meta-analysis of spontaneous coronary artery dissection identifies risk variants and genes related to artery integrity and tissue-mediated coagulation.,"Adlam D, Berrandou TE, Georges A, Nelson CP, Giannoulatou E, Henry J, Ma L, Blencowe M, Turley TN, Yang ML, Chopade S, Finan C, Braund PS, Sadeg-Sayoud I, Iismaa SE, Kosel ML, Zhou X, Hamby SE, Cheng J, Liu L, Tarr I, Muller DWM, d'Escamard V, King A, Brunham LR, Baranowska-Clarke AA, Debette S, Amouyel P, Olin JW, Patil S, Hesselson SE, Junday K, Kanoni S, Aragam KG, Butterworth AS, CARDIoGRAMPlusC4D, MEGASTROKE, International Stroke Genetics Consortium (ISGC) Intracranial Aneurysm Working Group, Tweet MS, Gulati R, Combaret N, DISCO register, Kadian-Dodov D, Kalman JM, Fatkin D, Hingorani AD, Saw J, Webb TR, Hayes SN, Yang X, Ganesh SK, Olson TM, Kovacic JC, Graham RM, Samani NJ, Bouatia-Naji N.",,Nature genetics,2023,2023-05-29,Y,,,,"Spontaneous coronary artery dissection (SCAD) is an understudied cause of myocardial infarction primarily affecting women. It is not known to what extent SCAD is genetically distinct from other cardiovascular diseases, including atherosclerotic coronary artery disease (CAD). Here we present a genome-wide association meta-analysis (1,917 cases and 9,292 controls) identifying 16 risk loci for SCAD. Integrative functional annotations prioritized genes that are likely to be regulated in vascular smooth muscle cells and artery fibroblasts and implicated in extracellular matrix biology. One locus containing the tissue factor gene F3, which is involved in blood coagulation cascade initiation, appears to be specific for SCAD risk. Several associated variants have diametrically opposite associations with CAD, suggesting that shared biological processes contribute to both diseases, but through different mechanisms. We also infer a causal role for high blood pressure in SCAD. Our findings provide novel pathophysiological insights involving arterial integrity and tissue-mediated coagulation in SCAD and set the stage for future specific therapeutics and preventions.",,pdf:https://www.nature.com/articles/s41588-023-01410-1.pdf; doi:https://doi.org/10.1038/s41588-023-01410-1; html:https://europepmc.org/articles/PMC10260398; pdf:https://europepmc.org/articles/PMC10260398?pdf=render
+32735845,https://doi.org/10.1016/j.immuni.2020.07.003,Differential IRF8 Transcription Factor Requirement Defines Two Pathways of Dendritic Cell Development in Humans.,"Cytlak U, Resteu A, Pagan S, Green K, Milne P, Maisuria S, McDonald D, Hulme G, Filby A, Carpenter B, Queen R, Hambleton S, Hague R, Lango Allen H, Thaventhiran JED, Doody G, Collin M, Bigley V.",,Immunity,2020,2020-07-30,Y,Transcription factor; Immunity; Hematopoiesis; Dendritic Cell; Primary Immunodeficiency; Irf8; Cytof; Single-cell Rna Sequencing,,,"The formation of mammalian dendritic cells (DCs) is controlled by multiple hematopoietic transcription factors, including IRF8. Loss of IRF8 exerts a differential effect on DC subsets, including plasmacytoid DCs (pDCs) and the classical DC lineages cDC1 and cDC2. In humans, cDC2-related subsets have been described including AXL<sup>+</sup>SIGLEC6<sup>+</sup> pre-DC, DC2 and DC3. The origin of this heterogeneity is unknown. Using high-dimensional analysis, in vitro differentiation, and an allelic series of human IRF8 deficiency, we demonstrated that cDC2 (CD1c<sup>+</sup>DC) heterogeneity originates from two distinct pathways of development. The lymphoid-primed IRF8<sup>hi</sup> pathway, marked by CD123 and BTLA, carried pDC, cDC1, and DC2 trajectories, while the common myeloid IRF8<sup>lo</sup> pathway, expressing SIRPA, formed DC3s and monocytes. We traced distinct trajectories through the granulocyte-macrophage progenitor (GMP) compartment showing that AXL<sup>+</sup>SIGLEC6<sup>+</sup> pre-DCs mapped exclusively to the DC2 pathway. In keeping with their lower requirement for IRF8, DC3s expand to replace DC2s in human partial IRF8 deficiency.",,pdf:http://www.cell.com/article/S1074761320302831/pdf; doi:https://doi.org/10.1016/j.immuni.2020.07.003; html:https://europepmc.org/articles/PMC7447982
 32139493,https://doi.org/10.1136/bmjopen-2019-035121,Community treatment orders and associations with readmission rates and duration of psychiatric hospital admission: a controlled electronic case register study.,"Barkhuizen W, Cullen AE, Shetty H, Pritchard M, Stewart R, McGuire P, Patel R.",,BMJ open,2020,2020-03-05,Y,Psychiatry; Mental health; epidemiology; Health Policy; Health Informatics; Medical Law,,,"<h4>Objectives</h4>Limited evidence is available regarding the effect of community treatment orders (CTOs) on mortality and readmission to psychiatric hospital. We compared clinical outcomes between patients placed on CTOs to a control group of patients discharged to voluntary community mental healthcare.<h4>Design and setting</h4>An observational study using deidentified electronic health record data from inpatients receiving mental healthcare in South London using the Clinical Record Interactive Search (CRIS) system. Data from patients discharged between November 2008 and May 2014 from compulsory inpatient treatment under the Mental Health Act were analysed.<h4>Participants</h4>830 participants discharged on a CTO (mean age 40 years; 63% male) and 3659 control participants discharged without a CTO (mean age 42 years; 53% male).<h4>Outcome measures</h4>The number of days spent in the community until readmission, the number of days spent in inpatient care in the 2 years prior to and the 2 years following the index admission and mortality.<h4>Results</h4>The mean duration of a CTO was 3.2 years. Patients receiving care from forensic psychiatry services were five times more likely and patients receiving a long-acting injectable antipsychotic were twice as likely to be placed on a CTO. There was a significant association between CTO receipt and readmission in adjusted models (HR: 1.60, 95% CI 1.42 to 1.80, p<0.001). Compared with controls, patients on a CTO spent 17.3 additional days (95% CI 4.0 to 30.6, p=0.011) in a psychiatric hospital in the 2 years following index admission and had a lower mortality rate (HR: 0.66, 95% CI 0.50 to 0.88, p=0.004).<h4>Conclusions</h4>Many patients spent longer on CTOs than initially anticipated by policymakers. Those on CTOs are readmitted sooner, spend more time in hospital and have a lower mortality rate. These findings merit consideration in future amendments to the UK Mental Health Act.",,pdf:https://bmjopen.bmj.com/content/bmjopen/10/3/e035121.full.pdf; doi:https://doi.org/10.1136/bmjopen-2019-035121; html:https://europepmc.org/articles/PMC7059496; pdf:https://europepmc.org/articles/PMC7059496?pdf=render
 32163302,https://doi.org/10.1161/circgen.119.002783,Reevaluation of the South Asian <i>MYBPC3</i><sup>Δ25bp</sup> Intronic Deletion in Hypertrophic Cardiomyopathy.,"Harper AR, Bowman M, Hayesmoore JBG, Sage H, Salatino S, Blair E, Campbell C, Currie B, Goel A, McGuire K, Ormondroyd E, Sergeant K, Waring A, Woodley J, Kramer CM, Neubauer S, Farrall M, Watkins H, Thomson KL, HCMR Investigators.",,Circulation. Genomic and precision medicine,2020,2020-03-12,Y,Genotype; Introns; haplotypes; Humans; Exome,,,"<h4>Background</h4>The common intronic deletion, <i>MYBPC3</i><sup>Δ25</sup>, detected in 4% to 8% of South Asian populations, is reported to be associated with cardiomyopathy, with ≈7-fold increased risk of disease in variant carriers. Here, we examine the contribution of <i>MYBPC3</i><sup>Δ25</sup> to hypertrophic cardiomyopathy (HCM) in a large patient cohort.<h4>Methods</h4>Sequence data from 2 HCM cohorts (n=5393) was analyzed to determine <i>MYBPC3</i><sup>Δ25</sup> frequency and co-occurrence of pathogenic variants in HCM genes. Case-control and haplotype analyses were performed to compare variant frequencies and assess disease association. Analyses were also undertaken to investigate the pathogenicity of a candidate variant <i>MYBPC3</i> c.1224-52G>A.<h4>Results</h4>Our data suggest that the risk of HCM, previously attributed to <i>MYBPC3</i><sup>Δ25</sup>, can be explained by enrichment of a derived haplotype, <i>MYBPC3</i><sup>Δ25/</sup><sup>-52</sup>, whereby a small subset of individuals bear both <i>MYBPC3</i><sup>Δ25</sup> and a rare pathogenic variant, <i>MYBPC3</i> c.1224-52G>A. The intronic <i>MYBPC3</i> c.1224-52G>A variant, which is not routinely evaluated by gene panel or exome sequencing, was detected in ≈1% of our HCM cohort.<h4>Conclusions</h4>The <i>MYBPC3</i> c.1224-52G>A variant explains the disease risk previously associated with <i>MYBPC3</i><sup>Δ25</sup> in the South Asian population and is one of the most frequent pathogenic variants in HCM in all populations; genotyping services should ensure coverage of this deep intronic mutation. Individuals carrying <i>MYBPC3</i><sup>Δ25</sup> alone are not at increased risk of HCM, and this variant should not be tested in isolation; this is important for the large majority of the 100 million individuals of South Asian ancestry who carry <i>MYBPC3</i><sup>Δ25</sup> and would previously have been declared at increased risk of HCM.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCGEN.119.002783; doi:https://doi.org/10.1161/CIRCGEN.119.002783; html:https://europepmc.org/articles/PMC7299222; pdf:https://europepmc.org/articles/PMC7299222?pdf=render
 36589292,https://doi.org/10.3389/fncel.2022.1050596,Telomere length analysis in amyotrophic lateral sclerosis using large-scale whole genome sequence data.,"Al Khleifat A, Iacoangeli A, Jones AR, van Vugt JJFA, Moisse M, Shatunov A, Zwamborn RAJ, van der Spek RAA, Cooper-Knock J, Topp S, van Rheenen W, Kenna B, Van Eijk KR, Kenna K, Byrne R, López V, Opie-Martin S, Vural A, Campos Y, Weber M, Smith B, Fogh I, Silani V, Morrison KE, Dobson R, van Es MA, McLaughlin RL, Vourc'h P, Chio A, Corcia P, de Carvalho M, Gotkine M, Panades MP, Mora JS, Shaw PJ, Landers JE, Glass JD, Shaw CE, Basak N, Hardiman O, Robberecht W, Van Damme P, van den Berg LH, Veldink JH, Al-Chalabi A.",,Frontiers in cellular neuroscience,2022,2022-12-15,Y,Genomics; Amyotrophic Lateral Sclerosis (Als); Bigdata; Telomere–Genetics; Mnd–Motor Neuron Disorders; Whole Genome Sequence (Wgs),,,"<h4>Background</h4>Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by the loss of upper and lower motor neurons, leading to progressive weakness of voluntary muscles, with death following from neuromuscular respiratory failure, typically within 3 to 5 years. There is a strong genetic contribution to ALS risk. In 10% or more, a family history of ALS or frontotemporal dementia is obtained, and the Mendelian genes responsible for ALS in such families have now been identified in about 50% of cases. Only about 14% of apparently sporadic ALS is explained by known genetic variation, suggesting that other forms of genetic variation are important. Telomeres maintain DNA integrity during cellular replication, differ between sexes, and shorten naturally with age. Sex and age are risk factors for ALS and we therefore investigated telomere length in ALS.<h4>Methods</h4>Samples were from Project MinE, an international ALS whole genome sequencing consortium that includes phenotype data. For validation we used donated brain samples from motor cortex from people with ALS and controls. Ancestry and relatedness were evaluated by principal components analysis and relationship matrices of DNA microarray data. Whole genome sequence data were from Illumina HiSeq platforms and aligned using the Isaac pipeline. TelSeq was used to quantify telomere length using whole genome sequence data. We tested the association of telomere length with ALS and ALS survival using Cox regression.<h4>Results</h4>There were 6,580 whole genome sequences, reducing to 6,195 samples (4,315 from people with ALS and 1,880 controls) after quality control, and 159 brain samples (106 ALS, 53 controls). Accounting for age and sex, there was a 20% (95% CI 14%, 25%) increase of telomere length in people with ALS compared to controls (p = 1.1 × 10<sup>-12</sup>), validated in the brain samples (p = 0.03). Those with shorter telomeres had a 10% increase in median survival (p = 5.0×10<sup>-7</sup>). Although there was no difference in telomere length between sporadic ALS and familial ALS (p=0.64), telomere length in 334 people with ALS due to expanded <i>C9orf72</i> repeats was shorter than in those without expanded <i>C9orf72</i> repeats (p = 5.0×10<sup>-4</sup>).<h4>Discussion</h4>Although telomeres shorten with age, longer telomeres are a risk factor for ALS and worsen prognosis. Longer telomeres are associated with ALS.",,pdf:https://www.frontiersin.org/articles/10.3389/fncel.2022.1050596/pdf; doi:https://doi.org/10.3389/fncel.2022.1050596; html:https://europepmc.org/articles/PMC9799999; pdf:https://europepmc.org/articles/PMC9799999?pdf=render
@@ -2705,8 +2707,8 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 35360896,https://doi.org/10.1021/acs.analchem.1c03592,Finding Correspondence between Metabolomic Features in Untargeted Liquid Chromatography-Mass Spectrometry Metabolomics Datasets.,"Climaco Pinto R, Karaman I, Lewis MR, Hällqvist J, Kaluarachchi M, Graça G, Chekmeneva E, Durainayagam B, Ghanbari M, Ikram MA, Zetterberg H, Griffin J, Elliott P, Tzoulaki I, Dehghan A, Herrington D, Ebbels T.",,Analytical chemistry,2022,2022-03-31,Y,,,,"Integration of multiple datasets can greatly enhance bioanalytical studies, for example, by increasing power to discover and validate biomarkers. In liquid chromatography-mass spectrometry (LC-MS) metabolomics, it is especially hard to combine untargeted datasets since the majority of metabolomic features are not annotated and thus cannot be matched by chemical identity. Typically, the information available for each feature is retention time (RT), mass-to-charge ratio (<i>m</i>/<i>z</i>), and feature intensity (FI). Pairs of features from the same metabolite in separate datasets can exhibit small but significant differences, making matching very challenging. Current methods to address this issue are too simple or rely on assumptions that cannot be met in all cases. We present a method to find feature correspondence between two similar LC-MS metabolomics experiments or batches using only the features' RT, <i>m</i>/<i>z</i>, and FI. We demonstrate the method on both real and synthetic datasets, using six orthogonal validation strategies to gauge the matching quality. In our main example, 4953 features were uniquely matched, of which 585 (96.8%) of 604 manually annotated features were correct. In a second example, 2324 features could be uniquely matched, with 79 (90.8%) out of 87 annotated features correctly matched. Most of the missed annotated matches are between features that behave very differently from modeled inter-dataset shifts of RT, MZ, and FI. In a third example with simulated data with 4755 features per dataset, 99.6% of the matches were correct. Finally, the results of matching three other dataset pairs using our method are compared with a published alternative method, metabCombiner, showing the advantages of our approach. The method can be applied using M2S (Match 2 Sets), a free, open-source MATLAB toolbox, available at https://github.com/rjdossan/M2S.",,pdf:https://pubs.acs.org/doi/pdf/10.1021/acs.analchem.1c03592; doi:https://doi.org/10.1021/acs.analchem.1c03592; html:https://europepmc.org/articles/PMC9008693; pdf:https://europepmc.org/articles/PMC9008693?pdf=render
 35135642,https://doi.org/10.1017/s0033291721004402,"Catatonia: demographic, clinical and laboratory associations.","Rogers JP, Pollak TA, Begum N, Griffin A, Carter B, Pritchard M, Broadbent M, Kolliakou A, Ke J, Stewart R, Patel R, Bomford A, Amad A, Zandi MS, Lewis G, Nicholson TR, David AS.",,Psychological medicine,2023,2021-11-02,Y,Mortality; Inflammation; NMDA receptor; epidemiology; incidence; Catatonia; Admission,,,"<h4>Background</h4>Catatonia, a severe neuropsychiatric syndrome, has few studies of sufficient scale to clarify its epidemiology or pathophysiology. We aimed to characterise demographic associations, peripheral inflammatory markers and outcome of catatonia.<h4>Methods</h4>Electronic healthcare records were searched for validated clinical diagnoses of catatonia. In a case-control study, demographics and inflammatory markers were compared in psychiatric inpatients with and without catatonia. In a cohort study, the two groups were compared in terms of their duration of admission and mortality.<h4>Results</h4>We identified 1456 patients with catatonia (of whom 25.1% had two or more episodes) and 24 956 psychiatric inpatients without catatonia. Incidence was 10.6 episodes of catatonia per 100 000 person-years. Patients with and without catatonia were similar in sex, younger and more likely to be of Black ethnicity. Serum iron was reduced in patients with catatonia [11.6 <i>v.</i> 14.2 μmol/L, odds ratio (OR) 0.65 (95% confidence interval (CI) 0.45-0.95), <i>p</i> = 0.03] and creatine kinase was raised [2545 <i>v.</i> 459 IU/L, OR 1.53 (95% CI 1.29-1.81), <i>p</i> < 0.001], but there was no difference in C-reactive protein or white cell count. <i>N</i>-Methyl-d-aspartate receptor antibodies were significantly associated with catatonia, but there were small numbers of positive results. Duration of hospitalisation was greater in the catatonia group (median: 43 <i>v.</i> 25 days), but there was no difference in mortality after adjustment.<h4>Conclusions</h4>In the largest clinical study of catatonia, we found catatonia occurred in approximately 1 per 10 000 person-years. Evidence for a proinflammatory state was mixed. Catatonia was associated with prolonged inpatient admission but not with increased mortality.",,pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/2676547CEE9AA7C0AC726A2E6CA4AA9B/S0033291721004402a.pdf/div-class-title-catatonia-demographic-clinical-and-laboratory-associations-div.pdf; doi:https://doi.org/10.1017/S0033291721004402; html:https://europepmc.org/articles/PMC10123832; pdf:https://europepmc.org/articles/PMC10123832?pdf=render
 34000257,https://doi.org/10.1016/s0140-6736(21)00897-7,"Convalescent plasma in patients admitted to hospital with COVID-19 (RECOVERY): a randomised controlled, open-label, platform trial.",RECOVERY Collaborative Group.,,"Lancet (London, England)",2021,2021-05-14,Y,,,,"<h4>Background</h4>Many patients with COVID-19 have been treated with plasma containing anti-SARS-CoV-2 antibodies. We aimed to evaluate the safety and efficacy of convalescent plasma therapy in patients admitted to hospital with COVID-19.<h4>Methods</h4>This randomised, controlled, open-label, platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]) is assessing several possible treatments in patients hospitalised with COVID-19 in the UK. The trial is underway at 177 NHS hospitals from across the UK. Eligible and consenting patients were randomly assigned (1:1) to receive either usual care alone (usual care group) or usual care plus high-titre convalescent plasma (convalescent plasma group). The primary outcome was 28-day mortality, analysed on an intention-to-treat basis. The trial is registered with ISRCTN, 50189673, and ClinicalTrials.gov, NCT04381936.<h4>Findings</h4>Between May 28, 2020, and Jan 15, 2021, 11558 (71%) of 16287 patients enrolled in RECOVERY were eligible to receive convalescent plasma and were assigned to either the convalescent plasma group or the usual care group. There was no significant difference in 28-day mortality between the two groups: 1399 (24%) of 5795 patients in the convalescent plasma group and 1408 (24%) of 5763 patients in the usual care group died within 28 days (rate ratio 1·00, 95% CI 0·93-1·07; p=0·95). The 28-day mortality rate ratio was similar in all prespecified subgroups of patients, including in those patients without detectable SARS-CoV-2 antibodies at randomisation. Allocation to convalescent plasma had no significant effect on the proportion of patients discharged from hospital within 28 days (3832 [66%] patients in the convalescent plasma group vs 3822 [66%] patients in the usual care group; rate ratio 0·99, 95% CI 0·94-1·03; p=0·57). Among those not on invasive mechanical ventilation at randomisation, there was no significant difference in the proportion of patients meeting the composite endpoint of progression to invasive mechanical ventilation or death (1568 [29%] of 5493 patients in the convalescent plasma group vs 1568 [29%] of 5448 patients in the usual care group; rate ratio 0·99, 95% CI 0·93-1·05; p=0·79).<h4>Interpretation</h4>In patients hospitalised with COVID-19, high-titre convalescent plasma did not improve survival or other prespecified clinical outcomes.<h4>Funding</h4>UK Research and Innovation (Medical Research Council) and National Institute of Health Research.",,pdf:https://aura.abdn.ac.uk/bitstream/2164/16629/1/Recovery_etal_TL_Convalescent_Plasma_In_VoR.pdf; doi:https://doi.org/10.1016/S0140-6736(21)00897-7; html:https://europepmc.org/articles/PMC8121538
-33444330,https://doi.org/10.1371/journal.pmed.1003498,Polygenic risk scores in cardiovascular risk prediction: A cohort study and modelling analyses.,"Sun L, Pennells L, Kaptoge S, Nelson CP, Ritchie SC, Abraham G, Arnold M, Bell S, Bolton T, Burgess S, Dudbridge F, Guo Q, Sofianopoulou E, Stevens D, Thompson JR, Butterworth AS, Wood A, Danesh J, Samani NJ, Inouye M, Di Angelantonio E.",,PLoS medicine,2021,2021-01-14,Y,,,,"<h4>Background</h4>Polygenic risk scores (PRSs) can stratify populations into cardiovascular disease (CVD) risk groups. We aimed to quantify the potential advantage of adding information on PRSs to conventional risk factors in the primary prevention of CVD.<h4>Methods and findings</h4>Using data from UK Biobank on 306,654 individuals without a history of CVD and not on lipid-lowering treatments (mean age [SD]: 56.0 [8.0] years; females: 57%; median follow-up: 8.1 years), we calculated measures of risk discrimination and reclassification upon addition of PRSs to risk factors in a conventional risk prediction model (i.e., age, sex, systolic blood pressure, smoking status, history of diabetes, and total and high-density lipoprotein cholesterol). We then modelled the implications of initiating guideline-recommended statin therapy in a primary care setting using incidence rates from 2.1 million individuals from the Clinical Practice Research Datalink. The C-index, a measure of risk discrimination, was 0.710 (95% CI 0.703-0.717) for a CVD prediction model containing conventional risk predictors alone. Addition of information on PRSs increased the C-index by 0.012 (95% CI 0.009-0.015), and resulted in continuous net reclassification improvements of about 10% and 12% in cases and non-cases, respectively. If a PRS were assessed in the entire UK primary care population aged 40-75 years, assuming that statin therapy would be initiated in accordance with the UK National Institute for Health and Care Excellence guidelines (i.e., for persons with a predicted risk of ≥10% and for those with certain other risk factors, such as diabetes, irrespective of their 10-year predicted risk), then it could help prevent 1 additional CVD event for approximately every 5,750 individuals screened. By contrast, targeted assessment only among people at intermediate (i.e., 5% to <10%) 10-year CVD risk could help prevent 1 additional CVD event for approximately every 340 individuals screened. Such a targeted strategy could help prevent 7% more CVD events than conventional risk prediction alone. Potential gains afforded by assessment of PRSs on top of conventional risk factors would be about 1.5-fold greater than those provided by assessment of C-reactive protein, a plasma biomarker included in some risk prediction guidelines. Potential limitations of this study include its restriction to European ancestry participants and a lack of health economic evaluation.<h4>Conclusions</h4>Our results suggest that addition of PRSs to conventional risk factors can modestly enhance prediction of first-onset CVD and could translate into population health benefits if used at scale.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003498&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003498; html:https://europepmc.org/articles/PMC7808664; pdf:https://europepmc.org/articles/PMC7808664?pdf=render
 32979922,https://doi.org/10.1186/s12933-020-01130-4,Diabetes as a risk factor for incident peripheral arterial disease in women compared to men: a systematic review and meta-analysis.,"Chase-Vilchez AZ, Chan IHY, Peters SAE, Woodward M.",,Cardiovascular diabetology,2020,2020-09-26,Y,Sex difference; Diabetes; Cardiovascular disease; Peripheral Arterial Disease; Peripheral Vascular Disease,,,"<h4>Aims/hypothesis</h4>Previous meta-analyses have suggested that diabetes confers a greater excess risk of coronary heart disease, stroke, vascular dementia, and heart failure in women compared to men. While the underlying mechanism that explains such greater excess risk is unknown, in the current meta-analysis we hypothesized that we would find a similar sex difference in the relationship between diabetes and peripheral arterial disease (PAD).<h4>Methods</h4>PubMed MEDLINE, the Cochrane Database of Systematic Reviews, and Embase were systematically searched for prospective population-based cohort studies, with no restriction on publication date, language, or country. We included studies that reported the relative risk (RR), and its variability, for incident PAD associated with diabetes in both sexes. We excluded studies that did not adjust at least for age, and in which participants had pre-existing PAD. In cases where sex-specific results were not reported, study authors were contacted. Random-effects meta-analyses with inverse variance weighting were used to obtain summary sex-specific RRs and the women: men ratio of RRs for PAD. The Newcastle-Ottawa scale was used to assess study quality.<h4>Results</h4>Data from seven cohorts, totalling 2071,260 participants (49.8% women), were included. The relative risk for incident PAD associated with diabetes compared with no diabetes was 1.96 (95% CI 1.29-2.63) in women and 1.84 (95% CI 1.29-2.86) in men, after adjusting for potential confounders. The multiple-adjusted RR ratio was 1.05 (95% CI 0.90-1.22), with virtually no heterogeneity between studies (I<sup>2</sup> = 0%). All studies scored 6-8, on the Newcastle-Ottawa scale of 0-9, indicating good quality. Eleven of the 12 studies that met review inclusion criteria did not report sex-specific relative risk, and these data were collected through direct correspondence with the study authors.<h4>Conclusion/interpretation</h4>Consistent with other studies, we found evidence that diabetes is an independent risk factor for PAD. However, in contrast to similar studies of other types of cardiovascular disease, we did not find evidence that diabetes confers a greater excess risk in women compared to men for PAD. More research is needed to explain this sex differential between PAD and other forms of CVD, in the sequelae of diabetes. In addition, we found that very few studies reported the sex-specific relative risk for the association between diabetes and PAD, adding to existing evidence for the need for improved reporting of sex-disaggregated results in cardiovascular disease research.",,pdf:https://cardiab.biomedcentral.com/track/pdf/10.1186/s12933-020-01130-4; doi:https://doi.org/10.1186/s12933-020-01130-4; html:https://europepmc.org/articles/PMC7520021; pdf:https://europepmc.org/articles/PMC7520021?pdf=render
+33444330,https://doi.org/10.1371/journal.pmed.1003498,Polygenic risk scores in cardiovascular risk prediction: A cohort study and modelling analyses.,"Sun L, Pennells L, Kaptoge S, Nelson CP, Ritchie SC, Abraham G, Arnold M, Bell S, Bolton T, Burgess S, Dudbridge F, Guo Q, Sofianopoulou E, Stevens D, Thompson JR, Butterworth AS, Wood A, Danesh J, Samani NJ, Inouye M, Di Angelantonio E.",,PLoS medicine,2021,2021-01-14,Y,,,,"<h4>Background</h4>Polygenic risk scores (PRSs) can stratify populations into cardiovascular disease (CVD) risk groups. We aimed to quantify the potential advantage of adding information on PRSs to conventional risk factors in the primary prevention of CVD.<h4>Methods and findings</h4>Using data from UK Biobank on 306,654 individuals without a history of CVD and not on lipid-lowering treatments (mean age [SD]: 56.0 [8.0] years; females: 57%; median follow-up: 8.1 years), we calculated measures of risk discrimination and reclassification upon addition of PRSs to risk factors in a conventional risk prediction model (i.e., age, sex, systolic blood pressure, smoking status, history of diabetes, and total and high-density lipoprotein cholesterol). We then modelled the implications of initiating guideline-recommended statin therapy in a primary care setting using incidence rates from 2.1 million individuals from the Clinical Practice Research Datalink. The C-index, a measure of risk discrimination, was 0.710 (95% CI 0.703-0.717) for a CVD prediction model containing conventional risk predictors alone. Addition of information on PRSs increased the C-index by 0.012 (95% CI 0.009-0.015), and resulted in continuous net reclassification improvements of about 10% and 12% in cases and non-cases, respectively. If a PRS were assessed in the entire UK primary care population aged 40-75 years, assuming that statin therapy would be initiated in accordance with the UK National Institute for Health and Care Excellence guidelines (i.e., for persons with a predicted risk of ≥10% and for those with certain other risk factors, such as diabetes, irrespective of their 10-year predicted risk), then it could help prevent 1 additional CVD event for approximately every 5,750 individuals screened. By contrast, targeted assessment only among people at intermediate (i.e., 5% to <10%) 10-year CVD risk could help prevent 1 additional CVD event for approximately every 340 individuals screened. Such a targeted strategy could help prevent 7% more CVD events than conventional risk prediction alone. Potential gains afforded by assessment of PRSs on top of conventional risk factors would be about 1.5-fold greater than those provided by assessment of C-reactive protein, a plasma biomarker included in some risk prediction guidelines. Potential limitations of this study include its restriction to European ancestry participants and a lack of health economic evaluation.<h4>Conclusions</h4>Our results suggest that addition of PRSs to conventional risk factors can modestly enhance prediction of first-onset CVD and could translate into population health benefits if used at scale.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003498&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003498; html:https://europepmc.org/articles/PMC7808664; pdf:https://europepmc.org/articles/PMC7808664?pdf=render
 34662348,https://doi.org/10.1371/journal.ppat.1009992,Genome-wide association studies reveal the role of polymorphisms affecting factor H binding protein expression in host invasion by Neisseria meningitidis.,"Earle SG, Lobanovska M, Lavender H, Tang C, Exley RM, Ramos-Sevillano E, Browning DF, Kostiou V, Harrison OB, Bratcher HB, Varani G, Tang CM, Wilson DJ, Maiden MCJ.",,PLoS pathogens,2021,2021-10-18,Y,,,,"Many invasive bacterial diseases are caused by organisms that are ordinarily harmless components of the human microbiome. Effective interventions against these microbes require an understanding of the processes whereby symbiotic or commensal relationships transition into pathology. Here, we describe bacterial genome-wide association studies (GWAS) of Neisseria meningitidis, a common commensal of the human respiratory tract that is nevertheless a leading cause of meningitis and sepsis. An initial GWAS discovered bacterial genetic variants, including single nucleotide polymorphisms (SNPs), associated with invasive meningococcal disease (IMD) versus carriage in several loci across the meningococcal genome, encoding antigens and other extracellular components, confirming the polygenic nature of the invasive phenotype. In particular, there was a significant peak of association around the fHbp locus, encoding factor H binding protein (fHbp), which promotes bacterial immune evasion of human complement by recruiting complement factor H (CFH) to the meningococcal surface. The association around fHbp with IMD was confirmed by a validation GWAS, and we found that the SNPs identified in the validation affected the 5' region of fHbp mRNA, altering secondary RNA structures, thereby increasing fHbp expression and enhancing bacterial escape from complement-mediated killing. This finding is consistent with the known link between complement deficiencies and CFH variation with human susceptibility to IMD. These observations demonstrate the importance of human and bacterial genetic variation across the fHbp:CFH interface in determining IMD susceptibility, the transition from carriage to disease.",,pdf:https://journals.plos.org/plospathogens/article/file?id=10.1371/journal.ppat.1009992&type=printable; doi:https://doi.org/10.1371/journal.ppat.1009992; html:https://europepmc.org/articles/PMC8553145; pdf:https://europepmc.org/articles/PMC8553145?pdf=render
 32956399,https://doi.org/10.1371/journal.pmed.1003336,Antibiotic prescribing for lower UTI in elderly patients in primary care and risk of bloodstream infection: A cohort study using electronic health records in England.,"Shallcross L, Rockenschaub P, Blackburn R, Nazareth I, Freemantle N, Hayward A.",,PLoS medicine,2020,2020-09-21,Y,,,,"<h4>Background</h4>Research has questioned the safety of delaying or withholding antibiotics for suspected urinary tract infection (UTI) in older patients. We evaluated the association between antibiotic treatment for lower UTI and risk of bloodstream infection (BSI) in adults aged ≥65 years in primary care.<h4>Methods and findings</h4>We analyzed primary care records from patients aged ≥65 years in England with community-onset UTI using the Clinical Practice Research Datalink (2007-2015) linked to Hospital Episode Statistics and census data. The primary outcome was BSI within 60 days, comparing patients treated immediately with antibiotics and those not treated immediately. Crude and adjusted associations between exposure and outcome were estimated using generalized estimating equations. A total of 147,334 patients were included representing 280,462 episodes of lower UTI. BSI occurred in 0.4% (1,025/244,963) of UTI episodes with immediate antibiotics versus 0.6% (228/35,499) of episodes without immediate antibiotics. After adjusting for patient demographics, year of consultation, comorbidities, smoking status, recent hospitalizations, recent accident and emergency (A&E) attendances, recent antibiotic prescribing, and home visits, the odds of BSI were equivalent in patients who were not treated with antibiotics immediately and those who were treated on the date of their UTI consultation (adjusted odds ratio [aOR] 1.13, 95% CI 0.97-1.32, p-value = 0.105). Delaying or withholding antibiotics was associated with increased odds of death in the subsequent 60 days (aOR 1.17, 95% CI 1.09-1.26, p-value < 0.001), but there was limited evidence that increased deaths were attributable to urinary-source BSI. Limitations include overlap between the categories of immediate and delayed antibiotic prescribing, residual confounding underlying differences between patients who were/were not treated with antibiotics, and lack of microbiological diagnosis for BSI.<h4>Conclusions</h4>In this study, we observed that delaying or withholding antibiotics in older adults with suspected UTI did not increase patients' risk of BSI, in contrast with a previous study that analyzed the same dataset, but mortality was increased. Our findings highlight uncertainty around the risks of delaying or withholding antibiotic treatment, which is exacerbated by systematic differences between patients who were and were not treated immediately with antibiotics. Overall, our findings emphasize the need for improved diagnostic/risk prediction strategies to guide antibiotic prescribing for suspected UTI in older adults.",,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003336&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003336; html:https://europepmc.org/articles/PMC7505443; pdf:https://europepmc.org/articles/PMC7505443?pdf=render
 30497795,https://doi.org/10.1016/s0140-6736(18)32207-4,Changes in health in the countries of the UK and 150 English Local Authority areas 1990-2016: a systematic analysis for the Global Burden of Disease Study 2016.,"Steel N, Ford JA, Newton JN, Davis ACJ, Vos T, Naghavi M, Glenn S, Hughes A, Dalton AM, Stockton D, Humphreys C, Dallat M, Schmidt J, Flowers J, Fox S, Abubakar I, Aldridge RW, Baker A, Brayne C, Brugha T, Capewell S, Car J, Cooper C, Ezzati M, Fitzpatrick J, Greaves F, Hay R, Hay S, Kee F, Larson HJ, Lyons RA, Majeed A, McKee M, Rawaf S, Rutter H, Saxena S, Sheikh A, Smeeth L, Viner RM, Vollset SE, Williams HC, Wolfe C, Woolf A, Murray CJL.",,"Lancet (London, England)",2018,2018-10-24,Y,,Improving Public Health,,"<h4>Background</h4>Previous studies have reported national and regional Global Burden of Disease (GBD) estimates for the UK. Because of substantial variation in health within the UK, action to improve it requires comparable estimates of disease burden and risks at country and local levels. The slowdown in the rate of improvement in life expectancy requires further investigation. We use GBD 2016 data on mortality, causes of death, and disability to analyse the burden of disease in the countries of the UK and within local authorities in England by deprivation quintile.<h4>Methods</h4>We extracted data from the GBD 2016 to estimate years of life lost (YLLs), years lived with disability (YLDs), disability-adjusted life-years (DALYs), and attributable risks from 1990 to 2016 for England, Scotland, Wales, Northern Ireland, the UK, and 150 English Upper-Tier Local Authorities. We estimated the burden of disease by cause of death, condition, year, and sex. We analysed the association between burden of disease and socioeconomic deprivation using the Index of Multiple Deprivation. We present results for all 264 GBD causes of death combined and the leading 20 specific causes, and all 84 GBD risks or risk clusters combined and 17 specific risks or risk clusters.<h4>Findings</h4>The leading causes of age-adjusted YLLs in all UK countries in 2016 were ischaemic heart disease, lung cancers, cerebrovascular disease, and chronic obstructive pulmonary disease. Age-standardised rates of YLLs for all causes varied by two times between local areas in England according to levels of socioeconomic deprivation (from 14 274 per 100 000 population [95% uncertainty interval 12 791-15 875] in Blackpool to 6888 [6145-7739] in Wokingham). Some Upper-Tier Local Authorities, particularly those in London, did better than expected for their level of deprivation. Allowing for differences in age structure, more deprived Upper-Tier Local Authorities had higher attributable YLLs for most major risk factors in the GBD. The population attributable fractions for all-cause YLLs for individual major risk factors varied across Upper-Tier Local Authorities. Life expectancy and YLLs have improved more slowly since 2010 in all UK countries compared with 1990-2010. In nine of 150 Upper-Tier Local Authorities, YLLs increased after 2010. For attributable YLLs, the rate of improvement slowed most substantially for cardiovascular disease and breast, colorectal, and lung cancers, and showed little change for Alzheimer's disease and other dementias. Morbidity makes an increasing contribution to overall burden in the UK compared with mortality. The age-standardised UK DALY rate for low back and neck pain (1795 [1258-2356]) was higher than for ischaemic heart disease (1200 [1155-1246]) or lung cancer (660 [642-679]). The leading causes of ill health (measured through YLDs) in the UK in 2016 were low back and neck pain, skin and subcutaneous diseases, migraine, depressive disorders, and sense organ disease. Age-standardised YLD rates varied much less than equivalent YLL rates across the UK, which reflects the relative scarcity of local data on causes of ill health.<h4>Interpretation</h4>These estimates at local, regional, and national level will allow policy makers to match resources and priorities to levels of burden and risk factors. Improvement in YLLs and life expectancy slowed notably after 2010, particularly in cardiovascular disease and cancer, and targeted actions are needed if the rate of improvement is to recover. A targeted policy response is also required to address the increasing proportion of burden due to morbidity, such as musculoskeletal problems and depression. Improving the quality and completeness of available data on these causes is an essential component of this response.<h4>Funding</h4>Bill & Melinda Gates Foundation and Public Health England.",,pdf:http://www.thelancet.com/article/S0140673618322074/pdf; doi:https://doi.org/10.1016/S0140-6736(18)32207-4; html:https://europepmc.org/articles/PMC6215773; pdf:https://europepmc.org/articles/PMC6215773?pdf=render
@@ -2730,9 +2732,9 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 32384159,https://doi.org/10.1093/jtm/taaa068,Effectiveness of interventions targeting air travellers for delaying local outbreaks of SARS-CoV-2.,"Clifford S, Pearson CAB, Klepac P, Van Zandvoort K, Quilty BJ, CMMID COVID-19 working group, Eggo RM, Flasche S.",,Journal of travel medicine,2020,2020-08-01,Y,Coronavirus; Public Health Emergency Of International Concern; Covid-19; Travel Screening,,,"<h4>Background</h4>We evaluated if interventions aimed at air travellers can delay local severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) community transmission in a previously unaffected country.<h4>Methods</h4>We simulated infected air travellers arriving into countries with no sustained SARS-CoV-2 transmission or other introduction routes from affected regions. We assessed the effectiveness of syndromic screening at departure and/or arrival and traveller sensitisation to the COVID-2019-like symptoms with the aim to trigger rapid self-isolation and reporting on symptom onset to enable contact tracing. We assumed that syndromic screening would reduce the number of infected arrivals and that traveller sensitisation reduces the average number of secondary cases. We use stochastic simulations to account for uncertainty in both arrival and secondary infections rates, and present sensitivity analyses on arrival rates of infected travellers and the effectiveness of traveller sensitisation. We report the median expected delay achievable in each scenario and an inner 50% interval.<h4>Results</h4>Under baseline assumptions, introducing exit and entry screening in combination with traveller sensitisation can delay a local SARS-CoV-2 outbreak by 8 days (50% interval: 3-14 days) when the rate of importation is 1 infected traveller per week at time of introduction. The additional benefit of entry screening is small if exit screening is effective: the combination of only exit screening and traveller sensitisation can delay an outbreak by 7 days (50% interval: 2-13 days). In the absence of screening, with less effective sensitisation, or a higher rate of importation, these delays shrink rapidly to <4 days.<h4>Conclusion</h4>Syndromic screening and traveller sensitisation in combination may have marginally delayed SARS-CoV-2 outbreaks in unaffected countries.",,pdf:https://academic.oup.com/jtm/article-pdf/27/5/taaa068/33666000/taaa068.pdf; doi:https://doi.org/10.1093/jtm/taaa068; html:https://europepmc.org/articles/PMC7239177; pdf:https://europepmc.org/articles/PMC7239177?pdf=render
 32543438,https://doi.org/10.1016/j.healthplace.2020.102355,Impact of air pollution on educational attainment for respiratory health treated students: A cross sectional data linkage study.,"Mizen A, Lyons J, Milojevic A, Doherty R, Wilkinson P, Carruthers D, Akbari A, Lake I, Davies GA, Al Sallakh M, Fry R, Dearden L, Rodgers SE.",,Health & place,2020,2020-05-12,Y,Air pollution; Asthma; poLLen; Data Linkage; Seasonal Allergic Rhinitis; Educational Attainment,,,"<h4>Introduction</h4>There is some evidence that exam results are worse when students are acutely exposed to air pollution. Studies investigating the association between air pollution and academic attainment have been constrained by small sample sizes.<h4>Methods</h4>Cross sectional educational attainment data (2009-2015) from students aged 15-16 years in Cardiff, Wales were linked to primary health care data, modelled air pollution and measured pollen data, and analysed using multilevel linear regression models. Annual cohort, school and individual level confounders were adjusted for in single and multi-pollutant/pollen models. We stratified by treatment of asthma and/or Seasonal Allergic Rhinitis (SAR).<h4>Results</h4>A unit (10μg/m<sup>3</sup>) increase of short-term exposure to NO<sub>2</sub> was associated with 0.044 (95% CI: -0.079, -0.008) reduction of standardised Capped Point Score (CPS) after adjusting for individual and household risk factors for 18,241 students. This association remained statistically significant after controlling for other pollutants and pollen. There was no association of PM<sub>2.5</sub>, O<sub>3</sub>, or Pollen with standardised CPS remaining after adjustment. We found no evidence that treatment for asthma or SAR modified the observed NO<sub>2</sub> effect on educational attainment.<h4>Conclusion</h4>Our study showed that short-term exposure to traffic-related air pollution, specifically NO<sub>2,</sub> was associated with detrimental educational attainment for students aged 15-16. Longitudinal investigations in different settings are required to confirm this possible impact and further work may uncover the long-term economic implications, and degree to which impacts are cumulative and permanent.",,doi:https://doi.org/10.1016/j.healthplace.2020.102355; doi:https://doi.org/10.1016/j.healthplace.2020.102355; html:https://europepmc.org/articles/PMC7214342
 32376654,https://doi.org/10.1136/bmj.m1203,Use of genetic variation to separate the effects of early and later life adiposity on disease risk: mendelian randomisation study.,"Richardson TG, Sanderson E, Elsworth B, Tilling K, Davey Smith G.",,BMJ (Clinical research ed.),2020,2020-05-06,Y,,,,"<h4>Objective</h4>To evaluate whether body size in early life has an independent effect on risk of disease in later life or whether its influence is mediated by body size in adulthood.<h4>Design</h4>Two sample univariable and multivariable mendelian randomisation.<h4>Setting</h4>The UK Biobank prospective cohort study and four large scale genome-wide association studies (GWAS) consortiums.<h4>Participants</h4>453 169 participants enrolled in UK Biobank and a combined total of more than 700 000 people from different GWAS consortiums.<h4>Exposures</h4>Measured body mass index during adulthood (mean age 56.5) and self-reported perceived body size at age 10.<h4>Main outcome measures</h4>Coronary artery disease, type 2 diabetes, breast cancer, and prostate cancer.<h4>Results</h4>Having a larger genetically predicted body size in early life was associated with an increased odds of coronary artery disease (odds ratio 1.49 for each change in body size category unless stated otherwise, 95% confidence interval 1.33 to 1.68) and type 2 diabetes (2.32, 1.76 to 3.05) based on univariable mendelian randomisation analyses. However, little evidence was found of a direct effect (ie, not through adult body size) based on multivariable mendelian randomisation estimates (coronary artery disease: 1.02, 0.86 to 1.22; type 2 diabetes:1.16, 0.74 to 1.82). In the multivariable mendelian randomisation analysis of breast cancer risk, strong evidence was found of a protective direct effect for larger body size in early life (0.59, 0.50 to 0.71), with less evidence of a direct effect of adult body size on this outcome (1.08, 0.93 to 1.27). Including age at menarche as an additional exposure provided weak evidence of a total causal effect (univariable mendelian randomisation odds ratio 0.98, 95% confidence interval 0.91 to 1.06) but strong evidence of a direct causal effect, independent of early life and adult body size (multivariable mendelian randomisation odds ratio 0.90, 0.85 to 0.95). No strong evidence was found of a causal effect of either early or later life measures on prostate cancer (early life body size odds ratio 1.06, 95% confidence interval 0.81 to 1.40; adult body size 0.87, 0.70 to 1.08).<h4>Conclusions</h4>The findings suggest that the positive association between body size in childhood and risk of coronary artery disease and type 2 diabetes in adulthood can be attributed to individuals remaining large into later life. However, having a smaller body size during childhood might increase the risk of breast cancer regardless of body size in adulthood, with timing of puberty also putatively playing a role.",,pdf:https://www.bmj.com/content/bmj/369/bmj.m1203.full.pdf; doi:https://doi.org/10.1136/bmj.m1203; html:https://europepmc.org/articles/PMC7201936
-32855398,https://doi.org/10.1038/s41467-020-18060-0,Multi-site clonality analysis uncovers pervasive heterogeneity across melanoma metastases.,"Rabbie R, Ansari-Pour N, Cast O, Lau D, Scott F, Welsh SJ, Parkinson C, Khoja L, Moore L, Tullett M, Wong K, Ferreira I, Gómez JMM, Levesque M, Gallagher FA, Jiménez-Sánchez A, Riva L, Miller ML, Allinson K, Campbell PJ, Corrie P, Wedge DC, Adams DJ.",,Nature communications,2020,2020-08-27,Y,,,,"Metastatic melanoma carries a poor prognosis despite modern systemic therapies. Understanding the evolution of the disease could help inform patient management. Through whole-genome sequencing of 13 melanoma metastases sampled at autopsy from a treatment naïve patient and by leveraging the analytical power of multi-sample analyses, we reveal evidence of diversification among metastatic lineages. UV-induced mutations dominate the trunk, whereas APOBEC-associated mutations are found in the branches of the evolutionary tree. Multi-sample analyses from a further seven patients confirmed that lineage diversification was pervasive, representing an important mode of melanoma dissemination. Our analyses demonstrate that joint analysis of cancer cell fraction estimates across multiple metastases can uncover previously unrecognised levels of tumour heterogeneity and highlight the limitations of inferring heterogeneity from a single biopsy.",,pdf:https://www.nature.com/articles/s41467-020-18060-0.pdf; doi:https://doi.org/10.1038/s41467-020-18060-0; html:https://europepmc.org/articles/PMC7453196; pdf:https://europepmc.org/articles/PMC7453196?pdf=render
-31666367,https://doi.org/10.1128/jcm.01037-19,Hash-Based Core Genome Multilocus Sequence Typing for Clostridium difficile.,"Eyre DW, Peto TEA, Crook DW, Walker AS, Wilcox MH.",,Journal of clinical microbiology,2019,2019-12-23,Y,Quality assurance; Clostridium Difficile; Whole-genome Sequencing; Core Genome Mlst,The Human Phenome,,"Pathogen whole-genome sequencing has huge potential as a tool to better understand infection transmission. However, rapidly identifying closely related genomes among a background of thousands of other genomes is challenging. Here, we describe a refinement to core genome multilocus sequence typing (cgMLST) in which alleles at each gene are reproducibly converted to a unique hash, or short string of letters (hash-cgMLST). This avoids the resource-intensive need for a single centralized database of sequentially numbered alleles. We test the reproducibility and discriminatory power of cgMLST/hash-cgMLST compared to those of mapping-based approaches in <i>Clostridium difficile</i>, using repeated sequencing of the same isolates (replicates) and data from consecutive infection isolates from six English hospitals. Hash-cgMLST provided the same results as standard cgMLST, with minimal performance penalty. Comparing 272 replicate sequence pairs using reference-based mapping, there were 0, 1, or 2 single-nucleotide polymorphisms (SNPs) between 262 (96%), 5 (2%), and 1 (<1%) of the pairs, respectively. Using hash-cgMLST, 218 (80%) of replicate pairs assembled with SPAdes had zero gene differences, and 31 (11%), 5 (2%), and 18 (7%) pairs had 1, 2, and >2 differences, respectively. False gene differences were clustered in specific genes and associated with fragmented assemblies, but were reduced using the SKESA assembler. Considering 412 pairs of infections with ≤2 SNPS, i.e., consistent with recent transmission, 376 (91%) had ≤2 gene differences and 16 (4%) had ≥4. Comparing a genome to 100,000 others took <1 min using hash-cgMLST. Hash-cgMLST is an effective surveillance tool for rapidly identifying clusters of related genomes. However, cgMLST/hash-cgMLST generate more false variants than mapping-based approaches. Follow-up mapping-based analyses are likely required to precisely define close genetic relationships.",,pdf:https://jcm.asm.org/content/jcm/58/1/e01037-19.full.pdf; doi:https://doi.org/10.1128/JCM.01037-19; html:https://europepmc.org/articles/PMC6935933; pdf:https://europepmc.org/articles/PMC6935933?pdf=render
 37681566,https://doi.org/10.1161/jaha.123.030280,Age at Menopause and the Risk of Stroke: Observational and Mendelian Randomization Analysis in 204 244 Postmenopausal Women.,"Tschiderer L, Peters SAE, van der Schouw YT, van Westing AC, Tong TYN, Willeit P, Seekircher L, Moreno-Iribas C, Huerta JM, Crous-Bou M, Söderholm M, Schulze MB, Johansson C, Själander S, Heath AK, Macciotta A, Dahm CC, Ibsen DB, Pala V, Mellemkjær L, Burgess S, Wood A, Kaaks R, Katzke V, Amiano P, Rodriguez-Barranco M, Engström G, Weiderpass E, Tjønneland A, Halkjær J, Panico S, Danesh J, Butterworth A, Onland-Moret NC.",,Journal of the American Heart Association,2023,2023-09-08,Y,Stroke; Age At Menopause; Mendelian Randomization Analysis; Observational Analysis,,,"Background Observational studies have shown that women with an early menopause are at higher risk of stroke compared with women with a later menopause. However, associations with stroke subtypes are inconsistent, and the causality is unclear. Methods and Results We analyzed data of the UK Biobank and EPIC-CVD (European Prospective Investigation Into Cancer and Nutrition-Cardiovascular Diseases) study. A total of 204 244 postmenopausal women without a history of stroke at baseline were included (7883 from EPIC-CVD [5292 from the subcohort], 196 361 from the UK Biobank). Pooled mean baseline age was 58.9 years (SD, 5.8), and pooled mean age at menopause was 47.8 years (SD, 6.2). Over a median follow-up of 12.6 years (interquartile range, 11.8-13.3), 6770 women experienced a stroke (5155 ischemic strokes, 1615 hemorrhagic strokes, 976 intracerebral hemorrhages, and 639 subarachnoid hemorrhages). In multivariable adjusted observational Cox regression analyses, the pooled hazard ratios per 5 years younger age at menopause were 1.09 (95% CI, 1.07-1.12) for stroke, 1.09 (95% CI, 1.06-1.13) for ischemic stroke, 1.10 (95% CI, 1.04-1.16) for hemorrhagic stroke, 1.14 (95% CI, 1.08-1.20) for intracerebral hemorrhage, and 1.00 (95% CI, 0.84-1.20) for subarachnoid hemorrhage. When using 2-sample Mendelian randomization analysis, we found no statistically significant association between genetically proxied age at menopause and risk of any type of stroke. Conclusions In our study, earlier age at menopause was related to a higher risk of stroke. We found no statistically significant association between genetically proxied age at menopause and risk of stroke, suggesting no causal relationship.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.123.030280; doi:https://doi.org/10.1161/JAHA.123.030280; html:https://europepmc.org/articles/PMC10547274; pdf:https://europepmc.org/articles/PMC10547274?pdf=render
+31666367,https://doi.org/10.1128/jcm.01037-19,Hash-Based Core Genome Multilocus Sequence Typing for Clostridium difficile.,"Eyre DW, Peto TEA, Crook DW, Walker AS, Wilcox MH.",,Journal of clinical microbiology,2019,2019-12-23,Y,Quality assurance; Clostridium Difficile; Whole-genome Sequencing; Core Genome Mlst,The Human Phenome,,"Pathogen whole-genome sequencing has huge potential as a tool to better understand infection transmission. However, rapidly identifying closely related genomes among a background of thousands of other genomes is challenging. Here, we describe a refinement to core genome multilocus sequence typing (cgMLST) in which alleles at each gene are reproducibly converted to a unique hash, or short string of letters (hash-cgMLST). This avoids the resource-intensive need for a single centralized database of sequentially numbered alleles. We test the reproducibility and discriminatory power of cgMLST/hash-cgMLST compared to those of mapping-based approaches in <i>Clostridium difficile</i>, using repeated sequencing of the same isolates (replicates) and data from consecutive infection isolates from six English hospitals. Hash-cgMLST provided the same results as standard cgMLST, with minimal performance penalty. Comparing 272 replicate sequence pairs using reference-based mapping, there were 0, 1, or 2 single-nucleotide polymorphisms (SNPs) between 262 (96%), 5 (2%), and 1 (<1%) of the pairs, respectively. Using hash-cgMLST, 218 (80%) of replicate pairs assembled with SPAdes had zero gene differences, and 31 (11%), 5 (2%), and 18 (7%) pairs had 1, 2, and >2 differences, respectively. False gene differences were clustered in specific genes and associated with fragmented assemblies, but were reduced using the SKESA assembler. Considering 412 pairs of infections with ≤2 SNPS, i.e., consistent with recent transmission, 376 (91%) had ≤2 gene differences and 16 (4%) had ≥4. Comparing a genome to 100,000 others took <1 min using hash-cgMLST. Hash-cgMLST is an effective surveillance tool for rapidly identifying clusters of related genomes. However, cgMLST/hash-cgMLST generate more false variants than mapping-based approaches. Follow-up mapping-based analyses are likely required to precisely define close genetic relationships.",,pdf:https://jcm.asm.org/content/jcm/58/1/e01037-19.full.pdf; doi:https://doi.org/10.1128/JCM.01037-19; html:https://europepmc.org/articles/PMC6935933; pdf:https://europepmc.org/articles/PMC6935933?pdf=render
+32855398,https://doi.org/10.1038/s41467-020-18060-0,Multi-site clonality analysis uncovers pervasive heterogeneity across melanoma metastases.,"Rabbie R, Ansari-Pour N, Cast O, Lau D, Scott F, Welsh SJ, Parkinson C, Khoja L, Moore L, Tullett M, Wong K, Ferreira I, Gómez JMM, Levesque M, Gallagher FA, Jiménez-Sánchez A, Riva L, Miller ML, Allinson K, Campbell PJ, Corrie P, Wedge DC, Adams DJ.",,Nature communications,2020,2020-08-27,Y,,,,"Metastatic melanoma carries a poor prognosis despite modern systemic therapies. Understanding the evolution of the disease could help inform patient management. Through whole-genome sequencing of 13 melanoma metastases sampled at autopsy from a treatment naïve patient and by leveraging the analytical power of multi-sample analyses, we reveal evidence of diversification among metastatic lineages. UV-induced mutations dominate the trunk, whereas APOBEC-associated mutations are found in the branches of the evolutionary tree. Multi-sample analyses from a further seven patients confirmed that lineage diversification was pervasive, representing an important mode of melanoma dissemination. Our analyses demonstrate that joint analysis of cancer cell fraction estimates across multiple metastases can uncover previously unrecognised levels of tumour heterogeneity and highlight the limitations of inferring heterogeneity from a single biopsy.",,pdf:https://www.nature.com/articles/s41467-020-18060-0.pdf; doi:https://doi.org/10.1038/s41467-020-18060-0; html:https://europepmc.org/articles/PMC7453196; pdf:https://europepmc.org/articles/PMC7453196?pdf=render
 34800427,https://doi.org/10.1016/s0140-6736(21)01825-0,"Aspirin in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial.",RECOVERY Collaborative Group.,,"Lancet (London, England)",2022,2021-11-17,Y,,,,"<h4>Background</h4>Aspirin has been proposed as a treatment for COVID-19 on the basis of its anti-thrombotic properties. We aimed to evaluate the efficacy and safety of aspirin in patients admitted to hospital with COVID-19.<h4>Methods</h4>In this randomised, controlled, open-label, platform trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19. The trial took place at 177 hospitals in the UK, two hospitals in Indonesia, and two hospitals in Nepal. Eligible and consenting adults were randomly allocated in a 1:1 ratio to either usual standard of care plus 150 mg aspirin once per day until discharge or usual standard of care alone using web-based simple (unstratified) randomisation with allocation concealment. The primary outcome was 28 day mortality. All analyses were done by intention to treat. The trial is registered with ISRCTN (50189673) and ClinicalTrials.gov (NCT04381936).<h4>Findings</h4>Between Nov 1, 2020, and March 21, 2021, 14 892 (66%) of 22 560 patients enrolled into the RECOVERY trial were eligible to be randomly allocated to aspirin. 7351 patients were randomly allocated (1:1) to receive aspirin and 7541 patients to receive usual care alone. Overall, 1222 (17%) of 7351 patients allocated to aspirin and 1299 (17%) of 7541 patients allocated to usual care died within 28 days (rate ratio 0·96, 95% CI 0·89-1·04; p=0·35). Consistent results were seen in all prespecified subgroups of patients. Patients allocated to aspirin had a slightly shorter duration of hospitalisation (median 8 days, IQR 5 to >28, vs 9 days, IQR 5 to >28) and a higher proportion were discharged from hospital alive within 28 days (75% vs 74%; rate ratio 1·06, 95% CI 1·02-1·10; p=0·0062). Among patients not on invasive mechanical ventilation at baseline, there was no significant difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (21% vs 22%; risk ratio 0·96, 95% CI 0·90-1·03; p=0·23). Aspirin use was associated with a reduction in thrombotic events (4·6% vs 5·3%; absolute reduction 0·6%, SE 0·4%) and an increase in major bleeding events (1·6% vs 1·0%; absolute increase 0·6%, SE 0·2%).<h4>Interpretation</h4>In patients hospitalised with COVID-19, aspirin was not associated with reductions in 28 day mortality or in the risk of progressing to invasive mechanical ventilation or death, but was associated with a small increase in the rate of being discharged alive within 28 days.<h4>Funding</h4>UK Research and Innovation (Medical Research Council), National Institute of Health Research, and the Wellcome Trust through the COVID-19 Therapeutics Accelerator.",,doi:https://doi.org/10.1016/s0140-6736(21)01825-0; doi:https://doi.org/10.1016/S0140-6736(21)01825-0; html:https://europepmc.org/articles/PMC8598213
 34090494,https://doi.org/10.1186/s13063-021-05284-8,A framework for handling missing accelerometer outcome data in trials.,"Tackney MS, Cook DG, Stahl D, Ismail K, Williamson E, Carpenter J.",,Trials,2021,2021-06-05,Y,Clinical Trial; Missing Data; Accelerometer; Multiple Imputation; Wearables,,,"Accelerometers and other wearable devices are increasingly being used in clinical trials to provide an objective measure of the impact of an intervention on physical activity. Missing data are ubiquitous in this setting, typically for one of two reasons: patients may not wear the device as per protocol, and/or the device may fail to collect data (e.g. flat battery, water damage). However, it is not always possible to distinguish whether the participant stopped wearing the device, or if the participant is wearing the device but staying still. Further, a lack of consensus in the literature on how to aggregate the data before analysis (hourly, daily, weekly) leads to a lack of consensus in how to define a ""missing"" outcome. Different trials have adopted different definitions (ranging from having insufficient step counts in a day, through to missing a certain number of days in a week). We propose an analysis framework that uses wear time to define missingness on the epoch and day level, and propose a multiple imputation approach, at the day level, which treats partially observed daily step counts as right censored. This flexible approach allows the inclusion of auxiliary variables, and is consistent with almost all the primary analysis models described in the literature, and readily allows sensitivity analysis (to the missing at random assumption) to be performed. Having presented our framework, we illustrate its application to the analysis of the 2019 MOVE-IT trial of motivational interviewing to increase exercise.",,pdf:https://trialsjournal.biomedcentral.com/track/pdf/10.1186/s13063-021-05284-8; doi:https://doi.org/10.1186/s13063-021-05284-8; html:https://europepmc.org/articles/PMC8178870; pdf:https://europepmc.org/articles/PMC8178870?pdf=render
 33203707,https://doi.org/10.2337/dc20-1328,Plasma Vitamin C and Type 2 Diabetes: Genome-Wide Association Study and Mendelian Randomization Analysis in European Populations.,"Zheng JS, Luan J, Sofianopoulou E, Imamura F, Stewart ID, Day FR, Pietzner M, Wheeler E, Lotta LA, Gundersen TE, Amiano P, Ardanaz E, Chirlaque MD, Fagherazzi G, Franks PW, Kaaks R, Laouali N, Mancini FR, Nilsson PM, Onland-Moret NC, Olsen A, Overvad K, Panico S, Palli D, Ricceri F, Rolandsson O, Spijkerman AMW, Sánchez MJ, Schulze MB, Sala N, Sieri S, Tjønneland A, Tumino R, van der Schouw YT, Weiderpass E, Riboli E, Danesh J, Butterworth AS, Sharp SJ, Langenberg C, Forouhi NG, Wareham NJ.",,Diabetes care,2021,2020-11-17,Y,,,,"<h4>Objective</h4>Higher plasma vitamin C levels are associated with lower type 2 diabetes risk, but whether this association is causal is uncertain. To investigate this, we studied the association of genetically predicted plasma vitamin C with type 2 diabetes.<h4>Research design and methods</h4>We conducted genome-wide association studies of plasma vitamin C among 52,018 individuals of European ancestry to discover novel genetic variants. We performed Mendelian randomization analyses to estimate the association of genetically predicted differences in plasma vitamin C with type 2 diabetes in up to 80,983 case participants and 842,909 noncase participants. We compared this estimate with the observational association between plasma vitamin C and incident type 2 diabetes, including 8,133 case participants and 11,073 noncase participants.<h4>Results</h4>We identified 11 genomic regions associated with plasma vitamin C (<i>P</i> < 5 × 10<sup>-8</sup>), with the strongest signal at <i>SLC23A1</i>, and 10 novel genetic loci including <i>SLC23A3</i>, <i>CHPT1</i>, <i>BCAS3</i>, <i>SNRPF</i>, <i>RER1</i>, <i>MAF</i>, <i>GSTA5</i>, <i>RGS14</i>, <i>AKT1</i>, and <i>FADS1</i>. Plasma vitamin C was inversely associated with type 2 diabetes (hazard ratio per SD 0.88; 95% CI 0.82, 0.94), but there was no association between genetically predicted plasma vitamin C (excluding <i>FADS1</i> variant due to its apparent pleiotropic effect) and type 2 diabetes (1.03; 95% CI 0.96, 1.10).<h4>Conclusions</h4>These findings indicate discordance between biochemically measured and genetically predicted plasma vitamin C levels in the association with type 2 diabetes among European populations. The null Mendelian randomization findings provide no strong evidence to suggest the use of vitamin C supplementation for type 2 diabetes prevention.",,pdf:https://diabetesjournals.org/care/article-pdf/44/1/98/532486/dc201328.pdf; doi:https://doi.org/10.2337/dc20-1328; html:https://europepmc.org/articles/PMC7783939; pdf:https://europepmc.org/articles/PMC7783939?pdf=render
@@ -2741,8 +2743,8 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 35609980,https://doi.org/10.1093/nar/gkac364,GEOexplorer: a webserver for gene expression analysis and visualisation.,"Hunt GP, Grassi L, Henkin R, Smeraldi F, Spargo TP, Kabiljo R, Koks S, Ibrahim Z, Dobson RJB, Al-Chalabi A, Barnes MR, Iacoangeli A.",,Nucleic acids research,2022,2022-07-01,Y,,,,"Gene Expression Omnibus (GEO) is a database repository hosting a substantial proportion of publicly available high throughput gene expression data. Gene expression analysis is a powerful tool to gain insight into the mechanisms and processes underlying the biological and phenotypic differences between sample groups. Despite the wide availability of gene expression datasets, their access, analysis, and integration are not trivial and require specific expertise and programming proficiency. We developed the GEOexplorer webserver to allow scientists to access, integrate and analyse gene expression datasets without requiring programming proficiency. Via its user-friendly graphic interface, users can easily apply GEOexplorer to perform interactive and reproducible gene expression analysis of microarray and RNA-seq datasets, while producing a wealth of interactive visualisations to facilitate data exploration and interpretation, and generating a range of publication ready figures. The webserver allows users to search and retrieve datasets from GEO as well as to upload user-generated data and combine and harmonise two datasets to perform joint analyses. GEOexplorer, available at https://geoexplorer.rosalind.kcl.ac.uk, provides a solution for performing interactive and reproducible analyses of microarray and RNA-seq gene expression data, empowering life scientists to perform exploratory data analysis and differential gene expression analysis on-the-fly without informatics proficiency.",,pdf:https://researchrepository.murdoch.edu.au/id/eprint/64965/1/geneexpression.pdf; doi:https://doi.org/10.1093/nar/gkac364; html:https://europepmc.org/articles/PMC9252785; pdf:https://europepmc.org/articles/PMC9252785?pdf=render
 31122927,https://doi.org/10.1136/bmj.l1778,Determinants of the decline in mortality from acute stroke in England: linked national database study of 795 869 adults.,"Seminog OO, Scarborough P, Wright FL, Rayner M, Goldacre MJ.",,BMJ (Clinical research ed.),2019,2019-05-22,Y,,Improving Public Health,,"<h4>Objectives</h4>To study trends in stroke mortality rates, event rates, and case fatality, and to explain the extent to which the reduction in stroke mortality rates was influenced by changes in stroke event rates or case fatality.<h4>Design</h4>Population based study.<h4>Setting</h4>Person linked routine hospital and mortality data, England.<h4>Participants</h4>795 869 adults aged 20 and older who were admitted to hospital with acute stroke or died from stroke.<h4>Main outcome measures</h4>Stroke mortality rates, stroke event rates (stroke admission or stroke death without admission), and case fatality within 30 days after stroke.<h4>Results</h4>Between 2001 and 2010 stroke mortality rates decreased by 55%, stroke event rates by 20%, and case fatality by 40%. The study population included 358 599 (45%) men and 437 270 (55%) women. Average annual change in mortality rate was -6.0% (95% confidence interval -6.2% to -5.8%) in men and -6.1% (-6.3% to -6.0%) in women, in stroke event rate was -1.3% (-1.4% to -1.2%) in men and -2.1% (-2.2 to -2.0) in women, and in case fatality was -4.7% (-4.9% to -4.5%) in men and -4.4% (-4.5% to -4.2%) in women. Mortality and case fatality but not event rate declined in all age groups: the stroke event rate decreased in older people but increased by 2% each year in adults aged 35 to 54 years. Of the total decline in mortality rates, 71% was attributed to the decline in case fatality (78% in men and 66% in women) and the remainder to the reduction in stroke event rates. The contribution of the two factors varied between age groups. Whereas the reduction in mortality rates in people younger than 55 years was due to the reduction in case fatality, in the oldest age group (≥85 years) reductions in case fatality and event rates contributed nearly equally.<h4>Conclusions</h4>Declines in case fatality, probably driven by improvements in stroke care, contributed more than declines in event rates to the overall reduction in stroke mortality. Mortality reduction in men and women younger than 55 was solely a result of a decrease in case fatality, whereas stroke event rates increased in the age group 35 to 54 years. The increase in stroke event rates in young adults is a concern. This suggests that stroke prevention needs to be strengthened to reduce the occurrence of stroke in people younger than 55 years.",,pdf:https://www.bmj.com/content/bmj/365/bmj.l1778.full.pdf; doi:https://doi.org/10.1136/bmj.l1778; html:https://europepmc.org/articles/PMC6529851
 32745807,https://doi.org/10.1016/j.neurobiolaging.2020.06.023,An epigenome-wide association study of Alzheimer's disease blood highlights robust DNA hypermethylation in the HOXB6 gene.,"Roubroeks JAY, Smith AR, Smith RG, Pishva E, Ibrahim Z, Sattlecker M, Hannon EJ, Kłoszewska I, Mecocci P, Soininen H, Tsolaki M, Vellas B, Wahlund LO, Aarsland D, Proitsi P, Hodges A, Lovestone S, Newhouse SJ, Dobson RJB, Mill J, van den Hove DLA, Lunnon K.",,Neurobiology of aging,2020,2020-07-03,Y,Blood; DNA methylation; Biomarker; Alzheimer's disease (AD); Mild Cognitive Impairment (Mci); Hoxb6,,,"A growing number of epigenome-wide association studies have demonstrated a role for DNA methylation in the brain in Alzheimer's disease. With the aim of exploring peripheral biomarker potential, we have examined DNA methylation patterns in whole blood collected from 284 individuals in the AddNeuroMed study, which included 89 nondemented controls, 86 patients with Alzheimer's disease, and 109 individuals with mild cognitive impairment, including 38 individuals who progressed to Alzheimer's disease within 1 year. We identified significant differentially methylated regions, including 12 adjacent hypermethylated probes in the HOXB6 gene in Alzheimer's disease, which we validated using pyrosequencing. Using weighted gene correlation network analysis, we identified comethylated modules of genes that were associated with key variables such as APOE genotype and diagnosis. In summary, this study represents the first large-scale epigenome-wide association study of Alzheimer's disease and mild cognitive impairment using blood. We highlight the differences in various loci and pathways in early disease, suggesting that these patterns relate to cognitive decline at an early stage.",,doi:https://doi.org/10.1016/j.neurobiolaging.2020.06.023; doi:https://doi.org/10.1016/j.neurobiolaging.2020.06.023; html:https://europepmc.org/articles/PMC7649340
-36113526,https://doi.org/10.1016/s2214-109x(22)00332-1,"Mapping development and health effects of cooking with solid fuels in low-income and middle-income countries, 2000-18: a geospatial modelling study.",Local Burden of Disease Household Air Pollution Collaborators.,,The Lancet. Global health,2022,2022-10-01,Y,,,,"<h4>Background</h4>More than 3 billion people do not have access to clean energy and primarily use solid fuels to cook. Use of solid fuels generates household air pollution, which was associated with more than 2 million deaths in 2019. Although local patterns in cooking vary systematically, subnational trends in use of solid fuels have yet to be comprehensively analysed. We estimated the prevalence of solid-fuel use with high spatial resolution to explore subnational inequalities, assess local progress, and assess the effects on health in low-income and middle-income countries (LMICs) without universal access to clean fuels.<h4>Methods</h4>We did a geospatial modelling study to map the prevalence of solid-fuel use for cooking at a 5 km × 5 km resolution in 98 LMICs based on 2·1 million household observations of the primary cooking fuel used from 663 population-based household surveys over the years 2000 to 2018. We use observed temporal patterns to forecast household air pollution in 2030 and to assess the probability of attaining the Sustainable Development Goal (SDG) target indicator for clean cooking. We aligned our estimates of household air pollution to geospatial estimates of ambient air pollution to establish the risk transition occurring in LMICs. Finally, we quantified the effect of residual primary solid-fuel use for cooking on child health by doing a counterfactual risk assessment to estimate the proportion of deaths from lower respiratory tract infections in children younger than 5 years that could be associated with household air pollution.<h4>Findings</h4>Although primary reliance on solid-fuel use for cooking has declined globally, it remains widespread. 593 million people live in districts where the prevalence of solid-fuel use for cooking exceeds 95%. 66% of people in LMICs live in districts that are not on track to meet the SDG target for universal access to clean energy by 2030. Household air pollution continues to be a major contributor to particulate exposure in LMICs, and rising ambient air pollution is undermining potential gains from reductions in the prevalence of solid-fuel use for cooking in many countries. We estimated that, in 2018, 205 000 (95% uncertainty interval 147 000-257 000) children younger than 5 years died from lower respiratory tract infections that could be attributed to household air pollution.<h4>Interpretation</h4>Efforts to accelerate the adoption of clean cooking fuels need to be substantially increased and recalibrated to account for subnational inequalities, because there are substantial opportunities to improve air quality and avert child mortality associated with household air pollution.<h4>Funding</h4>Bill & Melinda Gates Foundation.",,pdf:https://eprints.qut.edu.au/236269/1/1_s2.0_S2214109X22003321.pdf; doi:https://doi.org/10.1016/S2214-109X(22)00332-1; html:https://europepmc.org/articles/PMC9638039
 32664951,https://doi.org/10.1186/s13148-020-00895-5,H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts.,"Pei J, Harakalova M, Treibel TA, Lumbers RT, Boukens BJ, Efimov IR, van Dinter JT, González A, López B, El Azzouzi H, van den Dungen N, van Dijk CGM, Krebber MM, den Ruijter HM, Pasterkamp G, Duncker DJ, Nieuwenhuis EES, de Weger R, Huibers MM, Vink A, Moore JH, Moon JC, Verhaar MC, Kararigas G, Mokry M, Asselbergs FW, Cheng C.",,Clinical epigenetics,2020,2020-07-14,Y,Transcription factor; Histone acetylation; Transcriptome; Myocardial Remodeling,,,"<h4>Background</h4>H3K27ac histone acetylome changes contribute to the phenotypic response in heart diseases, particularly in end-stage heart failure. However, such epigenetic alterations have not been systematically investigated in remodeled non-failing human hearts. Therefore, valuable insight into cardiac dysfunction in early remodeling is lacking. This study aimed to reveal the acetylation changes of chromatin regions in response to myocardial remodeling and their correlations to transcriptional changes of neighboring genes.<h4>Results</h4>We detected chromatin regions with differential acetylation activity (DARs; P<sub>adj.</sub> < 0.05) between remodeled non-failing patient hearts and healthy donor hearts. The acetylation level of the chromatin region correlated with its RNA polymerase II occupancy level and the mRNA expression level of its adjacent gene per sample. Annotated genes from DARs were enriched in disease-related pathways, including fibrosis and cell metabolism regulation. DARs that change in the same direction have a tendency to cluster together, suggesting the well-reorganized chromatin architecture that facilitates the interactions of regulatory domains in response to myocardial remodeling. We further show the differences between the acetylation level and the mRNA expression level of cell-type-specific markers for cardiomyocytes and 11 non-myocyte cell types. Notably, we identified transcriptome factor (TF) binding motifs that were enriched in DARs and defined TFs that were predicted to bind to these motifs. We further showed 64 genes coding for these TFs that were differentially expressed in remodeled myocardium when compared with controls.<h4>Conclusions</h4>Our study reveals extensive novel insight on myocardial remodeling at the DNA regulatory level. Differences between the acetylation level and the transcriptional level of cell-type-specific markers suggest additional mechanism(s) between acetylome and transcriptome. By integrating these two layers of epigenetic profiles, we further provide promising TF-encoding genes that could serve as master regulators of myocardial remodeling. Combined, our findings highlight the important role of chromatin regulatory signatures in understanding disease etiology.",,pdf:https://clinicalepigeneticsjournal.biomedcentral.com/track/pdf/10.1186/s13148-020-00895-5; doi:https://doi.org/10.1186/s13148-020-00895-5; html:https://europepmc.org/articles/PMC7362435; pdf:https://europepmc.org/articles/PMC7362435?pdf=render
+36113526,https://doi.org/10.1016/s2214-109x(22)00332-1,"Mapping development and health effects of cooking with solid fuels in low-income and middle-income countries, 2000-18: a geospatial modelling study.",Local Burden of Disease Household Air Pollution Collaborators.,,The Lancet. Global health,2022,2022-10-01,Y,,,,"<h4>Background</h4>More than 3 billion people do not have access to clean energy and primarily use solid fuels to cook. Use of solid fuels generates household air pollution, which was associated with more than 2 million deaths in 2019. Although local patterns in cooking vary systematically, subnational trends in use of solid fuels have yet to be comprehensively analysed. We estimated the prevalence of solid-fuel use with high spatial resolution to explore subnational inequalities, assess local progress, and assess the effects on health in low-income and middle-income countries (LMICs) without universal access to clean fuels.<h4>Methods</h4>We did a geospatial modelling study to map the prevalence of solid-fuel use for cooking at a 5 km × 5 km resolution in 98 LMICs based on 2·1 million household observations of the primary cooking fuel used from 663 population-based household surveys over the years 2000 to 2018. We use observed temporal patterns to forecast household air pollution in 2030 and to assess the probability of attaining the Sustainable Development Goal (SDG) target indicator for clean cooking. We aligned our estimates of household air pollution to geospatial estimates of ambient air pollution to establish the risk transition occurring in LMICs. Finally, we quantified the effect of residual primary solid-fuel use for cooking on child health by doing a counterfactual risk assessment to estimate the proportion of deaths from lower respiratory tract infections in children younger than 5 years that could be associated with household air pollution.<h4>Findings</h4>Although primary reliance on solid-fuel use for cooking has declined globally, it remains widespread. 593 million people live in districts where the prevalence of solid-fuel use for cooking exceeds 95%. 66% of people in LMICs live in districts that are not on track to meet the SDG target for universal access to clean energy by 2030. Household air pollution continues to be a major contributor to particulate exposure in LMICs, and rising ambient air pollution is undermining potential gains from reductions in the prevalence of solid-fuel use for cooking in many countries. We estimated that, in 2018, 205 000 (95% uncertainty interval 147 000-257 000) children younger than 5 years died from lower respiratory tract infections that could be attributed to household air pollution.<h4>Interpretation</h4>Efforts to accelerate the adoption of clean cooking fuels need to be substantially increased and recalibrated to account for subnational inequalities, because there are substantial opportunities to improve air quality and avert child mortality associated with household air pollution.<h4>Funding</h4>Bill & Melinda Gates Foundation.",,pdf:https://eprints.qut.edu.au/236269/1/1_s2.0_S2214109X22003321.pdf; doi:https://doi.org/10.1016/S2214-109X(22)00332-1; html:https://europepmc.org/articles/PMC9638039
 32062083,https://doi.org/10.1016/j.neuroimage.2020.116604,Optimising network modelling methods for fMRI.,"Pervaiz U, Vidaurre D, Woolrich MW, Smith SM.",,NeuroImage,2020,2020-02-13,Y,Functional Connectivity; Connectome; Deep Learning; Riemannian Geometry; Convolutional Neural Networks; Netmat,,,"A major goal of neuroimaging studies is to develop predictive models to analyze the relationship between whole brain functional connectivity patterns and behavioural traits. However, there is no single widely-accepted standard pipeline for analyzing functional connectivity. The common procedure for designing functional connectivity based predictive models entails three main steps: parcellating the brain, estimating the interaction between defined parcels, and lastly, using these integrated associations between brain parcels as features fed to a classifier for predicting non-imaging variables e.g., behavioural traits, demographics, emotional measures, etc. There are also additional considerations when using correlation-based measures of functional connectivity, resulting in three supplementary steps: utilising Riemannian geometry tangent space parameterization to preserve the geometry of functional connectivity; penalizing the connectivity estimates with shrinkage approaches to handle challenges related to short time-series (and noisy) data; and removing confounding variables from brain-behaviour data. These six steps are contingent on each-other, and to optimise a general framework one should ideally examine these various methods simultaneously. In this paper, we investigated strengths and short-comings, both independently and jointly, of the following measures: parcellation techniques of four kinds (categorized further depending upon number of parcels), five measures of functional connectivity, the decision of staying in the ambient space of connectivity matrices or in tangent space, the choice of applying shrinkage estimators, six alternative techniques for handling confounds and finally four novel classifiers/predictors. For performance evaluation, we have selected two of the largest datasets, UK Biobank and the Human Connectome Project resting state fMRI data, and have run more than 9000 different pipeline variants on a total of ∼14000 individuals to determine the optimum pipeline. For independent performance validation, we have run some best-performing pipeline variants on ABIDE and ACPI datasets (∼1000 subjects) to evaluate the generalisability of proposed network modelling methods.",,doi:https://doi.org/10.1016/j.neuroimage.2020.116604; doi:https://doi.org/10.1016/j.neuroimage.2020.116604; html:https://europepmc.org/articles/PMC7086233
 30524708,https://doi.org/10.1093/ckj/sfy090,The potential for improving cardio-renal outcomes by sodium-glucose co-transporter-2 inhibition in people with chronic kidney disease: a rationale for the EMPA-KIDNEY study.,"Herrington WG, Preiss D, Haynes R, von Eynatten M, Staplin N, Hauske SJ, George JT, Green JB, Landray MJ, Baigent C, Wanner C.",,Clinical kidney journal,2018,2018-10-25,Y,Clinical Trial; cardiovascular; Ckd; Diabetic Kidney Disease; Sglt-2 Inhibitor,"Better, Faster and More Efficient Clinical Trials",,"Diabetes is a common cause of chronic kidney disease (CKD), but in aggregate, non-diabetic diseases account for a higher proportion of cases of CKD than diabetes in many parts of the world. Inhibition of the renin-angiotensin system reduces the risk of kidney disease progression and treatments that lower blood pressure (BP) or low-density lipoprotein cholesterol reduce cardiovascular (CV) risk in this population. Nevertheless, despite such interventions, considerable risks for kidney and CV complications remain. Recently, large placebo-controlled outcome trials have shown that sodium-glucose co-transporter-2 (SGLT-2) inhibitors reduce the risk of CV disease (including CV death and hospitalization for heart failure) in people with type 2 diabetes who are at high risk of atherosclerotic disease, and these effects were largely independent of improvements in hyperglycaemia, BP and body weight. In the kidney, increased sodium delivery to the macula densa mediated by SGLT-2 inhibition has the potential to reduce intraglomerular pressure, which may explain why SGLT-2 inhibitors reduce albuminuria and appear to slow kidney function decline in people with diabetes. Importantly, in the trials completed to date, these benefits appeared to be maintained at lower levels of kidney function, despite attenuation of glycosuric effects, and did not appear to be dependent on ambient hyperglycaemia. There is therefore a rationale for studying the cardio-renal effects of SGLT-2 inhibition in people at risk of CV disease and hyperfiltration (i.e. those with substantially reduced nephron mass and/or albuminuria), irrespective of whether they have diabetes.",,pdf:https://academic.oup.com/ckj/article-pdf/11/6/749/27765283/sfy090.pdf; doi:https://doi.org/10.1093/ckj/sfy090; html:https://europepmc.org/articles/PMC6275453; pdf:https://europepmc.org/articles/PMC6275453?pdf=render
 33830302,https://doi.org/10.1007/s00125-021-05428-0,Analysis of overlapping genetic association in type 1 and type 2 diabetes.,"Inshaw JRJ, Sidore C, Cucca F, Stefana MI, Crouch DJM, McCarthy MI, Mahajan A, Todd JA.",,Diabetologia,2021,2021-04-08,Y,Genetics; Insulin; Systematic; Statistics; Type 2 diabetes; type 1 diabetes; Analyses; Genome-wide Association Study; Co-localisation,,,"<h4>Aims/hypothesis</h4>Given the potential shared aetiology between type 1 and type 2 diabetes, we aimed to identify any genetic regions associated with both diseases. For associations where there is a shared signal and the allele that increases risk to one disease also increases risk to the other, inference about shared aetiology could be made, with the potential to develop therapeutic strategies to treat or prevent both diseases simultaneously. Alternatively, if a genetic signal co-localises with divergent effect directions, it could provide valuable biological insight into how the association affects the two diseases differently.<h4>Methods</h4>Using publicly available type 2 diabetes summary statistics from a genome-wide association study (GWAS) meta-analysis of European ancestry individuals (74,124 cases and 824,006 controls) and type 1 diabetes GWAS summary statistics from a meta-analysis of studies on individuals from the UK and Sardinia (7467 cases and 10,218 controls), we identified all regions of 0.5 Mb that contained variants associated with both diseases (false discovery rate <0.01). In each region, we performed forward stepwise logistic regression to identify independent association signals, then examined co-localisation of each type 1 diabetes signal with each type 2 diabetes signal using coloc. Any association with a co-localisation posterior probability of ≥0.9 was considered a genuine shared association with both diseases.<h4>Results</h4>Of the 81 association signals from 42 genetic regions that showed association with both type 1 and type 2 diabetes, four association signals co-localised between both diseases (posterior probability ≥0.9): (1) chromosome 16q23.1, near CTRB1/BCAR1, which has been previously identified; (2) chromosome 11p15.5, near the INS gene; (3) chromosome 4p16.3, near TMEM129 and (4) chromosome 1p31.3, near PGM1. In each of these regions, the effect of genetic variants on type 1 diabetes was in the opposite direction to the effect on type 2 diabetes. Use of additional datasets also supported the previously identified co-localisation on chromosome 9p24.2, near the GLIS3 gene, in this case with a concordant direction of effect.<h4>Conclusions/interpretation</h4>Four of five association signals that co-localise between type 1 diabetes and type 2 diabetes are in opposite directions, suggesting a complex genetic relationship between the two diseases.",,pdf:https://link.springer.com/content/pdf/10.1007/s00125-021-05428-0.pdf; doi:https://doi.org/10.1007/s00125-021-05428-0; html:https://europepmc.org/articles/PMC8099827; pdf:https://europepmc.org/articles/PMC8099827?pdf=render
@@ -2753,13 +2755,13 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 33757590,https://doi.org/10.1186/s13148-021-01043-3,Multi-omics integration identifies key upstream regulators of pathomechanisms in hypertrophic cardiomyopathy due to truncating MYBPC3 mutations.,"Pei J, Schuldt M, Nagyova E, Gu Z, El Bouhaddani S, Yiangou L, Jansen M, Calis JJA, Dorsch LM, Blok CS, van den Dungen NAM, Lansu N, Boukens BJ, Efimov IR, Michels M, Verhaar MC, de Weger R, Vink A, van Steenbeek FG, Baas AF, Davis RP, Uh HW, Kuster DWD, Cheng C, Mokry M, van der Velden J, Asselbergs FW, Harakalova M.",,Clinical epigenetics,2021,2021-03-23,Y,Transcription factors; Proteome; Transcriptome; Hcm; Mybpc3; Histone Acetylome,,,"<h4>Background</h4>Hypertrophic cardiomyopathy (HCM) is the most common genetic disease of the cardiac muscle, frequently caused by mutations in MYBPC3. However, little is known about the upstream pathways and key regulators causing the disease. Therefore, we employed a multi-omics approach to study the pathomechanisms underlying HCM comparing patient hearts harboring MYBPC3 mutations to control hearts.<h4>Results</h4>Using H3K27ac ChIP-seq and RNA-seq we obtained 9310 differentially acetylated regions and 2033 differentially expressed genes, respectively, between 13 HCM and 10 control hearts. We obtained 441 differentially expressed proteins between 11 HCM and 8 control hearts using proteomics. By integrating multi-omics datasets, we identified a set of DNA regions and genes that differentiate HCM from control hearts and 53 protein-coding genes as the major contributors. This comprehensive analysis consistently points toward altered extracellular matrix formation, muscle contraction, and metabolism. Therefore, we studied enriched transcription factor (TF) binding motifs and identified 9 motif-encoded TFs, including KLF15, ETV4, AR, CLOCK, ETS2, GATA5, MEIS1, RXRA, and ZFX. Selected candidates were examined in stem cell-derived cardiomyocytes with and without mutated MYBPC3. Furthermore, we observed an abundance of acetylation signals and transcripts derived from cardiomyocytes compared to non-myocyte populations.<h4>Conclusions</h4>By integrating histone acetylome, transcriptome, and proteome profiles, we identified major effector genes and protein networks that drive the pathological changes in HCM with mutated MYBPC3. Our work identifies 38 highly affected protein-coding genes as potential plasma HCM biomarkers and 9 TFs as potential upstream regulators of these pathomechanisms that may serve as possible therapeutic targets.",,pdf:https://clinicalepigeneticsjournal.biomedcentral.com/counter/pdf/10.1186/s13148-021-01043-3; doi:https://doi.org/10.1186/s13148-021-01043-3; html:https://europepmc.org/articles/PMC7989210; pdf:https://europepmc.org/articles/PMC7989210?pdf=render
 32246132,https://doi.org/10.1038/s41588-020-0603-8,A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer.,"Wagner AH, Walsh B, Mayfield G, Tamborero D, Sonkin D, Krysiak K, Deu-Pons J, Duren RP, Gao J, McMurry J, Patterson S, Del Vecchio Fitz C, Pitel BA, Sezerman OU, Ellrott K, Warner JL, Rieke DT, Aittokallio T, Cerami E, Ritter DI, Schriml LM, Freimuth RR, Haendel M, Raca G, Madhavan S, Baudis M, Beckmann JS, Dienstmann R, Chakravarty D, Li XS, Mockus S, Elemento O, Schultz N, Lopez-Bigas N, Lawler M, Goecks J, Griffith M, Griffith OL, Margolin AA, Variant Interpretation for Cancer Consortium.",,Nature genetics,2020,2020-04-03,Y,,,,"Precision oncology relies on accurate discovery and interpretation of genomic variants, enabling individualized diagnosis, prognosis and therapy selection. We found that six prominent somatic cancer variant knowledgebases were highly disparate in content, structure and supporting primary literature, impeding consensus when evaluating variants and their relevance in a clinical setting. We developed a framework for harmonizing variant interpretations to produce a meta-knowledgebase of 12,856 aggregate interpretations. We demonstrated large gains in overlap between resources across variants, diseases and drugs as a result of this harmonization. We subsequently demonstrated improved matching between a patient cohort and harmonized interpretations of potential clinical significance, observing an increase from an average of 33% per individual knowledgebase to 57% in aggregate. Our analyses illuminate the need for open, interoperable sharing of variant interpretation data. We also provide a freely available web interface (search.cancervariants.org) for exploring the harmonized interpretations from these six knowledgebases.",,pdf:https://www.nature.com/articles/s41588-020-0603-8.pdf; doi:https://doi.org/10.1038/s41588-020-0603-8; html:https://europepmc.org/articles/PMC7127986; pdf:https://europepmc.org/articles/PMC7127986?pdf=render
 35187482,https://doi.org/10.1093/braincomms/fcab291,Metabolic correlates of late midlife cognitive outcomes: findings from the 1946 British Birth Cohort.,"Green R, Lord J, Xu J, Maddock J, Kim M, Dobson R, Legido-Quigley C, Wong A, Richards M, Proitsi P.",,Brain communications,2022,2021-12-15,Y,Cognition; Dementia; Metabolomics; epidemiology; Network Analysis,,,"Investigating associations between metabolites and late midlife cognitive function could reveal potential markers and mechanisms relevant to early dementia. Here, we systematically explored the metabolic correlates of cognitive outcomes measured across the seventh decade of life, while untangling influencing life course factors. Using levels of 1019 metabolites profiled by liquid chromatography-mass spectrometry (age 60-64), we evaluated relationships between metabolites and cognitive outcomes in the British 1946 Birth Cohort (<i>N</i> = 1740). We additionally conducted pathway and network analyses to allow for greater insight into potential mechanisms, and sequentially adjusted for life course factors across four models, including sex and blood collection (Model 1), Model 1 + body mass index and lipid medication (Model 2), Model 2 + social factors and childhood cognition (Model 3) and Model 3 + lifestyle influences (Model 4). After adjusting for multiple tests, 155 metabolites, 10 pathways and 5 network modules were associated with cognitive outcomes. Of the 155, 35 metabolites were highly connected in their network module (termed 'hub' metabolites), presenting as promising marker candidates. Notably, we report relationships between a module comprised of acylcarnitines and processing speed which remained robust to life course adjustment, revealing palmitoylcarnitine (C16) as a hub (Model 4: <i>β</i> = -0.10, 95% confidence interval = -0.15 to -0.052, <i>P</i> = 5.99 × 10<sup>-5</sup>). Most associations were sensitive to adjustment for social factors and childhood cognition; in the final model, four metabolites remained after multiple testing correction, and 80 at <i>P</i> < 0.05. Two modules demonstrated associations that were partly or largely attenuated by life course factors: one enriched in modified nucleosides and amino acids (overall attenuation = 39.2-55.5%), and another in vitamin A and C metabolites (overall attenuation = 68.6-92.6%). Our other findings, including a module enriched in sphingolipid pathways, were entirely explained by life course factors, particularly childhood cognition and education. Using a large birth cohort study with information across the life course, we highlighted potential metabolic mechanisms associated with cognitive function in late midlife, suggesting marker candidates and life course relationships for further study.",,pdf:https://academic.oup.com/braincomms/article-pdf/4/1/fcab291/42546494/fcab291.pdf; doi:https://doi.org/10.1093/braincomms/fcab291; html:https://europepmc.org/articles/PMC8853724; pdf:https://europepmc.org/articles/PMC8853724?pdf=render
-31341063,https://doi.org/10.1126/scitranslmed.aan5662,The gut microbiota influences skeletal muscle mass and function in mice.,"Lahiri S, Kim H, Garcia-Perez I, Reza MM, Martin KA, Kundu P, Cox LM, Selkrig J, Posma JM, Zhang H, Padmanabhan P, Moret C, Gulyás B, Blaser MJ, Auwerx J, Holmes E, Nicholson J, Wahli W, Pettersson S.",,Science translational medicine,2019,2019-07-01,N,,,,"The functional interactions between the gut microbiota and the host are important for host physiology, homeostasis, and sustained health. We compared the skeletal muscle of germ-free mice that lacked a gut microbiota to the skeletal muscle of pathogen-free mice that had a gut microbiota. Compared to pathogen-free mouse skeletal muscle, germ-free mouse skeletal muscle showed atrophy, decreased expression of insulin-like growth factor 1, and reduced transcription of genes associated with skeletal muscle growth and mitochondrial function. Nuclear magnetic resonance spectrometry analysis of skeletal muscle, liver, and serum from germ-free mice revealed multiple changes in the amounts of amino acids, including glycine and alanine, compared to pathogen-free mice. Germ-free mice also showed reduced serum choline, the precursor of acetylcholine, the key neurotransmitter that signals between muscle and nerve at neuromuscular junctions. Reduced expression of genes encoding Rapsyn and Lrp4, two proteins important for neuromuscular junction assembly and function, was also observed in skeletal muscle from germ-free mice compared to pathogen-free mice. Transplanting the gut microbiota from pathogen-free mice into germ-free mice resulted in an increase in skeletal muscle mass, a reduction in muscle atrophy markers, improved oxidative metabolic capacity of the muscle, and elevated expression of the neuromuscular junction assembly genes <i>Rapsyn</i> and <i>Lrp4</i> Treating germ-free mice with short-chain fatty acids (microbial metabolites) partly reversed skeletal muscle impairments. Our results suggest a role for the gut microbiota in regulating skeletal muscle mass and function in mice.",,pdf:https://stm.sciencemag.org/content/scitransmed/11/502/eaan5662.full.pdf; doi:https://doi.org/10.1126/scitranslmed.aan5662; html:https://europepmc.org/articles/PMC7501733; pdf:https://europepmc.org/articles/PMC7501733?pdf=render; doi:https://doi.org/10.1126/scitranslmed.aan5662
 31607442,https://doi.org/10.1016/j.injury.2019.09.036,Over view of major traumatic injury in Australia--Implications for trauma system design.,"Cameron PA, Fitzgerald MC, Curtis K, McKie E, Gabbe B, Earnest A, Christey G, Clarke C, Crozier J, Dinh M, Ellis DY, Howard T, Joseph AP, McDermott K, Matthew J, Ogilvie R, Pollard C, Rao S, Reade M, Rushworth N, Zalstein S, Australian Trauma Quality Improvement Program (AusTQIP) collaboration.",,Injury,2020,2019-10-03,N,Quality improvement; epidemiology; Older Adults; Risk Adjustment; Trauma System; Major Trauma; System Of Care; Trauma Registries; Injury Burden,Improving Public Health,,"<h4>Background</h4>Trauma registries are known to drive improvements and optimise trauma systems worldwide. This is the first reported comparison of the epidemiology and outcomes at major centres across Australia.<h4>Methods</h4>The Australian Trauma Registry was a collaboration of 26 major trauma centres across Australia at the time of this study and currently collects information on patients admitted to these centres who die after injury and/or sustain major trauma (Injury Severity Score (ISS) > 12). Data from 1 July 2016 to 30 June 2017 were analysed. Primary endpoints were risk adjusted length of stay and mortality (adjusted for age, cause of injury, arrival Glasgow coma scale (GCS), shock-index grouped in quartiles and ISS).<h4>Results</h4>There were 8423 patients from 24 centres included. The median age (IQR) was 48 (28-68) years. Median (IQR) ISS was 17 (14-25). There was a predominance of males (72%) apart from the extremes of age. Transport-related cases accounted for 45% of major trauma, followed by falls (35.1%). Patients took 1.42 (1.03-2.12) h to reach hospital and spent 7.10 (3.64-15.00) days in hospital. Risk adjusted length of stay and mortality did not differ significantly across sites. Primary endpoints across sites were also similar in paediatric and older adult (>65) age groups.<h4>Conclusion</h4>Australia has the capability to identify national injury trends to target prevention and reduce the burden of injury. Quality of care following injury can now be benchmarked across Australia and with the planned enhancements to data collection and reporting, this will enable improved management of trauma victims.","This paper looks at the implications for trauma system design based on major traumatic injuries in Australia and aims to describe the current epidemiology of major trauma across the country, identifying improvements and future directions in the system of trauma care in Australia. This is the first reported comparison of the epidemiology and outcomes at major centres across Australia. They concluded that Australia now has the capability to identify national injury trends in patients admitted to major trauma services, optimising prevention and treamtnet strategies, thereby potentially reducing the burden of injury.",doi:https://doi.org/10.1016/j.injury.2019.09.036
+31341063,https://doi.org/10.1126/scitranslmed.aan5662,The gut microbiota influences skeletal muscle mass and function in mice.,"Lahiri S, Kim H, Garcia-Perez I, Reza MM, Martin KA, Kundu P, Cox LM, Selkrig J, Posma JM, Zhang H, Padmanabhan P, Moret C, Gulyás B, Blaser MJ, Auwerx J, Holmes E, Nicholson J, Wahli W, Pettersson S.",,Science translational medicine,2019,2019-07-01,N,,,,"The functional interactions between the gut microbiota and the host are important for host physiology, homeostasis, and sustained health. We compared the skeletal muscle of germ-free mice that lacked a gut microbiota to the skeletal muscle of pathogen-free mice that had a gut microbiota. Compared to pathogen-free mouse skeletal muscle, germ-free mouse skeletal muscle showed atrophy, decreased expression of insulin-like growth factor 1, and reduced transcription of genes associated with skeletal muscle growth and mitochondrial function. Nuclear magnetic resonance spectrometry analysis of skeletal muscle, liver, and serum from germ-free mice revealed multiple changes in the amounts of amino acids, including glycine and alanine, compared to pathogen-free mice. Germ-free mice also showed reduced serum choline, the precursor of acetylcholine, the key neurotransmitter that signals between muscle and nerve at neuromuscular junctions. Reduced expression of genes encoding Rapsyn and Lrp4, two proteins important for neuromuscular junction assembly and function, was also observed in skeletal muscle from germ-free mice compared to pathogen-free mice. Transplanting the gut microbiota from pathogen-free mice into germ-free mice resulted in an increase in skeletal muscle mass, a reduction in muscle atrophy markers, improved oxidative metabolic capacity of the muscle, and elevated expression of the neuromuscular junction assembly genes <i>Rapsyn</i> and <i>Lrp4</i> Treating germ-free mice with short-chain fatty acids (microbial metabolites) partly reversed skeletal muscle impairments. Our results suggest a role for the gut microbiota in regulating skeletal muscle mass and function in mice.",,pdf:https://stm.sciencemag.org/content/scitransmed/11/502/eaan5662.full.pdf; doi:https://doi.org/10.1126/scitranslmed.aan5662; html:https://europepmc.org/articles/PMC7501733; pdf:https://europepmc.org/articles/PMC7501733?pdf=render; doi:https://doi.org/10.1126/scitranslmed.aan5662
 31243008,https://doi.org/10.1136/archdischild-2018-316693,Origins of disparities in preventable child mortality in England and Sweden: a birth cohort study.,"Zylbersztejn A, Gilbert R, Hjern A, Hardelid P.",,Archives of disease in childhood,2020,2019-06-26,Y,Respiratory tract infection; Sweden; England; Child Mortality; Sudden Unexpected Death In Infancy,Improving Public Health,,"<h4>Objective</h4>To compare mortality in children aged <5 years from two causes amenable to healthcare prevention in England and Sweden: respiratory tract infection (RTI) and sudden unexpected death in infancy (SUDI).<h4>Design</h4>Birth cohort study using linked administrative health databases from England and Sweden.<h4>Setting and participants</h4>Singleton live births between 2003 and 2012 in England and Sweden, followed up from age 31 days until the fifth birthday, death or 31 December 2013.<h4>Main outcome measures</h4>The main outcome measures were HR for RTI-related mortality at 31-364 days and at 1-4 years and SUDI mortality at 31-364 days in England versus Sweden estimated using Cox proportional hazards models. We calculated unadjusted HRs and HRs adjusted for birth characteristics (gestational age, birth weight, sex and congenital anomalies) and socioeconomic factors (maternal age and socioeconomic status).<h4>Results</h4>The English cohort comprised 3 928 483 births, 768 RTI-related deaths at 31-364 days, 691 RTI-related deaths at 1-4 years and 1166 SUDIs; the corresponding figures for the Swedish cohort were 1 012 682, 131, 118 and 189. At 31-364 days, unadjusted HR for RTI-related death in England versus Sweden was 1.52 (95% CI 1.26 to 1.82). After adjusting for birth characteristics, the HR reduced to 1.16 (95% CI 0.96 to 1.40) and for socioeconomic factors to 1.11 (95% CI 0.92 to 1.34). At 1-4 years, unadjusted HR was 1.58 (95% CI 1.30 to 1.92) and decreased to 1.32 (95% CI 1.09 to 1.61) after adjusting for birth characteristics and to 1.30 (95% CI 1.07 to 1.59) after further adjustment for socioeconomic factors. For SUDI, the respective HRs were 1.59 (95% CI 1.36 to 1.85) in the unadjusted model, and 1.40 (95% CI 1.20 to 1.63) after accounting for birth characteristics and 1.19 (95% CI 1.02 to 1.39) in the fully adjusted model.<h4>Conclusion</h4>Interventions that improve maternal health before and during pregnancy to reduce the prevalence of adverse birth characteristics and address poverty could reduce child mortality due to RTIs and SUDIs in England.","Zylbersztejn et al. shown that helping mothers to have a healthier pregnancy: better mental health before and during pregnancy, reducing birth complications and addressing poverty are the potential areas which can affect reduction of child mortality at birth. ",pdf:https://adc.bmj.com/content/archdischild/105/1/53.full.pdf; doi:https://doi.org/10.1136/archdischild-2018-316693; html:https://europepmc.org/articles/PMC6951233; pdf:https://europepmc.org/articles/PMC6951233?pdf=render
 37291107,https://doi.org/10.1038/s41467-023-38766-1,South Asian medical cohorts reveal strong founder effects and high rates of homozygosity.,"Wall JD, Sathirapongsasuti JF, Gupta R, Rasheed A, Venkatesan R, Belsare S, Menon R, Phalke S, Mittal A, Fang J, Tanneeru D, Deshmukh M, Bassi A, Robinson J, Chaudhary R, Murugan S, Ul-Asar Z, Saleem I, Ishtiaq U, Fatima A, Sheikh SS, Hameed S, Ishaq M, Rasheed SZ, Memon FU, Jalal A, Abbas S, Frossard P, Fuchsberger C, Forer L, Schoenherr S, Bei Q, Bhangale T, Tom J, Gadde SGK, B V P, Naik NK, Wang M, Kwok PY, Khera AV, Lakshmi BR, Butterworth AS, Chowdhury R, Danesh J, di Angelantonio E, Naheed A, Goyal V, Kandadai RM, Kumar H, Borgohain R, Mukherjee A, Wadia PM, Yadav R, Desai S, Kumar N, Biswas A, Pal PK, Muthane UB, Das SK, Ramprasad VL, Kukkle PL, Seshagiri S, Kathiresan S, Ghosh A, Mohan V, Saleheen D, Stawiski EW, Peterson AS.",,Nature communications,2023,2023-06-08,Y,,,,"The benefits of large-scale genetic studies for healthcare of the populations studied are well documented, but these genetic studies have traditionally ignored people from some parts of the world, such as South Asia. Here we describe whole genome sequence (WGS) data from 4806 individuals recruited from the healthcare delivery systems of Pakistan, India and Bangladesh, combined with WGS from 927 individuals from isolated South Asian populations. We characterize population structure in South Asia and describe a genotyping array (SARGAM) and imputation reference panel that are optimized for South Asian genomes. We find evidence for high rates of reproductive isolation, endogamy and consanguinity that vary across the subcontinent and that lead to levels of rare homozygotes that reach 100 times that seen in outbred populations. Founder effects increase the power to associate functional variants with disease processes and make South Asia a uniquely powerful place for population-scale genetic studies.",,pdf:https://www.nature.com/articles/s41467-023-38766-1.pdf; doi:https://doi.org/10.1038/s41467-023-38766-1; html:https://europepmc.org/articles/PMC10250394; pdf:https://europepmc.org/articles/PMC10250394?pdf=render
 33033260,https://doi.org/10.1038/s41467-020-18843-5,Prostate cancer evolution from multilineage primary to single lineage metastases with implications for liquid biopsy.,"Woodcock DJ, Riabchenko E, Taavitsainen S, Kankainen M, Gundem G, Brewer DS, Ellonen P, Lepistö M, Golubeva YA, Warner AC, Tolonen T, Jasu J, Isaacs WB, Emmert-Buck MR, Nykter M, Visakorpi T, Bova GS, Wedge DC.",,Nature communications,2020,2020-10-08,Y,,,,"The evolutionary progression from primary to metastatic prostate cancer is largely uncharted, and the implications for liquid biopsy are unexplored. We infer detailed reconstructions of tumor phylogenies in ten prostate cancer patients with fatal disease, and investigate them in conjunction with histopathology and tumor DNA extracted from blood and cerebrospinal fluid. Substantial evolution occurs within the prostate, resulting in branching into multiple spatially intermixed lineages. One dominant lineage emerges that initiates and drives systemic metastasis, where polyclonal seeding between sites is common. Routes to metastasis differ between patients, and likely genetic drivers of metastasis distinguish the metastatic lineage from the lineage that remains confined to the prostate within each patient. Body fluids capture features of the dominant lineage, and subclonal expansions that occur in the metastatic phase are non-uniformly represented. Cerebrospinal fluid analysis reveals lineages not detected in blood-borne DNA, suggesting possible clinical utility.",,pdf:https://www.nature.com/articles/s41467-020-18843-5.pdf; doi:https://doi.org/10.1038/s41467-020-18843-5; html:https://europepmc.org/articles/PMC7545111; pdf:https://europepmc.org/articles/PMC7545111?pdf=render
-35304391,https://doi.org/10.1136/bmjopen-2021-050610,Results of a pilot feasibility randomised controlled trial exploring the use of an electronic patient-reported outcome measure in the management of UK patients with advanced chronic kidney disease.,"Kyte D, Anderson N, Bishop J, Bissell A, Brettell E, Calvert M, Chadburn M, Cockwell P, Dutton M, Eddington H, Forster E, Hadley G, Ives NJ, Jackson LJ, O'Brien S, Price G, Sharpe K, Stringer S, Verdi R, Waters J, Wilcockson A.",,BMJ open,2022,2022-03-18,Y,Clinical Trials; Nephrology; End Stage Renal Failure,,,"<h4>Objectives</h4>The use of routine remote follow-up of patients with chronic kidney disease (CKD) is increasing exponentially. It has been suggested that online electronic patient-reported outcome measures (ePROMs) could be used in parallel, to facilitate real-time symptom monitoring aimed at improving outcomes. We tested the feasibility of this approach in a pilot trial of ePROM symptom monitoring versus usual care in patients with advanced CKD not on dialysis.<h4>Design</h4>A 12-month, parallel, pilot randomised controlled trial (RCT) and qualitative substudy.<h4>Setting and participants</h4>Queen Elizabeth Hospital Birmingham, UK. Adult patients with advanced CKD (estimated glomerular filtration rate ≥6 and ≤15 mL/min/1.73 m<sup>2</sup>, or a projected risk of progression to kidney failure within 2 years ≥20%).<h4>Intervention</h4>Monthly online ePROM symptom reporting, including automated feedback of tailored self-management advice and triggered clinical notifications in the advent of severe symptoms. Real-time ePROM data were made available to the clinical team via the electronic medical record.<h4>Outcomes</h4>Feasibility (recruitment and retention rates, and acceptability/adherence to the ePROM intervention). Health-related quality of life, clinical data (eg, measures of kidney function, kidney failure, hospitalisation, death) and healthcare utilisation.<h4>Results</h4>52 patients were randomised (31% of approached). Case report form returns were high (99.5%), as was retention (96%). Overall, 73% of expected ePROM questionnaires were received. Intervention adherence was high beyond 90 days (74%) and 180 days (65%); but dropped beyond 270 days (46%). Qualitative interviews supported proof of concept and intervention acceptability, but highlighted necessary changes aimed at enhancing overall functionality/scalability of the ePROM system.<h4>Limitations</h4>Small sample size.<h4>Conclusions</h4>This pilot trial demonstrates that patients are willing to be randomised to a trial assessing ePROM symptom monitoring. The intervention was considered acceptable; though measures to improve longer-term engagement are needed. A full-scale RCT is considered feasible.<h4>Trial registration number</h4>ISRCTN12669006 and the UK NIHR Portfolio (CPMS ID: 36497).",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/3/e050610.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-050610; html:https://europepmc.org/articles/PMC8935185; pdf:https://europepmc.org/articles/PMC8935185?pdf=render
 31719529,https://doi.org/10.1038/s41467-019-12515-9,Genome-wide association study of eosinophilic granulomatosis with polyangiitis reveals genomic loci stratified by ANCA status.,"Lyons PA, Peters JE, Alberici F, Liley J, Coulson RMR, Astle W, Baldini C, Bonatti F, Cid MC, Elding H, Emmi G, Epplen J, Guillevin L, Jayne DRW, Jiang T, Gunnarsson I, Lamprecht P, Leslie S, Little MA, Martorana D, Moosig F, Neumann T, Ohlsson S, Quickert S, Ramirez GA, Rewerska B, Schett G, Sinico RA, Szczeklik W, Tesar V, Vukcevic D, European Vasculitis Genetics Consortium, Terrier B, Watts RA, Vaglio A, Holle JU, Wallace C, Smith KGC.",,Nature communications,2019,2019-11-12,Y,,Understanding the Causes of Disease,,"Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare inflammatory disease of unknown cause. 30% of patients have anti-neutrophil cytoplasmic antibodies (ANCA) specific for myeloperoxidase (MPO). Here, we describe a genome-wide association study in 676 EGPA cases and 6809 controls, that identifies 4 EGPA-associated loci through conventional case-control analysis, and 4 additional associations through a conditional false discovery rate approach. Many variants are also associated with asthma and six are associated with eosinophil count in the general population. Through Mendelian randomisation, we show that a primary tendency to eosinophilia contributes to EGPA susceptibility. Stratification by ANCA reveals that EGPA comprises two genetically and clinically distinct syndromes. MPO+ ANCA EGPA is an eosinophilic autoimmune disease sharing certain clinical features and an HLA-DQ association with MPO+ ANCA-associated vasculitis, while ANCA-negative EGPA may instead have a mucosal/barrier dysfunction origin. Four candidate genes are targets of therapies in development, supporting their exploration in EGPA.","This study aimed to identify parts of the genome that cause a rare inflammatory disease called EGPA, which usually starts with non-specific and common (asthma, raised levels of white blood cells) symptoms, followed by more distinctive patterns of symptoms as the disease progresses. The authors used two different statistical methods to compare the genomes of 534 people with EGPA and 6688 people without EGPA. They identified 8 parts of the genome that are likely to contribute to EGPA, but do not fully explain the disease. The study suggests that there are two types of EGPA that have different symptoms (with/without autoimmune vasculitis) and genetic causes. Four of the parts of the genome identified by the study are the target for drugs that are currently underdevelopment.",pdf:https://www.nature.com/articles/s41467-019-12515-9.pdf; doi:https://doi.org/10.1038/s41467-019-12515-9; html:https://europepmc.org/articles/PMC6851141; pdf:https://europepmc.org/articles/PMC6851141?pdf=render
+35304391,https://doi.org/10.1136/bmjopen-2021-050610,Results of a pilot feasibility randomised controlled trial exploring the use of an electronic patient-reported outcome measure in the management of UK patients with advanced chronic kidney disease.,"Kyte D, Anderson N, Bishop J, Bissell A, Brettell E, Calvert M, Chadburn M, Cockwell P, Dutton M, Eddington H, Forster E, Hadley G, Ives NJ, Jackson LJ, O'Brien S, Price G, Sharpe K, Stringer S, Verdi R, Waters J, Wilcockson A.",,BMJ open,2022,2022-03-18,Y,Clinical Trials; Nephrology; End Stage Renal Failure,,,"<h4>Objectives</h4>The use of routine remote follow-up of patients with chronic kidney disease (CKD) is increasing exponentially. It has been suggested that online electronic patient-reported outcome measures (ePROMs) could be used in parallel, to facilitate real-time symptom monitoring aimed at improving outcomes. We tested the feasibility of this approach in a pilot trial of ePROM symptom monitoring versus usual care in patients with advanced CKD not on dialysis.<h4>Design</h4>A 12-month, parallel, pilot randomised controlled trial (RCT) and qualitative substudy.<h4>Setting and participants</h4>Queen Elizabeth Hospital Birmingham, UK. Adult patients with advanced CKD (estimated glomerular filtration rate ≥6 and ≤15 mL/min/1.73 m<sup>2</sup>, or a projected risk of progression to kidney failure within 2 years ≥20%).<h4>Intervention</h4>Monthly online ePROM symptom reporting, including automated feedback of tailored self-management advice and triggered clinical notifications in the advent of severe symptoms. Real-time ePROM data were made available to the clinical team via the electronic medical record.<h4>Outcomes</h4>Feasibility (recruitment and retention rates, and acceptability/adherence to the ePROM intervention). Health-related quality of life, clinical data (eg, measures of kidney function, kidney failure, hospitalisation, death) and healthcare utilisation.<h4>Results</h4>52 patients were randomised (31% of approached). Case report form returns were high (99.5%), as was retention (96%). Overall, 73% of expected ePROM questionnaires were received. Intervention adherence was high beyond 90 days (74%) and 180 days (65%); but dropped beyond 270 days (46%). Qualitative interviews supported proof of concept and intervention acceptability, but highlighted necessary changes aimed at enhancing overall functionality/scalability of the ePROM system.<h4>Limitations</h4>Small sample size.<h4>Conclusions</h4>This pilot trial demonstrates that patients are willing to be randomised to a trial assessing ePROM symptom monitoring. The intervention was considered acceptable; though measures to improve longer-term engagement are needed. A full-scale RCT is considered feasible.<h4>Trial registration number</h4>ISRCTN12669006 and the UK NIHR Portfolio (CPMS ID: 36497).",,pdf:https://bmjopen.bmj.com/content/bmjopen/12/3/e050610.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-050610; html:https://europepmc.org/articles/PMC8935185; pdf:https://europepmc.org/articles/PMC8935185?pdf=render
 37221040,https://doi.org/10.1136/oemed-2022-108700,"Coverage, completion and outcomes of COVID-19 risk assessments in a multi-ethnic nationwide cohort of UK healthcare workers: a cross-sectional analysis from the UK-REACH Study.","Martin CA, Woolf K, Bryant L, Goss C, Gogoi M, Lagrata S, Papineni P, Qureshi I, Wobi F, Nellums L, Khunti K, Pareek M, UK-REACH Study Collaborative Group.",,Occupational and environmental medicine,2023,2023-05-23,Y,Ethnic Groups; risk assessment; Health Personnel; Covid-19,,,"<h4>Introduction</h4>There are limited data on the outcomes of COVID-19 risk assessment in healthcare workers (HCWs) or the association of ethnicity, other sociodemographic and occupational factors with risk assessment outcomes.<h4>Methods</h4>We used questionnaire data from UK-REACH (UK Research study into Ethnicity And COVID-19 outcomes in Healthcare workers), an ethnically diverse, nationwide cohort of UK HCWs. We derived four binary outcomes: (1) offered a risk assessment; (2) completed a risk assessment; (3) working practices changed as a result of the risk assessment; (4) wanted changes to working practices after risk assessment but working practices did not change.We examined the association of ethnicity, other sociodemographic/occupational factors and actual/perceived COVID-19 risk variables on our outcomes using multivariable logistic regression.<h4>Results</h4>8649 HCWs were included in total. HCWs from ethnic minority groups were more likely to report being offered a risk assessment than white HCWs, and those from Asian and black ethnic groups were more likely to report having completed an assessment if offered. Ethnic minority HCWs had lower odds of reporting having their work change as a result of risk assessment. Those from Asian and black ethnic groups were more likely to report no changes to their working practices despite wanting them.Previous SARS-CoV-2 infection was associated with lower odds of being offered a risk assessment and having adjustments made to working practices.<h4>Discussion</h4>We found differences in risk assessment outcomes by ethnicity, other sociodemographic/occupational factors and actual/perceived COVID-19 risk factors. These findings are concerning and warrant further research using actual (rather than reported) risk assessment outcomes in an unselected cohort.",,pdf:https://oem.bmj.com/content/oemed/80/7/399.full.pdf; doi:https://doi.org/10.1136/oemed-2022-108700; html:https://europepmc.org/articles/PMC10314065; pdf:https://europepmc.org/articles/PMC10314065?pdf=render
 32502668,https://doi.org/10.1016/j.neuroimage.2020.117002,Confound modelling in UK Biobank brain imaging.,"Alfaro-Almagro F, McCarthy P, Afyouni S, Andersson JLR, Bastiani M, Miller KL, Nichols TE, Smith SM.",,NeuroImage,2021,2020-06-02,Y,Image analysis; Machine Learning; Epidemiological Studies; Multi-modal Data Integration; Data Modelling; Confounds; Big Data Imaging; Statistica L Modelling,,,"Dealing with confounds is an essential step in large cohort studies to address problems such as unexplained variance and spurious correlations. UK Biobank is a powerful resource for studying associations between imaging and non-imaging measures such as lifestyle factors and health outcomes, in part because of the large subject numbers. However, the resulting high statistical power also raises the sensitivity to confound effects, which therefore have to be carefully considered. In this work we describe a set of possible confounds (including non-linear effects and interactions that researchers may wish to consider for their studies using such data). We include descriptions of how we can estimate the confounds, and study the extent to which each of these confounds affects the data, and the spurious correlations that may arise if they are not controlled. Finally, we discuss several issues that future studies should consider when dealing with confounds.",,doi:https://doi.org/10.1016/j.neuroimage.2020.117002; doi:https://doi.org/10.1016/j.neuroimage.2020.117002; html:https://europepmc.org/articles/PMC7610719; pdf:https://europepmc.org/articles/PMC7610719?pdf=render
 32025702,https://doi.org/10.1093/gigascience/giaa007,Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines.,"Bush SJ, Foster D, Eyre DW, Clark EL, De Maio N, Shaw LP, Stoesser N, Peto TEA, Crook DW, Walker AS.",,GigaScience,2020,2020-02-01,Y,Bacteria; Evaluation; Benchmarking; Variant Calling; Snp Calling,The Human Phenome,,"<h4>Background</h4>Accurately identifying single-nucleotide polymorphisms (SNPs) from bacterial sequencing data is an essential requirement for using genomics to track transmission and predict important phenotypes such as antimicrobial resistance. However, most previous performance evaluations of SNP calling have been restricted to eukaryotic (human) data. Additionally, bacterial SNP calling requires choosing an appropriate reference genome to align reads to, which, together with the bioinformatic pipeline, affects the accuracy and completeness of a set of SNP calls obtained. This study evaluates the performance of 209 SNP-calling pipelines using a combination of simulated data from 254 strains of 10 clinically common bacteria and real data from environmentally sourced and genomically diverse isolates within the genera Citrobacter, Enterobacter, Escherichia, and Klebsiella.<h4>Results</h4>We evaluated the performance of 209 SNP-calling pipelines, aligning reads to genomes of the same or a divergent strain. Irrespective of pipeline, a principal determinant of reliable SNP calling was reference genome selection. Across multiple taxa, there was a strong inverse relationship between pipeline sensitivity and precision, and the Mash distance (a proxy for average nucleotide divergence) between reads and reference genome. The effect was especially pronounced for diverse, recombinogenic bacteria such as Escherichia coli but less dominant for clonal species such as Mycobacterium tuberculosis.<h4>Conclusions</h4>The accuracy of SNP calling for a given species is compromised by increasing intra-species diversity. When reads were aligned to the same genome from which they were sequenced, among the highest-performing pipelines was Novoalign/GATK. By contrast, when reads were aligned to particularly divergent genomes, the highest-performing pipelines often used the aligners NextGenMap or SMALT, and/or the variant callers LoFreq, mpileup, or Strelka.","The authors compared the accuracy of data processing steps (called bioinformatics pipelines) for identifying different types of bacteria, and which antibiotics they are resistant to. They identified which processes were most likely to introduce errors for different bacteria, and make recommendations about which pipelines should be used.",pdf:https://watermark.silverchair.com/giaa007.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAArgwggK0BgkqhkiG9w0BBwagggKlMIICoQIBADCCApoGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM317Vywl4J0MoRskUAgEQgIICa7pwfJ56Mly4Anv1BPEAmwtKXOLcmFeMLRa66xhgPdK6Ci4Aw3rp4lJMizin326QALNQsODRERKONUxtXgEWVQAk130Fd7XbP6mDWd-0WqGT3cSidkfYveDUH3QNU5fMzLfCj598hrJEAk1z7LTkxKHEy9DQWfFNTCjY53IC7QawbMnwVvVq_lpTKlRP8_qZiTe8qiEKqWNVZ6woCjOc2Rro01EG5_atdzA8zpmJq2R4tx28FbVmIM7dsgYcT7L9DYQIcPQwJxaZSleSNtEyNXeo-WcHn_ezUiaRb0lthzfWPPdge5nY3tlFAelL_HeYo6jn4CkFdniFC28Gr7TuFnrJyj28_OsKYJICwvgwmNPj-T5rf9MGAMgBV3SLK6l87grZuO1r4Q8AfpvbJY9vHrDDayBzhuXMW_g2CFpQDYzMp4tGX8Yu3uS5qDWR81xG0Xqf5p0i0wsw1ZD1ZDA8tla87WrJCjbGwWjoXx2ihhyp6aXc4DC_8FCavms7sXqxQEsoVtDp6hvmpDsPPSvdGRAOjKeaQD2mWFi_3U7ndjd2_0dGVvsD5zDl0_GrRV8QEGNDocCzvibp-DyCby-tfRS4UsoqVA96Gs3ZgVtZzcQbcDt3C069xpbFOJD2rqJ4oyiGdUUh9uWDxgQFKiRvQZbblRH-htJ8tPKjv371GO1Wm6E-asCRSjCkT4vRP3lzDlab36iWZVp5vS5XoumjEnV9wxKBEqkYGywEdZUlG57ygWi11YTdMK3EYXbFqU0xFXvw34Sdl47d5bUDjYEEcxBciYLJqWhQKY9opr4bt5T3SCS107QDE4VOmd4; doi:https://doi.org/10.1093/gigascience/giaa007; html:https://europepmc.org/articles/PMC7002876; pdf:https://europepmc.org/articles/PMC7002876?pdf=render
@@ -2767,8 +2769,8 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 31485076,https://doi.org/10.1038/s41586-019-1530-7,Structures of influenza A virus RNA polymerase offer insight into viral genome replication.,"Fan H, Walker AP, Carrique L, Keown JR, Serna Martin I, Karia D, Sharps J, Hengrung N, Pardon E, Steyaert J, Grimes JM, Fodor E.",,Nature,2019,2019-09-04,Y,,,,"Influenza A viruses are responsible for seasonal epidemics, and pandemics can arise from the transmission of novel zoonotic influenza A viruses to humans<sup>1,2</sup>. Influenza A viruses contain a segmented negative-sense RNA genome, which is transcribed and replicated by the viral-RNA-dependent RNA polymerase (FluPol<sub>A</sub>) composed of PB1, PB2 and PA subunits<sup>3-5</sup>. Although the high-resolution crystal structure of FluPol<sub>A</sub> of bat influenza A virus has previously been reported<sup>6</sup>, there are no complete structures available for human and avian FluPol<sub>A</sub>. Furthermore, the molecular mechanisms of genomic viral RNA (vRNA) replication-which proceeds through a complementary RNA (cRNA) replicative intermediate, and requires oligomerization of the polymerase<sup>7-10</sup>-remain largely unknown. Here, using crystallography and cryo-electron microscopy, we determine the structures of FluPol<sub>A</sub> from human influenza A/NT/60/1968 (H3N2) and avian influenza A/duck/Fujian/01/2002 (H5N1) viruses at a resolution of 3.0-4.3 Å, in the presence or absence of a cRNA or vRNA template. In solution, FluPol<sub>A</sub> forms dimers of heterotrimers through the C-terminal domain of the PA subunit, the thumb subdomain of PB1 and the N1 subdomain of PB2. The cryo-electron microscopy structure of monomeric FluPol<sub>A</sub> bound to the cRNA template reveals a binding site for the 3' cRNA at the dimer interface. We use a combination of cell-based and in vitro assays to show that the interface of the FluPol<sub>A</sub> dimer is required for vRNA synthesis during replication of the viral genome. We also show that a nanobody (a single-domain antibody) that interferes with FluPol<sub>A</sub> dimerization inhibits the synthesis of vRNA and, consequently, inhibits virus replication in infected cells. Our study provides high-resolution structures of medically relevant FluPol<sub>A</sub>, as well as insights into the replication mechanisms of the viral RNA genome. In addition, our work identifies sites in FluPol<sub>A</sub> that could be targeted in the development of antiviral drugs.",,pdf:https://europepmc.org/articles/pmc6795553?pdf=render; doi:https://doi.org/10.1038/s41586-019-1530-7; html:https://europepmc.org/articles/PMC6795553; pdf:https://europepmc.org/articles/PMC6795553?pdf=render
 36109769,https://doi.org/10.1186/s13059-022-02757-0,Genetic regulation of RNA splicing in human pancreatic islets.,"Atla G, Bonàs-Guarch S, Cuenca-Ardura M, Beucher A, Crouch DJM, Garcia-Hurtado J, Moran I, T2DSystems Consortium, Irimia M, Prasad RB, Gloyn AL, Marselli L, Suleiman M, Berney T, de Koning EJP, Kerr-Conte J, Pattou F, Todd JA, Piemonti L, Ferrer J.",,Genome biology,2022,2022-09-15,Y,RNA splicing; Senescence; Quantitative trait loci; Type 2 diabetes; type 1 diabetes; pancreatic islets; Beta Cells; Twas; G-protein Signaling; Pancreatic Beta-cells; Ctrb2; Diabetes Pathophysiology,,,"<h4>Background</h4>Non-coding genetic variants that influence gene transcription in pancreatic islets play a major role in the susceptibility to type 2 diabetes (T2D), and likely also contribute to type 1 diabetes (T1D) risk. For many loci, however, the mechanisms through which non-coding variants influence diabetes susceptibility are unknown.<h4>Results</h4>We examine splicing QTLs (sQTLs) in pancreatic islets from 399 human donors and observe that common genetic variation has a widespread influence on the splicing of genes with established roles in islet biology and diabetes. In parallel, we profile expression QTLs (eQTLs) and use transcriptome-wide association as well as genetic co-localization studies to assign islet sQTLs or eQTLs to T2D and T1D susceptibility signals, many of which lack candidate effector genes. This analysis reveals biologically plausible mechanisms, including the association of T2D with an sQTL that creates a nonsense isoform in ERO1B, a regulator of ER-stress and proinsulin biosynthesis. The expanded list of T2D risk effector genes reveals overrepresented pathways, including regulators of G-protein-mediated cAMP production. The analysis of sQTLs also reveals candidate effector genes for T1D susceptibility such as DCLRE1B, a senescence regulator, and lncRNA MEG3.<h4>Conclusions</h4>These data expose widespread effects of common genetic variants on RNA splicing in pancreatic islets. The results support a role for splicing variation in diabetes susceptibility, and offer a new set of genetic targets with potential therapeutic benefit.",,pdf:https://genomebiology.biomedcentral.com/counter/pdf/10.1186/s13059-022-02757-0; doi:https://doi.org/10.1186/s13059-022-02757-0; html:https://europepmc.org/articles/PMC9479353; pdf:https://europepmc.org/articles/PMC9479353?pdf=render
 33595074,https://doi.org/10.1093/aje/kwab031,Prediction of Cardiovascular Disease Risk Accounting for Future Initiation of Statin Treatment.,"Xu Z, Arnold M, Stevens D, Kaptoge S, Pennells L, Sweeting MJ, Barrett J, Di Angelantonio E, Wood AM.",,American journal of epidemiology,2021,2021-10-01,Y,Longitudinal data; Cardiovascular disease; Risk Prediction; Electronic Health Records; Treatment Drop-in; Future Statin Initiation,,,"Cardiovascular disease (CVD) risk-prediction models are used to identify high-risk individuals and guide statin initiation. However, these models are usually derived from individuals who might initiate statins during follow-up. We present a simple approach to address statin initiation to predict ""statin-naive"" CVD risk. We analyzed primary care data (2004-2017) from the UK Clinical Practice Research Datalink for 1,678,727 individuals (aged 40-85 years) without CVD or statin treatment history at study entry. We derived age- and sex-specific prediction models including conventional risk factors and a time-dependent effect of statin initiation constrained to 25% risk reduction (from trial results). We compared predictive performance and measures of public-health impact (e.g., number needed to screen to prevent 1 event) against models ignoring statin initiation. During a median follow-up of 8.9 years, 103,163 individuals developed CVD. In models accounting for (versus ignoring) statin initiation, 10-year CVD risk predictions were slightly higher; predictive performance was moderately improved. However, few individuals were reclassified to a high-risk threshold, resulting in negligible improvements in number needed to screen to prevent 1 event. In conclusion, incorporating statin effects from trial results into risk-prediction models enables statin-naive CVD risk estimation and provides moderate gains in predictive ability but had a limited impact on treatment decision-making under current guidelines in this population.",,pdf:https://academic.oup.com/aje/article-pdf/190/10/2000/40491073/kwab031.pdf; doi:https://doi.org/10.1093/aje/kwab031; html:https://europepmc.org/articles/PMC8485151; pdf:https://europepmc.org/articles/PMC8485151?pdf=render
-32702746,https://doi.org/10.1093/eurheartj/ehaa531,Genetic variability in the absorption of dietary sterols affects the risk of coronary artery disease.,"Helgadottir A, Thorleifsson G, Alexandersson KF, Tragante V, Thorsteinsdottir M, Eiriksson FF, Gretarsdottir S, Björnsson E, Magnusson O, Sveinbjornsson G, Jonsdottir I, Steinthorsdottir V, Ferkingstad E, Jensson BÖ, Stefansson H, Olafsson I, Christensen AH, Torp-Pedersen C, Køber L, Pedersen OB, Erikstrup C, Sørensen E, Brunak S, Banasik K, Hansen TF, Nyegaard M, Eyjolfssson GI, Sigurdardottir O, Thorarinsson BL, Matthiasson SE, Steingrimsdottir T, Bjornsson ES, Danielsen R, Asselbergs FW, Arnar DO, Ullum H, Bundgaard H, Sulem P, Thorsteinsdottir U, Thorgeirsson G, Holm H, Gudbjartsson DF, Stefansson K.",,European heart journal,2020,2020-07-01,Y,Genetics; Absorption; phytosterols; Dietary Cholesterol; Abcg5/8,,,"<h4>Aims</h4>To explore whether variability in dietary cholesterol and phytosterol absorption impacts the risk of coronary artery disease (CAD) using as instruments sequence variants in the ABCG5/8 genes, key regulators of intestinal absorption of dietary sterols.<h4>Methods and results</h4>We examined the effects of ABCG5/8 variants on non-high-density lipoprotein (non-HDL) cholesterol (N up to 610 532) and phytosterol levels (N = 3039) and the risk of CAD in Iceland, Denmark, and the UK Biobank (105 490 cases and 844 025 controls). We used genetic scores for non-HDL cholesterol to determine whether ABCG5/8 variants confer greater risk of CAD than predicted by their effect on non-HDL cholesterol. We identified nine rare ABCG5/8 coding variants with substantial impact on non-HDL cholesterol. Carriers have elevated phytosterol levels and are at increased risk of CAD. Consistent with impact on ABCG5/8 transporter function in hepatocytes, eight rare ABCG5/8 variants associate with gallstones. A genetic score of ABCG5/8 variants predicting 1 mmol/L increase in non-HDL cholesterol associates with two-fold increase in CAD risk [odds ratio (OR) = 2.01, 95% confidence interval (CI) 1.75-2.31, P = 9.8 × 10-23] compared with a 54% increase in CAD risk (OR = 1.54, 95% CI 1.49-1.59, P = 1.1 × 10-154) associated with a score of other non-HDL cholesterol variants predicting the same increase in non-HDL cholesterol (P for difference in effects = 2.4 × 10-4).<h4>Conclusions</h4>Genetic variation in cholesterol absorption affects levels of circulating non-HDL cholesterol and risk of CAD. Our results indicate that both dietary cholesterol and phytosterols contribute directly to atherogenesis.",,pdf:https://academic.oup.com/eurheartj/article-pdf/41/28/2618/33526677/ehaa531.pdf; doi:https://doi.org/10.1093/eurheartj/ehaa531; html:https://europepmc.org/articles/PMC7377579; pdf:https://europepmc.org/articles/PMC7377579?pdf=render
 33277303,https://doi.org/10.2337/dc20-1137,Sex Differences in the Risk of Coronary Heart Disease Associated With Type 2 Diabetes: A Mendelian Randomization Analysis.,"Peters TM, Holmes MV, Richards JB, Palmer T, Forgetta V, Lindgren CM, Asselbergs FW, Nelson CP, Samani NJ, McCarthy MI, Mahajan A, Davey Smith G, Woodward M, O'Keeffe LM, Peters SAE.",,Diabetes care,2021,2020-12-04,Y,,,,"<h4>Objective</h4>Observational studies have demonstrated that type 2 diabetes is a stronger risk factor for coronary heart disease (CHD) in women compared with men. However, it is not clear whether this reflects a sex differential in the causal effect of diabetes on CHD risk or results from sex-specific residual confounding.<h4>Research design and methods</h4>Using 270 single nucleotide polymorphisms (SNPs) for type 2 diabetes identified in a type 2 diabetes genome-wide association study, we performed a sex-stratified Mendelian randomization (MR) study of type 2 diabetes and CHD using individual participant data in UK Biobank (251,420 women and 212,049 men). Weighted median, MR-Egger, MR-pleiotropy residual sum and outlier, and radial MR from summary-level analyses were used for pleiotropy assessment.<h4>Results</h4>MR analyses showed that genetic risk of type 2 diabetes increased the odds of CHD for women (odds ratio 1.13 [95% CI 1.08-1.18] per 1-log unit increase in odds of type 2 diabetes) and men (1.21 [1.17-1.26] per 1-log unit increase in odds of type 2 diabetes). Sensitivity analyses showed some evidence of directional pleiotropy; however, results were similar after correction for outlier SNPs.<h4>Conclusions</h4>This MR analysis supports a causal effect of genetic liability to type 2 diabetes on risk of CHD that is not stronger for women than men. Assuming a lack of bias, these findings suggest that the prevention and management of type 2 diabetes for CHD risk reduction is of equal priority in both sexes.",,pdf:https://care.diabetesjournals.org/content/diacare/44/2/556.full.pdf; doi:https://doi.org/10.2337/dc20-1137; html:https://europepmc.org/articles/PMC7818328; pdf:https://europepmc.org/articles/PMC7818328?pdf=render
+32702746,https://doi.org/10.1093/eurheartj/ehaa531,Genetic variability in the absorption of dietary sterols affects the risk of coronary artery disease.,"Helgadottir A, Thorleifsson G, Alexandersson KF, Tragante V, Thorsteinsdottir M, Eiriksson FF, Gretarsdottir S, Björnsson E, Magnusson O, Sveinbjornsson G, Jonsdottir I, Steinthorsdottir V, Ferkingstad E, Jensson BÖ, Stefansson H, Olafsson I, Christensen AH, Torp-Pedersen C, Køber L, Pedersen OB, Erikstrup C, Sørensen E, Brunak S, Banasik K, Hansen TF, Nyegaard M, Eyjolfssson GI, Sigurdardottir O, Thorarinsson BL, Matthiasson SE, Steingrimsdottir T, Bjornsson ES, Danielsen R, Asselbergs FW, Arnar DO, Ullum H, Bundgaard H, Sulem P, Thorsteinsdottir U, Thorgeirsson G, Holm H, Gudbjartsson DF, Stefansson K.",,European heart journal,2020,2020-07-01,Y,Genetics; Absorption; phytosterols; Dietary Cholesterol; Abcg5/8,,,"<h4>Aims</h4>To explore whether variability in dietary cholesterol and phytosterol absorption impacts the risk of coronary artery disease (CAD) using as instruments sequence variants in the ABCG5/8 genes, key regulators of intestinal absorption of dietary sterols.<h4>Methods and results</h4>We examined the effects of ABCG5/8 variants on non-high-density lipoprotein (non-HDL) cholesterol (N up to 610 532) and phytosterol levels (N = 3039) and the risk of CAD in Iceland, Denmark, and the UK Biobank (105 490 cases and 844 025 controls). We used genetic scores for non-HDL cholesterol to determine whether ABCG5/8 variants confer greater risk of CAD than predicted by their effect on non-HDL cholesterol. We identified nine rare ABCG5/8 coding variants with substantial impact on non-HDL cholesterol. Carriers have elevated phytosterol levels and are at increased risk of CAD. Consistent with impact on ABCG5/8 transporter function in hepatocytes, eight rare ABCG5/8 variants associate with gallstones. A genetic score of ABCG5/8 variants predicting 1 mmol/L increase in non-HDL cholesterol associates with two-fold increase in CAD risk [odds ratio (OR) = 2.01, 95% confidence interval (CI) 1.75-2.31, P = 9.8 × 10-23] compared with a 54% increase in CAD risk (OR = 1.54, 95% CI 1.49-1.59, P = 1.1 × 10-154) associated with a score of other non-HDL cholesterol variants predicting the same increase in non-HDL cholesterol (P for difference in effects = 2.4 × 10-4).<h4>Conclusions</h4>Genetic variation in cholesterol absorption affects levels of circulating non-HDL cholesterol and risk of CAD. Our results indicate that both dietary cholesterol and phytosterols contribute directly to atherogenesis.",,pdf:https://academic.oup.com/eurheartj/article-pdf/41/28/2618/33526677/ehaa531.pdf; doi:https://doi.org/10.1093/eurheartj/ehaa531; html:https://europepmc.org/articles/PMC7377579; pdf:https://europepmc.org/articles/PMC7377579?pdf=render
 32690604,https://doi.org/10.1136/gutjnl-2019-319866,Image-based consensus molecular subtype (imCMS) classification of colorectal cancer using deep learning.,"Sirinukunwattana K, Domingo E, Richman SD, Redmond KL, Blake A, Verrill C, Leedham SJ, Chatzipli A, Hardy C, Whalley CM, Wu CH, Beggs AD, McDermott U, Dunne PD, Meade A, Walker SM, Murray GI, Samuel L, Seymour M, Tomlinson I, Quirke P, Maughan T, Rittscher J, Koelzer VH, S:CORT consortium.",,Gut,2021,2020-07-20,Y,Molecular Pathology; Computerised Image Analysis; Colorectal Pathology,,,"<h4>Objective</h4>Complex phenotypes captured on histological slides represent the biological processes at play in individual cancers, but the link to underlying molecular classification has not been clarified or systematised. In colorectal cancer (CRC), histological grading is a poor predictor of disease progression, and consensus molecular subtypes (CMSs) cannot be distinguished without gene expression profiling. We hypothesise that image analysis is a cost-effective tool to associate complex features of tissue organisation with molecular and outcome data and to resolve unclassifiable or heterogeneous cases. In this study, we present an image-based approach to predict CRC CMS from standard H&E sections using deep learning.<h4>Design</h4>Training and evaluation of a neural network were performed using a total of n=1206 tissue sections with comprehensive multi-omic data from three independent datasets (training on FOCUS trial, n=278 patients; test on rectal cancer biopsies, GRAMPIAN cohort, n=144 patients; and The Cancer Genome Atlas (TCGA), n=430 patients). Ground truth CMS calls were ascertained by matching random forest and single sample predictions from CMS classifier.<h4>Results</h4>Image-based CMS (imCMS) accurately classified slides in unseen datasets from TCGA (n=431 slides, AUC)=0.84) and rectal cancer biopsies (n=265 slides, AUC=0.85). imCMS spatially resolved intratumoural heterogeneity and provided secondary calls correlating with bioinformatic prediction from molecular data. imCMS classified samples previously unclassifiable by RNA expression profiling, reproduced the expected correlations with genomic and epigenetic alterations and showed similar prognostic associations as transcriptomic CMS.<h4>Conclusion</h4>This study shows that a prediction of RNA expression classifiers can be made from H&E images, opening the door to simple, cheap and reliable biological stratification within routine workflows.",,pdf:https://gut.bmj.com/content/gutjnl/70/3/544.full.pdf; doi:https://doi.org/10.1136/gutjnl-2019-319866; html:https://europepmc.org/articles/PMC7873419; pdf:https://europepmc.org/articles/PMC7873419?pdf=render
 39437787,https://doi.org/10.1016/j.xgen.2024.100679,Mechanism-free repurposing of drugs for C9orf72-related ALS/FTD using large-scale genomic data.,"Saez-Atienzar S, Souza CDS, Chia R, Beal SN, Lorenzini I, Huang R, Levy J, Burciu C, Ding J, Gibbs JR, Jones A, Dewan R, Pensato V, Peverelli S, Corrado L, van Vugt JJFA, van Rheenen W, Tunca C, Bayraktar E, Xia M, International ALS Genomics Consortium, ITALSGEN Consortium, SLAGEN Consortium, Project MinE ALS Sequencing Consortium, Iacoangeli A, Shatunov A, Tiloca C, Ticozzi N, Verde F, Mazzini L, Kenna K, Al Khleifat A, Opie-Martin S, Raggi F, Filosto M, Piccinelli SC, Padovani A, Gagliardi S, Inghilleri M, Ferlini A, Vasta R, Calvo A, Moglia C, Canosa A, Manera U, Grassano M, Mandrioli J, Mora G, Lunetta C, Tanel R, Trojsi F, Cardinali P, Gallone S, Brunetti M, Galimberti D, Serpente M, Fenoglio C, Scarpini E, Comi GP, Corti S, Del Bo R, Ceroni M, Pinter GL, Taroni F, Bella ED, Bersano E, Curtis CJ, Lee SH, Chung R, Patel H, Morrison KE, Cooper-Knock J, Shaw PJ, Breen G, Dobson RJB, Dalgard CL, American Genome Center, Scholz SW, Al-Chalabi A, van den Berg LH, McLaughlin R, Hardiman O, Cereda C, Sorarù G, D'Alfonso S, Chandran S, Pal S, Ratti A, Gellera C, Johnson K, Doucet-O'Hare T, Pasternack N, Wang T, Nath A, Siciliano G, Silani V, Başak AN, Veldink JH, Camu W, Glass JD, Landers JE, Chiò A, Sattler R, Shaw CE, Ferraiuolo L, Fogh I, Traynor BJ.",,Cell genomics,2024,2024-10-19,N,Translation; Amyotrophic Lateral Sclerosis; Frontotemporal Dementia; Acamprosate; Drug Repurposing; Age At Onset; C9orf72,,,"Repeat expansions in the C9orf72 gene are the most common genetic cause of (ALS) and frontotemporal dementia (FTD). Like other genetic forms of neurodegeneration, pinpointing the precise mechanism(s) by which this mutation leads to neuronal death remains elusive, and this lack of knowledge hampers the development of therapy for C9orf72-related disease. We used an agnostic approach based on genomic data (n = 41,273 ALS and healthy samples, and n = 1,516 C9orf72 carriers) to overcome these bottlenecks. Our drug-repurposing screen, based on gene- and expression-pattern matching and information about the genetic variants influencing onset age among C9orf72 carriers, identified acamprosate, a γ-aminobutyric acid analog, as a potentially repurposable treatment for patients carrying C9orf72 repeat expansions. We validated its neuroprotective effect in cell models and showed comparable efficacy to riluzole, the current standard of care. Our work highlights the potential value of genomics in repurposing drugs in situations where the underlying pathomechanisms are inherently complex. VIDEO ABSTRACT.",,doi:https://doi.org/10.1016/j.xgen.2024.100679
 34107928,https://doi.org/10.1186/s12913-021-06509-x,Importance of patient bed pathways and length of stay differences in predicting COVID-19 hospital bed occupancy in England.,"Leclerc QJ, Fuller NM, Keogh RH, Diaz-Ordaz K, Sekula R, Semple MG, ISARIC4C Investigators, CMMID COVID-19 Working Group, Atkins KE, Procter SR, Knight GM.",,BMC health services research,2021,2021-06-09,Y,Length Of Stay; Hospitalisation; Bed Occupancy; Covid-19; Sars-cov-2; Bed Pathway,,,"<h4>Background</h4>Predicting bed occupancy for hospitalised patients with COVID-19 requires understanding of length of stay (LoS) in particular bed types. LoS can vary depending on the patient's ""bed pathway"" - the sequence of transfers of individual patients between bed types during a hospital stay. In this study, we characterise these pathways, and their impact on predicted hospital bed occupancy.<h4>Methods</h4>We obtained data from University College Hospital (UCH) and the ISARIC4C COVID-19 Clinical Information Network (CO-CIN) on hospitalised patients with COVID-19 who required care in general ward or critical care (CC) beds to determine possible bed pathways and LoS. We developed a discrete-time model to examine the implications of using either bed pathways or only average LoS by bed type to forecast bed occupancy. We compared model-predicted bed occupancy to publicly available bed occupancy data on COVID-19 in England between March and August 2020.<h4>Results</h4>In both the UCH and CO-CIN datasets, 82% of hospitalised patients with COVID-19 only received care in general ward beds. We identified four other bed pathways, present in both datasets: ""Ward, CC, Ward"", ""Ward, CC"", ""CC"" and ""CC, Ward"". Mean LoS varied by bed type, pathway, and dataset, between 1.78 and 13.53 days. For UCH, we found that using bed pathways improved the accuracy of bed occupancy predictions, while only using an average LoS for each bed type underestimated true bed occupancy. However, using the CO-CIN LoS dataset we were not able to replicate past data on bed occupancy in England, suggesting regional LoS heterogeneities.<h4>Conclusions</h4>We identified five bed pathways, with substantial variation in LoS by bed type, pathway, and geography. This might be caused by local differences in patient characteristics, clinical care strategies, or resource availability, and suggests that national LoS averages may not be appropriate for local forecasts of bed occupancy for COVID-19.<h4>Trial registration</h4>The ISARIC WHO CCP-UK study ISRCTN66726260 was retrospectively registered on 21/04/2020 and designated an Urgent Public Health Research Study by NIHR.",,pdf:https://bmchealthservres.biomedcentral.com/counter/pdf/10.1186/s12913-021-06509-x; doi:https://doi.org/10.1186/s12913-021-06509-x; html:https://europepmc.org/articles/PMC8188158; pdf:https://europepmc.org/articles/PMC8188158?pdf=render
@@ -2798,12 +2800,12 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 33991015,https://doi.org/10.1002/alz.12330,TMEM106B and CPOX are genetic determinants of cerebrospinal fluid Alzheimer's disease biomarker levels.,"Hong S, Dobricic V, Ohlei O, Bos I, Vos SJB, Prokopenko D, Tijms BM, Andreasson U, Blennow K, Vandenberghe R, Gabel S, Scheltens P, Teunissen CE, Engelborghs S, Frisoni G, Blin O, Richardson JC, Bordet R, Alzheimer's Disease Neuroimaging Initiative (ADNI), Lleó A, Alcolea D, Popp J, Clark C, Peyratout G, Martinez-Lage P, Tainta M, Dobson RJB, Legido-Quigley C, Sleegers K, Van Broeckhoven C, Tanzi RE, Ten Kate M, Wittig M, Franke A, Lill CM, Barkhof F, Lovestone S, Streffer J, Zetterberg H, Visser PJ, Bertram L.",,Alzheimer's & dementia : the journal of the Alzheimer's Association,2021,2021-05-14,N,Cerebrospinal fluid; Alzheimer's disease; Biomarker; Genome-wide Association Study; Neurogranin; Neurofilament Light; Chitinase-3-like Protein 1,,,"<h4>Introduction</h4>Neurofilament light (NfL), chitinase-3-like protein 1 (YKL-40), and neurogranin (Ng) are biomarkers for Alzheimer's disease (AD) to monitor axonal damage, astroglial activation, and synaptic degeneration, respectively.<h4>Methods</h4>We performed genome-wide association studies (GWAS) using DNA and cerebrospinal fluid (CSF) samples from the EMIF-AD Multimodal Biomarker Discovery study for discovery, and the Alzheimer's Disease Neuroimaging Initiative study for validation analyses. GWAS were performed for all three CSF biomarkers using linear regression models adjusting for relevant covariates.<h4>Results</h4>We identify novel genome-wide significant associations between DNA variants in TMEM106B and CSF levels of NfL, and between CPOX and YKL-40. We confirm previous work suggesting that YKL-40 levels are associated with DNA variants in CHI3L1.<h4>Discussion</h4>Our study provides important new insights into the genetic architecture underlying interindividual variation in three AD-related CSF biomarkers. In particular, our data shed light on the sequence of events regarding the initiation and progression of neuropathological processes relevant in AD.",,pdf:https://ddd.uab.cat/pub/artpub/2021/270272/270272.pdf; doi:https://doi.org/10.1002/alz.12330
 34759005,https://doi.org/10.1136/bmj-2021-065805,Effect of nutritionally modified infant formula on academic performance: linkage of seven dormant randomised controlled trials to national education data.,"Verfürden ML, Gilbert R, Lucas A, Jerrim J, Fewtrell M.",,BMJ (Clinical research ed.),2021,2021-11-10,Y,,,,"<h4>Objective</h4>To compare differences in academic performance between adolescents who were randomised in infancy to modified or standard infant formula.<h4>Design</h4>Linkage of seven dormant randomised controlled trials to national education data.<h4>Setting</h4>Five hospitals in England, 11 August 1993 to 29 October 2001, and schools in England, September 2002 to August 2016.<h4>Participants</h4>1763 adolescents (425 born preterm, 299 born at term and small for gestational age, 1039 born at term) who took part in one of seven randomised controlled trials of infant formula in infancy.<h4>Interventions</h4>Nutrient enriched versus standard term formula (two trials), long chain polyunsaturated fatty acid (LCPUFA) supplemented versus unsupplemented formula (two trials), high versus low iron follow-on formula (one trial), high versus low sn-2 palmitate formula (one trial), and nucleotide supplemented versus unsupplemented formula (one trial).<h4>Main outcome measures</h4>The primary outcome, determined by linkage of trial data to school data, was the mean difference in standard deviation scores for mandated examinations in mathematics at age 16 years. Secondary outcomes included differences in standard deviation scores in English (16 and 11 years) and mathematics (11 years). Analysis was by intention to treat with multiple imputation for participants missing the primary outcome.<h4>Results</h4>1607 (91.2%) participants were linked to school records. No benefit was found for performance in mathematics examinations at age 16 years for any modified formula: nutrient enriched in preterm infants after discharge from hospital, standard deviation score 0.02 (95% confidence interval -0.22 to 0.27), and nutrient enriched in small for gestational age term infants -0.11 (-0.33 to 0.12); LCPUFA supplemented in preterm infants -0.19 (-0.46 to 0.08) and in term infants -0.14 (-0.36 to 0.08); iron follow-on formula in term infants -0.12 (-0.31 to 0.07); and sn-2 palmitate supplemented formula in term infants -0.09 (-0.37 to 0.19). Participants from the nucleotide trial were too young to have sat their General Certificate of Secondary Education (GCSE) examinations at the time of linkage to school data. Secondary outcomes did not differ for nutrient enriched, high iron, sn-2 palmitate, or nucleotide supplemented formulas, but at 11 years, preterm and term participants randomised to LCPUFA supplemented formula scored lower in English and mathematics.<h4>Conclusions</h4>Evidence from these randomised controlled trials indicated that the infant formula modifications did not promote long term cognitive benefit compared with standard infant formulas.",,pdf:https://www.bmj.com/content/bmj/375/bmj-2021-065805.full.pdf; doi:https://doi.org/10.1136/bmj-2021-065805; html:https://europepmc.org/articles/PMC8579423
 34135082,https://doi.org/10.1681/asn.2020071070,Plasma Proteomics of Renal Function: A Transethnic Meta-Analysis and Mendelian Randomization Study.,"Matías-García PR, Wilson R, Guo Q, Zaghlool SB, Eales JM, Xu X, Charchar FJ, Dormer J, Maalmi H, Schlosser P, Elhadad MA, Nano J, Sharma S, Peters A, Fornoni A, Mook-Kanamori DO, Winkelmann J, Danesh J, Di Angelantonio E, Ouwehand WH, Watkins NA, Roberts DJ, Petrera A, Graumann J, Koenig W, Hveem K, Jonasson C, Köttgen A, Butterworth A, Prunotto M, Hauck SM, Herder C, Suhre K, Gieger C, Tomaszewski M, Teumer A, Teumer A, Waldenberger M, Human Kidney Tissue Resource.",,Journal of the American Society of Nephrology : JASN,2021,2021-06-16,N,Genetic epidemiology; glomerular filtration rate; Gene Expression; Plasma Proteomics; Chronic Kidney Disease; Biomarker Discovery; Mendelian Randomization; Epidemiology And Outcomes; Testican-2,,,"<h4>Background</h4>Studies on the relationship between renal function and the human plasma proteome have identified several potential biomarkers. However, investigations have been conducted largely in European populations, and causality of the associations between plasma proteins and kidney function has never been addressed.<h4>Methods</h4>A cross-sectional study of 993 plasma proteins among 2882 participants in four studies of European and admixed ancestries (KORA, INTERVAL, HUNT, QMDiab) identified transethnic associations between eGFR/CKD and proteomic biomarkers. For the replicated associations, two-sample bidirectional Mendelian randomization (MR) was used to investigate potential causal relationships. Publicly available datasets and transcriptomic data from independent studies were used to examine the association between gene expression in kidney tissue and eGFR.<h4>Results</h4>In total, 57 plasma proteins were associated with eGFR, including one novel protein. Of these, 23 were additionally associated with CKD. The strongest inferred causal effect was the positive effect of eGFR on testican-2, in line with the known biological role of this protein and the expression of its protein-coding gene (<i>SPOCK2</i>) in renal tissue. We also observed suggestive evidence of an effect of melanoma inhibitory activity (MIA), carbonic anhydrase III, and cystatin-M on eGFR.<h4>Conclusions</h4>In a discovery-replication setting, we identified 57 proteins transethnically associated with eGFR. The revealed causal relationships are an important stepping stone in establishing testican-2 as a clinically relevant physiological marker of kidney disease progression, and point to additional proteins warranting further investigation.",,pdf:https://jasn.asnjournals.org/content/jnephrol/32/7/1747.full.pdf; doi:https://doi.org/10.1681/ASN.2020071070; html:https://europepmc.org/articles/PMC8425654; doi:https://doi.org/10.1681/asn.2020071070
-32814572,https://doi.org/10.1186/s12916-020-01712-9,The effect of travel restrictions on the geographical spread of COVID-19 between large cities in China: a modelling study.,"Quilty BJ, Diamond C, Liu Y, Gibbs H, Russell TW, Jarvis CI, Prem K, Pearson CAB, Clifford S, Flasche S, CMMID COVID-19 working group, Klepac P, Eggo RM, Jit M.",,BMC medicine,2020,2020-08-19,Y,China; Wuhan; Mobility; Delay; Outbreaks; Modelling; Travel Restrictions; Covid-19; Sars-cov-2; Cordon Sanitaire,,,"<h4>Background</h4>To contain the spread of COVID-19, a cordon sanitaire was put in place in Wuhan prior to the Lunar New Year, on 23 January 2020. We assess the efficacy of the cordon sanitaire to delay the introduction and onset of local transmission of COVID-19 in other major cities in mainland China.<h4>Methods</h4>We estimated the number of infected travellers from Wuhan to other major cities in mainland China from November 2019 to February 2020 using previously estimated COVID-19 prevalence in Wuhan and publicly available mobility data. We focused on Beijing, Chongqing, Hangzhou, and Shenzhen as four representative major cities to identify the potential independent contribution of the cordon sanitaire and holiday travel. To do this, we simulated outbreaks generated by infected arrivals in these destination cities using stochastic branching processes. We also modelled the effect of the cordon sanitaire in combination with reduced transmissibility scenarios to simulate the effect of local non-pharmaceutical interventions.<h4>Results</h4>We find that in the four cities, given the potentially high prevalence of COVID-19 in Wuhan between December 2019 and early January 2020, local transmission may have been seeded as early as 1-8 January 2020. By the time the cordon sanitaire was imposed, infections were likely in the thousands. The cordon sanitaire alone did not substantially affect the epidemic progression in these cities, although it may have had some effect in smaller cities. Reduced transmissibility resulted in a notable decrease in the incidence of infection in the four studied cities.<h4>Conclusions</h4>Our results indicate that sustained transmission was likely occurring several weeks prior to the implementation of the cordon sanitaire in four major cities of mainland China and that the observed decrease in incidence was likely attributable to other non-pharmaceutical, transmission-reducing interventions.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-020-01712-9; doi:https://doi.org/10.1186/s12916-020-01712-9; html:https://europepmc.org/articles/PMC7437104; pdf:https://europepmc.org/articles/PMC7437104?pdf=render
+32814572,https://doi.org/10.1186/s12916-020-01712-9,The effect of travel restrictions on the geographical spread of COVID-19 between large cities in China: a modelling study.,"Quilty BJ, Diamond C, Liu Y, Gibbs H, Russell TW, Jarvis CI, Prem K, Pearson CAB, Clifford S, Flasche S, CMMID COVID-19 working group, Klepac P, Eggo RM, Jit M.",,BMC medicine,2020,2020-08-19,Y,China; Wuhan; Mobility; Delay; Outbreaks; Modelling; Travel Restrictions; Covid-19; Sars-cov-2; Cordon Sanitaire,,,"<h4>Background</h4>To contain the spread of COVID-19, a cordon sanitaire was put in place in Wuhan prior to the Lunar New Year, on 23 January 2020. We assess the efficacy of the cordon sanitaire to delay the introduction and onset of local transmission of COVID-19 in other major cities in mainland China.<h4>Methods</h4>We estimated the number of infected travellers from Wuhan to other major cities in mainland China from November 2019 to February 2020 using previously estimated COVID-19 prevalence in Wuhan and publicly available mobility data. We focused on Beijing, Chongqing, Hangzhou, and Shenzhen as four representative major cities to identify the potential independent contribution of the cordon sanitaire and holiday travel. To do this, we simulated outbreaks generated by infected arrivals in these destination cities using stochastic branching processes. We also modelled the effect of the cordon sanitaire in combination with reduced transmissibility scenarios to simulate the effect of local non-pharmaceutical interventions.<h4>Results</h4>We find that in the four cities, given the potentially high prevalence of COVID-19 in Wuhan between December 2019 and early January 2020, local transmission may have been seeded as early as 1-8 January 2020. By the time the cordon sanitaire was imposed, infections were likely in the thousands. The cordon sanitaire alone did not substantially affect the epidemic progression in these cities, although it may have had some effect in smaller cities. Reduced transmissibility resulted in a notable decrease in the incidence of infection in the four studied cities.<h4>Conclusions</h4>Our results indicate that sustained transmission was likely occurring several weeks prior to the implementation of the cordon sanitaire in four major cities of mainland China and that the observed decrease in incidence was likely attributable to other non-pharmaceutical, transmission-reducing interventions.",,doi:https://doi.org/10.1186/s12916-020-01712-9; doi:https://doi.org/10.1186/s12916-020-01712-9; html:https://europepmc.org/articles/PMC7437104; pdf:https://europepmc.org/articles/PMC7437104?pdf=render
 33536631,https://doi.org/10.1038/s42003-020-01575-z,A genome-wide meta-analysis yields 46 new loci associating with biomarkers of iron homeostasis.,"Bell S, Rigas AS, Magnusson MK, Ferkingstad E, Allara E, Bjornsdottir G, Ramond A, Sørensen E, Halldorsson GH, Paul DS, Burgdorf KS, Eggertsson HP, Howson JMM, Thørner LW, Kristmundsdottir S, Astle WJ, Erikstrup C, Sigurdsson JK, Vuckovic D, Dinh KM, Tragante V, Surendran P, Pedersen OB, Vidarsson B, Jiang T, Paarup HM, Onundarson PT, Akbari P, Nielsen KR, Lund SH, Juliusson K, Magnusson MI, Frigge ML, Oddsson A, Olafsson I, Kaptoge S, Hjalgrim H, Runarsson G, Wood AM, Jonsdottir I, Hansen TF, Sigurdardottir O, Stefansson H, Rye D, DBDS Genomic Consortium, Peters JE, Westergaard D, Holm H, Soranzo N, Banasik K, Thorleifsson G, Ouwehand WH, Thorsteinsdottir U, Roberts DJ, Sulem P, Butterworth AS, Gudbjartsson DF, Danesh J, Brunak S, Di Angelantonio E, Ullum H, Stefansson K.",,Communications biology,2021,2021-02-03,Y,,,,"Iron is essential for many biological functions and iron deficiency and overload have major health implications. We performed a meta-analysis of three genome-wide association studies from Iceland, the UK and Denmark of blood levels of ferritin (N = 246,139), total iron binding capacity (N = 135,430), iron (N = 163,511) and transferrin saturation (N = 131,471). We found 62 independent sequence variants associating with iron homeostasis parameters at 56 loci, including 46 novel loci. Variants at DUOX2, F5, SLC11A2 and TMPRSS6 associate with iron deficiency anemia, while variants at TF, HFE, TFR2 and TMPRSS6 associate with iron overload. A HBS1L-MYB intergenic region variant associates both with increased risk of iron overload and reduced risk of iron deficiency anemia. The DUOX2 missense variant is present in 14% of the population, associates with all iron homeostasis biomarkers, and increases the risk of iron deficiency anemia by 29%. The associations implicate proteins contributing to the main physiological processes involved in iron homeostasis: iron sensing and storage, inflammation, absorption of iron from the gut, iron recycling, erythropoiesis and bleeding/menstruation.",,pdf:https://www.nature.com/articles/s42003-020-01575-z.pdf; doi:https://doi.org/10.1038/s42003-020-01575-z; html:https://europepmc.org/articles/PMC7859200; pdf:https://europepmc.org/articles/PMC7859200?pdf=render
 34098341,https://doi.org/10.1016/j.ebiom.2021.103414,Accuracy of four lateral flow immunoassays for anti SARS-CoV-2 antibodies: a head-to-head comparative study.,"Jones HE, Mulchandani R, Taylor-Phillips S, Ades AE, Shute J, Perry KR, Chandra NL, Brooks T, Charlett A, Hickman M, Oliver I, Kaptoge S, Danesh J, Di Angelantonio E, Wyllie D, COMPARE study investigators, EDSAB-HOME investigators.",,EBioMedicine,2021,2021-06-04,Y,Seroepidemiology; Rapid Testing; Serosurveillance; Lateral Flow Devices; Covid-19,,,"<h4>Background</h4>SARS-CoV-2 antibody tests are used for population surveillance and might have a future role in individual risk assessment. Lateral flow immunoassays (LFIAs) can deliver results rapidly and at scale, but have widely varying accuracy.<h4>Methods</h4>In a laboratory setting, we performed head-to-head comparisons of four LFIAs: the Rapid Test Consortium's AbC-19<sup>TM</sup> Rapid Test, OrientGene COVID IgG/IgM Rapid Test Cassette, SureScreen COVID-19 Rapid Test Cassette, and Biomerica COVID-19 IgG/IgM Rapid Test. We analysed blood samples from 2,847 key workers and 1,995 pre-pandemic blood donors with all four devices.<h4>Findings</h4>We observed a clear trade-off between sensitivity and specificity: the IgG band of the SureScreen device and the AbC-19<sup>TM</sup> device had higher specificities but OrientGene and Biomerica higher sensitivities. Based on analysis of pre-pandemic samples, SureScreen IgG band had the highest specificity (98.9%, 95% confidence interval 98.3 to 99.3%), which translated to the highest positive predictive value across any pre-test probability: for example, 95.1% (95% uncertainty interval 92.6, 96.8%) at 20% pre-test probability. All four devices showed higher sensitivity at higher antibody concentrations (""spectrum effects""), but the extent of this varied by device.<h4>Interpretation</h4>The estimates of sensitivity and specificity can be used to adjust for test error rates when using these devices to estimate the prevalence of antibody. If tests were used to determine whether an individual has SARS-CoV-2 antibodies, in an example scenario in which 20% of individuals have antibodies we estimate around 5% of positive results on the most specific device would be false positives.<h4>Funding</h4>Public Health England.",,pdf:https://research-information.bris.ac.uk/files/280339070/1_s2.0_S2352396421002073_main.pdf; doi:https://doi.org/10.1016/j.ebiom.2021.103414; html:https://europepmc.org/articles/PMC8176919; pdf:https://europepmc.org/articles/PMC8176919?pdf=render
 31844323,https://doi.org/10.1038/s41588-019-0549-x,N<sup>6</sup>-methyladenosine regulates the stability of RNA:DNA hybrids in human cells.,"Abakir A, Giles TC, Cristini A, Foster JM, Dai N, Starczak M, Rubio-Roldan A, Li M, Eleftheriou M, Crutchley J, Flatt L, Young L, Gaffney DJ, Denning C, Dalhus B, Emes RD, Gackowski D, Corrêa IR, Garcia-Perez JL, Klungland A, Gromak N, Ruzov A.",,Nature genetics,2020,2019-12-16,Y,,,,"R-loops are nucleic acid structures formed by an RNA:DNA hybrid and unpaired single-stranded DNA that represent a source of genomic instability in mammalian cells<sup>1-4</sup>. Here we show that N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) modification, contributing to different aspects of messenger RNA metabolism<sup>5,6</sup>, is detectable on the majority of RNA:DNA hybrids in human pluripotent stem cells. We demonstrate that m<sup>6</sup>A-containing R-loops accumulate during G<sub>2</sub>/M and are depleted at G<sub>0</sub>/G<sub>1</sub> phases of the cell cycle, and that the m<sup>6</sup>A reader promoting mRNA degradation, YTHDF2 (ref. <sup>7</sup>), interacts with R-loop-enriched loci in dividing cells. Consequently, YTHDF2 knockout leads to increased R-loop levels, cell growth retardation and accumulation of γH2AX, a marker for DNA double-strand breaks, in mammalian cells. Our results suggest that m<sup>6</sup>A regulates accumulation of R-loops, implying a role for this modification in safeguarding genomic stability.",,pdf:https://europepmc.org/articles/pmc6974403?pdf=render; doi:https://doi.org/10.1038/s41588-019-0549-x; html:https://europepmc.org/articles/PMC6974403; pdf:https://europepmc.org/articles/PMC6974403?pdf=render
-38373851,https://doi.org/10.3399/bjgp.2023.0198,Long-term cardiovascular risks and the impact of statin treatment on socioeconomic inequalities: a microsimulation model.,"Wu R, Williams C, Zhou J, Schlackow I, Emberson J, Reith C, Keech A, Robson J, Armitage J, Gray A, Simes J, Baigent C, Mihaylova B, CTT Collaboration secretariat CTT Collaboration trialists: A to Z trial (phase Z) AFCAPS/TEXCAPS (AirForce/Texas Coronary Atherosclerosis Prevention Study)ALERT (Assessment of Lescol in Renal Transplantation)ALLHAT (Antihypertensive and Lipid-Lowering Treatment to Prevent Heart Attack Trial)ALLIANCE (Aggressive Lipid-Lowering Initiation Abates New Cardiac Events)ASCOT (Anglo-Scandinavian Cardiac Outcomes Trial)ASPEN (Atorvastatin Study for the Prevention of Coronary Heart Disease Endpoints in Non-Insulin Dependent Diabetes Mellitus)AURORA (A study to evaluate the Use of Rosuvastatin in subjects On Regular haemodialysis: an Assessment of survival and cardiovascular events)CARDS (Collaborative Atorvastatin Diabetes Study)CARE (Cholesterol And Recurrent Events Study)CORONA (Controlled Rosuvastatin Multinational Trial in Heart Failure)4D (Die Deutsche Diabetes Dialyse Studie)GISSI (Gruppo Italiano per lo Studio della Sopravvivenza nell’Infarto miocardico) Heart Failure and Prevention trialsHOPE-3HPS (Heart Protection Study)IDEAL (Incremental Decrease in Endpoints through Aggressive Lipid-lowering)JUPITER (Justification for the Use of Statins in Prevention: an Intervention Trial Evaluating Rosuvastatin)LIPID (Long-term Intervention with Pravastatin in Ischaemic Disease)LIPS (Lescol Intervention Prevention Study)Post-CABG (Post-Coronary Artery Bypass Graft Study)PROSPER (Prospective Study of Pravastatin in the Elderly at Risk)PROVE-IT (Pravastatin or Atorvastatin Evaluation and Infection Therapy)SEARCH (Study of Effectiveness of Additional Reductions in Cholesterol and Homocysteine)SPARCL (Stroke Prevention by Aggressive Reduction in Cholesterol Levels)4S (Scandinavian Simvastatin Survival Study)TNT (Treating to New Targets)WOSCOPS (West of Scotland Coronary Prevention Study)Other CTT Collaboration members.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2024,2024-02-29,Y,Cardiovascular disease; Socioeconomic status; Quality-adjusted Life Years; Inequality; Markov Microsimulation Model; Individual Patient Characteristics,,,"<h4>Background</h4>UK cardiovascular disease (CVD) incidence and mortality have declined in recent decades but socioeconomic inequalities persist.<h4>Aim</h4>To present a new CVD model, and project health outcomes and the impact of guideline-recommended statin treatment across quintiles of socioeconomic deprivation in the UK.<h4>Design and setting</h4>A lifetime microsimulation model was developed using 117 896 participants in 16 statin trials, 501 854 UK Biobank (UKB) participants, and quality-of-life data from national health surveys.<h4>Method</h4>A CVD microsimulation model was developed using risk equations for myocardial infarction, stroke, coronary revascularisation, cancer, and vascular and non-vascular death, estimated using trial data. The authors calibrated and further developed this model in the UKB cohort, including further characteristics and a diabetes risk equation, and validated the model in UKB and Whitehall II cohorts. The model was used to predict CVD incidence, life expectancy, quality-adjusted life years (QALYs), and the impact of UK guideline-recommended statin treatment across socioeconomic deprivation quintiles.<h4>Results</h4>Age, sex, socioeconomic deprivation, smoking, hypertension, diabetes, and cardiovascular events were key CVD risk determinants. Model-predicted event rates corresponded well to observed rates across participant categories. The model projected strong gradients in remaining life expectancy, with 4-5-year (5-8 QALYs) gaps between the least and most socioeconomically deprived quintiles. Guideline-recommended statin treatment was projected to increase QALYs, with larger gains in quintiles of higher deprivation.<h4>Conclusion</h4>The study demonstrated the potential of guideline-recommended statin treatment to reduce socioeconomic inequalities. This CVD model is a novel resource for individualised long-term projections of health outcomes of CVD treatments.",,pdf:https://bjgp.org/content/bjgp/early/2023/09/26/BJGP.2023.0198.full.pdf; doi:https://doi.org/10.3399/BJGP.2023.0198; html:https://europepmc.org/articles/PMC10904120; pdf:https://europepmc.org/articles/PMC10904120?pdf=render
 34051920,https://doi.org/10.1016/s2468-2667(21)00065-7,"Spatial, temporal, and demographic patterns in prevalence of chewing tobacco use in 204 countries and territories, 1990-2019: a systematic analysis from the Global Burden of Disease Study 2019.",GBD 2019 Chewing Tobacco Collaborators.,,The Lancet. Public health,2021,2021-05-28,Y,,,,"<h4>Background</h4>Chewing tobacco and other types of smokeless tobacco use have had less attention from the global health community than smoked tobacco use. However, the practice is popular in many parts of the world and has been linked to several adverse health outcomes. Understanding trends in prevalence with age, over time, and by location and sex is important for policy setting and in relation to monitoring and assessing commitment to the WHO Framework Convention on Tobacco Control.<h4>Methods</h4>We estimated prevalence of chewing tobacco use as part of the Global Burden of Diseases, Injuries, and Risk Factors Study 2019 using a modelling strategy that used information on multiple types of smokeless tobacco products. We generated a time series of prevalence of chewing tobacco use among individuals aged 15 years and older from 1990 to 2019 in 204 countries and territories, including age-sex specific estimates. We also compared these trends to those of smoked tobacco over the same time period.<h4>Findings</h4>In 2019, 273·9 million (95% uncertainty interval 258·5 to 290·9) people aged 15 years and older used chewing tobacco, and the global age-standardised prevalence of chewing tobacco use was 4·72% (4·46 to 5·01). 228·2 million (213·6 to 244·7; 83·29% [82·15 to 84·42]) chewing tobacco users lived in the south Asia region. Prevalence among young people aged 15-19 years was over 10% in seven locations in 2019. Although global age-standardised prevalence of smoking tobacco use decreased significantly between 1990 and 2019 (annualised rate of change: -1·21% [-1·26 to -1·16]), similar progress was not observed for chewing tobacco (0·46% [0·13 to 0·79]). Among the 12 highest prevalence countries (Bangladesh, Bhutan, Cambodia, India, Madagascar, Marshall Islands, Myanmar, Nepal, Pakistan, Palau, Sri Lanka, and Yemen), only Yemen had a significant decrease in the prevalence of chewing tobacco use, which was among males between 1990 and 2019 (-0·94% [-1·72 to -0·14]), compared with nine of 12 countries that had significant decreases in the prevalence of smoking tobacco. Among females, none of these 12 countries had significant decreases in prevalence of chewing tobacco use, whereas seven of 12 countries had a significant decrease in the prevalence of tobacco smoking use for the period.<h4>Interpretation</h4>Chewing tobacco remains a substantial public health problem in several regions of the world, and predominantly in south Asia. We found little change in the prevalence of chewing tobacco use between 1990 and 2019, and that control efforts have had much larger effects on the prevalence of smoking tobacco use than on chewing tobacco use in some countries. Mitigating the health effects of chewing tobacco requires stronger regulations and policies that specifically target use of chewing tobacco, especially in countries with high prevalence.<h4>Funding</h4>Bloomberg Philanthropies and the Bill & Melinda Gates Foundation.",,pdf:http://www.thelancet.com/article/S2468266721000657/pdf; doi:https://doi.org/10.1016/S2468-2667(21)00065-7; html:https://europepmc.org/articles/PMC8251505
+38373851,https://doi.org/10.3399/bjgp.2023.0198,Long-term cardiovascular risks and the impact of statin treatment on socioeconomic inequalities: a microsimulation model.,"Wu R, Williams C, Zhou J, Schlackow I, Emberson J, Reith C, Keech A, Robson J, Armitage J, Gray A, Simes J, Baigent C, Mihaylova B, CTT Collaboration secretariat CTT Collaboration trialists: A to Z trial (phase Z) AFCAPS/TEXCAPS (AirForce/Texas Coronary Atherosclerosis Prevention Study)ALERT (Assessment of Lescol in Renal Transplantation)ALLHAT (Antihypertensive and Lipid-Lowering Treatment to Prevent Heart Attack Trial)ALLIANCE (Aggressive Lipid-Lowering Initiation Abates New Cardiac Events)ASCOT (Anglo-Scandinavian Cardiac Outcomes Trial)ASPEN (Atorvastatin Study for the Prevention of Coronary Heart Disease Endpoints in Non-Insulin Dependent Diabetes Mellitus)AURORA (A study to evaluate the Use of Rosuvastatin in subjects On Regular haemodialysis: an Assessment of survival and cardiovascular events)CARDS (Collaborative Atorvastatin Diabetes Study)CARE (Cholesterol And Recurrent Events Study)CORONA (Controlled Rosuvastatin Multinational Trial in Heart Failure)4D (Die Deutsche Diabetes Dialyse Studie)GISSI (Gruppo Italiano per lo Studio della Sopravvivenza nell’Infarto miocardico) Heart Failure and Prevention trialsHOPE-3HPS (Heart Protection Study)IDEAL (Incremental Decrease in Endpoints through Aggressive Lipid-lowering)JUPITER (Justification for the Use of Statins in Prevention: an Intervention Trial Evaluating Rosuvastatin)LIPID (Long-term Intervention with Pravastatin in Ischaemic Disease)LIPS (Lescol Intervention Prevention Study)Post-CABG (Post-Coronary Artery Bypass Graft Study)PROSPER (Prospective Study of Pravastatin in the Elderly at Risk)PROVE-IT (Pravastatin or Atorvastatin Evaluation and Infection Therapy)SEARCH (Study of Effectiveness of Additional Reductions in Cholesterol and Homocysteine)SPARCL (Stroke Prevention by Aggressive Reduction in Cholesterol Levels)4S (Scandinavian Simvastatin Survival Study)TNT (Treating to New Targets)WOSCOPS (West of Scotland Coronary Prevention Study)Other CTT Collaboration members.",,The British journal of general practice : the journal of the Royal College of General Practitioners,2024,2024-02-29,Y,Cardiovascular disease; Socioeconomic status; Quality-adjusted Life Years; Inequality; Markov Microsimulation Model; Individual Patient Characteristics,,,"<h4>Background</h4>UK cardiovascular disease (CVD) incidence and mortality have declined in recent decades but socioeconomic inequalities persist.<h4>Aim</h4>To present a new CVD model, and project health outcomes and the impact of guideline-recommended statin treatment across quintiles of socioeconomic deprivation in the UK.<h4>Design and setting</h4>A lifetime microsimulation model was developed using 117 896 participants in 16 statin trials, 501 854 UK Biobank (UKB) participants, and quality-of-life data from national health surveys.<h4>Method</h4>A CVD microsimulation model was developed using risk equations for myocardial infarction, stroke, coronary revascularisation, cancer, and vascular and non-vascular death, estimated using trial data. The authors calibrated and further developed this model in the UKB cohort, including further characteristics and a diabetes risk equation, and validated the model in UKB and Whitehall II cohorts. The model was used to predict CVD incidence, life expectancy, quality-adjusted life years (QALYs), and the impact of UK guideline-recommended statin treatment across socioeconomic deprivation quintiles.<h4>Results</h4>Age, sex, socioeconomic deprivation, smoking, hypertension, diabetes, and cardiovascular events were key CVD risk determinants. Model-predicted event rates corresponded well to observed rates across participant categories. The model projected strong gradients in remaining life expectancy, with 4-5-year (5-8 QALYs) gaps between the least and most socioeconomically deprived quintiles. Guideline-recommended statin treatment was projected to increase QALYs, with larger gains in quintiles of higher deprivation.<h4>Conclusion</h4>The study demonstrated the potential of guideline-recommended statin treatment to reduce socioeconomic inequalities. This CVD model is a novel resource for individualised long-term projections of health outcomes of CVD treatments.",,pdf:https://bjgp.org/content/bjgp/early/2023/09/26/BJGP.2023.0198.full.pdf; doi:https://doi.org/10.3399/BJGP.2023.0198; html:https://europepmc.org/articles/PMC10904120; pdf:https://europepmc.org/articles/PMC10904120?pdf=render
 31770382,https://doi.org/10.1371/journal.pmed.1002974,"Long-term mortality in mothers of infants with neonatal abstinence syndrome: A population-based parallel-cohort study in England and Ontario, Canada.","Guttmann A, Blackburn R, Amartey A, Zhou L, Wijlaars L, Saunders N, Harron K, Chiu M, Gilbert R.",,PLoS medicine,2019,2019-11-26,Y,,Improving Public Health,,"<h4>Background</h4>Opioid addiction is a major public health threat to healthy life expectancy; however, little is known of long-term mortality for mothers with opioid use in pregnancy. Pregnancy and delivery care are opportunities to improve access to addiction and supportive services. Treating neonatal abstinence syndrome (NAS) as a marker of opioid use during pregnancy, this study reports long-term maternal mortality among mothers with a birth affected by NAS in relation to that of mothers without a NAS-affected birth in 2 high-prevalence jurisdictions, England and Ontario, Canada.<h4>Methods and findings</h4>We conducted a population-based study using linked administrative health data to develop parallel cohorts of mother-infant dyads in England and Ontario between 2002 and 2012. The study population comprised 13,577 and 4,966 mothers of infants with NAS and 4,205,675 and 929,985 control mothers in England and Ontario, respectively. Death records captured all-cause maternal mortality after delivery through March 31, 2016, and cause-specific maternal mortality to December 31, 2014. The primary exposure was a live birth of an infant with NAS, and the main outcome was all deaths among mothers following their date of delivery. We modelled the association between NAS and all-cause maternal mortality using Cox regression, and the cumulative incidence of cause-specific mortality within a competing risks framework. All-cause mortality rates, 10-year cumulative incidence risk of death, and crude and age-adjusted hazard ratios were calculated. Estimated crude 10-year mortality based on Kaplan-Meier curves in mothers of infants with NAS was 5.1% (95% CI 4.7%-5.6%) in England and 4.6% (95% CI 3.8%-5.5%) in Ontario versus 0.4% (95% CI 0.41%-0.42%) in England and 0.4% (95% CI 0.38%-0.41%) in Ontario for controls (p < 0.001 for all comparisons). Survival curves showed no clear inflection point or period of heightened risk. The crude hazard ratio for all-cause mortality was 12.1 (95% 11.1-13.2; p < 0.001) in England and 11.4 (9.7-13.4; p < 0.001) in Ontario; age adjustment did not reduce the hazard ratios. The cumulative incidence of death was higher among NAS mothers than controls for almost all causes of death. The majority of deaths were by avoidable causes, defined as those that are preventable, amenable to care, or both. Limitations included lack of direct measures of maternal opioid use, other substance misuse, and treatments or supports received.<h4>Conclusions</h4>In this study, we found that approximately 1 in 20 mothers of infants with NAS died within 10 years of delivery in both England and Canada-a mortality risk 11-12 times higher than for control mothers. Risk of death was not limited to the early postpartum period targeted by most public health programs. Policy responses to the current opioid epidemic require effective strategies for long-term support to improve the health and welfare of opioid-using mothers and their children.",This paper investigates the mortality of mothers of infants with Neonatal abstinence syndrome. This population has a greatly increased mortality compared to mothers who don't have NAS. The paper highlights the lack of long term support for this group.,pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1002974&type=printable; doi:https://doi.org/10.1371/journal.pmed.1002974; html:https://europepmc.org/articles/PMC6879118; pdf:https://europepmc.org/articles/PMC6879118?pdf=render
 33990564,https://doi.org/10.1038/s41467-021-22752-6,Epigenome-wide association meta-analysis of DNA methylation with coffee and tea consumption.,"Karabegović I, Portilla-Fernandez E, Li Y, Ma J, Maas SCE, Sun D, Hu EA, Kühnel B, Zhang Y, Ambatipudi S, Fiorito G, Huang J, Castillo-Fernandez JE, Wiggins KL, de Klein N, Grioni S, Swenson BR, Polidoro S, Treur JL, Cuenin C, Tsai PC, Costeira R, Chajes V, Braun K, Verweij N, Kretschmer A, Franke L, van Meurs JBJ, Uitterlinden AG, de Knegt RJ, Ikram MA, Dehghan A, Peters A, Schöttker B, Gharib SA, Sotoodehnia N, Bell JT, Elliott P, Vineis P, Relton C, Herceg Z, Brenner H, Waldenberger M, Rebholz CM, Voortman T, Pan Q, Fornage M, Levy D, Kayser M, Ghanbari M.",,Nature communications,2021,2021-05-14,Y,,,,"Coffee and tea are extensively consumed beverages worldwide which have received considerable attention regarding health. Intake of these beverages is consistently linked to, among others, reduced risk of diabetes and liver diseases; however, the mechanisms of action remain elusive. Epigenetics is suggested as a mechanism mediating the effects of dietary and lifestyle factors on disease onset. Here we report the results from epigenome-wide association studies (EWAS) on coffee and tea consumption in 15,789 participants of European and African-American ancestries from 15 cohorts. EWAS meta-analysis of coffee consumption reveals 11 CpGs surpassing the epigenome-wide significance threshold (P-value <1.1×10<sup>-7</sup>), which annotated to the AHRR, F2RL3, FLJ43663, HDAC4, GFI1 and PHGDH genes. Among them, cg14476101 is significantly associated with expression of the PHGDH and risk of fatty liver disease. Knockdown of PHGDH expression in liver cells shows a correlation with expression levels of genes associated with circulating lipids, suggesting a role of PHGDH in hepatic-lipid metabolism. EWAS meta-analysis on tea consumption reveals no significant association, only two CpGs annotated to CACNA1A and PRDM16 genes show suggestive association (P-value <5.0×10<sup>-6</sup>). These findings indicate that coffee-associated changes in DNA methylation levels may explain the mechanism of action of coffee consumption in conferring risk of diseases.",,pdf:https://www.nature.com/articles/s41467-021-22752-6.pdf; doi:https://doi.org/10.1038/s41467-021-22752-6; html:https://europepmc.org/articles/PMC8121846; pdf:https://europepmc.org/articles/PMC8121846?pdf=render
 32328990,https://doi.org/10.1007/s10654-020-00633-4,The Dementias Platform UK (DPUK) Data Portal.,"Bauermeister S, Orton C, Thompson S, Barker RA, Bauermeister JR, Ben-Shlomo Y, Brayne C, Burn D, Campbell A, Calvin C, Chandran S, Chaturvedi N, Chêne G, Chessell IP, Corbett A, Davis DHJ, Denis M, Dufouil C, Elliott P, Fox N, Hill D, Hofer SM, Hu MT, Jindra C, Kee F, Kim CH, Kim C, Kivimaki M, Koychev I, Lawson RA, Linden GJ, Lyons RA, Mackay C, Matthews PM, McGuiness B, Middleton L, Moody C, Moore K, Na DL, O'Brien JT, Ourselin S, Paranjothy S, Park KS, Porteous DJ, Richards M, Ritchie CW, Rohrer JD, Rossor MN, Rowe JB, Scahill R, Schnier C, Schott JM, Seo SW, South M, Steptoe M, Tabrizi SJ, Tales A, Tillin T, Timpson NJ, Toga AW, Visser PJ, Wade-Martins R, Wilkinson T, Williams J, Wong A, Gallacher JEJ.",,European journal of epidemiology,2020,2020-04-23,Y,Cohorts; epidemiology; data management; Data Access; Data Repository; Data Platform,,,"The Dementias Platform UK Data Portal is a data repository facilitating access to data for 3 370 929 individuals in 42 cohorts. The Data Portal is an end-to-end data management solution providing a secure, fully auditable, remote access environment for the analysis of cohort data. All projects utilising the data are by default collaborations with the cohort research teams generating the data. The Data Portal uses UK Secure eResearch Platform infrastructure to provide three core utilities: data discovery, access, and analysis. These are delivered using a 7 layered architecture comprising: data ingestion, data curation, platform interoperability, data discovery, access brokerage, data analysis and knowledge preservation. Automated, streamlined, and standardised procedures reduce the administrative burden for all stakeholders, particularly for requests involving multiple independent datasets, where a single request may be forwarded to multiple data controllers. Researchers are provided with their own secure 'lab' using VMware which is accessed using two factor authentication. Over the last 2 years, 160 project proposals involving 579 individual cohort data access requests were received. These were received from 268 applicants spanning 72 institutions (56 academic, 13 commercial, 3 government) in 16 countries with 84 requests involving multiple cohorts. Projects are varied including multi-modal, machine learning, and Mendelian randomisation analyses. Data access is usually free at point of use although a small number of cohorts require a data access fee.",,pdf:https://link.springer.com/content/pdf/10.1007/s10654-020-00633-4.pdf; doi:https://doi.org/10.1007/s10654-020-00633-4; html:https://europepmc.org/articles/PMC7320955; pdf:https://europepmc.org/articles/PMC7320955?pdf=render
@@ -2813,8 +2815,8 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 36314129,https://doi.org/10.1161/circulationaha.122.060700,Mild-to-Moderate Kidney Dysfunction and Cardiovascular Disease: Observational and Mendelian Randomization Analyses.,"Gaziano L, Sun L, Arnold M, Bell S, Cho K, Kaptoge SK, Song RJ, Burgess S, Posner DC, Mosconi K, Robinson-Cohen C, Mason AM, Bolton TR, Tao R, Allara E, Schubert P, Chen L, Staley JR, Staplin N, Altay S, Amiano P, Arndt V, Ärnlöv J, Barr ELM, Björkelund C, Boer JMA, Brenner H, Casiglia E, Chiodini P, Cooper JA, Coresh J, Cushman M, Dankner R, Davidson KW, de Jongh RT, Donfrancesco C, Engström G, Freisling H, de la Cámara AG, Gudnason V, Hankey GJ, Hansson PO, Heath AK, Hoorn EJ, Imano H, Jassal SK, Kaaks R, Katzke V, Kauhanen J, Kiechl S, Koenig W, Kronmal RA, Kyrø C, Lawlor DA, Ljungberg B, MacDonald C, Masala G, Meisinger C, Melander O, Moreno Iribas C, Ninomiya T, Nitsch D, Nordestgaard BG, Onland-Moret C, Palmieri L, Petrova D, Garcia JRQ, Rosengren A, Sacerdote C, Sakurai M, Santiuste C, Schulze MB, Sieri S, Sundström J, Tikhonoff V, Tjønneland A, Tong T, Tumino R, Tzoulaki I, van der Schouw YT, Monique Verschuren WM, Völzke H, Wallace RB, Wannamethee SG, Weiderpass E, Willeit P, Woodward M, Yamagishi K, Zamora-Ros R, Akwo EA, Pyarajan S, Gagnon DR, Tsao PS, Muralidhar S, Edwards TL, Damrauer SM, Joseph J, Pennells L, Wilson PWF, Harrison S, Gaziano TA, Inouye M, Baigent C, Casas JP, Langenberg C, Wareham N, Riboli E, Gaziano JM, Danesh J, Hung AM, Butterworth AS, Wood AM, Di Angelantonio E, Emerging Risk Factors Collaboration/EPIC-CVD/Million Veteran Program.",,Circulation,2022,2022-10-31,Y,Kidney diseases; Cardiovascular diseases; Coronary disease; Stroke,,,"<h4>Background</h4>End-stage renal disease is associated with a high risk of cardiovascular events. It is unknown, however, whether mild-to-moderate kidney dysfunction is causally related to coronary heart disease (CHD) and stroke.<h4>Methods</h4>Observational analyses were conducted using individual-level data from 4 population data sources (Emerging Risk Factors Collaboration, EPIC-CVD [European Prospective Investigation into Cancer and Nutrition-Cardiovascular Disease Study], Million Veteran Program, and UK Biobank), comprising 648 135 participants with no history of cardiovascular disease or diabetes at baseline, yielding 42 858 and 15 693 incident CHD and stroke events, respectively, during 6.8 million person-years of follow-up. Using a genetic risk score of 218 variants for estimated glomerular filtration rate (eGFR), we conducted Mendelian randomization analyses involving 413 718 participants (25 917 CHD and 8622 strokes) in EPIC-CVD, Million Veteran Program, and UK Biobank.<h4>Results</h4>There were U-shaped observational associations of creatinine-based eGFR with CHD and stroke, with higher risk in participants with eGFR values <60 or >105 mL·min<sup>-1</sup>·1.73 m<sup>-2</sup>, compared with those with eGFR between 60 and 105 mL·min<sup>-1</sup>·1.73 m<sup>-2</sup>. Mendelian randomization analyses for CHD showed an association among participants with eGFR <60 mL·min<sup>-1</sup>·1.73 m<sup>-2</sup>, with a 14% (95% CI, 3%-27%) higher CHD risk per 5 mL·min<sup>-1</sup>·1.73 m<sup>-2</sup> lower genetically predicted eGFR, but not for those with eGFR >105 mL·min<sup>-1</sup>·1.73 m<sup>-2</sup>. Results were not materially different after adjustment for factors associated with the eGFR genetic risk score, such as lipoprotein(a), triglycerides, hemoglobin A1c, and blood pressure. Mendelian randomization results for stroke were nonsignificant but broadly similar to those for CHD.<h4>Conclusions</h4>In people without manifest cardiovascular disease or diabetes, mild-to-moderate kidney dysfunction is causally related to risk of CHD, highlighting the potential value of preventive approaches that preserve and modulate kidney function.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCULATIONAHA.122.060700; doi:https://doi.org/10.1161/CIRCULATIONAHA.122.060700; html:https://europepmc.org/articles/PMC9662821; pdf:https://europepmc.org/articles/PMC9662821?pdf=render
 37880365,https://doi.org/10.1038/s41586-023-06630-3,Normative spatiotemporal fetal brain maturation with satisfactory development at 2 years.,"Namburete AIL, Papież BW, Fernandes M, Wyburd MK, Hesse LS, Moser FA, Ismail LC, Gunier RB, Squier W, Ohuma EO, Carvalho M, Jaffer Y, Gravett M, Wu Q, Lambert A, Winsey A, Restrepo-Méndez MC, Bertino E, Purwar M, Barros FC, Stein A, Noble JA, Molnár Z, Jenkinson M, Bhutta ZA, Papageorghiou AT, Villar J, Kennedy SH.",,Nature,2023,2023-10-25,Y,,,,"Maturation of the human fetal brain should follow precisely scheduled structural growth and folding of the cerebral cortex for optimal postnatal function<sup>1</sup>. We present a normative digital atlas of fetal brain maturation based on a prospective international cohort of healthy pregnant women<sup>2</sup>, selected using World Health Organization recommendations for growth standards<sup>3</sup>. Their fetuses were accurately dated in the first trimester, with satisfactory growth and neurodevelopment from early pregnancy to 2 years of age<sup>4,5</sup>. The atlas was produced using 1,059 optimal quality, three-dimensional ultrasound brain volumes from 899 of the fetuses and an automated analysis pipeline<sup>6-8</sup>. The atlas corresponds structurally to published magnetic resonance images<sup>9</sup>, but with finer anatomical details in deep grey matter. The between-study site variability represented less than 8.0% of the total variance of all brain measures, supporting pooling data from the eight study sites to produce patterns of normative maturation. We have thereby generated an average representation of each cerebral hemisphere between 14 and 31 weeks' gestation with quantification of intracranial volume variability and growth patterns. Emergent asymmetries were detectable from as early as 14 weeks, with peak asymmetries in regions associated with language development and functional lateralization between 20 and 26 weeks' gestation. These patterns were validated in 1,487 three-dimensional brain volumes from 1,295 different fetuses in the same cohort. We provide a unique spatiotemporal benchmark of fetal brain maturation from a large cohort with normative postnatal growth and neurodevelopment.",,pdf:https://www.nature.com/articles/s41586-023-06630-3.pdf; doi:https://doi.org/10.1038/s41586-023-06630-3; html:https://europepmc.org/articles/PMC10620088; pdf:https://europepmc.org/articles/PMC10620088?pdf=render
 35091648,https://doi.org/10.1038/s41525-021-00267-9,"Structural variation analysis of 6,500 whole genome sequences in amyotrophic lateral sclerosis.","Al Khleifat A, Iacoangeli A, van Vugt JJFA, Bowles H, Moisse M, Zwamborn RAJ, van der Spek RAA, Shatunov A, Cooper-Knock J, Topp S, Byrne R, Gellera C, López V, Jones AR, Opie-Martin S, Vural A, Campos Y, van Rheenen W, Kenna B, Van Eijk KR, Kenna K, Weber M, Smith B, Fogh I, Silani V, Morrison KE, Dobson R, van Es MA, McLaughlin RL, Vourc'h P, Chio A, Corcia P, de Carvalho M, Gotkine M, Panades MP, Mora JS, Shaw PJ, Landers JE, Glass JD, Shaw CE, Basak N, Hardiman O, Robberecht W, Van Damme P, van den Berg LH, Veldink JH, Al-Chalabi A.",,NPJ genomic medicine,2022,2022-01-28,Y,,,,"There is a strong genetic contribution to Amyotrophic lateral sclerosis (ALS) risk, with heritability estimates of up to 60%. Both Mendelian and small effect variants have been identified, but in common with other conditions, such variants only explain a little of the heritability. Genomic structural variation might account for some of this otherwise unexplained heritability. We therefore investigated association between structural variation in a set of 25 ALS genes, and ALS risk and phenotype. As expected, the repeat expansion in the C9orf72 gene was identified as associated with ALS. Two other ALS-associated structural variants were identified: inversion in the VCP gene and insertion in the ERBB4 gene. All three variants were associated both with increased risk of ALS and specific phenotypic patterns of disease expression. More than 70% of people with respiratory onset ALS harboured ERBB4 insertion compared with 25% of the general population, suggesting respiratory onset ALS may be a distinct genetic subtype.",,pdf:https://www.nature.com/articles/s41525-021-00267-9.pdf; doi:https://doi.org/10.1038/s41525-021-00267-9; html:https://europepmc.org/articles/PMC8799638; pdf:https://europepmc.org/articles/PMC8799638?pdf=render
-30498058,https://doi.org/10.1136/archdischild-2018-315866,Risk factors for permanent childhood hearing impairment.,"Butcher E, Dezateux C, Knowles RL.",,Archives of disease in childhood,2020,2018-11-28,Y,Deafness; epidemiology,Improving Public Health,,"<h4>Objective</h4>While several perinatal risk factors for permanent childhood hearing impairment (PCHI) are known, association with gestational length remains unclear. We hypothesised that shorter gestational length predicts higher PCHI risk.<h4>Design</h4>19 504 participants from the UK Millennium Cohort Study (born 2000-2002, prior to newborn screening).<h4>Methods</h4>Multivariable discrete-time survival analysis to examine associations between parent-reported PCHI by age 11 years and gestational length, plus other prespecified factors.<h4>Results</h4>PCHI affected 2.1 per 1000 children (95% CI 1.5 to 3.0) by age 11; however, gestational length did not predict PCHI risk (HR, 95% CI 1.00, 0.98 to 1.03 per day increase). Risk was increased in those with neonatal illness, with or without admission to neonatal care (6.33, 2.27 to 17.63 and 2.62, 1.15 to 5.97, respectively), of Bangladeshi or Pakistani ethnicity (2.78, 1.06 to 7.31) or born to younger mothers (0.92, 0.87 to 0.97 per year).<h4>Conclusion</h4>Neonatal illness, rather than gestational length, predicts PCHI risk. Further research should explore associations with ethnicity.","This study looked at whether there is a link between gestational length of a child (the length of time of pregnancy) and the likelihood of permanent hearing impairment. The authors looked at data from over 19000 children from a study called the Millenium Cohort Study. They found that shorter gestational length did not increase the likelihood of childhood permanent hearting impairment. However, they found that children who had neonatal illness (illness in the immediate days after birth), if they were Bangladeshi or Pakistani in ethnicity, or if they were born to younger mothers.",pdf:https://adc.bmj.com/content/archdischild/105/2/187.full.pdf; doi:https://doi.org/10.1136/archdischild-2018-315866; html:https://europepmc.org/articles/PMC7025723; pdf:https://europepmc.org/articles/PMC7025723?pdf=render
 30898389,https://doi.org/10.1016/j.injury.2019.03.003,Potentially preventable trauma deaths: A retrospective review.,"Beck B, Smith K, Mercier E, Bernard S, Jones C, Meadley B, Clair TS, Jennings PA, Nehme Z, Burke M, Bassed R, Fitzgerald M, Judson R, Teague W, Mitra B, Mathew J, Buck A, Varma D, Gabbe B, Bray J, McLellan S, Ford J, Siedenburg J, Cameron P.",,Injury,2019,2019-03-07,N,Mortality; Trauma; Emergency Medical Services; Pre-hospital Care; Trauma Systems; Preventable,Improving Public Health,,"<h4>Background</h4>Reviewing prehospital trauma deaths provides an opportunity to identify system improvements that may reduce trauma mortality. The objective of this study was to identify the number and rate of potentially preventable trauma deaths through expert panel reviews of prehospital and early in-hospital trauma deaths.<h4>Methods</h4>We conducted a retrospective review of prehospital and early in-hospital (<24 h) trauma deaths following a traumatic out-of-hospital cardiac arrest that were attended by Ambulance Victoria (AV) in the state of Victoria, Australia, between 2008 and 2014. Expert panels were used to review cases that had resuscitation attempted by paramedics and underwent a full autopsy. Patients with a mechanism of hanging, drowning or those with anatomical injuries deemed to be unsurvivable were excluded.<h4>Results</h4>Of the 1183 cases that underwent full autopsies, resuscitation was attempted by paramedics in 336 (28%) cases. Of these, 113 cases (34%) were deemed to have potentially survivable injuries and underwent expert panel review. There were 90 (80%) deaths that were not preventable, 19 (17%) potentially preventable deaths and 4 (3%) preventable deaths. Potentially preventable or preventable deaths represented 20% of those cases that underwent review and 7% of cases that had attempted resuscitation.<h4>Conclusions</h4>The number of potentially preventable or preventable trauma deaths in the pre-hospital and early in-hospital resuscitation phase was low. Specific circumstances were identified in which the trauma system could be further improved.",,pdf:http://www.injuryjournal.com/article/S0020138319301007/pdf; doi:https://doi.org/10.1016/j.injury.2019.03.003
+30498058,https://doi.org/10.1136/archdischild-2018-315866,Risk factors for permanent childhood hearing impairment.,"Butcher E, Dezateux C, Knowles RL.",,Archives of disease in childhood,2020,2018-11-28,Y,Deafness; epidemiology,Improving Public Health,,"<h4>Objective</h4>While several perinatal risk factors for permanent childhood hearing impairment (PCHI) are known, association with gestational length remains unclear. We hypothesised that shorter gestational length predicts higher PCHI risk.<h4>Design</h4>19 504 participants from the UK Millennium Cohort Study (born 2000-2002, prior to newborn screening).<h4>Methods</h4>Multivariable discrete-time survival analysis to examine associations between parent-reported PCHI by age 11 years and gestational length, plus other prespecified factors.<h4>Results</h4>PCHI affected 2.1 per 1000 children (95% CI 1.5 to 3.0) by age 11; however, gestational length did not predict PCHI risk (HR, 95% CI 1.00, 0.98 to 1.03 per day increase). Risk was increased in those with neonatal illness, with or without admission to neonatal care (6.33, 2.27 to 17.63 and 2.62, 1.15 to 5.97, respectively), of Bangladeshi or Pakistani ethnicity (2.78, 1.06 to 7.31) or born to younger mothers (0.92, 0.87 to 0.97 per year).<h4>Conclusion</h4>Neonatal illness, rather than gestational length, predicts PCHI risk. Further research should explore associations with ethnicity.","This study looked at whether there is a link between gestational length of a child (the length of time of pregnancy) and the likelihood of permanent hearing impairment. The authors looked at data from over 19000 children from a study called the Millenium Cohort Study. They found that shorter gestational length did not increase the likelihood of childhood permanent hearting impairment. However, they found that children who had neonatal illness (illness in the immediate days after birth), if they were Bangladeshi or Pakistani in ethnicity, or if they were born to younger mothers.",pdf:https://adc.bmj.com/content/archdischild/105/2/187.full.pdf; doi:https://doi.org/10.1136/archdischild-2018-315866; html:https://europepmc.org/articles/PMC7025723; pdf:https://europepmc.org/articles/PMC7025723?pdf=render
 35232957,https://doi.org/10.1038/s41398-022-01852-x,Correction: Association of low-frequency and rare coding variants with information processing speed.,"Bressler J, Davies G, Smith AV, Saba Y, Bis JC, Jian X, Hayward C, Yanek L, Smith JA, Mirza SS, Wang R, Adams HHH, Becker D, Boerwinkle E, Campbell A, Cox SR, Eiriksdottir G, Fawns-Ritchie C, Gottesman RF, Grove ML, Guo X, Hofer E, Kardia SLR, Knol MJ, Koini M, Lopez OL, Marioni RE, Nyquist P, Pattie A, Polasek O, Porteous DJ, Rudan I, Satizabal CL, Schmidt H, Schmidt R, Sidney S, Simino J, Smith BH, Turner ST, van der Lee SJ, Ware EB, Whitmer RA, Yaffe K, Yang Q, Zhao W, Gudnason V, Launer LJ, Fitzpatrick AL, Psaty BM, Fornage M, Arfan Ikram M, van Duijn CM, Seshadri S, Mosley TH, Deary IJ.",,Translational psychiatry,2022,2022-03-01,Y,,,,,,pdf:https://www.nature.com/articles/s41398-022-01852-x.pdf; doi:https://doi.org/10.1038/s41398-022-01852-x; html:https://europepmc.org/articles/PMC8888652; pdf:https://europepmc.org/articles/PMC8888652?pdf=render
 35726068,https://doi.org/10.1038/s41588-022-01126-8,"Author Correction: A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer's disease.","Wightman DP, Jansen IE, Savage JE, Shadrin AA, Bahrami S, Holland D, Rongve A, Børte S, Winsvold BS, Drange OK, Martinsen AE, Skogholt AH, Willer C, Bråthen G, Bosnes I, Nielsen JB, Fritsche LG, Thomas LF, Pedersen LM, Gabrielsen ME, Johnsen MB, Meisingset TW, Zhou W, Proitsi P, Hodges A, Dobson R, Velayudhan L, Heilbron K, Auton A, 23andMe Research Team, Sealock JM, Davis LK, Pedersen NL, Reynolds CA, Karlsson IK, Magnusson S, Stefansson H, Thordardottir S, Jonsson PV, Snaedal J, Zettergren A, Skoog I, Kern S, Waern M, Zetterberg H, Blennow K, Stordal E, Hveem K, Zwart JA, Athanasiu L, Selnes P, Saltvedt I, Sando SB, Ulstein I, Djurovic S, Fladby T, Aarsland D, Selbæk G, Ripke S, Stefansson K, Andreassen OA, Posthuma D.",,Nature genetics,2022,2022-07-01,N,,,,,,pdf:https://www.nature.com/articles/s41588-022-01126-8.pdf; doi:https://doi.org/10.1038/s41588-022-01126-8
 34516908,https://doi.org/10.1126/sciadv.abh0534,Cell-free DNA TAPS provides multimodal information for early cancer detection.,"Siejka-Zielińska P, Cheng J, Jackson F, Liu Y, Soonawalla Z, Reddy S, Silva M, Puta L, McCain MV, Culver EL, Bekkali N, Schuster-Böckler B, Palamara PF, Mann D, Reeves H, Barnes E, Sivakumar S, Song CX.",,Science advances,2021,2021-09-01,Y,,,,"Multimodal, genome-wide characterization of epigenetic and genetic information in circulating cell-free DNA (cfDNA) could enable more sensitive early cancer detection, but it is technologically challenging. Recently, we developed TET-assisted pyridine borane sequencing (TAPS), which is a mild, bisulfite-free method for base-resolution direct DNA methylation sequencing. Here, we optimized TAPS for cfDNA (cfTAPS) to provide high-quality and high-depth whole-genome cell-free methylomes. We applied cfTAPS to 85 cfDNA samples from patients with hepatocellular carcinoma (HCC) or pancreatic ductal adenocarcinoma (PDAC) and noncancer controls. From only 10 ng of cfDNA (1 to 3 ml of plasma), we generated the most comprehensive cfDNA methylome to date. We demonstrated that cfTAPS provides multimodal information about cfDNA characteristics, including DNA methylation, tissue of origin, and DNA fragmentation. Integrated analysis of these epigenetic and genetic features enables accurate identification of early HCC and PDAC.",,pdf:https://www.science.org/doi/pdf/10.1126/sciadv.abh0534?download=true; doi:https://doi.org/10.1126/sciadv.abh0534; html:https://europepmc.org/articles/PMC8442905; pdf:https://europepmc.org/articles/PMC8442905?pdf=render
@@ -2835,8 +2837,8 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 33495596,https://doi.org/10.1038/s41588-020-00762-2,Shared genetic pathways contribute to risk of hypertrophic and dilated cardiomyopathies with opposite directions of effect.,"Tadros R, Francis C, Xu X, Vermeer AMC, Harper AR, Huurman R, Kelu Bisabu K, Walsh R, Hoorntje ET, Te Rijdt WP, Buchan RJ, van Velzen HG, van Slegtenhorst MA, Vermeulen JM, Offerhaus JA, Bai W, de Marvao A, Lahrouchi N, Beekman L, Karper JC, Veldink JH, Kayvanpour E, Pantazis A, Baksi AJ, Whiffin N, Mazzarotto F, Sloane G, Suzuki H, Schneider-Luftman D, Elliott P, Richard P, Ader F, Villard E, Lichtner P, Meitinger T, Tanck MWT, van Tintelen JP, Thain A, McCarty D, Hegele RA, Roberts JD, Amyot J, Dubé MP, Cadrin-Tourigny J, Giraldeau G, L'Allier PL, Garceau P, Tardif JC, Boekholdt SM, Lumbers RT, Asselbergs FW, Barton PJR, Cook SA, Prasad SK, O'Regan DP, van der Velden J, Verweij KJH, Talajic M, Lettre G, Pinto YM, Meder B, Charron P, de Boer RA, Christiaans I, Michels M, Wilde AAM, Watkins H, Matthews PM, Ware JS, Bezzina CR.",,Nature genetics,2021,2021-01-25,Y,,,,"The heart muscle diseases hypertrophic (HCM) and dilated (DCM) cardiomyopathies are leading causes of sudden death and heart failure in young, otherwise healthy, individuals. We conducted genome-wide association studies and multi-trait analyses in HCM (1,733 cases), DCM (5,521 cases) and nine left ventricular (LV) traits (19,260 UK Biobank participants with structurally normal hearts). We identified 16 loci associated with HCM, 13 with DCM and 23 with LV traits. We show strong genetic correlations between LV traits and cardiomyopathies, with opposing effects in HCM and DCM. Two-sample Mendelian randomization supports a causal association linking increased LV contractility with HCM risk. A polygenic risk score explains a significant portion of phenotypic variability in carriers of HCM-causing rare variants. Our findings thus provide evidence that polygenic risk score may account for variability in Mendelian diseases. More broadly, we provide insights into how genetic pathways may lead to distinct disorders through opposing genetic effects.",,pdf:https://europepmc.org/articles/pmc7611259?pdf=render; doi:https://doi.org/10.1038/s41588-020-00762-2; html:https://europepmc.org/articles/PMC7611259; pdf:https://europepmc.org/articles/PMC7611259?pdf=render
 34228774,https://doi.org/10.1001/jama.2021.11330,Association Between Administration of IL-6 Antagonists and Mortality Among Patients Hospitalized for COVID-19: A Meta-analysis.,"WHO Rapid Evidence Appraisal for COVID-19 Therapies (REACT) Working Group, Shankar-Hari M, Vale CL, Godolphin PJ, Fisher D, Higgins JPT, Spiga F, Savovic J, Tierney J, Baron G, Benbenishty JS, Berry LR, Broman N, Cavalcanti AB, Colman R, De Buyser SL, Derde LPG, Domingo P, Omar SF, Fernandez-Cruz A, Feuth T, Garcia F, Garcia-Vicuna R, Gonzalez-Alvaro I, Gordon AC, Haynes R, Hermine O, Horby PW, Horick NK, Kumar K, Lambrecht BN, Landray MJ, Leal L, Lederer DJ, Lorenzi E, Mariette X, Merchante N, Misnan NA, Mohan SV, Nivens MC, Oksi J, Perez-Molina JA, Pizov R, Porcher R, Postma S, Rajasuriar R, Ramanan AV, Ravaud P, Reid PD, Rutgers A, Sancho-Lopez A, Seto TB, Sivapalasingam S, Soin AS, Staplin N, Stone JH, Strohbehn GW, Sunden-Cullberg J, Torre-Cisneros J, Tsai LW, van Hoogstraten H, van Meerten T, Veiga VC, Westerweel PE, Murthy S, Diaz JV, Marshall JC, Sterne JAC.",,JAMA,2021,2021-08-01,N,,,,"<h4>Importance</h4>Clinical trials assessing the efficacy of IL-6 antagonists in patients hospitalized for COVID-19 have variously reported benefit, no effect, and harm.<h4>Objective</h4>To estimate the association between administration of IL-6 antagonists compared with usual care or placebo and 28-day all-cause mortality and other outcomes.<h4>Data sources</h4>Trials were identified through systematic searches of electronic databases between October 2020 and January 2021. Searches were not restricted by trial status or language. Additional trials were identified through contact with experts.<h4>Study selection</h4>Eligible trials randomly assigned patients hospitalized for COVID-19 to a group in whom IL-6 antagonists were administered and to a group in whom neither IL-6 antagonists nor any other immunomodulators except corticosteroids were administered. Among 72 potentially eligible trials, 27 (37.5%) met study selection criteria.<h4>Data extraction and synthesis</h4>In this prospective meta-analysis, risk of bias was assessed using the Cochrane Risk of Bias Assessment Tool. Inconsistency among trial results was assessed using the I2 statistic. The primary analysis was an inverse variance-weighted fixed-effects meta-analysis of odds ratios (ORs) for 28-day all-cause mortality.<h4>Main outcomes and measures</h4>The primary outcome measure was all-cause mortality at 28 days after randomization. There were 9 secondary outcomes including progression to invasive mechanical ventilation or death and risk of secondary infection by 28 days.<h4>Results</h4>A total of 10 930 patients (median age, 61 years [range of medians, 52-68 years]; 3560 [33%] were women) participating in 27 trials were included. By 28 days, there were 1407 deaths among 6449 patients randomized to IL-6 antagonists and 1158 deaths among 4481 patients randomized to usual care or placebo (summary OR, 0.86 [95% CI, 0.79-0.95]; P = .003 based on a fixed-effects meta-analysis). This corresponds to an absolute mortality risk of 22% for IL-6 antagonists compared with an assumed mortality risk of 25% for usual care or placebo. The corresponding summary ORs were 0.83 (95% CI, 0.74-0.92; P < .001) for tocilizumab and 1.08 (95% CI, 0.86-1.36; P = .52) for sarilumab. The summary ORs for the association with mortality compared with usual care or placebo in those receiving corticosteroids were 0.77 (95% CI, 0.68-0.87) for tocilizumab and 0.92 (95% CI, 0.61-1.38) for sarilumab. The ORs for the association with progression to invasive mechanical ventilation or death, compared with usual care or placebo, were 0.77 (95% CI, 0.70-0.85) for all IL-6 antagonists, 0.74 (95% CI, 0.66-0.82) for tocilizumab, and 1.00 (95% CI, 0.74-1.34) for sarilumab. Secondary infections by 28 days occurred in 21.9% of patients treated with IL-6 antagonists vs 17.6% of patients treated with usual care or placebo (OR accounting for trial sample sizes, 0.99; 95% CI, 0.85-1.16).<h4>Conclusions and relevance</h4>In this prospective meta-analysis of clinical trials of patients hospitalized for COVID-19, administration of IL-6 antagonists, compared with usual care or placebo, was associated with lower 28-day all-cause mortality.<h4>Trial registration</h4>PROSPERO Identifier: CRD42021230155.",,pdf:https://biblio.ugent.be/publication/8716283/file/8716284.pdf; doi:https://doi.org/10.1001/jama.2021.11330; html:https://europepmc.org/articles/PMC8261689; doi:https://doi.org/10.1001/jama.2021.11330
 32553130,https://doi.org/10.1016/s2214-109x(20)30264-3,"Global, regional, and national estimates of the population at increased risk of severe COVID-19 due to underlying health conditions in 2020: a modelling study.","Clark A, Jit M, Warren-Gash C, Guthrie B, Wang HHX, Mercer SW, Sanderson C, McKee M, Troeger C, Ong KL, Checchi F, Perel P, Joseph S, Gibbs HP, Banerjee A, Eggo RM, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 working group.",,The Lancet. Global health,2020,2020-06-15,Y,,,,"<h4>Background</h4>The risk of severe COVID-19 if an individual becomes infected is known to be higher in older individuals and those with underlying health conditions. Understanding the number of individuals at increased risk of severe COVID-19 and how this varies between countries should inform the design of possible strategies to shield or vaccinate those at highest risk.<h4>Methods</h4>We estimated the number of individuals at increased risk of severe disease (defined as those with at least one condition listed as ""at increased risk of severe COVID-19"" in current guidelines) by age (5-year age groups), sex, and country for 188 countries using prevalence data from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017 and UN population estimates for 2020. The list of underlying conditions relevant to COVID-19 was determined by mapping the conditions listed in GBD 2017 to those listed in guidelines published by WHO and public health agencies in the UK and the USA. We analysed data from two large multimorbidity studies to determine appropriate adjustment factors for clustering and multimorbidity. To help interpretation of the degree of risk among those at increased risk, we also estimated the number of individuals at high risk (defined as those that would require hospital admission if infected) using age-specific infection-hospitalisation ratios for COVID-19 estimated for mainland China and making adjustments to reflect country-specific differences in the prevalence of underlying conditions and frailty. We assumed males were twice at likely as females to be at high risk. We also calculated the number of individuals without an underlying condition that could be considered at increased risk because of their age, using minimum ages from 50 to 70 years. We generated uncertainty intervals (UIs) for our estimates by running low and high scenarios using the lower and upper 95% confidence limits for country population size, disease prevalences, multimorbidity fractions, and infection-hospitalisation ratios, and plausible low and high estimates for the degree of clustering, informed by multimorbidity studies.<h4>Findings</h4>We estimated that 1·7 billion (UI 1·0-2·4) people, comprising 22% (UI 15-28) of the global population, have at least one underlying condition that puts them at increased risk of severe COVID-19 if infected (ranging from <5% of those younger than 20 years to >66% of those aged 70 years or older). We estimated that 349 million (186-787) people (4% [3-9] of the global population) are at high risk of severe COVID-19 and would require hospital admission if infected (ranging from <1% of those younger than 20 years to approximately 20% of those aged 70 years or older). We estimated 6% (3-12) of males to be at high risk compared with 3% (2-7) of females. The share of the population at increased risk was highest in countries with older populations, African countries with high HIV/AIDS prevalence, and small island nations with high diabetes prevalence. Estimates of the number of individuals at increased risk were most sensitive to the prevalence of chronic kidney disease, diabetes, cardiovascular disease, and chronic respiratory disease.<h4>Interpretation</h4>About one in five individuals worldwide could be at increased risk of severe COVID-19, should they become infected, due to underlying health conditions, but this risk varies considerably by age. Our estimates are uncertain, and focus on underlying conditions rather than other risk factors such as ethnicity, socioeconomic deprivation, and obesity, but provide a starting point for considering the number of individuals that might need to be shielded or vaccinated as the global pandemic unfolds.<h4>Funding</h4>UK Department for International Development, Wellcome Trust, Health Data Research UK, Medical Research Council, and National Institute for Health Research.",,pdf:http://www.thelancet.com/article/S2214109X20302643/pdf; doi:https://doi.org/10.1016/S2214-109X(20)30264-3; html:https://europepmc.org/articles/PMC7295519
-35104837,https://doi.org/10.1038/s41586-022-04474-x,Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity.,"Meng B, Abdullahi A, Ferreira IATM, Goonawardane N, Saito A, Kimura I, Yamasoba D, Gerber PP, Fatihi S, Rathore S, Zepeda SK, Papa G, Kemp SA, Ikeda T, Toyoda M, Tan TS, Kuramochi J, Mitsunaga S, Ueno T, Shirakawa K, Takaori-Kondo A, Brevini T, Mallery DL, Charles OJ, CITIID-NIHR BioResource COVID-19 Collaboration, Genotype to Phenotype Japan (G2P-Japan) Consortium, Ecuador-COVID19 Consortium, Bowen JE, Joshi A, Walls AC, Jackson L, Martin D, Smith KGC, Bradley J, Briggs JAG, Choi J, Madissoon E, Meyer KB, Mlcochova P, Ceron-Gutierrez L, Doffinger R, Teichmann SA, Fisher AJ, Pizzuto MS, de Marco A, Corti D, Hosmillo M, Lee JH, James LC, Thukral L, Veesler D, Sigal A, Sampaziotis F, Goodfellow IG, Matheson NJ, Sato K, Gupta RK.",,Nature,2022,2022-02-01,Y,,,,"The SARS-CoV-2 Omicron BA.1 variant emerged in 2021<sup>1</sup> and has multiple mutations in its spike protein<sup>2</sup>. Here we show that the spike protein of Omicron has a higher affinity for ACE2 compared with Delta, and a marked change in its antigenicity increases Omicron's evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralizing antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralization. Importantly, the antiviral drugs remdesivir and molnupiravir retain efficacy against Omicron BA.1. Replication was similar for Omicron and Delta virus isolates in human nasal epithelial cultures. However, in lung cells and gut cells, Omicron demonstrated lower replication. Omicron spike protein was less efficiently cleaved compared with Delta. The differences in replication were mapped to the entry efficiency of the virus on the basis of spike-pseudotyped virus assays. The defect in entry of Omicron pseudotyped virus to specific cell types effectively correlated with higher cellular RNA expression of TMPRSS2, and deletion of TMPRSS2 affected Delta entry to a greater extent than Omicron. Furthermore, drug inhibitors targeting specific entry pathways<sup>3</sup> demonstrated that the Omicron spike inefficiently uses the cellular protease TMPRSS2, which promotes cell entry through plasma membrane fusion, with greater dependency on cell entry through the endocytic pathway. Consistent with suboptimal S1/S2 cleavage and inability to use TMPRSS2, syncytium formation by the Omicron spike was substantially impaired compared with the Delta spike. The less efficient spike cleavage of Omicron at S1/S2 is associated with a shift in cellular tropism away from TMPRSS2-expressing cells, with implications for altered pathogenesis.",,pdf:https://www.nature.com/articles/s41586-022-04474-x.pdf; doi:https://doi.org/10.1038/s41586-022-04474-x; html:https://europepmc.org/articles/PMC8942856; pdf:https://europepmc.org/articles/PMC8942856?pdf=render
 32888493,https://doi.org/10.1016/j.cell.2020.06.045,"Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations.","Chen MH, Raffield LM, Mousas A, Sakaue S, Huffman JE, Moscati A, Trivedi B, Jiang T, Akbari P, Vuckovic D, Bao EL, Zhong X, Manansala R, Laplante V, Chen M, Lo KS, Qian H, Lareau CA, Beaudoin M, Hunt KA, Akiyama M, Bartz TM, Ben-Shlomo Y, Beswick A, Bork-Jensen J, Bottinger EP, Brody JA, van Rooij FJA, Chitrala K, Cho K, Choquet H, Correa A, Danesh J, Di Angelantonio E, Dimou N, Ding J, Elliott P, Esko T, Evans MK, Floyd JS, Broer L, Grarup N, Guo MH, Greinacher A, Haessler J, Hansen T, Howson JMM, Huang QQ, Huang W, Jorgenson E, Kacprowski T, Kähönen M, Kamatani Y, Kanai M, Karthikeyan S, Koskeridis F, Lange LA, Lehtimäki T, Lerch MM, Linneberg A, Liu Y, Lyytikäinen LP, Manichaikul A, Martin HC, Matsuda K, Mohlke KL, Mononen N, Murakami Y, Nadkarni GN, Nauck M, Nikus K, Ouwehand WH, Pankratz N, Pedersen O, Preuss M, Psaty BM, Raitakari OT, Roberts DJ, Rich SS, Rodriguez BAT, Rosen JD, Rotter JI, Schubert P, Spracklen CN, Surendran P, Tang H, Tardif JC, Trembath RC, Ghanbari M, Völker U, Völzke H, Watkins NA, Zonderman AB, VA Million Veteran Program, Wilson PWF, Li Y, Butterworth AS, Gauchat JF, Chiang CWK, Li B, Loos RJF, Astle WJ, Evangelou E, van Heel DA, Sankaran VG, Okada Y, Soranzo N, Johnson AD, Reiner AP, Auer PL, Lettre G.",,Cell,2020,2020-09-01,N,"Interleukin-7, Genetic Architecture, Fine-mapping, Selective Sweeps, Polygenic Trait Score, Phenome-wide Association Study",,,"Most loci identified by GWASs have been found in populations of European ancestry (EUR). In trans-ethnic meta-analyses for 15 hematological traits in 746,667 participants, including 184,535 non-EUR individuals, we identified 5,552 trait-variant associations at p < 5 × 10<sup>-9</sup>, including 71 novel associations not found in EUR populations. We also identified 28 additional novel variants in ancestry-specific, non-EUR meta-analyses, including an IL7 missense variant in South Asians associated with lymphocyte count in vivo and IL-7 secretion levels in vitro. Fine-mapping prioritized variants annotated as functional and generated 95% credible sets that were 30% smaller when using the trans-ethnic as opposed to the EUR-only results. We explored the clinical significance and predictive value of trans-ethnic variants in multiple populations and compared genetic architecture and the effect of natural selection on these blood phenotypes between populations. Altogether, our results for hematological traits highlight the value of a more global representation of populations in genetic studies.",,pdf:http://www.cell.com/article/S0092867420308229/pdf; doi:https://doi.org/10.1016/j.cell.2020.06.045; html:https://europepmc.org/articles/PMC7480402; pdf:https://europepmc.org/articles/PMC7480402?pdf=render; doi:https://doi.org/10.1016/j.cell.2020.06.045
+35104837,https://doi.org/10.1038/s41586-022-04474-x,Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity.,"Meng B, Abdullahi A, Ferreira IATM, Goonawardane N, Saito A, Kimura I, Yamasoba D, Gerber PP, Fatihi S, Rathore S, Zepeda SK, Papa G, Kemp SA, Ikeda T, Toyoda M, Tan TS, Kuramochi J, Mitsunaga S, Ueno T, Shirakawa K, Takaori-Kondo A, Brevini T, Mallery DL, Charles OJ, CITIID-NIHR BioResource COVID-19 Collaboration, Genotype to Phenotype Japan (G2P-Japan) Consortium, Ecuador-COVID19 Consortium, Bowen JE, Joshi A, Walls AC, Jackson L, Martin D, Smith KGC, Bradley J, Briggs JAG, Choi J, Madissoon E, Meyer KB, Mlcochova P, Ceron-Gutierrez L, Doffinger R, Teichmann SA, Fisher AJ, Pizzuto MS, de Marco A, Corti D, Hosmillo M, Lee JH, James LC, Thukral L, Veesler D, Sigal A, Sampaziotis F, Goodfellow IG, Matheson NJ, Sato K, Gupta RK.",,Nature,2022,2022-02-01,Y,,,,"The SARS-CoV-2 Omicron BA.1 variant emerged in 2021<sup>1</sup> and has multiple mutations in its spike protein<sup>2</sup>. Here we show that the spike protein of Omicron has a higher affinity for ACE2 compared with Delta, and a marked change in its antigenicity increases Omicron's evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralizing antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralization. Importantly, the antiviral drugs remdesivir and molnupiravir retain efficacy against Omicron BA.1. Replication was similar for Omicron and Delta virus isolates in human nasal epithelial cultures. However, in lung cells and gut cells, Omicron demonstrated lower replication. Omicron spike protein was less efficiently cleaved compared with Delta. The differences in replication were mapped to the entry efficiency of the virus on the basis of spike-pseudotyped virus assays. The defect in entry of Omicron pseudotyped virus to specific cell types effectively correlated with higher cellular RNA expression of TMPRSS2, and deletion of TMPRSS2 affected Delta entry to a greater extent than Omicron. Furthermore, drug inhibitors targeting specific entry pathways<sup>3</sup> demonstrated that the Omicron spike inefficiently uses the cellular protease TMPRSS2, which promotes cell entry through plasma membrane fusion, with greater dependency on cell entry through the endocytic pathway. Consistent with suboptimal S1/S2 cleavage and inability to use TMPRSS2, syncytium formation by the Omicron spike was substantially impaired compared with the Delta spike. The less efficient spike cleavage of Omicron at S1/S2 is associated with a shift in cellular tropism away from TMPRSS2-expressing cells, with implications for altered pathogenesis.",,pdf:https://www.nature.com/articles/s41586-022-04474-x.pdf; doi:https://doi.org/10.1038/s41586-022-04474-x; html:https://europepmc.org/articles/PMC8942856; pdf:https://europepmc.org/articles/PMC8942856?pdf=render
 37708900,https://doi.org/10.1016/s2213-8587(23)00223-1,Life expectancy associated with different ages at diagnosis of type 2 diabetes in high-income countries: 23 million person-years of observation.,Emerging Risk Factors Collaboration.,,The lancet. Diabetes & endocrinology,2023,2023-09-11,Y,,,,"<h4>Background</h4>The prevalence of type 2 diabetes is increasing rapidly, particularly among younger age groups. Estimates suggest that people with diabetes die, on average, 6 years earlier than people without diabetes. We aimed to provide reliable estimates of the associations between age at diagnosis of diabetes and all-cause mortality, cause-specific mortality, and reductions in life expectancy.<h4>Methods</h4>For this observational study, we conducted a combined analysis of individual-participant data from 19 high-income countries using two large-scale data sources: the Emerging Risk Factors Collaboration (96 cohorts, median baseline years 1961-2007, median latest follow-up years 1980-2013) and the UK Biobank (median baseline year 2006, median latest follow-up year 2020). We calculated age-adjusted and sex-adjusted hazard ratios (HRs) for all-cause mortality according to age at diagnosis of diabetes using data from 1 515 718 participants, in whom deaths were recorded during 23·1 million person-years of follow-up. We estimated cumulative survival by applying age-specific HRs to age-specific death rates from 2015 for the USA and the EU.<h4>Findings</h4>For participants with diabetes, we observed a linear dose-response association between earlier age at diagnosis and higher risk of all-cause mortality compared with participants without diabetes. HRs were 2·69 (95% CI 2·43-2·97) when diagnosed at 30-39 years, 2·26 (2·08-2·45) at 40-49 years, 1·84 (1·72-1·97) at 50-59 years, 1·57 (1·47-1·67) at 60-69 years, and 1·39 (1·29-1·51) at 70 years and older. HRs per decade of earlier diagnosis were similar for men and women. Using death rates from the USA, a 50-year-old individual with diabetes died on average 14 years earlier when diagnosed aged 30 years, 10 years earlier when diagnosed aged 40 years, or 6 years earlier when diagnosed aged 50 years than an individual without diabetes. Using EU death rates, the corresponding estimates were 13, 9, or 5 years earlier.<h4>Interpretation</h4>Every decade of earlier diagnosis of diabetes was associated with about 3-4 years of lower life expectancy, highlighting the need to develop and implement interventions that prevent or delay the onset of diabetes and to intensify the treatment of risk factors among young adults diagnosed with diabetes.<h4>Funding</h4>British Heart Foundation, Medical Research Council, National Institute for Health and Care Research, and Health Data Research UK.",,doi:https://doi.org/10.1016/S2213-8587(23)00223-1; html:https://europepmc.org/articles/PMC7615299; pdf:https://europepmc.org/articles/PMC7615299?pdf=render
 34582791,https://doi.org/10.1016/j.ajhg.2021.08.007,Whole-genome sequencing in diverse subjects identifies genetic correlates of leukocyte traits: The NHLBI TOPMed program.,"Mikhaylova AV, McHugh CP, Polfus LM, Raffield LM, Boorgula MP, Blackwell TW, Brody JA, Broome J, Chami N, Chen MH, Conomos MP, Cox C, Curran JE, Daya M, Ekunwe L, Glahn DC, Heard-Costa N, Highland HM, Hobbs BD, Ilboudo Y, Jain D, Lange LA, Miller-Fleming TW, Min N, Moon JY, Preuss MH, Rosen J, Ryan K, Smith AV, Sun Q, Surendran P, de Vries PS, Walter K, Wang Z, Wheeler M, Yanek LR, Zhong X, Abecasis GR, Almasy L, Barnes KC, Beaty TH, Becker LC, Blangero J, Boerwinkle E, Butterworth AS, Chavan S, Cho MH, Choquet H, Correa A, Cox N, DeMeo DL, Faraday N, Fornage M, Gerszten RE, Hou L, Johnson AD, Jorgenson E, Kaplan R, Kooperberg C, Kundu K, Laurie CA, Lettre G, Lewis JP, Li B, Li Y, Lloyd-Jones DM, Loos RJF, Manichaikul A, Meyers DA, Mitchell BD, Morrison AC, Ngo D, Nickerson DA, Nongmaithem S, North KE, O'Connell JR, Ortega VE, Pankratz N, Perry JA, Psaty BM, Rich SS, Soranzo N, Rotter JI, Silverman EK, Smith NL, Tang H, Tracy RP, Thornton TA, Vasan RS, Zein J, Mathias RA, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Reiner AP, Auer PL.",,American journal of human genetics,2021,2021-09-27,N,Whole-genome Sequencing; Blood-cell Counts,,,"Many common and rare variants associated with hematologic traits have been discovered through imputation on large-scale reference panels. However, the majority of genome-wide association studies (GWASs) have been conducted in Europeans, and determining causal variants has proved challenging. We performed a GWAS of total leukocyte, neutrophil, lymphocyte, monocyte, eosinophil, and basophil counts generated from 109,563,748 variants in the autosomes and the X chromosome in the Trans-Omics for Precision Medicine (TOPMed) program, which included data from 61,802 individuals of diverse ancestry. We discovered and replicated 7 leukocyte trait associations, including (1) the association between a chromosome X, pseudo-autosomal region (PAR), noncoding variant located between cytokine receptor genes (CSF2RA and CLRF2) and lower eosinophil count; and (2) associations between single variants found predominantly among African Americans at the S1PR3 (9q22.1) and HBB (11p15.4) loci and monocyte and lymphocyte counts, respectively. We further provide evidence indicating that the newly discovered eosinophil-lowering chromosome X PAR variant might be associated with reduced susceptibility to common allergic diseases such as atopic dermatitis and asthma. Additionally, we found a burden of very rare FLT3 (13q12.2) variants associated with monocyte counts. Together, these results emphasize the utility of whole-genome sequencing in diverse samples in identifying associations missed by European-ancestry-driven GWASs.",,pdf:http://www.cell.com/article/S0002929721003062/pdf; doi:https://doi.org/10.1016/j.ajhg.2021.08.007; html:https://europepmc.org/articles/PMC8546043; pdf:https://europepmc.org/articles/PMC8546043?pdf=render; doi:https://doi.org/10.1016/j.ajhg.2021.08.007
 34087097,https://doi.org/10.1016/s2352-3018(21)00051-5,"Subnational mapping of HIV incidence and mortality among individuals aged 15-49 years in sub-Saharan Africa, 2000-18: a modelling study.",Local Burden of Disease HIV Collaborators.,,The lancet. HIV,2021,2021-06-01,Y,,,,"<h4>Background</h4>High-resolution estimates of HIV burden across space and time provide an important tool for tracking and monitoring the progress of prevention and control efforts and assist with improving the precision and efficiency of targeting efforts. We aimed to assess HIV incidence and HIV mortality for all second-level administrative units across sub-Saharan Africa.<h4>Methods</h4>In this modelling study, we developed a framework that used the geographically specific HIV prevalence data collected in seroprevalence surveys and antenatal care clinics to train a model that estimates HIV incidence and mortality among individuals aged 15-49 years. We used a model-based geostatistical framework to estimate HIV prevalence at the second administrative level in 44 countries in sub-Saharan Africa for 2000-18 and sought data on the number of individuals on antiretroviral therapy (ART) by second-level administrative unit. We then modified the Estimation and Projection Package (EPP) to use these HIV prevalence and treatment estimates to estimate HIV incidence and mortality by second-level administrative unit.<h4>Findings</h4>The estimates suggest substantial variation in HIV incidence and mortality rates both between and within countries in sub-Saharan Africa, with 15 countries having a ten-times or greater difference in estimated HIV incidence between the second-level administrative units with the lowest and highest estimated incidence levels. Across all 44 countries in 2018, HIV incidence ranged from 2·8 (95% uncertainty interval 2·1-3·8) in Mauritania to 1585·9 (1369·4-1824·8) cases per 100 000 people in Lesotho and HIV mortality ranged from 0·8 (0·7-0·9) in Mauritania to 676·5 (513·6-888·0) deaths per 100 000 people in Lesotho. Variation in both incidence and mortality was substantially greater at the subnational level than at the national level and the highest estimated rates were accordingly higher. Among second-level administrative units, Guijá District, Gaza Province, Mozambique, had the highest estimated HIV incidence (4661·7 [2544·8-8120·3]) cases per 100 000 people in 2018 and Inhassunge District, Zambezia Province, Mozambique, had the highest estimated HIV mortality rate (1163·0 [679·0-1866·8]) deaths per 100 000 people. Further, the rate of reduction in HIV incidence and mortality from 2000 to 2018, as well as the ratio of new infections to the number of people living with HIV was highly variable. Although most second-level administrative units had declines in the number of new cases (3316 [81·1%] of 4087 units) and number of deaths (3325 [81·4%]), nearly all appeared well short of the targeted 75% reduction in new cases and deaths between 2010 and 2020.<h4>Interpretation</h4>Our estimates suggest that most second-level administrative units in sub-Saharan Africa are falling short of the targeted 75% reduction in new cases and deaths by 2020, which is further compounded by substantial within-country variability. These estimates will help decision makers and programme implementers expand access to ART and better target health resources to higher burden subnational areas.<h4>Funding</h4>Bill & Melinda Gates Foundation.",,pdf:https://digital.library.adelaide.edu.au/dspace/bitstream/2440/131776/2/hdl_131776.pdf; doi:https://doi.org/10.1016/S2352-3018(21)00051-5; html:https://europepmc.org/articles/PMC8187986
@@ -2854,8 +2856,8 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 35944070,https://doi.org/10.1371/journal.pbio.3001755,"Genome-wide association studies of global Mycobacterium tuberculosis resistance to 13 antimicrobials in 10,228 genomes identify new resistance mechanisms.",The CRyPTIC Consortium.,,PLoS biology,2022,2022-08-09,Y,,,,"The emergence of drug-resistant tuberculosis is a major global public health concern that threatens the ability to control the disease. Whole-genome sequencing as a tool to rapidly diagnose resistant infections can transform patient treatment and clinical practice. While resistance mechanisms are well understood for some drugs, there are likely many mechanisms yet to be uncovered, particularly for new and repurposed drugs. We sequenced 10,228 Mycobacterium tuberculosis (MTB) isolates worldwide and determined the minimum inhibitory concentration (MIC) on a grid of 2-fold concentration dilutions for 13 antimicrobials using quantitative microtiter plate assays. We performed oligopeptide- and oligonucleotide-based genome-wide association studies using linear mixed models to discover resistance-conferring mechanisms not currently catalogued. Use of MIC over binary resistance phenotypes increased sample heritability for the new and repurposed drugs by 26% to 37%, increasing our ability to detect novel associations. For all drugs, we discovered uncatalogued variants associated with MIC, including in the Rv1218c promoter binding site of the transcriptional repressor Rv1219c (isoniazid), upstream of the vapBC20 operon that cleaves 23S rRNA (linezolid) and in the region encoding an α-helix lining the active site of Cyp142 (clofazimine, all p < 10-7.7). We observed that artefactual signals of cross-resistance could be unravelled based on the relative effect size on MIC. Our study demonstrates the ability of very large-scale studies to substantially improve our knowledge of genetic variants associated with antimicrobial resistance in M. tuberculosis.",,pdf:https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.3001755&type=printable; doi:https://doi.org/10.1371/journal.pbio.3001755; html:https://europepmc.org/articles/PMC9363015; pdf:https://europepmc.org/articles/PMC9363015?pdf=render
 34083753,https://doi.org/10.1038/s41562-021-01108-6,"Mapping inequalities in exclusive breastfeeding in low- and middle-income countries, 2000-2018.","Bhattacharjee NV, Schaeffer LE, Hay SI, Local Burden of Disease Exclusive Breastfeeding Collaborators.",,Nature human behaviour,2021,2021-06-03,Y,,,,"Exclusive breastfeeding (EBF)-giving infants only breast-milk for the first 6 months of life-is a component of optimal breastfeeding practices effective in preventing child morbidity and mortality. EBF practices are known to vary by population and comparable subnational estimates of prevalence and progress across low- and middle-income countries (LMICs) are required for planning policy and interventions. Here we present a geospatial analysis of EBF prevalence estimates from 2000 to 2018 across 94 LMICs mapped to policy-relevant administrative units (for example, districts), quantify subnational inequalities and their changes over time, and estimate probabilities of meeting the World Health Organization's Global Nutrition Target (WHO GNT) of ≥70% EBF prevalence by 2030. While six LMICs are projected to meet the WHO GNT of ≥70% EBF prevalence at a national scale, only three are predicted to meet the target in all their district-level units by 2030.",,pdf:https://www.nature.com/articles/s41562-021-01108-6.pdf; doi:https://doi.org/10.1038/s41562-021-01108-6; html:https://europepmc.org/articles/PMC8373614; pdf:https://europepmc.org/articles/PMC8373614?pdf=render
 35023833,https://doi.org/10.7554/elife.71802,Epigenetic scores for the circulating proteome as tools for disease prediction.,"Gadd DA, Hillary RF, McCartney DL, Zaghlool SB, Stevenson AJ, Cheng Y, Fawns-Ritchie C, Nangle C, Campbell A, Flaig R, Harris SE, Walker RM, Shi L, Tucker-Drob EM, Gieger C, Peters A, Waldenberger M, Graumann J, McRae AF, Deary IJ, Porteous DJ, Hayward C, Visscher PM, Cox SR, Evans KL, McIntosh AM, Suhre K, Marioni RE.",,eLife,2022,2022-01-13,Y,Human; Prediction; Aging; Genetics; Proteomics; Genomics; Biomarker; epidemiology; Global Health; Epigenetic; Morbiditiy,,,"Protein biomarkers have been identified across many age-related morbidities. However, characterising epigenetic influences could further inform disease predictions. Here, we leverage epigenome-wide data to study links between the DNA methylation (DNAm) signatures of the circulating proteome and incident diseases. Using data from four cohorts, we trained and tested epigenetic scores (EpiScores) for 953 plasma proteins, identifying 109 scores that explained between 1% and 58% of the variance in protein levels after adjusting for known protein quantitative trait loci (pQTL) genetic effects. By projecting these EpiScores into an independent sample (Generation Scotland; n = 9537) and relating them to incident morbidities over a follow-up of 14 years, we uncovered 137 EpiScore-disease associations. These associations were largely independent of immune cell proportions, common lifestyle and health factors, and biological aging. Notably, we found that our diabetes-associated EpiScores highlighted previous top biomarker associations from proteome-wide assessments of diabetes. These EpiScores for protein levels can therefore be a valuable resource for disease prediction and risk stratification.",,doi:https://doi.org/10.7554/elife.71802; doi:https://doi.org/10.7554/eLife.71802; html:https://europepmc.org/articles/PMC8880990; pdf:https://europepmc.org/articles/PMC8880990?pdf=render
-39280063,https://doi.org/10.12688/wellcomeopenres.18754.1,Large-scale exome array summary statistics resources for glycemic traits to aid effector gene prioritization.,"Willems SM, Ng NHJ, Fernandez J, Fine RS, Wheeler E, Wessel J, Kitajima H, Marenne G, Sim X, Yaghootkar H, Wang S, Chen S, Chen Y, Chen YI, Grarup N, Li-Gao R, Varga TV, Asimit JL, Feng S, Strawbridge RJ, Kleinbrink EL, Ahluwalia TS, An P, Appel EV, Arking DE, Auvinen J, Bielak LF, Bihlmeyer NA, Bork-Jensen J, Brody JA, Campbell A, Chu AY, Davies G, Demirkan A, Floyd JS, Giulianini F, Guo X, Gustafsson S, Jackson AU, Jakobsdottir J, Järvelin MR, Jensen RA, Kanoni S, Keinanen-Kiukaanniemi S, Li M, Lu Y, Luan J, Manning AK, Marten J, Meidtner K, Mook-Kanamori DO, Muka T, Pistis G, Prins B, Rice KM, Sanna S, Smith AV, Smith JA, Southam L, Stringham HM, Tragante V, van der Laan SW, Warren HR, Yao J, Yiorkas AM, Zhang W, Zhao W, Graff M, Highland HM, Justice AE, Marouli E, Medina-Gomez C, Afaq S, Alhejily WA, Amin N, Asselbergs FW, Bonnycastle LL, Bots ML, Brandslund I, Chen J, Danesh J, de Mutsert R, Dehghan A, Ebeling T, Elliott P, EPIC-Interact Consortium, Farmaki AE, Faul JD, Franks PW, Franks S, Fritsche A, Gjesing AP, Goodarzi MO, Gudnason V, Hallmans G, Harris TB, Herzig KH, Hivert MF, Jørgensen T, Jørgensen ME, Jousilahti P, Kajantie E, Karaleftheri M, Kardia SLR, Kinnunen L, Koistinen HA, Komulainen P, Kovacs P, Kuusisto J, Laakso M, Lange LA, Launer LJ, Leong A, Lindström J, Manning Fox JE, Männistö S, Maruthur NM, Moilanen L, Mulas A, Nalls MA, Neville M, Pankow JS, Pattie A, Petersen ERB, Puolijoki H, Rasheed A, Redmond P, Renström F, Roden M, Saleheen D, Saltevo J, Savonen K, Sebert S, Skaaby T, Small KS, Stančáková A, Stokholm J, Strauch K, Tai ES, Taylor KD, Thuesen BH, Tönjes A, Tsafantakis E, Tuomi T, Tuomilehto J, Understanding Society Scientific Group, Uusitupa M, Vääräsmäki M, Vaartjes I, Zoledziewska M, Abecasis G, Balkau B, Bisgaard H, Blakemore AI, Blüher M, Boeing H, Boerwinkle E, Bønnelykke K, Bottinger EP, Caulfield MJ, Chambers JC, Chasman DI, Cheng CY, Collins FS, Coresh J, Cucca F, de Borst GJ, Deary IJ, Dedoussis G, Deloukas P, den Ruijter HM, Dupuis J, Evans MK, Ferrannini E, Franco OH, Grallert H, Hansen T, Hattersley AT, Hayward C, Hirschhorn JN, Ikram A, Ingelsson E, Karpe F, Kaw KT, Kiess W, Kooner JS, Körner A, Lakka T, Langenberg C, Lind L, Lindgren CM, Linneberg A, Lipovich L, Liu CT, Liu J, Liu Y, Loos RJF, MacDonald PE, Mohlke KL, Morris AD, Munroe PB, Murray A, Padmanabhan S, Palmer CNA, Pasterkamp G, Pedersen O, Peyser PA, Polasek O, Porteous D, Province MA, Psaty BM, Rauramaa R, Ridker PM, Rolandsson O, Rorsman P, Rosendaal FR, Rudan I, Salomaa V, Schulze MB, Sladek R, Smith BH, Spector TD, Starr JM, Stumvoll M, van Duijn CM, Walker M, Wareham NJ, Weir DR, Wilson JG, Wong TY, Zeggini E, Zonderman AB, Rotter JI, Morris AP, Boehnke M, Florez JC, McCarthy MI, Meigs JB, Mahajan A, Scott RA, Gloyn AL, Barroso I.",,Wellcome open research,2023,2023-10-20,Y,Effector Genes; Exome Chip; Glycaemic Traits; Genetic Discovery; Summary Statistics Resources,,,"<h4>Background</h4>Genome-wide association studies for glycemic traits have identified hundreds of loci associated with these biomarkers of glucose homeostasis. Despite this success, the challenge remains to link variant associations to genes, and underlying biological pathways.<h4>Methods</h4>To identify coding variant associations which may pinpoint effector genes at both novel and previously established genome-wide association loci, we performed meta-analyses of exome-array studies for four glycemic traits: glycated hemoglobin (HbA1c, up to 144,060 participants), fasting glucose (FG, up to 129,665 participants), fasting insulin (FI, up to 104,140) and 2hr glucose post-oral glucose challenge (2hGlu, up to 57,878). In addition, we performed network and pathway analyses.<h4>Results</h4>Single-variant and gene-based association analyses identified coding variant associations at more than 60 genes, which when combined with other datasets may be useful to nominate effector genes. Network and pathway analyses identified pathways related to insulin secretion, zinc transport and fatty acid metabolism. HbA1c associations were strongly enriched in pathways related to blood cell biology.<h4>Conclusions</h4>Our results provided novel glycemic trait associations and highlighted pathways implicated in glycemic regulation. Exome-array summary statistic results are being made available to the scientific community to enable further discoveries.",,doi:https://doi.org/10.12688/wellcomeopenres.18754.1; html:https://europepmc.org/articles/PMC11399760; pdf:https://europepmc.org/articles/PMC11399760?pdf=render
 32375776,https://doi.org/10.1186/s12916-020-01597-8,Quantifying the impact of physical distance measures on the transmission of COVID-19 in the UK.,"Jarvis CI, Van Zandvoort K, Gimma A, Prem K, CMMID COVID-19 working group, Klepac P, Rubin GJ, Edmunds WJ.",,BMC medicine,2020,2020-05-07,Y,Pandemic; Disease Outbreak; Reproduction Number; Ncov; Covid-19; Contact Survey,,,"<h4>Background</h4>To mitigate and slow the spread of COVID-19, many countries have adopted unprecedented physical distancing policies, including the UK. We evaluate whether these measures might be sufficient to control the epidemic by estimating their impact on the reproduction number (R<sub>0</sub>, the average number of secondary cases generated per case).<h4>Methods</h4>We asked a representative sample of UK adults about their contact patterns on the previous day. The questionnaire was conducted online via email recruitment and documents the age and location of contacts and a measure of their intimacy (whether physical contact was made or not). In addition, we asked about adherence to different physical distancing measures. The first surveys were sent on Tuesday, 24 March, 1 day after a ""lockdown"" was implemented across the UK. We compared measured contact patterns during the ""lockdown"" to patterns of social contact made during a non-epidemic period. By comparing these, we estimated the change in reproduction number as a consequence of the physical distancing measures imposed. We used a meta-analysis of published estimates to inform our estimates of the reproduction number before interventions were put in place.<h4>Results</h4>We found a 74% reduction in the average daily number of contacts observed per participant (from 10.8 to 2.8). This would be sufficient to reduce R<sub>0</sub> from 2.6 prior to lockdown to 0.62 (95% confidence interval [CI] 0.37-0.89) after the lockdown, based on all types of contact and 0.37 (95% CI = 0.22-0.53) for physical (skin to skin) contacts only.<h4>Conclusions</h4>The physical distancing measures adopted by the UK public have substantially reduced contact levels and will likely lead to a substantial impact and a decline in cases in the coming weeks. However, this projected decline in incidence will not occur immediately as there are significant delays between infection, the onset of symptomatic disease, and hospitalisation, as well as further delays to these events being reported. Tracking behavioural change can give a more rapid assessment of the impact of physical distancing measures than routine epidemiological surveillance.",This paper utilises questionaire data and modelling data to identify the likely reduction of contacts a person encounters in a day. The study estimated a 74 % reduction in contacts per day which will have an influence in the spread of COVID-19.,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-020-01597-8; doi:https://doi.org/10.1186/s12916-020-01597-8; html:https://europepmc.org/articles/PMC7202922; pdf:https://europepmc.org/articles/PMC7202922?pdf=render
+39280063,https://doi.org/10.12688/wellcomeopenres.18754.1,Large-scale exome array summary statistics resources for glycemic traits to aid effector gene prioritization.,"Willems SM, Ng NHJ, Fernandez J, Fine RS, Wheeler E, Wessel J, Kitajima H, Marenne G, Sim X, Yaghootkar H, Wang S, Chen S, Chen Y, Chen YI, Grarup N, Li-Gao R, Varga TV, Asimit JL, Feng S, Strawbridge RJ, Kleinbrink EL, Ahluwalia TS, An P, Appel EV, Arking DE, Auvinen J, Bielak LF, Bihlmeyer NA, Bork-Jensen J, Brody JA, Campbell A, Chu AY, Davies G, Demirkan A, Floyd JS, Giulianini F, Guo X, Gustafsson S, Jackson AU, Jakobsdottir J, Järvelin MR, Jensen RA, Kanoni S, Keinanen-Kiukaanniemi S, Li M, Lu Y, Luan J, Manning AK, Marten J, Meidtner K, Mook-Kanamori DO, Muka T, Pistis G, Prins B, Rice KM, Sanna S, Smith AV, Smith JA, Southam L, Stringham HM, Tragante V, van der Laan SW, Warren HR, Yao J, Yiorkas AM, Zhang W, Zhao W, Graff M, Highland HM, Justice AE, Marouli E, Medina-Gomez C, Afaq S, Alhejily WA, Amin N, Asselbergs FW, Bonnycastle LL, Bots ML, Brandslund I, Chen J, Danesh J, de Mutsert R, Dehghan A, Ebeling T, Elliott P, EPIC-Interact Consortium, Farmaki AE, Faul JD, Franks PW, Franks S, Fritsche A, Gjesing AP, Goodarzi MO, Gudnason V, Hallmans G, Harris TB, Herzig KH, Hivert MF, Jørgensen T, Jørgensen ME, Jousilahti P, Kajantie E, Karaleftheri M, Kardia SLR, Kinnunen L, Koistinen HA, Komulainen P, Kovacs P, Kuusisto J, Laakso M, Lange LA, Launer LJ, Leong A, Lindström J, Manning Fox JE, Männistö S, Maruthur NM, Moilanen L, Mulas A, Nalls MA, Neville M, Pankow JS, Pattie A, Petersen ERB, Puolijoki H, Rasheed A, Redmond P, Renström F, Roden M, Saleheen D, Saltevo J, Savonen K, Sebert S, Skaaby T, Small KS, Stančáková A, Stokholm J, Strauch K, Tai ES, Taylor KD, Thuesen BH, Tönjes A, Tsafantakis E, Tuomi T, Tuomilehto J, Understanding Society Scientific Group, Uusitupa M, Vääräsmäki M, Vaartjes I, Zoledziewska M, Abecasis G, Balkau B, Bisgaard H, Blakemore AI, Blüher M, Boeing H, Boerwinkle E, Bønnelykke K, Bottinger EP, Caulfield MJ, Chambers JC, Chasman DI, Cheng CY, Collins FS, Coresh J, Cucca F, de Borst GJ, Deary IJ, Dedoussis G, Deloukas P, den Ruijter HM, Dupuis J, Evans MK, Ferrannini E, Franco OH, Grallert H, Hansen T, Hattersley AT, Hayward C, Hirschhorn JN, Ikram A, Ingelsson E, Karpe F, Kaw KT, Kiess W, Kooner JS, Körner A, Lakka T, Langenberg C, Lind L, Lindgren CM, Linneberg A, Lipovich L, Liu CT, Liu J, Liu Y, Loos RJF, MacDonald PE, Mohlke KL, Morris AD, Munroe PB, Murray A, Padmanabhan S, Palmer CNA, Pasterkamp G, Pedersen O, Peyser PA, Polasek O, Porteous D, Province MA, Psaty BM, Rauramaa R, Ridker PM, Rolandsson O, Rorsman P, Rosendaal FR, Rudan I, Salomaa V, Schulze MB, Sladek R, Smith BH, Spector TD, Starr JM, Stumvoll M, van Duijn CM, Walker M, Wareham NJ, Weir DR, Wilson JG, Wong TY, Zeggini E, Zonderman AB, Rotter JI, Morris AP, Boehnke M, Florez JC, McCarthy MI, Meigs JB, Mahajan A, Scott RA, Gloyn AL, Barroso I.",,Wellcome open research,2023,2023-10-20,Y,Effector Genes; Exome Chip; Glycaemic Traits; Genetic Discovery; Summary Statistics Resources,,,"<h4>Background</h4>Genome-wide association studies for glycemic traits have identified hundreds of loci associated with these biomarkers of glucose homeostasis. Despite this success, the challenge remains to link variant associations to genes, and underlying biological pathways.<h4>Methods</h4>To identify coding variant associations which may pinpoint effector genes at both novel and previously established genome-wide association loci, we performed meta-analyses of exome-array studies for four glycemic traits: glycated hemoglobin (HbA1c, up to 144,060 participants), fasting glucose (FG, up to 129,665 participants), fasting insulin (FI, up to 104,140) and 2hr glucose post-oral glucose challenge (2hGlu, up to 57,878). In addition, we performed network and pathway analyses.<h4>Results</h4>Single-variant and gene-based association analyses identified coding variant associations at more than 60 genes, which when combined with other datasets may be useful to nominate effector genes. Network and pathway analyses identified pathways related to insulin secretion, zinc transport and fatty acid metabolism. HbA1c associations were strongly enriched in pathways related to blood cell biology.<h4>Conclusions</h4>Our results provided novel glycemic trait associations and highlighted pathways implicated in glycemic regulation. Exome-array summary statistic results are being made available to the scientific community to enable further discoveries.",,doi:https://doi.org/10.12688/wellcomeopenres.18754.1; html:https://europepmc.org/articles/PMC11399760; pdf:https://europepmc.org/articles/PMC11399760?pdf=render
 35202437,https://doi.org/10.1371/journal.pone.0264341,Protein prediction for trait mapping in diverse populations.,"Schubert R, Geoffroy E, Gregga I, Mulford AJ, Aguet F, Ardlie K, Gerszten R, Clish C, Van Den Berg D, Taylor KD, Durda P, Johnson WC, Cornell E, Guo X, Liu Y, Tracy R, Conomos M, Blackwell T, Papanicolaou G, Lappalainen T, Mikhaylova AV, Thornton TA, Cho MH, Gignoux CR, Lange L, Lange E, Rich SS, Rotter JI, NHLBI TOPMed Consortium, Manichaikul A, Im HK, Wheeler HE.",,PloS one,2022,2022-02-24,Y,,,,"Genetically regulated gene expression has helped elucidate the biological mechanisms underlying complex traits. Improved high-throughput technology allows similar interrogation of the genetically regulated proteome for understanding complex trait mechanisms. Here, we used the Trans-omics for Precision Medicine (TOPMed) Multi-omics pilot study, which comprises data from Multi-Ethnic Study of Atherosclerosis (MESA), to optimize genetic predictors of the plasma proteome for genetically regulated proteome-wide association studies (PWAS) in diverse populations. We built predictive models for protein abundances using data collected in TOPMed MESA, for which we have measured 1,305 proteins by a SOMAscan assay. We compared predictive models built via elastic net regression to models integrating posterior inclusion probabilities estimated by fine-mapping SNPs prior to elastic net. In order to investigate the transferability of predictive models across ancestries, we built protein prediction models in all four of the TOPMed MESA populations, African American (n = 183), Chinese (n = 71), European (n = 416), and Hispanic/Latino (n = 301), as well as in all populations combined. As expected, fine-mapping produced more significant protein prediction models, especially in African ancestries populations, potentially increasing opportunity for discovery. When we tested our TOPMed MESA models in the independent European INTERVAL study, fine-mapping improved cross-ancestries prediction for some proteins. Using GWAS summary statistics from the Population Architecture using Genomics and Epidemiology (PAGE) study, which comprises ∼50,000 Hispanic/Latinos, African Americans, Asians, Native Hawaiians, and Native Americans, we applied S-PrediXcan to perform PWAS for 28 complex traits. The most protein-trait associations were discovered, colocalized, and replicated in large independent GWAS using proteome prediction model training populations with similar ancestries to PAGE. At current training population sample sizes, performance between baseline and fine-mapped protein prediction models in PWAS was similar, highlighting the utility of elastic net. Our predictive models in diverse populations are publicly available for use in proteome mapping methods at https://doi.org/10.5281/zenodo.4837327.",,pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0264341&type=printable; doi:https://doi.org/10.1371/journal.pone.0264341; html:https://europepmc.org/articles/PMC8870552; pdf:https://europepmc.org/articles/PMC8870552?pdf=render
 37863501,https://doi.org/10.1136/bmj-2023-076387,Enhancing reporting quality and impact of early phase dose-finding clinical trials: CONSORT Dose-finding Extension (CONSORT-DEFINE) guidance.,"Yap C, Solovyeva O, de Bono J, Rekowski J, Patel D, Jaki T, Mander A, Evans TRJ, Peck R, Hayward KS, Hopewell S, Ursino M, Rantell KR, Calvert M, Lee S, Kightley A, Ashby D, Chan AW, Garrett-Mayer E, Isaacs JD, Golub R, Kholmanskikh O, Richards D, Boix O, Matcham J, Seymour L, Ivy SP, Marshall LV, Hommais A, Liu R, Tanaka Y, Berlin J, Espinasse A, Dimairo M, Weir CJ.",,BMJ (Clinical research ed.),2023,2023-10-20,Y,,,,,,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10583500; doi:https://doi.org/10.1136/bmj-2023-076387; html:https://europepmc.org/articles/PMC10583500
 33879890,https://doi.org/10.1038/s41591-021-01329-2,Single-cell multi-omics analysis of the immune response in COVID-19.,"Stephenson E, Reynolds G, Botting RA, Calero-Nieto FJ, Morgan MD, Tuong ZK, Bach K, Sungnak W, Worlock KB, Yoshida M, Kumasaka N, Kania K, Engelbert J, Olabi B, Spegarova JS, Wilson NK, Mende N, Jardine L, Gardner LCS, Goh I, Horsfall D, McGrath J, Webb S, Mather MW, Lindeboom RGH, Dann E, Huang N, Polanski K, Prigmore E, Gothe F, Scott J, Payne RP, Baker KF, Hanrath AT, Schim van der Loeff ICD, Barr AS, Sanchez-Gonzalez A, Bergamaschi L, Mescia F, Barnes JL, Kilich E, de Wilton A, Saigal A, Saleh A, Janes SM, Smith CM, Gopee N, Wilson C, Coupland P, Coxhead JM, Kiselev VY, van Dongen S, Bacardit J, King HW, Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID-19 BioResource Collaboration, Rostron AJ, Simpson AJ, Hambleton S, Laurenti E, Lyons PA, Meyer KB, Nikolić MZ, Duncan CJA, Smith KGC, Teichmann SA, Clatworthy MR, Marioni JC, Göttgens B, Haniffa M.",,Nature medicine,2021,2021-04-20,Y,,,,"Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19. We identified expansion of nonclassical monocytes expressing complement transcripts (CD16<sup>+</sup>C1QA/B/C<sup>+</sup>) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34<sup>+</sup> hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8<sup>+</sup> T cells and an increased ratio of CD8<sup>+</sup> effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease. We observed a relative loss of IgA2 in symptomatic disease despite an overall expansion of plasmablasts and plasma cells. Our study highlights the coordinated immune response that contributes to COVID-19 pathogenesis and reveals discrete cellular components that can be targeted for therapy.",,pdf:https://www.nature.com/articles/s41591-021-01329-2.pdf; doi:https://doi.org/10.1038/s41591-021-01329-2; html:https://europepmc.org/articles/PMC8121667; pdf:https://europepmc.org/articles/PMC8121667?pdf=render
@@ -2885,8 +2887,8 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 33532862,https://doi.org/10.1093/eurheartj/ehaa1040,Genome-wide analysis identifies novel susceptibility loci for myocardial infarction.,"Hartiala JA, Han Y, Jia Q, Hilser JR, Huang P, Gukasyan J, Schwartzman WS, Cai Z, Biswas S, Trégouët DA, Smith NL, INVENT Consortium, CHARGE Consortium Hemostasis Working Group, GENIUS-CHD Consortium, Seldin M, Pan C, Mehrabian M, Lusis AJ, Bazeley P, Sun YV, Liu C, Quyyumi AA, Scholz M, Thiery J, Delgado GE, Kleber ME, März W, Howe LJ, Asselbergs FW, van Vugt M, Vlachojannis GJ, Patel RS, Lyytikäinen LP, Kähönen M, Lehtimäki T, Nieminen TVM, Kuukasjärvi P, Laurikka JO, Chang X, Heng CK, Jiang R, Kraus WE, Hauser ER, Ferguson JF, Reilly MP, Ito K, Koyama S, Kamatani Y, Komuro I, Biobank Japan, Stolze LK, Romanoski CE, Khan MD, Turner AW, Miller CL, Aherrahrou R, Civelek M, Ma L, Björkegren JLM, Kumar SR, Tang WHW, Hazen SL, Allayee H.",,European heart journal,2021,2021-03-01,N,Myocardial infarction; Meta-analysis; genetic factors; Genome-wide Association Study; Slc44a3,,,"<h4>Aims</h4>While most patients with myocardial infarction (MI) have underlying coronary atherosclerosis, not all patients with coronary artery disease (CAD) develop MI. We sought to address the hypothesis that some of the genetic factors which establish atherosclerosis may be distinct from those that predispose to vulnerable plaques and thrombus formation.<h4>Methods and results</h4>We carried out a genome-wide association study for MI in the UK Biobank (n∼472 000), followed by a meta-analysis with summary statistics from the CARDIoGRAMplusC4D Consortium (n∼167 000). Multiple independent replication analyses and functional approaches were used to prioritize loci and evaluate positional candidate genes. Eight novel regions were identified for MI at the genome wide significance level, of which effect sizes at six loci were more robust for MI than for CAD without the presence of MI. Confirmatory evidence for association of a locus on chromosome 1p21.3 harbouring choline-like transporter 3 (SLC44A3) with MI in the context of CAD, but not with coronary atherosclerosis itself, was obtained in Biobank Japan (n∼165 000) and 16 independent angiography-based cohorts (n∼27 000). Follow-up analyses did not reveal association of the SLC44A3 locus with CAD risk factors, biomarkers of coagulation, other thrombotic diseases, or plasma levels of a broad array of metabolites, including choline, trimethylamine N-oxide, and betaine. However, aortic expression of SLC44A3 was increased in carriers of the MI risk allele at chromosome 1p21.3, increased in ischaemic (vs. non-diseased) coronary arteries, up-regulated in human aortic endothelial cells treated with interleukin-1β (vs. vehicle), and associated with smooth muscle cell migration in vitro.<h4>Conclusions</h4>A large-scale analysis comprising ∼831 000 subjects revealed novel genetic determinants of MI and implicated SLC44A3 in the pathophysiology of vulnerable plaques.",,pdf:https://academic.oup.com/eurheartj/article-pdf/42/9/919/36429038/ehaa1040.pdf; doi:https://doi.org/10.1093/eurheartj/ehaa1040; html:https://europepmc.org/articles/PMC7936531; pdf:https://europepmc.org/articles/PMC7936531?pdf=render; doi:https://doi.org/10.1093/eurheartj/ehaa1040
 34493870,https://doi.org/10.1038/s41588-021-00921-z,"A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer's disease.","Wightman DP, Jansen IE, Savage JE, Shadrin AA, Bahrami S, Holland D, Rongve A, Børte S, Winsvold BS, Drange OK, Martinsen AE, Skogholt AH, Willer C, Bråthen G, Bosnes I, Nielsen JB, Fritsche LG, Thomas LF, Pedersen LM, Gabrielsen ME, Johnsen MB, Meisingset TW, Zhou W, Proitsi P, Hodges A, Dobson R, Velayudhan L, Heilbron K, Auton A, 23andMe Research Team, Sealock JM, Davis LK, Pedersen NL, Reynolds CA, Karlsson IK, Magnusson S, Stefansson H, Thordardottir S, Jonsson PV, Snaedal J, Zettergren A, Skoog I, Kern S, Waern M, Zetterberg H, Blennow K, Stordal E, Hveem K, Zwart JA, Athanasiu L, Selnes P, Saltvedt I, Sando SB, Ulstein I, Djurovic S, Fladby T, Aarsland D, Selbæk G, Ripke S, Stefansson K, Andreassen OA, Posthuma D.",,Nature genetics,2021,2021-09-07,N,,,,"Late-onset Alzheimer's disease is a prevalent age-related polygenic disease that accounts for 50-70% of dementia cases. Currently, only a fraction of the genetic variants underlying Alzheimer's disease have been identified. Here we show that increased sample sizes allowed identification of seven previously unidentified genetic loci contributing to Alzheimer's disease. This study highlights microglia, immune cells and protein catabolism as relevant to late-onset Alzheimer's disease, while identifying and prioritizing previously unidentified genes of potential interest. We anticipate that these results can be included in larger meta-analyses of Alzheimer's disease to identify further genetic variants that contribute to Alzheimer's pathology.",,pdf:https://research.vu.nl/files/151770370/A_genomewide_association_study_with_112_563_individuals_identifies_new_risk_loci_for_Alzheimers_disease.pdf; doi:https://doi.org/10.1038/s41588-021-00921-z; html:https://europepmc.org/articles/PMC10243600; pdf:https://europepmc.org/articles/PMC10243600?pdf=render; doi:https://doi.org/10.1038/s41588-021-00921-z
 30879893,https://doi.org/10.1016/s1474-4422(18)30499-x,"Global, regional, and national burden of neurological disorders, 1990-2016: a systematic analysis for the Global Burden of Disease Study 2016.",GBD 2016 Neurology Collaborators.,,The Lancet. Neurology,2019,2019-03-14,Y,,Improving Public Health,,"<h4>Background</h4>Neurological disorders are increasingly recognised as major causes of death and disability worldwide. The aim of this analysis from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2016 is to provide the most comprehensive and up-to-date estimates of the global, regional, and national burden from neurological disorders.<h4>Methods</h4>We estimated prevalence, incidence, deaths, and disability-adjusted life-years (DALYs; the sum of years of life lost [YLLs] and years lived with disability [YLDs]) by age and sex for 15 neurological disorder categories (tetanus, meningitis, encephalitis, stroke, brain and other CNS cancers, traumatic brain injury, spinal cord injury, Alzheimer's disease and other dementias, Parkinson's disease, multiple sclerosis, motor neuron diseases, idiopathic epilepsy, migraine, tension-type headache, and a residual category for other less common neurological disorders) in 195 countries from 1990 to 2016. DisMod-MR 2.1, a Bayesian meta-regression tool, was the main method of estimation of prevalence and incidence, and the Cause of Death Ensemble model (CODEm) was used for mortality estimation. We quantified the contribution of 84 risks and combinations of risk to the disease estimates for the 15 neurological disorder categories using the GBD comparative risk assessment approach.<h4>Findings</h4>Globally, in 2016, neurological disorders were the leading cause of DALYs (276 million [95% UI 247-308]) and second leading cause of deaths (9·0 million [8·8-9·4]). The absolute number of deaths and DALYs from all neurological disorders combined increased (deaths by 39% [34-44] and DALYs by 15% [9-21]) whereas their age-standardised rates decreased (deaths by 28% [26-30] and DALYs by 27% [24-31]) between 1990 and 2016. The only neurological disorders that had a decrease in rates and absolute numbers of deaths and DALYs were tetanus, meningitis, and encephalitis. The four largest contributors of neurological DALYs were stroke (42·2% [38·6-46·1]), migraine (16·3% [11·7-20·8]), Alzheimer's and other dementias (10·4% [9·0-12·1]), and meningitis (7·9% [6·6-10·4]). For the combined neurological disorders, age-standardised DALY rates were significantly higher in males than in females (male-to-female ratio 1·12 [1·05-1·20]), but migraine, multiple sclerosis, and tension-type headache were more common and caused more burden in females, with male-to-female ratios of less than 0·7. The 84 risks quantified in GBD explain less than 10% of neurological disorder DALY burdens, except stroke, for which 88·8% (86·5-90·9) of DALYs are attributable to risk factors, and to a lesser extent Alzheimer's disease and other dementias (22·3% [11·8-35·1] of DALYs are risk attributable) and idiopathic epilepsy (14·1% [10·8-17·5] of DALYs are risk attributable).<h4>Interpretation</h4>Globally, the burden of neurological disorders, as measured by the absolute number of DALYs, continues to increase. As populations are growing and ageing, and the prevalence of major disabling neurological disorders steeply increases with age, governments will face increasing demand for treatment, rehabilitation, and support services for neurological disorders. The scarcity of established modifiable risks for most of the neurological burden demonstrates that new knowledge is required to develop effective prevention and treatment strategies.<h4>Funding</h4>Bill & Melinda Gates Foundation.",,pdf:http://www.thelancet.com/article/S147444221830499X/pdf; doi:https://doi.org/10.1016/S1474-4422(18)30499-X; html:https://europepmc.org/articles/PMC6459001; pdf:https://europepmc.org/articles/PMC6459001?pdf=render
-32710861,https://doi.org/10.1016/s2214-109x(20)30230-8,"Mapping geographical inequalities in oral rehydration therapy coverage in low-income and middle-income countries, 2000-17.",Local Burden of Disease Diarrhoea Collaborators.,,The Lancet. Global health,2020,2020-08-01,Y,,,,"<h4>Background</h4>Oral rehydration solution (ORS) is a form of oral rehydration therapy (ORT) for diarrhoea that has the potential to drastically reduce child mortality; yet, according to UNICEF estimates, less than half of children younger than 5 years with diarrhoea in low-income and middle-income countries (LMICs) received ORS in 2016. A variety of recommended home fluids (RHF) exist as alternative forms of ORT; however, it is unclear whether RHF prevent child mortality. Previous studies have shown considerable variation between countries in ORS and RHF use, but subnational variation is unknown. This study aims to produce high-resolution geospatial estimates of relative and absolute coverage of ORS, RHF, and ORT (use of either ORS or RHF) in LMICs.<h4>Methods</h4>We used a Bayesian geostatistical model including 15 spatial covariates and data from 385 household surveys across 94 LMICs to estimate annual proportions of children younger than 5 years of age with diarrhoea who received ORS or RHF (or both) on continuous continent-wide surfaces in 2000-17, and aggregated results to policy-relevant administrative units. Additionally, we analysed geographical inequality in coverage across administrative units and estimated the number of diarrhoeal deaths averted by increased coverage over the study period. Uncertainty in the mean coverage estimates was calculated by taking 250 draws from the posterior joint distribution of the model and creating uncertainty intervals (UIs) with the 2·5th and 97·5th percentiles of those 250 draws.<h4>Findings</h4>While ORS use among children with diarrhoea increased in some countries from 2000 to 2017, coverage remained below 50% in the majority (62·6%; 12 417 of 19 823) of second administrative-level units and an estimated 6 519 000 children (95% UI 5 254 000-7 733 000) with diarrhoea were not treated with any form of ORT in 2017. Increases in ORS use corresponded with declines in RHF in many locations, resulting in relatively constant overall ORT coverage from 2000 to 2017. Although ORS was uniformly distributed subnationally in some countries, within-country geographical inequalities persisted in others; 11 countries had at least a 50% difference in one of their units compared with the country mean. Increases in ORS use over time were correlated with declines in RHF use and in diarrhoeal mortality in many locations, and an estimated 52 230 diarrhoeal deaths (36 910-68 860) were averted by scaling up of ORS coverage between 2000 and 2017. Finally, we identified key subnational areas in Colombia, Nigeria, and Sudan as examples of where diarrhoeal mortality remains higher than average, while ORS coverage remains lower than average.<h4>Interpretation</h4>To our knowledge, this study is the first to produce and map subnational estimates of ORS, RHF, and ORT coverage and attributable child diarrhoeal deaths across LMICs from 2000 to 2017, allowing for tracking progress over time. Our novel results, combined with detailed subnational estimates of diarrhoeal morbidity and mortality, can support subnational needs assessments aimed at furthering policy makers' understanding of within-country disparities. Over 50 years after the discovery that led to this simple, cheap, and life-saving therapy, large gains in reducing mortality could still be made by reducing geographical inequalities in ORS coverage.<h4>Funding</h4>Bill & Melinda Gates Foundation.",,pdf:http://www.thelancet.com/article/S2214109X20302308/pdf; doi:https://doi.org/10.1016/S2214-109X(20)30230-8; html:https://europepmc.org/articles/PMC7388204
 32646569,https://doi.org/10.1016/j.jacc.2020.05.029,Clinical Features and Natural History of PRKAG2 Variant Cardiac Glycogenosis.,"Lopez-Sainz A, Dominguez F, Lopes LR, Ochoa JP, Barriales-Villa R, Climent V, Linschoten M, Tiron C, Chiriatti C, Marques N, Rasmussen TB, Espinosa MÁ, Beinart R, Quarta G, Cesar S, Field E, Garcia-Pinilla JM, Bilinska Z, Muir AR, Roberts AM, Santas E, Zorio E, Peña-Peña ML, Navarro M, Fernandez A, Palomino-Doza J, Azevedo O, Lorenzini M, García-Álvarez MI, Bento D, Jensen MK, Méndez I, Pezzoli L, Sarquella-Brugada G, Campuzano O, Gonzalez-Lopez E, Mogensen J, Kaski JP, Arad M, Brugada R, Asselbergs FW, Monserrat L, Olivotto I, Elliott PM, Garcia-Pavia P, European Genetic Cardiomyopathies Initiative Investigators.",,Journal of the American College of Cardiology,2020,2020-07-01,N,hypertrophic cardiomyopathy; Left ventricular hypertrophy; Pacemaker; Heart Failure; Sudden Cardiac Death; Pre-excitation; Prkag2; Glycogen-storage Disease,,,"<h4>Background</h4>PRKAG2 gene variants cause a syndrome characterized by cardiomyopathy, conduction disease, and ventricular pre-excitation. Only a small number of cases have been reported to date, and the natural history of the disease is poorly understood.<h4>Objectives</h4>The aim of this study was to describe phenotype and natural history of PRKAG2 variants in a large multicenter European cohort.<h4>Methods</h4>Clinical, electrocardiographic, and echocardiographic data from 90 subjects with PRKAG2 variants (53% men; median age 33 years; interquartile range [IQR]: 15 to 50 years) recruited from 27 centers were retrospectively studied.<h4>Results</h4>At first evaluation, 93% of patients were in New York Heart Association functional class I or II. Maximum left ventricular wall thickness was 18 ± 8 mm, and left ventricular ejection fraction was 61 ± 12%. Left ventricular hypertrophy (LVH) was present in 60 subjects (67%) at baseline. Thirty patients (33%) had ventricular pre-excitation or had undergone accessory pathway ablation; 17 (19%) had pacemakers (median age at implantation 36 years; IQR: 27 to 46 years), and 16 (18%) had atrial fibrillation (median age 43 years; IQR: 31 to 54 years). After a median follow-up period of 6 years (IQR: 2.3 to 13.9 years), 71% of subjects had LVH, 29% had AF, 21% required de novo pacemakers (median age at implantation 37 years; IQR: 29 to 48 years), 14% required admission for heart failure, 8% experienced sudden cardiac death or equivalent, 4% required heart transplantation, and 13% died.<h4>Conclusions</h4>PRKAG2 syndrome is a progressive cardiomyopathy characterized by high rates of atrial fibrillation, conduction disease, advanced heart failure, and life-threatening arrhythmias. Classical features of pre-excitation and severe LVH are not uniformly present, and diagnosis should be considered in patients with LVH who develop atrial fibrillation or require permanent pacemakers at a young age.",,doi:https://doi.org/10.1016/j.jacc.2020.05.029; doi:https://doi.org/10.1016/j.jacc.2020.05.029
+32710861,https://doi.org/10.1016/s2214-109x(20)30230-8,"Mapping geographical inequalities in oral rehydration therapy coverage in low-income and middle-income countries, 2000-17.",Local Burden of Disease Diarrhoea Collaborators.,,The Lancet. Global health,2020,2020-08-01,Y,,,,"<h4>Background</h4>Oral rehydration solution (ORS) is a form of oral rehydration therapy (ORT) for diarrhoea that has the potential to drastically reduce child mortality; yet, according to UNICEF estimates, less than half of children younger than 5 years with diarrhoea in low-income and middle-income countries (LMICs) received ORS in 2016. A variety of recommended home fluids (RHF) exist as alternative forms of ORT; however, it is unclear whether RHF prevent child mortality. Previous studies have shown considerable variation between countries in ORS and RHF use, but subnational variation is unknown. This study aims to produce high-resolution geospatial estimates of relative and absolute coverage of ORS, RHF, and ORT (use of either ORS or RHF) in LMICs.<h4>Methods</h4>We used a Bayesian geostatistical model including 15 spatial covariates and data from 385 household surveys across 94 LMICs to estimate annual proportions of children younger than 5 years of age with diarrhoea who received ORS or RHF (or both) on continuous continent-wide surfaces in 2000-17, and aggregated results to policy-relevant administrative units. Additionally, we analysed geographical inequality in coverage across administrative units and estimated the number of diarrhoeal deaths averted by increased coverage over the study period. Uncertainty in the mean coverage estimates was calculated by taking 250 draws from the posterior joint distribution of the model and creating uncertainty intervals (UIs) with the 2·5th and 97·5th percentiles of those 250 draws.<h4>Findings</h4>While ORS use among children with diarrhoea increased in some countries from 2000 to 2017, coverage remained below 50% in the majority (62·6%; 12 417 of 19 823) of second administrative-level units and an estimated 6 519 000 children (95% UI 5 254 000-7 733 000) with diarrhoea were not treated with any form of ORT in 2017. Increases in ORS use corresponded with declines in RHF in many locations, resulting in relatively constant overall ORT coverage from 2000 to 2017. Although ORS was uniformly distributed subnationally in some countries, within-country geographical inequalities persisted in others; 11 countries had at least a 50% difference in one of their units compared with the country mean. Increases in ORS use over time were correlated with declines in RHF use and in diarrhoeal mortality in many locations, and an estimated 52 230 diarrhoeal deaths (36 910-68 860) were averted by scaling up of ORS coverage between 2000 and 2017. Finally, we identified key subnational areas in Colombia, Nigeria, and Sudan as examples of where diarrhoeal mortality remains higher than average, while ORS coverage remains lower than average.<h4>Interpretation</h4>To our knowledge, this study is the first to produce and map subnational estimates of ORS, RHF, and ORT coverage and attributable child diarrhoeal deaths across LMICs from 2000 to 2017, allowing for tracking progress over time. Our novel results, combined with detailed subnational estimates of diarrhoeal morbidity and mortality, can support subnational needs assessments aimed at furthering policy makers' understanding of within-country disparities. Over 50 years after the discovery that led to this simple, cheap, and life-saving therapy, large gains in reducing mortality could still be made by reducing geographical inequalities in ORS coverage.<h4>Funding</h4>Bill & Melinda Gates Foundation.",,pdf:http://www.thelancet.com/article/S2214109X20302308/pdf; doi:https://doi.org/10.1016/S2214-109X(20)30230-8; html:https://europepmc.org/articles/PMC7388204
 38177345,https://doi.org/10.1038/s41588-023-01596-4,"Multi-ancestry genome-wide association study of major depression aids locus discovery, fine mapping, gene prioritization and causal inference.","Meng X, Navoly G, Giannakopoulou O, Levey DF, Koller D, Pathak GA, Koen N, Lin K, Adams MJ, Rentería ME, Feng Y, Gaziano JM, Stein DJ, Zar HJ, Campbell ML, van Heel DA, Trivedi B, Finer S, McQuillin A, Bass N, Chundru VK, Martin HC, Huang QQ, Valkovskaya M, Chu CY, Kanjira S, Kuo PH, Chen HC, Tsai SJ, Liu YL, Kendler KS, Peterson RE, Cai N, Fang Y, Sen S, Scott LJ, Burmeister M, Loos RJF, Preuss MH, Actkins KV, Davis LK, Uddin M, Wani AH, Wildman DE, Aiello AE, Ursano RJ, Kessler RC, Kanai M, Okada Y, Sakaue S, Rabinowitz JA, Maher BS, Uhl G, Eaton W, Cruz-Fuentes CS, Martinez-Levy GA, Campos AI, Millwood IY, Chen Z, Li L, Wassertheil-Smoller S, Jiang Y, Tian C, Martin NG, Mitchell BL, Byrne EM, Awasthi S, Coleman JRI, Ripke S, PGC-MDD Working Group, China Kadoorie Biobank Collaborative Group, 23andMe Research Team, Genes and Health Research Team, BioBank Japan Project, Sofer T, Walters RG, McIntosh AM, Polimanti R, Dunn EC, Stein MB, Gelernter J, Lewis CM, Kuchenbaecker K.",,Nature genetics,2024,2024-01-04,Y,,,,"Most genome-wide association studies (GWAS) of major depression (MD) have been conducted in samples of European ancestry. Here we report a multi-ancestry GWAS of MD, adding data from 21 cohorts with 88,316 MD cases and 902,757 controls to previously reported data. This analysis used a range of measures to define MD and included samples of African (36% of effective sample size), East Asian (26%) and South Asian (6%) ancestry and Hispanic/Latin American participants (32%). The multi-ancestry GWAS identified 53 significantly associated novel loci. For loci from GWAS in European ancestry samples, fewer than expected were transferable to other ancestry groups. Fine mapping benefited from additional sample diversity. A transcriptome-wide association study identified 205 significantly associated novel genes. These findings suggest that, for MD, increasing ancestral and global diversity in genetic studies may be particularly important to ensure discovery of core genes and inform about transferability of findings.",,pdf:https://www.nature.com/articles/s41588-023-01596-4.pdf; doi:https://doi.org/10.1038/s41588-023-01596-4; html:https://europepmc.org/articles/PMC10864182; pdf:https://europepmc.org/articles/PMC10864182?pdf=render
 32839249,https://doi.org/10.1136/injuryprev-2019-043531,Estimating global injuries morbidity and mortality: methods and data used in the Global Burden of Disease 2017 study.,"James SL, Castle CD, Dingels ZV, Fox JT, Hamilton EB, Liu Z, Roberts NLS, Sylte DO, Bertolacci GJ, Cunningham M, Henry NJ, LeGrand KE, Abdelalim A, Abdollahpour I, Abdulkader RS, Abedi A, Abegaz KH, Abosetugn AE, Abushouk AI, Adebayo OM, Adsuar JC, Advani SM, Agudelo-Botero M, Ahmad T, Ahmed MB, Ahmed R, Eddine Aichour MT, Alahdab F, Alanezi FM, Alema NM, Alemu BW, Alghnam SA, Ali BA, Ali S, Alinia C, Alipour V, Aljunid SM, Almasi-Hashiani A, Almasri NA, Altirkawi K, Abdeldayem Amer YS, Andrei CL, Ansari-Moghaddam A, T Antonio CA, Anvari D, Yaw Appiah SC, Arabloo J, Arab-Zozani M, Arefi Z, Aremu O, Ariani F, Arora A, Asaad M, Ayala Quintanilla BP, Ayano G, Ayanore MA, Azarian G, Badawi A, Badiye AD, Baig AA, Bairwa M, Bakhtiari A, Balachandran A, Banach M, Banerjee SK, Banik PC, Banstola A, Barker-Collo SL, Bärnighausen TW, Barzegar A, Bayati M, Bazargan-Hejazi S, Bedi N, Behzadifar M, Belete H, Bennett DA, Bensenor IM, Berhe K, Bhagavathula AS, Bhardwaj P, Bhat AG, Bhattacharyya K, Bhutta ZA, Bibi S, Bijani A, Boloor A, Borges G, Borschmann R, Borzì AM, Boufous S, Braithwaite D, Briko NI, Brugha T, Budhathoki SS, Car J, Cárdenas R, Carvalho F, Castaldelli-Maia JM, Castañeda-Orjuela CA, Castelpietra G, Catalá-López F, Cerin E, Chandan JS, Chapman JR, Chattu VK, Chattu SK, Chatziralli I, Chaudhary N, Cho DY, Choi JJ, Kabir Chowdhury MA, Christopher DJ, Chu DT, Cicuttini FM, Coelho JM, Costa VM, Dahlawi SMA, Daryani A, Dávila-Cervantes CA, Leo D, Demeke FM, Demoz GT, Demsie DG, Deribe K, Desai R, Nasab MD, Silva DDD, Dibaji Forooshani ZS, Do HT, Doyle KE, Driscoll TR, Dubljanin E, Adema BD, Eagan AW, Elemineh DA, El-Jaafary SI, El-Khatib Z, Ellingsen CL, Zaki MES, Eskandarieh S, Eyawo O, Faris PS, Faro A, Farzadfar F, Fereshtehnejad SM, Fernandes E, Ferrara P, Fischer F, Folayan MO, Fomenkov AA, Foroutan M, Francis JM, Franklin RC, Fukumoto T, Geberemariyam BS, Gebremariam H, Gebremedhin KB, Gebremeskel LG, Gebremeskel GG, Gebremichael B, Gedefaw GA, Geta B, Getenet AB, Ghafourifard M, Ghamari F, Gheshlagh RG, Gholamian A, Gilani SA, Gill TK, Goudarzian AH, Goulart AC, Grada A, Grivna M, Guimarães RA, Guo Y, Gupta G, Haagsma JA, Hall BJ, Hamadeh RR, Hamidi S, Handiso DW, Haro JM, Hasanzadeh A, Hassan S, Hassanipour S, Hassankhani H, Hassen HY, Havmoeller R, Hendrie D, Heydarpour F, Híjar M, Ho HC, Hoang CL, Hole MK, Holla R, Hossain N, Hosseinzadeh M, Hostiuc S, Hu G, Ibitoye SE, Ilesanmi OS, Inbaraj LR, Naghibi Irvani SS, Mofizul Islam M, Shariful Islam SM, Ivers RQ, Jahani MA, Jakovljevic M, Jalilian F, Jayaraman S, Jayatilleke AU, Jha RP, John-Akinola YO, Jonas JB, Jones KM, Joseph N, Joukar F, Jozwiak JJ, Jungari SB, Jürisson M, Kabir A, Kahsay A, Kalankesh LR, Kalhor R, Kamil TA, Kanchan T, Kapoor N, Karami M, Kasaeian A, Kassaye HG, Kavetskyy T, Kayode GA, Keiyoro PN, Kelbore AG, Khader YS, Khafaie MA, Khalid N, Khalil IA, Khalilov R, Khan M, Khan EA, Khan J, Khanna T, Khazaei S, Khazaie H, Khundkar R, Kiirithio DN, Kim YE, Kim YJ, Kim D, Kisa S, Kisa A, Komaki H, Kondlahalli SKM, Koolivand A, Korshunov VA, Koyanagi A, Kraemer MUG, Krishan K, Defo BK, Bicer BK, Kugbey N, Kumar N, Kumar M, Kumar V, Kumar N, Kumaresh G, Lami FH, Lansingh VC, Lasrado S, Latifi A, Lauriola P, Vecchia C, Leasher JL, Huey Lee SW, Li S, Liu X, Lopez AD, Lotufo PA, Lyons RA, Machado DB, Madadin M, Abd El Razek MM, Mahotra NB, Majdan M, Majeed A, Maled V, Malta DC, Manafi N, Manafi A, Manda AL, Manjunatha N, Mansour-Ghanaei F, Mansournia MA, Maravilla JC, Mason-Jones AJ, Masoumi SZ, Massenburg BB, Maulik PK, Mehndiratta MM, Melketsedik ZA, Memiah PTN, Mendoza W, Menezes RG, Mengesha MM, Meretoja TJ, Meretoja A, Merie HE, Mestrovic T, Miazgowski B, Miazgowski T, Miller TR, Mini GK, Mirica A, Mirrakhimov EM, Mirzaei-Alavijeh M, Mithra P, Moazen B, Moghadaszadeh M, Mohamadi E, Mohammad Y, Darwesh AM, Mohammadian-Hafshejani A, Mohammadpourhodki R, Mohammed S, Mohammed JA, Mohebi F, Mohseni Bandpei MA, Molokhia M, Monasta L, Moodley Y, Moradi M, Moradi G, Moradi-Lakeh M, Moradzadeh R, Morawska L, Velásquez IM, Morrison SD, Mossie TB, Muluneh AG, Musa KI, Mustafa G, Naderi M, Nagarajan AJ, Naik G, Naimzada MD, Najafi F, Nangia V, Nascimento BR, Naserbakht M, Nayak V, Nazari J, Ndwandwe DE, Negoi I, Ngunjiri JW, Nguyen TH, Nguyen CT, Nguyen DN, Thi Nguyen HL, Nikbakhsh R, Anggraini Ningrum DN, Nnaji CA, Ofori-Asenso R, Ogbo FA, Oghenetega OB, Oh IH, Olagunju AT, Olagunju TO, Bali AO, Onwujekwe OE, Orpana HM, Ota E, Otstavnov N, Otstavnov SS, P A M, Padubidri JR, Pakhale S, Pakshir K, Panda-Jonas S, Park EK, Patel SK, Pathak A, Pati S, Paulos K, Peden AE, Filipino Pepito VC, Pereira J, Phillips MR, Polibin RV, Polinder S, Pourmalek F, Pourshams A, Poustchi H, Prakash S, Angga Pribadi DR, Puri P, Syed ZQ, Rabiee N, Rabiee M, Radfar A, Rafay A, Rafiee A, Rafiei A, Rahim F, Rahimi S, Rahman MA, Rajabpour-Sanati A, Rajati F, Rakovac I, Rao SJ, Rashedi V, Rastogi P, Rathi P, Rawaf S, Rawal L, Rawassizadeh R, Renjith V, Resnikoff S, Rezapour A, Ribeiro AI, Rickard J, Rios González CM, Roever L, Ronfani L, Roshandel G, Saddik B, Safarpour H, Safdarian M, Mohammad Sajadi S, Salamati P, Rashad Salem MR, Salem H, Salz I, Samy AM, Sanabria J, Riera LS, Santric Milicevic MM, Sarker AR, Sarveazad A, Sathian B, Sawhney M, Sayyah M, Schwebel DC, Seedat S, Senthilkumaran S, Seyedmousavi S, Sha F, Shaahmadi F, Shahabi S, Shaikh MA, Shams-Beyranvand M, Sheikh A, Shigematsu M, Shin JI, Shiri R, Siabani S, Sigfusdottir ID, Singh JA, Singh PK, Sinha DN, Soheili A, Soriano JB, Sorrie MB, Soyiri IN, Stokes MA, Sufiyan MB, Sykes BL, Tabarés-Seisdedos R, Tabb KM, Taddele BW, Tefera YM, Tehrani-Banihashemi A, Tekulu GH, Tesema Tesema AK, Tesfay BE, Thapar R, Titova MV, Tlaye KG, Tohidinik HR, Topor-Madry R, Tran KB, Tran BX, Tripathy JP, Tsai AC, Tsatsakis A, Car LT, Ullah I, Ullah S, Unnikrishnan B, Upadhyay E, Uthman OA, Valdez PR, Vasankari TJ, Veisani Y, Venketasubramanian N, Violante FS, Vlassov V, Waheed Y, Wang YP, Wiangkham T, Wolde HF, Woldeyes DH, Wondmeneh TG, Wondmieneh AB, Wu AM, Wyper GMA, Yadav R, Yadollahpour A, Yano Y, Yaya S, Yazdi-Feyzabadi V, Ye P, Yip P, Yisma E, Yonemoto N, Yoon SJ, Youm Y, Younis MZ, Yousefi Z, Yu C, Yu Y, Moghadam TZ, Zaidi Z, Zaman SB, Zaman SB, Zamani M, Zandian H, Zarei F, Zhang ZJ, Zhang Y, Ziapour A, Zodpey S, Dandona R, Dharmaratne SD, Hay SI, Mokdad AH, Pigott DM, Reiner RC, Vos T.",,Injury prevention : journal of the International Society for Child and Adolescent Injury Prevention,2020,2020-08-24,Y,Methodology; Descriptive Epidemiology; Populations/contexts; Statistical Issues,,,"<h4>Background</h4>While there is a long history of measuring death and disability from injuries, modern research methods must account for the wide spectrum of disability that can occur in an injury, and must provide estimates with sufficient demographic, geographical and temporal detail to be useful for policy makers. The Global Burden of Disease (GBD) 2017 study used methods to provide highly detailed estimates of global injury burden that meet these criteria.<h4>Methods</h4>In this study, we report and discuss the methods used in GBD 2017 for injury morbidity and mortality burden estimation. In summary, these methods included estimating cause-specific mortality for every cause of injury, and then estimating incidence for every cause of injury. Non-fatal disability for each cause is then calculated based on the probabilities of suffering from different types of bodily injury experienced.<h4>Results</h4>GBD 2017 produced morbidity and mortality estimates for 38 causes of injury. Estimates were produced in terms of incidence, prevalence, years lived with disability, cause-specific mortality, years of life lost and disability-adjusted life-years for a 28-year period for 22 age groups, 195 countries and both sexes.<h4>Conclusions</h4>GBD 2017 demonstrated a complex and sophisticated series of analytical steps using the largest known database of morbidity and mortality data on injuries. GBD 2017 results should be used to help inform injury prevention policy making and resource allocation. We also identify important avenues for improving injury burden estimation in the future.",,pdf:https://injuryprevention.bmj.com/content/injuryprev/26/Suppl_2/i125.full.pdf; doi:https://doi.org/10.1136/injuryprev-2019-043531; html:https://europepmc.org/articles/PMC7571362; pdf:https://europepmc.org/articles/PMC7571362?pdf=render
 34732894,https://doi.org/10.1038/s41586-021-04088-9,MC3R links nutritional state to childhood growth and the timing of puberty.,"Lam BYH, Williamson A, Finer S, Day FR, Tadross JA, Gonçalves Soares A, Wade K, Sweeney P, Bedenbaugh MN, Porter DT, Melvin A, Ellacott KLJ, Lippert RN, Buller S, Rosmaninho-Salgado J, Dowsett GKC, Ridley KE, Xu Z, Cimino I, Rimmington D, Rainbow K, Duckett K, Holmqvist S, Khan A, Dai X, Bochukova EG, Genes & Health Research Team, Trembath RC, Martin HC, Coll AP, Rowitch DH, Wareham NJ, van Heel DA, Timpson N, Simerly RB, Ong KK, Cone RD, Langenberg C, Perry JRB, Yeo GS, O'Rahilly S.",,Nature,2021,2021-11-03,N,,,,"The state of somatic energy stores in metazoans is communicated to the brain, which regulates key aspects of behaviour, growth, nutrient partitioning and development<sup>1</sup>. The central melanocortin system acts through melanocortin 4 receptor (MC4R) to control appetite, food intake and energy expenditure<sup>2</sup>. Here we present evidence that MC3R regulates the timing of sexual maturation, the rate of linear growth and the accrual of lean mass, which are all energy-sensitive processes. We found that humans who carry loss-of-function mutations in MC3R, including a rare homozygote individual, have a later onset of puberty. Consistent with previous findings in mice, they also had reduced linear growth, lean mass and circulating levels of IGF1. Mice lacking Mc3r had delayed sexual maturation and an insensitivity of reproductive cycle length to nutritional perturbation. The expression of Mc3r is enriched in hypothalamic neurons that control reproduction and growth, and expression increases during postnatal development in a manner that is consistent with a role in the regulation of sexual maturation. These findings suggest a bifurcating model of nutrient sensing by the central melanocortin pathway with signalling through MC4R controlling the acquisition and retention of calories, whereas signalling through MC3R primarily regulates the disposition of calories into growth, lean mass and the timing of sexual maturation.",,html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8819628; doi:https://doi.org/10.1038/s41586-021-04088-9; html:https://europepmc.org/articles/PMC8819628; pdf:https://europepmc.org/articles/PMC8819628?pdf=render; doi:https://doi.org/10.1038/s41586-021-04088-9
@@ -2919,8 +2921,8 @@ PMC11210061,https://doi.org/,Plain language summary of a study looking at the ef
 36777997,https://doi.org/10.1016/j.xgen.2022.100181,Leveraging global multi-ancestry meta-analysis in the study of idiopathic pulmonary fibrosis genetics.,"Partanen JJ, Häppölä P, Zhou W, Lehisto AA, Ainola M, Sutinen E, Allen RJ, Stockwell AD, Leavy OC, Oldham JM, Guillen-Guio B, Cox NJ, Hirbo JB, Schwartz DA, Fingerlin TE, Flores C, Noth I, Yaspan BL, Jenkins RG, Wain LV, Ripatti S, Pirinen M, International IPF Genetics Consortium, Global Biobank Meta-Analysis Initiative (GBMI), Laitinen T, Kaarteenaho R, Myllärniemi M, Daly MJ, Koskela JT.",,Cell genomics,2022,2022-10-12,Y,Meta-analysis; idiopathic pulmonary fibrosis; Gwas; Ancestry; Muc5b; Fine-mapping; Cross-population Analysis; Covid-19; Global Biobank Meta-Analysis Initiative,,,"The research of rare and devastating orphan diseases, such as idiopathic pulmonary fibrosis (IPF) has been limited by the rarity of the disease itself. The prognosis is poor-the prevalence of IPF is only approximately four times the incidence, limiting the recruitment of patients to trials and studies of the underlying biology. Global biobanking efforts can dramatically alter the future of IPF research. We describe a large-scale meta-analysis of IPF, with 8,492 patients and 1,355,819 population controls from 13 biobanks around the globe. Finally, we combine this meta-analysis with the largest available meta-analysis of IPF, reaching 11,160 patients and 1,364,410 population controls. We identify seven novel genome-wide significant loci, only one of which would have been identified if the analysis had been limited to European ancestry individuals. We observe notable pleiotropy across IPF susceptibility and severe COVID-19 infection and note an unexplained sex-heterogeneity effect at the strongest IPF locus <i>MUC5B</i>.",,pdf:https://helda.helsinki.fi/bitstream/10138/355828/1/Leveraging_global_multi_ancestry_meta_a...pdf; doi:https://doi.org/10.1016/j.xgen.2022.100181; html:https://europepmc.org/articles/PMC9903787; pdf:https://europepmc.org/articles/PMC9903787?pdf=render
 36068517,https://doi.org/10.1186/s12916-022-02486-y,"The prevalence of onchocerciasis in Africa and Yemen, 2000-2018: a geospatial analysis.","Schmidt CA, Cromwell EA, Hill E, Donkers KM, Schipp MF, Johnson KB, Pigott DM, LBD 2019 Neglected Tropical Diseases Collaborators, Hay SI.",,BMC medicine,2022,2022-09-07,Y,Onchocerciasis; Neglected Tropical Diseases; Geospatial Model,,,"<h4>Background</h4>Onchocerciasis is a disease caused by infection with Onchocerca volvulus, which is transmitted to humans via the bite of several species of black fly, and is responsible for permanent blindness or vision loss, as well as severe skin disease. Predominantly endemic in parts of Africa and Yemen, preventive chemotherapy with mass drug administration of ivermectin is the primary intervention recommended for the elimination of its transmission.<h4>Methods</h4>A dataset of 18,116 geo-referenced prevalence survey datapoints was used to model annual 2000-2018 infection prevalence in Africa and Yemen. Using Bayesian model-based geostatistics, we generated spatially continuous estimates of all-age 2000-2018 onchocerciasis infection prevalence at the 5 × 5-km resolution as well as aggregations to the national level, along with corresponding estimates of the uncertainty in these predictions.<h4>Results</h4>As of 2018, the prevalence of onchocerciasis infection continues to be concentrated across central and western Africa, with the highest mean estimates at the national level in Ghana (12.2%, 95% uncertainty interval [UI] 5.0-22.7). Mean estimates exceed 5% infection prevalence at the national level for Cameroon, Central African Republic, Democratic Republic of the Congo (DRC), Guinea-Bissau, Sierra Leone, and South Sudan.<h4>Conclusions</h4>Our analysis suggests that onchocerciasis infection has declined over the last two decades throughout western and central Africa. Focal areas of Angola, Cameroon, the Democratic Republic of the Congo, Ethiopia, Ghana, Guinea, Mali, Nigeria, South Sudan, and Uganda continue to have mean microfiladermia prevalence estimates exceeding 25%. At and above this level, the continuation or initiation of mass drug administration with ivermectin is supported. If national programs aim to eliminate onchocerciasis infection, additional surveillance or supervision of areas of predicted high prevalence would be warranted to ensure sufficiently high coverage of program interventions.",,pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-022-02486-y; doi:https://doi.org/10.1186/s12916-022-02486-y; html:https://europepmc.org/articles/PMC9449300; pdf:https://europepmc.org/articles/PMC9449300?pdf=render
 32654539,https://doi.org/10.1161/circulationaha.119.045526,Association of Factor V Leiden With Subsequent Atherothrombotic Events: A GENIUS-CHD Study of Individual Participant Data.,"Mahmoodi BK, Tragante V, Kleber ME, Holmes MV, Schmidt AF, McCubrey RO, Howe LJ, Direk K, Allayee H, Baranova EV, Braund PS, Delgado GE, Eriksson N, Gijsberts CM, Gong Y, Hartiala J, Heydarpour M, Pasterkamp G, Kotti S, Kuukasjärvi P, Lenzini PA, Levin D, Lyytikäinen LP, Muehlschlegel JD, Nelson CP, Nikus K, Pilbrow AP, Wilson Tang WH, van der Laan SW, van Setten J, Vilmundarson RO, Deanfield J, Deloukas P, Dudbridge F, James S, Mordi IR, Teren A, Bergmeijer TO, Body SC, Bots M, Burkhardt R, Cooper-DeHoff RM, Cresci S, Danchin N, Doughty RN, Grobbee DE, Hagström E, Hazen SL, Held C, Hoefer IE, Hovingh GK, Johnson JA, Kaczor MP, Kähönen M, Klungel OH, Laurikka JO, Lehtimäki T, Maitland-van der Zee AH, McPherson R, Palmer CN, Kraaijeveld AO, Pepine CJ, Sanak M, Sattar N, Scholz M, Simon T, Spertus JA, Stewart AFR, Szczeklik W, Thiery J, Visseren FLJ, Waltenberger J, Richards AM, Lang CC, Cameron VA, Åkerblom A, Pare G, März W, Samani NJ, Hingorani AD, Ten Berg JM, Wallentin L, Asselbergs FW, Patel RS.",,Circulation,2020,2020-07-13,N,Thrombosis; Myocardial infarction; Single nucleotide polymorphism; Prognosis; coronary artery disease; Secondary Prevention; Genetic Association Studies,,,"<h4>Background</h4>Studies examining the role of factor V Leiden among patients at higher risk of atherothrombotic events, such as those with established coronary heart disease (CHD), are lacking. Given that coagulation is involved in the thrombus formation stage on atherosclerotic plaque rupture, we hypothesized that factor V Leiden may be a stronger risk factor for atherothrombotic events in patients with established CHD.<h4>Methods</h4>We performed an individual-level meta-analysis including 25 prospective studies (18 cohorts, 3 case-cohorts, 4 randomized trials) from the GENIUS-CHD (Genetics of Subsequent Coronary Heart Disease) consortium involving patients with established CHD at baseline. Participating studies genotyped factor V Leiden status and shared risk estimates for the outcomes of interest using a centrally developed statistical code with harmonized definitions across studies. Cox proportional hazards regression models were used to obtain age- and sex-adjusted estimates. The obtained estimates were pooled using fixed-effect meta-analysis. The primary outcome was composite of myocardial infarction and CHD death. Secondary outcomes included any stroke, ischemic stroke, coronary revascularization, cardiovascular mortality, and all-cause mortality.<h4>Results</h4>The studies included 69 681 individuals of whom 3190 (4.6%) were either heterozygous or homozygous (n=47) carriers of factor V Leiden. Median follow-up per study ranged from 1.0 to 10.6 years. A total of 20 studies with 61 147 participants and 6849 events contributed to analyses of the primary outcome. Factor V Leiden was not associated with the combined outcome of myocardial infarction and CHD death (hazard ratio, 1.03 [95% CI, 0.92-1.16]; <i>I</i><sup><i>2</i></sup>=28%; <i>P</i>-heterogeneity=0.12). Subgroup analysis according to baseline characteristics or strata of traditional cardiovascular risk factors did not show relevant differences. Similarly, risk estimates for the secondary outcomes including stroke, coronary revascularization, cardiovascular mortality, and all-cause mortality were also close to identity.<h4>Conclusions</h4>Factor V Leiden was not associated with increased risk of subsequent atherothrombotic events and mortality in high-risk participants with established and treated CHD. Routine assessment of factor V Leiden status is unlikely to improve atherothrombotic events risk stratification in this population.",,pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCULATIONAHA.119.045526; doi:https://doi.org/10.1161/CIRCULATIONAHA.119.045526; html:https://europepmc.org/articles/PMC7493828; pdf:https://europepmc.org/articles/PMC7493828?pdf=render; doi:https://doi.org/10.1161/circulationaha.119.045526
-38778362,https://doi.org/10.1186/s12889-024-18529-3,The state of health in the European Union (EU-27) in 2019: a systematic analysis for the Global Burden of Disease study 2019.,"Santos JV, Padron-Monedero A, Bikbov B, Grad DA, Plass D, Mechili EA, Gazzelloni F, Fischer F, Sulo G, Ngwa CH, Noguer-Zambrano I, Peñalvo JL, Haagsma JA, Kissimova-Skarbek K, Monasta L, Ghith N, Sarmiento-Suarez R, Hrzic R, Haneef R, O'Caoimh R, Cuschieri S, Mondello S, Kabir Z, GBD 2019 EU State of Health Collaborators, Freitas A, Devleesschauwer B.",,BMC public health,2024,2024-05-22,Y,Health Status; Population Health; European Union; Global Burden Of Diseases; European Burden Of Disease Network,,,"<h4>Background</h4>The European Union (EU) faces many health-related challenges. Burden of diseases information and the resulting trends over time are essential for health planning. This paper reports estimates of disease burden in the EU and individual 27 EU countries in 2019, and compares them with those in 2010.<h4>Methods</h4>We used the Global Burden of Disease 2019 study estimates and 95% uncertainty intervals for the whole EU and each country to evaluate age-standardised death, years of life lost (YLLs), years lived with disability (YLDs) and disability-adjusted life years (DALYs) rates for Level 2 causes, as well as life expectancy and healthy life expectancy (HALE).<h4>Results</h4>In 2019, the age-standardised death and DALY rates in the EU were 465.8 deaths and 20,251.0 DALYs per 100,000 inhabitants, respectively. Between 2010 and 2019, there were significant decreases in age-standardised death and YLL rates across EU countries. However, YLD rates remained mainly unchanged. The largest decreases in age-standardised DALY rates were observed for ""HIV/AIDS and sexually transmitted diseases"" and ""transport injuries"" (each -19%). ""Diabetes and kidney diseases"" showed a significant increase for age-standardised DALY rates across the EU (3.5%). In addition, ""mental disorders"" showed an increasing age-standardised YLL rate (14.5%).<h4>Conclusions</h4>There was a clear trend towards improvement in the overall health status of the EU but with differences between countries. EU health policymakers need to address the burden of diseases, paying specific attention to causes such as mental disorders. There are many opportunities for mutual learning among otherwise similar countries with different patterns of disease.",,pdf:https://bmcpublichealth.biomedcentral.com/counter/pdf/10.1186/s12889-024-18529-3; doi:https://doi.org/10.1186/s12889-024-18529-3; html:https://europepmc.org/articles/PMC11110444; pdf:https://europepmc.org/articles/PMC11110444?pdf=render
 30698716,https://doi.org/10.1093/aje/kwz005,Multiancestry Genome-Wide Association Study of Lipid Levels Incorporating Gene-Alcohol Interactions.,"de Vries PS, Brown MR, Bentley AR, Sung YJ, Winkler TW, Ntalla I, Schwander K, Kraja AT, Guo X, Franceschini N, Cheng CY, Sim X, Vojinovic D, Huffman JE, Musani SK, Li C, Feitosa MF, Richard MA, Noordam R, Aschard H, Bartz TM, Bielak LF, Deng X, Dorajoo R, Lohman KK, Manning AK, Rankinen T, Smith AV, Tajuddin SM, Evangelou E, Graff M, Alver M, Boissel M, Chai JF, Chen X, Divers J, Gandin I, Gao C, Goel A, Hagemeijer Y, Harris SE, Hartwig FP, He M, Horimoto ARVR, Hsu FC, Jackson AU, Kasturiratne A, Komulainen P, Kühnel B, Laguzzi F, Lee JH, Luan J, Lyytikäinen LP, Matoba N, Nolte IM, Pietzner M, Riaz M, Said MA, Scott RA, Sofer T, Stančáková A, Takeuchi F, Tayo BO, van der Most PJ, Varga TV, Wang Y, Ware EB, Wen W, Yanek LR, Zhang W, Zhao JH, Afaq S, Amin N, Amini M, Arking DE, Aung T, Ballantyne C, Boerwinkle E, Broeckel U, Campbell A, Canouil M, Charumathi S, Chen YI, Connell JM, de Faire U, de las Fuentes L, de Mutsert R, de Silva HJ, Ding J, Dominiczak AF, Duan Q, Eaton CB, Eppinga RN, Faul JD, Fisher V, Forrester T, Franco OH, Friedlander Y, Ghanbari M, Giulianini F, Grabe HJ, Grove ML, Gu CC, Harris TB, Heikkinen S, Heng CK, Hirata M, Hixson JE, Howard BV, Ikram MA, InterAct Consortium, Jacobs DR, Johnson C, Jonas JB, Kammerer CM, Katsuya T, Khor CC, Kilpeläinen TO, Koh WP, Koistinen HA, Kolcic I, Kooperberg C, Krieger JE, Kritchevsky SB, Kubo M, Kuusisto J, Lakka TA, Langefeld CD, Langenberg C, Launer LJ, Lehne B, Lemaitre RN, Li Y, Liang J, Liu J, Liu K, Loh M, Louie T, Mägi R, Manichaikul AW, McKenzie CA, Meitinger T, Metspalu A, Milaneschi Y, Milani L, Mohlke KL, Mosley TH, Mukamal KJ, Nalls MA, Nauck M, Nelson CP, Sotoodehnia N, O'Connell JR, Palmer ND, Pazoki R, Pedersen NL, Peters A, Peyser PA, Polasek O, Poulter N, Raffel LJ, Raitakari OT, Reiner AP, Rice TK, Rich SS, Robino A, Robinson JG, Rose LM, Rudan I, Schmidt CO, Schreiner PJ, Scott WR, Sever P, Shi Y, Sidney S, Sims M, Smith BH, Smith JA, Snieder H, Starr JM, Strauch K, Tan N, Taylor KD, Teo YY, Tham YC, Uitterlinden AG, van Heemst D, Vuckovic D, Waldenberger M, Wang L, Wang Y, Wang Z, Wei WB, Williams C, Wilson G, Wojczynski MK, Yao J, Yu B, Yu C, Yuan JM, Zhao W, Zonderman AB, Becker DM, Boehnke M, Bowden DW, Chambers JC, Deary IJ, Esko T, Farrall M, Franks PW, Freedman BI, Froguel P, Gasparini P, Gieger C, Horta BL, Kamatani Y, Kato N, Kooner JS, Laakso M, Leander K, Lehtimäki T, Lifelines Cohort, Groningen, The Netherlands (Lifelines Cohort Study), Magnusson PKE, Penninx B, Pereira AC, Rauramaa R, Samani NJ, Scott J, Shu XO, van der Harst P, Wagenknecht LE, Wang YX, Wareham NJ, Watkins H, Weir DR, Wickremasinghe AR, Zheng W, Elliott P, North KE, Bouchard C, Evans MK, Gudnason V, Liu CT, Liu Y, Psaty BM, Ridker PM, van Dam RM, Kardia SLR, Zhu X, Rotimi CN, Mook-Kanamori DO, Fornage M, Kelly TN, Fox ER, Hayward C, van Duijn CM, Tai ES, Wong TY, Liu J, Rotter JI, Gauderman WJ, Province MA, Munroe PB, Rice K, Chasman DI, Cupples LA, Rao DC, Morrison AC.",,American journal of epidemiology,2019,2019-06-01,N,Lipids; Cholesterol; Triglycerides; alcohol consumption; Genome-wide Association Studies; Gene-environment Interactions; Gene-lifestyle Interactions,,,"A person's lipid profile is influenced by genetic variants and alcohol consumption, but the contribution of interactions between these exposures has not been studied. We therefore incorporated gene-alcohol interactions into a multiancestry genome-wide association study of levels of high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides. We included 45 studies in stage 1 (genome-wide discovery) and 66 studies in stage 2 (focused follow-up), for a total of 394,584 individuals from 5 ancestry groups. Analyses covered the period July 2014-November 2017. Genetic main effects and interaction effects were jointly assessed by means of a 2-degrees-of-freedom (df) test, and a 1-df test was used to assess the interaction effects alone. Variants at 495 loci were at least suggestively associated (P < 1 × 10-6) with lipid levels in stage 1 and were evaluated in stage 2, followed by combined analyses of stage 1 and stage 2. In the combined analysis of stages 1 and 2, a total of 147 independent loci were associated with lipid levels at P < 5 × 10-8 using 2-df tests, of which 18 were novel. No genome-wide-significant associations were found testing the interaction effect alone. The novel loci included several genes (proprotein convertase subtilisin/kexin type 5 (PCSK5), vascular endothelial growth factor B (VEGFB), and apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1 (APOBEC1) complementation factor (A1CF)) that have a putative role in lipid metabolism on the basis of existing evidence from cellular and experimental models.",,pdf:https://academic.oup.com/aje/article-pdf/188/6/1033/32921017/kwz005.pdf; doi:https://doi.org/10.1093/aje/kwz005; html:https://europepmc.org/articles/PMC6545280; pdf:https://europepmc.org/articles/PMC6545280?pdf=render; doi:https://doi.org/10.1093/aje/kwz005
+38778362,https://doi.org/10.1186/s12889-024-18529-3,The state of health in the European Union (EU-27) in 2019: a systematic analysis for the Global Burden of Disease study 2019.,"Santos JV, Padron-Monedero A, Bikbov B, Grad DA, Plass D, Mechili EA, Gazzelloni F, Fischer F, Sulo G, Ngwa CH, Noguer-Zambrano I, Peñalvo JL, Haagsma JA, Kissimova-Skarbek K, Monasta L, Ghith N, Sarmiento-Suarez R, Hrzic R, Haneef R, O'Caoimh R, Cuschieri S, Mondello S, Kabir Z, GBD 2019 EU State of Health Collaborators, Freitas A, Devleesschauwer B.",,BMC public health,2024,2024-05-22,Y,Health Status; Population Health; European Union; Global Burden Of Diseases; European Burden Of Disease Network,,,"<h4>Background</h4>The European Union (EU) faces many health-related challenges. Burden of diseases information and the resulting trends over time are essential for health planning. This paper reports estimates of disease burden in the EU and individual 27 EU countries in 2019, and compares them with those in 2010.<h4>Methods</h4>We used the Global Burden of Disease 2019 study estimates and 95% uncertainty intervals for the whole EU and each country to evaluate age-standardised death, years of life lost (YLLs), years lived with disability (YLDs) and disability-adjusted life years (DALYs) rates for Level 2 causes, as well as life expectancy and healthy life expectancy (HALE).<h4>Results</h4>In 2019, the age-standardised death and DALY rates in the EU were 465.8 deaths and 20,251.0 DALYs per 100,000 inhabitants, respectively. Between 2010 and 2019, there were significant decreases in age-standardised death and YLL rates across EU countries. However, YLD rates remained mainly unchanged. The largest decreases in age-standardised DALY rates were observed for ""HIV/AIDS and sexually transmitted diseases"" and ""transport injuries"" (each -19%). ""Diabetes and kidney diseases"" showed a significant increase for age-standardised DALY rates across the EU (3.5%). In addition, ""mental disorders"" showed an increasing age-standardised YLL rate (14.5%).<h4>Conclusions</h4>There was a clear trend towards improvement in the overall health status of the EU but with differences between countries. EU health policymakers need to address the burden of diseases, paying specific attention to causes such as mental disorders. There are many opportunities for mutual learning among otherwise similar countries with different patterns of disease.",,pdf:https://bmcpublichealth.biomedcentral.com/counter/pdf/10.1186/s12889-024-18529-3; doi:https://doi.org/10.1186/s12889-024-18529-3; html:https://europepmc.org/articles/PMC11110444; pdf:https://europepmc.org/articles/PMC11110444?pdf=render
 33069326,https://doi.org/10.1016/s0140-6736(20)30925-9,"Global burden of 369 diseases and injuries in 204 countries and territories, 1990-2019: a systematic analysis for the Global Burden of Disease Study 2019.",GBD 2019 Diseases and Injuries Collaborators.,,"Lancet (London, England)",2020,2020-10-01,Y,,,,"<h4>Background</h4>In an era of shifting global agendas and expanded emphasis on non-communicable diseases and injuries along with communicable diseases, sound evidence on trends by cause at the national level is essential. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) provides a systematic scientific assessment of published, publicly available, and contributed data on incidence, prevalence, and mortality for a mutually exclusive and collectively exhaustive list of diseases and injuries.<h4>Methods</h4>GBD estimates incidence, prevalence, mortality, years of life lost (YLLs), years lived with disability (YLDs), and disability-adjusted life-years (DALYs) due to 369 diseases and injuries, for two sexes, and for 204 countries and territories. Input data were extracted from censuses, household surveys, civil registration and vital statistics, disease registries, health service use, air pollution monitors, satellite imaging, disease notifications, and other sources. Cause-specific death rates and cause fractions were calculated using the Cause of Death Ensemble model and spatiotemporal Gaussian process regression. Cause-specific deaths were adjusted to match the total all-cause deaths calculated as part of the GBD population, fertility, and mortality estimates. Deaths were multiplied by standard life expectancy at each age to calculate YLLs. A Bayesian meta-regression modelling tool, DisMod-MR 2.1, was used to ensure consistency between incidence, prevalence, remission, excess mortality, and cause-specific mortality for most causes. Prevalence estimates were multiplied by disability weights for mutually exclusive sequelae of diseases and injuries to calculate YLDs. We considered results in the context of the Socio-demographic Index (SDI), a composite indicator of income per capita, years of schooling, and fertility rate in females younger than 25 years. Uncertainty intervals (UIs) were generated for every metric using the 25th and 975th ordered 1000 draw values of the posterior distribution.<h4>Findings</h4>Global health has steadily improved over the past 30 years as measured by age-standardised DALY rates. After taking into account population growth and ageing, the absolute number of DALYs has remained stable. Since 2010, the pace of decline in global age-standardised DALY rates has accelerated in age groups younger than 50 years compared with the 1990-2010 time period, with the greatest annualised rate of decline occurring in the 0-9-year age group. Six infectious diseases were among the top ten causes of DALYs in children younger than 10 years in 2019: lower respiratory infections (ranked second), diarrhoeal diseases (third), malaria (fifth), meningitis (sixth), whooping cough (ninth), and sexually transmitted infections (which, in this age group, is fully accounted for by congenital syphilis; ranked tenth). In adolescents aged 10-24 years, three injury causes were among the top causes of DALYs: road injuries (ranked first), self-harm (third), and interpersonal violence (fifth). Five of the causes that were in the top ten for ages 10-24 years were also in the top ten in the 25-49-year age group: road injuries (ranked first), HIV/AIDS (second), low back pain (fourth), headache disorders (fifth), and depressive disorders (sixth). In 2019, ischaemic heart disease and stroke were the top-ranked causes of DALYs in both the 50-74-year and 75-years-and-older age groups. Since 1990, there has been a marked shift towards a greater proportion of burden due to YLDs from non-communicable diseases and injuries. In 2019, there were 11 countries where non-communicable disease and injury YLDs constituted more than half of all disease burden. Decreases in age-standardised DALY rates have accelerated over the past decade in countries at the lower end of the SDI range, while improvements have started to stagnate or even reverse in countries with higher SDI.<h4>Interpretation</h4>As disability becomes an increasingly large component of disease burden and a larger component of health expenditure, greater research and development investment is needed to identify new, more effective intervention strategies. With a rapidly ageing global population, the demands on health services to deal with disabling outcomes, which increase with age, will require policy makers to anticipate these changes. The mix of universal and more geographically specific influences on health reinforces the need for regular reporting on population health in detail and by underlying cause to help decision makers to identify success stories of disease control to emulate, as well as opportunities to improve.<h4>Funding</h4>Bill & Melinda Gates Foundation.",,pdf:http://www.thelancet.com/article/S0140673620309259/pdf; doi:https://doi.org/10.1016/S0140-6736(20)30925-9; html:https://europepmc.org/articles/PMC7567026
 35697829,https://doi.org/10.1038/s42003-022-03448-z,Differential and shared genetic effects on kidney function between diabetic and non-diabetic individuals.,"Winkler TW, Rasheed H, Teumer A, Gorski M, Rowan BX, Stanzick KJ, Thomas LF, Tin A, Hoppmann A, Chu AY, Tayo B, Thio CHL, Cusi D, Chai JF, Sieber KB, Horn K, Li M, Scholz M, Cocca M, Wuttke M, van der Most PJ, Yang Q, Ghasemi S, Nutile T, Li Y, Pontali G, Günther F, Dehghan A, Correa A, Parsa A, Feresin A, de Vries APJ, Zonderman AB, Smith AV, Oldehinkel AJ, De Grandi A, Rosenkranz AR, Franke A, Teren A, Metspalu A, Hicks AA, Morris AP, Tönjes A, Morgan A, Podgornaia AI, Peters A, Körner A, Mahajan A, Campbell A, Freedman BI, Spedicati B, Ponte B, Schöttker B, Brumpton B, Banas B, Krämer BK, Jung B, Åsvold BO, Smith BH, Ning B, Penninx BWJH, Vanderwerff BR, Psaty BM, Kammerer CM, Langefeld CD, Hayward C, Spracklen CN, Robinson-Cohen C, Hartman CA, Lindgren CM, Wang C, Sabanayagam C, Heng CK, Lanzani C, Khor CC, Cheng CY, Fuchsberger C, Gieger C, Shaffer CM, Schulz CA, Willer CJ, Chasman DI, Gudbjartsson DF, Ruggiero D, Toniolo D, Czamara D, Porteous DJ, Waterworth DM, Mascalzoni D, Mook-Kanamori DO, Reilly DF, Daw EW, Hofer E, Boerwinkle E, Salvi E, Bottinger EP, Tai ES, Catamo E, Rizzi F, Guo F, Rivadeneira F, Guilianini F, Sveinbjornsson G, Ehret G, Waeber G, Biino G, Girotto G, Pistis G, Nadkarni GN, Delgado GE, Montgomery GW, Snieder H, Campbell H, White HD, Gao H, Stringham HM, Schmidt H, Li H, Brenner H, Holm H, Kirsten H, Kramer H, Rudan I, Nolte IM, Tzoulaki I, Olafsson I, Martins J, Cook JP, Wilson JF, Halbritter J, Felix JF, Divers J, Kooner JS, Lee JJ, O'Connell J, Rotter JI, Liu J, Xu J, Thiery J, Ärnlöv J, Kuusisto J, Jakobsdottir J, Tremblay J, Chambers JC, Whitfield JB, Gaziano JM, Marten J, Coresh J, Jonas JB, Mychaleckyj JC, Christensen K, Eckardt KU, Mohlke KL, Endlich K, Dittrich K, Ryan KA, Rice KM, Taylor KD, Ho K, Nikus K, Matsuda K, Strauch K, Miliku K, Hveem K, Lind L, Wallentin L, Yerges-Armstrong LM, Raffield LM, Phillips LS, Launer LJ, Lyytikäinen LP, Lange LA, Citterio L, Klaric L, Ikram MA, Ising M, Kleber ME, Francescatto M, Concas MP, Ciullo M, Piratsu M, Orho-Melander M, Laakso M, Loeffler M, Perola M, de Borst MH, Gögele M, Bianca M, Lukas MA, Feitosa MF, Biggs ML, Wojczynski MK, Kavousi M, Kanai M, Akiyama M, Yasuda M, Nauck M, Waldenberger M, Chee ML, Chee ML, Boehnke M, Preuss MH, Stumvoll M, Province MA, Evans MK, O'Donoghue ML, Kubo M, Kähönen M, Kastarinen M, Nalls MA, Kuokkanen M, Ghanbari M, Bochud M, Josyula NS, Martin NG, Tan NYQ, Palmer ND, Pirastu N, Schupf N, Verweij N, Hutri-Kähönen N, Mononen N, Bansal N, Devuyst O, Melander O, Raitakari OT, Polasek O, Manunta P, Gasparini P, Mishra PP, Sulem P, Magnusson PKE, Elliott P, Ridker PM, Hamet P, Svensson PO, Joshi PK, Kovacs P, Pramstaller PP, Rossing P, Vollenweider P, van der Harst P, Dorajoo R, Sim RZH, Burkhardt R, Tao R, Noordam R, Mägi R, Schmidt R, de Mutsert R, Rueedi R, van Dam RM, Carroll RJ, Gansevoort RT, Loos RJF, Felicita SC, Sedaghat S, Padmanabhan S, Freitag-Wolf S, Pendergrass SA, Graham SE, Gordon SD, Hwang SJ, Kerr SM, Vaccargiu S, Patil SB, Hallan S, Bakker SJL, Lim SC, Lucae S, Vogelezang S, Bergmann S, Corre T, Ahluwalia TS, Lehtimäki T, Boutin TS, Meitinger T, Wong TY, Bergler T, Rabelink TJ, Esko T, Haller T, Thorsteinsdottir U, Völker U, Foo VHX, Salomaa V, Vitart V, Giedraitis V, Gudnason V, Jaddoe VWV, Huang W, Zhang W, Wei WB, Kiess W, März W, Koenig W, Lieb W, Gao X, Sim X, Wang YX, Friedlander Y, Tham YC, Kamatani Y, Okada Y, Milaneschi Y, Yu Z, Lifelines cohort study, DiscovEHR/MyCode study, VA Million Veteran Program, Stark KJ, Stefansson K, Böger CA, Hung AM, Kronenberg F, Köttgen A, Pattaro C, Heid IM.",,Communications biology,2022,2022-06-13,Y,,,,"Reduced glomerular filtration rate (GFR) can progress to kidney failure. Risk factors include genetics and diabetes mellitus (DM), but little is known about their interaction. We conducted genome-wide association meta-analyses for estimated GFR based on serum creatinine (eGFR), separately for individuals with or without DM (n<sub>DM</sub> = 178,691, n<sub>noDM</sub> = 1,296,113). Our genome-wide searches identified (i) seven eGFR loci with significant DM/noDM-difference, (ii) four additional novel loci with suggestive difference and (iii) 28 further novel loci (including CUBN) by allowing for potential difference. GWAS on eGFR among DM individuals identified 2 known and 27 potentially responsible loci for diabetic kidney disease. Gene prioritization highlighted 18 genes that may inform reno-protective drug development. We highlight the existence of DM-only and noDM-only effects, which can inform about the target group, if respective genes are advanced as drug targets. Largely shared effects suggest that most drug interventions to alter eGFR should be effective in DM and noDM.",,pdf:https://www.nature.com/articles/s42003-022-03448-z.pdf; doi:https://doi.org/10.1038/s42003-022-03448-z; html:https://europepmc.org/articles/PMC9192715; pdf:https://europepmc.org/articles/PMC9192715?pdf=render
 37595128,https://doi.org/10.1097/hep.0000000000000361,The global fatty liver disease Sustainable Development Goal country score for 195 countries and territories.,"Lazarus JV, Han H, Mark HE, Alqahtani SA, Schattenberg JM, Soriano JB, White TM, Zelber-Sagi S, Dirac MA, GBD Fatty Liver Disease Sustainable Development Goal Collaborators.",,"Hepatology (Baltimore, Md.)",2023,2023-04-18,Y,,,,"<h4>Background and aims</h4>Fatty liver disease is highly prevalent, resulting in overarching wellbeing and economic costs. Addressing it requires comprehensive and coordinated multisectoral action. We developed a fatty liver disease Sustainable Development Goal (SDG) country score to provide insights into country-level preparedness to address fatty liver disease through a whole-of-society lens.<h4>Approach and results</h4>We developed 2 fatty liver disease-SDG score sets. The first included 6 indicators (child wasting, child overweight, noncommunicable disease mortality, a universal health coverage service coverage index, health worker density, and education attainment), covering 195 countries and territories between 1990 and 2017. The second included the aforementioned indicators plus an urban green space indicator, covering 60 countries and territories for which 2017 data were available. To develop the fatty liver disease-SDG score, indicators were categorized as ""positive"" or ""negative"" and scaled from 0 to 100. Higher scores indicate better preparedness levels. Fatty liver disease-SDG scores varied between countries and territories (n = 195), from 14.6 (95% uncertainty interval: 8.9 to 19.4) in Niger to 93.5 (91.6 to 95.3) in Japan; 18 countries and territories scored > 85. Regionally, the high-income super-region had the highest score at 88.8 (87.3 to 90.1) in 2017, whereas south Asia had the lowest score at 44.1 (42.4 to 45.8). Between 1990 and 2017, the fatty liver disease-SDG score increased in all super-regions, with the greatest increase in south Asia, but decreased in 8 countries and territories.<h4>Conclusions</h4>The fatty liver disease-SDG score provides a strategic advocacy tool at the national and global levels for the liver health field and noncommunicable disease advocates, highlighting the multisectoral collaborations needed to address fatty liver disease, and noncommunicable diseases overall.",,html:https://journals.lww.com/hep/Abstract/9900/The_global_Fatty_Liver_Disease_Sustainable.395.aspx; doi:https://doi.org/10.1097/HEP.0000000000000361; html:https://europepmc.org/articles/PMC10442089; pdf:https://europepmc.org/articles/PMC10442089?pdf=render
diff --git a/data/papers.json b/data/papers.json
index c251be8e..41a29600 100644
--- a/data/papers.json
+++ b/data/papers.json
@@ -237,23 +237,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.vaccine.2023.01.023; doi:https://doi.org/10.1016/j.vaccine.2023.01.023; html:https://europepmc.org/articles/PMC9837216; pdf:https://europepmc.org/articles/PMC9837216?pdf=render"
   },
-  {
-    "id": "38562403",
-    "doi": "https://doi.org/10.1016/j.ssmph.2024.101655",
-    "title": "Pathways explaining racial/ethnic and socio-economic disparities in brain white matter integrity outcomes in the UK Biobank study.",
-    "authorString": "Weiss J, Beydoun MA, Beydoun HA, Georgescu MF, Hu YH, Noren Hooten N, Banerjee S, Launer LJ, Evans MK, Zonderman AB.",
-    "authorAffiliations": "",
-    "journalTitle": "SSM - population health",
-    "pubYear": "2024",
-    "date": "2024-03-20",
-    "isOpenAccess": "Y",
-    "keywords": "Aging; Magnetic Resonance Imaging; Racial Disparities; Socio-economic Status; White Matter Integrity",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Pathways explaining racial/ethnic and socio-economic status (SES) disparities in white matter integrity (WMI) reflecting brain health, remain underexplored, particularly in the UK population. We examined racial/ethnic and SES disparities in diffusion tensor brain magnetic resonance imaging (dMRI) markers, namely global and tract-specific mean fractional anisotropy (FA), and tested total, direct and indirect effects through lifestyle, health-related and cognition factors using a structural equations modeling approach among 36,184 UK Biobank participants aged 40-70\u00a0y at baseline assessment (47% men). Multiple linear regression models were conducted, testing independent associations of race/ethnicity, socio-economic and other downstream factors in relation to global mean FA, while stratifying by Alzheimer's Disease polygenic Risk Score (AD PRS) tertiles. Race (Non-White vs. White) and lower SES predicted poorer WMI (i.e. lower global mean FA) at follow-up, with racial/ethnic disparities in FA<sub>mean</sub> involving multiple pathways and SES playing a central role in those pathways. Mediational patterns differed across tract-specific FA outcomes, with SES-FA<sub>mean</sub> total effect being partially mediated (41% of total effect\u00a0=\u00a0indirect effect). Furthermore, the association of poor cognition with FA<sub>mean</sub> was markedly stronger in the two uppermost AD PRS tertiles compared to the lower tertile (T<sub>2</sub> and T<sub>3</sub>: \u03b2\u00b1SE: -0.0009\u00a0\u00b1\u00a00.0001 vs. T<sub>1</sub>: \u03b2\u00b1SE: -0.0005\u00a0\u00b1\u00a00.0001, <i>P</i>\u00a0<\u00a00.001), independently of potentially confounding factors. Race and lower SES were generally important determinants of adverse WMI outcomes, with partial mediation of socio-economic disparities in global mean FA through lifestyle, health-related and cognition factors. The association of poor cognition with lower global mean FA was stronger at higher AD polygenic risk.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.ssmph.2024.101655; html:https://europepmc.org/articles/PMC10982559; pdf:https://europepmc.org/articles/PMC10982559?pdf=render"
-  },
   {
     "id": "34994801",
     "doi": "https://doi.org/10.1093/pubmed/fdab400",
@@ -271,6 +254,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/jpubhealth/article-pdf/45/1/e65/49527132/fdab400.pdf; doi:https://doi.org/10.1093/pubmed/fdab400; html:https://europepmc.org/articles/PMC8755382; pdf:https://europepmc.org/articles/PMC8755382?pdf=render"
   },
+  {
+    "id": "38562403",
+    "doi": "https://doi.org/10.1016/j.ssmph.2024.101655",
+    "title": "Pathways explaining racial/ethnic and socio-economic disparities in brain white matter integrity outcomes in the UK Biobank study.",
+    "authorString": "Weiss J, Beydoun MA, Beydoun HA, Georgescu MF, Hu YH, Noren Hooten N, Banerjee S, Launer LJ, Evans MK, Zonderman AB.",
+    "authorAffiliations": "",
+    "journalTitle": "SSM - population health",
+    "pubYear": "2024",
+    "date": "2024-03-20",
+    "isOpenAccess": "Y",
+    "keywords": "Aging; Magnetic Resonance Imaging; Racial Disparities; Socio-economic Status; White Matter Integrity",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Pathways explaining racial/ethnic and socio-economic status (SES) disparities in white matter integrity (WMI) reflecting brain health, remain underexplored, particularly in the UK population. We examined racial/ethnic and SES disparities in diffusion tensor brain magnetic resonance imaging (dMRI) markers, namely global and tract-specific mean fractional anisotropy (FA), and tested total, direct and indirect effects through lifestyle, health-related and cognition factors using a structural equations modeling approach among 36,184 UK Biobank participants aged 40-70\u00a0y at baseline assessment (47% men). Multiple linear regression models were conducted, testing independent associations of race/ethnicity, socio-economic and other downstream factors in relation to global mean FA, while stratifying by Alzheimer's Disease polygenic Risk Score (AD PRS) tertiles. Race (Non-White vs. White) and lower SES predicted poorer WMI (i.e. lower global mean FA) at follow-up, with racial/ethnic disparities in FA<sub>mean</sub> involving multiple pathways and SES playing a central role in those pathways. Mediational patterns differed across tract-specific FA outcomes, with SES-FA<sub>mean</sub> total effect being partially mediated (41% of total effect\u00a0=\u00a0indirect effect). Furthermore, the association of poor cognition with FA<sub>mean</sub> was markedly stronger in the two uppermost AD PRS tertiles compared to the lower tertile (T<sub>2</sub> and T<sub>3</sub>: \u03b2\u00b1SE: -0.0009\u00a0\u00b1\u00a00.0001 vs. T<sub>1</sub>: \u03b2\u00b1SE: -0.0005\u00a0\u00b1\u00a00.0001, <i>P</i>\u00a0<\u00a00.001), independently of potentially confounding factors. Race and lower SES were generally important determinants of adverse WMI outcomes, with partial mediation of socio-economic disparities in global mean FA through lifestyle, health-related and cognition factors. The association of poor cognition with lower global mean FA was stronger at higher AD polygenic risk.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.ssmph.2024.101655; html:https://europepmc.org/articles/PMC10982559; pdf:https://europepmc.org/articles/PMC10982559?pdf=render"
+  },
   {
     "id": "37124948",
     "doi": "https://doi.org/10.1016/j.lanepe.2023.100638",
@@ -628,23 +628,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1007/s13300-023-01456-8; doi:https://doi.org/10.1007/s13300-023-01456-8; html:https://europepmc.org/articles/PMC10597906; pdf:https://europepmc.org/articles/PMC10597906?pdf=render"
   },
-  {
-    "id": "37308303",
-    "doi": "https://doi.org/10.3399/bjgp.2023.0044",
-    "title": "Diagnostic windows in non-neoplastic diseases: a systematic review.",
-    "authorString": "Whitfield E, White B, Denaxas S, Lyratzopoulos G.",
-    "authorAffiliations": "",
-    "journalTitle": "The British journal of general practice : the journal of the Royal College of General Practitioners",
-    "pubYear": "2023",
-    "date": "2023-08-31",
-    "isOpenAccess": "Y",
-    "keywords": "Diagnosis; Primary Health Care; Electronic Health Records",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Investigating changes in prediagnostic healthcare utilisation can help identify how much earlier conditions could be diagnosed. Such 'diagnostic windows' are established for cancer but remain relatively unexplored for non-neoplastic conditions.<h4>Aim</h4>To extract evidence on the presence and length of diagnostic windows for non-neoplastic conditions.<h4>Design and setting</h4>A systematic review of studies of prediagnostic healthcare utilisation was carried out.<h4>Method</h4>A search strategy was developed to identify relevant studies from PubMed and Connected Papers. Data were extracted on prediagnostic healthcare use, and evidence of diagnostic window presence and length was assessed.<h4>Results</h4>Of 4340 studies screened, 27 were included, covering 17 non-neoplastic conditions, including both chronic (for example, Parkinson's disease) and acute conditions (for example, stroke). Prediagnostic healthcare events included primary care encounters and presentations with relevant symptoms. For 10 conditions, sufficient evidence to determine diagnostic window presence and length was available, ranging from 28 days (herpes simplex encephalitis) to 9 years (ulcerative colitis). For the remaining conditions, diagnostic windows were likely to be present, but insufficient study duration was often a barrier to robustly determining their length, meaning that diagnostic window length may exceed 10 years for coeliac disease, for example.<h4>Conclusion</h4>Evidence of changing healthcare use before diagnosis exists for many non-neoplastic conditions, establishing that early diagnosis is possible, in principle. In particular, some conditions may be detectable many years earlier than they are currently diagnosed. Further research is required to accurately estimate diagnostic windows and to determine how much earlier diagnosis may be possible, and how this might be achieved.",
-    "laySummary": "",
-    "urls": "pdf:https://bjgp.org/content/bjgp/early/2023/04/04/BJGP.2023.0044.full.pdf; doi:https://doi.org/10.3399/BJGP.2023.0044; html:https://europepmc.org/articles/PMC10285689; pdf:https://europepmc.org/articles/PMC10285689?pdf=render"
-  },
   {
     "id": "38803829",
     "doi": "https://doi.org/10.1136/bmjmed-2023-000791",
@@ -662,6 +645,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1136/bmjmed-2023-000791; html:https://europepmc.org/articles/PMC11129040; pdf:https://europepmc.org/articles/PMC11129040?pdf=render"
   },
+  {
+    "id": "37308303",
+    "doi": "https://doi.org/10.3399/bjgp.2023.0044",
+    "title": "Diagnostic windows in non-neoplastic diseases: a systematic review.",
+    "authorString": "Whitfield E, White B, Denaxas S, Lyratzopoulos G.",
+    "authorAffiliations": "",
+    "journalTitle": "The British journal of general practice : the journal of the Royal College of General Practitioners",
+    "pubYear": "2023",
+    "date": "2023-08-31",
+    "isOpenAccess": "Y",
+    "keywords": "Diagnosis; Primary Health Care; Electronic Health Records",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Investigating changes in prediagnostic healthcare utilisation can help identify how much earlier conditions could be diagnosed. Such 'diagnostic windows' are established for cancer but remain relatively unexplored for non-neoplastic conditions.<h4>Aim</h4>To extract evidence on the presence and length of diagnostic windows for non-neoplastic conditions.<h4>Design and setting</h4>A systematic review of studies of prediagnostic healthcare utilisation was carried out.<h4>Method</h4>A search strategy was developed to identify relevant studies from PubMed and Connected Papers. Data were extracted on prediagnostic healthcare use, and evidence of diagnostic window presence and length was assessed.<h4>Results</h4>Of 4340 studies screened, 27 were included, covering 17 non-neoplastic conditions, including both chronic (for example, Parkinson's disease) and acute conditions (for example, stroke). Prediagnostic healthcare events included primary care encounters and presentations with relevant symptoms. For 10 conditions, sufficient evidence to determine diagnostic window presence and length was available, ranging from 28 days (herpes simplex encephalitis) to 9 years (ulcerative colitis). For the remaining conditions, diagnostic windows were likely to be present, but insufficient study duration was often a barrier to robustly determining their length, meaning that diagnostic window length may exceed 10 years for coeliac disease, for example.<h4>Conclusion</h4>Evidence of changing healthcare use before diagnosis exists for many non-neoplastic conditions, establishing that early diagnosis is possible, in principle. In particular, some conditions may be detectable many years earlier than they are currently diagnosed. Further research is required to accurately estimate diagnostic windows and to determine how much earlier diagnosis may be possible, and how this might be achieved.",
+    "laySummary": "",
+    "urls": "pdf:https://bjgp.org/content/bjgp/early/2023/04/04/BJGP.2023.0044.full.pdf; doi:https://doi.org/10.3399/BJGP.2023.0044; html:https://europepmc.org/articles/PMC10285689; pdf:https://europepmc.org/articles/PMC10285689?pdf=render"
+  },
   {
     "id": "39068671",
     "doi": "https://doi.org/10.18632/aging.206033",
@@ -815,23 +815,6 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/bcp.16030; doi:https://doi.org/10.1111/bcp.16030; html:https://europepmc.org/articles/PMC7616229; pdf:https://europepmc.org/articles/PMC7616229?pdf=render"
   },
-  {
-    "id": "37243092",
-    "doi": "https://doi.org/10.3390/vaccines11050988",
-    "title": "A Methodological Framework for Assessing the Benefit of SARS-CoV-2 Vaccination following Previous Infection: Case Study of Five- to Eleven-Year-Olds.",
-    "authorString": "Pagel C, Wilde H, Tomlinson C, Mateen B, Brown K.",
-    "authorAffiliations": "",
-    "journalTitle": "Vaccines",
-    "pubYear": "2023",
-    "date": "2023-05-16",
-    "isOpenAccess": "Y",
-    "keywords": "Health Policy; Mathematical Modelling; Covid-19; Paediatric Vaccines",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Vaccination rates against SARS-CoV-2 in children aged five to eleven years remain low in many countries. The current benefit of vaccination in this age group has been questioned given that the large majority of children have now experienced at least one SARS-CoV-2 infection. However, protection from infection, vaccination or both wanes over time. National decisions on offering vaccines to this age group have tended to be made without considering time since infection. There is an urgent need to evaluate the additional benefits of vaccination in previously infected children and under what circumstances those benefits accrue. We present a novel methodological framework for estimating the potential benefits of COVID-19 vaccination in previously infected children aged five to eleven, accounting for waning. We apply this framework to the UK context and for two adverse outcomes: hospitalisation related to SARS-CoV-2 infection and Long Covid. We show that the most important drivers of benefit are: the degree of protection provided by previous infection; the protection provided by vaccination; the time since previous infection; and future attack rates. Vaccination can be very beneficial for previously infected children if future attack rates are high and several months have elapsed since the previous major wave in this group. Benefits are generally larger for Long Covid than hospitalisation, because Long Covid is both more common than hospitalisation and previous infection offers less protection against it. Our framework provides a structure for policy makers to explore the additional benefit of vaccination across a range of adverse outcomes and different parameter assumptions. It can be easily updated as new evidence emerges.",
-    "laySummary": "",
-    "urls": "pdf:https://www.mdpi.com/2076-393X/11/5/988/pdf?version=1684231380; doi:https://doi.org/10.3390/vaccines11050988; html:https://europepmc.org/articles/PMC10220644; pdf:https://europepmc.org/articles/PMC10220644?pdf=render"
-  },
   {
     "id": "36261315",
     "doi": "https://doi.org/10.1002/ana.26536",
@@ -849,6 +832,23 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ana.26536; doi:https://doi.org/10.1002/ana.26536; html:https://europepmc.org/articles/PMC9874556; pdf:https://europepmc.org/articles/PMC9874556?pdf=render"
   },
+  {
+    "id": "37243092",
+    "doi": "https://doi.org/10.3390/vaccines11050988",
+    "title": "A Methodological Framework for Assessing the Benefit of SARS-CoV-2 Vaccination following Previous Infection: Case Study of Five- to Eleven-Year-Olds.",
+    "authorString": "Pagel C, Wilde H, Tomlinson C, Mateen B, Brown K.",
+    "authorAffiliations": "",
+    "journalTitle": "Vaccines",
+    "pubYear": "2023",
+    "date": "2023-05-16",
+    "isOpenAccess": "Y",
+    "keywords": "Health Policy; Mathematical Modelling; Covid-19; Paediatric Vaccines",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Vaccination rates against SARS-CoV-2 in children aged five to eleven years remain low in many countries. The current benefit of vaccination in this age group has been questioned given that the large majority of children have now experienced at least one SARS-CoV-2 infection. However, protection from infection, vaccination or both wanes over time. National decisions on offering vaccines to this age group have tended to be made without considering time since infection. There is an urgent need to evaluate the additional benefits of vaccination in previously infected children and under what circumstances those benefits accrue. We present a novel methodological framework for estimating the potential benefits of COVID-19 vaccination in previously infected children aged five to eleven, accounting for waning. We apply this framework to the UK context and for two adverse outcomes: hospitalisation related to SARS-CoV-2 infection and Long Covid. We show that the most important drivers of benefit are: the degree of protection provided by previous infection; the protection provided by vaccination; the time since previous infection; and future attack rates. Vaccination can be very beneficial for previously infected children if future attack rates are high and several months have elapsed since the previous major wave in this group. Benefits are generally larger for Long Covid than hospitalisation, because Long Covid is both more common than hospitalisation and previous infection offers less protection against it. Our framework provides a structure for policy makers to explore the additional benefit of vaccination across a range of adverse outcomes and different parameter assumptions. It can be easily updated as new evidence emerges.",
+    "laySummary": "",
+    "urls": "pdf:https://www.mdpi.com/2076-393X/11/5/988/pdf?version=1684231380; doi:https://doi.org/10.3390/vaccines11050988; html:https://europepmc.org/articles/PMC10220644; pdf:https://europepmc.org/articles/PMC10220644?pdf=render"
+  },
   {
     "id": "37407076",
     "doi": "https://doi.org/10.1136/bmj-2022-073639",
@@ -986,21 +986,21 @@
     "urls": "doi:https://doi.org/10.1136/bmjopen-2021-053402; doi:https://doi.org/10.1136/bmjopen-2021-053402; html:https://europepmc.org/articles/PMC8313303; pdf:https://europepmc.org/articles/PMC8313303?pdf=render"
   },
   {
-    "id": "37587102",
-    "doi": "https://doi.org/10.1038/s41467-023-40643-w",
-    "title": "SARS-CoV-2 rapid antibody test results and subsequent risk of hospitalisation and death in 361,801 people.",
-    "authorString": "Whitaker M, Davies B, Atchison C, Barclay W, Ashby D, Darzi A, Riley S, Cooke G, Donnelly CA, Chadeau-Hyam M, Elliott P, Ward H.",
+    "id": "35038629",
+    "doi": "https://doi.org/10.1016/j.puhe.2021.12.010",
+    "title": "Investigating the association between COVID-19 vaccination and care home outbreak frequency and duration.",
+    "authorString": "Bradley DT, Murphy S, McWilliams P, Arnold S, Lavery S, Murphy J, de Lusignan S, Hobbs R, Tsang RSM, Akbari A, Torabi F, Beggs J, Chuter A, Shi T, Vasileiou E, Robertson C, Sheikh A, Reid H, O'Reilly D.",
     "authorAffiliations": "",
-    "journalTitle": "Nature communications",
-    "pubYear": "2023",
-    "date": "2023-08-16",
+    "journalTitle": "Public health",
+    "pubYear": "2022",
+    "date": "2021-12-18",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Vaccination; outbreak; Care Homes; Covid-19; Sars-cov-2",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "The value of SARS-CoV-2 lateral flow immunoassay (LFIA) tests for estimating individual disease risk is unclear. The REACT-2 study in England, UK, obtained self-administered SARS-CoV-2 LFIA test results from 361,801 adults in January-May 2021. Here, we link to routine data on subsequent hospitalisation (to September 2021), and death (to December 2021). Among those who had received one or more vaccines, a negative LFIA is associated with increased risk of hospitalisation with COVID-19 (HR: 2.73 [95% confidence interval: 1.15,6.48]), death (all-cause) (HR: 1.59, 95% CI:1.07, 2.37), and death with COVID-19 as underlying cause (20.6 [1.83,232]). For people designated at high risk from COVID-19, who had received one or more vaccines, there is an additional risk of all-cause mortality of 1.9 per 1000 for those testing antibody negative compared to positive. However, the LFIA does not provide substantial predictive information over and above that which is available from detailed sociodemographic and health-related variables. Nonetheless, this simple test provides a marker which could be a valuable addition to understanding population and individual-level risk.",
+    "abstract": "<h4>Objectives</h4>At the end of 2020, many countries commenced a vaccination programme against SARS-CoV-2. Public health authorities aim to prevent and interrupt outbreaks of infectious disease in social care settings. We aimed to investigate the association between the introduction of the vaccination programme and the frequency and duration of COVID-19 outbreaks in Northern Ireland (NI).<h4>Study design</h4>We undertook an ecological study using routinely available national data.<h4>Methods</h4>We used Poisson regression to measure the relationship between the number of RT-PCR confirmed COVID-19 outbreaks in care homes, and as a measure of community COVID-19 prevalence, the Office for National Statistics COVID-19 Infection Survey estimated the number of people testing positive for COVID-19 in NI. We estimated the change in this relationship and estimated the expected number of care home outbreaks in the absence of the vaccination programme. A Cox proportional hazards model estimated the hazard ratio of a confirmed COVID-19 care home outbreak closure.<h4>Results</h4>Care home outbreaks reduced by two-thirds compared to expected following the introduction of the vaccination programme, from a projected 1625 COVID-19 outbreaks (95% prediction interval 1553-1694) between 7 December 2020 and 28 October 2021 to an observed 501. We estimated an adjusted hazard ratio of 2.53 of the outbreak closure assuming a 21-day lag for immunity.<h4>Conclusions</h4>These findings describe the association of the vaccination with a reduction in outbreak frequency and duration across NI care homes. This indicates probable reduced harm and disruption from COVID-19 in social care settings following vaccination. Future research using individual level data from care home residents will be needed to investigate the effectiveness of the vaccines and the duration of their effects.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1038/s41467-023-40643-w; html:https://europepmc.org/articles/PMC10432566; pdf:https://europepmc.org/articles/PMC10432566?pdf=render"
+    "urls": "pdf:https://cronfa.swan.ac.uk/Record/cronfa59048/Download/59048__22075__e4bbc8a7cad6434abac5984eb2422e06.pdf; doi:https://doi.org/10.1016/j.puhe.2021.12.010; html:https://europepmc.org/articles/PMC8683272; pdf:https://europepmc.org/articles/PMC8683272?pdf=render"
   },
   {
     "id": "36647111",
@@ -1019,6 +1019,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-022-02093-0; doi:https://doi.org/10.1186/s12911-022-02093-0; html:https://europepmc.org/articles/PMC9842203; pdf:https://europepmc.org/articles/PMC9842203?pdf=render"
   },
+  {
+    "id": "37587102",
+    "doi": "https://doi.org/10.1038/s41467-023-40643-w",
+    "title": "SARS-CoV-2 rapid antibody test results and subsequent risk of hospitalisation and death in 361,801 people.",
+    "authorString": "Whitaker M, Davies B, Atchison C, Barclay W, Ashby D, Darzi A, Riley S, Cooke G, Donnelly CA, Chadeau-Hyam M, Elliott P, Ward H.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature communications",
+    "pubYear": "2023",
+    "date": "2023-08-16",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The value of SARS-CoV-2 lateral flow immunoassay (LFIA) tests for estimating individual disease risk is unclear. The REACT-2 study in England, UK, obtained self-administered SARS-CoV-2 LFIA test results from 361,801 adults in January-May 2021. Here, we link to routine data on subsequent hospitalisation (to September 2021), and death (to December 2021). Among those who had received one or more vaccines, a negative LFIA is associated with increased risk of hospitalisation with COVID-19 (HR: 2.73 [95% confidence interval: 1.15,6.48]), death (all-cause) (HR: 1.59, 95% CI:1.07, 2.37), and death with COVID-19 as underlying cause (20.6 [1.83,232]). For people designated at high risk from COVID-19, who had received one or more vaccines, there is an additional risk of all-cause mortality of 1.9 per 1000 for those testing antibody negative compared to positive. However, the LFIA does not provide substantial predictive information over and above that which is available from detailed sociodemographic and health-related variables. Nonetheless, this simple test provides a marker which could be a valuable addition to understanding population and individual-level risk.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1038/s41467-023-40643-w; html:https://europepmc.org/articles/PMC10432566; pdf:https://europepmc.org/articles/PMC10432566?pdf=render"
+  },
   {
     "id": "38491011",
     "doi": "https://doi.org/10.1038/s41467-024-46451-0",
@@ -1036,23 +1053,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1038/s41467-024-46451-0; html:https://europepmc.org/articles/PMC10943015; pdf:https://europepmc.org/articles/PMC10943015?pdf=render"
   },
-  {
-    "id": "35038629",
-    "doi": "https://doi.org/10.1016/j.puhe.2021.12.010",
-    "title": "Investigating the association between COVID-19 vaccination and care home outbreak frequency and duration.",
-    "authorString": "Bradley DT, Murphy S, McWilliams P, Arnold S, Lavery S, Murphy J, de Lusignan S, Hobbs R, Tsang RSM, Akbari A, Torabi F, Beggs J, Chuter A, Shi T, Vasileiou E, Robertson C, Sheikh A, Reid H, O'Reilly D.",
-    "authorAffiliations": "",
-    "journalTitle": "Public health",
-    "pubYear": "2022",
-    "date": "2021-12-18",
-    "isOpenAccess": "Y",
-    "keywords": "Vaccination; outbreak; Care Homes; Covid-19; Sars-cov-2",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objectives</h4>At the end of 2020, many countries commenced a vaccination programme against SARS-CoV-2. Public health authorities aim to prevent and interrupt outbreaks of infectious disease in social care settings. We aimed to investigate the association between the introduction of the vaccination programme and the frequency and duration of COVID-19 outbreaks in Northern Ireland (NI).<h4>Study design</h4>We undertook an ecological study using routinely available national data.<h4>Methods</h4>We used Poisson regression to measure the relationship between the number of RT-PCR confirmed COVID-19 outbreaks in care homes, and as a measure of community COVID-19 prevalence, the Office for National Statistics COVID-19 Infection Survey estimated the number of people testing positive for COVID-19 in NI. We estimated the change in this relationship and estimated the expected number of care home outbreaks in the absence of the vaccination programme. A Cox proportional hazards model estimated the hazard ratio of a confirmed COVID-19 care home outbreak closure.<h4>Results</h4>Care home outbreaks reduced by two-thirds compared to expected following the introduction of the vaccination programme, from a projected 1625 COVID-19 outbreaks (95% prediction interval 1553-1694) between 7 December 2020 and 28 October 2021 to an observed 501. We estimated an adjusted hazard ratio of 2.53 of the outbreak closure assuming a 21-day lag for immunity.<h4>Conclusions</h4>These findings describe the association of the vaccination with a reduction in outbreak frequency and duration across NI care homes. This indicates probable reduced harm and disruption from COVID-19 in social care settings following vaccination. Future research using individual level data from care home residents will be needed to investigate the effectiveness of the vaccines and the duration of their effects.",
-    "laySummary": "",
-    "urls": "pdf:https://cronfa.swan.ac.uk/Record/cronfa59048/Download/59048__22075__e4bbc8a7cad6434abac5984eb2422e06.pdf; doi:https://doi.org/10.1016/j.puhe.2021.12.010; html:https://europepmc.org/articles/PMC8683272; pdf:https://europepmc.org/articles/PMC8683272?pdf=render"
-  },
   {
     "id": "PMC10929454",
     "doi": "https://doi.org/",
@@ -1139,21 +1139,21 @@
     "urls": "doi:https://doi.org/10.1016/j.lanepe.2024.100938; html:https://europepmc.org/articles/PMC11153226; pdf:https://europepmc.org/articles/PMC11153226?pdf=render"
   },
   {
-    "id": "38630417",
-    "doi": "https://doi.org/10.1007/s44192-024-00066-5",
-    "title": "Cerebrospinal fluid metabolomes of treatment-resistant depression subtypes and ketamine response: a pilot study.",
-    "authorString": "Berner J, Acharjee A.",
+    "id": "39011273",
+    "doi": "https://doi.org/10.34133/hds.0159",
+    "title": "The Time-Varying Impact of COVID-19 on the Acute Kidney Disorders: A Historical Matched Cohort Study and Mendelian Randomization Analysis.",
+    "authorString": "Li C, Zhang C, Chen J, Chen Y, Ying Z, Hu Y, Song H, Fu P, Zeng X.",
     "authorAffiliations": "",
-    "journalTitle": "Discover mental health",
+    "journalTitle": "Health data science",
     "pubYear": "2024",
-    "date": "2024-04-17",
+    "date": "2024-07-15",
     "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Depression is a disorder with variable presentation. Selecting treatments and dose-finding is, therefore, challenging and time-consuming. In addition, novel antidepressants such as ketamine have sparse optimization evidence. Insights obtained from metabolomics may improve the management of patients. The objective of this study was to determine whether compounds in the cerebrospinal fluid (CSF) metabolome correlate with scores on questionnaires and response to medication. We performed a retrospective pilot study to evaluate phenotypic and metabolomic variability in patients with treatment-resistant depression using multivariate data compression algorithms. Twenty-nine patients with treatment-resistant depression provided fasting CSF samples. Over 300 metabolites were analyzed in these samples with liquid chromatography-mass spectrometry. Chart review provided basic demographic information, clinical status with self-reported questionnaires, and response to medication. Of the 300 metabolites analyzed, 151 were present in all CSF samples and used in the analyses. Hypothesis-free multivariate analysis compressed the resultant data set into two dimensions using Principal Component (PC) analysis, accounting for\u2009~\u200932% of the variance. PC1 accounted for 16.9% of the variance and strongly correlated with age in one direction and 5-methyltetrahydrofolate, homocarnosine, and depression and anxiety scores in the opposite direction. PC2 accounted for 15.4% of the variance, with one end strongly correlated with autism scores, male gender, and cognitive fatigue scores, and the other end with bipolar diagnosis, lithium use, and ethylmalonate disturbance. This small pilot study suggests that complex treatment-resistant depression can be mapped onto a 2-dimensional pathophysiological domain. The results may have implications for treatment selection for depression subtypes.",
+    "abstract": "<b>Background:</b> This study aimed to explore the time-varying impact of COVID-19 on acute kidney disorders, including acute kidney injury and other acute kidney diseases. <b>Methods:</b> From the UK Biobank, 10,121 participants with COVID-19 were matched with up to 3 historically unexposed controls by age, sex, Townsend deprivation index, and the status of hospitalization or receiving critical care. We investigated the association between COVID-19 and incidence of acute kidney disorders, within the first 4 weeks after infection, using conditional and time-varying Cox proportional hazard regression. In addition, one-sample Mendelian randomization, utilizing the polygenic risk score for COVID-19 as an instrumental variable, was conducted to explore the potential causality of the association. <b>Results:</b> In the matched cohort study, we observed a significant association between COVID-19 and acute kidney disorders predominantly within the first 3 weeks. The impact of COVID-19 was time dependent, peaking in the second week (hazard ratio, 12.77; 95% confidence interval, 5.93 to 27.70) and decreasing by the fourth week (hazard ratio, 2.28; 95% confidence interval, 0.75 to 6.93). In subgroup analyses, only moderate to severe COVID-19 cases were associated with acute worsening of renal function in a time-dependent pattern. One-sample Mendelian randomization analyses further showed that COVID-19 might exert a \"short-term\" causal effect on the risk of acute kidney disorders, primarily confined to the first week after infection. <b>Conclusions:</b> The risk of acute kidney disorders following COVID-19 demonstrates a time-varying pattern. Hazard effects were observed only in patients with moderate or severe but not mild COVID-19.",
     "laySummary": "",
-    "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s44192-024-00066-5.pdf; doi:https://doi.org/10.1007/s44192-024-00066-5; html:https://europepmc.org/articles/PMC11024073; pdf:https://europepmc.org/articles/PMC11024073?pdf=render"
+    "urls": "doi:https://doi.org/10.34133/hds.0159; doi:https://doi.org/10.34133/hds.0159; html:https://europepmc.org/articles/PMC11246837; pdf:https://europepmc.org/articles/PMC11246837?pdf=render"
   },
   {
     "id": "37794179",
@@ -1173,21 +1173,21 @@
     "urls": "pdf:https://www.nature.com/articles/s41416-023-02450-4.pdf; doi:https://doi.org/10.1038/s41416-023-02450-4; html:https://europepmc.org/articles/PMC10645731; pdf:https://europepmc.org/articles/PMC10645731?pdf=render"
   },
   {
-    "id": "39011273",
-    "doi": "https://doi.org/10.34133/hds.0159",
-    "title": "The Time-Varying Impact of COVID-19 on the Acute Kidney Disorders: A Historical Matched Cohort Study and Mendelian Randomization Analysis.",
-    "authorString": "Li C, Zhang C, Chen J, Chen Y, Ying Z, Hu Y, Song H, Fu P, Zeng X.",
+    "id": "38630417",
+    "doi": "https://doi.org/10.1007/s44192-024-00066-5",
+    "title": "Cerebrospinal fluid metabolomes of treatment-resistant depression subtypes and ketamine response: a pilot study.",
+    "authorString": "Berner J, Acharjee A.",
     "authorAffiliations": "",
-    "journalTitle": "Health data science",
+    "journalTitle": "Discover mental health",
     "pubYear": "2024",
-    "date": "2024-07-15",
+    "date": "2024-04-17",
     "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<b>Background:</b> This study aimed to explore the time-varying impact of COVID-19 on acute kidney disorders, including acute kidney injury and other acute kidney diseases. <b>Methods:</b> From the UK Biobank, 10,121 participants with COVID-19 were matched with up to 3 historically unexposed controls by age, sex, Townsend deprivation index, and the status of hospitalization or receiving critical care. We investigated the association between COVID-19 and incidence of acute kidney disorders, within the first 4 weeks after infection, using conditional and time-varying Cox proportional hazard regression. In addition, one-sample Mendelian randomization, utilizing the polygenic risk score for COVID-19 as an instrumental variable, was conducted to explore the potential causality of the association. <b>Results:</b> In the matched cohort study, we observed a significant association between COVID-19 and acute kidney disorders predominantly within the first 3 weeks. The impact of COVID-19 was time dependent, peaking in the second week (hazard ratio, 12.77; 95% confidence interval, 5.93 to 27.70) and decreasing by the fourth week (hazard ratio, 2.28; 95% confidence interval, 0.75 to 6.93). In subgroup analyses, only moderate to severe COVID-19 cases were associated with acute worsening of renal function in a time-dependent pattern. One-sample Mendelian randomization analyses further showed that COVID-19 might exert a \"short-term\" causal effect on the risk of acute kidney disorders, primarily confined to the first week after infection. <b>Conclusions:</b> The risk of acute kidney disorders following COVID-19 demonstrates a time-varying pattern. Hazard effects were observed only in patients with moderate or severe but not mild COVID-19.",
+    "abstract": "Depression is a disorder with variable presentation. Selecting treatments and dose-finding is, therefore, challenging and time-consuming. In addition, novel antidepressants such as ketamine have sparse optimization evidence. Insights obtained from metabolomics may improve the management of patients. The objective of this study was to determine whether compounds in the cerebrospinal fluid (CSF) metabolome correlate with scores on questionnaires and response to medication. We performed a retrospective pilot study to evaluate phenotypic and metabolomic variability in patients with treatment-resistant depression using multivariate data compression algorithms. Twenty-nine patients with treatment-resistant depression provided fasting CSF samples. Over 300 metabolites were analyzed in these samples with liquid chromatography-mass spectrometry. Chart review provided basic demographic information, clinical status with self-reported questionnaires, and response to medication. Of the 300 metabolites analyzed, 151 were present in all CSF samples and used in the analyses. Hypothesis-free multivariate analysis compressed the resultant data set into two dimensions using Principal Component (PC) analysis, accounting for\u2009~\u200932% of the variance. PC1 accounted for 16.9% of the variance and strongly correlated with age in one direction and 5-methyltetrahydrofolate, homocarnosine, and depression and anxiety scores in the opposite direction. PC2 accounted for 15.4% of the variance, with one end strongly correlated with autism scores, male gender, and cognitive fatigue scores, and the other end with bipolar diagnosis, lithium use, and ethylmalonate disturbance. This small pilot study suggests that complex treatment-resistant depression can be mapped onto a 2-dimensional pathophysiological domain. The results may have implications for treatment selection for depression subtypes.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.34133/hds.0159; doi:https://doi.org/10.34133/hds.0159; html:https://europepmc.org/articles/PMC11246837; pdf:https://europepmc.org/articles/PMC11246837?pdf=render"
+    "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s44192-024-00066-5.pdf; doi:https://doi.org/10.1007/s44192-024-00066-5; html:https://europepmc.org/articles/PMC11024073; pdf:https://europepmc.org/articles/PMC11024073?pdf=render"
   },
   {
     "id": "37562853",
@@ -1240,23 +1240,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.degruyter.com/document/doi/10.1515/dx-2023-0062/pdf; doi:https://doi.org/10.1515/dx-2023-0062"
   },
-  {
-    "id": "38345538",
-    "doi": "https://doi.org/10.1177/01410768231223584",
-    "title": "Risk of winter hospitalisation and death from acute respiratory infections in Scotland: national retrospective cohort study.",
-    "authorString": "Shi T, Millington T, Robertson C, Jeffrey K, Katikireddi SV, McCowan C, Simpson CR, Woolford L, Daines L, Kerr S, Swallow B, Fagbamigbe A, Vallejos CA, Weatherill D, Jayacodi S, Marsh K, McMenamin J, Rudan I, Ritchie LD, Mueller T, Kurdi A, Sheikh A, Public Health Scotland and the EAVE II Collaborators.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of the Royal Society of Medicine",
-    "pubYear": "2024",
-    "date": "2024-02-12",
-    "isOpenAccess": "N",
-    "keywords": "epidemiology; Respiratory Medicine; Health Informatics",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objectives</h4>We undertook a national analysis to characterise and identify risk factors for acute respiratory infections (ARIs) resulting in hospitalisation during the winter period in Scotland.<h4>Design</h4>A population-based retrospective cohort analysis.<h4>Setting</h4>Scotland.<h4>Participants</h4>The study involved 5.4 million residents in Scotland.<h4>Main outcome measures</h4>Cox proportional hazard models were used to estimate adjusted hazard ratios (aHRs) and 95% confidence intervals (CIs) for the association between risk factors and ARI hospitalisation.<h4>Results</h4>Between 1 September 2022 and 31 January 2023, there were 22,284 (10.9% of 203,549 with any emergency hospitalisation) ARI hospitalisations (1759 in children and 20,525 in adults) in Scotland. Compared with the reference group of children aged 6-17 years, the risk of ARI hospitalisation was higher in children aged 3-5 years (aHR\u2009=\u20094.55; 95% CI: 4.11-5.04). Compared with those aged 25-29 years, the risk of ARI hospitalisation was highest among the oldest adults aged \u226580 years (aHR\u2009=\u20097.86; 95% CI: 7.06-8.76). Adults from more deprived areas (most deprived vs. least deprived, aHR\u2009=\u20091.64; 95% CI: 1.57-1.72), with existing health conditions (\u22655 vs. 0 health conditions, aHR\u2009=\u20094.84; 95% CI: 4.53-5.18) or with history of all-cause emergency admissions (\u22656 vs. 0 previous emergency admissions, aHR\u2009=\u20097.53; 95% CI: 5.48-10.35) were at a higher risk of ARI hospitalisations. The risk increased by the number of existing health conditions and previous emergency admission. Similar associations were seen in children.<h4>Conclusions</h4>Younger children, older adults, those from more deprived backgrounds and individuals with greater numbers of pre-existing conditions and previous emergency admission were at increased risk for winter hospitalisations for ARI.",
-    "laySummary": "",
-    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/01410768231223584; doi:https://doi.org/10.1177/01410768231223584; html:https://europepmc.org/articles/PMC11450722; pdf:https://europepmc.org/articles/PMC11450722?pdf=render; doi:https://doi.org/10.1177/01410768231223584"
-  },
   {
     "id": "38296356",
     "doi": "https://doi.org/10.3399/bjgp.2023.0492",
@@ -1274,6 +1257,23 @@
     "laySummary": "",
     "urls": "pdf:https://bjgp.org/content/bjgp/early/2024/01/26/BJGP.2023.0492.full.pdf; doi:https://doi.org/10.3399/BJGP.2023.0492; html:https://europepmc.org/articles/PMC11466294; pdf:https://europepmc.org/articles/PMC11466294?pdf=render"
   },
+  {
+    "id": "38345538",
+    "doi": "https://doi.org/10.1177/01410768231223584",
+    "title": "Risk of winter hospitalisation and death from acute respiratory infections in Scotland: national retrospective cohort study.",
+    "authorString": "Shi T, Millington T, Robertson C, Jeffrey K, Katikireddi SV, McCowan C, Simpson CR, Woolford L, Daines L, Kerr S, Swallow B, Fagbamigbe A, Vallejos CA, Weatherill D, Jayacodi S, Marsh K, McMenamin J, Rudan I, Ritchie LD, Mueller T, Kurdi A, Sheikh A, Public Health Scotland and the EAVE II Collaborators.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of the Royal Society of Medicine",
+    "pubYear": "2024",
+    "date": "2024-02-12",
+    "isOpenAccess": "N",
+    "keywords": "epidemiology; Respiratory Medicine; Health Informatics",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objectives</h4>We undertook a national analysis to characterise and identify risk factors for acute respiratory infections (ARIs) resulting in hospitalisation during the winter period in Scotland.<h4>Design</h4>A population-based retrospective cohort analysis.<h4>Setting</h4>Scotland.<h4>Participants</h4>The study involved 5.4 million residents in Scotland.<h4>Main outcome measures</h4>Cox proportional hazard models were used to estimate adjusted hazard ratios (aHRs) and 95% confidence intervals (CIs) for the association between risk factors and ARI hospitalisation.<h4>Results</h4>Between 1 September 2022 and 31 January 2023, there were 22,284 (10.9% of 203,549 with any emergency hospitalisation) ARI hospitalisations (1759 in children and 20,525 in adults) in Scotland. Compared with the reference group of children aged 6-17 years, the risk of ARI hospitalisation was higher in children aged 3-5 years (aHR\u2009=\u20094.55; 95% CI: 4.11-5.04). Compared with those aged 25-29 years, the risk of ARI hospitalisation was highest among the oldest adults aged \u226580 years (aHR\u2009=\u20097.86; 95% CI: 7.06-8.76). Adults from more deprived areas (most deprived vs. least deprived, aHR\u2009=\u20091.64; 95% CI: 1.57-1.72), with existing health conditions (\u22655 vs. 0 health conditions, aHR\u2009=\u20094.84; 95% CI: 4.53-5.18) or with history of all-cause emergency admissions (\u22656 vs. 0 previous emergency admissions, aHR\u2009=\u20097.53; 95% CI: 5.48-10.35) were at a higher risk of ARI hospitalisations. The risk increased by the number of existing health conditions and previous emergency admission. Similar associations were seen in children.<h4>Conclusions</h4>Younger children, older adults, those from more deprived backgrounds and individuals with greater numbers of pre-existing conditions and previous emergency admission were at increased risk for winter hospitalisations for ARI.",
+    "laySummary": "",
+    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/01410768231223584; doi:https://doi.org/10.1177/01410768231223584; html:https://europepmc.org/articles/PMC11450722; pdf:https://europepmc.org/articles/PMC11450722?pdf=render; doi:https://doi.org/10.1177/01410768231223584"
+  },
   {
     "id": "36356998",
     "doi": "https://doi.org/10.1136/bmjopen-2022-063271",
@@ -1308,23 +1308,6 @@
     "laySummary": "",
     "urls": "pdf:https://diabetesjournals.org/care/article-pdf/46/8/1531/729620/dc230294.pdf; doi:https://doi.org/10.2337/dc23-0294; html:https://europepmc.org/articles/PMC10369123; pdf:https://europepmc.org/articles/PMC10369123?pdf=render"
   },
-  {
-    "id": "35273122",
-    "doi": "https://doi.org/10.1136/heartjnl-2021-320325",
-    "title": "Evaluation of antithrombotic use and COVID-19 outcomes in a nationwide atrial fibrillation cohort.",
-    "authorString": "Handy A, Banerjee A, Wood AM, Dale C, Sudlow CLM, Tomlinson C, Bean D, Thygesen JH, Mizani MA, Katsoulis M, Takhar R, Hollings S, Denaxas S, Walker V, Dobson R, Sofat R, CVD-COVID-UK Consortium.",
-    "authorAffiliations": "",
-    "journalTitle": "Heart (British Cardiac Society)",
-    "pubYear": "2022",
-    "date": "2022-05-25",
-    "isOpenAccess": "Y",
-    "keywords": "Atrial fibrillation; epidemiology; Electronic Health Records; drug monitoring; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objective</h4>To evaluate antithrombotic (AT) use in individuals with atrial fibrillation (AF) and at high risk of stroke (CHA<sub>2</sub>DS<sub>2</sub>-VASc score \u22652) and investigate whether pre-existing AT use may improve COVID-19 outcomes.<h4>Methods</h4>Individuals with AF and CHA<sub>2</sub>DS<sub>2</sub>-VASc score \u22652 on 1 January 2020 were identified using electronic health records for 56\u2009million people in England and were followed up until 1 May 2021. Factors associated with pre-existing AT use were analysed using logistic regression. Differences in COVID-19-related hospitalisation and death were analysed using logistic and Cox regression in individuals with pre-existing AT use versus no AT use, anticoagulants (AC) versus antiplatelets (AP), and direct oral anticoagulants (DOACs) versus warfarin.<h4>Results</h4>From 972\u2009971 individuals with AF (age 79 (\u00b19.3), female 46.2%) and CHA<sub>2</sub>DS<sub>2</sub>-VASc score \u22652, 88.0% (n=856\u2009336) had pre-existing AT use, 3.8% (n=37\u2009418) had a COVID-19 hospitalisation and 2.2% (n=21\u2009116) died, followed up to 1 May 2021. Factors associated with no AT use included comorbidities that may contraindicate AT use (liver disease and history of falls) and demographics (socioeconomic status and ethnicity). Pre-existing AT use was associated with lower odds of death (OR=0.92, 95% CI 0.87 to 0.96), but higher odds of hospitalisation (OR=1.20, 95% CI 1.15 to 1.26). AC versus AP was associated with lower odds of death (OR=0.93, 95% CI 0.87 to 0.98) and higher hospitalisation (OR=1.17, 95% CI 1.11 to 1.24). For DOACs versus warfarin, lower odds were observed for hospitalisation (OR=0.86, 95% CI 0.82 to 0.89) but not for death (OR=1.00, 95% CI 0.95 to 1.05).<h4>Conclusions</h4>Pre-existing AT use may be associated with lower odds of COVID-19 death and, while not evidence of causality, provides further incentive to improve AT coverage for eligible individuals with AF.",
-    "laySummary": "",
-    "urls": "pdf:https://heart.bmj.com/content/heartjnl/108/12/923.full.pdf; doi:https://doi.org/10.1136/heartjnl-2021-320325; html:https://europepmc.org/articles/PMC8931797; pdf:https://europepmc.org/articles/PMC8931797?pdf=render"
-  },
   {
     "id": "34345715",
     "doi": "https://doi.org/10.23889/ijpds.v5i4.1656",
@@ -1342,6 +1325,23 @@
     "laySummary": "",
     "urls": "pdf:https://ijpds.org/article/download/1656/3219; doi:https://doi.org/10.23889/ijpds.v5i4.1656; html:https://europepmc.org/articles/PMC8280712; pdf:https://europepmc.org/articles/PMC8280712?pdf=render"
   },
+  {
+    "id": "35273122",
+    "doi": "https://doi.org/10.1136/heartjnl-2021-320325",
+    "title": "Evaluation of antithrombotic use and COVID-19 outcomes in a nationwide atrial fibrillation cohort.",
+    "authorString": "Handy A, Banerjee A, Wood AM, Dale C, Sudlow CLM, Tomlinson C, Bean D, Thygesen JH, Mizani MA, Katsoulis M, Takhar R, Hollings S, Denaxas S, Walker V, Dobson R, Sofat R, CVD-COVID-UK Consortium.",
+    "authorAffiliations": "",
+    "journalTitle": "Heart (British Cardiac Society)",
+    "pubYear": "2022",
+    "date": "2022-05-25",
+    "isOpenAccess": "Y",
+    "keywords": "Atrial fibrillation; epidemiology; Electronic Health Records; drug monitoring; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>To evaluate antithrombotic (AT) use in individuals with atrial fibrillation (AF) and at high risk of stroke (CHA<sub>2</sub>DS<sub>2</sub>-VASc score \u22652) and investigate whether pre-existing AT use may improve COVID-19 outcomes.<h4>Methods</h4>Individuals with AF and CHA<sub>2</sub>DS<sub>2</sub>-VASc score \u22652 on 1 January 2020 were identified using electronic health records for 56\u2009million people in England and were followed up until 1 May 2021. Factors associated with pre-existing AT use were analysed using logistic regression. Differences in COVID-19-related hospitalisation and death were analysed using logistic and Cox regression in individuals with pre-existing AT use versus no AT use, anticoagulants (AC) versus antiplatelets (AP), and direct oral anticoagulants (DOACs) versus warfarin.<h4>Results</h4>From 972\u2009971 individuals with AF (age 79 (\u00b19.3), female 46.2%) and CHA<sub>2</sub>DS<sub>2</sub>-VASc score \u22652, 88.0% (n=856\u2009336) had pre-existing AT use, 3.8% (n=37\u2009418) had a COVID-19 hospitalisation and 2.2% (n=21\u2009116) died, followed up to 1 May 2021. Factors associated with no AT use included comorbidities that may contraindicate AT use (liver disease and history of falls) and demographics (socioeconomic status and ethnicity). Pre-existing AT use was associated with lower odds of death (OR=0.92, 95% CI 0.87 to 0.96), but higher odds of hospitalisation (OR=1.20, 95% CI 1.15 to 1.26). AC versus AP was associated with lower odds of death (OR=0.93, 95% CI 0.87 to 0.98) and higher hospitalisation (OR=1.17, 95% CI 1.11 to 1.24). For DOACs versus warfarin, lower odds were observed for hospitalisation (OR=0.86, 95% CI 0.82 to 0.89) but not for death (OR=1.00, 95% CI 0.95 to 1.05).<h4>Conclusions</h4>Pre-existing AT use may be associated with lower odds of COVID-19 death and, while not evidence of causality, provides further incentive to improve AT coverage for eligible individuals with AF.",
+    "laySummary": "",
+    "urls": "pdf:https://heart.bmj.com/content/heartjnl/108/12/923.full.pdf; doi:https://doi.org/10.1136/heartjnl-2021-320325; html:https://europepmc.org/articles/PMC8931797; pdf:https://europepmc.org/articles/PMC8931797?pdf=render"
+  },
   {
     "id": "38645891",
     "doi": "https://doi.org/10.1136/bmjmed-2023-000807",
@@ -1563,23 +1563,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1038/s43856-024-00625-5; doi:https://doi.org/10.1038/s43856-024-00625-5; html:https://europepmc.org/articles/PMC11461613; pdf:https://europepmc.org/articles/PMC11461613?pdf=render"
   },
-  {
-    "id": "33969335",
-    "doi": "https://doi.org/10.1016/j.lanepe.2021.100098",
-    "title": "Prevalence of antibody positivity to SARS-CoV-2 following the first peak of infection in England: Serial cross-sectional studies of 365,000 adults.",
-    "authorString": "Ward H, Cooke GS, Atchison C, Whitaker M, Elliott J, Moshe M, Brown JC, Flower B, Daunt A, Ainslie K, Ashby D, Donnelly CA, Riley S, Darzi A, Barclay W, Elliott P.",
-    "authorAffiliations": "",
-    "journalTitle": "The Lancet regional health. Europe",
-    "pubYear": "2021",
-    "date": "2021-05-02",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>The time-concentrated nature of the first wave of the COVID-19 epidemic in England in March and April 2020 provides a natural experiment to measure changes in antibody positivity at the population level before onset of the second wave and initiation of the vaccination programme.<h4>Methods</h4>Three cross-sectional national surveys with non-overlapping random samples of the population in England undertaken between late June and September 2020 (REACT-2 study). 365,104 adults completed questionnaires and self-administered lateral flow immunoassay (LFIA) tests for IgG against SARS-CoV-2.<h4>Findings</h4>Overall, 17,576 people had detectable antibodies, a prevalence of 4.9% (95% confidence intervals 4.9, 5.0) when adjusted for test characteristics and weighted to the adult population of England. The prevalence declined from 6.0% (5.8, 6.1), to 4.8% (4.7, 5.0) and 4.4% (4.3, 4.5), over the three rounds of the study a difference of -26.5% (-29.0, -23.8). The highest prevalence and smallest overall decline in positivity was in the youngest age group (18-24 years) at -14.9% (-21.6, -8.1), and lowest prevalence and largest decline in the oldest group (>74 years) at -39.0% (-50.8, -27.2). The decline from June to September 2020 was largest in those who did not report a history of COVID-19 at -64.0% (-75.6, -52.3), compared to -22.3% (-27.0, -17.7) in those with SARS-CoV-2 infection confirmed on PCR.<h4>Interpretation</h4>A large proportion of the population remained susceptible to SARS-CoV-2 infection in England based on naturally acquired immunity from the first wave. Widespread vaccination is needed to confer immunity and control the epidemic at population level.<h4>Funding</h4>This work was funded by the Department of Health and Social Care in England.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.lanepe.2021.100098; doi:https://doi.org/10.1016/j.lanepe.2021.100098; html:https://europepmc.org/articles/PMC8088780; pdf:https://europepmc.org/articles/PMC8088780?pdf=render"
-  },
   {
     "id": "36719907",
     "doi": "https://doi.org/10.1371/journal.pmed.1004086",
@@ -1597,6 +1580,23 @@
     "laySummary": "",
     "urls": "pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004086&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004086; html:https://europepmc.org/articles/PMC9928075; pdf:https://europepmc.org/articles/PMC9928075?pdf=render"
   },
+  {
+    "id": "33969335",
+    "doi": "https://doi.org/10.1016/j.lanepe.2021.100098",
+    "title": "Prevalence of antibody positivity to SARS-CoV-2 following the first peak of infection in England: Serial cross-sectional studies of 365,000 adults.",
+    "authorString": "Ward H, Cooke GS, Atchison C, Whitaker M, Elliott J, Moshe M, Brown JC, Flower B, Daunt A, Ainslie K, Ashby D, Donnelly CA, Riley S, Darzi A, Barclay W, Elliott P.",
+    "authorAffiliations": "",
+    "journalTitle": "The Lancet regional health. Europe",
+    "pubYear": "2021",
+    "date": "2021-05-02",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>The time-concentrated nature of the first wave of the COVID-19 epidemic in England in March and April 2020 provides a natural experiment to measure changes in antibody positivity at the population level before onset of the second wave and initiation of the vaccination programme.<h4>Methods</h4>Three cross-sectional national surveys with non-overlapping random samples of the population in England undertaken between late June and September 2020 (REACT-2 study). 365,104 adults completed questionnaires and self-administered lateral flow immunoassay (LFIA) tests for IgG against SARS-CoV-2.<h4>Findings</h4>Overall, 17,576 people had detectable antibodies, a prevalence of 4.9% (95% confidence intervals 4.9, 5.0) when adjusted for test characteristics and weighted to the adult population of England. The prevalence declined from 6.0% (5.8, 6.1), to 4.8% (4.7, 5.0) and 4.4% (4.3, 4.5), over the three rounds of the study a difference of -26.5% (-29.0, -23.8). The highest prevalence and smallest overall decline in positivity was in the youngest age group (18-24 years) at -14.9% (-21.6, -8.1), and lowest prevalence and largest decline in the oldest group (>74 years) at -39.0% (-50.8, -27.2). The decline from June to September 2020 was largest in those who did not report a history of COVID-19 at -64.0% (-75.6, -52.3), compared to -22.3% (-27.0, -17.7) in those with SARS-CoV-2 infection confirmed on PCR.<h4>Interpretation</h4>A large proportion of the population remained susceptible to SARS-CoV-2 infection in England based on naturally acquired immunity from the first wave. Widespread vaccination is needed to confer immunity and control the epidemic at population level.<h4>Funding</h4>This work was funded by the Department of Health and Social Care in England.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.lanepe.2021.100098; doi:https://doi.org/10.1016/j.lanepe.2021.100098; html:https://europepmc.org/articles/PMC8088780; pdf:https://europepmc.org/articles/PMC8088780?pdf=render"
+  },
   {
     "id": "32873607",
     "doi": "https://doi.org/10.1136/bmjresp-2020-000644",
@@ -1614,23 +1614,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopenrespres.bmj.com/content/bmjresp/7/1/e000644.full.pdf; doi:https://doi.org/10.1136/bmjresp-2020-000644; html:https://europepmc.org/articles/PMC7467523; pdf:https://europepmc.org/articles/PMC7467523?pdf=render"
   },
-  {
-    "id": "37699667",
-    "doi": "https://doi.org/10.1136/jech-2023-220801",
-    "title": "Predictive value of metabolic profiling in cardiovascular risk scores: analysis of 75 000 adults in UK Biobank.",
-    "authorString": "Jin D, Trichia E, Islam N, Lewington S, Lacey B.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of epidemiology and community health",
-    "pubYear": "2023",
-    "date": "2023-09-12",
-    "isOpenAccess": "Y",
-    "keywords": "Cardiovascular diseases; epidemiology; Primary Health Care",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Metabolic profiling (the extensive measurement of circulating metabolites across multiple biological pathways) is increasingly employed in clinical care. However, there is little evidence on the benefit of metabolic profiling as compared with established atherosclerotic cardiovascular disease (CVD) risk scores.<h4>Methods</h4>UK Biobank is a prospective study of 0.5\u2009million participants, aged 40-69 at recruitment. Analyses were restricted to 74\u2009780 participants with metabolic profiling (measured using nuclear magnetic resonance) and without CVD at baseline. Cox regression was used to compare model performance before and after addition of metabolites to QRISK3 (an established CVD risk score used in primary care in England); analyses derived three models, with metabolites selected by association significance or by employing two different machine learning approaches.<h4>Results</h4>We identified 5097 incident CVD events within the 10-year follow-up. Harrell's C-index of QRISK3 was 0.750 (95% CI 0.739 to 0.763) for women and 0.706 (95% CI 0.696 to 0.716) for men. Adding selected metabolites did not significantly improve measures of discrimination in women (Harrell's C-index of three models are 0.759 (0.747 to 0.772), 0.759 (0.746 to 0.770) and 0.759 (0.748 to 0.771), respectively) or men (0.710 (0.701 to 0.720), 0.710 (0.700 to 0.719) and 0.710 (0.701 to 0.719), respectively), and neither did it improve reclassification or calibration.<h4>Conclusion</h4>This large-scale study applied both conventional and machine learning approaches to assess the potential benefit of metabolic profiling to well-established CVD risk scores. However, there was no evidence that metabolic profiling improved CVD risk prediction in this population.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1136/jech-2023-220801; html:https://europepmc.org/articles/PMC11418003; pdf:https://europepmc.org/articles/PMC11418003?pdf=render"
-  },
   {
     "id": "34127076",
     "doi": "https://doi.org/10.1186/s40900-021-00281-2",
@@ -1648,6 +1631,23 @@
     "laySummary": "",
     "urls": "pdf:https://researchinvolvement.biomedcentral.com/track/pdf/10.1186/s40900-021-00281-2; doi:https://doi.org/10.1186/s40900-021-00281-2; html:https://europepmc.org/articles/PMC8201435; pdf:https://europepmc.org/articles/PMC8201435?pdf=render"
   },
+  {
+    "id": "37699667",
+    "doi": "https://doi.org/10.1136/jech-2023-220801",
+    "title": "Predictive value of metabolic profiling in cardiovascular risk scores: analysis of 75 000 adults in UK Biobank.",
+    "authorString": "Jin D, Trichia E, Islam N, Lewington S, Lacey B.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of epidemiology and community health",
+    "pubYear": "2023",
+    "date": "2023-09-12",
+    "isOpenAccess": "Y",
+    "keywords": "Cardiovascular diseases; epidemiology; Primary Health Care",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Metabolic profiling (the extensive measurement of circulating metabolites across multiple biological pathways) is increasingly employed in clinical care. However, there is little evidence on the benefit of metabolic profiling as compared with established atherosclerotic cardiovascular disease (CVD) risk scores.<h4>Methods</h4>UK Biobank is a prospective study of 0.5\u2009million participants, aged 40-69 at recruitment. Analyses were restricted to 74\u2009780 participants with metabolic profiling (measured using nuclear magnetic resonance) and without CVD at baseline. Cox regression was used to compare model performance before and after addition of metabolites to QRISK3 (an established CVD risk score used in primary care in England); analyses derived three models, with metabolites selected by association significance or by employing two different machine learning approaches.<h4>Results</h4>We identified 5097 incident CVD events within the 10-year follow-up. Harrell's C-index of QRISK3 was 0.750 (95% CI 0.739 to 0.763) for women and 0.706 (95% CI 0.696 to 0.716) for men. Adding selected metabolites did not significantly improve measures of discrimination in women (Harrell's C-index of three models are 0.759 (0.747 to 0.772), 0.759 (0.746 to 0.770) and 0.759 (0.748 to 0.771), respectively) or men (0.710 (0.701 to 0.720), 0.710 (0.700 to 0.719) and 0.710 (0.701 to 0.719), respectively), and neither did it improve reclassification or calibration.<h4>Conclusion</h4>This large-scale study applied both conventional and machine learning approaches to assess the potential benefit of metabolic profiling to well-established CVD risk scores. However, there was no evidence that metabolic profiling improved CVD risk prediction in this population.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1136/jech-2023-220801; html:https://europepmc.org/articles/PMC11418003; pdf:https://europepmc.org/articles/PMC11418003?pdf=render"
+  },
   {
     "id": "38693557",
     "doi": "https://doi.org/10.1186/s12913-024-10931-2",
@@ -1699,6 +1699,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.gastha.2024.03.005; html:https://europepmc.org/articles/PMC11330930; pdf:https://europepmc.org/articles/PMC11330930?pdf=render"
   },
+  {
+    "id": "38251486",
+    "doi": "https://doi.org/10.1016/s2665-9913(23)00206-0",
+    "title": "Gout incidence and management during the COVID-19 pandemic in England, UK: a nationwide observational study using OpenSAFELY.",
+    "authorString": "Russell MD, Massey J, Roddy E, MacKenna B, Bacon S, Goldacre B, Andrews CD, Hickman G, Mehrkar A, Mahto A, Rutherford AI, Patel S, Adas MA, Alveyn E, Nagra D, Bechman K, Ledingham JM, Hudson J, Norton S, Cope AP, Galloway JB.",
+    "authorAffiliations": "",
+    "journalTitle": "The Lancet. Rheumatology",
+    "pubYear": "2023",
+    "date": "2023-08-31",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Gout is the most prevalent inflammatory arthritis, yet one of the worst managed. Our objective was to assess how the COVID-19 pandemic impacted incidence and quality of care for people with gout in England, UK.<h4>Methods</h4>With the approval of National Health Service England, we did a population-level cohort study using primary care and hospital electronic health record data for 17\u00b79 million adults registered with general practices using TPP health record software, via the OpenSAFELY platform. The study period was from March 1, 2015, to Feb 28, 2023. Individuals aged 18-110 years were defined as having incident gout if they were assigned index diagnostic codes for gout, were registered with TPP practices in England for at least 12 months before diagnosis, did not receive prescriptions for urate-lowering therapy more than 30 days before diagnosis, and had not been admitted to hospital or attended an emergency department for gout flares more than 30 days before diagnosis. Outcomes assessed were incidence and prevalence of people with recorded gout diagnoses, incidence of gout hospitalisations, initiation of urate-lowering therapy, and attainment of serum urate targets (\u2264360 \u03bcmol/L).<h4>Findings</h4>From a reference population of 17\u2008865\u2008145 adults, 246\u2008695 individuals were diagnosed with incident gout. The mean age of individuals with incident gout was 61\u00b73 years (SD 16\u00b72). 66\u2008265 (26\u00b79%) of 246\u2008695 individuals were female, 180\u2008430 (73\u00b71%) were male, and 189\u2008035 (90\u00b79%) of 208\u2008050 individuals with available ethnicity data were White. Incident gout diagnoses decreased by 30\u00b79% in the year beginning March, 2020, compared with the preceding year (1\u00b723 diagnoses vs 1\u00b778 diagnoses per 1000 adults). Gout prevalence was 3\u00b707% in 2015-16, and 3\u00b721% in 2022-23. Gout hospitalisations decreased by 30\u00b71% in the year commencing March, 2020, compared with the preceding year (9\u00b76 admissions vs 13\u00b77 admissions per 100\u2008000 adults). Of 228\u2008095 people with incident gout and available follow-up, 66\u2008560 (29\u00b72%) were prescribed urate-lowering therapy within 6 months. Of 65\u2008305 individuals who initiated urate-lowering therapy with available follow-up, 16\u2008790 (25\u00b77%) attained a serum urate concentration of 360 \u03bcmol/L or less within 6 months of urate-lowering therapy initiation. In interrupted time-series analyses, urate-lowering therapy prescribing improved modestly during the pandemic, compared with pre-pandemic, whereas urate target attainment was similar.<h4>Interpretation</h4>Using gout as an exemplar disease, we showed the complexity of how health care was impacted during the COVID-19 pandemic. We observed a reduction in gout diagnoses but no effect on treatment metrics. We showed how country-wide, routinely collected data can be used to map disease epidemiology and monitor care quality.<h4>Funding</h4>None.",
+    "laySummary": "",
+    "urls": "pdf:http://www.thelancet.com/article/S2665991323002060/pdf; doi:https://doi.org/10.1016/S2665-9913(23)00206-0; html:https://europepmc.org/articles/PMC7616140; pdf:https://europepmc.org/articles/PMC7616140?pdf=render"
+  },
   {
     "id": "39047204",
     "doi": "https://doi.org/10.1212/wnl.0000000000209659",
@@ -1716,23 +1733,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1212/WNL.0000000000209659; html:https://europepmc.org/articles/PMC11314951; pdf:https://europepmc.org/articles/PMC11314951?pdf=render"
   },
-  {
-    "id": "36901540",
-    "doi": "https://doi.org/10.3390/ijerph20054534",
-    "title": "Socioeconomic Background and Self-Reported Sleep Quality in Older Adults during the COVID-19 Pandemic: An Analysis of the English Longitudinal Study of Ageing (ELSA).",
-    "authorString": "Collinge AN, Bath PA, Bath PA.",
-    "authorAffiliations": "",
-    "journalTitle": "International journal of environmental research and public health",
-    "pubYear": "2023",
-    "date": "2023-03-03",
-    "isOpenAccess": "Y",
-    "keywords": "Mental health; Health Promotion; Wellness; Physical Health; Health Disparities; Health Behaviors; Older Adults; Sleep Quality; Socioeconomic Background; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The COVID-19 pandemic negatively impacted sleep quality. However, research regarding older adults' sleep quality during the pandemic has been limited. This study examined the association between socioeconomic background (SEB) and older adults' sleep quality during the COVID-19 pandemic. Data on 7040 adults aged \u226550 were acquired from a COVID-19 sub-study of the English Longitudinal Study of Ageing (ELSA). SEB was operationalized using educational attainment, previous financial situation, and concern about the future financial situation. Sociodemographic, mental health, physical health, and health behavior variables were included as covariates. Chi-squared tests and binary logistic regression were used to examine associations between SEB and sleep quality. Lower educational attainment and greater financial hardship and concerns were associated with poor sleep quality. The relationship between educational attainment and sleep quality was explained by the financial variables, while the relationship between previous financial difficulties and sleep quality was explained by physical health and health behavior variables. Greater financial concerns about the future, poor mental health, and poor physical health were independent risk factors for poor sleep quality in older adults during the pandemic. Healthcare professionals and service providers should consider these issues when supporting older patients with sleep problems and in promoting health and wellness.",
-    "laySummary": "",
-    "urls": "pdf:https://www.mdpi.com/1660-4601/20/5/4534/pdf?version=1677842613; doi:https://doi.org/10.3390/ijerph20054534; html:https://europepmc.org/articles/PMC10001974; pdf:https://europepmc.org/articles/PMC10001974?pdf=render"
-  },
   {
     "id": "36503414",
     "doi": "https://doi.org/10.1186/s12879-022-07856-8",
@@ -1751,21 +1751,21 @@
     "urls": "pdf:https://bmcinfectdis.biomedcentral.com/counter/pdf/10.1186/s12879-022-07856-8; doi:https://doi.org/10.1186/s12879-022-07856-8; html:https://europepmc.org/articles/PMC9742024; pdf:https://europepmc.org/articles/PMC9742024?pdf=render"
   },
   {
-    "id": "38251486",
-    "doi": "https://doi.org/10.1016/s2665-9913(23)00206-0",
-    "title": "Gout incidence and management during the COVID-19 pandemic in England, UK: a nationwide observational study using OpenSAFELY.",
-    "authorString": "Russell MD, Massey J, Roddy E, MacKenna B, Bacon S, Goldacre B, Andrews CD, Hickman G, Mehrkar A, Mahto A, Rutherford AI, Patel S, Adas MA, Alveyn E, Nagra D, Bechman K, Ledingham JM, Hudson J, Norton S, Cope AP, Galloway JB.",
+    "id": "36901540",
+    "doi": "https://doi.org/10.3390/ijerph20054534",
+    "title": "Socioeconomic Background and Self-Reported Sleep Quality in Older Adults during the COVID-19 Pandemic: An Analysis of the English Longitudinal Study of Ageing (ELSA).",
+    "authorString": "Collinge AN, Bath PA, Bath PA.",
     "authorAffiliations": "",
-    "journalTitle": "The Lancet. Rheumatology",
+    "journalTitle": "International journal of environmental research and public health",
     "pubYear": "2023",
-    "date": "2023-08-31",
+    "date": "2023-03-03",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Mental health; Health Promotion; Wellness; Physical Health; Health Disparities; Health Behaviors; Older Adults; Sleep Quality; Socioeconomic Background; Covid-19",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Gout is the most prevalent inflammatory arthritis, yet one of the worst managed. Our objective was to assess how the COVID-19 pandemic impacted incidence and quality of care for people with gout in England, UK.<h4>Methods</h4>With the approval of National Health Service England, we did a population-level cohort study using primary care and hospital electronic health record data for 17\u00b79 million adults registered with general practices using TPP health record software, via the OpenSAFELY platform. The study period was from March 1, 2015, to Feb 28, 2023. Individuals aged 18-110 years were defined as having incident gout if they were assigned index diagnostic codes for gout, were registered with TPP practices in England for at least 12 months before diagnosis, did not receive prescriptions for urate-lowering therapy more than 30 days before diagnosis, and had not been admitted to hospital or attended an emergency department for gout flares more than 30 days before diagnosis. Outcomes assessed were incidence and prevalence of people with recorded gout diagnoses, incidence of gout hospitalisations, initiation of urate-lowering therapy, and attainment of serum urate targets (\u2264360 \u03bcmol/L).<h4>Findings</h4>From a reference population of 17\u2008865\u2008145 adults, 246\u2008695 individuals were diagnosed with incident gout. The mean age of individuals with incident gout was 61\u00b73 years (SD 16\u00b72). 66\u2008265 (26\u00b79%) of 246\u2008695 individuals were female, 180\u2008430 (73\u00b71%) were male, and 189\u2008035 (90\u00b79%) of 208\u2008050 individuals with available ethnicity data were White. Incident gout diagnoses decreased by 30\u00b79% in the year beginning March, 2020, compared with the preceding year (1\u00b723 diagnoses vs 1\u00b778 diagnoses per 1000 adults). Gout prevalence was 3\u00b707% in 2015-16, and 3\u00b721% in 2022-23. Gout hospitalisations decreased by 30\u00b71% in the year commencing March, 2020, compared with the preceding year (9\u00b76 admissions vs 13\u00b77 admissions per 100\u2008000 adults). Of 228\u2008095 people with incident gout and available follow-up, 66\u2008560 (29\u00b72%) were prescribed urate-lowering therapy within 6 months. Of 65\u2008305 individuals who initiated urate-lowering therapy with available follow-up, 16\u2008790 (25\u00b77%) attained a serum urate concentration of 360 \u03bcmol/L or less within 6 months of urate-lowering therapy initiation. In interrupted time-series analyses, urate-lowering therapy prescribing improved modestly during the pandemic, compared with pre-pandemic, whereas urate target attainment was similar.<h4>Interpretation</h4>Using gout as an exemplar disease, we showed the complexity of how health care was impacted during the COVID-19 pandemic. We observed a reduction in gout diagnoses but no effect on treatment metrics. We showed how country-wide, routinely collected data can be used to map disease epidemiology and monitor care quality.<h4>Funding</h4>None.",
+    "abstract": "The COVID-19 pandemic negatively impacted sleep quality. However, research regarding older adults' sleep quality during the pandemic has been limited. This study examined the association between socioeconomic background (SEB) and older adults' sleep quality during the COVID-19 pandemic. Data on 7040 adults aged \u226550 were acquired from a COVID-19 sub-study of the English Longitudinal Study of Ageing (ELSA). SEB was operationalized using educational attainment, previous financial situation, and concern about the future financial situation. Sociodemographic, mental health, physical health, and health behavior variables were included as covariates. Chi-squared tests and binary logistic regression were used to examine associations between SEB and sleep quality. Lower educational attainment and greater financial hardship and concerns were associated with poor sleep quality. The relationship between educational attainment and sleep quality was explained by the financial variables, while the relationship between previous financial difficulties and sleep quality was explained by physical health and health behavior variables. Greater financial concerns about the future, poor mental health, and poor physical health were independent risk factors for poor sleep quality in older adults during the pandemic. Healthcare professionals and service providers should consider these issues when supporting older patients with sleep problems and in promoting health and wellness.",
     "laySummary": "",
-    "urls": "pdf:http://www.thelancet.com/article/S2665991323002060/pdf; doi:https://doi.org/10.1016/S2665-9913(23)00206-0; html:https://europepmc.org/articles/PMC7616140; pdf:https://europepmc.org/articles/PMC7616140?pdf=render"
+    "urls": "pdf:https://www.mdpi.com/1660-4601/20/5/4534/pdf?version=1677842613; doi:https://doi.org/10.3390/ijerph20054534; html:https://europepmc.org/articles/PMC10001974; pdf:https://europepmc.org/articles/PMC10001974?pdf=render"
   },
   {
     "id": "37935988",
@@ -1971,6 +1971,23 @@
     "laySummary": "",
     "urls": "pdf:https://mentalhealth.bmj.com/content/ebmental/26/1/e300775.full.pdf; doi:https://doi.org/10.1136/bmjment-2023-300775; html:https://europepmc.org/articles/PMC11146375; pdf:https://europepmc.org/articles/PMC11146375?pdf=render"
   },
+  {
+    "id": "39277617",
+    "doi": "https://doi.org/10.1038/s41467-024-52452-w",
+    "title": "Evaluating the cost-effectiveness of polygenic risk score-stratified screening for abdominal aortic aneurysm.",
+    "authorString": "Kelemen M, Danesh J, Di Angelantonio E, Inouye M, O'Sullivan J, Pennells L, Roychowdhury T, Sweeting MJ, Wood AM, Harrison S, Kim LG.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature communications",
+    "pubYear": "2024",
+    "date": "2024-09-14",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "As the heritability of abdominal aortic aneurysm (AAA) is high and AAA partially shares genetic architecture with other cardiovascular diseases, genetic information could help inform AAA screening strategies. Exploiting pleiotropy and meta-analysing summary data from large studies, we construct a polygenic risk score (PRS) for AAA. Leveraging related traits improves PRS performance (R<sup>2</sup>) by 22.7%, relative to using AAA alone. Compared with the low PRS tertile, intermediate and high tertiles have hazard ratios for AAA of 2.13 (95%CI 1.61, 2.82) and 3.70 (95%CI 2.86, 4.80) respectively, adjusted for clinical risk factors. Using simulation modelling, we compare PRS- and smoking-stratified screening with inviting men at age 65 and not inviting women (current UK strategy). In a futuristic scenario where genomic information is available, our modelling suggests inviting male current smokers with high PRS earlier than 65 and screening female smokers with high/intermediate PRS at 65 and 70 respectively, may improve cost-effectiveness.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1038/s41467-024-52452-w; html:https://europepmc.org/articles/PMC11401842; pdf:https://europepmc.org/articles/PMC11401842?pdf=render"
+  },
   {
     "id": "33993870",
     "doi": "https://doi.org/10.1186/s12916-021-02000-w",
@@ -2005,40 +2022,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-024-02487-2; doi:https://doi.org/10.1186/s12911-024-02487-2; html:https://europepmc.org/articles/PMC10979623; pdf:https://europepmc.org/articles/PMC10979623?pdf=render"
   },
-  {
-    "id": "39015764",
-    "doi": "https://doi.org/10.1093/braincomms/fcae220",
-    "title": "Head motion in the UK Biobank imaging subsample: longitudinal stability, associations with psychological and physical health, and risk of incomplete data.",
-    "authorString": "Ward J, Cox SR, Quinn T, Lyall LM, Strawbridge RJ, Russell E, Pell JP, Stewart W, Cullen B, Whalley H, Lyall DM.",
-    "authorAffiliations": "",
-    "journalTitle": "Brain communications",
-    "pubYear": "2024",
-    "date": "2024-07-02",
-    "isOpenAccess": "Y",
-    "keywords": "Motion; Imaging; Bias; epidemiology; Uk Biobank",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Participant motion in brain magnetic resonance imaging is associated with processing problems including potentially non-useable/incomplete data. This has implications for representativeness in research. Few large studies have investigated predictors of increased motion in the first instance. We exploratively tested for association between multiple psychological and physical health traits with concurrent motion during T<sub>1</sub> structural, diffusion, average resting-state and task functional magnetic resonance imaging in <i>N</i> = 52 951 UK Biobank imaging subsample participants. These traits included history of cardiometabolic, inflammatory, neurological and psychiatric conditions, as well as concurrent cognitive test scores and anthropometric traits. We tested for stability in motion in participants with longitudinal imaging data (<i>n</i> = 5305, average 2.64 years later). All functional and T<sub>1</sub> structural motion variables were significantly intercorrelated (Pearson <i>r</i> range 0.3-0.8, all <i>P</i> < 0.001). Diffusion motion variables showed weaker correlations around <i>r</i> = 0.1. Most physical and psychological phenotypes showed significant association with at least one measure of increased motion including specifically in participants with complete useable data (highest \u03b2 = 0.66 for diabetes versus resting-state functional magnetic resonance imaging motion). Poorer values in most health traits predicted lower odds of complete imaging data, with the largest association for history of traumatic brain injury (odds ratio = 0.720, 95% confidence interval = 0.562 to 0.923, <i>P</i> = 0.009). Worse psychological and physical health are consistent predictors of increased average functional and structural motion during brain imaging and associated with lower odds of complete data. Average motion levels were largely consistent across modalities and longitudinally in participants with repeat data. Together, these findings have implications for representativeness and bias in imaging studies of generally healthy population samples.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1093/braincomms/fcae220; html:https://europepmc.org/articles/PMC11249925; pdf:https://europepmc.org/articles/PMC11249925?pdf=render"
-  },
-  {
-    "id": "39277617",
-    "doi": "https://doi.org/10.1038/s41467-024-52452-w",
-    "title": "Evaluating the cost-effectiveness of polygenic risk score-stratified screening for abdominal aortic aneurysm.",
-    "authorString": "Kelemen M, Danesh J, Di Angelantonio E, Inouye M, O'Sullivan J, Pennells L, Roychowdhury T, Sweeting MJ, Wood AM, Harrison S, Kim LG.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature communications",
-    "pubYear": "2024",
-    "date": "2024-09-14",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "As the heritability of abdominal aortic aneurysm (AAA) is high and AAA partially shares genetic architecture with other cardiovascular diseases, genetic information could help inform AAA screening strategies. Exploiting pleiotropy and meta-analysing summary data from large studies, we construct a polygenic risk score (PRS) for AAA. Leveraging related traits improves PRS performance (R<sup>2</sup>) by 22.7%, relative to using AAA alone. Compared with the low PRS tertile, intermediate and high tertiles have hazard ratios for AAA of 2.13 (95%CI 1.61, 2.82) and 3.70 (95%CI 2.86, 4.80) respectively, adjusted for clinical risk factors. Using simulation modelling, we compare PRS- and smoking-stratified screening with inviting men at age 65 and not inviting women (current UK strategy). In a futuristic scenario where genomic information is available, our modelling suggests inviting male current smokers with high PRS earlier than 65 and screening female smokers with high/intermediate PRS at 65 and 70 respectively, may improve cost-effectiveness.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1038/s41467-024-52452-w; html:https://europepmc.org/articles/PMC11401842; pdf:https://europepmc.org/articles/PMC11401842?pdf=render"
-  },
   {
     "id": "37697235",
     "doi": "https://doi.org/10.1186/s12879-023-08555-8",
@@ -2056,6 +2039,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmcinfectdis.biomedcentral.com/counter/pdf/10.1186/s12879-023-08555-8; doi:https://doi.org/10.1186/s12879-023-08555-8; html:https://europepmc.org/articles/PMC10496238; pdf:https://europepmc.org/articles/PMC10496238?pdf=render"
   },
+  {
+    "id": "39015764",
+    "doi": "https://doi.org/10.1093/braincomms/fcae220",
+    "title": "Head motion in the UK Biobank imaging subsample: longitudinal stability, associations with psychological and physical health, and risk of incomplete data.",
+    "authorString": "Ward J, Cox SR, Quinn T, Lyall LM, Strawbridge RJ, Russell E, Pell JP, Stewart W, Cullen B, Whalley H, Lyall DM.",
+    "authorAffiliations": "",
+    "journalTitle": "Brain communications",
+    "pubYear": "2024",
+    "date": "2024-07-02",
+    "isOpenAccess": "Y",
+    "keywords": "Motion; Imaging; Bias; epidemiology; Uk Biobank",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Participant motion in brain magnetic resonance imaging is associated with processing problems including potentially non-useable/incomplete data. This has implications for representativeness in research. Few large studies have investigated predictors of increased motion in the first instance. We exploratively tested for association between multiple psychological and physical health traits with concurrent motion during T<sub>1</sub> structural, diffusion, average resting-state and task functional magnetic resonance imaging in <i>N</i> = 52 951 UK Biobank imaging subsample participants. These traits included history of cardiometabolic, inflammatory, neurological and psychiatric conditions, as well as concurrent cognitive test scores and anthropometric traits. We tested for stability in motion in participants with longitudinal imaging data (<i>n</i> = 5305, average 2.64 years later). All functional and T<sub>1</sub> structural motion variables were significantly intercorrelated (Pearson <i>r</i> range 0.3-0.8, all <i>P</i> < 0.001). Diffusion motion variables showed weaker correlations around <i>r</i> = 0.1. Most physical and psychological phenotypes showed significant association with at least one measure of increased motion including specifically in participants with complete useable data (highest \u03b2 = 0.66 for diabetes versus resting-state functional magnetic resonance imaging motion). Poorer values in most health traits predicted lower odds of complete imaging data, with the largest association for history of traumatic brain injury (odds ratio = 0.720, 95% confidence interval = 0.562 to 0.923, <i>P</i> = 0.009). Worse psychological and physical health are consistent predictors of increased average functional and structural motion during brain imaging and associated with lower odds of complete data. Average motion levels were largely consistent across modalities and longitudinally in participants with repeat data. Together, these findings have implications for representativeness and bias in imaging studies of generally healthy population samples.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1093/braincomms/fcae220; html:https://europepmc.org/articles/PMC11249925; pdf:https://europepmc.org/articles/PMC11249925?pdf=render"
+  },
   {
     "id": "38112489",
     "doi": "https://doi.org/10.1097/hep.0000000000000707",
@@ -2550,38 +2550,38 @@
     "urls": "pdf:https://emj.bmj.com/content/emermed/early/2022/04/27/emermed-2021-211706.full.pdf; doi:https://doi.org/10.1136/emermed-2021-211706; html:https://europepmc.org/articles/PMC9510399; pdf:https://europepmc.org/articles/PMC9510399?pdf=render"
   },
   {
-    "id": "35501391",
-    "doi": "https://doi.org/10.1038/s41416-022-01830-6",
-    "title": "Impact of the SARS-CoV-2 pandemic on female breast, colorectal and non-small\u00a0cell lung cancer incidence, stage and healthcare pathway to diagnosis during 2020 in Wales, UK, using a national cancer clinical record system.",
-    "authorString": "Greene G, Griffiths R, Han J, Akbari A, Jones M, Lyons J, Lyons RA, Rolles M, Torabi F, Warlow J, Morris ERA, Lawler M, Huws DW.",
+    "id": "35609019",
+    "doi": "https://doi.org/10.1371/journal.pone.0267176",
+    "title": "Population birth outcomes in 2020 and experiences of expectant mothers during the COVID-19 pandemic: A 'born in Wales' mixed methods study using routine data.",
+    "authorString": "Jones H, Seaborne M, Cowley L, Odd D, Paranjothy S, Akbari A, Brophy S.",
     "authorAffiliations": "",
-    "journalTitle": "British journal of cancer",
+    "journalTitle": "PloS one",
     "pubYear": "2022",
-    "date": "2022-05-02",
+    "date": "2022-05-24",
     "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>COVID-19 pandemic responses impacted behaviour and health services. We estimated the impact on incidence, stage and healthcare pathway to diagnosis for female breast, colorectal and non-small\u00a0cell lung cancers at population level in Wales.<h4>Methods</h4>Cancer e-record and hospital admission data linkage identified adult cases, stage and healthcare pathway to diagnosis (population ~2.5 million). Using multivariate Poisson regressions, we compared 2019 and 2020 counts and estimated incidence rate ratios (IRR).<h4>Results</h4>Cases decreased 15.2% (n\u2009=\u2009-1011) overall. Female breast annual IRR was 0.81 (95% CI: 0.76-0.86, p\u2009<\u20090.001), colorectal 0.80 (95% CI: 0.79-0.81, p\u2009<\u20090.001) and non-small\u00a0cell lung 0.91 (95% CI: 0.90-0.92, p\u2009<\u20090.001). Decreases were largest in 50-69 year olds for female breast and 80+ year olds for all cancers. Stage I female breast cancer declined 41.6%, but unknown stage increased 55.8%. Colorectal stages I-IV declined (range 26.6-29.9%), while unknown stage increased 803.6%. Colorectal Q2-2020 GP-urgent suspected cancer diagnoses decreased 50.0%, and 53.9% for non-small\u00a0cell lung cancer. Annual screen-detected female breast and colorectal cancers fell 47.8% and 13.3%, respectively. Non-smal\u00a0-cell lung cancer emergency presentation diagnoses increased 9.5% (Q2-2020) and 16.3% (Q3-2020).<h4>Conclusion</h4>Significantly fewer cases of three common cancers were diagnosed in 2020. Detrimental impacts on outcomes varied between cancers. Ongoing surveillance with health service optimisation will be needed to mitigate impacts.",
+    "abstract": "<h4>Background</h4>Pregnancy can be a stressful time and the COVID-19 pandemic has affected all aspects of life. This study aims to investigate the pandemic impact on pregnancy experience, rates of primary childhood immunisations and the differences in birth outcomes in during 2020 to those of previous years.<h4>Methods</h4>Self-reported pregnancy experience: 215 expectant mothers (aged 16+) in Wales completed an online survey about their experiences of pregnancy during the pandemic. The qualitative survey data was analysed using codebook thematic analysis. Population-level birth outcomes in Wales: Stillbirths, prematurity, birth weight and Caesarean section births before (2016-2019) and during (2020) the pandemic were compared using anonymised individual-level, population-scale routine data held in the Secure Anonymised Information Linkage (SAIL) Databank. Uptake of the first three scheduled primary childhood immunisations were compared between 2019 and 2020.<h4>Findings</h4>The pandemic had a negative impact on the mental health of 71% of survey respondents, who reported anxiety, stress and loneliness; this was associated with attending scans without their partner, giving birth alone, and minimal contact with midwives. There was no significant difference in annual outcomes including gestation and birth weight, stillbirths, and Caesarean sections for infants born in 2020 compared to 2016-2019. There was an increase in late term births (\u226542 weeks gestation) during the first lockdown (OR: 1.28, p = 0.019) and a decrease in moderate to late preterm births (32-36 weeks gestation) during the second lockdown (OR: 0.74, p = 0.001). Fewer babies were born in 2020 (N = 29,031) compared to 2016-2019 (average N = 32,582). All babies received their immunisations in 2020, but there were minor delays in the timings of immunisations. Those due at 8-weeks were 8% less likely to be on time (within 28-days) and at 16-weeks, they were 19% less likely to be on time.<h4>Interpretation</h4>Whilst the pandemic had a negative impact on mothers' experiences of pregnancy. Population-level data suggests that this did not translate to adverse birth outcomes for babies born during the pandemic.",
     "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41416-022-01830-6.pdf; doi:https://doi.org/10.1038/s41416-022-01830-6; html:https://europepmc.org/articles/PMC9060409; pdf:https://europepmc.org/articles/PMC9060409?pdf=render"
+    "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0267176&type=printable; doi:https://doi.org/10.1371/journal.pone.0267176; html:https://europepmc.org/articles/PMC9129046; pdf:https://europepmc.org/articles/PMC9129046?pdf=render"
   },
   {
-    "id": "35609019",
-    "doi": "https://doi.org/10.1371/journal.pone.0267176",
-    "title": "Population birth outcomes in 2020 and experiences of expectant mothers during the COVID-19 pandemic: A 'born in Wales' mixed methods study using routine data.",
-    "authorString": "Jones H, Seaborne M, Cowley L, Odd D, Paranjothy S, Akbari A, Brophy S.",
+    "id": "35501391",
+    "doi": "https://doi.org/10.1038/s41416-022-01830-6",
+    "title": "Impact of the SARS-CoV-2 pandemic on female breast, colorectal and non-small\u00a0cell lung cancer incidence, stage and healthcare pathway to diagnosis during 2020 in Wales, UK, using a national cancer clinical record system.",
+    "authorString": "Greene G, Griffiths R, Han J, Akbari A, Jones M, Lyons J, Lyons RA, Rolles M, Torabi F, Warlow J, Morris ERA, Lawler M, Huws DW.",
     "authorAffiliations": "",
-    "journalTitle": "PloS one",
+    "journalTitle": "British journal of cancer",
     "pubYear": "2022",
-    "date": "2022-05-24",
+    "date": "2022-05-02",
     "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Pregnancy can be a stressful time and the COVID-19 pandemic has affected all aspects of life. This study aims to investigate the pandemic impact on pregnancy experience, rates of primary childhood immunisations and the differences in birth outcomes in during 2020 to those of previous years.<h4>Methods</h4>Self-reported pregnancy experience: 215 expectant mothers (aged 16+) in Wales completed an online survey about their experiences of pregnancy during the pandemic. The qualitative survey data was analysed using codebook thematic analysis. Population-level birth outcomes in Wales: Stillbirths, prematurity, birth weight and Caesarean section births before (2016-2019) and during (2020) the pandemic were compared using anonymised individual-level, population-scale routine data held in the Secure Anonymised Information Linkage (SAIL) Databank. Uptake of the first three scheduled primary childhood immunisations were compared between 2019 and 2020.<h4>Findings</h4>The pandemic had a negative impact on the mental health of 71% of survey respondents, who reported anxiety, stress and loneliness; this was associated with attending scans without their partner, giving birth alone, and minimal contact with midwives. There was no significant difference in annual outcomes including gestation and birth weight, stillbirths, and Caesarean sections for infants born in 2020 compared to 2016-2019. There was an increase in late term births (\u226542 weeks gestation) during the first lockdown (OR: 1.28, p = 0.019) and a decrease in moderate to late preterm births (32-36 weeks gestation) during the second lockdown (OR: 0.74, p = 0.001). Fewer babies were born in 2020 (N = 29,031) compared to 2016-2019 (average N = 32,582). All babies received their immunisations in 2020, but there were minor delays in the timings of immunisations. Those due at 8-weeks were 8% less likely to be on time (within 28-days) and at 16-weeks, they were 19% less likely to be on time.<h4>Interpretation</h4>Whilst the pandemic had a negative impact on mothers' experiences of pregnancy. Population-level data suggests that this did not translate to adverse birth outcomes for babies born during the pandemic.",
+    "abstract": "<h4>Background</h4>COVID-19 pandemic responses impacted behaviour and health services. We estimated the impact on incidence, stage and healthcare pathway to diagnosis for female breast, colorectal and non-small\u00a0cell lung cancers at population level in Wales.<h4>Methods</h4>Cancer e-record and hospital admission data linkage identified adult cases, stage and healthcare pathway to diagnosis (population ~2.5 million). Using multivariate Poisson regressions, we compared 2019 and 2020 counts and estimated incidence rate ratios (IRR).<h4>Results</h4>Cases decreased 15.2% (n\u2009=\u2009-1011) overall. Female breast annual IRR was 0.81 (95% CI: 0.76-0.86, p\u2009<\u20090.001), colorectal 0.80 (95% CI: 0.79-0.81, p\u2009<\u20090.001) and non-small\u00a0cell lung 0.91 (95% CI: 0.90-0.92, p\u2009<\u20090.001). Decreases were largest in 50-69 year olds for female breast and 80+ year olds for all cancers. Stage I female breast cancer declined 41.6%, but unknown stage increased 55.8%. Colorectal stages I-IV declined (range 26.6-29.9%), while unknown stage increased 803.6%. Colorectal Q2-2020 GP-urgent suspected cancer diagnoses decreased 50.0%, and 53.9% for non-small\u00a0cell lung cancer. Annual screen-detected female breast and colorectal cancers fell 47.8% and 13.3%, respectively. Non-smal\u00a0-cell lung cancer emergency presentation diagnoses increased 9.5% (Q2-2020) and 16.3% (Q3-2020).<h4>Conclusion</h4>Significantly fewer cases of three common cancers were diagnosed in 2020. Detrimental impacts on outcomes varied between cancers. Ongoing surveillance with health service optimisation will be needed to mitigate impacts.",
     "laySummary": "",
-    "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0267176&type=printable; doi:https://doi.org/10.1371/journal.pone.0267176; html:https://europepmc.org/articles/PMC9129046; pdf:https://europepmc.org/articles/PMC9129046?pdf=render"
+    "urls": "pdf:https://www.nature.com/articles/s41416-022-01830-6.pdf; doi:https://doi.org/10.1038/s41416-022-01830-6; html:https://europepmc.org/articles/PMC9060409; pdf:https://europepmc.org/articles/PMC9060409?pdf=render"
   },
   {
     "id": "33045103",
@@ -2634,23 +2634,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1038/s41598-023-41476-9; html:https://europepmc.org/articles/PMC10480459; pdf:https://europepmc.org/articles/PMC10480459?pdf=render"
   },
-  {
-    "id": "34817387",
-    "doi": "https://doi.org/10.2196/29532",
-    "title": "Introduction of Systematized Nomenclature of Medicine-Clinical Terms Coding Into an Electronic Health Record and Evaluation of its Impact: Qualitative and Quantitative Study.",
-    "authorString": "Pankhurst T, Evison F, Atia J, Gallier S, Coleman J, Ball S, McKee D, Ryan S, Black R.",
-    "authorAffiliations": "",
-    "journalTitle": "JMIR medical informatics",
-    "pubYear": "2021",
-    "date": "2021-11-23",
-    "isOpenAccess": "Y",
-    "keywords": "Research; Diagnoses; data sharing; Clinical Decision Support; Population Health; Electronic Health Records; Coding Standards; Problem List; Health Data Exchange; Health Data Research; Clinician Led Design; International Classification Of Diseases Version 10 (Icd-10); National Health Service Blueprint; Systematized Nomenclature Of Medicine\u2013clinical Terms (Snomed-ct); Clinician Reported Experience; Electronic Health Record Standards; Patient Diagnoses; Use Of Electronic Health Data; User-led Design; Clinical Usability",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>This study describes the conversion within an existing electronic health record (EHR) from the International Classification of Diseases, Tenth Revision coding system to the SNOMED-CT (Systematized Nomenclature of Medicine-Clinical Terms) for the collection of patient histories and diagnoses. The setting is a large acute hospital that is designing and building its own EHR. Well-designed EHRs create opportunities for continuous data collection, which can be used in clinical decision support rules to drive patient safety. Collected data can be exchanged across health care systems to support patients in all health care settings. Data can be used for research to prevent diseases and protect future populations.<h4>Objective</h4>The aim of this study was to migrate a current EHR, with all relevant patient data, to the SNOMED-CT coding system to optimize clinical use and clinical decision support, facilitate data sharing across organizational boundaries for national programs, and enable remodeling of medical pathways.<h4>Methods</h4>The study used qualitative and quantitative data to understand the successes and gaps in the project, clinician attitudes toward the new tool, and the future use of the tool.<h4>Results</h4>The new coding system (tool) was well received and immediately widely used in all specialties. This resulted in increased, accurate, and clinically relevant data collection. Clinicians appreciated the increased depth and detail of the new coding, welcomed the potential for both data sharing and research, and provided extensive feedback for further development.<h4>Conclusions</h4>Successful implementation of the new system aligned the University Hospitals Birmingham NHS Foundation Trust with national strategy and can be used as a blueprint for similar projects in other health care settings.",
-    "laySummary": "",
-    "urls": "pdf:https://medinform.jmir.org/2021/11/e29532/PDF; doi:https://doi.org/10.2196/29532; html:https://europepmc.org/articles/PMC8663536"
-  },
   {
     "id": "38416166",
     "doi": "https://doi.org/10.1007/s00228-024-03656-y",
@@ -2668,6 +2651,23 @@
     "laySummary": "",
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s00228-024-03656-y.pdf; doi:https://doi.org/10.1007/s00228-024-03656-y; html:https://europepmc.org/articles/PMC11098902; pdf:https://europepmc.org/articles/PMC11098902?pdf=render"
   },
+  {
+    "id": "34817387",
+    "doi": "https://doi.org/10.2196/29532",
+    "title": "Introduction of Systematized Nomenclature of Medicine-Clinical Terms Coding Into an Electronic Health Record and Evaluation of its Impact: Qualitative and Quantitative Study.",
+    "authorString": "Pankhurst T, Evison F, Atia J, Gallier S, Coleman J, Ball S, McKee D, Ryan S, Black R.",
+    "authorAffiliations": "",
+    "journalTitle": "JMIR medical informatics",
+    "pubYear": "2021",
+    "date": "2021-11-23",
+    "isOpenAccess": "Y",
+    "keywords": "Research; Diagnoses; data sharing; Clinical Decision Support; Population Health; Electronic Health Records; Coding Standards; Problem List; Health Data Exchange; Health Data Research; Clinician Led Design; International Classification Of Diseases Version 10 (Icd-10); National Health Service Blueprint; Systematized Nomenclature Of Medicine\u2013clinical Terms (Snomed-ct); Clinician Reported Experience; Electronic Health Record Standards; Patient Diagnoses; Use Of Electronic Health Data; User-led Design; Clinical Usability",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>This study describes the conversion within an existing electronic health record (EHR) from the International Classification of Diseases, Tenth Revision coding system to the SNOMED-CT (Systematized Nomenclature of Medicine-Clinical Terms) for the collection of patient histories and diagnoses. The setting is a large acute hospital that is designing and building its own EHR. Well-designed EHRs create opportunities for continuous data collection, which can be used in clinical decision support rules to drive patient safety. Collected data can be exchanged across health care systems to support patients in all health care settings. Data can be used for research to prevent diseases and protect future populations.<h4>Objective</h4>The aim of this study was to migrate a current EHR, with all relevant patient data, to the SNOMED-CT coding system to optimize clinical use and clinical decision support, facilitate data sharing across organizational boundaries for national programs, and enable remodeling of medical pathways.<h4>Methods</h4>The study used qualitative and quantitative data to understand the successes and gaps in the project, clinician attitudes toward the new tool, and the future use of the tool.<h4>Results</h4>The new coding system (tool) was well received and immediately widely used in all specialties. This resulted in increased, accurate, and clinically relevant data collection. Clinicians appreciated the increased depth and detail of the new coding, welcomed the potential for both data sharing and research, and provided extensive feedback for further development.<h4>Conclusions</h4>Successful implementation of the new system aligned the University Hospitals Birmingham NHS Foundation Trust with national strategy and can be used as a blueprint for similar projects in other health care settings.",
+    "laySummary": "",
+    "urls": "pdf:https://medinform.jmir.org/2021/11/e29532/PDF; doi:https://doi.org/10.2196/29532; html:https://europepmc.org/articles/PMC8663536"
+  },
   {
     "id": "35356660",
     "doi": "https://doi.org/10.7189/jogh.12.05008",
@@ -2685,23 +2685,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.7189/jogh.12.05008; doi:https://doi.org/10.7189/jogh.12.05008; html:https://europepmc.org/articles/PMC8942298; pdf:https://europepmc.org/articles/PMC8942298?pdf=render"
   },
-  {
-    "id": "39152507",
-    "doi": "https://doi.org/10.1186/s13063-024-08330-3",
-    "title": "Towards an understanding of the ethics of electronic consent in clinical trials.",
-    "authorString": "Sahan K, Wijesurendra R, Preiss D, Mafham M, Sheehan M.",
-    "authorAffiliations": "",
-    "journalTitle": "Trials",
-    "pubYear": "2024",
-    "date": "2024-08-16",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "There are good practical reasons to use electronic consent (e-consent) in randomised trials, especially when conducting large-scale clinical trials to answer population-level health research questions. However, determining ethical reasons for e-consent is not so clear and depends on a proper understanding of what e-consent means when used in clinical trials and its ethical significance. Here we focus on four features of ethical significance which give rise to a range of ethical considerations relating to e-consent and merit further focused ethics research.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1186/s13063-024-08330-3; html:https://europepmc.org/articles/PMC11329992; pdf:https://europepmc.org/articles/PMC11329992?pdf=render"
-  },
   {
     "id": "38135323",
     "doi": "https://doi.org/10.1136/bmjopen-2023-076221",
@@ -2719,6 +2702,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1136/bmjopen-2023-076221; html:https://europepmc.org/articles/PMC10748981; pdf:https://europepmc.org/articles/PMC10748981?pdf=render"
   },
+  {
+    "id": "39152507",
+    "doi": "https://doi.org/10.1186/s13063-024-08330-3",
+    "title": "Towards an understanding of the ethics of electronic consent in clinical trials.",
+    "authorString": "Sahan K, Wijesurendra R, Preiss D, Mafham M, Sheehan M.",
+    "authorAffiliations": "",
+    "journalTitle": "Trials",
+    "pubYear": "2024",
+    "date": "2024-08-16",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "There are good practical reasons to use electronic consent (e-consent) in randomised trials, especially when conducting large-scale clinical trials to answer population-level health research questions. However, determining ethical reasons for e-consent is not so clear and depends on a proper understanding of what e-consent means when used in clinical trials and its ethical significance. Here we focus on four features of ethical significance which give rise to a range of ethical considerations relating to e-consent and merit further focused ethics research.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1186/s13063-024-08330-3; html:https://europepmc.org/articles/PMC11329992; pdf:https://europepmc.org/articles/PMC11329992?pdf=render"
+  },
   {
     "id": "34238721",
     "doi": "https://doi.org/10.1016/s2589-7500(21)00105-9",
@@ -2906,6 +2906,23 @@
     "laySummary": "",
     "urls": "pdf:https://discovery.ucl.ac.uk/id/eprint/10155637/1/ocac158.pdf; doi:https://doi.org/10.1093/jamia/ocac158; html:https://europepmc.org/articles/PMC9846670; pdf:https://europepmc.org/articles/PMC9846670?pdf=render"
   },
+  {
+    "id": "38783251",
+    "doi": "https://doi.org/10.1186/s12885-024-12344-0",
+    "title": "Prospective associations of leucocyte subtypes and obesity with the risk of developing cutaneous malignant melanoma in the UK Biobank cohort.",
+    "authorString": "Christakoudi S, Tsilidis KK, Riboli E.",
+    "authorAffiliations": "",
+    "journalTitle": "BMC cancer",
+    "pubYear": "2024",
+    "date": "2024-05-23",
+    "isOpenAccess": "Y",
+    "keywords": "Lymphocytes; Neutrophils; Monocytes; Obesity; BMI; abdominal obesity; Cutaneous Malignant Melanoma; Absi",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Obesity is associated with chronic low-grade inflammation, which is linked to cancer development. Abdominal obesity (a body mass index, ABSI), however, has unusually been associated inversely with cutaneous malignant melanoma (CMM), while general obesity (body mass index, BMI) is associated positively. Leucocytes participate in inflammation and are higher in obesity, but prospective associations of leucocytes with cutaneous malignant melanoma are unclear.<h4>Methods</h4>We examined the prospective associations of neutrophil, lymphocyte, and monocyte counts (each individually), as well as the prospective associations of ABSI and BMI, with cutaneous malignant melanoma in UK Biobank. We used multivariable Cox proportional hazards models and explored heterogeneity according to sex, menopausal status, age (\u2265\u200950 years at recruitment), smoking status, ABSI (dichotomised at the median: \u226573.5 women; \u226579.8 men), BMI (normal weight, overweight, obese), and time to diagnosis.<h4>Results</h4>During a mean follow-up of 10.2 years, 2174 CMM cases were ascertained in 398,450 participants. There was little evidence for associations with neutrophil or lymphocyte counts. Monocyte count, however, was associated inversely in participants overall (HR\u2009=\u20090.928; 95%CI: 0.888-0.971; per one standard deviation increase; SD\u2009=\u20090.144*10<sup>9</sup>/L women; SD\u2009=\u20090.169*10<sup>9</sup>/L men), specifically in older participants (HR\u2009=\u20090.906; 95%CI: 0.862-0.951), and more clearly in participants with low ABSI (HR\u2009=\u20090.880; 95%CI: 0.824-0.939), or with BMI\u2009\u2265\u200925\u00a0kg/m<sup>2</sup> (HR\u2009=\u20090.895; 95%CI: 0.837-0.958 for overweight; HR\u2009=\u20090.923; 95%CI: 0.848-1.005 for obese). ABSI was associated inversely in pre-menopausal women (HR\u2009=\u20090.810; 95%CI: 0.702-0.935; SD\u2009=\u20094.95) and men (HR\u2009=\u20090.925; 95%CI: 0.867-0.986; SD\u2009=\u20094.11). BMI was associated positively in men (HR\u2009=\u20091.148; 95%CI: 1.078-1.222; SD\u2009=\u20094.04\u00a0kg/m<sup>2</sup>). There was little evidence for heterogeneity according to smoking status. The associations with monocyte count and BMI were retained to at least 8 years prior to diagnosis, but the association with ABSI was observed up to 4 years prior to diagnosis and not for longer follow-up time.<h4>Conclusions</h4>Monocyte count is associated prospectively inversely with the risk of developing CMM in older individuals, while BMI is associated positively in men, suggesting a mechanistic involvement of factors related to monocytes and subcutaneous adipose tissue in melanoma development. An inverse association with ABSI closer to diagnosis may reflect reverse causality or glucocorticoid resistance.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1186/s12885-024-12344-0; html:https://europepmc.org/articles/PMC11112846; pdf:https://europepmc.org/articles/PMC11112846?pdf=render"
+  },
   {
     "id": "39323985",
     "doi": "https://doi.org/10.1214/23-aoas1849",
@@ -2940,6 +2957,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.cct.2024.107514"
   },
+  {
+    "id": "38529358",
+    "doi": "https://doi.org/10.1093/braincomms/fcae088",
+    "title": "<i>Helicobacter pylori</i>, persistent infection burden and structural brain imaging markers.",
+    "authorString": "Beydoun MA, Beydoun HA, Hu YH, El-Hajj ZW, Georgescu MF, Noren Hooten N, Li Z, Weiss J, Lyall DM, Waldstein SR, Hedges DW, Gale SD, Launer LJ, Evans MK, Zonderman AB.",
+    "authorAffiliations": "",
+    "journalTitle": "Brain communications",
+    "pubYear": "2024",
+    "date": "2024-03-13",
+    "isOpenAccess": "N",
+    "keywords": "Helicobacter Pylori; Persistent infection; Brain imaging; Cognitive Aging",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Persistent infections, whether viral, bacterial or parasitic, including <i>Helicobacter pylori</i> infection, have been implicated in non-communicable diseases, including dementia and other neurodegenerative diseases. In this cross-sectional study, data on 635 cognitively normal participants from the UK Biobank study (2006-21, age range: 40-70 years) were used to examine whether <i>H. pylori</i> seropositivity (e.g. presence of antibodies), serointensities of five <i>H. pylori</i> antigens and a measure of total persistent infection burden were associated with selected brain volumetric structural MRI (total, white, grey matter, frontal grey matter (left/right), white matter hyperintensity as percent intracranial volume and bi-lateral sub-cortical volumes) and diffusion-weighted MRI measures (global and tract-specific bi-lateral fractional anisotropy and mean diffusivity), after an average 9-10 years of lag time. Persistent infection burden was calculated as a cumulative score of seropositivity for over 20 different pathogens. Multivariable-adjusted linear regression analyses were conducted, whereby selected potential confounders (all measures) and intracranial volume (sub-cortical volumes) were adjusted, with stratification by Alzheimer's disease polygenic risk score tertile when exposures were <i>H. pylori</i> antigen serointensities. Type I error was adjusted to 0.007. We report little evidence of an association between <i>H. pylori</i> seropositivity and persistent infection burden with various volumetric outcomes (<i>P</i> > 0.007, from multivariable regression models), unlike previously reported in past research. However, <i>H. pylori</i> antigen serointensities, particularly immunoglobulin G against the vacuolating cytotoxin A, GroEL and outer membrane protein antigens, were associated with poorer tract-specific white matter integrity (<i>P</i> < 0.007), with outer membrane protein serointensity linked to worse outcomes in cognition-related tracts such as the external capsule, the anterior limb of the internal capsule and the cingulum, specifically at low Alzheimer's disease polygenic risk. Vacuolating cytotoxin A serointensity was associated with greater white matter hyperintensity volume among individuals with mid-level Alzheimer's disease polygenic risk, while among individuals with the highest Alzheimer's disease polygenic risk, the urease serointensity was consistently associated with reduced bi-lateral caudate volumes and the vacuolating cytotoxin A serointensity was linked to reduced right putamen volume (<i>P</i> < 0.007). Outer membrane protein and urease were associated with larger sub-cortical volumes (e.g. left putamen and right nucleus accumbens) at middle Alzheimer's disease polygenic risk levels (<i>P</i> < 0.007). Our results shed light on the relationship between <i>H. pylori</i> seropositivity, <i>H. pylori</i> antigen levels and persistent infection burden with brain volumetric structural measures. These data are important given the links between infectious agents and neurodegenerative diseases, including Alzheimer's disease, and can be used for the development of drugs and preventive interventions that would reduce the burden of those diseases.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1093/braincomms/fcae088; html:https://europepmc.org/articles/PMC10961948; pdf:https://europepmc.org/articles/PMC10961948?pdf=render; doi:https://doi.org/10.1093/braincomms/fcae088"
+  },
   {
     "id": "34706926",
     "doi": "https://doi.org/10.1136/jech-2021-217090",
@@ -2957,23 +2991,6 @@
     "laySummary": "",
     "urls": "pdf:https://jech.bmj.com/content/jech/76/3/223.full.pdf; doi:https://doi.org/10.1136/jech-2021-217090; html:https://europepmc.org/articles/PMC8862053; pdf:https://europepmc.org/articles/PMC8862053?pdf=render"
   },
-  {
-    "id": "38783251",
-    "doi": "https://doi.org/10.1186/s12885-024-12344-0",
-    "title": "Prospective associations of leucocyte subtypes and obesity with the risk of developing cutaneous malignant melanoma in the UK Biobank cohort.",
-    "authorString": "Christakoudi S, Tsilidis KK, Riboli E.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC cancer",
-    "pubYear": "2024",
-    "date": "2024-05-23",
-    "isOpenAccess": "Y",
-    "keywords": "Lymphocytes; Neutrophils; Monocytes; Obesity; BMI; abdominal obesity; Cutaneous Malignant Melanoma; Absi",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Obesity is associated with chronic low-grade inflammation, which is linked to cancer development. Abdominal obesity (a body mass index, ABSI), however, has unusually been associated inversely with cutaneous malignant melanoma (CMM), while general obesity (body mass index, BMI) is associated positively. Leucocytes participate in inflammation and are higher in obesity, but prospective associations of leucocytes with cutaneous malignant melanoma are unclear.<h4>Methods</h4>We examined the prospective associations of neutrophil, lymphocyte, and monocyte counts (each individually), as well as the prospective associations of ABSI and BMI, with cutaneous malignant melanoma in UK Biobank. We used multivariable Cox proportional hazards models and explored heterogeneity according to sex, menopausal status, age (\u2265\u200950 years at recruitment), smoking status, ABSI (dichotomised at the median: \u226573.5 women; \u226579.8 men), BMI (normal weight, overweight, obese), and time to diagnosis.<h4>Results</h4>During a mean follow-up of 10.2 years, 2174 CMM cases were ascertained in 398,450 participants. There was little evidence for associations with neutrophil or lymphocyte counts. Monocyte count, however, was associated inversely in participants overall (HR\u2009=\u20090.928; 95%CI: 0.888-0.971; per one standard deviation increase; SD\u2009=\u20090.144*10<sup>9</sup>/L women; SD\u2009=\u20090.169*10<sup>9</sup>/L men), specifically in older participants (HR\u2009=\u20090.906; 95%CI: 0.862-0.951), and more clearly in participants with low ABSI (HR\u2009=\u20090.880; 95%CI: 0.824-0.939), or with BMI\u2009\u2265\u200925\u00a0kg/m<sup>2</sup> (HR\u2009=\u20090.895; 95%CI: 0.837-0.958 for overweight; HR\u2009=\u20090.923; 95%CI: 0.848-1.005 for obese). ABSI was associated inversely in pre-menopausal women (HR\u2009=\u20090.810; 95%CI: 0.702-0.935; SD\u2009=\u20094.95) and men (HR\u2009=\u20090.925; 95%CI: 0.867-0.986; SD\u2009=\u20094.11). BMI was associated positively in men (HR\u2009=\u20091.148; 95%CI: 1.078-1.222; SD\u2009=\u20094.04\u00a0kg/m<sup>2</sup>). There was little evidence for heterogeneity according to smoking status. The associations with monocyte count and BMI were retained to at least 8 years prior to diagnosis, but the association with ABSI was observed up to 4 years prior to diagnosis and not for longer follow-up time.<h4>Conclusions</h4>Monocyte count is associated prospectively inversely with the risk of developing CMM in older individuals, while BMI is associated positively in men, suggesting a mechanistic involvement of factors related to monocytes and subcutaneous adipose tissue in melanoma development. An inverse association with ABSI closer to diagnosis may reflect reverse causality or glucocorticoid resistance.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1186/s12885-024-12344-0; html:https://europepmc.org/articles/PMC11112846; pdf:https://europepmc.org/articles/PMC11112846?pdf=render"
-  },
   {
     "id": "33319712",
     "doi": "https://doi.org/10.1186/s12911-020-01336-2",
@@ -3008,23 +3025,6 @@
     "laySummary": "",
     "urls": "pdf:https://diabetesjournals.org/care/article-pdf/45/5/1132/678515/dc211709.pdf; doi:https://doi.org/10.2337/dc21-1709; html:https://europepmc.org/articles/PMC9174963; pdf:https://europepmc.org/articles/PMC9174963?pdf=render; doi:https://doi.org/10.2337/dc21-1709"
   },
-  {
-    "id": "38529358",
-    "doi": "https://doi.org/10.1093/braincomms/fcae088",
-    "title": "<i>Helicobacter pylori</i>, persistent infection burden and structural brain imaging markers.",
-    "authorString": "Beydoun MA, Beydoun HA, Hu YH, El-Hajj ZW, Georgescu MF, Noren Hooten N, Li Z, Weiss J, Lyall DM, Waldstein SR, Hedges DW, Gale SD, Launer LJ, Evans MK, Zonderman AB.",
-    "authorAffiliations": "",
-    "journalTitle": "Brain communications",
-    "pubYear": "2024",
-    "date": "2024-03-13",
-    "isOpenAccess": "N",
-    "keywords": "Helicobacter Pylori; Persistent infection; Brain imaging; Cognitive Aging",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Persistent infections, whether viral, bacterial or parasitic, including <i>Helicobacter pylori</i> infection, have been implicated in non-communicable diseases, including dementia and other neurodegenerative diseases. In this cross-sectional study, data on 635 cognitively normal participants from the UK Biobank study (2006-21, age range: 40-70 years) were used to examine whether <i>H. pylori</i> seropositivity (e.g. presence of antibodies), serointensities of five <i>H. pylori</i> antigens and a measure of total persistent infection burden were associated with selected brain volumetric structural MRI (total, white, grey matter, frontal grey matter (left/right), white matter hyperintensity as percent intracranial volume and bi-lateral sub-cortical volumes) and diffusion-weighted MRI measures (global and tract-specific bi-lateral fractional anisotropy and mean diffusivity), after an average 9-10 years of lag time. Persistent infection burden was calculated as a cumulative score of seropositivity for over 20 different pathogens. Multivariable-adjusted linear regression analyses were conducted, whereby selected potential confounders (all measures) and intracranial volume (sub-cortical volumes) were adjusted, with stratification by Alzheimer's disease polygenic risk score tertile when exposures were <i>H. pylori</i> antigen serointensities. Type I error was adjusted to 0.007. We report little evidence of an association between <i>H. pylori</i> seropositivity and persistent infection burden with various volumetric outcomes (<i>P</i> > 0.007, from multivariable regression models), unlike previously reported in past research. However, <i>H. pylori</i> antigen serointensities, particularly immunoglobulin G against the vacuolating cytotoxin A, GroEL and outer membrane protein antigens, were associated with poorer tract-specific white matter integrity (<i>P</i> < 0.007), with outer membrane protein serointensity linked to worse outcomes in cognition-related tracts such as the external capsule, the anterior limb of the internal capsule and the cingulum, specifically at low Alzheimer's disease polygenic risk. Vacuolating cytotoxin A serointensity was associated with greater white matter hyperintensity volume among individuals with mid-level Alzheimer's disease polygenic risk, while among individuals with the highest Alzheimer's disease polygenic risk, the urease serointensity was consistently associated with reduced bi-lateral caudate volumes and the vacuolating cytotoxin A serointensity was linked to reduced right putamen volume (<i>P</i> < 0.007). Outer membrane protein and urease were associated with larger sub-cortical volumes (e.g. left putamen and right nucleus accumbens) at middle Alzheimer's disease polygenic risk levels (<i>P</i> < 0.007). Our results shed light on the relationship between <i>H. pylori</i> seropositivity, <i>H. pylori</i> antigen levels and persistent infection burden with brain volumetric structural measures. These data are important given the links between infectious agents and neurodegenerative diseases, including Alzheimer's disease, and can be used for the development of drugs and preventive interventions that would reduce the burden of those diseases.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1093/braincomms/fcae088; html:https://europepmc.org/articles/PMC10961948; pdf:https://europepmc.org/articles/PMC10961948?pdf=render; doi:https://doi.org/10.1093/braincomms/fcae088"
-  },
   {
     "id": "37193316",
     "doi": "https://doi.org/10.1016/j.xops.2023.100293",
@@ -3162,21 +3162,21 @@
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8192173; doi:https://doi.org/10.1016/j.bja.2021.05.018; html:https://europepmc.org/articles/PMC8192173; pdf:https://europepmc.org/articles/PMC8192173?pdf=render"
   },
   {
-    "id": "38331807",
-    "doi": "https://doi.org/10.1186/s12916-024-03271-9",
-    "title": "Childhood maltreatment and risk of endocrine diseases: an exploration of mediating pathways using sequential mediation analysis.",
-    "authorString": "Wen S, Zhu J, Han X, Li Y, Liu H, Yang H, Hou C, Xu S, Wang J, Hu Y, Qu Y, Liu D, Aspelund T, Fang F, Valdimarsd\u00f3ttir UA, Song H.",
+    "id": "38280379",
+    "doi": "https://doi.org/10.1016/j.xcrm.2023.101391",
+    "title": "Evidence for a causal link between intra-pancreatic fat deposition and pancreatic cancer: A prospective cohort and Mendelian randomization study.",
+    "authorString": "Yamazaki H, Streicher SA, Wu L, Fukuhara S, Wagner R, Heni M, Grossman SR, Lenz HJ, Setiawan VW, Le Marchand L, Huang BZ.",
     "authorAffiliations": "",
-    "journalTitle": "BMC medicine",
+    "journalTitle": "Cell reports. Medicine",
     "pubYear": "2024",
-    "date": "2024-02-08",
+    "date": "2024-01-26",
     "isOpenAccess": "Y",
-    "keywords": "Endocrine diseases; Childhood Maltreatment; Sequential Mediation Analysis; Psychological Adversities",
+    "keywords": "Pancreatic adenocarcinoma; Pancreas Cancer; Fatty Pancreas; Pancreatic Fat; Pancreatic Steatosis; Pancreas Fat",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Adverse childhood experiences (ACEs), including childhood maltreatment, have been linked with increased risk of diabetes and obesity during adulthood. A comprehensive assessment on the associations between childhood maltreatment and all major endocrine diseases, as well as the relative importance of different proposed mechanistic pathways on these associations, is currently lacking.<h4>Methods</h4>Based on the UK Biobank, we constructed a cohort including 151,659 participants with self-reported data on childhood maltreatment who were 30 years of age or older on/after January 1, 1985. All participants were followed from the index date (i.e., January 1, 1985, or their 30th birthday, whichever came later) until the first diagnosis of any or specific (12 individual diagnoses and 9 subtypes) endocrine diseases, death, or the end of follow-up (December 31, 2019), whichever occurred first. We used Cox models to examine the association of childhood maltreatment, treated as continuous (i.e., the cumulative number of experienced childhood maltreatment), ordinal (i.e., 0, 1 and\u2009\u2265\u20092), or binary (<\u20092 and\u2009\u2265\u20092) variable, with any and specific endocrine diseases, adjusted for multiple covariates. We further examined the risk of having multiple endocrine diseases using Linear or Logistic Regression models. Then, sequential mediation analyses were performed to assess the contribution of four possible mechanisms (i.e., suboptimal socioeconomic status (SES), psychological adversities, unfavorable lifestyle, and biological alterations) on the observed associations.<h4>Results</h4>During an average follow-up of 30.8 years, 20,885 participants received a diagnosis of endocrine diseases. We observed an association between the cumulative number of experienced childhood maltreatment and increased risk of being diagnosed with any endocrine disease (adjusted hazard ratio (HR)\u2009=\u20091.10, 95% confidence interval 1.09-1.12). The HR was 1.26 (1.22-1.30) when comparing individuals\u2009\u2265\u20092 with those with\u2009<\u20092 experienced childhood maltreatment. We further noted the most pronounced associations for type 2 diabetes (1.40 (1.33-1.48)) and hypothalamic-pituitary-adrenal (HPA)-axis-related endocrine diseases (1.38 (1.17-1.62)), and the association was stronger for having multiple endocrine diseases, compared to having one (odds ratio (95% CI)\u2009=\u20091.24 (1.19-1.30), 1.35 (1.27-1.44), and 1.52 (1.52-1.53) for 1, 2, and\u2009\u2265\u20093, respectively). Sequential mediation analyses showed that the association between childhood maltreatment and endocrine diseases was consistently and most distinctly mediated by psychological adversities (15.38\u2009~\u200944.97%), while unfavorable lifestyle (10.86\u2009~\u200925.32%) was additionally noted for type 2 diabetes whereas suboptimal SES (14.42\u2009~\u200939.33%) for HPA-axis-related endocrine diseases.<h4>Conclusions</h4>Our study demonstrates that adverse psychological sequel of childhood maltreatment constitutes the main pathway to multiple endocrine diseases, particularly type 2 diabetes and HPA-axis-related endocrine diseases. Therefore, increased access to evidence-based mental health services may also be pivotal in reducing the risk of endocrine diseases among childhood maltreatment-exposed individuals.",
+    "abstract": "Prior observational studies suggest an association between intra-pancreatic fat deposition (IPFD) and pancreatic ductal adenocarcinoma (PDAC); however, the causal relationship is unclear. To elucidate causality, we conduct a prospective observational study using magnetic resonance imaging (MRI)-measured IPFD data and also perform a Mendelian randomization study using genetic instruments for IPFD. In the observational study, we use UK Biobank data (N\u00a0= 29,463, median follow-up: 4.5 years) and find that high IPFD (>10%) is associated with PDAC risk (adjusted hazard ratio [HR]: 3.35, 95% confidence interval [95% CI]: 1.60-7.00). In the Mendelian randomization study, we leverage eight out of nine IPFD-associated genetic variants (p\u00a0<\u00a05\u00a0\u00d7\u00a010<sup>-8</sup>) from a genome-wide association study in the UK Biobank (N\u00a0= 25,617) and find that genetically determined IPFD is associated with PDAC (odds ratio [OR] per 1-standard deviation [SD] increase in IPFD: 2.46, 95% CI: 1.38-4.40) in the Pancreatic Cancer Cohort Consortium I, II, III (PanScan I-III)/Pancreatic Cancer Case-Control Consortium (PanC4) dataset (8,275 PDAC cases and 6,723 non-cases). This study provides evidence\u00a0for a potential causal role of IPFD in the pathogenesis of PDAC. Thus, reducing IPFD may lower PDAC risk.",
     "laySummary": "",
-    "urls": "pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-024-03271-9; doi:https://doi.org/10.1186/s12916-024-03271-9; html:https://europepmc.org/articles/PMC10854183; pdf:https://europepmc.org/articles/PMC10854183?pdf=render"
+    "urls": "doi:https://doi.org/10.1016/j.xcrm.2023.101391; html:https://europepmc.org/articles/PMC10897551; pdf:https://europepmc.org/articles/PMC10897551?pdf=render"
   },
   {
     "id": "34544601",
@@ -3196,21 +3196,38 @@
     "urls": "doi:https://doi.org/10.1016/j.vaccine.2021.09.019; doi:https://doi.org/10.1016/j.vaccine.2021.09.019; html:https://europepmc.org/articles/PMC8423991"
   },
   {
-    "id": "36332519",
-    "doi": "https://doi.org/10.1016/j.ijmedinf.2022.104905",
-    "title": "Creation of a core competency framework for clinical informatics: From genesis to maintaining relevance.",
-    "authorString": "Davies A, Hassey A, Williams J, Moulton G.",
+    "id": "38331807",
+    "doi": "https://doi.org/10.1186/s12916-024-03271-9",
+    "title": "Childhood maltreatment and risk of endocrine diseases: an exploration of mediating pathways using sequential mediation analysis.",
+    "authorString": "Wen S, Zhu J, Han X, Li Y, Liu H, Yang H, Hou C, Xu S, Wang J, Hu Y, Qu Y, Liu D, Aspelund T, Fang F, Valdimarsd\u00f3ttir UA, Song H.",
     "authorAffiliations": "",
-    "journalTitle": "International journal of medical informatics",
-    "pubYear": "2022",
-    "date": "2022-10-30",
-    "isOpenAccess": "N",
-    "keywords": "Informatics; Core Competencies; Competency Framework; Healthcare Workforce; Informaticians",
+    "journalTitle": "BMC medicine",
+    "pubYear": "2024",
+    "date": "2024-02-08",
+    "isOpenAccess": "Y",
+    "keywords": "Endocrine diseases; Childhood Maltreatment; Sequential Mediation Analysis; Psychological Adversities",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>The United Kingdom's Faculty of Clinical Informatics (FCI) embarked on the creation of a core competency framework in response to the need to provide support to those working in clinical and health and social care that also hold informatics roles.<h4>Methods</h4>The work spanned several phases and utilised a mixed-methods approach consisting of interviews, surveys, job listing analysis, expert discussions and a systematic literature review. The work presented here explores the lessons learnt from the process of creating the framework and the next steps for ensuring its use and continued relevance.<h4>Results</h4>A core competency framework was generated with six domains, 36 sub-domains and 111 individual competency statements. A discussion and eight key recommendations are presented based on the development of this framework.<h4>Conclusion</h4>Definition of the target audience is important to manage scope and define purpose. The use of robust reproducible methods helps to establish a strong evidence base. Competency frameworks should be living documents, ideally presented in an accessible digital form to enable easy use and embedding in other tools (e.g. for accreditation or to search competencies).",
+    "abstract": "<h4>Background</h4>Adverse childhood experiences (ACEs), including childhood maltreatment, have been linked with increased risk of diabetes and obesity during adulthood. A comprehensive assessment on the associations between childhood maltreatment and all major endocrine diseases, as well as the relative importance of different proposed mechanistic pathways on these associations, is currently lacking.<h4>Methods</h4>Based on the UK Biobank, we constructed a cohort including 151,659 participants with self-reported data on childhood maltreatment who were 30 years of age or older on/after January 1, 1985. All participants were followed from the index date (i.e., January 1, 1985, or their 30th birthday, whichever came later) until the first diagnosis of any or specific (12 individual diagnoses and 9 subtypes) endocrine diseases, death, or the end of follow-up (December 31, 2019), whichever occurred first. We used Cox models to examine the association of childhood maltreatment, treated as continuous (i.e., the cumulative number of experienced childhood maltreatment), ordinal (i.e., 0, 1 and\u2009\u2265\u20092), or binary (<\u20092 and\u2009\u2265\u20092) variable, with any and specific endocrine diseases, adjusted for multiple covariates. We further examined the risk of having multiple endocrine diseases using Linear or Logistic Regression models. Then, sequential mediation analyses were performed to assess the contribution of four possible mechanisms (i.e., suboptimal socioeconomic status (SES), psychological adversities, unfavorable lifestyle, and biological alterations) on the observed associations.<h4>Results</h4>During an average follow-up of 30.8 years, 20,885 participants received a diagnosis of endocrine diseases. We observed an association between the cumulative number of experienced childhood maltreatment and increased risk of being diagnosed with any endocrine disease (adjusted hazard ratio (HR)\u2009=\u20091.10, 95% confidence interval 1.09-1.12). The HR was 1.26 (1.22-1.30) when comparing individuals\u2009\u2265\u20092 with those with\u2009<\u20092 experienced childhood maltreatment. We further noted the most pronounced associations for type 2 diabetes (1.40 (1.33-1.48)) and hypothalamic-pituitary-adrenal (HPA)-axis-related endocrine diseases (1.38 (1.17-1.62)), and the association was stronger for having multiple endocrine diseases, compared to having one (odds ratio (95% CI)\u2009=\u20091.24 (1.19-1.30), 1.35 (1.27-1.44), and 1.52 (1.52-1.53) for 1, 2, and\u2009\u2265\u20093, respectively). Sequential mediation analyses showed that the association between childhood maltreatment and endocrine diseases was consistently and most distinctly mediated by psychological adversities (15.38\u2009~\u200944.97%), while unfavorable lifestyle (10.86\u2009~\u200925.32%) was additionally noted for type 2 diabetes whereas suboptimal SES (14.42\u2009~\u200939.33%) for HPA-axis-related endocrine diseases.<h4>Conclusions</h4>Our study demonstrates that adverse psychological sequel of childhood maltreatment constitutes the main pathway to multiple endocrine diseases, particularly type 2 diabetes and HPA-axis-related endocrine diseases. Therefore, increased access to evidence-based mental health services may also be pivotal in reducing the risk of endocrine diseases among childhood maltreatment-exposed individuals.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.ijmedinf.2022.104905"
+    "urls": "pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-024-03271-9; doi:https://doi.org/10.1186/s12916-024-03271-9; html:https://europepmc.org/articles/PMC10854183; pdf:https://europepmc.org/articles/PMC10854183?pdf=render"
+  },
+  {
+    "id": "38877008",
+    "doi": "https://doi.org/10.1038/s41541-024-00898-w",
+    "title": "Association between antibody responses post-vaccination and severe COVID-19 outcomes in Scotland.",
+    "authorString": "Macdonald C, Palmateer N, McAuley A, Lindsay L, Hasan T, Hameed SS, Hall E, Jeffrey K, Grange Z, Gousias P, Mavin S, Jarvis L, Cameron JC, Daines L, Tibble H, Simpson CR, McCowan C, Katikireddi SV, Rudan I, Fagbamigbe AF, Ritchie L, Swallow B, Moss P, Robertson C, Sheikh A, Murray J.",
+    "authorAffiliations": "",
+    "journalTitle": "NPJ vaccines",
+    "pubYear": "2024",
+    "date": "2024-06-14",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Several population-level studies have described individual clinical risk factors associated with suboptimal antibody responses following COVID-19 vaccination, but none have examined multimorbidity. Others have shown that suboptimal post-vaccination responses offer reduced protection to subsequent SARS-CoV-2 infection; however, the level of protection from COVID-19 hospitalisation/death remains unconfirmed. We use national Scottish datasets to investigate the association between multimorbidity and testing antibody-negative, examining the correlation between antibody levels and subsequent COVID-19 hospitalisation/death among double-vaccinated individuals. We found that individuals with multimorbidity (\u2009\u2265\u2009five conditions) were more likely to test antibody-negative post-vaccination and 13.37 [6.05-29.53] times more likely to be hospitalised/die from COVID-19 than individuals without conditions. We also show a dose-dependent association between post-vaccination antibody levels and COVID-19 hospitalisation or death, with those with undetectable antibody levels at a significantly higher risk (HR 9.21 [95% CI 4.63-18.29]) of these serious outcomes compared to those with high antibody levels.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41541-024-00898-w.pdf; doi:https://doi.org/10.1038/s41541-024-00898-w; html:https://europepmc.org/articles/PMC11178861; pdf:https://europepmc.org/articles/PMC11178861?pdf=render"
   },
   {
     "id": "37828061",
@@ -3230,55 +3247,38 @@
     "urls": "pdf:https://www.nature.com/articles/s41598-023-43193-9.pdf; doi:https://doi.org/10.1038/s41598-023-43193-9; html:https://europepmc.org/articles/PMC10570373; pdf:https://europepmc.org/articles/PMC10570373?pdf=render"
   },
   {
-    "id": "38280379",
-    "doi": "https://doi.org/10.1016/j.xcrm.2023.101391",
-    "title": "Evidence for a causal link between intra-pancreatic fat deposition and pancreatic cancer: A prospective cohort and Mendelian randomization study.",
-    "authorString": "Yamazaki H, Streicher SA, Wu L, Fukuhara S, Wagner R, Heni M, Grossman SR, Lenz HJ, Setiawan VW, Le Marchand L, Huang BZ.",
-    "authorAffiliations": "",
-    "journalTitle": "Cell reports. Medicine",
-    "pubYear": "2024",
-    "date": "2024-01-26",
-    "isOpenAccess": "Y",
-    "keywords": "Pancreatic adenocarcinoma; Pancreas Cancer; Fatty Pancreas; Pancreatic Fat; Pancreatic Steatosis; Pancreas Fat",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Prior observational studies suggest an association between intra-pancreatic fat deposition (IPFD) and pancreatic ductal adenocarcinoma (PDAC); however, the causal relationship is unclear. To elucidate causality, we conduct a prospective observational study using magnetic resonance imaging (MRI)-measured IPFD data and also perform a Mendelian randomization study using genetic instruments for IPFD. In the observational study, we use UK Biobank data (N\u00a0= 29,463, median follow-up: 4.5 years) and find that high IPFD (>10%) is associated with PDAC risk (adjusted hazard ratio [HR]: 3.35, 95% confidence interval [95% CI]: 1.60-7.00). In the Mendelian randomization study, we leverage eight out of nine IPFD-associated genetic variants (p\u00a0<\u00a05\u00a0\u00d7\u00a010<sup>-8</sup>) from a genome-wide association study in the UK Biobank (N\u00a0= 25,617) and find that genetically determined IPFD is associated with PDAC (odds ratio [OR] per 1-standard deviation [SD] increase in IPFD: 2.46, 95% CI: 1.38-4.40) in the Pancreatic Cancer Cohort Consortium I, II, III (PanScan I-III)/Pancreatic Cancer Case-Control Consortium (PanC4) dataset (8,275 PDAC cases and 6,723 non-cases). This study provides evidence\u00a0for a potential causal role of IPFD in the pathogenesis of PDAC. Thus, reducing IPFD may lower PDAC risk.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.xcrm.2023.101391; html:https://europepmc.org/articles/PMC10897551; pdf:https://europepmc.org/articles/PMC10897551?pdf=render"
-  },
-  {
-    "id": "38877008",
-    "doi": "https://doi.org/10.1038/s41541-024-00898-w",
-    "title": "Association between antibody responses post-vaccination and severe COVID-19 outcomes in Scotland.",
-    "authorString": "Macdonald C, Palmateer N, McAuley A, Lindsay L, Hasan T, Hameed SS, Hall E, Jeffrey K, Grange Z, Gousias P, Mavin S, Jarvis L, Cameron JC, Daines L, Tibble H, Simpson CR, McCowan C, Katikireddi SV, Rudan I, Fagbamigbe AF, Ritchie L, Swallow B, Moss P, Robertson C, Sheikh A, Murray J.",
+    "id": "38553835",
+    "doi": "https://doi.org/10.1002/jcsm.13461",
+    "title": "Leukocyte telomere length is associated with MRI-thigh fat-free muscle volume: data from 16 356 UK Biobank adults.",
+    "authorString": "Kirk B, Kuo CL, Liu P, Xiang M, Earp JE, Kositsawat J, Kuchel GA, Duque G.",
     "authorAffiliations": "",
-    "journalTitle": "NPJ vaccines",
+    "journalTitle": "Journal of cachexia, sarcopenia and muscle",
     "pubYear": "2024",
-    "date": "2024-06-14",
+    "date": "2024-03-29",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Skeletal muscle; Cellular senescence; Trabecular Bone; Osteosarcopenia",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Several population-level studies have described individual clinical risk factors associated with suboptimal antibody responses following COVID-19 vaccination, but none have examined multimorbidity. Others have shown that suboptimal post-vaccination responses offer reduced protection to subsequent SARS-CoV-2 infection; however, the level of protection from COVID-19 hospitalisation/death remains unconfirmed. We use national Scottish datasets to investigate the association between multimorbidity and testing antibody-negative, examining the correlation between antibody levels and subsequent COVID-19 hospitalisation/death among double-vaccinated individuals. We found that individuals with multimorbidity (\u2009\u2265\u2009five conditions) were more likely to test antibody-negative post-vaccination and 13.37 [6.05-29.53] times more likely to be hospitalised/die from COVID-19 than individuals without conditions. We also show a dose-dependent association between post-vaccination antibody levels and COVID-19 hospitalisation or death, with those with undetectable antibody levels at a significantly higher risk (HR 9.21 [95% CI 4.63-18.29]) of these serious outcomes compared to those with high antibody levels.",
+    "abstract": "<h4>Background</h4>Telomere attrition may share common biological mechanisms with bone and muscle loss with aging. Here, we investigated the association between these hallmarks of aging using data from UK Biobank, a large observational study.<h4>Methods</h4>Leukocyte telomere length (LTL as T/S ratio) was measured using a multiplex qPCR assay at baseline (2006-2010). Bone mineral density (whole body and regional; via dual-energy X-ray absorptiometry), trabecular bone score (via lumbar-spine dual-energy X-ray absorptiometry images), fat-free muscle volume (thighs; via magnetic resonance imaging), and muscle fat infiltration (thighs; via magnetic resonance imaging) were measured during the imaging visit (2014-2018). Regression models were used to model LTL against a muscle or bone outcome, unadjusted and adjusted for covariates.<h4>Results</h4>A total of 16\u00a0356 adults (mean age: 62.8\u00a0\u00b1\u00a07.5\u00a0years, 50.5% women) were included. In the fully adjusted model, thigh fat-free muscle volume was associated with LTL in the overall sample (adjusted standardized \u03b2 (a\u03b2)\u00a0=\u00a00.017, 95% CI 0.009 to 0.026, P\u00a0<\u00a00.001, per SD increase in LTL), with stronger associations in men (a\u03b2\u00a0=\u00a00.022, 95% CI 0.010 to 0.034, P\u00a0<\u00a00.001) than in women (a\u03b2\u00a0=\u00a00.013, 95% CI 0.000 to 0.025, P\u00a0=\u00a00.041) (sex-LTL P\u00a0=\u00a00.028). The adjusted odds ratio (aOR) for low thigh fat-free muscle volume (body mass index-adjusted, sex-specific bottom 20%) was 0.93 per SD increase in LTL (95% CI 0.89 to 0.96, P\u00a0<\u00a00.001) in the overall sample, with stronger associations in men (aOR\u00a0=\u00a00.92, 95% CI 0.87 to 0.99, P\u00a0=\u00a00.008) than women (aOR\u00a0=\u00a00.93, 95% CI 0.88 to 0.98, P\u00a0=\u00a00.009), although the sex difference was not statistically significant in this model (sex-LTL P\u00a0=\u00a00.37). LTL was not associated with bone mineral density, trabecular bone score, or muscle fat infiltration in the overall or subgroup analyses (P\u00a0>\u00a00.05).<h4>Conclusions</h4>LTL was consistently associated with thigh fat-free muscle volume in men and women. Future research should investigate moderating effects of lifestyle factors (e.g., physical activity, nutrition, or chronic diseases) in the association between LTL and muscle volume.",
     "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41541-024-00898-w.pdf; doi:https://doi.org/10.1038/s41541-024-00898-w; html:https://europepmc.org/articles/PMC11178861; pdf:https://europepmc.org/articles/PMC11178861?pdf=render"
+    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jcsm.13461; doi:https://doi.org/10.1002/jcsm.13461; html:https://europepmc.org/articles/PMC11154769; pdf:https://europepmc.org/articles/PMC11154769?pdf=render"
   },
   {
-    "id": "37309989",
-    "doi": "https://doi.org/10.1002/pds.5656",
-    "title": "Prevalent new user designs: A literature review of current implementation practice.",
-    "authorString": "Tazare J, Gibbons DC, Bokern M, Williamson EJ, Gillespie IA, Cunnington M, Logie J, Douglas IJ.",
+    "id": "36332519",
+    "doi": "https://doi.org/10.1016/j.ijmedinf.2022.104905",
+    "title": "Creation of a core competency framework for clinical informatics: From genesis to maintaining relevance.",
+    "authorString": "Davies A, Hassey A, Williams J, Moulton G.",
     "authorAffiliations": "",
-    "journalTitle": "Pharmacoepidemiology and drug safety",
-    "pubYear": "2023",
-    "date": "2023-06-22",
+    "journalTitle": "International journal of medical informatics",
+    "pubYear": "2022",
+    "date": "2022-10-30",
     "isOpenAccess": "N",
-    "keywords": "Literature review; Database Research; Prevalent New User Designs",
+    "keywords": "Informatics; Core Competencies; Competency Framework; Healthcare Workforce; Informaticians",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Purpose</h4>Prevalent new user (PNU) designs extend the active comparator new user design by allowing for the inclusion of initiators of the study drug who were previously on a comparator treatment. We performed a literature review summarising current practice.<h4>Methods</h4>PubMed was searched for studies applying the PNU design since its proposal in 2017. The review focused on three components. First, we extracted information on the overall study design, including the database used. We summarised information on implementation of the PNU design, including key decisions relating to exposure set definition and estimation of time-conditional propensity scores. Finally, we reviewed the analysis strategy of the matched cohort.<h4>Results</h4>Nineteen studies met the criteria for inclusion. Most studies (73%) implemented the PNU design in electronic health record or registry databases, with the remaining using insurance claims databases. Of 15 studies including a class of prevalent users, 40% deviated from the original exposure set definition proposals in favour of a more complex definition. Four studies did not include prevalent new users but used other aspects of the PNU framework. Several studies lacked details on exposure set definition (n\u2009=\u20092), time-conditional propensity score model (n\u2009=\u20092) or integration of complex analytical techniques, such as the high-dimensional propensity score algorithm (n\u2009=\u20093).<h4>Conclusion</h4>PNU designs have been applied in a range of therapeutic and disease areas. However, to encourage more widespread use of this design and help shape best practice, there is a need for improved accessibility, specifically through the provision of analytical code alongside guidance to support implementation and transparent reporting.",
+    "abstract": "<h4>Background</h4>The United Kingdom's Faculty of Clinical Informatics (FCI) embarked on the creation of a core competency framework in response to the need to provide support to those working in clinical and health and social care that also hold informatics roles.<h4>Methods</h4>The work spanned several phases and utilised a mixed-methods approach consisting of interviews, surveys, job listing analysis, expert discussions and a systematic literature review. The work presented here explores the lessons learnt from the process of creating the framework and the next steps for ensuring its use and continued relevance.<h4>Results</h4>A core competency framework was generated with six domains, 36 sub-domains and 111 individual competency statements. A discussion and eight key recommendations are presented based on the development of this framework.<h4>Conclusion</h4>Definition of the target audience is important to manage scope and define purpose. The use of robust reproducible methods helps to establish a strong evidence base. Competency frameworks should be living documents, ideally presented in an accessible digital form to enable easy use and embedding in other tools (e.g. for accreditation or to search competencies).",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1002/pds.5656; doi:https://doi.org/10.1002/pds.5656"
+    "urls": "doi:https://doi.org/10.1016/j.ijmedinf.2022.104905"
   },
   {
     "id": "35796183",
@@ -3297,23 +3297,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1177/01410768221107119; doi:https://doi.org/10.1177/01410768221107119; html:https://europepmc.org/articles/PMC9747896; pdf:https://europepmc.org/articles/PMC9747896?pdf=render"
   },
-  {
-    "id": "38553835",
-    "doi": "https://doi.org/10.1002/jcsm.13461",
-    "title": "Leukocyte telomere length is associated with MRI-thigh fat-free muscle volume: data from 16 356 UK Biobank adults.",
-    "authorString": "Kirk B, Kuo CL, Liu P, Xiang M, Earp JE, Kositsawat J, Kuchel GA, Duque G.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of cachexia, sarcopenia and muscle",
-    "pubYear": "2024",
-    "date": "2024-03-29",
-    "isOpenAccess": "Y",
-    "keywords": "Skeletal muscle; Cellular senescence; Trabecular Bone; Osteosarcopenia",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Telomere attrition may share common biological mechanisms with bone and muscle loss with aging. Here, we investigated the association between these hallmarks of aging using data from UK Biobank, a large observational study.<h4>Methods</h4>Leukocyte telomere length (LTL as T/S ratio) was measured using a multiplex qPCR assay at baseline (2006-2010). Bone mineral density (whole body and regional; via dual-energy X-ray absorptiometry), trabecular bone score (via lumbar-spine dual-energy X-ray absorptiometry images), fat-free muscle volume (thighs; via magnetic resonance imaging), and muscle fat infiltration (thighs; via magnetic resonance imaging) were measured during the imaging visit (2014-2018). Regression models were used to model LTL against a muscle or bone outcome, unadjusted and adjusted for covariates.<h4>Results</h4>A total of 16\u00a0356 adults (mean age: 62.8\u00a0\u00b1\u00a07.5\u00a0years, 50.5% women) were included. In the fully adjusted model, thigh fat-free muscle volume was associated with LTL in the overall sample (adjusted standardized \u03b2 (a\u03b2)\u00a0=\u00a00.017, 95% CI 0.009 to 0.026, P\u00a0<\u00a00.001, per SD increase in LTL), with stronger associations in men (a\u03b2\u00a0=\u00a00.022, 95% CI 0.010 to 0.034, P\u00a0<\u00a00.001) than in women (a\u03b2\u00a0=\u00a00.013, 95% CI 0.000 to 0.025, P\u00a0=\u00a00.041) (sex-LTL P\u00a0=\u00a00.028). The adjusted odds ratio (aOR) for low thigh fat-free muscle volume (body mass index-adjusted, sex-specific bottom 20%) was 0.93 per SD increase in LTL (95% CI 0.89 to 0.96, P\u00a0<\u00a00.001) in the overall sample, with stronger associations in men (aOR\u00a0=\u00a00.92, 95% CI 0.87 to 0.99, P\u00a0=\u00a00.008) than women (aOR\u00a0=\u00a00.93, 95% CI 0.88 to 0.98, P\u00a0=\u00a00.009), although the sex difference was not statistically significant in this model (sex-LTL P\u00a0=\u00a00.37). LTL was not associated with bone mineral density, trabecular bone score, or muscle fat infiltration in the overall or subgroup analyses (P\u00a0>\u00a00.05).<h4>Conclusions</h4>LTL was consistently associated with thigh fat-free muscle volume in men and women. Future research should investigate moderating effects of lifestyle factors (e.g., physical activity, nutrition, or chronic diseases) in the association between LTL and muscle volume.",
-    "laySummary": "",
-    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jcsm.13461; doi:https://doi.org/10.1002/jcsm.13461; html:https://europepmc.org/articles/PMC11154769; pdf:https://europepmc.org/articles/PMC11154769?pdf=render"
-  },
   {
     "id": "38237625",
     "doi": "https://doi.org/10.1016/s0140-6736(23)02467-4",
@@ -3331,6 +3314,23 @@
     "laySummary": "",
     "urls": "pdf:http://www.thelancet.com/article/S0140673623024674/pdf; doi:https://doi.org/10.1016/S0140-6736(23)02467-4"
   },
+  {
+    "id": "37309989",
+    "doi": "https://doi.org/10.1002/pds.5656",
+    "title": "Prevalent new user designs: A literature review of current implementation practice.",
+    "authorString": "Tazare J, Gibbons DC, Bokern M, Williamson EJ, Gillespie IA, Cunnington M, Logie J, Douglas IJ.",
+    "authorAffiliations": "",
+    "journalTitle": "Pharmacoepidemiology and drug safety",
+    "pubYear": "2023",
+    "date": "2023-06-22",
+    "isOpenAccess": "N",
+    "keywords": "Literature review; Database Research; Prevalent New User Designs",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Purpose</h4>Prevalent new user (PNU) designs extend the active comparator new user design by allowing for the inclusion of initiators of the study drug who were previously on a comparator treatment. We performed a literature review summarising current practice.<h4>Methods</h4>PubMed was searched for studies applying the PNU design since its proposal in 2017. The review focused on three components. First, we extracted information on the overall study design, including the database used. We summarised information on implementation of the PNU design, including key decisions relating to exposure set definition and estimation of time-conditional propensity scores. Finally, we reviewed the analysis strategy of the matched cohort.<h4>Results</h4>Nineteen studies met the criteria for inclusion. Most studies (73%) implemented the PNU design in electronic health record or registry databases, with the remaining using insurance claims databases. Of 15 studies including a class of prevalent users, 40% deviated from the original exposure set definition proposals in favour of a more complex definition. Four studies did not include prevalent new users but used other aspects of the PNU framework. Several studies lacked details on exposure set definition (n\u2009=\u20092), time-conditional propensity score model (n\u2009=\u20092) or integration of complex analytical techniques, such as the high-dimensional propensity score algorithm (n\u2009=\u20093).<h4>Conclusion</h4>PNU designs have been applied in a range of therapeutic and disease areas. However, to encourage more widespread use of this design and help shape best practice, there is a need for improved accessibility, specifically through the provision of analytical code alongside guidance to support implementation and transparent reporting.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1002/pds.5656; doi:https://doi.org/10.1002/pds.5656"
+  },
   {
     "id": "34216888",
     "doi": "https://doi.org/10.1016/j.compbiomed.2021.104556",
@@ -3382,23 +3382,6 @@
     "laySummary": "",
     "urls": "pdf:https://aura.abdn.ac.uk/bitstream/2164/18748/1/Sheikh_etal_LID_Severity_Omicron_Variant_VOR.pdf; doi:https://doi.org/10.1016/S1473-3099(22)00141-4; html:https://europepmc.org/articles/PMC9033213"
   },
-  {
-    "id": "39119202",
-    "doi": "https://doi.org/10.1093/ehjopen/oeae059",
-    "title": "Ventricular volume asymmetry as a novel imaging biomarker for disease discrimination and outcome prediction.",
-    "authorString": "McCracken C, Szabo L, Abdulelah ZA, Condurache DG, Vago H, Nichols TE, Petersen SE, Neubauer S, Raisi-Estabragh Z.",
-    "authorAffiliations": "",
-    "journalTitle": "European heart journal open",
-    "pubYear": "2024",
-    "date": "2024-07-25",
-    "isOpenAccess": "Y",
-    "keywords": "Cardiovascular disease; epidemiology; Cardiovascular Risk; Cardiovascular Magnetic Resonance; Imaging Biomarkers; Uk Biobank",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Aims</h4>Disruption of the predictable symmetry of the healthy heart may be an indicator of cardiovascular risk. This study defines the population distribution of ventricular asymmetry and its relationships across a range of prevalent and incident cardiorespiratory diseases.<h4>Methods and results</h4>The analysis includes 44 796 UK Biobank participants (average age 64.1 \u00b1 7.7 years; 51.9% women). Cardiovascular magnetic resonance (CMR) metrics were derived using previously validated automated pipelines. Ventricular asymmetry was expressed as the ratio of left and right ventricular (LV and RV) end-diastolic volumes. Clinical outcomes were defined through linked health records. Incident events were those occurring for the first time after imaging, longitudinally tracked over an average follow-up time of 4.75 \u00b1 1.52 years. The normal range for ventricular symmetry was defined in a healthy subset. Participants with values outside the 5th-95th percentiles of the healthy distribution were classed as either LV dominant (LV/RV > 112%) or RV dominant (LV/RV < 80%) asymmetry. Associations of LV and RV dominant asymmetry with vascular risk factors, CMR features, and prevalent and incident cardiovascular diseases (CVDs) were examined using regression models, adjusting for vascular risk factors, prevalent diseases, and conventional CMR measures. Left ventricular dominance was linked to an array of pre-existing vascular risk factors and CVDs, and a two-fold increased risk of incident heart failure, non-ischaemic cardiomyopathies, and left-sided valvular disorders. Right ventricular dominance was associated with an elevated risk of all-cause mortality.<h4>Conclusion</h4>Ventricular asymmetry has clinical utility for cardiovascular risk assessment, providing information that is incremental to traditional risk factors and conventional CMR metrics.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1093/ehjopen/oeae059; html:https://europepmc.org/articles/PMC11306927; pdf:https://europepmc.org/articles/PMC11306927?pdf=render"
-  },
   {
     "id": "39411544",
     "doi": "https://doi.org/10.1177/20552076241287450",
@@ -3416,6 +3399,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1177/20552076241287450; html:https://europepmc.org/articles/PMC11475109; pdf:https://europepmc.org/articles/PMC11475109?pdf=render"
   },
+  {
+    "id": "39119202",
+    "doi": "https://doi.org/10.1093/ehjopen/oeae059",
+    "title": "Ventricular volume asymmetry as a novel imaging biomarker for disease discrimination and outcome prediction.",
+    "authorString": "McCracken C, Szabo L, Abdulelah ZA, Condurache DG, Vago H, Nichols TE, Petersen SE, Neubauer S, Raisi-Estabragh Z.",
+    "authorAffiliations": "",
+    "journalTitle": "European heart journal open",
+    "pubYear": "2024",
+    "date": "2024-07-25",
+    "isOpenAccess": "Y",
+    "keywords": "Cardiovascular disease; epidemiology; Cardiovascular Risk; Cardiovascular Magnetic Resonance; Imaging Biomarkers; Uk Biobank",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Aims</h4>Disruption of the predictable symmetry of the healthy heart may be an indicator of cardiovascular risk. This study defines the population distribution of ventricular asymmetry and its relationships across a range of prevalent and incident cardiorespiratory diseases.<h4>Methods and results</h4>The analysis includes 44 796 UK Biobank participants (average age 64.1 \u00b1 7.7 years; 51.9% women). Cardiovascular magnetic resonance (CMR) metrics were derived using previously validated automated pipelines. Ventricular asymmetry was expressed as the ratio of left and right ventricular (LV and RV) end-diastolic volumes. Clinical outcomes were defined through linked health records. Incident events were those occurring for the first time after imaging, longitudinally tracked over an average follow-up time of 4.75 \u00b1 1.52 years. The normal range for ventricular symmetry was defined in a healthy subset. Participants with values outside the 5th-95th percentiles of the healthy distribution were classed as either LV dominant (LV/RV > 112%) or RV dominant (LV/RV < 80%) asymmetry. Associations of LV and RV dominant asymmetry with vascular risk factors, CMR features, and prevalent and incident cardiovascular diseases (CVDs) were examined using regression models, adjusting for vascular risk factors, prevalent diseases, and conventional CMR measures. Left ventricular dominance was linked to an array of pre-existing vascular risk factors and CVDs, and a two-fold increased risk of incident heart failure, non-ischaemic cardiomyopathies, and left-sided valvular disorders. Right ventricular dominance was associated with an elevated risk of all-cause mortality.<h4>Conclusion</h4>Ventricular asymmetry has clinical utility for cardiovascular risk assessment, providing information that is incremental to traditional risk factors and conventional CMR metrics.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1093/ehjopen/oeae059; html:https://europepmc.org/articles/PMC11306927; pdf:https://europepmc.org/articles/PMC11306927?pdf=render"
+  },
   {
     "id": "38905569",
     "doi": "https://doi.org/10.1056/evidoa2400179",
@@ -3467,23 +3467,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmcnephrol.biomedcentral.com/counter/pdf/10.1186/s12882-022-03031-y; doi:https://doi.org/10.1186/s12882-022-03031-y; html:https://europepmc.org/articles/PMC9843843; pdf:https://europepmc.org/articles/PMC9843843?pdf=render"
   },
-  {
-    "id": "35909577",
-    "doi": "https://doi.org/10.23889/ijpds.v7i1.1725",
-    "title": "Educational achievements of children aged 10-11 years with cystic fibrosis. A data linkage study in Wales.",
-    "authorString": "Schl\u00fcter DK, Griffiths R, Akbari A, Taylor-Robinson D.",
-    "authorAffiliations": "",
-    "journalTitle": "International journal of population data science",
-    "pubYear": "2022",
-    "date": "2022-06-27",
-    "isOpenAccess": "Y",
-    "keywords": "Education; Cystic Fibrosis; Data Linkage; Sail Databank",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>As people with cystic fibrosis (CF) lead longer, healthier lives, educational qualifications and employment prospects are increasingly important. However, little is known about the social consequences of CF, in particular, any impact on educational achievements and the support children with CF receive in schools.<h4>Objectives</h4>To assess the educational achievements of children with CF in Wales compared to the general Welsh population, and the additional learning support children with CF receive in schools.<h4>Methods</h4>We conducted a population-scale data linkage study of all children born in Wales using the Secure Anonymised Information Linkage (SAIL) Databank. We used anonymised individual-level population-scale health and administrative data sources to identify children with CF born between 2000 - 2015, linked to educational attainment records. We calculated the percentage of children that reached expected levels in statutory assessment at age 10-11, Key Stage 2 (KS2), and compared this to educational outcomes in the general population. We also assessed the percentage of children with CF that received extra learning support.<h4>Results</h4>Out of 150 eligible children, 119 had KS2 results. 77% (95% CI: 69%-84%) of children achieved expected levels in English, 81% (95% CI: 73% -87%) in Mathematics and 82% (95% CI: 75% - 88%) in Science. In the comparable general Welsh population, 83.4% to 91.1% achieved the expected level in English, 84.9% to 91.6% in Maths, and 87.1% to 92.2% in Science across the years of the study. 70% of children with CF received extra learning support.<h4>Conclusions</h4>Children with CF in Wales may have worse educational achievements than the general population. More research is needed to inform policies and interventions to better support children with CF to reach their full educational potential and employment opportunities.",
-    "laySummary": "",
-    "urls": "pdf:https://ijpds.org/article/download/1725/3455; doi:https://doi.org/10.23889/ijpds.v7i1.1725; html:https://europepmc.org/articles/PMC9284509; pdf:https://europepmc.org/articles/PMC9284509?pdf=render"
-  },
   {
     "id": "36447940",
     "doi": "https://doi.org/10.1016/s2665-9913(22)00305-8",
@@ -3501,6 +3484,23 @@
     "laySummary": "",
     "urls": "pdf:https://researchonline.lshtm.ac.uk/id/eprint/4669009/1/Russell_etal_2022_Incidence-and-management-of-inflammatory.pdf; doi:https://doi.org/10.1016/S2665-9913(22)00305-8; html:https://europepmc.org/articles/PMC9691150; pdf:https://europepmc.org/articles/PMC9691150?pdf=render"
   },
+  {
+    "id": "35909577",
+    "doi": "https://doi.org/10.23889/ijpds.v7i1.1725",
+    "title": "Educational achievements of children aged 10-11 years with cystic fibrosis. A data linkage study in Wales.",
+    "authorString": "Schl\u00fcter DK, Griffiths R, Akbari A, Taylor-Robinson D.",
+    "authorAffiliations": "",
+    "journalTitle": "International journal of population data science",
+    "pubYear": "2022",
+    "date": "2022-06-27",
+    "isOpenAccess": "Y",
+    "keywords": "Education; Cystic Fibrosis; Data Linkage; Sail Databank",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>As people with cystic fibrosis (CF) lead longer, healthier lives, educational qualifications and employment prospects are increasingly important. However, little is known about the social consequences of CF, in particular, any impact on educational achievements and the support children with CF receive in schools.<h4>Objectives</h4>To assess the educational achievements of children with CF in Wales compared to the general Welsh population, and the additional learning support children with CF receive in schools.<h4>Methods</h4>We conducted a population-scale data linkage study of all children born in Wales using the Secure Anonymised Information Linkage (SAIL) Databank. We used anonymised individual-level population-scale health and administrative data sources to identify children with CF born between 2000 - 2015, linked to educational attainment records. We calculated the percentage of children that reached expected levels in statutory assessment at age 10-11, Key Stage 2 (KS2), and compared this to educational outcomes in the general population. We also assessed the percentage of children with CF that received extra learning support.<h4>Results</h4>Out of 150 eligible children, 119 had KS2 results. 77% (95% CI: 69%-84%) of children achieved expected levels in English, 81% (95% CI: 73% -87%) in Mathematics and 82% (95% CI: 75% - 88%) in Science. In the comparable general Welsh population, 83.4% to 91.1% achieved the expected level in English, 84.9% to 91.6% in Maths, and 87.1% to 92.2% in Science across the years of the study. 70% of children with CF received extra learning support.<h4>Conclusions</h4>Children with CF in Wales may have worse educational achievements than the general population. More research is needed to inform policies and interventions to better support children with CF to reach their full educational potential and employment opportunities.",
+    "laySummary": "",
+    "urls": "pdf:https://ijpds.org/article/download/1725/3455; doi:https://doi.org/10.23889/ijpds.v7i1.1725; html:https://europepmc.org/articles/PMC9284509; pdf:https://europepmc.org/articles/PMC9284509?pdf=render"
+  },
   {
     "id": "37726825",
     "doi": "https://doi.org/10.1186/s13063-023-07606-4",
@@ -3552,6 +3552,23 @@
     "laySummary": "",
     "urls": "pdf:https://discovery.ucl.ac.uk/10138810/1/ForUCLDiscovery.pdf; doi:https://doi.org/10.1101/cshperspect.a039230; html:https://europepmc.org/articles/PMC8805642; pdf:https://europepmc.org/articles/PMC8805642?pdf=render; doi:https://doi.org/10.1101/cshperspect.a039230"
   },
+  {
+    "id": "37169862",
+    "doi": "https://doi.org/10.1038/s41591-023-02343-2",
+    "title": "Accelerated waning of the humoral response to COVID-19 vaccines in obesity.",
+    "authorString": "van der Klaauw AA, Horner EC, Pereyra-Gerber P, Agrawal U, Foster WS, Spencer S, Vergese B, Smith M, Henning E, Ramsay ID, Smith JA, Guillaume SM, Sharpe HJ, Hay IM, Thompson S, Innocentin S, Booth LH, Robertson C, McCowan C, Kerr S, Mulroney TE, O'Reilly MJ, Gurugama TP, Gurugama LP, Rust MA, Ferreira A, Ebrahimi S, Ceron-Gutierrez L, Scotucci J, Kronsteiner B, Dunachie SJ, Klenerman P, PITCH Consortium, Park AJ, Rubino F, Lamikanra AA, Stark H, Kingston N, Estcourt L, Harvala H, Roberts DJ, Doffinger R, Linterman MA, Matheson NJ, Sheikh A, Farooqi IS, Thaventhiran JED.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature medicine",
+    "pubYear": "2023",
+    "date": "2023-05-11",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Obesity is associated with an increased risk of severe Coronavirus Disease 2019 (COVID-19) infection and mortality. COVID-19 vaccines reduce the risk of serious COVID-19 outcomes; however, their effectiveness in people with obesity is incompletely understood. We studied the relationship among body mass index (BMI), hospitalization and mortality due to COVID-19 among 3.6 million people in Scotland using the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) surveillance platform. We found that vaccinated individuals with severe obesity (BMI\u2009>\u200940\u2009kg/m<sup>2</sup>) were 76% more likely to experience hospitalization or death from COVID-19 (adjusted rate ratio of 1.76 (95% confidence interval (CI), 1.60-1.94). We also conducted a prospective longitudinal study of a cohort of 28 individuals with severe obesity compared to 41 control individuals with normal BMI (BMI 18.5-24.9\u2009kg/m<sup>2</sup>). We found that 55% of individuals with severe obesity had unquantifiable titers of neutralizing antibody against authentic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus compared to 12% of individuals with normal BMI (P\u2009=\u20090.0003) 6\u2009months after their second vaccine dose. Furthermore, we observed that, for individuals with severe obesity, at any given anti-spike and anti-receptor-binding domain (RBD) antibody level, neutralizing capacity was lower than that of individuals with a normal BMI. Neutralizing capacity was restored by a third dose of vaccine but again declined more rapidly in people with severe obesity. We demonstrate that waning of COVID-19 vaccine-induced humoral immunity is accelerated in individuals with severe obesity. As obesity is associated with increased hospitalization and mortality from breakthrough infections, our findings have implications for vaccine prioritization policies.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41591-023-02343-2.pdf; doi:https://doi.org/10.1038/s41591-023-02343-2; html:https://europepmc.org/articles/PMC10202802; pdf:https://europepmc.org/articles/PMC10202802?pdf=render"
+  },
   {
     "id": "35915784",
     "doi": "https://doi.org/10.1016/j.lanepe.2022.100462",
@@ -3569,23 +3586,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.lanepe.2022.100462; doi:https://doi.org/10.1016/j.lanepe.2022.100462; html:https://europepmc.org/articles/PMC9330654; pdf:https://europepmc.org/articles/PMC9330654?pdf=render"
   },
-  {
-    "id": "38045451",
-    "doi": "https://doi.org/10.1002/joa3.12927",
-    "title": "Using machine learning to enhance prediction of atrial fibrillation recurrence after catheter ablation.",
-    "authorString": "Brahier MS, Zou F, Abdulkareem M, Kochi S, Migliarese F, Thomaides A, Ma X, Wu C, Sandfort V, Bergquist PJ, Srichai MB, Piccini JP, Petersen SE, Vargas JD.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of arrhythmia",
-    "pubYear": "2023",
-    "date": "2023-10-05",
-    "isOpenAccess": "Y",
-    "keywords": "Atrial fibrillation; Catheter ablation; Cardiac Computed Tomography; Machine Learning; Left Atrium",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Traditional risk scores for recurrent atrial fibrillation (AF) following catheter ablation utilize readily available clinical and echocardiographic variables and yet have limited discriminatory capacity. Use of data from cardiac imaging and deep learning may help improve accuracy and prediction of recurrent AF after ablation.<h4>Methods</h4>We evaluated patients with symptomatic, drug-refractory AF undergoing catheter ablation. All patients underwent pre-ablation cardiac computed tomography (cCT). LAVi was computed using a deep-learning algorithm. In a two-step analysis, random survival forest (RSF) was used to generate prognostic models with variables of highest importance, followed by Cox proportional hazard regression analysis of the selected variables. Events of interest included early and late recurrence.<h4>Results</h4>Among 653 patients undergoing AF ablation, the most important factors associated with late recurrence by RSF analysis at 24 (+/-18) months follow-up included LAVi and early recurrence. In total, 5 covariates were identified as independent predictors of late recurrence: LAVi (HR per mL/m<sup>2</sup> 1.01 [1.01-1.02]; <i>p</i>\u2009<\u2009.001), early recurrence (HR 2.42 [1.90-3.09]; <i>p</i>\u2009<\u2009.001), statin use (HR 1.38 [1.09-1.75]; <i>p</i>\u2009=\u2009.007), beta-blocker use (HR 1.29 [1.01-1.65]; <i>p</i>\u2009=\u2009.043), and adjunctive cavotricuspid isthmus ablation [HR 0.74 (0.57-0.96); <i>p</i>\u2009=\u2009.02]. Survival analysis demonstrated that patients with both LAVi >66.7\u2009mL/m<sup>2</sup> and early recurrence had the highest risk of late recurrence risk compared with those with LAVi <66.7\u2009mL/m<sup>2</sup> and no early recurrence (HR 4.52 [3.36-6.08], <i>p</i>\u2009<\u2009.001).<h4>Conclusions</h4>Machine learning-derived, full volumetric LAVi from cCT is the most important pre-procedural risk factor for late AF recurrence following catheter ablation. The combination of increased LAVi and early recurrence confers more than a four-fold increased risk of late recurrence.",
-    "laySummary": "",
-    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/joa3.12927; doi:https://doi.org/10.1002/joa3.12927; html:https://europepmc.org/articles/PMC10692862; pdf:https://europepmc.org/articles/PMC10692862?pdf=render"
-  },
   {
     "id": "35780805",
     "doi": "https://doi.org/10.1016/s2213-8587(22)00158-9",
@@ -3604,21 +3604,21 @@
     "urls": "pdf:http://www.thelancet.com/article/S2213858722001589/pdf; doi:https://doi.org/10.1016/S2213-8587(22)00158-9; html:https://europepmc.org/articles/PMC9246477; pdf:https://europepmc.org/articles/PMC9246477?pdf=render"
   },
   {
-    "id": "37169862",
-    "doi": "https://doi.org/10.1038/s41591-023-02343-2",
-    "title": "Accelerated waning of the humoral response to COVID-19 vaccines in obesity.",
-    "authorString": "van der Klaauw AA, Horner EC, Pereyra-Gerber P, Agrawal U, Foster WS, Spencer S, Vergese B, Smith M, Henning E, Ramsay ID, Smith JA, Guillaume SM, Sharpe HJ, Hay IM, Thompson S, Innocentin S, Booth LH, Robertson C, McCowan C, Kerr S, Mulroney TE, O'Reilly MJ, Gurugama TP, Gurugama LP, Rust MA, Ferreira A, Ebrahimi S, Ceron-Gutierrez L, Scotucci J, Kronsteiner B, Dunachie SJ, Klenerman P, PITCH Consortium, Park AJ, Rubino F, Lamikanra AA, Stark H, Kingston N, Estcourt L, Harvala H, Roberts DJ, Doffinger R, Linterman MA, Matheson NJ, Sheikh A, Farooqi IS, Thaventhiran JED.",
+    "id": "38045451",
+    "doi": "https://doi.org/10.1002/joa3.12927",
+    "title": "Using machine learning to enhance prediction of atrial fibrillation recurrence after catheter ablation.",
+    "authorString": "Brahier MS, Zou F, Abdulkareem M, Kochi S, Migliarese F, Thomaides A, Ma X, Wu C, Sandfort V, Bergquist PJ, Srichai MB, Piccini JP, Petersen SE, Vargas JD.",
     "authorAffiliations": "",
-    "journalTitle": "Nature medicine",
+    "journalTitle": "Journal of arrhythmia",
     "pubYear": "2023",
-    "date": "2023-05-11",
+    "date": "2023-10-05",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Atrial fibrillation; Catheter ablation; Cardiac Computed Tomography; Machine Learning; Left Atrium",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Obesity is associated with an increased risk of severe Coronavirus Disease 2019 (COVID-19) infection and mortality. COVID-19 vaccines reduce the risk of serious COVID-19 outcomes; however, their effectiveness in people with obesity is incompletely understood. We studied the relationship among body mass index (BMI), hospitalization and mortality due to COVID-19 among 3.6 million people in Scotland using the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) surveillance platform. We found that vaccinated individuals with severe obesity (BMI\u2009>\u200940\u2009kg/m<sup>2</sup>) were 76% more likely to experience hospitalization or death from COVID-19 (adjusted rate ratio of 1.76 (95% confidence interval (CI), 1.60-1.94). We also conducted a prospective longitudinal study of a cohort of 28 individuals with severe obesity compared to 41 control individuals with normal BMI (BMI 18.5-24.9\u2009kg/m<sup>2</sup>). We found that 55% of individuals with severe obesity had unquantifiable titers of neutralizing antibody against authentic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus compared to 12% of individuals with normal BMI (P\u2009=\u20090.0003) 6\u2009months after their second vaccine dose. Furthermore, we observed that, for individuals with severe obesity, at any given anti-spike and anti-receptor-binding domain (RBD) antibody level, neutralizing capacity was lower than that of individuals with a normal BMI. Neutralizing capacity was restored by a third dose of vaccine but again declined more rapidly in people with severe obesity. We demonstrate that waning of COVID-19 vaccine-induced humoral immunity is accelerated in individuals with severe obesity. As obesity is associated with increased hospitalization and mortality from breakthrough infections, our findings have implications for vaccine prioritization policies.",
+    "abstract": "<h4>Background</h4>Traditional risk scores for recurrent atrial fibrillation (AF) following catheter ablation utilize readily available clinical and echocardiographic variables and yet have limited discriminatory capacity. Use of data from cardiac imaging and deep learning may help improve accuracy and prediction of recurrent AF after ablation.<h4>Methods</h4>We evaluated patients with symptomatic, drug-refractory AF undergoing catheter ablation. All patients underwent pre-ablation cardiac computed tomography (cCT). LAVi was computed using a deep-learning algorithm. In a two-step analysis, random survival forest (RSF) was used to generate prognostic models with variables of highest importance, followed by Cox proportional hazard regression analysis of the selected variables. Events of interest included early and late recurrence.<h4>Results</h4>Among 653 patients undergoing AF ablation, the most important factors associated with late recurrence by RSF analysis at 24 (+/-18) months follow-up included LAVi and early recurrence. In total, 5 covariates were identified as independent predictors of late recurrence: LAVi (HR per mL/m<sup>2</sup> 1.01 [1.01-1.02]; <i>p</i>\u2009<\u2009.001), early recurrence (HR 2.42 [1.90-3.09]; <i>p</i>\u2009<\u2009.001), statin use (HR 1.38 [1.09-1.75]; <i>p</i>\u2009=\u2009.007), beta-blocker use (HR 1.29 [1.01-1.65]; <i>p</i>\u2009=\u2009.043), and adjunctive cavotricuspid isthmus ablation [HR 0.74 (0.57-0.96); <i>p</i>\u2009=\u2009.02]. Survival analysis demonstrated that patients with both LAVi >66.7\u2009mL/m<sup>2</sup> and early recurrence had the highest risk of late recurrence risk compared with those with LAVi <66.7\u2009mL/m<sup>2</sup> and no early recurrence (HR 4.52 [3.36-6.08], <i>p</i>\u2009<\u2009.001).<h4>Conclusions</h4>Machine learning-derived, full volumetric LAVi from cCT is the most important pre-procedural risk factor for late AF recurrence following catheter ablation. The combination of increased LAVi and early recurrence confers more than a four-fold increased risk of late recurrence.",
     "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41591-023-02343-2.pdf; doi:https://doi.org/10.1038/s41591-023-02343-2; html:https://europepmc.org/articles/PMC10202802; pdf:https://europepmc.org/articles/PMC10202802?pdf=render"
+    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/joa3.12927; doi:https://doi.org/10.1002/joa3.12927; html:https://europepmc.org/articles/PMC10692862; pdf:https://europepmc.org/articles/PMC10692862?pdf=render"
   },
   {
     "id": "36749628",
@@ -3688,23 +3688,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ageing/article-pdf/50/1/25/42362959/afaa207.pdf; doi:https://doi.org/10.1093/ageing/afaa207; html:https://europepmc.org/articles/PMC7546151; pdf:https://europepmc.org/articles/PMC7546151?pdf=render"
   },
-  {
-    "id": "32741245",
-    "doi": "https://doi.org/10.1177/0954411920946526",
-    "title": "Artificial intelligence approaches to predict coronary stenosis severity using non-invasive fractional flow reserve.",
-    "authorString": "Carson JM, Chakshu NK, Sazonov I, Nithiarasu P.",
-    "authorAffiliations": "",
-    "journalTitle": "Proceedings of the Institution of Mechanical Engineers. Part H, Journal of engineering in medicine",
-    "pubYear": "2020",
-    "date": "2020-08-03",
-    "isOpenAccess": "Y",
-    "keywords": "Artificial intelligence; Biomedical engineering; Coronary Heart Disease; Fractional Flow Reserve; Computational Mechanics; Haemodynamic Modelling",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Fractional flow reserve is the current reference standard in the assessment of the functional impact of a stenosis in coronary heart disease. In this study, three models of artificial intelligence of varying degrees of complexity were compared to fractional flow reserve measurements. The three models are the multivariate polynomial regression, which is a statistical method used primarily for correlation; the feed-forward neural network; and the long short-term memory, which is a type of recurrent neural network that is suited to modelling sequences. The models were initially trained using a virtual patient database that was generated from a validated one-dimensional physics-based model. The feed-forward neural network performed the best for all test cases considered, which were a single vessel case from a virtual patient database, a multi-vessel network from a virtual patient database, and 25 clinically invasive fractional flow reserve measurements from real patients. The feed-forward neural network model achieved around 99% diagnostic accuracy in both tests involving virtual patients, and a respectable 72% diagnostic accuracy when compared to the invasive fractional flow reserve measurements. The multivariate polynomial regression model performed well in the single vessel case, but struggled on network cases as the variation of input features was much larger. The long short-term memory performed well for the single vessel cases, but tended to have a bias towards a positive fractional flow reserve prediction for the virtual multi-vessel case, and for the patient cases. Overall, the feed-forward neural network shows promise in successfully predicting fractional flow reserve in real patients, and could be a viable option if trained using a large enough data set of real patients.",
-    "laySummary": "",
-    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/0954411920946526; doi:https://doi.org/10.1177/0954411920946526; html:https://europepmc.org/articles/PMC7675765; pdf:https://europepmc.org/articles/PMC7675765?pdf=render"
-  },
   {
     "id": "38809392",
     "doi": "https://doi.org/10.1007/s11357-024-01202-3",
@@ -3740,21 +3723,38 @@
     "urls": "pdf:https://bmjmedicine.bmj.com/content/bmjmed/2/1/e000371.full.pdf; doi:https://doi.org/10.1136/bmjmed-2022-000371; html:https://europepmc.org/articles/PMC9951384; pdf:https://europepmc.org/articles/PMC9951384?pdf=render"
   },
   {
-    "id": "34713086",
-    "doi": "https://doi.org/10.3389/fdgth.2021.598916",
-    "title": "Markup: A Web-Based Annotation Tool Powered by Active Learning.",
-    "authorString": "Dobbie S, Strafford H, Pickrell WO, Fonferko-Shadrach B, Jones C, Akbari A, Thompson S, Lacey A.",
+    "id": "32741245",
+    "doi": "https://doi.org/10.1177/0954411920946526",
+    "title": "Artificial intelligence approaches to predict coronary stenosis severity using non-invasive fractional flow reserve.",
+    "authorString": "Carson JM, Chakshu NK, Sazonov I, Nithiarasu P.",
     "authorAffiliations": "",
-    "journalTitle": "Frontiers in digital health",
-    "pubYear": "2021",
-    "date": "2021-07-26",
+    "journalTitle": "Proceedings of the Institution of Mechanical Engineers. Part H, Journal of engineering in medicine",
+    "pubYear": "2020",
+    "date": "2020-08-03",
     "isOpenAccess": "Y",
-    "keywords": "Active Learning; Annotation; Natural Language Processing; Unstructured Text; Sequence-to-sequence Learning",
+    "keywords": "Artificial intelligence; Biomedical engineering; Coronary Heart Disease; Fractional Flow Reserve; Computational Mechanics; Haemodynamic Modelling",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Across various domains, such as health and social care, law, news, and social media, there are increasing quantities of unstructured texts being produced. These potential data sources often contain rich information that could be used for domain-specific and research purposes. However, the unstructured nature of free-text data poses a significant challenge for its utilisation due to the necessity of substantial manual intervention from domain-experts to label embedded information. Annotation tools can assist with this process by providing functionality that enables the accurate capture and transformation of unstructured texts into structured annotations, which can be used individually, or as part of larger Natural Language Processing (NLP) pipelines. We present Markup (https://www.getmarkup.com/) an open-source, web-based annotation tool that is undergoing continued development for use across all domains. Markup incorporates NLP and Active Learning (AL) technologies to enable rapid and accurate annotation using custom user configurations, predictive annotation suggestions, and automated mapping suggestions to both domain-specific ontologies, such as the Unified Medical Language System (UMLS), and custom, user-defined ontologies. We demonstrate a real-world use case of how Markup has been used in a healthcare setting to annotate structured information from unstructured clinic letters, where captured annotations were used to build and test NLP applications.",
+    "abstract": "Fractional flow reserve is the current reference standard in the assessment of the functional impact of a stenosis in coronary heart disease. In this study, three models of artificial intelligence of varying degrees of complexity were compared to fractional flow reserve measurements. The three models are the multivariate polynomial regression, which is a statistical method used primarily for correlation; the feed-forward neural network; and the long short-term memory, which is a type of recurrent neural network that is suited to modelling sequences. The models were initially trained using a virtual patient database that was generated from a validated one-dimensional physics-based model. The feed-forward neural network performed the best for all test cases considered, which were a single vessel case from a virtual patient database, a multi-vessel network from a virtual patient database, and 25 clinically invasive fractional flow reserve measurements from real patients. The feed-forward neural network model achieved around 99% diagnostic accuracy in both tests involving virtual patients, and a respectable 72% diagnostic accuracy when compared to the invasive fractional flow reserve measurements. The multivariate polynomial regression model performed well in the single vessel case, but struggled on network cases as the variation of input features was much larger. The long short-term memory performed well for the single vessel cases, but tended to have a bias towards a positive fractional flow reserve prediction for the virtual multi-vessel case, and for the patient cases. Overall, the feed-forward neural network shows promise in successfully predicting fractional flow reserve in real patients, and could be a viable option if trained using a large enough data set of real patients.",
     "laySummary": "",
-    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fdgth.2021.598916/pdf; doi:https://doi.org/10.3389/fdgth.2021.598916; html:https://europepmc.org/articles/PMC8521860; pdf:https://europepmc.org/articles/PMC8521860?pdf=render"
+    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/0954411920946526; doi:https://doi.org/10.1177/0954411920946526; html:https://europepmc.org/articles/PMC7675765; pdf:https://europepmc.org/articles/PMC7675765?pdf=render"
+  },
+  {
+    "id": "34864250",
+    "doi": "https://doi.org/10.1016/j.seizure.2021.11.017",
+    "title": "Epilepsy mortality in Wales during COVID-19.",
+    "authorString": "Daniels H, Lacey AS, Mikadze D, Akbari A, Fonferko-Shadrach B, Hollinghurst J, Lyons RA, Rees MI, Sawhney IM, Powell RH, Kerr MP, Pickrell WO.",
+    "authorAffiliations": "",
+    "journalTitle": "Seizure",
+    "pubYear": "2022",
+    "date": "2021-11-27",
+    "isOpenAccess": "Y",
+    "keywords": "Pandemic; Data Linkage; Electronic Health Records; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Purpose</h4>The COVID-19 pandemic has increased mortality worldwide and those with chronic conditions may have been disproportionally affected. However, it is unknown whether the pandemic has changed mortality rates for people with epilepsy. We aimed to compare mortality rates in people with epilepsy in Wales during the pandemic with pre-pandemic rates.<h4>Methods</h4>We performed a retrospective study using individual-level linked population-scale anonymised electronic health records. We identified deaths in people with epilepsy (DPWE), i.e. those with a diagnosis of epilepsy, and deaths associated with epilepsy (DAE), where epilepsy was recorded as a cause of death on death certificates. We compared death rates in 2020 with average rates in 2015-2019 using Poisson models to calculate death rate ratios.<h4>Results</h4>There were 188 DAE and 628 DPWE in Wales in 2020 (death rates: 7.7/100,000/year and 25.7/100,000/year). The average rates for DAE and DPWE from 2015 to 2019 were 5.8/100,000/year and 23.8/100,000/year, respectively. Death rate ratios (2020 compared to 2015-2019) for DAE were 1.34 (95%CI 1.14-1.57, p<0.001) and for DPWE were 1.08 (0.99-1.17, p\u00a0=\u00a00.09). The death rate ratios for non-COVID deaths (deaths without COVID mentioned on death certificates) for DAE were 1.17 (0.99-1.39, p\u00a0=\u00a00.06) and for DPWE were 0.96 (0.87-1.05, p\u00a0=\u00a00.37).<h4>Conclusions</h4>The significant increase in DAE in Wales during 2020 could be explained by the direct effect of COVID-19 infection. Non-COVID-19 deaths have not increased significantly but further work is needed to assess the longer-term impact.",
+    "laySummary": "",
+    "urls": "pdf:http://www.seizure-journal.com/article/S1059131121003757/pdf; doi:https://doi.org/10.1016/j.seizure.2021.11.017; html:https://europepmc.org/articles/PMC8626872"
   },
   {
     "id": "34850818",
@@ -3773,6 +3773,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ageing/article-pdf/51/1/afab223/42083726/afab223.pdf; doi:https://doi.org/10.1093/ageing/afab223; html:https://europepmc.org/articles/PMC8690013; pdf:https://europepmc.org/articles/PMC8690013?pdf=render"
   },
+  {
+    "id": "34713086",
+    "doi": "https://doi.org/10.3389/fdgth.2021.598916",
+    "title": "Markup: A Web-Based Annotation Tool Powered by Active Learning.",
+    "authorString": "Dobbie S, Strafford H, Pickrell WO, Fonferko-Shadrach B, Jones C, Akbari A, Thompson S, Lacey A.",
+    "authorAffiliations": "",
+    "journalTitle": "Frontiers in digital health",
+    "pubYear": "2021",
+    "date": "2021-07-26",
+    "isOpenAccess": "Y",
+    "keywords": "Active Learning; Annotation; Natural Language Processing; Unstructured Text; Sequence-to-sequence Learning",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Across various domains, such as health and social care, law, news, and social media, there are increasing quantities of unstructured texts being produced. These potential data sources often contain rich information that could be used for domain-specific and research purposes. However, the unstructured nature of free-text data poses a significant challenge for its utilisation due to the necessity of substantial manual intervention from domain-experts to label embedded information. Annotation tools can assist with this process by providing functionality that enables the accurate capture and transformation of unstructured texts into structured annotations, which can be used individually, or as part of larger Natural Language Processing (NLP) pipelines. We present Markup (https://www.getmarkup.com/) an open-source, web-based annotation tool that is undergoing continued development for use across all domains. Markup incorporates NLP and Active Learning (AL) technologies to enable rapid and accurate annotation using custom user configurations, predictive annotation suggestions, and automated mapping suggestions to both domain-specific ontologies, such as the Unified Medical Language System (UMLS), and custom, user-defined ontologies. We demonstrate a real-world use case of how Markup has been used in a healthcare setting to annotate structured information from unstructured clinic letters, where captured annotations were used to build and test NLP applications.",
+    "laySummary": "",
+    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fdgth.2021.598916/pdf; doi:https://doi.org/10.3389/fdgth.2021.598916; html:https://europepmc.org/articles/PMC8521860; pdf:https://europepmc.org/articles/PMC8521860?pdf=render"
+  },
   {
     "id": "35501368",
     "doi": "https://doi.org/10.1038/s41431-022-01107-9",
@@ -3791,21 +3808,21 @@
     "urls": "pdf:https://www.nature.com/articles/s41431-022-01107-9.pdf; doi:https://doi.org/10.1038/s41431-022-01107-9; html:https://europepmc.org/articles/PMC9712543; pdf:https://europepmc.org/articles/PMC9712543?pdf=render"
   },
   {
-    "id": "34864250",
-    "doi": "https://doi.org/10.1016/j.seizure.2021.11.017",
-    "title": "Epilepsy mortality in Wales during COVID-19.",
-    "authorString": "Daniels H, Lacey AS, Mikadze D, Akbari A, Fonferko-Shadrach B, Hollinghurst J, Lyons RA, Rees MI, Sawhney IM, Powell RH, Kerr MP, Pickrell WO.",
+    "id": "35858680",
+    "doi": "https://doi.org/10.1136/bmj-2021-068946",
+    "title": "Comparative effectiveness of ChAdOx1 versus BNT162b2 covid-19 vaccines in health and social care workers in England: cohort study using OpenSAFELY.",
+    "authorString": "Hulme WJ, Williamson EJ, Green ACA, Bhaskaran K, McDonald HI, Rentsch CT, Schultze A, Tazare J, Curtis HJ, Walker AJ, Tomlinson LA, Palmer T, Horne EMF, MacKenna B, Morton CE, Mehrkar A, Morley J, Fisher L, Bacon SCJ, Evans D, Inglesby P, Hickman G, Davy S, Ward T, Croker R, Eggo RM, Wong AYS, Mathur R, Wing K, Forbes H, Grint DJ, Douglas IJ, Evans SJW, Smeeth L, Bates C, Cockburn J, Parry J, Hester F, Harper S, Sterne JAC, Hern\u00e1n MA, Goldacre B.",
     "authorAffiliations": "",
-    "journalTitle": "Seizure",
+    "journalTitle": "BMJ (Clinical research ed.)",
     "pubYear": "2022",
-    "date": "2021-11-27",
+    "date": "2022-07-20",
     "isOpenAccess": "Y",
-    "keywords": "Pandemic; Data Linkage; Electronic Health Records; Covid-19",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Purpose</h4>The COVID-19 pandemic has increased mortality worldwide and those with chronic conditions may have been disproportionally affected. However, it is unknown whether the pandemic has changed mortality rates for people with epilepsy. We aimed to compare mortality rates in people with epilepsy in Wales during the pandemic with pre-pandemic rates.<h4>Methods</h4>We performed a retrospective study using individual-level linked population-scale anonymised electronic health records. We identified deaths in people with epilepsy (DPWE), i.e. those with a diagnosis of epilepsy, and deaths associated with epilepsy (DAE), where epilepsy was recorded as a cause of death on death certificates. We compared death rates in 2020 with average rates in 2015-2019 using Poisson models to calculate death rate ratios.<h4>Results</h4>There were 188 DAE and 628 DPWE in Wales in 2020 (death rates: 7.7/100,000/year and 25.7/100,000/year). The average rates for DAE and DPWE from 2015 to 2019 were 5.8/100,000/year and 23.8/100,000/year, respectively. Death rate ratios (2020 compared to 2015-2019) for DAE were 1.34 (95%CI 1.14-1.57, p<0.001) and for DPWE were 1.08 (0.99-1.17, p\u00a0=\u00a00.09). The death rate ratios for non-COVID deaths (deaths without COVID mentioned on death certificates) for DAE were 1.17 (0.99-1.39, p\u00a0=\u00a00.06) and for DPWE were 0.96 (0.87-1.05, p\u00a0=\u00a00.37).<h4>Conclusions</h4>The significant increase in DAE in Wales during 2020 could be explained by the direct effect of COVID-19 infection. Non-COVID-19 deaths have not increased significantly but further work is needed to assess the longer-term impact.",
+    "abstract": "<h4>Objective</h4>To compare the effectiveness of the BNT162b2 mRNA (Pfizer-BioNTech) and the ChAdOx1 (Oxford-AstraZeneca) covid-19 vaccines against infection and covid-19 disease in health and social care workers.<h4>Design</h4>Cohort study, emulating a comparative effectiveness trial, on behalf of NHS England.<h4>Setting</h4>Linked primary care, hospital, and covid-19 surveillance records available within the OpenSAFELY-TPP research platform, covering a period when the SARS-CoV-2 Alpha variant was dominant.<h4>Participants</h4>317\u2009341 health and social care workers vaccinated between 4 January and 28 February 2021, registered with a general practice using the TPP SystmOne clinical information system in England, and not clinically extremely vulnerable.<h4>Interventions</h4>Vaccination with either BNT162b2 or ChAdOx1 administered as part of the national covid-19 vaccine roll-out.<h4>Main outcome measures</h4>Recorded SARS-CoV-2 positive test, or covid-19 related attendance at an accident and emergency (A&E) department or hospital admission occurring within 20 weeks of receipt of the first vaccine dose.<h4>Results</h4>Over the duration of 118\u2009771 person-years of follow-up there were 6962 positive SARS-CoV-2 tests, 282 covid-19 related A&E attendances, and 166 covid-19 related hospital admissions. The cumulative incidence of each outcome was similar for both vaccines during the first 20 weeks after vaccination. The cumulative incidence of recorded SARS-CoV-2 infection 20 weeks after first-dose vaccination with BNT162b2 was 21.7 per 1000 people (95% confidence interval 20.9 to 22.4) and with ChAdOx1 was 23.7 (21.8 to 25.6), representing a difference of 2.04 per 1000 people (0.04 to 4.04). The difference in the cumulative incidence per 1000 people of covid-19 related A&E attendance at 20 weeks was 0.06 per 1000 people (95% CI -0.31 to 0.43). For covid-19 related hospital admission, this difference was 0.11 per 1000 people (-0.22 to 0.44).<h4>Conclusions</h4>In this cohort of healthcare workers where we would not anticipate vaccine type to be related to health status, we found no substantial differences in the incidence of SARS-CoV-2 infection or covid-19 disease up to 20 weeks after vaccination. Incidence dropped sharply at 3-4 weeks after vaccination, and there were few covid-19 related hospital attendance and admission events after this period. This is in line with expected onset of vaccine induced immunity and suggests strong protection against Alpha variant covid-19 disease for both vaccines in this relatively young and healthy population of healthcare workers.",
     "laySummary": "",
-    "urls": "pdf:http://www.seizure-journal.com/article/S1059131121003757/pdf; doi:https://doi.org/10.1016/j.seizure.2021.11.017; html:https://europepmc.org/articles/PMC8626872"
+    "urls": "pdf:https://www.bmj.com/content/bmj/378/bmj-2021-068946.full.pdf; doi:https://doi.org/10.1136/bmj-2021-068946; html:https://europepmc.org/articles/PMC9295078; pdf:https://europepmc.org/articles/PMC9295078?pdf=render"
   },
   {
     "id": "37263685",
@@ -3825,38 +3842,21 @@
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/13/6/e070637.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-070637; html:https://europepmc.org/articles/PMC10255029; pdf:https://europepmc.org/articles/PMC10255029?pdf=render"
   },
   {
-    "id": "35858680",
-    "doi": "https://doi.org/10.1136/bmj-2021-068946",
-    "title": "Comparative effectiveness of ChAdOx1 versus BNT162b2 covid-19 vaccines in health and social care workers in England: cohort study using OpenSAFELY.",
-    "authorString": "Hulme WJ, Williamson EJ, Green ACA, Bhaskaran K, McDonald HI, Rentsch CT, Schultze A, Tazare J, Curtis HJ, Walker AJ, Tomlinson LA, Palmer T, Horne EMF, MacKenna B, Morton CE, Mehrkar A, Morley J, Fisher L, Bacon SCJ, Evans D, Inglesby P, Hickman G, Davy S, Ward T, Croker R, Eggo RM, Wong AYS, Mathur R, Wing K, Forbes H, Grint DJ, Douglas IJ, Evans SJW, Smeeth L, Bates C, Cockburn J, Parry J, Hester F, Harper S, Sterne JAC, Hern\u00e1n MA, Goldacre B.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ (Clinical research ed.)",
-    "pubYear": "2022",
-    "date": "2022-07-20",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objective</h4>To compare the effectiveness of the BNT162b2 mRNA (Pfizer-BioNTech) and the ChAdOx1 (Oxford-AstraZeneca) covid-19 vaccines against infection and covid-19 disease in health and social care workers.<h4>Design</h4>Cohort study, emulating a comparative effectiveness trial, on behalf of NHS England.<h4>Setting</h4>Linked primary care, hospital, and covid-19 surveillance records available within the OpenSAFELY-TPP research platform, covering a period when the SARS-CoV-2 Alpha variant was dominant.<h4>Participants</h4>317\u2009341 health and social care workers vaccinated between 4 January and 28 February 2021, registered with a general practice using the TPP SystmOne clinical information system in England, and not clinically extremely vulnerable.<h4>Interventions</h4>Vaccination with either BNT162b2 or ChAdOx1 administered as part of the national covid-19 vaccine roll-out.<h4>Main outcome measures</h4>Recorded SARS-CoV-2 positive test, or covid-19 related attendance at an accident and emergency (A&E) department or hospital admission occurring within 20 weeks of receipt of the first vaccine dose.<h4>Results</h4>Over the duration of 118\u2009771 person-years of follow-up there were 6962 positive SARS-CoV-2 tests, 282 covid-19 related A&E attendances, and 166 covid-19 related hospital admissions. The cumulative incidence of each outcome was similar for both vaccines during the first 20 weeks after vaccination. The cumulative incidence of recorded SARS-CoV-2 infection 20 weeks after first-dose vaccination with BNT162b2 was 21.7 per 1000 people (95% confidence interval 20.9 to 22.4) and with ChAdOx1 was 23.7 (21.8 to 25.6), representing a difference of 2.04 per 1000 people (0.04 to 4.04). The difference in the cumulative incidence per 1000 people of covid-19 related A&E attendance at 20 weeks was 0.06 per 1000 people (95% CI -0.31 to 0.43). For covid-19 related hospital admission, this difference was 0.11 per 1000 people (-0.22 to 0.44).<h4>Conclusions</h4>In this cohort of healthcare workers where we would not anticipate vaccine type to be related to health status, we found no substantial differences in the incidence of SARS-CoV-2 infection or covid-19 disease up to 20 weeks after vaccination. Incidence dropped sharply at 3-4 weeks after vaccination, and there were few covid-19 related hospital attendance and admission events after this period. This is in line with expected onset of vaccine induced immunity and suggests strong protection against Alpha variant covid-19 disease for both vaccines in this relatively young and healthy population of healthcare workers.",
-    "laySummary": "",
-    "urls": "pdf:https://www.bmj.com/content/bmj/378/bmj-2021-068946.full.pdf; doi:https://doi.org/10.1136/bmj-2021-068946; html:https://europepmc.org/articles/PMC9295078; pdf:https://europepmc.org/articles/PMC9295078?pdf=render"
-  },
-  {
-    "id": "39174061",
-    "doi": "https://doi.org/10.1136/bmjopen-2023-078108",
-    "title": "Risk factors for prolonged length of hospital stay following elective hip replacement surgery: a retrospective longitudinal observational study.",
-    "authorString": "Wilson R, Margelyte R, Redaniel MT, Eyles E, Jones T, Penfold C, Blom A, Elliott A, Harper A, Keen T, Pitt M, Judge A.",
+    "id": "37347268",
+    "doi": "https://doi.org/10.1177/01410768231181268",
+    "title": "Trends in SARS-CoV-2 infection and vaccination in school staff, students and their household members from 2020 to 2022 in Wales, UK: an electronic cohort study.",
+    "authorString": "Lowthian E, Abbasizanjani H, Bedston S, Akbari A, Cowley L, Fry R, Owen RK, Hollinghurst J, Rudan I, Beggs J, Marchant E, Torabi F, Lusignan S, Crick T, Moore G, Sheikh A, Lyons RA.",
     "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2024",
-    "date": "2024-08-21",
+    "journalTitle": "Journal of the Royal Society of Medicine",
+    "pubYear": "2023",
+    "date": "2023-06-22",
     "isOpenAccess": "Y",
-    "keywords": "Hip; Primary Health Care; Hospitalization; Adult Orthopaedics",
+    "keywords": "Pandemic; Schools; Population Health; Covid-19; Social Restrictions",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Objectives</h4>Our aim was to identify which patients are likely to stay in hospital longer following total hip replacement surgery.<h4>Design</h4>Longitudinal, observational study used routinely collected data.<h4>Setting</h4>Data were collected from an NHS Trust in South-West England between 2016 and 2019.<h4>Participants</h4>2352 hip replacement patients had complete data and were included in analysis.<h4>Primary and secondary outcome measures</h4>Three measures of length of stay were used: a count measure of number of days spent in hospital, a binary measure of \u22647\u2009days/>7\u2009days in hospital and a binary measure of remaining in hospital when medically fit for discharge.<h4>Results</h4>The mean length of stay was 5.4\u2009days following surgery, with 18% in hospital for more than 7\u2009days, and 11% staying in hospital when medically fit for discharge. Longer hospital stay was associated with older age (OR=1.06, 95%\u2009CI 1.05 to 1.08), being female (OR=1.42, 95%\u2009CI 1.12 to 1.81) and more comorbidities (OR=3.52, 95%\u2009CI 1.45 to 8.55) and shorter length of stay with not having had a recent hospital admission (OR=0.44, 95%\u2009CI 0.32 to 0.60). Results were similar for remaining in hospital when medically fit for discharge, with the addition of an association with highest socioeconomic deprivation (OR=2.08, 95%\u2009CI 1.37 to 3.16).<h4>Conclusions</h4>Older, female patients with more comorbidities and from more socioeconomically deprived areas are likely to remain in hospital for longer following surgery. This study produced regression models demonstrating consistent results across three measures of prolonged hospital stay following hip replacement surgery. These findings could be used to inform surgery planning and when supporting patient discharge following surgery.",
+    "abstract": "<h4>Objectives</h4>We investigated SARS-CoV-2 infection trends, risk of SARS-CoV-2 infection and COVID-19 vaccination uptake among school staff, students and their household members in Wales, UK.<h4>Design</h4>Seven-day average of SARS-CoV-2 infections and polymerase chain reaction tests per 1000 people daily, cumulative incidence of COVID-19 vaccination uptake and multi-level Poisson models with time-varying covariates.<h4>Setting</h4>National electronic cohort between September 2020 and May 2022 when several variants were predominant in the UK (Alpha, Delta and Omicron).<h4>Participants</h4>School students aged 4 to 10/11 years (primary school and younger middle school, <i>n</i>\u2009=\u2009238,163), and 11 to 15/16 years (secondary school and older middle school, <i>n</i>\u2009=\u2009182,775), school staff in Wales (<i>n</i>\u2009=\u200947,963) and the household members of students and staff (<i>n</i>\u2009=\u2009697,659).<h4>Main outcome measures</h4>SARS-CoV-2 infection and COVID-19 vaccination uptake.<h4>Results</h4>School students had a sustained period of high infection rates compared with household members after August 2021. Primary schedule vaccination uptake was highest among staff (96.3%) but lower for household members (72.2%), secondary and older middle school students (59.8%), and primary and younger middle school students (3.3%). Multi-level Poisson models showed that vaccination was associated with a lower risk of SARS-CoV-2 infection. The Delta variant posed a greater infection risk for students than the Alpha variant. However, Omicron was a larger risk for staff and household members.<h4>Conclusions</h4>Public health bodies should be informed of the protection COVID-19 vaccines afford, with more research being required for younger populations. Furthermore, schools require additional support in managing new, highly transmissible variants. Further research should examine the mechanisms between child deprivation and SARS-CoV-2 infection.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1136/bmjopen-2023-078108; html:https://europepmc.org/articles/PMC11340698; pdf:https://europepmc.org/articles/PMC11340698?pdf=render"
+    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/01410768231181268; doi:https://doi.org/10.1177/01410768231181268; html:https://europepmc.org/articles/PMC10767617; pdf:https://europepmc.org/articles/PMC10767617?pdf=render"
   },
   {
     "id": "37544968",
@@ -3875,6 +3875,23 @@
     "laySummary": "",
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s11357-023-00890-7.pdf; doi:https://doi.org/10.1007/s11357-023-00890-7; html:https://europepmc.org/articles/PMC10828302; pdf:https://europepmc.org/articles/PMC10828302?pdf=render"
   },
+  {
+    "id": "39174061",
+    "doi": "https://doi.org/10.1136/bmjopen-2023-078108",
+    "title": "Risk factors for prolonged length of hospital stay following elective hip replacement surgery: a retrospective longitudinal observational study.",
+    "authorString": "Wilson R, Margelyte R, Redaniel MT, Eyles E, Jones T, Penfold C, Blom A, Elliott A, Harper A, Keen T, Pitt M, Judge A.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2024",
+    "date": "2024-08-21",
+    "isOpenAccess": "Y",
+    "keywords": "Hip; Primary Health Care; Hospitalization; Adult Orthopaedics",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objectives</h4>Our aim was to identify which patients are likely to stay in hospital longer following total hip replacement surgery.<h4>Design</h4>Longitudinal, observational study used routinely collected data.<h4>Setting</h4>Data were collected from an NHS Trust in South-West England between 2016 and 2019.<h4>Participants</h4>2352 hip replacement patients had complete data and were included in analysis.<h4>Primary and secondary outcome measures</h4>Three measures of length of stay were used: a count measure of number of days spent in hospital, a binary measure of \u22647\u2009days/>7\u2009days in hospital and a binary measure of remaining in hospital when medically fit for discharge.<h4>Results</h4>The mean length of stay was 5.4\u2009days following surgery, with 18% in hospital for more than 7\u2009days, and 11% staying in hospital when medically fit for discharge. Longer hospital stay was associated with older age (OR=1.06, 95%\u2009CI 1.05 to 1.08), being female (OR=1.42, 95%\u2009CI 1.12 to 1.81) and more comorbidities (OR=3.52, 95%\u2009CI 1.45 to 8.55) and shorter length of stay with not having had a recent hospital admission (OR=0.44, 95%\u2009CI 0.32 to 0.60). Results were similar for remaining in hospital when medically fit for discharge, with the addition of an association with highest socioeconomic deprivation (OR=2.08, 95%\u2009CI 1.37 to 3.16).<h4>Conclusions</h4>Older, female patients with more comorbidities and from more socioeconomically deprived areas are likely to remain in hospital for longer following surgery. This study produced regression models demonstrating consistent results across three measures of prolonged hospital stay following hip replacement surgery. These findings could be used to inform surgery planning and when supporting patient discharge following surgery.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1136/bmjopen-2023-078108; html:https://europepmc.org/articles/PMC11340698; pdf:https://europepmc.org/articles/PMC11340698?pdf=render"
+  },
   {
     "id": "36526323",
     "doi": "https://doi.org/10.1136/bmjopen-2022-068252",
@@ -3892,23 +3909,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/12/e068252.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-068252; html:https://europepmc.org/articles/PMC9764602; pdf:https://europepmc.org/articles/PMC9764602?pdf=render"
   },
-  {
-    "id": "37347268",
-    "doi": "https://doi.org/10.1177/01410768231181268",
-    "title": "Trends in SARS-CoV-2 infection and vaccination in school staff, students and their household members from 2020 to 2022 in Wales, UK: an electronic cohort study.",
-    "authorString": "Lowthian E, Abbasizanjani H, Bedston S, Akbari A, Cowley L, Fry R, Owen RK, Hollinghurst J, Rudan I, Beggs J, Marchant E, Torabi F, Lusignan S, Crick T, Moore G, Sheikh A, Lyons RA.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of the Royal Society of Medicine",
-    "pubYear": "2023",
-    "date": "2023-06-22",
-    "isOpenAccess": "Y",
-    "keywords": "Pandemic; Schools; Population Health; Covid-19; Social Restrictions",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objectives</h4>We investigated SARS-CoV-2 infection trends, risk of SARS-CoV-2 infection and COVID-19 vaccination uptake among school staff, students and their household members in Wales, UK.<h4>Design</h4>Seven-day average of SARS-CoV-2 infections and polymerase chain reaction tests per 1000 people daily, cumulative incidence of COVID-19 vaccination uptake and multi-level Poisson models with time-varying covariates.<h4>Setting</h4>National electronic cohort between September 2020 and May 2022 when several variants were predominant in the UK (Alpha, Delta and Omicron).<h4>Participants</h4>School students aged 4 to 10/11 years (primary school and younger middle school, <i>n</i>\u2009=\u2009238,163), and 11 to 15/16 years (secondary school and older middle school, <i>n</i>\u2009=\u2009182,775), school staff in Wales (<i>n</i>\u2009=\u200947,963) and the household members of students and staff (<i>n</i>\u2009=\u2009697,659).<h4>Main outcome measures</h4>SARS-CoV-2 infection and COVID-19 vaccination uptake.<h4>Results</h4>School students had a sustained period of high infection rates compared with household members after August 2021. Primary schedule vaccination uptake was highest among staff (96.3%) but lower for household members (72.2%), secondary and older middle school students (59.8%), and primary and younger middle school students (3.3%). Multi-level Poisson models showed that vaccination was associated with a lower risk of SARS-CoV-2 infection. The Delta variant posed a greater infection risk for students than the Alpha variant. However, Omicron was a larger risk for staff and household members.<h4>Conclusions</h4>Public health bodies should be informed of the protection COVID-19 vaccines afford, with more research being required for younger populations. Furthermore, schools require additional support in managing new, highly transmissible variants. Further research should examine the mechanisms between child deprivation and SARS-CoV-2 infection.",
-    "laySummary": "",
-    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/01410768231181268; doi:https://doi.org/10.1177/01410768231181268; html:https://europepmc.org/articles/PMC10767617; pdf:https://europepmc.org/articles/PMC10767617?pdf=render"
-  },
   {
     "id": "34799365",
     "doi": "https://doi.org/10.1136/bmjopen-2021-054861",
@@ -3943,6 +3943,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1177/11779322211035921; doi:https://doi.org/10.1177/11779322211035921; html:https://europepmc.org/articles/PMC8323418; pdf:https://europepmc.org/articles/PMC8323418?pdf=render"
   },
+  {
+    "id": "34911741",
+    "doi": "https://doi.org/10.1136/heartjnl-2021-320047",
+    "title": "Impact of cardiometabolic multimorbidity and ethnicity on cardiovascular/renal complications in patients with COVID-19.",
+    "authorString": "Norris T, Razieh C, Zaccardi F, Yates T, Islam N, Gillies CL, Chudasama YV, Rowlands AV, Davies MJ, McCann GP, Banerjee A, Lam CSP, Docherty AB, Openshaw PJ, Baillie JK, Semple MG, Lawson CA, Khunti K, ISARIC4C investigators.",
+    "authorAffiliations": "",
+    "journalTitle": "Heart (British Cardiac Society)",
+    "pubYear": "2022",
+    "date": "2022-07-13",
+    "isOpenAccess": "Y",
+    "keywords": "epidemiology; risk factors; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>Using a large national database of people hospitalised with COVID-19, we investigated the contribution of cardio-metabolic conditions, multi-morbidity and ethnicity on the risk of in-hospital cardiovascular complications and death.<h4>Methods</h4>A multicentre, prospective cohort study in 302 UK healthcare facilities of adults hospitalised with COVID-19 between 6 February 2020 and 16 March 2021. Logistic models were used to explore associations between baseline patient ethnicity, cardiometabolic conditions and multimorbidity (0, 1, 2, >2 conditions), and in-hospital cardiovascular complications (heart failure, arrhythmia, cardiac ischaemia, cardiac arrest, coagulation complications, stroke), renal injury and death.<h4>Results</h4>Of 65 624 patients hospitalised with COVID-19, 44 598 (68.0%) reported at least one cardiometabolic condition on admission. Cardiovascular/renal complications or death occurred in 24 609 (38.0%) patients. Baseline cardiometabolic conditions were independently associated with increased odds of in-hospital complications and this risk increased in the presence of cardiometabolic multimorbidity. For example, compared with having no cardiometabolic conditions, 1, 2 or \u22653 conditions was associated with 1.46 (95% CI 1.39 to 1.54), 2.04 (95% CI 1.93 to 2.15) and 3.10 (95% CI 2.92 to 3.29) times higher odds of any cardiovascular/renal complication, respectively. A similar pattern was observed for all-cause death. Compared with the white group, the South Asian (OR 1.19, 95% CI 1.10 to 1.29) and black (OR 1.53 to 95% CI 1.37 to 1.72) ethnic groups had higher risk of any cardiovascular/renal complication.<h4>Conclusions</h4>In hospitalised patients with COVID-19, cardiovascular complications or death impacts just under half of all patients, with the highest risk in those of South Asian or Black ethnicity and in patients with cardiometabolic multimorbidity.",
+    "laySummary": "",
+    "urls": "pdf:https://heart.bmj.com/content/heartjnl/108/15/1200.full.pdf; doi:https://doi.org/10.1136/heartjnl-2021-320047; html:https://europepmc.org/articles/PMC8678560; pdf:https://europepmc.org/articles/PMC8678560?pdf=render"
+  },
   {
     "id": "36600681",
     "doi": "https://doi.org/10.1177/17562848221145612",
@@ -3961,21 +3978,38 @@
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9806427; doi:https://doi.org/10.1177/17562848221145612; html:https://europepmc.org/articles/PMC9806427; pdf:https://europepmc.org/articles/PMC9806427?pdf=render"
   },
   {
-    "id": "34911741",
-    "doi": "https://doi.org/10.1136/heartjnl-2021-320047",
-    "title": "Impact of cardiometabolic multimorbidity and ethnicity on cardiovascular/renal complications in patients with COVID-19.",
-    "authorString": "Norris T, Razieh C, Zaccardi F, Yates T, Islam N, Gillies CL, Chudasama YV, Rowlands AV, Davies MJ, McCann GP, Banerjee A, Lam CSP, Docherty AB, Openshaw PJ, Baillie JK, Semple MG, Lawson CA, Khunti K, ISARIC4C investigators.",
+    "id": "36860174",
+    "doi": "https://doi.org/10.1093/ije/dyad022",
+    "title": "Proxy gene-by-environment Mendelian randomization study of the association between cigarette smoking during pregnancy and offspring mental health.",
+    "authorString": "Sallis HM, Wootton RE, Davey Smith G, Munaf\u00f2 MR.",
     "authorAffiliations": "",
-    "journalTitle": "Heart (British Cardiac Society)",
+    "journalTitle": "International journal of epidemiology",
+    "pubYear": "2023",
+    "date": "2023-10-01",
+    "isOpenAccess": "Y",
+    "keywords": "Schizophrenia; Depression; Smoking; Mendelian Randomization",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Smoking prevalence is higher among individuals with schizophrenia or depression, and previous work has suggested this relationship is causal. However, this may be due to dynastic effects, for example reflecting maternal smoking during pregnancy rather than a direct effect of smoking. We used a proxy gene-by-environment Mendelian randomization approach to investigate whether there is a causal effect of maternal heaviness of smoking during pregnancy on offspring mental health.<h4>Methods</h4>Analyses were performed in the UK Biobank cohort. Individuals with data on smoking status, maternal smoking during pregnancy, a diagnosis of schizophrenia or depression, and genetic data were included. We used participants' genotype (rs16969968 in the CHRNA5 gene) as a proxy for their mothers' genotype. Analyses were stratified on participants' own smoking status in order to estimate the effect of maternal smoking heaviness during pregnancy independently of offspring smoking.<h4>Results</h4>The effect of maternal smoking on offspring schizophrenia was in opposing directions when stratifying on offspring smoking status. Among offspring of never smokers, each additional risk allele for maternal smoking heaviness appeared to have a protective effect [odds ratio (OR)\u2009=\u20090.77, 95% confidence interval (CI) 0.62 to 0.95, P\u2009=\u20090.015], whereas among ever smokers the effect of maternal smoking was in the reverse direction (OR\u2009=\u20091.23, 95% CI 1.05 to 1.45, P\u2009=\u20090.011, Pinteraction\u2009<0.001). There was no clear evidence of an association between maternal smoking heaviness and offspring depression.<h4>Conclusions</h4>These findings do not provide clear evidence of an effect of maternal smoking during pregnancy on offspring schizophrenia or depression, which implies that any causal effect of smoking on schizophrenia or depression is direct.",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/ije/advance-article-pdf/doi/10.1093/ije/dyad022/49393500/dyad022.pdf; doi:https://doi.org/10.1093/ije/dyad022; html:https://europepmc.org/articles/PMC10555861; pdf:https://europepmc.org/articles/PMC10555861?pdf=render"
+  },
+  {
+    "id": "34487522",
+    "doi": "https://doi.org/10.1093/cid/ciab754",
+    "title": "Severity of Severe Acute Respiratory System Coronavirus 2 (SARS-CoV-2) Alpha Variant (B.1.1.7) in England.",
+    "authorString": "Grint DJ, Wing K, Houlihan C, Gibbs HP, Evans SJW, Williamson E, McDonald HI, Bhaskaran K, Evans D, Walker AJ, Hickman G, Nightingale E, Schultze A, Rentsch CT, Bates C, Cockburn J, Curtis HJ, Morton CE, Bacon S, Davy S, Wong AYS, Mehrkar A, Tomlinson L, Douglas IJ, Mathur R, MacKenna B, Ingelsby P, Croker R, Parry J, Hester F, Harper S, DeVito NJ, Hulme W, Tazare J, Smeeth L, Goldacre B, Eggo RM.",
+    "authorAffiliations": "",
+    "journalTitle": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America",
     "pubYear": "2022",
-    "date": "2022-07-13",
+    "date": "2022-08-01",
     "isOpenAccess": "Y",
-    "keywords": "epidemiology; risk factors; Covid-19",
+    "keywords": "Alpha; Hospital Admission; Case Fatality; Sars-cov-2",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Objective</h4>Using a large national database of people hospitalised with COVID-19, we investigated the contribution of cardio-metabolic conditions, multi-morbidity and ethnicity on the risk of in-hospital cardiovascular complications and death.<h4>Methods</h4>A multicentre, prospective cohort study in 302 UK healthcare facilities of adults hospitalised with COVID-19 between 6 February 2020 and 16 March 2021. Logistic models were used to explore associations between baseline patient ethnicity, cardiometabolic conditions and multimorbidity (0, 1, 2, >2 conditions), and in-hospital cardiovascular complications (heart failure, arrhythmia, cardiac ischaemia, cardiac arrest, coagulation complications, stroke), renal injury and death.<h4>Results</h4>Of 65 624 patients hospitalised with COVID-19, 44 598 (68.0%) reported at least one cardiometabolic condition on admission. Cardiovascular/renal complications or death occurred in 24 609 (38.0%) patients. Baseline cardiometabolic conditions were independently associated with increased odds of in-hospital complications and this risk increased in the presence of cardiometabolic multimorbidity. For example, compared with having no cardiometabolic conditions, 1, 2 or \u22653 conditions was associated with 1.46 (95% CI 1.39 to 1.54), 2.04 (95% CI 1.93 to 2.15) and 3.10 (95% CI 2.92 to 3.29) times higher odds of any cardiovascular/renal complication, respectively. A similar pattern was observed for all-cause death. Compared with the white group, the South Asian (OR 1.19, 95% CI 1.10 to 1.29) and black (OR 1.53 to 95% CI 1.37 to 1.72) ethnic groups had higher risk of any cardiovascular/renal complication.<h4>Conclusions</h4>In hospitalised patients with COVID-19, cardiovascular complications or death impacts just under half of all patients, with the highest risk in those of South Asian or Black ethnicity and in patients with cardiometabolic multimorbidity.",
+    "abstract": "<h4>Background</h4>The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) alpha variant (B.1.1.7) is associated with higher transmissibility than wild-type virus, becoming the dominant variant in England by January 2021. We aimed to describe the severity of the alpha variant in terms of the pathway of disease from testing positive to hospital admission and death.<h4>Methods</h4>With the approval of NHS England, we linked individual-level data from primary care with SARS-CoV-2 community testing, hospital admission, and Office for National Statistics all-cause death data. We used testing data with S-gene target failure as a proxy for distinguishing alpha and wild-type cases, and stratified Cox proportional hazards regression to compare the relative severity of alpha cases with wild-type diagnosed from 16 November 2020 to 11 January 2021.<h4>Results</h4>Using data from 185 234 people who tested positive for SARS-CoV-2 in the community (alpha\u2005=\u200593 153; wild-type\u2005=\u200592 081), in fully adjusted analysis accounting for individual-level demographics and comorbidities as well as regional variation in infection incidence, we found alpha associated with 73% higher hazards of all-cause death (adjusted hazard ratio [aHR]: 1.73; 95% confidence interval [CI]: 1.41-2.13; P\u2005<\u2005.0001) and 62% higher hazards of hospital admission (1.62; 1.48-1.78; P\u2005<\u2005.0001) compared with wild-type virus. Among patients already admitted to the intensive care unit, the association between alpha and increased all-cause mortality was smaller and the CI included the null (aHR: 1.20; 95% CI: .74-1.95; P\u2005=\u2005.45).<h4>Conclusions</h4>The SARS-CoV-2 alpha variant is associated with an increased risk of both hospitalization and mortality than wild-type virus.",
     "laySummary": "",
-    "urls": "pdf:https://heart.bmj.com/content/heartjnl/108/15/1200.full.pdf; doi:https://doi.org/10.1136/heartjnl-2021-320047; html:https://europepmc.org/articles/PMC8678560; pdf:https://europepmc.org/articles/PMC8678560?pdf=render"
+    "urls": "pdf:https://academic.oup.com/cid/article-pdf/75/1/e1120/45513976/ciab754.pdf; doi:https://doi.org/10.1093/cid/ciab754; html:https://europepmc.org/articles/PMC8522415; pdf:https://europepmc.org/articles/PMC8522415?pdf=render"
   },
   {
     "id": "37126810",
@@ -3995,38 +4029,21 @@
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10152408; doi:https://doi.org/10.7326/M21-4269; html:https://europepmc.org/articles/PMC10152408; pdf:https://europepmc.org/articles/PMC10152408?pdf=render; doi:https://doi.org/10.7326/m21-4269"
   },
   {
-    "id": "34487522",
-    "doi": "https://doi.org/10.1093/cid/ciab754",
-    "title": "Severity of Severe Acute Respiratory System Coronavirus 2 (SARS-CoV-2) Alpha Variant (B.1.1.7) in England.",
-    "authorString": "Grint DJ, Wing K, Houlihan C, Gibbs HP, Evans SJW, Williamson E, McDonald HI, Bhaskaran K, Evans D, Walker AJ, Hickman G, Nightingale E, Schultze A, Rentsch CT, Bates C, Cockburn J, Curtis HJ, Morton CE, Bacon S, Davy S, Wong AYS, Mehrkar A, Tomlinson L, Douglas IJ, Mathur R, MacKenna B, Ingelsby P, Croker R, Parry J, Hester F, Harper S, DeVito NJ, Hulme W, Tazare J, Smeeth L, Goldacre B, Eggo RM.",
-    "authorAffiliations": "",
-    "journalTitle": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America",
-    "pubYear": "2022",
-    "date": "2022-08-01",
-    "isOpenAccess": "Y",
-    "keywords": "Alpha; Hospital Admission; Case Fatality; Sars-cov-2",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) alpha variant (B.1.1.7) is associated with higher transmissibility than wild-type virus, becoming the dominant variant in England by January 2021. We aimed to describe the severity of the alpha variant in terms of the pathway of disease from testing positive to hospital admission and death.<h4>Methods</h4>With the approval of NHS England, we linked individual-level data from primary care with SARS-CoV-2 community testing, hospital admission, and Office for National Statistics all-cause death data. We used testing data with S-gene target failure as a proxy for distinguishing alpha and wild-type cases, and stratified Cox proportional hazards regression to compare the relative severity of alpha cases with wild-type diagnosed from 16 November 2020 to 11 January 2021.<h4>Results</h4>Using data from 185 234 people who tested positive for SARS-CoV-2 in the community (alpha\u2005=\u200593 153; wild-type\u2005=\u200592 081), in fully adjusted analysis accounting for individual-level demographics and comorbidities as well as regional variation in infection incidence, we found alpha associated with 73% higher hazards of all-cause death (adjusted hazard ratio [aHR]: 1.73; 95% confidence interval [CI]: 1.41-2.13; P\u2005<\u2005.0001) and 62% higher hazards of hospital admission (1.62; 1.48-1.78; P\u2005<\u2005.0001) compared with wild-type virus. Among patients already admitted to the intensive care unit, the association between alpha and increased all-cause mortality was smaller and the CI included the null (aHR: 1.20; 95% CI: .74-1.95; P\u2005=\u2005.45).<h4>Conclusions</h4>The SARS-CoV-2 alpha variant is associated with an increased risk of both hospitalization and mortality than wild-type virus.",
-    "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/cid/article-pdf/75/1/e1120/45513976/ciab754.pdf; doi:https://doi.org/10.1093/cid/ciab754; html:https://europepmc.org/articles/PMC8522415; pdf:https://europepmc.org/articles/PMC8522415?pdf=render"
-  },
-  {
-    "id": "36860174",
-    "doi": "https://doi.org/10.1093/ije/dyad022",
-    "title": "Proxy gene-by-environment Mendelian randomization study of the association between cigarette smoking during pregnancy and offspring mental health.",
-    "authorString": "Sallis HM, Wootton RE, Davey Smith G, Munaf\u00f2 MR.",
+    "id": "37368589",
+    "doi": "https://doi.org/10.3390/toxics11060489",
+    "title": "Association between Residential Exposure to Air Pollution and Incident Coronary Heart Disease Is Not Mediated by Leukocyte Telomere Length: A UK Biobank Study.",
+    "authorString": "Kuo CL, Liu R, Godoy LDC, Pilling LC, Fortinsky RH, Brugge D.",
     "authorAffiliations": "",
-    "journalTitle": "International journal of epidemiology",
+    "journalTitle": "Toxics",
     "pubYear": "2023",
-    "date": "2023-10-01",
+    "date": "2023-05-28",
     "isOpenAccess": "Y",
-    "keywords": "Schizophrenia; Depression; Smoking; Mendelian Randomization",
+    "keywords": "Pm10; Pm2.5; No2; Nox; Pm2.5 Absorbance; Pm2.5\u201310",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Smoking prevalence is higher among individuals with schizophrenia or depression, and previous work has suggested this relationship is causal. However, this may be due to dynastic effects, for example reflecting maternal smoking during pregnancy rather than a direct effect of smoking. We used a proxy gene-by-environment Mendelian randomization approach to investigate whether there is a causal effect of maternal heaviness of smoking during pregnancy on offspring mental health.<h4>Methods</h4>Analyses were performed in the UK Biobank cohort. Individuals with data on smoking status, maternal smoking during pregnancy, a diagnosis of schizophrenia or depression, and genetic data were included. We used participants' genotype (rs16969968 in the CHRNA5 gene) as a proxy for their mothers' genotype. Analyses were stratified on participants' own smoking status in order to estimate the effect of maternal smoking heaviness during pregnancy independently of offspring smoking.<h4>Results</h4>The effect of maternal smoking on offspring schizophrenia was in opposing directions when stratifying on offspring smoking status. Among offspring of never smokers, each additional risk allele for maternal smoking heaviness appeared to have a protective effect [odds ratio (OR)\u2009=\u20090.77, 95% confidence interval (CI) 0.62 to 0.95, P\u2009=\u20090.015], whereas among ever smokers the effect of maternal smoking was in the reverse direction (OR\u2009=\u20091.23, 95% CI 1.05 to 1.45, P\u2009=\u20090.011, Pinteraction\u2009<0.001). There was no clear evidence of an association between maternal smoking heaviness and offspring depression.<h4>Conclusions</h4>These findings do not provide clear evidence of an effect of maternal smoking during pregnancy on offspring schizophrenia or depression, which implies that any causal effect of smoking on schizophrenia or depression is direct.",
+    "abstract": "Higher air pollution exposure and shorter leukocyte telomere length (LTL) are both associated with increased risk of coronary heart disease (CHD), and share plausible mechanisms, including inflammation. LTL may serve as a biomarker of air pollution exposure and may be intervened with to reduce the risk of CHD. To the best of our knowledge, we are the first to test the mediation effect of LTL in the relationship between air pollution exposure and incident CHD. Using the UK Biobank (UKB) data (<i>n</i> = 317,601), we conducted a prospective study linking residential air pollution exposure (PM<sub>2.5</sub>, PM<sub>10</sub>, NO<sub>2</sub>, NO<sub>x</sub>) and LTL to incident CHD during a mean follow-up of 12.6 years. Cox proportional hazards models and generalized additive models with penalized spline functions were used to model the associations of pollutant concentrations and LTL with incident CHD. We found non-linear associations of air pollution exposure with LTL and CHD. Pollutant concentrations in the lower range were decreasingly associated with longer LTL and reduced risk of CHD. The associations between lower pollutant concentrations and reduced risk of CHD, however, were minimally mediated by LTL (<3%). Our findings suggest that air pollution influences CHD through pathways that do not involve LTL. Replication is needed with improved measurements of air pollution that more accurately assesses personal exposure.",
     "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/ije/advance-article-pdf/doi/10.1093/ije/dyad022/49393500/dyad022.pdf; doi:https://doi.org/10.1093/ije/dyad022; html:https://europepmc.org/articles/PMC10555861; pdf:https://europepmc.org/articles/PMC10555861?pdf=render"
+    "urls": "doi:https://doi.org/10.3390/toxics11060489; html:https://europepmc.org/articles/PMC10301073; pdf:https://europepmc.org/articles/PMC10301073?pdf=render"
   },
   {
     "id": "33980500",
@@ -4045,23 +4062,6 @@
     "laySummary": "",
     "urls": "pdf:https://informatics.bmj.com/content/bmjhci/28/1/e100303.full.pdf; doi:https://doi.org/10.1136/bmjhci-2020-100303; html:https://europepmc.org/articles/PMC8117992; pdf:https://europepmc.org/articles/PMC8117992?pdf=render"
   },
-  {
-    "id": "37368589",
-    "doi": "https://doi.org/10.3390/toxics11060489",
-    "title": "Association between Residential Exposure to Air Pollution and Incident Coronary Heart Disease Is Not Mediated by Leukocyte Telomere Length: A UK Biobank Study.",
-    "authorString": "Kuo CL, Liu R, Godoy LDC, Pilling LC, Fortinsky RH, Brugge D.",
-    "authorAffiliations": "",
-    "journalTitle": "Toxics",
-    "pubYear": "2023",
-    "date": "2023-05-28",
-    "isOpenAccess": "Y",
-    "keywords": "Pm10; Pm2.5; No2; Nox; Pm2.5 Absorbance; Pm2.5\u201310",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Higher air pollution exposure and shorter leukocyte telomere length (LTL) are both associated with increased risk of coronary heart disease (CHD), and share plausible mechanisms, including inflammation. LTL may serve as a biomarker of air pollution exposure and may be intervened with to reduce the risk of CHD. To the best of our knowledge, we are the first to test the mediation effect of LTL in the relationship between air pollution exposure and incident CHD. Using the UK Biobank (UKB) data (<i>n</i> = 317,601), we conducted a prospective study linking residential air pollution exposure (PM<sub>2.5</sub>, PM<sub>10</sub>, NO<sub>2</sub>, NO<sub>x</sub>) and LTL to incident CHD during a mean follow-up of 12.6 years. Cox proportional hazards models and generalized additive models with penalized spline functions were used to model the associations of pollutant concentrations and LTL with incident CHD. We found non-linear associations of air pollution exposure with LTL and CHD. Pollutant concentrations in the lower range were decreasingly associated with longer LTL and reduced risk of CHD. The associations between lower pollutant concentrations and reduced risk of CHD, however, were minimally mediated by LTL (<3%). Our findings suggest that air pollution influences CHD through pathways that do not involve LTL. Replication is needed with improved measurements of air pollution that more accurately assesses personal exposure.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.3390/toxics11060489; html:https://europepmc.org/articles/PMC10301073; pdf:https://europepmc.org/articles/PMC10301073?pdf=render"
-  },
   {
     "id": "35381005",
     "doi": "https://doi.org/10.1371/journal.pone.0264828",
@@ -4283,23 +4283,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41467-022-33937-y.pdf; doi:https://doi.org/10.1038/s41467-022-33937-y; html:https://europepmc.org/articles/PMC9574832; pdf:https://europepmc.org/articles/PMC9574832?pdf=render"
   },
-  {
-    "id": "37435691",
-    "doi": "https://doi.org/10.1111/dom.15207",
-    "title": "Testing for associations between HbA1c levels, polygenic risk and brain health in UK Biobank (N\u2009=\u200939\u2009283).",
-    "authorString": "Ranglani S, Ward J, Sattar N, Strawbridge RJ, Lyall DM.",
-    "authorAffiliations": "",
-    "journalTitle": "Diabetes, obesity & metabolism",
-    "pubYear": "2023",
-    "date": "2023-07-12",
-    "isOpenAccess": "N",
-    "keywords": "Type 2 diabetes; Cohort study; Population Study",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Aim</h4>To investigate whether continuous HbA1c levels and HbA1c-polygenic risk scores (HbA1c-PRS) are significantly associated with worse brain health independent of type 2 diabetes (T2D) diagnosis (vs. not), by examining brain structure and cognitive test score phenotypes.<h4>Methods</h4>Using UK Biobank data (n\u2009=\u200939\u2009283), we tested whether HbA1c levels and/or HbA1c-PRS were associated with cognitive test scores and brain imaging phenotypes. We adjusted for confounders of age, sex, Townsend deprivation score, level of education, genotyping chip, eight genetic principal components, smoking, alcohol intake frequency, cholesterol medication, body mass index, T2D and apolipoprotein (APOE) e4 dosage.<h4>Results</h4>We found an association between higher HbA1c levels and poorer performance on symbol digit substitution scores (standardized beta [\u03b2]\u2009=\u2009-0.022, P\u2009=\u2009.001) in the fully adjusted model. We also found an association between higher HbA1c levels and worse brain MRI phenotypes of grey matter (GM; fully-adjusted \u03b2\u2009=\u2009-0.026, P\u2009<\u2009.001), whole brain volume (\u03b2\u2009=\u2009-0.072, P\u2009=\u2009.0113) and a general factor of frontal lobe GM (\u03b2\u2009=\u2009-0.022, P\u2009<\u2009.001) in partially and fully adjusted models. HbA1c-PRS were significantly associated with GM volume in the fully adjusted model (\u03b2\u2009=\u2009-0.010, P\u2009=\u2009.0113); however, when adjusted for HbA1c levels, the association was not significant.<h4>Conclusions</h4>Our findings suggest that measured HbA1c is associated with poorer cognitive health, and that HbA1c-PRS do not add significant information to this.",
-    "laySummary": "",
-    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/dom.15207; doi:https://doi.org/10.1111/dom.15207"
-  },
   {
     "id": "33827854",
     "doi": "https://doi.org/10.1136/bmj.n826",
@@ -4317,6 +4300,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.bmj.com/content/bmj/373/bmj.n826.full.pdf; doi:https://doi.org/10.1136/bmj.n826; html:https://europepmc.org/articles/PMC8413899; pdf:https://europepmc.org/articles/PMC8413899?pdf=render"
   },
+  {
+    "id": "37435691",
+    "doi": "https://doi.org/10.1111/dom.15207",
+    "title": "Testing for associations between HbA1c levels, polygenic risk and brain health in UK Biobank (N\u2009=\u200939\u2009283).",
+    "authorString": "Ranglani S, Ward J, Sattar N, Strawbridge RJ, Lyall DM.",
+    "authorAffiliations": "",
+    "journalTitle": "Diabetes, obesity & metabolism",
+    "pubYear": "2023",
+    "date": "2023-07-12",
+    "isOpenAccess": "N",
+    "keywords": "Type 2 diabetes; Cohort study; Population Study",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Aim</h4>To investigate whether continuous HbA1c levels and HbA1c-polygenic risk scores (HbA1c-PRS) are significantly associated with worse brain health independent of type 2 diabetes (T2D) diagnosis (vs. not), by examining brain structure and cognitive test score phenotypes.<h4>Methods</h4>Using UK Biobank data (n\u2009=\u200939\u2009283), we tested whether HbA1c levels and/or HbA1c-PRS were associated with cognitive test scores and brain imaging phenotypes. We adjusted for confounders of age, sex, Townsend deprivation score, level of education, genotyping chip, eight genetic principal components, smoking, alcohol intake frequency, cholesterol medication, body mass index, T2D and apolipoprotein (APOE) e4 dosage.<h4>Results</h4>We found an association between higher HbA1c levels and poorer performance on symbol digit substitution scores (standardized beta [\u03b2]\u2009=\u2009-0.022, P\u2009=\u2009.001) in the fully adjusted model. We also found an association between higher HbA1c levels and worse brain MRI phenotypes of grey matter (GM; fully-adjusted \u03b2\u2009=\u2009-0.026, P\u2009<\u2009.001), whole brain volume (\u03b2\u2009=\u2009-0.072, P\u2009=\u2009.0113) and a general factor of frontal lobe GM (\u03b2\u2009=\u2009-0.022, P\u2009<\u2009.001) in partially and fully adjusted models. HbA1c-PRS were significantly associated with GM volume in the fully adjusted model (\u03b2\u2009=\u2009-0.010, P\u2009=\u2009.0113); however, when adjusted for HbA1c levels, the association was not significant.<h4>Conclusions</h4>Our findings suggest that measured HbA1c is associated with poorer cognitive health, and that HbA1c-PRS do not add significant information to this.",
+    "laySummary": "",
+    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/dom.15207; doi:https://doi.org/10.1111/dom.15207"
+  },
   {
     "id": "36195871",
     "doi": "https://doi.org/10.1186/s12916-022-02533-8",
@@ -4335,21 +4335,38 @@
     "urls": "pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-022-02533-8; doi:https://doi.org/10.1186/s12916-022-02533-8; html:https://europepmc.org/articles/PMC9533594; pdf:https://europepmc.org/articles/PMC9533594?pdf=render"
   },
   {
-    "id": "33901420",
-    "doi": "https://doi.org/10.1016/s0140-6736(21)00677-2",
-    "title": "Interim findings from first-dose mass COVID-19 vaccination roll-out and COVID-19 hospital admissions in Scotland: a national prospective cohort study.",
-    "authorString": "Vasileiou E, Simpson CR, Shi T, Kerr S, Agrawal U, Akbari A, Bedston S, Beggs J, Bradley D, Chuter A, de Lusignan S, Docherty AB, Ford D, Hobbs FR, Joy M, Katikireddi SV, Marple J, McCowan C, McGagh D, McMenamin J, Moore E, Murray JL, Pan J, Ritchie L, Shah SA, Stock S, Torabi F, Tsang RS, Wood R, Woolhouse M, Robertson C, Sheikh A.",
+    "id": "37056776",
+    "doi": "https://doi.org/10.3389/fimmu.2023.1146702",
+    "title": "SARS-CoV-2 antibody responses associate with sex, age and disease severity in previously uninfected people admitted to hospital with COVID-19: An ISARIC4C prospective study.",
+    "authorString": "Parker E, Thomas J, Roper KJ, Ijaz S, Edwards T, Marchesin F, Katsanovskaja K, Lett L, Jones C, Hardwick HE, Davis C, Vink E, McDonald SE, Moore SC, Dicks S, Jegatheesan K, Cook NJ, Hope J, Cherepanov P, McClure MO, Baillie JK, Openshaw PJM, Turtle L, Ho A, Semple MG, Paxton WA, Tedder RS, Pollakis G, ISARIC4C Investigators.",
     "authorAffiliations": "",
-    "journalTitle": "Lancet (London, England)",
-    "pubYear": "2021",
-    "date": "2021-04-23",
+    "journalTitle": "Frontiers in immunology",
+    "pubYear": "2023",
+    "date": "2023-03-15",
+    "isOpenAccess": "Y",
+    "keywords": "Serology; Virus; Disease; immunology; Neutralisation; Covid-19; Sars-cov-2",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The SARS-CoV-2 pandemic enables the analysis of immune responses induced against a novel coronavirus infecting immunologically na\u00efve individuals. This provides an opportunity for analysis of immune responses and associations with age, sex and disease severity. Here we measured an array of solid-phase binding antibody and viral neutralising Ab (nAb) responses in participants (n=337) of the ISARIC4C cohort and characterised their correlation with peak disease severity during acute infection and early convalescence. Overall, the responses in a Double Antigen Binding Assay (DABA) for antibody to the receptor binding domain (anti-RBD) correlated well with IgM as well as IgG responses against viral spike, S1 and nucleocapsid protein (NP) antigens. DABA reactivity also correlated with nAb. As we and others reported previously, there is greater risk of severe disease and death in older men, whilst the sex ratio was found to be equal within each severity grouping in younger people. In older males with severe disease (mean age 68 years), peak antibody levels were found to be delayed by one to two weeks compared with women, and nAb responses were delayed further. Additionally, we demonstrated that solid-phase binding antibody responses reached higher levels in males as measured <i>via</i> DABA and IgM binding against Spike, NP and S1 antigens. In contrast, this was not observed for nAb responses. When measuring SARS-CoV-2 RNA transcripts (as a surrogate for viral shedding) in nasal swabs at recruitment, we saw no significant differences by sex or disease severity status. However, we have shown higher antibody levels associated with low nasal viral RNA indicating a role of antibody responses in controlling viral replication and shedding in the upper airway. In this study, we have shown discernible differences in the humoral immune responses between males and females and these differences associate with age as well as with resultant disease severity.",
+    "laySummary": "",
+    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fimmu.2023.1146702/pdf; doi:https://doi.org/10.3389/fimmu.2023.1146702; html:https://europepmc.org/articles/PMC10087108; pdf:https://europepmc.org/articles/PMC10087108?pdf=render"
+  },
+  {
+    "id": "35798890",
+    "doi": "https://doi.org/10.1038/s41564-022-01143-7",
+    "title": "SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway.",
+    "authorString": "Willett BJ, Grove J, MacLean OA, Wilkie C, De Lorenzo G, Furnon W, Cantoni D, Scott S, Logan N, Ashraf S, Manali M, Szemiel A, Cowton V, Vink E, Harvey WT, Davis C, Asamaphan P, Smollett K, Tong L, Orton R, Hughes J, Holland P, Silva V, Pascall DJ, Puxty K, da Silva Filipe A, Yebra G, Shaaban S, Holden MTG, Pinto RM, Gunson R, Templeton K, Murcia PR, Patel AH, Klenerman P, Dunachie S, PITCH Consortium, COVID-19 Genomics UK (COG-UK) Consortium, Haughney J, Robertson DL, Palmarini M, Ray S, Thomson EC.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature microbiology",
+    "pubYear": "2022",
+    "date": "2022-07-07",
     "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>The BNT162b2 mRNA (Pfizer-BioNTech) and ChAdOx1 nCoV-19 (Oxford-AstraZeneca) COVID-19 vaccines have shown high efficacy against disease in phase 3 clinical trials and are now being used in national vaccination programmes in the UK and several other countries. Studying the real-world effects of these vaccines is an urgent requirement. The aim of our study was to investigate the association between the mass roll-out of the first doses of these COVID-19 vaccines and hospital admissions for COVID-19.<h4>Methods</h4>We did a prospective cohort study using the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19-EAVE II-database comprising linked vaccination, primary care, real-time reverse transcription-PCR testing, and hospital admission patient records for 5\u00b74 million people in Scotland (about 99% of the population) registered at 940 general practices. Individuals who had previously tested positive were excluded from the analysis. A time-dependent Cox model and Poisson regression models with inverse propensity weights were fitted to estimate effectiveness against COVID-19 hospital admission (defined as 1-adjusted rate ratio) following the first dose of vaccine.<h4>Findings</h4>Between Dec 8, 2020, and Feb 22, 2021, a total of 1\u2009331\u2009993 people were vaccinated over the study period. The mean age of those vaccinated was 65\u00b70 years (SD 16\u00b72). The first dose of the BNT162b2 mRNA vaccine was associated with a vaccine effect of 91% (95% CI 85-94) for reduced COVID-19 hospital admission at 28-34 days post-vaccination. Vaccine effect at the same time interval for the ChAdOx1 vaccine was 88% (95% CI 75-94). Results of combined vaccine effects against hospital admission due to COVID-19 were similar when restricting the analysis to those aged 80 years and older (83%, 95% CI 72-89 at 28-34 days post-vaccination).<h4>Interpretation</h4>Mass roll-out of the first doses of the BNT162b2 mRNA and ChAdOx1 vaccines was associated with substantial reductions in the risk of hospital admission due to COVID-19 in Scotland. There remains the possibility that some of the observed effects might have been due to residual confounding.<h4>Funding</h4>UK Research and Innovation (Medical Research Council), Research and Innovation Industrial Strategy Challenge Fund, Health Data Research UK.",
+    "abstract": "Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant.",
     "laySummary": "",
-    "urls": "pdf:https://aura.abdn.ac.uk/bitstream/2164/17090/1/Vasileiou_etal_Lancet_Interim_Findings_FirstDose_VOR.pdf; doi:https://doi.org/10.1016/S0140-6736(21)00677-2; html:https://europepmc.org/articles/PMC8064669"
+    "urls": "pdf:https://www.nature.com/articles/s41564-022-01143-7.pdf; doi:https://doi.org/10.1038/s41564-022-01143-7; html:https://europepmc.org/articles/PMC9352574; pdf:https://europepmc.org/articles/PMC9352574?pdf=render"
   },
   {
     "id": "36720568",
@@ -4368,6 +4385,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/13/1/e066164.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-066164; html:https://europepmc.org/articles/PMC9890277; pdf:https://europepmc.org/articles/PMC9890277?pdf=render"
   },
+  {
+    "id": "33901420",
+    "doi": "https://doi.org/10.1016/s0140-6736(21)00677-2",
+    "title": "Interim findings from first-dose mass COVID-19 vaccination roll-out and COVID-19 hospital admissions in Scotland: a national prospective cohort study.",
+    "authorString": "Vasileiou E, Simpson CR, Shi T, Kerr S, Agrawal U, Akbari A, Bedston S, Beggs J, Bradley D, Chuter A, de Lusignan S, Docherty AB, Ford D, Hobbs FR, Joy M, Katikireddi SV, Marple J, McCowan C, McGagh D, McMenamin J, Moore E, Murray JL, Pan J, Ritchie L, Shah SA, Stock S, Torabi F, Tsang RS, Wood R, Woolhouse M, Robertson C, Sheikh A.",
+    "authorAffiliations": "",
+    "journalTitle": "Lancet (London, England)",
+    "pubYear": "2021",
+    "date": "2021-04-23",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>The BNT162b2 mRNA (Pfizer-BioNTech) and ChAdOx1 nCoV-19 (Oxford-AstraZeneca) COVID-19 vaccines have shown high efficacy against disease in phase 3 clinical trials and are now being used in national vaccination programmes in the UK and several other countries. Studying the real-world effects of these vaccines is an urgent requirement. The aim of our study was to investigate the association between the mass roll-out of the first doses of these COVID-19 vaccines and hospital admissions for COVID-19.<h4>Methods</h4>We did a prospective cohort study using the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19-EAVE II-database comprising linked vaccination, primary care, real-time reverse transcription-PCR testing, and hospital admission patient records for 5\u00b74 million people in Scotland (about 99% of the population) registered at 940 general practices. Individuals who had previously tested positive were excluded from the analysis. A time-dependent Cox model and Poisson regression models with inverse propensity weights were fitted to estimate effectiveness against COVID-19 hospital admission (defined as 1-adjusted rate ratio) following the first dose of vaccine.<h4>Findings</h4>Between Dec 8, 2020, and Feb 22, 2021, a total of 1\u2009331\u2009993 people were vaccinated over the study period. The mean age of those vaccinated was 65\u00b70 years (SD 16\u00b72). The first dose of the BNT162b2 mRNA vaccine was associated with a vaccine effect of 91% (95% CI 85-94) for reduced COVID-19 hospital admission at 28-34 days post-vaccination. Vaccine effect at the same time interval for the ChAdOx1 vaccine was 88% (95% CI 75-94). Results of combined vaccine effects against hospital admission due to COVID-19 were similar when restricting the analysis to those aged 80 years and older (83%, 95% CI 72-89 at 28-34 days post-vaccination).<h4>Interpretation</h4>Mass roll-out of the first doses of the BNT162b2 mRNA and ChAdOx1 vaccines was associated with substantial reductions in the risk of hospital admission due to COVID-19 in Scotland. There remains the possibility that some of the observed effects might have been due to residual confounding.<h4>Funding</h4>UK Research and Innovation (Medical Research Council), Research and Innovation Industrial Strategy Challenge Fund, Health Data Research UK.",
+    "laySummary": "",
+    "urls": "pdf:https://aura.abdn.ac.uk/bitstream/2164/17090/1/Vasileiou_etal_Lancet_Interim_Findings_FirstDose_VOR.pdf; doi:https://doi.org/10.1016/S0140-6736(21)00677-2; html:https://europepmc.org/articles/PMC8064669"
+  },
   {
     "id": "38539097",
     "doi": "https://doi.org/10.1186/s12877-024-04804-w",
@@ -4419,40 +4453,6 @@
     "laySummary": "",
     "urls": "pdf:https://ij-healthgeographics.biomedcentral.com/track/pdf/10.1186/s12942-020-00208-2; doi:https://doi.org/10.1186/s12942-020-00208-2; html:https://europepmc.org/articles/PMC7147039; pdf:https://europepmc.org/articles/PMC7147039?pdf=render"
   },
-  {
-    "id": "35798890",
-    "doi": "https://doi.org/10.1038/s41564-022-01143-7",
-    "title": "SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway.",
-    "authorString": "Willett BJ, Grove J, MacLean OA, Wilkie C, De Lorenzo G, Furnon W, Cantoni D, Scott S, Logan N, Ashraf S, Manali M, Szemiel A, Cowton V, Vink E, Harvey WT, Davis C, Asamaphan P, Smollett K, Tong L, Orton R, Hughes J, Holland P, Silva V, Pascall DJ, Puxty K, da Silva Filipe A, Yebra G, Shaaban S, Holden MTG, Pinto RM, Gunson R, Templeton K, Murcia PR, Patel AH, Klenerman P, Dunachie S, PITCH Consortium, COVID-19 Genomics UK (COG-UK) Consortium, Haughney J, Robertson DL, Palmarini M, Ray S, Thomson EC.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature microbiology",
-    "pubYear": "2022",
-    "date": "2022-07-07",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41564-022-01143-7.pdf; doi:https://doi.org/10.1038/s41564-022-01143-7; html:https://europepmc.org/articles/PMC9352574; pdf:https://europepmc.org/articles/PMC9352574?pdf=render"
-  },
-  {
-    "id": "37056776",
-    "doi": "https://doi.org/10.3389/fimmu.2023.1146702",
-    "title": "SARS-CoV-2 antibody responses associate with sex, age and disease severity in previously uninfected people admitted to hospital with COVID-19: An ISARIC4C prospective study.",
-    "authorString": "Parker E, Thomas J, Roper KJ, Ijaz S, Edwards T, Marchesin F, Katsanovskaja K, Lett L, Jones C, Hardwick HE, Davis C, Vink E, McDonald SE, Moore SC, Dicks S, Jegatheesan K, Cook NJ, Hope J, Cherepanov P, McClure MO, Baillie JK, Openshaw PJM, Turtle L, Ho A, Semple MG, Paxton WA, Tedder RS, Pollakis G, ISARIC4C Investigators.",
-    "authorAffiliations": "",
-    "journalTitle": "Frontiers in immunology",
-    "pubYear": "2023",
-    "date": "2023-03-15",
-    "isOpenAccess": "Y",
-    "keywords": "Serology; Virus; Disease; immunology; Neutralisation; Covid-19; Sars-cov-2",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The SARS-CoV-2 pandemic enables the analysis of immune responses induced against a novel coronavirus infecting immunologically na\u00efve individuals. This provides an opportunity for analysis of immune responses and associations with age, sex and disease severity. Here we measured an array of solid-phase binding antibody and viral neutralising Ab (nAb) responses in participants (n=337) of the ISARIC4C cohort and characterised their correlation with peak disease severity during acute infection and early convalescence. Overall, the responses in a Double Antigen Binding Assay (DABA) for antibody to the receptor binding domain (anti-RBD) correlated well with IgM as well as IgG responses against viral spike, S1 and nucleocapsid protein (NP) antigens. DABA reactivity also correlated with nAb. As we and others reported previously, there is greater risk of severe disease and death in older men, whilst the sex ratio was found to be equal within each severity grouping in younger people. In older males with severe disease (mean age 68 years), peak antibody levels were found to be delayed by one to two weeks compared with women, and nAb responses were delayed further. Additionally, we demonstrated that solid-phase binding antibody responses reached higher levels in males as measured <i>via</i> DABA and IgM binding against Spike, NP and S1 antigens. In contrast, this was not observed for nAb responses. When measuring SARS-CoV-2 RNA transcripts (as a surrogate for viral shedding) in nasal swabs at recruitment, we saw no significant differences by sex or disease severity status. However, we have shown higher antibody levels associated with low nasal viral RNA indicating a role of antibody responses in controlling viral replication and shedding in the upper airway. In this study, we have shown discernible differences in the humoral immune responses between males and females and these differences associate with age as well as with resultant disease severity.",
-    "laySummary": "",
-    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fimmu.2023.1146702/pdf; doi:https://doi.org/10.3389/fimmu.2023.1146702; html:https://europepmc.org/articles/PMC10087108; pdf:https://europepmc.org/articles/PMC10087108?pdf=render"
-  },
   {
     "id": "38894691",
     "doi": "https://doi.org/10.2337/dc24-0537",
@@ -4487,6 +4487,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-024-03477-x; doi:https://doi.org/10.1186/s12916-024-03477-x; html:https://europepmc.org/articles/PMC11188519; pdf:https://europepmc.org/articles/PMC11188519?pdf=render"
   },
+  {
+    "id": "39045545",
+    "doi": "https://doi.org/10.1016/j.eclinm.2024.102703",
+    "title": "Association of latent class analysis-derived multimorbidity clusters with adverse health outcomes in patients with multiple long-term conditions: comparative results across three UK cohorts.",
+    "authorString": "Krauth SJ, Steell L, Ahmed S, McIntosh E, Dibben GO, Hanlon P, Lewsey J, Nicholl BI, McAllister DA, Smith SM, Evans R, Ahmed Z, Dean S, Greaves C, Barber S, Doherty P, Gardiner N, Ibbotson T, Jolly K, Ormandy P, Simpson SA, Taylor RS, Singh SJ, Mair FS, Jani BD, PERFORM research team.",
+    "authorAffiliations": "",
+    "journalTitle": "EClinicalMedicine",
+    "pubYear": "2024",
+    "date": "2024-06-28",
+    "isOpenAccess": "Y",
+    "keywords": "Mortality; Clustering; Primary Health Care; Hospitalisation; Service Use; Multimorbidity",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>It remains unclear how to meaningfully classify people living with multimorbidity (multiple long-term conditions (MLTCs)), beyond counting the number of conditions. This paper aims to identify clusters of MLTCs in different age groups and associated risks of adverse health outcomes and service use.<h4>Methods</h4>Latent class analysis was used to identify MLTCs clusters in different age groups in three cohorts: Secure Anonymised Information Linkage Databank (SAIL) (n\u00a0=\u00a01,825,289), UK Biobank (n\u00a0=\u00a0502,363), and the UK Household Longitudinal Study (UKHLS) (n\u00a0=\u00a049,186). Incidence rate ratios (IRR) for MLTC clusters were computed for: all-cause mortality, hospitalisations, and general practice (GP) use over 10 years, using <2 MLTCs as reference. Information on health outcomes and service use were extracted for a ten year follow up period (between 01<sup>st</sup> Jan 2010 and 31st Dec 2019 for UK Biobank and UKHLS, and between 01<sup>st</sup> Jan 2011 and 31st Dec 2020 for SAIL).<h4>Findings</h4>Clustering MLTCs produced largely similar results across different age groups and cohorts. MLTC clusters had distinct associations with health outcomes and service use after accounting for LTC counts, in fully adjusted models. The largest associations with mortality, hospitalisations and GP use in SAIL were observed for the \"<i>Pain+</i>\" cluster in the age-group 18-36 years (mortality IRR\u00a0=\u00a04.47, hospitalisation IRR\u00a0=\u00a01.84; GP use IRR\u00a0=\u00a02.87) and the \"<i>Hypertension, Diabetes & Heart disease</i>\" cluster in the age-group 37-54 years (mortality IRR\u00a0=\u00a04.52, hospitalisation IRR\u00a0=\u00a01.53, GP use IRR\u00a0=\u00a02.36). In UK Biobank, the \"<i>Cancer, Thyroid disease & Rheumatoid arthritis</i>\" cluster in the age group 37-54 years had the largest association with mortality (IRR\u00a0=\u00a02.47). Cardiometabolic clusters across all age groups, pain/mental health clusters in younger groups, and cancer and pulmonary related clusters in older age groups had higher risk for all outcomes. In UKHLS, MLTC clusters were not significantly associated with higher risk of adverse outcomes, except for the hospitalisation in the age-group 18-36 years.<h4>Interpretation</h4>Personalising care around MLTC clusters that have higher risk of adverse outcomes may have important implications for practice (in relation to secondary prevention), policy (with allocation of health care resources), and research (intervention development and targeting), for people living with MLTCs.<h4>Funding</h4>This study was funded by the National Institute for Health and Care Research (NIHR; Personalised Exercise-Rehabilitation FOR people with Multiple long-term conditions (multimorbidity)-NIHR202020).",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.eclinm.2024.102703; html:https://europepmc.org/articles/PMC11261399; pdf:https://europepmc.org/articles/PMC11261399?pdf=render"
+  },
   {
     "id": "38939225",
     "doi": "https://doi.org/10.3389/fpsyg.2024.1395668",
@@ -4521,23 +4538,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.degruyter.com/document/doi/10.1515/dx-2022-0052/pdf; doi:https://doi.org/10.1515/dx-2022-0052"
   },
-  {
-    "id": "39045545",
-    "doi": "https://doi.org/10.1016/j.eclinm.2024.102703",
-    "title": "Association of latent class analysis-derived multimorbidity clusters with adverse health outcomes in patients with multiple long-term conditions: comparative results across three UK cohorts.",
-    "authorString": "Krauth SJ, Steell L, Ahmed S, McIntosh E, Dibben GO, Hanlon P, Lewsey J, Nicholl BI, McAllister DA, Smith SM, Evans R, Ahmed Z, Dean S, Greaves C, Barber S, Doherty P, Gardiner N, Ibbotson T, Jolly K, Ormandy P, Simpson SA, Taylor RS, Singh SJ, Mair FS, Jani BD, PERFORM research team.",
-    "authorAffiliations": "",
-    "journalTitle": "EClinicalMedicine",
-    "pubYear": "2024",
-    "date": "2024-06-28",
-    "isOpenAccess": "Y",
-    "keywords": "Mortality; Clustering; Primary Health Care; Hospitalisation; Service Use; Multimorbidity",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>It remains unclear how to meaningfully classify people living with multimorbidity (multiple long-term conditions (MLTCs)), beyond counting the number of conditions. This paper aims to identify clusters of MLTCs in different age groups and associated risks of adverse health outcomes and service use.<h4>Methods</h4>Latent class analysis was used to identify MLTCs clusters in different age groups in three cohorts: Secure Anonymised Information Linkage Databank (SAIL) (n\u00a0=\u00a01,825,289), UK Biobank (n\u00a0=\u00a0502,363), and the UK Household Longitudinal Study (UKHLS) (n\u00a0=\u00a049,186). Incidence rate ratios (IRR) for MLTC clusters were computed for: all-cause mortality, hospitalisations, and general practice (GP) use over 10 years, using <2 MLTCs as reference. Information on health outcomes and service use were extracted for a ten year follow up period (between 01<sup>st</sup> Jan 2010 and 31st Dec 2019 for UK Biobank and UKHLS, and between 01<sup>st</sup> Jan 2011 and 31st Dec 2020 for SAIL).<h4>Findings</h4>Clustering MLTCs produced largely similar results across different age groups and cohorts. MLTC clusters had distinct associations with health outcomes and service use after accounting for LTC counts, in fully adjusted models. The largest associations with mortality, hospitalisations and GP use in SAIL were observed for the \"<i>Pain+</i>\" cluster in the age-group 18-36 years (mortality IRR\u00a0=\u00a04.47, hospitalisation IRR\u00a0=\u00a01.84; GP use IRR\u00a0=\u00a02.87) and the \"<i>Hypertension, Diabetes & Heart disease</i>\" cluster in the age-group 37-54 years (mortality IRR\u00a0=\u00a04.52, hospitalisation IRR\u00a0=\u00a01.53, GP use IRR\u00a0=\u00a02.36). In UK Biobank, the \"<i>Cancer, Thyroid disease & Rheumatoid arthritis</i>\" cluster in the age group 37-54 years had the largest association with mortality (IRR\u00a0=\u00a02.47). Cardiometabolic clusters across all age groups, pain/mental health clusters in younger groups, and cancer and pulmonary related clusters in older age groups had higher risk for all outcomes. In UKHLS, MLTC clusters were not significantly associated with higher risk of adverse outcomes, except for the hospitalisation in the age-group 18-36 years.<h4>Interpretation</h4>Personalising care around MLTC clusters that have higher risk of adverse outcomes may have important implications for practice (in relation to secondary prevention), policy (with allocation of health care resources), and research (intervention development and targeting), for people living with MLTCs.<h4>Funding</h4>This study was funded by the National Institute for Health and Care Research (NIHR; Personalised Exercise-Rehabilitation FOR people with Multiple long-term conditions (multimorbidity)-NIHR202020).",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.eclinm.2024.102703; html:https://europepmc.org/articles/PMC11261399; pdf:https://europepmc.org/articles/PMC11261399?pdf=render"
-  },
   {
     "id": "39384575",
     "doi": "https://doi.org/10.1093/ehjqcco/qcae086",
@@ -4606,6 +4606,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1002/alz.13405; html:https://europepmc.org/articles/PMC10592296; pdf:https://europepmc.org/articles/PMC10592296?pdf=render; doi:https://doi.org/10.1002/alz.13405"
   },
+  {
+    "id": "37123891",
+    "doi": "https://doi.org/10.1016/j.heliyon.2023.e15143",
+    "title": "Disclosure control of machine learning models from trusted research environments (TRE): New challenges and opportunities.",
+    "authorString": "Mansouri-Benssassi E, Rogers S, Reel S, Malone M, Smith J, Ritchie F, Jefferson E.",
+    "authorAffiliations": "",
+    "journalTitle": "Heliyon",
+    "pubYear": "2023",
+    "date": "2023-04-03",
+    "isOpenAccess": "Y",
+    "keywords": "AI; Machine Learning; Data Privacy; Safe Haven; Disclosure Control; Trusted Research Environment",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>Artificial intelligence (AI) applications in healthcare and medicine have increased in recent years. To enable access to personal data, Trusted Research Environments (TREs) (otherwise known as Safe Havens) provide safe and secure environments in which researchers can access sensitive personal data and develop AI (in particular machine learning (ML)) models. However, currently few TREs support the training of ML models in part due to a gap in the practical decision-making guidance for TREs in handling model disclosure. Specifically, the training of ML models creates a need to disclose new types of outputs from TREs. Although TREs have clear policies for the disclosure of statistical outputs, the extent to which trained models can leak personal training data once released is not well understood.<h4>Background</h4>We review, for a general audience, different types of ML models and their applicability within healthcare. We explain the outputs from training a ML model and how trained ML models can be vulnerable to external attacks to discover personal data encoded within the model.<h4>Risks</h4>We present the challenges for disclosure control of trained ML models in the context of training and exporting models from TREs. We provide insights and analyse methods that could be introduced within TREs to mitigate the risk of privacy breaches when disclosing trained models.<h4>Discussion</h4>Although specific guidelines and policies exist for statistical disclosure controls in TREs, they do not satisfactorily address these new types of output requests; i.e., trained ML models. There is significant potential for new interdisciplinary research opportunities in developing and adapting policies and tools for safely disclosing ML outputs from TREs.",
+    "laySummary": "",
+    "urls": "pdf:http://www.cell.com/article/S2405844023023502/pdf; doi:https://doi.org/10.1016/j.heliyon.2023.e15143; html:https://europepmc.org/articles/PMC10130764; pdf:https://europepmc.org/articles/PMC10130764?pdf=render"
+  },
   {
     "id": "37494295",
     "doi": "https://doi.org/10.1371/journal.pone.0286840",
@@ -4658,21 +4675,21 @@
     "urls": "pdf:https://bmcmedimaging.biomedcentral.com/track/pdf/10.1186/s12880-021-00671-8; doi:https://doi.org/10.1186/s12880-021-00671-8; html:https://europepmc.org/articles/PMC8487512; pdf:https://europepmc.org/articles/PMC8487512?pdf=render"
   },
   {
-    "id": "37123891",
-    "doi": "https://doi.org/10.1016/j.heliyon.2023.e15143",
-    "title": "Disclosure control of machine learning models from trusted research environments (TRE): New challenges and opportunities.",
-    "authorString": "Mansouri-Benssassi E, Rogers S, Reel S, Malone M, Smith J, Ritchie F, Jefferson E.",
+    "id": "36918541",
+    "doi": "https://doi.org/10.1038/s41467-023-36997-w",
+    "title": "Genetic architecture of spatial electrical biomarkers for cardiac arrhythmia and relationship with cardiovascular disease.",
+    "authorString": "Young WJ, Haessler J, Benjamins JW, Repetto L, Yao J, Isaacs A, Harper AR, Ramirez J, Garnier S, van Duijvenboden S, Baldassari AR, Concas MP, Duong T, Foco L, Isaksen JL, Mei H, Noordam R, Nursyifa C, Richmond A, Santolalla ML, Sitlani CM, Soroush N, Th\u00e9riault S, Trompet S, Aeschbacher S, Ahmadizar F, Alonso A, Brody JA, Campbell A, Correa A, Darbar D, De Luca A, Deleuze JF, Ellervik C, Fuchsberger C, Goel A, Grace C, Guo X, Hansen T, Heckbert SR, Jackson RD, Kors JA, Lima-Costa MF, Linneberg A, Macfarlane PW, Morrison AC, Navarro P, Porteous DJ, Pramstaller PP, Reiner AP, Risch L, Schotten U, Shen X, Sinagra G, Soliman EZ, Stoll M, Tarazona-Santos E, Tinker A, Trajanoska K, Villard E, Warren HR, Whitsel EA, Wiggins KL, Arking DE, Avery CL, Conen D, Girotto G, Grarup N, Hayward C, Jukema JW, Mook-Kanamori DO, Olesen MS, Padmanabhan S, Psaty BM, Pattaro C, Ribeiro ALP, Rotter JI, Stricker BH, van der Harst P, van Duijn CM, Verweij N, Wilson JG, Orini M, Charron P, Watkins H, Kooperberg C, Lin HJ, Wilson JF, Kanters JK, Sotoodehnia N, Mifsud B, Lambiase PD, Tereshchenko LG, Munroe PB.",
     "authorAffiliations": "",
-    "journalTitle": "Heliyon",
+    "journalTitle": "Nature communications",
     "pubYear": "2023",
-    "date": "2023-04-03",
+    "date": "2023-03-14",
     "isOpenAccess": "Y",
-    "keywords": "AI; Machine Learning; Data Privacy; Safe Haven; Disclosure Control; Trusted Research Environment",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>Artificial intelligence (AI) applications in healthcare and medicine have increased in recent years. To enable access to personal data, Trusted Research Environments (TREs) (otherwise known as Safe Havens) provide safe and secure environments in which researchers can access sensitive personal data and develop AI (in particular machine learning (ML)) models. However, currently few TREs support the training of ML models in part due to a gap in the practical decision-making guidance for TREs in handling model disclosure. Specifically, the training of ML models creates a need to disclose new types of outputs from TREs. Although TREs have clear policies for the disclosure of statistical outputs, the extent to which trained models can leak personal training data once released is not well understood.<h4>Background</h4>We review, for a general audience, different types of ML models and their applicability within healthcare. We explain the outputs from training a ML model and how trained ML models can be vulnerable to external attacks to discover personal data encoded within the model.<h4>Risks</h4>We present the challenges for disclosure control of trained ML models in the context of training and exporting models from TREs. We provide insights and analyse methods that could be introduced within TREs to mitigate the risk of privacy breaches when disclosing trained models.<h4>Discussion</h4>Although specific guidelines and policies exist for statistical disclosure controls in TREs, they do not satisfactorily address these new types of output requests; i.e., trained ML models. There is significant potential for new interdisciplinary research opportunities in developing and adapting policies and tools for safely disclosing ML outputs from TREs.",
+    "abstract": "The 3-dimensional spatial and 2-dimensional frontal QRS-T angles are measures derived from the vectorcardiogram. They are independent risk predictors for arrhythmia, but the underlying biology is unknown. Using multi-ancestry genome-wide association studies we identify 61 (58 previously unreported) loci for the spatial QRS-T angle (N\u2009=\u2009118,780) and 11 for the frontal QRS-T angle (N\u2009=\u2009159,715). Seven out of the 61 spatial QRS-T angle loci have not been reported for other electrocardiographic measures. Enrichments are observed in pathways related to cardiac and vascular development, muscle contraction, and hypertrophy. Pairwise genome-wide association studies with classical ECG traits identify shared genetic influences with PR interval and QRS duration.\u00a0Phenome-wide scanning indicate associations with atrial fibrillation, atrioventricular block and arterial embolism\u00a0and\u00a0genetically determined QRS-T angle measures are associated with fascicular and bundle branch block (and also atrioventricular block for the frontal QRS-T angle). We identify potential biology involved in the QRS-T angle\u00a0and\u00a0their genetic relationships with cardiovascular traits and diseases, may inform future research and risk prediction.",
     "laySummary": "",
-    "urls": "pdf:http://www.cell.com/article/S2405844023023502/pdf; doi:https://doi.org/10.1016/j.heliyon.2023.e15143; html:https://europepmc.org/articles/PMC10130764; pdf:https://europepmc.org/articles/PMC10130764?pdf=render"
+    "urls": "pdf:https://www.nature.com/articles/s41467-023-36997-w.pdf; doi:https://doi.org/10.1038/s41467-023-36997-w; html:https://europepmc.org/articles/PMC10015012; pdf:https://europepmc.org/articles/PMC10015012?pdf=render"
   },
   {
     "id": "36035235",
@@ -4691,23 +4708,6 @@
     "laySummary": "",
     "urls": "pdf:https://ng.neurology.org/content/nng/8/5/e200015.full.pdf; doi:https://doi.org/10.1212/NXG.0000000000200015; html:https://europepmc.org/articles/PMC9403885; pdf:https://europepmc.org/articles/PMC9403885?pdf=render"
   },
-  {
-    "id": "37303488",
-    "doi": "https://doi.org/10.1136/bmjmed-2022-000392",
-    "title": "Changes in medication safety indicators in England throughout the covid-19 pandemic using OpenSAFELY: population based, retrospective cohort study of 57 million patients using federated analytics.",
-    "authorString": "Fisher L, Hopcroft LE, Rodgers S, Barrett J, Oliver K, Avery AJ, Evans D, Curtis H, Croker R, Macdonald O, Morley J, Mehrkar A, Bacon S, Davy S, Dillingham I, Evans D, Hickman G, Inglesby P, Morton CE, Smith B, Ward T, Hulme W, Green A, Massey J, Walker AJ, Bates C, Cockburn J, Parry J, Hester F, Harper S, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Griffiths P, Fowles A, Parkes N, Goldacre B, MacKenna B.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ medicine",
-    "pubYear": "2023",
-    "date": "2023-05-11",
-    "isOpenAccess": "Y",
-    "keywords": "Primary Health Care; Medical Informatics; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objective</h4>To implement complex, PINCER (pharmacist led information technology intervention) prescribing indicators, on a national scale with general practice data to describe the impact of the covid-19 pandemic on safe prescribing.<h4>Design</h4>Population based, retrospective cohort study using federated analytics.<h4>Setting</h4>Electronic general practice health record data from 56.8 million NHS patients by use of the OpenSAFELY platform, with the approval of the National Health Service (NHS) England.<h4>Participants</h4>NHS patients (aged 18-120 years) who were alive and registered at a general practice that used TPP or EMIS computer systems and were recorded as at risk of at least one potentially hazardous PINCER indicator.<h4>Main outcome measure</h4>Between 1 September 2019 and 1 September 2021, monthly trends and between practice variation for compliance with 13 PINCER indicators, as calculated on the first of every month, were reported. Prescriptions that do not adhere to these indicators are potentially hazardous and can cause gastrointestinal bleeds; are cautioned against in specific conditions (specifically heart failure, asthma, and chronic renal failure); or require blood test monitoring. The percentage for each indicator is formed of a numerator of patients deemed to be at risk of a potentially hazardous prescribing event and the denominator is of patients for which assessment of the indicator is clinically meaningful. Higher indicator percentages represent potentially poorer performance on medication safety.<h4>Results</h4>The PINCER indicators were successfully implemented across general practice data for 56.8 million patient records from 6367 practices in OpenSAFELY. Hazardous prescribing remained largely unchanged during the covid-19 pandemic, with no evidence of increases in indicators of harm as captured by the PINCER indicators. The percentage of patients at risk of potentially hazardous prescribing, as defined by each PINCER indicator, at mean quarter 1 (Q1) 2020 (representing before the pandemic) ranged from 1.11% (age \u226565 years and non-steroidal anti-inflammatory drugs) to 36.20% (amiodarone and no thyroid function test), while Q1 2021 (representing after the pandemic) percentages ranged from 0.75% (age \u226565 years and non-steroidal anti-inflammatory drugs) to 39.23% (amiodarone and no thyroid function test). Transient delays occurred in blood test monitoring for some medications, particularly angiotensin-converting enzyme inhibitors (where blood monitoring worsened from a mean of 5.16% in Q1 2020 to 12.14% in Q1 2021, and began to recover in June 2021). All indicators substantially recovered by September 2021. We identified 1 813 058 patients (3.1%) at risk of at least one potentially hazardous prescribing event.<h4>Conclusion</h4>NHS data from general practices can be analysed at national scale to generate insights into service delivery. Potentially hazardous prescribing was largely unaffected by the covid-19 pandemic in primary care health records in England.",
-    "laySummary": "",
-    "urls": "pdf:https://bmjmedicine.bmj.com/content/bmjmed/2/1/e000392.full.pdf; doi:https://doi.org/10.1136/bmjmed-2022-000392; html:https://europepmc.org/articles/PMC10254692; pdf:https://europepmc.org/articles/PMC10254692?pdf=render"
-  },
   {
     "id": "36581868",
     "doi": "https://doi.org/10.1186/s12911-022-02045-8",
@@ -4726,38 +4726,21 @@
     "urls": "pdf:https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-022-02045-8; doi:https://doi.org/10.1186/s12911-022-02045-8; html:https://europepmc.org/articles/PMC9798655; pdf:https://europepmc.org/articles/PMC9798655?pdf=render"
   },
   {
-    "id": "36918541",
-    "doi": "https://doi.org/10.1038/s41467-023-36997-w",
-    "title": "Genetic architecture of spatial electrical biomarkers for cardiac arrhythmia and relationship with cardiovascular disease.",
-    "authorString": "Young WJ, Haessler J, Benjamins JW, Repetto L, Yao J, Isaacs A, Harper AR, Ramirez J, Garnier S, van Duijvenboden S, Baldassari AR, Concas MP, Duong T, Foco L, Isaksen JL, Mei H, Noordam R, Nursyifa C, Richmond A, Santolalla ML, Sitlani CM, Soroush N, Th\u00e9riault S, Trompet S, Aeschbacher S, Ahmadizar F, Alonso A, Brody JA, Campbell A, Correa A, Darbar D, De Luca A, Deleuze JF, Ellervik C, Fuchsberger C, Goel A, Grace C, Guo X, Hansen T, Heckbert SR, Jackson RD, Kors JA, Lima-Costa MF, Linneberg A, Macfarlane PW, Morrison AC, Navarro P, Porteous DJ, Pramstaller PP, Reiner AP, Risch L, Schotten U, Shen X, Sinagra G, Soliman EZ, Stoll M, Tarazona-Santos E, Tinker A, Trajanoska K, Villard E, Warren HR, Whitsel EA, Wiggins KL, Arking DE, Avery CL, Conen D, Girotto G, Grarup N, Hayward C, Jukema JW, Mook-Kanamori DO, Olesen MS, Padmanabhan S, Psaty BM, Pattaro C, Ribeiro ALP, Rotter JI, Stricker BH, van der Harst P, van Duijn CM, Verweij N, Wilson JG, Orini M, Charron P, Watkins H, Kooperberg C, Lin HJ, Wilson JF, Kanters JK, Sotoodehnia N, Mifsud B, Lambiase PD, Tereshchenko LG, Munroe PB.",
+    "id": "37303488",
+    "doi": "https://doi.org/10.1136/bmjmed-2022-000392",
+    "title": "Changes in medication safety indicators in England throughout the covid-19 pandemic using OpenSAFELY: population based, retrospective cohort study of 57 million patients using federated analytics.",
+    "authorString": "Fisher L, Hopcroft LE, Rodgers S, Barrett J, Oliver K, Avery AJ, Evans D, Curtis H, Croker R, Macdonald O, Morley J, Mehrkar A, Bacon S, Davy S, Dillingham I, Evans D, Hickman G, Inglesby P, Morton CE, Smith B, Ward T, Hulme W, Green A, Massey J, Walker AJ, Bates C, Cockburn J, Parry J, Hester F, Harper S, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Griffiths P, Fowles A, Parkes N, Goldacre B, MacKenna B.",
     "authorAffiliations": "",
-    "journalTitle": "Nature communications",
+    "journalTitle": "BMJ medicine",
     "pubYear": "2023",
-    "date": "2023-03-14",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The 3-dimensional spatial and 2-dimensional frontal QRS-T angles are measures derived from the vectorcardiogram. They are independent risk predictors for arrhythmia, but the underlying biology is unknown. Using multi-ancestry genome-wide association studies we identify 61 (58 previously unreported) loci for the spatial QRS-T angle (N\u2009=\u2009118,780) and 11 for the frontal QRS-T angle (N\u2009=\u2009159,715). Seven out of the 61 spatial QRS-T angle loci have not been reported for other electrocardiographic measures. Enrichments are observed in pathways related to cardiac and vascular development, muscle contraction, and hypertrophy. Pairwise genome-wide association studies with classical ECG traits identify shared genetic influences with PR interval and QRS duration.\u00a0Phenome-wide scanning indicate associations with atrial fibrillation, atrioventricular block and arterial embolism\u00a0and\u00a0genetically determined QRS-T angle measures are associated with fascicular and bundle branch block (and also atrioventricular block for the frontal QRS-T angle). We identify potential biology involved in the QRS-T angle\u00a0and\u00a0their genetic relationships with cardiovascular traits and diseases, may inform future research and risk prediction.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41467-023-36997-w.pdf; doi:https://doi.org/10.1038/s41467-023-36997-w; html:https://europepmc.org/articles/PMC10015012; pdf:https://europepmc.org/articles/PMC10015012?pdf=render"
-  },
-  {
-    "id": "34183745",
-    "doi": "https://doi.org/10.1038/s41598-021-92874-w",
-    "title": "Frailty assessed by administrative tools and mortality in patients with pneumonia admitted to the hospital and ICU in Wales.",
-    "authorString": "Szakmany T, Hollinghurst J, Pugh R, Akbari A, Griffiths R, Bailey R, Lyons RA.",
-    "authorAffiliations": "",
-    "journalTitle": "Scientific reports",
-    "pubYear": "2021",
-    "date": "2021-06-28",
+    "date": "2023-05-11",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Primary Health Care; Medical Informatics; Covid-19",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "The ideal method of identifying frailty is uncertain, and data on long-term outcomes is relatively limited. We examined frailty indices derived from population-scale linked data on Intensive Care Unit (ICU) and hospitalised non-ICU patients with pneumonia to elucidate the influence of frailty on mortality. Longitudinal cohort study between 2010-2018 using population-scale anonymised data linkage of healthcare records for adults admitted to hospital with pneumonia in Wales. Primary outcome was in-patient mortality. Odds Ratios (ORs [95% confidence interval]) for age, hospital frailty risk score (HFRS), electronic frailty index (eFI), Charlson comorbidity index (CCI), and social deprivation index were estimated using multivariate logistic regression models. The area under the receiver operating characteristic curve (AUC) was estimated to determine the best fitting models. Of the 107,188 patients, mean (SD) age was 72.6 (16.6) years, 50% were men. The models adjusted for the two frailty indices and the comorbidity index had an increased odds of in-patient mortality for individuals with an ICU admission (ORs for ICU admission in the eFI model 2.67 [2.55, 2.79], HFRS model 2.30 [2.20, 2.41], CCI model 2.62 [2.51, 2.75]). Models indicated advancing age, increased frailty and comorbidity were also associated with an increased odds of in-patient mortality (eFI, baseline fit, ORs: mild 1.09 [1.04, 1.13], moderate 1.13 [1.08, 1.18], severe 1.17 [1.10, 1.23]. HFRS, baseline low, ORs: intermediate 2.65 [2.55, 2.75], high 3.31 [3.17, 3.45]). CCI, baseline\u2009<\u20091, ORs: '1-10' 1.15 [1.11, 1.20],\u2009>\u200910 2.50 [2.41, 2.60]). For predicting inpatient deaths, the CCI and HFRS based models were similar, however for longer term outcomes the CCI based model was superior. Frailty and comorbidity are significant risk factors for patients admitted to hospital with pneumonia. Frailty and comorbidity scores based on administrative data have only moderate ability to predict outcome.",
+    "abstract": "<h4>Objective</h4>To implement complex, PINCER (pharmacist led information technology intervention) prescribing indicators, on a national scale with general practice data to describe the impact of the covid-19 pandemic on safe prescribing.<h4>Design</h4>Population based, retrospective cohort study using federated analytics.<h4>Setting</h4>Electronic general practice health record data from 56.8 million NHS patients by use of the OpenSAFELY platform, with the approval of the National Health Service (NHS) England.<h4>Participants</h4>NHS patients (aged 18-120 years) who were alive and registered at a general practice that used TPP or EMIS computer systems and were recorded as at risk of at least one potentially hazardous PINCER indicator.<h4>Main outcome measure</h4>Between 1 September 2019 and 1 September 2021, monthly trends and between practice variation for compliance with 13 PINCER indicators, as calculated on the first of every month, were reported. Prescriptions that do not adhere to these indicators are potentially hazardous and can cause gastrointestinal bleeds; are cautioned against in specific conditions (specifically heart failure, asthma, and chronic renal failure); or require blood test monitoring. The percentage for each indicator is formed of a numerator of patients deemed to be at risk of a potentially hazardous prescribing event and the denominator is of patients for which assessment of the indicator is clinically meaningful. Higher indicator percentages represent potentially poorer performance on medication safety.<h4>Results</h4>The PINCER indicators were successfully implemented across general practice data for 56.8 million patient records from 6367 practices in OpenSAFELY. Hazardous prescribing remained largely unchanged during the covid-19 pandemic, with no evidence of increases in indicators of harm as captured by the PINCER indicators. The percentage of patients at risk of potentially hazardous prescribing, as defined by each PINCER indicator, at mean quarter 1 (Q1) 2020 (representing before the pandemic) ranged from 1.11% (age \u226565 years and non-steroidal anti-inflammatory drugs) to 36.20% (amiodarone and no thyroid function test), while Q1 2021 (representing after the pandemic) percentages ranged from 0.75% (age \u226565 years and non-steroidal anti-inflammatory drugs) to 39.23% (amiodarone and no thyroid function test). Transient delays occurred in blood test monitoring for some medications, particularly angiotensin-converting enzyme inhibitors (where blood monitoring worsened from a mean of 5.16% in Q1 2020 to 12.14% in Q1 2021, and began to recover in June 2021). All indicators substantially recovered by September 2021. We identified 1 813 058 patients (3.1%) at risk of at least one potentially hazardous prescribing event.<h4>Conclusion</h4>NHS data from general practices can be analysed at national scale to generate insights into service delivery. Potentially hazardous prescribing was largely unaffected by the covid-19 pandemic in primary care health records in England.",
     "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41598-021-92874-w.pdf; doi:https://doi.org/10.1038/s41598-021-92874-w; html:https://europepmc.org/articles/PMC8239046; pdf:https://europepmc.org/articles/PMC8239046?pdf=render"
+    "urls": "pdf:https://bmjmedicine.bmj.com/content/bmjmed/2/1/e000392.full.pdf; doi:https://doi.org/10.1136/bmjmed-2022-000392; html:https://europepmc.org/articles/PMC10254692; pdf:https://europepmc.org/articles/PMC10254692?pdf=render"
   },
   {
     "id": "39167370",
@@ -4777,38 +4760,21 @@
     "urls": "doi:https://doi.org/10.1001/jamapsychiatry.2024.2339; html:https://europepmc.org/articles/PMC11339697"
   },
   {
-    "id": "35255492",
-    "doi": "https://doi.org/10.1038/s41586-022-04576-6",
-    "title": "Whole-genome sequencing reveals host factors underlying critical COVID-19.",
-    "authorString": "Kousathanas A, Pairo-Castineira E, Rawlik K, Stuckey A, Odhams CA, Walker S, Russell CD, Malinauskas T, Wu Y, Millar J, Shen X, Elliott KS, Griffiths F, Oosthuyzen W, Morrice K, Keating S, Wang B, Rhodes D, Klaric L, Zechner M, Parkinson N, Siddiq A, Goddard P, Donovan S, Maslove D, Nichol A, Semple MG, Zainy T, Maleady-Crowe F, Todd L, Salehi S, Knight J, Elgar G, Chan G, Arumugam P, Patch C, Rendon A, Bentley D, Kingsley C, Kosmicki JA, Horowitz JE, Baras A, Abecasis GR, Ferreira MAR, Justice A, Mirshahi T, Oetjens M, Rader DJ, Ritchie MD, Verma A, Fowler TA, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Elliott P, Walsh T, Tenesa A, GenOMICC investigators, 23andMe investigators, COVID-19 Human Genetics Initiative, Fawkes A, Murphy L, Rowan K, Ponting CP, Vitart V, Wilson JF, Yang J, Bretherick AD, Scott RH, Hendry SC, Moutsianas L, Law A, Caulfield MJ, Baillie JK.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature",
-    "pubYear": "2022",
-    "date": "2022-03-07",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care<sup>1</sup> or hospitalization<sup>2-4</sup> after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41586-022-04576-6.pdf; doi:https://doi.org/10.1038/s41586-022-04576-6; html:https://europepmc.org/articles/PMC9259496; pdf:https://europepmc.org/articles/PMC9259496?pdf=render"
-  },
-  {
-    "id": "36609574",
-    "doi": "https://doi.org/10.1038/s41467-022-35771-8",
-    "title": "A population-based matched cohort study of major congenital anomalies following COVID-19 vaccination and SARS-CoV-2 infection.",
-    "authorString": "Calvert C, Carruthers J, Denny C, Donaghy J, Hopcroft LEM, Hopkins L, Goulding A, Lindsay L, McLaughlin T, Moore E, Taylor B, Loane M, Dolk H, Morris J, Auyeung B, Bhaskaran K, Gibbons CL, Katikireddi SV, O'Leary M, McAllister D, Shi T, Simpson CR, Robertson C, Sheikh A, Stock SJ, Wood R.",
+    "id": "34183745",
+    "doi": "https://doi.org/10.1038/s41598-021-92874-w",
+    "title": "Frailty assessed by administrative tools and mortality in patients with pneumonia admitted to the hospital and ICU in Wales.",
+    "authorString": "Szakmany T, Hollinghurst J, Pugh R, Akbari A, Griffiths R, Bailey R, Lyons RA.",
     "authorAffiliations": "",
-    "journalTitle": "Nature communications",
-    "pubYear": "2023",
-    "date": "2023-01-06",
+    "journalTitle": "Scientific reports",
+    "pubYear": "2021",
+    "date": "2021-06-28",
     "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Evidence on associations between COVID-19 vaccination or SARS-CoV-2 infection and the risk of congenital anomalies is limited. Here we report a national, population-based, matched cohort study using linked electronic health records from Scotland (May 2020-April 2022) to estimate the association between COVID-19 vaccination and, separately, SARS-CoV-2 infection between six weeks pre-conception and 19 weeks and six days gestation and the risk of [1] any major congenital anomaly and [2] any non-genetic major congenital anomaly. Mothers vaccinated in this pregnancy exposure period mostly received an mRNA vaccine (73.7% Pfizer-BioNTech BNT162b2 and 7.9% Moderna mRNA-1273). Of the 6731 babies whose mothers were vaccinated in the pregnancy exposure period, 153 had any anomaly and 120 had a non-genetic anomaly. Primary analyses find no association between any vaccination and any anomaly (adjusted Odds Ratio [aOR] = 1.01, 95% Confidence Interval [CI]\u2009=\u20090.83-1.24) or non-genetic anomalies (aOR = 1.00, 95% CI\u2009=\u20090.81-1.22). Primary analyses also find no association between SARS-CoV-2 infection and any anomaly (aOR\u2009=\u20091.02, 95% CI\u2009=\u20090.66-1.60) or non-genetic anomalies (aOR = 0.94, 95% CI\u2009=\u20090.57-1.54). Findings are robust to sensitivity analyses. These data provide reassurance on the safety of vaccination, in particular mRNA vaccines, just before or in early pregnancy.",
+    "abstract": "The ideal method of identifying frailty is uncertain, and data on long-term outcomes is relatively limited. We examined frailty indices derived from population-scale linked data on Intensive Care Unit (ICU) and hospitalised non-ICU patients with pneumonia to elucidate the influence of frailty on mortality. Longitudinal cohort study between 2010-2018 using population-scale anonymised data linkage of healthcare records for adults admitted to hospital with pneumonia in Wales. Primary outcome was in-patient mortality. Odds Ratios (ORs [95% confidence interval]) for age, hospital frailty risk score (HFRS), electronic frailty index (eFI), Charlson comorbidity index (CCI), and social deprivation index were estimated using multivariate logistic regression models. The area under the receiver operating characteristic curve (AUC) was estimated to determine the best fitting models. Of the 107,188 patients, mean (SD) age was 72.6 (16.6) years, 50% were men. The models adjusted for the two frailty indices and the comorbidity index had an increased odds of in-patient mortality for individuals with an ICU admission (ORs for ICU admission in the eFI model 2.67 [2.55, 2.79], HFRS model 2.30 [2.20, 2.41], CCI model 2.62 [2.51, 2.75]). Models indicated advancing age, increased frailty and comorbidity were also associated with an increased odds of in-patient mortality (eFI, baseline fit, ORs: mild 1.09 [1.04, 1.13], moderate 1.13 [1.08, 1.18], severe 1.17 [1.10, 1.23]. HFRS, baseline low, ORs: intermediate 2.65 [2.55, 2.75], high 3.31 [3.17, 3.45]). CCI, baseline\u2009<\u20091, ORs: '1-10' 1.15 [1.11, 1.20],\u2009>\u200910 2.50 [2.41, 2.60]). For predicting inpatient deaths, the CCI and HFRS based models were similar, however for longer term outcomes the CCI based model was superior. Frailty and comorbidity are significant risk factors for patients admitted to hospital with pneumonia. Frailty and comorbidity scores based on administrative data have only moderate ability to predict outcome.",
     "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41467-022-35771-8.pdf; doi:https://doi.org/10.1038/s41467-022-35771-8; html:https://europepmc.org/articles/PMC9821346; pdf:https://europepmc.org/articles/PMC9821346?pdf=render"
+    "urls": "pdf:https://www.nature.com/articles/s41598-021-92874-w.pdf; doi:https://doi.org/10.1038/s41598-021-92874-w; html:https://europepmc.org/articles/PMC8239046; pdf:https://europepmc.org/articles/PMC8239046?pdf=render"
   },
   {
     "id": "38332132",
@@ -4861,6 +4827,40 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41467-023-43661-w.pdf; doi:https://doi.org/10.1038/s41467-023-43661-w; html:https://europepmc.org/articles/PMC10689486; pdf:https://europepmc.org/articles/PMC10689486?pdf=render"
   },
+  {
+    "id": "36609574",
+    "doi": "https://doi.org/10.1038/s41467-022-35771-8",
+    "title": "A population-based matched cohort study of major congenital anomalies following COVID-19 vaccination and SARS-CoV-2 infection.",
+    "authorString": "Calvert C, Carruthers J, Denny C, Donaghy J, Hopcroft LEM, Hopkins L, Goulding A, Lindsay L, McLaughlin T, Moore E, Taylor B, Loane M, Dolk H, Morris J, Auyeung B, Bhaskaran K, Gibbons CL, Katikireddi SV, O'Leary M, McAllister D, Shi T, Simpson CR, Robertson C, Sheikh A, Stock SJ, Wood R.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature communications",
+    "pubYear": "2023",
+    "date": "2023-01-06",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Evidence on associations between COVID-19 vaccination or SARS-CoV-2 infection and the risk of congenital anomalies is limited. Here we report a national, population-based, matched cohort study using linked electronic health records from Scotland (May 2020-April 2022) to estimate the association between COVID-19 vaccination and, separately, SARS-CoV-2 infection between six weeks pre-conception and 19 weeks and six days gestation and the risk of [1] any major congenital anomaly and [2] any non-genetic major congenital anomaly. Mothers vaccinated in this pregnancy exposure period mostly received an mRNA vaccine (73.7% Pfizer-BioNTech BNT162b2 and 7.9% Moderna mRNA-1273). Of the 6731 babies whose mothers were vaccinated in the pregnancy exposure period, 153 had any anomaly and 120 had a non-genetic anomaly. Primary analyses find no association between any vaccination and any anomaly (adjusted Odds Ratio [aOR] = 1.01, 95% Confidence Interval [CI]\u2009=\u20090.83-1.24) or non-genetic anomalies (aOR = 1.00, 95% CI\u2009=\u20090.81-1.22). Primary analyses also find no association between SARS-CoV-2 infection and any anomaly (aOR\u2009=\u20091.02, 95% CI\u2009=\u20090.66-1.60) or non-genetic anomalies (aOR = 0.94, 95% CI\u2009=\u20090.57-1.54). Findings are robust to sensitivity analyses. These data provide reassurance on the safety of vaccination, in particular mRNA vaccines, just before or in early pregnancy.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41467-022-35771-8.pdf; doi:https://doi.org/10.1038/s41467-022-35771-8; html:https://europepmc.org/articles/PMC9821346; pdf:https://europepmc.org/articles/PMC9821346?pdf=render"
+  },
+  {
+    "id": "35255492",
+    "doi": "https://doi.org/10.1038/s41586-022-04576-6",
+    "title": "Whole-genome sequencing reveals host factors underlying critical COVID-19.",
+    "authorString": "Kousathanas A, Pairo-Castineira E, Rawlik K, Stuckey A, Odhams CA, Walker S, Russell CD, Malinauskas T, Wu Y, Millar J, Shen X, Elliott KS, Griffiths F, Oosthuyzen W, Morrice K, Keating S, Wang B, Rhodes D, Klaric L, Zechner M, Parkinson N, Siddiq A, Goddard P, Donovan S, Maslove D, Nichol A, Semple MG, Zainy T, Maleady-Crowe F, Todd L, Salehi S, Knight J, Elgar G, Chan G, Arumugam P, Patch C, Rendon A, Bentley D, Kingsley C, Kosmicki JA, Horowitz JE, Baras A, Abecasis GR, Ferreira MAR, Justice A, Mirshahi T, Oetjens M, Rader DJ, Ritchie MD, Verma A, Fowler TA, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Elliott P, Walsh T, Tenesa A, GenOMICC investigators, 23andMe investigators, COVID-19 Human Genetics Initiative, Fawkes A, Murphy L, Rowan K, Ponting CP, Vitart V, Wilson JF, Yang J, Bretherick AD, Scott RH, Hendry SC, Moutsianas L, Law A, Caulfield MJ, Baillie JK.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature",
+    "pubYear": "2022",
+    "date": "2022-03-07",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care<sup>1</sup> or hospitalization<sup>2-4</sup> after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41586-022-04576-6.pdf; doi:https://doi.org/10.1038/s41586-022-04576-6; html:https://europepmc.org/articles/PMC9259496; pdf:https://europepmc.org/articles/PMC9259496?pdf=render"
+  },
   {
     "id": "35077449",
     "doi": "https://doi.org/10.1371/journal.pmed.1003871",
@@ -4929,23 +4929,6 @@
     "laySummary": "",
     "urls": "pdf:http://www.thelancet.com/article/S2589537020300407/pdf; doi:https://doi.org/10.1016/j.eclinm.2020.100296; html:https://europepmc.org/articles/PMC7152819; pdf:https://europepmc.org/articles/PMC7152819?pdf=render"
   },
-  {
-    "id": "35340900",
-    "doi": "https://doi.org/10.1177/20552076221074122",
-    "title": "Magnetic resonance image-based brain tumour segmentation methods: A systematic review.",
-    "authorString": "Bhalodiya JM, Lim Choi Keung SN, Arvanitis TN.",
-    "authorAffiliations": "",
-    "journalTitle": "Digital health",
-    "pubYear": "2022",
-    "date": "2022-01-01",
-    "isOpenAccess": "Y",
-    "keywords": "Brain; Artificial intelligence; Segmentation; Systematic review; Magnetic Resonance Imaging; Brain Tumour",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Image segmentation is an essential step in the analysis and subsequent characterisation of brain tumours through magnetic resonance imaging. In the literature, segmentation methods are empowered by open-access magnetic resonance imaging datasets, such as the brain tumour segmentation dataset. Moreover, with the increased use of artificial intelligence methods in medical imaging, access to larger data repositories has become vital in method development.<h4>Purpose</h4>To determine what automated brain tumour segmentation techniques can medical imaging specialists and clinicians use to identify tumour components, compared to manual segmentation.<h4>Methods</h4>We conducted a systematic review of 572 brain tumour segmentation studies during 2015-2020. We reviewed segmentation techniques using T1-weighted, T2-weighted, gadolinium-enhanced T1-weighted, fluid-attenuated inversion recovery, diffusion-weighted and perfusion-weighted magnetic resonance imaging sequences. Moreover, we assessed physics or mathematics-based methods, deep learning methods, and software-based or semi-automatic methods, as applied to magnetic resonance imaging techniques. Particularly, we synthesised each method as per the utilised magnetic resonance imaging sequences, study population, technical approach (such as deep learning) and performance score measures (such as Dice score).<h4>Statistical tests</h4>We compared median Dice score in segmenting the whole tumour, tumour core and enhanced tumour.<h4>Results</h4>We found that T1-weighted, gadolinium-enhanced T1-weighted, T2-weighted and fluid-attenuated inversion recovery magnetic resonance imaging are used the most in various segmentation algorithms. However, there is limited use of perfusion-weighted and diffusion-weighted magnetic resonance imaging. Moreover, we found that the U-Net deep learning technology is cited the most, and has high accuracy (Dice score 0.9) for magnetic resonance imaging-based brain tumour segmentation.<h4>Conclusion</h4>U-Net is a promising deep learning technology for magnetic resonance imaging-based brain tumour segmentation. The community should be encouraged to contribute open-access datasets so training, testing and validation of deep learning algorithms can be improved, particularly for diffusion- and perfusion-weighted magnetic resonance imaging, where there are limited datasets available.",
-    "laySummary": "",
-    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/20552076221074122; doi:https://doi.org/10.1177/20552076221074122; html:https://europepmc.org/articles/PMC8943308; pdf:https://europepmc.org/articles/PMC8943308?pdf=render"
-  },
   {
     "id": "34384736",
     "doi": "https://doi.org/10.1016/s2589-7500(21)00175-8",
@@ -4964,21 +4947,21 @@
     "urls": "pdf:https://aura.abdn.ac.uk/bitstream/2164/21105/1/Shah_etal_Predicted_Covid_19_Positive_VOR.pdf; doi:https://doi.org/10.1016/S2589-7500(21)00175-8; html:https://europepmc.org/articles/PMC8352493; pdf:https://europepmc.org/articles/PMC8352493?pdf=render"
   },
   {
-    "id": "36874571",
-    "doi": "https://doi.org/10.12688/wellcomeopenres.17981.1",
-    "title": "Settings for non-household transmission of SARS-CoV-2 during the second lockdown in England and Wales - analysis of the Virus Watch household community cohort study.",
-    "authorString": "Hoskins S, Beale S, Nguyen V, Fragaszy E, Navaratnam AMD, Smith C, French C, Kovar J, Byrne T, Fong WLE, Geismar C, Patel P, Yavlinksy A, Johnson AM, Aldridge RW, Hayward A, Virus Watch Collaborative.",
+    "id": "35340900",
+    "doi": "https://doi.org/10.1177/20552076221074122",
+    "title": "Magnetic resonance image-based brain tumour segmentation methods: A systematic review.",
+    "authorString": "Bhalodiya JM, Lim Choi Keung SN, Arvanitis TN.",
     "authorAffiliations": "",
-    "journalTitle": "Wellcome open research",
+    "journalTitle": "Digital health",
     "pubYear": "2022",
-    "date": "2022-08-03",
+    "date": "2022-01-01",
     "isOpenAccess": "Y",
-    "keywords": "Transmission; Activities; Pandemic; Work; Public Transport; Shopping; Lockdown; Covid-19; Sars-cov-2",
+    "keywords": "Brain; Artificial intelligence; Segmentation; Systematic review; Magnetic Resonance Imaging; Brain Tumour",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<b>Background</b>: \"Lockdowns\" to control serious respiratory virus pandemics were widely used during the coronavirus disease 2019 (COVID-19) pandemic.\u00a0 However, there is limited information to understand the settings in which most transmission occurs during lockdowns, to support refinement of similar policies for future pandemics.\u00a0 <b>Methods</b>: Among Virus Watch household cohort participants we identified those infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outside the household.\u00a0 Using survey activity data, we undertook multivariable logistic regressions assessing the contribution of activities on non-household infection risk.\u00a0 We calculated adjusted population attributable fractions (APAF) to estimate which activity accounted for the greatest proportion of non-household infections during the pandemic's second wave. <b>Results</b>: Among 10,858 adults, 18% of cases were likely due to household transmission.\u00a0 Among 10,475 participants (household-acquired cases excluded), including 874 non-household-acquired infections, infection was associated with: leaving home for work or education (AOR 1.20 (1.02 - 1.42), APAF 6.9%); public transport (more than once per week AOR 1.82 (1.49 - 2.23), public transport APAF 12.42%); and shopping (more than once per week AOR 1.69 (1.29 - 2.21), shopping APAF 34.56%).\u00a0 Other non-household activities were rare and not significantly associated with infection. <b>Conclusions:</b> During lockdown, going to work and using public or shared transport independently increased infection risk, however only a minority did these activities.\u00a0 Most participants visited shops, accounting for one-third of non-household transmission. \u00a0Transmission in restricted hospitality and leisure settings was minimal suggesting these restrictions were effective.\u00a0 \u00a0If future respiratory infection pandemics emerge these findings highlight the value of working from home, using forms of transport that minimise exposure to others, minimising exposure to shops and restricting non-essential activities.",
+    "abstract": "<h4>Background</h4>Image segmentation is an essential step in the analysis and subsequent characterisation of brain tumours through magnetic resonance imaging. In the literature, segmentation methods are empowered by open-access magnetic resonance imaging datasets, such as the brain tumour segmentation dataset. Moreover, with the increased use of artificial intelligence methods in medical imaging, access to larger data repositories has become vital in method development.<h4>Purpose</h4>To determine what automated brain tumour segmentation techniques can medical imaging specialists and clinicians use to identify tumour components, compared to manual segmentation.<h4>Methods</h4>We conducted a systematic review of 572 brain tumour segmentation studies during 2015-2020. We reviewed segmentation techniques using T1-weighted, T2-weighted, gadolinium-enhanced T1-weighted, fluid-attenuated inversion recovery, diffusion-weighted and perfusion-weighted magnetic resonance imaging sequences. Moreover, we assessed physics or mathematics-based methods, deep learning methods, and software-based or semi-automatic methods, as applied to magnetic resonance imaging techniques. Particularly, we synthesised each method as per the utilised magnetic resonance imaging sequences, study population, technical approach (such as deep learning) and performance score measures (such as Dice score).<h4>Statistical tests</h4>We compared median Dice score in segmenting the whole tumour, tumour core and enhanced tumour.<h4>Results</h4>We found that T1-weighted, gadolinium-enhanced T1-weighted, T2-weighted and fluid-attenuated inversion recovery magnetic resonance imaging are used the most in various segmentation algorithms. However, there is limited use of perfusion-weighted and diffusion-weighted magnetic resonance imaging. Moreover, we found that the U-Net deep learning technology is cited the most, and has high accuracy (Dice score 0.9) for magnetic resonance imaging-based brain tumour segmentation.<h4>Conclusion</h4>U-Net is a promising deep learning technology for magnetic resonance imaging-based brain tumour segmentation. The community should be encouraged to contribute open-access datasets so training, testing and validation of deep learning algorithms can be improved, particularly for diffusion- and perfusion-weighted magnetic resonance imaging, where there are limited datasets available.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.12688/wellcomeopenres.17981.1; html:https://europepmc.org/articles/PMC9975411; pdf:https://europepmc.org/articles/PMC9975411?pdf=render"
+    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/20552076221074122; doi:https://doi.org/10.1177/20552076221074122; html:https://europepmc.org/articles/PMC8943308; pdf:https://europepmc.org/articles/PMC8943308?pdf=render"
   },
   {
     "id": "34605164",
@@ -4997,6 +4980,23 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/mnfr.202100316; doi:https://doi.org/10.1002/mnfr.202100316; html:https://europepmc.org/articles/PMC11475553; pdf:https://europepmc.org/articles/PMC11475553?pdf=render"
   },
+  {
+    "id": "36874571",
+    "doi": "https://doi.org/10.12688/wellcomeopenres.17981.1",
+    "title": "Settings for non-household transmission of SARS-CoV-2 during the second lockdown in England and Wales - analysis of the Virus Watch household community cohort study.",
+    "authorString": "Hoskins S, Beale S, Nguyen V, Fragaszy E, Navaratnam AMD, Smith C, French C, Kovar J, Byrne T, Fong WLE, Geismar C, Patel P, Yavlinksy A, Johnson AM, Aldridge RW, Hayward A, Virus Watch Collaborative.",
+    "authorAffiliations": "",
+    "journalTitle": "Wellcome open research",
+    "pubYear": "2022",
+    "date": "2022-08-03",
+    "isOpenAccess": "Y",
+    "keywords": "Transmission; Activities; Pandemic; Work; Public Transport; Shopping; Lockdown; Covid-19; Sars-cov-2",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<b>Background</b>: \"Lockdowns\" to control serious respiratory virus pandemics were widely used during the coronavirus disease 2019 (COVID-19) pandemic.\u00a0 However, there is limited information to understand the settings in which most transmission occurs during lockdowns, to support refinement of similar policies for future pandemics.\u00a0 <b>Methods</b>: Among Virus Watch household cohort participants we identified those infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outside the household.\u00a0 Using survey activity data, we undertook multivariable logistic regressions assessing the contribution of activities on non-household infection risk.\u00a0 We calculated adjusted population attributable fractions (APAF) to estimate which activity accounted for the greatest proportion of non-household infections during the pandemic's second wave. <b>Results</b>: Among 10,858 adults, 18% of cases were likely due to household transmission.\u00a0 Among 10,475 participants (household-acquired cases excluded), including 874 non-household-acquired infections, infection was associated with: leaving home for work or education (AOR 1.20 (1.02 - 1.42), APAF 6.9%); public transport (more than once per week AOR 1.82 (1.49 - 2.23), public transport APAF 12.42%); and shopping (more than once per week AOR 1.69 (1.29 - 2.21), shopping APAF 34.56%).\u00a0 Other non-household activities were rare and not significantly associated with infection. <b>Conclusions:</b> During lockdown, going to work and using public or shared transport independently increased infection risk, however only a minority did these activities.\u00a0 Most participants visited shops, accounting for one-third of non-household transmission. \u00a0Transmission in restricted hospitality and leisure settings was minimal suggesting these restrictions were effective.\u00a0 \u00a0If future respiratory infection pandemics emerge these findings highlight the value of working from home, using forms of transport that minimise exposure to others, minimising exposure to shops and restricting non-essential activities.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.12688/wellcomeopenres.17981.1; html:https://europepmc.org/articles/PMC9975411; pdf:https://europepmc.org/articles/PMC9975411?pdf=render"
+  },
   {
     "id": "36891499",
     "doi": "https://doi.org/10.1016/j.ssmph.2023.101370",
@@ -5014,23 +5014,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.ssmph.2023.101370; doi:https://doi.org/10.1016/j.ssmph.2023.101370; html:https://europepmc.org/articles/PMC9986621; pdf:https://europepmc.org/articles/PMC9986621?pdf=render"
   },
-  {
-    "id": "37088955",
-    "doi": "https://doi.org/10.1177/02692163231167212",
-    "title": "Deaths at home, area-based deprivation and the effect of the Covid-19 pandemic: An analysis of mortality data across four nations.",
-    "authorString": "Leniz J, Davies JM, Bone AE, Hocaoglu M, Verne J, Barclay S, Murtagh FEM, Fraser LK, Higginson IJ, Sleeman KE.",
-    "authorAffiliations": "",
-    "journalTitle": "Palliative medicine",
-    "pubYear": "2023",
-    "date": "2023-04-23",
-    "isOpenAccess": "Y",
-    "keywords": "Mortality; Palliative care; Terminal Care; Inequalities; Place Of Death; Deprivation; Pandemics; Socio-economic Position; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>The number and proportion of home deaths in the UK increased during the Covid-19 pandemic. It is not known whether these changes were experienced disproportionately by people from different socioeconomic groups.<h4>Aim</h4>To examine the association between home death and socioeconomic position during the Covid-19 pandemic, and how this changed between 2019 and 2020.<h4>Design</h4>Retrospective cohort study using population-based individual-level mortality data.<h4>Setting/participants</h4>All registered deaths in England, Wales, Scotland and Northern Ireland. The proportion of home deaths between 28th March and 31st December 2020 was compared with the same period in 2019. We used Poisson regression models to evaluate the association between decedent's area-based level of deprivation and risk of home death, as well as the interaction between deprivation and year of death, for each nation separately.<h4>Results</h4>Between the 28th March and 31st December 2020, 409,718 deaths were recorded in England, 46,372 in Scotland, 26,410 in Wales and 13,404 in Northern Ireland. All four nations showed an increase in the adjusted proportion of home deaths between 2019 and 2020, ranging from 21 to 28%. This increase was lowest for people living in the most deprived areas in all nations, with evidence of a deprivation gradient in England.<h4>Conclusions</h4>The Covid-19 pandemic exacerbated a previously described socioeconomic inequality in place of death in the UK. Further research to understand the reasons for this change and if this inequality has been sustained is needed.",
-    "laySummary": "",
-    "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10125882; doi:https://doi.org/10.1177/02692163231167212; html:https://europepmc.org/articles/PMC10125882; pdf:https://europepmc.org/articles/PMC10125882?pdf=render"
-  },
   {
     "id": "35476839",
     "doi": "https://doi.org/10.1371/journal.pone.0266967",
@@ -5049,21 +5032,21 @@
     "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0266967&type=printable; doi:https://doi.org/10.1371/journal.pone.0266967; html:https://europepmc.org/articles/PMC9045644; pdf:https://europepmc.org/articles/PMC9045644?pdf=render"
   },
   {
-    "id": "36497616",
-    "doi": "https://doi.org/10.3390/ijerph192315544",
-    "title": "Association between Internet Usage and Quality of Life of Elderly People in England: Evidence from the English Longitudinal Study of Ageing (ELSA).",
-    "authorString": "Vidiasratri AR, Bath PA, Bath PA.",
+    "id": "37088955",
+    "doi": "https://doi.org/10.1177/02692163231167212",
+    "title": "Deaths at home, area-based deprivation and the effect of the Covid-19 pandemic: An analysis of mortality data across four nations.",
+    "authorString": "Leniz J, Davies JM, Bone AE, Hocaoglu M, Verne J, Barclay S, Murtagh FEM, Fraser LK, Higginson IJ, Sleeman KE.",
     "authorAffiliations": "",
-    "journalTitle": "International journal of environmental research and public health",
-    "pubYear": "2022",
-    "date": "2022-11-23",
+    "journalTitle": "Palliative medicine",
+    "pubYear": "2023",
+    "date": "2023-04-23",
     "isOpenAccess": "Y",
-    "keywords": "Internet; Quality of life; Older People",
+    "keywords": "Mortality; Palliative care; Terminal Care; Inequalities; Place Of Death; Deprivation; Pandemics; Socio-economic Position; Covid-19",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "The WHO has stated that the number of senior citizens above age 65 across the world will double by the year 2050: in the UK, the whole population is projected to grow by about 2.5% over a decade, from mid-2018. Although people are living longer, they are not healthier in old age, and there is an increasing number of illnesses and disabilities in the ageing population, which have an impact on their overall well-being and quality of life (QoL). Alongside these trends, Internet technologies have improved and provide a wide range of information, including on medical and health issues. This study aimed to examine the association between the utilisation of the internet among older people in England and their QoL. This study utilised the English Longitudinal Study of Aging (ELSA), a longitudinal study of a representative sample of people aged 50 and over in England. The data from Wave 9 were analysed using bivariate analysis and logistic regression. The results show a strong association between QoL and utilisation of the Internet in older people, even when adjusting for demographic variables and health. Higher use of the internet was associated with older people being less likely to have higher QoL. The excessive use of the internet for communication and gathering information also contributed to lower QoL. From the findings, poorer QoL was also found in people in older age groups, in those who are married, and those who never suffer from chronic diseases. Our findings suggest that the quality of life in older people might not only be associated with the frequency of usage but also the purpose for which the internet is used; however, this relationship is complex and further research should explore this in greater depth. Further research should also investigate how older people's use of the Internet changed during the COVID-19 pandemic and the effects of this on the QoL in older age.",
+    "abstract": "<h4>Background</h4>The number and proportion of home deaths in the UK increased during the Covid-19 pandemic. It is not known whether these changes were experienced disproportionately by people from different socioeconomic groups.<h4>Aim</h4>To examine the association between home death and socioeconomic position during the Covid-19 pandemic, and how this changed between 2019 and 2020.<h4>Design</h4>Retrospective cohort study using population-based individual-level mortality data.<h4>Setting/participants</h4>All registered deaths in England, Wales, Scotland and Northern Ireland. The proportion of home deaths between 28th March and 31st December 2020 was compared with the same period in 2019. We used Poisson regression models to evaluate the association between decedent's area-based level of deprivation and risk of home death, as well as the interaction between deprivation and year of death, for each nation separately.<h4>Results</h4>Between the 28th March and 31st December 2020, 409,718 deaths were recorded in England, 46,372 in Scotland, 26,410 in Wales and 13,404 in Northern Ireland. All four nations showed an increase in the adjusted proportion of home deaths between 2019 and 2020, ranging from 21 to 28%. This increase was lowest for people living in the most deprived areas in all nations, with evidence of a deprivation gradient in England.<h4>Conclusions</h4>The Covid-19 pandemic exacerbated a previously described socioeconomic inequality in place of death in the UK. Further research to understand the reasons for this change and if this inequality has been sustained is needed.",
     "laySummary": "",
-    "urls": "pdf:https://www.mdpi.com/1660-4601/19/23/15544/pdf?version=1669349785; doi:https://doi.org/10.3390/ijerph192315544; html:https://europepmc.org/articles/PMC9738189; pdf:https://europepmc.org/articles/PMC9738189?pdf=render"
+    "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10125882; doi:https://doi.org/10.1177/02692163231167212; html:https://europepmc.org/articles/PMC10125882; pdf:https://europepmc.org/articles/PMC10125882?pdf=render"
   },
   {
     "id": "36385522",
@@ -5099,6 +5082,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41467-024-46497-0.pdf; doi:https://doi.org/10.1038/s41467-024-46497-0; html:https://europepmc.org/articles/PMC10928172; pdf:https://europepmc.org/articles/PMC10928172?pdf=render"
   },
+  {
+    "id": "36497616",
+    "doi": "https://doi.org/10.3390/ijerph192315544",
+    "title": "Association between Internet Usage and Quality of Life of Elderly People in England: Evidence from the English Longitudinal Study of Ageing (ELSA).",
+    "authorString": "Vidiasratri AR, Bath PA, Bath PA.",
+    "authorAffiliations": "",
+    "journalTitle": "International journal of environmental research and public health",
+    "pubYear": "2022",
+    "date": "2022-11-23",
+    "isOpenAccess": "Y",
+    "keywords": "Internet; Quality of life; Older People",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The WHO has stated that the number of senior citizens above age 65 across the world will double by the year 2050: in the UK, the whole population is projected to grow by about 2.5% over a decade, from mid-2018. Although people are living longer, they are not healthier in old age, and there is an increasing number of illnesses and disabilities in the ageing population, which have an impact on their overall well-being and quality of life (QoL). Alongside these trends, Internet technologies have improved and provide a wide range of information, including on medical and health issues. This study aimed to examine the association between the utilisation of the internet among older people in England and their QoL. This study utilised the English Longitudinal Study of Aging (ELSA), a longitudinal study of a representative sample of people aged 50 and over in England. The data from Wave 9 were analysed using bivariate analysis and logistic regression. The results show a strong association between QoL and utilisation of the Internet in older people, even when adjusting for demographic variables and health. Higher use of the internet was associated with older people being less likely to have higher QoL. The excessive use of the internet for communication and gathering information also contributed to lower QoL. From the findings, poorer QoL was also found in people in older age groups, in those who are married, and those who never suffer from chronic diseases. Our findings suggest that the quality of life in older people might not only be associated with the frequency of usage but also the purpose for which the internet is used; however, this relationship is complex and further research should explore this in greater depth. Further research should also investigate how older people's use of the Internet changed during the COVID-19 pandemic and the effects of this on the QoL in older age.",
+    "laySummary": "",
+    "urls": "pdf:https://www.mdpi.com/1660-4601/19/23/15544/pdf?version=1669349785; doi:https://doi.org/10.3390/ijerph192315544; html:https://europepmc.org/articles/PMC9738189; pdf:https://europepmc.org/articles/PMC9738189?pdf=render"
+  },
   {
     "id": "39076659",
     "doi": "https://doi.org/10.31083/j.rcm2312412",
@@ -5133,23 +5133,6 @@
     "laySummary": "",
     "urls": "pdf:https://systematicreviewsjournal.biomedcentral.com/counter/pdf/10.1186/s13643-024-02477-5; doi:https://doi.org/10.1186/s13643-024-02477-5; html:https://europepmc.org/articles/PMC10905869; pdf:https://europepmc.org/articles/PMC10905869?pdf=render"
   },
-  {
-    "id": "35168181",
-    "doi": "https://doi.org/10.1016/j.thromres.2022.01.023",
-    "title": "Potentially inappropriate prescribing of DOACs to people with mechanical heart valves: A federated analysis of 57.9 million patients' primary care records in situ using OpenSAFELY.",
-    "authorString": "OpenSAFELY Collaborative, Fisher L, Speed V, Curtis HJ, Rentsch CT, Wong AYS, Schultze A, Massey J, Inglesby P, Morton CE, Wood M, Walker AJ, Morley J, Mehrkar A, Bacon S, Hickman G, Bates C, Croker R, Evans D, Ward T, Cockburn J, Davy S, Bhaskaran K, Smith B, Williamson E, Hulme W, Green A, Eggo RM, Forbes H, Tazare J, Parry J, Hester F, Harper S, Meadows J, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Griffiths P, Fowles A, Parkes N, Douglas IJ, Evans SJW, Smeeth L, MacKenna B, Tomlinson L, Goldacre B.",
-    "authorAffiliations": "",
-    "journalTitle": "Thrombosis research",
-    "pubYear": "2022",
-    "date": "2022-01-29",
-    "isOpenAccess": "N",
-    "keywords": "Anticoagulants; Thrombosis; Heart valve prosthesis; Patient Safety; Electronic Health Records",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "",
-    "urls": "pdf:https://ora.ox.ac.uk/objects/uuid:aa50f867-d3a4-45ff-9173-1c9677a7ba4f/files/r3x816n268; doi:https://doi.org/10.1016/j.thromres.2022.01.023; html:https://europepmc.org/articles/PMC7616146; pdf:https://europepmc.org/articles/PMC7616146?pdf=render; doi:https://doi.org/10.1016/j.thromres.2022.01.023"
-  },
   {
     "id": "37468507",
     "doi": "https://doi.org/10.1038/s41598-023-37580-5",
@@ -5168,21 +5151,21 @@
     "urls": "pdf:https://www.nature.com/articles/s41598-023-37580-5.pdf; doi:https://doi.org/10.1038/s41598-023-37580-5; html:https://europepmc.org/articles/PMC10356957; pdf:https://europepmc.org/articles/PMC10356957?pdf=render"
   },
   {
-    "id": "36139476",
-    "doi": "https://doi.org/10.3390/cells11182901",
-    "title": "Dysregulated Neutrophil Phenotype and Function in Hospitalised Non-ICU COVID-19 Pneumonia.",
-    "authorString": "Belchamber KBR, Thein OS, Hazeldine J, Grudzinska FS, Faniyi AA, Hughes MJ, Jasper AE, Yip KP, Crowley LE, Lugg ST, Sapey E, Parekh D, Thickett DR, Scott A.",
+    "id": "35168181",
+    "doi": "https://doi.org/10.1016/j.thromres.2022.01.023",
+    "title": "Potentially inappropriate prescribing of DOACs to people with mechanical heart valves: A federated analysis of 57.9 million patients' primary care records in situ using OpenSAFELY.",
+    "authorString": "OpenSAFELY Collaborative, Fisher L, Speed V, Curtis HJ, Rentsch CT, Wong AYS, Schultze A, Massey J, Inglesby P, Morton CE, Wood M, Walker AJ, Morley J, Mehrkar A, Bacon S, Hickman G, Bates C, Croker R, Evans D, Ward T, Cockburn J, Davy S, Bhaskaran K, Smith B, Williamson E, Hulme W, Green A, Eggo RM, Forbes H, Tazare J, Parry J, Hester F, Harper S, Meadows J, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Griffiths P, Fowles A, Parkes N, Douglas IJ, Evans SJW, Smeeth L, MacKenna B, Tomlinson L, Goldacre B.",
     "authorAffiliations": "",
-    "journalTitle": "Cells",
+    "journalTitle": "Thrombosis research",
     "pubYear": "2022",
-    "date": "2022-09-16",
-    "isOpenAccess": "Y",
-    "keywords": "Inflammation; neutrophil; innate immunity; Covid-19",
+    "date": "2022-01-29",
+    "isOpenAccess": "N",
+    "keywords": "Anticoagulants; Thrombosis; Heart valve prosthesis; Patient Safety; Electronic Health Records",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<b>Rationale</b>: Infection with the SARS-CoV2 virus is associated with elevated neutrophil counts. Evidence of neutrophil dysfunction in COVID-19 is based on transcriptomics or single functional assays. Cell functions are interwoven pathways, and understanding the effect across the spectrum of neutrophil function may identify therapeutic targets. <b>Objectives</b>: Examine neutrophil phenotype and function in 41 hospitalised, non-ICU COVID-19 patients versus 23 age-matched controls (AMC) and 26 community acquired pneumonia patients (CAP). <b>Methods</b>: Isolated neutrophils underwent ex vivo analyses for migration, bacterial phagocytosis, ROS generation, NETosis and receptor expression. Circulating DNAse 1 activity, levels of cfDNA, MPO, VEGF, IL-6 and sTNFRI were measured and correlated to clinical outcome. Serial sampling on day three to five post hospitalization were also measured. The effect of ex vivo PI3K inhibition was measured in a further cohort of 18 COVID-19 patients. <b>Results</b>: Compared to AMC and CAP, COVID-19 neutrophils demonstrated elevated transmigration (<i>p</i> = 0.0397) and NETosis (<i>p</i> = 0.0332), and impaired phagocytosis (<i>p</i> = 0.0036) associated with impaired ROS generation (<i>p</i> < 0.0001). The percentage of CD54+ neutrophils (<i>p</i> < 0.001) was significantly increased, while surface expression of CD11b (<i>p</i> = 0.0014) and PD-L1 (<i>p</i> = 0.006) were significantly decreased in COVID-19. COVID-19 and CAP patients showed increased systemic markers of NETosis including increased cfDNA (<i>p</i> = 0.0396) and impaired DNAse activity (<i>p</i> < 0.0001). The ex vivo inhibition of PI3K \u03b3 and \u03b4 reduced NET release by COVID-19 neutrophils (<i>p</i> = 0.0129). <b>Conclusions</b>: COVID-19 is associated with neutrophil dysfunction across all main effector functions, with altered phenotype, elevated migration and NETosis, and impaired antimicrobial responses. These changes highlight that targeting neutrophil function may help modulate COVID-19 severity.",
+    "abstract": "",
     "laySummary": "",
-    "urls": "pdf:https://www.mdpi.com/2073-4409/11/18/2901/pdf?version=1663743438; doi:https://doi.org/10.3390/cells11182901; html:https://europepmc.org/articles/PMC9496854; pdf:https://europepmc.org/articles/PMC9496854?pdf=render"
+    "urls": "pdf:https://ora.ox.ac.uk/objects/uuid:aa50f867-d3a4-45ff-9173-1c9677a7ba4f/files/r3x816n268; doi:https://doi.org/10.1016/j.thromres.2022.01.023; html:https://europepmc.org/articles/PMC7616146; pdf:https://europepmc.org/articles/PMC7616146?pdf=render; doi:https://doi.org/10.1016/j.thromres.2022.01.023"
   },
   {
     "id": "37254630",
@@ -5219,21 +5202,21 @@
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cam4.6918; doi:https://doi.org/10.1002/cam4.6918; html:https://europepmc.org/articles/PMC10905680; pdf:https://europepmc.org/articles/PMC10905680?pdf=render"
   },
   {
-    "id": "31783849",
-    "doi": "https://doi.org/10.1186/s12911-019-0953-2",
-    "title": "Developing a standardised approach to the aggregation of inpatient episodes into person-based spells in all specialties and psychiatric specialties.",
-    "authorString": "Rees S, Akbari A, Collins H, Lee SC, Marchant A, Rees A, Thayer D, Wang T, Wood S, John A.",
+    "id": "36139476",
+    "doi": "https://doi.org/10.3390/cells11182901",
+    "title": "Dysregulated Neutrophil Phenotype and Function in Hospitalised Non-ICU COVID-19 Pneumonia.",
+    "authorString": "Belchamber KBR, Thein OS, Hazeldine J, Grudzinska FS, Faniyi AA, Hughes MJ, Jasper AE, Yip KP, Crowley LE, Lugg ST, Sapey E, Parekh D, Thickett DR, Scott A.",
     "authorAffiliations": "",
-    "journalTitle": "BMC medical informatics and decision making",
-    "pubYear": "2019",
-    "date": "2019-11-29",
+    "journalTitle": "Cells",
+    "pubYear": "2022",
+    "date": "2022-09-16",
     "isOpenAccess": "Y",
-    "keywords": "Data Quality; Data Linkage; Electronic Healthcare Record; Spells; Hospital Inpatient Episodes; Routine Health Data",
-    "nationalPriorities": "Improving Public Health",
+    "keywords": "Inflammation; neutrophil; innate immunity; Covid-19",
+    "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Electronic health record (EHR) data are available for research in all UK nations and cross-nation comparative studies are becoming more common. All UK inpatient EHRs are based around episodes, but episode-based analysis may not sufficiently capture the patient journey. There is no UK-wide method for aggregating episodes into standardised person-based spells. This study identifies two data quality issues affecting the creation of person-based spells, and tests four methods to create these spells, for implementation across all UK nations.<h4>Methods</h4>Welsh inpatient EHRs from 2013 to 2017 were analysed. Phase one described two data quality issues; transfers of care and episode sequencing. Phase two compared four methods for creating person spells. Measures were mean length of stay (LOS, expressed in days) and number of episodes per person spell for each method.<h4>Results</h4>3.5% of total admissions were transfers-in and 3.1% of total discharges were transfers-out. 68.7% of total transfers-in and 48.7% of psychiatric transfers-in had an identifiable preceding transfer-out, and 78.2% of total transfers-out and 59.0% of psychiatric transfers-out had an identifiable subsequent transfer-in. 0.2% of total episodes and 4.0% of psychiatric episodes overlapped with at least one other episode of any specialty. Method one (no evidence of transfer required; overlapping episodes grouped together) resulted in the longest mean LOS (4.0\u2009days for all specialties; 48.5\u2009days for psychiatric specialties) and the fewest single episode person spells (82.4% of all specialties; 69.7% for psychiatric specialties). Method three (evidence of transfer required; overlapping episodes separated) resulted in the shortest mean LOS (3.7\u2009days for all specialties; 45.8\u2009days for psychiatric specialties) and the most single episode person spells; (86.9% for all specialties; 86.3% for psychiatric specialties).<h4>Conclusions</h4>Transfers-in appear better recorded than transfers-out. Transfer coding is incomplete, particularly for psychiatric specialties. The proportion of episodes that overlap is small but psychiatric episodes are disproportionately affected. The most successful method for grouping episodes into person spells aggregated overlapping episodes and required no evidence of transfer from admission source/method or discharge destination codes. The least successful method treated overlapping episodes as distinct and required transfer coding. The impact of all four methods was greater for psychiatric specialties.",
-    "laySummary": "Rees et al used a Welsh database to examine inpatient episode/transfer coding coding for psychiatric patients. They identified deficiencies in the existing coding system for psychitatrics transfers and unexplained coding mistakes/problems, then they presesnt several different methods for constructing the inpatient spell to improve coding and avoid misclassification.",
-    "urls": "pdf:https://bmcmedinformdecismak.biomedcentral.com/track/pdf/10.1186/s12911-019-0953-2; doi:https://doi.org/10.1186/s12911-019-0953-2; html:https://europepmc.org/articles/PMC6884917; pdf:https://europepmc.org/articles/PMC6884917?pdf=render"
+    "abstract": "<b>Rationale</b>: Infection with the SARS-CoV2 virus is associated with elevated neutrophil counts. Evidence of neutrophil dysfunction in COVID-19 is based on transcriptomics or single functional assays. Cell functions are interwoven pathways, and understanding the effect across the spectrum of neutrophil function may identify therapeutic targets. <b>Objectives</b>: Examine neutrophil phenotype and function in 41 hospitalised, non-ICU COVID-19 patients versus 23 age-matched controls (AMC) and 26 community acquired pneumonia patients (CAP). <b>Methods</b>: Isolated neutrophils underwent ex vivo analyses for migration, bacterial phagocytosis, ROS generation, NETosis and receptor expression. Circulating DNAse 1 activity, levels of cfDNA, MPO, VEGF, IL-6 and sTNFRI were measured and correlated to clinical outcome. Serial sampling on day three to five post hospitalization were also measured. The effect of ex vivo PI3K inhibition was measured in a further cohort of 18 COVID-19 patients. <b>Results</b>: Compared to AMC and CAP, COVID-19 neutrophils demonstrated elevated transmigration (<i>p</i> = 0.0397) and NETosis (<i>p</i> = 0.0332), and impaired phagocytosis (<i>p</i> = 0.0036) associated with impaired ROS generation (<i>p</i> < 0.0001). The percentage of CD54+ neutrophils (<i>p</i> < 0.001) was significantly increased, while surface expression of CD11b (<i>p</i> = 0.0014) and PD-L1 (<i>p</i> = 0.006) were significantly decreased in COVID-19. COVID-19 and CAP patients showed increased systemic markers of NETosis including increased cfDNA (<i>p</i> = 0.0396) and impaired DNAse activity (<i>p</i> < 0.0001). The ex vivo inhibition of PI3K \u03b3 and \u03b4 reduced NET release by COVID-19 neutrophils (<i>p</i> = 0.0129). <b>Conclusions</b>: COVID-19 is associated with neutrophil dysfunction across all main effector functions, with altered phenotype, elevated migration and NETosis, and impaired antimicrobial responses. These changes highlight that targeting neutrophil function may help modulate COVID-19 severity.",
+    "laySummary": "",
+    "urls": "pdf:https://www.mdpi.com/2073-4409/11/18/2901/pdf?version=1663743438; doi:https://doi.org/10.3390/cells11182901; html:https://europepmc.org/articles/PMC9496854; pdf:https://europepmc.org/articles/PMC9496854?pdf=render"
   },
   {
     "id": "36807005",
@@ -5252,6 +5235,23 @@
     "laySummary": "",
     "urls": "pdf:http://www.thieme-connect.de/products/ejournals/pdf/10.1055/a-2038-0541.pdf; doi:https://doi.org/10.1055/a-2038-0541; html:https://europepmc.org/articles/PMC10465241; pdf:https://europepmc.org/articles/PMC10465241?pdf=render"
   },
+  {
+    "id": "31783849",
+    "doi": "https://doi.org/10.1186/s12911-019-0953-2",
+    "title": "Developing a standardised approach to the aggregation of inpatient episodes into person-based spells in all specialties and psychiatric specialties.",
+    "authorString": "Rees S, Akbari A, Collins H, Lee SC, Marchant A, Rees A, Thayer D, Wang T, Wood S, John A.",
+    "authorAffiliations": "",
+    "journalTitle": "BMC medical informatics and decision making",
+    "pubYear": "2019",
+    "date": "2019-11-29",
+    "isOpenAccess": "Y",
+    "keywords": "Data Quality; Data Linkage; Electronic Healthcare Record; Spells; Hospital Inpatient Episodes; Routine Health Data",
+    "nationalPriorities": "Improving Public Health",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Electronic health record (EHR) data are available for research in all UK nations and cross-nation comparative studies are becoming more common. All UK inpatient EHRs are based around episodes, but episode-based analysis may not sufficiently capture the patient journey. There is no UK-wide method for aggregating episodes into standardised person-based spells. This study identifies two data quality issues affecting the creation of person-based spells, and tests four methods to create these spells, for implementation across all UK nations.<h4>Methods</h4>Welsh inpatient EHRs from 2013 to 2017 were analysed. Phase one described two data quality issues; transfers of care and episode sequencing. Phase two compared four methods for creating person spells. Measures were mean length of stay (LOS, expressed in days) and number of episodes per person spell for each method.<h4>Results</h4>3.5% of total admissions were transfers-in and 3.1% of total discharges were transfers-out. 68.7% of total transfers-in and 48.7% of psychiatric transfers-in had an identifiable preceding transfer-out, and 78.2% of total transfers-out and 59.0% of psychiatric transfers-out had an identifiable subsequent transfer-in. 0.2% of total episodes and 4.0% of psychiatric episodes overlapped with at least one other episode of any specialty. Method one (no evidence of transfer required; overlapping episodes grouped together) resulted in the longest mean LOS (4.0\u2009days for all specialties; 48.5\u2009days for psychiatric specialties) and the fewest single episode person spells (82.4% of all specialties; 69.7% for psychiatric specialties). Method three (evidence of transfer required; overlapping episodes separated) resulted in the shortest mean LOS (3.7\u2009days for all specialties; 45.8\u2009days for psychiatric specialties) and the most single episode person spells; (86.9% for all specialties; 86.3% for psychiatric specialties).<h4>Conclusions</h4>Transfers-in appear better recorded than transfers-out. Transfer coding is incomplete, particularly for psychiatric specialties. The proportion of episodes that overlap is small but psychiatric episodes are disproportionately affected. The most successful method for grouping episodes into person spells aggregated overlapping episodes and required no evidence of transfer from admission source/method or discharge destination codes. The least successful method treated overlapping episodes as distinct and required transfer coding. The impact of all four methods was greater for psychiatric specialties.",
+    "laySummary": "Rees et al used a Welsh database to examine inpatient episode/transfer coding coding for psychiatric patients. They identified deficiencies in the existing coding system for psychitatrics transfers and unexplained coding mistakes/problems, then they presesnt several different methods for constructing the inpatient spell to improve coding and avoid misclassification.",
+    "urls": "pdf:https://bmcmedinformdecismak.biomedcentral.com/track/pdf/10.1186/s12911-019-0953-2; doi:https://doi.org/10.1186/s12911-019-0953-2; html:https://europepmc.org/articles/PMC6884917; pdf:https://europepmc.org/articles/PMC6884917?pdf=render"
+  },
   {
     "id": "35024157",
     "doi": "https://doi.org/10.1177/20552076211059350",
@@ -5269,6 +5269,23 @@
     "laySummary": "",
     "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/20552076211059350; doi:https://doi.org/10.1177/20552076211059350; html:https://europepmc.org/articles/PMC8744149; pdf:https://europepmc.org/articles/PMC8744149?pdf=render"
   },
+  {
+    "id": "34430796",
+    "doi": "https://doi.org/10.1016/j.mayocpiqo.2021.08.011",
+    "title": "Association Between Accelerometer-Assessed Physical Activity and Severity of COVID-19 in UK Biobank.",
+    "authorString": "Rowlands AV, Dempsey PC, Gillies C, Kloecker DE, Razieh C, Chudasama Y, Islam N, Zaccardi F, Lawson C, Norris T, Davies MJ, Khunti K, Yates T.",
+    "authorAffiliations": "",
+    "journalTitle": "Mayo Clinic proceedings. Innovations, quality & outcomes",
+    "pubYear": "2021",
+    "date": "2021-08-20",
+    "isOpenAccess": "Y",
+    "keywords": "Mvpa, Moderate To Vigorous Physical Activity; Covid-19, Coronavirus Disease 2019; Sars-cov-2, Severe Acute Respiratory Syndrome Coronavirus 2",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>To quantify the association between accelerometer-assessed physical activity and coronavirus disease 2019 (COVID-19) outcomes.<h4>Methods</h4>Data from 82,253 UK Biobank participants with accelerometer data (measured 2013-2015), complete covariate data, and linked COVID-19 data from March 16, 2020, to March 16, 2021, were included. Two outcomes were investigated: severe COVID-19 (positive test result from in-hospital setting or COVID-19 as primary cause of death) and nonsevere COVID-19 (positive test result from community setting). Logistic regressions were used to assess associations with moderate to vigorous physical activity (MVPA), total activity, and intensity gradient. A higher intensity gradient indicates a higher proportion of vigorous activity.<h4>Results</h4>Average MVPA was 48.1 (32.7) min/d. Physical activity was associated with lower odds of severe COVID-19 (adjusted odds ratio per standard deviation increase: MVPA, 0.75 [95% CI, 0.67 to 0.85]; total, 0.83 [0.74 to 0.92]; intensity, 0.77 [0.70 to 0.86]), with stronger associations in women (MVPA, 0.63 [0.52 to 0.77]; total, 0.76 [0.64 to 0.90]; intensity, 0.63 [0.53 to 0.74]) than in men (MVPA, 0.84 [0.73 to 0.97]; total, 0.88 [0.77 to 1.01]; intensity, 0.88 [0.77 to 1.00]). In contrast, when mutually adjusted, total activity was associated with higher odds of a nonsevere infection (1.10 [1.04 to 1.16]), whereas the intensity gradient was associated with lower odds (0.91 [0.86 to 0.97]).<h4>Conclusion</h4>Odds of severe COVID-19 were approximately 25% lower per standard deviation (\u223c30 min/d) MVPA. A greater proportion of vigorous activity was associated with lower odds of severe and nonsevere infections. The association between total activity and higher odds of a nonsevere infection may be through greater community engagement and thus more exposure to the virus. Results support calls for public health messaging highlighting the potential of MVPA for reducing the odds of severe COVID-19.",
+    "laySummary": "",
+    "urls": "pdf:http://www.mcpiqojournal.org/article/S2542454821001302/pdf; doi:https://doi.org/10.1016/j.mayocpiqo.2021.08.011; html:https://europepmc.org/articles/PMC8376658; pdf:https://europepmc.org/articles/PMC8376658?pdf=render"
+  },
   {
     "id": "37475157",
     "doi": "https://doi.org/10.1093/cvr/cvad106",
@@ -5303,23 +5320,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1167/tvst.11.9.34; doi:https://doi.org/10.1167/tvst.11.9.34; html:https://europepmc.org/articles/PMC9527330; pdf:https://europepmc.org/articles/PMC9527330?pdf=render"
   },
-  {
-    "id": "34430796",
-    "doi": "https://doi.org/10.1016/j.mayocpiqo.2021.08.011",
-    "title": "Association Between Accelerometer-Assessed Physical Activity and Severity of COVID-19 in UK Biobank.",
-    "authorString": "Rowlands AV, Dempsey PC, Gillies C, Kloecker DE, Razieh C, Chudasama Y, Islam N, Zaccardi F, Lawson C, Norris T, Davies MJ, Khunti K, Yates T.",
-    "authorAffiliations": "",
-    "journalTitle": "Mayo Clinic proceedings. Innovations, quality & outcomes",
-    "pubYear": "2021",
-    "date": "2021-08-20",
-    "isOpenAccess": "Y",
-    "keywords": "Mvpa, Moderate To Vigorous Physical Activity; Covid-19, Coronavirus Disease 2019; Sars-cov-2, Severe Acute Respiratory Syndrome Coronavirus 2",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objective</h4>To quantify the association between accelerometer-assessed physical activity and coronavirus disease 2019 (COVID-19) outcomes.<h4>Methods</h4>Data from 82,253 UK Biobank participants with accelerometer data (measured 2013-2015), complete covariate data, and linked COVID-19 data from March 16, 2020, to March 16, 2021, were included. Two outcomes were investigated: severe COVID-19 (positive test result from in-hospital setting or COVID-19 as primary cause of death) and nonsevere COVID-19 (positive test result from community setting). Logistic regressions were used to assess associations with moderate to vigorous physical activity (MVPA), total activity, and intensity gradient. A higher intensity gradient indicates a higher proportion of vigorous activity.<h4>Results</h4>Average MVPA was 48.1 (32.7) min/d. Physical activity was associated with lower odds of severe COVID-19 (adjusted odds ratio per standard deviation increase: MVPA, 0.75 [95% CI, 0.67 to 0.85]; total, 0.83 [0.74 to 0.92]; intensity, 0.77 [0.70 to 0.86]), with stronger associations in women (MVPA, 0.63 [0.52 to 0.77]; total, 0.76 [0.64 to 0.90]; intensity, 0.63 [0.53 to 0.74]) than in men (MVPA, 0.84 [0.73 to 0.97]; total, 0.88 [0.77 to 1.01]; intensity, 0.88 [0.77 to 1.00]). In contrast, when mutually adjusted, total activity was associated with higher odds of a nonsevere infection (1.10 [1.04 to 1.16]), whereas the intensity gradient was associated with lower odds (0.91 [0.86 to 0.97]).<h4>Conclusion</h4>Odds of severe COVID-19 were approximately 25% lower per standard deviation (\u223c30 min/d) MVPA. A greater proportion of vigorous activity was associated with lower odds of severe and nonsevere infections. The association between total activity and higher odds of a nonsevere infection may be through greater community engagement and thus more exposure to the virus. Results support calls for public health messaging highlighting the potential of MVPA for reducing the odds of severe COVID-19.",
-    "laySummary": "",
-    "urls": "pdf:http://www.mcpiqojournal.org/article/S2542454821001302/pdf; doi:https://doi.org/10.1016/j.mayocpiqo.2021.08.011; html:https://europepmc.org/articles/PMC8376658; pdf:https://europepmc.org/articles/PMC8376658?pdf=render"
-  },
   {
     "id": "38162515",
     "doi": "https://doi.org/10.1016/j.lanepe.2023.100816",
@@ -5728,6 +5728,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1093/ced/llae196; doi:https://doi.org/10.1093/ced/llae196"
   },
+  {
+    "id": "35027756",
+    "doi": "https://doi.org/10.1038/s41591-021-01666-2",
+    "title": "SARS-CoV-2 infection and COVID-19 vaccination rates in pregnant women in Scotland.",
+    "authorString": "Stock SJ, Carruthers J, Calvert C, Denny C, Donaghy J, Goulding A, Hopcroft LEM, Hopkins L, McLaughlin T, Pan J, Shi T, Taylor B, Agrawal U, Auyeung B, Katikireddi SV, McCowan C, Murray J, Simpson CR, Robertson C, Vasileiou E, Sheikh A, Wood R.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature medicine",
+    "pubYear": "2022",
+    "date": "2022-01-13",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Population-level data on COVID-19 vaccine uptake in pregnancy and SARS-CoV-2 infection outcomes are lacking. We describe COVID-19 vaccine uptake and SARS-CoV-2 infection in pregnant women in Scotland, using whole-population data from a national, prospective cohort. Between the start of a COVID-19 vaccine program in Scotland, on 8 December 2020 and 31 October 2021, 25,917 COVID-19 vaccinations were given to 18,457 pregnant women. Vaccine coverage was substantially lower in pregnant women than in the general female population of 18-44 years; 32.3% of women giving birth in October 2021 had two doses of vaccine compared to 77.4% in all women. The extended perinatal mortality rate for women who gave birth within 28\u2009d of a COVID-19 diagnosis was 22.6 per 1,000 births (95% CI 12.9-38.5; pandemic background rate 5.6 per 1,000 births; 452 out of 80,456; 95% CI 5.1-6.2). Overall, 77.4% (3,833 out of 4,950; 95% CI 76.2-78.6) of SARS-CoV-2 infections, 90.9% (748 out of 823; 95% CI 88.7-92.7) of SARS-CoV-2 associated with hospital admission and 98% (102 out of 104; 95% CI 92.5-99.7) of SARS-CoV-2 associated with critical care admission, as well as all baby deaths, occurred in pregnant women who were unvaccinated at the time of COVID-19 diagnosis. Addressing low vaccine uptake rates in pregnant women is imperative to protect the health of women and babies in the ongoing pandemic.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41591-021-01666-2.pdf; doi:https://doi.org/10.1038/s41591-021-01666-2; html:https://europepmc.org/articles/PMC8938271; pdf:https://europepmc.org/articles/PMC8938271?pdf=render"
+  },
   {
     "id": "36441117",
     "doi": "https://doi.org/10.1111/acps.13523",
@@ -5779,6 +5796,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.12688/wellcomeopenres.16058.2; html:https://europepmc.org/articles/PMC11411238; pdf:https://europepmc.org/articles/PMC11411238?pdf=render"
   },
+  {
+    "id": "38877563",
+    "doi": "https://doi.org/10.1186/s12911-024-02563-7",
+    "title": "Collaborative learning from distributed data with differentially private synthetic data.",
+    "authorString": "Prediger L, J\u00e4lk\u00f6 J, Honkela A, Kaski S.",
+    "authorAffiliations": "",
+    "journalTitle": "BMC medical informatics and decision making",
+    "pubYear": "2024",
+    "date": "2024-06-14",
+    "isOpenAccess": "Y",
+    "keywords": "Collaborative Learning; Health Informatics; Differential Privacy; Synthetic Data",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Consider a setting where multiple parties holding sensitive data aim to collaboratively learn population level statistics, but pooling the sensitive data sets is not possible due to privacy concerns and parties are unable to engage in centrally coordinated joint computation. We study the feasibility of combining privacy preserving synthetic data sets in place of the original data for collaborative learning on real-world health data from the UK Biobank.<h4>Methods</h4>We perform an empirical evaluation based on an existing prospective cohort study from the literature. Multiple parties were simulated by splitting the UK Biobank cohort along assessment centers, for which we generate synthetic data using differentially private generative modelling techniques. We then apply the original study's Poisson regression analysis on the combined synthetic data sets and evaluate the effects of 1) the size of local data set, 2) the number of participating parties, and 3) local shifts in distributions, on the obtained likelihood scores.<h4>Results</h4>We discover that parties engaging in the collaborative learning via shared synthetic data obtain more accurate estimates of the regression parameters compared to using only their local data. This finding extends to the difficult case of small heterogeneous data sets. Furthermore, the more parties participate, the larger and more consistent the improvements become up to a certain limit. Finally, we find that data sharing can especially help parties whose data contain underrepresented groups to perform better-adjusted analysis for said groups.<h4>Conclusions</h4>Based on our results we conclude that sharing of synthetic data is a viable method for enabling learning from sensitive data without violating privacy constraints even if individual data sets are small or do not represent the overall population well. Lack of access to distributed sensitive data is often a bottleneck in biomedical research, which our study shows can be alleviated with privacy-preserving collaborative learning methods.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1186/s12911-024-02563-7; html:https://europepmc.org/articles/PMC11179391; pdf:https://europepmc.org/articles/PMC11179391?pdf=render"
+  },
   {
     "id": "36322788",
     "doi": "https://doi.org/10.2196/40035",
@@ -5796,23 +5830,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.jmir.org/2022/12/e40035/PDF; doi:https://doi.org/10.2196/40035; html:https://europepmc.org/articles/PMC9822177"
   },
-  {
-    "id": "35027756",
-    "doi": "https://doi.org/10.1038/s41591-021-01666-2",
-    "title": "SARS-CoV-2 infection and COVID-19 vaccination rates in pregnant women in Scotland.",
-    "authorString": "Stock SJ, Carruthers J, Calvert C, Denny C, Donaghy J, Goulding A, Hopcroft LEM, Hopkins L, McLaughlin T, Pan J, Shi T, Taylor B, Agrawal U, Auyeung B, Katikireddi SV, McCowan C, Murray J, Simpson CR, Robertson C, Vasileiou E, Sheikh A, Wood R.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature medicine",
-    "pubYear": "2022",
-    "date": "2022-01-13",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Population-level data on COVID-19 vaccine uptake in pregnancy and SARS-CoV-2 infection outcomes are lacking. We describe COVID-19 vaccine uptake and SARS-CoV-2 infection in pregnant women in Scotland, using whole-population data from a national, prospective cohort. Between the start of a COVID-19 vaccine program in Scotland, on 8 December 2020 and 31 October 2021, 25,917 COVID-19 vaccinations were given to 18,457 pregnant women. Vaccine coverage was substantially lower in pregnant women than in the general female population of 18-44 years; 32.3% of women giving birth in October 2021 had two doses of vaccine compared to 77.4% in all women. The extended perinatal mortality rate for women who gave birth within 28\u2009d of a COVID-19 diagnosis was 22.6 per 1,000 births (95% CI 12.9-38.5; pandemic background rate 5.6 per 1,000 births; 452 out of 80,456; 95% CI 5.1-6.2). Overall, 77.4% (3,833 out of 4,950; 95% CI 76.2-78.6) of SARS-CoV-2 infections, 90.9% (748 out of 823; 95% CI 88.7-92.7) of SARS-CoV-2 associated with hospital admission and 98% (102 out of 104; 95% CI 92.5-99.7) of SARS-CoV-2 associated with critical care admission, as well as all baby deaths, occurred in pregnant women who were unvaccinated at the time of COVID-19 diagnosis. Addressing low vaccine uptake rates in pregnant women is imperative to protect the health of women and babies in the ongoing pandemic.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41591-021-01666-2.pdf; doi:https://doi.org/10.1038/s41591-021-01666-2; html:https://europepmc.org/articles/PMC8938271; pdf:https://europepmc.org/articles/PMC8938271?pdf=render"
-  },
   {
     "id": "34670038",
     "doi": "https://doi.org/10.1056/nejmc2113864",
@@ -5830,23 +5847,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1056/nejmc2113864; doi:https://doi.org/10.1056/NEJMc2113864; html:https://europepmc.org/articles/PMC8552534; pdf:https://europepmc.org/articles/PMC8552534?pdf=render"
   },
-  {
-    "id": "38877563",
-    "doi": "https://doi.org/10.1186/s12911-024-02563-7",
-    "title": "Collaborative learning from distributed data with differentially private synthetic data.",
-    "authorString": "Prediger L, J\u00e4lk\u00f6 J, Honkela A, Kaski S.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC medical informatics and decision making",
-    "pubYear": "2024",
-    "date": "2024-06-14",
-    "isOpenAccess": "Y",
-    "keywords": "Collaborative Learning; Health Informatics; Differential Privacy; Synthetic Data",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Consider a setting where multiple parties holding sensitive data aim to collaboratively learn population level statistics, but pooling the sensitive data sets is not possible due to privacy concerns and parties are unable to engage in centrally coordinated joint computation. We study the feasibility of combining privacy preserving synthetic data sets in place of the original data for collaborative learning on real-world health data from the UK Biobank.<h4>Methods</h4>We perform an empirical evaluation based on an existing prospective cohort study from the literature. Multiple parties were simulated by splitting the UK Biobank cohort along assessment centers, for which we generate synthetic data using differentially private generative modelling techniques. We then apply the original study's Poisson regression analysis on the combined synthetic data sets and evaluate the effects of 1) the size of local data set, 2) the number of participating parties, and 3) local shifts in distributions, on the obtained likelihood scores.<h4>Results</h4>We discover that parties engaging in the collaborative learning via shared synthetic data obtain more accurate estimates of the regression parameters compared to using only their local data. This finding extends to the difficult case of small heterogeneous data sets. Furthermore, the more parties participate, the larger and more consistent the improvements become up to a certain limit. Finally, we find that data sharing can especially help parties whose data contain underrepresented groups to perform better-adjusted analysis for said groups.<h4>Conclusions</h4>Based on our results we conclude that sharing of synthetic data is a viable method for enabling learning from sensitive data without violating privacy constraints even if individual data sets are small or do not represent the overall population well. Lack of access to distributed sensitive data is often a bottleneck in biomedical research, which our study shows can be alleviated with privacy-preserving collaborative learning methods.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1186/s12911-024-02563-7; html:https://europepmc.org/articles/PMC11179391; pdf:https://europepmc.org/articles/PMC11179391?pdf=render"
-  },
   {
     "id": "38818129",
     "doi": "https://doi.org/10.12688/wellcomeopenres.20750.1",
@@ -5915,23 +5915,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.lanepe.2022.100428; doi:https://doi.org/10.1016/j.lanepe.2022.100428; html:https://europepmc.org/articles/PMC9213032; pdf:https://europepmc.org/articles/PMC9213032?pdf=render"
   },
-  {
-    "id": "32043136",
-    "doi": "https://doi.org/10.1093/ageing/afaa018",
-    "title": "New Horizons in the use of routine data for ageing research.",
-    "authorString": "Todd OM, Burton JK, Dodds RM, Hollinghurst J, Lyons RA, Quinn TJ, Schneider A, Walesby KE, Wilkinson C, Conroy S, Gale CP, Hall M, Walters K, Clegg AP.",
-    "authorAffiliations": "",
-    "journalTitle": "Age and ageing",
-    "pubYear": "2020",
-    "date": "2020-08-01",
-    "isOpenAccess": "Y",
-    "keywords": "Ageing; Data Linkage; Older People; Big Data; Health Informatics; Electronic Health Records",
-    "nationalPriorities": "Improving Public Health",
-    "healthCategories": "",
-    "abstract": "The past three decades have seen a steady increase in the availability of routinely collected health and social care data and the processing power to analyse it. These developments represent a major opportunity for ageing research, especially with the integration of different datasets across traditional boundaries of health and social care, for prognostic research and novel evaluations of interventions with representative populations of older people. However, there are considerable challenges in using routine data at the level of coding, data analysis and in the application of findings to everyday care. New Horizons in applying routine data to investigate novel questions in ageing research require a collaborative approach between clinicians, data scientists, biostatisticians, epidemiologists and trial methodologists. This requires building capacity for the next generation of research leaders in this important area. There is a need to develop consensus code lists and standardised, validated algorithms for common conditions and outcomes that are relevant for older people to maximise the potential of routine data research in this group. Lastly, we must help drive the application of routine data to improve the care of older people, through the development of novel methods for evaluation of interventions using routine data infrastructure. We believe that harnessing routine data can help address knowledge gaps for older people living with multiple conditions and frailty, and design interventions and pathways of care to address the complex health issues we face in caring for older people.",
-    "laySummary": "This article looks at new horizons in the use of routine data for ageing research. This includes prognostic research, clinical trials, and service evaluations. The authors highlight the need for multidisciplinary collaboration. They identify three key areas where the application of routine data has major benefits for research in ageing - prediction (developing prediction tools to identify levels of future risk of outcomes thereby helping in decision making), clinical trials (routine data can help extend participation in clinical trials), and service evaluation (understanding performace of clinical services by measuring outcomes in routine data).",
-    "urls": "pdf:https://academic.oup.com/ageing/article-pdf/49/5/716/33676968/afaa018.pdf; doi:https://doi.org/10.1093/ageing/afaa018; html:https://europepmc.org/articles/PMC7444666; pdf:https://europepmc.org/articles/PMC7444666?pdf=render"
-  },
   {
     "id": "37765085",
     "doi": "https://doi.org/10.3390/ph16091277",
@@ -5949,6 +5932,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.3390/ph16091277; html:https://europepmc.org/articles/PMC10535191; pdf:https://europepmc.org/articles/PMC10535191?pdf=render"
   },
+  {
+    "id": "32043136",
+    "doi": "https://doi.org/10.1093/ageing/afaa018",
+    "title": "New Horizons in the use of routine data for ageing research.",
+    "authorString": "Todd OM, Burton JK, Dodds RM, Hollinghurst J, Lyons RA, Quinn TJ, Schneider A, Walesby KE, Wilkinson C, Conroy S, Gale CP, Hall M, Walters K, Clegg AP.",
+    "authorAffiliations": "",
+    "journalTitle": "Age and ageing",
+    "pubYear": "2020",
+    "date": "2020-08-01",
+    "isOpenAccess": "Y",
+    "keywords": "Ageing; Data Linkage; Older People; Big Data; Health Informatics; Electronic Health Records",
+    "nationalPriorities": "Improving Public Health",
+    "healthCategories": "",
+    "abstract": "The past three decades have seen a steady increase in the availability of routinely collected health and social care data and the processing power to analyse it. These developments represent a major opportunity for ageing research, especially with the integration of different datasets across traditional boundaries of health and social care, for prognostic research and novel evaluations of interventions with representative populations of older people. However, there are considerable challenges in using routine data at the level of coding, data analysis and in the application of findings to everyday care. New Horizons in applying routine data to investigate novel questions in ageing research require a collaborative approach between clinicians, data scientists, biostatisticians, epidemiologists and trial methodologists. This requires building capacity for the next generation of research leaders in this important area. There is a need to develop consensus code lists and standardised, validated algorithms for common conditions and outcomes that are relevant for older people to maximise the potential of routine data research in this group. Lastly, we must help drive the application of routine data to improve the care of older people, through the development of novel methods for evaluation of interventions using routine data infrastructure. We believe that harnessing routine data can help address knowledge gaps for older people living with multiple conditions and frailty, and design interventions and pathways of care to address the complex health issues we face in caring for older people.",
+    "laySummary": "This article looks at new horizons in the use of routine data for ageing research. This includes prognostic research, clinical trials, and service evaluations. The authors highlight the need for multidisciplinary collaboration. They identify three key areas where the application of routine data has major benefits for research in ageing - prediction (developing prediction tools to identify levels of future risk of outcomes thereby helping in decision making), clinical trials (routine data can help extend participation in clinical trials), and service evaluation (understanding performace of clinical services by measuring outcomes in routine data).",
+    "urls": "pdf:https://academic.oup.com/ageing/article-pdf/49/5/716/33676968/afaa018.pdf; doi:https://doi.org/10.1093/ageing/afaa018; html:https://europepmc.org/articles/PMC7444666; pdf:https://europepmc.org/articles/PMC7444666?pdf=render"
+  },
   {
     "id": "39319350",
     "doi": "https://doi.org/10.3389/fpsyt.2024.1181739",
@@ -5983,23 +5983,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ageing/article-pdf/53/3/afae057/57063252/afae057.pdf; doi:https://doi.org/10.1093/ageing/afae057; html:https://europepmc.org/articles/PMC10960070; pdf:https://europepmc.org/articles/PMC10960070?pdf=render"
   },
-  {
-    "id": "37363696",
-    "doi": "https://doi.org/10.1155/2023/5885059",
-    "title": "Gender Disparity in Expression of Sarcopenia in Haemodialysis Recipients: Analysis from the FITNESS Cohort.",
-    "authorString": "Anderson BM, Wilson DV, Qasim M, Correa G, Evison F, Gallier S, Ferro CJ, Jackson TA, Sharif A.",
-    "authorAffiliations": "",
-    "journalTitle": "International journal of nephrology",
-    "pubYear": "2023",
-    "date": "2023-06-17",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>There has been little exploration of the interplay between sarcopenia and frailty in haemodialysis, particularly regarding gender difference. We aimed to (1) assess whether ultrasound-derived low muscle mass (LMM) and sarcopenia are more common in male or female haemodialysis recipients; (2) assess whether age influences any observed gender difference, and (3) explore the interplay between sarcopenia, frailty, and gender in haemodialysis recipients.<h4>Methods</h4>This was an exploratory analysis of a subgroup of adult prevalent (\u22653\u2009months) haemodialysis with frailty phenotype (FP) scores. Bilateral anterior thigh thickness (BATT) was obtained according to an established ultrasound protocol. Associations with frailty were explored via both linear and logistic regressions for BATT, LMM, and sarcopenia with a priori covariables, stratified by gender.<h4>Results</h4>In total of 223 studies, participants had ultrasound measurements. Males showed greater prevalence of LMM. On adjusted analyses, LMM was associated with lower hand grip strength in males (<i>\u03b2</i>\u2009=\u2009-4.17; 95% C.I. -7.57 to -0.77; <i>P</i>=0.02), but not females (<i>\u03b2</i>\u2009=\u2009-1.88; 95% C.I. -5.41 to 1.64; <i>P</i>=0.29). LMM was also associated with slower walking speed in both males (<i>\u03b2</i>\u2009=\u2009-0.115; 95% C.I. -0.258 to -0.013; <i>P</i>=0.03) and females (<i>\u03b2</i>\u2009=\u2009-0.152; 95% C.I. -0.300 to -0.005; <i>P</i>=0.04). Sarcopenia was associated with greater odds of frailty on adjusted models in males (OR\u2009=\u20099.86; 95% C.I. 1.8 to 54.0; <i>P</i>=0.01), but not females (OR\u2009=\u20095.16; 95% C.I. 0.22 to 124; <i>P</i>=0.31).<h4>Conclusions</h4>The clinical expression and significance of sarcopenia differ substantially between males and females on haemodialysis. Further work is required to elucidate underlying mechanisms and guide tailored treatment.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1155/2023/5885059; html:https://europepmc.org/articles/PMC10290558; pdf:https://europepmc.org/articles/PMC10290558?pdf=render"
-  },
   {
     "id": "35715350",
     "doi": "https://doi.org/10.1016/j.vaccine.2022.06.010",
@@ -6035,21 +6018,21 @@
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cnm.3255; doi:https://doi.org/10.1002/cnm.3255; html:https://europepmc.org/articles/PMC7003475; pdf:https://europepmc.org/articles/PMC7003475?pdf=render"
   },
   {
-    "id": "36691218",
-    "doi": "https://doi.org/10.1136/bmjopen-2021-059813",
-    "title": "Evaluation of the shielding initiative in Wales (EVITE Immunity): protocol for a quasiexperimental study.",
-    "authorString": "Evans BA, Akbari A, Bailey R, Bethell L, Bufton S, Carson-Stevens A, Dixon L, Edwards A, John A, Jolles S, Kingston MR, Lyons J, Lyons R, Porter A, Sewell B, Thornton CA, Watkins A, Whiffen T, Snooks H.",
+    "id": "37363696",
+    "doi": "https://doi.org/10.1155/2023/5885059",
+    "title": "Gender Disparity in Expression of Sarcopenia in Haemodialysis Recipients: Analysis from the FITNESS Cohort.",
+    "authorString": "Anderson BM, Wilson DV, Qasim M, Correa G, Evison F, Gallier S, Ferro CJ, Jackson TA, Sharif A.",
     "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2022",
-    "date": "2022-09-08",
+    "journalTitle": "International journal of nephrology",
+    "pubYear": "2023",
+    "date": "2023-06-17",
     "isOpenAccess": "Y",
-    "keywords": "immunology; Public Health; Health Policy; Covid-19",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>Shielding aimed to protect those predicted to be at highest risk from COVID-19 and was uniquely implemented in the UK during the COVID-19 pandemic. Clinically extremely vulnerable people identified through algorithms and screening of routine National Health Service (NHS) data were individually and strongly advised to stay at home and strictly self-isolate even from others in their household. This study will generate a logic model of the intervention and evaluate the effects and costs of shielding to inform policy development and delivery during future pandemics.<h4>Methods and analysis</h4>This is a quasiexperimental study undertaken in Wales where records for people who were identified for shielding were already anonymously linked into integrated data systems for public health decision-making. We will: interview policy-makers to understand rationale for shielding advice to inform analysis and interpretation of results; use anonymised individual-level data to select people identified for shielding advice in March 2020 and a matched cohort, from routine electronic health data sources, to compare outcomes; survey a stratified random sample of each group about activities and quality of life at 12 months; use routine and newly collected blood data to assess immunity; interview people who were identified for shielding and their carers and NHS staff who delivered healthcare during shielding, to explore compliance and experiences; collect healthcare resource use data to calculate implementation costs and cost-consequences. Our team includes people who were shielding, who used their experience to help design and deliver this study.<h4>Ethics and dissemination</h4>The study has received approval from the Newcastle North Tyneside 2 Research Ethics Committee (IRAS 295050). We will disseminate results directly to UK government policy-makers, publish in peer-reviewed journals, present at scientific and policy conferences and share accessible summaries of results online and through public and patient networks.",
+    "abstract": "<h4>Background</h4>There has been little exploration of the interplay between sarcopenia and frailty in haemodialysis, particularly regarding gender difference. We aimed to (1) assess whether ultrasound-derived low muscle mass (LMM) and sarcopenia are more common in male or female haemodialysis recipients; (2) assess whether age influences any observed gender difference, and (3) explore the interplay between sarcopenia, frailty, and gender in haemodialysis recipients.<h4>Methods</h4>This was an exploratory analysis of a subgroup of adult prevalent (\u22653\u2009months) haemodialysis with frailty phenotype (FP) scores. Bilateral anterior thigh thickness (BATT) was obtained according to an established ultrasound protocol. Associations with frailty were explored via both linear and logistic regressions for BATT, LMM, and sarcopenia with a priori covariables, stratified by gender.<h4>Results</h4>In total of 223 studies, participants had ultrasound measurements. Males showed greater prevalence of LMM. On adjusted analyses, LMM was associated with lower hand grip strength in males (<i>\u03b2</i>\u2009=\u2009-4.17; 95% C.I. -7.57 to -0.77; <i>P</i>=0.02), but not females (<i>\u03b2</i>\u2009=\u2009-1.88; 95% C.I. -5.41 to 1.64; <i>P</i>=0.29). LMM was also associated with slower walking speed in both males (<i>\u03b2</i>\u2009=\u2009-0.115; 95% C.I. -0.258 to -0.013; <i>P</i>=0.03) and females (<i>\u03b2</i>\u2009=\u2009-0.152; 95% C.I. -0.300 to -0.005; <i>P</i>=0.04). Sarcopenia was associated with greater odds of frailty on adjusted models in males (OR\u2009=\u20099.86; 95% C.I. 1.8 to 54.0; <i>P</i>=0.01), but not females (OR\u2009=\u20095.16; 95% C.I. 0.22 to 124; <i>P</i>=0.31).<h4>Conclusions</h4>The clinical expression and significance of sarcopenia differ substantially between males and females on haemodialysis. Further work is required to elucidate underlying mechanisms and guide tailored treatment.",
     "laySummary": "",
-    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/9/e059813.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-059813; html:https://europepmc.org/articles/PMC9461087; pdf:https://europepmc.org/articles/PMC9461087?pdf=render"
+    "urls": "doi:https://doi.org/10.1155/2023/5885059; html:https://europepmc.org/articles/PMC10290558; pdf:https://europepmc.org/articles/PMC10290558?pdf=render"
   },
   {
     "id": "34385524",
@@ -6068,6 +6051,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41598-021-95802-0.pdf; doi:https://doi.org/10.1038/s41598-021-95802-0; html:https://europepmc.org/articles/PMC8360941; pdf:https://europepmc.org/articles/PMC8360941?pdf=render"
   },
+  {
+    "id": "36691218",
+    "doi": "https://doi.org/10.1136/bmjopen-2021-059813",
+    "title": "Evaluation of the shielding initiative in Wales (EVITE Immunity): protocol for a quasiexperimental study.",
+    "authorString": "Evans BA, Akbari A, Bailey R, Bethell L, Bufton S, Carson-Stevens A, Dixon L, Edwards A, John A, Jolles S, Kingston MR, Lyons J, Lyons R, Porter A, Sewell B, Thornton CA, Watkins A, Whiffen T, Snooks H.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2022",
+    "date": "2022-09-08",
+    "isOpenAccess": "Y",
+    "keywords": "immunology; Public Health; Health Policy; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>Shielding aimed to protect those predicted to be at highest risk from COVID-19 and was uniquely implemented in the UK during the COVID-19 pandemic. Clinically extremely vulnerable people identified through algorithms and screening of routine National Health Service (NHS) data were individually and strongly advised to stay at home and strictly self-isolate even from others in their household. This study will generate a logic model of the intervention and evaluate the effects and costs of shielding to inform policy development and delivery during future pandemics.<h4>Methods and analysis</h4>This is a quasiexperimental study undertaken in Wales where records for people who were identified for shielding were already anonymously linked into integrated data systems for public health decision-making. We will: interview policy-makers to understand rationale for shielding advice to inform analysis and interpretation of results; use anonymised individual-level data to select people identified for shielding advice in March 2020 and a matched cohort, from routine electronic health data sources, to compare outcomes; survey a stratified random sample of each group about activities and quality of life at 12 months; use routine and newly collected blood data to assess immunity; interview people who were identified for shielding and their carers and NHS staff who delivered healthcare during shielding, to explore compliance and experiences; collect healthcare resource use data to calculate implementation costs and cost-consequences. Our team includes people who were shielding, who used their experience to help design and deliver this study.<h4>Ethics and dissemination</h4>The study has received approval from the Newcastle North Tyneside 2 Research Ethics Committee (IRAS 295050). We will disseminate results directly to UK government policy-makers, publish in peer-reviewed journals, present at scientific and policy conferences and share accessible summaries of results online and through public and patient networks.",
+    "laySummary": "",
+    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/9/e059813.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-059813; html:https://europepmc.org/articles/PMC9461087; pdf:https://europepmc.org/articles/PMC9461087?pdf=render"
+  },
   {
     "id": "39226549",
     "doi": "https://doi.org/10.2196/47882",
@@ -6120,21 +6120,21 @@
     "urls": "pdf:https://aura.abdn.ac.uk/bitstream/2164/18431/1/Shi_etal_Lancet_Risk_COVID19_Hospital_VOR.pdf; doi:https://doi.org/10.1016/S2213-2600(21)00491-4; html:https://europepmc.org/articles/PMC8631918"
   },
   {
-    "id": "38774381",
-    "doi": "https://doi.org/10.1093/ehjdh/ztae011",
-    "title": "Remote monitoring of atrial fibrillation recurrence using mHealth technology (REMOTE-AF).",
-    "authorString": "Adasuriya G, Barsky A, Kralj-Hans I, Mohan S, Gill S, Chen Z, Jarman J, Jones D, Valli H, Gkoutos GV, Markides V, Hussain W, Wong T, Kotecha D, Haldar S.",
+    "id": "36653750",
+    "doi": "https://doi.org/10.1186/s12882-022-03043-8",
+    "title": "Ultrasound quadriceps muscle thickness is variably associated with frailty in haemodialysis recipients.",
+    "authorString": "Anderson BM, Wilson DV, Qasim M, Correa G, Evison F, Gallier S, Ferro CJ, Jackson TA, Sharif A.",
     "authorAffiliations": "",
-    "journalTitle": "European heart journal. Digital health",
-    "pubYear": "2024",
-    "date": "2024-02-12",
+    "journalTitle": "BMC nephrology",
+    "pubYear": "2023",
+    "date": "2023-01-18",
     "isOpenAccess": "Y",
-    "keywords": "Atrial fibrillation; Ablation; Remote Monitoring; Digital Health; Wearables",
+    "keywords": "Frailty; ultrasound; epidemiology; Sarcopenia",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Aims</h4>This proof-of-concept study sought to evaluate changes in heart rate (HR) obtained from a consumer wearable device and compare against implantable loop recorder (ILR)-detected recurrence of atrial fibrillation (AF) and atrial tachycardia (AT) after AF ablation.<h4>Methods and results</h4>REMOTE-AF (NCT05037136) was a prospectively designed sub-study of the CASA-AF randomized controlled trial (NCT04280042). Participants without a permanent pacemaker had an ILR implanted at their index ablation procedure for longstanding persistent AF. Heart rate and step count were continuously monitored using photoplethysmography (PPG) from a commercially available wrist-worn wearable. Photoplethysmography-recorded HR data were pre-processed with noise filtration and episodes at 1-min interval over 30\u2005min of HR elevations (<i>Z</i>-score = 2) were compared with corresponding ILR data. Thirty-five patients were enrolled, with mean age 70.3 \u00b1 6.8 years and median follow-up 10 months (interquartile range 8-12 months). Implantable loop recorder analysis revealed 17 out of 35 patients (49%) had recurrence of AF/AT. Compared with ILR recurrence, wearable-derived elevations in HR \u2265 110 beats per minute had a sensitivity of 95.3%, specificity 54.1%, positive predictive value (PPV) 15.8%, negative predictive value (NPV) 99.2%, and overall accuracy 57.4%. With PPG-recorded HR elevation spikes (non-exercise related), the sensitivity was 87.5%, specificity 62.2%, PPV 39.2%, NPV 92.3%, and overall accuracy 64.0% in the entire patient cohort. In the AF/AT recurrence only group, sensitivity was 87.6%, specificity 68.3%, PPV 53.6%, NPV 93.0%, and overall accuracy 75.0%.<h4>Conclusion</h4>Consumer wearable devices have the potential to contribute to arrhythmia detection after AF ablation.<h4>Study registration</h4>ClinicalTrials.gov Identifier: NCT05037136 https://clinicaltrials.gov/ct2/show/NCT05037136.",
+    "abstract": "<h4>Background</h4>Ultrasonographic quantitation of quadriceps muscle mass is increasingly used for assessment of sarcopenia, but its relationship with frailty in haemodialysis recipients is not known. This study explores the relationship between ultrasound-derived bilateral anterior thigh thickness (BATT), sarcopenia, and frailty by common frailty tools (Frailty Phenotype [FP], Frailty Index [FI], Edmonton Frailty [EFS], and Clinical Frailty Scale [CFS]).<h4>Methods</h4>This was an exploratory analysis of a subgroup of adult prevalent (\u22653\u2009months) haemodialysis recipients deeply phenotyped for frailty. Ultrasound assessment of BATT was obtained with participants at an angle of \u226445\u00b0, with legs outstretched and knees resting at 10\u00b0-20\u00b0, according to an established protocol. Associations with frailty were explored via both linear and logistic regressions for BATT, Low Muscle Mass (LMM), and sarcopenia with stepwise adjustment for a priori covariables.<h4>Results</h4>In total 223 study participants had ultrasound measurements. Frailty ranged from 34% for FP to 58% for FI. BATT was associated with increasing frailty on simple linear regression by all frailty tools, but lost significance on addition of covariables. Upon dichotomising frailty tools into Frail/Not Frail, BATT was associated with frailty by all tools on univariable analyses, but only retained association for EFS on the fully adjusted model (OR 0.97, 95% C.I. 0.94-1.00, P\u00a0=\u20090.05).<h4>Conclusions</h4>Ultrasound measures of quadriceps thickness is variably associated with frailty in prevalent haemodialysis recipients, dependent upon the frailty tool used, but not independent of other variables. Further work is required to establish the added value of sarcopenia measurement in frail haemodialysis patients.<h4>Trial registration</h4>Clinicaltrials.gov : NCT03071107 registered 06/03/2017.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1093/ehjdh/ztae011; html:https://europepmc.org/articles/PMC11104468; pdf:https://europepmc.org/articles/PMC11104468?pdf=render"
+    "urls": "pdf:https://bmcnephrol.biomedcentral.com/counter/pdf/10.1186/s12882-022-03043-8; doi:https://doi.org/10.1186/s12882-022-03043-8; html:https://europepmc.org/articles/PMC9847024; pdf:https://europepmc.org/articles/PMC9847024?pdf=render"
   },
   {
     "id": "33228632",
@@ -6153,23 +6153,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmcmedgenomics.biomedcentral.com/track/pdf/10.1186/s12920-020-00826-6; doi:https://doi.org/10.1186/s12920-020-00826-6; html:https://europepmc.org/articles/PMC7685541; pdf:https://europepmc.org/articles/PMC7685541?pdf=render"
   },
-  {
-    "id": "36653750",
-    "doi": "https://doi.org/10.1186/s12882-022-03043-8",
-    "title": "Ultrasound quadriceps muscle thickness is variably associated with frailty in haemodialysis recipients.",
-    "authorString": "Anderson BM, Wilson DV, Qasim M, Correa G, Evison F, Gallier S, Ferro CJ, Jackson TA, Sharif A.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC nephrology",
-    "pubYear": "2023",
-    "date": "2023-01-18",
-    "isOpenAccess": "Y",
-    "keywords": "Frailty; ultrasound; epidemiology; Sarcopenia",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Ultrasonographic quantitation of quadriceps muscle mass is increasingly used for assessment of sarcopenia, but its relationship with frailty in haemodialysis recipients is not known. This study explores the relationship between ultrasound-derived bilateral anterior thigh thickness (BATT), sarcopenia, and frailty by common frailty tools (Frailty Phenotype [FP], Frailty Index [FI], Edmonton Frailty [EFS], and Clinical Frailty Scale [CFS]).<h4>Methods</h4>This was an exploratory analysis of a subgroup of adult prevalent (\u22653\u2009months) haemodialysis recipients deeply phenotyped for frailty. Ultrasound assessment of BATT was obtained with participants at an angle of \u226445\u00b0, with legs outstretched and knees resting at 10\u00b0-20\u00b0, according to an established protocol. Associations with frailty were explored via both linear and logistic regressions for BATT, Low Muscle Mass (LMM), and sarcopenia with stepwise adjustment for a priori covariables.<h4>Results</h4>In total 223 study participants had ultrasound measurements. Frailty ranged from 34% for FP to 58% for FI. BATT was associated with increasing frailty on simple linear regression by all frailty tools, but lost significance on addition of covariables. Upon dichotomising frailty tools into Frail/Not Frail, BATT was associated with frailty by all tools on univariable analyses, but only retained association for EFS on the fully adjusted model (OR 0.97, 95% C.I. 0.94-1.00, P\u00a0=\u20090.05).<h4>Conclusions</h4>Ultrasound measures of quadriceps thickness is variably associated with frailty in prevalent haemodialysis recipients, dependent upon the frailty tool used, but not independent of other variables. Further work is required to establish the added value of sarcopenia measurement in frail haemodialysis patients.<h4>Trial registration</h4>Clinicaltrials.gov : NCT03071107 registered 06/03/2017.",
-    "laySummary": "",
-    "urls": "pdf:https://bmcnephrol.biomedcentral.com/counter/pdf/10.1186/s12882-022-03043-8; doi:https://doi.org/10.1186/s12882-022-03043-8; html:https://europepmc.org/articles/PMC9847024; pdf:https://europepmc.org/articles/PMC9847024?pdf=render"
-  },
   {
     "id": "36798088",
     "doi": "https://doi.org/10.1177/26335565221148616",
@@ -6187,6 +6170,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1177/26335565221148616; doi:https://doi.org/10.1177/26335565221148616; html:https://europepmc.org/articles/PMC9926377; pdf:https://europepmc.org/articles/PMC9926377?pdf=render"
   },
+  {
+    "id": "38774381",
+    "doi": "https://doi.org/10.1093/ehjdh/ztae011",
+    "title": "Remote monitoring of atrial fibrillation recurrence using mHealth technology (REMOTE-AF).",
+    "authorString": "Adasuriya G, Barsky A, Kralj-Hans I, Mohan S, Gill S, Chen Z, Jarman J, Jones D, Valli H, Gkoutos GV, Markides V, Hussain W, Wong T, Kotecha D, Haldar S.",
+    "authorAffiliations": "",
+    "journalTitle": "European heart journal. Digital health",
+    "pubYear": "2024",
+    "date": "2024-02-12",
+    "isOpenAccess": "Y",
+    "keywords": "Atrial fibrillation; Ablation; Remote Monitoring; Digital Health; Wearables",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Aims</h4>This proof-of-concept study sought to evaluate changes in heart rate (HR) obtained from a consumer wearable device and compare against implantable loop recorder (ILR)-detected recurrence of atrial fibrillation (AF) and atrial tachycardia (AT) after AF ablation.<h4>Methods and results</h4>REMOTE-AF (NCT05037136) was a prospectively designed sub-study of the CASA-AF randomized controlled trial (NCT04280042). Participants without a permanent pacemaker had an ILR implanted at their index ablation procedure for longstanding persistent AF. Heart rate and step count were continuously monitored using photoplethysmography (PPG) from a commercially available wrist-worn wearable. Photoplethysmography-recorded HR data were pre-processed with noise filtration and episodes at 1-min interval over 30\u2005min of HR elevations (<i>Z</i>-score = 2) were compared with corresponding ILR data. Thirty-five patients were enrolled, with mean age 70.3 \u00b1 6.8 years and median follow-up 10 months (interquartile range 8-12 months). Implantable loop recorder analysis revealed 17 out of 35 patients (49%) had recurrence of AF/AT. Compared with ILR recurrence, wearable-derived elevations in HR \u2265 110 beats per minute had a sensitivity of 95.3%, specificity 54.1%, positive predictive value (PPV) 15.8%, negative predictive value (NPV) 99.2%, and overall accuracy 57.4%. With PPG-recorded HR elevation spikes (non-exercise related), the sensitivity was 87.5%, specificity 62.2%, PPV 39.2%, NPV 92.3%, and overall accuracy 64.0% in the entire patient cohort. In the AF/AT recurrence only group, sensitivity was 87.6%, specificity 68.3%, PPV 53.6%, NPV 93.0%, and overall accuracy 75.0%.<h4>Conclusion</h4>Consumer wearable devices have the potential to contribute to arrhythmia detection after AF ablation.<h4>Study registration</h4>ClinicalTrials.gov Identifier: NCT05037136 https://clinicaltrials.gov/ct2/show/NCT05037136.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1093/ehjdh/ztae011; html:https://europepmc.org/articles/PMC11104468; pdf:https://europepmc.org/articles/PMC11104468?pdf=render"
+  },
   {
     "id": "35185750",
     "doi": "https://doi.org/10.3389/fneur.2021.787107",
@@ -6306,40 +6306,6 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pon.6225; doi:https://doi.org/10.1002/pon.6225; html:https://europepmc.org/articles/PMC10946963; pdf:https://europepmc.org/articles/PMC10946963?pdf=render"
   },
-  {
-    "id": "34942103",
-    "doi": "https://doi.org/10.1016/s0140-6736(21)02754-9",
-    "title": "Two-dose ChAdOx1 nCoV-19 vaccine protection against COVID-19 hospital admissions and deaths over time: a retrospective, population-based cohort study in Scotland and Brazil.",
-    "authorString": "Katikireddi SV, Cerqueira-Silva T, Vasileiou E, Robertson C, Amele S, Pan J, Taylor B, Boaventura V, Werneck GL, Flores-Ortiz R, Agrawal U, Docherty AB, McCowan C, McMenamin J, Moore E, Ritchie LD, Rudan I, Shah SA, Shi T, Simpson CR, Barreto ML, Oliveira VA, Barral-Netto M, Sheikh A.",
-    "authorAffiliations": "",
-    "journalTitle": "Lancet (London, England)",
-    "pubYear": "2022",
-    "date": "2021-12-20",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Reports suggest that COVID-19 vaccine effectiveness is decreasing, but whether this reflects waning or new SARS-CoV-2 variants-especially delta (B.1.617.2)-is unclear. We investigated the association between time since two doses of ChAdOx1 nCoV-19 vaccine and risk of severe COVID-19 outcomes in Scotland (where delta was dominant), with comparative analyses in Brazil (where delta was uncommon).<h4>Methods</h4>In this retrospective, population-based cohort study in Brazil and Scotland, we linked national databases from the EAVE II study in Scotland; and the COVID-19 Vaccination Campaign, Acute Respiratory Infection Suspected Cases, and Severe Acute Respiratory Infection/Illness datasets in Brazil) for vaccination, laboratory testing, clinical, and mortality data. We defined cohorts of adults (aged \u226518 years) who received two doses of ChAdOx1 nCoV-19 and compared rates of severe COVID-19 outcomes (ie, COVID-19 hospital admission or death) across fortnightly periods, relative to 2-3 weeks after the second dose. Entry to the Scotland cohort started from May 19, 2021, and entry to the Brazil cohort started from Jan 18, 2021. Follow-up in both cohorts was until Oct 25, 2021. Poisson regression was used to estimate rate ratios (RRs) and vaccine effectiveness, with 95% CIs.<h4>Findings</h4>1\u2009972\u2009454 adults received two doses of ChAdOx1 nCoV-19 in Scotland and 42\u2009558\u2009839 in Brazil, with longer follow-up in Scotland because two-dose vaccination began earlier in Scotland than in Brazil. In Scotland, RRs for severe COVID-19 increased to 2\u00b701 (95% CI 1\u00b754-2\u00b762) at 10-11 weeks, 3\u00b701 (2\u00b726-3\u00b799) at 14-15 weeks, and 5\u00b743 (4\u00b700-7\u00b738) at 18-19 weeks after the second dose. The pattern of results was similar in Brazil, with RRs of 2\u00b729 (2\u00b701-2\u00b761) at 10-11 weeks, 3\u00b710 (2\u00b763-3\u00b764) at 14-15 weeks, and 4\u00b771 (3\u00b783-5\u00b778) at 18-19 weeks after the second dose. In Scotland, vaccine effectiveness decreased from 83\u00b77% (95% CI 79\u00b77-87\u00b70) at 2-3 weeks, to 75\u00b79% (72\u00b79-78\u00b76) at 14-15 weeks, and 63\u00b77% (59\u00b76-67\u00b74) at 18-19 weeks after the second dose. In Brazil, vaccine effectiveness decreased from 86\u00b74% (85\u00b74-87\u00b73) at 2-3 weeks, to 59\u00b77% (54\u00b76-64\u00b72) at 14-15 weeks, and 42\u00b72% (32\u00b74-50\u00b76) at 18-19 weeks.<h4>Interpretation</h4>We found waning vaccine protection of ChAdOx1 nCoV-19 against COVID-19 hospital admissions and deaths in both Scotland and Brazil, this becoming evident within three months of the second vaccine dose. Consideration needs to be given to providing booster vaccine doses for people who have received ChAdOx1 nCoV-19.<h4>Funding</h4>UK Research and Innovation (Medical Research Council), Scottish Government, Research and Innovation Industrial Strategy Challenge Fund, Health Data Research UK, Fiocruz, Fazer o Bem Faz Bem Programme; Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico, Funda\u00e7\u00e3o Carlos Chagas Filho de Amparo \u00e0 Pesquisa do Estado do Rio de Janeiro.<h4>Translation</h4>For the Portuguese translation of the abstract see Supplementary Materials section.",
-    "laySummary": "",
-    "urls": "pdf:http://www.thelancet.com/article/S0140673621027549/pdf; doi:https://doi.org/10.1016/S0140-6736(21)02754-9; html:https://europepmc.org/articles/PMC8687670"
-  },
-  {
-    "id": "39192241",
-    "doi": "https://doi.org/10.1186/s12888-024-06022-5",
-    "title": "Developing a validated methodology for identifying clozapine treatment periods in electronic health records.",
-    "authorString": "Segev A, Govind R, Oloyede E, Morrin H, Jewell A, Jones R, Mangiaterra L, Bonora S, Iqbal E, Stewart R, Broadbent M, MacCabe JH.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC psychiatry",
-    "pubYear": "2024",
-    "date": "2024-08-27",
-    "isOpenAccess": "Y",
-    "keywords": "Databases; Schizophrenia; Algorithm; Clozapine; Psychosis; Ehr; Cris; Maudsley",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Clozapine is the only recommended antipsychotic medication for individuals diagnosed with treatment-resistant schizophrenia. Unfortunately, its wider use is hindered by several possible adverse effects, some of which are rare but potentially life threatening. As such, there is a growing interest in studying clozapine use and safety in routinely collected healthcare data. However, previous attempts to characterise clozapine treatment have had low accuracy.<h4>Aim</h4>To develop a methodology for identifying clozapine treatment dates by combining several data sources and implement this on a large clinical database.<h4>Methods</h4>Non-identifiable electronic health records from a large mental health provider in London and a linked database from a national clozapine blood monitoring service were used to obtain information regarding patients' clozapine treatment status, blood tests and pharmacy dispensing records. A rule-based algorithm was developed to determine the dates of starting and stopping treatment based on these data, and more than 10% of the outcomes were validated by manual review of de-identified case note text.<h4>Results</h4>A total of 3,212 possible clozapine treatment periods were identified, of which 425 (13.2%) were excluded due to insufficient data to verify clozapine administration. Of the 2,787 treatments remaining, 1,902 (68.2%) had an identified start-date. On evaluation, the algorithm identified treatments with 96.4% accuracy; start dates were 96.2% accurate within 15 days, and end dates were 85.1% accurate within 30 days.<h4>Conclusions</h4>The algorithm produced a reliable database of clozapine treatment periods. Beyond underpinning future observational clozapine studies, we envisage it will facilitate similar implementations on additional large clinical databases worldwide.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1186/s12888-024-06022-5; doi:https://doi.org/10.1186/s12888-024-06022-5; html:https://europepmc.org/articles/PMC11351314; pdf:https://europepmc.org/articles/PMC11351314?pdf=render"
-  },
   {
     "id": "36369736",
     "doi": "https://doi.org/10.1080/19490976.2022.2139979",
@@ -6357,6 +6323,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1080/19490976.2022.2139979; doi:https://doi.org/10.1080/19490976.2022.2139979; html:https://europepmc.org/articles/PMC9662191; pdf:https://europepmc.org/articles/PMC9662191?pdf=render"
   },
+  {
+    "id": "34942103",
+    "doi": "https://doi.org/10.1016/s0140-6736(21)02754-9",
+    "title": "Two-dose ChAdOx1 nCoV-19 vaccine protection against COVID-19 hospital admissions and deaths over time: a retrospective, population-based cohort study in Scotland and Brazil.",
+    "authorString": "Katikireddi SV, Cerqueira-Silva T, Vasileiou E, Robertson C, Amele S, Pan J, Taylor B, Boaventura V, Werneck GL, Flores-Ortiz R, Agrawal U, Docherty AB, McCowan C, McMenamin J, Moore E, Ritchie LD, Rudan I, Shah SA, Shi T, Simpson CR, Barreto ML, Oliveira VA, Barral-Netto M, Sheikh A.",
+    "authorAffiliations": "",
+    "journalTitle": "Lancet (London, England)",
+    "pubYear": "2022",
+    "date": "2021-12-20",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Reports suggest that COVID-19 vaccine effectiveness is decreasing, but whether this reflects waning or new SARS-CoV-2 variants-especially delta (B.1.617.2)-is unclear. We investigated the association between time since two doses of ChAdOx1 nCoV-19 vaccine and risk of severe COVID-19 outcomes in Scotland (where delta was dominant), with comparative analyses in Brazil (where delta was uncommon).<h4>Methods</h4>In this retrospective, population-based cohort study in Brazil and Scotland, we linked national databases from the EAVE II study in Scotland; and the COVID-19 Vaccination Campaign, Acute Respiratory Infection Suspected Cases, and Severe Acute Respiratory Infection/Illness datasets in Brazil) for vaccination, laboratory testing, clinical, and mortality data. We defined cohorts of adults (aged \u226518 years) who received two doses of ChAdOx1 nCoV-19 and compared rates of severe COVID-19 outcomes (ie, COVID-19 hospital admission or death) across fortnightly periods, relative to 2-3 weeks after the second dose. Entry to the Scotland cohort started from May 19, 2021, and entry to the Brazil cohort started from Jan 18, 2021. Follow-up in both cohorts was until Oct 25, 2021. Poisson regression was used to estimate rate ratios (RRs) and vaccine effectiveness, with 95% CIs.<h4>Findings</h4>1\u2009972\u2009454 adults received two doses of ChAdOx1 nCoV-19 in Scotland and 42\u2009558\u2009839 in Brazil, with longer follow-up in Scotland because two-dose vaccination began earlier in Scotland than in Brazil. In Scotland, RRs for severe COVID-19 increased to 2\u00b701 (95% CI 1\u00b754-2\u00b762) at 10-11 weeks, 3\u00b701 (2\u00b726-3\u00b799) at 14-15 weeks, and 5\u00b743 (4\u00b700-7\u00b738) at 18-19 weeks after the second dose. The pattern of results was similar in Brazil, with RRs of 2\u00b729 (2\u00b701-2\u00b761) at 10-11 weeks, 3\u00b710 (2\u00b763-3\u00b764) at 14-15 weeks, and 4\u00b771 (3\u00b783-5\u00b778) at 18-19 weeks after the second dose. In Scotland, vaccine effectiveness decreased from 83\u00b77% (95% CI 79\u00b77-87\u00b70) at 2-3 weeks, to 75\u00b79% (72\u00b79-78\u00b76) at 14-15 weeks, and 63\u00b77% (59\u00b76-67\u00b74) at 18-19 weeks after the second dose. In Brazil, vaccine effectiveness decreased from 86\u00b74% (85\u00b74-87\u00b73) at 2-3 weeks, to 59\u00b77% (54\u00b76-64\u00b72) at 14-15 weeks, and 42\u00b72% (32\u00b74-50\u00b76) at 18-19 weeks.<h4>Interpretation</h4>We found waning vaccine protection of ChAdOx1 nCoV-19 against COVID-19 hospital admissions and deaths in both Scotland and Brazil, this becoming evident within three months of the second vaccine dose. Consideration needs to be given to providing booster vaccine doses for people who have received ChAdOx1 nCoV-19.<h4>Funding</h4>UK Research and Innovation (Medical Research Council), Scottish Government, Research and Innovation Industrial Strategy Challenge Fund, Health Data Research UK, Fiocruz, Fazer o Bem Faz Bem Programme; Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico, Funda\u00e7\u00e3o Carlos Chagas Filho de Amparo \u00e0 Pesquisa do Estado do Rio de Janeiro.<h4>Translation</h4>For the Portuguese translation of the abstract see Supplementary Materials section.",
+    "laySummary": "",
+    "urls": "pdf:http://www.thelancet.com/article/S0140673621027549/pdf; doi:https://doi.org/10.1016/S0140-6736(21)02754-9; html:https://europepmc.org/articles/PMC8687670"
+  },
   {
     "id": "32935051",
     "doi": "https://doi.org/10.23889/ijpds.v5i1.1128",
@@ -6375,21 +6358,21 @@
     "urls": "pdf:https://ijpds.org/article/download/1128/2865; doi:https://doi.org/10.23889/ijpds.v5i1.1128; html:https://europepmc.org/articles/PMC7480324; pdf:https://europepmc.org/articles/PMC7480324?pdf=render"
   },
   {
-    "id": "38649271",
-    "doi": "https://doi.org/10.1136/thorax-2023-220856",
-    "title": "Rheumatoid arthritis and idiopathic pulmonary fibrosis: a bidirectional Mendelian randomisation study.",
-    "authorString": "Leavy OC, Kawano-Dourado L, Stewart ID, Quint JK, Solomon JJ, Borie R, Crestani B, Wain LV, Jenkins G, Dieud\u00e9 P, Minelli C.",
+    "id": "39192241",
+    "doi": "https://doi.org/10.1186/s12888-024-06022-5",
+    "title": "Developing a validated methodology for identifying clozapine treatment periods in electronic health records.",
+    "authorString": "Segev A, Govind R, Oloyede E, Morrin H, Jewell A, Jones R, Mangiaterra L, Bonora S, Iqbal E, Stewart R, Broadbent M, MacCabe JH.",
     "authorAffiliations": "",
-    "journalTitle": "Thorax",
+    "journalTitle": "BMC psychiatry",
     "pubYear": "2024",
-    "date": "2024-05-20",
+    "date": "2024-08-27",
     "isOpenAccess": "Y",
-    "keywords": "Interstitial fibrosis; idiopathic pulmonary fibrosis; Rheumatoid Lung Disease",
+    "keywords": "Databases; Schizophrenia; Algorithm; Clozapine; Psychosis; Ehr; Cris; Maudsley",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>A usual interstitial pneumonia (UIP) pattern of lung injury is a key feature of idiopathic pulmonary fibrosis (IPF) and is also observed in up to 40% of individuals with rheumatoid arthritis (RA)-associated interstitial lung disease (RA-ILD). The RA-UIP phenotype could result from either a causal relationship of RA on UIP or vice versa, or from a simple co-occurrence of RA and IPF due to shared demographic, genetic or environmental risk factors.<h4>Methods</h4>We used two-sample bidirectional Mendelian randomisation (MR) to test the hypothesis of a causal effect of RA on UIP and of UIP on RA, using variants from genome-wide association studies (GWAS) of RA (separately for seropositive (18\u2009019 cases and 991\u2009604 controls) and seronegative (8515 cases and 1\u2009015\u2009471 controls) RA) and of IPF (4125 cases and 20\u2009464 controls) as genetic instruments. Sensitivity analyses were conducted to assess the robustness of the results to violations of the MR assumptions.<h4>Findings</h4>IPF showed a significant causal effect on seropositive RA, with developing IPF increasing the risk of seropositive RA (OR=1.06, 95% CI: 1.04 to 1.08, p<0.001) which was robust under all models. For the MR in the other direction, seropositive RA showed a significant protective effect on IPF (OR=0.93; 95%\u2009CI: 0.87 to 0.99; p=0.032), but the effect was not significant when sensitivity analyses were applied. This was likely because of bias due to exclusion of patients with RA from among the cases in the IPF GWAS, or possibly because our genetic instruments did not fully capture the effect of the complex human leucocyte antigen region, the strongest RA genetic risk factor.<h4>Interpretation</h4>Our findings support the hypothesis that RA-UIP may be due to a cause-effect relationship between UIP and RA, rather than due to a coincidental occurrence of IPF in patients with RA. The significant causal effect of IPF on seropositive RA suggests that pathomechanisms involved in the development of UIP may promote RA, and this may help inform future guidelines on screening for ILD in patients with RA.",
+    "abstract": "<h4>Background</h4>Clozapine is the only recommended antipsychotic medication for individuals diagnosed with treatment-resistant schizophrenia. Unfortunately, its wider use is hindered by several possible adverse effects, some of which are rare but potentially life threatening. As such, there is a growing interest in studying clozapine use and safety in routinely collected healthcare data. However, previous attempts to characterise clozapine treatment have had low accuracy.<h4>Aim</h4>To develop a methodology for identifying clozapine treatment dates by combining several data sources and implement this on a large clinical database.<h4>Methods</h4>Non-identifiable electronic health records from a large mental health provider in London and a linked database from a national clozapine blood monitoring service were used to obtain information regarding patients' clozapine treatment status, blood tests and pharmacy dispensing records. A rule-based algorithm was developed to determine the dates of starting and stopping treatment based on these data, and more than 10% of the outcomes were validated by manual review of de-identified case note text.<h4>Results</h4>A total of 3,212 possible clozapine treatment periods were identified, of which 425 (13.2%) were excluded due to insufficient data to verify clozapine administration. Of the 2,787 treatments remaining, 1,902 (68.2%) had an identified start-date. On evaluation, the algorithm identified treatments with 96.4% accuracy; start dates were 96.2% accurate within 15 days, and end dates were 85.1% accurate within 30 days.<h4>Conclusions</h4>The algorithm produced a reliable database of clozapine treatment periods. Beyond underpinning future observational clozapine studies, we envisage it will facilitate similar implementations on additional large clinical databases worldwide.",
     "laySummary": "",
-    "urls": "pdf:https://thorax.bmj.com/content/thoraxjnl/early/2024/04/21/thorax-2023-220856.full.pdf; doi:https://doi.org/10.1136/thorax-2023-220856; html:https://europepmc.org/articles/PMC11137470; pdf:https://europepmc.org/articles/PMC11137470?pdf=render"
+    "urls": "doi:https://doi.org/10.1186/s12888-024-06022-5; doi:https://doi.org/10.1186/s12888-024-06022-5; html:https://europepmc.org/articles/PMC11351314; pdf:https://europepmc.org/articles/PMC11351314?pdf=render"
   },
   {
     "id": "36629285",
@@ -6408,6 +6391,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/eurheartj/advance-article-pdf/doi/10.1093/eurheartj/ehac758/48602276/ehac758.pdf; doi:https://doi.org/10.1093/eurheartj/ehac758; html:https://europepmc.org/articles/PMC9976986; pdf:https://europepmc.org/articles/PMC9976986?pdf=render"
   },
+  {
+    "id": "38649271",
+    "doi": "https://doi.org/10.1136/thorax-2023-220856",
+    "title": "Rheumatoid arthritis and idiopathic pulmonary fibrosis: a bidirectional Mendelian randomisation study.",
+    "authorString": "Leavy OC, Kawano-Dourado L, Stewart ID, Quint JK, Solomon JJ, Borie R, Crestani B, Wain LV, Jenkins G, Dieud\u00e9 P, Minelli C.",
+    "authorAffiliations": "",
+    "journalTitle": "Thorax",
+    "pubYear": "2024",
+    "date": "2024-05-20",
+    "isOpenAccess": "Y",
+    "keywords": "Interstitial fibrosis; idiopathic pulmonary fibrosis; Rheumatoid Lung Disease",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>A usual interstitial pneumonia (UIP) pattern of lung injury is a key feature of idiopathic pulmonary fibrosis (IPF) and is also observed in up to 40% of individuals with rheumatoid arthritis (RA)-associated interstitial lung disease (RA-ILD). The RA-UIP phenotype could result from either a causal relationship of RA on UIP or vice versa, or from a simple co-occurrence of RA and IPF due to shared demographic, genetic or environmental risk factors.<h4>Methods</h4>We used two-sample bidirectional Mendelian randomisation (MR) to test the hypothesis of a causal effect of RA on UIP and of UIP on RA, using variants from genome-wide association studies (GWAS) of RA (separately for seropositive (18\u2009019 cases and 991\u2009604 controls) and seronegative (8515 cases and 1\u2009015\u2009471 controls) RA) and of IPF (4125 cases and 20\u2009464 controls) as genetic instruments. Sensitivity analyses were conducted to assess the robustness of the results to violations of the MR assumptions.<h4>Findings</h4>IPF showed a significant causal effect on seropositive RA, with developing IPF increasing the risk of seropositive RA (OR=1.06, 95% CI: 1.04 to 1.08, p<0.001) which was robust under all models. For the MR in the other direction, seropositive RA showed a significant protective effect on IPF (OR=0.93; 95%\u2009CI: 0.87 to 0.99; p=0.032), but the effect was not significant when sensitivity analyses were applied. This was likely because of bias due to exclusion of patients with RA from among the cases in the IPF GWAS, or possibly because our genetic instruments did not fully capture the effect of the complex human leucocyte antigen region, the strongest RA genetic risk factor.<h4>Interpretation</h4>Our findings support the hypothesis that RA-UIP may be due to a cause-effect relationship between UIP and RA, rather than due to a coincidental occurrence of IPF in patients with RA. The significant causal effect of IPF on seropositive RA suggests that pathomechanisms involved in the development of UIP may promote RA, and this may help inform future guidelines on screening for ILD in patients with RA.",
+    "laySummary": "",
+    "urls": "pdf:https://thorax.bmj.com/content/thoraxjnl/early/2024/04/21/thorax-2023-220856.full.pdf; doi:https://doi.org/10.1136/thorax-2023-220856; html:https://europepmc.org/articles/PMC11137470; pdf:https://europepmc.org/articles/PMC11137470?pdf=render"
+  },
   {
     "id": "31088492",
     "doi": "https://doi.org/10.1186/s12967-019-1912-5",
@@ -6425,6 +6425,23 @@
     "laySummary": "",
     "urls": "pdf:https://translational-medicine.biomedcentral.com/track/pdf/10.1186/s12967-019-1912-5; doi:https://doi.org/10.1186/s12967-019-1912-5; html:https://europepmc.org/articles/PMC6518609; pdf:https://europepmc.org/articles/PMC6518609?pdf=render"
   },
+  {
+    "id": "34446426",
+    "doi": "https://doi.org/10.1136/bmj.n1931",
+    "title": "Risk of thrombocytopenia and thromboembolism after covid-19 vaccination and SARS-CoV-2 positive testing: self-controlled case series study.",
+    "authorString": "Hippisley-Cox J, Patone M, Mei XW, Saatci D, Dixon S, Khunti K, Zaccardi F, Watkinson P, Shankar-Hari M, Doidge J, Harrison DA, Griffin SJ, Sheikh A, Coupland CAC.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ (Clinical research ed.)",
+    "pubYear": "2021",
+    "date": "2021-08-26",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>To assess the association between covid-19 vaccines and risk of thrombocytopenia and thromboembolic events in England among adults.<h4>Design</h4>Self-controlled case series study using national data on covid-19 vaccination and hospital admissions.<h4>Setting</h4>Patient level data were obtained for approximately 30 million people vaccinated in England between 1 December 2020 and 24 April 2021. Electronic health records were linked with death data from the Office for National Statistics, SARS-CoV-2 positive test data, and hospital admission data from the United Kingdom's health service (NHS).<h4>Participants</h4>29\u2009121\u2009633 people were vaccinated with first doses (19\u2009608\u2009008 with Oxford-AstraZeneca (ChAdOx1 nCoV-19) and 9\u2009513\u2009625 with Pfizer-BioNTech (BNT162b2 mRNA)) and 1\u2009758\u2009095 people had a positive SARS-CoV-2 test. People aged \u226516 years who had first doses of the ChAdOx1 nCoV-19 or BNT162b2 mRNA vaccines and any outcome of interest were included in the study.<h4>Main outcome measures</h4>The primary outcomes were hospital admission or death associated with thrombocytopenia, venous thromboembolism, and arterial thromboembolism within 28 days of three exposures: first dose of the ChAdOx1 nCoV-19 vaccine; first dose of the BNT162b2 mRNA vaccine; and a SARS-CoV-2 positive test. Secondary outcomes were subsets of the primary outcomes: cerebral venous sinus thrombosis (CVST), ischaemic stroke, myocardial infarction, and other rare arterial thrombotic events.<h4>Results</h4>The study found increased risk of thrombocytopenia after ChAdOx1 nCoV-19 vaccination (incidence rate ratio 1.33, 95% confidence interval 1.19 to 1.47 at 8-14 days) and after a positive SARS-CoV-2 test (5.27, 4.34 to 6.40 at 8-14 days); increased risk of venous thromboembolism after ChAdOx1 nCoV-19 vaccination (1.10, 1.02 to 1.18 at 8-14 days) and after SARS-CoV-2 infection (13.86, 12.76 to 15.05 at 8-14 days); and increased risk of arterial thromboembolism after BNT162b2 mRNA vaccination (1.06, 1.01 to 1.10 at 15-21 days) and after SARS-CoV-2 infection (2.02, 1.82 to 2.24 at 15-21 days). Secondary analyses found increased risk of CVST after ChAdOx1 nCoV-19 vaccination (4.01, 2.08 to 7.71 at 8-14 days), after BNT162b2 mRNA vaccination (3.58, 1.39 to 9.27 at 15-21 days), and after a positive SARS-CoV-2 test; increased risk of ischaemic stroke after BNT162b2 mRNA vaccination (1.12, 1.04 to 1.20 at 15-21 days) and after a positive SARS-CoV-2 test; and increased risk of other rare arterial thrombotic events after ChAdOx1 nCoV-19 vaccination (1.21, 1.02 to 1.43 at 8-14 days) and after a positive SARS-CoV-2 test.<h4>Conclusion</h4>Increased risks of haematological and vascular events that led to hospital admission or death were observed for short time intervals after first doses of the ChAdOx1 nCoV-19 and BNT162b2 mRNA vaccines. The risks of most of these events were substantially higher and more prolonged after SARS-CoV-2 infection than after vaccination in the same population.",
+    "laySummary": "",
+    "urls": "pdf:https://www.bmj.com/content/bmj/374/bmj.n1931.full.pdf; doi:https://doi.org/10.1136/bmj.n1931; html:https://europepmc.org/articles/PMC8388189; pdf:https://europepmc.org/articles/PMC8388189?pdf=render"
+  },
   {
     "id": "35698725",
     "doi": "https://doi.org/10.1016/s2665-9913(22)00098-4",
@@ -6442,23 +6459,6 @@
     "laySummary": "",
     "urls": "pdf:http://www.thelancet.com/article/S2665991322000984/pdf; doi:https://doi.org/10.1016/S2665-9913(22)00098-4; html:https://europepmc.org/articles/PMC9179144; pdf:https://europepmc.org/articles/PMC9179144?pdf=render"
   },
-  {
-    "id": "33683514",
-    "doi": "https://doi.org/10.1007/s10237-021-01437-5",
-    "title": "A framework for incorporating 3D hyperelastic vascular wall models in 1D blood flow simulations.",
-    "authorString": "Coccarelli A, Carson JM, Aggarwal A, Pant S.",
-    "authorAffiliations": "",
-    "journalTitle": "Biomechanics and modeling in mechanobiology",
-    "pubYear": "2021",
-    "date": "2021-03-08",
-    "isOpenAccess": "Y",
-    "keywords": "Pulse wave velocity; Common carotid artery; Hyperelasticity; Tube Law; Axial Stretching; One-dimensional Blood Flow Modelling",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "We present a novel framework for investigating the role of vascular structure on arterial haemodynamics in large vessels, with a special focus on the human common carotid artery (CCA). The analysis is carried out by adopting a three-dimensional (3D) derived, fibre-reinforced, hyperelastic structural model, which is coupled with an axisymmetric, reduced order model describing blood flow. The vessel transmural pressure and lumen area are related via a Holzapfel-Ogden type of law, and the residual stresses along the thickness and length of the vessel are also accounted for. After a structural characterization of the adopted hyperelastic model, we investigate the link underlying the vascular wall response and blood-flow dynamics by comparing the proposed framework results against a popular tube law. The comparison shows that the behaviour of the model can be captured by the simpler linear surrogate only if a representative value of compliance is applied. Sobol's multi-variable sensitivity analysis is then carried out in order to identify the extent to which the structural parameters have an impact on the CCA haemodynamics. In this case, the local pulse wave velocity (PWV) is used as index for representing the arterial transmission capacity of blood pressure waveforms. The sensitivity analysis suggests that some geometrical factors, such as the stress-free inner radius and opening angle, play a major role on the system's haemodynamics. Subsequently, we quantified the differences in haemodynamic variables obtained from different virtual CCAs, tube laws and flow conditions. Although each artery presents a distinct vascular response, the differences obtained across different flow regimes are not significant. As expected, the linear tube law is unable to accurately capture all the haemodynamic features characterizing the current model. The findings from the sensitivity analysis are further confirmed by investigating the axial stretching effect on the CCA fluid dynamics. This factor does not seem to alter the pressure and flow waveforms. On the contrary, it is shown that, for an axially stretched vessel, the vascular wall exhibits an attenuation in absolute distension and an increase in circumferential stress, corroborating the findings of previous studies. This analysis shows that the new model offers a good balance between computational complexity and physics captured, making it an ideal framework for studies aiming to investigate the profound link between vascular mechanobiology and blood flow.",
-    "laySummary": "",
-    "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s10237-021-01437-5.pdf; doi:https://doi.org/10.1007/s10237-021-01437-5; html:https://europepmc.org/articles/PMC8298378; pdf:https://europepmc.org/articles/PMC8298378?pdf=render"
-  },
   {
     "id": "37120260",
     "doi": "https://doi.org/10.1016/s2468-2667(23)00079-8",
@@ -6476,6 +6476,23 @@
     "laySummary": "",
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10139026; doi:https://doi.org/10.1016/S2468-2667(23)00079-8; html:https://europepmc.org/articles/PMC10139026; pdf:https://europepmc.org/articles/PMC10139026?pdf=render"
   },
+  {
+    "id": "33683514",
+    "doi": "https://doi.org/10.1007/s10237-021-01437-5",
+    "title": "A framework for incorporating 3D hyperelastic vascular wall models in 1D blood flow simulations.",
+    "authorString": "Coccarelli A, Carson JM, Aggarwal A, Pant S.",
+    "authorAffiliations": "",
+    "journalTitle": "Biomechanics and modeling in mechanobiology",
+    "pubYear": "2021",
+    "date": "2021-03-08",
+    "isOpenAccess": "Y",
+    "keywords": "Pulse wave velocity; Common carotid artery; Hyperelasticity; Tube Law; Axial Stretching; One-dimensional Blood Flow Modelling",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "We present a novel framework for investigating the role of vascular structure on arterial haemodynamics in large vessels, with a special focus on the human common carotid artery (CCA). The analysis is carried out by adopting a three-dimensional (3D) derived, fibre-reinforced, hyperelastic structural model, which is coupled with an axisymmetric, reduced order model describing blood flow. The vessel transmural pressure and lumen area are related via a Holzapfel-Ogden type of law, and the residual stresses along the thickness and length of the vessel are also accounted for. After a structural characterization of the adopted hyperelastic model, we investigate the link underlying the vascular wall response and blood-flow dynamics by comparing the proposed framework results against a popular tube law. The comparison shows that the behaviour of the model can be captured by the simpler linear surrogate only if a representative value of compliance is applied. Sobol's multi-variable sensitivity analysis is then carried out in order to identify the extent to which the structural parameters have an impact on the CCA haemodynamics. In this case, the local pulse wave velocity (PWV) is used as index for representing the arterial transmission capacity of blood pressure waveforms. The sensitivity analysis suggests that some geometrical factors, such as the stress-free inner radius and opening angle, play a major role on the system's haemodynamics. Subsequently, we quantified the differences in haemodynamic variables obtained from different virtual CCAs, tube laws and flow conditions. Although each artery presents a distinct vascular response, the differences obtained across different flow regimes are not significant. As expected, the linear tube law is unable to accurately capture all the haemodynamic features characterizing the current model. The findings from the sensitivity analysis are further confirmed by investigating the axial stretching effect on the CCA fluid dynamics. This factor does not seem to alter the pressure and flow waveforms. On the contrary, it is shown that, for an axially stretched vessel, the vascular wall exhibits an attenuation in absolute distension and an increase in circumferential stress, corroborating the findings of previous studies. This analysis shows that the new model offers a good balance between computational complexity and physics captured, making it an ideal framework for studies aiming to investigate the profound link between vascular mechanobiology and blood flow.",
+    "laySummary": "",
+    "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s10237-021-01437-5.pdf; doi:https://doi.org/10.1007/s10237-021-01437-5; html:https://europepmc.org/articles/PMC8298378; pdf:https://europepmc.org/articles/PMC8298378?pdf=render"
+  },
   {
     "id": "32634370",
     "doi": "https://doi.org/10.1098/rsob.200121",
@@ -6494,21 +6511,21 @@
     "urls": "pdf:https://royalsocietypublishing.org/doi/pdf/10.1098/rsob.200121; doi:https://doi.org/10.1098/rsob.200121; html:https://europepmc.org/articles/PMC7574545; pdf:https://europepmc.org/articles/PMC7574545?pdf=render"
   },
   {
-    "id": "34446426",
-    "doi": "https://doi.org/10.1136/bmj.n1931",
-    "title": "Risk of thrombocytopenia and thromboembolism after covid-19 vaccination and SARS-CoV-2 positive testing: self-controlled case series study.",
-    "authorString": "Hippisley-Cox J, Patone M, Mei XW, Saatci D, Dixon S, Khunti K, Zaccardi F, Watkinson P, Shankar-Hari M, Doidge J, Harrison DA, Griffin SJ, Sheikh A, Coupland CAC.",
+    "id": "36583230",
+    "doi": "https://doi.org/10.1002/cam4.5556",
+    "title": "Circulating gamma-glutamyl transpeptidase and risk of pancreatic cancer: A prospective cohort study in the UK Biobank.",
+    "authorString": "Liao W, Yang Y, Yang H, Qu Y, Song H, Li Q.",
     "authorAffiliations": "",
-    "journalTitle": "BMJ (Clinical research ed.)",
-    "pubYear": "2021",
-    "date": "2021-08-26",
+    "journalTitle": "Cancer medicine",
+    "pubYear": "2023",
+    "date": "2022-12-29",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Prevention; Pancreatic cancer; Gamma-glutamyl Transpeptidase; European Ancestry",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Objective</h4>To assess the association between covid-19 vaccines and risk of thrombocytopenia and thromboembolic events in England among adults.<h4>Design</h4>Self-controlled case series study using national data on covid-19 vaccination and hospital admissions.<h4>Setting</h4>Patient level data were obtained for approximately 30 million people vaccinated in England between 1 December 2020 and 24 April 2021. Electronic health records were linked with death data from the Office for National Statistics, SARS-CoV-2 positive test data, and hospital admission data from the United Kingdom's health service (NHS).<h4>Participants</h4>29\u2009121\u2009633 people were vaccinated with first doses (19\u2009608\u2009008 with Oxford-AstraZeneca (ChAdOx1 nCoV-19) and 9\u2009513\u2009625 with Pfizer-BioNTech (BNT162b2 mRNA)) and 1\u2009758\u2009095 people had a positive SARS-CoV-2 test. People aged \u226516 years who had first doses of the ChAdOx1 nCoV-19 or BNT162b2 mRNA vaccines and any outcome of interest were included in the study.<h4>Main outcome measures</h4>The primary outcomes were hospital admission or death associated with thrombocytopenia, venous thromboembolism, and arterial thromboembolism within 28 days of three exposures: first dose of the ChAdOx1 nCoV-19 vaccine; first dose of the BNT162b2 mRNA vaccine; and a SARS-CoV-2 positive test. Secondary outcomes were subsets of the primary outcomes: cerebral venous sinus thrombosis (CVST), ischaemic stroke, myocardial infarction, and other rare arterial thrombotic events.<h4>Results</h4>The study found increased risk of thrombocytopenia after ChAdOx1 nCoV-19 vaccination (incidence rate ratio 1.33, 95% confidence interval 1.19 to 1.47 at 8-14 days) and after a positive SARS-CoV-2 test (5.27, 4.34 to 6.40 at 8-14 days); increased risk of venous thromboembolism after ChAdOx1 nCoV-19 vaccination (1.10, 1.02 to 1.18 at 8-14 days) and after SARS-CoV-2 infection (13.86, 12.76 to 15.05 at 8-14 days); and increased risk of arterial thromboembolism after BNT162b2 mRNA vaccination (1.06, 1.01 to 1.10 at 15-21 days) and after SARS-CoV-2 infection (2.02, 1.82 to 2.24 at 15-21 days). Secondary analyses found increased risk of CVST after ChAdOx1 nCoV-19 vaccination (4.01, 2.08 to 7.71 at 8-14 days), after BNT162b2 mRNA vaccination (3.58, 1.39 to 9.27 at 15-21 days), and after a positive SARS-CoV-2 test; increased risk of ischaemic stroke after BNT162b2 mRNA vaccination (1.12, 1.04 to 1.20 at 15-21 days) and after a positive SARS-CoV-2 test; and increased risk of other rare arterial thrombotic events after ChAdOx1 nCoV-19 vaccination (1.21, 1.02 to 1.43 at 8-14 days) and after a positive SARS-CoV-2 test.<h4>Conclusion</h4>Increased risks of haematological and vascular events that led to hospital admission or death were observed for short time intervals after first doses of the ChAdOx1 nCoV-19 and BNT162b2 mRNA vaccines. The risks of most of these events were substantially higher and more prolonged after SARS-CoV-2 infection than after vaccination in the same population.",
+    "abstract": "<h4>Background</h4>To determine whether serum gamma-glutamyl transpeptidase (GGT) level is associated with pancreatic cancer risk in a large prospective cohort.<h4>Methods</h4>The study analyzed serum GGT concentration at baseline of 421,032 participants recruited in the UK Biobank since 2006 through 2010. Information on incidence of pancreatic cancer was obtained from cancer and death registers, updated until 2015 in Scotland or 2016 in England and Wales. Adjusted Cox proportional hazards models were used to measure the association between serum GGT\u00a0and pancreatic cancer risk.<h4>Results</h4>The study identified 586 cases of pancreatic cancer over a median follow-up period of 7.16\u2009years. In the multivariable-adjusted Cox model, serum GGT level was associated with 14% higher pancreatic cancer risk (hazard ratio (HR) per one standard deviation increment of log2 GGT level\u00a0=\u00a01.14, 95% confidence interval (CI) 1.02-1.28, p\u00a0=\u20090.025). In the total population, the HR for the highest GGT group was 1.68 (95%CI: 1.22-2.30) versus the lowest GGT group. The HR for the highest GGT group in men (\u226550.2\u00a0U/L) was 1.72 (95%CI: 1.14-2.61) and that in women (\u226531.6\u00a0U/L) was 1.75 (95%CI: 1.06-2.88) versus the lowest GGT group.<h4>Conclusion</h4>Our findings suggested a positive association of serum GGT in pancreatic cancer etiology, implying the potential of monitoring GGT level for identifying at-risk individuals for pancreatic cancer.",
     "laySummary": "",
-    "urls": "pdf:https://www.bmj.com/content/bmj/374/bmj.n1931.full.pdf; doi:https://doi.org/10.1136/bmj.n1931; html:https://europepmc.org/articles/PMC8388189; pdf:https://europepmc.org/articles/PMC8388189?pdf=render"
+    "urls": "doi:https://doi.org/10.1002/cam4.5556; doi:https://doi.org/10.1002/cam4.5556; html:https://europepmc.org/articles/PMC10134379; pdf:https://europepmc.org/articles/PMC10134379?pdf=render"
   },
   {
     "id": "34829865",
@@ -6527,6 +6544,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.mdpi.com/2227-9059/9/11/1636/pdf?version=1637024773; doi:https://doi.org/10.3390/biomedicines9111636; html:https://europepmc.org/articles/PMC8615894; pdf:https://europepmc.org/articles/PMC8615894?pdf=render"
   },
+  {
+    "id": "35511729",
+    "doi": "https://doi.org/10.1093/ageing/afac084",
+    "title": "COVID-19 risk factors amongst 14,786 care home residents: an observational longitudinal analysis including daily community positive test rates of COVID-19, hospital stays and vaccination status in Wales (UK) between 1 September 2020 and 1 May 2021.",
+    "authorString": "Hollinghurst J, Hollinghurst R, North L, Mizen A, Akbari A, Long S, Lyons RA, Fry R.",
+    "authorAffiliations": "",
+    "journalTitle": "Age and ageing",
+    "pubYear": "2022",
+    "date": "2022-05-01",
+    "isOpenAccess": "Y",
+    "keywords": "Vaccination; Hospital infection; Older People; Care Homes; Covid-19; Pcr Tests",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>COVID-19 vaccinations have been prioritised for high risk individuals.<h4>Aim</h4>Determine individual-level risk factors for care home residents testing positive for SARS-CoV-2.<h4>Study design</h4>Longitudinal observational cohort study using individual-level linked data from the Secure Anonymised Information Linkage (SAIL) databank.<h4>Setting</h4>Fourteen thousand seven hundred and eighty-six older care home residents (aged 65+) living in Wales between 1 September 2020 and 1 May 2021. Our dataset consisted of 2,613,341 individual-level daily observations within 697 care homes.<h4>Methods</h4>We estimated odds ratios (ORs [95% confidence interval]) using multilevel logistic regression models. Our outcome of interest was a positive SARS-CoV-2 PCR test. We included time-dependent covariates for the estimated community positive test rate of COVID-19, hospital inpatient status, vaccination status and frailty. Additional covariates were included for age, sex and specialist care home services.<h4>Results</h4>The multivariable regression model indicated an increase in age (OR 1.01 [1.00,1.01] per year), community positive test rate (OR 1.13 [1.12,1.13] per percent increase), hospital inpatients (OR 7.40 [6.54,8.36]), and residents in care homes with non-specialist dementia care (OR 1.42 [1.01,1.99]) had an increased odds of a positive test. Having a positive test prior to the observation period (OR 0.58 [0.49,0.68]) and either one or two doses of a vaccine (0.21 [0.17,0.25] and 0.05 [0.02,0.09], respectively) were associated with a decreased odds.<h4>Conclusions</h4>Care providers need to remain vigilant despite the vaccination rollout, and extra precautions should be taken when caring for the most vulnerable. Minimising potential COVID-19 infection for care home residents when admitted to hospital should be prioritised.",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/ageing/article-pdf/51/5/afac084/43520659/afac084.pdf; doi:https://doi.org/10.1093/ageing/afac084; html:https://europepmc.org/articles/PMC9070807; pdf:https://europepmc.org/articles/PMC9070807?pdf=render"
+  },
   {
     "id": "33114263",
     "doi": "https://doi.org/10.3390/ijms21217886",
@@ -6544,23 +6578,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.mdpi.com/1422-0067/21/21/7886/pdf?version=1604329387; doi:https://doi.org/10.3390/ijms21217886; html:https://europepmc.org/articles/PMC7660606; pdf:https://europepmc.org/articles/PMC7660606?pdf=render"
   },
-  {
-    "id": "36583230",
-    "doi": "https://doi.org/10.1002/cam4.5556",
-    "title": "Circulating gamma-glutamyl transpeptidase and risk of pancreatic cancer: A prospective cohort study in the UK Biobank.",
-    "authorString": "Liao W, Yang Y, Yang H, Qu Y, Song H, Li Q.",
-    "authorAffiliations": "",
-    "journalTitle": "Cancer medicine",
-    "pubYear": "2023",
-    "date": "2022-12-29",
-    "isOpenAccess": "Y",
-    "keywords": "Prevention; Pancreatic cancer; Gamma-glutamyl Transpeptidase; European Ancestry",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>To determine whether serum gamma-glutamyl transpeptidase (GGT) level is associated with pancreatic cancer risk in a large prospective cohort.<h4>Methods</h4>The study analyzed serum GGT concentration at baseline of 421,032 participants recruited in the UK Biobank since 2006 through 2010. Information on incidence of pancreatic cancer was obtained from cancer and death registers, updated until 2015 in Scotland or 2016 in England and Wales. Adjusted Cox proportional hazards models were used to measure the association between serum GGT\u00a0and pancreatic cancer risk.<h4>Results</h4>The study identified 586 cases of pancreatic cancer over a median follow-up period of 7.16\u2009years. In the multivariable-adjusted Cox model, serum GGT level was associated with 14% higher pancreatic cancer risk (hazard ratio (HR) per one standard deviation increment of log2 GGT level\u00a0=\u00a01.14, 95% confidence interval (CI) 1.02-1.28, p\u00a0=\u20090.025). In the total population, the HR for the highest GGT group was 1.68 (95%CI: 1.22-2.30) versus the lowest GGT group. The HR for the highest GGT group in men (\u226550.2\u00a0U/L) was 1.72 (95%CI: 1.14-2.61) and that in women (\u226531.6\u00a0U/L) was 1.75 (95%CI: 1.06-2.88) versus the lowest GGT group.<h4>Conclusion</h4>Our findings suggested a positive association of serum GGT in pancreatic cancer etiology, implying the potential of monitoring GGT level for identifying at-risk individuals for pancreatic cancer.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1002/cam4.5556; doi:https://doi.org/10.1002/cam4.5556; html:https://europepmc.org/articles/PMC10134379; pdf:https://europepmc.org/articles/PMC10134379?pdf=render"
-  },
   {
     "id": "36750952",
     "doi": "https://doi.org/10.1186/s12911-023-02109-3",
@@ -6578,23 +6595,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-023-02109-3; doi:https://doi.org/10.1186/s12911-023-02109-3; html:https://europepmc.org/articles/PMC9903450; pdf:https://europepmc.org/articles/PMC9903450?pdf=render"
   },
-  {
-    "id": "35511729",
-    "doi": "https://doi.org/10.1093/ageing/afac084",
-    "title": "COVID-19 risk factors amongst 14,786 care home residents: an observational longitudinal analysis including daily community positive test rates of COVID-19, hospital stays and vaccination status in Wales (UK) between 1 September 2020 and 1 May 2021.",
-    "authorString": "Hollinghurst J, Hollinghurst R, North L, Mizen A, Akbari A, Long S, Lyons RA, Fry R.",
-    "authorAffiliations": "",
-    "journalTitle": "Age and ageing",
-    "pubYear": "2022",
-    "date": "2022-05-01",
-    "isOpenAccess": "Y",
-    "keywords": "Vaccination; Hospital infection; Older People; Care Homes; Covid-19; Pcr Tests",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>COVID-19 vaccinations have been prioritised for high risk individuals.<h4>Aim</h4>Determine individual-level risk factors for care home residents testing positive for SARS-CoV-2.<h4>Study design</h4>Longitudinal observational cohort study using individual-level linked data from the Secure Anonymised Information Linkage (SAIL) databank.<h4>Setting</h4>Fourteen thousand seven hundred and eighty-six older care home residents (aged 65+) living in Wales between 1 September 2020 and 1 May 2021. Our dataset consisted of 2,613,341 individual-level daily observations within 697 care homes.<h4>Methods</h4>We estimated odds ratios (ORs [95% confidence interval]) using multilevel logistic regression models. Our outcome of interest was a positive SARS-CoV-2 PCR test. We included time-dependent covariates for the estimated community positive test rate of COVID-19, hospital inpatient status, vaccination status and frailty. Additional covariates were included for age, sex and specialist care home services.<h4>Results</h4>The multivariable regression model indicated an increase in age (OR 1.01 [1.00,1.01] per year), community positive test rate (OR 1.13 [1.12,1.13] per percent increase), hospital inpatients (OR 7.40 [6.54,8.36]), and residents in care homes with non-specialist dementia care (OR 1.42 [1.01,1.99]) had an increased odds of a positive test. Having a positive test prior to the observation period (OR 0.58 [0.49,0.68]) and either one or two doses of a vaccine (0.21 [0.17,0.25] and 0.05 [0.02,0.09], respectively) were associated with a decreased odds.<h4>Conclusions</h4>Care providers need to remain vigilant despite the vaccination rollout, and extra precautions should be taken when caring for the most vulnerable. Minimising potential COVID-19 infection for care home residents when admitted to hospital should be prioritised.",
-    "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/ageing/article-pdf/51/5/afac084/43520659/afac084.pdf; doi:https://doi.org/10.1093/ageing/afac084; html:https://europepmc.org/articles/PMC9070807; pdf:https://europepmc.org/articles/PMC9070807?pdf=render"
-  },
   {
     "id": "37586846",
     "doi": "https://doi.org/10.1136/openhrt-2023-002378",
@@ -6680,6 +6680,23 @@
     "laySummary": "",
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s00247-021-05266-7.pdf; doi:https://doi.org/10.1007/s00247-021-05266-7; html:https://europepmc.org/articles/PMC9107460; pdf:https://europepmc.org/articles/PMC9107460?pdf=render"
   },
+  {
+    "id": "35913410",
+    "doi": "https://doi.org/10.1093/cid/ciac629",
+    "title": "Validity of Self-testing at Home With Rapid Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Detection by Lateral Flow Immunoassay.",
+    "authorString": "Atchison CJ, Moshe M, Brown JC, Whitaker M, Wong NCK, Bharath AA, McKendry RA, Darzi A, Ashby D, Donnelly CA, Riley S, Elliott P, Barclay WS, Cooke GS, Ward H.",
+    "authorAffiliations": "",
+    "journalTitle": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America",
+    "pubYear": "2023",
+    "date": "2023-02-01",
+    "isOpenAccess": "Y",
+    "keywords": "Antibodies; Lateral Flow Immunoassay; Home-testing; Covid-19; Sars-cov-2",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>We explore severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody lateral flow immunoassay (LFIA) performance under field conditions compared to laboratory-based electrochemiluminescence immunoassay (ECLIA) and live virus neutralization.<h4>Methods</h4>In July 2021, 3758 participants performed, at home, a self-administered Fortress LFIA on finger-prick blood, reported and submitted a photograph of the result, and provided a self-collected capillary blood sample for assessment of immunoglobulin G (IgG) antibodies using the Roche Elecsys\u00ae Anti-SARS-CoV-2 ECLIA. We compared the self-reported LFIA result to the quantitative ECLIA and checked the reading of the LFIA result with an automated image analysis (ALFA). In a subsample of 250 participants, we compared the results to live virus neutralization.<h4>Results</h4>Almost all participants (3593/3758, 95.6%) had been vaccinated or reported prior infection. Overall, 2777/3758 (73.9%) were positive on self-reported LFIA, 2811/3457 (81.3%) positive by LFIA when ALFA-reported, and 3622/3758 (96.4%) positive on ECLIA (using the manufacturer reference standard threshold for positivity of 0.8 U mL-1). Live virus neutralization was detected in 169 of 250 randomly selected samples (67.6%); 133/169 were positive with self-reported LFIA (sensitivity 78.7%; 95% confidence interval [CI]: 71.8, 84.6), 142/155 (91.6%; 95% CI: 86.1, 95.5) with ALFA, and 169 (100%; 95% CI: 97.8, 100.0) with ECLIA. There were 81 samples with no detectable virus neutralization; 47/81 were negative with self-reported LFIA (specificity 58.0%; 95% CI: 46.5, 68.9), 34/75 (45.3%; 95% CI: 33.8, 57.3) with ALFA, and 0/81 (0%; 95% CI: 0, 4.5) with ECLIA.<h4>Conclusions</h4>Self-administered LFIA is less sensitive than a quantitative antibody test, but the positivity in LFIA correlates better than the quantitative ECLIA with virus neutralization.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1093/cid/ciac629; doi:https://doi.org/10.1093/cid/ciac629; html:https://europepmc.org/articles/PMC9384551; pdf:https://europepmc.org/articles/PMC9384551?pdf=render"
+  },
   {
     "id": "31799783",
     "doi": "https://doi.org/10.1002/cnm.3267",
@@ -6714,23 +6731,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/4/e060413.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-060413; html:https://europepmc.org/articles/PMC9044550; pdf:https://europepmc.org/articles/PMC9044550?pdf=render"
   },
-  {
-    "id": "35913410",
-    "doi": "https://doi.org/10.1093/cid/ciac629",
-    "title": "Validity of Self-testing at Home With Rapid Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Detection by Lateral Flow Immunoassay.",
-    "authorString": "Atchison CJ, Moshe M, Brown JC, Whitaker M, Wong NCK, Bharath AA, McKendry RA, Darzi A, Ashby D, Donnelly CA, Riley S, Elliott P, Barclay WS, Cooke GS, Ward H.",
-    "authorAffiliations": "",
-    "journalTitle": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America",
-    "pubYear": "2023",
-    "date": "2023-02-01",
-    "isOpenAccess": "Y",
-    "keywords": "Antibodies; Lateral Flow Immunoassay; Home-testing; Covid-19; Sars-cov-2",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>We explore severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody lateral flow immunoassay (LFIA) performance under field conditions compared to laboratory-based electrochemiluminescence immunoassay (ECLIA) and live virus neutralization.<h4>Methods</h4>In July 2021, 3758 participants performed, at home, a self-administered Fortress LFIA on finger-prick blood, reported and submitted a photograph of the result, and provided a self-collected capillary blood sample for assessment of immunoglobulin G (IgG) antibodies using the Roche Elecsys\u00ae Anti-SARS-CoV-2 ECLIA. We compared the self-reported LFIA result to the quantitative ECLIA and checked the reading of the LFIA result with an automated image analysis (ALFA). In a subsample of 250 participants, we compared the results to live virus neutralization.<h4>Results</h4>Almost all participants (3593/3758, 95.6%) had been vaccinated or reported prior infection. Overall, 2777/3758 (73.9%) were positive on self-reported LFIA, 2811/3457 (81.3%) positive by LFIA when ALFA-reported, and 3622/3758 (96.4%) positive on ECLIA (using the manufacturer reference standard threshold for positivity of 0.8 U mL-1). Live virus neutralization was detected in 169 of 250 randomly selected samples (67.6%); 133/169 were positive with self-reported LFIA (sensitivity 78.7%; 95% confidence interval [CI]: 71.8, 84.6), 142/155 (91.6%; 95% CI: 86.1, 95.5) with ALFA, and 169 (100%; 95% CI: 97.8, 100.0) with ECLIA. There were 81 samples with no detectable virus neutralization; 47/81 were negative with self-reported LFIA (specificity 58.0%; 95% CI: 46.5, 68.9), 34/75 (45.3%; 95% CI: 33.8, 57.3) with ALFA, and 0/81 (0%; 95% CI: 0, 4.5) with ECLIA.<h4>Conclusions</h4>Self-administered LFIA is less sensitive than a quantitative antibody test, but the positivity in LFIA correlates better than the quantitative ECLIA with virus neutralization.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1093/cid/ciac629; doi:https://doi.org/10.1093/cid/ciac629; html:https://europepmc.org/articles/PMC9384551; pdf:https://europepmc.org/articles/PMC9384551?pdf=render"
-  },
   {
     "id": "35197114",
     "doi": "https://doi.org/10.1186/s41512-022-00120-2",
@@ -6765,6 +6765,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ije/article-pdf/52/1/e46/49127271/dyac189.pdf; doi:https://doi.org/10.1093/ije/dyac189; html:https://europepmc.org/articles/PMC9620716; pdf:https://europepmc.org/articles/PMC9620716?pdf=render; doi:https://doi.org/10.1093/ije/dyac189"
   },
+  {
+    "id": "35502909",
+    "doi": "https://doi.org/10.1177/01410768221095239",
+    "title": "Impact on emergency and elective hospital-based care in Scotland over the first 12 months of the pandemic: interrupted time-series analysis of national lockdowns.",
+    "authorString": "Shah SA, Mulholland RH, Wilkinson S, Katikireddi SV, Pan J, Shi T, Kerr S, Agrawal U, Rudan I, Simpson CR, Stock SJ, Macleod J, Murray JL, McCowan C, Ritchie L, Woolhouse M, Sheikh A.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of the Royal Society of Medicine",
+    "pubYear": "2022",
+    "date": "2022-05-03",
+    "isOpenAccess": "Y",
+    "keywords": "Public Health; Statistics And Research Methods; Population Trends",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objectives</h4>COVID-19 has resulted in the greatest disruption to National Health Service (NHS) care in its over 70-year history. Building on our previous work, we assessed the ongoing impact of pandemic-related disruption on provision of emergency and elective hospital-based care across Scotland over the first year of the pandemic.<h4>Design</h4>We undertook interrupted time-series analyses to evaluate the impact of ongoing pandemic-related disruption on hospital NHS care provision at national level and across demographics and clinical specialties spanning the period 29 March 2020-28 March 2021.<h4>Setting</h4>Scotland, UK.<h4>Participants</h4>Patients receiving hospital care from NHS Scotland.<h4>Main outcome measures</h4>We used the percentage change of accident and emergency attendances, and emergency and planned hospital admissions during the pandemic compared to the average admission rate for equivalent weeks in 2018-2019.<h4>Results</h4>As restrictions were gradually lifted in Scotland after the first lockdown, hospital-based admissions increased approaching pre-pandemic levels. Subsequent tightening of restrictions in September 2020 were associated with a change in slope of relative weekly admissions rate: -1.98% (-2.38, -1.58) in accident and emergency attendance, -1.36% (-1.68, -1.04) in emergency admissions and -2.31% (-2.95, -1.66) in planned admissions. A similar pattern was seen across sex, socioeconomic status and most age groups, except children (0-14 years) where accident and emergency attendance, and emergency admissions were persistently low over the study period.<h4>Conclusions</h4>We found substantial disruption to urgent and planned inpatient healthcare provision in hospitals across NHS Scotland. There is the need for urgent policy responses to address continuing unmet health needs and to ensure resilience in the context of future pandemics.",
+    "laySummary": "",
+    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/01410768221095239; doi:https://doi.org/10.1177/01410768221095239; html:https://europepmc.org/articles/PMC9723811; pdf:https://europepmc.org/articles/PMC9723811?pdf=render"
+  },
   {
     "id": "36051279",
     "doi": "https://doi.org/10.3389/fcvm.2022.894503",
@@ -6783,21 +6800,21 @@
     "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2022.894503/pdf; doi:https://doi.org/10.3389/fcvm.2022.894503; html:https://europepmc.org/articles/PMC9426684; pdf:https://europepmc.org/articles/PMC9426684?pdf=render"
   },
   {
-    "id": "35502909",
-    "doi": "https://doi.org/10.1177/01410768221095239",
-    "title": "Impact on emergency and elective hospital-based care in Scotland over the first 12 months of the pandemic: interrupted time-series analysis of national lockdowns.",
-    "authorString": "Shah SA, Mulholland RH, Wilkinson S, Katikireddi SV, Pan J, Shi T, Kerr S, Agrawal U, Rudan I, Simpson CR, Stock SJ, Macleod J, Murray JL, McCowan C, Ritchie L, Woolhouse M, Sheikh A.",
+    "id": "37198478",
+    "doi": "https://doi.org/10.1038/s41586-023-06034-3",
+    "title": "GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19.",
+    "authorString": "Pairo-Castineira E, Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, Oosthuyzen W, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Morrice K, Keating S, Maslove D, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Begg C, Walsh T, Tenesa A, Flores C, Riancho JA, Rojas-Martinez A, Lapunzina P, GenOMICC Investigators, SCOURGE Consortium, ISARICC Investigators, 23andMe COVID-19 Team, Yang J, Ponting CP, Wilson JF, Vitart V, Abedalthagafi M, Luchessi AD, Parra EJ, Cruz R, Carracedo A, Fawkes A, Murphy L, Rowan K, Pereira AC, Law A, Fairfax B, Hendry SC, Baillie JK.",
     "authorAffiliations": "",
-    "journalTitle": "Journal of the Royal Society of Medicine",
-    "pubYear": "2022",
-    "date": "2022-05-03",
+    "journalTitle": "Nature",
+    "pubYear": "2023",
+    "date": "2023-05-17",
     "isOpenAccess": "Y",
-    "keywords": "Public Health; Statistics And Research Methods; Population Trends",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Objectives</h4>COVID-19 has resulted in the greatest disruption to National Health Service (NHS) care in its over 70-year history. Building on our previous work, we assessed the ongoing impact of pandemic-related disruption on provision of emergency and elective hospital-based care across Scotland over the first year of the pandemic.<h4>Design</h4>We undertook interrupted time-series analyses to evaluate the impact of ongoing pandemic-related disruption on hospital NHS care provision at national level and across demographics and clinical specialties spanning the period 29 March 2020-28 March 2021.<h4>Setting</h4>Scotland, UK.<h4>Participants</h4>Patients receiving hospital care from NHS Scotland.<h4>Main outcome measures</h4>We used the percentage change of accident and emergency attendances, and emergency and planned hospital admissions during the pandemic compared to the average admission rate for equivalent weeks in 2018-2019.<h4>Results</h4>As restrictions were gradually lifted in Scotland after the first lockdown, hospital-based admissions increased approaching pre-pandemic levels. Subsequent tightening of restrictions in September 2020 were associated with a change in slope of relative weekly admissions rate: -1.98% (-2.38, -1.58) in accident and emergency attendance, -1.36% (-1.68, -1.04) in emergency admissions and -2.31% (-2.95, -1.66) in planned admissions. A similar pattern was seen across sex, socioeconomic status and most age groups, except children (0-14 years) where accident and emergency attendance, and emergency admissions were persistently low over the study period.<h4>Conclusions</h4>We found substantial disruption to urgent and planned inpatient healthcare provision in hospitals across NHS Scotland. There is the need for urgent policy responses to address continuing unmet health needs and to ensure resilience in the context of future pandemics.",
+    "abstract": "Critical illness in COVID-19 is an extreme and clinically homogeneous disease phenotype that we have previously shown<sup>1</sup> to be highly efficient for discovery of genetic associations<sup>2</sup>. Despite the advanced stage of illness at presentation, we have shown that host genetics in patients who are critically ill with COVID-19 can identify immunomodulatory therapies with strong beneficial effects in this group<sup>3</sup>. Here we analyse 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously. To investigate the therapeutic implications of these findings, we infer the structural consequences of protein-coding variants, and combine our GWAS results with gene expression data using a monocyte transcriptome-wide association study (TWAS) model, as well as gene and protein expression using Mendelian randomization. We identify potentially druggable targets in multiple systems, including inflammatory signalling (JAK1), monocyte-macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).",
     "laySummary": "",
-    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/01410768221095239; doi:https://doi.org/10.1177/01410768221095239; html:https://europepmc.org/articles/PMC9723811; pdf:https://europepmc.org/articles/PMC9723811?pdf=render"
+    "urls": "pdf:https://www.nature.com/articles/s41586-023-06034-3.pdf; doi:https://doi.org/10.1038/s41586-023-06034-3; html:https://europepmc.org/articles/PMC10208981; pdf:https://europepmc.org/articles/PMC10208981?pdf=render"
   },
   {
     "id": "38554132",
@@ -6884,23 +6901,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.mdpi.com/1422-0067/22/16/8527/pdf?version=1628431894; doi:https://doi.org/10.3390/ijms22168527; html:https://europepmc.org/articles/PMC8395220; pdf:https://europepmc.org/articles/PMC8395220?pdf=render"
   },
-  {
-    "id": "37198478",
-    "doi": "https://doi.org/10.1038/s41586-023-06034-3",
-    "title": "GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19.",
-    "authorString": "Pairo-Castineira E, Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, Oosthuyzen W, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Morrice K, Keating S, Maslove D, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Begg C, Walsh T, Tenesa A, Flores C, Riancho JA, Rojas-Martinez A, Lapunzina P, GenOMICC Investigators, SCOURGE Consortium, ISARICC Investigators, 23andMe COVID-19 Team, Yang J, Ponting CP, Wilson JF, Vitart V, Abedalthagafi M, Luchessi AD, Parra EJ, Cruz R, Carracedo A, Fawkes A, Murphy L, Rowan K, Pereira AC, Law A, Fairfax B, Hendry SC, Baillie JK.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature",
-    "pubYear": "2023",
-    "date": "2023-05-17",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Critical illness in COVID-19 is an extreme and clinically homogeneous disease phenotype that we have previously shown<sup>1</sup> to be highly efficient for discovery of genetic associations<sup>2</sup>. Despite the advanced stage of illness at presentation, we have shown that host genetics in patients who are critically ill with COVID-19 can identify immunomodulatory therapies with strong beneficial effects in this group<sup>3</sup>. Here we analyse 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously. To investigate the therapeutic implications of these findings, we infer the structural consequences of protein-coding variants, and combine our GWAS results with gene expression data using a monocyte transcriptome-wide association study (TWAS) model, as well as gene and protein expression using Mendelian randomization. We identify potentially druggable targets in multiple systems, including inflammatory signalling (JAK1), monocyte-macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41586-023-06034-3.pdf; doi:https://doi.org/10.1038/s41586-023-06034-3; html:https://europepmc.org/articles/PMC10208981; pdf:https://europepmc.org/articles/PMC10208981?pdf=render"
-  },
   {
     "id": "35165107",
     "doi": "https://doi.org/10.1136/bmjopen-2021-050062",
@@ -6935,23 +6935,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.ijid.2024.107155"
   },
-  {
-    "id": "38177425",
-    "doi": "https://doi.org/10.1038/s43588-023-00461-y",
-    "title": "GREENER principles for environmentally sustainable computational science.",
-    "authorString": "Lannelongue L, Aronson HG, Bateman A, Birney E, Caplan T, Juckes M, McEntyre J, Morris AD, Reilly G, Inouye M.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature computational science",
-    "pubYear": "2023",
-    "date": "2023-06-26",
-    "isOpenAccess": "N",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The carbon footprint of scientific computing is substantial, but environmentally sustainable computational science (ESCS) is a nascent field with many opportunities to thrive. To realize the immense green opportunities and continued, yet sustainable, growth of computer science, we must take a coordinated approach to our current challenges, including greater awareness and transparency, improved estimation and wider reporting of environmental impacts. Here, we present a snapshot of where ESCS stands today and introduce the GREENER set of principles, as well as guidance for best practices moving forward.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1038/s43588-023-00461-y"
-  },
   {
     "id": "35918110",
     "doi": "https://doi.org/10.1136/bmjopen-2021-057433",
@@ -6969,6 +6952,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/8/e057433.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-057433; html:https://europepmc.org/articles/PMC9351333; pdf:https://europepmc.org/articles/PMC9351333?pdf=render"
   },
+  {
+    "id": "38177425",
+    "doi": "https://doi.org/10.1038/s43588-023-00461-y",
+    "title": "GREENER principles for environmentally sustainable computational science.",
+    "authorString": "Lannelongue L, Aronson HG, Bateman A, Birney E, Caplan T, Juckes M, McEntyre J, Morris AD, Reilly G, Inouye M.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature computational science",
+    "pubYear": "2023",
+    "date": "2023-06-26",
+    "isOpenAccess": "N",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The carbon footprint of scientific computing is substantial, but environmentally sustainable computational science (ESCS) is a nascent field with many opportunities to thrive. To realize the immense green opportunities and continued, yet sustainable, growth of computer science, we must take a coordinated approach to our current challenges, including greater awareness and transparency, improved estimation and wider reporting of environmental impacts. Here, we present a snapshot of where ESCS stands today and introduce the GREENER set of principles, as well as guidance for best practices moving forward.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1038/s43588-023-00461-y"
+  },
   {
     "id": "35336739",
     "doi": "https://doi.org/10.3390/biology11030365",
@@ -7003,23 +7003,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmcmedinformdecismak.biomedcentral.com/track/pdf/10.1186/s12911-021-01693-6; doi:https://doi.org/10.1186/s12911-021-01693-6; html:https://europepmc.org/articles/PMC8653614; pdf:https://europepmc.org/articles/PMC8653614?pdf=render"
   },
-  {
-    "id": "37147628",
-    "doi": "https://doi.org/10.1186/s12911-023-02181-9",
-    "title": "Ontology-driven and weakly supervised rare disease identification from clinical notes.",
-    "authorString": "Dong H, Su\u00e1rez-Paniagua V, Zhang H, Wang M, Casey A, Davidson E, Chen J, Alex B, Whiteley W, Wu H.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC medical informatics and decision making",
-    "pubYear": "2023",
-    "date": "2023-05-05",
-    "isOpenAccess": "Y",
-    "keywords": "Phenotyping; Natural Language Processing; Rare Diseases; Ontology Matching; Clinical Notes; Weak Supervision",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Computational text phenotyping is the practice of identifying patients with certain disorders and traits from clinical notes. Rare diseases are challenging to be identified due to few cases available for machine learning and the need for data annotation from domain experts.<h4>Methods</h4>We propose a method using ontologies and weak supervision, with recent pre-trained contextual representations from Bi-directional Transformers (e.g. BERT). The ontology-driven framework includes two steps: (i) Text-to-UMLS, extracting phenotypes by contextually linking mentions to concepts in Unified Medical Language System (UMLS), with a Named Entity Recognition and Linking (NER+L) tool, SemEHR, and weak supervision with customised rules and contextual mention representation; (ii) UMLS-to-ORDO, matching UMLS concepts to rare diseases in Orphanet Rare Disease Ontology (ORDO). The weakly supervised approach is proposed to learn a phenotype confirmation model to improve Text-to-UMLS linking, without annotated data from domain experts. We evaluated the approach on three clinical datasets, MIMIC-III discharge summaries, MIMIC-III radiology reports, and NHS Tayside brain imaging reports from two institutions in the US and the UK, with annotations.<h4>Results</h4>The improvements in the precision were pronounced (by over 30% to 50% absolute score for Text-to-UMLS linking), with almost no loss of recall compared to the existing NER+L tool, SemEHR. Results on radiology reports from MIMIC-III and NHS Tayside were consistent with the discharge summaries. The overall pipeline processing clinical notes can extract rare disease cases, mostly uncaptured in structured data (manually assigned ICD codes).<h4>Conclusion</h4>The study provides empirical evidence for the task by applying a weakly supervised NLP pipeline on clinical notes. The proposed weak supervised deep learning approach requires no human annotation except for validation and testing, by leveraging ontologies, NER+L tools, and contextual representations. The study also demonstrates that Natural Language Processing (NLP) can complement traditional ICD-based approaches to better estimate rare diseases in clinical notes. We discuss the usefulness and limitations of the weak supervision approach and propose directions for future studies.",
-    "laySummary": "",
-    "urls": "pdf:https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-023-02181-9; doi:https://doi.org/10.1186/s12911-023-02181-9; html:https://europepmc.org/articles/PMC10162001; pdf:https://europepmc.org/articles/PMC10162001?pdf=render"
-  },
   {
     "id": "35572721",
     "doi": "https://doi.org/10.1016/j.eclinm.2022.101419",
@@ -7037,23 +7020,6 @@
     "laySummary": "",
     "urls": "pdf:http://www.thelancet.com/article/S2589537022001493/pdf; doi:https://doi.org/10.1016/j.eclinm.2022.101419; html:https://europepmc.org/articles/PMC9076030; pdf:https://europepmc.org/articles/PMC9076030?pdf=render"
   },
-  {
-    "id": "34007894",
-    "doi": "https://doi.org/10.23889/ijpds.v6i1.1373",
-    "title": "Visualisation and optimisation of alcohol-related hospital admissions ICD-10 codes in Welsh e-cohort data.",
-    "authorString": "Trefan L, Akbari A, Morgan JS, Farewell DM, Fone D, Lyons RA, Jones Hywel M, Moore SC.",
-    "authorAffiliations": "",
-    "journalTitle": "International journal of population data science",
-    "pubYear": "2021",
-    "date": "2021-03-24",
-    "isOpenAccess": "Y",
-    "keywords": "Alcohol; Hospital Admission; Optimisation; Icd-10 Codes; E-Cohort Data",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>The excessive consumption of alcohol is detrimental to long term health and increases the likelihood of hospital admission. However, definitions of alcohol-related hospital admission vary, giving rise to uncertainty in the effect of alcohol on alcohol-related health care utilization.<h4>Objectives</h4>To compare diagnostic codes on hospital admission and discharge and to determine the ideal combination of codes necessary for an accurate determination of alcohol-related hospital admission.<h4>Methods</h4>Routine population-linked e-cohort data were extracted from the Secure Anonymised Information Linkage (SAIL) Databank containing all alcohol-related hospital admissions (n,= 92,553) from 2006 to 2011 in Wales, United Kingdom. The distributions of the diagnostic codes recorded at admission and discharge were compared. By calculating a misclassification rate (sensitivity-like measure) the appropriate number of coding fields to examine for alcohol-codes was established.<h4>Results</h4>There was agreement between admission and discharge codes. When more than ten coding fields were used the misclassification rate was less than 1%.<h4>Conclusion</h4>With the data at present and alcohol-related codes used, codes recorded at admission and discharge can be used equivalently to identify alcohol-related admissions. The appropriate number of coding fields to examine was established: fewer than ten is likely to lead to under-reporting of alcohol-related admissions. The methods developed here can be applied to other medical conditions that can be described using a certain set of diagnostic codes, each of which can be a known sole cause of the condition and recorded in multiple positions in e-cohort data.",
-    "laySummary": "",
-    "urls": "pdf:https://ijpds.org/article/download/1373/3264; doi:https://doi.org/10.23889/ijpds.v6i1.1373; html:https://europepmc.org/articles/PMC8103565; pdf:https://europepmc.org/articles/PMC8103565?pdf=render"
-  },
   {
     "id": "34440368",
     "doi": "https://doi.org/10.3390/genes12081194",
@@ -7072,21 +7038,21 @@
     "urls": "pdf:https://www.mdpi.com/2073-4425/12/8/1194/pdf?version=1627984735; doi:https://doi.org/10.3390/genes12081194; html:https://europepmc.org/articles/PMC8391428; pdf:https://europepmc.org/articles/PMC8391428?pdf=render"
   },
   {
-    "id": "34108714",
-    "doi": "https://doi.org/10.1038/s41591-021-01408-4",
-    "title": "First-dose ChAdOx1 and BNT162b2 COVID-19 vaccines and thrombocytopenic, thromboembolic and hemorrhagic events in Scotland.",
-    "authorString": "Simpson CR, Shi T, Vasileiou E, Katikireddi SV, Kerr S, Moore E, McCowan C, Agrawal U, Shah SA, Ritchie LD, Murray J, Pan J, Bradley DT, Stock SJ, Wood R, Chuter A, Beggs J, Stagg HR, Joy M, Tsang RSM, de Lusignan S, Hobbs R, Lyons RA, Torabi F, Bedston S, O'Leary M, Akbari A, McMenamin J, Robertson C, Sheikh A.",
+    "id": "34007894",
+    "doi": "https://doi.org/10.23889/ijpds.v6i1.1373",
+    "title": "Visualisation and optimisation of alcohol-related hospital admissions ICD-10 codes in Welsh e-cohort data.",
+    "authorString": "Trefan L, Akbari A, Morgan JS, Farewell DM, Fone D, Lyons RA, Jones Hywel M, Moore SC.",
     "authorAffiliations": "",
-    "journalTitle": "Nature medicine",
+    "journalTitle": "International journal of population data science",
     "pubYear": "2021",
-    "date": "2021-06-09",
+    "date": "2021-03-24",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Alcohol; Hospital Admission; Optimisation; Icd-10 Codes; E-Cohort Data",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Reports of ChAdOx1 vaccine-associated thrombocytopenia and vascular adverse events have led to some countries restricting its use. Using a national prospective cohort, we estimated associations between exposure to first-dose ChAdOx1 or BNT162b2 vaccination and hematological and vascular adverse events using a nested incident-matched case-control study and a confirmatory self-controlled case series (SCCS) analysis. An association was found between ChAdOx1 vaccination and idiopathic thrombocytopenic purpura (ITP) (0-27 d after vaccination; adjusted rate ratio (aRR) = 5.77, 95% confidence interval (CI), 2.41-13.83), with an estimated incidence of 1.13 (0.62-1.63) cases per 100,000 doses. An SCCS analysis confirmed that this was unlikely due to bias (RR\u2009=\u20091.98 (1.29-3.02)). There was also an increased risk for arterial thromboembolic events (aRR = 1.22, 1.12-1.34) 0-27 d after vaccination, with an SCCS RR of 0.97 (0.93-1.02). For hemorrhagic events 0-27 d after vaccination, the aRR was 1.48 (1.12-1.96), with an SCCS RR of 0.95 (0.82-1.11). A first dose of ChAdOx1 was found to be associated with small increased risks of ITP, with suggestive evidence of an increased risk of arterial thromboembolic and hemorrhagic events. The attenuation of effect found in the SCCS analysis means that there is the potential for overestimation of the reported results, which might indicate the presence of some residual confounding or confounding by indication. Public health authorities should inform their jurisdictions of these relatively small increased risks associated with ChAdOx1. No positive associations were seen between BNT162b2 and thrombocytopenic, thromboembolic and hemorrhagic events.",
+    "abstract": "<h4>Introduction</h4>The excessive consumption of alcohol is detrimental to long term health and increases the likelihood of hospital admission. However, definitions of alcohol-related hospital admission vary, giving rise to uncertainty in the effect of alcohol on alcohol-related health care utilization.<h4>Objectives</h4>To compare diagnostic codes on hospital admission and discharge and to determine the ideal combination of codes necessary for an accurate determination of alcohol-related hospital admission.<h4>Methods</h4>Routine population-linked e-cohort data were extracted from the Secure Anonymised Information Linkage (SAIL) Databank containing all alcohol-related hospital admissions (n,= 92,553) from 2006 to 2011 in Wales, United Kingdom. The distributions of the diagnostic codes recorded at admission and discharge were compared. By calculating a misclassification rate (sensitivity-like measure) the appropriate number of coding fields to examine for alcohol-codes was established.<h4>Results</h4>There was agreement between admission and discharge codes. When more than ten coding fields were used the misclassification rate was less than 1%.<h4>Conclusion</h4>With the data at present and alcohol-related codes used, codes recorded at admission and discharge can be used equivalently to identify alcohol-related admissions. The appropriate number of coding fields to examine was established: fewer than ten is likely to lead to under-reporting of alcohol-related admissions. The methods developed here can be applied to other medical conditions that can be described using a certain set of diagnostic codes, each of which can be a known sole cause of the condition and recorded in multiple positions in e-cohort data.",
     "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41591-021-01408-4.pdf; doi:https://doi.org/10.1038/s41591-021-01408-4; html:https://europepmc.org/articles/PMC8282499; pdf:https://europepmc.org/articles/PMC8282499?pdf=render"
+    "urls": "pdf:https://ijpds.org/article/download/1373/3264; doi:https://doi.org/10.23889/ijpds.v6i1.1373; html:https://europepmc.org/articles/PMC8103565; pdf:https://europepmc.org/articles/PMC8103565?pdf=render"
   },
   {
     "id": "32990744",
@@ -7105,6 +7071,40 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/gigascience/article-pdf/9/10/giaa095/33802377/giaa095.pdf; doi:https://doi.org/10.1093/gigascience/giaa095; html:https://europepmc.org/articles/PMC7523405; pdf:https://europepmc.org/articles/PMC7523405?pdf=render"
   },
+  {
+    "id": "37147628",
+    "doi": "https://doi.org/10.1186/s12911-023-02181-9",
+    "title": "Ontology-driven and weakly supervised rare disease identification from clinical notes.",
+    "authorString": "Dong H, Su\u00e1rez-Paniagua V, Zhang H, Wang M, Casey A, Davidson E, Chen J, Alex B, Whiteley W, Wu H.",
+    "authorAffiliations": "",
+    "journalTitle": "BMC medical informatics and decision making",
+    "pubYear": "2023",
+    "date": "2023-05-05",
+    "isOpenAccess": "Y",
+    "keywords": "Phenotyping; Natural Language Processing; Rare Diseases; Ontology Matching; Clinical Notes; Weak Supervision",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Computational text phenotyping is the practice of identifying patients with certain disorders and traits from clinical notes. Rare diseases are challenging to be identified due to few cases available for machine learning and the need for data annotation from domain experts.<h4>Methods</h4>We propose a method using ontologies and weak supervision, with recent pre-trained contextual representations from Bi-directional Transformers (e.g. BERT). The ontology-driven framework includes two steps: (i) Text-to-UMLS, extracting phenotypes by contextually linking mentions to concepts in Unified Medical Language System (UMLS), with a Named Entity Recognition and Linking (NER+L) tool, SemEHR, and weak supervision with customised rules and contextual mention representation; (ii) UMLS-to-ORDO, matching UMLS concepts to rare diseases in Orphanet Rare Disease Ontology (ORDO). The weakly supervised approach is proposed to learn a phenotype confirmation model to improve Text-to-UMLS linking, without annotated data from domain experts. We evaluated the approach on three clinical datasets, MIMIC-III discharge summaries, MIMIC-III radiology reports, and NHS Tayside brain imaging reports from two institutions in the US and the UK, with annotations.<h4>Results</h4>The improvements in the precision were pronounced (by over 30% to 50% absolute score for Text-to-UMLS linking), with almost no loss of recall compared to the existing NER+L tool, SemEHR. Results on radiology reports from MIMIC-III and NHS Tayside were consistent with the discharge summaries. The overall pipeline processing clinical notes can extract rare disease cases, mostly uncaptured in structured data (manually assigned ICD codes).<h4>Conclusion</h4>The study provides empirical evidence for the task by applying a weakly supervised NLP pipeline on clinical notes. The proposed weak supervised deep learning approach requires no human annotation except for validation and testing, by leveraging ontologies, NER+L tools, and contextual representations. The study also demonstrates that Natural Language Processing (NLP) can complement traditional ICD-based approaches to better estimate rare diseases in clinical notes. We discuss the usefulness and limitations of the weak supervision approach and propose directions for future studies.",
+    "laySummary": "",
+    "urls": "pdf:https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-023-02181-9; doi:https://doi.org/10.1186/s12911-023-02181-9; html:https://europepmc.org/articles/PMC10162001; pdf:https://europepmc.org/articles/PMC10162001?pdf=render"
+  },
+  {
+    "id": "34108714",
+    "doi": "https://doi.org/10.1038/s41591-021-01408-4",
+    "title": "First-dose ChAdOx1 and BNT162b2 COVID-19 vaccines and thrombocytopenic, thromboembolic and hemorrhagic events in Scotland.",
+    "authorString": "Simpson CR, Shi T, Vasileiou E, Katikireddi SV, Kerr S, Moore E, McCowan C, Agrawal U, Shah SA, Ritchie LD, Murray J, Pan J, Bradley DT, Stock SJ, Wood R, Chuter A, Beggs J, Stagg HR, Joy M, Tsang RSM, de Lusignan S, Hobbs R, Lyons RA, Torabi F, Bedston S, O'Leary M, Akbari A, McMenamin J, Robertson C, Sheikh A.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature medicine",
+    "pubYear": "2021",
+    "date": "2021-06-09",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Reports of ChAdOx1 vaccine-associated thrombocytopenia and vascular adverse events have led to some countries restricting its use. Using a national prospective cohort, we estimated associations between exposure to first-dose ChAdOx1 or BNT162b2 vaccination and hematological and vascular adverse events using a nested incident-matched case-control study and a confirmatory self-controlled case series (SCCS) analysis. An association was found between ChAdOx1 vaccination and idiopathic thrombocytopenic purpura (ITP) (0-27 d after vaccination; adjusted rate ratio (aRR) = 5.77, 95% confidence interval (CI), 2.41-13.83), with an estimated incidence of 1.13 (0.62-1.63) cases per 100,000 doses. An SCCS analysis confirmed that this was unlikely due to bias (RR\u2009=\u20091.98 (1.29-3.02)). There was also an increased risk for arterial thromboembolic events (aRR = 1.22, 1.12-1.34) 0-27 d after vaccination, with an SCCS RR of 0.97 (0.93-1.02). For hemorrhagic events 0-27 d after vaccination, the aRR was 1.48 (1.12-1.96), with an SCCS RR of 0.95 (0.82-1.11). A first dose of ChAdOx1 was found to be associated with small increased risks of ITP, with suggestive evidence of an increased risk of arterial thromboembolic and hemorrhagic events. The attenuation of effect found in the SCCS analysis means that there is the potential for overestimation of the reported results, which might indicate the presence of some residual confounding or confounding by indication. Public health authorities should inform their jurisdictions of these relatively small increased risks associated with ChAdOx1. No positive associations were seen between BNT162b2 and thrombocytopenic, thromboembolic and hemorrhagic events.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41591-021-01408-4.pdf; doi:https://doi.org/10.1038/s41591-021-01408-4; html:https://europepmc.org/articles/PMC8282499; pdf:https://europepmc.org/articles/PMC8282499?pdf=render"
+  },
   {
     "id": "37949372",
     "doi": "https://doi.org/10.1016/j.jhin.2023.10.021",
@@ -7343,23 +7343,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1161/JAHA.123.029552; html:https://europepmc.org/articles/PMC10757541; pdf:https://europepmc.org/articles/PMC10757541?pdf=render"
   },
-  {
-    "id": "37346822",
-    "doi": "https://doi.org/10.12688/wellcomeopenres.18735.2",
-    "title": "First dose COVID-19 vaccine coverage amongst adolescents and children in England: an analysis of 3.21 million patients' primary care records in situ using OpenSAFELY.",
-    "authorString": "Hopcroft LE, Curtis HJ, Brown AD, Hulme WJ, Andrews CD, Morton CE, Inglesby P, Morley J, Mehrkar A, Bacon SC, Eggo RM, Mahalingasivam V, Parker EPK, Tomlinson LA, Bates C, Cockburn J, Parry J, Hester F, Harper S, Goldacre B, Walker AJ, MacKenna B.",
-    "authorAffiliations": "",
-    "journalTitle": "Wellcome open research",
-    "pubYear": "2023",
-    "date": "2023-06-09",
-    "isOpenAccess": "Y",
-    "keywords": "Vaccine; Primary Health Care; Public Health; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<b>Background:</b> The coronavirus disease 2019 (COVID-19) vaccination programme in England was extended to include all adolescents and children by April 2022. The aim of this paper is to describe trends and variation in vaccine coverage in different clinical and demographic groups amongst adolescents and children in England by August 2022. <b>Methods:</b> With the approval of NHS England, a cohort study was conducted of 3.21 million children and adolescents' records in general practice in England,\u00a0 <i>in situ</i>\u00a0and within the infrastructure of the electronic health record software vendor TPP using OpenSAFELY. Vaccine coverage across various demographic (sex, deprivation index and ethnicity) and clinical (risk status) populations is described. <b>Results:</b> Coverage is higher amongst adolescents than it is amongst children, with 53.5% adolescents and 10.8% children having received their first dose of the COVID-19 vaccine. Within those groups, coverage varies by ethnicity, deprivation index and risk status; there is no evidence of variation by sex. <b>Conclusion:</b> First dose COVID-19 vaccine coverage is shown to vary amongst various demographic and clinical groups of children and adolescents.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.12688/wellcomeopenres.18735.2; html:https://europepmc.org/articles/PMC10280033; pdf:https://europepmc.org/articles/PMC10280033?pdf=render"
-  },
   {
     "id": "32565483",
     "doi": "https://doi.org/10.1136/bmjopen-2020-039097",
@@ -7378,21 +7361,21 @@
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/10/6/e039097.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-039097; html:https://europepmc.org/articles/PMC7311023; pdf:https://europepmc.org/articles/PMC7311023?pdf=render"
   },
   {
-    "id": "38106617",
-    "doi": "https://doi.org/10.1016/j.patter.2023.100892",
-    "title": "Mortality prediction with adaptive feature importance recalibration for peritoneal dialysis patients.",
-    "authorString": "Ma L, Zhang C, Gao J, Jiao X, Yu Z, Zhu Y, Wang T, Ma X, Wang Y, Tang W, Zhao X, Ruan W, Wang T.",
+    "id": "37346822",
+    "doi": "https://doi.org/10.12688/wellcomeopenres.18735.2",
+    "title": "First dose COVID-19 vaccine coverage amongst adolescents and children in England: an analysis of 3.21 million patients' primary care records in situ using OpenSAFELY.",
+    "authorString": "Hopcroft LE, Curtis HJ, Brown AD, Hulme WJ, Andrews CD, Morton CE, Inglesby P, Morley J, Mehrkar A, Bacon SC, Eggo RM, Mahalingasivam V, Parker EPK, Tomlinson LA, Bates C, Cockburn J, Parry J, Hester F, Harper S, Goldacre B, Walker AJ, MacKenna B.",
     "authorAffiliations": "",
-    "journalTitle": "Patterns (New York, N.Y.)",
+    "journalTitle": "Wellcome open research",
     "pubYear": "2023",
-    "date": "2023-12-08",
+    "date": "2023-06-09",
     "isOpenAccess": "Y",
-    "keywords": "Peritoneal dialysis; PD; End-stage Renal Disease; Electronic Medical Record; Emr; Esrd; Mortality Prediction; Deep Learning; Model Interpretability",
+    "keywords": "Vaccine; Primary Health Care; Public Health; Covid-19",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "The study aims to develop AICare, an interpretable mortality prediction model, using electronic medical records (EMR) from follow-up visits for end-stage renal disease (ESRD) patients. AICare includes a multichannel feature extraction module and an adaptive feature importance recalibration module. It integrates dynamic records and static features to perform personalized health context representation learning. The dataset encompasses 13,091 visits and demographic data of 656 peritoneal dialysis (PD) patients spanning 12 years. An additional public dataset of 4,789 visits from 1,363 hemodialysis (HD) patients is also considered. AICare outperforms traditional deep learning models in mortality prediction while retaining interpretability. It uncovers mortality-feature relationships and variations in feature importance and provides reference values. An AI-doctor interaction system is developed for visualizing patients' health trajectories and risk indicators.",
+    "abstract": "<b>Background:</b> The coronavirus disease 2019 (COVID-19) vaccination programme in England was extended to include all adolescents and children by April 2022. The aim of this paper is to describe trends and variation in vaccine coverage in different clinical and demographic groups amongst adolescents and children in England by August 2022. <b>Methods:</b> With the approval of NHS England, a cohort study was conducted of 3.21 million children and adolescents' records in general practice in England,\u00a0 <i>in situ</i>\u00a0and within the infrastructure of the electronic health record software vendor TPP using OpenSAFELY. Vaccine coverage across various demographic (sex, deprivation index and ethnicity) and clinical (risk status) populations is described. <b>Results:</b> Coverage is higher amongst adolescents than it is amongst children, with 53.5% adolescents and 10.8% children having received their first dose of the COVID-19 vaccine. Within those groups, coverage varies by ethnicity, deprivation index and risk status; there is no evidence of variation by sex. <b>Conclusion:</b> First dose COVID-19 vaccine coverage is shown to vary amongst various demographic and clinical groups of children and adolescents.",
     "laySummary": "",
-    "urls": "pdf:http://www.cell.com/article/S2666389923002945/pdf; doi:https://doi.org/10.1016/j.patter.2023.100892; html:https://europepmc.org/articles/PMC10724364; pdf:https://europepmc.org/articles/PMC10724364?pdf=render"
+    "urls": "doi:https://doi.org/10.12688/wellcomeopenres.18735.2; html:https://europepmc.org/articles/PMC10280033; pdf:https://europepmc.org/articles/PMC10280033?pdf=render"
   },
   {
     "id": "35050151",
@@ -7411,6 +7394,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.mdpi.com/2218-1989/12/1/29/pdf?version=1642410547; doi:https://doi.org/10.3390/metabo12010029; html:https://europepmc.org/articles/PMC8780653; pdf:https://europepmc.org/articles/PMC8780653?pdf=render"
   },
+  {
+    "id": "38106617",
+    "doi": "https://doi.org/10.1016/j.patter.2023.100892",
+    "title": "Mortality prediction with adaptive feature importance recalibration for peritoneal dialysis patients.",
+    "authorString": "Ma L, Zhang C, Gao J, Jiao X, Yu Z, Zhu Y, Wang T, Ma X, Wang Y, Tang W, Zhao X, Ruan W, Wang T.",
+    "authorAffiliations": "",
+    "journalTitle": "Patterns (New York, N.Y.)",
+    "pubYear": "2023",
+    "date": "2023-12-08",
+    "isOpenAccess": "Y",
+    "keywords": "Peritoneal dialysis; PD; End-stage Renal Disease; Electronic Medical Record; Emr; Esrd; Mortality Prediction; Deep Learning; Model Interpretability",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The study aims to develop AICare, an interpretable mortality prediction model, using electronic medical records (EMR) from follow-up visits for end-stage renal disease (ESRD) patients. AICare includes a multichannel feature extraction module and an adaptive feature importance recalibration module. It integrates dynamic records and static features to perform personalized health context representation learning. The dataset encompasses 13,091 visits and demographic data of 656 peritoneal dialysis (PD) patients spanning 12 years. An additional public dataset of 4,789 visits from 1,363 hemodialysis (HD) patients is also considered. AICare outperforms traditional deep learning models in mortality prediction while retaining interpretability. It uncovers mortality-feature relationships and variations in feature importance and provides reference values. An AI-doctor interaction system is developed for visualizing patients' health trajectories and risk indicators.",
+    "laySummary": "",
+    "urls": "pdf:http://www.cell.com/article/S2666389923002945/pdf; doi:https://doi.org/10.1016/j.patter.2023.100892; html:https://europepmc.org/articles/PMC10724364; pdf:https://europepmc.org/articles/PMC10724364?pdf=render"
+  },
   {
     "id": "35910710",
     "doi": "https://doi.org/10.1093/rap/rkac056",
@@ -7462,23 +7462,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ije/article-pdf/49/5/1637/34947124/dyaa144.pdf; doi:https://doi.org/10.1093/ije/dyaa144; html:https://europepmc.org/articles/PMC7746409; pdf:https://europepmc.org/articles/PMC7746409?pdf=render; doi:https://doi.org/10.1093/ije/dyaa144"
   },
-  {
-    "id": "38444664",
-    "doi": "https://doi.org/10.1183/23120541.00010-2024",
-    "title": "Development and evaluation of a tool to optimise inhaler selection prior to hospital discharge following an exacerbation of COPD.",
-    "authorString": "Price E, Ahmad S, Althobiani MA, Ayoob T, Burgoyne T, De Soyza A, Dobson M, Echevarria C, Martin G, Mendes RG, Preston AM, Rahman NM, Sapey E, Usmani OS, Hurst JR.",
-    "authorAffiliations": "",
-    "journalTitle": "ERJ open research",
-    "pubYear": "2024",
-    "date": "2024-03-04",
-    "isOpenAccess": "N",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>Rates of mortality and re-admission after a hospitalised exacerbation of COPD are high and resistant to change. COPD guidelines do not give practical advice about the optimal selection of inhaled drugs and device in this situation. We hypothesised that a failure to optimise inhaled drug and drug delivery prior to discharge from hospital after an exacerbation would be associated with a modifiable increased risk of re-admission and death. We designed a study to 1) develop a practical inhaler selection tool to use at the point of hospital discharge and 2) implement this tool to understand the potential impact on modifying inhaler prescriptions, clinical outcomes, acceptability to clinicians and patients, and the feasibility of delivering a definitive trial to demonstrate potential benefit.<h4>Methods</h4>We iteratively developed an inhaler selection tool for use prior to discharge following a hospitalised exacerbation of COPD using surveys with multiprofessional clinicians and a focus group of people living with COPD. We surveyed clinicians to understand their views on the minimum clinically important difference (MCID) for death and re-admission following a hospitalised exacerbation of COPD. We conducted a mixed-methods implementation feasibility study using the tool at discharge, and collated 30- and 90-day follow-up data including death and re-admissions. Additionally, we observed the tool being used and interviewed clinicians and patients about use of the tool in this setting.<h4>Results</h4>We completed the design of an inhaler selection tool through two rounds of consultations with 94 multiprofessional clinicians, and a focus group of four expert patients. Regarding MCIDs, there was majority consensus for the following reductions from baseline being the MCID: 30-day readmissions 5-10%, 90-day readmissions 10-20%, 30-day mortality 5-10% and 90-day mortality 5-10%. 118 patients were assessed for eligibility and 26 had the tool applied. A change in inhaled medication was recommended in nine (35%) out of 26. Re-admission or death at 30\u2005days was seen in 33% of the switch group and 35% of the no-switch group. Re-admission or death at 90\u2005days was seen in 56% of the switch group and 41% of the no-switch group. Satisfaction with inhalers was generally high, and switching was associated with a small increase in the Feeling of Satisfaction with Inhaler questionnaire of 3 out of 50\u2005points. Delivery of a definitive study would be challenging.<h4>Conclusion</h4>We completed a mixed-methods study to design and implement a tool to aid optimisation of inhaled pharmacotherapy prior to discharge following a hospitalised exacerbation of COPD. This was not associated with fewer re-admissions, but was well received and one-third of people were eligible for a change in inhalers.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1183/23120541.00010-2024"
-  },
   {
     "id": "34977922",
     "doi": "https://doi.org/10.1093/ije/dyab243",
@@ -7496,6 +7479,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ije/article-pdf/51/5/e245/46495259/dyab243.pdf; doi:https://doi.org/10.1093/ije/dyab243; html:https://europepmc.org/articles/PMC9557859; pdf:https://europepmc.org/articles/PMC9557859?pdf=render"
   },
+  {
+    "id": "38444664",
+    "doi": "https://doi.org/10.1183/23120541.00010-2024",
+    "title": "Development and evaluation of a tool to optimise inhaler selection prior to hospital discharge following an exacerbation of COPD.",
+    "authorString": "Price E, Ahmad S, Althobiani MA, Ayoob T, Burgoyne T, De Soyza A, Dobson M, Echevarria C, Martin G, Mendes RG, Preston AM, Rahman NM, Sapey E, Usmani OS, Hurst JR.",
+    "authorAffiliations": "",
+    "journalTitle": "ERJ open research",
+    "pubYear": "2024",
+    "date": "2024-03-04",
+    "isOpenAccess": "N",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>Rates of mortality and re-admission after a hospitalised exacerbation of COPD are high and resistant to change. COPD guidelines do not give practical advice about the optimal selection of inhaled drugs and device in this situation. We hypothesised that a failure to optimise inhaled drug and drug delivery prior to discharge from hospital after an exacerbation would be associated with a modifiable increased risk of re-admission and death. We designed a study to 1) develop a practical inhaler selection tool to use at the point of hospital discharge and 2) implement this tool to understand the potential impact on modifying inhaler prescriptions, clinical outcomes, acceptability to clinicians and patients, and the feasibility of delivering a definitive trial to demonstrate potential benefit.<h4>Methods</h4>We iteratively developed an inhaler selection tool for use prior to discharge following a hospitalised exacerbation of COPD using surveys with multiprofessional clinicians and a focus group of people living with COPD. We surveyed clinicians to understand their views on the minimum clinically important difference (MCID) for death and re-admission following a hospitalised exacerbation of COPD. We conducted a mixed-methods implementation feasibility study using the tool at discharge, and collated 30- and 90-day follow-up data including death and re-admissions. Additionally, we observed the tool being used and interviewed clinicians and patients about use of the tool in this setting.<h4>Results</h4>We completed the design of an inhaler selection tool through two rounds of consultations with 94 multiprofessional clinicians, and a focus group of four expert patients. Regarding MCIDs, there was majority consensus for the following reductions from baseline being the MCID: 30-day readmissions 5-10%, 90-day readmissions 10-20%, 30-day mortality 5-10% and 90-day mortality 5-10%. 118 patients were assessed for eligibility and 26 had the tool applied. A change in inhaled medication was recommended in nine (35%) out of 26. Re-admission or death at 30\u2005days was seen in 33% of the switch group and 35% of the no-switch group. Re-admission or death at 90\u2005days was seen in 56% of the switch group and 41% of the no-switch group. Satisfaction with inhalers was generally high, and switching was associated with a small increase in the Feeling of Satisfaction with Inhaler questionnaire of 3 out of 50\u2005points. Delivery of a definitive study would be challenging.<h4>Conclusion</h4>We completed a mixed-methods study to design and implement a tool to aid optimisation of inhaled pharmacotherapy prior to discharge following a hospitalised exacerbation of COPD. This was not associated with fewer re-admissions, but was well received and one-third of people were eligible for a change in inhalers.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1183/23120541.00010-2024"
+  },
   {
     "id": "36526319",
     "doi": "https://doi.org/10.1136/bmjopen-2022-064910",
@@ -7547,23 +7547,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ije/advance-article-pdf/doi/10.1093/ije/dyac185/47708280/dyac185.pdf; doi:https://doi.org/10.1093/ije/dyac185; html:https://europepmc.org/articles/PMC10244047; pdf:https://europepmc.org/articles/PMC10244047?pdf=render"
   },
-  {
-    "id": "39009776",
-    "doi": "https://doi.org/10.1038/s41591-024-03094-4",
-    "title": "Consumer wearable devices for evaluation of heart rate control using digoxin versus beta-blockers: the RATE-AF randomized trial.",
-    "authorString": "Gill SK, Barsky A, Guan X, Bunting KV, Karwath A, Tica O, Stanbury M, Haynes S, Folarin A, Dobson R, Kurps J, Asselbergs FW, Grobbee DE, Camm AJ, Eijkemans MJC, Gkoutos GV, Kotecha D, BigData@Heart Consortium, cardAIc group, RATE-AF trial team.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature medicine",
-    "pubYear": "2024",
-    "date": "2024-07-15",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Consumer-grade wearable technology has the potential to support clinical research and patient management. Here, we report results from the RATE-AF trial wearables study, which was designed to compare heart rate in older, multimorbid patients with permanent atrial fibrillation and heart failure who were randomized to treatment with either digoxin or beta-blockers. Heart rate (n\u2009=\u2009143,379,796) and physical activity (n\u2009=\u200923,704,307) intervals were obtained from 53 participants (mean age 75.6\u2009years (s.d. 8.4), 40% women) using a wrist-worn wearable linked to a smartphone for 20\u2009weeks. Heart rates in participants treated with digoxin versus beta-blockers were not significantly different (regression coefficient 1.22 (95% confidence interval (CI) -2.82 to 5.27; P\u2009=\u20090.55); adjusted 0.66 (95% CI -3.45 to 4.77; P\u2009=\u20090.75)). No difference in heart rate was observed between the two groups of patients after accounting for physical activity (P\u2009=\u20090.74) or patients with high activity levels (\u226530,000\u2009steps per week; P\u2009=\u20090.97). Using a convolutional neural network designed to account for missing data, we found that wearable device data could predict New York Heart Association functional class 5\u2009months after baseline assessment similarly to standard clinical measures of electrocardiographic heart rate and 6-minute walk test (F1 score 0.56 (95% CI 0.41 to 0.70) versus 0.55 (95% CI 0.41 to 0.68); P\u2009=\u20090.88 for comparison). The results of this study indicate that digoxin and beta-blockers have equivalent effects on heart rate in atrial fibrillation at rest and on exertion, and suggest that dynamic monitoring of individuals with arrhythmia using wearable technology could be an alternative to in-person assessment. ClinicalTrials.gov identifier: NCT02391337 .",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1038/s41591-024-03094-4; html:https://europepmc.org/articles/PMC11271403; pdf:https://europepmc.org/articles/PMC11271403?pdf=render"
-  },
   {
     "id": "32635913",
     "doi": "https://doi.org/10.1186/s12911-020-01169-z",
@@ -7581,6 +7564,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmcmedinformdecismak.biomedcentral.com/track/pdf/10.1186/s12911-020-01169-z; doi:https://doi.org/10.1186/s12911-020-01169-z; html:https://europepmc.org/articles/PMC7339522; pdf:https://europepmc.org/articles/PMC7339522?pdf=render"
   },
+  {
+    "id": "33517931",
+    "doi": "https://doi.org/10.1192/j.eurpsy.2021.6",
+    "title": "The association between C-reactive protein, mood disorder, and cognitive function in UK Biobank.",
+    "authorString": "Milton DC, Ward J, Ward E, Lyall DM, Strawbridge RJ, Smith DJ, Cullen B.",
+    "authorAffiliations": "",
+    "journalTitle": "European psychiatry : the journal of the Association of European Psychiatrists",
+    "pubYear": "2021",
+    "date": "2021-02-01",
+    "isOpenAccess": "Y",
+    "keywords": "Inflammation; Cognitive function; C-reactive Protein; Mood Disorder",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Systemic inflammation has been linked with mood disorder and cognitive impairment. The extent of this relationship remains uncertain, with the effects of serum inflammatory biomarkers compared to genetic predisposition toward inflammation yet to be clearly established.<h4>Methods</h4>We investigated the magnitude of associations between C-reactive protein (CRP) measures, lifetime history of bipolar disorder or major depression, and cognitive function (reaction time and visuospatial memory) in 84,268 UK Biobank participants. CRP was measured in serum and a polygenic risk score for CRP was calculated, based on a published genome-wide association study. Multiple regression models adjusted for sociodemographic and clinical confounders.<h4>Results</h4>Increased serum CRP was significantly associated with mood disorder history (Kruskal-Wallis H\u00a0=\u00a0196.06, p\u00a0<\u00a00.001, \u03b72\u00a0=\u00a00.002) but increased polygenic risk for CRP was not (F\u00a0=\u00a00.668, p\u00a0=\u00a00.648, \u03b72\u00a0<\u00a00.001). Compared to the lowest quintile, the highest serum CRP quintile was significantly associated with both negative and positive differences in cognitive performance (fully adjusted models: reaction time B\u00a0=\u00a0-0.030, 95% CI\u00a0=\u00a0-0.052, -0.008; visuospatial memory B\u00a0=\u00a00.066, 95% CI\u00a0=\u00a00.042, 0.089). More severe mood disorder categories were significantly associated with worse cognitive performance and this was not moderated by serum or genetic CRP level.<h4>Conclusions</h4>In this large cohort study, we found that measured inflammation was associated with mood disorder history, but genetic predisposition to inflammation was not. The association between mood disorder and worse cognitive performance was very small and did not vary by CRP level. The inconsistent relationship between CRP measures and cognitive performance warrants further study.",
+    "laySummary": "",
+    "urls": "pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/DAB4F3EAD33B9437269C92D7A0A5DDC4/S0924933821000067a.pdf/div-class-title-the-association-between-c-reactive-protein-mood-disorder-and-cognitive-function-in-uk-biobank-div.pdf; doi:https://doi.org/10.1192/j.eurpsy.2021.6; html:https://europepmc.org/articles/PMC8057439; pdf:https://europepmc.org/articles/PMC8057439?pdf=render"
+  },
   {
     "id": "33745917",
     "doi": "https://doi.org/10.1016/j.jinf.2021.03.011",
@@ -7599,21 +7599,21 @@
     "urls": "pdf:http://www.journalofinfection.com/article/S0163445321001286/pdf; doi:https://doi.org/10.1016/j.jinf.2021.03.011; html:https://europepmc.org/articles/PMC7970419; pdf:https://europepmc.org/articles/PMC7970419?pdf=render"
   },
   {
-    "id": "33517931",
-    "doi": "https://doi.org/10.1192/j.eurpsy.2021.6",
-    "title": "The association between C-reactive protein, mood disorder, and cognitive function in UK Biobank.",
-    "authorString": "Milton DC, Ward J, Ward E, Lyall DM, Strawbridge RJ, Smith DJ, Cullen B.",
+    "id": "39009776",
+    "doi": "https://doi.org/10.1038/s41591-024-03094-4",
+    "title": "Consumer wearable devices for evaluation of heart rate control using digoxin versus beta-blockers: the RATE-AF randomized trial.",
+    "authorString": "Gill SK, Barsky A, Guan X, Bunting KV, Karwath A, Tica O, Stanbury M, Haynes S, Folarin A, Dobson R, Kurps J, Asselbergs FW, Grobbee DE, Camm AJ, Eijkemans MJC, Gkoutos GV, Kotecha D, BigData@Heart Consortium, cardAIc group, RATE-AF trial team.",
     "authorAffiliations": "",
-    "journalTitle": "European psychiatry : the journal of the Association of European Psychiatrists",
-    "pubYear": "2021",
-    "date": "2021-02-01",
+    "journalTitle": "Nature medicine",
+    "pubYear": "2024",
+    "date": "2024-07-15",
     "isOpenAccess": "Y",
-    "keywords": "Inflammation; Cognitive function; C-reactive Protein; Mood Disorder",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Systemic inflammation has been linked with mood disorder and cognitive impairment. The extent of this relationship remains uncertain, with the effects of serum inflammatory biomarkers compared to genetic predisposition toward inflammation yet to be clearly established.<h4>Methods</h4>We investigated the magnitude of associations between C-reactive protein (CRP) measures, lifetime history of bipolar disorder or major depression, and cognitive function (reaction time and visuospatial memory) in 84,268 UK Biobank participants. CRP was measured in serum and a polygenic risk score for CRP was calculated, based on a published genome-wide association study. Multiple regression models adjusted for sociodemographic and clinical confounders.<h4>Results</h4>Increased serum CRP was significantly associated with mood disorder history (Kruskal-Wallis H\u00a0=\u00a0196.06, p\u00a0<\u00a00.001, \u03b72\u00a0=\u00a00.002) but increased polygenic risk for CRP was not (F\u00a0=\u00a00.668, p\u00a0=\u00a00.648, \u03b72\u00a0<\u00a00.001). Compared to the lowest quintile, the highest serum CRP quintile was significantly associated with both negative and positive differences in cognitive performance (fully adjusted models: reaction time B\u00a0=\u00a0-0.030, 95% CI\u00a0=\u00a0-0.052, -0.008; visuospatial memory B\u00a0=\u00a00.066, 95% CI\u00a0=\u00a00.042, 0.089). More severe mood disorder categories were significantly associated with worse cognitive performance and this was not moderated by serum or genetic CRP level.<h4>Conclusions</h4>In this large cohort study, we found that measured inflammation was associated with mood disorder history, but genetic predisposition to inflammation was not. The association between mood disorder and worse cognitive performance was very small and did not vary by CRP level. The inconsistent relationship between CRP measures and cognitive performance warrants further study.",
+    "abstract": "Consumer-grade wearable technology has the potential to support clinical research and patient management. Here, we report results from the RATE-AF trial wearables study, which was designed to compare heart rate in older, multimorbid patients with permanent atrial fibrillation and heart failure who were randomized to treatment with either digoxin or beta-blockers. Heart rate (n\u2009=\u2009143,379,796) and physical activity (n\u2009=\u200923,704,307) intervals were obtained from 53 participants (mean age 75.6\u2009years (s.d. 8.4), 40% women) using a wrist-worn wearable linked to a smartphone for 20\u2009weeks. Heart rates in participants treated with digoxin versus beta-blockers were not significantly different (regression coefficient 1.22 (95% confidence interval (CI) -2.82 to 5.27; P\u2009=\u20090.55); adjusted 0.66 (95% CI -3.45 to 4.77; P\u2009=\u20090.75)). No difference in heart rate was observed between the two groups of patients after accounting for physical activity (P\u2009=\u20090.74) or patients with high activity levels (\u226530,000\u2009steps per week; P\u2009=\u20090.97). Using a convolutional neural network designed to account for missing data, we found that wearable device data could predict New York Heart Association functional class 5\u2009months after baseline assessment similarly to standard clinical measures of electrocardiographic heart rate and 6-minute walk test (F1 score 0.56 (95% CI 0.41 to 0.70) versus 0.55 (95% CI 0.41 to 0.68); P\u2009=\u20090.88 for comparison). The results of this study indicate that digoxin and beta-blockers have equivalent effects on heart rate in atrial fibrillation at rest and on exertion, and suggest that dynamic monitoring of individuals with arrhythmia using wearable technology could be an alternative to in-person assessment. ClinicalTrials.gov identifier: NCT02391337 .",
     "laySummary": "",
-    "urls": "pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/DAB4F3EAD33B9437269C92D7A0A5DDC4/S0924933821000067a.pdf/div-class-title-the-association-between-c-reactive-protein-mood-disorder-and-cognitive-function-in-uk-biobank-div.pdf; doi:https://doi.org/10.1192/j.eurpsy.2021.6; html:https://europepmc.org/articles/PMC8057439; pdf:https://europepmc.org/articles/PMC8057439?pdf=render"
+    "urls": "doi:https://doi.org/10.1038/s41591-024-03094-4; html:https://europepmc.org/articles/PMC11271403; pdf:https://europepmc.org/articles/PMC11271403?pdf=render"
   },
   {
     "id": "35448463",
@@ -7701,21 +7701,21 @@
     "urls": "pdf:https://www.nature.com/articles/s41467-022-29521-z.pdf; doi:https://doi.org/10.1038/s41467-022-29521-z; html:https://europepmc.org/articles/PMC9005552; pdf:https://europepmc.org/articles/PMC9005552?pdf=render"
   },
   {
-    "id": "38626948",
-    "doi": "https://doi.org/10.1136/bmj-2023-078378",
-    "title": "TRIPOD+AI statement: updated guidance for reporting clinical prediction models that use regression or machine learning methods.",
-    "authorString": "Collins GS, Moons KGM, Dhiman P, Riley RD, Beam AL, Van Calster B, Ghassemi M, Liu X, Reitsma JB, van Smeden M, Boulesteix AL, Camaradou JC, Celi LA, Denaxas S, Denniston AK, Glocker B, Golub RM, Harvey H, Heinze G, Hoffman MM, Kengne AP, Lam E, Lee N, Loder EW, Maier-Hein L, Mateen BA, McCradden MD, Oakden-Rayner L, Ordish J, Parnell R, Rose S, Singh K, Wynants L, Logullo P.",
+    "id": "37358897",
+    "doi": "https://doi.org/10.2196/45849",
+    "title": "Development of a Corpus Annotated With Mentions of Pain in Mental Health Records: Natural Language Processing Approach.",
+    "authorString": "Chaturvedi J, Chance N, Mirza L, Vernugopan V, Velupillai S, Stewart R, Roberts A.",
     "authorAffiliations": "",
-    "journalTitle": "BMJ (Clinical research ed.)",
-    "pubYear": "2024",
-    "date": "2024-04-16",
+    "journalTitle": "JMIR formative research",
+    "pubYear": "2023",
+    "date": "2023-06-26",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Pain; Mental health; Annotation; Information Extraction; Natural Language Processing",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "",
+    "abstract": "<h4>Background</h4>Pain is a widespread issue, with 20% of adults (1 in 5) experiencing it globally. A strong association has been demonstrated between pain and mental health conditions, and this association is known to exacerbate disability and impairment. Pain is also known to be strongly related to emotions, which can lead to damaging consequences. As pain is a common reason for people to access health care facilities, electronic health records (EHRs) are a potential source of information on this pain. Mental health EHRs could be particularly beneficial since they can show the overlap of pain with mental health. Most mental health EHRs contain the majority of their information within the free-text sections of the records. However, it is challenging to extract information from free text. Natural language processing (NLP) methods are therefore required to extract this information from the text.<h4>Objective</h4>This research describes the development of a corpus of manually labeled mentions of pain and pain-related entities from the documents of a mental health EHR database, for use in the development and evaluation of future NLP methods.<h4>Methods</h4>The EHR database used, Clinical Record Interactive Search, consists of anonymized patient records from The South London and Maudsley National Health Service Foundation Trust in the United Kingdom. The corpus was developed through a process of manual annotation where pain mentions were marked as relevant (ie, referring to physical pain afflicting the patient), negated (ie, indicating absence of pain), or not relevant (ie, referring to pain affecting someone other than the patient, or metaphorical and hypothetical mentions). Relevant mentions were also annotated with additional attributes such as anatomical location affected by pain, pain character, and pain management measures, if mentioned.<h4>Results</h4>A total of 5644 annotations were collected from 1985 documents (723 patients). Over 70% (n=4028) of the mentions found within the documents were annotated as relevant, and about half of these mentions also included the anatomical location affected by the pain. The most common pain character was chronic pain, and the most commonly mentioned anatomical location was the chest. Most annotations (n=1857, 33%) were from patients who had a primary diagnosis of mood disorders (International Classification of Diseases-10th edition, chapter F30-39).<h4>Conclusions</h4>This research has helped better understand how pain is mentioned within the context of mental health EHRs and provided insight into the kind of information that is typically mentioned around pain in such a data source. In future work, the extracted information will be used to develop and evaluate a machine learning-based NLP application to automatically extract relevant pain information from EHR databases.",
     "laySummary": "",
-    "urls": "pdf:https://www.bmj.com/content/bmj/385/bmj-2023-078378.full.pdf; doi:https://doi.org/10.1136/bmj-2023-078378; html:https://europepmc.org/articles/PMC11019967"
+    "urls": "pdf:https://formative.jmir.org/2023/1/e45849/PDF; doi:https://doi.org/10.2196/45849; html:https://europepmc.org/articles/PMC10337440; pdf:https://europepmc.org/articles/PMC10337440?pdf=render"
   },
   {
     "id": "38283541",
@@ -7734,23 +7734,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.ssmph.2023.101592; html:https://europepmc.org/articles/PMC10821139; pdf:https://europepmc.org/articles/PMC10821139?pdf=render"
   },
-  {
-    "id": "37358897",
-    "doi": "https://doi.org/10.2196/45849",
-    "title": "Development of a Corpus Annotated With Mentions of Pain in Mental Health Records: Natural Language Processing Approach.",
-    "authorString": "Chaturvedi J, Chance N, Mirza L, Vernugopan V, Velupillai S, Stewart R, Roberts A.",
-    "authorAffiliations": "",
-    "journalTitle": "JMIR formative research",
-    "pubYear": "2023",
-    "date": "2023-06-26",
-    "isOpenAccess": "Y",
-    "keywords": "Pain; Mental health; Annotation; Information Extraction; Natural Language Processing",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Pain is a widespread issue, with 20% of adults (1 in 5) experiencing it globally. A strong association has been demonstrated between pain and mental health conditions, and this association is known to exacerbate disability and impairment. Pain is also known to be strongly related to emotions, which can lead to damaging consequences. As pain is a common reason for people to access health care facilities, electronic health records (EHRs) are a potential source of information on this pain. Mental health EHRs could be particularly beneficial since they can show the overlap of pain with mental health. Most mental health EHRs contain the majority of their information within the free-text sections of the records. However, it is challenging to extract information from free text. Natural language processing (NLP) methods are therefore required to extract this information from the text.<h4>Objective</h4>This research describes the development of a corpus of manually labeled mentions of pain and pain-related entities from the documents of a mental health EHR database, for use in the development and evaluation of future NLP methods.<h4>Methods</h4>The EHR database used, Clinical Record Interactive Search, consists of anonymized patient records from The South London and Maudsley National Health Service Foundation Trust in the United Kingdom. The corpus was developed through a process of manual annotation where pain mentions were marked as relevant (ie, referring to physical pain afflicting the patient), negated (ie, indicating absence of pain), or not relevant (ie, referring to pain affecting someone other than the patient, or metaphorical and hypothetical mentions). Relevant mentions were also annotated with additional attributes such as anatomical location affected by pain, pain character, and pain management measures, if mentioned.<h4>Results</h4>A total of 5644 annotations were collected from 1985 documents (723 patients). Over 70% (n=4028) of the mentions found within the documents were annotated as relevant, and about half of these mentions also included the anatomical location affected by the pain. The most common pain character was chronic pain, and the most commonly mentioned anatomical location was the chest. Most annotations (n=1857, 33%) were from patients who had a primary diagnosis of mood disorders (International Classification of Diseases-10th edition, chapter F30-39).<h4>Conclusions</h4>This research has helped better understand how pain is mentioned within the context of mental health EHRs and provided insight into the kind of information that is typically mentioned around pain in such a data source. In future work, the extracted information will be used to develop and evaluate a machine learning-based NLP application to automatically extract relevant pain information from EHR databases.",
-    "laySummary": "",
-    "urls": "pdf:https://formative.jmir.org/2023/1/e45849/PDF; doi:https://doi.org/10.2196/45849; html:https://europepmc.org/articles/PMC10337440; pdf:https://europepmc.org/articles/PMC10337440?pdf=render"
-  },
   {
     "id": "33799834",
     "doi": "https://doi.org/10.3390/cancers13061239",
@@ -7768,6 +7751,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.mdpi.com/2072-6694/13/6/1239/pdf?version=1615817230; doi:https://doi.org/10.3390/cancers13061239; html:https://europepmc.org/articles/PMC7998932; pdf:https://europepmc.org/articles/PMC7998932?pdf=render"
   },
+  {
+    "id": "38626948",
+    "doi": "https://doi.org/10.1136/bmj-2023-078378",
+    "title": "TRIPOD+AI statement: updated guidance for reporting clinical prediction models that use regression or machine learning methods.",
+    "authorString": "Collins GS, Moons KGM, Dhiman P, Riley RD, Beam AL, Van Calster B, Ghassemi M, Liu X, Reitsma JB, van Smeden M, Boulesteix AL, Camaradou JC, Celi LA, Denaxas S, Denniston AK, Glocker B, Golub RM, Harvey H, Heinze G, Hoffman MM, Kengne AP, Lam E, Lee N, Loder EW, Maier-Hein L, Mateen BA, McCradden MD, Oakden-Rayner L, Ordish J, Parnell R, Rose S, Singh K, Wynants L, Logullo P.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ (Clinical research ed.)",
+    "pubYear": "2024",
+    "date": "2024-04-16",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "",
+    "laySummary": "",
+    "urls": "pdf:https://www.bmj.com/content/bmj/385/bmj-2023-078378.full.pdf; doi:https://doi.org/10.1136/bmj-2023-078378; html:https://europepmc.org/articles/PMC11019967"
+  },
   {
     "id": "37181393",
     "doi": "https://doi.org/10.1016/j.jacasi.2022.12.006",
@@ -7785,6 +7785,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.jacasi.2022.12.006; doi:https://doi.org/10.1016/j.jacasi.2022.12.006; html:https://europepmc.org/articles/PMC10167505; pdf:https://europepmc.org/articles/PMC10167505?pdf=render"
   },
+  {
+    "id": "38192590",
+    "doi": "https://doi.org/10.1016/j.eclinm.2023.102321",
+    "title": "Clinical and health inequality risk factors for non-COVID-related sepsis during the global COVID-19 pandemic: a national case-control and cohort study.",
+    "authorString": "Zhong X, Ashiru-Oredope D, Pate A, Martin GP, Sharma A, Dark P, Felton T, Lake C, MacKenna B, Mehrkar A, Bacon SCJ, Massey J, Inglesby P, Goldacre B, OpenSAFELY Collaborative, Hand K, Bladon S, Cunningham N, Gilham E, Brown CS, Mirfenderesky M, Palin V, van Staa TP.",
+    "authorAffiliations": "",
+    "journalTitle": "EClinicalMedicine",
+    "pubYear": "2023",
+    "date": "2023-11-23",
+    "isOpenAccess": "Y",
+    "keywords": "Sepsis; Morbidity; Primary Care; Deprivation; Health Inequality; Covid-19 Pandemic",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Sepsis, characterised by significant morbidity and mortality, is intricately linked to socioeconomic disparities and pre-admission clinical histories. This study aspires to elucidate the association between non-COVID-19 related sepsis and health inequality risk factors amidst the pandemic in England, with a secondary focus on their association with 30-day sepsis mortality.<h4>Methods</h4>With the approval of NHS England, we harnessed the OpenSAFELY platform to execute a cohort study and a 1:6 matched case-control study. A sepsis diagnosis was identified from the incident hospital admissions record using ICD-10 codes. This encompassed 248,767 cases with non-COVID-19 sepsis from a cohort of 22.0 million individuals spanning January 1, 2019, to June 31, 2022. Socioeconomic deprivation was gauged using the Index of Multiple Deprivation score, reflecting indicators like income, employment, and education. Hospitalisation-related sepsis diagnoses were categorised as community-acquired or hospital-acquired. Cases were matched to controls who had no recorded diagnosis of sepsis, based on age (stepwise), sex, and calendar month. The eligibility criteria for controls were established primarily on the absence of a recorded sepsis diagnosis. Associations between potential predictors and odds of developing non-COVID-19 sepsis underwent assessment through conditional logistic regression models, with multivariable regression determining odds ratios (ORs) for 30-day mortality.<h4>Findings</h4>The study included 224,361 (10.2%) cases with non-COVID-19 sepsis and 1,346,166 matched controls. The most socioeconomic deprived quintile was associated with higher odds of developing non-COVID-19 sepsis than the least deprived quintile (crude OR 1.80 [95% CI 1.77-1.83]). Other risk factors (after adjusting comorbidities) such as learning disability (adjusted OR 3.53 [3.35-3.73]), chronic liver disease (adjusted OR 3.08 [2.97-3.19]), chronic kidney disease (stage 4: adjusted OR 2.62 [2.55-2.70], stage 5: adjusted OR 6.23 [5.81-6.69]), cancer, neurological disease, immunosuppressive conditions were also associated with developing non-COVID-19 sepsis. The incidence rate of non-COVID-19 sepsis decreased during the COVID-19 pandemic and rebounded to pre-pandemic levels (April 2021) after national lockdowns had been lifted. The 30-day mortality risk in cases with non-COVID-19 sepsis was higher for the most deprived quintile across all periods.<h4>Interpretation</h4>Socioeconomic deprivation, comorbidity and learning disabilities were associated with an increased odds of developing non-COVID-19 related sepsis and 30-day mortality in England. This study highlights the need to improve the prevention of sepsis, including more precise targeting of antimicrobials to higher-risk patients.<h4>Funding</h4>The UK Health Security Agency, Health Data Research UK, and National Institute for Health Research.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.eclinm.2023.102321; html:https://europepmc.org/articles/PMC10772239; pdf:https://europepmc.org/articles/PMC10772239?pdf=render"
+  },
   {
     "id": "37624366",
     "doi": "https://doi.org/10.1039/d2an01350a",
@@ -7820,21 +7837,21 @@
     "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0248195&type=printable; doi:https://doi.org/10.1371/journal.pone.0248195; html:https://europepmc.org/articles/PMC8007012; pdf:https://europepmc.org/articles/PMC8007012?pdf=render"
   },
   {
-    "id": "38192590",
-    "doi": "https://doi.org/10.1016/j.eclinm.2023.102321",
-    "title": "Clinical and health inequality risk factors for non-COVID-related sepsis during the global COVID-19 pandemic: a national case-control and cohort study.",
-    "authorString": "Zhong X, Ashiru-Oredope D, Pate A, Martin GP, Sharma A, Dark P, Felton T, Lake C, MacKenna B, Mehrkar A, Bacon SCJ, Massey J, Inglesby P, Goldacre B, OpenSAFELY Collaborative, Hand K, Bladon S, Cunningham N, Gilham E, Brown CS, Mirfenderesky M, Palin V, van Staa TP.",
+    "id": "38509709",
+    "doi": "https://doi.org/10.1016/j.xhgg.2024.100284",
+    "title": "A power-based sliding window approach to evaluate the clinical impact of rare genetic variants in the nucleotide sequence or the spatial position of the folded protein.",
+    "authorString": "Cirulli ET, Schiabor Barrett KM, Bolze A, Judge DP, Pawloski PA, Grzymski JJ, Lee W, Washington NL.",
     "authorAffiliations": "",
-    "journalTitle": "EClinicalMedicine",
-    "pubYear": "2023",
-    "date": "2023-11-23",
+    "journalTitle": "HGG advances",
+    "pubYear": "2024",
+    "date": "2024-03-19",
     "isOpenAccess": "Y",
-    "keywords": "Sepsis; Morbidity; Primary Care; Deprivation; Health Inequality; Covid-19 Pandemic",
+    "keywords": "Genetic analysis; Sliding window; Rare Variants",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Sepsis, characterised by significant morbidity and mortality, is intricately linked to socioeconomic disparities and pre-admission clinical histories. This study aspires to elucidate the association between non-COVID-19 related sepsis and health inequality risk factors amidst the pandemic in England, with a secondary focus on their association with 30-day sepsis mortality.<h4>Methods</h4>With the approval of NHS England, we harnessed the OpenSAFELY platform to execute a cohort study and a 1:6 matched case-control study. A sepsis diagnosis was identified from the incident hospital admissions record using ICD-10 codes. This encompassed 248,767 cases with non-COVID-19 sepsis from a cohort of 22.0 million individuals spanning January 1, 2019, to June 31, 2022. Socioeconomic deprivation was gauged using the Index of Multiple Deprivation score, reflecting indicators like income, employment, and education. Hospitalisation-related sepsis diagnoses were categorised as community-acquired or hospital-acquired. Cases were matched to controls who had no recorded diagnosis of sepsis, based on age (stepwise), sex, and calendar month. The eligibility criteria for controls were established primarily on the absence of a recorded sepsis diagnosis. Associations between potential predictors and odds of developing non-COVID-19 sepsis underwent assessment through conditional logistic regression models, with multivariable regression determining odds ratios (ORs) for 30-day mortality.<h4>Findings</h4>The study included 224,361 (10.2%) cases with non-COVID-19 sepsis and 1,346,166 matched controls. The most socioeconomic deprived quintile was associated with higher odds of developing non-COVID-19 sepsis than the least deprived quintile (crude OR 1.80 [95% CI 1.77-1.83]). Other risk factors (after adjusting comorbidities) such as learning disability (adjusted OR 3.53 [3.35-3.73]), chronic liver disease (adjusted OR 3.08 [2.97-3.19]), chronic kidney disease (stage 4: adjusted OR 2.62 [2.55-2.70], stage 5: adjusted OR 6.23 [5.81-6.69]), cancer, neurological disease, immunosuppressive conditions were also associated with developing non-COVID-19 sepsis. The incidence rate of non-COVID-19 sepsis decreased during the COVID-19 pandemic and rebounded to pre-pandemic levels (April 2021) after national lockdowns had been lifted. The 30-day mortality risk in cases with non-COVID-19 sepsis was higher for the most deprived quintile across all periods.<h4>Interpretation</h4>Socioeconomic deprivation, comorbidity and learning disabilities were associated with an increased odds of developing non-COVID-19 related sepsis and 30-day mortality in England. This study highlights the need to improve the prevention of sepsis, including more precise targeting of antimicrobials to higher-risk patients.<h4>Funding</h4>The UK Health Security Agency, Health Data Research UK, and National Institute for Health Research.",
+    "abstract": "Systematic determination of novel variant pathogenicity remains a major challenge, even when there is an established association between a gene and phenotype. Here we present Power Window (PW), a sliding window technique that identifies the impactful regions of a gene using population-scale clinico-genomic datasets. By sizing analysis windows on the number of variant carriers, rather than the number of variants or nucleotides, statistical power is held constant, enabling the localization of clinical phenotypes and removal of unassociated gene regions. The windows can be built by sliding across either the nucleotide sequence of the gene (through 1D space) or the positions of the amino acids in the folded protein (through 3D space). Using a training set of 350k exomes from the UK Biobank (UKB), we developed PW models for well-established gene-disease associations and tested their accuracy in two independent cohorts (117k UKB exomes and 65k exomes sequenced at Helix in the Healthy Nevada Project, myGenetics, or In Our DNA SC studies). The significant models retained a median of 49% of the qualifying variant carriers in each gene (range 2%-98%), with quantitative traits showing a median effect size improvement of 66% compared with aggregating variants across the entire gene, and binary traits' odds ratios improving by a median of 2.2-fold. PW showcases that electronic health record-based statistical analyses can accurately distinguish between novel coding variants in established genes that will have high phenotypic penetrance and those that will not, unlocking new potential for human genomics research, drug development, variant interpretation, and precision medicine.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.eclinm.2023.102321; html:https://europepmc.org/articles/PMC10772239; pdf:https://europepmc.org/articles/PMC10772239?pdf=render"
+    "urls": "pdf:https://www.cell.com/article/S266624772400023X/pdf; doi:https://doi.org/10.1016/j.xhgg.2024.100284; html:https://europepmc.org/articles/PMC11004801; pdf:https://europepmc.org/articles/PMC11004801?pdf=render"
   },
   {
     "id": "38355631",
@@ -7853,40 +7870,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1186/s12916-024-03284-4; html:https://europepmc.org/articles/PMC10865714; pdf:https://europepmc.org/articles/PMC10865714?pdf=render"
   },
-  {
-    "id": "36217535",
-    "doi": "https://doi.org/10.1038/s43856-022-00185-6",
-    "title": "Multi-omic phenotyping reveals host-microbe responses to bariatric surgery, glycaemic control and obesity.",
-    "authorString": "Penney NC, Yeung DKT, Garcia-Perez I, Posma JM, Kopytek A, Garratt B, Ashrafian H, Frost G, Marchesi JR, Purkayastha S, Hoyles L, Darzi A, Holmes E.",
-    "authorAffiliations": "",
-    "journalTitle": "Communications medicine",
-    "pubYear": "2022",
-    "date": "2022-10-07",
-    "isOpenAccess": "Y",
-    "keywords": "Obesity; Type 2 diabetes; Dynamical Systems; Microbiome",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Resolution of type 2 diabetes (T2D) is common following bariatric surgery, particularly Roux-en-Y gastric bypass. However, the underlying mechanisms have not been fully elucidated.<h4>Methods</h4>To address this we compare the integrated serum, urine and faecal metabolic profiles of participants with obesity\u00a0\u00b1 T2D (<i>n</i>\u2009=\u200980, T2D\u2009=\u200942) with participants who underwent Roux-en-Y gastric bypass or sleeve gastrectomy (pre and 3-months post-surgery; <i>n</i>\u2009=\u200927), taking diet into account. We co-model these data with shotgun metagenomic profiles of the gut microbiota to provide a comprehensive atlas of host-gut microbe responses to bariatric surgery, weight-loss and glycaemic control at the systems level.<h4>Results</h4>Here we show that bariatric surgery reverses several disrupted pathways characteristic of T2D. The differential metabolite set representative of bariatric surgery overlaps with both diabetes (19.3% commonality) and body mass index (18.6% commonality). However, the percentage overlap between diabetes and body mass index is minimal (4.0% commonality), consistent with weight-independent mechanisms of T2D resolution. The gut microbiota is more strongly correlated to body mass index than T2D, although we identify some pathways such as amino acid metabolism that correlate with changes to the gut microbiota and which influence glycaemic control.<h4>Conclusion</h4>We identify multi-omic signatures associated with responses to surgery, body mass index, and glycaemic control. Improved understanding of gut microbiota - host co-metabolism may lead to novel therapies for weight-loss or diabetes. However, further experiments are required to provide mechanistic insight into the role of the gut microbiota in host metabolism and establish proof of causality.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s43856-022-00185-6.pdf; doi:https://doi.org/10.1038/s43856-022-00185-6; html:https://europepmc.org/articles/PMC9546886; pdf:https://europepmc.org/articles/PMC9546886?pdf=render"
-  },
-  {
-    "id": "38509709",
-    "doi": "https://doi.org/10.1016/j.xhgg.2024.100284",
-    "title": "A power-based sliding window approach to evaluate the clinical impact of rare genetic variants in the nucleotide sequence or the spatial position of the folded protein.",
-    "authorString": "Cirulli ET, Schiabor Barrett KM, Bolze A, Judge DP, Pawloski PA, Grzymski JJ, Lee W, Washington NL.",
-    "authorAffiliations": "",
-    "journalTitle": "HGG advances",
-    "pubYear": "2024",
-    "date": "2024-03-19",
-    "isOpenAccess": "Y",
-    "keywords": "Genetic analysis; Sliding window; Rare Variants",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Systematic determination of novel variant pathogenicity remains a major challenge, even when there is an established association between a gene and phenotype. Here we present Power Window (PW), a sliding window technique that identifies the impactful regions of a gene using population-scale clinico-genomic datasets. By sizing analysis windows on the number of variant carriers, rather than the number of variants or nucleotides, statistical power is held constant, enabling the localization of clinical phenotypes and removal of unassociated gene regions. The windows can be built by sliding across either the nucleotide sequence of the gene (through 1D space) or the positions of the amino acids in the folded protein (through 3D space). Using a training set of 350k exomes from the UK Biobank (UKB), we developed PW models for well-established gene-disease associations and tested their accuracy in two independent cohorts (117k UKB exomes and 65k exomes sequenced at Helix in the Healthy Nevada Project, myGenetics, or In Our DNA SC studies). The significant models retained a median of 49% of the qualifying variant carriers in each gene (range 2%-98%), with quantitative traits showing a median effect size improvement of 66% compared with aggregating variants across the entire gene, and binary traits' odds ratios improving by a median of 2.2-fold. PW showcases that electronic health record-based statistical analyses can accurately distinguish between novel coding variants in established genes that will have high phenotypic penetrance and those that will not, unlocking new potential for human genomics research, drug development, variant interpretation, and precision medicine.",
-    "laySummary": "",
-    "urls": "pdf:https://www.cell.com/article/S266624772400023X/pdf; doi:https://doi.org/10.1016/j.xhgg.2024.100284; html:https://europepmc.org/articles/PMC11004801; pdf:https://europepmc.org/articles/PMC11004801?pdf=render"
-  },
   {
     "id": "39171430",
     "doi": "https://doi.org/10.2196/43173",
@@ -7904,6 +7887,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.2196/43173; html:https://europepmc.org/articles/PMC11358661"
   },
+  {
+    "id": "36217535",
+    "doi": "https://doi.org/10.1038/s43856-022-00185-6",
+    "title": "Multi-omic phenotyping reveals host-microbe responses to bariatric surgery, glycaemic control and obesity.",
+    "authorString": "Penney NC, Yeung DKT, Garcia-Perez I, Posma JM, Kopytek A, Garratt B, Ashrafian H, Frost G, Marchesi JR, Purkayastha S, Hoyles L, Darzi A, Holmes E.",
+    "authorAffiliations": "",
+    "journalTitle": "Communications medicine",
+    "pubYear": "2022",
+    "date": "2022-10-07",
+    "isOpenAccess": "Y",
+    "keywords": "Obesity; Type 2 diabetes; Dynamical Systems; Microbiome",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Resolution of type 2 diabetes (T2D) is common following bariatric surgery, particularly Roux-en-Y gastric bypass. However, the underlying mechanisms have not been fully elucidated.<h4>Methods</h4>To address this we compare the integrated serum, urine and faecal metabolic profiles of participants with obesity\u00a0\u00b1 T2D (<i>n</i>\u2009=\u200980, T2D\u2009=\u200942) with participants who underwent Roux-en-Y gastric bypass or sleeve gastrectomy (pre and 3-months post-surgery; <i>n</i>\u2009=\u200927), taking diet into account. We co-model these data with shotgun metagenomic profiles of the gut microbiota to provide a comprehensive atlas of host-gut microbe responses to bariatric surgery, weight-loss and glycaemic control at the systems level.<h4>Results</h4>Here we show that bariatric surgery reverses several disrupted pathways characteristic of T2D. The differential metabolite set representative of bariatric surgery overlaps with both diabetes (19.3% commonality) and body mass index (18.6% commonality). However, the percentage overlap between diabetes and body mass index is minimal (4.0% commonality), consistent with weight-independent mechanisms of T2D resolution. The gut microbiota is more strongly correlated to body mass index than T2D, although we identify some pathways such as amino acid metabolism that correlate with changes to the gut microbiota and which influence glycaemic control.<h4>Conclusion</h4>We identify multi-omic signatures associated with responses to surgery, body mass index, and glycaemic control. Improved understanding of gut microbiota - host co-metabolism may lead to novel therapies for weight-loss or diabetes. However, further experiments are required to provide mechanistic insight into the role of the gut microbiota in host metabolism and establish proof of causality.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s43856-022-00185-6.pdf; doi:https://doi.org/10.1038/s43856-022-00185-6; html:https://europepmc.org/articles/PMC9546886; pdf:https://europepmc.org/articles/PMC9546886?pdf=render"
+  },
   {
     "id": "37171130",
     "doi": "https://doi.org/10.1093/gigascience/giad030",
@@ -7921,23 +7921,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/gigascience/article-pdf/doi/10.1093/gigascience/giad030/50383140/giad030.pdf; doi:https://doi.org/10.1093/gigascience/giad030; html:https://europepmc.org/articles/PMC10176503; pdf:https://europepmc.org/articles/PMC10176503?pdf=render"
   },
-  {
-    "id": "33087383",
-    "doi": "https://doi.org/10.1136/bmjopen-2020-043010",
-    "title": "Understanding and responding to COVID-19 in Wales: protocol for a privacy-protecting data platform for enhanced epidemiology and evaluation of interventions.",
-    "authorString": "Lyons J, Akbari A, Torabi F, Davies GI, North L, Griffiths R, Bailey R, Hollinghurst J, Fry R, Turner SL, Thompson D, Rafferty J, Mizen A, Orton C, Thompson S, Au-Yeung L, Cross L, Gravenor MB, Brophy S, Lucini B, John A, Szakmany T, Davies J, Davies C, Thomas DR, Williams C, Emmerson C, Cottrell S, Connor TR, Taylor C, Pugh RJ, Diggle P, John G, Scourfield S, Hunt J, Cunningham AM, Helliwell K, Lyons R.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2020",
-    "date": "2020-10-21",
-    "isOpenAccess": "Y",
-    "keywords": "epidemiology; Public Health; Health Informatics; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>The emergence of the novel respiratory SARS-CoV-2 and subsequent COVID-19 pandemic have required rapid assimilation of population-level data to understand and control the spread of infection in the general and vulnerable populations. Rapid analyses are needed to inform policy development and target interventions to at-risk groups to prevent serious health outcomes. We aim to provide an accessible research platform to determine demographic, socioeconomic and clinical risk factors for infection, morbidity and mortality of COVID-19, to measure the impact of COVID-19 on healthcare utilisation and long-term health, and to enable the evaluation of natural experiments of policy interventions.<h4>Methods and analysis</h4>Two privacy-protecting population-level cohorts have been created and derived from multisourced demographic and healthcare data. The C20 cohort consists of 3.2\u2009million people in Wales on the 1 January 2020 with follow-up until 31 May 2020. The complete cohort dataset will be updated monthly with some individual datasets available daily. The C16 cohort consists of 3\u2009million people in Wales on the 1 January 2016 with follow-up to 31 December 2019. C16 is designed as a counterfactual cohort to provide contextual comparative population data on disease, health service utilisation and mortality. Study outcomes will: (a) characterise the epidemiology of COVID-19, (b) assess socioeconomic and demographic influences on infection and outcomes, (c) measure the impact of COVID-19 on short -term and longer-term population outcomes and (d) undertake studies on the transmission and spatial spread of infection.<h4>Ethics and dissemination</h4>The Secure Anonymised Information Linkage-independent Information Governance Review Panel has approved this study. The study findings will be presented to policy groups, public meetings, national and international conferences, and published in peer-reviewed journals.",
-    "laySummary": "",
-    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/10/10/e043010.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-043010; html:https://europepmc.org/articles/PMC7580065; pdf:https://europepmc.org/articles/PMC7580065?pdf=render"
-  },
   {
     "id": "32341912",
     "doi": "https://doi.org/10.1177/2235042x19893470",
@@ -7955,6 +7938,23 @@
     "laySummary": "",
     "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/2235042X19893470; doi:https://doi.org/10.1177/2235042X19893470; html:https://europepmc.org/articles/PMC7171988; pdf:https://europepmc.org/articles/PMC7171988?pdf=render"
   },
+  {
+    "id": "33087383",
+    "doi": "https://doi.org/10.1136/bmjopen-2020-043010",
+    "title": "Understanding and responding to COVID-19 in Wales: protocol for a privacy-protecting data platform for enhanced epidemiology and evaluation of interventions.",
+    "authorString": "Lyons J, Akbari A, Torabi F, Davies GI, North L, Griffiths R, Bailey R, Hollinghurst J, Fry R, Turner SL, Thompson D, Rafferty J, Mizen A, Orton C, Thompson S, Au-Yeung L, Cross L, Gravenor MB, Brophy S, Lucini B, John A, Szakmany T, Davies J, Davies C, Thomas DR, Williams C, Emmerson C, Cottrell S, Connor TR, Taylor C, Pugh RJ, Diggle P, John G, Scourfield S, Hunt J, Cunningham AM, Helliwell K, Lyons R.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2020",
+    "date": "2020-10-21",
+    "isOpenAccess": "Y",
+    "keywords": "epidemiology; Public Health; Health Informatics; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>The emergence of the novel respiratory SARS-CoV-2 and subsequent COVID-19 pandemic have required rapid assimilation of population-level data to understand and control the spread of infection in the general and vulnerable populations. Rapid analyses are needed to inform policy development and target interventions to at-risk groups to prevent serious health outcomes. We aim to provide an accessible research platform to determine demographic, socioeconomic and clinical risk factors for infection, morbidity and mortality of COVID-19, to measure the impact of COVID-19 on healthcare utilisation and long-term health, and to enable the evaluation of natural experiments of policy interventions.<h4>Methods and analysis</h4>Two privacy-protecting population-level cohorts have been created and derived from multisourced demographic and healthcare data. The C20 cohort consists of 3.2\u2009million people in Wales on the 1 January 2020 with follow-up until 31 May 2020. The complete cohort dataset will be updated monthly with some individual datasets available daily. The C16 cohort consists of 3\u2009million people in Wales on the 1 January 2016 with follow-up to 31 December 2019. C16 is designed as a counterfactual cohort to provide contextual comparative population data on disease, health service utilisation and mortality. Study outcomes will: (a) characterise the epidemiology of COVID-19, (b) assess socioeconomic and demographic influences on infection and outcomes, (c) measure the impact of COVID-19 on short -term and longer-term population outcomes and (d) undertake studies on the transmission and spatial spread of infection.<h4>Ethics and dissemination</h4>The Secure Anonymised Information Linkage-independent Information Governance Review Panel has approved this study. The study findings will be presented to policy groups, public meetings, national and international conferences, and published in peer-reviewed journals.",
+    "laySummary": "",
+    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/10/10/e043010.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-043010; html:https://europepmc.org/articles/PMC7580065; pdf:https://europepmc.org/articles/PMC7580065?pdf=render"
+  },
   {
     "id": "33948220",
     "doi": "https://doi.org/10.1177/20552076211007661",
@@ -8091,6 +8091,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.3399/bjgp.2021.0376; doi:https://doi.org/10.3399/BJGP.2021.0376; html:https://europepmc.org/articles/PMC8589463; pdf:https://europepmc.org/articles/PMC8589463?pdf=render"
   },
+  {
+    "id": "34340970",
+    "doi": "https://doi.org/10.3399/bjgp.2021.0301",
+    "title": "Clinical coding of long COVID in English primary care: a federated analysis of 58 million patient records <i>in situ</i> using OpenSAFELY.",
+    "authorString": "Walker AJ, MacKenna B, Inglesby P, Tomlinson L, Rentsch CT, Curtis HJ, Morton CE, Morley J, Mehrkar A, Bacon S, Hickman G, Bates C, Croker R, Evans D, Ward T, Cockburn J, Davy S, Bhaskaran K, Schultze A, Williamson EJ, Hulme WJ, McDonald HI, Mathur R, Eggo RM, Wing K, Wong AY, Forbes H, Tazare J, Parry J, Hester F, Harper S, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Griffiths P, Fowles A, Parkes N, Douglas IJ, Evans SJ, (The OpenSAFELY Collaborative).",
+    "authorAffiliations": "",
+    "journalTitle": "The British journal of general practice : the journal of the Royal College of General Practitioners",
+    "pubYear": "2021",
+    "date": "2021-10-28",
+    "isOpenAccess": "Y",
+    "keywords": "Primary Health Care; General Practice; Electronic Health Records; Covid-19; Long Covid",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Long COVID describes new or persistent symptoms at least 4 weeks after onset of acute COVID-19. Clinical codes to describe this phenomenon were recently created.<h4>Aim</h4>To describe the use of long-COVID codes, and variation of use by general practice, demographic variables, and over time.<h4>Design and setting</h4>Population-based cohort study in English primary care.<h4>Method</h4>Working on behalf of NHS England, OpenSAFELY data were used encompassing 96% of the English population between 1 February 2020 and 25 May 2021. The proportion of people with a recorded code for long COVID was measured overall and by demographic factors, electronic health record software system (EMIS or TPP), and week.<h4>Results</h4>Long COVID was recorded for 23 273 people. Coding was unevenly distributed among practices, with 26.7% of practices having never used the codes. Regional variation ranged between 20.3 per 100 000 people for East of England (95% confidence interval [CI] = 19.3 to 21.4) and 55.6 per 100 000 people in London (95% CI = 54.1 to 57.1). Coding was higher among females (52.1, 95% CI = 51.3 to 52.9) than males (28.1, 95% CI = 27.5 to 28.7), and higher among practices using EMIS (53.7, 95% CI = 52.9 to 54.4) than those using TPP (20.9, 95% CI = 20.3 to 21.4).<h4>Conclusion</h4>Current recording of long COVID in primary care is very low, and variable between practices. This may reflect patients not presenting; clinicians and patients holding different diagnostic thresholds; or challenges with the design and communication of diagnostic codes. Increased awareness of diagnostic codes is recommended to facilitate research and planning of services, and also surveys with qualitative work to better evaluate clinicians' understanding of the diagnosis.",
+    "laySummary": "",
+    "urls": "pdf:https://bjgp.org/content/bjgp/71/712/e806.full.pdf; doi:https://doi.org/10.3399/BJGP.2021.0301; html:https://europepmc.org/articles/PMC8340730; pdf:https://europepmc.org/articles/PMC8340730?pdf=render"
+  },
   {
     "id": "37363796",
     "doi": "https://doi.org/10.1016/j.lanepe.2023.100636",
@@ -8109,21 +8126,21 @@
     "urls": "doi:https://doi.org/10.1016/j.lanepe.2023.100636; doi:https://doi.org/10.1016/j.lanepe.2023.100636; html:https://europepmc.org/articles/PMC10155829; pdf:https://europepmc.org/articles/PMC10155829?pdf=render"
   },
   {
-    "id": "34340970",
-    "doi": "https://doi.org/10.3399/bjgp.2021.0301",
-    "title": "Clinical coding of long COVID in English primary care: a federated analysis of 58 million patient records <i>in situ</i> using OpenSAFELY.",
-    "authorString": "Walker AJ, MacKenna B, Inglesby P, Tomlinson L, Rentsch CT, Curtis HJ, Morton CE, Morley J, Mehrkar A, Bacon S, Hickman G, Bates C, Croker R, Evans D, Ward T, Cockburn J, Davy S, Bhaskaran K, Schultze A, Williamson EJ, Hulme WJ, McDonald HI, Mathur R, Eggo RM, Wing K, Wong AY, Forbes H, Tazare J, Parry J, Hester F, Harper S, O'Hanlon S, Eavis A, Jarvis R, Avramov D, Griffiths P, Fowles A, Parkes N, Douglas IJ, Evans SJ, (The OpenSAFELY Collaborative).",
+    "id": "34598993",
+    "doi": "https://doi.org/10.1136/bmjopen-2021-054410",
+    "title": "Changes in neonatal admissions, care processes and outcomes in England and Wales during the COVID-19 pandemic: a whole population cohort study.",
+    "authorString": "Greenbury SF, Longford N, Ougham K, Angelini ED, Battersby C, Uthaya S, Modi N.",
     "authorAffiliations": "",
-    "journalTitle": "The British journal of general practice : the journal of the Royal College of General Practitioners",
+    "journalTitle": "BMJ open",
     "pubYear": "2021",
-    "date": "2021-10-28",
+    "date": "2021-10-01",
     "isOpenAccess": "Y",
-    "keywords": "Primary Health Care; General Practice; Electronic Health Records; Covid-19; Long Covid",
+    "keywords": "Public Health; Neonatology; Neonatal Intensive & Critical Care",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Long COVID describes new or persistent symptoms at least 4 weeks after onset of acute COVID-19. Clinical codes to describe this phenomenon were recently created.<h4>Aim</h4>To describe the use of long-COVID codes, and variation of use by general practice, demographic variables, and over time.<h4>Design and setting</h4>Population-based cohort study in English primary care.<h4>Method</h4>Working on behalf of NHS England, OpenSAFELY data were used encompassing 96% of the English population between 1 February 2020 and 25 May 2021. The proportion of people with a recorded code for long COVID was measured overall and by demographic factors, electronic health record software system (EMIS or TPP), and week.<h4>Results</h4>Long COVID was recorded for 23 273 people. Coding was unevenly distributed among practices, with 26.7% of practices having never used the codes. Regional variation ranged between 20.3 per 100 000 people for East of England (95% confidence interval [CI] = 19.3 to 21.4) and 55.6 per 100 000 people in London (95% CI = 54.1 to 57.1). Coding was higher among females (52.1, 95% CI = 51.3 to 52.9) than males (28.1, 95% CI = 27.5 to 28.7), and higher among practices using EMIS (53.7, 95% CI = 52.9 to 54.4) than those using TPP (20.9, 95% CI = 20.3 to 21.4).<h4>Conclusion</h4>Current recording of long COVID in primary care is very low, and variable between practices. This may reflect patients not presenting; clinicians and patients holding different diagnostic thresholds; or challenges with the design and communication of diagnostic codes. Increased awareness of diagnostic codes is recommended to facilitate research and planning of services, and also surveys with qualitative work to better evaluate clinicians' understanding of the diagnosis.",
+    "abstract": "<h4>Objectives</h4>The COVID-19 pandemic instigated multiple societal and healthcare interventions with potential to affect perinatal practice. We evaluated population-level changes in preterm and full-term admissions to neonatal units, care processes and outcomes.<h4>Design</h4>Observational cohort study using the UK National Neonatal Research Database.<h4>Setting</h4>England and Wales.<h4>Participants</h4>Admissions to National Health Service neonatal units from 2012 to 2020.<h4>Main outcome measures</h4>Admissions by gestational age, ethnicity and Index of Multiple Deprivation, and key care processes and outcomes.<h4>Methods</h4>We calculated differences in numbers and rates between April and June 2020 (spring), the first 3 months of national lockdown (COVID-19 period), and December 2019-February 2020 (winter), prior to introduction of mitigation measures, and compared them with the corresponding differences in the previous 7 years. We considered the COVID-19 period highly unusual if the spring-winter difference was smaller or larger than all previous corresponding differences, and calculated the level of confidence in this conclusion.<h4>Results</h4>Marked fluctuations occurred in all measures over the 8 years with several highly unusual changes during the COVID-19 period. Total admissions fell, having risen over all previous years (COVID-19 difference: -1492; previous 7-year difference range: +100, +1617; p<0.001); full-term black admissions rose (+66; -64, +35; p<0.001) whereas Asian (-137; -14, +101; p<0.001) and white (-319; -235, +643: p<0.001) admissions fell. Transfers to higher and lower designation neonatal units increased (+129; -4, +88; p<0.001) and decreased (-47; -25, +12; p<0.001), respectively. Total preterm admissions decreased (-350; -26, +479; p<0.001). The fall in extremely preterm admissions was most marked in the two lowest socioeconomic quintiles.<h4>Conclusions</h4>Our findings indicate substantial changes occurred in care pathways and clinical thresholds, with disproportionate effects on black ethnic groups, during the immediate COVID-19 period, and raise the intriguing possibility that non-healthcare interventions may reduce extremely preterm births.",
     "laySummary": "",
-    "urls": "pdf:https://bjgp.org/content/bjgp/71/712/e806.full.pdf; doi:https://doi.org/10.3399/BJGP.2021.0301; html:https://europepmc.org/articles/PMC8340730; pdf:https://europepmc.org/articles/PMC8340730?pdf=render"
+    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/11/10/e054410.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-054410; html:https://europepmc.org/articles/PMC8488283; pdf:https://europepmc.org/articles/PMC8488283?pdf=render"
   },
   {
     "id": "37387161",
@@ -8159,23 +8176,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ageing/article-pdf/52/8/afad141/51124726/afad141.pdf; doi:https://doi.org/10.1093/ageing/afad141; html:https://europepmc.org/articles/PMC10438206; pdf:https://europepmc.org/articles/PMC10438206?pdf=render"
   },
-  {
-    "id": "34598993",
-    "doi": "https://doi.org/10.1136/bmjopen-2021-054410",
-    "title": "Changes in neonatal admissions, care processes and outcomes in England and Wales during the COVID-19 pandemic: a whole population cohort study.",
-    "authorString": "Greenbury SF, Longford N, Ougham K, Angelini ED, Battersby C, Uthaya S, Modi N.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2021",
-    "date": "2021-10-01",
-    "isOpenAccess": "Y",
-    "keywords": "Public Health; Neonatology; Neonatal Intensive & Critical Care",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objectives</h4>The COVID-19 pandemic instigated multiple societal and healthcare interventions with potential to affect perinatal practice. We evaluated population-level changes in preterm and full-term admissions to neonatal units, care processes and outcomes.<h4>Design</h4>Observational cohort study using the UK National Neonatal Research Database.<h4>Setting</h4>England and Wales.<h4>Participants</h4>Admissions to National Health Service neonatal units from 2012 to 2020.<h4>Main outcome measures</h4>Admissions by gestational age, ethnicity and Index of Multiple Deprivation, and key care processes and outcomes.<h4>Methods</h4>We calculated differences in numbers and rates between April and June 2020 (spring), the first 3 months of national lockdown (COVID-19 period), and December 2019-February 2020 (winter), prior to introduction of mitigation measures, and compared them with the corresponding differences in the previous 7 years. We considered the COVID-19 period highly unusual if the spring-winter difference was smaller or larger than all previous corresponding differences, and calculated the level of confidence in this conclusion.<h4>Results</h4>Marked fluctuations occurred in all measures over the 8 years with several highly unusual changes during the COVID-19 period. Total admissions fell, having risen over all previous years (COVID-19 difference: -1492; previous 7-year difference range: +100, +1617; p<0.001); full-term black admissions rose (+66; -64, +35; p<0.001) whereas Asian (-137; -14, +101; p<0.001) and white (-319; -235, +643: p<0.001) admissions fell. Transfers to higher and lower designation neonatal units increased (+129; -4, +88; p<0.001) and decreased (-47; -25, +12; p<0.001), respectively. Total preterm admissions decreased (-350; -26, +479; p<0.001). The fall in extremely preterm admissions was most marked in the two lowest socioeconomic quintiles.<h4>Conclusions</h4>Our findings indicate substantial changes occurred in care pathways and clinical thresholds, with disproportionate effects on black ethnic groups, during the immediate COVID-19 period, and raise the intriguing possibility that non-healthcare interventions may reduce extremely preterm births.",
-    "laySummary": "",
-    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/11/10/e054410.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-054410; html:https://europepmc.org/articles/PMC8488283; pdf:https://europepmc.org/articles/PMC8488283?pdf=render"
-  },
   {
     "id": "37480048",
     "doi": "https://doi.org/10.1186/s12872-023-03394-6",
@@ -8227,23 +8227,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1210/clinem/dgae119; html:https://europepmc.org/articles/PMC11318998"
   },
-  {
-    "id": "35909058",
-    "doi": "https://doi.org/10.1016/s2589-7500(22)00123-6",
-    "title": "Remote COVID-19 Assessment in Primary Care (RECAP) risk prediction tool: derivation and real-world validation studies.",
-    "authorString": "Espinosa-Gonzalez A, Prociuk D, Fiorentino F, Ramtale C, Mi E, Mi E, Glampson B, Neves AL, Okusi C, Husain L, Macartney J, Brown M, Browne B, Warren C, Chowla R, Heaversedge J, Greenhalgh T, de Lusignan S, Mayer E, Delaney BC.",
-    "authorAffiliations": "",
-    "journalTitle": "The Lancet. Digital health",
-    "pubYear": "2022",
-    "date": "2022-07-28",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Accurate assessment of COVID-19 severity in the community is essential for patient care and requires COVID-19-specific risk prediction scores adequately validated in a community setting. Following a qualitative phase to identify signs, symptoms, and risk factors, we aimed to develop and validate two COVID-19-specific risk prediction scores. Remote COVID-19 Assessment in Primary Care-General Practice score (RECAP-GP; without peripheral oxygen saturation [SpO<sub>2</sub>]) and RECAP-oxygen saturation score (RECAP-O2; with SpO<sub>2</sub>).<h4>Methods</h4>RECAP was a prospective cohort study that used multivariable logistic regression. Data on signs and symptoms (predictors) of disease were collected from community-based patients with suspected COVID-19 via primary care electronic health records and linked with secondary data on hospital admission (outcome) within 28 days of symptom onset. Data sources for RECAP-GP were Oxford-Royal College of General Practitioners Research and Surveillance Centre (RCGP-RSC) primary care practices (development set), northwest London primary care practices (validation set), and the NHS COVID-19 Clinical Assessment Service (CCAS; validation set). The data source for RECAP-O2 was the Doctaly Assist platform (development set and validation set in subsequent sample). The two probabilistic risk prediction models were built by backwards elimination using the development sets and validated by application to the validation datasets. Estimated sample size per model, including the development and validation sets was 2880 people.<h4>Findings</h4>Data were available from 8311 individuals. Observations, such as SpO<sub>2</sub>, were mostly missing in the northwest London, RCGP-RSC, and CCAS data; however, SpO<sub>2</sub> was available for 1364 (70\u00b70%) of 1948 patients who used Doctaly. In the final predictive models, RECAP-GP (n=1863) included sex (male and female), age (years), degree of breathlessness (three point scale), temperature symptoms (two point scale), and presence of hypertension (yes or no); the area under the curve was 0\u00b780 (95% CI 0\u00b776-0\u00b785) and on validation the negative predictive value of a low risk designation was 99% (95% CI 98\u00b71-99\u00b72; 1435 of 1453). RECAP-O2 included age (years), degree of breathlessness (two point scale), fatigue (two point scale), and SpO<sub>2</sub> at rest (as a percentage); the area under the curve was 0\u00b784 (0\u00b778-0\u00b790) and on validation the negative predictive value of low risk designation was 99% (95% CI 98\u00b79-99\u00b77; 1176 of 1183).<h4>Interpretation</h4>Both RECAP models are valid tools to assess COVID-19 patients in the community. RECAP-GP can be used initially, without need for observations, to identify patients who require monitoring. If the patient is monitored and SpO<sub>2</sub> is available, RECAP-O2 is useful to assess the need for treatment escalation.<h4>Funding</h4>Community Jameel and the Imperial College President's Excellence Fund, the Economic and Social Research Council, UK Research and Innovation, and Health Data Research UK.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/s2589-7500(22)00123-6; doi:https://doi.org/10.1016/S2589-7500(22)00123-6; html:https://europepmc.org/articles/PMC9333950; pdf:https://europepmc.org/articles/PMC9333950?pdf=render"
-  },
   {
     "id": "34746717",
     "doi": "https://doi.org/10.1016/j.eclinm.2021.101100",
@@ -8261,6 +8244,23 @@
     "laySummary": "",
     "urls": "pdf:http://www.thelancet.com/article/S2589537021003801/pdf; doi:https://doi.org/10.1016/j.eclinm.2021.101100; html:https://europepmc.org/articles/PMC8548919; pdf:https://europepmc.org/articles/PMC8548919?pdf=render"
   },
+  {
+    "id": "35909058",
+    "doi": "https://doi.org/10.1016/s2589-7500(22)00123-6",
+    "title": "Remote COVID-19 Assessment in Primary Care (RECAP) risk prediction tool: derivation and real-world validation studies.",
+    "authorString": "Espinosa-Gonzalez A, Prociuk D, Fiorentino F, Ramtale C, Mi E, Mi E, Glampson B, Neves AL, Okusi C, Husain L, Macartney J, Brown M, Browne B, Warren C, Chowla R, Heaversedge J, Greenhalgh T, de Lusignan S, Mayer E, Delaney BC.",
+    "authorAffiliations": "",
+    "journalTitle": "The Lancet. Digital health",
+    "pubYear": "2022",
+    "date": "2022-07-28",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Accurate assessment of COVID-19 severity in the community is essential for patient care and requires COVID-19-specific risk prediction scores adequately validated in a community setting. Following a qualitative phase to identify signs, symptoms, and risk factors, we aimed to develop and validate two COVID-19-specific risk prediction scores. Remote COVID-19 Assessment in Primary Care-General Practice score (RECAP-GP; without peripheral oxygen saturation [SpO<sub>2</sub>]) and RECAP-oxygen saturation score (RECAP-O2; with SpO<sub>2</sub>).<h4>Methods</h4>RECAP was a prospective cohort study that used multivariable logistic regression. Data on signs and symptoms (predictors) of disease were collected from community-based patients with suspected COVID-19 via primary care electronic health records and linked with secondary data on hospital admission (outcome) within 28 days of symptom onset. Data sources for RECAP-GP were Oxford-Royal College of General Practitioners Research and Surveillance Centre (RCGP-RSC) primary care practices (development set), northwest London primary care practices (validation set), and the NHS COVID-19 Clinical Assessment Service (CCAS; validation set). The data source for RECAP-O2 was the Doctaly Assist platform (development set and validation set in subsequent sample). The two probabilistic risk prediction models were built by backwards elimination using the development sets and validated by application to the validation datasets. Estimated sample size per model, including the development and validation sets was 2880 people.<h4>Findings</h4>Data were available from 8311 individuals. Observations, such as SpO<sub>2</sub>, were mostly missing in the northwest London, RCGP-RSC, and CCAS data; however, SpO<sub>2</sub> was available for 1364 (70\u00b70%) of 1948 patients who used Doctaly. In the final predictive models, RECAP-GP (n=1863) included sex (male and female), age (years), degree of breathlessness (three point scale), temperature symptoms (two point scale), and presence of hypertension (yes or no); the area under the curve was 0\u00b780 (95% CI 0\u00b776-0\u00b785) and on validation the negative predictive value of a low risk designation was 99% (95% CI 98\u00b71-99\u00b72; 1435 of 1453). RECAP-O2 included age (years), degree of breathlessness (two point scale), fatigue (two point scale), and SpO<sub>2</sub> at rest (as a percentage); the area under the curve was 0\u00b784 (0\u00b778-0\u00b790) and on validation the negative predictive value of low risk designation was 99% (95% CI 98\u00b79-99\u00b77; 1176 of 1183).<h4>Interpretation</h4>Both RECAP models are valid tools to assess COVID-19 patients in the community. RECAP-GP can be used initially, without need for observations, to identify patients who require monitoring. If the patient is monitored and SpO<sub>2</sub> is available, RECAP-O2 is useful to assess the need for treatment escalation.<h4>Funding</h4>Community Jameel and the Imperial College President's Excellence Fund, the Economic and Social Research Council, UK Research and Innovation, and Health Data Research UK.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/s2589-7500(22)00123-6; doi:https://doi.org/10.1016/S2589-7500(22)00123-6; html:https://europepmc.org/articles/PMC9333950; pdf:https://europepmc.org/articles/PMC9333950?pdf=render"
+  },
   {
     "id": "36701357",
     "doi": "https://doi.org/10.1371/journal.pone.0280943",
@@ -8278,6 +8278,23 @@
     "laySummary": "",
     "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0280943&type=printable; doi:https://doi.org/10.1371/journal.pone.0280943; html:https://europepmc.org/articles/PMC9879384; pdf:https://europepmc.org/articles/PMC9879384?pdf=render"
   },
+  {
+    "id": "35079067",
+    "doi": "https://doi.org/10.1038/s41598-022-05414-5",
+    "title": "Asthma in paediatric intensive care in England residents: observational study.",
+    "authorString": "Mukherjee M, Cunningham S, Bhuia MR, Lo TM, Been JV, Sheikh A.",
+    "authorAffiliations": "",
+    "journalTitle": "Scientific reports",
+    "pubYear": "2022",
+    "date": "2022-01-25",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Despite high prevalence of asthma in children in the UK, there were no prior report on asthma admissions in paediatric intensive care units (PICU). We investigated the epidemiology and healthcare resource utilisation in children with asthma presenting to PICUs in England. PICANet, a UK national PICU database, was queried for asthma as the primary reason for admission, of children resident in England from April 2006 until March 2013. There were 2195 admissions to PICU for a median stay of 1.4\u00a0days. 59% were males and 51% aged 0-4\u00a0years. The fourth and fifth most\u00a0deprived quintiles represented 61% (1329) admissions and 73% (11) of the 15 deaths. Deaths were most frequent in 10-14\u00a0years age (n\u2009=\u200911, 73%), with no deaths in less than 5\u00a0years age. 38% of admissions (828/2193) received invasive ventilation, which was more frequent with increasing deprivation (13% (108/828) in least deprived to 31% (260/828) in most deprived) and with\u00a0decreasing age (0-4-year-olds: 49%, 409/828). This first multi-centre PICU study in England found that children from more deprived neighbourhoods represented the majority of asthma admissions, invasive ventilation and deaths in PICU. Children experiencing socioeconomic deprivation could benefit from enhanced asthma support in the community.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41598-022-05414-5.pdf; doi:https://doi.org/10.1038/s41598-022-05414-5; html:https://europepmc.org/articles/PMC8789863; pdf:https://europepmc.org/articles/PMC8789863?pdf=render"
+  },
   {
     "id": "37607793",
     "doi": "https://doi.org/10.1136/bmjopen-2023-076296",
@@ -8295,23 +8312,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1136/bmjopen-2023-076296; doi:https://doi.org/10.1136/bmjopen-2023-076296; html:https://europepmc.org/articles/PMC10445367; pdf:https://europepmc.org/articles/PMC10445367?pdf=render"
   },
-  {
-    "id": "35595824",
-    "doi": "https://doi.org/10.1038/s41598-022-12517-6",
-    "title": "Transmission dynamics of SARS-CoV-2 in a strictly-Orthodox Jewish community in the UK.",
-    "authorString": "Waites W, Pearson CAB, Gaskell KM, House T, Pellis L, Johnson M, Gould V, Hunt A, Stone NRH, Kasstan B, Chantler T, Lal S, Roberts CH, Goldblatt D, CMMID COVID-19 Working Group, Marks M, Eggo RM.",
-    "authorAffiliations": "",
-    "journalTitle": "Scientific reports",
-    "pubYear": "2022",
-    "date": "2022-05-20",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Some social settings such as households and workplaces, have been identified as high risk for SARS-CoV-2 transmission. Identifying and quantifying the importance of these settings is critical for designing interventions. A tightly-knit religious community in the UK experienced a very large COVID-19 epidemic in 2020, reaching 64.3% seroprevalence within 10 months, and we surveyed this community both for serological status and individual-level attendance at particular settings. Using these data, and a network model of people and places represented as a stochastic graph rewriting system, we estimated the relative contribution of transmission in households, schools and religious institutions to the epidemic, and the relative risk of infection in each of these settings. All congregate settings were important for transmission, with some such as primary schools and places of worship having a higher share of transmission than others. We found that the model needed a higher general-community transmission rate for women (3.3-fold), and lower susceptibility to infection in children to recreate the observed serological data. The precise share of transmission in each place was related to assumptions about the internal structure of those places. Identification of key settings of transmission can allow public health interventions to be targeted at these locations.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41598-022-12517-6.pdf; doi:https://doi.org/10.1038/s41598-022-12517-6; html:https://europepmc.org/articles/PMC9121858; pdf:https://europepmc.org/articles/PMC9121858?pdf=render"
-  },
   {
     "id": "34862222",
     "doi": "https://doi.org/10.7861/clinmed.2021-0386",
@@ -8330,38 +8330,21 @@
     "urls": "pdf:https://www.rcpjournals.org/content/clinmedicine/21/6/e620.full.pdf; doi:https://doi.org/10.7861/clinmed.2021-0386; html:https://europepmc.org/articles/PMC8806292; pdf:https://europepmc.org/articles/PMC8806292?pdf=render; doi:https://doi.org/10.7861/clinmed.2021-0386"
   },
   {
-    "id": "35079067",
-    "doi": "https://doi.org/10.1038/s41598-022-05414-5",
-    "title": "Asthma in paediatric intensive care in England residents: observational study.",
-    "authorString": "Mukherjee M, Cunningham S, Bhuia MR, Lo TM, Been JV, Sheikh A.",
+    "id": "35595824",
+    "doi": "https://doi.org/10.1038/s41598-022-12517-6",
+    "title": "Transmission dynamics of SARS-CoV-2 in a strictly-Orthodox Jewish community in the UK.",
+    "authorString": "Waites W, Pearson CAB, Gaskell KM, House T, Pellis L, Johnson M, Gould V, Hunt A, Stone NRH, Kasstan B, Chantler T, Lal S, Roberts CH, Goldblatt D, CMMID COVID-19 Working Group, Marks M, Eggo RM.",
     "authorAffiliations": "",
     "journalTitle": "Scientific reports",
     "pubYear": "2022",
-    "date": "2022-01-25",
+    "date": "2022-05-20",
     "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Despite high prevalence of asthma in children in the UK, there were no prior report on asthma admissions in paediatric intensive care units (PICU). We investigated the epidemiology and healthcare resource utilisation in children with asthma presenting to PICUs in England. PICANet, a UK national PICU database, was queried for asthma as the primary reason for admission, of children resident in England from April 2006 until March 2013. There were 2195 admissions to PICU for a median stay of 1.4\u00a0days. 59% were males and 51% aged 0-4\u00a0years. The fourth and fifth most\u00a0deprived quintiles represented 61% (1329) admissions and 73% (11) of the 15 deaths. Deaths were most frequent in 10-14\u00a0years age (n\u2009=\u200911, 73%), with no deaths in less than 5\u00a0years age. 38% of admissions (828/2193) received invasive ventilation, which was more frequent with increasing deprivation (13% (108/828) in least deprived to 31% (260/828) in most deprived) and with\u00a0decreasing age (0-4-year-olds: 49%, 409/828). This first multi-centre PICU study in England found that children from more deprived neighbourhoods represented the majority of asthma admissions, invasive ventilation and deaths in PICU. Children experiencing socioeconomic deprivation could benefit from enhanced asthma support in the community.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41598-022-05414-5.pdf; doi:https://doi.org/10.1038/s41598-022-05414-5; html:https://europepmc.org/articles/PMC8789863; pdf:https://europepmc.org/articles/PMC8789863?pdf=render"
-  },
-  {
-    "id": "37795045",
-    "doi": "https://doi.org/10.1177/26320843221147855",
-    "title": "Monitoring metrics over time: Why clinical trialists need to systematically collect site performance metrics.",
-    "authorString": "Yorke-Edwards V, Diaz-Montana C, Murray ML, Sydes MR, Love SB.",
-    "authorAffiliations": "",
-    "journalTitle": "Research methods in medicine & health sciences",
-    "pubYear": "2023",
-    "date": "2022-12-21",
-    "isOpenAccess": "N",
-    "keywords": "Clinical Trials; Risk-based Monitoring; Central Monitoring; Centralised Monitoring; Study-Within-A-Trial (Swat)",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Over the last decade, there has been an increasing interest in risk-based monitoring (RBM) in clinical trials, resulting in a number of guidelines from regulators and its inclusion in ICH GCP. However, there is a lack of detail on how to approach RBM from a practical perspective, and insufficient understanding of best practice.<h4>Purpose</h4>We present a method for clinical trials units to track their metrics within clinical trials using descriptive statistics and visualisations.<h4>Research design</h4>We suggest descriptive statistics and visualisations within a SWAT methodology.<h4>Study sample</h4>We illustrate this method using the metrics from TEMPER, a monitoring study carried out in three trials at the MRC Clinical Trials Unit at UCL.<h4>Data collection</h4>The data collection for TEMPER is described in <i>DOI: 10.1177/1740774518793379</i>.<h4>Results</h4>We show the results and discuss a protocol for a Study-Within-A-Trial (SWAT 167) for those wishing to use the method.<h4>Conclusions</h4>The potential benefits metric tracking brings to clinical trials include enhanced assessment of sites for potential corrective action, improved evaluation and contextualisation of the influence of metrics and their thresholds, and the establishment of best practice in RBM. The standardisation of the collection of such monitoring data would benefit both individual trials and the clinical trials community.",
+    "abstract": "Some social settings such as households and workplaces, have been identified as high risk for SARS-CoV-2 transmission. Identifying and quantifying the importance of these settings is critical for designing interventions. A tightly-knit religious community in the UK experienced a very large COVID-19 epidemic in 2020, reaching 64.3% seroprevalence within 10 months, and we surveyed this community both for serological status and individual-level attendance at particular settings. Using these data, and a network model of people and places represented as a stochastic graph rewriting system, we estimated the relative contribution of transmission in households, schools and religious institutions to the epidemic, and the relative risk of infection in each of these settings. All congregate settings were important for transmission, with some such as primary schools and places of worship having a higher share of transmission than others. We found that the model needed a higher general-community transmission rate for women (3.3-fold), and lower susceptibility to infection in children to recreate the observed serological data. The precise share of transmission in each place was related to assumptions about the internal structure of those places. Identification of key settings of transmission can allow public health interventions to be targeted at these locations.",
     "laySummary": "",
-    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/26320843221147855; doi:https://doi.org/10.1177/26320843221147855; html:https://europepmc.org/articles/PMC7615148; pdf:https://europepmc.org/articles/PMC7615148?pdf=render; doi:https://doi.org/10.1177/26320843221147855"
+    "urls": "pdf:https://www.nature.com/articles/s41598-022-12517-6.pdf; doi:https://doi.org/10.1038/s41598-022-12517-6; html:https://europepmc.org/articles/PMC9121858; pdf:https://europepmc.org/articles/PMC9121858?pdf=render"
   },
   {
     "id": "38096890",
@@ -8381,21 +8364,21 @@
     "urls": "pdf:http://www.thelancet.com/article/S1470204523005302/pdf; doi:https://doi.org/10.1016/S1470-2045(23)00530-2; html:https://europepmc.org/articles/PMC7615518; pdf:https://europepmc.org/articles/PMC7615518?pdf=render"
   },
   {
-    "id": "33079204",
-    "doi": "https://doi.org/10.1093/ehjqcco/qcaa079",
-    "title": "Impact of COVID-19 on cardiac procedure activity in England and associated 30-day mortality.",
-    "authorString": "Mohamed MO, Banerjee A, Clarke S, de Belder M, Patwala A, Goodwin AT, Kwok CS, Rashid M, Gale CP, Curzen N, Mamas MA.",
+    "id": "37795045",
+    "doi": "https://doi.org/10.1177/26320843221147855",
+    "title": "Monitoring metrics over time: Why clinical trialists need to systematically collect site performance metrics.",
+    "authorString": "Yorke-Edwards V, Diaz-Montana C, Murray ML, Sydes MR, Love SB.",
     "authorAffiliations": "",
-    "journalTitle": "European heart journal. Quality of care & clinical outcomes",
-    "pubYear": "2021",
-    "date": "2021-05-01",
-    "isOpenAccess": "Y",
-    "keywords": "Mortality; Cardiac; England; Procedures; Covid-19",
+    "journalTitle": "Research methods in medicine & health sciences",
+    "pubYear": "2023",
+    "date": "2022-12-21",
+    "isOpenAccess": "N",
+    "keywords": "Clinical Trials; Risk-based Monitoring; Central Monitoring; Centralised Monitoring; Study-Within-A-Trial (Swat)",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Aims</h4>Limited data exist on the impact of COVID-19 on national changes in cardiac procedure activity, including patient characteristics and clinical outcomes before and during the COVID-19 pandemic.<h4>Methods and results</h4>All major cardiac procedures (n\u2009=\u2009374\u00a0899) performed between 1 January and 31 May for the years 2018, 2019, and 2020 were analysed, stratified by procedure type and time-period (pre-COVID: January-May 2018 and 2019 and January-February 2020 and COVID: March-May 2020). Multivariable logistic regression was performed to examine the odds ratio (OR) of 30-day mortality for procedures performed in the COVID period. Overall, there was a deficit of 45\u00a0501 procedures during the COVID period compared to the monthly averages (March-May) in 2018-2019. Cardiac catheterization and device implantations were the most affected in terms of numbers (n\u2009=\u200919\u00a0637 and n\u2009=\u200910\u00a0453), whereas surgical procedures such as mitral valve replacement, other valve replacement/repair, atrioseptal defect/ventriculoseptal defect repair, and coronary artery bypass grafting were the most affected as a relative percentage difference (\u0394) to previous years' averages. Transcatheter aortic valve replacement was the least affected (\u0394 -10.6%). No difference in 30-day mortality was observed between pre-COVID and COVID time-periods for all cardiac procedures except cardiac catheterization [OR 1.25 95% confidence interval (CI) 1.07-1.47, P\u2009=\u20090.006] and cardiac device implantation (OR 1.35 95% CI 1.15-1.58, P\u2009<\u20090.001).<h4>Conclusion</h4>Cardiac procedural activity has significantly declined across England during the COVID-19 pandemic, with a deficit in excess of 45\u00a0000 procedures, without an increase in risk of mortality for most cardiac procedures performed during the pandemic. Major restructuring of cardiac services is necessary to deal with this deficit, which would inevitably impact long-term morbidity and mortality.",
+    "abstract": "<h4>Background</h4>Over the last decade, there has been an increasing interest in risk-based monitoring (RBM) in clinical trials, resulting in a number of guidelines from regulators and its inclusion in ICH GCP. However, there is a lack of detail on how to approach RBM from a practical perspective, and insufficient understanding of best practice.<h4>Purpose</h4>We present a method for clinical trials units to track their metrics within clinical trials using descriptive statistics and visualisations.<h4>Research design</h4>We suggest descriptive statistics and visualisations within a SWAT methodology.<h4>Study sample</h4>We illustrate this method using the metrics from TEMPER, a monitoring study carried out in three trials at the MRC Clinical Trials Unit at UCL.<h4>Data collection</h4>The data collection for TEMPER is described in <i>DOI: 10.1177/1740774518793379</i>.<h4>Results</h4>We show the results and discuss a protocol for a Study-Within-A-Trial (SWAT 167) for those wishing to use the method.<h4>Conclusions</h4>The potential benefits metric tracking brings to clinical trials include enhanced assessment of sites for potential corrective action, improved evaluation and contextualisation of the influence of metrics and their thresholds, and the establishment of best practice in RBM. The standardisation of the collection of such monitoring data would benefit both individual trials and the clinical trials community.",
     "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/ehjqcco/article-pdf/7/3/247/37776880/qcaa079.pdf; doi:https://doi.org/10.1093/ehjqcco/qcaa079; html:https://europepmc.org/articles/PMC7665465; pdf:https://europepmc.org/articles/PMC7665465?pdf=render"
+    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/26320843221147855; doi:https://doi.org/10.1177/26320843221147855; html:https://europepmc.org/articles/PMC7615148; pdf:https://europepmc.org/articles/PMC7615148?pdf=render; doi:https://doi.org/10.1177/26320843221147855"
   },
   {
     "id": "35192611",
@@ -8414,6 +8397,23 @@
     "laySummary": "",
     "urls": "pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003916&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003916; html:https://europepmc.org/articles/PMC8863286; pdf:https://europepmc.org/articles/PMC8863286?pdf=render"
   },
+  {
+    "id": "34232969",
+    "doi": "https://doi.org/10.23889/ijpds.v5i1.1151",
+    "title": "How effective are population health surveys for estimating prevalence of chronic conditions compared to anonymised clinical data?",
+    "authorString": "Whiffen T, Akbari A, Paget T, Lowe S, Lyons R.",
+    "authorAffiliations": "",
+    "journalTitle": "International journal of population data science",
+    "pubYear": "2020",
+    "date": "2020-06-12",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>Population health surveys are used to record person-reported outcome measures for chronic health conditions and provide a useful source of data when evaluating potential disease burdens. The reliability of survey-based prevalence estimates for chronic diseases is unclear nonetheless. This study applied methodological triangulation via a data linkage method to validate prevalence of selected chronic conditions (angina, myocardial infarction, heart failure, and asthma).<h4>Methods</h4>Linked healthcare records were used for a combined cohort of 11,323 adults from the 2013 and 2014 sweeps of the Welsh Health Survey (WHS). The approach utilised consented survey data linked to primary and secondary care electronic health record (EHR) data back to 2002 within the Secure Anonymised Information Linkage (SAIL) Databank.<h4>Results</h4>This descriptive study demonstrates validation of survey and clinical data using data linkage for selected chronic cardiovascular conditions and asthma with varied success. The results indicate that identifying cases for separate cardiovascular conditions was limited without specific medication codes for each condition, but more straightforward for asthma, where there was an extensive list of medications available. For asthma there was better agreement between prevalence estimates based on survey and clinical data as a result.<h4>Conclusion</h4>Whilst the results provide external validity for the WHS as an instrument for estimating the burden of chronic disease, they also indicate that a data linkage appproach can be used to produce comparable prevalence estimates using clinical data if a defined condition-specific set of clinical codes are available.",
+    "laySummary": "",
+    "urls": "pdf:https://ijpds.org/article/download/1151/2553; doi:https://doi.org/10.23889/ijpds.v5i1.1151; html:https://europepmc.org/articles/PMC7473295; pdf:https://europepmc.org/articles/PMC7473295?pdf=render"
+  },
   {
     "id": "39185668",
     "doi": "https://doi.org/10.1002/hbm.70003",
@@ -8432,21 +8432,21 @@
     "urls": "doi:https://doi.org/10.1002/hbm.70003; html:https://europepmc.org/articles/PMC11345634; pdf:https://europepmc.org/articles/PMC11345634?pdf=render"
   },
   {
-    "id": "34232969",
-    "doi": "https://doi.org/10.23889/ijpds.v5i1.1151",
-    "title": "How effective are population health surveys for estimating prevalence of chronic conditions compared to anonymised clinical data?",
-    "authorString": "Whiffen T, Akbari A, Paget T, Lowe S, Lyons R.",
+    "id": "33079204",
+    "doi": "https://doi.org/10.1093/ehjqcco/qcaa079",
+    "title": "Impact of COVID-19 on cardiac procedure activity in England and associated 30-day mortality.",
+    "authorString": "Mohamed MO, Banerjee A, Clarke S, de Belder M, Patwala A, Goodwin AT, Kwok CS, Rashid M, Gale CP, Curzen N, Mamas MA.",
     "authorAffiliations": "",
-    "journalTitle": "International journal of population data science",
-    "pubYear": "2020",
-    "date": "2020-06-12",
+    "journalTitle": "European heart journal. Quality of care & clinical outcomes",
+    "pubYear": "2021",
+    "date": "2021-05-01",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Mortality; Cardiac; England; Procedures; Covid-19",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>Population health surveys are used to record person-reported outcome measures for chronic health conditions and provide a useful source of data when evaluating potential disease burdens. The reliability of survey-based prevalence estimates for chronic diseases is unclear nonetheless. This study applied methodological triangulation via a data linkage method to validate prevalence of selected chronic conditions (angina, myocardial infarction, heart failure, and asthma).<h4>Methods</h4>Linked healthcare records were used for a combined cohort of 11,323 adults from the 2013 and 2014 sweeps of the Welsh Health Survey (WHS). The approach utilised consented survey data linked to primary and secondary care electronic health record (EHR) data back to 2002 within the Secure Anonymised Information Linkage (SAIL) Databank.<h4>Results</h4>This descriptive study demonstrates validation of survey and clinical data using data linkage for selected chronic cardiovascular conditions and asthma with varied success. The results indicate that identifying cases for separate cardiovascular conditions was limited without specific medication codes for each condition, but more straightforward for asthma, where there was an extensive list of medications available. For asthma there was better agreement between prevalence estimates based on survey and clinical data as a result.<h4>Conclusion</h4>Whilst the results provide external validity for the WHS as an instrument for estimating the burden of chronic disease, they also indicate that a data linkage appproach can be used to produce comparable prevalence estimates using clinical data if a defined condition-specific set of clinical codes are available.",
+    "abstract": "<h4>Aims</h4>Limited data exist on the impact of COVID-19 on national changes in cardiac procedure activity, including patient characteristics and clinical outcomes before and during the COVID-19 pandemic.<h4>Methods and results</h4>All major cardiac procedures (n\u2009=\u2009374\u00a0899) performed between 1 January and 31 May for the years 2018, 2019, and 2020 were analysed, stratified by procedure type and time-period (pre-COVID: January-May 2018 and 2019 and January-February 2020 and COVID: March-May 2020). Multivariable logistic regression was performed to examine the odds ratio (OR) of 30-day mortality for procedures performed in the COVID period. Overall, there was a deficit of 45\u00a0501 procedures during the COVID period compared to the monthly averages (March-May) in 2018-2019. Cardiac catheterization and device implantations were the most affected in terms of numbers (n\u2009=\u200919\u00a0637 and n\u2009=\u200910\u00a0453), whereas surgical procedures such as mitral valve replacement, other valve replacement/repair, atrioseptal defect/ventriculoseptal defect repair, and coronary artery bypass grafting were the most affected as a relative percentage difference (\u0394) to previous years' averages. Transcatheter aortic valve replacement was the least affected (\u0394 -10.6%). No difference in 30-day mortality was observed between pre-COVID and COVID time-periods for all cardiac procedures except cardiac catheterization [OR 1.25 95% confidence interval (CI) 1.07-1.47, P\u2009=\u20090.006] and cardiac device implantation (OR 1.35 95% CI 1.15-1.58, P\u2009<\u20090.001).<h4>Conclusion</h4>Cardiac procedural activity has significantly declined across England during the COVID-19 pandemic, with a deficit in excess of 45\u00a0000 procedures, without an increase in risk of mortality for most cardiac procedures performed during the pandemic. Major restructuring of cardiac services is necessary to deal with this deficit, which would inevitably impact long-term morbidity and mortality.",
     "laySummary": "",
-    "urls": "pdf:https://ijpds.org/article/download/1151/2553; doi:https://doi.org/10.23889/ijpds.v5i1.1151; html:https://europepmc.org/articles/PMC7473295; pdf:https://europepmc.org/articles/PMC7473295?pdf=render"
+    "urls": "pdf:https://academic.oup.com/ehjqcco/article-pdf/7/3/247/37776880/qcaa079.pdf; doi:https://doi.org/10.1093/ehjqcco/qcaa079; html:https://europepmc.org/articles/PMC7665465; pdf:https://europepmc.org/articles/PMC7665465?pdf=render"
   },
   {
     "id": "37674175",
@@ -8465,23 +8465,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmcpregnancychildbirth.biomedcentral.com/counter/pdf/10.1186/s12884-023-05958-y; doi:https://doi.org/10.1186/s12884-023-05958-y; html:https://europepmc.org/articles/PMC10481472; pdf:https://europepmc.org/articles/PMC10481472?pdf=render"
   },
-  {
-    "id": "35289755",
-    "doi": "https://doi.org/10.2196/31021",
-    "title": "Concept Libraries for Repeatable and Reusable Research: Qualitative Study Exploring the Needs of Users.",
-    "authorString": "Almowil Z, Zhou SM, Brophy S, Croxall J.",
-    "authorAffiliations": "",
-    "journalTitle": "JMIR human factors",
-    "pubYear": "2022",
-    "date": "2022-03-15",
-    "isOpenAccess": "Y",
-    "keywords": "Electronic Health Records; Record Linkage; Reproducible Research; Clinical Codes; Concept Libraries",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Big data research in the field of health sciences is hindered by a lack of agreement on how to identify and define different conditions and their medications. This means that researchers and health professionals often have different phenotype definitions for the same condition. This lack of agreement makes it difficult to compare different study findings and hinders the ability to conduct repeatable and reusable research.<h4>Objective</h4>This study aims to examine the requirements of various users, such as researchers, clinicians, machine learning experts, and managers, in the development of a data portal for phenotypes (a concept library).<h4>Methods</h4>This was a qualitative study using interviews and focus group discussion. One-to-one interviews were conducted with researchers, clinicians, machine learning experts, and senior research managers in health data science (N=6) to explore their specific needs in the development of a concept library. In addition, a focus group discussion with researchers (N=14) working with the Secured Anonymized Information Linkage databank, a national eHealth data linkage infrastructure, was held to perform a SWOT (strengths, weaknesses, opportunities, and threats) analysis for the phenotyping system and the proposed concept library. The interviews and focus group discussion were transcribed verbatim, and 2 thematic analyses were performed.<h4>Results</h4>Most of the participants thought that the prototype concept library would be a very helpful resource for conducting repeatable research, but they specified that many requirements are needed before its development. Although all the participants stated that they were aware of some existing concept libraries, most of them expressed negative perceptions about them. The participants mentioned several facilitators that would stimulate them to share their work and reuse the work of others, and they pointed out several barriers that could inhibit them from sharing their work and reusing the work of others. The participants suggested some developments that they would like to see to improve reproducible research output using routine data.<h4>Conclusions</h4>The study indicated that most interviewees valued a concept library for phenotypes. However, only half of the participants felt that they would contribute by providing definitions for the concept library, and they reported many barriers regarding sharing their work on a publicly accessible platform. Analysis of interviews and the focus group discussion revealed that different stakeholders have different requirements, facilitators, barriers, and concerns about a prototype concept library.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.2196/31021; doi:https://doi.org/10.2196/31021; html:https://europepmc.org/articles/PMC8965669"
-  },
   {
     "id": "38977844",
     "doi": "https://doi.org/10.1038/s43856-024-00506-x",
@@ -8499,6 +8482,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1038/s43856-024-00506-x; html:https://europepmc.org/articles/PMC11231221; pdf:https://europepmc.org/articles/PMC11231221?pdf=render"
   },
+  {
+    "id": "35289755",
+    "doi": "https://doi.org/10.2196/31021",
+    "title": "Concept Libraries for Repeatable and Reusable Research: Qualitative Study Exploring the Needs of Users.",
+    "authorString": "Almowil Z, Zhou SM, Brophy S, Croxall J.",
+    "authorAffiliations": "",
+    "journalTitle": "JMIR human factors",
+    "pubYear": "2022",
+    "date": "2022-03-15",
+    "isOpenAccess": "Y",
+    "keywords": "Electronic Health Records; Record Linkage; Reproducible Research; Clinical Codes; Concept Libraries",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Big data research in the field of health sciences is hindered by a lack of agreement on how to identify and define different conditions and their medications. This means that researchers and health professionals often have different phenotype definitions for the same condition. This lack of agreement makes it difficult to compare different study findings and hinders the ability to conduct repeatable and reusable research.<h4>Objective</h4>This study aims to examine the requirements of various users, such as researchers, clinicians, machine learning experts, and managers, in the development of a data portal for phenotypes (a concept library).<h4>Methods</h4>This was a qualitative study using interviews and focus group discussion. One-to-one interviews were conducted with researchers, clinicians, machine learning experts, and senior research managers in health data science (N=6) to explore their specific needs in the development of a concept library. In addition, a focus group discussion with researchers (N=14) working with the Secured Anonymized Information Linkage databank, a national eHealth data linkage infrastructure, was held to perform a SWOT (strengths, weaknesses, opportunities, and threats) analysis for the phenotyping system and the proposed concept library. The interviews and focus group discussion were transcribed verbatim, and 2 thematic analyses were performed.<h4>Results</h4>Most of the participants thought that the prototype concept library would be a very helpful resource for conducting repeatable research, but they specified that many requirements are needed before its development. Although all the participants stated that they were aware of some existing concept libraries, most of them expressed negative perceptions about them. The participants mentioned several facilitators that would stimulate them to share their work and reuse the work of others, and they pointed out several barriers that could inhibit them from sharing their work and reusing the work of others. The participants suggested some developments that they would like to see to improve reproducible research output using routine data.<h4>Conclusions</h4>The study indicated that most interviewees valued a concept library for phenotypes. However, only half of the participants felt that they would contribute by providing definitions for the concept library, and they reported many barriers regarding sharing their work on a publicly accessible platform. Analysis of interviews and the focus group discussion revealed that different stakeholders have different requirements, facilitators, barriers, and concerns about a prototype concept library.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.2196/31021; doi:https://doi.org/10.2196/31021; html:https://europepmc.org/articles/PMC8965669"
+  },
   {
     "id": "37400731",
     "doi": "https://doi.org/10.1007/s10802-023-01086-5",
@@ -8551,21 +8551,21 @@
     "urls": "pdf:http://www.cell.com/article/S2666389922000514/pdf; doi:https://doi.org/10.1016/j.patter.2022.100471; html:https://europepmc.org/articles/PMC9122960; pdf:https://europepmc.org/articles/PMC9122960?pdf=render"
   },
   {
-    "id": "34474011",
-    "doi": "https://doi.org/10.1016/s0140-6736(21)01638-x",
-    "title": "Redefining \u03b2-blocker response in heart failure patients with sinus rhythm and atrial fibrillation: a machine learning cluster analysis.",
-    "authorString": "Karwath A, Bunting KV, Gill SK, Tica O, Pendleton S, Aziz F, Barsky AD, Chernbumroong S, Duan J, Mobley AR, Cardoso VR, Slater K, Williams JA, Bruce EJ, Wang X, Flather MD, Coats AJS, Gkoutos GV, Kotecha D, card AIc group and the Beta-blockers in Heart Failure Collaborative Group.",
+    "id": "31757986",
+    "doi": "https://doi.org/10.1038/s41598-019-53454-1",
+    "title": "Ontology-based prediction of cancer driver genes.",
+    "authorString": "Althubaiti S, Karwath A, Dallol A, Noor A, Alkhayyat SS, Alwassia R, Mineta K, Gojobori T, Beggs AD, Schofield PN, Gkoutos GV, Hoehndorf R.",
     "authorAffiliations": "",
-    "journalTitle": "Lancet (London, England)",
-    "pubYear": "2021",
-    "date": "2021-08-30",
+    "journalTitle": "Scientific reports",
+    "pubYear": "2019",
+    "date": "2019-11-22",
     "isOpenAccess": "Y",
     "keywords": "",
-    "nationalPriorities": "",
+    "nationalPriorities": "Applied Analytics",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Mortality remains unacceptably high in patients with heart failure and reduced left ventricular ejection fraction (LVEF) despite advances in therapeutics. We hypothesised that a novel artificial intelligence approach could better assess multiple and higher-dimension interactions of comorbidities, and define clusters of \u03b2-blocker efficacy in patients with sinus rhythm and atrial fibrillation.<h4>Methods</h4>Neural network-based variational autoencoders and hierarchical clustering were applied to pooled individual patient data from nine double-blind, randomised, placebo-controlled trials of \u03b2 blockers. All-cause mortality during median 1\u00b73 years of follow-up was assessed by intention to treat, stratified by electrocardiographic heart rhythm. The number of clusters and dimensions was determined objectively, with results validated using a leave-one-trial-out approach. This study was prospectively registered with ClinicalTrials.gov (NCT00832442) and the PROSPERO database of systematic reviews (CRD42014010012).<h4>Findings</h4>15\u2008659 patients with heart failure and LVEF of less than 50% were included, with median age 65 years (IQR 56-72) and LVEF 27% (IQR 21-33). 3708 (24%) patients were women. In sinus rhythm (n=12\u2008822), most clusters demonstrated a consistent overall mortality benefit from \u03b2 blockers, with odds ratios (ORs) ranging from 0\u00b754 to 0\u00b774. One cluster in sinus rhythm of older patients with less severe symptoms showed no significant efficacy (OR 0\u00b786, 95% CI 0\u00b767-1\u00b710; p=0\u00b722). In atrial fibrillation (n=2837), four of five clusters were consistent with the overall neutral effect of \u03b2 blockers versus placebo (OR 0\u00b792, 0\u00b777-1\u00b710; p=0\u00b737). One cluster of younger atrial fibrillation patients at lower mortality risk but similar LVEF to average had a statistically significant reduction in mortality with \u03b2 blockers (OR 0\u00b757, 0\u00b735-0\u00b793; p=0\u00b7023). The robustness and consistency of clustering was confirmed for all models (p<0\u00b70001 vs random), and cluster membership was externally validated across the nine independent trials.<h4>Interpretation</h4>An artificial intelligence-based clustering approach was able to distinguish prognostic response from \u03b2 blockers in patients with heart failure and reduced LVEF. This included patients in sinus rhythm with suboptimal efficacy, as well as a cluster of patients with atrial fibrillation where \u03b2 blockers did reduce mortality.<h4>Funding</h4>Medical Research Council, UK, and EU/EFPIA Innovative Medicines Initiative BigData@Heart.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/s0140-6736(21)01638-x; doi:https://doi.org/10.1016/S0140-6736(21)01638-X; html:https://europepmc.org/articles/PMC8542730; pdf:https://europepmc.org/articles/PMC8542730?pdf=render"
+    "abstract": "Identifying and distinguishing cancer driver genes among thousands of candidate mutations remains a major challenge. Accurate identification of driver genes and driver mutations is critical for advancing cancer research and personalizing treatment based on accurate stratification of patients. Due to inter-tumor genetic heterogeneity many driver mutations within a gene occur at low frequencies, which make it challenging to distinguish them from non-driver mutations. We have developed a novel method for identifying cancer driver genes. Our approach utilizes multiple complementary types of information, specifically cellular phenotypes, cellular locations, functions, and whole body physiological phenotypes as features. We demonstrate that our method can accurately identify known cancer driver genes and distinguish between their role in different types of cancer. In addition to confirming known driver genes, we identify several novel candidate driver genes. We demonstrate the utility of our method by validating its predictions in nasopharyngeal cancer and colorectal cancer using whole exome and whole genome sequencing.",
+    "laySummary": "This study investigated which genes encourage cancer tumors to grow. The study identifies genes and distinguishes their role in different types of cancers. Their method is validated using whole exome and whole genome sequencing",
+    "urls": "pdf:https://www.nature.com/articles/s41598-019-53454-1.pdf; doi:https://doi.org/10.1038/s41598-019-53454-1; html:https://europepmc.org/articles/PMC6874647; pdf:https://europepmc.org/articles/PMC6874647?pdf=render"
   },
   {
     "id": "37678881",
@@ -8585,38 +8585,21 @@
     "urls": "doi:https://doi.org/10.1093/ageing/afad157; html:https://europepmc.org/articles/PMC10484725; pdf:https://europepmc.org/articles/PMC10484725?pdf=render"
   },
   {
-    "id": "31757986",
-    "doi": "https://doi.org/10.1038/s41598-019-53454-1",
-    "title": "Ontology-based prediction of cancer driver genes.",
-    "authorString": "Althubaiti S, Karwath A, Dallol A, Noor A, Alkhayyat SS, Alwassia R, Mineta K, Gojobori T, Beggs AD, Schofield PN, Gkoutos GV, Hoehndorf R.",
+    "id": "34474011",
+    "doi": "https://doi.org/10.1016/s0140-6736(21)01638-x",
+    "title": "Redefining \u03b2-blocker response in heart failure patients with sinus rhythm and atrial fibrillation: a machine learning cluster analysis.",
+    "authorString": "Karwath A, Bunting KV, Gill SK, Tica O, Pendleton S, Aziz F, Barsky AD, Chernbumroong S, Duan J, Mobley AR, Cardoso VR, Slater K, Williams JA, Bruce EJ, Wang X, Flather MD, Coats AJS, Gkoutos GV, Kotecha D, card AIc group and the Beta-blockers in Heart Failure Collaborative Group.",
     "authorAffiliations": "",
-    "journalTitle": "Scientific reports",
-    "pubYear": "2019",
-    "date": "2019-11-22",
+    "journalTitle": "Lancet (London, England)",
+    "pubYear": "2021",
+    "date": "2021-08-30",
     "isOpenAccess": "Y",
     "keywords": "",
-    "nationalPriorities": "Applied Analytics",
-    "healthCategories": "",
-    "abstract": "Identifying and distinguishing cancer driver genes among thousands of candidate mutations remains a major challenge. Accurate identification of driver genes and driver mutations is critical for advancing cancer research and personalizing treatment based on accurate stratification of patients. Due to inter-tumor genetic heterogeneity many driver mutations within a gene occur at low frequencies, which make it challenging to distinguish them from non-driver mutations. We have developed a novel method for identifying cancer driver genes. Our approach utilizes multiple complementary types of information, specifically cellular phenotypes, cellular locations, functions, and whole body physiological phenotypes as features. We demonstrate that our method can accurately identify known cancer driver genes and distinguish between their role in different types of cancer. In addition to confirming known driver genes, we identify several novel candidate driver genes. We demonstrate the utility of our method by validating its predictions in nasopharyngeal cancer and colorectal cancer using whole exome and whole genome sequencing.",
-    "laySummary": "This study investigated which genes encourage cancer tumors to grow. The study identifies genes and distinguishes their role in different types of cancers. Their method is validated using whole exome and whole genome sequencing",
-    "urls": "pdf:https://www.nature.com/articles/s41598-019-53454-1.pdf; doi:https://doi.org/10.1038/s41598-019-53454-1; html:https://europepmc.org/articles/PMC6874647; pdf:https://europepmc.org/articles/PMC6874647?pdf=render"
-  },
-  {
-    "id": "37536152",
-    "doi": "https://doi.org/10.1016/j.seizure.2023.07.016",
-    "title": "Association of comorbid-socioeconomic clusters with mortality in late onset epilepsy derived through unsupervised machine learning.",
-    "authorString": "Josephson CB, Gonzalez-Izquierdo A, Engbers JDT, Denaxas S, Delgado-Garcia G, Sajobi TT, Wang M, Keezer MR, Wiebe S.",
-    "authorAffiliations": "",
-    "journalTitle": "Seizure",
-    "pubYear": "2023",
-    "date": "2023-07-29",
-    "isOpenAccess": "N",
-    "keywords": "Epilepsy; Elderly; Cohort study; Electronic Health Records; Unsupervised Machine Learning; Late-onset Epilepsy",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background and objectives</h4>Late-onset epilepsy is a heterogenous entity associated with specific aetiologies and an elevated risk of premature mortality. Specific multimorbid-socioeconomic profiles and their unique prognostic trajectories have not been described. We sought to determine if specific clusters of late onset epilepsy exist, and whether they have unique hazards of premature mortality.<h4>Methods</h4>We performed a retrospective observational cohort study linking primary and hospital-based UK electronic health records with vital statistics data (covering years 1998-2019) to identify all cases of incident late onset epilepsy (from people aged \u226565) and 1:10 age, sex, and GP practice-matched controls. We applied hierarchical agglomerative clustering using common aetiologies identified at baseline to define multimorbid-socioeconomic profiles, compare hazards of early mortality, and tabulating causes of death stratified by cluster.<h4>Results</h4>From 1,032,129 people aged \u226565, we identified 1048 cases of late onset epilepsy who were matched to 10,259 controls. Median age at epilepsy diagnosis was 68 (interquartile range: 66-72) and 474 (45%) were female. The hazard of premature mortality related to late-onset epilepsy was higher than matched controls (hazard ratio [HR] 1.73; 95% confidence interval [95%CI] 1.51-1.99). Ten unique phenotypic clusters were identified, defined by 'healthy' males and females, ischaemic stroke, intracerebral haemorrhage (ICH), ICH and alcohol misuse, dementia and anxiety, anxiety, depression in males and females, and brain tumours. Cluster-specific hazards were often similar to that derived for late-onset epilepsy as a whole. Clusters that differed significantly from the base late-onset epilepsy hazard were 'dementia and anxiety' (HR 5.36; 95%CI 3.31-8.68), 'brain tumour' (HR 4.97; 95%CI 2.89-8.56), 'ICH and alcohol misuse' (HR 2.91; 95%CI 1.76-4.81), and 'ischaemic stroke' (HR 2.83; 95%CI 1.83-4.04). These cluster-specific risks were also elevated compared to those derived for tumours, dementia, ischaemic stroke, and ICH in the whole population. Seizure-related cause of death was uncommon and restricted to the ICH, ICH and alcohol misuse, and healthy female clusters.<h4>Significance</h4>Late-onset epilepsy is an amalgam of unique phenotypic clusters that can be quantitatively defined. Late-onset epilepsy and cluster-specific comorbid profiles have complex effects on premature mortality above and beyond the base rates attributed to epilepsy and cluster-defining comorbidities alone.",
+    "abstract": "<h4>Background</h4>Mortality remains unacceptably high in patients with heart failure and reduced left ventricular ejection fraction (LVEF) despite advances in therapeutics. We hypothesised that a novel artificial intelligence approach could better assess multiple and higher-dimension interactions of comorbidities, and define clusters of \u03b2-blocker efficacy in patients with sinus rhythm and atrial fibrillation.<h4>Methods</h4>Neural network-based variational autoencoders and hierarchical clustering were applied to pooled individual patient data from nine double-blind, randomised, placebo-controlled trials of \u03b2 blockers. All-cause mortality during median 1\u00b73 years of follow-up was assessed by intention to treat, stratified by electrocardiographic heart rhythm. The number of clusters and dimensions was determined objectively, with results validated using a leave-one-trial-out approach. This study was prospectively registered with ClinicalTrials.gov (NCT00832442) and the PROSPERO database of systematic reviews (CRD42014010012).<h4>Findings</h4>15\u2008659 patients with heart failure and LVEF of less than 50% were included, with median age 65 years (IQR 56-72) and LVEF 27% (IQR 21-33). 3708 (24%) patients were women. In sinus rhythm (n=12\u2008822), most clusters demonstrated a consistent overall mortality benefit from \u03b2 blockers, with odds ratios (ORs) ranging from 0\u00b754 to 0\u00b774. One cluster in sinus rhythm of older patients with less severe symptoms showed no significant efficacy (OR 0\u00b786, 95% CI 0\u00b767-1\u00b710; p=0\u00b722). In atrial fibrillation (n=2837), four of five clusters were consistent with the overall neutral effect of \u03b2 blockers versus placebo (OR 0\u00b792, 0\u00b777-1\u00b710; p=0\u00b737). One cluster of younger atrial fibrillation patients at lower mortality risk but similar LVEF to average had a statistically significant reduction in mortality with \u03b2 blockers (OR 0\u00b757, 0\u00b735-0\u00b793; p=0\u00b7023). The robustness and consistency of clustering was confirmed for all models (p<0\u00b70001 vs random), and cluster membership was externally validated across the nine independent trials.<h4>Interpretation</h4>An artificial intelligence-based clustering approach was able to distinguish prognostic response from \u03b2 blockers in patients with heart failure and reduced LVEF. This included patients in sinus rhythm with suboptimal efficacy, as well as a cluster of patients with atrial fibrillation where \u03b2 blockers did reduce mortality.<h4>Funding</h4>Medical Research Council, UK, and EU/EFPIA Innovative Medicines Initiative BigData@Heart.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.seizure.2023.07.016"
+    "urls": "doi:https://doi.org/10.1016/s0140-6736(21)01638-x; doi:https://doi.org/10.1016/S0140-6736(21)01638-X; html:https://europepmc.org/articles/PMC8542730; pdf:https://europepmc.org/articles/PMC8542730?pdf=render"
   },
   {
     "id": "36333839",
@@ -8636,21 +8619,21 @@
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/gps.5834; doi:https://doi.org/10.1002/gps.5834; html:https://europepmc.org/articles/PMC9828419; pdf:https://europepmc.org/articles/PMC9828419?pdf=render"
   },
   {
-    "id": "36755846",
-    "doi": "https://doi.org/10.1093/ckj/sfac241",
-    "title": "Depression is associated with frailty and lower quality of life in haemodialysis recipients, but not with mortality or hospitalization.",
-    "authorString": "Anderson BM, Qasim M, Correa G, Evison F, Gallier S, Ferro CJ, Jackson TA, Sharif A.",
+    "id": "37536152",
+    "doi": "https://doi.org/10.1016/j.seizure.2023.07.016",
+    "title": "Association of comorbid-socioeconomic clusters with mortality in late onset epilepsy derived through unsupervised machine learning.",
+    "authorString": "Josephson CB, Gonzalez-Izquierdo A, Engbers JDT, Denaxas S, Delgado-Garcia G, Sajobi TT, Wang M, Keezer MR, Wiebe S.",
     "authorAffiliations": "",
-    "journalTitle": "Clinical kidney journal",
+    "journalTitle": "Seizure",
     "pubYear": "2023",
-    "date": "2022-10-31",
-    "isOpenAccess": "Y",
-    "keywords": "Mortality; Depression; Frailty; Haemodialysis; Hospitalization; Health-related Quality Of Life",
+    "date": "2023-07-29",
+    "isOpenAccess": "N",
+    "keywords": "Epilepsy; Elderly; Cohort study; Electronic Health Records; Unsupervised Machine Learning; Late-onset Epilepsy",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Frailty and depression are highly prevalent in haemodialysis recipients, exhibit a reciprocal relationship, and are associated with increased mortality and hospitalization, and lower quality of life. Despite this, there has been little exploration of the relationship between depression and frailty upon patient outcomes. We aimed to explore the relationship between depression and frailty, and their associations with mortality, hospitalization and quality of life.<h4>Methods</h4>We performed a prospective cohort study of prevalent haemodialysis recipients linked to national datasets for outcomes including mortality and hospitalization. Depression was assessed using the Patient Health Questionnaire-9 (PHQ-9), frailty using the Clinical Frailty Scale (CFS) and quality of life using the EuroQol 5-Dimension (EQ-5D) Summary Index.<h4>Results</h4>A total of 485 prevalent haemodialysis recipients were recruited, with 111 deaths and 1241 hospitalizations during follow-up. CFS was independently associated with mortality [hazard ratio (HR) 1.31; 95% confidence interval (CI) 1.08, 1.59; <i>P</i>\u00a0=\u00a0.006], hospitalization [incidence rate ratio (IRR) 1.13; 95% CI 1.03, 1.25; <i>P</i>\u00a0=\u00a0.010] and lower quality of life (Coef. -0.401; 95% CI -0.511, -0.292; <i>P</i>\u00a0<\u00a0.001). PHQ-9 score was independently associated with lower quality of life (Coef. -0.042; 95% CI -0.063, -0.021; <i>P</i>\u00a0<\u00a0.001), but not mortality (HR 1.00; 95% CI 0.96, 1.04; <i>P</i>\u00a0=\u00a0.901) or hospitalization (IRR 0.99; 95% CI 0.97, 1.01; <i>P</i>\u00a0=\u00a0.351). In an adjusted model including CFS, moderate depression was associated with reduced hospitalization (IRR 0.72; 95% CI 0.56, 0.93; <i>P</i>\u00a0=\u00a0.013).<h4>Conclusions</h4>With the addition of frailty, depression was associated with lower hospital admissions, but poorer quality of life. The relationship between frailty and depression, and their influence on outcomes is complex, requiring further study.",
+    "abstract": "<h4>Background and objectives</h4>Late-onset epilepsy is a heterogenous entity associated with specific aetiologies and an elevated risk of premature mortality. Specific multimorbid-socioeconomic profiles and their unique prognostic trajectories have not been described. We sought to determine if specific clusters of late onset epilepsy exist, and whether they have unique hazards of premature mortality.<h4>Methods</h4>We performed a retrospective observational cohort study linking primary and hospital-based UK electronic health records with vital statistics data (covering years 1998-2019) to identify all cases of incident late onset epilepsy (from people aged \u226565) and 1:10 age, sex, and GP practice-matched controls. We applied hierarchical agglomerative clustering using common aetiologies identified at baseline to define multimorbid-socioeconomic profiles, compare hazards of early mortality, and tabulating causes of death stratified by cluster.<h4>Results</h4>From 1,032,129 people aged \u226565, we identified 1048 cases of late onset epilepsy who were matched to 10,259 controls. Median age at epilepsy diagnosis was 68 (interquartile range: 66-72) and 474 (45%) were female. The hazard of premature mortality related to late-onset epilepsy was higher than matched controls (hazard ratio [HR] 1.73; 95% confidence interval [95%CI] 1.51-1.99). Ten unique phenotypic clusters were identified, defined by 'healthy' males and females, ischaemic stroke, intracerebral haemorrhage (ICH), ICH and alcohol misuse, dementia and anxiety, anxiety, depression in males and females, and brain tumours. Cluster-specific hazards were often similar to that derived for late-onset epilepsy as a whole. Clusters that differed significantly from the base late-onset epilepsy hazard were 'dementia and anxiety' (HR 5.36; 95%CI 3.31-8.68), 'brain tumour' (HR 4.97; 95%CI 2.89-8.56), 'ICH and alcohol misuse' (HR 2.91; 95%CI 1.76-4.81), and 'ischaemic stroke' (HR 2.83; 95%CI 1.83-4.04). These cluster-specific risks were also elevated compared to those derived for tumours, dementia, ischaemic stroke, and ICH in the whole population. Seizure-related cause of death was uncommon and restricted to the ICH, ICH and alcohol misuse, and healthy female clusters.<h4>Significance</h4>Late-onset epilepsy is an amalgam of unique phenotypic clusters that can be quantitatively defined. Late-onset epilepsy and cluster-specific comorbid profiles have complex effects on premature mortality above and beyond the base rates attributed to epilepsy and cluster-defining comorbidities alone.",
     "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/ckj/article-pdf/16/2/342/49100412/sfac241.pdf; doi:https://doi.org/10.1093/ckj/sfac241; html:https://europepmc.org/articles/PMC9900564; pdf:https://europepmc.org/articles/PMC9900564?pdf=render"
+    "urls": "doi:https://doi.org/10.1016/j.seizure.2023.07.016"
   },
   {
     "id": "36544046",
@@ -8670,21 +8653,21 @@
     "urls": "pdf:https://www.nature.com/articles/s41746-022-00730-6.pdf; doi:https://doi.org/10.1038/s41746-022-00730-6; html:https://europepmc.org/articles/PMC9770568; pdf:https://europepmc.org/articles/PMC9770568?pdf=render"
   },
   {
-    "id": "37528841",
-    "doi": "https://doi.org/10.1016/j.eclinm.2023.102064",
-    "title": "Repeated antibiotic exposure and risk of hospitalisation and death following COVID-19 infection (OpenSAFELY): a matched case-control study.",
-    "authorString": "Yang YT, Wong D, Ashcroft DM, Massey J, MacKenna B, Fisher L, Mehrkar A, Bacon SC, OpenSAFELY collaborative, Hand K, Zhong X, Fahmi A, Goldacre B, van Staa T, Palin V.",
+    "id": "36755846",
+    "doi": "https://doi.org/10.1093/ckj/sfac241",
+    "title": "Depression is associated with frailty and lower quality of life in haemodialysis recipients, but not with mortality or hospitalization.",
+    "authorString": "Anderson BM, Qasim M, Correa G, Evison F, Gallier S, Ferro CJ, Jackson TA, Sharif A.",
     "authorAffiliations": "",
-    "journalTitle": "EClinicalMedicine",
+    "journalTitle": "Clinical kidney journal",
     "pubYear": "2023",
-    "date": "2023-07-05",
+    "date": "2022-10-31",
     "isOpenAccess": "Y",
-    "keywords": "Antibiotics; Primary Care; Severe Outcome; Covid-19",
+    "keywords": "Mortality; Depression; Frailty; Haemodialysis; Hospitalization; Health-related Quality Of Life",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Identifying potential risk factors related to severe COVID-19 outcomes is important. Repeated intermittent antibiotic use is known be associated with adverse outcomes. This study aims to examine whether prior frequent antibiotic exposure is associated with severe COVID-19 outcomes.<h4>Methods</h4>With the approval of NHS England, we used the OpenSAFELY platform, which integrated primary and secondary care, COVID-19 test, and death registration data. This matched case-control study included 0.67 million patients (aged 18-110 years) from an eligible 2.47 million patients with incident COVID-19 by matching with replacement. Inclusion criteria included registration within one general practice for at least 3 years and infection with incident COVID-19. Cases were identified according to different severity of COVID-19 outcomes. Cases and eligible controls were 1:6 matched on age, sex, region of GP practice, and index year and month of COVID-19 infection. Five quintile groups, based on the number of previous 3-year antibiotic prescriptions, were created to indicate the frequency of prior antibiotic exposure. Conditional logistic regression used to compare the differences between case and control groups, adjusting for ethnicity, body mass index, comorbidities, vaccination history, deprivation, and care home status. Sensitivity analyses were done to explore potential confounding and the effects of missing data.<h4>Findings</h4>Based on our inclusion criteria, between February 1, 2020 and December 31, 2021, 98,420 patients were admitted to hospitals and 22,660 died. 55 unique antibiotics were prescribed. A dose-response relationship between number of antibiotic prescriptions and risk of severe COVID-19 outcome was observed. Patients in the highest quintile with history of prior antibiotic exposure had 1.80 times greater odds of hospitalisation compared to patients without antibiotic exposure (adjusted odds ratio [OR] 1.80, 95% Confidence Interval [CI] 1.75-1.84). Similarly, the adjusted OR for hospitalised patients with death outcomes was 1.34 (95% CI 1.28-1.41). Larger number of prior antibiotic type was also associated with more severe COVID-19 related hospital admission. The adjusted OR of quintile 5 exposure (the most frequent) with more than 3 antibiotic types was around 2 times larger than quintile 1 (only 1 type; OR 1.80, 95% CI 1.75-1.84 vs. OR 1.03, 95% CI 1.01-1.05).<h4>Interpretation</h4>Our observational study has provided evidence that antibiotic exposure frequency and diversity may be associated with COVID-19 severity, potentially suggesting adverse effects of repeated intermittent antibiotic use. Future work could work to elucidate causal links and potential mechanisms. Antibiotic stewardship should put more emphasis on long-term antibiotic exposure and its adverse outcome to increase the awareness of appropriate antibiotics use.<h4>Funding</h4>Health Data Research UK and National Institute for Health Research.",
+    "abstract": "<h4>Background</h4>Frailty and depression are highly prevalent in haemodialysis recipients, exhibit a reciprocal relationship, and are associated with increased mortality and hospitalization, and lower quality of life. Despite this, there has been little exploration of the relationship between depression and frailty upon patient outcomes. We aimed to explore the relationship between depression and frailty, and their associations with mortality, hospitalization and quality of life.<h4>Methods</h4>We performed a prospective cohort study of prevalent haemodialysis recipients linked to national datasets for outcomes including mortality and hospitalization. Depression was assessed using the Patient Health Questionnaire-9 (PHQ-9), frailty using the Clinical Frailty Scale (CFS) and quality of life using the EuroQol 5-Dimension (EQ-5D) Summary Index.<h4>Results</h4>A total of 485 prevalent haemodialysis recipients were recruited, with 111 deaths and 1241 hospitalizations during follow-up. CFS was independently associated with mortality [hazard ratio (HR) 1.31; 95% confidence interval (CI) 1.08, 1.59; <i>P</i>\u00a0=\u00a0.006], hospitalization [incidence rate ratio (IRR) 1.13; 95% CI 1.03, 1.25; <i>P</i>\u00a0=\u00a0.010] and lower quality of life (Coef. -0.401; 95% CI -0.511, -0.292; <i>P</i>\u00a0<\u00a0.001). PHQ-9 score was independently associated with lower quality of life (Coef. -0.042; 95% CI -0.063, -0.021; <i>P</i>\u00a0<\u00a0.001), but not mortality (HR 1.00; 95% CI 0.96, 1.04; <i>P</i>\u00a0=\u00a0.901) or hospitalization (IRR 0.99; 95% CI 0.97, 1.01; <i>P</i>\u00a0=\u00a0.351). In an adjusted model including CFS, moderate depression was associated with reduced hospitalization (IRR 0.72; 95% CI 0.56, 0.93; <i>P</i>\u00a0=\u00a0.013).<h4>Conclusions</h4>With the addition of frailty, depression was associated with lower hospital admissions, but poorer quality of life. The relationship between frailty and depression, and their influence on outcomes is complex, requiring further study.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.eclinm.2023.102064; html:https://europepmc.org/articles/PMC10388579; pdf:https://europepmc.org/articles/PMC10388579?pdf=render"
+    "urls": "pdf:https://academic.oup.com/ckj/article-pdf/16/2/342/49100412/sfac241.pdf; doi:https://doi.org/10.1093/ckj/sfac241; html:https://europepmc.org/articles/PMC9900564; pdf:https://europepmc.org/articles/PMC9900564?pdf=render"
   },
   {
     "id": "37046692",
@@ -8703,6 +8686,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.mdpi.com/2072-6694/15/7/2031/pdf?version=1680080044; doi:https://doi.org/10.3390/cancers15072031; html:https://europepmc.org/articles/PMC10093616; pdf:https://europepmc.org/articles/PMC10093616?pdf=render"
   },
+  {
+    "id": "37528841",
+    "doi": "https://doi.org/10.1016/j.eclinm.2023.102064",
+    "title": "Repeated antibiotic exposure and risk of hospitalisation and death following COVID-19 infection (OpenSAFELY): a matched case-control study.",
+    "authorString": "Yang YT, Wong D, Ashcroft DM, Massey J, MacKenna B, Fisher L, Mehrkar A, Bacon SC, OpenSAFELY collaborative, Hand K, Zhong X, Fahmi A, Goldacre B, van Staa T, Palin V.",
+    "authorAffiliations": "",
+    "journalTitle": "EClinicalMedicine",
+    "pubYear": "2023",
+    "date": "2023-07-05",
+    "isOpenAccess": "Y",
+    "keywords": "Antibiotics; Primary Care; Severe Outcome; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Identifying potential risk factors related to severe COVID-19 outcomes is important. Repeated intermittent antibiotic use is known be associated with adverse outcomes. This study aims to examine whether prior frequent antibiotic exposure is associated with severe COVID-19 outcomes.<h4>Methods</h4>With the approval of NHS England, we used the OpenSAFELY platform, which integrated primary and secondary care, COVID-19 test, and death registration data. This matched case-control study included 0.67 million patients (aged 18-110 years) from an eligible 2.47 million patients with incident COVID-19 by matching with replacement. Inclusion criteria included registration within one general practice for at least 3 years and infection with incident COVID-19. Cases were identified according to different severity of COVID-19 outcomes. Cases and eligible controls were 1:6 matched on age, sex, region of GP practice, and index year and month of COVID-19 infection. Five quintile groups, based on the number of previous 3-year antibiotic prescriptions, were created to indicate the frequency of prior antibiotic exposure. Conditional logistic regression used to compare the differences between case and control groups, adjusting for ethnicity, body mass index, comorbidities, vaccination history, deprivation, and care home status. Sensitivity analyses were done to explore potential confounding and the effects of missing data.<h4>Findings</h4>Based on our inclusion criteria, between February 1, 2020 and December 31, 2021, 98,420 patients were admitted to hospitals and 22,660 died. 55 unique antibiotics were prescribed. A dose-response relationship between number of antibiotic prescriptions and risk of severe COVID-19 outcome was observed. Patients in the highest quintile with history of prior antibiotic exposure had 1.80 times greater odds of hospitalisation compared to patients without antibiotic exposure (adjusted odds ratio [OR] 1.80, 95% Confidence Interval [CI] 1.75-1.84). Similarly, the adjusted OR for hospitalised patients with death outcomes was 1.34 (95% CI 1.28-1.41). Larger number of prior antibiotic type was also associated with more severe COVID-19 related hospital admission. The adjusted OR of quintile 5 exposure (the most frequent) with more than 3 antibiotic types was around 2 times larger than quintile 1 (only 1 type; OR 1.80, 95% CI 1.75-1.84 vs. OR 1.03, 95% CI 1.01-1.05).<h4>Interpretation</h4>Our observational study has provided evidence that antibiotic exposure frequency and diversity may be associated with COVID-19 severity, potentially suggesting adverse effects of repeated intermittent antibiotic use. Future work could work to elucidate causal links and potential mechanisms. Antibiotic stewardship should put more emphasis on long-term antibiotic exposure and its adverse outcome to increase the awareness of appropriate antibiotics use.<h4>Funding</h4>Health Data Research UK and National Institute for Health Research.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.eclinm.2023.102064; html:https://europepmc.org/articles/PMC10388579; pdf:https://europepmc.org/articles/PMC10388579?pdf=render"
+  },
   {
     "id": "39145098",
     "doi": "https://doi.org/10.3310/nihropenres.13530.1",
@@ -8720,23 +8720,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.3310/nihropenres.13530.1; html:https://europepmc.org/articles/PMC11319897; pdf:https://europepmc.org/articles/PMC11319897?pdf=render"
   },
-  {
-    "id": "32946449",
-    "doi": "https://doi.org/10.1371/journal.pone.0237676",
-    "title": "Proton pump inhibitors and dementia risk: Evidence from a cohort study using linked routinely collected national health data in Wales, UK.",
-    "authorString": "Cooksey R, Kennedy J, Dennis MS, Escott-Price V, Lyons RA, Seaborne M, Brophy S.",
-    "authorAffiliations": "",
-    "journalTitle": "PloS one",
-    "pubYear": "2020",
-    "date": "2020-09-18",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objectives</h4>Proton pump inhibitors (PPIs) are commonly prescribed for prevention and treatment of gastrointestinal conditions or for gastroprotection from other drugs. Research suggests they are linked to increased dementia risk. We use linked national health data to examine the association between PPI use and the development of incident dementia.<h4>Methods and findings</h4>A population-based study using electronic health-data from the Secure Anonymised Information Linkage (SAIL) Databank, Wales (UK) from 1999 to 2015. Of data available on 3,765,744 individuals, a cohort who had ever been prescribed a PPI was developed (n = 183,968) for people aged 55 years and over and compared to non-PPI exposed individuals (131,110). Those with prior dementia, mild-cognitive-impairment or delirium codes were excluded. Confounding factors included comorbidities and/or drugs associated with them. Comorbidities might include head injury and some examples of medications include antidepressants, antiplatelets and anticoagulants. These commonly prescribed drugs were investigated as it was not feasible to explore all drugs in this study. The main outcome was a diagnosis of incident dementia. Cox proportional hazard regression modelling was used to calculate the Hazard ratio (HR) of developing dementia in PPI-exposed compared to unexposed individuals while controlling for potential confounders. The mean age of the PPI exposed individuals was 69.9 years and 39.8% male while the mean age of the unexposed individuals was 72.1 years and 41.1% male. The rate of PPI usage was 58.4% (183,968) and incident dementia rate was 11.8% (37,148/315,078). PPI use was associated with decreased dementia risk (HR: 0.67, 95% CI: 0.65 to 0.67, p<0.01).<h4>Conclusions</h4>This study, using large-scale, multi-centre health-data was unable to confirm an association between PPI use and increased dementia risk. Previously reported links may be associated with confounders of people using PPI's, such as increased risk of cardiovascular disease and/or depression and their associated medications which may be responsible for any increased risk of developing dementia.",
-    "laySummary": "",
-    "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0237676&type=printable; doi:https://doi.org/10.1371/journal.pone.0237676; html:https://europepmc.org/articles/PMC7500586; pdf:https://europepmc.org/articles/PMC7500586?pdf=render"
-  },
   {
     "id": "34089614",
     "doi": "https://doi.org/10.1093/ije/dyab028",
@@ -8755,21 +8738,21 @@
     "urls": "pdf:https://academic.oup.com/ije/article-pdf/50/4/1064/40146583/dyab028.pdf; doi:https://doi.org/10.1093/ije/dyab028; html:https://europepmc.org/articles/PMC8195245; pdf:https://europepmc.org/articles/PMC8195245?pdf=render; doi:https://doi.org/10.1093/ije/dyab028"
   },
   {
-    "id": "36992188",
-    "doi": "https://doi.org/10.3390/vaccines11030604",
-    "title": "Household Composition and Inequalities in COVID-19 Vaccination in Wales, UK.",
-    "authorString": "Lench A, Perry M, Johnson RD, Fry R, Richardson G, Lyons RA, Akbari A, Edwards A, Collins B, Joseph-Williams N, Cooper A, Cottrell S.",
+    "id": "32946449",
+    "doi": "https://doi.org/10.1371/journal.pone.0237676",
+    "title": "Proton pump inhibitors and dementia risk: Evidence from a cohort study using linked routinely collected national health data in Wales, UK.",
+    "authorString": "Cooksey R, Kennedy J, Dennis MS, Escott-Price V, Lyons RA, Seaborne M, Brophy S.",
     "authorAffiliations": "",
-    "journalTitle": "Vaccines",
-    "pubYear": "2023",
-    "date": "2023-03-07",
+    "journalTitle": "PloS one",
+    "pubYear": "2020",
+    "date": "2020-09-18",
     "isOpenAccess": "Y",
-    "keywords": "Vaccines; Vaccination; Households; Inequalities; Immunisation; Household Composition; Inequities; Covid-19",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "The uptake of COVID-19 vaccination in Wales is high at a population level but many inequalities exist. Household composition may be an important factor in COVID-19 vaccination uptake due to the practical, social, and psychological implications associated with different living arrangements. In this study, the role of household composition in the uptake of COVID-19 vaccination in Wales was examined with the aim of identifying areas for intervention to address inequalities. Records within the Wales Immunisation System (WIS) COVID-19 vaccination register were linked to the Welsh Demographic Service Dataset (WDSD; a population register for Wales) held within the Secure Anonymised Information Linkage (SAIL) databank. Eight household types were defined based on household size, the presence or absence of children, and the presence of single or multiple generations. Uptake of the second dose of any COVID-19 vaccine was analysed using logistic regression. Gender, age group, health board, rural/urban residential classification, ethnic group, and deprivation quintile were included as covariates for multivariable regression. Compared to two-adult households, all other household types were associated with lower uptake. The most significantly reduced uptake was observed for large, multigenerational, adult group households (aOR 0.45, 95%CI 0.43-0.46). Comparing multivariable regression with and without incorporation of household composition as a variable produced significant differences in odds of vaccination for health board, age group, and ethnic group categories. These results indicate that household composition is an important factor for the uptake of COVID-19 vaccination and consideration of differences in household composition is necessary to mitigate vaccination inequalities.",
+    "abstract": "<h4>Objectives</h4>Proton pump inhibitors (PPIs) are commonly prescribed for prevention and treatment of gastrointestinal conditions or for gastroprotection from other drugs. Research suggests they are linked to increased dementia risk. We use linked national health data to examine the association between PPI use and the development of incident dementia.<h4>Methods and findings</h4>A population-based study using electronic health-data from the Secure Anonymised Information Linkage (SAIL) Databank, Wales (UK) from 1999 to 2015. Of data available on 3,765,744 individuals, a cohort who had ever been prescribed a PPI was developed (n = 183,968) for people aged 55 years and over and compared to non-PPI exposed individuals (131,110). Those with prior dementia, mild-cognitive-impairment or delirium codes were excluded. Confounding factors included comorbidities and/or drugs associated with them. Comorbidities might include head injury and some examples of medications include antidepressants, antiplatelets and anticoagulants. These commonly prescribed drugs were investigated as it was not feasible to explore all drugs in this study. The main outcome was a diagnosis of incident dementia. Cox proportional hazard regression modelling was used to calculate the Hazard ratio (HR) of developing dementia in PPI-exposed compared to unexposed individuals while controlling for potential confounders. The mean age of the PPI exposed individuals was 69.9 years and 39.8% male while the mean age of the unexposed individuals was 72.1 years and 41.1% male. The rate of PPI usage was 58.4% (183,968) and incident dementia rate was 11.8% (37,148/315,078). PPI use was associated with decreased dementia risk (HR: 0.67, 95% CI: 0.65 to 0.67, p<0.01).<h4>Conclusions</h4>This study, using large-scale, multi-centre health-data was unable to confirm an association between PPI use and increased dementia risk. Previously reported links may be associated with confounders of people using PPI's, such as increased risk of cardiovascular disease and/or depression and their associated medications which may be responsible for any increased risk of developing dementia.",
     "laySummary": "",
-    "urls": "pdf:https://www.mdpi.com/2076-393X/11/3/604/pdf?version=1678670919; doi:https://doi.org/10.3390/vaccines11030604; html:https://europepmc.org/articles/PMC10055803; pdf:https://europepmc.org/articles/PMC10055803?pdf=render"
+    "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0237676&type=printable; doi:https://doi.org/10.1371/journal.pone.0237676; html:https://europepmc.org/articles/PMC7500586; pdf:https://europepmc.org/articles/PMC7500586?pdf=render"
   },
   {
     "id": "33240522",
@@ -8788,6 +8771,23 @@
     "laySummary": "",
     "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/2055207620965046; doi:https://doi.org/10.1177/2055207620965046; html:https://europepmc.org/articles/PMC7675911; pdf:https://europepmc.org/articles/PMC7675911?pdf=render"
   },
+  {
+    "id": "36992188",
+    "doi": "https://doi.org/10.3390/vaccines11030604",
+    "title": "Household Composition and Inequalities in COVID-19 Vaccination in Wales, UK.",
+    "authorString": "Lench A, Perry M, Johnson RD, Fry R, Richardson G, Lyons RA, Akbari A, Edwards A, Collins B, Joseph-Williams N, Cooper A, Cottrell S.",
+    "authorAffiliations": "",
+    "journalTitle": "Vaccines",
+    "pubYear": "2023",
+    "date": "2023-03-07",
+    "isOpenAccess": "Y",
+    "keywords": "Vaccines; Vaccination; Households; Inequalities; Immunisation; Household Composition; Inequities; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The uptake of COVID-19 vaccination in Wales is high at a population level but many inequalities exist. Household composition may be an important factor in COVID-19 vaccination uptake due to the practical, social, and psychological implications associated with different living arrangements. In this study, the role of household composition in the uptake of COVID-19 vaccination in Wales was examined with the aim of identifying areas for intervention to address inequalities. Records within the Wales Immunisation System (WIS) COVID-19 vaccination register were linked to the Welsh Demographic Service Dataset (WDSD; a population register for Wales) held within the Secure Anonymised Information Linkage (SAIL) databank. Eight household types were defined based on household size, the presence or absence of children, and the presence of single or multiple generations. Uptake of the second dose of any COVID-19 vaccine was analysed using logistic regression. Gender, age group, health board, rural/urban residential classification, ethnic group, and deprivation quintile were included as covariates for multivariable regression. Compared to two-adult households, all other household types were associated with lower uptake. The most significantly reduced uptake was observed for large, multigenerational, adult group households (aOR 0.45, 95%CI 0.43-0.46). Comparing multivariable regression with and without incorporation of household composition as a variable produced significant differences in odds of vaccination for health board, age group, and ethnic group categories. These results indicate that household composition is an important factor for the uptake of COVID-19 vaccination and consideration of differences in household composition is necessary to mitigate vaccination inequalities.",
+    "laySummary": "",
+    "urls": "pdf:https://www.mdpi.com/2076-393X/11/3/604/pdf?version=1678670919; doi:https://doi.org/10.3390/vaccines11030604; html:https://europepmc.org/articles/PMC10055803; pdf:https://europepmc.org/articles/PMC10055803?pdf=render"
+  },
   {
     "id": "38269898",
     "doi": "https://doi.org/10.3233/shti231054",
@@ -8822,23 +8822,6 @@
     "laySummary": "",
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s40258-022-00777-2.pdf; doi:https://doi.org/10.1007/s40258-022-00777-2; html:https://europepmc.org/articles/PMC9760184; pdf:https://europepmc.org/articles/PMC9760184?pdf=render"
   },
-  {
-    "id": "37558806",
-    "doi": "https://doi.org/10.1038/s41598-023-40215-4",
-    "title": "Associations of the serotonin transporter gene polymorphism, 5-HTTLPR, and adverse life events with late life depression in the elderly Lithuanian population.",
-    "authorString": "Simonyte S, Grabauskyte I, Macijauskiene J, Lesauskaite V, Lesauskaite V, Kvaal KS, Stewart R.",
-    "authorAffiliations": "",
-    "journalTitle": "Scientific reports",
-    "pubYear": "2023",
-    "date": "2023-08-09",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Late-life depression (LLD) is a multifactorial disorder, with susceptibility and vulnerability potentially influenced by gene-environment interaction. The aim of this study was to investigate whether the 5-HTTLPR polymorphism is associated with LLD. The sample of 353 participants aged 65\u00a0years and over was randomly selected from the list of Kaunas city inhabitants by Residents' Register Service of Lithuania. Depressive symptoms were ascertained using the EURO-D scale. The List of Threatening Events Questionnaire was used to identify stressful life events that happened over the last 6\u00a0months and during lifetime. A 5-HTTLPR and lifetime stressful events interaction was indicated by higher odds of depression in those with s/s genotype who experienced high stress compared to l/l carriers with low or medium stress, while 5-HTTLPR and current stressful events interaction analysis revealed that carriers of either one or two copies of the s allele had increased odds of depressive symptoms associated with stress compared to participants with the l/l genotype not exposed to stressful situations. Although no significant direct association was found between the 5-HTTLPR short allele and depression, our findings demonstrated that lifetime or current stressful life events and their modification by 5-HTTLPR genotype are risk factors for late-life depression.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41598-023-40215-4.pdf; doi:https://doi.org/10.1038/s41598-023-40215-4; html:https://europepmc.org/articles/PMC10412533; pdf:https://europepmc.org/articles/PMC10412533?pdf=render"
-  },
   {
     "id": "34582457",
     "doi": "https://doi.org/10.1371/journal.pmed.1003777",
@@ -8856,6 +8839,23 @@
     "laySummary": "",
     "urls": "pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003777&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003777; html:https://europepmc.org/articles/PMC8478234; pdf:https://europepmc.org/articles/PMC8478234?pdf=render"
   },
+  {
+    "id": "37558806",
+    "doi": "https://doi.org/10.1038/s41598-023-40215-4",
+    "title": "Associations of the serotonin transporter gene polymorphism, 5-HTTLPR, and adverse life events with late life depression in the elderly Lithuanian population.",
+    "authorString": "Simonyte S, Grabauskyte I, Macijauskiene J, Lesauskaite V, Lesauskaite V, Kvaal KS, Stewart R.",
+    "authorAffiliations": "",
+    "journalTitle": "Scientific reports",
+    "pubYear": "2023",
+    "date": "2023-08-09",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Late-life depression (LLD) is a multifactorial disorder, with susceptibility and vulnerability potentially influenced by gene-environment interaction. The aim of this study was to investigate whether the 5-HTTLPR polymorphism is associated with LLD. The sample of 353 participants aged 65\u00a0years and over was randomly selected from the list of Kaunas city inhabitants by Residents' Register Service of Lithuania. Depressive symptoms were ascertained using the EURO-D scale. The List of Threatening Events Questionnaire was used to identify stressful life events that happened over the last 6\u00a0months and during lifetime. A 5-HTTLPR and lifetime stressful events interaction was indicated by higher odds of depression in those with s/s genotype who experienced high stress compared to l/l carriers with low or medium stress, while 5-HTTLPR and current stressful events interaction analysis revealed that carriers of either one or two copies of the s allele had increased odds of depressive symptoms associated with stress compared to participants with the l/l genotype not exposed to stressful situations. Although no significant direct association was found between the 5-HTTLPR short allele and depression, our findings demonstrated that lifetime or current stressful life events and their modification by 5-HTTLPR genotype are risk factors for late-life depression.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41598-023-40215-4.pdf; doi:https://doi.org/10.1038/s41598-023-40215-4; html:https://europepmc.org/articles/PMC10412533; pdf:https://europepmc.org/articles/PMC10412533?pdf=render"
+  },
   {
     "id": "37006328",
     "doi": "https://doi.org/10.1093/braincomms/fcad065",
@@ -8873,23 +8873,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/braincomms/advance-article-pdf/doi/10.1093/braincomms/fcad065/49588224/fcad065.pdf; doi:https://doi.org/10.1093/braincomms/fcad065; html:https://europepmc.org/articles/PMC10053639; pdf:https://europepmc.org/articles/PMC10053639?pdf=render"
   },
-  {
-    "id": "36649943",
-    "doi": "https://doi.org/10.1136/bmjoq-2021-001704",
-    "title": "Benefits of electronic charts in intensive care and during a world health pandemic: advantages of the technology age.",
-    "authorString": "Pankhurst T, Lucas L, Ryan S, Ragdale C, Gyves H, Denner L, Young I, Rathbone L, Shah A, McKee D, Coleman JJ, Evison F, Atia J, Rosser D, Garrick M, Baker R, Gallier S, Ball S.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open quality",
-    "pubYear": "2023",
-    "date": "2023-01-01",
-    "isOpenAccess": "Y",
-    "keywords": "Evaluation Methodology; Critical Care; Electronic Health Records",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Aims and objectives</h4>This study sets out to describe benefits from the implementation of electronic observation charting in intensive care units (ICU). This was an extension to the existing hospital wide digital health system. We evaluated error reduction, time-savings and the costs associated with conversion from paper to digital records. The world health emergency of COVID-19 placed extraordinary strain on ICU and staff opinion was evaluated to test how well the electronic system performed.<h4>Methods</h4>A clinically led project group working directly with programmers developed an electronic patient record for intensive care. Data error rates, time to add data and to make calculations were studied before and after the introduction of electronic charts. User feedback was sought pre and post go-live (during the COVID-19 pandemic) and financial implications were calculated by the hospital finance teams.<h4>Results</h4>Error rates equating to 219\u2009000/year were avoided by conversion to electronic charts. Time saved was the equivalent of a nursing shift each day. Recurrent cost savings per year were estimated to be \u00a3257k. Staff were overwhelmingly positive about electronic charts in ICU, even during a health pandemic and despite redeployment into intensive care where they were using the electronic charts for the first time.<h4>Discussion</h4>Electronic ICU charts have been successfully introduced into our institution with benefits in terms of patient safety through error reduction and improved care through release of nursing time. Costs have been reduced. Staff feel supported by the digital system and report it to be helpful even during redeployment and in the unfamiliar environment of intensive care.",
-    "laySummary": "",
-    "urls": "pdf:https://bmjopenquality.bmj.com/content/bmjqir/12/1/e001704.full.pdf; doi:https://doi.org/10.1136/bmjoq-2021-001704; html:https://europepmc.org/articles/PMC9853220; pdf:https://europepmc.org/articles/PMC9853220?pdf=render"
-  },
   {
     "id": "34599903",
     "doi": "https://doi.org/10.1016/s2213-2600(21)00380-5",
@@ -8907,6 +8890,23 @@
     "laySummary": "",
     "urls": "pdf:https://aura.abdn.ac.uk/bitstream/2164/17801/1/Agrawal_etal_LRM_COVID19_Hospital_Admissions_VOR.pdf; doi:https://doi.org/10.1016/S2213-2600(21)00380-5; html:https://europepmc.org/articles/PMC8480963"
   },
+  {
+    "id": "36649943",
+    "doi": "https://doi.org/10.1136/bmjoq-2021-001704",
+    "title": "Benefits of electronic charts in intensive care and during a world health pandemic: advantages of the technology age.",
+    "authorString": "Pankhurst T, Lucas L, Ryan S, Ragdale C, Gyves H, Denner L, Young I, Rathbone L, Shah A, McKee D, Coleman JJ, Evison F, Atia J, Rosser D, Garrick M, Baker R, Gallier S, Ball S.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open quality",
+    "pubYear": "2023",
+    "date": "2023-01-01",
+    "isOpenAccess": "Y",
+    "keywords": "Evaluation Methodology; Critical Care; Electronic Health Records",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Aims and objectives</h4>This study sets out to describe benefits from the implementation of electronic observation charting in intensive care units (ICU). This was an extension to the existing hospital wide digital health system. We evaluated error reduction, time-savings and the costs associated with conversion from paper to digital records. The world health emergency of COVID-19 placed extraordinary strain on ICU and staff opinion was evaluated to test how well the electronic system performed.<h4>Methods</h4>A clinically led project group working directly with programmers developed an electronic patient record for intensive care. Data error rates, time to add data and to make calculations were studied before and after the introduction of electronic charts. User feedback was sought pre and post go-live (during the COVID-19 pandemic) and financial implications were calculated by the hospital finance teams.<h4>Results</h4>Error rates equating to 219\u2009000/year were avoided by conversion to electronic charts. Time saved was the equivalent of a nursing shift each day. Recurrent cost savings per year were estimated to be \u00a3257k. Staff were overwhelmingly positive about electronic charts in ICU, even during a health pandemic and despite redeployment into intensive care where they were using the electronic charts for the first time.<h4>Discussion</h4>Electronic ICU charts have been successfully introduced into our institution with benefits in terms of patient safety through error reduction and improved care through release of nursing time. Costs have been reduced. Staff feel supported by the digital system and report it to be helpful even during redeployment and in the unfamiliar environment of intensive care.",
+    "laySummary": "",
+    "urls": "pdf:https://bmjopenquality.bmj.com/content/bmjqir/12/1/e001704.full.pdf; doi:https://doi.org/10.1136/bmjoq-2021-001704; html:https://europepmc.org/articles/PMC9853220; pdf:https://europepmc.org/articles/PMC9853220?pdf=render"
+  },
   {
     "id": "34461893",
     "doi": "https://doi.org/10.1186/s12916-021-02096-0",
@@ -8924,6 +8924,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-021-02096-0; doi:https://doi.org/10.1186/s12916-021-02096-0; html:https://europepmc.org/articles/PMC8404408; pdf:https://europepmc.org/articles/PMC8404408?pdf=render"
   },
+  {
+    "id": "37415095",
+    "doi": "https://doi.org/10.1186/s12889-023-16202-9",
+    "title": "Multi-morbidity and its association with common cancer diagnoses: a UK Biobank prospective study.",
+    "authorString": "Conroy MC, Reeves GK, Allen NE.",
+    "authorAffiliations": "",
+    "journalTitle": "BMC public health",
+    "pubYear": "2023",
+    "date": "2023-07-06",
+    "isOpenAccess": "Y",
+    "keywords": "Cancer Risk; Uk Biobank; Multi-morbidity",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Whilst multi-morbidity is known to be a concern in people with cancer, very little is known about the risk of cancer in multi-morbid patients. This study aims to investigate the risk of being diagnosed with lung, colorectal, breast and prostate cancer associated with multi-morbidity.<h4>Methods</h4>We investigated the association between multi-morbidity and subsequent risk of cancer diagnosis in UK Biobank. Cox models were used to estimate the relative risks of each cancer of interest in multi-morbid participants, using the Cambridge Multimorbidity Score. The extent to which reverse causation, residual confounding and ascertainment bias may have impacted on the findings was robustly investigated.<h4>Results</h4>Of the 436,990 participants included in the study who were cancer-free at baseline, 21.6% (99,965) were multi-morbid (\u2265\u20092 diseases). Over a median follow-up time of 10.9 [IQR 10.0-11.7] years, 9,019 prostate, 7,994 breast, 5,241 colorectal, and 3,591 lung cancers were diagnosed. After exclusion of the first year of follow-up, there was no clear association between multi-morbidity and risk of colorectal, prostate or breast cancer diagnosis. Those with\u2009\u2265\u20094 diseases at recruitment had double the risk of a subsequent lung cancer diagnosis compared to those with no diseases (HR 2.00 [95% CI 1.70-2.35] p for trend\u2009<\u20090.001). These findings were robust to sensitivity analyses aimed at reducing the impact of reverse causation, residual confounding from known cancer risk factors and ascertainment bias.<h4>Conclusions</h4>Individuals with multi-morbidity are at an increased risk of lung cancer diagnosis. While this association did not appear to be due to common sources of bias in observational studies, further research is needed to understand what underlies this association.",
+    "laySummary": "",
+    "urls": "pdf:https://bmcpublichealth.biomedcentral.com/counter/pdf/10.1186/s12889-023-16202-9; doi:https://doi.org/10.1186/s12889-023-16202-9; html:https://europepmc.org/articles/PMC10326925; pdf:https://europepmc.org/articles/PMC10326925?pdf=render"
+  },
   {
     "id": "34209840",
     "doi": "https://doi.org/10.3390/cancers13133257",
@@ -8958,6 +8975,23 @@
     "laySummary": "",
     "urls": "pdf:https://openheart.bmj.com/content/openhrt/9/2/e002142.full.pdf; doi:https://doi.org/10.1136/openhrt-2022-002142; html:https://europepmc.org/articles/PMC9639145; pdf:https://europepmc.org/articles/PMC9639145?pdf=render"
   },
+  {
+    "id": "38233744",
+    "doi": "https://doi.org/10.1186/s12874-024-02143-3",
+    "title": "Novel linkage approach to join community-acquired and national data.",
+    "authorString": "Tochel C, Pead E, McTrusty A, Buckmaster F, MacGillivray T, Tatham AJ, Strang NC, Dhillon B, Bernabeu MO.",
+    "authorAffiliations": "",
+    "journalTitle": "BMC medical research methodology",
+    "pubYear": "2024",
+    "date": "2024-01-17",
+    "isOpenAccess": "Y",
+    "keywords": "Image analysis; Longitudinal data; Data Linkage; Early Disease Detection; Community Optometry",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Community optometrists in Scotland have performed regular free-at-point-of-care eye examinations for all, for over 15 years. Eye examinations include retinal imaging but image storage is fragmented and they are not used for research. The Scottish Collaborative Optometry-Ophthalmology Network e-research project aimed to collect these images and create a repository linked to routinely collected healthcare data, supporting the development of pre-symptomatic diagnostic tools.<h4>Methods</h4>As the image record was usually separate from the patient record and contained minimal patient information, we developed an efficient matching algorithm using a combination of deterministic and probabilistic steps which minimised the risk of false positives, to facilitate national health record linkage. We visited two practices and assessed the data contained in their image device and Practice Management Systems. Practice activities were explored to understand the context of data collection processes. Iteratively, we tested a series of matching rules which captured a high proportion of true positive records compared to manual matches. The approach was validated by testing manual matching against automated steps in three further practices.<h4>Results</h4>A sequence of deterministic rules successfully matched 95% of records in the three test practices compared to manual matching. Adding two probabilistic rules to the algorithm successfully matched 99% of records.<h4>Conclusions</h4>The potential value of community-acquired retinal images can be harnessed only if they are linked to centrally-held healthcare care data. Despite the lack of interoperability between systems within optometry practices and inconsistent use of unique identifiers, data linkage is possible using robust, almost entirely automated processes.",
+    "laySummary": "",
+    "urls": "pdf:https://bmcmedresmethodol.biomedcentral.com/counter/pdf/10.1186/s12874-024-02143-3; doi:https://doi.org/10.1186/s12874-024-02143-3; html:https://europepmc.org/articles/PMC10792819; pdf:https://europepmc.org/articles/PMC10792819?pdf=render"
+  },
   {
     "id": "36857859",
     "doi": "https://doi.org/10.1016/j.ebiom.2023.104489",
@@ -8992,40 +9026,6 @@
     "laySummary": "",
     "urls": "pdf:https://ijpds.org/article/download/1121/2984; doi:https://doi.org/10.23889/ijpds.v5i1.1121; html:https://europepmc.org/articles/PMC7473277; pdf:https://europepmc.org/articles/PMC7473277?pdf=render"
   },
-  {
-    "id": "38233744",
-    "doi": "https://doi.org/10.1186/s12874-024-02143-3",
-    "title": "Novel linkage approach to join community-acquired and national data.",
-    "authorString": "Tochel C, Pead E, McTrusty A, Buckmaster F, MacGillivray T, Tatham AJ, Strang NC, Dhillon B, Bernabeu MO.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC medical research methodology",
-    "pubYear": "2024",
-    "date": "2024-01-17",
-    "isOpenAccess": "Y",
-    "keywords": "Image analysis; Longitudinal data; Data Linkage; Early Disease Detection; Community Optometry",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Community optometrists in Scotland have performed regular free-at-point-of-care eye examinations for all, for over 15 years. Eye examinations include retinal imaging but image storage is fragmented and they are not used for research. The Scottish Collaborative Optometry-Ophthalmology Network e-research project aimed to collect these images and create a repository linked to routinely collected healthcare data, supporting the development of pre-symptomatic diagnostic tools.<h4>Methods</h4>As the image record was usually separate from the patient record and contained minimal patient information, we developed an efficient matching algorithm using a combination of deterministic and probabilistic steps which minimised the risk of false positives, to facilitate national health record linkage. We visited two practices and assessed the data contained in their image device and Practice Management Systems. Practice activities were explored to understand the context of data collection processes. Iteratively, we tested a series of matching rules which captured a high proportion of true positive records compared to manual matches. The approach was validated by testing manual matching against automated steps in three further practices.<h4>Results</h4>A sequence of deterministic rules successfully matched 95% of records in the three test practices compared to manual matching. Adding two probabilistic rules to the algorithm successfully matched 99% of records.<h4>Conclusions</h4>The potential value of community-acquired retinal images can be harnessed only if they are linked to centrally-held healthcare care data. Despite the lack of interoperability between systems within optometry practices and inconsistent use of unique identifiers, data linkage is possible using robust, almost entirely automated processes.",
-    "laySummary": "",
-    "urls": "pdf:https://bmcmedresmethodol.biomedcentral.com/counter/pdf/10.1186/s12874-024-02143-3; doi:https://doi.org/10.1186/s12874-024-02143-3; html:https://europepmc.org/articles/PMC10792819; pdf:https://europepmc.org/articles/PMC10792819?pdf=render"
-  },
-  {
-    "id": "37415095",
-    "doi": "https://doi.org/10.1186/s12889-023-16202-9",
-    "title": "Multi-morbidity and its association with common cancer diagnoses: a UK Biobank prospective study.",
-    "authorString": "Conroy MC, Reeves GK, Allen NE.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC public health",
-    "pubYear": "2023",
-    "date": "2023-07-06",
-    "isOpenAccess": "Y",
-    "keywords": "Cancer Risk; Uk Biobank; Multi-morbidity",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Whilst multi-morbidity is known to be a concern in people with cancer, very little is known about the risk of cancer in multi-morbid patients. This study aims to investigate the risk of being diagnosed with lung, colorectal, breast and prostate cancer associated with multi-morbidity.<h4>Methods</h4>We investigated the association between multi-morbidity and subsequent risk of cancer diagnosis in UK Biobank. Cox models were used to estimate the relative risks of each cancer of interest in multi-morbid participants, using the Cambridge Multimorbidity Score. The extent to which reverse causation, residual confounding and ascertainment bias may have impacted on the findings was robustly investigated.<h4>Results</h4>Of the 436,990 participants included in the study who were cancer-free at baseline, 21.6% (99,965) were multi-morbid (\u2265\u20092 diseases). Over a median follow-up time of 10.9 [IQR 10.0-11.7] years, 9,019 prostate, 7,994 breast, 5,241 colorectal, and 3,591 lung cancers were diagnosed. After exclusion of the first year of follow-up, there was no clear association between multi-morbidity and risk of colorectal, prostate or breast cancer diagnosis. Those with\u2009\u2265\u20094 diseases at recruitment had double the risk of a subsequent lung cancer diagnosis compared to those with no diseases (HR 2.00 [95% CI 1.70-2.35] p for trend\u2009<\u20090.001). These findings were robust to sensitivity analyses aimed at reducing the impact of reverse causation, residual confounding from known cancer risk factors and ascertainment bias.<h4>Conclusions</h4>Individuals with multi-morbidity are at an increased risk of lung cancer diagnosis. While this association did not appear to be due to common sources of bias in observational studies, further research is needed to understand what underlies this association.",
-    "laySummary": "",
-    "urls": "pdf:https://bmcpublichealth.biomedcentral.com/counter/pdf/10.1186/s12889-023-16202-9; doi:https://doi.org/10.1186/s12889-023-16202-9; html:https://europepmc.org/articles/PMC10326925; pdf:https://europepmc.org/articles/PMC10326925?pdf=render"
-  },
   {
     "id": "36882868",
     "doi": "https://doi.org/10.1186/s12916-023-02784-z",
@@ -9383,6 +9383,40 @@
     "laySummary": "",
     "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.119.012812; doi:https://doi.org/10.1161/JAHA.119.012812; html:https://europepmc.org/articles/PMC6898825; pdf:https://europepmc.org/articles/PMC6898825?pdf=render"
   },
+  {
+    "id": "38434747",
+    "doi": "https://doi.org/10.12688/wellcomeopenres.19858.1",
+    "title": "Interpreting pathology test result values with comparators (< , >) in Electronic Health Records research: an OpenSAFELY short data report.",
+    "authorString": "Curtis HJ, Fisher L, Evans D, OpenSAFELY Collaborative, Bacon S, Mehrkar A, Goldacre B, MacKenna B.",
+    "authorAffiliations": "",
+    "journalTitle": "Wellcome open research",
+    "pubYear": "2023",
+    "date": "2023-01-01",
+    "isOpenAccess": "Y",
+    "keywords": "Pathology; Kidney function tests; Electronic Health Records",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Numeric results of pathology tests are sometimes returned as a range rather than a precise value, e.g. \"<10\". In health data research, test result values above or below clinical threshold values are often used to categorise patients into groups; however comparators (<, > etc) are typically stored separately to the numeric values and often ignored, but may influence interpretation.<h4>Methods</h4>With the approval of NHS England we used routine clinical data from 24 million patients in OpenSAFELY to identify pathology tests with comparators commonly attached to result values. For each test we report: the proportion returned with comparators present, split by comparator type and geographic region; the specific numeric result values returned with comparators, and the associated reference limits.<h4>Results</h4>We identified 11 common test codes where at least one in four results had comparators. Three codes related to glomerular filtration rate (GFR) tests/calculations, with 31-45% of results returned with \"\u2265\" comparators. At least 90% of tests with numeric values 60 and 90 represented ranges (\u226560 and \u226590 respectively) rather than exact values. The other tests - four blood tests (Nucleated red blood cell count, Plasma C reactive protein, Tissue transglutaminase immunoglobulin A, and Rheumatoid factor), two urine tests (albumin/microalbumin) and two faecal tests (calprotectin and quantitative faecal immunochemical test) - were returned with \"\u2264\" comparators (29-86%).<h4>Conclusions</h4>Comparators appear commonly in certain pathology tests in electronic health records. For most common affected tests, we expect there to be minimal implications for researchers for most use-cases. However, care should be taken around whether results falling exactly on clinical threshold values should be considered \"normal\" or \"abnormal\". Results from GFR tests/calculations cannot reliably distinguish between mild kidney disease (stage G2, 60-<90) versus healthy kidney function (90+). More broadly, health data researchers using numeric test result values should consider the impact of comparators.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.12688/wellcomeopenres.19858.1; html:https://europepmc.org/articles/PMC10904973; pdf:https://europepmc.org/articles/PMC10904973?pdf=render"
+  },
+  {
+    "id": "34599527",
+    "doi": "https://doi.org/10.1111/dme.14707",
+    "title": "Comparing survival outcomes for kidney transplant recipients with pre-existing diabetes versus those who develop post-transplantation diabetes.",
+    "authorString": "Hussain A, Culliford A, Phagura N, Evison F, Gallier S, Sharif A.",
+    "authorAffiliations": "",
+    "journalTitle": "Diabetic medicine : a journal of the British Diabetic Association",
+    "pubYear": "2022",
+    "date": "2021-10-08",
+    "isOpenAccess": "N",
+    "keywords": "Survival; Management; Diabetes; Kidney Transplant; Post-transplant Diabetes",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>The aim of this study was to compare the management strategy and clinical outcomes for kidney transplant recipients with pre-transplant versus post-transplantation diabetes (PTDM) in a contemporary cohort.<h4>Methods</h4>This is a single-centre, retrospective. observational study of kidney transplant recipients between 2007 and 2018 with follow-up to 31 December 2020. Data were extracted from hospital electronic patient records, with clinical outcomes linked to national data sets. PTDM was diagnosed by international consensus guidelines. Unadjusted and adjusted survival outcomes were assessed with Kaplan-Meier curves and Cox regression models, respectively, with PTDM handled as a time-varying covariate.<h4>Results</h4>Data were analysed for 1,757\u00a0kidney transplant recipients, of whom 11.8% (n\u00a0=\u00a0207) had pre-transplant diabetes, and 13.8% (n\u00a0=\u00a0243) developed PTDM with median time to onset 108\u00a0days (IQR 46-549\u00a0days). Median follow-up was 1,839\u00a0days (IQR 928-2985\u00a0days). Disparate management strategies were observed, although insulin was the commonest glucose-lowering therapy for all patients with diabetes. In adjusted models, PTDM was associated with lower mortality (HR 0.663, 95% CI 0.543-0.810) and pre-diabetes with higher mortality (HR 1.675, 95% CI 1.396-2.011). However, if analyses are restricted to those with at least 5-year follow-up, then PTDM has no association with mortality (HR 0.771, 95% CI 0.419-1.096), but pre-transplant diabetes remains associated with higher mortality (HR 2.029, 95% CI 1.367-3.012).<h4>Conclusions</h4>Pre-transplant diabetes remains associated with increased mortality risk after kidney transplantation, but PTDM effects are time dependent. Development of PTDM should be encouraged as a mandated registry return to study the long-term impact on survival outcomes.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1111/dme.14707"
+  },
   {
     "id": "33004880",
     "doi": "https://doi.org/10.1038/s41598-020-73228-4",
@@ -9417,40 +9451,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/5/e054186.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-054186; html:https://europepmc.org/articles/PMC9086620; pdf:https://europepmc.org/articles/PMC9086620?pdf=render"
   },
-  {
-    "id": "34599527",
-    "doi": "https://doi.org/10.1111/dme.14707",
-    "title": "Comparing survival outcomes for kidney transplant recipients with pre-existing diabetes versus those who develop post-transplantation diabetes.",
-    "authorString": "Hussain A, Culliford A, Phagura N, Evison F, Gallier S, Sharif A.",
-    "authorAffiliations": "",
-    "journalTitle": "Diabetic medicine : a journal of the British Diabetic Association",
-    "pubYear": "2022",
-    "date": "2021-10-08",
-    "isOpenAccess": "N",
-    "keywords": "Survival; Management; Diabetes; Kidney Transplant; Post-transplant Diabetes",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>The aim of this study was to compare the management strategy and clinical outcomes for kidney transplant recipients with pre-transplant versus post-transplantation diabetes (PTDM) in a contemporary cohort.<h4>Methods</h4>This is a single-centre, retrospective. observational study of kidney transplant recipients between 2007 and 2018 with follow-up to 31 December 2020. Data were extracted from hospital electronic patient records, with clinical outcomes linked to national data sets. PTDM was diagnosed by international consensus guidelines. Unadjusted and adjusted survival outcomes were assessed with Kaplan-Meier curves and Cox regression models, respectively, with PTDM handled as a time-varying covariate.<h4>Results</h4>Data were analysed for 1,757\u00a0kidney transplant recipients, of whom 11.8% (n\u00a0=\u00a0207) had pre-transplant diabetes, and 13.8% (n\u00a0=\u00a0243) developed PTDM with median time to onset 108\u00a0days (IQR 46-549\u00a0days). Median follow-up was 1,839\u00a0days (IQR 928-2985\u00a0days). Disparate management strategies were observed, although insulin was the commonest glucose-lowering therapy for all patients with diabetes. In adjusted models, PTDM was associated with lower mortality (HR 0.663, 95% CI 0.543-0.810) and pre-diabetes with higher mortality (HR 1.675, 95% CI 1.396-2.011). However, if analyses are restricted to those with at least 5-year follow-up, then PTDM has no association with mortality (HR 0.771, 95% CI 0.419-1.096), but pre-transplant diabetes remains associated with higher mortality (HR 2.029, 95% CI 1.367-3.012).<h4>Conclusions</h4>Pre-transplant diabetes remains associated with increased mortality risk after kidney transplantation, but PTDM effects are time dependent. Development of PTDM should be encouraged as a mandated registry return to study the long-term impact on survival outcomes.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1111/dme.14707"
-  },
-  {
-    "id": "38434747",
-    "doi": "https://doi.org/10.12688/wellcomeopenres.19858.1",
-    "title": "Interpreting pathology test result values with comparators (< , >) in Electronic Health Records research: an OpenSAFELY short data report.",
-    "authorString": "Curtis HJ, Fisher L, Evans D, OpenSAFELY Collaborative, Bacon S, Mehrkar A, Goldacre B, MacKenna B.",
-    "authorAffiliations": "",
-    "journalTitle": "Wellcome open research",
-    "pubYear": "2023",
-    "date": "2023-01-01",
-    "isOpenAccess": "Y",
-    "keywords": "Pathology; Kidney function tests; Electronic Health Records",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Numeric results of pathology tests are sometimes returned as a range rather than a precise value, e.g. \"<10\". In health data research, test result values above or below clinical threshold values are often used to categorise patients into groups; however comparators (<, > etc) are typically stored separately to the numeric values and often ignored, but may influence interpretation.<h4>Methods</h4>With the approval of NHS England we used routine clinical data from 24 million patients in OpenSAFELY to identify pathology tests with comparators commonly attached to result values. For each test we report: the proportion returned with comparators present, split by comparator type and geographic region; the specific numeric result values returned with comparators, and the associated reference limits.<h4>Results</h4>We identified 11 common test codes where at least one in four results had comparators. Three codes related to glomerular filtration rate (GFR) tests/calculations, with 31-45% of results returned with \"\u2265\" comparators. At least 90% of tests with numeric values 60 and 90 represented ranges (\u226560 and \u226590 respectively) rather than exact values. The other tests - four blood tests (Nucleated red blood cell count, Plasma C reactive protein, Tissue transglutaminase immunoglobulin A, and Rheumatoid factor), two urine tests (albumin/microalbumin) and two faecal tests (calprotectin and quantitative faecal immunochemical test) - were returned with \"\u2264\" comparators (29-86%).<h4>Conclusions</h4>Comparators appear commonly in certain pathology tests in electronic health records. For most common affected tests, we expect there to be minimal implications for researchers for most use-cases. However, care should be taken around whether results falling exactly on clinical threshold values should be considered \"normal\" or \"abnormal\". Results from GFR tests/calculations cannot reliably distinguish between mild kidney disease (stage G2, 60-<90) versus healthy kidney function (90+). More broadly, health data researchers using numeric test result values should consider the impact of comparators.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.12688/wellcomeopenres.19858.1; html:https://europepmc.org/articles/PMC10904973; pdf:https://europepmc.org/articles/PMC10904973?pdf=render"
-  },
   {
     "id": "37018139",
     "doi": "https://doi.org/10.1093/rheumatology/kead150",
@@ -9485,23 +9485,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1177/08862605231163885; doi:https://doi.org/10.1177/08862605231163885; html:https://europepmc.org/articles/PMC10064198; pdf:https://europepmc.org/articles/PMC10064198?pdf=render"
   },
-  {
-    "id": "36691170",
-    "doi": "https://doi.org/10.1136/bmjopen-2022-061344",
-    "title": "Pre-COVID-19 pandemic health-related behaviours in children (2018-2020) and association with being tested for SARS-CoV-2 and testing positive for SARS-CoV-2 (2020-2021): a retrospective cohort study using survey data linked with routine health data in Wales, UK.",
-    "authorString": "Marchant E, Lowthian E, Crick T, Griffiths LJ, Fry R, Dadaczynski K, Okan O, James M, Cowley L, Torabi F, Kennedy J, Akbari A, Lyons R, Brophy S.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2022",
-    "date": "2022-09-07",
-    "isOpenAccess": "Y",
-    "keywords": "epidemiology; Public Health; Community Child Health; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objectives</h4>Examine if pre-COVID-19 pandemic (prior March 2020) health-related behaviours during primary school are associated with (1) being tested for SARS-CoV-2 and (2) testing positive between 1 March 2020 and 31 August 2021.<h4>Design</h4>Retrospective cohort study using an online cohort survey (January 2018 to February 2020) linked with routine PCR SARS-CoV-2 test results.<h4>Setting</h4>Children attending primary schools in Wales (2018-2020), UK, who were part of the Health and Attainment of Pupils in a Primary Education Network (HAPPEN)_school network.<h4>Participants</h4>Complete linked records of eligible participants were obtained for n=7062 individuals. 39.1% (n=2764) were tested (age 10.6\u00b10.9; 48.9% girls) and 8.1% (n=569) tested positive for SARS-CoV-2 (age 10.6\u00b11.0; 54.5% girls).<h4>Main outcome measures</h4>Logistic regression of health-related behaviours and demographics were used to determine the ORs of factors associated with (1) being tested for SARS-CoV-2 and (2) testing positive for SARS-CoV-2.<h4>Results</h4>Consuming sugary snacks (1-2\u2009days/week OR=1.24, 95% CI 1.04 to 1.49; 5-6\u2009days/week OR=1.31, 95% CI 1.07 to 1.61; reference 0 days), can swim 25 m (OR=1.21, 95% CI 1.06 to 1.39) and age (OR=1.25, 95% CI 1.16 to 1.35) were associated with an increased likelihood of being tested for SARS-CoV-2. Eating breakfast (OR=1.52, 95% CI 1.01 to 2.27), weekly physical activity \u226560 min (1-2\u2009days OR=1.69, 95% CI 1.04 to 2.74; 3-4\u2009days OR=1.76, 95% CI 1.10 to 2.82; reference 0 days), out-of-school club participation (OR=1.06, 95% CI 1.02 to 1.10), can ride a bike (OR=1.39, 95% CI 1.00 to 1.93), age (OR=1.16, 95% CI 1.05 to 1.28) and girls (OR=1.21, 95% CI 1.00 to 1.46) were associated with an increased likelihood of testing positive for SARS-CoV-2. Living in least deprived areas (quintile 4 OR=0.64, 95% CI 0.46 to 0.90; quintile 5 OR=0.64, 95% CI 0.46 to 0.89) compared with the most deprived (quintile 1) was associated with a decreased likelihood.<h4>Conclusions</h4>Associations may be related to parental health literacy and monitoring behaviours. Physically active behaviours may include coparticipation with others and exposure to SARS-CoV-2. A risk-versus-benefit approach must be considered in relation to promoting these health behaviours, given the importance of health-related behaviours such as childhood physical activity for development.",
-    "laySummary": "",
-    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/9/e061344.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-061344; html:https://europepmc.org/articles/PMC9453425; pdf:https://europepmc.org/articles/PMC9453425?pdf=render"
-  },
   {
     "id": "37068964",
     "doi": "https://doi.org/10.3399/bjgp.2022.0301",
@@ -9536,6 +9519,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/eurpub/advance-article-pdf/doi/10.1093/eurpub/ckad075/50504334/ckad075.pdf; doi:https://doi.org/10.1093/eurpub/ckad075; html:https://europepmc.org/articles/PMC10393497; pdf:https://europepmc.org/articles/PMC10393497?pdf=render"
   },
+  {
+    "id": "36691170",
+    "doi": "https://doi.org/10.1136/bmjopen-2022-061344",
+    "title": "Pre-COVID-19 pandemic health-related behaviours in children (2018-2020) and association with being tested for SARS-CoV-2 and testing positive for SARS-CoV-2 (2020-2021): a retrospective cohort study using survey data linked with routine health data in Wales, UK.",
+    "authorString": "Marchant E, Lowthian E, Crick T, Griffiths LJ, Fry R, Dadaczynski K, Okan O, James M, Cowley L, Torabi F, Kennedy J, Akbari A, Lyons R, Brophy S.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2022",
+    "date": "2022-09-07",
+    "isOpenAccess": "Y",
+    "keywords": "epidemiology; Public Health; Community Child Health; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objectives</h4>Examine if pre-COVID-19 pandemic (prior March 2020) health-related behaviours during primary school are associated with (1) being tested for SARS-CoV-2 and (2) testing positive between 1 March 2020 and 31 August 2021.<h4>Design</h4>Retrospective cohort study using an online cohort survey (January 2018 to February 2020) linked with routine PCR SARS-CoV-2 test results.<h4>Setting</h4>Children attending primary schools in Wales (2018-2020), UK, who were part of the Health and Attainment of Pupils in a Primary Education Network (HAPPEN)_school network.<h4>Participants</h4>Complete linked records of eligible participants were obtained for n=7062 individuals. 39.1% (n=2764) were tested (age 10.6\u00b10.9; 48.9% girls) and 8.1% (n=569) tested positive for SARS-CoV-2 (age 10.6\u00b11.0; 54.5% girls).<h4>Main outcome measures</h4>Logistic regression of health-related behaviours and demographics were used to determine the ORs of factors associated with (1) being tested for SARS-CoV-2 and (2) testing positive for SARS-CoV-2.<h4>Results</h4>Consuming sugary snacks (1-2\u2009days/week OR=1.24, 95% CI 1.04 to 1.49; 5-6\u2009days/week OR=1.31, 95% CI 1.07 to 1.61; reference 0 days), can swim 25 m (OR=1.21, 95% CI 1.06 to 1.39) and age (OR=1.25, 95% CI 1.16 to 1.35) were associated with an increased likelihood of being tested for SARS-CoV-2. Eating breakfast (OR=1.52, 95% CI 1.01 to 2.27), weekly physical activity \u226560 min (1-2\u2009days OR=1.69, 95% CI 1.04 to 2.74; 3-4\u2009days OR=1.76, 95% CI 1.10 to 2.82; reference 0 days), out-of-school club participation (OR=1.06, 95% CI 1.02 to 1.10), can ride a bike (OR=1.39, 95% CI 1.00 to 1.93), age (OR=1.16, 95% CI 1.05 to 1.28) and girls (OR=1.21, 95% CI 1.00 to 1.46) were associated with an increased likelihood of testing positive for SARS-CoV-2. Living in least deprived areas (quintile 4 OR=0.64, 95% CI 0.46 to 0.90; quintile 5 OR=0.64, 95% CI 0.46 to 0.89) compared with the most deprived (quintile 1) was associated with a decreased likelihood.<h4>Conclusions</h4>Associations may be related to parental health literacy and monitoring behaviours. Physically active behaviours may include coparticipation with others and exposure to SARS-CoV-2. A risk-versus-benefit approach must be considered in relation to promoting these health behaviours, given the importance of health-related behaviours such as childhood physical activity for development.",
+    "laySummary": "",
+    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/9/e061344.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-061344; html:https://europepmc.org/articles/PMC9453425; pdf:https://europepmc.org/articles/PMC9453425?pdf=render"
+  },
   {
     "id": "37340474",
     "doi": "https://doi.org/10.1186/s12916-023-02877-9",
@@ -9604,6 +9604,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/11/6/e048333.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-048333; html:https://europepmc.org/articles/PMC8228811; pdf:https://europepmc.org/articles/PMC8228811?pdf=render"
   },
+  {
+    "id": "36863848",
+    "doi": "https://doi.org/10.1136/archdischild-2022-325152",
+    "title": "Characteristics and predictors of persistent symptoms post-COVID-19 in children and young people: a large community cross-sectional study in England.",
+    "authorString": "Atchison CJ, Whitaker M, Donnelly CA, Chadeau-Hyam M, Riley S, Darzi A, Ashby D, Barclay W, Cooke GS, Elliott P, Ward H.",
+    "authorAffiliations": "",
+    "journalTitle": "Archives of disease in childhood",
+    "pubYear": "2023",
+    "date": "2023-03-02",
+    "isOpenAccess": "Y",
+    "keywords": "epidemiology; Paediatrics; Adolescent Health; Infectious Disease Medicine; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>To estimate the prevalence of, and associated risk factors for, persistent symptoms post-COVID-19 among children aged 5-17 years in England.<h4>Design</h4>Serial cross-sectional study.<h4>Setting</h4>Rounds 10-19 (March 2021 to March 2022) of the REal-time Assessment of Community Transmission-1 study (monthly cross-sectional surveys of random samples of the population in England).<h4>Study population</h4>Children aged 5-17 years in the community.<h4>Predictors</h4>Age, sex, ethnicity, presence of a pre-existing health condition, index of multiple deprivation, COVID-19 vaccination status and dominant UK circulating SARS-CoV-2 variant at time of symptom onset.<h4>Main outcome measures</h4>Prevalence of persistent symptoms, reported as those lasting \u22653 months post-COVID-19.<h4>Results</h4>Overall, 4.4% (95% CI 3.7 to 5.1) of 3173 5-11\u2009year-olds and 13.3% (95% CI 12.5 to 14.1) of 6886 12-17\u2009year-olds with prior symptomatic infection reported at least one symptom lasting \u22653 months post-COVID-19, of whom 13.5% (95% CI 8.4 to 20.9) and 10.9% (95% CI 9.0 to 13.2), respectively, reported their ability to carry out day-to-day activities was reduced 'a lot' due to their symptoms. The most common symptoms among participants with persistent symptoms were persistent coughing (27.4%) and headaches (25.4%) in children aged 5-11 years and loss or change of sense of smell (52.2%) and taste (40.7%) in participants aged 12-17 years. Higher age and having a pre-existing health condition were associated with higher odds of reporting persistent symptoms.<h4>Conclusions</h4>One in 23 5-11\u2009year-olds and one in eight 12-17\u2009year-olds post-COVID-19 report persistent symptoms lasting \u22653 months, of which one in nine report a large impact on performing day-to-day activities.",
+    "laySummary": "",
+    "urls": "pdf:https://adc.bmj.com/content/archdischild/early/2023/03/01/archdischild-2022-325152.full.pdf; doi:https://doi.org/10.1136/archdischild-2022-325152; html:https://europepmc.org/articles/PMC10313975; pdf:https://europepmc.org/articles/PMC10313975?pdf=render"
+  },
   {
     "id": "38627354",
     "doi": "https://doi.org/10.1007/s15010-024-02235-8",
@@ -9638,23 +9655,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.3389/fepid.2024.1326306; html:https://europepmc.org/articles/PMC11021700; pdf:https://europepmc.org/articles/PMC11021700?pdf=render"
   },
-  {
-    "id": "36863848",
-    "doi": "https://doi.org/10.1136/archdischild-2022-325152",
-    "title": "Characteristics and predictors of persistent symptoms post-COVID-19 in children and young people: a large community cross-sectional study in England.",
-    "authorString": "Atchison CJ, Whitaker M, Donnelly CA, Chadeau-Hyam M, Riley S, Darzi A, Ashby D, Barclay W, Cooke GS, Elliott P, Ward H.",
-    "authorAffiliations": "",
-    "journalTitle": "Archives of disease in childhood",
-    "pubYear": "2023",
-    "date": "2023-03-02",
-    "isOpenAccess": "Y",
-    "keywords": "epidemiology; Paediatrics; Adolescent Health; Infectious Disease Medicine; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objective</h4>To estimate the prevalence of, and associated risk factors for, persistent symptoms post-COVID-19 among children aged 5-17 years in England.<h4>Design</h4>Serial cross-sectional study.<h4>Setting</h4>Rounds 10-19 (March 2021 to March 2022) of the REal-time Assessment of Community Transmission-1 study (monthly cross-sectional surveys of random samples of the population in England).<h4>Study population</h4>Children aged 5-17 years in the community.<h4>Predictors</h4>Age, sex, ethnicity, presence of a pre-existing health condition, index of multiple deprivation, COVID-19 vaccination status and dominant UK circulating SARS-CoV-2 variant at time of symptom onset.<h4>Main outcome measures</h4>Prevalence of persistent symptoms, reported as those lasting \u22653 months post-COVID-19.<h4>Results</h4>Overall, 4.4% (95% CI 3.7 to 5.1) of 3173 5-11\u2009year-olds and 13.3% (95% CI 12.5 to 14.1) of 6886 12-17\u2009year-olds with prior symptomatic infection reported at least one symptom lasting \u22653 months post-COVID-19, of whom 13.5% (95% CI 8.4 to 20.9) and 10.9% (95% CI 9.0 to 13.2), respectively, reported their ability to carry out day-to-day activities was reduced 'a lot' due to their symptoms. The most common symptoms among participants with persistent symptoms were persistent coughing (27.4%) and headaches (25.4%) in children aged 5-11 years and loss or change of sense of smell (52.2%) and taste (40.7%) in participants aged 12-17 years. Higher age and having a pre-existing health condition were associated with higher odds of reporting persistent symptoms.<h4>Conclusions</h4>One in 23 5-11\u2009year-olds and one in eight 12-17\u2009year-olds post-COVID-19 report persistent symptoms lasting \u22653 months, of which one in nine report a large impact on performing day-to-day activities.",
-    "laySummary": "",
-    "urls": "pdf:https://adc.bmj.com/content/archdischild/early/2023/03/01/archdischild-2022-325152.full.pdf; doi:https://doi.org/10.1136/archdischild-2022-325152; html:https://europepmc.org/articles/PMC10313975; pdf:https://europepmc.org/articles/PMC10313975?pdf=render"
-  },
   {
     "id": "34376451",
     "doi": "https://doi.org/10.1136/bmjopen-2021-048852",
@@ -9774,40 +9774,6 @@
     "laySummary": "",
     "urls": "pdf:http://spiral.imperial.ac.uk/bitstream/10044/1/94586/2/science.abn8347.pdf; doi:https://doi.org/10.1126/science.abn8347; html:https://europepmc.org/articles/PMC8939772; pdf:https://europepmc.org/articles/PMC8939772?pdf=render"
   },
-  {
-    "id": "38373998",
-    "doi": "https://doi.org/10.1186/s13073-024-01304-9",
-    "title": "Recent advances in polygenic scores: translation, equitability, methods and FAIR tools.",
-    "authorString": "Xiang R, Kelemen M, Xu Y, Harris LW, Parkinson H, Inouye M, Lambert SA.",
-    "authorAffiliations": "",
-    "journalTitle": "Genome medicine",
-    "pubYear": "2024",
-    "date": "2024-02-19",
-    "isOpenAccess": "Y",
-    "keywords": "transferability; Clinical Utility; Genome-wide Association Studies (Gwas); Open-access; Accessible; Interoperable; Responsible Use; Polygenic Score (Pgs); Fair (Findable; And Reusable)",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Polygenic scores (PGS) can be used for risk stratification by quantifying individuals' genetic predisposition to disease, and many potentially clinically useful applications have been proposed. Here, we review the latest potential benefits of PGS in the clinic and challenges to implementation. PGS could augment risk stratification through combined use with traditional risk factors (demographics, disease-specific risk factors, family history, etc.), to support diagnostic pathways, to predict groups with therapeutic benefits, and to increase the efficiency of clinical trials. However, there exist challenges to maximizing the clinical utility of PGS, including FAIR (Findable, Accessible, Interoperable, and Reusable) use and standardized sharing of the genomic data needed to develop and recalculate PGS, the equitable performance of PGS across populations and ancestries, the generation of robust and reproducible PGS calculations, and the responsible communication and interpretation of results. We outline how these challenges may be overcome analytically and with more diverse data as well as highlight sustained community efforts to achieve equitable, impactful, and responsible use of PGS in healthcare.",
-    "laySummary": "",
-    "urls": "pdf:https://genomemedicine.biomedcentral.com/counter/pdf/10.1186/s13073-024-01304-9; doi:https://doi.org/10.1186/s13073-024-01304-9; html:https://europepmc.org/articles/PMC10875792; pdf:https://europepmc.org/articles/PMC10875792?pdf=render"
-  },
-  {
-    "id": "38895652",
-    "doi": "https://doi.org/10.1093/jamiaopen/ooae049",
-    "title": "Creating a next-generation phenotype library: the health data research UK Phenotype Library.",
-    "authorString": "Thayer DS, Mumtaz S, Elmessary MA, Scanlon I, Zinnurov A, Coldea AI, Scanlon J, Chapman M, Curcin V, John A, DelPozo-Banos M, Davies H, Karwath A, Gkoutos GV, Fitzpatrick NK, Quint JK, Varma S, Milner C, Oliveira C, Parkinson H, Denaxas S, Hemingway H, Jefferson E.",
-    "authorAffiliations": "",
-    "journalTitle": "JAMIA open",
-    "pubYear": "2024",
-    "date": "2024-06-17",
-    "isOpenAccess": "Y",
-    "keywords": "Phenotyping; Medical Informatics; Algorithms; Public Health Informatics; Electronic Health Records; Application Programming Interface",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objective</h4>To enable reproducible research at scale by creating a platform that enables health data users to find, access, curate, and re-use electronic health record phenotyping algorithms.<h4>Materials and methods</h4>We undertook a structured approach to identifying requirements for a phenotype algorithm platform by engaging with key stakeholders. User experience analysis was used to inform the design, which we implemented as a web application featuring a novel metadata standard for defining phenotyping algorithms, access via Application Programming Interface (API), support for computable data flows, and version control. The application has creation and editing functionality, enabling researchers to submit phenotypes directly.<h4>Results</h4>We created and launched the Phenotype Library in October 2021. The platform currently hosts 1049 phenotype definitions defined against 40 health data sources and >200K terms across 16 medical ontologies. We present several case studies demonstrating its utility for supporting and enabling research: the library hosts curated phenotype collections for the BREATHE respiratory health research hub and the Adolescent Mental Health Data Platform, and it is supporting the development of an informatics tool to generate clinical evidence for clinical guideline development groups.<h4>Discussion</h4>This platform makes an impact by being open to all health data users and accepting all appropriate content, as well as implementing key features that have not been widely available, including managing structured metadata, access via an API, and support for computable phenotypes.<h4>Conclusions</h4>We have created the first openly available, programmatically accessible resource enabling the global health research community to store and manage phenotyping algorithms. Removing barriers to describing, sharing, and computing phenotypes will help unleash the potential benefit of health data for patients and the public.",
-    "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/jamiaopen/article-pdf/7/2/ooae049/58255810/ooae049.pdf; doi:https://doi.org/10.1093/jamiaopen/ooae049; html:https://europepmc.org/articles/PMC11182945; pdf:https://europepmc.org/articles/PMC11182945?pdf=render"
-  },
   {
     "id": "33611594",
     "doi": "https://doi.org/10.1093/eurjpc/zwaa155",
@@ -9842,6 +9808,40 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/4/e049441.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-049441; html:https://europepmc.org/articles/PMC9013997; pdf:https://europepmc.org/articles/PMC9013997?pdf=render"
   },
+  {
+    "id": "38895652",
+    "doi": "https://doi.org/10.1093/jamiaopen/ooae049",
+    "title": "Creating a next-generation phenotype library: the health data research UK Phenotype Library.",
+    "authorString": "Thayer DS, Mumtaz S, Elmessary MA, Scanlon I, Zinnurov A, Coldea AI, Scanlon J, Chapman M, Curcin V, John A, DelPozo-Banos M, Davies H, Karwath A, Gkoutos GV, Fitzpatrick NK, Quint JK, Varma S, Milner C, Oliveira C, Parkinson H, Denaxas S, Hemingway H, Jefferson E.",
+    "authorAffiliations": "",
+    "journalTitle": "JAMIA open",
+    "pubYear": "2024",
+    "date": "2024-06-17",
+    "isOpenAccess": "Y",
+    "keywords": "Phenotyping; Medical Informatics; Algorithms; Public Health Informatics; Electronic Health Records; Application Programming Interface",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>To enable reproducible research at scale by creating a platform that enables health data users to find, access, curate, and re-use electronic health record phenotyping algorithms.<h4>Materials and methods</h4>We undertook a structured approach to identifying requirements for a phenotype algorithm platform by engaging with key stakeholders. User experience analysis was used to inform the design, which we implemented as a web application featuring a novel metadata standard for defining phenotyping algorithms, access via Application Programming Interface (API), support for computable data flows, and version control. The application has creation and editing functionality, enabling researchers to submit phenotypes directly.<h4>Results</h4>We created and launched the Phenotype Library in October 2021. The platform currently hosts 1049 phenotype definitions defined against 40 health data sources and >200K terms across 16 medical ontologies. We present several case studies demonstrating its utility for supporting and enabling research: the library hosts curated phenotype collections for the BREATHE respiratory health research hub and the Adolescent Mental Health Data Platform, and it is supporting the development of an informatics tool to generate clinical evidence for clinical guideline development groups.<h4>Discussion</h4>This platform makes an impact by being open to all health data users and accepting all appropriate content, as well as implementing key features that have not been widely available, including managing structured metadata, access via an API, and support for computable phenotypes.<h4>Conclusions</h4>We have created the first openly available, programmatically accessible resource enabling the global health research community to store and manage phenotyping algorithms. Removing barriers to describing, sharing, and computing phenotypes will help unleash the potential benefit of health data for patients and the public.",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/jamiaopen/article-pdf/7/2/ooae049/58255810/ooae049.pdf; doi:https://doi.org/10.1093/jamiaopen/ooae049; html:https://europepmc.org/articles/PMC11182945; pdf:https://europepmc.org/articles/PMC11182945?pdf=render"
+  },
+  {
+    "id": "38373998",
+    "doi": "https://doi.org/10.1186/s13073-024-01304-9",
+    "title": "Recent advances in polygenic scores: translation, equitability, methods and FAIR tools.",
+    "authorString": "Xiang R, Kelemen M, Xu Y, Harris LW, Parkinson H, Inouye M, Lambert SA.",
+    "authorAffiliations": "",
+    "journalTitle": "Genome medicine",
+    "pubYear": "2024",
+    "date": "2024-02-19",
+    "isOpenAccess": "Y",
+    "keywords": "transferability; Clinical Utility; Genome-wide Association Studies (Gwas); Open-access; Accessible; Interoperable; Responsible Use; Polygenic Score (Pgs); Fair (Findable; And Reusable)",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Polygenic scores (PGS) can be used for risk stratification by quantifying individuals' genetic predisposition to disease, and many potentially clinically useful applications have been proposed. Here, we review the latest potential benefits of PGS in the clinic and challenges to implementation. PGS could augment risk stratification through combined use with traditional risk factors (demographics, disease-specific risk factors, family history, etc.), to support diagnostic pathways, to predict groups with therapeutic benefits, and to increase the efficiency of clinical trials. However, there exist challenges to maximizing the clinical utility of PGS, including FAIR (Findable, Accessible, Interoperable, and Reusable) use and standardized sharing of the genomic data needed to develop and recalculate PGS, the equitable performance of PGS across populations and ancestries, the generation of robust and reproducible PGS calculations, and the responsible communication and interpretation of results. We outline how these challenges may be overcome analytically and with more diverse data as well as highlight sustained community efforts to achieve equitable, impactful, and responsible use of PGS in healthcare.",
+    "laySummary": "",
+    "urls": "pdf:https://genomemedicine.biomedcentral.com/counter/pdf/10.1186/s13073-024-01304-9; doi:https://doi.org/10.1186/s13073-024-01304-9; html:https://europepmc.org/articles/PMC10875792; pdf:https://europepmc.org/articles/PMC10875792?pdf=render"
+  },
   {
     "id": "35197134",
     "doi": "https://doi.org/10.1192/bjo.2022.24",
@@ -9910,23 +9910,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-023-02921-8; doi:https://doi.org/10.1186/s12916-023-02921-8; html:https://europepmc.org/articles/PMC10280894; pdf:https://europepmc.org/articles/PMC10280894?pdf=render"
   },
-  {
-    "id": "38459430",
-    "doi": "https://doi.org/10.1186/s12859-024-05682-0",
-    "title": "Bayesian inference for identifying tumour-specific cancer dependencies through integration of ex-vivo drug response assays and drug-protein profiling.",
-    "authorString": "Xing H, Yau C.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC bioinformatics",
-    "pubYear": "2024",
-    "date": "2024-03-08",
-    "isOpenAccess": "Y",
-    "keywords": "Gaussian Process; Chemical Perturbation; Spike-and-slab Regression; Tumor-specific Molecular Dependencies",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The identification of tumor-specific molecular dependencies is essential for the development of effective cancer therapies. Genetic and chemical perturbations are powerful tools for discovering these dependencies. Even though chemical perturbations can be applied to primary cancer samples at large scale, the interpretation of experiment outcomes is often complicated by the fact that one chemical compound can affect multiple proteins. To overcome this challenge, Batzilla et al. (PLoS Comput Biol 18(8): e1010438, 2022) proposed DepInfeR, a regularized multi-response regression model designed to identify and estimate specific molecular dependencies of individual cancers from their ex-vivo drug sensitivity profiles. Inspired by their work, we propose a Bayesian extension to DepInfeR. Our proposed approach offers several advantages over DepInfeR, including e.g. the ability to handle missing values in both protein-drug affinity and drug sensitivity profiles without the need for data pre-processing steps such as imputation. Moreover, our approach uses Gaussian Processes to capture more complex molecular dependency structures, and provides probabilistic statements about whether a protein in the protein-drug affinity profiles is informative to the drug sensitivity profiles. Simulation studies demonstrate that our proposed approach achieves better prediction accuracy, and is able to discover unreported dependency structures.",
-    "laySummary": "",
-    "urls": "pdf:https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05682-0; doi:https://doi.org/10.1186/s12859-024-05682-0; html:https://europepmc.org/articles/PMC10921766; pdf:https://europepmc.org/articles/PMC10921766?pdf=render"
-  },
   {
     "id": "30474191",
     "doi": "https://doi.org/10.1111/dme.13870",
@@ -9961,6 +9944,23 @@
     "laySummary": "",
     "urls": "pdf:https://jech.bmj.com/content/jech/74/10/861.full.pdf; doi:https://doi.org/10.1136/jech-2020-214051; html:https://europepmc.org/articles/PMC7307459; pdf:https://europepmc.org/articles/PMC7307459?pdf=render"
   },
+  {
+    "id": "38459430",
+    "doi": "https://doi.org/10.1186/s12859-024-05682-0",
+    "title": "Bayesian inference for identifying tumour-specific cancer dependencies through integration of ex-vivo drug response assays and drug-protein profiling.",
+    "authorString": "Xing H, Yau C.",
+    "authorAffiliations": "",
+    "journalTitle": "BMC bioinformatics",
+    "pubYear": "2024",
+    "date": "2024-03-08",
+    "isOpenAccess": "Y",
+    "keywords": "Gaussian Process; Chemical Perturbation; Spike-and-slab Regression; Tumor-specific Molecular Dependencies",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The identification of tumor-specific molecular dependencies is essential for the development of effective cancer therapies. Genetic and chemical perturbations are powerful tools for discovering these dependencies. Even though chemical perturbations can be applied to primary cancer samples at large scale, the interpretation of experiment outcomes is often complicated by the fact that one chemical compound can affect multiple proteins. To overcome this challenge, Batzilla et al. (PLoS Comput Biol 18(8): e1010438, 2022) proposed DepInfeR, a regularized multi-response regression model designed to identify and estimate specific molecular dependencies of individual cancers from their ex-vivo drug sensitivity profiles. Inspired by their work, we propose a Bayesian extension to DepInfeR. Our proposed approach offers several advantages over DepInfeR, including e.g. the ability to handle missing values in both protein-drug affinity and drug sensitivity profiles without the need for data pre-processing steps such as imputation. Moreover, our approach uses Gaussian Processes to capture more complex molecular dependency structures, and provides probabilistic statements about whether a protein in the protein-drug affinity profiles is informative to the drug sensitivity profiles. Simulation studies demonstrate that our proposed approach achieves better prediction accuracy, and is able to discover unreported dependency structures.",
+    "laySummary": "",
+    "urls": "pdf:https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05682-0; doi:https://doi.org/10.1186/s12859-024-05682-0; html:https://europepmc.org/articles/PMC10921766; pdf:https://europepmc.org/articles/PMC10921766?pdf=render"
+  },
   {
     "id": "36481043",
     "doi": "https://doi.org/10.1016/s2468-1253(22)00389-2",
@@ -10063,23 +10063,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/biomedgerontology/article-pdf/75/12/2320/34289886/glaa216.pdf; doi:https://doi.org/10.1093/gerona/glaa216; html:https://europepmc.org/articles/PMC7662170; pdf:https://europepmc.org/articles/PMC7662170?pdf=render"
   },
-  {
-    "id": "37408471",
-    "doi": "https://doi.org/10.1093/eurheartj/ehad424",
-    "title": "The CODE-EHR global framework: lifting the veil on health record data.",
-    "authorString": "Asselbergs FW, Kotecha D.",
-    "authorAffiliations": "",
-    "journalTitle": "European heart journal",
-    "pubYear": "2023",
-    "date": "2023-09-01",
-    "isOpenAccess": "N",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/eurheartj/advance-article-pdf/doi/10.1093/eurheartj/ehad424/50827856/ehad424.pdf; doi:https://doi.org/10.1093/eurheartj/ehad424"
-  },
   {
     "id": "34722933",
     "doi": "https://doi.org/10.12688/wellcomeopenres.16507.1",
@@ -10098,21 +10081,21 @@
     "urls": "doi:https://doi.org/10.12688/wellcomeopenres.16507.1; html:https://europepmc.org/articles/PMC8524299; pdf:https://europepmc.org/articles/PMC8524299?pdf=render"
   },
   {
-    "id": "37596262",
-    "doi": "https://doi.org/10.1038/s41467-023-40679-y",
-    "title": "A genome-wide association study of blood cell morphology identifies cellular proteins implicated in disease aetiology.",
-    "authorString": "Akbari P, Vuckovic D, Stefanucci L, Jiang T, Kundu K, Kreuzhuber R, Bao EL, Collins JH, Downes K, Grassi L, Guerrero JA, Kaptoge S, Knight JC, Meacham S, Sambrook J, Seyres D, Stegle O, Verboon JM, Walter K, Watkins NA, Danesh J, Roberts DJ, Di Angelantonio E, Sankaran VG, Frontini M, Burgess S, Kuijpers T, Peters JE, Butterworth AS, Ouwehand WH, Soranzo N, Astle WJ.",
+    "id": "37408471",
+    "doi": "https://doi.org/10.1093/eurheartj/ehad424",
+    "title": "The CODE-EHR global framework: lifting the veil on health record data.",
+    "authorString": "Asselbergs FW, Kotecha D.",
     "authorAffiliations": "",
-    "journalTitle": "Nature communications",
+    "journalTitle": "European heart journal",
     "pubYear": "2023",
-    "date": "2023-08-18",
-    "isOpenAccess": "Y",
+    "date": "2023-09-01",
+    "isOpenAccess": "N",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Blood cells contain functionally important intracellular structures, such as granules, critical to immunity and thrombosis. Quantitative variation in these structures has not been subjected previously to large-scale genetic analysis. We perform genome-wide association studies of 63 flow-cytometry derived cellular phenotypes-including cell-type specific measures of granularity, nucleic acid content and reactivity-in 41,515 participants in the INTERVAL study. We identify 2172 distinct variant-trait associations, including associations near genes coding for proteins in organelles implicated in inflammatory and thrombotic diseases. By integrating with epigenetic data we show that many intracellular structures are likely to be determined in immature precursor cells. By integrating with proteomic data we identify the transcription factor FOG2 as an early regulator of platelet formation and \u03b1-granularity. Finally, we show that colocalisation of our associations with disease risk signals can suggest aetiological cell-types-variants in IL2RA and ITGA4 respectively mirror the known effects of daclizumab in multiple sclerosis and vedolizumab in inflammatory bowel disease.",
+    "abstract": "",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1038/s41467-023-40679-y; html:https://europepmc.org/articles/PMC10439125; pdf:https://europepmc.org/articles/PMC10439125?pdf=render"
+    "urls": "pdf:https://academic.oup.com/eurheartj/advance-article-pdf/doi/10.1093/eurheartj/ehad424/50827856/ehad424.pdf; doi:https://doi.org/10.1093/eurheartj/ehad424"
   },
   {
     "id": "37927438",
@@ -10131,6 +10114,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.lanepe.2023.100741; doi:https://doi.org/10.1016/j.lanepe.2023.100741; html:https://europepmc.org/articles/PMC10624988; pdf:https://europepmc.org/articles/PMC10624988?pdf=render"
   },
+  {
+    "id": "37596262",
+    "doi": "https://doi.org/10.1038/s41467-023-40679-y",
+    "title": "A genome-wide association study of blood cell morphology identifies cellular proteins implicated in disease aetiology.",
+    "authorString": "Akbari P, Vuckovic D, Stefanucci L, Jiang T, Kundu K, Kreuzhuber R, Bao EL, Collins JH, Downes K, Grassi L, Guerrero JA, Kaptoge S, Knight JC, Meacham S, Sambrook J, Seyres D, Stegle O, Verboon JM, Walter K, Watkins NA, Danesh J, Roberts DJ, Di Angelantonio E, Sankaran VG, Frontini M, Burgess S, Kuijpers T, Peters JE, Butterworth AS, Ouwehand WH, Soranzo N, Astle WJ.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature communications",
+    "pubYear": "2023",
+    "date": "2023-08-18",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Blood cells contain functionally important intracellular structures, such as granules, critical to immunity and thrombosis. Quantitative variation in these structures has not been subjected previously to large-scale genetic analysis. We perform genome-wide association studies of 63 flow-cytometry derived cellular phenotypes-including cell-type specific measures of granularity, nucleic acid content and reactivity-in 41,515 participants in the INTERVAL study. We identify 2172 distinct variant-trait associations, including associations near genes coding for proteins in organelles implicated in inflammatory and thrombotic diseases. By integrating with epigenetic data we show that many intracellular structures are likely to be determined in immature precursor cells. By integrating with proteomic data we identify the transcription factor FOG2 as an early regulator of platelet formation and \u03b1-granularity. Finally, we show that colocalisation of our associations with disease risk signals can suggest aetiological cell-types-variants in IL2RA and ITGA4 respectively mirror the known effects of daclizumab in multiple sclerosis and vedolizumab in inflammatory bowel disease.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1038/s41467-023-40679-y; html:https://europepmc.org/articles/PMC10439125; pdf:https://europepmc.org/articles/PMC10439125?pdf=render"
+  },
   {
     "id": "35677101",
     "doi": "https://doi.org/10.23889/ijpds.v5i4.1715",
@@ -10200,21 +10200,21 @@
     "urls": "doi:https://doi.org/10.1177/10398562221103117; doi:https://doi.org/10.1177/10398562221103117; html:https://europepmc.org/articles/PMC9379386; pdf:https://europepmc.org/articles/PMC9379386?pdf=render"
   },
   {
-    "id": "34786063",
-    "doi": "https://doi.org/",
-    "title": "Immune infiltration and prognostic and diagnostic use of LGALS4 in colon adenocarcinoma and bladder urothelial carcinoma.",
-    "authorString": "Acharjee A, Agarwal P, Nash K, Bano S, Rahman T, Gkoutos GV.",
+    "id": "33565992",
+    "doi": "https://doi.org/10.2196/22164",
+    "title": "Identifying Myocardial Infarction Using Hierarchical Template Matching-Based Myocardial Strain: Algorithm Development and Usability Study.",
+    "authorString": "Bhalodiya JM, Palit A, Giblin G, Tiwari MK, Prasad SK, Bhudia SK, Arvanitis TN, Williams MA.",
     "authorAffiliations": "",
-    "journalTitle": "American journal of translational research",
+    "journalTitle": "JMIR medical informatics",
     "pubYear": "2021",
-    "date": "2021-10-15",
-    "isOpenAccess": "N",
-    "keywords": "Biomarker; Translational Research; Immune Infiltration; Omics Integration; Blca; Lgals4",
+    "date": "2021-02-10",
+    "isOpenAccess": "Y",
+    "keywords": "Myocardium; Strain; Myocardial infarction; Left ventricle",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Colon adenocarcinoma (COAD) is a common tumor of the gastrointestinal tract with a high mortality rate. Current research has identified many genes associated with immune infiltration that play a vital role in the development of COAD. In this study, we analysed the prognostic and diagnostic features of such immune-related genes in the context of colonic adenocarcinoma (COAD). We analysed 17 overlapping gene expression profiles of COAD and healthy samples obtained from TCGA-COAD and public single-cell sequencing resources, to identify potential therapeutic COAD targets. We evaluated the abundance of immune infiltration with those genes using the TIMER (Tumor Immune Estimation Resource) deconvolution method. Subsequently, we developed predictive and survival models to assess the prognostic value of these genes. The LGALS4 (Galectin-4) gene was found to be significantly (P<0.05) downregulated in COAD and bladder urothelial carcinoma (BLCA) compared to healthy samples. We identified LGALS4 as a prognostic and diagnostic marker for multiple cancer types, including COAD and BLCA. Our analysis reveals a series of novel candidate drug targets, as well as candidate molecular markers, that may explain the pathogenesis of COAD and BLCA. LGALS4 gene is associated with multiple cancer types and is a possible prognostic, as well as diagnostic, marker of COAD and BLCA.",
+    "abstract": "<h4>Background</h4>Myocardial infarction (MI; location and extent of infarction) can be determined by late enhancement cardiac magnetic resonance (CMR) imaging, which requires the injection of a potentially harmful gadolinium-based contrast agent (GBCA). Alternatively, emerging research in the area of myocardial strain has shown potential to identify MI using strain values.<h4>Objective</h4>This study aims to identify the location of MI by developing an applied algorithmic method of circumferential strain (CS) values, which are derived through a novel hierarchical template matching (HTM) method.<h4>Methods</h4>HTM-based CS H-spread from end-diastole to end-systole was used to develop an applied method. Grid-tagging magnetic resonance imaging was used to calculate strain values in the left ventricular (LV) myocardium, followed by the 16-segment American Heart Association model. The data set was used with k-fold cross-validation to estimate the percentage reduction of H-spread among infarcted and noninfarcted LV segments. A total of 43 participants (38 MI and 5 healthy) who underwent CMR imaging were retrospectively selected. Infarcted segments detected by using this method were validated by comparison with late enhancement CMR, and the diagnostic performance of the applied algorithmic method was evaluated with a receiver operating characteristic curve test.<h4>Results</h4>The H-spread of the CS was reduced in infarcted segments compared with noninfarcted segments of the LV. The reductions were 30% in basal segments, 30% in midventricular segments, and 20% in apical LV segments. The diagnostic accuracy of detection, using the reported method, was represented by area under the curve values, which were 0.85, 0.82, and 0.87 for basal, midventricular, and apical slices, respectively, demonstrating good agreement with the late-gadolinium enhancement-based detections.<h4>Conclusions</h4>The proposed applied algorithmic method has the potential to accurately identify the location of infarcted LV segments without the administration of late-gadolinium enhancement. Such an approach adds the potential to safely identify MI, potentially reduce patient scanning time, and extend the utility of CMR in patients who are contraindicated for the use of GBCA.",
     "laySummary": "",
-    "urls": "html:https://europepmc.org/articles/PMC8581917; pdf:https://europepmc.org/articles/PMC8581917?pdf=render"
+    "urls": "pdf:https://medinform.jmir.org/2021/2/e22164/PDF; doi:https://doi.org/10.2196/22164; html:https://europepmc.org/articles/PMC7904396"
   },
   {
     "id": "34693751",
@@ -10234,21 +10234,21 @@
     "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/14799731211053332; doi:https://doi.org/10.1177/14799731211053332; html:https://europepmc.org/articles/PMC8543738; pdf:https://europepmc.org/articles/PMC8543738?pdf=render"
   },
   {
-    "id": "33565992",
-    "doi": "https://doi.org/10.2196/22164",
-    "title": "Identifying Myocardial Infarction Using Hierarchical Template Matching-Based Myocardial Strain: Algorithm Development and Usability Study.",
-    "authorString": "Bhalodiya JM, Palit A, Giblin G, Tiwari MK, Prasad SK, Bhudia SK, Arvanitis TN, Williams MA.",
+    "id": "34786063",
+    "doi": "https://doi.org/",
+    "title": "Immune infiltration and prognostic and diagnostic use of LGALS4 in colon adenocarcinoma and bladder urothelial carcinoma.",
+    "authorString": "Acharjee A, Agarwal P, Nash K, Bano S, Rahman T, Gkoutos GV.",
     "authorAffiliations": "",
-    "journalTitle": "JMIR medical informatics",
+    "journalTitle": "American journal of translational research",
     "pubYear": "2021",
-    "date": "2021-02-10",
-    "isOpenAccess": "Y",
-    "keywords": "Myocardium; Strain; Myocardial infarction; Left ventricle",
+    "date": "2021-10-15",
+    "isOpenAccess": "N",
+    "keywords": "Biomarker; Translational Research; Immune Infiltration; Omics Integration; Blca; Lgals4",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Myocardial infarction (MI; location and extent of infarction) can be determined by late enhancement cardiac magnetic resonance (CMR) imaging, which requires the injection of a potentially harmful gadolinium-based contrast agent (GBCA). Alternatively, emerging research in the area of myocardial strain has shown potential to identify MI using strain values.<h4>Objective</h4>This study aims to identify the location of MI by developing an applied algorithmic method of circumferential strain (CS) values, which are derived through a novel hierarchical template matching (HTM) method.<h4>Methods</h4>HTM-based CS H-spread from end-diastole to end-systole was used to develop an applied method. Grid-tagging magnetic resonance imaging was used to calculate strain values in the left ventricular (LV) myocardium, followed by the 16-segment American Heart Association model. The data set was used with k-fold cross-validation to estimate the percentage reduction of H-spread among infarcted and noninfarcted LV segments. A total of 43 participants (38 MI and 5 healthy) who underwent CMR imaging were retrospectively selected. Infarcted segments detected by using this method were validated by comparison with late enhancement CMR, and the diagnostic performance of the applied algorithmic method was evaluated with a receiver operating characteristic curve test.<h4>Results</h4>The H-spread of the CS was reduced in infarcted segments compared with noninfarcted segments of the LV. The reductions were 30% in basal segments, 30% in midventricular segments, and 20% in apical LV segments. The diagnostic accuracy of detection, using the reported method, was represented by area under the curve values, which were 0.85, 0.82, and 0.87 for basal, midventricular, and apical slices, respectively, demonstrating good agreement with the late-gadolinium enhancement-based detections.<h4>Conclusions</h4>The proposed applied algorithmic method has the potential to accurately identify the location of infarcted LV segments without the administration of late-gadolinium enhancement. Such an approach adds the potential to safely identify MI, potentially reduce patient scanning time, and extend the utility of CMR in patients who are contraindicated for the use of GBCA.",
+    "abstract": "Colon adenocarcinoma (COAD) is a common tumor of the gastrointestinal tract with a high mortality rate. Current research has identified many genes associated with immune infiltration that play a vital role in the development of COAD. In this study, we analysed the prognostic and diagnostic features of such immune-related genes in the context of colonic adenocarcinoma (COAD). We analysed 17 overlapping gene expression profiles of COAD and healthy samples obtained from TCGA-COAD and public single-cell sequencing resources, to identify potential therapeutic COAD targets. We evaluated the abundance of immune infiltration with those genes using the TIMER (Tumor Immune Estimation Resource) deconvolution method. Subsequently, we developed predictive and survival models to assess the prognostic value of these genes. The LGALS4 (Galectin-4) gene was found to be significantly (P<0.05) downregulated in COAD and bladder urothelial carcinoma (BLCA) compared to healthy samples. We identified LGALS4 as a prognostic and diagnostic marker for multiple cancer types, including COAD and BLCA. Our analysis reveals a series of novel candidate drug targets, as well as candidate molecular markers, that may explain the pathogenesis of COAD and BLCA. LGALS4 gene is associated with multiple cancer types and is a possible prognostic, as well as diagnostic, marker of COAD and BLCA.",
     "laySummary": "",
-    "urls": "pdf:https://medinform.jmir.org/2021/2/e22164/PDF; doi:https://doi.org/10.2196/22164; html:https://europepmc.org/articles/PMC7904396"
+    "urls": "html:https://europepmc.org/articles/PMC8581917; pdf:https://europepmc.org/articles/PMC8581917?pdf=render"
   },
   {
     "id": "36735963",
@@ -10267,23 +10267,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1080/09553002.2023.2173823; doi:https://doi.org/10.1080/09553002.2023.2173823"
   },
-  {
-    "id": "39311593",
-    "doi": "https://doi.org/10.1111/trf.17963",
-    "title": "The power of arts-based film interventions to encourage Black blood donors.",
-    "authorString": "Mills R, Okubanjo A, Acheampong N, Croucher M, Eaton N, Kazi A, di Angelantonio E, Wood A, Masser B, Ferguson E.",
-    "authorAffiliations": "",
-    "journalTitle": "Transfusion",
-    "pubYear": "2024",
-    "date": "2024-09-23",
-    "isOpenAccess": "N",
-    "keywords": "Donors | Co\u2010design | Art\u2010based | Film Campaigns",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Blood services must consider innovative ways to encourage more Black people to donate to enhance the efficacy of treatments. We evaluate how two innovative arts-based approaches (co-designed and locally produced films and a large-scale Marvel Studios'/NHSBT collaboration) can achieve this by generalizing to a wider audience from their target audiences.<h4>Study design and methods</h4>Four co-designed short community films were produced in the United Kingdom: Comedy, Reciprocity, Donor-Recipient, and Sliding Doors. In Study 1 (N\u2009=\u200944: Black people), these films were evaluated in the target community in which they were produced. In Study 2 (N\u2009=\u20091237: Black\u2009=\u2009638, White\u2009=\u2009599), the community and Marvel Black Panther/NHSBT films were evaluated in a nontarget general population sample. Evaluations were in terms of campaign behavioral efficacy (e.g., willingness to donate, encourage others to donate) and affect. These analyses were segmented by donor status, age, and gender.<h4>Results</h4>Study 1 shows that the community groups rated the films very positively, with over 90% stating that they would be convinced to donate blood. Study 2 shows the results from the community films generalized to the general population, with the Black Panther film also rated positively in the general population. Three community films and the Black Panther film were rated equally positively. There were notable differences across generations and by donor status.<h4>Discussion</h4>The results highlight the power of arts-based approaches (both locally co-produced community films and franchise collaborations) in encouraging donors within their target audiences and, importantly, on the broader population.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1111/trf.17963"
-  },
   {
     "id": "36745545",
     "doi": "https://doi.org/10.1099/mgen.0.000887",
@@ -10301,6 +10284,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1099/mgen.0.000887; html:https://europepmc.org/articles/PMC9997751; pdf:https://europepmc.org/articles/PMC9997751?pdf=render"
   },
+  {
+    "id": "39311593",
+    "doi": "https://doi.org/10.1111/trf.17963",
+    "title": "The power of arts-based film interventions to encourage Black blood donors.",
+    "authorString": "Mills R, Okubanjo A, Acheampong N, Croucher M, Eaton N, Kazi A, di Angelantonio E, Wood A, Masser B, Ferguson E.",
+    "authorAffiliations": "",
+    "journalTitle": "Transfusion",
+    "pubYear": "2024",
+    "date": "2024-09-23",
+    "isOpenAccess": "N",
+    "keywords": "Donors | Co\u2010design | Art\u2010based | Film Campaigns",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Blood services must consider innovative ways to encourage more Black people to donate to enhance the efficacy of treatments. We evaluate how two innovative arts-based approaches (co-designed and locally produced films and a large-scale Marvel Studios'/NHSBT collaboration) can achieve this by generalizing to a wider audience from their target audiences.<h4>Study design and methods</h4>Four co-designed short community films were produced in the United Kingdom: Comedy, Reciprocity, Donor-Recipient, and Sliding Doors. In Study 1 (N\u2009=\u200944: Black people), these films were evaluated in the target community in which they were produced. In Study 2 (N\u2009=\u20091237: Black\u2009=\u2009638, White\u2009=\u2009599), the community and Marvel Black Panther/NHSBT films were evaluated in a nontarget general population sample. Evaluations were in terms of campaign behavioral efficacy (e.g., willingness to donate, encourage others to donate) and affect. These analyses were segmented by donor status, age, and gender.<h4>Results</h4>Study 1 shows that the community groups rated the films very positively, with over 90% stating that they would be convinced to donate blood. Study 2 shows the results from the community films generalized to the general population, with the Black Panther film also rated positively in the general population. Three community films and the Black Panther film were rated equally positively. There were notable differences across generations and by donor status.<h4>Discussion</h4>The results highlight the power of arts-based approaches (both locally co-produced community films and franchise collaborations) in encouraging donors within their target audiences and, importantly, on the broader population.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1111/trf.17963"
+  },
   {
     "id": "34356905",
     "doi": "https://doi.org/10.3390/biomedicines9070841",
@@ -10318,23 +10318,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.mdpi.com/2227-9059/9/7/841/pdf?version=1626837519; doi:https://doi.org/10.3390/biomedicines9070841; html:https://europepmc.org/articles/PMC8301759; pdf:https://europepmc.org/articles/PMC8301759?pdf=render"
   },
-  {
-    "id": "39033821",
-    "doi": "https://doi.org/10.1016/j.clinme.2024.100230",
-    "title": "Strategies to identify medical patients suitable for management through same-day emergency care services: A systematic review.",
-    "authorString": "Atkin C, Khosla R, Belsham J, Hegarty H, Hennessy C, Sapey E.",
-    "authorAffiliations": "",
-    "journalTitle": "Clinical medicine (London, England)",
-    "pubYear": "2024",
-    "date": "2024-07-19",
-    "isOpenAccess": "Y",
-    "keywords": "Scoring; Acute Medicine; Same Day Emergency Care; Admission Pathways",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Same-day emergency care (SDEC) in unplanned and emergency care is an NHS England (NHSE) priority. Optimal use of these services requires rapid identification of suitable patients. NHSE suggests the use of one tool for this purpose. This systematic review compares studies that evaluate the performance of selection tools for SDEC pathways. Nine studies met the inclusion criteria. Three scores were evaluated: the Amb score (seven studies), Glasgow Admission Prediction Score (GAPS) (six studies) and Sydney Triage to Admission Risk Tool (START) (two studies). There was heterogeneity in the populations assessed, exclusion criteria used and definitions used for SDEC suitability, with proportions of patients deemed 'suitable' for SDEC ranging from 20 to 80%. Reported score sensitivity and specificity ranged between 18-99% and 10-89%. Score performance could not be compared due to heterogeneity between studies. No studies assessed clinical implementation. The current evidence to support the use of a specific tool for SDEC is limited and requires further evaluation.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.clinme.2024.100230; html:https://europepmc.org/articles/PMC11359741; pdf:https://europepmc.org/articles/PMC11359741?pdf=render"
-  },
   {
     "id": "35379238",
     "doi": "https://doi.org/10.1186/s12933-022-01482-z",
@@ -10403,6 +10386,23 @@
     "laySummary": "",
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9161371; doi:https://doi.org/10.1126/science.abq4411; html:https://europepmc.org/articles/PMC9161371; pdf:https://europepmc.org/articles/PMC9161371?pdf=render"
   },
+  {
+    "id": "39033821",
+    "doi": "https://doi.org/10.1016/j.clinme.2024.100230",
+    "title": "Strategies to identify medical patients suitable for management through same-day emergency care services: A systematic review.",
+    "authorString": "Atkin C, Khosla R, Belsham J, Hegarty H, Hennessy C, Sapey E.",
+    "authorAffiliations": "",
+    "journalTitle": "Clinical medicine (London, England)",
+    "pubYear": "2024",
+    "date": "2024-07-19",
+    "isOpenAccess": "Y",
+    "keywords": "Scoring; Acute Medicine; Same Day Emergency Care; Admission Pathways",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Same-day emergency care (SDEC) in unplanned and emergency care is an NHS England (NHSE) priority. Optimal use of these services requires rapid identification of suitable patients. NHSE suggests the use of one tool for this purpose. This systematic review compares studies that evaluate the performance of selection tools for SDEC pathways. Nine studies met the inclusion criteria. Three scores were evaluated: the Amb score (seven studies), Glasgow Admission Prediction Score (GAPS) (six studies) and Sydney Triage to Admission Risk Tool (START) (two studies). There was heterogeneity in the populations assessed, exclusion criteria used and definitions used for SDEC suitability, with proportions of patients deemed 'suitable' for SDEC ranging from 20 to 80%. Reported score sensitivity and specificity ranged between 18-99% and 10-89%. Score performance could not be compared due to heterogeneity between studies. No studies assessed clinical implementation. The current evidence to support the use of a specific tool for SDEC is limited and requires further evaluation.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.clinme.2024.100230; html:https://europepmc.org/articles/PMC11359741; pdf:https://europepmc.org/articles/PMC11359741?pdf=render"
+  },
   {
     "id": "33879450",
     "doi": "https://doi.org/10.1136/heartjnl-2021-319118",
@@ -10421,21 +10421,21 @@
     "urls": "pdf:https://heart.bmj.com/content/heartjnl/107/18/1480.full.pdf; doi:https://doi.org/10.1136/heartjnl-2021-319118; html:https://europepmc.org/articles/PMC8408584; pdf:https://europepmc.org/articles/PMC8408584?pdf=render"
   },
   {
-    "id": "37656609",
-    "doi": "https://doi.org/10.1093/aje/kwad179",
-    "title": "CHALLENGES IN ESTIMATING THE EFFECTIVENESS OF 2 DOSES OF COVID-19 VACCINE BEYOND 6 MONTHS IN ENGLAND.",
-    "authorString": "Horne EMF, Hulme WJ, Keogh RH, Palmer TM, Williamson EJ, Parker EPK, Walker VM, Knight R, Wei Y, Taylor K, Fisher L, Morley J, Mehrkar A, Dillingham I, Bacon S, Goldacre B, Sterne JAC, OpenSAFELY Collaborative FT.",
+    "id": "38079428",
+    "doi": "https://doi.org/10.1371/journal.pone.0273596",
+    "title": "Factors associated with low school readiness, a linked health and education data study in Wales, UK.",
+    "authorString": "Bandyopadhyay A, Marchant E, Jones H, Parker M, Evans J, Brophy S.",
     "authorAffiliations": "",
-    "journalTitle": "American journal of epidemiology",
-    "pubYear": "2024",
-    "date": "2024-01-01",
+    "journalTitle": "PloS one",
+    "pubYear": "2023",
+    "date": "2023-12-11",
     "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "",
+    "abstract": "<h4>Background</h4>School readiness is a measure of a child's cognitive, social, and emotional readiness to begin formal schooling. Children with low school readiness need additional support from schools for learning, developing required social and academic skills, and catching-up with their school-ready peers. This study aims to identify the most significant risk factors associated with low school readiness using linked routine data for children in Wales.<h4>Method</h4>This was a longitudinal cohort study using linked data. The cohort comprises of children who completed the Foundation Phase assessment between 2012 and 2018. Individuals were identified by linking Welsh Demographic Service and Pre16 Education Attainment datasets. School readiness was assessed via the binary outcome of the Foundation Phase assessment (achieved/not achieved). This study used multivariable logistic regression model and a decision tree to identify and weight the most important risk factors associated with low school readiness.<h4>Results</h4>In order of importance, logistic regression identified maternal learning difficulties (adjusted odds ratio 5.35(95% confidence interval 3.97-7.22)), childhood epilepsy (2.95(2.39-3.66)), very low birth weight (2.24(1.86-2.70), being a boy (2.11(2.04-2.19)), being on free school meals (1.85(1.78-1.93)), living in the most deprived areas (1.67(1.57-1.77)), maternal death (1.47(1.09-1.98)), and maternal diabetes (1.46(1.23-1.78)) as factors associated with low school readiness. Using a decision tree, eligibility for free school meals, being a boy, absence/low attendance at school, being born late in the academic year, being a low birthweight child, and not being breastfed were factors which were associated with low school readiness.<h4>Conclusion</h4>This work suggests that public health interventions focusing on children who are: boys, living in deprived areas, have poor early years attendance, have parents with learning difficulties, have parents with an illness or have illnesses themselves, would make the most difference to school readiness in the population.",
     "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/aje/advance-article-pdf/doi/10.1093/aje/kwad179/51329819/kwad179.pdf; doi:https://doi.org/10.1093/aje/kwad179; html:https://europepmc.org/articles/PMC10773473; pdf:https://europepmc.org/articles/PMC10773473?pdf=render"
+    "urls": "doi:https://doi.org/10.1371/journal.pone.0273596; html:https://europepmc.org/articles/PMC10712842; pdf:https://europepmc.org/articles/PMC10712842?pdf=render"
   },
   {
     "id": "37248229",
@@ -10454,23 +10454,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1038/s41467-023-38756-3; doi:https://doi.org/10.1038/s41467-023-38756-3; html:https://europepmc.org/articles/PMC10226446; pdf:https://europepmc.org/articles/PMC10226446?pdf=render"
   },
-  {
-    "id": "38079428",
-    "doi": "https://doi.org/10.1371/journal.pone.0273596",
-    "title": "Factors associated with low school readiness, a linked health and education data study in Wales, UK.",
-    "authorString": "Bandyopadhyay A, Marchant E, Jones H, Parker M, Evans J, Brophy S.",
-    "authorAffiliations": "",
-    "journalTitle": "PloS one",
-    "pubYear": "2023",
-    "date": "2023-12-11",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>School readiness is a measure of a child's cognitive, social, and emotional readiness to begin formal schooling. Children with low school readiness need additional support from schools for learning, developing required social and academic skills, and catching-up with their school-ready peers. This study aims to identify the most significant risk factors associated with low school readiness using linked routine data for children in Wales.<h4>Method</h4>This was a longitudinal cohort study using linked data. The cohort comprises of children who completed the Foundation Phase assessment between 2012 and 2018. Individuals were identified by linking Welsh Demographic Service and Pre16 Education Attainment datasets. School readiness was assessed via the binary outcome of the Foundation Phase assessment (achieved/not achieved). This study used multivariable logistic regression model and a decision tree to identify and weight the most important risk factors associated with low school readiness.<h4>Results</h4>In order of importance, logistic regression identified maternal learning difficulties (adjusted odds ratio 5.35(95% confidence interval 3.97-7.22)), childhood epilepsy (2.95(2.39-3.66)), very low birth weight (2.24(1.86-2.70), being a boy (2.11(2.04-2.19)), being on free school meals (1.85(1.78-1.93)), living in the most deprived areas (1.67(1.57-1.77)), maternal death (1.47(1.09-1.98)), and maternal diabetes (1.46(1.23-1.78)) as factors associated with low school readiness. Using a decision tree, eligibility for free school meals, being a boy, absence/low attendance at school, being born late in the academic year, being a low birthweight child, and not being breastfed were factors which were associated with low school readiness.<h4>Conclusion</h4>This work suggests that public health interventions focusing on children who are: boys, living in deprived areas, have poor early years attendance, have parents with learning difficulties, have parents with an illness or have illnesses themselves, would make the most difference to school readiness in the population.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1371/journal.pone.0273596; html:https://europepmc.org/articles/PMC10712842; pdf:https://europepmc.org/articles/PMC10712842?pdf=render"
-  },
   {
     "id": "34966903",
     "doi": "https://doi.org/10.3389/fdgth.2021.778305",
@@ -10489,21 +10472,21 @@
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8710455; doi:https://doi.org/10.3389/fdgth.2021.778305; html:https://europepmc.org/articles/PMC8710455; pdf:https://europepmc.org/articles/PMC8710455?pdf=render"
   },
   {
-    "id": "39446320",
-    "doi": "https://doi.org/10.1001/jamanetworkopen.2024.41166",
-    "title": "Pharmacologic Treatments for Dementia and the Risk of Developing Age-Related Macular Degeneration.",
-    "authorString": "Wang J, Antza C, Lee WH, Coker J, Keane PA, Denniston AK, Nirantharakumar K, Adderley NJ.",
+    "id": "37656609",
+    "doi": "https://doi.org/10.1093/aje/kwad179",
+    "title": "CHALLENGES IN ESTIMATING THE EFFECTIVENESS OF 2 DOSES OF COVID-19 VACCINE BEYOND 6 MONTHS IN ENGLAND.",
+    "authorString": "Horne EMF, Hulme WJ, Keogh RH, Palmer TM, Williamson EJ, Parker EPK, Walker VM, Knight R, Wei Y, Taylor K, Fisher L, Morley J, Mehrkar A, Dillingham I, Bacon S, Goldacre B, Sterne JAC, OpenSAFELY Collaborative FT.",
     "authorAffiliations": "",
-    "journalTitle": "JAMA network open",
+    "journalTitle": "American journal of epidemiology",
     "pubYear": "2024",
-    "date": "2024-10-01",
-    "isOpenAccess": "N",
+    "date": "2024-01-01",
+    "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Importance</h4>Age-related macular degeneration (AMD) is the leading cause of blindness among people aged 50 years or older worldwide. There is a need for new strategies for the prevention and treatment of AMD. There is some limited evidence to suggest the possibility of a protective association of dementia medications with the development of some types of AMD, but the evidence is weak.<h4>Objective</h4>To investigate whether the dementia medications memantine and donepezil are associated with the risk of developing AMD.<h4>Design, setting, and participants</h4>Three population-based cohort studies were performed using data from the Clinical Practice Research Datalink GOLD and Aurum databases from May 15, 2002, to June 21, 2022. Participants included individuals with dementia (vascular dementia, nonvascular dementia, or Alzheimer disease) aged 40 years or older. Statistical analysis was carried out between February and November 2023.<h4>Exposures</h4>Exposures were dementia medications. Cohort 1 compared patients prescribed donepezil with those prescribed rivastigmine or galantamine using the new-user design. Cohort 2 compared memantine with donepezil, rivastigmine, or galantamine using the prevalent new-user design. In a sensitivity analysis, cohort 3 compared memantine with rivastigmine or galantamine only.<h4>Main outcomes and measures</h4>New diagnosis of AMD.<h4>Results</h4>There were 132\u202f846 individuals (mean [SD] age, 80.4 [7.6] years; 61.8% women; mean [SD] body mass index [BMI], 25.5 [4.6]) with a diagnosis of dementia included in cohort 1, 159\u202f419 individuals (mean [SD] age, 81.2 [7.6] years; 59.7% women; mean [SD] body mass index [BMI], 25.6 [4.7]) with a diagnosis of dementia included in cohort 2, and 92\u202f328 individuals with a diagnosis of dementia included in cohort 3 (mean [SD] age, 80.9 [7.7] years; 58.5% women; mean [SD] body mass index [BMI], 25.5 [4.7]). The adjusted hazard ratio (HR) for donepezil compared with rivastigmine or galantamine (cohort 1) was 0.95 (95% CI, 0.67-1.35). The adjusted HR for memantine compared with donepezil, rivastigmine, or galantamine (cohort 2) was 1.03 (95% CI, 0.83-1.27). The adjusted HR for memantine vs rivastigmine or galantamine only (cohort 3) was 1.24 (95% CI, 0.83-1.86).<h4>Conclusions and relevance</h4>This cohort study of patients with dementia found no significant associations between memantine or donepezil compared with other dementia medications and the risk of development of AMD. Further research is recommended to examine any possible pathophysiological protective action of memantine and other dementia medications against the development of AMD.",
+    "abstract": "",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1001/jamanetworkopen.2024.41166"
+    "urls": "pdf:https://academic.oup.com/aje/advance-article-pdf/doi/10.1093/aje/kwad179/51329819/kwad179.pdf; doi:https://doi.org/10.1093/aje/kwad179; html:https://europepmc.org/articles/PMC10773473; pdf:https://europepmc.org/articles/PMC10773473?pdf=render"
   },
   {
     "id": "34261639",
@@ -10522,6 +10505,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.bmj.com/content/bmj/374/bmj.n1592.full.pdf; doi:https://doi.org/10.1136/bmj.n1592; html:https://europepmc.org/articles/PMC8278652; pdf:https://europepmc.org/articles/PMC8278652?pdf=render"
   },
+  {
+    "id": "39446320",
+    "doi": "https://doi.org/10.1001/jamanetworkopen.2024.41166",
+    "title": "Pharmacologic Treatments for Dementia and the Risk of Developing Age-Related Macular Degeneration.",
+    "authorString": "Wang J, Antza C, Lee WH, Coker J, Keane PA, Denniston AK, Nirantharakumar K, Adderley NJ.",
+    "authorAffiliations": "",
+    "journalTitle": "JAMA network open",
+    "pubYear": "2024",
+    "date": "2024-10-01",
+    "isOpenAccess": "N",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Importance</h4>Age-related macular degeneration (AMD) is the leading cause of blindness among people aged 50 years or older worldwide. There is a need for new strategies for the prevention and treatment of AMD. There is some limited evidence to suggest the possibility of a protective association of dementia medications with the development of some types of AMD, but the evidence is weak.<h4>Objective</h4>To investigate whether the dementia medications memantine and donepezil are associated with the risk of developing AMD.<h4>Design, setting, and participants</h4>Three population-based cohort studies were performed using data from the Clinical Practice Research Datalink GOLD and Aurum databases from May 15, 2002, to June 21, 2022. Participants included individuals with dementia (vascular dementia, nonvascular dementia, or Alzheimer disease) aged 40 years or older. Statistical analysis was carried out between February and November 2023.<h4>Exposures</h4>Exposures were dementia medications. Cohort 1 compared patients prescribed donepezil with those prescribed rivastigmine or galantamine using the new-user design. Cohort 2 compared memantine with donepezil, rivastigmine, or galantamine using the prevalent new-user design. In a sensitivity analysis, cohort 3 compared memantine with rivastigmine or galantamine only.<h4>Main outcomes and measures</h4>New diagnosis of AMD.<h4>Results</h4>There were 132\u202f846 individuals (mean [SD] age, 80.4 [7.6] years; 61.8% women; mean [SD] body mass index [BMI], 25.5 [4.6]) with a diagnosis of dementia included in cohort 1, 159\u202f419 individuals (mean [SD] age, 81.2 [7.6] years; 59.7% women; mean [SD] body mass index [BMI], 25.6 [4.7]) with a diagnosis of dementia included in cohort 2, and 92\u202f328 individuals with a diagnosis of dementia included in cohort 3 (mean [SD] age, 80.9 [7.7] years; 58.5% women; mean [SD] body mass index [BMI], 25.5 [4.7]). The adjusted hazard ratio (HR) for donepezil compared with rivastigmine or galantamine (cohort 1) was 0.95 (95% CI, 0.67-1.35). The adjusted HR for memantine compared with donepezil, rivastigmine, or galantamine (cohort 2) was 1.03 (95% CI, 0.83-1.27). The adjusted HR for memantine vs rivastigmine or galantamine only (cohort 3) was 1.24 (95% CI, 0.83-1.86).<h4>Conclusions and relevance</h4>This cohort study of patients with dementia found no significant associations between memantine or donepezil compared with other dementia medications and the risk of development of AMD. Further research is recommended to examine any possible pathophysiological protective action of memantine and other dementia medications against the development of AMD.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1001/jamanetworkopen.2024.41166"
+  },
   {
     "id": "34957254",
     "doi": "https://doi.org/10.3389/fcvm.2021.766287",
@@ -10574,21 +10574,21 @@
     "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fdgth.2022.874237/pdf; doi:https://doi.org/10.3389/fdgth.2022.874237; html:https://europepmc.org/articles/PMC9490173; pdf:https://europepmc.org/articles/PMC9490173?pdf=render"
   },
   {
-    "id": "39175920",
-    "doi": "https://doi.org/10.1136/bmjmed-2023-000633",
-    "title": "Age and sex specific thresholds for risk stratification of cardiovascular disease and clinical decision making: prospective open cohort study.",
-    "authorString": "Xu Z, Usher-Smith J, Pennells L, Chung R, Arnold M, Kim L, Kaptoge S, Sperrin M, Di Angelantonio E, Wood AM.",
+    "id": "31591592",
+    "doi": "https://doi.org/10.1038/s41591-019-0597-x",
+    "title": "Avoidable flaws in observational analyses: an application to statins and cancer.",
+    "authorString": "Dickerman BA, Garc\u00eda-Alb\u00e9niz X, Logan RW, Denaxas S, Hern\u00e1n MA.",
     "authorAffiliations": "",
-    "journalTitle": "BMJ medicine",
-    "pubYear": "2024",
-    "date": "2024-08-12",
-    "isOpenAccess": "Y",
-    "keywords": "Cardiovascular disease; Risk stratification; Risk Prediction; Statin Treatment",
+    "journalTitle": "Nature medicine",
+    "pubYear": "2019",
+    "date": "2019-10-07",
+    "isOpenAccess": "N",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Objective</h4>To quantify the potential advantages of using 10 year risk prediction models for cardiovascular disease, in combination with risk thresholds specific to both age and sex, to identify individuals at high risk of cardiovascular disease for allocation of statin treatment.<h4>Design</h4>Prospective open cohort study.<h4>Setting</h4>Primary care data from the UK Clinical Practice Research Datalink GOLD, linked with hospital admissions from Hospital Episode Statistics and national mortality records from the Office for National Statistics in England, 1 January 2006 to 31 May 2019.<h4>Participants</h4>1\u2009046\u2009736 individuals (aged 40-85 years) with no cardiovascular disease, diabetes, or a history of statin treatment at baseline using data from electronic health records.<h4>Main outcome measures</h4>10 year risk of cardiovascular disease, calculated with version 2 of the QRISK cardiovascular disease risk algorithm (QRISK2), with two main strategies to identify individuals at high risk: in strategy A, estimated risk was a fixed cut-off value of \u226510% (ie, as per the UK National Institute for Health and Care Excellence guidelines); in strategy B, estimated risk was \u226510%\u2009or \u226590th centile of age and sex specific risk distributions.<h4>Results</h4>Compared with strategy A, strategy B stratified 20\u2009241 (149.8%) more women aged \u226453 years and 9832 (150.2%) more men aged \u226447 years as having a high risk of cardiovascular disease; for all other ages the strategies were the same. Assuming that treatment with statins would be initiated in those identified as high risk, differences in the estimated gain in cardiovascular disease-free life years from statin treatment for strategy B versus strategy A were 0.14 and 0.16 years for women and men aged 40 years, respectively; among individuals aged 40-49 years, the numbers needed to treat to prevent one cardiovascular disease event for strategy B versus strategy A were 39 versus 21 in women and 19 versus 15 in men, respectively.<h4>Conclusions</h4>This study quantified the potential gains in cardiovascular disease-free life years when implementing prevention strategies based on age and sex specific risk thresholds instead of a fixed risk threshold for allocation of statin treatment. Such gains should be weighed against the costs of treating more younger people with statins for longer.",
+    "abstract": "The increasing availability of large healthcare databases is fueling an intense debate on whether real-world data should play a role in the assessment of the benefit-risk of medical treatments. In many observational studies, for example, statin users were found to have a substantially lower risk of cancer than in meta-analyses of randomized trials. Although such discrepancies are often attributed to a lack of randomization in the observational studies, they might be explained by flaws that can be avoided by explicitly emulating a target trial (the randomized trial that would answer the question of interest). Using the electronic health records of 733,804 UK adults, we emulated a target trial of statins and cancer and compared our estimates with those obtained using previously applied analytic approaches. Over the 10-yr follow-up, 28,408 individuals developed cancer. Under the target trial approach, estimated observational analogs of intention-to-treat and per-protocol 10-yr cancer-free survival differences were -0.5% (95% confidence interval (CI) -1.0%, 0.0%) and -0.3% (95% CI -1.5%, 0.5%), respectively. By contrast, previous analytic approaches yielded estimates that appeared to be strongly protective. Our findings highlight the importance of explicitly emulating a target trial to reduce bias in the effect estimates derived from observational analyses.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1136/bmjmed-2023-000633; html:https://europepmc.org/articles/PMC11340247; pdf:https://europepmc.org/articles/PMC11340247?pdf=render"
+    "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7076561; doi:https://doi.org/10.1038/s41591-019-0597-x; html:https://europepmc.org/articles/PMC7076561; pdf:https://europepmc.org/articles/PMC7076561?pdf=render; doi:https://doi.org/10.1038/s41591-019-0597-x"
   },
   {
     "id": "35474585",
@@ -10608,38 +10608,38 @@
     "urls": "doi:https://doi.org/10.1111/bcp.15366; doi:https://doi.org/10.1111/bcp.15366; html:https://europepmc.org/articles/PMC9541840; pdf:https://europepmc.org/articles/PMC9541840?pdf=render"
   },
   {
-    "id": "31591592",
-    "doi": "https://doi.org/10.1038/s41591-019-0597-x",
-    "title": "Avoidable flaws in observational analyses: an application to statins and cancer.",
-    "authorString": "Dickerman BA, Garc\u00eda-Alb\u00e9niz X, Logan RW, Denaxas S, Hern\u00e1n MA.",
+    "id": "34282121",
+    "doi": "https://doi.org/10.1038/s41398-021-01522-4",
+    "title": "Phenotypic and genetic associations between anhedonia and brain structure in UK Biobank.",
+    "authorString": "Zhu X, Ward J, Cullen B, Lyall DM, Strawbridge RJ, Lyall LM, Smith DJ.",
     "authorAffiliations": "",
-    "journalTitle": "Nature medicine",
-    "pubYear": "2019",
-    "date": "2019-10-07",
-    "isOpenAccess": "N",
+    "journalTitle": "Translational psychiatry",
+    "pubYear": "2021",
+    "date": "2021-07-16",
+    "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "The increasing availability of large healthcare databases is fueling an intense debate on whether real-world data should play a role in the assessment of the benefit-risk of medical treatments. In many observational studies, for example, statin users were found to have a substantially lower risk of cancer than in meta-analyses of randomized trials. Although such discrepancies are often attributed to a lack of randomization in the observational studies, they might be explained by flaws that can be avoided by explicitly emulating a target trial (the randomized trial that would answer the question of interest). Using the electronic health records of 733,804 UK adults, we emulated a target trial of statins and cancer and compared our estimates with those obtained using previously applied analytic approaches. Over the 10-yr follow-up, 28,408 individuals developed cancer. Under the target trial approach, estimated observational analogs of intention-to-treat and per-protocol 10-yr cancer-free survival differences were -0.5% (95% confidence interval (CI) -1.0%, 0.0%) and -0.3% (95% CI -1.5%, 0.5%), respectively. By contrast, previous analytic approaches yielded estimates that appeared to be strongly protective. Our findings highlight the importance of explicitly emulating a target trial to reduce bias in the effect estimates derived from observational analyses.",
+    "abstract": "Anhedonia is a core symptom of multiple psychiatric disorders and has been associated with alterations in brain structure. Genome-wide association studies suggest that anhedonia is heritable, with a polygenic architecture, but few studies have explored the association between genetic loading for anhedonia-indexed by polygenic risk scores for anhedonia (PRS-anhedonia)-and structural brain imaging phenotypes. Here, we investigated how anhedonia and PRS-anhedonia were associated with brain structure within the UK Biobank cohort. Brain measures (including total grey/white matter volumes, subcortical volumes, cortical thickness (CT) and white matter integrity) were analysed using linear mixed models in relation to anhedonia and PRS-anhedonia in 19,592 participants (9225 males; mean age\u2009=\u200962.6 years, SD\u2009=\u20097.44). We found that state anhedonia was significantly associated with reduced total grey matter volume (GMV); increased total white matter volume (WMV); smaller volumes in thalamus and nucleus accumbens; reduced CT within the paracentral cortex, the opercular part of inferior frontal gyrus, precentral cortex, insula and rostral anterior cingulate cortex; and poorer integrity of many white matter tracts. PRS-anhedonia was associated with reduced total GMV; increased total WMV; reduced white matter integrity; and reduced CT within the parahippocampal cortex, superior temporal gyrus and insula. Overall, both state anhedonia and PRS-anhedonia were associated with individual differences in multiple brain structures, including within reward-related circuits. These associations may represent vulnerability markers for psychopathology relevant to a range of psychiatric disorders.",
     "laySummary": "",
-    "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7076561; doi:https://doi.org/10.1038/s41591-019-0597-x; html:https://europepmc.org/articles/PMC7076561; pdf:https://europepmc.org/articles/PMC7076561?pdf=render; doi:https://doi.org/10.1038/s41591-019-0597-x"
+    "urls": "pdf:https://www.nature.com/articles/s41398-021-01522-4.pdf; doi:https://doi.org/10.1038/s41398-021-01522-4; html:https://europepmc.org/articles/PMC8289859; pdf:https://europepmc.org/articles/PMC8289859?pdf=render"
   },
   {
-    "id": "38317644",
-    "doi": "https://doi.org/10.1177/03331024241229410",
-    "title": "How migraine and its associated treatment impact on pregnancy outcomes: Umbrella review with updated systematic review and meta-analysis.",
-    "authorString": "Phillips K, Clerkin-Oliver C, Nirantharakumar K, Crowe FL, Wakerley BR.",
+    "id": "39175920",
+    "doi": "https://doi.org/10.1136/bmjmed-2023-000633",
+    "title": "Age and sex specific thresholds for risk stratification of cardiovascular disease and clinical decision making: prospective open cohort study.",
+    "authorString": "Xu Z, Usher-Smith J, Pennells L, Chung R, Arnold M, Kim L, Kaptoge S, Sperrin M, Di Angelantonio E, Wood AM.",
     "authorAffiliations": "",
-    "journalTitle": "Cephalalgia : an international journal of headache",
+    "journalTitle": "BMJ medicine",
     "pubYear": "2024",
-    "date": "2024-02-01",
-    "isOpenAccess": "N",
-    "keywords": "Pregnancy; Migraine",
+    "date": "2024-08-12",
+    "isOpenAccess": "Y",
+    "keywords": "Cardiovascular disease; Risk stratification; Risk Prediction; Statin Treatment",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Migraine is common in reproductive aged women. Understanding the impact of migraine and associated treatments on pregnancy outcomes remains very important. An umbrella review of systematic reviews, with or without meta-analyses, examined the link between migraine and pregnancy outcomes.<h4>Methods</h4>We systematically searched Medline, Embase and Cochrane to 27 October 2022. Quality appraisal was carried out using the AMSTAR2 tool. An established framework was used to determine whether included reviews were eligible for update.<h4>Results</h4>Four studies met review criteria. Migraine was reported to be associated with increased odds ratio (OR) of pre-eclampsia, low birth weight and peripartum mental illness (pooled OR\u2009=\u20093.54 (2.24-5.59)). Triptan-exposed women had increased odds of miscarriage compared to women without migraine (pooled OR\u2009=\u20093.54 (2.24-5.59)). In updated meta-analyses, migraine was associated with an increased odds of pre-eclampsia and preterm birth (pooled OR\u2009=\u20092.05 (1.47-2.84) and 1.26 (1.21-1.32) respectively).<h4>Conclusions</h4>Migraine is associated with increased odds of pre-eclampsia, peripartum mental illness and preterm birth. Further investigation of the relationship between migraine and placental abruption, low birth weight and small for gestational age is warranted, as well as the relationship between migraine, triptans and miscarriage risk.<b>Systematic Review Registration:</b> Prospero CRD42022357630.",
+    "abstract": "<h4>Objective</h4>To quantify the potential advantages of using 10 year risk prediction models for cardiovascular disease, in combination with risk thresholds specific to both age and sex, to identify individuals at high risk of cardiovascular disease for allocation of statin treatment.<h4>Design</h4>Prospective open cohort study.<h4>Setting</h4>Primary care data from the UK Clinical Practice Research Datalink GOLD, linked with hospital admissions from Hospital Episode Statistics and national mortality records from the Office for National Statistics in England, 1 January 2006 to 31 May 2019.<h4>Participants</h4>1\u2009046\u2009736 individuals (aged 40-85 years) with no cardiovascular disease, diabetes, or a history of statin treatment at baseline using data from electronic health records.<h4>Main outcome measures</h4>10 year risk of cardiovascular disease, calculated with version 2 of the QRISK cardiovascular disease risk algorithm (QRISK2), with two main strategies to identify individuals at high risk: in strategy A, estimated risk was a fixed cut-off value of \u226510% (ie, as per the UK National Institute for Health and Care Excellence guidelines); in strategy B, estimated risk was \u226510%\u2009or \u226590th centile of age and sex specific risk distributions.<h4>Results</h4>Compared with strategy A, strategy B stratified 20\u2009241 (149.8%) more women aged \u226453 years and 9832 (150.2%) more men aged \u226447 years as having a high risk of cardiovascular disease; for all other ages the strategies were the same. Assuming that treatment with statins would be initiated in those identified as high risk, differences in the estimated gain in cardiovascular disease-free life years from statin treatment for strategy B versus strategy A were 0.14 and 0.16 years for women and men aged 40 years, respectively; among individuals aged 40-49 years, the numbers needed to treat to prevent one cardiovascular disease event for strategy B versus strategy A were 39 versus 21 in women and 19 versus 15 in men, respectively.<h4>Conclusions</h4>This study quantified the potential gains in cardiovascular disease-free life years when implementing prevention strategies based on age and sex specific risk thresholds instead of a fixed risk threshold for allocation of statin treatment. Such gains should be weighed against the costs of treating more younger people with statins for longer.",
     "laySummary": "",
-    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/03331024241229410; doi:https://doi.org/10.1177/03331024241229410"
+    "urls": "doi:https://doi.org/10.1136/bmjmed-2023-000633; html:https://europepmc.org/articles/PMC11340247; pdf:https://europepmc.org/articles/PMC11340247?pdf=render"
   },
   {
     "id": "32180562",
@@ -10659,21 +10659,21 @@
     "urls": "doi:https://doi.org/10.1016/j.molmet.2020.01.009; doi:https://doi.org/10.1016/j.molmet.2020.01.009; html:https://europepmc.org/articles/PMC7021539; pdf:https://europepmc.org/articles/PMC7021539?pdf=render"
   },
   {
-    "id": "34282121",
-    "doi": "https://doi.org/10.1038/s41398-021-01522-4",
-    "title": "Phenotypic and genetic associations between anhedonia and brain structure in UK Biobank.",
-    "authorString": "Zhu X, Ward J, Cullen B, Lyall DM, Strawbridge RJ, Lyall LM, Smith DJ.",
+    "id": "38317644",
+    "doi": "https://doi.org/10.1177/03331024241229410",
+    "title": "How migraine and its associated treatment impact on pregnancy outcomes: Umbrella review with updated systematic review and meta-analysis.",
+    "authorString": "Phillips K, Clerkin-Oliver C, Nirantharakumar K, Crowe FL, Wakerley BR.",
     "authorAffiliations": "",
-    "journalTitle": "Translational psychiatry",
-    "pubYear": "2021",
-    "date": "2021-07-16",
-    "isOpenAccess": "Y",
-    "keywords": "",
+    "journalTitle": "Cephalalgia : an international journal of headache",
+    "pubYear": "2024",
+    "date": "2024-02-01",
+    "isOpenAccess": "N",
+    "keywords": "Pregnancy; Migraine",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Anhedonia is a core symptom of multiple psychiatric disorders and has been associated with alterations in brain structure. Genome-wide association studies suggest that anhedonia is heritable, with a polygenic architecture, but few studies have explored the association between genetic loading for anhedonia-indexed by polygenic risk scores for anhedonia (PRS-anhedonia)-and structural brain imaging phenotypes. Here, we investigated how anhedonia and PRS-anhedonia were associated with brain structure within the UK Biobank cohort. Brain measures (including total grey/white matter volumes, subcortical volumes, cortical thickness (CT) and white matter integrity) were analysed using linear mixed models in relation to anhedonia and PRS-anhedonia in 19,592 participants (9225 males; mean age\u2009=\u200962.6 years, SD\u2009=\u20097.44). We found that state anhedonia was significantly associated with reduced total grey matter volume (GMV); increased total white matter volume (WMV); smaller volumes in thalamus and nucleus accumbens; reduced CT within the paracentral cortex, the opercular part of inferior frontal gyrus, precentral cortex, insula and rostral anterior cingulate cortex; and poorer integrity of many white matter tracts. PRS-anhedonia was associated with reduced total GMV; increased total WMV; reduced white matter integrity; and reduced CT within the parahippocampal cortex, superior temporal gyrus and insula. Overall, both state anhedonia and PRS-anhedonia were associated with individual differences in multiple brain structures, including within reward-related circuits. These associations may represent vulnerability markers for psychopathology relevant to a range of psychiatric disorders.",
+    "abstract": "<h4>Background</h4>Migraine is common in reproductive aged women. Understanding the impact of migraine and associated treatments on pregnancy outcomes remains very important. An umbrella review of systematic reviews, with or without meta-analyses, examined the link between migraine and pregnancy outcomes.<h4>Methods</h4>We systematically searched Medline, Embase and Cochrane to 27 October 2022. Quality appraisal was carried out using the AMSTAR2 tool. An established framework was used to determine whether included reviews were eligible for update.<h4>Results</h4>Four studies met review criteria. Migraine was reported to be associated with increased odds ratio (OR) of pre-eclampsia, low birth weight and peripartum mental illness (pooled OR\u2009=\u20093.54 (2.24-5.59)). Triptan-exposed women had increased odds of miscarriage compared to women without migraine (pooled OR\u2009=\u20093.54 (2.24-5.59)). In updated meta-analyses, migraine was associated with an increased odds of pre-eclampsia and preterm birth (pooled OR\u2009=\u20092.05 (1.47-2.84) and 1.26 (1.21-1.32) respectively).<h4>Conclusions</h4>Migraine is associated with increased odds of pre-eclampsia, peripartum mental illness and preterm birth. Further investigation of the relationship between migraine and placental abruption, low birth weight and small for gestational age is warranted, as well as the relationship between migraine, triptans and miscarriage risk.<b>Systematic Review Registration:</b> Prospero CRD42022357630.",
     "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41398-021-01522-4.pdf; doi:https://doi.org/10.1038/s41398-021-01522-4; html:https://europepmc.org/articles/PMC8289859; pdf:https://europepmc.org/articles/PMC8289859?pdf=render"
+    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/03331024241229410; doi:https://doi.org/10.1177/03331024241229410"
   },
   {
     "id": "34782484",
@@ -10743,23 +10743,6 @@
     "laySummary": "",
     "urls": "pdf:https://orca.cardiff.ac.uk/161774/1/SCHIZR~1.PDF; doi:https://doi.org/10.1016/j.schres.2023.08.014"
   },
-  {
-    "id": "33842409",
-    "doi": "https://doi.org/10.3389/fped.2021.630036",
-    "title": "Microtia: A Data Linkage Study of Epidemiology and Implications for Service Delivery.",
-    "authorString": "Jovic TH, Gibson JAG, Griffiths R, Dobbs TD, Akbari A, Wilson-Jones N, Costello R, Evans P, Cooper M, Key S, Lyons R, Whitaker IS.",
-    "authorAffiliations": "",
-    "journalTitle": "Frontiers in pediatrics",
-    "pubYear": "2021",
-    "date": "2021-03-26",
-    "isOpenAccess": "Y",
-    "keywords": "epidemiology; congenital; Otology; Reconstructive Surgery; Microtia",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<b>Introduction:</b> Previous studies of microtia epidemiology globally have demonstrated significant geographical and ethnic variation, cited broadly as affecting 3-5 in 10,000 live births. The aim of this study was to determine the incidence of microtia in a largely homogeneous ethnic population in the United Kingdom (Wales) and to identify factors, such as distance and socioeconomic status, which may influence the access to surgical intervention. <b>Materials and Methods:</b> A retrospective cohort study was conducted using data linkage to identify patients born between 2000 and 2018 with a diagnosis of microtia. Microtia incidence was calculated using annual and geographic birth rates. Surgical operation codes were used to classify patients into those that had no surgery, autologous reconstruction or prosthetic reconstruction. Sociodemographic attributes were compared using descriptive statistics to determine differences in access to each type of surgical intervention. <b>Results:</b> A total of 101 patients were identified, 64.4% were male and the median age was 12 (8-16). The mean annual incidence was 2.13 microtia cases per 10,000 births over the 19-year study period. Both temporal and geographic variation was noted. The majority of patients undergoing surgery opted for autologous reconstruction (72.9%) at a median age of 9 (7-10) compared to 7 (5-8) for prosthetic reconstruction. Autologous reconstruction had a higher median number of surgeries (2, 1-3) than prosthetic (1.5, 1-2) and a higher median socioeconomic status of 3 (2-4) compared to 2 (1-4) for the prosthetic cohort. There were no statistically significant differences in the distance traveled for surgery. <b>Discussion:</b> This study highlights a role for data linkage in epidemiological analyses and provides a revised incidence of microtia in Wales. Although the majority of patients opted for autologous reconstruction, demographic disparities in socioeconomic status warrant further investigation, emphasizing the importance of striving for equity in accessibility to surgical intervention.",
-    "laySummary": "",
-    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fped.2021.630036/pdf; doi:https://doi.org/10.3389/fped.2021.630036; html:https://europepmc.org/articles/PMC8033003; pdf:https://europepmc.org/articles/PMC8033003?pdf=render"
-  },
   {
     "id": "33182605",
     "doi": "https://doi.org/10.3390/genes11111326",
@@ -10777,6 +10760,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.mdpi.com/2073-4425/11/11/1326/pdf?version=1605520057; doi:https://doi.org/10.3390/genes11111326; html:https://europepmc.org/articles/PMC7697406; pdf:https://europepmc.org/articles/PMC7697406?pdf=render"
   },
+  {
+    "id": "33842409",
+    "doi": "https://doi.org/10.3389/fped.2021.630036",
+    "title": "Microtia: A Data Linkage Study of Epidemiology and Implications for Service Delivery.",
+    "authorString": "Jovic TH, Gibson JAG, Griffiths R, Dobbs TD, Akbari A, Wilson-Jones N, Costello R, Evans P, Cooper M, Key S, Lyons R, Whitaker IS.",
+    "authorAffiliations": "",
+    "journalTitle": "Frontiers in pediatrics",
+    "pubYear": "2021",
+    "date": "2021-03-26",
+    "isOpenAccess": "Y",
+    "keywords": "epidemiology; congenital; Otology; Reconstructive Surgery; Microtia",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<b>Introduction:</b> Previous studies of microtia epidemiology globally have demonstrated significant geographical and ethnic variation, cited broadly as affecting 3-5 in 10,000 live births. The aim of this study was to determine the incidence of microtia in a largely homogeneous ethnic population in the United Kingdom (Wales) and to identify factors, such as distance and socioeconomic status, which may influence the access to surgical intervention. <b>Materials and Methods:</b> A retrospective cohort study was conducted using data linkage to identify patients born between 2000 and 2018 with a diagnosis of microtia. Microtia incidence was calculated using annual and geographic birth rates. Surgical operation codes were used to classify patients into those that had no surgery, autologous reconstruction or prosthetic reconstruction. Sociodemographic attributes were compared using descriptive statistics to determine differences in access to each type of surgical intervention. <b>Results:</b> A total of 101 patients were identified, 64.4% were male and the median age was 12 (8-16). The mean annual incidence was 2.13 microtia cases per 10,000 births over the 19-year study period. Both temporal and geographic variation was noted. The majority of patients undergoing surgery opted for autologous reconstruction (72.9%) at a median age of 9 (7-10) compared to 7 (5-8) for prosthetic reconstruction. Autologous reconstruction had a higher median number of surgeries (2, 1-3) than prosthetic (1.5, 1-2) and a higher median socioeconomic status of 3 (2-4) compared to 2 (1-4) for the prosthetic cohort. There were no statistically significant differences in the distance traveled for surgery. <b>Discussion:</b> This study highlights a role for data linkage in epidemiological analyses and provides a revised incidence of microtia in Wales. Although the majority of patients opted for autologous reconstruction, demographic disparities in socioeconomic status warrant further investigation, emphasizing the importance of striving for equity in accessibility to surgical intervention.",
+    "laySummary": "",
+    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fped.2021.630036/pdf; doi:https://doi.org/10.3389/fped.2021.630036; html:https://europepmc.org/articles/PMC8033003; pdf:https://europepmc.org/articles/PMC8033003?pdf=render"
+  },
   {
     "id": "34983063",
     "doi": "https://doi.org/10.1093/bioinformatics/btab879",
@@ -10794,6 +10794,40 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/bioinformatics/article-pdf/38/6/1639/42744567/btab879.pdf; doi:https://doi.org/10.1093/bioinformatics/btab879; html:https://europepmc.org/articles/PMC8896646; pdf:https://europepmc.org/articles/PMC8896646?pdf=render"
   },
+  {
+    "id": "33965593",
+    "doi": "https://doi.org/10.1016/j.jaip.2021.04.055",
+    "title": "Intolerance to Angiotensin Converting Enzyme Inhibitors in Asthma and the General Population: A UK Population-Based Cohort Study.",
+    "authorString": "Morales DR, Lipworth BJ, Donnan PT, Wang H.",
+    "authorAffiliations": "",
+    "journalTitle": "The journal of allergy and clinical immunology. In practice",
+    "pubYear": "2021",
+    "date": "2021-05-06",
+    "isOpenAccess": "Y",
+    "keywords": "Hypertension; Angiotensin converting enzyme; Asthma; epidemiology; Cough",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Angiotensin converting enzyme inhibitor (ACEI) intolerance commonly occurs, requiring switching to an angiotensin-II receptor blocker (ARB). Angiotensin converting enzyme inhibitor intolerance may be mediated by bradykinin, potentially affecting airway hyperresponsiveness.<h4>Objective</h4>To assess the risk for switching to ARBs in asthma.<h4>Methods</h4>We conducted a new-user cohort study of ACEI initiators identified from electronic health records from the UK Clinical Practice Research Datalink. The risk for switching to ARBs in people with asthma or chronic obstructive pulmonary disease and the general population was compared. Adjusted hazard ratios (HRs) were calculated using Cox regression, stratified by British Thoracic Society (BTS) treatment step and ACEI type.<h4>Results</h4>Of 642,336 new users of ACEI, 6.4% had active asthma. The hazard of switching to ARB was greater in people with asthma (HR\u00a0= 1.16; 95% confidence interval [CI], 1.14-1.18; P \u2264 .001) and highest in those at BTS step 3 or greater\u00a0(HR\u00a0= 1.35, 95% CI, 1.32-1.39; and HR\u00a0= 1.18, 95% CI, 1.15-1.22, P \u2264 .001 for patients aged \u226560 and <60 years, respectively). Hazard was highest with enalapril (HR\u00a0= 1.25, 95% CI, 1.18-1.34, P \u2264 .001; HR\u00a0= 1.44, 95% CI, 1.32-1.58, P\u00a0\u2264 .001 for BTS step 3 or greater asthma). No increased hazard was observed in chronic obstructive pulmonary disease or those younger than age 60 years at BTS step 1/2. The number needed to treat varied by age, sex, and body mass index (BMI), ranging between 21 and 4, and was lowest in older women with a BMI of 25 or greater.<h4>Conclusions</h4>People with active asthma are more likely to switch to ARBs after commencing ACEI therapy. The number needed to treat varies by age, sex, BMI, and BTS step. Angiotensin-II receptor blocker could potentially be considered first-line in people with asthma and in those with high-risk characteristics.",
+    "laySummary": "",
+    "urls": "pdf:https://europepmc.org/articles/pmc8443840?pdf=render; doi:https://doi.org/10.1016/j.jaip.2021.04.055; html:https://europepmc.org/articles/PMC8443840; pdf:https://europepmc.org/articles/PMC8443840?pdf=render"
+  },
+  {
+    "id": "34514500",
+    "doi": "https://doi.org/10.1093/infdis/jiab459",
+    "title": "The Impact of Cocirculating Pathogens on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/Coronavirus Disease 2019 Surveillance: How Concurrent Epidemics May Introduce Bias and Decrease the Observed SARS-CoV-2 Percentage Positivity.",
+    "authorString": "Kovacevic A, Eggo RM, Baguelin M, Domenech de Cell\u00e8s M, Opatowski L.",
+    "authorAffiliations": "",
+    "journalTitle": "The Journal of infectious diseases",
+    "pubYear": "2022",
+    "date": "2022-01-01",
+    "isOpenAccess": "Y",
+    "keywords": "Mathematical Modeling; Multiplex Testing; Sars-cov-2; Covid-19 Surveillance; Cocirculating Respiratory Viruses",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Circulation of seasonal non-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) respiratory viruses with syndromic overlap during the coronavirus disease 2019 (COVID-19) pandemic may alter the quality of COVID-19 surveillance, with possible consequences for real-time analysis and delay in implementation of control measures.<h4>Methods</h4>Using a multipathogen susceptible-exposed-infectious-recovered (SEIR) transmission model formalizing cocirculation of SARS-CoV-2 and another respiratory virus, we assessed how an outbreak of secondary virus may affect 2 COVID-19 surveillance indicators: testing demand and positivity. Using simulation, we assessed to what extent the use of multiplex polymerase chain reaction tests on a subsample of symptomatic individuals can help correct the observed SARS-CoV-2 percentage positivity and improve surveillance quality.<h4>Results</h4>We find that a non-SARS-CoV-2 epidemic strongly increases SARS-CoV-2 daily testing demand and artificially reduces the observed SARS-CoV-2 percentage positivity for the duration of the outbreak. We estimate that performing 1 multiplex test for every 1000 COVID-19 tests on symptomatic individuals could be sufficient to maintain surveillance of other respiratory viruses in the population and correct the observed SARS-CoV-2 percentage positivity.<h4>Conclusions</h4>This study showed that cocirculating respiratory viruses can distort SARS-CoV-2 surveillance. Correction of the positivity rate can be achieved by using multiplex polymerase chain reaction tests, and a low number of samples is sufficient to avoid bias in SARS-CoV-2 surveillance.",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/jid/article-pdf/225/2/199/42224165/jiab459.pdf; doi:https://doi.org/10.1093/infdis/jiab459; html:https://europepmc.org/articles/PMC8763960; pdf:https://europepmc.org/articles/PMC8763960?pdf=render"
+  },
   {
     "id": "38833617",
     "doi": "https://doi.org/10.1093/cvr/cvae123",
@@ -10811,23 +10845,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1093/cvr/cvae123; html:https://europepmc.org/articles/PMC11416056; pdf:https://europepmc.org/articles/PMC11416056?pdf=render"
   },
-  {
-    "id": "36936594",
-    "doi": "https://doi.org/10.1136/bmjmed-2022-000247",
-    "title": "Measuring multimorbidity in research: Delphi consensus study.",
-    "authorString": "Ho ISS, Azcoaga-Lorenzo A, Akbari A, Davies J, Khunti K, Kadam UT, Lyons RA, McCowan C, Mercer SW, Nirantharakumar K, Staniszewska S, Guthrie B.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ medicine",
-    "pubYear": "2022",
-    "date": "2022-07-27",
-    "isOpenAccess": "Y",
-    "keywords": "Medicine; epidemiology; Primary Health Care; Public Health; Research Design",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objective</h4>To develop international consensus on the definition and measurement of multimorbidity in research.<h4>Design</h4>Delphi consensus study.<h4>Setting</h4>International consensus; data collected in three online rounds from participants between 30 November 2020 and 18 May 2021.<h4>Participants</h4>Professionals interested in multimorbidity and people with long term conditions were recruited to professional and public panels.<h4>Results</h4>150 professional and 25 public participants completed the first survey round. Response rates for rounds 2/3 were 83%/92% for professionals and 88%/93% in the public panel, respectively. Across both panels, the consensus was that multimorbidity should be defined as two or more long term conditions. Complex multimorbidity was perceived to be a useful concept, but the panels were unable to agree on how to define it. Both panels agreed that conditions should be included in a multimorbidity measure if they were one or more of the following: currently active; permanent in their effects; requiring current treatment, care, or therapy; requiring surveillance; or relapsing-remitting conditions requiring ongoing care. Consensus was reached for 24 conditions to always include in multimorbidity measures, and 35 conditions to usually include unless a good reason not to existed. Simple counts were preferred for estimating prevalence and examining clustering or trajectories, and weighted measures were preferred for risk adjustment and outcome prediction.<h4>Conclusions</h4>Previous multimorbidity research is limited by inconsistent definitions and approaches to measuring multimorbidity. This Delphi study identifies professional and public panel consensus guidance to facilitate consistency of definition and measurement, and to improve study comparability and reproducibility.",
-    "laySummary": "",
-    "urls": "pdf:https://bmjmedicine.bmj.com/content/bmjmed/1/1/e000247.full.pdf; doi:https://doi.org/10.1136/bmjmed-2022-000247; html:https://europepmc.org/articles/PMC9978673; pdf:https://europepmc.org/articles/PMC9978673?pdf=render"
-  },
   {
     "id": "35505353",
     "doi": "https://doi.org/10.1186/s12916-022-02349-6",
@@ -10846,38 +10863,38 @@
     "urls": "pdf:https://bmcmedicine.biomedcentral.com/track/pdf/10.1186/s12916-022-02349-6; doi:https://doi.org/10.1186/s12916-022-02349-6; html:https://europepmc.org/articles/PMC9066924; pdf:https://europepmc.org/articles/PMC9066924?pdf=render"
   },
   {
-    "id": "33965593",
-    "doi": "https://doi.org/10.1016/j.jaip.2021.04.055",
-    "title": "Intolerance to Angiotensin Converting Enzyme Inhibitors in Asthma and the General Population: A UK Population-Based Cohort Study.",
-    "authorString": "Morales DR, Lipworth BJ, Donnan PT, Wang H.",
+    "id": "36936594",
+    "doi": "https://doi.org/10.1136/bmjmed-2022-000247",
+    "title": "Measuring multimorbidity in research: Delphi consensus study.",
+    "authorString": "Ho ISS, Azcoaga-Lorenzo A, Akbari A, Davies J, Khunti K, Kadam UT, Lyons RA, McCowan C, Mercer SW, Nirantharakumar K, Staniszewska S, Guthrie B.",
     "authorAffiliations": "",
-    "journalTitle": "The journal of allergy and clinical immunology. In practice",
-    "pubYear": "2021",
-    "date": "2021-05-06",
+    "journalTitle": "BMJ medicine",
+    "pubYear": "2022",
+    "date": "2022-07-27",
     "isOpenAccess": "Y",
-    "keywords": "Hypertension; Angiotensin converting enzyme; Asthma; epidemiology; Cough",
+    "keywords": "Medicine; epidemiology; Primary Health Care; Public Health; Research Design",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Angiotensin converting enzyme inhibitor (ACEI) intolerance commonly occurs, requiring switching to an angiotensin-II receptor blocker (ARB). Angiotensin converting enzyme inhibitor intolerance may be mediated by bradykinin, potentially affecting airway hyperresponsiveness.<h4>Objective</h4>To assess the risk for switching to ARBs in asthma.<h4>Methods</h4>We conducted a new-user cohort study of ACEI initiators identified from electronic health records from the UK Clinical Practice Research Datalink. The risk for switching to ARBs in people with asthma or chronic obstructive pulmonary disease and the general population was compared. Adjusted hazard ratios (HRs) were calculated using Cox regression, stratified by British Thoracic Society (BTS) treatment step and ACEI type.<h4>Results</h4>Of 642,336 new users of ACEI, 6.4% had active asthma. The hazard of switching to ARB was greater in people with asthma (HR\u00a0= 1.16; 95% confidence interval [CI], 1.14-1.18; P \u2264 .001) and highest in those at BTS step 3 or greater\u00a0(HR\u00a0= 1.35, 95% CI, 1.32-1.39; and HR\u00a0= 1.18, 95% CI, 1.15-1.22, P \u2264 .001 for patients aged \u226560 and <60 years, respectively). Hazard was highest with enalapril (HR\u00a0= 1.25, 95% CI, 1.18-1.34, P \u2264 .001; HR\u00a0= 1.44, 95% CI, 1.32-1.58, P\u00a0\u2264 .001 for BTS step 3 or greater asthma). No increased hazard was observed in chronic obstructive pulmonary disease or those younger than age 60 years at BTS step 1/2. The number needed to treat varied by age, sex, and body mass index (BMI), ranging between 21 and 4, and was lowest in older women with a BMI of 25 or greater.<h4>Conclusions</h4>People with active asthma are more likely to switch to ARBs after commencing ACEI therapy. The number needed to treat varies by age, sex, BMI, and BTS step. Angiotensin-II receptor blocker could potentially be considered first-line in people with asthma and in those with high-risk characteristics.",
+    "abstract": "<h4>Objective</h4>To develop international consensus on the definition and measurement of multimorbidity in research.<h4>Design</h4>Delphi consensus study.<h4>Setting</h4>International consensus; data collected in three online rounds from participants between 30 November 2020 and 18 May 2021.<h4>Participants</h4>Professionals interested in multimorbidity and people with long term conditions were recruited to professional and public panels.<h4>Results</h4>150 professional and 25 public participants completed the first survey round. Response rates for rounds 2/3 were 83%/92% for professionals and 88%/93% in the public panel, respectively. Across both panels, the consensus was that multimorbidity should be defined as two or more long term conditions. Complex multimorbidity was perceived to be a useful concept, but the panels were unable to agree on how to define it. Both panels agreed that conditions should be included in a multimorbidity measure if they were one or more of the following: currently active; permanent in their effects; requiring current treatment, care, or therapy; requiring surveillance; or relapsing-remitting conditions requiring ongoing care. Consensus was reached for 24 conditions to always include in multimorbidity measures, and 35 conditions to usually include unless a good reason not to existed. Simple counts were preferred for estimating prevalence and examining clustering or trajectories, and weighted measures were preferred for risk adjustment and outcome prediction.<h4>Conclusions</h4>Previous multimorbidity research is limited by inconsistent definitions and approaches to measuring multimorbidity. This Delphi study identifies professional and public panel consensus guidance to facilitate consistency of definition and measurement, and to improve study comparability and reproducibility.",
     "laySummary": "",
-    "urls": "pdf:https://europepmc.org/articles/pmc8443840?pdf=render; doi:https://doi.org/10.1016/j.jaip.2021.04.055; html:https://europepmc.org/articles/PMC8443840; pdf:https://europepmc.org/articles/PMC8443840?pdf=render"
+    "urls": "pdf:https://bmjmedicine.bmj.com/content/bmjmed/1/1/e000247.full.pdf; doi:https://doi.org/10.1136/bmjmed-2022-000247; html:https://europepmc.org/articles/PMC9978673; pdf:https://europepmc.org/articles/PMC9978673?pdf=render"
   },
   {
-    "id": "34514500",
-    "doi": "https://doi.org/10.1093/infdis/jiab459",
-    "title": "The Impact of Cocirculating Pathogens on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/Coronavirus Disease 2019 Surveillance: How Concurrent Epidemics May Introduce Bias and Decrease the Observed SARS-CoV-2 Percentage Positivity.",
-    "authorString": "Kovacevic A, Eggo RM, Baguelin M, Domenech de Cell\u00e8s M, Opatowski L.",
+    "id": "36841835",
+    "doi": "https://doi.org/10.1038/s41541-023-00614-0",
+    "title": "Incidence determinants and serological correlates of reactive symptoms following SARS-CoV-2 vaccination.",
+    "authorString": "Holt H, Jolliffe DA, Talaei M, Faustini S, Vivaldi G, Greenig M, Richter AG, Lyons RA, Griffiths CJ, Kee F, Sheikh A, Davies GA, Shaheen SO, Martineau AR.",
     "authorAffiliations": "",
-    "journalTitle": "The Journal of infectious diseases",
-    "pubYear": "2022",
-    "date": "2022-01-01",
+    "journalTitle": "NPJ vaccines",
+    "pubYear": "2023",
+    "date": "2023-02-25",
     "isOpenAccess": "Y",
-    "keywords": "Mathematical Modeling; Multiplex Testing; Sars-cov-2; Covid-19 Surveillance; Cocirculating Respiratory Viruses",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Circulation of seasonal non-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) respiratory viruses with syndromic overlap during the coronavirus disease 2019 (COVID-19) pandemic may alter the quality of COVID-19 surveillance, with possible consequences for real-time analysis and delay in implementation of control measures.<h4>Methods</h4>Using a multipathogen susceptible-exposed-infectious-recovered (SEIR) transmission model formalizing cocirculation of SARS-CoV-2 and another respiratory virus, we assessed how an outbreak of secondary virus may affect 2 COVID-19 surveillance indicators: testing demand and positivity. Using simulation, we assessed to what extent the use of multiplex polymerase chain reaction tests on a subsample of symptomatic individuals can help correct the observed SARS-CoV-2 percentage positivity and improve surveillance quality.<h4>Results</h4>We find that a non-SARS-CoV-2 epidemic strongly increases SARS-CoV-2 daily testing demand and artificially reduces the observed SARS-CoV-2 percentage positivity for the duration of the outbreak. We estimate that performing 1 multiplex test for every 1000 COVID-19 tests on symptomatic individuals could be sufficient to maintain surveillance of other respiratory viruses in the population and correct the observed SARS-CoV-2 percentage positivity.<h4>Conclusions</h4>This study showed that cocirculating respiratory viruses can distort SARS-CoV-2 surveillance. Correction of the positivity rate can be achieved by using multiplex polymerase chain reaction tests, and a low number of samples is sufficient to avoid bias in SARS-CoV-2 surveillance.",
+    "abstract": "Prospective population-based studies investigating associations between reactive symptoms following SARS-CoV-2 vaccination and serologic responses to vaccination are lacking. We therefore conducted a study in 9003 adults from the UK general population receiving SARS-CoV-2 vaccines as part of the national vaccination programme. Titres of combined IgG/IgA/IgM responses to SARS-CoV-2 spike (S) glycoprotein were determined in eluates of dried blood spots collected from all participants before and after vaccination. 4262 (47.3%) participants experienced systemic reactive symptoms after a first vaccine dose. Factors associating with lower risk of such symptoms included older age (aOR per additional 10 years of age 0.85, 95% CI: 0.81-0.90), male vs. female sex (0.59, 0.53-0.65) and receipt of an mRNA vaccine vs. ChAdOx1 nCoV-19 (0.29, 0.26-0.32 for BNT162b2; 0.06, 0.01-0.26 for mRNA-1273). Higher risk of such symptoms was associated with SARS-CoV-2 seropositivity and COVID-19 symptoms prior to vaccination (2.23, 1.78-2.81), but not with SARS-CoV-2 seropositivity in the absence of COVID-19 symptoms (0.94, 0.81-1.09). Presence vs. absence of self-reported anxiety or depression at enrolment associated with higher risk of such symptoms (1.24, 1.12-1.39). Post-vaccination anti-S titres were higher among participants who experienced reactive symptoms after vaccination vs. those who did not (P\u2009<\u20090.001). We conclude that factors influencing risk of systemic symptoms after SARS-CoV-2 vaccination include demographic characteristics, pre-vaccination SARS-CoV-2 serostatus and vaccine type. Participants experiencing reactive symptoms following SARS-CoV-2 vaccination had higher post-vaccination titres of IgG/A/M anti-S antibodies. Improved public understanding of the frequency of reactogenic symptoms and their positive association with vaccine immunogenicity could potentially increase vaccine uptake.",
     "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/jid/article-pdf/225/2/199/42224165/jiab459.pdf; doi:https://doi.org/10.1093/infdis/jiab459; html:https://europepmc.org/articles/PMC8763960; pdf:https://europepmc.org/articles/PMC8763960?pdf=render"
+    "urls": "pdf:https://www.nature.com/articles/s41541-023-00614-0.pdf; doi:https://doi.org/10.1038/s41541-023-00614-0; html:https://europepmc.org/articles/PMC9959934; pdf:https://europepmc.org/articles/PMC9959934?pdf=render"
   },
   {
     "id": "36224173",
@@ -10913,23 +10930,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1371/journal.pdig.0000218; doi:https://doi.org/10.1371/journal.pdig.0000218; html:https://europepmc.org/articles/PMC10168555; pdf:https://europepmc.org/articles/PMC10168555?pdf=render"
   },
-  {
-    "id": "36841835",
-    "doi": "https://doi.org/10.1038/s41541-023-00614-0",
-    "title": "Incidence determinants and serological correlates of reactive symptoms following SARS-CoV-2 vaccination.",
-    "authorString": "Holt H, Jolliffe DA, Talaei M, Faustini S, Vivaldi G, Greenig M, Richter AG, Lyons RA, Griffiths CJ, Kee F, Sheikh A, Davies GA, Shaheen SO, Martineau AR.",
-    "authorAffiliations": "",
-    "journalTitle": "NPJ vaccines",
-    "pubYear": "2023",
-    "date": "2023-02-25",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Prospective population-based studies investigating associations between reactive symptoms following SARS-CoV-2 vaccination and serologic responses to vaccination are lacking. We therefore conducted a study in 9003 adults from the UK general population receiving SARS-CoV-2 vaccines as part of the national vaccination programme. Titres of combined IgG/IgA/IgM responses to SARS-CoV-2 spike (S) glycoprotein were determined in eluates of dried blood spots collected from all participants before and after vaccination. 4262 (47.3%) participants experienced systemic reactive symptoms after a first vaccine dose. Factors associating with lower risk of such symptoms included older age (aOR per additional 10 years of age 0.85, 95% CI: 0.81-0.90), male vs. female sex (0.59, 0.53-0.65) and receipt of an mRNA vaccine vs. ChAdOx1 nCoV-19 (0.29, 0.26-0.32 for BNT162b2; 0.06, 0.01-0.26 for mRNA-1273). Higher risk of such symptoms was associated with SARS-CoV-2 seropositivity and COVID-19 symptoms prior to vaccination (2.23, 1.78-2.81), but not with SARS-CoV-2 seropositivity in the absence of COVID-19 symptoms (0.94, 0.81-1.09). Presence vs. absence of self-reported anxiety or depression at enrolment associated with higher risk of such symptoms (1.24, 1.12-1.39). Post-vaccination anti-S titres were higher among participants who experienced reactive symptoms after vaccination vs. those who did not (P\u2009<\u20090.001). We conclude that factors influencing risk of systemic symptoms after SARS-CoV-2 vaccination include demographic characteristics, pre-vaccination SARS-CoV-2 serostatus and vaccine type. Participants experiencing reactive symptoms following SARS-CoV-2 vaccination had higher post-vaccination titres of IgG/A/M anti-S antibodies. Improved public understanding of the frequency of reactogenic symptoms and their positive association with vaccine immunogenicity could potentially increase vaccine uptake.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41541-023-00614-0.pdf; doi:https://doi.org/10.1038/s41541-023-00614-0; html:https://europepmc.org/articles/PMC9959934; pdf:https://europepmc.org/articles/PMC9959934?pdf=render"
-  },
   {
     "id": "35213664",
     "doi": "https://doi.org/10.1371/journal.pone.0264529",
@@ -11168,6 +11168,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.isci.2024.110298; doi:https://doi.org/10.1016/j.isci.2024.110298; html:https://europepmc.org/articles/PMC11261406; pdf:https://europepmc.org/articles/PMC11261406?pdf=render"
   },
+  {
+    "id": "35003715",
+    "doi": "https://doi.org/10.7189/jogh.11.05026",
+    "title": "Uptake, effectiveness and safety of COVID-19 vaccines in children and young people in Scotland: Protocol for early pandemic evaluation and enhanced surveillance of COVID-19 (EAVE II).",
+    "authorString": "Adeloye D, Katikireddi SV, Woolford L, Simpson CR, Shah SA, Agrawal U, Richie LD, Swann OV, Stock SJ, Robertson C, Sheikh A, Rudan I.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of global health",
+    "pubYear": "2021",
+    "date": "2021-12-25",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>The dynamics of acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and severity of disease among children and young people (CYP) across different settings are of considerable clinical, public health and societal interest. Severe COVID-19 cases, requiring hospitalisations, and deaths have been reported in some CYP suggesting a need to extend vaccinations to these age groups. As part of the ongoing Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) study, we aim to investigate the uptake, effectiveness and safety of COVID-19 vaccines in children and young people (CYP) aged 0 to 17 years in Scotland. Specifically, we will estimate: (i) uptake of vaccines against COVID-19, (ii) vaccine effectiveness (VE) against the outcomes of symptomatic SARS-CoV-2 infection, hospitalisation, intensive care unit (ICU) admissions, and death; (iii) VE for first/second dose timing among different age groups and risk groups; and (iv) the safety of vaccines.<h4>Methods and analysis</h4>We will conduct an open prospective cohort study classifying exposure as time-varying. We will compare outcomes amongst first dose vaccinated and second dose vaccinated CYP to those not yet vaccinated. A Test Negative Design (TND) case control study will be nested within this national cohort to investigate VE against symptomatic infection. The primary outcomes will be (i) uptake of vaccines against COVID-19, (ii) time to COVID-19 infection, hospitalisation, ICU admissions or death, and (iii) adverse events related to vaccines. Vaccination status (unvaccinated, one dose and two doses) will be defined as a time-varying exposure. Data from multiple sources will be linked using a unique identifier. We will conduct descriptive analyses to explore trends in vaccine uptake, and association between different exposure variables and vaccine uptake will be determined using multivariable logistic regression models. VE will be assessed from time-dependent Cox models or Poisson regression models, adjusted for relevant confounders, including age, sex, socioeconomic status, and comorbidities. We will employ self-controlled study designs to determine the risk of adverse events following COVID-19 vaccination.<h4>Ethics and dissemination</h4>Ethics approval was obtained from the National Research Ethics Committee, South East Scotland 02. We will present findings of this study at international conferences, in peer-reviewed journals and to policy-makers.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.7189/jogh.11.05026; doi:https://doi.org/10.7189/jogh.11.05026; html:https://europepmc.org/articles/PMC8709900; pdf:https://europepmc.org/articles/PMC8709900?pdf=render"
+  },
   {
     "id": "32463370",
     "doi": "https://doi.org/10.2196/16452",
@@ -11202,23 +11219,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ageing/article-pdf/51/5/afac072/43616755/afac072.pdf; doi:https://doi.org/10.1093/ageing/afac072; html:https://europepmc.org/articles/PMC8992303; pdf:https://europepmc.org/articles/PMC8992303?pdf=render"
   },
-  {
-    "id": "35003715",
-    "doi": "https://doi.org/10.7189/jogh.11.05026",
-    "title": "Uptake, effectiveness and safety of COVID-19 vaccines in children and young people in Scotland: Protocol for early pandemic evaluation and enhanced surveillance of COVID-19 (EAVE II).",
-    "authorString": "Adeloye D, Katikireddi SV, Woolford L, Simpson CR, Shah SA, Agrawal U, Richie LD, Swann OV, Stock SJ, Robertson C, Sheikh A, Rudan I.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of global health",
-    "pubYear": "2021",
-    "date": "2021-12-25",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>The dynamics of acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and severity of disease among children and young people (CYP) across different settings are of considerable clinical, public health and societal interest. Severe COVID-19 cases, requiring hospitalisations, and deaths have been reported in some CYP suggesting a need to extend vaccinations to these age groups. As part of the ongoing Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) study, we aim to investigate the uptake, effectiveness and safety of COVID-19 vaccines in children and young people (CYP) aged 0 to 17 years in Scotland. Specifically, we will estimate: (i) uptake of vaccines against COVID-19, (ii) vaccine effectiveness (VE) against the outcomes of symptomatic SARS-CoV-2 infection, hospitalisation, intensive care unit (ICU) admissions, and death; (iii) VE for first/second dose timing among different age groups and risk groups; and (iv) the safety of vaccines.<h4>Methods and analysis</h4>We will conduct an open prospective cohort study classifying exposure as time-varying. We will compare outcomes amongst first dose vaccinated and second dose vaccinated CYP to those not yet vaccinated. A Test Negative Design (TND) case control study will be nested within this national cohort to investigate VE against symptomatic infection. The primary outcomes will be (i) uptake of vaccines against COVID-19, (ii) time to COVID-19 infection, hospitalisation, ICU admissions or death, and (iii) adverse events related to vaccines. Vaccination status (unvaccinated, one dose and two doses) will be defined as a time-varying exposure. Data from multiple sources will be linked using a unique identifier. We will conduct descriptive analyses to explore trends in vaccine uptake, and association between different exposure variables and vaccine uptake will be determined using multivariable logistic regression models. VE will be assessed from time-dependent Cox models or Poisson regression models, adjusted for relevant confounders, including age, sex, socioeconomic status, and comorbidities. We will employ self-controlled study designs to determine the risk of adverse events following COVID-19 vaccination.<h4>Ethics and dissemination</h4>Ethics approval was obtained from the National Research Ethics Committee, South East Scotland 02. We will present findings of this study at international conferences, in peer-reviewed journals and to policy-makers.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.7189/jogh.11.05026; doi:https://doi.org/10.7189/jogh.11.05026; html:https://europepmc.org/articles/PMC8709900; pdf:https://europepmc.org/articles/PMC8709900?pdf=render"
-  },
   {
     "id": "37399490",
     "doi": "https://doi.org/10.1182/bloodadvances.2023010562",
@@ -11338,23 +11338,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41588-023-01585-7.pdf; doi:https://doi.org/10.1038/s41588-023-01585-7; html:https://europepmc.org/articles/PMC10786720; pdf:https://europepmc.org/articles/PMC10786720?pdf=render"
   },
-  {
-    "id": "37658166",
-    "doi": "https://doi.org/10.1007/s00392-023-02295-0",
-    "title": "Efficacy and safety of intravenous beta-blockers in acute atrial fibrillation and flutter is dependent on beta-1 selectivity: a systematic review and meta-analysis of randomised trials.",
-    "authorString": "Perrett M, Gohil N, Tica O, Bunting KV, Kotecha D.",
-    "authorAffiliations": "",
-    "journalTitle": "Clinical research in cardiology : official journal of the German Cardiac Society",
-    "pubYear": "2024",
-    "date": "2023-09-01",
-    "isOpenAccess": "Y",
-    "keywords": "Meta-analysis; Atrial fibrillation; Acute; Atrial flutter; Systematic review; Beta-blockers",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Intravenous beta-blockers are commonly used to manage patients with acute atrial fibrillation (AF) and atrial flutter (AFl), but the choice of specific agent is often not evidence-based.<h4>Methods</h4>A prospectively-registered systematic review and meta-analysis of randomised trials (PROSPERO: CRD42020204772) to compare the safety and efficacy of intravenous beta-blockers against alternative pharmacological agents.<h4>Results</h4>Twelve trials comparing beta-blockers with diltiazem, digoxin, verapamil, anti-arrhythmic drugs and placebo were included, with variable risk of bias and 1152 participants. With high heterogeneity (I<sup>2</sup>\u2009=\u200987%; p\u2009<\u20090.001), there was no difference in the primary outcomes of heart rate reduction (standardised mean difference -\u00a00.65 beats/minute compared to control, 95% CI -\u00a01.63 to 0.32; p\u2009=\u20090.19) or the proportion that achieved target heart rate (risk ratio [RR] 0.85, 95% CI 0.36-1.97; p\u2009=\u20090.70). Conventional selective beta-1 blockers were inferior for target heart rate reduction versus control (RR 0.33, 0.17-0.64; p\u2009<\u20090.001), whereas super-selective beta-1 blockers were superior (RR 1.98, 1.54-2.54; p\u2009<\u20090.001). There was no significant difference between beta-blockers and comparators for secondary outcomes of conversion to sinus rhythm (RR 1.15, 0.90-1.46; p\u2009=\u20090.28), hypotension (RR 1.85, 0.87-3.93; p\u2009=\u20090.11), bradycardia (RR 1.29, 0.25-6.82; p\u2009=\u20090.76) or adverse events leading to drug discontinuation (RR 1.03, 0.49-2.17; p\u2009=\u20090.93). The incidence of hypotension and bradycardia were greater with non-selective beta-blockers (p\u2009=\u20090.031 and p\u2009<\u20090.001).<h4>Conclusions</h4>Across all intravenous beta-blockers, there was no difference with other medications for acute heart rate control in atrial fibrillation and flutter. Efficacy and safety may be improved by choosing beta-blockers with higher beta-1 selectivity.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1007/s00392-023-02295-0; html:https://europepmc.org/articles/PMC11108934; pdf:https://europepmc.org/articles/PMC11108934?pdf=render"
-  },
   {
     "id": "35944928",
     "doi": "https://doi.org/10.1136/bmjhci-2021-100488",
@@ -11390,21 +11373,21 @@
     "urls": "doi:https://doi.org/10.1016/j.ijmedinf.2021.104400; doi:https://doi.org/10.1016/j.ijmedinf.2021.104400; html:https://europepmc.org/articles/PMC7843148"
   },
   {
-    "id": "39035417",
-    "doi": "https://doi.org/10.1093/braincomms/fcae219",
-    "title": "Multimodal subtypes identified in Alzheimer's Disease Neuroimaging Initiative participants by missing-data-enabled subtype and stage inference.",
-    "authorString": "Estarellas M, Oxtoby NP, Schott JM, Alexander DC, Young AL.",
+    "id": "37658166",
+    "doi": "https://doi.org/10.1007/s00392-023-02295-0",
+    "title": "Efficacy and safety of intravenous beta-blockers in acute atrial fibrillation and flutter is dependent on beta-1 selectivity: a systematic review and meta-analysis of randomised trials.",
+    "authorString": "Perrett M, Gohil N, Tica O, Bunting KV, Kotecha D.",
     "authorAffiliations": "",
-    "journalTitle": "Brain communications",
+    "journalTitle": "Clinical research in cardiology : official journal of the German Cardiac Society",
     "pubYear": "2024",
-    "date": "2024-06-25",
+    "date": "2023-09-01",
     "isOpenAccess": "Y",
-    "keywords": "Heterogeneity; Alzheimer\u2019s disease; Subtyping; Missing Data; Multimodal",
+    "keywords": "Meta-analysis; Atrial fibrillation; Acute; Atrial flutter; Systematic review; Beta-blockers",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Alzheimer's disease is a highly heterogeneous disease in which different biomarkers are dynamic over different windows of the decades-long pathophysiological processes, and potentially have distinct involvement in different subgroups. Subtype and Stage Inference is an unsupervised learning algorithm that disentangles the phenotypic heterogeneity and temporal progression of disease biomarkers, providing disease insight and quantitative estimates of individual subtype and stage. However, a key limitation of Subtype and Stage Inference is that it requires a complete set of biomarkers for each subject, reducing the number of datapoints available for model fitting and limiting applications of Subtype and Stage Inference to modalities that are widely collected, e.g. volumetric biomarkers derived from structural MRI. In this study, we adapted the Subtype and Stage Inference algorithm to handle missing data, enabling the application of Subtype and Stage Inference to multimodal data (magnetic resonance imaging, positron emission tomography, cerebrospinal fluid and cognitive tests) from 789 participants in the Alzheimer's Disease Neuroimaging Initiative. Missing-data Subtype and Stage Inference identified five subtypes having distinct progression patterns, which we describe by the earliest unique abnormality as 'Typical AD with Early Tau', 'Typical AD with Late Tau', 'Cortical', 'Cognitive' and 'Subcortical'. These new multimodal subtypes were differentially associated with age, years of education, Apolipoprotein E (APOE4) status, white matter hyperintensity burden and the rate of conversion from mild cognitive impairment to Alzheimer's disease, with the 'Cognitive' subtype showing the fastest clinical progression, and the 'Subcortical' subtype the slowest. Overall, we demonstrate that missing-data Subtype and Stage Inference reveals a finer landscape of Alzheimer's disease subtypes, each of which are associated with different risk factors. Missing-data Subtype and Stage Inference has broad utility, enabling the prediction of progression in a much wider set of individuals, rather than being restricted to those with complete data.",
+    "abstract": "<h4>Background</h4>Intravenous beta-blockers are commonly used to manage patients with acute atrial fibrillation (AF) and atrial flutter (AFl), but the choice of specific agent is often not evidence-based.<h4>Methods</h4>A prospectively-registered systematic review and meta-analysis of randomised trials (PROSPERO: CRD42020204772) to compare the safety and efficacy of intravenous beta-blockers against alternative pharmacological agents.<h4>Results</h4>Twelve trials comparing beta-blockers with diltiazem, digoxin, verapamil, anti-arrhythmic drugs and placebo were included, with variable risk of bias and 1152 participants. With high heterogeneity (I<sup>2</sup>\u2009=\u200987%; p\u2009<\u20090.001), there was no difference in the primary outcomes of heart rate reduction (standardised mean difference -\u00a00.65 beats/minute compared to control, 95% CI -\u00a01.63 to 0.32; p\u2009=\u20090.19) or the proportion that achieved target heart rate (risk ratio [RR] 0.85, 95% CI 0.36-1.97; p\u2009=\u20090.70). Conventional selective beta-1 blockers were inferior for target heart rate reduction versus control (RR 0.33, 0.17-0.64; p\u2009<\u20090.001), whereas super-selective beta-1 blockers were superior (RR 1.98, 1.54-2.54; p\u2009<\u20090.001). There was no significant difference between beta-blockers and comparators for secondary outcomes of conversion to sinus rhythm (RR 1.15, 0.90-1.46; p\u2009=\u20090.28), hypotension (RR 1.85, 0.87-3.93; p\u2009=\u20090.11), bradycardia (RR 1.29, 0.25-6.82; p\u2009=\u20090.76) or adverse events leading to drug discontinuation (RR 1.03, 0.49-2.17; p\u2009=\u20090.93). The incidence of hypotension and bradycardia were greater with non-selective beta-blockers (p\u2009=\u20090.031 and p\u2009<\u20090.001).<h4>Conclusions</h4>Across all intravenous beta-blockers, there was no difference with other medications for acute heart rate control in atrial fibrillation and flutter. Efficacy and safety may be improved by choosing beta-blockers with higher beta-1 selectivity.",
     "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/braincomms/advance-article-pdf/doi/10.1093/braincomms/fcae219/58327048/fcae219.pdf; doi:https://doi.org/10.1093/braincomms/fcae219; html:https://europepmc.org/articles/PMC11259979; pdf:https://europepmc.org/articles/PMC11259979?pdf=render"
+    "urls": "doi:https://doi.org/10.1007/s00392-023-02295-0; html:https://europepmc.org/articles/PMC11108934; pdf:https://europepmc.org/articles/PMC11108934?pdf=render"
   },
   {
     "id": "34164795",
@@ -11424,21 +11407,21 @@
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s40801-021-00256-5.pdf; doi:https://doi.org/10.1007/s40801-021-00256-5; html:https://europepmc.org/articles/PMC8605959; pdf:https://europepmc.org/articles/PMC8605959?pdf=render"
   },
   {
-    "id": "33780550",
-    "doi": "https://doi.org/10.1111/anae.15457",
-    "title": "Impact of a physician - critical care practitioner pre-hospital service in Wales on trauma survival: a retrospective analysis of linked registry data.",
-    "authorString": "Lyons J, Gabbe BJ, Rawlinson D, Lockey D, Fry RJ, Akbari A, Lyons RA.",
+    "id": "39035417",
+    "doi": "https://doi.org/10.1093/braincomms/fcae219",
+    "title": "Multimodal subtypes identified in Alzheimer's Disease Neuroimaging Initiative participants by missing-data-enabled subtype and stage inference.",
+    "authorString": "Estarellas M, Oxtoby NP, Schott JM, Alexander DC, Young AL.",
     "authorAffiliations": "",
-    "journalTitle": "Anaesthesia",
-    "pubYear": "2021",
-    "date": "2021-03-29",
+    "journalTitle": "Brain communications",
+    "pubYear": "2024",
+    "date": "2024-06-25",
     "isOpenAccess": "Y",
-    "keywords": "Trauma; Survival; Critical Care; Pre-hospital Care",
+    "keywords": "Heterogeneity; Alzheimer\u2019s disease; Subtyping; Missing Data; Multimodal",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "The Emergency Medical Retrieval and Transfer Service for Wales launched in 2015. This service delivers senior pre-hospital doctors and advanced critical care practitioners to the scene of time-critical life- and limb-threatening incidents to provide advanced decision-making and pre-hospital clinical care. The impact of the service on 30-day mortality was evaluated retrospectively using a data linkage system. The study included patients who sustained moderate-to-severe blunt traumatic injuries (injury severity score\u00a0\u2265\u00a09) between 27 April 2015 and 30 November 2018. The association between pre-hospital management by the Emergency Medical Retrieval and Transfer Service and 30-day mortality was assessed using multivariable logistic regression. In total, data from 4035 patients were analysed, of which 412 (10%) were treated by the Emergency Medical Retrieval and Transfer Service. A greater proportion of patients treated by the Emergency Medical Retrieval and Transfer Service had an injury severity score\u00a0\u2265\u00a016 and Glasgow coma scale\u00a0\u2264\u00a012 (288 (70%) vs. 1435 (40%) and 126 (31%) vs. 325 (9%), respectively). The unadjusted 30-day mortality rate was 11.7% for patients managed by the Emergency Medical Retrieval and Transfer Service compared with 9.6% for patients managed by standard pre-hospital care services. However, after adjustment for differences in case-mix, the 30-day mortality rate for patients treated by the Emergency Medical Retrieval and Transfer Service was 37% lower (adjusted odds ratio 0.63 (95%CI 0.41-0.97); p\u00a0=\u00a00.037). The introduction of an emergency medical retrieval service was associated with a reduction in 30-day mortality for patients with blunt traumatic injury.",
+    "abstract": "Alzheimer's disease is a highly heterogeneous disease in which different biomarkers are dynamic over different windows of the decades-long pathophysiological processes, and potentially have distinct involvement in different subgroups. Subtype and Stage Inference is an unsupervised learning algorithm that disentangles the phenotypic heterogeneity and temporal progression of disease biomarkers, providing disease insight and quantitative estimates of individual subtype and stage. However, a key limitation of Subtype and Stage Inference is that it requires a complete set of biomarkers for each subject, reducing the number of datapoints available for model fitting and limiting applications of Subtype and Stage Inference to modalities that are widely collected, e.g. volumetric biomarkers derived from structural MRI. In this study, we adapted the Subtype and Stage Inference algorithm to handle missing data, enabling the application of Subtype and Stage Inference to multimodal data (magnetic resonance imaging, positron emission tomography, cerebrospinal fluid and cognitive tests) from 789 participants in the Alzheimer's Disease Neuroimaging Initiative. Missing-data Subtype and Stage Inference identified five subtypes having distinct progression patterns, which we describe by the earliest unique abnormality as 'Typical AD with Early Tau', 'Typical AD with Late Tau', 'Cortical', 'Cognitive' and 'Subcortical'. These new multimodal subtypes were differentially associated with age, years of education, Apolipoprotein E (APOE4) status, white matter hyperintensity burden and the rate of conversion from mild cognitive impairment to Alzheimer's disease, with the 'Cognitive' subtype showing the fastest clinical progression, and the 'Subcortical' subtype the slowest. Overall, we demonstrate that missing-data Subtype and Stage Inference reveals a finer landscape of Alzheimer's disease subtypes, each of which are associated with different risk factors. Missing-data Subtype and Stage Inference has broad utility, enabling the prediction of progression in a much wider set of individuals, rather than being restricted to those with complete data.",
     "laySummary": "",
-    "urls": "pdf:https://cronfa.swan.ac.uk/Record/cronfa56616/Download/56616__19761__8c6edaf906b846a69c8b19bdb94d015d.pdf; doi:https://doi.org/10.1111/anae.15457; html:https://europepmc.org/articles/PMC11497344; pdf:https://europepmc.org/articles/PMC11497344?pdf=render"
+    "urls": "pdf:https://academic.oup.com/braincomms/advance-article-pdf/doi/10.1093/braincomms/fcae219/58327048/fcae219.pdf; doi:https://doi.org/10.1093/braincomms/fcae219; html:https://europepmc.org/articles/PMC11259979; pdf:https://europepmc.org/articles/PMC11259979?pdf=render"
   },
   {
     "id": "33801002",
@@ -11457,6 +11440,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.mdpi.com/1424-8220/21/6/2190/pdf?version=1616388230; doi:https://doi.org/10.3390/s21062190; html:https://europepmc.org/articles/PMC8003942; pdf:https://europepmc.org/articles/PMC8003942?pdf=render"
   },
+  {
+    "id": "33780550",
+    "doi": "https://doi.org/10.1111/anae.15457",
+    "title": "Impact of a physician - critical care practitioner pre-hospital service in Wales on trauma survival: a retrospective analysis of linked registry data.",
+    "authorString": "Lyons J, Gabbe BJ, Rawlinson D, Lockey D, Fry RJ, Akbari A, Lyons RA.",
+    "authorAffiliations": "",
+    "journalTitle": "Anaesthesia",
+    "pubYear": "2021",
+    "date": "2021-03-29",
+    "isOpenAccess": "Y",
+    "keywords": "Trauma; Survival; Critical Care; Pre-hospital Care",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The Emergency Medical Retrieval and Transfer Service for Wales launched in 2015. This service delivers senior pre-hospital doctors and advanced critical care practitioners to the scene of time-critical life- and limb-threatening incidents to provide advanced decision-making and pre-hospital clinical care. The impact of the service on 30-day mortality was evaluated retrospectively using a data linkage system. The study included patients who sustained moderate-to-severe blunt traumatic injuries (injury severity score\u00a0\u2265\u00a09) between 27 April 2015 and 30 November 2018. The association between pre-hospital management by the Emergency Medical Retrieval and Transfer Service and 30-day mortality was assessed using multivariable logistic regression. In total, data from 4035 patients were analysed, of which 412 (10%) were treated by the Emergency Medical Retrieval and Transfer Service. A greater proportion of patients treated by the Emergency Medical Retrieval and Transfer Service had an injury severity score\u00a0\u2265\u00a016 and Glasgow coma scale\u00a0\u2264\u00a012 (288 (70%) vs. 1435 (40%) and 126 (31%) vs. 325 (9%), respectively). The unadjusted 30-day mortality rate was 11.7% for patients managed by the Emergency Medical Retrieval and Transfer Service compared with 9.6% for patients managed by standard pre-hospital care services. However, after adjustment for differences in case-mix, the 30-day mortality rate for patients treated by the Emergency Medical Retrieval and Transfer Service was 37% lower (adjusted odds ratio 0.63 (95%CI 0.41-0.97); p\u00a0=\u00a00.037). The introduction of an emergency medical retrieval service was associated with a reduction in 30-day mortality for patients with blunt traumatic injury.",
+    "laySummary": "",
+    "urls": "pdf:https://cronfa.swan.ac.uk/Record/cronfa56616/Download/56616__19761__8c6edaf906b846a69c8b19bdb94d015d.pdf; doi:https://doi.org/10.1111/anae.15457; html:https://europepmc.org/articles/PMC11497344; pdf:https://europepmc.org/articles/PMC11497344?pdf=render"
+  },
   {
     "id": "37144149",
     "doi": "https://doi.org/10.3389/fped.2023.1148975",
@@ -11542,23 +11542,6 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/ene.15114; doi:https://doi.org/10.1111/ene.15114; html:https://europepmc.org/articles/PMC9377012; pdf:https://europepmc.org/articles/PMC9377012?pdf=render"
   },
-  {
-    "id": "37996473",
-    "doi": "https://doi.org/10.1038/s41598-023-47371-7",
-    "title": "Evidence for involvement of the alcohol consumption WDPCP gene in lipid metabolism, and liver cirrhosis.",
-    "authorString": "O'Farrell F, Aleyakpo B, Mustafa R, Jiang X, Pinto RC, Elliott P, Tzoulaki I, Dehghan A, Loh SHY, Barclay JW, Martins LM, Pazoki R.",
-    "authorAffiliations": "",
-    "journalTitle": "Scientific reports",
-    "pubYear": "2023",
-    "date": "2023-11-23",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Biological pathways between alcohol consumption and alcohol liver disease (ALD) are not fully understood. We selected genes with known effect on (1) alcohol consumption, (2) liver function, and (3) gene expression. Expression of the orthologs of these genes in Caenorhabditis elegans and Drosophila melanogaster was suppressed using mutations and/or RNA interference (RNAi). In humans, association analysis, pathway analysis, and Mendelian randomization analysis were performed to identify metabolic changes due to alcohol consumption. In C. elegans, we found a reduction in locomotion rate after exposure to ethanol for RNAi knockdown of ACTR1B and MAPT. In Drosophila, we observed (1) a change in sedative effect of ethanol for RNAi knockdown of WDPCP, TENM2, GPN1, ARPC1B, and SCN8A, (2) a reduction in ethanol consumption for RNAi knockdown of TENM2, (3) a reduction in triradylglycerols (TAG) levels for RNAi knockdown of WDPCP, TENM2, and GPN1. In human, we observed (1) a link between alcohol consumption and several metabolites including TAG, (2) an enrichment of the candidate (alcohol-associated) metabolites within the linoleic acid (LNA) and alpha-linolenic acid (ALA) metabolism pathways, (3) a causal link between gene expression of WDPCP to liver fibrosis and liver cirrhosis. Our results imply that WDPCP might be involved in ALD.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41598-023-47371-7.pdf; doi:https://doi.org/10.1038/s41598-023-47371-7; html:https://europepmc.org/articles/PMC10667215; pdf:https://europepmc.org/articles/PMC10667215?pdf=render"
-  },
   {
     "id": "30928998",
     "doi": "https://doi.org/10.4193/rhin18.237",
@@ -11593,6 +11576,40 @@
     "laySummary": "",
     "urls": "pdf:https://adc.bmj.com/content/archdischild/early/2024/06/07/archdischild-2023-326756.full.pdf; doi:https://doi.org/10.1136/archdischild-2023-326756; html:https://europepmc.org/articles/PMC11347208; pdf:https://europepmc.org/articles/PMC11347208?pdf=render"
   },
+  {
+    "id": "37996473",
+    "doi": "https://doi.org/10.1038/s41598-023-47371-7",
+    "title": "Evidence for involvement of the alcohol consumption WDPCP gene in lipid metabolism, and liver cirrhosis.",
+    "authorString": "O'Farrell F, Aleyakpo B, Mustafa R, Jiang X, Pinto RC, Elliott P, Tzoulaki I, Dehghan A, Loh SHY, Barclay JW, Martins LM, Pazoki R.",
+    "authorAffiliations": "",
+    "journalTitle": "Scientific reports",
+    "pubYear": "2023",
+    "date": "2023-11-23",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Biological pathways between alcohol consumption and alcohol liver disease (ALD) are not fully understood. We selected genes with known effect on (1) alcohol consumption, (2) liver function, and (3) gene expression. Expression of the orthologs of these genes in Caenorhabditis elegans and Drosophila melanogaster was suppressed using mutations and/or RNA interference (RNAi). In humans, association analysis, pathway analysis, and Mendelian randomization analysis were performed to identify metabolic changes due to alcohol consumption. In C. elegans, we found a reduction in locomotion rate after exposure to ethanol for RNAi knockdown of ACTR1B and MAPT. In Drosophila, we observed (1) a change in sedative effect of ethanol for RNAi knockdown of WDPCP, TENM2, GPN1, ARPC1B, and SCN8A, (2) a reduction in ethanol consumption for RNAi knockdown of TENM2, (3) a reduction in triradylglycerols (TAG) levels for RNAi knockdown of WDPCP, TENM2, and GPN1. In human, we observed (1) a link between alcohol consumption and several metabolites including TAG, (2) an enrichment of the candidate (alcohol-associated) metabolites within the linoleic acid (LNA) and alpha-linolenic acid (ALA) metabolism pathways, (3) a causal link between gene expression of WDPCP to liver fibrosis and liver cirrhosis. Our results imply that WDPCP might be involved in ALD.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41598-023-47371-7.pdf; doi:https://doi.org/10.1038/s41598-023-47371-7; html:https://europepmc.org/articles/PMC10667215; pdf:https://europepmc.org/articles/PMC10667215?pdf=render"
+  },
+  {
+    "id": "33495722",
+    "doi": "https://doi.org/10.1109/access.2021.3050524",
+    "title": "Remote Assessment of Parkinson's Disease Symptom Severity Using the Simulated Cellular Mobile Telephone Network.",
+    "authorString": "Tsanas A, Little MA, Ramig LO.",
+    "authorAffiliations": "",
+    "journalTitle": "IEEE access : practical innovations, open solutions",
+    "pubYear": "2021",
+    "date": "2021-01-11",
+    "isOpenAccess": "Y",
+    "keywords": "Telemedicine; Parkinson\u2019s Disease; Decision Support Tool; Nonlinear Speech Signal Processing",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Telemonitoring of Parkinson's Disease (PD) has attracted considerable research interest because of its potential to make a lasting, positive impact on the life of patients and their carers. Purpose-built devices have been developed that record various signals which can be associated with average PD symptom severity, as quantified on standard clinical metrics such as the Unified Parkinson's Disease Rating Scale (UPDRS). Speech signals are particularly promising in this regard, because they can be easily recorded without the use of expensive, dedicated hardware. Previous studies have demonstrated replication of UPDRS to within less than 2 points of a clinical raters' assessment of symptom severity, using high-quality speech signals collected using dedicated telemonitoring hardware. Here, we investigate the potential of using the standard voice-over-GSM (2G) or UMTS (3G) cellular mobile telephone networks for PD telemonitoring, networks that, together, have greater than 5 billion subscribers worldwide. We test the robustness of this approach using a simulated noisy mobile communication network over which speech signals are transmitted, and approximately 6000 recordings from 42 PD subjects. We show that UPDRS can be estimated to within less than 3.5 points difference from the clinical raters' assessment, which is clinically useful given that the inter-rater variability for UPDRS can be as high as 4-5 UPDRS points. This provides compelling evidence that the existing voice telephone network has potential towards facilitating inexpensive, mass-scale PD symptom telemonitoring applications.",
+    "laySummary": "",
+    "urls": "pdf:https://ieeexplore.ieee.org/ielx7/6287639/9312710/09319241.pdf; doi:https://doi.org/10.1109/ACCESS.2021.3050524; html:https://europepmc.org/articles/PMC7821632; pdf:https://europepmc.org/articles/PMC7821632?pdf=render"
+  },
   {
     "id": "39406990",
     "doi": "https://doi.org/10.1038/s42003-024-06984-y",
@@ -11627,23 +11644,6 @@
     "laySummary": "",
     "urls": "pdf:https://aacrjournals.org/mct/article-pdf/20/9/1627/3076208/1627.pdf; doi:https://doi.org/10.1158/1535-7163.MCT-20-1050; html:https://europepmc.org/articles/PMC7611622; pdf:https://europepmc.org/articles/PMC7611622?pdf=render"
   },
-  {
-    "id": "33495722",
-    "doi": "https://doi.org/10.1109/access.2021.3050524",
-    "title": "Remote Assessment of Parkinson's Disease Symptom Severity Using the Simulated Cellular Mobile Telephone Network.",
-    "authorString": "Tsanas A, Little MA, Ramig LO.",
-    "authorAffiliations": "",
-    "journalTitle": "IEEE access : practical innovations, open solutions",
-    "pubYear": "2021",
-    "date": "2021-01-11",
-    "isOpenAccess": "Y",
-    "keywords": "Telemedicine; Parkinson\u2019s Disease; Decision Support Tool; Nonlinear Speech Signal Processing",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Telemonitoring of Parkinson's Disease (PD) has attracted considerable research interest because of its potential to make a lasting, positive impact on the life of patients and their carers. Purpose-built devices have been developed that record various signals which can be associated with average PD symptom severity, as quantified on standard clinical metrics such as the Unified Parkinson's Disease Rating Scale (UPDRS). Speech signals are particularly promising in this regard, because they can be easily recorded without the use of expensive, dedicated hardware. Previous studies have demonstrated replication of UPDRS to within less than 2 points of a clinical raters' assessment of symptom severity, using high-quality speech signals collected using dedicated telemonitoring hardware. Here, we investigate the potential of using the standard voice-over-GSM (2G) or UMTS (3G) cellular mobile telephone networks for PD telemonitoring, networks that, together, have greater than 5 billion subscribers worldwide. We test the robustness of this approach using a simulated noisy mobile communication network over which speech signals are transmitted, and approximately 6000 recordings from 42 PD subjects. We show that UPDRS can be estimated to within less than 3.5 points difference from the clinical raters' assessment, which is clinically useful given that the inter-rater variability for UPDRS can be as high as 4-5 UPDRS points. This provides compelling evidence that the existing voice telephone network has potential towards facilitating inexpensive, mass-scale PD symptom telemonitoring applications.",
-    "laySummary": "",
-    "urls": "pdf:https://ieeexplore.ieee.org/ielx7/6287639/9312710/09319241.pdf; doi:https://doi.org/10.1109/ACCESS.2021.3050524; html:https://europepmc.org/articles/PMC7821632; pdf:https://europepmc.org/articles/PMC7821632?pdf=render"
-  },
   {
     "id": "36794597",
     "doi": "https://doi.org/10.1111/trf.17277",
@@ -11695,23 +11695,6 @@
     "laySummary": "",
     "urls": "pdf:https://informatics.bmj.com/content/bmjhci/28/1/e100254.full.pdf; doi:https://doi.org/10.1136/bmjhci-2020-100254; html:https://europepmc.org/articles/PMC7798427; pdf:https://europepmc.org/articles/PMC7798427?pdf=render"
   },
-  {
-    "id": "38238056",
-    "doi": "https://doi.org/10.1136/bmjopen-2023-076711",
-    "title": "Cohort profile: Born in Wales-a birth cohort with maternity, parental and child data linkage for life course research in Wales, UK.",
-    "authorString": "Jones H, Seaborne MJ, Kennedy NL, James M, Dredge S, Bandyopadhyay A, Battaglia A, Davies S, Brophy S.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2024",
-    "date": "2024-01-18",
-    "isOpenAccess": "Y",
-    "keywords": "epidemiology; Public Health; Community Child Health; Surveys And Questionnaires",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Purpose</h4>Using Wales's national dataset for maternity and births as a core dataset, we have linked related datasets to create a more complete and comprehensive entire country birth cohort. Data of anonymised identified persons are linked on the individual level to data from health, social care and education data within the Secure Anonymised Information Linkage (SAIL) Databank. Each individual is assigned an encrypted Anonymised Linking Field; this field is used to link anonymised individuals across datasets. We present the descriptive data available in the core dataset, and the future expansion plans for the database beyond its initial development stage.<h4>Participants</h4>Descriptive information from 2011 to 2023 has been gathered from the National Community Child Health Database (NCCHD) in SAIL. This comprehensive dataset comprises over 400\u2009000 child electronic records. Additionally, survey responses about health and well-being from a cross-section of the population including 2500 parents and 30\u2009000 primary school children have been collected for enriched personal responses and linkage to the data spine.<h4>Findings to date</h4>The electronic cohort comprises all children born in Wales since 2011, with follow-up conducted until they finish primary school at age 11. The child cohort is 51%: 49% female: male, and 7.8% are from ethnic minority backgrounds. When considering age distribution, 26.8% of children are under the age of 5, while 63.2% fall within the age range of 5-11.<h4>Future plans</h4>Born in Wales will expand by 30\u2009000 new births annually in Wales (in NCCHD), while including follow-up data of children and parents already in the database. Supplementary datasets complement the existing linkage, including primary care, hospital data, educational attainment and social care. Future research includes exploring the long-term implications of COVID-19 on child health and development, and examining the impact of parental work environment on child health and development.",
-    "laySummary": "",
-    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/14/1/e076711.full.pdf; doi:https://doi.org/10.1136/bmjopen-2023-076711; html:https://europepmc.org/articles/PMC10806724; pdf:https://europepmc.org/articles/PMC10806724?pdf=render"
-  },
   {
     "id": "34489241",
     "doi": "https://doi.org/10.1136/bjsports-2021-104050",
@@ -11729,6 +11712,23 @@
     "laySummary": "",
     "urls": "pdf:https://bjsm.bmj.com/content/bjsports/early/2022/02/15/bjsports-2021-104050.full.pdf; doi:https://doi.org/10.1136/bjsports-2021-104050; html:https://europepmc.org/articles/PMC9484395; pdf:https://europepmc.org/articles/PMC9484395?pdf=render"
   },
+  {
+    "id": "38238056",
+    "doi": "https://doi.org/10.1136/bmjopen-2023-076711",
+    "title": "Cohort profile: Born in Wales-a birth cohort with maternity, parental and child data linkage for life course research in Wales, UK.",
+    "authorString": "Jones H, Seaborne MJ, Kennedy NL, James M, Dredge S, Bandyopadhyay A, Battaglia A, Davies S, Brophy S.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2024",
+    "date": "2024-01-18",
+    "isOpenAccess": "Y",
+    "keywords": "epidemiology; Public Health; Community Child Health; Surveys And Questionnaires",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Purpose</h4>Using Wales's national dataset for maternity and births as a core dataset, we have linked related datasets to create a more complete and comprehensive entire country birth cohort. Data of anonymised identified persons are linked on the individual level to data from health, social care and education data within the Secure Anonymised Information Linkage (SAIL) Databank. Each individual is assigned an encrypted Anonymised Linking Field; this field is used to link anonymised individuals across datasets. We present the descriptive data available in the core dataset, and the future expansion plans for the database beyond its initial development stage.<h4>Participants</h4>Descriptive information from 2011 to 2023 has been gathered from the National Community Child Health Database (NCCHD) in SAIL. This comprehensive dataset comprises over 400\u2009000 child electronic records. Additionally, survey responses about health and well-being from a cross-section of the population including 2500 parents and 30\u2009000 primary school children have been collected for enriched personal responses and linkage to the data spine.<h4>Findings to date</h4>The electronic cohort comprises all children born in Wales since 2011, with follow-up conducted until they finish primary school at age 11. The child cohort is 51%: 49% female: male, and 7.8% are from ethnic minority backgrounds. When considering age distribution, 26.8% of children are under the age of 5, while 63.2% fall within the age range of 5-11.<h4>Future plans</h4>Born in Wales will expand by 30\u2009000 new births annually in Wales (in NCCHD), while including follow-up data of children and parents already in the database. Supplementary datasets complement the existing linkage, including primary care, hospital data, educational attainment and social care. Future research includes exploring the long-term implications of COVID-19 on child health and development, and examining the impact of parental work environment on child health and development.",
+    "laySummary": "",
+    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/14/1/e076711.full.pdf; doi:https://doi.org/10.1136/bmjopen-2023-076711; html:https://europepmc.org/articles/PMC10806724; pdf:https://europepmc.org/articles/PMC10806724?pdf=render"
+  },
   {
     "id": "35813279",
     "doi": "https://doi.org/10.1016/s2666-7568(22)00147-7",
@@ -11797,23 +11797,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1136/bmjdrc-2024-004191; doi:https://doi.org/10.1136/bmjdrc-2024-004191"
   },
-  {
-    "id": "35836669",
-    "doi": "https://doi.org/10.1097/txd.0000000000001188",
-    "title": "HLA Alleles Cw12 and DQ4 in Kidney Transplant Recipients Are Independent Risk Factors for the Development of Posttransplantation Diabetes.",
-    "authorString": "Phagura N, Hussain A, Culliford A, Hodson J, Evison F, Gallier S, Borrows R, Lane HA, Briggs D, Sharif A.",
-    "authorAffiliations": "",
-    "journalTitle": "Transplantation direct",
-    "pubYear": "2021",
-    "date": "2021-07-23",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The association between specific HLA alleles and risk for posttransplantation diabetes (PTDM) in a contemporary and multiethnic kidney transplant recipient cohort is not clear.<h4>Methods</h4>In this single-center analysis, data were retrospectively analyzed for 1560 nondiabetic kidney transplant recipients at a single center between 2007 and 2018, with median follow-up of 33 mo (interquartile range 8-73). HLA typing methodology was by DNA analysis and reported at the resolution required for the national allocation scheme. Diagnosis of PTDM was aligned with International Consensus recommendations.<h4>Results</h4>PTDM developed in 231 kidney transplant recipients. Exploring 99 HLA alleles, the presence of Cw12, B52, B38, B58, DQ4, A80, and DR13 and the absence of DQ3 and DR04 were associated with significant increases in PTDM risk. In a multivariable Cox regression model, adjusting for other clinical risk factors for PTDM, the presence of Cw12 (hazard ratio [HR], 1.57; 95% CI, 1.08-2.27; <i>P</i>\u2009=\u20090.017) and DQ4 (HR, 1.78; 95% CI, 1.07-2.96; <i>P</i>\u2009=\u20090.026) were found to be independent risk factors for PTDM. There was also evidence that the presence of B58 increases PTDM risk within the subgroup of recipients of White ethnicity (HR, 5.01; 95% CI, 2.20-11.42; <i>P</i>\u2009<\u20090.001).<h4>Conclusion</h4>Our data suggest that specific HLA alleles can be associated with PTDM risk, which can be used pretransplantation for PTDM risk stratification. However, association is not causality, and this work requires replication and further investigation to understand underlying biological mechanisms.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1097/txd.0000000000001188; doi:https://doi.org/10.1097/TXD.0000000000001188; html:https://europepmc.org/articles/PMC9276282; pdf:https://europepmc.org/articles/PMC9276282?pdf=render"
-  },
   {
     "id": "35997000",
     "doi": "https://doi.org/10.1111/ene.15530",
@@ -11831,6 +11814,23 @@
     "laySummary": "",
     "urls": "pdf:https://cronfa.swan.ac.uk/Record/cronfa62203/Download/62203__26254__0c88bfc9ff7e4fe2acaea5e2a2d74058.pdf; doi:https://doi.org/10.1111/ene.15530; html:https://europepmc.org/articles/PMC9826317; pdf:https://europepmc.org/articles/PMC9826317?pdf=render"
   },
+  {
+    "id": "35836669",
+    "doi": "https://doi.org/10.1097/txd.0000000000001188",
+    "title": "HLA Alleles Cw12 and DQ4 in Kidney Transplant Recipients Are Independent Risk Factors for the Development of Posttransplantation Diabetes.",
+    "authorString": "Phagura N, Hussain A, Culliford A, Hodson J, Evison F, Gallier S, Borrows R, Lane HA, Briggs D, Sharif A.",
+    "authorAffiliations": "",
+    "journalTitle": "Transplantation direct",
+    "pubYear": "2021",
+    "date": "2021-07-23",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The association between specific HLA alleles and risk for posttransplantation diabetes (PTDM) in a contemporary and multiethnic kidney transplant recipient cohort is not clear.<h4>Methods</h4>In this single-center analysis, data were retrospectively analyzed for 1560 nondiabetic kidney transplant recipients at a single center between 2007 and 2018, with median follow-up of 33 mo (interquartile range 8-73). HLA typing methodology was by DNA analysis and reported at the resolution required for the national allocation scheme. Diagnosis of PTDM was aligned with International Consensus recommendations.<h4>Results</h4>PTDM developed in 231 kidney transplant recipients. Exploring 99 HLA alleles, the presence of Cw12, B52, B38, B58, DQ4, A80, and DR13 and the absence of DQ3 and DR04 were associated with significant increases in PTDM risk. In a multivariable Cox regression model, adjusting for other clinical risk factors for PTDM, the presence of Cw12 (hazard ratio [HR], 1.57; 95% CI, 1.08-2.27; <i>P</i>\u2009=\u20090.017) and DQ4 (HR, 1.78; 95% CI, 1.07-2.96; <i>P</i>\u2009=\u20090.026) were found to be independent risk factors for PTDM. There was also evidence that the presence of B58 increases PTDM risk within the subgroup of recipients of White ethnicity (HR, 5.01; 95% CI, 2.20-11.42; <i>P</i>\u2009<\u20090.001).<h4>Conclusion</h4>Our data suggest that specific HLA alleles can be associated with PTDM risk, which can be used pretransplantation for PTDM risk stratification. However, association is not causality, and this work requires replication and further investigation to understand underlying biological mechanisms.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1097/txd.0000000000001188; doi:https://doi.org/10.1097/TXD.0000000000001188; html:https://europepmc.org/articles/PMC9276282; pdf:https://europepmc.org/articles/PMC9276282?pdf=render"
+  },
   {
     "id": "38842977",
     "doi": "https://doi.org/10.1016/j.jacep.2024.04.006",
@@ -11934,38 +11934,38 @@
     "urls": "pdf:https://nutrition.bmj.com/content/bmjnph/4/1/174.full.pdf; doi:https://doi.org/10.1136/bmjnph-2020-000225; html:https://europepmc.org/articles/PMC8258022; pdf:https://europepmc.org/articles/PMC8258022?pdf=render"
   },
   {
-    "id": "33623985",
-    "doi": "https://doi.org/10.1093/cid/ciab159",
-    "title": "Shorter and Longer Courses of Antibiotics for Common Infections and the Association With Reductions of Infection-Related Complications Including Hospital Admissions.",
-    "authorString": "Palin V, Welfare W, Ashcroft DM, van Staa TP.",
+    "id": "38383048",
+    "doi": "https://doi.org/10.1093/bioinformatics/btae101",
+    "title": "LAVASET: Latent Variable Stochastic Ensemble of Trees. An ensemble method for correlated datasets with spatial, spectral, and temporal dependencies.",
+    "authorString": "Kasapi M, Xu K, Ebbels TMD, O'Regan DP, Ware JS, Posma JM.",
     "authorAffiliations": "",
-    "journalTitle": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America",
-    "pubYear": "2021",
-    "date": "2021-11-01",
+    "journalTitle": "Bioinformatics (Oxford, England)",
+    "pubYear": "2024",
+    "date": "2024-03-01",
     "isOpenAccess": "Y",
-    "keywords": "Antibiotics; Antimicrobial resistance; Antibiotic Duration; Infection Complication",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Antimicrobial resistance is a serious global health concern that emphasizes completing treatment course. Recently, the effectiveness of short versus longer antibiotic courses has been questioned. This study investigated the duration of prescribed antibiotics, their effectiveness, and associated risk of infection-related complications.<h4>Methods</h4>Clinical Practice Research Datalink identified 4 million acute infection episodes prescribed an antibiotic in primary care between January 2014-June 2014, England. Prescriptions were categorized by duration. Risk of infection-related hospitalizations within 30 days was modelled overall and by infection type. Risk was assessed immediately after or within 30 days follow-up to measure confounders given similar and varying exposure, respectively. An interaction term with follow-up time assessed whether hazard ratios (HRs) remained parallel with different antibiotic durations.<h4>Results</h4>The duration of antibiotic courses increased over the study period (5.2-19.1%); 6-7 days were most common (66.9%). Most infection-related hospitalizations occurred with prescriptions of 8-15 days (0.21%), accompanied by greater risk of infection-related complications compared to patients who received a short prescription (HR: 1.75 [95% CI: 1.54-2.00]). Comparing HRs in the first 5 days versus remaining follow-up showed longer antibiotic courses were no more effective than shorter courses (1.02 [95% CI: 0.90-1.16] and 0.92 [95% CI: 0.75-1.12]). No variation by infection-type was observed.<h4>Conclusions</h4>Equal effectiveness was found between shorter and longer antibiotic courses and the reduction of infection-related hospitalizations. Stewardship programs should recommend shorter courses of antibiotics for acute infections. Further research is required for treating patients with a complex medical history.SummaryPrescribing of longer courses increased over the study period. The majority of hospitalizations occurred for patients receiving longer courses. Risk of developing a complication (immediate vs remaining follow-up) found longer courses were no more effective than shorter courses.",
+    "abstract": "<h4>Motivation</h4>Random forests (RFs) can deal with a large number of variables, achieve reasonable prediction scores, and yield highly interpretable feature importance values. As such, RFs are appropriate models for feature selection and further dimension reduction. However, RFs are often not appropriate for correlated datasets due to their mode of selecting individual features for splitting. Addressing correlation relationships in high-dimensional datasets is imperative for reducing the number of variables that are assigned high importance, hence making the dimension reduction most efficient. Here, we propose the LAtent VAriable Stochastic Ensemble of Trees (LAVASET) method that derives latent variables based on the distance characteristics of each feature and aims to incorporate the correlation factor in the splitting step.<h4>Results</h4>Without compromising on performance in the majority of examples, LAVASET outperforms RF by accurately determining feature importance across all correlated variables and ensuring proper distribution of importance values. LAVASET yields mostly non-inferior prediction accuracies to traditional RFs when tested in simulated and real 1D datasets, as well as more complex and high-dimensional 3D datatypes. Unlike traditional RFs, LAVASET is unaffected by single 'important' noisy features (false positives), as it considers the local neighbourhood. LAVASET, therefore, highlights neighbourhoods of features, reflecting real signals that collectively impact the model's predictive ability.<h4>Availability and implementation</h4>LAVASET is freely available as a standalone package from https://github.com/melkasapi/LAVASET.",
     "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/cid/advance-article-pdf/doi/10.1093/cid/ciab159/37414330/ciab159.pdf; doi:https://doi.org/10.1093/cid/ciab159; html:https://europepmc.org/articles/PMC8599204; pdf:https://europepmc.org/articles/PMC8599204?pdf=render"
+    "urls": "pdf:https://academic.oup.com/bioinformatics/article-pdf/40/3/btae101/56904442/btae101.pdf; doi:https://doi.org/10.1093/bioinformatics/btae101; html:https://europepmc.org/articles/PMC11212485; pdf:https://europepmc.org/articles/PMC11212485?pdf=render"
   },
   {
-    "id": "38316529",
-    "doi": "https://doi.org/10.1111/dar.13816",
-    "title": "Approaches and reporting of alcohol and other drug testing for injured patients in hospital-based studies: A systematic review.",
-    "authorString": "Lau G, Ang JY, Kim N, Gabbe BJ, Mitra B, Dietze PM, Reeder S, Beck B.",
+    "id": "35749561",
+    "doi": "https://doi.org/10.1371/journal.pcbi.1010234",
+    "title": "Evidence for influenza and RSV interaction from 10 years of enhanced surveillance in Nha Trang, Vietnam, a modelling study.",
+    "authorString": "Waterlow NR, Toizumi M, van Leeuwen E, Thi Nguyen HA, Myint-Yoshida L, Eggo RM, Flasche S.",
     "authorAffiliations": "",
-    "journalTitle": "Drug and alcohol review",
-    "pubYear": "2024",
-    "date": "2024-02-05",
-    "isOpenAccess": "N",
-    "keywords": "Alcohol; Injury; Emergency Department; Illicit Drug; Substance Abuse Detection",
+    "journalTitle": "PLoS computational biology",
+    "pubYear": "2022",
+    "date": "2022-06-24",
+    "isOpenAccess": "Y",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Issue</h4>Hospital alcohol and/or other drug (AOD) testing is important for identifying AOD-related injuries; however, testing methods vary. This systematic review aimed to examine biological AOD testing methods from hospital-based studies of injured patients and quantify what proportion reported key information on those testing methods.<h4>Approach</h4>Observational studies published in English from 2010 onwards involving biological AOD testing for injured patients presenting to hospital were included. Studies examining single injury causes were excluded. Extracted data included concentration thresholds for AOD detection (e.g., lower limits of detection, author-defined cut-offs), test type (e.g., immunoassay, breathalyser) and approach (e.g., routine, clinical discretion), timing of testing, sample type and the proportion of injured cases tested for AODs.<h4>Key findings</h4>Of 83 included studies, 76 measured alcohol and 37 other drugs. Forty-nine studies defined blood alcohol concentration thresholds (ranging from 0 to 0.1\u2009g/100\u2009mL). Seven studies defined concentration thresholds for other drugs. Testing approach was reported in 39/76 alcohol and 18/37 other drug studies. Sample type was commonly reported (alcohol: n\u2009=\u200969/76; other drugs: n\u2009=\u200928/37); alcohol was typically measured using blood (n\u2009=\u200960) and other drugs using urine (n\u2009=\u200920). Studies that reported the proportion of cases tested (alcohol: n\u2009=\u200953/76; other drugs: n\u2009=\u200928/37), reported that between 0% and 89% of cases were not tested for alcohol and 0% and 91% for other drugs. Timing of testing was often unreported (alcohol: n\u2009=\u200961; other drugs: n\u2009=\u200930).<h4>Implications and conclusion</h4>Variation in AOD testing methods alongside incomplete reporting of those methods limits data comparability and interpretation. Standardised reporting of testing methods will assist AOD-related injury surveillance and prevention.",
+    "abstract": "Influenza and Respiratory Syncytial Virus (RSV) interact within their host posing the concern for impacts on heterologous viruses following vaccination. We aimed to estimate the population level impact of their interaction. We developed a dynamic age-stratified two-pathogen mathematical model that includes pathogen interaction through competition for infection and enhanced severity of dual infections. We used parallel tempering to fit its parameters to 11 years of enhanced hospital-based surveillance for acute respiratory illnesses (ARI) in children under 5 years old in Nha Trang, Vietnam. The data supported either a 41% (95%CrI: 36-54) reduction in susceptibility following infection and for 10.0 days (95%CrI 7.1-12.8) thereafter, or no change in susceptibility following infection. We estimate that co-infection increased the probability for an infection in <2y old children to be reported 7.2 fold (95%CrI 5.0-11.4); or 16.6 fold (95%CrI 14.5-18.4) in the moderate or low interaction scenarios. Absence of either pathogen was not to the detriment of the other. We find stronger evidence for severity enhancing than for acquisition limiting interaction. In this setting vaccination against either pathogen is unlikely to have a major detrimental effect on the burden of disease caused by the other.",
     "laySummary": "",
-    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/dar.13816; doi:https://doi.org/10.1111/dar.13816"
+    "urls": "pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010234&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1010234; html:https://europepmc.org/articles/PMC9262224; pdf:https://europepmc.org/articles/PMC9262224?pdf=render"
   },
   {
     "id": "34518162",
@@ -11985,38 +11985,38 @@
     "urls": "pdf:https://discovery.ucl.ac.uk/10164981/1/267.full.pdf; doi:https://doi.org/10.1136/bjophthalmol-2021-319383; html:https://europepmc.org/articles/PMC9887382; pdf:https://europepmc.org/articles/PMC9887382?pdf=render"
   },
   {
-    "id": "35749561",
-    "doi": "https://doi.org/10.1371/journal.pcbi.1010234",
-    "title": "Evidence for influenza and RSV interaction from 10 years of enhanced surveillance in Nha Trang, Vietnam, a modelling study.",
-    "authorString": "Waterlow NR, Toizumi M, van Leeuwen E, Thi Nguyen HA, Myint-Yoshida L, Eggo RM, Flasche S.",
+    "id": "33623985",
+    "doi": "https://doi.org/10.1093/cid/ciab159",
+    "title": "Shorter and Longer Courses of Antibiotics for Common Infections and the Association With Reductions of Infection-Related Complications Including Hospital Admissions.",
+    "authorString": "Palin V, Welfare W, Ashcroft DM, van Staa TP.",
     "authorAffiliations": "",
-    "journalTitle": "PLoS computational biology",
-    "pubYear": "2022",
-    "date": "2022-06-24",
+    "journalTitle": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America",
+    "pubYear": "2021",
+    "date": "2021-11-01",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Antibiotics; Antimicrobial resistance; Antibiotic Duration; Infection Complication",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Influenza and Respiratory Syncytial Virus (RSV) interact within their host posing the concern for impacts on heterologous viruses following vaccination. We aimed to estimate the population level impact of their interaction. We developed a dynamic age-stratified two-pathogen mathematical model that includes pathogen interaction through competition for infection and enhanced severity of dual infections. We used parallel tempering to fit its parameters to 11 years of enhanced hospital-based surveillance for acute respiratory illnesses (ARI) in children under 5 years old in Nha Trang, Vietnam. The data supported either a 41% (95%CrI: 36-54) reduction in susceptibility following infection and for 10.0 days (95%CrI 7.1-12.8) thereafter, or no change in susceptibility following infection. We estimate that co-infection increased the probability for an infection in <2y old children to be reported 7.2 fold (95%CrI 5.0-11.4); or 16.6 fold (95%CrI 14.5-18.4) in the moderate or low interaction scenarios. Absence of either pathogen was not to the detriment of the other. We find stronger evidence for severity enhancing than for acquisition limiting interaction. In this setting vaccination against either pathogen is unlikely to have a major detrimental effect on the burden of disease caused by the other.",
+    "abstract": "<h4>Background</h4>Antimicrobial resistance is a serious global health concern that emphasizes completing treatment course. Recently, the effectiveness of short versus longer antibiotic courses has been questioned. This study investigated the duration of prescribed antibiotics, their effectiveness, and associated risk of infection-related complications.<h4>Methods</h4>Clinical Practice Research Datalink identified 4 million acute infection episodes prescribed an antibiotic in primary care between January 2014-June 2014, England. Prescriptions were categorized by duration. Risk of infection-related hospitalizations within 30 days was modelled overall and by infection type. Risk was assessed immediately after or within 30 days follow-up to measure confounders given similar and varying exposure, respectively. An interaction term with follow-up time assessed whether hazard ratios (HRs) remained parallel with different antibiotic durations.<h4>Results</h4>The duration of antibiotic courses increased over the study period (5.2-19.1%); 6-7 days were most common (66.9%). Most infection-related hospitalizations occurred with prescriptions of 8-15 days (0.21%), accompanied by greater risk of infection-related complications compared to patients who received a short prescription (HR: 1.75 [95% CI: 1.54-2.00]). Comparing HRs in the first 5 days versus remaining follow-up showed longer antibiotic courses were no more effective than shorter courses (1.02 [95% CI: 0.90-1.16] and 0.92 [95% CI: 0.75-1.12]). No variation by infection-type was observed.<h4>Conclusions</h4>Equal effectiveness was found between shorter and longer antibiotic courses and the reduction of infection-related hospitalizations. Stewardship programs should recommend shorter courses of antibiotics for acute infections. Further research is required for treating patients with a complex medical history.SummaryPrescribing of longer courses increased over the study period. The majority of hospitalizations occurred for patients receiving longer courses. Risk of developing a complication (immediate vs remaining follow-up) found longer courses were no more effective than shorter courses.",
     "laySummary": "",
-    "urls": "pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010234&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1010234; html:https://europepmc.org/articles/PMC9262224; pdf:https://europepmc.org/articles/PMC9262224?pdf=render"
+    "urls": "pdf:https://academic.oup.com/cid/advance-article-pdf/doi/10.1093/cid/ciab159/37414330/ciab159.pdf; doi:https://doi.org/10.1093/cid/ciab159; html:https://europepmc.org/articles/PMC8599204; pdf:https://europepmc.org/articles/PMC8599204?pdf=render"
   },
   {
-    "id": "38383048",
-    "doi": "https://doi.org/10.1093/bioinformatics/btae101",
-    "title": "LAVASET: Latent Variable Stochastic Ensemble of Trees. An ensemble method for correlated datasets with spatial, spectral, and temporal dependencies.",
-    "authorString": "Kasapi M, Xu K, Ebbels TMD, O'Regan DP, Ware JS, Posma JM.",
+    "id": "38316529",
+    "doi": "https://doi.org/10.1111/dar.13816",
+    "title": "Approaches and reporting of alcohol and other drug testing for injured patients in hospital-based studies: A systematic review.",
+    "authorString": "Lau G, Ang JY, Kim N, Gabbe BJ, Mitra B, Dietze PM, Reeder S, Beck B.",
     "authorAffiliations": "",
-    "journalTitle": "Bioinformatics (Oxford, England)",
+    "journalTitle": "Drug and alcohol review",
     "pubYear": "2024",
-    "date": "2024-03-01",
-    "isOpenAccess": "Y",
-    "keywords": "",
+    "date": "2024-02-05",
+    "isOpenAccess": "N",
+    "keywords": "Alcohol; Injury; Emergency Department; Illicit Drug; Substance Abuse Detection",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Motivation</h4>Random forests (RFs) can deal with a large number of variables, achieve reasonable prediction scores, and yield highly interpretable feature importance values. As such, RFs are appropriate models for feature selection and further dimension reduction. However, RFs are often not appropriate for correlated datasets due to their mode of selecting individual features for splitting. Addressing correlation relationships in high-dimensional datasets is imperative for reducing the number of variables that are assigned high importance, hence making the dimension reduction most efficient. Here, we propose the LAtent VAriable Stochastic Ensemble of Trees (LAVASET) method that derives latent variables based on the distance characteristics of each feature and aims to incorporate the correlation factor in the splitting step.<h4>Results</h4>Without compromising on performance in the majority of examples, LAVASET outperforms RF by accurately determining feature importance across all correlated variables and ensuring proper distribution of importance values. LAVASET yields mostly non-inferior prediction accuracies to traditional RFs when tested in simulated and real 1D datasets, as well as more complex and high-dimensional 3D datatypes. Unlike traditional RFs, LAVASET is unaffected by single 'important' noisy features (false positives), as it considers the local neighbourhood. LAVASET, therefore, highlights neighbourhoods of features, reflecting real signals that collectively impact the model's predictive ability.<h4>Availability and implementation</h4>LAVASET is freely available as a standalone package from https://github.com/melkasapi/LAVASET.",
+    "abstract": "<h4>Issue</h4>Hospital alcohol and/or other drug (AOD) testing is important for identifying AOD-related injuries; however, testing methods vary. This systematic review aimed to examine biological AOD testing methods from hospital-based studies of injured patients and quantify what proportion reported key information on those testing methods.<h4>Approach</h4>Observational studies published in English from 2010 onwards involving biological AOD testing for injured patients presenting to hospital were included. Studies examining single injury causes were excluded. Extracted data included concentration thresholds for AOD detection (e.g., lower limits of detection, author-defined cut-offs), test type (e.g., immunoassay, breathalyser) and approach (e.g., routine, clinical discretion), timing of testing, sample type and the proportion of injured cases tested for AODs.<h4>Key findings</h4>Of 83 included studies, 76 measured alcohol and 37 other drugs. Forty-nine studies defined blood alcohol concentration thresholds (ranging from 0 to 0.1\u2009g/100\u2009mL). Seven studies defined concentration thresholds for other drugs. Testing approach was reported in 39/76 alcohol and 18/37 other drug studies. Sample type was commonly reported (alcohol: n\u2009=\u200969/76; other drugs: n\u2009=\u200928/37); alcohol was typically measured using blood (n\u2009=\u200960) and other drugs using urine (n\u2009=\u200920). Studies that reported the proportion of cases tested (alcohol: n\u2009=\u200953/76; other drugs: n\u2009=\u200928/37), reported that between 0% and 89% of cases were not tested for alcohol and 0% and 91% for other drugs. Timing of testing was often unreported (alcohol: n\u2009=\u200961; other drugs: n\u2009=\u200930).<h4>Implications and conclusion</h4>Variation in AOD testing methods alongside incomplete reporting of those methods limits data comparability and interpretation. Standardised reporting of testing methods will assist AOD-related injury surveillance and prevention.",
     "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/bioinformatics/article-pdf/40/3/btae101/56904442/btae101.pdf; doi:https://doi.org/10.1093/bioinformatics/btae101; html:https://europepmc.org/articles/PMC11212485; pdf:https://europepmc.org/articles/PMC11212485?pdf=render"
+    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/dar.13816; doi:https://doi.org/10.1111/dar.13816"
   },
   {
     "id": "35067242",
@@ -12171,23 +12171,6 @@
     "laySummary": "",
     "urls": "pdf:https://n.neurology.org/content/neurology/96/8/e1251.full.pdf; doi:https://doi.org/10.1212/WNL.0000000000011463; html:https://europepmc.org/articles/PMC8055349; pdf:https://europepmc.org/articles/PMC8055349?pdf=render"
   },
-  {
-    "id": "31818272",
-    "doi": "https://doi.org/10.1186/s12889-019-8015-3",
-    "title": "Drinking beer, wine or spirits - does it matter for inequalities in alcohol-related hospital admission? A record-linked longitudinal study in Wales.",
-    "authorString": "Gartner A, Trefan L, Moore S, Akbari A, Paranjothy S, Farewell D.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC public health",
-    "pubYear": "2019",
-    "date": "2019-12-09",
-    "isOpenAccess": "Y",
-    "keywords": "Alcohol; Inequalities; Deprivation; Hospital Admission; Beverage Type; Record Linked",
-    "nationalPriorities": "Improving Public Health",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Alcohol-related harm has been found to be higher in disadvantaged groups, despite similar alcohol consumption to advantaged groups. This is known as the alcohol harm paradox. Beverage type is reportedly socioeconomically patterned but has not been included in longitudinal studies investigating record-linked alcohol consumption and harm. We aimed to investigate whether and to what extent consumption by beverage type, BMI, smoking and other factors explain inequalities in alcohol-related harm.<h4>Methods</h4>11,038 respondents to the Welsh Health Survey answered questions on their health and lifestyle. Responses were record-linked to wholly attributable alcohol-related hospital admissions (ARHA) eight years before the survey month and until the end of 2016 within the Secure Anonymised Information Linkage (SAIL) Databank. We used survival analysis, specifically multi-level and multi-failure Cox mixed effects models, to calculate the hazard ratios of ARHA. In adjusted models we included the number of units consumed by beverage type and other factors, censoring for death or moving out of Wales.<h4>Results</h4>People living in more deprived areas had a higher risk of admission (HR 1.75; 95% CI 1.23-2.48) compared to less deprived. Adjustment for the number of units by type of alcohol consumed only reduced the risk of ARHA for more deprived areas by 4% (HR 1.72; 95% CI 1.21-2.44), whilst adding smoking and BMI reduced these inequalities by 35.7% (HR 1.48; 95% CI 1.01-2.17). These social patterns were similar for individual-level social class, employment, housing tenure and highest qualification. Inequalities were further reduced by including either health status (16.6%) or mental health condition (5%). Unit increases of spirits drunk were positively associated with increasing risk of ARHA (HR 1.06; 95% CI 1.01-1.12), higher than for other drink types.<h4>Conclusions</h4>Although consumption by beverage type was socioeconomically patterned, it did not help explain inequalities in alcohol-related harm. Smoking and BMI explained around a third of inequalities, but lower socioeconomic groups had a persistently higher risk of (multiple) ARHA. Comorbidities also explained a further proportion of inequalities and need further investigation, including the contribution of specific conditions. The increased harms from consumption of stronger alcoholic beverages may inform public health policy.",
-    "laySummary": "This longitudinal study investigated whether and to what extent consumption by beverage type, BMI, smoking and other factors explained inequalities in alcohol-related hospital admission (ARHA). Using statistical analysis methods, it was found that people living in more deprived areas had a higher risk of ARHA compared to less deprived. Smokers and people currently being treated for mental illness had higher risk of ARHA, while BMI appeared to be slightly protective. ",
-    "urls": "pdf:https://bmcpublichealth.biomedcentral.com/track/pdf/10.1186/s12889-019-8015-3; doi:https://doi.org/10.1186/s12889-019-8015-3; html:https://europepmc.org/articles/PMC6902530; pdf:https://europepmc.org/articles/PMC6902530?pdf=render"
-  },
   {
     "id": "34431993",
     "doi": "https://doi.org/10.1093/eurheartj/ehab581",
@@ -12205,6 +12188,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/eurheartj/article-pdf/43/2/127/42182731/ehab581.pdf; doi:https://doi.org/10.1093/eurheartj/ehab581; html:https://europepmc.org/articles/PMC8757580; pdf:https://europepmc.org/articles/PMC8757580?pdf=render"
   },
+  {
+    "id": "31818272",
+    "doi": "https://doi.org/10.1186/s12889-019-8015-3",
+    "title": "Drinking beer, wine or spirits - does it matter for inequalities in alcohol-related hospital admission? A record-linked longitudinal study in Wales.",
+    "authorString": "Gartner A, Trefan L, Moore S, Akbari A, Paranjothy S, Farewell D.",
+    "authorAffiliations": "",
+    "journalTitle": "BMC public health",
+    "pubYear": "2019",
+    "date": "2019-12-09",
+    "isOpenAccess": "Y",
+    "keywords": "Alcohol; Inequalities; Deprivation; Hospital Admission; Beverage Type; Record Linked",
+    "nationalPriorities": "Improving Public Health",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Alcohol-related harm has been found to be higher in disadvantaged groups, despite similar alcohol consumption to advantaged groups. This is known as the alcohol harm paradox. Beverage type is reportedly socioeconomically patterned but has not been included in longitudinal studies investigating record-linked alcohol consumption and harm. We aimed to investigate whether and to what extent consumption by beverage type, BMI, smoking and other factors explain inequalities in alcohol-related harm.<h4>Methods</h4>11,038 respondents to the Welsh Health Survey answered questions on their health and lifestyle. Responses were record-linked to wholly attributable alcohol-related hospital admissions (ARHA) eight years before the survey month and until the end of 2016 within the Secure Anonymised Information Linkage (SAIL) Databank. We used survival analysis, specifically multi-level and multi-failure Cox mixed effects models, to calculate the hazard ratios of ARHA. In adjusted models we included the number of units consumed by beverage type and other factors, censoring for death or moving out of Wales.<h4>Results</h4>People living in more deprived areas had a higher risk of admission (HR 1.75; 95% CI 1.23-2.48) compared to less deprived. Adjustment for the number of units by type of alcohol consumed only reduced the risk of ARHA for more deprived areas by 4% (HR 1.72; 95% CI 1.21-2.44), whilst adding smoking and BMI reduced these inequalities by 35.7% (HR 1.48; 95% CI 1.01-2.17). These social patterns were similar for individual-level social class, employment, housing tenure and highest qualification. Inequalities were further reduced by including either health status (16.6%) or mental health condition (5%). Unit increases of spirits drunk were positively associated with increasing risk of ARHA (HR 1.06; 95% CI 1.01-1.12), higher than for other drink types.<h4>Conclusions</h4>Although consumption by beverage type was socioeconomically patterned, it did not help explain inequalities in alcohol-related harm. Smoking and BMI explained around a third of inequalities, but lower socioeconomic groups had a persistently higher risk of (multiple) ARHA. Comorbidities also explained a further proportion of inequalities and need further investigation, including the contribution of specific conditions. The increased harms from consumption of stronger alcoholic beverages may inform public health policy.",
+    "laySummary": "This longitudinal study investigated whether and to what extent consumption by beverage type, BMI, smoking and other factors explained inequalities in alcohol-related hospital admission (ARHA). Using statistical analysis methods, it was found that people living in more deprived areas had a higher risk of ARHA compared to less deprived. Smokers and people currently being treated for mental illness had higher risk of ARHA, while BMI appeared to be slightly protective. ",
+    "urls": "pdf:https://bmcpublichealth.biomedcentral.com/track/pdf/10.1186/s12889-019-8015-3; doi:https://doi.org/10.1186/s12889-019-8015-3; html:https://europepmc.org/articles/PMC6902530; pdf:https://europepmc.org/articles/PMC6902530?pdf=render"
+  },
   {
     "id": "37935836",
     "doi": "https://doi.org/10.1093/eurheartj/ehad736",
@@ -12273,6 +12273,23 @@
     "laySummary": "",
     "urls": "pdf:https://discovery.ucl.ac.uk/10145154/1/Bean_An%20open%20source%2C%20expert%20designed%20decision%20tree%20application%20to%20support%20accurate%20diagnosis%20of%20myeloid%20malignancies_VoR.pdf; doi:https://doi.org/10.1002/jha2.182; html:https://europepmc.org/articles/PMC9175663; pdf:https://europepmc.org/articles/PMC9175663?pdf=render"
   },
+  {
+    "id": "37185641",
+    "doi": "https://doi.org/10.1136/bmjopen-2022-070022",
+    "title": "EXAcerbations of COPD and their OutcomeS on CardioVascular diseases (EXACOS-CV) Programme: protocol of multicountry observational cohort studies.",
+    "authorString": "Nordon C, Rhodes K, Quint JK, Vogelmeier CF, Simons SO, Hawkins NM, Marshall J, Ouwens M, Garbe E, M\u00fcllerov\u00e1 H.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2023",
+    "date": "2023-04-26",
+    "isOpenAccess": "Y",
+    "keywords": "epidemiology; Cardiology; Vascular Medicine; Chronic Airways Disease",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>In patients with chronic obstructive pulmonary disease (COPD), the risk of certain cardiovascular (CV) events is increased by threefold to fivefold in the year following acute exacerbation of COPD (AECOPD), compared with a non-exacerbation period. While the effect of severe AECOPD is well established, the relationship of moderate exacerbation or prior exacerbation to elevated risk of CV events is less clear. We will conduct cohort studies in multiple countries to further characterise the association between AECOPD and CV events.<h4>Methods and analysis</h4>Retrospective longitudinal cohort studies will be conducted within routinely collected electronic healthcare records or claims databases. The study cohorts will include patients meeting inclusion criteria for COPD between 1 January 2014 and 31 December 2018. Moderate exacerbation is defined as an outpatient visit and/or medication dispensation/prescription for exacerbation; severe exacerbation is defined as hospitalisation for COPD. The primary outcomes of interest are the time to (1) first hospitalisation for a CV event (including acute coronary syndrome, heart failure, arrhythmias or cerebral ischaemia) since cohort entry or (2) death. Time-dependent Cox proportional hazards models will compare the hazard of a CV event between exposed periods following exacerbation (split into these periods: 1-7, 8-14, 15-30, 31-180 and 181-365 days) and the unexposed reference time period, adjusted on time-fixed and time-varying confounders.<h4>Ethics and dissemination</h4>Studies have been approved in Canada, Japan, the Netherlands, Spain and the UK, where an institutional review board is mandated. For each study, the results will be published in peer-reviewed journals.",
+    "laySummary": "",
+    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/13/4/e070022.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-070022; html:https://europepmc.org/articles/PMC10151875; pdf:https://europepmc.org/articles/PMC10151875?pdf=render"
+  },
   {
     "id": "PMC9644982",
     "doi": "https://doi.org/",
@@ -12307,23 +12324,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2022.983091/pdf; doi:https://doi.org/10.3389/fcvm.2022.983091; html:https://europepmc.org/articles/PMC9537599; pdf:https://europepmc.org/articles/PMC9537599?pdf=render"
   },
-  {
-    "id": "37185641",
-    "doi": "https://doi.org/10.1136/bmjopen-2022-070022",
-    "title": "EXAcerbations of COPD and their OutcomeS on CardioVascular diseases (EXACOS-CV) Programme: protocol of multicountry observational cohort studies.",
-    "authorString": "Nordon C, Rhodes K, Quint JK, Vogelmeier CF, Simons SO, Hawkins NM, Marshall J, Ouwens M, Garbe E, M\u00fcllerov\u00e1 H.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2023",
-    "date": "2023-04-26",
-    "isOpenAccess": "Y",
-    "keywords": "epidemiology; Cardiology; Vascular Medicine; Chronic Airways Disease",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>In patients with chronic obstructive pulmonary disease (COPD), the risk of certain cardiovascular (CV) events is increased by threefold to fivefold in the year following acute exacerbation of COPD (AECOPD), compared with a non-exacerbation period. While the effect of severe AECOPD is well established, the relationship of moderate exacerbation or prior exacerbation to elevated risk of CV events is less clear. We will conduct cohort studies in multiple countries to further characterise the association between AECOPD and CV events.<h4>Methods and analysis</h4>Retrospective longitudinal cohort studies will be conducted within routinely collected electronic healthcare records or claims databases. The study cohorts will include patients meeting inclusion criteria for COPD between 1 January 2014 and 31 December 2018. Moderate exacerbation is defined as an outpatient visit and/or medication dispensation/prescription for exacerbation; severe exacerbation is defined as hospitalisation for COPD. The primary outcomes of interest are the time to (1) first hospitalisation for a CV event (including acute coronary syndrome, heart failure, arrhythmias or cerebral ischaemia) since cohort entry or (2) death. Time-dependent Cox proportional hazards models will compare the hazard of a CV event between exposed periods following exacerbation (split into these periods: 1-7, 8-14, 15-30, 31-180 and 181-365 days) and the unexposed reference time period, adjusted on time-fixed and time-varying confounders.<h4>Ethics and dissemination</h4>Studies have been approved in Canada, Japan, the Netherlands, Spain and the UK, where an institutional review board is mandated. For each study, the results will be published in peer-reviewed journals.",
-    "laySummary": "",
-    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/13/4/e070022.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-070022; html:https://europepmc.org/articles/PMC10151875; pdf:https://europepmc.org/articles/PMC10151875?pdf=render"
-  },
   {
     "id": "33739254",
     "doi": "https://doi.org/10.2807/1560-7917.es.2021.26.11.2100256",
@@ -12358,23 +12358,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ehjdh/advance-article-pdf/doi/10.1093/ehjdh/ztae001/56332468/ztae001.pdf; doi:https://doi.org/10.1093/ehjdh/ztae001; html:https://europepmc.org/articles/PMC10944683; pdf:https://europepmc.org/articles/PMC10944683?pdf=render"
   },
-  {
-    "id": "35868811",
-    "doi": "https://doi.org/10.1016/s2589-7500(22)00122-4",
-    "title": "Data provenance and integrity of health-care systems data for clinical trials.",
-    "authorString": "Murray ML, Love SB, Carpenter JR, Hartley S, Landray MJ, Mafham M, Parmar MKB, Pinches H, Sydes MR, Healthcare Systems Data for Clinical Trials Collaborative Group.",
-    "authorAffiliations": "",
-    "journalTitle": "The Lancet. Digital health",
-    "pubYear": "2022",
-    "date": "2022-08-01",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "",
-    "urls": "pdf:http://www.thelancet.com/article/S2589750022001224/pdf; doi:https://doi.org/10.1016/S2589-7500(22)00122-4; html:https://europepmc.org/articles/PMC9296098; pdf:https://europepmc.org/articles/PMC9296098?pdf=render"
-  },
   {
     "id": "38053867",
     "doi": "https://doi.org/10.1016/j.heliyon.2023.e21734",
@@ -12392,6 +12375,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.heliyon.2023.e21734; html:https://europepmc.org/articles/PMC10694161; pdf:https://europepmc.org/articles/PMC10694161?pdf=render"
   },
+  {
+    "id": "35868811",
+    "doi": "https://doi.org/10.1016/s2589-7500(22)00122-4",
+    "title": "Data provenance and integrity of health-care systems data for clinical trials.",
+    "authorString": "Murray ML, Love SB, Carpenter JR, Hartley S, Landray MJ, Mafham M, Parmar MKB, Pinches H, Sydes MR, Healthcare Systems Data for Clinical Trials Collaborative Group.",
+    "authorAffiliations": "",
+    "journalTitle": "The Lancet. Digital health",
+    "pubYear": "2022",
+    "date": "2022-08-01",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "",
+    "laySummary": "",
+    "urls": "pdf:http://www.thelancet.com/article/S2589750022001224/pdf; doi:https://doi.org/10.1016/S2589-7500(22)00122-4; html:https://europepmc.org/articles/PMC9296098; pdf:https://europepmc.org/articles/PMC9296098?pdf=render"
+  },
   {
     "id": "36545688",
     "doi": "https://doi.org/10.1192/bjb.2022.83",
@@ -12495,21 +12495,21 @@
     "urls": "pdf:https://academic.oup.com/nar/article-pdf/48/D1/D933/31697824/gkz895.pdf; doi:https://doi.org/10.1093/nar/gkz895; html:https://europepmc.org/articles/PMC7145571; pdf:https://europepmc.org/articles/PMC7145571?pdf=render"
   },
   {
-    "id": "38378812",
-    "doi": "https://doi.org/10.1007/s00127-024-02620-6",
-    "title": "Understanding social and clinical associations with unemployment for people with schizophrenia and bipolar disorders: large-scale health records study.",
-    "authorString": "Chilman N, Laporte D, Dorrington S, Hatch SL, Morgan C, Okoroji C, Stewart R, Das-Munshi J.",
+    "id": "36472984",
+    "doi": "https://doi.org/10.1371/journal.pmed.1004124",
+    "title": "Association between antidementia medication use and mortality in people diagnosed with dementia with Lewy bodies in the UK: A retrospective cohort study.",
+    "authorString": "Chen S, Price AC, Cardinal RN, Moylett S, Kershenbaum AD, Fitzgerald J, Mueller C, Stewart R, O'Brien JT.",
     "authorAffiliations": "",
-    "journalTitle": "Social psychiatry and psychiatric epidemiology",
-    "pubYear": "2024",
-    "date": "2024-02-20",
+    "journalTitle": "PLoS medicine",
+    "pubYear": "2022",
+    "date": "2022-12-06",
     "isOpenAccess": "Y",
-    "keywords": "Schizophrenia; Bipolar disorder; Employment; Ethnicity; Occupation; Natural Language Processing",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Purpose</h4>People with severe mental illness (SMI) experience high levels of unemployment. We aimed to better understand the associations between clinical, social, and demographic inequality indicators and unemployment.<h4>Methods</h4>Data were extracted from de-identified health records of people with SMI in contact with secondary mental health services in south London, UK. A Natural Language Processing text-mining application was applied to extract information on unemployment in the health records. Multivariable logistic regression was used to assess associations with unemployment, in people with SMI.<h4>Results</h4>Records from 19,768 service users were used for analysis, 84.9% (n\u2009=\u200916,778) had experienced unemployment. In fully adjusted models, Black Caribbean and Black African service users were more likely to experience unemployment compared with White British service users (Black Caribbean: aOR 1.62, 95% CI 1.45-1.80; Black African: 1.32, 1.15-1.51). Although men were more likely to have experienced unemployment relative to women in unadjusted models (OR 1.36, 95% CI 1.26-1.47), differences were no longer apparent in the fully adjusted models (aOR 1.05, 95% CI 0.97-1.15). The presence of a non-affective (compared to affective) diagnosis (1.24, 1.13-1.35), comorbid substance use (2.02, 1.76-2.33), previous inpatient admissions (4.18, 3.71-4.70), longer inpatient stays (78\u2009+\u2009days: 7.78, 6.34-9.54), and compulsory admissions (3.45, 3.04-3.92) were associated with unemployment, in fully adjusted models.<h4>Conclusion</h4>People with SMI experience high levels of unemployment, and we found that unemployment was associated with several clinical and social factors. Interventions to address low employment may need to also address these broader inequalities.",
+    "abstract": "<h4>Background</h4>Dementia with Lewy bodies (DLBs) is a common cause of dementia but has higher mortality than Alzheimer's disease (AD). The reasons for this are unclear, but antidementia drugs (including acetylcholinesterase inhibitors [AChEIs] and memantine) symptomatically benefit people with DLB and might improve outcomes. We investigated whether AChEIs and/or memantine were associated with reduced hospital admissions and mortality.<h4>Methods and findings</h4>We performed a retrospective cohort study of those diagnosed with DLB between 1 January 2005 and 31 December 2019, using data from electronic clinical records of secondary care mental health services in Cambridgeshire and Peterborough NHS Foundation Trust (CPFT), United Kingdom (catchment area population approximately 0.86 million), as well as linked records from national Hospital Episode Statistics (HES) data. Eligible patients were those who started AChEIs or memantine within 3 months of their diagnosis (cases) and those who never used AChEIs or memantine (controls). Outcomes included admission, length of stay, and mortality. Cox proportional hazard and linear regression models were used. Of 592 patients with DLB, 219 never took AChEIs or memantine, 100 took AChEIs only, and 273 took both AChEIs and memantine. The cohorts were followed up for an average of 896 days, 981 days, and 1,004 days, respectively. There were no significant differences in the cohorts' baseline characteristics, except for socioeconomic status that was lower in patients who never took AChEIs or memantine (\u03c72 = 23.34, P = 0.003). After controlling for confounding by sociodemographic factors (age, sex, marital status, ethnicity, socioeconomic status), antipsychotic use, antidepressant use, cognitive status, physical comorbidity, anticholinergic burden, and global health performance, compared with patients who never took AChEIs or memantine, patients taking AChEIs only or taking both had a significantly lower risk of death (adjusted hazard ratio (HR) = 0.67, 95% CI = 0.48 to 0.93, p = 0.02; adjusted HR = 0.64, 95% CI = 0.50 to 0.83, P = 0.001, respectively). Those taking AChEIs or both AChEIs and memantine had significantly shorter periods of unplanned hospital admission for physical disorders (adjusted coefficient -13.48, 95% CI = [-26.87, -0.09], P = 0.049; adjusted coefficient -14.21, 95% CI = [-24.58, -3.85], P = 0.007, respectively), but no difference in length of stay for planned admissions for physical disorders, or for admissions for mental health disorders. No significant additional associations of memantine on admission, length of stay, and mortality were found (all P > 0.05). The main limitation was that this was a naturalistic study and possible confounds cannot be fully controlled, and there may be selection bias resulting from nonrandom prescription behaviour in clinical practice. However, we mimicked the intention-to-treat design of clinical trials, and the majority of baseline characters were balanced between cohorts. In addition, our series of sensitivity analyses confirmed the consistency of our results.<h4>Conclusion</h4>In this study, we observed that use of AChEIs with or without memantine in DLB was associated with shorter duration of hospital admissions and decreased risk of mortality. Although our study was naturalistic, it supports further the use of AChEIs in DLB.",
     "laySummary": "",
-    "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s00127-024-02620-6.pdf; doi:https://doi.org/10.1007/s00127-024-02620-6; html:https://europepmc.org/articles/PMC11464607; pdf:https://europepmc.org/articles/PMC11464607?pdf=render"
+    "urls": "pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004124&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004124; html:https://europepmc.org/articles/PMC9725132; pdf:https://europepmc.org/articles/PMC9725132?pdf=render"
   },
   {
     "id": "36992264",
@@ -12546,21 +12546,21 @@
     "urls": "pdf:https://academic.oup.com/jamia/article-pdf/30/1/103/47829607/ocac203.pdf; doi:https://doi.org/10.1093/jamia/ocac203; html:https://europepmc.org/articles/PMC9619789; pdf:https://europepmc.org/articles/PMC9619789?pdf=render"
   },
   {
-    "id": "36472984",
-    "doi": "https://doi.org/10.1371/journal.pmed.1004124",
-    "title": "Association between antidementia medication use and mortality in people diagnosed with dementia with Lewy bodies in the UK: A retrospective cohort study.",
-    "authorString": "Chen S, Price AC, Cardinal RN, Moylett S, Kershenbaum AD, Fitzgerald J, Mueller C, Stewart R, O'Brien JT.",
+    "id": "38378812",
+    "doi": "https://doi.org/10.1007/s00127-024-02620-6",
+    "title": "Understanding social and clinical associations with unemployment for people with schizophrenia and bipolar disorders: large-scale health records study.",
+    "authorString": "Chilman N, Laporte D, Dorrington S, Hatch SL, Morgan C, Okoroji C, Stewart R, Das-Munshi J.",
     "authorAffiliations": "",
-    "journalTitle": "PLoS medicine",
-    "pubYear": "2022",
-    "date": "2022-12-06",
+    "journalTitle": "Social psychiatry and psychiatric epidemiology",
+    "pubYear": "2024",
+    "date": "2024-02-20",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Schizophrenia; Bipolar disorder; Employment; Ethnicity; Occupation; Natural Language Processing",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Dementia with Lewy bodies (DLBs) is a common cause of dementia but has higher mortality than Alzheimer's disease (AD). The reasons for this are unclear, but antidementia drugs (including acetylcholinesterase inhibitors [AChEIs] and memantine) symptomatically benefit people with DLB and might improve outcomes. We investigated whether AChEIs and/or memantine were associated with reduced hospital admissions and mortality.<h4>Methods and findings</h4>We performed a retrospective cohort study of those diagnosed with DLB between 1 January 2005 and 31 December 2019, using data from electronic clinical records of secondary care mental health services in Cambridgeshire and Peterborough NHS Foundation Trust (CPFT), United Kingdom (catchment area population approximately 0.86 million), as well as linked records from national Hospital Episode Statistics (HES) data. Eligible patients were those who started AChEIs or memantine within 3 months of their diagnosis (cases) and those who never used AChEIs or memantine (controls). Outcomes included admission, length of stay, and mortality. Cox proportional hazard and linear regression models were used. Of 592 patients with DLB, 219 never took AChEIs or memantine, 100 took AChEIs only, and 273 took both AChEIs and memantine. The cohorts were followed up for an average of 896 days, 981 days, and 1,004 days, respectively. There were no significant differences in the cohorts' baseline characteristics, except for socioeconomic status that was lower in patients who never took AChEIs or memantine (\u03c72 = 23.34, P = 0.003). After controlling for confounding by sociodemographic factors (age, sex, marital status, ethnicity, socioeconomic status), antipsychotic use, antidepressant use, cognitive status, physical comorbidity, anticholinergic burden, and global health performance, compared with patients who never took AChEIs or memantine, patients taking AChEIs only or taking both had a significantly lower risk of death (adjusted hazard ratio (HR) = 0.67, 95% CI = 0.48 to 0.93, p = 0.02; adjusted HR = 0.64, 95% CI = 0.50 to 0.83, P = 0.001, respectively). Those taking AChEIs or both AChEIs and memantine had significantly shorter periods of unplanned hospital admission for physical disorders (adjusted coefficient -13.48, 95% CI = [-26.87, -0.09], P = 0.049; adjusted coefficient -14.21, 95% CI = [-24.58, -3.85], P = 0.007, respectively), but no difference in length of stay for planned admissions for physical disorders, or for admissions for mental health disorders. No significant additional associations of memantine on admission, length of stay, and mortality were found (all P > 0.05). The main limitation was that this was a naturalistic study and possible confounds cannot be fully controlled, and there may be selection bias resulting from nonrandom prescription behaviour in clinical practice. However, we mimicked the intention-to-treat design of clinical trials, and the majority of baseline characters were balanced between cohorts. In addition, our series of sensitivity analyses confirmed the consistency of our results.<h4>Conclusion</h4>In this study, we observed that use of AChEIs with or without memantine in DLB was associated with shorter duration of hospital admissions and decreased risk of mortality. Although our study was naturalistic, it supports further the use of AChEIs in DLB.",
+    "abstract": "<h4>Purpose</h4>People with severe mental illness (SMI) experience high levels of unemployment. We aimed to better understand the associations between clinical, social, and demographic inequality indicators and unemployment.<h4>Methods</h4>Data were extracted from de-identified health records of people with SMI in contact with secondary mental health services in south London, UK. A Natural Language Processing text-mining application was applied to extract information on unemployment in the health records. Multivariable logistic regression was used to assess associations with unemployment, in people with SMI.<h4>Results</h4>Records from 19,768 service users were used for analysis, 84.9% (n\u2009=\u200916,778) had experienced unemployment. In fully adjusted models, Black Caribbean and Black African service users were more likely to experience unemployment compared with White British service users (Black Caribbean: aOR 1.62, 95% CI 1.45-1.80; Black African: 1.32, 1.15-1.51). Although men were more likely to have experienced unemployment relative to women in unadjusted models (OR 1.36, 95% CI 1.26-1.47), differences were no longer apparent in the fully adjusted models (aOR 1.05, 95% CI 0.97-1.15). The presence of a non-affective (compared to affective) diagnosis (1.24, 1.13-1.35), comorbid substance use (2.02, 1.76-2.33), previous inpatient admissions (4.18, 3.71-4.70), longer inpatient stays (78\u2009+\u2009days: 7.78, 6.34-9.54), and compulsory admissions (3.45, 3.04-3.92) were associated with unemployment, in fully adjusted models.<h4>Conclusion</h4>People with SMI experience high levels of unemployment, and we found that unemployment was associated with several clinical and social factors. Interventions to address low employment may need to also address these broader inequalities.",
     "laySummary": "",
-    "urls": "pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004124&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004124; html:https://europepmc.org/articles/PMC9725132; pdf:https://europepmc.org/articles/PMC9725132?pdf=render"
+    "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s00127-024-02620-6.pdf; doi:https://doi.org/10.1007/s00127-024-02620-6; html:https://europepmc.org/articles/PMC11464607; pdf:https://europepmc.org/articles/PMC11464607?pdf=render"
   },
   {
     "id": "37158960",
@@ -12630,6 +12630,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.ejvs.2024.05.010"
   },
+  {
+    "id": "36384890",
+    "doi": "https://doi.org/10.1136/bmj-2022-071932",
+    "title": "Comparative effectiveness of sotrovimab and molnupiravir for prevention of severe covid-19 outcomes in patients in the community: observational cohort study with the OpenSAFELY platform.",
+    "authorString": "Zheng B, Green ACA, Tazare J, Curtis HJ, Fisher L, Nab L, Schultze A, Mahalingasivam V, Parker EPK, Hulme WJ, Bacon SCJ, DeVito NJ, Bates C, Evans D, Inglesby P, Drysdale H, Davy S, Cockburn J, Morton CE, Hickman G, Ward T, Smith RM, Parry J, Hester F, Harper S, Mehrkar A, Eggo RM, Walker AJ, Evans SJW, Douglas IJ, MacKenna B, Goldacre B, Tomlinson LA.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ (Clinical research ed.)",
+    "pubYear": "2022",
+    "date": "2022-11-16",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>To compare the effectiveness of sotrovimab (a neutralising monoclonal antibody) with molnupiravir (an antiviral) in preventing severe outcomes of covid-19 in adult patients infected with SARS-CoV-2 in the community and at high risk of severe outcomes from covid-19.<h4>Design</h4>Observational cohort study with the OpenSAFELY platform.<h4>Setting</h4>With the approval of NHS England, a real world cohort study was conducted with the OpenSAFELY-TPP platform (a secure, transparent, open source software platform for analysis of NHS electronic health records), and patient level electronic health record data were obtained from 24 million people registered with a general practice in England that uses TPP software. The primary care data were securely linked with data on SARS-CoV-2 infection and treatments, hospital admission, and death, over a period when both drug treatments were frequently prescribed in community settings.<h4>Participants</h4>Adult patients with covid-19 in the community at high risk of severe outcomes from covid-19, treated with sotrovimab or molnupiravir from 16 December 2021.<h4>Interventions</h4>Sotrovimab or molnupiravir given in the community by covid-19 medicine delivery units.<h4>Main outcome measures</h4>Admission to hospital with covid-19 (ie, with covid-19 as the primary diagnosis) or death from covid-19 (ie, with covid-19 as the underlying or contributing cause of death) within 28 days of the start of treatment.<h4>Results</h4>Between 16 December 2021 and 10 February 2022, 3331 and 2689 patients were treated with sotrovimab and molnupiravir, respectively, with no substantial differences in baseline characteristics. Mean age of all 6020 patients was 52 (standard deviation 16) years; 59% were women, 89% were white, and 88% had received three or more covid-19 vaccinations. Within 28 days of the start of treatment, 87 (1.4%) patients were admitted to hospital or died of infection from SARS-CoV-2 (32 treated with sotrovimab and 55 with molnupiravir). Cox proportional hazards models stratified by area showed that after adjusting for demographic information, high risk cohort categories, vaccination status, calendar time, body mass index, and other comorbidities, treatment with sotrovimab was associated with a substantially lower risk than treatment with molnupiravir (hazard ratio 0.54, 95% confidence interval 0.33 to 0.88, P=0.01). Consistent results were found from propensity score weighted Cox models (0.50, 0.31 to 0.81, P=0.005) and when restricted to people who were fully vaccinated (0.53, 0.31 to 0.90, P=0.02). No substantial effect modifications by other characteristics were detected (all P values for interaction >0.10). The findings were similar in an exploratory analysis of patients treated between 16 February and 1 May 2022 when omicron BA.2 was the predominant variant in England.<h4>Conclusions</h4>In routine care of adult patients in England with covid-19 in the community, at high risk of severe outcomes from covid-19, those who received sotrovimab were at lower risk of severe outcomes of covid-19 than those treated with molnupiravir.",
+    "laySummary": "",
+    "urls": "pdf:https://www.bmj.com/content/bmj/379/bmj-2022-071932.full.pdf; doi:https://doi.org/10.1136/bmj-2022-071932; html:https://europepmc.org/articles/PMC9667468"
+  },
   {
     "id": "39132877",
     "doi": "https://doi.org/10.1002/ehf2.15011",
@@ -12648,21 +12665,21 @@
     "urls": "doi:https://doi.org/10.1002/ehf2.15011; doi:https://doi.org/10.1002/ehf2.15011"
   },
   {
-    "id": "36384890",
-    "doi": "https://doi.org/10.1136/bmj-2022-071932",
-    "title": "Comparative effectiveness of sotrovimab and molnupiravir for prevention of severe covid-19 outcomes in patients in the community: observational cohort study with the OpenSAFELY platform.",
-    "authorString": "Zheng B, Green ACA, Tazare J, Curtis HJ, Fisher L, Nab L, Schultze A, Mahalingasivam V, Parker EPK, Hulme WJ, Bacon SCJ, DeVito NJ, Bates C, Evans D, Inglesby P, Drysdale H, Davy S, Cockburn J, Morton CE, Hickman G, Ward T, Smith RM, Parry J, Hester F, Harper S, Mehrkar A, Eggo RM, Walker AJ, Evans SJW, Douglas IJ, MacKenna B, Goldacre B, Tomlinson LA.",
+    "id": "37128667",
+    "doi": "https://doi.org/10.1111/bjhp.12666",
+    "title": "A qualitative process evaluation using the behaviour change wheel approach: Did a whole genome sequence report form (SRF) used to reduce nosocomial SARS-CoV-2 within UK hospitals operate as anticipated?",
+    "authorString": "Flowers P, Leiser R, Mapp F, McLeod J, Stirrup O, Illingworth CJR, Blackstone J, Breuer J.",
     "authorAffiliations": "",
-    "journalTitle": "BMJ (Clinical research ed.)",
-    "pubYear": "2022",
-    "date": "2022-11-16",
+    "journalTitle": "British journal of health psychology",
+    "pubYear": "2023",
+    "date": "2023-05-01",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Hospital; Behaviour Change; Infection Prevention And Control; Behaviour Change Wheel; Covid-19; Sequence Report Form",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Objective</h4>To compare the effectiveness of sotrovimab (a neutralising monoclonal antibody) with molnupiravir (an antiviral) in preventing severe outcomes of covid-19 in adult patients infected with SARS-CoV-2 in the community and at high risk of severe outcomes from covid-19.<h4>Design</h4>Observational cohort study with the OpenSAFELY platform.<h4>Setting</h4>With the approval of NHS England, a real world cohort study was conducted with the OpenSAFELY-TPP platform (a secure, transparent, open source software platform for analysis of NHS electronic health records), and patient level electronic health record data were obtained from 24 million people registered with a general practice in England that uses TPP software. The primary care data were securely linked with data on SARS-CoV-2 infection and treatments, hospital admission, and death, over a period when both drug treatments were frequently prescribed in community settings.<h4>Participants</h4>Adult patients with covid-19 in the community at high risk of severe outcomes from covid-19, treated with sotrovimab or molnupiravir from 16 December 2021.<h4>Interventions</h4>Sotrovimab or molnupiravir given in the community by covid-19 medicine delivery units.<h4>Main outcome measures</h4>Admission to hospital with covid-19 (ie, with covid-19 as the primary diagnosis) or death from covid-19 (ie, with covid-19 as the underlying or contributing cause of death) within 28 days of the start of treatment.<h4>Results</h4>Between 16 December 2021 and 10 February 2022, 3331 and 2689 patients were treated with sotrovimab and molnupiravir, respectively, with no substantial differences in baseline characteristics. Mean age of all 6020 patients was 52 (standard deviation 16) years; 59% were women, 89% were white, and 88% had received three or more covid-19 vaccinations. Within 28 days of the start of treatment, 87 (1.4%) patients were admitted to hospital or died of infection from SARS-CoV-2 (32 treated with sotrovimab and 55 with molnupiravir). Cox proportional hazards models stratified by area showed that after adjusting for demographic information, high risk cohort categories, vaccination status, calendar time, body mass index, and other comorbidities, treatment with sotrovimab was associated with a substantially lower risk than treatment with molnupiravir (hazard ratio 0.54, 95% confidence interval 0.33 to 0.88, P=0.01). Consistent results were found from propensity score weighted Cox models (0.50, 0.31 to 0.81, P=0.005) and when restricted to people who were fully vaccinated (0.53, 0.31 to 0.90, P=0.02). No substantial effect modifications by other characteristics were detected (all P values for interaction >0.10). The findings were similar in an exploratory analysis of patients treated between 16 February and 1 May 2022 when omicron BA.2 was the predominant variant in England.<h4>Conclusions</h4>In routine care of adult patients in England with covid-19 in the community, at high risk of severe outcomes from covid-19, those who received sotrovimab were at lower risk of severe outcomes of covid-19 than those treated with molnupiravir.",
+    "abstract": "<h4>Purpose</h4>The aim of this study was to conduct a process evaluation of a whole-genome sequence report form (SRF) used to reduce nosocomial SARS-CoV-2 through changing infection prevention and control (IPC) behaviours within the COVID-19 pandemic.<h4>Methods</h4>We used a three-staged design. Firstly, we described and theorized the purported content of the SRF using the behaviour change wheel (BCW). Secondly, we used inductive thematic analysis of one-to-one interviews (n\u2009=\u200939) to explore contextual accounts of using the SRF. Thirdly, further deductive analysis gauged support for the intervention working as earlier anticipated.<h4>Results</h4>It was possible to theorize the SRF using the BCW approach and visualize it within a simple logic model. Inductive thematic analyses identified the SRF's acceptability, ease of use and perceived effectiveness. However, major challenges to embedding it in routine practice during the unfolding COVID-19 crisis were reported. Notwithstanding this insight, deductive analysis showed support for the putative intervention functions 'Education', 'Persuasion' and 'Enablement'; behaviour change techniques '1.2 Problem solving', '2.6 Biofeedback', '2.7 Feedback on outcomes of behaviour' and '7.1 Prompts and cues'; and theoretical domains framework domains 'Knowledge' and 'Behavioural regulation'.<h4>Conclusions</h4>Our process evaluation of the SRF, using the BCW approach to describe and theorize its content, provided granular support for the SRF working to change IPC behaviours as anticipated. However, our complementary inductive thematic analysis highlighted the importance of the local context in constraining its routine use. For SRFs to reach their full potential in reducing nosocomial infections, further implementation research is needed.",
     "laySummary": "",
-    "urls": "pdf:https://www.bmj.com/content/bmj/379/bmj-2022-071932.full.pdf; doi:https://doi.org/10.1136/bmj-2022-071932; html:https://europepmc.org/articles/PMC9667468"
+    "urls": "doi:https://doi.org/10.1111/bjhp.12666; doi:https://doi.org/10.1111/bjhp.12666; html:https://europepmc.org/articles/PMC11497355; pdf:https://europepmc.org/articles/PMC11497355?pdf=render"
   },
   {
     "id": "33200120",
@@ -12682,21 +12699,21 @@
     "urls": "pdf:https://figshare.com/articles/journal_contribution/Ethnicity_and_clinical_outcomes_in_COVID-19_A_Systematic_Review_and_Meta-analysis/13147892/1/files/25502810.pdf; doi:https://doi.org/10.1016/j.eclinm.2020.100630; html:https://europepmc.org/articles/PMC7658622; pdf:https://europepmc.org/articles/PMC7658622?pdf=render"
   },
   {
-    "id": "37128667",
-    "doi": "https://doi.org/10.1111/bjhp.12666",
-    "title": "A qualitative process evaluation using the behaviour change wheel approach: Did a whole genome sequence report form (SRF) used to reduce nosocomial SARS-CoV-2 within UK hospitals operate as anticipated?",
-    "authorString": "Flowers P, Leiser R, Mapp F, McLeod J, Stirrup O, Illingworth CJR, Blackstone J, Breuer J.",
+    "id": "33185672",
+    "doi": "https://doi.org/10.1093/jamia/ocaa295",
+    "title": "Ensemble learning for poor prognosis predictions: A case study on SARS-CoV-2.",
+    "authorString": "Wu H, Zhang H, Karwath A, Ibrahim Z, Shi T, Zhang X, Wang K, Sun J, Dhaliwal K, Bean D, Cardoso VR, Li K, Teo JT, Banerjee A, Gao-Smith F, Whitehouse T, Veenith T, Gkoutos GV, Wu X, Dobson R, Guthrie B.",
     "authorAffiliations": "",
-    "journalTitle": "British journal of health psychology",
-    "pubYear": "2023",
-    "date": "2023-05-01",
+    "journalTitle": "Journal of the American Medical Informatics Association : JAMIA",
+    "pubYear": "2021",
+    "date": "2021-03-01",
     "isOpenAccess": "Y",
-    "keywords": "Hospital; Behaviour Change; Infection Prevention And Control; Behaviour Change Wheel; Covid-19; Sequence Report Form",
+    "keywords": "Decision Support; Risk Prediction; Ensemble Learning; Covid-19; Model Synergy",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Purpose</h4>The aim of this study was to conduct a process evaluation of a whole-genome sequence report form (SRF) used to reduce nosocomial SARS-CoV-2 through changing infection prevention and control (IPC) behaviours within the COVID-19 pandemic.<h4>Methods</h4>We used a three-staged design. Firstly, we described and theorized the purported content of the SRF using the behaviour change wheel (BCW). Secondly, we used inductive thematic analysis of one-to-one interviews (n\u2009=\u200939) to explore contextual accounts of using the SRF. Thirdly, further deductive analysis gauged support for the intervention working as earlier anticipated.<h4>Results</h4>It was possible to theorize the SRF using the BCW approach and visualize it within a simple logic model. Inductive thematic analyses identified the SRF's acceptability, ease of use and perceived effectiveness. However, major challenges to embedding it in routine practice during the unfolding COVID-19 crisis were reported. Notwithstanding this insight, deductive analysis showed support for the putative intervention functions 'Education', 'Persuasion' and 'Enablement'; behaviour change techniques '1.2 Problem solving', '2.6 Biofeedback', '2.7 Feedback on outcomes of behaviour' and '7.1 Prompts and cues'; and theoretical domains framework domains 'Knowledge' and 'Behavioural regulation'.<h4>Conclusions</h4>Our process evaluation of the SRF, using the BCW approach to describe and theorize its content, provided granular support for the SRF working to change IPC behaviours as anticipated. However, our complementary inductive thematic analysis highlighted the importance of the local context in constraining its routine use. For SRFs to reach their full potential in reducing nosocomial infections, further implementation research is needed.",
+    "abstract": "<h4>Objective</h4>Risk prediction models are widely used to inform evidence-based clinical decision making. However, few models developed from single cohorts can perform consistently well at population level where diverse prognoses exist (such as the SARS-CoV-2 [severe acute respiratory syndrome coronavirus 2] pandemic). This study aims at tackling this challenge by synergizing prediction models from the literature using ensemble learning.<h4>Materials and methods</h4>In this study, we selected and reimplemented 7 prediction models for COVID-19 (coronavirus disease 2019) that were derived from diverse cohorts and used different implementation techniques. A novel ensemble learning framework was proposed to synergize them for realizing personalized predictions for individual patients. Four diverse international cohorts (2 from the United Kingdom and 2 from China; N\u2009=\u20095394) were used to validate all 8 models on discrimination, calibration, and clinical usefulness.<h4>Results</h4>Results showed that individual prediction models could perform well on some cohorts while poorly on others. Conversely, the ensemble model achieved the best performances consistently on all metrics quantifying discrimination, calibration, and clinical usefulness. Performance disparities were observed in cohorts from the 2 countries: all models achieved better performances on the China cohorts.<h4>Discussion</h4>When individual models were learned from complementary cohorts, the synergized model had the potential to achieve better performances than any individual model. Results indicate that blood parameters and physiological measurements might have better predictive powers when collected early, which remains to be confirmed by further studies.<h4>Conclusions</h4>Combining a diverse set of individual prediction models, the ensemble method can synergize a robust and well-performing model by choosing the most competent ones for individual patients.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1111/bjhp.12666; doi:https://doi.org/10.1111/bjhp.12666; html:https://europepmc.org/articles/PMC11497355; pdf:https://europepmc.org/articles/PMC11497355?pdf=render"
+    "urls": "pdf:https://academic.oup.com/jamia/article-pdf/28/4/791/41182395/ocaa295.pdf; doi:https://doi.org/10.1093/jamia/ocaa295; html:https://europepmc.org/articles/PMC7717299; pdf:https://europepmc.org/articles/PMC7717299?pdf=render"
   },
   {
     "id": "PMC9644860",
@@ -12715,23 +12732,6 @@
     "laySummary": "",
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9644860/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9644860/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC9644860; pdf:https://europepmc.org/articles/PMC9644860?pdf=render"
   },
-  {
-    "id": "33185672",
-    "doi": "https://doi.org/10.1093/jamia/ocaa295",
-    "title": "Ensemble learning for poor prognosis predictions: A case study on SARS-CoV-2.",
-    "authorString": "Wu H, Zhang H, Karwath A, Ibrahim Z, Shi T, Zhang X, Wang K, Sun J, Dhaliwal K, Bean D, Cardoso VR, Li K, Teo JT, Banerjee A, Gao-Smith F, Whitehouse T, Veenith T, Gkoutos GV, Wu X, Dobson R, Guthrie B.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of the American Medical Informatics Association : JAMIA",
-    "pubYear": "2021",
-    "date": "2021-03-01",
-    "isOpenAccess": "Y",
-    "keywords": "Decision Support; Risk Prediction; Ensemble Learning; Covid-19; Model Synergy",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objective</h4>Risk prediction models are widely used to inform evidence-based clinical decision making. However, few models developed from single cohorts can perform consistently well at population level where diverse prognoses exist (such as the SARS-CoV-2 [severe acute respiratory syndrome coronavirus 2] pandemic). This study aims at tackling this challenge by synergizing prediction models from the literature using ensemble learning.<h4>Materials and methods</h4>In this study, we selected and reimplemented 7 prediction models for COVID-19 (coronavirus disease 2019) that were derived from diverse cohorts and used different implementation techniques. A novel ensemble learning framework was proposed to synergize them for realizing personalized predictions for individual patients. Four diverse international cohorts (2 from the United Kingdom and 2 from China; N\u2009=\u20095394) were used to validate all 8 models on discrimination, calibration, and clinical usefulness.<h4>Results</h4>Results showed that individual prediction models could perform well on some cohorts while poorly on others. Conversely, the ensemble model achieved the best performances consistently on all metrics quantifying discrimination, calibration, and clinical usefulness. Performance disparities were observed in cohorts from the 2 countries: all models achieved better performances on the China cohorts.<h4>Discussion</h4>When individual models were learned from complementary cohorts, the synergized model had the potential to achieve better performances than any individual model. Results indicate that blood parameters and physiological measurements might have better predictive powers when collected early, which remains to be confirmed by further studies.<h4>Conclusions</h4>Combining a diverse set of individual prediction models, the ensemble method can synergize a robust and well-performing model by choosing the most competent ones for individual patients.",
-    "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/jamia/article-pdf/28/4/791/41182395/ocaa295.pdf; doi:https://doi.org/10.1093/jamia/ocaa295; html:https://europepmc.org/articles/PMC7717299; pdf:https://europepmc.org/articles/PMC7717299?pdf=render"
-  },
   {
     "id": "35953587",
     "doi": "https://doi.org/10.1038/s41588-022-01153-5",
@@ -12749,23 +12749,6 @@
     "laySummary": "",
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7613894; doi:https://doi.org/10.1038/s41588-022-01153-5; html:https://europepmc.org/articles/PMC7613894; pdf:https://europepmc.org/articles/PMC7613894?pdf=render"
   },
-  {
-    "id": "38811438",
-    "doi": "https://doi.org/10.1007/s00586-024-08315-5",
-    "title": "Early evaluation of a natural language processing tool to improve access to educational resources for surgical patients.",
-    "authorString": "Booker J, Penn J, Noor K, Dobson RJB, Funnell JP, Koh CH, Khan DZ, Newall N, Rowland D, Sinha S, Williams SC, Sayal P, Marcus HJ.",
-    "authorAffiliations": "",
-    "journalTitle": "European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society",
-    "pubYear": "2024",
-    "date": "2024-05-30",
-    "isOpenAccess": "Y",
-    "keywords": "Spine; Education; Machine Learning; Natural Language Processing; automation",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Purpose</h4>Accessible patient information sources are vital in educating patients about the benefits and risks of spinal surgery, which is crucial for obtaining informed consent. We aim to assess the effectiveness of a natural language processing (NLP) pipeline in recognizing surgical procedures from clinic letters and linking this with educational resources.<h4>Methods</h4>Retrospective examination of letters from patients seeking surgery for degenerative spinal disease at a single neurosurgical center. We utilized MedCAT, a named entity recognition and linking NLP, integrated into the electronic health record (EHR), which extracts concepts and links them to systematized nomenclature of medicine-clinical terms (SNOMED-CT). Investigators reviewed clinic letters, identifying words or phrases that described or identified operations and recording the SNOMED-CT terms as ground truth. This was compared to SNOMED-CT terms identified by the model, untrained on our dataset. A pipeline linking clinic letters to patient-specific educational resources was established, and precision, recall, and F1 scores were calculated.<h4>Results</h4>Across 199 letters the model identified 582 surgical procedures, and the overall pipeline after adding rules a total of 784 procedures (precision\u2009=\u20090.94, recall\u2009=\u20090.86, F1\u2009=\u20090.91). Across 187 letters with identified SNOMED-CT terms the integrated pipeline linking education resources directly to the EHR was successful in 157 (78%) patients (precision\u2009=\u20090.99, recall\u2009=\u20090.87, F1\u2009=\u20090.92).<h4>Conclusions</h4>NLP accurately identifies surgical procedures in pre-operative clinic letters within an untrained subspecialty. Performance varies among letter authors and depends on the language used by clinicians. The identified procedures can be linked to patient education resources, potentially improving patients' understanding of surgical procedures.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1007/s00586-024-08315-5; doi:https://doi.org/10.1007/s00586-024-08315-5; html:https://europepmc.org/articles/PMC11269391; pdf:https://europepmc.org/articles/PMC11269391?pdf=render"
-  },
   {
     "id": "31249320",
     "doi": "https://doi.org/10.1038/s41598-019-45562-9",
@@ -12784,21 +12767,21 @@
     "urls": "pdf:https://www.nature.com/articles/s41598-019-45562-9.pdf; doi:https://doi.org/10.1038/s41598-019-45562-9; html:https://europepmc.org/articles/PMC6597711; pdf:https://europepmc.org/articles/PMC6597711?pdf=render"
   },
   {
-    "id": "37800588",
-    "doi": "https://doi.org/10.1097/js9.0000000000000781",
-    "title": "Safety outcomes of bariatric surgery in patients with advanced organ disease: the ONWARD study: a prospective cohort study.",
-    "authorString": "Singhal R, Cardoso VR, Wiggins T, Rajeev Y, Ludwig C, Gkoutos GV, Hanif W, Mahawar K, ONWARD & GENEVA collaborators.",
+    "id": "38811438",
+    "doi": "https://doi.org/10.1007/s00586-024-08315-5",
+    "title": "Early evaluation of a natural language processing tool to improve access to educational resources for surgical patients.",
+    "authorString": "Booker J, Penn J, Noor K, Dobson RJB, Funnell JP, Koh CH, Khan DZ, Newall N, Rowland D, Sinha S, Williams SC, Sayal P, Marcus HJ.",
     "authorAffiliations": "",
-    "journalTitle": "International journal of surgery (London, England)",
+    "journalTitle": "European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society",
     "pubYear": "2024",
-    "date": "2024-01-01",
+    "date": "2024-05-30",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Spine; Education; Machine Learning; Natural Language Processing; automation",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>Increasing numbers of patients with advanced organ disease are being considered for bariatric and metabolic surgery (BMS). There is no prospective study on the safety of BMS in these patients. This study aimed to capture outcomes for patients with advanced cardiac, renal, or liver disease undergoing BMS.<h4>Materials and methods</h4>This was a multinational, prospective cohort study on the safety of elective BMS in adults (\u226518\u00a0years) with advanced disease of the heart, liver, or kidney.<h4>Results</h4>Data on 177 patients with advanced diseases of heart, liver, or kidney were submitted by 75 centres in 33 countries. Mean age and BMI was 48.56\u00b111.23 years and 45.55\u00b17.35\u00a0kg/m 2 , respectively. Laparoscopic sleeve gastrectomy was performed in 124 patients (70%). The 30-day morbidity and mortality were 15.9% ( n =28) and 1.1% ( n =2), respectively. Thirty-day morbidity was 16.4%, 11.7%, 20.5%, and 50.0% in patients with advanced heart ( n =11/61), liver ( n =8/68), kidney ( n =9/44), and multi-organ disease ( n =2/4), respectively. Cardiac patients with left ventricular ejection fraction less than or equal to 35% and New York Heart Association classification 3 or 4, liver patients with model for end-stage liver disease score greater than or equal to 12, and patients with advanced renal disease not on dialysis were at increased risk of complications. Comparison with a propensity score-matched cohort found advanced disease of the heart, liver, or kidney to be significantly associated with higher 30-day morbidity.<h4>Conclusion</h4>Patients with advanced organ disease are at increased risk of 30-day morbidity following BMS. This prospective study quantifies that risk and identifies patients at the highest risk.",
+    "abstract": "<h4>Purpose</h4>Accessible patient information sources are vital in educating patients about the benefits and risks of spinal surgery, which is crucial for obtaining informed consent. We aim to assess the effectiveness of a natural language processing (NLP) pipeline in recognizing surgical procedures from clinic letters and linking this with educational resources.<h4>Methods</h4>Retrospective examination of letters from patients seeking surgery for degenerative spinal disease at a single neurosurgical center. We utilized MedCAT, a named entity recognition and linking NLP, integrated into the electronic health record (EHR), which extracts concepts and links them to systematized nomenclature of medicine-clinical terms (SNOMED-CT). Investigators reviewed clinic letters, identifying words or phrases that described or identified operations and recording the SNOMED-CT terms as ground truth. This was compared to SNOMED-CT terms identified by the model, untrained on our dataset. A pipeline linking clinic letters to patient-specific educational resources was established, and precision, recall, and F1 scores were calculated.<h4>Results</h4>Across 199 letters the model identified 582 surgical procedures, and the overall pipeline after adding rules a total of 784 procedures (precision\u2009=\u20090.94, recall\u2009=\u20090.86, F1\u2009=\u20090.91). Across 187 letters with identified SNOMED-CT terms the integrated pipeline linking education resources directly to the EHR was successful in 157 (78%) patients (precision\u2009=\u20090.99, recall\u2009=\u20090.87, F1\u2009=\u20090.92).<h4>Conclusions</h4>NLP accurately identifies surgical procedures in pre-operative clinic letters within an untrained subspecialty. Performance varies among letter authors and depends on the language used by clinicians. The identified procedures can be linked to patient education resources, potentially improving patients' understanding of surgical procedures.",
     "laySummary": "",
-    "urls": "html:https://journals.lww.com/international-journal-of-surgery/abstract/9900/safety_outcomes_of_bariatric_surgery_in_patients.696.aspx; doi:https://doi.org/10.1097/JS9.0000000000000781; html:https://europepmc.org/articles/PMC10793784; pdf:https://europepmc.org/articles/PMC10793784?pdf=render"
+    "urls": "doi:https://doi.org/10.1007/s00586-024-08315-5; doi:https://doi.org/10.1007/s00586-024-08315-5; html:https://europepmc.org/articles/PMC11269391; pdf:https://europepmc.org/articles/PMC11269391?pdf=render"
   },
   {
     "id": "36434299",
@@ -12817,6 +12800,23 @@
     "laySummary": "",
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s00127-022-02393-w.pdf; doi:https://doi.org/10.1007/s00127-022-02393-w; html:https://europepmc.org/articles/PMC9702612; pdf:https://europepmc.org/articles/PMC9702612?pdf=render"
   },
+  {
+    "id": "37800588",
+    "doi": "https://doi.org/10.1097/js9.0000000000000781",
+    "title": "Safety outcomes of bariatric surgery in patients with advanced organ disease: the ONWARD study: a prospective cohort study.",
+    "authorString": "Singhal R, Cardoso VR, Wiggins T, Rajeev Y, Ludwig C, Gkoutos GV, Hanif W, Mahawar K, ONWARD & GENEVA collaborators.",
+    "authorAffiliations": "",
+    "journalTitle": "International journal of surgery (London, England)",
+    "pubYear": "2024",
+    "date": "2024-01-01",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>Increasing numbers of patients with advanced organ disease are being considered for bariatric and metabolic surgery (BMS). There is no prospective study on the safety of BMS in these patients. This study aimed to capture outcomes for patients with advanced cardiac, renal, or liver disease undergoing BMS.<h4>Materials and methods</h4>This was a multinational, prospective cohort study on the safety of elective BMS in adults (\u226518\u00a0years) with advanced disease of the heart, liver, or kidney.<h4>Results</h4>Data on 177 patients with advanced diseases of heart, liver, or kidney were submitted by 75 centres in 33 countries. Mean age and BMI was 48.56\u00b111.23 years and 45.55\u00b17.35\u00a0kg/m 2 , respectively. Laparoscopic sleeve gastrectomy was performed in 124 patients (70%). The 30-day morbidity and mortality were 15.9% ( n =28) and 1.1% ( n =2), respectively. Thirty-day morbidity was 16.4%, 11.7%, 20.5%, and 50.0% in patients with advanced heart ( n =11/61), liver ( n =8/68), kidney ( n =9/44), and multi-organ disease ( n =2/4), respectively. Cardiac patients with left ventricular ejection fraction less than or equal to 35% and New York Heart Association classification 3 or 4, liver patients with model for end-stage liver disease score greater than or equal to 12, and patients with advanced renal disease not on dialysis were at increased risk of complications. Comparison with a propensity score-matched cohort found advanced disease of the heart, liver, or kidney to be significantly associated with higher 30-day morbidity.<h4>Conclusion</h4>Patients with advanced organ disease are at increased risk of 30-day morbidity following BMS. This prospective study quantifies that risk and identifies patients at the highest risk.",
+    "laySummary": "",
+    "urls": "html:https://journals.lww.com/international-journal-of-surgery/abstract/9900/safety_outcomes_of_bariatric_surgery_in_patients.696.aspx; doi:https://doi.org/10.1097/JS9.0000000000000781; html:https://europepmc.org/articles/PMC10793784; pdf:https://europepmc.org/articles/PMC10793784?pdf=render"
+  },
   {
     "id": "32525266",
     "doi": "https://doi.org/10.1002/jmri.27209",
@@ -13039,21 +13039,21 @@
     "urls": "pdf:https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-022-08562-0; doi:https://doi.org/10.1186/s12864-022-08562-0; html:https://europepmc.org/articles/PMC9063233; pdf:https://europepmc.org/articles/PMC9063233?pdf=render"
   },
   {
-    "id": "36713473",
-    "doi": "https://doi.org/10.1093/ofid/ofac694",
-    "title": "Clinical Effectiveness of SARS-CoV-2 Booster Vaccine Against Omicron Infection in Residents and Staff of Long-term Care Facilities: A Prospective Cohort Study (VIVALDI).",
-    "authorString": "Stirrup O, Shrotri M, Adams NL, Krutikov M, Nacer-Laidi H, Azmi B, Palmer T, Fuller C, Irwin-Singer A, Baynton V, Tut G, Moss P, Hayward A, Copas A, Shallcross L.",
+    "id": "39486906",
+    "doi": "https://doi.org/10.1016/s2468-2667(24)00228-7",
+    "title": "Alcohol and mortality in Mexico: prospective study of 150\u2008000 adults.",
+    "authorString": "Trichia E, Alegre-D\u00edaz J, Aguilar-Ramirez D, Ramirez-Reyes R, Garcilazo-\u00c1vila A, Gonz\u00e1lez-Carballo C, Bragg F, Friedrichs LG, Herrington WG, Holland L, Torres J, Wade R, Collins R, Peto R, Berumen J, Tapia-Conyer R, Kuri-Morales P, Emberson JR.",
     "authorAffiliations": "",
-    "journalTitle": "Open forum infectious diseases",
-    "pubYear": "2023",
-    "date": "2022-12-29",
-    "isOpenAccess": "Y",
-    "keywords": "Vaccine Effectiveness; Long-term Care Facilities; Covid-19; Sars-cov-2; Omicron",
+    "journalTitle": "The Lancet. Public health",
+    "pubYear": "2024",
+    "date": "2024-11-01",
+    "isOpenAccess": "N",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Successive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have caused severe disease in long-term care facility (LTCF) residents. Primary vaccination provides strong short-term protection, but data are limited on duration of protection following booster vaccines, particularly against the Omicron variant. We investigated the effectiveness of booster vaccination against infections, hospitalizations, and deaths among LTCF residents and staff in England.<h4>Methods</h4>We included residents and staff of LTCFs within the VIVALDI study (ISRCTN 14447421) who underwent routine, asymptomatic testing (December 12, 2021-March 31, 2022). Cox regression was used to estimate relative hazards of SARS-CoV-2 infection, and associated hospitalization and death at 0-13, 14-48, 49-83, 84-111, 112-139, and 140+ days after dose 3 of SARS-CoV-2 vaccination compared with 2 doses (after 84+ days), stratified by previous SARS-CoV-2 infection and adjusting for age, sex, LTCF capacity, and local SARS-CoV-2 incidence.<h4>Results</h4>A total of 14 175 residents and 19 793 staff were included. In residents without prior SARS-CoV-2 infection, infection risk was reduced 0-111 days after the first booster, but no protection was apparent after 112 days. Additional protection following booster vaccination waned but was still present at 140+ days for COVID-associated hospitalization (adjusted hazard ratio [aHR], 0.20; 95% CI, 0.06-0.63) and death (aHR, 0.50; 95% CI, 0.20-1.27). Most residents (64.4%) had received primary course vaccine of AstraZeneca, but this did not impact pre- or postbooster risk. Staff showed a similar pattern of waning booster effectiveness against infection, with few hospitalizations and no deaths.<h4>Conclusions</h4>Our findings suggest that booster vaccination provided sustained protection against severe outcomes following infection with the Omicron variant, but no protection against infection from 4 months onwards. Ongoing surveillance for SARS-CoV-2 in LTCFs is crucial.",
+    "abstract": "<h4>Background</h4>Alcohol consumption is a leading cause of premature death globally, but there is no large-scale prospective evidence from Mexico.<h4>Methods</h4>The Mexico City Prospective Study recruited 150\u2008000 adults aged 35 years or older between 1998 and 2004. Participants were followed up until Oct 1, 2022 for cause-specific mortality. Cox regression in those with no self-reported chronic disease at entry (adjusted for age, sex, district, education, physical activity, smoking, and diabetes) was used to relate baseline-reported alcohol consumption (never, former, occasional [less than monthly], and regular [at least monthly, split into <70, \u226570 to <140, \u2265140 to <210, and \u2265210 g/week]) to mortality at ages 35-74 from all causes, and from a pre-specified alcohol-related set of underlying causes. Heavy episodic drinking (normally consuming >5 [men] or >4 [women] drinks on a single occasion) and type of preferred drink were also examined.<h4>Findings</h4>Among 138\u2008413 participants aged 35-74 years at recruitment, 21\u2008136 (15%) were regular alcohol drinkers (14\u2008863 [33%] men, 6273 [7%] women), of whom 13\u2008383 (63%) favoured spirits and 6580 (31%) favoured beer. During follow-up, there were 13\u2008889 deaths at ages 35-74 years, including 3067 deaths from the pre-specified alcohol-related causes. Overall, J-shaped associations with mortality were observed. Compared with occasional drinkers, those with baseline-reported consumption \u2265210 g/week had 43% higher all-cause mortality (rate ratio [RR] 1\u00b743 [95% CI 1\u00b730-1\u00b756]) and nearly three times the mortality from the pre-specified alcohol-related causes (2\u00b777 [2\u00b739-3\u00b720]). Death from liver disease was strongly related to alcohol consumption; the RR comparing regular drinkers of \u2265140 g/week with occasional drinkers was 4\u00b703 (3\u00b736-4\u00b783). Compared with occasional light drinking, occasional heavy episodic drinking was associated with 20% higher alcohol-related mortality (1\u00b720 [1\u00b706-1\u00b735]), and regular heavy episodic drinking was associated with 89% higher alcohol-related mortality (1\u00b789 [1\u00b767-2\u00b715]). Drinks with alcohol percentages higher than spirits were associated with the greatest increased mortality risk, even after accounting for the total alcohol consumed.<h4>Interpretation</h4>In this Mexican population, higher alcohol consumption, episodic drinking, and very high percentage alcoholic products were all associated with increased mortality.<h4>Funding</h4>Wellcome Trust, the Mexican Health Ministry, the National Council of Science and Technology for Mexico, Cancer Research UK, British Heart Foundation, and the UK Medical Research Council.<h4>Translation</h4>For the Spanish translation of the abstract see Supplementary Materials section.",
     "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/ofid/article-pdf/10/1/ofac694/48846221/ofac694.pdf; doi:https://doi.org/10.1093/ofid/ofac694; html:https://europepmc.org/articles/PMC9874026; pdf:https://europepmc.org/articles/PMC9874026?pdf=render"
+    "urls": "doi:https://doi.org/10.1016/S2468-2667(24)00228-7"
   },
   {
     "id": "36812617",
@@ -13073,21 +13073,21 @@
     "urls": "pdf:https://journals.plos.org/digitalhealth/article/file?id=10.1371/journal.pdig.0000162&type=printable; doi:https://doi.org/10.1371/journal.pdig.0000162; html:https://europepmc.org/articles/PMC9931350; pdf:https://europepmc.org/articles/PMC9931350?pdf=render"
   },
   {
-    "id": "36748660",
-    "doi": "https://doi.org/10.1111/head.14465",
-    "title": "Depression and anxiety in women with idiopathic intracranial hypertension compared to migraine: A matched controlled cohort study.",
-    "authorString": "Mollan SP, Subramanian A, Perrins M, Nirantharakumar K, Adderley NJ, Sinclair AJ.",
+    "id": "36713473",
+    "doi": "https://doi.org/10.1093/ofid/ofac694",
+    "title": "Clinical Effectiveness of SARS-CoV-2 Booster Vaccine Against Omicron Infection in Residents and Staff of Long-term Care Facilities: A Prospective Cohort Study (VIVALDI).",
+    "authorString": "Stirrup O, Shrotri M, Adams NL, Krutikov M, Nacer-Laidi H, Azmi B, Palmer T, Fuller C, Irwin-Singer A, Baynton V, Tut G, Moss P, Hayward A, Copas A, Shallcross L.",
     "authorAffiliations": "",
-    "journalTitle": "Headache",
+    "journalTitle": "Open forum infectious diseases",
     "pubYear": "2023",
-    "date": "2023-02-07",
+    "date": "2022-12-29",
     "isOpenAccess": "Y",
-    "keywords": "Depression; Migraine; Anxiety; epidemiology; Primary Care; Idiopathic Intracranial Hypertension",
+    "keywords": "Vaccine Effectiveness; Long-term Care Facilities; Covid-19; Sars-cov-2; Omicron",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Objective</h4>To evaluate mental health burden in women with idiopathic intracranial hypertension (IIH) compared to matched women with migraine and population controls.<h4>Background</h4>Depression and anxiety are recognized comorbid conditions in those with IIH and lead to worse predicted medical outcomes. The mental health burden in IIH has not been previously evaluated in a large, matched cohort study.<h4>Methods</h4>We performed a population-based matched, retrospective cohort study to explore mental health outcomes (depression and anxiety). We used data from IQVIA Medical Research Data, an anonymized, nationally representative primary care electronic medical records database in the United Kingdom, from January 1, 1995, to September 25, 2019. Women aged \u226516\u2009years were eligible for inclusion. Women with IIH (exposure) were matched by age and body mass index with up to 10 control women without IIH but with migraine (migraine controls), and without IIH or migraine (population controls).<h4>Results</h4>A total of 3411 women with IIH, 30,879 migraine controls and 33,495 population controls were included. Of these, 237, 2372 and 1695 women with IIH, migraine controls and population controls, respectively, developed depression during follow-up, and 179, 1826 and 1197, respectively, developed anxiety. There was a greater hazard of depression and anxiety in IIH compared to population controls (adjusted hazard ratio [aHR] 1.38, 95% confidence interval [CI] 1.20-1.58; and aHR 1.40, 95% CI 1.19-1.64, respectively), while hazards were similar to migraine controls (aHR 0.98, 95% CI 0.86-1.13; and aHR 0.98, 95% CI 0.83-1.14, respectively).<h4>Conclusion</h4>Depression and anxiety burden in women with IIH is higher than in the general population, and comparable to that in matched women with migraine. This may indicate that presence of headache is a potential driver for comorbid depression and anxiety in IIH.",
+    "abstract": "<h4>Background</h4>Successive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have caused severe disease in long-term care facility (LTCF) residents. Primary vaccination provides strong short-term protection, but data are limited on duration of protection following booster vaccines, particularly against the Omicron variant. We investigated the effectiveness of booster vaccination against infections, hospitalizations, and deaths among LTCF residents and staff in England.<h4>Methods</h4>We included residents and staff of LTCFs within the VIVALDI study (ISRCTN 14447421) who underwent routine, asymptomatic testing (December 12, 2021-March 31, 2022). Cox regression was used to estimate relative hazards of SARS-CoV-2 infection, and associated hospitalization and death at 0-13, 14-48, 49-83, 84-111, 112-139, and 140+ days after dose 3 of SARS-CoV-2 vaccination compared with 2 doses (after 84+ days), stratified by previous SARS-CoV-2 infection and adjusting for age, sex, LTCF capacity, and local SARS-CoV-2 incidence.<h4>Results</h4>A total of 14 175 residents and 19 793 staff were included. In residents without prior SARS-CoV-2 infection, infection risk was reduced 0-111 days after the first booster, but no protection was apparent after 112 days. Additional protection following booster vaccination waned but was still present at 140+ days for COVID-associated hospitalization (adjusted hazard ratio [aHR], 0.20; 95% CI, 0.06-0.63) and death (aHR, 0.50; 95% CI, 0.20-1.27). Most residents (64.4%) had received primary course vaccine of AstraZeneca, but this did not impact pre- or postbooster risk. Staff showed a similar pattern of waning booster effectiveness against infection, with few hospitalizations and no deaths.<h4>Conclusions</h4>Our findings suggest that booster vaccination provided sustained protection against severe outcomes following infection with the Omicron variant, but no protection against infection from 4 months onwards. Ongoing surveillance for SARS-CoV-2 in LTCFs is crucial.",
     "laySummary": "",
-    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/head.14465; doi:https://doi.org/10.1111/head.14465; html:https://europepmc.org/articles/PMC10952318; pdf:https://europepmc.org/articles/PMC10952318?pdf=render"
+    "urls": "pdf:https://academic.oup.com/ofid/article-pdf/10/1/ofac694/48846221/ofac694.pdf; doi:https://doi.org/10.1093/ofid/ofac694; html:https://europepmc.org/articles/PMC9874026; pdf:https://europepmc.org/articles/PMC9874026?pdf=render"
   },
   {
     "id": "31398891",
@@ -13123,6 +13123,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1186/s12916-024-03399-8; html:https://europepmc.org/articles/PMC11304908; pdf:https://europepmc.org/articles/PMC11304908?pdf=render"
   },
+  {
+    "id": "36748660",
+    "doi": "https://doi.org/10.1111/head.14465",
+    "title": "Depression and anxiety in women with idiopathic intracranial hypertension compared to migraine: A matched controlled cohort study.",
+    "authorString": "Mollan SP, Subramanian A, Perrins M, Nirantharakumar K, Adderley NJ, Sinclair AJ.",
+    "authorAffiliations": "",
+    "journalTitle": "Headache",
+    "pubYear": "2023",
+    "date": "2023-02-07",
+    "isOpenAccess": "Y",
+    "keywords": "Depression; Migraine; Anxiety; epidemiology; Primary Care; Idiopathic Intracranial Hypertension",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>To evaluate mental health burden in women with idiopathic intracranial hypertension (IIH) compared to matched women with migraine and population controls.<h4>Background</h4>Depression and anxiety are recognized comorbid conditions in those with IIH and lead to worse predicted medical outcomes. The mental health burden in IIH has not been previously evaluated in a large, matched cohort study.<h4>Methods</h4>We performed a population-based matched, retrospective cohort study to explore mental health outcomes (depression and anxiety). We used data from IQVIA Medical Research Data, an anonymized, nationally representative primary care electronic medical records database in the United Kingdom, from January 1, 1995, to September 25, 2019. Women aged \u226516\u2009years were eligible for inclusion. Women with IIH (exposure) were matched by age and body mass index with up to 10 control women without IIH but with migraine (migraine controls), and without IIH or migraine (population controls).<h4>Results</h4>A total of 3411 women with IIH, 30,879 migraine controls and 33,495 population controls were included. Of these, 237, 2372 and 1695 women with IIH, migraine controls and population controls, respectively, developed depression during follow-up, and 179, 1826 and 1197, respectively, developed anxiety. There was a greater hazard of depression and anxiety in IIH compared to population controls (adjusted hazard ratio [aHR] 1.38, 95% confidence interval [CI] 1.20-1.58; and aHR 1.40, 95% CI 1.19-1.64, respectively), while hazards were similar to migraine controls (aHR 0.98, 95% CI 0.86-1.13; and aHR 0.98, 95% CI 0.83-1.14, respectively).<h4>Conclusion</h4>Depression and anxiety burden in women with IIH is higher than in the general population, and comparable to that in matched women with migraine. This may indicate that presence of headache is a potential driver for comorbid depression and anxiety in IIH.",
+    "laySummary": "",
+    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/head.14465; doi:https://doi.org/10.1111/head.14465; html:https://europepmc.org/articles/PMC10952318; pdf:https://europepmc.org/articles/PMC10952318?pdf=render"
+  },
   {
     "id": "36720882",
     "doi": "https://doi.org/10.1038/s41597-023-01949-y",
@@ -13191,23 +13208,6 @@
     "laySummary": "",
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7612723; doi:https://doi.org/10.1097/MCP.0000000000000863; html:https://europepmc.org/articles/PMC7612723; pdf:https://europepmc.org/articles/PMC7612723?pdf=render; doi:https://doi.org/10.1097/mcp.0000000000000863"
   },
-  {
-    "id": "38662697",
-    "doi": "https://doi.org/10.1093/cid/ciae108",
-    "title": "Reducing the Antigen Prevalence Target Threshold for Stopping and Restarting Mass Drug Administration for Lymphatic Filariasis Elimination: A Model-Based Cost-effectiveness Simulation in Tanzania, India and Haiti.",
-    "authorString": "Antony Oliver MC, Graham M, Gass KM, Medley GF, Clark J, Davis EL, Reimer LJ, King JD, Pouwels KB, Hollingsworth TD.",
-    "authorAffiliations": "",
-    "journalTitle": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America",
-    "pubYear": "2024",
-    "date": "2024-04-01",
-    "isOpenAccess": "Y",
-    "keywords": "Threshold; Modeling; Elimination; Health Economics; Lymphatic Filariasis",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>The Global Programme to Eliminate Lymphatic Filariasis (GPELF) aims to reduce and maintain infection levels through mass drug administration (MDA), but there is evidence of ongoing transmission after MDA in areas where Culex mosquitoes are the main transmission vector, suggesting that a more stringent criterion is required for MDA decision making in these settings.<h4>Methods</h4>We use a transmission model to investigate how a lower prevalence threshold (<1% antigenemia [Ag] prevalence compared with <2% Ag prevalence) for MDA decision making would affect the probability of local elimination, health outcomes, the number of MDA rounds, including restarts, and program costs associated with MDA and surveys across different scenarios. To determine the cost-effectiveness of switching to a lower threshold, we simulated 65% and 80% MDA coverage of the total population for different willingness to pay per disability-adjusted life-year averted for India ($446.07), Tanzania ($389.83), and Haiti ($219.84).<h4>Results</h4>Our results suggest that with a lower Ag threshold, there is a small proportion of simulations where extra rounds are required to reach the target, but this also reduces the need to restart MDA later in the program. For 80% coverage, the lower threshold is cost-effective across all baseline prevalences for India, Tanzania, and Haiti. For 65% MDA coverage, the lower threshold is not cost-effective due to additional MDA rounds, although it increases the probability of local elimination. Valuing the benefits of elimination to align with the GPELF goals, we find that a willingness to pay per capita government expenditure of approximately $1000-$4000 for 1% increase in the probability of local elimination would be required to make a lower threshold cost-effective.<h4>Conclusions</h4>Lower Ag thresholds for stopping MDAs generally mean a higher probability of local elimination, reducing long-term costs and health impacts. However, they may also lead to an increased number of MDA rounds required to reach the lower threshold and, therefore, increased short-term costs. Collectively, our analyses highlight that lower target Ag thresholds have the potential to assist programs in achieving lymphatic filariasis goals.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1093/cid/ciae108; doi:https://doi.org/10.1093/cid/ciae108; html:https://europepmc.org/articles/PMC11045020; pdf:https://europepmc.org/articles/PMC11045020?pdf=render"
-  },
   {
     "id": "34308306",
     "doi": "https://doi.org/10.1016/j.eclinm.2021.100888",
@@ -13225,6 +13225,23 @@
     "laySummary": "",
     "urls": "pdf:http://www.thelancet.com/article/S2589537021001681/pdf; doi:https://doi.org/10.1016/j.eclinm.2021.100888; html:https://europepmc.org/articles/PMC8257989; pdf:https://europepmc.org/articles/PMC8257989?pdf=render"
   },
+  {
+    "id": "38662697",
+    "doi": "https://doi.org/10.1093/cid/ciae108",
+    "title": "Reducing the Antigen Prevalence Target Threshold for Stopping and Restarting Mass Drug Administration for Lymphatic Filariasis Elimination: A Model-Based Cost-effectiveness Simulation in Tanzania, India and Haiti.",
+    "authorString": "Antony Oliver MC, Graham M, Gass KM, Medley GF, Clark J, Davis EL, Reimer LJ, King JD, Pouwels KB, Hollingsworth TD.",
+    "authorAffiliations": "",
+    "journalTitle": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America",
+    "pubYear": "2024",
+    "date": "2024-04-01",
+    "isOpenAccess": "Y",
+    "keywords": "Threshold; Modeling; Elimination; Health Economics; Lymphatic Filariasis",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>The Global Programme to Eliminate Lymphatic Filariasis (GPELF) aims to reduce and maintain infection levels through mass drug administration (MDA), but there is evidence of ongoing transmission after MDA in areas where Culex mosquitoes are the main transmission vector, suggesting that a more stringent criterion is required for MDA decision making in these settings.<h4>Methods</h4>We use a transmission model to investigate how a lower prevalence threshold (<1% antigenemia [Ag] prevalence compared with <2% Ag prevalence) for MDA decision making would affect the probability of local elimination, health outcomes, the number of MDA rounds, including restarts, and program costs associated with MDA and surveys across different scenarios. To determine the cost-effectiveness of switching to a lower threshold, we simulated 65% and 80% MDA coverage of the total population for different willingness to pay per disability-adjusted life-year averted for India ($446.07), Tanzania ($389.83), and Haiti ($219.84).<h4>Results</h4>Our results suggest that with a lower Ag threshold, there is a small proportion of simulations where extra rounds are required to reach the target, but this also reduces the need to restart MDA later in the program. For 80% coverage, the lower threshold is cost-effective across all baseline prevalences for India, Tanzania, and Haiti. For 65% MDA coverage, the lower threshold is not cost-effective due to additional MDA rounds, although it increases the probability of local elimination. Valuing the benefits of elimination to align with the GPELF goals, we find that a willingness to pay per capita government expenditure of approximately $1000-$4000 for 1% increase in the probability of local elimination would be required to make a lower threshold cost-effective.<h4>Conclusions</h4>Lower Ag thresholds for stopping MDAs generally mean a higher probability of local elimination, reducing long-term costs and health impacts. However, they may also lead to an increased number of MDA rounds required to reach the lower threshold and, therefore, increased short-term costs. Collectively, our analyses highlight that lower target Ag thresholds have the potential to assist programs in achieving lymphatic filariasis goals.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1093/cid/ciae108; doi:https://doi.org/10.1093/cid/ciae108; html:https://europepmc.org/articles/PMC11045020; pdf:https://europepmc.org/articles/PMC11045020?pdf=render"
+  },
   {
     "id": "39461360",
     "doi": "https://doi.org/10.1016/s2213-8587(24)00242-0",
@@ -13395,23 +13412,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ije/article-pdf/51/6/1745/47882630/dyac158.pdf; doi:https://doi.org/10.1093/ije/dyac158; html:https://europepmc.org/articles/PMC9384728; pdf:https://europepmc.org/articles/PMC9384728?pdf=render"
   },
-  {
-    "id": "33545096",
-    "doi": "https://doi.org/10.1016/s0140-6736(21)00149-5",
-    "title": "Azithromycin in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial.",
-    "authorString": "RECOVERY Collaborative Group.",
-    "authorAffiliations": "",
-    "journalTitle": "Lancet (London, England)",
-    "pubYear": "2021",
-    "date": "2021-02-02",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Azithromycin has been proposed as a treatment for COVID-19 on the basis of its immunomodulatory actions. We aimed to evaluate the safety and efficacy of azithromycin in patients admitted to hospital with COVID-19.<h4>Methods</h4>In this randomised, controlled, open-label, adaptive platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), several possible treatments were compared with usual care in patients admitted to hospital with COVID-19 in the UK. The trial is underway at 176 hospitals in the UK. Eligible and consenting patients were randomly allocated to either usual standard of care alone or usual standard of care plus azithromycin 500 mg once per day by mouth or intravenously for 10 days or until discharge (or allocation to one of the other RECOVERY treatment groups). Patients were assigned via web-based simple (unstratified) randomisation with allocation concealment and were twice as likely to be randomly assigned to usual care than to any of the active treatment groups. Participants and local study staff were not masked to the allocated treatment, but all others involved in the trial were masked to the outcome data during the trial. The primary outcome was 28-day all-cause mortality, assessed in the intention-to-treat population. The trial is registered with ISRCTN, 50189673, and ClinicalTrials.gov, NCT04381936.<h4>Findings</h4>Between April 7 and Nov 27, 2020, of 16\u2008442 patients enrolled in the RECOVERY trial, 9433 (57%) were eligible and 7763 were included in the assessment of azithromycin. The mean age of these study participants was 65\u00b73 years (SD 15\u00b77) and approximately a third were women (2944 [38%] of 7763). 2582 patients were randomly allocated to receive azithromycin and 5181 patients were randomly allocated to usual care alone. Overall, 561 (22%) patients allocated to azithromycin and 1162 (22%) patients allocated to usual care died within 28 days (rate ratio 0\u00b797, 95% CI 0\u00b787-1\u00b707; p=0\u00b750). No significant difference was seen in duration of hospital stay (median 10 days [IQR 5 to >28] vs 11 days [5 to >28]) or the proportion of patients discharged from hospital alive within 28 days (rate ratio 1\u00b704, 95% CI 0\u00b798-1\u00b710; p=0\u00b719). Among those not on invasive mechanical ventilation at baseline, no significant difference was seen in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (risk ratio 0\u00b795, 95% CI 0\u00b787-1\u00b703; p=0\u00b724).<h4>Interpretation</h4>In patients admitted to hospital with COVID-19, azithromycin did not improve survival or other prespecified clinical outcomes. Azithromycin use in patients admitted to hospital with COVID-19 should be restricted to patients in whom there is a clear antimicrobial indication.<h4>Funding</h4>UK Research and Innovation (Medical Research Council) and National Institute of Health Research.",
-    "laySummary": "",
-    "urls": "pdf:http://www.thelancet.com/article/S0140673621001495/pdf; doi:https://doi.org/10.1016/S0140-6736(21)00149-5; html:https://europepmc.org/articles/PMC7884931; pdf:https://europepmc.org/articles/PMC7884931?pdf=render"
-  },
   {
     "id": "34240125",
     "doi": "https://doi.org/10.1093/clinchem/hvab109",
@@ -13429,6 +13429,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/clinchem/article-pdf/67/10/1351/40494927/hvab109.pdf; doi:https://doi.org/10.1093/clinchem/hvab109; html:https://europepmc.org/articles/PMC8486023; pdf:https://europepmc.org/articles/PMC8486023?pdf=render"
   },
+  {
+    "id": "36929232",
+    "doi": "https://doi.org/10.1002/jmri.28675",
+    "title": "Image-Based Biological Heart Age Estimation Reveals Differential Aging Patterns Across Cardiac Chambers.",
+    "authorString": "Salih AM, Pujadas ER, Campello VM, McCracken C, Harvey NC, Neubauer S, Lekadir K, Nichols TE, Petersen SE, Raisi-Estabragh Z.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of magnetic resonance imaging : JMRI",
+    "pubYear": "2023",
+    "date": "2023-03-16",
+    "isOpenAccess": "Y",
+    "keywords": "Aging; Cardiac Imaging; Cardiac Health; Radiomics",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Biological heart age estimation can provide insights into cardiac aging. However, existing studies do not consider differential aging across cardiac regions.<h4>Purpose</h4>To estimate biological age of the left ventricle (LV), right ventricle (RV), myocardium, left atrium, and right atrium using magnetic resonance imaging radiomics phenotypes and to investigate determinants of aging by cardiac region.<h4>Study type</h4>Cross-sectional.<h4>Population</h4>A total of 18,117 healthy UK Biobank participants including 8338 men (mean age\u00a0=\u00a064.2\u00a0\u00b1\u20097.5) and 9779 women (mean age\u00a0=\u00a063.0\u2009\u00b1\u20097.4).<h4>Field strength/sequence</h4>A 1.5\u00a0T/balanced steady-state free precession.<h4>Assessment</h4>An automated algorithm was used to segment the five cardiac regions, from which radiomic features were extracted. Bayesian ridge regression was used to estimate biological age of each cardiac region with radiomics features as predictors and chronological age as the output. The \"age gap\" was the difference between biological and chronological age. Linear regression was used to calculate associations of age gap from each cardiac region with socioeconomic, lifestyle, body composition, blood pressure and arterial stiffness, blood biomarkers, mental well-being, multiorgan health, and sex hormone exposures (n\u00a0=\u200949).<h4>Statistical test</h4>Multiple testing correction with false discovery method (threshold\u00a0=\u00a05%).<h4>Results</h4>The largest model error was with RV and the smallest with LV age (mean absolute error in men: 5.26 vs. 4.96\u2009years). There were 172 statistically significant age gap associations. Greater visceral adiposity was the strongest correlate of larger age gaps, for example, myocardial age gap in women (Beta\u00a0=\u00a00.85, P\u00a0=\u20091.69\u2009\u00d7\u200910<sup>-26</sup> ). Poor mental health associated with large age gaps, for example, \"disinterested\" episodes and myocardial age gap in men (Beta\u00a0=\u00a00.25, P\u00a0=\u20090.001), as did a history of dental problems (eg LV in men Beta\u00a0=\u00a00.19, P\u00a0=\u20090.02). Higher bone mineral density was the strongest associate of smaller age gaps, for example, myocardial age gap in men (Beta\u00a0=\u00a0-1.52, P\u00a0=\u20097.44\u2009\u00d7\u200910<sup>-6</sup> ).<h4>Data conclusion</h4>This work demonstrates image-based heart age estimation as a novel method for understanding cardiac aging.<h4>Evidence level</h4>1.<h4>Technical efficacy</h4>Stage 1.",
+    "laySummary": "",
+    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jmri.28675; doi:https://doi.org/10.1002/jmri.28675; html:https://europepmc.org/articles/PMC10947470; pdf:https://europepmc.org/articles/PMC10947470?pdf=render"
+  },
   {
     "id": "37934728",
     "doi": "https://doi.org/10.1093/jamia/ocad212",
@@ -13447,21 +13464,21 @@
     "urls": "doi:https://doi.org/10.1093/jamia/ocad212"
   },
   {
-    "id": "36929232",
-    "doi": "https://doi.org/10.1002/jmri.28675",
-    "title": "Image-Based Biological Heart Age Estimation Reveals Differential Aging Patterns Across Cardiac Chambers.",
-    "authorString": "Salih AM, Pujadas ER, Campello VM, McCracken C, Harvey NC, Neubauer S, Lekadir K, Nichols TE, Petersen SE, Raisi-Estabragh Z.",
+    "id": "33545096",
+    "doi": "https://doi.org/10.1016/s0140-6736(21)00149-5",
+    "title": "Azithromycin in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial.",
+    "authorString": "RECOVERY Collaborative Group.",
     "authorAffiliations": "",
-    "journalTitle": "Journal of magnetic resonance imaging : JMRI",
-    "pubYear": "2023",
-    "date": "2023-03-16",
+    "journalTitle": "Lancet (London, England)",
+    "pubYear": "2021",
+    "date": "2021-02-02",
     "isOpenAccess": "Y",
-    "keywords": "Aging; Cardiac Imaging; Cardiac Health; Radiomics",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Biological heart age estimation can provide insights into cardiac aging. However, existing studies do not consider differential aging across cardiac regions.<h4>Purpose</h4>To estimate biological age of the left ventricle (LV), right ventricle (RV), myocardium, left atrium, and right atrium using magnetic resonance imaging radiomics phenotypes and to investigate determinants of aging by cardiac region.<h4>Study type</h4>Cross-sectional.<h4>Population</h4>A total of 18,117 healthy UK Biobank participants including 8338 men (mean age\u00a0=\u00a064.2\u00a0\u00b1\u20097.5) and 9779 women (mean age\u00a0=\u00a063.0\u2009\u00b1\u20097.4).<h4>Field strength/sequence</h4>A 1.5\u00a0T/balanced steady-state free precession.<h4>Assessment</h4>An automated algorithm was used to segment the five cardiac regions, from which radiomic features were extracted. Bayesian ridge regression was used to estimate biological age of each cardiac region with radiomics features as predictors and chronological age as the output. The \"age gap\" was the difference between biological and chronological age. Linear regression was used to calculate associations of age gap from each cardiac region with socioeconomic, lifestyle, body composition, blood pressure and arterial stiffness, blood biomarkers, mental well-being, multiorgan health, and sex hormone exposures (n\u00a0=\u200949).<h4>Statistical test</h4>Multiple testing correction with false discovery method (threshold\u00a0=\u00a05%).<h4>Results</h4>The largest model error was with RV and the smallest with LV age (mean absolute error in men: 5.26 vs. 4.96\u2009years). There were 172 statistically significant age gap associations. Greater visceral adiposity was the strongest correlate of larger age gaps, for example, myocardial age gap in women (Beta\u00a0=\u00a00.85, P\u00a0=\u20091.69\u2009\u00d7\u200910<sup>-26</sup> ). Poor mental health associated with large age gaps, for example, \"disinterested\" episodes and myocardial age gap in men (Beta\u00a0=\u00a00.25, P\u00a0=\u20090.001), as did a history of dental problems (eg LV in men Beta\u00a0=\u00a00.19, P\u00a0=\u20090.02). Higher bone mineral density was the strongest associate of smaller age gaps, for example, myocardial age gap in men (Beta\u00a0=\u00a0-1.52, P\u00a0=\u20097.44\u2009\u00d7\u200910<sup>-6</sup> ).<h4>Data conclusion</h4>This work demonstrates image-based heart age estimation as a novel method for understanding cardiac aging.<h4>Evidence level</h4>1.<h4>Technical efficacy</h4>Stage 1.",
+    "abstract": "<h4>Background</h4>Azithromycin has been proposed as a treatment for COVID-19 on the basis of its immunomodulatory actions. We aimed to evaluate the safety and efficacy of azithromycin in patients admitted to hospital with COVID-19.<h4>Methods</h4>In this randomised, controlled, open-label, adaptive platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), several possible treatments were compared with usual care in patients admitted to hospital with COVID-19 in the UK. The trial is underway at 176 hospitals in the UK. Eligible and consenting patients were randomly allocated to either usual standard of care alone or usual standard of care plus azithromycin 500 mg once per day by mouth or intravenously for 10 days or until discharge (or allocation to one of the other RECOVERY treatment groups). Patients were assigned via web-based simple (unstratified) randomisation with allocation concealment and were twice as likely to be randomly assigned to usual care than to any of the active treatment groups. Participants and local study staff were not masked to the allocated treatment, but all others involved in the trial were masked to the outcome data during the trial. The primary outcome was 28-day all-cause mortality, assessed in the intention-to-treat population. The trial is registered with ISRCTN, 50189673, and ClinicalTrials.gov, NCT04381936.<h4>Findings</h4>Between April 7 and Nov 27, 2020, of 16\u2008442 patients enrolled in the RECOVERY trial, 9433 (57%) were eligible and 7763 were included in the assessment of azithromycin. The mean age of these study participants was 65\u00b73 years (SD 15\u00b77) and approximately a third were women (2944 [38%] of 7763). 2582 patients were randomly allocated to receive azithromycin and 5181 patients were randomly allocated to usual care alone. Overall, 561 (22%) patients allocated to azithromycin and 1162 (22%) patients allocated to usual care died within 28 days (rate ratio 0\u00b797, 95% CI 0\u00b787-1\u00b707; p=0\u00b750). No significant difference was seen in duration of hospital stay (median 10 days [IQR 5 to >28] vs 11 days [5 to >28]) or the proportion of patients discharged from hospital alive within 28 days (rate ratio 1\u00b704, 95% CI 0\u00b798-1\u00b710; p=0\u00b719). Among those not on invasive mechanical ventilation at baseline, no significant difference was seen in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (risk ratio 0\u00b795, 95% CI 0\u00b787-1\u00b703; p=0\u00b724).<h4>Interpretation</h4>In patients admitted to hospital with COVID-19, azithromycin did not improve survival or other prespecified clinical outcomes. Azithromycin use in patients admitted to hospital with COVID-19 should be restricted to patients in whom there is a clear antimicrobial indication.<h4>Funding</h4>UK Research and Innovation (Medical Research Council) and National Institute of Health Research.",
     "laySummary": "",
-    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jmri.28675; doi:https://doi.org/10.1002/jmri.28675; html:https://europepmc.org/articles/PMC10947470; pdf:https://europepmc.org/articles/PMC10947470?pdf=render"
+    "urls": "pdf:http://www.thelancet.com/article/S0140673621001495/pdf; doi:https://doi.org/10.1016/S0140-6736(21)00149-5; html:https://europepmc.org/articles/PMC7884931; pdf:https://europepmc.org/articles/PMC7884931?pdf=render"
   },
   {
     "id": "35443953",
@@ -13531,23 +13548,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1177/20552076241272570; html:https://europepmc.org/articles/PMC11363038; pdf:https://europepmc.org/articles/PMC11363038?pdf=render"
   },
-  {
-    "id": "39004446",
-    "doi": "https://doi.org/10.1136/jmg-2023-109791",
-    "title": "Estimating cancer risk in carriers of Lynch syndrome variants in UK Biobank.",
-    "authorString": "Fummey E, Navarro P, Plazzer JP, Frayling IM, Knott S, Tenesa A.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of medical genetics",
-    "pubYear": "2024",
-    "date": "2024-08-29",
-    "isOpenAccess": "Y",
-    "keywords": "Neoplasms; Human genetics; Genetic predisposition to disease; Germ-line Mutation; Whole Exome Sequencing",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "BackgroundLynch syndrome (LS) is an inherited cancer predisposition syndrome caused by genetic variants affecting DNA mismatch repair (MMR) genes <i>MLH1</i>, <i>MSH2</i>, <i>MSH6</i> and <i>PMS2</i> Cancer risk in LS is estimated from cohorts of individuals ascertained by individual or family history of cancer, which may upwardly bias estimates.<h4>Methods</h4>830 carriers of pathogenic or likely pathogenic (<i>path_MMR</i>) MMR gene variants classified by InSiGHT were identified in 454\u2009756 UK Biobank (UKB) participants using whole-exome sequence. Nelson-Aalen survival analysis was used to estimate cumulative incidence of colorectal, endometrial and breast cancer (BC).<h4>Results</h4>Cumulative incidence of colorectal and endometrial cancer (EC) by age 70 years was elevated in <i>path_MMR</i> carriers compared with non-carriers (colorectal: 11.8% (95% confidence interval (CI): 9.5% to 14.6%) vs 1.7% (95% CI: 1.6% to 1.7%), endometrial: 13.4% (95% CI: 10.2% to 17.6%) vs 1.0% (95% CI: 0.9% to 1.0%)), but the magnitude of this increase differed between genes. Cumulative BC incidence by age 70 years was not elevated in <i>path_MMR</i> carriers compared with non-carriers (8.9% (95% CI: 6.3% to 12.4%) vs 7.5% (95% CI: 7.4% to 7.6%)). Cumulative cancer incidence estimates in UKB were similar to estimates from the Prospective Lynch Syndrome Database for all genes and cancers, except there was no evidence for elevated EC risk in carriers of pathogenic <i>PMS2</i> variants in UKB.<h4>Conclusion</h4>These results support offering incidentally identified carriers of any <i>path_MMR</i> surveillance to manage colorectal cancer risk. Incidentally identified carriers of pathogenic variants in <i>MLH1</i>, <i>MSH2</i> and <i>MSH6</i> would also benefit from interventions to reduce EC risk. The results suggest that BC is not an LS-related cancer.",
-    "laySummary": "",
-    "urls": "pdf:https://jmg.bmj.com/content/jmedgenet/early/2024/08/06/jmg-2023-109791.full.pdf; doi:https://doi.org/10.1136/jmg-2023-109791; html:https://europepmc.org/articles/PMC11420727; pdf:https://europepmc.org/articles/PMC11420727?pdf=render"
-  },
   {
     "id": "37650026",
     "doi": "https://doi.org/10.23889/ijpds.v7i1.1727",
@@ -13565,6 +13565,23 @@
     "laySummary": "",
     "urls": "pdf:https://ijpds.org/article/download/1727/3395; doi:https://doi.org/10.23889/ijpds.v7i1.1727; html:https://europepmc.org/articles/PMC10464868; pdf:https://europepmc.org/articles/PMC10464868?pdf=render"
   },
+  {
+    "id": "39004446",
+    "doi": "https://doi.org/10.1136/jmg-2023-109791",
+    "title": "Estimating cancer risk in carriers of Lynch syndrome variants in UK Biobank.",
+    "authorString": "Fummey E, Navarro P, Plazzer JP, Frayling IM, Knott S, Tenesa A.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of medical genetics",
+    "pubYear": "2024",
+    "date": "2024-08-29",
+    "isOpenAccess": "Y",
+    "keywords": "Neoplasms; Human genetics; Genetic predisposition to disease; Germ-line Mutation; Whole Exome Sequencing",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "BackgroundLynch syndrome (LS) is an inherited cancer predisposition syndrome caused by genetic variants affecting DNA mismatch repair (MMR) genes <i>MLH1</i>, <i>MSH2</i>, <i>MSH6</i> and <i>PMS2</i> Cancer risk in LS is estimated from cohorts of individuals ascertained by individual or family history of cancer, which may upwardly bias estimates.<h4>Methods</h4>830 carriers of pathogenic or likely pathogenic (<i>path_MMR</i>) MMR gene variants classified by InSiGHT were identified in 454\u2009756 UK Biobank (UKB) participants using whole-exome sequence. Nelson-Aalen survival analysis was used to estimate cumulative incidence of colorectal, endometrial and breast cancer (BC).<h4>Results</h4>Cumulative incidence of colorectal and endometrial cancer (EC) by age 70 years was elevated in <i>path_MMR</i> carriers compared with non-carriers (colorectal: 11.8% (95% confidence interval (CI): 9.5% to 14.6%) vs 1.7% (95% CI: 1.6% to 1.7%), endometrial: 13.4% (95% CI: 10.2% to 17.6%) vs 1.0% (95% CI: 0.9% to 1.0%)), but the magnitude of this increase differed between genes. Cumulative BC incidence by age 70 years was not elevated in <i>path_MMR</i> carriers compared with non-carriers (8.9% (95% CI: 6.3% to 12.4%) vs 7.5% (95% CI: 7.4% to 7.6%)). Cumulative cancer incidence estimates in UKB were similar to estimates from the Prospective Lynch Syndrome Database for all genes and cancers, except there was no evidence for elevated EC risk in carriers of pathogenic <i>PMS2</i> variants in UKB.<h4>Conclusion</h4>These results support offering incidentally identified carriers of any <i>path_MMR</i> surveillance to manage colorectal cancer risk. Incidentally identified carriers of pathogenic variants in <i>MLH1</i>, <i>MSH2</i> and <i>MSH6</i> would also benefit from interventions to reduce EC risk. The results suggest that BC is not an LS-related cancer.",
+    "laySummary": "",
+    "urls": "pdf:https://jmg.bmj.com/content/jmedgenet/early/2024/08/06/jmg-2023-109791.full.pdf; doi:https://doi.org/10.1136/jmg-2023-109791; html:https://europepmc.org/articles/PMC11420727; pdf:https://europepmc.org/articles/PMC11420727?pdf=render"
+  },
   {
     "id": "38837525",
     "doi": "https://doi.org/10.1002/alz.13870",
@@ -13582,23 +13599,6 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/alz.13870; doi:https://doi.org/10.1002/alz.13870; html:https://europepmc.org/articles/PMC11247702; pdf:https://europepmc.org/articles/PMC11247702?pdf=render"
   },
-  {
-    "id": "36073628",
-    "doi": "https://doi.org/10.1161/jaha.122.026432",
-    "title": "Differential Patterns and Outcomes of 20.6\u00a0Million Cardiovascular Emergency Department Encounters for Men and Women in the United States.",
-    "authorString": "Raisi-Estabragh Z, Kobo O, Elbadawi A, Velagapudi P, Sharma G, Bullock-Palmer RP, Petersen SE, Mehta LS, Ullah W, Roguin A, Sun LY, Mamas MA.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of the American Heart Association",
-    "pubYear": "2022",
-    "date": "2022-09-08",
-    "isOpenAccess": "Y",
-    "keywords": "Men; Essential hypertension; Atrial fibrillation; Stroke; Women; Sex characteristics; United States",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Background We describe sex-differential disease patterns and outcomes of >20.6\u00a0million cardiovascular emergency department encounters in the United States. Methods and Results We analyzed primary cardiovascular encounters from the Nationwide Emergency Department Sample between 2016 and 2018. We grouped cardiovascular diagnoses into 15 disease categories. The sample included 48.7% women; median age was 67 (interquartile range, 54-78) years. Men had greater overall baseline comorbidity burden; however, women had higher rates of obesity, hypertension, and cerebrovascular disease. For women, the most common emergency department encounters were essential hypertension (16.0%), hypertensive heart or kidney disease (14.1%), and atrial fibrillation/flutter (10.2%). For men, the most common encounters were hypertensive heart or kidney disease (14.7%), essential hypertension (10.8%), and acute myocardial infarction (10.7%). Women were more likely to present with essential hypertension, hypertensive crisis, atrial fibrillation/flutter, supraventricular tachycardia, pulmonary embolism, or ischemic stroke. Men were more likely to present with acute myocardial infarction or cardiac arrest. In logistic regression models adjusted for baseline covariates, compared with men, women with intracranial hemorrhage had higher risk of hospitalization and death. Women presenting with pulmonary embolism or deep vein thrombosis were less likely to be hospitalized. Women with aortic aneurysm/dissection had higher odds of hospitalization and death. Men were more likely to die following presentations with hypertensive heart or kidney disease, atrial fibrillation/flutter, acute myocardial infarction, or cardiac arrest. Conclusions In this large nationally representative sample of cardiovascular emergency department presentations, we demonstrate significant sex differences in disease distribution, hospitalization, and death.",
-    "laySummary": "",
-    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.122.026432; doi:https://doi.org/10.1161/JAHA.122.026432; html:https://europepmc.org/articles/PMC9673731; pdf:https://europepmc.org/articles/PMC9673731?pdf=render"
-  },
   {
     "id": "37868035",
     "doi": "https://doi.org/10.1016/j.xgen.2023.100385",
@@ -13616,6 +13616,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.xgen.2023.100385; doi:https://doi.org/10.1016/j.xgen.2023.100385; html:https://europepmc.org/articles/PMC10589627; pdf:https://europepmc.org/articles/PMC10589627?pdf=render"
   },
+  {
+    "id": "36073628",
+    "doi": "https://doi.org/10.1161/jaha.122.026432",
+    "title": "Differential Patterns and Outcomes of 20.6\u00a0Million Cardiovascular Emergency Department Encounters for Men and Women in the United States.",
+    "authorString": "Raisi-Estabragh Z, Kobo O, Elbadawi A, Velagapudi P, Sharma G, Bullock-Palmer RP, Petersen SE, Mehta LS, Ullah W, Roguin A, Sun LY, Mamas MA.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of the American Heart Association",
+    "pubYear": "2022",
+    "date": "2022-09-08",
+    "isOpenAccess": "Y",
+    "keywords": "Men; Essential hypertension; Atrial fibrillation; Stroke; Women; Sex characteristics; United States",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Background We describe sex-differential disease patterns and outcomes of >20.6\u00a0million cardiovascular emergency department encounters in the United States. Methods and Results We analyzed primary cardiovascular encounters from the Nationwide Emergency Department Sample between 2016 and 2018. We grouped cardiovascular diagnoses into 15 disease categories. The sample included 48.7% women; median age was 67 (interquartile range, 54-78) years. Men had greater overall baseline comorbidity burden; however, women had higher rates of obesity, hypertension, and cerebrovascular disease. For women, the most common emergency department encounters were essential hypertension (16.0%), hypertensive heart or kidney disease (14.1%), and atrial fibrillation/flutter (10.2%). For men, the most common encounters were hypertensive heart or kidney disease (14.7%), essential hypertension (10.8%), and acute myocardial infarction (10.7%). Women were more likely to present with essential hypertension, hypertensive crisis, atrial fibrillation/flutter, supraventricular tachycardia, pulmonary embolism, or ischemic stroke. Men were more likely to present with acute myocardial infarction or cardiac arrest. In logistic regression models adjusted for baseline covariates, compared with men, women with intracranial hemorrhage had higher risk of hospitalization and death. Women presenting with pulmonary embolism or deep vein thrombosis were less likely to be hospitalized. Women with aortic aneurysm/dissection had higher odds of hospitalization and death. Men were more likely to die following presentations with hypertensive heart or kidney disease, atrial fibrillation/flutter, acute myocardial infarction, or cardiac arrest. Conclusions In this large nationally representative sample of cardiovascular emergency department presentations, we demonstrate significant sex differences in disease distribution, hospitalization, and death.",
+    "laySummary": "",
+    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.122.026432; doi:https://doi.org/10.1161/JAHA.122.026432; html:https://europepmc.org/articles/PMC9673731; pdf:https://europepmc.org/articles/PMC9673731?pdf=render"
+  },
   {
     "id": "31256764",
     "doi": "https://doi.org/10.1192/bjp.2019.153",
@@ -13684,23 +13701,6 @@
     "laySummary": "",
     "urls": "html:https://europepmc.org/articles/PMC8861677; pdf:https://europepmc.org/articles/PMC8861677?pdf=render"
   },
-  {
-    "id": "39074912",
-    "doi": "https://doi.org/10.1136/bmjhci-2023-100963",
-    "title": "Communicating exploratory unsupervised machine learning analysis in age clustering for paediatric disease.",
-    "authorString": "Spear JW, Pissaridou E, Bowyer S, Bryant WA, Key D, Booth J, Spiridou A, Denaxas S, Pope R, Taylor AM, Hemingway H, Sebire NJ.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ health & care informatics",
-    "pubYear": "2024",
-    "date": "2024-07-29",
-    "isOpenAccess": "Y",
-    "keywords": "Data Visualization; Machine Learning; Electronic Health Records; Data Science",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Despite the increasing availability of electronic healthcare record (EHR) data and wide availability of plug-and-play machine learning (ML) Application Programming Interfaces, the adoption of data-driven decision-making within routine hospital workflows thus far, has remained limited. Through the lens of deriving clusters of diagnoses by age, this study investigated the type of ML analysis that can be performed using EHR data and how results could be communicated to lay stakeholders.<h4>Methods</h4>Observational EHR data from a tertiary paediatric hospital, containing 61\u2009522 unique patients and 3315 unique ICD-10 diagnosis codes was used, after preprocessing. K-means clustering was applied to identify age distributions of patient diagnoses. The final model was selected using quantitative metrics and expert assessment of the clinical validity of the clusters. Additionally, uncertainty over preprocessing decisions was analysed.<h4>Findings</h4>Four age clusters of diseases were identified, broadly aligning to ages between: 0 and 1; 1 and 5; 5 and 13; 13 and 18. Diagnoses, within the clusters, aligned to existing knowledge regarding the propensity of presentation at different ages, and sequential clusters presented known disease progressions. The results validated similar methodologies within the literature. The impact of uncertainty induced by preprocessing decisions was large at the individual diagnoses but not at a population level. Strategies for mitigating, or communicating, this uncertainty were successfully demonstrated.<h4>Conclusion</h4>Unsupervised ML applied to EHR data identifies clinically relevant age distributions of diagnoses which can augment existing decision making. However, biases within healthcare datasets dramatically impact results if not appropriately mitigated or communicated.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1136/bmjhci-2023-100963; html:https://europepmc.org/articles/PMC11288139; pdf:https://europepmc.org/articles/PMC11288139?pdf=render"
-  },
   {
     "id": "36680646",
     "doi": "https://doi.org/10.1007/s10654-022-00962-6",
@@ -13718,6 +13718,23 @@
     "laySummary": "",
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s10654-022-00962-6.pdf; doi:https://doi.org/10.1007/s10654-022-00962-6; html:https://europepmc.org/articles/PMC9860244; pdf:https://europepmc.org/articles/PMC9860244?pdf=render"
   },
+  {
+    "id": "39074912",
+    "doi": "https://doi.org/10.1136/bmjhci-2023-100963",
+    "title": "Communicating exploratory unsupervised machine learning analysis in age clustering for paediatric disease.",
+    "authorString": "Spear JW, Pissaridou E, Bowyer S, Bryant WA, Key D, Booth J, Spiridou A, Denaxas S, Pope R, Taylor AM, Hemingway H, Sebire NJ.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ health & care informatics",
+    "pubYear": "2024",
+    "date": "2024-07-29",
+    "isOpenAccess": "Y",
+    "keywords": "Data Visualization; Machine Learning; Electronic Health Records; Data Science",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Despite the increasing availability of electronic healthcare record (EHR) data and wide availability of plug-and-play machine learning (ML) Application Programming Interfaces, the adoption of data-driven decision-making within routine hospital workflows thus far, has remained limited. Through the lens of deriving clusters of diagnoses by age, this study investigated the type of ML analysis that can be performed using EHR data and how results could be communicated to lay stakeholders.<h4>Methods</h4>Observational EHR data from a tertiary paediatric hospital, containing 61\u2009522 unique patients and 3315 unique ICD-10 diagnosis codes was used, after preprocessing. K-means clustering was applied to identify age distributions of patient diagnoses. The final model was selected using quantitative metrics and expert assessment of the clinical validity of the clusters. Additionally, uncertainty over preprocessing decisions was analysed.<h4>Findings</h4>Four age clusters of diseases were identified, broadly aligning to ages between: 0 and 1; 1 and 5; 5 and 13; 13 and 18. Diagnoses, within the clusters, aligned to existing knowledge regarding the propensity of presentation at different ages, and sequential clusters presented known disease progressions. The results validated similar methodologies within the literature. The impact of uncertainty induced by preprocessing decisions was large at the individual diagnoses but not at a population level. Strategies for mitigating, or communicating, this uncertainty were successfully demonstrated.<h4>Conclusion</h4>Unsupervised ML applied to EHR data identifies clinically relevant age distributions of diagnoses which can augment existing decision making. However, biases within healthcare datasets dramatically impact results if not appropriately mitigated or communicated.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1136/bmjhci-2023-100963; html:https://europepmc.org/articles/PMC11288139; pdf:https://europepmc.org/articles/PMC11288139?pdf=render"
+  },
   {
     "id": "37550086",
     "doi": "https://doi.org/10.1136/bmjment-2023-300762",
@@ -13735,23 +13752,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1136/bmjment-2023-300762; html:https://europepmc.org/articles/PMC10577765; pdf:https://europepmc.org/articles/PMC10577765?pdf=render"
   },
-  {
-    "id": "39272070",
-    "doi": "https://doi.org/10.1186/s12889-024-19999-1",
-    "title": "Prevalence of undiagnosed hypertension and associated factors in Ndera sector, Gasabo district of Rwanda: a cross-sectional study.",
-    "authorString": "Okesina AA, Habineza JC, Mbazumutima R, Mignonne U, Mahirwe C, Hakizimana S, Gbadamosi MA, Uppal A, Wabwire FP.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC public health",
-    "pubYear": "2024",
-    "date": "2024-09-13",
-    "isOpenAccess": "Y",
-    "keywords": "Hypertension; risk factors; Rwanda; Low- And Middle-income Countries; Healthcare Services; Undiagnosed Hypertension",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Hypertension remains a major global health challenge, including in low- and middle-income countries. In Rwanda, a lack of adequate information and healthcare services impacts healthcare-seeking behaviors, contributing to undiagnosed hypertension in rural areas. Therefore, the need to determine its prevalence and associated factors.<h4>Methods</h4>A cross-sectional study was conducted with 393 adults in the Ndera Sector, of Rwanda's Gasabo District, through a multistage sampling technique. Data was gathered using the WHO STEP-wise approach to non-communicable disease risk factor surveillance (STEPS) questionnaire; physical examination was done to determine blood pressure and body-mass index (BMI), after which the data collected was analyzed using SPSS. Newly diagnosed hypertension was determined when on two different intervals, systolic blood pressure readings was >\u2009140 mmHg, and/or the diastolic blood pressure readings was >\u200990 mmHg, in the absence of previous hypertension diagnosis.<h4>Results</h4>The overall prevalence of hypertension among patients at Ndera sector was 15%, all of which were newly diagnosed. The mean (SD) age of the participants was 37 (13.7) years and half (53%) were women. The mean systolic blood pressure for men was 124.3 mmHg compared to 120.9 mmHg for women (p\u2009=\u20090.043, 95%CI: 0.12-6.74). Women had a significantly higher mean BMI (26.0) compared to men (22.8) (p\u2009<\u20090.001, 95%CI: -4.18 - -2.31). Age (\u03c7\u00b2 = 37.400, p\u2009<\u20090.001), residence (\u03c7\u00b2 = 10.200, p\u2009<\u20090.001), BMI (\u03c7\u00b2 = 22.1, p\u2009<\u20090.001), and lack of knowledge about hypertension (\u03c7\u00b2 = 25.1, p\u2009<\u20090.001) were the factors with significantly undiagnosed hypertension.<h4>Conclusions</h4>The high prevalence of undiagnosed hypertension in Ndera Sector is linked to gender, older age, higher BMI, location, and lack of hypertension knowledge. These findings call for multifaceted approaches, combining educational initiatives, geographical targeting, lifestyle modifications, and policy implementations, all aimed at mitigating the burden of undiagnosed hypertension and enhancing community health within the Ndera Sector.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1186/s12889-024-19999-1; html:https://europepmc.org/articles/PMC11397070; pdf:https://europepmc.org/articles/PMC11397070?pdf=render"
-  },
   {
     "id": "37004203",
     "doi": "https://doi.org/10.1093/qjmed/hcad050",
@@ -13769,6 +13769,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/qjmed/advance-article-pdf/doi/10.1093/qjmed/hcad050/50051055/hcad050.pdf; doi:https://doi.org/10.1093/qjmed/hcad050; html:https://europepmc.org/articles/PMC10250078; pdf:https://europepmc.org/articles/PMC10250078?pdf=render"
   },
+  {
+    "id": "39272070",
+    "doi": "https://doi.org/10.1186/s12889-024-19999-1",
+    "title": "Prevalence of undiagnosed hypertension and associated factors in Ndera sector, Gasabo district of Rwanda: a cross-sectional study.",
+    "authorString": "Okesina AA, Habineza JC, Mbazumutima R, Mignonne U, Mahirwe C, Hakizimana S, Gbadamosi MA, Uppal A, Wabwire FP.",
+    "authorAffiliations": "",
+    "journalTitle": "BMC public health",
+    "pubYear": "2024",
+    "date": "2024-09-13",
+    "isOpenAccess": "Y",
+    "keywords": "Hypertension; risk factors; Rwanda; Low- And Middle-income Countries; Healthcare Services; Undiagnosed Hypertension",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Hypertension remains a major global health challenge, including in low- and middle-income countries. In Rwanda, a lack of adequate information and healthcare services impacts healthcare-seeking behaviors, contributing to undiagnosed hypertension in rural areas. Therefore, the need to determine its prevalence and associated factors.<h4>Methods</h4>A cross-sectional study was conducted with 393 adults in the Ndera Sector, of Rwanda's Gasabo District, through a multistage sampling technique. Data was gathered using the WHO STEP-wise approach to non-communicable disease risk factor surveillance (STEPS) questionnaire; physical examination was done to determine blood pressure and body-mass index (BMI), after which the data collected was analyzed using SPSS. Newly diagnosed hypertension was determined when on two different intervals, systolic blood pressure readings was >\u2009140 mmHg, and/or the diastolic blood pressure readings was >\u200990 mmHg, in the absence of previous hypertension diagnosis.<h4>Results</h4>The overall prevalence of hypertension among patients at Ndera sector was 15%, all of which were newly diagnosed. The mean (SD) age of the participants was 37 (13.7) years and half (53%) were women. The mean systolic blood pressure for men was 124.3 mmHg compared to 120.9 mmHg for women (p\u2009=\u20090.043, 95%CI: 0.12-6.74). Women had a significantly higher mean BMI (26.0) compared to men (22.8) (p\u2009<\u20090.001, 95%CI: -4.18 - -2.31). Age (\u03c7\u00b2 = 37.400, p\u2009<\u20090.001), residence (\u03c7\u00b2 = 10.200, p\u2009<\u20090.001), BMI (\u03c7\u00b2 = 22.1, p\u2009<\u20090.001), and lack of knowledge about hypertension (\u03c7\u00b2 = 25.1, p\u2009<\u20090.001) were the factors with significantly undiagnosed hypertension.<h4>Conclusions</h4>The high prevalence of undiagnosed hypertension in Ndera Sector is linked to gender, older age, higher BMI, location, and lack of hypertension knowledge. These findings call for multifaceted approaches, combining educational initiatives, geographical targeting, lifestyle modifications, and policy implementations, all aimed at mitigating the burden of undiagnosed hypertension and enhancing community health within the Ndera Sector.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1186/s12889-024-19999-1; html:https://europepmc.org/articles/PMC11397070; pdf:https://europepmc.org/articles/PMC11397070?pdf=render"
+  },
   {
     "id": "36329425",
     "doi": "https://doi.org/10.1186/s12890-022-02189-3",
@@ -13854,23 +13871,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.12688/wellcomeopenres.20278.2; html:https://europepmc.org/articles/PMC11447437; pdf:https://europepmc.org/articles/PMC11447437?pdf=render"
   },
-  {
-    "id": "38909207",
-    "doi": "https://doi.org/10.1186/s12887-024-04848-2",
-    "title": "Educational outcomes among children with congenital heart disease compared to peers: a Scotland-wide record-linkage study of 715,850 schoolchildren.",
-    "authorString": "Fleming M, Athanasopoulos P, Mackay DF, Pell JP.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC pediatrics",
-    "pubYear": "2024",
-    "date": "2024-06-22",
-    "isOpenAccess": "Y",
-    "keywords": "Congenital heart disease; Population Study; Educational Outcomes; Record Linkage",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Nine in every thousand children born in the United Kingdom have congenital heart disease, and 250,000 adults are living with the condition. This study aims to investigate the associations between congenital heart disease and educational outcomes among school-aged children in Scotland.<h4>Methods</h4>Routine health and education databases were linked to produce a cohort of all singleton children born in Scotland and attending a local authority run primary, secondary, or special school in Scotland at some point between 2009 and 2013. Children with congenital heart disease within this cohort were compared with children unaffected by congenital conditions. Outcomes investigated were special educational need (SEN), absenteeism, exclusion, academic attainment, and unemployment. All analyses were adjusted for sociodemographic and maternity confounders. Absenteeism was investigated as a mediating factor in the associations with attainment and unemployment.<h4>Results</h4>Of the 715,850 children, 6,295 (0.9%) had congenital heart disease and 4,412 (6.1%) had isolated congenital heart disease. Congenital heart disease and isolated congenital heart disease were both significantly associated with subsequent special educational need (OR 3.45, 95% CI 3.26-3.65, p\u2009<\u20090.001 and OR 1.98, 95% CI 1.84-2.13, p\u2009<\u20090.001 respectively), absenteeism (IRR 1.13, 95% CI 1.10-1.16, p\u2009<\u20090.001 and IRR 1.10, 95% CI 1.06-1.13, p\u2009<\u20090.001 respectively), and low academic attainment (OR 1.69, 95% CI 1.39-2.07, p\u2009<\u20090.001 and OR 1.35, 95% CI 1.07-1.69, p\u2009=\u20090.011 respectively). Neither congenital heart disease nor isolated congenital heart disease were associated with school exclusion. Only congenital heart disease (OR 1.21, 95% CI 1.03-1.42, p\u2009= 0.022) but not isolated congenital heart disease was associated with unemployment. When days absent were included in the analyses investigating attainment and unemployment, the conclusions were not altered.<h4>Conclusion</h4>Children with congenital heart disease have greater special educational need, lower school attendance, attain lower examination grades and have greater unemployment compared to peers. In addition to healthcare support, affected children need educational support to avoid additional impact on their long-term wellbeing.",
-    "laySummary": "",
-    "urls": "pdf:https://bmcpediatr.biomedcentral.com/counter/pdf/10.1186/s12887-024-04848-2; doi:https://doi.org/10.1186/s12887-024-04848-2; html:https://europepmc.org/articles/PMC11193247; pdf:https://europepmc.org/articles/PMC11193247?pdf=render"
-  },
   {
     "id": "34842128",
     "doi": "https://doi.org/10.1192/j.eurpsy.2021.2255",
@@ -13923,21 +13923,21 @@
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s10461-021-03551-y.pdf; doi:https://doi.org/10.1007/s10461-021-03551-y; html:https://europepmc.org/articles/PMC9046343; pdf:https://europepmc.org/articles/PMC9046343?pdf=render"
   },
   {
-    "id": "33577558",
-    "doi": "https://doi.org/10.1371/journal.pmed.1003497",
-    "title": "Association of socioeconomic deprivation with asthma care, outcomes, and deaths in Wales: A 5-year national linked primary and secondary care cohort study.",
-    "authorString": "Alsallakh MA, Rodgers SE, Lyons RA, Sheikh A, Davies GA.",
+    "id": "38909207",
+    "doi": "https://doi.org/10.1186/s12887-024-04848-2",
+    "title": "Educational outcomes among children with congenital heart disease compared to peers: a Scotland-wide record-linkage study of 715,850 schoolchildren.",
+    "authorString": "Fleming M, Athanasopoulos P, Mackay DF, Pell JP.",
     "authorAffiliations": "",
-    "journalTitle": "PLoS medicine",
-    "pubYear": "2021",
-    "date": "2021-02-12",
+    "journalTitle": "BMC pediatrics",
+    "pubYear": "2024",
+    "date": "2024-06-22",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Congenital heart disease; Population Study; Educational Outcomes; Record Linkage",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Socioeconomic deprivation is known to be associated with worse outcomes in asthma, but there is a lack of population-based evidence of its impact across all stages of patient care. We investigated the association of socioeconomic deprivation with asthma-related care and outcomes across primary and secondary care and with asthma-related death in Wales.<h4>Methods and findings</h4>We constructed a national cohort, identified from 76% (2.4 million) of the Welsh population, of continuously treated asthma patients between 2013 and 2017 using anonymised, person-level, linked, routinely collected primary and secondary care data in the Secure Anonymised Information Linkage (SAIL) Databank. We investigated the association between asthma-related health service utilisation, prescribing, and deaths with the 2011 Welsh Index of Multiple Deprivation (WIMD) and its domains. We studied 106,926 patients (534,630 person-years), 56.3% were female, with mean age of 47.5 years (SD = 20.3). Compared to the least deprived patients, the most deprived patients had slightly fewer total asthma-related primary care consultations per patient (incidence rate ratio [IRR] = 0.98, 95% CI 0.97-0.99, p-value < 0.001), slightly fewer routine asthma reviews (IRR = 0.98, 0.97-0.99, p-value < 0.001), lower controller-to-total asthma medication ratios (AMRs; 0.50 versus 0.56, p-value < 0.001), more asthma-related accident and emergency (A&E) attendances (IRR = 1.27, 1.10-1.46, p-value = 0.001), more asthma emergency admissions (IRR = 1.56, 1.39-1.76, p-value < 0.001), longer asthma-related hospital stay (IRR = 1.64, 1.39-1.94, p-value < 0.001), and were at higher risk of asthma-related death (risk ratio of deaths with any mention of asthma 1.56, 1.18-2.07, p-value = 0.002). Study limitations include the deprivation index being area based and the potential for residual confounders and mediators.<h4>Conclusions</h4>In this study, we observed that the most deprived asthma patients in Wales had different prescribing patterns, more A&E attendances, more emergency hospital admissions, and substantially higher risk of death. Interventions specifically designed to improve treatment and outcomes for these disadvantaged groups are urgently needed.",
+    "abstract": "<h4>Background</h4>Nine in every thousand children born in the United Kingdom have congenital heart disease, and 250,000 adults are living with the condition. This study aims to investigate the associations between congenital heart disease and educational outcomes among school-aged children in Scotland.<h4>Methods</h4>Routine health and education databases were linked to produce a cohort of all singleton children born in Scotland and attending a local authority run primary, secondary, or special school in Scotland at some point between 2009 and 2013. Children with congenital heart disease within this cohort were compared with children unaffected by congenital conditions. Outcomes investigated were special educational need (SEN), absenteeism, exclusion, academic attainment, and unemployment. All analyses were adjusted for sociodemographic and maternity confounders. Absenteeism was investigated as a mediating factor in the associations with attainment and unemployment.<h4>Results</h4>Of the 715,850 children, 6,295 (0.9%) had congenital heart disease and 4,412 (6.1%) had isolated congenital heart disease. Congenital heart disease and isolated congenital heart disease were both significantly associated with subsequent special educational need (OR 3.45, 95% CI 3.26-3.65, p\u2009<\u20090.001 and OR 1.98, 95% CI 1.84-2.13, p\u2009<\u20090.001 respectively), absenteeism (IRR 1.13, 95% CI 1.10-1.16, p\u2009<\u20090.001 and IRR 1.10, 95% CI 1.06-1.13, p\u2009<\u20090.001 respectively), and low academic attainment (OR 1.69, 95% CI 1.39-2.07, p\u2009<\u20090.001 and OR 1.35, 95% CI 1.07-1.69, p\u2009=\u20090.011 respectively). Neither congenital heart disease nor isolated congenital heart disease were associated with school exclusion. Only congenital heart disease (OR 1.21, 95% CI 1.03-1.42, p\u2009= 0.022) but not isolated congenital heart disease was associated with unemployment. When days absent were included in the analyses investigating attainment and unemployment, the conclusions were not altered.<h4>Conclusion</h4>Children with congenital heart disease have greater special educational need, lower school attendance, attain lower examination grades and have greater unemployment compared to peers. In addition to healthcare support, affected children need educational support to avoid additional impact on their long-term wellbeing.",
     "laySummary": "",
-    "urls": "pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003497&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003497; html:https://europepmc.org/articles/PMC7880491; pdf:https://europepmc.org/articles/PMC7880491?pdf=render"
+    "urls": "pdf:https://bmcpediatr.biomedcentral.com/counter/pdf/10.1186/s12887-024-04848-2; doi:https://doi.org/10.1186/s12887-024-04848-2; html:https://europepmc.org/articles/PMC11193247; pdf:https://europepmc.org/articles/PMC11193247?pdf=render"
   },
   {
     "id": "31857590",
@@ -13956,6 +13956,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41597-019-0337-6.pdf; doi:https://doi.org/10.1038/s41597-019-0337-6; html:https://europepmc.org/articles/PMC6923383; pdf:https://europepmc.org/articles/PMC6923383?pdf=render"
   },
+  {
+    "id": "33577558",
+    "doi": "https://doi.org/10.1371/journal.pmed.1003497",
+    "title": "Association of socioeconomic deprivation with asthma care, outcomes, and deaths in Wales: A 5-year national linked primary and secondary care cohort study.",
+    "authorString": "Alsallakh MA, Rodgers SE, Lyons RA, Sheikh A, Davies GA.",
+    "authorAffiliations": "",
+    "journalTitle": "PLoS medicine",
+    "pubYear": "2021",
+    "date": "2021-02-12",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Socioeconomic deprivation is known to be associated with worse outcomes in asthma, but there is a lack of population-based evidence of its impact across all stages of patient care. We investigated the association of socioeconomic deprivation with asthma-related care and outcomes across primary and secondary care and with asthma-related death in Wales.<h4>Methods and findings</h4>We constructed a national cohort, identified from 76% (2.4 million) of the Welsh population, of continuously treated asthma patients between 2013 and 2017 using anonymised, person-level, linked, routinely collected primary and secondary care data in the Secure Anonymised Information Linkage (SAIL) Databank. We investigated the association between asthma-related health service utilisation, prescribing, and deaths with the 2011 Welsh Index of Multiple Deprivation (WIMD) and its domains. We studied 106,926 patients (534,630 person-years), 56.3% were female, with mean age of 47.5 years (SD = 20.3). Compared to the least deprived patients, the most deprived patients had slightly fewer total asthma-related primary care consultations per patient (incidence rate ratio [IRR] = 0.98, 95% CI 0.97-0.99, p-value < 0.001), slightly fewer routine asthma reviews (IRR = 0.98, 0.97-0.99, p-value < 0.001), lower controller-to-total asthma medication ratios (AMRs; 0.50 versus 0.56, p-value < 0.001), more asthma-related accident and emergency (A&E) attendances (IRR = 1.27, 1.10-1.46, p-value = 0.001), more asthma emergency admissions (IRR = 1.56, 1.39-1.76, p-value < 0.001), longer asthma-related hospital stay (IRR = 1.64, 1.39-1.94, p-value < 0.001), and were at higher risk of asthma-related death (risk ratio of deaths with any mention of asthma 1.56, 1.18-2.07, p-value = 0.002). Study limitations include the deprivation index being area based and the potential for residual confounders and mediators.<h4>Conclusions</h4>In this study, we observed that the most deprived asthma patients in Wales had different prescribing patterns, more A&E attendances, more emergency hospital admissions, and substantially higher risk of death. Interventions specifically designed to improve treatment and outcomes for these disadvantaged groups are urgently needed.",
+    "laySummary": "",
+    "urls": "pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003497&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003497; html:https://europepmc.org/articles/PMC7880491; pdf:https://europepmc.org/articles/PMC7880491?pdf=render"
+  },
   {
     "id": "37736873",
     "doi": "https://doi.org/10.1002/ehf2.14527",
@@ -14024,6 +14041,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/11/5/e049964.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-049964; html:https://europepmc.org/articles/PMC8103393; pdf:https://europepmc.org/articles/PMC8103393?pdf=render"
   },
+  {
+    "id": "34141852",
+    "doi": "https://doi.org/10.1016/j.ssmph.2021.100828",
+    "title": "Media representations of opposition to the 'junk food advertising ban' on the Transport for London (TfL) network: A thematic content analysis of UK news and trade press.",
+    "authorString": "Thompson C, Clary C, Er V, Adams J, Boyland E, Burgoine T, Cornelsen L, de Vocht F, Egan M, Lake AA, Lock K, Mytton O, Petticrew M, White M, Yau A, Cummins S.",
+    "authorAffiliations": "",
+    "journalTitle": "SSM - population health",
+    "pubYear": "2021",
+    "date": "2021-05-27",
+    "isOpenAccess": "Y",
+    "keywords": "Regulation; Media; Advertising; Childhood Obesity",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Advertising of less healthy foods and drinks is hypothesised to be associated with obesity in adults and children. In February 2019, Transport for London implemented restrictions on advertisements for foods and beverages high in fat, salt or sugar across its network as part of a city-wide strategy to tackle childhood obesity. The policy was extensively debated in the press. This paper identifies arguments for and against the restrictions. Focusing on arguments against the restrictions, it then goes on to deconstruct the discursive strategies underpinning them.<h4>Methods</h4>A qualitative thematic content analysis of media coverage of the restrictions (the 'ban') in UK newspapers and trade press was followed by a document analysis of arguments against the ban. A search period of March 1, 2018 to May 31, 2019 covered: (i) the launch of the public consultation on the ban in May 2018; (ii) the announcement of the ban in November 2018; and (iii) its implementation in February 2019. A systematic search of printed and online publications in English distributed in the UK or published on UK-specific websites identified 152 articles.<h4>Results</h4>Arguments in favour of the ban focused on inequalities and childhood obesity. Arguments against the ban centred on two claims: that childhood obesity was not the 'right' priority; and that an advertising ban was not an effective way to address childhood obesity. These claims were justified via three discursive approaches: (i) claiming more 'important' priorities for action; (ii) disputing the science behind the ban; (iii) emphasising potential financial costs of the ban.<h4>Conclusion</h4>The discursive tactics used in media sources to argue against the ban draw on frames widely used by unhealthy commodities industries in response to structural public health interventions. Our analyses highlight the need for interventions to be framed in ways that can pre-emptively counter common criticisms.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.ssmph.2021.100828; doi:https://doi.org/10.1016/j.ssmph.2021.100828; html:https://europepmc.org/articles/PMC8184652; pdf:https://europepmc.org/articles/PMC8184652?pdf=render"
+  },
   {
     "id": "32856160",
     "doi": "https://doi.org/10.1007/s10654-020-00677-6",
@@ -14059,21 +14093,21 @@
     "urls": "doi:https://doi.org/10.1161/CIRCEP.123.012570"
   },
   {
-    "id": "34141852",
-    "doi": "https://doi.org/10.1016/j.ssmph.2021.100828",
-    "title": "Media representations of opposition to the 'junk food advertising ban' on the Transport for London (TfL) network: A thematic content analysis of UK news and trade press.",
-    "authorString": "Thompson C, Clary C, Er V, Adams J, Boyland E, Burgoine T, Cornelsen L, de Vocht F, Egan M, Lake AA, Lock K, Mytton O, Petticrew M, White M, Yau A, Cummins S.",
+    "id": "34556677",
+    "doi": "https://doi.org/10.1038/s41598-021-96189-8",
+    "title": "Combining multi-site magnetic resonance imaging with machine learning predicts survival in pediatric brain tumors.",
+    "authorString": "Grist JT, Withey S, Bennett C, Rose HEL, MacPherson L, Oates A, Powell S, Novak J, Abernethy L, Pizer B, Bailey S, Clifford SC, Mitra D, Arvanitis TN, Auer DP, Avula S, Grundy R, Peet AC.",
     "authorAffiliations": "",
-    "journalTitle": "SSM - population health",
+    "journalTitle": "Scientific reports",
     "pubYear": "2021",
-    "date": "2021-05-27",
+    "date": "2021-09-23",
     "isOpenAccess": "Y",
-    "keywords": "Regulation; Media; Advertising; Childhood Obesity",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Advertising of less healthy foods and drinks is hypothesised to be associated with obesity in adults and children. In February 2019, Transport for London implemented restrictions on advertisements for foods and beverages high in fat, salt or sugar across its network as part of a city-wide strategy to tackle childhood obesity. The policy was extensively debated in the press. This paper identifies arguments for and against the restrictions. Focusing on arguments against the restrictions, it then goes on to deconstruct the discursive strategies underpinning them.<h4>Methods</h4>A qualitative thematic content analysis of media coverage of the restrictions (the 'ban') in UK newspapers and trade press was followed by a document analysis of arguments against the ban. A search period of March 1, 2018 to May 31, 2019 covered: (i) the launch of the public consultation on the ban in May 2018; (ii) the announcement of the ban in November 2018; and (iii) its implementation in February 2019. A systematic search of printed and online publications in English distributed in the UK or published on UK-specific websites identified 152 articles.<h4>Results</h4>Arguments in favour of the ban focused on inequalities and childhood obesity. Arguments against the ban centred on two claims: that childhood obesity was not the 'right' priority; and that an advertising ban was not an effective way to address childhood obesity. These claims were justified via three discursive approaches: (i) claiming more 'important' priorities for action; (ii) disputing the science behind the ban; (iii) emphasising potential financial costs of the ban.<h4>Conclusion</h4>The discursive tactics used in media sources to argue against the ban draw on frames widely used by unhealthy commodities industries in response to structural public health interventions. Our analyses highlight the need for interventions to be framed in ways that can pre-emptively counter common criticisms.",
+    "abstract": "Brain tumors represent the highest cause of mortality in the pediatric oncological population. Diagnosis is commonly performed with magnetic resonance imaging. Survival biomarkers are challenging to identify due to the relatively low numbers of individual tumor types. 69 children with biopsy-confirmed brain tumors were recruited into this study. All participants had perfusion and diffusion weighted imaging performed at diagnosis. Imaging data were processed using conventional methods, and a Bayesian survival analysis performed. Unsupervised and supervised machine learning were performed with the survival features, to determine novel sub-groups related to survival. Sub-group analysis was undertaken to understand differences in imaging features. Survival analysis showed that a combination of diffusion and perfusion imaging were able to determine two novel sub-groups of brain tumors with different survival characteristics (p\u2009<\u20090.01), which were subsequently classified with high accuracy (98%) by a neural network. Analysis of high-grade tumors showed a marked difference in survival (p\u2009=\u20090.029) between the two clusters with high risk and low risk imaging features. This study has developed a novel model of survival for pediatric brain tumors. Tumor perfusion plays a key role in determining survival and should be considered as a high priority for future imaging protocols.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.ssmph.2021.100828; doi:https://doi.org/10.1016/j.ssmph.2021.100828; html:https://europepmc.org/articles/PMC8184652; pdf:https://europepmc.org/articles/PMC8184652?pdf=render"
+    "urls": "pdf:https://www.nature.com/articles/s41598-021-96189-8.pdf; doi:https://doi.org/10.1038/s41598-021-96189-8; html:https://europepmc.org/articles/PMC8460620; pdf:https://europepmc.org/articles/PMC8460620?pdf=render"
   },
   {
     "id": "35814295",
@@ -14092,23 +14126,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s43856-022-00146-z.pdf; doi:https://doi.org/10.1038/s43856-022-00146-z; html:https://europepmc.org/articles/PMC9259560; pdf:https://europepmc.org/articles/PMC9259560?pdf=render"
   },
-  {
-    "id": "34556677",
-    "doi": "https://doi.org/10.1038/s41598-021-96189-8",
-    "title": "Combining multi-site magnetic resonance imaging with machine learning predicts survival in pediatric brain tumors.",
-    "authorString": "Grist JT, Withey S, Bennett C, Rose HEL, MacPherson L, Oates A, Powell S, Novak J, Abernethy L, Pizer B, Bailey S, Clifford SC, Mitra D, Arvanitis TN, Auer DP, Avula S, Grundy R, Peet AC.",
-    "authorAffiliations": "",
-    "journalTitle": "Scientific reports",
-    "pubYear": "2021",
-    "date": "2021-09-23",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Brain tumors represent the highest cause of mortality in the pediatric oncological population. Diagnosis is commonly performed with magnetic resonance imaging. Survival biomarkers are challenging to identify due to the relatively low numbers of individual tumor types. 69 children with biopsy-confirmed brain tumors were recruited into this study. All participants had perfusion and diffusion weighted imaging performed at diagnosis. Imaging data were processed using conventional methods, and a Bayesian survival analysis performed. Unsupervised and supervised machine learning were performed with the survival features, to determine novel sub-groups related to survival. Sub-group analysis was undertaken to understand differences in imaging features. Survival analysis showed that a combination of diffusion and perfusion imaging were able to determine two novel sub-groups of brain tumors with different survival characteristics (p\u2009<\u20090.01), which were subsequently classified with high accuracy (98%) by a neural network. Analysis of high-grade tumors showed a marked difference in survival (p\u2009=\u20090.029) between the two clusters with high risk and low risk imaging features. This study has developed a novel model of survival for pediatric brain tumors. Tumor perfusion plays a key role in determining survival and should be considered as a high priority for future imaging protocols.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41598-021-96189-8.pdf; doi:https://doi.org/10.1038/s41598-021-96189-8; html:https://europepmc.org/articles/PMC8460620; pdf:https://europepmc.org/articles/PMC8460620?pdf=render"
-  },
   {
     "id": "33971933",
     "doi": "https://doi.org/10.1186/s13063-021-05295-5",
@@ -14177,6 +14194,23 @@
     "laySummary": "",
     "urls": "pdf:https://aura.abdn.ac.uk/bitstream/2164/16630/1/Recovery_etal_TL_Tocilizumab_In_Patients_VoR.pdf; doi:https://doi.org/10.1016/S0140-6736(21)00676-0; html:https://europepmc.org/articles/PMC8084355"
   },
+  {
+    "id": "35497059",
+    "doi": "https://doi.org/10.1016/j.eclinm.2022.101392",
+    "title": "Health conditions in adults with HIV compared with the general population: A population-based cross-sectional analysis.",
+    "authorString": "Morales DR, Moreno-Martos D, Matin N, McGettigan P.",
+    "authorAffiliations": "",
+    "journalTitle": "EClinicalMedicine",
+    "pubYear": "2022",
+    "date": "2022-04-21",
+    "isOpenAccess": "Y",
+    "keywords": "HIV; Comorbidity; Multimorbidity",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Life expectancy in adults with human immunodeficiency virus (HIV) has increased and managing other health conditions is increasingly important for patients and healthcare planning. The aim of this study was to examine the prevalence and association between different health conditions and HIV status.<h4>Methods</h4>We performed a cross-sectional analysis of adult UK Clinical Practice Research Datalink primary care electronic medical records linked to hospital admissions as of Nov 30, 2015. We examined 47 health condition groups and 304 physical and mental health conditions by HIV status, after adjustment for age, sex, social deprivation status using logistic regression.<h4>Findings</h4>There were 964 patients with HIV (61.7% male; 92.8% aged <65 years) and 941,113 non-HIV patients (49.4% male; 75.2% aged <65 years). Condition groups with the greatest prevalence in HIV that were also highly prevalent in adults without HIV included: lipid disorder (41.4% vs 40.2%), and hypertension (19.1% vs 24.6%). Following adjustment, 18 (37.5%) condition groups were more likely in adults with HIV and ten (20.8%) were less likely. Individual conditions that were less likely in adults with HIV included: atrial fibrillation (odds ratio [OR] 0.37 [95% CI 0.20-0.64]) and hypertension (OR_0.78 [0.65-0.94]); rheumatoid arthritis (OR 0.27 [0.05-0.84]); asthma (OR_0.65 (0.53-0.80]); and certain eye diseases such as macular degeneration (OR_0.30 [0.09-0.70]). Meanwhile individual conditions that were more likely included: liver fibrosis, sclerosis, and cirrhosis (OR_3.23 [1.85-5.20]); pulmonary embolism (OR_2.06 [1.15-3.36]); male infertility (OR_2.23 [1.50-3.16]) and female infertility (OR_2.01 [1.34-2.88]); bipolar disorder (OR_2.93 [1.52-5.05]) and depression (OR_1.49 [1.28-1.71]); cervical malignancy (OR_4.64 [1.15-12.15]); and infections.<h4>Interpretation</h4>Comorbidity is common in adults with HIV, with physical and mental health conditions spanning a wide spectrum. HIV management should consider multidisciplinary care models to provide optimal patient care.<h4>Funding</h4>The project was funded by the Bart's Charity; DRM was funded by a Wellcome Trust Clinical Research Career Development Fellowship; DRM and DMM received funding from the HDR-UK Precision therapeutics programme.",
+    "laySummary": "",
+    "urls": "pdf:http://www.thelancet.com/article/S2589537022001225/pdf; doi:https://doi.org/10.1016/j.eclinm.2022.101392; html:https://europepmc.org/articles/PMC9046106; pdf:https://europepmc.org/articles/PMC9046106?pdf=render"
+  },
   {
     "id": "37478175",
     "doi": "https://doi.org/10.1126/sciadv.adh8839",
@@ -14194,23 +14228,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1126/sciadv.adh8839; html:https://europepmc.org/articles/PMC10361594; pdf:https://europepmc.org/articles/PMC10361594?pdf=render"
   },
-  {
-    "id": "38388753",
-    "doi": "https://doi.org/10.1007/s00125-024-06099-3",
-    "title": "Phenotype-based targeted treatment of SGLT2 inhibitors and GLP-1 receptor agonists in type 2 diabetes.",
-    "authorString": "Cardoso P, Young KG, Nair ATN, Hopkins R, McGovern AP, Haider E, Karunaratne P, Donnelly L, Mateen BA, Sattar N, Holman RR, Bowden J, Hattersley AT, Pearson ER, Jones AG, Shields BM, McKinley TJ, Dennis JM, MASTERMIND consortium.",
-    "authorAffiliations": "",
-    "journalTitle": "Diabetologia",
-    "pubYear": "2024",
-    "date": "2024-02-22",
-    "isOpenAccess": "Y",
-    "keywords": "Type 2 diabetes; Precision Medicine; Sglt2-inhibitors; Heterogeneous Treatment Effects; Glp1-receptor Agonists; Bayesian Non-parametric Modelling",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Aims/hypothesis</h4>A precision medicine approach in type 2 diabetes could enhance targeting specific glucose-lowering therapies to individual patients most likely to benefit. We aimed to use the recently developed Bayesian causal forest (BCF) method to develop and validate an individualised treatment selection algorithm for two major type 2 diabetes drug classes, sodium-glucose cotransporter 2 inhibitors (SGLT2i) and glucagon-like peptide-1 receptor agonists (GLP1-RA).<h4>Methods</h4>We designed a predictive algorithm using BCF to estimate individual-level conditional average treatment effects for 12-month glycaemic outcome (HbA<sub>1c</sub>) between SGLT2i and GLP1-RA, based on routine clinical features of 46,394 people with type 2 diabetes in primary care in England (Clinical Practice Research Datalink; 27,319 for model development, 19,075 for hold-out validation), with additional external validation in 2252 people with type 2 diabetes from Scotland (SCI-Diabetes [Tayside & Fife]). Differences in glycaemic outcome with GLP1-RA by sex seen in clinical data were replicated in clinical trial data (HARMONY programme: liraglutide [n=389] and albiglutide [n=1682]). As secondary outcomes, we evaluated the impacts of targeting therapy based on glycaemic response on weight change, tolerability and longer-term risk of new-onset microvascular complications, macrovascular complications and adverse kidney events.<h4>Results</h4>Model development identified marked heterogeneity in glycaemic response, with 4787 (17.5%) of the development cohort having a predicted HbA<sub>1c</sub> benefit >3 mmol/mol (>0.3%) with SGLT2i over GLP1-RA and 5551 (20.3%) having a predicted HbA<sub>1c</sub> benefit >3 mmol/mol with GLP1-RA over SGLT2i. Calibration was good in hold-back validation, and external validation in an independent Scottish dataset identified clear differences in glycaemic outcomes between those predicted to benefit from each therapy. Sex, with women markedly more responsive to GLP1-RA, was identified as a major treatment effect modifier in both the UK observational datasets and in clinical trial data: HARMONY-7 liraglutide (GLP1-RA): 4.4 mmol/mol (95% credible interval [95% CrI] 2.2, 6.3) (0.4% [95% CrI 0.2, 0.6]) greater response in women than men. Targeting the two therapies based on predicted glycaemic response was also associated with improvements in short-term tolerability and long-term risk of new-onset microvascular complications.<h4>Conclusions/interpretation</h4>Precision medicine approaches can facilitate effective individualised treatment choice between SGLT2i and GLP1-RA therapies, and the use of routinely collected clinical features for treatment selection could support low-cost deployment in many countries.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1007/s00125-024-06099-3; html:https://europepmc.org/articles/PMC10955037; pdf:https://europepmc.org/articles/PMC10955037?pdf=render"
-  },
   {
     "id": "37398988",
     "doi": "https://doi.org/10.1007/s40258-023-00821-9",
@@ -14229,21 +14246,21 @@
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s40258-023-00821-9.pdf; doi:https://doi.org/10.1007/s40258-023-00821-9; html:https://europepmc.org/articles/PMC10403424; pdf:https://europepmc.org/articles/PMC10403424?pdf=render"
   },
   {
-    "id": "35497059",
-    "doi": "https://doi.org/10.1016/j.eclinm.2022.101392",
-    "title": "Health conditions in adults with HIV compared with the general population: A population-based cross-sectional analysis.",
-    "authorString": "Morales DR, Moreno-Martos D, Matin N, McGettigan P.",
+    "id": "38388753",
+    "doi": "https://doi.org/10.1007/s00125-024-06099-3",
+    "title": "Phenotype-based targeted treatment of SGLT2 inhibitors and GLP-1 receptor agonists in type 2 diabetes.",
+    "authorString": "Cardoso P, Young KG, Nair ATN, Hopkins R, McGovern AP, Haider E, Karunaratne P, Donnelly L, Mateen BA, Sattar N, Holman RR, Bowden J, Hattersley AT, Pearson ER, Jones AG, Shields BM, McKinley TJ, Dennis JM, MASTERMIND consortium.",
     "authorAffiliations": "",
-    "journalTitle": "EClinicalMedicine",
-    "pubYear": "2022",
-    "date": "2022-04-21",
+    "journalTitle": "Diabetologia",
+    "pubYear": "2024",
+    "date": "2024-02-22",
     "isOpenAccess": "Y",
-    "keywords": "HIV; Comorbidity; Multimorbidity",
+    "keywords": "Type 2 diabetes; Precision Medicine; Sglt2-inhibitors; Heterogeneous Treatment Effects; Glp1-receptor Agonists; Bayesian Non-parametric Modelling",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Life expectancy in adults with human immunodeficiency virus (HIV) has increased and managing other health conditions is increasingly important for patients and healthcare planning. The aim of this study was to examine the prevalence and association between different health conditions and HIV status.<h4>Methods</h4>We performed a cross-sectional analysis of adult UK Clinical Practice Research Datalink primary care electronic medical records linked to hospital admissions as of Nov 30, 2015. We examined 47 health condition groups and 304 physical and mental health conditions by HIV status, after adjustment for age, sex, social deprivation status using logistic regression.<h4>Findings</h4>There were 964 patients with HIV (61.7% male; 92.8% aged <65 years) and 941,113 non-HIV patients (49.4% male; 75.2% aged <65 years). Condition groups with the greatest prevalence in HIV that were also highly prevalent in adults without HIV included: lipid disorder (41.4% vs 40.2%), and hypertension (19.1% vs 24.6%). Following adjustment, 18 (37.5%) condition groups were more likely in adults with HIV and ten (20.8%) were less likely. Individual conditions that were less likely in adults with HIV included: atrial fibrillation (odds ratio [OR] 0.37 [95% CI 0.20-0.64]) and hypertension (OR_0.78 [0.65-0.94]); rheumatoid arthritis (OR 0.27 [0.05-0.84]); asthma (OR_0.65 (0.53-0.80]); and certain eye diseases such as macular degeneration (OR_0.30 [0.09-0.70]). Meanwhile individual conditions that were more likely included: liver fibrosis, sclerosis, and cirrhosis (OR_3.23 [1.85-5.20]); pulmonary embolism (OR_2.06 [1.15-3.36]); male infertility (OR_2.23 [1.50-3.16]) and female infertility (OR_2.01 [1.34-2.88]); bipolar disorder (OR_2.93 [1.52-5.05]) and depression (OR_1.49 [1.28-1.71]); cervical malignancy (OR_4.64 [1.15-12.15]); and infections.<h4>Interpretation</h4>Comorbidity is common in adults with HIV, with physical and mental health conditions spanning a wide spectrum. HIV management should consider multidisciplinary care models to provide optimal patient care.<h4>Funding</h4>The project was funded by the Bart's Charity; DRM was funded by a Wellcome Trust Clinical Research Career Development Fellowship; DRM and DMM received funding from the HDR-UK Precision therapeutics programme.",
+    "abstract": "<h4>Aims/hypothesis</h4>A precision medicine approach in type 2 diabetes could enhance targeting specific glucose-lowering therapies to individual patients most likely to benefit. We aimed to use the recently developed Bayesian causal forest (BCF) method to develop and validate an individualised treatment selection algorithm for two major type 2 diabetes drug classes, sodium-glucose cotransporter 2 inhibitors (SGLT2i) and glucagon-like peptide-1 receptor agonists (GLP1-RA).<h4>Methods</h4>We designed a predictive algorithm using BCF to estimate individual-level conditional average treatment effects for 12-month glycaemic outcome (HbA<sub>1c</sub>) between SGLT2i and GLP1-RA, based on routine clinical features of 46,394 people with type 2 diabetes in primary care in England (Clinical Practice Research Datalink; 27,319 for model development, 19,075 for hold-out validation), with additional external validation in 2252 people with type 2 diabetes from Scotland (SCI-Diabetes [Tayside & Fife]). Differences in glycaemic outcome with GLP1-RA by sex seen in clinical data were replicated in clinical trial data (HARMONY programme: liraglutide [n=389] and albiglutide [n=1682]). As secondary outcomes, we evaluated the impacts of targeting therapy based on glycaemic response on weight change, tolerability and longer-term risk of new-onset microvascular complications, macrovascular complications and adverse kidney events.<h4>Results</h4>Model development identified marked heterogeneity in glycaemic response, with 4787 (17.5%) of the development cohort having a predicted HbA<sub>1c</sub> benefit >3 mmol/mol (>0.3%) with SGLT2i over GLP1-RA and 5551 (20.3%) having a predicted HbA<sub>1c</sub> benefit >3 mmol/mol with GLP1-RA over SGLT2i. Calibration was good in hold-back validation, and external validation in an independent Scottish dataset identified clear differences in glycaemic outcomes between those predicted to benefit from each therapy. Sex, with women markedly more responsive to GLP1-RA, was identified as a major treatment effect modifier in both the UK observational datasets and in clinical trial data: HARMONY-7 liraglutide (GLP1-RA): 4.4 mmol/mol (95% credible interval [95% CrI] 2.2, 6.3) (0.4% [95% CrI 0.2, 0.6]) greater response in women than men. Targeting the two therapies based on predicted glycaemic response was also associated with improvements in short-term tolerability and long-term risk of new-onset microvascular complications.<h4>Conclusions/interpretation</h4>Precision medicine approaches can facilitate effective individualised treatment choice between SGLT2i and GLP1-RA therapies, and the use of routinely collected clinical features for treatment selection could support low-cost deployment in many countries.",
     "laySummary": "",
-    "urls": "pdf:http://www.thelancet.com/article/S2589537022001225/pdf; doi:https://doi.org/10.1016/j.eclinm.2022.101392; html:https://europepmc.org/articles/PMC9046106; pdf:https://europepmc.org/articles/PMC9046106?pdf=render"
+    "urls": "doi:https://doi.org/10.1007/s00125-024-06099-3; html:https://europepmc.org/articles/PMC10955037; pdf:https://europepmc.org/articles/PMC10955037?pdf=render"
   },
   {
     "id": "35176022",
@@ -14364,23 +14381,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/11/4/e045077.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-045077; html:https://europepmc.org/articles/PMC8057071; pdf:https://europepmc.org/articles/PMC8057071?pdf=render"
   },
-  {
-    "id": "39266635",
-    "doi": "https://doi.org/10.1038/s41598-024-68543-z",
-    "title": "Oculomic stratification of COVID-19 patients' intensive therapy unit admission status and mortality by retinal morphological findings.",
-    "authorString": "Courtie E, Taylor M, Danks D, Acharjee A, Jackson T, Logan A, Veenith T, Blanch RJ.",
-    "authorAffiliations": "",
-    "journalTitle": "Scientific reports",
-    "pubYear": "2024",
-    "date": "2024-09-12",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "To investigate if retinal thickness has predictive utility in COVID-19 outcomes by evaluating the statistical association between retinal thickness using OCT and of COVID-19-related mortality. Secondary outcomes included associations between retinal thickness and length of stay (LoS) in hospital. In this retrospective cohort study, OCT scans from 230 COVID-19 patients admitted to the Intensive Care Unit (ITU) were compared with age and gender-matched patients with pneumonia from before March 2020. Total retinal, GCL\u2009+\u2009IPL, and RNFL thicknesses were recorded, and analysed with systemic measures collected at the time of admission and mortality outcomes, using linear regression models, Pearson's R correlation, and Principal Component Analysis. Retinal thickness was significantly associated with all-time mortality on follow up in the COVID-19 group (p\u2009=\u20090.015), but not 28-day mortality (p\u2009=\u20090.151). Retinal and GCL\u2009+\u2009IPL layer thicknesses were both significantly associated with LoS in hospital for COVID-19 patients (p\u2009=\u20090.006 for both), but not for patients with pneumonia (p\u2009=\u20090.706 and 0.989 respectively). RNFL thickness was not associated with LoS in either group (COVID-19 p\u2009=\u20090.097, pneumonia p\u2009=\u20090.692). Retinal thickness associated with LoS in hospital and long-term mortality in COVID-19 patients, suggesting that retinal structure could be a surrogate marker for frailty and predictor of disease severity in this group of patients, but not in patients with pneumonia from other causes.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1038/s41598-024-68543-z; doi:https://doi.org/10.1038/s41598-024-68543-z; html:https://europepmc.org/articles/PMC11393335; pdf:https://europepmc.org/articles/PMC11393335?pdf=render"
-  },
   {
     "id": "34148732",
     "doi": "https://doi.org/10.1016/j.bja.2021.05.001",
@@ -14398,6 +14398,23 @@
     "laySummary": "",
     "urls": "pdf:http://www.bjanaesthesia.org/article/S0007091221002737/pdf; doi:https://doi.org/10.1016/j.bja.2021.05.001; html:https://europepmc.org/articles/PMC8277602; pdf:https://europepmc.org/articles/PMC8277602?pdf=render"
   },
+  {
+    "id": "39266635",
+    "doi": "https://doi.org/10.1038/s41598-024-68543-z",
+    "title": "Oculomic stratification of COVID-19 patients' intensive therapy unit admission status and mortality by retinal morphological findings.",
+    "authorString": "Courtie E, Taylor M, Danks D, Acharjee A, Jackson T, Logan A, Veenith T, Blanch RJ.",
+    "authorAffiliations": "",
+    "journalTitle": "Scientific reports",
+    "pubYear": "2024",
+    "date": "2024-09-12",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "To investigate if retinal thickness has predictive utility in COVID-19 outcomes by evaluating the statistical association between retinal thickness using OCT and of COVID-19-related mortality. Secondary outcomes included associations between retinal thickness and length of stay (LoS) in hospital. In this retrospective cohort study, OCT scans from 230 COVID-19 patients admitted to the Intensive Care Unit (ITU) were compared with age and gender-matched patients with pneumonia from before March 2020. Total retinal, GCL\u2009+\u2009IPL, and RNFL thicknesses were recorded, and analysed with systemic measures collected at the time of admission and mortality outcomes, using linear regression models, Pearson's R correlation, and Principal Component Analysis. Retinal thickness was significantly associated with all-time mortality on follow up in the COVID-19 group (p\u2009=\u20090.015), but not 28-day mortality (p\u2009=\u20090.151). Retinal and GCL\u2009+\u2009IPL layer thicknesses were both significantly associated with LoS in hospital for COVID-19 patients (p\u2009=\u20090.006 for both), but not for patients with pneumonia (p\u2009=\u20090.706 and 0.989 respectively). RNFL thickness was not associated with LoS in either group (COVID-19 p\u2009=\u20090.097, pneumonia p\u2009=\u20090.692). Retinal thickness associated with LoS in hospital and long-term mortality in COVID-19 patients, suggesting that retinal structure could be a surrogate marker for frailty and predictor of disease severity in this group of patients, but not in patients with pneumonia from other causes.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1038/s41598-024-68543-z; doi:https://doi.org/10.1038/s41598-024-68543-z; html:https://europepmc.org/articles/PMC11393335; pdf:https://europepmc.org/articles/PMC11393335?pdf=render"
+  },
   {
     "id": "36374585",
     "doi": "https://doi.org/10.1177/01410768221131897",
@@ -14442,7 +14459,7 @@
     "pubYear": "2021",
     "date": "2021-07-15",
     "isOpenAccess": "Y",
-    "keywords": "Infectious diseases; epidemiology; Public Health; Respiratory Medicine; Health Service Research; Covid-19; Long Covid; Post-Covid-19 Syndrome; Persistent Covid-19 Symptoms",
+    "keywords": "Infectious diseases; epidemiology; Public Health; Respiratory Medicine; Health Service Research; Covid-19; Long Covid; Persistent Covid-19 Symptoms; Post-Covid-19 Syndrome",
     "nationalPriorities": "",
     "healthCategories": "",
     "abstract": "Globally, there are now over 160 million confirmed cases of COVID-19 and more than 3 million deaths. While the majority of infected individuals recover, a significant proportion continue to experience symptoms and complications after their acute illness. Patients with 'long COVID' experience a wide range of physical and mental/psychological symptoms. Pooled prevalence data showed the 10 most prevalent reported symptoms were fatigue, shortness of breath, muscle pain, joint pain, headache, cough, chest pain, altered smell, altered taste and diarrhoea. Other common symptoms were cognitive impairment, memory loss, anxiety and sleep disorders. Beyond symptoms and complications, people with long COVID often reported impaired quality of life, mental health and employment issues. These individuals may require multidisciplinary care involving the long-term monitoring of symptoms, to identify potential complications, physical rehabilitation, mental health and social services support. Resilient healthcare systems are needed to ensure efficient and effective responses to future health challenges.",
@@ -14484,21 +14501,21 @@
     "urls": "doi:https://doi.org/10.1016/j.lanepe.2022.100475; doi:https://doi.org/10.1016/j.lanepe.2022.100475; html:https://europepmc.org/articles/PMC9340533; pdf:https://europepmc.org/articles/PMC9340533?pdf=render"
   },
   {
-    "id": "37080566",
-    "doi": "https://doi.org/10.1183/13993003.01720-2022",
-    "title": "Collaboration between explainable artificial intelligence and pulmonologists improves the accuracy of pulmonary function test interpretation.",
-    "authorString": "Das N, Happaerts S, Gyselinck I, Staes M, Derom E, Brusselle G, Burgos F, Contoli M, Dinh-Xuan AT, Franssen FME, Gonem S, Greening N, Haenebalcke C, Man WD, Mois\u00e9s J, Pech\u00e9 R, Poberezhets V, Quint JK, Steiner MC, Vanderhelst E, Abdo M, Topalovic M, Janssens W.",
+    "id": "31315158",
+    "doi": "https://doi.org/10.1002/cnm.3235",
+    "title": "Non-invasive coronary CT angiography-derived fractional flow reserve: A benchmark study comparing the diagnostic performance of four different computational methodologies.",
+    "authorString": "Carson JM, Pant S, Roobottom C, Alcock R, Javier Blanco P, Alberto Bulant C, Vassilevski Y, Simakov S, Gamilov T, Pryamonosov R, Liang F, Ge X, Liu Y, Nithiarasu P.",
     "authorAffiliations": "",
-    "journalTitle": "The European respiratory journal",
-    "pubYear": "2023",
-    "date": "2023-05-18",
+    "journalTitle": "International journal for numerical methods in biomedical engineering",
+    "pubYear": "2019",
+    "date": "2019-08-16",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Fractional Flow Reserve; Benchmark; Haemodynamic Models",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Few studies have investigated the collaborative potential between artificial intelligence (AI) and pulmonologists for diagnosing pulmonary disease. We hypothesised that the collaboration between a pulmonologist and AI with explanations (explainable AI (XAI)) is superior in diagnostic interpretation of pulmonary function tests (PFTs) than the pulmonologist without support.<h4>Methods</h4>The study was conducted in two phases, a monocentre study (phase 1) and a multicentre intervention study (phase 2). Each phase utilised two different sets of 24 PFT reports of patients with a clinically validated gold standard diagnosis. Each PFT was interpreted without (control) and with XAI's suggestions (intervention). Pulmonologists provided a differential diagnosis consisting of a preferential diagnosis and optionally up to three additional diagnoses. The primary end-point compared accuracy of preferential and additional diagnoses between control and intervention. Secondary end-points were the number of diagnoses in differential diagnosis, diagnostic confidence and inter-rater agreement. We also analysed how XAI influenced pulmonologists' decisions.<h4>Results</h4>In phase 1 (n=16 pulmonologists), mean preferential and differential diagnostic accuracy significantly increased by 10.4% and 9.4%, respectively, between control and intervention (p<0.001). Improvements were somewhat lower but highly significant (p<0.0001) in phase 2 (5.4% and 8.7%, respectively; n=62 pulmonologists). In both phases, the number of diagnoses in the differential diagnosis did not reduce, but diagnostic confidence and inter-rater agreement significantly increased during intervention. Pulmonologists updated their decisions with XAI's feedback and consistently improved their baseline performance if AI provided correct predictions.<h4>Conclusion</h4>A collaboration between a pulmonologist and XAI is better at interpreting PFTs than individual pulmonologists reading without XAI support or XAI alone.",
-    "laySummary": "",
-    "urls": "pdf:https://erj.ersjournals.com/content/erj/early/2023/03/15/13993003.01720-2022.full.pdf; doi:https://doi.org/10.1183/13993003.01720-2022; html:https://europepmc.org/articles/PMC10196345; pdf:https://europepmc.org/articles/PMC10196345?pdf=render"
+    "abstract": "Non-invasive coronary computed tomography (CT) angiography-derived fractional flow reserve (cFFR) is an emergent approach to determine the functional relevance of obstructive coronary lesions. Its feasibility and diagnostic performance has been reported in several studies. It is unclear if differences in sensitivity and specificity between these studies are due to study design, population, or \"computational methodology.\" We evaluate the diagnostic performance of four different computational workflows for the prediction of cFFR using a limited data set of 10 patients, three based on reduced-order modelling and one based on a 3D rigid-wall model. The results for three of these methodologies yield similar accuracy of 6.5%\u00a0to 10.5% mean absolute difference between computed and measured FFR. The main aspects of modelling which affected cFFR estimation were choice of inlet and outlet boundary conditions and estimation of flow distribution in the coronary network. One of the reduced-order models showed the lowest overall deviation from the clinical FFR measurements, indicating that reduced-order models are capable of a similar level of accuracy to a 3D model. In addition, this reduced-order model did not include a lumped pressure-drop model for a stenosis, which implies that the additional effort of isolating a stenosis and inserting a pressure-drop element in the spatial mesh may not be required for FFR estimation. The present benchmark study is the first of this kind, in which we attempt to homogenize the data required to compute FFR using mathematical models. The clinical data utilised in the cFFR workflows are made publicly available online.",
+    "laySummary": "Retrospective case series of 10 patients having coronary angiogram and invasive fractional flow reserve measurement. The authors used 4 different techniques to estimate coronary vessel flow rate and compared their measurement agreement with clinical FFA measurements and with each other. They found that all 4 methods gave different results, but one approach was more similar with the clinical gold standard. They propose this method with most worthy of further investigaiton.",
+    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cnm.3235; doi:https://doi.org/10.1002/cnm.3235; html:https://europepmc.org/articles/PMC6851543; pdf:https://europepmc.org/articles/PMC6851543?pdf=render"
   },
   {
     "id": "36384749",
@@ -14517,6 +14534,23 @@
     "laySummary": "",
     "urls": "pdf:https://heart.bmj.com/content/heartjnl/early/2022/11/15/heartjnl-2022-321733.full.pdf; doi:https://doi.org/10.1136/heartjnl-2022-321733; html:https://europepmc.org/articles/PMC10086465; pdf:https://europepmc.org/articles/PMC10086465?pdf=render"
   },
+  {
+    "id": "37080566",
+    "doi": "https://doi.org/10.1183/13993003.01720-2022",
+    "title": "Collaboration between explainable artificial intelligence and pulmonologists improves the accuracy of pulmonary function test interpretation.",
+    "authorString": "Das N, Happaerts S, Gyselinck I, Staes M, Derom E, Brusselle G, Burgos F, Contoli M, Dinh-Xuan AT, Franssen FME, Gonem S, Greening N, Haenebalcke C, Man WD, Mois\u00e9s J, Pech\u00e9 R, Poberezhets V, Quint JK, Steiner MC, Vanderhelst E, Abdo M, Topalovic M, Janssens W.",
+    "authorAffiliations": "",
+    "journalTitle": "The European respiratory journal",
+    "pubYear": "2023",
+    "date": "2023-05-18",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Few studies have investigated the collaborative potential between artificial intelligence (AI) and pulmonologists for diagnosing pulmonary disease. We hypothesised that the collaboration between a pulmonologist and AI with explanations (explainable AI (XAI)) is superior in diagnostic interpretation of pulmonary function tests (PFTs) than the pulmonologist without support.<h4>Methods</h4>The study was conducted in two phases, a monocentre study (phase 1) and a multicentre intervention study (phase 2). Each phase utilised two different sets of 24 PFT reports of patients with a clinically validated gold standard diagnosis. Each PFT was interpreted without (control) and with XAI's suggestions (intervention). Pulmonologists provided a differential diagnosis consisting of a preferential diagnosis and optionally up to three additional diagnoses. The primary end-point compared accuracy of preferential and additional diagnoses between control and intervention. Secondary end-points were the number of diagnoses in differential diagnosis, diagnostic confidence and inter-rater agreement. We also analysed how XAI influenced pulmonologists' decisions.<h4>Results</h4>In phase 1 (n=16 pulmonologists), mean preferential and differential diagnostic accuracy significantly increased by 10.4% and 9.4%, respectively, between control and intervention (p<0.001). Improvements were somewhat lower but highly significant (p<0.0001) in phase 2 (5.4% and 8.7%, respectively; n=62 pulmonologists). In both phases, the number of diagnoses in the differential diagnosis did not reduce, but diagnostic confidence and inter-rater agreement significantly increased during intervention. Pulmonologists updated their decisions with XAI's feedback and consistently improved their baseline performance if AI provided correct predictions.<h4>Conclusion</h4>A collaboration between a pulmonologist and XAI is better at interpreting PFTs than individual pulmonologists reading without XAI support or XAI alone.",
+    "laySummary": "",
+    "urls": "pdf:https://erj.ersjournals.com/content/erj/early/2023/03/15/13993003.01720-2022.full.pdf; doi:https://doi.org/10.1183/13993003.01720-2022; html:https://europepmc.org/articles/PMC10196345; pdf:https://europepmc.org/articles/PMC10196345?pdf=render"
+  },
   {
     "id": "37118449",
     "doi": "https://doi.org/10.1038/s43587-022-00224-w",
@@ -14551,23 +14585,6 @@
     "laySummary": "",
     "urls": "pdf:https://qmro.qmul.ac.uk/xmlui/bitstream/123456789/80022/2/Petersen%20Autonomic%20Cardiovascular%20Control%202022%20Accepted.pdf; doi:https://doi.org/10.1002/cphy.c210037; html:https://europepmc.org/articles/PMC10406398; pdf:https://europepmc.org/articles/PMC10406398?pdf=render; doi:https://doi.org/10.1002/cphy.c210037"
   },
-  {
-    "id": "31315158",
-    "doi": "https://doi.org/10.1002/cnm.3235",
-    "title": "Non-invasive coronary CT angiography-derived fractional flow reserve: A benchmark study comparing the diagnostic performance of four different computational methodologies.",
-    "authorString": "Carson JM, Pant S, Roobottom C, Alcock R, Javier Blanco P, Alberto Bulant C, Vassilevski Y, Simakov S, Gamilov T, Pryamonosov R, Liang F, Ge X, Liu Y, Nithiarasu P.",
-    "authorAffiliations": "",
-    "journalTitle": "International journal for numerical methods in biomedical engineering",
-    "pubYear": "2019",
-    "date": "2019-08-16",
-    "isOpenAccess": "Y",
-    "keywords": "Fractional Flow Reserve; Benchmark; Haemodynamic Models",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Non-invasive coronary computed tomography (CT) angiography-derived fractional flow reserve (cFFR) is an emergent approach to determine the functional relevance of obstructive coronary lesions. Its feasibility and diagnostic performance has been reported in several studies. It is unclear if differences in sensitivity and specificity between these studies are due to study design, population, or \"computational methodology.\" We evaluate the diagnostic performance of four different computational workflows for the prediction of cFFR using a limited data set of 10 patients, three based on reduced-order modelling and one based on a 3D rigid-wall model. The results for three of these methodologies yield similar accuracy of 6.5%\u00a0to 10.5% mean absolute difference between computed and measured FFR. The main aspects of modelling which affected cFFR estimation were choice of inlet and outlet boundary conditions and estimation of flow distribution in the coronary network. One of the reduced-order models showed the lowest overall deviation from the clinical FFR measurements, indicating that reduced-order models are capable of a similar level of accuracy to a 3D model. In addition, this reduced-order model did not include a lumped pressure-drop model for a stenosis, which implies that the additional effort of isolating a stenosis and inserting a pressure-drop element in the spatial mesh may not be required for FFR estimation. The present benchmark study is the first of this kind, in which we attempt to homogenize the data required to compute FFR using mathematical models. The clinical data utilised in the cFFR workflows are made publicly available online.",
-    "laySummary": "Retrospective case series of 10 patients having coronary angiogram and invasive fractional flow reserve measurement. The authors used 4 different techniques to estimate coronary vessel flow rate and compared their measurement agreement with clinical FFA measurements and with each other. They found that all 4 methods gave different results, but one approach was more similar with the clinical gold standard. They propose this method with most worthy of further investigaiton.",
-    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cnm.3235; doi:https://doi.org/10.1002/cnm.3235; html:https://europepmc.org/articles/PMC6851543; pdf:https://europepmc.org/articles/PMC6851543?pdf=render"
-  },
   {
     "id": "38022395",
     "doi": "https://doi.org/10.1088/2515-7620/acf81b",
@@ -14619,6 +14636,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.jbi.2021.103916; doi:https://doi.org/10.1016/j.jbi.2021.103916; html:https://europepmc.org/articles/PMC8524321"
   },
+  {
+    "id": "35256633",
+    "doi": "https://doi.org/10.1038/s41598-022-07291-4",
+    "title": "Shared genetic loci for body fat storage and adipocyte lipolysis in humans.",
+    "authorString": "Kulyt\u00e9 A, Lundb\u00e4ck V, Arner P, Strawbridge RJ, Dahlman I.",
+    "authorAffiliations": "",
+    "journalTitle": "Scientific reports",
+    "pubYear": "2022",
+    "date": "2022-03-07",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Total body fat and central fat distribution are heritable traits and well-established predictors of adverse metabolic outcomes. Lipolysis is the process responsible for the hydrolysis of triacylglycerols stored in adipocytes. To increase our understanding of the genetic regulation of body fat distribution and total body fat, we set out to determine if genetic variants associated with body mass index (BMI) or waist-hip-ratio adjusted for BMI (WHRadjBMI) in genome-wide association studies (GWAS) mediate their effect by influencing adipocyte lipolysis. We utilized data from the recent GWAS of spontaneous and isoprenaline-stimulated lipolysis in the unique GENetics of Adipocyte Lipolysis (GENiAL) cohort. GENiAL consists of 939 participants who have undergone abdominal subcutaneous adipose biopsy for the determination of spontaneous and isoprenaline-stimulated lipolysis in adipocytes. We report 11 BMI and 15 WHRadjBMI loci with SNPs displaying nominal association with lipolysis and allele-dependent gene expression in adipose tissue according to in silico analysis. Functional evaluation of candidate genes in these loci by small interfering RNAs (siRNA)-mediated knock-down in adipose-derived stem cells identified ZNF436 and NUP85 as intrinsic regulators of lipolysis consistent with the associations observed in the clinical cohorts. Furthermore, candidate genes in another BMI-locus (STX17) and two more WHRadjBMI loci (NID2, GGA3, GRB2) control lipolysis alone, or in conjunction with lipid storage, and may hereby be involved in genetic control of body fat. The findings expand our understanding of how genetic variants mediate their impact on the complex traits of fat storage and distribution.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41598-022-07291-4.pdf; doi:https://doi.org/10.1038/s41598-022-07291-4; html:https://europepmc.org/articles/PMC8901764; pdf:https://europepmc.org/articles/PMC8901764?pdf=render"
+  },
   {
     "id": "38689316",
     "doi": "https://doi.org/10.1186/s13643-024-02540-1",
@@ -14670,23 +14704,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/S0140-6736(24)00537-3"
   },
-  {
-    "id": "35256633",
-    "doi": "https://doi.org/10.1038/s41598-022-07291-4",
-    "title": "Shared genetic loci for body fat storage and adipocyte lipolysis in humans.",
-    "authorString": "Kulyt\u00e9 A, Lundb\u00e4ck V, Arner P, Strawbridge RJ, Dahlman I.",
-    "authorAffiliations": "",
-    "journalTitle": "Scientific reports",
-    "pubYear": "2022",
-    "date": "2022-03-07",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Total body fat and central fat distribution are heritable traits and well-established predictors of adverse metabolic outcomes. Lipolysis is the process responsible for the hydrolysis of triacylglycerols stored in adipocytes. To increase our understanding of the genetic regulation of body fat distribution and total body fat, we set out to determine if genetic variants associated with body mass index (BMI) or waist-hip-ratio adjusted for BMI (WHRadjBMI) in genome-wide association studies (GWAS) mediate their effect by influencing adipocyte lipolysis. We utilized data from the recent GWAS of spontaneous and isoprenaline-stimulated lipolysis in the unique GENetics of Adipocyte Lipolysis (GENiAL) cohort. GENiAL consists of 939 participants who have undergone abdominal subcutaneous adipose biopsy for the determination of spontaneous and isoprenaline-stimulated lipolysis in adipocytes. We report 11 BMI and 15 WHRadjBMI loci with SNPs displaying nominal association with lipolysis and allele-dependent gene expression in adipose tissue according to in silico analysis. Functional evaluation of candidate genes in these loci by small interfering RNAs (siRNA)-mediated knock-down in adipose-derived stem cells identified ZNF436 and NUP85 as intrinsic regulators of lipolysis consistent with the associations observed in the clinical cohorts. Furthermore, candidate genes in another BMI-locus (STX17) and two more WHRadjBMI loci (NID2, GGA3, GRB2) control lipolysis alone, or in conjunction with lipid storage, and may hereby be involved in genetic control of body fat. The findings expand our understanding of how genetic variants mediate their impact on the complex traits of fat storage and distribution.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41598-022-07291-4.pdf; doi:https://doi.org/10.1038/s41598-022-07291-4; html:https://europepmc.org/articles/PMC8901764; pdf:https://europepmc.org/articles/PMC8901764?pdf=render"
-  },
   {
     "id": "37649988",
     "doi": "https://doi.org/10.1093/jamiaopen/ooad078",
@@ -14721,6 +14738,23 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.14814/phy2.15546; doi:https://doi.org/10.14814/phy2.15546; html:https://europepmc.org/articles/PMC9768724; pdf:https://europepmc.org/articles/PMC9768724?pdf=render"
   },
+  {
+    "id": "35440469",
+    "doi": "https://doi.org/10.3399/bjgp.2022.0083",
+    "title": "Colchicine for COVID-19 in the community (PRINCIPLE): a randomised, controlled, adaptive platform trial.",
+    "authorString": "Dorward J, Yu LM, Hayward G, Saville BR, Gbinigie O, Van Hecke O, Ogburn E, Evans PH, Thomas NP, Patel MG, Richards D, Berry N, Detry MA, Saunders C, Fitzgerald M, Harris V, Shanyinde M, de Lusignan S, Andersson MI, Butler CC, Hobbs FR, PRINCIPLE Trial Collaborative Group.",
+    "authorAffiliations": "",
+    "journalTitle": "The British journal of general practice : the journal of the Royal College of General Practitioners",
+    "pubYear": "2022",
+    "date": "2022-06-30",
+    "isOpenAccess": "Y",
+    "keywords": "Colchicine; Community; Primary Health Care; Randomised Controlled Trial; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Colchicine has been proposed as a COVID-19 treatment.<h4>Aim</h4>To determine whether colchicine reduces time to recovery and COVID-19-related admissions to hospital and/or deaths among people in the community.<h4>Design and setting</h4>Prospective, multicentre, open-label, multi-arm, randomised, controlled, adaptive platform trial (PRINCIPLE).<h4>Method</h4>Adults aged \u226565 years or \u226518 years with comorbidities or shortness of breath, and unwell for \u226414 days with suspected COVID-19 in the community, were randomised to usual care, usual care plus colchicine (500 \u00b5g daily for 14 days), or usual care plus other interventions. The co-primary endpoints were time to first self-reported recovery and admission to hospital/death related to COVID-19, within 28 days, analysed using Bayesian models.<h4>Results</h4>The trial opened on 2 April 2020. Randomisation to colchicine started on 4 March 2021 and stopped on 26 May 2021 because the prespecified time to recovery futility criterion was met. The primary analysis model included 2755 participants who were SARS-CoV-2 positive, randomised to colchicine (<i>n</i> = 156), usual care (<i>n</i> = 1145), and other treatments (<i>n</i> = 1454). Time to first self-reported recovery was similar in the colchicine group compared with usual care with an estimated hazard ratio of 0.92 (95% credible interval (CrI) = 0.72 to 1.16) and an estimated increase of 1.4 days in median time to self-reported recovery for colchicine versus usual care. The probability of meaningful benefit in time to recovery was very low at 1.8%. COVID-19-related admissions to hospital/deaths were similar in the colchicine group versus usual care, with an estimated odds ratio of 0.76 (95% CrI = 0.28 to 1.89) and an estimated difference of -0.4% (95% CrI = -2.7 to 2.4).<h4>Conclusion</h4>Colchicine did not improve time to recovery in people at higher risk of complications with COVID-19 in the community.",
+    "laySummary": "",
+    "urls": "pdf:https://bjgp.org/content/bjgp/72/720/e446.full.pdf; doi:https://doi.org/10.3399/BJGP.2022.0083; html:https://europepmc.org/articles/PMC9037186; pdf:https://europepmc.org/articles/PMC9037186?pdf=render"
+  },
   {
     "id": "38216198",
     "doi": "https://doi.org/10.1136/bmjopen-2023-080410",
@@ -14755,23 +14789,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.bmj.com/content/bmj/380/bmj-2022-072808.full.pdf; doi:https://doi.org/10.1136/bmj-2022-072808; html:https://europepmc.org/articles/PMC10014664; pdf:https://europepmc.org/articles/PMC10014664?pdf=render"
   },
-  {
-    "id": "35440469",
-    "doi": "https://doi.org/10.3399/bjgp.2022.0083",
-    "title": "Colchicine for COVID-19 in the community (PRINCIPLE): a randomised, controlled, adaptive platform trial.",
-    "authorString": "Dorward J, Yu LM, Hayward G, Saville BR, Gbinigie O, Van Hecke O, Ogburn E, Evans PH, Thomas NP, Patel MG, Richards D, Berry N, Detry MA, Saunders C, Fitzgerald M, Harris V, Shanyinde M, de Lusignan S, Andersson MI, Butler CC, Hobbs FR, PRINCIPLE Trial Collaborative Group.",
-    "authorAffiliations": "",
-    "journalTitle": "The British journal of general practice : the journal of the Royal College of General Practitioners",
-    "pubYear": "2022",
-    "date": "2022-06-30",
-    "isOpenAccess": "Y",
-    "keywords": "Colchicine; Community; Primary Health Care; Randomised Controlled Trial; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Colchicine has been proposed as a COVID-19 treatment.<h4>Aim</h4>To determine whether colchicine reduces time to recovery and COVID-19-related admissions to hospital and/or deaths among people in the community.<h4>Design and setting</h4>Prospective, multicentre, open-label, multi-arm, randomised, controlled, adaptive platform trial (PRINCIPLE).<h4>Method</h4>Adults aged \u226565 years or \u226518 years with comorbidities or shortness of breath, and unwell for \u226414 days with suspected COVID-19 in the community, were randomised to usual care, usual care plus colchicine (500 \u00b5g daily for 14 days), or usual care plus other interventions. The co-primary endpoints were time to first self-reported recovery and admission to hospital/death related to COVID-19, within 28 days, analysed using Bayesian models.<h4>Results</h4>The trial opened on 2 April 2020. Randomisation to colchicine started on 4 March 2021 and stopped on 26 May 2021 because the prespecified time to recovery futility criterion was met. The primary analysis model included 2755 participants who were SARS-CoV-2 positive, randomised to colchicine (<i>n</i> = 156), usual care (<i>n</i> = 1145), and other treatments (<i>n</i> = 1454). Time to first self-reported recovery was similar in the colchicine group compared with usual care with an estimated hazard ratio of 0.92 (95% credible interval (CrI) = 0.72 to 1.16) and an estimated increase of 1.4 days in median time to self-reported recovery for colchicine versus usual care. The probability of meaningful benefit in time to recovery was very low at 1.8%. COVID-19-related admissions to hospital/deaths were similar in the colchicine group versus usual care, with an estimated odds ratio of 0.76 (95% CrI = 0.28 to 1.89) and an estimated difference of -0.4% (95% CrI = -2.7 to 2.4).<h4>Conclusion</h4>Colchicine did not improve time to recovery in people at higher risk of complications with COVID-19 in the community.",
-    "laySummary": "",
-    "urls": "pdf:https://bjgp.org/content/bjgp/72/720/e446.full.pdf; doi:https://doi.org/10.3399/BJGP.2022.0083; html:https://europepmc.org/articles/PMC9037186; pdf:https://europepmc.org/articles/PMC9037186?pdf=render"
-  },
   {
     "id": "33203640",
     "doi": "https://doi.org/10.1136/bmjopen-2020-043828",
@@ -14789,23 +14806,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/10/11/e043828.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-043828; html:https://europepmc.org/articles/PMC7674020; pdf:https://europepmc.org/articles/PMC7674020?pdf=render"
   },
-  {
-    "id": "39039249",
-    "doi": "https://doi.org/10.1038/s41591-024-03142-z",
-    "title": "Proteomic signatures improve risk prediction for common and rare diseases.",
-    "authorString": "Carrasco-Zanini J, Pietzner M, Davitte J, Surendran P, Croteau-Chonka DC, Robins C, Torralbo A, Tomlinson C, Gr\u00fcnschl\u00e4ger F, Fitzpatrick N, Ytsma C, Kanno T, Gade S, Freitag D, Ziebell F, Haas S, Denaxas S, Betts JC, Wareham NJ, Hemingway H, Scott RA, Langenberg C.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature medicine",
-    "pubYear": "2024",
-    "date": "2024-07-22",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "For many diseases there are delays in diagnosis due to a lack of objective biomarkers for disease onset. Here, in 41,931 individuals from the United Kingdom Biobank Pharma Proteomics Project, we integrated measurements of ~3,000 plasma proteins with clinical information to derive sparse prediction models for the 10-year incidence of 218 common and rare diseases (81-6,038 cases). We then compared prediction models developed using proteomic data with models developed using either basic clinical information alone or clinical information combined with data from 37 clinical assays. The predictive performance of sparse models including as few as 5 to 20 proteins was superior to the performance of models developed using basic clinical information for 67 pathologically diverse diseases (median delta C-index\u2009=\u20090.07; range\u2009=\u20090.02-0.31). Sparse protein models further outperformed models developed using basic information combined with clinical assay data for 52 diseases, including multiple myeloma, non-Hodgkin lymphoma, motor neuron disease, pulmonary fibrosis and dilated cardiomyopathy. For multiple myeloma, single-cell RNA sequencing from bone marrow in newly diagnosed patients showed that four of the five predictor proteins were expressed specifically in plasma cells, consistent with the strong predictive power of these proteins. External replication of sparse protein models in the EPIC-Norfolk study showed good generalizability for prediction of the six diseases tested. These findings show that sparse plasma protein signatures, including both disease-specific proteins and protein predictors shared across several diseases, offer clinically useful prediction of common and rare diseases.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1038/s41591-024-03142-z; html:https://europepmc.org/articles/PMC11405273; pdf:https://europepmc.org/articles/PMC11405273?pdf=render"
-  },
   {
     "id": "34217220",
     "doi": "https://doi.org/10.1186/s12872-021-02137-9",
@@ -14823,6 +14823,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmccardiovascdisord.biomedcentral.com/counter/pdf/10.1186/s12872-021-02137-9; doi:https://doi.org/10.1186/s12872-021-02137-9; html:https://europepmc.org/articles/PMC8254437; pdf:https://europepmc.org/articles/PMC8254437?pdf=render"
   },
+  {
+    "id": "39039249",
+    "doi": "https://doi.org/10.1038/s41591-024-03142-z",
+    "title": "Proteomic signatures improve risk prediction for common and rare diseases.",
+    "authorString": "Carrasco-Zanini J, Pietzner M, Davitte J, Surendran P, Croteau-Chonka DC, Robins C, Torralbo A, Tomlinson C, Gr\u00fcnschl\u00e4ger F, Fitzpatrick N, Ytsma C, Kanno T, Gade S, Freitag D, Ziebell F, Haas S, Denaxas S, Betts JC, Wareham NJ, Hemingway H, Scott RA, Langenberg C.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature medicine",
+    "pubYear": "2024",
+    "date": "2024-07-22",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "For many diseases there are delays in diagnosis due to a lack of objective biomarkers for disease onset. Here, in 41,931 individuals from the United Kingdom Biobank Pharma Proteomics Project, we integrated measurements of ~3,000 plasma proteins with clinical information to derive sparse prediction models for the 10-year incidence of 218 common and rare diseases (81-6,038 cases). We then compared prediction models developed using proteomic data with models developed using either basic clinical information alone or clinical information combined with data from 37 clinical assays. The predictive performance of sparse models including as few as 5 to 20 proteins was superior to the performance of models developed using basic clinical information for 67 pathologically diverse diseases (median delta C-index\u2009=\u20090.07; range\u2009=\u20090.02-0.31). Sparse protein models further outperformed models developed using basic information combined with clinical assay data for 52 diseases, including multiple myeloma, non-Hodgkin lymphoma, motor neuron disease, pulmonary fibrosis and dilated cardiomyopathy. For multiple myeloma, single-cell RNA sequencing from bone marrow in newly diagnosed patients showed that four of the five predictor proteins were expressed specifically in plasma cells, consistent with the strong predictive power of these proteins. External replication of sparse protein models in the EPIC-Norfolk study showed good generalizability for prediction of the six diseases tested. These findings show that sparse plasma protein signatures, including both disease-specific proteins and protein predictors shared across several diseases, offer clinically useful prediction of common and rare diseases.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1038/s41591-024-03142-z; html:https://europepmc.org/articles/PMC11405273; pdf:https://europepmc.org/articles/PMC11405273?pdf=render"
+  },
   {
     "id": "35172999",
     "doi": "https://doi.org/10.1136/bmjopen-2021-052911",
@@ -14841,21 +14858,21 @@
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/2/e052911.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-052911; html:https://europepmc.org/articles/PMC8852656; pdf:https://europepmc.org/articles/PMC8852656?pdf=render"
   },
   {
-    "id": "38102763",
-    "doi": "https://doi.org/10.1177/15353702231214253",
-    "title": "Explainable hierarchical clustering for patient subtyping and risk prediction.",
-    "authorString": "Werner E, Clark JN, Hepburn A, Bhamber RS, Ambler M, Bourdeaux CP, McWilliams CJ, Santos-Rodriguez R.",
+    "id": "32206896",
+    "doi": "https://doi.org/10.1007/s00394-020-02220-5",
+    "title": "Alcohol consumption in relation to carotid subclinical atherosclerosis and its progression: results from a European longitudinal multicentre study.",
+    "authorString": "Laguzzi F, Baldassarre D, Veglia F, Strawbridge RJ, Humphries SE, Rauramaa R, Smit AJ, Giral P, Silveira A, Tremoli E, Hamsten A, de Faire U, Frumento P, Leander K, IMPROVE Study group.",
     "authorAffiliations": "",
-    "journalTitle": "Experimental biology and medicine (Maywood, N.J.)",
-    "pubYear": "2023",
-    "date": "2023-12-15",
+    "journalTitle": "European journal of nutrition",
+    "pubYear": "2021",
+    "date": "2020-03-24",
     "isOpenAccess": "Y",
-    "keywords": "Clinical evaluation; hierarchical clustering; Mortality Prediction; Early Warning Score; Explainability; Patient Subtypes",
+    "keywords": "Atherosclerosis; epidemiology; Carotid intima-media thickness; Alcohol drinking; Progression",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "We present a pipeline in which machine learning techniques are used to automatically identify and evaluate subtypes of hospital patients admitted between 2017 and 2021 in a large UK teaching hospital. Patient clusters are determined using routinely collected hospital data, such as those used in the UK's National Early Warning Score 2 (NEWS2). An iterative, hierarchical clustering process was used to identify the minimum set of relevant features for cluster separation. With the use of state-of-the-art explainability techniques, the identified subtypes are interpreted and assigned clinical meaning, illustrating their robustness. In parallel, clinicians assessed intracluster similarities and intercluster differences of the identified patient subtypes within the context of their clinical knowledge. For each cluster, outcome prediction models were trained and their forecasting ability was illustrated against the NEWS2 of the unclustered patient cohort. These preliminary results suggest that subtype models can outperform the established NEWS2 method, providing improved prediction of patient deterioration. By considering both the computational outputs and clinician-based explanations in patient subtyping, we aim to highlight the mutual benefit of combining machine learning techniques with clinical expertise.",
+    "abstract": "<h4>Background/aim</h4>The association between alcohol consumption and subclinical atherosclerosis is still unclear. Using data from a European multicentre study, we assess subclinical atherosclerosis and its 30-month progression by carotid intima-media thickness (C-IMT) measurements, and correlate this information with self-reported data on alcohol consumption.<h4>Methods</h4>Between 2002-2004, 1772 men and 1931 women aged 54-79\u00a0years with at least three risk factors for cardiovascular disease (CVD) were recruited in Italy, France, Netherlands, Sweden, and Finland. Self-reported alcohol consumption, assessed at baseline, was categorized as follows: none (0\u00a0g/d), very-low (0\u2009-\u20095\u00a0g/d), low (>\u20095 to \u2009\u2264\u200910\u00a0g/d), moderate (>\u200910 to \u2264\u200920\u00a0g/d for women, \u2009>\u200910 to \u2264\u200930\u00a0g/d for men) and high (>\u200920\u00a0g/d for women,\u2009>\u200930\u00a0g/d for men). C-IMT was measured in millimeters at baseline and after 30\u00a0months. Measurements consisted of the mean and maximum values of the common carotids (CC), internal carotid artery (ICA), and bifurcations (Bif) and whole carotid tree. We used quantile regression to describe the associations between C-IMT measures and alcohol consumption categories, adjusting for sex, age, physical activity, education, smoking, diet, and latitude.<h4>Results</h4>Adjusted differences between median C-IMT values in different levels of alcohol consumption (vs. very-low) showed that moderate alcohol consumption was associated with lower C-IMT<sub>max</sub>[-\u20090.17(95%CI -\u20090.32; -\u20090.02)], and Bif-IMT<sub>mean</sub>[-\u20090.07(95%CI -\u20090.13; -\u20090.01)] at baseline and decreasing C-IMT<sub>mean</sub>[-\u20090.006 (95%CI -\u20090.011; -\u20090.000)], Bif-IMT<sub>mean</sub>[-\u20090.016(95%CI -\u20090.027; -\u20090.005)], ICA-IMT<sub>mean</sub>[-\u20090.009(95% -\u20090.016;\u2009-\u20090.002)] and ICA-IMT<sub>max</sub>[-\u20090.016(95%: -\u20090.032; -\u20090.000)] after 30\u00a0months. There was no evidence of departure from linearity in the association between alcohol consumption and C-IMT.<h4>Conclusion</h4>In this European population at high risk of CVD, findings show an inverse relation between moderate alcohol consumption and carotid subclinical atherosclerosis and its 30-month progression, independently of several potential confounders.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1177/15353702231214253; html:https://europepmc.org/articles/PMC10854470; pdf:https://europepmc.org/articles/PMC10854470?pdf=render"
+    "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s00394-020-02220-5.pdf; doi:https://doi.org/10.1007/s00394-020-02220-5; html:https://europepmc.org/articles/PMC7867553; pdf:https://europepmc.org/articles/PMC7867553?pdf=render"
   },
   {
     "id": "36350656",
@@ -14875,38 +14892,38 @@
     "urls": "pdf:https://academic.oup.com/nar/article-pdf/51/D1/D977/48440802/gkac1010.pdf; doi:https://doi.org/10.1093/nar/gkac1010; html:https://europepmc.org/articles/PMC9825413; pdf:https://europepmc.org/articles/PMC9825413?pdf=render"
   },
   {
-    "id": "38434152",
-    "doi": "https://doi.org/10.5334/gh.1298",
-    "title": "Characterization of Non-Ischemic Dilated Cardiomyopathy in a Native Tanzanian Cohort: MOYO Study.",
-    "authorString": "Fundikira LS, Chillo P, Alimohamed MZ, Mayala H, Kifai E, Aloyce GM, Kamuhabwa A, Kwesigabo G, van Laake LW, Asselbergs FW.",
+    "id": "38102763",
+    "doi": "https://doi.org/10.1177/15353702231214253",
+    "title": "Explainable hierarchical clustering for patient subtyping and risk prediction.",
+    "authorString": "Werner E, Clark JN, Hepburn A, Bhamber RS, Ambler M, Bourdeaux CP, McWilliams CJ, Santos-Rodriguez R.",
     "authorAffiliations": "",
-    "journalTitle": "Global heart",
-    "pubYear": "2024",
-    "date": "2024-02-29",
+    "journalTitle": "Experimental biology and medicine (Maywood, N.J.)",
+    "pubYear": "2023",
+    "date": "2023-12-15",
     "isOpenAccess": "Y",
-    "keywords": "Echocardiography; Heart Failure; Non-ischemic Dilated Cardiomyopathy",
+    "keywords": "Clinical evaluation; hierarchical clustering; Mortality Prediction; Early Warning Score; Explainability; Patient Subtypes",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Non-ischemic dilated cardiomyopathy (NIDCM) is a common cause of heart failure with progressive tendency. The disease occurs in one in every 2,500 individuals in the developed world, with high morbidity and mortality. However, detailed data on the role of NIDCM in heart failure in Tanzania is lacking.<h4>Aim</h4>To characterize NIDCM in a Tanzanian cohort with respect to demographics, clinical profile, imaging findings and management.<h4>Methods</h4>Characterization of non-ischemic dilated cardioMyOpathY in a native Tanzanian cOhort (MOYO) is a prospective cohort study of NIDCM patients seen at the Jakaya Kikwete Cardiac Institute. Patients aged \u226518 years with a clinical diagnosis of heart failure, an ejection fraction of \u226445% on echocardiography and no evidence of ischemia were enrolled. Clinical data, echocardiography, electrocardiography (ECG), coronary angiography and stress ECG information were collected from February 2020 to March 2022.<h4>Results</h4>Of 402 patients, n = 220 (54.7%) were males with a median (IQR) age of 55.0 (41.0, 66.0) years. Causes of NIDCM were presumably hypertensive n = 218 (54.2%), idiopathic n = 116 (28.9%), PPCM n = 45 (11.2%), alcoholic n = 10 (2.5%) and other causes n = 13 (3.2%). The most common presenting symptoms were dyspnea n = 342 (85.1%), with the majority of patients presenting with New York Heart Association (NYHA) Class III n = 195 (48.5%). The mean (SD) left ventricular ejection fraction (LVEF) was 29.4% (\u00b17.7), and severe systolic dysfunction (LVEF <30%) was common n = 208 (51.7%). Compared with other forms of DCM, idiopathic DCM patients were significantly younger, had more advanced NYHA class (p < 0.001) and presented more often with left bundle branch block on ECG (p = 0.0042). There was suboptimal use of novel guidelines recommended medications ARNI n = 10 (2.5%) and SGLT2 2-inhibitors n = 2 (0.5%).<h4>Conclusions</h4>In our Tanzanian cohort, the majority of patients with NIDCM have an identified underlying cause, and they present at late stages of the disease. Patients with idiopathic DCM are younger with more severe disease compared to other forms of NIDCM.",
+    "abstract": "We present a pipeline in which machine learning techniques are used to automatically identify and evaluate subtypes of hospital patients admitted between 2017 and 2021 in a large UK teaching hospital. Patient clusters are determined using routinely collected hospital data, such as those used in the UK's National Early Warning Score 2 (NEWS2). An iterative, hierarchical clustering process was used to identify the minimum set of relevant features for cluster separation. With the use of state-of-the-art explainability techniques, the identified subtypes are interpreted and assigned clinical meaning, illustrating their robustness. In parallel, clinicians assessed intracluster similarities and intercluster differences of the identified patient subtypes within the context of their clinical knowledge. For each cluster, outcome prediction models were trained and their forecasting ability was illustrated against the NEWS2 of the unclustered patient cohort. These preliminary results suggest that subtype models can outperform the established NEWS2 method, providing improved prediction of patient deterioration. By considering both the computational outputs and clinician-based explanations in patient subtyping, we aim to highlight the mutual benefit of combining machine learning techniques with clinical expertise.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.5334/gh.1298; html:https://europepmc.org/articles/PMC10906337; pdf:https://europepmc.org/articles/PMC10906337?pdf=render"
+    "urls": "doi:https://doi.org/10.1177/15353702231214253; html:https://europepmc.org/articles/PMC10854470; pdf:https://europepmc.org/articles/PMC10854470?pdf=render"
   },
   {
-    "id": "32206896",
-    "doi": "https://doi.org/10.1007/s00394-020-02220-5",
-    "title": "Alcohol consumption in relation to carotid subclinical atherosclerosis and its progression: results from a European longitudinal multicentre study.",
-    "authorString": "Laguzzi F, Baldassarre D, Veglia F, Strawbridge RJ, Humphries SE, Rauramaa R, Smit AJ, Giral P, Silveira A, Tremoli E, Hamsten A, de Faire U, Frumento P, Leander K, IMPROVE Study group.",
+    "id": "33587202",
+    "doi": "https://doi.org/10.1007/s10654-021-00722-y",
+    "title": "COVID-19 mortality in the UK Biobank cohort: revisiting and evaluating risk factors.",
+    "authorString": "Elliott J, Bodinier B, Whitaker M, Delpierre C, Vermeulen R, Tzoulaki I, Elliott P, Chadeau-Hyam M.",
     "authorAffiliations": "",
-    "journalTitle": "European journal of nutrition",
+    "journalTitle": "European journal of epidemiology",
     "pubYear": "2021",
-    "date": "2020-03-24",
+    "date": "2021-02-15",
     "isOpenAccess": "Y",
-    "keywords": "Atherosclerosis; epidemiology; Carotid intima-media thickness; Alcohol drinking; Progression",
+    "keywords": "Risk factor; Prospective Cohort; Uk Biobank; Sars-cov-2; Covid-19 Mortality",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background/aim</h4>The association between alcohol consumption and subclinical atherosclerosis is still unclear. Using data from a European multicentre study, we assess subclinical atherosclerosis and its 30-month progression by carotid intima-media thickness (C-IMT) measurements, and correlate this information with self-reported data on alcohol consumption.<h4>Methods</h4>Between 2002-2004, 1772 men and 1931 women aged 54-79\u00a0years with at least three risk factors for cardiovascular disease (CVD) were recruited in Italy, France, Netherlands, Sweden, and Finland. Self-reported alcohol consumption, assessed at baseline, was categorized as follows: none (0\u00a0g/d), very-low (0\u2009-\u20095\u00a0g/d), low (>\u20095 to \u2009\u2264\u200910\u00a0g/d), moderate (>\u200910 to \u2264\u200920\u00a0g/d for women, \u2009>\u200910 to \u2264\u200930\u00a0g/d for men) and high (>\u200920\u00a0g/d for women,\u2009>\u200930\u00a0g/d for men). C-IMT was measured in millimeters at baseline and after 30\u00a0months. Measurements consisted of the mean and maximum values of the common carotids (CC), internal carotid artery (ICA), and bifurcations (Bif) and whole carotid tree. We used quantile regression to describe the associations between C-IMT measures and alcohol consumption categories, adjusting for sex, age, physical activity, education, smoking, diet, and latitude.<h4>Results</h4>Adjusted differences between median C-IMT values in different levels of alcohol consumption (vs. very-low) showed that moderate alcohol consumption was associated with lower C-IMT<sub>max</sub>[-\u20090.17(95%CI -\u20090.32; -\u20090.02)], and Bif-IMT<sub>mean</sub>[-\u20090.07(95%CI -\u20090.13; -\u20090.01)] at baseline and decreasing C-IMT<sub>mean</sub>[-\u20090.006 (95%CI -\u20090.011; -\u20090.000)], Bif-IMT<sub>mean</sub>[-\u20090.016(95%CI -\u20090.027; -\u20090.005)], ICA-IMT<sub>mean</sub>[-\u20090.009(95% -\u20090.016;\u2009-\u20090.002)] and ICA-IMT<sub>max</sub>[-\u20090.016(95%: -\u20090.032; -\u20090.000)] after 30\u00a0months. There was no evidence of departure from linearity in the association between alcohol consumption and C-IMT.<h4>Conclusion</h4>In this European population at high risk of CVD, findings show an inverse relation between moderate alcohol consumption and carotid subclinical atherosclerosis and its 30-month progression, independently of several potential confounders.",
+    "abstract": "Most studies of severe/fatal COVID-19 risk have used routine/hospitalisation data without detailed pre-morbid characterisation. Using the community-based UK Biobank cohort, we investigate risk factors for COVID-19 mortality in comparison with non-COVID-19 mortality. We investigated demographic, social (education, income, housing, employment), lifestyle (smoking, drinking, body mass index), biological (lipids, cystatin C, vitamin D), medical (comorbidities, medications) and environmental (air pollution) data from UK Biobank (N\u2009=\u2009473,550) in relation to 459 COVID-19 and 2626 non-COVID-19 deaths to 21 September 2020. We used univariate, multivariable and penalised regression models. Age (OR\u2009=\u20092.76 [2.18-3.49] per S.D. [8.1\u00a0years], p\u2009=\u20092.6\u2009\u00d7\u200910<sup>-17</sup>), male sex (OR\u2009=\u20091.47 [1.26-1.73], p\u2009=\u20091.3\u2009\u00d7\u200910<sup>-6</sup>) and Black versus White ethnicity (OR\u2009=\u20091.21 [1.12-1.29], p\u2009=\u20093.0\u2009\u00d7\u200910<sup>-7</sup>) were independently associated with and jointly explanatory of (area under receiver operating characteristic curve, AUC\u2009=\u20090.79) increased risk of COVID-19 mortality. In multivariable regression, alongside demographic covariates, being a healthcare worker, current smoker, having cardiovascular disease, hypertension, diabetes, autoimmune disease, and oral steroid use at enrolment were independently associated with COVID-19 mortality. Penalised regression models selected income, cardiovascular disease, hypertension, diabetes, cystatin C, and oral steroid use as jointly contributing to COVID-19 mortality risk; Black ethnicity, hypertension and oral steroid use contributed to COVID-19 but not non-COVID-19 mortality. Age, male sex and Black ethnicity, as well as comorbidities and oral steroid use at enrolment were associated with increased risk of COVID-19 death. Our results suggest that previously reported associations of COVID-19 mortality with body mass index, low vitamin D, air pollutants, renin-angiotensin-aldosterone system inhibitors may be explained by the aforementioned factors.",
     "laySummary": "",
-    "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s00394-020-02220-5.pdf; doi:https://doi.org/10.1007/s00394-020-02220-5; html:https://europepmc.org/articles/PMC7867553; pdf:https://europepmc.org/articles/PMC7867553?pdf=render"
+    "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s10654-021-00722-y.pdf; doi:https://doi.org/10.1007/s10654-021-00722-y; html:https://europepmc.org/articles/PMC7882869; pdf:https://europepmc.org/articles/PMC7882869?pdf=render"
   },
   {
     "id": "33634312",
@@ -14926,21 +14943,21 @@
     "urls": "pdf:https://www.pure.ed.ac.uk/ws/files/198917679/bbab006.pdf; doi:https://doi.org/10.1093/bib/bbab006; html:https://europepmc.org/articles/PMC8425308; pdf:https://europepmc.org/articles/PMC8425308?pdf=render"
   },
   {
-    "id": "38941600",
-    "doi": "https://doi.org/10.2196/55302",
-    "title": "Longitudinal Assessment of Seasonal Impacts and Depression Associations on Circadian Rhythm Using Multimodal Wearable Sensing: Retrospective Analysis.",
-    "authorString": "Zhang Y, Folarin AA, Sun S, Cummins N, Ranjan Y, Rashid Z, Stewart C, Conde P, Sankesara H, Laiou P, Matcham F, White KM, Oetzmann C, Lamers F, Siddi S, Simblett S, Vairavan S, Myin-Germeys I, Mohr DC, Wykes T, Haro JM, Annas P, Penninx BW, Narayan VA, Hotopf M, Dobson RJ, RADAR-CNS consortium.",
+    "id": "38434152",
+    "doi": "https://doi.org/10.5334/gh.1298",
+    "title": "Characterization of Non-Ischemic Dilated Cardiomyopathy in a Native Tanzanian Cohort: MOYO Study.",
+    "authorString": "Fundikira LS, Chillo P, Alimohamed MZ, Mayala H, Kifai E, Aloyce GM, Kamuhabwa A, Kwesigabo G, van Laake LW, Asselbergs FW.",
     "authorAffiliations": "",
-    "journalTitle": "Journal of medical Internet research",
+    "journalTitle": "Global heart",
     "pubYear": "2024",
-    "date": "2024-06-28",
+    "date": "2024-02-29",
     "isOpenAccess": "Y",
-    "keywords": "Circadian rhythm; Monitoring; Mental health; Major Depressive Disorder; Biological Rhythms; Mdd; Wearable; Mhealth; Mobile Health; Digital Health",
+    "keywords": "Echocardiography; Heart Failure; Non-ischemic Dilated Cardiomyopathy",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Previous mobile health (mHealth) studies have revealed significant links between depression and circadian rhythm features measured via wearables. However, the comprehensive impact of seasonal variations was not fully considered in these studies, potentially biasing interpretations in real-world settings.<h4>Objective</h4>This study aims to explore the associations between depression severity and wearable-measured circadian rhythms while accounting for seasonal impacts.<h4>Methods</h4>Data were sourced from a large longitudinal mHealth study, wherein participants' depression severity was assessed biweekly using the 8-item Patient Health Questionnaire (PHQ-8), and participants' behaviors, including sleep, step count, and heart rate (HR), were tracked via Fitbit devices for up to 2 years. We extracted 12 circadian rhythm features from the 14-day Fitbit data preceding each PHQ-8 assessment, including cosinor variables, such as HR peak timing (HR acrophase), and nonparametric features, such as the onset of the most active continuous 10-hour period (M10 onset). To investigate the association between depression severity and circadian rhythms while also assessing the seasonal impacts, we used three nested linear mixed-effects models for each circadian rhythm feature: (1) incorporating the PHQ-8 score as an independent variable, (2) adding seasonality, and (3) adding an interaction term between season and the PHQ-8 score.<h4>Results</h4>Analyzing 10,018 PHQ-8 records alongside Fitbit data from 543 participants (n=414, 76.2% female; median age 48, IQR 32-58 years), we found that after adjusting for seasonal effects, higher PHQ-8 scores were associated with reduced daily steps (\u03b2=-93.61, P<.001), increased sleep variability (\u03b2=0.96, P<.001), and delayed circadian rhythms (ie, sleep onset: \u03b2=0.55, P=.001; sleep offset: \u03b2=1.12, P<.001; M10 onset: \u03b2=0.73, P=.003; HR acrophase: \u03b2=0.71, P=.001). Notably, the negative association with daily steps was more pronounced in spring (\u03b2 of PHQ-8 \u00d7 spring = -31.51, P=.002) and summer (\u03b2 of PHQ-8 \u00d7 summer = -42.61, P<.001) compared with winter. Additionally, the significant correlation with delayed M10 onset was observed solely in summer (\u03b2 of PHQ-8 \u00d7 summer = 1.06, P=.008). Moreover, compared with winter, participants experienced a shorter sleep duration by 16.6 minutes, an increase in daily steps by 394.5, a delay in M10 onset by 20.5 minutes, and a delay in HR peak time by 67.9 minutes during summer.<h4>Conclusions</h4>Our findings highlight significant seasonal influences on human circadian rhythms and their associations with depression, underscoring the importance of considering seasonal variations in mHealth research for real-world applications. This study also indicates the potential of wearable-measured circadian rhythms as digital biomarkers for depression.",
+    "abstract": "<h4>Background</h4>Non-ischemic dilated cardiomyopathy (NIDCM) is a common cause of heart failure with progressive tendency. The disease occurs in one in every 2,500 individuals in the developed world, with high morbidity and mortality. However, detailed data on the role of NIDCM in heart failure in Tanzania is lacking.<h4>Aim</h4>To characterize NIDCM in a Tanzanian cohort with respect to demographics, clinical profile, imaging findings and management.<h4>Methods</h4>Characterization of non-ischemic dilated cardioMyOpathY in a native Tanzanian cOhort (MOYO) is a prospective cohort study of NIDCM patients seen at the Jakaya Kikwete Cardiac Institute. Patients aged \u226518 years with a clinical diagnosis of heart failure, an ejection fraction of \u226445% on echocardiography and no evidence of ischemia were enrolled. Clinical data, echocardiography, electrocardiography (ECG), coronary angiography and stress ECG information were collected from February 2020 to March 2022.<h4>Results</h4>Of 402 patients, n = 220 (54.7%) were males with a median (IQR) age of 55.0 (41.0, 66.0) years. Causes of NIDCM were presumably hypertensive n = 218 (54.2%), idiopathic n = 116 (28.9%), PPCM n = 45 (11.2%), alcoholic n = 10 (2.5%) and other causes n = 13 (3.2%). The most common presenting symptoms were dyspnea n = 342 (85.1%), with the majority of patients presenting with New York Heart Association (NYHA) Class III n = 195 (48.5%). The mean (SD) left ventricular ejection fraction (LVEF) was 29.4% (\u00b17.7), and severe systolic dysfunction (LVEF <30%) was common n = 208 (51.7%). Compared with other forms of DCM, idiopathic DCM patients were significantly younger, had more advanced NYHA class (p < 0.001) and presented more often with left bundle branch block on ECG (p = 0.0042). There was suboptimal use of novel guidelines recommended medications ARNI n = 10 (2.5%) and SGLT2 2-inhibitors n = 2 (0.5%).<h4>Conclusions</h4>In our Tanzanian cohort, the majority of patients with NIDCM have an identified underlying cause, and they present at late stages of the disease. Patients with idiopathic DCM are younger with more severe disease compared to other forms of NIDCM.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.2196/55302; html:https://europepmc.org/articles/PMC11245656"
+    "urls": "doi:https://doi.org/10.5334/gh.1298; html:https://europepmc.org/articles/PMC10906337; pdf:https://europepmc.org/articles/PMC10906337?pdf=render"
   },
   {
     "id": "35780515",
@@ -14959,6 +14976,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.epidem.2022.100604; doi:https://doi.org/10.1016/j.epidem.2022.100604; html:https://europepmc.org/articles/PMC9220254; pdf:https://europepmc.org/articles/PMC9220254?pdf=render"
   },
+  {
+    "id": "38941600",
+    "doi": "https://doi.org/10.2196/55302",
+    "title": "Longitudinal Assessment of Seasonal Impacts and Depression Associations on Circadian Rhythm Using Multimodal Wearable Sensing: Retrospective Analysis.",
+    "authorString": "Zhang Y, Folarin AA, Sun S, Cummins N, Ranjan Y, Rashid Z, Stewart C, Conde P, Sankesara H, Laiou P, Matcham F, White KM, Oetzmann C, Lamers F, Siddi S, Simblett S, Vairavan S, Myin-Germeys I, Mohr DC, Wykes T, Haro JM, Annas P, Penninx BW, Narayan VA, Hotopf M, Dobson RJ, RADAR-CNS consortium.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of medical Internet research",
+    "pubYear": "2024",
+    "date": "2024-06-28",
+    "isOpenAccess": "Y",
+    "keywords": "Circadian rhythm; Monitoring; Mental health; Major Depressive Disorder; Biological Rhythms; Mdd; Wearable; Mhealth; Mobile Health; Digital Health",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Previous mobile health (mHealth) studies have revealed significant links between depression and circadian rhythm features measured via wearables. However, the comprehensive impact of seasonal variations was not fully considered in these studies, potentially biasing interpretations in real-world settings.<h4>Objective</h4>This study aims to explore the associations between depression severity and wearable-measured circadian rhythms while accounting for seasonal impacts.<h4>Methods</h4>Data were sourced from a large longitudinal mHealth study, wherein participants' depression severity was assessed biweekly using the 8-item Patient Health Questionnaire (PHQ-8), and participants' behaviors, including sleep, step count, and heart rate (HR), were tracked via Fitbit devices for up to 2 years. We extracted 12 circadian rhythm features from the 14-day Fitbit data preceding each PHQ-8 assessment, including cosinor variables, such as HR peak timing (HR acrophase), and nonparametric features, such as the onset of the most active continuous 10-hour period (M10 onset). To investigate the association between depression severity and circadian rhythms while also assessing the seasonal impacts, we used three nested linear mixed-effects models for each circadian rhythm feature: (1) incorporating the PHQ-8 score as an independent variable, (2) adding seasonality, and (3) adding an interaction term between season and the PHQ-8 score.<h4>Results</h4>Analyzing 10,018 PHQ-8 records alongside Fitbit data from 543 participants (n=414, 76.2% female; median age 48, IQR 32-58 years), we found that after adjusting for seasonal effects, higher PHQ-8 scores were associated with reduced daily steps (\u03b2=-93.61, P<.001), increased sleep variability (\u03b2=0.96, P<.001), and delayed circadian rhythms (ie, sleep onset: \u03b2=0.55, P=.001; sleep offset: \u03b2=1.12, P<.001; M10 onset: \u03b2=0.73, P=.003; HR acrophase: \u03b2=0.71, P=.001). Notably, the negative association with daily steps was more pronounced in spring (\u03b2 of PHQ-8 \u00d7 spring = -31.51, P=.002) and summer (\u03b2 of PHQ-8 \u00d7 summer = -42.61, P<.001) compared with winter. Additionally, the significant correlation with delayed M10 onset was observed solely in summer (\u03b2 of PHQ-8 \u00d7 summer = 1.06, P=.008). Moreover, compared with winter, participants experienced a shorter sleep duration by 16.6 minutes, an increase in daily steps by 394.5, a delay in M10 onset by 20.5 minutes, and a delay in HR peak time by 67.9 minutes during summer.<h4>Conclusions</h4>Our findings highlight significant seasonal influences on human circadian rhythms and their associations with depression, underscoring the importance of considering seasonal variations in mHealth research for real-world applications. This study also indicates the potential of wearable-measured circadian rhythms as digital biomarkers for depression.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.2196/55302; html:https://europepmc.org/articles/PMC11245656"
+  },
   {
     "id": "33635829",
     "doi": "https://doi.org/10.1530/eje-20-1163",
@@ -14976,23 +15010,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ejendo/article-pdf/184/5/637/45221794/eje-20-1163.pdf; doi:https://doi.org/10.1530/EJE-20-1163; html:https://europepmc.org/articles/PMC8052516; pdf:https://europepmc.org/articles/PMC8052516?pdf=render"
   },
-  {
-    "id": "33587202",
-    "doi": "https://doi.org/10.1007/s10654-021-00722-y",
-    "title": "COVID-19 mortality in the UK Biobank cohort: revisiting and evaluating risk factors.",
-    "authorString": "Elliott J, Bodinier B, Whitaker M, Delpierre C, Vermeulen R, Tzoulaki I, Elliott P, Chadeau-Hyam M.",
-    "authorAffiliations": "",
-    "journalTitle": "European journal of epidemiology",
-    "pubYear": "2021",
-    "date": "2021-02-15",
-    "isOpenAccess": "Y",
-    "keywords": "Risk factor; Prospective Cohort; Uk Biobank; Sars-cov-2; Covid-19 Mortality",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Most studies of severe/fatal COVID-19 risk have used routine/hospitalisation data without detailed pre-morbid characterisation. Using the community-based UK Biobank cohort, we investigate risk factors for COVID-19 mortality in comparison with non-COVID-19 mortality. We investigated demographic, social (education, income, housing, employment), lifestyle (smoking, drinking, body mass index), biological (lipids, cystatin C, vitamin D), medical (comorbidities, medications) and environmental (air pollution) data from UK Biobank (N\u2009=\u2009473,550) in relation to 459 COVID-19 and 2626 non-COVID-19 deaths to 21 September 2020. We used univariate, multivariable and penalised regression models. Age (OR\u2009=\u20092.76 [2.18-3.49] per S.D. [8.1\u00a0years], p\u2009=\u20092.6\u2009\u00d7\u200910<sup>-17</sup>), male sex (OR\u2009=\u20091.47 [1.26-1.73], p\u2009=\u20091.3\u2009\u00d7\u200910<sup>-6</sup>) and Black versus White ethnicity (OR\u2009=\u20091.21 [1.12-1.29], p\u2009=\u20093.0\u2009\u00d7\u200910<sup>-7</sup>) were independently associated with and jointly explanatory of (area under receiver operating characteristic curve, AUC\u2009=\u20090.79) increased risk of COVID-19 mortality. In multivariable regression, alongside demographic covariates, being a healthcare worker, current smoker, having cardiovascular disease, hypertension, diabetes, autoimmune disease, and oral steroid use at enrolment were independently associated with COVID-19 mortality. Penalised regression models selected income, cardiovascular disease, hypertension, diabetes, cystatin C, and oral steroid use as jointly contributing to COVID-19 mortality risk; Black ethnicity, hypertension and oral steroid use contributed to COVID-19 but not non-COVID-19 mortality. Age, male sex and Black ethnicity, as well as comorbidities and oral steroid use at enrolment were associated with increased risk of COVID-19 death. Our results suggest that previously reported associations of COVID-19 mortality with body mass index, low vitamin D, air pollutants, renin-angiotensin-aldosterone system inhibitors may be explained by the aforementioned factors.",
-    "laySummary": "",
-    "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s10654-021-00722-y.pdf; doi:https://doi.org/10.1007/s10654-021-00722-y; html:https://europepmc.org/articles/PMC7882869; pdf:https://europepmc.org/articles/PMC7882869?pdf=render"
-  },
   {
     "id": "38589621",
     "doi": "https://doi.org/10.1038/s41590-024-01778-0",
@@ -15061,23 +15078,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1177/20552076231211551; html:https://europepmc.org/articles/PMC10638880; pdf:https://europepmc.org/articles/PMC10638880?pdf=render"
   },
-  {
-    "id": "35105585",
-    "doi": "https://doi.org/10.1136/bmjopen-2021-054376",
-    "title": "Development of an algorithm to classify primary care electronic health records of alcohol consumption: experience using data linkage from UK Biobank and primary care electronic health data sources.",
-    "authorString": "Fraile-Navarro D, Azcoaga-Lorenzo A, Agrawal U, Jani B, Fagbamigbe A, Currie D, Baldacchino A, Sullivan F.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2022",
-    "date": "2022-02-01",
-    "isOpenAccess": "Y",
-    "keywords": "Public Health; Primary Care; Health Informatics",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objectives</h4>Develop a novel algorithm to categorise alcohol consumption using primary care electronic health records (EHRs) and asses its reliability by comparing this classification with self-reported alcohol consumption data obtained from the UK Biobank (UKB) cohort.<h4>Design</h4>Cross-sectional study.<h4>Setting</h4>The UKB, a population-based cohort with participants aged between 40 and 69 years recruited across the UK between 2006 and 2010.<h4>Participants</h4>UKB participants from Scotland with linked primary care data.<h4>Primary and secondary outcome measures</h4>Create a rule-based multiclass algorithm to classify alcohol consumption reported by Scottish UKB participants and compare it with their classification using data present in primary care EHRs based on Read Codes. We evaluated agreement metrics (simple agreement and kappa statistic).<h4>Results</h4>Among the Scottish UKB participants, 18\u2009838 (69%) had at least one Read Code related to alcohol consumption and were used in the classification. The agreement of alcohol consumption categories between UKB and primary care data, including assessments within 5 years was 59.6%, and kappa was 0.23 (95% CI 0.21 to 0.24). Differences in classification between the two sources were statistically significant (p<0.001); More individuals were classified as 'sensible drinkers' and in lower alcohol consumption levels in primary care records compared with the UKB. Agreement improved slightly when using only numerical values (k=0.29; 95%\u2009CI 0.27 to 0.31) and decreased when using qualitative descriptors only (k=0.18;95% CI 0.16 to 0.20).<h4>Conclusion</h4>Our algorithm classifies alcohol consumption recorded in Primary Care EHRs into discrete meaningful categories. These results suggest that alcohol consumption may be underestimated in primary care EHRs. Using numerical values (alcohol units) may improve classification when compared with qualitative descriptors.",
-    "laySummary": "",
-    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/2/e054376.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-054376; html:https://europepmc.org/articles/PMC8808438; pdf:https://europepmc.org/articles/PMC8808438?pdf=render"
-  },
   {
     "id": "33469151",
     "doi": "https://doi.org/10.1038/s42003-020-01613-w",
@@ -15113,21 +15113,21 @@
     "urls": "doi:https://doi.org/10.1136/bmjopen-2024-088600; html:https://europepmc.org/articles/PMC11487931; pdf:https://europepmc.org/articles/PMC11487931?pdf=render"
   },
   {
-    "id": "37272361",
-    "doi": "https://doi.org/10.2340/actadv.v103.5268",
-    "title": "Relationship between Eczema and Self-reported Difficulties Keeping up with School Education: A Cross-sectional Study.",
-    "authorString": "Beckman L, Hagquist C, Svensson \u00c5, Langan SM, Von Kobyletzki L.",
+    "id": "35105585",
+    "doi": "https://doi.org/10.1136/bmjopen-2021-054376",
+    "title": "Development of an algorithm to classify primary care electronic health records of alcohol consumption: experience using data linkage from UK Biobank and primary care electronic health data sources.",
+    "authorString": "Fraile-Navarro D, Azcoaga-Lorenzo A, Agrawal U, Jani B, Fagbamigbe A, Currie D, Baldacchino A, Sullivan F.",
     "authorAffiliations": "",
-    "journalTitle": "Acta dermato-venereologica",
-    "pubYear": "2023",
-    "date": "2023-06-05",
+    "journalTitle": "BMJ open",
+    "pubYear": "2022",
+    "date": "2022-02-01",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Public Health; Primary Care; Health Informatics",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Eczema is a common chronic disease that affects both children and adults, and may have an adverse impact on school performance, as it is characteristically pruritic, and hence may lead to poor concentration and inadequate sleep. The aim of this study was to elucidate the relationship between eczema and self-reported difficulties keeping up with school education. The study was based on cross-sectional questionnaire data collected in schools among all 9th graders (15-16 years old) within a Swedish county. Logistic regression analyses were used to assess the association between having eczema and self-reported difficulties keeping up with school education. A total of 2,620 pupils participated (50.1% female). An increased odds ratio (OR) of self-reported difficulties keeping up with school education was found in adolescents with eczema compared with those without eczema after adjustment for sex and\u00a0 family residence (OR 2.13, 95% confidence interval (95% CI) 1.32-3.44), and with additional adjustment for sleeping problems, attention-deficit hyperactivity disorder, allergy, rhinitis, asthma, and alcohol consumption (adjusted OR 1.78, CI 1.05-3.00). Eczema may be a relevant risk factor for difficulty keeping up with school education in adolescents. However, studies that can assess temporality, based in different settings with objective reports of both eczema and self-reported difficulties at school, are needed to confirm these findings.",
+    "abstract": "<h4>Objectives</h4>Develop a novel algorithm to categorise alcohol consumption using primary care electronic health records (EHRs) and asses its reliability by comparing this classification with self-reported alcohol consumption data obtained from the UK Biobank (UKB) cohort.<h4>Design</h4>Cross-sectional study.<h4>Setting</h4>The UKB, a population-based cohort with participants aged between 40 and 69 years recruited across the UK between 2006 and 2010.<h4>Participants</h4>UKB participants from Scotland with linked primary care data.<h4>Primary and secondary outcome measures</h4>Create a rule-based multiclass algorithm to classify alcohol consumption reported by Scottish UKB participants and compare it with their classification using data present in primary care EHRs based on Read Codes. We evaluated agreement metrics (simple agreement and kappa statistic).<h4>Results</h4>Among the Scottish UKB participants, 18\u2009838 (69%) had at least one Read Code related to alcohol consumption and were used in the classification. The agreement of alcohol consumption categories between UKB and primary care data, including assessments within 5 years was 59.6%, and kappa was 0.23 (95% CI 0.21 to 0.24). Differences in classification between the two sources were statistically significant (p<0.001); More individuals were classified as 'sensible drinkers' and in lower alcohol consumption levels in primary care records compared with the UKB. Agreement improved slightly when using only numerical values (k=0.29; 95%\u2009CI 0.27 to 0.31) and decreased when using qualitative descriptors only (k=0.18;95% CI 0.16 to 0.20).<h4>Conclusion</h4>Our algorithm classifies alcohol consumption recorded in Primary Care EHRs into discrete meaningful categories. These results suggest that alcohol consumption may be underestimated in primary care EHRs. Using numerical values (alcohol units) may improve classification when compared with qualitative descriptors.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.2340/actadv.v103.5268; html:https://europepmc.org/articles/PMC10259463; pdf:https://europepmc.org/articles/PMC10259463?pdf=render"
+    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/2/e054376.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-054376; html:https://europepmc.org/articles/PMC8808438; pdf:https://europepmc.org/articles/PMC8808438?pdf=render"
   },
   {
     "id": "32620158",
@@ -15146,6 +15146,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmcbiol.biomedcentral.com/counter/pdf/10.1186/s12915-020-00792-6; doi:https://doi.org/10.1186/s12915-020-00792-6; html:https://europepmc.org/articles/PMC7334855; pdf:https://europepmc.org/articles/PMC7334855?pdf=render"
   },
+  {
+    "id": "37272361",
+    "doi": "https://doi.org/10.2340/actadv.v103.5268",
+    "title": "Relationship between Eczema and Self-reported Difficulties Keeping up with School Education: A Cross-sectional Study.",
+    "authorString": "Beckman L, Hagquist C, Svensson \u00c5, Langan SM, Von Kobyletzki L.",
+    "authorAffiliations": "",
+    "journalTitle": "Acta dermato-venereologica",
+    "pubYear": "2023",
+    "date": "2023-06-05",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Eczema is a common chronic disease that affects both children and adults, and may have an adverse impact on school performance, as it is characteristically pruritic, and hence may lead to poor concentration and inadequate sleep. The aim of this study was to elucidate the relationship between eczema and self-reported difficulties keeping up with school education. The study was based on cross-sectional questionnaire data collected in schools among all 9th graders (15-16 years old) within a Swedish county. Logistic regression analyses were used to assess the association between having eczema and self-reported difficulties keeping up with school education. A total of 2,620 pupils participated (50.1% female). An increased odds ratio (OR) of self-reported difficulties keeping up with school education was found in adolescents with eczema compared with those without eczema after adjustment for sex and\u00a0 family residence (OR 2.13, 95% confidence interval (95% CI) 1.32-3.44), and with additional adjustment for sleeping problems, attention-deficit hyperactivity disorder, allergy, rhinitis, asthma, and alcohol consumption (adjusted OR 1.78, CI 1.05-3.00). Eczema may be a relevant risk factor for difficulty keeping up with school education in adolescents. However, studies that can assess temporality, based in different settings with objective reports of both eczema and self-reported difficulties at school, are needed to confirm these findings.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.2340/actadv.v103.5268; html:https://europepmc.org/articles/PMC10259463; pdf:https://europepmc.org/articles/PMC10259463?pdf=render"
+  },
   {
     "id": "30727941",
     "doi": "https://doi.org/10.1186/s12859-019-2633-8",
@@ -15163,6 +15180,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2633-8; doi:https://doi.org/10.1186/s12859-019-2633-8; html:https://europepmc.org/articles/PMC6364462; pdf:https://europepmc.org/articles/PMC6364462?pdf=render"
   },
+  {
+    "id": "34249083",
+    "doi": "https://doi.org/10.3389/fgene.2021.652878",
+    "title": "Polymorphism in <i>INSR</i> Locus Modifies Risk of Atrial Fibrillation in Patients on Thyroid Hormone Replacement Therapy.",
+    "authorString": "Soto-Pedre E, Siddiqui MK, Maroteau C, Dawed AY, Doney AS, Palmer CNA, Pearson ER, Leese GP.",
+    "authorAffiliations": "",
+    "journalTitle": "Frontiers in genetics",
+    "pubYear": "2021",
+    "date": "2021-06-23",
+    "isOpenAccess": "Y",
+    "keywords": "Genetics; Insulin receptor; Hypothyroidism; Atrial fibrillation; Thyroid Hormone Replacement Therapy",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Aims</h4>Atrial fibrillation (AF) is a risk for patients receiving thyroid hormone replacement therapy. No published work has focused on pharmacogenetics relevant to thyroid dysfunction and AF risk. We aimed to assess the effect of L-thyroxine on AF risk stratified by a variation in a candidate gene.<h4>Methods and results</h4>A retrospective follow-up study was done among European Caucasian patients from the Genetics of Diabetes Audit and Research in Tayside Scotland cohort (Scotland, United Kingdom). Linked data on biochemistry, prescribing, hospital admissions, demographics, and genetic biobank were used to ascertain patients on L-thyroxine and diagnosis of AF. A GWAS-identified insulin receptor-<i>INSR</i> locus (rs4804416) was the candidate gene. Cox survival models and sensitivity analyses by taking competing risk of death into account were used. Replication was performed in additional sample (The Genetics of Scottish Health Research register, GoSHARE), and meta-analyses across the results of the study and replication cohorts were done. We analyzed 962 exposed to L-thyroxine and 5,840 unexposed patients who were rs4804416 genotyped. The rarer G/G genotype was present in 18% of the study population. The total follow-up was up to 20 years, and there was a significant increased AF risk for patients homozygous carriers of the G allele exposed to L-thyroxine (RHR = 2.35, <i>P</i> = 1.6e-02). The adjusted increased risk was highest within the first 3 years of exposure (RHR = 9.10, <i>P</i> = 8.5e-04). Sensitivity analysis yielded similar results. Effects were replicated in GoSHARE (<i>n</i> = 3,190).<h4>Conclusion</h4>Homozygous G/G genotype at the <i>INSR</i> locus (rs4804416) is associated with an increased risk of AF in patients on L-thyroxine, independent of serum of free thyroxine and thyroid-stimulating hormone serum concentrations.",
+    "laySummary": "",
+    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fgene.2021.652878/pdf; doi:https://doi.org/10.3389/fgene.2021.652878; html:https://europepmc.org/articles/PMC8260687; pdf:https://europepmc.org/articles/PMC8260687?pdf=render"
+  },
   {
     "id": "31845899",
     "doi": "https://doi.org/10.2196/14782",
@@ -15181,21 +15215,21 @@
     "urls": "doi:https://doi.org/10.2196/14782; doi:https://doi.org/10.2196/14782; html:https://europepmc.org/articles/PMC6938594"
   },
   {
-    "id": "34249083",
-    "doi": "https://doi.org/10.3389/fgene.2021.652878",
-    "title": "Polymorphism in <i>INSR</i> Locus Modifies Risk of Atrial Fibrillation in Patients on Thyroid Hormone Replacement Therapy.",
-    "authorString": "Soto-Pedre E, Siddiqui MK, Maroteau C, Dawed AY, Doney AS, Palmer CNA, Pearson ER, Leese GP.",
+    "id": "34353320",
+    "doi": "https://doi.org/10.1186/s12916-021-02045-x",
+    "title": "Adverse childhood experiences and child mental health: an electronic birth cohort study.",
+    "authorString": "Lowthian E, Anthony R, Evans A, Daniel R, Long S, Bandyopadhyay A, John A, Bellis MA, Paranjothy S.",
     "authorAffiliations": "",
-    "journalTitle": "Frontiers in genetics",
+    "journalTitle": "BMC medicine",
     "pubYear": "2021",
-    "date": "2021-06-23",
+    "date": "2021-08-06",
     "isOpenAccess": "Y",
-    "keywords": "Genetics; Insulin receptor; Hypothyroidism; Atrial fibrillation; Thyroid Hormone Replacement Therapy",
+    "keywords": "Survival analysis; Cohort; Mental health; Wales; Administrative Data; Adverse Childhood Experiences",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Aims</h4>Atrial fibrillation (AF) is a risk for patients receiving thyroid hormone replacement therapy. No published work has focused on pharmacogenetics relevant to thyroid dysfunction and AF risk. We aimed to assess the effect of L-thyroxine on AF risk stratified by a variation in a candidate gene.<h4>Methods and results</h4>A retrospective follow-up study was done among European Caucasian patients from the Genetics of Diabetes Audit and Research in Tayside Scotland cohort (Scotland, United Kingdom). Linked data on biochemistry, prescribing, hospital admissions, demographics, and genetic biobank were used to ascertain patients on L-thyroxine and diagnosis of AF. A GWAS-identified insulin receptor-<i>INSR</i> locus (rs4804416) was the candidate gene. Cox survival models and sensitivity analyses by taking competing risk of death into account were used. Replication was performed in additional sample (The Genetics of Scottish Health Research register, GoSHARE), and meta-analyses across the results of the study and replication cohorts were done. We analyzed 962 exposed to L-thyroxine and 5,840 unexposed patients who were rs4804416 genotyped. The rarer G/G genotype was present in 18% of the study population. The total follow-up was up to 20 years, and there was a significant increased AF risk for patients homozygous carriers of the G allele exposed to L-thyroxine (RHR = 2.35, <i>P</i> = 1.6e-02). The adjusted increased risk was highest within the first 3 years of exposure (RHR = 9.10, <i>P</i> = 8.5e-04). Sensitivity analysis yielded similar results. Effects were replicated in GoSHARE (<i>n</i> = 3,190).<h4>Conclusion</h4>Homozygous G/G genotype at the <i>INSR</i> locus (rs4804416) is associated with an increased risk of AF in patients on L-thyroxine, independent of serum of free thyroxine and thyroid-stimulating hormone serum concentrations.",
+    "abstract": "<h4>Background</h4>Adverse childhood experiences (ACEs) are negatively associated with a range of child health outcomes. In this study, we explored associations between five individual ACEs and child mental health diagnoses or symptoms. ACEs included living with someone who had an alcohol-related problem, common mental health disorder or serious mental illness, or experienced victimisation or death of a household member.<h4>Methods</h4>We analysed data from a population-level electronic cohort of children in Wales, UK, (N = 191,035) between the years of 1998 and 2012. We used Cox regression with discrete time-varying exposure variables to model time to child mental health diagnosis during the first 15 years of life. Child mental health diagnoses include five categories: (i) externalising symptoms (anti-social behaviour), (ii) internalising symptoms (stress, anxiety, depression), (iii) developmental delay (e.g. learning disability), (iv) other (e.g. eating disorder, personality disorders),\u00a0and (v) any mental health diagnosis, which was created by combining externalising symptoms, internalising symptoms and other. Our analyses were adjusted for social deprivation and perinatal risk factors.<h4>Results</h4>There were strong univariable associations between the five individual ACEs, sociodemographic and perinatal factors (e.g. gestational weight at birth) and an increased risk of child mental health diagnoses. After adjusting for sociodemographic and perinatal aspects, there was a remaining conditional increased risk of any child mental health diagnosis, associated with victimisation (conditional hazard ratio (cHR) 1.90, CI 95% 1.34-2.69), and living with an adult with a common mental health diagnosis (cHR 1.63, CI 95% 1.52-1.75). Coefficients of product terms between ACEs and deprivation were not statistically significant.<h4>Conclusion</h4>The increased risk of child mental health diagnosis associated with victimisation, or exposure to common mental health diagnoses, and alcohol problems in the household supports the need for policy measures and intervention strategies for children and their families.",
     "laySummary": "",
-    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fgene.2021.652878/pdf; doi:https://doi.org/10.3389/fgene.2021.652878; html:https://europepmc.org/articles/PMC8260687; pdf:https://europepmc.org/articles/PMC8260687?pdf=render"
+    "urls": "pdf:https://bmcmedicine.biomedcentral.com/track/pdf/10.1186/s12916-021-02045-x; doi:https://doi.org/10.1186/s12916-021-02045-x; html:https://europepmc.org/articles/PMC8344166; pdf:https://europepmc.org/articles/PMC8344166?pdf=render"
   },
   {
     "id": "38419411",
@@ -15214,23 +15248,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/bjd/advance-article-pdf/doi/10.1093/bjd/ljae080/56794617/ljae080.pdf; doi:https://doi.org/10.1093/bjd/ljae080; html:https://europepmc.org/articles/PMC11188926; pdf:https://europepmc.org/articles/PMC11188926?pdf=render"
   },
-  {
-    "id": "34353320",
-    "doi": "https://doi.org/10.1186/s12916-021-02045-x",
-    "title": "Adverse childhood experiences and child mental health: an electronic birth cohort study.",
-    "authorString": "Lowthian E, Anthony R, Evans A, Daniel R, Long S, Bandyopadhyay A, John A, Bellis MA, Paranjothy S.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC medicine",
-    "pubYear": "2021",
-    "date": "2021-08-06",
-    "isOpenAccess": "Y",
-    "keywords": "Survival analysis; Cohort; Mental health; Wales; Administrative Data; Adverse Childhood Experiences",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Adverse childhood experiences (ACEs) are negatively associated with a range of child health outcomes. In this study, we explored associations between five individual ACEs and child mental health diagnoses or symptoms. ACEs included living with someone who had an alcohol-related problem, common mental health disorder or serious mental illness, or experienced victimisation or death of a household member.<h4>Methods</h4>We analysed data from a population-level electronic cohort of children in Wales, UK, (N = 191,035) between the years of 1998 and 2012. We used Cox regression with discrete time-varying exposure variables to model time to child mental health diagnosis during the first 15 years of life. Child mental health diagnoses include five categories: (i) externalising symptoms (anti-social behaviour), (ii) internalising symptoms (stress, anxiety, depression), (iii) developmental delay (e.g. learning disability), (iv) other (e.g. eating disorder, personality disorders),\u00a0and (v) any mental health diagnosis, which was created by combining externalising symptoms, internalising symptoms and other. Our analyses were adjusted for social deprivation and perinatal risk factors.<h4>Results</h4>There were strong univariable associations between the five individual ACEs, sociodemographic and perinatal factors (e.g. gestational weight at birth) and an increased risk of child mental health diagnoses. After adjusting for sociodemographic and perinatal aspects, there was a remaining conditional increased risk of any child mental health diagnosis, associated with victimisation (conditional hazard ratio (cHR) 1.90, CI 95% 1.34-2.69), and living with an adult with a common mental health diagnosis (cHR 1.63, CI 95% 1.52-1.75). Coefficients of product terms between ACEs and deprivation were not statistically significant.<h4>Conclusion</h4>The increased risk of child mental health diagnosis associated with victimisation, or exposure to common mental health diagnoses, and alcohol problems in the household supports the need for policy measures and intervention strategies for children and their families.",
-    "laySummary": "",
-    "urls": "pdf:https://bmcmedicine.biomedcentral.com/track/pdf/10.1186/s12916-021-02045-x; doi:https://doi.org/10.1186/s12916-021-02045-x; html:https://europepmc.org/articles/PMC8344166; pdf:https://europepmc.org/articles/PMC8344166?pdf=render"
-  },
   {
     "id": "32641105",
     "doi": "https://doi.org/10.1186/s12874-020-01025-8",
@@ -15418,23 +15435,6 @@
     "laySummary": "",
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11198649/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11198649/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC11198649; pdf:https://europepmc.org/articles/PMC11198649?pdf=render"
   },
-  {
-    "id": "37745706",
-    "doi": "https://doi.org/10.3389/fendo.2023.1266557",
-    "title": "Editorial: Integrative multi-modal, multi-omics analytics for the better understanding of metabolic diseases.",
-    "authorString": "Acharjee A, Agarwal P, Gkoutos GV.",
-    "authorAffiliations": "",
-    "journalTitle": "Frontiers in endocrinology",
-    "pubYear": "2023",
-    "date": "2023-09-08",
-    "isOpenAccess": "Y",
-    "keywords": "Biomarker; Therapeutic; Diagnostic; Metabolic Disease; Omics",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.3389/fendo.2023.1266557; html:https://europepmc.org/articles/PMC10516571; pdf:https://europepmc.org/articles/PMC10516571?pdf=render"
-  },
   {
     "id": "35932242",
     "doi": "https://doi.org/10.1093/ageing/afac176",
@@ -15452,6 +15452,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1093/ageing/afac176; doi:https://doi.org/10.1093/ageing/afac176; html:https://europepmc.org/articles/PMC9356534; pdf:https://europepmc.org/articles/PMC9356534?pdf=render"
   },
+  {
+    "id": "37745706",
+    "doi": "https://doi.org/10.3389/fendo.2023.1266557",
+    "title": "Editorial: Integrative multi-modal, multi-omics analytics for the better understanding of metabolic diseases.",
+    "authorString": "Acharjee A, Agarwal P, Gkoutos GV.",
+    "authorAffiliations": "",
+    "journalTitle": "Frontiers in endocrinology",
+    "pubYear": "2023",
+    "date": "2023-09-08",
+    "isOpenAccess": "Y",
+    "keywords": "Biomarker; Therapeutic; Diagnostic; Metabolic Disease; Omics",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.3389/fendo.2023.1266557; html:https://europepmc.org/articles/PMC10516571; pdf:https://europepmc.org/articles/PMC10516571?pdf=render"
+  },
   {
     "id": "35079022",
     "doi": "https://doi.org/10.1038/s41467-022-28157-3",
@@ -15486,23 +15503,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.3389/fcvm.2023.1141026; html:https://europepmc.org/articles/PMC10541220; pdf:https://europepmc.org/articles/PMC10541220?pdf=render"
   },
-  {
-    "id": "39374974",
-    "doi": "https://doi.org/10.1136/bmj-2024-080528",
-    "title": "Non-pharmaceutical interventions: evaluating challenges and priorities for future health shocks.",
-    "authorString": "Majeed A, Quint JK, Bhatt S, Davies F, Islam N.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ (Clinical research ed.)",
-    "pubYear": "2024",
-    "date": "2024-10-07",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1136/bmj-2024-080528; html:https://europepmc.org/articles/PMC11450877"
-  },
   {
     "id": "31971603",
     "doi": "https://doi.org/10.2340/00015555-3384",
@@ -15520,6 +15520,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.2340/00015555-3384; doi:https://doi.org/10.2340/00015555-3384; html:https://europepmc.org/articles/PMC9128944; pdf:https://europepmc.org/articles/PMC9128944?pdf=render"
   },
+  {
+    "id": "39374974",
+    "doi": "https://doi.org/10.1136/bmj-2024-080528",
+    "title": "Non-pharmaceutical interventions: evaluating challenges and priorities for future health shocks.",
+    "authorString": "Majeed A, Quint JK, Bhatt S, Davies F, Islam N.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ (Clinical research ed.)",
+    "pubYear": "2024",
+    "date": "2024-10-07",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1136/bmj-2024-080528; html:https://europepmc.org/articles/PMC11450877"
+  },
   {
     "id": "38727134",
     "doi": "https://doi.org/10.1002/epi4.12957",
@@ -15554,23 +15571,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.cct.2023.107162; doi:https://doi.org/10.1016/j.cct.2023.107162"
   },
-  {
-    "id": "35216844",
-    "doi": "https://doi.org/10.1016/j.vaccine.2022.02.056",
-    "title": "Localising vaccination services: Qualitative insights on public health and minority group collaborations to co-deliver coronavirus vaccines.",
-    "authorString": "Kasstan B, Mounier-Jack S, Letley L, Gaskell KM, Roberts CH, Stone NRH, Lal S, Eggo RM, Marks M, Chantler T.",
-    "authorAffiliations": "",
-    "journalTitle": "Vaccine",
-    "pubYear": "2022",
-    "date": "2022-02-17",
-    "isOpenAccess": "Y",
-    "keywords": "Qualitative Research; Ethnic Minorities; Coronavirus Vaccine; Localising Services; Public Health Collaboration",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Ethnic and religious minorities have been disproportionately affected by the SARS-CoV-2 pandemic and are less likely to accept coronavirus vaccinations. Orthodox (Haredi) Jewish neighbourhoods in England experienced high incidences of SARS-CoV-2 in 2020-21 and measles outbreaks (2018-19) due to suboptimal childhood vaccination coverage. The objective of our study was to explore how the coronavirus vaccination programme (CVP) was co-delivered between public health services and an Orthodox Jewish health organisation. Methods included 28 semi-structured interviews conducted virtually with public health professionals, community welfare and religious representatives, and household members. We examined CVP delivery from the perspectives of those involved in organising services and vaccine beneficiaries. Interview data was contextualised within debates of the CVP in Orthodox (Haredi) Jewish print and social media. Thematic analysis generated five considerations: i) Prior immunisation-related collaboration with public health services carved a role for Jewish health organisations to host and promote coronavirus vaccination sessions, distribute appointments, and administer vaccines ii) Public health services maintained responsibility for training, logistics, and maintaining vaccination records; iii) The localised approach to service delivery promoted vaccination in a minority with historically suboptimal levels of coverage; iv) Co-delivery promoted trust in the CVP, though a minority of participants maintained concerns around safety; v) Provision of CVP information and stakeholders' response to situated (context-specific) challenges and concerns. Drawing on this example of CVP co-delivery, we propose that a localised approach to delivering immunisation programmes could address service provision gaps in ways that involve trusted community organisations. Localisation of vaccination services can include communication or implementation strategies, but both approaches involve consideration of investment, engagement and coordination, which are not cost-neutral. Localising vaccination services in collaboration with welfare groups raises opportunities for the on-going CVP and other immunisation programmes, and constitutes an opportunity for ethnic and religious minorities to collaborate in safeguarding community health.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.vaccine.2022.02.056; doi:https://doi.org/10.1016/j.vaccine.2022.02.056; html:https://europepmc.org/articles/PMC8849863"
-  },
   {
     "id": "38286672",
     "doi": "https://doi.org/10.1136/bmjopen-2023-073582",
@@ -15588,6 +15588,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1136/bmjopen-2023-073582; html:https://europepmc.org/articles/PMC10826590; pdf:https://europepmc.org/articles/PMC10826590?pdf=render"
   },
+  {
+    "id": "35216844",
+    "doi": "https://doi.org/10.1016/j.vaccine.2022.02.056",
+    "title": "Localising vaccination services: Qualitative insights on public health and minority group collaborations to co-deliver coronavirus vaccines.",
+    "authorString": "Kasstan B, Mounier-Jack S, Letley L, Gaskell KM, Roberts CH, Stone NRH, Lal S, Eggo RM, Marks M, Chantler T.",
+    "authorAffiliations": "",
+    "journalTitle": "Vaccine",
+    "pubYear": "2022",
+    "date": "2022-02-17",
+    "isOpenAccess": "Y",
+    "keywords": "Qualitative Research; Ethnic Minorities; Coronavirus Vaccine; Localising Services; Public Health Collaboration",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Ethnic and religious minorities have been disproportionately affected by the SARS-CoV-2 pandemic and are less likely to accept coronavirus vaccinations. Orthodox (Haredi) Jewish neighbourhoods in England experienced high incidences of SARS-CoV-2 in 2020-21 and measles outbreaks (2018-19) due to suboptimal childhood vaccination coverage. The objective of our study was to explore how the coronavirus vaccination programme (CVP) was co-delivered between public health services and an Orthodox Jewish health organisation. Methods included 28 semi-structured interviews conducted virtually with public health professionals, community welfare and religious representatives, and household members. We examined CVP delivery from the perspectives of those involved in organising services and vaccine beneficiaries. Interview data was contextualised within debates of the CVP in Orthodox (Haredi) Jewish print and social media. Thematic analysis generated five considerations: i) Prior immunisation-related collaboration with public health services carved a role for Jewish health organisations to host and promote coronavirus vaccination sessions, distribute appointments, and administer vaccines ii) Public health services maintained responsibility for training, logistics, and maintaining vaccination records; iii) The localised approach to service delivery promoted vaccination in a minority with historically suboptimal levels of coverage; iv) Co-delivery promoted trust in the CVP, though a minority of participants maintained concerns around safety; v) Provision of CVP information and stakeholders' response to situated (context-specific) challenges and concerns. Drawing on this example of CVP co-delivery, we propose that a localised approach to delivering immunisation programmes could address service provision gaps in ways that involve trusted community organisations. Localisation of vaccination services can include communication or implementation strategies, but both approaches involve consideration of investment, engagement and coordination, which are not cost-neutral. Localising vaccination services in collaboration with welfare groups raises opportunities for the on-going CVP and other immunisation programmes, and constitutes an opportunity for ethnic and religious minorities to collaborate in safeguarding community health.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.vaccine.2022.02.056; doi:https://doi.org/10.1016/j.vaccine.2022.02.056; html:https://europepmc.org/articles/PMC8849863"
+  },
   {
     "id": "35074819",
     "doi": "https://doi.org/10.1136/bmjopen-2021-054414",
@@ -15707,23 +15724,6 @@
     "laySummary": "",
     "urls": "pdf:https://genomebiology.biomedcentral.com/counter/pdf/10.1186/s13059-022-02745-4; doi:https://doi.org/10.1186/s13059-022-02745-4; html:https://europepmc.org/articles/PMC9394047; pdf:https://europepmc.org/articles/PMC9394047?pdf=render"
   },
-  {
-    "id": "35580876",
-    "doi": "https://doi.org/10.1136/bmj-2021-069704",
-    "title": "Long term impact of prophylactic antibiotic use before incision versus after cord clamping on children born by caesarean section: longitudinal study of UK electronic health records.",
-    "authorString": "\u0160umilo D, Nirantharakumar K, Willis BH, Rudge GM, Martin J, Gokhale K, Thayakaran R, Adderley NJ, Chandan JS, Okoth K, Harris IM, Hewston R, Skrybant M, Deeks JJ, Brocklehurst P.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ (Clinical research ed.)",
-    "pubYear": "2022",
-    "date": "2022-05-17",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objective</h4>To investigate the impact on child health up to age 5 years of a policy to use antibiotic prophylaxis for caesarean section before incision compared with after cord clamping.<h4>Design</h4>Observational controlled interrupted time series study.<h4>Setting</h4>UK primary and secondary care.<h4>Participants</h4>515\u2009945 children born in 2006-18 with linked maternal records and registered with general practices contributing to two UK primary care databases (The Health Improvement Network and Clinical Practice Research Datalink), and 7\u2009147\u2009884 children with linked maternal records in the Hospital Episode Statistics database covering England, of which 3\u2009945\u2009351 were linked to hospitals that reported the year of policy change to administer prophylactic antibiotics for caesarean section before incision rather than after cord clamping.<h4>Intervention</h4>Fetal exposure to antibiotics shortly before birth (using pre-incision antibiotic policy as proxy) compared with no exposure.<h4>Main outcome measures</h4>The primary outcomes were incidence rate ratios of asthma and eczema in children born by caesarean section when pre-incision prophylactic antibiotics were recommended compared with those born when antibiotics were administered post-cord clamping, adjusted for temporal changes in the incidence rates in children born vaginally.<h4>Results</h4>Prophylactic antibiotics administered before incision for caesarean section compared with after cord clamping were not associated with a significantly higher risk of asthma (incidence rate ratio 0.91, 95% confidence interval 0.78 to 1.05) or eczema (0.98, 0.94 to 1.03), including asthma and eczema resulting in hospital admission (1.05, 0.99 to 1.11 and 0.96, 0.71 to 1.29, respectively), up to age 5 years.<h4>Conclusions</h4>This study found no evidence of an association between pre-incision prophylactic antibiotic use and risk of asthma and eczema in early childhood in children born by caesarean section.",
-    "laySummary": "",
-    "urls": "pdf:https://www.bmj.com/content/bmj/377/bmj-2021-069704.full.pdf; doi:https://doi.org/10.1136/bmj-2021-069704; html:https://europepmc.org/articles/PMC9112858"
-  },
   {
     "id": "33436761",
     "doi": "https://doi.org/10.1038/s41598-020-79964-x",
@@ -15741,6 +15741,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41598-020-79964-x.pdf; doi:https://doi.org/10.1038/s41598-020-79964-x; html:https://europepmc.org/articles/PMC7804422; pdf:https://europepmc.org/articles/PMC7804422?pdf=render"
   },
+  {
+    "id": "35580876",
+    "doi": "https://doi.org/10.1136/bmj-2021-069704",
+    "title": "Long term impact of prophylactic antibiotic use before incision versus after cord clamping on children born by caesarean section: longitudinal study of UK electronic health records.",
+    "authorString": "\u0160umilo D, Nirantharakumar K, Willis BH, Rudge GM, Martin J, Gokhale K, Thayakaran R, Adderley NJ, Chandan JS, Okoth K, Harris IM, Hewston R, Skrybant M, Deeks JJ, Brocklehurst P.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ (Clinical research ed.)",
+    "pubYear": "2022",
+    "date": "2022-05-17",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>To investigate the impact on child health up to age 5 years of a policy to use antibiotic prophylaxis for caesarean section before incision compared with after cord clamping.<h4>Design</h4>Observational controlled interrupted time series study.<h4>Setting</h4>UK primary and secondary care.<h4>Participants</h4>515\u2009945 children born in 2006-18 with linked maternal records and registered with general practices contributing to two UK primary care databases (The Health Improvement Network and Clinical Practice Research Datalink), and 7\u2009147\u2009884 children with linked maternal records in the Hospital Episode Statistics database covering England, of which 3\u2009945\u2009351 were linked to hospitals that reported the year of policy change to administer prophylactic antibiotics for caesarean section before incision rather than after cord clamping.<h4>Intervention</h4>Fetal exposure to antibiotics shortly before birth (using pre-incision antibiotic policy as proxy) compared with no exposure.<h4>Main outcome measures</h4>The primary outcomes were incidence rate ratios of asthma and eczema in children born by caesarean section when pre-incision prophylactic antibiotics were recommended compared with those born when antibiotics were administered post-cord clamping, adjusted for temporal changes in the incidence rates in children born vaginally.<h4>Results</h4>Prophylactic antibiotics administered before incision for caesarean section compared with after cord clamping were not associated with a significantly higher risk of asthma (incidence rate ratio 0.91, 95% confidence interval 0.78 to 1.05) or eczema (0.98, 0.94 to 1.03), including asthma and eczema resulting in hospital admission (1.05, 0.99 to 1.11 and 0.96, 0.71 to 1.29, respectively), up to age 5 years.<h4>Conclusions</h4>This study found no evidence of an association between pre-incision prophylactic antibiotic use and risk of asthma and eczema in early childhood in children born by caesarean section.",
+    "laySummary": "",
+    "urls": "pdf:https://www.bmj.com/content/bmj/377/bmj-2021-069704.full.pdf; doi:https://doi.org/10.1136/bmj-2021-069704; html:https://europepmc.org/articles/PMC9112858"
+  },
   {
     "id": "33711543",
     "doi": "https://doi.org/10.1016/j.jbi.2021.103728",
@@ -15758,23 +15775,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.jbi.2021.103728; doi:https://doi.org/10.1016/j.jbi.2021.103728"
   },
-  {
-    "id": "35802764",
-    "doi": "https://doi.org/10.7189/jogh.12.05025",
-    "title": "COVID-19 vaccine effectiveness against symptomatic SARS-CoV-2 infection and severe COVID-19 outcomes from Delta AY.4.2: Cohort and test-negative study of 5.4 million individuals in Scotland.",
-    "authorString": "Kerr S, Vasileiou E, Robertson C, Sheikh A.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of global health",
-    "pubYear": "2022",
-    "date": "2022-07-09",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>In July 2021, a new variant of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in the Delta lineage was detected in the United Kingdom (UK), named AY.4.2 or \"Delta plus\". By October 2021, the AY.4.2 variant accounted for approximately 10-11% of cases in the UK. AY.4.2 was designated as a variant under investigation by the UK Health and Security Agency on 20 October 2021. This study aimed to investigate vaccine effectiveness (VE) against symptomatic COVID-19 (Coronavirus disease 2019) infection and COVID-19 hospitalisation/death for the AY.4.2 variant.<h4>Methods</h4>We used the Scotland-wide Early Pandemic Evaluation and Enhanced Surveillance (EAVE-II) platform to estimate the VE of the ChAdOx1, BNT162b2, and mRNA-1273 vaccines against symptomatic infection and severe COVID-19 outcomes in adults. The study was conducted from June 8 to October 25, 2021. We used a test-negative design (TND) to estimate VE against reverse transcriptase polymerase chain reaction (RT-PCR) confirmed symptomatic SARS-CoV-2 infection while adjusting for sex, socioeconomic status, number of coexisting conditions, and splines in time and age. We also performed a cohort study using a Cox proportional hazards model to estimate VE against a composite outcome of COVID-19 hospital admission or death, with the same adjustments.<h4>Results</h4>We found an overall VE against symptomatic SARS-CoV-2 infection due to AY.4.2 of 73% (95% confidence interval (CI)\u2009=\u200962-81) for >14 days post-second vaccine dose. Good protection against AY.4.2 symptomatic infection was observed for BNT162b2, ChAdOx1, and mRNA-1273. In unvaccinated individuals, the hazard ratio (HR) for COVID-19 hospital admission or death from AY.4.2 among community detected cases was 1.77 (95% CI\u2009=\u20091.02-3.07) relative to unvaccinated individuals who were infected with Delta, after adjusting for multiple potential confounders. VE against AY.4.2 COVID-19 admissions or deaths was 87% (95% CI\u2009=\u200974-93) >28 days post-second vaccination relative to unvaccinated.<h4>Conclusions</h4>We found that AY.4.2 was associated with an increased risk of COVID-19 hospitalisations or deaths in unvaccinated individuals compared with Delta and that vaccination provided substantial protection against symptomatic SARS-CoV-2 and severe COVID-19 outcomes following Delta AY.4.2 infection. High levels of vaccine uptake and protection offered by existing vaccines, as well as the rapid emergence of the Omicron variant may have contributed to the AY.4.2 variant never progressing to a variant of concern.",
-    "laySummary": "",
-    "urls": "pdf:https://jogh.org/wp-content/uploads/2022/07/jogh-12-05025.pdf; doi:https://doi.org/10.7189/jogh.12.05025; html:https://europepmc.org/articles/PMC9269984; pdf:https://europepmc.org/articles/PMC9269984?pdf=render"
-  },
   {
     "id": "34044910",
     "doi": "https://doi.org/10.1016/bs.acc.2020.08.002",
@@ -15792,6 +15792,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/bs.acc.2020.08.002"
   },
+  {
+    "id": "35802764",
+    "doi": "https://doi.org/10.7189/jogh.12.05025",
+    "title": "COVID-19 vaccine effectiveness against symptomatic SARS-CoV-2 infection and severe COVID-19 outcomes from Delta AY.4.2: Cohort and test-negative study of 5.4 million individuals in Scotland.",
+    "authorString": "Kerr S, Vasileiou E, Robertson C, Sheikh A.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of global health",
+    "pubYear": "2022",
+    "date": "2022-07-09",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>In July 2021, a new variant of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in the Delta lineage was detected in the United Kingdom (UK), named AY.4.2 or \"Delta plus\". By October 2021, the AY.4.2 variant accounted for approximately 10-11% of cases in the UK. AY.4.2 was designated as a variant under investigation by the UK Health and Security Agency on 20 October 2021. This study aimed to investigate vaccine effectiveness (VE) against symptomatic COVID-19 (Coronavirus disease 2019) infection and COVID-19 hospitalisation/death for the AY.4.2 variant.<h4>Methods</h4>We used the Scotland-wide Early Pandemic Evaluation and Enhanced Surveillance (EAVE-II) platform to estimate the VE of the ChAdOx1, BNT162b2, and mRNA-1273 vaccines against symptomatic infection and severe COVID-19 outcomes in adults. The study was conducted from June 8 to October 25, 2021. We used a test-negative design (TND) to estimate VE against reverse transcriptase polymerase chain reaction (RT-PCR) confirmed symptomatic SARS-CoV-2 infection while adjusting for sex, socioeconomic status, number of coexisting conditions, and splines in time and age. We also performed a cohort study using a Cox proportional hazards model to estimate VE against a composite outcome of COVID-19 hospital admission or death, with the same adjustments.<h4>Results</h4>We found an overall VE against symptomatic SARS-CoV-2 infection due to AY.4.2 of 73% (95% confidence interval (CI)\u2009=\u200962-81) for >14 days post-second vaccine dose. Good protection against AY.4.2 symptomatic infection was observed for BNT162b2, ChAdOx1, and mRNA-1273. In unvaccinated individuals, the hazard ratio (HR) for COVID-19 hospital admission or death from AY.4.2 among community detected cases was 1.77 (95% CI\u2009=\u20091.02-3.07) relative to unvaccinated individuals who were infected with Delta, after adjusting for multiple potential confounders. VE against AY.4.2 COVID-19 admissions or deaths was 87% (95% CI\u2009=\u200974-93) >28 days post-second vaccination relative to unvaccinated.<h4>Conclusions</h4>We found that AY.4.2 was associated with an increased risk of COVID-19 hospitalisations or deaths in unvaccinated individuals compared with Delta and that vaccination provided substantial protection against symptomatic SARS-CoV-2 and severe COVID-19 outcomes following Delta AY.4.2 infection. High levels of vaccine uptake and protection offered by existing vaccines, as well as the rapid emergence of the Omicron variant may have contributed to the AY.4.2 variant never progressing to a variant of concern.",
+    "laySummary": "",
+    "urls": "pdf:https://jogh.org/wp-content/uploads/2022/07/jogh-12-05025.pdf; doi:https://doi.org/10.7189/jogh.12.05025; html:https://europepmc.org/articles/PMC9269984; pdf:https://europepmc.org/articles/PMC9269984?pdf=render"
+  },
   {
     "id": "33521768",
     "doi": "https://doi.org/10.1016/s2666-7568(20)30011-8",
@@ -15809,23 +15826,6 @@
     "laySummary": "",
     "urls": "pdf:https://eprint.ncl.ac.uk/fulltext.aspx?url=271502/147E40FC-6152-4060-81B1-702AE3B1D66A.pdf&pub_id=271502; doi:https://doi.org/10.1016/S2666-7568(20)30011-8; html:https://europepmc.org/articles/PMC7834195; pdf:https://europepmc.org/articles/PMC7834195?pdf=render"
   },
-  {
-    "id": "36001371",
-    "doi": "https://doi.org/10.2196/38122",
-    "title": "Deployment of a Free-Text Analytics Platform at a UK National Health Service Research Hospital: CogStack at University College London Hospitals.",
-    "authorString": "Noor K, Roguski L, Bai X, Handy A, Klapaukh R, Folarin A, Romao L, Matteson J, Lea N, Zhu L, Asselbergs FW, Wong WK, Shah A, Dobson RJ.",
-    "authorAffiliations": "",
-    "journalTitle": "JMIR medical informatics",
-    "pubYear": "2022",
-    "date": "2022-08-24",
-    "isOpenAccess": "Y",
-    "keywords": "Information Retrieval; Natural Language Processing; Text Mining; Electronic Health Record System; Clinical Support",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>As more health care organizations transition to using electronic health record (EHR) systems, it is important for these organizations to maximize the secondary use of their data to support service improvement and clinical research. These organizations will find it challenging to have systems capable of harnessing the unstructured data fields in the record (clinical notes, letters, etc) and more practically have such systems interact with all of the hospital data systems (legacy and current).<h4>Objective</h4>We describe the deployment of the EHR interfacing information extraction and retrieval platform CogStack at University College London Hospitals (UCLH).<h4>Methods</h4>At UCLH, we have deployed the CogStack platform, an information retrieval platform with natural language processing capabilities. The platform addresses the problem of data ingestion and harmonization from multiple data sources using the Apache NiFi module for managing complex data flows. The platform also facilitates the extraction of structured data from free-text records through use of the MedCAT natural language processing library. Finally, data science tools are made available to support data scientists and the development of downstream applications dependent upon data ingested and analyzed by CogStack.<h4>Results</h4>The platform has been deployed at the hospital, and in particular, it has facilitated a number of research and service evaluation projects. To date, we have processed over 30 million records, and the insights produced from CogStack have informed a number of clinical research use cases at the hospital.<h4>Conclusions</h4>The CogStack platform can be configured to handle the data ingestion and harmonization challenges faced by a hospital. More importantly, the platform enables the hospital to unlock important clinical information from the unstructured portion of the record using natural language processing technology.",
-    "laySummary": "",
-    "urls": "pdf:https://medinform.jmir.org/2022/8/e38122/PDF; doi:https://doi.org/10.2196/38122; html:https://europepmc.org/articles/PMC9453582"
-  },
   {
     "id": "38837310",
     "doi": "https://doi.org/10.1002/ejhf.3306",
@@ -15843,6 +15843,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1002/ejhf.3306; doi:https://doi.org/10.1002/ejhf.3306"
   },
+  {
+    "id": "36001371",
+    "doi": "https://doi.org/10.2196/38122",
+    "title": "Deployment of a Free-Text Analytics Platform at a UK National Health Service Research Hospital: CogStack at University College London Hospitals.",
+    "authorString": "Noor K, Roguski L, Bai X, Handy A, Klapaukh R, Folarin A, Romao L, Matteson J, Lea N, Zhu L, Asselbergs FW, Wong WK, Shah A, Dobson RJ.",
+    "authorAffiliations": "",
+    "journalTitle": "JMIR medical informatics",
+    "pubYear": "2022",
+    "date": "2022-08-24",
+    "isOpenAccess": "Y",
+    "keywords": "Information Retrieval; Natural Language Processing; Text Mining; Electronic Health Record System; Clinical Support",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>As more health care organizations transition to using electronic health record (EHR) systems, it is important for these organizations to maximize the secondary use of their data to support service improvement and clinical research. These organizations will find it challenging to have systems capable of harnessing the unstructured data fields in the record (clinical notes, letters, etc) and more practically have such systems interact with all of the hospital data systems (legacy and current).<h4>Objective</h4>We describe the deployment of the EHR interfacing information extraction and retrieval platform CogStack at University College London Hospitals (UCLH).<h4>Methods</h4>At UCLH, we have deployed the CogStack platform, an information retrieval platform with natural language processing capabilities. The platform addresses the problem of data ingestion and harmonization from multiple data sources using the Apache NiFi module for managing complex data flows. The platform also facilitates the extraction of structured data from free-text records through use of the MedCAT natural language processing library. Finally, data science tools are made available to support data scientists and the development of downstream applications dependent upon data ingested and analyzed by CogStack.<h4>Results</h4>The platform has been deployed at the hospital, and in particular, it has facilitated a number of research and service evaluation projects. To date, we have processed over 30 million records, and the insights produced from CogStack have informed a number of clinical research use cases at the hospital.<h4>Conclusions</h4>The CogStack platform can be configured to handle the data ingestion and harmonization challenges faced by a hospital. More importantly, the platform enables the hospital to unlock important clinical information from the unstructured portion of the record using natural language processing technology.",
+    "laySummary": "",
+    "urls": "pdf:https://medinform.jmir.org/2022/8/e38122/PDF; doi:https://doi.org/10.2196/38122; html:https://europepmc.org/articles/PMC9453582"
+  },
   {
     "id": "33446033",
     "doi": "https://doi.org/10.1177/1460458220977579",
@@ -15877,6 +15894,40 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1038/s41586-024-07773-7; html:https://europepmc.org/articles/PMC11338827; pdf:https://europepmc.org/articles/PMC11338827?pdf=render"
   },
+  {
+    "id": "34649997",
+    "doi": "https://doi.org/10.2337/dc21-0437",
+    "title": "Polycystic Ovary Syndrome, Combined Oral Contraceptives, and the Risk of Dysglycemia: A Population-Based Cohort Study With a Nested Pharmacoepidemiological Case-Control Study.",
+    "authorString": "Kumarendran B, O'Reilly MW, Subramanian A, \u0160umilo D, Toulis K, Gokhale KM, Wijeratne CN, Coomarasamy A, Tahrani AA, Azoulay L, Arlt W, Nirantharakumar K.",
+    "authorAffiliations": "",
+    "journalTitle": "Diabetes care",
+    "pubYear": "2021",
+    "date": "2021-10-14",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>Irregular menstrual cycles are associated with increased cardiovascular mortality. Polycystic ovary syndrome (PCOS) is characterized by androgen excess and irregular menses; androgens are drivers of increased metabolic risk in women with PCOS. Combined oral contraceptive pills (COCPs) are used in PCOS both for cycle regulation and to reduce the biologically active androgen fraction. We examined COCP use and risk of dysglycemia (prediabetes and type 2 diabetes) in women with PCOS.<h4>Research design and methods</h4>Using a large U.K. primary care database (The Health Improvement Network [THIN]; 3.7 million patients from 787 practices), we carried out a retrospective population-based cohort study to determine dysglycemia risk (64,051 women with PCOS and 123,545 matched control subjects), as well as a nested pharmacoepidemiological case-control study to investigate COCP use in relation to dysglycemia risk (2,407 women with PCOS with [case subjects] and without [control subjects] a diagnosis of dysglycemia during follow-up). Cox models were used to estimate the unadjusted and adjusted hazard ratio, and conditional logistic regression was used to obtain adjusted odds ratios (aORs).<h4>Results</h4>The adjusted hazard ratio for dysglycemia in women with PCOS was 1.87 (95% CI 1.78-1.97, <i>P</i> < 0.001; adjustment for age, social deprivation, BMI, ethnicity, and smoking), with increased rates of dysglycemia in all BMI subgroups. Women with PCOS and COCP use had a reduced dysglycemia risk (aOR 0.72, 95% CI 0.59-0.87).<h4>Conclusions</h4>In this study, limited by its retrospective nature and the use of routinely collected electronic general practice record data, which does not allow for exclusion of the impact of prescription-by-indication bias, women with PCOS exposed to COCPs had a reduced risk of dysglycemia across all BMI subgroups. Future prospective studies should be considered for further understanding of these observations and potential causality.",
+    "laySummary": "",
+    "urls": "pdf:https://diabetesjournals.org/care/article-pdf/44/12/2758/631597/dc210437.pdf; doi:https://doi.org/10.2337/dc21-0437; html:https://europepmc.org/articles/PMC8669537; pdf:https://europepmc.org/articles/PMC8669537?pdf=render"
+  },
+  {
+    "id": "35301875",
+    "doi": "https://doi.org/10.1161/jaha.121.023146",
+    "title": "Long-Term Cardiovascular Risk and Management of Patients Recorded in Primary Care With Unattributed Chest Pain: An Electronic Health Record Study.",
+    "authorString": "Jordan KP, Rathod-Mistry T, Bailey J, Chen Y, Clarson L, Denaxas S, Hayward RA, Hemingway H, van der Windt DA, Mamas MA.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of the American Heart Association",
+    "pubYear": "2022",
+    "date": "2022-03-18",
+    "isOpenAccess": "Y",
+    "keywords": "Cardiovascular disease; Chest pain; Primary Care; Electronic Health Records",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Background Most adults presenting with chest pain will not receive a diagnosis and be recorded with unattributed chest pain. The objective was to assess if they have increased risk of cardiovascular disease compared with those with noncoronary chest pain and determine whether investigations and interventions are targeted at those at highest risk. Methods and Results We used records from general practices in England linked to hospitalization and mortality information. The study population included patients aged 18\u00a0years or over with a new record of chest pain with a noncoronary cause or unattributed between 2002 and 2018, and no cardiovascular disease recorded up to 6\u00a0months (diagnostic window) afterward. We compared risk of a future cardiovascular event by type of chest pain, adjusting for cardiovascular risk factors and alternative explanations for chest pain. We determined prevalence of cardiac diagnostic investigations and preventative medication during the diagnostic window in patients with estimated cardiovascular risk \u226510%. There were 375\u00a0240 patients with unattributed chest pain (245\u00a0329 noncoronary chest pain). There was an increased risk of cardiovascular events for patients with unattributed chest pain, highest in the first year (hazard ratio, 1.25 [95% CI, 1.21-1.29]), persistent up to 10\u00a0years. Patients with unattributed chest pain had consistently increased risk of myocardial infarction over time but no increased risk of stroke. Thirty percent of patients at higher risk were prescribed lipid-lowering medication. Conclusions Patients presenting to primary care with unattributed chest pain are at increased risk of cardiovascular events. Primary prevention to reduce cardiovascular events appears suboptimal in those at higher risk.",
+    "laySummary": "",
+    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.121.023146; doi:https://doi.org/10.1161/JAHA.121.023146; html:https://europepmc.org/articles/PMC9075433; pdf:https://europepmc.org/articles/PMC9075433?pdf=render"
+  },
   {
     "id": "39141307",
     "doi": "https://doi.org/10.1007/s12471-024-01886-4",
@@ -15911,23 +15962,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ije/article-pdf/53/4/dyae079/58242858/dyae079.pdf; doi:https://doi.org/10.1093/ije/dyae079; html:https://europepmc.org/articles/PMC11180225; pdf:https://europepmc.org/articles/PMC11180225?pdf=render"
   },
-  {
-    "id": "35301875",
-    "doi": "https://doi.org/10.1161/jaha.121.023146",
-    "title": "Long-Term Cardiovascular Risk and Management of Patients Recorded in Primary Care With Unattributed Chest Pain: An Electronic Health Record Study.",
-    "authorString": "Jordan KP, Rathod-Mistry T, Bailey J, Chen Y, Clarson L, Denaxas S, Hayward RA, Hemingway H, van der Windt DA, Mamas MA.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of the American Heart Association",
-    "pubYear": "2022",
-    "date": "2022-03-18",
-    "isOpenAccess": "Y",
-    "keywords": "Cardiovascular disease; Chest pain; Primary Care; Electronic Health Records",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Background Most adults presenting with chest pain will not receive a diagnosis and be recorded with unattributed chest pain. The objective was to assess if they have increased risk of cardiovascular disease compared with those with noncoronary chest pain and determine whether investigations and interventions are targeted at those at highest risk. Methods and Results We used records from general practices in England linked to hospitalization and mortality information. The study population included patients aged 18\u00a0years or over with a new record of chest pain with a noncoronary cause or unattributed between 2002 and 2018, and no cardiovascular disease recorded up to 6\u00a0months (diagnostic window) afterward. We compared risk of a future cardiovascular event by type of chest pain, adjusting for cardiovascular risk factors and alternative explanations for chest pain. We determined prevalence of cardiac diagnostic investigations and preventative medication during the diagnostic window in patients with estimated cardiovascular risk \u226510%. There were 375\u00a0240 patients with unattributed chest pain (245\u00a0329 noncoronary chest pain). There was an increased risk of cardiovascular events for patients with unattributed chest pain, highest in the first year (hazard ratio, 1.25 [95% CI, 1.21-1.29]), persistent up to 10\u00a0years. Patients with unattributed chest pain had consistently increased risk of myocardial infarction over time but no increased risk of stroke. Thirty percent of patients at higher risk were prescribed lipid-lowering medication. Conclusions Patients presenting to primary care with unattributed chest pain are at increased risk of cardiovascular events. Primary prevention to reduce cardiovascular events appears suboptimal in those at higher risk.",
-    "laySummary": "",
-    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.121.023146; doi:https://doi.org/10.1161/JAHA.121.023146; html:https://europepmc.org/articles/PMC9075433; pdf:https://europepmc.org/articles/PMC9075433?pdf=render"
-  },
   {
     "id": "38216884",
     "doi": "https://doi.org/10.1186/s12859-024-05642-8",
@@ -15962,23 +15996,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.eclinm.2021.101163; doi:https://doi.org/10.1016/j.eclinm.2021.101163; html:https://europepmc.org/articles/PMC8571171; pdf:https://europepmc.org/articles/PMC8571171?pdf=render"
   },
-  {
-    "id": "34649997",
-    "doi": "https://doi.org/10.2337/dc21-0437",
-    "title": "Polycystic Ovary Syndrome, Combined Oral Contraceptives, and the Risk of Dysglycemia: A Population-Based Cohort Study With a Nested Pharmacoepidemiological Case-Control Study.",
-    "authorString": "Kumarendran B, O'Reilly MW, Subramanian A, \u0160umilo D, Toulis K, Gokhale KM, Wijeratne CN, Coomarasamy A, Tahrani AA, Azoulay L, Arlt W, Nirantharakumar K.",
-    "authorAffiliations": "",
-    "journalTitle": "Diabetes care",
-    "pubYear": "2021",
-    "date": "2021-10-14",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objective</h4>Irregular menstrual cycles are associated with increased cardiovascular mortality. Polycystic ovary syndrome (PCOS) is characterized by androgen excess and irregular menses; androgens are drivers of increased metabolic risk in women with PCOS. Combined oral contraceptive pills (COCPs) are used in PCOS both for cycle regulation and to reduce the biologically active androgen fraction. We examined COCP use and risk of dysglycemia (prediabetes and type 2 diabetes) in women with PCOS.<h4>Research design and methods</h4>Using a large U.K. primary care database (The Health Improvement Network [THIN]; 3.7 million patients from 787 practices), we carried out a retrospective population-based cohort study to determine dysglycemia risk (64,051 women with PCOS and 123,545 matched control subjects), as well as a nested pharmacoepidemiological case-control study to investigate COCP use in relation to dysglycemia risk (2,407 women with PCOS with [case subjects] and without [control subjects] a diagnosis of dysglycemia during follow-up). Cox models were used to estimate the unadjusted and adjusted hazard ratio, and conditional logistic regression was used to obtain adjusted odds ratios (aORs).<h4>Results</h4>The adjusted hazard ratio for dysglycemia in women with PCOS was 1.87 (95% CI 1.78-1.97, <i>P</i> < 0.001; adjustment for age, social deprivation, BMI, ethnicity, and smoking), with increased rates of dysglycemia in all BMI subgroups. Women with PCOS and COCP use had a reduced dysglycemia risk (aOR 0.72, 95% CI 0.59-0.87).<h4>Conclusions</h4>In this study, limited by its retrospective nature and the use of routinely collected electronic general practice record data, which does not allow for exclusion of the impact of prescription-by-indication bias, women with PCOS exposed to COCPs had a reduced risk of dysglycemia across all BMI subgroups. Future prospective studies should be considered for further understanding of these observations and potential causality.",
-    "laySummary": "",
-    "urls": "pdf:https://diabetesjournals.org/care/article-pdf/44/12/2758/631597/dc210437.pdf; doi:https://doi.org/10.2337/dc21-0437; html:https://europepmc.org/articles/PMC8669537; pdf:https://europepmc.org/articles/PMC8669537?pdf=render"
-  },
   {
     "id": "36377225",
     "doi": "https://doi.org/10.1177/18333583221135710",
@@ -16081,23 +16098,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/braincomms/advance-article-pdf/doi/10.1093/braincomms/fcad211/51001698/fcad211.pdf; doi:https://doi.org/10.1093/braincomms/fcad211; html:https://europepmc.org/articles/PMC10412752; pdf:https://europepmc.org/articles/PMC10412752?pdf=render"
   },
-  {
-    "id": "29716529",
-    "doi": "https://doi.org/10.1186/s12883-018-1058-8",
-    "title": "Severe localised granulomatosis with polyangiitis (Wegener's granulomatosis) manifesting with extensive cranial nerve palsies and cranial diabetes insipidus: a case report and literature review.",
-    "authorString": "Peters JE, Gupta V, Saeed IT, Offiah C, Jawad ASM.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC neurology",
-    "pubYear": "2018",
-    "date": "2018-05-01",
-    "isOpenAccess": "Y",
-    "keywords": "Diabetes insipidus; Cyclophosphamide; pituitary; Vasculitis; Rituximab; Anca; Cavernous Sinus Syndrome; Collet-sicard Syndrome; Granulomatosis With Polyangiitis; Wegener\u2019s Granulomatosis",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Granulomatosis with polyangiitis (GPA,\u00a0formerly Wegener's granulomatosis) is a multisystem vasculitis of small- to medium-sized blood vessels. Cranial involvement can result in cranial nerve palsies and, rarely, pituitary infiltration.<h4>Case presentation</h4>We describe the case of a 32\u00a0year-old woman with limited but severe GPA manifesting as progressive cranial nerve palsies and pituitary dysfunction. Our patient initially presented with localised ENT involvement, but despite treatment with methotrexate, she deteriorated. Granulomatous inflammatory tissue around the skull base resulted in cavernous sinus syndrome, facial nerve palsy, palsies of cranial nerves IX-XII (Collet-Sicard syndrome), and the rare complication of cranial diabetes insipidus due to pituitary infiltration. The glossopharyngeal, vagus and accessory nerve palsies resulted in severe dysphagia and she required nasogastric tube feeding. Her neurological deficits substantially improved with treatment including high dose corticosteroid, cyclophosphamide and rituximab.<h4>Conclusions</h4>This case emphasises that serious morbidity can arise from localised cranial Wegener's granulomatosis in the absence of systemic disease. In such cases intensive induction immunosuppression is required.\u00a0Analysis of previously reported cases of pituitary involvement in GPA reveals that this rare complication predominantly affects female patients.",
-    "laySummary": "",
-    "urls": "pdf:https://bmcneurol.biomedcentral.com/track/pdf/10.1186/s12883-018-1058-8; doi:https://doi.org/10.1186/s12883-018-1058-8; html:https://europepmc.org/articles/PMC5930853; pdf:https://europepmc.org/articles/PMC5930853?pdf=render"
-  },
   {
     "id": "34508578",
     "doi": "https://doi.org/10.1093/gigascience/giab059",
@@ -16115,6 +16115,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/gigascience/article-pdf/10/9/giab059/40348225/giab059.pdf; doi:https://doi.org/10.1093/gigascience/giab059; html:https://europepmc.org/articles/PMC8434766; pdf:https://europepmc.org/articles/PMC8434766?pdf=render"
   },
+  {
+    "id": "29716529",
+    "doi": "https://doi.org/10.1186/s12883-018-1058-8",
+    "title": "Severe localised granulomatosis with polyangiitis (Wegener's granulomatosis) manifesting with extensive cranial nerve palsies and cranial diabetes insipidus: a case report and literature review.",
+    "authorString": "Peters JE, Gupta V, Saeed IT, Offiah C, Jawad ASM.",
+    "authorAffiliations": "",
+    "journalTitle": "BMC neurology",
+    "pubYear": "2018",
+    "date": "2018-05-01",
+    "isOpenAccess": "Y",
+    "keywords": "Diabetes insipidus; Cyclophosphamide; pituitary; Vasculitis; Rituximab; Anca; Cavernous Sinus Syndrome; Collet-sicard Syndrome; Granulomatosis With Polyangiitis; Wegener\u2019s Granulomatosis",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Granulomatosis with polyangiitis (GPA,\u00a0formerly Wegener's granulomatosis) is a multisystem vasculitis of small- to medium-sized blood vessels. Cranial involvement can result in cranial nerve palsies and, rarely, pituitary infiltration.<h4>Case presentation</h4>We describe the case of a 32\u00a0year-old woman with limited but severe GPA manifesting as progressive cranial nerve palsies and pituitary dysfunction. Our patient initially presented with localised ENT involvement, but despite treatment with methotrexate, she deteriorated. Granulomatous inflammatory tissue around the skull base resulted in cavernous sinus syndrome, facial nerve palsy, palsies of cranial nerves IX-XII (Collet-Sicard syndrome), and the rare complication of cranial diabetes insipidus due to pituitary infiltration. The glossopharyngeal, vagus and accessory nerve palsies resulted in severe dysphagia and she required nasogastric tube feeding. Her neurological deficits substantially improved with treatment including high dose corticosteroid, cyclophosphamide and rituximab.<h4>Conclusions</h4>This case emphasises that serious morbidity can arise from localised cranial Wegener's granulomatosis in the absence of systemic disease. In such cases intensive induction immunosuppression is required.\u00a0Analysis of previously reported cases of pituitary involvement in GPA reveals that this rare complication predominantly affects female patients.",
+    "laySummary": "",
+    "urls": "pdf:https://bmcneurol.biomedcentral.com/track/pdf/10.1186/s12883-018-1058-8; doi:https://doi.org/10.1186/s12883-018-1058-8; html:https://europepmc.org/articles/PMC5930853; pdf:https://europepmc.org/articles/PMC5930853?pdf=render"
+  },
   {
     "id": "37139857",
     "doi": "https://doi.org/10.1111/dom.15102",
@@ -16132,23 +16149,6 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/dom.15102; doi:https://doi.org/10.1111/dom.15102"
   },
-  {
-    "id": "39469534",
-    "doi": "https://doi.org/10.1016/j.eclinm.2024.102887",
-    "title": "Diagnostic performance of deep learning for infectious keratitis: a systematic review and meta-analysis.",
-    "authorString": "Ong ZZ, Sadek Y, Qureshi R, Liu SH, Li T, Liu X, Takwoingi Y, Sounderajah V, Ashrafian H, Ting DSW, Mehta JS, Rauz S, Said DG, Dua HS, Burton MJ, Ting DSJ.",
-    "authorAffiliations": "",
-    "journalTitle": "EClinicalMedicine",
-    "pubYear": "2024",
-    "date": "2024-10-18",
-    "isOpenAccess": "Y",
-    "keywords": "Artificial intelligence; Corneal Ulcer; Microbial Keratitis; Infectious Keratitis; Corneal Infection; Deep Learning",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Infectious keratitis (IK) is the leading cause of corneal blindness globally. Deep learning (DL) is an emerging tool for medical diagnosis, though its value in IK is unclear. We aimed to assess the diagnostic accuracy of DL for IK and its comparative accuracy with ophthalmologists.<h4>Methods</h4>In this systematic review and meta-analysis, we searched EMBASE, MEDLINE, and clinical registries for studies related to DL for IK published between 1974 and July 16, 2024. We performed meta-analyses using bivariate models to estimate summary sensitivities and specificities. This systematic review was registered with PROSPERO (CRD42022348596).<h4>Findings</h4>Of 963 studies identified, 35 studies (136,401 corneal images from >56,011 patients) were included. Most studies had low risk of bias (68.6%) and low applicability concern (91.4%) in all domains of QUADAS-2, except the index test domain. Against the reference standard of expert consensus and/or microbiological results (seven external validation studies; 10,675 images), the summary estimates (95% CI) for sensitivity and specificity of DL for IK were 86.2% (71.6-93.9) and 96.3% (91.5-98.5). From 28 internal validation studies (16,059 images), summary estimates for sensitivity and specificity were 91.6% (86.8-94.8) and 90.7% (84.8-94.5). Based on seven studies (4007 images), DL and ophthalmologists had comparable summary sensitivity [89.2% (82.2-93.6) versus 82.2% (71.5-89.5); P\u00a0=\u00a00.20] and specificity [(93.2% (85.5-97.0) versus 89.6% (78.8-95.2); P\u00a0=\u00a00.45].<h4>Interpretation</h4>DL models may have good diagnostic accuracy for IK and comparable performance to ophthalmologists. These findings should be interpreted with caution due to the image-based analysis that did not account for potential correlation within individuals, relatively homogeneous population studies, lack of pre-specification of DL thresholds, and limited external validation. Future studies should improve their reporting, data diversity, external validation, transparency, and explainability to increase the reliability and generalisability of DL models for clinical deployment.<h4>Funding</h4>NIH, Wellcome Trust, MRC, Fight for Sight, BHP, and ESCRS.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.eclinm.2024.102887; html:https://europepmc.org/articles/PMC11513659; pdf:https://europepmc.org/articles/PMC11513659?pdf=render"
-  },
   {
     "id": "36447757",
     "doi": "https://doi.org/10.1136/gpsych-2022-100819",
@@ -16184,21 +16184,21 @@
     "urls": "doi:https://doi.org/10.7554/eLife.85332; html:https://europepmc.org/articles/PMC10414967; pdf:https://europepmc.org/articles/PMC10414967?pdf=render"
   },
   {
-    "id": "38528230",
-    "doi": "https://doi.org/10.1038/s43587-024-00590-7",
-    "title": "Integration of polygenic and gut metagenomic risk prediction for common diseases.",
-    "authorString": "Liu Y, Ritchie SC, Teo SM, Ruuskanen MO, Kambur O, Zhu Q, Sanders J, V\u00e1zquez-Baeza Y, Verspoor K, Jousilahti P, Lahti L, Niiranen T, Salomaa V, Havulinna AS, Knight R, M\u00e9ric G, Inouye M.",
+    "id": "39469534",
+    "doi": "https://doi.org/10.1016/j.eclinm.2024.102887",
+    "title": "Diagnostic performance of deep learning for infectious keratitis: a systematic review and meta-analysis.",
+    "authorString": "Ong ZZ, Sadek Y, Qureshi R, Liu SH, Li T, Liu X, Takwoingi Y, Sounderajah V, Ashrafian H, Ting DSW, Mehta JS, Rauz S, Said DG, Dua HS, Burton MJ, Ting DSJ.",
     "authorAffiliations": "",
-    "journalTitle": "Nature aging",
+    "journalTitle": "EClinicalMedicine",
     "pubYear": "2024",
-    "date": "2024-03-25",
+    "date": "2024-10-18",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Artificial intelligence; Corneal Ulcer; Microbial Keratitis; Infectious Keratitis; Corneal Infection; Deep Learning",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Multiomics has shown promise in noninvasive risk profiling and early detection of various common diseases. In the present study, in a prospective population-based cohort with ~18\u2009years of e-health record follow-up, we investigated the incremental and combined value of genomic and gut metagenomic risk assessment compared with conventional risk factors for predicting incident coronary artery disease (CAD), type 2 diabetes (T2D), Alzheimer disease and prostate cancer. We found that polygenic risk scores (PRSs) improved prediction over conventional risk factors for all diseases. Gut microbiome scores improved predictive capacity over baseline age for CAD, T2D and prostate cancer. Integrated risk models of PRSs, gut microbiome scores and conventional risk factors achieved the highest predictive performance for all diseases studied compared with models based on conventional risk factors alone. The present study demonstrates that integrated PRSs and gut metagenomic risk models improve the predictive value over conventional risk factors for common chronic diseases.",
+    "abstract": "<h4>Background</h4>Infectious keratitis (IK) is the leading cause of corneal blindness globally. Deep learning (DL) is an emerging tool for medical diagnosis, though its value in IK is unclear. We aimed to assess the diagnostic accuracy of DL for IK and its comparative accuracy with ophthalmologists.<h4>Methods</h4>In this systematic review and meta-analysis, we searched EMBASE, MEDLINE, and clinical registries for studies related to DL for IK published between 1974 and July 16, 2024. We performed meta-analyses using bivariate models to estimate summary sensitivities and specificities. This systematic review was registered with PROSPERO (CRD42022348596).<h4>Findings</h4>Of 963 studies identified, 35 studies (136,401 corneal images from >56,011 patients) were included. Most studies had low risk of bias (68.6%) and low applicability concern (91.4%) in all domains of QUADAS-2, except the index test domain. Against the reference standard of expert consensus and/or microbiological results (seven external validation studies; 10,675 images), the summary estimates (95% CI) for sensitivity and specificity of DL for IK were 86.2% (71.6-93.9) and 96.3% (91.5-98.5). From 28 internal validation studies (16,059 images), summary estimates for sensitivity and specificity were 91.6% (86.8-94.8) and 90.7% (84.8-94.5). Based on seven studies (4007 images), DL and ophthalmologists had comparable summary sensitivity [89.2% (82.2-93.6) versus 82.2% (71.5-89.5); P\u00a0=\u00a00.20] and specificity [(93.2% (85.5-97.0) versus 89.6% (78.8-95.2); P\u00a0=\u00a00.45].<h4>Interpretation</h4>DL models may have good diagnostic accuracy for IK and comparable performance to ophthalmologists. These findings should be interpreted with caution due to the image-based analysis that did not account for potential correlation within individuals, relatively homogeneous population studies, lack of pre-specification of DL thresholds, and limited external validation. Future studies should improve their reporting, data diversity, external validation, transparency, and explainability to increase the reliability and generalisability of DL models for clinical deployment.<h4>Funding</h4>NIH, Wellcome Trust, MRC, Fight for Sight, BHP, and ESCRS.",
     "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s43587-024-00590-7.pdf; doi:https://doi.org/10.1038/s43587-024-00590-7; html:https://europepmc.org/articles/PMC11031402; pdf:https://europepmc.org/articles/PMC11031402?pdf=render"
+    "urls": "doi:https://doi.org/10.1016/j.eclinm.2024.102887; html:https://europepmc.org/articles/PMC11513659; pdf:https://europepmc.org/articles/PMC11513659?pdf=render"
   },
   {
     "id": "29938349",
@@ -16217,6 +16217,40 @@
     "laySummary": "",
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s11892-018-1021-5.pdf; doi:https://doi.org/10.1007/s11892-018-1021-5; html:https://europepmc.org/articles/PMC6015804; pdf:https://europepmc.org/articles/PMC6015804?pdf=render"
   },
+  {
+    "id": "31797917",
+    "doi": "https://doi.org/10.1038/s41398-019-0635-y",
+    "title": "Novel genome-wide associations for anhedonia, genetic correlation with psychiatric disorders, and polygenic association with brain structure.",
+    "authorString": "Ward J, Lyall LM, Bethlehem RAI, Ferguson A, Strawbridge RJ, Lyall DM, Cullen B, Graham N, Johnston KJA, Bailey MES, Murray GK, Smith DJ.",
+    "authorAffiliations": "",
+    "journalTitle": "Translational psychiatry",
+    "pubYear": "2019",
+    "date": "2019-12-04",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Anhedonia is a core symptom of several psychiatric disorders but its biological underpinnings are poorly understood. We performed a genome-wide association study of state anhedonia in 375,275 UK Biobank participants and assessed for genetic correlation between anhedonia and neuropsychiatric conditions (major depressive disorder, schizophrenia, bipolar disorder, obsessive compulsive disorder and Parkinson's Disease). We then used a polygenic risk score approach to test for association between genetic loading for anhedonia and both brain structure and brain function. This included: magnetic resonance imaging (MRI) assessments of total grey matter volume, white matter volume, cerebrospinal fluid volume, and 15 cortical/subcortical regions of interest; diffusion tensor imaging (DTI) measures of white matter tract integrity; and functional MRI activity during an emotion processing task. We identified 11 novel loci associated at genome-wide significance with anhedonia, with a SNP heritability estimate (h<sub>2</sub>SNP) of 5.6%. Strong positive genetic correlations were found between anhedonia and major depressive disorder, schizophrenia and bipolar disorder; but not with obsessive compulsive disorder or Parkinson's Disease. Polygenic risk for anhedonia was associated with poorer brain white matter integrity, smaller total grey matter volume, and smaller volumes of brain regions linked to reward and pleasure processing, including orbito-frontal cortex. In summary, the identification of novel anhedonia-associated loci substantially expands our current understanding of the biological basis of state anhedonia and genetic correlations with several psychiatric disorders confirm the utility of this phenotype as a transdiagnostic marker of vulnerability to mental illness. We also provide the first evidence that genetic risk for state anhedonia influences brain structure, including in regions associated with reward and pleasure processing.",
+    "laySummary": "This study assessed for genetic correlation between anhedonia and neuropsychiatric conditions. A polygenic risk score approach was applied to test for association between anhedonia and brain structure and brain function. Findings confirm that using anhedonia as a marker of vulnerability to mental illness. Findings also suggest that genetic risk for state anhedonia influences brain structure",
+    "urls": "pdf:https://www.nature.com/articles/s41398-019-0635-y.pdf; doi:https://doi.org/10.1038/s41398-019-0635-y; html:https://europepmc.org/articles/PMC6892870; pdf:https://europepmc.org/articles/PMC6892870?pdf=render"
+  },
+  {
+    "id": "38528230",
+    "doi": "https://doi.org/10.1038/s43587-024-00590-7",
+    "title": "Integration of polygenic and gut metagenomic risk prediction for common diseases.",
+    "authorString": "Liu Y, Ritchie SC, Teo SM, Ruuskanen MO, Kambur O, Zhu Q, Sanders J, V\u00e1zquez-Baeza Y, Verspoor K, Jousilahti P, Lahti L, Niiranen T, Salomaa V, Havulinna AS, Knight R, M\u00e9ric G, Inouye M.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature aging",
+    "pubYear": "2024",
+    "date": "2024-03-25",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Multiomics has shown promise in noninvasive risk profiling and early detection of various common diseases. In the present study, in a prospective population-based cohort with ~18\u2009years of e-health record follow-up, we investigated the incremental and combined value of genomic and gut metagenomic risk assessment compared with conventional risk factors for predicting incident coronary artery disease (CAD), type 2 diabetes (T2D), Alzheimer disease and prostate cancer. We found that polygenic risk scores (PRSs) improved prediction over conventional risk factors for all diseases. Gut microbiome scores improved predictive capacity over baseline age for CAD, T2D and prostate cancer. Integrated risk models of PRSs, gut microbiome scores and conventional risk factors achieved the highest predictive performance for all diseases studied compared with models based on conventional risk factors alone. The present study demonstrates that integrated PRSs and gut metagenomic risk models improve the predictive value over conventional risk factors for common chronic diseases.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s43587-024-00590-7.pdf; doi:https://doi.org/10.1038/s43587-024-00590-7; html:https://europepmc.org/articles/PMC11031402; pdf:https://europepmc.org/articles/PMC11031402?pdf=render"
+  },
   {
     "id": "35365351",
     "doi": "https://doi.org/10.1016/j.injury.2022.03.039",
@@ -16268,23 +16302,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/s2589-7500(22)00147-9; doi:https://doi.org/10.1016/S2589-7500(22)00147-9; html:https://europepmc.org/articles/PMC9489064; pdf:https://europepmc.org/articles/PMC9489064?pdf=render"
   },
-  {
-    "id": "31797917",
-    "doi": "https://doi.org/10.1038/s41398-019-0635-y",
-    "title": "Novel genome-wide associations for anhedonia, genetic correlation with psychiatric disorders, and polygenic association with brain structure.",
-    "authorString": "Ward J, Lyall LM, Bethlehem RAI, Ferguson A, Strawbridge RJ, Lyall DM, Cullen B, Graham N, Johnston KJA, Bailey MES, Murray GK, Smith DJ.",
-    "authorAffiliations": "",
-    "journalTitle": "Translational psychiatry",
-    "pubYear": "2019",
-    "date": "2019-12-04",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Anhedonia is a core symptom of several psychiatric disorders but its biological underpinnings are poorly understood. We performed a genome-wide association study of state anhedonia in 375,275 UK Biobank participants and assessed for genetic correlation between anhedonia and neuropsychiatric conditions (major depressive disorder, schizophrenia, bipolar disorder, obsessive compulsive disorder and Parkinson's Disease). We then used a polygenic risk score approach to test for association between genetic loading for anhedonia and both brain structure and brain function. This included: magnetic resonance imaging (MRI) assessments of total grey matter volume, white matter volume, cerebrospinal fluid volume, and 15 cortical/subcortical regions of interest; diffusion tensor imaging (DTI) measures of white matter tract integrity; and functional MRI activity during an emotion processing task. We identified 11 novel loci associated at genome-wide significance with anhedonia, with a SNP heritability estimate (h<sub>2</sub>SNP) of 5.6%. Strong positive genetic correlations were found between anhedonia and major depressive disorder, schizophrenia and bipolar disorder; but not with obsessive compulsive disorder or Parkinson's Disease. Polygenic risk for anhedonia was associated with poorer brain white matter integrity, smaller total grey matter volume, and smaller volumes of brain regions linked to reward and pleasure processing, including orbito-frontal cortex. In summary, the identification of novel anhedonia-associated loci substantially expands our current understanding of the biological basis of state anhedonia and genetic correlations with several psychiatric disorders confirm the utility of this phenotype as a transdiagnostic marker of vulnerability to mental illness. We also provide the first evidence that genetic risk for state anhedonia influences brain structure, including in regions associated with reward and pleasure processing.",
-    "laySummary": "This study assessed for genetic correlation between anhedonia and neuropsychiatric conditions. A polygenic risk score approach was applied to test for association between anhedonia and brain structure and brain function. Findings confirm that using anhedonia as a marker of vulnerability to mental illness. Findings also suggest that genetic risk for state anhedonia influences brain structure",
-    "urls": "pdf:https://www.nature.com/articles/s41398-019-0635-y.pdf; doi:https://doi.org/10.1038/s41398-019-0635-y; html:https://europepmc.org/articles/PMC6892870; pdf:https://europepmc.org/articles/PMC6892870?pdf=render"
-  },
   {
     "id": "34784292",
     "doi": "https://doi.org/10.2196/32587",
@@ -16455,23 +16472,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41467-022-32095-5.pdf; doi:https://doi.org/10.1038/s41467-022-32095-5; html:https://europepmc.org/articles/PMC9363492; pdf:https://europepmc.org/articles/PMC9363492?pdf=render"
   },
-  {
-    "id": "39053121",
-    "doi": "https://doi.org/10.1016/j.jdiacomp.2024.108813",
-    "title": "The effect of bariatric surgery on diabetes related foot complications among patients with type 2 diabetes: A systematic review.",
-    "authorString": "Wang Z, Crowe FL, Tahrani AA, Singh P, Wang J, Tan L, Nirantharakumar K, Hazlehurst J.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of diabetes and its complications",
-    "pubYear": "2024",
-    "date": "2024-07-14",
-    "isOpenAccess": "N",
-    "keywords": "Type 2 diabetes; Bariatric Surgery; Diabetes Related Foot Complications",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Bariatric surgery leads to considerable weight loss and improved glycaemic control and seems to have a favourable impact on diabetes related foot complications (DFC).<h4>Objectives</h4>To assess the effect of bariatric surgery on diabetes related foot complications in patients with type 2 diabetes and determine whether DFC symptoms are improved after bariatric surgery.<h4>Methods</h4>We searched MEDLINE, Embase and Cochrane Central Register of Controlled Trials. The primary outcome was the presence of DFC after bariatric surgery. The secondary outcome was the improvement of DFC after bariatric surgery among patients who already had DFC before surgery.<h4>Results</h4>There were nine studies showing the presence of DFC post bariatric surgery and six detailing the changes in DFC post bariatric surgery. Bariatric surgery was not associated with a lower risk of developing or worsening DFC compared to conventional medical treatment based on 4 randomised control trials (IR 0.87, 95\u00a0% CI, 0.26, 2.98), while from observational studies was associated with 51\u00a0% lower risk of DFC (IR 0.49, 95\u00a0% CI, 0.31, 0.77). Bariatric surgery was associated with improvement in diabetic neuropathy assessment parameters including toe tuning fork score, self-reported neuropathy symptoms, neuropathy symptom score, and neuropathy symptom profile.<h4>Conclusion</h4>Bariatric surgery led to a greater reduction in developing or worsening DFC among patients with type 2 diabetes compared to medical treatment in observational studies, but not among RCTs. Bariatric surgery was associated with improvements in diabetic neuropathy related assessment parameters and symptoms. Bariatric surgery could be a promising treatment for patients with type 2 diabetes who are at high risk of DFC.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.jdiacomp.2024.108813"
-  },
   {
     "id": "29925668",
     "doi": "https://doi.org/10.1136/jech-2017-210370",
@@ -16489,6 +16489,23 @@
     "laySummary": "",
     "urls": "pdf:https://jech.bmj.com/content/jech/72/10/896.full.pdf; doi:https://doi.org/10.1136/jech-2017-210370; html:https://europepmc.org/articles/PMC6161658; pdf:https://europepmc.org/articles/PMC6161658?pdf=render"
   },
+  {
+    "id": "39053121",
+    "doi": "https://doi.org/10.1016/j.jdiacomp.2024.108813",
+    "title": "The effect of bariatric surgery on diabetes related foot complications among patients with type 2 diabetes: A systematic review.",
+    "authorString": "Wang Z, Crowe FL, Tahrani AA, Singh P, Wang J, Tan L, Nirantharakumar K, Hazlehurst J.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of diabetes and its complications",
+    "pubYear": "2024",
+    "date": "2024-07-14",
+    "isOpenAccess": "N",
+    "keywords": "Type 2 diabetes; Bariatric Surgery; Diabetes Related Foot Complications",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Bariatric surgery leads to considerable weight loss and improved glycaemic control and seems to have a favourable impact on diabetes related foot complications (DFC).<h4>Objectives</h4>To assess the effect of bariatric surgery on diabetes related foot complications in patients with type 2 diabetes and determine whether DFC symptoms are improved after bariatric surgery.<h4>Methods</h4>We searched MEDLINE, Embase and Cochrane Central Register of Controlled Trials. The primary outcome was the presence of DFC after bariatric surgery. The secondary outcome was the improvement of DFC after bariatric surgery among patients who already had DFC before surgery.<h4>Results</h4>There were nine studies showing the presence of DFC post bariatric surgery and six detailing the changes in DFC post bariatric surgery. Bariatric surgery was not associated with a lower risk of developing or worsening DFC compared to conventional medical treatment based on 4 randomised control trials (IR 0.87, 95\u00a0% CI, 0.26, 2.98), while from observational studies was associated with 51\u00a0% lower risk of DFC (IR 0.49, 95\u00a0% CI, 0.31, 0.77). Bariatric surgery was associated with improvement in diabetic neuropathy assessment parameters including toe tuning fork score, self-reported neuropathy symptoms, neuropathy symptom score, and neuropathy symptom profile.<h4>Conclusion</h4>Bariatric surgery led to a greater reduction in developing or worsening DFC among patients with type 2 diabetes compared to medical treatment in observational studies, but not among RCTs. Bariatric surgery was associated with improvements in diabetic neuropathy related assessment parameters and symptoms. Bariatric surgery could be a promising treatment for patients with type 2 diabetes who are at high risk of DFC.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.jdiacomp.2024.108813"
+  },
   {
     "id": "34514354",
     "doi": "https://doi.org/10.1093/jamiaopen/ooab001",
@@ -16642,23 +16659,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1371/journal.pgph.0002022; html:https://europepmc.org/articles/PMC10707482; pdf:https://europepmc.org/articles/PMC10707482?pdf=render"
   },
-  {
-    "id": "38045436",
-    "doi": "https://doi.org/10.1093/ehjdh/ztad062",
-    "title": "Monitoring left ventricular assist device parameters to detect flow- and power-impacting complications: a proof of concept.",
-    "authorString": "Moazeni M, Numan L, Szymanski MK, Van der Kaaij NP, Asselbergs FW, van Laake LW, Aarts E.",
-    "authorAffiliations": "",
-    "journalTitle": "European heart journal. Digital health",
-    "pubYear": "2023",
-    "date": "2023-10-27",
-    "isOpenAccess": "Y",
-    "keywords": "Lvad; Intensive Longitudinal Data; Remote Patient Monitoring; Patient-Specific Monitoring",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Aims</h4>The number of patients on left ventricular assist device (LVAD) support increases due to the growing number of patients with end-stage heart failure and the limited number of donor hearts. Despite improving survival rates, patients frequently suffer from adverse events such as cardiac arrhythmia and major bleeding. Telemonitoring is a potentially powerful tool to early detect deteriorations and may further improve outcome after LVAD implantation. Hence, we developed a personalized algorithm to remotely monitor HeartMate3 (HM3) pump parameters aiming to early detect unscheduled admissions due to cardiac arrhythmia or major bleeding.<h4>Methods and results</h4>The source code of the algorithm is published in an open repository. The algorithm was optimized and tested retrospectively using HeartMate 3 (HM3) power and flow data of 120 patients, including 29 admissions due to cardiac arrhythmia and 14 admissions due to major bleeding. Using a true alarm window of 14 days prior to the admission date, the algorithm detected 59 and 79% of unscheduled admissions due to cardiac arrhythmia and major bleeding, respectively, with a false alarm rate of 2%.<h4>Conclusion</h4>The proposed algorithm showed that the personalized algorithm is a viable approach to early identify cardiac arrhythmia and major bleeding by monitoring HM3 pump parameters. External validation is needed and integration with other clinical parameters could potentially improve the predictive value. In addition, the algorithm can be further enhanced using continuous data.",
-    "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/ehjdh/article-pdf/4/6/488/53897330/ztad062.pdf; doi:https://doi.org/10.1093/ehjdh/ztad062; html:https://europepmc.org/articles/PMC10689906; pdf:https://europepmc.org/articles/PMC10689906?pdf=render"
-  },
   {
     "id": "30423068",
     "doi": "https://doi.org/10.1093/bioinformatics/bty605",
@@ -16677,21 +16677,21 @@
     "urls": "pdf:https://academic.oup.com/bioinformatics/article-pdf/34/17/i857/25702307/bty605.pdf; doi:https://doi.org/10.1093/bioinformatics/bty605; html:https://europepmc.org/articles/PMC6129279; pdf:https://europepmc.org/articles/PMC6129279?pdf=render"
   },
   {
-    "id": "31616478",
-    "doi": "https://doi.org/10.3389/fgene.2019.00922",
-    "title": "Machine Learning Predicts Accurately <i>Mycobacterium tuberculosis</i> Drug Resistance From Whole Genome Sequencing Data.",
-    "authorString": "Deelder W, Christakoudi S, Phelan J, Benavente ED, Campino S, McNerney R, Palla L, Clark TG.",
+    "id": "38045436",
+    "doi": "https://doi.org/10.1093/ehjdh/ztad062",
+    "title": "Monitoring left ventricular assist device parameters to detect flow- and power-impacting complications: a proof of concept.",
+    "authorString": "Moazeni M, Numan L, Szymanski MK, Van der Kaaij NP, Asselbergs FW, van Laake LW, Aarts E.",
     "authorAffiliations": "",
-    "journalTitle": "Frontiers in genetics",
-    "pubYear": "2019",
-    "date": "2019-09-26",
+    "journalTitle": "European heart journal. Digital health",
+    "pubYear": "2023",
+    "date": "2023-10-27",
     "isOpenAccess": "Y",
-    "keywords": "Mycobacterium tuberculosis; Drug resistance; Mdr-tb; Xdr-tb; Machine Learning",
-    "nationalPriorities": "Applied Analytics",
+    "keywords": "Lvad; Intensive Longitudinal Data; Remote Patient Monitoring; Patient-Specific Monitoring",
+    "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<b>Background:</b> Tuberculosis disease, caused by <i>Mycobacterium tuberculosis</i>, is a major public health problem. The emergence of <i>M. tuberculosis</i> strains resistant to existing treatments threatens to derail control efforts. Resistance is mainly conferred by mutations in genes coding for drug targets or converting enzymes, but our knowledge of these mutations is incomplete. Whole genome sequencing (WGS) is an increasingly common approach to rapidly characterize isolates and identify mutations predicting antimicrobial resistance and thereby providing a diagnostic tool to assist clinical decision making. <b>Methods:</b> We applied machine learning approaches to 16,688 <i>M. tuberculosis</i> isolates that have undergone WGS and laboratory drug-susceptibility testing (DST) across 14 antituberculosis drugs, with 22.5% of samples being multidrug resistant and 2.1% being extensively drug resistant. We used non-parametric classification-tree and gradient-boosted-tree models to predict drug resistance and uncover any associated novel putative mutations. We fitted separate models for each drug, with and without \"co-occurrent resistance\" markers known to be causing resistance to drugs other than the one of interest. Predictive performance was measured using sensitivity, specificity, and the area under the receiver operating characteristic curve, assuming DST results as the gold standard. <b>Results:</b> The predictive performance was highest for resistance to first-line drugs, amikacin, kanamycin, ciprofloxacin, moxifloxacin, and multidrug-resistant tuberculosis (area under the receiver operating characteristic curve above 96%), and lowest for third-line drugs such as D-cycloserine and Para-aminosalisylic acid (area under the curve below 85%). The inclusion of co-occurrent resistance markers led to improved performance for some drugs and superior results when compared to similar models in other large-scale studies, which had smaller sample sizes. Overall, the gradient-boosted-tree models performed better than the classification-tree models. The mutation-rank analysis detected no new single nucleotide polymorphisms linked to drug resistance. Discordance between DST and genotypically inferred resistance may be explained by DST errors, novel rare mutations, hetero-resistance, and nongenomic drivers such as efflux-pump upregulation. <b>Conclusion:</b> Our work demonstrates the utility of machine learning as a flexible approach to drug resistance prediction that is able to accommodate a much larger number of predictors and to summarize their predictive ability, thus assisting clinical decision making and single nucleotide polymorphism detection in an era of increasing WGS data generation.",
+    "abstract": "<h4>Aims</h4>The number of patients on left ventricular assist device (LVAD) support increases due to the growing number of patients with end-stage heart failure and the limited number of donor hearts. Despite improving survival rates, patients frequently suffer from adverse events such as cardiac arrhythmia and major bleeding. Telemonitoring is a potentially powerful tool to early detect deteriorations and may further improve outcome after LVAD implantation. Hence, we developed a personalized algorithm to remotely monitor HeartMate3 (HM3) pump parameters aiming to early detect unscheduled admissions due to cardiac arrhythmia or major bleeding.<h4>Methods and results</h4>The source code of the algorithm is published in an open repository. The algorithm was optimized and tested retrospectively using HeartMate 3 (HM3) power and flow data of 120 patients, including 29 admissions due to cardiac arrhythmia and 14 admissions due to major bleeding. Using a true alarm window of 14 days prior to the admission date, the algorithm detected 59 and 79% of unscheduled admissions due to cardiac arrhythmia and major bleeding, respectively, with a false alarm rate of 2%.<h4>Conclusion</h4>The proposed algorithm showed that the personalized algorithm is a viable approach to early identify cardiac arrhythmia and major bleeding by monitoring HM3 pump parameters. External validation is needed and integration with other clinical parameters could potentially improve the predictive value. In addition, the algorithm can be further enhanced using continuous data.",
     "laySummary": "",
-    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fgene.2019.00922/pdf; doi:https://doi.org/10.3389/fgene.2019.00922; html:https://europepmc.org/articles/PMC6775242; pdf:https://europepmc.org/articles/PMC6775242?pdf=render"
+    "urls": "pdf:https://academic.oup.com/ehjdh/article-pdf/4/6/488/53897330/ztad062.pdf; doi:https://doi.org/10.1093/ehjdh/ztad062; html:https://europepmc.org/articles/PMC10689906; pdf:https://europepmc.org/articles/PMC10689906?pdf=render"
   },
   {
     "id": "33827849",
@@ -16710,6 +16710,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/11/4/e048139.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-048139; html:https://europepmc.org/articles/PMC8031692; pdf:https://europepmc.org/articles/PMC8031692?pdf=render"
   },
+  {
+    "id": "31616478",
+    "doi": "https://doi.org/10.3389/fgene.2019.00922",
+    "title": "Machine Learning Predicts Accurately <i>Mycobacterium tuberculosis</i> Drug Resistance From Whole Genome Sequencing Data.",
+    "authorString": "Deelder W, Christakoudi S, Phelan J, Benavente ED, Campino S, McNerney R, Palla L, Clark TG.",
+    "authorAffiliations": "",
+    "journalTitle": "Frontiers in genetics",
+    "pubYear": "2019",
+    "date": "2019-09-26",
+    "isOpenAccess": "Y",
+    "keywords": "Mycobacterium tuberculosis; Drug resistance; Mdr-tb; Xdr-tb; Machine Learning",
+    "nationalPriorities": "Applied Analytics",
+    "healthCategories": "",
+    "abstract": "<b>Background:</b> Tuberculosis disease, caused by <i>Mycobacterium tuberculosis</i>, is a major public health problem. The emergence of <i>M. tuberculosis</i> strains resistant to existing treatments threatens to derail control efforts. Resistance is mainly conferred by mutations in genes coding for drug targets or converting enzymes, but our knowledge of these mutations is incomplete. Whole genome sequencing (WGS) is an increasingly common approach to rapidly characterize isolates and identify mutations predicting antimicrobial resistance and thereby providing a diagnostic tool to assist clinical decision making. <b>Methods:</b> We applied machine learning approaches to 16,688 <i>M. tuberculosis</i> isolates that have undergone WGS and laboratory drug-susceptibility testing (DST) across 14 antituberculosis drugs, with 22.5% of samples being multidrug resistant and 2.1% being extensively drug resistant. We used non-parametric classification-tree and gradient-boosted-tree models to predict drug resistance and uncover any associated novel putative mutations. We fitted separate models for each drug, with and without \"co-occurrent resistance\" markers known to be causing resistance to drugs other than the one of interest. Predictive performance was measured using sensitivity, specificity, and the area under the receiver operating characteristic curve, assuming DST results as the gold standard. <b>Results:</b> The predictive performance was highest for resistance to first-line drugs, amikacin, kanamycin, ciprofloxacin, moxifloxacin, and multidrug-resistant tuberculosis (area under the receiver operating characteristic curve above 96%), and lowest for third-line drugs such as D-cycloserine and Para-aminosalisylic acid (area under the curve below 85%). The inclusion of co-occurrent resistance markers led to improved performance for some drugs and superior results when compared to similar models in other large-scale studies, which had smaller sample sizes. Overall, the gradient-boosted-tree models performed better than the classification-tree models. The mutation-rank analysis detected no new single nucleotide polymorphisms linked to drug resistance. Discordance between DST and genotypically inferred resistance may be explained by DST errors, novel rare mutations, hetero-resistance, and nongenomic drivers such as efflux-pump upregulation. <b>Conclusion:</b> Our work demonstrates the utility of machine learning as a flexible approach to drug resistance prediction that is able to accommodate a much larger number of predictors and to summarize their predictive ability, thus assisting clinical decision making and single nucleotide polymorphism detection in an era of increasing WGS data generation.",
+    "laySummary": "",
+    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fgene.2019.00922/pdf; doi:https://doi.org/10.3389/fgene.2019.00922; html:https://europepmc.org/articles/PMC6775242; pdf:https://europepmc.org/articles/PMC6775242?pdf=render"
+  },
   {
     "id": "32855306",
     "doi": "https://doi.org/10.1136/gutjnl-2020-321650",
@@ -16778,6 +16795,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41433-020-01326-8.pdf; doi:https://doi.org/10.1038/s41433-020-01326-8; html:https://europepmc.org/articles/PMC8452782; pdf:https://europepmc.org/articles/PMC8452782?pdf=render; doi:https://doi.org/10.1038/s41433-020-01326-8"
   },
+  {
+    "id": "32737300",
+    "doi": "https://doi.org/10.1038/s41467-020-17696-2",
+    "title": "Distinct genetic architectures and environmental factors associate with host response to the \u03b32-herpesvirus infections.",
+    "authorString": "Sallah N, Miley W, Labo N, Carstensen T, Fatumo S, Gurdasani D, Pollard MO, Dilthey AT, Mentzer AJ, Marshall V, Cornejo Castro EM, Pomilla C, Young EH, Asiki G, Hibberd ML, Sandhu M, Kellam P, Newton R, Whitby D, Barroso I.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature communications",
+    "pubYear": "2020",
+    "date": "2020-07-31",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr Virus (EBV) establish life-long infections and are associated with malignancies. Striking geographic variation in incidence and the fact that virus alone is insufficient to cause disease, suggests other co-factors are involved. Here we present epidemiological analysis and genome-wide association study (GWAS) in 4365 individuals from an African population cohort, to assess the influence of host genetic and non-genetic factors on virus antibody responses. EBV/KSHV co-infection (OR\u2009=\u20095.71(1.58-7.12)), HIV positivity (OR\u2009=\u20092.22(1.32-3.73)) and living in a more rural area (OR\u2009=\u20091.38(1.01-1.89)) are strongly associated with immunogenicity. GWAS reveals associations with KSHV antibody response in the HLA-B/C region (p\u2009=\u20096.64\u2009\u00d7\u200910<sup>-09</sup>). For EBV, associations are identified for VCA (rs71542439, p\u2009=\u20091.15\u2009\u00d7\u200910<sup>-12</sup>). Human leucocyte antigen (HLA) and trans-ancestry fine-mapping substantiate that distinct variants in HLA-DQA1 (p\u2009=\u20095.24\u2009\u00d7\u200910<sup>-44</sup>) are driving associations for EBNA-1 in Africa. This study highlights complex interactions between KSHV and EBV, in addition to distinct genetic architectures resulting in important differences in pathogenesis and transmission.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41467-020-17696-2.pdf; doi:https://doi.org/10.1038/s41467-020-17696-2; html:https://europepmc.org/articles/PMC7395761; pdf:https://europepmc.org/articles/PMC7395761?pdf=render"
+  },
   {
     "id": "34135032",
     "doi": "https://doi.org/10.1136/bmjopen-2020-043906",
@@ -16795,23 +16829,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/11/6/e043906.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-043906; html:https://europepmc.org/articles/PMC8211043; pdf:https://europepmc.org/articles/PMC8211043?pdf=render"
   },
-  {
-    "id": "36806317",
-    "doi": "https://doi.org/10.1038/s41746-023-00749-3",
-    "title": "Long-term participant retention and engagement patterns in an app and wearable-based multinational remote digital depression study.",
-    "authorString": "Zhang Y, Pratap A, Folarin AA, Sun S, Cummins N, Matcham F, Vairavan S, Dineley J, Ranjan Y, Rashid Z, Conde P, Stewart C, White KM, Oetzmann C, Ivan A, Lamers F, Siddi S, Rambla CH, Simblett S, Nica R, Mohr DC, Myin-Germeys I, Wykes T, Haro JM, Penninx BWJH, Annas P, Narayan VA, Hotopf M, Dobson RJB, RADAR-CNS consortium.",
-    "authorAffiliations": "",
-    "journalTitle": "NPJ digital medicine",
-    "pubYear": "2023",
-    "date": "2023-02-17",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Recent growth in digital technologies has enabled the recruitment and monitoring of large and diverse populations in remote health studies. However, the generalizability of inference drawn from remotely collected health data could be severely impacted by uneven participant engagement and attrition over the course of the study. We report findings on long-term participant retention and engagement patterns in a large multinational observational digital study for depression containing active (surveys) and passive sensor data collected via Android smartphones, and Fitbit devices from 614 participants for up to 2 years. Majority of participants (67.6%) continued to remain engaged in the study after 43 weeks. Unsupervised clustering of participants' study apps and Fitbit usage data showed 3 distinct engagement subgroups for each data stream. We found: (i) the least engaged group had the highest depression severity (4 PHQ8 points higher) across all data streams; (ii) the least engaged group (completed 4 bi-weekly surveys) took significantly longer to respond to survey notifications (3.8\u2009h more) and were 5 years younger compared to the most engaged group (completed 20 bi-weekly surveys); and (iii) a considerable proportion (44.6%) of the participants who stopped completing surveys after 8 weeks continued to share passive Fitbit data for significantly longer (average 42 weeks). Additionally, multivariate survival models showed participants' age, ownership and brand of smartphones, and recruitment sites to be associated with retention in the study. Together these findings could inform the design of future digital health studies to enable equitable and balanced data collection from diverse populations.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41746-023-00749-3.pdf; doi:https://doi.org/10.1038/s41746-023-00749-3; html:https://europepmc.org/articles/PMC9938183; pdf:https://europepmc.org/articles/PMC9938183?pdf=render"
-  },
   {
     "id": "33845766",
     "doi": "https://doi.org/10.1186/s12879-021-05992-1",
@@ -16830,21 +16847,21 @@
     "urls": "pdf:https://bmcinfectdis.biomedcentral.com/counter/pdf/10.1186/s12879-021-05992-1; doi:https://doi.org/10.1186/s12879-021-05992-1; html:https://europepmc.org/articles/PMC8040367; pdf:https://europepmc.org/articles/PMC8040367?pdf=render"
   },
   {
-    "id": "32737300",
-    "doi": "https://doi.org/10.1038/s41467-020-17696-2",
-    "title": "Distinct genetic architectures and environmental factors associate with host response to the \u03b32-herpesvirus infections.",
-    "authorString": "Sallah N, Miley W, Labo N, Carstensen T, Fatumo S, Gurdasani D, Pollard MO, Dilthey AT, Mentzer AJ, Marshall V, Cornejo Castro EM, Pomilla C, Young EH, Asiki G, Hibberd ML, Sandhu M, Kellam P, Newton R, Whitby D, Barroso I.",
+    "id": "36806317",
+    "doi": "https://doi.org/10.1038/s41746-023-00749-3",
+    "title": "Long-term participant retention and engagement patterns in an app and wearable-based multinational remote digital depression study.",
+    "authorString": "Zhang Y, Pratap A, Folarin AA, Sun S, Cummins N, Matcham F, Vairavan S, Dineley J, Ranjan Y, Rashid Z, Conde P, Stewart C, White KM, Oetzmann C, Ivan A, Lamers F, Siddi S, Rambla CH, Simblett S, Nica R, Mohr DC, Myin-Germeys I, Wykes T, Haro JM, Penninx BWJH, Annas P, Narayan VA, Hotopf M, Dobson RJB, RADAR-CNS consortium.",
     "authorAffiliations": "",
-    "journalTitle": "Nature communications",
-    "pubYear": "2020",
-    "date": "2020-07-31",
+    "journalTitle": "NPJ digital medicine",
+    "pubYear": "2023",
+    "date": "2023-02-17",
     "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr Virus (EBV) establish life-long infections and are associated with malignancies. Striking geographic variation in incidence and the fact that virus alone is insufficient to cause disease, suggests other co-factors are involved. Here we present epidemiological analysis and genome-wide association study (GWAS) in 4365 individuals from an African population cohort, to assess the influence of host genetic and non-genetic factors on virus antibody responses. EBV/KSHV co-infection (OR\u2009=\u20095.71(1.58-7.12)), HIV positivity (OR\u2009=\u20092.22(1.32-3.73)) and living in a more rural area (OR\u2009=\u20091.38(1.01-1.89)) are strongly associated with immunogenicity. GWAS reveals associations with KSHV antibody response in the HLA-B/C region (p\u2009=\u20096.64\u2009\u00d7\u200910<sup>-09</sup>). For EBV, associations are identified for VCA (rs71542439, p\u2009=\u20091.15\u2009\u00d7\u200910<sup>-12</sup>). Human leucocyte antigen (HLA) and trans-ancestry fine-mapping substantiate that distinct variants in HLA-DQA1 (p\u2009=\u20095.24\u2009\u00d7\u200910<sup>-44</sup>) are driving associations for EBNA-1 in Africa. This study highlights complex interactions between KSHV and EBV, in addition to distinct genetic architectures resulting in important differences in pathogenesis and transmission.",
+    "abstract": "Recent growth in digital technologies has enabled the recruitment and monitoring of large and diverse populations in remote health studies. However, the generalizability of inference drawn from remotely collected health data could be severely impacted by uneven participant engagement and attrition over the course of the study. We report findings on long-term participant retention and engagement patterns in a large multinational observational digital study for depression containing active (surveys) and passive sensor data collected via Android smartphones, and Fitbit devices from 614 participants for up to 2 years. Majority of participants (67.6%) continued to remain engaged in the study after 43 weeks. Unsupervised clustering of participants' study apps and Fitbit usage data showed 3 distinct engagement subgroups for each data stream. We found: (i) the least engaged group had the highest depression severity (4 PHQ8 points higher) across all data streams; (ii) the least engaged group (completed 4 bi-weekly surveys) took significantly longer to respond to survey notifications (3.8\u2009h more) and were 5 years younger compared to the most engaged group (completed 20 bi-weekly surveys); and (iii) a considerable proportion (44.6%) of the participants who stopped completing surveys after 8 weeks continued to share passive Fitbit data for significantly longer (average 42 weeks). Additionally, multivariate survival models showed participants' age, ownership and brand of smartphones, and recruitment sites to be associated with retention in the study. Together these findings could inform the design of future digital health studies to enable equitable and balanced data collection from diverse populations.",
     "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41467-020-17696-2.pdf; doi:https://doi.org/10.1038/s41467-020-17696-2; html:https://europepmc.org/articles/PMC7395761; pdf:https://europepmc.org/articles/PMC7395761?pdf=render"
+    "urls": "pdf:https://www.nature.com/articles/s41746-023-00749-3.pdf; doi:https://doi.org/10.1038/s41746-023-00749-3; html:https://europepmc.org/articles/PMC9938183; pdf:https://europepmc.org/articles/PMC9938183?pdf=render"
   },
   {
     "id": "39054034",
@@ -16863,6 +16880,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/S2213-8587(24)00159-1"
   },
+  {
+    "id": "35976089",
+    "doi": "https://doi.org/10.1515/cclm-2022-0135",
+    "title": "Reference ranges for GDF-15, and risk factors associated with GDF-15, in a large general population cohort.",
+    "authorString": "Welsh P, Kimenai DM, Marioni RE, Hayward C, Campbell A, Porteous D, Mills NL, O'Rahilly S, Sattar N.",
+    "authorAffiliations": "",
+    "journalTitle": "Clinical chemistry and laboratory medicine",
+    "pubYear": "2022",
+    "date": "2022-08-18",
+    "isOpenAccess": "N",
+    "keywords": "Biochemical markers; Guidelines; Reference Ranges",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objectives</h4>Growth differentiation factor (GDF)-15 is attracting interest as a biomarker in several areas of medicine. We aimed to evaluate the reference range for GDF-15 in\u00a0a\u00a0general population, and to explore demographics, classical cardiovascular disease risk factors, and other cardiac biomarkers associated with GDF-15.<h4>Methods</h4>GDF-15 was measured in serum from 19,462 individuals in the Generation Scotland Scottish Family Health Study. Associations of cardiometabolic risk factors with GDF-15 were tested using adjusted linear regression. Among 18,507 participants with no heart disease, heart failure, or stroke, and not pregnant, reference ranges (median and 97.5th centiles) were derived by decade age bands and sex.<h4>Results</h4>Among males in the reference range population, median (97.5th centile) GDF-15 concentration at age <30 years was 537 (1,135)\u00a0pg/mL, rising to 931 (2,492)\u00a0pg/mL at 50-59\u00a0years, and 2,152 (5,972) pg/mL at\u00a0\u226580 years. In females, median GDF-15 at age <30\u00a0years was 628 (2,195)\u00a0pg/mL, 881 (2,323)\u00a0pg/mL at 50-59\u00a0years, and 1847 (6,830)\u00a0pg/mL at\u00a0\u226580\u00a0years. Among those known to be pregnant, median GDF-15 was 19,311\u00a0pg/mL. After adjustment, GDF-15 was\u00a0higher in participants with adverse cardiovascular risk factors, including current smoking (+26.1%), those with previous heart disease (+12.7%), stroke (+17.1%), heart failure (+25.3%), and particularly diabetes (+60.2%). GDF-15 had positive associations with cardiac biomarkers cardiac troponin I, cardiac troponin T, and N-terminal pro B-type natriuretic peptide (NT-proBNP).<h4>Conclusions</h4>These data define reference ranges for GDF-15 for comparison in future studies, and identify potentially confounding risk factors and mediators to be considered in interpreting GDF-15 concentrations.",
+    "laySummary": "",
+    "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9524804; doi:https://doi.org/10.1515/cclm-2022-0135; html:https://europepmc.org/articles/PMC9524804; pdf:https://europepmc.org/articles/PMC9524804?pdf=render; doi:https://doi.org/10.1515/cclm-2022-0135"
+  },
   {
     "id": "34785588",
     "doi": "https://doi.org/10.1136/openhrt-2021-001784",
@@ -16897,40 +16931,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1177/09622802211055853; doi:https://doi.org/10.1177/09622802211055853; html:https://europepmc.org/articles/PMC9465559; pdf:https://europepmc.org/articles/PMC9465559?pdf=render"
   },
-  {
-    "id": "36879385",
-    "doi": "https://doi.org/10.1097/ta.0000000000003950",
-    "title": "Cost-effectiveness of a purpose-built ward environment and new allied health model of care for major trauma.",
-    "authorString": "Gabbe BJ, Reeder S, Ekegren CL, Mather A, Kimmel L, Cameron PA, Higgins AM.",
-    "authorAffiliations": "",
-    "journalTitle": "The journal of trauma and acute care surgery",
-    "pubYear": "2023",
-    "date": "2023-03-07",
-    "isOpenAccess": "N",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Targeted rehabilitation within the acute inpatient setting could have a substantial impact on improving outcomes for major trauma patients. The aim of this study was to investigate the cost-effectiveness of the introduction of a purpose-built ward environment, and a new allied health model of care (AHMOC) delivered in the acute inpatient setting, in a major trauma population.<h4>Methods</h4>The statewide trauma registry, the trauma center's data warehouse, and electronic medical record data were used for this observational study. There were three phases: baseline, new ward, and new AHMOC. Cost-effectiveness was measured as cost per quality-adjusted life year using preinjury, hospital discharge, 1-month and 6-month 5-level, EQ-5D utility scores. Total costs included initial acute and inpatient rehabilitation care, as well as outpatient, readmission and ED presentations to 6-months.<h4>Results</h4>Four hundred eleven patients were included. Case-mix was stable between phases. The median (IQR) number of allied health services received by patients was 8 (5-17) at baseline, 10 (5-19) in the new ward phase, and 17 (9-23) in the AHMOC phase. The proportion discharged to rehabilitation was 37% at baseline, 45% with the new ward and 28% with the new AHMOC. Mean (SD) total Australian dollar costs were $69,335 ($141,175) at baseline, $55,943 ($82,706) with the new ward and $37,833 ($49,004) with the AHMOC. The probability of the AHMOC being cost-effective at a willingness-to-pay threshold of $50,000 per quality-adjusted life year was 99.4% compared with baseline and 98% compared with the new ward.<h4>Conclusion</h4>The new allied health model of care was found to be a cost-effective intervention. Uptake of this model of allied health care at other trauma centers has the potential to reduce the cost and burden of major trauma.<h4>Level of evidence</h4>Economic and Value-based Evaluations; Level III.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1097/TA.0000000000003950"
-  },
-  {
-    "id": "35976089",
-    "doi": "https://doi.org/10.1515/cclm-2022-0135",
-    "title": "Reference ranges for GDF-15, and risk factors associated with GDF-15, in a large general population cohort.",
-    "authorString": "Welsh P, Kimenai DM, Marioni RE, Hayward C, Campbell A, Porteous D, Mills NL, O'Rahilly S, Sattar N.",
-    "authorAffiliations": "",
-    "journalTitle": "Clinical chemistry and laboratory medicine",
-    "pubYear": "2022",
-    "date": "2022-08-18",
-    "isOpenAccess": "N",
-    "keywords": "Biochemical markers; Guidelines; Reference Ranges",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objectives</h4>Growth differentiation factor (GDF)-15 is attracting interest as a biomarker in several areas of medicine. We aimed to evaluate the reference range for GDF-15 in\u00a0a\u00a0general population, and to explore demographics, classical cardiovascular disease risk factors, and other cardiac biomarkers associated with GDF-15.<h4>Methods</h4>GDF-15 was measured in serum from 19,462 individuals in the Generation Scotland Scottish Family Health Study. Associations of cardiometabolic risk factors with GDF-15 were tested using adjusted linear regression. Among 18,507 participants with no heart disease, heart failure, or stroke, and not pregnant, reference ranges (median and 97.5th centiles) were derived by decade age bands and sex.<h4>Results</h4>Among males in the reference range population, median (97.5th centile) GDF-15 concentration at age <30 years was 537 (1,135)\u00a0pg/mL, rising to 931 (2,492)\u00a0pg/mL at 50-59\u00a0years, and 2,152 (5,972) pg/mL at\u00a0\u226580 years. In females, median GDF-15 at age <30\u00a0years was 628 (2,195)\u00a0pg/mL, 881 (2,323)\u00a0pg/mL at 50-59\u00a0years, and 1847 (6,830)\u00a0pg/mL at\u00a0\u226580\u00a0years. Among those known to be pregnant, median GDF-15 was 19,311\u00a0pg/mL. After adjustment, GDF-15 was\u00a0higher in participants with adverse cardiovascular risk factors, including current smoking (+26.1%), those with previous heart disease (+12.7%), stroke (+17.1%), heart failure (+25.3%), and particularly diabetes (+60.2%). GDF-15 had positive associations with cardiac biomarkers cardiac troponin I, cardiac troponin T, and N-terminal pro B-type natriuretic peptide (NT-proBNP).<h4>Conclusions</h4>These data define reference ranges for GDF-15 for comparison in future studies, and identify potentially confounding risk factors and mediators to be considered in interpreting GDF-15 concentrations.",
-    "laySummary": "",
-    "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9524804; doi:https://doi.org/10.1515/cclm-2022-0135; html:https://europepmc.org/articles/PMC9524804; pdf:https://europepmc.org/articles/PMC9524804?pdf=render; doi:https://doi.org/10.1515/cclm-2022-0135"
-  },
   {
     "id": "32310142",
     "doi": "https://doi.org/10.2196/14306",
@@ -16948,6 +16948,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.2196/14306; doi:https://doi.org/10.2196/14306; html:https://europepmc.org/articles/PMC7199134"
   },
+  {
+    "id": "36879385",
+    "doi": "https://doi.org/10.1097/ta.0000000000003950",
+    "title": "Cost-effectiveness of a purpose-built ward environment and new allied health model of care for major trauma.",
+    "authorString": "Gabbe BJ, Reeder S, Ekegren CL, Mather A, Kimmel L, Cameron PA, Higgins AM.",
+    "authorAffiliations": "",
+    "journalTitle": "The journal of trauma and acute care surgery",
+    "pubYear": "2023",
+    "date": "2023-03-07",
+    "isOpenAccess": "N",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Targeted rehabilitation within the acute inpatient setting could have a substantial impact on improving outcomes for major trauma patients. The aim of this study was to investigate the cost-effectiveness of the introduction of a purpose-built ward environment, and a new allied health model of care (AHMOC) delivered in the acute inpatient setting, in a major trauma population.<h4>Methods</h4>The statewide trauma registry, the trauma center's data warehouse, and electronic medical record data were used for this observational study. There were three phases: baseline, new ward, and new AHMOC. Cost-effectiveness was measured as cost per quality-adjusted life year using preinjury, hospital discharge, 1-month and 6-month 5-level, EQ-5D utility scores. Total costs included initial acute and inpatient rehabilitation care, as well as outpatient, readmission and ED presentations to 6-months.<h4>Results</h4>Four hundred eleven patients were included. Case-mix was stable between phases. The median (IQR) number of allied health services received by patients was 8 (5-17) at baseline, 10 (5-19) in the new ward phase, and 17 (9-23) in the AHMOC phase. The proportion discharged to rehabilitation was 37% at baseline, 45% with the new ward and 28% with the new AHMOC. Mean (SD) total Australian dollar costs were $69,335 ($141,175) at baseline, $55,943 ($82,706) with the new ward and $37,833 ($49,004) with the AHMOC. The probability of the AHMOC being cost-effective at a willingness-to-pay threshold of $50,000 per quality-adjusted life year was 99.4% compared with baseline and 98% compared with the new ward.<h4>Conclusion</h4>The new allied health model of care was found to be a cost-effective intervention. Uptake of this model of allied health care at other trauma centers has the potential to reduce the cost and burden of major trauma.<h4>Level of evidence</h4>Economic and Value-based Evaluations; Level III.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1097/TA.0000000000003950"
+  },
   {
     "id": "38066209",
     "doi": "https://doi.org/10.1038/s41591-023-02665-1",
@@ -16965,23 +16982,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1038/s41591-023-02665-1; html:https://europepmc.org/articles/PMC10719102; pdf:https://europepmc.org/articles/PMC10719102?pdf=render"
   },
-  {
-    "id": "38304287",
-    "doi": "https://doi.org/10.3389/fpsyt.2024.1347358",
-    "title": "How will AI make sense of our messy lives and improve our mental health?",
-    "authorString": "Speechley J, McTernan M.",
-    "authorAffiliations": "",
-    "journalTitle": "Frontiers in psychiatry",
-    "pubYear": "2024",
-    "date": "2024-01-18",
-    "isOpenAccess": "Y",
-    "keywords": "Artificial intelligence; Data; Mental health; TRUST; Patient And Public Engagement",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.3389/fpsyt.2024.1347358; html:https://europepmc.org/articles/PMC10832992; pdf:https://europepmc.org/articles/PMC10832992?pdf=render"
-  },
   {
     "id": "36805366",
     "doi": "https://doi.org/10.2196/43419",
@@ -16999,6 +16999,23 @@
     "laySummary": "",
     "urls": "pdf:https://publichealth.jmir.org/2023/1/e43419/PDF; doi:https://doi.org/10.2196/43419; html:https://europepmc.org/articles/PMC9989910"
   },
+  {
+    "id": "38304287",
+    "doi": "https://doi.org/10.3389/fpsyt.2024.1347358",
+    "title": "How will AI make sense of our messy lives and improve our mental health?",
+    "authorString": "Speechley J, McTernan M.",
+    "authorAffiliations": "",
+    "journalTitle": "Frontiers in psychiatry",
+    "pubYear": "2024",
+    "date": "2024-01-18",
+    "isOpenAccess": "Y",
+    "keywords": "Artificial intelligence; Data; Mental health; TRUST; Patient And Public Engagement",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.3389/fpsyt.2024.1347358; html:https://europepmc.org/articles/PMC10832992; pdf:https://europepmc.org/articles/PMC10832992?pdf=render"
+  },
   {
     "id": "37381004",
     "doi": "https://doi.org/10.1186/s12913-023-09545-x",
@@ -17016,23 +17033,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmchealthservres.biomedcentral.com/counter/pdf/10.1186/s12913-023-09545-x; doi:https://doi.org/10.1186/s12913-023-09545-x; html:https://europepmc.org/articles/PMC10308762; pdf:https://europepmc.org/articles/PMC10308762?pdf=render"
   },
-  {
-    "id": "34189274",
-    "doi": "https://doi.org/10.23889/ijpds.v5i1.1362",
-    "title": "Concept libraries for automatic electronic health record based phenotyping: A review.",
-    "authorString": "Almowil ZA, Zhou SM, Brophy S.",
-    "authorAffiliations": "",
-    "journalTitle": "International journal of population data science",
-    "pubYear": "2021",
-    "date": "2021-06-16",
-    "isOpenAccess": "Y",
-    "keywords": "Review; Phenotype Algorithms; Linked Electronic Health Records; Concept Libraries",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>Electronic health records (EHR) are linked together to examine disease history and to undertake research into the causes and outcomes of disease. However, the process of constructing algorithms for phenotyping (e.g., identifying disease characteristics) or health characteristics (e.g., smoker) is very time consuming and resource costly. In addition, results can vary greatly between researchers. Reusing or building on algorithms that others have created is a compelling solution to these problems. However, sharing algorithms is not a common practice and many published studies do not detail the clinical code lists used by the researchers in the disease/characteristic definition. To address these challenges, a number of centres across the world have developed health data portals which contain concept libraries (e.g., algorithms for defining concepts such as disease and characteristics) in order to facilitate disease phenotyping and health studies.<h4>Objectives</h4>This study aims to review the literature of existing concept libraries, examine their utilities, identify the current gaps, and suggest future developments.<h4>Methods</h4>The five-stage framework of Arksey and O'Malley was used for the literature search. This approach included defining the research questions, identifying relevant studies through literature review, selecting eligible studies, charting and extracting data, and summarising and reporting the findings.<h4>Results</h4>This review identified seven publicly accessible Electronic Health data concept libraries which were developed in different countries including UK, USA, and Canada. The concept libraries (n = 7) investigated were either general libraries that hold phenotypes of multiple specialties (n = 4) or specialized libraries that manage only certain specialities such as rare diseases (n = 3). There were some clear differences between the general libraries such as archiving data from different electronic sources, and using a range of different types of coding systems. However, they share some clear similarities such as enabling users to upload their own code lists, and allowing users to use/download the publicly accessible code. In addition, there were some differences between the specialized libraries such as difference in ability to search, and if it was possible to use different searching queries such as simple or complex searches. Conversely, there were some similarities between the specialized libraries such as enabling users to upload their own concepts into the libraries and to show where they were published, which facilitates assessing the validity of the concepts. All the specialized libraries aimed to encourage the reuse of research methods such as lists of clinical code and/or metadata.<h4>Conclusion</h4>The seven libraries identified have been developed independently and appear to replicate similar concepts but in different ways. Collaboration between similar libraries would greatly facilitate the use of these libraries for the user. The process of building code lists takes time and effort. Access to existing code lists increases consistency and accuracy of definitions across studies. Concept library developers should collaborate with each other to raise awareness of their existence and of their various functions, which could increase users' contributions to those libraries and promote their wide-ranging adoption.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.23889/ijpds.v5i1.1362; html:https://europepmc.org/articles/PMC8210840; pdf:https://europepmc.org/articles/PMC8210840?pdf=render"
-  },
   {
     "id": "36773891",
     "doi": "https://doi.org/10.1016/j.jinf.2023.02.012",
@@ -17050,6 +17050,23 @@
     "laySummary": "",
     "urls": "pdf:http://www.journalofinfection.com/article/S0163445323000828/pdf; doi:https://doi.org/10.1016/j.jinf.2023.02.012; html:https://europepmc.org/articles/PMC9911979; pdf:https://europepmc.org/articles/PMC9911979?pdf=render"
   },
+  {
+    "id": "34189274",
+    "doi": "https://doi.org/10.23889/ijpds.v5i1.1362",
+    "title": "Concept libraries for automatic electronic health record based phenotyping: A review.",
+    "authorString": "Almowil ZA, Zhou SM, Brophy S.",
+    "authorAffiliations": "",
+    "journalTitle": "International journal of population data science",
+    "pubYear": "2021",
+    "date": "2021-06-16",
+    "isOpenAccess": "Y",
+    "keywords": "Review; Phenotype Algorithms; Linked Electronic Health Records; Concept Libraries",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>Electronic health records (EHR) are linked together to examine disease history and to undertake research into the causes and outcomes of disease. However, the process of constructing algorithms for phenotyping (e.g., identifying disease characteristics) or health characteristics (e.g., smoker) is very time consuming and resource costly. In addition, results can vary greatly between researchers. Reusing or building on algorithms that others have created is a compelling solution to these problems. However, sharing algorithms is not a common practice and many published studies do not detail the clinical code lists used by the researchers in the disease/characteristic definition. To address these challenges, a number of centres across the world have developed health data portals which contain concept libraries (e.g., algorithms for defining concepts such as disease and characteristics) in order to facilitate disease phenotyping and health studies.<h4>Objectives</h4>This study aims to review the literature of existing concept libraries, examine their utilities, identify the current gaps, and suggest future developments.<h4>Methods</h4>The five-stage framework of Arksey and O'Malley was used for the literature search. This approach included defining the research questions, identifying relevant studies through literature review, selecting eligible studies, charting and extracting data, and summarising and reporting the findings.<h4>Results</h4>This review identified seven publicly accessible Electronic Health data concept libraries which were developed in different countries including UK, USA, and Canada. The concept libraries (n = 7) investigated were either general libraries that hold phenotypes of multiple specialties (n = 4) or specialized libraries that manage only certain specialities such as rare diseases (n = 3). There were some clear differences between the general libraries such as archiving data from different electronic sources, and using a range of different types of coding systems. However, they share some clear similarities such as enabling users to upload their own code lists, and allowing users to use/download the publicly accessible code. In addition, there were some differences between the specialized libraries such as difference in ability to search, and if it was possible to use different searching queries such as simple or complex searches. Conversely, there were some similarities between the specialized libraries such as enabling users to upload their own concepts into the libraries and to show where they were published, which facilitates assessing the validity of the concepts. All the specialized libraries aimed to encourage the reuse of research methods such as lists of clinical code and/or metadata.<h4>Conclusion</h4>The seven libraries identified have been developed independently and appear to replicate similar concepts but in different ways. Collaboration between similar libraries would greatly facilitate the use of these libraries for the user. The process of building code lists takes time and effort. Access to existing code lists increases consistency and accuracy of definitions across studies. Concept library developers should collaborate with each other to raise awareness of their existence and of their various functions, which could increase users' contributions to those libraries and promote their wide-ranging adoption.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.23889/ijpds.v5i1.1362; html:https://europepmc.org/articles/PMC8210840; pdf:https://europepmc.org/articles/PMC8210840?pdf=render"
+  },
   {
     "id": "37699069",
     "doi": "https://doi.org/10.1093/ehjci/jead218",
@@ -17135,6 +17152,23 @@
     "laySummary": "",
     "urls": "pdf:https://bjgp.org/content/bjgp/73/726/e43.full.pdf; doi:https://doi.org/10.3399/BJGP.2022.0156; html:https://europepmc.org/articles/PMC9799341; pdf:https://europepmc.org/articles/PMC9799341?pdf=render"
   },
+  {
+    "id": "34716166",
+    "doi": "https://doi.org/10.1136/bmjopen-2021-053268",
+    "title": "Electronic reminders and rewards to improve adherence to inhaled asthma treatment in adolescents: a non-randomised feasibility study in tertiary care.",
+    "authorString": "De Simoni A, Fleming L, Holliday L, Horne R, Priebe S, Bush A, Sheikh A, Griffiths C.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2021",
+    "date": "2021-10-29",
+    "isOpenAccess": "Y",
+    "keywords": "Asthma; Respiratory Medicine (See Thoracic Medicine); Paediatric Thoracic Medicine",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>To test the feasibility and acceptability of a short-term reminder and incentives intervention in adolescents with low adherence to asthma medications.<h4>Methods</h4>Mixed-methods feasibility study in a tertiary care clinic. Adolescents recruited to a 24-week programme with three 8-weekly visits, receiving electronic reminders to prompt inhaled corticosteroid (ICS) inhalation through a mobile app coupled with electronic monitoring devices (EMD). From the second visit, monetary incentives based on adherence of ICS inhalation: \u00a31 per dose, maximum \u00a32\u2009/day, up to \u00a3112/study, collected as gift cards at the third visit. End of study interviews and questionnaires assessing perceptions of asthma and ICS, analysed using the Perceptions and Practicalities Framework.<h4>Participants</h4>Adolescents (11-18 years) with documented low ICS adherence (<80% by EMD), and poor asthma control at the first clinic visit.<h4>Results</h4>10 out of 12 adolescents approached were recruited (7 males, 3 females, 12-16 years). Eight participants provided adherence measures up to the fourth visits and received rewards. Mean study duration was 281 days, with 7/10 participants unable to attend their fourth visit due to COVID-19 lockdown. Only 3/10 participants managed to pair the app/EMD up to the fourth visit, which was associated with improved ICS adherence (from 0.51, SD 0.07 to 0.86, SD 0.05). Adherence did not change in adolescents unable to pair the app/EMD. The intervention was acceptable to participants and parents/guardians. Exit interviews showed that participants welcomed reminders and incentives, though expressed frustration with app/EMD technological difficulties. Participants stated the intervention helped through reminding ICS doses, promoting self-monitoring and increasing motivation to take inhalers.<h4>Conclusions</h4>An intervention using electronic reminders and incentives through an app coupled with an EMD was feasible and acceptable to adolescents with asthma. A pilot randomised controlled trial is warranted to better estimate the effect size on adherence, with improved technical support for the EMD.",
+    "laySummary": "",
+    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/11/10/e053268.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-053268; html:https://europepmc.org/articles/PMC8559117; pdf:https://europepmc.org/articles/PMC8559117?pdf=render"
+  },
   {
     "id": "34641870",
     "doi": "https://doi.org/10.1186/s12911-021-01638-z",
@@ -17169,23 +17203,6 @@
     "laySummary": "",
     "urls": "pdf:https://systematicreviewsjournal.biomedcentral.com/counter/pdf/10.1186/s13643-024-02558-5; doi:https://doi.org/10.1186/s13643-024-02558-5"
   },
-  {
-    "id": "34716166",
-    "doi": "https://doi.org/10.1136/bmjopen-2021-053268",
-    "title": "Electronic reminders and rewards to improve adherence to inhaled asthma treatment in adolescents: a non-randomised feasibility study in tertiary care.",
-    "authorString": "De Simoni A, Fleming L, Holliday L, Horne R, Priebe S, Bush A, Sheikh A, Griffiths C.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2021",
-    "date": "2021-10-29",
-    "isOpenAccess": "Y",
-    "keywords": "Asthma; Respiratory Medicine (See Thoracic Medicine); Paediatric Thoracic Medicine",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objective</h4>To test the feasibility and acceptability of a short-term reminder and incentives intervention in adolescents with low adherence to asthma medications.<h4>Methods</h4>Mixed-methods feasibility study in a tertiary care clinic. Adolescents recruited to a 24-week programme with three 8-weekly visits, receiving electronic reminders to prompt inhaled corticosteroid (ICS) inhalation through a mobile app coupled with electronic monitoring devices (EMD). From the second visit, monetary incentives based on adherence of ICS inhalation: \u00a31 per dose, maximum \u00a32\u2009/day, up to \u00a3112/study, collected as gift cards at the third visit. End of study interviews and questionnaires assessing perceptions of asthma and ICS, analysed using the Perceptions and Practicalities Framework.<h4>Participants</h4>Adolescents (11-18 years) with documented low ICS adherence (<80% by EMD), and poor asthma control at the first clinic visit.<h4>Results</h4>10 out of 12 adolescents approached were recruited (7 males, 3 females, 12-16 years). Eight participants provided adherence measures up to the fourth visits and received rewards. Mean study duration was 281 days, with 7/10 participants unable to attend their fourth visit due to COVID-19 lockdown. Only 3/10 participants managed to pair the app/EMD up to the fourth visit, which was associated with improved ICS adherence (from 0.51, SD 0.07 to 0.86, SD 0.05). Adherence did not change in adolescents unable to pair the app/EMD. The intervention was acceptable to participants and parents/guardians. Exit interviews showed that participants welcomed reminders and incentives, though expressed frustration with app/EMD technological difficulties. Participants stated the intervention helped through reminding ICS doses, promoting self-monitoring and increasing motivation to take inhalers.<h4>Conclusions</h4>An intervention using electronic reminders and incentives through an app coupled with an EMD was feasible and acceptable to adolescents with asthma. A pilot randomised controlled trial is warranted to better estimate the effect size on adherence, with improved technical support for the EMD.",
-    "laySummary": "",
-    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/11/10/e053268.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-053268; html:https://europepmc.org/articles/PMC8559117; pdf:https://europepmc.org/articles/PMC8559117?pdf=render"
-  },
   {
     "id": "37526977",
     "doi": "https://doi.org/10.5830/cvja-2023-037",
@@ -17203,23 +17220,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.5830/CVJA-2023-037"
   },
-  {
-    "id": "37468148",
-    "doi": "https://doi.org/10.1136/bmj-2023-075133",
-    "title": "Associations between self-reported healthcare disruption due to covid-19 and avoidable hospital admission: evidence from seven linked longitudinal studies for England.",
-    "authorString": "Green MA, McKee M, Hamilton OK, Shaw RJ, Macleod J, Boyd A, Katikireddi SV, LH&W NCS Collaborative.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ (Clinical research ed.)",
-    "pubYear": "2023",
-    "date": "2023-07-19",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objectives</h4>To examine whether there is an association between people who experienced disrupted access to healthcare during the covid-19 pandemic and risk of an avoidable hospital admission.<h4>Design</h4>Observational analysis using evidence from seven linked longitudinal cohort studies for England.<h4>Setting</h4>Studies linked to electronic health records from NHS Digital from 1 March 2020 to 25 August 2022. Data were accessed using the UK Longitudinal Linkage Collaboration trusted research environment.<h4>Participants</h4>Individual level records for 29\u2009276 people.<h4>Main outcome measures</h4>Avoidable hospital admissions defined as emergency hospital admissions for ambulatory care sensitive and emergency urgent care sensitive conditions.<h4>Results</h4>9742 participants (weighted percentage 35%, adjusted for sample structure of longitudinal cohorts) self-reported some form of disrupted access to healthcare during the covid-19 pandemic. People with disrupted access were at increased risk of any (odds ratio 1.80, 95% confidence interval 1.39 to 2.34), acute (2.01, 1.39 to 2.92), and chronic (1.80, 1.31 to 2.48) ambulatory care sensitive hospital admissions. For people who experienced disrupted access to appointments (eg, visiting their doctor or an outpatient department) and procedures (eg, surgery, cancer treatment), positive associations were found with measures of avoidable hospital admissions.<h4>Conclusions</h4>Evidence from linked individual level data shows that people whose access to healthcare was disrupted were more likely to have a potentially preventable hospital admission. The findings highlight the need to increase healthcare investment to tackle the short and long term implications of the pandemic, and to protect treatments and procedures during future pandemics.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1136/bmj-2023-075133; html:https://europepmc.org/articles/PMC10354595; pdf:https://europepmc.org/articles/PMC10354595?pdf=render"
-  },
   {
     "id": "35896970",
     "doi": "https://doi.org/10.1186/s12879-022-07628-4",
@@ -17237,6 +17237,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmcinfectdis.biomedcentral.com/counter/pdf/10.1186/s12879-022-07628-4; doi:https://doi.org/10.1186/s12879-022-07628-4; html:https://europepmc.org/articles/PMC9326417; pdf:https://europepmc.org/articles/PMC9326417?pdf=render"
   },
+  {
+    "id": "37468148",
+    "doi": "https://doi.org/10.1136/bmj-2023-075133",
+    "title": "Associations between self-reported healthcare disruption due to covid-19 and avoidable hospital admission: evidence from seven linked longitudinal studies for England.",
+    "authorString": "Green MA, McKee M, Hamilton OK, Shaw RJ, Macleod J, Boyd A, Katikireddi SV, LH&W NCS Collaborative.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ (Clinical research ed.)",
+    "pubYear": "2023",
+    "date": "2023-07-19",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objectives</h4>To examine whether there is an association between people who experienced disrupted access to healthcare during the covid-19 pandemic and risk of an avoidable hospital admission.<h4>Design</h4>Observational analysis using evidence from seven linked longitudinal cohort studies for England.<h4>Setting</h4>Studies linked to electronic health records from NHS Digital from 1 March 2020 to 25 August 2022. Data were accessed using the UK Longitudinal Linkage Collaboration trusted research environment.<h4>Participants</h4>Individual level records for 29\u2009276 people.<h4>Main outcome measures</h4>Avoidable hospital admissions defined as emergency hospital admissions for ambulatory care sensitive and emergency urgent care sensitive conditions.<h4>Results</h4>9742 participants (weighted percentage 35%, adjusted for sample structure of longitudinal cohorts) self-reported some form of disrupted access to healthcare during the covid-19 pandemic. People with disrupted access were at increased risk of any (odds ratio 1.80, 95% confidence interval 1.39 to 2.34), acute (2.01, 1.39 to 2.92), and chronic (1.80, 1.31 to 2.48) ambulatory care sensitive hospital admissions. For people who experienced disrupted access to appointments (eg, visiting their doctor or an outpatient department) and procedures (eg, surgery, cancer treatment), positive associations were found with measures of avoidable hospital admissions.<h4>Conclusions</h4>Evidence from linked individual level data shows that people whose access to healthcare was disrupted were more likely to have a potentially preventable hospital admission. The findings highlight the need to increase healthcare investment to tackle the short and long term implications of the pandemic, and to protect treatments and procedures during future pandemics.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1136/bmj-2023-075133; html:https://europepmc.org/articles/PMC10354595; pdf:https://europepmc.org/articles/PMC10354595?pdf=render"
+  },
   {
     "id": "37432340",
     "doi": "https://doi.org/10.1093/rheumatology/kead346",
@@ -17254,23 +17271,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/rheumatology/advance-article-pdf/doi/10.1093/rheumatology/kead346/50930066/kead346.pdf; doi:https://doi.org/10.1093/rheumatology/kead346; html:https://europepmc.org/articles/PMC10986805; pdf:https://europepmc.org/articles/PMC10986805?pdf=render"
   },
-  {
-    "id": "37022975",
-    "doi": "https://doi.org/10.1210/clinem/dgad201",
-    "title": "Stable Incidence and Increasing Prevalence of Primary Hyperparathyroidism in a Population-based Study in Scotland.",
-    "authorString": "Soto-Pedre E, Newey PJ, Leese GP.",
-    "authorAffiliations": "",
-    "journalTitle": "The Journal of clinical endocrinology and metabolism",
-    "pubYear": "2023",
-    "date": "2023-09-01",
-    "isOpenAccess": "Y",
-    "keywords": "Parathyroid gland; Prevalence; epidemiology; incidence; Primary Hyperparathyroidism",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Context</h4>Previous studies, including our own, have demonstrated a highly variable incidence of primary hyperparathyroidism (PHPT) from year to year.<h4>Objective</h4>We planned to provide a current estimate of the incidence and prevalence of PHPT in a community-based study.<h4>Methods</h4>A population-based retrospective follow-up study was conducted in Tayside (Scotland) from 2007 to 2018. Record-linkage technology (demography, biochemistry, prescribing, hospital admissions, radiology, and mortality data) was used to identify all patients. Cases of PHPT were defined as those with at least 2 raised serum corrected calcium concentration CCA (> 2.55 mmol/L) and/or hospital admissions with PHPT diagnoses and/or surgery records with parathyroidectomy during the follow-up period. The number of prevalent and incident cases of PHPT per calendar year by age and sex were estimated.<h4>Results</h4>A total of 2118 people (72.3% female, mean age 65 years) were identified with an incident case of PHPT. The overall prevalence of PHPT over the 12 years of the study was 0.84% (95% CI, 0.68%-1.02%), steadily increasing from 0.71% in 2007 to 1.02% in 2018. From 2008, the incidence of PHPT was relatively stable from 4 to 6 cases per 10 000 person-years, declining from 11.5 per 10 000 person-years in 2007. The incidence varied from 0.59 per 10 000 person-years (95% CI, 0.40%-0.77%) for those aged 20 to 29 years, to 12.4 per 10 000 person-years (95% CI, 11.2%-13.3%) in those aged 70 to 79 years. Incidence of PHPT was 2.5 times higher in women than in men.<h4>Conclusion</h4>This study is the first showing a relatively steady annual incidence of PHPT at 4 to 6 per 10 000 person-years. This population-based study reports a PHPT prevalence of 0.84%.",
-    "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/jcem/advance-article-pdf/doi/10.1210/clinem/dgad201/50034331/dgad201.pdf; doi:https://doi.org/10.1210/clinem/dgad201; html:https://europepmc.org/articles/PMC10505547"
-  },
   {
     "id": "33052324",
     "doi": "https://doi.org/10.1016/j.eclinm.2020.100574",
@@ -17289,21 +17289,21 @@
     "urls": "pdf:http://www.thelancet.com/article/S2589537020303187/pdf; doi:https://doi.org/10.1016/j.eclinm.2020.100574; html:https://europepmc.org/articles/PMC7545271; pdf:https://europepmc.org/articles/PMC7545271?pdf=render"
   },
   {
-    "id": "35032176",
-    "doi": "https://doi.org/10.1007/s00125-021-05640-y",
-    "title": "Cardiovascular risk prediction in type 2 diabetes: a comparison of 22 risk scores in primary care settings.",
-    "authorString": "Dziopa K, Asselbergs FW, Gratton J, Chaturvedi N, Schmidt AF.",
+    "id": "37022975",
+    "doi": "https://doi.org/10.1210/clinem/dgad201",
+    "title": "Stable Incidence and Increasing Prevalence of Primary Hyperparathyroidism in a Population-based Study in Scotland.",
+    "authorString": "Soto-Pedre E, Newey PJ, Leese GP.",
     "authorAffiliations": "",
-    "journalTitle": "Diabetologia",
-    "pubYear": "2022",
-    "date": "2022-01-15",
+    "journalTitle": "The Journal of clinical endocrinology and metabolism",
+    "pubYear": "2023",
+    "date": "2023-09-01",
     "isOpenAccess": "Y",
-    "keywords": "Prediction; Diabetes; Cardiovascular disease; Risk Score",
+    "keywords": "Parathyroid gland; Prevalence; epidemiology; incidence; Primary Hyperparathyroidism",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Aims/hypothesis</h4>We aimed to compare the performance of risk prediction scores for CVD (i.e., coronary heart disease and stroke), and a broader definition of CVD including atrial fibrillation and heart failure (CVD+), in individuals with type 2 diabetes.<h4>Methods</h4>Scores were identified through a literature review and were included irrespective of the type of predicted cardiovascular outcome or the inclusion of individuals with type 2 diabetes. Performance was assessed in a contemporary, representative sample of 168,871 UK-based individuals with type 2 diabetes (age\u2009\u226518\u00a0years without pre-existing CVD+). Missing observations were addressed using multiple imputation.<h4>Results</h4>We evaluated 22 scores: 13 derived in the general population and nine in individuals with type 2 diabetes. The Systemic Coronary Risk Evaluation (SCORE) CVD rule derived in the general population performed best for both CVD (C statistic 0.67 [95% CI 0.67, 0.67]) and CVD+ (C statistic 0.69 [95% CI 0.69, 0.70]). The C statistic of the remaining scores ranged from 0.62 to 0.67 for CVD, and from 0.64 to 0.69 for CVD+. Calibration slopes (1 indicates perfect calibration) ranged from 0.38 (95% CI 0.37, 0.39) to 0.74 (95% CI 0.72, 0.76) for CVD, and from 0.41 (95% CI 0.40, 0.42) to 0.88 (95% CI 0.86, 0.90) for CVD+. A simple recalibration process considerably improved the performance of the scores, with calibration slopes now ranging between 0.96 and 1.04 for CVD. Scores with more predictors did not outperform scores with fewer predictors: for CVD+, QRISK3 (19 variables) had a C statistic of 0.68 (95% CI 0.68, 0.69), compared with SCORE CVD (six variables) which had a C statistic of 0.69 (95% CI 0.69, 0.70). Scores specific to individuals with diabetes did not discriminate better than scores derived in the general population: the UK Prospective Diabetes Study (UKPDS) scores performed significantly worse than SCORE CVD (p value <0.001).<h4>Conclusions/interpretation</h4>CVD risk prediction scores could not accurately identify individuals with type 2 diabetes who experienced a CVD event in the 10\u00a0years of follow-up. All 22 evaluated models had a comparable and modest discriminative ability.",
+    "abstract": "<h4>Context</h4>Previous studies, including our own, have demonstrated a highly variable incidence of primary hyperparathyroidism (PHPT) from year to year.<h4>Objective</h4>We planned to provide a current estimate of the incidence and prevalence of PHPT in a community-based study.<h4>Methods</h4>A population-based retrospective follow-up study was conducted in Tayside (Scotland) from 2007 to 2018. Record-linkage technology (demography, biochemistry, prescribing, hospital admissions, radiology, and mortality data) was used to identify all patients. Cases of PHPT were defined as those with at least 2 raised serum corrected calcium concentration CCA (> 2.55 mmol/L) and/or hospital admissions with PHPT diagnoses and/or surgery records with parathyroidectomy during the follow-up period. The number of prevalent and incident cases of PHPT per calendar year by age and sex were estimated.<h4>Results</h4>A total of 2118 people (72.3% female, mean age 65 years) were identified with an incident case of PHPT. The overall prevalence of PHPT over the 12 years of the study was 0.84% (95% CI, 0.68%-1.02%), steadily increasing from 0.71% in 2007 to 1.02% in 2018. From 2008, the incidence of PHPT was relatively stable from 4 to 6 cases per 10 000 person-years, declining from 11.5 per 10 000 person-years in 2007. The incidence varied from 0.59 per 10 000 person-years (95% CI, 0.40%-0.77%) for those aged 20 to 29 years, to 12.4 per 10 000 person-years (95% CI, 11.2%-13.3%) in those aged 70 to 79 years. Incidence of PHPT was 2.5 times higher in women than in men.<h4>Conclusion</h4>This study is the first showing a relatively steady annual incidence of PHPT at 4 to 6 per 10 000 person-years. This population-based study reports a PHPT prevalence of 0.84%.",
     "laySummary": "",
-    "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s00125-021-05640-y.pdf; doi:https://doi.org/10.1007/s00125-021-05640-y; html:https://europepmc.org/articles/PMC8894164; pdf:https://europepmc.org/articles/PMC8894164?pdf=render"
+    "urls": "pdf:https://academic.oup.com/jcem/advance-article-pdf/doi/10.1210/clinem/dgad201/50034331/dgad201.pdf; doi:https://doi.org/10.1210/clinem/dgad201; html:https://europepmc.org/articles/PMC10505547"
   },
   {
     "id": "33112263",
@@ -17340,21 +17340,21 @@
     "urls": ""
   },
   {
-    "id": "31960476",
-    "doi": "https://doi.org/10.1111/ppe.12627",
-    "title": "Phenotyping congenital anomalies in administrative hospital records.",
-    "authorString": "Zylbersztejn A, Verf\u00fcrden M, Hardelid P, Gilbert R, Wijlaars L.",
+    "id": "35032176",
+    "doi": "https://doi.org/10.1007/s00125-021-05640-y",
+    "title": "Cardiovascular risk prediction in type 2 diabetes: a comparison of 22 risk scores in primary care settings.",
+    "authorString": "Dziopa K, Asselbergs FW, Gratton J, Chaturvedi N, Schmidt AF.",
     "authorAffiliations": "",
-    "journalTitle": "Paediatric and perinatal epidemiology",
-    "pubYear": "2020",
-    "date": "2020-01-01",
+    "journalTitle": "Diabetologia",
+    "pubYear": "2022",
+    "date": "2022-01-15",
     "isOpenAccess": "Y",
-    "keywords": "Phenotyping; Congenital Anomalies; International Comparison; Administrative Data",
-    "nationalPriorities": "Improving Public Health",
+    "keywords": "Prediction; Diabetes; Cardiovascular disease; Risk Score",
+    "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Congenital anomalies are a major cause of co-morbidity in children. Diagnostic code lists are increasingly used to identify congenital anomalies in administrative health records. Evidence is lacking on comparability of these code lists.<h4>Objectives</h4>To compare prevalence of congenital anomalies and prognostic outcomes for children with congenital anomalies identified in administrative health records using three different code lists.<h4>Methods</h4>We developed national cohorts of singleton livebirths in England (n\u00a0=\u00a07\u00a0354\u00a0363, 2003-2014) and Scotland (n\u00a0=\u00a0493\u00a0556, 2003-2011). Children with congenital anomalies were identified if congenital anomaly diagnosis was recorded at birth, during subsequent hospital admission or as cause of death before 2\u00a0years old. We used three code lists: the EUROCAT list for congenital anomaly surveillance in Europe; the Hardelid list developed to identify children with chronic conditions (including congenital anomalies) admitted to hospital in England; and the Feudtner list developed to indicate children with complex chronic conditions (including congenital anomalies) admitted to hospitals in the United States. We compared prevalence, and risks of postnatal hospital readmission and death according to each code list in England and Scotland.<h4>Results</h4>Prevalence of congenital anomalies was highest using the EUROCAT list (4.1% of livebirths in England, 3.7% in Scotland), followed by Hardelid (3.1% and 3.0% of livebirths, respectively) and Feudtner (1.8% and 1.5% of livebirths, respectively). 67.2%-73.3% of children with congenital anomalies in England and 65.2%-77.0% in Scotland had at least one postnatal hospital admission across the three code lists; mortality ranged between 42.6-75.4 and 41.5-88.7 deaths per 1000 births in England Scotland, respectively. The risk of these adverse outcomes was highest using Feudtner and lowest using EUROCAT code lists.<h4>Conclusions</h4>The prevalence of congenital anomalies varied by congenital anomaly code list, over time and between countries, reflecting in part differences in hospital coding practices and admission thresholds. As a minimum, researchers using administrative health data to study congenital anomalies should report sensitivity analyses using different code lists.",
-    "laySummary": "This study identifies children born with congenital anomalies from administrative health data. The the prevalence of congenital anomalies and prognostic outcomes for children with congenital anomalies are compared using three different code lists. The study found that the prevalence of congenital anomalies varied by code list, over time and between countries. This reflects differences in hospital coding practices and admission thresholds.",
-    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/ppe.12627; doi:https://doi.org/10.1111/ppe.12627; html:https://europepmc.org/articles/PMC7003968; pdf:https://europepmc.org/articles/PMC7003968?pdf=render"
+    "abstract": "<h4>Aims/hypothesis</h4>We aimed to compare the performance of risk prediction scores for CVD (i.e., coronary heart disease and stroke), and a broader definition of CVD including atrial fibrillation and heart failure (CVD+), in individuals with type 2 diabetes.<h4>Methods</h4>Scores were identified through a literature review and were included irrespective of the type of predicted cardiovascular outcome or the inclusion of individuals with type 2 diabetes. Performance was assessed in a contemporary, representative sample of 168,871 UK-based individuals with type 2 diabetes (age\u2009\u226518\u00a0years without pre-existing CVD+). Missing observations were addressed using multiple imputation.<h4>Results</h4>We evaluated 22 scores: 13 derived in the general population and nine in individuals with type 2 diabetes. The Systemic Coronary Risk Evaluation (SCORE) CVD rule derived in the general population performed best for both CVD (C statistic 0.67 [95% CI 0.67, 0.67]) and CVD+ (C statistic 0.69 [95% CI 0.69, 0.70]). The C statistic of the remaining scores ranged from 0.62 to 0.67 for CVD, and from 0.64 to 0.69 for CVD+. Calibration slopes (1 indicates perfect calibration) ranged from 0.38 (95% CI 0.37, 0.39) to 0.74 (95% CI 0.72, 0.76) for CVD, and from 0.41 (95% CI 0.40, 0.42) to 0.88 (95% CI 0.86, 0.90) for CVD+. A simple recalibration process considerably improved the performance of the scores, with calibration slopes now ranging between 0.96 and 1.04 for CVD. Scores with more predictors did not outperform scores with fewer predictors: for CVD+, QRISK3 (19 variables) had a C statistic of 0.68 (95% CI 0.68, 0.69), compared with SCORE CVD (six variables) which had a C statistic of 0.69 (95% CI 0.69, 0.70). Scores specific to individuals with diabetes did not discriminate better than scores derived in the general population: the UK Prospective Diabetes Study (UKPDS) scores performed significantly worse than SCORE CVD (p value <0.001).<h4>Conclusions/interpretation</h4>CVD risk prediction scores could not accurately identify individuals with type 2 diabetes who experienced a CVD event in the 10\u00a0years of follow-up. All 22 evaluated models had a comparable and modest discriminative ability.",
+    "laySummary": "",
+    "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s00125-021-05640-y.pdf; doi:https://doi.org/10.1007/s00125-021-05640-y; html:https://europepmc.org/articles/PMC8894164; pdf:https://europepmc.org/articles/PMC8894164?pdf=render"
   },
   {
     "id": "34161326",
@@ -17374,21 +17374,21 @@
     "urls": "pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009121&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1009121; html:https://europepmc.org/articles/PMC8259985; pdf:https://europepmc.org/articles/PMC8259985?pdf=render"
   },
   {
-    "id": "36620207",
-    "doi": "https://doi.org/10.3389/fphys.2022.1089343",
-    "title": "Incorporating structural abnormalities in equivalent dipole layer based ECG simulations.",
-    "authorString": "Boonstra MJ, Oostendorp TF, Roudijk RW, Kloosterman M, Asselbergs FW, Loh P, Van Dam PM.",
+    "id": "31960476",
+    "doi": "https://doi.org/10.1111/ppe.12627",
+    "title": "Phenotyping congenital anomalies in administrative hospital records.",
+    "authorString": "Zylbersztejn A, Verf\u00fcrden M, Hardelid P, Gilbert R, Wijlaars L.",
     "authorAffiliations": "",
-    "journalTitle": "Frontiers in physiology",
-    "pubYear": "2022",
-    "date": "2022-12-22",
+    "journalTitle": "Paediatric and perinatal epidemiology",
+    "pubYear": "2020",
+    "date": "2020-01-01",
     "isOpenAccess": "Y",
-    "keywords": "Simulation; Myocardial Disease; Electrocardiogram (Ecg); Cardiac Activation; Ecgsim; Equivalent Dipole Layer",
-    "nationalPriorities": "",
+    "keywords": "Phenotyping; Congenital Anomalies; International Comparison; Administrative Data",
+    "nationalPriorities": "Improving Public Health",
     "healthCategories": "",
-    "abstract": "<b>Introduction:</b> Electrical activity of the myocardium is recorded with the 12-lead ECG. ECG simulations can improve our understanding of the relation between abnormal ventricular activation in diseased myocardium and body surface potentials (BSP). However, in equivalent dipole layer (EDL)-based ECG simulations, the presence of diseased myocardium breaks the equivalence of the dipole layer. To simulate diseased myocardium, patches with altered electrophysiological characteristics were incorporated within the model. The relation between diseased myocardium and corresponding BSP was investigated in a simulation study. <b>Methods:</b> Activation sequences in normal and diseased myocardium were simulated and corresponding 64-lead BSP were computed in four models with distinct patch locations. QRS-complexes were compared using correlation coefficient (CC). The effect of different types of patch activation was assessed. Of one patient, simulated electrograms were compared to electrograms recorded during invasive electro-anatomical mapping. <b>Results:</b> Hundred-fifty-three abnormal activation sequences were simulated. Median QRS-CC of delayed versus dyssynchronous were significantly different (1.00 vs. 0.97, <i>p</i> < 0.001). Depending on the location of the patch, BSP leads were affected differently. Within diseased regions, fragmentation, low bipolar voltages and late potentials were observed in both recorded and simulated electrograms. <b>Discussion:</b> A novel method to simulate cardiomyopathy in EDL-based ECG simulations was established and evaluated. The new patch-based approach created a realistic relation between ECG waveforms and underlying activation sequences. Findings in the simulated cases were in agreement with clinical observations. With this method, our understanding of disease progression in cardiomyopathies may be further improved and used in advanced inverse ECG procedures.",
-    "laySummary": "",
-    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fphys.2022.1089343/pdf; doi:https://doi.org/10.3389/fphys.2022.1089343; html:https://europepmc.org/articles/PMC9814485; pdf:https://europepmc.org/articles/PMC9814485?pdf=render"
+    "abstract": "<h4>Background</h4>Congenital anomalies are a major cause of co-morbidity in children. Diagnostic code lists are increasingly used to identify congenital anomalies in administrative health records. Evidence is lacking on comparability of these code lists.<h4>Objectives</h4>To compare prevalence of congenital anomalies and prognostic outcomes for children with congenital anomalies identified in administrative health records using three different code lists.<h4>Methods</h4>We developed national cohorts of singleton livebirths in England (n\u00a0=\u00a07\u00a0354\u00a0363, 2003-2014) and Scotland (n\u00a0=\u00a0493\u00a0556, 2003-2011). Children with congenital anomalies were identified if congenital anomaly diagnosis was recorded at birth, during subsequent hospital admission or as cause of death before 2\u00a0years old. We used three code lists: the EUROCAT list for congenital anomaly surveillance in Europe; the Hardelid list developed to identify children with chronic conditions (including congenital anomalies) admitted to hospital in England; and the Feudtner list developed to indicate children with complex chronic conditions (including congenital anomalies) admitted to hospitals in the United States. We compared prevalence, and risks of postnatal hospital readmission and death according to each code list in England and Scotland.<h4>Results</h4>Prevalence of congenital anomalies was highest using the EUROCAT list (4.1% of livebirths in England, 3.7% in Scotland), followed by Hardelid (3.1% and 3.0% of livebirths, respectively) and Feudtner (1.8% and 1.5% of livebirths, respectively). 67.2%-73.3% of children with congenital anomalies in England and 65.2%-77.0% in Scotland had at least one postnatal hospital admission across the three code lists; mortality ranged between 42.6-75.4 and 41.5-88.7 deaths per 1000 births in England Scotland, respectively. The risk of these adverse outcomes was highest using Feudtner and lowest using EUROCAT code lists.<h4>Conclusions</h4>The prevalence of congenital anomalies varied by congenital anomaly code list, over time and between countries, reflecting in part differences in hospital coding practices and admission thresholds. As a minimum, researchers using administrative health data to study congenital anomalies should report sensitivity analyses using different code lists.",
+    "laySummary": "This study identifies children born with congenital anomalies from administrative health data. The the prevalence of congenital anomalies and prognostic outcomes for children with congenital anomalies are compared using three different code lists. The study found that the prevalence of congenital anomalies varied by code list, over time and between countries. This reflects differences in hospital coding practices and admission thresholds.",
+    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/ppe.12627; doi:https://doi.org/10.1111/ppe.12627; html:https://europepmc.org/articles/PMC7003968; pdf:https://europepmc.org/articles/PMC7003968?pdf=render"
   },
   {
     "id": "35039282",
@@ -17407,6 +17407,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/1/e049506.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-049506; html:https://europepmc.org/articles/PMC8764710; pdf:https://europepmc.org/articles/PMC8764710?pdf=render"
   },
+  {
+    "id": "36620207",
+    "doi": "https://doi.org/10.3389/fphys.2022.1089343",
+    "title": "Incorporating structural abnormalities in equivalent dipole layer based ECG simulations.",
+    "authorString": "Boonstra MJ, Oostendorp TF, Roudijk RW, Kloosterman M, Asselbergs FW, Loh P, Van Dam PM.",
+    "authorAffiliations": "",
+    "journalTitle": "Frontiers in physiology",
+    "pubYear": "2022",
+    "date": "2022-12-22",
+    "isOpenAccess": "Y",
+    "keywords": "Simulation; Myocardial Disease; Electrocardiogram (Ecg); Cardiac Activation; Ecgsim; Equivalent Dipole Layer",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<b>Introduction:</b> Electrical activity of the myocardium is recorded with the 12-lead ECG. ECG simulations can improve our understanding of the relation between abnormal ventricular activation in diseased myocardium and body surface potentials (BSP). However, in equivalent dipole layer (EDL)-based ECG simulations, the presence of diseased myocardium breaks the equivalence of the dipole layer. To simulate diseased myocardium, patches with altered electrophysiological characteristics were incorporated within the model. The relation between diseased myocardium and corresponding BSP was investigated in a simulation study. <b>Methods:</b> Activation sequences in normal and diseased myocardium were simulated and corresponding 64-lead BSP were computed in four models with distinct patch locations. QRS-complexes were compared using correlation coefficient (CC). The effect of different types of patch activation was assessed. Of one patient, simulated electrograms were compared to electrograms recorded during invasive electro-anatomical mapping. <b>Results:</b> Hundred-fifty-three abnormal activation sequences were simulated. Median QRS-CC of delayed versus dyssynchronous were significantly different (1.00 vs. 0.97, <i>p</i> < 0.001). Depending on the location of the patch, BSP leads were affected differently. Within diseased regions, fragmentation, low bipolar voltages and late potentials were observed in both recorded and simulated electrograms. <b>Discussion:</b> A novel method to simulate cardiomyopathy in EDL-based ECG simulations was established and evaluated. The new patch-based approach created a realistic relation between ECG waveforms and underlying activation sequences. Findings in the simulated cases were in agreement with clinical observations. With this method, our understanding of disease progression in cardiomyopathies may be further improved and used in advanced inverse ECG procedures.",
+    "laySummary": "",
+    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fphys.2022.1089343/pdf; doi:https://doi.org/10.3389/fphys.2022.1089343; html:https://europepmc.org/articles/PMC9814485; pdf:https://europepmc.org/articles/PMC9814485?pdf=render"
+  },
   {
     "id": "35985824",
     "doi": "https://doi.org/10.1212/wnl.0000000000201064",
@@ -17510,21 +17527,21 @@
     "urls": "pdf:https://academic.oup.com/brain/article-pdf/144/9/2670/40880367/awab253.pdf; doi:https://doi.org/10.1093/brain/awab253; html:https://europepmc.org/articles/PMC8557338; pdf:https://europepmc.org/articles/PMC8557338?pdf=render; doi:https://doi.org/10.1093/brain/awab253"
   },
   {
-    "id": "37042240",
-    "doi": "https://doi.org/10.1161/circimaging.122.014519",
-    "title": "Explainable Artificial Intelligence and Cardiac Imaging: Toward More Interpretable Models.",
-    "authorString": "Salih A, Boscolo Galazzo I, Gkontra P, Lee AM, Lekadir K, Raisi-Estabragh Z, Petersen SE.",
+    "id": "36098502",
+    "doi": "https://doi.org/10.7554/elife.78427",
+    "title": "Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study.",
+    "authorString": "Stirrup O, Blackstone J, Mapp F, MacNeil A, Panca M, Holmes A, Machin N, Shin GY, Mahungu T, Saeed K, Saluja T, Taha Y, Mahida N, Pope C, Chawla A, Cutino-Moguel MT, Tamuri A, Williams R, Darby A, Robertson DL, Flaviani F, Nastouli E, Robson S, Smith D, Loose M, Laing K, Monahan I, Kele B, Haldenby S, George R, Bashton M, Witney AA, Byott M, Coll F, Chapman M, Peacock SJ, COG-UK HOCI Investigators, COVID-19 Genomics UK (COG-UK) consortium, Hughes J, Nebbia G, Partridge DG, Parker M, Price JR, Peters C, Roy S, Snell LB, de Silva TI, Thomson E, Flowers P, Copas A, Breuer J.",
     "authorAffiliations": "",
-    "journalTitle": "Circulation. Cardiovascular imaging",
-    "pubYear": "2023",
-    "date": "2023-04-12",
-    "isOpenAccess": "N",
-    "keywords": "Artificial intelligence; Diagnostic Imaging; Machine Learning; Cardiac Imaging Techniques",
+    "journalTitle": "eLife",
+    "pubYear": "2022",
+    "date": "2022-09-13",
+    "isOpenAccess": "Y",
+    "keywords": "Human; Microbiology; Infectious disease; Molecular epidemiology; Infection control; epidemiology; Global Health; Hospital-acquired Infection; Infection Prevention; Viral Genomics; Healthcare-associated Infection; Covid-19",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Artificial intelligence applications have shown success in different medical and health care domains, and cardiac imaging is no exception. However, some machine learning models, especially deep learning, are considered black box as they do not provide an explanation or rationale for model outcomes. Complexity and vagueness in these models necessitate a transition to explainable artificial intelligence (XAI) methods to ensure that model results are both transparent and understandable to end users. In cardiac imaging studies, there are a limited number of papers that use XAI methodologies. This article provides a comprehensive literature review of state-of-the-art works using XAI methods for cardiac imaging. Moreover, it provides simple and comprehensive guidelines on XAI. Finally, open issues and directions for XAI in cardiac imaging are discussed.",
+    "abstract": "<h4>Background</h4>Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings.<h4>Methods</h4>We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data collection period, followed by intervention periods comprising 8 weeks of 'rapid' (<48 hr) and 4 weeks of 'longer-turnaround' (5-10 days) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital-onset COVID-19 infections (HOCIs; detected \u226548 hr from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on the incidence of probable/definite hospital-acquired infections (HAIs), was evaluated.<h4>Results</h4>A total of 2170 HOCI cases were recorded from October 2020 to April 2021, corresponding to a period of extreme strain on the health service, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (incidence rate ratio 1.60, 95% CI 0.85-3.01; p<i>=</i>0.14) or rapid (0.85, 0.48-1.50; p<i>=</i>0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8 and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2 and 11.6% of cases where the report was returned. In a 'per-protocol' sensitivity analysis, there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. Capacity to respond effectively to insights from sequencing was breached in most sites by the volume of cases and limited resources.<h4>Conclusions</h4>While we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days.<h4>Funding</h4>COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) (grant code: MC_PC_19027), and Genome Research Limited, operating as the Wellcome Sanger Institute.<h4>Clinical trial number</h4>NCT04405934.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1161/CIRCIMAGING.122.014519"
+    "urls": "doi:https://doi.org/10.7554/elife.78427; doi:https://doi.org/10.7554/eLife.78427; html:https://europepmc.org/articles/PMC9596156; pdf:https://europepmc.org/articles/PMC9596156?pdf=render"
   },
   {
     "id": "35139069",
@@ -17544,21 +17561,21 @@
     "urls": "doi:https://doi.org/10.1371/journal.pcbi.1009806; doi:https://doi.org/10.1371/journal.pcbi.1009806; html:https://europepmc.org/articles/PMC10138267; pdf:https://europepmc.org/articles/PMC10138267?pdf=render"
   },
   {
-    "id": "36382153",
-    "doi": "https://doi.org/10.5334/gh.1166",
-    "title": "Risk Factors and Prevalence of Dilated Cardiomyopathy in Sub-Saharan Africa: A Systematic Review.",
-    "authorString": "Fundikira LS, Chillo P, Mutagaywa R, Kamuhabwa A, Kwesigabo G, Asselbergs FW, van Laake LW.",
+    "id": "37042240",
+    "doi": "https://doi.org/10.1161/circimaging.122.014519",
+    "title": "Explainable Artificial Intelligence and Cardiac Imaging: Toward More Interpretable Models.",
+    "authorString": "Salih A, Boscolo Galazzo I, Gkontra P, Lee AM, Lekadir K, Raisi-Estabragh Z, Petersen SE.",
     "authorAffiliations": "",
-    "journalTitle": "Global heart",
-    "pubYear": "2022",
-    "date": "2022-10-21",
-    "isOpenAccess": "Y",
-    "keywords": "Dilated cardiomyopathy; Sub-Saharan Africa; Cardiovascular risk factors",
+    "journalTitle": "Circulation. Cardiovascular imaging",
+    "pubYear": "2023",
+    "date": "2023-04-12",
+    "isOpenAccess": "N",
+    "keywords": "Artificial intelligence; Diagnostic Imaging; Machine Learning; Cardiac Imaging Techniques",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<b>Highlights</b>\u00a0 Prevalence of DCM varies widely in SSA.Cardiovascular risk factors are important in patients with DCM.The role of genetics in idiopathic DCM is not studied in major part of SSA.",
+    "abstract": "Artificial intelligence applications have shown success in different medical and health care domains, and cardiac imaging is no exception. However, some machine learning models, especially deep learning, are considered black box as they do not provide an explanation or rationale for model outcomes. Complexity and vagueness in these models necessitate a transition to explainable artificial intelligence (XAI) methods to ensure that model results are both transparent and understandable to end users. In cardiac imaging studies, there are a limited number of papers that use XAI methodologies. This article provides a comprehensive literature review of state-of-the-art works using XAI methods for cardiac imaging. Moreover, it provides simple and comprehensive guidelines on XAI. Finally, open issues and directions for XAI in cardiac imaging are discussed.",
     "laySummary": "",
-    "urls": "pdf:http://globalheartjournal.com/articles/10.5334/gh.1166/galley/1329/download/; doi:https://doi.org/10.5334/gh.1166; html:https://europepmc.org/articles/PMC9585983; pdf:https://europepmc.org/articles/PMC9585983?pdf=render"
+    "urls": "doi:https://doi.org/10.1161/CIRCIMAGING.122.014519"
   },
   {
     "id": "30984881",
@@ -17577,6 +17594,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.12688/wellcomeopenres.15151.1; html:https://europepmc.org/articles/PMC6449792; pdf:https://europepmc.org/articles/PMC6449792?pdf=render"
   },
+  {
+    "id": "36382153",
+    "doi": "https://doi.org/10.5334/gh.1166",
+    "title": "Risk Factors and Prevalence of Dilated Cardiomyopathy in Sub-Saharan Africa: A Systematic Review.",
+    "authorString": "Fundikira LS, Chillo P, Mutagaywa R, Kamuhabwa A, Kwesigabo G, Asselbergs FW, van Laake LW.",
+    "authorAffiliations": "",
+    "journalTitle": "Global heart",
+    "pubYear": "2022",
+    "date": "2022-10-21",
+    "isOpenAccess": "Y",
+    "keywords": "Dilated cardiomyopathy; Sub-Saharan Africa; Cardiovascular risk factors",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<b>Highlights</b>\u00a0 Prevalence of DCM varies widely in SSA.Cardiovascular risk factors are important in patients with DCM.The role of genetics in idiopathic DCM is not studied in major part of SSA.",
+    "laySummary": "",
+    "urls": "pdf:http://globalheartjournal.com/articles/10.5334/gh.1166/galley/1329/download/; doi:https://doi.org/10.5334/gh.1166; html:https://europepmc.org/articles/PMC9585983; pdf:https://europepmc.org/articles/PMC9585983?pdf=render"
+  },
   {
     "id": "36038914",
     "doi": "https://doi.org/10.1186/s12916-022-02473-3",
@@ -17594,40 +17628,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-022-02473-3; doi:https://doi.org/10.1186/s12916-022-02473-3; html:https://europepmc.org/articles/PMC9425992; pdf:https://europepmc.org/articles/PMC9425992?pdf=render"
   },
-  {
-    "id": "36098502",
-    "doi": "https://doi.org/10.7554/elife.78427",
-    "title": "Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study.",
-    "authorString": "Stirrup O, Blackstone J, Mapp F, MacNeil A, Panca M, Holmes A, Machin N, Shin GY, Mahungu T, Saeed K, Saluja T, Taha Y, Mahida N, Pope C, Chawla A, Cutino-Moguel MT, Tamuri A, Williams R, Darby A, Robertson DL, Flaviani F, Nastouli E, Robson S, Smith D, Loose M, Laing K, Monahan I, Kele B, Haldenby S, George R, Bashton M, Witney AA, Byott M, Coll F, Chapman M, Peacock SJ, COG-UK HOCI Investigators, COVID-19 Genomics UK (COG-UK) consortium, Hughes J, Nebbia G, Partridge DG, Parker M, Price JR, Peters C, Roy S, Snell LB, de Silva TI, Thomson E, Flowers P, Copas A, Breuer J.",
-    "authorAffiliations": "",
-    "journalTitle": "eLife",
-    "pubYear": "2022",
-    "date": "2022-09-13",
-    "isOpenAccess": "Y",
-    "keywords": "Human; Microbiology; Infectious disease; Molecular epidemiology; Infection control; epidemiology; Global Health; Hospital-acquired Infection; Infection Prevention; Viral Genomics; Healthcare-associated Infection; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings.<h4>Methods</h4>We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data collection period, followed by intervention periods comprising 8 weeks of 'rapid' (<48 hr) and 4 weeks of 'longer-turnaround' (5-10 days) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital-onset COVID-19 infections (HOCIs; detected \u226548 hr from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on the incidence of probable/definite hospital-acquired infections (HAIs), was evaluated.<h4>Results</h4>A total of 2170 HOCI cases were recorded from October 2020 to April 2021, corresponding to a period of extreme strain on the health service, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (incidence rate ratio 1.60, 95% CI 0.85-3.01; p<i>=</i>0.14) or rapid (0.85, 0.48-1.50; p<i>=</i>0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8 and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2 and 11.6% of cases where the report was returned. In a 'per-protocol' sensitivity analysis, there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. Capacity to respond effectively to insights from sequencing was breached in most sites by the volume of cases and limited resources.<h4>Conclusions</h4>While we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days.<h4>Funding</h4>COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) (grant code: MC_PC_19027), and Genome Research Limited, operating as the Wellcome Sanger Institute.<h4>Clinical trial number</h4>NCT04405934.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.7554/elife.78427; doi:https://doi.org/10.7554/eLife.78427; html:https://europepmc.org/articles/PMC9596156; pdf:https://europepmc.org/articles/PMC9596156?pdf=render"
-  },
-  {
-    "id": "39293053",
-    "doi": "https://doi.org/10.2196/57334",
-    "title": "Metagenomics in the Diagnosis of Pneumonia: Protocol for a Systematic Review.",
-    "authorString": "Quarton S, Livesey A, Jeff C, Hatton C, Scott A, Parekh D, Thickett D, McNally A, Sapey E.",
-    "authorAffiliations": "",
-    "journalTitle": "JMIR research protocols",
-    "pubYear": "2024",
-    "date": "2024-09-18",
-    "isOpenAccess": "Y",
-    "keywords": "Diagnosis; Ventilator-associated pneumonia; Pneumonia; HAP; Systematic review; Community-acquired pneumonia; Respiratory tract infection; Cap; Metagenomics; Hospital-acquired Pneumonia; Vap",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Causative pathogens are currently identified in only a minority of pneumonia cases, which affects antimicrobial stewardship. Metagenomic next-generation sequencing (mNGS) has potential to enhance pathogen detection due to its sensitivity and broad applicability. However, while studies have shown improved sensitivity compared with conventional microbiological methods for pneumonia diagnosis, it remains unclear whether this can translate into clinical benefit. Most existing studies focus on patients who are ventilated, readily allowing for analysis of bronchoalveolar lavage fluid (BALF). The impact of sample type on the use of metagenomic analysis remains poorly defined. Similarly, previous studies rarely differentiate between the types of pneumonia involved-community-acquired pneumonia (CAP), hospital-acquired pneumonia (HAP), or ventilator-associated pneumonia (VAP)-which have different clinical profiles.<h4>Objective</h4>This study aims to determine the clinical use of mNGS in CAP, HAP, and VAP, compared with traditional microbiological methods.<h4>Methods</h4>We aim to review all studies (excluding case reports of a series of fewer than 10 people) of adult patients with suspected or confirmed pneumonia that compare metagenomic analysis with traditional microbiology techniques, including culture, antigen-based testing, and polymerase chain reaction-based assays. Relevant studies will be identified through systematic searches of the Embase, MEDLINE, Scopus, and Cochrane CENTRAL databases. Screening of titles, abstracts, and subsequent review of eligible full texts will be done by 2 separate reviewers (SQ and 1 of AL, CJ, or CH), with a third clinician (ES) providing adjudication in case of disagreement. Our focus is on the clinical use of metagenomics for patients with CAP, HAP, and VAP. Data extracted will focus on clinically important outcomes-pathogen positivity rate, laboratory turnaround time, impact on clinical decision-making, length of stay, and 30-day mortality. Subgroup analyses will be performed based on the type of pneumonia (CAP, HAP, or VAP) and sample type used. The risk of bias will be assessed using the QUADAS-2 tool for diagnostic accuracy studies. Outcome data will be combined in a random-effects meta-analysis, and where this is not possible, a narrative synthesis will be undertaken.<h4>Results</h4>The searches were completed with the assistance of a medical librarian on January 13, 2024, returning 5750 records. Screening and data extraction are anticipated to be completed by September 2024.<h4>Conclusions</h4>Despite significant promise, the impact of metagenomic analysis on clinical pathways remains unclear. Furthermore, it is unclear whether the use of this technique will alter depending on whether the pneumonia is a CAP, HAP, or VAP or the sample type that is collected. This systematic review will assess the current evidence base to support the benefit of clinical outcomes for metagenomic analysis, depending on the setting of pneumonia diagnosis or specimen type used. It will identify areas where further research is needed to advance this methodology into routine care.<h4>Trial registration</h4>PROSPERO CRD42023488096; https://tinyurl.com/3suy7cma.<h4>International registered report identifier (irrid)</h4>DERR1-10.2196/57334.",
-    "laySummary": "",
-    "urls": "pdf:https://s3.ca-central-1.amazonaws.com/assets.jmir.org/assets/preprints/preprint-57334-accepted.pdf; doi:https://doi.org/10.2196/57334; html:https://europepmc.org/articles/PMC11447427"
-  },
   {
     "id": "36475361",
     "doi": "https://doi.org/10.1302/2633-1462.312.bjo-2022-0130.r1",
@@ -17662,6 +17662,23 @@
     "laySummary": "",
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s12687-023-00635-1.pdf; doi:https://doi.org/10.1007/s12687-023-00635-1; html:https://europepmc.org/articles/PMC10576689; pdf:https://europepmc.org/articles/PMC10576689?pdf=render"
   },
+  {
+    "id": "39293053",
+    "doi": "https://doi.org/10.2196/57334",
+    "title": "Metagenomics in the Diagnosis of Pneumonia: Protocol for a Systematic Review.",
+    "authorString": "Quarton S, Livesey A, Jeff C, Hatton C, Scott A, Parekh D, Thickett D, McNally A, Sapey E.",
+    "authorAffiliations": "",
+    "journalTitle": "JMIR research protocols",
+    "pubYear": "2024",
+    "date": "2024-09-18",
+    "isOpenAccess": "Y",
+    "keywords": "Diagnosis; Ventilator-associated pneumonia; Pneumonia; HAP; Systematic review; Community-acquired pneumonia; Respiratory tract infection; Cap; Metagenomics; Hospital-acquired Pneumonia; Vap",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Causative pathogens are currently identified in only a minority of pneumonia cases, which affects antimicrobial stewardship. Metagenomic next-generation sequencing (mNGS) has potential to enhance pathogen detection due to its sensitivity and broad applicability. However, while studies have shown improved sensitivity compared with conventional microbiological methods for pneumonia diagnosis, it remains unclear whether this can translate into clinical benefit. Most existing studies focus on patients who are ventilated, readily allowing for analysis of bronchoalveolar lavage fluid (BALF). The impact of sample type on the use of metagenomic analysis remains poorly defined. Similarly, previous studies rarely differentiate between the types of pneumonia involved-community-acquired pneumonia (CAP), hospital-acquired pneumonia (HAP), or ventilator-associated pneumonia (VAP)-which have different clinical profiles.<h4>Objective</h4>This study aims to determine the clinical use of mNGS in CAP, HAP, and VAP, compared with traditional microbiological methods.<h4>Methods</h4>We aim to review all studies (excluding case reports of a series of fewer than 10 people) of adult patients with suspected or confirmed pneumonia that compare metagenomic analysis with traditional microbiology techniques, including culture, antigen-based testing, and polymerase chain reaction-based assays. Relevant studies will be identified through systematic searches of the Embase, MEDLINE, Scopus, and Cochrane CENTRAL databases. Screening of titles, abstracts, and subsequent review of eligible full texts will be done by 2 separate reviewers (SQ and 1 of AL, CJ, or CH), with a third clinician (ES) providing adjudication in case of disagreement. Our focus is on the clinical use of metagenomics for patients with CAP, HAP, and VAP. Data extracted will focus on clinically important outcomes-pathogen positivity rate, laboratory turnaround time, impact on clinical decision-making, length of stay, and 30-day mortality. Subgroup analyses will be performed based on the type of pneumonia (CAP, HAP, or VAP) and sample type used. The risk of bias will be assessed using the QUADAS-2 tool for diagnostic accuracy studies. Outcome data will be combined in a random-effects meta-analysis, and where this is not possible, a narrative synthesis will be undertaken.<h4>Results</h4>The searches were completed with the assistance of a medical librarian on January 13, 2024, returning 5750 records. Screening and data extraction are anticipated to be completed by September 2024.<h4>Conclusions</h4>Despite significant promise, the impact of metagenomic analysis on clinical pathways remains unclear. Furthermore, it is unclear whether the use of this technique will alter depending on whether the pneumonia is a CAP, HAP, or VAP or the sample type that is collected. This systematic review will assess the current evidence base to support the benefit of clinical outcomes for metagenomic analysis, depending on the setting of pneumonia diagnosis or specimen type used. It will identify areas where further research is needed to advance this methodology into routine care.<h4>Trial registration</h4>PROSPERO CRD42023488096; https://tinyurl.com/3suy7cma.<h4>International registered report identifier (irrid)</h4>DERR1-10.2196/57334.",
+    "laySummary": "",
+    "urls": "pdf:https://s3.ca-central-1.amazonaws.com/assets.jmir.org/assets/preprints/preprint-57334-accepted.pdf; doi:https://doi.org/10.2196/57334; html:https://europepmc.org/articles/PMC11447427"
+  },
   {
     "id": "37657941",
     "doi": "https://doi.org/10.1212/wnl.0000000000207777",
@@ -17696,23 +17713,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.jacasi.2024.01.005; html:https://europepmc.org/articles/PMC11099820; pdf:https://europepmc.org/articles/PMC11099820?pdf=render"
   },
-  {
-    "id": "35429382",
-    "doi": "https://doi.org/10.1093/infdis/jiac146",
-    "title": "Severe Acute Respiratory Syndrome Coronavirus 2 Anti-Spike Antibody Levels Following Second Dose of ChAdOx1 nCov-19 or BNT162b2 Vaccine in Residents of Long-term Care Facilities in England (VIVALDI).",
-    "authorString": "Stirrup O, Krutikov M, Tut G, Palmer T, Bone D, Bruton R, Fuller C, Azmi B, Lancaster T, Sylla P, Kaur N, Spalkova E, Bentley C, Amin U, Jadir A, Hulme S, Giddings R, Nacer-Laidi H, Baynton V, Irwin-Singer A, Hayward A, Moss P, Copas A, Shallcross L.",
-    "authorAffiliations": "",
-    "journalTitle": "The Journal of infectious diseases",
-    "pubYear": "2022",
-    "date": "2022-11-01",
-    "isOpenAccess": "Y",
-    "keywords": "Antibodies; Vaccination; Waning; Long-term Care Facilities; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "General population studies have shown strong humoral response following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination with subsequent waning of anti-spike antibody levels. Vaccine-induced immune responses are often attenuated in frail and older populations, but published data are scarce. We measured SARS-CoV-2 anti-spike antibody levels in long-term care facility residents and staff following a second vaccination dose with Oxford-AstraZeneca or Pfizer-BioNTech. Vaccination elicited robust antibody responses in older residents, suggesting comparable levels of vaccine-induced immunity to that in the general population. Antibody levels are higher after Pfizer-BioNTech vaccination but fall more rapidly compared to Oxford-AstraZeneca recipients and are enhanced by prior infection in both groups.",
-    "laySummary": "",
-    "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9047242; doi:https://doi.org/10.1093/infdis/jiac146; html:https://europepmc.org/articles/PMC9047242; pdf:https://europepmc.org/articles/PMC9047242?pdf=render"
-  },
   {
     "id": "33413610",
     "doi": "https://doi.org/10.1186/s13073-020-00822-6",
@@ -17730,6 +17730,23 @@
     "laySummary": "",
     "urls": "pdf:https://genomemedicine.biomedcentral.com/counter/pdf/10.1186/s13073-020-00822-6; doi:https://doi.org/10.1186/s13073-020-00822-6; html:https://europepmc.org/articles/PMC7790334; pdf:https://europepmc.org/articles/PMC7790334?pdf=render"
   },
+  {
+    "id": "35429382",
+    "doi": "https://doi.org/10.1093/infdis/jiac146",
+    "title": "Severe Acute Respiratory Syndrome Coronavirus 2 Anti-Spike Antibody Levels Following Second Dose of ChAdOx1 nCov-19 or BNT162b2 Vaccine in Residents of Long-term Care Facilities in England (VIVALDI).",
+    "authorString": "Stirrup O, Krutikov M, Tut G, Palmer T, Bone D, Bruton R, Fuller C, Azmi B, Lancaster T, Sylla P, Kaur N, Spalkova E, Bentley C, Amin U, Jadir A, Hulme S, Giddings R, Nacer-Laidi H, Baynton V, Irwin-Singer A, Hayward A, Moss P, Copas A, Shallcross L.",
+    "authorAffiliations": "",
+    "journalTitle": "The Journal of infectious diseases",
+    "pubYear": "2022",
+    "date": "2022-11-01",
+    "isOpenAccess": "Y",
+    "keywords": "Antibodies; Vaccination; Waning; Long-term Care Facilities; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "General population studies have shown strong humoral response following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination with subsequent waning of anti-spike antibody levels. Vaccine-induced immune responses are often attenuated in frail and older populations, but published data are scarce. We measured SARS-CoV-2 anti-spike antibody levels in long-term care facility residents and staff following a second vaccination dose with Oxford-AstraZeneca or Pfizer-BioNTech. Vaccination elicited robust antibody responses in older residents, suggesting comparable levels of vaccine-induced immunity to that in the general population. Antibody levels are higher after Pfizer-BioNTech vaccination but fall more rapidly compared to Oxford-AstraZeneca recipients and are enhanced by prior infection in both groups.",
+    "laySummary": "",
+    "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9047242; doi:https://doi.org/10.1093/infdis/jiac146; html:https://europepmc.org/articles/PMC9047242; pdf:https://europepmc.org/articles/PMC9047242?pdf=render"
+  },
   {
     "id": "33307988",
     "doi": "https://doi.org/10.1177/0961203320979045",
@@ -17748,21 +17765,21 @@
     "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/0961203320979045; doi:https://doi.org/10.1177/0961203320979045; html:https://europepmc.org/articles/PMC7854491; pdf:https://europepmc.org/articles/PMC7854491?pdf=render"
   },
   {
-    "id": "39426795",
-    "doi": "https://doi.org/10.1016/j.jpeds.2024.114370",
-    "title": "Trends in Pediatric Hospital Admissions Caused or Contributed by SARS-CoV-2 Infection in England.",
-    "authorString": "Wilde H, Tomlinson C, Mateen BA, Selby D, Kanthimathinathan HK, Denaxas S, Flaxman S, Vollmer S, Pagel C, Brown K, CVD-COVID-UK/COVID-IMPACT Consortium.",
+    "id": "39486903",
+    "doi": "https://doi.org/10.1016/s2468-2667(24)00215-9",
+    "title": "Contemporary epidemiology of hospitalised heart failure with reduced versus preserved ejection fraction in England: a retrospective, cohort study of whole-population electronic health records.",
+    "authorString": "Fletcher RA, Rockenschaub P, Neuen BL, Walter IJ, Conrad N, Mizani MA, Bolton T, Lawson CA, Tomlinson C, Logothetis SB, Petitjean C, Brizzi LF, Kaptoge S, Raffetti E, Calvert PA, Di Angelantonio E, Banerjee A, Mamas MA, Squire I, Denaxas S, McDonagh TA, Sudlow C, Petersen SE, Chertow GM, Khunti K, Sundstr\u00f6m J, Arnott C, Cleland JGF, Danesh J, McMurray JJV, Vaduganathan M, Wood AM, CVD-COVID-UK/COVID-IMPACT Consortium.",
     "authorAffiliations": "",
-    "journalTitle": "The Journal of pediatrics",
+    "journalTitle": "The Lancet. Public health",
     "pubYear": "2024",
-    "date": "2024-10-17",
+    "date": "2024-11-01",
     "isOpenAccess": "N",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Objective</h4>To investigate the changing characteristics of SARS-CoV-2 related pediatric hospital admissions over time.<h4>Study design</h4>A national, observational cohort study from 1, July 2020, to August 31, 2023, using English population-linked electronic health records. We identified 45,203 children under 18 years old in whom SARS-CoV-2 either caused or contributed to hospitalization, excluding those admitted with \"incidental\" infection. Studied outcomes were types of hospitalization and severe hospitalizations involving either critical care or PIMS-TS.<h4>Results</h4>There were 45,920 SARS-CoV-2 related hospitalizations in children: 34,870 (75.9%) due to COVID-19; 1,845 (4.0%) due to pediatric inflammatory multisystem syndrome - temporally associated with SARS-CoV-2 (PIMS-TS); 8,330 (18.1%) with SARS-CoV-2 as contributor to admission; and 875 (1.9%) acquired nosocomial SARS-CoV-2 infection. The most notable changes between the first three waves (March 2020 through November 2021) and the omicron era (December 2021 onwards) were: a fall in PIMS-TS from 1,575 of 14,020 (11.2%) to 270 of 31,905 (0.8%); a reduction in critical care use from 1,175 of 14,020 (8.4%) to 1,390 of 31,905 (4.4%); a fall in mortality rate among those hospitalized from 521 per 100,000 to 249 per 100,000; and a drop in the median age of hospitalized children from 4.7 (IQR 0.6,12.3) to 1.1 (IQR 0.3,6.4) years. Of children hospitalized, infants, 10.2% of whom had a recorded underlying health condition, comprised 4,225 of 14,020 (30.1%) admissions 2020 through 2021 and 15,555 of 31,900 (48.8%) since 2022. (p<0.001 for all comparisons).<h4>Conclusions</h4>Infants are now the most affected age group by SARS-CoV2, at least partially related to having the least immunity to the virus, and are most vulnerable to respiratory illnesses.",
+    "abstract": "<h4>Background</h4>Heart failure is common, complex, and often associated with coexisting chronic medical conditions and a high mortality. We aimed to assess the epidemiology of people admitted to hospital with heart failure with reduced ejection fraction (HFrEF) and heart failure with preserved ejection fraction (HFpEF), including the period covering the COVID-19 pandemic, which was previously not well characterised.<h4>Methods</h4>In this retrospective, cohort study, we used whole-population electronic health records with 57 million individuals in England to identify patients hospitalised with heart failure as the primary diagnosis in any consultant episode of an in-patient admission to a National Health Service (NHS) hospital. We excluded individuals with less than 1 year of medical history records in primary or secondary care; admissions to NHS hospitals for which less than 10% of heart failure cases were linkable to the National Heart Failure Audit (NHFA); individuals younger than 18 years at the time of the heart failure hospitalisation; and patients who died in hospital during the index heart failure admission. For patients with new onset heart failure, we assessed incidence rates of 30-day and 1-year all-cause and cause-specific (cardiovascular, non-cardiovascular, and heart failure-related) emergency rehospitalisation and mortality after discharge, and dispensed guideline-recommended medical therapy (GRMT). Follow-up occurred from the index admission to the earliest occurrence of the event of interest, death, or end of data coverage. We estimated adjusted hazard ratios (HRs) to compare HFrEF with HFpEF. We computed population-attributable fractions to quantify the percentage of outcomes attributable to coexisting chronic medical conditions.<h4>Findings</h4>Among 233\u2008320 patients identified who survived the index heart failure admission across 335 NHS hospitals between Jan 1, 2019, and Dec 31, 2022, 101\u2008320 (43\u00b74%) had HFrEF, 71\u2008910 (30\u00b78%) had HFpEF, and 60\u2008090 (25\u00b78%) had an unknown classification. In patients with new onset heart failure, there were reductions in all-cause 30-day (-5\u00b72% [95% CI -7\u00b77 to -2\u00b76] in 2019-22) and 1-year rehospitalisation rates (-3\u00b79% [-6\u00b76 to -1\u00b72]). Declining 30-day rehospitalisation rates affected patients with HFpEF (-4\u00b78% [-9\u00b72 to -0\u00b72]) and HFrEF (-6\u00b72% [-10\u00b75 to -1\u00b76]), although 1-year rates were not statistically significant for patients with HFpEF (-2\u00b72% [-6\u00b76 to 2\u00b73] vs -5\u00b77% [-10\u00b76 to -0\u00b75] for HFrEF). There were no temporal trends in incidence rates of 30-day or 1-year mortality after discharge. The rates of all-cause (HR 1\u00b720 [1\u00b718-1\u00b722]) and cause-specific rehospitalisation were uniformly higher in those with HFpEF than those with HFrEF. Patients with HFpEF also had higher rates of 1-year all-cause mortality after discharge (HR 1\u00b707 [1\u00b705-1\u00b709]), driven by excess risk of non-cardiovascular death (HR 1\u00b725 [1\u00b721-1\u00b729]). Rates of rehospitalisation and mortality were highest in patients with coexisting chronic kidney disease, chronic obstructive pulmonary disease, dementia, and liver disease. Chronic kidney disease contributed to 6\u00b75% (5\u00b76-7\u00b74) of rehospitalisations within 1 year for HFrEF and 5\u00b70% (4\u00b71-5\u00b79) of rehospitalisations for HFpEF, double that of any other coexisting condition. There was swift implementation of newer GRMT, but markedly lower dispensing of these medications in patients with coexisting chronic kidney disease.<h4>Interpretation</h4>Rates of rehospitalisation in patients with heart failure in England have decreased during 2019-22. Further population health improvements could be reached through enhanced implementation of GRMT, particularly in patients with coexisting chronic kidney disease, who, despite being at high risk, remain undertreated.<h4>Funding</h4>Wellcome Trust, Health Data Research UK, British Heart Foundation Data Science Centre.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.jpeds.2024.114370"
+    "urls": "doi:https://doi.org/10.1016/S2468-2667(24)00215-9"
   },
   {
     "id": "33710281",
@@ -17782,21 +17799,21 @@
     "urls": "pdf:https://academic.oup.com/ageing/article-pdf/50/4/1019/40971734/afab060.pdf; doi:https://doi.org/10.1093/ageing/afab060; html:https://europepmc.org/articles/PMC7989651; pdf:https://europepmc.org/articles/PMC7989651?pdf=render"
   },
   {
-    "id": "35776101",
-    "doi": "https://doi.org/10.1093/ije/dyac140",
-    "title": "Incremental value of risk factor variability for cardiovascular risk prediction in individuals with type 2 diabetes: results from UK primary care electronic health records.",
-    "authorString": "Xu Z, Arnold M, Sun L, Stevens D, Chung R, Ip S, Barrett J, Kaptoge S, Pennells L, Di Angelantonio E, Wood AM.",
+    "id": "39426795",
+    "doi": "https://doi.org/10.1016/j.jpeds.2024.114370",
+    "title": "Trends in Pediatric Hospital Admissions Caused or Contributed by SARS-CoV-2 Infection in England.",
+    "authorString": "Wilde H, Tomlinson C, Mateen BA, Selby D, Kanthimathinathan HK, Denaxas S, Flaxman S, Vollmer S, Pagel C, Brown K, CVD-COVID-UK/COVID-IMPACT Consortium.",
     "authorAffiliations": "",
-    "journalTitle": "International journal of epidemiology",
-    "pubYear": "2022",
-    "date": "2022-12-01",
-    "isOpenAccess": "Y",
-    "keywords": "Variability; Cardiovascular disease; Type 2 diabetes; Risk Prediction; Repeated Measurements; Electronic Health Records",
+    "journalTitle": "The Journal of pediatrics",
+    "pubYear": "2024",
+    "date": "2024-10-17",
+    "isOpenAccess": "N",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Cardiovascular disease (CVD) risk prediction models for individuals with type 2 diabetes are important tools to guide intensification of interventions for CVD prevention. We aimed to assess the added value of incorporating risk factors variability in CVD risk prediction for people with type 2 diabetes.<h4>Methods</h4>We used electronic health records (EHRs) data from 83\u200a910 adults with type 2 diabetes but without pre-existing CVD from the UK Clinical Practice Research Datalink for 2004-2017. Using a landmark-modelling approach, we developed and validated sex-specific Cox models, incorporating conventional predictors and trajectories plus variability of systolic blood pressure (SBP), total and high-density lipoprotein (HDL) cholesterol, and glycated haemoglobin (HbA1c). Such models were compared against simpler models using single last observed values or means.<h4>Results</h4>The standard deviations (SDs) of SBP, HDL cholesterol and HbA1c were associated with higher CVD risk (P\u2009<\u20090.05). Models incorporating trajectories and variability of continuous predictors demonstrated improvement in risk discrimination (C-index\u2009=\u20090.659, 95% CI: 0.654-0.663) as compared with using last observed values (C-index\u2009=\u20090.651, 95% CI: 0.646-0.656) or means (C-index\u2009=\u20090.650, 95% CI: 0.645-0.655). Inclusion of SDs of SBP yielded the greatest improvement in discrimination (C-index increase\u2009=\u20090.005, 95% CI: 0.004-0.007) in comparison to incorporating SDs of total cholesterol (C-index\u2009increase =\u20090.002, 95% CI: 0.000-0.003), HbA1c (C-index increase\u2009=\u20090.002, 95% CI: 0.000-0.003) or HDL cholesterol (C-index\u2009increase=\u20090.003, 95% CI: 0.002-0.005).<h4>Conclusion</h4>Incorporating variability of predictors from EHRs provides a modest improvement in CVD risk discrimination for individuals with type 2 diabetes. Given that repeat measures are readily available in EHRs especially for regularly monitored patients with diabetes, this improvement could easily be achieved.",
+    "abstract": "<h4>Objective</h4>To investigate the changing characteristics of SARS-CoV-2 related pediatric hospital admissions over time.<h4>Study design</h4>A national, observational cohort study from 1, July 2020, to August 31, 2023, using English population-linked electronic health records. We identified 45,203 children under 18 years old in whom SARS-CoV-2 either caused or contributed to hospitalization, excluding those admitted with \"incidental\" infection. Studied outcomes were types of hospitalization and severe hospitalizations involving either critical care or PIMS-TS.<h4>Results</h4>There were 45,920 SARS-CoV-2 related hospitalizations in children: 34,870 (75.9%) due to COVID-19; 1,845 (4.0%) due to pediatric inflammatory multisystem syndrome - temporally associated with SARS-CoV-2 (PIMS-TS); 8,330 (18.1%) with SARS-CoV-2 as contributor to admission; and 875 (1.9%) acquired nosocomial SARS-CoV-2 infection. The most notable changes between the first three waves (March 2020 through November 2021) and the omicron era (December 2021 onwards) were: a fall in PIMS-TS from 1,575 of 14,020 (11.2%) to 270 of 31,905 (0.8%); a reduction in critical care use from 1,175 of 14,020 (8.4%) to 1,390 of 31,905 (4.4%); a fall in mortality rate among those hospitalized from 521 per 100,000 to 249 per 100,000; and a drop in the median age of hospitalized children from 4.7 (IQR 0.6,12.3) to 1.1 (IQR 0.3,6.4) years. Of children hospitalized, infants, 10.2% of whom had a recorded underlying health condition, comprised 4,225 of 14,020 (30.1%) admissions 2020 through 2021 and 15,555 of 31,900 (48.8%) since 2022. (p<0.001 for all comparisons).<h4>Conclusions</h4>Infants are now the most affected age group by SARS-CoV2, at least partially related to having the least immunity to the virus, and are most vulnerable to respiratory illnesses.",
     "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/ije/advance-article-pdf/doi/10.1093/ije/dyac140/45030523/dyac140.pdf; doi:https://doi.org/10.1093/ije/dyac140; html:https://europepmc.org/articles/PMC9749723; pdf:https://europepmc.org/articles/PMC9749723?pdf=render"
+    "urls": "doi:https://doi.org/10.1016/j.jpeds.2024.114370"
   },
   {
     "id": "31000744",
@@ -17815,6 +17832,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41598-019-42036-w.pdf; doi:https://doi.org/10.1038/s41598-019-42036-w; html:https://europepmc.org/articles/PMC6473002; pdf:https://europepmc.org/articles/PMC6473002?pdf=render"
   },
+  {
+    "id": "35776101",
+    "doi": "https://doi.org/10.1093/ije/dyac140",
+    "title": "Incremental value of risk factor variability for cardiovascular risk prediction in individuals with type 2 diabetes: results from UK primary care electronic health records.",
+    "authorString": "Xu Z, Arnold M, Sun L, Stevens D, Chung R, Ip S, Barrett J, Kaptoge S, Pennells L, Di Angelantonio E, Wood AM.",
+    "authorAffiliations": "",
+    "journalTitle": "International journal of epidemiology",
+    "pubYear": "2022",
+    "date": "2022-12-01",
+    "isOpenAccess": "Y",
+    "keywords": "Variability; Cardiovascular disease; Type 2 diabetes; Risk Prediction; Repeated Measurements; Electronic Health Records",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Cardiovascular disease (CVD) risk prediction models for individuals with type 2 diabetes are important tools to guide intensification of interventions for CVD prevention. We aimed to assess the added value of incorporating risk factors variability in CVD risk prediction for people with type 2 diabetes.<h4>Methods</h4>We used electronic health records (EHRs) data from 83\u200a910 adults with type 2 diabetes but without pre-existing CVD from the UK Clinical Practice Research Datalink for 2004-2017. Using a landmark-modelling approach, we developed and validated sex-specific Cox models, incorporating conventional predictors and trajectories plus variability of systolic blood pressure (SBP), total and high-density lipoprotein (HDL) cholesterol, and glycated haemoglobin (HbA1c). Such models were compared against simpler models using single last observed values or means.<h4>Results</h4>The standard deviations (SDs) of SBP, HDL cholesterol and HbA1c were associated with higher CVD risk (P\u2009<\u20090.05). Models incorporating trajectories and variability of continuous predictors demonstrated improvement in risk discrimination (C-index\u2009=\u20090.659, 95% CI: 0.654-0.663) as compared with using last observed values (C-index\u2009=\u20090.651, 95% CI: 0.646-0.656) or means (C-index\u2009=\u20090.650, 95% CI: 0.645-0.655). Inclusion of SDs of SBP yielded the greatest improvement in discrimination (C-index increase\u2009=\u20090.005, 95% CI: 0.004-0.007) in comparison to incorporating SDs of total cholesterol (C-index\u2009increase =\u20090.002, 95% CI: 0.000-0.003), HbA1c (C-index increase\u2009=\u20090.002, 95% CI: 0.000-0.003) or HDL cholesterol (C-index\u2009increase=\u20090.003, 95% CI: 0.002-0.005).<h4>Conclusion</h4>Incorporating variability of predictors from EHRs provides a modest improvement in CVD risk discrimination for individuals with type 2 diabetes. Given that repeat measures are readily available in EHRs especially for regularly monitored patients with diabetes, this improvement could easily be achieved.",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/ije/advance-article-pdf/doi/10.1093/ije/dyac140/45030523/dyac140.pdf; doi:https://doi.org/10.1093/ije/dyac140; html:https://europepmc.org/articles/PMC9749723; pdf:https://europepmc.org/articles/PMC9749723?pdf=render"
+  },
   {
     "id": "38035863",
     "doi": "https://doi.org/10.1016/j.injury.2023.111200",
@@ -17849,6 +17883,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.bmj.com/content/bmj/368/bmj.l6927.full.pdf; doi:https://doi.org/10.1136/bmj.l6927; html:https://europepmc.org/articles/PMC11515850"
   },
+  {
+    "id": "31607513",
+    "doi": "https://doi.org/10.1016/j.cell.2019.08.051",
+    "title": "Genome-wide Association Studies in Ancestrally Diverse Populations: Opportunities, Methods, Pitfalls, and Recommendations.",
+    "authorString": "Peterson RE, Kuchenbaecker K, Walters RK, Chen CY, Popejoy AB, Periyasamy S, Lam M, Iyegbe C, Strawbridge RJ, Brick L, Carey CE, Martin AR, Meyers JL, Su J, Chen J, Edwards AC, Kalungi A, Koen N, Majara L, Schwarz E, Smoller JW, Stahl EA, Sullivan PF, Vassos E, Mowry B, Prieto ML, Cuellar-Barboza A, Bigdeli TB, Edenberg HJ, Huang H, Duncan LE.",
+    "authorAffiliations": "",
+    "journalTitle": "Cell",
+    "pubYear": "2019",
+    "date": "2019-10-10",
+    "isOpenAccess": "N",
+    "keywords": "Population genetics; Diversity; Psychiatry; complex disease; Gwas; Ancestry; Admixed Populations; Trans-ethnic; Trans-ancestry; Cross-ancestry",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Genome-wide association studies (GWASs) have focused primarily on populations of European descent, but it is essential that diverse populations become better represented. Increasing diversity among study participants will advance our understanding of genetic architecture in all populations and ensure that genetic research is broadly applicable. To facilitate and promote research in multi-ancestry and admixed cohorts, we outline key methodological considerations and highlight opportunities, challenges, solutions, and areas in need of development. Despite the perception that analyzing genetic data from diverse populations is difficult, it is scientifically and ethically imperative, and there is an expanding analytical toolbox to do it well.",
+    "laySummary": "",
+    "urls": "pdf:http://www.cell.com/article/S0092867419310025/pdf; doi:https://doi.org/10.1016/j.cell.2019.08.051; html:https://europepmc.org/articles/PMC6939869; pdf:https://europepmc.org/articles/PMC6939869?pdf=render; doi:https://doi.org/10.1016/j.cell.2019.08.051"
+  },
   {
     "id": "37859783",
     "doi": "https://doi.org/10.1136/bmjmed-2023-000554",
@@ -17867,21 +17918,21 @@
     "urls": "doi:https://doi.org/10.1136/bmjmed-2023-000554; html:https://europepmc.org/articles/PMC10582890; pdf:https://europepmc.org/articles/PMC10582890?pdf=render"
   },
   {
-    "id": "31607513",
-    "doi": "https://doi.org/10.1016/j.cell.2019.08.051",
-    "title": "Genome-wide Association Studies in Ancestrally Diverse Populations: Opportunities, Methods, Pitfalls, and Recommendations.",
-    "authorString": "Peterson RE, Kuchenbaecker K, Walters RK, Chen CY, Popejoy AB, Periyasamy S, Lam M, Iyegbe C, Strawbridge RJ, Brick L, Carey CE, Martin AR, Meyers JL, Su J, Chen J, Edwards AC, Kalungi A, Koen N, Majara L, Schwarz E, Smoller JW, Stahl EA, Sullivan PF, Vassos E, Mowry B, Prieto ML, Cuellar-Barboza A, Bigdeli TB, Edenberg HJ, Huang H, Duncan LE.",
+    "id": "33402395",
+    "doi": "https://doi.org/10.1136/jech-2020-215204",
+    "title": "Hospital readmission among people experiencing homelessness in England: a cohort study of 2772 matched homeless and housed inpatients.",
+    "authorString": "Lewer D, Menezes D, Cornes M, Blackburn RM, Byng R, Clark M, Denaxas S, Evans H, Fuller J, Hewett N, Kilmister A, Luchenski SA, Manthorpe J, McKee M, Neale J, Story A, Tinelli M, Whiteford M, Wurie F, Yavlinsky A, Hayward A, Aldridge R.",
     "authorAffiliations": "",
-    "journalTitle": "Cell",
-    "pubYear": "2019",
-    "date": "2019-10-10",
-    "isOpenAccess": "N",
-    "keywords": "Population genetics; Diversity; Psychiatry; complex disease; Gwas; Ancestry; Admixed Populations; Trans-ethnic; Trans-ancestry; Cross-ancestry",
+    "journalTitle": "Journal of epidemiology and community health",
+    "pubYear": "2021",
+    "date": "2021-01-05",
+    "isOpenAccess": "Y",
+    "keywords": "Homelessness; Health Inequalities; Record Linkage; Access To Hlth Care",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Genome-wide association studies (GWASs) have focused primarily on populations of European descent, but it is essential that diverse populations become better represented. Increasing diversity among study participants will advance our understanding of genetic architecture in all populations and ensure that genetic research is broadly applicable. To facilitate and promote research in multi-ancestry and admixed cohorts, we outline key methodological considerations and highlight opportunities, challenges, solutions, and areas in need of development. Despite the perception that analyzing genetic data from diverse populations is difficult, it is scientifically and ethically imperative, and there is an expanding analytical toolbox to do it well.",
+    "abstract": "<h4>Background</h4>Inpatients experiencing homelessness are often discharged to unstable accommodation or the street, which may increase the risk of readmission.<h4>Methods</h4>We conducted a cohort study of 2772 homeless patients discharged after an emergency admission at 78 hospitals across England between November 2013 and November 2016. For each individual, we selected a housed patient who lived in a socioeconomically deprived area, matched on age, sex, hospital, and year of discharge. Counts of emergency readmissions, planned readmissions, and Accident and Emergency (A&E) visits post-discharge were derived from national hospital databases, with a median of 2.8 years of follow-up. We estimated the cumulative incidence of readmission over 12 months, and used negative binomial regression to estimate rate ratios.<h4>Results</h4>After adjusting for health measured at the index admission, homeless patients had 2.49 (95% CI 2.29 to 2.70) times the rate of emergency readmission, 0.60 (95% CI 0.53 to 0.68) times the rate of planned readmission and 2.57 (95% CI 2.41 to 2.73) times the rate of A&E visits compared with housed patients. The 12-month risk of emergency readmission was higher for homeless patients (61%, 95% CI 59% to 64%) than housed patients (33%, 95% CI 30% to 36%); and the risk of planned readmission was lower for homeless patients (17%, 95% CI 14% to 19%) than for housed patients (30%, 95% CI 28% to 32%). While the risk of emergency readmission varied with the reason for admission for housed patients, for example being higher for admissions due to cancers than for those due to accidents, the risk was high across all causes for homeless patients.<h4>Conclusions</h4>Hospital patients experiencing homelessness have high rates of emergency readmission that are not explained by health. This highlights the need for discharge arrangements that address their health, housing and social care needs.",
     "laySummary": "",
-    "urls": "pdf:http://www.cell.com/article/S0092867419310025/pdf; doi:https://doi.org/10.1016/j.cell.2019.08.051; html:https://europepmc.org/articles/PMC6939869; pdf:https://europepmc.org/articles/PMC6939869?pdf=render; doi:https://doi.org/10.1016/j.cell.2019.08.051"
+    "urls": "pdf:https://jech.bmj.com/content/jech/75/7/681.full.pdf; doi:https://doi.org/10.1136/jech-2020-215204; html:https://europepmc.org/articles/PMC8223662; pdf:https://europepmc.org/articles/PMC8223662?pdf=render"
   },
   {
     "id": "35085490",
@@ -17918,21 +17969,21 @@
     "urls": "pdf:https://formative.jmir.org/2022/8/e37821/PDF; doi:https://doi.org/10.2196/37821; html:https://europepmc.org/articles/PMC9400842; pdf:https://europepmc.org/articles/PMC9400842?pdf=render"
   },
   {
-    "id": "33402395",
-    "doi": "https://doi.org/10.1136/jech-2020-215204",
-    "title": "Hospital readmission among people experiencing homelessness in England: a cohort study of 2772 matched homeless and housed inpatients.",
-    "authorString": "Lewer D, Menezes D, Cornes M, Blackburn RM, Byng R, Clark M, Denaxas S, Evans H, Fuller J, Hewett N, Kilmister A, Luchenski SA, Manthorpe J, McKee M, Neale J, Story A, Tinelli M, Whiteford M, Wurie F, Yavlinsky A, Hayward A, Aldridge R.",
+    "id": "33356394",
+    "doi": "https://doi.org/10.1161/hypertensionaha.120.16547",
+    "title": "Urate, Blood Pressure, and Cardiovascular Disease: Evidence From Mendelian Randomization and Meta-Analysis of Clinical Trials.",
+    "authorString": "Gill D, Cameron AC, Burgess S, Li X, Doherty DJ, Karhunen V, Abdul-Rahim AH, Taylor-Rowan M, Zuber V, Tsao PS, Klarin D, VA Million Veteran Program, Evangelou E, Elliott P, Damrauer SM, Quinn TJ, Dehghan A, Theodoratou E, Dawson J, Tzoulaki I.",
     "authorAffiliations": "",
-    "journalTitle": "Journal of epidemiology and community health",
+    "journalTitle": "Hypertension (Dallas, Tex. : 1979)",
     "pubYear": "2021",
-    "date": "2021-01-05",
+    "date": "2020-12-28",
     "isOpenAccess": "Y",
-    "keywords": "Homelessness; Health Inequalities; Record Linkage; Access To Hlth Care",
+    "keywords": "Cardiovascular diseases; Blood pressure; Uric acid; Systematic review; Odds Ratio",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Inpatients experiencing homelessness are often discharged to unstable accommodation or the street, which may increase the risk of readmission.<h4>Methods</h4>We conducted a cohort study of 2772 homeless patients discharged after an emergency admission at 78 hospitals across England between November 2013 and November 2016. For each individual, we selected a housed patient who lived in a socioeconomically deprived area, matched on age, sex, hospital, and year of discharge. Counts of emergency readmissions, planned readmissions, and Accident and Emergency (A&E) visits post-discharge were derived from national hospital databases, with a median of 2.8 years of follow-up. We estimated the cumulative incidence of readmission over 12 months, and used negative binomial regression to estimate rate ratios.<h4>Results</h4>After adjusting for health measured at the index admission, homeless patients had 2.49 (95% CI 2.29 to 2.70) times the rate of emergency readmission, 0.60 (95% CI 0.53 to 0.68) times the rate of planned readmission and 2.57 (95% CI 2.41 to 2.73) times the rate of A&E visits compared with housed patients. The 12-month risk of emergency readmission was higher for homeless patients (61%, 95% CI 59% to 64%) than housed patients (33%, 95% CI 30% to 36%); and the risk of planned readmission was lower for homeless patients (17%, 95% CI 14% to 19%) than for housed patients (30%, 95% CI 28% to 32%). While the risk of emergency readmission varied with the reason for admission for housed patients, for example being higher for admissions due to cancers than for those due to accidents, the risk was high across all causes for homeless patients.<h4>Conclusions</h4>Hospital patients experiencing homelessness have high rates of emergency readmission that are not explained by health. This highlights the need for discharge arrangements that address their health, housing and social care needs.",
+    "abstract": "Serum urate has been implicated in hypertension and cardiovascular disease, but it is not known whether it is exerting a causal effect. To investigate this, we performed Mendelian randomization analysis using data from UK Biobank, Million Veterans Program and genome-wide association study consortia, and meta-analysis of randomized controlled trials. The main Mendelian randomization analyses showed that every 1-SD increase in genetically predicted serum urate was associated with an increased risk of coronary heart disease (odds ratio, 1.19 [95% CI, 1.10-1.30]; <i>P</i>=4\u00d710<sup>-5</sup>), peripheral artery disease (1.12 [95% CI, 1.03-1.21]; <i>P</i>=9\u00d710<sup>-3</sup>), and stroke (1.11 [95% CI, 1.05-1.18]; <i>P</i>=2\u00d710<sup>-4</sup>). In Mendelian randomization mediation analyses, elevated blood pressure was estimated to mediate approximately one-third of the effect of urate on cardiovascular disease risk. Systematic review and meta-analysis of randomized controlled trials showed a favorable effect of urate-lowering treatment on systolic blood pressure (mean difference, -2.55 mm\u2009Hg [95% CI, -4.06 to -1.05]; <i>P</i>=1\u00d710<sup>-3</sup>) and major adverse cardiovascular events in those with previous cardiovascular disease (odds ratio, 0.40 [95% CI, 0.22-0.73]; <i>P</i>=3\u00d710<sup>-3</sup>) but no significant effect on major adverse cardiovascular events in all individuals (odds ratio, 0.67 [95% CI, 0.44-1.03]; <i>P</i>=0.07). In summary, these Mendelian randomization and clinical trial data support an effect of higher serum urate on increasing blood pressure, which may mediate a consequent effect on cardiovascular disease risk. High-quality trials are necessary to provide definitive evidence on the specific clinical contexts where urate lowering may be of cardiovascular benefit.",
     "laySummary": "",
-    "urls": "pdf:https://jech.bmj.com/content/jech/75/7/681.full.pdf; doi:https://doi.org/10.1136/jech-2020-215204; html:https://europepmc.org/articles/PMC8223662; pdf:https://europepmc.org/articles/PMC8223662?pdf=render"
+    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/HYPERTENSIONAHA.120.16547; doi:https://doi.org/10.1161/HYPERTENSIONAHA.120.16547; html:https://europepmc.org/articles/PMC7803439; pdf:https://europepmc.org/articles/PMC7803439?pdf=render"
   },
   {
     "id": "38855982",
@@ -17968,23 +18019,6 @@
     "laySummary": "",
     "urls": "pdf:https://cronfa.swan.ac.uk/Record/cronfa62055/Download/62055__26915__ae11794993454389b6ceddbb7f50caaa.pdf; doi:https://doi.org/10.1093/bjd/ljac090"
   },
-  {
-    "id": "33356394",
-    "doi": "https://doi.org/10.1161/hypertensionaha.120.16547",
-    "title": "Urate, Blood Pressure, and Cardiovascular Disease: Evidence From Mendelian Randomization and Meta-Analysis of Clinical Trials.",
-    "authorString": "Gill D, Cameron AC, Burgess S, Li X, Doherty DJ, Karhunen V, Abdul-Rahim AH, Taylor-Rowan M, Zuber V, Tsao PS, Klarin D, VA Million Veteran Program, Evangelou E, Elliott P, Damrauer SM, Quinn TJ, Dehghan A, Theodoratou E, Dawson J, Tzoulaki I.",
-    "authorAffiliations": "",
-    "journalTitle": "Hypertension (Dallas, Tex. : 1979)",
-    "pubYear": "2021",
-    "date": "2020-12-28",
-    "isOpenAccess": "Y",
-    "keywords": "Cardiovascular diseases; Blood pressure; Uric acid; Systematic review; Odds Ratio",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Serum urate has been implicated in hypertension and cardiovascular disease, but it is not known whether it is exerting a causal effect. To investigate this, we performed Mendelian randomization analysis using data from UK Biobank, Million Veterans Program and genome-wide association study consortia, and meta-analysis of randomized controlled trials. The main Mendelian randomization analyses showed that every 1-SD increase in genetically predicted serum urate was associated with an increased risk of coronary heart disease (odds ratio, 1.19 [95% CI, 1.10-1.30]; <i>P</i>=4\u00d710<sup>-5</sup>), peripheral artery disease (1.12 [95% CI, 1.03-1.21]; <i>P</i>=9\u00d710<sup>-3</sup>), and stroke (1.11 [95% CI, 1.05-1.18]; <i>P</i>=2\u00d710<sup>-4</sup>). In Mendelian randomization mediation analyses, elevated blood pressure was estimated to mediate approximately one-third of the effect of urate on cardiovascular disease risk. Systematic review and meta-analysis of randomized controlled trials showed a favorable effect of urate-lowering treatment on systolic blood pressure (mean difference, -2.55 mm\u2009Hg [95% CI, -4.06 to -1.05]; <i>P</i>=1\u00d710<sup>-3</sup>) and major adverse cardiovascular events in those with previous cardiovascular disease (odds ratio, 0.40 [95% CI, 0.22-0.73]; <i>P</i>=3\u00d710<sup>-3</sup>) but no significant effect on major adverse cardiovascular events in all individuals (odds ratio, 0.67 [95% CI, 0.44-1.03]; <i>P</i>=0.07). In summary, these Mendelian randomization and clinical trial data support an effect of higher serum urate on increasing blood pressure, which may mediate a consequent effect on cardiovascular disease risk. High-quality trials are necessary to provide definitive evidence on the specific clinical contexts where urate lowering may be of cardiovascular benefit.",
-    "laySummary": "",
-    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/HYPERTENSIONAHA.120.16547; doi:https://doi.org/10.1161/HYPERTENSIONAHA.120.16547; html:https://europepmc.org/articles/PMC7803439; pdf:https://europepmc.org/articles/PMC7803439?pdf=render"
-  },
   {
     "id": "38984466",
     "doi": "https://doi.org/10.1002/ehf2.14751",
@@ -18036,23 +18070,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmcmedresmethodol.biomedcentral.com/counter/pdf/10.1186/s12874-024-02175-9; doi:https://doi.org/10.1186/s12874-024-02175-9; html:https://europepmc.org/articles/PMC10953059; pdf:https://europepmc.org/articles/PMC10953059?pdf=render"
   },
-  {
-    "id": "36935397",
-    "doi": "https://doi.org/10.1093/bjs/znad055",
-    "title": "Validating a novel natural language processing pathway for automated quality assurance in surgical oncology: incomplete excision rates of 34 955 basal cell carcinomas.",
-    "authorString": "Ali SR, Dobbs TD, Jovic M, Strafford H, Fonferko-Shadrach B, Lacey AS, Williams N, Pickrell WO, Hutchings HA, Whitaker IS.",
-    "authorAffiliations": "",
-    "journalTitle": "The British journal of surgery",
-    "pubYear": "2023",
-    "date": "2023-08-01",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/bjs/advance-article-pdf/doi/10.1093/bjs/znad055/49561408/znad055.pdf; doi:https://doi.org/10.1093/bjs/znad055; html:https://europepmc.org/articles/PMC10416688; pdf:https://europepmc.org/articles/PMC10416688?pdf=render"
-  },
   {
     "id": "36654802",
     "doi": "https://doi.org/10.1002/lrh2.10315",
@@ -18070,6 +18087,23 @@
     "laySummary": "",
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9835047; doi:https://doi.org/10.1002/lrh2.10315; html:https://europepmc.org/articles/PMC9835047; pdf:https://europepmc.org/articles/PMC9835047?pdf=render"
   },
+  {
+    "id": "36935397",
+    "doi": "https://doi.org/10.1093/bjs/znad055",
+    "title": "Validating a novel natural language processing pathway for automated quality assurance in surgical oncology: incomplete excision rates of 34 955 basal cell carcinomas.",
+    "authorString": "Ali SR, Dobbs TD, Jovic M, Strafford H, Fonferko-Shadrach B, Lacey AS, Williams N, Pickrell WO, Hutchings HA, Whitaker IS.",
+    "authorAffiliations": "",
+    "journalTitle": "The British journal of surgery",
+    "pubYear": "2023",
+    "date": "2023-08-01",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/bjs/advance-article-pdf/doi/10.1093/bjs/znad055/49561408/znad055.pdf; doi:https://doi.org/10.1093/bjs/znad055; html:https://europepmc.org/articles/PMC10416688; pdf:https://europepmc.org/articles/PMC10416688?pdf=render"
+  },
   {
     "id": "32626822",
     "doi": "https://doi.org/10.1007/s41109-020-00273-3",
@@ -18461,6 +18495,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fdgth.2023.1184919/pdf?isPublishedV2=False; doi:https://doi.org/10.3389/fdgth.2023.1184919; html:https://europepmc.org/articles/PMC10569314; pdf:https://europepmc.org/articles/PMC10569314?pdf=render"
   },
+  {
+    "id": "30240446",
+    "doi": "https://doi.org/10.1371/journal.pone.0203896",
+    "title": "Polygenic risk scores for major depressive disorder and neuroticism as predictors of antidepressant response: Meta-analysis of three treatment cohorts.",
+    "authorString": "Ward J, Graham N, Strawbridge RJ, Ferguson A, Jenkins G, Chen W, Hodgson K, Frye M, Weinshilboum R, Uher R, Lewis CM, Biernacka J, Smith DJ.",
+    "authorAffiliations": "",
+    "journalTitle": "PloS one",
+    "pubYear": "2018",
+    "date": "2018-09-21",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "Better Care",
+    "healthCategories": "",
+    "abstract": "There are currently no reliable approaches for correctly identifying which patients with major depressive disorder (MDD) will respond well to antidepressant therapy. However, recent genetic advances suggest that Polygenic Risk Scores (PRS) could allow MDD patients to be stratified for antidepressant response. We used PRS for MDD and PRS for neuroticism as putative predictors of antidepressant response within three treatment cohorts: The Genome-based Therapeutic Drugs for Depression (GENDEP) cohort, and 2 sub-cohorts from the Pharmacogenomics Research Network Antidepressant Medication Pharmacogenomics Study PRGN-AMPS (total patient number = 760). Results across cohorts were combined via meta-analysis within a random effects model. Overall, PRS for MDD and neuroticism did not significantly predict antidepressant response but there was a consistent direction of effect, whereby greater genetic loading for both MDD (best MDD result, p < 5*10-5 MDD-PRS at 4 weeks, \u03b2 = -0.019, S.E = 0.008, p = 0.01) and neuroticism (best neuroticism result, p < 0.1 neuroticism-PRS at 8 weeks, \u03b2 = -0.017, S.E = 0.008, p = 0.03) were associated with less favourable response. We conclude that the PRS approach may offer some promise for treatment stratification in MDD and should now be assessed within larger clinical cohorts.",
+    "laySummary": "",
+    "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0203896&type=printable; doi:https://doi.org/10.1371/journal.pone.0203896; html:https://europepmc.org/articles/PMC6150505; pdf:https://europepmc.org/articles/PMC6150505?pdf=render"
+  },
   {
     "id": "33280008",
     "doi": "https://doi.org/10.1093/cercor/bhaa345",
@@ -18478,23 +18529,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/cercor/article-pdf/31/4/2071/36458400/bhaa345.pdf; doi:https://doi.org/10.1093/cercor/bhaa345; html:https://europepmc.org/articles/PMC7945030; pdf:https://europepmc.org/articles/PMC7945030?pdf=render"
   },
-  {
-    "id": "37294923",
-    "doi": "https://doi.org/10.1093/eurjpc/zwad192",
-    "title": "Incidence of 12 common cardiovascular diseases and subsequent mortality risk in the general population.",
-    "authorString": "Prugger C, Perier MC, Gonzalez-Izquierdo A, Hemingway H, Denaxas S, Empana JP.",
-    "authorAffiliations": "",
-    "journalTitle": "European journal of preventive cardiology",
-    "pubYear": "2023",
-    "date": "2023-10-01",
-    "isOpenAccess": "N",
-    "keywords": "Prevention; Survival analysis; Stroke; epidemiology; Coronary Heart Disease; incidence",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Incident events of cardiovascular diseases (CVDs) are heterogenous and may result in different mortality risks. Such evidence may help inform patient and physician decisions in CVD prevention and risk factor management.<h4>Aims</h4>This study aimed to determine the extent to which incident events of common CVD show heterogeneous associations with subsequent mortality risk in the general population.<h4>Methods and results</h4>Based on England-wide linked electronic health records, we established a cohort of 1 310 518 people \u226530 years of age initially free of CVD and followed up for non-fatal events of 12 common CVD and cause-specific mortality. The 12 CVDs were considered as time-varying exposures in Cox's proportional hazards models to estimate hazard rate ratios (HRRs) with 95% confidence intervals (CIs). Over the median follow-up of 4.2 years (2010-16), 81 516 non-fatal CVD, 10 906 cardiovascular deaths, and 40 843 non-cardiovascular deaths occurred. All 12 CVDs were associated with increased risk of cardiovascular mortality, with HRR (95% CI) ranging from 1.67 (1.47-1.89) for stable angina to 7.85 (6.62-9.31) for haemorrhagic stroke. All 12 CVDs were also associated with increased non-cardiovascular and all-cause mortality risk but to a lesser extent: HRR (95% CI) ranged from 1.10 (1.00-1.22) to 4.55 (4.03-5.13) and from 1.24 (1.13-1.35) to 4.92 (4.44-5.46) for transient ischaemic attack and sudden cardiac arrest, respectively.<h4>Conclusion</h4>Incident events of 12 common CVD show significant adverse and markedly differential associations with subsequent cardiovascular, non-cardiovascular, and all-cause mortality risk in the general population.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1093/eurjpc/zwad192"
-  },
   {
     "id": "36302124",
     "doi": "https://doi.org/10.1080/21645515.2022.2127572",
@@ -18513,21 +18547,21 @@
     "urls": "doi:https://doi.org/10.1080/21645515.2022.2127572; doi:https://doi.org/10.1080/21645515.2022.2127572; html:https://europepmc.org/articles/PMC9746546; pdf:https://europepmc.org/articles/PMC9746546?pdf=render"
   },
   {
-    "id": "30240446",
-    "doi": "https://doi.org/10.1371/journal.pone.0203896",
-    "title": "Polygenic risk scores for major depressive disorder and neuroticism as predictors of antidepressant response: Meta-analysis of three treatment cohorts.",
-    "authorString": "Ward J, Graham N, Strawbridge RJ, Ferguson A, Jenkins G, Chen W, Hodgson K, Frye M, Weinshilboum R, Uher R, Lewis CM, Biernacka J, Smith DJ.",
+    "id": "37294923",
+    "doi": "https://doi.org/10.1093/eurjpc/zwad192",
+    "title": "Incidence of 12 common cardiovascular diseases and subsequent mortality risk in the general population.",
+    "authorString": "Prugger C, Perier MC, Gonzalez-Izquierdo A, Hemingway H, Denaxas S, Empana JP.",
     "authorAffiliations": "",
-    "journalTitle": "PloS one",
-    "pubYear": "2018",
-    "date": "2018-09-21",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "Better Care",
+    "journalTitle": "European journal of preventive cardiology",
+    "pubYear": "2023",
+    "date": "2023-10-01",
+    "isOpenAccess": "N",
+    "keywords": "Prevention; Survival analysis; Stroke; epidemiology; Coronary Heart Disease; incidence",
+    "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "There are currently no reliable approaches for correctly identifying which patients with major depressive disorder (MDD) will respond well to antidepressant therapy. However, recent genetic advances suggest that Polygenic Risk Scores (PRS) could allow MDD patients to be stratified for antidepressant response. We used PRS for MDD and PRS for neuroticism as putative predictors of antidepressant response within three treatment cohorts: The Genome-based Therapeutic Drugs for Depression (GENDEP) cohort, and 2 sub-cohorts from the Pharmacogenomics Research Network Antidepressant Medication Pharmacogenomics Study PRGN-AMPS (total patient number = 760). Results across cohorts were combined via meta-analysis within a random effects model. Overall, PRS for MDD and neuroticism did not significantly predict antidepressant response but there was a consistent direction of effect, whereby greater genetic loading for both MDD (best MDD result, p < 5*10-5 MDD-PRS at 4 weeks, \u03b2 = -0.019, S.E = 0.008, p = 0.01) and neuroticism (best neuroticism result, p < 0.1 neuroticism-PRS at 8 weeks, \u03b2 = -0.017, S.E = 0.008, p = 0.03) were associated with less favourable response. We conclude that the PRS approach may offer some promise for treatment stratification in MDD and should now be assessed within larger clinical cohorts.",
+    "abstract": "<h4>Background</h4>Incident events of cardiovascular diseases (CVDs) are heterogenous and may result in different mortality risks. Such evidence may help inform patient and physician decisions in CVD prevention and risk factor management.<h4>Aims</h4>This study aimed to determine the extent to which incident events of common CVD show heterogeneous associations with subsequent mortality risk in the general population.<h4>Methods and results</h4>Based on England-wide linked electronic health records, we established a cohort of 1 310 518 people \u226530 years of age initially free of CVD and followed up for non-fatal events of 12 common CVD and cause-specific mortality. The 12 CVDs were considered as time-varying exposures in Cox's proportional hazards models to estimate hazard rate ratios (HRRs) with 95% confidence intervals (CIs). Over the median follow-up of 4.2 years (2010-16), 81 516 non-fatal CVD, 10 906 cardiovascular deaths, and 40 843 non-cardiovascular deaths occurred. All 12 CVDs were associated with increased risk of cardiovascular mortality, with HRR (95% CI) ranging from 1.67 (1.47-1.89) for stable angina to 7.85 (6.62-9.31) for haemorrhagic stroke. All 12 CVDs were also associated with increased non-cardiovascular and all-cause mortality risk but to a lesser extent: HRR (95% CI) ranged from 1.10 (1.00-1.22) to 4.55 (4.03-5.13) and from 1.24 (1.13-1.35) to 4.92 (4.44-5.46) for transient ischaemic attack and sudden cardiac arrest, respectively.<h4>Conclusion</h4>Incident events of 12 common CVD show significant adverse and markedly differential associations with subsequent cardiovascular, non-cardiovascular, and all-cause mortality risk in the general population.",
     "laySummary": "",
-    "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0203896&type=printable; doi:https://doi.org/10.1371/journal.pone.0203896; html:https://europepmc.org/articles/PMC6150505; pdf:https://europepmc.org/articles/PMC6150505?pdf=render"
+    "urls": "doi:https://doi.org/10.1093/eurjpc/zwad192"
   },
   {
     "id": "38740716",
@@ -18597,23 +18631,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/eurheartj/advance-article-pdf/doi/10.1093/eurheartj/ehad376/50684614/ehad376.pdf; doi:https://doi.org/10.1093/eurheartj/ehad376; html:https://europepmc.org/articles/PMC10406338; pdf:https://europepmc.org/articles/PMC10406338?pdf=render"
   },
-  {
-    "id": "35940584",
-    "doi": "https://doi.org/10.1123/pes.2021-0174",
-    "title": "Clusters of Activity-Related Social and Physical Home Environmental Factors and Their Association With Children's Home-Based Physical Activity and Sitting.",
-    "authorString": "Sheldrick MP, Maitland C, Mackintosh KA, Rosenberg M, Griffiths LJ, Fry R, Stratton G.",
-    "authorAffiliations": "",
-    "journalTitle": "Pediatric exercise science",
-    "pubYear": "2023",
-    "date": "2022-08-08",
-    "isOpenAccess": "N",
-    "keywords": "Families; Physical environment; Social Environment; Sedentary Behavior; Correlates; Screen Time",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Purpose</h4>Understanding which physical activity (PA) and sedentary behavior correlates cluster in children is important, particularly in the home, where children spend significant time. Therefore, this study aimed to assess clustering of physical and social activity-related factors at home, and whether these clusters are related to home-based sitting and PA in children. A secondary aim was to explore whether the clusters were associated with child, parent, and family characteristics.<h4>Methods</h4>Altogether, 235 children (55% girls, mean age = 10.2 [0.7]\u00a0y) and their parents took part. Physical (eg,\u00a0PA and electronic media equipment, house and garden size, layout) and social (eg,\u00a0activity preferences, priorities, parental rules) home environmental factors were obtained via the HomeSPACE-II audit and self-report, respectively. Principal component analysis was used to identify clusters of physical and social environmental factors. Backward regression analysis and partial correlations were used to examine relationships between clusters, children's device-measured home-based activity behaviors, and background characteristics.<h4>Results</h4>The findings show that physical and social environment activity-related factors at home cluster. The clusters were associated with several background characteristics, with socioeconomic factors appearing to be particularly influential. The clusters were also associated with home-based activity behaviors in the hypothesized directions.<h4>Conclusion</h4>Interventions which target clusters of social and physical factors at home, especially among low-socioeconomic status families, are warranted.",
-    "laySummary": "",
-    "urls": "pdf:https://cronfa.swan.ac.uk/Record/cronfa60257/Download/60257__24327__e83f9d0502424e5e9075c668a2672db1.pdf; doi:https://doi.org/10.1123/pes.2021-0174"
-  },
   {
     "id": "32460529",
     "doi": "https://doi.org/10.1161/circimaging.119.010389",
@@ -18632,21 +18649,21 @@
     "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCIMAGING.119.010389; doi:https://doi.org/10.1161/CIRCIMAGING.119.010389; html:https://europepmc.org/articles/PMC7610536; pdf:https://europepmc.org/articles/PMC7610536?pdf=render; doi:https://doi.org/10.1161/circimaging.119.010389"
   },
   {
-    "id": "39002770",
-    "doi": "https://doi.org/10.1016/j.ijid.2024.107169",
-    "title": "Incidence and mortality rates of 14 site-specific infectious diseases in 10 diverse areas of China: findings from China Kadoorie Biobank, 2006-2018.",
-    "authorString": "Huang R, Kartsonaki C, Turnbull I, Pei P, Chen Y, Liu J, Du H, Sun D, Yang L, Barnard M, Lv J, Yu C, Chen J, Li L, Chen Z, Bragg F.",
+    "id": "35940584",
+    "doi": "https://doi.org/10.1123/pes.2021-0174",
+    "title": "Clusters of Activity-Related Social and Physical Home Environmental Factors and Their Association With Children's Home-Based Physical Activity and Sitting.",
+    "authorString": "Sheldrick MP, Maitland C, Mackintosh KA, Rosenberg M, Griffiths LJ, Fry R, Stratton G.",
     "authorAffiliations": "",
-    "journalTitle": "International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases",
-    "pubYear": "2024",
-    "date": "2024-07-11",
+    "journalTitle": "Pediatric exercise science",
+    "pubYear": "2023",
+    "date": "2022-08-08",
     "isOpenAccess": "N",
-    "keywords": "China; Infectious diseases; Mortality; Hospitalization; incidence; Case Fatality",
+    "keywords": "Families; Physical environment; Social Environment; Sedentary Behavior; Correlates; Screen Time",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Infectious diseases remain a major global health concern, including in China, with an estimated >10 million cases of infectious disease in 2019. We describe the burden of site-specific infectious diseases among Chinese adults.<h4>Methods</h4>From 2004 to 2008, the prospective China Kadoorie Biobank enrolled 512,726 adults aged 30-79 years from 10 diverse areas (5 rural, 5 urban) of China. During the 12 years of follow-up, 101,673 participants were hospitalized for any infectious disease. Descriptive analyses examined standardized incidence, mortality and case fatality of infections.<h4>Findings</h4>The incidence of any infectious disease was 1856 per 100,000 person-years; respiratory tract infections (1069) were most common. The infectious disease mortality rate was 31.8 per 100,000 person-years (20.3 and 9.4 for respiratory and non-respiratory infections, respectively) and case fatality was 2.2% (2.6% and 1.6% for respiratory and non-respiratory infections, respectively). Infectious disease incidence and mortality rates were higher at older ages and in rural areas. There were no clear sex differences in infectious disease incidence rates, but mortality and case fatality rates were twice as high in men as in women.<h4>Interpretation</h4>Infectious diseases were common in Chinese adults. The observed burden of, and disparities in, site-specific infections can inform targeted prevention efforts.<h4>Funding</h4>Kadoorie Foundation, Wellcome Trust, MRC, BHF, CR-UK, MoST, NNSF.",
+    "abstract": "<h4>Purpose</h4>Understanding which physical activity (PA) and sedentary behavior correlates cluster in children is important, particularly in the home, where children spend significant time. Therefore, this study aimed to assess clustering of physical and social activity-related factors at home, and whether these clusters are related to home-based sitting and PA in children. A secondary aim was to explore whether the clusters were associated with child, parent, and family characteristics.<h4>Methods</h4>Altogether, 235 children (55% girls, mean age = 10.2 [0.7]\u00a0y) and their parents took part. Physical (eg,\u00a0PA and electronic media equipment, house and garden size, layout) and social (eg,\u00a0activity preferences, priorities, parental rules) home environmental factors were obtained via the HomeSPACE-II audit and self-report, respectively. Principal component analysis was used to identify clusters of physical and social environmental factors. Backward regression analysis and partial correlations were used to examine relationships between clusters, children's device-measured home-based activity behaviors, and background characteristics.<h4>Results</h4>The findings show that physical and social environment activity-related factors at home cluster. The clusters were associated with several background characteristics, with socioeconomic factors appearing to be particularly influential. The clusters were also associated with home-based activity behaviors in the hypothesized directions.<h4>Conclusion</h4>Interventions which target clusters of social and physical factors at home, especially among low-socioeconomic status families, are warranted.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.ijid.2024.107169"
+    "urls": "pdf:https://cronfa.swan.ac.uk/Record/cronfa60257/Download/60257__24327__e83f9d0502424e5e9075c668a2672db1.pdf; doi:https://doi.org/10.1123/pes.2021-0174"
   },
   {
     "id": "37367415",
@@ -18665,6 +18682,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.mdpi.com/2308-3425/10/6/250/pdf?version=1686288586; doi:https://doi.org/10.3390/jcdd10060250; html:https://europepmc.org/articles/PMC10299045; pdf:https://europepmc.org/articles/PMC10299045?pdf=render"
   },
+  {
+    "id": "39002770",
+    "doi": "https://doi.org/10.1016/j.ijid.2024.107169",
+    "title": "Incidence and mortality rates of 14 site-specific infectious diseases in 10 diverse areas of China: findings from China Kadoorie Biobank, 2006-2018.",
+    "authorString": "Huang R, Kartsonaki C, Turnbull I, Pei P, Chen Y, Liu J, Du H, Sun D, Yang L, Barnard M, Lv J, Yu C, Chen J, Li L, Chen Z, Bragg F.",
+    "authorAffiliations": "",
+    "journalTitle": "International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases",
+    "pubYear": "2024",
+    "date": "2024-07-11",
+    "isOpenAccess": "N",
+    "keywords": "China; Infectious diseases; Mortality; Hospitalization; incidence; Case Fatality",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Infectious diseases remain a major global health concern, including in China, with an estimated >10 million cases of infectious disease in 2019. We describe the burden of site-specific infectious diseases among Chinese adults.<h4>Methods</h4>From 2004 to 2008, the prospective China Kadoorie Biobank enrolled 512,726 adults aged 30-79 years from 10 diverse areas (5 rural, 5 urban) of China. During the 12 years of follow-up, 101,673 participants were hospitalized for any infectious disease. Descriptive analyses examined standardized incidence, mortality and case fatality of infections.<h4>Findings</h4>The incidence of any infectious disease was 1856 per 100,000 person-years; respiratory tract infections (1069) were most common. The infectious disease mortality rate was 31.8 per 100,000 person-years (20.3 and 9.4 for respiratory and non-respiratory infections, respectively) and case fatality was 2.2% (2.6% and 1.6% for respiratory and non-respiratory infections, respectively). Infectious disease incidence and mortality rates were higher at older ages and in rural areas. There were no clear sex differences in infectious disease incidence rates, but mortality and case fatality rates were twice as high in men as in women.<h4>Interpretation</h4>Infectious diseases were common in Chinese adults. The observed burden of, and disparities in, site-specific infections can inform targeted prevention efforts.<h4>Funding</h4>Kadoorie Foundation, Wellcome Trust, MRC, BHF, CR-UK, MoST, NNSF.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.ijid.2024.107169"
+  },
   {
     "id": "32398093",
     "doi": "https://doi.org/10.1186/s13063-020-04329-8",
@@ -18801,23 +18835,6 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jcsm.12971; doi:https://doi.org/10.1002/jcsm.12971; html:https://europepmc.org/articles/PMC9178164; pdf:https://europepmc.org/articles/PMC9178164?pdf=render"
   },
-  {
-    "id": "36564466",
-    "doi": "https://doi.org/10.1038/s41598-022-26141-x",
-    "title": "Assessing and removing the effect of unwanted technical variations in microbiome data.",
-    "authorString": "Fachrul M, M\u00e9ric G, Inouye M, Pamp SJ, Salim A.",
-    "authorAffiliations": "",
-    "journalTitle": "Scientific reports",
-    "pubYear": "2022",
-    "date": "2022-12-23",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Varying technologies and experimental approaches used in microbiome studies often lead to irreproducible results due to unwanted technical variations. Such variations, often unaccounted for and of unknown source, may interfere with true biological signals, resulting in misleading biological conclusions. In this work, we aim to characterize the major sources of technical variations in microbiome data and demonstrate how in-silico approaches can minimize their impact. We analyzed 184 pig faecal metagenomes encompassing 21 specific combinations of deliberately introduced factors of technical and biological variations. Using the novel Removing Unwanted Variations-III-Negative Binomial (RUV-III-NB), we identified several known experimental factors, specifically storage conditions and freeze-thaw cycles, as likely major sources of unwanted variation in metagenomes. We also observed that these unwanted technical variations do not affect taxa uniformly, with freezing samples affecting taxa of class Bacteroidia the most, for example. Additionally, we benchmarked the performances of different correction methods, including ComBat, ComBat-seq, RUVg, RUVs, and RUV-III-NB. While RUV-III-NB performed consistently robust across our sensitivity and specificity metrics, most other methods did not remove unwanted variations optimally. Our analyses suggest that a careful consideration of possible technical confounders is critical during experimental design of microbiome studies, and that the inclusion of technical replicates is necessary to efficiently remove unwanted variations computationally.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41598-022-26141-x.pdf; doi:https://doi.org/10.1038/s41598-022-26141-x; html:https://europepmc.org/articles/PMC9789116; pdf:https://europepmc.org/articles/PMC9789116?pdf=render"
-  },
   {
     "id": "38069915",
     "doi": "https://doi.org/10.1093/clinchem/hvad205",
@@ -18835,6 +18852,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1093/clinchem/hvad205"
   },
+  {
+    "id": "36564466",
+    "doi": "https://doi.org/10.1038/s41598-022-26141-x",
+    "title": "Assessing and removing the effect of unwanted technical variations in microbiome data.",
+    "authorString": "Fachrul M, M\u00e9ric G, Inouye M, Pamp SJ, Salim A.",
+    "authorAffiliations": "",
+    "journalTitle": "Scientific reports",
+    "pubYear": "2022",
+    "date": "2022-12-23",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Varying technologies and experimental approaches used in microbiome studies often lead to irreproducible results due to unwanted technical variations. Such variations, often unaccounted for and of unknown source, may interfere with true biological signals, resulting in misleading biological conclusions. In this work, we aim to characterize the major sources of technical variations in microbiome data and demonstrate how in-silico approaches can minimize their impact. We analyzed 184 pig faecal metagenomes encompassing 21 specific combinations of deliberately introduced factors of technical and biological variations. Using the novel Removing Unwanted Variations-III-Negative Binomial (RUV-III-NB), we identified several known experimental factors, specifically storage conditions and freeze-thaw cycles, as likely major sources of unwanted variation in metagenomes. We also observed that these unwanted technical variations do not affect taxa uniformly, with freezing samples affecting taxa of class Bacteroidia the most, for example. Additionally, we benchmarked the performances of different correction methods, including ComBat, ComBat-seq, RUVg, RUVs, and RUV-III-NB. While RUV-III-NB performed consistently robust across our sensitivity and specificity metrics, most other methods did not remove unwanted variations optimally. Our analyses suggest that a careful consideration of possible technical confounders is critical during experimental design of microbiome studies, and that the inclusion of technical replicates is necessary to efficiently remove unwanted variations computationally.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41598-022-26141-x.pdf; doi:https://doi.org/10.1038/s41598-022-26141-x; html:https://europepmc.org/articles/PMC9789116; pdf:https://europepmc.org/articles/PMC9789116?pdf=render"
+  },
   {
     "id": "32788201",
     "doi": "https://doi.org/10.1136/archdischild-2020-319027",
@@ -18852,23 +18886,6 @@
     "laySummary": "",
     "urls": "pdf:https://adc.bmj.com/content/archdischild/106/1/44.full.pdf; doi:https://doi.org/10.1136/archdischild-2020-319027; html:https://europepmc.org/articles/PMC7788194; pdf:https://europepmc.org/articles/PMC7788194?pdf=render"
   },
-  {
-    "id": "39170762",
-    "doi": "https://doi.org/10.2196/preprints.42449",
-    "title": "Charting a course for smartphones and wearables to transform population health research.",
-    "authorString": "Dixon WG, van der Veer SN, Ali SM, Laidlaw L, Dobson RJ, Sudlow C, Chico T, MacArthur JA, Doherty A.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of medical Internet research",
-    "pubYear": "2023",
-    "date": "2023-02-07",
-    "isOpenAccess": "N",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The use of data from smartphones and wearable devices has huge potential for population health research given high device ownership, the range of novel health-relevant data types available from consumer devices, and the frequency and duration over which data are, or could be, collected. Yet the uptake and success of large-scale mobile health research in the last decade has not matched the hyped opportunity. We make the argument that digital person-generated health data is required and necessary to answer many top priority research questions through illustrative examples taken from the James Lind Alliance Priority Setting Partnership. We then summarise the findings from two UK initiatives that considered the challenges and possible solutions for what needs to be done, and in what way, to realise the future opportunities of digital person-generated health data for clinically important population health research. Examples of important areas to be addressed to advance the field include digital inequality and addressing possible selection bias, easy access for researchers to the appropriate data collection tools including how best to harmonise data items, analysis methodology for time series data, methods for patient and public involvement and engagement to optimise recruitment, retention and public trust, and providing greater control of their data to research participants. There is also a major opportunity through the linkage of digital persongenerated health data to routinely-collected data to support novel population health research, bringing together clinician-reported and patient-reported measures. We recognise that well conducted studies need a wide range of diverse challenges to be skilfully addressed in unison: for example, epidemiology, data science and biostatistics, psychometrics, behavioural and social science, software engineering, user interface design, information governance, data management and patient and public involvement and engagement. Consequently, progress would be accelerated by the establishment of a new interdisciplinary community where all relevant and necessary skills are brought together to allow excellence throughout the lifecycle of a research study. This will require a partnership of diverse people, of methods and of technology. Get this right and the synergy has the potential to transform many millions of people's lives for the better.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.2196/preprints.42449"
-  },
   {
     "id": "36571960",
     "doi": "https://doi.org/10.1016/j.bjps.2022.11.049",
@@ -18886,6 +18903,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.bjps.2022.11.049"
   },
+  {
+    "id": "39170762",
+    "doi": "https://doi.org/10.2196/preprints.42449",
+    "title": "Charting a course for smartphones and wearables to transform population health research.",
+    "authorString": "Dixon WG, van der Veer SN, Ali SM, Laidlaw L, Dobson RJ, Sudlow C, Chico T, MacArthur JA, Doherty A.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of medical Internet research",
+    "pubYear": "2023",
+    "date": "2023-02-07",
+    "isOpenAccess": "N",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The use of data from smartphones and wearable devices has huge potential for population health research given high device ownership, the range of novel health-relevant data types available from consumer devices, and the frequency and duration over which data are, or could be, collected. Yet the uptake and success of large-scale mobile health research in the last decade has not matched the hyped opportunity. We make the argument that digital person-generated health data is required and necessary to answer many top priority research questions through illustrative examples taken from the James Lind Alliance Priority Setting Partnership. We then summarise the findings from two UK initiatives that considered the challenges and possible solutions for what needs to be done, and in what way, to realise the future opportunities of digital person-generated health data for clinically important population health research. Examples of important areas to be addressed to advance the field include digital inequality and addressing possible selection bias, easy access for researchers to the appropriate data collection tools including how best to harmonise data items, analysis methodology for time series data, methods for patient and public involvement and engagement to optimise recruitment, retention and public trust, and providing greater control of their data to research participants. There is also a major opportunity through the linkage of digital persongenerated health data to routinely-collected data to support novel population health research, bringing together clinician-reported and patient-reported measures. We recognise that well conducted studies need a wide range of diverse challenges to be skilfully addressed in unison: for example, epidemiology, data science and biostatistics, psychometrics, behavioural and social science, software engineering, user interface design, information governance, data management and patient and public involvement and engagement. Consequently, progress would be accelerated by the establishment of a new interdisciplinary community where all relevant and necessary skills are brought together to allow excellence throughout the lifecycle of a research study. This will require a partnership of diverse people, of methods and of technology. Get this right and the synergy has the potential to transform many millions of people's lives for the better.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.2196/preprints.42449"
+  },
   {
     "id": "39053458",
     "doi": "https://doi.org/10.1016/j.ajhg.2024.06.017",
@@ -18955,21 +18989,38 @@
     "urls": "pdf:https://royalsocietypublishing.org/doi/pdf/10.1098/rstb.2018.0276; doi:https://doi.org/10.1098/rstb.2018.0276; html:https://europepmc.org/articles/PMC6558557; pdf:https://europepmc.org/articles/PMC6558557?pdf=render"
   },
   {
-    "id": "39453837",
-    "doi": "https://doi.org/10.1056/nejmoa2409183",
-    "title": "Long-Term Effects of Empagliflozin in Patients with Chronic Kidney Disease.",
-    "authorString": "EMPA-KIDNEY Collaborative Group, Herrington WG, Staplin N, Agrawal N, Wanner C, Green JB, Hauske SJ, Emberson JR, Preiss D, Judge P, Zhu D, Dayanandan R, Arimoto R, Mayne KJ, Ng SYA, Sammons E, Hill M, Stevens W, Wallendszus K, Brenner S, Cheung AK, Liu ZH, Li J, Hooi LS, Liu W, Kadowaki T, Nangaku M, Levin A, Cherney DZI, Maggioni AP, Pontremoli R, Deo R, Goto S, Rossello X, Tuttle KR, Steubl D, Massey D, Brueckmann M, Landray MJ, Baigent C, Haynes R.",
+    "id": "36299367",
+    "doi": "https://doi.org/10.1183/23120541.00211-2022",
+    "title": "Mortality associated with metabolic syndrome in people with COPD managed in primary care.",
+    "authorString": "Karsanji U, Evans RA, Quint JK, Khunti K, Lawson CA, Petherick E, Greening NJ, Singh SJ, Richardson M, Steiner MC.",
     "authorAffiliations": "",
-    "journalTitle": "The New England journal of medicine",
-    "pubYear": "2024",
-    "date": "2024-10-25",
+    "journalTitle": "ERJ open research",
+    "pubYear": "2022",
+    "date": "2022-10-24",
     "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>In the EMPA-KIDNEY trial, empagliflozin, a sodium-glucose cotransporter 2 (SGLT2) inhibitor, had positive cardiorenal effects in patients with chronic kidney disease who were at risk for disease progression. Post-trial follow-up was designed to assess how the effects of empagliflozin would evolve after the discontinuation of the trial drug.<h4>Methods</h4>In the active trial, patients with chronic kidney disease were randomly assigned to receive either empagliflozin (10 mg once daily) or matching placebo and were followed for a median of 2 years. All the patients had an estimated glomerular filtration rate (eGFR) of at least 20 but less than 45 ml per minute per 1.73 m<sup>2</sup> of body-surface area or an eGFR of at least 45 but less than 90 ml per minute per 1.73 m<sup>2</sup> with a urinary albumin-to-creatinine ratio (with albumin measured in milligrams and creatinine measured in grams) of at least 200. Subsequently, surviving patients who consented were observed for 2 additional years. No trial empagliflozin or placebo was administered during the post-trial period, but local practitioners could prescribe open-label SGLT2 inhibitors, including open-label empagliflozin. The primary composite outcome was kidney disease progression or cardiovascular death as assessed from the start of the active-trial period to the end of the post-trial period.<h4>Results</h4>Of the 6609 patients who had undergone randomization in the active trial, 4891 (74%) were enrolled in the post-trial period. During this period, the use of open-label SGLT2 inhibitors was similar in the two groups (43% in the empagliflozin group and 40% in the placebo group). During the combined active- and post-trial periods, a primary-outcome event occurred in 865 of 3304 patients (26.2%) in the empagliflozin group and in 1001 of 3305 patients (30.3%) in the placebo group (hazard ratio, 0.79; 95% confidence interval [CI], 0.72 to 0.87). During the post-trial period only, the hazard ratio for a primary-outcome event was 0.87 (95% CI, 0.76 to 0.99). During the combined periods, the risk of kidney disease progression was 23.5% in the empagliflozin group and 27.1% in the placebo group; the risk of the composite of death or end-stage kidney disease was 16.9% and 19.6%, respectively; and the risk of cardiovascular death was 3.8% and 4.9%, respectively. There was no effect of empagliflozin on death from noncardiovascular causes (5.3% in both groups).<h4>Conclusions</h4>In a broad range of patients with chronic kidney disease at risk for progression, empagliflozin continued to have additional cardiorenal benefits for up to 12 months after it was discontinued. (Funded by Boehringer Ingelheim and others; EMPA-KIDNEY ClinicalTrials.gov number, NCT03594110; EuDRACT number, 2017-002971-24.).",
+    "abstract": "<h4>Objective</h4>The prevalence of metabolic syndrome (MetS) has been reported to be higher in selected populations of people with COPD. The impact of MetS on mortality in COPD is unknown. We used routinely collected healthcare data to estimate the prevalence of MetS in people with COPD managed in primary care and determine its impact on 5-year mortality.<h4>Methods</h4>Records from 103\u2009955 patients with COPD from the Clinical Practice Research Datalink (CPRD-GOLD) between 2009 to 2017 were scrutinised. MetS was defined as the presence of three or more of: obesity, hypertension, lowered high-density lipoprotein cholesterol, elevated triglycerides or type 2 diabetes mellitus (T2DM). Univariate and multivariable Cox regression models were constructed to determine the prognostic impact of MetS on 5-year mortality. Similar univariate models were constructed for individual components of the definition of MetS.<h4>Results</h4>The prevalence of MetS in the COPD cohort was 10.1%. Univariate analyses showed the presence of MetS increased mortality (hazard ratio (HR) 1.19, 95% CI: 1.12-1.27, p<0.001), but this risk was substantially attenuated in the multivariable analysis (HR 1.06, 95% CI: 0.99-1.13, p<i>=</i>0.085). The presence of hypertension (HR 1.70, 95% CI: 1.63-1.77, p<0.001) and T2DM (HR 1.41, 95% CI: 1.34-1.48, p<0.001) increased and obesity (HR 0.74, 95% CI: 0.71-0.78, p<0.001) reduced mortality risk.<h4>Conclusion</h4>MetS in patients with COPD is associated with higher 5-year mortality, but this impact was minimal when adjusted for indices of COPD disease severity and other comorbidities. Individual components of the MetS definition exerted differential impacts on mortality suggesting limitation to the use of MetS as a multicomponent condition in predicting outcome in COPD.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1056/NEJMoa2409183; html:https://europepmc.org/articles/PMC7616743; pdf:https://europepmc.org/articles/PMC7616743?pdf=render"
+    "urls": "pdf:https://openres.ersjournals.com/content/erjor/8/4/00211-2022.full.pdf; doi:https://doi.org/10.1183/23120541.00211-2022; html:https://europepmc.org/articles/PMC9589337; pdf:https://europepmc.org/articles/PMC9589337?pdf=render"
+  },
+  {
+    "id": "34543272",
+    "doi": "https://doi.org/10.1371/journal.pcbi.1009324",
+    "title": "Ten simple rules to make your computing more environmentally sustainable.",
+    "authorString": "Lannelongue L, Grealey J, Bateman A, Inouye M.",
+    "authorAffiliations": "",
+    "journalTitle": "PLoS computational biology",
+    "pubYear": "2021",
+    "date": "2021-09-20",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "",
+    "laySummary": "",
+    "urls": "pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009324&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1009324; html:https://europepmc.org/articles/PMC8452068; pdf:https://europepmc.org/articles/PMC8452068?pdf=render"
   },
   {
     "id": "35143670",
@@ -18989,21 +19040,21 @@
     "urls": "pdf:https://academic.oup.com/mbe/article-pdf/39/3/msac034/42692776/msac034.pdf; doi:https://doi.org/10.1093/molbev/msac034; html:https://europepmc.org/articles/PMC8892942; pdf:https://europepmc.org/articles/PMC8892942?pdf=render"
   },
   {
-    "id": "34543272",
-    "doi": "https://doi.org/10.1371/journal.pcbi.1009324",
-    "title": "Ten simple rules to make your computing more environmentally sustainable.",
-    "authorString": "Lannelongue L, Grealey J, Bateman A, Inouye M.",
+    "id": "39453837",
+    "doi": "https://doi.org/10.1056/nejmoa2409183",
+    "title": "Long-Term Effects of Empagliflozin in Patients with Chronic Kidney Disease.",
+    "authorString": "EMPA-KIDNEY Collaborative Group, Herrington WG, Staplin N, Agrawal N, Wanner C, Green JB, Hauske SJ, Emberson JR, Preiss D, Judge P, Zhu D, Dayanandan R, Arimoto R, Mayne KJ, Ng SYA, Sammons E, Hill M, Stevens W, Wallendszus K, Brenner S, Cheung AK, Liu ZH, Li J, Hooi LS, Liu W, Kadowaki T, Nangaku M, Levin A, Cherney DZI, Maggioni AP, Pontremoli R, Deo R, Goto S, Rossello X, Tuttle KR, Steubl D, Massey D, Brueckmann M, Landray MJ, Baigent C, Haynes R.",
     "authorAffiliations": "",
-    "journalTitle": "PLoS computational biology",
-    "pubYear": "2021",
-    "date": "2021-09-20",
+    "journalTitle": "The New England journal of medicine",
+    "pubYear": "2024",
+    "date": "2024-10-25",
     "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "",
+    "abstract": "<h4>Background</h4>In the EMPA-KIDNEY trial, empagliflozin, a sodium-glucose cotransporter 2 (SGLT2) inhibitor, had positive cardiorenal effects in patients with chronic kidney disease who were at risk for disease progression. Post-trial follow-up was designed to assess how the effects of empagliflozin would evolve after the discontinuation of the trial drug.<h4>Methods</h4>In the active trial, patients with chronic kidney disease were randomly assigned to receive either empagliflozin (10 mg once daily) or matching placebo and were followed for a median of 2 years. All the patients had an estimated glomerular filtration rate (eGFR) of at least 20 but less than 45 ml per minute per 1.73 m<sup>2</sup> of body-surface area or an eGFR of at least 45 but less than 90 ml per minute per 1.73 m<sup>2</sup> with a urinary albumin-to-creatinine ratio (with albumin measured in milligrams and creatinine measured in grams) of at least 200. Subsequently, surviving patients who consented were observed for 2 additional years. No trial empagliflozin or placebo was administered during the post-trial period, but local practitioners could prescribe open-label SGLT2 inhibitors, including open-label empagliflozin. The primary composite outcome was kidney disease progression or cardiovascular death as assessed from the start of the active-trial period to the end of the post-trial period.<h4>Results</h4>Of the 6609 patients who had undergone randomization in the active trial, 4891 (74%) were enrolled in the post-trial period. During this period, the use of open-label SGLT2 inhibitors was similar in the two groups (43% in the empagliflozin group and 40% in the placebo group). During the combined active- and post-trial periods, a primary-outcome event occurred in 865 of 3304 patients (26.2%) in the empagliflozin group and in 1001 of 3305 patients (30.3%) in the placebo group (hazard ratio, 0.79; 95% confidence interval [CI], 0.72 to 0.87). During the post-trial period only, the hazard ratio for a primary-outcome event was 0.87 (95% CI, 0.76 to 0.99). During the combined periods, the risk of kidney disease progression was 23.5% in the empagliflozin group and 27.1% in the placebo group; the risk of the composite of death or end-stage kidney disease was 16.9% and 19.6%, respectively; and the risk of cardiovascular death was 3.8% and 4.9%, respectively. There was no effect of empagliflozin on death from noncardiovascular causes (5.3% in both groups).<h4>Conclusions</h4>In a broad range of patients with chronic kidney disease at risk for progression, empagliflozin continued to have additional cardiorenal benefits for up to 12 months after it was discontinued. (Funded by Boehringer Ingelheim and others; EMPA-KIDNEY ClinicalTrials.gov number, NCT03594110; EuDRACT number, 2017-002971-24.).",
     "laySummary": "",
-    "urls": "pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009324&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1009324; html:https://europepmc.org/articles/PMC8452068; pdf:https://europepmc.org/articles/PMC8452068?pdf=render"
+    "urls": "doi:https://doi.org/10.1056/NEJMoa2409183; html:https://europepmc.org/articles/PMC7616743; pdf:https://europepmc.org/articles/PMC7616743?pdf=render"
   },
   {
     "id": "37794871",
@@ -19023,21 +19074,21 @@
     "urls": "pdf:https://academic.oup.com/ehjdh/advance-article-pdf/doi/10.1093/ehjdh/ztad044/50878931/ztad044.pdf; doi:https://doi.org/10.1093/ehjdh/ztad044; html:https://europepmc.org/articles/PMC10545512; pdf:https://europepmc.org/articles/PMC10545512?pdf=render"
   },
   {
-    "id": "36299367",
-    "doi": "https://doi.org/10.1183/23120541.00211-2022",
-    "title": "Mortality associated with metabolic syndrome in people with COPD managed in primary care.",
-    "authorString": "Karsanji U, Evans RA, Quint JK, Khunti K, Lawson CA, Petherick E, Greening NJ, Singh SJ, Richardson M, Steiner MC.",
+    "id": "35964473",
+    "doi": "https://doi.org/10.1016/j.socscimed.2022.115237",
+    "title": "\"We've all got the virus inside us now\": Disaggregating public health relations and responsibilities for health protection in pandemic London.",
+    "authorString": "Kasstan B, Mounier-Jack S, Gaskell KM, Eggo RM, Marks M, Chantler T.",
     "authorAffiliations": "",
-    "journalTitle": "ERJ open research",
+    "journalTitle": "Social science & medicine (1982)",
     "pubYear": "2022",
-    "date": "2022-10-24",
+    "date": "2022-08-07",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Pandemic; Public Health; Judaism; Responsibility; London; Covid-19",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Objective</h4>The prevalence of metabolic syndrome (MetS) has been reported to be higher in selected populations of people with COPD. The impact of MetS on mortality in COPD is unknown. We used routinely collected healthcare data to estimate the prevalence of MetS in people with COPD managed in primary care and determine its impact on 5-year mortality.<h4>Methods</h4>Records from 103\u2009955 patients with COPD from the Clinical Practice Research Datalink (CPRD-GOLD) between 2009 to 2017 were scrutinised. MetS was defined as the presence of three or more of: obesity, hypertension, lowered high-density lipoprotein cholesterol, elevated triglycerides or type 2 diabetes mellitus (T2DM). Univariate and multivariable Cox regression models were constructed to determine the prognostic impact of MetS on 5-year mortality. Similar univariate models were constructed for individual components of the definition of MetS.<h4>Results</h4>The prevalence of MetS in the COPD cohort was 10.1%. Univariate analyses showed the presence of MetS increased mortality (hazard ratio (HR) 1.19, 95% CI: 1.12-1.27, p<0.001), but this risk was substantially attenuated in the multivariable analysis (HR 1.06, 95% CI: 0.99-1.13, p<i>=</i>0.085). The presence of hypertension (HR 1.70, 95% CI: 1.63-1.77, p<0.001) and T2DM (HR 1.41, 95% CI: 1.34-1.48, p<0.001) increased and obesity (HR 0.74, 95% CI: 0.71-0.78, p<0.001) reduced mortality risk.<h4>Conclusion</h4>MetS in patients with COPD is associated with higher 5-year mortality, but this impact was minimal when adjusted for indices of COPD disease severity and other comorbidities. Individual components of the MetS definition exerted differential impacts on mortality suggesting limitation to the use of MetS as a multicomponent condition in predicting outcome in COPD.",
+    "abstract": "The COVID-19 pandemic has disproportionately impacted ethnic minorities in the global north, evidenced by higher rates of transmission, morbidity, and mortality relative to population sizes. Orthodox Jewish neighbourhoods in London had extremely high SARS-CoV-2 seroprevalence rates, reflecting patterns in Israel and the US. The aim of this paper is to examine how responsibilities over health protection are conveyed, and to what extent responsibility is sought by, and shared between, state services, and 'community' stakeholders or representative groups, and families in public health emergencies. The study investigates how public health and statutory services stakeholders, Orthodox Jewish communal custodians and households sought to enact health protection in London during the first year of the pandemic (March 2020-March 2021). Twenty-eight semi-structured interviews were conducted across these cohorts. Findings demonstrate that institutional relations - both their formation and at times fragmentation - were directly shaped by issues surrounding COVID-19 control measures. Exchanges around protective interventions (whether control measures, contact tracing technologies, or vaccines) reveal diverse and diverging attributions of responsibility and authority. The paper develops a framework of public health relations to understand negotiations between statutory services and minority groups over responsiveness and accountability in health protection. Disaggregating public health relations can help social scientists to critique who and what characterises institutional relationships with minority groups, and what ideas of responsibility and responsiveness are projected by differently-positioned stakeholders in health protection.",
     "laySummary": "",
-    "urls": "pdf:https://openres.ersjournals.com/content/erjor/8/4/00211-2022.full.pdf; doi:https://doi.org/10.1183/23120541.00211-2022; html:https://europepmc.org/articles/PMC9589337; pdf:https://europepmc.org/articles/PMC9589337?pdf=render"
+    "urls": "doi:https://doi.org/10.1016/j.socscimed.2022.115237; doi:https://doi.org/10.1016/j.socscimed.2022.115237; html:https://europepmc.org/articles/PMC9357441; pdf:https://europepmc.org/articles/PMC9357441?pdf=render"
   },
   {
     "id": "36962513",
@@ -19107,23 +19158,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1089/neur.2023.0127; html:https://europepmc.org/articles/PMC11035854; pdf:https://europepmc.org/articles/PMC11035854?pdf=render"
   },
-  {
-    "id": "35964473",
-    "doi": "https://doi.org/10.1016/j.socscimed.2022.115237",
-    "title": "\"We've all got the virus inside us now\": Disaggregating public health relations and responsibilities for health protection in pandemic London.",
-    "authorString": "Kasstan B, Mounier-Jack S, Gaskell KM, Eggo RM, Marks M, Chantler T.",
-    "authorAffiliations": "",
-    "journalTitle": "Social science & medicine (1982)",
-    "pubYear": "2022",
-    "date": "2022-08-07",
-    "isOpenAccess": "Y",
-    "keywords": "Pandemic; Public Health; Judaism; Responsibility; London; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The COVID-19 pandemic has disproportionately impacted ethnic minorities in the global north, evidenced by higher rates of transmission, morbidity, and mortality relative to population sizes. Orthodox Jewish neighbourhoods in London had extremely high SARS-CoV-2 seroprevalence rates, reflecting patterns in Israel and the US. The aim of this paper is to examine how responsibilities over health protection are conveyed, and to what extent responsibility is sought by, and shared between, state services, and 'community' stakeholders or representative groups, and families in public health emergencies. The study investigates how public health and statutory services stakeholders, Orthodox Jewish communal custodians and households sought to enact health protection in London during the first year of the pandemic (March 2020-March 2021). Twenty-eight semi-structured interviews were conducted across these cohorts. Findings demonstrate that institutional relations - both their formation and at times fragmentation - were directly shaped by issues surrounding COVID-19 control measures. Exchanges around protective interventions (whether control measures, contact tracing technologies, or vaccines) reveal diverse and diverging attributions of responsibility and authority. The paper develops a framework of public health relations to understand negotiations between statutory services and minority groups over responsiveness and accountability in health protection. Disaggregating public health relations can help social scientists to critique who and what characterises institutional relationships with minority groups, and what ideas of responsibility and responsiveness are projected by differently-positioned stakeholders in health protection.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.socscimed.2022.115237; doi:https://doi.org/10.1016/j.socscimed.2022.115237; html:https://europepmc.org/articles/PMC9357441; pdf:https://europepmc.org/articles/PMC9357441?pdf=render"
-  },
   {
     "id": "37982176",
     "doi": "https://doi.org/10.1093/ehjci/jead285",
@@ -19141,23 +19175,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ehjcimaging/advance-article-pdf/doi/10.1093/ehjci/jead285/53585728/jead285.pdf; doi:https://doi.org/10.1093/ehjci/jead285; html:https://europepmc.org/articles/PMC10966332; pdf:https://europepmc.org/articles/PMC10966332?pdf=render"
   },
-  {
-    "id": "36745557",
-    "doi": "https://doi.org/10.1093/bjd/ljac132",
-    "title": "Factors associated with depression, anxiety and severe mental illness among adults with atopic eczema or psoriasis: a systematic review and meta-analysis.",
-    "authorString": "Adesanya EI, Matthewman J, Schonmann Y, Hayes JF, Henderson A, Mathur R, Mulick AR, Smith CH, Langan SM, Mansfield KE.",
-    "authorAffiliations": "",
-    "journalTitle": "The British journal of dermatology",
-    "pubYear": "2023",
-    "date": "2023-03-01",
-    "isOpenAccess": "N",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Evidence suggests an association between atopic eczema (AE) or psoriasis and mental illness; however, the factors associated with mental illness are unclear.<h4>Objectives</h4>To synthesize and evaluate all available evidence on factors associated with depression, anxiety and severe mental illness (SMI) among adults with AE or psoriasis.<h4>Methods</h4>We searched electronic databases, grey literature databases and clinical trial registries from inception to February 2022 for studies of adults with AE or psoriasis. Eligible studies included randomized controlled trials (RCTs), cohort, cross-sectional or case-control studies where effect estimates of factors associated with depression, anxiety or SMI were reported. We did not apply language or geographical restrictions. We assessed risk of bias using the Quality in Prognosis Studies tool. We synthesized results narratively, and if at least two studies were sufficiently homogeneous, we pooled effect estimates in a random effects meta-analysis.<h4>Results</h4>We included 21 studies (11 observational, 10 RCTs). No observational studies in AE fulfilled our eligibility criteria. Observational studies in people with psoriasis mostly investigated factors associated with depression or anxiety - one cross-sectional study investigated factors associated with schizophrenia. Pooled effect estimates suggest that female sex and psoriatic arthritis were associated with depression [female sex: odds ratio (OR) 1.62, 95% confidence interval (CI) 1.09-2.40, 95% prediction intervals (PIs) 0.62-4.23, I2 = 24.90%, \u03c42 = 0.05; psoriatic arthritis: OR 2.26, 95% CI 1.56-3.25, 95% PI 0.21-24.23, I2 = 0.00%, \u03c42 = 0.00] and anxiety (female sex: OR 2.59, 95% CI 1.32-5.07, 95% PI 0.00-3956.27, I2 = 61.90%, \u03c42 = 0.22; psoriatic arthritis: OR 1.98, 95% CI 1.33-2.94, I2 = 0.00%, \u03c42 = 0.00). Moderate/severe psoriasis was associated with anxiety (OR 1.14, 95% CI 1.05-1.25, I2 0.00%, \u03c42 = 0.00), but not depression. Evidence from RCTs suggested that adults with AE or psoriasis given placebo had higher depression and anxiety scores compared with comparators given targeted treatment (e.g. biologic agents).<h4>Conclusions</h4>Our review highlights limited existing research on factors associated with depression, anxiety and SMI in adults with AE or psoriasis. Observational evidence on factors associated with depression or anxiety in people with psoriasis was conflicting or from single studies, but some identified factors were consistent with those in the general population. Evidence on factors associated with SMIs in people with AE or psoriasis was particularly limited. Evidence from RCTs suggested that AE and psoriasis treated with placebo was associated with higher depression and anxiety scores compared with skin disease treated with targeted therapy; however, follow-up was limited. Therefore, long-term effects on mental health are unclear.",
-    "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/bjd/article-pdf/188/4/460/51790111/ljac132.pdf; doi:https://doi.org/10.1093/bjd/ljac132"
-  },
   {
     "id": "34227657",
     "doi": "https://doi.org/10.1093/bjs/znab183",
@@ -19175,6 +19192,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/bjs/article-pdf/108/11/1274/47371055/znab183.pdf; doi:https://doi.org/10.1093/bjs/znab183; html:https://europepmc.org/articles/PMC8344569; pdf:https://europepmc.org/articles/PMC8344569?pdf=render"
   },
+  {
+    "id": "36745557",
+    "doi": "https://doi.org/10.1093/bjd/ljac132",
+    "title": "Factors associated with depression, anxiety and severe mental illness among adults with atopic eczema or psoriasis: a systematic review and meta-analysis.",
+    "authorString": "Adesanya EI, Matthewman J, Schonmann Y, Hayes JF, Henderson A, Mathur R, Mulick AR, Smith CH, Langan SM, Mansfield KE.",
+    "authorAffiliations": "",
+    "journalTitle": "The British journal of dermatology",
+    "pubYear": "2023",
+    "date": "2023-03-01",
+    "isOpenAccess": "N",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Evidence suggests an association between atopic eczema (AE) or psoriasis and mental illness; however, the factors associated with mental illness are unclear.<h4>Objectives</h4>To synthesize and evaluate all available evidence on factors associated with depression, anxiety and severe mental illness (SMI) among adults with AE or psoriasis.<h4>Methods</h4>We searched electronic databases, grey literature databases and clinical trial registries from inception to February 2022 for studies of adults with AE or psoriasis. Eligible studies included randomized controlled trials (RCTs), cohort, cross-sectional or case-control studies where effect estimates of factors associated with depression, anxiety or SMI were reported. We did not apply language or geographical restrictions. We assessed risk of bias using the Quality in Prognosis Studies tool. We synthesized results narratively, and if at least two studies were sufficiently homogeneous, we pooled effect estimates in a random effects meta-analysis.<h4>Results</h4>We included 21 studies (11 observational, 10 RCTs). No observational studies in AE fulfilled our eligibility criteria. Observational studies in people with psoriasis mostly investigated factors associated with depression or anxiety - one cross-sectional study investigated factors associated with schizophrenia. Pooled effect estimates suggest that female sex and psoriatic arthritis were associated with depression [female sex: odds ratio (OR) 1.62, 95% confidence interval (CI) 1.09-2.40, 95% prediction intervals (PIs) 0.62-4.23, I2 = 24.90%, \u03c42 = 0.05; psoriatic arthritis: OR 2.26, 95% CI 1.56-3.25, 95% PI 0.21-24.23, I2 = 0.00%, \u03c42 = 0.00] and anxiety (female sex: OR 2.59, 95% CI 1.32-5.07, 95% PI 0.00-3956.27, I2 = 61.90%, \u03c42 = 0.22; psoriatic arthritis: OR 1.98, 95% CI 1.33-2.94, I2 = 0.00%, \u03c42 = 0.00). Moderate/severe psoriasis was associated with anxiety (OR 1.14, 95% CI 1.05-1.25, I2 0.00%, \u03c42 = 0.00), but not depression. Evidence from RCTs suggested that adults with AE or psoriasis given placebo had higher depression and anxiety scores compared with comparators given targeted treatment (e.g. biologic agents).<h4>Conclusions</h4>Our review highlights limited existing research on factors associated with depression, anxiety and SMI in adults with AE or psoriasis. Observational evidence on factors associated with depression or anxiety in people with psoriasis was conflicting or from single studies, but some identified factors were consistent with those in the general population. Evidence on factors associated with SMIs in people with AE or psoriasis was particularly limited. Evidence from RCTs suggested that AE and psoriasis treated with placebo was associated with higher depression and anxiety scores compared with skin disease treated with targeted therapy; however, follow-up was limited. Therefore, long-term effects on mental health are unclear.",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/bjd/article-pdf/188/4/460/51790111/ljac132.pdf; doi:https://doi.org/10.1093/bjd/ljac132"
+  },
   {
     "id": "32616677",
     "doi": "https://doi.org/10.1212/wnl.0000000000009924",
@@ -19277,23 +19311,6 @@
     "laySummary": "",
     "urls": "pdf:https://orca.cardiff.ac.uk/136801/8/ACEs%20academic%20attainment%20at%20age%207%20and%2011%20years_FINALaccepted_v2.pdf; doi:https://doi.org/10.1016/j.puhe.2020.08.027"
   },
-  {
-    "id": "37562944",
-    "doi": "https://doi.org/10.1136/emermed-2023-213186",
-    "title": "Biases in the collection of blood alcohol data for adult major trauma patients in Victoria, Australia.",
-    "authorString": "Lau G, Gabbe B, Mitra B, Dietze P, Reeder S, Cameron P, Read DJ, Symons E, Beck B.",
-    "authorAffiliations": "",
-    "journalTitle": "Emergency medicine journal : EMJ",
-    "pubYear": "2023",
-    "date": "2023-08-10",
-    "isOpenAccess": "N",
-    "keywords": "epidemiology; wounds and injuries; toxicology; Alcohol Abuse",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>In-hospital alcohol testing provides an opportunity to implement prevention strategies for patients with high risk of experiencing repeated alcohol-related injuries. However, barriers to alcohol testing in emergency settings can prevent patients from being tested. In this study, we aimed to understand potential biases in current data on the completion of blood alcohol tests for major trauma patients at hospitals in Victoria, Australia.<h4>Methods</h4>Victorian State Trauma Registry data on all adult major trauma patients from 1 January 2018 to 31 December 2021 were used. Characteristics associated with having a blood alcohol test recorded in the registry were assessed using logistic regression models.<h4>Results</h4>This study included 14\u2009221 major trauma patients, of which 4563 (32.1%) had a blood alcohol test recorded. Having a blood alcohol test completed was significantly associated with age, socioeconomic disadvantage level, preferred language, having pre-existing mental health or substance use conditions, smoking status, presenting during times associated with heavy community alcohol consumption, injury cause and intent, and Glasgow Coma Scale scores (p<0.05). Restricting analyses to patients from a trauma centre where blood alcohol testing was part of routine clinical care mitigated most biases. However, relative to patients injured while driving a motor vehicle/motorcycle, lower odds of testing were still observed for patients with injuries from flames/scalds/contact burns (adjusted OR (aOR)=0.33, 95%\u2009CI 0.18 to 0.61) and low falls (aOR=0.17, 95% CI 0.12 to 0.25). Higher odds of testing were associated with pre-existing mental health (aOR=1.39, 95% CI 1.02 to 1.89) or substance use conditions (aOR=2.33, 95% CI to 1.47-3.70), and living in a more disadvantaged area (most disadvantaged quintile relative to least disadvantaged quintile: aOR=2.30, 95% CI 1.52 to 3.48).<h4>Conclusion</h4>Biases in the collection of blood alcohol data likely impact the surveillance of alcohol-related injuries. Routine alcohol testing after major trauma is needed to accurately inform epidemiology and the subsequent implementation of strategies for reducing alcohol-related injuries.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1136/emermed-2023-213186"
-  },
   {
     "id": "31685485",
     "doi": "https://doi.org/10.1136/bmjopen-2019-031365",
@@ -19328,6 +19345,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41598-019-51562-6.pdf; doi:https://doi.org/10.1038/s41598-019-51562-6; html:https://europepmc.org/articles/PMC6802378; pdf:https://europepmc.org/articles/PMC6802378?pdf=render"
   },
+  {
+    "id": "37562944",
+    "doi": "https://doi.org/10.1136/emermed-2023-213186",
+    "title": "Biases in the collection of blood alcohol data for adult major trauma patients in Victoria, Australia.",
+    "authorString": "Lau G, Gabbe B, Mitra B, Dietze P, Reeder S, Cameron P, Read DJ, Symons E, Beck B.",
+    "authorAffiliations": "",
+    "journalTitle": "Emergency medicine journal : EMJ",
+    "pubYear": "2023",
+    "date": "2023-08-10",
+    "isOpenAccess": "N",
+    "keywords": "epidemiology; wounds and injuries; toxicology; Alcohol Abuse",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>In-hospital alcohol testing provides an opportunity to implement prevention strategies for patients with high risk of experiencing repeated alcohol-related injuries. However, barriers to alcohol testing in emergency settings can prevent patients from being tested. In this study, we aimed to understand potential biases in current data on the completion of blood alcohol tests for major trauma patients at hospitals in Victoria, Australia.<h4>Methods</h4>Victorian State Trauma Registry data on all adult major trauma patients from 1 January 2018 to 31 December 2021 were used. Characteristics associated with having a blood alcohol test recorded in the registry were assessed using logistic regression models.<h4>Results</h4>This study included 14\u2009221 major trauma patients, of which 4563 (32.1%) had a blood alcohol test recorded. Having a blood alcohol test completed was significantly associated with age, socioeconomic disadvantage level, preferred language, having pre-existing mental health or substance use conditions, smoking status, presenting during times associated with heavy community alcohol consumption, injury cause and intent, and Glasgow Coma Scale scores (p<0.05). Restricting analyses to patients from a trauma centre where blood alcohol testing was part of routine clinical care mitigated most biases. However, relative to patients injured while driving a motor vehicle/motorcycle, lower odds of testing were still observed for patients with injuries from flames/scalds/contact burns (adjusted OR (aOR)=0.33, 95%\u2009CI 0.18 to 0.61) and low falls (aOR=0.17, 95% CI 0.12 to 0.25). Higher odds of testing were associated with pre-existing mental health (aOR=1.39, 95% CI 1.02 to 1.89) or substance use conditions (aOR=2.33, 95% CI to 1.47-3.70), and living in a more disadvantaged area (most disadvantaged quintile relative to least disadvantaged quintile: aOR=2.30, 95% CI 1.52 to 3.48).<h4>Conclusion</h4>Biases in the collection of blood alcohol data likely impact the surveillance of alcohol-related injuries. Routine alcohol testing after major trauma is needed to accurately inform epidemiology and the subsequent implementation of strategies for reducing alcohol-related injuries.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1136/emermed-2023-213186"
+  },
   {
     "id": "37812323",
     "doi": "https://doi.org/10.1186/s41687-023-00634-3",
@@ -19481,6 +19515,23 @@
     "laySummary": "",
     "urls": "pdf:https://adc.bmj.com/content/archdischild/105/4/347.full.pdf; doi:https://doi.org/10.1136/archdischild-2019-317248; html:https://europepmc.org/articles/PMC7146921; pdf:https://europepmc.org/articles/PMC7146921?pdf=render"
   },
+  {
+    "id": "31765395",
+    "doi": "https://doi.org/10.1371/journal.pone.0225625",
+    "title": "Semantic computational analysis of anticoagulation use in atrial fibrillation from real world data.",
+    "authorString": "Bean DM, Teo J, Wu H, Oliveira R, Patel R, Bendayan R, Shah AM, Dobson RJB, Scott PA.",
+    "authorAffiliations": "",
+    "journalTitle": "PloS one",
+    "pubYear": "2019",
+    "date": "2019-11-25",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Atrial fibrillation (AF) is the most common arrhythmia and significantly increases stroke risk. This risk is effectively managed by oral anticoagulation. Recent studies using national registry data indicate increased use of anticoagulation resulting from changes in guidelines and the availability of newer drugs. The aim of this study is to develop and validate an open source risk scoring pipeline for free-text electronic health record data using natural language processing. AF patients discharged from 1st January 2011 to 1st October 2017 were identified from discharge summaries (N = 10,030, 64.6% male, average age 75.3 \u00b1 12.3 years). A natural language processing pipeline was developed to identify risk factors in clinical text and calculate risk for ischaemic stroke (CHA2DS2-VASc) and bleeding (HAS-BLED). Scores were validated vs two independent experts for 40 patients. Automatic risk scores were in strong agreement with the two independent experts for CHA2DS2-VASc (average kappa 0.78 vs experts, compared to 0.85 between experts). Agreement was lower for HAS-BLED (average kappa 0.54 vs experts, compared to 0.74 between experts). In high-risk patients (CHA2DS2-VASc \u22652) OAC use has increased significantly over the last 7 years, driven by the availability of DOACs and the transitioning of patients from AP medication alone to OAC. Factors independently associated with OAC use included components of the CHA2DS2-VASc and HAS-BLED scores as well as discharging specialty and frailty. OAC use was highest in patients discharged under cardiology (69%). Electronic health record text can be used for automatic calculation of clinical risk scores at scale. Open source tools are available today for this task but require further validation. Analysis of routinely collected EHR data can replicate findings from large-scale curated registries.",
+    "laySummary": "Bean et al. looked at using clinical notes to calculate risk scores: CHADSVASC and HASBLED for 10,030 AF patients from 2011 to October 2017), they\u2019ve validated their natural language processing algorithm with getting clinicians to calculate the risk in conventional manner for 40 of cases, the two scores were in higher agreement for stroke risk compared to HAS-BLED They\u2019ve concluded on usefulness of NLP method in risk calculation at the large scale.",
+    "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0225625&type=printable; doi:https://doi.org/10.1371/journal.pone.0225625; html:https://europepmc.org/articles/PMC6876873; pdf:https://europepmc.org/articles/PMC6876873?pdf=render"
+  },
   {
     "id": "32657853",
     "doi": "https://doi.org/10.1097/sap.0000000000002434",
@@ -19515,23 +19566,6 @@
     "laySummary": "",
     "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0266521&type=printable; doi:https://doi.org/10.1371/journal.pone.0266521; html:https://europepmc.org/articles/PMC9258853; pdf:https://europepmc.org/articles/PMC9258853?pdf=render"
   },
-  {
-    "id": "31765395",
-    "doi": "https://doi.org/10.1371/journal.pone.0225625",
-    "title": "Semantic computational analysis of anticoagulation use in atrial fibrillation from real world data.",
-    "authorString": "Bean DM, Teo J, Wu H, Oliveira R, Patel R, Bendayan R, Shah AM, Dobson RJB, Scott PA.",
-    "authorAffiliations": "",
-    "journalTitle": "PloS one",
-    "pubYear": "2019",
-    "date": "2019-11-25",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Atrial fibrillation (AF) is the most common arrhythmia and significantly increases stroke risk. This risk is effectively managed by oral anticoagulation. Recent studies using national registry data indicate increased use of anticoagulation resulting from changes in guidelines and the availability of newer drugs. The aim of this study is to develop and validate an open source risk scoring pipeline for free-text electronic health record data using natural language processing. AF patients discharged from 1st January 2011 to 1st October 2017 were identified from discharge summaries (N = 10,030, 64.6% male, average age 75.3 \u00b1 12.3 years). A natural language processing pipeline was developed to identify risk factors in clinical text and calculate risk for ischaemic stroke (CHA2DS2-VASc) and bleeding (HAS-BLED). Scores were validated vs two independent experts for 40 patients. Automatic risk scores were in strong agreement with the two independent experts for CHA2DS2-VASc (average kappa 0.78 vs experts, compared to 0.85 between experts). Agreement was lower for HAS-BLED (average kappa 0.54 vs experts, compared to 0.74 between experts). In high-risk patients (CHA2DS2-VASc \u22652) OAC use has increased significantly over the last 7 years, driven by the availability of DOACs and the transitioning of patients from AP medication alone to OAC. Factors independently associated with OAC use included components of the CHA2DS2-VASc and HAS-BLED scores as well as discharging specialty and frailty. OAC use was highest in patients discharged under cardiology (69%). Electronic health record text can be used for automatic calculation of clinical risk scores at scale. Open source tools are available today for this task but require further validation. Analysis of routinely collected EHR data can replicate findings from large-scale curated registries.",
-    "laySummary": "Bean et al. looked at using clinical notes to calculate risk scores: CHADSVASC and HASBLED for 10,030 AF patients from 2011 to October 2017), they\u2019ve validated their natural language processing algorithm with getting clinicians to calculate the risk in conventional manner for 40 of cases, the two scores were in higher agreement for stroke risk compared to HAS-BLED They\u2019ve concluded on usefulness of NLP method in risk calculation at the large scale.",
-    "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0225625&type=printable; doi:https://doi.org/10.1371/journal.pone.0225625; html:https://europepmc.org/articles/PMC6876873; pdf:https://europepmc.org/articles/PMC6876873?pdf=render"
-  },
   {
     "id": "35459950",
     "doi": "https://doi.org/10.1093/intqhc/mzac031",
@@ -19549,23 +19583,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/intqhc/article-pdf/34/2/mzac031/43704475/mzac031.pdf; doi:https://doi.org/10.1093/intqhc/mzac031"
   },
-  {
-    "id": "37953241",
-    "doi": "https://doi.org/10.1186/s12916-023-03153-6",
-    "title": "Cardiovascular events and venous thromboembolism after primary malignant or non-malignant brain tumour diagnosis: a population matched cohort study in Wales (United Kingdom).",
-    "authorString": "Poon MTC, Brennan PM, Jin K, Sudlow CLM, Figueroa JD.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC medicine",
-    "pubYear": "2023",
-    "date": "2023-11-13",
-    "isOpenAccess": "Y",
-    "keywords": "Brain cancer; Cerebrovascular disease; Neuro-oncology; Population-based",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Elevated standardised mortality ratio of cardiovascular diseases (CVD) in patients with brain tumours may result from differences in the CVD incidences and cardiovascular risk factors. We compared the risk of CVD among patients with a primary malignant or non-malignant brain tumour to a matched general population cohort, accounting for other co-morbidities.<h4>Methods</h4>Using data from the Secured Anonymised Information Linkage (SAIL) Databank in Wales (United Kingdom), we identified all adults aged\u2009\u2265\u200918\u00a0years in the primary care database with first diagnosis of malignant or non-malignant brain tumour identified in the cancer registry in 2000-2014 and a matched cohort (case-to-control ratio 1:5) by age, sex and primary care provider from the general population without any cancer diagnosis. Outcomes included fatal and non-fatal major vascular events (stroke, ischaemic heart disease, aortic and peripheral vascular diseases) and venous thromboembolism (VTE). We used multivariable Cox models adjusted for clinical risk factors to compare risks, stratified by tumour behaviour (malignant or non-malignant) and follow-up period.<h4>Results</h4>There were 2869 and 3931 people diagnosed with malignant or non-malignant brain tumours, respectively, between 2000 and 2014 in Wales. They were matched to 33,785 controls. Within the first year of tumour diagnosis, malignant tumour was associated with a higher risk of VTE (hazard ratio [HR] 21.58, 95% confidence interval 16.12-28.88) and stroke (HR 3.32, 2.44-4.53). After the first year, the risks of VTE (HR 2.20, 1.52-3.18) and stroke (HR 1.45, 1.00-2.10) remained higher than controls. Patients with non-malignant tumours had higher risks of VTE (HR 3.72, 2.73-5.06), stroke (HR 4.06, 3.35-4.93) and aortic and peripheral arterial disease (HR 2.09, 1.26-3.48) within the first year of diagnosis compared with their controls.<h4>Conclusions</h4>The elevated CVD and VTE risks suggested risk reduction may be a strategy to improve life quality and survival in people with a brain tumour.",
-    "laySummary": "",
-    "urls": "pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-023-03153-6; doi:https://doi.org/10.1186/s12916-023-03153-6; html:https://europepmc.org/articles/PMC10641987; pdf:https://europepmc.org/articles/PMC10641987?pdf=render"
-  },
   {
     "id": "31153319",
     "doi": "https://doi.org/10.1121/1.5100272",
@@ -19584,21 +19601,21 @@
     "urls": "pdf:https://asa.scitation.org/doi/pdf/10.1121/1.5100272; doi:https://doi.org/10.1121/1.5100272; html:https://europepmc.org/articles/PMC6509044; pdf:https://europepmc.org/articles/PMC6509044?pdf=render; doi:https://doi.org/10.1121/1.5100272"
   },
   {
-    "id": "37327673",
-    "doi": "https://doi.org/10.1016/j.ebiom.2023.104655",
-    "title": "HFrEF subphenotypes based on 4210 repeatedly measured circulating proteins are driven by different biological mechanisms.",
-    "authorString": "Petersen TB, de Bakker M, Asselbergs FW, Harakalova M, Akkerhuis KM, Brugts JJ, van Ramshorst J, Lumbers RT, Ostroff RM, Katsikis PD, van der Spek PJ, Umans VA, Boersma E, Rizopoulos D, Kardys I.",
+    "id": "37953241",
+    "doi": "https://doi.org/10.1186/s12916-023-03153-6",
+    "title": "Cardiovascular events and venous thromboembolism after primary malignant or non-malignant brain tumour diagnosis: a population matched cohort study in Wales (United Kingdom).",
+    "authorString": "Poon MTC, Brennan PM, Jin K, Sudlow CLM, Figueroa JD.",
     "authorAffiliations": "",
-    "journalTitle": "EBioMedicine",
+    "journalTitle": "BMC medicine",
     "pubYear": "2023",
-    "date": "2023-06-14",
+    "date": "2023-11-13",
     "isOpenAccess": "Y",
-    "keywords": "Proteomics; Phenotypes; Biomarkers; Heart Failure; Unsupervised Machine Learning",
+    "keywords": "Brain cancer; Cerebrovascular disease; Neuro-oncology; Population-based",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>HFrEF is a heterogenous condition with high mortality. We used serial assessments of 4210 circulating proteins to identify distinct novel protein-based HFrEF subphenotypes and to investigate underlying dynamic biological mechanisms. Herewith we aimed to gain pathophysiological insights and fuel opportunities for personalised treatment.<h4>Methods</h4>In 382 patients, we performed trimonthly blood sampling during a median follow-up of 2.1 [IQR:1.1-2.6] years. We selected all baseline samples and two samples closest to the primary endpoint (PEP; composite of cardiovascular mortality, HF hospitalization, LVAD implantation, and heart transplantation) or censoring, and applied an aptamer-based multiplex proteomic approach. Using unsupervised machine learning methods, we derived clusters from 4210 repeatedly measured proteomic biomarkers. Sets of proteins that drove cluster allocation were analysed via an enrichment analysis. Differences in clinical characteristics and PEP occurrence were evaluated.<h4>Findings</h4>We identified four subphenotypes with different protein profiles, prognosis and clinical characteristics, including age (median [IQR] for subphenotypes 1-4, respectively:70 [64, 76], 68 [60, 79], 57 [47, 65], 59 [56, 66]years), EF (30 [26, 36], 26 [20, 38], 26 [22, 32], 33 [28, 37]%), and chronic renal failure (45%, 65%, 36%, 37%). Subphenotype allocation was driven by subsets of proteins associated with various biological functions, such as oxidative stress, inflammation and extracellular matrix organisation. Clinical characteristics of the subphenotypes were aligned with these associations. Subphenotypes 2 and 3 had the worst prognosis compared to subphenotype 1 (adjHR (95%CI):3.43 (1.76-6.69), and 2.88 (1.37-6.03), respectively).<h4>Interpretation</h4>Four circulating-protein based subphenotypes are present in HFrEF, which are driven by varying combinations of protein subsets, and have different clinical characteristics and prognosis.<h4>Clinical trial registration</h4>ClinicalTrials.gov Identifier: NCT01851538https://clinicaltrials.gov/ct2/show/NCT01851538.<h4>Funding</h4>EU/EFPIA IMI2JU BigData@Heart grant n\u00b0116074, Jaap Schouten Foundation and Noordwest Academie.",
+    "abstract": "<h4>Background</h4>Elevated standardised mortality ratio of cardiovascular diseases (CVD) in patients with brain tumours may result from differences in the CVD incidences and cardiovascular risk factors. We compared the risk of CVD among patients with a primary malignant or non-malignant brain tumour to a matched general population cohort, accounting for other co-morbidities.<h4>Methods</h4>Using data from the Secured Anonymised Information Linkage (SAIL) Databank in Wales (United Kingdom), we identified all adults aged\u2009\u2265\u200918\u00a0years in the primary care database with first diagnosis of malignant or non-malignant brain tumour identified in the cancer registry in 2000-2014 and a matched cohort (case-to-control ratio 1:5) by age, sex and primary care provider from the general population without any cancer diagnosis. Outcomes included fatal and non-fatal major vascular events (stroke, ischaemic heart disease, aortic and peripheral vascular diseases) and venous thromboembolism (VTE). We used multivariable Cox models adjusted for clinical risk factors to compare risks, stratified by tumour behaviour (malignant or non-malignant) and follow-up period.<h4>Results</h4>There were 2869 and 3931 people diagnosed with malignant or non-malignant brain tumours, respectively, between 2000 and 2014 in Wales. They were matched to 33,785 controls. Within the first year of tumour diagnosis, malignant tumour was associated with a higher risk of VTE (hazard ratio [HR] 21.58, 95% confidence interval 16.12-28.88) and stroke (HR 3.32, 2.44-4.53). After the first year, the risks of VTE (HR 2.20, 1.52-3.18) and stroke (HR 1.45, 1.00-2.10) remained higher than controls. Patients with non-malignant tumours had higher risks of VTE (HR 3.72, 2.73-5.06), stroke (HR 4.06, 3.35-4.93) and aortic and peripheral arterial disease (HR 2.09, 1.26-3.48) within the first year of diagnosis compared with their controls.<h4>Conclusions</h4>The elevated CVD and VTE risks suggested risk reduction may be a strategy to improve life quality and survival in people with a brain tumour.",
     "laySummary": "",
-    "urls": "pdf:http://www.thelancet.com/article/S2352396423002207/pdf; doi:https://doi.org/10.1016/j.ebiom.2023.104655; html:https://europepmc.org/articles/PMC10279550; pdf:https://europepmc.org/articles/PMC10279550?pdf=render"
+    "urls": "pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-023-03153-6; doi:https://doi.org/10.1186/s12916-023-03153-6; html:https://europepmc.org/articles/PMC10641987; pdf:https://europepmc.org/articles/PMC10641987?pdf=render"
   },
   {
     "id": "32864476",
@@ -19618,21 +19635,38 @@
     "urls": "pdf:https://ijpds.org/article/download/1157/2531; doi:https://doi.org/10.23889/ijpds.v5i1.1157; html:https://europepmc.org/articles/PMC7115985; pdf:https://europepmc.org/articles/PMC7115985?pdf=render"
   },
   {
-    "id": "37717234",
-    "doi": "https://doi.org/10.1111/1742-6723.14312",
-    "title": "Prevalence of alcohol and other drug detections in non-transport injury events.",
-    "authorString": "Lau G, Mitra B, Gabbe BJ, Dietze PM, Reeder S, Cameron PA, Smit V, Schneider HG, Symons E, Koolstra C, Stewart C, Beck B.",
+    "id": "37327673",
+    "doi": "https://doi.org/10.1016/j.ebiom.2023.104655",
+    "title": "HFrEF subphenotypes based on 4210 repeatedly measured circulating proteins are driven by different biological mechanisms.",
+    "authorString": "Petersen TB, de Bakker M, Asselbergs FW, Harakalova M, Akkerhuis KM, Brugts JJ, van Ramshorst J, Lumbers RT, Ostroff RM, Katsikis PD, van der Spek PJ, Umans VA, Boersma E, Rizopoulos D, Kardys I.",
     "authorAffiliations": "",
-    "journalTitle": "Emergency medicine Australasia : EMA",
-    "pubYear": "2024",
-    "date": "2023-09-17",
+    "journalTitle": "EBioMedicine",
+    "pubYear": "2023",
+    "date": "2023-06-14",
     "isOpenAccess": "Y",
-    "keywords": "Alcoholic Intoxication; Illicit Drug; Blood Alcohol Content; Wounds And Injury; Substance-related Disorder; Substance Use Detection",
+    "keywords": "Proteomics; Phenotypes; Biomarkers; Heart Failure; Unsupervised Machine Learning",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Objective</h4>To measure the prevalence of alcohol and/or other drug (AOD) detections in suspected major trauma patients with non-transport injuries who presented to an adult major trauma centre.<h4>Methods</h4>This registry-based cohort study examined the prevalence of AOD detections in patients aged \u226518\u2009years who: (i) sustained non-transport injuries; and (ii) met predefined trauma call-out criteria and were therefore managed by an interdisciplinary trauma team between 1 July 2021 and 31 December 2022. Prevalence was measured using routine in-hospital blood alcohol and urine drug screens.<h4>Results</h4>A total of 1469 cases met the inclusion criteria. Of cases with a valid blood test (n\u2009=\u20091248, 85.0%), alcohol was detected in 313 (25.1%) patients. Of the 733 (49.9%) cases with urine drug screen results, cannabinoids were most commonly detected (n\u2009=\u2009103, 14.1%), followed by benzodiazepines (n\u2009=\u200998, 13.4%), amphetamine-type substances (n\u2009= 80, 10.9%), opioids (n\u2009=\u200928, 3.8%) and cocaine (n\u2009=\u200917, 2.3%). Alcohol and/or at least one other drug was detected in 37.4% (n\u2009=\u2009472) of cases with either a blood alcohol or urine drug test completed (n\u2009=\u20091263, 86.0%). Multiple substances were detected in 16.6% (n\u2009=\u2009119) of cases with both blood alcohol and urine drug screens (n\u2009=\u2009718, 48.9%). Detections were prevalent in cases of interpersonal violence (n\u2009=\u2009123/179, 68.7%) and intentional self-harm (n\u2009=\u200950/106, 47.2%), and in those occurring on Friday and Saturday nights (n\u2009=\u2009118/191, 61.8%).<h4>Conclusion</h4>AOD detections were common in trauma patients with non-transport injury causes. Population-level surveillance is needed to inform prevention strategies that address AOD use as a significant risk factor for serious injury.",
+    "abstract": "<h4>Background</h4>HFrEF is a heterogenous condition with high mortality. We used serial assessments of 4210 circulating proteins to identify distinct novel protein-based HFrEF subphenotypes and to investigate underlying dynamic biological mechanisms. Herewith we aimed to gain pathophysiological insights and fuel opportunities for personalised treatment.<h4>Methods</h4>In 382 patients, we performed trimonthly blood sampling during a median follow-up of 2.1 [IQR:1.1-2.6] years. We selected all baseline samples and two samples closest to the primary endpoint (PEP; composite of cardiovascular mortality, HF hospitalization, LVAD implantation, and heart transplantation) or censoring, and applied an aptamer-based multiplex proteomic approach. Using unsupervised machine learning methods, we derived clusters from 4210 repeatedly measured proteomic biomarkers. Sets of proteins that drove cluster allocation were analysed via an enrichment analysis. Differences in clinical characteristics and PEP occurrence were evaluated.<h4>Findings</h4>We identified four subphenotypes with different protein profiles, prognosis and clinical characteristics, including age (median [IQR] for subphenotypes 1-4, respectively:70 [64, 76], 68 [60, 79], 57 [47, 65], 59 [56, 66]years), EF (30 [26, 36], 26 [20, 38], 26 [22, 32], 33 [28, 37]%), and chronic renal failure (45%, 65%, 36%, 37%). Subphenotype allocation was driven by subsets of proteins associated with various biological functions, such as oxidative stress, inflammation and extracellular matrix organisation. Clinical characteristics of the subphenotypes were aligned with these associations. Subphenotypes 2 and 3 had the worst prognosis compared to subphenotype 1 (adjHR (95%CI):3.43 (1.76-6.69), and 2.88 (1.37-6.03), respectively).<h4>Interpretation</h4>Four circulating-protein based subphenotypes are present in HFrEF, which are driven by varying combinations of protein subsets, and have different clinical characteristics and prognosis.<h4>Clinical trial registration</h4>ClinicalTrials.gov Identifier: NCT01851538https://clinicaltrials.gov/ct2/show/NCT01851538.<h4>Funding</h4>EU/EFPIA IMI2JU BigData@Heart grant n\u00b0116074, Jaap Schouten Foundation and Noordwest Academie.",
     "laySummary": "",
-    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/1742-6723.14312; doi:https://doi.org/10.1111/1742-6723.14312; html:https://europepmc.org/articles/PMC10952644; pdf:https://europepmc.org/articles/PMC10952644?pdf=render"
+    "urls": "pdf:http://www.thelancet.com/article/S2352396423002207/pdf; doi:https://doi.org/10.1016/j.ebiom.2023.104655; html:https://europepmc.org/articles/PMC10279550; pdf:https://europepmc.org/articles/PMC10279550?pdf=render"
+  },
+  {
+    "id": "32790708",
+    "doi": "https://doi.org/10.1371/journal.pone.0237298",
+    "title": "Clinical academic research in the time of Corona: A simulation study in England and a call for action.",
+    "authorString": "Banerjee A, Katsoulis M, Lai AG, Pasea L, Treibel TA, Manisty C, Denaxas S, Quarta G, Hemingway H, Cavalcante JL, Noursadeghi M, Moon JC.",
+    "authorAffiliations": "",
+    "journalTitle": "PloS one",
+    "pubYear": "2020",
+    "date": "2020-08-13",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objectives</h4>We aimed to model the impact of coronavirus (COVID-19) on the clinical academic response in England, and to provide recommendations for COVID-related research.<h4>Design</h4>A stochastic model to determine clinical academic capacity in England, incorporating the following key factors which affect the ability to conduct research in the COVID-19 climate: (i) infection growth rate and population infection rate (from UK COVID-19 statistics and WHO); (ii) strain on the healthcare system (from published model); and (iii) availability of clinical academic staff with appropriate skillsets affected by frontline clinical activity and sickness (from UK statistics).<h4>Setting</h4>Clinical academics in primary and secondary care in England.<h4>Participants</h4>Equivalent of 3200 full-time clinical academics in England.<h4>Interventions</h4>Four policy approaches to COVID-19 with differing population infection rates: \"Italy model\" (6%), \"mitigation\" (10%), \"relaxed mitigation\" (40%) and \"do-nothing\" (80%) scenarios. Low and high strain on the health system (no clinical academics able to do research at 10% and 5% infection rate, respectively.<h4>Main outcome measures</h4>Number of full-time clinical academics available to conduct clinical research during the pandemic in England.<h4>Results</h4>In the \"Italy model\", \"mitigation\", \"relaxed mitigation\" and \"do-nothing\" scenarios, from 5 March 2020 the duration (days) and peak infection rates (%) are 95(2.4%), 115(2.5%), 240(5.3%) and 240(16.7%) respectively. Near complete attrition of academia (87% reduction, <400 clinical academics) occurs 35 days after pandemic start for 11, 34, 62, 76 days respectively-with no clinical academics at all for 37 days in the \"do-nothing\" scenario. Restoration of normal academic workforce (80% of normal capacity) takes 11, 12, 30 and 26 weeks respectively.<h4>Conclusions</h4>Pandemic COVID-19 crushes the science needed at system level. National policies mitigate, but the academic community needs to adapt. We highlight six key strategies: radical prioritisation (eg 3-4 research ideas per institution), deep resourcing, non-standard leadership (repurposing of key non-frontline teams), rationalisation (profoundly simple approaches), careful site selection (eg protected sites with large academic backup) and complete suspension of academic competition with collaborative approaches.",
+    "laySummary": "",
+    "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0237298&type=printable; doi:https://doi.org/10.1371/journal.pone.0237298; html:https://europepmc.org/articles/PMC7425844; pdf:https://europepmc.org/articles/PMC7425844?pdf=render"
   },
   {
     "id": "31951005",
@@ -19652,21 +19686,38 @@
     "urls": "pdf:https://academic.oup.com/jamia/article-pdf/27/3/437/34153319/ocz211.pdf; doi:https://doi.org/10.1093/jamia/ocz211; html:https://europepmc.org/articles/PMC7025363; pdf:https://europepmc.org/articles/PMC7025363?pdf=render"
   },
   {
-    "id": "32790708",
-    "doi": "https://doi.org/10.1371/journal.pone.0237298",
-    "title": "Clinical academic research in the time of Corona: A simulation study in England and a call for action.",
-    "authorString": "Banerjee A, Katsoulis M, Lai AG, Pasea L, Treibel TA, Manisty C, Denaxas S, Quarta G, Hemingway H, Cavalcante JL, Noursadeghi M, Moon JC.",
+    "id": "31416346",
+    "doi": "https://doi.org/10.1161/circulationaha.119.041980",
+    "title": "Machine Learning to Predict the Likelihood of Acute Myocardial Infarction.",
+    "authorString": "Than MP, Pickering JW, Sandoval Y, Shah ASV, Tsanas A, Apple FS, Blankenberg S, Cullen L, Mueller C, Neumann JT, Twerenbold R, Westermann D, Beshiri A, Mills NL, MI3 Collaborative.",
     "authorAffiliations": "",
-    "journalTitle": "PloS one",
-    "pubYear": "2020",
-    "date": "2020-08-13",
+    "journalTitle": "Circulation",
+    "pubYear": "2019",
+    "date": "2019-08-16",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Troponin; Myocardial infarction; acute coronary syndrome; Machine Learning",
+    "nationalPriorities": "Applied Analytics",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Variations in cardiac troponin concentrations by age, sex, and time between samples in patients with suspected myocardial infarction are not currently accounted for in diagnostic approaches. We aimed to combine these variables through machine learning to improve the assessment of risk for individual patients.<h4>Methods</h4>A machine learning algorithm (myocardial-ischemic-injury-index [MI<sup>3</sup>]) incorporating age, sex, and paired high-sensitivity cardiac troponin I concentrations, was trained on 3013 patients and tested on 7998 patients with suspected myocardial infarction. MI<sup>3</sup> uses gradient boosting to compute a value (0-100) reflecting an individual's likelihood of a diagnosis of type 1 myocardial infarction and estimates the sensitivity, negative predictive value, specificity and positive predictive value for that individual. Assessment was by calibration and area under the receiver operating characteristic curve. Secondary analysis evaluated example MI<sup>3</sup> thresholds from the training set that identified patients as low risk (99% sensitivity) and high risk (75% positive predictive value), and performance at these thresholds was compared in the test set to the 99th percentile and European Society of Cardiology rule-out pathways.<h4>Results</h4>Myocardial infarction occurred in 404 (13.4%) patients in the training set and 849 (10.6%) patients in the test set. MI<sup>3</sup> was well calibrated with a very high area under the receiver operating characteristic curve of 0.963 [0.956-0.971] in the test set and similar performance in early and late presenters. Example MI<sup>3</sup> thresholds identifying low- and high-risk patients in the training set were 1.6 and 49.7, respectively. In the test set, MI<sup>3</sup> values were <1.6 in 69.5% with a negative predictive value of 99.7% (99.5-99.8%) and sensitivity of 97.8% (96.7-98.7%), and were \u226549.7 in 10.6% with a positive predictive value of 71.8% (68.9-75.0%) and specificity of 96.7% (96.3-97.1%). Using these thresholds, MI<sup>3</sup> performed better than the European Society of Cardiology 0/3-hour pathway (sensitivity, 82.5% [74.5-88.8%]; specificity, 92.2% [90.7-93.5%]) and the 99th percentile at any time point (sensitivity, 89.6% [87.4-91.6%]); specificity, 89.3% [88.6-90.0%]).<h4>Conclusions</h4>Using machine learning, MI<sup>3</sup> provides an individualized and objective assessment of the likelihood of myocardial infarction, which can be used to identify low- and high-risk patients who may benefit from earlier clinical decisions.<h4>Clinical trial registration</h4>URL: https://www.anzctr.org.au. Unique identifier: ACTRN12616001441404.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1161/circulationaha.119.041980; doi:https://doi.org/10.1161/CIRCULATIONAHA.119.041980; html:https://europepmc.org/articles/PMC6749969; pdf:https://europepmc.org/articles/PMC6749969?pdf=render"
+  },
+  {
+    "id": "37717234",
+    "doi": "https://doi.org/10.1111/1742-6723.14312",
+    "title": "Prevalence of alcohol and other drug detections in non-transport injury events.",
+    "authorString": "Lau G, Mitra B, Gabbe BJ, Dietze PM, Reeder S, Cameron PA, Smit V, Schneider HG, Symons E, Koolstra C, Stewart C, Beck B.",
+    "authorAffiliations": "",
+    "journalTitle": "Emergency medicine Australasia : EMA",
+    "pubYear": "2024",
+    "date": "2023-09-17",
+    "isOpenAccess": "Y",
+    "keywords": "Alcoholic Intoxication; Illicit Drug; Blood Alcohol Content; Wounds And Injury; Substance-related Disorder; Substance Use Detection",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Objectives</h4>We aimed to model the impact of coronavirus (COVID-19) on the clinical academic response in England, and to provide recommendations for COVID-related research.<h4>Design</h4>A stochastic model to determine clinical academic capacity in England, incorporating the following key factors which affect the ability to conduct research in the COVID-19 climate: (i) infection growth rate and population infection rate (from UK COVID-19 statistics and WHO); (ii) strain on the healthcare system (from published model); and (iii) availability of clinical academic staff with appropriate skillsets affected by frontline clinical activity and sickness (from UK statistics).<h4>Setting</h4>Clinical academics in primary and secondary care in England.<h4>Participants</h4>Equivalent of 3200 full-time clinical academics in England.<h4>Interventions</h4>Four policy approaches to COVID-19 with differing population infection rates: \"Italy model\" (6%), \"mitigation\" (10%), \"relaxed mitigation\" (40%) and \"do-nothing\" (80%) scenarios. Low and high strain on the health system (no clinical academics able to do research at 10% and 5% infection rate, respectively.<h4>Main outcome measures</h4>Number of full-time clinical academics available to conduct clinical research during the pandemic in England.<h4>Results</h4>In the \"Italy model\", \"mitigation\", \"relaxed mitigation\" and \"do-nothing\" scenarios, from 5 March 2020 the duration (days) and peak infection rates (%) are 95(2.4%), 115(2.5%), 240(5.3%) and 240(16.7%) respectively. Near complete attrition of academia (87% reduction, <400 clinical academics) occurs 35 days after pandemic start for 11, 34, 62, 76 days respectively-with no clinical academics at all for 37 days in the \"do-nothing\" scenario. Restoration of normal academic workforce (80% of normal capacity) takes 11, 12, 30 and 26 weeks respectively.<h4>Conclusions</h4>Pandemic COVID-19 crushes the science needed at system level. National policies mitigate, but the academic community needs to adapt. We highlight six key strategies: radical prioritisation (eg 3-4 research ideas per institution), deep resourcing, non-standard leadership (repurposing of key non-frontline teams), rationalisation (profoundly simple approaches), careful site selection (eg protected sites with large academic backup) and complete suspension of academic competition with collaborative approaches.",
+    "abstract": "<h4>Objective</h4>To measure the prevalence of alcohol and/or other drug (AOD) detections in suspected major trauma patients with non-transport injuries who presented to an adult major trauma centre.<h4>Methods</h4>This registry-based cohort study examined the prevalence of AOD detections in patients aged \u226518\u2009years who: (i) sustained non-transport injuries; and (ii) met predefined trauma call-out criteria and were therefore managed by an interdisciplinary trauma team between 1 July 2021 and 31 December 2022. Prevalence was measured using routine in-hospital blood alcohol and urine drug screens.<h4>Results</h4>A total of 1469 cases met the inclusion criteria. Of cases with a valid blood test (n\u2009=\u20091248, 85.0%), alcohol was detected in 313 (25.1%) patients. Of the 733 (49.9%) cases with urine drug screen results, cannabinoids were most commonly detected (n\u2009=\u2009103, 14.1%), followed by benzodiazepines (n\u2009=\u200998, 13.4%), amphetamine-type substances (n\u2009= 80, 10.9%), opioids (n\u2009=\u200928, 3.8%) and cocaine (n\u2009=\u200917, 2.3%). Alcohol and/or at least one other drug was detected in 37.4% (n\u2009=\u2009472) of cases with either a blood alcohol or urine drug test completed (n\u2009=\u20091263, 86.0%). Multiple substances were detected in 16.6% (n\u2009=\u2009119) of cases with both blood alcohol and urine drug screens (n\u2009=\u2009718, 48.9%). Detections were prevalent in cases of interpersonal violence (n\u2009=\u2009123/179, 68.7%) and intentional self-harm (n\u2009=\u200950/106, 47.2%), and in those occurring on Friday and Saturday nights (n\u2009=\u2009118/191, 61.8%).<h4>Conclusion</h4>AOD detections were common in trauma patients with non-transport injury causes. Population-level surveillance is needed to inform prevention strategies that address AOD use as a significant risk factor for serious injury.",
     "laySummary": "",
-    "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0237298&type=printable; doi:https://doi.org/10.1371/journal.pone.0237298; html:https://europepmc.org/articles/PMC7425844; pdf:https://europepmc.org/articles/PMC7425844?pdf=render"
+    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/1742-6723.14312; doi:https://doi.org/10.1111/1742-6723.14312; html:https://europepmc.org/articles/PMC10952644; pdf:https://europepmc.org/articles/PMC10952644?pdf=render"
   },
   {
     "id": "36812613",
@@ -19685,23 +19736,6 @@
     "laySummary": "",
     "urls": "pdf:https://journals.plos.org/digitalhealth/article/file?id=10.1371/journal.pdig.0000190&type=printable; doi:https://doi.org/10.1371/journal.pdig.0000190; html:https://europepmc.org/articles/PMC9931327; pdf:https://europepmc.org/articles/PMC9931327?pdf=render"
   },
-  {
-    "id": "31416346",
-    "doi": "https://doi.org/10.1161/circulationaha.119.041980",
-    "title": "Machine Learning to Predict the Likelihood of Acute Myocardial Infarction.",
-    "authorString": "Than MP, Pickering JW, Sandoval Y, Shah ASV, Tsanas A, Apple FS, Blankenberg S, Cullen L, Mueller C, Neumann JT, Twerenbold R, Westermann D, Beshiri A, Mills NL, MI3 Collaborative.",
-    "authorAffiliations": "",
-    "journalTitle": "Circulation",
-    "pubYear": "2019",
-    "date": "2019-08-16",
-    "isOpenAccess": "Y",
-    "keywords": "Troponin; Myocardial infarction; acute coronary syndrome; Machine Learning",
-    "nationalPriorities": "Applied Analytics",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Variations in cardiac troponin concentrations by age, sex, and time between samples in patients with suspected myocardial infarction are not currently accounted for in diagnostic approaches. We aimed to combine these variables through machine learning to improve the assessment of risk for individual patients.<h4>Methods</h4>A machine learning algorithm (myocardial-ischemic-injury-index [MI<sup>3</sup>]) incorporating age, sex, and paired high-sensitivity cardiac troponin I concentrations, was trained on 3013 patients and tested on 7998 patients with suspected myocardial infarction. MI<sup>3</sup> uses gradient boosting to compute a value (0-100) reflecting an individual's likelihood of a diagnosis of type 1 myocardial infarction and estimates the sensitivity, negative predictive value, specificity and positive predictive value for that individual. Assessment was by calibration and area under the receiver operating characteristic curve. Secondary analysis evaluated example MI<sup>3</sup> thresholds from the training set that identified patients as low risk (99% sensitivity) and high risk (75% positive predictive value), and performance at these thresholds was compared in the test set to the 99th percentile and European Society of Cardiology rule-out pathways.<h4>Results</h4>Myocardial infarction occurred in 404 (13.4%) patients in the training set and 849 (10.6%) patients in the test set. MI<sup>3</sup> was well calibrated with a very high area under the receiver operating characteristic curve of 0.963 [0.956-0.971] in the test set and similar performance in early and late presenters. Example MI<sup>3</sup> thresholds identifying low- and high-risk patients in the training set were 1.6 and 49.7, respectively. In the test set, MI<sup>3</sup> values were <1.6 in 69.5% with a negative predictive value of 99.7% (99.5-99.8%) and sensitivity of 97.8% (96.7-98.7%), and were \u226549.7 in 10.6% with a positive predictive value of 71.8% (68.9-75.0%) and specificity of 96.7% (96.3-97.1%). Using these thresholds, MI<sup>3</sup> performed better than the European Society of Cardiology 0/3-hour pathway (sensitivity, 82.5% [74.5-88.8%]; specificity, 92.2% [90.7-93.5%]) and the 99th percentile at any time point (sensitivity, 89.6% [87.4-91.6%]); specificity, 89.3% [88.6-90.0%]).<h4>Conclusions</h4>Using machine learning, MI<sup>3</sup> provides an individualized and objective assessment of the likelihood of myocardial infarction, which can be used to identify low- and high-risk patients who may benefit from earlier clinical decisions.<h4>Clinical trial registration</h4>URL: https://www.anzctr.org.au. Unique identifier: ACTRN12616001441404.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1161/circulationaha.119.041980; doi:https://doi.org/10.1161/CIRCULATIONAHA.119.041980; html:https://europepmc.org/articles/PMC6749969; pdf:https://europepmc.org/articles/PMC6749969?pdf=render"
-  },
   {
     "id": "36712153",
     "doi": "https://doi.org/10.1093/ehjdh/ztac046",
@@ -19940,23 +19974,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1001/jamaneurol.2023.1580; html:https://europepmc.org/articles/PMC10262059; doi:https://doi.org/10.1001/jamaneurol.2023.1580"
   },
-  {
-    "id": "33851963",
-    "doi": "https://doi.org/10.1001/jamadermatol.2021.0009",
-    "title": "Association Between Atopic Dermatitis and Educational Attainment in Denmark.",
-    "authorString": "Schmidt SAJ, Mailhac A, Darvalics B, Mulick A, Deleuran MS, S\u00f8rensen HT, Riis JL, Langan SM.",
-    "authorAffiliations": "",
-    "journalTitle": "JAMA dermatology",
-    "pubYear": "2021",
-    "date": "2021-04-14",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Importance</h4>Atopic dermatitis (AD) may affect academic performance through multiple pathways, including poor concentration associated with itching, sleep deprivation, or adverse effects of medications. Because educational attainment is associated with health and well-being, any association with a prevalent condition such as AD is of major importance.<h4>Objective</h4>To examine whether a childhood diagnosis of AD is associated with lower educational attainment.<h4>Design, setting, and participants</h4>This population-based cohort study used linked routine health care data from January 1, 1977, to June 30, 2017 (end of registry follow-up), in Denmark. The study population included all children born in Denmark on June 30, 1987, or earlier with an inpatient or outpatient hospital clinic diagnosis of AD recorded before their 13th birthday (baseline) and a comparison cohort of children from the general population matched by birth year and sex. A secondary analysis included exposure-discordant full siblings as a comparison cohort to account for familial factors. Data were analyzed from September 11, 2019, to January 21, 2021.<h4>Exposures</h4>Hospital-diagnosed AD.<h4>Main outcomes and measures</h4>Estimated probability or risk of not attaining specific educational levels (lower secondary, upper secondary, and higher) by 30 years of age among children with AD compared with children in the matched general population cohort. Corresponding risk ratios (RRs) were computed using Poisson regression that was conditioned on matched sets and adjusted for age. The sibling analysis was conditioned on family and adjusted for sex and age.<h4>Results</h4>The study included a total of 61 153 children, 5927 in the AD cohort (3341 male [56.4%]) and 55\u202f226 from the general population (31 182 male [56.5%]). Compared with matched children from the general population, children with AD were at increased risk of not attaining lower secondary education (150 of 5927 [2.5%] vs 924 of 55 226 [1.7%]; adjusted RR, 1.50; 95% CI, 1.26-1.78) and upper secondary education (1141 of 5777 [19.8%] vs 8690 of 52 899 [16.4%]; RR, 1.16; 95% CI, 1.09-1.24), but not higher education (2406 of 4636 [51.9%] vs 18 785 of 35 408 [53.1%]; RR, 0.95; 95% CI, 0.91-1.00). The absolute differences in probability were less than 3.5%. The comparison of 3259 children with AD and 4046 of their full siblings yielded estimates that were less pronounced than those in the main analysis (adjusted RR for lower secondary education, 1.29 [95% CI, 0.92-1.82]; adjusted RR for upper secondary education, 1.05 [95% CI, 0.93-1.18]; adjusted RR for higher education, 0.94 [95% CI, 0.87-1.02]).<h4>Conclusions and relevance</h4>This population-based cohort study found that hospital-diagnosed AD was associated with reduced educational attainment, but the clinical importance was uncertain owing to small absolute differences and possible confounding by familial factors in this study. Future studies should examine for replicability in other populations and variation by AD phenotype.",
-    "laySummary": "",
-    "urls": "pdf:https://jamanetwork.com/journals/jamadermatology/articlepdf/2778389/jamadermatology_schmidt_2021_oi_210002_1623774349.64965.pdf; doi:https://doi.org/10.1001/jamadermatol.2021.0009; html:https://europepmc.org/articles/PMC8047754"
-  },
   {
     "id": "32954362",
     "doi": "https://doi.org/10.1038/s43016-020-0093-y",
@@ -19974,6 +19991,23 @@
     "laySummary": "",
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7497842; doi:https://doi.org/10.1038/s43016-020-0093-y; html:https://europepmc.org/articles/PMC7497842; pdf:https://europepmc.org/articles/PMC7497842?pdf=render; doi:https://doi.org/10.1038/s43016-020-0093-y"
   },
+  {
+    "id": "33851963",
+    "doi": "https://doi.org/10.1001/jamadermatol.2021.0009",
+    "title": "Association Between Atopic Dermatitis and Educational Attainment in Denmark.",
+    "authorString": "Schmidt SAJ, Mailhac A, Darvalics B, Mulick A, Deleuran MS, S\u00f8rensen HT, Riis JL, Langan SM.",
+    "authorAffiliations": "",
+    "journalTitle": "JAMA dermatology",
+    "pubYear": "2021",
+    "date": "2021-04-14",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Importance</h4>Atopic dermatitis (AD) may affect academic performance through multiple pathways, including poor concentration associated with itching, sleep deprivation, or adverse effects of medications. Because educational attainment is associated with health and well-being, any association with a prevalent condition such as AD is of major importance.<h4>Objective</h4>To examine whether a childhood diagnosis of AD is associated with lower educational attainment.<h4>Design, setting, and participants</h4>This population-based cohort study used linked routine health care data from January 1, 1977, to June 30, 2017 (end of registry follow-up), in Denmark. The study population included all children born in Denmark on June 30, 1987, or earlier with an inpatient or outpatient hospital clinic diagnosis of AD recorded before their 13th birthday (baseline) and a comparison cohort of children from the general population matched by birth year and sex. A secondary analysis included exposure-discordant full siblings as a comparison cohort to account for familial factors. Data were analyzed from September 11, 2019, to January 21, 2021.<h4>Exposures</h4>Hospital-diagnosed AD.<h4>Main outcomes and measures</h4>Estimated probability or risk of not attaining specific educational levels (lower secondary, upper secondary, and higher) by 30 years of age among children with AD compared with children in the matched general population cohort. Corresponding risk ratios (RRs) were computed using Poisson regression that was conditioned on matched sets and adjusted for age. The sibling analysis was conditioned on family and adjusted for sex and age.<h4>Results</h4>The study included a total of 61 153 children, 5927 in the AD cohort (3341 male [56.4%]) and 55\u202f226 from the general population (31 182 male [56.5%]). Compared with matched children from the general population, children with AD were at increased risk of not attaining lower secondary education (150 of 5927 [2.5%] vs 924 of 55 226 [1.7%]; adjusted RR, 1.50; 95% CI, 1.26-1.78) and upper secondary education (1141 of 5777 [19.8%] vs 8690 of 52 899 [16.4%]; RR, 1.16; 95% CI, 1.09-1.24), but not higher education (2406 of 4636 [51.9%] vs 18 785 of 35 408 [53.1%]; RR, 0.95; 95% CI, 0.91-1.00). The absolute differences in probability were less than 3.5%. The comparison of 3259 children with AD and 4046 of their full siblings yielded estimates that were less pronounced than those in the main analysis (adjusted RR for lower secondary education, 1.29 [95% CI, 0.92-1.82]; adjusted RR for upper secondary education, 1.05 [95% CI, 0.93-1.18]; adjusted RR for higher education, 0.94 [95% CI, 0.87-1.02]).<h4>Conclusions and relevance</h4>This population-based cohort study found that hospital-diagnosed AD was associated with reduced educational attainment, but the clinical importance was uncertain owing to small absolute differences and possible confounding by familial factors in this study. Future studies should examine for replicability in other populations and variation by AD phenotype.",
+    "laySummary": "",
+    "urls": "pdf:https://jamanetwork.com/journals/jamadermatology/articlepdf/2778389/jamadermatology_schmidt_2021_oi_210002_1623774349.64965.pdf; doi:https://doi.org/10.1001/jamadermatol.2021.0009; html:https://europepmc.org/articles/PMC8047754"
+  },
   {
     "id": "37609702",
     "doi": "https://doi.org/10.1002/pds.5681",
@@ -20229,23 +20263,6 @@
     "laySummary": "",
     "urls": "pdf:http://www.aginganddisease.org/EN/PDF/10.14336/AD.2022.1107; doi:https://doi.org/10.14336/AD.2022.1107; html:https://europepmc.org/articles/PMC10187689; pdf:https://europepmc.org/articles/PMC10187689?pdf=render"
   },
-  {
-    "id": "33704068",
-    "doi": "https://doi.org/10.7554/elife.64827",
-    "title": "Longitudinal proteomic profiling of dialysis patients with COVID-19 reveals markers of severity and predictors of death.",
-    "authorString": "Gisby J, Clarke CL, Medjeral-Thomas N, Malik TH, Papadaki A, Mortimer PM, Buang NB, Lewis S, Pereira M, Toulza F, Fagnano E, Mawhin MA, Dutton EE, Tapeng L, Richard AC, Kirk PD, Behmoaras J, Sandhu E, McAdoo SP, Prendecki MF, Pickering MC, Botto M, Willicombe M, Thomas DC, Peters JE.",
-    "authorAffiliations": "",
-    "journalTitle": "eLife",
-    "pubYear": "2021",
-    "date": "2021-03-11",
-    "isOpenAccess": "Y",
-    "keywords": "Human; Cytokines; Proteomics; Inflammation; Medicine; Biomarkers; immunology; Longitudinal; End-stage Kidney Disease; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "End-stage kidney disease (ESKD) patients are at high risk of severe COVID-19. We measured 436 circulating proteins in serial blood samples from hospitalised and non-hospitalised ESKD patients with COVID-19 (n = 256 samples from 55 patients). Comparison to 51 non-infected patients revealed 221 differentially expressed proteins, with consistent results in a separate subcohort of 46 COVID-19 patients. Two hundred and three proteins were associated with clinical severity, including IL6, markers of monocyte recruitment (e.g. CCL2, CCL7), neutrophil activation (e.g. proteinase-3), and epithelial injury (e.g. KRT19). Machine-learning identified predictors of severity including IL18BP, CTSD, GDF15, and KRT19. Survival analysis with joint models revealed 69 predictors of death. Longitudinal modelling with linear mixed models uncovered 32 proteins displaying different temporal profiles in severe versus non-severe disease, including integrins and adhesion molecules. These data implicate epithelial damage, innate immune activation, and leucocyte-endothelial interactions in the pathology of severe COVID-19 and provide a resource for identifying drug targets.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.7554/elife.64827; doi:https://doi.org/10.7554/eLife.64827; html:https://europepmc.org/articles/PMC8064756; pdf:https://europepmc.org/articles/PMC8064756?pdf=render"
-  },
   {
     "id": "34399584",
     "doi": "https://doi.org/10.1161/strokeaha.120.032619",
@@ -20263,6 +20280,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/STROKEAHA.120.032619; doi:https://doi.org/10.1161/STROKEAHA.120.032619; html:https://europepmc.org/articles/PMC7611731; pdf:https://europepmc.org/articles/PMC7611731?pdf=render; doi:https://doi.org/10.1161/strokeaha.120.032619"
   },
+  {
+    "id": "33704068",
+    "doi": "https://doi.org/10.7554/elife.64827",
+    "title": "Longitudinal proteomic profiling of dialysis patients with COVID-19 reveals markers of severity and predictors of death.",
+    "authorString": "Gisby J, Clarke CL, Medjeral-Thomas N, Malik TH, Papadaki A, Mortimer PM, Buang NB, Lewis S, Pereira M, Toulza F, Fagnano E, Mawhin MA, Dutton EE, Tapeng L, Richard AC, Kirk PD, Behmoaras J, Sandhu E, McAdoo SP, Prendecki MF, Pickering MC, Botto M, Willicombe M, Thomas DC, Peters JE.",
+    "authorAffiliations": "",
+    "journalTitle": "eLife",
+    "pubYear": "2021",
+    "date": "2021-03-11",
+    "isOpenAccess": "Y",
+    "keywords": "Human; Cytokines; Proteomics; Inflammation; Medicine; Biomarkers; immunology; Longitudinal; End-stage Kidney Disease; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "End-stage kidney disease (ESKD) patients are at high risk of severe COVID-19. We measured 436 circulating proteins in serial blood samples from hospitalised and non-hospitalised ESKD patients with COVID-19 (n = 256 samples from 55 patients). Comparison to 51 non-infected patients revealed 221 differentially expressed proteins, with consistent results in a separate subcohort of 46 COVID-19 patients. Two hundred and three proteins were associated with clinical severity, including IL6, markers of monocyte recruitment (e.g. CCL2, CCL7), neutrophil activation (e.g. proteinase-3), and epithelial injury (e.g. KRT19). Machine-learning identified predictors of severity including IL18BP, CTSD, GDF15, and KRT19. Survival analysis with joint models revealed 69 predictors of death. Longitudinal modelling with linear mixed models uncovered 32 proteins displaying different temporal profiles in severe versus non-severe disease, including integrins and adhesion molecules. These data implicate epithelial damage, innate immune activation, and leucocyte-endothelial interactions in the pathology of severe COVID-19 and provide a resource for identifying drug targets.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.7554/elife.64827; doi:https://doi.org/10.7554/eLife.64827; html:https://europepmc.org/articles/PMC8064756; pdf:https://europepmc.org/articles/PMC8064756?pdf=render"
+  },
   {
     "id": "35322592",
     "doi": "https://doi.org/10.1002/ehf2.13910",
@@ -20484,23 +20518,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.researchprotocols.org/2020/8/e18690/PDF; doi:https://doi.org/10.2196/18690; html:https://europepmc.org/articles/PMC7442945"
   },
-  {
-    "id": "35997594",
-    "doi": "https://doi.org/10.1099/mic.0.001223",
-    "title": "Diagnostic MALDI-TOF MS can differentiate between high and low toxic <i>Staphylococcus aureus</i> bacteraemia isolates as a predictor of patient outcome.",
-    "authorString": "Brignoli T, Recker M, Lee WWY, Dong T, Bhamber R, Albur M, Williams P, Dowsey AW, Massey RC.",
-    "authorAffiliations": "",
-    "journalTitle": "Microbiology (Reading, England)",
-    "pubYear": "2022",
-    "date": "2022-08-01",
-    "isOpenAccess": "Y",
-    "keywords": "Toxicity; Staphylococcus aureus; Bacteraemia; agr; Maldi-tof Ms Diagnosis",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<i>Staphylococcus aureus</i> bacteraemia (SAB) is a major cause of blood-stream infection (BSI) in both healthcare and community settings. While the underlying comorbidities of a patient significantly contributes to their susceptibility to and outcome following SAB, recent studies show the importance of the level of cytolytic toxin production by the infecting bacterium. In this study we demonstrate that this cytotoxicity can be determined directly from the diagnostic MALDI-TOF mass spectrum generated in a routine diagnostic laboratory. With further development this information could be used to guide the management and improve the outcomes for SAB patients.",
-    "laySummary": "",
-    "urls": "pdf:https://research-information.bris.ac.uk/files/356539118/mic001223.pdf; doi:https://doi.org/10.1099/mic.0.001223; html:https://europepmc.org/articles/PMC10323763; pdf:https://europepmc.org/articles/PMC10323763?pdf=render"
-  },
   {
     "id": "31711534",
     "doi": "https://doi.org/10.1186/s13326-019-0216-2",
@@ -20518,6 +20535,23 @@
     "laySummary": "",
     "urls": "pdf:https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-019-0216-2; doi:https://doi.org/10.1186/s13326-019-0216-2; html:https://europepmc.org/articles/PMC6849162; pdf:https://europepmc.org/articles/PMC6849162?pdf=render"
   },
+  {
+    "id": "35997594",
+    "doi": "https://doi.org/10.1099/mic.0.001223",
+    "title": "Diagnostic MALDI-TOF MS can differentiate between high and low toxic <i>Staphylococcus aureus</i> bacteraemia isolates as a predictor of patient outcome.",
+    "authorString": "Brignoli T, Recker M, Lee WWY, Dong T, Bhamber R, Albur M, Williams P, Dowsey AW, Massey RC.",
+    "authorAffiliations": "",
+    "journalTitle": "Microbiology (Reading, England)",
+    "pubYear": "2022",
+    "date": "2022-08-01",
+    "isOpenAccess": "Y",
+    "keywords": "Toxicity; Staphylococcus aureus; Bacteraemia; agr; Maldi-tof Ms Diagnosis",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<i>Staphylococcus aureus</i> bacteraemia (SAB) is a major cause of blood-stream infection (BSI) in both healthcare and community settings. While the underlying comorbidities of a patient significantly contributes to their susceptibility to and outcome following SAB, recent studies show the importance of the level of cytolytic toxin production by the infecting bacterium. In this study we demonstrate that this cytotoxicity can be determined directly from the diagnostic MALDI-TOF mass spectrum generated in a routine diagnostic laboratory. With further development this information could be used to guide the management and improve the outcomes for SAB patients.",
+    "laySummary": "",
+    "urls": "pdf:https://research-information.bris.ac.uk/files/356539118/mic001223.pdf; doi:https://doi.org/10.1099/mic.0.001223; html:https://europepmc.org/articles/PMC10323763; pdf:https://europepmc.org/articles/PMC10323763?pdf=render"
+  },
   {
     "id": "34673925",
     "doi": "https://doi.org/10.1093/ageing/afab201",
@@ -20553,21 +20587,21 @@
     "urls": "pdf:https://academic.oup.com/ageing/article-pdf/49/6/1056/33993322/afaa158.pdf; doi:https://doi.org/10.1093/ageing/afaa158; html:https://europepmc.org/articles/PMC7583515; pdf:https://europepmc.org/articles/PMC7583515?pdf=render"
   },
   {
-    "id": "36439548",
-    "doi": "https://doi.org/10.3389/fsurg.2022.870494",
-    "title": "Development and validation of an automated basal cell carcinoma histopathology information extraction system using natural language processing.",
-    "authorString": "Ali SR, Strafford H, Dobbs TD, Fonferko-Shadrach B, Lacey AS, Pickrell WO, Hutchings HA, Whitaker IS.",
+    "id": "33653161",
+    "doi": "https://doi.org/10.1177/1740774520976617",
+    "title": "Making a distinction between data cleaning and central monitoring in clinical trials.",
+    "authorString": "Love SB, Yorke-Edwards V, Diaz-Montana C, Murray ML, Masters L, Gabriel M, Joffe N, Sydes MR.",
     "authorAffiliations": "",
-    "journalTitle": "Frontiers in surgery",
-    "pubYear": "2022",
-    "date": "2022-08-24",
+    "journalTitle": "Clinical trials (London, England)",
+    "pubYear": "2021",
+    "date": "2021-03-02",
     "isOpenAccess": "Y",
-    "keywords": "Electronic Health Records (Ehrs); Natural Language Processing (Nlp); Basal Cell Carcinoma (Bcc); Non-melanoma Skin Cancer (Nmsc); Information Extraction (Ie)",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>Routinely collected healthcare data are a powerful research resource, but often lack detailed disease-specific information that is collected in clinical free text such as histopathology reports. We aim to use natural Language Processing (NLP) techniques to extract detailed clinical and pathological information from histopathology reports to enrich routinely collected data.<h4>Methods</h4>We used the general architecture for text engineering (GATE) framework to build an NLP information extraction system using rule-based techniques. During validation, we deployed our rule-based NLP pipeline on 200 previously unseen, de-identified and pseudonymised basal cell carcinoma (BCC) histopathological reports from Swansea Bay University Health Board, Wales, UK. The results of our algorithm were compared with gold standard human annotation by two independent and blinded expert clinicians involved in skin cancer care.<h4>Results</h4>We identified 11,224 items of information with a mean precision, recall, and F1 score of 86.0% (95% CI: 75.1-96.9), 84.2% (95% CI: 72.8-96.1), and 84.5% (95% CI: 73.0-95.1), respectively. The difference between clinician annotator F1 scores was 7.9% in comparison with 15.5% between the NLP pipeline and the gold standard corpus. Cohen's Kappa score on annotated tokens was 0.85.<h4>Conclusion</h4>Using an NLP rule-based approach for named entity recognition in BCC, we have been able to develop and validate a pipeline with a potential application in improving the quality of cancer registry data, supporting service planning, and enhancing the quality of routinely collected data for research.",
+    "abstract": "",
     "laySummary": "",
-    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fsurg.2022.870494/pdf; doi:https://doi.org/10.3389/fsurg.2022.870494; html:https://europepmc.org/articles/PMC9683031; pdf:https://europepmc.org/articles/PMC9683031?pdf=render"
+    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/1740774520976617; doi:https://doi.org/10.1177/1740774520976617; html:https://europepmc.org/articles/PMC8174009; pdf:https://europepmc.org/articles/PMC8174009?pdf=render"
   },
   {
     "id": "34026049",
@@ -20587,21 +20621,21 @@
     "urls": "pdf:https://f1000research.com/articles/9-1095/v2/pdf; doi:https://doi.org/10.12688/f1000research.25484.2; html:https://europepmc.org/articles/PMC8108552; pdf:https://europepmc.org/articles/PMC8108552?pdf=render"
   },
   {
-    "id": "33653161",
-    "doi": "https://doi.org/10.1177/1740774520976617",
-    "title": "Making a distinction between data cleaning and central monitoring in clinical trials.",
-    "authorString": "Love SB, Yorke-Edwards V, Diaz-Montana C, Murray ML, Masters L, Gabriel M, Joffe N, Sydes MR.",
+    "id": "36439548",
+    "doi": "https://doi.org/10.3389/fsurg.2022.870494",
+    "title": "Development and validation of an automated basal cell carcinoma histopathology information extraction system using natural language processing.",
+    "authorString": "Ali SR, Strafford H, Dobbs TD, Fonferko-Shadrach B, Lacey AS, Pickrell WO, Hutchings HA, Whitaker IS.",
     "authorAffiliations": "",
-    "journalTitle": "Clinical trials (London, England)",
-    "pubYear": "2021",
-    "date": "2021-03-02",
+    "journalTitle": "Frontiers in surgery",
+    "pubYear": "2022",
+    "date": "2022-08-24",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Electronic Health Records (Ehrs); Natural Language Processing (Nlp); Basal Cell Carcinoma (Bcc); Non-melanoma Skin Cancer (Nmsc); Information Extraction (Ie)",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "",
+    "abstract": "<h4>Introduction</h4>Routinely collected healthcare data are a powerful research resource, but often lack detailed disease-specific information that is collected in clinical free text such as histopathology reports. We aim to use natural Language Processing (NLP) techniques to extract detailed clinical and pathological information from histopathology reports to enrich routinely collected data.<h4>Methods</h4>We used the general architecture for text engineering (GATE) framework to build an NLP information extraction system using rule-based techniques. During validation, we deployed our rule-based NLP pipeline on 200 previously unseen, de-identified and pseudonymised basal cell carcinoma (BCC) histopathological reports from Swansea Bay University Health Board, Wales, UK. The results of our algorithm were compared with gold standard human annotation by two independent and blinded expert clinicians involved in skin cancer care.<h4>Results</h4>We identified 11,224 items of information with a mean precision, recall, and F1 score of 86.0% (95% CI: 75.1-96.9), 84.2% (95% CI: 72.8-96.1), and 84.5% (95% CI: 73.0-95.1), respectively. The difference between clinician annotator F1 scores was 7.9% in comparison with 15.5% between the NLP pipeline and the gold standard corpus. Cohen's Kappa score on annotated tokens was 0.85.<h4>Conclusion</h4>Using an NLP rule-based approach for named entity recognition in BCC, we have been able to develop and validate a pipeline with a potential application in improving the quality of cancer registry data, supporting service planning, and enhancing the quality of routinely collected data for research.",
     "laySummary": "",
-    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/1740774520976617; doi:https://doi.org/10.1177/1740774520976617; html:https://europepmc.org/articles/PMC8174009; pdf:https://europepmc.org/articles/PMC8174009?pdf=render"
+    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fsurg.2022.870494/pdf; doi:https://doi.org/10.3389/fsurg.2022.870494; html:https://europepmc.org/articles/PMC9683031; pdf:https://europepmc.org/articles/PMC9683031?pdf=render"
   },
   {
     "id": "33249608",
@@ -20756,23 +20790,6 @@
     "laySummary": "",
     "urls": "pdf:https://jech.bmj.com/content/jech/early/2023/10/11/jech-2023-220975.full.pdf; doi:https://doi.org/10.1136/jech-2023-220975; html:https://europepmc.org/articles/PMC10715544; pdf:https://europepmc.org/articles/PMC10715544?pdf=render"
   },
-  {
-    "id": "33468531",
-    "doi": "https://doi.org/10.1136/bmjopen-2020-047101",
-    "title": "Protocol for the development of the Wales Multimorbidity e-Cohort (WMC): data sources and methods to construct a population-based research platform to investigate multimorbidity.",
-    "authorString": "Lyons J, Akbari A, Agrawal U, Harper G, Azcoaga-Lorenzo A, Bailey R, Rafferty J, Watkins A, Fry R, McCowan C, Dezateux C, Robson JP, Peek N, Holmes C, Denaxas S, Owen R, Abrams KR, John A, O'Reilly D, Richardson S, Hall M, Gale CP, Davies J, Davies C, Cross L, Gallacher J, Chess J, Brookes AJ, Lyons RA.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2021",
-    "date": "2021-01-19",
-    "isOpenAccess": "Y",
-    "keywords": "epidemiology; Public Health; Primary Care; Geriatric Medicine; Health Policy",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>Multimorbidity is widely recognised as the presence of two or more concurrent long-term conditions, yet remains a poorly understood global issue despite increasing in prevalence.We have created the Wales Multimorbidity e-Cohort (WMC) to provide an accessible research ready data asset to further the understanding of multimorbidity. Our objectives are to create a platform to support research which would help to understand prevalence, trajectories and determinants in multimorbidity, characterise clusters that lead to highest burden on individuals and healthcare services, and evaluate and provide new multimorbidity phenotypes and algorithms to the National Health Service and research communities to support prevention, healthcare planning and the management of individuals with multimorbidity.<h4>Methods and analysis</h4>The WMC has been created and derived from multisourced demographic, administrative and electronic health record data relating to the Welsh population in the Secure Anonymised Information Linkage (SAIL) Databank. The WMC consists of 2.9 million people alive and living in Wales on the 1 January 2000 with follow-up until 31 December 2019, Welsh residency break or death. Published comorbidity indices and phenotype code lists will be used to measure and conceptualise multimorbidity.Study outcomes will include: (1) a description of multimorbidity using published data phenotype algorithms/ontologies, (2) investigation of the associations between baseline demographic factors and multimorbidity, (3) identification of temporal trajectories of clusters of conditions and multimorbidity and (4) investigation of multimorbidity clusters with poor outcomes such as mortality and high healthcare service utilisation.<h4>Ethics and dissemination</h4>The SAIL Databank independent Information Governance Review Panel has approved this study (SAIL Project: 0911). Study findings will be presented to policy groups, public meetings, national and international conferences, and published in peer-reviewed journals.",
-    "laySummary": "",
-    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/11/1/e047101.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-047101; html:https://europepmc.org/articles/PMC7817800; pdf:https://europepmc.org/articles/PMC7817800?pdf=render"
-  },
   {
     "id": "37717030",
     "doi": "https://doi.org/10.1186/s13756-023-01280-6",
@@ -20807,6 +20824,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.mdpi.com/2073-4409/9/3/665/pdf?version=1584361130; doi:https://doi.org/10.3390/cells9030665; html:https://europepmc.org/articles/PMC7140647; pdf:https://europepmc.org/articles/PMC7140647?pdf=render"
   },
+  {
+    "id": "33468531",
+    "doi": "https://doi.org/10.1136/bmjopen-2020-047101",
+    "title": "Protocol for the development of the Wales Multimorbidity e-Cohort (WMC): data sources and methods to construct a population-based research platform to investigate multimorbidity.",
+    "authorString": "Lyons J, Akbari A, Agrawal U, Harper G, Azcoaga-Lorenzo A, Bailey R, Rafferty J, Watkins A, Fry R, McCowan C, Dezateux C, Robson JP, Peek N, Holmes C, Denaxas S, Owen R, Abrams KR, John A, O'Reilly D, Richardson S, Hall M, Gale CP, Davies J, Davies C, Cross L, Gallacher J, Chess J, Brookes AJ, Lyons RA.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2021",
+    "date": "2021-01-19",
+    "isOpenAccess": "Y",
+    "keywords": "epidemiology; Public Health; Primary Care; Geriatric Medicine; Health Policy",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>Multimorbidity is widely recognised as the presence of two or more concurrent long-term conditions, yet remains a poorly understood global issue despite increasing in prevalence.We have created the Wales Multimorbidity e-Cohort (WMC) to provide an accessible research ready data asset to further the understanding of multimorbidity. Our objectives are to create a platform to support research which would help to understand prevalence, trajectories and determinants in multimorbidity, characterise clusters that lead to highest burden on individuals and healthcare services, and evaluate and provide new multimorbidity phenotypes and algorithms to the National Health Service and research communities to support prevention, healthcare planning and the management of individuals with multimorbidity.<h4>Methods and analysis</h4>The WMC has been created and derived from multisourced demographic, administrative and electronic health record data relating to the Welsh population in the Secure Anonymised Information Linkage (SAIL) Databank. The WMC consists of 2.9 million people alive and living in Wales on the 1 January 2000 with follow-up until 31 December 2019, Welsh residency break or death. Published comorbidity indices and phenotype code lists will be used to measure and conceptualise multimorbidity.Study outcomes will include: (1) a description of multimorbidity using published data phenotype algorithms/ontologies, (2) investigation of the associations between baseline demographic factors and multimorbidity, (3) identification of temporal trajectories of clusters of conditions and multimorbidity and (4) investigation of multimorbidity clusters with poor outcomes such as mortality and high healthcare service utilisation.<h4>Ethics and dissemination</h4>The SAIL Databank independent Information Governance Review Panel has approved this study (SAIL Project: 0911). Study findings will be presented to policy groups, public meetings, national and international conferences, and published in peer-reviewed journals.",
+    "laySummary": "",
+    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/11/1/e047101.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-047101; html:https://europepmc.org/articles/PMC7817800; pdf:https://europepmc.org/articles/PMC7817800?pdf=render"
+  },
   {
     "id": "37814053",
     "doi": "https://doi.org/10.1038/s41588-023-01522-8",
@@ -20892,23 +20926,6 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/aor.14537; doi:https://doi.org/10.1111/aor.14537"
   },
-  {
-    "id": "37194197",
-    "doi": "https://doi.org/10.1111/acps.13566",
-    "title": "Low risk of some common cancers in women with anorexia nervosa: Evidence from a national record-linkage study.",
-    "authorString": "Seminog O, Thakrar DB, James AC, Goldacre MJ.",
-    "authorAffiliations": "",
-    "journalTitle": "Acta psychiatrica Scandinavica",
-    "pubYear": "2023",
-    "date": "2023-05-16",
-    "isOpenAccess": "Y",
-    "keywords": "Cancer; Caloric restriction; epidemiology; Anorexia Nervosa; risk",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Some studies report that women with anorexia nervosa (AN) have lower risk than others of breast cancer, but increased risk of cancers of other sites. No work has been done to quantify the risk in the English population.<h4>Methods</h4>Retrospective cohort study using a national linked dataset of Hospital Episode Statistics for 1999-2021. We selected individuals with a hospital admission for AN, and compared their relative risk (RR) of developing site-specific cancers, with that in a reference cohort.<h4>Results</h4>We identified 75 cancers in 15,029 women hospitalised with AN. There was a low RR of all cancers combined at 0.75 (95%CI 0.59-0.94), and, notably, low RR for breast cancer 0.43 (0.20-0.81), cancers of secondary and ill-defined sites 0.52 (0.26-0.93). The RR for parotid gland cancer was 4.4 (1.4-10.6) within a year of first recorded diagnosis of AN. In men, we found 12 cancers in 1413 individuals hospitalised with AN, but no increased risks beyond the first year of diagnosis of AN.<h4>Conclusions</h4>This is the first report on the association between AN and cancers in the all-England population. The study showed low rates of breast cancer, and of all cancers combined, in women hospitalised with AN. It is possible that some of the metabolic or hormonal changes observed in AN could work as a protective factor for breast cancer. More experimental work is needed to identify and explain these factors. The new finding on the higher risk of salivary gland tumours could inform clinicians caring for patients with AN.",
-    "laySummary": "",
-    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/acps.13566; doi:https://doi.org/10.1111/acps.13566; html:https://europepmc.org/articles/PMC10953461; pdf:https://europepmc.org/articles/PMC10953461?pdf=render"
-  },
   {
     "id": "37649471",
     "doi": "https://doi.org/10.23889/ijpds.v6i3.1705",
@@ -20943,6 +20960,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.12688/wellcomeopenres.17231.2; html:https://europepmc.org/articles/PMC9152464; pdf:https://europepmc.org/articles/PMC9152464?pdf=render"
   },
+  {
+    "id": "37194197",
+    "doi": "https://doi.org/10.1111/acps.13566",
+    "title": "Low risk of some common cancers in women with anorexia nervosa: Evidence from a national record-linkage study.",
+    "authorString": "Seminog O, Thakrar DB, James AC, Goldacre MJ.",
+    "authorAffiliations": "",
+    "journalTitle": "Acta psychiatrica Scandinavica",
+    "pubYear": "2023",
+    "date": "2023-05-16",
+    "isOpenAccess": "Y",
+    "keywords": "Cancer; Caloric restriction; epidemiology; Anorexia Nervosa; risk",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Some studies report that women with anorexia nervosa (AN) have lower risk than others of breast cancer, but increased risk of cancers of other sites. No work has been done to quantify the risk in the English population.<h4>Methods</h4>Retrospective cohort study using a national linked dataset of Hospital Episode Statistics for 1999-2021. We selected individuals with a hospital admission for AN, and compared their relative risk (RR) of developing site-specific cancers, with that in a reference cohort.<h4>Results</h4>We identified 75 cancers in 15,029 women hospitalised with AN. There was a low RR of all cancers combined at 0.75 (95%CI 0.59-0.94), and, notably, low RR for breast cancer 0.43 (0.20-0.81), cancers of secondary and ill-defined sites 0.52 (0.26-0.93). The RR for parotid gland cancer was 4.4 (1.4-10.6) within a year of first recorded diagnosis of AN. In men, we found 12 cancers in 1413 individuals hospitalised with AN, but no increased risks beyond the first year of diagnosis of AN.<h4>Conclusions</h4>This is the first report on the association between AN and cancers in the all-England population. The study showed low rates of breast cancer, and of all cancers combined, in women hospitalised with AN. It is possible that some of the metabolic or hormonal changes observed in AN could work as a protective factor for breast cancer. More experimental work is needed to identify and explain these factors. The new finding on the higher risk of salivary gland tumours could inform clinicians caring for patients with AN.",
+    "laySummary": "",
+    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/acps.13566; doi:https://doi.org/10.1111/acps.13566; html:https://europepmc.org/articles/PMC10953461; pdf:https://europepmc.org/articles/PMC10953461?pdf=render"
+  },
   {
     "id": "38100737",
     "doi": "https://doi.org/10.1371/journal.pdig.0000383",
@@ -21079,23 +21113,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.science.org/doi/pdf/10.1126/scitranslmed.abq4810?download=true; doi:https://doi.org/10.1126/scitranslmed.abq4810"
   },
-  {
-    "id": "38050140",
-    "doi": "https://doi.org/10.1136/jnnp-2023-332322",
-    "title": "Premorbid brain structure influences risk of amyotrophic lateral sclerosis.",
-    "authorString": "Thompson AG, Taschler B, Smith SM, Turner MR.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of neurology, neurosurgery, and psychiatry",
-    "pubYear": "2024",
-    "date": "2024-03-13",
-    "isOpenAccess": "Y",
-    "keywords": "MRI; ALS",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Amyotrophic lateral sclerosis (ALS) is a disease of the motor network associated with brain structure and functional connectivity alterations that are implicated in disease progression. Whether such changes have a causal role in ALS, fitting with a postulated influence of premorbid cerebral architecture on the phenotypes associated with neurodegenerative disorders is not known.<h4>Methods</h4>This study considered causal effects and shared genetic risk of 2240 structural and functional MRI brain scan imaging-derived phenotypes (IDPs) on ALS using two sample Mendelian randomisation, with putative associations further examined with extensive sensitivity analysis. Shared genetic predisposition between IDPs and ALS was explored using genetic correlation analysis.<h4>Results</h4>Increased white matter volume in the cerebral hemispheres was causally associated with ALS. Weaker causal associations were observed for brain stem grey matter volume, parieto-occipital white matter surface and volume of the left thalamic ventral anterior nucleus. Genetic correlation was observed between ALS and intracellular volume fraction and isotropic free water volume fraction within the posterior limb of the internal capsule.<h4>Conclusions</h4>This study provides evidence that premorbid brain structure, in particular white matter volume, contributes to the risk of ALS.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1136/jnnp-2023-332322; html:https://europepmc.org/articles/PMC10958375; pdf:https://europepmc.org/articles/PMC10958375?pdf=render"
-  },
   {
     "id": "38374065",
     "doi": "https://doi.org/10.1038/s41467-024-45779-x",
@@ -21131,21 +21148,21 @@
     "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fphys.2021.730736/pdf; doi:https://doi.org/10.3389/fphys.2021.730736; html:https://europepmc.org/articles/PMC8521153; pdf:https://europepmc.org/articles/PMC8521153?pdf=render"
   },
   {
-    "id": "32896935",
-    "doi": "https://doi.org/10.1002/cbm.2166",
-    "title": "Are Liaison and Diversion interventions in policing delivering the planned impact: A longitudinal evaluation in two constabularies?",
-    "authorString": "Kane E, Evans E, Mitsch J, Jilani T.",
+    "id": "38050140",
+    "doi": "https://doi.org/10.1136/jnnp-2023-332322",
+    "title": "Premorbid brain structure influences risk of amyotrophic lateral sclerosis.",
+    "authorString": "Thompson AG, Taschler B, Smith SM, Turner MR.",
     "authorAffiliations": "",
-    "journalTitle": "Criminal behaviour and mental health : CBMH",
-    "pubYear": "2020",
-    "date": "2020-09-08",
-    "isOpenAccess": "N",
-    "keywords": "Mental health; Outcomes; Offending; Policing; Liaison & Diversion",
+    "journalTitle": "Journal of neurology, neurosurgery, and psychiatry",
+    "pubYear": "2024",
+    "date": "2024-03-13",
+    "isOpenAccess": "Y",
+    "keywords": "MRI; ALS",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Liaison and Diversion (L&D) has twin objectives: improving mental health outcomes and reducing re-offending. Early diversion from police custody seems promising, but evidence of benefit is required to sustain such programmes. To test the hypothesis that contact with L&D services while in police custody would lead to improved mental health outcomes and a reduction in type and level of offending, we used a pre-post service use design. National Health Service (NHS) records in two counties were searched for evidence that patients had been involved with L&D services while in police custody during the period July 2009-December 2017. We defined January 2009-July 2014 as the pre-intervention period and any time after contact as the post-intervention period. Data from the Police National Computer were gathered for each period for these individuals, to assess their pre-post L&D contact offending histories. NHS Trust data were similarly gathered to assess their pre-post use of mental health legislation. 4,462 individuals were identified who had used L&D services in police custody. There were statistically significant reductions in the amount of offending following contact with the L&D service (whether one or two contacts), regardless of offence type. Statistically significant reductions were also observed in use of the four most commonly used legislative powers for detaining patients in hospital on mental disorder grounds, regardless of offending status (prolific/non-prolific). Our results indicate positive associations between the L&D interventions and change in offending and use of compulsory hospital detention. Whilst our research does not allow a direct causal relationship to be established in either area, the findings go beyond other impact assessments of L&D which have either been with small samples or relied only on qualitative data or expert opinion.",
+    "abstract": "<h4>Background</h4>Amyotrophic lateral sclerosis (ALS) is a disease of the motor network associated with brain structure and functional connectivity alterations that are implicated in disease progression. Whether such changes have a causal role in ALS, fitting with a postulated influence of premorbid cerebral architecture on the phenotypes associated with neurodegenerative disorders is not known.<h4>Methods</h4>This study considered causal effects and shared genetic risk of 2240 structural and functional MRI brain scan imaging-derived phenotypes (IDPs) on ALS using two sample Mendelian randomisation, with putative associations further examined with extensive sensitivity analysis. Shared genetic predisposition between IDPs and ALS was explored using genetic correlation analysis.<h4>Results</h4>Increased white matter volume in the cerebral hemispheres was causally associated with ALS. Weaker causal associations were observed for brain stem grey matter volume, parieto-occipital white matter surface and volume of the left thalamic ventral anterior nucleus. Genetic correlation was observed between ALS and intracellular volume fraction and isotropic free water volume fraction within the posterior limb of the internal capsule.<h4>Conclusions</h4>This study provides evidence that premorbid brain structure, in particular white matter volume, contributes to the risk of ALS.",
     "laySummary": "",
-    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cbm.2166; doi:https://doi.org/10.1002/cbm.2166"
+    "urls": "doi:https://doi.org/10.1136/jnnp-2023-332322; html:https://europepmc.org/articles/PMC10958375; pdf:https://europepmc.org/articles/PMC10958375?pdf=render"
   },
   {
     "id": "36682888",
@@ -21165,21 +21182,21 @@
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/cch.13097; doi:https://doi.org/10.1111/cch.13097; html:https://europepmc.org/articles/PMC10946723; pdf:https://europepmc.org/articles/PMC10946723?pdf=render"
   },
   {
-    "id": "37008054",
-    "doi": "https://doi.org/10.14336/ad.2022.0829",
-    "title": "Identifying Dynamic Patterns of Polypharmacy for Patients with Dementia from Primary Care Electronic Health Records: A Machine Learning Driven Longitudinal Study.",
-    "authorString": "Longo E, Burnett B, Bauermeister S, Zhou SM.",
+    "id": "32896935",
+    "doi": "https://doi.org/10.1002/cbm.2166",
+    "title": "Are Liaison and Diversion interventions in policing delivering the planned impact: A longitudinal evaluation in two constabularies?",
+    "authorString": "Kane E, Evans E, Mitsch J, Jilani T.",
     "authorAffiliations": "",
-    "journalTitle": "Aging and disease",
-    "pubYear": "2023",
-    "date": "2023-04-01",
-    "isOpenAccess": "Y",
-    "keywords": "Diagnosis; Dementia; Patient Safety; Machine Learning; Polypharmacy; Electronic Health Records; Exploratory Factor Analysis",
+    "journalTitle": "Criminal behaviour and mental health : CBMH",
+    "pubYear": "2020",
+    "date": "2020-09-08",
+    "isOpenAccess": "N",
+    "keywords": "Mental health; Outcomes; Offending; Policing; Liaison & Diversion",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "It is unclear how medication use evolved before diagnosis of dementia (DoD). This study aims to identify varied patterns of polypharmacy before DoD, their prevalence and possible complications. We collected primary care e-health records for 33,451 dementia patients in Wales from 1990 to 2015. The medication uses in every 5-year period along with 20-years prior to dementia diagnosis were considered. Exploratory factor analysis was used to identify clusters of medicines for every 5-year period. The prevalence of patients taking three or more medications was 82.16%, 69.7%, 41.1% and 5.5% in the Period 1 (0-5 years before DoD) ~ Period 4 (16-20 years before DoD) respectively. The Period 1 showed 3 clusters of polypharmacy - medicines for respiratory/urinary infections, arthropathies and rheumatism, and cardio-vascular disease (CVD) (66.55%); medicines for infections, arthropathies and rheumatism (AR), cardio-metabolic disease (CMD) and depression (22.02%); and medicines for arthropathies, rheumatism and osteoarthritis (2.6%). The Period 2 showed 4 clusters of polypharmacy - medicines for infections, arthropathies, and CVD (69.7%); medicines for CVD and depression (3%); medicines for CMD and arthropathies (0.3%); and medicines for AR, and CVD (2,5%). The Period 3 showed 6 clusters of polypharmacy - medicines for infections, arthropathies, and CVD (41.1%); medicines for CVD, acute-respiratory-infection (ARI), and arthropathies (1.25%); medicines for AR (1.16%); medicines for depression, anxiety (0.06%); medicines for CMD (1.4%); and medicines for dermatologic disorders (0.9%). The Period 4 showed 3 main clusters of polypharmacy - medicines for infections, arthropathy, and CVD (5.5%); medicines for anxiety, ARI (2.4%); and medicines for ARI and CVD (2.1%). As the development towards dementia progressed, the associative diseases tended to cluster with a larger prevalence in each cluster. Farther away before DoD, the clusters of polypharmacy tended to be clearly distinct between each other, resulting in an increasing number of patterns, but in a smaller prevalence.",
+    "abstract": "Liaison and Diversion (L&D) has twin objectives: improving mental health outcomes and reducing re-offending. Early diversion from police custody seems promising, but evidence of benefit is required to sustain such programmes. To test the hypothesis that contact with L&D services while in police custody would lead to improved mental health outcomes and a reduction in type and level of offending, we used a pre-post service use design. National Health Service (NHS) records in two counties were searched for evidence that patients had been involved with L&D services while in police custody during the period July 2009-December 2017. We defined January 2009-July 2014 as the pre-intervention period and any time after contact as the post-intervention period. Data from the Police National Computer were gathered for each period for these individuals, to assess their pre-post L&D contact offending histories. NHS Trust data were similarly gathered to assess their pre-post use of mental health legislation. 4,462 individuals were identified who had used L&D services in police custody. There were statistically significant reductions in the amount of offending following contact with the L&D service (whether one or two contacts), regardless of offence type. Statistically significant reductions were also observed in use of the four most commonly used legislative powers for detaining patients in hospital on mental disorder grounds, regardless of offending status (prolific/non-prolific). Our results indicate positive associations between the L&D interventions and change in offending and use of compulsory hospital detention. Whilst our research does not allow a direct causal relationship to be established in either area, the findings go beyond other impact assessments of L&D which have either been with small samples or relied only on qualitative data or expert opinion.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.14336/ad.2022.0829; doi:https://doi.org/10.14336/AD.2022.0829; html:https://europepmc.org/articles/PMC10017143; pdf:https://europepmc.org/articles/PMC10017143?pdf=render"
+    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cbm.2166; doi:https://doi.org/10.1002/cbm.2166"
   },
   {
     "id": "35135774",
@@ -21198,6 +21215,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/2/e055603.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-055603; html:https://europepmc.org/articles/PMC8830221; pdf:https://europepmc.org/articles/PMC8830221?pdf=render"
   },
+  {
+    "id": "37008054",
+    "doi": "https://doi.org/10.14336/ad.2022.0829",
+    "title": "Identifying Dynamic Patterns of Polypharmacy for Patients with Dementia from Primary Care Electronic Health Records: A Machine Learning Driven Longitudinal Study.",
+    "authorString": "Longo E, Burnett B, Bauermeister S, Zhou SM.",
+    "authorAffiliations": "",
+    "journalTitle": "Aging and disease",
+    "pubYear": "2023",
+    "date": "2023-04-01",
+    "isOpenAccess": "Y",
+    "keywords": "Diagnosis; Dementia; Patient Safety; Machine Learning; Polypharmacy; Electronic Health Records; Exploratory Factor Analysis",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "It is unclear how medication use evolved before diagnosis of dementia (DoD). This study aims to identify varied patterns of polypharmacy before DoD, their prevalence and possible complications. We collected primary care e-health records for 33,451 dementia patients in Wales from 1990 to 2015. The medication uses in every 5-year period along with 20-years prior to dementia diagnosis were considered. Exploratory factor analysis was used to identify clusters of medicines for every 5-year period. The prevalence of patients taking three or more medications was 82.16%, 69.7%, 41.1% and 5.5% in the Period 1 (0-5 years before DoD) ~ Period 4 (16-20 years before DoD) respectively. The Period 1 showed 3 clusters of polypharmacy - medicines for respiratory/urinary infections, arthropathies and rheumatism, and cardio-vascular disease (CVD) (66.55%); medicines for infections, arthropathies and rheumatism (AR), cardio-metabolic disease (CMD) and depression (22.02%); and medicines for arthropathies, rheumatism and osteoarthritis (2.6%). The Period 2 showed 4 clusters of polypharmacy - medicines for infections, arthropathies, and CVD (69.7%); medicines for CVD and depression (3%); medicines for CMD and arthropathies (0.3%); and medicines for AR, and CVD (2,5%). The Period 3 showed 6 clusters of polypharmacy - medicines for infections, arthropathies, and CVD (41.1%); medicines for CVD, acute-respiratory-infection (ARI), and arthropathies (1.25%); medicines for AR (1.16%); medicines for depression, anxiety (0.06%); medicines for CMD (1.4%); and medicines for dermatologic disorders (0.9%). The Period 4 showed 3 main clusters of polypharmacy - medicines for infections, arthropathy, and CVD (5.5%); medicines for anxiety, ARI (2.4%); and medicines for ARI and CVD (2.1%). As the development towards dementia progressed, the associative diseases tended to cluster with a larger prevalence in each cluster. Farther away before DoD, the clusters of polypharmacy tended to be clearly distinct between each other, resulting in an increasing number of patterns, but in a smaller prevalence.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.14336/ad.2022.0829; doi:https://doi.org/10.14336/AD.2022.0829; html:https://europepmc.org/articles/PMC10017143; pdf:https://europepmc.org/articles/PMC10017143?pdf=render"
+  },
   {
     "id": "36050271",
     "doi": "https://doi.org/10.1016/s2589-7500(22)00151-0",
@@ -21215,23 +21249,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/s2589-7500(22)00151-0; doi:https://doi.org/10.1016/S2589-7500(22)00151-0"
   },
-  {
-    "id": "37140153",
-    "doi": "https://doi.org/10.1093/ehjci/jead093",
-    "title": "Determinants of post-operative left ventricular dysfunction in degenerative mitral regurgitation.",
-    "authorString": "Althunayyan AM, Alborikan S, Badiani S, Wong K, Uppal R, Patel N, Petersen SE, Lloyd G, Bhattacharyya S.",
-    "authorAffiliations": "",
-    "journalTitle": "European heart journal. Cardiovascular Imaging",
-    "pubYear": "2023",
-    "date": "2023-08-01",
-    "isOpenAccess": "N",
-    "keywords": "Surgery; Mitral regurgitation; Mitral Valve Prolapse; Global Longitudinal Strain; Lv Volumes",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Aims</h4>Chronic degenerative mitral regurgitation leads to volume overload causing left ventricular (LV) enlargement and eventually LV impairment. Current guidelines determining thresholds for intervention are based on LV diameters and ejection fraction (LVEF). There are sparse data examining the value of LV volumes and newer markers of LV performance on outcomes of surgery in mitral valve prolapse. The aim of this study is to identify the best marker of LV impairment after mitral valve surgery.<h4>Methods and results</h4>Prospective, observational study of patients with mitral valve prolapse undergoing mitral valve surgery. Pre-operative LV diameters, volumes, LVEF, global longitudinal strain (GLS), and myocardial work measured. Post-operative LV impairment defined as LVEF < 50% at 1 year post-surgery. Eighty-seven patients included. Thirteen percent developed post-operative LV impairment. Patients with post-operative LV dysfunction showed significantly larger indexed LV end-systolic diameters, indexed LV end-systolic volumes (LVESVi), lower LVEF, and more abnormal GLS than patients without post-operative LV dysfunction. In multivariate analysis, LVESVi [odds ratio 1.11 (95% CI 1.01-1.23), P = 0.039] and GLS [odds ratio 1.46 (95% CI 1.00-2.14), P = 0.054] were the only independent predictors of post-operative LV dysfunction. The optimal cut-off of 36.3 mL/m2 for LVESVi had a sensitivity of 82% and specificity of 78% for detection of post-operative LV impairment.<h4>Conclusion</h4>Post-operative LV impairment is common. Indexed LV volumes (36.3 mL/m2) provided the best marker of post-operative LV impairment.",
-    "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/ehjcimaging/advance-article-pdf/doi/10.1093/ehjci/jead093/50200028/jead093.pdf; doi:https://doi.org/10.1093/ehjci/jead093"
-  },
   {
     "id": "36276403",
     "doi": "https://doi.org/10.3389/fpubh.2022.875198",
@@ -21249,6 +21266,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fpubh.2022.875198/pdf; doi:https://doi.org/10.3389/fpubh.2022.875198; html:https://europepmc.org/articles/PMC9582845; pdf:https://europepmc.org/articles/PMC9582845?pdf=render"
   },
+  {
+    "id": "37140153",
+    "doi": "https://doi.org/10.1093/ehjci/jead093",
+    "title": "Determinants of post-operative left ventricular dysfunction in degenerative mitral regurgitation.",
+    "authorString": "Althunayyan AM, Alborikan S, Badiani S, Wong K, Uppal R, Patel N, Petersen SE, Lloyd G, Bhattacharyya S.",
+    "authorAffiliations": "",
+    "journalTitle": "European heart journal. Cardiovascular Imaging",
+    "pubYear": "2023",
+    "date": "2023-08-01",
+    "isOpenAccess": "N",
+    "keywords": "Surgery; Mitral regurgitation; Mitral Valve Prolapse; Global Longitudinal Strain; Lv Volumes",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Aims</h4>Chronic degenerative mitral regurgitation leads to volume overload causing left ventricular (LV) enlargement and eventually LV impairment. Current guidelines determining thresholds for intervention are based on LV diameters and ejection fraction (LVEF). There are sparse data examining the value of LV volumes and newer markers of LV performance on outcomes of surgery in mitral valve prolapse. The aim of this study is to identify the best marker of LV impairment after mitral valve surgery.<h4>Methods and results</h4>Prospective, observational study of patients with mitral valve prolapse undergoing mitral valve surgery. Pre-operative LV diameters, volumes, LVEF, global longitudinal strain (GLS), and myocardial work measured. Post-operative LV impairment defined as LVEF < 50% at 1 year post-surgery. Eighty-seven patients included. Thirteen percent developed post-operative LV impairment. Patients with post-operative LV dysfunction showed significantly larger indexed LV end-systolic diameters, indexed LV end-systolic volumes (LVESVi), lower LVEF, and more abnormal GLS than patients without post-operative LV dysfunction. In multivariate analysis, LVESVi [odds ratio 1.11 (95% CI 1.01-1.23), P = 0.039] and GLS [odds ratio 1.46 (95% CI 1.00-2.14), P = 0.054] were the only independent predictors of post-operative LV dysfunction. The optimal cut-off of 36.3 mL/m2 for LVESVi had a sensitivity of 82% and specificity of 78% for detection of post-operative LV impairment.<h4>Conclusion</h4>Post-operative LV impairment is common. Indexed LV volumes (36.3 mL/m2) provided the best marker of post-operative LV impairment.",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/ehjcimaging/advance-article-pdf/doi/10.1093/ehjci/jead093/50200028/jead093.pdf; doi:https://doi.org/10.1093/ehjci/jead093"
+  },
   {
     "id": "30279426",
     "doi": "https://doi.org/10.1038/s41598-018-32876-3",
@@ -21266,23 +21300,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41598-018-32876-3.pdf; doi:https://doi.org/10.1038/s41598-018-32876-3; html:https://europepmc.org/articles/PMC6168481; pdf:https://europepmc.org/articles/PMC6168481?pdf=render"
   },
-  {
-    "id": "37963560",
-    "doi": "https://doi.org/10.1098/rsif.2023.0410",
-    "title": "Spatio-temporal surveillance and early detection of SARS-CoV-2 variants of concern: a retrospective analysis.",
-    "authorString": "Cavallaro M, Dyson L, Tildesley MJ, Todkill D, Keeling MJ.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of the Royal Society, Interface",
-    "pubYear": "2023",
-    "date": "2023-11-15",
-    "isOpenAccess": "Y",
-    "keywords": "Disease Emergence; Anomaly Detection; Early Warning Signals; Sars-cov-2",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The SARS-CoV-2 pandemic has been characterized by the repeated emergence of genetically distinct virus variants of increased transmissibility and immune evasion compared to pre-existing lineages. In many countries, their containment required the intervention of public health authorities and the imposition of control measures. While the primary role of testing is to identify infection, target treatment, and limit spread (through isolation and contact tracing), a secondary benefit is in terms of surveillance and the early detection of new variants. Here we study the spatial invasion and early spread of the Alpha, Delta and Omicron (BA.1 and BA.2) variants in England from September 2020 to February 2022 using the random neighbourhood covering (RaNCover) method. This is a statistical technique for the detection of aberrations in spatial point processes, which we tailored here to community PCR (polymerase-chain-reaction) test data where the TaqPath kit provides a proxy measure of the switch between variants. Retrospectively, RaNCover detected the earliest signals associated with the four novel variants that led to large infection waves in England. With suitable data our method therefore has the potential to rapidly detect outbreaks of future SARS-CoV-2 variants, thus helping to inform targeted public health interventions.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1098/rsif.2023.0410; html:https://europepmc.org/articles/PMC10645511; pdf:https://europepmc.org/articles/PMC10645511?pdf=render"
-  },
   {
     "id": "38195748",
     "doi": "https://doi.org/10.1038/s41591-023-02715-8",
@@ -21300,6 +21317,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1038/s41591-023-02715-8"
   },
+  {
+    "id": "37963560",
+    "doi": "https://doi.org/10.1098/rsif.2023.0410",
+    "title": "Spatio-temporal surveillance and early detection of SARS-CoV-2 variants of concern: a retrospective analysis.",
+    "authorString": "Cavallaro M, Dyson L, Tildesley MJ, Todkill D, Keeling MJ.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of the Royal Society, Interface",
+    "pubYear": "2023",
+    "date": "2023-11-15",
+    "isOpenAccess": "Y",
+    "keywords": "Disease Emergence; Anomaly Detection; Early Warning Signals; Sars-cov-2",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The SARS-CoV-2 pandemic has been characterized by the repeated emergence of genetically distinct virus variants of increased transmissibility and immune evasion compared to pre-existing lineages. In many countries, their containment required the intervention of public health authorities and the imposition of control measures. While the primary role of testing is to identify infection, target treatment, and limit spread (through isolation and contact tracing), a secondary benefit is in terms of surveillance and the early detection of new variants. Here we study the spatial invasion and early spread of the Alpha, Delta and Omicron (BA.1 and BA.2) variants in England from September 2020 to February 2022 using the random neighbourhood covering (RaNCover) method. This is a statistical technique for the detection of aberrations in spatial point processes, which we tailored here to community PCR (polymerase-chain-reaction) test data where the TaqPath kit provides a proxy measure of the switch between variants. Retrospectively, RaNCover detected the earliest signals associated with the four novel variants that led to large infection waves in England. With suitable data our method therefore has the potential to rapidly detect outbreaks of future SARS-CoV-2 variants, thus helping to inform targeted public health interventions.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1098/rsif.2023.0410; html:https://europepmc.org/articles/PMC10645511; pdf:https://europepmc.org/articles/PMC10645511?pdf=render"
+  },
   {
     "id": "36942567",
     "doi": "https://doi.org/10.1161/circep.122.011585",
@@ -21334,23 +21368,6 @@
     "laySummary": "",
     "urls": "pdf:https://jogh.org/wp-content/uploads/2022/10/jogh-12-05044.pdf; doi:https://doi.org/10.7189/jogh.12.05044; html:https://europepmc.org/articles/PMC9494196; pdf:https://europepmc.org/articles/PMC9494196?pdf=render"
   },
-  {
-    "id": "39169209",
-    "doi": "https://doi.org/10.1038/s43856-024-00590-z",
-    "title": "Predicting 1, 2 and 3 year emergent referable diabetic retinopathy and maculopathy using deep learning.",
-    "authorString": "Nderitu P, Nunez do Rio JM, Webster L, Mann S, Cardoso MJ, Modat M, Hopkins D, Bergeles C, Jackson TL.",
-    "authorAffiliations": "",
-    "journalTitle": "Communications medicine",
-    "pubYear": "2024",
-    "date": "2024-08-21",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Predicting diabetic retinopathy (DR) progression could enable individualised screening with prompt referral for high-risk individuals for sight-saving treatment, whilst reducing screening burden for low-risk individuals. We developed and validated deep learning systems (DLS) that predict 1, 2 and 3 year emergent referable DR and maculopathy using risk factor characteristics (tabular DLS), colour fundal photographs (image DLS) or both (multimodal DLS).<h4>Methods</h4>From 162,339 development-set eyes from south-east London (UK) diabetic eye screening programme (DESP), 110,837 had eligible longitudinal data, with the remaining 51,502 used for pretraining. Internal and external (Birmingham DESP, UK) test datasets included 27,996, and 6928 eyes respectively.<h4>Results</h4>Internal multimodal DLS emergent referable DR, maculopathy or either area-under-the receiver operating characteristic (AUROC) were 0.95 (95% CI: 0.92-0.98), 0.84 (0.82-0.86), 0.85 (0.83-0.87) for 1 year, 0.92 (0.87-0.96), 0.84 (0.82-0.87), 0.85 (0.82-0.87) for 2 years, and 0.85 (0.80-0.90), 0.79 (0.76-0.82), 0.79 (0.76-0.82) for 3 years. External multimodal DLS emergent referable DR, maculopathy or either AUROC were 0.93 (0.88-0.97), 0.85 (0.80-0.89), 0.85 (0.76-0.85) for 1 year, 0.93 (0.89-0.97), 0.79 (0.74-0.84), 0.80 (0.76-0.85) for 2 years, and 0.91 (0.84-0.98), 0.79 (0.74-0.83), 0.79 (0.74-0.84) for 3 years.<h4>Conclusions</h4>Multimodal and image DLS performance is significantly better than tabular DLS at all intervals. DLS accurately predict 1, 2 and 3 year emergent referable DR and referable maculopathy using colour fundal photographs, with additional risk factor characteristics conferring improvements in prognostic performance. Proposed DLS are a step towards individualised risk-based screening, whereby AI-assistance allows high-risk individuals to be closely monitored while reducing screening burden for low-risk individuals.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1038/s43856-024-00590-z; doi:https://doi.org/10.1038/s43856-024-00590-z; html:https://europepmc.org/articles/PMC11339445; pdf:https://europepmc.org/articles/PMC11339445?pdf=render"
-  },
   {
     "id": "37662524",
     "doi": "https://doi.org/10.1016/j.eclinm.2023.102172",
@@ -21368,6 +21385,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.eclinm.2023.102172; html:https://europepmc.org/articles/PMC10474377; pdf:https://europepmc.org/articles/PMC10474377?pdf=render"
   },
+  {
+    "id": "39169209",
+    "doi": "https://doi.org/10.1038/s43856-024-00590-z",
+    "title": "Predicting 1, 2 and 3 year emergent referable diabetic retinopathy and maculopathy using deep learning.",
+    "authorString": "Nderitu P, Nunez do Rio JM, Webster L, Mann S, Cardoso MJ, Modat M, Hopkins D, Bergeles C, Jackson TL.",
+    "authorAffiliations": "",
+    "journalTitle": "Communications medicine",
+    "pubYear": "2024",
+    "date": "2024-08-21",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Predicting diabetic retinopathy (DR) progression could enable individualised screening with prompt referral for high-risk individuals for sight-saving treatment, whilst reducing screening burden for low-risk individuals. We developed and validated deep learning systems (DLS) that predict 1, 2 and 3 year emergent referable DR and maculopathy using risk factor characteristics (tabular DLS), colour fundal photographs (image DLS) or both (multimodal DLS).<h4>Methods</h4>From 162,339 development-set eyes from south-east London (UK) diabetic eye screening programme (DESP), 110,837 had eligible longitudinal data, with the remaining 51,502 used for pretraining. Internal and external (Birmingham DESP, UK) test datasets included 27,996, and 6928 eyes respectively.<h4>Results</h4>Internal multimodal DLS emergent referable DR, maculopathy or either area-under-the receiver operating characteristic (AUROC) were 0.95 (95% CI: 0.92-0.98), 0.84 (0.82-0.86), 0.85 (0.83-0.87) for 1 year, 0.92 (0.87-0.96), 0.84 (0.82-0.87), 0.85 (0.82-0.87) for 2 years, and 0.85 (0.80-0.90), 0.79 (0.76-0.82), 0.79 (0.76-0.82) for 3 years. External multimodal DLS emergent referable DR, maculopathy or either AUROC were 0.93 (0.88-0.97), 0.85 (0.80-0.89), 0.85 (0.76-0.85) for 1 year, 0.93 (0.89-0.97), 0.79 (0.74-0.84), 0.80 (0.76-0.85) for 2 years, and 0.91 (0.84-0.98), 0.79 (0.74-0.83), 0.79 (0.74-0.84) for 3 years.<h4>Conclusions</h4>Multimodal and image DLS performance is significantly better than tabular DLS at all intervals. DLS accurately predict 1, 2 and 3 year emergent referable DR and referable maculopathy using colour fundal photographs, with additional risk factor characteristics conferring improvements in prognostic performance. Proposed DLS are a step towards individualised risk-based screening, whereby AI-assistance allows high-risk individuals to be closely monitored while reducing screening burden for low-risk individuals.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1038/s43856-024-00590-z; doi:https://doi.org/10.1038/s43856-024-00590-z; html:https://europepmc.org/articles/PMC11339445; pdf:https://europepmc.org/articles/PMC11339445?pdf=render"
+  },
   {
     "id": "34798287",
     "doi": "https://doi.org/10.1016/j.jclinepi.2021.11.023",
@@ -21436,23 +21470,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmchealthservres.biomedcentral.com/counter/pdf/10.1186/s12913-019-4286-8; doi:https://doi.org/10.1186/s12913-019-4286-8; html:https://europepmc.org/articles/PMC6720086; pdf:https://europepmc.org/articles/PMC6720086?pdf=render"
   },
-  {
-    "id": "34847088",
-    "doi": "https://doi.org/10.1097/ede.0000000000001429",
-    "title": "The Authors Respond.",
-    "authorString": "Katsoulis M, De Stavola B, Lai AG, Gomes M, Diaz-Ordaz K.",
-    "authorAffiliations": "",
-    "journalTitle": "Epidemiology (Cambridge, Mass.)",
-    "pubYear": "2022",
-    "date": "2022-01-01",
-    "isOpenAccess": "N",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "",
-    "urls": "html:https://journals.lww.com/epidem/Fulltext/2022/01000/The_Authors_Respond.22.aspx; doi:https://doi.org/10.1097/EDE.0000000000001429"
-  },
   {
     "id": "32908284",
     "doi": "https://doi.org/10.1038/s41591-020-1037-7",
@@ -21470,6 +21487,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41591-020-1037-7.pdf; doi:https://doi.org/10.1038/s41591-020-1037-7; html:https://europepmc.org/articles/PMC7598944; pdf:https://europepmc.org/articles/PMC7598944?pdf=render"
   },
+  {
+    "id": "34847088",
+    "doi": "https://doi.org/10.1097/ede.0000000000001429",
+    "title": "The Authors Respond.",
+    "authorString": "Katsoulis M, De Stavola B, Lai AG, Gomes M, Diaz-Ordaz K.",
+    "authorAffiliations": "",
+    "journalTitle": "Epidemiology (Cambridge, Mass.)",
+    "pubYear": "2022",
+    "date": "2022-01-01",
+    "isOpenAccess": "N",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "",
+    "laySummary": "",
+    "urls": "html:https://journals.lww.com/epidem/Fulltext/2022/01000/The_Authors_Respond.22.aspx; doi:https://doi.org/10.1097/EDE.0000000000001429"
+  },
   {
     "id": "32908283",
     "doi": "https://doi.org/10.1038/s41591-020-1034-x",
@@ -21640,23 +21674,6 @@
     "laySummary": "",
     "urls": "pdf:https://medinform.jmir.org/2022/12/e41200/PDF; doi:https://doi.org/10.2196/41200; html:https://europepmc.org/articles/PMC9812268"
   },
-  {
-    "id": "37951941",
-    "doi": "https://doi.org/10.1186/s12920-023-01710-9",
-    "title": "A phenome-wide approach to identify causal risk factors for deep vein thrombosis.",
-    "authorString": "Constantinescu AE, Bull CJ, Goudswaard LJ, Zheng J, Elsworth B, Timpson NJ, Moore SF, Hers I, Vincent EE.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC medical genomics",
-    "pubYear": "2023",
-    "date": "2023-11-11",
-    "isOpenAccess": "Y",
-    "keywords": "Deep vein thrombosis; Alspac; Genome-wide Association Study; Mendelian Randomization; Protein Quantitative Trait Loci",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Deep vein thrombosis (DVT) is the formation of a blood clot in a deep vein. DVT can lead to a venous thromboembolism (VTE), the combined term for DVT and pulmonary embolism, a leading cause of death and disability worldwide. Despite the prevalence and associated morbidity of DVT, the underlying causes are not well understood. Our aim was to leverage publicly available genetic summary association statistics to identify causal risk factors for DVT. We conducted a Mendelian randomization phenome-wide association study (MR-PheWAS) using genetic summary association statistics for 973 exposures and DVT (6,767 cases and 330,392 controls in UK Biobank). There was evidence for a causal effect of 57 exposures on DVT risk, including previously reported risk factors (e.g. body mass index-BMI and height) and novel risk factors (e.g. hyperthyroidism and varicose veins). As the majority of identified risk factors were adiposity-related, we explored the molecular link with DVT by undertaking a two-sample MR mediation analysis of BMI-associated circulating proteins on DVT risk. Our results indicate that circulating neurogenic locus notch homolog protein 1 (NOTCH1), inhibin beta C chain (INHBC) and plasminogen activator inhibitor 1 (PAI-1) influence DVT risk, with PAI-1 mediating the BMI-DVT relationship. Using a phenome-wide approach, we provide putative causal evidence that hyperthyroidism, varicose veins and BMI enhance the risk of DVT. Furthermore, the circulating protein PAI-1 has a causal role in DVT aetiology and is involved in mediating the BMI-DVT relationship.",
-    "laySummary": "",
-    "urls": "pdf:https://bmcmedgenomics.biomedcentral.com/counter/pdf/10.1186/s12920-023-01710-9; doi:https://doi.org/10.1186/s12920-023-01710-9; html:https://europepmc.org/articles/PMC10640748; pdf:https://europepmc.org/articles/PMC10640748?pdf=render"
-  },
   {
     "id": "31442537",
     "doi": "https://doi.org/10.1016/j.jaad.2019.08.039",
@@ -21675,21 +21692,21 @@
     "urls": "pdf:http://www.jaad.org/article/S0190962219326143/pdf; doi:https://doi.org/10.1016/j.jaad.2019.08.039; html:https://europepmc.org/articles/PMC7704103; pdf:https://europepmc.org/articles/PMC7704103?pdf=render"
   },
   {
-    "id": "35921096",
-    "doi": "https://doi.org/10.1001/jamacardio.2022.2333",
-    "title": "Joint Genetic Inhibition of PCSK9 and CETP and the Association With Coronary Artery Disease: A Factorial Mendelian Randomization Study.",
-    "authorString": "Cupido AJ, Reeskamp LF, Hingorani AD, Finan C, Asselbergs FW, Hovingh GK, Schmidt AF.",
+    "id": "37951941",
+    "doi": "https://doi.org/10.1186/s12920-023-01710-9",
+    "title": "A phenome-wide approach to identify causal risk factors for deep vein thrombosis.",
+    "authorString": "Constantinescu AE, Bull CJ, Goudswaard LJ, Zheng J, Elsworth B, Timpson NJ, Moore SF, Hers I, Vincent EE.",
     "authorAffiliations": "",
-    "journalTitle": "JAMA cardiology",
-    "pubYear": "2022",
-    "date": "2022-09-01",
-    "isOpenAccess": "N",
-    "keywords": "",
+    "journalTitle": "BMC medical genomics",
+    "pubYear": "2023",
+    "date": "2023-11-11",
+    "isOpenAccess": "Y",
+    "keywords": "Deep vein thrombosis; Alspac; Genome-wide Association Study; Mendelian Randomization; Protein Quantitative Trait Loci",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Importance</h4>Cholesteryl ester transfer protein inhibition (CETP) has been shown to increase levels of high-density lipoprotein cholesterol (HDL-C) and reduce levels of low-density lipoprotein cholesterol (LDL-C). Current LDL-C target attainment is low, and novel phase 3 trials are underway to investigate whether CETP inhibitors result in reduction of cardiovascular disease risk in high-risk patients who may be treated with PCSK9-inhibiting agents.<h4>Objective</h4>To explore the associations of combined reduction of CETP and PCSK9 concentrations with risk of coronary artery disease (CAD) and other clinical and safety outcomes.<h4>Design, setting, and participants</h4>Two-sample 2\u2009\u00d7\u20092 factorial Mendelian randomization study in a general population sample that includes data for UK Biobank participants of European ancestry.<h4>Exposures</h4>Separate genetic scores were constructed for CETP and PCSK9 plasma protein concentrations, which were combined to determine the associations of combined genetically reduced CETP and PCSK9 concentrations with disease.<h4>Main outcomes and measures</h4>Blood lipid and lipoprotein concentrations, blood pressure, CAD, age-related macular degeneration, type 2 diabetes, any stroke and ischemic stroke, Alzheimer disease, vascular dementia, heart failure, atrial fibrillation, chronic kidney disease, asthma, and multiple sclerosis.<h4>Results</h4>Data for 425\u202f354 UKB participants were included; the median (IQR) age was 59 years (51-64), and 229\u202f399 (53.9%) were female. The associations of lower CETP and lower PCSK9 concentrations with CAD are similar when scaled per 10-mg/dL reduction in LDL-C concentrations (CETP: odds ratio [OR], 0.74; 95% CI, 0.67 to 0.81; PCSK9: OR, 0.75; 95% CI, 0.71 to 0.79). Combined exposure to lower CETP and PCSK9 concentrations was associated with an additive magnitude with lipids and all outcomes, and we did not observe any nonadditive interactions, most notably for LDL-C (CETP: effect size, -1.11 mg/dL; 95% CI, -1.40 to -0.82; PCSK9: effect size, -2.13 mg/dL; 95% CI, -2.43 to -1.84; combined: effect size, -3.47 mg/dL; 95% CI, -3.76 to -3.18; P\u2009=\u2009.34 for interaction) and CAD (CETP: OR, 0.96; 95% CI, 0.94 to 1.00; PCSK9: OR, 0.94; 95% CI, 0.91 to 0.97; combined: OR, 0.90; 95% CI, 0.87 to 0.93; P\u2009=\u2009.83 for interaction). In addition, when corrected for multiple testing, lower CETP concentrations were associated with increased age-related macular degeneration (OR, 1.11; 95% CI, 1.04 to 1.19).<h4>Conclusions and relevance</h4>Our results suggest that joint inhibition of CETP and PCSK9 has additive effects on lipid traits and disease risk, including a lower risk of CAD. Further research may explore whether a combination of CETP- and PCSK9-related therapeutics can benefit high-risk patients who are unable to reach treatment targets with existing options.",
+    "abstract": "Deep vein thrombosis (DVT) is the formation of a blood clot in a deep vein. DVT can lead to a venous thromboembolism (VTE), the combined term for DVT and pulmonary embolism, a leading cause of death and disability worldwide. Despite the prevalence and associated morbidity of DVT, the underlying causes are not well understood. Our aim was to leverage publicly available genetic summary association statistics to identify causal risk factors for DVT. We conducted a Mendelian randomization phenome-wide association study (MR-PheWAS) using genetic summary association statistics for 973 exposures and DVT (6,767 cases and 330,392 controls in UK Biobank). There was evidence for a causal effect of 57 exposures on DVT risk, including previously reported risk factors (e.g. body mass index-BMI and height) and novel risk factors (e.g. hyperthyroidism and varicose veins). As the majority of identified risk factors were adiposity-related, we explored the molecular link with DVT by undertaking a two-sample MR mediation analysis of BMI-associated circulating proteins on DVT risk. Our results indicate that circulating neurogenic locus notch homolog protein 1 (NOTCH1), inhibin beta C chain (INHBC) and plasminogen activator inhibitor 1 (PAI-1) influence DVT risk, with PAI-1 mediating the BMI-DVT relationship. Using a phenome-wide approach, we provide putative causal evidence that hyperthyroidism, varicose veins and BMI enhance the risk of DVT. Furthermore, the circulating protein PAI-1 has a causal role in DVT aetiology and is involved in mediating the BMI-DVT relationship.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1001/jamacardio.2022.2333; html:https://europepmc.org/articles/PMC9350849; doi:https://doi.org/10.1001/jamacardio.2022.2333"
+    "urls": "pdf:https://bmcmedgenomics.biomedcentral.com/counter/pdf/10.1186/s12920-023-01710-9; doi:https://doi.org/10.1186/s12920-023-01710-9; html:https://europepmc.org/articles/PMC10640748; pdf:https://europepmc.org/articles/PMC10640748?pdf=render"
   },
   {
     "id": "37456658",
@@ -21708,6 +21725,23 @@
     "laySummary": "",
     "urls": "pdf:https://hrbopenresearch.org/articles/6-10/pdf; doi:https://doi.org/10.12688/hrbopenres.13667.1; html:https://europepmc.org/articles/PMC10345597; pdf:https://europepmc.org/articles/PMC10345597?pdf=render"
   },
+  {
+    "id": "35921096",
+    "doi": "https://doi.org/10.1001/jamacardio.2022.2333",
+    "title": "Joint Genetic Inhibition of PCSK9 and CETP and the Association With Coronary Artery Disease: A Factorial Mendelian Randomization Study.",
+    "authorString": "Cupido AJ, Reeskamp LF, Hingorani AD, Finan C, Asselbergs FW, Hovingh GK, Schmidt AF.",
+    "authorAffiliations": "",
+    "journalTitle": "JAMA cardiology",
+    "pubYear": "2022",
+    "date": "2022-09-01",
+    "isOpenAccess": "N",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Importance</h4>Cholesteryl ester transfer protein inhibition (CETP) has been shown to increase levels of high-density lipoprotein cholesterol (HDL-C) and reduce levels of low-density lipoprotein cholesterol (LDL-C). Current LDL-C target attainment is low, and novel phase 3 trials are underway to investigate whether CETP inhibitors result in reduction of cardiovascular disease risk in high-risk patients who may be treated with PCSK9-inhibiting agents.<h4>Objective</h4>To explore the associations of combined reduction of CETP and PCSK9 concentrations with risk of coronary artery disease (CAD) and other clinical and safety outcomes.<h4>Design, setting, and participants</h4>Two-sample 2\u2009\u00d7\u20092 factorial Mendelian randomization study in a general population sample that includes data for UK Biobank participants of European ancestry.<h4>Exposures</h4>Separate genetic scores were constructed for CETP and PCSK9 plasma protein concentrations, which were combined to determine the associations of combined genetically reduced CETP and PCSK9 concentrations with disease.<h4>Main outcomes and measures</h4>Blood lipid and lipoprotein concentrations, blood pressure, CAD, age-related macular degeneration, type 2 diabetes, any stroke and ischemic stroke, Alzheimer disease, vascular dementia, heart failure, atrial fibrillation, chronic kidney disease, asthma, and multiple sclerosis.<h4>Results</h4>Data for 425\u202f354 UKB participants were included; the median (IQR) age was 59 years (51-64), and 229\u202f399 (53.9%) were female. The associations of lower CETP and lower PCSK9 concentrations with CAD are similar when scaled per 10-mg/dL reduction in LDL-C concentrations (CETP: odds ratio [OR], 0.74; 95% CI, 0.67 to 0.81; PCSK9: OR, 0.75; 95% CI, 0.71 to 0.79). Combined exposure to lower CETP and PCSK9 concentrations was associated with an additive magnitude with lipids and all outcomes, and we did not observe any nonadditive interactions, most notably for LDL-C (CETP: effect size, -1.11 mg/dL; 95% CI, -1.40 to -0.82; PCSK9: effect size, -2.13 mg/dL; 95% CI, -2.43 to -1.84; combined: effect size, -3.47 mg/dL; 95% CI, -3.76 to -3.18; P\u2009=\u2009.34 for interaction) and CAD (CETP: OR, 0.96; 95% CI, 0.94 to 1.00; PCSK9: OR, 0.94; 95% CI, 0.91 to 0.97; combined: OR, 0.90; 95% CI, 0.87 to 0.93; P\u2009=\u2009.83 for interaction). In addition, when corrected for multiple testing, lower CETP concentrations were associated with increased age-related macular degeneration (OR, 1.11; 95% CI, 1.04 to 1.19).<h4>Conclusions and relevance</h4>Our results suggest that joint inhibition of CETP and PCSK9 has additive effects on lipid traits and disease risk, including a lower risk of CAD. Further research may explore whether a combination of CETP- and PCSK9-related therapeutics can benefit high-risk patients who are unable to reach treatment targets with existing options.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1001/jamacardio.2022.2333; html:https://europepmc.org/articles/PMC9350849; doi:https://doi.org/10.1001/jamacardio.2022.2333"
+  },
   {
     "id": "33655079",
     "doi": "https://doi.org/10.12688/wellcomeopenres.16304.2",
@@ -21742,23 +21776,6 @@
     "laySummary": "",
     "urls": "pdf:https://cronfa.swan.ac.uk/Record/cronfa56833/Download/56833__19829__9b0bb77f67e84342b525fbccaba98e67.pdf; doi:https://doi.org/10.1080/02640414.2021.1928409"
   },
-  {
-    "id": "38965219",
-    "doi": "https://doi.org/10.1038/s41398-024-02997-7",
-    "title": "Vitamin D, chronic pain, and depression: linear and non-linear Mendelian randomization analyses.",
-    "authorString": "Bassett E, Gjekmarkaj E, Mason AM, Zhao SS, Burgess S.",
-    "authorAffiliations": "",
-    "journalTitle": "Translational psychiatry",
-    "pubYear": "2024",
-    "date": "2024-07-04",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Vitamin D deficiency has been linked to various chronic pain conditions. However, randomized trials of vitamin D supplementation have had mixed results. In contrast, systematic reviews of randomized trials indicate a protective effect of vitamin D supplementation on depression. We undertake a Mendelian randomization investigation in UK Biobank, a study of UK residents aged 40-65 at recruitment. We perform linear and non-linear Mendelian randomization analyses for four outcomes: fibromyalgia, clinical fatigue, chronic widespread pain, and probable lifetime major depression. We use genetic variants from four gene regions with known links to vitamin D biology as instruments. In linear analyses, genetically-predicted levels of 25-hydroxyvitamin D [25(OH)D], a clinical marker of vitamin D status, were not associated with fibromyalgia (odds ratio [OR] per 10 nmol/L higher 25(OH)D 1.02, 95% confidence interval [CI] 0.93, 1.12), clinical fatigue (OR 0.99, 95% CI 0.94, 1.05), chronic widespread pain (OR 0.95, 95% CI 0.89, 1.02), or probable lifetime major depression (OR 0.97, 95% CI 0.93, 1.01). In non-linear analyses, an association was observed between genetically-predicted 25(OH)D levels and depression in the quintile of the population with the lowest 25(OH)D levels (OR 0.75, 95% CI 0.59, 0.94); associations were null in other strata. Our findings suggest that population-wide vitamin D supplementation will not substantially reduce pain or depression; however, targeted supplementation of deficient individuals may reduce risk of depression.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1038/s41398-024-02997-7; html:https://europepmc.org/articles/PMC11224391; pdf:https://europepmc.org/articles/PMC11224391?pdf=render"
-  },
   {
     "id": "36864090",
     "doi": "https://doi.org/10.1038/s41598-023-30369-6",
@@ -21776,6 +21793,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41598-023-30369-6.pdf; doi:https://doi.org/10.1038/s41598-023-30369-6; html:https://europepmc.org/articles/PMC9981672; pdf:https://europepmc.org/articles/PMC9981672?pdf=render"
   },
+  {
+    "id": "38965219",
+    "doi": "https://doi.org/10.1038/s41398-024-02997-7",
+    "title": "Vitamin D, chronic pain, and depression: linear and non-linear Mendelian randomization analyses.",
+    "authorString": "Bassett E, Gjekmarkaj E, Mason AM, Zhao SS, Burgess S.",
+    "authorAffiliations": "",
+    "journalTitle": "Translational psychiatry",
+    "pubYear": "2024",
+    "date": "2024-07-04",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Vitamin D deficiency has been linked to various chronic pain conditions. However, randomized trials of vitamin D supplementation have had mixed results. In contrast, systematic reviews of randomized trials indicate a protective effect of vitamin D supplementation on depression. We undertake a Mendelian randomization investigation in UK Biobank, a study of UK residents aged 40-65 at recruitment. We perform linear and non-linear Mendelian randomization analyses for four outcomes: fibromyalgia, clinical fatigue, chronic widespread pain, and probable lifetime major depression. We use genetic variants from four gene regions with known links to vitamin D biology as instruments. In linear analyses, genetically-predicted levels of 25-hydroxyvitamin D [25(OH)D], a clinical marker of vitamin D status, were not associated with fibromyalgia (odds ratio [OR] per 10 nmol/L higher 25(OH)D 1.02, 95% confidence interval [CI] 0.93, 1.12), clinical fatigue (OR 0.99, 95% CI 0.94, 1.05), chronic widespread pain (OR 0.95, 95% CI 0.89, 1.02), or probable lifetime major depression (OR 0.97, 95% CI 0.93, 1.01). In non-linear analyses, an association was observed between genetically-predicted 25(OH)D levels and depression in the quintile of the population with the lowest 25(OH)D levels (OR 0.75, 95% CI 0.59, 0.94); associations were null in other strata. Our findings suggest that population-wide vitamin D supplementation will not substantially reduce pain or depression; however, targeted supplementation of deficient individuals may reduce risk of depression.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1038/s41398-024-02997-7; html:https://europepmc.org/articles/PMC11224391; pdf:https://europepmc.org/articles/PMC11224391?pdf=render"
+  },
   {
     "id": "34939031",
     "doi": "https://doi.org/10.1093/braincomms/fcab241",
@@ -21912,23 +21946,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41598-022-16639-9.pdf; doi:https://doi.org/10.1038/s41598-022-16639-9; html:https://europepmc.org/articles/PMC9329281; pdf:https://europepmc.org/articles/PMC9329281?pdf=render"
   },
-  {
-    "id": "34427560",
-    "doi": "https://doi.org/10.1684/ejd.2021.4108",
-    "title": "The association between immunosuppression and skin cancer in solid organ transplant recipients: a control-matched cohort study of 2,852 patients.",
-    "authorString": "Gibson JAG, Cordaro A, Dobbs TD, Griffiths R, Akbari A, Whitaker S, Hutchings HA, Lyons RA, Whitaker IS.",
-    "authorAffiliations": "",
-    "journalTitle": "European journal of dermatology : EJD",
-    "pubYear": "2021",
-    "date": "2021-12-01",
-    "isOpenAccess": "N",
-    "keywords": "Transplant; Oncology; immunosuppression; Skin Cancer",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Skin cancer is more common in transplant recipients, although the quoted incidence is variable. This study investigated the incidence of skin cancer in solid organ transplant recipients (OTRs) in a national cohort and the effect of pharmacotherapeutic agents Transplant patients were identified from Patient Episode Database for Wales (PEDW) using Office of Population Census and Surveys Classifications of Interventions and Procedures-4 (OPCS-4) codes. Controls were matched to cases according to age, sex and socioeconomic status. Skin cancer data were obtained from linkage with other national data sources. Incidence was calculated per 100,000 person-years at risk (PYAR). Negative binomial regression was used to calculate adjusted incidence rate ratios (IRRs) for each organ type. During 2000-2018, 2,852 Welsh patients underwent solid organ transplantation. A total of 13,527 controls were matched from the general population. The incidence of skin cancer within the OTR cohort was 1203.2 per 100,000 PYAR vs 133.9 in the matched control group. Age, male gender and azathioprine use were all associated with an increased risk of skin cancer. Contemporary immunomodulators such as tacrolimus and mycophenolate were associated with a reduction in skin cancer risk when compared to their predecessors, cyclosporin and azathioprine. The highest adjusted IRR was observed in heart transplant recipients (IRR: 10.82; 95%\u00a0CI: 3.64-32.19) and the lowest in liver transplant recipients (IRR: 2.86; 95%\u00a0CI: 1.15-7.13). This study highlights the need for long-term routine skin cancer surveillance for all OTRs and the importance of using contemporary immunomodulators, when possible, for risk reduction.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1684/ejd.2021.4108"
-  },
   {
     "id": "32771960",
     "doi": "https://doi.org/10.1016/j.ijmedinf.2020.104237",
@@ -21947,21 +21964,21 @@
     "urls": "doi:https://doi.org/10.1016/j.ijmedinf.2020.104237"
   },
   {
-    "id": "34435642",
-    "doi": "https://doi.org/10.1093/eurheartj/ehab350",
-    "title": "Evidence to support magnetic resonance conditional labelling of all pacemaker and defibrillator leads in patients with cardiac implantable electronic devices.",
-    "authorString": "Bhuva AN, Moralee R, Brunker T, Lascelles K, Cash L, Patel KP, Lowe M, Sekhri N, Alpendurada F, Pennell DJ, Schilling R, Lambiase PD, Chow A, Moon JC, Litt H, Baksi AJ, Manisty CH.",
+    "id": "34427560",
+    "doi": "https://doi.org/10.1684/ejd.2021.4108",
+    "title": "The association between immunosuppression and skin cancer in solid organ transplant recipients: a control-matched cohort study of 2,852 patients.",
+    "authorString": "Gibson JAG, Cordaro A, Dobbs TD, Griffiths R, Akbari A, Whitaker S, Hutchings HA, Lyons RA, Whitaker IS.",
     "authorAffiliations": "",
-    "journalTitle": "European heart journal",
-    "pubYear": "2022",
-    "date": "2022-07-01",
-    "isOpenAccess": "Y",
-    "keywords": "Pacemaker; Magnetic Resonance Imaging; Defibrillator",
+    "journalTitle": "European journal of dermatology : EJD",
+    "pubYear": "2021",
+    "date": "2021-12-01",
+    "isOpenAccess": "N",
+    "keywords": "Transplant; Oncology; immunosuppression; Skin Cancer",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Aims</h4>Many cardiac pacemakers and defibrillators are not approved by regulators for magnetic resonance imaging (MRI). Even following generator exchange to an approved magnetic resonance (MR)-conditional model, many systems remain classified 'non-MR conditional' due to the leads. This classification makes patient access to MRI challenging, but there is no evidence of increased clinical risk. We compared the effect of MRI on non-MR conditional and MR-conditional pacemaker and defibrillator leads.<h4>Methods and results</h4>Patients undergoing clinical 1.5T MRI with pacemakers and defibrillators in three centres over 5 years were included. Magnetic resonance imaging protocols were similar for MR-conditional and non-MR conditional systems. Devices were interrogated pre- and immediately post-scan, and at follow-up, and adverse clinical events recorded. Lead parameter changes peri-scan were stratified by MR-conditional labelling. A total of 1148 MRI examinations were performed in 970 patients (54% non-MR conditional systems, 39% defibrillators, 15% pacing-dependent) with 2268 leads. There were no lead-related adverse clinical events, and no clinically significant immediate or late lead parameter changes following MRI in either MR-conditional or non-MR conditional leads. Small reductions in atrial and right ventricular sensed amplitudes and impedances were similar between groups, with no difference in the proportion of leads with parameter changes greater than pre-defined thresholds (7.1%, 95% confidence interval: 6.1-8.3).<h4>Conclusions</h4>There was no increased risk of MRI in patients with non-MR conditional pacemaker or defibrillator leads when following recommended protocols. Standardizing MR conditions for all leads would significantly improve access to MRI by enabling patients to be scanned in non-specialist centres, with no discernible incremental risk.",
+    "abstract": "Skin cancer is more common in transplant recipients, although the quoted incidence is variable. This study investigated the incidence of skin cancer in solid organ transplant recipients (OTRs) in a national cohort and the effect of pharmacotherapeutic agents Transplant patients were identified from Patient Episode Database for Wales (PEDW) using Office of Population Census and Surveys Classifications of Interventions and Procedures-4 (OPCS-4) codes. Controls were matched to cases according to age, sex and socioeconomic status. Skin cancer data were obtained from linkage with other national data sources. Incidence was calculated per 100,000 person-years at risk (PYAR). Negative binomial regression was used to calculate adjusted incidence rate ratios (IRRs) for each organ type. During 2000-2018, 2,852 Welsh patients underwent solid organ transplantation. A total of 13,527 controls were matched from the general population. The incidence of skin cancer within the OTR cohort was 1203.2 per 100,000 PYAR vs 133.9 in the matched control group. Age, male gender and azathioprine use were all associated with an increased risk of skin cancer. Contemporary immunomodulators such as tacrolimus and mycophenolate were associated with a reduction in skin cancer risk when compared to their predecessors, cyclosporin and azathioprine. The highest adjusted IRR was observed in heart transplant recipients (IRR: 10.82; 95%\u00a0CI: 3.64-32.19) and the lowest in liver transplant recipients (IRR: 2.86; 95%\u00a0CI: 1.15-7.13). This study highlights the need for long-term routine skin cancer surveillance for all OTRs and the importance of using contemporary immunomodulators, when possible, for risk reduction.",
     "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/eurheartj/advance-article-pdf/doi/10.1093/eurheartj/ehab350/39932149/ehab350.pdf; doi:https://doi.org/10.1093/eurheartj/ehab350; html:https://europepmc.org/articles/PMC9259370; pdf:https://europepmc.org/articles/PMC9259370?pdf=render"
+    "urls": "doi:https://doi.org/10.1684/ejd.2021.4108"
   },
   {
     "id": "35151869",
@@ -21980,6 +21997,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.jbi.2022.104010; doi:https://doi.org/10.1016/j.jbi.2022.104010; html:https://europepmc.org/articles/PMC8894882"
   },
+  {
+    "id": "34435642",
+    "doi": "https://doi.org/10.1093/eurheartj/ehab350",
+    "title": "Evidence to support magnetic resonance conditional labelling of all pacemaker and defibrillator leads in patients with cardiac implantable electronic devices.",
+    "authorString": "Bhuva AN, Moralee R, Brunker T, Lascelles K, Cash L, Patel KP, Lowe M, Sekhri N, Alpendurada F, Pennell DJ, Schilling R, Lambiase PD, Chow A, Moon JC, Litt H, Baksi AJ, Manisty CH.",
+    "authorAffiliations": "",
+    "journalTitle": "European heart journal",
+    "pubYear": "2022",
+    "date": "2022-07-01",
+    "isOpenAccess": "Y",
+    "keywords": "Pacemaker; Magnetic Resonance Imaging; Defibrillator",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Aims</h4>Many cardiac pacemakers and defibrillators are not approved by regulators for magnetic resonance imaging (MRI). Even following generator exchange to an approved magnetic resonance (MR)-conditional model, many systems remain classified 'non-MR conditional' due to the leads. This classification makes patient access to MRI challenging, but there is no evidence of increased clinical risk. We compared the effect of MRI on non-MR conditional and MR-conditional pacemaker and defibrillator leads.<h4>Methods and results</h4>Patients undergoing clinical 1.5T MRI with pacemakers and defibrillators in three centres over 5 years were included. Magnetic resonance imaging protocols were similar for MR-conditional and non-MR conditional systems. Devices were interrogated pre- and immediately post-scan, and at follow-up, and adverse clinical events recorded. Lead parameter changes peri-scan were stratified by MR-conditional labelling. A total of 1148 MRI examinations were performed in 970 patients (54% non-MR conditional systems, 39% defibrillators, 15% pacing-dependent) with 2268 leads. There were no lead-related adverse clinical events, and no clinically significant immediate or late lead parameter changes following MRI in either MR-conditional or non-MR conditional leads. Small reductions in atrial and right ventricular sensed amplitudes and impedances were similar between groups, with no difference in the proportion of leads with parameter changes greater than pre-defined thresholds (7.1%, 95% confidence interval: 6.1-8.3).<h4>Conclusions</h4>There was no increased risk of MRI in patients with non-MR conditional pacemaker or defibrillator leads when following recommended protocols. Standardizing MR conditions for all leads would significantly improve access to MRI by enabling patients to be scanned in non-specialist centres, with no discernible incremental risk.",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/eurheartj/advance-article-pdf/doi/10.1093/eurheartj/ehab350/39932149/ehab350.pdf; doi:https://doi.org/10.1093/eurheartj/ehab350; html:https://europepmc.org/articles/PMC9259370; pdf:https://europepmc.org/articles/PMC9259370?pdf=render"
+  },
   {
     "id": "33707775",
     "doi": "https://doi.org/10.1038/s41591-021-01266-0",
@@ -21997,23 +22031,6 @@
     "laySummary": "",
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8127079; doi:https://doi.org/10.1038/s41591-021-01266-0; html:https://europepmc.org/articles/PMC8127079; pdf:https://europepmc.org/articles/PMC8127079?pdf=render; doi:https://doi.org/10.1038/s41591-021-01266-0"
   },
-  {
-    "id": "38450564",
-    "doi": "https://doi.org/10.1089/neu.2023.0462",
-    "title": "The Australian Traumatic Brain Injury Initiative: Systematic Review and Consensus Process to Determine the Predictive Value of Pre-existing Health Conditions for People with Moderate-Severe Traumatic Brain Injury.",
-    "authorString": "Antonic-Baker A, Auvrez C, Tao G, Bagg MK, Gadowski A, McKimmie A, Hicks AJ, Hill R, Romero L, Ponsford JL, Lannin NA, Gabbe BJ, Cameron PA, Cooper DJ, Rushworth N, Fitzgerald M, O'Brien TJ.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of neurotrauma",
-    "pubYear": "2024",
-    "date": "2024-04-15",
-    "isOpenAccess": "N",
-    "keywords": "Health care; Mental health; Comorbidity; Common Data Elements; Multiple Chronic Conditions; Brain Injuries, Traumatic; Outcome Assessment, Systematic Review [Publication Type]",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The first aim of the Australian Traumatic Brain Injury Initiative (AUS-TBI) encompasses development of a set of measures that comprehensively predict outcomes for people with moderate-severe TBI across Australia. This process engaged diverse stakeholders and information sources across six areas: social, health, and clinical factors; biological markers; treatments; and longer-term outcomes. Here, we report the systematic review of pre-existing health conditions as predictors of outcome for people with moderate-severe TBI. Standardized searches were implemented across databases until March 31, 2022. English-language reports of studies evaluating association between pre-existing health conditions and clinical outcome in at least 10 patients with moderate-severe TBI were included. A predefined algorithm was used to assign a judgement of predictive value to each observed association. The list of identified pre-existing health conditions was then discussed with key stakeholders during a consensus meeting to determine the feasibility of incorporating them into standard care. The searches retrieved 22,217 records, of which 47 articles were included. The process led to identification of 88 unique health predictors (homologized to 21 predictor categories) of 55 outcomes (homologized to 19 outcome categories). Only pre-existing health conditions with high and moderate predictive values were discussed during the consensus meeting. Following the consensus meeting, 5 out of 11 were included (migraine, mental health conditions, \u22654 pre-existing health conditions, osteoporosis, and body mass index [BMI]) as common data elements in the AUS-TBI data dictionary. Upon further discussion, 3 additional pre-existing health conditions were included. These are pre-existing heart disease, frailty score, and previous incidence of TBI.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1089/neu.2023.0462"
-  },
   {
     "id": "36936265",
     "doi": "https://doi.org/10.1136/bmjmed-2022-000276",
@@ -22031,6 +22048,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmjmedicine.bmj.com/content/bmjmed/2/1/e000276.full.pdf; doi:https://doi.org/10.1136/bmjmed-2022-000276; html:https://europepmc.org/articles/PMC9951378; pdf:https://europepmc.org/articles/PMC9951378?pdf=render"
   },
+  {
+    "id": "38450564",
+    "doi": "https://doi.org/10.1089/neu.2023.0462",
+    "title": "The Australian Traumatic Brain Injury Initiative: Systematic Review and Consensus Process to Determine the Predictive Value of Pre-existing Health Conditions for People with Moderate-Severe Traumatic Brain Injury.",
+    "authorString": "Antonic-Baker A, Auvrez C, Tao G, Bagg MK, Gadowski A, McKimmie A, Hicks AJ, Hill R, Romero L, Ponsford JL, Lannin NA, Gabbe BJ, Cameron PA, Cooper DJ, Rushworth N, Fitzgerald M, O'Brien TJ.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of neurotrauma",
+    "pubYear": "2024",
+    "date": "2024-04-15",
+    "isOpenAccess": "N",
+    "keywords": "Health care; Mental health; Comorbidity; Common Data Elements; Multiple Chronic Conditions; Brain Injuries, Traumatic; Outcome Assessment, Systematic Review [Publication Type]",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The first aim of the Australian Traumatic Brain Injury Initiative (AUS-TBI) encompasses development of a set of measures that comprehensively predict outcomes for people with moderate-severe TBI across Australia. This process engaged diverse stakeholders and information sources across six areas: social, health, and clinical factors; biological markers; treatments; and longer-term outcomes. Here, we report the systematic review of pre-existing health conditions as predictors of outcome for people with moderate-severe TBI. Standardized searches were implemented across databases until March 31, 2022. English-language reports of studies evaluating association between pre-existing health conditions and clinical outcome in at least 10 patients with moderate-severe TBI were included. A predefined algorithm was used to assign a judgement of predictive value to each observed association. The list of identified pre-existing health conditions was then discussed with key stakeholders during a consensus meeting to determine the feasibility of incorporating them into standard care. The searches retrieved 22,217 records, of which 47 articles were included. The process led to identification of 88 unique health predictors (homologized to 21 predictor categories) of 55 outcomes (homologized to 19 outcome categories). Only pre-existing health conditions with high and moderate predictive values were discussed during the consensus meeting. Following the consensus meeting, 5 out of 11 were included (migraine, mental health conditions, \u22654 pre-existing health conditions, osteoporosis, and body mass index [BMI]) as common data elements in the AUS-TBI data dictionary. Upon further discussion, 3 additional pre-existing health conditions were included. These are pre-existing heart disease, frailty score, and previous incidence of TBI.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1089/neu.2023.0462"
+  },
   {
     "id": "33328049",
     "doi": "https://doi.org/10.1016/s2589-7500(20)30219-3",
@@ -22065,6 +22099,23 @@
     "laySummary": "",
     "urls": "pdf:http://www.thelancet.com/article/S2589750020303174/pdf; doi:https://doi.org/10.1016/S2589-7500(20)30317-4"
   },
+  {
+    "id": "32065794",
+    "doi": "https://doi.org/10.3233/jad-191163",
+    "title": "Working Towards a Blood-Derived Gene Expression Biomarker Specific for Alzheimer's Disease.",
+    "authorString": "Patel H, Iniesta R, Stahl D, Dobson RJB, Newhouse SJ.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of Alzheimer's disease : JAD",
+    "pubYear": "2020",
+    "date": "2020-01-01",
+    "isOpenAccess": "Y",
+    "keywords": "Human; Biomarkers; Alzheimer\u2019s disease; Dementia; Gene Expression; Neurodegenerative Disorders; Machine Learning; Microarray Analysis; Age-related Memory Disorders",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>The typical approach to identify blood-derived gene expression signatures as a biomarker for Alzheimer's disease (AD) have relied on training classification models using AD and healthy controls only. This may inadvertently result in the identification of markers for general illness rather than being disease-specific.<h4>Objective</h4>Investigate whether incorporating additional related disorders in the classification model development process can lead to the discovery of an AD-specific gene expression signature.<h4>Methods</h4>Two types of XGBoost classification models were developed. The first used 160 AD and 127 healthy controls and the second used the same 160 AD with 6,318 upsampled mixed controls consisting of Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis, bipolar disorder, schizophrenia, coronary artery disease, rheumatoid arthritis, chronic obstructive pulmonary disease, and cognitively healthy subjects. Both classification models were evaluated in an independent cohort consisting of 127 AD and 687 mixed controls.<h4>Results</h4>The AD versus healthy control models resulted in an average 48.7% sensitivity (95% CI\u200a=\u200a34.7-64.6), 41.9% specificity (95% CI\u200a=\u200a26.8-54.3), 13.6% PPV (95% CI\u200a=\u200a9.9-18.5), and 81.1% NPV (95% CI\u200a=\u200a73.3-87.7). In contrast, the mixed control models resulted in an average of 40.8% sensitivity (95% CI\u200a=\u200a27.5-52.0), 95.3% specificity (95% CI\u200a=\u200a93.3-97.1), 61.4% PPV (95% CI\u200a=\u200a53.8-69.6), and 89.7% NPV (95% CI\u200a=\u200a87.8-91.4).<h4>Conclusions</h4>This early work demonstrates the value of incorporating additional related disorders into the classification model developmental process, which can result in models with improved ability to distinguish AD from a heterogeneous aging population. However, further improvement to the sensitivity of the test is still required.",
+    "laySummary": "",
+    "urls": "pdf:https://content.iospress.com:443/download/journal-of-alzheimers-disease/jad191163?id=journal-of-alzheimers-disease%2Fjad191163; doi:https://doi.org/10.3233/JAD-191163; html:https://europepmc.org/articles/PMC7175937; pdf:https://europepmc.org/articles/PMC7175937?pdf=render"
+  },
   {
     "id": "37440761",
     "doi": "https://doi.org/10.1093/ehjci/jead166",
@@ -22099,23 +22150,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.jtha.2023.07.008"
   },
-  {
-    "id": "32065794",
-    "doi": "https://doi.org/10.3233/jad-191163",
-    "title": "Working Towards a Blood-Derived Gene Expression Biomarker Specific for Alzheimer's Disease.",
-    "authorString": "Patel H, Iniesta R, Stahl D, Dobson RJB, Newhouse SJ.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of Alzheimer's disease : JAD",
-    "pubYear": "2020",
-    "date": "2020-01-01",
-    "isOpenAccess": "Y",
-    "keywords": "Human; Biomarkers; Alzheimer\u2019s disease; Dementia; Gene Expression; Neurodegenerative Disorders; Machine Learning; Microarray Analysis; Age-related Memory Disorders",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>The typical approach to identify blood-derived gene expression signatures as a biomarker for Alzheimer's disease (AD) have relied on training classification models using AD and healthy controls only. This may inadvertently result in the identification of markers for general illness rather than being disease-specific.<h4>Objective</h4>Investigate whether incorporating additional related disorders in the classification model development process can lead to the discovery of an AD-specific gene expression signature.<h4>Methods</h4>Two types of XGBoost classification models were developed. The first used 160 AD and 127 healthy controls and the second used the same 160 AD with 6,318 upsampled mixed controls consisting of Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis, bipolar disorder, schizophrenia, coronary artery disease, rheumatoid arthritis, chronic obstructive pulmonary disease, and cognitively healthy subjects. Both classification models were evaluated in an independent cohort consisting of 127 AD and 687 mixed controls.<h4>Results</h4>The AD versus healthy control models resulted in an average 48.7% sensitivity (95% CI\u200a=\u200a34.7-64.6), 41.9% specificity (95% CI\u200a=\u200a26.8-54.3), 13.6% PPV (95% CI\u200a=\u200a9.9-18.5), and 81.1% NPV (95% CI\u200a=\u200a73.3-87.7). In contrast, the mixed control models resulted in an average of 40.8% sensitivity (95% CI\u200a=\u200a27.5-52.0), 95.3% specificity (95% CI\u200a=\u200a93.3-97.1), 61.4% PPV (95% CI\u200a=\u200a53.8-69.6), and 89.7% NPV (95% CI\u200a=\u200a87.8-91.4).<h4>Conclusions</h4>This early work demonstrates the value of incorporating additional related disorders into the classification model developmental process, which can result in models with improved ability to distinguish AD from a heterogeneous aging population. However, further improvement to the sensitivity of the test is still required.",
-    "laySummary": "",
-    "urls": "pdf:https://content.iospress.com:443/download/journal-of-alzheimers-disease/jad191163?id=journal-of-alzheimers-disease%2Fjad191163; doi:https://doi.org/10.3233/JAD-191163; html:https://europepmc.org/articles/PMC7175937; pdf:https://europepmc.org/articles/PMC7175937?pdf=render"
-  },
   {
     "id": "33085509",
     "doi": "https://doi.org/10.7326/m20-4986",
@@ -22558,23 +22592,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1002/edm2.309; doi:https://doi.org/10.1002/edm2.309; html:https://europepmc.org/articles/PMC8754243; pdf:https://europepmc.org/articles/PMC8754243?pdf=render"
   },
-  {
-    "id": "38113090",
-    "doi": "https://doi.org/10.2196/41540",
-    "title": "Association Between Household Online Grocery Delivery Service Use and Food and Drink Purchase Behavior in England: Cross-Sectional Analysis.",
-    "authorString": "Yau A, Law C, Cornelsen L, Adams J, Boyland E, Burgoine T, de Vocht F, White M, Cummins S.",
-    "authorAffiliations": "",
-    "journalTitle": "JMIR public health and surveillance",
-    "pubYear": "2023",
-    "date": "2023-12-19",
-    "isOpenAccess": "Y",
-    "keywords": "Delivery; Diet; Internet; Public Health; Lifestyle; Consumer Behavior; Inequality; Sociodemographic Factors; Online; Food Preferences; Food Purchase; Supermarkets; Food And Beverages; Online Purchase; Grocery Purchase; Grocery; Online Grocery",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Online grocery delivery services (OGDSs) are a popular way of acquiring food. However, it is unclear whether OGDS use is associated with the healthiness of purchases and whether there are sociodemographic differences in OGDS use. If so, the increased prevalence of OGDS use may have implications for population diet, and differential OGDS use could contribute to diet inequalities.<h4>Objective</h4>This study aimed to examine whether OGDS use varies by sociodemographic characteristics and is associated with the amount and types of groceries purchased.<h4>Methods</h4>Item-level take-home food and drink purchase data (n=3,233,920 items) from households in London and the North of England were available from the 2019 UK Kantar fast-moving consumer goods panel (N=1911). Purchases were categorized as being bought online or in-store. We used logistic regression to estimate the likelihood of an above-median frequency of OGDS use by sociodemographic characteristics. We used Poisson regression to estimate the differences in energy and nutrients purchased by households that had above- and below-median OGDS use and the proportion of energy purchased from products high in fat, salt, and sugar (HFSS) online versus in-store among households that used both shopping methods (n=665).<h4>Results</h4>In total, 668 (35%) households used OGDSs at least once in 2019. Of the households that used OGDSs, the median use was 5 occasions in 2019. Households were more likely to have above-median use in London versus in the North of England (odds ratio 1.29, 95% CI 1.01-1.65) and if they had a higher annual household income (odds ratio 1.56, 95% CI 1.02-2.38 for \u2265\u00a350,000 [US $64,000] vs <\u00a320,000 [$25,600]). Households with above-median OGDS use had a higher weekly mean purchase of energy by 1461 (95% CI 1448-1474) kcal per person compared with households with below-median OGDS use. For households that used a combination of in-store and online shopping, HFSS products made up a lower proportion (-10.1%, 95% CI -12% to -8.1%) of energy purchased online compared to in-store.<h4>Conclusions</h4>Differences in grocery purchases between households with above- and below-median OGDS use could have positive or negative consequences. The extra energy purchased among households with above-median OGDS use could lead to overconsumption or food waste, which has negative consequences for population and environmental health. Alternatively, this extra energy may be replacing out-of-home purchasing, which tends to be less healthy, and may be beneficial for the population diet. Households made fewer HFSS purchases when shopping online compared to in-store, which may be due to differences in the shopping environment or experience, such as fewer promotions and advertisements when shopping online or not having to transport and carry purchases home. As higher-income households used OGDS more frequently, the implications of this sociodemographic pattern on dietary inequalities must be explored.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.2196/41540; html:https://europepmc.org/articles/PMC10762614"
-  },
   {
     "id": "36369983",
     "doi": "https://doi.org/10.1093/eurheartj/ehac650",
@@ -22592,6 +22609,23 @@
     "laySummary": "",
     "urls": "pdf:https://discovery.ucl.ac.uk/10159909/1/Asselbergs_EHJ%20digital%20viewpoint%202022_final%20accepted.pdf; doi:https://doi.org/10.1093/eurheartj/ehac650"
   },
+  {
+    "id": "38113090",
+    "doi": "https://doi.org/10.2196/41540",
+    "title": "Association Between Household Online Grocery Delivery Service Use and Food and Drink Purchase Behavior in England: Cross-Sectional Analysis.",
+    "authorString": "Yau A, Law C, Cornelsen L, Adams J, Boyland E, Burgoine T, de Vocht F, White M, Cummins S.",
+    "authorAffiliations": "",
+    "journalTitle": "JMIR public health and surveillance",
+    "pubYear": "2023",
+    "date": "2023-12-19",
+    "isOpenAccess": "Y",
+    "keywords": "Delivery; Diet; Internet; Public Health; Lifestyle; Consumer Behavior; Inequality; Sociodemographic Factors; Online; Food Preferences; Food Purchase; Supermarkets; Food And Beverages; Online Purchase; Grocery Purchase; Grocery; Online Grocery",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Online grocery delivery services (OGDSs) are a popular way of acquiring food. However, it is unclear whether OGDS use is associated with the healthiness of purchases and whether there are sociodemographic differences in OGDS use. If so, the increased prevalence of OGDS use may have implications for population diet, and differential OGDS use could contribute to diet inequalities.<h4>Objective</h4>This study aimed to examine whether OGDS use varies by sociodemographic characteristics and is associated with the amount and types of groceries purchased.<h4>Methods</h4>Item-level take-home food and drink purchase data (n=3,233,920 items) from households in London and the North of England were available from the 2019 UK Kantar fast-moving consumer goods panel (N=1911). Purchases were categorized as being bought online or in-store. We used logistic regression to estimate the likelihood of an above-median frequency of OGDS use by sociodemographic characteristics. We used Poisson regression to estimate the differences in energy and nutrients purchased by households that had above- and below-median OGDS use and the proportion of energy purchased from products high in fat, salt, and sugar (HFSS) online versus in-store among households that used both shopping methods (n=665).<h4>Results</h4>In total, 668 (35%) households used OGDSs at least once in 2019. Of the households that used OGDSs, the median use was 5 occasions in 2019. Households were more likely to have above-median use in London versus in the North of England (odds ratio 1.29, 95% CI 1.01-1.65) and if they had a higher annual household income (odds ratio 1.56, 95% CI 1.02-2.38 for \u2265\u00a350,000 [US $64,000] vs <\u00a320,000 [$25,600]). Households with above-median OGDS use had a higher weekly mean purchase of energy by 1461 (95% CI 1448-1474) kcal per person compared with households with below-median OGDS use. For households that used a combination of in-store and online shopping, HFSS products made up a lower proportion (-10.1%, 95% CI -12% to -8.1%) of energy purchased online compared to in-store.<h4>Conclusions</h4>Differences in grocery purchases between households with above- and below-median OGDS use could have positive or negative consequences. The extra energy purchased among households with above-median OGDS use could lead to overconsumption or food waste, which has negative consequences for population and environmental health. Alternatively, this extra energy may be replacing out-of-home purchasing, which tends to be less healthy, and may be beneficial for the population diet. Households made fewer HFSS purchases when shopping online compared to in-store, which may be due to differences in the shopping environment or experience, such as fewer promotions and advertisements when shopping online or not having to transport and carry purchases home. As higher-income households used OGDS more frequently, the implications of this sociodemographic pattern on dietary inequalities must be explored.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.2196/41540; html:https://europepmc.org/articles/PMC10762614"
+  },
   {
     "id": "32301135",
     "doi": "https://doi.org/10.1111/opo.12685",
@@ -22626,40 +22660,6 @@
     "laySummary": "This study investiages whether there is a smoking and socioeconomic status is linked to the risk of developing melanoma (a skin cancer). They used a Welsh database to find data on individuals who had melanoma and linked this data with smoking status and socioeconomic status on other national databases. They found that melanoma was less likely in those who smoked, but was associated with less chance of survival (due to health problems other than melanoma). Those in higher socioeconomic status had overall higher likelihood of survival.",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/bjd.18526; doi:https://doi.org/10.1111/bjd.18526; html:https://europepmc.org/articles/PMC7383980; pdf:https://europepmc.org/articles/PMC7383980?pdf=render"
   },
-  {
-    "id": "38633019",
-    "doi": "https://doi.org/10.1002/lrh2.10391",
-    "title": "ROAD2H: Development and evaluation of an open-source explainable artificial intelligence approach for managing co-morbidity and clinical guidelines.",
-    "authorString": "Dom\u00ednguez J, Prociuk D, Marovi\u0107 B, \u010cyras K, Cocarascu O, Ruiz F, Mi E, Mi E, Ramtale C, Rago A, Darzi A, Toni F, Curcin V, Delaney B.",
-    "authorAffiliations": "",
-    "journalTitle": "Learning health systems",
-    "pubYear": "2024",
-    "date": "2023-09-12",
-    "isOpenAccess": "Y",
-    "keywords": "Clinical Decision Support Systems; Argumentation; Fhir; Cds Hooks; Transition\u2010based Medical Recommendation Model; Co\u2010morbidity",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>Clinical decision support (CDS) systems (CDSSs) that integrate clinical guidelines need to reflect real-world co-morbidity. In patient-specific clinical contexts, transparent recommendations that allow for contraindications and other conflicts arising from co-morbidity are a requirement. In this work, we develop and evaluate a non-proprietary, standards-based approach to the deployment of computable guidelines with explainable argumentation, integrated with a commercial electronic health record (EHR) system in Serbia, a middle-income country in West Balkans.<h4>Methods</h4>We used an ontological framework, the Transition-based Medical Recommendation (TMR) model, to represent, and reason about, guideline concepts, and chose the 2017 International global initiative for chronic obstructive lung disease (GOLD) guideline and a Serbian hospital as the deployment and evaluation site, respectively. To mitigate potential guideline conflicts, we used a TMR-based implementation of the Assumptions-Based Argumentation framework extended with preferences and Goals (ABA+G). Remote EHR integration of computable guidelines was via a microservice architecture based on HL7 FHIR and CDS Hooks. A prototype integration was developed to manage chronic obstructive pulmonary disease (COPD) with comorbid cardiovascular or chronic kidney diseases, and a mixed-methods evaluation was conducted with 20 simulated cases and five pulmonologists.<h4>Results</h4>Pulmonologists agreed 97% of the time with the GOLD-based COPD symptom severity assessment assigned to each patient by the CDSS, and 98% of the time with one of the proposed COPD care plans. Comments were favourable on the principles of explainable argumentation; inclusion of additional co-morbidities was suggested in the future along with customisation of the level of explanation with expertise.<h4>Conclusion</h4>An ontological model provided a flexible means of providing argumentation and explainable artificial intelligence for a long-term condition. Extension to other guidelines and multiple co-morbidities is needed to test the approach further.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1002/lrh2.10391; html:https://europepmc.org/articles/PMC11019374; pdf:https://europepmc.org/articles/PMC11019374?pdf=render"
-  },
-  {
-    "id": "37293269",
-    "doi": "https://doi.org/10.1140/epjds/s13688-023-00394-6",
-    "title": "Do poverty and wealth look the same the world over? A comparative study of 12 cities from five high-income countries using street images.",
-    "authorString": "Suel E, Muller E, Bennett JE, Blakely T, Doyle Y, Lynch J, Mackenbach JD, Middel A, Mizdrak A, Nathvani R, Brauer M, Ezzati M.",
-    "authorAffiliations": "",
-    "journalTitle": "EPJ data science",
-    "pubYear": "2023",
-    "date": "2023-06-07",
-    "isOpenAccess": "Y",
-    "keywords": "Computer vision; Visual Similarity; Urban Inequalities; Street Images",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Urbanization and inequalities are two of the major policy themes of our time, intersecting in large cities where social and economic inequalities are particularly pronounced. Large scale street-level images are a source of city-wide visual information and allow for comparative analyses of multiple cities. Computer vision methods based on deep learning applied to street images have been shown to successfully measure inequalities in socioeconomic and environmental features, yet existing work has been within specific geographies and have not looked at how visual environments compare across different cities and countries. In this study, we aim to apply existing methods to understand whether, and to what extent, poor and wealthy groups live in visually similar neighborhoods across cities and countries. We present novel insights on similarity of neighborhoods using street-level images and deep learning methods. We analyzed 7.2 million images from 12 cities in five high-income countries, home to more than 85 million people: Auckland (New Zealand), Sydney (Australia), Toronto and Vancouver (Canada), Atlanta, Boston, Chicago, Los Angeles, New York, San Francisco, and Washington D.C. (United States of America), and London (United Kingdom). Visual features associated with neighborhood disadvantage are more distinct and unique to each city than those associated with affluence. For example, from what is visible from street images, high density poor neighborhoods located near the city center (e.g., in London) are visually distinct from poor suburban neighborhoods characterized by lower density and lower accessibility (e.g., in Atlanta). This suggests that differences between two cities is also driven by historical factors, policies, and local geography. Our results also have implications for image-based measures of inequality in cities especially when trained on data from cities that are visually distinct from target cities. We showed that these are more prone to errors for disadvantaged areas especially when transferring across cities, suggesting more attention needs to be paid to improving methods for capturing heterogeneity in poor environment across cities around the world.<h4>Supplementary information</h4>The online version contains supplementary material available at 10.1140/epjds/s13688-023-00394-6.",
-    "laySummary": "",
-    "urls": "pdf:https://epjdatascience.springeropen.com/counter/pdf/10.1140/epjds/s13688-023-00394-6; doi:https://doi.org/10.1140/epjds/s13688-023-00394-6; html:https://europepmc.org/articles/PMC10245348; pdf:https://europepmc.org/articles/PMC10245348?pdf=render"
-  },
   {
     "id": "39081663",
     "doi": "https://doi.org/10.1089/neur.2023.0111",
@@ -22677,6 +22677,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1089/neur.2023.0111"
   },
+  {
+    "id": "38633019",
+    "doi": "https://doi.org/10.1002/lrh2.10391",
+    "title": "ROAD2H: Development and evaluation of an open-source explainable artificial intelligence approach for managing co-morbidity and clinical guidelines.",
+    "authorString": "Dom\u00ednguez J, Prociuk D, Marovi\u0107 B, \u010cyras K, Cocarascu O, Ruiz F, Mi E, Mi E, Ramtale C, Rago A, Darzi A, Toni F, Curcin V, Delaney B.",
+    "authorAffiliations": "",
+    "journalTitle": "Learning health systems",
+    "pubYear": "2024",
+    "date": "2023-09-12",
+    "isOpenAccess": "Y",
+    "keywords": "Clinical Decision Support Systems; Argumentation; Fhir; Cds Hooks; Transition\u2010based Medical Recommendation Model; Co\u2010morbidity",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>Clinical decision support (CDS) systems (CDSSs) that integrate clinical guidelines need to reflect real-world co-morbidity. In patient-specific clinical contexts, transparent recommendations that allow for contraindications and other conflicts arising from co-morbidity are a requirement. In this work, we develop and evaluate a non-proprietary, standards-based approach to the deployment of computable guidelines with explainable argumentation, integrated with a commercial electronic health record (EHR) system in Serbia, a middle-income country in West Balkans.<h4>Methods</h4>We used an ontological framework, the Transition-based Medical Recommendation (TMR) model, to represent, and reason about, guideline concepts, and chose the 2017 International global initiative for chronic obstructive lung disease (GOLD) guideline and a Serbian hospital as the deployment and evaluation site, respectively. To mitigate potential guideline conflicts, we used a TMR-based implementation of the Assumptions-Based Argumentation framework extended with preferences and Goals (ABA+G). Remote EHR integration of computable guidelines was via a microservice architecture based on HL7 FHIR and CDS Hooks. A prototype integration was developed to manage chronic obstructive pulmonary disease (COPD) with comorbid cardiovascular or chronic kidney diseases, and a mixed-methods evaluation was conducted with 20 simulated cases and five pulmonologists.<h4>Results</h4>Pulmonologists agreed 97% of the time with the GOLD-based COPD symptom severity assessment assigned to each patient by the CDSS, and 98% of the time with one of the proposed COPD care plans. Comments were favourable on the principles of explainable argumentation; inclusion of additional co-morbidities was suggested in the future along with customisation of the level of explanation with expertise.<h4>Conclusion</h4>An ontological model provided a flexible means of providing argumentation and explainable artificial intelligence for a long-term condition. Extension to other guidelines and multiple co-morbidities is needed to test the approach further.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1002/lrh2.10391; html:https://europepmc.org/articles/PMC11019374; pdf:https://europepmc.org/articles/PMC11019374?pdf=render"
+  },
   {
     "id": "33990383",
     "doi": "https://doi.org/10.1136/gutjnl-2020-323546",
@@ -22694,6 +22711,23 @@
     "laySummary": "",
     "urls": "pdf:https://gut.bmj.com/content/gutjnl/71/4/705.full.pdf; doi:https://doi.org/10.1136/gutjnl-2020-323546; html:https://europepmc.org/articles/PMC8921573; pdf:https://europepmc.org/articles/PMC8921573?pdf=render"
   },
+  {
+    "id": "37293269",
+    "doi": "https://doi.org/10.1140/epjds/s13688-023-00394-6",
+    "title": "Do poverty and wealth look the same the world over? A comparative study of 12 cities from five high-income countries using street images.",
+    "authorString": "Suel E, Muller E, Bennett JE, Blakely T, Doyle Y, Lynch J, Mackenbach JD, Middel A, Mizdrak A, Nathvani R, Brauer M, Ezzati M.",
+    "authorAffiliations": "",
+    "journalTitle": "EPJ data science",
+    "pubYear": "2023",
+    "date": "2023-06-07",
+    "isOpenAccess": "Y",
+    "keywords": "Computer vision; Visual Similarity; Urban Inequalities; Street Images",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Urbanization and inequalities are two of the major policy themes of our time, intersecting in large cities where social and economic inequalities are particularly pronounced. Large scale street-level images are a source of city-wide visual information and allow for comparative analyses of multiple cities. Computer vision methods based on deep learning applied to street images have been shown to successfully measure inequalities in socioeconomic and environmental features, yet existing work has been within specific geographies and have not looked at how visual environments compare across different cities and countries. In this study, we aim to apply existing methods to understand whether, and to what extent, poor and wealthy groups live in visually similar neighborhoods across cities and countries. We present novel insights on similarity of neighborhoods using street-level images and deep learning methods. We analyzed 7.2 million images from 12 cities in five high-income countries, home to more than 85 million people: Auckland (New Zealand), Sydney (Australia), Toronto and Vancouver (Canada), Atlanta, Boston, Chicago, Los Angeles, New York, San Francisco, and Washington D.C. (United States of America), and London (United Kingdom). Visual features associated with neighborhood disadvantage are more distinct and unique to each city than those associated with affluence. For example, from what is visible from street images, high density poor neighborhoods located near the city center (e.g., in London) are visually distinct from poor suburban neighborhoods characterized by lower density and lower accessibility (e.g., in Atlanta). This suggests that differences between two cities is also driven by historical factors, policies, and local geography. Our results also have implications for image-based measures of inequality in cities especially when trained on data from cities that are visually distinct from target cities. We showed that these are more prone to errors for disadvantaged areas especially when transferring across cities, suggesting more attention needs to be paid to improving methods for capturing heterogeneity in poor environment across cities around the world.<h4>Supplementary information</h4>The online version contains supplementary material available at 10.1140/epjds/s13688-023-00394-6.",
+    "laySummary": "",
+    "urls": "pdf:https://epjdatascience.springeropen.com/counter/pdf/10.1140/epjds/s13688-023-00394-6; doi:https://doi.org/10.1140/epjds/s13688-023-00394-6; html:https://europepmc.org/articles/PMC10245348; pdf:https://europepmc.org/articles/PMC10245348?pdf=render"
+  },
   {
     "id": "32128788",
     "doi": "https://doi.org/10.1111/bjd.18889",
@@ -22745,6 +22779,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/11/3/e043290.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-043290; html:https://europepmc.org/articles/PMC7929882; pdf:https://europepmc.org/articles/PMC7929882?pdf=render"
   },
+  {
+    "id": "32249120",
+    "doi": "https://doi.org/10.1016/j.schres.2020.03.044",
+    "title": "Area deprivation, urbanicity, severe mental illness and social drift - A population-based linkage study using routinely collected primary and secondary care data.",
+    "authorString": "Lee SC, DelPozo-Banos M, Lloyd K, Jones I, Walters JTR, Owen MJ, O'Donovan M, John A.",
+    "authorAffiliations": "",
+    "journalTitle": "Schizophrenia research",
+    "pubYear": "2020",
+    "date": "2020-04-02",
+    "isOpenAccess": "N",
+    "keywords": "Schizophrenia; Bipolar disorder; Deprivation; Severe Mental Illness; Urbanicity; Social Drift",
+    "nationalPriorities": "Improving Public Health",
+    "healthCategories": "mental health",
+    "abstract": "We investigated whether associations between area deprivation, urbanicity and elevated risk of severe mental illnesses (SMIs, including schizophrenia and bipolar disorder) is accounted for by social drift or social causation. We extracted primary and secondary care electronic health records from 2004 to 2015 from a population of 3.9 million. We identified prevalent and incident individuals with SMIs and their level of deprivation and urbanicity using the Welsh Index of Multiple Deprivation (WIMD) and urban/rural indicator. The presence of social drift was determined by whether odds ratios (ORs) from logistic regression is greater than the incidence rate ratios (IRRs) from Poisson regression. Additionally, we performed longitudinal analysis to measure the proportion of change in deprivation level and rural/urban residence 10\u00a0years after an incident diagnosis of SMI and compared it to the general population using standardised rate ratios (SRRs). Prevalence and incidence of SMIs were significantly associated with deprivation and urbanicity (all ORs and IRRs significantly >1). ORs and IRRs were similar across all conditions and cohorts (ranging from 1.1 to 1.4). Results from the longitudinal analysis showed individuals with SMIs are more likely to move compared to the general population. However, they did not preferentially move to more deprived or urban areas. There was little evidence of downward social drift over a 10-year period. These findings have implications for the allocation of resources, service configuration and access to services in deprived communities, as well as, for broader public health interventions addressing poverty, and social and environmental contexts.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.schres.2020.03.044; doi:https://doi.org/10.1016/j.schres.2020.03.044"
+  },
   {
     "id": "31744503",
     "doi": "https://doi.org/10.1186/s12916-019-1438-y",
@@ -22779,23 +22830,6 @@
     "laySummary": "",
     "urls": "pdf:https://cronfa.swan.ac.uk/Record/cronfa60128/Download/60128__24479__4d74009536e649b0b17180e2bfd80435.pdf; doi:https://doi.org/10.1111/bjhp.12606; html:https://europepmc.org/articles/PMC9347957; pdf:https://europepmc.org/articles/PMC9347957?pdf=render"
   },
-  {
-    "id": "32249120",
-    "doi": "https://doi.org/10.1016/j.schres.2020.03.044",
-    "title": "Area deprivation, urbanicity, severe mental illness and social drift - A population-based linkage study using routinely collected primary and secondary care data.",
-    "authorString": "Lee SC, DelPozo-Banos M, Lloyd K, Jones I, Walters JTR, Owen MJ, O'Donovan M, John A.",
-    "authorAffiliations": "",
-    "journalTitle": "Schizophrenia research",
-    "pubYear": "2020",
-    "date": "2020-04-02",
-    "isOpenAccess": "N",
-    "keywords": "Schizophrenia; Bipolar disorder; Deprivation; Severe Mental Illness; Urbanicity; Social Drift",
-    "nationalPriorities": "Improving Public Health",
-    "healthCategories": "mental health",
-    "abstract": "We investigated whether associations between area deprivation, urbanicity and elevated risk of severe mental illnesses (SMIs, including schizophrenia and bipolar disorder) is accounted for by social drift or social causation. We extracted primary and secondary care electronic health records from 2004 to 2015 from a population of 3.9 million. We identified prevalent and incident individuals with SMIs and their level of deprivation and urbanicity using the Welsh Index of Multiple Deprivation (WIMD) and urban/rural indicator. The presence of social drift was determined by whether odds ratios (ORs) from logistic regression is greater than the incidence rate ratios (IRRs) from Poisson regression. Additionally, we performed longitudinal analysis to measure the proportion of change in deprivation level and rural/urban residence 10\u00a0years after an incident diagnosis of SMI and compared it to the general population using standardised rate ratios (SRRs). Prevalence and incidence of SMIs were significantly associated with deprivation and urbanicity (all ORs and IRRs significantly >1). ORs and IRRs were similar across all conditions and cohorts (ranging from 1.1 to 1.4). Results from the longitudinal analysis showed individuals with SMIs are more likely to move compared to the general population. However, they did not preferentially move to more deprived or urban areas. There was little evidence of downward social drift over a 10-year period. These findings have implications for the allocation of resources, service configuration and access to services in deprived communities, as well as, for broader public health interventions addressing poverty, and social and environmental contexts.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.schres.2020.03.044; doi:https://doi.org/10.1016/j.schres.2020.03.044"
-  },
   {
     "id": "30729733",
     "doi": "https://doi.org/10.1111/ijpo.12512",
@@ -22881,23 +22915,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/eurheartj/article-pdf/41/2/227/31731687/ehz569.pdf; doi:https://doi.org/10.1093/eurheartj/ehz569"
   },
-  {
-    "id": "36644660",
-    "doi": "https://doi.org/10.1177/20552076221128677",
-    "title": "Evaluation of prototype risk prediction tools for clinicians and people living with type 2 diabetes in North West London using the think aloud method.",
-    "authorString": "Gardner C, Wake D, Brodie D, Silverstein A, Young S, Cunningham S, Sainsbury C, Ilia M, Lucas A, Willis T, Halligan J.",
-    "authorAffiliations": "",
-    "journalTitle": "Digital health",
-    "pubYear": "2023",
-    "date": "2023-01-08",
-    "isOpenAccess": "Y",
-    "keywords": "Artificial intelligence; Internet; Diabetes; Qualitative; risk factors; Machine Learning; Health Informatics; Behaviour Change; Personalised Medicine; Digital Health",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The prevalence of type 2 diabetes in North West London (NWL) is relatively high compared to other parts of the United Kingdom with outcomes suboptimal. This presents a need for more effective strategies to identify people living with type 2 diabetes who need additional support. An emerging subset of web-based interventions for diabetes self-management and population management has used artificial intelligence and machine learning models to stratify the risk of complications from diabetes and identify patients in need of immediate support. In this study, two prototype risk prediction tools on the MyWay Diabetes and MyWay Clinical platforms were evaluated with six clinicians and six people living with type 2 diabetes in NWL using the think aloud method. The results of the sessions with people living with type 2 diabetes showed that the concept of the tool was intuitive, however, more instruction on how to correctly use the risk prediction tool would be valuable. The feedback from the sessions with clinicians was that the data presented in the tool aligned with the key diabetes targets in NWL, and that this would be useful for identifying and inviting patients to the practice who are overdue for tests and at risk of complications. The findings of the evaluation have been used to support the development of the prototype risk predictions tools. This study demonstrates the value of conducting usability testing on web-based interventions designed to support the targeted management of type 2 diabetes in local communities.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1177/20552076221128677; doi:https://doi.org/10.1177/20552076221128677; html:https://europepmc.org/articles/PMC9834412; pdf:https://europepmc.org/articles/PMC9834412?pdf=render"
-  },
   {
     "id": "34230034",
     "doi": "https://doi.org/10.1136/bmjresp-2021-000967",
@@ -22915,6 +22932,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopenrespres.bmj.com/content/bmjresp/8/1/e000967.full.pdf; doi:https://doi.org/10.1136/bmjresp-2021-000967; html:https://europepmc.org/articles/PMC8261886; pdf:https://europepmc.org/articles/PMC8261886?pdf=render"
   },
+  {
+    "id": "36644660",
+    "doi": "https://doi.org/10.1177/20552076221128677",
+    "title": "Evaluation of prototype risk prediction tools for clinicians and people living with type 2 diabetes in North West London using the think aloud method.",
+    "authorString": "Gardner C, Wake D, Brodie D, Silverstein A, Young S, Cunningham S, Sainsbury C, Ilia M, Lucas A, Willis T, Halligan J.",
+    "authorAffiliations": "",
+    "journalTitle": "Digital health",
+    "pubYear": "2023",
+    "date": "2023-01-08",
+    "isOpenAccess": "Y",
+    "keywords": "Artificial intelligence; Internet; Diabetes; Qualitative; risk factors; Machine Learning; Health Informatics; Behaviour Change; Personalised Medicine; Digital Health",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The prevalence of type 2 diabetes in North West London (NWL) is relatively high compared to other parts of the United Kingdom with outcomes suboptimal. This presents a need for more effective strategies to identify people living with type 2 diabetes who need additional support. An emerging subset of web-based interventions for diabetes self-management and population management has used artificial intelligence and machine learning models to stratify the risk of complications from diabetes and identify patients in need of immediate support. In this study, two prototype risk prediction tools on the MyWay Diabetes and MyWay Clinical platforms were evaluated with six clinicians and six people living with type 2 diabetes in NWL using the think aloud method. The results of the sessions with people living with type 2 diabetes showed that the concept of the tool was intuitive, however, more instruction on how to correctly use the risk prediction tool would be valuable. The feedback from the sessions with clinicians was that the data presented in the tool aligned with the key diabetes targets in NWL, and that this would be useful for identifying and inviting patients to the practice who are overdue for tests and at risk of complications. The findings of the evaluation have been used to support the development of the prototype risk predictions tools. This study demonstrates the value of conducting usability testing on web-based interventions designed to support the targeted management of type 2 diabetes in local communities.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1177/20552076221128677; doi:https://doi.org/10.1177/20552076221128677; html:https://europepmc.org/articles/PMC9834412; pdf:https://europepmc.org/articles/PMC9834412?pdf=render"
+  },
   {
     "id": "34544691",
     "doi": "https://doi.org/10.3399/bjgp.2021.0153",
@@ -22949,23 +22983,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2022.1016032/pdf; doi:https://doi.org/10.3389/fcvm.2022.1016032; html:https://europepmc.org/articles/PMC9681217; pdf:https://europepmc.org/articles/PMC9681217?pdf=render"
   },
-  {
-    "id": "37143831",
-    "doi": "https://doi.org/10.1183/23120541.00591-2022",
-    "title": "Ethnic variation in asthma healthcare utilisation and exacerbation: systematic review and meta-analysis.",
-    "authorString": "Akin-Imran A, Bajpai A, McCartan D, Heaney LG, Kee F, Redmond C, Busby J.",
-    "authorAffiliations": "",
-    "journalTitle": "ERJ open research",
-    "pubYear": "2023",
-    "date": "2023-05-02",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Patients from ethnic minority groups (EMGs) frequently report poorer asthma outcomes; however, a broad synthesis summarising ethnic disparities is yet to be undertaken. What is the magnitude of ethnic disparities in asthma healthcare utilisation, exacerbations and mortality?<h4>Methods</h4>MEDLINE, Embase and Web of Science databases were searched for studies reporting ethnic variation in asthma healthcare outcomes (primary care attendance, exacerbation, emergency department (ED) visits, hospitalisation, hospital readmission, ventilation/intubation and mortality) between White patients and those from EMGs. Estimates were displayed using forest plots and random-effects models were used to calculate pooled estimates. We conducted subgroup analyses to explore heterogeneity, including by specific ethnicity (Black, Hispanic, Asian and other).<h4>Results</h4>65 studies, comprising 699\u2009882 patients, were included. Most studies (92.3%) were conducted in the United States of America (USA). Patients from EMGs had evidence suggestive of lower levels of primary care attendance (OR 0.72, 95% CI 0.48-1.09), but substantially higher ED visits (OR 1.74, 95% CI 1.53-1.98), hospitalisations (OR 1.63, 95% CI 1.48-1.79) and ventilation/intubation (OR 2.67, 95% CI 1.65-4.31) when compared to White patients. In addition, we found evidence suggestive of increased hospital readmissions (OR 1.19, 95% CI 0.90-1.57) and exacerbation rates (OR 1.10, 95% CI 0.94-1.28) among EMGs. No eligible studies explored disparities in mortality. ED visits were much higher among Black and Hispanic patients, while Asian and other ethnicities had similar rates to White patients.<h4>Conclusions</h4>EMGs had higher secondary care utilisation and exacerbations. Despite the global importance of this issue, the majority of studies were performed in the USA. Further research into the causes of these disparities, including whether these vary by specific ethnicity, is required to aid the design of effective interventions.",
-    "laySummary": "",
-    "urls": "pdf:https://openres.ersjournals.com/content/erjor/early/2023/02/16/23120541.00591-2022.full.pdf; doi:https://doi.org/10.1183/23120541.00591-2022; html:https://europepmc.org/articles/PMC10152257; pdf:https://europepmc.org/articles/PMC10152257?pdf=render"
-  },
   {
     "id": "33168126",
     "doi": "https://doi.org/10.1192/bjo.2020.42",
@@ -22984,21 +23001,21 @@
     "urls": "pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/A00360A347FCC91E2E9D0B39FBDCE887/S2056472420000423a.pdf/div-class-title-impact-of-schizophrenia-genetic-liability-on-the-association-between-schizophrenia-and-physical-illness-data-linkage-study-div.pdf; doi:https://doi.org/10.1192/bjo.2020.42; html:https://europepmc.org/articles/PMC7745237; pdf:https://europepmc.org/articles/PMC7745237?pdf=render"
   },
   {
-    "id": "37338108",
-    "doi": "https://doi.org/10.1093/eurjpc/zwad202",
-    "title": "The relevance of competing risk adjustment in cardiovascular risk prediction models for clinical practice.",
-    "authorString": "Hageman SHJ, Dorresteijn JAN, Pennells L, van Smeden M, Bots ML, Di Angelantonio E, Visseren FLJ.",
+    "id": "37143831",
+    "doi": "https://doi.org/10.1183/23120541.00591-2022",
+    "title": "Ethnic variation in asthma healthcare utilisation and exacerbation: systematic review and meta-analysis.",
+    "authorString": "Akin-Imran A, Bajpai A, McCartan D, Heaney LG, Kee F, Redmond C, Busby J.",
     "authorAffiliations": "",
-    "journalTitle": "European journal of preventive cardiology",
+    "journalTitle": "ERJ open research",
     "pubYear": "2023",
-    "date": "2023-11-01",
-    "isOpenAccess": "N",
-    "keywords": "Education; Personalized Medicine; Risk Prediction; Competing Risks; Score2",
+    "date": "2023-05-02",
+    "isOpenAccess": "Y",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Many models developed for predicting the risk of cardiovascular disease (CVD) are adjusted for the competing risk of non-CVD mortality, which has been suggested to reduce potential overestimation of cumulative incidence in populations where the risk of competing events is high. The objective was to evaluate and illustrate the clinical impact of competing risk adjustment when deriving a CVD prediction model in a high-risk population.<h4>Methods and results</h4>Individuals with established atherosclerotic CVD were included from the Utrecht Cardiovascular Cohort-Secondary Manifestations of ARTerial disease (UCC-SMART). In 8355 individuals, followed for a median of 8.2 years (IQR 4.2-12.5), two similar prediction models for the estimation of 10-year residual CVD risk were derived: with competing risk adjustment using a Fine and Gray model and without competing risk adjustment using a Cox proportional hazards model. On average, predictions were higher from the Cox model. The Cox model predictions overestimated the cumulative incidence [predicted-observed ratio 1.14 (95% CI 1.09-1.20)], which was most apparent in the highest risk quartiles and in older persons. Discrimination of both models was similar. When determining treatment eligibility on thresholds of predicted risks, more individuals would be treated based on the Cox model predictions. If, for example, individuals with a predicted risk > 20% were considered eligible for treatment, 34% of the population would be treated according to the Fine and Gray model predictions and 44% according to the Cox model predictions.<h4>Interpretation</h4>Individual predictions from the model unadjusted for competing risks were higher, reflecting the different interpretations of both models. For models aiming to accurately predict absolute risks, especially in high-risk populations, competing risk adjustment must be considered.",
+    "abstract": "<h4>Background</h4>Patients from ethnic minority groups (EMGs) frequently report poorer asthma outcomes; however, a broad synthesis summarising ethnic disparities is yet to be undertaken. What is the magnitude of ethnic disparities in asthma healthcare utilisation, exacerbations and mortality?<h4>Methods</h4>MEDLINE, Embase and Web of Science databases were searched for studies reporting ethnic variation in asthma healthcare outcomes (primary care attendance, exacerbation, emergency department (ED) visits, hospitalisation, hospital readmission, ventilation/intubation and mortality) between White patients and those from EMGs. Estimates were displayed using forest plots and random-effects models were used to calculate pooled estimates. We conducted subgroup analyses to explore heterogeneity, including by specific ethnicity (Black, Hispanic, Asian and other).<h4>Results</h4>65 studies, comprising 699\u2009882 patients, were included. Most studies (92.3%) were conducted in the United States of America (USA). Patients from EMGs had evidence suggestive of lower levels of primary care attendance (OR 0.72, 95% CI 0.48-1.09), but substantially higher ED visits (OR 1.74, 95% CI 1.53-1.98), hospitalisations (OR 1.63, 95% CI 1.48-1.79) and ventilation/intubation (OR 2.67, 95% CI 1.65-4.31) when compared to White patients. In addition, we found evidence suggestive of increased hospital readmissions (OR 1.19, 95% CI 0.90-1.57) and exacerbation rates (OR 1.10, 95% CI 0.94-1.28) among EMGs. No eligible studies explored disparities in mortality. ED visits were much higher among Black and Hispanic patients, while Asian and other ethnicities had similar rates to White patients.<h4>Conclusions</h4>EMGs had higher secondary care utilisation and exacerbations. Despite the global importance of this issue, the majority of studies were performed in the USA. Further research into the causes of these disparities, including whether these vary by specific ethnicity, is required to aid the design of effective interventions.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1093/eurjpc/zwad202; doi:https://doi.org/10.1093/eurjpc/zwad202"
+    "urls": "pdf:https://openres.ersjournals.com/content/erjor/early/2023/02/16/23120541.00591-2022.full.pdf; doi:https://doi.org/10.1183/23120541.00591-2022; html:https://europepmc.org/articles/PMC10152257; pdf:https://europepmc.org/articles/PMC10152257?pdf=render"
   },
   {
     "id": "30969971",
@@ -23017,6 +23034,23 @@
     "laySummary": "",
     "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0213435&type=printable; doi:https://doi.org/10.1371/journal.pone.0213435; html:https://europepmc.org/articles/PMC6457613; pdf:https://europepmc.org/articles/PMC6457613?pdf=render"
   },
+  {
+    "id": "37338108",
+    "doi": "https://doi.org/10.1093/eurjpc/zwad202",
+    "title": "The relevance of competing risk adjustment in cardiovascular risk prediction models for clinical practice.",
+    "authorString": "Hageman SHJ, Dorresteijn JAN, Pennells L, van Smeden M, Bots ML, Di Angelantonio E, Visseren FLJ.",
+    "authorAffiliations": "",
+    "journalTitle": "European journal of preventive cardiology",
+    "pubYear": "2023",
+    "date": "2023-11-01",
+    "isOpenAccess": "N",
+    "keywords": "Education; Personalized Medicine; Risk Prediction; Competing Risks; Score2",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Many models developed for predicting the risk of cardiovascular disease (CVD) are adjusted for the competing risk of non-CVD mortality, which has been suggested to reduce potential overestimation of cumulative incidence in populations where the risk of competing events is high. The objective was to evaluate and illustrate the clinical impact of competing risk adjustment when deriving a CVD prediction model in a high-risk population.<h4>Methods and results</h4>Individuals with established atherosclerotic CVD were included from the Utrecht Cardiovascular Cohort-Secondary Manifestations of ARTerial disease (UCC-SMART). In 8355 individuals, followed for a median of 8.2 years (IQR 4.2-12.5), two similar prediction models for the estimation of 10-year residual CVD risk were derived: with competing risk adjustment using a Fine and Gray model and without competing risk adjustment using a Cox proportional hazards model. On average, predictions were higher from the Cox model. The Cox model predictions overestimated the cumulative incidence [predicted-observed ratio 1.14 (95% CI 1.09-1.20)], which was most apparent in the highest risk quartiles and in older persons. Discrimination of both models was similar. When determining treatment eligibility on thresholds of predicted risks, more individuals would be treated based on the Cox model predictions. If, for example, individuals with a predicted risk > 20% were considered eligible for treatment, 34% of the population would be treated according to the Fine and Gray model predictions and 44% according to the Cox model predictions.<h4>Interpretation</h4>Individual predictions from the model unadjusted for competing risks were higher, reflecting the different interpretations of both models. For models aiming to accurately predict absolute risks, especially in high-risk populations, competing risk adjustment must be considered.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1093/eurjpc/zwad202; doi:https://doi.org/10.1093/eurjpc/zwad202"
+  },
   {
     "id": "38784722",
     "doi": "https://doi.org/10.1093/jbmrpl/ziae058",
@@ -23034,6 +23068,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/jbmrplus/advance-article-pdf/doi/10.1093/jbmrpl/ziae058/57334584/ziae058.pdf; doi:https://doi.org/10.1093/jbmrpl/ziae058; html:https://europepmc.org/articles/PMC11114472; pdf:https://europepmc.org/articles/PMC11114472?pdf=render"
   },
+  {
+    "id": "29457906",
+    "doi": "https://doi.org/10.1021/acs.jproteome.7b00879",
+    "title": "Optimized Phenotypic Biomarker Discovery and Confounder Elimination via Covariate-Adjusted Projection to Latent Structures from Metabolic Spectroscopy Data.",
+    "authorString": "Posma JM, Garcia-Perez I, Ebbels TMD, Lindon JC, Stamler J, Elliott P, Holmes E, Nicholson JK.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of proteome research",
+    "pubYear": "2018",
+    "date": "2018-02-27",
+    "isOpenAccess": "Y",
+    "keywords": "Chemometrics; multivariate data analysis; Biomarker Discovery; Sampling Bias; Covariate Adjustment; Metabolic Phenotyping; Random Matrix Theory; Reanalysis; Monte Carlo Cross-validation; Confounder Elimination",
+    "nationalPriorities": "Applied Analytics",
+    "healthCategories": "",
+    "abstract": "Metabolism is altered by genetics, diet, disease status, environment, and many other factors. Modeling either one of these is often done without considering the effects of the other covariates. Attributing differences in metabolic profile to one of these factors needs to be done while controlling for the metabolic influence of the rest. We describe here a data analysis framework and novel confounder-adjustment algorithm for multivariate analysis of metabolic profiling data. Using simulated data, we show that similar numbers of true associations and significantly less false positives are found compared to other commonly used methods. Covariate-adjusted projections to latent structures (CA-PLS) are exemplified here using a large-scale metabolic phenotyping study of two Chinese populations at different risks for cardiovascular disease. Using CA-PLS, we find that some previously reported differences are actually associated with external factors and discover a number of previously unreported biomarkers linked to different metabolic pathways. CA-PLS can be applied to any multivariate data where confounding may be an issue and the confounder-adjustment procedure is translatable to other multivariate regression techniques.",
+    "laySummary": "",
+    "urls": "pdf:https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.7b00879; doi:https://doi.org/10.1021/acs.jproteome.7b00879; html:https://europepmc.org/articles/PMC5891819; pdf:https://europepmc.org/articles/PMC5891819?pdf=render"
+  },
   {
     "id": "35589356",
     "doi": "https://doi.org/10.1136/bmjopen-2021-057343",
@@ -23102,40 +23153,6 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/ppe.12959; doi:https://doi.org/10.1111/ppe.12959; html:https://europepmc.org/articles/PMC10946523; pdf:https://europepmc.org/articles/PMC10946523?pdf=render"
   },
-  {
-    "id": "29457906",
-    "doi": "https://doi.org/10.1021/acs.jproteome.7b00879",
-    "title": "Optimized Phenotypic Biomarker Discovery and Confounder Elimination via Covariate-Adjusted Projection to Latent Structures from Metabolic Spectroscopy Data.",
-    "authorString": "Posma JM, Garcia-Perez I, Ebbels TMD, Lindon JC, Stamler J, Elliott P, Holmes E, Nicholson JK.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of proteome research",
-    "pubYear": "2018",
-    "date": "2018-02-27",
-    "isOpenAccess": "Y",
-    "keywords": "Chemometrics; multivariate data analysis; Biomarker Discovery; Sampling Bias; Covariate Adjustment; Metabolic Phenotyping; Random Matrix Theory; Reanalysis; Monte Carlo Cross-validation; Confounder Elimination",
-    "nationalPriorities": "Applied Analytics",
-    "healthCategories": "",
-    "abstract": "Metabolism is altered by genetics, diet, disease status, environment, and many other factors. Modeling either one of these is often done without considering the effects of the other covariates. Attributing differences in metabolic profile to one of these factors needs to be done while controlling for the metabolic influence of the rest. We describe here a data analysis framework and novel confounder-adjustment algorithm for multivariate analysis of metabolic profiling data. Using simulated data, we show that similar numbers of true associations and significantly less false positives are found compared to other commonly used methods. Covariate-adjusted projections to latent structures (CA-PLS) are exemplified here using a large-scale metabolic phenotyping study of two Chinese populations at different risks for cardiovascular disease. Using CA-PLS, we find that some previously reported differences are actually associated with external factors and discover a number of previously unreported biomarkers linked to different metabolic pathways. CA-PLS can be applied to any multivariate data where confounding may be an issue and the confounder-adjustment procedure is translatable to other multivariate regression techniques.",
-    "laySummary": "",
-    "urls": "pdf:https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.7b00879; doi:https://doi.org/10.1021/acs.jproteome.7b00879; html:https://europepmc.org/articles/PMC5891819; pdf:https://europepmc.org/articles/PMC5891819?pdf=render"
-  },
-  {
-    "id": "36580444",
-    "doi": "https://doi.org/10.1371/journal.pmed.1004141",
-    "title": "Associations of genetically predicted fatty acid levels across the phenome: A mendelian randomisation study.",
-    "authorString": "Zagkos L, Dib MJ, Pinto R, Gill D, Koskeridis F, Drenos F, Markozannes G, Elliott P, Zuber V, Tsilidis K, Dehghan A, Tzoulaki I.",
-    "authorAffiliations": "",
-    "journalTitle": "PLoS medicine",
-    "pubYear": "2022",
-    "date": "2022-12-29",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Fatty acids are important dietary factors that have been extensively studied for their implication in health and disease. Evidence from epidemiological studies and randomised controlled trials on their role in cardiovascular, inflammatory, and other diseases remains inconsistent. The objective of this study was to assess whether genetically predicted fatty acid concentrations affect the risk of disease across a wide variety of clinical health outcomes.<h4>Methods and findings</h4>The UK Biobank (UKB) is a large study involving over 500,000 participants aged 40 to 69 years at recruitment from 2006 to 2010. We used summary-level data for 117,143 UKB samples (base dataset), to extract genetic associations of fatty acids, and individual-level data for 322,232 UKB participants (target dataset) to conduct our discovery analysis. We studied potentially causal relationships of circulating fatty acids with 845 clinical diagnoses, using mendelian randomisation (MR) approach, within a phenome-wide association study (PheWAS) framework. Regression models in PheWAS were adjusted for sex, age, and the first 10 genetic principal components. External summary statistics were used for replication. When several fatty acids were associated with a health outcome, multivariable MR and MR-Bayesian method averaging (MR-BMA) was applied to disentangle their causal role. Genetic predisposition to higher docosahexaenoic acid (DHA) was associated with cholelithiasis and cholecystitis (odds ratio per mmol/L: 0.76, 95% confidence interval: 0.66 to 0.87). This was supported in replication analysis (FinnGen study) and by the genetically predicted omega-3 fatty acids analyses. Genetically predicted linoleic acid (LA), omega-6, polyunsaturated fatty acids (PUFAs), and total fatty acids (total FAs) showed positive associations with cardiovascular outcomes with support from replication analysis. Finally, higher genetically predicted levels of DHA (0.83, 0.73 to 0.95) and omega-3 (0.83, 0.75 to 0.92) were found to have a protective effect on obesity, which was supported using body mass index (BMI) in the GIANT consortium as replication analysis. Multivariable MR analysis suggested a direct detrimental effect of LA (1.64, 1.07 to 2.50) and omega-6 fatty acids (1.81, 1.06 to 3.09) on coronary heart disease (CHD). MR-BMA prioritised LA and omega-6 fatty acids as the top risk factors for CHD. Although we present a range of sensitivity analyses to the address MR assumptions, horizontal pleiotropy may still bias the reported associations and further evaluation in clinical trials is needed.<h4>Conclusions</h4>Our study suggests potentially protective effects of circulating DHA and omega-3 concentrations on cholelithiasis and cholecystitis and on obesity, highlighting the need to further assess them as prevention treatments in clinical trials. Moreover, our findings do not support the supplementation of unsaturated fatty acids for cardiovascular disease prevention.",
-    "laySummary": "",
-    "urls": "pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004141&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004141; html:https://europepmc.org/articles/PMC9799317; pdf:https://europepmc.org/articles/PMC9799317?pdf=render"
-  },
   {
     "id": "36543768",
     "doi": "https://doi.org/10.1038/s41467-022-35321-2",
@@ -23170,6 +23187,23 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/advs.202100707; doi:https://doi.org/10.1002/advs.202100707; html:https://europepmc.org/articles/PMC8224424; pdf:https://europepmc.org/articles/PMC8224424?pdf=render"
   },
+  {
+    "id": "36580444",
+    "doi": "https://doi.org/10.1371/journal.pmed.1004141",
+    "title": "Associations of genetically predicted fatty acid levels across the phenome: A mendelian randomisation study.",
+    "authorString": "Zagkos L, Dib MJ, Pinto R, Gill D, Koskeridis F, Drenos F, Markozannes G, Elliott P, Zuber V, Tsilidis K, Dehghan A, Tzoulaki I.",
+    "authorAffiliations": "",
+    "journalTitle": "PLoS medicine",
+    "pubYear": "2022",
+    "date": "2022-12-29",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Fatty acids are important dietary factors that have been extensively studied for their implication in health and disease. Evidence from epidemiological studies and randomised controlled trials on their role in cardiovascular, inflammatory, and other diseases remains inconsistent. The objective of this study was to assess whether genetically predicted fatty acid concentrations affect the risk of disease across a wide variety of clinical health outcomes.<h4>Methods and findings</h4>The UK Biobank (UKB) is a large study involving over 500,000 participants aged 40 to 69 years at recruitment from 2006 to 2010. We used summary-level data for 117,143 UKB samples (base dataset), to extract genetic associations of fatty acids, and individual-level data for 322,232 UKB participants (target dataset) to conduct our discovery analysis. We studied potentially causal relationships of circulating fatty acids with 845 clinical diagnoses, using mendelian randomisation (MR) approach, within a phenome-wide association study (PheWAS) framework. Regression models in PheWAS were adjusted for sex, age, and the first 10 genetic principal components. External summary statistics were used for replication. When several fatty acids were associated with a health outcome, multivariable MR and MR-Bayesian method averaging (MR-BMA) was applied to disentangle their causal role. Genetic predisposition to higher docosahexaenoic acid (DHA) was associated with cholelithiasis and cholecystitis (odds ratio per mmol/L: 0.76, 95% confidence interval: 0.66 to 0.87). This was supported in replication analysis (FinnGen study) and by the genetically predicted omega-3 fatty acids analyses. Genetically predicted linoleic acid (LA), omega-6, polyunsaturated fatty acids (PUFAs), and total fatty acids (total FAs) showed positive associations with cardiovascular outcomes with support from replication analysis. Finally, higher genetically predicted levels of DHA (0.83, 0.73 to 0.95) and omega-3 (0.83, 0.75 to 0.92) were found to have a protective effect on obesity, which was supported using body mass index (BMI) in the GIANT consortium as replication analysis. Multivariable MR analysis suggested a direct detrimental effect of LA (1.64, 1.07 to 2.50) and omega-6 fatty acids (1.81, 1.06 to 3.09) on coronary heart disease (CHD). MR-BMA prioritised LA and omega-6 fatty acids as the top risk factors for CHD. Although we present a range of sensitivity analyses to the address MR assumptions, horizontal pleiotropy may still bias the reported associations and further evaluation in clinical trials is needed.<h4>Conclusions</h4>Our study suggests potentially protective effects of circulating DHA and omega-3 concentrations on cholelithiasis and cholecystitis and on obesity, highlighting the need to further assess them as prevention treatments in clinical trials. Moreover, our findings do not support the supplementation of unsaturated fatty acids for cardiovascular disease prevention.",
+    "laySummary": "",
+    "urls": "pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004141&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004141; html:https://europepmc.org/articles/PMC9799317; pdf:https://europepmc.org/articles/PMC9799317?pdf=render"
+  },
   {
     "id": "37395705",
     "doi": "https://doi.org/10.1167/tvst.12.7.3",
@@ -23187,23 +23221,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1167/tvst.12.7.3; doi:https://doi.org/10.1167/tvst.12.7.3; html:https://europepmc.org/articles/PMC10324418; pdf:https://europepmc.org/articles/PMC10324418?pdf=render"
   },
-  {
-    "id": "38091687",
-    "doi": "https://doi.org/10.1016/j.bjps.2023.10.106",
-    "title": "Revisiting basal cell carcinoma clinical margins: Leveraging natural language processing and multivariate analysis with updated Royal College of Pathologists histological reporting standards.",
-    "authorString": "Ali SR, Dobbs TD, Jovic M, Strafford H, Lacey AS, Williams N, Pickrell WO, Hutchings HA, Whitaker IS.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of plastic, reconstructive & aesthetic surgery : JPRAS",
-    "pubYear": "2024",
-    "date": "2023-10-20",
-    "isOpenAccess": "N",
-    "keywords": "multivariate analysis; Royal College Of Pathologists; Basal Cell Carcinoma; Natural Language Processing; Clinical Margins; Histological Reporting Guidelines",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>Data supporting the current British Association of Dermatologists guidelines for the management of basal cell carcinoma (BCC) are based on historic studies and do not consider the updated Royal College of Pathologists (RCPath) histological reporting standards. The aim of this study was to use natural language processing (NLP)-derived data and undertake a multivariate analysis with updated RCPath standards, providing a contemporary update on the excision margins required to achieve histological clearance in BCC.<h4>Methods</h4>A validated NLP information extraction model was used to perform a rapid multi-centre, pan-specialty, consecutive retrospective analysis of BCCs, managed with surgical excision using a pre-determined clinical margin, over a 17-year period (2004-2021) at Swansea Bay University Health Board. Logistic regression assessed the relationship between the peripheral and deep margins and histological clearance.<h4>Results</h4>We ran our NLP algorithm on 34,955 BCCs. Out of the 1447 BCCs that met the inclusion criteria, the peripheral margin clearance was not influenced by the BCC risk level (p\u00a0=\u00a00.670). A clinical peripheral margin of 6\u00a0mm achieved a 95% histological clearance rate (95% confidence interval [CI], 0.93-0.98). Tumour thickness inversely affected deep-margin histological clearance (OR 0.720, 95% CI, 0.525-0.991, p\u00a0<\u00a00.05). Depth level 2 had a 97% probability of achieving deep-margin histological clearance across all tumour thicknesses.<h4>Conclusion</h4>Updated RCPath reporting standards minimally impact the peripheral margin histological clearance in BCC. Larger clinical peripheral margins than those indicated by current guidelines may be necessary to achieve excision rates of \u226595%. These findings emphasise the need for continuous reassessment of clinical standards to enhance patient care.",
-    "laySummary": "",
-    "urls": "pdf:http://www.jprasurg.com/article/S1748681523006769/pdf; doi:https://doi.org/10.1016/j.bjps.2023.10.106"
-  },
   {
     "id": "34304048",
     "doi": "https://doi.org/10.1016/j.ebiom.2021.103485",
@@ -23221,6 +23238,23 @@
     "laySummary": "",
     "urls": "pdf:http://www.thelancet.com/article/S2352396421002784/pdf; doi:https://doi.org/10.1016/j.ebiom.2021.103485; html:https://europepmc.org/articles/PMC8299112; pdf:https://europepmc.org/articles/PMC8299112?pdf=render"
   },
+  {
+    "id": "38091687",
+    "doi": "https://doi.org/10.1016/j.bjps.2023.10.106",
+    "title": "Revisiting basal cell carcinoma clinical margins: Leveraging natural language processing and multivariate analysis with updated Royal College of Pathologists histological reporting standards.",
+    "authorString": "Ali SR, Dobbs TD, Jovic M, Strafford H, Lacey AS, Williams N, Pickrell WO, Hutchings HA, Whitaker IS.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of plastic, reconstructive & aesthetic surgery : JPRAS",
+    "pubYear": "2024",
+    "date": "2023-10-20",
+    "isOpenAccess": "N",
+    "keywords": "multivariate analysis; Royal College Of Pathologists; Basal Cell Carcinoma; Natural Language Processing; Clinical Margins; Histological Reporting Guidelines",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>Data supporting the current British Association of Dermatologists guidelines for the management of basal cell carcinoma (BCC) are based on historic studies and do not consider the updated Royal College of Pathologists (RCPath) histological reporting standards. The aim of this study was to use natural language processing (NLP)-derived data and undertake a multivariate analysis with updated RCPath standards, providing a contemporary update on the excision margins required to achieve histological clearance in BCC.<h4>Methods</h4>A validated NLP information extraction model was used to perform a rapid multi-centre, pan-specialty, consecutive retrospective analysis of BCCs, managed with surgical excision using a pre-determined clinical margin, over a 17-year period (2004-2021) at Swansea Bay University Health Board. Logistic regression assessed the relationship between the peripheral and deep margins and histological clearance.<h4>Results</h4>We ran our NLP algorithm on 34,955 BCCs. Out of the 1447 BCCs that met the inclusion criteria, the peripheral margin clearance was not influenced by the BCC risk level (p\u00a0=\u00a00.670). A clinical peripheral margin of 6\u00a0mm achieved a 95% histological clearance rate (95% confidence interval [CI], 0.93-0.98). Tumour thickness inversely affected deep-margin histological clearance (OR 0.720, 95% CI, 0.525-0.991, p\u00a0<\u00a00.05). Depth level 2 had a 97% probability of achieving deep-margin histological clearance across all tumour thicknesses.<h4>Conclusion</h4>Updated RCPath reporting standards minimally impact the peripheral margin histological clearance in BCC. Larger clinical peripheral margins than those indicated by current guidelines may be necessary to achieve excision rates of \u226595%. These findings emphasise the need for continuous reassessment of clinical standards to enhance patient care.",
+    "laySummary": "",
+    "urls": "pdf:http://www.jprasurg.com/article/S1748681523006769/pdf; doi:https://doi.org/10.1016/j.bjps.2023.10.106"
+  },
   {
     "id": "37337639",
     "doi": "https://doi.org/10.1002/ctm2.1291",
@@ -23459,23 +23493,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1210/clinem/dgad276; doi:https://doi.org/10.1210/clinem/dgad276; html:https://europepmc.org/articles/PMC10584009"
   },
-  {
-    "id": "38528983",
-    "doi": "https://doi.org/10.3389/fpsyt.2024.1347100",
-    "title": "Machine learning in mental health and its relationship with epidemiological practice.",
-    "authorString": "DelPozo-Banos M, Stewart R, John A.",
-    "authorAffiliations": "",
-    "journalTitle": "Frontiers in psychiatry",
-    "pubYear": "2024",
-    "date": "2024-03-11",
-    "isOpenAccess": "Y",
-    "keywords": "Research methods; Mental health; epidemiology; Machine Learning; Challenges And Opportunities",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "",
-    "urls": "pdf:https://www.frontiersin.org/journals/psychiatry/articles/10.3389/fpsyt.2024.1347100/pdf; doi:https://doi.org/10.3389/fpsyt.2024.1347100; html:https://europepmc.org/articles/PMC10961376; pdf:https://europepmc.org/articles/PMC10961376?pdf=render"
-  },
   {
     "id": "34873584",
     "doi": "https://doi.org/10.1016/j.eclinm.2021.101212",
@@ -23494,21 +23511,21 @@
     "urls": "pdf:https://discovery.ucl.ac.uk/10139946/1/Sudre_PIIS2589537021004934.pdf; doi:https://doi.org/10.1016/j.eclinm.2021.101212; html:https://europepmc.org/articles/PMC8635464; pdf:https://europepmc.org/articles/PMC8635464?pdf=render"
   },
   {
-    "id": "36501061",
-    "doi": "https://doi.org/10.3390/nu14235031",
-    "title": "Associations of Genetically Predicted Vitamin B<sub>12</sub> Status across the Phenome.",
-    "authorString": "Dib MJ, Ahmadi KR, Zagkos L, Gill D, Morris B, Elliott P, Dehghan A, Tzoulaki I.",
+    "id": "38528983",
+    "doi": "https://doi.org/10.3389/fpsyt.2024.1347100",
+    "title": "Machine learning in mental health and its relationship with epidemiological practice.",
+    "authorString": "DelPozo-Banos M, Stewart R, John A.",
     "authorAffiliations": "",
-    "journalTitle": "Nutrients",
-    "pubYear": "2022",
-    "date": "2022-11-26",
+    "journalTitle": "Frontiers in psychiatry",
+    "pubYear": "2024",
+    "date": "2024-03-11",
     "isOpenAccess": "Y",
-    "keywords": "Vitamin B12; Deficiency; epidemiology; Mendelian Randomisation; Pernicious Anaemia",
+    "keywords": "Research methods; Mental health; epidemiology; Machine Learning; Challenges And Opportunities",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Variation in vitamin B<sub>12</sub> levels has been associated with a range of diseases across the life-course, the causal nature of which remains elusive. We aimed to interrogate genetically predicted vitamin B<sub>12</sub> status in relation to a plethora of clinical outcomes available in the UK Biobank. Genome-wide association study (GWAS) summary data obtained from a Danish and Icelandic cohort of 45,576 individuals were used to identify 8 genetic variants associated with vitamin B<sub>12</sub> levels, serving as genetic instruments for vitamin B<sub>12</sub> status in subsequent analyses. We conducted a Mendelian randomisation (MR)-phenome-wide association study (PheWAS) of vitamin B<sub>12</sub> status with 945 distinct phenotypes in 439,738 individuals from the UK Biobank using these 8 genetic instruments to proxy alterations in vitamin B<sub>12</sub> status. We used external GWAS summary statistics for replication of significant findings. Correction for multiple testing was taken into consideration using a 5% false discovery rate (FDR) threshold. MR analysis identified an association between higher genetically predicted vitamin B<sub>12</sub> status and lower risk of vitamin B deficiency (including all B vitamin deficiencies), serving as a positive control outcome. We further identified associations between higher genetically predicted vitamin B<sub>12</sub> status and a reduced risk of megaloblastic anaemia (OR = 0.35, 95% CI: 0.20-0.50) and pernicious anaemia (0.29, 0.19-0.45), which was supported in replication analyses. Our study highlights that higher genetically predicted vitamin B<sub>12</sub> status is potentially protective of risk of vitamin B<sub>12</sub> deficiency associated with pernicious anaemia diagnosis, and reduces risk of megaloblastic anaemia. The potential use of genetically predicted vitamin B<sub>12</sub> status in disease diagnosis, progression and management remains to be investigated.",
+    "abstract": "",
     "laySummary": "",
-    "urls": "pdf:https://www.mdpi.com/2072-6643/14/23/5031/pdf?version=1669449806; doi:https://doi.org/10.3390/nu14235031; html:https://europepmc.org/articles/PMC9740080; pdf:https://europepmc.org/articles/PMC9740080?pdf=render"
+    "urls": "pdf:https://www.frontiersin.org/journals/psychiatry/articles/10.3389/fpsyt.2024.1347100/pdf; doi:https://doi.org/10.3389/fpsyt.2024.1347100; html:https://europepmc.org/articles/PMC10961376; pdf:https://europepmc.org/articles/PMC10961376?pdf=render"
   },
   {
     "id": "36194451",
@@ -23528,21 +23545,21 @@
     "urls": "pdf:https://mhealth.jmir.org/2022/10/e40667/PDF; doi:https://doi.org/10.2196/40667; html:https://europepmc.org/articles/PMC9579931"
   },
   {
-    "id": "36707908",
-    "doi": "https://doi.org/10.1186/s13643-023-02173-w",
-    "title": "A comparison of international modelling methods to evaluate health economics of colorectal cancer screening: a systematic review protocol.",
-    "authorString": "Adair O, McFerran E, Owen T, McKee C, Lamrock F, Lawler M.",
+    "id": "36501061",
+    "doi": "https://doi.org/10.3390/nu14235031",
+    "title": "Associations of Genetically Predicted Vitamin B<sub>12</sub> Status across the Phenome.",
+    "authorString": "Dib MJ, Ahmadi KR, Zagkos L, Gill D, Morris B, Elliott P, Dehghan A, Tzoulaki I.",
     "authorAffiliations": "",
-    "journalTitle": "Systematic reviews",
-    "pubYear": "2023",
-    "date": "2023-01-27",
+    "journalTitle": "Nutrients",
+    "pubYear": "2022",
+    "date": "2022-11-26",
     "isOpenAccess": "Y",
-    "keywords": "Screening; Economic evaluation; Colorectal Cancer; Health Economics; Cost-effectiveness Analysis; Quality-adjusted Life Years; Cost-utility; Incremental Cost-effectiveness Ratio; Cost\u2013benefit; Life Years Gained",
+    "keywords": "Vitamin B12; Deficiency; epidemiology; Mendelian Randomisation; Pernicious Anaemia",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Colorectal cancer (CRC) is becoming an increasing health problem worldwide. However, with the help of screening, early diagnosis can reduce incidence and mortality rates. To elevate the economic burden that CRC can cause, cost-effectiveness analysis (CEA) can assist healthcare systems to make screening programmes more cost-effective and prolong survival for early-stage CRC patients. This review aims to identify different CEA modelling methods used internationally to evaluate health economics of CRC screening.<h4>Methods</h4>This review will systematically search electronic databases which include MEDLINE, EMBASE, Web of Science and Scopus. The Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidance recommendations will design the review, and the Consolidated Health Economic Evaluation Reporting Standards (CHEERS) statement will be used to extract relevant data from studies retrieved. Two reviewers will screen through the evidence using the PICOS (Participant, Intervention, Comparators, Outcomes, Study Design) framework, with a third reviewer to settle any disagreements. Once data extraction and quality assessment are complete, the results will be presented qualitatively and tabulated using the CHEERS checklist.<h4>Discussion</h4>The results obtained from the systematic review will highlight how different CRC screening programmes around the world utilise and incorporate health economic modelling methods to be more cost-effective. This information can help modellers develop CEA models which can be adapted to suit the specific screening programmes that they are evaluating.<h4>Systematic review registration</h4>PROSPERO CRD42022296113.",
+    "abstract": "Variation in vitamin B<sub>12</sub> levels has been associated with a range of diseases across the life-course, the causal nature of which remains elusive. We aimed to interrogate genetically predicted vitamin B<sub>12</sub> status in relation to a plethora of clinical outcomes available in the UK Biobank. Genome-wide association study (GWAS) summary data obtained from a Danish and Icelandic cohort of 45,576 individuals were used to identify 8 genetic variants associated with vitamin B<sub>12</sub> levels, serving as genetic instruments for vitamin B<sub>12</sub> status in subsequent analyses. We conducted a Mendelian randomisation (MR)-phenome-wide association study (PheWAS) of vitamin B<sub>12</sub> status with 945 distinct phenotypes in 439,738 individuals from the UK Biobank using these 8 genetic instruments to proxy alterations in vitamin B<sub>12</sub> status. We used external GWAS summary statistics for replication of significant findings. Correction for multiple testing was taken into consideration using a 5% false discovery rate (FDR) threshold. MR analysis identified an association between higher genetically predicted vitamin B<sub>12</sub> status and lower risk of vitamin B deficiency (including all B vitamin deficiencies), serving as a positive control outcome. We further identified associations between higher genetically predicted vitamin B<sub>12</sub> status and a reduced risk of megaloblastic anaemia (OR = 0.35, 95% CI: 0.20-0.50) and pernicious anaemia (0.29, 0.19-0.45), which was supported in replication analyses. Our study highlights that higher genetically predicted vitamin B<sub>12</sub> status is potentially protective of risk of vitamin B<sub>12</sub> deficiency associated with pernicious anaemia diagnosis, and reduces risk of megaloblastic anaemia. The potential use of genetically predicted vitamin B<sub>12</sub> status in disease diagnosis, progression and management remains to be investigated.",
     "laySummary": "",
-    "urls": "pdf:https://systematicreviewsjournal.biomedcentral.com/counter/pdf/10.1186/s13643-023-02173-w; doi:https://doi.org/10.1186/s13643-023-02173-w; html:https://europepmc.org/articles/PMC9883863; pdf:https://europepmc.org/articles/PMC9883863?pdf=render"
+    "urls": "pdf:https://www.mdpi.com/2072-6643/14/23/5031/pdf?version=1669449806; doi:https://doi.org/10.3390/nu14235031; html:https://europepmc.org/articles/PMC9740080; pdf:https://europepmc.org/articles/PMC9740080?pdf=render"
   },
   {
     "id": "34639458",
@@ -23578,6 +23595,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCGEN.121.003542; doi:https://doi.org/10.1161/CIRCGEN.121.003542; html:https://europepmc.org/articles/PMC10525909; pdf:https://europepmc.org/articles/PMC10525909?pdf=render; doi:https://doi.org/10.1161/circgen.121.003542"
   },
+  {
+    "id": "36707908",
+    "doi": "https://doi.org/10.1186/s13643-023-02173-w",
+    "title": "A comparison of international modelling methods to evaluate health economics of colorectal cancer screening: a systematic review protocol.",
+    "authorString": "Adair O, McFerran E, Owen T, McKee C, Lamrock F, Lawler M.",
+    "authorAffiliations": "",
+    "journalTitle": "Systematic reviews",
+    "pubYear": "2023",
+    "date": "2023-01-27",
+    "isOpenAccess": "Y",
+    "keywords": "Screening; Economic evaluation; Colorectal Cancer; Health Economics; Cost-effectiveness Analysis; Quality-adjusted Life Years; Cost-utility; Incremental Cost-effectiveness Ratio; Cost\u2013benefit; Life Years Gained",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Colorectal cancer (CRC) is becoming an increasing health problem worldwide. However, with the help of screening, early diagnosis can reduce incidence and mortality rates. To elevate the economic burden that CRC can cause, cost-effectiveness analysis (CEA) can assist healthcare systems to make screening programmes more cost-effective and prolong survival for early-stage CRC patients. This review aims to identify different CEA modelling methods used internationally to evaluate health economics of CRC screening.<h4>Methods</h4>This review will systematically search electronic databases which include MEDLINE, EMBASE, Web of Science and Scopus. The Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidance recommendations will design the review, and the Consolidated Health Economic Evaluation Reporting Standards (CHEERS) statement will be used to extract relevant data from studies retrieved. Two reviewers will screen through the evidence using the PICOS (Participant, Intervention, Comparators, Outcomes, Study Design) framework, with a third reviewer to settle any disagreements. Once data extraction and quality assessment are complete, the results will be presented qualitatively and tabulated using the CHEERS checklist.<h4>Discussion</h4>The results obtained from the systematic review will highlight how different CRC screening programmes around the world utilise and incorporate health economic modelling methods to be more cost-effective. This information can help modellers develop CEA models which can be adapted to suit the specific screening programmes that they are evaluating.<h4>Systematic review registration</h4>PROSPERO CRD42022296113.",
+    "laySummary": "",
+    "urls": "pdf:https://systematicreviewsjournal.biomedcentral.com/counter/pdf/10.1186/s13643-023-02173-w; doi:https://doi.org/10.1186/s13643-023-02173-w; html:https://europepmc.org/articles/PMC9883863; pdf:https://europepmc.org/articles/PMC9883863?pdf=render"
+  },
   {
     "id": "39215973",
     "doi": "https://doi.org/10.1093/eurheartj/ehae611",
@@ -23646,23 +23680,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ageing/article-pdf/52/9/afad176/51729004/afad176.pdf; doi:https://doi.org/10.1093/ageing/afad176; html:https://europepmc.org/articles/PMC10517713; pdf:https://europepmc.org/articles/PMC10517713?pdf=render"
   },
-  {
-    "id": "37645022",
-    "doi": "https://doi.org/10.1183/20734735.0058-2023",
-    "title": "The impact of poor housing and indoor air quality on respiratory health in children.",
-    "authorString": "Holden KA, Lee AR, Hawcutt DB, Sinha IP.",
-    "authorAffiliations": "",
-    "journalTitle": "Breathe (Sheffield, England)",
-    "pubYear": "2023",
-    "date": "2023-06-01",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "It is becoming increasingly apparent that poor housing quality affects indoor air quality, significantly impacting on respiratory health in children and young people. Exposure to damp and/or mould in the home, cold homes and the presence of pests and pollutants all have a significant detrimental impact on child respiratory health. There is a complex relationship between features of poor-quality housing, such as being in a state of disrepair, poor ventilation, overcrowding and being cold, that favour an environment resulting in poor indoor air quality. Children living in rented (private or public) housing are more likely to come from lower-income backgrounds and are most at risk of living in substandard housing posing a serious threat to respiratory health. Children have the right to safe and adequate housing, and research has shown that either rehousing or making modifications to poor-quality housing to improve indoor air quality results in improved respiratory health. Urgent action is needed to address this threat to health. All stakeholders should understand the relationship between poor-quality housing and respiratory health in children and act, working with families, to redress this modifiable risk factor.<h4>Educational aims</h4>The reader should understand how housing quality and indoor air quality affect respiratory health in children.The reader should understand which children are at most risk of living in poor-quality housing.The reader should understand what policy recommendations have been made and what actions need to be undertaken to improve housing quality and respiratory health in children and young people.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1183/20734735.0058-2023; html:https://europepmc.org/articles/PMC10461733; pdf:https://europepmc.org/articles/PMC10461733?pdf=render"
-  },
   {
     "id": "37505992",
     "doi": "https://doi.org/10.1093/ageing/afad136",
@@ -23680,6 +23697,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ageing/article-pdf/52/7/afad136/50976589/afad136.pdf; doi:https://doi.org/10.1093/ageing/afad136; html:https://europepmc.org/articles/PMC10378723; pdf:https://europepmc.org/articles/PMC10378723?pdf=render"
   },
+  {
+    "id": "37645022",
+    "doi": "https://doi.org/10.1183/20734735.0058-2023",
+    "title": "The impact of poor housing and indoor air quality on respiratory health in children.",
+    "authorString": "Holden KA, Lee AR, Hawcutt DB, Sinha IP.",
+    "authorAffiliations": "",
+    "journalTitle": "Breathe (Sheffield, England)",
+    "pubYear": "2023",
+    "date": "2023-06-01",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "It is becoming increasingly apparent that poor housing quality affects indoor air quality, significantly impacting on respiratory health in children and young people. Exposure to damp and/or mould in the home, cold homes and the presence of pests and pollutants all have a significant detrimental impact on child respiratory health. There is a complex relationship between features of poor-quality housing, such as being in a state of disrepair, poor ventilation, overcrowding and being cold, that favour an environment resulting in poor indoor air quality. Children living in rented (private or public) housing are more likely to come from lower-income backgrounds and are most at risk of living in substandard housing posing a serious threat to respiratory health. Children have the right to safe and adequate housing, and research has shown that either rehousing or making modifications to poor-quality housing to improve indoor air quality results in improved respiratory health. Urgent action is needed to address this threat to health. All stakeholders should understand the relationship between poor-quality housing and respiratory health in children and act, working with families, to redress this modifiable risk factor.<h4>Educational aims</h4>The reader should understand how housing quality and indoor air quality affect respiratory health in children.The reader should understand which children are at most risk of living in poor-quality housing.The reader should understand what policy recommendations have been made and what actions need to be undertaken to improve housing quality and respiratory health in children and young people.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1183/20734735.0058-2023; html:https://europepmc.org/articles/PMC10461733; pdf:https://europepmc.org/articles/PMC10461733?pdf=render"
+  },
   {
     "id": "37532769",
     "doi": "https://doi.org/10.1038/s42003-023-05171-9",
@@ -23901,23 +23935,6 @@
     "laySummary": "",
     "urls": "pdf:https://formative.jmir.org/2023/1/e44126/PDF; doi:https://doi.org/10.2196/44126; html:https://europepmc.org/articles/PMC10365629; pdf:https://europepmc.org/articles/PMC10365629?pdf=render"
   },
-  {
-    "id": "34125897",
-    "doi": "https://doi.org/10.1093/nar/gkab449",
-    "title": "DGLinker: flexible knowledge-graph prediction of disease-gene associations.",
-    "authorString": "Hu J, Lepore R, Dobson RJB, Al-Chalabi A, M Bean D, Iacoangeli A.",
-    "authorAffiliations": "",
-    "journalTitle": "Nucleic acids research",
-    "pubYear": "2021",
-    "date": "2021-07-01",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "As a result of the advent of high-throughput technologies, there has been rapid progress in our understanding of the genetics underlying biological processes. However, despite such advances, the genetic landscape of human diseases has only marginally been disclosed. Exploiting the present availability of large amounts of biological and phenotypic data, we can use our current understanding of disease genetics to train machine learning models to predict novel genetic factors associated with the disease. To this end, we developed DGLinker, a webserver for the prediction of novel candidate genes for human diseases given a set of known disease genes. DGLinker has a user-friendly interface that allows non-expert users to exploit biomedical information from a wide range of biological and phenotypic databases, and/or to upload their own data, to generate a knowledge-graph and use machine learning to predict new disease-associated genes. The webserver includes tools to explore and interpret the results and generates publication-ready figures. DGLinker is available at https://dglinker.rosalind.kcl.ac.uk. The webserver is free and open to all users without the need for registration.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1093/nar/gkab449; doi:https://doi.org/10.1093/nar/gkab449; html:https://europepmc.org/articles/PMC8262728; pdf:https://europepmc.org/articles/PMC8262728?pdf=render"
-  },
   {
     "id": "33655501",
     "doi": "https://doi.org/10.1111/bjd.19885",
@@ -23935,6 +23952,23 @@
     "laySummary": "",
     "urls": "pdf:https://researchonline.lshtm.ac.uk/id/eprint/4660846/7/Mulick_etal_2021_Four-childhood-atopic-dermatitis-subtypes.pdf; doi:https://doi.org/10.1111/bjd.19885; html:https://europepmc.org/articles/PMC8410876; pdf:https://europepmc.org/articles/PMC8410876?pdf=render; doi:https://doi.org/10.1111/bjd.19885"
   },
+  {
+    "id": "34125897",
+    "doi": "https://doi.org/10.1093/nar/gkab449",
+    "title": "DGLinker: flexible knowledge-graph prediction of disease-gene associations.",
+    "authorString": "Hu J, Lepore R, Dobson RJB, Al-Chalabi A, M Bean D, Iacoangeli A.",
+    "authorAffiliations": "",
+    "journalTitle": "Nucleic acids research",
+    "pubYear": "2021",
+    "date": "2021-07-01",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "As a result of the advent of high-throughput technologies, there has been rapid progress in our understanding of the genetics underlying biological processes. However, despite such advances, the genetic landscape of human diseases has only marginally been disclosed. Exploiting the present availability of large amounts of biological and phenotypic data, we can use our current understanding of disease genetics to train machine learning models to predict novel genetic factors associated with the disease. To this end, we developed DGLinker, a webserver for the prediction of novel candidate genes for human diseases given a set of known disease genes. DGLinker has a user-friendly interface that allows non-expert users to exploit biomedical information from a wide range of biological and phenotypic databases, and/or to upload their own data, to generate a knowledge-graph and use machine learning to predict new disease-associated genes. The webserver includes tools to explore and interpret the results and generates publication-ready figures. DGLinker is available at https://dglinker.rosalind.kcl.ac.uk. The webserver is free and open to all users without the need for registration.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1093/nar/gkab449; doi:https://doi.org/10.1093/nar/gkab449; html:https://europepmc.org/articles/PMC8262728; pdf:https://europepmc.org/articles/PMC8262728?pdf=render"
+  },
   {
     "id": "38023948",
     "doi": "https://doi.org/10.18332/ejm/171802",
@@ -23969,23 +24003,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ajcn/article-pdf/112/6/1485/34844146/nqaa266.pdf; doi:https://doi.org/10.1093/ajcn/nqaa266"
   },
-  {
-    "id": "38932357",
-    "doi": "https://doi.org/10.3390/vaccines12060628",
-    "title": "COVID-19 Vaccine Uptake and Effectiveness by Time since Vaccination in the Western Cape Province, South Africa: An Observational Cohort Study during 2020-2022.",
-    "authorString": "Kassanjee R, Davies MA, Heekes A, Mahomed H, Hawkridge AJ, Morden E, Jacobs T, Cohen C, Moultrie H, Lessells RJ, Van Der Walt N, Arendse JO, Wolter N, Walaza S, Jassat W, von Gottberg A, Hannan PL, Feikin DR, Cloete K, Boulle A.",
-    "authorAffiliations": "",
-    "journalTitle": "Vaccines",
-    "pubYear": "2024",
-    "date": "2024-06-05",
-    "isOpenAccess": "Y",
-    "keywords": "Cohort; South Africa; Vaccine Effectiveness; Observational; Covid-19; Sars-cov-2",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "There are few data on the real-world effectiveness of COVID-19 vaccines and boosting in Africa, which experienced widespread SARS-CoV-2 infection before vaccine availability. We assessed the association between vaccination and severe COVID-19 in the Western Cape, South Africa, in an observational cohort study of >2 million adults during 2020-2022. We described SARS-CoV-2 testing, COVID-19 outcomes, and vaccine uptake over time. We used multivariable cox models to estimate the association of BNT162b2 and Ad26.COV2.S vaccination with COVID-19-related hospitalization and death, adjusting for demographic characteristics, underlying health conditions, socioeconomic status proxies, and healthcare utilization. We found that by the end of 2022, 41% of surviving adults had completed vaccination and 8% had received a booster dose. Recent vaccination was associated with notable reductions in severe COVID-19 during periods dominated by Delta, and Omicron BA.1/2 and BA.4/5 (sub)lineages. During the latest Omicron BA.4/5 wave, within 3 months of vaccination or boosting, BNT162b2 and Ad26.COV2.S were each 84% effective against death (95% CIs: 57-94 and 49-95, respectively). However, distinct reductions of effectiveness occurred at longer times post completing or boosting vaccination. Results highlight the importance of continued emphasis on COVID-19 vaccination and boosting for those at high risk of severe COVID-19, even in settings with widespread infection-induced immunity.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.3390/vaccines12060628; html:https://europepmc.org/articles/PMC11209070; pdf:https://europepmc.org/articles/PMC11209070?pdf=render"
-  },
   {
     "id": "36648036",
     "doi": "https://doi.org/10.1016/j.jcmg.2022.06.011",
@@ -24003,6 +24020,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.jcmg.2022.06.011; doi:https://doi.org/10.1016/j.jcmg.2022.06.011; html:https://europepmc.org/articles/PMC10102720; pdf:https://europepmc.org/articles/PMC10102720?pdf=render"
   },
+  {
+    "id": "38932357",
+    "doi": "https://doi.org/10.3390/vaccines12060628",
+    "title": "COVID-19 Vaccine Uptake and Effectiveness by Time since Vaccination in the Western Cape Province, South Africa: An Observational Cohort Study during 2020-2022.",
+    "authorString": "Kassanjee R, Davies MA, Heekes A, Mahomed H, Hawkridge AJ, Morden E, Jacobs T, Cohen C, Moultrie H, Lessells RJ, Van Der Walt N, Arendse JO, Wolter N, Walaza S, Jassat W, von Gottberg A, Hannan PL, Feikin DR, Cloete K, Boulle A.",
+    "authorAffiliations": "",
+    "journalTitle": "Vaccines",
+    "pubYear": "2024",
+    "date": "2024-06-05",
+    "isOpenAccess": "Y",
+    "keywords": "Cohort; South Africa; Vaccine Effectiveness; Observational; Covid-19; Sars-cov-2",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "There are few data on the real-world effectiveness of COVID-19 vaccines and boosting in Africa, which experienced widespread SARS-CoV-2 infection before vaccine availability. We assessed the association between vaccination and severe COVID-19 in the Western Cape, South Africa, in an observational cohort study of >2 million adults during 2020-2022. We described SARS-CoV-2 testing, COVID-19 outcomes, and vaccine uptake over time. We used multivariable cox models to estimate the association of BNT162b2 and Ad26.COV2.S vaccination with COVID-19-related hospitalization and death, adjusting for demographic characteristics, underlying health conditions, socioeconomic status proxies, and healthcare utilization. We found that by the end of 2022, 41% of surviving adults had completed vaccination and 8% had received a booster dose. Recent vaccination was associated with notable reductions in severe COVID-19 during periods dominated by Delta, and Omicron BA.1/2 and BA.4/5 (sub)lineages. During the latest Omicron BA.4/5 wave, within 3 months of vaccination or boosting, BNT162b2 and Ad26.COV2.S were each 84% effective against death (95% CIs: 57-94 and 49-95, respectively). However, distinct reductions of effectiveness occurred at longer times post completing or boosting vaccination. Results highlight the importance of continued emphasis on COVID-19 vaccination and boosting for those at high risk of severe COVID-19, even in settings with widespread infection-induced immunity.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.3390/vaccines12060628; html:https://europepmc.org/articles/PMC11209070; pdf:https://europepmc.org/articles/PMC11209070?pdf=render"
+  },
   {
     "id": "36357675",
     "doi": "https://doi.org/10.1038/s41591-022-02046-0",
@@ -24071,23 +24105,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s43587-022-00328-3.pdf; doi:https://doi.org/10.1038/s43587-022-00328-3; html:https://europepmc.org/articles/PMC10154221; pdf:https://europepmc.org/articles/PMC10154221?pdf=render"
   },
-  {
-    "id": "35537476",
-    "doi": "https://doi.org/10.1177/01410768221095245",
-    "title": "Indirect effects of the pandemic: highlighting the need for data-driven policy and preparedness.",
-    "authorString": "Banerjee A, Sudlow C, Lawler M.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of the Royal Society of Medicine",
-    "pubYear": "2022",
-    "date": "2022-05-10",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "",
-    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/01410768221095245; doi:https://doi.org/10.1177/01410768221095245; html:https://europepmc.org/articles/PMC9234890; pdf:https://europepmc.org/articles/PMC9234890?pdf=render"
-  },
   {
     "id": "31194737",
     "doi": "https://doi.org/10.1371/journal.pgen.1008164",
@@ -24105,6 +24122,23 @@
     "laySummary": "",
     "urls": "pdf:https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1008164&type=printable; doi:https://doi.org/10.1371/journal.pgen.1008164; html:https://europepmc.org/articles/PMC6592570; pdf:https://europepmc.org/articles/PMC6592570?pdf=render"
   },
+  {
+    "id": "35537476",
+    "doi": "https://doi.org/10.1177/01410768221095245",
+    "title": "Indirect effects of the pandemic: highlighting the need for data-driven policy and preparedness.",
+    "authorString": "Banerjee A, Sudlow C, Lawler M.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of the Royal Society of Medicine",
+    "pubYear": "2022",
+    "date": "2022-05-10",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "",
+    "laySummary": "",
+    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/01410768221095245; doi:https://doi.org/10.1177/01410768221095245; html:https://europepmc.org/articles/PMC9234890; pdf:https://europepmc.org/articles/PMC9234890?pdf=render"
+  },
   {
     "id": "35487738",
     "doi": "https://doi.org/10.1136/bmjopen-2021-057017",
@@ -24326,23 +24360,6 @@
     "laySummary": "",
     "urls": "pdf:https://heart.bmj.com/content/heartjnl/early/2022/03/10/heartjnl-2021-320417.full.pdf; doi:https://doi.org/10.1136/heartjnl-2021-320417; html:https://europepmc.org/articles/PMC9554073; pdf:https://europepmc.org/articles/PMC9554073?pdf=render"
   },
-  {
-    "id": "37119604",
-    "doi": "https://doi.org/10.1016/j.canep.2023.102367",
-    "title": "Whole-population trends in pathology-confirmed cancer incidence in Northern Ireland, Scotland and Wales during the SARS-CoV-2 pandemic: A retrospective observational study.",
-    "authorString": "Greene GJ, Thomson CS, Donnelly D, Chung D, Bhatti L, Gavin AT, Lawler M, Huws DW, Rolles MJ, Benn\u00e9e F, Morrison DS.",
-    "authorAffiliations": "",
-    "journalTitle": "Cancer epidemiology",
-    "pubYear": "2023",
-    "date": "2023-04-21",
-    "isOpenAccess": "Y",
-    "keywords": "Pandemic; Population-based Incidence; Covid-19; Sars-cov-2; Pathology-Confirmed Cancer",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>The COVID-19 epidemic interrupted normal cancer diagnosis procedures. Population-based cancer registries report incidence at least 18 months after it happens. Our goal was to make more timely estimates by using pathologically confirmed cancers (PDC) as a proxy for incidence. We compared the 2020 and 2021 PDC with the 2019 pre-pandemic baseline in Scotland, Wales, and Northern Ireland (NI).<h4>Methods</h4>Numbers of female breast (ICD-10 C50), lung (C33-34), colorectal (C18-20), gynaecological (C51-58), prostate (C61), head and neck (C00-C14, C30-32), upper gastro-intestinal (C15-16), urological (C64-68), malignant melanoma (C43), and non-melanoma skin (NMSC) (C44) cancers were counted. Multiple pairwise comparisons generated incidence rate ratios (IRR).<h4>Results</h4>Data were accessible within 5 months of the pathological diagnosis date. Between 2019 and 2020, the number of pathologically confirmed malignancies (excluding NMSC) decreased by 7315 (14.1 %). Scotland experienced early monthly declines of up to 64 % (colorectal cancers, April 2020 versus April 2019). Wales experienced the greatest overall change in 2020, but Northern Ireland experienced the quickest recovery. The pandemic's effects varied by cancer type, with no significant change in lung cancer diagnoses in Wales in 2020 (IRR 0.97 (95 % CI 0.90-1.05)), followed by an increase in 2021 (IRR 1.11 (1.03-1.20).<h4>Conclusion</h4>PDC are useful in reporting cancer incidence quicker than cancer registrations. Temporal and geographical differences between participating countries mirrored differences in responses to the COVID-19 pandemic, indicating face validity and the potential for quick cancer diagnosis assessment. To verify their sensitivity and specificity against the gold standard of cancer registrations, however, additional research is required.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.canep.2023.102367; html:https://europepmc.org/articles/PMC10121133; pdf:https://europepmc.org/articles/PMC10121133?pdf=render"
-  },
   {
     "id": "34137744",
     "doi": "https://doi.org/10.1097/ta.0000000000003317",
@@ -24360,6 +24377,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1097/TA.0000000000003317"
   },
+  {
+    "id": "37119604",
+    "doi": "https://doi.org/10.1016/j.canep.2023.102367",
+    "title": "Whole-population trends in pathology-confirmed cancer incidence in Northern Ireland, Scotland and Wales during the SARS-CoV-2 pandemic: A retrospective observational study.",
+    "authorString": "Greene GJ, Thomson CS, Donnelly D, Chung D, Bhatti L, Gavin AT, Lawler M, Huws DW, Rolles MJ, Benn\u00e9e F, Morrison DS.",
+    "authorAffiliations": "",
+    "journalTitle": "Cancer epidemiology",
+    "pubYear": "2023",
+    "date": "2023-04-21",
+    "isOpenAccess": "Y",
+    "keywords": "Pandemic; Population-based Incidence; Covid-19; Sars-cov-2; Pathology-Confirmed Cancer",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>The COVID-19 epidemic interrupted normal cancer diagnosis procedures. Population-based cancer registries report incidence at least 18 months after it happens. Our goal was to make more timely estimates by using pathologically confirmed cancers (PDC) as a proxy for incidence. We compared the 2020 and 2021 PDC with the 2019 pre-pandemic baseline in Scotland, Wales, and Northern Ireland (NI).<h4>Methods</h4>Numbers of female breast (ICD-10 C50), lung (C33-34), colorectal (C18-20), gynaecological (C51-58), prostate (C61), head and neck (C00-C14, C30-32), upper gastro-intestinal (C15-16), urological (C64-68), malignant melanoma (C43), and non-melanoma skin (NMSC) (C44) cancers were counted. Multiple pairwise comparisons generated incidence rate ratios (IRR).<h4>Results</h4>Data were accessible within 5 months of the pathological diagnosis date. Between 2019 and 2020, the number of pathologically confirmed malignancies (excluding NMSC) decreased by 7315 (14.1 %). Scotland experienced early monthly declines of up to 64 % (colorectal cancers, April 2020 versus April 2019). Wales experienced the greatest overall change in 2020, but Northern Ireland experienced the quickest recovery. The pandemic's effects varied by cancer type, with no significant change in lung cancer diagnoses in Wales in 2020 (IRR 0.97 (95 % CI 0.90-1.05)), followed by an increase in 2021 (IRR 1.11 (1.03-1.20).<h4>Conclusion</h4>PDC are useful in reporting cancer incidence quicker than cancer registrations. Temporal and geographical differences between participating countries mirrored differences in responses to the COVID-19 pandemic, indicating face validity and the potential for quick cancer diagnosis assessment. To verify their sensitivity and specificity against the gold standard of cancer registrations, however, additional research is required.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.canep.2023.102367; html:https://europepmc.org/articles/PMC10121133; pdf:https://europepmc.org/articles/PMC10121133?pdf=render"
+  },
   {
     "id": "33543581",
     "doi": "https://doi.org/10.1111/ans.16578",
@@ -24428,23 +24462,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.jid.2021.02.744"
   },
-  {
-    "id": "38660106",
-    "doi": "https://doi.org/10.1016/j.jacasi.2024.02.003",
-    "title": "Depression and Incident Cardiovascular\u00a0Disease.",
-    "authorString": "Pennells L, Mascie-Taylor CGN.",
-    "authorAffiliations": "",
-    "journalTitle": "JACC. Asia",
-    "pubYear": "2024",
-    "date": "2024-04-03",
-    "isOpenAccess": "Y",
-    "keywords": "Sex difference; Depression; Cardiovascular disease; epidemiology",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.jacasi.2024.02.003; html:https://europepmc.org/articles/PMC11035929; pdf:https://europepmc.org/articles/PMC11035929?pdf=render"
-  },
   {
     "id": "33517835",
     "doi": "https://doi.org/10.1080/17457300.2021.1876736",
@@ -24462,6 +24479,23 @@
     "laySummary": "",
     "urls": "pdf:https://figshare.com/articles/journal_contribution/Identify_the_key_characteristics_of_pedestrian_collisions_through_in-depth_interviews_a_pilot_study/13671482/1/files/26241158.pdf; doi:https://doi.org/10.1080/17457300.2021.1876736"
   },
+  {
+    "id": "38660106",
+    "doi": "https://doi.org/10.1016/j.jacasi.2024.02.003",
+    "title": "Depression and Incident Cardiovascular\u00a0Disease.",
+    "authorString": "Pennells L, Mascie-Taylor CGN.",
+    "authorAffiliations": "",
+    "journalTitle": "JACC. Asia",
+    "pubYear": "2024",
+    "date": "2024-04-03",
+    "isOpenAccess": "Y",
+    "keywords": "Sex difference; Depression; Cardiovascular disease; epidemiology",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.jacasi.2024.02.003; html:https://europepmc.org/articles/PMC11035929; pdf:https://europepmc.org/articles/PMC11035929?pdf=render"
+  },
   {
     "id": "36224187",
     "doi": "https://doi.org/10.1038/s41467-022-33826-4",
@@ -24496,23 +24530,6 @@
     "laySummary": "",
     "urls": "pdf:https://content.iospress.com:443/download/journal-of-alzheimers-disease/jad181085?id=journal-of-alzheimers-disease%2Fjad181085; doi:https://doi.org/10.3233/JAD-181085; html:https://europepmc.org/articles/PMC6484273; pdf:https://europepmc.org/articles/PMC6484273?pdf=render"
   },
-  {
-    "id": "38526449",
-    "doi": "https://doi.org/10.1002/clt2.12348",
-    "title": "Ethnic differences in depression and anxiety among adults with atopic eczema: Population-based matched cohort studies within UK primary care.",
-    "authorString": "Adesanya EI, Henderson A, Hayes JF, Lewin A, Mathur R, Mulick A, Morton C, Smith C, Langan SM, Mansfield KE.",
-    "authorAffiliations": "",
-    "journalTitle": "Clinical and translational allergy",
-    "pubYear": "2024",
-    "date": "2024-03-01",
-    "isOpenAccess": "Y",
-    "keywords": "Depression; Anxiety; epidemiology; Atopic Eczema; Ethnicity",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Evidence demonstrates that individuals with atopic eczema (eczema) have increased depression and anxiety; however, the role of ethnicity in these associations is poorly understood. We aimed to investigate whether associations between eczema and depression or anxiety differed between adults from white and minority ethnic groups in the UK.<h4>Methods</h4>We used UK Clinical Practice Research Datalink GOLD to conduct matched cohort studies of adults (\u226518\u00a0years) with ethnicity recorded in primary care electronic health records (April 2006-January 2020). We matched (age, sex, practice) adults with eczema to up to five adults without. We used stratified Cox regression with an interaction between eczema and ethnicity, to estimate hazard ratios (HRs) for associations between eczema and incident depression and anxiety in individuals from white ethnic groups and a pooled minority ethnic group (adults from Black, South Asian, Mixed and Other groups).<h4>Results</h4>We identified separate cohorts for depression (215,073 with eczema matched to 646,539 without) and anxiety (242,598 with eczema matched to 774,113 without). After adjusting for matching variables and potential confounders (age, sex, practice, deprivation, calendar period), we found strong evidence (p\u00a0<\u00a00.01) of ethnic differences in associations between eczema and depression (minority ethnic groups: HR\u00a0=\u00a01.33, 95% CI\u00a0=\u00a01.22,1.45; white ethnic groups: HR\u00a0=\u00a01.15, 95% CI\u00a0=\u00a01.12,1.17) and anxiety (minority ethnic groups: HR\u00a0=\u00a01.41, 95% CI\u00a0=\u00a01.28,1.55; white ethnic groups: HR\u00a0=\u00a01.17, 95% CI\u00a0=\u00a01.14,1.19).<h4>Conclusions</h4>Adults with eczema from minority ethnic groups appear to be at increased depression and anxiety risk compared with their white counterparts. Culturally adapted mental health promotion and prevention strategies should be considered in individuals with eczema from minority ethnic groups.",
-    "laySummary": "",
-    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/clt2.12348; doi:https://doi.org/10.1002/clt2.12348; html:https://europepmc.org/articles/PMC10962487; pdf:https://europepmc.org/articles/PMC10962487?pdf=render"
-  },
   {
     "id": "35816976",
     "doi": "https://doi.org/10.1016/j.jpsychires.2022.06.044",
@@ -24531,21 +24548,21 @@
     "urls": "doi:https://doi.org/10.1016/j.jpsychires.2022.06.044; doi:https://doi.org/10.1016/j.jpsychires.2022.06.044"
   },
   {
-    "id": "39277784",
-    "doi": "https://doi.org/10.1093/ndt/gfae203",
-    "title": "Empagliflozin lowers serum uric acid in chronic kidney disease: exploratory analyses from the EMPA-KIDNEY trial.",
-    "authorString": "Mayne KJ, Sardell RJ, Staplin N, Judge PK, Zhu D, Sammons E, Cherney DZI, Green JB, Levin A, Pontremoli R, Hauske SJ, Emberson J, Preiss D, Landray MJ, Baigent C, Wanner C, Haynes R, Herrington WG, EMPA-KIDNEY Collaborative Group\n.",
+    "id": "38526449",
+    "doi": "https://doi.org/10.1002/clt2.12348",
+    "title": "Ethnic differences in depression and anxiety among adults with atopic eczema: Population-based matched cohort studies within UK primary care.",
+    "authorString": "Adesanya EI, Henderson A, Hayes JF, Lewin A, Mathur R, Mulick A, Morton C, Smith C, Langan SM, Mansfield KE.",
     "authorAffiliations": "",
-    "journalTitle": "Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association",
+    "journalTitle": "Clinical and translational allergy",
     "pubYear": "2024",
-    "date": "2024-09-14",
+    "date": "2024-03-01",
     "isOpenAccess": "Y",
-    "keywords": "Uric acid; Gout; Sglt2 Inhibitor; Ckd; Empagliflozin",
+    "keywords": "Depression; Anxiety; epidemiology; Atopic Eczema; Ethnicity",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background and hypothesis</h4>Hyperuricaemia and gout are common in chronic kidney disease (CKD). We aimed to assess the effects of sodium-glucose co-transporter-2 (SGLT2) inhibition on uric acid (urate) and gout in patients with CKD.<h4>Methods</h4>The EMPA-KIDNEY trial randomised 6609 patients with CKD (estimated glomerular filtration rate [eGFR] \u226520 and <90\u00a0mL/min/1.73m2) to receive either empagliflozin 10\u00a0mg daily or matching placebo over a median of two years follow-up. Serum uric acid was measured at randomisation then 2 and 18 months of follow-up and the effects of empagliflozin were analysed using a pre-specified mixed model repeated measures approach. Participant-reported gout events were analysed in Cox regression models (first events) with the Andersen-Gill extension (total events). A post-hoc composite outcome included new initiation of uric acid lowering therapy or colchicine. EMPA-KIDNEY primary and kidney disease progression outcomes were also assessed in subgroups of baseline serum uric acid.<h4>Results</h4>Baseline mean\u00a0\u00b1\u00a0SD serum uric acid concentration was 431\u00b1114\u00a0\u00b5mol/L. Allocation to empagliflozin resulted in a study-average between-group difference in serum uric acid of -25.6 (95%CI -30.3,-21.0) \u00b5mol/L with larger effects in those with higher eGFR (trend P\u00a0<\u00a00.001) and without diabetes (heterogeneity P\u00a0<\u00a00.001). Compared to placebo, empagliflozin did not significantly reduce first or total gout events (HR 0.87, 95%CI 0.74-1.02 for the 595 first events, and 0.86, 0.72-1.03 for the 869 total events) with similar hazard ratios for the post-hoc composite and across subgroups, including by diabetes and eGFR. The effect of empagliflozin on the primary outcome and kidney disease progression outcomes were similar irrespective of baseline level of uric acid.<h4>Conclusion</h4>SGLT2 inhibition reduces serum uric acid in patients with CKD with larger effects at higher eGFR and in the absence of diabetes. However, the effect on uric acid is modest and did not translate into reduced risk of gout in EMPA-KIDNEY.",
+    "abstract": "<h4>Background</h4>Evidence demonstrates that individuals with atopic eczema (eczema) have increased depression and anxiety; however, the role of ethnicity in these associations is poorly understood. We aimed to investigate whether associations between eczema and depression or anxiety differed between adults from white and minority ethnic groups in the UK.<h4>Methods</h4>We used UK Clinical Practice Research Datalink GOLD to conduct matched cohort studies of adults (\u226518\u00a0years) with ethnicity recorded in primary care electronic health records (April 2006-January 2020). We matched (age, sex, practice) adults with eczema to up to five adults without. We used stratified Cox regression with an interaction between eczema and ethnicity, to estimate hazard ratios (HRs) for associations between eczema and incident depression and anxiety in individuals from white ethnic groups and a pooled minority ethnic group (adults from Black, South Asian, Mixed and Other groups).<h4>Results</h4>We identified separate cohorts for depression (215,073 with eczema matched to 646,539 without) and anxiety (242,598 with eczema matched to 774,113 without). After adjusting for matching variables and potential confounders (age, sex, practice, deprivation, calendar period), we found strong evidence (p\u00a0<\u00a00.01) of ethnic differences in associations between eczema and depression (minority ethnic groups: HR\u00a0=\u00a01.33, 95% CI\u00a0=\u00a01.22,1.45; white ethnic groups: HR\u00a0=\u00a01.15, 95% CI\u00a0=\u00a01.12,1.17) and anxiety (minority ethnic groups: HR\u00a0=\u00a01.41, 95% CI\u00a0=\u00a01.28,1.55; white ethnic groups: HR\u00a0=\u00a01.17, 95% CI\u00a0=\u00a01.14,1.19).<h4>Conclusions</h4>Adults with eczema from minority ethnic groups appear to be at increased depression and anxiety risk compared with their white counterparts. Culturally adapted mental health promotion and prevention strategies should be considered in individuals with eczema from minority ethnic groups.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1093/ndt/gfae203; html:https://europepmc.org/articles/PMC7616479; pdf:https://europepmc.org/articles/PMC7616479?pdf=render"
+    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/clt2.12348; doi:https://doi.org/10.1002/clt2.12348; html:https://europepmc.org/articles/PMC10962487; pdf:https://europepmc.org/articles/PMC10962487?pdf=render"
   },
   {
     "id": "32946613",
@@ -24564,6 +24581,23 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/cea.13741; doi:https://doi.org/10.1111/cea.13741"
   },
+  {
+    "id": "39277784",
+    "doi": "https://doi.org/10.1093/ndt/gfae203",
+    "title": "Empagliflozin lowers serum uric acid in chronic kidney disease: exploratory analyses from the EMPA-KIDNEY trial.",
+    "authorString": "Mayne KJ, Sardell RJ, Staplin N, Judge PK, Zhu D, Sammons E, Cherney DZI, Green JB, Levin A, Pontremoli R, Hauske SJ, Emberson J, Preiss D, Landray MJ, Baigent C, Wanner C, Haynes R, Herrington WG, EMPA-KIDNEY Collaborative Group\n.",
+    "authorAffiliations": "",
+    "journalTitle": "Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association",
+    "pubYear": "2024",
+    "date": "2024-09-14",
+    "isOpenAccess": "Y",
+    "keywords": "Uric acid; Gout; Sglt2 Inhibitor; Ckd; Empagliflozin",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background and hypothesis</h4>Hyperuricaemia and gout are common in chronic kidney disease (CKD). We aimed to assess the effects of sodium-glucose co-transporter-2 (SGLT2) inhibition on uric acid (urate) and gout in patients with CKD.<h4>Methods</h4>The EMPA-KIDNEY trial randomised 6609 patients with CKD (estimated glomerular filtration rate [eGFR] \u226520 and <90\u00a0mL/min/1.73m2) to receive either empagliflozin 10\u00a0mg daily or matching placebo over a median of two years follow-up. Serum uric acid was measured at randomisation then 2 and 18 months of follow-up and the effects of empagliflozin were analysed using a pre-specified mixed model repeated measures approach. Participant-reported gout events were analysed in Cox regression models (first events) with the Andersen-Gill extension (total events). A post-hoc composite outcome included new initiation of uric acid lowering therapy or colchicine. EMPA-KIDNEY primary and kidney disease progression outcomes were also assessed in subgroups of baseline serum uric acid.<h4>Results</h4>Baseline mean\u00a0\u00b1\u00a0SD serum uric acid concentration was 431\u00b1114\u00a0\u00b5mol/L. Allocation to empagliflozin resulted in a study-average between-group difference in serum uric acid of -25.6 (95%CI -30.3,-21.0) \u00b5mol/L with larger effects in those with higher eGFR (trend P\u00a0<\u00a00.001) and without diabetes (heterogeneity P\u00a0<\u00a00.001). Compared to placebo, empagliflozin did not significantly reduce first or total gout events (HR 0.87, 95%CI 0.74-1.02 for the 595 first events, and 0.86, 0.72-1.03 for the 869 total events) with similar hazard ratios for the post-hoc composite and across subgroups, including by diabetes and eGFR. The effect of empagliflozin on the primary outcome and kidney disease progression outcomes were similar irrespective of baseline level of uric acid.<h4>Conclusion</h4>SGLT2 inhibition reduces serum uric acid in patients with CKD with larger effects at higher eGFR and in the absence of diabetes. However, the effect on uric acid is modest and did not translate into reduced risk of gout in EMPA-KIDNEY.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1093/ndt/gfae203; html:https://europepmc.org/articles/PMC7616479; pdf:https://europepmc.org/articles/PMC7616479?pdf=render"
+  },
   {
     "id": "32975552",
     "doi": "https://doi.org/10.1001/jamapediatrics.2020.4573",
@@ -24615,23 +24649,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1136/injuryprev-2021-044513"
   },
-  {
-    "id": "38355192",
-    "doi": "https://doi.org/10.1136/bmjopen-2023-080678",
-    "title": "How far back do we need to look to capture diagnoses in electronic health records? A retrospective observational study of hospital electronic health record data.",
-    "authorString": "Lewis J, Evison F, Doal R, Field J, Gallier S, Harris S, le Roux P, Osman M, Plummer C, Sapey E, Singer M, Sayer AA, Witham MD, ADMISSION Research Collaborative.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2024",
-    "date": "2024-02-13",
-    "isOpenAccess": "Y",
-    "keywords": "Hospitals; Electronic Health Records; Information Extraction",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objectives</h4>Analysis of routinely collected electronic health data is a key tool for long-term condition research and practice for hospitalised patients. This requires accurate and complete ascertainment of a broad range of diagnoses, something not always recorded on an admission document at a single point in time. This study aimed to ascertain how far back in time electronic hospital records need to be interrogated to capture long-term condition diagnoses.<h4>Design</h4>Retrospective observational study of routinely collected hospital electronic health record data.<h4>Setting</h4>Queen Elizabeth Hospital Birmingham (UK)-linked data held by the PIONEER acute care data hub.<h4>Participants</h4>Patients whose first recorded admission for chronic obstructive pulmonary disease (COPD) exacerbation (n=560) or acute stroke (n=2142) was between January and December 2018 and who had a minimum of 10 years of data prior to the index date.<h4>Outcome measures</h4>We identified the most common International Classification of Diseases version 10-coded diagnoses received by patients with COPD and acute stroke separately. For each diagnosis, we derived the number of patients with the diagnosis recorded at least once over the full 10-year lookback period, and then compared this with shorter lookback periods from 1 year to 9 years prior to the index admission.<h4>Results</h4>Seven of the top 10 most common diagnoses in the COPD dataset reached >90% completeness by 6 years of lookback. Atrial fibrillation and diabetes were >90% coded with 2-3 years of lookback, but hypertension and asthma completeness continued to rise all the way out to 10 years of lookback. For stroke, 4 of the top 10 reached 90% completeness by 5 years of lookback; angina pectoris was >90% coded at 7 years and previous transient ischaemic attack completeness continued to rise out to 10 years of lookback.<h4>Conclusion</h4>A 7-year lookback captures most, but not all, common diagnoses. Lookback duration should be tailored to the conditions being studied.",
-    "laySummary": "",
-    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/14/2/e080678.full.pdf; doi:https://doi.org/10.1136/bmjopen-2023-080678; html:https://europepmc.org/articles/PMC10868273; pdf:https://europepmc.org/articles/PMC10868273?pdf=render"
-  },
   {
     "id": "37658971",
     "doi": "https://doi.org/10.1007/s11897-023-00626-w",
@@ -24666,6 +24683,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ehjcimaging/advance-article-pdf/doi/10.1093/ehjci/jeac270/48798234/jeac270.pdf; doi:https://doi.org/10.1093/ehjci/jeac270; html:https://europepmc.org/articles/PMC10284050; pdf:https://europepmc.org/articles/PMC10284050?pdf=render"
   },
+  {
+    "id": "38355192",
+    "doi": "https://doi.org/10.1136/bmjopen-2023-080678",
+    "title": "How far back do we need to look to capture diagnoses in electronic health records? A retrospective observational study of hospital electronic health record data.",
+    "authorString": "Lewis J, Evison F, Doal R, Field J, Gallier S, Harris S, le Roux P, Osman M, Plummer C, Sapey E, Singer M, Sayer AA, Witham MD, ADMISSION Research Collaborative.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2024",
+    "date": "2024-02-13",
+    "isOpenAccess": "Y",
+    "keywords": "Hospitals; Electronic Health Records; Information Extraction",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objectives</h4>Analysis of routinely collected electronic health data is a key tool for long-term condition research and practice for hospitalised patients. This requires accurate and complete ascertainment of a broad range of diagnoses, something not always recorded on an admission document at a single point in time. This study aimed to ascertain how far back in time electronic hospital records need to be interrogated to capture long-term condition diagnoses.<h4>Design</h4>Retrospective observational study of routinely collected hospital electronic health record data.<h4>Setting</h4>Queen Elizabeth Hospital Birmingham (UK)-linked data held by the PIONEER acute care data hub.<h4>Participants</h4>Patients whose first recorded admission for chronic obstructive pulmonary disease (COPD) exacerbation (n=560) or acute stroke (n=2142) was between January and December 2018 and who had a minimum of 10 years of data prior to the index date.<h4>Outcome measures</h4>We identified the most common International Classification of Diseases version 10-coded diagnoses received by patients with COPD and acute stroke separately. For each diagnosis, we derived the number of patients with the diagnosis recorded at least once over the full 10-year lookback period, and then compared this with shorter lookback periods from 1 year to 9 years prior to the index admission.<h4>Results</h4>Seven of the top 10 most common diagnoses in the COPD dataset reached >90% completeness by 6 years of lookback. Atrial fibrillation and diabetes were >90% coded with 2-3 years of lookback, but hypertension and asthma completeness continued to rise all the way out to 10 years of lookback. For stroke, 4 of the top 10 reached 90% completeness by 5 years of lookback; angina pectoris was >90% coded at 7 years and previous transient ischaemic attack completeness continued to rise out to 10 years of lookback.<h4>Conclusion</h4>A 7-year lookback captures most, but not all, common diagnoses. Lookback duration should be tailored to the conditions being studied.",
+    "laySummary": "",
+    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/14/2/e080678.full.pdf; doi:https://doi.org/10.1136/bmjopen-2023-080678; html:https://europepmc.org/articles/PMC10868273; pdf:https://europepmc.org/articles/PMC10868273?pdf=render"
+  },
   {
     "id": "37827807",
     "doi": "https://doi.org/10.1136/bmjresp-2023-001806",
@@ -24734,23 +24768,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopengastro.bmj.com/content/bmjgast/10/1/e001139.full.pdf; doi:https://doi.org/10.1136/bmjgast-2023-001139; html:https://europepmc.org/articles/PMC10230891; pdf:https://europepmc.org/articles/PMC10230891?pdf=render"
   },
-  {
-    "id": "37751239",
-    "doi": "https://doi.org/10.2196/49438",
-    "title": "Design and Evaluation of an Intensive Care Unit Dashboard Built in Response to the COVID-19 Pandemic: Semistructured Interview Study.",
-    "authorString": "Wac M, Craddock I, Chantziara S, Campbell T, Santos-Rodriguez R, Davidson B, McWilliams C.",
-    "authorAffiliations": "",
-    "journalTitle": "JMIR human factors",
-    "pubYear": "2023",
-    "date": "2023-09-26",
-    "isOpenAccess": "Y",
-    "keywords": "Design; Health; ICU; EPR; intensive care unit; Interview; Intensive Care; Critical Care; Electronic Patient Record; Participatory Design; Ehr; Electronic Health Record; Software Engineering; Clinical Information System; Cis; Thematic Analysis; Dashboard; Human-centered Design; Covid-19; Interactive Display",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Dashboards and interactive displays are becoming increasingly prevalent in most health care settings and have the potential to streamline access to information, consolidate disparate data sources and deliver new insights. Our research focuses on intensive care units (ICUs) which are heavily instrumented, critical care environments that generate vast amounts of data and frequently require individualized support for each patient. Consequently, clinicians experience a high cognitive load, which can translate to suboptimal performance. The global COVID-19 pandemic exacerbated this problem by generating a large number of additional hospitalizations, which necessitated a new tool that would help manage ICUs' census. In a previous study, we interviewed clinicians at the University Hospitals Bristol and Weston National Health Service Foundation Trust to capture the requirements for bespoke dashboards that would alleviate this problem.<h4>Objective</h4>This study aims to design, implement, and evaluate an ICU dashboard to allow for monitoring of the high volume of patients in need of critical care, particularly tailored to high-demand situations, such as those seen during the COVID-19 pandemic.<h4>Methods</h4>Building upon the previously gathered requirements, we developed a dashboard, integrated it within the ICU of a National Health Service trust, and allowed all staff to access our tool. For evaluation purposes, participants were recruited and interviewed following a 25-day period during which they were able to use the dashboard clinically. The semistructured interviews followed a topic guide aimed at capturing the usability of the dashboard, supplemented with additional questions asked post hoc to probe themes established during the interview. Interview transcripts were analyzed using a thematic analysis framework that combined inductive and deductive approaches and integrated the Technology Acceptance Model.<h4>Results</h4>A total of 10 participants with 4 different roles in the ICU (6 consultants, 2 junior doctors, 1 nurse, and 1 advanced clinical practitioner) participated in the interviews. Our analysis generated 4 key topics that prevailed across the data: our dashboard met the usability requirements of the participants and was found useful and intuitive; participants perceived that it impacted their delivery of patient care by improving the access to the information and better equipping them to do their job; the tool was used in a variety of ways and for different reasons and tasks; and there were barriers to integration of our dashboard into practice, including familiarity with existing systems, which stifled the adoption of our tool.<h4>Conclusions</h4>Our findings show that the perceived utility of the dashboard had a positive impact on the clinicians' workflows in the ICU. Improving access to information translated into more efficient patient care and transformed some of the existing processes. The introduction of our tool was met with positive reception, but its integration during the COVID-19 pandemic limited its adoption into practice.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.2196/49438; doi:https://doi.org/10.2196/49438; html:https://europepmc.org/articles/PMC10565627"
-  },
   {
     "id": "32895316",
     "doi": "https://doi.org/10.1136/thoraxjnl-2020-215566",
@@ -24768,6 +24785,23 @@
     "laySummary": "",
     "urls": "pdf:https://thorax.bmj.com/content/thoraxjnl/75/10/826.full.pdf; doi:https://doi.org/10.1136/thoraxjnl-2020-215566"
   },
+  {
+    "id": "37751239",
+    "doi": "https://doi.org/10.2196/49438",
+    "title": "Design and Evaluation of an Intensive Care Unit Dashboard Built in Response to the COVID-19 Pandemic: Semistructured Interview Study.",
+    "authorString": "Wac M, Craddock I, Chantziara S, Campbell T, Santos-Rodriguez R, Davidson B, McWilliams C.",
+    "authorAffiliations": "",
+    "journalTitle": "JMIR human factors",
+    "pubYear": "2023",
+    "date": "2023-09-26",
+    "isOpenAccess": "Y",
+    "keywords": "Design; Health; ICU; EPR; intensive care unit; Interview; Intensive Care; Critical Care; Electronic Patient Record; Participatory Design; Ehr; Electronic Health Record; Software Engineering; Clinical Information System; Cis; Thematic Analysis; Dashboard; Human-centered Design; Covid-19; Interactive Display",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Dashboards and interactive displays are becoming increasingly prevalent in most health care settings and have the potential to streamline access to information, consolidate disparate data sources and deliver new insights. Our research focuses on intensive care units (ICUs) which are heavily instrumented, critical care environments that generate vast amounts of data and frequently require individualized support for each patient. Consequently, clinicians experience a high cognitive load, which can translate to suboptimal performance. The global COVID-19 pandemic exacerbated this problem by generating a large number of additional hospitalizations, which necessitated a new tool that would help manage ICUs' census. In a previous study, we interviewed clinicians at the University Hospitals Bristol and Weston National Health Service Foundation Trust to capture the requirements for bespoke dashboards that would alleviate this problem.<h4>Objective</h4>This study aims to design, implement, and evaluate an ICU dashboard to allow for monitoring of the high volume of patients in need of critical care, particularly tailored to high-demand situations, such as those seen during the COVID-19 pandemic.<h4>Methods</h4>Building upon the previously gathered requirements, we developed a dashboard, integrated it within the ICU of a National Health Service trust, and allowed all staff to access our tool. For evaluation purposes, participants were recruited and interviewed following a 25-day period during which they were able to use the dashboard clinically. The semistructured interviews followed a topic guide aimed at capturing the usability of the dashboard, supplemented with additional questions asked post hoc to probe themes established during the interview. Interview transcripts were analyzed using a thematic analysis framework that combined inductive and deductive approaches and integrated the Technology Acceptance Model.<h4>Results</h4>A total of 10 participants with 4 different roles in the ICU (6 consultants, 2 junior doctors, 1 nurse, and 1 advanced clinical practitioner) participated in the interviews. Our analysis generated 4 key topics that prevailed across the data: our dashboard met the usability requirements of the participants and was found useful and intuitive; participants perceived that it impacted their delivery of patient care by improving the access to the information and better equipping them to do their job; the tool was used in a variety of ways and for different reasons and tasks; and there were barriers to integration of our dashboard into practice, including familiarity with existing systems, which stifled the adoption of our tool.<h4>Conclusions</h4>Our findings show that the perceived utility of the dashboard had a positive impact on the clinicians' workflows in the ICU. Improving access to information translated into more efficient patient care and transformed some of the existing processes. The introduction of our tool was met with positive reception, but its integration during the COVID-19 pandemic limited its adoption into practice.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.2196/49438; doi:https://doi.org/10.2196/49438; html:https://europepmc.org/articles/PMC10565627"
+  },
   {
     "id": "37230417",
     "doi": "https://doi.org/10.1016/j.jtha.2023.05.012",
@@ -24904,23 +24938,6 @@
     "laySummary": "",
     "urls": "pdf:https://adc.bmj.com/content/archdischild/early/2023/03/30/archdischild-2022-325219.full.pdf; doi:https://doi.org/10.1136/archdischild-2022-325219; html:https://europepmc.org/articles/PMC10314013; pdf:https://europepmc.org/articles/PMC10314013?pdf=render"
   },
-  {
-    "id": "38491524",
-    "doi": "https://doi.org/10.1186/s40246-024-00585-w",
-    "title": "A genome-wide association study of neutrophil count in individuals associated to an African continental ancestry group facilitates studies of malaria pathogenesis.",
-    "authorString": "Constantinescu AE, Hughes DA, Bull CJ, Fleming K, Mitchell RE, Zheng J, Kar S, Timpson NJ, Amulic B, Vincent EE.",
-    "authorAffiliations": "",
-    "journalTitle": "Human genomics",
-    "pubYear": "2024",
-    "date": "2024-03-15",
-    "isOpenAccess": "Y",
-    "keywords": "Malaria; Gwas; Mendelian Randomization; Neutrophil Count; African Ancestry",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>'Benign ethnic neutropenia' (BEN) is a heritable condition characterized by lower neutrophil counts, predominantly observed in individuals of African ancestry, and the genetic basis of BEN remains a subject of extensive research. In this study, we aimed to dissect the genetic architecture underlying neutrophil count variation through a linear-mixed model genome-wide association study (GWAS) in a population of African ancestry (N\u2009=\u20095976). Malaria caused by P. falciparum imposes a tremendous public health burden on people living in sub-Saharan Africa. Individuals living in malaria endemic regions often have a reduced circulating neutrophil count due to BEN, raising the possibility that reduced neutrophil counts modulate severity of malaria in susceptible populations. As a follow-up, we tested this hypothesis by conducting a Mendelian randomization (MR) analysis of neutrophil counts on severe malaria (MalariaGEN, N\u2009=\u200917,056).<h4>Results</h4>We carried out a GWAS of neutrophil count in individuals associated to an African continental ancestry group within UK Biobank, identifying 73 loci (r<sup>2</sup>\u2009=\u20090.1) and 10 index SNPs (GCTA-COJO loci) associated with neutrophil count, including previously unknown rare loci regulating neutrophil count in a non-European population. BOLT-LMM was reliable when conducted in a non-European population, and additional covariates added to the model did not largely alter the results of the top loci or index SNPs. The two-sample bi-directional MR analysis between neutrophil count and severe malaria showed the greatest evidence for an effect between neutrophil count and severe anaemia, although the confidence intervals crossed the null.<h4>Conclusion</h4>Our GWAS of neutrophil count revealed unique loci present in individuals of African ancestry. We note that a small sample-size reduced our power to identify variants with low allele frequencies and/or low effect sizes in our GWAS. Our work highlights the need for conducting large-scale biobank studies in Africa and for further exploring the link between neutrophils and severe malaria.",
-    "laySummary": "",
-    "urls": "pdf:https://humgenomics.biomedcentral.com/counter/pdf/10.1186/s40246-024-00585-w; doi:https://doi.org/10.1186/s40246-024-00585-w; html:https://europepmc.org/articles/PMC10941368; pdf:https://europepmc.org/articles/PMC10941368?pdf=render"
-  },
   {
     "id": "35038301",
     "doi": "https://doi.org/10.2196/30523",
@@ -24938,6 +24955,23 @@
     "laySummary": "",
     "urls": "pdf:https://humanfactors.jmir.org/2022/2/e30523/PDF; doi:https://doi.org/10.2196/30523; html:https://europepmc.org/articles/PMC9009380"
   },
+  {
+    "id": "38491524",
+    "doi": "https://doi.org/10.1186/s40246-024-00585-w",
+    "title": "A genome-wide association study of neutrophil count in individuals associated to an African continental ancestry group facilitates studies of malaria pathogenesis.",
+    "authorString": "Constantinescu AE, Hughes DA, Bull CJ, Fleming K, Mitchell RE, Zheng J, Kar S, Timpson NJ, Amulic B, Vincent EE.",
+    "authorAffiliations": "",
+    "journalTitle": "Human genomics",
+    "pubYear": "2024",
+    "date": "2024-03-15",
+    "isOpenAccess": "Y",
+    "keywords": "Malaria; Gwas; Mendelian Randomization; Neutrophil Count; African Ancestry",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>'Benign ethnic neutropenia' (BEN) is a heritable condition characterized by lower neutrophil counts, predominantly observed in individuals of African ancestry, and the genetic basis of BEN remains a subject of extensive research. In this study, we aimed to dissect the genetic architecture underlying neutrophil count variation through a linear-mixed model genome-wide association study (GWAS) in a population of African ancestry (N\u2009=\u20095976). Malaria caused by P. falciparum imposes a tremendous public health burden on people living in sub-Saharan Africa. Individuals living in malaria endemic regions often have a reduced circulating neutrophil count due to BEN, raising the possibility that reduced neutrophil counts modulate severity of malaria in susceptible populations. As a follow-up, we tested this hypothesis by conducting a Mendelian randomization (MR) analysis of neutrophil counts on severe malaria (MalariaGEN, N\u2009=\u200917,056).<h4>Results</h4>We carried out a GWAS of neutrophil count in individuals associated to an African continental ancestry group within UK Biobank, identifying 73 loci (r<sup>2</sup>\u2009=\u20090.1) and 10 index SNPs (GCTA-COJO loci) associated with neutrophil count, including previously unknown rare loci regulating neutrophil count in a non-European population. BOLT-LMM was reliable when conducted in a non-European population, and additional covariates added to the model did not largely alter the results of the top loci or index SNPs. The two-sample bi-directional MR analysis between neutrophil count and severe malaria showed the greatest evidence for an effect between neutrophil count and severe anaemia, although the confidence intervals crossed the null.<h4>Conclusion</h4>Our GWAS of neutrophil count revealed unique loci present in individuals of African ancestry. We note that a small sample-size reduced our power to identify variants with low allele frequencies and/or low effect sizes in our GWAS. Our work highlights the need for conducting large-scale biobank studies in Africa and for further exploring the link between neutrophils and severe malaria.",
+    "laySummary": "",
+    "urls": "pdf:https://humgenomics.biomedcentral.com/counter/pdf/10.1186/s40246-024-00585-w; doi:https://doi.org/10.1186/s40246-024-00585-w; html:https://europepmc.org/articles/PMC10941368; pdf:https://europepmc.org/articles/PMC10941368?pdf=render"
+  },
   {
     "id": "35210898",
     "doi": "https://doi.org/10.2147/por.s353400",
@@ -24972,23 +25006,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41467-022-28729-3.pdf; doi:https://doi.org/10.1038/s41467-022-28729-3; html:https://europepmc.org/articles/PMC8907312; pdf:https://europepmc.org/articles/PMC8907312?pdf=render"
   },
-  {
-    "id": "37679551",
-    "doi": "https://doi.org/10.1038/s41590-023-01635-6",
-    "title": "Author Correction: Genetics of circulating inflammatory proteins identifies drivers of immune-mediated disease risk and therapeutic targets.",
-    "authorString": "Zhao JH, Stacey D, Eriksson N, Macdonald-Dunlop E, Hedman \u00c5K, Kalnapenkis A, Enroth S, Cozzetto D, Digby-Bell J, Marten J, Folkersen L, Herder C, Jonsson L, Bergen SE, Gieger C, Needham EJ, Surendran P, Estonian Biobank Research Team, Paul DS, Polasek O, Thorand B, Grallert H, Roden M, V\u00f5sa U, Esko T, Hayward C, Johansson \u00c5, Gyllensten U, Powell N, Hansson O, Mattsson-Carlgren N, Joshi PK, Danesh J, Padyukov L, Klareskog L, Land\u00e9n M, Wilson JF, Siegbahn A, Wallentin L, M\u00e4larstig A, Butterworth AS, Peters JE.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature immunology",
-    "pubYear": "2023",
-    "date": "2023-11-01",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1038/s41590-023-01635-6; html:https://europepmc.org/articles/PMC10602847; pdf:https://europepmc.org/articles/PMC10602847?pdf=render"
-  },
   {
     "id": "35776955",
     "doi": "https://doi.org/10.1093/ehjqcco/qcac039",
@@ -25007,21 +25024,21 @@
     "urls": "doi:https://doi.org/10.1093/ehjqcco/qcac039; html:https://europepmc.org/articles/PMC9442847; pdf:https://europepmc.org/articles/PMC9442847?pdf=render; doi:https://doi.org/10.1093/ehjqcco/qcac039"
   },
   {
-    "id": "38346686",
-    "doi": "https://doi.org/10.1093/ageing/afae004",
-    "title": "The impact of digital technology in care homes on unplanned secondary care usage and associated costs.",
-    "authorString": "Garner A, Lewis J, Dixon S, Preston N, Caiado CCS, Hanratty B, Jones M, Knight J, Mason SM.",
+    "id": "37679551",
+    "doi": "https://doi.org/10.1038/s41590-023-01635-6",
+    "title": "Author Correction: Genetics of circulating inflammatory proteins identifies drivers of immune-mediated disease risk and therapeutic targets.",
+    "authorString": "Zhao JH, Stacey D, Eriksson N, Macdonald-Dunlop E, Hedman \u00c5K, Kalnapenkis A, Enroth S, Cozzetto D, Digby-Bell J, Marten J, Folkersen L, Herder C, Jonsson L, Bergen SE, Gieger C, Needham EJ, Surendran P, Estonian Biobank Research Team, Paul DS, Polasek O, Thorand B, Grallert H, Roden M, V\u00f5sa U, Esko T, Hayward C, Johansson \u00c5, Gyllensten U, Powell N, Hansson O, Mattsson-Carlgren N, Joshi PK, Danesh J, Padyukov L, Klareskog L, Land\u00e9n M, Wilson JF, Siegbahn A, Wallentin L, M\u00e4larstig A, Butterworth AS, Peters JE.",
     "authorAffiliations": "",
-    "journalTitle": "Age and ageing",
-    "pubYear": "2024",
-    "date": "2024-02-01",
+    "journalTitle": "Nature immunology",
+    "pubYear": "2023",
+    "date": "2023-11-01",
     "isOpenAccess": "Y",
-    "keywords": "Older People; Emergency Medicine; Care Homes; Long-term Care; Telehealth; Routinely Collected Data",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>A substantial number of Emergency Department (ED) attendances by care home residents are potentially avoidable. Health Call Digital Care Homes is an app-based technology that aims to streamline residents' care by recording their observations such as vital parameters electronically. Observations are triaged by remote clinical staff. This study assessed the effectiveness of the Health Call technology to reduce unplanned secondary care usage and associated costs.<h4>Methods</h4>A retrospective analysis of health outcomes and economic impact based on an intervention. The study involved 118 care homes across the North East of UK from 2018 to 2021. Routinely collected NHS secondary care data from County Durham and Darlington NHS Foundation Trust was linked with data from the Health Call app. Three outcomes were modelled monthly using Generalised Linear Mixed Models: counts of emergency attendances, emergency admissions and length of stay of emergency admissions. A similar approach was taken for costs. The impact of Health Call was tested on each outcome using the models.<h4>Findings</h4>Data from 8,702 residents were used in the analysis. Results show Health Call reduces the number of emergency attendances by 11% [6-15%], emergency admissions by 25% [20-39%] and length of stay by 11% [3-18%] (with an additional month-by-month decrease of 28% [24-34%]). The cost analysis found a cost reduction of \u00a357 per resident in 2018, increasing to \u00a3113 in 2021.<h4>Interpretation</h4>The introduction of a digital technology, such as Health Call, could significantly reduce contacts with and costs resulting from unplanned secondary care usage by care home residents.",
+    "abstract": "",
     "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/ageing/article-pdf/53/2/afae004/56661196/afae004.pdf; doi:https://doi.org/10.1093/ageing/afae004; html:https://europepmc.org/articles/PMC10861323; pdf:https://europepmc.org/articles/PMC10861323?pdf=render"
+    "urls": "doi:https://doi.org/10.1038/s41590-023-01635-6; html:https://europepmc.org/articles/PMC10602847; pdf:https://europepmc.org/articles/PMC10602847?pdf=render"
   },
   {
     "id": "30183734",
@@ -25040,6 +25057,23 @@
     "laySummary": "",
     "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0202359&type=printable; doi:https://doi.org/10.1371/journal.pone.0202359; html:https://europepmc.org/articles/PMC6124703; pdf:https://europepmc.org/articles/PMC6124703?pdf=render"
   },
+  {
+    "id": "38346686",
+    "doi": "https://doi.org/10.1093/ageing/afae004",
+    "title": "The impact of digital technology in care homes on unplanned secondary care usage and associated costs.",
+    "authorString": "Garner A, Lewis J, Dixon S, Preston N, Caiado CCS, Hanratty B, Jones M, Knight J, Mason SM.",
+    "authorAffiliations": "",
+    "journalTitle": "Age and ageing",
+    "pubYear": "2024",
+    "date": "2024-02-01",
+    "isOpenAccess": "Y",
+    "keywords": "Older People; Emergency Medicine; Care Homes; Long-term Care; Telehealth; Routinely Collected Data",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>A substantial number of Emergency Department (ED) attendances by care home residents are potentially avoidable. Health Call Digital Care Homes is an app-based technology that aims to streamline residents' care by recording their observations such as vital parameters electronically. Observations are triaged by remote clinical staff. This study assessed the effectiveness of the Health Call technology to reduce unplanned secondary care usage and associated costs.<h4>Methods</h4>A retrospective analysis of health outcomes and economic impact based on an intervention. The study involved 118 care homes across the North East of UK from 2018 to 2021. Routinely collected NHS secondary care data from County Durham and Darlington NHS Foundation Trust was linked with data from the Health Call app. Three outcomes were modelled monthly using Generalised Linear Mixed Models: counts of emergency attendances, emergency admissions and length of stay of emergency admissions. A similar approach was taken for costs. The impact of Health Call was tested on each outcome using the models.<h4>Findings</h4>Data from 8,702 residents were used in the analysis. Results show Health Call reduces the number of emergency attendances by 11% [6-15%], emergency admissions by 25% [20-39%] and length of stay by 11% [3-18%] (with an additional month-by-month decrease of 28% [24-34%]). The cost analysis found a cost reduction of \u00a357 per resident in 2018, increasing to \u00a3113 in 2021.<h4>Interpretation</h4>The introduction of a digital technology, such as Health Call, could significantly reduce contacts with and costs resulting from unplanned secondary care usage by care home residents.",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/ageing/article-pdf/53/2/afae004/56661196/afae004.pdf; doi:https://doi.org/10.1093/ageing/afae004; html:https://europepmc.org/articles/PMC10861323; pdf:https://europepmc.org/articles/PMC10861323?pdf=render"
+  },
   {
     "id": "35699189",
     "doi": "https://doi.org/10.1161/jaha.121.024248",
@@ -25074,23 +25108,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/painmedicine/article-pdf/21/2/291/32739506/pnz209.pdf; doi:https://doi.org/10.1093/pm/pnz209"
   },
-  {
-    "id": "38904124",
-    "doi": "https://doi.org/10.1136/bmjopen-2023-079169",
-    "title": "10-year multimorbidity patterns among people with and without rheumatic and musculoskeletal diseases: an observational cohort study using linked electronic health records from Wales, UK.",
-    "authorString": "Jalali-Najafabadi F, Bailey R, Lyons J, Akbari A, Ba Dhafari T, Azadbakht N, Rafferty J, Watkins A, Martin GP, Bowes J, Lyons RA, Barton A, Peek N.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2024",
-    "date": "2024-06-19",
-    "isOpenAccess": "Y",
-    "keywords": "epidemiology; Rheumatology; Electronic Health Records",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objectives</h4>To compare the patterns of multimorbidity between people with and without rheumatic and musculoskeletal diseases (RMDs) and to describe how these patterns change by age and sex over time, between 2010 and 2019.<h4>Participants</h4>103\u2009426 people with RMDs and 2.9\u2009million comparators registered in 395 Wales general practices (GPs). Each patient with an RMD aged 0-100 years between January 2010 and December 2019 registered in Clinical Practice Research Welsh practices was matched with up to five comparators without an RMD, based on age, gender and GP code.<h4>Primary outcome measures</h4>The prevalence of 29 Elixhauser-defined comorbidities in people with RMDs and comparators categorised by age, gender and GP practices. Conditional logistic regression models were fitted to calculate differences (OR, 95%\u2009CI) in associations with comorbidities between cohorts.<h4>Results</h4>The most prevalent comorbidities were cardiovascular risk factors, hypertension and diabetes. Having an RMD diagnosis was associated with a significantly higher odds for many conditions including deficiency anaemia (OR 1.39, 95%\u2009CI (1.32 to 1.46)), hypothyroidism (OR 1.34, 95%\u2009CI (1.19 to 1.50)), pulmonary circulation disorders (OR 1.39, 95%\u2009CI 1.12 to 1.73) diabetes (OR 1.17, 95%\u2009CI (1.11 to 1.23)) and fluid and electrolyte disorders (OR 1.27, 95%\u2009CI (1.17 to 1.38)). RMDs have a higher proportion of multimorbidity (two or more conditions in addition to the RMD) compared with non-RMD group (81% and 73%, respectively in 2019) and the mean number of comorbidities was higher in women from the age of 25 and 50 in men than in non-RMDs group.<h4>Conclusion</h4>People with RMDs are approximately 1.5 times as likely to have multimorbidity as the general population and provide a high-risk group for targeted intervention studies. The individuals with RMDs experience a greater load of coexisting health conditions, which tend to manifest at earlier ages. This phenomenon is particularly pronounced among women. Additionally, there is an under-reporting of comorbidities in individuals with RMDs.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1136/bmjopen-2023-079169; doi:https://doi.org/10.1136/bmjopen-2023-079169; html:https://europepmc.org/articles/PMC11191776; pdf:https://europepmc.org/articles/PMC11191776?pdf=render"
-  },
   {
     "id": "36691123",
     "doi": "https://doi.org/10.1136/bmjopen-2022-063199",
@@ -25125,6 +25142,23 @@
     "laySummary": "",
     "urls": "pdf:https://heart.bmj.com/content/heartjnl/107/21/1748.full.pdf; doi:https://doi.org/10.1136/heartjnl-2021-319229; html:https://europepmc.org/articles/PMC8522453; pdf:https://europepmc.org/articles/PMC8522453?pdf=render"
   },
+  {
+    "id": "38904124",
+    "doi": "https://doi.org/10.1136/bmjopen-2023-079169",
+    "title": "10-year multimorbidity patterns among people with and without rheumatic and musculoskeletal diseases: an observational cohort study using linked electronic health records from Wales, UK.",
+    "authorString": "Jalali-Najafabadi F, Bailey R, Lyons J, Akbari A, Ba Dhafari T, Azadbakht N, Rafferty J, Watkins A, Martin GP, Bowes J, Lyons RA, Barton A, Peek N.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2024",
+    "date": "2024-06-19",
+    "isOpenAccess": "Y",
+    "keywords": "epidemiology; Rheumatology; Electronic Health Records",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objectives</h4>To compare the patterns of multimorbidity between people with and without rheumatic and musculoskeletal diseases (RMDs) and to describe how these patterns change by age and sex over time, between 2010 and 2019.<h4>Participants</h4>103\u2009426 people with RMDs and 2.9\u2009million comparators registered in 395 Wales general practices (GPs). Each patient with an RMD aged 0-100 years between January 2010 and December 2019 registered in Clinical Practice Research Welsh practices was matched with up to five comparators without an RMD, based on age, gender and GP code.<h4>Primary outcome measures</h4>The prevalence of 29 Elixhauser-defined comorbidities in people with RMDs and comparators categorised by age, gender and GP practices. Conditional logistic regression models were fitted to calculate differences (OR, 95%\u2009CI) in associations with comorbidities between cohorts.<h4>Results</h4>The most prevalent comorbidities were cardiovascular risk factors, hypertension and diabetes. Having an RMD diagnosis was associated with a significantly higher odds for many conditions including deficiency anaemia (OR 1.39, 95%\u2009CI (1.32 to 1.46)), hypothyroidism (OR 1.34, 95%\u2009CI (1.19 to 1.50)), pulmonary circulation disorders (OR 1.39, 95%\u2009CI 1.12 to 1.73) diabetes (OR 1.17, 95%\u2009CI (1.11 to 1.23)) and fluid and electrolyte disorders (OR 1.27, 95%\u2009CI (1.17 to 1.38)). RMDs have a higher proportion of multimorbidity (two or more conditions in addition to the RMD) compared with non-RMD group (81% and 73%, respectively in 2019) and the mean number of comorbidities was higher in women from the age of 25 and 50 in men than in non-RMDs group.<h4>Conclusion</h4>People with RMDs are approximately 1.5 times as likely to have multimorbidity as the general population and provide a high-risk group for targeted intervention studies. The individuals with RMDs experience a greater load of coexisting health conditions, which tend to manifest at earlier ages. This phenomenon is particularly pronounced among women. Additionally, there is an under-reporting of comorbidities in individuals with RMDs.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1136/bmjopen-2023-079169; doi:https://doi.org/10.1136/bmjopen-2023-079169; html:https://europepmc.org/articles/PMC11191776; pdf:https://europepmc.org/articles/PMC11191776?pdf=render"
+  },
   {
     "id": "31827124",
     "doi": "https://doi.org/10.1038/s41598-019-54849-w",
@@ -25160,21 +25194,21 @@
     "urls": "pdf:http://www.jacionline.org/article/S0091674922025775/pdf; doi:https://doi.org/10.1016/j.jaci.2022.12.810; html:https://europepmc.org/articles/PMC10109092; pdf:https://europepmc.org/articles/PMC10109092?pdf=render"
   },
   {
-    "id": "36403308",
-    "doi": "https://doi.org/10.1016/j.media.2022.102678",
-    "title": "DragNet: Learning-based deformable registration for realistic cardiac MR sequence generation from a single frame.",
-    "authorString": "Zakeri A, Hokmabadi A, Bi N, Wijesinghe I, Nix MG, Petersen SE, Frangi AF, Taylor ZA, Gooya A.",
+    "id": "PMC8855010",
+    "doi": "https://doi.org/",
+    "title": "POS-894 PREDICTING PANDEMIC-RELATED EXCESS-DEATH USING PRE-PANDEMIC RISK OF MORTALITY IN INDIVIDUALS WITH CHRONIC KIDNEY DISEASE",
+    "authorString": "Dashtban M, Mizani M, Gonazalez-Izquierdo A, Corbett R, Denaxas S, Quint J, Mamza J, Morris T, Hemingway H, Sudlow C, Banerjee A.",
     "authorAffiliations": "",
-    "journalTitle": "Medical image analysis",
-    "pubYear": "2023",
-    "date": "2022-11-02",
-    "isOpenAccess": "N",
-    "keywords": "Uncertainty Estimation; Uk Biobank; Deep Learning; Deformable Temporal Image Registration; Sequential Image Data Generation; Variational Recurrent Neural Networks",
+    "journalTitle": "Kidney international reports",
+    "pubYear": "2022",
+    "date": "2022-02-01",
+    "isOpenAccess": "Y",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Deformable image registration (DIR) can be used to track cardiac motion. Conventional DIR algorithms aim to establish a dense and non-linear correspondence between independent pairs of images. They are, nevertheless, computationally intensive and do not consider temporal dependencies to regulate the estimated motion in a cardiac cycle. In this paper, leveraging deep learning methods, we formulate a novel hierarchical probabilistic model, termed DragNet, for fast and reliable spatio-temporal registration in cine cardiac magnetic resonance (CMR) images and for generating synthetic heart motion sequences. DragNet is a variational inference framework, which takes an image from the sequence in combination with the hidden states of a recurrent neural network (RNN) as inputs to an inference network per time step. As part of this framework, we condition the prior probability of the latent variables on the hidden states of the RNN utilised to capture temporal dependencies. We further condition the posterior of the motion field on a latent variable from hierarchy and features from the moving image. Subsequently, the RNN updates the hidden state variables based on the feature maps of the fixed image and the latent variables. Different from traditional methods, DragNet performs registration on unseen sequences in a forward pass, which significantly expedites the registration process. Besides, DragNet enables generating a large number of realistic synthetic image sequences given only one frame, where the corresponding deformations are also retrieved. The probabilistic framework allows for computing spatio-temporal uncertainties in the estimated motion fields. Our results show that DragNet performance is comparable with state-of-the-art methods in terms of registration accuracy, with the advantage of offering analytical pixel-wise motion uncertainty estimation across a cardiac cycle and being a motion generator. We will make our code publicly available.",
+    "abstract": "",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.media.2022.102678; doi:https://doi.org/10.1016/j.media.2022.102678"
+    "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8855010/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8855010/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC8855010; pdf:https://europepmc.org/articles/PMC8855010?pdf=render"
   },
   {
     "id": "34000735",
@@ -25194,21 +25228,21 @@
     "urls": "pdf:https://academic.oup.com/ije/article-pdf/50/2/457/37947593/dyab025.pdf; doi:https://doi.org/10.1093/ije/dyab025"
   },
   {
-    "id": "PMC8855010",
-    "doi": "https://doi.org/",
-    "title": "POS-894 PREDICTING PANDEMIC-RELATED EXCESS-DEATH USING PRE-PANDEMIC RISK OF MORTALITY IN INDIVIDUALS WITH CHRONIC KIDNEY DISEASE",
-    "authorString": "Dashtban M, Mizani M, Gonazalez-Izquierdo A, Corbett R, Denaxas S, Quint J, Mamza J, Morris T, Hemingway H, Sudlow C, Banerjee A.",
+    "id": "36403308",
+    "doi": "https://doi.org/10.1016/j.media.2022.102678",
+    "title": "DragNet: Learning-based deformable registration for realistic cardiac MR sequence generation from a single frame.",
+    "authorString": "Zakeri A, Hokmabadi A, Bi N, Wijesinghe I, Nix MG, Petersen SE, Frangi AF, Taylor ZA, Gooya A.",
     "authorAffiliations": "",
-    "journalTitle": "Kidney international reports",
-    "pubYear": "2022",
-    "date": "2022-02-01",
-    "isOpenAccess": "Y",
-    "keywords": "",
+    "journalTitle": "Medical image analysis",
+    "pubYear": "2023",
+    "date": "2022-11-02",
+    "isOpenAccess": "N",
+    "keywords": "Uncertainty Estimation; Uk Biobank; Deep Learning; Deformable Temporal Image Registration; Sequential Image Data Generation; Variational Recurrent Neural Networks",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "",
+    "abstract": "Deformable image registration (DIR) can be used to track cardiac motion. Conventional DIR algorithms aim to establish a dense and non-linear correspondence between independent pairs of images. They are, nevertheless, computationally intensive and do not consider temporal dependencies to regulate the estimated motion in a cardiac cycle. In this paper, leveraging deep learning methods, we formulate a novel hierarchical probabilistic model, termed DragNet, for fast and reliable spatio-temporal registration in cine cardiac magnetic resonance (CMR) images and for generating synthetic heart motion sequences. DragNet is a variational inference framework, which takes an image from the sequence in combination with the hidden states of a recurrent neural network (RNN) as inputs to an inference network per time step. As part of this framework, we condition the prior probability of the latent variables on the hidden states of the RNN utilised to capture temporal dependencies. We further condition the posterior of the motion field on a latent variable from hierarchy and features from the moving image. Subsequently, the RNN updates the hidden state variables based on the feature maps of the fixed image and the latent variables. Different from traditional methods, DragNet performs registration on unseen sequences in a forward pass, which significantly expedites the registration process. Besides, DragNet enables generating a large number of realistic synthetic image sequences given only one frame, where the corresponding deformations are also retrieved. The probabilistic framework allows for computing spatio-temporal uncertainties in the estimated motion fields. Our results show that DragNet performance is comparable with state-of-the-art methods in terms of registration accuracy, with the advantage of offering analytical pixel-wise motion uncertainty estimation across a cardiac cycle and being a motion generator. We will make our code publicly available.",
     "laySummary": "",
-    "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8855010/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8855010/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC8855010; pdf:https://europepmc.org/articles/PMC8855010?pdf=render"
+    "urls": "doi:https://doi.org/10.1016/j.media.2022.102678; doi:https://doi.org/10.1016/j.media.2022.102678"
   },
   {
     "id": "38388919",
@@ -25227,23 +25261,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1186/s12913-024-10716-7; html:https://europepmc.org/articles/PMC10882730; pdf:https://europepmc.org/articles/PMC10882730?pdf=render"
   },
-  {
-    "id": "35487318",
-    "doi": "https://doi.org/10.1016/j.ijcard.2022.04.067",
-    "title": "Implications of elevated troponin on time-to-surgery in non-ST elevation myocardial infarction (NIHR Health Informatics Collaborative: TROP-CABG study).",
-    "authorString": "Benedetto U, Sinha S, Mulla A, Glampson B, Davies J, Panoulas V, Gautama S, Papadimitriou D, Woods K, Elliott P, Hemingway H, Williams B, Asselbergs FW, Melikian N, Krasopoulos G, Sayeed R, Wendler O, Baig K, Chukwuemeka A, Angelini GD, Sterne JAC, Johnson T, Shah AM, Perera D, Patel RS, Kharbanda R, Channon KM, Mayet J, Kaura A.",
-    "authorAffiliations": "",
-    "journalTitle": "International journal of cardiology",
-    "pubYear": "2022",
-    "date": "2022-04-27",
-    "isOpenAccess": "N",
-    "keywords": "Troponin; Myocardial infarction; Coronary Artery Bypass Grafting; Timing-to-surgery",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Implications of elevated troponin on time-to-surgery in non-ST elevation myocardial infarction(NIHR Health Informatics Collaborative:TROP-CABG study). Benedetto et al. BACKGROUND: The optimal timing of coronary artery bypass grafting (CABG) in patients with non-ST elevation myocardial infarction (NSTEMI) and the utility of pre-operative troponin levels in decision-making remains unclear. We investigated (a) the association between peak pre-operative troponin and survival post-CABG in a large cohort of NSTEMI patients and (b) the interaction between troponin and time-to-surgery. METHODS AND RESULTS: Our cohort consisted of 1746 patients (1684 NSTEMI; 62 unstable angina) (mean age 69\u00a0\u00b1\u00a011\u00a0years,21% female) with recorded troponins that had CABG at five United Kingdom centers between 2010 and 2017. Time-segmented Cox regression was used to investigate the interaction of peak troponin and time-to-surgery on early (within 30\u00a0days) and late (beyond 30\u00a0days) survival. Average interval from peak troponin to surgery was 9\u00a0\u00b1\u00a015\u00a0days, with 1466 (84.0%) patients having CABG during the same admission. Sixty patients died within 30-days and another 211 died after a mean follow-up of 4\u00a0\u00b1\u00a02\u00a0years (30-day survival 0.97\u00a0\u00b1\u00a00.004 and 5-year survival 0.83\u00a0\u00b1\u00a00.01). Peak troponin was a strong predictor of early survival (adjusted P\u00a0=\u00a00.002) with a significant interaction with time-to-surgery (P interaction\u00a0=\u00a00.007). For peak troponin levels <100 times the upper limit of normal, there was no improvement in early survival with longer time-to-surgery. However, in patients with higher troponins, early survival increased progressively with a longer time-to-surgery, till day 10. Peak troponin did not influence survival beyond 30\u00a0days (adjusted P\u00a0=\u00a00.64). CONCLUSIONS: Peak troponin in NSTEMI patients undergoing CABG was a significant predictor of early mortality, strongly influenced the time-to-surgery and may prove to be a clinically useful biomarker in the management of these patients.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.ijcard.2022.04.067"
-  },
   {
     "id": "32717063",
     "doi": "https://doi.org/10.1093/cvr/cvaa233",
@@ -25261,6 +25278,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1093/cvr/cvaa233; doi:https://doi.org/10.1093/cvr/cvaa233; html:https://europepmc.org/articles/PMC8152696; pdf:https://europepmc.org/articles/PMC8152696?pdf=render"
   },
+  {
+    "id": "35487318",
+    "doi": "https://doi.org/10.1016/j.ijcard.2022.04.067",
+    "title": "Implications of elevated troponin on time-to-surgery in non-ST elevation myocardial infarction (NIHR Health Informatics Collaborative: TROP-CABG study).",
+    "authorString": "Benedetto U, Sinha S, Mulla A, Glampson B, Davies J, Panoulas V, Gautama S, Papadimitriou D, Woods K, Elliott P, Hemingway H, Williams B, Asselbergs FW, Melikian N, Krasopoulos G, Sayeed R, Wendler O, Baig K, Chukwuemeka A, Angelini GD, Sterne JAC, Johnson T, Shah AM, Perera D, Patel RS, Kharbanda R, Channon KM, Mayet J, Kaura A.",
+    "authorAffiliations": "",
+    "journalTitle": "International journal of cardiology",
+    "pubYear": "2022",
+    "date": "2022-04-27",
+    "isOpenAccess": "N",
+    "keywords": "Troponin; Myocardial infarction; Coronary Artery Bypass Grafting; Timing-to-surgery",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Implications of elevated troponin on time-to-surgery in non-ST elevation myocardial infarction(NIHR Health Informatics Collaborative:TROP-CABG study). Benedetto et al. BACKGROUND: The optimal timing of coronary artery bypass grafting (CABG) in patients with non-ST elevation myocardial infarction (NSTEMI) and the utility of pre-operative troponin levels in decision-making remains unclear. We investigated (a) the association between peak pre-operative troponin and survival post-CABG in a large cohort of NSTEMI patients and (b) the interaction between troponin and time-to-surgery. METHODS AND RESULTS: Our cohort consisted of 1746 patients (1684 NSTEMI; 62 unstable angina) (mean age 69\u00a0\u00b1\u00a011\u00a0years,21% female) with recorded troponins that had CABG at five United Kingdom centers between 2010 and 2017. Time-segmented Cox regression was used to investigate the interaction of peak troponin and time-to-surgery on early (within 30\u00a0days) and late (beyond 30\u00a0days) survival. Average interval from peak troponin to surgery was 9\u00a0\u00b1\u00a015\u00a0days, with 1466 (84.0%) patients having CABG during the same admission. Sixty patients died within 30-days and another 211 died after a mean follow-up of 4\u00a0\u00b1\u00a02\u00a0years (30-day survival 0.97\u00a0\u00b1\u00a00.004 and 5-year survival 0.83\u00a0\u00b1\u00a00.01). Peak troponin was a strong predictor of early survival (adjusted P\u00a0=\u00a00.002) with a significant interaction with time-to-surgery (P interaction\u00a0=\u00a00.007). For peak troponin levels <100 times the upper limit of normal, there was no improvement in early survival with longer time-to-surgery. However, in patients with higher troponins, early survival increased progressively with a longer time-to-surgery, till day 10. Peak troponin did not influence survival beyond 30\u00a0days (adjusted P\u00a0=\u00a00.64). CONCLUSIONS: Peak troponin in NSTEMI patients undergoing CABG was a significant predictor of early mortality, strongly influenced the time-to-surgery and may prove to be a clinically useful biomarker in the management of these patients.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.ijcard.2022.04.067"
+  },
   {
     "id": "33652931",
     "doi": "https://doi.org/10.3390/jcm10050921",
@@ -25431,23 +25465,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.3233/SHTI190058"
   },
-  {
-    "id": "36332947",
-    "doi": "https://doi.org/10.1136/bmjopen-2022-061843",
-    "title": "Numbers and types of neurological emergencies in England and the influence of socioeconomic deprivation: a retrospective analysis of hospital episode statistics data.",
-    "authorString": "Jackson M, Szczepaniak M, Wall J, Maskery M, Mummery C, Morrish P, Williams A, Knight J, Emsley HCA.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2022",
-    "date": "2022-11-04",
-    "isOpenAccess": "Y",
-    "keywords": "Epilepsy; Neurology; Public Health",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objectives</h4>In this first large-scale analysis of neurological emergency admissions in England, we determine the number and types of emergency admissions with neurological emergency diagnostic codes, how many are under the care of a neurologist or neurosurgeon and how such admissions vary by levels of deprivation.<h4>Design</h4>Retrospective empirical research employing a derived list of neurological emergency diagnostic codes SETTING: This study used the Hospital Episode Statistics data set for the financial year 2019/2020 based on 17\u2009million in-year inpatient admissions in England including 6.5\u2009million (100%) emergency admissions with any diagnosis codes.<h4>Results</h4>There were 1.4\u2009million (21.2%) emergency inpatient admissions with a mention of any neurological code, approx. 248\u2009455 (3.8%) with mention of a specific neurological emergency code from the derived list, and 72\u2009485 (1.1%) included such a code as the primary reason for admission. The highest number of in-year admissions for adults was for epilepsy (145 995), with epilepsy as the primary diagnostic code in 15\u2009945 (10.9%). Acute nerve root/spinal cord syndrome (41 215), head injury (29 235) and subarachnoid haemorrhage (18 505) accounted for the next three highest number of admissions. 3230 (1.4%) in-year emergency hospital admissions with mention of a neurological emergency code were under the care of a neurologist or neurosurgeon, with only 1315 (0.9%) admissions with mention of an epilepsy code under a neurologist. There was significant variation for epilepsy and functional neurological disorders (FNDs) in particular by Index of Multiple Deprivation decile. The association between deprivation and epilepsy and FND was significant with p-values of 2.5e-6 and 1.5e-8, respectively.<h4>Conclusions</h4>This study has identified important findings in relation to the burden of neurological emergency admissions but further work is needed, with greater clinical engagement in diagnostic coding, to better understand the implications for workforce and changes to service delivery needing to be implemented.",
-    "laySummary": "",
-    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/11/e061843.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-061843; html:https://europepmc.org/articles/PMC9639083; pdf:https://europepmc.org/articles/PMC9639083?pdf=render"
-  },
   {
     "id": "32861307",
     "doi": "https://doi.org/10.1016/s0140-6736(20)30930-2",
@@ -25465,6 +25482,23 @@
     "laySummary": "",
     "urls": "pdf:http://www.thelancet.com/article/S0140673620309302/pdf; doi:https://doi.org/10.1016/S0140-6736(20)30930-2; html:https://europepmc.org/articles/PMC7456783; pdf:https://europepmc.org/articles/PMC7456783?pdf=render"
   },
+  {
+    "id": "36332947",
+    "doi": "https://doi.org/10.1136/bmjopen-2022-061843",
+    "title": "Numbers and types of neurological emergencies in England and the influence of socioeconomic deprivation: a retrospective analysis of hospital episode statistics data.",
+    "authorString": "Jackson M, Szczepaniak M, Wall J, Maskery M, Mummery C, Morrish P, Williams A, Knight J, Emsley HCA.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2022",
+    "date": "2022-11-04",
+    "isOpenAccess": "Y",
+    "keywords": "Epilepsy; Neurology; Public Health",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objectives</h4>In this first large-scale analysis of neurological emergency admissions in England, we determine the number and types of emergency admissions with neurological emergency diagnostic codes, how many are under the care of a neurologist or neurosurgeon and how such admissions vary by levels of deprivation.<h4>Design</h4>Retrospective empirical research employing a derived list of neurological emergency diagnostic codes SETTING: This study used the Hospital Episode Statistics data set for the financial year 2019/2020 based on 17\u2009million in-year inpatient admissions in England including 6.5\u2009million (100%) emergency admissions with any diagnosis codes.<h4>Results</h4>There were 1.4\u2009million (21.2%) emergency inpatient admissions with a mention of any neurological code, approx. 248\u2009455 (3.8%) with mention of a specific neurological emergency code from the derived list, and 72\u2009485 (1.1%) included such a code as the primary reason for admission. The highest number of in-year admissions for adults was for epilepsy (145 995), with epilepsy as the primary diagnostic code in 15\u2009945 (10.9%). Acute nerve root/spinal cord syndrome (41 215), head injury (29 235) and subarachnoid haemorrhage (18 505) accounted for the next three highest number of admissions. 3230 (1.4%) in-year emergency hospital admissions with mention of a neurological emergency code were under the care of a neurologist or neurosurgeon, with only 1315 (0.9%) admissions with mention of an epilepsy code under a neurologist. There was significant variation for epilepsy and functional neurological disorders (FNDs) in particular by Index of Multiple Deprivation decile. The association between deprivation and epilepsy and FND was significant with p-values of 2.5e-6 and 1.5e-8, respectively.<h4>Conclusions</h4>This study has identified important findings in relation to the burden of neurological emergency admissions but further work is needed, with greater clinical engagement in diagnostic coding, to better understand the implications for workforce and changes to service delivery needing to be implemented.",
+    "laySummary": "",
+    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/11/e061843.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-061843; html:https://europepmc.org/articles/PMC9639083; pdf:https://europepmc.org/articles/PMC9639083?pdf=render"
+  },
   {
     "id": "31558464",
     "doi": "https://doi.org/10.1136/bmjopen-2019-033013",
@@ -25737,23 +25771,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/schizophreniabulletin/article-pdf/47/2/575/36620724/sbaa176.pdf; doi:https://doi.org/10.1093/schbul/sbaa176; html:https://europepmc.org/articles/PMC7965055; pdf:https://europepmc.org/articles/PMC7965055?pdf=render; doi:https://doi.org/10.1093/schbul/sbaa176"
   },
-  {
-    "id": "37750555",
-    "doi": "https://doi.org/10.1161/jaha.123.030766",
-    "title": "Impact of New Cardiovascular Events on Quality of Life and Hospital Costs in People With Cardiovascular Disease in the United Kingdom and United States.",
-    "authorString": "Lui JNM, Williams C, Keng MJ, Hopewell JC, Sammons E, Chen F, Gray A, Bowman L, Landray SMJ, Mihaylova B, REVEAL Collaborative Group.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of the American Heart Association",
-    "pubYear": "2023",
-    "date": "2023-09-26",
-    "isOpenAccess": "Y",
-    "keywords": "Cardiovascular diseases; Quality of life; United States; United Kingdom; Secondary Prevention; Health Care Costs",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Despite optimized risk factor control, people with prior cardiovascular disease remain at high cardiovascular disease risk. We assess the immediate- and longer-term impacts of new vascular and nonvascular events on quality of life (QoL) and hospital costs among participants in the REVEAL (Randomized Evaluation of the Effects of Anacetrapib Through Lipid Modification) trial in secondary prevention.<h4>Methods and results</h4>Data on demographic and clinical characteristics, health-related quality of life (QoL: EuroQoL 5-Dimension-5-Level), adverse events, and hospital admissions during the 4-year follow-up of the 21\u2009820 participants recruited in Europe and North America informed assessments of the impacts of new adverse events on QoL and hospital costs from the UK and US health systems' perspectives using generalized linear regression models. Reductions in QoL were estimated in the years of event occurrence for nonhemorrhagic stroke (-0.067 [United Kingdom], -0.069 [US]), heart failure admission (-0.072 [United Kingdom], -0.103 [US]), incident cancer (-0.064 [United Kingdom], -0.068 [US]), and noncoronary revascularization (-0.071 [United Kingdom], -0.061 [US]), as well as in subsequent years following these events. Myocardial infarction and coronary revascularization (CRV) procedures were not found to affect QoL. All adverse events were associated with additional hospital costs in the years of events and in subsequent years, with the highest additional costs in the years of noncoronary revascularization (\u00a35830 [United Kingdom], $14\u2009133 [US Medicare]), of myocardial infarction with urgent CRV procedure (\u00a35614, $24722), and of urgent/nonurgent CRV procedure without myocardial infarction (\u00a34674/\u00a34651 and $15\u2009251/$17\u2009539).<h4>Conclusions</h4>Stroke, heart failure, and noncoronary revascularization procedures substantially reduce QoL, and all cardiovascular disease events increase hospital costs. These estimates are useful in informing cost-effectiveness of interventions to reduce cardiovascular disease risk in secondary prevention.<h4>Registration</h4>URL: https://www.clinicaltrials.gov; Unique identifier: NCT01252953; https://www.Isrctn.com. Unique identifier: ISRCTN48678192; https://www.clinicaltrialsregister.eu. Unique identifier: 2010-023467-18.",
-    "laySummary": "",
-    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.123.030766; doi:https://doi.org/10.1161/JAHA.123.030766; html:https://europepmc.org/articles/PMC7615160; pdf:https://europepmc.org/articles/PMC7615160?pdf=render"
-  },
   {
     "id": "32929109",
     "doi": "https://doi.org/10.1038/s41598-020-72060-0",
@@ -25771,6 +25788,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41598-020-72060-0.pdf; doi:https://doi.org/10.1038/s41598-020-72060-0; html:https://europepmc.org/articles/PMC7490405; pdf:https://europepmc.org/articles/PMC7490405?pdf=render"
   },
+  {
+    "id": "37750555",
+    "doi": "https://doi.org/10.1161/jaha.123.030766",
+    "title": "Impact of New Cardiovascular Events on Quality of Life and Hospital Costs in People With Cardiovascular Disease in the United Kingdom and United States.",
+    "authorString": "Lui JNM, Williams C, Keng MJ, Hopewell JC, Sammons E, Chen F, Gray A, Bowman L, Landray SMJ, Mihaylova B, REVEAL Collaborative Group.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of the American Heart Association",
+    "pubYear": "2023",
+    "date": "2023-09-26",
+    "isOpenAccess": "Y",
+    "keywords": "Cardiovascular diseases; Quality of life; United States; United Kingdom; Secondary Prevention; Health Care Costs",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Despite optimized risk factor control, people with prior cardiovascular disease remain at high cardiovascular disease risk. We assess the immediate- and longer-term impacts of new vascular and nonvascular events on quality of life (QoL) and hospital costs among participants in the REVEAL (Randomized Evaluation of the Effects of Anacetrapib Through Lipid Modification) trial in secondary prevention.<h4>Methods and results</h4>Data on demographic and clinical characteristics, health-related quality of life (QoL: EuroQoL 5-Dimension-5-Level), adverse events, and hospital admissions during the 4-year follow-up of the 21\u2009820 participants recruited in Europe and North America informed assessments of the impacts of new adverse events on QoL and hospital costs from the UK and US health systems' perspectives using generalized linear regression models. Reductions in QoL were estimated in the years of event occurrence for nonhemorrhagic stroke (-0.067 [United Kingdom], -0.069 [US]), heart failure admission (-0.072 [United Kingdom], -0.103 [US]), incident cancer (-0.064 [United Kingdom], -0.068 [US]), and noncoronary revascularization (-0.071 [United Kingdom], -0.061 [US]), as well as in subsequent years following these events. Myocardial infarction and coronary revascularization (CRV) procedures were not found to affect QoL. All adverse events were associated with additional hospital costs in the years of events and in subsequent years, with the highest additional costs in the years of noncoronary revascularization (\u00a35830 [United Kingdom], $14\u2009133 [US Medicare]), of myocardial infarction with urgent CRV procedure (\u00a35614, $24722), and of urgent/nonurgent CRV procedure without myocardial infarction (\u00a34674/\u00a34651 and $15\u2009251/$17\u2009539).<h4>Conclusions</h4>Stroke, heart failure, and noncoronary revascularization procedures substantially reduce QoL, and all cardiovascular disease events increase hospital costs. These estimates are useful in informing cost-effectiveness of interventions to reduce cardiovascular disease risk in secondary prevention.<h4>Registration</h4>URL: https://www.clinicaltrials.gov; Unique identifier: NCT01252953; https://www.Isrctn.com. Unique identifier: ISRCTN48678192; https://www.clinicaltrialsregister.eu. Unique identifier: 2010-023467-18.",
+    "laySummary": "",
+    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.123.030766; doi:https://doi.org/10.1161/JAHA.123.030766; html:https://europepmc.org/articles/PMC7615160; pdf:https://europepmc.org/articles/PMC7615160?pdf=render"
+  },
   {
     "id": "31302040",
     "doi": "https://doi.org/10.1016/j.jchf.2019.03.009",
@@ -25941,23 +25975,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1080/17434440.2022.2132147; doi:https://doi.org/10.1080/17434440.2022.2132147"
   },
-  {
-    "id": "39054354",
-    "doi": "https://doi.org/10.1038/s41594-024-01357-9",
-    "title": "Structural basis for activity switching in polymerases determining the fate of let-7 pre-miRNAs.",
-    "authorString": "Yi G, Ye M, Carrique L, El-Sagheer A, Brown T, Norbury CJ, Zhang P, Gilbert RJC.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature structural & molecular biology",
-    "pubYear": "2024",
-    "date": "2024-07-25",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Tumor-suppressor let-7 pre-microRNAs (miRNAs) are regulated by terminal uridylyltransferases TUT7 and TUT4 that either promote let-7 maturation by adding a single uridine nucleotide to the pre-miRNA 3' end or mark them for degradation by the addition of multiple uridines. Oligo-uridylation is increased in cells by enhanced TUT7/4 expression and especially by the RNA-binding pluripotency factor LIN28A. Using cryogenic electron microscopy, we captured high-resolution structures of active forms of TUT7 alone, of TUT7 plus pre-miRNA and of both TUT7 and TUT4 bound with pre-miRNA and LIN28A. Our structures reveal that pre-miRNAs engage the enzymes in fundamentally different ways depending on the presence of LIN28A, which clamps them onto the TUTs to enable processive 3' oligo-uridylation. This study reveals the molecular basis for mono- versus oligo-uridylation by TUT7/4, as determined by the presence of LIN28A, and thus their mechanism of action in the regulation of cell fate and in cancer.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1038/s41594-024-01357-9; doi:https://doi.org/10.1038/s41594-024-01357-9; html:https://europepmc.org/articles/PMC11402785; pdf:https://europepmc.org/articles/PMC11402785?pdf=render"
-  },
   {
     "id": "35103964",
     "doi": "https://doi.org/10.1007/978-1-0716-2140-0_6",
@@ -25992,6 +26009,23 @@
     "laySummary": "",
     "urls": "pdf:https://discovery.ucl.ac.uk/10149151/1/Dobson_The%20COPILOT%20Raw%20Illumina%20Genotyping%20QC%20Protocol_VoR.pdf; doi:https://doi.org/10.1002/cpz1.373"
   },
+  {
+    "id": "39054354",
+    "doi": "https://doi.org/10.1038/s41594-024-01357-9",
+    "title": "Structural basis for activity switching in polymerases determining the fate of let-7 pre-miRNAs.",
+    "authorString": "Yi G, Ye M, Carrique L, El-Sagheer A, Brown T, Norbury CJ, Zhang P, Gilbert RJC.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature structural & molecular biology",
+    "pubYear": "2024",
+    "date": "2024-07-25",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Tumor-suppressor let-7 pre-microRNAs (miRNAs) are regulated by terminal uridylyltransferases TUT7 and TUT4 that either promote let-7 maturation by adding a single uridine nucleotide to the pre-miRNA 3' end or mark them for degradation by the addition of multiple uridines. Oligo-uridylation is increased in cells by enhanced TUT7/4 expression and especially by the RNA-binding pluripotency factor LIN28A. Using cryogenic electron microscopy, we captured high-resolution structures of active forms of TUT7 alone, of TUT7 plus pre-miRNA and of both TUT7 and TUT4 bound with pre-miRNA and LIN28A. Our structures reveal that pre-miRNAs engage the enzymes in fundamentally different ways depending on the presence of LIN28A, which clamps them onto the TUTs to enable processive 3' oligo-uridylation. This study reveals the molecular basis for mono- versus oligo-uridylation by TUT7/4, as determined by the presence of LIN28A, and thus their mechanism of action in the regulation of cell fate and in cancer.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1038/s41594-024-01357-9; doi:https://doi.org/10.1038/s41594-024-01357-9; html:https://europepmc.org/articles/PMC11402785; pdf:https://europepmc.org/articles/PMC11402785?pdf=render"
+  },
   {
     "id": "36809311",
     "doi": "https://doi.org/10.1093/ejendo/lvad024",
@@ -26009,23 +26043,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ejendo/article-pdf/188/3/290/49630912/lvad024.pdf; doi:https://doi.org/10.1093/ejendo/lvad024"
   },
-  {
-    "id": "38821540",
-    "doi": "https://doi.org/10.1038/s41591-024-03085-5",
-    "title": "Mutations in the U4 snRNA gene RNU4-2 cause one of the most prevalent monogenic neurodevelopmental disorders.",
-    "authorString": "Greene D, Thys C, Berry IR, Jarvis J, Ortibus E, Mumford AD, Freson K, Turro E.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature medicine",
-    "pubYear": "2024",
-    "date": "2024-05-31",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Most people with intellectual disability (ID) do not receive a molecular diagnosis following genetic testing. To identify new etiologies of ID, we performed a genetic association analysis comparing the burden of rare variants in 41,132 noncoding genes between 5,529 unrelated cases and 46,401 unrelated controls. RNU4-2, which encodes U4 small nuclear RNA, a critical component of the spliceosome, was the most strongly associated gene. We implicated de novo variants among 47 cases in two regions of RNU4-2 in the etiology of a syndrome characterized by ID, microcephaly, short stature, hypotonia, seizures and motor delay. We replicated this finding in three collections, bringing the number of unrelated cases to 73. Analysis of national genomic diagnostic data showed RNU4-2 to be a more common etiological gene for neurodevelopmental abnormality than any previously reported autosomal gene. Our findings add to the growing evidence of spliceosome dysfunction in the etiologies of neurological disorders.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1038/s41591-024-03085-5; html:https://europepmc.org/articles/PMC11333284; pdf:https://europepmc.org/articles/PMC11333284?pdf=render"
-  },
   {
     "id": "35022215",
     "doi": "https://doi.org/10.1136/bmj-2021-067519",
@@ -26044,21 +26061,21 @@
     "urls": "pdf:https://www.bmj.com/content/bmj/376/bmj-2021-067519.full.pdf; doi:https://doi.org/10.1136/bmj-2021-067519; html:https://europepmc.org/articles/PMC8753487; pdf:https://europepmc.org/articles/PMC8753487?pdf=render"
   },
   {
-    "id": "36576811",
-    "doi": "https://doi.org/10.1001/jamacardio.2022.4466",
-    "title": "Predictive Utility of a Coronary Artery Disease Polygenic Risk Score in Primary Prevention.",
-    "authorString": "Marston NA, Pirruccello JP, Melloni GEM, Koyama S, Kamanu FK, Weng LC, Roselli C, Kamatani Y, Komuro I, Aragam KG, Butterworth AS, Ito K, Lubitz SA, Ellinor PT, Sabatine MS, Ruff CT.",
+    "id": "38821540",
+    "doi": "https://doi.org/10.1038/s41591-024-03085-5",
+    "title": "Mutations in the U4 snRNA gene RNU4-2 cause one of the most prevalent monogenic neurodevelopmental disorders.",
+    "authorString": "Greene D, Thys C, Berry IR, Jarvis J, Ortibus E, Mumford AD, Freson K, Turro E.",
     "authorAffiliations": "",
-    "journalTitle": "JAMA cardiology",
-    "pubYear": "2023",
-    "date": "2023-02-01",
-    "isOpenAccess": "N",
+    "journalTitle": "Nature medicine",
+    "pubYear": "2024",
+    "date": "2024-05-31",
+    "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Importance</h4>The clinical utility of polygenic risk scores (PRS) for coronary artery disease (CAD) has not yet been established.<h4>Objective</h4>To investigate the ability of a CAD PRS to potentially guide statin initiation in primary prevention after accounting for age and clinical risk.<h4>Design, setting, and participants</h4>This was a longitudinal cohort study with enrollment starting on January 1, 2006, and ending on December 31, 2010, with data updated to mid-2021, using data from the UK Biobank, a long-term population study of UK citizens. A replication analysis was performed in Biobank Japan. The analysis included all patients without a history of CAD and who were not taking lipid-lowering therapy. Data were analyzed from January 1 to June 30, 2022.<h4>Exposures</h4>Polygenic risk for CAD was defined as low (bottom 20%), intermediate, and high (top 20%) using a CAD PRS including 241 genome-wide significant single-nucleotide variations (SNVs). The pooled cohort equations were used to estimate 10-year atherosclerotic cardiovascular disease (ASCVD) risk and classify individuals as low (<5%), borderline (5-<7.5%), intermediate (7.5-<20%), or high risk (\u226520%).<h4>Main outcomes and measures</h4>Myocardial infarction (MI) and ASCVD events (defined as incident clinical CAD [including MI], stroke, or CV death).<h4>Results</h4>A total of 330\u202f201 patients (median [IQR] age, 57 [40-74] years; 189\u202f107 female individuals [57%]) were included from the UK Biobank. Over the 10-year follow-up, 4454 individuals had an MI. The CAD PRS was significantly associated with the risk of MI in all age groups but had significantly stronger risk prediction at younger ages (age <50 years: hazard ratio [HR] per 1 SD of PRS, 1.72; 95% CI, 1.56-1.89; age 50-60 years: HR, 1.46; 95% CI, 1.38-1.53; age >60 years: HR, 1.42; 95% CI, 1.37-1.48; P for interaction <.001). In patients younger than 50 years, those with high PRS had a 3- to 4-fold increased associated risk of MI compared with those in the low PRS category. A significant interaction between CAD PRS and age was replicated in Biobank Japan. When CAD PRS testing was added to the clinical ASCVD risk score in individuals younger than 50 years, 591 of 4373 patients (20%) with borderline risk were risk stratified into intermediate risk, warranting initiation of statin therapy and 3198 of 7477 patients (20%) with both borderline or intermediate risk were stratified as low risk, thus not warranting therapy.<h4>Conclusions and relevance</h4>Results of this cohort study suggest that the predictive ability of a CAD PRS was greater in younger individuals and can be used to better identify patients with borderline and intermediate clinical risk who should initiate statin therapy.",
+    "abstract": "Most people with intellectual disability (ID) do not receive a molecular diagnosis following genetic testing. To identify new etiologies of ID, we performed a genetic association analysis comparing the burden of rare variants in 41,132 noncoding genes between 5,529 unrelated cases and 46,401 unrelated controls. RNU4-2, which encodes U4 small nuclear RNA, a critical component of the spliceosome, was the most strongly associated gene. We implicated de novo variants among 47 cases in two regions of RNU4-2 in the etiology of a syndrome characterized by ID, microcephaly, short stature, hypotonia, seizures and motor delay. We replicated this finding in three collections, bringing the number of unrelated cases to 73. Analysis of national genomic diagnostic data showed RNU4-2 to be a more common etiological gene for neurodevelopmental abnormality than any previously reported autosomal gene. Our findings add to the growing evidence of spliceosome dysfunction in the etiologies of neurological disorders.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1001/jamacardio.2022.4466; html:https://europepmc.org/articles/PMC9857431; doi:https://doi.org/10.1001/jamacardio.2022.4466"
+    "urls": "doi:https://doi.org/10.1038/s41591-024-03085-5; html:https://europepmc.org/articles/PMC11333284; pdf:https://europepmc.org/articles/PMC11333284?pdf=render"
   },
   {
     "id": "35242820",
@@ -26078,21 +26095,21 @@
     "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2021.816985/pdf; doi:https://doi.org/10.3389/fcvm.2021.816985; html:https://europepmc.org/articles/PMC8886212; pdf:https://europepmc.org/articles/PMC8886212?pdf=render"
   },
   {
-    "id": "37284234",
-    "doi": "https://doi.org/10.1140/epjds/s13688-023-00391-9",
-    "title": "The shock, the coping, the resilience: smartphone application use reveals Covid-19 lockdown effects on human behaviors.",
-    "authorString": "Liu XF, Wang ZZ, Xu XK, Wu Y, Zhao Z, Deng H, Wang P, Chao N, Huang YC.",
+    "id": "36576811",
+    "doi": "https://doi.org/10.1001/jamacardio.2022.4466",
+    "title": "Predictive Utility of a Coronary Artery Disease Polygenic Risk Score in Primary Prevention.",
+    "authorString": "Marston NA, Pirruccello JP, Melloni GEM, Koyama S, Kamanu FK, Weng LC, Roselli C, Kamatani Y, Komuro I, Aragam KG, Butterworth AS, Ito K, Lubitz SA, Ellinor PT, Sabatine MS, Ruff CT.",
     "authorAffiliations": "",
-    "journalTitle": "EPJ data science",
+    "journalTitle": "JAMA cardiology",
     "pubYear": "2023",
-    "date": "2023-06-05",
-    "isOpenAccess": "Y",
-    "keywords": "Human behaviors; Natural Experiment; Lockdown; Smartphone Apps; Covid-19",
+    "date": "2023-02-01",
+    "isOpenAccess": "N",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Human mobility restriction policies have been widely used to contain the coronavirus disease-19 (COVID-19). However, a critical question is how these policies affect individuals' behavioral and psychological well-being during and after confinement periods. Here, we analyze China's five most stringent city-level lockdowns in 2021, treating them as natural experiments that allow for examining behavioral changes in millions of people through smartphone application use. We made three fundamental observations. First, the use of physical and economic activity-related apps experienced a steep decline, yet apps that provide daily necessities maintained normal usage. Second, apps that fulfilled lower-level human needs, such as working, socializing, information seeking, and entertainment, saw an immediate and substantial increase in screen time. Those that satisfied higher-level needs, such as education, only attracted delayed attention. Third, human behaviors demonstrated resilience as most routines resumed after the lockdowns were lifted. Nonetheless, long-term lifestyle changes were observed, as significant numbers of people chose to continue working and learning online, becoming \"digital residents.\" This study also demonstrates the capability of smartphone screen time analytics in the study of human behaviors.<h4>Supplementary information</h4>The online version contains supplementary material available at 10.1140/epjds/s13688-023-00391-9.",
+    "abstract": "<h4>Importance</h4>The clinical utility of polygenic risk scores (PRS) for coronary artery disease (CAD) has not yet been established.<h4>Objective</h4>To investigate the ability of a CAD PRS to potentially guide statin initiation in primary prevention after accounting for age and clinical risk.<h4>Design, setting, and participants</h4>This was a longitudinal cohort study with enrollment starting on January 1, 2006, and ending on December 31, 2010, with data updated to mid-2021, using data from the UK Biobank, a long-term population study of UK citizens. A replication analysis was performed in Biobank Japan. The analysis included all patients without a history of CAD and who were not taking lipid-lowering therapy. Data were analyzed from January 1 to June 30, 2022.<h4>Exposures</h4>Polygenic risk for CAD was defined as low (bottom 20%), intermediate, and high (top 20%) using a CAD PRS including 241 genome-wide significant single-nucleotide variations (SNVs). The pooled cohort equations were used to estimate 10-year atherosclerotic cardiovascular disease (ASCVD) risk and classify individuals as low (<5%), borderline (5-<7.5%), intermediate (7.5-<20%), or high risk (\u226520%).<h4>Main outcomes and measures</h4>Myocardial infarction (MI) and ASCVD events (defined as incident clinical CAD [including MI], stroke, or CV death).<h4>Results</h4>A total of 330\u202f201 patients (median [IQR] age, 57 [40-74] years; 189\u202f107 female individuals [57%]) were included from the UK Biobank. Over the 10-year follow-up, 4454 individuals had an MI. The CAD PRS was significantly associated with the risk of MI in all age groups but had significantly stronger risk prediction at younger ages (age <50 years: hazard ratio [HR] per 1 SD of PRS, 1.72; 95% CI, 1.56-1.89; age 50-60 years: HR, 1.46; 95% CI, 1.38-1.53; age >60 years: HR, 1.42; 95% CI, 1.37-1.48; P for interaction <.001). In patients younger than 50 years, those with high PRS had a 3- to 4-fold increased associated risk of MI compared with those in the low PRS category. A significant interaction between CAD PRS and age was replicated in Biobank Japan. When CAD PRS testing was added to the clinical ASCVD risk score in individuals younger than 50 years, 591 of 4373 patients (20%) with borderline risk were risk stratified into intermediate risk, warranting initiation of statin therapy and 3198 of 7477 patients (20%) with both borderline or intermediate risk were stratified as low risk, thus not warranting therapy.<h4>Conclusions and relevance</h4>Results of this cohort study suggest that the predictive ability of a CAD PRS was greater in younger individuals and can be used to better identify patients with borderline and intermediate clinical risk who should initiate statin therapy.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1140/epjds/s13688-023-00391-9; doi:https://doi.org/10.1140/epjds/s13688-023-00391-9; html:https://europepmc.org/articles/PMC10240109; pdf:https://europepmc.org/articles/PMC10240109?pdf=render"
+    "urls": "doi:https://doi.org/10.1001/jamacardio.2022.4466; html:https://europepmc.org/articles/PMC9857431; doi:https://doi.org/10.1001/jamacardio.2022.4466"
   },
   {
     "id": "37269003",
@@ -26111,6 +26128,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1186/s13643-023-02261-x; doi:https://doi.org/10.1186/s13643-023-02261-x; html:https://europepmc.org/articles/PMC10237080; pdf:https://europepmc.org/articles/PMC10237080?pdf=render"
   },
+  {
+    "id": "37284234",
+    "doi": "https://doi.org/10.1140/epjds/s13688-023-00391-9",
+    "title": "The shock, the coping, the resilience: smartphone application use reveals Covid-19 lockdown effects on human behaviors.",
+    "authorString": "Liu XF, Wang ZZ, Xu XK, Wu Y, Zhao Z, Deng H, Wang P, Chao N, Huang YC.",
+    "authorAffiliations": "",
+    "journalTitle": "EPJ data science",
+    "pubYear": "2023",
+    "date": "2023-06-05",
+    "isOpenAccess": "Y",
+    "keywords": "Human behaviors; Natural Experiment; Lockdown; Smartphone Apps; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Human mobility restriction policies have been widely used to contain the coronavirus disease-19 (COVID-19). However, a critical question is how these policies affect individuals' behavioral and psychological well-being during and after confinement periods. Here, we analyze China's five most stringent city-level lockdowns in 2021, treating them as natural experiments that allow for examining behavioral changes in millions of people through smartphone application use. We made three fundamental observations. First, the use of physical and economic activity-related apps experienced a steep decline, yet apps that provide daily necessities maintained normal usage. Second, apps that fulfilled lower-level human needs, such as working, socializing, information seeking, and entertainment, saw an immediate and substantial increase in screen time. Those that satisfied higher-level needs, such as education, only attracted delayed attention. Third, human behaviors demonstrated resilience as most routines resumed after the lockdowns were lifted. Nonetheless, long-term lifestyle changes were observed, as significant numbers of people chose to continue working and learning online, becoming \"digital residents.\" This study also demonstrates the capability of smartphone screen time analytics in the study of human behaviors.<h4>Supplementary information</h4>The online version contains supplementary material available at 10.1140/epjds/s13688-023-00391-9.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1140/epjds/s13688-023-00391-9; doi:https://doi.org/10.1140/epjds/s13688-023-00391-9; html:https://europepmc.org/articles/PMC10240109; pdf:https://europepmc.org/articles/PMC10240109?pdf=render"
+  },
   {
     "id": "37538142",
     "doi": "https://doi.org/10.1093/ehjdh/ztad037",
@@ -26179,6 +26213,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/bjs/article-pdf/107/7/e220/35705126/bjs11580.pdf; doi:https://doi.org/10.1002/bjs.11580"
   },
+  {
+    "id": "35440446",
+    "doi": "https://doi.org/10.1136/bmjopen-2021-052514",
+    "title": "Protocol for the COG-UK hospital-onset COVID-19 infection (HOCI) multicentre interventional clinical study: evaluating the efficacy of rapid genome sequencing of SARS-CoV-2 in limiting the spread of COVID-19 in UK NHS hospitals.",
+    "authorString": "Blackstone J, Stirrup O, Mapp F, Panca M, Copas A, Flowers P, Hockey L, Price J, Partridge D, Peters C, de Silva T, Nebbia G, Snell LB, McComish R, COVID-19 Genomics UK (COG-UK) Consortium, Breuer J.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2022",
+    "date": "2022-04-19",
+    "isOpenAccess": "Y",
+    "keywords": "Molecular biology; Infection control; epidemiology; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objectives</h4>Nosocomial transmission of SARS-CoV-2 has been a significant cause of mortality in National Health Service (NHS) hospitals during the COVID-19 pandemic. The COG-UK Consortium Hospital-Onset COVID-19 Infections (COG-UK HOCI) study aims to evaluate whether the use of rapid whole-genome sequencing of SARS-CoV-2, supported by a novel probabilistic reporting methodology, can inform infection prevention and control (IPC) practice within NHS hospital settings.<h4>Design</h4>Multicentre, prospective, interventional, superiority study.<h4>Setting</h4>14 participating NHS hospitals over winter-spring 2020/2021 in the UK.<h4>Participants</h4>Eligible patients must be admitted to hospital with first-confirmed SARS-CoV-2 PCR-positive test result >48\u2009hour from time of admission, where COVID-19 diagnosis not suspected on admission. The projected sample size is 2380 patients.<h4>Intervention</h4>The intervention is the return of a sequence report, within 48 hours in one phase (rapid local lab processing) and within 5-10\u2009days in a second phase (mimicking central lab), comparing the viral genome from an eligible study participant with others within and outside the hospital site.<h4>Primary and secondary outcome measures</h4>The primary outcomes are incidence of Public Health England (PHE)/IPC-defined SARS-CoV-2 hospital-acquired infection during the baseline and two interventional phases, and proportion of hospital-onset cases with genomic evidence of transmission linkage following implementation of the intervention where such linkage was not suspected by initial IPC investigation. Secondary outcomes include incidence of hospital outbreaks, with and without sequencing data; actual and desirable changes to IPC actions; periods of healthcare worker (HCW) absence. Health economic analysis will be conducted to determine cost benefit of the intervention. A process evaluation using qualitative interviews with HCWs will be conducted alongside the study.<h4>Trial registration number</h4>ISRCTN50212645. Pre-results stage. This manuscript is based on protocol V.6.0. 2 September 2021.",
+    "laySummary": "",
+    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/4/e052514.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-052514; html:https://europepmc.org/articles/PMC9019828; pdf:https://europepmc.org/articles/PMC9019828?pdf=render"
+  },
   {
     "id": "32856398",
     "doi": "https://doi.org/10.1111/1742-6723.13604",
@@ -26213,23 +26264,6 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/jdv.17450; doi:https://doi.org/10.1111/jdv.17450; html:https://europepmc.org/articles/PMC8447018; pdf:https://europepmc.org/articles/PMC8447018?pdf=render"
   },
-  {
-    "id": "35440446",
-    "doi": "https://doi.org/10.1136/bmjopen-2021-052514",
-    "title": "Protocol for the COG-UK hospital-onset COVID-19 infection (HOCI) multicentre interventional clinical study: evaluating the efficacy of rapid genome sequencing of SARS-CoV-2 in limiting the spread of COVID-19 in UK NHS hospitals.",
-    "authorString": "Blackstone J, Stirrup O, Mapp F, Panca M, Copas A, Flowers P, Hockey L, Price J, Partridge D, Peters C, de Silva T, Nebbia G, Snell LB, McComish R, COVID-19 Genomics UK (COG-UK) Consortium, Breuer J.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2022",
-    "date": "2022-04-19",
-    "isOpenAccess": "Y",
-    "keywords": "Molecular biology; Infection control; epidemiology; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objectives</h4>Nosocomial transmission of SARS-CoV-2 has been a significant cause of mortality in National Health Service (NHS) hospitals during the COVID-19 pandemic. The COG-UK Consortium Hospital-Onset COVID-19 Infections (COG-UK HOCI) study aims to evaluate whether the use of rapid whole-genome sequencing of SARS-CoV-2, supported by a novel probabilistic reporting methodology, can inform infection prevention and control (IPC) practice within NHS hospital settings.<h4>Design</h4>Multicentre, prospective, interventional, superiority study.<h4>Setting</h4>14 participating NHS hospitals over winter-spring 2020/2021 in the UK.<h4>Participants</h4>Eligible patients must be admitted to hospital with first-confirmed SARS-CoV-2 PCR-positive test result >48\u2009hour from time of admission, where COVID-19 diagnosis not suspected on admission. The projected sample size is 2380 patients.<h4>Intervention</h4>The intervention is the return of a sequence report, within 48 hours in one phase (rapid local lab processing) and within 5-10\u2009days in a second phase (mimicking central lab), comparing the viral genome from an eligible study participant with others within and outside the hospital site.<h4>Primary and secondary outcome measures</h4>The primary outcomes are incidence of Public Health England (PHE)/IPC-defined SARS-CoV-2 hospital-acquired infection during the baseline and two interventional phases, and proportion of hospital-onset cases with genomic evidence of transmission linkage following implementation of the intervention where such linkage was not suspected by initial IPC investigation. Secondary outcomes include incidence of hospital outbreaks, with and without sequencing data; actual and desirable changes to IPC actions; periods of healthcare worker (HCW) absence. Health economic analysis will be conducted to determine cost benefit of the intervention. A process evaluation using qualitative interviews with HCWs will be conducted alongside the study.<h4>Trial registration number</h4>ISRCTN50212645. Pre-results stage. This manuscript is based on protocol V.6.0. 2 September 2021.",
-    "laySummary": "",
-    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/4/e052514.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-052514; html:https://europepmc.org/articles/PMC9019828; pdf:https://europepmc.org/articles/PMC9019828?pdf=render"
-  },
   {
     "id": "34304930",
     "doi": "https://doi.org/10.1016/j.burns.2021.06.007",
@@ -26247,6 +26281,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.burns.2021.06.007"
   },
+  {
+    "id": "32119825",
+    "doi": "https://doi.org/10.1016/s2214-109x(20)30074-7",
+    "title": "Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts.",
+    "authorString": "Hellewell J, Abbott S, Gimma A, Bosse NI, Jarvis CI, Russell TW, Munday JD, Kucharski AJ, Edmunds WJ, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Funk S, Eggo RM.",
+    "authorAffiliations": "",
+    "journalTitle": "The Lancet. Global health",
+    "pubYear": "2020",
+    "date": "2020-02-28",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "Improving Public Health",
+    "healthCategories": "COVID-19",
+    "abstract": "<h4>Background</h4>Isolation of cases and contact tracing is used to control outbreaks of infectious diseases, and has been used for coronavirus disease 2019 (COVID-19). Whether this strategy will achieve control depends on characteristics of both the pathogen and the response. Here we use a mathematical model to assess if isolation and contact tracing are able to control onwards transmission from imported cases of COVID-19.<h4>Methods</h4>We developed a stochastic transmission model, parameterised to the COVID-19 outbreak. We used the model to quantify the potential effectiveness of contact tracing and isolation of cases at controlling a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-like pathogen. We considered scenarios that varied in the number of initial cases, the basic reproduction number (R<sub>0</sub>), the delay from symptom onset to isolation, the probability that contacts were traced, the proportion of transmission that occurred before symptom onset, and the proportion of subclinical infections. We assumed isolation prevented all further transmission in the model. Outbreaks were deemed controlled if transmission ended within 12 weeks or before 5000 cases in total. We measured the success of controlling outbreaks using isolation and contact tracing, and quantified the weekly maximum number of cases traced to measure feasibility of public health effort.<h4>Findings</h4>Simulated outbreaks starting with five initial cases, an R<sub>0</sub> of 1\u00b75, and 0% transmission before symptom onset could be controlled even with low contact tracing probability; however, the probability of controlling an outbreak decreased with the number of initial cases, when R<sub>0</sub> was 2\u00b75 or 3\u00b75 and with more transmission before symptom onset. Across different initial numbers of cases, the majority of scenarios with an R<sub>0</sub> of 1\u00b75 were controllable with less than 50% of contacts successfully traced. To control the majority of outbreaks, for R<sub>0</sub> of 2\u00b75 more than 70% of contacts had to be traced, and for an R<sub>0</sub> of 3\u00b75 more than 90% of contacts had to be traced. The delay between symptom onset and isolation had the largest role in determining whether an outbreak was controllable when R<sub>0</sub> was 1\u00b75. For R<sub>0</sub> values of 2\u00b75 or 3\u00b75, if there were 40 initial cases, contact tracing and isolation were only potentially feasible when less than 1% of transmission occurred before symptom onset.<h4>Interpretation</h4>In most scenarios, highly effective contact tracing and case isolation is enough to control a new outbreak of COVID-19 within 3 months. The probability of control decreases with long delays from symptom onset to isolation, fewer cases ascertained by contact tracing, and increasing transmission before symptoms. This model can be modified to reflect updated transmission characteristics and more specific definitions of outbreak control to assess the potential success of local response efforts.<h4>Funding</h4>Wellcome Trust, Global Challenges Research Fund, and Health Data Research UK.",
+    "laySummary": "",
+    "urls": "pdf:https://europepmc.org/articles/pmc7097845?pdf=render; doi:https://doi.org/10.1016/S2214-109X(20)30074-7; html:https://europepmc.org/articles/PMC7097845; pdf:https://europepmc.org/articles/PMC7097845?pdf=render"
+  },
   {
     "id": "37964568",
     "doi": "https://doi.org/10.1192/bjo.2023.547",
@@ -26281,23 +26332,6 @@
     "laySummary": "",
     "urls": "pdf:https://downloads.hindawi.com/journals/jhe/2021/6663884.pdf; doi:https://doi.org/10.1155/2021/6663884; html:https://europepmc.org/articles/PMC8285182; pdf:https://europepmc.org/articles/PMC8285182?pdf=render"
   },
-  {
-    "id": "32119825",
-    "doi": "https://doi.org/10.1016/s2214-109x(20)30074-7",
-    "title": "Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts.",
-    "authorString": "Hellewell J, Abbott S, Gimma A, Bosse NI, Jarvis CI, Russell TW, Munday JD, Kucharski AJ, Edmunds WJ, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Funk S, Eggo RM.",
-    "authorAffiliations": "",
-    "journalTitle": "The Lancet. Global health",
-    "pubYear": "2020",
-    "date": "2020-02-28",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "Improving Public Health",
-    "healthCategories": "COVID-19",
-    "abstract": "<h4>Background</h4>Isolation of cases and contact tracing is used to control outbreaks of infectious diseases, and has been used for coronavirus disease 2019 (COVID-19). Whether this strategy will achieve control depends on characteristics of both the pathogen and the response. Here we use a mathematical model to assess if isolation and contact tracing are able to control onwards transmission from imported cases of COVID-19.<h4>Methods</h4>We developed a stochastic transmission model, parameterised to the COVID-19 outbreak. We used the model to quantify the potential effectiveness of contact tracing and isolation of cases at controlling a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-like pathogen. We considered scenarios that varied in the number of initial cases, the basic reproduction number (R<sub>0</sub>), the delay from symptom onset to isolation, the probability that contacts were traced, the proportion of transmission that occurred before symptom onset, and the proportion of subclinical infections. We assumed isolation prevented all further transmission in the model. Outbreaks were deemed controlled if transmission ended within 12 weeks or before 5000 cases in total. We measured the success of controlling outbreaks using isolation and contact tracing, and quantified the weekly maximum number of cases traced to measure feasibility of public health effort.<h4>Findings</h4>Simulated outbreaks starting with five initial cases, an R<sub>0</sub> of 1\u00b75, and 0% transmission before symptom onset could be controlled even with low contact tracing probability; however, the probability of controlling an outbreak decreased with the number of initial cases, when R<sub>0</sub> was 2\u00b75 or 3\u00b75 and with more transmission before symptom onset. Across different initial numbers of cases, the majority of scenarios with an R<sub>0</sub> of 1\u00b75 were controllable with less than 50% of contacts successfully traced. To control the majority of outbreaks, for R<sub>0</sub> of 2\u00b75 more than 70% of contacts had to be traced, and for an R<sub>0</sub> of 3\u00b75 more than 90% of contacts had to be traced. The delay between symptom onset and isolation had the largest role in determining whether an outbreak was controllable when R<sub>0</sub> was 1\u00b75. For R<sub>0</sub> values of 2\u00b75 or 3\u00b75, if there were 40 initial cases, contact tracing and isolation were only potentially feasible when less than 1% of transmission occurred before symptom onset.<h4>Interpretation</h4>In most scenarios, highly effective contact tracing and case isolation is enough to control a new outbreak of COVID-19 within 3 months. The probability of control decreases with long delays from symptom onset to isolation, fewer cases ascertained by contact tracing, and increasing transmission before symptoms. This model can be modified to reflect updated transmission characteristics and more specific definitions of outbreak control to assess the potential success of local response efforts.<h4>Funding</h4>Wellcome Trust, Global Challenges Research Fund, and Health Data Research UK.",
-    "laySummary": "",
-    "urls": "pdf:https://europepmc.org/articles/pmc7097845?pdf=render; doi:https://doi.org/10.1016/S2214-109X(20)30074-7; html:https://europepmc.org/articles/PMC7097845; pdf:https://europepmc.org/articles/PMC7097845?pdf=render"
-  },
   {
     "id": "33240510",
     "doi": "https://doi.org/10.15420/aer.2020.26",
@@ -26349,6 +26383,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1002/ejhf.2868; doi:https://doi.org/10.1002/ejhf.2868"
   },
+  {
+    "id": "36243582",
+    "doi": "https://doi.org/10.1016/j.injury.2022.09.052",
+    "title": "Older trauma patients with isolated chest injuries have low rates of complications.",
+    "authorString": "Ferrah N, Beck B, Ibrahim J, Gabbe B, McLellan MS, Cameron P.",
+    "authorAffiliations": "",
+    "journalTitle": "Injury",
+    "pubYear": "2022",
+    "date": "2022-10-07",
+    "isOpenAccess": "N",
+    "keywords": "Geriatric; Complication; Pneumonia; Chest Trauma; Older; Trauma Centre",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>The number of older adults hospitalised for injury is growing rapidly. The population-adjusted incidence of isolated thoracic injuries in older adults is also growing. While some older adults are at high risk of post-traumatic complications, not all older adults will need treatment in a major trauma service (MTS). The aim of this study was to characterise older patients with isolated chest injuries, determine the rates of post-traumatic complications, including respiratory failure and pneumonia, and the factors associated with the risk of developing these complications.<h4>Patients and methods</h4>This was a retrospective review of patients aged 65 years and over with isolated chest trauma, from January 2007 to June 2017, using data from the Victorian State Trauma Registry. Patient characteristics and rates of complications were compared between patients with 1. isolated rib fractures, and 2. complex chest injury. Multivariable logistic regression was used to identify predictors of respiratory failure, and pneumonia.<h4>Results</h4>The study population comprised 5401 patients aged 65 years or more, with isolated chest injuries. Two-thirds (65%) of all patients had isolated rib fractures, and 58% of patients (n\u00a0=\u00a03156) were directly admitted to a non-major trauma centre. Complications were uncommon, with 5.45% of all patients (n\u00a0=\u00a0295) having pneumonia and 3.2% (n\u00a0=\u00a0175) having respiratory failure. Factors associated with increased risk of pneumonia and respiratory failure included advancing age, smoking, chronic obstructive pulmonary disease, congestive heart failure, and more severe and complex chest injury. The adjusted odds of complications were lowest amongst patients not classified as major trauma and receiving definitive treatment in non-MTS.<h4>Discussion</h4>Our findings suggest that rates of complications in older patients with isolated chest trauma in this study were low, and that there is a large group of patients with isolated, uncomplicated rib fractures, who may not need to be treated in a major trauma centre. Further work should be undertaken to appropriately risk stratify and manage older adults with isolated chest trauma.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.injury.2022.09.052"
+  },
   {
     "id": "34907415",
     "doi": "https://doi.org/10.1093/ehjci/jeab266",
@@ -26383,23 +26434,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.jcmg.2022.11.012; doi:https://doi.org/10.1016/j.jcmg.2022.11.012; html:https://europepmc.org/articles/PMC11229671; pdf:https://europepmc.org/articles/PMC11229671?pdf=render; doi:https://doi.org/10.1016/j.jcmg.2022.11.012"
   },
-  {
-    "id": "36243582",
-    "doi": "https://doi.org/10.1016/j.injury.2022.09.052",
-    "title": "Older trauma patients with isolated chest injuries have low rates of complications.",
-    "authorString": "Ferrah N, Beck B, Ibrahim J, Gabbe B, McLellan MS, Cameron P.",
-    "authorAffiliations": "",
-    "journalTitle": "Injury",
-    "pubYear": "2022",
-    "date": "2022-10-07",
-    "isOpenAccess": "N",
-    "keywords": "Geriatric; Complication; Pneumonia; Chest Trauma; Older; Trauma Centre",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>The number of older adults hospitalised for injury is growing rapidly. The population-adjusted incidence of isolated thoracic injuries in older adults is also growing. While some older adults are at high risk of post-traumatic complications, not all older adults will need treatment in a major trauma service (MTS). The aim of this study was to characterise older patients with isolated chest injuries, determine the rates of post-traumatic complications, including respiratory failure and pneumonia, and the factors associated with the risk of developing these complications.<h4>Patients and methods</h4>This was a retrospective review of patients aged 65 years and over with isolated chest trauma, from January 2007 to June 2017, using data from the Victorian State Trauma Registry. Patient characteristics and rates of complications were compared between patients with 1. isolated rib fractures, and 2. complex chest injury. Multivariable logistic regression was used to identify predictors of respiratory failure, and pneumonia.<h4>Results</h4>The study population comprised 5401 patients aged 65 years or more, with isolated chest injuries. Two-thirds (65%) of all patients had isolated rib fractures, and 58% of patients (n\u00a0=\u00a03156) were directly admitted to a non-major trauma centre. Complications were uncommon, with 5.45% of all patients (n\u00a0=\u00a0295) having pneumonia and 3.2% (n\u00a0=\u00a0175) having respiratory failure. Factors associated with increased risk of pneumonia and respiratory failure included advancing age, smoking, chronic obstructive pulmonary disease, congestive heart failure, and more severe and complex chest injury. The adjusted odds of complications were lowest amongst patients not classified as major trauma and receiving definitive treatment in non-MTS.<h4>Discussion</h4>Our findings suggest that rates of complications in older patients with isolated chest trauma in this study were low, and that there is a large group of patients with isolated, uncomplicated rib fractures, who may not need to be treated in a major trauma centre. Further work should be undertaken to appropriately risk stratify and manage older adults with isolated chest trauma.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.injury.2022.09.052"
-  },
   {
     "id": "32379357",
     "doi": "https://doi.org/10.1002/sim.8563",
@@ -26502,23 +26536,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.bmj.com/content/bmj/377/bmj-2022-070230.full.pdf; doi:https://doi.org/10.1136/bmj-2022-070230; html:https://europepmc.org/articles/PMC9043395; pdf:https://europepmc.org/articles/PMC9043395?pdf=render"
   },
-  {
-    "id": "39174501",
-    "doi": "https://doi.org/10.1038/s41467-024-51451-1",
-    "title": "Structural insights into Frizzled3 through nanobody modulators.",
-    "authorString": "Hillier J, Zhao Y, Carrique L, Malinauskas T, Ruza RR, Chang TH, Yi G, Duyvesteyn HME, Yu J, Lu W, Pardon E, Steyaert J, Zhu Y, Ni T, Jones EY.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature communications",
-    "pubYear": "2024",
-    "date": "2024-08-22",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The Wnt receptor Frizzled3 (FZD3) is important for brain axonal development and cancer progression. We report structures of FZD3 in complex with extracellular and intracellular binding nanobodies (Nb). The crystal structure of Nb8 in complex with the FZD3 cysteine-rich domain (CRD) reveals that the nanobody binds at the base of the lipid-binding groove and can compete with Wnt5a. Nb8 fused with the Dickkopf-1 C-terminal domain behaves as a FZD3-specific Wnt surrogate, activating \u03b2-catenin signalling. The cryo-EM structure of FZD3 in complex with Nb9 reveals partially resolved density for the CRD, which exhibits positional flexibility, and a transmembrane conformation that resembles active GPCRs. Nb9 binds to the cytoplasmic region of FZD3 at the putative Dishevelled (DVL) or G protein-binding site, competes with DVL binding, and inhibits G\u03b1S coupling. In combination, our FZD3 structures with nanobody modulators map extracellular and intracellular interaction surfaces of functional, and potentially therapeutic, relevance.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1038/s41467-024-51451-1; html:https://europepmc.org/articles/PMC11341715; pdf:https://europepmc.org/articles/PMC11341715?pdf=render"
-  },
   {
     "id": "35048949",
     "doi": "https://doi.org/10.1093/eurjpc/zwac008",
@@ -26536,6 +26553,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/eurjpc/article-pdf/29/6/982/43589594/zwac008.pdf; doi:https://doi.org/10.1093/eurjpc/zwac008"
   },
+  {
+    "id": "39174501",
+    "doi": "https://doi.org/10.1038/s41467-024-51451-1",
+    "title": "Structural insights into Frizzled3 through nanobody modulators.",
+    "authorString": "Hillier J, Zhao Y, Carrique L, Malinauskas T, Ruza RR, Chang TH, Yi G, Duyvesteyn HME, Yu J, Lu W, Pardon E, Steyaert J, Zhu Y, Ni T, Jones EY.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature communications",
+    "pubYear": "2024",
+    "date": "2024-08-22",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The Wnt receptor Frizzled3 (FZD3) is important for brain axonal development and cancer progression. We report structures of FZD3 in complex with extracellular and intracellular binding nanobodies (Nb). The crystal structure of Nb8 in complex with the FZD3 cysteine-rich domain (CRD) reveals that the nanobody binds at the base of the lipid-binding groove and can compete with Wnt5a. Nb8 fused with the Dickkopf-1 C-terminal domain behaves as a FZD3-specific Wnt surrogate, activating \u03b2-catenin signalling. The cryo-EM structure of FZD3 in complex with Nb9 reveals partially resolved density for the CRD, which exhibits positional flexibility, and a transmembrane conformation that resembles active GPCRs. Nb9 binds to the cytoplasmic region of FZD3 at the putative Dishevelled (DVL) or G protein-binding site, competes with DVL binding, and inhibits G\u03b1S coupling. In combination, our FZD3 structures with nanobody modulators map extracellular and intracellular interaction surfaces of functional, and potentially therapeutic, relevance.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1038/s41467-024-51451-1; html:https://europepmc.org/articles/PMC11341715; pdf:https://europepmc.org/articles/PMC11341715?pdf=render"
+  },
   {
     "id": "35028631",
     "doi": "https://doi.org/10.1016/s2666-7568(21)00281-6",
@@ -26587,23 +26621,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1093/gigascience/giab076; doi:https://doi.org/10.1093/gigascience/giab076; html:https://europepmc.org/articles/PMC8633457; pdf:https://europepmc.org/articles/PMC8633457?pdf=render"
   },
-  {
-    "id": "33728815",
-    "doi": "https://doi.org/10.1002/art.41709",
-    "title": "Epidemiology of Scleritis in the United Kingdom From 1997 to 2018: Population-Based Analysis of 11 Million Patients and Association Between Scleritis and Infectious and Immune-Mediated Inflammatory Disease.",
-    "authorString": "Braithwaite T, Adderley NJ, Subramanian A, Galloway J, Kempen JH, Gokhale K, Cope AP, Dick AD, Nirantharakumar K, Denniston AK.",
-    "authorAffiliations": "",
-    "journalTitle": "Arthritis & rheumatology (Hoboken, N.J.)",
-    "pubYear": "2021",
-    "date": "2021-06-06",
-    "isOpenAccess": "N",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objective</h4>To estimate 22-year trends in the prevalence and incidence of scleritis, and the associations of scleritis with infectious and immune-mediated inflammatory diseases (I-IMIDs) in the UK.<h4>Methods</h4>The retrospective cross-sectional and population cohort study (1997-2018) included 10,939,823 patients (2,946 incident scleritis cases) in The Health Improvement Network, a nationally representative primary care records database. The case-control and matched cohort study (1995-2019) included 3,005 incident scleritis cases and 12,020 control patients matched by age, sex, region, and Townsend deprivation index. Data were analyzed using multivariable Poisson regression, multivariable logistic regression, and Cox proportional hazards multivariable models adjusted for age, sex, Townsend deprivation index, race/ethnicity, smoking status, nation within the UK, and body mass index. Incidence rate ratios (IRRs) and 95% confidence intervals (95% CIs) were calculated.<h4>Results</h4>Scleritis incidence rates per 100,000 person-years declined from 4.23 (95% CI 2.16-6.31) to 2.79 (95% CI 2.19-3.39) between 1997 and 2018. The prevalence of scleritis per 100,000 person-years was 93.62 (95% CI 90.17-97.07) in 2018 (61,650 UK patients). Among 2,946 patients with incident scleritis, 1,831 (62.2%) were female, the mean \u00b1 SD age was 44.9 \u00b1 17.6 years (range 1-93), and 1,257 (88.8%) were White. Higher risk of incident scleritis was associated with female sex (adjusted IRR 1.53 [95% CI 1.43-1.66], P < 0.001), Black race/ethnicity (adjusted IRR 1.52 [95% CI 1.14-2.01], P = 0.004 compared to White race/ethnicity), or South Asian race/ethnicity (adjusted IRR 1.50 [95% CI 1.19-1.90], P < 0.001 compared to White race/ethnicity), and older age (peak adjusted IRR 4.95 [95% CI 3.99-6.14], P < 0.001 for patients ages 51-60 years versus those ages \u226410 years). Compared to controls, scleritis patients had a 2-fold increased risk of a prior I-IMID diagnosis (17 I-IMIDs, P < 0.001) and significantly increased risk of subsequent diagnosis (13 I-IMIDs). The I-IMIDs most strongly associated with scleritis included granulomatosis with polyangiitis, Beh\u00e7et's disease, and Sj\u00f6gren's syndrome.<h4>Conclusion</h4>From 1997 through 2018, the UK incidence of scleritis declined from 4.23 to 2.79/100,000 person-years. Incident scleritis was associated with 19 I-IMIDs, providing data for rational investigation and cross-specialty engagement.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1002/art.41709; doi:https://doi.org/10.1002/art.41709"
-  },
   {
     "id": "31757515",
     "doi": "https://doi.org/10.1016/j.jaci.2019.09.015",
@@ -26621,6 +26638,23 @@
     "laySummary": "This population-wide study used datalinkage methods to create a matched cohort study between 1998-2016. The study estimated hazard ratios and compared the risk of major fractures and any fracture in people with and without atopic eczema. Findings suggest that people with atopic eczema have an increased fracture risk.",
     "urls": "pdf:http://www.jacionline.org/article/S0091674919312515/pdf; doi:https://doi.org/10.1016/j.jaci.2019.09.015; html:https://europepmc.org/articles/PMC7014587; pdf:https://europepmc.org/articles/PMC7014587?pdf=render"
   },
+  {
+    "id": "33728815",
+    "doi": "https://doi.org/10.1002/art.41709",
+    "title": "Epidemiology of Scleritis in the United Kingdom From 1997 to 2018: Population-Based Analysis of 11 Million Patients and Association Between Scleritis and Infectious and Immune-Mediated Inflammatory Disease.",
+    "authorString": "Braithwaite T, Adderley NJ, Subramanian A, Galloway J, Kempen JH, Gokhale K, Cope AP, Dick AD, Nirantharakumar K, Denniston AK.",
+    "authorAffiliations": "",
+    "journalTitle": "Arthritis & rheumatology (Hoboken, N.J.)",
+    "pubYear": "2021",
+    "date": "2021-06-06",
+    "isOpenAccess": "N",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>To estimate 22-year trends in the prevalence and incidence of scleritis, and the associations of scleritis with infectious and immune-mediated inflammatory diseases (I-IMIDs) in the UK.<h4>Methods</h4>The retrospective cross-sectional and population cohort study (1997-2018) included 10,939,823 patients (2,946 incident scleritis cases) in The Health Improvement Network, a nationally representative primary care records database. The case-control and matched cohort study (1995-2019) included 3,005 incident scleritis cases and 12,020 control patients matched by age, sex, region, and Townsend deprivation index. Data were analyzed using multivariable Poisson regression, multivariable logistic regression, and Cox proportional hazards multivariable models adjusted for age, sex, Townsend deprivation index, race/ethnicity, smoking status, nation within the UK, and body mass index. Incidence rate ratios (IRRs) and 95% confidence intervals (95% CIs) were calculated.<h4>Results</h4>Scleritis incidence rates per 100,000 person-years declined from 4.23 (95% CI 2.16-6.31) to 2.79 (95% CI 2.19-3.39) between 1997 and 2018. The prevalence of scleritis per 100,000 person-years was 93.62 (95% CI 90.17-97.07) in 2018 (61,650 UK patients). Among 2,946 patients with incident scleritis, 1,831 (62.2%) were female, the mean \u00b1 SD age was 44.9 \u00b1 17.6 years (range 1-93), and 1,257 (88.8%) were White. Higher risk of incident scleritis was associated with female sex (adjusted IRR 1.53 [95% CI 1.43-1.66], P < 0.001), Black race/ethnicity (adjusted IRR 1.52 [95% CI 1.14-2.01], P = 0.004 compared to White race/ethnicity), or South Asian race/ethnicity (adjusted IRR 1.50 [95% CI 1.19-1.90], P < 0.001 compared to White race/ethnicity), and older age (peak adjusted IRR 4.95 [95% CI 3.99-6.14], P < 0.001 for patients ages 51-60 years versus those ages \u226410 years). Compared to controls, scleritis patients had a 2-fold increased risk of a prior I-IMID diagnosis (17 I-IMIDs, P < 0.001) and significantly increased risk of subsequent diagnosis (13 I-IMIDs). The I-IMIDs most strongly associated with scleritis included granulomatosis with polyangiitis, Beh\u00e7et's disease, and Sj\u00f6gren's syndrome.<h4>Conclusion</h4>From 1997 through 2018, the UK incidence of scleritis declined from 4.23 to 2.79/100,000 person-years. Incident scleritis was associated with 19 I-IMIDs, providing data for rational investigation and cross-specialty engagement.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1002/art.41709; doi:https://doi.org/10.1002/art.41709"
+  },
   {
     "id": "34378227",
     "doi": "https://doi.org/10.1111/tri.14010",
@@ -26825,23 +26859,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1161/CIRCGEN.124.004755"
   },
-  {
-    "id": "37438684",
-    "doi": "https://doi.org/10.1186/s12874-023-01935-3",
-    "title": "Estimating medication adherence from Electronic Health Records: comparing methods for mining and processing asthma treatment prescriptions.",
-    "authorString": "Tibble H, Sheikh A, Tsanas A.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC medical research methodology",
-    "pubYear": "2023",
-    "date": "2023-07-12",
-    "isOpenAccess": "Y",
-    "keywords": "Adherence; Asthma; Compliance; corticosteroid; Electronic Health Records",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Medication adherence is usually defined as the extent of the agreement between the medication regimen agreed to by patients with their healthcare provider and the real-world implementation. Proactive identification of those with poor adherence may be useful to identify those with poor disease control and offers the opportunity for ameliorative action. Adherence can be estimated from Electronic Health Records (EHRs) by comparing medication dispensing records to the prescribed regimen. Several methods have been developed in the literature to infer adherence from EHRs, however there is no clear consensus on what should be considered the gold standard in each use case. Our objectives were to critically evaluate different measures of medication adherence in a large longitudinal Scottish EHR dataset. We used asthma, a chronic condition with high prevalence and high rates of non-adherence, as a case study.<h4>Methods</h4>Over 1.6 million asthma controllers were prescribed for our cohort of 91,334 individuals, between January 2009 and March 2017. Eight adherence measures were calculated, and different approaches to estimating the amount of medication supply available at any time were compared.<h4>Results</h4>Estimates from different measures of adherence varied substantially. Three of the main drivers of the differences between adherence measures were the expected duration (if taken as in accordance with the dose directions), whether there was overlapping supply between prescriptions, and whether treatment had been discontinued. However, there are also wider, study-related, factors which are crucial to consider when comparing the adherence measures.<h4>Conclusions</h4>We evaluated the limitations of various medication adherence measures, and highlight key considerations about the underlying data, condition, and population to guide researchers choose appropriate adherence measures. This guidance will enable researchers to make more informed decisions about the methodology they employ, ensuring that adherence is captured in the most meaningful way for their particular application needs.",
-    "laySummary": "",
-    "urls": "pdf:https://bmcmedresmethodol.biomedcentral.com/counter/pdf/10.1186/s12874-023-01935-3; doi:https://doi.org/10.1186/s12874-023-01935-3; html:https://europepmc.org/articles/PMC10337150; pdf:https://europepmc.org/articles/PMC10337150?pdf=render"
-  },
   {
     "id": "33830993",
     "doi": "https://doi.org/10.1371/journal.pgen.1009428",
@@ -26859,6 +26876,23 @@
     "laySummary": "",
     "urls": "pdf:https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1009428&type=printable; doi:https://doi.org/10.1371/journal.pgen.1009428; html:https://europepmc.org/articles/PMC8031124; pdf:https://europepmc.org/articles/PMC8031124?pdf=render"
   },
+  {
+    "id": "37438684",
+    "doi": "https://doi.org/10.1186/s12874-023-01935-3",
+    "title": "Estimating medication adherence from Electronic Health Records: comparing methods for mining and processing asthma treatment prescriptions.",
+    "authorString": "Tibble H, Sheikh A, Tsanas A.",
+    "authorAffiliations": "",
+    "journalTitle": "BMC medical research methodology",
+    "pubYear": "2023",
+    "date": "2023-07-12",
+    "isOpenAccess": "Y",
+    "keywords": "Adherence; Asthma; Compliance; corticosteroid; Electronic Health Records",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Medication adherence is usually defined as the extent of the agreement between the medication regimen agreed to by patients with their healthcare provider and the real-world implementation. Proactive identification of those with poor adherence may be useful to identify those with poor disease control and offers the opportunity for ameliorative action. Adherence can be estimated from Electronic Health Records (EHRs) by comparing medication dispensing records to the prescribed regimen. Several methods have been developed in the literature to infer adherence from EHRs, however there is no clear consensus on what should be considered the gold standard in each use case. Our objectives were to critically evaluate different measures of medication adherence in a large longitudinal Scottish EHR dataset. We used asthma, a chronic condition with high prevalence and high rates of non-adherence, as a case study.<h4>Methods</h4>Over 1.6 million asthma controllers were prescribed for our cohort of 91,334 individuals, between January 2009 and March 2017. Eight adherence measures were calculated, and different approaches to estimating the amount of medication supply available at any time were compared.<h4>Results</h4>Estimates from different measures of adherence varied substantially. Three of the main drivers of the differences between adherence measures were the expected duration (if taken as in accordance with the dose directions), whether there was overlapping supply between prescriptions, and whether treatment had been discontinued. However, there are also wider, study-related, factors which are crucial to consider when comparing the adherence measures.<h4>Conclusions</h4>We evaluated the limitations of various medication adherence measures, and highlight key considerations about the underlying data, condition, and population to guide researchers choose appropriate adherence measures. This guidance will enable researchers to make more informed decisions about the methodology they employ, ensuring that adherence is captured in the most meaningful way for their particular application needs.",
+    "laySummary": "",
+    "urls": "pdf:https://bmcmedresmethodol.biomedcentral.com/counter/pdf/10.1186/s12874-023-01935-3; doi:https://doi.org/10.1186/s12874-023-01935-3; html:https://europepmc.org/articles/PMC10337150; pdf:https://europepmc.org/articles/PMC10337150?pdf=render"
+  },
   {
     "id": "33749694",
     "doi": "https://doi.org/",
@@ -26910,23 +26944,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.apmr.2021.12.014"
   },
-  {
-    "id": "31345952",
-    "doi": "https://doi.org/10.1136/heartjnl-2018-313855",
-    "title": "Do beta-blockers and inhibitors of the renin-angiotensin aldosterone system improve outcomes in patients with heart failure and left ventricular ejection fraction >40%?",
-    "authorString": "Lumbers RT, Martin N, Manoharan K, Thomas J, Davies LC.",
-    "authorAffiliations": "",
-    "journalTitle": "Heart (British Cardiac Society)",
-    "pubYear": "2019",
-    "date": "2019-07-25",
-    "isOpenAccess": "N",
-    "keywords": "Pharmacology; Meta-analysis; epidemiology; Heart Failure With Preserved Ejection Fraction; Systemic Review",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1136/heartjnl-2018-313855"
-  },
   {
     "id": "34734970",
     "doi": "https://doi.org/10.1001/jamaophthalmol.2021.4601",
@@ -26944,23 +26961,6 @@
     "laySummary": "",
     "urls": "pdf:https://jamanetwork.com/journals/jamaophthalmology/articlepdf/2785704/jamaophthalmology_kuan_2021_oi_210068_1639510445.31311.pdf; doi:https://doi.org/10.1001/jamaophthalmol.2021.4601; html:https://europepmc.org/articles/PMC8569599"
   },
-  {
-    "id": "31361079",
-    "doi": "https://doi.org/10.1111/1742-6723.13361",
-    "title": "Animal-vehicle collisions in Victoria, Australia: An under-recognised cause of road traffic crashes.",
-    "authorString": "Ang JY, Gabbe B, Cameron P, Beck B.",
-    "authorAffiliations": "",
-    "journalTitle": "Emergency medicine Australasia : EMA",
-    "pubYear": "2019",
-    "date": "2019-07-30",
-    "isOpenAccess": "N",
-    "keywords": "Injury; Prevention; Traffic; Motor Vehicle",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objective</h4>Non-fatal injuries sustained from animal-vehicle collisions are a globally under-recognised road safety issue, with limited data on these crash types. The present study aimed to quantify the number and causes of major trauma events resulting from animal-vehicle collisions.<h4>Methods</h4>The study was a retrospective analysis of major trauma cases occurring in Victoria, Australia, between 2007 and 2016, using data from the population-based Victorian State Trauma Registry. To identify animal-vehicle collisions, Victorian State Trauma Registry injury codes were combined with text-mining of the text description of the injury event.<h4>Results</h4>Over the 10 year period, there were 152 major trauma patients who were admitted to Victorian trauma-receiving hospitals due to vehicle collisions with animals. The crude population-based incidence rate for animal-vehicle collisions increased by 6.7% per year (incidence rate ratio 1.07; 95% confidence interval 1.01-1.13; P = 0.02).<h4>Conclusion</h4>Development of systematic recording methods of animal-vehicle collisions will improve reporting of these crash types to assist future studies in implementing effective countermeasures.",
-    "laySummary": "",
-    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/1742-6723.13361; doi:https://doi.org/10.1111/1742-6723.13361"
-  },
   {
     "id": "33127858",
     "doi": "https://doi.org/10.1681/asn.2020050679",
@@ -26978,6 +26978,40 @@
     "laySummary": "",
     "urls": "pdf:https://jasn.asnjournals.org/content/jnephrol/32/1/127.full.pdf; doi:https://doi.org/10.1681/ASN.2020050679; html:https://europepmc.org/articles/PMC7894659; doi:https://doi.org/10.1681/asn.2020050679"
   },
+  {
+    "id": "31345952",
+    "doi": "https://doi.org/10.1136/heartjnl-2018-313855",
+    "title": "Do beta-blockers and inhibitors of the renin-angiotensin aldosterone system improve outcomes in patients with heart failure and left ventricular ejection fraction >40%?",
+    "authorString": "Lumbers RT, Martin N, Manoharan K, Thomas J, Davies LC.",
+    "authorAffiliations": "",
+    "journalTitle": "Heart (British Cardiac Society)",
+    "pubYear": "2019",
+    "date": "2019-07-25",
+    "isOpenAccess": "N",
+    "keywords": "Pharmacology; Meta-analysis; epidemiology; Heart Failure With Preserved Ejection Fraction; Systemic Review",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1136/heartjnl-2018-313855"
+  },
+  {
+    "id": "31361079",
+    "doi": "https://doi.org/10.1111/1742-6723.13361",
+    "title": "Animal-vehicle collisions in Victoria, Australia: An under-recognised cause of road traffic crashes.",
+    "authorString": "Ang JY, Gabbe B, Cameron P, Beck B.",
+    "authorAffiliations": "",
+    "journalTitle": "Emergency medicine Australasia : EMA",
+    "pubYear": "2019",
+    "date": "2019-07-30",
+    "isOpenAccess": "N",
+    "keywords": "Injury; Prevention; Traffic; Motor Vehicle",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>Non-fatal injuries sustained from animal-vehicle collisions are a globally under-recognised road safety issue, with limited data on these crash types. The present study aimed to quantify the number and causes of major trauma events resulting from animal-vehicle collisions.<h4>Methods</h4>The study was a retrospective analysis of major trauma cases occurring in Victoria, Australia, between 2007 and 2016, using data from the population-based Victorian State Trauma Registry. To identify animal-vehicle collisions, Victorian State Trauma Registry injury codes were combined with text-mining of the text description of the injury event.<h4>Results</h4>Over the 10 year period, there were 152 major trauma patients who were admitted to Victorian trauma-receiving hospitals due to vehicle collisions with animals. The crude population-based incidence rate for animal-vehicle collisions increased by 6.7% per year (incidence rate ratio 1.07; 95% confidence interval 1.01-1.13; P = 0.02).<h4>Conclusion</h4>Development of systematic recording methods of animal-vehicle collisions will improve reporting of these crash types to assist future studies in implementing effective countermeasures.",
+    "laySummary": "",
+    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/1742-6723.13361; doi:https://doi.org/10.1111/1742-6723.13361"
+  },
   {
     "id": "30972781",
     "doi": "https://doi.org/10.1111/apt.15232",
@@ -27029,6 +27063,23 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cnm.3180; doi:https://doi.org/10.1002/cnm.3180; html:https://europepmc.org/articles/PMC6593817; pdf:https://europepmc.org/articles/PMC6593817?pdf=render"
   },
+  {
+    "id": "34642218",
+    "doi": "https://doi.org/10.1136/bcr-2021-243424",
+    "title": "Neurological injury from virtual reality mishap.",
+    "authorString": "Warner N, Teo JT.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ case reports",
+    "pubYear": "2021",
+    "date": "2021-10-12",
+    "isOpenAccess": "Y",
+    "keywords": "Cranial nerves; Neurology; Neurological Injury; Trauma Cns /Pns",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Consumer virtual reality systems are becoming increasingly popular with the increasing availability of devices and gamified technologies. Self-sustained injury risks exist with the use of this technology in the uncontrolled home environment, however, the public awareness of these risks may not be recognised. We present a case of a low- impact virtual reality fall resulting in spinal cord injury, hypoglossal nerve injury, vertebral artery dissection and traumatic brain injury.",
+    "laySummary": "",
+    "urls": "pdf:https://casereports.bmj.com/content/bmjcr/14/10/e243424.full.pdf; doi:https://doi.org/10.1136/bcr-2021-243424; html:https://europepmc.org/articles/PMC8513217; pdf:https://europepmc.org/articles/PMC8513217?pdf=render"
+  },
   {
     "id": "38894942",
     "doi": "https://doi.org/10.1177/20552076241258276",
@@ -27063,23 +27114,6 @@
     "laySummary": "",
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s00787-021-01817-3.pdf; doi:https://doi.org/10.1007/s00787-021-01817-3; html:https://europepmc.org/articles/PMC9663394; pdf:https://europepmc.org/articles/PMC9663394?pdf=render"
   },
-  {
-    "id": "34642218",
-    "doi": "https://doi.org/10.1136/bcr-2021-243424",
-    "title": "Neurological injury from virtual reality mishap.",
-    "authorString": "Warner N, Teo JT.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ case reports",
-    "pubYear": "2021",
-    "date": "2021-10-12",
-    "isOpenAccess": "Y",
-    "keywords": "Cranial nerves; Neurology; Neurological Injury; Trauma Cns /Pns",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Consumer virtual reality systems are becoming increasingly popular with the increasing availability of devices and gamified technologies. Self-sustained injury risks exist with the use of this technology in the uncontrolled home environment, however, the public awareness of these risks may not be recognised. We present a case of a low- impact virtual reality fall resulting in spinal cord injury, hypoglossal nerve injury, vertebral artery dissection and traumatic brain injury.",
-    "laySummary": "",
-    "urls": "pdf:https://casereports.bmj.com/content/bmjcr/14/10/e243424.full.pdf; doi:https://doi.org/10.1136/bcr-2021-243424; html:https://europepmc.org/articles/PMC8513217; pdf:https://europepmc.org/articles/PMC8513217?pdf=render"
-  },
   {
     "id": "34409990",
     "doi": "https://doi.org/10.1093/dote/doab058",
@@ -27097,23 +27131,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/dote/article-pdf/35/1/doab058/42098674/doab058.pdf; doi:https://doi.org/10.1093/dote/doab058"
   },
-  {
-    "id": "36729586",
-    "doi": "https://doi.org/10.2196/42965",
-    "title": "Assessing the Feasibility of a Text-Based Conversational Agent for Asthma Support: Protocol for a Mixed Methods Observational Study.",
-    "authorString": "Calvo RA, Peters D, Moradbakhti L, Cook D, Rizos G, Schuller B, Kallis C, Wong E, Quint J.",
-    "authorAffiliations": "",
-    "journalTitle": "JMIR research protocols",
-    "pubYear": "2023",
-    "date": "2023-02-02",
-    "isOpenAccess": "Y",
-    "keywords": "Artificial intelligence; Health; Asthma; Health education; Well-being; Behavior Change; Conversational Agent; Chatbot",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Despite efforts, the UK death rate from asthma is the highest in Europe, and 65% of people with asthma in the United Kingdom do not receive the professional care they are entitled to. Experts have recommended the use of digital innovations to help address the issues of poor outcomes and lack of care access. An automated SMS text messaging-based conversational agent (ie, chatbot) created to provide access to asthma support in a familiar format via a mobile phone has the potential to help people with asthma across demographics and at scale. Such a chatbot could help improve the accuracy of self-assessed risk, improve asthma self-management, increase access to professional care, and ultimately reduce asthma attacks and emergencies.<h4>Objective</h4>The aims of this study are to determine the feasibility and usability of a text-based conversational agent that processes a patient's text responses and short sample voice recordings to calculate an estimate of their risk for an asthma exacerbation and then offers follow-up information for lowering risk and improving asthma control; assess the levels of engagement for different groups of users, particularly those who do not access professional services and those with poor asthma control; and assess the extent to which users of the chatbot perceive it as helpful for improving their understanding and self-management of their condition.<h4>Methods</h4>We will recruit 300 adults through four channels for broad reach: Facebook, YouGov, Asthma + Lung UK social media, and the website Healthily (a health self-management app). Participants will be screened, and those who meet inclusion criteria (adults diagnosed with asthma and who use WhatsApp) will be provided with a link to access the conversational agent through WhatsApp on their mobile phones. Participants will be sent scheduled and randomly timed messages to invite them to engage in dialogue about their asthma risk during the period of study. After a data collection period (28 days), participants will respond to questionnaire items related to the quality of the interaction. A pre- and postquestionnaire will measure asthma control before and after the intervention.<h4>Results</h4>This study was funded in March 2021 and started in January 2022. We developed a prototype conversational agent, which was iteratively improved with feedback from people with asthma, asthma nurses, and specialist doctors. Fortnightly reviews of iterations by the clinical team began in September 2022 and are ongoing. This feasibility study will start recruitment in January 2023. The anticipated completion of the study is July 2023. A future randomized controlled trial will depend on the outcomes of this study and funding.<h4>Conclusions</h4>This feasibility study will inform a follow-up pilot and larger randomized controlled trial to assess the impact of a conversational agent on asthma outcomes, self-management, behavior change, and access to care.<h4>International registered report identifier (irrid)</h4>PRR1-10.2196/42965.",
-    "laySummary": "",
-    "urls": "pdf:https://www.researchprotocols.org/2023/1/e42965/PDF; doi:https://doi.org/10.2196/42965; html:https://europepmc.org/articles/PMC9936366"
-  },
   {
     "id": "37730605",
     "doi": "https://doi.org/10.1186/s12889-023-16523-9",
@@ -27131,6 +27148,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmcpublichealth.biomedcentral.com/counter/pdf/10.1186/s12889-023-16523-9; doi:https://doi.org/10.1186/s12889-023-16523-9; html:https://europepmc.org/articles/PMC10510114; pdf:https://europepmc.org/articles/PMC10510114?pdf=render"
   },
+  {
+    "id": "36729586",
+    "doi": "https://doi.org/10.2196/42965",
+    "title": "Assessing the Feasibility of a Text-Based Conversational Agent for Asthma Support: Protocol for a Mixed Methods Observational Study.",
+    "authorString": "Calvo RA, Peters D, Moradbakhti L, Cook D, Rizos G, Schuller B, Kallis C, Wong E, Quint J.",
+    "authorAffiliations": "",
+    "journalTitle": "JMIR research protocols",
+    "pubYear": "2023",
+    "date": "2023-02-02",
+    "isOpenAccess": "Y",
+    "keywords": "Artificial intelligence; Health; Asthma; Health education; Well-being; Behavior Change; Conversational Agent; Chatbot",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Despite efforts, the UK death rate from asthma is the highest in Europe, and 65% of people with asthma in the United Kingdom do not receive the professional care they are entitled to. Experts have recommended the use of digital innovations to help address the issues of poor outcomes and lack of care access. An automated SMS text messaging-based conversational agent (ie, chatbot) created to provide access to asthma support in a familiar format via a mobile phone has the potential to help people with asthma across demographics and at scale. Such a chatbot could help improve the accuracy of self-assessed risk, improve asthma self-management, increase access to professional care, and ultimately reduce asthma attacks and emergencies.<h4>Objective</h4>The aims of this study are to determine the feasibility and usability of a text-based conversational agent that processes a patient's text responses and short sample voice recordings to calculate an estimate of their risk for an asthma exacerbation and then offers follow-up information for lowering risk and improving asthma control; assess the levels of engagement for different groups of users, particularly those who do not access professional services and those with poor asthma control; and assess the extent to which users of the chatbot perceive it as helpful for improving their understanding and self-management of their condition.<h4>Methods</h4>We will recruit 300 adults through four channels for broad reach: Facebook, YouGov, Asthma + Lung UK social media, and the website Healthily (a health self-management app). Participants will be screened, and those who meet inclusion criteria (adults diagnosed with asthma and who use WhatsApp) will be provided with a link to access the conversational agent through WhatsApp on their mobile phones. Participants will be sent scheduled and randomly timed messages to invite them to engage in dialogue about their asthma risk during the period of study. After a data collection period (28 days), participants will respond to questionnaire items related to the quality of the interaction. A pre- and postquestionnaire will measure asthma control before and after the intervention.<h4>Results</h4>This study was funded in March 2021 and started in January 2022. We developed a prototype conversational agent, which was iteratively improved with feedback from people with asthma, asthma nurses, and specialist doctors. Fortnightly reviews of iterations by the clinical team began in September 2022 and are ongoing. This feasibility study will start recruitment in January 2023. The anticipated completion of the study is July 2023. A future randomized controlled trial will depend on the outcomes of this study and funding.<h4>Conclusions</h4>This feasibility study will inform a follow-up pilot and larger randomized controlled trial to assess the impact of a conversational agent on asthma outcomes, self-management, behavior change, and access to care.<h4>International registered report identifier (irrid)</h4>PRR1-10.2196/42965.",
+    "laySummary": "",
+    "urls": "pdf:https://www.researchprotocols.org/2023/1/e42965/PDF; doi:https://doi.org/10.2196/42965; html:https://europepmc.org/articles/PMC9936366"
+  },
   {
     "id": "33632741",
     "doi": "https://doi.org/10.2337/db20-0895",
@@ -27148,23 +27182,6 @@
     "laySummary": "",
     "urls": "pdf:https://diabetesjournals.org/diabetes/article-pdf/70/10/2313/628539/db200895.pdf; doi:https://doi.org/10.2337/db20-0895"
   },
-  {
-    "id": "31500613",
-    "doi": "https://doi.org/10.1186/s12911-019-0908-7",
-    "title": "A validated natural language processing algorithm for brain imaging phenotypes from radiology reports in UK electronic health records.",
-    "authorString": "Wheater E, Mair G, Sudlow C, Alex B, Grover C, Whiteley W.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC medical informatics and decision making",
-    "pubYear": "2019",
-    "date": "2019-09-09",
-    "isOpenAccess": "Y",
-    "keywords": "Stroke; Phenotyping; Brain imaging; Radiology; Natural Language Processing; Radiology Reports",
-    "nationalPriorities": "Applied Analytics, Better Care",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Manual coding of phenotypes in brain radiology reports is time consuming. We developed a natural language processing (NLP) algorithm to enable automatic identification of brain imaging in radiology reports performed in routine clinical practice in the UK National Health Service (NHS).<h4>Methods</h4>We used anonymized text brain imaging reports from a cohort study of stroke/TIA patients and from a regional hospital to develop and test an NLP algorithm. Two experts marked up text in 1692 reports for 24 cerebrovascular and other neurological phenotypes. We developed and tested a rule-based NLP algorithm first within the cohort study, and further evaluated it in the reports from the regional hospital.<h4>Results</h4>The agreement between expert readers was excellent (Cohen's \u03ba =0.93) in both datasets. In the final test dataset (n\u00a0=\u2009700) in unseen regional hospital reports, the algorithm had very good performance for a report of any ischaemic stroke [sensitivity 89% (95% CI:81-94); positive predictive value (PPV) 85% (76-90); specificity 100% (95% CI:0.99-1.00)]; any haemorrhagic stroke [sensitivity 96% (95% CI: 80-99), PPV 72% (95% CI:55-84); specificity 100% (95% CI:0.99-1.00)]; brain tumours [sensitivity 96% (CI:87-99); PPV 84% (73-91); specificity: 100% (95% CI:0.99-1.00)] and cerebral small vessel disease and cerebral atrophy (sensitivity, PPV and specificity all >\u200997%). We obtained few reports of subarachnoid haemorrhage, microbleeds or subdural haematomas. In 110,695 reports from NHS Tayside, atrophy (n\u00a0=\u200928,757, 26%), small vessel disease (15,015, 14%) and old, deep ischaemic strokes (10,636, 10%) were the commonest findings.<h4>Conclusions</h4>An NLP algorithm can be developed in UK NHS radiology records to allow identification of cohorts of patients with important brain imaging phenotypes at a scale that would otherwise not be possible.",
-    "laySummary": "",
-    "urls": "pdf:https://bmcmedinformdecismak.biomedcentral.com/track/pdf/10.1186/s12911-019-0908-7; doi:https://doi.org/10.1186/s12911-019-0908-7; html:https://europepmc.org/articles/PMC6734359; pdf:https://europepmc.org/articles/PMC6734359?pdf=render"
-  },
   {
     "id": "37072241",
     "doi": "https://doi.org/10.1136/heartjnl-2022-321888",
@@ -27182,6 +27199,23 @@
     "laySummary": "",
     "urls": "pdf:https://heart.bmj.com/content/heartjnl/early/2023/03/21/heartjnl-2022-321888.full.pdf; doi:https://doi.org/10.1136/heartjnl-2022-321888; html:https://europepmc.org/articles/PMC10314020; pdf:https://europepmc.org/articles/PMC10314020?pdf=render"
   },
+  {
+    "id": "31500613",
+    "doi": "https://doi.org/10.1186/s12911-019-0908-7",
+    "title": "A validated natural language processing algorithm for brain imaging phenotypes from radiology reports in UK electronic health records.",
+    "authorString": "Wheater E, Mair G, Sudlow C, Alex B, Grover C, Whiteley W.",
+    "authorAffiliations": "",
+    "journalTitle": "BMC medical informatics and decision making",
+    "pubYear": "2019",
+    "date": "2019-09-09",
+    "isOpenAccess": "Y",
+    "keywords": "Stroke; Phenotyping; Brain imaging; Radiology; Natural Language Processing; Radiology Reports",
+    "nationalPriorities": "Applied Analytics, Better Care",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Manual coding of phenotypes in brain radiology reports is time consuming. We developed a natural language processing (NLP) algorithm to enable automatic identification of brain imaging in radiology reports performed in routine clinical practice in the UK National Health Service (NHS).<h4>Methods</h4>We used anonymized text brain imaging reports from a cohort study of stroke/TIA patients and from a regional hospital to develop and test an NLP algorithm. Two experts marked up text in 1692 reports for 24 cerebrovascular and other neurological phenotypes. We developed and tested a rule-based NLP algorithm first within the cohort study, and further evaluated it in the reports from the regional hospital.<h4>Results</h4>The agreement between expert readers was excellent (Cohen's \u03ba =0.93) in both datasets. In the final test dataset (n\u00a0=\u2009700) in unseen regional hospital reports, the algorithm had very good performance for a report of any ischaemic stroke [sensitivity 89% (95% CI:81-94); positive predictive value (PPV) 85% (76-90); specificity 100% (95% CI:0.99-1.00)]; any haemorrhagic stroke [sensitivity 96% (95% CI: 80-99), PPV 72% (95% CI:55-84); specificity 100% (95% CI:0.99-1.00)]; brain tumours [sensitivity 96% (CI:87-99); PPV 84% (73-91); specificity: 100% (95% CI:0.99-1.00)] and cerebral small vessel disease and cerebral atrophy (sensitivity, PPV and specificity all >\u200997%). We obtained few reports of subarachnoid haemorrhage, microbleeds or subdural haematomas. In 110,695 reports from NHS Tayside, atrophy (n\u00a0=\u200928,757, 26%), small vessel disease (15,015, 14%) and old, deep ischaemic strokes (10,636, 10%) were the commonest findings.<h4>Conclusions</h4>An NLP algorithm can be developed in UK NHS radiology records to allow identification of cohorts of patients with important brain imaging phenotypes at a scale that would otherwise not be possible.",
+    "laySummary": "",
+    "urls": "pdf:https://bmcmedinformdecismak.biomedcentral.com/track/pdf/10.1186/s12911-019-0908-7; doi:https://doi.org/10.1186/s12911-019-0908-7; html:https://europepmc.org/articles/PMC6734359; pdf:https://europepmc.org/articles/PMC6734359?pdf=render"
+  },
   {
     "id": "37805492",
     "doi": "https://doi.org/10.1186/s12864-023-09663-0",
@@ -27199,23 +27233,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1186/s12864-023-09663-0; html:https://europepmc.org/articles/PMC10559536; pdf:https://europepmc.org/articles/PMC10559536?pdf=render"
   },
-  {
-    "id": "34761838",
-    "doi": "https://doi.org/10.1002/biof.1801",
-    "title": "Neutrophil to lymphocyte ratio is not related to carotid atherosclerosis progression and cardiovascular events in the primary prevention of cardiovascular disease: Results from the IMPROVE study.",
-    "authorString": "Mannarino MR, Bianconi V, Gigante B, Strawbridge RJ, Savonen K, Kurl S, Giral P, Smit A, Eriksson P, Tremoli E, Veglia F, Baldassarre D, Pirro M, IMPROVE study group.",
-    "authorAffiliations": "",
-    "journalTitle": "BioFactors (Oxford, England)",
-    "pubYear": "2022",
-    "date": "2021-11-11",
-    "isOpenAccess": "Y",
-    "keywords": "Lymphocyte; neutrophil; cardiovascular; Carotid; Prospective; Imt; Nlr",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Inflammation is a component of the pathogenesis of atherosclerosis and is associated with an increased risk of atherosclerotic cardiovascular disease (ASCVD). The neutrophil to lymphocyte ratio (NLR) is a possible inflammation metric for the detection of ASCVD risk, although results of prospective studies are highly inconsistent on this topic. We investigated the cross-sectional relationship between NLR and carotid intima-media thickness (cIMT) in subjects at moderate-to-high ASCVD risk. The prospective association between NLR, cIMT progression, and incident vascular events (VEs) was also explored. In 3341 subjects from the IMT-Progression as Predictors of VEs (IMPROVE) study, we analyzed the association between NLR, cIMT, and its 15-month progression. The association between NLR and incident VEs was also investigated. NLR was positively associated with cross-sectional measures of cIMT, but not with cIMT progression. The association between NLR and cross-sectional cIMT measures was abolished when adjusted for confounders. No association was found between NRL and incident VEs. Similarly, there were no significant differences in the hazard ratios (HRs) of VEs across NLR quartiles. NLR was neither associated with the presence and progression of carotid atherosclerosis, nor with the risk of VEs. Our findings do not support the role of NLR as a predictor of the risk of atherosclerosis progression and ASCVD events in subjects at moderate-to-high ASCVD risk, in primary prevention. However, the usefulness of NLR for patients at a different level of ASCVD risk cannot be inferred from this study.",
-    "laySummary": "",
-    "urls": "pdf:https://air.unimi.it/bitstream/2434/890337/2/0127%20IMPROVE%20mannarino%20Neutrophil%20to%20lymphocyte%20e%20suppl%20.pdf; doi:https://doi.org/10.1002/biof.1801; html:https://europepmc.org/articles/PMC9299016; pdf:https://europepmc.org/articles/PMC9299016?pdf=render"
-  },
   {
     "id": "34095541",
     "doi": "https://doi.org/10.23889/ijpds.v4i2.1134",
@@ -27234,21 +27251,21 @@
     "urls": "pdf:https://ijpds.org/article/download/1134/2643; doi:https://doi.org/10.23889/ijpds.v4i2.1134; html:https://europepmc.org/articles/PMC8142954; pdf:https://europepmc.org/articles/PMC8142954?pdf=render"
   },
   {
-    "id": "34095527",
-    "doi": "https://doi.org/10.23889/ijpds.v4i1.581",
-    "title": "Electronic Longitudinal Alcohol Study in Communities (ELAStiC) Wales - protocol for platform development.",
-    "authorString": "Trefan L, Akbari A, Paranjothy S, Farewell DM, Gartner A, Fone D, Greene J, Evans A, Smith A, Adekanmbi V, Kennedy J, Lyons RA, Moore SC.",
+    "id": "34761838",
+    "doi": "https://doi.org/10.1002/biof.1801",
+    "title": "Neutrophil to lymphocyte ratio is not related to carotid atherosclerosis progression and cardiovascular events in the primary prevention of cardiovascular disease: Results from the IMPROVE study.",
+    "authorString": "Mannarino MR, Bianconi V, Gigante B, Strawbridge RJ, Savonen K, Kurl S, Giral P, Smit A, Eriksson P, Tremoli E, Veglia F, Baldassarre D, Pirro M, IMPROVE study group.",
     "authorAffiliations": "",
-    "journalTitle": "International journal of population data science",
-    "pubYear": "2019",
-    "date": "2019-05-20",
+    "journalTitle": "BioFactors (Oxford, England)",
+    "pubYear": "2022",
+    "date": "2021-11-11",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Lymphocyte; neutrophil; cardiovascular; Carotid; Prospective; Imt; Nlr",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>Excessive alcohol consumption has adverse effects on health and there is a recognised need for the longitudinal analysis of population data to improve our understanding of the patterns of alcohol use, harms to consumers and those in their immediate environment. The UK has a number of linkable, longitudinal databases that if assembled properly could support valuable research on this topic.<h4>Aims and objectives</h4>This paper describes the development of a broad set of cross-linked cohorts, e-cohorts, surveys and linked electronic healthcare records (EHRs) to construct an alcohol-specific analytical platform in the United Kingdom using datasets on the population of Wales.The objective of this paper is to provide a description of existing key datasets integrated with existing, routinely collected electronic health data on a secure platform, and relevant derived variables to enable population-based research on alcohol-related harm in Wales. We illustrate our use of these data with some exemplar research questions that are currently under investigation.<h4>Methods</h4>Record-linkage of routine and observational datasets. Routine data includes hospital admissions, general practice, and cohorts specific to children. Two observational studies were included. Routine socioeconomic descriptors and mortality data were also linked.<h4>Conclusion</h4>We described a record-linked, population-based research protocol for alcohol related harm on a secure platform. As the datasets used here are available in many countries, ELAStiC provides a template for setting up similar initiatives in other countries. We have also defined a number of alcohol specific variables using routinely-collected available data that can be used in other epidemiological studies into alcohol related outcomes. With over 10 years of longitudinal data, it will help to understand alcohol-related disease and health trajectories across the lifespan.",
+    "abstract": "Inflammation is a component of the pathogenesis of atherosclerosis and is associated with an increased risk of atherosclerotic cardiovascular disease (ASCVD). The neutrophil to lymphocyte ratio (NLR) is a possible inflammation metric for the detection of ASCVD risk, although results of prospective studies are highly inconsistent on this topic. We investigated the cross-sectional relationship between NLR and carotid intima-media thickness (cIMT) in subjects at moderate-to-high ASCVD risk. The prospective association between NLR, cIMT progression, and incident vascular events (VEs) was also explored. In 3341 subjects from the IMT-Progression as Predictors of VEs (IMPROVE) study, we analyzed the association between NLR, cIMT, and its 15-month progression. The association between NLR and incident VEs was also investigated. NLR was positively associated with cross-sectional measures of cIMT, but not with cIMT progression. The association between NLR and cross-sectional cIMT measures was abolished when adjusted for confounders. No association was found between NRL and incident VEs. Similarly, there were no significant differences in the hazard ratios (HRs) of VEs across NLR quartiles. NLR was neither associated with the presence and progression of carotid atherosclerosis, nor with the risk of VEs. Our findings do not support the role of NLR as a predictor of the risk of atherosclerosis progression and ASCVD events in subjects at moderate-to-high ASCVD risk, in primary prevention. However, the usefulness of NLR for patients at a different level of ASCVD risk cannot be inferred from this study.",
     "laySummary": "",
-    "urls": "pdf:https://ijpds.org/article/download/581/2923; doi:https://doi.org/10.23889/ijpds.v4i1.581; html:https://europepmc.org/articles/PMC8142962; pdf:https://europepmc.org/articles/PMC8142962?pdf=render"
+    "urls": "pdf:https://air.unimi.it/bitstream/2434/890337/2/0127%20IMPROVE%20mannarino%20Neutrophil%20to%20lymphocyte%20e%20suppl%20.pdf; doi:https://doi.org/10.1002/biof.1801; html:https://europepmc.org/articles/PMC9299016; pdf:https://europepmc.org/articles/PMC9299016?pdf=render"
   },
   {
     "id": "33144367",
@@ -27267,6 +27284,23 @@
     "laySummary": "",
     "urls": "pdf:https://bjgpopen.org/content/bjgpoa/4/5/bjgpopen20X101109.full.pdf; doi:https://doi.org/10.3399/bjgpopen20X101109; html:https://europepmc.org/articles/PMC7880177; pdf:https://europepmc.org/articles/PMC7880177?pdf=render"
   },
+  {
+    "id": "34095527",
+    "doi": "https://doi.org/10.23889/ijpds.v4i1.581",
+    "title": "Electronic Longitudinal Alcohol Study in Communities (ELAStiC) Wales - protocol for platform development.",
+    "authorString": "Trefan L, Akbari A, Paranjothy S, Farewell DM, Gartner A, Fone D, Greene J, Evans A, Smith A, Adekanmbi V, Kennedy J, Lyons RA, Moore SC.",
+    "authorAffiliations": "",
+    "journalTitle": "International journal of population data science",
+    "pubYear": "2019",
+    "date": "2019-05-20",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>Excessive alcohol consumption has adverse effects on health and there is a recognised need for the longitudinal analysis of population data to improve our understanding of the patterns of alcohol use, harms to consumers and those in their immediate environment. The UK has a number of linkable, longitudinal databases that if assembled properly could support valuable research on this topic.<h4>Aims and objectives</h4>This paper describes the development of a broad set of cross-linked cohorts, e-cohorts, surveys and linked electronic healthcare records (EHRs) to construct an alcohol-specific analytical platform in the United Kingdom using datasets on the population of Wales.The objective of this paper is to provide a description of existing key datasets integrated with existing, routinely collected electronic health data on a secure platform, and relevant derived variables to enable population-based research on alcohol-related harm in Wales. We illustrate our use of these data with some exemplar research questions that are currently under investigation.<h4>Methods</h4>Record-linkage of routine and observational datasets. Routine data includes hospital admissions, general practice, and cohorts specific to children. Two observational studies were included. Routine socioeconomic descriptors and mortality data were also linked.<h4>Conclusion</h4>We described a record-linked, population-based research protocol for alcohol related harm on a secure platform. As the datasets used here are available in many countries, ELAStiC provides a template for setting up similar initiatives in other countries. We have also defined a number of alcohol specific variables using routinely-collected available data that can be used in other epidemiological studies into alcohol related outcomes. With over 10 years of longitudinal data, it will help to understand alcohol-related disease and health trajectories across the lifespan.",
+    "laySummary": "",
+    "urls": "pdf:https://ijpds.org/article/download/581/2923; doi:https://doi.org/10.23889/ijpds.v4i1.581; html:https://europepmc.org/articles/PMC8142962; pdf:https://europepmc.org/articles/PMC8142962?pdf=render"
+  },
   {
     "id": "35579056",
     "doi": "https://doi.org/10.1111/eci.13814",
@@ -27284,23 +27318,6 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/eci.13814; doi:https://doi.org/10.1111/eci.13814; html:https://europepmc.org/articles/PMC9540114; pdf:https://europepmc.org/articles/PMC9540114?pdf=render"
   },
-  {
-    "id": "32838035",
-    "doi": "https://doi.org/10.1002/lrh2.10236",
-    "title": "Rapid translation of clinical guidelines into executable knowledge: A case study of COVID-19 and online demonstration.",
-    "authorString": "Fox J, Khan O, Curtis H, Wright A, Pal C, Cockburn N, Cooper J, Chandan JS, Nirantharakumar K.",
-    "authorAffiliations": "",
-    "journalTitle": "Learning health systems",
-    "pubYear": "2021",
-    "date": "2020-07-14",
-    "isOpenAccess": "Y",
-    "keywords": "Artificial intelligence; Covid\u201019; Rapid Learning Systems",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>We report a pathfinder study of AI/knowledge engineering methods to rapidly formalise COVID-19 guidelines into an executable model of decision making and care pathways. The knowledge source for the study was material published by BMJ Best Practice in March 2020.<h4>Methods</h4>The <i>PROforma</i> guideline modelling language and OpenClinical.net authoring and publishing platform were used to create a data model for care of COVID-19 patients together with executable models of rules, decisions and plans that interpret patient data and give personalised care advice.<h4>Results</h4><i>PROforma</i> and OpenClinical.net proved to be an effective combination for rapidly creating the COVID-19 model; the Pathfinder 1 demonstrator is available for assessment at https://www.openclinical.net/index.php?id=746.<h4>Conclusions</h4>This is believed to be the first use of AI/knowledge engineering methods for disseminating best-practice in COVID-19 care. It demonstrates a novel and promising approach to the rapid translation of clinical guidelines into point of care services, and a foundation for rapid learning systems in many areas of healthcare.",
-    "laySummary": "",
-    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/lrh2.10236; doi:https://doi.org/10.1002/lrh2.10236; html:https://europepmc.org/articles/PMC7323421; pdf:https://europepmc.org/articles/PMC7323421?pdf=render"
-  },
   {
     "id": "34772649",
     "doi": "https://doi.org/10.1016/s2589-7500(21)00252-1",
@@ -27335,6 +27352,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/s2589-7500(22)00249-7; doi:https://doi.org/10.1016/S2589-7500(22)00249-7"
   },
+  {
+    "id": "32838035",
+    "doi": "https://doi.org/10.1002/lrh2.10236",
+    "title": "Rapid translation of clinical guidelines into executable knowledge: A case study of COVID-19 and online demonstration.",
+    "authorString": "Fox J, Khan O, Curtis H, Wright A, Pal C, Cockburn N, Cooper J, Chandan JS, Nirantharakumar K.",
+    "authorAffiliations": "",
+    "journalTitle": "Learning health systems",
+    "pubYear": "2021",
+    "date": "2020-07-14",
+    "isOpenAccess": "Y",
+    "keywords": "Artificial intelligence; Covid\u201019; Rapid Learning Systems",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>We report a pathfinder study of AI/knowledge engineering methods to rapidly formalise COVID-19 guidelines into an executable model of decision making and care pathways. The knowledge source for the study was material published by BMJ Best Practice in March 2020.<h4>Methods</h4>The <i>PROforma</i> guideline modelling language and OpenClinical.net authoring and publishing platform were used to create a data model for care of COVID-19 patients together with executable models of rules, decisions and plans that interpret patient data and give personalised care advice.<h4>Results</h4><i>PROforma</i> and OpenClinical.net proved to be an effective combination for rapidly creating the COVID-19 model; the Pathfinder 1 demonstrator is available for assessment at https://www.openclinical.net/index.php?id=746.<h4>Conclusions</h4>This is believed to be the first use of AI/knowledge engineering methods for disseminating best-practice in COVID-19 care. It demonstrates a novel and promising approach to the rapid translation of clinical guidelines into point of care services, and a foundation for rapid learning systems in many areas of healthcare.",
+    "laySummary": "",
+    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/lrh2.10236; doi:https://doi.org/10.1002/lrh2.10236; html:https://europepmc.org/articles/PMC7323421; pdf:https://europepmc.org/articles/PMC7323421?pdf=render"
+  },
   {
     "id": "36355406",
     "doi": "https://doi.org/10.2196/40707",
@@ -27386,23 +27420,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.ejrad.2022.110366"
   },
-  {
-    "id": "35804579",
-    "doi": "https://doi.org/10.3390/ani12131679",
-    "title": "Genetic Basis of Dilated Cardiomyopathy in Dogs and Its Potential as a Bidirectional Model.",
-    "authorString": "Gaar-Humphreys KR, Spanjersberg TCF, Santarelli G, Grinwis GCM, Szatm\u00e1ri V, Roelen BAJ, Vink A, van Tintelen JP, Asselbergs FW, Fieten H, Harakalova M, van Steenbeek FG.",
-    "authorAffiliations": "",
-    "journalTitle": "Animals : an open access journal from MDPI",
-    "pubYear": "2022",
-    "date": "2022-06-29",
-    "isOpenAccess": "Y",
-    "keywords": "cardiovascular; Human Induced Pluripotent Stem Cells; Fibrofatty Infiltration; Canine Induced Pluripotent Stem Cells; Attenuated Wavy Fibers",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Cardiac disease is a leading cause of death for both humans and dogs. Genetic cardiomyopathies, including dilated cardiomyopathy (DCM), account for a proportion of these cases in both species. Patients may suffer from ventricular enlargement and systolic dysfunction resulting in congestive heart failure and ventricular arrhythmias with high risk for sudden cardiac death. Although canine DCM has similar disease progression and subtypes as in humans, only a few candidate genes have been found to be associated with DCM while the genetic background of human DCM has been more thoroughly studied. Additionally, experimental disease models using induced pluripotent stem cells have been widely adopted in the study of human genetic cardiomyopathy but have not yet been fully adapted for the in-depth study of canine genetic cardiomyopathies. The clinical presentation of DCM is extremely heterogeneous for both species with differences occurring based on sex predisposition, age of onset, and the rate of disease progression. Both genetic predisposition and environmental factors play a role in disease development which are identical in dogs and humans in contrast to other experimental animals. Interestingly, different dog breeds have been shown to develop distinct DCM phenotypes, and this presents a unique opportunity for modeling as there are multiple breed-specific models for DCM with less genetic variance than human DCM. A better understanding of DCM in dogs has the potential for improved selection for breeding and could lead to better overall care and treatment for human and canine DCM patients. At the same time, progress in research made for human DCM can have a positive impact on the care given to dogs affected by DCM. Therefore, this review will analyze the feasibility of canines as a naturally occurring bidirectional disease model for DCM in both species. The histopathology of the myocardium in canine DCM will be evaluated in three different breeds compared to control tissue, and the known genetics that contributes to both canine and human DCM will be summarized. Lastly, the prospect of canine iPSCs as a novel method to uncover the contributions of genetic variants to the pathogenesis of canine DCM will be introduced along with the applications for disease modeling and treatment.",
-    "laySummary": "",
-    "urls": "pdf:https://www.mdpi.com/2076-2615/12/13/1679/pdf?version=1656561768; doi:https://doi.org/10.3390/ani12131679; html:https://europepmc.org/articles/PMC9265105; pdf:https://europepmc.org/articles/PMC9265105?pdf=render"
-  },
   {
     "id": "34390586",
     "doi": "https://doi.org/10.1111/ejn.15423",
@@ -27420,6 +27437,23 @@
     "laySummary": "",
     "urls": "pdf:https://discovery.dundee.ac.uk/files/66344502/ejn.15423.pdf; doi:https://doi.org/10.1111/ejn.15423"
   },
+  {
+    "id": "35804579",
+    "doi": "https://doi.org/10.3390/ani12131679",
+    "title": "Genetic Basis of Dilated Cardiomyopathy in Dogs and Its Potential as a Bidirectional Model.",
+    "authorString": "Gaar-Humphreys KR, Spanjersberg TCF, Santarelli G, Grinwis GCM, Szatm\u00e1ri V, Roelen BAJ, Vink A, van Tintelen JP, Asselbergs FW, Fieten H, Harakalova M, van Steenbeek FG.",
+    "authorAffiliations": "",
+    "journalTitle": "Animals : an open access journal from MDPI",
+    "pubYear": "2022",
+    "date": "2022-06-29",
+    "isOpenAccess": "Y",
+    "keywords": "cardiovascular; Human Induced Pluripotent Stem Cells; Fibrofatty Infiltration; Canine Induced Pluripotent Stem Cells; Attenuated Wavy Fibers",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Cardiac disease is a leading cause of death for both humans and dogs. Genetic cardiomyopathies, including dilated cardiomyopathy (DCM), account for a proportion of these cases in both species. Patients may suffer from ventricular enlargement and systolic dysfunction resulting in congestive heart failure and ventricular arrhythmias with high risk for sudden cardiac death. Although canine DCM has similar disease progression and subtypes as in humans, only a few candidate genes have been found to be associated with DCM while the genetic background of human DCM has been more thoroughly studied. Additionally, experimental disease models using induced pluripotent stem cells have been widely adopted in the study of human genetic cardiomyopathy but have not yet been fully adapted for the in-depth study of canine genetic cardiomyopathies. The clinical presentation of DCM is extremely heterogeneous for both species with differences occurring based on sex predisposition, age of onset, and the rate of disease progression. Both genetic predisposition and environmental factors play a role in disease development which are identical in dogs and humans in contrast to other experimental animals. Interestingly, different dog breeds have been shown to develop distinct DCM phenotypes, and this presents a unique opportunity for modeling as there are multiple breed-specific models for DCM with less genetic variance than human DCM. A better understanding of DCM in dogs has the potential for improved selection for breeding and could lead to better overall care and treatment for human and canine DCM patients. At the same time, progress in research made for human DCM can have a positive impact on the care given to dogs affected by DCM. Therefore, this review will analyze the feasibility of canines as a naturally occurring bidirectional disease model for DCM in both species. The histopathology of the myocardium in canine DCM will be evaluated in three different breeds compared to control tissue, and the known genetics that contributes to both canine and human DCM will be summarized. Lastly, the prospect of canine iPSCs as a novel method to uncover the contributions of genetic variants to the pathogenesis of canine DCM will be introduced along with the applications for disease modeling and treatment.",
+    "laySummary": "",
+    "urls": "pdf:https://www.mdpi.com/2076-2615/12/13/1679/pdf?version=1656561768; doi:https://doi.org/10.3390/ani12131679; html:https://europepmc.org/articles/PMC9265105; pdf:https://europepmc.org/articles/PMC9265105?pdf=render"
+  },
   {
     "id": "35435219",
     "doi": "https://doi.org/10.1093/ehjqcco/qcac016",
@@ -27437,23 +27471,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ehjqcco/advance-article-pdf/doi/10.1093/ehjqcco/qcac016/43887262/qcac016.pdf; doi:https://doi.org/10.1093/ehjqcco/qcac016; html:https://europepmc.org/articles/PMC9745666; pdf:https://europepmc.org/articles/PMC9745666?pdf=render"
   },
-  {
-    "id": "34275648",
-    "doi": "https://doi.org/10.1016/j.injury.2021.06.037",
-    "title": "Patterns and predictors of personal responsibility attributions after major trauma.",
-    "authorString": "Lau G, Gabbe BJ, Giummarra MJ.",
-    "authorAffiliations": "",
-    "journalTitle": "Injury",
-    "pubYear": "2021",
-    "date": "2021-07-06",
-    "isOpenAccess": "N",
-    "keywords": "wounds and injuries; Insurance, Accident; Violence; Guilt; Accidental Injuries; Liability, Legal",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>External responsibility attributions after injury are associated with worse recovery. However, there remains limited understanding of who accepts personal responsibilityfor their injury and whether or how responsibility attributions change over time.<h4>Methods</h4>This prospective cohort study included patients who received care from recovery co-ordinators following serious injury and admission to a major trauma centre in Victoria, Australia (n=850). Self-reported personal responsibility attributions (totally, partially, not responsible, or did not know) were collected at three timepoints (admission, discharge, and six months post-injury) and linked to demographic, injury and clinical characteristics from the Victorian State Trauma Registry.<h4>Results</h4>Mixed effects multinomial analyses revealed that female sex (adjusted relative risk ratio, aRRR=3.11-4.66) and compensable injury (aRRR=7.83-15.27) were associated with reporting lower personal responsibility relative to total responsibility. Falls and motorcyclists had decreased risk of reporting lower personal responsibility than non-drivers (motor vehicle/motorcycle passengers, cyclists and pedestrians) (aRRR=0.11-0.19). More than one-third of participants changed their personal responsibility attribution within six months post-injury. Kappa analyses revealed fair to moderate agreement between the three timepoints (kappa=0.38-0.59), and Stuart-Maxwell tests showed unidirectional bias towards reporting lower levels of personal responsibility between admission and discharge (p<0.001). No demographic, health or injury characteristics predicted a change in responsibility attributions in logistic regression analyses.<h4>Conclusions</h4>Personal responsibility attributions often change over time. Therefore, responsibility attributions should not be considered static, and attributions made at different times post-injury should not be used interchangeably in research or clinical settings. Given that external responsibility attributions are associated with worse post-injury outcomes, potential interventions to optimise recovery should be prioritised for patients who predominantly report lower levels of personal responsibility, especially women and people with compensable injuries. Meanwhile, factors associated with high levels of personal responsibility highlight opportunities to implement targeted injury prevention strategies.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.injury.2021.06.037"
-  },
   {
     "id": "32142356",
     "doi": "https://doi.org/10.1164/rccm.201902-0286oc",
@@ -27471,6 +27488,23 @@
     "laySummary": "",
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7328307; doi:https://doi.org/10.1164/rccm.201902-0286OC; html:https://europepmc.org/articles/PMC7328307; pdf:https://europepmc.org/articles/PMC7328307?pdf=render; doi:https://doi.org/10.1164/rccm.201902-0286oc"
   },
+  {
+    "id": "34275648",
+    "doi": "https://doi.org/10.1016/j.injury.2021.06.037",
+    "title": "Patterns and predictors of personal responsibility attributions after major trauma.",
+    "authorString": "Lau G, Gabbe BJ, Giummarra MJ.",
+    "authorAffiliations": "",
+    "journalTitle": "Injury",
+    "pubYear": "2021",
+    "date": "2021-07-06",
+    "isOpenAccess": "N",
+    "keywords": "wounds and injuries; Insurance, Accident; Violence; Guilt; Accidental Injuries; Liability, Legal",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>External responsibility attributions after injury are associated with worse recovery. However, there remains limited understanding of who accepts personal responsibilityfor their injury and whether or how responsibility attributions change over time.<h4>Methods</h4>This prospective cohort study included patients who received care from recovery co-ordinators following serious injury and admission to a major trauma centre in Victoria, Australia (n=850). Self-reported personal responsibility attributions (totally, partially, not responsible, or did not know) were collected at three timepoints (admission, discharge, and six months post-injury) and linked to demographic, injury and clinical characteristics from the Victorian State Trauma Registry.<h4>Results</h4>Mixed effects multinomial analyses revealed that female sex (adjusted relative risk ratio, aRRR=3.11-4.66) and compensable injury (aRRR=7.83-15.27) were associated with reporting lower personal responsibility relative to total responsibility. Falls and motorcyclists had decreased risk of reporting lower personal responsibility than non-drivers (motor vehicle/motorcycle passengers, cyclists and pedestrians) (aRRR=0.11-0.19). More than one-third of participants changed their personal responsibility attribution within six months post-injury. Kappa analyses revealed fair to moderate agreement between the three timepoints (kappa=0.38-0.59), and Stuart-Maxwell tests showed unidirectional bias towards reporting lower levels of personal responsibility between admission and discharge (p<0.001). No demographic, health or injury characteristics predicted a change in responsibility attributions in logistic regression analyses.<h4>Conclusions</h4>Personal responsibility attributions often change over time. Therefore, responsibility attributions should not be considered static, and attributions made at different times post-injury should not be used interchangeably in research or clinical settings. Given that external responsibility attributions are associated with worse post-injury outcomes, potential interventions to optimise recovery should be prioritised for patients who predominantly report lower levels of personal responsibility, especially women and people with compensable injuries. Meanwhile, factors associated with high levels of personal responsibility highlight opportunities to implement targeted injury prevention strategies.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.injury.2021.06.037"
+  },
   {
     "id": "35089148",
     "doi": "https://doi.org/10.2196/28095",
@@ -27488,23 +27522,6 @@
     "laySummary": "",
     "urls": "pdf:https://mhealth.jmir.org/2022/1/e28095/PDF; doi:https://doi.org/10.2196/28095; html:https://europepmc.org/articles/PMC8838593"
   },
-  {
-    "id": "33866023",
-    "doi": "https://doi.org/10.1016/j.oret.2021.04.001",
-    "title": "Evolving Treatment Patterns and Outcomes of Neovascular Age-Related Macular Degeneration Over a Decade.",
-    "authorString": "Schwartz R, Warwick A, Olvera-Barrios A, Pikoula M, Lee AY, Denaxas S, Taylor P, Egan C, Chakravarthy U, Lip PL, Tufail A, of the UK EMR Users Group.",
-    "authorAffiliations": "",
-    "journalTitle": "Ophthalmology. Retina",
-    "pubYear": "2021",
-    "date": "2021-04-16",
-    "isOpenAccess": "N",
-    "keywords": "AMD; Ranibizumab; Anti-vegf; Aflibercept; Electronic Health Records; Etdrs; Early Treatment Diabetic Retinopathy Study",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Purpose</h4>Management of neovascular age-related macular degeneration (nAMD) has evolved over the last decade with several treatment regimens and medications. This study describes the treatment patterns and visual outcomes over 10 years in a large cohort of patients.<h4>Design</h4>Retrospective analysis of electronic health records from 27 National Health Service secondary care healthcare providers in the UK.<h4>Participants</h4>Treatment-na\u00efve patients receiving at least 3 intravitreal anti-vascular endothelial growth factor (VEGF) injections for nAMD in their first 6 months of follow-up were included. Patients with missing data for age or gender and those aged less than 55 years were excluded.<h4>Methods</h4>Eyes with at least 3 years of follow-up were grouped by years of treatment initiation, and 3-year outcomes were compared between the groups. Data were generated during routine clinical care between September 2008 and December\u00a02018.<h4>Main outcome measures</h4>Visual acuity (VA), number of injections, and number of visits.<h4>Results</h4>A total of 15 810 eyes of 13 705 patients receiving 195 104 injections were included. Visual acuity improved from baseline during the first year, but decreased thereafter, resulting in loss of visual gains. This trend remained consistent throughout the past decade. Although an increasing proportion of eyes remained in the driving standard, this was driven by better presenting VA over the decade. The number of injections decreased substantially between the first and subsequent years, from a mean of 6.25 in year 1 to 3 in year 2 and 2.5 in year 3, without improvement over the decade. In a multivariable regression analysis, final VA improved by 0.24 letters for each year since 2008, and younger age and baseline VA were significantly associated with VA at 3 years.<h4>Conclusions</h4>Our findings show that despite improvement in functional VA over the years, primarily driven by improving baseline VA, patients continue to lose vision after the first year of treatment, with only marginal change over the past decade. The data suggest these results may be related to suboptimal treatment patterns, which have not improved over the years. Rethinking treatment strategies may be warranted, possibly on a national level or through the introduction of longer-acting therapies.",
-    "laySummary": "",
-    "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9165682; doi:https://doi.org/10.1016/j.oret.2021.04.001; html:https://europepmc.org/articles/PMC9165682; pdf:https://europepmc.org/articles/PMC9165682?pdf=render; doi:https://doi.org/10.1016/j.oret.2021.04.001"
-  },
   {
     "id": "34850874",
     "doi": "https://doi.org/10.1093/gigascience/giab083",
@@ -27522,6 +27539,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/gigascience/article-pdf/10/12/giab083/41395049/giab083.pdf; doi:https://doi.org/10.1093/gigascience/giab083; html:https://europepmc.org/articles/PMC8634578; pdf:https://europepmc.org/articles/PMC8634578?pdf=render"
   },
+  {
+    "id": "33866023",
+    "doi": "https://doi.org/10.1016/j.oret.2021.04.001",
+    "title": "Evolving Treatment Patterns and Outcomes of Neovascular Age-Related Macular Degeneration Over a Decade.",
+    "authorString": "Schwartz R, Warwick A, Olvera-Barrios A, Pikoula M, Lee AY, Denaxas S, Taylor P, Egan C, Chakravarthy U, Lip PL, Tufail A, of the UK EMR Users Group.",
+    "authorAffiliations": "",
+    "journalTitle": "Ophthalmology. Retina",
+    "pubYear": "2021",
+    "date": "2021-04-16",
+    "isOpenAccess": "N",
+    "keywords": "AMD; Ranibizumab; Anti-vegf; Aflibercept; Electronic Health Records; Etdrs; Early Treatment Diabetic Retinopathy Study",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Purpose</h4>Management of neovascular age-related macular degeneration (nAMD) has evolved over the last decade with several treatment regimens and medications. This study describes the treatment patterns and visual outcomes over 10 years in a large cohort of patients.<h4>Design</h4>Retrospective analysis of electronic health records from 27 National Health Service secondary care healthcare providers in the UK.<h4>Participants</h4>Treatment-na\u00efve patients receiving at least 3 intravitreal anti-vascular endothelial growth factor (VEGF) injections for nAMD in their first 6 months of follow-up were included. Patients with missing data for age or gender and those aged less than 55 years were excluded.<h4>Methods</h4>Eyes with at least 3 years of follow-up were grouped by years of treatment initiation, and 3-year outcomes were compared between the groups. Data were generated during routine clinical care between September 2008 and December\u00a02018.<h4>Main outcome measures</h4>Visual acuity (VA), number of injections, and number of visits.<h4>Results</h4>A total of 15 810 eyes of 13 705 patients receiving 195 104 injections were included. Visual acuity improved from baseline during the first year, but decreased thereafter, resulting in loss of visual gains. This trend remained consistent throughout the past decade. Although an increasing proportion of eyes remained in the driving standard, this was driven by better presenting VA over the decade. The number of injections decreased substantially between the first and subsequent years, from a mean of 6.25 in year 1 to 3 in year 2 and 2.5 in year 3, without improvement over the decade. In a multivariable regression analysis, final VA improved by 0.24 letters for each year since 2008, and younger age and baseline VA were significantly associated with VA at 3 years.<h4>Conclusions</h4>Our findings show that despite improvement in functional VA over the years, primarily driven by improving baseline VA, patients continue to lose vision after the first year of treatment, with only marginal change over the past decade. The data suggest these results may be related to suboptimal treatment patterns, which have not improved over the years. Rethinking treatment strategies may be warranted, possibly on a national level or through the introduction of longer-acting therapies.",
+    "laySummary": "",
+    "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9165682; doi:https://doi.org/10.1016/j.oret.2021.04.001; html:https://europepmc.org/articles/PMC9165682; pdf:https://europepmc.org/articles/PMC9165682?pdf=render; doi:https://doi.org/10.1016/j.oret.2021.04.001"
+  },
   {
     "id": "35536740",
     "doi": "https://doi.org/10.1136/bmjopen-2021-052884",
@@ -27556,23 +27590,6 @@
     "laySummary": "",
     "urls": "pdf:https://jech.bmj.com/content/jech/76/12/991.full.pdf; doi:https://doi.org/10.1136/jech-2021-217986; html:https://europepmc.org/articles/PMC9664100; pdf:https://europepmc.org/articles/PMC9664100?pdf=render"
   },
-  {
-    "id": "38383544",
-    "doi": "https://doi.org/10.1038/s41467-024-45761-7",
-    "title": "The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies.",
-    "authorString": "Lipworth S, Matlock W, Shaw L, Vihta KD, Rodger G, Chau K, Barker L, George S, Kavanagh J, Davies T, Vaughan A, Andersson M, Jeffery K, Oakley S, Morgan M, Hopkins S, Peto T, Crook D, Walker AS, Stoesser N.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature communications",
-    "pubYear": "2024",
-    "date": "2024-02-22",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Plasmids carry genes conferring antimicrobial resistance and other clinically important traits, and contribute to the rapid dissemination of such genes. Previous studies using complete plasmid assemblies, which are essential for reliable inference, have been small and/or limited to plasmids carrying antimicrobial resistance genes (ARGs). In this study, we sequenced 1,880 complete plasmids from 738 isolates from bloodstream infections in Oxfordshire, UK. The bacteria had been originally isolated in 2009 (194 isolates) and 2018 (368 isolates), plus a stratified selection from intervening years (176 isolates). We demonstrate that plasmids are largely, but not entirely, constrained to a single host species, although there is substantial overlap between species of plasmid gene-repertoire. Most ARGs are carried by a relatively small number of plasmid groups with biological features that are predictable. Plasmids carrying ARGs (including those encoding carbapenemases) share a putative 'backbone' of core genes with those carrying no such genes. These findings suggest that future surveillance should, in addition to tracking plasmids currently associated with clinically important genes, focus on identifying and monitoring the dissemination of high-risk plasmid groups with the potential to rapidly acquire and disseminate these genes.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1038/s41467-024-45761-7; html:https://europepmc.org/articles/PMC10881496; pdf:https://europepmc.org/articles/PMC10881496?pdf=render"
-  },
   {
     "id": "34038519",
     "doi": "https://doi.org/10.1093/ageing/afab084",
@@ -27590,6 +27607,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ageing/article-pdf/50/5/1762/40349116/afab084.pdf; doi:https://doi.org/10.1093/ageing/afab084; html:https://europepmc.org/articles/PMC8437066; pdf:https://europepmc.org/articles/PMC8437066?pdf=render"
   },
+  {
+    "id": "38383544",
+    "doi": "https://doi.org/10.1038/s41467-024-45761-7",
+    "title": "The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies.",
+    "authorString": "Lipworth S, Matlock W, Shaw L, Vihta KD, Rodger G, Chau K, Barker L, George S, Kavanagh J, Davies T, Vaughan A, Andersson M, Jeffery K, Oakley S, Morgan M, Hopkins S, Peto T, Crook D, Walker AS, Stoesser N.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature communications",
+    "pubYear": "2024",
+    "date": "2024-02-22",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Plasmids carry genes conferring antimicrobial resistance and other clinically important traits, and contribute to the rapid dissemination of such genes. Previous studies using complete plasmid assemblies, which are essential for reliable inference, have been small and/or limited to plasmids carrying antimicrobial resistance genes (ARGs). In this study, we sequenced 1,880 complete plasmids from 738 isolates from bloodstream infections in Oxfordshire, UK. The bacteria had been originally isolated in 2009 (194 isolates) and 2018 (368 isolates), plus a stratified selection from intervening years (176 isolates). We demonstrate that plasmids are largely, but not entirely, constrained to a single host species, although there is substantial overlap between species of plasmid gene-repertoire. Most ARGs are carried by a relatively small number of plasmid groups with biological features that are predictable. Plasmids carrying ARGs (including those encoding carbapenemases) share a putative 'backbone' of core genes with those carrying no such genes. These findings suggest that future surveillance should, in addition to tracking plasmids currently associated with clinically important genes, focus on identifying and monitoring the dissemination of high-risk plasmid groups with the potential to rapidly acquire and disseminate these genes.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1038/s41467-024-45761-7; html:https://europepmc.org/articles/PMC10881496; pdf:https://europepmc.org/articles/PMC10881496?pdf=render"
+  },
   {
     "id": "31822919",
     "doi": "https://doi.org/10.1093/pubmed/fdz172",
@@ -27607,6 +27641,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/jpubhealth/article-pdf/42/4/e516/34469316/fdz172.pdf; doi:https://doi.org/10.1093/pubmed/fdz172"
   },
+  {
+    "id": "30745170",
+    "doi": "https://doi.org/10.1016/j.ebiom.2019.02.005",
+    "title": "Identification of novel genome-wide associations for suicidality in UK Biobank, genetic correlation with psychiatric disorders and polygenic association with completed suicide.",
+    "authorString": "Strawbridge RJ, Ward J, Ferguson A, Graham N, Shaw RJ, Cullen B, Pearsall R, Lyall LM, Johnston KJA, Niedzwiedz CL, Pell JP, Mackay D, Martin JL, Lyall DM, Bailey MES, Smith DJ.",
+    "authorAffiliations": "",
+    "journalTitle": "EBioMedicine",
+    "pubYear": "2019",
+    "date": "2019-02-08",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "Understanding the Causes of Disease",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Suicide is a major issue for global public health. Suicidality describes a broad spectrum of thoughts and behaviours, some of which are common in the general population. Although suicide results from a complex interaction of multiple social and psychological factors, predisposition to suicidality is at least partly genetic.<h4>Methods</h4>Ordinal genome-wide association study of suicidality in the UK Biobank cohort comparing: 'no suicidality' controls (N\u202f=\u202f83,557); 'thoughts that life was not worth living' (N\u202f=\u202f21,063); 'ever contemplated self-harm' (N\u202f=\u202f13,038); 'act of deliberate self-harm in the past' (N\u202f=\u202f2498); and 'previous suicide attempt' (N\u202f=\u202f2666).<h4>Outcomes</h4>We identified three novel genome-wide significant loci for suicidality (on chromosomes nine, 11 and 13) and moderate-to-strong genetic correlations between suicidality and a range of psychiatric disorders, most notably depression (r<sub>g</sub> 0\u00b781).<h4>Interpretation</h4>These findings provide new information about genetic variants relating to increased risk of suicidal thoughts and behaviours. Future work should assess the extent to which polygenic risk scores for suicidality, in combination with non-genetic risk factors, may be useful for stratified approaches to suicide prevention at a population level. FUND: UKRI Innovation-HDR-UK Fellowship (MR/S003061/1). MRC Mental Health Data Pathfinder Award (MC_PC_17217). MRC Doctoral Training Programme Studentship at the University of Glasgow (MR/K501335/1). MRC Doctoral Training Programme Studentship at the Universities of Glasgow and Edinburgh. UKRI Innovation Fellowship (MR/R024774/1).",
+    "laySummary": "",
+    "urls": "pdf:http://www.thelancet.com/article/S2352396419300775/pdf; doi:https://doi.org/10.1016/j.ebiom.2019.02.005; html:https://europepmc.org/articles/PMC6442001; pdf:https://europepmc.org/articles/PMC6442001?pdf=render"
+  },
   {
     "id": "30940752",
     "doi": "https://doi.org/10.1136/bmjopen-2018-023232",
@@ -27641,23 +27692,6 @@
     "laySummary": "",
     "urls": "pdf:https://eprints.gla.ac.uk/217500/1/217500.pdf; doi:https://doi.org/10.3233/JAD-200338"
   },
-  {
-    "id": "37319288",
-    "doi": "https://doi.org/10.1371/journal.pone.0287264",
-    "title": "Evaluation of data processing pipelines on real-world electronic health records data for the purpose of measuring patient similarity.",
-    "authorString": "Pikoula M, Kallis C, Madjiheurem S, Quint JK, Bafadhel M, Denaxas S.",
-    "authorAffiliations": "",
-    "journalTitle": "PloS one",
-    "pubYear": "2023",
-    "date": "2023-06-15",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>The ever-growing size, breadth, and availability of patient data allows for a wide variety of clinical features to serve as inputs for phenotype discovery using cluster analysis. Data of mixed types in particular are not straightforward to combine into a single feature vector, and techniques used to address this can be biased towards certain data types in ways that are not immediately obvious or intended. In this context, the process of constructing clinically meaningful patient representations from complex datasets has not been systematically evaluated.<h4>Aims</h4>Our aim was to a) outline and b) implement an analytical framework to evaluate distinct methods of constructing patient representations from routine electronic health record data for the purpose of measuring patient similarity. We applied the analysis on a patient cohort diagnosed with chronic obstructive pulmonary disease.<h4>Methods</h4>Using data from the CALIBER data resource, we extracted clinically relevant features for a cohort of patients diagnosed with chronic obstructive pulmonary disease. We used four different data processing pipelines to construct lower dimensional patient representations from which we calculated patient similarity scores. We described the resulting representations, ranked the influence of each individual feature on patient similarity and evaluated the effect of different pipelines on clustering outcomes. Experts evaluated the resulting representations by rating the clinical relevance of similar patient suggestions with regard to a reference patient.<h4>Results</h4>Each of the four pipelines resulted in similarity scores primarily driven by a unique set of features. It was demonstrated that data transformations according to each pipeline prior to clustering can result in a variation of clustering results of over 40%. The most appropriate pipeline was selected on the basis of feature ranking and clinical expertise. There was moderate agreement between clinicians as measured by Cohen's kappa coefficient.<h4>Conclusions</h4>Data transformation has downstream and unforeseen consequences in cluster analysis. Rather than viewing this process as a black box, we have shown ways to quantitatively and qualitatively evaluate and select the appropriate preprocessing pipeline.",
-    "laySummary": "",
-    "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0287264&type=printable; doi:https://doi.org/10.1371/journal.pone.0287264; html:https://europepmc.org/articles/PMC10270623; pdf:https://europepmc.org/articles/PMC10270623?pdf=render"
-  },
   {
     "id": "36855161",
     "doi": "https://doi.org/10.1186/s13073-023-01161-y",
@@ -27676,21 +27710,21 @@
     "urls": "pdf:https://genomemedicine.biomedcentral.com/counter/pdf/10.1186/s13073-023-01161-y; doi:https://doi.org/10.1186/s13073-023-01161-y; html:https://europepmc.org/articles/PMC9976489; pdf:https://europepmc.org/articles/PMC9976489?pdf=render"
   },
   {
-    "id": "30745170",
-    "doi": "https://doi.org/10.1016/j.ebiom.2019.02.005",
-    "title": "Identification of novel genome-wide associations for suicidality in UK Biobank, genetic correlation with psychiatric disorders and polygenic association with completed suicide.",
-    "authorString": "Strawbridge RJ, Ward J, Ferguson A, Graham N, Shaw RJ, Cullen B, Pearsall R, Lyall LM, Johnston KJA, Niedzwiedz CL, Pell JP, Mackay D, Martin JL, Lyall DM, Bailey MES, Smith DJ.",
+    "id": "37319288",
+    "doi": "https://doi.org/10.1371/journal.pone.0287264",
+    "title": "Evaluation of data processing pipelines on real-world electronic health records data for the purpose of measuring patient similarity.",
+    "authorString": "Pikoula M, Kallis C, Madjiheurem S, Quint JK, Bafadhel M, Denaxas S.",
     "authorAffiliations": "",
-    "journalTitle": "EBioMedicine",
-    "pubYear": "2019",
-    "date": "2019-02-08",
+    "journalTitle": "PloS one",
+    "pubYear": "2023",
+    "date": "2023-06-15",
     "isOpenAccess": "Y",
     "keywords": "",
-    "nationalPriorities": "Understanding the Causes of Disease",
+    "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Suicide is a major issue for global public health. Suicidality describes a broad spectrum of thoughts and behaviours, some of which are common in the general population. Although suicide results from a complex interaction of multiple social and psychological factors, predisposition to suicidality is at least partly genetic.<h4>Methods</h4>Ordinal genome-wide association study of suicidality in the UK Biobank cohort comparing: 'no suicidality' controls (N\u202f=\u202f83,557); 'thoughts that life was not worth living' (N\u202f=\u202f21,063); 'ever contemplated self-harm' (N\u202f=\u202f13,038); 'act of deliberate self-harm in the past' (N\u202f=\u202f2498); and 'previous suicide attempt' (N\u202f=\u202f2666).<h4>Outcomes</h4>We identified three novel genome-wide significant loci for suicidality (on chromosomes nine, 11 and 13) and moderate-to-strong genetic correlations between suicidality and a range of psychiatric disorders, most notably depression (r<sub>g</sub> 0\u00b781).<h4>Interpretation</h4>These findings provide new information about genetic variants relating to increased risk of suicidal thoughts and behaviours. Future work should assess the extent to which polygenic risk scores for suicidality, in combination with non-genetic risk factors, may be useful for stratified approaches to suicide prevention at a population level. FUND: UKRI Innovation-HDR-UK Fellowship (MR/S003061/1). MRC Mental Health Data Pathfinder Award (MC_PC_17217). MRC Doctoral Training Programme Studentship at the University of Glasgow (MR/K501335/1). MRC Doctoral Training Programme Studentship at the Universities of Glasgow and Edinburgh. UKRI Innovation Fellowship (MR/R024774/1).",
+    "abstract": "<h4>Background</h4>The ever-growing size, breadth, and availability of patient data allows for a wide variety of clinical features to serve as inputs for phenotype discovery using cluster analysis. Data of mixed types in particular are not straightforward to combine into a single feature vector, and techniques used to address this can be biased towards certain data types in ways that are not immediately obvious or intended. In this context, the process of constructing clinically meaningful patient representations from complex datasets has not been systematically evaluated.<h4>Aims</h4>Our aim was to a) outline and b) implement an analytical framework to evaluate distinct methods of constructing patient representations from routine electronic health record data for the purpose of measuring patient similarity. We applied the analysis on a patient cohort diagnosed with chronic obstructive pulmonary disease.<h4>Methods</h4>Using data from the CALIBER data resource, we extracted clinically relevant features for a cohort of patients diagnosed with chronic obstructive pulmonary disease. We used four different data processing pipelines to construct lower dimensional patient representations from which we calculated patient similarity scores. We described the resulting representations, ranked the influence of each individual feature on patient similarity and evaluated the effect of different pipelines on clustering outcomes. Experts evaluated the resulting representations by rating the clinical relevance of similar patient suggestions with regard to a reference patient.<h4>Results</h4>Each of the four pipelines resulted in similarity scores primarily driven by a unique set of features. It was demonstrated that data transformations according to each pipeline prior to clustering can result in a variation of clustering results of over 40%. The most appropriate pipeline was selected on the basis of feature ranking and clinical expertise. There was moderate agreement between clinicians as measured by Cohen's kappa coefficient.<h4>Conclusions</h4>Data transformation has downstream and unforeseen consequences in cluster analysis. Rather than viewing this process as a black box, we have shown ways to quantitatively and qualitatively evaluate and select the appropriate preprocessing pipeline.",
     "laySummary": "",
-    "urls": "pdf:http://www.thelancet.com/article/S2352396419300775/pdf; doi:https://doi.org/10.1016/j.ebiom.2019.02.005; html:https://europepmc.org/articles/PMC6442001; pdf:https://europepmc.org/articles/PMC6442001?pdf=render"
+    "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0287264&type=printable; doi:https://doi.org/10.1371/journal.pone.0287264; html:https://europepmc.org/articles/PMC10270623; pdf:https://europepmc.org/articles/PMC10270623?pdf=render"
   },
   {
     "id": "31711543",
@@ -27862,6 +27896,23 @@
     "laySummary": "",
     "urls": "pdf:https://n.neurology.org/content/neurology/95/4/e353.full.pdf; doi:https://doi.org/10.1212/WNL.0000000000009814; html:https://europepmc.org/articles/PMC7455321; pdf:https://europepmc.org/articles/PMC7455321?pdf=render"
   },
+  {
+    "id": "36692937",
+    "doi": "https://doi.org/10.2196/42866",
+    "title": "The Feasibility of Implementing Remote Measurement Technologies in Psychological Treatment for Depression: Mixed Methods Study on Engagement.",
+    "authorString": "de Angel V, Adeleye F, Zhang Y, Cummins N, Munir S, Lewis S, Laporta Puyal E, Matcham F, Sun S, Folarin AA, Ranjan Y, Conde P, Rashid Z, Dobson R, Hotopf M.",
+    "authorAffiliations": "",
+    "journalTitle": "JMIR mental health",
+    "pubYear": "2023",
+    "date": "2023-01-24",
+    "isOpenAccess": "Y",
+    "keywords": "Depression; Mobile phone; Anxiety; Smartphone; Mhealth; Mobile Health; Wearable Devices; Digital Health; Digital Phenotyping; Passive Sensing",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Remote measurement technologies (RMTs) such as smartphones and wearables can help improve treatment for depression by providing objective, continuous, and ecologically valid insights into mood and behavior. Engagement with RMTs is varied and highly context dependent; however, few studies have investigated their feasibility in the context of treatment.<h4>Objective</h4>A mixed methods design was used to evaluate engagement with active and passive data collection via RMT in people with depression undergoing psychotherapy. We evaluated the effects of treatment on 2 different types of engagement: study attrition (engagement with study protocol) and patterns of missing data (engagement with digital devices), which we termed data availability. Qualitative interviews were conducted to help interpret the differences in engagement.<h4>Methods</h4>A total of 66 people undergoing psychological therapy for depression were followed up for 7 months. Active data were gathered from weekly questionnaires and speech and cognitive tasks, and passive data were gathered from smartphone sensors and a Fitbit (Fitbit Inc) wearable device.<h4>Results</h4>The overall retention rate was 60%. Higher-intensity treatment (\u03c7<sup>2</sup><sub>1</sub>=4.6; P=.03) and higher baseline anxiety (t<sub>56.28</sub>=-2.80, 2-tailed; P=.007) were associated with attrition, but depression severity was not (t<sub>50.4</sub>=-0.18; P=.86). A trend toward significance was found for the association between longer treatments and increased attrition (U=339.5; P=.05). Data availability was higher for active data than for passive data initially but declined at a sharper rate (90%-30% drop in 7 months). As for passive data, wearable data availability fell from a maximum of 80% to 45% at 7 months but showed higher overall data availability than smartphone-based data, which remained stable at the range of 20%-40% throughout. Missing data were more prevalent among GPS location data, followed by among Bluetooth data, then among accelerometry data. As for active data, speech and cognitive tasks had lower completion rates than clinical questionnaires. The participants in treatment provided less Fitbit data but more active data than those on the waiting list.<h4>Conclusions</h4>Different data streams showed varied patterns of missing data, despite being gathered from the same device. Longer and more complex treatments and clinical characteristics such as higher baseline anxiety may reduce long-term engagement with RMTs, and different devices may show opposite patterns of missingness during treatment. This has implications for the scalability and uptake of RMTs in health care settings, the generalizability and accuracy of the data collected by these methods, feature construction, and the appropriateness of RMT use in the long term.",
+    "laySummary": "",
+    "urls": "pdf:https://mental.jmir.org/2023/1/e42866/PDF; doi:https://doi.org/10.2196/42866; html:https://europepmc.org/articles/PMC9906314"
+  },
   {
     "id": "35144240",
     "doi": "https://doi.org/10.2196/32543",
@@ -27879,23 +27930,6 @@
     "laySummary": "",
     "urls": "pdf:https://publichealth.jmir.org/2022/5/e32543/PDF; doi:https://doi.org/10.2196/32543; html:https://europepmc.org/articles/PMC9150729"
   },
-  {
-    "id": "38279797",
-    "doi": "https://doi.org/10.1089/neu.2023.0465",
-    "title": "The Australian Traumatic Brain Injury Initiative: Systematic Review of the Effect of Acute Interventions on Outcome for People With Moderate-Severe Traumatic Brain Injury.",
-    "authorString": "Keeves J, Gadowski A, McKimmie A, Bagg MK, Antonic-Baker A, Hicks AJ, Clarke N, Brown A, McNamara R, Reeder S, Roman C, Jeffcote T, Romero L, Hill R, Ponsford JL, Lannin NA, O'Brien TJ, Cameron PA, Rushworth N, Fitzgerald M, Gabbe BJ, Cooper DJ.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of neurotrauma",
-    "pubYear": "2024",
-    "date": "2024-04-08",
-    "isOpenAccess": "N",
-    "keywords": "Common Data Elements; Brain Injuries, Traumatic; Outcome Assessment, Health Care; Systematic Review [Publication Type]; Emergency Medical Services, Critical Care, Early Medical Intervention",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The Australian Traumatic Brain Injury Initiative (AUS-TBI) is developing a data resource to enable improved outcome prediction for people with moderate-severe TBI (msTBI) across Australia. Fundamental to this resource is the collaboratively designed data dictionary. This systematic review and consultation aimed to identify acute interventions with potential to modify clinical outcomes for people after msTBI, for inclusion in a data dictionary. Standardized searches were implemented across bibliographic databases from inception through April 2022. English-language reports of randomized controlled trials (RCTs) evaluating any association between any acute intervention and clinical outcome in at least 100 patients with msTBI, were included. A predefined algorithm was used to assign a value to each observed association. Consultation with AUS-TBI clinicians and researchers formed the consensus process for interventions to be included in a single data dictionary. Searches retrieved 14,455 records, of which 124 full-length RCTs were screened, with 35 studies included. These studies evaluated 26 unique acute interventions across 21 unique clinical outcomes. Only 4 interventions were considered to have medium modifying value for any outcome from the review, with an additional 8 interventions agreed upon through the consensus process. The interventions with medium value were tranexamic acid and phenytoin, which had a positive effect on an outcome; and decompressive craniectomy surgery and hypothermia, which negatively affected outcomes. From the systematic review and consensus process, 12 interventions were identified as potential modifiers to be included in the AUS-TBI national data resource.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1089/neu.2023.0465"
-  },
   {
     "id": "36929968",
     "doi": "https://doi.org/10.1016/s0140-6736(22)02235-8",
@@ -27914,21 +27948,21 @@
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9691043; doi:https://doi.org/10.1016/S0140-6736(22)02235-8; html:https://europepmc.org/articles/PMC9691043; pdf:https://europepmc.org/articles/PMC9691043?pdf=render"
   },
   {
-    "id": "36692937",
-    "doi": "https://doi.org/10.2196/42866",
-    "title": "The Feasibility of Implementing Remote Measurement Technologies in Psychological Treatment for Depression: Mixed Methods Study on Engagement.",
-    "authorString": "de Angel V, Adeleye F, Zhang Y, Cummins N, Munir S, Lewis S, Laporta Puyal E, Matcham F, Sun S, Folarin AA, Ranjan Y, Conde P, Rashid Z, Dobson R, Hotopf M.",
+    "id": "38279797",
+    "doi": "https://doi.org/10.1089/neu.2023.0465",
+    "title": "The Australian Traumatic Brain Injury Initiative: Systematic Review of the Effect of Acute Interventions on Outcome for People With Moderate-Severe Traumatic Brain Injury.",
+    "authorString": "Keeves J, Gadowski A, McKimmie A, Bagg MK, Antonic-Baker A, Hicks AJ, Clarke N, Brown A, McNamara R, Reeder S, Roman C, Jeffcote T, Romero L, Hill R, Ponsford JL, Lannin NA, O'Brien TJ, Cameron PA, Rushworth N, Fitzgerald M, Gabbe BJ, Cooper DJ.",
     "authorAffiliations": "",
-    "journalTitle": "JMIR mental health",
-    "pubYear": "2023",
-    "date": "2023-01-24",
-    "isOpenAccess": "Y",
-    "keywords": "Depression; Mobile phone; Anxiety; Smartphone; Mhealth; Mobile Health; Wearable Devices; Digital Health; Digital Phenotyping; Passive Sensing",
+    "journalTitle": "Journal of neurotrauma",
+    "pubYear": "2024",
+    "date": "2024-04-08",
+    "isOpenAccess": "N",
+    "keywords": "Common Data Elements; Brain Injuries, Traumatic; Outcome Assessment, Health Care; Systematic Review [Publication Type]; Emergency Medical Services, Critical Care, Early Medical Intervention",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Remote measurement technologies (RMTs) such as smartphones and wearables can help improve treatment for depression by providing objective, continuous, and ecologically valid insights into mood and behavior. Engagement with RMTs is varied and highly context dependent; however, few studies have investigated their feasibility in the context of treatment.<h4>Objective</h4>A mixed methods design was used to evaluate engagement with active and passive data collection via RMT in people with depression undergoing psychotherapy. We evaluated the effects of treatment on 2 different types of engagement: study attrition (engagement with study protocol) and patterns of missing data (engagement with digital devices), which we termed data availability. Qualitative interviews were conducted to help interpret the differences in engagement.<h4>Methods</h4>A total of 66 people undergoing psychological therapy for depression were followed up for 7 months. Active data were gathered from weekly questionnaires and speech and cognitive tasks, and passive data were gathered from smartphone sensors and a Fitbit (Fitbit Inc) wearable device.<h4>Results</h4>The overall retention rate was 60%. Higher-intensity treatment (\u03c7<sup>2</sup><sub>1</sub>=4.6; P=.03) and higher baseline anxiety (t<sub>56.28</sub>=-2.80, 2-tailed; P=.007) were associated with attrition, but depression severity was not (t<sub>50.4</sub>=-0.18; P=.86). A trend toward significance was found for the association between longer treatments and increased attrition (U=339.5; P=.05). Data availability was higher for active data than for passive data initially but declined at a sharper rate (90%-30% drop in 7 months). As for passive data, wearable data availability fell from a maximum of 80% to 45% at 7 months but showed higher overall data availability than smartphone-based data, which remained stable at the range of 20%-40% throughout. Missing data were more prevalent among GPS location data, followed by among Bluetooth data, then among accelerometry data. As for active data, speech and cognitive tasks had lower completion rates than clinical questionnaires. The participants in treatment provided less Fitbit data but more active data than those on the waiting list.<h4>Conclusions</h4>Different data streams showed varied patterns of missing data, despite being gathered from the same device. Longer and more complex treatments and clinical characteristics such as higher baseline anxiety may reduce long-term engagement with RMTs, and different devices may show opposite patterns of missingness during treatment. This has implications for the scalability and uptake of RMTs in health care settings, the generalizability and accuracy of the data collected by these methods, feature construction, and the appropriateness of RMT use in the long term.",
+    "abstract": "The Australian Traumatic Brain Injury Initiative (AUS-TBI) is developing a data resource to enable improved outcome prediction for people with moderate-severe TBI (msTBI) across Australia. Fundamental to this resource is the collaboratively designed data dictionary. This systematic review and consultation aimed to identify acute interventions with potential to modify clinical outcomes for people after msTBI, for inclusion in a data dictionary. Standardized searches were implemented across bibliographic databases from inception through April 2022. English-language reports of randomized controlled trials (RCTs) evaluating any association between any acute intervention and clinical outcome in at least 100 patients with msTBI, were included. A predefined algorithm was used to assign a value to each observed association. Consultation with AUS-TBI clinicians and researchers formed the consensus process for interventions to be included in a single data dictionary. Searches retrieved 14,455 records, of which 124 full-length RCTs were screened, with 35 studies included. These studies evaluated 26 unique acute interventions across 21 unique clinical outcomes. Only 4 interventions were considered to have medium modifying value for any outcome from the review, with an additional 8 interventions agreed upon through the consensus process. The interventions with medium value were tranexamic acid and phenytoin, which had a positive effect on an outcome; and decompressive craniectomy surgery and hypothermia, which negatively affected outcomes. From the systematic review and consensus process, 12 interventions were identified as potential modifiers to be included in the AUS-TBI national data resource.",
     "laySummary": "",
-    "urls": "pdf:https://mental.jmir.org/2023/1/e42866/PDF; doi:https://doi.org/10.2196/42866; html:https://europepmc.org/articles/PMC9906314"
+    "urls": "doi:https://doi.org/10.1089/neu.2023.0465"
   },
   {
     "id": "33903145",
@@ -27981,23 +28015,6 @@
     "laySummary": "",
     "urls": "pdf:https://cronfa.swan.ac.uk/Record/cronfa50163/Download/0050163-25062019060819.pdf; doi:https://doi.org/10.1136/injuryprev-2018-043085"
   },
-  {
-    "id": "37190768",
-    "doi": "https://doi.org/10.1017/s2045796023000276",
-    "title": "The mental health of all children in contact with social services: a population-wide record-linkage study in Northern Ireland.",
-    "authorString": "McKenna S, O'Reilly D, Maguire A.",
-    "authorAffiliations": "",
-    "journalTitle": "Epidemiology and psychiatric sciences",
-    "pubYear": "2023",
-    "date": "2023-05-16",
-    "isOpenAccess": "Y",
-    "keywords": "Mental health; Data Linkage; Children\u2019s Social Care",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Aims</h4>Children in contact with social services are at high risk for mental ill health, but it is not known what proportion of the child population has contact with social services or how risk varies within this group compared to unexposed peers. We aim to quantify the extent and nature of contact with social services within the child population in Northern Ireland (NI) and the association with mental ill health. We also examine which social care experiences identify those most at risk.<h4>Methods</h4>This is a population-based record-linkage study of 497,269 children (aged under 18\u00a0years) alive and resident in NI in 2015 using routinely collected health and social care data. Exposure was categorized as (1) no contact, (2) referred but assessed as not in need (NIN), (3) child in need (CIN) and (4) child in care (CIC). Multilevel logistic regression analyses estimated odds ratios (ORs) for mental ill health indicated by receipt of psychotropic medication (antidepressants, anxiolytics, antipsychotics and hypnotics), psychiatric hospital admission and hospital-presenting self-harm or ideation.<h4>Results</h4>Over one in six children (17.2%, <i>n</i>\u00a0=\u00a085,792) were currently or previously in contact with social services, and almost one child in every 20 (4.8%, <i>n</i>\u00a0=\u00a023,975) had contact in 2015. Likelihood of any mental ill health outcome increased incrementally with the level of contact with social services relative to unexposed peers: NIN (OR 5.90 [95% confidence interval (CI) 5.10-6.83]), CIN (OR 5.99 [95% CI 5.50-6.53]) and CIC (OR 12.60 [95% CI 10.63-14.95]). All tiers of contact, number of referrals, number of care episodes and placement type were strongly associated with the likelihood of mental ill health.<h4>Conclusion</h4>Children who have contact with social services account for a large and disproportionate amount of mental ill health in the child population. Likelihood of poor mental health across indicators is highest in care experienced children but also extends to the much larger population of children in contact with social services but never in care. Findings suggest a need for targeted mental health screening and enhanced support for all children in contact with social services.",
-    "laySummary": "",
-    "urls": "pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/A60E6D761449A937DCE08F3A075B236D/S2045796023000276a.pdf/div-class-title-the-mental-health-of-all-children-in-contact-with-social-services-a-population-wide-record-linkage-study-in-northern-ireland-div.pdf; doi:https://doi.org/10.1017/S2045796023000276; html:https://europepmc.org/articles/PMC10227534; pdf:https://europepmc.org/articles/PMC10227534?pdf=render"
-  },
   {
     "id": "32524641",
     "doi": "https://doi.org/10.1002/sim.8556",
@@ -28015,6 +28032,23 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/sim.8556; doi:https://doi.org/10.1002/sim.8556; html:https://europepmc.org/articles/PMC8432147; pdf:https://europepmc.org/articles/PMC8432147?pdf=render"
   },
+  {
+    "id": "37190768",
+    "doi": "https://doi.org/10.1017/s2045796023000276",
+    "title": "The mental health of all children in contact with social services: a population-wide record-linkage study in Northern Ireland.",
+    "authorString": "McKenna S, O'Reilly D, Maguire A.",
+    "authorAffiliations": "",
+    "journalTitle": "Epidemiology and psychiatric sciences",
+    "pubYear": "2023",
+    "date": "2023-05-16",
+    "isOpenAccess": "Y",
+    "keywords": "Mental health; Data Linkage; Children\u2019s Social Care",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Aims</h4>Children in contact with social services are at high risk for mental ill health, but it is not known what proportion of the child population has contact with social services or how risk varies within this group compared to unexposed peers. We aim to quantify the extent and nature of contact with social services within the child population in Northern Ireland (NI) and the association with mental ill health. We also examine which social care experiences identify those most at risk.<h4>Methods</h4>This is a population-based record-linkage study of 497,269 children (aged under 18\u00a0years) alive and resident in NI in 2015 using routinely collected health and social care data. Exposure was categorized as (1) no contact, (2) referred but assessed as not in need (NIN), (3) child in need (CIN) and (4) child in care (CIC). Multilevel logistic regression analyses estimated odds ratios (ORs) for mental ill health indicated by receipt of psychotropic medication (antidepressants, anxiolytics, antipsychotics and hypnotics), psychiatric hospital admission and hospital-presenting self-harm or ideation.<h4>Results</h4>Over one in six children (17.2%, <i>n</i>\u00a0=\u00a085,792) were currently or previously in contact with social services, and almost one child in every 20 (4.8%, <i>n</i>\u00a0=\u00a023,975) had contact in 2015. Likelihood of any mental ill health outcome increased incrementally with the level of contact with social services relative to unexposed peers: NIN (OR 5.90 [95% confidence interval (CI) 5.10-6.83]), CIN (OR 5.99 [95% CI 5.50-6.53]) and CIC (OR 12.60 [95% CI 10.63-14.95]). All tiers of contact, number of referrals, number of care episodes and placement type were strongly associated with the likelihood of mental ill health.<h4>Conclusion</h4>Children who have contact with social services account for a large and disproportionate amount of mental ill health in the child population. Likelihood of poor mental health across indicators is highest in care experienced children but also extends to the much larger population of children in contact with social services but never in care. Findings suggest a need for targeted mental health screening and enhanced support for all children in contact with social services.",
+    "laySummary": "",
+    "urls": "pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/A60E6D761449A937DCE08F3A075B236D/S2045796023000276a.pdf/div-class-title-the-mental-health-of-all-children-in-contact-with-social-services-a-population-wide-record-linkage-study-in-northern-ireland-div.pdf; doi:https://doi.org/10.1017/S2045796023000276; html:https://europepmc.org/articles/PMC10227534; pdf:https://europepmc.org/articles/PMC10227534?pdf=render"
+  },
   {
     "id": "38345865",
     "doi": "https://doi.org/10.1113/jp284597",
@@ -28253,23 +28287,6 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ejhf.3339; doi:https://doi.org/10.1002/ejhf.3339"
   },
-  {
-    "id": "33033797",
-    "doi": "https://doi.org/10.1016/j.eclinm.2020.100560",
-    "title": "Investigating the effects of comprehensive smoke-free legislation on neonatal and infant mortality in Thailand using the synthetic control method.",
-    "authorString": "Rad\u00f3 MK, van Lenthe FJ, Sheikh A, Been JV.",
-    "authorAffiliations": "",
-    "journalTitle": "EClinicalMedicine",
-    "pubYear": "2020",
-    "date": "2020-10-02",
-    "isOpenAccess": "Y",
-    "keywords": "Thailand; Infant Mortality; Child Health; Smoke-free Legislation; Synthetic Control Method",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Almost all of the evidence on the benefits of smoke-free legislation on child health comes from evaluations in high-income countries. We investigated the effects of Thailand's 2010 comprehensive smoke-free legislation on neonatal and infant mortality.<h4>Methods</h4>To overcome some of the methodological issues inherent to traditional quasi-experimental methods, we applied the novel synthetic control approach. Using 2001-2017 country-level panel data from the World Bank and Penn World datasets, we estimated the effects of smoke-free legislation as the difference between the outcome trends in Thailand versus those in a synthetic control country. The synthetic control country was composed of 'control' middle-income countries without comprehensive smoke-free legislation to recreate trends in Thailand in the 2001-2009 pre-legislation outcomes and covariates. We compared the legislation effects to 'placebo effects' obtained for each control country by fictitiously assuming that comprehensive smoke-free legislation was introduced there in 2010, similar to Thailand.<h4>Findings</h4>Neonatal and infant mortality decreased by 2.9% and 2.8%/year respectively following smoke-free legislation, with an estimated 7463 infant deaths (including 4623 neonatal deaths) having been averted over eight years. The results were robust to different specifications of the control countries. Comparison with placebo effects indicated that the findings were unlikely to be attributable to factors other than the smoke-free legislation.<h4>Interpretation</h4>Expanding comprehensive smoke-free policies to middle-income countries can support national efforts to achieve Sustainable Development Goal 3.2 for reducing preventable early-life deaths.<h4>Funding</h4>Netherlands Lung Foundation, HDRUK, Asthma UK center for Applied Research and NIHR Global Respiratory Health Unit (RESPIRE).",
-    "laySummary": "",
-    "urls": "pdf:http://www.thelancet.com/article/S2589537020303047/pdf; doi:https://doi.org/10.1016/j.eclinm.2020.100560; html:https://europepmc.org/articles/PMC7533363; pdf:https://europepmc.org/articles/PMC7533363?pdf=render"
-  },
   {
     "id": "35259281",
     "doi": "https://doi.org/10.1111/acel.13524",
@@ -28287,6 +28304,23 @@
     "laySummary": "",
     "urls": "pdf:https://discovery.ucl.ac.uk/10145565/1/Hignorani_Biological%20mechanisms%20of%20aging%20predict%20age-related%20disease%20co-occurrence%20in%20patients_AOP.pdf; doi:https://doi.org/10.1111/acel.13524; html:https://europepmc.org/articles/PMC9009120; pdf:https://europepmc.org/articles/PMC9009120?pdf=render"
   },
+  {
+    "id": "34873059",
+    "doi": "https://doi.org/10.1073/pnas.2108395118",
+    "title": "How immunity from and interaction with seasonal coronaviruses can shape SARS-CoV-2 epidemiology.",
+    "authorString": "Waterlow NR, van Leeuwen E, Davies NG, CMMID COVID-19 Working Group, Flasche S, Eggo RM.",
+    "authorAffiliations": "",
+    "journalTitle": "Proceedings of the National Academy of Sciences of the United States of America",
+    "pubYear": "2021",
+    "date": "2021-12-01",
+    "isOpenAccess": "Y",
+    "keywords": "Immunity; Coronaviruses; Cross-protection; Covid-19; Sars-cov-2",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "We hypothesized that cross-protection from seasonal epidemics of human coronaviruses (HCoVs) could have affected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, including generating reduced susceptibility in children. To determine what the prepandemic distribution of immunity to HCoVs was, we fitted a mathematical model to 6 y of seasonal coronavirus surveillance data from England and Wales. We estimated a duration of immunity to seasonal HCoVs of 7.8 y (95% CI 6.3 to 8.1) and show that, while cross-protection between HCoV and SARS-CoV-2 may contribute to the age distribution, it is insufficient to explain the age pattern of SARS-CoV-2 infections in the first wave of the pandemic in England and Wales. Projections from our model illustrate how different strengths of cross-protection between circulating coronaviruses could determine the frequency and magnitude of SARS-CoV-2 epidemics over the coming decade, as well as the potential impact of cross-protection on future seasonal coronavirus transmission.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1073/pnas.2108395118; doi:https://doi.org/10.1073/pnas.2108395118; html:https://europepmc.org/articles/PMC8670441; pdf:https://europepmc.org/articles/PMC8670441?pdf=render"
+  },
   {
     "id": "PMC9023380",
     "doi": "https://doi.org/",
@@ -28305,21 +28339,21 @@
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9023380/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9023380/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC9023380; pdf:https://europepmc.org/articles/PMC9023380?pdf=render"
   },
   {
-    "id": "34873059",
-    "doi": "https://doi.org/10.1073/pnas.2108395118",
-    "title": "How immunity from and interaction with seasonal coronaviruses can shape SARS-CoV-2 epidemiology.",
-    "authorString": "Waterlow NR, van Leeuwen E, Davies NG, CMMID COVID-19 Working Group, Flasche S, Eggo RM.",
+    "id": "33033797",
+    "doi": "https://doi.org/10.1016/j.eclinm.2020.100560",
+    "title": "Investigating the effects of comprehensive smoke-free legislation on neonatal and infant mortality in Thailand using the synthetic control method.",
+    "authorString": "Rad\u00f3 MK, van Lenthe FJ, Sheikh A, Been JV.",
     "authorAffiliations": "",
-    "journalTitle": "Proceedings of the National Academy of Sciences of the United States of America",
-    "pubYear": "2021",
-    "date": "2021-12-01",
+    "journalTitle": "EClinicalMedicine",
+    "pubYear": "2020",
+    "date": "2020-10-02",
     "isOpenAccess": "Y",
-    "keywords": "Immunity; Coronaviruses; Cross-protection; Covid-19; Sars-cov-2",
+    "keywords": "Thailand; Infant Mortality; Child Health; Smoke-free Legislation; Synthetic Control Method",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "We hypothesized that cross-protection from seasonal epidemics of human coronaviruses (HCoVs) could have affected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, including generating reduced susceptibility in children. To determine what the prepandemic distribution of immunity to HCoVs was, we fitted a mathematical model to 6 y of seasonal coronavirus surveillance data from England and Wales. We estimated a duration of immunity to seasonal HCoVs of 7.8 y (95% CI 6.3 to 8.1) and show that, while cross-protection between HCoV and SARS-CoV-2 may contribute to the age distribution, it is insufficient to explain the age pattern of SARS-CoV-2 infections in the first wave of the pandemic in England and Wales. Projections from our model illustrate how different strengths of cross-protection between circulating coronaviruses could determine the frequency and magnitude of SARS-CoV-2 epidemics over the coming decade, as well as the potential impact of cross-protection on future seasonal coronavirus transmission.",
+    "abstract": "<h4>Background</h4>Almost all of the evidence on the benefits of smoke-free legislation on child health comes from evaluations in high-income countries. We investigated the effects of Thailand's 2010 comprehensive smoke-free legislation on neonatal and infant mortality.<h4>Methods</h4>To overcome some of the methodological issues inherent to traditional quasi-experimental methods, we applied the novel synthetic control approach. Using 2001-2017 country-level panel data from the World Bank and Penn World datasets, we estimated the effects of smoke-free legislation as the difference between the outcome trends in Thailand versus those in a synthetic control country. The synthetic control country was composed of 'control' middle-income countries without comprehensive smoke-free legislation to recreate trends in Thailand in the 2001-2009 pre-legislation outcomes and covariates. We compared the legislation effects to 'placebo effects' obtained for each control country by fictitiously assuming that comprehensive smoke-free legislation was introduced there in 2010, similar to Thailand.<h4>Findings</h4>Neonatal and infant mortality decreased by 2.9% and 2.8%/year respectively following smoke-free legislation, with an estimated 7463 infant deaths (including 4623 neonatal deaths) having been averted over eight years. The results were robust to different specifications of the control countries. Comparison with placebo effects indicated that the findings were unlikely to be attributable to factors other than the smoke-free legislation.<h4>Interpretation</h4>Expanding comprehensive smoke-free policies to middle-income countries can support national efforts to achieve Sustainable Development Goal 3.2 for reducing preventable early-life deaths.<h4>Funding</h4>Netherlands Lung Foundation, HDRUK, Asthma UK center for Applied Research and NIHR Global Respiratory Health Unit (RESPIRE).",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1073/pnas.2108395118; doi:https://doi.org/10.1073/pnas.2108395118; html:https://europepmc.org/articles/PMC8670441; pdf:https://europepmc.org/articles/PMC8670441?pdf=render"
+    "urls": "pdf:http://www.thelancet.com/article/S2589537020303047/pdf; doi:https://doi.org/10.1016/j.eclinm.2020.100560; html:https://europepmc.org/articles/PMC7533363; pdf:https://europepmc.org/articles/PMC7533363?pdf=render"
   },
   {
     "id": "32817390",
@@ -28389,6 +28423,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ndt/advance-article-pdf/doi/10.1093/ndt/gfac224/45505736/gfac224.pdf; doi:https://doi.org/10.1093/ndt/gfac224; html:https://europepmc.org/articles/PMC10157789; pdf:https://europepmc.org/articles/PMC10157789?pdf=render"
   },
+  {
+    "id": "36711167",
+    "doi": "https://doi.org/10.1093/ehjdh/ztaa016",
+    "title": "Real-time imputation of missing predictor values in clinical practice.",
+    "authorString": "Nijman SWJ, Hoogland J, Groenhof TKJ, Brandjes M, Jacobs JJL, Bots ML, Asselbergs FW, Moons KGM, Debray TPA.",
+    "authorAffiliations": "",
+    "journalTitle": "European heart journal. Digital health",
+    "pubYear": "2021",
+    "date": "2020-12-19",
+    "isOpenAccess": "Y",
+    "keywords": "Prediction; Missing Data; Electronic Health Records; Computerized Decision Support System; Real-time Imputation; Joint Modelling Imputation",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Aims</h4>Use of prediction models is widely recommended by clinical guidelines, but usually requires complete information on all predictors, which is not always available in daily practice. We aim to describe two methods for real-time handling of missing predictor values when using prediction models in practice.<h4>Methods and results</h4>We compare the widely used method of mean imputation (M-imp) to a method that personalizes the imputations by taking advantage of the observed patient characteristics. These characteristics may include both prediction model variables and other characteristics (auxiliary variables). The method was implemented using imputation from a joint multivariate normal model of the patient characteristics (joint modelling imputation; JMI). Data from two different cardiovascular cohorts with cardiovascular predictors and outcome were used to evaluate the real-time imputation methods. We quantified the prediction model's overall performance [mean squared error (MSE) of linear predictor], discrimination (c-index), calibration (intercept and slope), and net benefit (decision curve analysis). When compared with mean imputation, JMI substantially improved the MSE (0.10 vs. 0.13), c-index (0.70 vs. 0.68), and calibration (calibration-in-the-large: 0.04 vs. 0.06; calibration slope: 1.01 vs. 0.92), especially when incorporating auxiliary variables. When the imputation method was based on an external cohort, calibration deteriorated, but discrimination remained similar.<h4>Conclusions</h4>We recommend JMI with auxiliary variables for real-time imputation of missing values, and to update imputation models when implementing them in new settings or (sub)populations.",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/ehjdh/article-pdf/2/1/154/37807088/ztaa016.pdf; doi:https://doi.org/10.1093/ehjdh/ztaa016; html:https://europepmc.org/articles/PMC9707891; pdf:https://europepmc.org/articles/PMC9707891?pdf=render"
+  },
   {
     "id": "35842920",
     "doi": "https://doi.org/10.1002/ehf2.14073",
@@ -28407,21 +28458,21 @@
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ehf2.14073; doi:https://doi.org/10.1002/ehf2.14073; html:https://europepmc.org/articles/PMC9715795; pdf:https://europepmc.org/articles/PMC9715795?pdf=render"
   },
   {
-    "id": "36711167",
-    "doi": "https://doi.org/10.1093/ehjdh/ztaa016",
-    "title": "Real-time imputation of missing predictor values in clinical practice.",
-    "authorString": "Nijman SWJ, Hoogland J, Groenhof TKJ, Brandjes M, Jacobs JJL, Bots ML, Asselbergs FW, Moons KGM, Debray TPA.",
+    "id": "34769922",
+    "doi": "https://doi.org/10.3390/ijerph182111380",
+    "title": "Driver, Collision and Meteorological Characteristics of Motor Vehicle Collisions among Road Trauma Survivors.",
+    "authorString": "Giummarra MJ, Xu R, Guo Y, Dipnall JF, Ponsford J, Cameron PA, Ameratunga S, Gabbe BJ.",
     "authorAffiliations": "",
-    "journalTitle": "European heart journal. Digital health",
+    "journalTitle": "International journal of environmental research and public health",
     "pubYear": "2021",
-    "date": "2020-12-19",
+    "date": "2021-10-29",
     "isOpenAccess": "Y",
-    "keywords": "Prediction; Missing Data; Electronic Health Records; Computerized Decision Support System; Real-time Imputation; Joint Modelling Imputation",
+    "keywords": "Trauma; Prevention; Traffic; Motor Vehicle",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Aims</h4>Use of prediction models is widely recommended by clinical guidelines, but usually requires complete information on all predictors, which is not always available in daily practice. We aim to describe two methods for real-time handling of missing predictor values when using prediction models in practice.<h4>Methods and results</h4>We compare the widely used method of mean imputation (M-imp) to a method that personalizes the imputations by taking advantage of the observed patient characteristics. These characteristics may include both prediction model variables and other characteristics (auxiliary variables). The method was implemented using imputation from a joint multivariate normal model of the patient characteristics (joint modelling imputation; JMI). Data from two different cardiovascular cohorts with cardiovascular predictors and outcome were used to evaluate the real-time imputation methods. We quantified the prediction model's overall performance [mean squared error (MSE) of linear predictor], discrimination (c-index), calibration (intercept and slope), and net benefit (decision curve analysis). When compared with mean imputation, JMI substantially improved the MSE (0.10 vs. 0.13), c-index (0.70 vs. 0.68), and calibration (calibration-in-the-large: 0.04 vs. 0.06; calibration slope: 1.01 vs. 0.92), especially when incorporating auxiliary variables. When the imputation method was based on an external cohort, calibration deteriorated, but discrimination remained similar.<h4>Conclusions</h4>We recommend JMI with auxiliary variables for real-time imputation of missing values, and to update imputation models when implementing them in new settings or (sub)populations.",
+    "abstract": "Road trauma remains a significant public health problem. We aimed to identify sub-groups of motor vehicle collisions in Victoria, Australia, and the association between collision characteristics and outcomes up to 24 months post-injury. Data were extracted from the Victorian State Trauma Registry for injured drivers aged \u226516 years, from 2010 to 2016, with a compensation claim who survived \u226512 months post-injury. People with intentional or severe head injury were excluded, resulting in 2735 cases. Latent class analysis was used to identify collision classes for driver fault and blood alcohol concentration (BAC), day and time of collision, weather conditions, single vs. multi-vehicle and regional vs. metropolitan injury location. Five classes were identified: (1) daytime multi-vehicle collisions, no other at fault; (2) daytime single-vehicle predominantly weekday collisions; (3) evening single-vehicle collisions, no other at fault, 36% with BAC \u2265 0.05; (4) sunrise or sunset weekday collisions; and (5) dusk and evening multi-vehicle in metropolitan areas with BAC < 0.05. Mixed linear and logistic regression analyses examined associations between collision class and return to work, health (EQ-5D-3L summary score) and independent function Glasgow Outcome Scale - Extended at 6, 12 and 24 months. After adjusting for demographic, health and injury characteristics, collision class was not associated with outcomes. Rather, risk of poor outcomes was associated with age, sex and socioeconomic disadvantage, education, pre-injury health and injury severity. People at risk of poor recovery may be identified from factors available during the hospital admission and may benefit from clinical assessment and targeted referrals and treatments.",
     "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/ehjdh/article-pdf/2/1/154/37807088/ztaa016.pdf; doi:https://doi.org/10.1093/ehjdh/ztaa016; html:https://europepmc.org/articles/PMC9707891; pdf:https://europepmc.org/articles/PMC9707891?pdf=render"
+    "urls": "pdf:https://www.mdpi.com/1660-4601/18/21/11380/pdf?version=1635513758; doi:https://doi.org/10.3390/ijerph182111380; html:https://europepmc.org/articles/PMC8583338; pdf:https://europepmc.org/articles/PMC8583338?pdf=render"
   },
   {
     "id": "32738956",
@@ -28440,23 +28491,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/S0140-6736(20)31286-1"
   },
-  {
-    "id": "34769922",
-    "doi": "https://doi.org/10.3390/ijerph182111380",
-    "title": "Driver, Collision and Meteorological Characteristics of Motor Vehicle Collisions among Road Trauma Survivors.",
-    "authorString": "Giummarra MJ, Xu R, Guo Y, Dipnall JF, Ponsford J, Cameron PA, Ameratunga S, Gabbe BJ.",
-    "authorAffiliations": "",
-    "journalTitle": "International journal of environmental research and public health",
-    "pubYear": "2021",
-    "date": "2021-10-29",
-    "isOpenAccess": "Y",
-    "keywords": "Trauma; Prevention; Traffic; Motor Vehicle",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Road trauma remains a significant public health problem. We aimed to identify sub-groups of motor vehicle collisions in Victoria, Australia, and the association between collision characteristics and outcomes up to 24 months post-injury. Data were extracted from the Victorian State Trauma Registry for injured drivers aged \u226516 years, from 2010 to 2016, with a compensation claim who survived \u226512 months post-injury. People with intentional or severe head injury were excluded, resulting in 2735 cases. Latent class analysis was used to identify collision classes for driver fault and blood alcohol concentration (BAC), day and time of collision, weather conditions, single vs. multi-vehicle and regional vs. metropolitan injury location. Five classes were identified: (1) daytime multi-vehicle collisions, no other at fault; (2) daytime single-vehicle predominantly weekday collisions; (3) evening single-vehicle collisions, no other at fault, 36% with BAC \u2265 0.05; (4) sunrise or sunset weekday collisions; and (5) dusk and evening multi-vehicle in metropolitan areas with BAC < 0.05. Mixed linear and logistic regression analyses examined associations between collision class and return to work, health (EQ-5D-3L summary score) and independent function Glasgow Outcome Scale - Extended at 6, 12 and 24 months. After adjusting for demographic, health and injury characteristics, collision class was not associated with outcomes. Rather, risk of poor outcomes was associated with age, sex and socioeconomic disadvantage, education, pre-injury health and injury severity. People at risk of poor recovery may be identified from factors available during the hospital admission and may benefit from clinical assessment and targeted referrals and treatments.",
-    "laySummary": "",
-    "urls": "pdf:https://www.mdpi.com/1660-4601/18/21/11380/pdf?version=1635513758; doi:https://doi.org/10.3390/ijerph182111380; html:https://europepmc.org/articles/PMC8583338; pdf:https://europepmc.org/articles/PMC8583338?pdf=render"
-  },
   {
     "id": "38170504",
     "doi": "https://doi.org/10.1001/jamacardio.2023.4994",
@@ -28525,23 +28559,6 @@
     "laySummary": "",
     "urls": "pdf:https://informatics.bmj.com/content/bmjhci/28/1/e100385.full.pdf; doi:https://doi.org/10.1136/bmjhci-2021-100385; html:https://europepmc.org/articles/PMC8383863; pdf:https://europepmc.org/articles/PMC8383863?pdf=render"
   },
-  {
-    "id": "38326875",
-    "doi": "https://doi.org/10.1186/s13059-024-03172-3",
-    "title": "IDHwt glioblastomas can be stratified by their transcriptional response to standard treatment, with implications for targeted therapy.",
-    "authorString": "Tanner G, Barrow R, Ajaib S, Al-Jabri M, Ahmed N, Pollock S, Finetti M, Rippaus N, Bruns AF, Syed K, Poulter JA, Matthews L, Hughes T, Wilson E, Johnson C, Varn FS, Br\u00fcning-Richardson A, Hogg C, Droop A, Gusnanto A, Care MA, Cutillo L, Westhead DR, Short SC, Jenkinson MD, Brodbelt A, Chakrabarty A, Ismail A, Verhaak RGW, Stead LF.",
-    "authorAffiliations": "",
-    "journalTitle": "Genome biology",
-    "pubYear": "2024",
-    "date": "2024-02-07",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Glioblastoma (GBM) brain tumors lacking IDH1 mutations (IDHwt) have the worst prognosis of all brain neoplasms. Patients receive surgery and chemoradiotherapy but tumors almost always fatally recur.<h4>Results</h4>Using RNA sequencing data from 107 pairs of pre- and post-standard treatment locally recurrent IDHwt GBM tumors, we identify two responder subtypes based on longitudinal changes in gene expression. In two thirds of patients, a specific subset of genes is upregulated from primary to recurrence (Up responders), and in one third, the same genes are downregulated (Down responders), specifically in neoplastic cells. Characterization of the responder subtypes indicates subtype-specific adaptive treatment resistance mechanisms that are associated with distinct changes in the tumor microenvironment. In Up responders, recurrent tumors are enriched in quiescent proneural GBM stem cells and differentiated neoplastic cells, with increased interaction with the surrounding normal brain and neurotransmitter signaling, whereas Down responders commonly undergo mesenchymal transition. ChIP-sequencing data from longitudinal GBM tumors suggests that the observed transcriptional reprogramming could be driven by Polycomb-based chromatin remodeling rather than DNA methylation.<h4>Conclusions</h4>We show that the responder subtype is cancer-cell intrinsic, recapitulated in in vitro GBM cell models, and influenced by the presence of the tumor microenvironment. Stratifying GBM tumors by responder subtype may lead to more effective treatment.",
-    "laySummary": "",
-    "urls": "pdf:https://genomebiology.biomedcentral.com/counter/pdf/10.1186/s13059-024-03172-3; doi:https://doi.org/10.1186/s13059-024-03172-3; html:https://europepmc.org/articles/PMC10848526; pdf:https://europepmc.org/articles/PMC10848526?pdf=render"
-  },
   {
     "id": "34018481",
     "doi": "https://doi.org/10.2807/1560-7917.es.2021.26.20.2100428",
@@ -28559,23 +28576,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.eurosurveillance.org/deliver/fulltext/eurosurveillance/26/20/eurosurv-26-20-1.pdf?itemId=%2Fcontent%2F10.2807%2F1560-7917.ES.2021.26.20.2100428&mimeType=pdf&containerItemId=content/eurosurveillance; doi:https://doi.org/10.2807/1560-7917.ES.2021.26.20.2100428; html:https://europepmc.org/articles/PMC8138959; pdf:https://europepmc.org/articles/PMC8138959?pdf=render"
   },
-  {
-    "id": "34429368",
-    "doi": "https://doi.org/10.1136/heartjnl-2021-319566",
-    "title": "Sex disparity in subsequent outcomes in survivors of coronary heart disease.",
-    "authorString": "Akyea RK, Kontopantelis E, Kai J, Weng SF, Patel RS, Asselbergs FW, Qureshi N.",
-    "authorAffiliations": "",
-    "journalTitle": "Heart (British Cardiac Society)",
-    "pubYear": "2022",
-    "date": "2021-08-24",
-    "isOpenAccess": "N",
-    "keywords": "Sex difference; Coronary Heart Disease; Secondary Prevention; Competing Risks; Major Adverse Cardiovascular Events",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objective</h4>Evidence on sex differences in outcomes after developing coronary heart disease (CHD) has focused on recurrent CHD, all-cause mortality or revascularisation. We assessed sex disparities in subsequent major adverse cardiovascular events (MACE) in adults surviving their first-time CHD.<h4>Methods</h4>Using a population-based cohort obtained from the Clinical Practice Research Datalink (CPRD GOLD) linked to hospitalisation and death records in the UK, we identified 143\u2009702 adults (aged \u226518 years) between 1 January 1998 and 31 December 2017 with no prior history of MACE. MACE outcome was a composite of recurrent CHD, stroke, peripheral vascular disease, heart failure and cardiovascular-related mortality. Multivariable models (Cox and competing risks regressions) were used to assess differences between sexes.<h4>Results</h4>There were 143\u2009702 adults with any incident CHD (either angina, myocardial infarction or coronary revascularisation). Women (n=63\u2009078, 43.9%) were older than men (median age, 73 vs 66 years). First subsequent MACE outcome was observed in 91\u2009706 (63.8%). Women had a significantly lower risk of MACE (hazard ratio (HR), 0.68 (95% CI 0.67 to 0.69); sub-hazard ratio (HRsd), 0.71 (0.70 to 0.72), respectively) and recurrent CHD (n=66\u2009543, 46.3%) (HR, 0.60 (0.59 to 0.61); HRsd, 0.62 (0.61 to 0.63)) when compared with men after incident CHD. However, women had a significantly higher risk of stroke (n=5740, 4.0%) (HR, 1.26 (1.19 to 1.33); HRsd, 1.32 (1.25 to 1.39)), heart failure (n=7905, 5.5%) (HR, 1.09 (1.04 to 1.15); HRsd, 1.13 (1.07 to 1.18)) and all-cause mortality (n=29\u2009503, 20.5%) (HR, 1.05 (1.02 to 1.07); HRsd, 1.11 (1.08 to 1.13)).<h4>Conclusions</h4>After incident CHD, women have lower risk of composite MACE and recurrent CHD outcomes but higher risk of stroke, heart failure, and all-cause mortality compared with men.",
-    "laySummary": "",
-    "urls": "pdf:https://heart.bmj.com/content/heartjnl/108/1/37.full.pdf; doi:https://doi.org/10.1136/heartjnl-2021-319566"
-  },
   {
     "id": "35351727",
     "doi": "https://doi.org/10.1136/bmjopen-2021-057909",
@@ -28594,21 +28594,38 @@
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/3/e057909.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-057909; html:https://europepmc.org/articles/PMC8961119; pdf:https://europepmc.org/articles/PMC8961119?pdf=render"
   },
   {
-    "id": "37519214",
-    "doi": "https://doi.org/10.1177/09622802231188518",
-    "title": "Multiple imputation approaches for epoch-level accelerometer data in trials.",
-    "authorString": "Tackney MS, Williamson E, Cook DG, Limb E, Harris T, Carpenter J.",
+    "id": "34429368",
+    "doi": "https://doi.org/10.1136/heartjnl-2021-319566",
+    "title": "Sex disparity in subsequent outcomes in survivors of coronary heart disease.",
+    "authorString": "Akyea RK, Kontopantelis E, Kai J, Weng SF, Patel RS, Asselbergs FW, Qureshi N.",
     "authorAffiliations": "",
-    "journalTitle": "Statistical methods in medical research",
-    "pubYear": "2023",
-    "date": "2023-07-31",
+    "journalTitle": "Heart (British Cardiac Society)",
+    "pubYear": "2022",
+    "date": "2021-08-24",
+    "isOpenAccess": "N",
+    "keywords": "Sex difference; Coronary Heart Disease; Secondary Prevention; Competing Risks; Major Adverse Cardiovascular Events",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>Evidence on sex differences in outcomes after developing coronary heart disease (CHD) has focused on recurrent CHD, all-cause mortality or revascularisation. We assessed sex disparities in subsequent major adverse cardiovascular events (MACE) in adults surviving their first-time CHD.<h4>Methods</h4>Using a population-based cohort obtained from the Clinical Practice Research Datalink (CPRD GOLD) linked to hospitalisation and death records in the UK, we identified 143\u2009702 adults (aged \u226518 years) between 1 January 1998 and 31 December 2017 with no prior history of MACE. MACE outcome was a composite of recurrent CHD, stroke, peripheral vascular disease, heart failure and cardiovascular-related mortality. Multivariable models (Cox and competing risks regressions) were used to assess differences between sexes.<h4>Results</h4>There were 143\u2009702 adults with any incident CHD (either angina, myocardial infarction or coronary revascularisation). Women (n=63\u2009078, 43.9%) were older than men (median age, 73 vs 66 years). First subsequent MACE outcome was observed in 91\u2009706 (63.8%). Women had a significantly lower risk of MACE (hazard ratio (HR), 0.68 (95% CI 0.67 to 0.69); sub-hazard ratio (HRsd), 0.71 (0.70 to 0.72), respectively) and recurrent CHD (n=66\u2009543, 46.3%) (HR, 0.60 (0.59 to 0.61); HRsd, 0.62 (0.61 to 0.63)) when compared with men after incident CHD. However, women had a significantly higher risk of stroke (n=5740, 4.0%) (HR, 1.26 (1.19 to 1.33); HRsd, 1.32 (1.25 to 1.39)), heart failure (n=7905, 5.5%) (HR, 1.09 (1.04 to 1.15); HRsd, 1.13 (1.07 to 1.18)) and all-cause mortality (n=29\u2009503, 20.5%) (HR, 1.05 (1.02 to 1.07); HRsd, 1.11 (1.08 to 1.13)).<h4>Conclusions</h4>After incident CHD, women have lower risk of composite MACE and recurrent CHD outcomes but higher risk of stroke, heart failure, and all-cause mortality compared with men.",
+    "laySummary": "",
+    "urls": "pdf:https://heart.bmj.com/content/heartjnl/108/1/37.full.pdf; doi:https://doi.org/10.1136/heartjnl-2021-319566"
+  },
+  {
+    "id": "38326875",
+    "doi": "https://doi.org/10.1186/s13059-024-03172-3",
+    "title": "IDHwt glioblastomas can be stratified by their transcriptional response to standard treatment, with implications for targeted therapy.",
+    "authorString": "Tanner G, Barrow R, Ajaib S, Al-Jabri M, Ahmed N, Pollock S, Finetti M, Rippaus N, Bruns AF, Syed K, Poulter JA, Matthews L, Hughes T, Wilson E, Johnson C, Varn FS, Br\u00fcning-Richardson A, Hogg C, Droop A, Gusnanto A, Care MA, Cutillo L, Westhead DR, Short SC, Jenkinson MD, Brodbelt A, Chakrabarty A, Ismail A, Verhaak RGW, Stead LF.",
+    "authorAffiliations": "",
+    "journalTitle": "Genome biology",
+    "pubYear": "2024",
+    "date": "2024-02-07",
     "isOpenAccess": "Y",
-    "keywords": "Missing Data; Accelerometer; Multiple Imputation; Wearables; Physical Activity Trial",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Clinical trials that investigate physical activity interventions often use accelerometers to measure step count at a very granular level, for example in 5-second epochs. Participants typically wear the accelerometer for a week-long period at baseline, and for one or more week-long follow-up periods after the intervention. The data is aggregated to provide daily or weekly step counts for the primary analysis. Missing data are common as participants may not wear the device as per protocol. Approaches to handling missing data in the literature have defined missingness on the day level using a threshold on daily weartime, which leads to loss of information on the time of day when data are missing. We propose an approach to identifying and classifying missingness at the finer epoch-level and present two approaches to handling missingness using multiple imputation. Firstly, we present a parametric approach which accounts for the number of missing epochs per day. Secondly, we describe a non-parametric approach where missing periods during the day are replaced by donor data from the same person where possible, or data from a different person who is matched on demographic and physical activity-related variables. Our simulation studies show that the non-parametric approach leads to estimates of the effect of treatment that are least biased while maintaining small standard errors. We illustrate the application of these different multiple imputation strategies to the analysis of the 2017 PACE-UP trial. The proposed framework is likely to be applicable to other digital health outcomes and to other wearable devices.",
+    "abstract": "<h4>Background</h4>Glioblastoma (GBM) brain tumors lacking IDH1 mutations (IDHwt) have the worst prognosis of all brain neoplasms. Patients receive surgery and chemoradiotherapy but tumors almost always fatally recur.<h4>Results</h4>Using RNA sequencing data from 107 pairs of pre- and post-standard treatment locally recurrent IDHwt GBM tumors, we identify two responder subtypes based on longitudinal changes in gene expression. In two thirds of patients, a specific subset of genes is upregulated from primary to recurrence (Up responders), and in one third, the same genes are downregulated (Down responders), specifically in neoplastic cells. Characterization of the responder subtypes indicates subtype-specific adaptive treatment resistance mechanisms that are associated with distinct changes in the tumor microenvironment. In Up responders, recurrent tumors are enriched in quiescent proneural GBM stem cells and differentiated neoplastic cells, with increased interaction with the surrounding normal brain and neurotransmitter signaling, whereas Down responders commonly undergo mesenchymal transition. ChIP-sequencing data from longitudinal GBM tumors suggests that the observed transcriptional reprogramming could be driven by Polycomb-based chromatin remodeling rather than DNA methylation.<h4>Conclusions</h4>We show that the responder subtype is cancer-cell intrinsic, recapitulated in in vitro GBM cell models, and influenced by the presence of the tumor microenvironment. Stratifying GBM tumors by responder subtype may lead to more effective treatment.",
     "laySummary": "",
-    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/09622802231188518; doi:https://doi.org/10.1177/09622802231188518; html:https://europepmc.org/articles/PMC10563375; pdf:https://europepmc.org/articles/PMC10563375?pdf=render"
+    "urls": "pdf:https://genomebiology.biomedcentral.com/counter/pdf/10.1186/s13059-024-03172-3; doi:https://doi.org/10.1186/s13059-024-03172-3; html:https://europepmc.org/articles/PMC10848526; pdf:https://europepmc.org/articles/PMC10848526?pdf=render"
   },
   {
     "id": "35504525",
@@ -28644,6 +28661,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.123.031646; doi:https://doi.org/10.1161/JAHA.123.031646; html:https://europepmc.org/articles/PMC10926784; pdf:https://europepmc.org/articles/PMC10926784?pdf=render"
   },
+  {
+    "id": "37519214",
+    "doi": "https://doi.org/10.1177/09622802231188518",
+    "title": "Multiple imputation approaches for epoch-level accelerometer data in trials.",
+    "authorString": "Tackney MS, Williamson E, Cook DG, Limb E, Harris T, Carpenter J.",
+    "authorAffiliations": "",
+    "journalTitle": "Statistical methods in medical research",
+    "pubYear": "2023",
+    "date": "2023-07-31",
+    "isOpenAccess": "Y",
+    "keywords": "Missing Data; Accelerometer; Multiple Imputation; Wearables; Physical Activity Trial",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Clinical trials that investigate physical activity interventions often use accelerometers to measure step count at a very granular level, for example in 5-second epochs. Participants typically wear the accelerometer for a week-long period at baseline, and for one or more week-long follow-up periods after the intervention. The data is aggregated to provide daily or weekly step counts for the primary analysis. Missing data are common as participants may not wear the device as per protocol. Approaches to handling missing data in the literature have defined missingness on the day level using a threshold on daily weartime, which leads to loss of information on the time of day when data are missing. We propose an approach to identifying and classifying missingness at the finer epoch-level and present two approaches to handling missingness using multiple imputation. Firstly, we present a parametric approach which accounts for the number of missing epochs per day. Secondly, we describe a non-parametric approach where missing periods during the day are replaced by donor data from the same person where possible, or data from a different person who is matched on demographic and physical activity-related variables. Our simulation studies show that the non-parametric approach leads to estimates of the effect of treatment that are least biased while maintaining small standard errors. We illustrate the application of these different multiple imputation strategies to the analysis of the 2017 PACE-UP trial. The proposed framework is likely to be applicable to other digital health outcomes and to other wearable devices.",
+    "laySummary": "",
+    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/09622802231188518; doi:https://doi.org/10.1177/09622802231188518; html:https://europepmc.org/articles/PMC10563375; pdf:https://europepmc.org/articles/PMC10563375?pdf=render"
+  },
   {
     "id": "35177264",
     "doi": "https://doi.org/10.1016/j.injury.2022.02.027",
@@ -28729,23 +28763,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.amjcard.2023.05.039"
   },
-  {
-    "id": "37813531",
-    "doi": "https://doi.org/10.1136/bmjopen-2023-073162",
-    "title": "Detection and evaluation of signals associated with exposure to individual and combination of medications in pregnancy: a signal detection study protocol.",
-    "authorString": "Subramanian A, Lee SI, Hemali Sudasinghe SPB, Wambua S, Phillips K, Singh M, Azcoaga-Lorenzo A, Cockburn N, Wang J, Fagbamigbe A, Usman M, Damase-Michel C, Yau C, Kent L, McCowan C, OReilly D, Santorelli G, Hope H, Kennedy J, Mhereeg M, Abel KM, Eastwood KA, Black M, Loane M, Moss N, Brophy S, Brocklehurst P, Dolk H, Nelson-Piercy C, Nirantharakumar K, MuM-PreDiCT Group.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2023",
-    "date": "2023-10-09",
-    "isOpenAccess": "Y",
-    "keywords": "Obstetrics; epidemiology; Maternal Medicine",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>Considering the high prevalence of polypharmacy in pregnant women and the knowledge gap in the risk-benefit safety profile of their often-complex treatment plan, more research is needed to optimise prescribing. In this study, we aim to detect adverse and protective effect signals of exposure to individual and pairwise combinations of medications during pregnancy.<h4>Methods and analysis</h4>Using a range of real-world data sources from the UK, we aim to conduct a pharmacovigilance study to assess the safety of medications prescribed during the preconception period (3\u2009months prior to conception) and first trimester of pregnancy. Women aged between 15 and 49 years with a record of pregnancy within the Clinical Practice Research Datalink (CPRD) Pregnancy Register, the Welsh Secure Anonymised Information Linkage (SAIL), the Scottish Morbidity Record (SMR) data sets and the Northern Ireland Maternity System (NIMATS) will be included. A series of case control studies will be conducted to estimate measures of disproportionality, detecting signals of association between a range of pregnancy outcomes and exposure to individual and combinations of medications. A multidisciplinary expert team will be invited to a signal detection workshop. By employing a structured framework, signals will be transparently assessed by each member of the team using a questionnaire appraising the signals on aspects of temporality, selection, time and measurement-related biases and confounding by underlying disease or comedications. Through group discussion, the expert team will reach consensus on each of the medication exposure-outcome signal, thereby excluding spurious signals, leaving signals suggestive of causal associations for further evaluation.<h4>Ethics and dissemination</h4>Ethical approval has been obtained from the Independent Scientific Advisory Committee, SAIL Information Governance Review Panel, University of St. Andrews Teaching and Research Ethics Committee and Office for Research Ethics Committees Northern Ireland (ORECNI) for access and use of CPRD, SAIL, SMR and NIMATS data, respectively.",
-    "laySummary": "",
-    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/13/10/e073162.full.pdf; doi:https://doi.org/10.1136/bmjopen-2023-073162; html:https://europepmc.org/articles/PMC10565241; pdf:https://europepmc.org/articles/PMC10565241?pdf=render"
-  },
   {
     "id": "33206055",
     "doi": "https://doi.org/10.2196/19650",
@@ -28763,23 +28780,6 @@
     "laySummary": "",
     "urls": "pdf:https://diabetes.jmir.org/2020/4/e19650/PDF; doi:https://doi.org/10.2196/19650; html:https://europepmc.org/articles/PMC7710444; pdf:https://europepmc.org/articles/PMC7710444?pdf=render"
   },
-  {
-    "id": "31984563",
-    "doi": "https://doi.org/10.1111/jce.14368",
-    "title": "Early recurrences of atrial tachyarrhythmias post pulmonary vein isolation.",
-    "authorString": "von Olshausen G, Uijl A, Jensen-Urstad M, Schwieler J, Drca N, Bastani H, Tapanainen J, Saluveer O, Bourke T, Kenneb\u00e4ck G, Insulander P, Deisenhofer I, Braunschweig F.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of cardiovascular electrophysiology",
-    "pubYear": "2020",
-    "date": "2020-01-31",
-    "isOpenAccess": "N",
-    "keywords": "Atrial fibrillation; Catheter ablation; Late Recurrence; Early Recurrence; Blanking Period",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Aims</h4>To investigate the significance of early recurrence (ER) of atrial tachyarrhythmias after pulmonary vein isolation (PVI) on the development of late recurrence (LR) and to redefine the blanking period during which an ER is considered nonspecific.<h4>Methods</h4>Data of 713 patients undergoing their first PVI for paroxysmal or persistent atrial fibrillation between January 2012 and December 2017 were included. All patients were followed-up for 12 months according to clinical and outpatient routine and were screened for any atrial tachyarrhythmia lasting >30 seconds occurring during the first 3 months postablation (ER) and after the 3 months blanking period (LR).<h4>Results</h4>Patients with ER compared to those without ER had significantly more LR (74.5% vs 16.5% vs, P\u2009<\u2009.001). The occurrence of ER during the first, second and third months showed increasing LR rates of 35.2%, 67.9%, and 94.8%, respectively (P\u2009<\u2009.001). Receiver operator characteristic analysis revealed a blanking period of 46 days with the highest sensitivity (68.1%) and specificity (96.5%). Later timing and longer time span of ER were independent predictors for LR in multivariable analysis.<h4>Conclusion</h4>ER is a strong predictor for LR. Our study advocates a shortening of the post-PVI blanking period followed by a \"gray zone\" up to 3 months where individualized therapeutic decisions based on additional risk factors should be considered. We suggest that the ER time span might serve as such a predictor identifying patients at the highest risk for LR.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1111/jce.14368"
-  },
   {
     "id": "34019073",
     "doi": "https://doi.org/10.1093/ibd/izab059",
@@ -28797,6 +28797,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ibdjournal/article-pdf/27/11/1719/40784408/izab059.pdf; doi:https://doi.org/10.1093/ibd/izab059; html:https://europepmc.org/articles/PMC8528147; pdf:https://europepmc.org/articles/PMC8528147?pdf=render"
   },
+  {
+    "id": "31984563",
+    "doi": "https://doi.org/10.1111/jce.14368",
+    "title": "Early recurrences of atrial tachyarrhythmias post pulmonary vein isolation.",
+    "authorString": "von Olshausen G, Uijl A, Jensen-Urstad M, Schwieler J, Drca N, Bastani H, Tapanainen J, Saluveer O, Bourke T, Kenneb\u00e4ck G, Insulander P, Deisenhofer I, Braunschweig F.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of cardiovascular electrophysiology",
+    "pubYear": "2020",
+    "date": "2020-01-31",
+    "isOpenAccess": "N",
+    "keywords": "Atrial fibrillation; Catheter ablation; Late Recurrence; Early Recurrence; Blanking Period",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Aims</h4>To investigate the significance of early recurrence (ER) of atrial tachyarrhythmias after pulmonary vein isolation (PVI) on the development of late recurrence (LR) and to redefine the blanking period during which an ER is considered nonspecific.<h4>Methods</h4>Data of 713 patients undergoing their first PVI for paroxysmal or persistent atrial fibrillation between January 2012 and December 2017 were included. All patients were followed-up for 12 months according to clinical and outpatient routine and were screened for any atrial tachyarrhythmia lasting >30 seconds occurring during the first 3 months postablation (ER) and after the 3 months blanking period (LR).<h4>Results</h4>Patients with ER compared to those without ER had significantly more LR (74.5% vs 16.5% vs, P\u2009<\u2009.001). The occurrence of ER during the first, second and third months showed increasing LR rates of 35.2%, 67.9%, and 94.8%, respectively (P\u2009<\u2009.001). Receiver operator characteristic analysis revealed a blanking period of 46 days with the highest sensitivity (68.1%) and specificity (96.5%). Later timing and longer time span of ER were independent predictors for LR in multivariable analysis.<h4>Conclusion</h4>ER is a strong predictor for LR. Our study advocates a shortening of the post-PVI blanking period followed by a \"gray zone\" up to 3 months where individualized therapeutic decisions based on additional risk factors should be considered. We suggest that the ER time span might serve as such a predictor identifying patients at the highest risk for LR.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1111/jce.14368"
+  },
   {
     "id": "32017129",
     "doi": "https://doi.org/10.5694/mja2.50485",
@@ -28814,6 +28831,40 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.5694/mja2.50485; doi:https://doi.org/10.5694/mja2.50485"
   },
+  {
+    "id": "37813531",
+    "doi": "https://doi.org/10.1136/bmjopen-2023-073162",
+    "title": "Detection and evaluation of signals associated with exposure to individual and combination of medications in pregnancy: a signal detection study protocol.",
+    "authorString": "Subramanian A, Lee SI, Hemali Sudasinghe SPB, Wambua S, Phillips K, Singh M, Azcoaga-Lorenzo A, Cockburn N, Wang J, Fagbamigbe A, Usman M, Damase-Michel C, Yau C, Kent L, McCowan C, OReilly D, Santorelli G, Hope H, Kennedy J, Mhereeg M, Abel KM, Eastwood KA, Black M, Loane M, Moss N, Brophy S, Brocklehurst P, Dolk H, Nelson-Piercy C, Nirantharakumar K, MuM-PreDiCT Group.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2023",
+    "date": "2023-10-09",
+    "isOpenAccess": "Y",
+    "keywords": "Obstetrics; epidemiology; Maternal Medicine",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>Considering the high prevalence of polypharmacy in pregnant women and the knowledge gap in the risk-benefit safety profile of their often-complex treatment plan, more research is needed to optimise prescribing. In this study, we aim to detect adverse and protective effect signals of exposure to individual and pairwise combinations of medications during pregnancy.<h4>Methods and analysis</h4>Using a range of real-world data sources from the UK, we aim to conduct a pharmacovigilance study to assess the safety of medications prescribed during the preconception period (3\u2009months prior to conception) and first trimester of pregnancy. Women aged between 15 and 49 years with a record of pregnancy within the Clinical Practice Research Datalink (CPRD) Pregnancy Register, the Welsh Secure Anonymised Information Linkage (SAIL), the Scottish Morbidity Record (SMR) data sets and the Northern Ireland Maternity System (NIMATS) will be included. A series of case control studies will be conducted to estimate measures of disproportionality, detecting signals of association between a range of pregnancy outcomes and exposure to individual and combinations of medications. A multidisciplinary expert team will be invited to a signal detection workshop. By employing a structured framework, signals will be transparently assessed by each member of the team using a questionnaire appraising the signals on aspects of temporality, selection, time and measurement-related biases and confounding by underlying disease or comedications. Through group discussion, the expert team will reach consensus on each of the medication exposure-outcome signal, thereby excluding spurious signals, leaving signals suggestive of causal associations for further evaluation.<h4>Ethics and dissemination</h4>Ethical approval has been obtained from the Independent Scientific Advisory Committee, SAIL Information Governance Review Panel, University of St. Andrews Teaching and Research Ethics Committee and Office for Research Ethics Committees Northern Ireland (ORECNI) for access and use of CPRD, SAIL, SMR and NIMATS data, respectively.",
+    "laySummary": "",
+    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/13/10/e073162.full.pdf; doi:https://doi.org/10.1136/bmjopen-2023-073162; html:https://europepmc.org/articles/PMC10565241; pdf:https://europepmc.org/articles/PMC10565241?pdf=render"
+  },
+  {
+    "id": "35089054",
+    "doi": "https://doi.org/10.1161/circep.121.010221",
+    "title": "Integrating Exercise Into Personalized Ventricular Arrhythmia Risk Prediction in Arrhythmogenic Right Ventricular Cardiomyopathy.",
+    "authorString": "Bosman LP, Wang W, Lie \u00d8H, van Lint FHM, Rootwelt-Norberg C, Murray B, Tichnell C, Cadrin-Tourigny J, van Tintelen JP, Asselbergs FW, Calkins H, Te Riele ASJM, Haugaa KH, James CA.",
+    "authorAffiliations": "",
+    "journalTitle": "Circulation. Arrhythmia and electrophysiology",
+    "pubYear": "2022",
+    "date": "2022-01-28",
+    "isOpenAccess": "N",
+    "keywords": "Prognosis; Exercise; Arrhythmogenic right ventricular dysplasia",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Exercise is associated with sustained ventricular arrhythmias (VA) in Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC) but is not included in the ARVC risk calculator (arvcrisk.com). The objective of this study is to quantify the influence of exercise at diagnosis on incident VA risk and evaluate whether the risk calculator needs adjustment for exercise.<h4>Methods</h4>We interviewed ARVC patients without sustained VA at diagnosis about their exercise history. The relationship between exercise dose 3 years preceding diagnosis (average METh/wk) and incident VA during follow-up was analyzed with time-to-event analysis. The incremental prognostic value of exercise to the risk calculator was evaluated by Cox models.<h4>Results</h4>We included 176 patients (male, 43.2%; age, 37.6\u00b116.1 years) from 3 ARVC centers, of whom 53 (30.1%) developed sustained VA during 5.4 (2.7-9.7) years of follow-up. Exercise at diagnosis showed a dose-dependent nonlinear relationship with VA, with no significant risk increase <15 to 30 METh/wk. Athlete status, using 3 definitions from literature (>18, >24, and >36 METh/wk), was significantly associated with VA (hazard ratios, 2.53-2.91) but was also correlated with risk factors currently in the risk calculator model. Thus, adding athlete status to the model did not change the C index of 0.77 (0.71-0.84) and showed no significant improvement (Akaike information criterion change, <2).<h4>Conclusions</h4>Exercise at diagnosis was dose dependently associated with risk of sustained VA in ARVC patients but only above 15 to 30 METh/wk. Exercise does not appear to have incremental prognostic value over the risk calculator. The ARVC risk calculator can be used accurately in athletic patients without modification.",
+    "laySummary": "",
+    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCEP.121.010221; doi:https://doi.org/10.1161/CIRCEP.121.010221"
+  },
   {
     "id": "35297548",
     "doi": "https://doi.org/10.1002/humu.24369",
@@ -28848,23 +28899,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.injury.2019.05.004"
   },
-  {
-    "id": "35089054",
-    "doi": "https://doi.org/10.1161/circep.121.010221",
-    "title": "Integrating Exercise Into Personalized Ventricular Arrhythmia Risk Prediction in Arrhythmogenic Right Ventricular Cardiomyopathy.",
-    "authorString": "Bosman LP, Wang W, Lie \u00d8H, van Lint FHM, Rootwelt-Norberg C, Murray B, Tichnell C, Cadrin-Tourigny J, van Tintelen JP, Asselbergs FW, Calkins H, Te Riele ASJM, Haugaa KH, James CA.",
-    "authorAffiliations": "",
-    "journalTitle": "Circulation. Arrhythmia and electrophysiology",
-    "pubYear": "2022",
-    "date": "2022-01-28",
-    "isOpenAccess": "N",
-    "keywords": "Prognosis; Exercise; Arrhythmogenic right ventricular dysplasia",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Exercise is associated with sustained ventricular arrhythmias (VA) in Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC) but is not included in the ARVC risk calculator (arvcrisk.com). The objective of this study is to quantify the influence of exercise at diagnosis on incident VA risk and evaluate whether the risk calculator needs adjustment for exercise.<h4>Methods</h4>We interviewed ARVC patients without sustained VA at diagnosis about their exercise history. The relationship between exercise dose 3 years preceding diagnosis (average METh/wk) and incident VA during follow-up was analyzed with time-to-event analysis. The incremental prognostic value of exercise to the risk calculator was evaluated by Cox models.<h4>Results</h4>We included 176 patients (male, 43.2%; age, 37.6\u00b116.1 years) from 3 ARVC centers, of whom 53 (30.1%) developed sustained VA during 5.4 (2.7-9.7) years of follow-up. Exercise at diagnosis showed a dose-dependent nonlinear relationship with VA, with no significant risk increase <15 to 30 METh/wk. Athlete status, using 3 definitions from literature (>18, >24, and >36 METh/wk), was significantly associated with VA (hazard ratios, 2.53-2.91) but was also correlated with risk factors currently in the risk calculator model. Thus, adding athlete status to the model did not change the C index of 0.77 (0.71-0.84) and showed no significant improvement (Akaike information criterion change, <2).<h4>Conclusions</h4>Exercise at diagnosis was dose dependently associated with risk of sustained VA in ARVC patients but only above 15 to 30 METh/wk. Exercise does not appear to have incremental prognostic value over the risk calculator. The ARVC risk calculator can be used accurately in athletic patients without modification.",
-    "laySummary": "",
-    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCEP.121.010221; doi:https://doi.org/10.1161/CIRCEP.121.010221"
-  },
   {
     "id": "35743743",
     "doi": "https://doi.org/10.3390/jpm12060958",
@@ -28882,23 +28916,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.mdpi.com/2075-4426/12/6/958/pdf?version=1655284846; doi:https://doi.org/10.3390/jpm12060958; html:https://europepmc.org/articles/PMC9225330; pdf:https://europepmc.org/articles/PMC9225330?pdf=render"
   },
-  {
-    "id": "37477360",
-    "doi": "https://doi.org/10.1097/ypg.0000000000000349",
-    "title": "Schizophrenia polygenic risk score and type 2 diabetes onset in older adults with no schizophrenia diagnosis.",
-    "authorString": "Shamsutdinova D, Ajnakina O, Roberts A, Stahl D.",
-    "authorAffiliations": "",
-    "journalTitle": "Psychiatric genetics",
-    "pubYear": "2023",
-    "date": "2023-07-04",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objectives</h4>An association between type 2 diabetes (T2DM) and schizophrenia has long been observed, and recent research revealed presence of shared genetic factors. However, epidemiological evidence was inconsistent, some reported insignificant contribution of genetic factors to T2DM-schizophrenia comorbidity. Prior works studied people with schizophrenia, particularly, antipsychotic-naive patients, or those during the first psychotic experience to limit schizophrenia-related environmental factors. In contrast, we controlled such factors by utilizing a general population sample of individuals undiagnosed with schizophrenia. We hypothesized that if schizophrenia genetics impact T2DM development and such impact is not fully mediated by schizophrenia-related environment, people with high polygenic schizophrenia risk would exhibit elevated T2DM incidence.<h4>Methods</h4>Using a population-representative sample of adults aged \u226550 from English Longitudinal Study of Ageing ( n \u2005=\u20055968, 493 T2DM cases, average follow-up 8.7 years), we investigated if schizophrenia polygenic risk score (PGS-SZ) is associated with T2DM onset. A proportional hazards model with interval censoring was adjusted for age and sex (Model 1), and age, sex, BMI, hypertension, cardiovascular diseases, exercise, smoking, depressive symptoms and T2DM polygenic risk score (Model 2). According to the power calculations, hazard rates > 1.14 per standard deviation in PGS-SZ could be detected.<h4>Results</h4>We did not observe a significant association between PGS-SZ and T2DM incidence (hazard ratio 1.04; 95% CI 0.93-1.15; and\u20051.01, 95% CI\u20050.94-1.09).<h4>Conclusion</h4>Our results suggest low contribution of the intrinsic biological mechanisms driven by the polygenic risk of schizophrenia on future T2DM onset. Further research is needed.",
-    "laySummary": "",
-    "urls": "html:https://journals.lww.com/psychgenetics/fulltext/9900/schizophrenia_polygenic_risk_score_and_type_2.34.aspx; doi:https://doi.org/10.1097/YPG.0000000000000349; html:https://europepmc.org/articles/PMC10501355; pdf:https://europepmc.org/articles/PMC10501355?pdf=render"
-  },
   {
     "id": "36828609",
     "doi": "https://doi.org/10.1016/s2589-7500(22)00252-7",
@@ -28933,6 +28950,23 @@
     "laySummary": "",
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8718341/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8718341/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC8718341; pdf:https://europepmc.org/articles/PMC8718341?pdf=render"
   },
+  {
+    "id": "37477360",
+    "doi": "https://doi.org/10.1097/ypg.0000000000000349",
+    "title": "Schizophrenia polygenic risk score and type 2 diabetes onset in older adults with no schizophrenia diagnosis.",
+    "authorString": "Shamsutdinova D, Ajnakina O, Roberts A, Stahl D.",
+    "authorAffiliations": "",
+    "journalTitle": "Psychiatric genetics",
+    "pubYear": "2023",
+    "date": "2023-07-04",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objectives</h4>An association between type 2 diabetes (T2DM) and schizophrenia has long been observed, and recent research revealed presence of shared genetic factors. However, epidemiological evidence was inconsistent, some reported insignificant contribution of genetic factors to T2DM-schizophrenia comorbidity. Prior works studied people with schizophrenia, particularly, antipsychotic-naive patients, or those during the first psychotic experience to limit schizophrenia-related environmental factors. In contrast, we controlled such factors by utilizing a general population sample of individuals undiagnosed with schizophrenia. We hypothesized that if schizophrenia genetics impact T2DM development and such impact is not fully mediated by schizophrenia-related environment, people with high polygenic schizophrenia risk would exhibit elevated T2DM incidence.<h4>Methods</h4>Using a population-representative sample of adults aged \u226550 from English Longitudinal Study of Ageing ( n \u2005=\u20055968, 493 T2DM cases, average follow-up 8.7 years), we investigated if schizophrenia polygenic risk score (PGS-SZ) is associated with T2DM onset. A proportional hazards model with interval censoring was adjusted for age and sex (Model 1), and age, sex, BMI, hypertension, cardiovascular diseases, exercise, smoking, depressive symptoms and T2DM polygenic risk score (Model 2). According to the power calculations, hazard rates > 1.14 per standard deviation in PGS-SZ could be detected.<h4>Results</h4>We did not observe a significant association between PGS-SZ and T2DM incidence (hazard ratio 1.04; 95% CI 0.93-1.15; and\u20051.01, 95% CI\u20050.94-1.09).<h4>Conclusion</h4>Our results suggest low contribution of the intrinsic biological mechanisms driven by the polygenic risk of schizophrenia on future T2DM onset. Further research is needed.",
+    "laySummary": "",
+    "urls": "html:https://journals.lww.com/psychgenetics/fulltext/9900/schizophrenia_polygenic_risk_score_and_type_2.34.aspx; doi:https://doi.org/10.1097/YPG.0000000000000349; html:https://europepmc.org/articles/PMC10501355; pdf:https://europepmc.org/articles/PMC10501355?pdf=render"
+  },
   {
     "id": "35072885",
     "doi": "https://doi.org/10.1007/s10439-022-02905-4",
@@ -29001,23 +29035,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.jove.com/pdf/60794/implementation-real-time-psychosis-risk-detection-alerting-system; doi:https://doi.org/10.3791/60794; html:https://europepmc.org/articles/PMC7272223; pdf:https://europepmc.org/articles/PMC7272223?pdf=render; doi:https://doi.org/10.3791/60794"
   },
-  {
-    "id": "35748342",
-    "doi": "https://doi.org/10.1093/ije/dyac130",
-    "title": "Linkage of multiple electronic health record datasets using a 'spine linkage' approach compared with all 'pairwise linkages'.",
-    "authorString": "Blake HA, Sharples LD, Harron K, van der Meulen JH, Walker K.",
-    "authorAffiliations": "",
-    "journalTitle": "International journal of epidemiology",
-    "pubYear": "2023",
-    "date": "2023-02-01",
-    "isOpenAccess": "Y",
-    "keywords": "Electronic Health Records; Record Linkage; Pairwise Linkage; Spine Linkage Approach",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Methods for linking records between two datasets are well established. However, guidance is needed for linking more than two datasets. Using all 'pairwise linkages'-linking each dataset to every other dataset-is the most inclusive, but resource-intensive, approach. The 'spine' approach links each dataset to a designated 'spine dataset', reducing the number of linkages, but potentially reducing linkage quality.<h4>Methods</h4>We compared the pairwise and spine linkage approaches using real-world data on patients undergoing emergency bowel cancer surgery between 31\u00a0October\u00a02013 and 30\u00a0April\u00a02018. We linked an administrative hospital dataset (Hospital Episode Statistics; HES) capturing patients admitted to hospitals in England, and two clinical datasets comprising patients diagnosed with bowel cancer and patients undergoing emergency bowel surgery.<h4>Results</h4>The spine linkage approach, with HES as the spine dataset, created an analysis cohort of 15\u200a826 patients, equating to 98.3% of the 16\u200a100 patients identified using the pairwise linkage approach. There were no systematic differences in patient characteristics between these analysis cohorts. Associations of patient and tumour characteristics with mortality, complications and length of stay were not sensitive to the linkage approach. When eligibility criteria were applied before linkage, spine linkage included 14\u200a509 patients (90.0% compared with pairwise linkage).<h4>Conclusion</h4>Spine linkage can be used as an efficient alternative to pairwise linkage if case ascertainment in the spine dataset and data quality of linkage variables are high. These aspects should be systematically evaluated in the nominated spine dataset before spine linkage is used to create the analysis cohort.",
-    "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/ije/advance-article-pdf/doi/10.1093/ije/dyac130/44245961/dyac130.pdf; doi:https://doi.org/10.1093/ije/dyac130; html:https://europepmc.org/articles/PMC9908066; pdf:https://europepmc.org/articles/PMC9908066?pdf=render"
-  },
   {
     "id": "35275087",
     "doi": "https://doi.org/10.2196/34898",
@@ -29052,6 +29069,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-022-02399-w; doi:https://doi.org/10.1186/s12916-022-02399-w; html:https://europepmc.org/articles/PMC9190170; pdf:https://europepmc.org/articles/PMC9190170?pdf=render"
   },
+  {
+    "id": "35748342",
+    "doi": "https://doi.org/10.1093/ije/dyac130",
+    "title": "Linkage of multiple electronic health record datasets using a 'spine linkage' approach compared with all 'pairwise linkages'.",
+    "authorString": "Blake HA, Sharples LD, Harron K, van der Meulen JH, Walker K.",
+    "authorAffiliations": "",
+    "journalTitle": "International journal of epidemiology",
+    "pubYear": "2023",
+    "date": "2023-02-01",
+    "isOpenAccess": "Y",
+    "keywords": "Electronic Health Records; Record Linkage; Pairwise Linkage; Spine Linkage Approach",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Methods for linking records between two datasets are well established. However, guidance is needed for linking more than two datasets. Using all 'pairwise linkages'-linking each dataset to every other dataset-is the most inclusive, but resource-intensive, approach. The 'spine' approach links each dataset to a designated 'spine dataset', reducing the number of linkages, but potentially reducing linkage quality.<h4>Methods</h4>We compared the pairwise and spine linkage approaches using real-world data on patients undergoing emergency bowel cancer surgery between 31\u00a0October\u00a02013 and 30\u00a0April\u00a02018. We linked an administrative hospital dataset (Hospital Episode Statistics; HES) capturing patients admitted to hospitals in England, and two clinical datasets comprising patients diagnosed with bowel cancer and patients undergoing emergency bowel surgery.<h4>Results</h4>The spine linkage approach, with HES as the spine dataset, created an analysis cohort of 15\u200a826 patients, equating to 98.3% of the 16\u200a100 patients identified using the pairwise linkage approach. There were no systematic differences in patient characteristics between these analysis cohorts. Associations of patient and tumour characteristics with mortality, complications and length of stay were not sensitive to the linkage approach. When eligibility criteria were applied before linkage, spine linkage included 14\u200a509 patients (90.0% compared with pairwise linkage).<h4>Conclusion</h4>Spine linkage can be used as an efficient alternative to pairwise linkage if case ascertainment in the spine dataset and data quality of linkage variables are high. These aspects should be systematically evaluated in the nominated spine dataset before spine linkage is used to create the analysis cohort.",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/ije/advance-article-pdf/doi/10.1093/ije/dyac130/44245961/dyac130.pdf; doi:https://doi.org/10.1093/ije/dyac130; html:https://europepmc.org/articles/PMC9908066; pdf:https://europepmc.org/articles/PMC9908066?pdf=render"
+  },
   {
     "id": "31409800",
     "doi": "https://doi.org/10.1038/s41467-019-11451-y",
@@ -29069,23 +29103,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41467-019-11451-y.pdf; doi:https://doi.org/10.1038/s41467-019-11451-y; html:https://europepmc.org/articles/PMC6692500; pdf:https://europepmc.org/articles/PMC6692500?pdf=render"
   },
-  {
-    "id": "36701266",
-    "doi": "https://doi.org/10.1371/journal.pmed.1004036",
-    "title": "Gestational age at birth and body size from infancy through adolescence: An individual participant data meta-analysis on 253,810 singletons in 16 birth cohort studies.",
-    "authorString": "Vinther JL, Cadman T, Avraam D, Ekstr\u00f8m CT, S\u00f8rensen TIA, Elhakeem A, Santos AC, Pinot de Moira A, Heude B, I\u00f1iguez C, Pizzi C, Simons E, Voerman E, Corpeleijn E, Zariouh F, Santorelli G, Inskip HM, Barros H, Carson J, Harris JR, Nader JL, Ronkainen J, Strandberg-Larsen K, Santa-Marina L, Calas L, Cederkvist L, Popovic M, Charles MA, Welten M, Vrijheid M, Azad M, Subbarao P, Burton P, Mandhane PJ, Huang RC, Wilson RC, Haakma S, Fern\u00e1ndez-Barr\u00e9s S, Turvey S, Santos S, Tough SC, Tough SC, Sebert S, Moraes TJ, Salika T, Jaddoe VWV, Lawlor DA, Nybo Andersen AM.",
-    "authorAffiliations": "",
-    "journalTitle": "PLoS medicine",
-    "pubYear": "2023",
-    "date": "2023-01-26",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Preterm birth is the leading cause of perinatal morbidity and mortality and is associated with adverse developmental and long-term health outcomes, including several cardiometabolic risk factors and outcomes. However, evidence about the association of preterm birth with later body size derives mainly from studies using birth weight as a proxy of prematurity rather than an actual length of gestation. We investigated the association of gestational age (GA) at birth with body size from infancy through adolescence.<h4>Methods and findings</h4>We conducted a two-stage individual participant data (IPD) meta-analysis using data from 253,810 mother-child dyads from 16 general population-based cohort studies in Europe (Denmark, Finland, France, Italy, Norway, Portugal, Spain, the Netherlands, United Kingdom), North America (Canada), and Australasia (Australia) to estimate the association of GA with body mass index (BMI) and overweight (including obesity) adjusted for the following maternal characteristics as potential confounders: education, height, prepregnancy BMI, ethnic background, parity, smoking during pregnancy, age at child's birth, gestational diabetes and hypertension, and preeclampsia. Pregnancy and birth cohort studies from the LifeCycle and the EUCAN-Connect projects were invited and were eligible for inclusion if they had information on GA and minimum one measurement of BMI between infancy and adolescence. Using a federated analytical tool (DataSHIELD), we fitted linear and logistic regression models in each cohort separately with a complete-case approach and combined the regression estimates and standard errors through random-effects study-level meta-analysis providing an overall effect estimate at early infancy (>0.0 to 0.5 years), late infancy (>0.5 to 2.0 years), early childhood (>2.0 to 5.0 years), mid-childhood (>5.0 to 9.0 years), late childhood (>9.0 to 14.0 years), and adolescence (>14.0 to 19.0 years). GA was positively associated with BMI in the first decade of life, with the greatest increase in mean BMI z-score during early infancy (0.02, 95% confidence interval (CI): 0.00; 0.05, p < 0.05) per week of increase in GA, while in adolescence, preterm individuals reached similar levels of BMI (0.00, 95% CI: -0.01; 0.01, p 0.9) as term counterparts. The association between GA and overweight revealed a similar pattern of association with an increase in odds ratio (OR) of overweight from late infancy through mid-childhood (OR 1.01 to 1.02) per week increase in GA. By adolescence, however, GA was slightly negatively associated with the risk of overweight (OR 0.98 [95% CI: 0.97; 1.00], p 0.1) per week of increase in GA. Although based on only four cohorts (n = 32,089) that reached the age of adolescence, data suggest that individuals born very preterm may be at increased odds of overweight (OR 1.46 [95% CI: 1.03; 2.08], p < 0.05) compared with term counterparts. Findings were consistent across cohorts and sensitivity analyses despite considerable heterogeneity in cohort characteristics. However, residual confounding may be a limitation in this study, while findings may be less generalisable to settings in low- and middle-income countries.<h4>Conclusions</h4>This study based on data from infancy through adolescence from 16 cohort studies found that GA may be important for body size in infancy, but the strength of association attenuates consistently with age. By adolescence, preterm individuals have on average a similar mean BMI to peers born at term.",
-    "laySummary": "",
-    "urls": "pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004036&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004036; html:https://europepmc.org/articles/PMC9879424; pdf:https://europepmc.org/articles/PMC9879424?pdf=render"
-  },
   {
     "id": "34688720",
     "doi": "https://doi.org/10.1016/j.ijcard.2021.10.029",
@@ -29103,6 +29120,40 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.ijcard.2021.10.029"
   },
+  {
+    "id": "32234121",
+    "doi": "https://doi.org/10.2807/1560-7917.es.2020.25.12.2000256",
+    "title": "Estimating the infection and case fatality ratio for coronavirus disease (COVID-19) using age-adjusted data from the outbreak on the Diamond Princess cruise ship, February 2020.",
+    "authorString": "Russell TW, Hellewell J, Jarvis CI, van Zandvoort K, Abbott S, Ratnayake R, CMMID COVID-19 working group, Flasche S, Eggo RM, Edmunds WJ, Kucharski AJ.",
+    "authorAffiliations": "",
+    "journalTitle": "Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin",
+    "pubYear": "2020",
+    "date": "2020-03-01",
+    "isOpenAccess": "Y",
+    "keywords": "Coronavirus; outbreak; Severity; Asymptomatic; Case Fatality Ratio; Cruise Ship; Covid-19; Infection Fatality Ratio",
+    "nationalPriorities": "COVID-19, Improving Public Health",
+    "healthCategories": "COVID-19, infection",
+    "abstract": "Adjusting for delay from confirmation to death, we estimated case and infection fatality ratios (CFR, IFR) for coronavirus disease (COVID-19) on the Diamond Princess ship as 2.6% (95% confidence interval (CI): 0.89-6.7) and 1.3% (95% CI: 0.38-3.6), respectively. Comparing deaths on board with expected deaths based on naive CFR estimates from China, we estimated CFR and IFR in China to be 1.2% (95% CI: 0.3-2.7) and 0.6% (95% CI: 0.2-1.3), respectively.",
+    "laySummary": "",
+    "urls": "pdf:https://www.eurosurveillance.org/deliver/fulltext/eurosurveillance/25/12/eurosurv-25-12-3.pdf?itemId=%2Fcontent%2F10.2807%2F1560-7917.ES.2020.25.12.2000256&mimeType=pdf&containerItemId=content/eurosurveillance; doi:https://doi.org/10.2807/1560-7917.ES.2020.25.12.2000256; html:https://europepmc.org/articles/PMC7118348; pdf:https://europepmc.org/articles/PMC7118348?pdf=render"
+  },
+  {
+    "id": "36701266",
+    "doi": "https://doi.org/10.1371/journal.pmed.1004036",
+    "title": "Gestational age at birth and body size from infancy through adolescence: An individual participant data meta-analysis on 253,810 singletons in 16 birth cohort studies.",
+    "authorString": "Vinther JL, Cadman T, Avraam D, Ekstr\u00f8m CT, S\u00f8rensen TIA, Elhakeem A, Santos AC, Pinot de Moira A, Heude B, I\u00f1iguez C, Pizzi C, Simons E, Voerman E, Corpeleijn E, Zariouh F, Santorelli G, Inskip HM, Barros H, Carson J, Harris JR, Nader JL, Ronkainen J, Strandberg-Larsen K, Santa-Marina L, Calas L, Cederkvist L, Popovic M, Charles MA, Welten M, Vrijheid M, Azad M, Subbarao P, Burton P, Mandhane PJ, Huang RC, Wilson RC, Haakma S, Fern\u00e1ndez-Barr\u00e9s S, Turvey S, Santos S, Tough SC, Tough SC, Sebert S, Moraes TJ, Salika T, Jaddoe VWV, Lawlor DA, Nybo Andersen AM.",
+    "authorAffiliations": "",
+    "journalTitle": "PLoS medicine",
+    "pubYear": "2023",
+    "date": "2023-01-26",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Preterm birth is the leading cause of perinatal morbidity and mortality and is associated with adverse developmental and long-term health outcomes, including several cardiometabolic risk factors and outcomes. However, evidence about the association of preterm birth with later body size derives mainly from studies using birth weight as a proxy of prematurity rather than an actual length of gestation. We investigated the association of gestational age (GA) at birth with body size from infancy through adolescence.<h4>Methods and findings</h4>We conducted a two-stage individual participant data (IPD) meta-analysis using data from 253,810 mother-child dyads from 16 general population-based cohort studies in Europe (Denmark, Finland, France, Italy, Norway, Portugal, Spain, the Netherlands, United Kingdom), North America (Canada), and Australasia (Australia) to estimate the association of GA with body mass index (BMI) and overweight (including obesity) adjusted for the following maternal characteristics as potential confounders: education, height, prepregnancy BMI, ethnic background, parity, smoking during pregnancy, age at child's birth, gestational diabetes and hypertension, and preeclampsia. Pregnancy and birth cohort studies from the LifeCycle and the EUCAN-Connect projects were invited and were eligible for inclusion if they had information on GA and minimum one measurement of BMI between infancy and adolescence. Using a federated analytical tool (DataSHIELD), we fitted linear and logistic regression models in each cohort separately with a complete-case approach and combined the regression estimates and standard errors through random-effects study-level meta-analysis providing an overall effect estimate at early infancy (>0.0 to 0.5 years), late infancy (>0.5 to 2.0 years), early childhood (>2.0 to 5.0 years), mid-childhood (>5.0 to 9.0 years), late childhood (>9.0 to 14.0 years), and adolescence (>14.0 to 19.0 years). GA was positively associated with BMI in the first decade of life, with the greatest increase in mean BMI z-score during early infancy (0.02, 95% confidence interval (CI): 0.00; 0.05, p < 0.05) per week of increase in GA, while in adolescence, preterm individuals reached similar levels of BMI (0.00, 95% CI: -0.01; 0.01, p 0.9) as term counterparts. The association between GA and overweight revealed a similar pattern of association with an increase in odds ratio (OR) of overweight from late infancy through mid-childhood (OR 1.01 to 1.02) per week increase in GA. By adolescence, however, GA was slightly negatively associated with the risk of overweight (OR 0.98 [95% CI: 0.97; 1.00], p 0.1) per week of increase in GA. Although based on only four cohorts (n = 32,089) that reached the age of adolescence, data suggest that individuals born very preterm may be at increased odds of overweight (OR 1.46 [95% CI: 1.03; 2.08], p < 0.05) compared with term counterparts. Findings were consistent across cohorts and sensitivity analyses despite considerable heterogeneity in cohort characteristics. However, residual confounding may be a limitation in this study, while findings may be less generalisable to settings in low- and middle-income countries.<h4>Conclusions</h4>This study based on data from infancy through adolescence from 16 cohort studies found that GA may be important for body size in infancy, but the strength of association attenuates consistently with age. By adolescence, preterm individuals have on average a similar mean BMI to peers born at term.",
+    "laySummary": "",
+    "urls": "pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004036&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004036; html:https://europepmc.org/articles/PMC9879424; pdf:https://europepmc.org/articles/PMC9879424?pdf=render"
+  },
   {
     "id": "35355205",
     "doi": "https://doi.org/10.1007/s11897-022-00544-3",
@@ -29120,23 +29171,6 @@
     "laySummary": "",
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s11897-022-00544-3.pdf; doi:https://doi.org/10.1007/s11897-022-00544-3; html:https://europepmc.org/articles/PMC9177497; pdf:https://europepmc.org/articles/PMC9177497?pdf=render"
   },
-  {
-    "id": "35922433",
-    "doi": "https://doi.org/10.1038/s41467-022-32219-x",
-    "title": "Genome-wide associations of aortic distensibility suggest causality for aortic aneurysms and brain white matter hyperintensities.",
-    "authorString": "Francis CM, Futschik ME, Huang J, Bai W, Sargurupremraj M, Teumer A, Breteler MMB, Petretto E, Ho ASR, Amouyel P, Engelter ST, B\u00fclow R, V\u00f6lker U, V\u00f6lzke H, D\u00f6rr M, Imtiaz MA, Aziz NA, Lohner V, Ware JS, Debette S, Elliott P, Dehghan A, Matthews PM.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature communications",
-    "pubYear": "2022",
-    "date": "2022-08-03",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Aortic dimensions and distensibility are key risk factors for aortic aneurysms and dissections, as well as for other cardiovascular and cerebrovascular diseases. We present genome-wide associations of ascending and descending aortic distensibility and area derived from cardiac magnetic resonance imaging (MRI) data of up to 32,590 Caucasian individuals in UK Biobank. We identify 102 loci (including 27 novel associations) tagging genes related to cardiovascular development, extracellular matrix production, smooth muscle cell contraction and heritable aortic diseases. Functional analyses highlight four signalling pathways associated with aortic distensibility (TGF-\u03b2, IGF, VEGF and PDGF). We identify distinct sex-specific associations with aortic traits. We develop co-expression networks associated with aortic traits and apply phenome-wide Mendelian randomization (MR-PheWAS), generating evidence for a causal role for aortic distensibility in development of aortic aneurysms. Multivariable MR suggests a causal relationship between aortic distensibility and cerebral white matter hyperintensities, mechanistically linking aortic traits and brain small vessel disease.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41467-022-32219-x.pdf; doi:https://doi.org/10.1038/s41467-022-32219-x; html:https://europepmc.org/articles/PMC9349177; pdf:https://europepmc.org/articles/PMC9349177?pdf=render"
-  },
   {
     "id": "31446403",
     "doi": "https://doi.org/10.1136/bmjopen-2018-026677",
@@ -29154,6 +29188,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/9/8/e026677.full.pdf; doi:https://doi.org/10.1136/bmjopen-2018-026677; html:https://europepmc.org/articles/PMC6720466; pdf:https://europepmc.org/articles/PMC6720466?pdf=render"
   },
+  {
+    "id": "35922433",
+    "doi": "https://doi.org/10.1038/s41467-022-32219-x",
+    "title": "Genome-wide associations of aortic distensibility suggest causality for aortic aneurysms and brain white matter hyperintensities.",
+    "authorString": "Francis CM, Futschik ME, Huang J, Bai W, Sargurupremraj M, Teumer A, Breteler MMB, Petretto E, Ho ASR, Amouyel P, Engelter ST, B\u00fclow R, V\u00f6lker U, V\u00f6lzke H, D\u00f6rr M, Imtiaz MA, Aziz NA, Lohner V, Ware JS, Debette S, Elliott P, Dehghan A, Matthews PM.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature communications",
+    "pubYear": "2022",
+    "date": "2022-08-03",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Aortic dimensions and distensibility are key risk factors for aortic aneurysms and dissections, as well as for other cardiovascular and cerebrovascular diseases. We present genome-wide associations of ascending and descending aortic distensibility and area derived from cardiac magnetic resonance imaging (MRI) data of up to 32,590 Caucasian individuals in UK Biobank. We identify 102 loci (including 27 novel associations) tagging genes related to cardiovascular development, extracellular matrix production, smooth muscle cell contraction and heritable aortic diseases. Functional analyses highlight four signalling pathways associated with aortic distensibility (TGF-\u03b2, IGF, VEGF and PDGF). We identify distinct sex-specific associations with aortic traits. We develop co-expression networks associated with aortic traits and apply phenome-wide Mendelian randomization (MR-PheWAS), generating evidence for a causal role for aortic distensibility in development of aortic aneurysms. Multivariable MR suggests a causal relationship between aortic distensibility and cerebral white matter hyperintensities, mechanistically linking aortic traits and brain small vessel disease.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41467-022-32219-x.pdf; doi:https://doi.org/10.1038/s41467-022-32219-x; html:https://europepmc.org/articles/PMC9349177; pdf:https://europepmc.org/articles/PMC9349177?pdf=render"
+  },
   {
     "id": "31671849",
     "doi": "https://doi.org/10.3390/ijerph16214178",
@@ -29171,40 +29222,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.mdpi.com/1660-4601/16/21/4178/pdf?version=1573119054; doi:https://doi.org/10.3390/ijerph16214178; html:https://europepmc.org/articles/PMC6862192; pdf:https://europepmc.org/articles/PMC6862192?pdf=render"
   },
-  {
-    "id": "38746859",
-    "doi": "https://doi.org/10.1183/23120541.00430-2023",
-    "title": "Prevalence, incidence and healthcare burden of eosinophilic granulomatosis with polyangiitis in the UK.",
-    "authorString": "Hwee J, Harper L, Fu Q, Nirantharakumar K, Mu G, Jakes RW.",
-    "authorAffiliations": "",
-    "journalTitle": "ERJ open research",
-    "pubYear": "2024",
-    "date": "2024-05-13",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare but serious disease characterised by the combination of small-to-medium vessel vasculitis, blood and tissue eosinophilia, and asthma and/or sinonasal disease. This study estimated the prevalence and incidence of diagnosed EGPA in the United Kingdom (UK), and described the demographics, clinical characteristics and healthcare resource utilisation (HCRU) of this population.<h4>Methods</h4>This retrospective longitudinal study of patients with newly diagnosed EGPA (index) (2005-2019) used the Clinical Practice Research Datalink AURUM and Hospital Episode Statistics databases. The primary outcomes were the annual prevalence (2005-2019) and incidence (2006-2019) of EGPA, and secondary outcomes included patient demographics and clinical characteristics, and HCRU in the year pre- and post-index (diagnosis).<h4>Results</h4>Populations of patients with EGPA comprised 940 prevalent cases and 502 incident cases, of which 377 were linked to Hospital Episode Statistics. EGPA prevalence increased from 22.7 to 45.6 cases per 1\u2009000\u2009000 (2005-2019), driven by patients aged \u226518\u2005years. Incidence ranged from 2.3 to 4.0 per 1\u2009000\u2009000 person-years (2006-2019). Pre-index, the most common clinical symptoms were respiratory related, and the most common comorbidities were asthma (80.6%) and nasal polyps (32.1%). Post-index, 19.1% had an EGPA-related inpatient stay (median length of stay 11.0\u2005days) and 38.7% had five or more oral corticosteroid (OCS) prescriptions with a mean OCS possession ratio per patient of 47.0%.<h4>Conclusions</h4>Although EGPA incidence in the UK remains relatively stable, prevalence is increasing, and HCRU and OCS use remain frequent, suggesting considerable healthcare burden for patients with EGPA.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1183/23120541.00430-2023; html:https://europepmc.org/articles/PMC11089387; pdf:https://europepmc.org/articles/PMC11089387?pdf=render"
-  },
-  {
-    "id": "32234121",
-    "doi": "https://doi.org/10.2807/1560-7917.es.2020.25.12.2000256",
-    "title": "Estimating the infection and case fatality ratio for coronavirus disease (COVID-19) using age-adjusted data from the outbreak on the Diamond Princess cruise ship, February 2020.",
-    "authorString": "Russell TW, Hellewell J, Jarvis CI, van Zandvoort K, Abbott S, Ratnayake R, CMMID COVID-19 working group, Flasche S, Eggo RM, Edmunds WJ, Kucharski AJ.",
-    "authorAffiliations": "",
-    "journalTitle": "Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin",
-    "pubYear": "2020",
-    "date": "2020-03-01",
-    "isOpenAccess": "Y",
-    "keywords": "Coronavirus; outbreak; Severity; Asymptomatic; Case Fatality Ratio; Cruise Ship; Covid-19; Infection Fatality Ratio",
-    "nationalPriorities": "COVID-19, Improving Public Health",
-    "healthCategories": "COVID-19, infection",
-    "abstract": "Adjusting for delay from confirmation to death, we estimated case and infection fatality ratios (CFR, IFR) for coronavirus disease (COVID-19) on the Diamond Princess ship as 2.6% (95% confidence interval (CI): 0.89-6.7) and 1.3% (95% CI: 0.38-3.6), respectively. Comparing deaths on board with expected deaths based on naive CFR estimates from China, we estimated CFR and IFR in China to be 1.2% (95% CI: 0.3-2.7) and 0.6% (95% CI: 0.2-1.3), respectively.",
-    "laySummary": "",
-    "urls": "pdf:https://www.eurosurveillance.org/deliver/fulltext/eurosurveillance/25/12/eurosurv-25-12-3.pdf?itemId=%2Fcontent%2F10.2807%2F1560-7917.ES.2020.25.12.2000256&mimeType=pdf&containerItemId=content/eurosurveillance; doi:https://doi.org/10.2807/1560-7917.ES.2020.25.12.2000256; html:https://europepmc.org/articles/PMC7118348; pdf:https://europepmc.org/articles/PMC7118348?pdf=render"
-  },
   {
     "id": "33905476",
     "doi": "https://doi.org/10.1093/cid/ciab192",
@@ -29222,6 +29239,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/cid/article-pdf/72/Supplement_3/S172/38618862/ciab192.pdf; doi:https://doi.org/10.1093/cid/ciab192; html:https://europepmc.org/articles/PMC8201574; pdf:https://europepmc.org/articles/PMC8201574?pdf=render"
   },
+  {
+    "id": "38746859",
+    "doi": "https://doi.org/10.1183/23120541.00430-2023",
+    "title": "Prevalence, incidence and healthcare burden of eosinophilic granulomatosis with polyangiitis in the UK.",
+    "authorString": "Hwee J, Harper L, Fu Q, Nirantharakumar K, Mu G, Jakes RW.",
+    "authorAffiliations": "",
+    "journalTitle": "ERJ open research",
+    "pubYear": "2024",
+    "date": "2024-05-13",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare but serious disease characterised by the combination of small-to-medium vessel vasculitis, blood and tissue eosinophilia, and asthma and/or sinonasal disease. This study estimated the prevalence and incidence of diagnosed EGPA in the United Kingdom (UK), and described the demographics, clinical characteristics and healthcare resource utilisation (HCRU) of this population.<h4>Methods</h4>This retrospective longitudinal study of patients with newly diagnosed EGPA (index) (2005-2019) used the Clinical Practice Research Datalink AURUM and Hospital Episode Statistics databases. The primary outcomes were the annual prevalence (2005-2019) and incidence (2006-2019) of EGPA, and secondary outcomes included patient demographics and clinical characteristics, and HCRU in the year pre- and post-index (diagnosis).<h4>Results</h4>Populations of patients with EGPA comprised 940 prevalent cases and 502 incident cases, of which 377 were linked to Hospital Episode Statistics. EGPA prevalence increased from 22.7 to 45.6 cases per 1\u2009000\u2009000 (2005-2019), driven by patients aged \u226518\u2005years. Incidence ranged from 2.3 to 4.0 per 1\u2009000\u2009000 person-years (2006-2019). Pre-index, the most common clinical symptoms were respiratory related, and the most common comorbidities were asthma (80.6%) and nasal polyps (32.1%). Post-index, 19.1% had an EGPA-related inpatient stay (median length of stay 11.0\u2005days) and 38.7% had five or more oral corticosteroid (OCS) prescriptions with a mean OCS possession ratio per patient of 47.0%.<h4>Conclusions</h4>Although EGPA incidence in the UK remains relatively stable, prevalence is increasing, and HCRU and OCS use remain frequent, suggesting considerable healthcare burden for patients with EGPA.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1183/23120541.00430-2023; html:https://europepmc.org/articles/PMC11089387; pdf:https://europepmc.org/articles/PMC11089387?pdf=render"
+  },
   {
     "id": "35802687",
     "doi": "https://doi.org/10.1371/journal.pone.0270668",
@@ -29307,23 +29341,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/4C20CD00C92C75F4F0B4FACD8418B244/S2056472424000231a.pdf/div-class-title-contacts-with-primary-and-secondary-healthcare-before-suicide-by-those-under-the-care-of-mental-health-services-case-control-whole-population-based-study-using-person-level-linked-routine-data-in-wales-uk-during-2000-2015-div.pdf; doi:https://doi.org/10.1192/bjo.2024.23; html:https://europepmc.org/articles/PMC11094447; pdf:https://europepmc.org/articles/PMC11094447?pdf=render"
   },
-  {
-    "id": "38951929",
-    "doi": "https://doi.org/10.1186/s13063-024-08273-9",
-    "title": "Clinical trial results in context: comparison of baseline characteristics and outcomes of 38,510 RECOVERY trial participants versus a reference population of 346,271 people hospitalised with COVID-19 in England.",
-    "authorString": "Pessoa-Amorim G, Goldacre R, Crichton C, Stevens W, Nunn M, King A, Murray D, Welsh R, Pinches H, Rees A, Morris EJA, Landray MJ, Haynes R, Horby P, Wallendszus K, Peto L, Campbell M, Harper C, Mafham M.",
-    "authorAffiliations": "",
-    "journalTitle": "Trials",
-    "pubYear": "2024",
-    "date": "2024-06-29",
-    "isOpenAccess": "Y",
-    "keywords": "Recovery; Randomised Trials; Evidence Translation; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Randomised trials are essential to reliably assess medical interventions. Nevertheless, interpretation of such studies, particularly when considering absolute effects, is enhanced by understanding how the trial population may differ from the populations it aims to represent.<h4>Methods</h4>We compared baseline characteristics and mortality of RECOVERY participants recruited in England (n\u2009=\u200938,510) with a reference population hospitalised with COVID-19 in England (n\u2009=\u2009346,271) from March 2020 to November 2021. We used linked hospitalisation and mortality data for both cohorts to extract demographics, comorbidity/frailty scores, and crude and age- and sex-adjusted 28-day all-cause mortality.<h4>Results</h4>Demographics of RECOVERY participants were broadly similar to the reference population, but RECOVERY participants were younger (mean age [standard deviation]: RECOVERY 62.6 [15.3] vs reference 65.7 [18.5] years) and less frequently female (37% vs 45%). Comorbidity and frailty scores were lower in RECOVERY, but differences were attenuated after age stratification. Age- and sex-adjusted 28-day mortality declined over time but was similar between cohorts across the study period (RECOVERY 23.7% [95% confidence interval: 23.3-24.1%]; vs reference 24.8% [24.6-25.0%]), except during the first pandemic wave in the UK (March-May 2020) when adjusted mortality was lower in RECOVERY.<h4>Conclusions</h4>Adjusted 28-day mortality in RECOVERY was similar to a nationwide reference population of patients admitted with COVID-19 in England during the same period but varied substantially over time in both cohorts. Therefore, the absolute effect estimates from RECOVERY were broadly applicable to the target population at the time but should be interpreted in the light of current mortality estimates.<h4>Trial registration</h4>ISRCTN50189673- Feb. 04, 2020, NCT04381936- May 11, 2020.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1186/s13063-024-08273-9; doi:https://doi.org/10.1186/s13063-024-08273-9; html:https://europepmc.org/articles/PMC11218071; pdf:https://europepmc.org/articles/PMC11218071?pdf=render"
-  },
   {
     "id": "35916366",
     "doi": "https://doi.org/10.7554/elife.76272",
@@ -29341,23 +29358,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.7554/elife.76272; doi:https://doi.org/10.7554/eLife.76272; html:https://europepmc.org/articles/PMC9391041; pdf:https://europepmc.org/articles/PMC9391041?pdf=render"
   },
-  {
-    "id": "31479767",
-    "doi": "https://doi.org/10.1016/j.jaip.2019.08.030",
-    "title": "Atopic Eczema in Adulthood and Risk of Depression and Anxiety: A Population-Based Cohort Study.",
-    "authorString": "Schonmann Y, Mansfield KE, Hayes JF, Abuabara K, Roberts A, Smeeth L, Langan SM.",
-    "authorAffiliations": "",
-    "journalTitle": "The journal of allergy and clinical immunology. In practice",
-    "pubYear": "2020",
-    "date": "2019-08-31",
-    "isOpenAccess": "Y",
-    "keywords": "Depression; Anxiety; Atopic Eczema; Atopic Dermatitis; Severity; Population-based",
-    "nationalPriorities": "Understanding the Causes of Disease",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Atopic eczema is a common and debilitating condition associated with depression and anxiety, but the nature of this association remains unclear.<h4>Objective</h4>To explore the temporal relationship between atopic eczema and new depression/anxiety.<h4>Methods</h4>This matched cohort study used routinely collected data from the UK Clinical Practice Research Datalink, linked to hospital admissions data. We identified adults with atopic eczema (1998-2016) using a validated algorithm, and up to 5 individuals without atopic eczema matched on date of diagnosis, age, sex, and general practice. We estimated the hazard ratio (HR) for new depression/anxiety using stratified Cox regression to account for age, sex, calendar period, Index of Multiple Deprivation, glucocorticoid treatment, obesity, smoking, and harmful alcohol use.<h4>Results</h4>We identified 526,808 adults with atopic eczema who were matched to 2,569,030 without. Atopic eczema was associated with increased incidence of new depression (HR, 1.14; 99% CI, 1.12-1.16) and anxiety (HR, 1.17; 99% CI, 1.14-1.19). We observed a stronger effect of atopic eczema on depression with increasing atopic eczema severity (HR [99% CI] compared with no atopic eczema: mild, 1.10 [1.08-1.13]; moderate, 1.19 [1.15-1.23]; and severe, 1.26 [1.17-1.37]). A dose-response association, however, was less apparent for new anxiety diagnosis (HR [99% CI] compared with no atopic eczema: mild, 1.14 [1.11-1.18]; moderate, 1.21 [1.17-1.26]; and severe, 1.15; [1.05-1.25]).<h4>Conclusions</h4>Adults with atopic eczema are more likely to develop new depression and anxiety. For depression, we observed a dose-response relationship with atopic eczema severity.",
-    "laySummary": "",
-    "urls": "pdf:http://www.jaci-inpractice.org/article/S2213219819307536/pdf; doi:https://doi.org/10.1016/j.jaip.2019.08.030; html:https://europepmc.org/articles/PMC6947493; pdf:https://europepmc.org/articles/PMC6947493?pdf=render"
-  },
   {
     "id": "32685698",
     "doi": "https://doi.org/10.12688/wellcomeopenres.15842.3",
@@ -29375,6 +29375,40 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.12688/wellcomeopenres.15842.3; html:https://europepmc.org/articles/PMC7338915; pdf:https://europepmc.org/articles/PMC7338915?pdf=render"
   },
+  {
+    "id": "38951929",
+    "doi": "https://doi.org/10.1186/s13063-024-08273-9",
+    "title": "Clinical trial results in context: comparison of baseline characteristics and outcomes of 38,510 RECOVERY trial participants versus a reference population of 346,271 people hospitalised with COVID-19 in England.",
+    "authorString": "Pessoa-Amorim G, Goldacre R, Crichton C, Stevens W, Nunn M, King A, Murray D, Welsh R, Pinches H, Rees A, Morris EJA, Landray MJ, Haynes R, Horby P, Wallendszus K, Peto L, Campbell M, Harper C, Mafham M.",
+    "authorAffiliations": "",
+    "journalTitle": "Trials",
+    "pubYear": "2024",
+    "date": "2024-06-29",
+    "isOpenAccess": "Y",
+    "keywords": "Recovery; Randomised Trials; Evidence Translation; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Randomised trials are essential to reliably assess medical interventions. Nevertheless, interpretation of such studies, particularly when considering absolute effects, is enhanced by understanding how the trial population may differ from the populations it aims to represent.<h4>Methods</h4>We compared baseline characteristics and mortality of RECOVERY participants recruited in England (n\u2009=\u200938,510) with a reference population hospitalised with COVID-19 in England (n\u2009=\u2009346,271) from March 2020 to November 2021. We used linked hospitalisation and mortality data for both cohorts to extract demographics, comorbidity/frailty scores, and crude and age- and sex-adjusted 28-day all-cause mortality.<h4>Results</h4>Demographics of RECOVERY participants were broadly similar to the reference population, but RECOVERY participants were younger (mean age [standard deviation]: RECOVERY 62.6 [15.3] vs reference 65.7 [18.5] years) and less frequently female (37% vs 45%). Comorbidity and frailty scores were lower in RECOVERY, but differences were attenuated after age stratification. Age- and sex-adjusted 28-day mortality declined over time but was similar between cohorts across the study period (RECOVERY 23.7% [95% confidence interval: 23.3-24.1%]; vs reference 24.8% [24.6-25.0%]), except during the first pandemic wave in the UK (March-May 2020) when adjusted mortality was lower in RECOVERY.<h4>Conclusions</h4>Adjusted 28-day mortality in RECOVERY was similar to a nationwide reference population of patients admitted with COVID-19 in England during the same period but varied substantially over time in both cohorts. Therefore, the absolute effect estimates from RECOVERY were broadly applicable to the target population at the time but should be interpreted in the light of current mortality estimates.<h4>Trial registration</h4>ISRCTN50189673- Feb. 04, 2020, NCT04381936- May 11, 2020.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1186/s13063-024-08273-9; doi:https://doi.org/10.1186/s13063-024-08273-9; html:https://europepmc.org/articles/PMC11218071; pdf:https://europepmc.org/articles/PMC11218071?pdf=render"
+  },
+  {
+    "id": "31479767",
+    "doi": "https://doi.org/10.1016/j.jaip.2019.08.030",
+    "title": "Atopic Eczema in Adulthood and Risk of Depression and Anxiety: A Population-Based Cohort Study.",
+    "authorString": "Schonmann Y, Mansfield KE, Hayes JF, Abuabara K, Roberts A, Smeeth L, Langan SM.",
+    "authorAffiliations": "",
+    "journalTitle": "The journal of allergy and clinical immunology. In practice",
+    "pubYear": "2020",
+    "date": "2019-08-31",
+    "isOpenAccess": "Y",
+    "keywords": "Depression; Anxiety; Atopic Eczema; Atopic Dermatitis; Severity; Population-based",
+    "nationalPriorities": "Understanding the Causes of Disease",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Atopic eczema is a common and debilitating condition associated with depression and anxiety, but the nature of this association remains unclear.<h4>Objective</h4>To explore the temporal relationship between atopic eczema and new depression/anxiety.<h4>Methods</h4>This matched cohort study used routinely collected data from the UK Clinical Practice Research Datalink, linked to hospital admissions data. We identified adults with atopic eczema (1998-2016) using a validated algorithm, and up to 5 individuals without atopic eczema matched on date of diagnosis, age, sex, and general practice. We estimated the hazard ratio (HR) for new depression/anxiety using stratified Cox regression to account for age, sex, calendar period, Index of Multiple Deprivation, glucocorticoid treatment, obesity, smoking, and harmful alcohol use.<h4>Results</h4>We identified 526,808 adults with atopic eczema who were matched to 2,569,030 without. Atopic eczema was associated with increased incidence of new depression (HR, 1.14; 99% CI, 1.12-1.16) and anxiety (HR, 1.17; 99% CI, 1.14-1.19). We observed a stronger effect of atopic eczema on depression with increasing atopic eczema severity (HR [99% CI] compared with no atopic eczema: mild, 1.10 [1.08-1.13]; moderate, 1.19 [1.15-1.23]; and severe, 1.26 [1.17-1.37]). A dose-response association, however, was less apparent for new anxiety diagnosis (HR [99% CI] compared with no atopic eczema: mild, 1.14 [1.11-1.18]; moderate, 1.21 [1.17-1.26]; and severe, 1.15; [1.05-1.25]).<h4>Conclusions</h4>Adults with atopic eczema are more likely to develop new depression and anxiety. For depression, we observed a dose-response relationship with atopic eczema severity.",
+    "laySummary": "",
+    "urls": "pdf:http://www.jaci-inpractice.org/article/S2213219819307536/pdf; doi:https://doi.org/10.1016/j.jaip.2019.08.030; html:https://europepmc.org/articles/PMC6947493; pdf:https://europepmc.org/articles/PMC6947493?pdf=render"
+  },
   {
     "id": "34606520",
     "doi": "https://doi.org/10.1371/journal.pmed.1003815",
@@ -29393,21 +29427,21 @@
     "urls": "pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003815&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003815; html:https://europepmc.org/articles/PMC8523052; pdf:https://europepmc.org/articles/PMC8523052?pdf=render"
   },
   {
-    "id": "31747863",
-    "doi": "https://doi.org/10.1161/jaha.119.012551",
-    "title": "UVA and Seasonal Patterning of 56\u00a0370 Myocardial Infarctions Across Scotland, 2000-2011.",
-    "authorString": "Mackay DF, Clemens TL, Hastie CE, Cherrie MPC, Dibben C, Pell JP.",
+    "id": "32814581",
+    "doi": "https://doi.org/10.1186/s12916-020-01687-7",
+    "title": "Seasonal influenza vaccination in Kenya: an economic evaluation using dynamic transmission modelling.",
+    "authorString": "Dawa J, Emukule GO, Barasa E, Widdowson MA, Anzala O, van Leeuwen E, Baguelin M, Chaves SS, Eggo RM.",
     "authorAffiliations": "",
-    "journalTitle": "Journal of the American Heart Association",
-    "pubYear": "2019",
-    "date": "2019-11-21",
+    "journalTitle": "BMC medicine",
+    "pubYear": "2020",
+    "date": "2020-08-20",
     "isOpenAccess": "Y",
-    "keywords": "Environmental factors; UV radiation; Myocardial infarction; epidemiology",
-    "nationalPriorities": "Improving Public Health, Understanding the Causes of Disease",
+    "keywords": "Economic evaluation; Influenza vaccine; Cost-effectiveness; Low- And Middle-income Countries; Dynamic Transmission Model; Vaccine Timing; Vaccine Target Group",
+    "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Background Myocardial infarction exhibits seasonal patterning, with higher amplitude at increased latitude. Epidemiological evidence suggests that sunlight is protective against cardiovascular disease, independent of ambient temperature, but ultraviolet B-mediated vitamin D production has been discounted as causal. We aimed to determine whether ultraviolet A is associated with the seasonal patterning of myocardial infarction. Methods and Results Routine hospitalization data were used to determine monthly incidence of myocardial infarction in Scotland between 2000 and 2011. Small-area-level aggregated data were obtained on ambient temperature from the Meteorological Office and ultraviolet A and ultraviolet B irradiance from NASA satellites. Autoregressive distributed lag models were run for ultraviolet A and myocardial infarction, including adjustment for ambient temperature and ultraviolet B. Monthly incidence of myocardial infarction displayed winter peaks and summer troughs superimposed on the underlying trend, with a mean amplitude of 0.31 (95% CI: 0.21, 0.41) myocardial infarctions per 100\u00a0000 population per month. Ultraviolet A exposure was inversely associated with myocardial infarction independent of ambient temperature (coefficient, -0.05; 95% CI, -0.09, -0.01; <i>P</i>=0.015) and ultraviolet B UVB (coefficient, -0.05; 95% CI, -0.09, -0.02; <i>P</i>=0.004). Conclusions Further research is required to explore whether an ultraviolet-mediated mechanism different to vitamin D, such as nitric oxide-mediated vasodilatation, may play a causal role in the seasonal and geographical patterning of myocardial infarction.",
+    "abstract": "<h4>Background</h4>There is substantial burden of seasonal influenza in Kenya, which led the government to consider introducing a national influenza vaccination programme. Given the cost implications of a nationwide programme, local economic evaluation data are needed to inform policy on the design and benefits of influenza vaccination. We set out to estimate the cost-effectiveness of seasonal influenza vaccination in Kenya.<h4>Methods</h4>We fitted an age-stratified dynamic transmission model to active surveillance data from patients with influenza from 2010 to 2018. Using a societal perspective, we developed a decision tree cost-effectiveness model and estimated the incremental cost-effectiveness ratio (ICER) per disability-adjusted life year (DALY) averted for three vaccine target groups: children 6-23\u2009months (strategy I), 2-5\u2009years (strategy II) and 6-14\u2009years (strategy III) with either the Southern Hemisphere influenza vaccine (Strategy A) or Northern Hemisphere vaccine (Strategy B) or both (Strategy C: twice yearly vaccination campaigns, or Strategy D: year-round vaccination campaigns). We assessed cost-effectiveness by calculating incremental net monetary benefits (INMB) using a willingness-to-pay (WTP) threshold of 1-51% of the annual gross domestic product per capita ($17-$872).<h4>Results</h4>The mean number of infections across all ages was 2-15 million per year. When vaccination was well timed to influenza activity, the annual mean ICER per DALY averted for vaccinating children 6-23\u2009months ranged between $749 and $1385 for strategy IA, $442 and $1877 for strategy IB, $678 and $4106 for strategy IC and $1147 and $7933 for strategy ID. For children 2-5\u2009years, it ranged between $945 and $1573 for strategy IIA, $563 and $1869 for strategy IIB, $662 and $4085 for strategy IIC, and $1169 and $7897 for strategy IID. For children 6-14\u2009years, it ranged between $923 and $3116 for strategy IIIA, $1005 and $2223 for strategy IIIB, $883 and $4727 for strategy IIIC and $1467 and $6813 for strategy IIID. Overall, no vaccination strategy was cost-effective at the minimum ($17) and median ($445) WTP thresholds. Vaccinating children 6-23\u2009months once a year had the highest mean INMB value at $872 (WTP threshold upper limit); however, this strategy had very low probability of the highest net benefit.<h4>Conclusion</h4>Vaccinating children 6-23\u2009months once a year was the most favourable vaccination option; however, the strategy is unlikely to be cost-effective given the current WTP thresholds.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1161/jaha.119.012551; doi:https://doi.org/10.1161/JAHA.119.012551; html:https://europepmc.org/articles/PMC6912961; pdf:https://europepmc.org/articles/PMC6912961?pdf=render"
+    "urls": "pdf:https://bmcmedicine.biomedcentral.com/track/pdf/10.1186/s12916-020-01687-7; doi:https://doi.org/10.1186/s12916-020-01687-7; html:https://europepmc.org/articles/PMC7438179; pdf:https://europepmc.org/articles/PMC7438179?pdf=render"
   },
   {
     "id": "37198662",
@@ -29427,21 +29461,21 @@
     "urls": "pdf:https://bsd.biomedcentral.com/counter/pdf/10.1186/s13293-023-00516-9; doi:https://doi.org/10.1186/s13293-023-00516-9; html:https://europepmc.org/articles/PMC10193800; pdf:https://europepmc.org/articles/PMC10193800?pdf=render"
   },
   {
-    "id": "32814581",
-    "doi": "https://doi.org/10.1186/s12916-020-01687-7",
-    "title": "Seasonal influenza vaccination in Kenya: an economic evaluation using dynamic transmission modelling.",
-    "authorString": "Dawa J, Emukule GO, Barasa E, Widdowson MA, Anzala O, van Leeuwen E, Baguelin M, Chaves SS, Eggo RM.",
+    "id": "31747863",
+    "doi": "https://doi.org/10.1161/jaha.119.012551",
+    "title": "UVA and Seasonal Patterning of 56\u00a0370 Myocardial Infarctions Across Scotland, 2000-2011.",
+    "authorString": "Mackay DF, Clemens TL, Hastie CE, Cherrie MPC, Dibben C, Pell JP.",
     "authorAffiliations": "",
-    "journalTitle": "BMC medicine",
-    "pubYear": "2020",
-    "date": "2020-08-20",
+    "journalTitle": "Journal of the American Heart Association",
+    "pubYear": "2019",
+    "date": "2019-11-21",
     "isOpenAccess": "Y",
-    "keywords": "Economic evaluation; Influenza vaccine; Cost-effectiveness; Low- And Middle-income Countries; Dynamic Transmission Model; Vaccine Timing; Vaccine Target Group",
-    "nationalPriorities": "",
+    "keywords": "Environmental factors; UV radiation; Myocardial infarction; epidemiology",
+    "nationalPriorities": "Improving Public Health, Understanding the Causes of Disease",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>There is substantial burden of seasonal influenza in Kenya, which led the government to consider introducing a national influenza vaccination programme. Given the cost implications of a nationwide programme, local economic evaluation data are needed to inform policy on the design and benefits of influenza vaccination. We set out to estimate the cost-effectiveness of seasonal influenza vaccination in Kenya.<h4>Methods</h4>We fitted an age-stratified dynamic transmission model to active surveillance data from patients with influenza from 2010 to 2018. Using a societal perspective, we developed a decision tree cost-effectiveness model and estimated the incremental cost-effectiveness ratio (ICER) per disability-adjusted life year (DALY) averted for three vaccine target groups: children 6-23\u2009months (strategy I), 2-5\u2009years (strategy II) and 6-14\u2009years (strategy III) with either the Southern Hemisphere influenza vaccine (Strategy A) or Northern Hemisphere vaccine (Strategy B) or both (Strategy C: twice yearly vaccination campaigns, or Strategy D: year-round vaccination campaigns). We assessed cost-effectiveness by calculating incremental net monetary benefits (INMB) using a willingness-to-pay (WTP) threshold of 1-51% of the annual gross domestic product per capita ($17-$872).<h4>Results</h4>The mean number of infections across all ages was 2-15 million per year. When vaccination was well timed to influenza activity, the annual mean ICER per DALY averted for vaccinating children 6-23\u2009months ranged between $749 and $1385 for strategy IA, $442 and $1877 for strategy IB, $678 and $4106 for strategy IC and $1147 and $7933 for strategy ID. For children 2-5\u2009years, it ranged between $945 and $1573 for strategy IIA, $563 and $1869 for strategy IIB, $662 and $4085 for strategy IIC, and $1169 and $7897 for strategy IID. For children 6-14\u2009years, it ranged between $923 and $3116 for strategy IIIA, $1005 and $2223 for strategy IIIB, $883 and $4727 for strategy IIIC and $1467 and $6813 for strategy IIID. Overall, no vaccination strategy was cost-effective at the minimum ($17) and median ($445) WTP thresholds. Vaccinating children 6-23\u2009months once a year had the highest mean INMB value at $872 (WTP threshold upper limit); however, this strategy had very low probability of the highest net benefit.<h4>Conclusion</h4>Vaccinating children 6-23\u2009months once a year was the most favourable vaccination option; however, the strategy is unlikely to be cost-effective given the current WTP thresholds.",
+    "abstract": "Background Myocardial infarction exhibits seasonal patterning, with higher amplitude at increased latitude. Epidemiological evidence suggests that sunlight is protective against cardiovascular disease, independent of ambient temperature, but ultraviolet B-mediated vitamin D production has been discounted as causal. We aimed to determine whether ultraviolet A is associated with the seasonal patterning of myocardial infarction. Methods and Results Routine hospitalization data were used to determine monthly incidence of myocardial infarction in Scotland between 2000 and 2011. Small-area-level aggregated data were obtained on ambient temperature from the Meteorological Office and ultraviolet A and ultraviolet B irradiance from NASA satellites. Autoregressive distributed lag models were run for ultraviolet A and myocardial infarction, including adjustment for ambient temperature and ultraviolet B. Monthly incidence of myocardial infarction displayed winter peaks and summer troughs superimposed on the underlying trend, with a mean amplitude of 0.31 (95% CI: 0.21, 0.41) myocardial infarctions per 100\u00a0000 population per month. Ultraviolet A exposure was inversely associated with myocardial infarction independent of ambient temperature (coefficient, -0.05; 95% CI, -0.09, -0.01; <i>P</i>=0.015) and ultraviolet B UVB (coefficient, -0.05; 95% CI, -0.09, -0.02; <i>P</i>=0.004). Conclusions Further research is required to explore whether an ultraviolet-mediated mechanism different to vitamin D, such as nitric oxide-mediated vasodilatation, may play a causal role in the seasonal and geographical patterning of myocardial infarction.",
     "laySummary": "",
-    "urls": "pdf:https://bmcmedicine.biomedcentral.com/track/pdf/10.1186/s12916-020-01687-7; doi:https://doi.org/10.1186/s12916-020-01687-7; html:https://europepmc.org/articles/PMC7438179; pdf:https://europepmc.org/articles/PMC7438179?pdf=render"
+    "urls": "doi:https://doi.org/10.1161/jaha.119.012551; doi:https://doi.org/10.1161/JAHA.119.012551; html:https://europepmc.org/articles/PMC6912961; pdf:https://europepmc.org/articles/PMC6912961?pdf=render"
   },
   {
     "id": "PMC11210061",
@@ -29460,23 +29494,6 @@
     "laySummary": "",
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11210061/?tool=EBI; pdf:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11210061/pdf/?tool=EBI; html:https://europepmc.org/articles/PMC11210061; pdf:https://europepmc.org/articles/PMC11210061?pdf=render"
   },
-  {
-    "id": "37993464",
-    "doi": "https://doi.org/10.1038/s41467-023-43434-5",
-    "title": "Structure of the N-RNA/P interface indicates mode of L/P recruitment to the nucleocapsid of human metapneumovirus.",
-    "authorString": "Whitehead JD, Decool H, Leyrat C, Carrique L, Fix J, El\u00e9ou\u00ebt JF, Galloux M, Renner M.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature communications",
-    "pubYear": "2023",
-    "date": "2023-11-22",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Human metapneumovirus (HMPV) is a major cause of respiratory illness in young children. The HMPV polymerase (L) binds an obligate cofactor, the phosphoprotein (P). During replication and transcription, the L/P complex traverses the viral RNA genome, which is encapsidated within nucleoproteins (N). An essential interaction between N and a C-terminal region of P tethers the L/P polymerase to the template. This N-P interaction is also involved in the formation of cytoplasmic viral factories in infected cells, called inclusion bodies. To define how the polymerase component P recognizes N-encapsidated RNA (N-RNA) we employed cryogenic electron microscopy (cryo-EM) and molecular dynamics simulations, coupled to activity assays and imaging of inclusion bodies in cells. We report a 2.9\u2009\u00c5 resolution structure of a triple-complex between multimeric N, bound to both RNA and the C-terminal region of P. Furthermore, we also present cryo-EM structures of assembled N in different oligomeric states, highlighting the plasticity of N. Combined with our functional assays, these structural data delineate in molecular detail how P attaches to N-RNA whilst retaining substantial conformational dynamics. Moreover, the N-RNA-P triple complex structure provides a molecular blueprint for the design of therapeutics to potentially disrupt the attachment of L/P to its template.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41467-023-43434-5.pdf; doi:https://doi.org/10.1038/s41467-023-43434-5; html:https://europepmc.org/articles/PMC10665349; pdf:https://europepmc.org/articles/PMC10665349?pdf=render"
-  },
   {
     "id": "35410933",
     "doi": "https://doi.org/10.1136/bmjopen-2021-057885",
@@ -29494,6 +29511,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/4/e057885.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-057885; html:https://europepmc.org/articles/PMC9002258; pdf:https://europepmc.org/articles/PMC9002258?pdf=render"
   },
+  {
+    "id": "37993464",
+    "doi": "https://doi.org/10.1038/s41467-023-43434-5",
+    "title": "Structure of the N-RNA/P interface indicates mode of L/P recruitment to the nucleocapsid of human metapneumovirus.",
+    "authorString": "Whitehead JD, Decool H, Leyrat C, Carrique L, Fix J, El\u00e9ou\u00ebt JF, Galloux M, Renner M.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature communications",
+    "pubYear": "2023",
+    "date": "2023-11-22",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Human metapneumovirus (HMPV) is a major cause of respiratory illness in young children. The HMPV polymerase (L) binds an obligate cofactor, the phosphoprotein (P). During replication and transcription, the L/P complex traverses the viral RNA genome, which is encapsidated within nucleoproteins (N). An essential interaction between N and a C-terminal region of P tethers the L/P polymerase to the template. This N-P interaction is also involved in the formation of cytoplasmic viral factories in infected cells, called inclusion bodies. To define how the polymerase component P recognizes N-encapsidated RNA (N-RNA) we employed cryogenic electron microscopy (cryo-EM) and molecular dynamics simulations, coupled to activity assays and imaging of inclusion bodies in cells. We report a 2.9\u2009\u00c5 resolution structure of a triple-complex between multimeric N, bound to both RNA and the C-terminal region of P. Furthermore, we also present cryo-EM structures of assembled N in different oligomeric states, highlighting the plasticity of N. Combined with our functional assays, these structural data delineate in molecular detail how P attaches to N-RNA whilst retaining substantial conformational dynamics. Moreover, the N-RNA-P triple complex structure provides a molecular blueprint for the design of therapeutics to potentially disrupt the attachment of L/P to its template.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41467-023-43434-5.pdf; doi:https://doi.org/10.1038/s41467-023-43434-5; html:https://europepmc.org/articles/PMC10665349; pdf:https://europepmc.org/articles/PMC10665349?pdf=render"
+  },
   {
     "id": "37180793",
     "doi": "https://doi.org/10.3389/fcvm.2023.1136764",
@@ -29511,23 +29545,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2023.1136764/pdf; doi:https://doi.org/10.3389/fcvm.2023.1136764; html:https://europepmc.org/articles/PMC10167048; pdf:https://europepmc.org/articles/PMC10167048?pdf=render"
   },
-  {
-    "id": "36273236",
-    "doi": "https://doi.org/10.1038/s41746-022-00705-7",
-    "title": "Automated clinical coding: what, why, and where we are?",
-    "authorString": "Dong H, Falis M, Whiteley W, Alex B, Matterson J, Ji S, Chen J, Wu H.",
-    "authorAffiliations": "",
-    "journalTitle": "NPJ digital medicine",
-    "pubYear": "2022",
-    "date": "2022-10-22",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Clinical coding is the task of transforming medical information in a patient's health records into structured codes so that they can be used for statistical analysis. This is a cognitive and time-consuming task that follows a standard process in order to achieve a high level of consistency. Clinical coding could potentially be supported by an automated system to improve the efficiency and accuracy of the process. We introduce the idea of automated clinical coding and summarise its challenges from the perspective of Artificial Intelligence (AI) and Natural Language Processing (NLP), based on the literature, our project experience over the past two and half years (late 2019-early 2022), and discussions with clinical coding experts in Scotland and the UK. Our research reveals the gaps between the current deep learning-based approach applied to clinical coding and the need for explainability and consistency in real-world practice. Knowledge-based methods that represent and reason the standard, explainable process of a task may need to be incorporated into deep learning-based methods for clinical coding. Automated clinical coding is a promising task for AI, despite the technical and organisational challenges. Coders are needed to be involved in the development process. There is much to achieve to develop and deploy an AI-based automated system to support coding in the next five years and beyond.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41746-022-00705-7.pdf; doi:https://doi.org/10.1038/s41746-022-00705-7; html:https://europepmc.org/articles/PMC9588058; pdf:https://europepmc.org/articles/PMC9588058?pdf=render"
-  },
   {
     "id": "33779119",
     "doi": "https://doi.org/10.1002/ejhf.2169",
@@ -29545,6 +29562,23 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ejhf.2169; doi:https://doi.org/10.1002/ejhf.2169; html:https://europepmc.org/articles/PMC8359985; pdf:https://europepmc.org/articles/PMC8359985?pdf=render"
   },
+  {
+    "id": "36273236",
+    "doi": "https://doi.org/10.1038/s41746-022-00705-7",
+    "title": "Automated clinical coding: what, why, and where we are?",
+    "authorString": "Dong H, Falis M, Whiteley W, Alex B, Matterson J, Ji S, Chen J, Wu H.",
+    "authorAffiliations": "",
+    "journalTitle": "NPJ digital medicine",
+    "pubYear": "2022",
+    "date": "2022-10-22",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Clinical coding is the task of transforming medical information in a patient's health records into structured codes so that they can be used for statistical analysis. This is a cognitive and time-consuming task that follows a standard process in order to achieve a high level of consistency. Clinical coding could potentially be supported by an automated system to improve the efficiency and accuracy of the process. We introduce the idea of automated clinical coding and summarise its challenges from the perspective of Artificial Intelligence (AI) and Natural Language Processing (NLP), based on the literature, our project experience over the past two and half years (late 2019-early 2022), and discussions with clinical coding experts in Scotland and the UK. Our research reveals the gaps between the current deep learning-based approach applied to clinical coding and the need for explainability and consistency in real-world practice. Knowledge-based methods that represent and reason the standard, explainable process of a task may need to be incorporated into deep learning-based methods for clinical coding. Automated clinical coding is a promising task for AI, despite the technical and organisational challenges. Coders are needed to be involved in the development process. There is much to achieve to develop and deploy an AI-based automated system to support coding in the next five years and beyond.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41746-022-00705-7.pdf; doi:https://doi.org/10.1038/s41746-022-00705-7; html:https://europepmc.org/articles/PMC9588058; pdf:https://europepmc.org/articles/PMC9588058?pdf=render"
+  },
   {
     "id": "37735103",
     "doi": "https://doi.org/10.1136/bmjresp-2023-001895",
@@ -29597,21 +29631,21 @@
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8288152; doi:https://doi.org/10.1016/j.lanepe.2021.100267; html:https://europepmc.org/articles/PMC8629724; pdf:https://europepmc.org/articles/PMC8629724?pdf=render"
   },
   {
-    "id": "31994239",
-    "doi": "https://doi.org/10.1002/bimj.201900041",
-    "title": "Estimating treatment effects with partially observed covariates using outcome regression with missing indicators.",
-    "authorString": "Blake HA, Leyrat C, Mansfield KE, Tomlinson LA, Carpenter J, Williamson EJ.",
+    "id": "35381001",
+    "doi": "https://doi.org/10.1371/journal.pgen.1010093",
+    "title": "Analyzing human knockouts to validate GPR151 as a therapeutic target for reduction of body mass index.",
+    "authorString": "Gurtan A, Dominy J, Khalid S, Vong L, Caplan S, Currie T, Richards S, Lamarche L, Denning D, Shpektor D, Gurinovich A, Rasheed A, Hameed S, Saeed S, Saleem I, Jalal A, Abbas S, Sultana R, Rasheed SZ, Memon FU, Shah N, Ishaq M, Khera AV, Danesh J, Frossard P, Saleheen D.",
     "authorAffiliations": "",
-    "journalTitle": "Biometrical journal. Biometrische Zeitschrift",
-    "pubYear": "2020",
-    "date": "2020-01-29",
-    "isOpenAccess": "N",
-    "keywords": "Average Treatment Effect; Outcome Regression; Missing Covariate Data; Missing Indicator; Missing Confounder Data",
+    "journalTitle": "PLoS genetics",
+    "pubYear": "2022",
+    "date": "2022-04-05",
+    "isOpenAccess": "Y",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Missing data is a common issue in research using observational studies to investigate the effect of treatments on health outcomes. When missingness occurs only in the covariates, a simple approach is to use missing indicators to handle the partially observed covariates. The missing indicator approach has been criticized for giving biased results in outcome regression. However, recent papers have suggested that the missing indicator approach can provide unbiased results in propensity score analysis under certain assumptions. We consider assumptions under which the missing indicator approach can provide valid inferences, namely, (1) no unmeasured confounding within missingness patterns; either (2a) covariate values of patients with missing data were conditionally independent of treatment or (2b) these values were conditionally independent of outcome; and (3) the outcome model is correctly specified: specifically, the true outcome model does not include interactions between missing indicators and fully observed covariates. We prove that, under the assumptions above, the missing indicator approach with outcome regression can provide unbiased estimates of the average treatment effect. We use a simulation study to investigate the extent of bias in estimates of the treatment effect when the assumptions are violated and we illustrate our findings using data from electronic health records. In conclusion, the missing indicator approach can provide valid inferences for outcome regression, but the plausibility of its assumptions must first be considered\u00a0carefully.",
+    "abstract": "Novel drug targets for sustained reduction in body mass index (BMI) are needed to curb the epidemic of obesity, which affects 650 million individuals worldwide and is a causal driver of cardiovascular and metabolic disease and mortality. Previous studies reported that the Arg95Ter nonsense variant of GPR151, an orphan G protein-coupled receptor, is associated with reduced BMI and reduced risk of Type 2 Diabetes (T2D). Here, we further investigate GPR151 with the Pakistan Genome Resource (PGR), which is one of the largest exome biobanks of human homozygous loss-of-function carriers (knockouts) in the world. Among PGR participants, we identify eleven GPR151 putative loss-of-function (plof) variants, three of which are present at homozygosity (Arg95Ter, Tyr99Ter, and Phe175LeufsTer7), with a cumulative allele frequency of 2.2%. We confirm these alleles in vitro as loss-of-function. We test if GPR151 plof is associated with BMI, T2D, or other metabolic traits and find that GPR151 deficiency in complete human knockouts is not associated with clinically significant differences in these traits. Relative to Gpr151+/+ mice, Gpr151-/- animals exhibit no difference in body weight on normal chow and higher body weight on a high-fat diet. Together, our findings indicate that GPR151 antagonism is not a compelling therapeutic approach to treatment of obesity.",
     "laySummary": "",
-    "urls": "pdf:https://researchonline.lshtm.ac.uk/id/eprint/4655332/1/Estimating-treatment-effects-with-partially-observed-covariates-using-outcome-regression-with-missing-indicators.pdf; doi:https://doi.org/10.1002/bimj.201900041"
+    "urls": "pdf:https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1010093&type=printable; doi:https://doi.org/10.1371/journal.pgen.1010093; html:https://europepmc.org/articles/PMC9022822; pdf:https://europepmc.org/articles/PMC9022822?pdf=render"
   },
   {
     "id": "31282950",
@@ -29631,21 +29665,21 @@
     "urls": "pdf:https://jamanetwork.com/journals/jamaneurology/articlepdf/2737044/jamaneurology_adderley_2019_oi_190046.pdf; doi:https://doi.org/10.1001/jamaneurol.2019.1812; html:https://europepmc.org/articles/PMC6618853"
   },
   {
-    "id": "35381001",
-    "doi": "https://doi.org/10.1371/journal.pgen.1010093",
-    "title": "Analyzing human knockouts to validate GPR151 as a therapeutic target for reduction of body mass index.",
-    "authorString": "Gurtan A, Dominy J, Khalid S, Vong L, Caplan S, Currie T, Richards S, Lamarche L, Denning D, Shpektor D, Gurinovich A, Rasheed A, Hameed S, Saeed S, Saleem I, Jalal A, Abbas S, Sultana R, Rasheed SZ, Memon FU, Shah N, Ishaq M, Khera AV, Danesh J, Frossard P, Saleheen D.",
+    "id": "31994239",
+    "doi": "https://doi.org/10.1002/bimj.201900041",
+    "title": "Estimating treatment effects with partially observed covariates using outcome regression with missing indicators.",
+    "authorString": "Blake HA, Leyrat C, Mansfield KE, Tomlinson LA, Carpenter J, Williamson EJ.",
     "authorAffiliations": "",
-    "journalTitle": "PLoS genetics",
-    "pubYear": "2022",
-    "date": "2022-04-05",
-    "isOpenAccess": "Y",
-    "keywords": "",
+    "journalTitle": "Biometrical journal. Biometrische Zeitschrift",
+    "pubYear": "2020",
+    "date": "2020-01-29",
+    "isOpenAccess": "N",
+    "keywords": "Average Treatment Effect; Outcome Regression; Missing Covariate Data; Missing Indicator; Missing Confounder Data",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Novel drug targets for sustained reduction in body mass index (BMI) are needed to curb the epidemic of obesity, which affects 650 million individuals worldwide and is a causal driver of cardiovascular and metabolic disease and mortality. Previous studies reported that the Arg95Ter nonsense variant of GPR151, an orphan G protein-coupled receptor, is associated with reduced BMI and reduced risk of Type 2 Diabetes (T2D). Here, we further investigate GPR151 with the Pakistan Genome Resource (PGR), which is one of the largest exome biobanks of human homozygous loss-of-function carriers (knockouts) in the world. Among PGR participants, we identify eleven GPR151 putative loss-of-function (plof) variants, three of which are present at homozygosity (Arg95Ter, Tyr99Ter, and Phe175LeufsTer7), with a cumulative allele frequency of 2.2%. We confirm these alleles in vitro as loss-of-function. We test if GPR151 plof is associated with BMI, T2D, or other metabolic traits and find that GPR151 deficiency in complete human knockouts is not associated with clinically significant differences in these traits. Relative to Gpr151+/+ mice, Gpr151-/- animals exhibit no difference in body weight on normal chow and higher body weight on a high-fat diet. Together, our findings indicate that GPR151 antagonism is not a compelling therapeutic approach to treatment of obesity.",
+    "abstract": "Missing data is a common issue in research using observational studies to investigate the effect of treatments on health outcomes. When missingness occurs only in the covariates, a simple approach is to use missing indicators to handle the partially observed covariates. The missing indicator approach has been criticized for giving biased results in outcome regression. However, recent papers have suggested that the missing indicator approach can provide unbiased results in propensity score analysis under certain assumptions. We consider assumptions under which the missing indicator approach can provide valid inferences, namely, (1) no unmeasured confounding within missingness patterns; either (2a) covariate values of patients with missing data were conditionally independent of treatment or (2b) these values were conditionally independent of outcome; and (3) the outcome model is correctly specified: specifically, the true outcome model does not include interactions between missing indicators and fully observed covariates. We prove that, under the assumptions above, the missing indicator approach with outcome regression can provide unbiased estimates of the average treatment effect. We use a simulation study to investigate the extent of bias in estimates of the treatment effect when the assumptions are violated and we illustrate our findings using data from electronic health records. In conclusion, the missing indicator approach can provide valid inferences for outcome regression, but the plausibility of its assumptions must first be considered\u00a0carefully.",
     "laySummary": "",
-    "urls": "pdf:https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1010093&type=printable; doi:https://doi.org/10.1371/journal.pgen.1010093; html:https://europepmc.org/articles/PMC9022822; pdf:https://europepmc.org/articles/PMC9022822?pdf=render"
+    "urls": "pdf:https://researchonline.lshtm.ac.uk/id/eprint/4655332/1/Estimating-treatment-effects-with-partially-observed-covariates-using-outcome-regression-with-missing-indicators.pdf; doi:https://doi.org/10.1002/bimj.201900041"
   },
   {
     "id": "32709646",
@@ -29749,23 +29783,6 @@
     "laySummary": "",
     "urls": "pdf:http://pure-oai.bham.ac.uk/ws/files/143736502/ceo.13943.pdf; doi:https://doi.org/10.1111/ceo.13943"
   },
-  {
-    "id": "35953815",
-    "doi": "https://doi.org/10.1186/s12931-022-02130-6",
-    "title": "Dynamic early warning scores for predicting clinical deterioration in patients with respiratory disease.",
-    "authorString": "Gonem S, Taylor A, Figueredo G, Forster S, Quinlan P, Garibaldi JM, McKeever TM, Shaw D.",
-    "authorAffiliations": "",
-    "journalTitle": "Respiratory research",
-    "pubYear": "2022",
-    "date": "2022-08-11",
-    "isOpenAccess": "Y",
-    "keywords": "Risk Prediction; Clinical Deterioration; Early Warning Score",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>The National Early Warning Score-2 (NEWS-2) is used to detect patient deterioration in UK hospitals but fails to take account of the detailed granularity or temporal trends in clinical observations. We used data-driven methods to develop dynamic early warning scores (DEWS) to address these deficiencies, and tested their accuracy in patients with respiratory disease for predicting (1) death or intensive care unit admission, occurring within 24\u00a0h (D/ICU), and (2) clinically significant deterioration requiring urgent intervention, occurring within 4\u00a0h (CSD).<h4>Methods</h4>Clinical observations data were extracted from electronic records for 31,590 respiratory in-patient episodes from April 2015 to December 2020 at a large acute NHS Trust. The timing of D/ICU was extracted for all episodes. 1100 in-patient episodes were annotated manually to record the timing of CSD, defined as a specific event requiring a change in treatment. Time series features were entered into logistic regression models to derive DEWS for each of the clinical outcomes. Area under the receiver operating characteristic curve (AUROC) was the primary measure of model accuracy.<h4>Results</h4>AUROC (95% confidence interval) for predicting D/ICU was 0.857 (0.852-0.862) for NEWS-2 and 0.906 (0.899-0.914) for DEWS in the validation data. AUROC for predicting CSD was 0.829 (0.817-0.842) for NEWS-2 and 0.877 (0.862-0.892) for DEWS. NEWS-2\u2009\u2265\u20095 had sensitivity of 88.2% and specificity of 54.2% for predicting CSD, while DEWS\u2009\u2265\u20090.021 had higher sensitivity of 93.6% and approximately the same specificity of 54.3% for the same outcome. Using these cut-offs, 315 out of 347 (90.8%) CSD events were detected by both NEWS-2 and DEWS, at the time of the event or within the previous 4\u00a0h; 12 (3.5%) were detected by DEWS but not by NEWS-2, while 4 (1.2%) were detected by NEWS-2 but not by DEWS; 16 (4.6%) were not detected by either scoring system.<h4>Conclusion</h4>We have developed DEWS that display greater accuracy than NEWS-2 for predicting clinical deterioration events in patients with respiratory disease. Prospective validation studies are required to assess whether DEWS can be used to reduce missed deteriorations and false alarms in real-life clinical settings.",
-    "laySummary": "",
-    "urls": "pdf:https://respiratory-research.biomedcentral.com/counter/pdf/10.1186/s12931-022-02130-6; doi:https://doi.org/10.1186/s12931-022-02130-6; html:https://europepmc.org/articles/PMC9367123; pdf:https://europepmc.org/articles/PMC9367123?pdf=render"
-  },
   {
     "id": "39421942",
     "doi": "https://doi.org/10.7189/jogh.14.03042",
@@ -29800,6 +29817,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1007/s11136-021-02876-4"
   },
+  {
+    "id": "35953815",
+    "doi": "https://doi.org/10.1186/s12931-022-02130-6",
+    "title": "Dynamic early warning scores for predicting clinical deterioration in patients with respiratory disease.",
+    "authorString": "Gonem S, Taylor A, Figueredo G, Forster S, Quinlan P, Garibaldi JM, McKeever TM, Shaw D.",
+    "authorAffiliations": "",
+    "journalTitle": "Respiratory research",
+    "pubYear": "2022",
+    "date": "2022-08-11",
+    "isOpenAccess": "Y",
+    "keywords": "Risk Prediction; Clinical Deterioration; Early Warning Score",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>The National Early Warning Score-2 (NEWS-2) is used to detect patient deterioration in UK hospitals but fails to take account of the detailed granularity or temporal trends in clinical observations. We used data-driven methods to develop dynamic early warning scores (DEWS) to address these deficiencies, and tested their accuracy in patients with respiratory disease for predicting (1) death or intensive care unit admission, occurring within 24\u00a0h (D/ICU), and (2) clinically significant deterioration requiring urgent intervention, occurring within 4\u00a0h (CSD).<h4>Methods</h4>Clinical observations data were extracted from electronic records for 31,590 respiratory in-patient episodes from April 2015 to December 2020 at a large acute NHS Trust. The timing of D/ICU was extracted for all episodes. 1100 in-patient episodes were annotated manually to record the timing of CSD, defined as a specific event requiring a change in treatment. Time series features were entered into logistic regression models to derive DEWS for each of the clinical outcomes. Area under the receiver operating characteristic curve (AUROC) was the primary measure of model accuracy.<h4>Results</h4>AUROC (95% confidence interval) for predicting D/ICU was 0.857 (0.852-0.862) for NEWS-2 and 0.906 (0.899-0.914) for DEWS in the validation data. AUROC for predicting CSD was 0.829 (0.817-0.842) for NEWS-2 and 0.877 (0.862-0.892) for DEWS. NEWS-2\u2009\u2265\u20095 had sensitivity of 88.2% and specificity of 54.2% for predicting CSD, while DEWS\u2009\u2265\u20090.021 had higher sensitivity of 93.6% and approximately the same specificity of 54.3% for the same outcome. Using these cut-offs, 315 out of 347 (90.8%) CSD events were detected by both NEWS-2 and DEWS, at the time of the event or within the previous 4\u00a0h; 12 (3.5%) were detected by DEWS but not by NEWS-2, while 4 (1.2%) were detected by NEWS-2 but not by DEWS; 16 (4.6%) were not detected by either scoring system.<h4>Conclusion</h4>We have developed DEWS that display greater accuracy than NEWS-2 for predicting clinical deterioration events in patients with respiratory disease. Prospective validation studies are required to assess whether DEWS can be used to reduce missed deteriorations and false alarms in real-life clinical settings.",
+    "laySummary": "",
+    "urls": "pdf:https://respiratory-research.biomedcentral.com/counter/pdf/10.1186/s12931-022-02130-6; doi:https://doi.org/10.1186/s12931-022-02130-6; html:https://europepmc.org/articles/PMC9367123; pdf:https://europepmc.org/articles/PMC9367123?pdf=render"
+  },
   {
     "id": "34348396",
     "doi": "https://doi.org/10.1097/ede.0000000000001393",
@@ -29851,23 +29885,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41588-021-00991-z.pdf; doi:https://doi.org/10.1038/s41588-021-00991-z; html:https://europepmc.org/articles/PMC9883041; pdf:https://europepmc.org/articles/PMC9883041?pdf=render; doi:https://doi.org/10.1038/s41588-021-00991-z"
   },
-  {
-    "id": "37419925",
-    "doi": "https://doi.org/10.1038/s41467-023-38930-7",
-    "title": "Optimal strategies for learning multi-ancestry polygenic scores vary across traits.",
-    "authorString": "Lehmann B, Mackintosh M, McVean G, Holmes C.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature communications",
-    "pubYear": "2023",
-    "date": "2023-07-07",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Polygenic scores (PGSs) are individual-level measures that aggregate the genome-wide genetic predisposition to a given trait. As PGS have predominantly been developed using European-ancestry samples, trait prediction using such European ancestry-derived PGS is less accurate in non-European ancestry individuals. Although there has been recent progress in combining multiple PGS trained on distinct populations, the problem of how to maximize performance given a multiple-ancestry cohort is largely unexplored. Here, we investigate the effect of sample size and ancestry composition on PGS performance for fifteen traits in UK Biobank. For some traits, PGS estimated using a relatively small African-ancestry training set outperformed, on an African-ancestry test set, PGS estimated using a much larger European-ancestry only training set. We observe similar, but not identical, results when considering other minority-ancestry groups within UK Biobank. Our results emphasise the importance of targeted data collection from underrepresented groups in order to address existing disparities in PGS performance.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41467-023-38930-7.pdf; doi:https://doi.org/10.1038/s41467-023-38930-7; html:https://europepmc.org/articles/PMC10328935; pdf:https://europepmc.org/articles/PMC10328935?pdf=render"
-  },
   {
     "id": "34753797",
     "doi": "https://doi.org/10.2337/db21-0320",
@@ -29885,6 +29902,23 @@
     "laySummary": "",
     "urls": "pdf:https://diabetesjournals.org/diabetes/article-pdf/71/2/359/640867/db210320.pdf; doi:https://doi.org/10.2337/db21-0320; html:https://europepmc.org/articles/PMC8914280; pdf:https://europepmc.org/articles/PMC8914280?pdf=render; doi:https://doi.org/10.2337/db21-0320"
   },
+  {
+    "id": "37419925",
+    "doi": "https://doi.org/10.1038/s41467-023-38930-7",
+    "title": "Optimal strategies for learning multi-ancestry polygenic scores vary across traits.",
+    "authorString": "Lehmann B, Mackintosh M, McVean G, Holmes C.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature communications",
+    "pubYear": "2023",
+    "date": "2023-07-07",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Polygenic scores (PGSs) are individual-level measures that aggregate the genome-wide genetic predisposition to a given trait. As PGS have predominantly been developed using European-ancestry samples, trait prediction using such European ancestry-derived PGS is less accurate in non-European ancestry individuals. Although there has been recent progress in combining multiple PGS trained on distinct populations, the problem of how to maximize performance given a multiple-ancestry cohort is largely unexplored. Here, we investigate the effect of sample size and ancestry composition on PGS performance for fifteen traits in UK Biobank. For some traits, PGS estimated using a relatively small African-ancestry training set outperformed, on an African-ancestry test set, PGS estimated using a much larger European-ancestry only training set. We observe similar, but not identical, results when considering other minority-ancestry groups within UK Biobank. Our results emphasise the importance of targeted data collection from underrepresented groups in order to address existing disparities in PGS performance.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41467-023-38930-7.pdf; doi:https://doi.org/10.1038/s41467-023-38930-7; html:https://europepmc.org/articles/PMC10328935; pdf:https://europepmc.org/articles/PMC10328935?pdf=render"
+  },
   {
     "id": "39266746",
     "doi": "https://doi.org/10.1038/s41591-024-03246-6",
@@ -30021,23 +30055,6 @@
     "laySummary": "",
     "urls": "pdf:http://www.jclinepi.com/article/S0895435621001074/pdf; doi:https://doi.org/10.1016/j.jclinepi.2021.03.025"
   },
-  {
-    "id": "35087703",
-    "doi": "https://doi.org/10.5334/aogh.3465",
-    "title": "Household Air Pollution and Respiratory Symptoms a Month Before and During the Stringent COVID-19 Lockdown Levels 5 and 4 in South Africa.",
-    "authorString": "Wright CY, Kapwata T, Abdelatif N, Batini C, Wernecke B, Kunene Z, Millar DA, Mathee A, Street R, Panchal R, Hansell A, Cordell R, Hey JV.",
-    "authorAffiliations": "",
-    "journalTitle": "Annals of global health",
-    "pubYear": "2022",
-    "date": "2022-01-10",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Household air pollution (HAP) is associated with adverse human health impacts. During COVID-19 Lockdown Levels 5 and 4 (the most stringent levels), South Africans remained at home, potentially increasing their exposure to HAP.<h4>Objectives</h4>To investigate changes in fuel use behaviours/patterns of use affecting HAP exposure and associated HAP-related respiratory health outcomes during COVID-19 Lockdown Levels 5 and 4.<h4>Methods</h4>This was a cross-sectional online and telephonic survey of participants from an existing database. Logistic regression and McNemar's test were used to analyse household-level data.<h4>Results</h4>Among 2 505 participants, while electricity was the main energy source for cooking and heating the month before and during Lockdown Levels 5 and 4, some households used less electricity during Lockdown Levels 5 and 4 or switched to \"dirty fuels.\" One third of participants reported presence of environmental tobacco smoke in the home, a source of HAP associated with respiratory illnesses. Prevalence of HAP-related respiratory health outcomes were <10% (except dry cough). Majority of households reported cooking more, cleaning more and spending more time indoors during Lockdown Levels 5 and 4 - potentially exposed to HAP.<h4>Conclusion</h4>Should South Africa return to Lockdown Levels 5 or 4, awareness raising about the risks associated with HAP as well as messaging information for prevention of exposure to HAP, including environmental tobacco smoke, and associated adverse health impacts will be necessary.",
-    "laySummary": "",
-    "urls": "pdf:http://www.annalsofglobalhealth.org/articles/10.5334/aogh.3465/galley/3414/download/; doi:https://doi.org/10.5334/aogh.3465; html:https://europepmc.org/articles/PMC8757382; pdf:https://europepmc.org/articles/PMC8757382?pdf=render"
-  },
   {
     "id": "34535484",
     "doi": "https://doi.org/10.1136/bmjopen-2021-050647",
@@ -30056,21 +30073,21 @@
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/11/9/e050647.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-050647; html:https://europepmc.org/articles/PMC8450967; pdf:https://europepmc.org/articles/PMC8450967?pdf=render"
   },
   {
-    "id": "39009924",
-    "doi": "https://doi.org/10.1007/s10654-024-01141-5",
-    "title": "Multi-biobank Mendelian randomization analyses identify opposing pathways in plasma low-density lipoprotein-cholesterol lowering and gallstone disease.",
-    "authorString": "Yang G, Mason AM, Gill D, Schooling CM, Burgess S.",
+    "id": "35087703",
+    "doi": "https://doi.org/10.5334/aogh.3465",
+    "title": "Household Air Pollution and Respiratory Symptoms a Month Before and During the Stringent COVID-19 Lockdown Levels 5 and 4 in South Africa.",
+    "authorString": "Wright CY, Kapwata T, Abdelatif N, Batini C, Wernecke B, Kunene Z, Millar DA, Mathee A, Street R, Panchal R, Hansell A, Cordell R, Hey JV.",
     "authorAffiliations": "",
-    "journalTitle": "European journal of epidemiology",
-    "pubYear": "2024",
-    "date": "2024-07-15",
+    "journalTitle": "Annals of global health",
+    "pubYear": "2022",
+    "date": "2022-01-10",
     "isOpenAccess": "Y",
-    "keywords": "Gallstone Disease; Ldl-cholesterol; Drug-target Mendelian Randomization; Clustered Mendelian Randomization",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Plasma low-density lipoprotein (LDL)-cholesterol is positively associated with coronary artery disease risk while biliary cholesterol promotes gallstone formation. Different plasma LDL-cholesterol lowering pathways may have distinct effects on biliary cholesterol and thereby gallstone disease risk. We conducted a Mendelian randomization (MR) study using data from the UK Biobank (30,547 gallstone disease cases/336,742 controls), FinnGen (34,461 cases/301,383 controls) and Biobank Japan (9,305 cases/168,253 controls). We first performed drug-target MR analyses substantiated by colocalization to investigate the effects of plasma LDL-cholesterol lowering therapies on gallstone disease risk. We then performed clustered MR analyses and pathway analyses to identify distinct mechanisms underlying the association of plasma LDL-cholesterol with gallstone disease risk. For a 1-standard deviation reduction in plasma LDL-cholesterol, genetic mimics of statins were associated with lower gallstone disease risk (odds ratio 0.72 [95% confidence interval 0.62, 0.83]), but genetic mimics of PCSK9 inhibitors and targeting apolipoprotein B were associated with higher risk (1.11 [1.03, 1.19] and 1.23 [1.13, 1.35]). The association for statins was supported by colocalization (posterior probability 98.7%). Clustered MR analyses identified variant clusters showing opposing associations of plasma LDL-cholesterol with gallstone disease risk, with some evidence for ancestry-and sex-specific associations. Among variants lowering plasma LDL-cholesterol, those associated with lower gallstone disease risk were mapped to glycosphingolipid biosynthesis pathway, while those associated with higher risk were mapped to pathways relating to plasma lipoprotein assembly, remodelling, and clearance and ATP-binding cassette transporters. This MR study provides genetic evidence that different plasma LDL-cholesterol lowering pathways have opposing effects on gallstone disease risk.",
+    "abstract": "<h4>Background</h4>Household air pollution (HAP) is associated with adverse human health impacts. During COVID-19 Lockdown Levels 5 and 4 (the most stringent levels), South Africans remained at home, potentially increasing their exposure to HAP.<h4>Objectives</h4>To investigate changes in fuel use behaviours/patterns of use affecting HAP exposure and associated HAP-related respiratory health outcomes during COVID-19 Lockdown Levels 5 and 4.<h4>Methods</h4>This was a cross-sectional online and telephonic survey of participants from an existing database. Logistic regression and McNemar's test were used to analyse household-level data.<h4>Results</h4>Among 2 505 participants, while electricity was the main energy source for cooking and heating the month before and during Lockdown Levels 5 and 4, some households used less electricity during Lockdown Levels 5 and 4 or switched to \"dirty fuels.\" One third of participants reported presence of environmental tobacco smoke in the home, a source of HAP associated with respiratory illnesses. Prevalence of HAP-related respiratory health outcomes were <10% (except dry cough). Majority of households reported cooking more, cleaning more and spending more time indoors during Lockdown Levels 5 and 4 - potentially exposed to HAP.<h4>Conclusion</h4>Should South Africa return to Lockdown Levels 5 or 4, awareness raising about the risks associated with HAP as well as messaging information for prevention of exposure to HAP, including environmental tobacco smoke, and associated adverse health impacts will be necessary.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1007/s10654-024-01141-5; html:https://europepmc.org/articles/PMC11410903; pdf:https://europepmc.org/articles/PMC11410903?pdf=render"
+    "urls": "pdf:http://www.annalsofglobalhealth.org/articles/10.5334/aogh.3465/galley/3414/download/; doi:https://doi.org/10.5334/aogh.3465; html:https://europepmc.org/articles/PMC8757382; pdf:https://europepmc.org/articles/PMC8757382?pdf=render"
   },
   {
     "id": "33692568",
@@ -30089,6 +30106,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.medrxiv.org/content/medrxiv/early/2020/05/23/2020.05.20.20108217.full.pdf; doi:https://doi.org/10.1038/s41588-021-00783-5"
   },
+  {
+    "id": "39009924",
+    "doi": "https://doi.org/10.1007/s10654-024-01141-5",
+    "title": "Multi-biobank Mendelian randomization analyses identify opposing pathways in plasma low-density lipoprotein-cholesterol lowering and gallstone disease.",
+    "authorString": "Yang G, Mason AM, Gill D, Schooling CM, Burgess S.",
+    "authorAffiliations": "",
+    "journalTitle": "European journal of epidemiology",
+    "pubYear": "2024",
+    "date": "2024-07-15",
+    "isOpenAccess": "Y",
+    "keywords": "Gallstone Disease; Ldl-cholesterol; Drug-target Mendelian Randomization; Clustered Mendelian Randomization",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Plasma low-density lipoprotein (LDL)-cholesterol is positively associated with coronary artery disease risk while biliary cholesterol promotes gallstone formation. Different plasma LDL-cholesterol lowering pathways may have distinct effects on biliary cholesterol and thereby gallstone disease risk. We conducted a Mendelian randomization (MR) study using data from the UK Biobank (30,547 gallstone disease cases/336,742 controls), FinnGen (34,461 cases/301,383 controls) and Biobank Japan (9,305 cases/168,253 controls). We first performed drug-target MR analyses substantiated by colocalization to investigate the effects of plasma LDL-cholesterol lowering therapies on gallstone disease risk. We then performed clustered MR analyses and pathway analyses to identify distinct mechanisms underlying the association of plasma LDL-cholesterol with gallstone disease risk. For a 1-standard deviation reduction in plasma LDL-cholesterol, genetic mimics of statins were associated with lower gallstone disease risk (odds ratio 0.72 [95% confidence interval 0.62, 0.83]), but genetic mimics of PCSK9 inhibitors and targeting apolipoprotein B were associated with higher risk (1.11 [1.03, 1.19] and 1.23 [1.13, 1.35]). The association for statins was supported by colocalization (posterior probability 98.7%). Clustered MR analyses identified variant clusters showing opposing associations of plasma LDL-cholesterol with gallstone disease risk, with some evidence for ancestry-and sex-specific associations. Among variants lowering plasma LDL-cholesterol, those associated with lower gallstone disease risk were mapped to glycosphingolipid biosynthesis pathway, while those associated with higher risk were mapped to pathways relating to plasma lipoprotein assembly, remodelling, and clearance and ATP-binding cassette transporters. This MR study provides genetic evidence that different plasma LDL-cholesterol lowering pathways have opposing effects on gallstone disease risk.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1007/s10654-024-01141-5; html:https://europepmc.org/articles/PMC11410903; pdf:https://europepmc.org/articles/PMC11410903?pdf=render"
+  },
   {
     "id": "32743489",
     "doi": "https://doi.org/10.1016/j.eclinm.2020.100469",
@@ -30106,6 +30140,23 @@
     "laySummary": "",
     "urls": "pdf:http://www.thelancet.com/article/S2589537020302133/pdf; doi:https://doi.org/10.1016/j.eclinm.2020.100469; html:https://europepmc.org/articles/PMC7385442; pdf:https://europepmc.org/articles/PMC7385442?pdf=render"
   },
+  {
+    "id": "35585575",
+    "doi": "https://doi.org/10.1186/s12889-022-13219-4",
+    "title": "The impact of COVID-19 vaccination in prisons in England and Wales: a metapopulation model.",
+    "authorString": "McCarthy CV, O'Mara O, van Leeuwen E, CMMID COVID-19 Working Group, Jit M, Sandmann F.",
+    "authorAffiliations": "",
+    "journalTitle": "BMC public health",
+    "pubYear": "2022",
+    "date": "2022-05-18",
+    "isOpenAccess": "Y",
+    "keywords": "Vaccination; mathematical model; Public Health; Prisons; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>High incidence of cases and deaths due to coronavirus disease 2019 (COVID-19) have been reported in prisons worldwide. This study aimed to evaluate the impact of different COVID-19 vaccination strategies in epidemiologically semi-enclosed settings such as prisons, where staff interact regularly with those incarcerated and the wider community.<h4>Methods</h4>We used a metapopulation transmission-dynamic model of a local prison in England and Wales. Two-dose vaccination strategies included no vaccination, vaccination of all individuals\u00a0who are\u00a0incarcerated and/or staff, and an age-based approach. Outcomes were quantified in terms of COVID-19-related symptomatic cases, losses in quality-adjusted life-years (QALYs), and deaths.<h4>Results</h4>Compared to no vaccination, vaccinating all people living and working in prison reduced cases, QALY loss and deaths over a one-year period by 41%, 32% and 36% respectively. However, if vaccine introduction was delayed until the start of an outbreak, the impact was negligible. Vaccinating individuals who are incarcerated and staff over 50\u00a0years old averted one death for every 104 vaccination\u00a0courses administered. All-staff-only strategies reduced cases by up to 5%. Increasing coverage from 30 to 90% among those who are incarcerated reduced cases by around 30 percentage points.<h4>Conclusions</h4>The impact of vaccination in prison settings was highly dependent on early and rapid vaccine delivery. If administered to both those living and working in prison prior to an outbreak occurring, vaccines could substantially reduce COVID-19-related morbidity and mortality in prison settings.",
+    "laySummary": "",
+    "urls": "pdf:https://bmcpublichealth.biomedcentral.com/track/pdf/10.1186/s12889-022-13219-4; doi:https://doi.org/10.1186/s12889-022-13219-4; html:https://europepmc.org/articles/PMC9115545; pdf:https://europepmc.org/articles/PMC9115545?pdf=render"
+  },
   {
     "id": "35477354",
     "doi": "https://doi.org/10.1186/s12877-022-03077-5",
@@ -30124,21 +30175,21 @@
     "urls": "pdf:https://bmcgeriatr.biomedcentral.com/track/pdf/10.1186/s12877-022-03077-5; doi:https://doi.org/10.1186/s12877-022-03077-5; html:https://europepmc.org/articles/PMC9043890; pdf:https://europepmc.org/articles/PMC9043890?pdf=render"
   },
   {
-    "id": "35585575",
-    "doi": "https://doi.org/10.1186/s12889-022-13219-4",
-    "title": "The impact of COVID-19 vaccination in prisons in England and Wales: a metapopulation model.",
-    "authorString": "McCarthy CV, O'Mara O, van Leeuwen E, CMMID COVID-19 Working Group, Jit M, Sandmann F.",
+    "id": "30742608",
+    "doi": "https://doi.org/10.1371/journal.pcbi.1006785",
+    "title": "Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15.",
+    "authorString": "Funk S, Camacho A, Kucharski AJ, Lowe R, Eggo RM, Edmunds WJ.",
     "authorAffiliations": "",
-    "journalTitle": "BMC public health",
-    "pubYear": "2022",
-    "date": "2022-05-18",
+    "journalTitle": "PLoS computational biology",
+    "pubYear": "2019",
+    "date": "2019-02-11",
     "isOpenAccess": "Y",
-    "keywords": "Vaccination; mathematical model; Public Health; Prisons; Covid-19",
-    "nationalPriorities": "",
+    "keywords": "",
+    "nationalPriorities": "Applied Analytics",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>High incidence of cases and deaths due to coronavirus disease 2019 (COVID-19) have been reported in prisons worldwide. This study aimed to evaluate the impact of different COVID-19 vaccination strategies in epidemiologically semi-enclosed settings such as prisons, where staff interact regularly with those incarcerated and the wider community.<h4>Methods</h4>We used a metapopulation transmission-dynamic model of a local prison in England and Wales. Two-dose vaccination strategies included no vaccination, vaccination of all individuals\u00a0who are\u00a0incarcerated and/or staff, and an age-based approach. Outcomes were quantified in terms of COVID-19-related symptomatic cases, losses in quality-adjusted life-years (QALYs), and deaths.<h4>Results</h4>Compared to no vaccination, vaccinating all people living and working in prison reduced cases, QALY loss and deaths over a one-year period by 41%, 32% and 36% respectively. However, if vaccine introduction was delayed until the start of an outbreak, the impact was negligible. Vaccinating individuals who are incarcerated and staff over 50\u00a0years old averted one death for every 104 vaccination\u00a0courses administered. All-staff-only strategies reduced cases by up to 5%. Increasing coverage from 30 to 90% among those who are incarcerated reduced cases by around 30 percentage points.<h4>Conclusions</h4>The impact of vaccination in prison settings was highly dependent on early and rapid vaccine delivery. If administered to both those living and working in prison prior to an outbreak occurring, vaccines could substantially reduce COVID-19-related morbidity and mortality in prison settings.",
+    "abstract": "Real-time forecasts based on mathematical models can inform critical decision-making during infectious disease outbreaks. Yet, epidemic forecasts are rarely evaluated during or after the event, and there is little guidance on the best metrics for assessment. Here, we propose an evaluation approach that disentangles different components of forecasting ability using metrics that separately assess the calibration, sharpness and bias of forecasts. This makes it possible to assess not just how close a forecast was to reality but also how well uncertainty has been quantified. We used this approach to analyse the performance of weekly forecasts we generated in real time for Western Area, Sierra Leone, during the 2013-16 Ebola epidemic in West Africa. We investigated a range of forecast model variants based on the model fits generated at the time with a semi-mechanistic model, and found that good probabilistic calibration was achievable at short time horizons of one or two weeks ahead but model predictions were increasingly unreliable at longer forecasting horizons. This suggests that forecasts may have been of good enough quality to inform decision making based on predictions a few weeks ahead of time but not longer, reflecting the high level of uncertainty in the processes driving the trajectory of the epidemic. Comparing forecasts based on the semi-mechanistic model to simpler null models showed that the best semi-mechanistic model variant performed better than the null models with respect to probabilistic calibration, and that this would have been identified from the earliest stages of the outbreak. As forecasts become a routine part of the toolkit in public health, standards for evaluation of performance will be important for assessing quality and improving credibility of mathematical models, and for elucidating difficulties and trade-offs when aiming to make the most useful and reliable forecasts.",
     "laySummary": "",
-    "urls": "pdf:https://bmcpublichealth.biomedcentral.com/track/pdf/10.1186/s12889-022-13219-4; doi:https://doi.org/10.1186/s12889-022-13219-4; html:https://europepmc.org/articles/PMC9115545; pdf:https://europepmc.org/articles/PMC9115545?pdf=render"
+    "urls": "pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006785&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1006785; html:https://europepmc.org/articles/PMC6386417; pdf:https://europepmc.org/articles/PMC6386417?pdf=render"
   },
   {
     "id": "36240828",
@@ -30157,23 +30208,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.repository.cam.ac.uk/bitstreams/bb5465bd-c08f-4c3d-ab0e-87fee39fc92b/download; doi:https://doi.org/10.1016/S2214-109X(22)00358-8; html:https://europepmc.org/articles/PMC9573849"
   },
-  {
-    "id": "36331190",
-    "doi": "https://doi.org/10.1056/nejmoa2204233",
-    "title": "Empagliflozin in Patients with Chronic Kidney Disease.",
-    "authorString": "The EMPA-KIDNEY Collaborative Group, Herrington WG, Staplin N, Wanner C, Green JB, Hauske SJ, Emberson JR, Preiss D, Judge P, Mayne KJ, Ng SYA, Sammons E, Zhu D, Hill M, Stevens W, Wallendszus K, Brenner S, Cheung AK, Liu ZH, Li J, Hooi LS, Liu W, Kadowaki T, Nangaku M, Levin A, Cherney D, Maggioni AP, Pontremoli R, Deo R, Goto S, Rossello X, Tuttle KR, Steubl D, Petrini M, Massey D, Eilbracht J, Brueckmann M, Landray MJ, Baigent C, Haynes R.",
-    "authorAffiliations": "",
-    "journalTitle": "The New England journal of medicine",
-    "pubYear": "2023",
-    "date": "2022-11-04",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>The effects of empagliflozin in patients with chronic kidney disease who are at risk for disease progression are not well understood. The EMPA-KIDNEY trial was designed to assess the effects of treatment with empagliflozin in a broad range of such patients.<h4>Methods</h4>We enrolled patients with chronic kidney disease who had an estimated glomerular filtration rate (eGFR) of at least 20 but less than 45 ml per minute per 1.73 m<sup>2</sup> of body-surface area, or who had an eGFR of at least 45 but less than 90 ml per minute per 1.73 m<sup>2</sup> with a urinary albumin-to-creatinine ratio (with albumin measured in milligrams and creatinine measured in grams) of at least 200. Patients were randomly assigned to receive empagliflozin (10 mg once daily) or matching placebo. The primary outcome was a composite of progression of kidney disease (defined as end-stage kidney disease, a sustained decrease in eGFR to <10 ml per minute per 1.73 m<sup>2</sup>, a sustained decrease in eGFR of \u226540% from baseline, or death from renal causes) or death from cardiovascular causes.<h4>Results</h4>A total of 6609 patients underwent randomization. During a median of 2.0 years of follow-up, progression of kidney disease or death from cardiovascular causes occurred in 432 of 3304 patients (13.1%) in the empagliflozin group and in 558 of 3305 patients (16.9%) in the placebo group (hazard ratio, 0.72; 95% confidence interval [CI], 0.64 to 0.82; P<0.001). Results were consistent among patients with or without diabetes and across subgroups defined according to eGFR ranges. The rate of hospitalization from any cause was lower in the empagliflozin group than in the placebo group (hazard ratio, 0.86; 95% CI, 0.78 to 0.95; P\u2009=\u20090.003), but there were no significant between-group differences with respect to the composite outcome of hospitalization for heart failure or death from cardiovascular causes (which occurred in 4.0% in the empagliflozin group and 4.6% in the placebo group) or death from any cause (in 4.5% and 5.1%, respectively). The rates of serious adverse events were similar in the two groups.<h4>Conclusions</h4>Among a wide range of patients with chronic kidney disease who were at risk for disease progression, empagliflozin therapy led to a lower risk of progression of kidney disease or death from cardiovascular causes than placebo. (Funded by Boehringer Ingelheim and others; EMPA-KIDNEY ClinicalTrials.gov number, NCT03594110; EudraCT number, 2017-002971-24.).",
-    "laySummary": "",
-    "urls": "pdf:https://www.nejm.org/doi/pdf/10.1056/NEJMoa2204233?articleTools=true; doi:https://doi.org/10.1056/NEJMoa2204233; html:https://europepmc.org/articles/PMC7614055; pdf:https://europepmc.org/articles/PMC7614055?pdf=render"
-  },
   {
     "id": "35072137",
     "doi": "https://doi.org/10.1016/j.xgen.2021.100086",
@@ -30192,21 +30226,21 @@
     "urls": "doi:https://doi.org/10.1016/j.xgen.2021.100086; doi:https://doi.org/10.1016/j.xgen.2021.100086; html:https://europepmc.org/articles/PMC8758502; pdf:https://europepmc.org/articles/PMC8758502?pdf=render"
   },
   {
-    "id": "30742608",
-    "doi": "https://doi.org/10.1371/journal.pcbi.1006785",
-    "title": "Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15.",
-    "authorString": "Funk S, Camacho A, Kucharski AJ, Lowe R, Eggo RM, Edmunds WJ.",
+    "id": "36331190",
+    "doi": "https://doi.org/10.1056/nejmoa2204233",
+    "title": "Empagliflozin in Patients with Chronic Kidney Disease.",
+    "authorString": "The EMPA-KIDNEY Collaborative Group, Herrington WG, Staplin N, Wanner C, Green JB, Hauske SJ, Emberson JR, Preiss D, Judge P, Mayne KJ, Ng SYA, Sammons E, Zhu D, Hill M, Stevens W, Wallendszus K, Brenner S, Cheung AK, Liu ZH, Li J, Hooi LS, Liu W, Kadowaki T, Nangaku M, Levin A, Cherney D, Maggioni AP, Pontremoli R, Deo R, Goto S, Rossello X, Tuttle KR, Steubl D, Petrini M, Massey D, Eilbracht J, Brueckmann M, Landray MJ, Baigent C, Haynes R.",
     "authorAffiliations": "",
-    "journalTitle": "PLoS computational biology",
-    "pubYear": "2019",
-    "date": "2019-02-11",
+    "journalTitle": "The New England journal of medicine",
+    "pubYear": "2023",
+    "date": "2022-11-04",
     "isOpenAccess": "Y",
     "keywords": "",
-    "nationalPriorities": "Applied Analytics",
+    "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Real-time forecasts based on mathematical models can inform critical decision-making during infectious disease outbreaks. Yet, epidemic forecasts are rarely evaluated during or after the event, and there is little guidance on the best metrics for assessment. Here, we propose an evaluation approach that disentangles different components of forecasting ability using metrics that separately assess the calibration, sharpness and bias of forecasts. This makes it possible to assess not just how close a forecast was to reality but also how well uncertainty has been quantified. We used this approach to analyse the performance of weekly forecasts we generated in real time for Western Area, Sierra Leone, during the 2013-16 Ebola epidemic in West Africa. We investigated a range of forecast model variants based on the model fits generated at the time with a semi-mechanistic model, and found that good probabilistic calibration was achievable at short time horizons of one or two weeks ahead but model predictions were increasingly unreliable at longer forecasting horizons. This suggests that forecasts may have been of good enough quality to inform decision making based on predictions a few weeks ahead of time but not longer, reflecting the high level of uncertainty in the processes driving the trajectory of the epidemic. Comparing forecasts based on the semi-mechanistic model to simpler null models showed that the best semi-mechanistic model variant performed better than the null models with respect to probabilistic calibration, and that this would have been identified from the earliest stages of the outbreak. As forecasts become a routine part of the toolkit in public health, standards for evaluation of performance will be important for assessing quality and improving credibility of mathematical models, and for elucidating difficulties and trade-offs when aiming to make the most useful and reliable forecasts.",
+    "abstract": "<h4>Background</h4>The effects of empagliflozin in patients with chronic kidney disease who are at risk for disease progression are not well understood. The EMPA-KIDNEY trial was designed to assess the effects of treatment with empagliflozin in a broad range of such patients.<h4>Methods</h4>We enrolled patients with chronic kidney disease who had an estimated glomerular filtration rate (eGFR) of at least 20 but less than 45 ml per minute per 1.73 m<sup>2</sup> of body-surface area, or who had an eGFR of at least 45 but less than 90 ml per minute per 1.73 m<sup>2</sup> with a urinary albumin-to-creatinine ratio (with albumin measured in milligrams and creatinine measured in grams) of at least 200. Patients were randomly assigned to receive empagliflozin (10 mg once daily) or matching placebo. The primary outcome was a composite of progression of kidney disease (defined as end-stage kidney disease, a sustained decrease in eGFR to <10 ml per minute per 1.73 m<sup>2</sup>, a sustained decrease in eGFR of \u226540% from baseline, or death from renal causes) or death from cardiovascular causes.<h4>Results</h4>A total of 6609 patients underwent randomization. During a median of 2.0 years of follow-up, progression of kidney disease or death from cardiovascular causes occurred in 432 of 3304 patients (13.1%) in the empagliflozin group and in 558 of 3305 patients (16.9%) in the placebo group (hazard ratio, 0.72; 95% confidence interval [CI], 0.64 to 0.82; P<0.001). Results were consistent among patients with or without diabetes and across subgroups defined according to eGFR ranges. The rate of hospitalization from any cause was lower in the empagliflozin group than in the placebo group (hazard ratio, 0.86; 95% CI, 0.78 to 0.95; P\u2009=\u20090.003), but there were no significant between-group differences with respect to the composite outcome of hospitalization for heart failure or death from cardiovascular causes (which occurred in 4.0% in the empagliflozin group and 4.6% in the placebo group) or death from any cause (in 4.5% and 5.1%, respectively). The rates of serious adverse events were similar in the two groups.<h4>Conclusions</h4>Among a wide range of patients with chronic kidney disease who were at risk for disease progression, empagliflozin therapy led to a lower risk of progression of kidney disease or death from cardiovascular causes than placebo. (Funded by Boehringer Ingelheim and others; EMPA-KIDNEY ClinicalTrials.gov number, NCT03594110; EudraCT number, 2017-002971-24.).",
     "laySummary": "",
-    "urls": "pdf:https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006785&type=printable; doi:https://doi.org/10.1371/journal.pcbi.1006785; html:https://europepmc.org/articles/PMC6386417; pdf:https://europepmc.org/articles/PMC6386417?pdf=render"
+    "urls": "pdf:https://www.nejm.org/doi/pdf/10.1056/NEJMoa2204233?articleTools=true; doi:https://doi.org/10.1056/NEJMoa2204233; html:https://europepmc.org/articles/PMC7614055; pdf:https://europepmc.org/articles/PMC7614055?pdf=render"
   },
   {
     "id": "37573145",
@@ -30225,23 +30259,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ndt/advance-article-pdf/doi/10.1093/ndt/gfad180/51104398/gfad180.pdf; doi:https://doi.org/10.1093/ndt/gfad180; html:https://europepmc.org/articles/PMC10899778; pdf:https://europepmc.org/articles/PMC10899778?pdf=render"
   },
-  {
-    "id": "37321240",
-    "doi": "https://doi.org/10.1016/s2215-0366(23)00113-x",
-    "title": "Mental health in Europe during the COVID-19 pandemic: a systematic review.",
-    "authorString": "Ahmed N, Barnett P, Greenburgh A, Pemovska T, Stefanidou T, Lyons N, Ikhtabi S, Talwar S, Francis ER, Harris SM, Shah P, Machin K, Jeffreys S, Mitchell L, Lynch C, Foye U, Schlief M, Appleton R, Saunders KRK, Baldwin H, Allan SM, Sheridan-Rains L, Kharboutly O, Kular A, Goldblatt P, Stewart R, Kirkbride JB, Lloyd-Evans B, Johnson S.",
-    "authorAffiliations": "",
-    "journalTitle": "The lancet. Psychiatry",
-    "pubYear": "2023",
-    "date": "2023-06-12",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The COVID-19 pandemic caused immediate and far-reaching disruption to society, the economy, and health-care services. We synthesised evidence on the effect of the pandemic on mental health and mental health care in high-income European countries. We included 177 longitudinal and repeated cross-sectional studies comparing prevalence or incidence of mental health problems, mental health symptom severity in people with pre-existing mental health conditions, or mental health service use before versus during the pandemic, or between different timepoints of the pandemic. We found that epidemiological studies reported higher prevalence of some mental health problems during the pandemic compared with before it, but that in most cases this increase reduced over time. Conversely, studies of health records showed reduced incidence of new diagnoses at the start of the pandemic, which further declined during 2020. Mental health service use also declined at the onset of the pandemic but increased later in 2020 and through 2021, although rates of use did not return to pre-pandemic levels for some services. We found mixed patterns of effects of the pandemic on mental health and social outcome for adults already living with mental health conditions.",
-    "laySummary": "",
-    "urls": "pdf:http://www.thelancet.com/article/S221503662300113X/pdf; doi:https://doi.org/10.1016/S2215-0366(23)00113-X; html:https://europepmc.org/articles/PMC10259832; pdf:https://europepmc.org/articles/PMC10259832?pdf=render"
-  },
   {
     "id": "33782427",
     "doi": "https://doi.org/10.1038/s41598-021-86266-3",
@@ -30259,6 +30276,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41598-021-86266-3.pdf; doi:https://doi.org/10.1038/s41598-021-86266-3; html:https://europepmc.org/articles/PMC8007605; pdf:https://europepmc.org/articles/PMC8007605?pdf=render"
   },
+  {
+    "id": "37321240",
+    "doi": "https://doi.org/10.1016/s2215-0366(23)00113-x",
+    "title": "Mental health in Europe during the COVID-19 pandemic: a systematic review.",
+    "authorString": "Ahmed N, Barnett P, Greenburgh A, Pemovska T, Stefanidou T, Lyons N, Ikhtabi S, Talwar S, Francis ER, Harris SM, Shah P, Machin K, Jeffreys S, Mitchell L, Lynch C, Foye U, Schlief M, Appleton R, Saunders KRK, Baldwin H, Allan SM, Sheridan-Rains L, Kharboutly O, Kular A, Goldblatt P, Stewart R, Kirkbride JB, Lloyd-Evans B, Johnson S.",
+    "authorAffiliations": "",
+    "journalTitle": "The lancet. Psychiatry",
+    "pubYear": "2023",
+    "date": "2023-06-12",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The COVID-19 pandemic caused immediate and far-reaching disruption to society, the economy, and health-care services. We synthesised evidence on the effect of the pandemic on mental health and mental health care in high-income European countries. We included 177 longitudinal and repeated cross-sectional studies comparing prevalence or incidence of mental health problems, mental health symptom severity in people with pre-existing mental health conditions, or mental health service use before versus during the pandemic, or between different timepoints of the pandemic. We found that epidemiological studies reported higher prevalence of some mental health problems during the pandemic compared with before it, but that in most cases this increase reduced over time. Conversely, studies of health records showed reduced incidence of new diagnoses at the start of the pandemic, which further declined during 2020. Mental health service use also declined at the onset of the pandemic but increased later in 2020 and through 2021, although rates of use did not return to pre-pandemic levels for some services. We found mixed patterns of effects of the pandemic on mental health and social outcome for adults already living with mental health conditions.",
+    "laySummary": "",
+    "urls": "pdf:http://www.thelancet.com/article/S221503662300113X/pdf; doi:https://doi.org/10.1016/S2215-0366(23)00113-X; html:https://europepmc.org/articles/PMC10259832; pdf:https://europepmc.org/articles/PMC10259832?pdf=render"
+  },
   {
     "id": "34957541",
     "doi": "https://doi.org/10.1111/bjh.18013",
@@ -30327,23 +30361,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.xpro.2021.100334; doi:https://doi.org/10.1016/j.xpro.2021.100334; html:https://europepmc.org/articles/PMC7881265; pdf:https://europepmc.org/articles/PMC7881265?pdf=render"
   },
-  {
-    "id": "33521535",
-    "doi": "https://doi.org/10.1136/bmjnph-2020-000107",
-    "title": "Genetic risk of obesity as a modifier of associations between neighbourhood environment and body mass index: an observational study of 335 046 UK Biobank participants.",
-    "authorString": "Mason KE, Palla L, Pearce N, Phelan J, Cummins S.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ nutrition, prevention & health",
-    "pubYear": "2020",
-    "date": "2020-10-05",
-    "isOpenAccess": "Y",
-    "keywords": "Malnutrition; Dietary Patterns",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>There is growing recognition that recent global increases in obesity are the product of a complex interplay between genetic and environmental factors. However, in gene-environment studies of obesity, 'environment' usually refers to individual behavioural factors that influence energy balance, whereas more upstream environmental factors are overlooked. We examined gene-environment interactions between genetic risk of obesity and two neighbourhood characteristics likely to be associated with obesity (proximity to takeaway/fast-food outlets and availability of physical activity facilities).<h4>Methods</h4>We used data from 335 046 adults aged 40-70 in the UK Biobank cohort to conduct a population-based cross-sectional study of interactions between neighbourhood characteristics and genetic risk of obesity, in relation to body mass index (BMI). Proximity to a fast-food outlet was defined as distance from home address to nearest takeaway/fast-food outlet, and availability of physical activity facilities as the number of formal physical activity facilities within 1 km of home address. Genetic risk of obesity was operationalised by weighted Genetic Risk Scores of 91 or 69 single nucleotide polymorphisms (SNP), and by six individual SNPs considered separately. Multivariable, mixed-effects models with product terms for the gene-environment interactions were estimated.<h4>Results</h4>After accounting for likely confounding, the association between proximity to takeaway/fast-food outlets and BMI was stronger among those at increased genetic risk of obesity, with evidence of an interaction with polygenic risk scores (p=0.018 and p=0.028 for 69-SNP and 91-SNP scores, respectively) and in particular with a SNP linked to <i>MC4R</i> (p=0.009), a gene known to regulate food intake. We found very little evidence of gene-environment interaction for the availability of physical activity facilities.<h4>Conclusions</h4>Individuals at an increased genetic risk of obesity may be more sensitive to exposure to the local fast-food environment. Ensuring that neighbourhood residential environments are designed to promote a healthy weight may be particularly important for those with greater genetic susceptibility to obesity.",
-    "laySummary": "",
-    "urls": "pdf:https://nutrition.bmj.com/content/bmjnph/3/2/247.full.pdf; doi:https://doi.org/10.1136/bmjnph-2020-000107; html:https://europepmc.org/articles/PMC7841812; pdf:https://europepmc.org/articles/PMC7841812?pdf=render"
-  },
   {
     "id": "36029662",
     "doi": "https://doi.org/10.1016/j.bios.2022.114623",
@@ -30362,21 +30379,21 @@
     "urls": "pdf:https://research-information.bris.ac.uk/files/338519213/1_s2.0_S0956566322006637_main.pdf; doi:https://doi.org/10.1016/j.bios.2022.114623"
   },
   {
-    "id": "36066609",
-    "doi": "https://doi.org/10.1007/s00392-022-02088-x",
-    "title": "Towards automatic classification of cardiovascular magnetic resonance Task Force Criteria for diagnosis of arrhythmogenic right ventricular cardiomyopathy.",
-    "authorString": "Bourfiss M, Sander J, de Vos BD, Te Riele ASJM, Asselbergs FW, I\u0161gum I, Velthuis BK.",
+    "id": "33521535",
+    "doi": "https://doi.org/10.1136/bmjnph-2020-000107",
+    "title": "Genetic risk of obesity as a modifier of associations between neighbourhood environment and body mass index: an observational study of 335 046 UK Biobank participants.",
+    "authorString": "Mason KE, Palla L, Pearce N, Phelan J, Cummins S.",
     "authorAffiliations": "",
-    "journalTitle": "Clinical research in cardiology : official journal of the German Cardiac Society",
-    "pubYear": "2023",
-    "date": "2022-09-06",
+    "journalTitle": "BMJ nutrition, prevention & health",
+    "pubYear": "2020",
+    "date": "2020-10-05",
     "isOpenAccess": "Y",
-    "keywords": "Cardiac Magnetic Resonance Imaging; Arrhythmogenic Right Ventricular Cardiomyopathy; Automatic Segmentation; Deep Learning",
+    "keywords": "Malnutrition; Dietary Patterns",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Arrhythmogenic right ventricular cardiomyopathy (ARVC) is diagnosed according to the Task Force Criteria (TFC) in which cardiovascular magnetic resonance (CMR) imaging plays an important role. Our study aims to apply an automatic deep learning-based segmentation for right and left ventricular CMR assessment and evaluate this approach for classification of the CMR TFC.<h4>Methods</h4>We included 227 subjects suspected of ARVC who underwent CMR. Subjects were classified into (1) ARVC patients fulfilling TFC; (2) at-risk family members; and (3) controls. To perform automatic segmentation, a Bayesian Dilated Residual Neural Network was trained and tested. Performance of automatic versus manual segmentation was assessed using Dice-coefficient and Hausdorff distance. Since automatic segmentation is most challenging in basal slices, manual correction of the automatic segmentation in the most basal slice was simulated (automatic<sup>-basal</sup>). CMR TFC calculated using manual and automatic<sup>-basal</sup> segmentation were compared using Cohen's Kappa (\u03ba).<h4>Results</h4>Automatic segmentation was trained on CMRs of 70 subjects (39.6\u2009\u00b1\u200918.1\u00a0years, 47% female) and tested on 157 subjects (36.9\u2009\u00b1\u200917.6\u00a0years, 59% female). Dice-coefficient and Hausdorff distance showed good agreement between manual and automatic segmentations (\u2265\u20090.89 and\u2009\u2264\u200910.6\u00a0mm, respectively) which further improved after simulated correction of the most basal slice (\u2265\u20090.92 and\u2009\u2264\u20099.2\u00a0mm, p\u2009<\u20090.001). Pearson correlation of volumetric and functional CMR measurements was good to excellent (automatic (r\u2009=\u20090.78-0.99, p\u2009<\u20090.001) and automatic<sup>-basal</sup> (r\u2009=\u20090.88-0.99, p\u2009<\u20090.001) measurements). CMR TFC classification using automatic<sup>-basal</sup> segmentations was comparable to manual segmentations (\u03ba 0.98\u2009\u00b1\u20090.02) with comparable diagnostic performance.<h4>Conclusions</h4>Combining automatic segmentation of CMRs with correction of the most basal slice results in accurate CMR TFC classification of subjects suspected of ARVC.",
+    "abstract": "<h4>Background</h4>There is growing recognition that recent global increases in obesity are the product of a complex interplay between genetic and environmental factors. However, in gene-environment studies of obesity, 'environment' usually refers to individual behavioural factors that influence energy balance, whereas more upstream environmental factors are overlooked. We examined gene-environment interactions between genetic risk of obesity and two neighbourhood characteristics likely to be associated with obesity (proximity to takeaway/fast-food outlets and availability of physical activity facilities).<h4>Methods</h4>We used data from 335 046 adults aged 40-70 in the UK Biobank cohort to conduct a population-based cross-sectional study of interactions between neighbourhood characteristics and genetic risk of obesity, in relation to body mass index (BMI). Proximity to a fast-food outlet was defined as distance from home address to nearest takeaway/fast-food outlet, and availability of physical activity facilities as the number of formal physical activity facilities within 1 km of home address. Genetic risk of obesity was operationalised by weighted Genetic Risk Scores of 91 or 69 single nucleotide polymorphisms (SNP), and by six individual SNPs considered separately. Multivariable, mixed-effects models with product terms for the gene-environment interactions were estimated.<h4>Results</h4>After accounting for likely confounding, the association between proximity to takeaway/fast-food outlets and BMI was stronger among those at increased genetic risk of obesity, with evidence of an interaction with polygenic risk scores (p=0.018 and p=0.028 for 69-SNP and 91-SNP scores, respectively) and in particular with a SNP linked to <i>MC4R</i> (p=0.009), a gene known to regulate food intake. We found very little evidence of gene-environment interaction for the availability of physical activity facilities.<h4>Conclusions</h4>Individuals at an increased genetic risk of obesity may be more sensitive to exposure to the local fast-food environment. Ensuring that neighbourhood residential environments are designed to promote a healthy weight may be particularly important for those with greater genetic susceptibility to obesity.",
     "laySummary": "",
-    "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s00392-022-02088-x.pdf; doi:https://doi.org/10.1007/s00392-022-02088-x; html:https://europepmc.org/articles/PMC9998324; pdf:https://europepmc.org/articles/PMC9998324?pdf=render"
+    "urls": "pdf:https://nutrition.bmj.com/content/bmjnph/3/2/247.full.pdf; doi:https://doi.org/10.1136/bmjnph-2020-000107; html:https://europepmc.org/articles/PMC7841812; pdf:https://europepmc.org/articles/PMC7841812?pdf=render"
   },
   {
     "id": "32570434",
@@ -30395,6 +30412,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.3233/SHTI200210"
   },
+  {
+    "id": "36066609",
+    "doi": "https://doi.org/10.1007/s00392-022-02088-x",
+    "title": "Towards automatic classification of cardiovascular magnetic resonance Task Force Criteria for diagnosis of arrhythmogenic right ventricular cardiomyopathy.",
+    "authorString": "Bourfiss M, Sander J, de Vos BD, Te Riele ASJM, Asselbergs FW, I\u0161gum I, Velthuis BK.",
+    "authorAffiliations": "",
+    "journalTitle": "Clinical research in cardiology : official journal of the German Cardiac Society",
+    "pubYear": "2023",
+    "date": "2022-09-06",
+    "isOpenAccess": "Y",
+    "keywords": "Cardiac Magnetic Resonance Imaging; Arrhythmogenic Right Ventricular Cardiomyopathy; Automatic Segmentation; Deep Learning",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Arrhythmogenic right ventricular cardiomyopathy (ARVC) is diagnosed according to the Task Force Criteria (TFC) in which cardiovascular magnetic resonance (CMR) imaging plays an important role. Our study aims to apply an automatic deep learning-based segmentation for right and left ventricular CMR assessment and evaluate this approach for classification of the CMR TFC.<h4>Methods</h4>We included 227 subjects suspected of ARVC who underwent CMR. Subjects were classified into (1) ARVC patients fulfilling TFC; (2) at-risk family members; and (3) controls. To perform automatic segmentation, a Bayesian Dilated Residual Neural Network was trained and tested. Performance of automatic versus manual segmentation was assessed using Dice-coefficient and Hausdorff distance. Since automatic segmentation is most challenging in basal slices, manual correction of the automatic segmentation in the most basal slice was simulated (automatic<sup>-basal</sup>). CMR TFC calculated using manual and automatic<sup>-basal</sup> segmentation were compared using Cohen's Kappa (\u03ba).<h4>Results</h4>Automatic segmentation was trained on CMRs of 70 subjects (39.6\u2009\u00b1\u200918.1\u00a0years, 47% female) and tested on 157 subjects (36.9\u2009\u00b1\u200917.6\u00a0years, 59% female). Dice-coefficient and Hausdorff distance showed good agreement between manual and automatic segmentations (\u2265\u20090.89 and\u2009\u2264\u200910.6\u00a0mm, respectively) which further improved after simulated correction of the most basal slice (\u2265\u20090.92 and\u2009\u2264\u20099.2\u00a0mm, p\u2009<\u20090.001). Pearson correlation of volumetric and functional CMR measurements was good to excellent (automatic (r\u2009=\u20090.78-0.99, p\u2009<\u20090.001) and automatic<sup>-basal</sup> (r\u2009=\u20090.88-0.99, p\u2009<\u20090.001) measurements). CMR TFC classification using automatic<sup>-basal</sup> segmentations was comparable to manual segmentations (\u03ba 0.98\u2009\u00b1\u20090.02) with comparable diagnostic performance.<h4>Conclusions</h4>Combining automatic segmentation of CMRs with correction of the most basal slice results in accurate CMR TFC classification of subjects suspected of ARVC.",
+    "laySummary": "",
+    "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s00392-022-02088-x.pdf; doi:https://doi.org/10.1007/s00392-022-02088-x; html:https://europepmc.org/articles/PMC9998324; pdf:https://europepmc.org/articles/PMC9998324?pdf=render"
+  },
   {
     "id": "32400358",
     "doi": "https://doi.org/10.2807/1560-7917.es.2020.25.18.2000632",
@@ -30412,23 +30446,6 @@
     "laySummary": "The authors of this paper estimate the number of cases and spread of COVID-19 using data on critical care admissions within the UK, from a period of February to March 2020. Their results suggest that the UK had hundreds of thousands of COVID-19 cases by the time the national lockdown was implemented. They highlight the usefulness of surveilling critical care data to better understand the dynamics of the epidemic and better inform the response measures.",
     "urls": "pdf:https://www.eurosurveillance.org/deliver/fulltext/eurosurveillance/25/18/eurosurv-25-18-2.pdf?itemId=%2Fcontent%2F10.2807%2F1560-7917.ES.2020.25.18.2000632&mimeType=pdf&containerItemId=content/eurosurveillance; doi:https://doi.org/10.2807/1560-7917.ES.2020.25.18.2000632; html:https://europepmc.org/articles/PMC7219029; pdf:https://europepmc.org/articles/PMC7219029?pdf=render"
   },
-  {
-    "id": "37046260",
-    "doi": "https://doi.org/10.1186/s12913-023-09363-1",
-    "title": "Associations between the stringency of COVID-19 containment policies and health service disruptions in 10 countries.",
-    "authorString": "Reddy T, Kapoor NR, Kubota S, Doubova SV, Asai D, Mariam DH, Ayele W, Mebratie AD, Thermidor R, Sapag JC, Bedregal P, Passi-Solar \u00c1, Gordon-Strachan G, Dulal M, Gadeka DD, Mehata S, Margozzini P, Leerapan B, Rittiphairoj T, Kaewkamjornchai P, Nega A, Awoonor-Williams JK, Kruk ME, Arsenault C.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC health services research",
-    "pubYear": "2023",
-    "date": "2023-04-12",
-    "isOpenAccess": "Y",
-    "keywords": "Health Services; Health Systems; Pandemic Response; Health System Resilience; Covid-19 Restrictions; Health Care Disruptions",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Disruptions in essential health services during the COVID-19 pandemic have been reported in several countries. Yet, patterns in health service disruption according to country responses remain unclear.\u00a0In this paper, we investigate associations between the stringency of COVID-19 containment policies and disruptions in 31 health services in 10 low- middle- and high-income countries in 2020.<h4>Methods</h4>Using routine health information systems and administrative data from 10 countries (Chile, Ethiopia, Ghana, Haiti, Lao People's Democratic Republic, Mexico, Nepal, South Africa, South Korea, and Thailand) we estimated health service disruptions for the period of April to December 2020 by dividing monthly service provision at national levels by the average service provision in the 15\u00a0months pre-COVID (January 2019-March 2020). We used the\u00a0Oxford COVID-19 Government Response Tracker (OxCGRT) index and\u00a0multi-level linear regression analyses to assess associations between the stringency of restrictions and health service disruptions over nine months. We extended the analysis by examining associations between 11 individual containment or closure policies and health service disruptions. Models were adjusted for COVID caseload, health service category and country GDP and included robust standard errors.<h4>Findings</h4>Chronic disease care was among the most affected services. Regression analyses revealed that a 10% increase in the mean stringency index was associated with a 3.3 percentage-point (95% CI -3.9, -2.7) reduction in relative service volumes. Among individual policies, curfews, and the presence of a state of emergency, had the largest coefficients and were associated with 14.1 (95% CI -19.6, 8.7) and 10.7 (95% CI -12.7, -8.7) percentage-point lower relative service volumes, respectively. In contrast, number of COVID-19 cases in 2020 was not associated with health service disruptions in any model.<h4>Conclusions</h4>Although containment policies were crucial in reducing COVID-19 mortality in many contexts, it is important to consider the indirect effects of these restrictions. Strategies to improve the resilience of health systems should be designed to ensure that populations can continue accessing essential health care despite the presence of containment policies during future infectious disease outbreaks.",
-    "laySummary": "",
-    "urls": "pdf:https://bmchealthservres.biomedcentral.com/counter/pdf/10.1186/s12913-023-09363-1; doi:https://doi.org/10.1186/s12913-023-09363-1; html:https://europepmc.org/articles/PMC10096103; pdf:https://europepmc.org/articles/PMC10096103?pdf=render"
-  },
   {
     "id": "36253349",
     "doi": "https://doi.org/10.1038/s41467-022-33675-1",
@@ -30447,21 +30464,21 @@
     "urls": "pdf:https://www.nature.com/articles/s41467-022-33675-1.pdf; doi:https://doi.org/10.1038/s41467-022-33675-1; html:https://europepmc.org/articles/PMC9576777; pdf:https://europepmc.org/articles/PMC9576777?pdf=render"
   },
   {
-    "id": "34950917",
-    "doi": "https://doi.org/10.1016/j.lanepe.2021.100248",
-    "title": "Late effects of cancer in children, teenagers and young adults: Population-based study on the burden of 183 conditions, in-patient and critical care admissions and years of life lost.",
-    "authorString": "Chang WH, Katsoulis M, Tan YY, Mueller SH, Green K, Lai AG.",
+    "id": "37046260",
+    "doi": "https://doi.org/10.1186/s12913-023-09363-1",
+    "title": "Associations between the stringency of COVID-19 containment policies and health service disruptions in 10 countries.",
+    "authorString": "Reddy T, Kapoor NR, Kubota S, Doubova SV, Asai D, Mariam DH, Ayele W, Mebratie AD, Thermidor R, Sapag JC, Bedregal P, Passi-Solar \u00c1, Gordon-Strachan G, Dulal M, Gadeka DD, Mehata S, Margozzini P, Leerapan B, Rittiphairoj T, Kaewkamjornchai P, Nega A, Awoonor-Williams JK, Kruk ME, Arsenault C.",
     "authorAffiliations": "",
-    "journalTitle": "The Lancet regional health. Europe",
-    "pubYear": "2022",
-    "date": "2021-11-14",
+    "journalTitle": "BMC health services research",
+    "pubYear": "2023",
+    "date": "2023-04-12",
     "isOpenAccess": "Y",
-    "keywords": "Primary Care; Hospitalisation; Cancer Treatment; Years Of Life Lost; Cancer Late Effects; Children, Teenagers And Young Adults",
+    "keywords": "Health Services; Health Systems; Pandemic Response; Health System Resilience; Covid-19 Restrictions; Health Care Disruptions",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Children, teenagers and young adults who survived cancer are prone to developing late effects. The burden of late effects across a large number of conditions, in-patient hospitalisation and critical care admissions have not been described using a population-based dataset. We aim to systematically quantify the cumulative burden of late effects across all cancer subtypes, treatment modalities and chemotherapy drug classes.<h4>Methods</h4>We employed primary care records linked to hospitals, the death registry and cancer registry from 1998-2020. CTYA survivors were 25 years or younger at the time of cancer diagnosis had survived \u22655 years post-diagnosis. Year-of-birth and sex-matched community controls were used for comparison. We considered nine treatment types, nine chemotherapy classes and 183 physical and mental health late effects. Cumulative burden was estimated using mean cumulative count, which considers recurring events. Multivariable logistic regression was used to investigate the association between treatment exposures and late effects. Excess years of life lost (YLL) attributable to late effects were estimated.<h4>Findings</h4>Among 4,063 patients diagnosed with cancer, 3,466 survived \u2265 5 years (85%); 13,517 matched controls were identified. The cumulative burden of late effects at age 35 was the highest in survivors of leukaemia (23.52 per individual [95% CI:19.85-29.33]) and lowest in survivors of germ cell tumours (CI:6.04 [5.32-6.91]). In controls, the cumulative burden was 3.99 (CI:3.93-4.08) at age 35 years. When survivors reach age 45, the cumulative burden for immunological conditions and infections was the highest (3.27 [CI:3.01-3.58]), followed by cardiovascular conditions (3.08 [CI:1.98-3.29]). Survivors who received chemotherapy and radiotherapy had the highest disease burden compared to those who received surgery only. These patients also had the highest burden of hospitalisation (by age 45: 10.43 [CI:8.27-11.95]). Survivors who received antimetabolite chemotherapy had the highest disease and hospitalisation burden, while the lowest burden is observed in those receiving antitumour antibiotics. Regression analyses revealed that survivors who received only surgery had lower odds of developing cardiovascular (adjusted odds ratio 0.73 [CI:0.56-0.94]), haematological (aOR 0.51 [CI:0.37-0.70]), immunology and infection (aOR 0.84 [CI:0.71-0.99]) and renal (aOR 0.51 [CI:0.39-0.66]) late effects. By contrast, the opposite trend was observed in survivors who received chemo-radiotherapy. High antimetabolite chemotherapy cumulative dose was associated with increased risks of subsequent cancer (aOR 2.32 [CI:1.06-4.84]), metastatic cancer (aOR 4.44 [CI:1.29-11.66]) and renal (aOR 3.48 [CI:1.36-7.86]) conditions. Patients who received radiation dose of \u226550\u202fGy experienced higher risks of developing metastatic cancer (aOR 5.51 [CI:2.21-11.86]), cancer (aOR 3.77 [CI:2.22-6.34]), haematological (aOR 3.43 [CI:1.54-6.83]) and neurological (aOR 3.24 [CI:1.78-5.66]) conditions. Similar trends were observed in survivors who received more than three teletherapy fields. Cumulative burden analyses on 183 conditions separately revealed varying dominance of different late effects across cancer types, socioeconomic deprivation and treatment modalities. Late effects are associated with excess YLL (i.e., the difference in YLL between survivors with or without late effects), which was the most pronounced among survivors with haematological comorbidities.<h4>Interpretation</h4>To our knowledge, this is the first study to dissect and quantify the importance of late morbidities on subsequent survival using linked electronic health records from multiple settings. The burden of late effects is heterogeneous, as is the risk of premature mortality associated with late effects. We provide an extensive knowledgebase to help inform treatment decisions at the point of diagnosis, future interventional trials and late-effects screening centred on the holistic needs of this vulnerable population.",
+    "abstract": "<h4>Background</h4>Disruptions in essential health services during the COVID-19 pandemic have been reported in several countries. Yet, patterns in health service disruption according to country responses remain unclear.\u00a0In this paper, we investigate associations between the stringency of COVID-19 containment policies and disruptions in 31 health services in 10 low- middle- and high-income countries in 2020.<h4>Methods</h4>Using routine health information systems and administrative data from 10 countries (Chile, Ethiopia, Ghana, Haiti, Lao People's Democratic Republic, Mexico, Nepal, South Africa, South Korea, and Thailand) we estimated health service disruptions for the period of April to December 2020 by dividing monthly service provision at national levels by the average service provision in the 15\u00a0months pre-COVID (January 2019-March 2020). We used the\u00a0Oxford COVID-19 Government Response Tracker (OxCGRT) index and\u00a0multi-level linear regression analyses to assess associations between the stringency of restrictions and health service disruptions over nine months. We extended the analysis by examining associations between 11 individual containment or closure policies and health service disruptions. Models were adjusted for COVID caseload, health service category and country GDP and included robust standard errors.<h4>Findings</h4>Chronic disease care was among the most affected services. Regression analyses revealed that a 10% increase in the mean stringency index was associated with a 3.3 percentage-point (95% CI -3.9, -2.7) reduction in relative service volumes. Among individual policies, curfews, and the presence of a state of emergency, had the largest coefficients and were associated with 14.1 (95% CI -19.6, 8.7) and 10.7 (95% CI -12.7, -8.7) percentage-point lower relative service volumes, respectively. In contrast, number of COVID-19 cases in 2020 was not associated with health service disruptions in any model.<h4>Conclusions</h4>Although containment policies were crucial in reducing COVID-19 mortality in many contexts, it is important to consider the indirect effects of these restrictions. Strategies to improve the resilience of health systems should be designed to ensure that populations can continue accessing essential health care despite the presence of containment policies during future infectious disease outbreaks.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.lanepe.2021.100248; doi:https://doi.org/10.1016/j.lanepe.2021.100248; html:https://europepmc.org/articles/PMC8672041; pdf:https://europepmc.org/articles/PMC8672041?pdf=render"
+    "urls": "pdf:https://bmchealthservres.biomedcentral.com/counter/pdf/10.1186/s12913-023-09363-1; doi:https://doi.org/10.1186/s12913-023-09363-1; html:https://europepmc.org/articles/PMC10096103; pdf:https://europepmc.org/articles/PMC10096103?pdf=render"
   },
   {
     "id": "32735830",
@@ -30480,6 +30497,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/S2352-3026(20)30228-3"
   },
+  {
+    "id": "34950917",
+    "doi": "https://doi.org/10.1016/j.lanepe.2021.100248",
+    "title": "Late effects of cancer in children, teenagers and young adults: Population-based study on the burden of 183 conditions, in-patient and critical care admissions and years of life lost.",
+    "authorString": "Chang WH, Katsoulis M, Tan YY, Mueller SH, Green K, Lai AG.",
+    "authorAffiliations": "",
+    "journalTitle": "The Lancet regional health. Europe",
+    "pubYear": "2022",
+    "date": "2021-11-14",
+    "isOpenAccess": "Y",
+    "keywords": "Primary Care; Hospitalisation; Cancer Treatment; Years Of Life Lost; Cancer Late Effects; Children, Teenagers And Young Adults",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Children, teenagers and young adults who survived cancer are prone to developing late effects. The burden of late effects across a large number of conditions, in-patient hospitalisation and critical care admissions have not been described using a population-based dataset. We aim to systematically quantify the cumulative burden of late effects across all cancer subtypes, treatment modalities and chemotherapy drug classes.<h4>Methods</h4>We employed primary care records linked to hospitals, the death registry and cancer registry from 1998-2020. CTYA survivors were 25 years or younger at the time of cancer diagnosis had survived \u22655 years post-diagnosis. Year-of-birth and sex-matched community controls were used for comparison. We considered nine treatment types, nine chemotherapy classes and 183 physical and mental health late effects. Cumulative burden was estimated using mean cumulative count, which considers recurring events. Multivariable logistic regression was used to investigate the association between treatment exposures and late effects. Excess years of life lost (YLL) attributable to late effects were estimated.<h4>Findings</h4>Among 4,063 patients diagnosed with cancer, 3,466 survived \u2265 5 years (85%); 13,517 matched controls were identified. The cumulative burden of late effects at age 35 was the highest in survivors of leukaemia (23.52 per individual [95% CI:19.85-29.33]) and lowest in survivors of germ cell tumours (CI:6.04 [5.32-6.91]). In controls, the cumulative burden was 3.99 (CI:3.93-4.08) at age 35 years. When survivors reach age 45, the cumulative burden for immunological conditions and infections was the highest (3.27 [CI:3.01-3.58]), followed by cardiovascular conditions (3.08 [CI:1.98-3.29]). Survivors who received chemotherapy and radiotherapy had the highest disease burden compared to those who received surgery only. These patients also had the highest burden of hospitalisation (by age 45: 10.43 [CI:8.27-11.95]). Survivors who received antimetabolite chemotherapy had the highest disease and hospitalisation burden, while the lowest burden is observed in those receiving antitumour antibiotics. Regression analyses revealed that survivors who received only surgery had lower odds of developing cardiovascular (adjusted odds ratio 0.73 [CI:0.56-0.94]), haematological (aOR 0.51 [CI:0.37-0.70]), immunology and infection (aOR 0.84 [CI:0.71-0.99]) and renal (aOR 0.51 [CI:0.39-0.66]) late effects. By contrast, the opposite trend was observed in survivors who received chemo-radiotherapy. High antimetabolite chemotherapy cumulative dose was associated with increased risks of subsequent cancer (aOR 2.32 [CI:1.06-4.84]), metastatic cancer (aOR 4.44 [CI:1.29-11.66]) and renal (aOR 3.48 [CI:1.36-7.86]) conditions. Patients who received radiation dose of \u226550\u202fGy experienced higher risks of developing metastatic cancer (aOR 5.51 [CI:2.21-11.86]), cancer (aOR 3.77 [CI:2.22-6.34]), haematological (aOR 3.43 [CI:1.54-6.83]) and neurological (aOR 3.24 [CI:1.78-5.66]) conditions. Similar trends were observed in survivors who received more than three teletherapy fields. Cumulative burden analyses on 183 conditions separately revealed varying dominance of different late effects across cancer types, socioeconomic deprivation and treatment modalities. Late effects are associated with excess YLL (i.e., the difference in YLL between survivors with or without late effects), which was the most pronounced among survivors with haematological comorbidities.<h4>Interpretation</h4>To our knowledge, this is the first study to dissect and quantify the importance of late morbidities on subsequent survival using linked electronic health records from multiple settings. The burden of late effects is heterogeneous, as is the risk of premature mortality associated with late effects. We provide an extensive knowledgebase to help inform treatment decisions at the point of diagnosis, future interventional trials and late-effects screening centred on the holistic needs of this vulnerable population.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.lanepe.2021.100248; doi:https://doi.org/10.1016/j.lanepe.2021.100248; html:https://europepmc.org/articles/PMC8672041; pdf:https://europepmc.org/articles/PMC8672041?pdf=render"
+  },
   {
     "id": "38479550",
     "doi": "https://doi.org/10.1016/j.ajcnut.2024.03.006",
@@ -30565,23 +30599,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/cei/advance-article-pdf/doi/10.1093/cei/uxad008/49549101/uxad008.pdf; doi:https://doi.org/10.1093/cei/uxad008; html:https://europepmc.org/articles/PMC10128160; pdf:https://europepmc.org/articles/PMC10128160?pdf=render"
   },
-  {
-    "id": "39107017",
-    "doi": "https://doi.org/10.1136/bmjopen-2023-083497",
-    "title": "COVID-19 pandemic impact on hypertension management in North East London: an observational cohort study using electronic health records.",
-    "authorString": "Rison SCG, Redfern OC, Mathur R, Dostal I, Carvalho C, Raisi-Estabragh Z, Robson J.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2024",
-    "date": "2024-08-06",
-    "isOpenAccess": "Y",
-    "keywords": "Hypertension; Blood pressure; Cardiovascular disease; Public Health; Primary Care; Health Equity",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objective</h4>There are established inequities in the monitoring and management of hypertension in England. The COVID-19 pandemic had a major impact on primary care management of long-term conditions such as hypertension. This study investigated the possible disproportionate impact of the pandemic across patient groups.<h4>Design</h4>Open cohort of people with diagnosed hypertension.<h4>Settings</h4>North East London primary care practices from January 2019 to October 2022.<h4>Participants</h4>All 224\u2009329 adults with hypertension registered in 193 primary care practices.<h4>Outcomes</h4>Monitoring and management of hypertension were assessed using two indicators: (i) blood pressure recorded within 1 year of the index date and (ii) blood pressure control to national clinical practice guidelines.<h4>Results</h4>The proportion of patients with a contemporaneous blood pressure recording fell from a 91% pre-pandemic peak to 62% at the end of the pandemic lockdown and improved to 77% by the end of the study. This was paralleled by the proportion of individuals with controlled hypertension which fell from a 73% pre-pandemic peak to 50% at the end of the pandemic lockdown and improved to 60% by the end of the study. However, when excluding patients without a recent blood pressure recording, the proportions of patients with controlled hypertension increased to 81%, 80% and 78% respectively.Throughout the study, in comparison to the White ethnic group, the Black ethnic group was less likely to achieve adequate blood pressure control (ORs 0.81 (95% CI 0.78 to 0.85, p<0.001) to 0.87 (95% CI 0.84 to 0.91, p<0.001)). Conversely, the Asian ethnic group was more likely to have controlled blood pressure (ORs 1.09 (95% CI 1.05 to 1.14, p<0.001) to 1.28 (95% CI 1.23 to 1.32, p<0.001)). Men, younger individuals, more affluent individuals, individuals with unknown or unrecorded ethnicity or those untreated were also less likely to have blood pressure control to target throughout the study.<h4>Conclusion</h4>The COVID-19 pandemic had a greater impact on blood pressure recording than on blood pressure control. Inequities in blood pressure control persisted during the pandemic and remain outstanding.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1136/bmjopen-2023-083497; html:https://europepmc.org/articles/PMC11308888; pdf:https://europepmc.org/articles/PMC11308888?pdf=render"
-  },
   {
     "id": "33653287",
     "doi": "https://doi.org/10.1186/s12875-021-01384-1",
@@ -30599,6 +30616,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmcfampract.biomedcentral.com/track/pdf/10.1186/s12875-021-01384-1; doi:https://doi.org/10.1186/s12875-021-01384-1; html:https://europepmc.org/articles/PMC7927406; pdf:https://europepmc.org/articles/PMC7927406?pdf=render"
   },
+  {
+    "id": "39107017",
+    "doi": "https://doi.org/10.1136/bmjopen-2023-083497",
+    "title": "COVID-19 pandemic impact on hypertension management in North East London: an observational cohort study using electronic health records.",
+    "authorString": "Rison SCG, Redfern OC, Mathur R, Dostal I, Carvalho C, Raisi-Estabragh Z, Robson J.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2024",
+    "date": "2024-08-06",
+    "isOpenAccess": "Y",
+    "keywords": "Hypertension; Blood pressure; Cardiovascular disease; Public Health; Primary Care; Health Equity",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>There are established inequities in the monitoring and management of hypertension in England. The COVID-19 pandemic had a major impact on primary care management of long-term conditions such as hypertension. This study investigated the possible disproportionate impact of the pandemic across patient groups.<h4>Design</h4>Open cohort of people with diagnosed hypertension.<h4>Settings</h4>North East London primary care practices from January 2019 to October 2022.<h4>Participants</h4>All 224\u2009329 adults with hypertension registered in 193 primary care practices.<h4>Outcomes</h4>Monitoring and management of hypertension were assessed using two indicators: (i) blood pressure recorded within 1 year of the index date and (ii) blood pressure control to national clinical practice guidelines.<h4>Results</h4>The proportion of patients with a contemporaneous blood pressure recording fell from a 91% pre-pandemic peak to 62% at the end of the pandemic lockdown and improved to 77% by the end of the study. This was paralleled by the proportion of individuals with controlled hypertension which fell from a 73% pre-pandemic peak to 50% at the end of the pandemic lockdown and improved to 60% by the end of the study. However, when excluding patients without a recent blood pressure recording, the proportions of patients with controlled hypertension increased to 81%, 80% and 78% respectively.Throughout the study, in comparison to the White ethnic group, the Black ethnic group was less likely to achieve adequate blood pressure control (ORs 0.81 (95% CI 0.78 to 0.85, p<0.001) to 0.87 (95% CI 0.84 to 0.91, p<0.001)). Conversely, the Asian ethnic group was more likely to have controlled blood pressure (ORs 1.09 (95% CI 1.05 to 1.14, p<0.001) to 1.28 (95% CI 1.23 to 1.32, p<0.001)). Men, younger individuals, more affluent individuals, individuals with unknown or unrecorded ethnicity or those untreated were also less likely to have blood pressure control to target throughout the study.<h4>Conclusion</h4>The COVID-19 pandemic had a greater impact on blood pressure recording than on blood pressure control. Inequities in blood pressure control persisted during the pandemic and remain outstanding.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1136/bmjopen-2023-083497; html:https://europepmc.org/articles/PMC11308888; pdf:https://europepmc.org/articles/PMC11308888?pdf=render"
+  },
   {
     "id": "36819459",
     "doi": "https://doi.org/10.1210/jendso/bvad020",
@@ -30650,23 +30684,6 @@
     "laySummary": "",
     "urls": "pdf:https://discovery.ucl.ac.uk/10143945/1/Keane_T2DM%20metformin%20and%20risk%20of%20AMD%20BJO%2020220111%20clean.pdf; doi:https://doi.org/10.1136/bjophthalmol-2021-319641"
   },
-  {
-    "id": "36228971",
-    "doi": "https://doi.org/10.1016/j.jclinepi.2022.10.011",
-    "title": "In simulated data and health records, latent class analysis was the optimum multimorbidity clustering algorithm.",
-    "authorString": "Nichols L, Taverner T, Crowe F, Richardson S, Yau C, Kiddle S, Kirk P, Barrett J, Nirantharakumar K, Griffin S, Edwards D, Marshall T.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of clinical epidemiology",
-    "pubYear": "2022",
-    "date": "2022-10-11",
-    "isOpenAccess": "Y",
-    "keywords": "Hierarchical cluster analysis; Clustering Methods; Latent Class Analysis; Electronic Medical Records; Multimorbidity; K-means; Multiple Correspondence Analysis",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background and objectives</h4>To investigate the reproducibility and validity of latent class analysis (LCA) and hierarchical cluster analysis (HCA), multiple correspondence analysis followed by k-means (MCA-kmeans) and k-means (kmeans) for multimorbidity clustering.<h4>Methods</h4>We first investigated clustering algorithms in simulated datasets with 26 diseases of varying prevalence in predetermined clusters, comparing the derived clusters to known clusters using the adjusted Rand Index (aRI). We then them investigated the medical records of male patients, aged 65 to 84 years from 50 UK general practices, with 49 long-term health conditions. We compared within cluster morbidity profiles using the Pearson correlation coefficient and assessed cluster stability using in 400 bootstrap samples.<h4>Results</h4>In the simulated datasets, the closest agreement (largest aRI) to known clusters was with LCA and then MCA-kmeans algorithms. In the medical records dataset, all four algorithms identified one cluster of 20-25% of the dataset with about 82% of the same patients across all four algorithms. LCA and MCA-kmeans both found a second cluster of 7% of the dataset. Other clusters were found by only one algorithm. LCA and MCA-kmeans clustering gave the most similar partitioning (aRI 0.54).<h4>Conclusion</h4>LCA achieved higher aRI than other clustering algorithms.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.jclinepi.2022.10.011; doi:https://doi.org/10.1016/j.jclinepi.2022.10.011; html:https://europepmc.org/articles/PMC7613854; pdf:https://europepmc.org/articles/PMC7613854?pdf=render"
-  },
   {
     "id": "34396190",
     "doi": "https://doi.org/10.1016/j.jaccao.2019.09.007",
@@ -30684,6 +30701,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.jaccao.2019.09.007; doi:https://doi.org/10.1016/j.jaccao.2019.09.007; html:https://europepmc.org/articles/PMC8352330; pdf:https://europepmc.org/articles/PMC8352330?pdf=render"
   },
+  {
+    "id": "36228971",
+    "doi": "https://doi.org/10.1016/j.jclinepi.2022.10.011",
+    "title": "In simulated data and health records, latent class analysis was the optimum multimorbidity clustering algorithm.",
+    "authorString": "Nichols L, Taverner T, Crowe F, Richardson S, Yau C, Kiddle S, Kirk P, Barrett J, Nirantharakumar K, Griffin S, Edwards D, Marshall T.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of clinical epidemiology",
+    "pubYear": "2022",
+    "date": "2022-10-11",
+    "isOpenAccess": "Y",
+    "keywords": "Hierarchical cluster analysis; Clustering Methods; Latent Class Analysis; Electronic Medical Records; Multimorbidity; K-means; Multiple Correspondence Analysis",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background and objectives</h4>To investigate the reproducibility and validity of latent class analysis (LCA) and hierarchical cluster analysis (HCA), multiple correspondence analysis followed by k-means (MCA-kmeans) and k-means (kmeans) for multimorbidity clustering.<h4>Methods</h4>We first investigated clustering algorithms in simulated datasets with 26 diseases of varying prevalence in predetermined clusters, comparing the derived clusters to known clusters using the adjusted Rand Index (aRI). We then them investigated the medical records of male patients, aged 65 to 84 years from 50 UK general practices, with 49 long-term health conditions. We compared within cluster morbidity profiles using the Pearson correlation coefficient and assessed cluster stability using in 400 bootstrap samples.<h4>Results</h4>In the simulated datasets, the closest agreement (largest aRI) to known clusters was with LCA and then MCA-kmeans algorithms. In the medical records dataset, all four algorithms identified one cluster of 20-25% of the dataset with about 82% of the same patients across all four algorithms. LCA and MCA-kmeans both found a second cluster of 7% of the dataset. Other clusters were found by only one algorithm. LCA and MCA-kmeans clustering gave the most similar partitioning (aRI 0.54).<h4>Conclusion</h4>LCA achieved higher aRI than other clustering algorithms.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.jclinepi.2022.10.011; doi:https://doi.org/10.1016/j.jclinepi.2022.10.011; html:https://europepmc.org/articles/PMC7613854; pdf:https://europepmc.org/articles/PMC7613854?pdf=render"
+  },
   {
     "id": "33174528",
     "doi": "https://doi.org/10.3310/hta24570",
@@ -30718,6 +30752,40 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1167/tvst.11.1.3; doi:https://doi.org/10.1167/tvst.11.1.3; html:https://europepmc.org/articles/PMC8742534; pdf:https://europepmc.org/articles/PMC8742534?pdf=render"
   },
+  {
+    "id": "34002035",
+    "doi": "https://doi.org/10.1038/s41366-021-00807-4",
+    "title": "Risk factors mediating the effect of body mass index and waist-to-hip ratio on cardiovascular outcomes: Mendelian randomization analysis.",
+    "authorString": "Gill D, Zuber V, Dawson J, Pearson-Stuttard J, Carter AR, Sanderson E, Karhunen V, Levin MG, Wootton RE, Klarin D, Tsao PS, Tsilidis KK, Damrauer SM, Burgess S, Elliott P.",
+    "authorAffiliations": "",
+    "journalTitle": "International journal of obesity (2005)",
+    "pubYear": "2021",
+    "date": "2021-05-17",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Higher body mass index (BMI) and waist-to-hip ratio (WHR) increase the risk of cardiovascular disease, but the extent to which this is mediated by blood pressure, diabetes, lipid traits, and smoking is not fully understood.<h4>Methods</h4>Using consortia and UK Biobank genetic association summary data from 140,595 to 898,130 participants predominantly of European ancestry, Mendelian randomization mediation analysis was performed to investigate the degree to which systolic blood pressure (SBP), diabetes, lipid traits, and smoking mediated an effect of BMI and WHR on the risk of coronary artery disease (CAD), peripheral artery disease (PAD) and stroke.<h4>Results</h4>The odds ratio of CAD per 1-standard deviation increase in genetically predicted BMI was 1.49 (95% CI 1.39 to 1.60). This attenuated to 1.34 (95% CI 1.24 to 1.45) after adjusting for genetically predicted SBP (proportion mediated 27%, 95% CI 3% to 50%), to 1.27 (95% CI 1.17 to 1.37) after adjusting for genetically predicted diabetes (41% mediated, 95% CI 18% to 63%), to 1.47 (95% CI 1.36 to 1.59) after adjusting for genetically predicted lipids (3% mediated, 95% -23% to 29%), and to 1.46 (95% CI 1.34 to 1.58) after adjusting for genetically predicted smoking (6% mediated, 95% CI -20% to 32%). Adjusting for all the mediators together, the estimate attenuated to 1.14 (95% CI 1.04 to 1.26; 66% mediated, 95% CI 42% to 91%). A similar pattern was observed when considering genetically predicted WHR as the exposure, and PAD or stroke as the outcome.<h4>Conclusions</h4>Measures to reduce obesity will lower the risk of cardiovascular disease primarily by impacting downstream metabolic risk factors, particularly diabetes and hypertension. Reduction of obesity prevalence alongside control and management of its mediators is likely to be most effective for minimizing the burden of obesity.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41366-021-00807-4.pdf; doi:https://doi.org/10.1038/s41366-021-00807-4; html:https://europepmc.org/articles/PMC8236409; pdf:https://europepmc.org/articles/PMC8236409?pdf=render"
+  },
+  {
+    "id": "34425897",
+    "doi": "https://doi.org/10.1186/s13326-021-00249-x",
+    "title": "Linking common human diseases to their phenotypes; development of a resource for human phenomics.",
+    "authorString": "Kafkas \u015e, Althubaiti S, Gkoutos GV, Hoehndorf R, Schofield PN.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of biomedical semantics",
+    "pubYear": "2021",
+    "date": "2021-08-23",
+    "isOpenAccess": "Y",
+    "keywords": "Ontologies; Text Mining; Uk Biobank; Disease\u2013phenotype Associations",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>In recent years a large volume of clinical genomics data has become available due to rapid advances in sequencing technologies. Efficient exploitation of this genomics data requires linkage to patient phenotype profiles. Current resources providing disease-phenotype associations are not comprehensive, and they often do not have broad coverage of the disease terminologies, particularly ICD-10, which is still the primary terminology used in clinical settings.<h4>Methods</h4>We developed two approaches to gather disease-phenotype associations. First, we used a text mining method that utilizes semantic relations in phenotype ontologies, and applies statistical methods to extract associations between diseases in ICD-10 and phenotype ontology classes from the literature. Second, we developed a semi-automatic way to collect ICD-10-phenotype associations from existing resources containing known relationships.<h4>Results</h4>We generated four datasets. Two of them are independent datasets linking diseases to their phenotypes based on text mining and semi-automatic strategies. The remaining two datasets are generated from these datasets and cover a subset of ICD-10 classes of common diseases contained in UK Biobank. We extensively validated our text mined and semi-automatically curated datasets by: comparing them against an expert-curated validation dataset containing disease-phenotype associations, measuring their similarity to disease-phenotype associations found in public databases, and assessing how well they could be used to recover gene-disease associations using phenotype similarity.<h4>Conclusion</h4>We find that our text mining method can produce phenotype annotations of diseases that are correct but often too general to have significant information content, or too specific to accurately reflect the typical manifestations of the sporadic disease. On the other hand, the datasets generated from integrating multiple knowledgebases are more complete (i.e., cover more of the required phenotype annotations for a given disease). We make all data freely available at https://doi.org/10.5281/zenodo.4726713 .",
+    "laySummary": "",
+    "urls": "pdf:https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-021-00249-x; doi:https://doi.org/10.1186/s13326-021-00249-x; html:https://europepmc.org/articles/PMC8383460; pdf:https://europepmc.org/articles/PMC8383460?pdf=render"
+  },
   {
     "id": "33654696",
     "doi": "https://doi.org/10.1093/burnst/tkaa044",
@@ -30752,40 +30820,6 @@
     "laySummary": "",
     "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0249258&type=printable; doi:https://doi.org/10.1371/journal.pone.0249258; html:https://europepmc.org/articles/PMC8011734; pdf:https://europepmc.org/articles/PMC8011734?pdf=render"
   },
-  {
-    "id": "34425897",
-    "doi": "https://doi.org/10.1186/s13326-021-00249-x",
-    "title": "Linking common human diseases to their phenotypes; development of a resource for human phenomics.",
-    "authorString": "Kafkas \u015e, Althubaiti S, Gkoutos GV, Hoehndorf R, Schofield PN.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of biomedical semantics",
-    "pubYear": "2021",
-    "date": "2021-08-23",
-    "isOpenAccess": "Y",
-    "keywords": "Ontologies; Text Mining; Uk Biobank; Disease\u2013phenotype Associations",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>In recent years a large volume of clinical genomics data has become available due to rapid advances in sequencing technologies. Efficient exploitation of this genomics data requires linkage to patient phenotype profiles. Current resources providing disease-phenotype associations are not comprehensive, and they often do not have broad coverage of the disease terminologies, particularly ICD-10, which is still the primary terminology used in clinical settings.<h4>Methods</h4>We developed two approaches to gather disease-phenotype associations. First, we used a text mining method that utilizes semantic relations in phenotype ontologies, and applies statistical methods to extract associations between diseases in ICD-10 and phenotype ontology classes from the literature. Second, we developed a semi-automatic way to collect ICD-10-phenotype associations from existing resources containing known relationships.<h4>Results</h4>We generated four datasets. Two of them are independent datasets linking diseases to their phenotypes based on text mining and semi-automatic strategies. The remaining two datasets are generated from these datasets and cover a subset of ICD-10 classes of common diseases contained in UK Biobank. We extensively validated our text mined and semi-automatically curated datasets by: comparing them against an expert-curated validation dataset containing disease-phenotype associations, measuring their similarity to disease-phenotype associations found in public databases, and assessing how well they could be used to recover gene-disease associations using phenotype similarity.<h4>Conclusion</h4>We find that our text mining method can produce phenotype annotations of diseases that are correct but often too general to have significant information content, or too specific to accurately reflect the typical manifestations of the sporadic disease. On the other hand, the datasets generated from integrating multiple knowledgebases are more complete (i.e., cover more of the required phenotype annotations for a given disease). We make all data freely available at https://doi.org/10.5281/zenodo.4726713 .",
-    "laySummary": "",
-    "urls": "pdf:https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-021-00249-x; doi:https://doi.org/10.1186/s13326-021-00249-x; html:https://europepmc.org/articles/PMC8383460; pdf:https://europepmc.org/articles/PMC8383460?pdf=render"
-  },
-  {
-    "id": "34002035",
-    "doi": "https://doi.org/10.1038/s41366-021-00807-4",
-    "title": "Risk factors mediating the effect of body mass index and waist-to-hip ratio on cardiovascular outcomes: Mendelian randomization analysis.",
-    "authorString": "Gill D, Zuber V, Dawson J, Pearson-Stuttard J, Carter AR, Sanderson E, Karhunen V, Levin MG, Wootton RE, Klarin D, Tsao PS, Tsilidis KK, Damrauer SM, Burgess S, Elliott P.",
-    "authorAffiliations": "",
-    "journalTitle": "International journal of obesity (2005)",
-    "pubYear": "2021",
-    "date": "2021-05-17",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Higher body mass index (BMI) and waist-to-hip ratio (WHR) increase the risk of cardiovascular disease, but the extent to which this is mediated by blood pressure, diabetes, lipid traits, and smoking is not fully understood.<h4>Methods</h4>Using consortia and UK Biobank genetic association summary data from 140,595 to 898,130 participants predominantly of European ancestry, Mendelian randomization mediation analysis was performed to investigate the degree to which systolic blood pressure (SBP), diabetes, lipid traits, and smoking mediated an effect of BMI and WHR on the risk of coronary artery disease (CAD), peripheral artery disease (PAD) and stroke.<h4>Results</h4>The odds ratio of CAD per 1-standard deviation increase in genetically predicted BMI was 1.49 (95% CI 1.39 to 1.60). This attenuated to 1.34 (95% CI 1.24 to 1.45) after adjusting for genetically predicted SBP (proportion mediated 27%, 95% CI 3% to 50%), to 1.27 (95% CI 1.17 to 1.37) after adjusting for genetically predicted diabetes (41% mediated, 95% CI 18% to 63%), to 1.47 (95% CI 1.36 to 1.59) after adjusting for genetically predicted lipids (3% mediated, 95% -23% to 29%), and to 1.46 (95% CI 1.34 to 1.58) after adjusting for genetically predicted smoking (6% mediated, 95% CI -20% to 32%). Adjusting for all the mediators together, the estimate attenuated to 1.14 (95% CI 1.04 to 1.26; 66% mediated, 95% CI 42% to 91%). A similar pattern was observed when considering genetically predicted WHR as the exposure, and PAD or stroke as the outcome.<h4>Conclusions</h4>Measures to reduce obesity will lower the risk of cardiovascular disease primarily by impacting downstream metabolic risk factors, particularly diabetes and hypertension. Reduction of obesity prevalence alongside control and management of its mediators is likely to be most effective for minimizing the burden of obesity.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41366-021-00807-4.pdf; doi:https://doi.org/10.1038/s41366-021-00807-4; html:https://europepmc.org/articles/PMC8236409; pdf:https://europepmc.org/articles/PMC8236409?pdf=render"
-  },
   {
     "id": "30554166",
     "doi": "https://doi.org/10.1136/injuryprev-2018-043019",
@@ -30803,23 +30837,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1136/injuryprev-2018-043019"
   },
-  {
-    "id": "31816119",
-    "doi": "https://doi.org/10.1002/sim.8443",
-    "title": "Dynamic predictive probabilities to monitor rapid cystic fibrosis disease progression.",
-    "authorString": "Szczesniak RD, Su W, Brokamp C, Keogh RH, Pestian JP, Seid M, Diggle PJ, Clancy JP.",
-    "authorAffiliations": "",
-    "journalTitle": "Statistics in medicine",
-    "pubYear": "2020",
-    "date": "2019-12-09",
-    "isOpenAccess": "Y",
-    "keywords": "Longitudinal Data Analysis; Medical Monitoring; Nonstationary Process; Nowcasting; Predictive Probability Distributions",
-    "nationalPriorities": "Understanding the Causes of Disease",
-    "healthCategories": "",
-    "abstract": "Cystic fibrosis (CF) is a progressive, genetic disease characterized by frequent, prolonged drops in lung function. Accurately predicting rapid underlying lung-function decline is essential for clinical decision support and timely intervention. Determining whether an individual is experiencing a period of rapid decline is complicated due to its heterogeneous timing and extent, and error component of the measured lung function. We construct individualized predictive probabilities for \"nowcasting\" rapid decline. We assume each patient's true longitudinal lung function, S(t), follows a nonlinear, nonstationary stochastic process, and accommodate between-patient heterogeneity through random effects. Corresponding lung-function decline at time t is defined as the rate of change, S'(t). We predict S'(t) conditional on observed covariate and measurement history by modeling a measured lung function as a noisy version of S(t). The method is applied to data on 30\u2009879 US CF Registry patients. Results are contrasted with a currently employed decision rule using single-center data on 212 individuals. Rapid decline is identified earlier using predictive probabilities than the center's currently employed decision rule (mean difference: 0.65\u2009years; 95% confidence interval (CI): 0.41, 0.89). We constructed a bootstrapping algorithm to obtain CIs for predictive probabilities. We illustrate real-time implementation with R Shiny. Predictive accuracy is investigated using empirical simulations, which suggest this approach more accurately detects peak decline, compared with a uniform threshold of rapid decline. Median area under the ROC curve estimates (Q1-Q3) were 0.817 (0.814-0.822) and 0.745 (0.741-0.747), respectively, implying reasonable accuracy for both. This article demonstrates how individualized rate of change estimates can be coupled with probabilistic predictive inference and implementation for a useful medical-monitoring approach.",
-    "laySummary": "The objective of this paper was to construct individualised dynamic predictive probabilities to monitor rapid Cystic Fibrosis (CF) disease progression. The results demonstrated how individualised rate of change estimates can be coupled with probabilitic predictive inference and implementation for a useful medical-monitoring approach.",
-    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/sim.8443; doi:https://doi.org/10.1002/sim.8443; html:https://europepmc.org/articles/PMC7028099; pdf:https://europepmc.org/articles/PMC7028099?pdf=render"
-  },
   {
     "id": "35983770",
     "doi": "https://doi.org/10.2807/1560-7917.es.2022.27.33.2100885",
@@ -30837,6 +30854,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.eurosurveillance.org/deliver/fulltext/eurosurveillance/27/33/eurosurv-27-33-5.pdf?itemId=%2Fcontent%2F10.2807%2F1560-7917.ES.2022.27.33.2100885&mimeType=pdf&containerItemId=content/eurosurveillance; doi:https://doi.org/10.2807/1560-7917.ES.2022.27.33.2100885; html:https://europepmc.org/articles/PMC9389857"
   },
+  {
+    "id": "31816119",
+    "doi": "https://doi.org/10.1002/sim.8443",
+    "title": "Dynamic predictive probabilities to monitor rapid cystic fibrosis disease progression.",
+    "authorString": "Szczesniak RD, Su W, Brokamp C, Keogh RH, Pestian JP, Seid M, Diggle PJ, Clancy JP.",
+    "authorAffiliations": "",
+    "journalTitle": "Statistics in medicine",
+    "pubYear": "2020",
+    "date": "2019-12-09",
+    "isOpenAccess": "Y",
+    "keywords": "Longitudinal Data Analysis; Medical Monitoring; Nonstationary Process; Nowcasting; Predictive Probability Distributions",
+    "nationalPriorities": "Understanding the Causes of Disease",
+    "healthCategories": "",
+    "abstract": "Cystic fibrosis (CF) is a progressive, genetic disease characterized by frequent, prolonged drops in lung function. Accurately predicting rapid underlying lung-function decline is essential for clinical decision support and timely intervention. Determining whether an individual is experiencing a period of rapid decline is complicated due to its heterogeneous timing and extent, and error component of the measured lung function. We construct individualized predictive probabilities for \"nowcasting\" rapid decline. We assume each patient's true longitudinal lung function, S(t), follows a nonlinear, nonstationary stochastic process, and accommodate between-patient heterogeneity through random effects. Corresponding lung-function decline at time t is defined as the rate of change, S'(t). We predict S'(t) conditional on observed covariate and measurement history by modeling a measured lung function as a noisy version of S(t). The method is applied to data on 30\u2009879 US CF Registry patients. Results are contrasted with a currently employed decision rule using single-center data on 212 individuals. Rapid decline is identified earlier using predictive probabilities than the center's currently employed decision rule (mean difference: 0.65\u2009years; 95% confidence interval (CI): 0.41, 0.89). We constructed a bootstrapping algorithm to obtain CIs for predictive probabilities. We illustrate real-time implementation with R Shiny. Predictive accuracy is investigated using empirical simulations, which suggest this approach more accurately detects peak decline, compared with a uniform threshold of rapid decline. Median area under the ROC curve estimates (Q1-Q3) were 0.817 (0.814-0.822) and 0.745 (0.741-0.747), respectively, implying reasonable accuracy for both. This article demonstrates how individualized rate of change estimates can be coupled with probabilistic predictive inference and implementation for a useful medical-monitoring approach.",
+    "laySummary": "The objective of this paper was to construct individualised dynamic predictive probabilities to monitor rapid Cystic Fibrosis (CF) disease progression. The results demonstrated how individualised rate of change estimates can be coupled with probabilitic predictive inference and implementation for a useful medical-monitoring approach.",
+    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/sim.8443; doi:https://doi.org/10.1002/sim.8443; html:https://europepmc.org/articles/PMC7028099; pdf:https://europepmc.org/articles/PMC7028099?pdf=render"
+  },
   {
     "id": "34931349",
     "doi": "https://doi.org/10.1111/bcp.15191",
@@ -30888,23 +30922,6 @@
     "laySummary": "",
     "urls": "pdf:http://www.thelancet.com/article/S2468266723001780/pdf; doi:https://doi.org/10.1016/S2468-2667(23)00178-0; html:https://europepmc.org/articles/PMC10851157; pdf:https://europepmc.org/articles/PMC10851157?pdf=render"
   },
-  {
-    "id": "35866236",
-    "doi": "https://doi.org/10.7189/jogh.12.05033",
-    "title": "The road to recovery: an interrupted time series analysis of policy intervention to restore essential health services in Mexico during the COVID-19 pandemic.",
-    "authorString": "Doubova SV, Arsenault C, Contreras-S\u00e1nchez SE, Borrayo-S\u00e1nchez G, Leslie HH.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of global health",
-    "pubYear": "2022",
-    "date": "2022-07-23",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Recovery of health services disrupted by the COVID-19 pandemic represents a significant challenge in low- and middle-income countries. In April 2021, the Mexican Institute of Social Security (IMSS), which provides health care to 68.5 million people, launched the National Strategy for Health Services Recovery (Recovery policy). The study objective was to evaluate whether the Recovery policy addressed COVID-related declines in maternal, child health, and non-communicable diseases (NCDs) services.<h4>Methods</h4>We analysed the data of 35 IMSS delegations from January 2019 to November 2021 on contraceptive visits, antenatal care consultations, deliveries, caesarean sections, sick children's consultations, child vaccination, breast and cervical cancer screening, diabetes and hypertension consultations, and control. We focused on the period before (April 2020 - March 2021) and during (April 2021 - November 2021) the Recovery policy and used an interrupted time series design and Poisson Generalized Estimating Equation models to estimate the association of this policy with service use and outcomes and change in their trends.<h4>Results</h4>Despite the third wave of the pandemic in 2021, service utilization increased in the Recovery period, reaching (at minimum) 49% of pre-pandemic levels for sick children's consultations and (at maximum) 106% of pre-pandemic levels for breast cancer screenings. Evidence for the Recovery policy role was mixed: the policy was associated with increased facility deliveries (IRR\u2009=\u20091.15, 95%CI\u2009=\u20091.11-1.19) with a growing trend over time (IRR\u2009=\u20091.04, 95%CI\u2009=\u20091.03-1.05); antenatal care and child health services saw strong level effects but decrease over time. Additionally, the Recovery policy was associated with diabetes and hypertension control. Services recovery varied across delegations.<h4>Conclusions</h4>Health service utilization and NCDs control demonstrated important gains in 2021, but evidence suggests the policy had inconsistent effects across services and decreasing impact over time. Further efforts to strengthen essential health services and ensure consistent recovery across delegations are warranted.",
-    "laySummary": "",
-    "urls": "pdf:https://jogh.org/wp-content/uploads/2022/07/jogh-12-05033.pdf; doi:https://doi.org/10.7189/jogh.12.05033; html:https://europepmc.org/articles/PMC9304921; pdf:https://europepmc.org/articles/PMC9304921?pdf=render"
-  },
   {
     "id": "32763829",
     "doi": "https://doi.org/10.1016/j.ebiom.2020.102932",
@@ -30923,21 +30940,21 @@
     "urls": "pdf:http://www.thelancet.com/article/S235239642030308X/pdf; doi:https://doi.org/10.1016/j.ebiom.2020.102932; html:https://europepmc.org/articles/PMC7406914; pdf:https://europepmc.org/articles/PMC7406914?pdf=render"
   },
   {
-    "id": "36082306",
-    "doi": "https://doi.org/10.1016/j.xgen.2021.100004",
-    "title": "Workshop proceedings: GWAS summary statistics standards and sharing.",
-    "authorString": "MacArthur JAL, Buniello A, Harris LW, Hayhurst J, McMahon A, Sollis E, Cerezo M, Hall P, Lewis E, Whetzel PL, Bahcall OG, Barroso I, Carroll RJ, Inouye M, Manolio TA, Rich SS, Hindorff LA, Wiley K, Parkinson H.",
+    "id": "35866236",
+    "doi": "https://doi.org/10.7189/jogh.12.05033",
+    "title": "The road to recovery: an interrupted time series analysis of policy intervention to restore essential health services in Mexico during the COVID-19 pandemic.",
+    "authorString": "Doubova SV, Arsenault C, Contreras-S\u00e1nchez SE, Borrayo-S\u00e1nchez G, Leslie HH.",
     "authorAffiliations": "",
-    "journalTitle": "Cell genomics",
-    "pubYear": "2021",
-    "date": "2021-10-01",
+    "journalTitle": "Journal of global health",
+    "pubYear": "2022",
+    "date": "2022-07-23",
     "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Genome-wide association studies (GWASs) have enabled robust mapping of complex traits in humans. The open sharing of GWAS summary statistics (SumStats) is essential in facilitating the larger meta-analyses needed for increased power in resolving the genetic basis of disease. However, most GWAS SumStats are not readily accessible because of limited sharing and a lack of defined standards. With the aim of increasing the availability, quality, and utility of GWAS SumStats, the National Human Genome Research Institute-European Bioinformatics Institute (NHGRI-EBI) GWAS Catalog organized a community workshop to address the standards, infrastructure, and incentives required to promote and enable sharing. We evaluated the barriers to SumStats sharing, both technological and sociological, and developed an action plan to address those challenges and ensure that SumStats and study metadata are findable, accessible, interoperable, and reusable (FAIR). We encourage early deposition of datasets in the GWAS Catalog as the recognized central repository. We recommend standard requirements for reporting elements and formats for SumStats and accompanying metadata as guidelines for community standards and a basis for submission to the GWAS Catalog. Finally, we provide recommendations to enable, promote, and incentivize broader data sharing, standards and FAIRness in order to advance genomic medicine.",
+    "abstract": "<h4>Background</h4>Recovery of health services disrupted by the COVID-19 pandemic represents a significant challenge in low- and middle-income countries. In April 2021, the Mexican Institute of Social Security (IMSS), which provides health care to 68.5 million people, launched the National Strategy for Health Services Recovery (Recovery policy). The study objective was to evaluate whether the Recovery policy addressed COVID-related declines in maternal, child health, and non-communicable diseases (NCDs) services.<h4>Methods</h4>We analysed the data of 35 IMSS delegations from January 2019 to November 2021 on contraceptive visits, antenatal care consultations, deliveries, caesarean sections, sick children's consultations, child vaccination, breast and cervical cancer screening, diabetes and hypertension consultations, and control. We focused on the period before (April 2020 - March 2021) and during (April 2021 - November 2021) the Recovery policy and used an interrupted time series design and Poisson Generalized Estimating Equation models to estimate the association of this policy with service use and outcomes and change in their trends.<h4>Results</h4>Despite the third wave of the pandemic in 2021, service utilization increased in the Recovery period, reaching (at minimum) 49% of pre-pandemic levels for sick children's consultations and (at maximum) 106% of pre-pandemic levels for breast cancer screenings. Evidence for the Recovery policy role was mixed: the policy was associated with increased facility deliveries (IRR\u2009=\u20091.15, 95%CI\u2009=\u20091.11-1.19) with a growing trend over time (IRR\u2009=\u20091.04, 95%CI\u2009=\u20091.03-1.05); antenatal care and child health services saw strong level effects but decrease over time. Additionally, the Recovery policy was associated with diabetes and hypertension control. Services recovery varied across delegations.<h4>Conclusions</h4>Health service utilization and NCDs control demonstrated important gains in 2021, but evidence suggests the policy had inconsistent effects across services and decreasing impact over time. Further efforts to strengthen essential health services and ensure consistent recovery across delegations are warranted.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.xgen.2021.100004; doi:https://doi.org/10.1016/j.xgen.2021.100004; html:https://europepmc.org/articles/PMC9451133; pdf:https://europepmc.org/articles/PMC9451133?pdf=render"
+    "urls": "pdf:https://jogh.org/wp-content/uploads/2022/07/jogh-12-05033.pdf; doi:https://doi.org/10.7189/jogh.12.05033; html:https://europepmc.org/articles/PMC9304921; pdf:https://europepmc.org/articles/PMC9304921?pdf=render"
   },
   {
     "id": "34750571",
@@ -30956,6 +30973,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s42255-021-00478-5.pdf; doi:https://doi.org/10.1038/s42255-021-00478-5; html:https://europepmc.org/articles/PMC8574944; pdf:https://europepmc.org/articles/PMC8574944?pdf=render"
   },
+  {
+    "id": "36082306",
+    "doi": "https://doi.org/10.1016/j.xgen.2021.100004",
+    "title": "Workshop proceedings: GWAS summary statistics standards and sharing.",
+    "authorString": "MacArthur JAL, Buniello A, Harris LW, Hayhurst J, McMahon A, Sollis E, Cerezo M, Hall P, Lewis E, Whetzel PL, Bahcall OG, Barroso I, Carroll RJ, Inouye M, Manolio TA, Rich SS, Hindorff LA, Wiley K, Parkinson H.",
+    "authorAffiliations": "",
+    "journalTitle": "Cell genomics",
+    "pubYear": "2021",
+    "date": "2021-10-01",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Genome-wide association studies (GWASs) have enabled robust mapping of complex traits in humans. The open sharing of GWAS summary statistics (SumStats) is essential in facilitating the larger meta-analyses needed for increased power in resolving the genetic basis of disease. However, most GWAS SumStats are not readily accessible because of limited sharing and a lack of defined standards. With the aim of increasing the availability, quality, and utility of GWAS SumStats, the National Human Genome Research Institute-European Bioinformatics Institute (NHGRI-EBI) GWAS Catalog organized a community workshop to address the standards, infrastructure, and incentives required to promote and enable sharing. We evaluated the barriers to SumStats sharing, both technological and sociological, and developed an action plan to address those challenges and ensure that SumStats and study metadata are findable, accessible, interoperable, and reusable (FAIR). We encourage early deposition of datasets in the GWAS Catalog as the recognized central repository. We recommend standard requirements for reporting elements and formats for SumStats and accompanying metadata as guidelines for community standards and a basis for submission to the GWAS Catalog. Finally, we provide recommendations to enable, promote, and incentivize broader data sharing, standards and FAIRness in order to advance genomic medicine.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.xgen.2021.100004; doi:https://doi.org/10.1016/j.xgen.2021.100004; html:https://europepmc.org/articles/PMC9451133; pdf:https://europepmc.org/articles/PMC9451133?pdf=render"
+  },
   {
     "id": "38180742",
     "doi": "https://doi.org/10.1097/qai.0000000000003326",
@@ -30973,23 +31007,6 @@
     "laySummary": "",
     "urls": "html:https://journals.lww.com/jaids/fulltext/2024/01011/estimation_of_improvements_in_mortality_in.10.aspx; doi:https://doi.org/10.1097/QAI.0000000000003326; html:https://europepmc.org/articles/PMC10769170; pdf:https://europepmc.org/articles/PMC10769170?pdf=render"
   },
-  {
-    "id": "38190103",
-    "doi": "https://doi.org/10.1016/j.xgen.2023.100469",
-    "title": "Genome-wide classification of epigenetic activity reveals regions of enriched heritability in immune-related traits.",
-    "authorString": "Stricker M, Zhang W, Cheng WY, Gazal S, Dendrou C, Nahkuri S, Palamara PF.",
-    "authorAffiliations": "",
-    "journalTitle": "Cell genomics",
-    "pubYear": "2024",
-    "date": "2023-12-28",
-    "isOpenAccess": "Y",
-    "keywords": "Immune system; Heritability; Epigenetics; Machine Learning",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Epigenetics underpins the regulation of genes known to play a key role in the adaptive and innate immune system (AIIS). We developed a method, EpiNN, that leverages epigenetic data to detect AIIS-relevant genomic regions and used it to detect 2,765 putative AIIS loci. Experimental validation of one of these loci, DNMT1, provided evidence for a novel AIIS-specific transcription start site. We built a genome-wide AIIS\u00a0annotation and used linkage disequilibrium (LD) score regression to test whether it predicts regional heritability using association statistics for 176 traits. We detected significant heritability effects (average |\u03c4<sup>\u2217</sup>|=1.65) for 20 out of 26 immune-relevant traits. In a meta-analysis, immune-relevant traits and diseases were 4.45\u00d7 more enriched for heritability than other traits. The EpiNN annotation was also depleted of trans-ancestry genetic correlation, indicating ancestry-specific effects. These results underscore the effectiveness of leveraging supervised learning algorithms and epigenetic data to detect loci implicated in specific classes of traits and diseases.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.xgen.2023.100469; html:https://europepmc.org/articles/PMC10794845; pdf:https://europepmc.org/articles/PMC10794845?pdf=render"
-  },
   {
     "id": "33837377",
     "doi": "https://doi.org/10.1038/s41591-021-01310-z",
@@ -31024,6 +31041,23 @@
     "laySummary": "",
     "urls": "pdf:http://www.internationaljournalofcardiology.com/article/S0167527320335579/pdf; doi:https://doi.org/10.1016/j.ijcard.2020.08.030"
   },
+  {
+    "id": "38190103",
+    "doi": "https://doi.org/10.1016/j.xgen.2023.100469",
+    "title": "Genome-wide classification of epigenetic activity reveals regions of enriched heritability in immune-related traits.",
+    "authorString": "Stricker M, Zhang W, Cheng WY, Gazal S, Dendrou C, Nahkuri S, Palamara PF.",
+    "authorAffiliations": "",
+    "journalTitle": "Cell genomics",
+    "pubYear": "2024",
+    "date": "2023-12-28",
+    "isOpenAccess": "Y",
+    "keywords": "Immune system; Heritability; Epigenetics; Machine Learning",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Epigenetics underpins the regulation of genes known to play a key role in the adaptive and innate immune system (AIIS). We developed a method, EpiNN, that leverages epigenetic data to detect AIIS-relevant genomic regions and used it to detect 2,765 putative AIIS loci. Experimental validation of one of these loci, DNMT1, provided evidence for a novel AIIS-specific transcription start site. We built a genome-wide AIIS\u00a0annotation and used linkage disequilibrium (LD) score regression to test whether it predicts regional heritability using association statistics for 176 traits. We detected significant heritability effects (average |\u03c4<sup>\u2217</sup>|=1.65) for 20 out of 26 immune-relevant traits. In a meta-analysis, immune-relevant traits and diseases were 4.45\u00d7 more enriched for heritability than other traits. The EpiNN annotation was also depleted of trans-ancestry genetic correlation, indicating ancestry-specific effects. These results underscore the effectiveness of leveraging supervised learning algorithms and epigenetic data to detect loci implicated in specific classes of traits and diseases.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.xgen.2023.100469; html:https://europepmc.org/articles/PMC10794845; pdf:https://europepmc.org/articles/PMC10794845?pdf=render"
+  },
   {
     "id": "33072403",
     "doi": "https://doi.org/10.1186/s40959-020-00079-3",
@@ -31041,23 +31075,6 @@
     "laySummary": "",
     "urls": "pdf:https://cardiooncologyjournal.biomedcentral.com/track/pdf/10.1186/s40959-020-00079-3; doi:https://doi.org/10.1186/s40959-020-00079-3; html:https://europepmc.org/articles/PMC7557080; pdf:https://europepmc.org/articles/PMC7557080?pdf=render"
   },
-  {
-    "id": "38663408",
-    "doi": "https://doi.org/10.1016/j.xgen.2024.100541",
-    "title": "Characterization of the genetic determinants of context-specific DNA methylation in primary monocytes.",
-    "authorString": "Gilchrist JJ, Fang H, Danielli S, Tomkova M, Nassiri I, Ng E, Tong O, Taylor C, Muldoon D, Cohen LRZ, Al-Mossawi H, Lau E, Neville M, Schuster-Boeckler B, Knight JC, Fairfax BP.",
-    "authorAffiliations": "",
-    "journalTitle": "Cell genomics",
-    "pubYear": "2024",
-    "date": "2024-04-24",
-    "isOpenAccess": "Y",
-    "keywords": "Genetics; Monocytes; Cancer; LPS; DNA methylation; Innate Immune Activation; Mqtl; Epigenetic Aging",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "To better understand inter-individual variation in sensitivity of DNA methylation (DNAm) to immune activity, we characterized effects of inflammatory stimuli on primary monocyte DNAm (n\u00a0= 190). We find that monocyte DNAm is site-dependently sensitive to lipopolysaccharide (LPS), with LPS-induced demethylation occurring following hydroxymethylation. We identify 7,359 high-confidence immune-modulated CpGs (imCpGs) that differ in genomic localization and transcription factor usage according to whether they represent a gain or loss in DNAm. Demethylated imCpGs are profoundly enriched for enhancers and colocalize to genes enriched for disease associations, especially cancer. DNAm is age associated, and we find that 24-h LPS exposure triggers approximately 6\u00a0months of gain in epigenetic age, directly linking epigenetic aging with innate immune activity. By integrating LPS-induced changes in DNAm with genetic variation, we identify 234 imCpGs under local genetic control. Exploring shared causal loci between LPS-induced DNAm responses and human disease traits highlights examples of disease-associated loci that modulate imCpG formation.",
-    "laySummary": "",
-    "urls": "pdf:https://ora.ox.ac.uk/objects/uuid:d3672019-795b-477f-a48c-8bcd9d51ecfb/files/sjw827d50r; doi:https://doi.org/10.1016/j.xgen.2024.100541; html:https://europepmc.org/articles/PMC11099345; pdf:https://europepmc.org/articles/PMC11099345?pdf=render"
-  },
   {
     "id": "32247548",
     "doi": "https://doi.org/10.1016/j.tips.2020.03.003",
@@ -31075,6 +31092,23 @@
     "laySummary": "",
     "urls": "pdf:https://discovery.ucl.ac.uk/10097090/3/Denaxas_Electronic%20Health%20Records%20to%20Predict%20Gestational%20Diabetes%20Risk_AAM.pdf; doi:https://doi.org/10.1016/j.tips.2020.03.003"
   },
+  {
+    "id": "38663408",
+    "doi": "https://doi.org/10.1016/j.xgen.2024.100541",
+    "title": "Characterization of the genetic determinants of context-specific DNA methylation in primary monocytes.",
+    "authorString": "Gilchrist JJ, Fang H, Danielli S, Tomkova M, Nassiri I, Ng E, Tong O, Taylor C, Muldoon D, Cohen LRZ, Al-Mossawi H, Lau E, Neville M, Schuster-Boeckler B, Knight JC, Fairfax BP.",
+    "authorAffiliations": "",
+    "journalTitle": "Cell genomics",
+    "pubYear": "2024",
+    "date": "2024-04-24",
+    "isOpenAccess": "Y",
+    "keywords": "Genetics; Monocytes; Cancer; LPS; DNA methylation; Innate Immune Activation; Mqtl; Epigenetic Aging",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "To better understand inter-individual variation in sensitivity of DNA methylation (DNAm) to immune activity, we characterized effects of inflammatory stimuli on primary monocyte DNAm (n\u00a0= 190). We find that monocyte DNAm is site-dependently sensitive to lipopolysaccharide (LPS), with LPS-induced demethylation occurring following hydroxymethylation. We identify 7,359 high-confidence immune-modulated CpGs (imCpGs) that differ in genomic localization and transcription factor usage according to whether they represent a gain or loss in DNAm. Demethylated imCpGs are profoundly enriched for enhancers and colocalize to genes enriched for disease associations, especially cancer. DNAm is age associated, and we find that 24-h LPS exposure triggers approximately 6\u00a0months of gain in epigenetic age, directly linking epigenetic aging with innate immune activity. By integrating LPS-induced changes in DNAm with genetic variation, we identify 234 imCpGs under local genetic control. Exploring shared causal loci between LPS-induced DNAm responses and human disease traits highlights examples of disease-associated loci that modulate imCpG formation.",
+    "laySummary": "",
+    "urls": "pdf:https://ora.ox.ac.uk/objects/uuid:d3672019-795b-477f-a48c-8bcd9d51ecfb/files/sjw827d50r; doi:https://doi.org/10.1016/j.xgen.2024.100541; html:https://europepmc.org/articles/PMC11099345; pdf:https://europepmc.org/articles/PMC11099345?pdf=render"
+  },
   {
     "id": "37984978",
     "doi": "https://doi.org/10.1136/bmj-2023-076754",
@@ -31126,23 +31160,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.12688/gatesopenres.13654.1; html:https://europepmc.org/articles/PMC10663174; pdf:https://europepmc.org/articles/PMC10663174?pdf=render"
   },
-  {
-    "id": "32200692",
-    "doi": "https://doi.org/10.1080/09602011.2020.1744453",
-    "title": "Factors facilitating recovery following severe traumatic brain injury: A qualitative study.",
-    "authorString": "Downing M, Hicks A, Braaf S, Myles D, Gabbe B, Cameron P, Ameratunga S, Ponsford J.",
-    "authorAffiliations": "",
-    "journalTitle": "Neuropsychological rehabilitation",
-    "pubYear": "2021",
-    "date": "2020-03-23",
-    "isOpenAccess": "N",
-    "keywords": "Recovery; Traumatic brain injury; Qualitative; Outcome; Positive Factors",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Given the significant impact of severe traumatic brain injury (TBI), understanding factors influencing recovery is critical to inform prognostication and treatment planning. Previous research has focussed primarily on factors negatively associated with outcome, with less focus on factors facilitating the recovery process. The current qualitative study examined positive factors identified for recovery by individuals who had sustained severe TBI three years earlier. Semi-structured interviews were conducted with nine participants with TBI and 16 close-others. Participants were asked to identify factors about themselves (or the injured individual), those around them, and the care they received that they felt were positive for recovery. Using reflexive thematic analysis, three themes were identified as positive for recovery after a TBI. <i>Having a support network</i> included social supports such as family and friends, and receiving other funded/non-funded assistance towards improving independence and participation. <i>Being positive and engaged</i> included being able to participate, being positive, using compensatory strategies, and becoming fit, healthy and happy. <i>Getting good care</i> included patients perceiving they had a comprehensive and good quality hospital experience, and access to multidisciplinary outpatient services. A focus on enhancing these positive environmental, personal and service factors in service provision may enhance outcomes following severe TBI.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1080/09602011.2020.1744453"
-  },
   {
     "id": "32238333",
     "doi": "https://doi.org/10.2196/16400",
@@ -31160,6 +31177,23 @@
     "laySummary": "",
     "urls": "pdf:https://medinform.jmir.org/2020/4/e16400/PDF; doi:https://doi.org/10.2196/16400; html:https://europepmc.org/articles/PMC7163416"
   },
+  {
+    "id": "32200692",
+    "doi": "https://doi.org/10.1080/09602011.2020.1744453",
+    "title": "Factors facilitating recovery following severe traumatic brain injury: A qualitative study.",
+    "authorString": "Downing M, Hicks A, Braaf S, Myles D, Gabbe B, Cameron P, Ameratunga S, Ponsford J.",
+    "authorAffiliations": "",
+    "journalTitle": "Neuropsychological rehabilitation",
+    "pubYear": "2021",
+    "date": "2020-03-23",
+    "isOpenAccess": "N",
+    "keywords": "Recovery; Traumatic brain injury; Qualitative; Outcome; Positive Factors",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Given the significant impact of severe traumatic brain injury (TBI), understanding factors influencing recovery is critical to inform prognostication and treatment planning. Previous research has focussed primarily on factors negatively associated with outcome, with less focus on factors facilitating the recovery process. The current qualitative study examined positive factors identified for recovery by individuals who had sustained severe TBI three years earlier. Semi-structured interviews were conducted with nine participants with TBI and 16 close-others. Participants were asked to identify factors about themselves (or the injured individual), those around them, and the care they received that they felt were positive for recovery. Using reflexive thematic analysis, three themes were identified as positive for recovery after a TBI. <i>Having a support network</i> included social supports such as family and friends, and receiving other funded/non-funded assistance towards improving independence and participation. <i>Being positive and engaged</i> included being able to participate, being positive, using compensatory strategies, and becoming fit, healthy and happy. <i>Getting good care</i> included patients perceiving they had a comprehensive and good quality hospital experience, and access to multidisciplinary outpatient services. A focus on enhancing these positive environmental, personal and service factors in service provision may enhance outcomes following severe TBI.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1080/09602011.2020.1744453"
+  },
   {
     "id": "33591566",
     "doi": "https://doi.org/10.1007/s43441-021-00263-2",
@@ -31313,23 +31347,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.eclinm.2023.102251; html:https://europepmc.org/articles/PMC10721552; pdf:https://europepmc.org/articles/PMC10721552?pdf=render"
   },
-  {
-    "id": "38751312",
-    "doi": "https://doi.org/10.1093/aje/kwae039",
-    "title": "Regression calibration of self-reported mobile phone use to optimize quantitative risk estimation in the COSMOS study.",
-    "authorString": "Reedijk M, Portengen L, Auvinen A, Kojo K, Hein\u00e4vaara S, Feychting M, Tettamanti G, Hillert L, Elliott P, Toledano MB, Smith RB, Heller J, Sch\u00fcz J, Deltour I, Poulsen AH, Johansen C, Verheij R, Peeters P, Rookus M, Traini E, Huss A, Kromhout H, Vermeulen R, COSMOS Study Group.",
-    "authorAffiliations": "",
-    "journalTitle": "American journal of epidemiology",
-    "pubYear": "2024",
-    "date": "2024-10-01",
-    "isOpenAccess": "Y",
-    "keywords": "Cohort Analysis; Measurement error; Regression calibration; Health Outcomes; Exposure assessment; Mobile Phone Use",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The Cohort Study of Mobile Phone Use and Health (COSMOS) has repeatedly collected self-reported and operator-recorded data on mobile phone use. Assessing health effects using self-reported information is prone to measurement error, but operator data were available prospectively for only part of the study population and did not cover past mobile phone use. To optimize the available data and reduce bias, we evaluated different statistical approaches for constructing mobile phone exposure histories within COSMOS. We evaluated and compared the performance of 4 regression calibration (RC) methods (simple, direct, inverse, and generalized additive model for location, shape, and scale), complete-case analysis, and multiple imputation in a simulation study with a binary health outcome. We used self-reported and operator-recorded mobile phone call data collected at baseline (2007-2012) from participants in Denmark, Finland, the Netherlands, Sweden, and the United Kingdom. Parameter estimates obtained using simple, direct, and inverse RC methods were associated with less bias and lower mean squared error than those obtained with complete-case analysis or multiple imputation. We showed that RC methods resulted in more accurate estimation of the relationship between mobile phone use and health outcomes by combining self-reported data with objective operator-recorded data available for a subset of participants.",
-    "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/aje/advance-article-pdf/doi/10.1093/aje/kwae039/57572723/kwae039.pdf; doi:https://doi.org/10.1093/aje/kwae039; html:https://europepmc.org/articles/PMC11458186; pdf:https://europepmc.org/articles/PMC11458186?pdf=render"
-  },
   {
     "id": "37671353",
     "doi": "https://doi.org/10.23889/ijpds.v5i3.2133",
@@ -31347,6 +31364,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.23889/ijpds.v5i3.2133; html:https://europepmc.org/articles/PMC10476697; pdf:https://europepmc.org/articles/PMC10476697?pdf=render"
   },
+  {
+    "id": "38751312",
+    "doi": "https://doi.org/10.1093/aje/kwae039",
+    "title": "Regression calibration of self-reported mobile phone use to optimize quantitative risk estimation in the COSMOS study.",
+    "authorString": "Reedijk M, Portengen L, Auvinen A, Kojo K, Hein\u00e4vaara S, Feychting M, Tettamanti G, Hillert L, Elliott P, Toledano MB, Smith RB, Heller J, Sch\u00fcz J, Deltour I, Poulsen AH, Johansen C, Verheij R, Peeters P, Rookus M, Traini E, Huss A, Kromhout H, Vermeulen R, COSMOS Study Group.",
+    "authorAffiliations": "",
+    "journalTitle": "American journal of epidemiology",
+    "pubYear": "2024",
+    "date": "2024-10-01",
+    "isOpenAccess": "Y",
+    "keywords": "Cohort Analysis; Measurement error; Regression calibration; Health Outcomes; Exposure assessment; Mobile Phone Use",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The Cohort Study of Mobile Phone Use and Health (COSMOS) has repeatedly collected self-reported and operator-recorded data on mobile phone use. Assessing health effects using self-reported information is prone to measurement error, but operator data were available prospectively for only part of the study population and did not cover past mobile phone use. To optimize the available data and reduce bias, we evaluated different statistical approaches for constructing mobile phone exposure histories within COSMOS. We evaluated and compared the performance of 4 regression calibration (RC) methods (simple, direct, inverse, and generalized additive model for location, shape, and scale), complete-case analysis, and multiple imputation in a simulation study with a binary health outcome. We used self-reported and operator-recorded mobile phone call data collected at baseline (2007-2012) from participants in Denmark, Finland, the Netherlands, Sweden, and the United Kingdom. Parameter estimates obtained using simple, direct, and inverse RC methods were associated with less bias and lower mean squared error than those obtained with complete-case analysis or multiple imputation. We showed that RC methods resulted in more accurate estimation of the relationship between mobile phone use and health outcomes by combining self-reported data with objective operator-recorded data available for a subset of participants.",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/aje/advance-article-pdf/doi/10.1093/aje/kwae039/57572723/kwae039.pdf; doi:https://doi.org/10.1093/aje/kwae039; html:https://europepmc.org/articles/PMC11458186; pdf:https://europepmc.org/articles/PMC11458186?pdf=render"
+  },
   {
     "id": "32900377",
     "doi": "https://doi.org/10.1186/s12916-020-01754-z",
@@ -31398,23 +31432,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/s2352-3018(23)00028-0; doi:https://doi.org/10.1016/S2352-3018(23)00028-0; html:https://europepmc.org/articles/PMC10288029; pdf:https://europepmc.org/articles/PMC10288029?pdf=render; doi:https://doi.org/10.1016/s2352-3018(23)00028-0"
   },
-  {
-    "id": "35241573",
-    "doi": "https://doi.org/10.1136/bmjqs-2020-012108",
-    "title": "Comparing antibiotic prescribing between clinicians in UK primary care: an analysis in a cohort study of eight different measures of antibiotic prescribing.",
-    "authorString": "Van Staa T, Li Y, Gold N, Chadborn T, Welfare W, Palin V, Ashcroft DM, Bircher J.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ quality & safety",
-    "pubYear": "2022",
-    "date": "2022-10-19",
-    "isOpenAccess": "Y",
-    "keywords": "General Practice; Antibiotic Management; Healthcare Quality Improvement",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>There is a need to reduce antimicrobial uses in humans. Previous studies have found variations in antibiotic (AB) prescribing between practices in primary care. This study assessed variability of AB prescribing between clinicians.<h4>Methods</h4>Clinical Practice Research Datalink, which collects electronic health records in primary care, was used to select anonymised clinicians providing 500+ consultations during 2012-2017. Eight measures of AB prescribing were assessed, such as overall and incidental AB prescribing, repeat AB courses and extent of risk-based prescribing. Poisson regression models with random effect for clinicians were fitted.<h4>Results</h4>6111 clinicians from 466 general practices were included. Considerable variability between individual clinicians was found for most AB measures. For example, the rate of AB prescribing varied between 77.4 and 350.3 per 1000 consultations; percentage of repeat AB courses within 30 days ranged from 13.1% to 34.3%; predicted patient risk of hospital admission for infection-related complications in those prescribed AB ranged from 0.03% to 0.32% (5th and 95th percentiles). The adjusted relative rate between clinicians in rates of AB prescribing was 5.23. Weak correlation coefficients (<0.5) were found between most AB measures. There was considerable variability in case mix seen by clinicians. The largest potential impact to reduce AB prescribing could be around encouraging risk-based prescribing and addressing repeat issues of ABs. Reduction of repeat AB courses to prescribing habit of median clinician would save 21 813 AB prescriptions per 1000 clinicians per year.<h4>Conclusions</h4>The wide variation seen in all measures of AB prescribing and weak correlation between them suggests that a single AB measure, such as prescribing rate, is not sufficient to underpin the optimisation of AB prescribing.",
-    "laySummary": "",
-    "urls": "pdf:https://qualitysafety.bmj.com/content/qhc/early/2022/03/02/bmjqs-2020-012108.full.pdf; doi:https://doi.org/10.1136/bmjqs-2020-012108; html:https://europepmc.org/articles/PMC9606525; pdf:https://europepmc.org/articles/PMC9606525?pdf=render"
-  },
   {
     "id": "34237806",
     "doi": "https://doi.org/10.1515/dmdi-2021-0104",
@@ -31432,6 +31449,23 @@
     "laySummary": "",
     "urls": "pdf:https://discovery.ucl.ac.uk/10135735/1/Asselbergs_10.1515_dmdi-2021-0104.pdf; doi:https://doi.org/10.1515/dmdi-2021-0104"
   },
+  {
+    "id": "35241573",
+    "doi": "https://doi.org/10.1136/bmjqs-2020-012108",
+    "title": "Comparing antibiotic prescribing between clinicians in UK primary care: an analysis in a cohort study of eight different measures of antibiotic prescribing.",
+    "authorString": "Van Staa T, Li Y, Gold N, Chadborn T, Welfare W, Palin V, Ashcroft DM, Bircher J.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ quality & safety",
+    "pubYear": "2022",
+    "date": "2022-10-19",
+    "isOpenAccess": "Y",
+    "keywords": "General Practice; Antibiotic Management; Healthcare Quality Improvement",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>There is a need to reduce antimicrobial uses in humans. Previous studies have found variations in antibiotic (AB) prescribing between practices in primary care. This study assessed variability of AB prescribing between clinicians.<h4>Methods</h4>Clinical Practice Research Datalink, which collects electronic health records in primary care, was used to select anonymised clinicians providing 500+ consultations during 2012-2017. Eight measures of AB prescribing were assessed, such as overall and incidental AB prescribing, repeat AB courses and extent of risk-based prescribing. Poisson regression models with random effect for clinicians were fitted.<h4>Results</h4>6111 clinicians from 466 general practices were included. Considerable variability between individual clinicians was found for most AB measures. For example, the rate of AB prescribing varied between 77.4 and 350.3 per 1000 consultations; percentage of repeat AB courses within 30 days ranged from 13.1% to 34.3%; predicted patient risk of hospital admission for infection-related complications in those prescribed AB ranged from 0.03% to 0.32% (5th and 95th percentiles). The adjusted relative rate between clinicians in rates of AB prescribing was 5.23. Weak correlation coefficients (<0.5) were found between most AB measures. There was considerable variability in case mix seen by clinicians. The largest potential impact to reduce AB prescribing could be around encouraging risk-based prescribing and addressing repeat issues of ABs. Reduction of repeat AB courses to prescribing habit of median clinician would save 21 813 AB prescriptions per 1000 clinicians per year.<h4>Conclusions</h4>The wide variation seen in all measures of AB prescribing and weak correlation between them suggests that a single AB measure, such as prescribing rate, is not sufficient to underpin the optimisation of AB prescribing.",
+    "laySummary": "",
+    "urls": "pdf:https://qualitysafety.bmj.com/content/qhc/early/2022/03/02/bmjqs-2020-012108.full.pdf; doi:https://doi.org/10.1136/bmjqs-2020-012108; html:https://europepmc.org/articles/PMC9606525; pdf:https://europepmc.org/articles/PMC9606525?pdf=render"
+  },
   {
     "id": "35385889",
     "doi": "https://doi.org/10.1515/dmpt-2021-0104",
@@ -31466,6 +31500,23 @@
     "laySummary": "",
     "urls": "pdf:https://ieeexplore.ieee.org/ielx7/6221039/9246949/09268962.pdf; doi:https://doi.org/10.1109/JTEHM.2020.3040236; html:https://europepmc.org/articles/PMC7737850; pdf:https://europepmc.org/articles/PMC7737850?pdf=render"
   },
+  {
+    "id": "31168069",
+    "doi": "https://doi.org/10.1038/s41380-019-0439-8",
+    "title": "The genomic basis of mood instability: identification of 46 loci in 363,705 UK Biobank participants, genetic correlation with psychiatric disorders, and association with gene expression and function.",
+    "authorString": "Ward J, Tunbridge EM, Sandor C, Lyall LM, Ferguson A, Strawbridge RJ, Lyall DM, Cullen B, Graham N, Johnston KJA, Webber C, Escott-Price V, O'Donovan M, Pell JP, Bailey MES, Harrison PJ, Smith DJ.",
+    "authorAffiliations": "",
+    "journalTitle": "Molecular psychiatry",
+    "pubYear": "2020",
+    "date": "2019-06-05",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Genome-wide association studies (GWAS) of psychiatric phenotypes have tended to focus on categorical diagnoses, but to understand the biology of mental illness it may be more useful to study traits which cut across traditional boundaries. Here, we report the results of a GWAS of mood instability as a trait in a large population cohort (UK Biobank, n\u2009=\u2009363,705). We also assess the clinical and biological relevance of the findings, including whether genetic associations show enrichment for nervous system pathways. Forty six unique loci associated with mood instability were identified with a SNP heritability estimate of 9%. Linkage Disequilibrium Score Regression (LDSR) analyses identified genetic correlations with Major Depressive Disorder (MDD), Bipolar Disorder (BD), Schizophrenia, anxiety, and Post Traumatic Stress Disorder (PTSD). Gene-level and gene set analyses identified 244 significant genes and 6 enriched gene sets. Tissue expression analysis of the SNP-level data found enrichment in multiple brain regions, and eQTL analyses highlighted an inversion on chromosome 17 plus two brain-specific eQTLs. In addition, we used a Phenotype Linkage Network (PLN) analysis and community analysis to assess for enrichment of nervous system gene sets using mouse orthologue databases. The PLN analysis found enrichment in nervous system PLNs for a community containing serotonin and melatonin receptors. In summary, this work has identified novel loci, tissues and gene sets contributing to mood instability. These findings may be relevant for the identification of novel trans-diagnostic drug targets and could help to inform future stratified medicine innovations in mental health.",
+    "laySummary": "",
+    "urls": "pdf:https://eprints.gla.ac.uk/185493/1/185493.pdf; doi:https://doi.org/10.1038/s41380-019-0439-8; html:https://europepmc.org/articles/PMC7116257; pdf:https://europepmc.org/articles/PMC7116257?pdf=render"
+  },
   {
     "id": "30848519",
     "doi": "https://doi.org/10.1111/dme.13945",
@@ -31483,23 +31534,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1111/dme.13945"
   },
-  {
-    "id": "36060542",
-    "doi": "https://doi.org/10.3389/fdgth.2022.939292",
-    "title": "Clinical deployment environments: Five pillars of translational machine learning for health.",
-    "authorString": "Harris S, Bonnici T, Keen T, Lilaonitkul W, White MJ, Swanepoel N.",
-    "authorAffiliations": "",
-    "journalTitle": "Frontiers in digital health",
-    "pubYear": "2022",
-    "date": "2022-08-19",
-    "isOpenAccess": "Y",
-    "keywords": "Safety; Artificial intelligence; Machine Learning; Health Informatics; Translational Medicine; Ml-ops",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Machine Learning for Health (ML4H) has demonstrated efficacy in computer imaging and other self-contained digital workflows, but has failed to substantially impact routine clinical care. This is no longer because of poor adoption of Electronic Health Records Systems (EHRS), but because ML4H needs an infrastructure for development, deployment and evaluation within the healthcare institution. In this paper, we propose a design pattern called a Clinical Deployment Environment (CDE). We sketch the five pillars of the CDE: (1) real world development supported by live data where ML4H teams can iteratively build and test at the bedside (2) an ML-Ops platform that brings the rigour and standards of continuous deployment to ML4H (3) design and supervision by those with expertise in AI safety (4) the methods of implementation science that enable the algorithmic insights to influence the behaviour of clinicians and patients and (5) continuous evaluation that uses randomisation to avoid bias but in an agile manner. The CDE is intended to answer the same requirements that bio-medicine articulated in establishing the translational medicine domain. It envisions a transition from \"real-world\" data to \"real-world\" development.",
-    "laySummary": "",
-    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fdgth.2022.939292/pdf; doi:https://doi.org/10.3389/fdgth.2022.939292; html:https://europepmc.org/articles/PMC9437594; pdf:https://europepmc.org/articles/PMC9437594?pdf=render"
-  },
   {
     "id": "36814324",
     "doi": "https://doi.org/10.1186/s13195-023-01184-y",
@@ -31518,21 +31552,21 @@
     "urls": "pdf:https://alzres.biomedcentral.com/counter/pdf/10.1186/s13195-023-01184-y; doi:https://doi.org/10.1186/s13195-023-01184-y; html:https://europepmc.org/articles/PMC9945600; pdf:https://europepmc.org/articles/PMC9945600?pdf=render"
   },
   {
-    "id": "31168069",
-    "doi": "https://doi.org/10.1038/s41380-019-0439-8",
-    "title": "The genomic basis of mood instability: identification of 46 loci in 363,705 UK Biobank participants, genetic correlation with psychiatric disorders, and association with gene expression and function.",
-    "authorString": "Ward J, Tunbridge EM, Sandor C, Lyall LM, Ferguson A, Strawbridge RJ, Lyall DM, Cullen B, Graham N, Johnston KJA, Webber C, Escott-Price V, O'Donovan M, Pell JP, Bailey MES, Harrison PJ, Smith DJ.",
+    "id": "36060542",
+    "doi": "https://doi.org/10.3389/fdgth.2022.939292",
+    "title": "Clinical deployment environments: Five pillars of translational machine learning for health.",
+    "authorString": "Harris S, Bonnici T, Keen T, Lilaonitkul W, White MJ, Swanepoel N.",
     "authorAffiliations": "",
-    "journalTitle": "Molecular psychiatry",
-    "pubYear": "2020",
-    "date": "2019-06-05",
+    "journalTitle": "Frontiers in digital health",
+    "pubYear": "2022",
+    "date": "2022-08-19",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Safety; Artificial intelligence; Machine Learning; Health Informatics; Translational Medicine; Ml-ops",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Genome-wide association studies (GWAS) of psychiatric phenotypes have tended to focus on categorical diagnoses, but to understand the biology of mental illness it may be more useful to study traits which cut across traditional boundaries. Here, we report the results of a GWAS of mood instability as a trait in a large population cohort (UK Biobank, n\u2009=\u2009363,705). We also assess the clinical and biological relevance of the findings, including whether genetic associations show enrichment for nervous system pathways. Forty six unique loci associated with mood instability were identified with a SNP heritability estimate of 9%. Linkage Disequilibrium Score Regression (LDSR) analyses identified genetic correlations with Major Depressive Disorder (MDD), Bipolar Disorder (BD), Schizophrenia, anxiety, and Post Traumatic Stress Disorder (PTSD). Gene-level and gene set analyses identified 244 significant genes and 6 enriched gene sets. Tissue expression analysis of the SNP-level data found enrichment in multiple brain regions, and eQTL analyses highlighted an inversion on chromosome 17 plus two brain-specific eQTLs. In addition, we used a Phenotype Linkage Network (PLN) analysis and community analysis to assess for enrichment of nervous system gene sets using mouse orthologue databases. The PLN analysis found enrichment in nervous system PLNs for a community containing serotonin and melatonin receptors. In summary, this work has identified novel loci, tissues and gene sets contributing to mood instability. These findings may be relevant for the identification of novel trans-diagnostic drug targets and could help to inform future stratified medicine innovations in mental health.",
+    "abstract": "Machine Learning for Health (ML4H) has demonstrated efficacy in computer imaging and other self-contained digital workflows, but has failed to substantially impact routine clinical care. This is no longer because of poor adoption of Electronic Health Records Systems (EHRS), but because ML4H needs an infrastructure for development, deployment and evaluation within the healthcare institution. In this paper, we propose a design pattern called a Clinical Deployment Environment (CDE). We sketch the five pillars of the CDE: (1) real world development supported by live data where ML4H teams can iteratively build and test at the bedside (2) an ML-Ops platform that brings the rigour and standards of continuous deployment to ML4H (3) design and supervision by those with expertise in AI safety (4) the methods of implementation science that enable the algorithmic insights to influence the behaviour of clinicians and patients and (5) continuous evaluation that uses randomisation to avoid bias but in an agile manner. The CDE is intended to answer the same requirements that bio-medicine articulated in establishing the translational medicine domain. It envisions a transition from \"real-world\" data to \"real-world\" development.",
     "laySummary": "",
-    "urls": "pdf:https://eprints.gla.ac.uk/185493/1/185493.pdf; doi:https://doi.org/10.1038/s41380-019-0439-8; html:https://europepmc.org/articles/PMC7116257; pdf:https://europepmc.org/articles/PMC7116257?pdf=render"
+    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fdgth.2022.939292/pdf; doi:https://doi.org/10.3389/fdgth.2022.939292; html:https://europepmc.org/articles/PMC9437594; pdf:https://europepmc.org/articles/PMC9437594?pdf=render"
   },
   {
     "id": "32079223",
@@ -31637,21 +31671,21 @@
     "urls": "doi:https://doi.org/10.1016/j.neuroimage.2022.119779; doi:https://doi.org/10.1016/j.neuroimage.2022.119779; html:https://europepmc.org/articles/PMC10933815; pdf:https://europepmc.org/articles/PMC10933815?pdf=render"
   },
   {
-    "id": "37705296",
-    "doi": "https://doi.org/10.1002/sim.9898",
-    "title": "Using temporal recalibration to improve the calibration of risk prediction models in competing risk settings when there are trends in survival over time.",
-    "authorString": "Booth S, Mozumder SI, Archer L, Ensor J, Riley RD, Lambert PC, Rutherford MJ.",
+    "id": "31089183",
+    "doi": "https://doi.org/10.1038/s41598-019-43861-9",
+    "title": "Genetic variation in CADM2 as a link between psychological traits and obesity.",
+    "authorString": "Morris J, Bailey MES, Baldassarre D, Cullen B, de Faire U, Ferguson A, Gigante B, Giral P, Goel A, Graham N, Hamsten A, Humphries SE, Johnston KJA, Lyall DM, Lyall LM, Sennblad B, Silveira A, Smit AJ, Tremoli E, Veglia F, Ward J, Watkins H, Smith DJ, Strawbridge RJ.",
     "authorAffiliations": "",
-    "journalTitle": "Statistics in medicine",
-    "pubYear": "2023",
-    "date": "2023-09-13",
+    "journalTitle": "Scientific reports",
+    "pubYear": "2019",
+    "date": "2019-05-14",
     "isOpenAccess": "Y",
-    "keywords": "calibration; Risk Prediction; Competing Risks; Temporal Recalibration; Prognostic Models",
-    "nationalPriorities": "",
+    "keywords": "",
+    "nationalPriorities": "Understanding the Causes of Disease",
     "healthCategories": "",
-    "abstract": "We have previously proposed temporal recalibration to account for trends in survival over time to improve the calibration of predictions from prognostic models for new patients. This involves first estimating the predictor effects using data from all individuals (full dataset) and then re-estimating the baseline using a subset of the most recent data whilst constraining the predictor effects to remain the same. In this article, we demonstrate how temporal recalibration can be applied in competing risk settings by recalibrating each cause-specific (or subdistribution) hazard model separately. We illustrate this using an example of colon cancer survival with data from the Surveillance Epidemiology and End Results (SEER) program. Data from patients diagnosed in 1995-2004 were used to fit two models for deaths due to colon cancer and other causes respectively. We discuss considerations that need to be made in order to apply temporal recalibration such as the choice of data used in the recalibration step. We also demonstrate how to assess the calibration of these models in new data for patients diagnosed subsequently in 2005. Comparison was made to a standard analysis (when improvements over time are not taken into account) and a period analysis which is similar to temporal recalibration but differs in the data used to estimate the predictor effects. The 10-year calibration plots demonstrated that using the standard approach over-estimated the risk of death due to colon cancer and the total risk of death and that calibration was improved using temporal recalibration or period analysis.",
+    "abstract": "CADM2 has been associated with a range of behavioural and metabolic traits, including physical activity, risk-taking, educational attainment, alcohol and cannabis use and obesity. Here, we set out to determine whether CADM2 contributes to mechanisms shared between mental and physical health disorders. We assessed genetic variants in the CADM2 locus for association with phenotypes in the UK Biobank, IMPROVE, PROCARDIS and SCARFSHEEP studies, before performing meta-analyses. A wide range of metabolic phenotypes were meta-analysed. Psychological phenotypes analysed in UK Biobank only were major depressive disorder, generalised anxiety disorder, bipolar disorder, neuroticism, mood instability and risk-taking behaviour. In UK Biobank, four, 88 and 172 genetic variants were significantly (p\u2009<\u20091\u2009\u00d7\u200910<sup>-5</sup>) associated with neuroticism, mood instability and risk-taking respectively. In meta-analyses of 4 cohorts, we identified 362, 63 and 11 genetic variants significantly (p\u2009<\u20091\u2009\u00d7\u200910<sup>-5</sup>) associated with BMI, SBP and CRP respectively. Genetic effects on BMI, CRP and risk-taking were all positively correlated, and were consistently inversely correlated with genetic effects on SBP, mood instability and neuroticism. Conditional analyses suggested an overlap in the signals for physical and psychological traits. Many significant variants had genotype-specific effects on CADM2 expression levels in adult brain and adipose tissues. CADM2 variants influence a wide range of both psychological and metabolic traits, suggesting common biological mechanisms across phenotypes via regulation of CADM2 expression levels in adipose tissue. Functional studies of CADM2 are required to fully understand mechanisms connecting mental and physical health conditions.",
     "laySummary": "",
-    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/sim.9898; doi:https://doi.org/10.1002/sim.9898; html:https://europepmc.org/articles/PMC10946485; pdf:https://europepmc.org/articles/PMC10946485?pdf=render"
+    "urls": "pdf:https://www.nature.com/articles/s41598-019-43861-9.pdf; doi:https://doi.org/10.1038/s41598-019-43861-9; html:https://europepmc.org/articles/PMC6517397; pdf:https://europepmc.org/articles/PMC6517397?pdf=render"
   },
   {
     "id": "31481394",
@@ -31671,21 +31705,21 @@
     "urls": "pdf:https://www.bmj.com/content/bmj/366/bmj.l4892.full.pdf; doi:https://doi.org/10.1136/bmj.l4892; html:https://europepmc.org/articles/PMC6719286"
   },
   {
-    "id": "31089183",
-    "doi": "https://doi.org/10.1038/s41598-019-43861-9",
-    "title": "Genetic variation in CADM2 as a link between psychological traits and obesity.",
-    "authorString": "Morris J, Bailey MES, Baldassarre D, Cullen B, de Faire U, Ferguson A, Gigante B, Giral P, Goel A, Graham N, Hamsten A, Humphries SE, Johnston KJA, Lyall DM, Lyall LM, Sennblad B, Silveira A, Smit AJ, Tremoli E, Veglia F, Ward J, Watkins H, Smith DJ, Strawbridge RJ.",
+    "id": "37705296",
+    "doi": "https://doi.org/10.1002/sim.9898",
+    "title": "Using temporal recalibration to improve the calibration of risk prediction models in competing risk settings when there are trends in survival over time.",
+    "authorString": "Booth S, Mozumder SI, Archer L, Ensor J, Riley RD, Lambert PC, Rutherford MJ.",
     "authorAffiliations": "",
-    "journalTitle": "Scientific reports",
-    "pubYear": "2019",
-    "date": "2019-05-14",
+    "journalTitle": "Statistics in medicine",
+    "pubYear": "2023",
+    "date": "2023-09-13",
     "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "Understanding the Causes of Disease",
+    "keywords": "calibration; Risk Prediction; Competing Risks; Temporal Recalibration; Prognostic Models",
+    "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "CADM2 has been associated with a range of behavioural and metabolic traits, including physical activity, risk-taking, educational attainment, alcohol and cannabis use and obesity. Here, we set out to determine whether CADM2 contributes to mechanisms shared between mental and physical health disorders. We assessed genetic variants in the CADM2 locus for association with phenotypes in the UK Biobank, IMPROVE, PROCARDIS and SCARFSHEEP studies, before performing meta-analyses. A wide range of metabolic phenotypes were meta-analysed. Psychological phenotypes analysed in UK Biobank only were major depressive disorder, generalised anxiety disorder, bipolar disorder, neuroticism, mood instability and risk-taking behaviour. In UK Biobank, four, 88 and 172 genetic variants were significantly (p\u2009<\u20091\u2009\u00d7\u200910<sup>-5</sup>) associated with neuroticism, mood instability and risk-taking respectively. In meta-analyses of 4 cohorts, we identified 362, 63 and 11 genetic variants significantly (p\u2009<\u20091\u2009\u00d7\u200910<sup>-5</sup>) associated with BMI, SBP and CRP respectively. Genetic effects on BMI, CRP and risk-taking were all positively correlated, and were consistently inversely correlated with genetic effects on SBP, mood instability and neuroticism. Conditional analyses suggested an overlap in the signals for physical and psychological traits. Many significant variants had genotype-specific effects on CADM2 expression levels in adult brain and adipose tissues. CADM2 variants influence a wide range of both psychological and metabolic traits, suggesting common biological mechanisms across phenotypes via regulation of CADM2 expression levels in adipose tissue. Functional studies of CADM2 are required to fully understand mechanisms connecting mental and physical health conditions.",
+    "abstract": "We have previously proposed temporal recalibration to account for trends in survival over time to improve the calibration of predictions from prognostic models for new patients. This involves first estimating the predictor effects using data from all individuals (full dataset) and then re-estimating the baseline using a subset of the most recent data whilst constraining the predictor effects to remain the same. In this article, we demonstrate how temporal recalibration can be applied in competing risk settings by recalibrating each cause-specific (or subdistribution) hazard model separately. We illustrate this using an example of colon cancer survival with data from the Surveillance Epidemiology and End Results (SEER) program. Data from patients diagnosed in 1995-2004 were used to fit two models for deaths due to colon cancer and other causes respectively. We discuss considerations that need to be made in order to apply temporal recalibration such as the choice of data used in the recalibration step. We also demonstrate how to assess the calibration of these models in new data for patients diagnosed subsequently in 2005. Comparison was made to a standard analysis (when improvements over time are not taken into account) and a period analysis which is similar to temporal recalibration but differs in the data used to estimate the predictor effects. The 10-year calibration plots demonstrated that using the standard approach over-estimated the risk of death due to colon cancer and the total risk of death and that calibration was improved using temporal recalibration or period analysis.",
     "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41598-019-43861-9.pdf; doi:https://doi.org/10.1038/s41598-019-43861-9; html:https://europepmc.org/articles/PMC6517397; pdf:https://europepmc.org/articles/PMC6517397?pdf=render"
+    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/sim.9898; doi:https://doi.org/10.1002/sim.9898; html:https://europepmc.org/articles/PMC10946485; pdf:https://europepmc.org/articles/PMC10946485?pdf=render"
   },
   {
     "id": "33036417",
@@ -31721,23 +31755,6 @@
     "laySummary": "",
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8081749; doi:https://doi.org/10.1016/j.jinf.2021.04.027; html:https://europepmc.org/articles/PMC8081749; pdf:https://europepmc.org/articles/PMC8081749?pdf=render"
   },
-  {
-    "id": "34939832",
-    "doi": "https://doi.org/10.1308/rcsann.2021.0206",
-    "title": "Projections for primary hip and knee replacement surgery up to the year 2060: an analysis based on data from The National Joint Registry for England, Wales, Northern Ireland and the Isle of Man.",
-    "authorString": "Matharu GS, Culliford DJ, Blom AW, Judge A.",
-    "authorAffiliations": "",
-    "journalTitle": "Annals of the Royal College of Surgeons of England",
-    "pubYear": "2022",
-    "date": "2021-12-23",
-    "isOpenAccess": "N",
-    "keywords": "Total hip replacement; Total Knee Replacement; Demand; Future Numbers",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>We estimated the number of primary total hip and knee replacements (THR and TKR) that will need to be performed up to the year 2060.<h4>Methods</h4>We used data from The National Joint Registry for England, Wales, Northern Ireland and the Isle of Man on the volume of primary THRs (<i>n</i>=94,936) and TKRs (<i>n</i>=100,547) performed in 2018. We projected future numbers of THR and TKR using a static estimated rate from 2018 applied to population growth forecast data from the UK Office for National Statistics up to 2060.<h4>Results</h4>By 2060, THR and TKR volume would increase from 2018 levels by an estimated 37.7% (<i>n</i>=130,766) and 36.6% (<i>n</i>=137,341), respectively. For both males and females demand for surgery was also higher for patients aged 70 and over, with older patients having the biggest relative increase in volume over time: 70-79 years (44.6% males, 41.2% females); 80-89 years (112.4% males, 85.6% females); 90 years and older (348.0% males, 198.2% females).<h4>Conclusion</h4>By 2060 demand for hip and knee joint replacement is estimated to increase by almost 40%. Demand will be greatest in older patients (70+ years), which will have significant implications for the health service requiring forward planning given that morbidity and resource use is higher in this population. These issues, coupled with two waves of COVID-19, will impact the ability of health services to deliver timely joint replacement to many patients for a number of years, requiring urgent planning.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1308/rcsann.2021.0206; html:https://europepmc.org/articles/PMC9157920; pdf:https://europepmc.org/articles/PMC9157920?pdf=render; doi:https://doi.org/10.1308/rcsann.2021.0206"
-  },
   {
     "id": "31964672",
     "doi": "https://doi.org/10.1136/bmjopen-2019-033318",
@@ -31755,6 +31772,23 @@
     "laySummary": "This study which includes over 40 thousant adults in the UK, aims to assess whether there are links between different levels of physical activity and educational achievements. It found that lower educational achievement was associated with higher travel and work related physical activity, but not leisure time activity. They found this difference to be larger in men than in women, and also in white compared to black individuals.",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/10/1/e033318.full.pdf; doi:https://doi.org/10.1136/bmjopen-2019-033318; html:https://europepmc.org/articles/PMC7045199; pdf:https://europepmc.org/articles/PMC7045199?pdf=render"
   },
+  {
+    "id": "34939832",
+    "doi": "https://doi.org/10.1308/rcsann.2021.0206",
+    "title": "Projections for primary hip and knee replacement surgery up to the year 2060: an analysis based on data from The National Joint Registry for England, Wales, Northern Ireland and the Isle of Man.",
+    "authorString": "Matharu GS, Culliford DJ, Blom AW, Judge A.",
+    "authorAffiliations": "",
+    "journalTitle": "Annals of the Royal College of Surgeons of England",
+    "pubYear": "2022",
+    "date": "2021-12-23",
+    "isOpenAccess": "N",
+    "keywords": "Total hip replacement; Total Knee Replacement; Demand; Future Numbers",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>We estimated the number of primary total hip and knee replacements (THR and TKR) that will need to be performed up to the year 2060.<h4>Methods</h4>We used data from The National Joint Registry for England, Wales, Northern Ireland and the Isle of Man on the volume of primary THRs (<i>n</i>=94,936) and TKRs (<i>n</i>=100,547) performed in 2018. We projected future numbers of THR and TKR using a static estimated rate from 2018 applied to population growth forecast data from the UK Office for National Statistics up to 2060.<h4>Results</h4>By 2060, THR and TKR volume would increase from 2018 levels by an estimated 37.7% (<i>n</i>=130,766) and 36.6% (<i>n</i>=137,341), respectively. For both males and females demand for surgery was also higher for patients aged 70 and over, with older patients having the biggest relative increase in volume over time: 70-79 years (44.6% males, 41.2% females); 80-89 years (112.4% males, 85.6% females); 90 years and older (348.0% males, 198.2% females).<h4>Conclusion</h4>By 2060 demand for hip and knee joint replacement is estimated to increase by almost 40%. Demand will be greatest in older patients (70+ years), which will have significant implications for the health service requiring forward planning given that morbidity and resource use is higher in this population. These issues, coupled with two waves of COVID-19, will impact the ability of health services to deliver timely joint replacement to many patients for a number of years, requiring urgent planning.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1308/rcsann.2021.0206; html:https://europepmc.org/articles/PMC9157920; pdf:https://europepmc.org/articles/PMC9157920?pdf=render; doi:https://doi.org/10.1308/rcsann.2021.0206"
+  },
   {
     "id": "32393804",
     "doi": "https://doi.org/10.1038/s41591-020-0916-2",
@@ -32078,23 +32112,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1038/s41467-024-50297-x; html:https://europepmc.org/articles/PMC11269703; pdf:https://europepmc.org/articles/PMC11269703?pdf=render"
   },
-  {
-    "id": "38198570",
-    "doi": "https://doi.org/10.1126/scitranslmed.adf4428",
-    "title": "Prospective study design and data analysis in UK Biobank.",
-    "authorString": "Allen NE, Lacey B, Lawlor DA, Pell JP, Gallacher J, Smeeth L, Elliott P, Matthews PM, Lyons RA, Whetton AD, Lucassen A, Hurles ME, Chapman M, Roddam AW, Fitzpatrick NK, Hansell AL, Hardy R, Marioni RE, O'Donnell VB, Williams J, Lindgren CM, Effingham M, Sellors J, Danesh J, Collins R.",
-    "authorAffiliations": "",
-    "journalTitle": "Science translational medicine",
-    "pubYear": "2024",
-    "date": "2024-01-10",
-    "isOpenAccess": "N",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Population-based prospective studies, such as UK Biobank, are valuable for generating and testing hypotheses about the potential causes of human disease. We describe how UK Biobank's study design, data access policies, and approaches to statistical analysis can help to minimize error and improve the interpretability of research findings, with implications for other population-based prospective studies being established worldwide.",
-    "laySummary": "",
-    "urls": "pdf:https://www.pure.ed.ac.uk/ws/files/405264227/scitranslmed.adf4428.pdf; doi:https://doi.org/10.1126/scitranslmed.adf4428"
-  },
   {
     "id": "38597854",
     "doi": "https://doi.org/10.1016/j.jcmg.2024.03.001",
@@ -32112,6 +32129,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.jcmg.2024.03.001; doi:https://doi.org/10.1016/j.jcmg.2024.03.001"
   },
+  {
+    "id": "38198570",
+    "doi": "https://doi.org/10.1126/scitranslmed.adf4428",
+    "title": "Prospective study design and data analysis in UK Biobank.",
+    "authorString": "Allen NE, Lacey B, Lawlor DA, Pell JP, Gallacher J, Smeeth L, Elliott P, Matthews PM, Lyons RA, Whetton AD, Lucassen A, Hurles ME, Chapman M, Roddam AW, Fitzpatrick NK, Hansell AL, Hardy R, Marioni RE, O'Donnell VB, Williams J, Lindgren CM, Effingham M, Sellors J, Danesh J, Collins R.",
+    "authorAffiliations": "",
+    "journalTitle": "Science translational medicine",
+    "pubYear": "2024",
+    "date": "2024-01-10",
+    "isOpenAccess": "N",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Population-based prospective studies, such as UK Biobank, are valuable for generating and testing hypotheses about the potential causes of human disease. We describe how UK Biobank's study design, data access policies, and approaches to statistical analysis can help to minimize error and improve the interpretability of research findings, with implications for other population-based prospective studies being established worldwide.",
+    "laySummary": "",
+    "urls": "pdf:https://www.pure.ed.ac.uk/ws/files/405264227/scitranslmed.adf4428.pdf; doi:https://doi.org/10.1126/scitranslmed.adf4428"
+  },
   {
     "id": "33310109",
     "doi": "https://doi.org/10.1016/j.ijid.2020.12.006",
@@ -32197,6 +32231,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.120.019814; doi:https://doi.org/10.1161/JAHA.120.019814; html:https://europepmc.org/articles/PMC9075396; pdf:https://europepmc.org/articles/PMC9075396?pdf=render"
   },
+  {
+    "id": "34930919",
+    "doi": "https://doi.org/10.1038/s41467-021-26280-1",
+    "title": "Finding genetically-supported drug targets for Parkinson's disease using Mendelian randomization of the druggable genome.",
+    "authorString": "Storm CS, Kia DA, Almramhi MM, Bandres-Ciga S, Finan C, International Parkinson\u2019s Disease Genomics Consortium (IPDGC), Hingorani AD, Wood NW.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature communications",
+    "pubYear": "2021",
+    "date": "2021-12-20",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Parkinson's disease is a neurodegenerative movement disorder that currently has no disease-modifying treatment, partly owing to inefficiencies in drug target identification and validation. We use Mendelian randomization to investigate over 3,000 genes that encode druggable proteins and predict their efficacy as drug targets for Parkinson's disease. We use expression and protein quantitative trait loci to mimic exposure to medications, and we examine the causal effect on Parkinson's disease risk (in two large cohorts), age at onset and progression. We propose 23 drug-targeting mechanisms for Parkinson's disease, including four possible drug repurposing opportunities and two drugs which may increase Parkinson's disease risk. Of these, we put forward six drug targets with the strongest Mendelian randomization evidence. There is remarkably little overlap between our drug targets to reduce Parkinson's disease risk versus progression, suggesting different molecular mechanisms. Drugs with genetic support are considerably more likely to succeed in clinical trials, and we provide compelling genetic evidence and an analysis pipeline to prioritise Parkinson's disease drug development.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41467-021-26280-1.pdf; doi:https://doi.org/10.1038/s41467-021-26280-1; html:https://europepmc.org/articles/PMC8688480; pdf:https://europepmc.org/articles/PMC8688480?pdf=render"
+  },
   {
     "id": "38115598",
     "doi": "https://doi.org/10.1089/neu.2023.0461",
@@ -32215,21 +32266,21 @@
     "urls": "doi:https://doi.org/10.1089/neu.2023.0461"
   },
   {
-    "id": "34930919",
-    "doi": "https://doi.org/10.1038/s41467-021-26280-1",
-    "title": "Finding genetically-supported drug targets for Parkinson's disease using Mendelian randomization of the druggable genome.",
-    "authorString": "Storm CS, Kia DA, Almramhi MM, Bandres-Ciga S, Finan C, International Parkinson\u2019s Disease Genomics Consortium (IPDGC), Hingorani AD, Wood NW.",
+    "id": "32909959",
+    "doi": "https://doi.org/10.1136/bmj.m3164",
+    "title": "Reporting guidelines for clinical trial reports for interventions involving artificial intelligence: the CONSORT-AI Extension.",
+    "authorString": "Liu X, Rivera SC, Moher D, Calvert MJ, Denniston AK, SPIRIT-AI and CONSORT-AI Working Group.",
     "authorAffiliations": "",
-    "journalTitle": "Nature communications",
-    "pubYear": "2021",
-    "date": "2021-12-20",
+    "journalTitle": "BMJ (Clinical research ed.)",
+    "pubYear": "2020",
+    "date": "2020-09-09",
     "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Parkinson's disease is a neurodegenerative movement disorder that currently has no disease-modifying treatment, partly owing to inefficiencies in drug target identification and validation. We use Mendelian randomization to investigate over 3,000 genes that encode druggable proteins and predict their efficacy as drug targets for Parkinson's disease. We use expression and protein quantitative trait loci to mimic exposure to medications, and we examine the causal effect on Parkinson's disease risk (in two large cohorts), age at onset and progression. We propose 23 drug-targeting mechanisms for Parkinson's disease, including four possible drug repurposing opportunities and two drugs which may increase Parkinson's disease risk. Of these, we put forward six drug targets with the strongest Mendelian randomization evidence. There is remarkably little overlap between our drug targets to reduce Parkinson's disease risk versus progression, suggesting different molecular mechanisms. Drugs with genetic support are considerably more likely to succeed in clinical trials, and we provide compelling genetic evidence and an analysis pipeline to prioritise Parkinson's disease drug development.",
+    "abstract": "The CONSORT 2010 (Consolidated Standards of Reporting Trials) statement provides minimum guidelines for reporting randomised trials. Its widespread use has been instrumental in ensuring transparency when evaluating new interventions. More recently, there has been a growing recognition that interventions involving artificial intelligence (AI) need to undergo rigorous, prospective evaluation to demonstrate impact on health outcomes.The CONSORT-AI extension is a new reporting guideline for clinical trials evaluating interventions with an AI component. It was developed in parallel with its companion statement for clinical trial protocols: SPIRIT-AI. Both guidelines were developed through a staged consensus process, involving a literature review and expert consultation to generate 29 candidate items, which were assessed by an international multi-stakeholder group in a two-stage Delphi survey (103 stakeholders), agreed on in a two-day consensus meeting (31 stakeholders) and refined through a checklist pilot (34 participants).The CONSORT-AI extension includes 14 new items, which were considered sufficiently important for AI interventions, that they should be routinely reported in addition to the core CONSORT 2010 items. CONSORT-AI recommends that investigators provide clear descriptions of the AI intervention, including instructions and skills required for use, the setting in which the AI intervention is integrated, the handling of inputs and outputs of the AI intervention, the human-AI interaction and providing analysis of error cases.CONSORT-AI will help promote transparency and completeness in reporting clinical trials for AI interventions. It will assist editors and peer-reviewers, as well as the general readership, to understand, interpret and critically appraise the quality of clinical trial design and risk of bias in the reported outcomes.",
     "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41467-021-26280-1.pdf; doi:https://doi.org/10.1038/s41467-021-26280-1; html:https://europepmc.org/articles/PMC8688480; pdf:https://europepmc.org/articles/PMC8688480?pdf=render"
+    "urls": "pdf:https://www.bmj.com/content/bmj/370/bmj.m3164.full.pdf; doi:https://doi.org/10.1136/bmj.m3164; html:https://europepmc.org/articles/PMC7490784"
   },
   {
     "id": "32735547",
@@ -32266,21 +32317,21 @@
     "urls": "pdf:https://www.nature.com/articles/s41467-023-36439-7.pdf; doi:https://doi.org/10.1038/s41467-023-36439-7; html:https://europepmc.org/articles/PMC9922305; pdf:https://europepmc.org/articles/PMC9922305?pdf=render"
   },
   {
-    "id": "32909959",
-    "doi": "https://doi.org/10.1136/bmj.m3164",
-    "title": "Reporting guidelines for clinical trial reports for interventions involving artificial intelligence: the CONSORT-AI Extension.",
-    "authorString": "Liu X, Rivera SC, Moher D, Calvert MJ, Denniston AK, SPIRIT-AI and CONSORT-AI Working Group.",
+    "id": "32935062",
+    "doi": "https://doi.org/10.23889/ijpds.v5i2.1383",
+    "title": "Prospective data linkage to facilitate COVID-19 trials - A call to action.",
+    "authorString": "Paprica PA, Sydes MR, McGrail KM, Morris AD, Schull MJ, Walker R.",
     "authorAffiliations": "",
-    "journalTitle": "BMJ (Clinical research ed.)",
+    "journalTitle": "International journal of population data science",
     "pubYear": "2020",
-    "date": "2020-09-09",
+    "date": "2020-08-11",
     "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "The CONSORT 2010 (Consolidated Standards of Reporting Trials) statement provides minimum guidelines for reporting randomised trials. Its widespread use has been instrumental in ensuring transparency when evaluating new interventions. More recently, there has been a growing recognition that interventions involving artificial intelligence (AI) need to undergo rigorous, prospective evaluation to demonstrate impact on health outcomes.The CONSORT-AI extension is a new reporting guideline for clinical trials evaluating interventions with an AI component. It was developed in parallel with its companion statement for clinical trial protocols: SPIRIT-AI. Both guidelines were developed through a staged consensus process, involving a literature review and expert consultation to generate 29 candidate items, which were assessed by an international multi-stakeholder group in a two-stage Delphi survey (103 stakeholders), agreed on in a two-day consensus meeting (31 stakeholders) and refined through a checklist pilot (34 participants).The CONSORT-AI extension includes 14 new items, which were considered sufficiently important for AI interventions, that they should be routinely reported in addition to the core CONSORT 2010 items. CONSORT-AI recommends that investigators provide clear descriptions of the AI intervention, including instructions and skills required for use, the setting in which the AI intervention is integrated, the handling of inputs and outputs of the AI intervention, the human-AI interaction and providing analysis of error cases.CONSORT-AI will help promote transparency and completeness in reporting clinical trials for AI interventions. It will assist editors and peer-reviewers, as well as the general readership, to understand, interpret and critically appraise the quality of clinical trial design and risk of bias in the reported outcomes.",
+    "abstract": "",
     "laySummary": "",
-    "urls": "pdf:https://www.bmj.com/content/bmj/370/bmj.m3164.full.pdf; doi:https://doi.org/10.1136/bmj.m3164; html:https://europepmc.org/articles/PMC7490784"
+    "urls": "pdf:https://ijpds.org/article/download/1383/2566; doi:https://doi.org/10.23889/ijpds.v5i2.1383; html:https://europepmc.org/articles/PMC7473253; pdf:https://europepmc.org/articles/PMC7473253?pdf=render"
   },
   {
     "id": "38642613",
@@ -32316,23 +32367,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.3399/BJGP.2023.0077; html:https://europepmc.org/articles/PMC10523336; pdf:https://europepmc.org/articles/PMC10523336?pdf=render"
   },
-  {
-    "id": "32935062",
-    "doi": "https://doi.org/10.23889/ijpds.v5i2.1383",
-    "title": "Prospective data linkage to facilitate COVID-19 trials - A call to action.",
-    "authorString": "Paprica PA, Sydes MR, McGrail KM, Morris AD, Schull MJ, Walker R.",
-    "authorAffiliations": "",
-    "journalTitle": "International journal of population data science",
-    "pubYear": "2020",
-    "date": "2020-08-11",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "",
-    "urls": "pdf:https://ijpds.org/article/download/1383/2566; doi:https://doi.org/10.23889/ijpds.v5i2.1383; html:https://europepmc.org/articles/PMC7473253; pdf:https://europepmc.org/articles/PMC7473253?pdf=render"
-  },
   {
     "id": "37494011",
     "doi": "https://doi.org/10.1001/jamacardio.2023.2167",
@@ -32384,23 +32418,6 @@
     "laySummary": "",
     "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0290583&type=printable; doi:https://doi.org/10.1371/journal.pone.0290583; html:https://europepmc.org/articles/PMC10521988; pdf:https://europepmc.org/articles/PMC10521988?pdf=render"
   },
-  {
-    "id": "38987242",
-    "doi": "https://doi.org/10.1038/s41467-024-49998-0",
-    "title": "Characterising the genetic architecture of changes in adiposity during adulthood using electronic health records.",
-    "authorString": "Venkatesh SS, Ganjgahi H, Palmer DS, Coley K, Linchangco GV, Hui Q, Wilson P, Ho YL, Cho K, Arum\u00e4e K, Million Veteran Program, Estonian Biobank Research Team, Wittemans LBL, Nell\u00e5ker C, Vainik U, Sun YV, Holmes C, Lindgren CM, Nicholson G.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature communications",
-    "pubYear": "2024",
-    "date": "2024-07-10",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Obesity is a heritable disease, characterised by excess adiposity that is measured by body mass index (BMI). While over 1,000 genetic loci are associated with BMI, less is known about the genetic contribution to adiposity trajectories over adulthood. We derive adiposity-change phenotypes from 24.5 million primary-care health records in over 740,000 individuals in the UK Biobank, Million Veteran Program USA, and Estonian Biobank, to discover and validate the genetic architecture of adiposity trajectories. Using multiple BMI measurements over time increases power to identify genetic factors affecting baseline BMI by 14%. In the largest reported genome-wide study of adiposity-change in adulthood, we identify novel associations with BMI-change at six independent loci, including rs429358 (APOE missense variant). The SNP-based heritability of BMI-change (1.98%) is 9-fold lower than that of BMI. The modest genetic correlation between BMI-change and BMI (45.2%) indicates that genetic studies of longitudinal trajectories could uncover novel biology of quantitative traits in adulthood.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1038/s41467-024-49998-0; doi:https://doi.org/10.1038/s41467-024-49998-0; html:https://europepmc.org/articles/PMC11237142; pdf:https://europepmc.org/articles/PMC11237142?pdf=render"
-  },
   {
     "id": "30551632",
     "doi": "https://doi.org/10.3390/ijerph15122845",
@@ -32418,6 +32435,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.mdpi.com/1660-4601/15/12/2845/pdf?version=1544701398; doi:https://doi.org/10.3390/ijerph15122845; html:https://europepmc.org/articles/PMC6313538; pdf:https://europepmc.org/articles/PMC6313538?pdf=render"
   },
+  {
+    "id": "38987242",
+    "doi": "https://doi.org/10.1038/s41467-024-49998-0",
+    "title": "Characterising the genetic architecture of changes in adiposity during adulthood using electronic health records.",
+    "authorString": "Venkatesh SS, Ganjgahi H, Palmer DS, Coley K, Linchangco GV, Hui Q, Wilson P, Ho YL, Cho K, Arum\u00e4e K, Million Veteran Program, Estonian Biobank Research Team, Wittemans LBL, Nell\u00e5ker C, Vainik U, Sun YV, Holmes C, Lindgren CM, Nicholson G.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature communications",
+    "pubYear": "2024",
+    "date": "2024-07-10",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Obesity is a heritable disease, characterised by excess adiposity that is measured by body mass index (BMI). While over 1,000 genetic loci are associated with BMI, less is known about the genetic contribution to adiposity trajectories over adulthood. We derive adiposity-change phenotypes from 24.5 million primary-care health records in over 740,000 individuals in the UK Biobank, Million Veteran Program USA, and Estonian Biobank, to discover and validate the genetic architecture of adiposity trajectories. Using multiple BMI measurements over time increases power to identify genetic factors affecting baseline BMI by 14%. In the largest reported genome-wide study of adiposity-change in adulthood, we identify novel associations with BMI-change at six independent loci, including rs429358 (APOE missense variant). The SNP-based heritability of BMI-change (1.98%) is 9-fold lower than that of BMI. The modest genetic correlation between BMI-change and BMI (45.2%) indicates that genetic studies of longitudinal trajectories could uncover novel biology of quantitative traits in adulthood.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1038/s41467-024-49998-0; doi:https://doi.org/10.1038/s41467-024-49998-0; html:https://europepmc.org/articles/PMC11237142; pdf:https://europepmc.org/articles/PMC11237142?pdf=render"
+  },
   {
     "id": "32692755",
     "doi": "https://doi.org/10.1371/journal.pone.0236193",
@@ -32452,23 +32486,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1098/rsob.220373; doi:https://doi.org/10.1098/rsob.220373; html:https://europepmc.org/articles/PMC10030265; pdf:https://europepmc.org/articles/PMC10030265?pdf=render"
   },
-  {
-    "id": "30993728",
-    "doi": "https://doi.org/10.1111/cen.13990",
-    "title": "Risk of incident circulatory disease in patients treated for differentiated thyroid carcinoma with no history of cardiovascular disease.",
-    "authorString": "Toulis KA, Viola D, Gkoutos G, Keerthy D, Boelaert K, Nirantharakumar K.",
-    "authorAffiliations": "",
-    "journalTitle": "Clinical endocrinology",
-    "pubYear": "2019",
-    "date": "2019-05-17",
-    "isOpenAccess": "N",
-    "keywords": "Atrial fibrillation; Cardiovascular events; Thyroid cancer; Differentiated Thyroid Carcinoma",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Context</h4>The incidence of differentiated thyroid cancer (DTC) is increasing, yet the prognosis is favourable and long-term survival is expected. Exogenous TSH suppression has been used for many years to prevent DTC recurrence and may be associated with increased risks of circulatory diseases.<h4>Design</h4>Risks of circulatory disease in patients treated for DTC were compared to randomly matched patients without DTC (controls) up to a 1:5 ratio using age, sex, body mass index (BMI) and smoking as the matching parameters in a population-based, open cohort study using The Health Improvement Network.<h4>Patients</h4>A total of 3009 patients treated for DTC with no pre-existing cardiovascular disease were identified and matched to 11\u00a0303 controls, followed up to median of 5\u00a0years.<h4>Results</h4>A total of 1259 incident circulatory events were recorded during the observation period. No difference in the risk of ischaemic heart disease (IHD) (adjusted hazards ratio [aHR]: 1.04, 95% CI: 0.80-1.36) or heart failure (HF) (aHR: 1.27, 95% CI: 0.89-1.81) was detected. The risk of atrial fibrillation (AF) and stroke was significantly higher in patients with DTC (aHR: 1.71, 95% CI: 1.36-2.15 and aHR: 1.34, 95% CI: 1.05-1.72, respectively). In a sensitivity analysis limited to newly diagnosed patients with DTC, only the risk of AF was consistently elevated (aHR: 1.86, 95% CI: 1.33-2.60).<h4>Conclusions</h4>The increased risk of AF in patients who have undergone treatment for DTC but without pre-existing CVD may warrant periodic screening for this arrhythmia. Whereas no evidence of increased risk of IHD or HF was observed, the increased risk of stroke/TIA warrants further investigation.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1111/cen.13990"
-  },
   {
     "id": "34785789",
     "doi": "https://doi.org/10.1038/s41591-021-01546-9",
@@ -32487,21 +32504,21 @@
     "urls": "pdf:http://pure-oai.bham.ac.uk/ws/files/149366889/The_role_of_PROs_MedicalDevices_NatMed_FINAL_Sep_REVISED_CLEANCOPY2.pdf; doi:https://doi.org/10.1038/s41591-021-01546-9"
   },
   {
-    "id": "34970633",
-    "doi": "https://doi.org/10.23889/ijpds.v6i1.1674",
-    "title": "Evaluation of the ASSIGN open-source deterministic address-matching algorithm for allocating unique property reference numbers to general practitioner-recorded patient addresses.",
-    "authorString": "Harper G, Stables D, Simon P, Ahmed Z, Smith K, Robson J, Dezateux C.",
+    "id": "30993728",
+    "doi": "https://doi.org/10.1111/cen.13990",
+    "title": "Risk of incident circulatory disease in patients treated for differentiated thyroid carcinoma with no history of cardiovascular disease.",
+    "authorString": "Toulis KA, Viola D, Gkoutos G, Keerthy D, Boelaert K, Nirantharakumar K.",
     "authorAffiliations": "",
-    "journalTitle": "International journal of population data science",
-    "pubYear": "2021",
-    "date": "2021-12-08",
-    "isOpenAccess": "Y",
-    "keywords": "Quality assurance; Data Linkage; Population Health; Electronic Health Record; Addresses; Address-matching; Place-based Health",
+    "journalTitle": "Clinical endocrinology",
+    "pubYear": "2019",
+    "date": "2019-05-17",
+    "isOpenAccess": "N",
+    "keywords": "Atrial fibrillation; Cardiovascular events; Thyroid cancer; Differentiated Thyroid Carcinoma",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>Linking places to people is a core element of the UK government's geospatial strategy. Matching patient addresses in electronic health records to their Unique Property Reference Numbers (UPRNs) enables spatial linkage for research, innovation and public benefit. Available algorithms are not transparent or evaluated for use with addresses recorded by health care providers.<h4>Objectives</h4>To describe and quality assure the open-source deterministic ASSIGN address-matching algorithm applied to general practitioner-recorded patient addresses.<h4>Methods</h4>Best practice standards were used to report the ASSIGN algorithm match rate, sensitivity and positive predictive value using gold-standard datasets from London and Wales. We applied the ASSIGN algorithm to the recorded addresses of a sample of 1,757,018 patients registered with all general practices in north east London. We examined bias in match results for the study population using multivariable analyses to estimate the likelihood of an address-matched UPRN by demographic, registration, and organisational variables.<h4>Results</h4>We found a 99.5% and 99.6% match rate with high sensitivity (0.999,0.998) and positive predictive value (0.996,0.998) for the Welsh and London gold standard datasets respectively, and a 98.6% match rate for the study population.The 1.4% of the study population without a UPRN match were more likely to have changed registered address in the last 12 months (match rate: 95.4%), be from a Chinese ethnic background (95.5%), or registered with a general practice using the SystmOne clinical record system (94.4%). Conversely, people registered for more than 6.5 years with their general practitioner were more likely to have a match (99.4%) than those with shorter registration durations.<h4>Conclusions</h4>ASSIGN is a highly accurate open-source address-matching algorithm with a high match rate and minimal biases when evaluated against a large sample of general practice-recorded patient addresses. ASSIGN has potential to be used in other address-based datasets including those with information relevant to the wider determinants of health.",
+    "abstract": "<h4>Context</h4>The incidence of differentiated thyroid cancer (DTC) is increasing, yet the prognosis is favourable and long-term survival is expected. Exogenous TSH suppression has been used for many years to prevent DTC recurrence and may be associated with increased risks of circulatory diseases.<h4>Design</h4>Risks of circulatory disease in patients treated for DTC were compared to randomly matched patients without DTC (controls) up to a 1:5 ratio using age, sex, body mass index (BMI) and smoking as the matching parameters in a population-based, open cohort study using The Health Improvement Network.<h4>Patients</h4>A total of 3009 patients treated for DTC with no pre-existing cardiovascular disease were identified and matched to 11\u00a0303 controls, followed up to median of 5\u00a0years.<h4>Results</h4>A total of 1259 incident circulatory events were recorded during the observation period. No difference in the risk of ischaemic heart disease (IHD) (adjusted hazards ratio [aHR]: 1.04, 95% CI: 0.80-1.36) or heart failure (HF) (aHR: 1.27, 95% CI: 0.89-1.81) was detected. The risk of atrial fibrillation (AF) and stroke was significantly higher in patients with DTC (aHR: 1.71, 95% CI: 1.36-2.15 and aHR: 1.34, 95% CI: 1.05-1.72, respectively). In a sensitivity analysis limited to newly diagnosed patients with DTC, only the risk of AF was consistently elevated (aHR: 1.86, 95% CI: 1.33-2.60).<h4>Conclusions</h4>The increased risk of AF in patients who have undergone treatment for DTC but without pre-existing CVD may warrant periodic screening for this arrhythmia. Whereas no evidence of increased risk of IHD or HF was observed, the increased risk of stroke/TIA warrants further investigation.",
     "laySummary": "",
-    "urls": "pdf:https://ijpds.org/article/download/1674/3300; doi:https://doi.org/10.23889/ijpds.v6i1.1674; html:https://europepmc.org/articles/PMC8678979; pdf:https://europepmc.org/articles/PMC8678979?pdf=render"
+    "urls": "doi:https://doi.org/10.1111/cen.13990"
   },
   {
     "id": "30120083",
@@ -32521,21 +32538,21 @@
     "urls": "pdf:http://www.thelancet.com/article/S2352396418302925/pdf; doi:https://doi.org/10.1016/j.ebiom.2018.08.004; html:https://europepmc.org/articles/PMC6154782; pdf:https://europepmc.org/articles/PMC6154782?pdf=render"
   },
   {
-    "id": "36545235",
-    "doi": "https://doi.org/10.1177/26335565221145493",
-    "title": "The DynAIRx Project Protocol: Artificial Intelligence for dynamic prescribing optimisation and care integration in multimorbidity.",
-    "authorString": "Walker LE, Abuzour AS, Bollegala D, Clegg A, Gabbay M, Griffiths A, Kullu C, Leeming G, Mair FS, Maskell S, Relton S, Ruddle RA, Shantsila E, Sperrin M, Van Staa T, Woodall A, Buchan I.",
+    "id": "34970633",
+    "doi": "https://doi.org/10.23889/ijpds.v6i1.1674",
+    "title": "Evaluation of the ASSIGN open-source deterministic address-matching algorithm for allocating unique property reference numbers to general practitioner-recorded patient addresses.",
+    "authorString": "Harper G, Stables D, Simon P, Ahmed Z, Smith K, Robson J, Dezateux C.",
     "authorAffiliations": "",
-    "journalTitle": "Journal of multimorbidity and comorbidity",
-    "pubYear": "2022",
-    "date": "2022-01-01",
+    "journalTitle": "International journal of population data science",
+    "pubYear": "2021",
+    "date": "2021-12-08",
     "isOpenAccess": "Y",
-    "keywords": "Artificial intelligence; Frailty; Mental health; Polypharmacy; Multimorbidity; Medicines Optimisation",
+    "keywords": "Quality assurance; Data Linkage; Population Health; Electronic Health Record; Addresses; Address-matching; Place-based Health",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Structured Medication Reviews (SMRs) are intended to help deliver the NHS Long Term Plan for medicines optimisation in people living with multiple long-term conditions and polypharmacy. It is challenging to gather the information needed for these reviews due to poor integration of health records across providers and there is little guidance on how to identify those patients most urgently requiring review.<h4>Objective</h4>To extract information from scattered clinical records on how health and medications change over time, apply interpretable artificial intelligence (AI) approaches to predict risks of poor outcomes and overlay this information on care records to inform SMRs. We will pilot this approach in primary care prescribing audit and feedback systems, and co-design future medicines optimisation decision support systems.<h4>Design</h4>DynAIRx will target potentially problematic polypharmacy in three key multimorbidity groups, namely, people with (a) mental and physical health problems, (b) four or more long-term conditions taking ten or more drugs and (c) older age and frailty. Structured clinical data will be drawn from integrated care records (general practice, hospital, and social care) covering an \u223c11m population supplemented with Natural Language Processing (NLP) of unstructured clinical text. AI systems will be trained to identify patterns of conditions, medications, tests, and clinical contacts preceding adverse events in order to identify individuals who might benefit most from an SMR.<h4>Discussion</h4>By implementing and evaluating an AI-augmented visualisation of care records in an existing prescribing audit and feedback system we will create a learning system for medicines optimisation, co-designed throughout with end-users and patients.",
+    "abstract": "<h4>Introduction</h4>Linking places to people is a core element of the UK government's geospatial strategy. Matching patient addresses in electronic health records to their Unique Property Reference Numbers (UPRNs) enables spatial linkage for research, innovation and public benefit. Available algorithms are not transparent or evaluated for use with addresses recorded by health care providers.<h4>Objectives</h4>To describe and quality assure the open-source deterministic ASSIGN address-matching algorithm applied to general practitioner-recorded patient addresses.<h4>Methods</h4>Best practice standards were used to report the ASSIGN algorithm match rate, sensitivity and positive predictive value using gold-standard datasets from London and Wales. We applied the ASSIGN algorithm to the recorded addresses of a sample of 1,757,018 patients registered with all general practices in north east London. We examined bias in match results for the study population using multivariable analyses to estimate the likelihood of an address-matched UPRN by demographic, registration, and organisational variables.<h4>Results</h4>We found a 99.5% and 99.6% match rate with high sensitivity (0.999,0.998) and positive predictive value (0.996,0.998) for the Welsh and London gold standard datasets respectively, and a 98.6% match rate for the study population.The 1.4% of the study population without a UPRN match were more likely to have changed registered address in the last 12 months (match rate: 95.4%), be from a Chinese ethnic background (95.5%), or registered with a general practice using the SystmOne clinical record system (94.4%). Conversely, people registered for more than 6.5 years with their general practitioner were more likely to have a match (99.4%) than those with shorter registration durations.<h4>Conclusions</h4>ASSIGN is a highly accurate open-source address-matching algorithm with a high match rate and minimal biases when evaluated against a large sample of general practice-recorded patient addresses. ASSIGN has potential to be used in other address-based datasets including those with information relevant to the wider determinants of health.",
     "laySummary": "",
-    "urls": "pdf:https://eprints.whiterose.ac.uk/197084/1/26335565221145493.pdf; doi:https://doi.org/10.1177/26335565221145493; html:https://europepmc.org/articles/PMC9761229; pdf:https://europepmc.org/articles/PMC9761229?pdf=render"
+    "urls": "pdf:https://ijpds.org/article/download/1674/3300; doi:https://doi.org/10.23889/ijpds.v6i1.1674; html:https://europepmc.org/articles/PMC8678979; pdf:https://europepmc.org/articles/PMC8678979?pdf=render"
   },
   {
     "id": "35639667",
@@ -32554,6 +32571,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/eurheartj/article-pdf/43/31/2921/45333809/ehac238.pdf; doi:https://doi.org/10.1093/eurheartj/ehac238; html:https://europepmc.org/articles/PMC9443991; pdf:https://europepmc.org/articles/PMC9443991?pdf=render"
   },
+  {
+    "id": "36545235",
+    "doi": "https://doi.org/10.1177/26335565221145493",
+    "title": "The DynAIRx Project Protocol: Artificial Intelligence for dynamic prescribing optimisation and care integration in multimorbidity.",
+    "authorString": "Walker LE, Abuzour AS, Bollegala D, Clegg A, Gabbay M, Griffiths A, Kullu C, Leeming G, Mair FS, Maskell S, Relton S, Ruddle RA, Shantsila E, Sperrin M, Van Staa T, Woodall A, Buchan I.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of multimorbidity and comorbidity",
+    "pubYear": "2022",
+    "date": "2022-01-01",
+    "isOpenAccess": "Y",
+    "keywords": "Artificial intelligence; Frailty; Mental health; Polypharmacy; Multimorbidity; Medicines Optimisation",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Structured Medication Reviews (SMRs) are intended to help deliver the NHS Long Term Plan for medicines optimisation in people living with multiple long-term conditions and polypharmacy. It is challenging to gather the information needed for these reviews due to poor integration of health records across providers and there is little guidance on how to identify those patients most urgently requiring review.<h4>Objective</h4>To extract information from scattered clinical records on how health and medications change over time, apply interpretable artificial intelligence (AI) approaches to predict risks of poor outcomes and overlay this information on care records to inform SMRs. We will pilot this approach in primary care prescribing audit and feedback systems, and co-design future medicines optimisation decision support systems.<h4>Design</h4>DynAIRx will target potentially problematic polypharmacy in three key multimorbidity groups, namely, people with (a) mental and physical health problems, (b) four or more long-term conditions taking ten or more drugs and (c) older age and frailty. Structured clinical data will be drawn from integrated care records (general practice, hospital, and social care) covering an \u223c11m population supplemented with Natural Language Processing (NLP) of unstructured clinical text. AI systems will be trained to identify patterns of conditions, medications, tests, and clinical contacts preceding adverse events in order to identify individuals who might benefit most from an SMR.<h4>Discussion</h4>By implementing and evaluating an AI-augmented visualisation of care records in an existing prescribing audit and feedback system we will create a learning system for medicines optimisation, co-designed throughout with end-users and patients.",
+    "laySummary": "",
+    "urls": "pdf:https://eprints.whiterose.ac.uk/197084/1/26335565221145493.pdf; doi:https://doi.org/10.1177/26335565221145493; html:https://europepmc.org/articles/PMC9761229; pdf:https://europepmc.org/articles/PMC9761229?pdf=render"
+  },
   {
     "id": "39195987",
     "doi": "https://doi.org/10.1038/s44161-021-00012-6",
@@ -32639,23 +32673,6 @@
     "laySummary": "",
     "urls": "pdf:https://cronfa.swan.ac.uk/Record/cronfa50368/Download/0050368-25062019091637.pdf; doi:https://doi.org/10.1016/j.burns.2019.04.006"
   },
-  {
-    "id": "32401709",
-    "doi": "https://doi.org/10.1016/s2468-2667(20)30112-2",
-    "title": "COVID-19: a public health approach to manage domestic violence is needed.",
-    "authorString": "Chandan JS, Taylor J, Bradbury-Jones C, Nirantharakumar K, Kane E, Bandyopadhyay S.",
-    "authorAffiliations": "",
-    "journalTitle": "The Lancet. Public health",
-    "pubYear": "2020",
-    "date": "2020-05-10",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "Chandan et al. comment on the effect the covid pandemic may have on domestic violence and propose surveillance for domestic violence is needed. ",
-    "urls": "pdf:http://www.thelancet.com/article/S2468266720301122/pdf; doi:https://doi.org/10.1016/S2468-2667(20)30112-2; html:https://europepmc.org/articles/PMC7252171; pdf:https://europepmc.org/articles/PMC7252171?pdf=render"
-  },
   {
     "id": "32346541",
     "doi": "https://doi.org/10.1093/burnst/tkz004",
@@ -32674,21 +32691,21 @@
     "urls": "pdf:https://academic.oup.com/burnstrauma/article-pdf/doi/10.1093/burnst/tkz004/33423529/tkz004.pdf; doi:https://doi.org/10.1093/burnst/tkz004; html:https://europepmc.org/articles/PMC7175773; pdf:https://europepmc.org/articles/PMC7175773?pdf=render"
   },
   {
-    "id": "34040552",
-    "doi": "https://doi.org/10.3389/fpsyt.2021.627996",
-    "title": "Optimising a Simple Fully Convolutional Network for Accurate Brain Age Prediction in the PAC 2019 Challenge.",
-    "authorString": "Gong W, Beckmann CF, Vedaldi A, Smith SM, Peng H.",
+    "id": "32401709",
+    "doi": "https://doi.org/10.1016/s2468-2667(20)30112-2",
+    "title": "COVID-19: a public health approach to manage domestic violence is needed.",
+    "authorString": "Chandan JS, Taylor J, Bradbury-Jones C, Nirantharakumar K, Kane E, Bandyopadhyay S.",
     "authorAffiliations": "",
-    "journalTitle": "Frontiers in psychiatry",
-    "pubYear": "2021",
-    "date": "2021-05-10",
+    "journalTitle": "The Lancet. Public health",
+    "pubYear": "2020",
+    "date": "2020-05-10",
     "isOpenAccess": "Y",
-    "keywords": "Brain imaging; Predictive Analysis; Big Data; Deep Learning; Convolution Neural Network; Brain Age Prediction",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Brain age prediction from brain MRI scans not only helps improve brain ageing modelling generally, but also provides benchmarks for predictive analysis methods. Brain-age delta, which is the difference between a subject's predicted age and true age, has become a meaningful biomarker for the health of the brain. Here, we report the details of our brain age prediction models and results in the Predictive Analysis Challenge 2019. The aim of the challenge was to use T1-weighted brain MRIs to predict a subject's age in multicentre datasets. We apply a lightweight deep convolutional neural network architecture, Simple Fully Convolutional Neural Network (SFCN), and combined several techniques including data augmentation, transfer learning, model ensemble, and bias correction for brain age prediction. The model achieved first place in both of the two objectives in the PAC 2019 brain age prediction challenge: Mean absolute error (MAE) = 2.90 years without bias removal (Second Place = 3.09 yrs; Third Place = 3.33 yrs), and MAE = 2.95 years with bias removal, leading by a large margin (Second Place = 3.80 yrs; Third Place = 3.92 yrs).",
-    "laySummary": "",
-    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fpsyt.2021.627996/pdf; doi:https://doi.org/10.3389/fpsyt.2021.627996; html:https://europepmc.org/articles/PMC8141616; pdf:https://europepmc.org/articles/PMC8141616?pdf=render"
+    "abstract": "",
+    "laySummary": "Chandan et al. comment on the effect the covid pandemic may have on domestic violence and propose surveillance for domestic violence is needed. ",
+    "urls": "pdf:http://www.thelancet.com/article/S2468266720301122/pdf; doi:https://doi.org/10.1016/S2468-2667(20)30112-2; html:https://europepmc.org/articles/PMC7252171; pdf:https://europepmc.org/articles/PMC7252171?pdf=render"
   },
   {
     "id": "34236053",
@@ -32707,6 +32724,23 @@
     "laySummary": "",
     "urls": "pdf:http://insight.jci.org/articles/view/149446/files/pdf; doi:https://doi.org/10.1172/jci.insight.149446; html:https://europepmc.org/articles/PMC8410072; pdf:https://europepmc.org/articles/PMC8410072?pdf=render"
   },
+  {
+    "id": "34040552",
+    "doi": "https://doi.org/10.3389/fpsyt.2021.627996",
+    "title": "Optimising a Simple Fully Convolutional Network for Accurate Brain Age Prediction in the PAC 2019 Challenge.",
+    "authorString": "Gong W, Beckmann CF, Vedaldi A, Smith SM, Peng H.",
+    "authorAffiliations": "",
+    "journalTitle": "Frontiers in psychiatry",
+    "pubYear": "2021",
+    "date": "2021-05-10",
+    "isOpenAccess": "Y",
+    "keywords": "Brain imaging; Predictive Analysis; Big Data; Deep Learning; Convolution Neural Network; Brain Age Prediction",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Brain age prediction from brain MRI scans not only helps improve brain ageing modelling generally, but also provides benchmarks for predictive analysis methods. Brain-age delta, which is the difference between a subject's predicted age and true age, has become a meaningful biomarker for the health of the brain. Here, we report the details of our brain age prediction models and results in the Predictive Analysis Challenge 2019. The aim of the challenge was to use T1-weighted brain MRIs to predict a subject's age in multicentre datasets. We apply a lightweight deep convolutional neural network architecture, Simple Fully Convolutional Neural Network (SFCN), and combined several techniques including data augmentation, transfer learning, model ensemble, and bias correction for brain age prediction. The model achieved first place in both of the two objectives in the PAC 2019 brain age prediction challenge: Mean absolute error (MAE) = 2.90 years without bias removal (Second Place = 3.09 yrs; Third Place = 3.33 yrs), and MAE = 2.95 years with bias removal, leading by a large margin (Second Place = 3.80 yrs; Third Place = 3.92 yrs).",
+    "laySummary": "",
+    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fpsyt.2021.627996/pdf; doi:https://doi.org/10.3389/fpsyt.2021.627996; html:https://europepmc.org/articles/PMC8141616; pdf:https://europepmc.org/articles/PMC8141616?pdf=render"
+  },
   {
     "id": "34112101",
     "doi": "https://doi.org/10.1186/s12872-021-02020-7",
@@ -32724,23 +32758,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmccardiovascdisord.biomedcentral.com/counter/pdf/10.1186/s12872-021-02020-7; doi:https://doi.org/10.1186/s12872-021-02020-7; html:https://europepmc.org/articles/PMC8191101; pdf:https://europepmc.org/articles/PMC8191101?pdf=render"
   },
-  {
-    "id": "35869125",
-    "doi": "https://doi.org/10.1038/s41598-022-16375-0",
-    "title": "Minimising multi-centre radiomics variability through image normalisation: a pilot study.",
-    "authorString": "Campello VM, Mart\u00edn-Isla C, Izquierdo C, Guala A, Palomares JFR, Vilad\u00e9s D, Descalzo ML, Karakas M, \u00c7avu\u015f E, Raisi-Estabragh Z, Petersen SE, Escalera S, Segu\u00ed S, Lekadir K.",
-    "authorAffiliations": "",
-    "journalTitle": "Scientific reports",
-    "pubYear": "2022",
-    "date": "2022-07-22",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Radiomics is an emerging technique for the quantification of imaging data that has recently shown great promise for deeper phenotyping of cardiovascular disease. Thus far, the technique has been mostly applied in single-centre studies. However, one of the main difficulties in multi-centre imaging studies is the inherent variability of image characteristics due to centre differences. In this paper, a comprehensive analysis of radiomics variability under several image- and feature-based normalisation techniques was conducted using a multi-centre cardiovascular magnetic resonance dataset. 218 subjects divided into healthy (n\u00a0=\u00a0112) and hypertrophic cardiomyopathy (n\u00a0=\u00a0106, HCM) groups from five different centres were considered. First and second order texture radiomic features were extracted from three regions of interest, namely the left and right ventricular cavities and the left ventricular myocardium. Two methods were used to assess features' variability. First, feature distributions were compared across centres to obtain a distribution similarity index. Second, two classification tasks were proposed to assess: (1) the amount of centre-related information encoded in normalised features (centre identification) and (2) the generalisation ability for a classification model when trained on these features (healthy versus HCM classification). The results showed that the feature-based harmonisation technique ComBat is able to remove the variability introduced by centre information from radiomic features, at the expense of slightly degrading classification performance. Piecewise linear histogram matching normalisation gave features with greater generalisation ability for classification ( balanced accuracy in between 0.78\u00a0\u00b1\u00a00.08 and 0.79\u00a0\u00b1\u00a00.09). Models trained with features from images without normalisation showed the worst performance overall ( balanced accuracy in between 0.45\u00a0\u00b1\u00a00.28 and 0.60\u00a0\u00b1\u00a00.22). In conclusion, centre-related information removal did not imply good generalisation ability for classification.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41598-022-16375-0.pdf; doi:https://doi.org/10.1038/s41598-022-16375-0; html:https://europepmc.org/articles/PMC9307565; pdf:https://europepmc.org/articles/PMC9307565?pdf=render"
-  },
   {
     "id": "32807724",
     "doi": "https://doi.org/10.1016/j.auec.2020.07.007",
@@ -32758,6 +32775,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.auec.2020.07.007"
   },
+  {
+    "id": "35869125",
+    "doi": "https://doi.org/10.1038/s41598-022-16375-0",
+    "title": "Minimising multi-centre radiomics variability through image normalisation: a pilot study.",
+    "authorString": "Campello VM, Mart\u00edn-Isla C, Izquierdo C, Guala A, Palomares JFR, Vilad\u00e9s D, Descalzo ML, Karakas M, \u00c7avu\u015f E, Raisi-Estabragh Z, Petersen SE, Escalera S, Segu\u00ed S, Lekadir K.",
+    "authorAffiliations": "",
+    "journalTitle": "Scientific reports",
+    "pubYear": "2022",
+    "date": "2022-07-22",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Radiomics is an emerging technique for the quantification of imaging data that has recently shown great promise for deeper phenotyping of cardiovascular disease. Thus far, the technique has been mostly applied in single-centre studies. However, one of the main difficulties in multi-centre imaging studies is the inherent variability of image characteristics due to centre differences. In this paper, a comprehensive analysis of radiomics variability under several image- and feature-based normalisation techniques was conducted using a multi-centre cardiovascular magnetic resonance dataset. 218 subjects divided into healthy (n\u00a0=\u00a0112) and hypertrophic cardiomyopathy (n\u00a0=\u00a0106, HCM) groups from five different centres were considered. First and second order texture radiomic features were extracted from three regions of interest, namely the left and right ventricular cavities and the left ventricular myocardium. Two methods were used to assess features' variability. First, feature distributions were compared across centres to obtain a distribution similarity index. Second, two classification tasks were proposed to assess: (1) the amount of centre-related information encoded in normalised features (centre identification) and (2) the generalisation ability for a classification model when trained on these features (healthy versus HCM classification). The results showed that the feature-based harmonisation technique ComBat is able to remove the variability introduced by centre information from radiomic features, at the expense of slightly degrading classification performance. Piecewise linear histogram matching normalisation gave features with greater generalisation ability for classification ( balanced accuracy in between 0.78\u00a0\u00b1\u00a00.08 and 0.79\u00a0\u00b1\u00a00.09). Models trained with features from images without normalisation showed the worst performance overall ( balanced accuracy in between 0.45\u00a0\u00b1\u00a00.28 and 0.60\u00a0\u00b1\u00a00.22). In conclusion, centre-related information removal did not imply good generalisation ability for classification.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41598-022-16375-0.pdf; doi:https://doi.org/10.1038/s41598-022-16375-0; html:https://europepmc.org/articles/PMC9307565; pdf:https://europepmc.org/articles/PMC9307565?pdf=render"
+  },
   {
     "id": "34980174",
     "doi": "https://doi.org/10.1186/s12967-021-03210-9",
@@ -32792,6 +32826,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41467-024-49956-w.pdf; doi:https://doi.org/10.1038/s41467-024-49956-w; html:https://europepmc.org/articles/PMC11286847; pdf:https://europepmc.org/articles/PMC11286847?pdf=render"
   },
+  {
+    "id": "33472714",
+    "doi": "https://doi.org/10.1017/s1368980021000197",
+    "title": "Diet and risk of gastro-oesophageal reflux disease in the Melbourne Collaborative Cohort Study.",
+    "authorString": "Wang SE, Hodge AM, Dashti SG, Dixon-Suen SC, Mitchell H, Thomas RJ, Williamson EM, Makalic E, Boussioutas A, Haydon AM, Giles GG, Milne RL, Kendall BJ, English DR.",
+    "authorAffiliations": "",
+    "journalTitle": "Public health nutrition",
+    "pubYear": "2021",
+    "date": "2021-01-21",
+    "isOpenAccess": "N",
+    "keywords": "Fat; Diet; Prospective Cohort Study; Gastro-oesophageal Reflux Disease; Carbonated Beverages",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>To examine associations between diet and risk of developing gastro-oesophageal reflux disease (GERD).<h4>Design</h4>Prospective cohort with a median follow-up of 15\u00b78 years. Baseline diet was measured using a FFQ. GERD was defined as self-reported current or history of daily heartburn or acid regurgitation beginning at least 2 years after baseline. Sex-specific logistic regressions were performed to estimate OR for GERD associated with diet quality scores and intakes of nutrients, food groups and individual foods and beverages. The effect of substituting saturated fat for monounsaturated or polyunsaturated fat on GERD risk was examined.<h4>Setting</h4>Melbourne, Australia.<h4>Participants</h4>A cohort of 20 926 participants (62 % women) aged 40-59 years at recruitment between 1990 and 1994.<h4>Results</h4>For men, total fat intake was associated with increased risk of GERD (OR 1\u00b705 per 5 g/d; 95 % CI 1\u00b701, 1\u00b709; P = 0\u00b7016), whereas total carbohydrate (OR 0\u00b789 per 30 g/d; 95 % CI 0\u00b782, 0\u00b798; P = 0\u00b7010) and starch intakes (OR 0\u00b784 per 30 g/d; 95 % CI 0\u00b775, 0\u00b794; P = 0\u00b7005) were associated with reduced risk. Nutrients were not associated with risk for women. For both sexes, substituting saturated fat for polyunsaturated or monounsaturated fat did not change risk. For both sexes, fish, chicken, cruciferous vegetables and carbonated beverages were associated with increased risk, whereas total fruit and citrus were associated with reduced risk. No association was observed with diet quality scores.<h4>Conclusions</h4>Diet is a possible risk factor for GERD, but food considered as triggers of GERD symptoms might not necessarily contribute to disease development. Potential differential associations for men and women warrant further investigation.",
+    "laySummary": "",
+    "urls": "pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/274F1A424FA99A10625C3447D256A318/S1368980021000197a.pdf/div-class-title-diet-and-risk-of-gastro-oesophageal-reflux-disease-in-the-melbourne-collaborative-cohort-study-div.pdf; doi:https://doi.org/10.1017/S1368980021000197; html:https://europepmc.org/articles/PMC11082811; pdf:https://europepmc.org/articles/PMC11082811?pdf=render; doi:https://doi.org/10.1017/s1368980021000197"
+  },
   {
     "id": "37477760",
     "doi": "https://doi.org/10.1007/s10875-023-01547-y",
@@ -32826,23 +32877,6 @@
     "laySummary": "",
     "urls": "pdf:https://thorax.bmj.com/content/thoraxjnl/early/2023/05/24/thorax-2023-220057.full.pdf; doi:https://doi.org/10.1136/thorax-2023-220057; html:https://europepmc.org/articles/PMC10715514; pdf:https://europepmc.org/articles/PMC10715514?pdf=render"
   },
-  {
-    "id": "33472714",
-    "doi": "https://doi.org/10.1017/s1368980021000197",
-    "title": "Diet and risk of gastro-oesophageal reflux disease in the Melbourne Collaborative Cohort Study.",
-    "authorString": "Wang SE, Hodge AM, Dashti SG, Dixon-Suen SC, Mitchell H, Thomas RJ, Williamson EM, Makalic E, Boussioutas A, Haydon AM, Giles GG, Milne RL, Kendall BJ, English DR.",
-    "authorAffiliations": "",
-    "journalTitle": "Public health nutrition",
-    "pubYear": "2021",
-    "date": "2021-01-21",
-    "isOpenAccess": "N",
-    "keywords": "Fat; Diet; Prospective Cohort Study; Gastro-oesophageal Reflux Disease; Carbonated Beverages",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objective</h4>To examine associations between diet and risk of developing gastro-oesophageal reflux disease (GERD).<h4>Design</h4>Prospective cohort with a median follow-up of 15\u00b78 years. Baseline diet was measured using a FFQ. GERD was defined as self-reported current or history of daily heartburn or acid regurgitation beginning at least 2 years after baseline. Sex-specific logistic regressions were performed to estimate OR for GERD associated with diet quality scores and intakes of nutrients, food groups and individual foods and beverages. The effect of substituting saturated fat for monounsaturated or polyunsaturated fat on GERD risk was examined.<h4>Setting</h4>Melbourne, Australia.<h4>Participants</h4>A cohort of 20 926 participants (62 % women) aged 40-59 years at recruitment between 1990 and 1994.<h4>Results</h4>For men, total fat intake was associated with increased risk of GERD (OR 1\u00b705 per 5 g/d; 95 % CI 1\u00b701, 1\u00b709; P = 0\u00b7016), whereas total carbohydrate (OR 0\u00b789 per 30 g/d; 95 % CI 0\u00b782, 0\u00b798; P = 0\u00b7010) and starch intakes (OR 0\u00b784 per 30 g/d; 95 % CI 0\u00b775, 0\u00b794; P = 0\u00b7005) were associated with reduced risk. Nutrients were not associated with risk for women. For both sexes, substituting saturated fat for polyunsaturated or monounsaturated fat did not change risk. For both sexes, fish, chicken, cruciferous vegetables and carbonated beverages were associated with increased risk, whereas total fruit and citrus were associated with reduced risk. No association was observed with diet quality scores.<h4>Conclusions</h4>Diet is a possible risk factor for GERD, but food considered as triggers of GERD symptoms might not necessarily contribute to disease development. Potential differential associations for men and women warrant further investigation.",
-    "laySummary": "",
-    "urls": "pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/274F1A424FA99A10625C3447D256A318/S1368980021000197a.pdf/div-class-title-diet-and-risk-of-gastro-oesophageal-reflux-disease-in-the-melbourne-collaborative-cohort-study-div.pdf; doi:https://doi.org/10.1017/S1368980021000197; html:https://europepmc.org/articles/PMC11082811; pdf:https://europepmc.org/articles/PMC11082811?pdf=render; doi:https://doi.org/10.1017/s1368980021000197"
-  },
   {
     "id": "36449515",
     "doi": "https://doi.org/10.1371/journal.pcbi.1010726",
@@ -32895,21 +32929,38 @@
     "urls": "doi:https://doi.org/10.1089/neu.2023.0464"
   },
   {
-    "id": "36823471",
-    "doi": "https://doi.org/10.1038/s42255-023-00753-7",
-    "title": "Proteogenomic links to human metabolic diseases.",
-    "authorString": "Koprulu M, Carrasco-Zanini J, Wheeler E, Lockhart S, Kerrison ND, Wareham NJ, Pietzner M, Langenberg C.",
+    "id": "37348789",
+    "doi": "https://doi.org/10.1016/j.jhep.2023.05.046",
+    "title": "Liver disease is a significant risk factor for cardiovascular outcomes - A UK Biobank study.",
+    "authorString": "Roca-Fernandez A, Banerjee R, Thomaides-Brears H, Telford A, Sanyal A, Neubauer S, Nichols TE, Raman B, McCracken C, Petersen SE, Ntusi NA, Cuthbertson DJ, Lai M, Dennis A, Banerjee A.",
     "authorAffiliations": "",
-    "journalTitle": "Nature metabolism",
+    "journalTitle": "Journal of hepatology",
     "pubYear": "2023",
-    "date": "2023-02-23",
+    "date": "2023-06-20",
+    "isOpenAccess": "N",
+    "keywords": "Cardiac; MRI; Imaging; Hepatic; Heart Failure; liver disease; Cvd; Nafld; Atrial Fibrilliation",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background & aims</h4>Chronic liver disease (CLD) is associated with increased cardiovascular disease (CVD) risk. We investigated whether early signs of liver disease (measured by iron-corrected T1-mapping [cT1]) were associated with an increased risk of major CVD events.<h4>Methods</h4>Liver disease activity (cT1) and fat (proton density fat fraction [PDFF]) were measured using LiverMultiScan\u00ae between January 2016 and February 2020 in the UK Biobank imaging sub-study. Using multivariable Cox regression, we explored associations between liver cT1 (MRI) and primary CVD (coronary artery disease, atrial fibrillation [AF], embolism/vascular events, heart failure [HF] and stroke), and CVD hospitalisation and all-cause mortality. Liver blood biomarkers, general metabolism biomarkers, and demographics were also included. Subgroup analysis was conducted in those without metabolic syndrome (defined as at least three of: a large waist, high triglycerides, low high-density lipoprotein cholesterol, increased systolic blood pressure, or elevated haemoglobin A1c).<h4>Results</h4>A total of 33,616 participants (mean age 65 years, mean BMI 26\u00a0kg/m<sup>2</sup>, mean haemoglobin A1c 35\u00a0mmol/mol) had complete MRI liver data with linked clinical outcomes (median time to major CVD event onset: 1.4 years [range: 0.002-5.1]; follow-up: 2.5 years [range: 1.1-5.2]). Liver disease activity (cT1), but not liver fat (PDFF), was associated with higher risk of any major CVD event (hazard ratio 1.14; 95% CI 1.03-1.26; p\u00a0= 0.008), AF (1.30; 1.12-1.51; p <0.001); HF (1.30; 1.09-1.56; p= 0.004); CVD hospitalisation (1.27; 1.18-1.37; p <0.001) and all-cause mortality (1.19; 1.02-1.38; p\u00a0= 0.026). FIB-4 index was associated with HF (1.06; 1.01-1.10; p\u00a0= 0.007). Risk of CVD hospitalisation was independently associated with cT1 in individuals without metabolic syndrome (1.26; 1.13-1.4; p <0.001).<h4>Conclusion</h4>Liver disease activity, by cT1, was independently associated with a higher risk of incident CVD and all-cause mortality, independent of pre-existing metabolic syndrome, liver fibrosis or fat.<h4>Impact and implications</h4>Chronic liver disease (CLD) is associated with a twofold greater incidence of cardiovascular disease. Our work shows that early liver disease on iron-corrected T1 mapping was associated with a higher risk of major cardiovascular disease (14%), cardiovascular disease hospitalisation (27%) and all-cause mortality (19%). These findings highlight the prognostic relevance of a comprehensive evaluation of liver health in populations at risk of CVD and/or CLD, even in the absence of clinical manifestations or metabolic syndrome, when there is an opportunity to modify/address risk factors and prevent disease progression. As such, they are relevant to patients, carers, clinicians, and policymakers.",
+    "laySummary": "",
+    "urls": "pdf:http://www.journal-of-hepatology.eu/article/S0168827823004208/pdf; doi:https://doi.org/10.1016/j.jhep.2023.05.046"
+  },
+  {
+    "id": "34173614",
+    "doi": "https://doi.org/10.1016/s2666-7568(20)30012-x",
+    "title": "Evolution and effects of COVID-19 outbreaks in care homes: a population analysis in 189 care homes in one geographical region of the UK.",
+    "authorString": "Burton JK, Bayne G, Evans C, Garbe F, Gorman D, Honhold N, McCormick D, Othieno R, Stevenson JE, Swietlik S, Templeton KE, Tranter M, Willocks L, Guthrie B.",
+    "authorAffiliations": "",
+    "journalTitle": "The lancet. Healthy longevity",
+    "pubYear": "2020",
+    "date": "2020-10-20",
     "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Studying the plasma proteome as the intermediate layer between the genome and the phenome has the potential to identify new disease processes. Here, we conducted a cis-focused proteogenomic analysis of 2,923 plasma proteins measured in 1,180 individuals using antibody-based assays. We (1) identify 256 unreported protein quantitative trait loci (pQTL); (2) demonstrate shared genetic regulation of 224 cis-pQTLs with 575 specific health outcomes, revealing examples for notable metabolic diseases (such as gastrin-releasing peptide as a potential therapeutic target for type 2 diabetes); (3) improve causal gene assignment at 40% (n\u2009=\u2009192) of overlapping risk loci; and (4) observe convergence of phenotypic consequences of cis-pQTLs and rare loss-of-function gene burden for 12 proteins, such as TIMD4 for lipoprotein metabolism. Our findings demonstrate the value of integrating complementary proteomic technologies with genomics even at moderate scale to identify new mediators of metabolic diseases with the potential for therapeutic interventions.",
+    "abstract": "<h4>Background</h4>COVID-19 has affected care home residents internationally, but detailed information on outbreaks is scarce. We aimed to describe the evolution of outbreaks of COVID-19 in all care homes in one large health region in Scotland.<h4>Methods</h4>We did a population analysis of testing, cases, and deaths in care homes in the National Health Service (NHS) Lothian health region of the UK. We obtained data for COVID-19 testing (PCR testing of nasopharyngeal swabs for severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) and deaths (COVID-19-related and non-COVID-19-related), and we analysed data by several variables including type of care home, number of beds, and locality. Outcome measures were timing of outbreaks, number of confirmed cases of COVID-19 in care home residents, care home characteristics associated with the presence of an outbreak, and deaths of residents in both care homes and hospitals. We calculated excess deaths (both COVID-19-related and non-COVID-19-related), which we defined as the sum of deaths over and above the historical average in the same period over the past 5 years.<h4>Findings</h4>Between March 10 and Aug 2, 2020, residents at 189 care homes (5843 beds) were tested for COVID-19 when symptomatic. A COVID-19 outbreak was confirmed at 69 (37%) care homes, of which 66 (96%) were care homes for older people. The size of care homes for older people was strongly associated with a COVID-19 outbreak (odds ratio per 20-bed increase 3\u00b735, 95% CI 1\u00b799-5\u00b763). 907 confirmed cases of SARS-CoV-2 infection were recorded during the study period, and 432 COVID-19-related deaths. 229 (25%) COVID-19-related cases and 99 (24%) COVID-related deaths occurred in five (3%) of 189 care homes, and 441 (49%) cases and 207 (50%) deaths were in 13 (7%) care homes. 411 (95%) COVID-19-related deaths occurred in the 69 care homes with a confirmed COVID-19 outbreak, 19 (4%) deaths were in hospital, and two (<1%) were in one of the 120 care homes without a confirmed COVID-19 outbreak. At the 69 care homes with a confirmed COVID-19 outbreak, 74 excess non-COVID-19-related deaths were reported, whereas ten non-COVID-19-related excess deaths were observed in the 120 care homes without a confirmed COVID-19 outbreak. 32 fewer non-COVID-19-related deaths than expected were reported among care home residents in hospital.<h4>Interpretation</h4>The effect of COVID-19 on care homes has been substantial but concentrated in care homes with known outbreaks. A key implication from our findings is that, if community incidence of COVID-19 increases again, many care home residents will be susceptible. Shielding care home residents from potential sources of SARS-CoV-2 infection, and ensuring rapid action to minimise outbreak size if infection is introduced, will be important for any second wave.<h4>Funding</h4>None.",
     "laySummary": "",
-    "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7614946; doi:https://doi.org/10.1038/s42255-023-00753-7; html:https://europepmc.org/articles/PMC7614946; pdf:https://europepmc.org/articles/PMC7614946?pdf=render"
+    "urls": "doi:https://doi.org/10.1016/s2666-7568(20)30012-x; doi:https://doi.org/10.1016/S2666-7568(20)30012-X; html:https://europepmc.org/articles/PMC7574931; pdf:https://europepmc.org/articles/PMC7574931?pdf=render"
   },
   {
     "id": "38745010",
@@ -32929,38 +32980,21 @@
     "urls": "pdf:https://www.nature.com/articles/s41591-024-02960-5.pdf; doi:https://doi.org/10.1038/s41591-024-02960-5; html:https://europepmc.org/articles/PMC11186791; pdf:https://europepmc.org/articles/PMC11186791?pdf=render"
   },
   {
-    "id": "34173614",
-    "doi": "https://doi.org/10.1016/s2666-7568(20)30012-x",
-    "title": "Evolution and effects of COVID-19 outbreaks in care homes: a population analysis in 189 care homes in one geographical region of the UK.",
-    "authorString": "Burton JK, Bayne G, Evans C, Garbe F, Gorman D, Honhold N, McCormick D, Othieno R, Stevenson JE, Swietlik S, Templeton KE, Tranter M, Willocks L, Guthrie B.",
+    "id": "36823471",
+    "doi": "https://doi.org/10.1038/s42255-023-00753-7",
+    "title": "Proteogenomic links to human metabolic diseases.",
+    "authorString": "Koprulu M, Carrasco-Zanini J, Wheeler E, Lockhart S, Kerrison ND, Wareham NJ, Pietzner M, Langenberg C.",
     "authorAffiliations": "",
-    "journalTitle": "The lancet. Healthy longevity",
-    "pubYear": "2020",
-    "date": "2020-10-20",
+    "journalTitle": "Nature metabolism",
+    "pubYear": "2023",
+    "date": "2023-02-23",
     "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>COVID-19 has affected care home residents internationally, but detailed information on outbreaks is scarce. We aimed to describe the evolution of outbreaks of COVID-19 in all care homes in one large health region in Scotland.<h4>Methods</h4>We did a population analysis of testing, cases, and deaths in care homes in the National Health Service (NHS) Lothian health region of the UK. We obtained data for COVID-19 testing (PCR testing of nasopharyngeal swabs for severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) and deaths (COVID-19-related and non-COVID-19-related), and we analysed data by several variables including type of care home, number of beds, and locality. Outcome measures were timing of outbreaks, number of confirmed cases of COVID-19 in care home residents, care home characteristics associated with the presence of an outbreak, and deaths of residents in both care homes and hospitals. We calculated excess deaths (both COVID-19-related and non-COVID-19-related), which we defined as the sum of deaths over and above the historical average in the same period over the past 5 years.<h4>Findings</h4>Between March 10 and Aug 2, 2020, residents at 189 care homes (5843 beds) were tested for COVID-19 when symptomatic. A COVID-19 outbreak was confirmed at 69 (37%) care homes, of which 66 (96%) were care homes for older people. The size of care homes for older people was strongly associated with a COVID-19 outbreak (odds ratio per 20-bed increase 3\u00b735, 95% CI 1\u00b799-5\u00b763). 907 confirmed cases of SARS-CoV-2 infection were recorded during the study period, and 432 COVID-19-related deaths. 229 (25%) COVID-19-related cases and 99 (24%) COVID-related deaths occurred in five (3%) of 189 care homes, and 441 (49%) cases and 207 (50%) deaths were in 13 (7%) care homes. 411 (95%) COVID-19-related deaths occurred in the 69 care homes with a confirmed COVID-19 outbreak, 19 (4%) deaths were in hospital, and two (<1%) were in one of the 120 care homes without a confirmed COVID-19 outbreak. At the 69 care homes with a confirmed COVID-19 outbreak, 74 excess non-COVID-19-related deaths were reported, whereas ten non-COVID-19-related excess deaths were observed in the 120 care homes without a confirmed COVID-19 outbreak. 32 fewer non-COVID-19-related deaths than expected were reported among care home residents in hospital.<h4>Interpretation</h4>The effect of COVID-19 on care homes has been substantial but concentrated in care homes with known outbreaks. A key implication from our findings is that, if community incidence of COVID-19 increases again, many care home residents will be susceptible. Shielding care home residents from potential sources of SARS-CoV-2 infection, and ensuring rapid action to minimise outbreak size if infection is introduced, will be important for any second wave.<h4>Funding</h4>None.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/s2666-7568(20)30012-x; doi:https://doi.org/10.1016/S2666-7568(20)30012-X; html:https://europepmc.org/articles/PMC7574931; pdf:https://europepmc.org/articles/PMC7574931?pdf=render"
-  },
-  {
-    "id": "37348789",
-    "doi": "https://doi.org/10.1016/j.jhep.2023.05.046",
-    "title": "Liver disease is a significant risk factor for cardiovascular outcomes - A UK Biobank study.",
-    "authorString": "Roca-Fernandez A, Banerjee R, Thomaides-Brears H, Telford A, Sanyal A, Neubauer S, Nichols TE, Raman B, McCracken C, Petersen SE, Ntusi NA, Cuthbertson DJ, Lai M, Dennis A, Banerjee A.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of hepatology",
-    "pubYear": "2023",
-    "date": "2023-06-20",
-    "isOpenAccess": "N",
-    "keywords": "Cardiac; MRI; Imaging; Hepatic; Heart Failure; liver disease; Cvd; Nafld; Atrial Fibrilliation",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background & aims</h4>Chronic liver disease (CLD) is associated with increased cardiovascular disease (CVD) risk. We investigated whether early signs of liver disease (measured by iron-corrected T1-mapping [cT1]) were associated with an increased risk of major CVD events.<h4>Methods</h4>Liver disease activity (cT1) and fat (proton density fat fraction [PDFF]) were measured using LiverMultiScan\u00ae between January 2016 and February 2020 in the UK Biobank imaging sub-study. Using multivariable Cox regression, we explored associations between liver cT1 (MRI) and primary CVD (coronary artery disease, atrial fibrillation [AF], embolism/vascular events, heart failure [HF] and stroke), and CVD hospitalisation and all-cause mortality. Liver blood biomarkers, general metabolism biomarkers, and demographics were also included. Subgroup analysis was conducted in those without metabolic syndrome (defined as at least three of: a large waist, high triglycerides, low high-density lipoprotein cholesterol, increased systolic blood pressure, or elevated haemoglobin A1c).<h4>Results</h4>A total of 33,616 participants (mean age 65 years, mean BMI 26\u00a0kg/m<sup>2</sup>, mean haemoglobin A1c 35\u00a0mmol/mol) had complete MRI liver data with linked clinical outcomes (median time to major CVD event onset: 1.4 years [range: 0.002-5.1]; follow-up: 2.5 years [range: 1.1-5.2]). Liver disease activity (cT1), but not liver fat (PDFF), was associated with higher risk of any major CVD event (hazard ratio 1.14; 95% CI 1.03-1.26; p\u00a0= 0.008), AF (1.30; 1.12-1.51; p <0.001); HF (1.30; 1.09-1.56; p= 0.004); CVD hospitalisation (1.27; 1.18-1.37; p <0.001) and all-cause mortality (1.19; 1.02-1.38; p\u00a0= 0.026). FIB-4 index was associated with HF (1.06; 1.01-1.10; p\u00a0= 0.007). Risk of CVD hospitalisation was independently associated with cT1 in individuals without metabolic syndrome (1.26; 1.13-1.4; p <0.001).<h4>Conclusion</h4>Liver disease activity, by cT1, was independently associated with a higher risk of incident CVD and all-cause mortality, independent of pre-existing metabolic syndrome, liver fibrosis or fat.<h4>Impact and implications</h4>Chronic liver disease (CLD) is associated with a twofold greater incidence of cardiovascular disease. Our work shows that early liver disease on iron-corrected T1 mapping was associated with a higher risk of major cardiovascular disease (14%), cardiovascular disease hospitalisation (27%) and all-cause mortality (19%). These findings highlight the prognostic relevance of a comprehensive evaluation of liver health in populations at risk of CVD and/or CLD, even in the absence of clinical manifestations or metabolic syndrome, when there is an opportunity to modify/address risk factors and prevent disease progression. As such, they are relevant to patients, carers, clinicians, and policymakers.",
+    "abstract": "Studying the plasma proteome as the intermediate layer between the genome and the phenome has the potential to identify new disease processes. Here, we conducted a cis-focused proteogenomic analysis of 2,923 plasma proteins measured in 1,180 individuals using antibody-based assays. We (1) identify 256 unreported protein quantitative trait loci (pQTL); (2) demonstrate shared genetic regulation of 224 cis-pQTLs with 575 specific health outcomes, revealing examples for notable metabolic diseases (such as gastrin-releasing peptide as a potential therapeutic target for type 2 diabetes); (3) improve causal gene assignment at 40% (n\u2009=\u2009192) of overlapping risk loci; and (4) observe convergence of phenotypic consequences of cis-pQTLs and rare loss-of-function gene burden for 12 proteins, such as TIMD4 for lipoprotein metabolism. Our findings demonstrate the value of integrating complementary proteomic technologies with genomics even at moderate scale to identify new mediators of metabolic diseases with the potential for therapeutic interventions.",
     "laySummary": "",
-    "urls": "pdf:http://www.journal-of-hepatology.eu/article/S0168827823004208/pdf; doi:https://doi.org/10.1016/j.jhep.2023.05.046"
+    "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7614946; doi:https://doi.org/10.1038/s42255-023-00753-7; html:https://europepmc.org/articles/PMC7614946; pdf:https://europepmc.org/articles/PMC7614946?pdf=render"
   },
   {
     "id": "33496075",
@@ -33081,6 +33115,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1038/s41397-023-00317-8; html:https://europepmc.org/articles/PMC10661738; pdf:https://europepmc.org/articles/PMC10661738?pdf=render"
   },
+  {
+    "id": "33986429",
+    "doi": "https://doi.org/10.1038/s41598-021-89743-x",
+    "title": "Predicting sex from retinal fundus photographs using automated deep learning.",
+    "authorString": "Korot E, Pontikos N, Liu X, Wagner SK, Faes L, Huemer J, Balaskas K, Denniston AK, Khawaja A, Keane PA.",
+    "authorAffiliations": "",
+    "journalTitle": "Scientific reports",
+    "pubYear": "2021",
+    "date": "2021-05-13",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Deep learning may transform health care, but model development has largely been dependent on availability of advanced technical expertise. Herein we present the development of a deep learning model by clinicians without coding, which predicts reported sex from retinal fundus photographs. A model was trained on 84,743 retinal fundus photos from the UK Biobank dataset. External validation was performed on 252 fundus photos from a tertiary ophthalmic referral center. For internal validation, the area under the receiver operating characteristic curve (AUROC) of the code free deep learning (CFDL) model was 0.93. Sensitivity, specificity, positive predictive value (PPV) and accuracy (ACC) were 88.8%, 83.6%, 87.3% and 86.5%, and for external validation were 83.9%, 72.2%, 78.2% and 78.6% respectively. Clinicians are currently unaware of distinct retinal feature variations between males and females, highlighting the importance of model explainability for this task. The model performed significantly worse when foveal pathology was present in the external validation dataset, ACC: 69.4%, compared to 85.4% in healthy eyes, suggesting the fovea is a salient region for model performance OR (95% CI): 0.36 (0.19, 0.70) p\u2009=\u20090.0022. Automated machine learning (AutoML) may enable clinician-driven automated discovery of novel insights and disease biomarkers.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41598-021-89743-x.pdf; doi:https://doi.org/10.1038/s41598-021-89743-x; html:https://europepmc.org/articles/PMC8119673; pdf:https://europepmc.org/articles/PMC8119673?pdf=render"
+  },
   {
     "id": "31363735",
     "doi": "https://doi.org/10.1093/hmg/ddz187",
@@ -33099,21 +33150,21 @@
     "urls": "pdf:https://academic.oup.com/hmg/article-pdf/28/R2/R133/31081033/ddz187.pdf; doi:https://doi.org/10.1093/hmg/ddz187"
   },
   {
-    "id": "33986429",
-    "doi": "https://doi.org/10.1038/s41598-021-89743-x",
-    "title": "Predicting sex from retinal fundus photographs using automated deep learning.",
-    "authorString": "Korot E, Pontikos N, Liu X, Wagner SK, Faes L, Huemer J, Balaskas K, Denniston AK, Khawaja A, Keane PA.",
+    "id": "32781946",
+    "doi": "https://doi.org/10.1098/rspb.2020.1405",
+    "title": "Key questions for modelling COVID-19 exit strategies.",
+    "authorString": "Thompson RN, Hollingsworth TD, Isham V, Arribas-Bel D, Ashby B, Britton T, Challenor P, Chappell LHK, Clapham H, Cunniffe NJ, Dawid AP, Donnelly CA, Eggo RM, Funk S, Gilbert N, Glendinning P, Gog JR, Hart WS, Heesterbeek H, House T, Keeling M, Kiss IZ, Kretzschmar ME, Lloyd AL, McBryde ES, McCaw JM, McKinley TJ, Miller JC, Morris M, O'Neill PD, Parag KV, Pearson CAB, Pellis L, Pulliam JRC, Ross JV, Tomba GS, Silverman BW, Struchiner CJ, Tildesley MJ, Trapman P, Webb CR, Mollison D, Restif O.",
     "authorAffiliations": "",
-    "journalTitle": "Scientific reports",
-    "pubYear": "2021",
-    "date": "2021-05-13",
+    "journalTitle": "Proceedings. Biological sciences",
+    "pubYear": "2020",
+    "date": "2020-08-12",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Uncertainty; Mathematical Modelling; Epidemic Control; Exit Strategy; Covid-19; Sars-cov-2",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Deep learning may transform health care, but model development has largely been dependent on availability of advanced technical expertise. Herein we present the development of a deep learning model by clinicians without coding, which predicts reported sex from retinal fundus photographs. A model was trained on 84,743 retinal fundus photos from the UK Biobank dataset. External validation was performed on 252 fundus photos from a tertiary ophthalmic referral center. For internal validation, the area under the receiver operating characteristic curve (AUROC) of the code free deep learning (CFDL) model was 0.93. Sensitivity, specificity, positive predictive value (PPV) and accuracy (ACC) were 88.8%, 83.6%, 87.3% and 86.5%, and for external validation were 83.9%, 72.2%, 78.2% and 78.6% respectively. Clinicians are currently unaware of distinct retinal feature variations between males and females, highlighting the importance of model explainability for this task. The model performed significantly worse when foveal pathology was present in the external validation dataset, ACC: 69.4%, compared to 85.4% in healthy eyes, suggesting the fovea is a salient region for model performance OR (95% CI): 0.36 (0.19, 0.70) p\u2009=\u20090.0022. Automated machine learning (AutoML) may enable clinician-driven automated discovery of novel insights and disease biomarkers.",
+    "abstract": "Combinations of intense non-pharmaceutical interventions (lockdowns) were introduced worldwide to reduce SARS-CoV-2 transmission. Many governments have begun to implement exit strategies that relax restrictions while attempting to control the risk of a surge in cases. Mathematical modelling has played a central role in guiding interventions, but the challenge of designing optimal exit strategies in the face of ongoing transmission is unprecedented. Here, we report discussions from the Isaac Newton Institute 'Models for an exit strategy' workshop (11-15 May 2020). A diverse community of modellers who are providing evidence to governments worldwide were asked to identify the main questions that, if answered, would allow for more accurate predictions of the effects of different exit strategies. Based on these questions, we propose a roadmap to facilitate the development of reliable models to guide exit strategies. This roadmap requires a global collaborative effort from the scientific community and policymakers, and has three parts: (i) improve estimation of key epidemiological parameters; (ii) understand sources of heterogeneity in populations; and (iii) focus on requirements for data collection, particularly in low-to-middle-income countries. This will provide important information for planning exit strategies that balance socio-economic benefits with public health.",
     "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41598-021-89743-x.pdf; doi:https://doi.org/10.1038/s41598-021-89743-x; html:https://europepmc.org/articles/PMC8119673; pdf:https://europepmc.org/articles/PMC8119673?pdf=render"
+    "urls": "doi:https://doi.org/10.1098/rspb.2020.1405; doi:https://doi.org/10.1098/rspb.2020.1405; html:https://europepmc.org/articles/PMC7575516; pdf:https://europepmc.org/articles/PMC7575516?pdf=render"
   },
   {
     "id": "34611362",
@@ -33149,23 +33200,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41366-021-00896-1.pdf; doi:https://doi.org/10.1038/s41366-021-00896-1; html:https://europepmc.org/articles/PMC8455324; pdf:https://europepmc.org/articles/PMC8455324?pdf=render"
   },
-  {
-    "id": "32781946",
-    "doi": "https://doi.org/10.1098/rspb.2020.1405",
-    "title": "Key questions for modelling COVID-19 exit strategies.",
-    "authorString": "Thompson RN, Hollingsworth TD, Isham V, Arribas-Bel D, Ashby B, Britton T, Challenor P, Chappell LHK, Clapham H, Cunniffe NJ, Dawid AP, Donnelly CA, Eggo RM, Funk S, Gilbert N, Glendinning P, Gog JR, Hart WS, Heesterbeek H, House T, Keeling M, Kiss IZ, Kretzschmar ME, Lloyd AL, McBryde ES, McCaw JM, McKinley TJ, Miller JC, Morris M, O'Neill PD, Parag KV, Pearson CAB, Pellis L, Pulliam JRC, Ross JV, Tomba GS, Silverman BW, Struchiner CJ, Tildesley MJ, Trapman P, Webb CR, Mollison D, Restif O.",
-    "authorAffiliations": "",
-    "journalTitle": "Proceedings. Biological sciences",
-    "pubYear": "2020",
-    "date": "2020-08-12",
-    "isOpenAccess": "Y",
-    "keywords": "Uncertainty; Mathematical Modelling; Epidemic Control; Exit Strategy; Covid-19; Sars-cov-2",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Combinations of intense non-pharmaceutical interventions (lockdowns) were introduced worldwide to reduce SARS-CoV-2 transmission. Many governments have begun to implement exit strategies that relax restrictions while attempting to control the risk of a surge in cases. Mathematical modelling has played a central role in guiding interventions, but the challenge of designing optimal exit strategies in the face of ongoing transmission is unprecedented. Here, we report discussions from the Isaac Newton Institute 'Models for an exit strategy' workshop (11-15 May 2020). A diverse community of modellers who are providing evidence to governments worldwide were asked to identify the main questions that, if answered, would allow for more accurate predictions of the effects of different exit strategies. Based on these questions, we propose a roadmap to facilitate the development of reliable models to guide exit strategies. This roadmap requires a global collaborative effort from the scientific community and policymakers, and has three parts: (i) improve estimation of key epidemiological parameters; (ii) understand sources of heterogeneity in populations; and (iii) focus on requirements for data collection, particularly in low-to-middle-income countries. This will provide important information for planning exit strategies that balance socio-economic benefits with public health.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1098/rspb.2020.1405; doi:https://doi.org/10.1098/rspb.2020.1405; html:https://europepmc.org/articles/PMC7575516; pdf:https://europepmc.org/articles/PMC7575516?pdf=render"
-  },
   {
     "id": "30537243",
     "doi": "https://doi.org/10.1002/ejhf.1370",
@@ -33234,23 +33268,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41591-022-01781-8.pdf; doi:https://doi.org/10.1038/s41591-022-01781-8"
   },
-  {
-    "id": "32679111",
-    "doi": "https://doi.org/10.1016/s0140-6736(20)31356-8",
-    "title": "COVID-19 pandemic and admission rates for and management of acute coronary syndromes in England.",
-    "authorString": "Mafham MM, Spata E, Goldacre R, Gair D, Curnow P, Bray M, Hollings S, Roebuck C, Gale CP, Mamas MA, Deanfield JE, de Belder MA, Luescher TF, Denwood T, Landray MJ, Emberson JR, Collins R, Morris EJA, Casadei B, Baigent C.",
-    "authorAffiliations": "",
-    "journalTitle": "Lancet (London, England)",
-    "pubYear": "2020",
-    "date": "2020-07-14",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Several countries affected by the COVID-19 pandemic have reported a substantial drop in the number of patients attending the emergency department with acute coronary syndromes and a reduced number of cardiac procedures. We aimed to understand the scale, nature, and duration of changes to admissions for different types of acute coronary syndrome in England and to evaluate whether in-hospital management of patients has been affected as a result of the COVID-19 pandemic.<h4>Methods</h4>We analysed data on hospital admissions in England for types of acute coronary syndrome from Jan 1, 2019, to May 24, 2020, that were recorded in the Secondary Uses Service Admitted Patient Care database. Admissions were classified as ST-elevation myocardial infarction (STEMI), non-STEMI (NSTEMI), myocardial infarction of unknown type, or other acute coronary syndromes (including unstable angina). We identified revascularisation procedures undertaken during these admissions (ie, coronary angiography without percutaneous coronary intervention [PCI], PCI, and coronary artery bypass graft surgery). We calculated the numbers of weekly admissions and procedures undertaken; percentage reductions in weekly admissions and across subgroups were also calculated, with 95% CIs.<h4>Findings</h4>Hospital admissions for acute coronary syndrome declined from mid-February, 2020, falling from a 2019 baseline rate of 3017 admissions per week to 1813 per week by the end of March, 2020, a reduction of 40% (95% CI 37-43). This decline was partly reversed during April and May, 2020, such that by the last week of May, 2020, there were 2522 admissions, representing a 16% (95% CI 13-20) reduction from baseline. During the period of declining admissions, there were reductions in the numbers of admissions for all types of acute coronary syndrome, including both STEMI and NSTEMI, but relative and absolute reductions were larger for NSTEMI, with 1267 admissions per week in 2019 and 733 per week by the end of March, 2020, a percent reduction of 42% (95% CI 38-46). In parallel, reductions were recorded in the number of PCI procedures for patients with both STEMI (438 PCI procedures per week in 2019 vs 346 by the end of March, 2020; percent reduction 21%, 95% CI 12-29) and NSTEMI (383 PCI procedures per week in 2019 vs 240 by the end of March, 2020; percent reduction 37%, 29-45). The median length of stay among patients with acute coronary syndrome fell from 4 days (IQR 2-9) in 2019 to 3 days (1-5) by the end of March, 2020.<h4>Interpretation</h4>Compared with the weekly average in 2019, there was a substantial reduction in the weekly numbers of patients with acute coronary syndrome who were admitted to hospital in England by the end of March, 2020, which had been partly reversed by the end of May, 2020. The reduced number of admissions during this period is likely to have resulted in increases in out-of-hospital deaths and long-term complications of myocardial infarction and missed opportunities to offer secondary prevention treatment for patients with coronary heart disease. The full extent of the effect of COVID-19 on the management of patients with acute coronary syndrome will continue to be assessed by updating these analyses.<h4>Funding</h4>UK Medical Research Council, British Heart Foundation, Public Health England, Health Data Research UK, and the National Institute for Health Research Oxford Biomedical Research Centre.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/s0140-6736(20)31356-8; doi:https://doi.org/10.1016/S0140-6736(20)31356-8; html:https://europepmc.org/articles/PMC7429983; pdf:https://europepmc.org/articles/PMC7429983?pdf=render"
-  },
   {
     "id": "31443926",
     "doi": "https://doi.org/10.1016/s0140-6736(19)31674-5",
@@ -33268,6 +33285,23 @@
     "laySummary": "",
     "urls": "pdf:http://www.thelancet.com/article/S0140673619316745/pdf; doi:https://doi.org/10.1016/S0140-6736(19)31674-5; html:https://europepmc.org/articles/PMC6857444; pdf:https://europepmc.org/articles/PMC6857444?pdf=render"
   },
+  {
+    "id": "32679111",
+    "doi": "https://doi.org/10.1016/s0140-6736(20)31356-8",
+    "title": "COVID-19 pandemic and admission rates for and management of acute coronary syndromes in England.",
+    "authorString": "Mafham MM, Spata E, Goldacre R, Gair D, Curnow P, Bray M, Hollings S, Roebuck C, Gale CP, Mamas MA, Deanfield JE, de Belder MA, Luescher TF, Denwood T, Landray MJ, Emberson JR, Collins R, Morris EJA, Casadei B, Baigent C.",
+    "authorAffiliations": "",
+    "journalTitle": "Lancet (London, England)",
+    "pubYear": "2020",
+    "date": "2020-07-14",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Several countries affected by the COVID-19 pandemic have reported a substantial drop in the number of patients attending the emergency department with acute coronary syndromes and a reduced number of cardiac procedures. We aimed to understand the scale, nature, and duration of changes to admissions for different types of acute coronary syndrome in England and to evaluate whether in-hospital management of patients has been affected as a result of the COVID-19 pandemic.<h4>Methods</h4>We analysed data on hospital admissions in England for types of acute coronary syndrome from Jan 1, 2019, to May 24, 2020, that were recorded in the Secondary Uses Service Admitted Patient Care database. Admissions were classified as ST-elevation myocardial infarction (STEMI), non-STEMI (NSTEMI), myocardial infarction of unknown type, or other acute coronary syndromes (including unstable angina). We identified revascularisation procedures undertaken during these admissions (ie, coronary angiography without percutaneous coronary intervention [PCI], PCI, and coronary artery bypass graft surgery). We calculated the numbers of weekly admissions and procedures undertaken; percentage reductions in weekly admissions and across subgroups were also calculated, with 95% CIs.<h4>Findings</h4>Hospital admissions for acute coronary syndrome declined from mid-February, 2020, falling from a 2019 baseline rate of 3017 admissions per week to 1813 per week by the end of March, 2020, a reduction of 40% (95% CI 37-43). This decline was partly reversed during April and May, 2020, such that by the last week of May, 2020, there were 2522 admissions, representing a 16% (95% CI 13-20) reduction from baseline. During the period of declining admissions, there were reductions in the numbers of admissions for all types of acute coronary syndrome, including both STEMI and NSTEMI, but relative and absolute reductions were larger for NSTEMI, with 1267 admissions per week in 2019 and 733 per week by the end of March, 2020, a percent reduction of 42% (95% CI 38-46). In parallel, reductions were recorded in the number of PCI procedures for patients with both STEMI (438 PCI procedures per week in 2019 vs 346 by the end of March, 2020; percent reduction 21%, 95% CI 12-29) and NSTEMI (383 PCI procedures per week in 2019 vs 240 by the end of March, 2020; percent reduction 37%, 29-45). The median length of stay among patients with acute coronary syndrome fell from 4 days (IQR 2-9) in 2019 to 3 days (1-5) by the end of March, 2020.<h4>Interpretation</h4>Compared with the weekly average in 2019, there was a substantial reduction in the weekly numbers of patients with acute coronary syndrome who were admitted to hospital in England by the end of March, 2020, which had been partly reversed by the end of May, 2020. The reduced number of admissions during this period is likely to have resulted in increases in out-of-hospital deaths and long-term complications of myocardial infarction and missed opportunities to offer secondary prevention treatment for patients with coronary heart disease. The full extent of the effect of COVID-19 on the management of patients with acute coronary syndrome will continue to be assessed by updating these analyses.<h4>Funding</h4>UK Medical Research Council, British Heart Foundation, Public Health England, Health Data Research UK, and the National Institute for Health Research Oxford Biomedical Research Centre.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/s0140-6736(20)31356-8; doi:https://doi.org/10.1016/S0140-6736(20)31356-8; html:https://europepmc.org/articles/PMC7429983; pdf:https://europepmc.org/articles/PMC7429983?pdf=render"
+  },
   {
     "id": "37719788",
     "doi": "https://doi.org/10.1093/noajnl/vdad096",
@@ -33285,6 +33319,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/noa/advance-article-pdf/doi/10.1093/noajnl/vdad096/51026152/vdad096.pdf; doi:https://doi.org/10.1093/noajnl/vdad096; html:https://europepmc.org/articles/PMC10503650; pdf:https://europepmc.org/articles/PMC10503650?pdf=render"
   },
+  {
+    "id": "35410184",
+    "doi": "https://doi.org/10.1186/s12889-022-13069-0",
+    "title": "The local burden of disease during the first wave of the COVID-19 epidemic in England: estimation using different data sources from changing surveillance practices.",
+    "authorString": "Nightingale ES, Abbott S, Russell TW, CMMID Covid-19 Working Group, Lowe R, Medley GF, Brady OJ.",
+    "authorAffiliations": "",
+    "journalTitle": "BMC public health",
+    "pubYear": "2022",
+    "date": "2022-04-11",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>The COVID-19 epidemic has differentially impacted communities across England, with regional variation in rates of confirmed cases, hospitalisations and deaths. Measurement of this burden changed substantially over the first months, as surveillance was expanded to accommodate the escalating epidemic. Laboratory confirmation was initially restricted to clinical need (\"pillar 1\") before expanding to community-wide symptomatics (\"pillar 2\"). This study aimed to ascertain whether inconsistent measurement of case data resulting from varying testing coverage could be reconciled by drawing inference from COVID-19-related deaths.<h4>Methods</h4>We fit a Bayesian spatio-temporal model to weekly COVID-19-related deaths per local authority (LTLA) throughout the first wave (1 January 2020-30 June 2020), adjusting for the local epidemic timing and the age, deprivation and ethnic composition of its population. We combined predictions from this model with case data under community-wide, symptomatic testing and infection prevalence estimates from the ONS infection survey, to infer the likely trajectory of infections implied by the deaths in each LTLA.<h4>Results</h4>A model including temporally- and spatially-correlated random effects was found to best accommodate the observed variation in COVID-19-related deaths, after accounting for local population characteristics. Predicted case counts under community-wide symptomatic testing suggest a total of 275,000-420,000 cases over the first wave - a median of over 100,000 additional to the total confirmed in practice under varying testing coverage. This translates to a peak incidence of around 200,000 total infections per week across England. The extent to which estimated total infections are reflected in confirmed case counts was found to vary substantially across LTLAs, ranging from 7% in Leicester to 96% in Gloucester with a median of 23%.<h4>Conclusions</h4>Limitations in testing capacity biased the observed trajectory of COVID-19 infections throughout the first wave. Basing inference on COVID-19-related mortality and higher-coverage testing later in the time period, we could explore the extent of this bias more explicitly. Evidence points towards substantial under-representation of initial growth and peak magnitude of infections nationally, to which different parts of the country contribute unequally.",
+    "laySummary": "",
+    "urls": "pdf:https://bmcpublichealth.biomedcentral.com/track/pdf/10.1186/s12889-022-13069-0; doi:https://doi.org/10.1186/s12889-022-13069-0; html:https://europepmc.org/articles/PMC8996221; pdf:https://europepmc.org/articles/PMC8996221?pdf=render"
+  },
   {
     "id": "36996819",
     "doi": "https://doi.org/10.1016/j.chom.2023.03.004",
@@ -33319,23 +33370,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/13/2/e067254.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-067254; html:https://europepmc.org/articles/PMC9923317; pdf:https://europepmc.org/articles/PMC9923317?pdf=render"
   },
-  {
-    "id": "35410184",
-    "doi": "https://doi.org/10.1186/s12889-022-13069-0",
-    "title": "The local burden of disease during the first wave of the COVID-19 epidemic in England: estimation using different data sources from changing surveillance practices.",
-    "authorString": "Nightingale ES, Abbott S, Russell TW, CMMID Covid-19 Working Group, Lowe R, Medley GF, Brady OJ.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC public health",
-    "pubYear": "2022",
-    "date": "2022-04-11",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>The COVID-19 epidemic has differentially impacted communities across England, with regional variation in rates of confirmed cases, hospitalisations and deaths. Measurement of this burden changed substantially over the first months, as surveillance was expanded to accommodate the escalating epidemic. Laboratory confirmation was initially restricted to clinical need (\"pillar 1\") before expanding to community-wide symptomatics (\"pillar 2\"). This study aimed to ascertain whether inconsistent measurement of case data resulting from varying testing coverage could be reconciled by drawing inference from COVID-19-related deaths.<h4>Methods</h4>We fit a Bayesian spatio-temporal model to weekly COVID-19-related deaths per local authority (LTLA) throughout the first wave (1 January 2020-30 June 2020), adjusting for the local epidemic timing and the age, deprivation and ethnic composition of its population. We combined predictions from this model with case data under community-wide, symptomatic testing and infection prevalence estimates from the ONS infection survey, to infer the likely trajectory of infections implied by the deaths in each LTLA.<h4>Results</h4>A model including temporally- and spatially-correlated random effects was found to best accommodate the observed variation in COVID-19-related deaths, after accounting for local population characteristics. Predicted case counts under community-wide symptomatic testing suggest a total of 275,000-420,000 cases over the first wave - a median of over 100,000 additional to the total confirmed in practice under varying testing coverage. This translates to a peak incidence of around 200,000 total infections per week across England. The extent to which estimated total infections are reflected in confirmed case counts was found to vary substantially across LTLAs, ranging from 7% in Leicester to 96% in Gloucester with a median of 23%.<h4>Conclusions</h4>Limitations in testing capacity biased the observed trajectory of COVID-19 infections throughout the first wave. Basing inference on COVID-19-related mortality and higher-coverage testing later in the time period, we could explore the extent of this bias more explicitly. Evidence points towards substantial under-representation of initial growth and peak magnitude of infections nationally, to which different parts of the country contribute unequally.",
-    "laySummary": "",
-    "urls": "pdf:https://bmcpublichealth.biomedcentral.com/track/pdf/10.1186/s12889-022-13069-0; doi:https://doi.org/10.1186/s12889-022-13069-0; html:https://europepmc.org/articles/PMC8996221; pdf:https://europepmc.org/articles/PMC8996221?pdf=render"
-  },
   {
     "id": "35244709",
     "doi": "https://doi.org/10.1093/europace/euac022",
@@ -33370,23 +33404,6 @@
     "laySummary": "",
     "urls": "pdf:https://mhealth.jmir.org/2021/7/e29840/PDF; doi:https://doi.org/10.2196/29840; html:https://europepmc.org/articles/PMC8367113"
   },
-  {
-    "id": "36330526",
-    "doi": "https://doi.org/10.3389/fimmu.2022.1032331",
-    "title": "Levels of soluble complement regulators predict severity of COVID-19 symptoms.",
-    "authorString": "Tierney AL, Alali WM, Scott T, Rees-Unwin KS, CITIID-NIHR BioResource COVID-19 Collaboration, Clark SJ, Unwin RD.",
-    "authorAffiliations": "",
-    "journalTitle": "Frontiers in immunology",
-    "pubYear": "2022",
-    "date": "2022-10-18",
-    "isOpenAccess": "Y",
-    "keywords": "Complement; Mass spectrometry; Biomarkers; Factor H; Factor H-related Proteins; Covid-19; Sars-cov-2",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The SARS-CoV-2 virus continues to cause significant morbidity and mortality worldwide from COVID-19. One of the major challenges of patient management is the broad range of symptoms observed. While the majority of individuals experience relatively mild disease, a significant minority of patients require hospitalisation, with COVID-19 still proving fatal for some. As such, there remains a desperate need to better understand what drives this severe disease, both in terms of the underlying biology, but also to potentially predict at diagnosis which patients are likely to require further interventions, thus enabling better outcomes for both patients and healthcare systems. Several lines of evidence have pointed to dysregulation of the complement cascade as a major factor in severe COVID-19 outcomes. How this is underpinned mechanistically is not known. Here, we have focussed on the role of the soluble complement regulators Complement Factor H (FH), its splice variant Factor H-like 1 (FHL-1) and five Factor H-Related proteins (FHR1-5). Using a targeted mass spectrometry approach, we quantified these proteins in a cohort of 188 plasma samples from controls and SARS-CoV-2 patients taken at diagnosis. This analysis revealed significant elevations in all FHR proteins, but not FH, in patients with more severe disease, particularly FHR2 and FHR5 (FHR2: 1.97-fold, p&lt;0.0001; FHR5: 2.4-fold, p&lt;0.0001). Furthermore, for a subset of 77 SARS-CoV-2 +ve patients we also analysed time course samples taken approximately 28 days post-diagnosis. Here, we see complement regulator levels drop in all individuals with asymptomatic or mild disease, but regulators remain high in those with more severe outcomes, with elevations in FHR2 over baseline levels in this group. These data support the hypothesis that elevation of circulating levels of the FHR family of proteins could predict disease severity in COVID-19 patients, and that the duration of elevation (or lack of immune activation resolution) may be partly responsible for driving poor outcomes in COVID-19.",
-    "laySummary": "",
-    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fimmu.2022.1032331/pdf; doi:https://doi.org/10.3389/fimmu.2022.1032331; html:https://europepmc.org/articles/PMC9624227; pdf:https://europepmc.org/articles/PMC9624227?pdf=render"
-  },
   {
     "id": "31234639",
     "doi": "https://doi.org/10.1161/circulationaha.118.038814",
@@ -33405,21 +33422,21 @@
     "urls": "doi:https://doi.org/10.1161/circulationaha.118.038814; doi:https://doi.org/10.1161/CIRCULATIONAHA.118.038814; html:https://europepmc.org/articles/PMC6687408; pdf:https://europepmc.org/articles/PMC6687408?pdf=render"
   },
   {
-    "id": "33048945",
-    "doi": "https://doi.org/10.1371/journal.pmed.1003290",
-    "title": "Neurodevelopmental multimorbidity and educational outcomes of Scottish schoolchildren: A population-based record linkage cohort study.",
-    "authorString": "Fleming M, Salim EE, Mackay DF, Henderson A, Kinnear D, Clark D, King A, McLay JS, Cooper SA, Pell JP.",
+    "id": "36330526",
+    "doi": "https://doi.org/10.3389/fimmu.2022.1032331",
+    "title": "Levels of soluble complement regulators predict severity of COVID-19 symptoms.",
+    "authorString": "Tierney AL, Alali WM, Scott T, Rees-Unwin KS, CITIID-NIHR BioResource COVID-19 Collaboration, Clark SJ, Unwin RD.",
     "authorAffiliations": "",
-    "journalTitle": "PLoS medicine",
-    "pubYear": "2020",
-    "date": "2020-10-13",
+    "journalTitle": "Frontiers in immunology",
+    "pubYear": "2022",
+    "date": "2022-10-18",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Complement; Mass spectrometry; Biomarkers; Factor H; Factor H-related Proteins; Covid-19; Sars-cov-2",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Neurodevelopmental conditions commonly coexist in children, but compared to adults, childhood multimorbidity attracts less attention in research and clinical practice. We previously reported that children treated for attention deficit hyperactivity disorder (ADHD) and depression have more school absences and exclusions, additional support needs, poorer attainment, and increased unemployment. They are also more likely to have coexisting conditions, including autism and intellectual disability. We investigated prevalence of neurodevelopmental multimorbidity (\u22652 conditions) among Scottish schoolchildren and their educational outcomes compared to peers.<h4>Methods and findings</h4>We retrospectively linked 6 Scotland-wide databases to analyse 766,244 children (390,290 [50.9%] boys; 375,954 [49.1%] girls) aged 4 to 19 years (mean = 10.9) attending Scottish schools between 2009 and 2013. Children were distributed across all deprivation quintiles (most to least deprived: 22.7%, 20.1%, 19.3%, 19.5%, 18.4%). The majority (96.2%) were white ethnicity. We ascertained autism spectrum disorder (ASD) and intellectual disabilities from records of additional support needs and ADHD and depression through relevant encashed prescriptions. We identified neurodevelopmental multimorbidity (\u22652 of these conditions) in 4,789 (0.6%) children, with ASD and intellectual disability the most common combination. On adjusting for sociodemographic (sex, age, ethnicity, deprivation) and maternity (maternal age, maternal smoking, sex-gestation-specific birth weight centile, gestational age, 5-minute Apgar score, mode of delivery, parity) factors, multimorbidity was associated with increased school absenteeism and exclusion, unemployment, and poorer exam attainment. Significant dose relationships were evident between number of conditions (0, 1, \u22652) and the last 3 outcomes. Compared to children with no conditions, children with 1 condition, and children with 2 or more conditions, had more absenteeism (1 condition adjusted incidence rate ratio [IRR] 1.28, 95% CI 1.27-1.30, p < 0.001 and 2 or more conditions adjusted IRR 1.23, 95% CI 1.20-1.28, p < 0.001), greater exclusion (adjusted IRR 2.37, 95% CI 2.25-2.48, p < 0.001 and adjusted IRR 3.04, 95% CI 2.74-3.38, p < 0.001), poorer attainment (adjusted odds ratio [OR] 3.92, 95% CI 3.63-4.23, p < 0.001 and adjusted OR 12.07, 95% CI 9.15-15.94, p < 0.001), and increased unemployment (adjusted OR 1.57, 95% CI 1.49-1.66, p < 0.001 and adjusted OR 2.11, 95% CI 1.83-2.45, p < 0.001). Associations remained after further adjustment for comorbid physical conditions and additional support needs. Coexisting depression was the strongest driver of absenteeism and coexisting ADHD the strongest driver of exclusion. Absence of formal primary care diagnoses was a limitation since ascertaining depression and ADHD from prescriptions omitted affected children receiving alternative or no treatment and some antidepressants can be prescribed for other indications.<h4>Conclusions</h4>Structuring clinical practice and training around single conditions may disadvantage children with neurodevelopmental multimorbidity, who we observed had significantly poorer educational outcomes compared to children with 1 condition and no conditions.",
+    "abstract": "The SARS-CoV-2 virus continues to cause significant morbidity and mortality worldwide from COVID-19. One of the major challenges of patient management is the broad range of symptoms observed. While the majority of individuals experience relatively mild disease, a significant minority of patients require hospitalisation, with COVID-19 still proving fatal for some. As such, there remains a desperate need to better understand what drives this severe disease, both in terms of the underlying biology, but also to potentially predict at diagnosis which patients are likely to require further interventions, thus enabling better outcomes for both patients and healthcare systems. Several lines of evidence have pointed to dysregulation of the complement cascade as a major factor in severe COVID-19 outcomes. How this is underpinned mechanistically is not known. Here, we have focussed on the role of the soluble complement regulators Complement Factor H (FH), its splice variant Factor H-like 1 (FHL-1) and five Factor H-Related proteins (FHR1-5). Using a targeted mass spectrometry approach, we quantified these proteins in a cohort of 188 plasma samples from controls and SARS-CoV-2 patients taken at diagnosis. This analysis revealed significant elevations in all FHR proteins, but not FH, in patients with more severe disease, particularly FHR2 and FHR5 (FHR2: 1.97-fold, p&lt;0.0001; FHR5: 2.4-fold, p&lt;0.0001). Furthermore, for a subset of 77 SARS-CoV-2 +ve patients we also analysed time course samples taken approximately 28 days post-diagnosis. Here, we see complement regulator levels drop in all individuals with asymptomatic or mild disease, but regulators remain high in those with more severe outcomes, with elevations in FHR2 over baseline levels in this group. These data support the hypothesis that elevation of circulating levels of the FHR family of proteins could predict disease severity in COVID-19 patients, and that the duration of elevation (or lack of immune activation resolution) may be partly responsible for driving poor outcomes in COVID-19.",
     "laySummary": "",
-    "urls": "pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003290&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003290; html:https://europepmc.org/articles/PMC7553326; pdf:https://europepmc.org/articles/PMC7553326?pdf=render"
+    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fimmu.2022.1032331/pdf; doi:https://doi.org/10.3389/fimmu.2022.1032331; html:https://europepmc.org/articles/PMC9624227; pdf:https://europepmc.org/articles/PMC9624227?pdf=render"
   },
   {
     "id": "33482294",
@@ -33439,21 +33456,21 @@
     "urls": "pdf:http://www.jclinepi.com/article/S0895435621000056/pdf; doi:https://doi.org/10.1016/j.jclinepi.2021.01.003"
   },
   {
-    "id": "33306713",
-    "doi": "https://doi.org/10.1371/journal.pone.0243383",
-    "title": "Health, educational and employment outcomes among children treated for a skin disorder: Scotland-wide retrospective record linkage cohort study of 766,244 children.",
-    "authorString": "Fleming M, McLay JS, Clark D, King A, Mackay DF, Pell JP.",
+    "id": "33048945",
+    "doi": "https://doi.org/10.1371/journal.pmed.1003290",
+    "title": "Neurodevelopmental multimorbidity and educational outcomes of Scottish schoolchildren: A population-based record linkage cohort study.",
+    "authorString": "Fleming M, Salim EE, Mackay DF, Henderson A, Kinnear D, Clark D, King A, McLay JS, Cooper SA, Pell JP.",
     "authorAffiliations": "",
-    "journalTitle": "PloS one",
+    "journalTitle": "PLoS medicine",
     "pubYear": "2020",
-    "date": "2020-12-11",
+    "date": "2020-10-13",
     "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>To compare health, educational and employment outcomes of schoolchildren receiving medication for a skin disorder with peers.<h4>Methods</h4>This retrospective population cohort study linked eight Scotland-wide databases, covering dispensed prescriptions, hospital admissions, maternity records, death certificates, annual pupil census, school examinations, school absences/exclusions and unemployment to investigate educational (absence, exclusion, special educational need, academic attainment), employment, and health (admissions and mortality) outcomes of 766,244 children attending local authority run primary, secondary and special schools in Scotland between 2009 and 2013.<h4>Results</h4>After adjusting for sociodemographic and maternity confounders the 130,087 (17.0%) children treated for a skin disorder had increased hospitalisation, particularly within one year of commencing treatment (IRR 1.38, 95% CI 1.35-1.41, p<0.001) and mortality (HR 1.50, 95% CI 1.18-1.90, p<0.001). They had greater special educational need (OR 1.19, 95% CI 1.17-1.21, p<0.001) and more frequent absences from school (IRR 1.07, 95% CI 1.06-1.08, p<0.001) but did not exhibit poorer exam attainment or increased post-school unemployment. The associations remained after further adjustment for comorbid chronic conditions.<h4>Conclusions</h4>Despite increased hospitalisation, school absenteeism, and special educational need, children treated for a skin disorder did not have poorer exam attainment or employment outcomes. Whilst findings relating to educational and employment outcomes are reassuring, the association with increased risk of mortality is alarming and merits further investigation.",
+    "abstract": "<h4>Background</h4>Neurodevelopmental conditions commonly coexist in children, but compared to adults, childhood multimorbidity attracts less attention in research and clinical practice. We previously reported that children treated for attention deficit hyperactivity disorder (ADHD) and depression have more school absences and exclusions, additional support needs, poorer attainment, and increased unemployment. They are also more likely to have coexisting conditions, including autism and intellectual disability. We investigated prevalence of neurodevelopmental multimorbidity (\u22652 conditions) among Scottish schoolchildren and their educational outcomes compared to peers.<h4>Methods and findings</h4>We retrospectively linked 6 Scotland-wide databases to analyse 766,244 children (390,290 [50.9%] boys; 375,954 [49.1%] girls) aged 4 to 19 years (mean = 10.9) attending Scottish schools between 2009 and 2013. Children were distributed across all deprivation quintiles (most to least deprived: 22.7%, 20.1%, 19.3%, 19.5%, 18.4%). The majority (96.2%) were white ethnicity. We ascertained autism spectrum disorder (ASD) and intellectual disabilities from records of additional support needs and ADHD and depression through relevant encashed prescriptions. We identified neurodevelopmental multimorbidity (\u22652 of these conditions) in 4,789 (0.6%) children, with ASD and intellectual disability the most common combination. On adjusting for sociodemographic (sex, age, ethnicity, deprivation) and maternity (maternal age, maternal smoking, sex-gestation-specific birth weight centile, gestational age, 5-minute Apgar score, mode of delivery, parity) factors, multimorbidity was associated with increased school absenteeism and exclusion, unemployment, and poorer exam attainment. Significant dose relationships were evident between number of conditions (0, 1, \u22652) and the last 3 outcomes. Compared to children with no conditions, children with 1 condition, and children with 2 or more conditions, had more absenteeism (1 condition adjusted incidence rate ratio [IRR] 1.28, 95% CI 1.27-1.30, p < 0.001 and 2 or more conditions adjusted IRR 1.23, 95% CI 1.20-1.28, p < 0.001), greater exclusion (adjusted IRR 2.37, 95% CI 2.25-2.48, p < 0.001 and adjusted IRR 3.04, 95% CI 2.74-3.38, p < 0.001), poorer attainment (adjusted odds ratio [OR] 3.92, 95% CI 3.63-4.23, p < 0.001 and adjusted OR 12.07, 95% CI 9.15-15.94, p < 0.001), and increased unemployment (adjusted OR 1.57, 95% CI 1.49-1.66, p < 0.001 and adjusted OR 2.11, 95% CI 1.83-2.45, p < 0.001). Associations remained after further adjustment for comorbid physical conditions and additional support needs. Coexisting depression was the strongest driver of absenteeism and coexisting ADHD the strongest driver of exclusion. Absence of formal primary care diagnoses was a limitation since ascertaining depression and ADHD from prescriptions omitted affected children receiving alternative or no treatment and some antidepressants can be prescribed for other indications.<h4>Conclusions</h4>Structuring clinical practice and training around single conditions may disadvantage children with neurodevelopmental multimorbidity, who we observed had significantly poorer educational outcomes compared to children with 1 condition and no conditions.",
     "laySummary": "",
-    "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0243383&type=printable; doi:https://doi.org/10.1371/journal.pone.0243383; html:https://europepmc.org/articles/PMC7732076; pdf:https://europepmc.org/articles/PMC7732076?pdf=render"
+    "urls": "pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003290&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003290; html:https://europepmc.org/articles/PMC7553326; pdf:https://europepmc.org/articles/PMC7553326?pdf=render"
   },
   {
     "id": "35165324",
@@ -33472,6 +33489,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41598-022-06315-3.pdf; doi:https://doi.org/10.1038/s41598-022-06315-3; html:https://europepmc.org/articles/PMC8844403; pdf:https://europepmc.org/articles/PMC8844403?pdf=render"
   },
+  {
+    "id": "33306713",
+    "doi": "https://doi.org/10.1371/journal.pone.0243383",
+    "title": "Health, educational and employment outcomes among children treated for a skin disorder: Scotland-wide retrospective record linkage cohort study of 766,244 children.",
+    "authorString": "Fleming M, McLay JS, Clark D, King A, Mackay DF, Pell JP.",
+    "authorAffiliations": "",
+    "journalTitle": "PloS one",
+    "pubYear": "2020",
+    "date": "2020-12-11",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>To compare health, educational and employment outcomes of schoolchildren receiving medication for a skin disorder with peers.<h4>Methods</h4>This retrospective population cohort study linked eight Scotland-wide databases, covering dispensed prescriptions, hospital admissions, maternity records, death certificates, annual pupil census, school examinations, school absences/exclusions and unemployment to investigate educational (absence, exclusion, special educational need, academic attainment), employment, and health (admissions and mortality) outcomes of 766,244 children attending local authority run primary, secondary and special schools in Scotland between 2009 and 2013.<h4>Results</h4>After adjusting for sociodemographic and maternity confounders the 130,087 (17.0%) children treated for a skin disorder had increased hospitalisation, particularly within one year of commencing treatment (IRR 1.38, 95% CI 1.35-1.41, p<0.001) and mortality (HR 1.50, 95% CI 1.18-1.90, p<0.001). They had greater special educational need (OR 1.19, 95% CI 1.17-1.21, p<0.001) and more frequent absences from school (IRR 1.07, 95% CI 1.06-1.08, p<0.001) but did not exhibit poorer exam attainment or increased post-school unemployment. The associations remained after further adjustment for comorbid chronic conditions.<h4>Conclusions</h4>Despite increased hospitalisation, school absenteeism, and special educational need, children treated for a skin disorder did not have poorer exam attainment or employment outcomes. Whilst findings relating to educational and employment outcomes are reassuring, the association with increased risk of mortality is alarming and merits further investigation.",
+    "laySummary": "",
+    "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0243383&type=printable; doi:https://doi.org/10.1371/journal.pone.0243383; html:https://europepmc.org/articles/PMC7732076; pdf:https://europepmc.org/articles/PMC7732076?pdf=render"
+  },
   {
     "id": "33659712",
     "doi": "https://doi.org/10.12688/wellcomeopenres.16431.2",
@@ -33625,23 +33659,6 @@
     "laySummary": "",
     "urls": "pdf:https://genomebiology.biomedcentral.com/counter/pdf/10.1186/s13059-021-02395-y; doi:https://doi.org/10.1186/s13059-021-02395-y; html:https://europepmc.org/articles/PMC8247108; pdf:https://europepmc.org/articles/PMC8247108?pdf=render"
   },
-  {
-    "id": "35047183",
-    "doi": "https://doi.org/10.7189/jogh.11.01011",
-    "title": "The COVID-19 pandemic in children and young people during 2020-2021: A complex discussion on vaccination.",
-    "authorString": "Rudan I, Adeloye D, Katikireddi V, Murray J, Simpson C, Shah SA, Robertson C, Sheikh A, EAVE II collaboration.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of global health",
-    "pubYear": "2021",
-    "date": "2021-12-25",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.7189/jogh.11.01011; doi:https://doi.org/10.7189/jogh.11.01011; html:https://europepmc.org/articles/PMC8763337; pdf:https://europepmc.org/articles/PMC8763337?pdf=render"
-  },
   {
     "id": "37755828",
     "doi": "https://doi.org/10.1001/jamanetworkopen.2023.36023",
@@ -33659,6 +33676,23 @@
     "laySummary": "",
     "urls": "pdf:https://jamanetwork.com/journals/jamanetworkopen/articlepdf/2809945/hansford_2023_oi_231035_1695236241.69575.pdf; doi:https://doi.org/10.1001/jamanetworkopen.2023.36023; html:https://europepmc.org/articles/PMC10534275"
   },
+  {
+    "id": "35047183",
+    "doi": "https://doi.org/10.7189/jogh.11.01011",
+    "title": "The COVID-19 pandemic in children and young people during 2020-2021: A complex discussion on vaccination.",
+    "authorString": "Rudan I, Adeloye D, Katikireddi V, Murray J, Simpson C, Shah SA, Robertson C, Sheikh A, EAVE II collaboration.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of global health",
+    "pubYear": "2021",
+    "date": "2021-12-25",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.7189/jogh.11.01011; doi:https://doi.org/10.7189/jogh.11.01011; html:https://europepmc.org/articles/PMC8763337; pdf:https://europepmc.org/articles/PMC8763337?pdf=render"
+  },
   {
     "id": "30102210",
     "doi": "https://doi.org/10.1016/s1470-2045(18)30425-x",
@@ -33693,6 +33727,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/s2589-7500(19)30012-3; doi:https://doi.org/10.1016/S2589-7500(19)30012-3; html:https://europepmc.org/articles/PMC6798263; pdf:https://europepmc.org/articles/PMC6798263?pdf=render"
   },
+  {
+    "id": "34345870",
+    "doi": "https://doi.org/10.1016/j.bbih.2021.100286",
+    "title": "The effects of genotype on inflammatory response in hippocampal progenitor cells: A computational approach.",
+    "authorString": "Lee H, Metz A, McDiarmid A, Palmos A, Lee SH, Curtis CJ, Patel H, Newhouse SJ, Thuret S.",
+    "authorAffiliations": "",
+    "journalTitle": "Brain, behavior, & immunity - health",
+    "pubYear": "2021",
+    "date": "2021-08-01",
+    "isOpenAccess": "Y",
+    "keywords": "Hippocampus; Neurogenesis; Inflammation; Neural stem cells; in vitro model; single nucleotide polymorphisms SNP; Eqtl; Gene Variants",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Cell culture models are valuable tools to study biological mechanisms underlying health and disease in a controlled environment. Although their genotype influences their phenotype, subtle genetic variations in cell lines are rarely characterised and taken into account for in vitro studies. To investigate how the genetic makeup of a cell line might affect the cellular response to inflammation, we characterised the single nucleotide variants (SNPs) relevant to inflammation-related genes in an established hippocampal progenitor cell line (HPC0A07/03C) that is frequently used as an in vitro model for hippocampal neurogenesis (HN). SNPs were identified using a genotyping array, and genes associated with chronic inflammatory and neuroinflammatory response gene ontology terms were retrieved using the AmiGO application. SNPs associated with these genes were then extracted from the genotyping dataset, for which a literature search was conducted, yielding relevant research articles for a total of 17 SNPs. Of these variants, 10 were found to potentially affect hippocampal neurogenesis whereby a majority (n=7) is likely to reduce neurogenesis under inflammatory conditions. Taken together, the existing literature seems to suggest that all stages of hippocampal neurogenesis could be negatively affected due to the genetic makeup in HPC0A07/03C cells under inflammation. Additional experiments will be needed to validate these specific findings in a laboratory setting. However, this computational approach already confirms that in vitro studies in general should control for cell lines subtle genetic variations which could mask or exacerbate findings.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.bbih.2021.100286; doi:https://doi.org/10.1016/j.bbih.2021.100286; html:https://europepmc.org/articles/PMC8261829; pdf:https://europepmc.org/articles/PMC8261829?pdf=render"
+  },
   {
     "id": "36100927",
     "doi": "https://doi.org/10.28920/dhm52.3.164-174",
@@ -33710,6 +33761,40 @@
     "laySummary": "",
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9536848; doi:https://doi.org/10.28920/dhm52.3.164-174; html:https://europepmc.org/articles/PMC9536848; pdf:https://europepmc.org/articles/PMC9536848?pdf=render; doi:https://doi.org/10.28920/dhm52.3.164-174"
   },
+  {
+    "id": "37339333",
+    "doi": "https://doi.org/10.1002/jia2.26104",
+    "title": "COVID-19 among adults living with HIV: correlates of mortality among public sector healthcare users in Western Cape, South Africa.",
+    "authorString": "Kassanjee R, Davies MA, Ngwenya O, Osei-Yeboah R, Jacobs T, Morden E, Timmerman V, Britz S, Mendelson M, Taljaard J, Riou J, Boulle A, Tiffin N, Zinyakatira N.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of the International AIDS Society",
+    "pubYear": "2023",
+    "date": "2023-06-01",
+    "isOpenAccess": "Y",
+    "keywords": "Mortality; HIV; South Africa; Cd4 Count; Covid-19; Sars-cov-2",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>While a large proportion of people with HIV (PWH) have experienced SARS-CoV-2 infections, there is uncertainty about the role of HIV disease severity on COVID-19 outcomes, especially in lower-income settings. We studied the association of mortality with characteristics of HIV severity and management, and vaccination, among adult PWH.<h4>Methods</h4>We analysed observational cohort data on all PWH aged \u226515 years experiencing a diagnosed SARS-CoV-2 infection (until March 2022), who accessed public sector healthcare in the Western Cape province of South Africa. Logistic regression was used to study the association of mortality with evidence of antiretroviral therapy (ART) collection, time since first HIV evidence, CD4 cell count, viral load (among those with evidence of ART collection) and COVID-19 vaccination, adjusting for demographic characteristics, comorbidities, admission pressure, location and time period.<h4>Results</h4>Mortality occurred in 5.7% (95% CI: 5.3,6.0) of 17,831 first-diagnosed infections. Higher mortality was associated with lower recent CD4, no evidence of ART collection, high or unknown recent viral load and recent first HIV evidence, differentially by age. Vaccination was protective. The burden of comorbidities was high, and tuberculosis (especially more recent episodes of tuberculosis), chronic kidney disease, diabetes and hypertension were associated with higher mortality, more strongly in younger adults.<h4>Conclusions</h4>Mortality was strongly associated with suboptimal HIV control, and the prevalence of these risk factors increased in later COVID-19 waves. It remains a public health priority to ensure PWH are on suppressive ART and vaccinated, and manage any disruptions in care that occurred during the pandemic. The diagnosis and management of comorbidities, including for tuberculosis, should be optimized.",
+    "laySummary": "",
+    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jia2.26104; doi:https://doi.org/10.1002/jia2.26104; html:https://europepmc.org/articles/PMC10281639; pdf:https://europepmc.org/articles/PMC10281639?pdf=render"
+  },
+  {
+    "id": "32212911",
+    "doi": "https://doi.org/10.1161/jaha.119.013684",
+    "title": "Prognostic significance of troponin level in 3121 patients presenting with atrial fibrillation (The NIHR Health Informatics Collaborative TROP-AF study).",
+    "authorString": "Kaura A, Arnold AD, Panoulas V, Glampson B, Davies J, Mulla A, Woods K, Omigie J, Shah AD, Channon KM, Weber JN, Thursz MR, Elliott P, Hemingway H, Williams B, Asselbergs FW, O'Sullivan M, Lord GM, Melikian N, Lefroy DC, Francis DP, Shah AM, Kharbanda R, Perera D, Patel RS, Mayet J.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of the American Heart Association",
+    "pubYear": "2020",
+    "date": "2020-03-26",
+    "isOpenAccess": "Y",
+    "keywords": "Troponin; Mortality; Atrial fibrillation; coronary artery disease; angiography",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Background Patients presenting with atrial fibrillation (AF) often undergo a blood test to measure troponin, but interpretation of the result is impeded by uncertainty about its clinical importance. We investigated the relationship between troponin level, coronary angiography, and all-cause mortality in real-world patients presenting with AF. Methods and Results We used National Institute of Health Research Health Informatics Collaborative data to identify patients admitted between 2010 and 2017 at 5 tertiary centers in the United Kingdom with a primary diagnosis of AF. Peak troponin results were scaled as multiples of the upper limit of normal. A total of 3121 patients were included in the analysis. Over a median follow-up of 1462 (interquartile range, 929-1975) days, there were 586 deaths (18.8%). The adjusted hazard ratio for mortality associated with a positive troponin (value above upper limit of normal) was 1.20 (95% CI, 1.01-1.43; <i>P</i><0.05). Higher troponin levels were associated with higher risk of mortality, reaching a maximum hazard ratio of 2.6 (95% CI, 1.9-3.4) at \u2248250 multiples of the upper limit of normal. There was an exponential relationship between higher troponin levels and increased odds of coronary angiography. The mortality risk was 36% lower in patients undergoing coronary angiography than in those who did not (adjusted hazard ratio, 0.61; 95% CI, 0.42-0.89; <i>P</i>=0.01). Conclusions Increased troponin was associated with increased risk of mortality in patients presenting with AF. The lower hazard ratio in patients undergoing invasive management raises the possibility that the clinical importance of troponin release in AF may be mediated by coronary artery disease, which may be responsive to revascularization.",
+    "laySummary": "",
+    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.119.013684; doi:https://doi.org/10.1161/JAHA.119.013684; html:https://europepmc.org/articles/PMC7428631; pdf:https://europepmc.org/articles/PMC7428631?pdf=render"
+  },
   {
     "id": "39414775",
     "doi": "https://doi.org/10.1038/s41467-024-53091-x",
@@ -33744,40 +33829,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41746-024-01062-3.pdf; doi:https://doi.org/10.1038/s41746-024-01062-3; html:https://europepmc.org/articles/PMC11015005; pdf:https://europepmc.org/articles/PMC11015005?pdf=render"
   },
-  {
-    "id": "34345870",
-    "doi": "https://doi.org/10.1016/j.bbih.2021.100286",
-    "title": "The effects of genotype on inflammatory response in hippocampal progenitor cells: A computational approach.",
-    "authorString": "Lee H, Metz A, McDiarmid A, Palmos A, Lee SH, Curtis CJ, Patel H, Newhouse SJ, Thuret S.",
-    "authorAffiliations": "",
-    "journalTitle": "Brain, behavior, & immunity - health",
-    "pubYear": "2021",
-    "date": "2021-08-01",
-    "isOpenAccess": "Y",
-    "keywords": "Hippocampus; Neurogenesis; Inflammation; Neural stem cells; in vitro model; single nucleotide polymorphisms SNP; Eqtl; Gene Variants",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Cell culture models are valuable tools to study biological mechanisms underlying health and disease in a controlled environment. Although their genotype influences their phenotype, subtle genetic variations in cell lines are rarely characterised and taken into account for in vitro studies. To investigate how the genetic makeup of a cell line might affect the cellular response to inflammation, we characterised the single nucleotide variants (SNPs) relevant to inflammation-related genes in an established hippocampal progenitor cell line (HPC0A07/03C) that is frequently used as an in vitro model for hippocampal neurogenesis (HN). SNPs were identified using a genotyping array, and genes associated with chronic inflammatory and neuroinflammatory response gene ontology terms were retrieved using the AmiGO application. SNPs associated with these genes were then extracted from the genotyping dataset, for which a literature search was conducted, yielding relevant research articles for a total of 17 SNPs. Of these variants, 10 were found to potentially affect hippocampal neurogenesis whereby a majority (n=7) is likely to reduce neurogenesis under inflammatory conditions. Taken together, the existing literature seems to suggest that all stages of hippocampal neurogenesis could be negatively affected due to the genetic makeup in HPC0A07/03C cells under inflammation. Additional experiments will be needed to validate these specific findings in a laboratory setting. However, this computational approach already confirms that in vitro studies in general should control for cell lines subtle genetic variations which could mask or exacerbate findings.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.bbih.2021.100286; doi:https://doi.org/10.1016/j.bbih.2021.100286; html:https://europepmc.org/articles/PMC8261829; pdf:https://europepmc.org/articles/PMC8261829?pdf=render"
-  },
-  {
-    "id": "37339333",
-    "doi": "https://doi.org/10.1002/jia2.26104",
-    "title": "COVID-19 among adults living with HIV: correlates of mortality among public sector healthcare users in Western Cape, South Africa.",
-    "authorString": "Kassanjee R, Davies MA, Ngwenya O, Osei-Yeboah R, Jacobs T, Morden E, Timmerman V, Britz S, Mendelson M, Taljaard J, Riou J, Boulle A, Tiffin N, Zinyakatira N.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of the International AIDS Society",
-    "pubYear": "2023",
-    "date": "2023-06-01",
-    "isOpenAccess": "Y",
-    "keywords": "Mortality; HIV; South Africa; Cd4 Count; Covid-19; Sars-cov-2",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>While a large proportion of people with HIV (PWH) have experienced SARS-CoV-2 infections, there is uncertainty about the role of HIV disease severity on COVID-19 outcomes, especially in lower-income settings. We studied the association of mortality with characteristics of HIV severity and management, and vaccination, among adult PWH.<h4>Methods</h4>We analysed observational cohort data on all PWH aged \u226515 years experiencing a diagnosed SARS-CoV-2 infection (until March 2022), who accessed public sector healthcare in the Western Cape province of South Africa. Logistic regression was used to study the association of mortality with evidence of antiretroviral therapy (ART) collection, time since first HIV evidence, CD4 cell count, viral load (among those with evidence of ART collection) and COVID-19 vaccination, adjusting for demographic characteristics, comorbidities, admission pressure, location and time period.<h4>Results</h4>Mortality occurred in 5.7% (95% CI: 5.3,6.0) of 17,831 first-diagnosed infections. Higher mortality was associated with lower recent CD4, no evidence of ART collection, high or unknown recent viral load and recent first HIV evidence, differentially by age. Vaccination was protective. The burden of comorbidities was high, and tuberculosis (especially more recent episodes of tuberculosis), chronic kidney disease, diabetes and hypertension were associated with higher mortality, more strongly in younger adults.<h4>Conclusions</h4>Mortality was strongly associated with suboptimal HIV control, and the prevalence of these risk factors increased in later COVID-19 waves. It remains a public health priority to ensure PWH are on suppressive ART and vaccinated, and manage any disruptions in care that occurred during the pandemic. The diagnosis and management of comorbidities, including for tuberculosis, should be optimized.",
-    "laySummary": "",
-    "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jia2.26104; doi:https://doi.org/10.1002/jia2.26104; html:https://europepmc.org/articles/PMC10281639; pdf:https://europepmc.org/articles/PMC10281639?pdf=render"
-  },
   {
     "id": "35045937",
     "doi": "https://doi.org/10.1016/j.amjcard.2021.12.022",
@@ -33796,21 +33847,21 @@
     "urls": "pdf:http://www.ajconline.org/article/S0002914921012418/pdf; doi:https://doi.org/10.1016/j.amjcard.2021.12.022"
   },
   {
-    "id": "32212911",
-    "doi": "https://doi.org/10.1161/jaha.119.013684",
-    "title": "Prognostic significance of troponin level in 3121 patients presenting with atrial fibrillation (The NIHR Health Informatics Collaborative TROP-AF study).",
-    "authorString": "Kaura A, Arnold AD, Panoulas V, Glampson B, Davies J, Mulla A, Woods K, Omigie J, Shah AD, Channon KM, Weber JN, Thursz MR, Elliott P, Hemingway H, Williams B, Asselbergs FW, O'Sullivan M, Lord GM, Melikian N, Lefroy DC, Francis DP, Shah AM, Kharbanda R, Perera D, Patel RS, Mayet J.",
+    "id": "33928785",
+    "doi": "https://doi.org/10.1161/circulationaha.120.049844",
+    "title": "Unfolded Protein Response as a Compensatory Mechanism and Potential Therapeutic Target in PLN R14del Cardiomyopathy.",
+    "authorString": "Feyen DAM, Perea-Gil I, Maas RGC, Harakalova M, Gavidia AA, Arthur Ataam J, Wu TH, Vink A, Pei J, Vadgama N, Suurmeijer AJ, Te Rijdt WP, Vu M, Amatya PL, Prado M, Zhang Y, Dunkenberger L, Sluijter JPG, Sallam K, Asselbergs FW, Mercola M, Karakikes I.",
     "authorAffiliations": "",
-    "journalTitle": "Journal of the American Heart Association",
-    "pubYear": "2020",
-    "date": "2020-03-26",
-    "isOpenAccess": "Y",
-    "keywords": "Troponin; Mortality; Atrial fibrillation; coronary artery disease; angiography",
+    "journalTitle": "Circulation",
+    "pubYear": "2021",
+    "date": "2021-04-30",
+    "isOpenAccess": "N",
+    "keywords": "Unfolded protein response; Models, Biological; Induced Pluripotent Stem Cells; Phospholamban; Cardiomyopathy, Dilated; Sequence Analysis, Rna",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Background Patients presenting with atrial fibrillation (AF) often undergo a blood test to measure troponin, but interpretation of the result is impeded by uncertainty about its clinical importance. We investigated the relationship between troponin level, coronary angiography, and all-cause mortality in real-world patients presenting with AF. Methods and Results We used National Institute of Health Research Health Informatics Collaborative data to identify patients admitted between 2010 and 2017 at 5 tertiary centers in the United Kingdom with a primary diagnosis of AF. Peak troponin results were scaled as multiples of the upper limit of normal. A total of 3121 patients were included in the analysis. Over a median follow-up of 1462 (interquartile range, 929-1975) days, there were 586 deaths (18.8%). The adjusted hazard ratio for mortality associated with a positive troponin (value above upper limit of normal) was 1.20 (95% CI, 1.01-1.43; <i>P</i><0.05). Higher troponin levels were associated with higher risk of mortality, reaching a maximum hazard ratio of 2.6 (95% CI, 1.9-3.4) at \u2248250 multiples of the upper limit of normal. There was an exponential relationship between higher troponin levels and increased odds of coronary angiography. The mortality risk was 36% lower in patients undergoing coronary angiography than in those who did not (adjusted hazard ratio, 0.61; 95% CI, 0.42-0.89; <i>P</i>=0.01). Conclusions Increased troponin was associated with increased risk of mortality in patients presenting with AF. The lower hazard ratio in patients undergoing invasive management raises the possibility that the clinical importance of troponin release in AF may be mediated by coronary artery disease, which may be responsive to revascularization.",
+    "abstract": "<h4>Background</h4>Phospholamban (PLN) is a critical regulator of calcium cycling and contractility in the heart. The loss of arginine at position 14 in PLN (R14del) is associated with dilated cardiomyopathy with a high prevalence of ventricular arrhythmias. How the R14 deletion causes dilated cardiomyopathy is poorly understood, and there are no disease-specific therapies.<h4>Methods</h4>We used single-cell RNA sequencing to uncover PLN R14del disease mechanisms in human induced pluripotent stem cells (hiPSC-CMs). We used both 2-dimensional and 3-dimensional functional contractility assays to evaluate the impact of modulating disease-relevant pathways in PLN R14del hiPSC-CMs.<h4>Results</h4>Modeling of the PLN R14del cardiomyopathy with isogenic pairs of hiPSC-CMs recapitulated the contractile deficit associated with the disease in vitro. Single-cell RNA sequencing revealed the induction of the unfolded protein response (UPR) pathway in PLN R14del compared with isogenic control hiPSC-CMs. The activation of UPR was also evident in the hearts from PLN R14del patients. Silencing of each of the 3 main UPR signaling branches (IRE1, ATF6, or PERK) by siRNA exacerbated the contractile dysfunction of PLN R14del hiPSC-CMs. We explored the therapeutic potential of activating the UPR with a small molecule activator, BiP (binding immunoglobulin protein) inducer X. PLN R14del hiPSC-CMs treated with BiP protein inducer X showed a dose-dependent amelioration of the contractility deficit in both 2-dimensional cultures and 3-dimensional engineered heart tissues without affecting calcium homeostasis.<h4>Conclusions</h4>Together, these findings suggest that the UPR exerts a protective effect in the setting of PLN R14del cardiomyopathy and that modulation of the UPR might be exploited therapeutically.",
     "laySummary": "",
-    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.119.013684; doi:https://doi.org/10.1161/JAHA.119.013684; html:https://europepmc.org/articles/PMC7428631; pdf:https://europepmc.org/articles/PMC7428631?pdf=render"
+    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCULATIONAHA.120.049844; doi:https://doi.org/10.1161/CIRCULATIONAHA.120.049844; html:https://europepmc.org/articles/PMC8667423; pdf:https://europepmc.org/articles/PMC8667423?pdf=render; doi:https://doi.org/10.1161/circulationaha.120.049844"
   },
   {
     "id": "36869930",
@@ -33829,23 +33880,6 @@
     "laySummary": "",
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s00520-023-07633-6.pdf; doi:https://doi.org/10.1007/s00520-023-07633-6; html:https://europepmc.org/articles/PMC9985568; pdf:https://europepmc.org/articles/PMC9985568?pdf=render"
   },
-  {
-    "id": "33928785",
-    "doi": "https://doi.org/10.1161/circulationaha.120.049844",
-    "title": "Unfolded Protein Response as a Compensatory Mechanism and Potential Therapeutic Target in PLN R14del Cardiomyopathy.",
-    "authorString": "Feyen DAM, Perea-Gil I, Maas RGC, Harakalova M, Gavidia AA, Arthur Ataam J, Wu TH, Vink A, Pei J, Vadgama N, Suurmeijer AJ, Te Rijdt WP, Vu M, Amatya PL, Prado M, Zhang Y, Dunkenberger L, Sluijter JPG, Sallam K, Asselbergs FW, Mercola M, Karakikes I.",
-    "authorAffiliations": "",
-    "journalTitle": "Circulation",
-    "pubYear": "2021",
-    "date": "2021-04-30",
-    "isOpenAccess": "N",
-    "keywords": "Unfolded protein response; Models, Biological; Induced Pluripotent Stem Cells; Phospholamban; Cardiomyopathy, Dilated; Sequence Analysis, Rna",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Phospholamban (PLN) is a critical regulator of calcium cycling and contractility in the heart. The loss of arginine at position 14 in PLN (R14del) is associated with dilated cardiomyopathy with a high prevalence of ventricular arrhythmias. How the R14 deletion causes dilated cardiomyopathy is poorly understood, and there are no disease-specific therapies.<h4>Methods</h4>We used single-cell RNA sequencing to uncover PLN R14del disease mechanisms in human induced pluripotent stem cells (hiPSC-CMs). We used both 2-dimensional and 3-dimensional functional contractility assays to evaluate the impact of modulating disease-relevant pathways in PLN R14del hiPSC-CMs.<h4>Results</h4>Modeling of the PLN R14del cardiomyopathy with isogenic pairs of hiPSC-CMs recapitulated the contractile deficit associated with the disease in vitro. Single-cell RNA sequencing revealed the induction of the unfolded protein response (UPR) pathway in PLN R14del compared with isogenic control hiPSC-CMs. The activation of UPR was also evident in the hearts from PLN R14del patients. Silencing of each of the 3 main UPR signaling branches (IRE1, ATF6, or PERK) by siRNA exacerbated the contractile dysfunction of PLN R14del hiPSC-CMs. We explored the therapeutic potential of activating the UPR with a small molecule activator, BiP (binding immunoglobulin protein) inducer X. PLN R14del hiPSC-CMs treated with BiP protein inducer X showed a dose-dependent amelioration of the contractility deficit in both 2-dimensional cultures and 3-dimensional engineered heart tissues without affecting calcium homeostasis.<h4>Conclusions</h4>Together, these findings suggest that the UPR exerts a protective effect in the setting of PLN R14del cardiomyopathy and that modulation of the UPR might be exploited therapeutically.",
-    "laySummary": "",
-    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCULATIONAHA.120.049844; doi:https://doi.org/10.1161/CIRCULATIONAHA.120.049844; html:https://europepmc.org/articles/PMC8667423; pdf:https://europepmc.org/articles/PMC8667423?pdf=render; doi:https://doi.org/10.1161/circulationaha.120.049844"
-  },
   {
     "id": "38352035",
     "doi": "https://doi.org/10.26633/rpsp.2024.13",
@@ -33948,23 +33982,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.karger.com/Article/Pdf/517521; doi:https://doi.org/10.1159/000517521"
   },
-  {
-    "id": "36343994",
-    "doi": "https://doi.org/10.1136/bmjopen-2022-063159",
-    "title": "Demographic, behavioural and occupational risk factors associated with SARS-CoV-2 infection in UK healthcare workers: a retrospective observational study.",
-    "authorString": "Cooper DJ, Lear S, Sithole N, Shaw A, Stark H, Ferris M, CITIID-NIHR BioResource COVID-19 collaboration consortium, Bradley J, Maxwell P, Goodfellow I, Weekes MP, Seaman S, Baker S.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2022",
-    "date": "2022-11-07",
-    "isOpenAccess": "Y",
-    "keywords": "Infection control; epidemiology; Public Health; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objective</h4>Healthcare workers (HCWs) are at higher risk of SARS-CoV-2 infection than the general population. This group is pivotal to healthcare system resilience during the COVID-19, and future, pandemics. We investigated demographic, social, behavioural and occupational risk factors for SARS-CoV-2 infection among HCWs.<h4>Design/setting/participants</h4>HCWs enrolled in a large-scale sero-epidemiological study at a UK university teaching hospital were sent questionnaires spanning a 5-month period from March to July 2020. In a retrospective observational cohort study, univariate logistic regression was used to assess factors associated with SARS-CoV-2 infection. A Least Absolute Shrinkage Selection Operator regression model was used to identify variables to include in a multivariate logistic regression model.<h4>Results</h4>Among 2258 HCWs, highest ORs associated with SARS-CoV-2 antibody seropositivity on multivariate analysis were having a household member previously testing positive for SARS-CoV-2 antibodies (OR 6.94 (95% CI 4.15 to 11.6); p&lt;0.0001) and being of black ethnicity (6.21 (95% CI 2.69 to 14.3); p&lt;0.0001). Occupational factors associated with a higher risk of seropositivity included working as a physiotherapist (OR 2.78 (95% CI 1.21 to 6.36); p=0.015) and working predominantly in acute medicine (OR 2.72 (95% CI 1.57 to 4.69); p&lt;0.0001) or medical subspecialties (not including infectious diseases) (OR 2.33 (95% CI 1.4 to 3.88); p=0.001). Reporting that adequate personal protective equipment (PPE) was 'rarely' available had an OR of 2.83 (95% CI 1.29 to 6.25; p=0.01). Reporting attending a handover where social distancing was not possible had an OR of 1.39 (95% CI 1.02 to 1.9; p=0.038).<h4>Conclusions</h4>The emergence of SARS-CoV-2 variants and potential vaccine escape continue to threaten stability of healthcare systems worldwide, and sustained vigilance against HCW infection remains a priority. Enhanced risk assessments should be considered for HCWs of black ethnicity, physiotherapists and those working in acute medicine or medical subspecialties. Workplace risk reduction measures include ongoing access to high-quality PPE and effective social distancing measures.",
-    "laySummary": "",
-    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/11/e063159.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-063159; html:https://europepmc.org/articles/PMC9644078; pdf:https://europepmc.org/articles/PMC9644078?pdf=render"
-  },
   {
     "id": "38280393",
     "doi": "https://doi.org/10.1016/s2352-3018(23)00272-2",
@@ -33999,6 +34016,23 @@
     "laySummary": "",
     "urls": "pdf:https://pure.rug.nl/ws/files/89611268/Manduchi_et_al_2019_Genetic_Epidemiology.pdf; doi:https://doi.org/10.1002/gepi.22215; html:https://europepmc.org/articles/PMC6687530; pdf:https://europepmc.org/articles/PMC6687530?pdf=render; doi:https://doi.org/10.1002/gepi.22215"
   },
+  {
+    "id": "36343994",
+    "doi": "https://doi.org/10.1136/bmjopen-2022-063159",
+    "title": "Demographic, behavioural and occupational risk factors associated with SARS-CoV-2 infection in UK healthcare workers: a retrospective observational study.",
+    "authorString": "Cooper DJ, Lear S, Sithole N, Shaw A, Stark H, Ferris M, CITIID-NIHR BioResource COVID-19 collaboration consortium, Bradley J, Maxwell P, Goodfellow I, Weekes MP, Seaman S, Baker S.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2022",
+    "date": "2022-11-07",
+    "isOpenAccess": "Y",
+    "keywords": "Infection control; epidemiology; Public Health; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>Healthcare workers (HCWs) are at higher risk of SARS-CoV-2 infection than the general population. This group is pivotal to healthcare system resilience during the COVID-19, and future, pandemics. We investigated demographic, social, behavioural and occupational risk factors for SARS-CoV-2 infection among HCWs.<h4>Design/setting/participants</h4>HCWs enrolled in a large-scale sero-epidemiological study at a UK university teaching hospital were sent questionnaires spanning a 5-month period from March to July 2020. In a retrospective observational cohort study, univariate logistic regression was used to assess factors associated with SARS-CoV-2 infection. A Least Absolute Shrinkage Selection Operator regression model was used to identify variables to include in a multivariate logistic regression model.<h4>Results</h4>Among 2258 HCWs, highest ORs associated with SARS-CoV-2 antibody seropositivity on multivariate analysis were having a household member previously testing positive for SARS-CoV-2 antibodies (OR 6.94 (95% CI 4.15 to 11.6); p&lt;0.0001) and being of black ethnicity (6.21 (95% CI 2.69 to 14.3); p&lt;0.0001). Occupational factors associated with a higher risk of seropositivity included working as a physiotherapist (OR 2.78 (95% CI 1.21 to 6.36); p=0.015) and working predominantly in acute medicine (OR 2.72 (95% CI 1.57 to 4.69); p&lt;0.0001) or medical subspecialties (not including infectious diseases) (OR 2.33 (95% CI 1.4 to 3.88); p=0.001). Reporting that adequate personal protective equipment (PPE) was 'rarely' available had an OR of 2.83 (95% CI 1.29 to 6.25; p=0.01). Reporting attending a handover where social distancing was not possible had an OR of 1.39 (95% CI 1.02 to 1.9; p=0.038).<h4>Conclusions</h4>The emergence of SARS-CoV-2 variants and potential vaccine escape continue to threaten stability of healthcare systems worldwide, and sustained vigilance against HCW infection remains a priority. Enhanced risk assessments should be considered for HCWs of black ethnicity, physiotherapists and those working in acute medicine or medical subspecialties. Workplace risk reduction measures include ongoing access to high-quality PPE and effective social distancing measures.",
+    "laySummary": "",
+    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/11/e063159.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-063159; html:https://europepmc.org/articles/PMC9644078; pdf:https://europepmc.org/articles/PMC9644078?pdf=render"
+  },
   {
     "id": "31863937",
     "doi": "https://doi.org/10.1016/j.aap.2019.105333",
@@ -34050,6 +34084,23 @@
     "laySummary": "",
     "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/0141076820961776; doi:https://doi.org/10.1177/0141076820961776; html:https://europepmc.org/articles/PMC7809339; pdf:https://europepmc.org/articles/PMC7809339?pdf=render"
   },
+  {
+    "id": "33323251",
+    "doi": "https://doi.org/10.1016/s2589-7500(19)30123-2",
+    "title": "A comparison of deep learning performance against health-care professionals in detecting diseases from medical imaging: a systematic review and meta-analysis.",
+    "authorString": "Liu X, Faes L, Kale AU, Wagner SK, Fu DJ, Bruynseels A, Mahendiran T, Moraes G, Shamdas M, Kern C, Ledsam JR, Schmid MK, Balaskas K, Topol EJ, Bachmann LM, Keane PA, Denniston AK.",
+    "authorAffiliations": "",
+    "journalTitle": "The Lancet. Digital health",
+    "pubYear": "2019",
+    "date": "2019-09-25",
+    "isOpenAccess": "N",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Deep learning offers considerable promise for medical diagnostics. We aimed to evaluate the diagnostic accuracy of deep learning algorithms versus health-care professionals in classifying diseases using medical imaging.<h4>Methods</h4>In this systematic review and meta-analysis, we searched Ovid-MEDLINE, Embase, Science Citation Index, and Conference Proceedings Citation Index for studies published from Jan 1, 2012, to June 6, 2019. Studies comparing the diagnostic performance of deep learning models and health-care professionals based on medical imaging, for any disease, were included. We excluded studies that used medical waveform data graphics material or investigated the accuracy of image segmentation rather than disease classification. We extracted binary diagnostic accuracy data and constructed contingency tables to derive the outcomes of interest: sensitivity and specificity. Studies undertaking an out-of-sample external validation were included in a meta-analysis, using a unified hierarchical model. This study is registered with PROSPERO, CRD42018091176.<h4>Findings</h4>Our search identified 31\u2008587 studies, of which 82 (describing 147 patient cohorts) were included. 69 studies provided enough data to construct contingency tables, enabling calculation of test accuracy, with sensitivity ranging from 9\u00b77% to 100\u00b70% (mean 79\u00b71%, SD 0\u00b72) and specificity ranging from 38\u00b79% to 100\u00b70% (mean 88\u00b73%, SD 0\u00b71). An out-of-sample external validation was done in 25 studies, of which 14 made the comparison between deep learning models and health-care professionals in the same sample. Comparison of the performance between health-care professionals in these 14 studies, when restricting the analysis to the contingency table for each study reporting the highest accuracy, found a pooled sensitivity of 87\u00b70% (95% CI 83\u00b70-90\u00b72) for deep learning models and 86\u00b74% (79\u00b79-91\u00b70) for health-care professionals, and a pooled specificity of 92\u00b75% (95% CI 85\u00b71-96\u00b74) for deep learning models and 90\u00b75% (80\u00b76-95\u00b77) for health-care professionals.<h4>Interpretation</h4>Our review found the diagnostic performance of deep learning models to be equivalent to that of health-care professionals. However, a major finding of the review is that few studies presented externally validated results or compared the performance of deep learning models and health-care professionals using the same sample. Additionally, poor reporting is prevalent in deep learning studies, which limits reliable interpretation of the reported diagnostic accuracy. New reporting standards that address specific challenges of deep learning could improve future studies, enabling greater confidence in the results of future evaluations of this promising technology.<h4>Funding</h4>None.",
+    "laySummary": "",
+    "urls": "pdf:http://www.thelancet.com/article/S2589750019301232/pdf; doi:https://doi.org/10.1016/S2589-7500(19)30123-2"
+  },
   {
     "id": "38351061",
     "doi": "https://doi.org/10.1038/s41467-024-45419-4",
@@ -34068,21 +34119,21 @@
     "urls": "pdf:https://www.nature.com/articles/s41467-024-45419-4.pdf; doi:https://doi.org/10.1038/s41467-024-45419-4; html:https://europepmc.org/articles/PMC10864358; pdf:https://europepmc.org/articles/PMC10864358?pdf=render"
   },
   {
-    "id": "33323251",
-    "doi": "https://doi.org/10.1016/s2589-7500(19)30123-2",
-    "title": "A comparison of deep learning performance against health-care professionals in detecting diseases from medical imaging: a systematic review and meta-analysis.",
-    "authorString": "Liu X, Faes L, Kale AU, Wagner SK, Fu DJ, Bruynseels A, Mahendiran T, Moraes G, Shamdas M, Kern C, Ledsam JR, Schmid MK, Balaskas K, Topol EJ, Bachmann LM, Keane PA, Denniston AK.",
+    "id": "32619549",
+    "doi": "https://doi.org/10.1016/j.cels.2020.05.012",
+    "title": "Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection.",
+    "authorString": "Messner CB, Demichev V, Wendisch D, Michalick L, White M, Freiwald A, Textoris-Taube K, Vernardis SI, Egger AS, Kreidl M, Ludwig D, Kilian C, Agostini F, Zelezniak A, Thibeault C, Pfeiffer M, Hippenstiel S, Hocke A, von Kalle C, Campbell A, Hayward C, Porteous DJ, Marioni RE, Langenberg C, Lilley KS, Kuebler WM, M\u00fclleder M, Drosten C, Suttorp N, Witzenrath M, Kurth F, Sander LE, Ralser M.",
     "authorAffiliations": "",
-    "journalTitle": "The Lancet. Digital health",
-    "pubYear": "2019",
-    "date": "2019-09-25",
-    "isOpenAccess": "N",
-    "keywords": "",
+    "journalTitle": "Cell systems",
+    "pubYear": "2020",
+    "date": "2020-06-02",
+    "isOpenAccess": "Y",
+    "keywords": "Mass spectrometry; High-throughput Proteomics; Swath-ms; Antiviral Immune Response; Clinical Classifiers; Covid-19 Infection",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Deep learning offers considerable promise for medical diagnostics. We aimed to evaluate the diagnostic accuracy of deep learning algorithms versus health-care professionals in classifying diseases using medical imaging.<h4>Methods</h4>In this systematic review and meta-analysis, we searched Ovid-MEDLINE, Embase, Science Citation Index, and Conference Proceedings Citation Index for studies published from Jan 1, 2012, to June 6, 2019. Studies comparing the diagnostic performance of deep learning models and health-care professionals based on medical imaging, for any disease, were included. We excluded studies that used medical waveform data graphics material or investigated the accuracy of image segmentation rather than disease classification. We extracted binary diagnostic accuracy data and constructed contingency tables to derive the outcomes of interest: sensitivity and specificity. Studies undertaking an out-of-sample external validation were included in a meta-analysis, using a unified hierarchical model. This study is registered with PROSPERO, CRD42018091176.<h4>Findings</h4>Our search identified 31\u2008587 studies, of which 82 (describing 147 patient cohorts) were included. 69 studies provided enough data to construct contingency tables, enabling calculation of test accuracy, with sensitivity ranging from 9\u00b77% to 100\u00b70% (mean 79\u00b71%, SD 0\u00b72) and specificity ranging from 38\u00b79% to 100\u00b70% (mean 88\u00b73%, SD 0\u00b71). An out-of-sample external validation was done in 25 studies, of which 14 made the comparison between deep learning models and health-care professionals in the same sample. Comparison of the performance between health-care professionals in these 14 studies, when restricting the analysis to the contingency table for each study reporting the highest accuracy, found a pooled sensitivity of 87\u00b70% (95% CI 83\u00b70-90\u00b72) for deep learning models and 86\u00b74% (79\u00b79-91\u00b70) for health-care professionals, and a pooled specificity of 92\u00b75% (95% CI 85\u00b71-96\u00b74) for deep learning models and 90\u00b75% (80\u00b76-95\u00b77) for health-care professionals.<h4>Interpretation</h4>Our review found the diagnostic performance of deep learning models to be equivalent to that of health-care professionals. However, a major finding of the review is that few studies presented externally validated results or compared the performance of deep learning models and health-care professionals using the same sample. Additionally, poor reporting is prevalent in deep learning studies, which limits reliable interpretation of the reported diagnostic accuracy. New reporting standards that address specific challenges of deep learning could improve future studies, enabling greater confidence in the results of future evaluations of this promising technology.<h4>Funding</h4>None.",
+    "abstract": "The COVID-19 pandemic is an unprecedented global challenge, and point-of-care diagnostic classifiers are urgently required. Here, we present a platform for ultra-high-throughput serum and plasma proteomics that builds on ISO13485 standardization to facilitate simple implementation in regulated clinical laboratories. Our low-cost workflow handles up to 180 samples per day, enables high precision quantification, and reduces batch effects for large-scale and longitudinal studies. We use our platform on samples collected from a cohort of early hospitalized cases of the SARS-CoV-2 pandemic and identify 27 potential biomarkers that are differentially expressed depending on the WHO severity grade of COVID-19. They include complement factors, the coagulation system, inflammation modulators, and pro-inflammatory factors upstream and downstream of interleukin 6. All protocols and software for implementing our approach are freely available. In total, this work supports the development of routine proteomic assays to aid clinical decision making and generate hypotheses about potential COVID-19 therapeutic targets.",
     "laySummary": "",
-    "urls": "pdf:http://www.thelancet.com/article/S2589750019301232/pdf; doi:https://doi.org/10.1016/S2589-7500(19)30123-2"
+    "urls": "pdf:http://www.cell.com/article/S2405471220301976/pdf; doi:https://doi.org/10.1016/j.cels.2020.05.012; html:https://europepmc.org/articles/PMC7264033"
   },
   {
     "id": "36093379",
@@ -34102,21 +34153,38 @@
     "urls": "pdf:http://www.cell.com/article/S2589004222013517/pdf; doi:https://doi.org/10.1016/j.isci.2022.105079; html:https://europepmc.org/articles/PMC9441477; pdf:https://europepmc.org/articles/PMC9441477?pdf=render"
   },
   {
-    "id": "32619549",
-    "doi": "https://doi.org/10.1016/j.cels.2020.05.012",
-    "title": "Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection.",
-    "authorString": "Messner CB, Demichev V, Wendisch D, Michalick L, White M, Freiwald A, Textoris-Taube K, Vernardis SI, Egger AS, Kreidl M, Ludwig D, Kilian C, Agostini F, Zelezniak A, Thibeault C, Pfeiffer M, Hippenstiel S, Hocke A, von Kalle C, Campbell A, Hayward C, Porteous DJ, Marioni RE, Langenberg C, Lilley KS, Kuebler WM, M\u00fclleder M, Drosten C, Suttorp N, Witzenrath M, Kurth F, Sander LE, Ralser M.",
+    "id": "32255392",
+    "doi": "https://doi.org/10.1080/09273948.2019.1709650",
+    "title": "Non-invasive Instrument-Based Tests for Quantifying Anterior Chamber Flare in Uveitis: A Systematic Review.",
+    "authorString": "Liu X, McNally TW, Beese S, Downie LE, Solebo AL, Faes L, Husain S, Keane PA, Moore DJ, Denniston AK.",
     "authorAffiliations": "",
-    "journalTitle": "Cell systems",
-    "pubYear": "2020",
-    "date": "2020-06-02",
+    "journalTitle": "Ocular immunology and inflammation",
+    "pubYear": "2021",
+    "date": "2020-04-07",
+    "isOpenAccess": "N",
+    "keywords": "Diagnostic test; Systematic review; Uveitis; optical coherence tomography; Laser Flare Photometry; Anterior Chamber Flare; Tyndall Effect; Aqueous Humor, Aqueous Humour; Aqueous Protein Concentration",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<b>Purpose</b>: Anterior chamber (AC) flare is a key sign for anterior uveitis. New instrument-based techniques for measuring AC flare can offer automation and objectivity. This review aims to identify objective instrument-based measures for AC flare.<b>Methods</b>: In this systematic review, we identified studies reporting correlation between instrument-based tests versus clinician AC flare grading, and/or aqueous protein concentration, as well as test reliability.<b>Results</b>: Four index tests were identified in 11 studies: laser-flare photometry (LFP), optical coherence tomography, ocular flare analysis meter (OFAM) and the double-pass technique. The correlation between LFP and clinician grading was 0.40-0.93 and 0.87-0.94 for LFP and protein concentration. The double-pass technique showed no correlation with clinician grading and insufficient information was available for OFAM.<b>Conclusion</b>: LFP shows moderate to strong correlation with clinician grading and aqueous protein concentration. LFP could be a superior reference test compared to clinician AC flare grading for validating new index tests.",
+    "laySummary": "",
+    "urls": "pdf:https://discovery.ucl.ac.uk/10097154/3/Solebo_Liu%20AC%20Flare%20SR%20290919.pdf; doi:https://doi.org/10.1080/09273948.2019.1709650"
+  },
+  {
+    "id": "35434685",
+    "doi": "https://doi.org/10.1016/j.lanepe.2022.100381",
+    "title": "Dosing interval strategies for two-dose COVID-19 vaccination in 13 middle-income countries of Europe: Health impact modelling and benefit-risk analysis.",
+    "authorString": "Liu Y, Pearson CAB, Sandmann FG, Barnard RC, Kim JH, CMMID COVID-19 Working Group, Flasche S, Jit M, Abbas K.",
+    "authorAffiliations": "",
+    "journalTitle": "The Lancet regional health. Europe",
+    "pubYear": "2022",
+    "date": "2022-04-11",
     "isOpenAccess": "Y",
-    "keywords": "Mass spectrometry; High-throughput Proteomics; Swath-ms; Antiviral Immune Response; Clinical Classifiers; Covid-19 Infection",
+    "keywords": "Quantitative Methods; Mathematical Modelling; Public Health Intervention; Vaccine Policy; Ve, Vaccine Efficacy; Covid-19; Sars-cov-2; Voc, Variant Of Concern; Aefi, Adverse Events Following Immunisation; Mic, Middle Income Country",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "The COVID-19 pandemic is an unprecedented global challenge, and point-of-care diagnostic classifiers are urgently required. Here, we present a platform for ultra-high-throughput serum and plasma proteomics that builds on ISO13485 standardization to facilitate simple implementation in regulated clinical laboratories. Our low-cost workflow handles up to 180 samples per day, enables high precision quantification, and reduces batch effects for large-scale and longitudinal studies. We use our platform on samples collected from a cohort of early hospitalized cases of the SARS-CoV-2 pandemic and identify 27 potential biomarkers that are differentially expressed depending on the WHO severity grade of COVID-19. They include complement factors, the coagulation system, inflammation modulators, and pro-inflammatory factors upstream and downstream of interleukin 6. All protocols and software for implementing our approach are freely available. In total, this work supports the development of routine proteomic assays to aid clinical decision making and generate hypotheses about potential COVID-19 therapeutic targets.",
+    "abstract": "<h4>Background</h4>In settings where the COVID-19 vaccine supply is constrained, extending the intervals between the first and second doses of the COVID-19 vaccine may allow more people receive their first doses earlier. Our aim is to estimate the health impact of COVID-19 vaccination alongside benefit-risk assessment of different dosing intervals in 13 middle-income countries (MICs) of Europe.<h4>Methods</h4>We fitted a dynamic transmission model to country-level daily reported COVID-19 mortality in 13 MICs in Europe (Albania, Armenia, Azerbaijan, Belarus, Bosnia and Herzegovina, Bulgaria, Georgia, Republic of Moldova, Russian Federation, Serbia, North Macedonia, Turkey, and Ukraine). A vaccine product with characteristics similar to those of the Oxford/AstraZeneca COVID-19 (AZD1222) vaccine was used in the base case scenario and was complemented by sensitivity analyses around efficacies similar to other COVID-19 vaccines. Both fixed dosing intervals at 4, 8, 12, 16, and 20 weeks and dose-specific intervals that prioritise specific doses for certain age groups were tested. Optimal intervals minimise COVID-19 mortality between March 2021 and December 2022. We incorporated the emergence of variants of concern (VOCs) into the model and conducted a benefit-risk assessment to quantify the tradeoff between health benefits versus adverse events following immunisation.<h4>Findings</h4>In all countries modelled, optimal strategies are those that prioritise the first doses among older adults (60+ years) or adults (20+ years), which lead to dosing intervals longer than six months. In comparison, a four-week fixed dosing interval may incur 10.1% [range: 4.3% - 19.0%; n\u00a0=\u00a013 (countries)] more deaths. The rapid waning of the immunity induced by the first dose (i.e. with means ranging 60-120 days as opposed to 360 days in the base case) resulted in shorter optimal dosing intervals of 8-20 weeks. Benefit-risk ratios were the highest for fixed dosing intervals of 8-12 weeks.<h4>Interpretation</h4>We infer that longer dosing intervals of over six months could reduce COVID-19 mortality in MICs of Europe. Certain parameters, such as rapid waning of first-dose induced immunity and increased immune escape through the emergence of VOCs, could significantly shorten the optimal dosing intervals.<h4>Funding</h4>World Health Organization.",
     "laySummary": "",
-    "urls": "pdf:http://www.cell.com/article/S2405471220301976/pdf; doi:https://doi.org/10.1016/j.cels.2020.05.012; html:https://europepmc.org/articles/PMC7264033"
+    "urls": "doi:https://doi.org/10.1016/j.lanepe.2022.100381; doi:https://doi.org/10.1016/j.lanepe.2022.100381; html:https://europepmc.org/articles/PMC8996067; pdf:https://europepmc.org/articles/PMC8996067?pdf=render"
   },
   {
     "id": "38082486",
@@ -34152,40 +34220,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/mbe/advance-article-pdf/doi/10.1093/molbev/msad070/49594873/msad070.pdf; doi:https://doi.org/10.1093/molbev/msad070; html:https://europepmc.org/articles/PMC10118308; pdf:https://europepmc.org/articles/PMC10118308?pdf=render"
   },
-  {
-    "id": "32255392",
-    "doi": "https://doi.org/10.1080/09273948.2019.1709650",
-    "title": "Non-invasive Instrument-Based Tests for Quantifying Anterior Chamber Flare in Uveitis: A Systematic Review.",
-    "authorString": "Liu X, McNally TW, Beese S, Downie LE, Solebo AL, Faes L, Husain S, Keane PA, Moore DJ, Denniston AK.",
-    "authorAffiliations": "",
-    "journalTitle": "Ocular immunology and inflammation",
-    "pubYear": "2021",
-    "date": "2020-04-07",
-    "isOpenAccess": "N",
-    "keywords": "Diagnostic test; Systematic review; Uveitis; optical coherence tomography; Laser Flare Photometry; Anterior Chamber Flare; Tyndall Effect; Aqueous Humor, Aqueous Humour; Aqueous Protein Concentration",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<b>Purpose</b>: Anterior chamber (AC) flare is a key sign for anterior uveitis. New instrument-based techniques for measuring AC flare can offer automation and objectivity. This review aims to identify objective instrument-based measures for AC flare.<b>Methods</b>: In this systematic review, we identified studies reporting correlation between instrument-based tests versus clinician AC flare grading, and/or aqueous protein concentration, as well as test reliability.<b>Results</b>: Four index tests were identified in 11 studies: laser-flare photometry (LFP), optical coherence tomography, ocular flare analysis meter (OFAM) and the double-pass technique. The correlation between LFP and clinician grading was 0.40-0.93 and 0.87-0.94 for LFP and protein concentration. The double-pass technique showed no correlation with clinician grading and insufficient information was available for OFAM.<b>Conclusion</b>: LFP shows moderate to strong correlation with clinician grading and aqueous protein concentration. LFP could be a superior reference test compared to clinician AC flare grading for validating new index tests.",
-    "laySummary": "",
-    "urls": "pdf:https://discovery.ucl.ac.uk/10097154/3/Solebo_Liu%20AC%20Flare%20SR%20290919.pdf; doi:https://doi.org/10.1080/09273948.2019.1709650"
-  },
-  {
-    "id": "35568032",
-    "doi": "https://doi.org/10.1016/j.ajhg.2022.04.009",
-    "title": "Whole-exome sequencing identifies rare genetic variants associated with human plasma metabolites.",
-    "authorString": "Bomba L, Walter K, Guo Q, Surendran P, Kundu K, Nongmaithem S, Karim MA, Stewart ID, Langenberg C, Danesh J, Di Angelantonio E, Roberts DJ, Ouwehand WH, INTERVAL study, Dunham I, Butterworth AS, Soranzo N.",
-    "authorAffiliations": "",
-    "journalTitle": "American journal of human genetics",
-    "pubYear": "2022",
-    "date": "2022-05-13",
-    "isOpenAccess": "Y",
-    "keywords": "Sequencing; Proteomics; drug targets; Metabolomics; Endophenotypes; Loss-of-function; Metabolon; Wgs; Wes; Rare Genetic Variant",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Metabolite levels measured in the human population are endophenotypes for biological processes. We combined sequencing data for 3,924 (whole-exome sequencing, WES, discovery) and 2,805 (whole-genome sequencing, WGS, replication) donors from a prospective cohort of blood donors in England. We used multiple approaches to select and aggregate rare genetic variants (minor allele frequency [MAF]\u00a0<\u00a00.1%) in protein-coding regions and tested their associations with 995 metabolites measured in plasma by using ultra-high-performance liquid chromatography-tandem mass spectrometry. We identified 40 novel associations implicating rare coding variants (27 genes and 38 metabolites), of which 28 (15 genes and 28 metabolites) were replicated. We developed algorithms to prioritize putative driver variants at each locus and used mediation and Mendelian randomization analyses to test directionality at associations of metabolite and protein levels at the ACY1 locus. Overall, 66% of reported associations implicate gene targets of approved drugs or bioactive drug-like compounds, contributing to drug targets' validating efforts.",
-    "laySummary": "",
-    "urls": "pdf:https://www.repository.cam.ac.uk/bitstreams/ce3ed268-a258-488b-b08c-4948d71b7460/download; doi:https://doi.org/10.1016/j.ajhg.2022.04.009; html:https://europepmc.org/articles/PMC9247822; pdf:https://europepmc.org/articles/PMC9247822?pdf=render"
-  },
   {
     "id": "33184391",
     "doi": "https://doi.org/10.1038/s41598-020-76816-6",
@@ -34204,21 +34238,21 @@
     "urls": "pdf:https://www.nature.com/articles/s41598-020-76816-6.pdf; doi:https://doi.org/10.1038/s41598-020-76816-6; html:https://europepmc.org/articles/PMC7661535; pdf:https://europepmc.org/articles/PMC7661535?pdf=render"
   },
   {
-    "id": "35434685",
-    "doi": "https://doi.org/10.1016/j.lanepe.2022.100381",
-    "title": "Dosing interval strategies for two-dose COVID-19 vaccination in 13 middle-income countries of Europe: Health impact modelling and benefit-risk analysis.",
-    "authorString": "Liu Y, Pearson CAB, Sandmann FG, Barnard RC, Kim JH, CMMID COVID-19 Working Group, Flasche S, Jit M, Abbas K.",
+    "id": "35568032",
+    "doi": "https://doi.org/10.1016/j.ajhg.2022.04.009",
+    "title": "Whole-exome sequencing identifies rare genetic variants associated with human plasma metabolites.",
+    "authorString": "Bomba L, Walter K, Guo Q, Surendran P, Kundu K, Nongmaithem S, Karim MA, Stewart ID, Langenberg C, Danesh J, Di Angelantonio E, Roberts DJ, Ouwehand WH, INTERVAL study, Dunham I, Butterworth AS, Soranzo N.",
     "authorAffiliations": "",
-    "journalTitle": "The Lancet regional health. Europe",
+    "journalTitle": "American journal of human genetics",
     "pubYear": "2022",
-    "date": "2022-04-11",
+    "date": "2022-05-13",
     "isOpenAccess": "Y",
-    "keywords": "Quantitative Methods; Mathematical Modelling; Public Health Intervention; Vaccine Policy; Ve, Vaccine Efficacy; Covid-19; Sars-cov-2; Voc, Variant Of Concern; Aefi, Adverse Events Following Immunisation; Mic, Middle Income Country",
+    "keywords": "Sequencing; Proteomics; drug targets; Metabolomics; Endophenotypes; Loss-of-function; Metabolon; Wgs; Wes; Rare Genetic Variant",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>In settings where the COVID-19 vaccine supply is constrained, extending the intervals between the first and second doses of the COVID-19 vaccine may allow more people receive their first doses earlier. Our aim is to estimate the health impact of COVID-19 vaccination alongside benefit-risk assessment of different dosing intervals in 13 middle-income countries (MICs) of Europe.<h4>Methods</h4>We fitted a dynamic transmission model to country-level daily reported COVID-19 mortality in 13 MICs in Europe (Albania, Armenia, Azerbaijan, Belarus, Bosnia and Herzegovina, Bulgaria, Georgia, Republic of Moldova, Russian Federation, Serbia, North Macedonia, Turkey, and Ukraine). A vaccine product with characteristics similar to those of the Oxford/AstraZeneca COVID-19 (AZD1222) vaccine was used in the base case scenario and was complemented by sensitivity analyses around efficacies similar to other COVID-19 vaccines. Both fixed dosing intervals at 4, 8, 12, 16, and 20 weeks and dose-specific intervals that prioritise specific doses for certain age groups were tested. Optimal intervals minimise COVID-19 mortality between March 2021 and December 2022. We incorporated the emergence of variants of concern (VOCs) into the model and conducted a benefit-risk assessment to quantify the tradeoff between health benefits versus adverse events following immunisation.<h4>Findings</h4>In all countries modelled, optimal strategies are those that prioritise the first doses among older adults (60+ years) or adults (20+ years), which lead to dosing intervals longer than six months. In comparison, a four-week fixed dosing interval may incur 10.1% [range: 4.3% - 19.0%; n\u00a0=\u00a013 (countries)] more deaths. The rapid waning of the immunity induced by the first dose (i.e. with means ranging 60-120 days as opposed to 360 days in the base case) resulted in shorter optimal dosing intervals of 8-20 weeks. Benefit-risk ratios were the highest for fixed dosing intervals of 8-12 weeks.<h4>Interpretation</h4>We infer that longer dosing intervals of over six months could reduce COVID-19 mortality in MICs of Europe. Certain parameters, such as rapid waning of first-dose induced immunity and increased immune escape through the emergence of VOCs, could significantly shorten the optimal dosing intervals.<h4>Funding</h4>World Health Organization.",
+    "abstract": "Metabolite levels measured in the human population are endophenotypes for biological processes. We combined sequencing data for 3,924 (whole-exome sequencing, WES, discovery) and 2,805 (whole-genome sequencing, WGS, replication) donors from a prospective cohort of blood donors in England. We used multiple approaches to select and aggregate rare genetic variants (minor allele frequency [MAF]\u00a0<\u00a00.1%) in protein-coding regions and tested their associations with 995 metabolites measured in plasma by using ultra-high-performance liquid chromatography-tandem mass spectrometry. We identified 40 novel associations implicating rare coding variants (27 genes and 38 metabolites), of which 28 (15 genes and 28 metabolites) were replicated. We developed algorithms to prioritize putative driver variants at each locus and used mediation and Mendelian randomization analyses to test directionality at associations of metabolite and protein levels at the ACY1 locus. Overall, 66% of reported associations implicate gene targets of approved drugs or bioactive drug-like compounds, contributing to drug targets' validating efforts.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.lanepe.2022.100381; doi:https://doi.org/10.1016/j.lanepe.2022.100381; html:https://europepmc.org/articles/PMC8996067; pdf:https://europepmc.org/articles/PMC8996067?pdf=render"
+    "urls": "pdf:https://www.repository.cam.ac.uk/bitstreams/ce3ed268-a258-488b-b08c-4948d71b7460/download; doi:https://doi.org/10.1016/j.ajhg.2022.04.009; html:https://europepmc.org/articles/PMC9247822; pdf:https://europepmc.org/articles/PMC9247822?pdf=render"
   },
   {
     "id": "31055854",
@@ -34254,23 +34288,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41598-021-82214-3.pdf; doi:https://doi.org/10.1038/s41598-021-82214-3; html:https://europepmc.org/articles/PMC7862387; pdf:https://europepmc.org/articles/PMC7862387?pdf=render"
   },
-  {
-    "id": "34903266",
-    "doi": "https://doi.org/10.1186/s13059-021-02561-2",
-    "title": "CIDER: an interpretable meta-clustering framework for single-cell RNA-seq data integration and evaluation.",
-    "authorString": "Hu Z, Ahmed AA, Yau C.",
-    "authorAffiliations": "",
-    "journalTitle": "Genome biology",
-    "pubYear": "2021",
-    "date": "2021-12-13",
-    "isOpenAccess": "Y",
-    "keywords": "Clustering; Confounding Factors; Single-cell Rna-seq",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Clustering of joint single-cell RNA-Seq (scRNA-Seq) data is often challenged by confounding factors, such as batch effects and biologically relevant variability. Existing batch effect removal methods typically require strong assumptions on the composition of cell populations being near identical across samples. Here, we present CIDER, a meta-clustering workflow based on inter-group similarity measures. We demonstrate that CIDER outperforms other scRNA-Seq clustering methods and integration approaches in both simulated and real datasets. Moreover, we show that CIDER can be used to assess the biological correctness of integration in real datasets, while it does not require the existence of prior cellular annotations.",
-    "laySummary": "",
-    "urls": "pdf:https://genomebiology.biomedcentral.com/counter/pdf/10.1186/s13059-021-02561-2; doi:https://doi.org/10.1186/s13059-021-02561-2; html:https://europepmc.org/articles/PMC8667531; pdf:https://europepmc.org/articles/PMC8667531?pdf=render"
-  },
   {
     "id": "33560344",
     "doi": "https://doi.org/10.1210/clinem/dgab067",
@@ -34288,6 +34305,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/jcem/article-pdf/106/5/1255/41848481/dgab067.pdf; doi:https://doi.org/10.1210/clinem/dgab067; html:https://europepmc.org/articles/PMC7928949"
   },
+  {
+    "id": "34903266",
+    "doi": "https://doi.org/10.1186/s13059-021-02561-2",
+    "title": "CIDER: an interpretable meta-clustering framework for single-cell RNA-seq data integration and evaluation.",
+    "authorString": "Hu Z, Ahmed AA, Yau C.",
+    "authorAffiliations": "",
+    "journalTitle": "Genome biology",
+    "pubYear": "2021",
+    "date": "2021-12-13",
+    "isOpenAccess": "Y",
+    "keywords": "Clustering; Confounding Factors; Single-cell Rna-seq",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Clustering of joint single-cell RNA-Seq (scRNA-Seq) data is often challenged by confounding factors, such as batch effects and biologically relevant variability. Existing batch effect removal methods typically require strong assumptions on the composition of cell populations being near identical across samples. Here, we present CIDER, a meta-clustering workflow based on inter-group similarity measures. We demonstrate that CIDER outperforms other scRNA-Seq clustering methods and integration approaches in both simulated and real datasets. Moreover, we show that CIDER can be used to assess the biological correctness of integration in real datasets, while it does not require the existence of prior cellular annotations.",
+    "laySummary": "",
+    "urls": "pdf:https://genomebiology.biomedcentral.com/counter/pdf/10.1186/s13059-021-02561-2; doi:https://doi.org/10.1186/s13059-021-02561-2; html:https://europepmc.org/articles/PMC8667531; pdf:https://europepmc.org/articles/PMC8667531?pdf=render"
+  },
   {
     "id": "32702311",
     "doi": "https://doi.org/10.1016/s1470-2045(20)30392-2",
@@ -34407,23 +34441,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/bioinformatics/article-pdf/36/6/1772/36089203/btz796.pdf; doi:https://doi.org/10.1093/bioinformatics/btz796; html:https://europepmc.org/articles/PMC7703753; pdf:https://europepmc.org/articles/PMC7703753?pdf=render"
   },
-  {
-    "id": "35861818",
-    "doi": "https://doi.org/10.1161/jaha.121.025473",
-    "title": "Interatrial Block Predicts Life-Threatening Arrhythmias in Dilated Cardiomyopathy.",
-    "authorString": "Henkens MTHM, L\u00f3pez Mart\u00ednez H, Weerts J, Sammani A, Raafs AG, Verdonschot JAJ, van de Leur RR, Sikking MA, Stroeks S, van Empel VPM, Brunner-La Rocca HP, van Stipdonk AMW, Farmakis D, Hazebroek MR, Vernooy K, Bay\u00e9s-de-Luna A, Asselbergs FW, Bay\u00e9s-Gen\u00eds A, Heymans SRB.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of the American Heart Association",
-    "pubYear": "2022",
-    "date": "2022-07-15",
-    "isOpenAccess": "Y",
-    "keywords": "Electrocardiography; Dilated cardiomyopathy; Sudden Cardiac Death; Interatrial Block; Non\u2010ischemic Cardiomyopathy; Life\u2010threatening Arrhythmias",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Background Interatrial block (IAB) has been associated with supraventricular arrhythmias and stroke, and even with sudden cardiac death in the general population. Whether IAB is associated with life-threatening arrhythmias (LTA) and sudden cardiac death in dilated cardiomyopathy (DCM) remains unknown. This study aimed to determine the association between IAB and LTA in ambulant patients with DCM. Methods and Results A derivation cohort (Maastricht Dilated Cardiomyopathy Registry; N=469) and an external validation cohort (Utrecht Cardiomyopathy Cohort; N=321) were used for this study. The presence of IAB (P-wave duration>120\u00a0milliseconds) or atrial fibrillation (AF) was determined using digital calipers by physicians blinded to the study data. In the derivation cohort, IAB and AF were present in 291 (62%) and 70 (15%) patients with DCM, respectively. LTA (defined as sudden cardiac death, justified shock from implantable cardioverter-defibrillator or anti-tachypacing, or hemodynamic unstable ventricular fibrillation/tachycardia) occurred in 49 patients (3 with no IAB, 35 with IAB, and 11 patients with AF, respectively; median follow-up, 4.4\u00a0years [2.1; 7.4]). The LTA-free survival distribution significantly differed between IAB or AF versus no IAB (both <i>P</i><0.01), but not between IAB versus AF (<i>P</i>=0.999). This association remained statistically significant in the multivariable model (IAB: HR, 4.8 (1.4-16.1), <i>P</i>=0.013; AF: HR, 6.4 (1.7-24.0), <i>P</i>=0.007). In the external validation cohort, the survival distribution was also significantly worse for IAB or AF versus no IAB (<i>P</i>=0.037; <i>P</i>=0.005), but not for IAB versus AF (<i>P</i>=0.836). Conclusions IAB is an easy to assess, widely applicable marker associated with LTA in DCM. IAB and AF seem to confer similar risk of LTA. Further research on IAB in DCM, and on the management of IAB in DCM is warranted.",
-    "laySummary": "",
-    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.121.025473; doi:https://doi.org/10.1161/JAHA.121.025473; html:https://europepmc.org/articles/PMC9707810; pdf:https://europepmc.org/articles/PMC9707810?pdf=render"
-  },
   {
     "id": "31653530",
     "doi": "https://doi.org/10.1016/j.echo.2019.08.015",
@@ -34441,6 +34458,23 @@
     "laySummary": "",
     "urls": "pdf:http://www.onlinejase.com/article/S0894731719309460/pdf; doi:https://doi.org/10.1016/j.echo.2019.08.015"
   },
+  {
+    "id": "35861818",
+    "doi": "https://doi.org/10.1161/jaha.121.025473",
+    "title": "Interatrial Block Predicts Life-Threatening Arrhythmias in Dilated Cardiomyopathy.",
+    "authorString": "Henkens MTHM, L\u00f3pez Mart\u00ednez H, Weerts J, Sammani A, Raafs AG, Verdonschot JAJ, van de Leur RR, Sikking MA, Stroeks S, van Empel VPM, Brunner-La Rocca HP, van Stipdonk AMW, Farmakis D, Hazebroek MR, Vernooy K, Bay\u00e9s-de-Luna A, Asselbergs FW, Bay\u00e9s-Gen\u00eds A, Heymans SRB.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of the American Heart Association",
+    "pubYear": "2022",
+    "date": "2022-07-15",
+    "isOpenAccess": "Y",
+    "keywords": "Electrocardiography; Dilated cardiomyopathy; Sudden Cardiac Death; Interatrial Block; Non\u2010ischemic Cardiomyopathy; Life\u2010threatening Arrhythmias",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Background Interatrial block (IAB) has been associated with supraventricular arrhythmias and stroke, and even with sudden cardiac death in the general population. Whether IAB is associated with life-threatening arrhythmias (LTA) and sudden cardiac death in dilated cardiomyopathy (DCM) remains unknown. This study aimed to determine the association between IAB and LTA in ambulant patients with DCM. Methods and Results A derivation cohort (Maastricht Dilated Cardiomyopathy Registry; N=469) and an external validation cohort (Utrecht Cardiomyopathy Cohort; N=321) were used for this study. The presence of IAB (P-wave duration>120\u00a0milliseconds) or atrial fibrillation (AF) was determined using digital calipers by physicians blinded to the study data. In the derivation cohort, IAB and AF were present in 291 (62%) and 70 (15%) patients with DCM, respectively. LTA (defined as sudden cardiac death, justified shock from implantable cardioverter-defibrillator or anti-tachypacing, or hemodynamic unstable ventricular fibrillation/tachycardia) occurred in 49 patients (3 with no IAB, 35 with IAB, and 11 patients with AF, respectively; median follow-up, 4.4\u00a0years [2.1; 7.4]). The LTA-free survival distribution significantly differed between IAB or AF versus no IAB (both <i>P</i><0.01), but not between IAB versus AF (<i>P</i>=0.999). This association remained statistically significant in the multivariable model (IAB: HR, 4.8 (1.4-16.1), <i>P</i>=0.013; AF: HR, 6.4 (1.7-24.0), <i>P</i>=0.007). In the external validation cohort, the survival distribution was also significantly worse for IAB or AF versus no IAB (<i>P</i>=0.037; <i>P</i>=0.005), but not for IAB versus AF (<i>P</i>=0.836). Conclusions IAB is an easy to assess, widely applicable marker associated with LTA in DCM. IAB and AF seem to confer similar risk of LTA. Further research on IAB in DCM, and on the management of IAB in DCM is warranted.",
+    "laySummary": "",
+    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.121.025473; doi:https://doi.org/10.1161/JAHA.121.025473; html:https://europepmc.org/articles/PMC9707810; pdf:https://europepmc.org/articles/PMC9707810?pdf=render"
+  },
   {
     "id": "34396248",
     "doi": "https://doi.org/10.1016/j.jaccao.2020.07.001",
@@ -34577,6 +34611,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.jacc.2023.05.005"
   },
+  {
+    "id": "37474660",
+    "doi": "https://doi.org/10.1038/s41591-023-02445-x",
+    "title": "Considerations for patient and public involvement and engagement in health research.",
+    "authorString": "Aiyegbusi OL, McMullan C, Hughes SE, Turner GM, Subramanian A, Hotham R, Davies EH, Frost C, Alder Y, Agyen L, Buckland L, Camaradou J, Chong A, Jeyes F, Kumar S, Matthews KL, Moore P, Ormerod J, Price G, Saint-Cricq M, Stanton D, Walker A, Haroon S, Denniston AK, Calvert MJ, TLC Study Group.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature medicine",
+    "pubYear": "2023",
+    "date": "2023-07-20",
+    "isOpenAccess": "N",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Patient and public involvement and engagement (PPIE) can provide valuable insights into the experiences of those living with and affected by a disease or health condition. Inclusive collaboration between patients, the public and researchers can lead to productive relationships, ensuring that health research addresses patient needs. Guidelines are available to support effective PPIE; however, evaluation of the impact of PPIE strategies in health research is limited. In this Review, we evaluate the impact of PPIE in the 'Therapies for Long COVID in non-hospitalised individuals' (TLC) Study, using a combination of group discussions and interviews with patient partners and researchers. We identify areas of good practice and reflect on areas for improvement. Using these insights and the results of a survey, we synthesize two checklists of considerations for PPIE, and we propose that research teams use these checklists to optimize the impact of PPIE for both patients and researchers in future studies.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1038/s41591-023-02445-x"
+  },
   {
     "id": "38429458",
     "doi": "https://doi.org/10.1038/s41590-024-01754-8",
@@ -34611,23 +34662,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmjmedicine.bmj.com/content/bmjmed/1/1/e000151.full.pdf; doi:https://doi.org/10.1136/bmjmed-2022-000151; html:https://europepmc.org/articles/PMC9951363; pdf:https://europepmc.org/articles/PMC9951363?pdf=render"
   },
-  {
-    "id": "37474660",
-    "doi": "https://doi.org/10.1038/s41591-023-02445-x",
-    "title": "Considerations for patient and public involvement and engagement in health research.",
-    "authorString": "Aiyegbusi OL, McMullan C, Hughes SE, Turner GM, Subramanian A, Hotham R, Davies EH, Frost C, Alder Y, Agyen L, Buckland L, Camaradou J, Chong A, Jeyes F, Kumar S, Matthews KL, Moore P, Ormerod J, Price G, Saint-Cricq M, Stanton D, Walker A, Haroon S, Denniston AK, Calvert MJ, TLC Study Group.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature medicine",
-    "pubYear": "2023",
-    "date": "2023-07-20",
-    "isOpenAccess": "N",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Patient and public involvement and engagement (PPIE) can provide valuable insights into the experiences of those living with and affected by a disease or health condition. Inclusive collaboration between patients, the public and researchers can lead to productive relationships, ensuring that health research addresses patient needs. Guidelines are available to support effective PPIE; however, evaluation of the impact of PPIE strategies in health research is limited. In this Review, we evaluate the impact of PPIE in the 'Therapies for Long COVID in non-hospitalised individuals' (TLC) Study, using a combination of group discussions and interviews with patient partners and researchers. We identify areas of good practice and reflect on areas for improvement. Using these insights and the results of a survey, we synthesize two checklists of considerations for PPIE, and we propose that research teams use these checklists to optimize the impact of PPIE for both patients and researchers in future studies.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1038/s41591-023-02445-x"
-  },
   {
     "id": "36048760",
     "doi": "https://doi.org/10.1371/journal.pgen.1010294",
@@ -34645,23 +34679,6 @@
     "laySummary": "",
     "urls": "pdf:https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1010294&type=printable; doi:https://doi.org/10.1371/journal.pgen.1010294; html:https://europepmc.org/articles/PMC9436054; pdf:https://europepmc.org/articles/PMC9436054?pdf=render"
   },
-  {
-    "id": "34791170",
-    "doi": "https://doi.org/10.1093/eurheartj/ehab759",
-    "title": "A sex-specific prediction model is not enough to achieve equality for women in preventative cardiovascular medicine.",
-    "authorString": "Kimenai DM, Shah ASV, Mills NL.",
-    "authorAffiliations": "",
-    "journalTitle": "European heart journal",
-    "pubYear": "2022",
-    "date": "2022-01-01",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/eurheartj/article-pdf/43/3/239/42296399/ehab759.pdf; doi:https://doi.org/10.1093/eurheartj/ehab759; html:https://europepmc.org/articles/PMC8790764; pdf:https://europepmc.org/articles/PMC8790764?pdf=render"
-  },
   {
     "id": "30082368",
     "doi": "https://doi.org/10.1136/bmjopen-2018-024755",
@@ -34679,6 +34696,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/8/8/e024755.full.pdf; doi:https://doi.org/10.1136/bmjopen-2018-024755; html:https://europepmc.org/articles/PMC6078268; pdf:https://europepmc.org/articles/PMC6078268?pdf=render"
   },
+  {
+    "id": "34791170",
+    "doi": "https://doi.org/10.1093/eurheartj/ehab759",
+    "title": "A sex-specific prediction model is not enough to achieve equality for women in preventative cardiovascular medicine.",
+    "authorString": "Kimenai DM, Shah ASV, Mills NL.",
+    "authorAffiliations": "",
+    "journalTitle": "European heart journal",
+    "pubYear": "2022",
+    "date": "2022-01-01",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/eurheartj/article-pdf/43/3/239/42296399/ehab759.pdf; doi:https://doi.org/10.1093/eurheartj/ehab759; html:https://europepmc.org/articles/PMC8790764; pdf:https://europepmc.org/articles/PMC8790764?pdf=render"
+  },
   {
     "id": "36719157",
     "doi": "https://doi.org/10.2215/cjn.05080422",
@@ -34781,23 +34815,6 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/bjd.19052; doi:https://doi.org/10.1111/bjd.19052"
   },
-  {
-    "id": "38594327",
-    "doi": "https://doi.org/10.1038/s41698-024-00580-3",
-    "title": "Image-based consensus molecular subtyping in rectal cancer biopsies and response to neoadjuvant chemoradiotherapy.",
-    "authorString": "Lafarge MW, Domingo E, Sirinukunwattana K, Wood R, Samuel L, Murray G, Richman SD, Blake A, Sebag-Montefiore D, Gollins S, Klieser E, Neureiter D, Huemer F, Greil R, Dunne P, Quirke P, Weiss L, Rittscher J, Maughan T, Koelzer VH.",
-    "authorAffiliations": "",
-    "journalTitle": "NPJ precision oncology",
-    "pubYear": "2024",
-    "date": "2024-04-09",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The development of deep learning (DL) models to predict the consensus molecular subtypes (CMS) from histopathology images (imCMS) is a promising and cost-effective strategy to support patient stratification. Here, we investigate whether imCMS calls generated from whole slide histopathology images (WSIs) of rectal cancer (RC) pre-treatment biopsies are associated with pathological complete response (pCR) to neoadjuvant long course chemoradiotherapy (LCRT) with single agent fluoropyrimidine. DL models were trained to classify WSIs of colorectal cancers stained with hematoxylin and eosin into one of the four CMS classes using a multi-centric dataset of resection and biopsy specimens (n\u2009=\u20091057 WSIs) with paired transcriptional data. Classifiers were tested on a held out RC biopsy cohort (ARISTOTLE) and correlated with pCR to LCRT in an independent dataset merging two RC cohorts (ARISTOTLE, n\u2009=\u2009114 and SALZBURG, n\u2009=\u200955 patients). DL models predicted CMS with high classification performance in multiple comparative analyses. In the independent cohorts (ARISTOTLE, SALZBURG), cases with WSIs classified as imCMS1 had a significantly higher likelihood of achieving pCR (OR\u2009=\u20092.69, 95% CI 1.01-7.17, p\u2009=\u20090.048). Conversely, imCMS4 was associated with lack of pCR (OR\u2009=\u20090.25, 95% CI 0.07-0.88, p\u2009=\u20090.031). Classification maps demonstrated pathologist-interpretable associations with high stromal content in imCMS4 cases, associated with poor outcome. No significant association was found in imCMS2 or imCMS3. imCMS classification of pre-treatment biopsies is a fast and inexpensive solution to identify patient groups that could benefit from neoadjuvant LCRT. The significant associations between imCMS1/imCMS4 with pCR suggest the existence of predictive morphological features that could enhance standard pathological assessment.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41698-024-00580-3.pdf; doi:https://doi.org/10.1038/s41698-024-00580-3; html:https://europepmc.org/articles/PMC11003957; pdf:https://europepmc.org/articles/PMC11003957?pdf=render"
-  },
   {
     "id": "33090454",
     "doi": "https://doi.org/10.1111/bjd.19597",
@@ -34815,6 +34832,23 @@
     "laySummary": "",
     "urls": "pdf:https://researchonline.lshtm.ac.uk/id/eprint/4658151/1/Ascott-etal-2020_Atopic_eczema_and-obesity.pdf; doi:https://doi.org/10.1111/bjd.19597"
   },
+  {
+    "id": "38594327",
+    "doi": "https://doi.org/10.1038/s41698-024-00580-3",
+    "title": "Image-based consensus molecular subtyping in rectal cancer biopsies and response to neoadjuvant chemoradiotherapy.",
+    "authorString": "Lafarge MW, Domingo E, Sirinukunwattana K, Wood R, Samuel L, Murray G, Richman SD, Blake A, Sebag-Montefiore D, Gollins S, Klieser E, Neureiter D, Huemer F, Greil R, Dunne P, Quirke P, Weiss L, Rittscher J, Maughan T, Koelzer VH.",
+    "authorAffiliations": "",
+    "journalTitle": "NPJ precision oncology",
+    "pubYear": "2024",
+    "date": "2024-04-09",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The development of deep learning (DL) models to predict the consensus molecular subtypes (CMS) from histopathology images (imCMS) is a promising and cost-effective strategy to support patient stratification. Here, we investigate whether imCMS calls generated from whole slide histopathology images (WSIs) of rectal cancer (RC) pre-treatment biopsies are associated with pathological complete response (pCR) to neoadjuvant long course chemoradiotherapy (LCRT) with single agent fluoropyrimidine. DL models were trained to classify WSIs of colorectal cancers stained with hematoxylin and eosin into one of the four CMS classes using a multi-centric dataset of resection and biopsy specimens (n\u2009=\u20091057 WSIs) with paired transcriptional data. Classifiers were tested on a held out RC biopsy cohort (ARISTOTLE) and correlated with pCR to LCRT in an independent dataset merging two RC cohorts (ARISTOTLE, n\u2009=\u2009114 and SALZBURG, n\u2009=\u200955 patients). DL models predicted CMS with high classification performance in multiple comparative analyses. In the independent cohorts (ARISTOTLE, SALZBURG), cases with WSIs classified as imCMS1 had a significantly higher likelihood of achieving pCR (OR\u2009=\u20092.69, 95% CI 1.01-7.17, p\u2009=\u20090.048). Conversely, imCMS4 was associated with lack of pCR (OR\u2009=\u20090.25, 95% CI 0.07-0.88, p\u2009=\u20090.031). Classification maps demonstrated pathologist-interpretable associations with high stromal content in imCMS4 cases, associated with poor outcome. No significant association was found in imCMS2 or imCMS3. imCMS classification of pre-treatment biopsies is a fast and inexpensive solution to identify patient groups that could benefit from neoadjuvant LCRT. The significant associations between imCMS1/imCMS4 with pCR suggest the existence of predictive morphological features that could enhance standard pathological assessment.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41698-024-00580-3.pdf; doi:https://doi.org/10.1038/s41698-024-00580-3; html:https://europepmc.org/articles/PMC11003957; pdf:https://europepmc.org/articles/PMC11003957?pdf=render"
+  },
   {
     "id": "37748493",
     "doi": "https://doi.org/10.1016/s2213-2600(23)00262-x",
@@ -34832,23 +34866,6 @@
     "laySummary": "",
     "urls": "pdf:http://www.thelancet.com/article/S221326002300262X/pdf; doi:https://doi.org/10.1016/S2213-2600(23)00262-X; html:https://europepmc.org/articles/PMC7615263; pdf:https://europepmc.org/articles/PMC7615263?pdf=render"
   },
-  {
-    "id": "35386996",
-    "doi": "https://doi.org/10.3389/falgy.2021.677677",
-    "title": "Purinergic Receptors in the Airways: Potential Therapeutic Targets for Asthma?",
-    "authorString": "Thompson RJ, Sayers I, Kuokkanen K, Hall IP.",
-    "authorAffiliations": "",
-    "journalTitle": "Frontiers in allergy",
-    "pubYear": "2021",
-    "date": "2021-05-31",
-    "isOpenAccess": "Y",
-    "keywords": "Lung; Bioinformatics; Asthma; airway; Gene Expression; purinergic receptor; Purinergic Signaling",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Extracellular ATP functions as a signaling messenger through its actions on purinergic receptors, and is known to be involved in numerous physiological and pathophysiological processes throughout the body, including in the lungs and airways. Consequently, purinergic receptors are considered to be promising therapeutic targets for many respiratory diseases, including asthma. This review explores how online bioinformatics resources combined with recently generated datasets can be utilized to investigate purinergic receptor gene expression in tissues and cell types of interest in respiratory disease to identify potential therapeutic targets, which can then be investigated further. These approaches show that different purinergic receptors are expressed at different levels in lung tissue, and that purinergic receptors tend to be expressed at higher levels in immune cells and at more moderate levels in airway structural cells. Notably, P2RX1, P2RX4, P2RX7, P2RY1, P2RY11, and P2RY14 were revealed as the most highly expressed purinergic receptors in lung tissue, therefore suggesting that these receptors have good potential as therapeutic targets for asthma and other respiratory diseases.",
-    "laySummary": "",
-    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/falgy.2021.677677/pdf; doi:https://doi.org/10.3389/falgy.2021.677677; html:https://europepmc.org/articles/PMC8974712; pdf:https://europepmc.org/articles/PMC8974712?pdf=render"
-  },
   {
     "id": "33635119",
     "doi": "https://doi.org/10.1161/circgen.120.002963",
@@ -34866,6 +34883,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCGEN.120.002963; doi:https://doi.org/10.1161/CIRCGEN.120.002963; html:https://europepmc.org/articles/PMC8284356; pdf:https://europepmc.org/articles/PMC8284356?pdf=render; doi:https://doi.org/10.1161/circgen.120.002963"
   },
+  {
+    "id": "35386996",
+    "doi": "https://doi.org/10.3389/falgy.2021.677677",
+    "title": "Purinergic Receptors in the Airways: Potential Therapeutic Targets for Asthma?",
+    "authorString": "Thompson RJ, Sayers I, Kuokkanen K, Hall IP.",
+    "authorAffiliations": "",
+    "journalTitle": "Frontiers in allergy",
+    "pubYear": "2021",
+    "date": "2021-05-31",
+    "isOpenAccess": "Y",
+    "keywords": "Lung; Bioinformatics; Asthma; airway; Gene Expression; purinergic receptor; Purinergic Signaling",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Extracellular ATP functions as a signaling messenger through its actions on purinergic receptors, and is known to be involved in numerous physiological and pathophysiological processes throughout the body, including in the lungs and airways. Consequently, purinergic receptors are considered to be promising therapeutic targets for many respiratory diseases, including asthma. This review explores how online bioinformatics resources combined with recently generated datasets can be utilized to investigate purinergic receptor gene expression in tissues and cell types of interest in respiratory disease to identify potential therapeutic targets, which can then be investigated further. These approaches show that different purinergic receptors are expressed at different levels in lung tissue, and that purinergic receptors tend to be expressed at higher levels in immune cells and at more moderate levels in airway structural cells. Notably, P2RX1, P2RX4, P2RX7, P2RY1, P2RY11, and P2RY14 were revealed as the most highly expressed purinergic receptors in lung tissue, therefore suggesting that these receptors have good potential as therapeutic targets for asthma and other respiratory diseases.",
+    "laySummary": "",
+    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/falgy.2021.677677/pdf; doi:https://doi.org/10.3389/falgy.2021.677677; html:https://europepmc.org/articles/PMC8974712; pdf:https://europepmc.org/articles/PMC8974712?pdf=render"
+  },
   {
     "id": "33246414",
     "doi": "https://doi.org/10.1186/s12874-020-01163-z",
@@ -34917,23 +34951,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.neuroimage.2022.119452; doi:https://doi.org/10.1016/j.neuroimage.2022.119452; html:https://europepmc.org/articles/PMC10933779; pdf:https://europepmc.org/articles/PMC10933779?pdf=render"
   },
-  {
-    "id": "38424462",
-    "doi": "https://doi.org/10.1038/s41588-024-01693-y",
-    "title": "Author Correction: Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort.",
-    "authorString": "Qin Y, Havulinna AS, Liu Y, Jousilahti P, Ritchie SC, Tokolyi A, Sanders JG, Valsta L, Bro\u017cy\u0144ska M, Zhu Q, Tripathi A, V\u00e1zquez-Baeza Y, Loomba R, Cheng S, Jain M, Niiranen T, Lahti L, Knight R, Salomaa V, Inouye M, M\u00e9ric G.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature genetics",
-    "pubYear": "2024",
-    "date": "2024-03-01",
-    "isOpenAccess": "N",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41588-024-01693-y.pdf; doi:https://doi.org/10.1038/s41588-024-01693-y"
-  },
   {
     "id": "35880304",
     "doi": "https://doi.org/10.1002/jbmr.4664",
@@ -34951,6 +34968,23 @@
     "laySummary": "",
     "urls": "pdf:https://research-information.bris.ac.uk/files/341783442/J_of_Bone_Mineral_Res_2022_Curtis_Telomere_Length_and_Risk_of_Incident_Fracture_and_Arthroplasty_Findings_From_UK_1_.pdf; doi:https://doi.org/10.1002/jbmr.4664; html:https://europepmc.org/articles/PMC9826022; pdf:https://europepmc.org/articles/PMC9826022?pdf=render"
   },
+  {
+    "id": "38424462",
+    "doi": "https://doi.org/10.1038/s41588-024-01693-y",
+    "title": "Author Correction: Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort.",
+    "authorString": "Qin Y, Havulinna AS, Liu Y, Jousilahti P, Ritchie SC, Tokolyi A, Sanders JG, Valsta L, Bro\u017cy\u0144ska M, Zhu Q, Tripathi A, V\u00e1zquez-Baeza Y, Loomba R, Cheng S, Jain M, Niiranen T, Lahti L, Knight R, Salomaa V, Inouye M, M\u00e9ric G.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature genetics",
+    "pubYear": "2024",
+    "date": "2024-03-01",
+    "isOpenAccess": "N",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41588-024-01693-y.pdf; doi:https://doi.org/10.1038/s41588-024-01693-y"
+  },
   {
     "id": "33637859",
     "doi": "https://doi.org/10.1038/s41746-021-00404-9",
@@ -35019,23 +35053,6 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/jvh.13863; doi:https://doi.org/10.1111/jvh.13863; html:https://europepmc.org/articles/PMC10526649; pdf:https://europepmc.org/articles/PMC10526649?pdf=render"
   },
-  {
-    "id": "36335192",
-    "doi": "https://doi.org/10.1038/s41598-022-22218-9",
-    "title": "Genetic insights into smoking behaviours in 10,558 men of African ancestry from continental Africa and the UK.",
-    "authorString": "Piga NN, Boua PR, Soremekun C, Shrine N, Coley K, Brandenburg JT, Tobin MD, Ramsay M, Fatumo S, Choudhury A, Batini C.",
-    "authorAffiliations": "",
-    "journalTitle": "Scientific reports",
-    "pubYear": "2022",
-    "date": "2022-11-05",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Smoking is a leading risk factor for many of the top ten causes of death worldwide. Of the 1.3 billion smokers globally, 80% live in low- and middle-income countries, where the number of deaths due to tobacco use is expected to double in the next decade according to the World Health Organization. Genetic studies have helped to identify biological pathways for smoking behaviours, but have mostly focussed on individuals of European ancestry or living in either North America or Europe. We performed a genome-wide association study of two smoking behaviour traits in 10,558 men of African ancestry living in five African countries and the UK. Eight independent variants were associated with either smoking initiation or cessation at P-value\u2009<\u20095\u2009\u00d7\u200910<sup>-6</sup>, four being monomorphic or rare in European populations. Gene prioritisation strategy highlighted five genes, including SEMA6D, previously described as associated with several smoking behaviour traits. These results confirm the importance of analysing underrepresented populations in genetic epidemiology, and the urgent need for larger genomic studies to boost discovery power to better understand smoking behaviours, as well as many other traits.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41598-022-22218-9.pdf; doi:https://doi.org/10.1038/s41598-022-22218-9; html:https://europepmc.org/articles/PMC9637114; pdf:https://europepmc.org/articles/PMC9637114?pdf=render"
-  },
   {
     "id": "31699727",
     "doi": "https://doi.org/10.1136/bmjopen-2019-030882",
@@ -35053,6 +35070,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/9/11/e030882.full.pdf; doi:https://doi.org/10.1136/bmjopen-2019-030882; html:https://europepmc.org/articles/PMC6858135; pdf:https://europepmc.org/articles/PMC6858135?pdf=render"
   },
+  {
+    "id": "36335192",
+    "doi": "https://doi.org/10.1038/s41598-022-22218-9",
+    "title": "Genetic insights into smoking behaviours in 10,558 men of African ancestry from continental Africa and the UK.",
+    "authorString": "Piga NN, Boua PR, Soremekun C, Shrine N, Coley K, Brandenburg JT, Tobin MD, Ramsay M, Fatumo S, Choudhury A, Batini C.",
+    "authorAffiliations": "",
+    "journalTitle": "Scientific reports",
+    "pubYear": "2022",
+    "date": "2022-11-05",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Smoking is a leading risk factor for many of the top ten causes of death worldwide. Of the 1.3 billion smokers globally, 80% live in low- and middle-income countries, where the number of deaths due to tobacco use is expected to double in the next decade according to the World Health Organization. Genetic studies have helped to identify biological pathways for smoking behaviours, but have mostly focussed on individuals of European ancestry or living in either North America or Europe. We performed a genome-wide association study of two smoking behaviour traits in 10,558 men of African ancestry living in five African countries and the UK. Eight independent variants were associated with either smoking initiation or cessation at P-value\u2009<\u20095\u2009\u00d7\u200910<sup>-6</sup>, four being monomorphic or rare in European populations. Gene prioritisation strategy highlighted five genes, including SEMA6D, previously described as associated with several smoking behaviour traits. These results confirm the importance of analysing underrepresented populations in genetic epidemiology, and the urgent need for larger genomic studies to boost discovery power to better understand smoking behaviours, as well as many other traits.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41598-022-22218-9.pdf; doi:https://doi.org/10.1038/s41598-022-22218-9; html:https://europepmc.org/articles/PMC9637114; pdf:https://europepmc.org/articles/PMC9637114?pdf=render"
+  },
   {
     "id": "37391266",
     "doi": "https://doi.org/10.1016/s2589-7500(23)00087-0",
@@ -35155,23 +35189,6 @@
     "laySummary": "",
     "urls": "pdf:https://journals.plos.org/globalpublichealth/article/file?id=10.1371/journal.pgph.0000292&type=printable; doi:https://doi.org/10.1371/journal.pgph.0000292; html:https://europepmc.org/articles/PMC10021216; pdf:https://europepmc.org/articles/PMC10021216?pdf=render"
   },
-  {
-    "id": "38371671",
-    "doi": "https://doi.org/10.1016/j.jdin.2023.09.007",
-    "title": "Fasting blood glucose and insulin are not associated with atopic dermatitis in a pediatric population: A longitudinal cohort study from the Avon Longitudinal Study of Parents and Children.",
-    "authorString": "Shan J, Ye M, Ku E, McCulloch CE, Langan SM, Abuabara K.",
-    "authorAffiliations": "",
-    "journalTitle": "JAAD international",
-    "pubYear": "2024",
-    "date": "2023-10-23",
-    "isOpenAccess": "N",
-    "keywords": "Diabetes mellitus; Biomarkers; Clinical research; epidemiology; endocrinology; Atopic Dermatitis; Alspac; Pediatric Dermatology",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.jdin.2023.09.007; html:https://europepmc.org/articles/PMC10869312; pdf:https://europepmc.org/articles/PMC10869312?pdf=render; doi:https://doi.org/10.1016/j.jdin.2023.09.007"
-  },
   {
     "id": "35099396",
     "doi": "https://doi.org/10.2196/21341",
@@ -35189,6 +35206,23 @@
     "laySummary": "",
     "urls": "pdf:https://formative.jmir.org/2022/1/e21341/PDF; doi:https://doi.org/10.2196/21341; html:https://europepmc.org/articles/PMC8845013; pdf:https://europepmc.org/articles/PMC8845013?pdf=render"
   },
+  {
+    "id": "38371671",
+    "doi": "https://doi.org/10.1016/j.jdin.2023.09.007",
+    "title": "Fasting blood glucose and insulin are not associated with atopic dermatitis in a pediatric population: A longitudinal cohort study from the Avon Longitudinal Study of Parents and Children.",
+    "authorString": "Shan J, Ye M, Ku E, McCulloch CE, Langan SM, Abuabara K.",
+    "authorAffiliations": "",
+    "journalTitle": "JAAD international",
+    "pubYear": "2024",
+    "date": "2023-10-23",
+    "isOpenAccess": "N",
+    "keywords": "Diabetes mellitus; Biomarkers; Clinical research; epidemiology; endocrinology; Atopic Dermatitis; Alspac; Pediatric Dermatology",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.jdin.2023.09.007; html:https://europepmc.org/articles/PMC10869312; pdf:https://europepmc.org/articles/PMC10869312?pdf=render; doi:https://doi.org/10.1016/j.jdin.2023.09.007"
+  },
   {
     "id": "29966429",
     "doi": "https://doi.org/10.1177/2047487318785228",
@@ -35495,23 +35529,6 @@
     "laySummary": "",
     "urls": "pdf:https://cardiab.biomedcentral.com/track/pdf/10.1186/s12933-019-0972-4; doi:https://doi.org/10.1186/s12933-019-0972-4; html:https://europepmc.org/articles/PMC6900858; pdf:https://europepmc.org/articles/PMC6900858?pdf=render"
   },
-  {
-    "id": "35279265",
-    "doi": "https://doi.org/10.1016/s2213-2600(21)00511-7",
-    "title": "Global, regional, and national prevalence of, and risk factors for, chronic obstructive pulmonary disease (COPD) in 2019: a systematic review and modelling analysis.",
-    "authorString": "Adeloye D, Song P, Zhu Y, Campbell H, Sheikh A, Rudan I, NIHR RESPIRE Global Respiratory Health Unit.",
-    "authorAffiliations": "",
-    "journalTitle": "The Lancet. Respiratory medicine",
-    "pubYear": "2022",
-    "date": "2022-03-10",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Chronic obstructive pulmonary disease (COPD) is an increasingly important cause of morbidity, disability, and mortality worldwide. We aimed to estimate global, regional, and national COPD prevalence and risk factors to guide policy and population interventions.<h4>Methods</h4>For this systematic review and modelling study, we searched MEDLINE, Embase, Global Health, and CINAHL, for population-based studies on COPD prevalence published between Jan 1, 1990, and Dec 31, 2019. We included data reported using the two main case definitions: the Global Initiative for Chronic Obstructive Lung Disease fixed ratio (GOLD; FEV<sub>1</sub>/FVC<0\u00b77) and the lower limit of normal (LLN; FEV<sub>1</sub>/FVC<LLN). We employed a multilevel multivariable mixed-effects meta-regression approach to generate the age-specific and sex-specific prevalence of COPD in 2019 for high-income countries (HICs) and low-income and middle-income countries (LMICs) according to the World Bank definition. Common risk factors for GOLD-COPD were evaluated using a random-effects meta-analysis.<h4>Findings</h4>We identified 162 articles reporting population-based studies conducted across 260 sites in 65 countries. In 2019, the global prevalence of COPD among people aged 30-79 years was 10\u00b73% (95% CI 8\u00b72-12\u00b78) using the GOLD case definition, which translates to 391\u00b79 million people (95% CI 312\u00b76-487\u00b79), and 7\u00b76% (5\u00b78-10\u00b71) using the LLN definition, which translates to 292\u00b70 million people (219\u00b78-385\u00b76). Using the GOLD definition, we estimated that 391\u00b79 million (95% CI 312\u00b76-487\u00b79) people aged 30-79 years had COPD worldwide in 2019, with most (315\u00b75 million [246\u00b77-399\u00b76]; 80\u00b75%) living in LMICs. The overall prevalence of GOLD-COPD among people aged 30-79 years was the highest in the Western Pacific region (11\u00b77% [95% CI 9\u00b73-14\u00b76]) and lowest in the region of the Americas (6\u00b78% [95% CI 5\u00b76-8\u00b72]). Globally, male sex (OR 2\u00b71 [95% CI 1\u00b78-2\u00b73]), smoking (current smoker 3\u00b72 [2\u00b75-4\u00b70]; ever smoker 2\u00b73 [2\u00b70-2\u00b75]), body-mass index of less than 18\u00b75 kg/m<sup>2</sup> (2\u00b72 [1\u00b77-2\u00b77]), biomass exposure (1\u00b74 [1\u00b72-1\u00b77]), and occupational exposure to dust or smoke (1\u00b74 [1\u00b73-1\u00b76]) were all substantial risk factors for COPD.<h4>Interpretation</h4>With more than three-quarters of global COPD cases in LMICs, tackling this chronic condition is a major and increasing challenge for health systems in these settings. In the absence of targeted population-wide efforts and health system reforms in these settings, many of which are under-resourced, achieving a substantial reduction in the burden of COPD globally might remain a difficult task.<h4>Funding</h4>National Institute for Health Research and Health Data Research UK.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/s2213-2600(21)00511-7; doi:https://doi.org/10.1016/S2213-2600(21)00511-7; html:https://europepmc.org/articles/PMC9050565"
-  },
   {
     "id": "37104291",
     "doi": "https://doi.org/10.1371/journal.pmed.1004221",
@@ -35529,6 +35546,23 @@
     "laySummary": "",
     "urls": "pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1004221&type=printable; doi:https://doi.org/10.1371/journal.pmed.1004221; html:https://europepmc.org/articles/PMC10138823; pdf:https://europepmc.org/articles/PMC10138823?pdf=render"
   },
+  {
+    "id": "35279265",
+    "doi": "https://doi.org/10.1016/s2213-2600(21)00511-7",
+    "title": "Global, regional, and national prevalence of, and risk factors for, chronic obstructive pulmonary disease (COPD) in 2019: a systematic review and modelling analysis.",
+    "authorString": "Adeloye D, Song P, Zhu Y, Campbell H, Sheikh A, Rudan I, NIHR RESPIRE Global Respiratory Health Unit.",
+    "authorAffiliations": "",
+    "journalTitle": "The Lancet. Respiratory medicine",
+    "pubYear": "2022",
+    "date": "2022-03-10",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Chronic obstructive pulmonary disease (COPD) is an increasingly important cause of morbidity, disability, and mortality worldwide. We aimed to estimate global, regional, and national COPD prevalence and risk factors to guide policy and population interventions.<h4>Methods</h4>For this systematic review and modelling study, we searched MEDLINE, Embase, Global Health, and CINAHL, for population-based studies on COPD prevalence published between Jan 1, 1990, and Dec 31, 2019. We included data reported using the two main case definitions: the Global Initiative for Chronic Obstructive Lung Disease fixed ratio (GOLD; FEV<sub>1</sub>/FVC<0\u00b77) and the lower limit of normal (LLN; FEV<sub>1</sub>/FVC<LLN). We employed a multilevel multivariable mixed-effects meta-regression approach to generate the age-specific and sex-specific prevalence of COPD in 2019 for high-income countries (HICs) and low-income and middle-income countries (LMICs) according to the World Bank definition. Common risk factors for GOLD-COPD were evaluated using a random-effects meta-analysis.<h4>Findings</h4>We identified 162 articles reporting population-based studies conducted across 260 sites in 65 countries. In 2019, the global prevalence of COPD among people aged 30-79 years was 10\u00b73% (95% CI 8\u00b72-12\u00b78) using the GOLD case definition, which translates to 391\u00b79 million people (95% CI 312\u00b76-487\u00b79), and 7\u00b76% (5\u00b78-10\u00b71) using the LLN definition, which translates to 292\u00b70 million people (219\u00b78-385\u00b76). Using the GOLD definition, we estimated that 391\u00b79 million (95% CI 312\u00b76-487\u00b79) people aged 30-79 years had COPD worldwide in 2019, with most (315\u00b75 million [246\u00b77-399\u00b76]; 80\u00b75%) living in LMICs. The overall prevalence of GOLD-COPD among people aged 30-79 years was the highest in the Western Pacific region (11\u00b77% [95% CI 9\u00b73-14\u00b76]) and lowest in the region of the Americas (6\u00b78% [95% CI 5\u00b76-8\u00b72]). Globally, male sex (OR 2\u00b71 [95% CI 1\u00b78-2\u00b73]), smoking (current smoker 3\u00b72 [2\u00b75-4\u00b70]; ever smoker 2\u00b73 [2\u00b70-2\u00b75]), body-mass index of less than 18\u00b75 kg/m<sup>2</sup> (2\u00b72 [1\u00b77-2\u00b77]), biomass exposure (1\u00b74 [1\u00b72-1\u00b77]), and occupational exposure to dust or smoke (1\u00b74 [1\u00b73-1\u00b76]) were all substantial risk factors for COPD.<h4>Interpretation</h4>With more than three-quarters of global COPD cases in LMICs, tackling this chronic condition is a major and increasing challenge for health systems in these settings. In the absence of targeted population-wide efforts and health system reforms in these settings, many of which are under-resourced, achieving a substantial reduction in the burden of COPD globally might remain a difficult task.<h4>Funding</h4>National Institute for Health Research and Health Data Research UK.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/s2213-2600(21)00511-7; doi:https://doi.org/10.1016/S2213-2600(21)00511-7; html:https://europepmc.org/articles/PMC9050565"
+  },
   {
     "id": "33062309",
     "doi": "https://doi.org/10.1177/2059513120952336",
@@ -35597,6 +35631,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.bmj.com/content/bmj/368/bmj.m331.full.pdf; doi:https://doi.org/10.1136/bmj.m331; html:https://europepmc.org/articles/PMC7190043"
   },
+  {
+    "id": "33713332",
+    "doi": "https://doi.org/10.1007/s40620-021-00996-1",
+    "title": "End-stage kidney disease in patients with clinically manifest vascular disease; incidence and risk factors: results from the UCC-SMART cohort study.",
+    "authorString": "\u00d8stergaard HB, Westerink J, Verhaar MC, Bots ML, Asselbergs FW, de Borst GJ, Kappelle LJ, Visseren FLJ, van der Leeuw J, UCC-SMART studygroup.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of nephrology",
+    "pubYear": "2021",
+    "date": "2021-03-13",
+    "isOpenAccess": "Y",
+    "keywords": "Cardiovascular disease; incidence; End-stage Kidney Disease; Modifiable Risk Factors",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Patients with cardiovascular disease (CVD) are at increased risk of end-stage kidney disease (ESKD). Insights into the incidence and role of modifiable risk factors for end-stage kidney disease may provide means for prevention in patients with cardiovascular disease.<h4>Methods</h4>We included 8402 patients with stable cardiovascular disease. Incidence rates (IRs) for end-stage kidney disease were determined stratified according to vascular disease location. Cox proportional hazard models were used to assess the risk of end-stage kidney disease for the different determinants.<h4>Results</h4>Sixty-five events were observed with a median follow-up of 8.6\u00a0years. The overall incidence rate of end-stage kidney disease was 0.9/1000 person-years. Patients with polyvascular disease had the highest incidence rate (1.8/1000 person-years). Smoking (Hazard ratio (HR) 1.87; 95% CI 1.10-3.19), type 2 diabetes (HR 1.81; 95% CI 1.05-3.14), higher systolic blood pressure (HR 1.37; 95% CI 1.24-1.52/10\u00a0mmHg), lower estimated glomerular filtration rate (eGFR) (HR 2.86; 95% CI 2.44-3.23/10\u00a0mL/min/1.73\u00a0m<sup>2</sup>) and higher urine albumin/creatinine ratio (uACR) (HR 1.19; 95% CI 1.15-1.23/10\u00a0mg/mmol) were independently associated with elevated risk of end-stage kidney disease. Body mass index (BMI), waist circumference, non-HDL-cholesterol and exercise were not independently associated with risk of end-stage kidney disease.<h4>Conclusions</h4>Incidence of end-stage kidney disease in patients with cardiovascular disease varies according to vascular disease location. Several modifiable risk factors for end-stage kidney disease were identified in patients with cardiovascular disease. These findings highlight the potential of risk factor management in patients with manifest cardiovascular disease.",
+    "laySummary": "",
+    "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s40620-021-00996-1.pdf; doi:https://doi.org/10.1007/s40620-021-00996-1; html:https://europepmc.org/articles/PMC8494654; pdf:https://europepmc.org/articles/PMC8494654?pdf=render"
+  },
   {
     "id": "35835762",
     "doi": "https://doi.org/10.1038/s41467-022-31626-4",
@@ -35615,38 +35666,21 @@
     "urls": "pdf:https://www.nature.com/articles/s41467-022-31626-4.pdf; doi:https://doi.org/10.1038/s41467-022-31626-4; html:https://europepmc.org/articles/PMC9283523; pdf:https://europepmc.org/articles/PMC9283523?pdf=render"
   },
   {
-    "id": "33713332",
-    "doi": "https://doi.org/10.1007/s40620-021-00996-1",
-    "title": "End-stage kidney disease in patients with clinically manifest vascular disease; incidence and risk factors: results from the UCC-SMART cohort study.",
-    "authorString": "\u00d8stergaard HB, Westerink J, Verhaar MC, Bots ML, Asselbergs FW, de Borst GJ, Kappelle LJ, Visseren FLJ, van der Leeuw J, UCC-SMART studygroup.",
+    "id": "33947203",
+    "doi": "https://doi.org/10.1161/circulationaha.120.053033",
+    "title": "Evidence-Based Assessment of Genes in Dilated Cardiomyopathy.",
+    "authorString": "Jordan E, Peterson L, Ai T, Asatryan B, Bronicki L, Brown E, Celeghin R, Edwards M, Fan J, Ingles J, James CA, Jarinova O, Johnson R, Judge DP, Lahrouchi N, Lekanne Deprez RH, Lumbers RT, Mazzarotto F, Medeiros Domingo A, Miller RL, Morales A, Murray B, Peters S, Pilichou K, Protonotarios A, Semsarian C, Shah P, Syrris P, Thaxton C, van Tintelen JP, Walsh R, Wang J, Ware J, Hershberger RE.",
     "authorAffiliations": "",
-    "journalTitle": "Journal of nephrology",
+    "journalTitle": "Circulation",
     "pubYear": "2021",
-    "date": "2021-03-13",
-    "isOpenAccess": "Y",
-    "keywords": "Cardiovascular disease; incidence; End-stage Kidney Disease; Modifiable Risk Factors",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Patients with cardiovascular disease (CVD) are at increased risk of end-stage kidney disease (ESKD). Insights into the incidence and role of modifiable risk factors for end-stage kidney disease may provide means for prevention in patients with cardiovascular disease.<h4>Methods</h4>We included 8402 patients with stable cardiovascular disease. Incidence rates (IRs) for end-stage kidney disease were determined stratified according to vascular disease location. Cox proportional hazard models were used to assess the risk of end-stage kidney disease for the different determinants.<h4>Results</h4>Sixty-five events were observed with a median follow-up of 8.6\u00a0years. The overall incidence rate of end-stage kidney disease was 0.9/1000 person-years. Patients with polyvascular disease had the highest incidence rate (1.8/1000 person-years). Smoking (Hazard ratio (HR) 1.87; 95% CI 1.10-3.19), type 2 diabetes (HR 1.81; 95% CI 1.05-3.14), higher systolic blood pressure (HR 1.37; 95% CI 1.24-1.52/10\u00a0mmHg), lower estimated glomerular filtration rate (eGFR) (HR 2.86; 95% CI 2.44-3.23/10\u00a0mL/min/1.73\u00a0m<sup>2</sup>) and higher urine albumin/creatinine ratio (uACR) (HR 1.19; 95% CI 1.15-1.23/10\u00a0mg/mmol) were independently associated with elevated risk of end-stage kidney disease. Body mass index (BMI), waist circumference, non-HDL-cholesterol and exercise were not independently associated with risk of end-stage kidney disease.<h4>Conclusions</h4>Incidence of end-stage kidney disease in patients with cardiovascular disease varies according to vascular disease location. Several modifiable risk factors for end-stage kidney disease were identified in patients with cardiovascular disease. These findings highlight the potential of risk factor management in patients with manifest cardiovascular disease.",
-    "laySummary": "",
-    "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s40620-021-00996-1.pdf; doi:https://doi.org/10.1007/s40620-021-00996-1; html:https://europepmc.org/articles/PMC8494654; pdf:https://europepmc.org/articles/PMC8494654?pdf=render"
-  },
-  {
-    "id": "38438269",
-    "doi": "https://doi.org/10.3399/bjgp.2023.0214",
-    "title": "Post-hospitalisation asthma management in primary care: a retrospective cohort study.",
-    "authorString": "Punyadasa D, Simms-Williams N, Adderley NJ, Thayakaran R, Mansur AH, Nirantharakumar K, Nagakumar P, Haroon S.",
-    "authorAffiliations": "",
-    "journalTitle": "The British journal of general practice : the journal of the Royal College of General Practitioners",
-    "pubYear": "2024",
-    "date": "2024-05-30",
+    "date": "2021-05-05",
     "isOpenAccess": "Y",
-    "keywords": "Management; Asthma; Cohort studies; Primary Health Care; Ethnic And Racial Minorities; Post-hospitalisation",
+    "keywords": "Genetics; Cardiomyopathy",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Clinical guidelines recommend that patients admitted to hospital for asthma attacks are reviewed in primary care following hospital discharge.<h4>Aim</h4>To evaluate asthma management in primary care following a hospital admission for asthma and its associations with patient characteristics.<h4>Design and setting</h4>A retrospective cohort study using English primary care data from the Clinical Practice Research Datalink Aurum database and linked Hospital Episode Statistics Admitted Patient Care data.<h4>Method</h4>Patients with asthma aged \u22655 years who had at least one asthma-related hospital admission from 1 January 2017 to 31 December 2019 were included. The primary outcome was a composite of any of the following delivered in primary care within 28 days from hospital discharge: asthma review, asthma management plan, asthma medication prescriptions, demonstration of inhaler technique, or smoking cessation counselling. The association between patient characteristics and delivery of clinical care was assessed using logistic regression.<h4>Results</h4>The study included 17 457 patients. A total of 10 515 (60.2%) patients received the primary outcome within 28 days of hospital discharge. There were 2311 (13.2%) who received an asthma review, 1459 (8.4%) an asthma management plan, 9996 (57.3%) an asthma medication, 1500 (8.6%) a demonstration of inhaler technique, and 52 (1.2% of smokers) had smoking cessation counselling. Patients from Black ethnic minority groups received less of this care (27%-54% lower odds, depending on age). However, short-acting bronchodilator prescriptions in the previous year were associated with an increased likelihood of the primary outcome.<h4>Conclusion</h4>A significant proportion of patients do not receive timely follow-up in primary care following asthma-related admissions to hospital, particularly among Black ethnic minority groups.",
+    "abstract": "<h4>Background</h4>Each of the cardiomyopathies, classically categorized as hypertrophic cardiomyopathy, dilated cardiomyopathy (DCM), and arrhythmogenic right ventricular cardiomyopathy, has a signature genetic theme. Hypertrophic cardiomyopathy and arrhythmogenic right ventricular cardiomyopathy are largely understood as genetic diseases of sarcomere or desmosome proteins, respectively. In contrast, >250 genes spanning >10 gene ontologies have been implicated in DCM, representing a complex and diverse genetic architecture. To clarify this, a systematic curation of evidence to establish the relationship of genes with DCM was conducted.<h4>Methods</h4>An international panel with clinical and scientific expertise in DCM genetics evaluated evidence supporting monogenic relationships of genes with idiopathic DCM. The panel used the Clinical Genome Resource semiquantitative gene-disease clinical validity classification framework with modifications for DCM genetics to classify genes into categories on the basis of the strength of currently available evidence. Representation of DCM genes on clinically available genetic testing panels was evaluated.<h4>Results</h4>Fifty-one genes with human genetic evidence were curated. Twelve genes (23%) from 8 gene ontologies were classified as having definitive (<i>BAG3</i>, <i>DES</i>, <i>FLNC</i>, <i>LMNA</i>, <i>MYH7</i>, <i>PLN</i>, <i>RBM20</i>, <i>SCN5A</i>, <i>TNNC1</i>, <i>TNNT2</i>, <i>TTN</i>) or strong (<i>DSP</i>) evidence. Seven genes (14%; <i>ACTC1</i>, <i>ACTN2</i>, <i>JPH2</i>, <i>NEXN</i>, <i>TNNI3</i>, <i>TPM1</i>, <i>VCL</i>) including 2 additional ontologies were classified as moderate evidence; these genes are likely to emerge as strong or definitive with additional evidence. Of these 19 genes, 6 were similarly classified for hypertrophic cardiomyopathy and 3 for arrhythmogenic right ventricular cardiomyopathy. Of the remaining 32 genes (63%), 25 (49%) had limited evidence, 4 (8%) were disputed, 2 (4%) had no disease relationship, and 1 (2%) was supported by animal model data only. Of the 16 evaluated clinical genetic testing panels, most definitive genes were included, but panels also included numerous genes with minimal human evidence.<h4>Conclusions</h4>In the curation of 51 genes, 19 had high evidence (12 definitive/strong, 7 moderate). It is notable that these 19 genes explain only a minority of cases, leaving the remainder of DCM genetic architecture incompletely addressed. Clinical genetic testing panels include most high-evidence genes; however, genes lacking robust evidence are also commonly included. We recommend that high-evidence DCM genes be used for clinical practice and that caution be exercised in the interpretation of variants in variable-evidence DCM genes.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.3399/BJGP.2023.0214; html:https://europepmc.org/articles/PMC10947362; pdf:https://europepmc.org/articles/PMC10947362?pdf=render"
+    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCULATIONAHA.120.053033; doi:https://doi.org/10.1161/CIRCULATIONAHA.120.053033; html:https://europepmc.org/articles/PMC8247549; pdf:https://europepmc.org/articles/PMC8247549?pdf=render"
   },
   {
     "id": "35538704",
@@ -35666,21 +35700,21 @@
     "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/1357633X221093434; doi:https://doi.org/10.1177/1357633X221093434; html:https://europepmc.org/articles/PMC11027437; pdf:https://europepmc.org/articles/PMC11027437?pdf=render"
   },
   {
-    "id": "33947203",
-    "doi": "https://doi.org/10.1161/circulationaha.120.053033",
-    "title": "Evidence-Based Assessment of Genes in Dilated Cardiomyopathy.",
-    "authorString": "Jordan E, Peterson L, Ai T, Asatryan B, Bronicki L, Brown E, Celeghin R, Edwards M, Fan J, Ingles J, James CA, Jarinova O, Johnson R, Judge DP, Lahrouchi N, Lekanne Deprez RH, Lumbers RT, Mazzarotto F, Medeiros Domingo A, Miller RL, Morales A, Murray B, Peters S, Pilichou K, Protonotarios A, Semsarian C, Shah P, Syrris P, Thaxton C, van Tintelen JP, Walsh R, Wang J, Ware J, Hershberger RE.",
+    "id": "38438269",
+    "doi": "https://doi.org/10.3399/bjgp.2023.0214",
+    "title": "Post-hospitalisation asthma management in primary care: a retrospective cohort study.",
+    "authorString": "Punyadasa D, Simms-Williams N, Adderley NJ, Thayakaran R, Mansur AH, Nirantharakumar K, Nagakumar P, Haroon S.",
     "authorAffiliations": "",
-    "journalTitle": "Circulation",
-    "pubYear": "2021",
-    "date": "2021-05-05",
+    "journalTitle": "The British journal of general practice : the journal of the Royal College of General Practitioners",
+    "pubYear": "2024",
+    "date": "2024-05-30",
     "isOpenAccess": "Y",
-    "keywords": "Genetics; Cardiomyopathy",
+    "keywords": "Management; Asthma; Cohort studies; Primary Health Care; Ethnic And Racial Minorities; Post-hospitalisation",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Each of the cardiomyopathies, classically categorized as hypertrophic cardiomyopathy, dilated cardiomyopathy (DCM), and arrhythmogenic right ventricular cardiomyopathy, has a signature genetic theme. Hypertrophic cardiomyopathy and arrhythmogenic right ventricular cardiomyopathy are largely understood as genetic diseases of sarcomere or desmosome proteins, respectively. In contrast, >250 genes spanning >10 gene ontologies have been implicated in DCM, representing a complex and diverse genetic architecture. To clarify this, a systematic curation of evidence to establish the relationship of genes with DCM was conducted.<h4>Methods</h4>An international panel with clinical and scientific expertise in DCM genetics evaluated evidence supporting monogenic relationships of genes with idiopathic DCM. The panel used the Clinical Genome Resource semiquantitative gene-disease clinical validity classification framework with modifications for DCM genetics to classify genes into categories on the basis of the strength of currently available evidence. Representation of DCM genes on clinically available genetic testing panels was evaluated.<h4>Results</h4>Fifty-one genes with human genetic evidence were curated. Twelve genes (23%) from 8 gene ontologies were classified as having definitive (<i>BAG3</i>, <i>DES</i>, <i>FLNC</i>, <i>LMNA</i>, <i>MYH7</i>, <i>PLN</i>, <i>RBM20</i>, <i>SCN5A</i>, <i>TNNC1</i>, <i>TNNT2</i>, <i>TTN</i>) or strong (<i>DSP</i>) evidence. Seven genes (14%; <i>ACTC1</i>, <i>ACTN2</i>, <i>JPH2</i>, <i>NEXN</i>, <i>TNNI3</i>, <i>TPM1</i>, <i>VCL</i>) including 2 additional ontologies were classified as moderate evidence; these genes are likely to emerge as strong or definitive with additional evidence. Of these 19 genes, 6 were similarly classified for hypertrophic cardiomyopathy and 3 for arrhythmogenic right ventricular cardiomyopathy. Of the remaining 32 genes (63%), 25 (49%) had limited evidence, 4 (8%) were disputed, 2 (4%) had no disease relationship, and 1 (2%) was supported by animal model data only. Of the 16 evaluated clinical genetic testing panels, most definitive genes were included, but panels also included numerous genes with minimal human evidence.<h4>Conclusions</h4>In the curation of 51 genes, 19 had high evidence (12 definitive/strong, 7 moderate). It is notable that these 19 genes explain only a minority of cases, leaving the remainder of DCM genetic architecture incompletely addressed. Clinical genetic testing panels include most high-evidence genes; however, genes lacking robust evidence are also commonly included. We recommend that high-evidence DCM genes be used for clinical practice and that caution be exercised in the interpretation of variants in variable-evidence DCM genes.",
+    "abstract": "<h4>Background</h4>Clinical guidelines recommend that patients admitted to hospital for asthma attacks are reviewed in primary care following hospital discharge.<h4>Aim</h4>To evaluate asthma management in primary care following a hospital admission for asthma and its associations with patient characteristics.<h4>Design and setting</h4>A retrospective cohort study using English primary care data from the Clinical Practice Research Datalink Aurum database and linked Hospital Episode Statistics Admitted Patient Care data.<h4>Method</h4>Patients with asthma aged \u22655 years who had at least one asthma-related hospital admission from 1 January 2017 to 31 December 2019 were included. The primary outcome was a composite of any of the following delivered in primary care within 28 days from hospital discharge: asthma review, asthma management plan, asthma medication prescriptions, demonstration of inhaler technique, or smoking cessation counselling. The association between patient characteristics and delivery of clinical care was assessed using logistic regression.<h4>Results</h4>The study included 17 457 patients. A total of 10 515 (60.2%) patients received the primary outcome within 28 days of hospital discharge. There were 2311 (13.2%) who received an asthma review, 1459 (8.4%) an asthma management plan, 9996 (57.3%) an asthma medication, 1500 (8.6%) a demonstration of inhaler technique, and 52 (1.2% of smokers) had smoking cessation counselling. Patients from Black ethnic minority groups received less of this care (27%-54% lower odds, depending on age). However, short-acting bronchodilator prescriptions in the previous year were associated with an increased likelihood of the primary outcome.<h4>Conclusion</h4>A significant proportion of patients do not receive timely follow-up in primary care following asthma-related admissions to hospital, particularly among Black ethnic minority groups.",
     "laySummary": "",
-    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCULATIONAHA.120.053033; doi:https://doi.org/10.1161/CIRCULATIONAHA.120.053033; html:https://europepmc.org/articles/PMC8247549; pdf:https://europepmc.org/articles/PMC8247549?pdf=render"
+    "urls": "doi:https://doi.org/10.3399/BJGP.2023.0214; html:https://europepmc.org/articles/PMC10947362; pdf:https://europepmc.org/articles/PMC10947362?pdf=render"
   },
   {
     "id": "31820220",
@@ -35699,23 +35733,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1007/s10926-019-09867-w"
   },
-  {
-    "id": "39444499",
-    "doi": "https://doi.org/10.1002/lrh2.10461",
-    "title": "Creating a learning health system to include environmental determinants of health: The GroundsWell experience.",
-    "authorString": "Rodgers SE, Geary RS, Villegas-Diaz R, Buchan IE, Burnett H, Clemens T, Crook R, Duckworth H, Green MA, King E, Zhang W, Butters O.",
-    "authorAffiliations": "",
-    "journalTitle": "Learning health systems",
-    "pubYear": "2024",
-    "date": "2024-10-10",
-    "isOpenAccess": "Y",
-    "keywords": "Public Health Research; Data Privacy; Household Record Linkage; Public Health Learning System; Record Linkage Complex Systems",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>Policies aiming to prevent ill health and reduce health inequalities need to consider the full complexity of health systems, including environmental determinants. A learning health system that incorporates environmental factors needs healthcare, social care and non-health data linkage at individual and small-area levels. Our objective was to establish privacy-preserving household record linkage for England to ensure person-level data remain secure and private when linked with data from households or the wider environment.<h4>Methods</h4>A stakeholder workshop with participants from our regional health board, together with the regional data processor, and the national data provider. The workshop discussed the risks and benefits of household linkages. This group then co-designed actionable dataflows between national and local data controllers and processors.<h4>Results</h4>A process was defined whereby the Personal Demographics Service, which includes the addresses of all patients of the National Health Service (NHS) in England, was used to match patients to a home identifier, for the time they are recorded as living at that address. Discussions with NHS England resulted in secure and quality-assured data linkages and a plan to flow these pseudonymised data onwards into regional health boards. Methods were established, including the generation of matching algorithms, transfer processes and information governance approvals. Our collaboration accelerated the development of a new data governance application, facilitating future public health intervention evaluations.<h4>Conclusion</h4>These activities have established a secure method for protecting the privacy of NHS patients in England, while allowing linkage of wider environmental data. This enables local health systems to learn from their data and improve health by optimizing non-health factors. Proportionate governance of health and linked non-health data is practical in England for incorporating key environmental factors into a learning health system.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1002/lrh2.10461; html:https://europepmc.org/articles/PMC11493545; pdf:https://europepmc.org/articles/PMC11493545?pdf=render"
-  },
   {
     "id": "35728939",
     "doi": "https://doi.org/10.1136/archdischild-2021-323681",
@@ -35750,6 +35767,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.12688/wellcomeopenres.19470.2; html:https://europepmc.org/articles/PMC11292189; pdf:https://europepmc.org/articles/PMC11292189?pdf=render"
   },
+  {
+    "id": "39444499",
+    "doi": "https://doi.org/10.1002/lrh2.10461",
+    "title": "Creating a learning health system to include environmental determinants of health: The GroundsWell experience.",
+    "authorString": "Rodgers SE, Geary RS, Villegas-Diaz R, Buchan IE, Burnett H, Clemens T, Crook R, Duckworth H, Green MA, King E, Zhang W, Butters O.",
+    "authorAffiliations": "",
+    "journalTitle": "Learning health systems",
+    "pubYear": "2024",
+    "date": "2024-10-10",
+    "isOpenAccess": "Y",
+    "keywords": "Public Health Research; Data Privacy; Household Record Linkage; Public Health Learning System; Record Linkage Complex Systems",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>Policies aiming to prevent ill health and reduce health inequalities need to consider the full complexity of health systems, including environmental determinants. A learning health system that incorporates environmental factors needs healthcare, social care and non-health data linkage at individual and small-area levels. Our objective was to establish privacy-preserving household record linkage for England to ensure person-level data remain secure and private when linked with data from households or the wider environment.<h4>Methods</h4>A stakeholder workshop with participants from our regional health board, together with the regional data processor, and the national data provider. The workshop discussed the risks and benefits of household linkages. This group then co-designed actionable dataflows between national and local data controllers and processors.<h4>Results</h4>A process was defined whereby the Personal Demographics Service, which includes the addresses of all patients of the National Health Service (NHS) in England, was used to match patients to a home identifier, for the time they are recorded as living at that address. Discussions with NHS England resulted in secure and quality-assured data linkages and a plan to flow these pseudonymised data onwards into regional health boards. Methods were established, including the generation of matching algorithms, transfer processes and information governance approvals. Our collaboration accelerated the development of a new data governance application, facilitating future public health intervention evaluations.<h4>Conclusion</h4>These activities have established a secure method for protecting the privacy of NHS patients in England, while allowing linkage of wider environmental data. This enables local health systems to learn from their data and improve health by optimizing non-health factors. Proportionate governance of health and linked non-health data is practical in England for incorporating key environmental factors into a learning health system.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1002/lrh2.10461; html:https://europepmc.org/articles/PMC11493545; pdf:https://europepmc.org/articles/PMC11493545?pdf=render"
+  },
   {
     "id": "34647377",
     "doi": "https://doi.org/10.1002/nbm.4630",
@@ -35836,21 +35870,21 @@
     "urls": "doi:https://doi.org/10.1016/j.rse.2021.112339; doi:https://doi.org/10.1016/j.rse.2021.112339; html:https://europepmc.org/articles/PMC7985619; pdf:https://europepmc.org/articles/PMC7985619?pdf=render"
   },
   {
-    "id": "37730620",
-    "doi": "https://doi.org/10.1186/s13643-023-02333-y",
-    "title": "What is known about what works in community-involved decision-making relating to urban green and blue spaces? A realist review protocol.",
-    "authorString": "Rahtz E, Bell SL, Nurse A, Wheeler BW, Guell C, Elliott LR, Thompson CW, McDougall CW, Lovell R.",
+    "id": "37117689",
+    "doi": "https://doi.org/10.1038/s43016-021-00309-6",
+    "title": "Author Correction: Nutriome-metabolome relationships provide insights into dietary intake and metabolism.",
+    "authorString": "Posma JM, Garcia-Perez I, Frost G, Aljuraiban GS, Chan Q, Van Horn L, Daviglus M, Stamler J, Holmes E, Elliott P, Nicholson JK.",
     "authorAffiliations": "",
-    "journalTitle": "Systematic reviews",
-    "pubYear": "2023",
-    "date": "2023-09-20",
-    "isOpenAccess": "Y",
+    "journalTitle": "Nature food",
+    "pubYear": "2021",
+    "date": "2021-07-01",
+    "isOpenAccess": "N",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>There is now a relatively well-established evidence base suggesting that greener living environments and time spent in urban green and blue spaces (UGBS) can be beneficial for human health and wellbeing. However, benefits are not universal and there remain widespread social inequalities in access to such resources and experiences, particularly along axes of class, race, ethnicity, age and disability, and in relation to efforts to increase the availability and accessibility of such spaces. These injustices often relate to distributive, procedural and recognition-based processes. There is growing interest in how to ensure that efforts to increase access to or use of UGBS (whether through infrastructural or social programmes) result in equitable outcomes whilst minimising potential for exacerbating existing inequalities and injustices. Community engagement is considered an important step towards more inclusive UGBS decision-making, from planning and design to management and maintenance processes. It is thought to contribute to better and more widely trusted decisions, enhanced democracy, community satisfaction, civic interest and feelings of green space ownership, and greater longevity of UGBS projects. However, uneven representation and barriers to participation can create imbalances and undermine these benefits.<h4>Methods</h4>An iterative, multi-stage realist-inspired review will be conducted to ask what works, in what context and in what ways relating to the meaningful involvement of communities in UGBS decision-making, focusing on the skills, capacities and capabilities of different stakeholders and the role of contexts and processes. 'Effectiveness' (or what works) will be understood as a multifaceted outcome, encompassing both the processes and results of community engagement efforts. Following a scoping stage to identify initial programme theory, inclusion/exclusion criteria and derive search terms, relevant databases and grey literature will be searched to identify interdisciplinary literature in two phases. The first phase will be used to further develop programme theories, which will be articulated as 'if then' statements. The second phase searches will be used to identify sources to further explore and evidence the programme and formal theory. We will assess all includable evidence for conceptual richness, prioritising more conceptually rich sources if needed.<h4>Discussion</h4>The realist synthesis will explore the key context, mechanism and outcome configurations that appear to explain if and how different approaches to community-involved UGBS decision-making are or are not effective. We will consider factors such as different conceptualisations of community, and if and how they have been involved in UGBS decision-making; the types of tools and approaches used; and the socio-cultural and political or governance structures within which decision-making takes place.",
+    "abstract": "",
     "laySummary": "",
-    "urls": "pdf:https://systematicreviewsjournal.biomedcentral.com/counter/pdf/10.1186/s13643-023-02333-y; doi:https://doi.org/10.1186/s13643-023-02333-y; html:https://europepmc.org/articles/PMC10512649; pdf:https://europepmc.org/articles/PMC10512649?pdf=render"
+    "urls": "pdf:https://www.nature.com/articles/s43016-021-00309-6.pdf; doi:https://doi.org/10.1038/s43016-021-00309-6"
   },
   {
     "id": "35193920",
@@ -35870,21 +35904,21 @@
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/2/e055773.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-055773; html:https://europepmc.org/articles/PMC8867343; pdf:https://europepmc.org/articles/PMC8867343?pdf=render"
   },
   {
-    "id": "37117689",
-    "doi": "https://doi.org/10.1038/s43016-021-00309-6",
-    "title": "Author Correction: Nutriome-metabolome relationships provide insights into dietary intake and metabolism.",
-    "authorString": "Posma JM, Garcia-Perez I, Frost G, Aljuraiban GS, Chan Q, Van Horn L, Daviglus M, Stamler J, Holmes E, Elliott P, Nicholson JK.",
+    "id": "37730620",
+    "doi": "https://doi.org/10.1186/s13643-023-02333-y",
+    "title": "What is known about what works in community-involved decision-making relating to urban green and blue spaces? A realist review protocol.",
+    "authorString": "Rahtz E, Bell SL, Nurse A, Wheeler BW, Guell C, Elliott LR, Thompson CW, McDougall CW, Lovell R.",
     "authorAffiliations": "",
-    "journalTitle": "Nature food",
-    "pubYear": "2021",
-    "date": "2021-07-01",
-    "isOpenAccess": "N",
+    "journalTitle": "Systematic reviews",
+    "pubYear": "2023",
+    "date": "2023-09-20",
+    "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "",
+    "abstract": "<h4>Background</h4>There is now a relatively well-established evidence base suggesting that greener living environments and time spent in urban green and blue spaces (UGBS) can be beneficial for human health and wellbeing. However, benefits are not universal and there remain widespread social inequalities in access to such resources and experiences, particularly along axes of class, race, ethnicity, age and disability, and in relation to efforts to increase the availability and accessibility of such spaces. These injustices often relate to distributive, procedural and recognition-based processes. There is growing interest in how to ensure that efforts to increase access to or use of UGBS (whether through infrastructural or social programmes) result in equitable outcomes whilst minimising potential for exacerbating existing inequalities and injustices. Community engagement is considered an important step towards more inclusive UGBS decision-making, from planning and design to management and maintenance processes. It is thought to contribute to better and more widely trusted decisions, enhanced democracy, community satisfaction, civic interest and feelings of green space ownership, and greater longevity of UGBS projects. However, uneven representation and barriers to participation can create imbalances and undermine these benefits.<h4>Methods</h4>An iterative, multi-stage realist-inspired review will be conducted to ask what works, in what context and in what ways relating to the meaningful involvement of communities in UGBS decision-making, focusing on the skills, capacities and capabilities of different stakeholders and the role of contexts and processes. 'Effectiveness' (or what works) will be understood as a multifaceted outcome, encompassing both the processes and results of community engagement efforts. Following a scoping stage to identify initial programme theory, inclusion/exclusion criteria and derive search terms, relevant databases and grey literature will be searched to identify interdisciplinary literature in two phases. The first phase will be used to further develop programme theories, which will be articulated as 'if then' statements. The second phase searches will be used to identify sources to further explore and evidence the programme and formal theory. We will assess all includable evidence for conceptual richness, prioritising more conceptually rich sources if needed.<h4>Discussion</h4>The realist synthesis will explore the key context, mechanism and outcome configurations that appear to explain if and how different approaches to community-involved UGBS decision-making are or are not effective. We will consider factors such as different conceptualisations of community, and if and how they have been involved in UGBS decision-making; the types of tools and approaches used; and the socio-cultural and political or governance structures within which decision-making takes place.",
     "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s43016-021-00309-6.pdf; doi:https://doi.org/10.1038/s43016-021-00309-6"
+    "urls": "pdf:https://systematicreviewsjournal.biomedcentral.com/counter/pdf/10.1186/s13643-023-02333-y; doi:https://doi.org/10.1186/s13643-023-02333-y; html:https://europepmc.org/articles/PMC10512649; pdf:https://europepmc.org/articles/PMC10512649?pdf=render"
   },
   {
     "id": "39117403",
@@ -35903,23 +35937,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1136/bmjopen-2023-082413; html:https://europepmc.org/articles/PMC11331951; pdf:https://europepmc.org/articles/PMC11331951?pdf=render"
   },
-  {
-    "id": "35251129",
-    "doi": "https://doi.org/10.3389/fgene.2022.818574",
-    "title": "Calculating Polygenic Risk Scores (PRS) in UK Biobank: A Practical Guide for Epidemiologists.",
-    "authorString": "Collister JA, Liu X, Clifton L.",
-    "authorAffiliations": "",
-    "journalTitle": "Frontiers in genetics",
-    "pubYear": "2022",
-    "date": "2022-02-18",
-    "isOpenAccess": "Y",
-    "keywords": "Polygenic Score; Genetic Risk Score; Uk Biobank; Polygenic Risk Score; Worked Example",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "A polygenic risk score estimates the genetic risk of an individual for some disease or trait, calculated by aggregating the effect of many common variants associated with the condition. With the increasing availability of genetic data in large cohort studies such as the UK Biobank, inclusion of this genetic risk as a covariate in statistical analyses is becoming more widespread. Previously this required specialist knowledge, but as tooling and data availability have improved it has become more feasible for statisticians and epidemiologists to calculate existing scores themselves for use in analyses. While tutorial resources exist for conducting genome-wide association studies and generating of new polygenic risk scores, fewer guides exist for the simple calculation and application of existing genetic scores. This guide outlines the key steps of this process: selection of suitable polygenic risk scores from the literature, extraction of relevant genetic variants and verification of their quality, calculation of the risk score and key considerations of its inclusion in statistical models, using the UK Biobank imputed data as a model data set. Many of the techniques in this guide will generalize to other datasets, however we also focus on some of the specific techniques required for using data in the formats UK Biobank have selected. This includes some of the challenges faced when working with large numbers of variants, where the computation time required by some tools is impractical. While we have focused on only a couple of tools, which may not be the best ones for every given aspect of the process, one barrier to working with genetic data is the sheer volume of tools available, and the difficulty for a novice to assess their viability. By discussing in depth a couple of tools that are adequate for the calculation even at large scale, we hope to make polygenic risk scores more accessible to a wider range of researchers.",
-    "laySummary": "",
-    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fgene.2022.818574/pdf; doi:https://doi.org/10.3389/fgene.2022.818574; html:https://europepmc.org/articles/PMC8894758; pdf:https://europepmc.org/articles/PMC8894758?pdf=render"
-  },
   {
     "id": "34648354",
     "doi": "https://doi.org/10.1126/science.abj1541",
@@ -35937,6 +35954,23 @@
     "laySummary": "",
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9904207; doi:https://doi.org/10.1126/science.abj1541; html:https://europepmc.org/articles/PMC9904207; pdf:https://europepmc.org/articles/PMC9904207?pdf=render; doi:https://doi.org/10.1126/science.abj1541"
   },
+  {
+    "id": "35251129",
+    "doi": "https://doi.org/10.3389/fgene.2022.818574",
+    "title": "Calculating Polygenic Risk Scores (PRS) in UK Biobank: A Practical Guide for Epidemiologists.",
+    "authorString": "Collister JA, Liu X, Clifton L.",
+    "authorAffiliations": "",
+    "journalTitle": "Frontiers in genetics",
+    "pubYear": "2022",
+    "date": "2022-02-18",
+    "isOpenAccess": "Y",
+    "keywords": "Polygenic Score; Genetic Risk Score; Uk Biobank; Polygenic Risk Score; Worked Example",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "A polygenic risk score estimates the genetic risk of an individual for some disease or trait, calculated by aggregating the effect of many common variants associated with the condition. With the increasing availability of genetic data in large cohort studies such as the UK Biobank, inclusion of this genetic risk as a covariate in statistical analyses is becoming more widespread. Previously this required specialist knowledge, but as tooling and data availability have improved it has become more feasible for statisticians and epidemiologists to calculate existing scores themselves for use in analyses. While tutorial resources exist for conducting genome-wide association studies and generating of new polygenic risk scores, fewer guides exist for the simple calculation and application of existing genetic scores. This guide outlines the key steps of this process: selection of suitable polygenic risk scores from the literature, extraction of relevant genetic variants and verification of their quality, calculation of the risk score and key considerations of its inclusion in statistical models, using the UK Biobank imputed data as a model data set. Many of the techniques in this guide will generalize to other datasets, however we also focus on some of the specific techniques required for using data in the formats UK Biobank have selected. This includes some of the challenges faced when working with large numbers of variants, where the computation time required by some tools is impractical. While we have focused on only a couple of tools, which may not be the best ones for every given aspect of the process, one barrier to working with genetic data is the sheer volume of tools available, and the difficulty for a novice to assess their viability. By discussing in depth a couple of tools that are adequate for the calculation even at large scale, we hope to make polygenic risk scores more accessible to a wider range of researchers.",
+    "laySummary": "",
+    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fgene.2022.818574/pdf; doi:https://doi.org/10.3389/fgene.2022.818574; html:https://europepmc.org/articles/PMC8894758; pdf:https://europepmc.org/articles/PMC8894758?pdf=render"
+  },
   {
     "id": "31564467",
     "doi": "https://doi.org/10.1016/s2215-0366(19)30369-4",
@@ -36124,23 +36158,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/11/e065142.full.pdf; doi:https://doi.org/10.1136/bmjopen-2022-065142; html:https://europepmc.org/articles/PMC9709810; pdf:https://europepmc.org/articles/PMC9709810?pdf=render"
   },
-  {
-    "id": "33888728",
-    "doi": "https://doi.org/10.1038/s41598-021-86331-x",
-    "title": "A multidimensional measure of polypharmacy for older adults using the Health and Retirement Study.",
-    "authorString": "Carr E, Federman A, Dzahini O, Dobson RJ, Bendayan R.",
-    "authorAffiliations": "",
-    "journalTitle": "Scientific reports",
-    "pubYear": "2021",
-    "date": "2021-04-22",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Polypharmacy is commonly defined based on the number of medications taken concurrently using standard cut-offs, but several studies have highlighted the need for a multidimensional assessment. We developed a multidimensional measure of polypharmacy and compared with standard cut-offs. Data were extracted for 2141 respondents of the 2007 Prescription Drug Survey, a sub-study of the Health Retirement Study. Latent classes were identified based on multiple indicators of polypharmacy, including quantity, temporality and risk profile. A four-class model was selected based on fit statistics and clinical interpretability: 'High risk, long-term' (Class 1), 'Low risk, long-term' (Class 2), 'High risk, short-term' (Class 3), and 'High risk for drug interactions, medium-term, regular' (Class 4). Classes differed regarding sex, cohabitation, disability and multimorbidity. Participants in the 'low risk' class tended to be male, cohabitating, and reported fewer health conditions, compared to 'high risk' classes. Polypharmacy classes were compared to standard cut-offs (5+ or 9+ medications) in terms of overlap and mortality risk. The three 'high risk' classes overlapped with the groups concurrently taking 5+ and 9+ medications per month. However, the multidimensional measure further differentiated individuals in terms of risk profile and temporality of medication taking, thus offering a richer assessment of polypharmacy.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41598-021-86331-x.pdf; doi:https://doi.org/10.1038/s41598-021-86331-x; html:https://europepmc.org/articles/PMC8062687; pdf:https://europepmc.org/articles/PMC8062687?pdf=render"
-  },
   {
     "id": "34053260",
     "doi": "https://doi.org/10.1098/rstb.2020.0283",
@@ -36158,6 +36175,23 @@
     "laySummary": "",
     "urls": "pdf:https://royalsocietypublishing.org/doi/pdf/10.1098/rstb.2020.0283; doi:https://doi.org/10.1098/rstb.2020.0283; html:https://europepmc.org/articles/PMC8165604; pdf:https://europepmc.org/articles/PMC8165604?pdf=render"
   },
+  {
+    "id": "33888728",
+    "doi": "https://doi.org/10.1038/s41598-021-86331-x",
+    "title": "A multidimensional measure of polypharmacy for older adults using the Health and Retirement Study.",
+    "authorString": "Carr E, Federman A, Dzahini O, Dobson RJ, Bendayan R.",
+    "authorAffiliations": "",
+    "journalTitle": "Scientific reports",
+    "pubYear": "2021",
+    "date": "2021-04-22",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Polypharmacy is commonly defined based on the number of medications taken concurrently using standard cut-offs, but several studies have highlighted the need for a multidimensional assessment. We developed a multidimensional measure of polypharmacy and compared with standard cut-offs. Data were extracted for 2141 respondents of the 2007 Prescription Drug Survey, a sub-study of the Health Retirement Study. Latent classes were identified based on multiple indicators of polypharmacy, including quantity, temporality and risk profile. A four-class model was selected based on fit statistics and clinical interpretability: 'High risk, long-term' (Class 1), 'Low risk, long-term' (Class 2), 'High risk, short-term' (Class 3), and 'High risk for drug interactions, medium-term, regular' (Class 4). Classes differed regarding sex, cohabitation, disability and multimorbidity. Participants in the 'low risk' class tended to be male, cohabitating, and reported fewer health conditions, compared to 'high risk' classes. Polypharmacy classes were compared to standard cut-offs (5+ or 9+ medications) in terms of overlap and mortality risk. The three 'high risk' classes overlapped with the groups concurrently taking 5+ and 9+ medications per month. However, the multidimensional measure further differentiated individuals in terms of risk profile and temporality of medication taking, thus offering a richer assessment of polypharmacy.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41598-021-86331-x.pdf; doi:https://doi.org/10.1038/s41598-021-86331-x; html:https://europepmc.org/articles/PMC8062687; pdf:https://europepmc.org/articles/PMC8062687?pdf=render"
+  },
   {
     "id": "32285648",
     "doi": "https://doi.org/10.1002/ehf2.12689",
@@ -36226,23 +36260,6 @@
     "laySummary": "",
     "urls": "pdf:https://medinform.jmir.org/2020/12/e23530/PDF; doi:https://doi.org/10.2196/23530; html:https://europepmc.org/articles/PMC7773511"
   },
-  {
-    "id": "38553074",
-    "doi": "https://doi.org/10.1136/bmjopen-2024-085392",
-    "title": "Protocol for a mixed-methods study to develop and feasibility test a digital system for the capture of patient-reported outcomes (PROs) in patients receiving chimeric antigen receptor T-cell (CAR-T) therapies (the PRO-CAR-T study).",
-    "authorString": "Hughes SE, McMullan C, Aiyegbusi OL, Shaw K, Kinsella F, Ferguson P, Khatsuria F, Burns D, Pyatt L, Ansell J, Chakera E, Richardson-Abraham J, Denniston AK, Davies EH, Craddock C, Calvert M.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2024",
-    "date": "2024-03-29",
-    "isOpenAccess": "Y",
-    "keywords": "Gene therapy; Quality of life; Haematology; Patient-centered Care; Ehealth; Patient Reported Outcome Measures",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>Chimeric antigen receptor (CAR) T-cell therapies are novel, potentially curative therapies for haematological malignancies. CAR T-cell therapies are associated with severe toxicities, meaning patients require monitoring during acute and postacute treatment phases. Electronic patient-reported outcomes (ePROs), self-reports of health status provided via online questionnaires, can complement clinician observation with potential to improve patient outcomes. This study will develop and evaluate feasibility of a new ePRO system for CAR-T patients in routine care.<h4>Methods and analysis</h4>Multiphase, mixed-methods study involving multiple stakeholder groups (patients, family members, carers, clinicians, academics/researchers and policy-makers). The intervention development phase comprises a Delphi study to select PRO measures for the digital system, a codesign workshop and consensus meetings to establish thresholds for notifications to the clinical team if a patient reports severe symptoms or side effects. Usability testing will evaluate how users interact with the digital system and, lastly, we will evaluate ePRO system feasibility with 30 CAR-T patients (adults aged 18+ years) when used in addition to usual care. Feasibility study participants will use the ePRO system to submit self-reports of symptoms, treatment tolerability and quality of life at specific time points. The CAR-T clinical team will respond to system notifications triggered by patients' submitted responses with actions in line with standard clinical practice. Feasibility measures will be collected at prespecified time points following CAR T-cell infusion. A qualitative substudy involving patients and clinical team members will explore acceptability of the ePRO system.<h4>Ethics and dissemination</h4>Favourable ethical opinion was granted by the Health and Social Care Research Ethics Committee B(HSC REC B) (ref: 23/NI/0104) on 28 September 2023. Findings will be submitted for publication in high-quality, peer-reviewed journals. Summaries of results, codeveloped with the Blood and Transplant Research Unit Patient and Public Involvement and Engagement group, will be disseminated to all interested groups.<h4>Trial registration number</h4>ISCTRN11232653.",
-    "laySummary": "",
-    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/14/3/e085392.full.pdf; doi:https://doi.org/10.1136/bmjopen-2024-085392; html:https://europepmc.org/articles/PMC10982800; pdf:https://europepmc.org/articles/PMC10982800?pdf=render"
-  },
   {
     "id": "35247983",
     "doi": "https://doi.org/10.1186/s12877-021-02673-1",
@@ -36260,6 +36277,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1186/s12877-021-02673-1; doi:https://doi.org/10.1186/s12877-021-02673-1; html:https://europepmc.org/articles/PMC8897728; pdf:https://europepmc.org/articles/PMC8897728?pdf=render"
   },
+  {
+    "id": "38553074",
+    "doi": "https://doi.org/10.1136/bmjopen-2024-085392",
+    "title": "Protocol for a mixed-methods study to develop and feasibility test a digital system for the capture of patient-reported outcomes (PROs) in patients receiving chimeric antigen receptor T-cell (CAR-T) therapies (the PRO-CAR-T study).",
+    "authorString": "Hughes SE, McMullan C, Aiyegbusi OL, Shaw K, Kinsella F, Ferguson P, Khatsuria F, Burns D, Pyatt L, Ansell J, Chakera E, Richardson-Abraham J, Denniston AK, Davies EH, Craddock C, Calvert M.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2024",
+    "date": "2024-03-29",
+    "isOpenAccess": "Y",
+    "keywords": "Gene therapy; Quality of life; Haematology; Patient-centered Care; Ehealth; Patient Reported Outcome Measures",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>Chimeric antigen receptor (CAR) T-cell therapies are novel, potentially curative therapies for haematological malignancies. CAR T-cell therapies are associated with severe toxicities, meaning patients require monitoring during acute and postacute treatment phases. Electronic patient-reported outcomes (ePROs), self-reports of health status provided via online questionnaires, can complement clinician observation with potential to improve patient outcomes. This study will develop and evaluate feasibility of a new ePRO system for CAR-T patients in routine care.<h4>Methods and analysis</h4>Multiphase, mixed-methods study involving multiple stakeholder groups (patients, family members, carers, clinicians, academics/researchers and policy-makers). The intervention development phase comprises a Delphi study to select PRO measures for the digital system, a codesign workshop and consensus meetings to establish thresholds for notifications to the clinical team if a patient reports severe symptoms or side effects. Usability testing will evaluate how users interact with the digital system and, lastly, we will evaluate ePRO system feasibility with 30 CAR-T patients (adults aged 18+ years) when used in addition to usual care. Feasibility study participants will use the ePRO system to submit self-reports of symptoms, treatment tolerability and quality of life at specific time points. The CAR-T clinical team will respond to system notifications triggered by patients' submitted responses with actions in line with standard clinical practice. Feasibility measures will be collected at prespecified time points following CAR T-cell infusion. A qualitative substudy involving patients and clinical team members will explore acceptability of the ePRO system.<h4>Ethics and dissemination</h4>Favourable ethical opinion was granted by the Health and Social Care Research Ethics Committee B(HSC REC B) (ref: 23/NI/0104) on 28 September 2023. Findings will be submitted for publication in high-quality, peer-reviewed journals. Summaries of results, codeveloped with the Blood and Transplant Research Unit Patient and Public Involvement and Engagement group, will be disseminated to all interested groups.<h4>Trial registration number</h4>ISCTRN11232653.",
+    "laySummary": "",
+    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/14/3/e085392.full.pdf; doi:https://doi.org/10.1136/bmjopen-2024-085392; html:https://europepmc.org/articles/PMC10982800; pdf:https://europepmc.org/articles/PMC10982800?pdf=render"
+  },
   {
     "id": "34581777",
     "doi": "https://doi.org/10.1182/bloodadvances.2021005453",
@@ -36481,23 +36515,6 @@
     "laySummary": "",
     "urls": "pdf:http://www.thelancet.com/article/S2589537020304028/pdf; doi:https://doi.org/10.1016/j.eclinm.2020.100658; html:https://europepmc.org/articles/PMC7788440; pdf:https://europepmc.org/articles/PMC7788440?pdf=render"
   },
-  {
-    "id": "38296965",
-    "doi": "https://doi.org/10.1038/s41467-023-43644-x",
-    "title": "Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial.",
-    "authorString": "RECOVERY Collaborative Group, Horby PW, Peto L, Staplin N, Campbell M, Pessoa-Amorim G, Mafham M, Emberson JR, Stewart R, Prudon B, Uriel A, Green CA, Dhasmana DJ, Malein F, Majumdar J, Collini P, Shurmer J, Yates B, Baillie JK, Buch MH, Day J, Faust SN, Jaki T, Jeffery K, Juszczak E, Knight M, Lim WS, Montgomery A, Mumford A, Rowan K, Thwaites G, Haynes R, Landray MJ.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature communications",
-    "pubYear": "2024",
-    "date": "2024-01-31",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Dimethyl fumarate (DMF) inhibits inflammasome-mediated inflammation and has been proposed as a treatment for patients hospitalised with COVID-19. This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple treatments in patients hospitalised for COVID-19 (NCT04381936, ISRCTN50189673). In this assessment of DMF performed at 27 UK hospitals, adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. Between 2 March 2021 and 18 November 2021, 713 patients were enroled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients received corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.86-1.47; p\u2009=\u20090.40). There was no significant effect of DMF on any secondary outcome.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41467-023-43644-x.pdf; doi:https://doi.org/10.1038/s41467-023-43644-x; html:https://europepmc.org/articles/PMC10831058; pdf:https://europepmc.org/articles/PMC10831058?pdf=render"
-  },
   {
     "id": "33185016",
     "doi": "https://doi.org/10.1002/art.41593",
@@ -36515,6 +36532,23 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/art.41593; doi:https://doi.org/10.1002/art.41593; html:https://europepmc.org/articles/PMC8252419; pdf:https://europepmc.org/articles/PMC8252419?pdf=render"
   },
+  {
+    "id": "38296965",
+    "doi": "https://doi.org/10.1038/s41467-023-43644-x",
+    "title": "Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial.",
+    "authorString": "RECOVERY Collaborative Group, Horby PW, Peto L, Staplin N, Campbell M, Pessoa-Amorim G, Mafham M, Emberson JR, Stewart R, Prudon B, Uriel A, Green CA, Dhasmana DJ, Malein F, Majumdar J, Collini P, Shurmer J, Yates B, Baillie JK, Buch MH, Day J, Faust SN, Jaki T, Jeffery K, Juszczak E, Knight M, Lim WS, Montgomery A, Mumford A, Rowan K, Thwaites G, Haynes R, Landray MJ.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature communications",
+    "pubYear": "2024",
+    "date": "2024-01-31",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Dimethyl fumarate (DMF) inhibits inflammasome-mediated inflammation and has been proposed as a treatment for patients hospitalised with COVID-19. This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple treatments in patients hospitalised for COVID-19 (NCT04381936, ISRCTN50189673). In this assessment of DMF performed at 27 UK hospitals, adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. Between 2 March 2021 and 18 November 2021, 713 patients were enroled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients received corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.86-1.47; p\u2009=\u20090.40). There was no significant effect of DMF on any secondary outcome.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41467-023-43644-x.pdf; doi:https://doi.org/10.1038/s41467-023-43644-x; html:https://europepmc.org/articles/PMC10831058; pdf:https://europepmc.org/articles/PMC10831058?pdf=render"
+  },
   {
     "id": "35354069",
     "doi": "https://doi.org/10.1016/j.cmet.2022.03.002",
@@ -36600,23 +36634,6 @@
     "laySummary": "",
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8609771; doi:https://doi.org/10.1038/s41586-021-03243-6; html:https://europepmc.org/articles/PMC8609771; pdf:https://europepmc.org/articles/PMC8609771?pdf=render; doi:https://doi.org/10.1038/s41586-021-03243-6"
   },
-  {
-    "id": "38964793",
-    "doi": "https://doi.org/10.1136/bmjopen-2023-072314",
-    "title": "Impact of the first year of COVID-19 vaccination strategy in Brazil: an ecological study.",
-    "authorString": "Aguilar S, Bastos LSL, Ma\u00e7aira P, Bai\u00e3o F, Sim\u00f5es P, Cerbino-Neto J, Ranzani O, Hamacher S, Bozza FA.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2024",
-    "date": "2024-07-04",
-    "isOpenAccess": "Y",
-    "keywords": "epidemiology; Public Health; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objectives</h4>No consensus exists about the best COVID-19 vaccination strategy to be adopted by low-income and middle-income countries. Brazil adopted an age-based calendar strategy to reduce mortality and the burden on the healthcare system. This study evaluates the impact of the vaccination campaign in Brazil on the progression of the reported COVID-19 deaths.<h4>Methods</h4>This ecological study analyses the dynamic of vaccination coverage and COVID-19 deaths in hospitalised adults (\u226520 years) during the first year of the COVID-19 vaccination roll-out (January to December 2021) using nationwide data (DATASUS). We stratified the adult population into 20-49, 50-59, 60-69 and 70+ years. The dynamic effect of the vaccination campaign on mortality rates was estimated by applying a negative binomial regression. The prevented and possible preventable deaths (observed deaths higher than expected) and potential years of life lost (PYLL) for each age group were obtained in a counterfactual analysis.<h4>Results</h4>During the first year of COVID-19 vaccination, 266\u2009153\u2009517 doses were administered, achieving 91% first-dose coverage. A total of 380\u2009594 deaths were reported, 154\u2009091 (40%) in 70+ years\u2009and 136\u2009804 (36%) from 50-59 or 20-49 years. The mortality rates of 70+ decreased by 52% (rate ratio [95%\u2009CI]: 0.48 [0.43-0.53]) in 6 months, whereas rates for 20-49 were still increasing due to low coverage (52%). The vaccination roll-out strategy prevented 59\u2009618 deaths, 53\u2009088 (89%) from those aged 70+ years. However, the strategy did not prevent 54\u2009797 deaths, 85% from those under 60 years, being 26\u2009344 (45%) only in 20-49, corresponding to 1 589 271 PYLL, being 1 080 104 PYLL (68%) from those aged 20-49 years.<h4>Conclusion</h4>The adopted aged-based calendar vaccination strategy initially reduced mortality in the oldest but did not prevent the deaths of the youngest as effectively as compared with the older age group. Countries with a high burden, limited vaccine supply and young populations should consider other factors beyond the age to prioritise who should be vaccinated first.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1136/bmjopen-2023-072314; html:https://europepmc.org/articles/PMC11227766; pdf:https://europepmc.org/articles/PMC11227766?pdf=render"
-  },
   {
     "id": "33769566",
     "doi": "https://doi.org/10.1111/bph.15459",
@@ -36634,6 +36651,23 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/bph.15459; doi:https://doi.org/10.1111/bph.15459"
   },
+  {
+    "id": "38964793",
+    "doi": "https://doi.org/10.1136/bmjopen-2023-072314",
+    "title": "Impact of the first year of COVID-19 vaccination strategy in Brazil: an ecological study.",
+    "authorString": "Aguilar S, Bastos LSL, Ma\u00e7aira P, Bai\u00e3o F, Sim\u00f5es P, Cerbino-Neto J, Ranzani O, Hamacher S, Bozza FA.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2024",
+    "date": "2024-07-04",
+    "isOpenAccess": "Y",
+    "keywords": "epidemiology; Public Health; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objectives</h4>No consensus exists about the best COVID-19 vaccination strategy to be adopted by low-income and middle-income countries. Brazil adopted an age-based calendar strategy to reduce mortality and the burden on the healthcare system. This study evaluates the impact of the vaccination campaign in Brazil on the progression of the reported COVID-19 deaths.<h4>Methods</h4>This ecological study analyses the dynamic of vaccination coverage and COVID-19 deaths in hospitalised adults (\u226520 years) during the first year of the COVID-19 vaccination roll-out (January to December 2021) using nationwide data (DATASUS). We stratified the adult population into 20-49, 50-59, 60-69 and 70+ years. The dynamic effect of the vaccination campaign on mortality rates was estimated by applying a negative binomial regression. The prevented and possible preventable deaths (observed deaths higher than expected) and potential years of life lost (PYLL) for each age group were obtained in a counterfactual analysis.<h4>Results</h4>During the first year of COVID-19 vaccination, 266\u2009153\u2009517 doses were administered, achieving 91% first-dose coverage. A total of 380\u2009594 deaths were reported, 154\u2009091 (40%) in 70+ years\u2009and 136\u2009804 (36%) from 50-59 or 20-49 years. The mortality rates of 70+ decreased by 52% (rate ratio [95%\u2009CI]: 0.48 [0.43-0.53]) in 6 months, whereas rates for 20-49 were still increasing due to low coverage (52%). The vaccination roll-out strategy prevented 59\u2009618 deaths, 53\u2009088 (89%) from those aged 70+ years. However, the strategy did not prevent 54\u2009797 deaths, 85% from those under 60 years, being 26\u2009344 (45%) only in 20-49, corresponding to 1 589 271 PYLL, being 1 080 104 PYLL (68%) from those aged 20-49 years.<h4>Conclusion</h4>The adopted aged-based calendar vaccination strategy initially reduced mortality in the oldest but did not prevent the deaths of the youngest as effectively as compared with the older age group. Countries with a high burden, limited vaccine supply and young populations should consider other factors beyond the age to prioritise who should be vaccinated first.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1136/bmjopen-2023-072314; html:https://europepmc.org/articles/PMC11227766; pdf:https://europepmc.org/articles/PMC11227766?pdf=render"
+  },
   {
     "id": "35068290",
     "doi": "https://doi.org/10.1080/09537104.2021.2003317",
@@ -36669,21 +36703,21 @@
     "urls": "pdf:https://www.nature.com/articles/s41467-023-43522-6.pdf; doi:https://doi.org/10.1038/s41467-023-43522-6; html:https://europepmc.org/articles/PMC10692198; pdf:https://europepmc.org/articles/PMC10692198?pdf=render"
   },
   {
-    "id": "35751107",
-    "doi": "https://doi.org/10.1186/s13059-022-02702-1",
-    "title": "Epigenomic analysis reveals a dynamic and context-specific macrophage enhancer landscape associated with innate immune activation and tolerance.",
-    "authorString": "Zhang P, Amarasinghe HE, Whalley JP, Tay C, Fang H, Migliorini G, Brown AC, Allcock A, Scozzafava G, Rath P, Davies B, Knight JC.",
+    "id": "34593247",
+    "doi": "https://doi.org/10.1016/j.injury.2021.09.027",
+    "title": "An evaluation of the association between fault attribution and healthcare costs and trajectories in the first three years after transport\u00a0injury.",
+    "authorString": "Melita J G, Joanna F D, Alex C, Jennie P, Shanthi A, Belinda J G.",
     "authorAffiliations": "",
-    "journalTitle": "Genome biology",
-    "pubYear": "2022",
-    "date": "2022-06-24",
-    "isOpenAccess": "Y",
-    "keywords": "",
+    "journalTitle": "Injury",
+    "pubYear": "2021",
+    "date": "2021-09-20",
+    "isOpenAccess": "N",
+    "keywords": "Trauma; Compensation; Insurance; Biopsychosocial; Health Service Use",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Chromatin states and enhancers associate gene expression, cell identity and disease. Here, we systematically delineate the acute innate immune response to endotoxin in terms of human macrophage enhancer activity and contrast with endotoxin tolerance, profiling the coding and non-coding transcriptome, chromatin accessibility and epigenetic modifications.<h4>Results</h4>We describe the spectrum of enhancers under acute and tolerance conditions and the regulatory networks between these enhancers and biological processes including gene expression, splicing regulation, transcription factor binding and enhancer RNA signatures. We demonstrate that the vast majority of differentially regulated enhancers on acute stimulation are subject to tolerance and that expression quantitative trait loci, disease-risk variants and eRNAs are enriched in these regulatory regions and related to context-specific gene expression. We find enrichment for context-specific eQTL involving endotoxin response and specific infections and delineate specific differential regions informative for GWAS variants in inflammatory bowel disease and multiple sclerosis, together with a context-specific enhancer involving a bacterial infection eQTL for KLF4. We show enrichment in differential enhancers for tolerance involving transcription factors NF\u03baB-p65, STATs and IRFs and prioritize putative causal genes directly linking genetic variants and disease risk enhancers. We further delineate similarities and differences in epigenetic landscape between stem cell-derived macrophages and primary cells and characterize the context-specific enhancer activities for key innate immune response genes KLF4, SLAMF1 and IL2RA.<h4>Conclusions</h4>Our study demonstrates the importance of context-specific macrophage enhancers in gene regulation and utility for interpreting disease associations, providing a roadmap to link genetic variants with molecular and cellular functions.",
+    "abstract": "<h4>Background</h4>People with complex medical and psychosocial issues have high healthcare needs. This registry-based cohort study sought to quantify the association between external fault attribution, recorded during compensation claim lodgement, and the cost and patterns of healthcare utilisation.<h4>Methods</h4>6,144 survivors of transport-related major trauma between 1 July 2010 and 30 June 2016 were extracted from the Victorian State Trauma Registry (VSTR) and linked to treatment payments from the Transport Accident Commission (TAC). Associations between fault and healthcare costs were examined with Generalised Linear Regression. Healthcare trajectories were identified using Group-Based Multi-Trajectory Modelling and included medical treatments from a physician, or pain, mental health and physical therapy treatments for the first three years post-injury. Trajectories were validated against the EQ-5D-3L health status summary score using mixed linear regression.<h4>Results</h4>While injury severity had the strongest association with healthcare use, people who attributed fault to another had 9% higher healthcare costs. Six multi-trajectory groups were identified: 36% had low treatments over time; 25% had a rapid decline from high medical and physical therapy by 12-months; 12% had moderate to high medical and physical therapy that declined by 2-3 years; 11% had a gradual decline in medical treatment, an early increase in physical therapy but low pain and mental health treatment; 8% had high or increasing medical and physical therapy, moderate mental health therapy and low pain treatment; and 7% had moderate-high treatment across all domains. All groups had poorer health status compared with the group with low treatment levels, and people who attributed fault to another had higher risk of following trajectories with higher levels of treatment versus the low treatment group (beta=0.34, SE=0.12, p=0.01).<h4>Conclusion</h4>These findings highlight the need to provide pro-active multidisciplinary care coordination for people with complex needs after injury to better optimise recovery.",
     "laySummary": "",
-    "urls": "pdf:https://genomebiology.biomedcentral.com/counter/pdf/10.1186/s13059-022-02702-1; doi:https://doi.org/10.1186/s13059-022-02702-1; html:https://europepmc.org/articles/PMC9229144; pdf:https://europepmc.org/articles/PMC9229144?pdf=render"
+    "urls": "doi:https://doi.org/10.1016/j.injury.2021.09.027"
   },
   {
     "id": "35520099",
@@ -36703,38 +36737,21 @@
     "urls": "doi:https://doi.org/10.23889/ijpds.v6i1.1718; html:https://europepmc.org/articles/PMC9052961; pdf:https://europepmc.org/articles/PMC9052961?pdf=render"
   },
   {
-    "id": "34593247",
-    "doi": "https://doi.org/10.1016/j.injury.2021.09.027",
-    "title": "An evaluation of the association between fault attribution and healthcare costs and trajectories in the first three years after transport\u00a0injury.",
-    "authorString": "Melita J G, Joanna F D, Alex C, Jennie P, Shanthi A, Belinda J G.",
-    "authorAffiliations": "",
-    "journalTitle": "Injury",
-    "pubYear": "2021",
-    "date": "2021-09-20",
-    "isOpenAccess": "N",
-    "keywords": "Trauma; Compensation; Insurance; Biopsychosocial; Health Service Use",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>People with complex medical and psychosocial issues have high healthcare needs. This registry-based cohort study sought to quantify the association between external fault attribution, recorded during compensation claim lodgement, and the cost and patterns of healthcare utilisation.<h4>Methods</h4>6,144 survivors of transport-related major trauma between 1 July 2010 and 30 June 2016 were extracted from the Victorian State Trauma Registry (VSTR) and linked to treatment payments from the Transport Accident Commission (TAC). Associations between fault and healthcare costs were examined with Generalised Linear Regression. Healthcare trajectories were identified using Group-Based Multi-Trajectory Modelling and included medical treatments from a physician, or pain, mental health and physical therapy treatments for the first three years post-injury. Trajectories were validated against the EQ-5D-3L health status summary score using mixed linear regression.<h4>Results</h4>While injury severity had the strongest association with healthcare use, people who attributed fault to another had 9% higher healthcare costs. Six multi-trajectory groups were identified: 36% had low treatments over time; 25% had a rapid decline from high medical and physical therapy by 12-months; 12% had moderate to high medical and physical therapy that declined by 2-3 years; 11% had a gradual decline in medical treatment, an early increase in physical therapy but low pain and mental health treatment; 8% had high or increasing medical and physical therapy, moderate mental health therapy and low pain treatment; and 7% had moderate-high treatment across all domains. All groups had poorer health status compared with the group with low treatment levels, and people who attributed fault to another had higher risk of following trajectories with higher levels of treatment versus the low treatment group (beta=0.34, SE=0.12, p=0.01).<h4>Conclusion</h4>These findings highlight the need to provide pro-active multidisciplinary care coordination for people with complex needs after injury to better optimise recovery.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.injury.2021.09.027"
-  },
-  {
-    "id": "31588514",
-    "doi": "https://doi.org/10.1093/ptj/pzz151",
-    "title": "Physical Activity and Sedentary Behavior 6\u00a0Months After Musculoskeletal Trauma: What Factors Predict Recovery?",
-    "authorString": "Ekegren CL, Climie RE, Simpson PM, Owen N, Dunstan DW, Veitch W, Gabbe BJ.",
+    "id": "35751107",
+    "doi": "https://doi.org/10.1186/s13059-022-02702-1",
+    "title": "Epigenomic analysis reveals a dynamic and context-specific macrophage enhancer landscape associated with innate immune activation and tolerance.",
+    "authorString": "Zhang P, Amarasinghe HE, Whalley JP, Tay C, Fang H, Migliorini G, Brown AC, Allcock A, Scozzafava G, Rath P, Davies B, Knight JC.",
     "authorAffiliations": "",
-    "journalTitle": "Physical therapy",
-    "pubYear": "2020",
-    "date": "2020-02-01",
-    "isOpenAccess": "N",
+    "journalTitle": "Genome biology",
+    "pubYear": "2022",
+    "date": "2022-06-24",
+    "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Physical activity is increasingly recognized as an important marker of functional recovery following fracture.<h4>Objective</h4>The objectives of this study were to measure sedentary behavior and physical activity 2\u00a0weeks and 6\u00a0months following fracture and to determine associated demographic and injury factors.<h4>Design</h4>This was an observational study.<h4>Methods</h4>Two weeks and 6\u00a0months following fracture, 83 adults who were 18 to 69\u00a0years old and had upper limb (UL) or lower limb (LL) fractures wore an accelerometer and an inclinometer for 10\u00a0days. We calculated sitting time, steps, moderate-intensity physical activity (MPA), and vigorous-intensity physical activity and conducted linear mixed-effects multivariable regression analyses to determine factors associated with temporal changes in activity.<h4>Results</h4>At 6\u00a0months versus 2\u00a0weeks after fracture, participants sat less, took more steps, and engaged in more MPA. Participants with LL fractures sat 2\u00a0hours more, took 66% fewer steps, and engaged in 77% less MPA than participants with UL fractures. Greater reductions in sitting time were observed for participants in the youngest age group and with LL fractures, participants with high preinjury activity, and participants who were overweight or obese. For steps, greater improvement was observed for participants in the youngest and middle-aged groups and those with LL fractures. For MPA, greater improvement was observed for middle-aged participants and those with LL fractures.<h4>Limitations</h4>Although this study was sufficiently powered for the analysis of major categories, a convenience sample that may not be representative of all people with musculoskeletal trauma was used.<h4>Conclusions</h4>Working-age adults with LL fractures had lower levels of physical activity 6\u00a0months after fracture than those with UL fractures. Older adults showed less improvement over time, suggesting that they are an important target group for interventions aimed at regaining preinjury activity levels.",
+    "abstract": "<h4>Background</h4>Chromatin states and enhancers associate gene expression, cell identity and disease. Here, we systematically delineate the acute innate immune response to endotoxin in terms of human macrophage enhancer activity and contrast with endotoxin tolerance, profiling the coding and non-coding transcriptome, chromatin accessibility and epigenetic modifications.<h4>Results</h4>We describe the spectrum of enhancers under acute and tolerance conditions and the regulatory networks between these enhancers and biological processes including gene expression, splicing regulation, transcription factor binding and enhancer RNA signatures. We demonstrate that the vast majority of differentially regulated enhancers on acute stimulation are subject to tolerance and that expression quantitative trait loci, disease-risk variants and eRNAs are enriched in these regulatory regions and related to context-specific gene expression. We find enrichment for context-specific eQTL involving endotoxin response and specific infections and delineate specific differential regions informative for GWAS variants in inflammatory bowel disease and multiple sclerosis, together with a context-specific enhancer involving a bacterial infection eQTL for KLF4. We show enrichment in differential enhancers for tolerance involving transcription factors NF\u03baB-p65, STATs and IRFs and prioritize putative causal genes directly linking genetic variants and disease risk enhancers. We further delineate similarities and differences in epigenetic landscape between stem cell-derived macrophages and primary cells and characterize the context-specific enhancer activities for key innate immune response genes KLF4, SLAMF1 and IL2RA.<h4>Conclusions</h4>Our study demonstrates the importance of context-specific macrophage enhancers in gene regulation and utility for interpreting disease associations, providing a roadmap to link genetic variants with molecular and cellular functions.",
     "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/ptj/article-pdf/100/2/332/32901113/pzz151.pdf; doi:https://doi.org/10.1093/ptj/pzz151"
+    "urls": "pdf:https://genomebiology.biomedcentral.com/counter/pdf/10.1186/s13059-022-02702-1; doi:https://doi.org/10.1186/s13059-022-02702-1; html:https://europepmc.org/articles/PMC9229144; pdf:https://europepmc.org/articles/PMC9229144?pdf=render"
   },
   {
     "id": "34432797",
@@ -36753,6 +36770,23 @@
     "laySummary": "",
     "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0255748&type=printable; doi:https://doi.org/10.1371/journal.pone.0255748; html:https://europepmc.org/articles/PMC8386866; pdf:https://europepmc.org/articles/PMC8386866?pdf=render"
   },
+  {
+    "id": "31588514",
+    "doi": "https://doi.org/10.1093/ptj/pzz151",
+    "title": "Physical Activity and Sedentary Behavior 6\u00a0Months After Musculoskeletal Trauma: What Factors Predict Recovery?",
+    "authorString": "Ekegren CL, Climie RE, Simpson PM, Owen N, Dunstan DW, Veitch W, Gabbe BJ.",
+    "authorAffiliations": "",
+    "journalTitle": "Physical therapy",
+    "pubYear": "2020",
+    "date": "2020-02-01",
+    "isOpenAccess": "N",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Physical activity is increasingly recognized as an important marker of functional recovery following fracture.<h4>Objective</h4>The objectives of this study were to measure sedentary behavior and physical activity 2\u00a0weeks and 6\u00a0months following fracture and to determine associated demographic and injury factors.<h4>Design</h4>This was an observational study.<h4>Methods</h4>Two weeks and 6\u00a0months following fracture, 83 adults who were 18 to 69\u00a0years old and had upper limb (UL) or lower limb (LL) fractures wore an accelerometer and an inclinometer for 10\u00a0days. We calculated sitting time, steps, moderate-intensity physical activity (MPA), and vigorous-intensity physical activity and conducted linear mixed-effects multivariable regression analyses to determine factors associated with temporal changes in activity.<h4>Results</h4>At 6\u00a0months versus 2\u00a0weeks after fracture, participants sat less, took more steps, and engaged in more MPA. Participants with LL fractures sat 2\u00a0hours more, took 66% fewer steps, and engaged in 77% less MPA than participants with UL fractures. Greater reductions in sitting time were observed for participants in the youngest age group and with LL fractures, participants with high preinjury activity, and participants who were overweight or obese. For steps, greater improvement was observed for participants in the youngest and middle-aged groups and those with LL fractures. For MPA, greater improvement was observed for middle-aged participants and those with LL fractures.<h4>Limitations</h4>Although this study was sufficiently powered for the analysis of major categories, a convenience sample that may not be representative of all people with musculoskeletal trauma was used.<h4>Conclusions</h4>Working-age adults with LL fractures had lower levels of physical activity 6\u00a0months after fracture than those with UL fractures. Older adults showed less improvement over time, suggesting that they are an important target group for interventions aimed at regaining preinjury activity levels.",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/ptj/article-pdf/100/2/332/32901113/pzz151.pdf; doi:https://doi.org/10.1093/ptj/pzz151"
+  },
   {
     "id": "37075078",
     "doi": "https://doi.org/10.1371/journal.pmed.1004223",
@@ -36821,23 +36855,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41467-022-29641-6.pdf; doi:https://doi.org/10.1038/s41467-022-29641-6; html:https://europepmc.org/articles/PMC8986867; pdf:https://europepmc.org/articles/PMC8986867?pdf=render"
   },
-  {
-    "id": "34645794",
-    "doi": "https://doi.org/10.1038/s41467-021-25914-8",
-    "title": "A cross-sectional analysis of meteorological factors and SARS-CoV-2 transmission in 409 cities across 26 countries.",
-    "authorString": "Sera F, Armstrong B, Abbott S, Meakin S, O'Reilly K, von Borries R, Schneider R, Roy\u00e9 D, Hashizume M, Pascal M, Tobias A, Vicedo-Cabrera AM, MCC Collaborative Research Network, CMMID COVID-19 Working Group, Gasparrini A, Lowe R.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature communications",
-    "pubYear": "2021",
-    "date": "2021-10-13",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "There is conflicting evidence on the influence of weather on COVID-19 transmission. Our aim is to estimate weather-dependent signatures in the early phase of the pandemic, while controlling for socio-economic factors and non-pharmaceutical interventions. We identify a modest non-linear association between mean temperature and the effective reproduction number (R<sub>e</sub>) in 409 cities in 26 countries, with a decrease of 0.087 (95% CI: 0.025; 0.148) for a 10\u2009\u00b0C increase. Early interventions have a greater effect on R<sub>e</sub> with a decrease of 0.285 (95% CI 0.223; 0.347) for a 5th - 95th percentile increase in the government response index. The variation in the effective reproduction number explained by government interventions is 6 times greater than for mean temperature. We find little evidence of meteorological conditions having influenced the early stages of local epidemics and conclude that population behaviour and government interventions are more important drivers of transmission.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1038/s41467-021-25914-8; doi:https://doi.org/10.1038/s41467-021-25914-8; html:https://europepmc.org/articles/PMC8514574; pdf:https://europepmc.org/articles/PMC8514574?pdf=render"
-  },
   {
     "id": "29780001",
     "doi": "https://doi.org/10.1016/s2352-3026(18)30053-x",
@@ -36856,21 +36873,21 @@
     "urls": "pdf:http://www.thelancet.com/article/S235230261830053X/pdf; doi:https://doi.org/10.1016/S2352-3026(18)30053-X; html:https://europepmc.org/articles/PMC6438177; pdf:https://europepmc.org/articles/PMC6438177?pdf=render; doi:https://doi.org/10.1016/s2352-3026(18)30053-x"
   },
   {
-    "id": "34888366",
-    "doi": "https://doi.org/10.3389/fcvm.2021.768245",
-    "title": "MOCOnet: Robust Motion Correction of Cardiovascular Magnetic Resonance T1 Mapping Using Convolutional Neural Networks.",
-    "authorString": "Gonzales RA, Zhang Q, Papie\u017c BW, Werys K, Lukaschuk E, Popescu IA, Burrage MK, Shanmuganathan M, Ferreira VM, Piechnik SK.",
+    "id": "34645794",
+    "doi": "https://doi.org/10.1038/s41467-021-25914-8",
+    "title": "A cross-sectional analysis of meteorological factors and SARS-CoV-2 transmission in 409 cities across 26 countries.",
+    "authorString": "Sera F, Armstrong B, Abbott S, Meakin S, O'Reilly K, von Borries R, Schneider R, Roy\u00e9 D, Hashizume M, Pascal M, Tobias A, Vicedo-Cabrera AM, MCC Collaborative Research Network, CMMID COVID-19 Working Group, Gasparrini A, Lowe R.",
     "authorAffiliations": "",
-    "journalTitle": "Frontiers in cardiovascular medicine",
+    "journalTitle": "Nature communications",
     "pubYear": "2021",
-    "date": "2021-11-23",
+    "date": "2021-10-13",
     "isOpenAccess": "Y",
-    "keywords": "image registration; Cardiovascular Magnetic Resonance; T1 Mapping; Deep Learning; Shmolli",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<b>Background:</b> Quantitative cardiovascular magnetic resonance (CMR) T1 mapping has shown promise for advanced tissue characterisation in routine clinical practise. However, T1 mapping is prone to motion artefacts, which affects its robustness and clinical interpretation. Current methods for motion correction on T1 mapping are model-driven with no guarantee on generalisability, limiting its widespread use. In contrast, emerging data-driven deep learning approaches have shown good performance in general image registration tasks. We propose MOCOnet, a convolutional neural network solution, for generalisable motion artefact correction in T1 maps. <b>Methods:</b> The network architecture employs U-Net for producing distance vector fields and utilises warping layers to apply deformation to the feature maps in a coarse-to-fine manner. Using the UK Biobank imaging dataset scanned at 1.5T, MOCOnet was trained on 1,536 mid-ventricular T1 maps (acquired using the ShMOLLI method) with motion artefacts, generated by a customised deformation procedure, and tested on a different set of 200 samples with a diverse range of motion. MOCOnet was compared to a well-validated baseline multi-modal image registration method. Motion reduction was visually assessed by 3 human experts, with motion scores ranging from 0% (strictly no motion) to 100% (very severe motion). <b>Results:</b> MOCOnet achieved fast image registration (<1 second per T1 map) and successfully suppressed a wide range of motion artefacts. MOCOnet significantly reduced motion scores from 37.1\u00b121.5 to 13.3\u00b110.5 (<i>p</i> < 0.001), whereas the baseline method reduced it to 15.8\u00b115.6 (<i>p</i> < 0.001). MOCOnet was significantly better than the baseline method in suppressing motion artefacts and more consistently (<i>p</i> = 0.007). <b>Conclusion:</b> MOCOnet demonstrated significantly better motion correction performance compared to a traditional image registration approach. Salvaging data affected by motion with robustness and in a time-efficient manner may enable better image quality and reliable images for immediate clinical interpretation.",
+    "abstract": "There is conflicting evidence on the influence of weather on COVID-19 transmission. Our aim is to estimate weather-dependent signatures in the early phase of the pandemic, while controlling for socio-economic factors and non-pharmaceutical interventions. We identify a modest non-linear association between mean temperature and the effective reproduction number (R<sub>e</sub>) in 409 cities in 26 countries, with a decrease of 0.087 (95% CI: 0.025; 0.148) for a 10\u2009\u00b0C increase. Early interventions have a greater effect on R<sub>e</sub> with a decrease of 0.285 (95% CI 0.223; 0.347) for a 5th - 95th percentile increase in the government response index. The variation in the effective reproduction number explained by government interventions is 6 times greater than for mean temperature. We find little evidence of meteorological conditions having influenced the early stages of local epidemics and conclude that population behaviour and government interventions are more important drivers of transmission.",
     "laySummary": "",
-    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2021.768245/pdf; doi:https://doi.org/10.3389/fcvm.2021.768245; html:https://europepmc.org/articles/PMC8649951; pdf:https://europepmc.org/articles/PMC8649951?pdf=render"
+    "urls": "doi:https://doi.org/10.1038/s41467-021-25914-8; doi:https://doi.org/10.1038/s41467-021-25914-8; html:https://europepmc.org/articles/PMC8514574; pdf:https://europepmc.org/articles/PMC8514574?pdf=render"
   },
   {
     "id": "35000827",
@@ -36889,6 +36906,23 @@
     "laySummary": "",
     "urls": "pdf:http://www.clinicaloncologyonline.net/article/S0936655521005161/pdf; doi:https://doi.org/10.1016/j.clon.2021.12.017"
   },
+  {
+    "id": "34888366",
+    "doi": "https://doi.org/10.3389/fcvm.2021.768245",
+    "title": "MOCOnet: Robust Motion Correction of Cardiovascular Magnetic Resonance T1 Mapping Using Convolutional Neural Networks.",
+    "authorString": "Gonzales RA, Zhang Q, Papie\u017c BW, Werys K, Lukaschuk E, Popescu IA, Burrage MK, Shanmuganathan M, Ferreira VM, Piechnik SK.",
+    "authorAffiliations": "",
+    "journalTitle": "Frontiers in cardiovascular medicine",
+    "pubYear": "2021",
+    "date": "2021-11-23",
+    "isOpenAccess": "Y",
+    "keywords": "image registration; Cardiovascular Magnetic Resonance; T1 Mapping; Deep Learning; Shmolli",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<b>Background:</b> Quantitative cardiovascular magnetic resonance (CMR) T1 mapping has shown promise for advanced tissue characterisation in routine clinical practise. However, T1 mapping is prone to motion artefacts, which affects its robustness and clinical interpretation. Current methods for motion correction on T1 mapping are model-driven with no guarantee on generalisability, limiting its widespread use. In contrast, emerging data-driven deep learning approaches have shown good performance in general image registration tasks. We propose MOCOnet, a convolutional neural network solution, for generalisable motion artefact correction in T1 maps. <b>Methods:</b> The network architecture employs U-Net for producing distance vector fields and utilises warping layers to apply deformation to the feature maps in a coarse-to-fine manner. Using the UK Biobank imaging dataset scanned at 1.5T, MOCOnet was trained on 1,536 mid-ventricular T1 maps (acquired using the ShMOLLI method) with motion artefacts, generated by a customised deformation procedure, and tested on a different set of 200 samples with a diverse range of motion. MOCOnet was compared to a well-validated baseline multi-modal image registration method. Motion reduction was visually assessed by 3 human experts, with motion scores ranging from 0% (strictly no motion) to 100% (very severe motion). <b>Results:</b> MOCOnet achieved fast image registration (<1 second per T1 map) and successfully suppressed a wide range of motion artefacts. MOCOnet significantly reduced motion scores from 37.1\u00b121.5 to 13.3\u00b110.5 (<i>p</i> < 0.001), whereas the baseline method reduced it to 15.8\u00b115.6 (<i>p</i> < 0.001). MOCOnet was significantly better than the baseline method in suppressing motion artefacts and more consistently (<i>p</i> = 0.007). <b>Conclusion:</b> MOCOnet demonstrated significantly better motion correction performance compared to a traditional image registration approach. Salvaging data affected by motion with robustness and in a time-efficient manner may enable better image quality and reliable images for immediate clinical interpretation.",
+    "laySummary": "",
+    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2021.768245/pdf; doi:https://doi.org/10.3389/fcvm.2021.768245; html:https://europepmc.org/articles/PMC8649951; pdf:https://europepmc.org/articles/PMC8649951?pdf=render"
+  },
   {
     "id": "33821553",
     "doi": "https://doi.org/10.1002/jia2.25697",
@@ -37144,23 +37178,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/schizophreniabulletin/article-pdf/47/2/405/36620462/sbaa126.pdf; doi:https://doi.org/10.1093/schbul/sbaa126; html:https://europepmc.org/articles/PMC7965059; pdf:https://europepmc.org/articles/PMC7965059?pdf=render; doi:https://doi.org/10.1093/schbul/sbaa126"
   },
-  {
-    "id": "34437535",
-    "doi": "https://doi.org/10.1371/journal.pgen.1009723",
-    "title": "The impact of age on genetic risk for common diseases.",
-    "authorString": "Jiang X, Holmes C, McVean G.",
-    "authorAffiliations": "",
-    "journalTitle": "PLoS genetics",
-    "pubYear": "2021",
-    "date": "2021-08-26",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Inherited genetic variation contributes to individual risk for many complex diseases and is increasingly being used for predictive patient stratification. Previous work has shown that genetic factors are not equally relevant to human traits across age and other contexts, though the reasons for such variation are not clear. Here, we introduce methods to infer the form of the longitudinal relationship between genetic relative risk for disease and age and to test whether all genetic risk factors behave similarly. We use a proportional hazards model within an interval-based censoring methodology to estimate age-varying individual variant contributions to genetic relative risk for 24 common diseases within the British ancestry subset of UK Biobank, applying a Bayesian clustering approach to group variants by their relative risk profile over age and permutation tests for age dependency and multiplicity of profiles. We find evidence for age-varying relative risk profiles in nine diseases, including hypertension, skin cancer, atherosclerotic heart disease, hypothyroidism and calculus of gallbladder, several of which show evidence, albeit weak, for multiple distinct profiles of genetic relative risk. The predominant pattern shows genetic risk factors having the greatest relative impact on risk of early disease, with a monotonic decrease over time, at least for the majority of variants, although the magnitude and form of the decrease varies among diseases. As a consequence, for diseases where genetic relative risk decreases over age, genetic risk factors have stronger explanatory power among younger populations, compared to older ones. We show that these patterns cannot be explained by a simple model involving the presence of unobserved covariates such as environmental factors. We discuss possible models that can explain our observations and the implications for genetic risk prediction.",
-    "laySummary": "",
-    "urls": "pdf:https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1009723&type=printable; doi:https://doi.org/10.1371/journal.pgen.1009723; html:https://europepmc.org/articles/PMC8389405; pdf:https://europepmc.org/articles/PMC8389405?pdf=render"
-  },
   {
     "id": "31848017",
     "doi": "https://doi.org/10.1016/j.injury.2019.12.016",
@@ -37178,6 +37195,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.injury.2019.12.016"
   },
+  {
+    "id": "34437535",
+    "doi": "https://doi.org/10.1371/journal.pgen.1009723",
+    "title": "The impact of age on genetic risk for common diseases.",
+    "authorString": "Jiang X, Holmes C, McVean G.",
+    "authorAffiliations": "",
+    "journalTitle": "PLoS genetics",
+    "pubYear": "2021",
+    "date": "2021-08-26",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Inherited genetic variation contributes to individual risk for many complex diseases and is increasingly being used for predictive patient stratification. Previous work has shown that genetic factors are not equally relevant to human traits across age and other contexts, though the reasons for such variation are not clear. Here, we introduce methods to infer the form of the longitudinal relationship between genetic relative risk for disease and age and to test whether all genetic risk factors behave similarly. We use a proportional hazards model within an interval-based censoring methodology to estimate age-varying individual variant contributions to genetic relative risk for 24 common diseases within the British ancestry subset of UK Biobank, applying a Bayesian clustering approach to group variants by their relative risk profile over age and permutation tests for age dependency and multiplicity of profiles. We find evidence for age-varying relative risk profiles in nine diseases, including hypertension, skin cancer, atherosclerotic heart disease, hypothyroidism and calculus of gallbladder, several of which show evidence, albeit weak, for multiple distinct profiles of genetic relative risk. The predominant pattern shows genetic risk factors having the greatest relative impact on risk of early disease, with a monotonic decrease over time, at least for the majority of variants, although the magnitude and form of the decrease varies among diseases. As a consequence, for diseases where genetic relative risk decreases over age, genetic risk factors have stronger explanatory power among younger populations, compared to older ones. We show that these patterns cannot be explained by a simple model involving the presence of unobserved covariates such as environmental factors. We discuss possible models that can explain our observations and the implications for genetic risk prediction.",
+    "laySummary": "",
+    "urls": "pdf:https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1009723&type=printable; doi:https://doi.org/10.1371/journal.pgen.1009723; html:https://europepmc.org/articles/PMC8389405; pdf:https://europepmc.org/articles/PMC8389405?pdf=render"
+  },
   {
     "id": "34991479",
     "doi": "https://doi.org/10.1186/s12877-021-02684-y",
@@ -37263,23 +37297,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/s0140-6736(23)00510-x; doi:https://doi.org/10.1016/S0140-6736(23)00510-X; html:https://europepmc.org/articles/PMC10156147; pdf:https://europepmc.org/articles/PMC10156147?pdf=render"
   },
-  {
-    "id": "35717168",
-    "doi": "https://doi.org/10.1186/s12879-022-07490-4",
-    "title": "The contribution of hospital-acquired infections to the COVID-19 epidemic in England in the first half of 2020.",
-    "authorString": "Knight GM, Pham TM, Stimson J, Funk S, Jafari Y, Pople D, Evans S, Yin M, Brown CS, Bhattacharya A, Hope R, Semple MG, ISARIC4C Investigators, CMMID COVID-19 Working Group, Read JM, Cooper BS, Robotham JV.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC infectious diseases",
-    "pubYear": "2022",
-    "date": "2022-06-18",
-    "isOpenAccess": "Y",
-    "keywords": "Mathematical Modelling; Nosocomial Transmission; Covid-19; Sars-cov-2",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>SARS-CoV-2 is known to transmit in hospital settings, but the contribution of infections acquired in hospitals to the epidemic at a national scale is unknown.<h4>Methods</h4>We used comprehensive national English datasets to determine the number of COVID-19 patients with identified hospital-acquired infections (with symptom onset >\u20097\u00a0days after admission and before discharge) in acute English hospitals up to August 2020. As patients may leave the hospital prior to detection of infection or have rapid symptom onset, we combined measures of the length of stay and the incubation period distribution to estimate how many hospital-acquired infections may have been missed. We used simulations to estimate the total number (identified and unidentified) of symptomatic hospital-acquired infections, as well as infections due to onward community transmission from missed hospital-acquired infections, to 31st July 2020.<h4>Results</h4>In our dataset of hospitalised COVID-19 patients in acute English hospitals with a recorded symptom onset date (n\u2009=\u200965,028), 7% were classified as hospital-acquired. We estimated that only 30% (range across weeks and 200 simulations: 20-41%) of symptomatic hospital-acquired infections would be identified, with up to 15% (mean, 95% range over 200 simulations: 14.1-15.8%) of cases currently classified as community-acquired COVID-19 potentially linked to hospital transmission. We estimated that 26,600 (25,900 to 27,700) individuals acquired a symptomatic SARS-CoV-2 infection in an acute Trust in England before 31st July 2020, resulting in 15,900 (15,200-16,400) or 20.1% (19.2-20.7%) of all identified hospitalised COVID-19 cases.<h4>Conclusions</h4>Transmission of SARS-CoV-2 to hospitalised patients likely caused approximately a fifth of identified cases of hospitalised COVID-19 in the \"first wave\" in England, but less than 1% of all infections in England. Using time to symptom onset from admission for inpatients as a detection method likely misses a substantial proportion (>\u200960%) of hospital-acquired infections.",
-    "laySummary": "",
-    "urls": "pdf:https://bmcinfectdis.biomedcentral.com/counter/pdf/10.1186/s12879-022-07490-4; doi:https://doi.org/10.1186/s12879-022-07490-4; html:https://europepmc.org/articles/PMC9206097; pdf:https://europepmc.org/articles/PMC9206097?pdf=render"
-  },
   {
     "id": "33737684",
     "doi": "https://doi.org/10.1038/s41598-021-85877-0",
@@ -37297,6 +37314,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41598-021-85877-0.pdf; doi:https://doi.org/10.1038/s41598-021-85877-0; html:https://europepmc.org/articles/PMC7973581; pdf:https://europepmc.org/articles/PMC7973581?pdf=render"
   },
+  {
+    "id": "35717168",
+    "doi": "https://doi.org/10.1186/s12879-022-07490-4",
+    "title": "The contribution of hospital-acquired infections to the COVID-19 epidemic in England in the first half of 2020.",
+    "authorString": "Knight GM, Pham TM, Stimson J, Funk S, Jafari Y, Pople D, Evans S, Yin M, Brown CS, Bhattacharya A, Hope R, Semple MG, ISARIC4C Investigators, CMMID COVID-19 Working Group, Read JM, Cooper BS, Robotham JV.",
+    "authorAffiliations": "",
+    "journalTitle": "BMC infectious diseases",
+    "pubYear": "2022",
+    "date": "2022-06-18",
+    "isOpenAccess": "Y",
+    "keywords": "Mathematical Modelling; Nosocomial Transmission; Covid-19; Sars-cov-2",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>SARS-CoV-2 is known to transmit in hospital settings, but the contribution of infections acquired in hospitals to the epidemic at a national scale is unknown.<h4>Methods</h4>We used comprehensive national English datasets to determine the number of COVID-19 patients with identified hospital-acquired infections (with symptom onset >\u20097\u00a0days after admission and before discharge) in acute English hospitals up to August 2020. As patients may leave the hospital prior to detection of infection or have rapid symptom onset, we combined measures of the length of stay and the incubation period distribution to estimate how many hospital-acquired infections may have been missed. We used simulations to estimate the total number (identified and unidentified) of symptomatic hospital-acquired infections, as well as infections due to onward community transmission from missed hospital-acquired infections, to 31st July 2020.<h4>Results</h4>In our dataset of hospitalised COVID-19 patients in acute English hospitals with a recorded symptom onset date (n\u2009=\u200965,028), 7% were classified as hospital-acquired. We estimated that only 30% (range across weeks and 200 simulations: 20-41%) of symptomatic hospital-acquired infections would be identified, with up to 15% (mean, 95% range over 200 simulations: 14.1-15.8%) of cases currently classified as community-acquired COVID-19 potentially linked to hospital transmission. We estimated that 26,600 (25,900 to 27,700) individuals acquired a symptomatic SARS-CoV-2 infection in an acute Trust in England before 31st July 2020, resulting in 15,900 (15,200-16,400) or 20.1% (19.2-20.7%) of all identified hospitalised COVID-19 cases.<h4>Conclusions</h4>Transmission of SARS-CoV-2 to hospitalised patients likely caused approximately a fifth of identified cases of hospitalised COVID-19 in the \"first wave\" in England, but less than 1% of all infections in England. Using time to symptom onset from admission for inpatients as a detection method likely misses a substantial proportion (>\u200960%) of hospital-acquired infections.",
+    "laySummary": "",
+    "urls": "pdf:https://bmcinfectdis.biomedcentral.com/counter/pdf/10.1186/s12879-022-07490-4; doi:https://doi.org/10.1186/s12879-022-07490-4; html:https://europepmc.org/articles/PMC9206097; pdf:https://europepmc.org/articles/PMC9206097?pdf=render"
+  },
   {
     "id": "35188939",
     "doi": "https://doi.org/10.1097/pts.0000000000000867",
@@ -37416,23 +37450,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41746-020-00357-5.pdf; doi:https://doi.org/10.1038/s41746-020-00357-5; html:https://europepmc.org/articles/PMC7648058; pdf:https://europepmc.org/articles/PMC7648058?pdf=render"
   },
-  {
-    "id": "35849350",
-    "doi": "https://doi.org/10.1093/nar/gkac612",
-    "title": "Whole-genome long-read TAPS deciphers DNA methylation patterns at base resolution using PacBio SMRT sequencing technology.",
-    "authorString": "Chen J, Cheng J, Chen X, Inoue M, Liu Y, Song CX.",
-    "authorAffiliations": "",
-    "journalTitle": "Nucleic acids research",
-    "pubYear": "2022",
-    "date": "2022-10-01",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Long-read sequencing provides valuable information on difficult-to-map genomic regions, which can complement short-read sequencing to improve genome assembly, yet limited methods are available to accurately detect DNA methylation over long distances at a whole-genome scale. By combining our recently developed TET-assisted pyridine borane sequencing (TAPS) method, which enables direct detection of 5-methylcytosine and 5-hydroxymethylcytosine, with PacBio single-molecule real-time sequencing, we present here whole-genome long-read TAPS (wglrTAPS). To evaluate the performance of wglrTAPS, we applied it to mouse embryonic stem cells as a proof of concept, and an N50 read length of 3.5 kb is achieved. By sequencing wglrTAPS to 8.2\u00d7\u00a0depth, we discovered a significant proportion of CpG sites that\u00a0were not covered in previous 27.5\u00d7 short-read TAPS. Our results demonstrate that wglrTAPS facilitates methylation profiling on problematic genomic regions with repetitive elements or structural variations, and also in an allelic manner, all of which are extremely difficult for short-read sequencing methods to resolve. This method therefore enhances applications of third-generation sequencing technologies for DNA epigenetics.",
-    "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/nar/article-pdf/50/18/e104/46501243/gkac612.pdf; doi:https://doi.org/10.1093/nar/gkac612; html:https://europepmc.org/articles/PMC9561279; pdf:https://europepmc.org/articles/PMC9561279?pdf=render"
-  },
   {
     "id": "34173574",
     "doi": "https://doi.org/10.1016/j.puhip.2020.100039",
@@ -37450,6 +37467,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.puhip.2020.100039; doi:https://doi.org/10.1016/j.puhip.2020.100039; html:https://europepmc.org/articles/PMC7486860; pdf:https://europepmc.org/articles/PMC7486860?pdf=render"
   },
+  {
+    "id": "35849350",
+    "doi": "https://doi.org/10.1093/nar/gkac612",
+    "title": "Whole-genome long-read TAPS deciphers DNA methylation patterns at base resolution using PacBio SMRT sequencing technology.",
+    "authorString": "Chen J, Cheng J, Chen X, Inoue M, Liu Y, Song CX.",
+    "authorAffiliations": "",
+    "journalTitle": "Nucleic acids research",
+    "pubYear": "2022",
+    "date": "2022-10-01",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Long-read sequencing provides valuable information on difficult-to-map genomic regions, which can complement short-read sequencing to improve genome assembly, yet limited methods are available to accurately detect DNA methylation over long distances at a whole-genome scale. By combining our recently developed TET-assisted pyridine borane sequencing (TAPS) method, which enables direct detection of 5-methylcytosine and 5-hydroxymethylcytosine, with PacBio single-molecule real-time sequencing, we present here whole-genome long-read TAPS (wglrTAPS). To evaluate the performance of wglrTAPS, we applied it to mouse embryonic stem cells as a proof of concept, and an N50 read length of 3.5 kb is achieved. By sequencing wglrTAPS to 8.2\u00d7\u00a0depth, we discovered a significant proportion of CpG sites that\u00a0were not covered in previous 27.5\u00d7 short-read TAPS. Our results demonstrate that wglrTAPS facilitates methylation profiling on problematic genomic regions with repetitive elements or structural variations, and also in an allelic manner, all of which are extremely difficult for short-read sequencing methods to resolve. This method therefore enhances applications of third-generation sequencing technologies for DNA epigenetics.",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/nar/article-pdf/50/18/e104/46501243/gkac612.pdf; doi:https://doi.org/10.1093/nar/gkac612; html:https://europepmc.org/articles/PMC9561279; pdf:https://europepmc.org/articles/PMC9561279?pdf=render"
+  },
   {
     "id": "33407780",
     "doi": "https://doi.org/10.1186/s13063-020-04951-6",
@@ -37637,23 +37671,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/eurheartj/article-pdf/43/14/1416/43292041/ehab863.pdf; doi:https://doi.org/10.1093/eurheartj/ehab863; html:https://europepmc.org/articles/PMC8986460; pdf:https://europepmc.org/articles/PMC8986460?pdf=render"
   },
-  {
-    "id": "39365172",
-    "doi": "https://doi.org/10.1093/eurjpc/zwae315",
-    "title": "Association of circulating fatty acids with cardiovascular disease risk: Analysis of individual-level data in three large prospective cohorts and updated meta-analysis.",
-    "authorString": "Shi F, Chowdhury R, Sofianopoulou E, Koulman A, Sun L, Steur M, Aleksandrova K, Dahm CC, Schulze MB, van der Schouw YT, Agnoli C, Amiano P, Boer JMA, Bork CS, Cabrera-Castro N, Eichelmann F, Elbaz A, Farr\u00e0s M, Heath AK, Kaaks R, Katzke V, Keski-Rahkonen P, Masala G, Moreno-Iribas C, Panico S, Papier K, Petrova D, Quir\u00f3s JR, Ricceri F, Severi G, Tj\u00f8nneland A, Tong TYN, Tumino R, Wareham N, Weiderpass E, Di Angelantonio E, Forouhi N, Danesh J, Butterworth AS, Kaptoge S.",
-    "authorAffiliations": "",
-    "journalTitle": "European journal of preventive cardiology",
-    "pubYear": "2024",
-    "date": "2024-10-04",
-    "isOpenAccess": "N",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Associations of saturated and unsaturated fatty acids (FAs) with cardiovascular disease (CVD) remain controversial. We therefore aimed to investigate the prospective associations of objectively measured FAs with CVD, including incident coronary heart disease (CHD) and stroke, as well as CVD mortality.<h4>Methods</h4>Circulating FA concentrations expressed as the percentage of total FAs were assayed in 172,891 participants without prior vascular disease at baseline from the European Prospective Investigation into Cancer and Nutrition-CVD (EPIC-CVD) (7,343 CHD; 6,499 stroke), UK Biobank (1,825; 1,474), and INTERVAL (285; 209) cohort studies. Hazard ratio (HR) per 1-standard deviation (SD) higher FA concentrations was estimated using Cox regression models and pooled by random-effects meta-analysis. Systematic reviews with meta-analysis published by 6 May 2023 on associations between FAs and CVDs were systematically searched and updated meta-analyses using random-effects model were conducted. Evidence from randomized controlled trials (RCTs) was also summarized.<h4>Results</h4>Higher concentrations of total saturated FAs (SFAs) were associated with higher cardiovascular risks in the combined analysis, with differential findings noted for SFA subtypes in further analysis restricted to EPIC-CVD: positive associations for even-chain SFA [HR for CHD 1.24 (95% CI: 1.18-1.32); stroke 1.23 (1.10-1.38)] and negative associations for odd-chain [0.82 (0.76-0.87); 0.73 (0.67-0.78)] and longer-chain [0.95 (0.80-1.12); 0.84 (0.72-0.99)] SFA. In the combined analysis, total n-3 polyunsaturated FA (PUFA) [0.91 (0.85-0.97)], including docosahexaenoic acid (DHA) [0.91 (0.84-0.98)], was negatively associated with incident CHD risk. Similarly, total n-6 PUFA [0.94 (0.91-0.98)], including linoleic acid (LA) [0.89 (0.83-0.95)], was negatively associated with incident stroke risk. By contrast, more detailed analyses in EPIC-CVD revealed that several downstream n-6 PUFAs of LA were positively associated with CHD risk. Updated meta-analyses of 37 FAs including 49 non-overlapping studies, involving between 7,787 to 22,802 CHD and 6,499 to 14,221 stroke cases, showed broadly similar results as our combined empirical analysis and further suggested significant inverse associations of individual long-chain n-3 PUFAs and LA on both CHD and stroke. The findings of long-chain n-3 PUFAs were consistent with those from published RCTs on CHD despite insufficient evidence in monotherapy, while RCT evidence remained unclear for the rest of the explored FAs.<h4>Conclusions</h4>Our study provides an overview of the most recent evidence on the associations between objectively measured FAs and CVD outcomes. Collectively, the data reveals notable differences in associations by SFA subtypes and calls for further studies, especially RCTs, to explore these links.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1093/eurjpc/zwae315"
-  },
   {
     "id": "34555069",
     "doi": "https://doi.org/10.1371/journal.pone.0257361",
@@ -37671,6 +37688,23 @@
     "laySummary": "",
     "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0257361&type=printable; doi:https://doi.org/10.1371/journal.pone.0257361; html:https://europepmc.org/articles/PMC8460020; pdf:https://europepmc.org/articles/PMC8460020?pdf=render"
   },
+  {
+    "id": "39365172",
+    "doi": "https://doi.org/10.1093/eurjpc/zwae315",
+    "title": "Association of circulating fatty acids with cardiovascular disease risk: Analysis of individual-level data in three large prospective cohorts and updated meta-analysis.",
+    "authorString": "Shi F, Chowdhury R, Sofianopoulou E, Koulman A, Sun L, Steur M, Aleksandrova K, Dahm CC, Schulze MB, van der Schouw YT, Agnoli C, Amiano P, Boer JMA, Bork CS, Cabrera-Castro N, Eichelmann F, Elbaz A, Farr\u00e0s M, Heath AK, Kaaks R, Katzke V, Keski-Rahkonen P, Masala G, Moreno-Iribas C, Panico S, Papier K, Petrova D, Quir\u00f3s JR, Ricceri F, Severi G, Tj\u00f8nneland A, Tong TYN, Tumino R, Wareham N, Weiderpass E, Di Angelantonio E, Forouhi N, Danesh J, Butterworth AS, Kaptoge S.",
+    "authorAffiliations": "",
+    "journalTitle": "European journal of preventive cardiology",
+    "pubYear": "2024",
+    "date": "2024-10-04",
+    "isOpenAccess": "N",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Associations of saturated and unsaturated fatty acids (FAs) with cardiovascular disease (CVD) remain controversial. We therefore aimed to investigate the prospective associations of objectively measured FAs with CVD, including incident coronary heart disease (CHD) and stroke, as well as CVD mortality.<h4>Methods</h4>Circulating FA concentrations expressed as the percentage of total FAs were assayed in 172,891 participants without prior vascular disease at baseline from the European Prospective Investigation into Cancer and Nutrition-CVD (EPIC-CVD) (7,343 CHD; 6,499 stroke), UK Biobank (1,825; 1,474), and INTERVAL (285; 209) cohort studies. Hazard ratio (HR) per 1-standard deviation (SD) higher FA concentrations was estimated using Cox regression models and pooled by random-effects meta-analysis. Systematic reviews with meta-analysis published by 6 May 2023 on associations between FAs and CVDs were systematically searched and updated meta-analyses using random-effects model were conducted. Evidence from randomized controlled trials (RCTs) was also summarized.<h4>Results</h4>Higher concentrations of total saturated FAs (SFAs) were associated with higher cardiovascular risks in the combined analysis, with differential findings noted for SFA subtypes in further analysis restricted to EPIC-CVD: positive associations for even-chain SFA [HR for CHD 1.24 (95% CI: 1.18-1.32); stroke 1.23 (1.10-1.38)] and negative associations for odd-chain [0.82 (0.76-0.87); 0.73 (0.67-0.78)] and longer-chain [0.95 (0.80-1.12); 0.84 (0.72-0.99)] SFA. In the combined analysis, total n-3 polyunsaturated FA (PUFA) [0.91 (0.85-0.97)], including docosahexaenoic acid (DHA) [0.91 (0.84-0.98)], was negatively associated with incident CHD risk. Similarly, total n-6 PUFA [0.94 (0.91-0.98)], including linoleic acid (LA) [0.89 (0.83-0.95)], was negatively associated with incident stroke risk. By contrast, more detailed analyses in EPIC-CVD revealed that several downstream n-6 PUFAs of LA were positively associated with CHD risk. Updated meta-analyses of 37 FAs including 49 non-overlapping studies, involving between 7,787 to 22,802 CHD and 6,499 to 14,221 stroke cases, showed broadly similar results as our combined empirical analysis and further suggested significant inverse associations of individual long-chain n-3 PUFAs and LA on both CHD and stroke. The findings of long-chain n-3 PUFAs were consistent with those from published RCTs on CHD despite insufficient evidence in monotherapy, while RCT evidence remained unclear for the rest of the explored FAs.<h4>Conclusions</h4>Our study provides an overview of the most recent evidence on the associations between objectively measured FAs and CVD outcomes. Collectively, the data reveals notable differences in associations by SFA subtypes and calls for further studies, especially RCTs, to explore these links.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1093/eurjpc/zwae315"
+  },
   {
     "id": "35380004",
     "doi": "https://doi.org/10.1042/bcj20220105",
@@ -37739,6 +37773,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41467-021-22213-0.pdf; doi:https://doi.org/10.1038/s41467-021-22213-0; html:https://europepmc.org/articles/PMC8007691; pdf:https://europepmc.org/articles/PMC8007691?pdf=render"
   },
+  {
+    "id": "33829489",
+    "doi": "https://doi.org/10.1111/bjd.20140",
+    "title": "Defining trajectories of response in patients with psoriasis treated with biologic therapies.",
+    "authorString": "Geifman N, Azadbakht N, Zeng J, Wilkinson T, Dand N, Buchan I, Stocken D, Di Meglio P, Warren RB, Barker JN, Reynolds NJ, Barnes MR, Smith CH, Griffiths CEM, Peek N, BADBIR Study Group, on behalf of the PSORT Consortium.",
+    "authorAffiliations": "",
+    "journalTitle": "The British journal of dermatology",
+    "pubYear": "2021",
+    "date": "2021-06-04",
+    "isOpenAccess": "N",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>The effectiveness and cost-effectiveness of biologic therapies for psoriasis are significantly compromised by variable treatment responses. Thus, more precise management of psoriasis is needed.<h4>Objectives</h4>To identify subgroups of patients with psoriasis treated with biologic therapies, based on changes in their disease activity over time, that may better inform patient management.<h4>Methods</h4>We applied latent class mixed modelling to identify trajectory-based patient subgroups from longitudinal, routine clinical data on disease severity, as measured by the Psoriasis Area and Severity Index (PASI), from 3546 patients in the British Association of Dermatologists Biologics and Immunomodulators Register, as well as in an independent cohort of 2889 patients pooled across four clinical trials.<h4>Results</h4>We discovered four discrete classes of global response trajectories, each characterized in terms of time to response, size of effect and relapse. Each class was associated with differing clinical characteristics, e.g. body mass index, baseline PASI and prevalence of different manifestations. The results were verified in a second cohort of clinical trial participants, where similar trajectories following the initiation of biologic therapy were identified. Further, we found differential associations of the genetic marker HLA-C*06:02 between our registry-identified trajectories.<h4>Conclusions</h4>These subgroups, defined by change in disease over time, may be indicative of distinct endotypes driven by different biological mechanisms and may help inform the management of patients with psoriasis. Future work will aim to further delineate these mechanisms by extensively characterizing the subgroups with additional molecular and pharmacological data.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1111/bjd.20140"
+  },
   {
     "id": "38381822",
     "doi": "https://doi.org/10.1126/sciadv.adi9379",
@@ -37773,23 +37824,6 @@
     "laySummary": "",
     "urls": "pdf:https://journals.plos.org/globalpublichealth/article/file?id=10.1371/journal.pgph.0000843&type=printable; doi:https://doi.org/10.1371/journal.pgph.0000843; html:https://europepmc.org/articles/PMC10021875; pdf:https://europepmc.org/articles/PMC10021875?pdf=render"
   },
-  {
-    "id": "33829489",
-    "doi": "https://doi.org/10.1111/bjd.20140",
-    "title": "Defining trajectories of response in patients with psoriasis treated with biologic therapies.",
-    "authorString": "Geifman N, Azadbakht N, Zeng J, Wilkinson T, Dand N, Buchan I, Stocken D, Di Meglio P, Warren RB, Barker JN, Reynolds NJ, Barnes MR, Smith CH, Griffiths CEM, Peek N, BADBIR Study Group, on behalf of the PSORT Consortium.",
-    "authorAffiliations": "",
-    "journalTitle": "The British journal of dermatology",
-    "pubYear": "2021",
-    "date": "2021-06-04",
-    "isOpenAccess": "N",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>The effectiveness and cost-effectiveness of biologic therapies for psoriasis are significantly compromised by variable treatment responses. Thus, more precise management of psoriasis is needed.<h4>Objectives</h4>To identify subgroups of patients with psoriasis treated with biologic therapies, based on changes in their disease activity over time, that may better inform patient management.<h4>Methods</h4>We applied latent class mixed modelling to identify trajectory-based patient subgroups from longitudinal, routine clinical data on disease severity, as measured by the Psoriasis Area and Severity Index (PASI), from 3546 patients in the British Association of Dermatologists Biologics and Immunomodulators Register, as well as in an independent cohort of 2889 patients pooled across four clinical trials.<h4>Results</h4>We discovered four discrete classes of global response trajectories, each characterized in terms of time to response, size of effect and relapse. Each class was associated with differing clinical characteristics, e.g. body mass index, baseline PASI and prevalence of different manifestations. The results were verified in a second cohort of clinical trial participants, where similar trajectories following the initiation of biologic therapy were identified. Further, we found differential associations of the genetic marker HLA-C*06:02 between our registry-identified trajectories.<h4>Conclusions</h4>These subgroups, defined by change in disease over time, may be indicative of distinct endotypes driven by different biological mechanisms and may help inform the management of patients with psoriasis. Future work will aim to further delineate these mechanisms by extensively characterizing the subgroups with additional molecular and pharmacological data.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1111/bjd.20140"
-  },
   {
     "id": "35094586",
     "doi": "https://doi.org/10.1177/17407745221077691",
@@ -37808,21 +37842,21 @@
     "urls": "pdf:http://pure-oai.bham.ac.uk/ws/files/160459757/17407745221077691.pdf; doi:https://doi.org/10.1177/17407745221077691; html:https://europepmc.org/articles/PMC9203669; pdf:https://europepmc.org/articles/PMC9203669?pdf=render"
   },
   {
-    "id": "37208429",
-    "doi": "https://doi.org/10.1038/s41598-023-33391-w",
-    "title": "Rare variant contribution to cholestatic liver disease in a South Asian population in the United Kingdom.",
-    "authorString": "Z\u00f6llner J, Finer S, Linton KJ, Genes and Health Research Team, van Heel DA, Williamson C, Dixon PH.",
+    "id": "30949070",
+    "doi": "https://doi.org/10.3389/fpsyt.2019.00109",
+    "title": "Real World Implementation of a Transdiagnostic Risk Calculator for the Automatic Detection of Individuals at Risk of Psychosis in Clinical Routine: Study Protocol.",
+    "authorString": "Fusar-Poli P, Oliver D, Spada G, Patel R, Stewart R, Dobson R, McGuire P.",
     "authorAffiliations": "",
-    "journalTitle": "Scientific reports",
-    "pubYear": "2023",
-    "date": "2023-05-19",
+    "journalTitle": "Frontiers in psychiatry",
+    "pubYear": "2019",
+    "date": "2019-03-13",
     "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
+    "keywords": "Schizophrenia; Prevention; risk; Psychosis; Transdiagnostic",
+    "nationalPriorities": "Applied Analytics, Better Care",
     "healthCategories": "",
-    "abstract": "This study assessed the contribution of five genes previously known to be involved in cholestatic liver disease in British Bangladeshi and Pakistani people. Five genes (ABCB4, ABCB11, ATP8B1, NR1H4, TJP2) were interrogated by exome sequencing data of 5236 volunteers. Included were non-synonymous or loss of function (LoF) variants with a minor allele frequency\u2009<\u20095%. Variants were filtered, and annotated to perform rare variant burden analysis, protein structure, and modelling analysis in-silico. Out of 314 non-synonymous variants, 180 fulfilled the inclusion criteria and were mostly heterozygous unless specified. 90 were novel and of those variants, 22 were considered likely pathogenic and 9 pathogenic. We identified variants in volunteers with gallstone disease (n\u2009=\u200931), intrahepatic cholestasis of pregnancy (ICP, n\u2009=\u200916), cholangiocarcinoma and cirrhosis (n\u2009=\u20092). Fourteen novel LoF variants were identified: 7 frameshift, 5 introduction of premature stop codon and 2 splice acceptor variants. The rare variant burden was significantly increased in ABCB11. Protein modelling demonstrated variants that appeared to likely cause significant structural alterations. This study highlights the significant genetic burden contributing to cholestatic liver disease. Novel likely pathogenic and pathogenic variants were identified addressing the underrepresentation of diverse ancestry groups in genomic research.",
+    "abstract": "<b>Background:</b> Primary indicated prevention in individuals at-risk for psychosis has the potential to improve the outcomes of this disorder. The ability to detect the majority of at-risk individuals is the main barrier toward extending benefits for the lives of many adolescents and young adults. Current detection strategies are highly inefficient. Only 5% (standalone specialized early detection services) to 12% (youth mental health services) of individuals who will develop a first psychotic disorder can be detected at the time of their at-risk stage. To overcome these challenges a pragmatic, clinically-based, individualized, transdiagnostic risk calculator has been developed to detect individuals at-risk of psychosis in secondary mental health care at scale. This calculator has been externally validated and has demonstrated good prognostic performance. However, it is not known whether it can be used in the real world clinical routine. For example, clinicians may not be willing to adhere to the recommendations made by the transdiagnostic risk calculator. Implementation studies are needed to address pragmatic challenges relating to the real world use of the transdiagnostic risk calculator. The aim of the current study is to provide <i>in-vitro</i> and <i>in-vivo</i> feasibility data to support the implementation of the transdiagnostic risk calculator in clinical routine. <b>Method:</b> This is a study which comprises of two subsequent phases: an <i>in-vitro</i> phase of 1 month and an <i>in-vivo</i> phase of 11 months. The <i>in-vitro</i> phase aims at developing and integrating the transdiagnostic risk calculator in the local electronic health register (primary outcome). The <i>in-vivo</i> phase aims at addressing the clinicians' adherence to the recommendations made by the transdiagnostic risk calculator (primary outcome) and other secondary feasibility parameters that are necessary to estimate the resources needed for its implementation. <b>Discussion:</b> This is the first implementation study for risk prediction models in individuals at-risk for psychosis. Ultimately, successful implementation is the true measure of a prediction model's utility. Therefore, the overall translational deliverable of the current study would be to extend the benefits of primary indicated prevention and improve outcomes of first episode psychosis. This may produce significant social benefits for many adolescents and young adults and their families.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1038/s41598-023-33391-w; doi:https://doi.org/10.1038/s41598-023-33391-w; html:https://europepmc.org/articles/PMC10199085; pdf:https://europepmc.org/articles/PMC10199085?pdf=render"
+    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fpsyt.2019.00109/pdf; doi:https://doi.org/10.3389/fpsyt.2019.00109; html:https://europepmc.org/articles/PMC6436079; pdf:https://europepmc.org/articles/PMC6436079?pdf=render"
   },
   {
     "id": "34091032",
@@ -37842,21 +37876,21 @@
     "urls": "doi:https://doi.org/10.1016/j.neuroimage.2021.118235; doi:https://doi.org/10.1016/j.neuroimage.2021.118235; html:https://europepmc.org/articles/PMC7611820; pdf:https://europepmc.org/articles/PMC7611820?pdf=render"
   },
   {
-    "id": "30949070",
-    "doi": "https://doi.org/10.3389/fpsyt.2019.00109",
-    "title": "Real World Implementation of a Transdiagnostic Risk Calculator for the Automatic Detection of Individuals at Risk of Psychosis in Clinical Routine: Study Protocol.",
-    "authorString": "Fusar-Poli P, Oliver D, Spada G, Patel R, Stewart R, Dobson R, McGuire P.",
+    "id": "37208429",
+    "doi": "https://doi.org/10.1038/s41598-023-33391-w",
+    "title": "Rare variant contribution to cholestatic liver disease in a South Asian population in the United Kingdom.",
+    "authorString": "Z\u00f6llner J, Finer S, Linton KJ, Genes and Health Research Team, van Heel DA, Williamson C, Dixon PH.",
     "authorAffiliations": "",
-    "journalTitle": "Frontiers in psychiatry",
-    "pubYear": "2019",
-    "date": "2019-03-13",
+    "journalTitle": "Scientific reports",
+    "pubYear": "2023",
+    "date": "2023-05-19",
     "isOpenAccess": "Y",
-    "keywords": "Schizophrenia; Prevention; risk; Psychosis; Transdiagnostic",
-    "nationalPriorities": "Applied Analytics, Better Care",
+    "keywords": "",
+    "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<b>Background:</b> Primary indicated prevention in individuals at-risk for psychosis has the potential to improve the outcomes of this disorder. The ability to detect the majority of at-risk individuals is the main barrier toward extending benefits for the lives of many adolescents and young adults. Current detection strategies are highly inefficient. Only 5% (standalone specialized early detection services) to 12% (youth mental health services) of individuals who will develop a first psychotic disorder can be detected at the time of their at-risk stage. To overcome these challenges a pragmatic, clinically-based, individualized, transdiagnostic risk calculator has been developed to detect individuals at-risk of psychosis in secondary mental health care at scale. This calculator has been externally validated and has demonstrated good prognostic performance. However, it is not known whether it can be used in the real world clinical routine. For example, clinicians may not be willing to adhere to the recommendations made by the transdiagnostic risk calculator. Implementation studies are needed to address pragmatic challenges relating to the real world use of the transdiagnostic risk calculator. The aim of the current study is to provide <i>in-vitro</i> and <i>in-vivo</i> feasibility data to support the implementation of the transdiagnostic risk calculator in clinical routine. <b>Method:</b> This is a study which comprises of two subsequent phases: an <i>in-vitro</i> phase of 1 month and an <i>in-vivo</i> phase of 11 months. The <i>in-vitro</i> phase aims at developing and integrating the transdiagnostic risk calculator in the local electronic health register (primary outcome). The <i>in-vivo</i> phase aims at addressing the clinicians' adherence to the recommendations made by the transdiagnostic risk calculator (primary outcome) and other secondary feasibility parameters that are necessary to estimate the resources needed for its implementation. <b>Discussion:</b> This is the first implementation study for risk prediction models in individuals at-risk for psychosis. Ultimately, successful implementation is the true measure of a prediction model's utility. Therefore, the overall translational deliverable of the current study would be to extend the benefits of primary indicated prevention and improve outcomes of first episode psychosis. This may produce significant social benefits for many adolescents and young adults and their families.",
+    "abstract": "This study assessed the contribution of five genes previously known to be involved in cholestatic liver disease in British Bangladeshi and Pakistani people. Five genes (ABCB4, ABCB11, ATP8B1, NR1H4, TJP2) were interrogated by exome sequencing data of 5236 volunteers. Included were non-synonymous or loss of function (LoF) variants with a minor allele frequency\u2009<\u20095%. Variants were filtered, and annotated to perform rare variant burden analysis, protein structure, and modelling analysis in-silico. Out of 314 non-synonymous variants, 180 fulfilled the inclusion criteria and were mostly heterozygous unless specified. 90 were novel and of those variants, 22 were considered likely pathogenic and 9 pathogenic. We identified variants in volunteers with gallstone disease (n\u2009=\u200931), intrahepatic cholestasis of pregnancy (ICP, n\u2009=\u200916), cholangiocarcinoma and cirrhosis (n\u2009=\u20092). Fourteen novel LoF variants were identified: 7 frameshift, 5 introduction of premature stop codon and 2 splice acceptor variants. The rare variant burden was significantly increased in ABCB11. Protein modelling demonstrated variants that appeared to likely cause significant structural alterations. This study highlights the significant genetic burden contributing to cholestatic liver disease. Novel likely pathogenic and pathogenic variants were identified addressing the underrepresentation of diverse ancestry groups in genomic research.",
     "laySummary": "",
-    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fpsyt.2019.00109/pdf; doi:https://doi.org/10.3389/fpsyt.2019.00109; html:https://europepmc.org/articles/PMC6436079; pdf:https://europepmc.org/articles/PMC6436079?pdf=render"
+    "urls": "doi:https://doi.org/10.1038/s41598-023-33391-w; doi:https://doi.org/10.1038/s41598-023-33391-w; html:https://europepmc.org/articles/PMC10199085; pdf:https://europepmc.org/articles/PMC10199085?pdf=render"
   },
   {
     "id": "35073907",
@@ -37875,23 +37909,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-021-02218-8; doi:https://doi.org/10.1186/s12916-021-02218-8; html:https://europepmc.org/articles/PMC8787919; pdf:https://europepmc.org/articles/PMC8787919?pdf=render"
   },
-  {
-    "id": "35482474",
-    "doi": "https://doi.org/10.1111/bjd.21627",
-    "title": "Biomarkers of disease progression in people with psoriasis: a scoping review.",
-    "authorString": "Ramessur R, Corbett M, Marshall D, Acencio ML, Barbosa IA, Dand N, Di Meglio P, Haddad S, Jensen AHM, Koopmann W, Mahil SK, Ostaszewski M, Rahmatulla S, Rastrick J, Saklatvala J, Weidinger S, Wright K, Eyerich K, Ndlovu M, Barker JN, Skov L, Conrad C, Smith CH, BIOMAP consortium.",
-    "authorAffiliations": "",
-    "journalTitle": "The British journal of dermatology",
-    "pubYear": "2022",
-    "date": "2022-07-11",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Identification of those at risk of more severe psoriasis and/or associated morbidities offers opportunity for early intervention, reduced disease burden and more cost-effective healthcare. Prognostic biomarkers of disease progression have thus been the focus of intense research, but none are part of routine practice.<h4>Objectives</h4>To identify and catalogue candidate biomarkers of disease progression in psoriasis for the translational research community.<h4>Methods</h4>A systematic search of CENTRAL, Embase, LILACS and MEDLINE was performed for relevant articles published between 1990 and December 2021. Eligibility criteria were studies involving patients with psoriasis (any age, n\u2009\u2265\u200950) reporting biomarkers associated with disease progression. The main outcomes were any measure of skin severity or any prespecified psoriasis comorbidity. Data were extracted by one reviewer and checked by a second; studies meeting minimal quality criteria (longitudinal design and/or use of methods to control for confounding) were formally assessed for bias. Candidate biomarkers were identified by an expert multistakeholder group using a majority voting consensus exercise, and mapped to relevant cellular and molecular pathways.<h4>Results</h4>Of 181 included studies, most investigated genomic or proteomic biomarkers associated with disease severity (n\u2009=\u2009145) or psoriatic arthritis (n\u2009=\u200930). Methodological and reporting limitations compromised interpretation of findings, most notably a lack of longitudinal studies, and inadequate control for key prognostic factors. The following candidate biomarkers with future potential utility were identified for predicting disease severity: LCE3D, interleukin (IL)23R, IL23A, NFKBIL1 loci, HLA-C*06:02 (genomic), IL-17A, IgG aHDL, GlycA, I-FABP and kallikrein 8 (proteomic), tyramine (metabolomic); psoriatic arthritis: HLA-C*06:02, HLA-B*27, HLA-B*38, HLA-B*08, and variation at the IL23R and IL13 loci (genomic); IL-17A, CXCL10, Mac-2 binding protein, integrin b5, matrix metalloproteinase-3 and macrophage-colony stimulating factor (proteomic) and tyramine and mucic acid (metabolomic); and type 2 diabetes mellitus: variation in IL12B and IL23R loci (genomic). No biomarkers were supported by sufficient evidence for clinical use without further validation.<h4>Conclusions</h4>This review provides a comprehensive catalogue of investigated biomarkers of disease progression in psoriasis. Future studies must address the common methodological limitations identified herein to expedite discovery and validation of biomarkers for clinical use. What is already known about this topic? The current treatment paradigm in psoriasis is reactive. There is a need to develop effective risk-stratified management approaches that can proactively attenuate the substantial burden of disease. Prognostic biomarkers of disease progression have therefore been the focus of intense research. What does this study add? This review is the first to scope, collate and catalogue research investigating biomarkers of disease progression in psoriasis. The review identifies potentially promising candidate biomarkers for further investigation and highlights common important limitations that should be considered when designing and conducting future studies in this area.",
-    "laySummary": "",
-    "urls": "pdf:https://kclpure.kcl.ac.uk/ws/files/177671246/Br_J_Dermatol_2022_Ramessur_Biomarkers_of_disease_progression_in_people_with_psoriasis_a_scoping_review.pdf; doi:https://doi.org/10.1111/bjd.21627; html:https://europepmc.org/articles/PMC9796834; pdf:https://europepmc.org/articles/PMC9796834?pdf=render"
-  },
   {
     "id": "31040096",
     "doi": "https://doi.org/10.1016/s2352-4642(19)30114-2",
@@ -37926,6 +37943,23 @@
     "laySummary": "",
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s12471-019-1288-4.pdf; doi:https://doi.org/10.1007/s12471-019-1288-4; html:https://europepmc.org/articles/PMC6712144; pdf:https://europepmc.org/articles/PMC6712144?pdf=render"
   },
+  {
+    "id": "35482474",
+    "doi": "https://doi.org/10.1111/bjd.21627",
+    "title": "Biomarkers of disease progression in people with psoriasis: a scoping review.",
+    "authorString": "Ramessur R, Corbett M, Marshall D, Acencio ML, Barbosa IA, Dand N, Di Meglio P, Haddad S, Jensen AHM, Koopmann W, Mahil SK, Ostaszewski M, Rahmatulla S, Rastrick J, Saklatvala J, Weidinger S, Wright K, Eyerich K, Ndlovu M, Barker JN, Skov L, Conrad C, Smith CH, BIOMAP consortium.",
+    "authorAffiliations": "",
+    "journalTitle": "The British journal of dermatology",
+    "pubYear": "2022",
+    "date": "2022-07-11",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Identification of those at risk of more severe psoriasis and/or associated morbidities offers opportunity for early intervention, reduced disease burden and more cost-effective healthcare. Prognostic biomarkers of disease progression have thus been the focus of intense research, but none are part of routine practice.<h4>Objectives</h4>To identify and catalogue candidate biomarkers of disease progression in psoriasis for the translational research community.<h4>Methods</h4>A systematic search of CENTRAL, Embase, LILACS and MEDLINE was performed for relevant articles published between 1990 and December 2021. Eligibility criteria were studies involving patients with psoriasis (any age, n\u2009\u2265\u200950) reporting biomarkers associated with disease progression. The main outcomes were any measure of skin severity or any prespecified psoriasis comorbidity. Data were extracted by one reviewer and checked by a second; studies meeting minimal quality criteria (longitudinal design and/or use of methods to control for confounding) were formally assessed for bias. Candidate biomarkers were identified by an expert multistakeholder group using a majority voting consensus exercise, and mapped to relevant cellular and molecular pathways.<h4>Results</h4>Of 181 included studies, most investigated genomic or proteomic biomarkers associated with disease severity (n\u2009=\u2009145) or psoriatic arthritis (n\u2009=\u200930). Methodological and reporting limitations compromised interpretation of findings, most notably a lack of longitudinal studies, and inadequate control for key prognostic factors. The following candidate biomarkers with future potential utility were identified for predicting disease severity: LCE3D, interleukin (IL)23R, IL23A, NFKBIL1 loci, HLA-C*06:02 (genomic), IL-17A, IgG aHDL, GlycA, I-FABP and kallikrein 8 (proteomic), tyramine (metabolomic); psoriatic arthritis: HLA-C*06:02, HLA-B*27, HLA-B*38, HLA-B*08, and variation at the IL23R and IL13 loci (genomic); IL-17A, CXCL10, Mac-2 binding protein, integrin b5, matrix metalloproteinase-3 and macrophage-colony stimulating factor (proteomic) and tyramine and mucic acid (metabolomic); and type 2 diabetes mellitus: variation in IL12B and IL23R loci (genomic). No biomarkers were supported by sufficient evidence for clinical use without further validation.<h4>Conclusions</h4>This review provides a comprehensive catalogue of investigated biomarkers of disease progression in psoriasis. Future studies must address the common methodological limitations identified herein to expedite discovery and validation of biomarkers for clinical use. What is already known about this topic? The current treatment paradigm in psoriasis is reactive. There is a need to develop effective risk-stratified management approaches that can proactively attenuate the substantial burden of disease. Prognostic biomarkers of disease progression have therefore been the focus of intense research. What does this study add? This review is the first to scope, collate and catalogue research investigating biomarkers of disease progression in psoriasis. The review identifies potentially promising candidate biomarkers for further investigation and highlights common important limitations that should be considered when designing and conducting future studies in this area.",
+    "laySummary": "",
+    "urls": "pdf:https://kclpure.kcl.ac.uk/ws/files/177671246/Br_J_Dermatol_2022_Ramessur_Biomarkers_of_disease_progression_in_people_with_psoriasis_a_scoping_review.pdf; doi:https://doi.org/10.1111/bjd.21627; html:https://europepmc.org/articles/PMC9796834; pdf:https://europepmc.org/articles/PMC9796834?pdf=render"
+  },
   {
     "id": "32479194",
     "doi": "https://doi.org/10.1161/circulationaha.120.045826",
@@ -37977,23 +38011,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.cels.2021.05.005; doi:https://doi.org/10.1016/j.cels.2021.05.005; html:https://europepmc.org/articles/PMC8201874"
   },
-  {
-    "id": "37118290",
-    "doi": "https://doi.org/10.1038/s43587-022-00293-x",
-    "title": "Immune system-wide Mendelian randomization and triangulation analyses support autoimmunity as a modifiable component in dementia-causing diseases.",
-    "authorString": "Lindbohm JV, Mars N, Sipil\u00e4 PN, Singh-Manoux A, Runz H, FinnGen, Livingston G, Seshadri S, Xavier R, Hingorani AD, Ripatti S, Kivim\u00e4ki M.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature aging",
-    "pubYear": "2022",
-    "date": "2022-10-14",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Immune system and blood-brain barrier dysfunction are implicated in the development of Alzheimer's and other dementia-causing diseases, but their causal role remains unknown. We performed Mendelian randomization for 1,827\u2009immune system- and blood-brain barrier-related biomarkers and identified 127\u2009potential causal risk factors for dementia-causing diseases. Pathway analyses linked these biomarkers to amyloid-\u03b2, tau and \u03b1-synuclein pathways and to autoimmunity-related processes. A phenome-wide analysis using Mendelian randomization-based polygenic risk score in the FinnGen study (n\u2009=\u2009339,233) for the biomarkers indicated shared genetic background for dementias and autoimmune diseases. This association was further supported by human leukocyte antigen analyses. In inverse-probability-weighted analyses that simulate randomized controlled drug trials in observational data, anti-inflammatory methotrexate treatment reduced the incidence of Alzheimer's disease in high-risk individuals (hazard ratio compared with no treatment, 0.64, 95% confidence interval 0.49-0.88, P\u2009=\u20090.005). These converging results from different lines of human research suggest that autoimmunity is a modifiable component in dementia-causing diseases.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s43587-022-00293-x.pdf; doi:https://doi.org/10.1038/s43587-022-00293-x; html:https://europepmc.org/articles/PMC10154235; pdf:https://europepmc.org/articles/PMC10154235?pdf=render"
-  },
   {
     "id": "37770476",
     "doi": "https://doi.org/10.1038/s41467-023-41249-y",
@@ -38011,6 +38028,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41467-023-41249-y.pdf; doi:https://doi.org/10.1038/s41467-023-41249-y; html:https://europepmc.org/articles/PMC10539313; pdf:https://europepmc.org/articles/PMC10539313?pdf=render"
   },
+  {
+    "id": "37118290",
+    "doi": "https://doi.org/10.1038/s43587-022-00293-x",
+    "title": "Immune system-wide Mendelian randomization and triangulation analyses support autoimmunity as a modifiable component in dementia-causing diseases.",
+    "authorString": "Lindbohm JV, Mars N, Sipil\u00e4 PN, Singh-Manoux A, Runz H, FinnGen, Livingston G, Seshadri S, Xavier R, Hingorani AD, Ripatti S, Kivim\u00e4ki M.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature aging",
+    "pubYear": "2022",
+    "date": "2022-10-14",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Immune system and blood-brain barrier dysfunction are implicated in the development of Alzheimer's and other dementia-causing diseases, but their causal role remains unknown. We performed Mendelian randomization for 1,827\u2009immune system- and blood-brain barrier-related biomarkers and identified 127\u2009potential causal risk factors for dementia-causing diseases. Pathway analyses linked these biomarkers to amyloid-\u03b2, tau and \u03b1-synuclein pathways and to autoimmunity-related processes. A phenome-wide analysis using Mendelian randomization-based polygenic risk score in the FinnGen study (n\u2009=\u2009339,233) for the biomarkers indicated shared genetic background for dementias and autoimmune diseases. This association was further supported by human leukocyte antigen analyses. In inverse-probability-weighted analyses that simulate randomized controlled drug trials in observational data, anti-inflammatory methotrexate treatment reduced the incidence of Alzheimer's disease in high-risk individuals (hazard ratio compared with no treatment, 0.64, 95% confidence interval 0.49-0.88, P\u2009=\u20090.005). These converging results from different lines of human research suggest that autoimmunity is a modifiable component in dementia-causing diseases.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s43587-022-00293-x.pdf; doi:https://doi.org/10.1038/s43587-022-00293-x; html:https://europepmc.org/articles/PMC10154235; pdf:https://europepmc.org/articles/PMC10154235?pdf=render"
+  },
   {
     "id": "30014898",
     "doi": "https://doi.org/10.1016/j.envres.2018.07.015",
@@ -38028,23 +38062,6 @@
     "laySummary": "",
     "urls": "pdf:https://researchonline.lshtm.ac.uk/id/eprint/4648566/1/Estimation%20of%20TETRA%20radio_GREEN%20AAM.pdf; doi:https://doi.org/10.1016/j.envres.2018.07.015"
   },
-  {
-    "id": "33550229",
-    "doi": "https://doi.org/10.1136/bmjopen-2020-040167",
-    "title": "Assessing public support for extending smoke-free policies beyond enclosed public places and workplaces: protocol for a systematic review and meta-analysis.",
-    "authorString": "Boderie NW, M\u00f6lenberg FJ, Sheikh A, Bramer WM, Burdorf A, van Lenthe FJ, Been JV.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2021",
-    "date": "2021-02-05",
-    "isOpenAccess": "Y",
-    "keywords": "Tobacco smoke pollution; Attitude; Smoke-free Policy",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>Smoke-free enclosed public environments are effective in reducing exposure to secondhand smoke and yield major public health benefits. Building on this, many countries are now implementing smoke-free policies regulating smoking beyond enclosed public places and workplaces. In order to successfully implement such 'novel smoke-free policies', public support is essential. We aim to provide the first comprehensive systematic review and meta-analysis assessing levels and determinants of public support for novel smoke-free policies.<h4>Methods and analysis</h4>The primary objective of this review is to summarise the level of public support for novel smoke-free policies. Eight online databases (Embase.com, Medline ALL Ovid, Web of Science Core Collection, WHO Library Database, Latin American and Caribbean Health Sciences Literature, Scientific Online Library Online, PsychINFO and Google Scholar) will be searched from 1 January 2004 by two independent researchers with no language restrictions. The initial search was performed on 15 April 2020 and will be updated prior to finalisation of the report. Studies are eligible if assessing support for novel smoke-free policies in the general population (age \u226516 years) and have a sample size of n\u2265400. Studies funded by the tobacco industry or evaluating support among groups with vested interest are excluded. The primary outcome is proportion of public support for smoke-free policies, subdivided according to the spaces covered: (1) indoor private spaces (eg, cars) (2) indoor semiprivate spaces (eg, multi-unit housing) (3) outdoor (semi)private spaces (eg, courtyards) (4) non-hospitality outdoor public spaces (eg, parks, hospital grounds, playgrounds) and (5) hospitality outdoor public spaces (eg, restaurant terraces). The secondary objective is to identify determinants associated with public support on three levels: (1) within-study determinants (eg, smoking status) (2) between-study determinants (eg, survey year) and (3) context-specific determinants (eg, social norms). Risk of bias will be assessed using the Mixed Methods Appraisal Tool and a sensitivity analysis will be performed excluding studies at high risk of bias.<h4>Ethics and dissemination</h4>No formal ethical approval is required. Findings will be disseminated to academics, policymakers and the general public.",
-    "laySummary": "",
-    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/11/2/e040167.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-040167; html:https://europepmc.org/articles/PMC7925902; pdf:https://europepmc.org/articles/PMC7925902?pdf=render"
-  },
   {
     "id": "34708157",
     "doi": "https://doi.org/10.12688/wellcomeopenres.16701.3",
@@ -38062,6 +38079,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.12688/wellcomeopenres.16701.3; html:https://europepmc.org/articles/PMC8517721; pdf:https://europepmc.org/articles/PMC8517721?pdf=render"
   },
+  {
+    "id": "33550229",
+    "doi": "https://doi.org/10.1136/bmjopen-2020-040167",
+    "title": "Assessing public support for extending smoke-free policies beyond enclosed public places and workplaces: protocol for a systematic review and meta-analysis.",
+    "authorString": "Boderie NW, M\u00f6lenberg FJ, Sheikh A, Bramer WM, Burdorf A, van Lenthe FJ, Been JV.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2021",
+    "date": "2021-02-05",
+    "isOpenAccess": "Y",
+    "keywords": "Tobacco smoke pollution; Attitude; Smoke-free Policy",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>Smoke-free enclosed public environments are effective in reducing exposure to secondhand smoke and yield major public health benefits. Building on this, many countries are now implementing smoke-free policies regulating smoking beyond enclosed public places and workplaces. In order to successfully implement such 'novel smoke-free policies', public support is essential. We aim to provide the first comprehensive systematic review and meta-analysis assessing levels and determinants of public support for novel smoke-free policies.<h4>Methods and analysis</h4>The primary objective of this review is to summarise the level of public support for novel smoke-free policies. Eight online databases (Embase.com, Medline ALL Ovid, Web of Science Core Collection, WHO Library Database, Latin American and Caribbean Health Sciences Literature, Scientific Online Library Online, PsychINFO and Google Scholar) will be searched from 1 January 2004 by two independent researchers with no language restrictions. The initial search was performed on 15 April 2020 and will be updated prior to finalisation of the report. Studies are eligible if assessing support for novel smoke-free policies in the general population (age \u226516 years) and have a sample size of n\u2265400. Studies funded by the tobacco industry or evaluating support among groups with vested interest are excluded. The primary outcome is proportion of public support for smoke-free policies, subdivided according to the spaces covered: (1) indoor private spaces (eg, cars) (2) indoor semiprivate spaces (eg, multi-unit housing) (3) outdoor (semi)private spaces (eg, courtyards) (4) non-hospitality outdoor public spaces (eg, parks, hospital grounds, playgrounds) and (5) hospitality outdoor public spaces (eg, restaurant terraces). The secondary objective is to identify determinants associated with public support on three levels: (1) within-study determinants (eg, smoking status) (2) between-study determinants (eg, survey year) and (3) context-specific determinants (eg, social norms). Risk of bias will be assessed using the Mixed Methods Appraisal Tool and a sensitivity analysis will be performed excluding studies at high risk of bias.<h4>Ethics and dissemination</h4>No formal ethical approval is required. Findings will be disseminated to academics, policymakers and the general public.",
+    "laySummary": "",
+    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/11/2/e040167.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-040167; html:https://europepmc.org/articles/PMC7925902; pdf:https://europepmc.org/articles/PMC7925902?pdf=render"
+  },
   {
     "id": "35991675",
     "doi": "https://doi.org/10.1016/j.lana.2022.100335",
@@ -38130,23 +38164,6 @@
     "laySummary": "",
     "urls": "html:http://hdl.handle.net/10044/1/80100; doi:https://doi.org/10.1038/s43016-020-0092-z"
   },
-  {
-    "id": "37723491",
-    "doi": "https://doi.org/10.1186/s13073-023-01221-3",
-    "title": "Identification of novel genetic risk factors of dilated cardiomyopathy: from canine to human.",
-    "authorString": "Niskanen JE, Ohlsson \u00c5, Ljungvall I, Dr\u00f6gem\u00fcller M, Ernst RF, Dooijes D, van Deutekom HWM, van Tintelen JP, Snijders Blok CJB, van Vugt M, van Setten J, Asselbergs FW, Petri\u010d AD, Salonen M, Hundi S, H\u00f6rtenhuber M, DoGA consortium, Kere J, Pyle WG, Donner J, Postma AV, Leeb T, Andersson G, Hyt\u00f6nen MK, H\u00e4ggstr\u00f6m J, Wiberg M, Friederich J, Eberhard J, Harakalova M, van Steenbeek FG, Wess G, Lohi H.",
-    "authorAffiliations": "",
-    "journalTitle": "Genome medicine",
-    "pubYear": "2023",
-    "date": "2023-09-18",
-    "isOpenAccess": "Y",
-    "keywords": "Genetics; Cardiac; Arrhythmia; Cardiology; Gwas; Transcriptomics; Complex Trait; Companion Animal",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Dilated cardiomyopathy (DCM) is a life-threatening heart disease and a common cause of heart failure due to systolic dysfunction and subsequent left or biventricular dilatation. A significant number of cases have a genetic etiology; however, as a complex disease, the exact genetic risk factors are largely unknown, and many patients remain without a molecular diagnosis.<h4>Methods</h4>We performed GWAS followed by whole-genome, transcriptome, and immunohistochemical analyses in a spontaneously occurring canine model of DCM. Canine gene discovery was followed up in three human DCM cohorts.<h4>Results</h4>Our results revealed two independent additive loci associated with the typical DCM phenotype comprising left ventricular systolic dysfunction and dilatation. We highlight two novel candidate genes, RNF207 and PRKAA2, known for their involvement in cardiac action potentials, energy homeostasis, and morphology. We further illustrate the distinct genetic etiologies underlying the typical DCM phenotype and ventricular premature contractions. Finally, we followed up on the canine discoveries in human DCM patients and discovered candidate variants in our two novel genes.<h4>Conclusions</h4>Collectively, our study yields insight into the molecular pathophysiology of DCM and provides a large animal model for preclinical studies.",
-    "laySummary": "",
-    "urls": "pdf:https://genomemedicine.biomedcentral.com/counter/pdf/10.1186/s13073-023-01221-3; doi:https://doi.org/10.1186/s13073-023-01221-3; html:https://europepmc.org/articles/PMC10506233; pdf:https://europepmc.org/articles/PMC10506233?pdf=render"
-  },
   {
     "id": "35416614",
     "doi": "https://doi.org/10.1007/s43441-022-00394-0",
@@ -38164,6 +38181,23 @@
     "laySummary": "",
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s43441-022-00394-0.pdf; doi:https://doi.org/10.1007/s43441-022-00394-0; html:https://europepmc.org/articles/PMC9007047; pdf:https://europepmc.org/articles/PMC9007047?pdf=render"
   },
+  {
+    "id": "37723491",
+    "doi": "https://doi.org/10.1186/s13073-023-01221-3",
+    "title": "Identification of novel genetic risk factors of dilated cardiomyopathy: from canine to human.",
+    "authorString": "Niskanen JE, Ohlsson \u00c5, Ljungvall I, Dr\u00f6gem\u00fcller M, Ernst RF, Dooijes D, van Deutekom HWM, van Tintelen JP, Snijders Blok CJB, van Vugt M, van Setten J, Asselbergs FW, Petri\u010d AD, Salonen M, Hundi S, H\u00f6rtenhuber M, DoGA consortium, Kere J, Pyle WG, Donner J, Postma AV, Leeb T, Andersson G, Hyt\u00f6nen MK, H\u00e4ggstr\u00f6m J, Wiberg M, Friederich J, Eberhard J, Harakalova M, van Steenbeek FG, Wess G, Lohi H.",
+    "authorAffiliations": "",
+    "journalTitle": "Genome medicine",
+    "pubYear": "2023",
+    "date": "2023-09-18",
+    "isOpenAccess": "Y",
+    "keywords": "Genetics; Cardiac; Arrhythmia; Cardiology; Gwas; Transcriptomics; Complex Trait; Companion Animal",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Dilated cardiomyopathy (DCM) is a life-threatening heart disease and a common cause of heart failure due to systolic dysfunction and subsequent left or biventricular dilatation. A significant number of cases have a genetic etiology; however, as a complex disease, the exact genetic risk factors are largely unknown, and many patients remain without a molecular diagnosis.<h4>Methods</h4>We performed GWAS followed by whole-genome, transcriptome, and immunohistochemical analyses in a spontaneously occurring canine model of DCM. Canine gene discovery was followed up in three human DCM cohorts.<h4>Results</h4>Our results revealed two independent additive loci associated with the typical DCM phenotype comprising left ventricular systolic dysfunction and dilatation. We highlight two novel candidate genes, RNF207 and PRKAA2, known for their involvement in cardiac action potentials, energy homeostasis, and morphology. We further illustrate the distinct genetic etiologies underlying the typical DCM phenotype and ventricular premature contractions. Finally, we followed up on the canine discoveries in human DCM patients and discovered candidate variants in our two novel genes.<h4>Conclusions</h4>Collectively, our study yields insight into the molecular pathophysiology of DCM and provides a large animal model for preclinical studies.",
+    "laySummary": "",
+    "urls": "pdf:https://genomemedicine.biomedcentral.com/counter/pdf/10.1186/s13073-023-01221-3; doi:https://doi.org/10.1186/s13073-023-01221-3; html:https://europepmc.org/articles/PMC10506233; pdf:https://europepmc.org/articles/PMC10506233?pdf=render"
+  },
   {
     "id": "31810636",
     "doi": "https://doi.org/10.1016/j.injury.2019.11.034",
@@ -38283,23 +38317,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/s2589-7500(20)30134-5; doi:https://doi.org/10.1016/S2589-7500(20)30134-5; html:https://europepmc.org/articles/PMC7292602; pdf:https://europepmc.org/articles/PMC7292602?pdf=render"
   },
-  {
-    "id": "34547359",
-    "doi": "https://doi.org/10.1016/j.jaad.2021.09.018",
-    "title": "Mixed evidence on the relationship between socioeconomic position and atopic dermatitis: A systematic review.",
-    "authorString": "Bajwa H, Baghchechi M, Mujahid M, Kang Dufour MS, Langan SM, Abuabara K.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of the American Academy of Dermatology",
-    "pubYear": "2022",
-    "date": "2021-09-20",
-    "isOpenAccess": "N",
-    "keywords": "dermatitis; Socioeconomic status; Eczema; Atopic; Socioeconomic Position",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Lower socioeconomic position usually portends worse health outcomes, but multiple studies have found that atopic dermatitis is associated with higher socioeconomic position. The nature of this relationship remains unclear.<h4>Objective</h4>To systematically review the literature on socioeconomic position and atopic dermatitis and determine whether the association varies by patient or study characteristics.<h4>Methods</h4>A literature search was conducted in the PubMed and Embase databases. Individual-level studies addressing the association between all measures of socioeconomic position and the prevalence or incidence of atopic dermatitis were eligible for inclusion. Two independent reviewers screened all texts and extracted all data for qualitative synthesis.<h4>Results</h4>Eighty-eight studies met the inclusion criteria. Of the 88 studies, 42% (37) found a positive association between atopic dermatitis and socioeconomic position, 15% (13) found a negative association, and 43% (38) found a null or inconsistent association. Studies conducted in Europe, among children, and based on self-report of eczema were more likely to find a positive association with socioeconomic position.<h4>Limitations</h4>Studies varied both in terms of the measurement of socioeconomic position and the definition of atopic dermatitis, limiting quantitative synthesis.<h4>Conclusion</h4>The evidence of a positive association between atopic dermatitis and socioeconomic position is not consistent.",
-    "laySummary": "",
-    "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8810617; doi:https://doi.org/10.1016/j.jaad.2021.09.018; html:https://europepmc.org/articles/PMC8810617; pdf:https://europepmc.org/articles/PMC8810617?pdf=render; doi:https://doi.org/10.1016/j.jaad.2021.09.018"
-  },
   {
     "id": "32724101",
     "doi": "https://doi.org/10.1038/s41467-020-17477-x",
@@ -38317,6 +38334,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41467-020-17477-x.pdf; doi:https://doi.org/10.1038/s41467-020-17477-x; html:https://europepmc.org/articles/PMC7387553; pdf:https://europepmc.org/articles/PMC7387553?pdf=render"
   },
+  {
+    "id": "34547359",
+    "doi": "https://doi.org/10.1016/j.jaad.2021.09.018",
+    "title": "Mixed evidence on the relationship between socioeconomic position and atopic dermatitis: A systematic review.",
+    "authorString": "Bajwa H, Baghchechi M, Mujahid M, Kang Dufour MS, Langan SM, Abuabara K.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of the American Academy of Dermatology",
+    "pubYear": "2022",
+    "date": "2021-09-20",
+    "isOpenAccess": "N",
+    "keywords": "dermatitis; Socioeconomic status; Eczema; Atopic; Socioeconomic Position",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Lower socioeconomic position usually portends worse health outcomes, but multiple studies have found that atopic dermatitis is associated with higher socioeconomic position. The nature of this relationship remains unclear.<h4>Objective</h4>To systematically review the literature on socioeconomic position and atopic dermatitis and determine whether the association varies by patient or study characteristics.<h4>Methods</h4>A literature search was conducted in the PubMed and Embase databases. Individual-level studies addressing the association between all measures of socioeconomic position and the prevalence or incidence of atopic dermatitis were eligible for inclusion. Two independent reviewers screened all texts and extracted all data for qualitative synthesis.<h4>Results</h4>Eighty-eight studies met the inclusion criteria. Of the 88 studies, 42% (37) found a positive association between atopic dermatitis and socioeconomic position, 15% (13) found a negative association, and 43% (38) found a null or inconsistent association. Studies conducted in Europe, among children, and based on self-report of eczema were more likely to find a positive association with socioeconomic position.<h4>Limitations</h4>Studies varied both in terms of the measurement of socioeconomic position and the definition of atopic dermatitis, limiting quantitative synthesis.<h4>Conclusion</h4>The evidence of a positive association between atopic dermatitis and socioeconomic position is not consistent.",
+    "laySummary": "",
+    "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8810617; doi:https://doi.org/10.1016/j.jaad.2021.09.018; html:https://europepmc.org/articles/PMC8810617; pdf:https://europepmc.org/articles/PMC8810617?pdf=render; doi:https://doi.org/10.1016/j.jaad.2021.09.018"
+  },
   {
     "id": "33201485",
     "doi": "https://doi.org/10.1007/s12471-020-01517-8",
@@ -38453,23 +38487,6 @@
     "laySummary": "",
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s12471-022-01670-2.pdf; doi:https://doi.org/10.1007/s12471-022-01670-2; html:https://europepmc.org/articles/PMC8929464; pdf:https://europepmc.org/articles/PMC8929464?pdf=render"
   },
-  {
-    "id": "32678323",
-    "doi": "https://doi.org/10.1038/s41366-020-0642-3",
-    "title": "Cross-sectional associations between central and general adiposity with albuminuria: observations from 400,000 people in UK Biobank.",
-    "authorString": "Zhu P, Lewington S, Haynes R, Emberson J, Landray MJ, Cherney D, Woodward M, Baigent C, Herrington WG, Staplin N.",
-    "authorAffiliations": "",
-    "journalTitle": "International journal of obesity (2005)",
-    "pubYear": "2020",
-    "date": "2020-07-16",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Whether measures of central adiposity are more or less strongly associated with risk of albuminuria than body mass index (BMI), and by how much diabetes/levels of glycosylated haemoglobin (HbA1c) explain or modify these associations, is uncertain.<h4>Methods</h4>Ordinal logistic regression was used to estimate associations between values of central adiposity (waist-to-hip ratio) and, separately, general adiposity (BMI) with categories of urinary albumin-to-creatinine ratio (uACR) in 408,527 UK Biobank participants. Separate central and general adiposity-based models were initially adjusted for potential confounders and measurement error, then sequentially, models were mutually adjusted (e.g. waist-to-hip ratio adjusted for BMI, and vice versa), and finally they were adjusted for potential mediators.<h4>Results</h4>Levels of albuminuria were generally low: 20,425 (5%) had a uACR \u22653\u2009mg/mmol. After adjustment for confounders and measurement error, each 0.06 higher waist-to-hip ratio was associated with a 55% (95%CI 53-57%) increase in the odds of being in a higher uACR category. After adjustment for baseline BMI, this association was reduced to 32% (30-34%). Each 5\u2009kg/m<sup>2</sup> higher BMI was associated with a 47% (46-49%) increase in the odds of being in a higher uACR category. Adjustment for baseline waist-to-hip ratio reduced this association to 35% (33-37%). Those with higher HbA1c were at progressively higher odds of albuminuria, but positive associations between both waist-to-hip ratio and BMI were apparent irrespective of HbA1c. Altogether, about 40% of central adiposity associations appeared to be mediated by diabetes, vascular disease and blood pressure.<h4>Conclusions</h4>Conventional epidemiological approaches suggest that higher waist-to-hip ratio and BMI are independently positively associated with albuminuria. Adiposity-albuminuria associations appear strong among people with normal HbA1c, as well as people with pre-diabetes or diabetes.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41366-020-0642-3.pdf; doi:https://doi.org/10.1038/s41366-020-0642-3; html:https://europepmc.org/articles/PMC7577847; pdf:https://europepmc.org/articles/PMC7577847?pdf=render"
-  },
   {
     "id": "31204027",
     "doi": "https://doi.org/10.1016/j.injury.2019.06.012",
@@ -38487,6 +38504,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.injury.2019.06.012"
   },
+  {
+    "id": "32678323",
+    "doi": "https://doi.org/10.1038/s41366-020-0642-3",
+    "title": "Cross-sectional associations between central and general adiposity with albuminuria: observations from 400,000 people in UK Biobank.",
+    "authorString": "Zhu P, Lewington S, Haynes R, Emberson J, Landray MJ, Cherney D, Woodward M, Baigent C, Herrington WG, Staplin N.",
+    "authorAffiliations": "",
+    "journalTitle": "International journal of obesity (2005)",
+    "pubYear": "2020",
+    "date": "2020-07-16",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Whether measures of central adiposity are more or less strongly associated with risk of albuminuria than body mass index (BMI), and by how much diabetes/levels of glycosylated haemoglobin (HbA1c) explain or modify these associations, is uncertain.<h4>Methods</h4>Ordinal logistic regression was used to estimate associations between values of central adiposity (waist-to-hip ratio) and, separately, general adiposity (BMI) with categories of urinary albumin-to-creatinine ratio (uACR) in 408,527 UK Biobank participants. Separate central and general adiposity-based models were initially adjusted for potential confounders and measurement error, then sequentially, models were mutually adjusted (e.g. waist-to-hip ratio adjusted for BMI, and vice versa), and finally they were adjusted for potential mediators.<h4>Results</h4>Levels of albuminuria were generally low: 20,425 (5%) had a uACR \u22653\u2009mg/mmol. After adjustment for confounders and measurement error, each 0.06 higher waist-to-hip ratio was associated with a 55% (95%CI 53-57%) increase in the odds of being in a higher uACR category. After adjustment for baseline BMI, this association was reduced to 32% (30-34%). Each 5\u2009kg/m<sup>2</sup> higher BMI was associated with a 47% (46-49%) increase in the odds of being in a higher uACR category. Adjustment for baseline waist-to-hip ratio reduced this association to 35% (33-37%). Those with higher HbA1c were at progressively higher odds of albuminuria, but positive associations between both waist-to-hip ratio and BMI were apparent irrespective of HbA1c. Altogether, about 40% of central adiposity associations appeared to be mediated by diabetes, vascular disease and blood pressure.<h4>Conclusions</h4>Conventional epidemiological approaches suggest that higher waist-to-hip ratio and BMI are independently positively associated with albuminuria. Adiposity-albuminuria associations appear strong among people with normal HbA1c, as well as people with pre-diabetes or diabetes.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41366-020-0642-3.pdf; doi:https://doi.org/10.1038/s41366-020-0642-3; html:https://europepmc.org/articles/PMC7577847; pdf:https://europepmc.org/articles/PMC7577847?pdf=render"
+  },
   {
     "id": "32888427",
     "doi": "https://doi.org/10.1016/j.ajhg.2020.08.009",
@@ -38555,23 +38589,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41588-024-01763-1.pdf; doi:https://doi.org/10.1038/s41588-024-01763-1; html:https://europepmc.org/articles/PMC11176086; pdf:https://europepmc.org/articles/PMC11176086?pdf=render"
   },
-  {
-    "id": "37575973",
-    "doi": "https://doi.org/10.2147/clep.s417176",
-    "title": "Anxiety and Depression in People with Eczema or Psoriasis: A Comparison of Associations in UK Biobank and Linked Primary Care Data.",
-    "authorString": "Matthewman J, Mansfield KE, Hayes JF, Adesanya EI, Smith CH, Roberts A, Langan SM, Henderson AD.",
-    "authorAffiliations": "",
-    "journalTitle": "Clinical epidemiology",
-    "pubYear": "2023",
-    "date": "2023-08-07",
-    "isOpenAccess": "Y",
-    "keywords": "Depression; Psoriasis; Anxiety; Eczema; Cross-sectional study; Data Linkage; Electronic Health Records; Ascertainment; Uk Biobank",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>Previous research has shown associations between eczema and psoriasis and anxiety and depression. We investigated whether associations are consistent across different settings of ascertainment for depression and anxiety, including interview and survey responses from UK Biobank (a large longitudinal cohort recruiting individuals aged 40-69 years between 2006-2010), and linked primary care data, with the aim of drawing more reliable conclusions through triangulation.<h4>Methods</h4>In cross-sectional studies, we estimated associations between eczema or psoriasis and anxiety or depression, defining anxiety or depression as 1) self-reported previous diagnosis at UK Biobank recruitment interview; 2) PHQ-9/GAD-7 score indicating depression or anxiety from a UK Biobank mental health follow-up survey in 2016; and 3) diagnosis in linked primary care electronic health record data.<h4>Results</h4>We analysed 230,047 people with linked Biobank and primary care data. We found poor agreement between the data sources for eczema, psoriasis, anxiety, and depression. Eg, 9474 had a previous eczema diagnosis in primary care data, 4069 self-reported previous eczema diagnosis at the UK biobank interview, and 1536 had eczema in both data sources (for depression 40,455; 13,320; and 9588 respectively). Having eczema or psoriasis (recorded in primary care or baseline interview) was associated with higher odds of anxiety and depression. Eg, the adjusted odds ratio for depression comparing those with eczema to those without was greater than 1 when defining the outcome from 1) the recruitment interview (1.36, 95% confidence interval 1.27-1.45); 2) the follow-up survey (1.24, 1.09-1.39), and 3) primary care records (1.56, 1.50-1.62).<h4>Discussion</h4>Our findings support increased prevalence of mental illness in people with psoriasis and eczema across multiple data sources, which should be considered in planning of mental health services. However, we found poor agreement in disease ascertainment between settings, with implications for data interpretation in electronic health records.",
-    "laySummary": "",
-    "urls": "pdf:https://www.dovepress.com/getfile.php?fileID=91773; doi:https://doi.org/10.2147/CLEP.S417176; html:https://europepmc.org/articles/PMC10421744; pdf:https://europepmc.org/articles/PMC10421744?pdf=render"
-  },
   {
     "id": "35288697",
     "doi": "https://doi.org/10.1038/s41591-022-01750-1",
@@ -38589,6 +38606,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41591-022-01750-1.pdf; doi:https://doi.org/10.1038/s41591-022-01750-1; html:https://europepmc.org/articles/PMC9205770; pdf:https://europepmc.org/articles/PMC9205770?pdf=render"
   },
+  {
+    "id": "37575973",
+    "doi": "https://doi.org/10.2147/clep.s417176",
+    "title": "Anxiety and Depression in People with Eczema or Psoriasis: A Comparison of Associations in UK Biobank and Linked Primary Care Data.",
+    "authorString": "Matthewman J, Mansfield KE, Hayes JF, Adesanya EI, Smith CH, Roberts A, Langan SM, Henderson AD.",
+    "authorAffiliations": "",
+    "journalTitle": "Clinical epidemiology",
+    "pubYear": "2023",
+    "date": "2023-08-07",
+    "isOpenAccess": "Y",
+    "keywords": "Depression; Psoriasis; Anxiety; Eczema; Cross-sectional study; Data Linkage; Electronic Health Records; Ascertainment; Uk Biobank",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>Previous research has shown associations between eczema and psoriasis and anxiety and depression. We investigated whether associations are consistent across different settings of ascertainment for depression and anxiety, including interview and survey responses from UK Biobank (a large longitudinal cohort recruiting individuals aged 40-69 years between 2006-2010), and linked primary care data, with the aim of drawing more reliable conclusions through triangulation.<h4>Methods</h4>In cross-sectional studies, we estimated associations between eczema or psoriasis and anxiety or depression, defining anxiety or depression as 1) self-reported previous diagnosis at UK Biobank recruitment interview; 2) PHQ-9/GAD-7 score indicating depression or anxiety from a UK Biobank mental health follow-up survey in 2016; and 3) diagnosis in linked primary care electronic health record data.<h4>Results</h4>We analysed 230,047 people with linked Biobank and primary care data. We found poor agreement between the data sources for eczema, psoriasis, anxiety, and depression. Eg, 9474 had a previous eczema diagnosis in primary care data, 4069 self-reported previous eczema diagnosis at the UK biobank interview, and 1536 had eczema in both data sources (for depression 40,455; 13,320; and 9588 respectively). Having eczema or psoriasis (recorded in primary care or baseline interview) was associated with higher odds of anxiety and depression. Eg, the adjusted odds ratio for depression comparing those with eczema to those without was greater than 1 when defining the outcome from 1) the recruitment interview (1.36, 95% confidence interval 1.27-1.45); 2) the follow-up survey (1.24, 1.09-1.39), and 3) primary care records (1.56, 1.50-1.62).<h4>Discussion</h4>Our findings support increased prevalence of mental illness in people with psoriasis and eczema across multiple data sources, which should be considered in planning of mental health services. However, we found poor agreement in disease ascertainment between settings, with implications for data interpretation in electronic health records.",
+    "laySummary": "",
+    "urls": "pdf:https://www.dovepress.com/getfile.php?fileID=91773; doi:https://doi.org/10.2147/CLEP.S417176; html:https://europepmc.org/articles/PMC10421744; pdf:https://europepmc.org/articles/PMC10421744?pdf=render"
+  },
   {
     "id": "32714939",
     "doi": "https://doi.org/10.3389/fnut.2020.00080",
@@ -38742,23 +38776,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41467-024-46982-6.pdf; doi:https://doi.org/10.1038/s41467-024-46982-6; html:https://europepmc.org/articles/PMC10978878; pdf:https://europepmc.org/articles/PMC10978878?pdf=render"
   },
-  {
-    "id": "33480434",
-    "doi": "https://doi.org/10.1093/pubmed/fdaa267",
-    "title": "Complex differences in infection rates between ethnic groups in Scotland: a retrospective, national census-linked cohort study of 1.65 million cases.",
-    "authorString": "Gruer LD, C\u00e9zard GI, Wallace LA, Hutchinson SJ, Douglas AF, Buchanan D, Katikireddi SV, Millard AD, Goldberg DJ, Sheikh A, Bhopal RS.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of public health (Oxford, England)",
-    "pubYear": "2022",
-    "date": "2022-03-01",
-    "isOpenAccess": "Y",
-    "keywords": "Infectious disease; epidemiology; Ethnicity",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Ethnicity can influence susceptibility to infection, as COVID-19 has shown. Few countries have systematically investigated ethnic variations in infection.<h4>Methods</h4>We linked the Scotland 2001 Census, including ethnic group, to national databases of hospitalizations/deaths and serological diagnoses of bloodborne viruses for 2001-2013. We calculated age-adjusted rate ratios (RRs) in 12 ethnic groups for all infections combined, 15 infection categories, and human immunodeficiency virus (HIV), hepatitis B (HBV) and hepatitis C (HCV) viruses.<h4>Results</h4>We analysed over 1.65 million infection-related hospitalisations/deaths. Compared with White Scottish, RRs for all infections combined were 0.8 or lower for Other White British, Other White and Chinese males and females, and 1.2-1.4 for Pakistani and African males and females. Adjustment for socioeconomic status or birthplace had little effect. RRs for specific infection categories followed similar patterns with striking exceptions. For HIV, RRs were 136 in African females and 14 in males; for HBV, 125 in Chinese females and 59 in males, 55 in African females and 24 in males; and for HCV, 2.3-3.1 in Pakistanis and Africans.<h4>Conclusions</h4>Ethnic differences were found in overall rates and many infection categories, suggesting multiple causative pathways. We recommend census linkage as a powerful method for studying the disproportionate impact of COVID-19.",
-    "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/jpubhealth/advance-article-pdf/doi/10.1093/pubmed/fdaa267/36684631/fdaa267.pdf; doi:https://doi.org/10.1093/pubmed/fdaa267; html:https://europepmc.org/articles/PMC7928762; pdf:https://europepmc.org/articles/PMC7928762?pdf=render"
-  },
   {
     "id": "31372838",
     "doi": "https://doi.org/10.1007/s12471-019-01308-w",
@@ -38776,6 +38793,23 @@
     "laySummary": "",
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s12471-019-01308-w.pdf; doi:https://doi.org/10.1007/s12471-019-01308-w; html:https://europepmc.org/articles/PMC6712110; pdf:https://europepmc.org/articles/PMC6712110?pdf=render"
   },
+  {
+    "id": "33480434",
+    "doi": "https://doi.org/10.1093/pubmed/fdaa267",
+    "title": "Complex differences in infection rates between ethnic groups in Scotland: a retrospective, national census-linked cohort study of 1.65 million cases.",
+    "authorString": "Gruer LD, C\u00e9zard GI, Wallace LA, Hutchinson SJ, Douglas AF, Buchanan D, Katikireddi SV, Millard AD, Goldberg DJ, Sheikh A, Bhopal RS.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of public health (Oxford, England)",
+    "pubYear": "2022",
+    "date": "2022-03-01",
+    "isOpenAccess": "Y",
+    "keywords": "Infectious disease; epidemiology; Ethnicity",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Ethnicity can influence susceptibility to infection, as COVID-19 has shown. Few countries have systematically investigated ethnic variations in infection.<h4>Methods</h4>We linked the Scotland 2001 Census, including ethnic group, to national databases of hospitalizations/deaths and serological diagnoses of bloodborne viruses for 2001-2013. We calculated age-adjusted rate ratios (RRs) in 12 ethnic groups for all infections combined, 15 infection categories, and human immunodeficiency virus (HIV), hepatitis B (HBV) and hepatitis C (HCV) viruses.<h4>Results</h4>We analysed over 1.65 million infection-related hospitalisations/deaths. Compared with White Scottish, RRs for all infections combined were 0.8 or lower for Other White British, Other White and Chinese males and females, and 1.2-1.4 for Pakistani and African males and females. Adjustment for socioeconomic status or birthplace had little effect. RRs for specific infection categories followed similar patterns with striking exceptions. For HIV, RRs were 136 in African females and 14 in males; for HBV, 125 in Chinese females and 59 in males, 55 in African females and 24 in males; and for HCV, 2.3-3.1 in Pakistanis and Africans.<h4>Conclusions</h4>Ethnic differences were found in overall rates and many infection categories, suggesting multiple causative pathways. We recommend census linkage as a powerful method for studying the disproportionate impact of COVID-19.",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/jpubhealth/advance-article-pdf/doi/10.1093/pubmed/fdaa267/36684631/fdaa267.pdf; doi:https://doi.org/10.1093/pubmed/fdaa267; html:https://europepmc.org/articles/PMC7928762; pdf:https://europepmc.org/articles/PMC7928762?pdf=render"
+  },
   {
     "id": "35505938",
     "doi": "https://doi.org/10.1016/j.eclinm.2022.101417",
@@ -38810,6 +38844,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-020-01872-8; doi:https://doi.org/10.1186/s12916-020-01872-8; html:https://europepmc.org/articles/PMC7861967; pdf:https://europepmc.org/articles/PMC7861967?pdf=render"
   },
+  {
+    "id": "33725121",
+    "doi": "https://doi.org/10.1093/rheumatology/keab250",
+    "title": "COVID-19 in patients with autoimmune diseases: characteristics and outcomes in a multinational network of cohorts across three countries.",
+    "authorString": "Tan EH, Sena AG, Prats-Uribe A, You SC, Ahmed WU, Kostka K, Reich C, Duvall SL, Lynch KE, Matheny ME, Duarte-Salles T, Bertolin SF, Hripcsak G, Natarajan K, Falconer T, Spotnitz M, Ostropolets A, Blacketer C, Alshammari TM, Alghoul H, Alser O, Lane JCE, Dawoud DM, Shah K, Yang Y, Zhang L, Areia C, Golozar A, Recalde M, Casajust P, Jonnagaddala J, Subbian V, Vizcaya D, Lai LYH, Nyberg F, Morales DR, Posada JD, Shah NH, Gong M, Vivekanantham A, Abend A, Minty EP, Suchard M, Rijnbeek P, Ryan PB, Prieto-Alhambra D.",
+    "authorAffiliations": "",
+    "journalTitle": "Rheumatology (Oxford, England)",
+    "pubYear": "2021",
+    "date": "2021-10-01",
+    "isOpenAccess": "Y",
+    "keywords": "Mortality; Hospitalization; Open Science; Autoimmune Condition; Observational Health Data Sciences And Informatics (Ohdsi); Observational Medical Outcomes Partnership (Omop); Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>Patients with autoimmune diseases were advised to shield to avoid coronavirus disease 2019 (COVID-19), but information on their prognosis is lacking. We characterized 30-day outcomes and mortality after hospitalization with COVID-19 among patients with prevalent autoimmune diseases, and compared outcomes after hospital admissions among similar patients with seasonal influenza.<h4>Methods</h4>A multinational network cohort study was conducted using electronic health records data from Columbia University Irving Medical Center [USA, Optum (USA), Department of Veterans Affairs (USA), Information System for Research in Primary Care-Hospitalization Linked Data (Spain) and claims data from IQVIA Open Claims (USA) and Health Insurance and Review Assessment (South Korea). All patients with prevalent autoimmune diseases, diagnosed and/or hospitalized between January and June 2020 with COVID-19, and similar patients hospitalized with influenza in 2017-18 were included. Outcomes were death and complications within 30\u2009days of hospitalization.<h4>Results</h4>We studied 133\u2009589 patients diagnosed and 48\u2009418 hospitalized with COVID-19 with prevalent autoimmune diseases. Most patients were female, aged \u226550\u2009years with previous comorbidities. The prevalence of hypertension (45.5-93.2%), chronic kidney disease (14.0-52.7%) and heart disease (29.0-83.8%) was higher in hospitalized vs diagnosed patients with COVID-19. Compared with 70\u2009660 hospitalized with influenza, those admitted with COVID-19 had more respiratory complications including pneumonia and acute respiratory distress syndrome, and higher 30-day mortality (2.2-4.3% vs 6.32-24.6%).<h4>Conclusion</h4>Compared with influenza, COVID-19 is a more severe disease, leading to more complications and higher mortality.",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/rheumatology/article-pdf/60/SI/SI37/40544680/keab250.pdf; doi:https://doi.org/10.1093/rheumatology/keab250; html:https://europepmc.org/articles/PMC7989171; pdf:https://europepmc.org/articles/PMC7989171?pdf=render"
+  },
   {
     "id": "33664499",
     "doi": "https://doi.org/10.1038/s41431-021-00835-8",
@@ -38845,21 +38896,21 @@
     "urls": "doi:https://doi.org/10.1128/jcm.00670-20; doi:https://doi.org/10.1128/JCM.00670-20; html:https://europepmc.org/articles/PMC7512152; pdf:https://europepmc.org/articles/PMC7512152?pdf=render"
   },
   {
-    "id": "33725121",
-    "doi": "https://doi.org/10.1093/rheumatology/keab250",
-    "title": "COVID-19 in patients with autoimmune diseases: characteristics and outcomes in a multinational network of cohorts across three countries.",
-    "authorString": "Tan EH, Sena AG, Prats-Uribe A, You SC, Ahmed WU, Kostka K, Reich C, Duvall SL, Lynch KE, Matheny ME, Duarte-Salles T, Bertolin SF, Hripcsak G, Natarajan K, Falconer T, Spotnitz M, Ostropolets A, Blacketer C, Alshammari TM, Alghoul H, Alser O, Lane JCE, Dawoud DM, Shah K, Yang Y, Zhang L, Areia C, Golozar A, Recalde M, Casajust P, Jonnagaddala J, Subbian V, Vizcaya D, Lai LYH, Nyberg F, Morales DR, Posada JD, Shah NH, Gong M, Vivekanantham A, Abend A, Minty EP, Suchard M, Rijnbeek P, Ryan PB, Prieto-Alhambra D.",
+    "id": "31782492",
+    "doi": "https://doi.org/10.1093/ajcn/nqz293",
+    "title": "The association of fish consumption and its urinary metabolites with cardiovascular risk factors: the International Study of Macro-/Micronutrients and Blood Pressure (INTERMAP).",
+    "authorString": "Gibson R, Lau CE, Loo RL, Ebbels TMD, Chekmeneva E, Dyer AR, Miura K, Ueshima H, Zhao L, Daviglus ML, Stamler J, Van Horn L, Elliott P, Holmes E, Chan Q.",
     "authorAffiliations": "",
-    "journalTitle": "Rheumatology (Oxford, England)",
-    "pubYear": "2021",
-    "date": "2021-10-01",
+    "journalTitle": "The American journal of clinical nutrition",
+    "pubYear": "2020",
+    "date": "2020-02-01",
     "isOpenAccess": "Y",
-    "keywords": "Mortality; Hospitalization; Open Science; Autoimmune Condition; Observational Health Data Sciences And Informatics (Ohdsi); Observational Medical Outcomes Partnership (Omop); Covid-19",
-    "nationalPriorities": "",
+    "keywords": "Hypertension; Blood pressure; FISH; Shellfish; Biomarkers; body mass index; Seafood; Metabonomics; Homarine; Intermap Metabolomics",
+    "nationalPriorities": "Improving Public Health",
     "healthCategories": "",
-    "abstract": "<h4>Objective</h4>Patients with autoimmune diseases were advised to shield to avoid coronavirus disease 2019 (COVID-19), but information on their prognosis is lacking. We characterized 30-day outcomes and mortality after hospitalization with COVID-19 among patients with prevalent autoimmune diseases, and compared outcomes after hospital admissions among similar patients with seasonal influenza.<h4>Methods</h4>A multinational network cohort study was conducted using electronic health records data from Columbia University Irving Medical Center [USA, Optum (USA), Department of Veterans Affairs (USA), Information System for Research in Primary Care-Hospitalization Linked Data (Spain) and claims data from IQVIA Open Claims (USA) and Health Insurance and Review Assessment (South Korea). All patients with prevalent autoimmune diseases, diagnosed and/or hospitalized between January and June 2020 with COVID-19, and similar patients hospitalized with influenza in 2017-18 were included. Outcomes were death and complications within 30\u2009days of hospitalization.<h4>Results</h4>We studied 133\u2009589 patients diagnosed and 48\u2009418 hospitalized with COVID-19 with prevalent autoimmune diseases. Most patients were female, aged \u226550\u2009years with previous comorbidities. The prevalence of hypertension (45.5-93.2%), chronic kidney disease (14.0-52.7%) and heart disease (29.0-83.8%) was higher in hospitalized vs diagnosed patients with COVID-19. Compared with 70\u2009660 hospitalized with influenza, those admitted with COVID-19 had more respiratory complications including pneumonia and acute respiratory distress syndrome, and higher 30-day mortality (2.2-4.3% vs 6.32-24.6%).<h4>Conclusion</h4>Compared with influenza, COVID-19 is a more severe disease, leading to more complications and higher mortality.",
-    "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/rheumatology/article-pdf/60/SI/SI37/40544680/keab250.pdf; doi:https://doi.org/10.1093/rheumatology/keab250; html:https://europepmc.org/articles/PMC7989171; pdf:https://europepmc.org/articles/PMC7989171?pdf=render"
+    "abstract": "<h4>Background</h4>Results from observational studies regarding associations between fish (including shellfish) intake and cardiovascular disease risk factors, including blood pressure (BP) and BMI, are inconsistent.<h4>Objective</h4>To investigate associations of fish consumption and associated urinary metabolites with BP and BMI in free-living populations.<h4>Methods</h4>We used cross-sectional data from the International Study of Macro-/Micronutrients and Blood Pressure (INTERMAP), including 4680 men and women (40-59 y) from Japan, China, the United Kingdom, and United States. Dietary intakes were assessed by four 24-h dietary recalls and BP from 8 measurements. Urinary metabolites (2 timed 24-h urinary samples) associated with fish intake acquired from NMR spectroscopy were identified. Linear models were used to estimate BP and BMI differences across categories of intake and per 2 SD higher intake of fish and its biomarkers.<h4>Results</h4>No significant associations were observed between fish intake and BP. There was a direct association with fish intake and BMI in the Japanese population sample (P trend\u00a0=\u00a00.03; fully adjusted model). In Japan, trimethylamine-N-oxide (TMAO) and taurine, respectively, demonstrated area under the receiver operating characteristic curve (AUC) values of 0.81 and 0.78 in discriminating high against low fish intake, whereas homarine (a metabolite found in shellfish muscle) demonstrated an AUC of 0.80 for high/nonshellfish intake. Direct associations were observed between urinary TMAO and BMI for all regions except Japan (P\u00a0<\u00a00.0001) and in Western populations between TMAO and BP (diastolic blood pressure: mean difference 1.28; 95% CI: 0.55, 2.02 mmHg; P\u00a0=\u00a00.0006, systolic blood pressure: mean difference 1.67; 95% CI: 0.60, 2.73 mmHg; P\u00a0=\u00a00.002).<h4>Conclusions</h4>Urinary TMAO showed a stronger association with fish intake in the Japanese compared with the Western population sample. Urinary TMAO was directly associated with BP in the Western but not the Japanese population sample. Associations between fish intake and its biomarkers and downstream associations with BP/BMI appear to be context specific. INTERMAP is registered at www.clinicaltrials.gov as NCT00005271.",
+    "laySummary": "Gibson et al.\u2019s study investigates whether having fish in diet will have an effect on urinary metabolism. They\u2019ve assessed dietary and BP measurement across Asian and Westerns and shown that the relationship was stronger in Japanese population compared to Western population and is highly context dependant. ",
+    "urls": "doi:https://doi.org/10.1093/ajcn/nqz293; doi:https://doi.org/10.1093/ajcn/nqz293; html:https://europepmc.org/articles/PMC6997096; pdf:https://europepmc.org/articles/PMC6997096?pdf=render"
   },
   {
     "id": "34653419",
@@ -38896,21 +38947,21 @@
     "urls": "pdf:http://www.thelancet.com/article/S2666756821002828/pdf; doi:https://doi.org/10.1016/S2666-7568(21)00282-8; html:https://europepmc.org/articles/PMC8676418"
   },
   {
-    "id": "31782492",
-    "doi": "https://doi.org/10.1093/ajcn/nqz293",
-    "title": "The association of fish consumption and its urinary metabolites with cardiovascular risk factors: the International Study of Macro-/Micronutrients and Blood Pressure (INTERMAP).",
-    "authorString": "Gibson R, Lau CE, Loo RL, Ebbels TMD, Chekmeneva E, Dyer AR, Miura K, Ueshima H, Zhao L, Daviglus ML, Stamler J, Van Horn L, Elliott P, Holmes E, Chan Q.",
+    "id": "36208161",
+    "doi": "https://doi.org/10.1093/eurheartj/ehac426",
+    "title": "CODE-EHR best practice framework for the use of structured electronic healthcare records in clinical research.",
+    "authorString": "Kotecha D, Asselbergs FW, Achenbach S, Anker SD, Atar D, Baigent C, Banerjee A, Beger B, Brobert G, Casadei B, Ceccarelli C, Cowie MR, Crea F, Cronin M, Denaxas S, Derix A, Fitzsimons D, Fredriksson M, Gale CP, Gkoutos GV, Goettsch W, Hemingway H, Ingvar M, Jonas A, Kazmierski R, L\u00f8gstrup S, Thomas Lumbers R, L\u00fcscher TF, McGreavy P, Pi\u00f1a IL, Roessig L, Steinbeisser C, Sundgren M, Tyl B, van Thiel G, van Bochove K, Vardas PE, Villanueva T, Vrana M, Weber W, Weidinger F, Windecker S, Wood A, Grobbee DE, Innovative Medicines Initiative BigData@Heart Consortium, European Society of Cardiology, CODE-EHR international consensus group.",
     "authorAffiliations": "",
-    "journalTitle": "The American journal of clinical nutrition",
-    "pubYear": "2020",
-    "date": "2020-02-01",
+    "journalTitle": "European heart journal",
+    "pubYear": "2022",
+    "date": "2022-10-01",
     "isOpenAccess": "Y",
-    "keywords": "Hypertension; Blood pressure; FISH; Shellfish; Biomarkers; body mass index; Seafood; Metabonomics; Homarine; Intermap Metabolomics",
-    "nationalPriorities": "Improving Public Health",
+    "keywords": "",
+    "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Results from observational studies regarding associations between fish (including shellfish) intake and cardiovascular disease risk factors, including blood pressure (BP) and BMI, are inconsistent.<h4>Objective</h4>To investigate associations of fish consumption and associated urinary metabolites with BP and BMI in free-living populations.<h4>Methods</h4>We used cross-sectional data from the International Study of Macro-/Micronutrients and Blood Pressure (INTERMAP), including 4680 men and women (40-59 y) from Japan, China, the United Kingdom, and United States. Dietary intakes were assessed by four 24-h dietary recalls and BP from 8 measurements. Urinary metabolites (2 timed 24-h urinary samples) associated with fish intake acquired from NMR spectroscopy were identified. Linear models were used to estimate BP and BMI differences across categories of intake and per 2 SD higher intake of fish and its biomarkers.<h4>Results</h4>No significant associations were observed between fish intake and BP. There was a direct association with fish intake and BMI in the Japanese population sample (P trend\u00a0=\u00a00.03; fully adjusted model). In Japan, trimethylamine-N-oxide (TMAO) and taurine, respectively, demonstrated area under the receiver operating characteristic curve (AUC) values of 0.81 and 0.78 in discriminating high against low fish intake, whereas homarine (a metabolite found in shellfish muscle) demonstrated an AUC of 0.80 for high/nonshellfish intake. Direct associations were observed between urinary TMAO and BMI for all regions except Japan (P\u00a0<\u00a00.0001) and in Western populations between TMAO and BP (diastolic blood pressure: mean difference 1.28; 95% CI: 0.55, 2.02 mmHg; P\u00a0=\u00a00.0006, systolic blood pressure: mean difference 1.67; 95% CI: 0.60, 2.73 mmHg; P\u00a0=\u00a00.002).<h4>Conclusions</h4>Urinary TMAO showed a stronger association with fish intake in the Japanese compared with the Western population sample. Urinary TMAO was directly associated with BP in the Western but not the Japanese population sample. Associations between fish intake and its biomarkers and downstream associations with BP/BMI appear to be context specific. INTERMAP is registered at www.clinicaltrials.gov as NCT00005271.",
-    "laySummary": "Gibson et al.\u2019s study investigates whether having fish in diet will have an effect on urinary metabolism. They\u2019ve assessed dietary and BP measurement across Asian and Westerns and shown that the relationship was stronger in Japanese population compared to Western population and is highly context dependant. ",
-    "urls": "doi:https://doi.org/10.1093/ajcn/nqz293; doi:https://doi.org/10.1093/ajcn/nqz293; html:https://europepmc.org/articles/PMC6997096; pdf:https://europepmc.org/articles/PMC6997096?pdf=render"
+    "abstract": "Big data is central to new developments in global clinical science aiming to improve the lives of patients. Technological advances have led to the routine use of structured electronic healthcare records with the potential to address key gaps in clinical evidence. The covid-19 pandemic has demonstrated the potential of big data and related analytics, but also important pitfalls. Verification, validation, and data privacy, as well as the social mandate to undertake research are key challenges. The European Society of Cardiology and the BigData@Heart consortium have brought together a range of international stakeholders, including patient representatives, clinicians, scientists, regulators, journal editors and industry. We propose the CODE-EHR Minimum Standards Framework as a means to improve the design of studies, enhance transparency and develop a roadmap towards more robust and effective utilisation of healthcare data for research purposes.",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/eurheartj/article-pdf/43/37/3578/46535456/ehac426.pdf; doi:https://doi.org/10.1093/eurheartj/ehac426; html:https://europepmc.org/articles/PMC9452067; pdf:https://europepmc.org/articles/PMC9452067?pdf=render"
   },
   {
     "id": "35710247",
@@ -38929,23 +38980,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/6/e060280.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-060280; html:https://europepmc.org/articles/PMC9207897; pdf:https://europepmc.org/articles/PMC9207897?pdf=render"
   },
-  {
-    "id": "36208161",
-    "doi": "https://doi.org/10.1093/eurheartj/ehac426",
-    "title": "CODE-EHR best practice framework for the use of structured electronic healthcare records in clinical research.",
-    "authorString": "Kotecha D, Asselbergs FW, Achenbach S, Anker SD, Atar D, Baigent C, Banerjee A, Beger B, Brobert G, Casadei B, Ceccarelli C, Cowie MR, Crea F, Cronin M, Denaxas S, Derix A, Fitzsimons D, Fredriksson M, Gale CP, Gkoutos GV, Goettsch W, Hemingway H, Ingvar M, Jonas A, Kazmierski R, L\u00f8gstrup S, Thomas Lumbers R, L\u00fcscher TF, McGreavy P, Pi\u00f1a IL, Roessig L, Steinbeisser C, Sundgren M, Tyl B, van Thiel G, van Bochove K, Vardas PE, Villanueva T, Vrana M, Weber W, Weidinger F, Windecker S, Wood A, Grobbee DE, Innovative Medicines Initiative BigData@Heart Consortium, European Society of Cardiology, CODE-EHR international consensus group.",
-    "authorAffiliations": "",
-    "journalTitle": "European heart journal",
-    "pubYear": "2022",
-    "date": "2022-10-01",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Big data is central to new developments in global clinical science aiming to improve the lives of patients. Technological advances have led to the routine use of structured electronic healthcare records with the potential to address key gaps in clinical evidence. The covid-19 pandemic has demonstrated the potential of big data and related analytics, but also important pitfalls. Verification, validation, and data privacy, as well as the social mandate to undertake research are key challenges. The European Society of Cardiology and the BigData@Heart consortium have brought together a range of international stakeholders, including patient representatives, clinicians, scientists, regulators, journal editors and industry. We propose the CODE-EHR Minimum Standards Framework as a means to improve the design of studies, enhance transparency and develop a roadmap towards more robust and effective utilisation of healthcare data for research purposes.",
-    "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/eurheartj/article-pdf/43/37/3578/46535456/ehac426.pdf; doi:https://doi.org/10.1093/eurheartj/ehac426; html:https://europepmc.org/articles/PMC9452067; pdf:https://europepmc.org/articles/PMC9452067?pdf=render"
-  },
   {
     "id": "36539756",
     "doi": "https://doi.org/10.1186/s12888-022-04429-6",
@@ -38963,6 +38997,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmcpsychiatry.biomedcentral.com/counter/pdf/10.1186/s12888-022-04429-6; doi:https://doi.org/10.1186/s12888-022-04429-6; html:https://europepmc.org/articles/PMC9764531; pdf:https://europepmc.org/articles/PMC9764531?pdf=render"
   },
+  {
+    "id": "35498042",
+    "doi": "https://doi.org/10.3389/fcvm.2022.768972",
+    "title": "Unravelling the Difference Between Men and Women in Post-CABG Survival.",
+    "authorString": "Schmidt AF, Haitjema S, Sartipy U, Holzmann MJ, Malenka DJ, Ross CS, van Gilst W, Rouleau JL, Meeder AM, Baker RA, Shiomi H, Kimura T, Tran L, Smith JA, Reid CM, Asselbergs FW, den Ruijter HM.",
+    "authorAffiliations": "",
+    "journalTitle": "Frontiers in cardiovascular medicine",
+    "pubYear": "2022",
+    "date": "2022-04-13",
+    "isOpenAccess": "Y",
+    "keywords": "Atherosclerosis; Sex; Gender; Prognosis; Cabg; Outcome",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objectives</h4>Women have a worse prognosis after coronary artery bypass grafting (CABG) surgery compared to men. We sought to quantify to what extent this difference in post-CABG survival could be attributed to sex itself, or whether this was mediated by difference between men and women at the time of intervention. Additionally, we explored to what extent these effects were homogenous across patient subgroups.<h4>Methods</h4>Time to all-cause mortality was available for 102,263 CABG patients, including 20,988 (21%) women, sourced through an individual participant data meta-analysis of five cohort studies. Difference between men and women in survival duration was assessed using Kaplan-Meier estimates, and Cox's proportional hazards model.<h4>Results</h4>During a median follow-up of 5 years, 13,598 (13%) patients died, with women more likely to die than men: female HR 1.20 (95%CI 1.16; 1.25). We found that differences in patient characteristics at the time of CABG procedure mediated this sex effect, and accounting for these resulted in a neutral female HR 0.98 (95%CI 0.94; 1.02). Next we performed <i>a priori</i> defined subgroup analyses of the five most prominent mediators: age, creatinine, peripheral vascular disease, type 2 diabetes, and heart failure. We found that women without peripheral vascular disease (PVD) or women aged 70+, survived longer than men (interaction <i>p</i>-values 0.04 and 6 \u00d7 10<sup>-5</sup>, respectively), with an effect reversal in younger women.<h4>Conclusion</h4>Sex differences in post-CABG survival were readily explained by difference in patient characteristics and comorbidities. Pre-planned analyses revealed patient subgroups (aged 70+, or without PVD) of women that survived longer than men, and a subgroup of younger women with comparatively poorer survival.",
+    "laySummary": "",
+    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2022.768972/pdf; doi:https://doi.org/10.3389/fcvm.2022.768972; html:https://europepmc.org/articles/PMC9043514; pdf:https://europepmc.org/articles/PMC9043514?pdf=render"
+  },
   {
     "id": "33528799",
     "doi": "https://doi.org/10.1007/s12471-021-01542-1",
@@ -38981,21 +39032,21 @@
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s12471-021-01542-1.pdf; doi:https://doi.org/10.1007/s12471-021-01542-1; html:https://europepmc.org/articles/PMC8160055; pdf:https://europepmc.org/articles/PMC8160055?pdf=render"
   },
   {
-    "id": "35498042",
-    "doi": "https://doi.org/10.3389/fcvm.2022.768972",
-    "title": "Unravelling the Difference Between Men and Women in Post-CABG Survival.",
-    "authorString": "Schmidt AF, Haitjema S, Sartipy U, Holzmann MJ, Malenka DJ, Ross CS, van Gilst W, Rouleau JL, Meeder AM, Baker RA, Shiomi H, Kimura T, Tran L, Smith JA, Reid CM, Asselbergs FW, den Ruijter HM.",
+    "id": "33532905",
+    "doi": "https://doi.org/10.1007/s12471-021-01539-w",
+    "title": "BIO FOr CARE: biomarkers of hypertrophic cardiomyopathy development and progression in carriers of Dutch founder truncating MYBPC3 variants-design and status.",
+    "authorString": "Jansen M, Christiaans I, van der Crabben SN, Michels M, Huurman R, Hoedemaekers YM, Dooijes D, Jongbloed JDH, Boven LG, Lekanne Deprez RH, Wilde AAM, Jans JJM, van der Velden J, de Boer RA, van Tintelen JP, Asselbergs FW, Baas AF.",
     "authorAffiliations": "",
-    "journalTitle": "Frontiers in cardiovascular medicine",
-    "pubYear": "2022",
-    "date": "2022-04-13",
+    "journalTitle": "Netherlands heart journal : monthly journal of the Netherlands Society of Cardiology and the Netherlands Heart Foundation",
+    "pubYear": "2021",
+    "date": "2021-02-02",
     "isOpenAccess": "Y",
-    "keywords": "Atherosclerosis; Sex; Gender; Prognosis; Cabg; Outcome",
+    "keywords": "Prognosis; Biomarkers; hypertrophic cardiomyopathy; Mybpc3",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Objectives</h4>Women have a worse prognosis after coronary artery bypass grafting (CABG) surgery compared to men. We sought to quantify to what extent this difference in post-CABG survival could be attributed to sex itself, or whether this was mediated by difference between men and women at the time of intervention. Additionally, we explored to what extent these effects were homogenous across patient subgroups.<h4>Methods</h4>Time to all-cause mortality was available for 102,263 CABG patients, including 20,988 (21%) women, sourced through an individual participant data meta-analysis of five cohort studies. Difference between men and women in survival duration was assessed using Kaplan-Meier estimates, and Cox's proportional hazards model.<h4>Results</h4>During a median follow-up of 5 years, 13,598 (13%) patients died, with women more likely to die than men: female HR 1.20 (95%CI 1.16; 1.25). We found that differences in patient characteristics at the time of CABG procedure mediated this sex effect, and accounting for these resulted in a neutral female HR 0.98 (95%CI 0.94; 1.02). Next we performed <i>a priori</i> defined subgroup analyses of the five most prominent mediators: age, creatinine, peripheral vascular disease, type 2 diabetes, and heart failure. We found that women without peripheral vascular disease (PVD) or women aged 70+, survived longer than men (interaction <i>p</i>-values 0.04 and 6 \u00d7 10<sup>-5</sup>, respectively), with an effect reversal in younger women.<h4>Conclusion</h4>Sex differences in post-CABG survival were readily explained by difference in patient characteristics and comorbidities. Pre-planned analyses revealed patient subgroups (aged 70+, or without PVD) of women that survived longer than men, and a subgroup of younger women with comparatively poorer survival.",
+    "abstract": "<h4>Background</h4>Hypertrophic cardiomyopathy (HCM) is the most prevalent monogenic heart disease, commonly caused by truncating variants in the MYBPC3 gene. HCM is an important cause of sudden cardiac death; however, overall prognosis is good and penetrance in genotype-positive individuals is incomplete. The underlying mechanisms are poorly understood and risk stratification remains limited.<h4>Aim</h4>To create a\u00a0nationwide cohort of carriers of truncating MYBPC3 variants for identification of predictive biomarkers for HCM development and progression.<h4>Methods</h4>In the multicentre, observational BIO FOr CARe (Identification of BIOmarkers of hypertrophic cardiomyopathy development and progression in Dutch MYBPC3 FOunder variant CARriers) cohort, carriers of the c.2373dupG, c.2827C\u202f>\u202fT, c.2864_2865delCT and c.3776delA MYBPC3 variants are included and prospectively undergo longitudinal blood collection. Clinical data are collected from first presentation onwards. The primary outcome constitutes a\u00a0composite endpoint of HCM progression (maximum wall thickness \u2265\u202f20\u202fmm, septal reduction therapy, heart failure occurrence, sustained ventricular arrhythmia and sudden cardiac death).<h4>Results</h4>So far, 250 subjects (median age 54.9\u00a0years (interquartile range 43.3, 66.6), 54.8% male) have been included. HCM was diagnosed in 169 subjects and dilated cardiomyopathy in\u00a04. The primary outcome was met in 115 subjects. Blood samples were collected from 131 subjects.<h4>Conclusion</h4>BIO FOr CARe is a\u00a0genetically homogeneous, phenotypically heterogeneous cohort incorporating a\u00a0clinical data registry and longitudinal blood collection. This provides a\u00a0unique opportunity to study biomarkers for HCM development and prognosis. The established infrastructure can be extended to study other genetic variants. Other centres are invited to join our consortium.",
     "laySummary": "",
-    "urls": "pdf:https://www.frontiersin.org/articles/10.3389/fcvm.2022.768972/pdf; doi:https://doi.org/10.3389/fcvm.2022.768972; html:https://europepmc.org/articles/PMC9043514; pdf:https://europepmc.org/articles/PMC9043514?pdf=render"
+    "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s12471-021-01539-w.pdf; doi:https://doi.org/10.1007/s12471-021-01539-w; html:https://europepmc.org/articles/PMC8160056; pdf:https://europepmc.org/articles/PMC8160056?pdf=render"
   },
   {
     "id": "31950891",
@@ -39014,23 +39065,6 @@
     "laySummary": "This study uses data from a mental healthcare provider to predict 3 things: 1) extended duration of stay in a hospital, 2) the likelihood of needing to be admitted to hospital again after discharge, and 3) likehood of needing 'high intesity service' (high cost services). The authors developed a natural language processing model (a computer system than aims to interpret text and draw out useful information) to review the text, diagnoses, medications and the patient symptoms to work out which patients would fall within those 3 categories. They conclude that their model could be used to improve services through predicting users who will require the most intense and costly care.",
     "urls": "pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/6EF9FC74DC5A744C9D841DD649992ABE/S2056472419000966a.pdf/div-class-title-predicting-high-cost-care-in-a-mental-health-setting-div.pdf; doi:https://doi.org/10.1192/bjo.2019.96; html:https://europepmc.org/articles/PMC7001466; pdf:https://europepmc.org/articles/PMC7001466?pdf=render"
   },
-  {
-    "id": "33532905",
-    "doi": "https://doi.org/10.1007/s12471-021-01539-w",
-    "title": "BIO FOr CARE: biomarkers of hypertrophic cardiomyopathy development and progression in carriers of Dutch founder truncating MYBPC3 variants-design and status.",
-    "authorString": "Jansen M, Christiaans I, van der Crabben SN, Michels M, Huurman R, Hoedemaekers YM, Dooijes D, Jongbloed JDH, Boven LG, Lekanne Deprez RH, Wilde AAM, Jans JJM, van der Velden J, de Boer RA, van Tintelen JP, Asselbergs FW, Baas AF.",
-    "authorAffiliations": "",
-    "journalTitle": "Netherlands heart journal : monthly journal of the Netherlands Society of Cardiology and the Netherlands Heart Foundation",
-    "pubYear": "2021",
-    "date": "2021-02-02",
-    "isOpenAccess": "Y",
-    "keywords": "Prognosis; Biomarkers; hypertrophic cardiomyopathy; Mybpc3",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Hypertrophic cardiomyopathy (HCM) is the most prevalent monogenic heart disease, commonly caused by truncating variants in the MYBPC3 gene. HCM is an important cause of sudden cardiac death; however, overall prognosis is good and penetrance in genotype-positive individuals is incomplete. The underlying mechanisms are poorly understood and risk stratification remains limited.<h4>Aim</h4>To create a\u00a0nationwide cohort of carriers of truncating MYBPC3 variants for identification of predictive biomarkers for HCM development and progression.<h4>Methods</h4>In the multicentre, observational BIO FOr CARe (Identification of BIOmarkers of hypertrophic cardiomyopathy development and progression in Dutch MYBPC3 FOunder variant CARriers) cohort, carriers of the c.2373dupG, c.2827C\u202f>\u202fT, c.2864_2865delCT and c.3776delA MYBPC3 variants are included and prospectively undergo longitudinal blood collection. Clinical data are collected from first presentation onwards. The primary outcome constitutes a\u00a0composite endpoint of HCM progression (maximum wall thickness \u2265\u202f20\u202fmm, septal reduction therapy, heart failure occurrence, sustained ventricular arrhythmia and sudden cardiac death).<h4>Results</h4>So far, 250 subjects (median age 54.9\u00a0years (interquartile range 43.3, 66.6), 54.8% male) have been included. HCM was diagnosed in 169 subjects and dilated cardiomyopathy in\u00a04. The primary outcome was met in 115 subjects. Blood samples were collected from 131 subjects.<h4>Conclusion</h4>BIO FOr CARe is a\u00a0genetically homogeneous, phenotypically heterogeneous cohort incorporating a\u00a0clinical data registry and longitudinal blood collection. This provides a\u00a0unique opportunity to study biomarkers for HCM development and prognosis. The established infrastructure can be extended to study other genetic variants. Other centres are invited to join our consortium.",
-    "laySummary": "",
-    "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s12471-021-01539-w.pdf; doi:https://doi.org/10.1007/s12471-021-01539-w; html:https://europepmc.org/articles/PMC8160056; pdf:https://europepmc.org/articles/PMC8160056?pdf=render"
-  },
   {
     "id": "30984759",
     "doi": "https://doi.org/10.3389/fmed.2019.00048",
@@ -39303,23 +39337,6 @@
     "laySummary": "",
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s00127-022-02257-3.pdf; doi:https://doi.org/10.1007/s00127-022-02257-3; html:https://europepmc.org/articles/PMC9246775; pdf:https://europepmc.org/articles/PMC9246775?pdf=render"
   },
-  {
-    "id": "34442458",
-    "doi": "https://doi.org/10.3390/jpm11080814",
-    "title": "Reduced MIP-1\u03b2 as a Trait Marker and Reduced IL-7 and IL-12 as State Markers of Anorexia Nervosa.",
-    "authorString": "Keeler JL, Patsalos O, Chung R, Schmidt U, Breen G, Treasure J, Himmerich H, Dalton B.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of personalized medicine",
-    "pubYear": "2021",
-    "date": "2021-08-20",
-    "isOpenAccess": "Y",
-    "keywords": "Cytokines; Chemokines; Brain-derived neurotrophic factor; Anorexia Nervosa; cross-sectional; Inflammatory Markers",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Alterations in certain inflammatory markers have been found in individuals with anorexia nervosa (AN). However, their relation to clinical characteristics has not been extensively explored, nor is it clear whether they are trait or state features of the disorder. This cross-sectional study measured serum concentrations of 36 inflammatory markers in people with acute AN (<i>n</i> = 56), recovered AN (rec-AN; <i>n</i> = 24) and healthy controls (HC; <i>n</i> = 51). The relationship between body mass index (BMI), eating disorder psychopathology, depression symptoms and inflammatory markers was assessed. Statistical models controlled for variables known to influence cytokine concentrations (i.e., age, ethnicity, smoking status and medication usage). Overall, most inflammatory markers including pro-inflammatory cytokines were unchanged in AN and rec-AN. However, in AN and rec-AN, concentrations of macrophage inflammatory protein (MIP)-1\u03b2 were lower than HCs. Interleukin (IL)-7 and IL-12/IL-23p40 were reduced in AN, and concentrations of macrophage-derived chemokine, MIP-1\u03b1 and tumor necrosis factor-\u03b1 were reduced in rec-AN compared to HC. In conclusion, a reduction in MIP-1\u03b2 may be a trait marker of the illness, whereas reductions in IL-7 and IL-12/IL-23p40 may be state markers. The absence of increased pro-inflammatory cytokines in AN is contradictory to the wider literature, although the inclusion of covariates may explain our differing findings.",
-    "laySummary": "",
-    "urls": "pdf:https://www.mdpi.com/2075-4426/11/8/814/pdf?version=1629458822; doi:https://doi.org/10.3390/jpm11080814; html:https://europepmc.org/articles/PMC8399452; pdf:https://europepmc.org/articles/PMC8399452?pdf=render"
-  },
   {
     "id": "32891970",
     "doi": "https://doi.org/10.1016/j.chiabu.2020.104689",
@@ -39337,6 +39354,23 @@
     "laySummary": "",
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7613165; doi:https://doi.org/10.1016/j.chiabu.2020.104689; html:https://europepmc.org/articles/PMC7613165; pdf:https://europepmc.org/articles/PMC7613165?pdf=render; doi:https://doi.org/10.1016/j.chiabu.2020.104689"
   },
+  {
+    "id": "34442458",
+    "doi": "https://doi.org/10.3390/jpm11080814",
+    "title": "Reduced MIP-1\u03b2 as a Trait Marker and Reduced IL-7 and IL-12 as State Markers of Anorexia Nervosa.",
+    "authorString": "Keeler JL, Patsalos O, Chung R, Schmidt U, Breen G, Treasure J, Himmerich H, Dalton B.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of personalized medicine",
+    "pubYear": "2021",
+    "date": "2021-08-20",
+    "isOpenAccess": "Y",
+    "keywords": "Cytokines; Chemokines; Brain-derived neurotrophic factor; Anorexia Nervosa; cross-sectional; Inflammatory Markers",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Alterations in certain inflammatory markers have been found in individuals with anorexia nervosa (AN). However, their relation to clinical characteristics has not been extensively explored, nor is it clear whether they are trait or state features of the disorder. This cross-sectional study measured serum concentrations of 36 inflammatory markers in people with acute AN (<i>n</i> = 56), recovered AN (rec-AN; <i>n</i> = 24) and healthy controls (HC; <i>n</i> = 51). The relationship between body mass index (BMI), eating disorder psychopathology, depression symptoms and inflammatory markers was assessed. Statistical models controlled for variables known to influence cytokine concentrations (i.e., age, ethnicity, smoking status and medication usage). Overall, most inflammatory markers including pro-inflammatory cytokines were unchanged in AN and rec-AN. However, in AN and rec-AN, concentrations of macrophage inflammatory protein (MIP)-1\u03b2 were lower than HCs. Interleukin (IL)-7 and IL-12/IL-23p40 were reduced in AN, and concentrations of macrophage-derived chemokine, MIP-1\u03b1 and tumor necrosis factor-\u03b1 were reduced in rec-AN compared to HC. In conclusion, a reduction in MIP-1\u03b2 may be a trait marker of the illness, whereas reductions in IL-7 and IL-12/IL-23p40 may be state markers. The absence of increased pro-inflammatory cytokines in AN is contradictory to the wider literature, although the inclusion of covariates may explain our differing findings.",
+    "laySummary": "",
+    "urls": "pdf:https://www.mdpi.com/2075-4426/11/8/814/pdf?version=1629458822; doi:https://doi.org/10.3390/jpm11080814; html:https://europepmc.org/articles/PMC8399452; pdf:https://europepmc.org/articles/PMC8399452?pdf=render"
+  },
   {
     "id": "34167318",
     "doi": "https://doi.org/10.1161/circulationaha.121.054302",
@@ -39371,23 +39405,6 @@
     "laySummary": "Kaura et al. used a large database of about a quarter of a million patients who had toponin measurements and concluded that there was an association between positive troponin results and mortality regardless of age ",
     "urls": "pdf:https://www.bmj.com/content/bmj/367/bmj.l6055.full.pdf; doi:https://doi.org/10.1136/bmj.l6055; html:https://europepmc.org/articles/PMC6865859"
   },
-  {
-    "id": "33628949",
-    "doi": "https://doi.org/10.12688/wellcomeopenres.16020.2",
-    "title": "The Avon Longitudinal Study of Parents and Children - A resource for COVID-19 research: Questionnaire data capture April-May 2020.",
-    "authorString": "Northstone K, Howarth S, Smith D, Bowring C, Wells N, Timpson NJ.",
-    "authorAffiliations": "",
-    "journalTitle": "Wellcome open research",
-    "pubYear": "2020",
-    "date": "2020-11-20",
-    "isOpenAccess": "Y",
-    "keywords": "Coronavirus; Mental health; Alspac; Birth Cohort Study; Online Questionnaire; Children Of The 90S; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The Avon Longitudinal Study of Parents and Children (ALSPAC) is a prospective population-based cohort study which recruited pregnant women in 1990-1992. The resource provides an informative and efficient setting for collecting data on the current coronavirus 2019 (COVID-19) pandemic. In early March 2020, a questionnaire was developed in collaboration with other longitudinal population studies to ensure cross-cohort comparability. It targeted retrospective and current COVID-19 infection information (exposure assessment, symptom tracking and reported clinical outcomes) and the impact of both disease and mitigating measures implemented to manage the COVID-19 crisis more broadly. Data were collected on symptoms of COVID-19 and seasonal flu, travel prior to the pandemic, mental health and social, behavioural and lifestyle factors. The online questionnaire was deployed across parent (G0) and offspring (G1) generations between 9 <sup>th</sup> April and 15 <sup>th</sup> May 2020. 6807 participants completed the questionnaire (2706 original mothers, 1014 original fathers/partners, 2973 offspring (mean age ~28 years) and 114 offspring partners). Eight (0.01%) participants (4 G0 and 4 G1) reported a positive test for COVID-19, 77 (1.13%; 28 G0 and 49 G1) reported that they had been told by a doctor they likely had COVID-19 and 865 (12.7%; 426 G0 and 439 G1) suspected that they have had COVID-19.\u00a0 Using algorithmically defined cases, we estimate that the predicted proportion of COVID-19 cases ranged from 1.03% - 4.19% depending on timing during the period of reporting (October 2019-March 2020). Data from this first questionnaire will be complemented with at least two more follow-up questionnaires, linkage to health records and results of biological testing as they become available. Data has been released as: 1) a standard dataset containing <i>all</i> participant responses with key sociodemographic factors and 2) as a composite release coordinating data from the existing resource, thus enabling bespoke research across all areas supported by the study.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.12688/wellcomeopenres.16020.2; html:https://europepmc.org/articles/PMC7883314; pdf:https://europepmc.org/articles/PMC7883314?pdf=render"
-  },
   {
     "id": "35477539",
     "doi": "https://doi.org/10.1136/gutjnl-2021-326183",
@@ -39405,6 +39422,23 @@
     "laySummary": "",
     "urls": "pdf:https://gut.bmj.com/content/gutjnl/early/2022/04/10/gutjnl-2021-326183.full.pdf; doi:https://doi.org/10.1136/gutjnl-2021-326183; html:https://europepmc.org/articles/PMC9664095; pdf:https://europepmc.org/articles/PMC9664095?pdf=render"
   },
+  {
+    "id": "33628949",
+    "doi": "https://doi.org/10.12688/wellcomeopenres.16020.2",
+    "title": "The Avon Longitudinal Study of Parents and Children - A resource for COVID-19 research: Questionnaire data capture April-May 2020.",
+    "authorString": "Northstone K, Howarth S, Smith D, Bowring C, Wells N, Timpson NJ.",
+    "authorAffiliations": "",
+    "journalTitle": "Wellcome open research",
+    "pubYear": "2020",
+    "date": "2020-11-20",
+    "isOpenAccess": "Y",
+    "keywords": "Coronavirus; Mental health; Alspac; Birth Cohort Study; Online Questionnaire; Children Of The 90S; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The Avon Longitudinal Study of Parents and Children (ALSPAC) is a prospective population-based cohort study which recruited pregnant women in 1990-1992. The resource provides an informative and efficient setting for collecting data on the current coronavirus 2019 (COVID-19) pandemic. In early March 2020, a questionnaire was developed in collaboration with other longitudinal population studies to ensure cross-cohort comparability. It targeted retrospective and current COVID-19 infection information (exposure assessment, symptom tracking and reported clinical outcomes) and the impact of both disease and mitigating measures implemented to manage the COVID-19 crisis more broadly. Data were collected on symptoms of COVID-19 and seasonal flu, travel prior to the pandemic, mental health and social, behavioural and lifestyle factors. The online questionnaire was deployed across parent (G0) and offspring (G1) generations between 9 <sup>th</sup> April and 15 <sup>th</sup> May 2020. 6807 participants completed the questionnaire (2706 original mothers, 1014 original fathers/partners, 2973 offspring (mean age ~28 years) and 114 offspring partners). Eight (0.01%) participants (4 G0 and 4 G1) reported a positive test for COVID-19, 77 (1.13%; 28 G0 and 49 G1) reported that they had been told by a doctor they likely had COVID-19 and 865 (12.7%; 426 G0 and 439 G1) suspected that they have had COVID-19.\u00a0 Using algorithmically defined cases, we estimate that the predicted proportion of COVID-19 cases ranged from 1.03% - 4.19% depending on timing during the period of reporting (October 2019-March 2020). Data from this first questionnaire will be complemented with at least two more follow-up questionnaires, linkage to health records and results of biological testing as they become available. Data has been released as: 1) a standard dataset containing <i>all</i> participant responses with key sociodemographic factors and 2) as a composite release coordinating data from the existing resource, thus enabling bespoke research across all areas supported by the study.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.12688/wellcomeopenres.16020.2; html:https://europepmc.org/articles/PMC7883314; pdf:https://europepmc.org/articles/PMC7883314?pdf=render"
+  },
   {
     "id": "33627748",
     "doi": "https://doi.org/10.1038/s41746-021-00406-7",
@@ -39643,23 +39677,6 @@
     "laySummary": "",
     "urls": "html:http://hdl.handle.net/10044/1/85586; doi:https://doi.org/10.1038/s41591-020-0941-1"
   },
-  {
-    "id": "30981377",
-    "doi": "https://doi.org/10.1016/j.aap.2019.03.007",
-    "title": "How much space do drivers provide when passing cyclists? Understanding the impact of motor vehicle and infrastructure characteristics on passing distance.",
-    "authorString": "Beck B, Chong D, Olivier J, Perkins M, Tsay A, Rushford A, Li L, Cameron P, Fry R, Johnson M.",
-    "authorAffiliations": "",
-    "journalTitle": "Accident; analysis and prevention",
-    "pubYear": "2019",
-    "date": "2019-04-10",
-    "isOpenAccess": "N",
-    "keywords": "Road Infrastructure; Overtaking; Cyclist Safety; Passing Distance",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Understanding factors that influence the distance that drivers provide when passing cyclists is critical to reducing subjective risk and improving cycling participation. This study aimed to quantify passing distance and assess the impact of motor vehicle and road infrastructure characteristics on passing distance.<h4>Methods</h4>An on-road observational study was conducted in Victoria, Australia. Participants had a custom device installed on their bicycle and rode as per their usual cycling for one to two weeks. A hierarchical linear model was used to investigate the relationship between motor vehicle and infrastructure characteristics (location, presence of on-road marked bicycle lane and the presence of parked cars on the kerbside) and passing distance (defined as the lateral distance between the end of the bicycle handlebars and the passing motor vehicle).<h4>Results</h4>Sixty cyclists recorded 18,527 passing events over 422 trips. The median passing distance was 173\u2009cm (Q1: 137\u2009cm, Q3: 224\u2009cm) and 1085 (5.9%) passing events were less than 100\u2009cm. Relative to sedans, 4WDs had a reduced mean passing distance of 15\u2009cm (Q1: 12\u2009cm, Q3: 17\u2009cm) and buses had a reduced mean passing distance of 28\u2009cm (Q1: 16\u2009cm, Q3: 40\u2009cm). Relative to passing events that occurred on roads without a marked bicycle lane and without parked cars, passing events on roads with a bike lane with no parked cars had a reduced mean passing distance of 27\u2009cm (Q1: 25\u2009cm, Q3: 29\u2009cm), and passing events on roads with a bike lane and parked cars had a mean lower passing distance of 40\u2009cm (Q1: 37\u2009cm, Q3: 43\u2009cm).<h4>Conclusions</h4>One in every 17 passing events was a close (<100\u2009cm) passing event. We identified that on-road bicycle lanes and parked cars reduced passing distance. These data can be used to inform the selection and design of cycling-related infrastructure and road use with the aim of improving safety for cyclists.",
-    "laySummary": "",
-    "urls": "pdf:https://cronfa.swan.ac.uk/Record/cronfa50030/Download/0050030-20052019102229.pdf; doi:https://doi.org/10.1016/j.aap.2019.03.007"
-  },
   {
     "id": "35353173",
     "doi": "https://doi.org/10.1001/jamapsychiatry.2022.0407",
@@ -39677,6 +39694,23 @@
     "laySummary": "",
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8968718; doi:https://doi.org/10.1001/jamapsychiatry.2022.0407; html:https://europepmc.org/articles/PMC8968718"
   },
+  {
+    "id": "30981377",
+    "doi": "https://doi.org/10.1016/j.aap.2019.03.007",
+    "title": "How much space do drivers provide when passing cyclists? Understanding the impact of motor vehicle and infrastructure characteristics on passing distance.",
+    "authorString": "Beck B, Chong D, Olivier J, Perkins M, Tsay A, Rushford A, Li L, Cameron P, Fry R, Johnson M.",
+    "authorAffiliations": "",
+    "journalTitle": "Accident; analysis and prevention",
+    "pubYear": "2019",
+    "date": "2019-04-10",
+    "isOpenAccess": "N",
+    "keywords": "Road Infrastructure; Overtaking; Cyclist Safety; Passing Distance",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Understanding factors that influence the distance that drivers provide when passing cyclists is critical to reducing subjective risk and improving cycling participation. This study aimed to quantify passing distance and assess the impact of motor vehicle and road infrastructure characteristics on passing distance.<h4>Methods</h4>An on-road observational study was conducted in Victoria, Australia. Participants had a custom device installed on their bicycle and rode as per their usual cycling for one to two weeks. A hierarchical linear model was used to investigate the relationship between motor vehicle and infrastructure characteristics (location, presence of on-road marked bicycle lane and the presence of parked cars on the kerbside) and passing distance (defined as the lateral distance between the end of the bicycle handlebars and the passing motor vehicle).<h4>Results</h4>Sixty cyclists recorded 18,527 passing events over 422 trips. The median passing distance was 173\u2009cm (Q1: 137\u2009cm, Q3: 224\u2009cm) and 1085 (5.9%) passing events were less than 100\u2009cm. Relative to sedans, 4WDs had a reduced mean passing distance of 15\u2009cm (Q1: 12\u2009cm, Q3: 17\u2009cm) and buses had a reduced mean passing distance of 28\u2009cm (Q1: 16\u2009cm, Q3: 40\u2009cm). Relative to passing events that occurred on roads without a marked bicycle lane and without parked cars, passing events on roads with a bike lane with no parked cars had a reduced mean passing distance of 27\u2009cm (Q1: 25\u2009cm, Q3: 29\u2009cm), and passing events on roads with a bike lane and parked cars had a mean lower passing distance of 40\u2009cm (Q1: 37\u2009cm, Q3: 43\u2009cm).<h4>Conclusions</h4>One in every 17 passing events was a close (<100\u2009cm) passing event. We identified that on-road bicycle lanes and parked cars reduced passing distance. These data can be used to inform the selection and design of cycling-related infrastructure and road use with the aim of improving safety for cyclists.",
+    "laySummary": "",
+    "urls": "pdf:https://cronfa.swan.ac.uk/Record/cronfa50030/Download/0050030-20052019102229.pdf; doi:https://doi.org/10.1016/j.aap.2019.03.007"
+  },
   {
     "id": "39422666",
     "doi": "https://doi.org/10.1099/jgv.0.002032",
@@ -39694,23 +39728,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1099/jgv.0.002032; html:https://europepmc.org/articles/PMC11488517; pdf:https://europepmc.org/articles/PMC11488517?pdf=render"
   },
-  {
-    "id": "34732073",
-    "doi": "https://doi.org/10.1161/strokeaha.121.034787",
-    "title": "Risk, Clinical Course, and Outcome of Ischemic Stroke in Patients Hospitalized With COVID-19: A Multicenter Cohort Study.",
-    "authorString": "Sluis WM, Linschoten M, Buijs JE, Biesbroek JM, den Hertog HM, Ribbers T, Nieuwkamp DJ, van Houwelingen RC, Dias A, van Uden IWM, Kerklaan JP, Bienfait HP, Vermeer SE, de Jong SW, Ali M, Wermer MJH, de Graaf MT, Brouwers PJAM, Asselbergs FW, Kappelle LJ, van der Worp HB, Algra AM, CAPACITY-COVID Collaborative Consortium*.",
-    "authorAffiliations": "",
-    "journalTitle": "Stroke",
-    "pubYear": "2021",
-    "date": "2021-11-04",
-    "isOpenAccess": "N",
-    "keywords": "Intensive care units; Pulmonary embolism; incidence; Hospital Mortality; Patient Discharge; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background and purpose</h4>The frequency of ischemic stroke in patients with coronavirus disease 2019 (COVID-19) varies in the current literature, and risk factors are unknown. We assessed the incidence, risk factors, and outcomes of acute ischemic stroke in hospitalized patients with COVID-19.<h4>Methods</h4>We included patients with a laboratory-confirmed SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) infection admitted in 16 Dutch hospitals participating in the international CAPACITY-COVID registry between March 1 and August 1, 2020. Patients were screened for the occurrence of acute ischemic stroke. We calculated the cumulative incidence of ischemic stroke and compared risk factors, cardiovascular complications, and in-hospital mortality in patients with and without ischemic stroke.<h4>Results</h4>We included 2147 patients with COVID-19, of whom 586 (27.3%) needed treatment at an intensive care unit. Thirty-eight patients (1.8%) had an ischemic stroke. Patients with stroke were older but did not differ in sex or cardiovascular risk factors. Median time between the onset of COVID-19 symptoms and diagnosis of stroke was 2 weeks. The incidence of ischemic stroke was higher among patients who were treated at an intensive care unit (16/586; 2.7% versus nonintensive care unit, 22/1561; 1.4%; <i>P</i>=0.039). Pulmonary embolism was more common in patients with (8/38; 21.1%) than in those without stroke (160/2109; 7.6%; adjusted risk ratio, 2.08 [95% CI, 1.52-2.84]). Twenty-seven patients with ischemic stroke (71.1%) died during admission or were functionally dependent at discharge. Patients with ischemic stroke were at a higher risk of in-hospital mortality (adjusted risk ratio, 1.56 [95% CI, 1.13-2.15]) than patients without stroke.<h4>Conclusions</h4>In this multicenter cohort study, the cumulative incidence of acute ischemic stroke in hospitalized patients with COVID-19 was \u22482%, with a higher risk in patients treated at an intensive care unit. The majority of stroke patients had a poor outcome. The association between ischemic stroke and pulmonary embolism warrants further investigation.",
-    "laySummary": "",
-    "urls": "pdf:https://europepmc.org/articles/pmc8607920?pdf=render; doi:https://doi.org/10.1161/STROKEAHA.121.034787; html:https://europepmc.org/articles/PMC8607920; pdf:https://europepmc.org/articles/PMC8607920?pdf=render; doi:https://doi.org/10.1161/strokeaha.121.034787"
-  },
   {
     "id": "33012285",
     "doi": "https://doi.org/10.1186/s12916-020-01779-4",
@@ -39728,6 +39745,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-020-01779-4; doi:https://doi.org/10.1186/s12916-020-01779-4; html:https://europepmc.org/articles/PMC7533154; pdf:https://europepmc.org/articles/PMC7533154?pdf=render"
   },
+  {
+    "id": "34732073",
+    "doi": "https://doi.org/10.1161/strokeaha.121.034787",
+    "title": "Risk, Clinical Course, and Outcome of Ischemic Stroke in Patients Hospitalized With COVID-19: A Multicenter Cohort Study.",
+    "authorString": "Sluis WM, Linschoten M, Buijs JE, Biesbroek JM, den Hertog HM, Ribbers T, Nieuwkamp DJ, van Houwelingen RC, Dias A, van Uden IWM, Kerklaan JP, Bienfait HP, Vermeer SE, de Jong SW, Ali M, Wermer MJH, de Graaf MT, Brouwers PJAM, Asselbergs FW, Kappelle LJ, van der Worp HB, Algra AM, CAPACITY-COVID Collaborative Consortium*.",
+    "authorAffiliations": "",
+    "journalTitle": "Stroke",
+    "pubYear": "2021",
+    "date": "2021-11-04",
+    "isOpenAccess": "N",
+    "keywords": "Intensive care units; Pulmonary embolism; incidence; Hospital Mortality; Patient Discharge; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background and purpose</h4>The frequency of ischemic stroke in patients with coronavirus disease 2019 (COVID-19) varies in the current literature, and risk factors are unknown. We assessed the incidence, risk factors, and outcomes of acute ischemic stroke in hospitalized patients with COVID-19.<h4>Methods</h4>We included patients with a laboratory-confirmed SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) infection admitted in 16 Dutch hospitals participating in the international CAPACITY-COVID registry between March 1 and August 1, 2020. Patients were screened for the occurrence of acute ischemic stroke. We calculated the cumulative incidence of ischemic stroke and compared risk factors, cardiovascular complications, and in-hospital mortality in patients with and without ischemic stroke.<h4>Results</h4>We included 2147 patients with COVID-19, of whom 586 (27.3%) needed treatment at an intensive care unit. Thirty-eight patients (1.8%) had an ischemic stroke. Patients with stroke were older but did not differ in sex or cardiovascular risk factors. Median time between the onset of COVID-19 symptoms and diagnosis of stroke was 2 weeks. The incidence of ischemic stroke was higher among patients who were treated at an intensive care unit (16/586; 2.7% versus nonintensive care unit, 22/1561; 1.4%; <i>P</i>=0.039). Pulmonary embolism was more common in patients with (8/38; 21.1%) than in those without stroke (160/2109; 7.6%; adjusted risk ratio, 2.08 [95% CI, 1.52-2.84]). Twenty-seven patients with ischemic stroke (71.1%) died during admission or were functionally dependent at discharge. Patients with ischemic stroke were at a higher risk of in-hospital mortality (adjusted risk ratio, 1.56 [95% CI, 1.13-2.15]) than patients without stroke.<h4>Conclusions</h4>In this multicenter cohort study, the cumulative incidence of acute ischemic stroke in hospitalized patients with COVID-19 was \u22482%, with a higher risk in patients treated at an intensive care unit. The majority of stroke patients had a poor outcome. The association between ischemic stroke and pulmonary embolism warrants further investigation.",
+    "laySummary": "",
+    "urls": "pdf:https://europepmc.org/articles/pmc8607920?pdf=render; doi:https://doi.org/10.1161/STROKEAHA.121.034787; html:https://europepmc.org/articles/PMC8607920; pdf:https://europepmc.org/articles/PMC8607920?pdf=render; doi:https://doi.org/10.1161/strokeaha.121.034787"
+  },
   {
     "id": "32656368",
     "doi": "https://doi.org/10.12688/wellcomeopenres.15889.2",
@@ -39881,23 +39915,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/11/11/e056601.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-056601; html:https://europepmc.org/articles/PMC8573296; pdf:https://europepmc.org/articles/PMC8573296?pdf=render"
   },
-  {
-    "id": "34732839",
-    "doi": "https://doi.org/10.1038/s41379-021-00953-0",
-    "title": "Stratification of chemotherapy-treated stage III colorectal cancer patients using multiplexed imaging and single-cell analysis of T-cell populations.",
-    "authorString": "Stachtea X, Loughrey MB, Salvucci M, Lindner AU, Cho S, McDonough E, Sood A, Graf J, Santamaria-Pang A, Corwin A, Laurent-Puig P, Dasgupta S, Shia J, Owens JR, Abate S, Van Schaeybroeck S, Lawler M, Prehn JHM, Ginty F, Longley DB.",
-    "authorAffiliations": "",
-    "journalTitle": "Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc",
-    "pubYear": "2022",
-    "date": "2021-11-03",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Colorectal cancer (CRC) has one of the highest cancer incidences and mortality rates. In stage III, postoperative chemotherapy benefits <20% of patients, while more than 50% will develop distant metastases. Biomarkers for identification of patients at increased risk of disease recurrence following adjuvant chemotherapy are currently lacking. In this study, we assessed immune signatures in the tumor and tumor microenvironment (TME) using an in situ multiplexed immunofluorescence imaging and single-cell analysis technology (Cell DIVE<sup>TM</sup>) and evaluated their\u00a0correlations with patient outcomes. Tissue microarrays (TMAs) with up to three 1\u2009mm diameter cores per patient were prepared from 117 stage III CRC patients treated with adjuvant fluoropyrimidine/oxaliplatin (FOLFOX) chemotherapy. Single sections underwent multiplexed immunofluorescence staining for immune cell markers (CD45, CD3, CD4, CD8, FOXP3, PD1) and tumor/cell segmentation markers (DAPI, pan-cytokeratin, AE1, NaKATPase, and S6). We used annotations and a probabilistic classification algorithm to build statistical models of immune cell types. Images were also qualitatively assessed independently by a Pathologist as 'high', 'moderate' or 'low', for stromal and total immune cell content. Excellent agreement was found between manual assessment and total automated scores (p\u2009<\u20090.0001). Moreover, compared to single markers, a multi-marker classification of regulatory T cells (Tregs: CD3+/CD4+FOXP3+/PD1-) was significantly associated with disease-free survival (DFS) and overall survival (OS) (p\u2009=\u20090.049 and 0.032) of FOLFOX-treated patients. Our results also showed that PD1- Tregs rather than PD1+ Tregs were associated with improved survival. These findings were supported by results from an independent FOLFOX-treated cohort of 191 stage III CRC patients, where higher PD1- Tregs were associated with an increase overall survival (p\u2009=\u20090.015) for CD3+/CD4+/FOXP3+/PD1-. Overall, compared to single markers, multi-marker classification provided more accurate quantitation of immune cell types with\u00a0stronger correlations with outcomes.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41379-021-00953-0.pdf; doi:https://doi.org/10.1038/s41379-021-00953-0; html:https://europepmc.org/articles/PMC8964416; pdf:https://europepmc.org/articles/PMC8964416?pdf=render"
-  },
   {
     "id": "31675503",
     "doi": "https://doi.org/10.1016/j.cell.2019.10.004",
@@ -39915,6 +39932,23 @@
     "laySummary": "",
     "urls": "pdf:http://www.cell.com/article/S0092867419311201/pdf; doi:https://doi.org/10.1016/j.cell.2019.10.004; html:https://europepmc.org/articles/PMC7202134; pdf:https://europepmc.org/articles/PMC7202134?pdf=render; doi:https://doi.org/10.1016/j.cell.2019.10.004"
   },
+  {
+    "id": "34732839",
+    "doi": "https://doi.org/10.1038/s41379-021-00953-0",
+    "title": "Stratification of chemotherapy-treated stage III colorectal cancer patients using multiplexed imaging and single-cell analysis of T-cell populations.",
+    "authorString": "Stachtea X, Loughrey MB, Salvucci M, Lindner AU, Cho S, McDonough E, Sood A, Graf J, Santamaria-Pang A, Corwin A, Laurent-Puig P, Dasgupta S, Shia J, Owens JR, Abate S, Van Schaeybroeck S, Lawler M, Prehn JHM, Ginty F, Longley DB.",
+    "authorAffiliations": "",
+    "journalTitle": "Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc",
+    "pubYear": "2022",
+    "date": "2021-11-03",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Colorectal cancer (CRC) has one of the highest cancer incidences and mortality rates. In stage III, postoperative chemotherapy benefits <20% of patients, while more than 50% will develop distant metastases. Biomarkers for identification of patients at increased risk of disease recurrence following adjuvant chemotherapy are currently lacking. In this study, we assessed immune signatures in the tumor and tumor microenvironment (TME) using an in situ multiplexed immunofluorescence imaging and single-cell analysis technology (Cell DIVE<sup>TM</sup>) and evaluated their\u00a0correlations with patient outcomes. Tissue microarrays (TMAs) with up to three 1\u2009mm diameter cores per patient were prepared from 117 stage III CRC patients treated with adjuvant fluoropyrimidine/oxaliplatin (FOLFOX) chemotherapy. Single sections underwent multiplexed immunofluorescence staining for immune cell markers (CD45, CD3, CD4, CD8, FOXP3, PD1) and tumor/cell segmentation markers (DAPI, pan-cytokeratin, AE1, NaKATPase, and S6). We used annotations and a probabilistic classification algorithm to build statistical models of immune cell types. Images were also qualitatively assessed independently by a Pathologist as 'high', 'moderate' or 'low', for stromal and total immune cell content. Excellent agreement was found between manual assessment and total automated scores (p\u2009<\u20090.0001). Moreover, compared to single markers, a multi-marker classification of regulatory T cells (Tregs: CD3+/CD4+FOXP3+/PD1-) was significantly associated with disease-free survival (DFS) and overall survival (OS) (p\u2009=\u20090.049 and 0.032) of FOLFOX-treated patients. Our results also showed that PD1- Tregs rather than PD1+ Tregs were associated with improved survival. These findings were supported by results from an independent FOLFOX-treated cohort of 191 stage III CRC patients, where higher PD1- Tregs were associated with an increase overall survival (p\u2009=\u20090.015) for CD3+/CD4+/FOXP3+/PD1-. Overall, compared to single markers, multi-marker classification provided more accurate quantitation of immune cell types with\u00a0stronger correlations with outcomes.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41379-021-00953-0.pdf; doi:https://doi.org/10.1038/s41379-021-00953-0; html:https://europepmc.org/articles/PMC8964416; pdf:https://europepmc.org/articles/PMC8964416?pdf=render"
+  },
   {
     "id": "35386118",
     "doi": "https://doi.org/10.3389/fnagi.2022.840651",
@@ -40136,6 +40170,23 @@
     "laySummary": "",
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9463529; doi:https://doi.org/10.1016/j.ebiom.2022.104243; html:https://europepmc.org/articles/PMC9463529; pdf:https://europepmc.org/articles/PMC9463529?pdf=render"
   },
+  {
+    "id": "33024096",
+    "doi": "https://doi.org/10.1038/s41467-020-18783-0",
+    "title": "Changing travel patterns in China during the early stages of the COVID-19 pandemic.",
+    "authorString": "Gibbs H, Liu Y, Pearson CAB, Jarvis CI, Grundy C, Quilty BJ, Diamond C, LSHTM CMMID COVID-19 working group, Eggo RM.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature communications",
+    "pubYear": "2020",
+    "date": "2020-10-06",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Understanding changes in human mobility in the early stages of the COVID-19 pandemic is crucial for assessing the impacts of travel restrictions designed to reduce disease spread. Here, relying on data from mainland China, we investigate the spatio-temporal characteristics of human mobility between 1st January and 1st March 2020, and discuss their public health implications. An outbound travel surge from Wuhan before travel restrictions were implemented was also observed across China due to the Lunar New Year, indicating that holiday travel may have played a larger role in mobility changes compared to impending travel restrictions. Holiday travel also shifted healthcare pressure related to COVID-19 towards locations with lower healthcare capacity. Network analyses showed no sign of major changes in the transportation network after Lunar New Year. Changes observed were temporary and did not lead to structural reorganisation of the transportation network during the study period.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41467-020-18783-0.pdf; doi:https://doi.org/10.1038/s41467-020-18783-0; html:https://europepmc.org/articles/PMC7538915; pdf:https://europepmc.org/articles/PMC7538915?pdf=render"
+  },
   {
     "id": "37315048",
     "doi": "https://doi.org/10.1371/journal.pone.0287091",
@@ -40170,23 +40221,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ije/article-pdf/48/3/678/29005217/dyz073.pdf; doi:https://doi.org/10.1093/ije/dyz073; html:https://europepmc.org/articles/PMC6659362; pdf:https://europepmc.org/articles/PMC6659362?pdf=render"
   },
-  {
-    "id": "33024096",
-    "doi": "https://doi.org/10.1038/s41467-020-18783-0",
-    "title": "Changing travel patterns in China during the early stages of the COVID-19 pandemic.",
-    "authorString": "Gibbs H, Liu Y, Pearson CAB, Jarvis CI, Grundy C, Quilty BJ, Diamond C, LSHTM CMMID COVID-19 working group, Eggo RM.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature communications",
-    "pubYear": "2020",
-    "date": "2020-10-06",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Understanding changes in human mobility in the early stages of the COVID-19 pandemic is crucial for assessing the impacts of travel restrictions designed to reduce disease spread. Here, relying on data from mainland China, we investigate the spatio-temporal characteristics of human mobility between 1st January and 1st March 2020, and discuss their public health implications. An outbound travel surge from Wuhan before travel restrictions were implemented was also observed across China due to the Lunar New Year, indicating that holiday travel may have played a larger role in mobility changes compared to impending travel restrictions. Holiday travel also shifted healthcare pressure related to COVID-19 towards locations with lower healthcare capacity. Network analyses showed no sign of major changes in the transportation network after Lunar New Year. Changes observed were temporary and did not lead to structural reorganisation of the transportation network during the study period.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41467-020-18783-0.pdf; doi:https://doi.org/10.1038/s41467-020-18783-0; html:https://europepmc.org/articles/PMC7538915; pdf:https://europepmc.org/articles/PMC7538915?pdf=render"
-  },
   {
     "id": "34110679",
     "doi": "https://doi.org/10.1002/1878-0261.13038",
@@ -40307,21 +40341,21 @@
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/10/5/e038530.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-038530; html:https://europepmc.org/articles/PMC7239518; pdf:https://europepmc.org/articles/PMC7239518?pdf=render"
   },
   {
-    "id": "34244281",
-    "doi": "https://doi.org/10.1136/bmjopen-2021-049611",
-    "title": "Ethnicity and COVID-19 outcomes among healthcare workers in the UK: UK-REACH ethico-legal research, qualitative research on healthcare workers' experiences and stakeholder engagement protocol.",
-    "authorString": "Gogoi M, Reed-Berendt R, Al-Oraibi A, Hassan O, Wobi F, Gupta A, Abubakar I, Dove E, Nellums LB, Pareek M, UK-REACH Collaborative Group.",
+    "id": "39210026",
+    "doi": "https://doi.org/10.1038/s41562-024-01963-z",
+    "title": "The genetic landscape of neuro-related proteins in human plasma.",
+    "authorString": "Repetto L, Chen J, Yang Z, Zhai R, Timmers PRHJ, Feng X, Li T, Yao Y, Maslov D, Timoshchuk A, Tu F, Twait EL, May-Wilson S, Muckian MD, Prins BP, Png G, Kooperberg C, Johansson \u00c5, Hillary RF, Wheeler E, Pan L, He Y, Klasson S, Ahmad S, Peters JE, Gilly A, Karaleftheri M, Tsafantakis E, Haessler J, Gyllensten U, Harris SE, Wareham NJ, G\u00f6teson A, Lagging C, Ikram MA, van Duijn CM, Jern C, Land\u00e9n M, Langenberg C, Deary IJ, Marioni RE, Enroth S, Reiner AP, Dedoussis G, Zeggini E, Sharapov S, Aulchenko YS, Butterworth AS, M\u00e4larstig A, Wilson JF, Navarro P, Shen X.",
     "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2021",
-    "date": "2021-07-09",
-    "isOpenAccess": "Y",
-    "keywords": "Medical Ethics; Qualitative Research; Medical Law; Covid-19",
+    "journalTitle": "Nature human behaviour",
+    "pubYear": "2024",
+    "date": "2024-08-29",
+    "isOpenAccess": "N",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>As the world continues to grapple with the COVID-19 pandemic, emerging evidence suggests that individuals from ethnic minority backgrounds may be disproportionately affected. The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers (UK-REACH) project has been initiated to generate rapid evidence on whether and why ethnicity affects COVID-19 diagnosis and clinical outcomes in healthcare workers (HCWs) in the UK, through five interlinked work packages/work streams, three of which form the basis of this protocol. The ethico-legal work (Work Package 3) aims to understand and address legal, ethical and acceptability issues around big data research; the HCWs' experiences study (Work Package 4) explores their work and personal experiences, perceptions of risk, support and coping mechanisms; the stakeholder engagement work (Work Package 5) aims to provide feedback and support with the formulation and dissemination of the project recommendations.<h4>Methods and analysis</h4>Work Package 3 has two different research strands: (A) desk-based doctrinal research; and (B) empirical qualitative research with key opinion leaders. For the empirical research, in-depth interviews will be conducted digitally and recorded with participants' permission. Recordings will be transcribed, coded and analysed using thematic analysis. In Work Package 4, online in-depth interviews and focus groups will be conducted with approximately 150 HCWs, from across the UK, and these will be recorded with participants' consent. The recordings will be transcribed and coded and data will be analysed using thematic analysis. Work Package 5 will achieve its objectives through regular group meetings and in-group discussions.<h4>Ethics and dissemination</h4>Ethical approval has been received from the London-Brighton & Sussex Research Ethics Committee of the Health Research Authority (Ref No 20/HRA/4718). Results of the study will be published in open-access journals, and disseminated through conference presentations, project website, stakeholder organisations, media and scientific advisory groups.<h4>Trial registration number</h4>ISRCTN11811602.",
+    "abstract": "Understanding the genetic basis of neuro-related proteins is essential for dissecting the molecular basis of human behavioural traits and the disease aetiology of neuropsychiatric disorders. Here the SCALLOP Consortium conducted a genome-wide association meta-analysis of over 12,000 individuals for 184 neuro-related proteins in human plasma. The analysis identified 125 cis-regulatory protein quantitative trait loci (cis-pQTL) and 164 trans-pQTL. The mapped pQTL capture on average 50% of each protein's heritability. At the cis-pQTL, multiple proteins shared a genetic basis with human behavioural traits such as alcohol and food intake, smoking and educational attainment, as well as neurological conditions and psychiatric disorders such as pain, neuroticism and schizophrenia. Integrating with established drug information, the causal inference analysis validated 52 out of 66 matched combinations of protein targets and diseases or side effects with available drugs while suggesting hundreds of repurposing and new therapeutic targets.",
     "laySummary": "",
-    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/11/7/e049611.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-049611; html:https://europepmc.org/articles/PMC8275361; pdf:https://europepmc.org/articles/PMC8275361?pdf=render"
+    "urls": "doi:https://doi.org/10.1038/s41562-024-01963-z"
   },
   {
     "id": "31196905",
@@ -40340,6 +40374,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/9/6/e028929.full.pdf; doi:https://doi.org/10.1136/bmjopen-2019-028929; html:https://europepmc.org/articles/PMC6577359; pdf:https://europepmc.org/articles/PMC6577359?pdf=render"
   },
+  {
+    "id": "34244281",
+    "doi": "https://doi.org/10.1136/bmjopen-2021-049611",
+    "title": "Ethnicity and COVID-19 outcomes among healthcare workers in the UK: UK-REACH ethico-legal research, qualitative research on healthcare workers' experiences and stakeholder engagement protocol.",
+    "authorString": "Gogoi M, Reed-Berendt R, Al-Oraibi A, Hassan O, Wobi F, Gupta A, Abubakar I, Dove E, Nellums LB, Pareek M, UK-REACH Collaborative Group.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2021",
+    "date": "2021-07-09",
+    "isOpenAccess": "Y",
+    "keywords": "Medical Ethics; Qualitative Research; Medical Law; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>As the world continues to grapple with the COVID-19 pandemic, emerging evidence suggests that individuals from ethnic minority backgrounds may be disproportionately affected. The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers (UK-REACH) project has been initiated to generate rapid evidence on whether and why ethnicity affects COVID-19 diagnosis and clinical outcomes in healthcare workers (HCWs) in the UK, through five interlinked work packages/work streams, three of which form the basis of this protocol. The ethico-legal work (Work Package 3) aims to understand and address legal, ethical and acceptability issues around big data research; the HCWs' experiences study (Work Package 4) explores their work and personal experiences, perceptions of risk, support and coping mechanisms; the stakeholder engagement work (Work Package 5) aims to provide feedback and support with the formulation and dissemination of the project recommendations.<h4>Methods and analysis</h4>Work Package 3 has two different research strands: (A) desk-based doctrinal research; and (B) empirical qualitative research with key opinion leaders. For the empirical research, in-depth interviews will be conducted digitally and recorded with participants' permission. Recordings will be transcribed, coded and analysed using thematic analysis. In Work Package 4, online in-depth interviews and focus groups will be conducted with approximately 150 HCWs, from across the UK, and these will be recorded with participants' consent. The recordings will be transcribed and coded and data will be analysed using thematic analysis. Work Package 5 will achieve its objectives through regular group meetings and in-group discussions.<h4>Ethics and dissemination</h4>Ethical approval has been received from the London-Brighton & Sussex Research Ethics Committee of the Health Research Authority (Ref No 20/HRA/4718). Results of the study will be published in open-access journals, and disseminated through conference presentations, project website, stakeholder organisations, media and scientific advisory groups.<h4>Trial registration number</h4>ISRCTN11811602.",
+    "laySummary": "",
+    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/11/7/e049611.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-049611; html:https://europepmc.org/articles/PMC8275361; pdf:https://europepmc.org/articles/PMC8275361?pdf=render"
+  },
   {
     "id": "35584845",
     "doi": "https://doi.org/10.1136/bmj-2022-070904",
@@ -40357,23 +40408,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.bmj.com/content/bmj/377/bmj-2022-070904.full.pdf; doi:https://doi.org/10.1136/bmj-2022-070904; html:https://europepmc.org/articles/PMC9116198"
   },
-  {
-    "id": "39210026",
-    "doi": "https://doi.org/10.1038/s41562-024-01963-z",
-    "title": "The genetic landscape of neuro-related proteins in human plasma.",
-    "authorString": "Repetto L, Chen J, Yang Z, Zhai R, Timmers PRHJ, Feng X, Li T, Yao Y, Maslov D, Timoshchuk A, Tu F, Twait EL, May-Wilson S, Muckian MD, Prins BP, Png G, Kooperberg C, Johansson \u00c5, Hillary RF, Wheeler E, Pan L, He Y, Klasson S, Ahmad S, Peters JE, Gilly A, Karaleftheri M, Tsafantakis E, Haessler J, Gyllensten U, Harris SE, Wareham NJ, G\u00f6teson A, Lagging C, Ikram MA, van Duijn CM, Jern C, Land\u00e9n M, Langenberg C, Deary IJ, Marioni RE, Enroth S, Reiner AP, Dedoussis G, Zeggini E, Sharapov S, Aulchenko YS, Butterworth AS, M\u00e4larstig A, Wilson JF, Navarro P, Shen X.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature human behaviour",
-    "pubYear": "2024",
-    "date": "2024-08-29",
-    "isOpenAccess": "N",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Understanding the genetic basis of neuro-related proteins is essential for dissecting the molecular basis of human behavioural traits and the disease aetiology of neuropsychiatric disorders. Here the SCALLOP Consortium conducted a genome-wide association meta-analysis of over 12,000 individuals for 184 neuro-related proteins in human plasma. The analysis identified 125 cis-regulatory protein quantitative trait loci (cis-pQTL) and 164 trans-pQTL. The mapped pQTL capture on average 50% of each protein's heritability. At the cis-pQTL, multiple proteins shared a genetic basis with human behavioural traits such as alcohol and food intake, smoking and educational attainment, as well as neurological conditions and psychiatric disorders such as pain, neuroticism and schizophrenia. Integrating with established drug information, the causal inference analysis validated 52 out of 66 matched combinations of protein targets and diseases or side effects with available drugs while suggesting hundreds of repurposing and new therapeutic targets.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1038/s41562-024-01963-z"
-  },
   {
     "id": "34568827",
     "doi": "https://doi.org/10.1093/schizbullopen/sgab041",
@@ -40442,23 +40476,6 @@
     "laySummary": "Grist et al. team trained computers to analyse brain images from children for identification of tumours. They\u2019ve shown that applying analytical methods to enable machine distinguishes between the entire brain area and the tumour area in the images more than 80% improves how machine analyses the image to identify exact tumour area. ",
     "urls": "doi:https://doi.org/10.1016/j.nicl.2020.102172; doi:https://doi.org/10.1016/j.nicl.2020.102172; html:https://europepmc.org/articles/PMC7005468; pdf:https://europepmc.org/articles/PMC7005468?pdf=render"
   },
-  {
-    "id": "33602244",
-    "doi": "https://doi.org/10.1186/s12916-021-01924-7",
-    "title": "The impact of local and national restrictions in response to COVID-19 on social contacts in England: a longitudinal natural experiment.",
-    "authorString": "Jarvis CI, Gimma A, van Zandvoort K, Wong KLM, CMMID COVID-19 working group, Edmunds WJ.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC medicine",
-    "pubYear": "2021",
-    "date": "2021-02-19",
-    "isOpenAccess": "Y",
-    "keywords": "Pandemic; England; United Kingdom; Disease Outbreak; Non-pharmaceutical Interventions; Covid-19; Contact Survey; Lockdowns",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>England's COVID-19 response transitioned from a national lockdown to localised interventions. In response to rising cases, these were supplemented by national restrictions on contacts (the Rule of Six), then 10\u2009pm closing for bars and restaurants, and encouragement to work from home. These were quickly followed by a 3-tier system applying different restrictions in different localities. As cases continued to rise, a second national lockdown was declared. We used a national survey to quantify the impact of these restrictions on epidemiologically relevant contacts.<h4>Methods</h4>We compared paired measures on setting-specific contacts before and after each restriction started and tested for differences using paired permutation tests on the mean change in contacts and the proportion of individuals decreasing their contacts.<h4>Results</h4>Following the imposition of each measure, individuals tended to report fewer contacts than they had before. However, the magnitude of the changes was relatively small and variable. For instance, although early closure of bars and restaurants appeared to have no measurable effect on contacts, the work from home directive reduced mean daily work contacts by 0.99 (95% confidence interval CI] 0.03-1.94), and the Rule of Six reduced non-work and school contacts by a mean of 0.25 (0.01-0.5) per day. Whilst Tier 3 appeared to also reduce non-work and school contacts, the evidence for an effect of the lesser restrictions (Tiers 1 and 2) was much weaker. There may also have been some evidence of saturation of effects, with those who were in Tier 1 (least restrictive) reducing their contacts markedly when they entered lockdown, which was not reflected in similar changes in those who were already under tighter restrictions (Tiers 2 and 3).<h4>Conclusions</h4>The imposition of various local and national measures in England during the summer and autumn of 2020 has gradually reduced contacts. However, these changes are smaller than the initial lockdown in March. This may partly be because many individuals were already starting from a lower number of contacts.",
-    "laySummary": "",
-    "urls": "pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-021-01924-7; doi:https://doi.org/10.1186/s12916-021-01924-7; html:https://europepmc.org/articles/PMC7892289; pdf:https://europepmc.org/articles/PMC7892289?pdf=render"
-  },
   {
     "id": "33879569",
     "doi": "https://doi.org/10.1073/pnas.2009808118",
@@ -40476,6 +40493,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1073/pnas.2009808118; doi:https://doi.org/10.1073/pnas.2009808118; html:https://europepmc.org/articles/PMC8072203; pdf:https://europepmc.org/articles/PMC8072203?pdf=render"
   },
+  {
+    "id": "33602244",
+    "doi": "https://doi.org/10.1186/s12916-021-01924-7",
+    "title": "The impact of local and national restrictions in response to COVID-19 on social contacts in England: a longitudinal natural experiment.",
+    "authorString": "Jarvis CI, Gimma A, van Zandvoort K, Wong KLM, CMMID COVID-19 working group, Edmunds WJ.",
+    "authorAffiliations": "",
+    "journalTitle": "BMC medicine",
+    "pubYear": "2021",
+    "date": "2021-02-19",
+    "isOpenAccess": "Y",
+    "keywords": "Pandemic; England; United Kingdom; Disease Outbreak; Non-pharmaceutical Interventions; Covid-19; Contact Survey; Lockdowns",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>England's COVID-19 response transitioned from a national lockdown to localised interventions. In response to rising cases, these were supplemented by national restrictions on contacts (the Rule of Six), then 10\u2009pm closing for bars and restaurants, and encouragement to work from home. These were quickly followed by a 3-tier system applying different restrictions in different localities. As cases continued to rise, a second national lockdown was declared. We used a national survey to quantify the impact of these restrictions on epidemiologically relevant contacts.<h4>Methods</h4>We compared paired measures on setting-specific contacts before and after each restriction started and tested for differences using paired permutation tests on the mean change in contacts and the proportion of individuals decreasing their contacts.<h4>Results</h4>Following the imposition of each measure, individuals tended to report fewer contacts than they had before. However, the magnitude of the changes was relatively small and variable. For instance, although early closure of bars and restaurants appeared to have no measurable effect on contacts, the work from home directive reduced mean daily work contacts by 0.99 (95% confidence interval CI] 0.03-1.94), and the Rule of Six reduced non-work and school contacts by a mean of 0.25 (0.01-0.5) per day. Whilst Tier 3 appeared to also reduce non-work and school contacts, the evidence for an effect of the lesser restrictions (Tiers 1 and 2) was much weaker. There may also have been some evidence of saturation of effects, with those who were in Tier 1 (least restrictive) reducing their contacts markedly when they entered lockdown, which was not reflected in similar changes in those who were already under tighter restrictions (Tiers 2 and 3).<h4>Conclusions</h4>The imposition of various local and national measures in England during the summer and autumn of 2020 has gradually reduced contacts. However, these changes are smaller than the initial lockdown in March. This may partly be because many individuals were already starting from a lower number of contacts.",
+    "laySummary": "",
+    "urls": "pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-021-01924-7; doi:https://doi.org/10.1186/s12916-021-01924-7; html:https://europepmc.org/articles/PMC7892289; pdf:https://europepmc.org/articles/PMC7892289?pdf=render"
+  },
   {
     "id": "35477868",
     "doi": "https://doi.org/10.1136/bmjopen-2021-057579",
@@ -40561,6 +40595,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.3399/bjgp.2021.0380; doi:https://doi.org/10.3399/BJGP.2021.0380; html:https://europepmc.org/articles/PMC8589464; pdf:https://europepmc.org/articles/PMC8589464?pdf=render"
   },
+  {
+    "id": "32546850",
+    "doi": "https://doi.org/10.1038/s41598-020-66737-9",
+    "title": "Genetic aetiology of self-harm ideation and behaviour.",
+    "authorString": "Campos AI, Verweij KJH, Statham DJ, Madden PAF, Maciejewski DF, Davis KAS, John A, Hotopf M, Heath AC, Martin NG, Renter\u00eda ME.",
+    "authorAffiliations": "",
+    "journalTitle": "Scientific reports",
+    "pubYear": "2020",
+    "date": "2020-06-16",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Family studies have identified a heritable component to self-harm that is partially independent from comorbid psychiatric disorders. However, the genetic aetiology of broad sense (non-suicidal and suicidal) self-harm has not been characterised on the molecular level. In addition, controversy exists about the degree to which suicidal and non-suicidal self-harm share a common genetic aetiology. In the present study, we conduct genome-wide association studies (GWAS) on lifetime self-harm ideation and self-harm behaviour (i.e. any lifetime self-harm act regardless of suicidal intent) using data from the UK Biobank (n\u2009>\u2009156,000). We also perform genome wide gene-based tests and characterize the SNP heritability and genetic correlations between these traits. Finally, we test whether polygenic risk scores (PRS) for self-harm ideation and self-harm behaviour predict suicide attempt, suicide thoughts and non-suicidal self-harm (NSSH) in an independent target sample of 8,703 Australian adults. Our GWAS results identified one genome-wide significant locus associated with each of the two phenotypes. SNP heritability (h<sub>snp</sub><sup>2</sup>) estimates were ~10%, and both traits were highly genetically correlated (LDSC r<sub>g</sub>\u2009>\u20090.8). Gene-based tests identified seven genes associated with self-harm ideation and four with self-harm behaviour. Furthermore, in the target sample, PRS for self-harm ideation were significantly associated with suicide thoughts and NSSH, and PRS for self-harm behaviour predicted suicide thoughts and suicide attempt. Follow up regressions identified a shared genetic aetiology between NSSH and suicide thoughts, and between suicide thoughts and suicide attempt. Evidence for shared genetic aetiology between NSSH and suicide attempt was not statistically significant.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41598-020-66737-9.pdf; doi:https://doi.org/10.1038/s41598-020-66737-9; html:https://europepmc.org/articles/PMC7297971; pdf:https://europepmc.org/articles/PMC7297971?pdf=render"
+  },
   {
     "id": "34503493",
     "doi": "https://doi.org/10.1186/s12916-021-02107-0",
@@ -40595,23 +40646,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41397-023-00307-w.pdf; doi:https://doi.org/10.1038/s41397-023-00307-w; html:https://europepmc.org/articles/PMC10506906; pdf:https://europepmc.org/articles/PMC10506906?pdf=render"
   },
-  {
-    "id": "32546850",
-    "doi": "https://doi.org/10.1038/s41598-020-66737-9",
-    "title": "Genetic aetiology of self-harm ideation and behaviour.",
-    "authorString": "Campos AI, Verweij KJH, Statham DJ, Madden PAF, Maciejewski DF, Davis KAS, John A, Hotopf M, Heath AC, Martin NG, Renter\u00eda ME.",
-    "authorAffiliations": "",
-    "journalTitle": "Scientific reports",
-    "pubYear": "2020",
-    "date": "2020-06-16",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Family studies have identified a heritable component to self-harm that is partially independent from comorbid psychiatric disorders. However, the genetic aetiology of broad sense (non-suicidal and suicidal) self-harm has not been characterised on the molecular level. In addition, controversy exists about the degree to which suicidal and non-suicidal self-harm share a common genetic aetiology. In the present study, we conduct genome-wide association studies (GWAS) on lifetime self-harm ideation and self-harm behaviour (i.e. any lifetime self-harm act regardless of suicidal intent) using data from the UK Biobank (n\u2009>\u2009156,000). We also perform genome wide gene-based tests and characterize the SNP heritability and genetic correlations between these traits. Finally, we test whether polygenic risk scores (PRS) for self-harm ideation and self-harm behaviour predict suicide attempt, suicide thoughts and non-suicidal self-harm (NSSH) in an independent target sample of 8,703 Australian adults. Our GWAS results identified one genome-wide significant locus associated with each of the two phenotypes. SNP heritability (h<sub>snp</sub><sup>2</sup>) estimates were ~10%, and both traits were highly genetically correlated (LDSC r<sub>g</sub>\u2009>\u20090.8). Gene-based tests identified seven genes associated with self-harm ideation and four with self-harm behaviour. Furthermore, in the target sample, PRS for self-harm ideation were significantly associated with suicide thoughts and NSSH, and PRS for self-harm behaviour predicted suicide thoughts and suicide attempt. Follow up regressions identified a shared genetic aetiology between NSSH and suicide thoughts, and between suicide thoughts and suicide attempt. Evidence for shared genetic aetiology between NSSH and suicide attempt was not statistically significant.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41598-020-66737-9.pdf; doi:https://doi.org/10.1038/s41598-020-66737-9; html:https://europepmc.org/articles/PMC7297971; pdf:https://europepmc.org/articles/PMC7297971?pdf=render"
-  },
   {
     "id": "36245269",
     "doi": "https://doi.org/10.15252/embj.2022111857",
@@ -40799,23 +40833,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1136/bmjgh-2022-009997; doi:https://doi.org/10.1136/bmjgh-2022-009997; html:https://europepmc.org/articles/PMC10230340; pdf:https://europepmc.org/articles/PMC10230340?pdf=render"
   },
-  {
-    "id": "35322056",
-    "doi": "https://doi.org/10.1038/s41598-022-08351-5",
-    "title": "Automated quality assessment of large digitised histology cohorts by artificial intelligence.",
-    "authorString": "Haghighat M, Browning L, Sirinukunwattana K, Malacrino S, Khalid Alham N, Colling R, Cui Y, Rakha E, Hamdy FC, Verrill C, Rittscher J.",
-    "authorAffiliations": "",
-    "journalTitle": "Scientific reports",
-    "pubYear": "2022",
-    "date": "2022-03-23",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Research using whole slide images (WSIs) of histopathology slides has increased exponentially over recent years. Glass slides from retrospective cohorts, some with patient follow-up data are digitised for the development and validation of artificial intelligence (AI) tools. Such resources, therefore, become very important, with the need to ensure that their quality is of the standard necessary for downstream AI development. However, manual quality control of large cohorts of WSIs by visual assessment is unfeasible, and whilst quality control AI algorithms exist, these focus on bespoke aspects of image quality, e.g. focus, or use traditional machine-learning methods, which are unable to classify the range of potential image artefacts that should be considered. In this study, we have trained and validated a multi-task deep neural network to automate the process of quality control of a large retrospective cohort of prostate cases from which glass slides have been scanned several years after production, to determine both the usability of the images at the diagnostic level (considered in this study to be the minimal standard for research) and the common image artefacts present. Using a two-layer approach, quality overlays of WSIs were generated from a quality assessment (QA) undertaken at patch-level at [Formula: see text] magnification. From these quality overlays the slide-level quality scores were predicted and then compared to those generated by three specialist urological pathologists, with a Pearson correlation of 0.89 for overall 'usability' (at a diagnostic level), and 0.87 and 0.82 for focus and H&E staining quality scores respectively. To demonstrate its wider potential utility, we subsequently applied our QA pipeline to the TCGA prostate cancer cohort and to a colorectal cancer cohort, for comparison. Our model, designated as PathProfiler, indicates comparable predicted usability of images from the cohorts assessed (86-90% of WSIs predicted to be usable), and perhaps more significantly is able to predict WSIs that could benefit from an intervention such as re-scanning or re-staining for quality improvement. We have shown in this study that AI can be used to automate the process of quality control of large retrospective WSI cohorts to maximise their utility for research.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41598-022-08351-5.pdf; doi:https://doi.org/10.1038/s41598-022-08351-5; html:https://europepmc.org/articles/PMC8943120; pdf:https://europepmc.org/articles/PMC8943120?pdf=render"
-  },
   {
     "id": "31792462",
     "doi": "https://doi.org/10.1038/s41591-019-0665-2",
@@ -40833,6 +40850,23 @@
     "laySummary": "",
     "urls": "pdf:https://europepmc.org/articles/pmc6922049?pdf=render; doi:https://doi.org/10.1038/s41591-019-0665-2; html:https://europepmc.org/articles/PMC6922049; pdf:https://europepmc.org/articles/PMC6922049?pdf=render; doi:https://doi.org/10.1038/s41591-019-0665-2"
   },
+  {
+    "id": "35322056",
+    "doi": "https://doi.org/10.1038/s41598-022-08351-5",
+    "title": "Automated quality assessment of large digitised histology cohorts by artificial intelligence.",
+    "authorString": "Haghighat M, Browning L, Sirinukunwattana K, Malacrino S, Khalid Alham N, Colling R, Cui Y, Rakha E, Hamdy FC, Verrill C, Rittscher J.",
+    "authorAffiliations": "",
+    "journalTitle": "Scientific reports",
+    "pubYear": "2022",
+    "date": "2022-03-23",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Research using whole slide images (WSIs) of histopathology slides has increased exponentially over recent years. Glass slides from retrospective cohorts, some with patient follow-up data are digitised for the development and validation of artificial intelligence (AI) tools. Such resources, therefore, become very important, with the need to ensure that their quality is of the standard necessary for downstream AI development. However, manual quality control of large cohorts of WSIs by visual assessment is unfeasible, and whilst quality control AI algorithms exist, these focus on bespoke aspects of image quality, e.g. focus, or use traditional machine-learning methods, which are unable to classify the range of potential image artefacts that should be considered. In this study, we have trained and validated a multi-task deep neural network to automate the process of quality control of a large retrospective cohort of prostate cases from which glass slides have been scanned several years after production, to determine both the usability of the images at the diagnostic level (considered in this study to be the minimal standard for research) and the common image artefacts present. Using a two-layer approach, quality overlays of WSIs were generated from a quality assessment (QA) undertaken at patch-level at [Formula: see text] magnification. From these quality overlays the slide-level quality scores were predicted and then compared to those generated by three specialist urological pathologists, with a Pearson correlation of 0.89 for overall 'usability' (at a diagnostic level), and 0.87 and 0.82 for focus and H&E staining quality scores respectively. To demonstrate its wider potential utility, we subsequently applied our QA pipeline to the TCGA prostate cancer cohort and to a colorectal cancer cohort, for comparison. Our model, designated as PathProfiler, indicates comparable predicted usability of images from the cohorts assessed (86-90% of WSIs predicted to be usable), and perhaps more significantly is able to predict WSIs that could benefit from an intervention such as re-scanning or re-staining for quality improvement. We have shown in this study that AI can be used to automate the process of quality control of large retrospective WSI cohorts to maximise their utility for research.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41598-022-08351-5.pdf; doi:https://doi.org/10.1038/s41598-022-08351-5; html:https://europepmc.org/articles/PMC8943120; pdf:https://europepmc.org/articles/PMC8943120?pdf=render"
+  },
   {
     "id": "36474045",
     "doi": "https://doi.org/10.1038/s41588-022-01233-6",
@@ -40850,6 +40884,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41588-022-01233-6.pdf; doi:https://doi.org/10.1038/s41588-022-01233-6; html:https://europepmc.org/articles/PMC9729111; pdf:https://europepmc.org/articles/PMC9729111?pdf=render"
   },
+  {
+    "id": "33531015",
+    "doi": "https://doi.org/10.1186/s12916-021-01906-9",
+    "title": "The importance of supplementary immunisation activities to prevent measles outbreaks during the COVID-19 pandemic in Kenya.",
+    "authorString": "Mburu CN, Ojal J, Chebet R, Akech D, Karia B, Tuju J, Sigilai A, Abbas K, Jit M, Funk S, Smits G, van Gageldonk PGM, van der Klis FRM, Tabu C, Nokes DJ, LSHTM CMMID COVID-19 Working Group, Scott J, Flasche S, Adetifa I.",
+    "authorAffiliations": "",
+    "journalTitle": "BMC medicine",
+    "pubYear": "2021",
+    "date": "2021-02-03",
+    "isOpenAccess": "Y",
+    "keywords": "outbreak; Measles; Vaccination Coverage; Supplementary Immunisation Activities; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>The COVID-19 pandemic has disrupted routine measles immunisation and supplementary immunisation activities (SIAs) in most countries including Kenya. We assessed the risk of measles outbreaks during the pandemic in Kenya as a case study for the African Region.<h4>Methods</h4>Combining measles serological data, local contact patterns, and vaccination coverage into a cohort model, we predicted the age-adjusted population immunity in Kenya and estimated the probability of outbreaks when contact-reducing COVID-19 interventions are lifted. We considered various scenarios for reduced measles vaccination coverage from April 2020.<h4>Results</h4>In February 2020, when a scheduled SIA was postponed, population immunity was close to the herd immunity threshold and the probability of a large outbreak was 34% (8-54). As the COVID-19 contact restrictions are nearly fully eased, from December 2020, the probability of a large measles outbreak will increase to 38% (19-54), 46% (30-59), and 54% (43-64) assuming a 15%, 50%, and 100% reduction in measles vaccination coverage. By December 2021, this risk increases further to 43% (25-56), 54% (43-63), and 67% (59-72) for the same coverage scenarios respectively. However, the increased risk of a measles outbreak following the lifting of all restrictions can be overcome by conducting a SIA with \u2265\u200995% coverage in under-fives.<h4>Conclusion</h4>While contact restrictions sufficient for SAR-CoV-2 control temporarily reduce measles transmissibility and the risk of an outbreak from a measles immunity gap, this risk rises rapidly once these restrictions are lifted. Implementing delayed SIAs will be critical for prevention of measles outbreaks given the roll-back of contact restrictions in Kenya.",
+    "laySummary": "",
+    "urls": "pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-021-01906-9; doi:https://doi.org/10.1186/s12916-021-01906-9; html:https://europepmc.org/articles/PMC7854026; pdf:https://europepmc.org/articles/PMC7854026?pdf=render"
+  },
   {
     "id": "30609404",
     "doi": "https://doi.org/10.1016/j.ajhg.2018.11.014",
@@ -40884,23 +40935,6 @@
     "laySummary": "",
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7885692; doi:https://doi.org/10.1016/j.mayocp.2021.02.007; html:https://europepmc.org/articles/PMC7885692; pdf:https://europepmc.org/articles/PMC7885692?pdf=render"
   },
-  {
-    "id": "33531015",
-    "doi": "https://doi.org/10.1186/s12916-021-01906-9",
-    "title": "The importance of supplementary immunisation activities to prevent measles outbreaks during the COVID-19 pandemic in Kenya.",
-    "authorString": "Mburu CN, Ojal J, Chebet R, Akech D, Karia B, Tuju J, Sigilai A, Abbas K, Jit M, Funk S, Smits G, van Gageldonk PGM, van der Klis FRM, Tabu C, Nokes DJ, LSHTM CMMID COVID-19 Working Group, Scott J, Flasche S, Adetifa I.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC medicine",
-    "pubYear": "2021",
-    "date": "2021-02-03",
-    "isOpenAccess": "Y",
-    "keywords": "outbreak; Measles; Vaccination Coverage; Supplementary Immunisation Activities; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>The COVID-19 pandemic has disrupted routine measles immunisation and supplementary immunisation activities (SIAs) in most countries including Kenya. We assessed the risk of measles outbreaks during the pandemic in Kenya as a case study for the African Region.<h4>Methods</h4>Combining measles serological data, local contact patterns, and vaccination coverage into a cohort model, we predicted the age-adjusted population immunity in Kenya and estimated the probability of outbreaks when contact-reducing COVID-19 interventions are lifted. We considered various scenarios for reduced measles vaccination coverage from April 2020.<h4>Results</h4>In February 2020, when a scheduled SIA was postponed, population immunity was close to the herd immunity threshold and the probability of a large outbreak was 34% (8-54). As the COVID-19 contact restrictions are nearly fully eased, from December 2020, the probability of a large measles outbreak will increase to 38% (19-54), 46% (30-59), and 54% (43-64) assuming a 15%, 50%, and 100% reduction in measles vaccination coverage. By December 2021, this risk increases further to 43% (25-56), 54% (43-63), and 67% (59-72) for the same coverage scenarios respectively. However, the increased risk of a measles outbreak following the lifting of all restrictions can be overcome by conducting a SIA with \u2265\u200995% coverage in under-fives.<h4>Conclusion</h4>While contact restrictions sufficient for SAR-CoV-2 control temporarily reduce measles transmissibility and the risk of an outbreak from a measles immunity gap, this risk rises rapidly once these restrictions are lifted. Implementing delayed SIAs will be critical for prevention of measles outbreaks given the roll-back of contact restrictions in Kenya.",
-    "laySummary": "",
-    "urls": "pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-021-01906-9; doi:https://doi.org/10.1186/s12916-021-01906-9; html:https://europepmc.org/articles/PMC7854026; pdf:https://europepmc.org/articles/PMC7854026?pdf=render"
-  },
   {
     "id": "38361499",
     "doi": "https://doi.org/10.26633/rpsp.2023.149",
@@ -40935,23 +40969,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ije/article-pdf/51/1/17/42555483/dyab149.pdf; doi:https://doi.org/10.1093/ije/dyab149; html:https://europepmc.org/articles/PMC8856003; pdf:https://europepmc.org/articles/PMC8856003?pdf=render"
   },
-  {
-    "id": "38296292",
-    "doi": "https://doi.org/10.1136/bmjopen-2023-078135",
-    "title": "Risk factor associations for severe COVID-19, influenza and pneumonia in people with diabetes to inform future pandemic preparations: UK population-based cohort study.",
-    "authorString": "Hopkins R, Young KG, Thomas NJ, Godwin J, Raja D, Mateen BA, Challen RJ, Vollmer SJ, Shields BM, McGovern AP, Dennis JM.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2024",
-    "date": "2024-01-31",
-    "isOpenAccess": "Y",
-    "keywords": "risk factors; Electronic Health Records; Diabetes & Endocrinology; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objective</h4>This study aimed to compare clinical and sociodemographic risk factors for severe COVID-19, influenza and pneumonia, in people with diabetes.<h4>Design</h4>Population-based cohort study.<h4>Setting</h4>UK primary care records (Clinical Practice Research Datalink) linked to mortality and hospital records.<h4>Participants</h4>Individuals with type 1 and type 2 diabetes (COVID-19 cohort: n=43\u2009033\u2009type 1 diabetes and n=584\u2009854\u2009type 2 diabetes, influenza and pneumonia cohort: n=42\u2009488\u2009type 1 diabetes and n=585\u2009289\u2009type 2 diabetes).<h4>Primary and secondary outcome measures</h4>COVID-19 hospitalisation from 1 February 2020 to 31 October 2020 (pre-COVID-19 vaccination roll-out), and influenza and pneumonia hospitalisation from 1 September 2016 to 31 May 2019 (pre-COVID-19 pandemic). Secondary outcomes were COVID-19 and pneumonia mortality. Associations between clinical and sociodemographic risk factors and each outcome were assessed using multivariable Cox proportional hazards models. In people with type 2 diabetes, we explored modifying effects of glycated haemoglobin (HbA1c) and body mass index (BMI) by age, sex and ethnicity.<h4>Results</h4>In type 2 diabetes, poor glycaemic control and severe obesity were consistently associated with increased risk of hospitalisation for COVID-19, influenza and pneumonia. The highest HbA1c and BMI-associated relative risks were observed in people aged under 70 years. Sociodemographic-associated risk differed markedly by respiratory infection, particularly for ethnicity. Compared with people of white ethnicity, black and south Asian groups had a greater risk of COVID-19 hospitalisation, but a lesser risk of pneumonia hospitalisation. Risk factor associations for type 1 diabetes and for type 2 diabetes mortality were broadly consistent with the primary analysis.<h4>Conclusions</h4>Clinical risk factors of high HbA1c and severe obesity are consistently associated with severe outcomes from COVID-19, influenza and pneumonia, especially in younger people. In contrast, associations with sociodemographic risk factors differed by type of respiratory infection. This emphasises that risk stratification should be specific to individual respiratory infections.",
-    "laySummary": "",
-    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/14/1/e078135.full.pdf; doi:https://doi.org/10.1136/bmjopen-2023-078135; html:https://europepmc.org/articles/PMC10831438; pdf:https://europepmc.org/articles/PMC10831438?pdf=render"
-  },
   {
     "id": "33777379",
     "doi": "https://doi.org/10.1093/ckj/sfaa045",
@@ -40969,6 +40986,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/ckj/article-pdf/14/3/950/36670473/sfaa045.pdf; doi:https://doi.org/10.1093/ckj/sfaa045; html:https://europepmc.org/articles/PMC7986362; pdf:https://europepmc.org/articles/PMC7986362?pdf=render"
   },
+  {
+    "id": "38296292",
+    "doi": "https://doi.org/10.1136/bmjopen-2023-078135",
+    "title": "Risk factor associations for severe COVID-19, influenza and pneumonia in people with diabetes to inform future pandemic preparations: UK population-based cohort study.",
+    "authorString": "Hopkins R, Young KG, Thomas NJ, Godwin J, Raja D, Mateen BA, Challen RJ, Vollmer SJ, Shields BM, McGovern AP, Dennis JM.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2024",
+    "date": "2024-01-31",
+    "isOpenAccess": "Y",
+    "keywords": "risk factors; Electronic Health Records; Diabetes & Endocrinology; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>This study aimed to compare clinical and sociodemographic risk factors for severe COVID-19, influenza and pneumonia, in people with diabetes.<h4>Design</h4>Population-based cohort study.<h4>Setting</h4>UK primary care records (Clinical Practice Research Datalink) linked to mortality and hospital records.<h4>Participants</h4>Individuals with type 1 and type 2 diabetes (COVID-19 cohort: n=43\u2009033\u2009type 1 diabetes and n=584\u2009854\u2009type 2 diabetes, influenza and pneumonia cohort: n=42\u2009488\u2009type 1 diabetes and n=585\u2009289\u2009type 2 diabetes).<h4>Primary and secondary outcome measures</h4>COVID-19 hospitalisation from 1 February 2020 to 31 October 2020 (pre-COVID-19 vaccination roll-out), and influenza and pneumonia hospitalisation from 1 September 2016 to 31 May 2019 (pre-COVID-19 pandemic). Secondary outcomes were COVID-19 and pneumonia mortality. Associations between clinical and sociodemographic risk factors and each outcome were assessed using multivariable Cox proportional hazards models. In people with type 2 diabetes, we explored modifying effects of glycated haemoglobin (HbA1c) and body mass index (BMI) by age, sex and ethnicity.<h4>Results</h4>In type 2 diabetes, poor glycaemic control and severe obesity were consistently associated with increased risk of hospitalisation for COVID-19, influenza and pneumonia. The highest HbA1c and BMI-associated relative risks were observed in people aged under 70 years. Sociodemographic-associated risk differed markedly by respiratory infection, particularly for ethnicity. Compared with people of white ethnicity, black and south Asian groups had a greater risk of COVID-19 hospitalisation, but a lesser risk of pneumonia hospitalisation. Risk factor associations for type 1 diabetes and for type 2 diabetes mortality were broadly consistent with the primary analysis.<h4>Conclusions</h4>Clinical risk factors of high HbA1c and severe obesity are consistently associated with severe outcomes from COVID-19, influenza and pneumonia, especially in younger people. In contrast, associations with sociodemographic risk factors differed by type of respiratory infection. This emphasises that risk stratification should be specific to individual respiratory infections.",
+    "laySummary": "",
+    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/14/1/e078135.full.pdf; doi:https://doi.org/10.1136/bmjopen-2023-078135; html:https://europepmc.org/articles/PMC10831438; pdf:https://europepmc.org/articles/PMC10831438?pdf=render"
+  },
   {
     "id": "34172543",
     "doi": "https://doi.org/10.1136/bmjopen-2020-042893",
@@ -41088,23 +41122,6 @@
     "laySummary": "",
     "urls": "pdf:https://bjgpopen.org/content/bjgpoa/5/4/BJGPO.2021.0020.full.pdf; doi:https://doi.org/10.3399/BJGPO.2021.0020; html:https://europepmc.org/articles/PMC8450889; pdf:https://europepmc.org/articles/PMC8450889?pdf=render"
   },
-  {
-    "id": "37918923",
-    "doi": "https://doi.org/10.1136/bmjopen-2023-072531",
-    "title": "Evaluation of variation in special educational needs provision and its impact on health and education using administrative records for England: umbrella protocol for a mixed-methods research programme.",
-    "authorString": "Zylbersztejn A, Lewis K, Nguyen V, Matthews J, Winterburn I, Karwatowska L, Barnes S, Lilliman M, Saxton J, Stone A, Boddy K, Downs J, Logan S, Rahi J, Black-Hawkins K, Dearden L, Ford T, Harron K, De Stavola B, Gilbert R.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2023",
-    "date": "2023-11-02",
-    "isOpenAccess": "Y",
-    "keywords": "epidemiology; Public Health; Qualitative Research; Health Informatics; Statistics & Research Methods; Health Equity",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>One-third of children in England have special educational needs (SEN) provision recorded during their school career. The proportion of children with SEN provision varies between schools and demographic groups, which may reflect variation in need, inequitable provision and/or systemic factors. There is scant evidence on whether SEN provision improves health and education outcomes.<h4>Methods</h4>The Health Outcomes of young People in Education (HOPE) research programme uses administrative data from the Education and Child Health Insights from Linked Data-ECHILD-which contains data from all state schools, and contacts with National Health Service hospitals in England, to explore variation in SEN provision and its impact on health and education outcomes. This umbrella protocol sets out analyses across four work packages (WP). WP1 defined a range of 'health phenotypes', that is health conditions expected to need SEN provision in primary school. Next, we describe health and education outcomes (WP1) and individual, school-level and area-level factors affecting variation in SEN provision across different phenotypes (WP2). WP3 assesses the impact of SEN provision on health and education outcomes for specific health phenotypes using a range of causal inference methods to account for confounding factors and possible selection bias. In WP4 we review local policies and synthesise findings from surveys, interviews and focus groups of service users and providers to understand factors associated with variation in and experiences of identification, assessment and provision for SEN. Triangulation of findings on outcomes, variation and impact of SEN provision for different health phenotypes in ECHILD, with experiences of SEN provision will inform interpretation of findings for policy, practice and families and methods for future evaluation.<h4>Ethics and dissemination</h4>Research ethics committees have approved the use of the ECHILD database and, separately, the survey, interviews and focus groups of young people, parents and service providers. These stakeholders will contribute to the design, interpretation and communication of findings.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1136/bmjopen-2023-072531; html:https://europepmc.org/articles/PMC10626865; pdf:https://europepmc.org/articles/PMC10626865?pdf=render"
-  },
   {
     "id": "30681347",
     "doi": "https://doi.org/10.1161/circgen.118.002328",
@@ -41122,6 +41139,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCGEN.118.002328; doi:https://doi.org/10.1161/CIRCGEN.118.002328; html:https://europepmc.org/articles/PMC6380958; pdf:https://europepmc.org/articles/PMC6380958?pdf=render; doi:https://doi.org/10.1161/circgen.118.002328"
   },
+  {
+    "id": "37918923",
+    "doi": "https://doi.org/10.1136/bmjopen-2023-072531",
+    "title": "Evaluation of variation in special educational needs provision and its impact on health and education using administrative records for England: umbrella protocol for a mixed-methods research programme.",
+    "authorString": "Zylbersztejn A, Lewis K, Nguyen V, Matthews J, Winterburn I, Karwatowska L, Barnes S, Lilliman M, Saxton J, Stone A, Boddy K, Downs J, Logan S, Rahi J, Black-Hawkins K, Dearden L, Ford T, Harron K, De Stavola B, Gilbert R.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2023",
+    "date": "2023-11-02",
+    "isOpenAccess": "Y",
+    "keywords": "epidemiology; Public Health; Qualitative Research; Health Informatics; Statistics & Research Methods; Health Equity",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>One-third of children in England have special educational needs (SEN) provision recorded during their school career. The proportion of children with SEN provision varies between schools and demographic groups, which may reflect variation in need, inequitable provision and/or systemic factors. There is scant evidence on whether SEN provision improves health and education outcomes.<h4>Methods</h4>The Health Outcomes of young People in Education (HOPE) research programme uses administrative data from the Education and Child Health Insights from Linked Data-ECHILD-which contains data from all state schools, and contacts with National Health Service hospitals in England, to explore variation in SEN provision and its impact on health and education outcomes. This umbrella protocol sets out analyses across four work packages (WP). WP1 defined a range of 'health phenotypes', that is health conditions expected to need SEN provision in primary school. Next, we describe health and education outcomes (WP1) and individual, school-level and area-level factors affecting variation in SEN provision across different phenotypes (WP2). WP3 assesses the impact of SEN provision on health and education outcomes for specific health phenotypes using a range of causal inference methods to account for confounding factors and possible selection bias. In WP4 we review local policies and synthesise findings from surveys, interviews and focus groups of service users and providers to understand factors associated with variation in and experiences of identification, assessment and provision for SEN. Triangulation of findings on outcomes, variation and impact of SEN provision for different health phenotypes in ECHILD, with experiences of SEN provision will inform interpretation of findings for policy, practice and families and methods for future evaluation.<h4>Ethics and dissemination</h4>Research ethics committees have approved the use of the ECHILD database and, separately, the survey, interviews and focus groups of young people, parents and service providers. These stakeholders will contribute to the design, interpretation and communication of findings.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1136/bmjopen-2023-072531; html:https://europepmc.org/articles/PMC10626865; pdf:https://europepmc.org/articles/PMC10626865?pdf=render"
+  },
   {
     "id": "34810237",
     "doi": "https://doi.org/10.1136/thoraxjnl-2021-217629",
@@ -41225,21 +41259,21 @@
     "urls": "pdf:https://www.researchprotocols.org/2022/2/e31885/PDF; doi:https://doi.org/10.2196/31885; html:https://europepmc.org/articles/PMC8874931"
   },
   {
-    "id": "35545669",
-    "doi": "https://doi.org/10.1038/s41586-022-04712-2",
-    "title": "Genetic and chemotherapeutic influences on germline hypermutation.",
-    "authorString": "Kaplanis J, Ide B, Sanghvi R, Neville M, Danecek P, Coorens T, Prigmore E, Short P, Gallone G, McRae J, Genomics England Research Consortium, Carmichael J, Barnicoat A, Firth H, O'Brien P, Rahbari R, Hurles M.",
+    "id": "32184442",
+    "doi": "https://doi.org/10.1038/s42003-020-0857-9",
+    "title": "Genome-wide association identifies seven loci for pelvic organ prolapse in Iceland and the UK Biobank.",
+    "authorString": "Olafsdottir T, Thorleifsson G, Sulem P, Stefansson OA, Medek H, Olafsson K, Ingthorsson O, Gudmundsson V, Jonsdottir I, Halldorsson GH, Kristjansson RP, Frigge ML, Stefansdottir L, Sigurdsson JK, Oddsson A, Sigurdsson A, Eggertsson HP, Melsted P, Halldorsson BV, Lund SH, Styrkarsdottir U, Steinthorsdottir V, Gudmundsson J, Holm H, Tragante V, Asselbergs FW, Thorsteinsdottir U, Gudbjartsson DF, Jonsdottir K, Rafnar T, Stefansson K.",
     "authorAffiliations": "",
-    "journalTitle": "Nature",
-    "pubYear": "2022",
-    "date": "2022-05-11",
+    "journalTitle": "Communications biology",
+    "pubYear": "2020",
+    "date": "2020-03-17",
     "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Mutations in the germline generates all evolutionary genetic variation and is a cause of genetic disease. Parental age is the primary determinant of the number of new germline mutations in an individual's genome<sup>1,2</sup>. Here we analysed the genome-wide sequences of 21,879 families with rare genetic diseases and identified 12 individuals with a hypermutated genome with between two and seven times more de novo single-nucleotide variants than expected. In most families (9 out of 12), the excess mutations came from the father. Two families had genetic drivers of germline hypermutation, with fathers carrying damaging genetic variation in DNA-repair genes. For five of the families, paternal exposure to chemotherapeutic agents before conception was probably a key driver of hypermutation. Our results suggest that the germline is well protected from mutagenic effects, hypermutation is rare, the number of excess\u00a0mutations is relatively modest and most individuals with a hypermutated genome will not have a genetic disease.",
+    "abstract": "Pelvic organ prolapse (POP) is a downward descent of one or more of the pelvic organs, resulting in a protrusion of the vaginal wall and/or uterus. We performed a genome-wide association study of POP using data from Iceland and the UK Biobank, a total of 15,010 cases with hospital-based diagnosis code and 340,734 female controls, and found eight sequence variants at seven loci associating with POP (P\u2009<\u20095 \u00d7 10<sup>-8</sup>); seven common (minor allele frequency >5%) and one with minor allele frequency of 4.87%. Some of the variants associating with POP also associated with traits of similar pathophysiology. Of these, rs3820282, which may alter the estrogen-based regulation of WNT4, also associates with leiomyoma of uterus, gestational duration and endometriosis. Rs3791675 at EFEMP1, a gene involved in connective tissue homeostasis, also associates with hernias and carpal tunnel syndrome. Our results highlight the role of connective tissue metabolism and estrogen exposure in the etiology of POP.",
     "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41586-022-04712-2.pdf; doi:https://doi.org/10.1038/s41586-022-04712-2; html:https://europepmc.org/articles/PMC9117138; pdf:https://europepmc.org/articles/PMC9117138?pdf=render"
+    "urls": "pdf:https://www.nature.com/articles/s42003-020-0857-9.pdf; doi:https://doi.org/10.1038/s42003-020-0857-9; html:https://europepmc.org/articles/PMC7078216; pdf:https://europepmc.org/articles/PMC7078216?pdf=render"
   },
   {
     "id": "31794059",
@@ -41259,21 +41293,21 @@
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/bjd.18778; doi:https://doi.org/10.1111/bjd.18778; html:https://europepmc.org/articles/PMC7496176; pdf:https://europepmc.org/articles/PMC7496176?pdf=render"
   },
   {
-    "id": "32184442",
-    "doi": "https://doi.org/10.1038/s42003-020-0857-9",
-    "title": "Genome-wide association identifies seven loci for pelvic organ prolapse in Iceland and the UK Biobank.",
-    "authorString": "Olafsdottir T, Thorleifsson G, Sulem P, Stefansson OA, Medek H, Olafsson K, Ingthorsson O, Gudmundsson V, Jonsdottir I, Halldorsson GH, Kristjansson RP, Frigge ML, Stefansdottir L, Sigurdsson JK, Oddsson A, Sigurdsson A, Eggertsson HP, Melsted P, Halldorsson BV, Lund SH, Styrkarsdottir U, Steinthorsdottir V, Gudmundsson J, Holm H, Tragante V, Asselbergs FW, Thorsteinsdottir U, Gudbjartsson DF, Jonsdottir K, Rafnar T, Stefansson K.",
+    "id": "35545669",
+    "doi": "https://doi.org/10.1038/s41586-022-04712-2",
+    "title": "Genetic and chemotherapeutic influences on germline hypermutation.",
+    "authorString": "Kaplanis J, Ide B, Sanghvi R, Neville M, Danecek P, Coorens T, Prigmore E, Short P, Gallone G, McRae J, Genomics England Research Consortium, Carmichael J, Barnicoat A, Firth H, O'Brien P, Rahbari R, Hurles M.",
     "authorAffiliations": "",
-    "journalTitle": "Communications biology",
-    "pubYear": "2020",
-    "date": "2020-03-17",
+    "journalTitle": "Nature",
+    "pubYear": "2022",
+    "date": "2022-05-11",
     "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Pelvic organ prolapse (POP) is a downward descent of one or more of the pelvic organs, resulting in a protrusion of the vaginal wall and/or uterus. We performed a genome-wide association study of POP using data from Iceland and the UK Biobank, a total of 15,010 cases with hospital-based diagnosis code and 340,734 female controls, and found eight sequence variants at seven loci associating with POP (P\u2009<\u20095 \u00d7 10<sup>-8</sup>); seven common (minor allele frequency >5%) and one with minor allele frequency of 4.87%. Some of the variants associating with POP also associated with traits of similar pathophysiology. Of these, rs3820282, which may alter the estrogen-based regulation of WNT4, also associates with leiomyoma of uterus, gestational duration and endometriosis. Rs3791675 at EFEMP1, a gene involved in connective tissue homeostasis, also associates with hernias and carpal tunnel syndrome. Our results highlight the role of connective tissue metabolism and estrogen exposure in the etiology of POP.",
+    "abstract": "Mutations in the germline generates all evolutionary genetic variation and is a cause of genetic disease. Parental age is the primary determinant of the number of new germline mutations in an individual's genome<sup>1,2</sup>. Here we analysed the genome-wide sequences of 21,879 families with rare genetic diseases and identified 12 individuals with a hypermutated genome with between two and seven times more de novo single-nucleotide variants than expected. In most families (9 out of 12), the excess mutations came from the father. Two families had genetic drivers of germline hypermutation, with fathers carrying damaging genetic variation in DNA-repair genes. For five of the families, paternal exposure to chemotherapeutic agents before conception was probably a key driver of hypermutation. Our results suggest that the germline is well protected from mutagenic effects, hypermutation is rare, the number of excess\u00a0mutations is relatively modest and most individuals with a hypermutated genome will not have a genetic disease.",
     "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s42003-020-0857-9.pdf; doi:https://doi.org/10.1038/s42003-020-0857-9; html:https://europepmc.org/articles/PMC7078216; pdf:https://europepmc.org/articles/PMC7078216?pdf=render"
+    "urls": "pdf:https://www.nature.com/articles/s41586-022-04712-2.pdf; doi:https://doi.org/10.1038/s41586-022-04712-2; html:https://europepmc.org/articles/PMC9117138; pdf:https://europepmc.org/articles/PMC9117138?pdf=render"
   },
   {
     "id": "35962208",
@@ -41411,23 +41445,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1002/ajmg.b.32938; html:https://europepmc.org/articles/PMC10952822; pdf:https://europepmc.org/articles/PMC10952822?pdf=render"
   },
-  {
-    "id": "35879886",
-    "doi": "https://doi.org/10.1017/s0033291722002501",
-    "title": "Depression, anxiety and PTSD symptoms before and during the COVID-19 pandemic in the UK.",
-    "authorString": "Young KS, Purves KL, H\u00fcbel C, Davies MR, Thompson KN, Bristow S, Krebs G, Danese A, Hirsch C, Parsons CE, Vassos E, Adey BN, Bright S, Hegemann L, Lee YT, Kalsi G, Monssen D, Mundy J, Peel AJ, Rayner C, Rogers HC, Ter Kuile A, Ward C, York K, Lin Y, Palmos AB, Schmidt U, Veale D, Nicholson TR, Pollak TA, Stevelink SAM, Moukhtarian T, Martineau AR, Holt H, Maughan B, Al-Chalabi A, Chaudhuri KR, Richardson MP, Bradley JR, Chinnery PF, Kingston N, Papadia S, Stirrups KE, Linger R, Hotopf M, Eley TC, Breen G.",
-    "authorAffiliations": "",
-    "journalTitle": "Psychological medicine",
-    "pubYear": "2023",
-    "date": "2022-07-26",
-    "isOpenAccess": "Y",
-    "keywords": "Depression; Anxiety; Ptsd; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>The impact of the coronavirus disease 2019 (COVID-19) pandemic on mental health is still being unravelled. It is important to identify which individuals are at greatest risk of worsening symptoms. This study aimed to examine changes in depression, anxiety and post-traumatic stress disorder (PTSD) symptoms using prospective and retrospective symptom change assessments, and to find and examine the effect of key risk factors.<h4>Method</h4>Online questionnaires were administered to 34 465 individuals (aged 16 years or above) in April/May 2020 in the UK, recruited from existing cohorts or via social media. Around one-third (<i>n</i> = 12 718) of included participants had prior diagnoses of depression or anxiety and had completed pre-pandemic mental health assessments (between September 2018 and February 2020), allowing prospective investigation of symptom change.<h4>Results</h4>Prospective symptom analyses showed small decreases in depression (PHQ-9: -0.43 points) and anxiety [generalised anxiety disorder scale - 7 items (GAD)-7: -0.33 points] and increases in PTSD (PCL-6: 0.22 points). Conversely, retrospective symptom analyses demonstrated significant large increases (PHQ-9: 2.40; GAD-7 = 1.97), with 55% reported worsening mental health since the beginning of the pandemic on a global change rating. Across both prospective and retrospective measures of symptom change, worsening depression, anxiety and PTSD symptoms were associated with prior mental health diagnoses, female gender, young age and unemployed/student status.<h4>Conclusions</h4>We highlight the effect of prior mental health diagnoses on worsening mental health during the pandemic and confirm previously reported sociodemographic risk factors. Discrepancies between prospective and retrospective measures of changes in mental health may be related to recall bias-related underestimation of prior symptom severity.",
-    "laySummary": "",
-    "urls": "pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/8C3760ED596F1ED8B80F729AC5E47B9B/S0033291722002501a.pdf/div-class-title-depression-anxiety-and-ptsd-symptoms-before-and-during-the-covid-19-pandemic-in-the-uk-div.pdf; doi:https://doi.org/10.1017/S0033291722002501; html:https://europepmc.org/articles/PMC10482709; pdf:https://europepmc.org/articles/PMC10482709?pdf=render"
-  },
   {
     "id": "32862087",
     "doi": "https://doi.org/10.1016/j.atherosclerosis.2020.07.014",
@@ -41445,6 +41462,23 @@
     "laySummary": "",
     "urls": "pdf:http://www.atherosclerosis-journal.com/article/S0021915020303816/pdf; doi:https://doi.org/10.1016/j.atherosclerosis.2020.07.014"
   },
+  {
+    "id": "35879886",
+    "doi": "https://doi.org/10.1017/s0033291722002501",
+    "title": "Depression, anxiety and PTSD symptoms before and during the COVID-19 pandemic in the UK.",
+    "authorString": "Young KS, Purves KL, H\u00fcbel C, Davies MR, Thompson KN, Bristow S, Krebs G, Danese A, Hirsch C, Parsons CE, Vassos E, Adey BN, Bright S, Hegemann L, Lee YT, Kalsi G, Monssen D, Mundy J, Peel AJ, Rayner C, Rogers HC, Ter Kuile A, Ward C, York K, Lin Y, Palmos AB, Schmidt U, Veale D, Nicholson TR, Pollak TA, Stevelink SAM, Moukhtarian T, Martineau AR, Holt H, Maughan B, Al-Chalabi A, Chaudhuri KR, Richardson MP, Bradley JR, Chinnery PF, Kingston N, Papadia S, Stirrups KE, Linger R, Hotopf M, Eley TC, Breen G.",
+    "authorAffiliations": "",
+    "journalTitle": "Psychological medicine",
+    "pubYear": "2023",
+    "date": "2022-07-26",
+    "isOpenAccess": "Y",
+    "keywords": "Depression; Anxiety; Ptsd; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>The impact of the coronavirus disease 2019 (COVID-19) pandemic on mental health is still being unravelled. It is important to identify which individuals are at greatest risk of worsening symptoms. This study aimed to examine changes in depression, anxiety and post-traumatic stress disorder (PTSD) symptoms using prospective and retrospective symptom change assessments, and to find and examine the effect of key risk factors.<h4>Method</h4>Online questionnaires were administered to 34 465 individuals (aged 16 years or above) in April/May 2020 in the UK, recruited from existing cohorts or via social media. Around one-third (<i>n</i> = 12 718) of included participants had prior diagnoses of depression or anxiety and had completed pre-pandemic mental health assessments (between September 2018 and February 2020), allowing prospective investigation of symptom change.<h4>Results</h4>Prospective symptom analyses showed small decreases in depression (PHQ-9: -0.43 points) and anxiety [generalised anxiety disorder scale - 7 items (GAD)-7: -0.33 points] and increases in PTSD (PCL-6: 0.22 points). Conversely, retrospective symptom analyses demonstrated significant large increases (PHQ-9: 2.40; GAD-7 = 1.97), with 55% reported worsening mental health since the beginning of the pandemic on a global change rating. Across both prospective and retrospective measures of symptom change, worsening depression, anxiety and PTSD symptoms were associated with prior mental health diagnoses, female gender, young age and unemployed/student status.<h4>Conclusions</h4>We highlight the effect of prior mental health diagnoses on worsening mental health during the pandemic and confirm previously reported sociodemographic risk factors. Discrepancies between prospective and retrospective measures of changes in mental health may be related to recall bias-related underestimation of prior symptom severity.",
+    "laySummary": "",
+    "urls": "pdf:https://www.cambridge.org/core/services/aop-cambridge-core/content/view/8C3760ED596F1ED8B80F729AC5E47B9B/S0033291722002501a.pdf/div-class-title-depression-anxiety-and-ptsd-symptoms-before-and-during-the-covid-19-pandemic-in-the-uk-div.pdf; doi:https://doi.org/10.1017/S0033291722002501; html:https://europepmc.org/articles/PMC10482709; pdf:https://europepmc.org/articles/PMC10482709?pdf=render"
+  },
   {
     "id": "32505923",
     "doi": "https://doi.org/10.1016/j.ebiom.2020.102818",
@@ -41598,23 +41632,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.aucc.2021.05.013"
   },
-  {
-    "id": "36608816",
-    "doi": "https://doi.org/10.1016/j.diabet.2022.101418",
-    "title": "Empagliflozin cardiovascular and renal effectiveness and safety compared to dipeptidyl peptidase-4 inhibitors across 11 countries in Europe and Asia: Results from the EMPagliflozin compaRative effectIveness and SafEty (EMPRISE) study.",
-    "authorString": "Karasik A, Lanzinger S, Chia-Hui Tan E, Yabe D, Kim DJ, Sheu WH, Melzer-Cohen C, Holl RW, Ha KH, Khunti K, Zaccardi F, Subramanian A, Nirantharakumar K, Nystr\u00f6m T, Niskanen L, Linnemann Jensen M, Hoti F, Klement R, D\u00e9ruaz-Luyet A, Kyaw MH, Koeneman L, Vistisen D, Carstensen B, Halvorsen S, Langslet G, Fazeli Farsani S, Patorno E, N\u00fa\u00f1ez J, EMPRISE Europe and Asia Study Group.",
-    "authorAffiliations": "",
-    "journalTitle": "Diabetes & metabolism",
-    "pubYear": "2023",
-    "date": "2023-01-03",
-    "isOpenAccess": "N",
-    "keywords": "Cardiovascular diseases; Meta-analysis; Heart Failure; All-cause Mortality; Pharmacoepidemiology; Observational Study; Comparative Effectiveness; Dipeptidyl Peptidase-4 Inhibitors; Empagliflozin; Sodium-glucose Transporter 2 Inhibitors",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Continued expansion of indications for sodium-glucose cotransporter-2 inhibitors increases importance of evaluating cardiovascular and kidney efficacy and safety of empagliflozin in patients with type 2 diabetes compared to similar therapies.<h4>Methods</h4>The EMPRISE Europe and Asia study is a non-interventional cohort study using data from 2014-2019 in seven European (Denmark, Finland, Germany, Norway, Spain, Sweden, United Kingdom) and four Asian (Israel, Japan, South Korea, Taiwan) countries. Patients with type 2 diabetes initiating empagliflozin were 1:1 propensity score matched to patients initiating dipeptidyl peptidase-4 inhibitors. Primary endpoints included hospitalization for heart failure, all-cause mortality, myocardial infarction and stroke. Other cardiovascular, renal, and safety outcomes were examined.<h4>Findings</h4>Among 83,946 matched patient pairs, (0\u00b77 years overall mean follow-up time), initiation of empagliflozin was associated with lower risk of hospitalization for heart failure compared to dipeptidyl peptidase-4 inhibitors (Hazard Ratio 0\u00b770; 95% CI 0.60 to 0.83). Risks of all-cause mortality (0\u00b755; 0\u00b748 to 0\u00b763), stroke (0\u00b782; 0\u00b771 to 0\u00b796), and end-stage renal disease (0\u00b743; 0\u00b730 to 0\u00b763) were lower and risk for myocardial infarction, bone fracture, severe hypoglycemia, and lower-limb amputation were similar between initiators of empagliflozin and dipeptidyl peptidase-4 inhibitors. Initiation of empagliflozin was associated with higher risk for diabetic ketoacidosis (1\u00b797; 1\u00b728 to 3\u00b703) compared to dipeptidyl peptidase-4 inhibitors. Results were consistent across continents and regions.<h4>Interpretation</h4>Results from this EMPRISE Europe and Asia study complements previous clinical trials and real-world studies by providing further evidence of the beneficial cardiorenal effects and overall safety of empagliflozin compared to dipeptidyl peptidase-4 inhibitors.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.diabet.2022.101418; doi:https://doi.org/10.1016/j.diabet.2022.101418"
-  },
   {
     "id": "32681152",
     "doi": "https://doi.org/10.1038/s41596-020-0343-3",
@@ -41632,6 +41649,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1038/s41596-020-0343-3"
   },
+  {
+    "id": "36608816",
+    "doi": "https://doi.org/10.1016/j.diabet.2022.101418",
+    "title": "Empagliflozin cardiovascular and renal effectiveness and safety compared to dipeptidyl peptidase-4 inhibitors across 11 countries in Europe and Asia: Results from the EMPagliflozin compaRative effectIveness and SafEty (EMPRISE) study.",
+    "authorString": "Karasik A, Lanzinger S, Chia-Hui Tan E, Yabe D, Kim DJ, Sheu WH, Melzer-Cohen C, Holl RW, Ha KH, Khunti K, Zaccardi F, Subramanian A, Nirantharakumar K, Nystr\u00f6m T, Niskanen L, Linnemann Jensen M, Hoti F, Klement R, D\u00e9ruaz-Luyet A, Kyaw MH, Koeneman L, Vistisen D, Carstensen B, Halvorsen S, Langslet G, Fazeli Farsani S, Patorno E, N\u00fa\u00f1ez J, EMPRISE Europe and Asia Study Group.",
+    "authorAffiliations": "",
+    "journalTitle": "Diabetes & metabolism",
+    "pubYear": "2023",
+    "date": "2023-01-03",
+    "isOpenAccess": "N",
+    "keywords": "Cardiovascular diseases; Meta-analysis; Heart Failure; All-cause Mortality; Pharmacoepidemiology; Observational Study; Comparative Effectiveness; Dipeptidyl Peptidase-4 Inhibitors; Empagliflozin; Sodium-glucose Transporter 2 Inhibitors",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Continued expansion of indications for sodium-glucose cotransporter-2 inhibitors increases importance of evaluating cardiovascular and kidney efficacy and safety of empagliflozin in patients with type 2 diabetes compared to similar therapies.<h4>Methods</h4>The EMPRISE Europe and Asia study is a non-interventional cohort study using data from 2014-2019 in seven European (Denmark, Finland, Germany, Norway, Spain, Sweden, United Kingdom) and four Asian (Israel, Japan, South Korea, Taiwan) countries. Patients with type 2 diabetes initiating empagliflozin were 1:1 propensity score matched to patients initiating dipeptidyl peptidase-4 inhibitors. Primary endpoints included hospitalization for heart failure, all-cause mortality, myocardial infarction and stroke. Other cardiovascular, renal, and safety outcomes were examined.<h4>Findings</h4>Among 83,946 matched patient pairs, (0\u00b77 years overall mean follow-up time), initiation of empagliflozin was associated with lower risk of hospitalization for heart failure compared to dipeptidyl peptidase-4 inhibitors (Hazard Ratio 0\u00b770; 95% CI 0.60 to 0.83). Risks of all-cause mortality (0\u00b755; 0\u00b748 to 0\u00b763), stroke (0\u00b782; 0\u00b771 to 0\u00b796), and end-stage renal disease (0\u00b743; 0\u00b730 to 0\u00b763) were lower and risk for myocardial infarction, bone fracture, severe hypoglycemia, and lower-limb amputation were similar between initiators of empagliflozin and dipeptidyl peptidase-4 inhibitors. Initiation of empagliflozin was associated with higher risk for diabetic ketoacidosis (1\u00b797; 1\u00b728 to 3\u00b703) compared to dipeptidyl peptidase-4 inhibitors. Results were consistent across continents and regions.<h4>Interpretation</h4>Results from this EMPRISE Europe and Asia study complements previous clinical trials and real-world studies by providing further evidence of the beneficial cardiorenal effects and overall safety of empagliflozin compared to dipeptidyl peptidase-4 inhibitors.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.diabet.2022.101418; doi:https://doi.org/10.1016/j.diabet.2022.101418"
+  },
   {
     "id": "32935027",
     "doi": "https://doi.org/10.23889/ijpds.v4i1.1093",
@@ -41751,23 +41785,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.neuroimage.2019.02.028; doi:https://doi.org/10.1016/j.neuroimage.2019.02.028; html:https://europepmc.org/articles/PMC6503942"
   },
-  {
-    "id": "32097451",
-    "doi": "https://doi.org/10.1093/ije/dyaa015",
-    "title": "Commentary: Using human genetics to guide the repurposing of medicines.",
-    "authorString": "Bovijn J, Censin JC, Lindgren CM, Holmes MV.",
-    "authorAffiliations": "",
-    "journalTitle": "International journal of epidemiology",
-    "pubYear": "2020",
-    "date": "2020-08-01",
-    "isOpenAccess": "N",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/ije/article-pdf/49/4/1140/34275903/dyaa015.pdf; doi:https://doi.org/10.1093/ije/dyaa015; html:https://europepmc.org/articles/PMC7660148; pdf:https://europepmc.org/articles/PMC7660148?pdf=render; doi:https://doi.org/10.1093/ije/dyaa015"
-  },
   {
     "id": "31063847",
     "doi": "https://doi.org/10.1016/j.bbi.2019.05.009",
@@ -41785,6 +41802,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.bbi.2019.05.009; doi:https://doi.org/10.1016/j.bbi.2019.05.009"
   },
+  {
+    "id": "32097451",
+    "doi": "https://doi.org/10.1093/ije/dyaa015",
+    "title": "Commentary: Using human genetics to guide the repurposing of medicines.",
+    "authorString": "Bovijn J, Censin JC, Lindgren CM, Holmes MV.",
+    "authorAffiliations": "",
+    "journalTitle": "International journal of epidemiology",
+    "pubYear": "2020",
+    "date": "2020-08-01",
+    "isOpenAccess": "N",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/ije/article-pdf/49/4/1140/34275903/dyaa015.pdf; doi:https://doi.org/10.1093/ije/dyaa015; html:https://europepmc.org/articles/PMC7660148; pdf:https://europepmc.org/articles/PMC7660148?pdf=render; doi:https://doi.org/10.1093/ije/dyaa015"
+  },
   {
     "id": "34039579",
     "doi": "https://doi.org/10.1136/bmjopen-2021-049721",
@@ -41870,23 +41904,6 @@
     "laySummary": "",
     "urls": "pdf:http://spiral.imperial.ac.uk/bitstream/10044/1/95846/7/1-s2.0-S1201971222001291-main.pdf; doi:https://doi.org/10.1016/j.ijid.2022.02.051; html:https://europepmc.org/articles/PMC8882068; pdf:https://europepmc.org/articles/PMC8882068?pdf=render"
   },
-  {
-    "id": "34796246",
-    "doi": "https://doi.org/10.1093/ofid/ofab496",
-    "title": "Acceptability, Usability, and Performance of Lateral Flow Immunoassay Tests for Severe Acute Respiratory Syndrome Coronavirus 2 Antibodies: REACT-2 Study of Self-Testing in Nonhealthcare Key Workers.",
-    "authorString": "Davies B, Araghi M, Moshe M, Gao H, Bennet K, Jenkins J, Atchison C, Darzi A, Ashby D, Riley S, Barclay W, Elliott P, Ward H, Cooke G.",
-    "authorAffiliations": "",
-    "journalTitle": "Open forum infectious diseases",
-    "pubYear": "2021",
-    "date": "2021-10-04",
-    "isOpenAccess": "Y",
-    "keywords": "Sensitivity and specificity; Antibody testing; Sars-cov-2; Covid-19 Diagnostic Testing",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Seroprevalence studies are essential to understand the epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Various technologies, including laboratory assays and point-of-care self-tests, are available for antibody testing. The interpretation of seroprevalence studies requires comparative data on the performance of antibody tests.<h4>Methods</h4>In June 2020, current and former members of the United Kingdom police forces and fire service performed a self-test lateral flow immunoassay (LFIA), had a nurse-performed LFIA, and provided a venous blood sample for enzyme-linked immunosorbent assay (ELISA). We present the prevalence of antibodies to SARS-CoV-2 and the acceptability and usability of self-test LFIAs, and we determine the sensitivity and specificity of LFIAs compared with laboratory ELISA.<h4>Results</h4>In this cohort of 5189 current and former members of the police service and 263 members of the fire service, 7.4% (396 of 5348; 95% confidence interval [CI], 6.7-8.1) were antibody positive. Seroprevalence was 8.9% (95% CI, 6.9-11.4) in those under 40 years, 11.5% (95% CI, 8.8-15.0) in those of nonwhite ethnicity, and 7.8% (95% CI, 7.1-8.7) in those currently working. Self-test LFIA had an acceptability of 97.7% and a usability of 90.0%. There was substantial agreement between within-participant LFIA results (kappa 0.80; 95% CI, 0.77-0.83). The LFIAs had a similar performance: compared with ELISA, sensitivity was 82.1% (95% CI, 77.7-86.0) self-test and 76.4% (95% CI, 71.9-80.5) nurse-performed with specificity of 97.8% (95% CI, 97.3-98.2) and 98.5% (95% CI, 98.1-98.8), respectively.<h4>Conclusions</h4>A greater proportion of this nonhealthcare key worker cohort showed evidence of previous infection with SARS-CoV-2 than the general population at 6.0% (95% CI, 5.8-6.1) after the first wave in England. The high acceptability and usability reported by participants and similar performance of self-test and nurse-performed LFIAs indicate that the self-test LFIA is fit for purpose for home testing in occupational and community prevalence studies.",
-    "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/ofid/article-pdf/8/11/ofab496/41174715/ofab496.pdf; doi:https://doi.org/10.1093/ofid/ofab496; html:https://europepmc.org/articles/PMC8522420; pdf:https://europepmc.org/articles/PMC8522420?pdf=render"
-  },
   {
     "id": "31013802",
     "doi": "https://doi.org/10.3390/ijerph16081325",
@@ -41904,6 +41921,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.mdpi.com/1660-4601/16/8/1325/pdf?version=1555077276; doi:https://doi.org/10.3390/ijerph16081325; html:https://europepmc.org/articles/PMC6517898; pdf:https://europepmc.org/articles/PMC6517898?pdf=render"
   },
+  {
+    "id": "34796246",
+    "doi": "https://doi.org/10.1093/ofid/ofab496",
+    "title": "Acceptability, Usability, and Performance of Lateral Flow Immunoassay Tests for Severe Acute Respiratory Syndrome Coronavirus 2 Antibodies: REACT-2 Study of Self-Testing in Nonhealthcare Key Workers.",
+    "authorString": "Davies B, Araghi M, Moshe M, Gao H, Bennet K, Jenkins J, Atchison C, Darzi A, Ashby D, Riley S, Barclay W, Elliott P, Ward H, Cooke G.",
+    "authorAffiliations": "",
+    "journalTitle": "Open forum infectious diseases",
+    "pubYear": "2021",
+    "date": "2021-10-04",
+    "isOpenAccess": "Y",
+    "keywords": "Sensitivity and specificity; Antibody testing; Sars-cov-2; Covid-19 Diagnostic Testing",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Seroprevalence studies are essential to understand the epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Various technologies, including laboratory assays and point-of-care self-tests, are available for antibody testing. The interpretation of seroprevalence studies requires comparative data on the performance of antibody tests.<h4>Methods</h4>In June 2020, current and former members of the United Kingdom police forces and fire service performed a self-test lateral flow immunoassay (LFIA), had a nurse-performed LFIA, and provided a venous blood sample for enzyme-linked immunosorbent assay (ELISA). We present the prevalence of antibodies to SARS-CoV-2 and the acceptability and usability of self-test LFIAs, and we determine the sensitivity and specificity of LFIAs compared with laboratory ELISA.<h4>Results</h4>In this cohort of 5189 current and former members of the police service and 263 members of the fire service, 7.4% (396 of 5348; 95% confidence interval [CI], 6.7-8.1) were antibody positive. Seroprevalence was 8.9% (95% CI, 6.9-11.4) in those under 40 years, 11.5% (95% CI, 8.8-15.0) in those of nonwhite ethnicity, and 7.8% (95% CI, 7.1-8.7) in those currently working. Self-test LFIA had an acceptability of 97.7% and a usability of 90.0%. There was substantial agreement between within-participant LFIA results (kappa 0.80; 95% CI, 0.77-0.83). The LFIAs had a similar performance: compared with ELISA, sensitivity was 82.1% (95% CI, 77.7-86.0) self-test and 76.4% (95% CI, 71.9-80.5) nurse-performed with specificity of 97.8% (95% CI, 97.3-98.2) and 98.5% (95% CI, 98.1-98.8), respectively.<h4>Conclusions</h4>A greater proportion of this nonhealthcare key worker cohort showed evidence of previous infection with SARS-CoV-2 than the general population at 6.0% (95% CI, 5.8-6.1) after the first wave in England. The high acceptability and usability reported by participants and similar performance of self-test and nurse-performed LFIAs indicate that the self-test LFIA is fit for purpose for home testing in occupational and community prevalence studies.",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/ofid/article-pdf/8/11/ofab496/41174715/ofab496.pdf; doi:https://doi.org/10.1093/ofid/ofab496; html:https://europepmc.org/articles/PMC8522420; pdf:https://europepmc.org/articles/PMC8522420?pdf=render"
+  },
   {
     "id": "37188768",
     "doi": "https://doi.org/10.1038/s42003-023-04836-9",
@@ -41989,23 +42023,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.eclinm.2023.101932; doi:https://doi.org/10.1016/j.eclinm.2023.101932; html:https://europepmc.org/articles/PMC10072853; pdf:https://europepmc.org/articles/PMC10072853?pdf=render"
   },
-  {
-    "id": "38575161",
-    "doi": "https://doi.org/10.1183/13993003.01853-2023",
-    "title": "Symptoms before and after COVID-19: a population and case-control study using prospective data.",
-    "authorString": "Sudre CH, Antonelli M, Cheetham NJ, Molteni E, Canas LS, Bowyer V, Murray B, Rjoob K, Modat M, Capdevila Pujol J, Hu C, Wolf J, Spector TD, Hammers A, Steves CJ, Ourselin S, Duncan EL.",
-    "authorAffiliations": "",
-    "journalTitle": "The European respiratory journal",
-    "pubYear": "2024",
-    "date": "2024-07-18",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Some individuals experience prolonged illness after acute coronavirus disease 2019 (COVID-19). We assessed whether pre-infection symptoms affected post-acute COVID illness duration.<h4>Methods</h4>Survival analysis was performed in adults (n=23\u2009452) with community-managed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection prospectively self-logging data through the ZOE COVID Symptom Study app, at least weekly, from 8\u2005weeks before to 12\u2005weeks after COVID-19 onset, conditioned on presence <i>versus</i> absence of baseline symptoms (4-8\u2005weeks before COVID-19). A case-control study was performed in 1350 individuals with long illness (\u22658\u2005weeks, including 906 individuals (67.1%) with illness \u226512\u2005weeks), matched 1:1 (for age, sex, body mass index, testing week, prior infection, vaccination, smoking, index of multiple deprivation) with 1350 individuals with short illness (<4\u2005weeks). Baseline symptoms were compared between the two groups, and against post-COVID symptoms.<h4>Results</h4>Individuals reporting baseline symptoms had longer COVID-related symptom duration (median 15\u2005days <i>versus</i> 10 days for individuals without baseline symptoms) with baseline fatigue nearly doubling duration. Two-thirds (910 (67.4%) of 1350) of individuals with long illness were asymptomatic beforehand. However, 440 (32.6%) had baseline symptoms, <i>versus</i> 255 (18.9%) of 1350 individuals with short illness (p<0.0001). Baseline symptoms doubled the odds ratio for long illness (2.14, 95% CI 1.78-2.57). Prior comorbidities were more common in individuals with long <i>versus</i> short illness. In individuals with long illness, baseline symptomatic (<i>versus</i> asymptomatic) individuals were more likely to be female, younger, and have prior comorbidities; and baseline and post-acute symptoms, and symptom burden, correlated strongly.<h4>Conclusions</h4>Individuals experiencing symptoms before COVID-19 had longer illness duration and increased odds of long illness. However, many individuals with long illness were well before SARS-CoV-2 infection.",
-    "laySummary": "",
-    "urls": "pdf:https://erj.ersjournals.com/content/erj/early/2024/03/21/13993003.01853-2023.full.pdf; doi:https://doi.org/10.1183/13993003.01853-2023; html:https://europepmc.org/articles/PMC11255388; pdf:https://europepmc.org/articles/PMC11255388?pdf=render"
-  },
   {
     "id": "31666709",
     "doi": "https://doi.org/10.1038/s41433-019-0657-y",
@@ -42023,6 +42040,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41433-019-0657-y.pdf; doi:https://doi.org/10.1038/s41433-019-0657-y; html:https://europepmc.org/articles/PMC7376231; pdf:https://europepmc.org/articles/PMC7376231?pdf=render; doi:https://doi.org/10.1038/s41433-019-0657-y"
   },
+  {
+    "id": "38575161",
+    "doi": "https://doi.org/10.1183/13993003.01853-2023",
+    "title": "Symptoms before and after COVID-19: a population and case-control study using prospective data.",
+    "authorString": "Sudre CH, Antonelli M, Cheetham NJ, Molteni E, Canas LS, Bowyer V, Murray B, Rjoob K, Modat M, Capdevila Pujol J, Hu C, Wolf J, Spector TD, Hammers A, Steves CJ, Ourselin S, Duncan EL.",
+    "authorAffiliations": "",
+    "journalTitle": "The European respiratory journal",
+    "pubYear": "2024",
+    "date": "2024-07-18",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Some individuals experience prolonged illness after acute coronavirus disease 2019 (COVID-19). We assessed whether pre-infection symptoms affected post-acute COVID illness duration.<h4>Methods</h4>Survival analysis was performed in adults (n=23\u2009452) with community-managed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection prospectively self-logging data through the ZOE COVID Symptom Study app, at least weekly, from 8\u2005weeks before to 12\u2005weeks after COVID-19 onset, conditioned on presence <i>versus</i> absence of baseline symptoms (4-8\u2005weeks before COVID-19). A case-control study was performed in 1350 individuals with long illness (\u22658\u2005weeks, including 906 individuals (67.1%) with illness \u226512\u2005weeks), matched 1:1 (for age, sex, body mass index, testing week, prior infection, vaccination, smoking, index of multiple deprivation) with 1350 individuals with short illness (<4\u2005weeks). Baseline symptoms were compared between the two groups, and against post-COVID symptoms.<h4>Results</h4>Individuals reporting baseline symptoms had longer COVID-related symptom duration (median 15\u2005days <i>versus</i> 10 days for individuals without baseline symptoms) with baseline fatigue nearly doubling duration. Two-thirds (910 (67.4%) of 1350) of individuals with long illness were asymptomatic beforehand. However, 440 (32.6%) had baseline symptoms, <i>versus</i> 255 (18.9%) of 1350 individuals with short illness (p<0.0001). Baseline symptoms doubled the odds ratio for long illness (2.14, 95% CI 1.78-2.57). Prior comorbidities were more common in individuals with long <i>versus</i> short illness. In individuals with long illness, baseline symptomatic (<i>versus</i> asymptomatic) individuals were more likely to be female, younger, and have prior comorbidities; and baseline and post-acute symptoms, and symptom burden, correlated strongly.<h4>Conclusions</h4>Individuals experiencing symptoms before COVID-19 had longer illness duration and increased odds of long illness. However, many individuals with long illness were well before SARS-CoV-2 infection.",
+    "laySummary": "",
+    "urls": "pdf:https://erj.ersjournals.com/content/erj/early/2024/03/21/13993003.01853-2023.full.pdf; doi:https://doi.org/10.1183/13993003.01853-2023; html:https://europepmc.org/articles/PMC11255388; pdf:https://europepmc.org/articles/PMC11255388?pdf=render"
+  },
   {
     "id": "38230350",
     "doi": "https://doi.org/10.1016/j.gimo.2023.100811",
@@ -42227,23 +42261,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.jchf.2019.01.009; doi:https://doi.org/10.1016/j.jchf.2019.01.009"
   },
-  {
-    "id": "34036180",
-    "doi": "https://doi.org/10.23889/ijpds.v5i2.1385",
-    "title": "Linking data on women in public family law court proceedings concerning their children to mental health service records in South London.",
-    "authorString": "Pearson RJ, Jewell A, Wijlaars L, Bedston S, Finch E, Broadhurst K, Downs J, Gilbert R.",
-    "authorAffiliations": "",
-    "journalTitle": "International journal of population data science",
-    "pubYear": "2021",
-    "date": "2021-02-24",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>Maternal mental health problems and substance misuse are key risk factors for child neglect or abuse and court-mandated placement into care. Linkage between mental health records and family court data could raise awareness about parent mental health needs and inform approaches to address them.<h4>Objectives</h4>To evaluate data linkage between administrative family court data and electronic mental health records for a population-based mental health service for 1.3 million people in South London.<h4>Methods</h4>We deterministically linked administrative family court data for women (n=5463) involved in care proceedings in South London with service user records from the South London and Maudsley NHS Mental Health Trust (SLaM). We restricted the cohort to women involved in proceedings between 2007 and 2019, in local authorities where SLaM solely provides secondary/tertiary mental health services and the Improving Access to Psychological Therapies (IAPT) (n=3226). We analysed the associations between match status and sociodemographic/case characteristics using multivariable logistic regression.<h4>Results</h4>Two-thirds (2317/3226; 66%) of women linked to a SLaM service user record at some point; most (91%) who linked accessed secondary/tertiary mental health services, indicating serious mental illness. Accounting for possible missed matches, we estimated that 70-83% of women accessed SLaM services at some point. Older women at index proceedings (>35yrs OR: 0.69, 95%CI: 0.54-0.88vs <25yrs) and Black women or women from other ethnic groups (Black ethnic groups 0.65, 0.50-0.83; other ethnicity 0.59, 0.43-0.81 vs White ethnic groups) had lower odds of linking. Odds of linking were higher for women with an infant in proceedings (1.42, 1.18-1.71), or with curtailed/terminated parental responsibility (1.44, 1.20-1.73).<h4>Conclusion</h4>Our linkage supports growing evidence of a high burden of mental health problems and substance misuse among women whose children enter care in England, compared to the general population. Research using this linkage should inform strategies to address the considerable mental health needs of vulnerable women and their children.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.23889/ijpds.v5i2.1385; html:https://europepmc.org/articles/PMC8133060; pdf:https://europepmc.org/articles/PMC8133060?pdf=render"
-  },
   {
     "id": "37286573",
     "doi": "https://doi.org/10.1038/s41467-023-38383-y",
@@ -42261,6 +42278,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41467-023-38383-y.pdf; doi:https://doi.org/10.1038/s41467-023-38383-y; html:https://europepmc.org/articles/PMC10247781; pdf:https://europepmc.org/articles/PMC10247781?pdf=render"
   },
+  {
+    "id": "34036180",
+    "doi": "https://doi.org/10.23889/ijpds.v5i2.1385",
+    "title": "Linking data on women in public family law court proceedings concerning their children to mental health service records in South London.",
+    "authorString": "Pearson RJ, Jewell A, Wijlaars L, Bedston S, Finch E, Broadhurst K, Downs J, Gilbert R.",
+    "authorAffiliations": "",
+    "journalTitle": "International journal of population data science",
+    "pubYear": "2021",
+    "date": "2021-02-24",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Introduction</h4>Maternal mental health problems and substance misuse are key risk factors for child neglect or abuse and court-mandated placement into care. Linkage between mental health records and family court data could raise awareness about parent mental health needs and inform approaches to address them.<h4>Objectives</h4>To evaluate data linkage between administrative family court data and electronic mental health records for a population-based mental health service for 1.3 million people in South London.<h4>Methods</h4>We deterministically linked administrative family court data for women (n=5463) involved in care proceedings in South London with service user records from the South London and Maudsley NHS Mental Health Trust (SLaM). We restricted the cohort to women involved in proceedings between 2007 and 2019, in local authorities where SLaM solely provides secondary/tertiary mental health services and the Improving Access to Psychological Therapies (IAPT) (n=3226). We analysed the associations between match status and sociodemographic/case characteristics using multivariable logistic regression.<h4>Results</h4>Two-thirds (2317/3226; 66%) of women linked to a SLaM service user record at some point; most (91%) who linked accessed secondary/tertiary mental health services, indicating serious mental illness. Accounting for possible missed matches, we estimated that 70-83% of women accessed SLaM services at some point. Older women at index proceedings (>35yrs OR: 0.69, 95%CI: 0.54-0.88vs <25yrs) and Black women or women from other ethnic groups (Black ethnic groups 0.65, 0.50-0.83; other ethnicity 0.59, 0.43-0.81 vs White ethnic groups) had lower odds of linking. Odds of linking were higher for women with an infant in proceedings (1.42, 1.18-1.71), or with curtailed/terminated parental responsibility (1.44, 1.20-1.73).<h4>Conclusion</h4>Our linkage supports growing evidence of a high burden of mental health problems and substance misuse among women whose children enter care in England, compared to the general population. Research using this linkage should inform strategies to address the considerable mental health needs of vulnerable women and their children.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.23889/ijpds.v5i2.1385; html:https://europepmc.org/articles/PMC8133060; pdf:https://europepmc.org/articles/PMC8133060?pdf=render"
+  },
   {
     "id": "35188868",
     "doi": "https://doi.org/10.1080/19490976.2022.2038863",
@@ -42363,6 +42397,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41591-022-01772-9.pdf; doi:https://doi.org/10.1038/s41591-022-01772-9"
   },
+  {
+    "id": "31844048",
+    "doi": "https://doi.org/10.1038/s41467-019-13585-5",
+    "title": "Genome-wide analysis identifies molecular systems and 149 genetic loci associated with income.",
+    "authorString": "Hill WD, Davies NM, Ritchie SJ, Skene NG, Bryois J, Bell S, Di Angelantonio E, Roberts DJ, Xueyi S, Davies G, Liewald DCM, Porteous DJ, Hayward C, Butterworth AS, McIntosh AM, Gale CR, Deary IJ.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature communications",
+    "pubYear": "2019",
+    "date": "2019-12-16",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "Understanding the Causes of Disease",
+    "healthCategories": "",
+    "abstract": "Socioeconomic position (SEP) is a multi-dimensional construct reflecting (and influencing) multiple socio-cultural, physical, and environmental factors. In a sample of 286,301 participants from UK Biobank, we identify 30\u00a0(29 previously\u00a0unreported) independent-loci associated with income. Using a method to meta-analyze data from genetically-correlated traits, we identify an additional 120 income-associated loci. These loci show clear evidence of functionality, with transcriptional differences identified across multiple cortical tissues, and links to GABAergic and serotonergic neurotransmission. By combining our genome wide association study\u00a0on income with data from eQTL studies and chromatin interactions, 24 genes are prioritized for follow up, 18 of which were previously associated with intelligence. We identify intelligence as one of the likely causal, partly-heritable phenotypes that might bridge the gap between molecular genetic inheritance and phenotypic consequence in terms of income differences. These results indicate that, in modern era\u00a0Great Britain, genetic effects contribute towards some of the observed socioeconomic inequalities.",
+    "laySummary": "This study linked genetic sequencing data and information on household income to identify parts of the genome that are more common in people who live in more affluent households. The authors identified 150 parts of the genome that were associated with income, and found that these genetic regions were more commonly expressed in the brain and testes. The results indicate that intelligence and income are causally linked, and suggest that genetics partly explain a small amount of variation (~2%) in household income in the UK.",
+    "urls": "pdf:https://www.nature.com/articles/s41467-019-13585-5.pdf; doi:https://doi.org/10.1038/s41467-019-13585-5; html:https://europepmc.org/articles/PMC6915786; pdf:https://europepmc.org/articles/PMC6915786?pdf=render"
+  },
   {
     "id": "30921401",
     "doi": "https://doi.org/10.1371/journal.pone.0214607",
@@ -42381,21 +42432,21 @@
     "urls": "pdf:https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0214607&type=printable; doi:https://doi.org/10.1371/journal.pone.0214607; html:https://europepmc.org/articles/PMC6438638; pdf:https://europepmc.org/articles/PMC6438638?pdf=render"
   },
   {
-    "id": "31844048",
-    "doi": "https://doi.org/10.1038/s41467-019-13585-5",
-    "title": "Genome-wide analysis identifies molecular systems and 149 genetic loci associated with income.",
-    "authorString": "Hill WD, Davies NM, Ritchie SJ, Skene NG, Bryois J, Bell S, Di Angelantonio E, Roberts DJ, Xueyi S, Davies G, Liewald DCM, Porteous DJ, Hayward C, Butterworth AS, McIntosh AM, Gale CR, Deary IJ.",
+    "id": "32423943",
+    "doi": "https://doi.org/10.1136/bmjopen-2020-038974",
+    "title": "Study protocol for a multicentre longitudinal mixed methods study to explore the Outcomes of ChildrEn and fAmilies in the first year after paediatric Intensive Care: the OCEANIC study.",
+    "authorString": "Manning JC, Latour JM, Curley MAQ, Draper ES, Jilani T, Quinlan PR, Watson RS, Rennick JE, Colville G, Pinto N, Latif A, Popejoy E, Coad J, OCEANIC Study Investigators.",
     "authorAffiliations": "",
-    "journalTitle": "Nature communications",
-    "pubYear": "2019",
-    "date": "2019-12-16",
+    "journalTitle": "BMJ open",
+    "pubYear": "2020",
+    "date": "2020-05-17",
     "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "Understanding the Causes of Disease",
+    "keywords": "Qualitative Research; Statistics & Research Methods; Paediatric Intensive & Critical Care",
+    "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Socioeconomic position (SEP) is a multi-dimensional construct reflecting (and influencing) multiple socio-cultural, physical, and environmental factors. In a sample of 286,301 participants from UK Biobank, we identify 30\u00a0(29 previously\u00a0unreported) independent-loci associated with income. Using a method to meta-analyze data from genetically-correlated traits, we identify an additional 120 income-associated loci. These loci show clear evidence of functionality, with transcriptional differences identified across multiple cortical tissues, and links to GABAergic and serotonergic neurotransmission. By combining our genome wide association study\u00a0on income with data from eQTL studies and chromatin interactions, 24 genes are prioritized for follow up, 18 of which were previously associated with intelligence. We identify intelligence as one of the likely causal, partly-heritable phenotypes that might bridge the gap between molecular genetic inheritance and phenotypic consequence in terms of income differences. These results indicate that, in modern era\u00a0Great Britain, genetic effects contribute towards some of the observed socioeconomic inequalities.",
-    "laySummary": "This study linked genetic sequencing data and information on household income to identify parts of the genome that are more common in people who live in more affluent households. The authors identified 150 parts of the genome that were associated with income, and found that these genetic regions were more commonly expressed in the brain and testes. The results indicate that intelligence and income are causally linked, and suggest that genetics partly explain a small amount of variation (~2%) in household income in the UK.",
-    "urls": "pdf:https://www.nature.com/articles/s41467-019-13585-5.pdf; doi:https://doi.org/10.1038/s41467-019-13585-5; html:https://europepmc.org/articles/PMC6915786; pdf:https://europepmc.org/articles/PMC6915786?pdf=render"
+    "abstract": "<h4>Introduction</h4>Annually in the UK, 20 000 children become very ill or injured and need specialist care within a paediatric intensive care unit (PICU). Most children survive. However, some children and their families may experience problems after they have left the PICU including physical, functional and/or emotional problems. It is unknown which children and families experience such problems, when these occur or what causes them. The aim of this mixed-method longitudinal cohort study is to understand the physical, functional, emotional and social impact of children surviving PICU (aged: 1\u2009month-17 years), their parents and siblings, during the first year after a PICU admission.<h4>Methods and analysis</h4>A quantitative study involving 300 child survivors of PICU; 300 parents; and 150-300 siblings will collect data (using self-completion questionnaires) at baseline, PICU discharge, 1, 3, 6 and 12 months post-PICU discharge. Questionnaires will comprise validated and reliable instruments. Demographic data, PICU admission and treatment data, health-related quality of life, functional status, strengths and difficulties behaviour and post-traumatic stress symptoms will be collected from the child. Parent and sibling data will be collected on the impact of paediatric health conditions on the family's functioning capabilities, levels of anxiety and social impact of the child's PICU admission. Data will be analysed using descriptive and inferential statistics. Concurrently, an embedded qualitative study involving semistructured interviews with 24 enrolled families at 3 months and 9 months post-PICU discharge will be undertaken. Framework analysis will be used to analyse the qualitative data.<h4>Ethics and dissemination</h4>The study has received ethical approval from the National Health Services Research Ethics Committee (Ref: 19/WM/0290) and full governance clearance. This will be the first UK study to comprehensively investigate physical, functional, emotional and social consequences of PICU survival in the first-year postdischarge.Clinical Trials Registration Number: ISRCTN28072812 [Pre-results].",
+    "laySummary": "",
+    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/10/5/e038974.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-038974; html:https://europepmc.org/articles/PMC7239532; pdf:https://europepmc.org/articles/PMC7239532?pdf=render"
   },
   {
     "id": "33186544",
@@ -42431,23 +42482,6 @@
     "laySummary": "",
     "urls": "pdf:http://www.thelancet.com/article/S2468266720302103/pdf; doi:https://doi.org/10.1016/S2468-2667(20)30210-3; html:https://europepmc.org/articles/PMC7848754; pdf:https://europepmc.org/articles/PMC7848754?pdf=render"
   },
-  {
-    "id": "32423943",
-    "doi": "https://doi.org/10.1136/bmjopen-2020-038974",
-    "title": "Study protocol for a multicentre longitudinal mixed methods study to explore the Outcomes of ChildrEn and fAmilies in the first year after paediatric Intensive Care: the OCEANIC study.",
-    "authorString": "Manning JC, Latour JM, Curley MAQ, Draper ES, Jilani T, Quinlan PR, Watson RS, Rennick JE, Colville G, Pinto N, Latif A, Popejoy E, Coad J, OCEANIC Study Investigators.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2020",
-    "date": "2020-05-17",
-    "isOpenAccess": "Y",
-    "keywords": "Qualitative Research; Statistics & Research Methods; Paediatric Intensive & Critical Care",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Introduction</h4>Annually in the UK, 20 000 children become very ill or injured and need specialist care within a paediatric intensive care unit (PICU). Most children survive. However, some children and their families may experience problems after they have left the PICU including physical, functional and/or emotional problems. It is unknown which children and families experience such problems, when these occur or what causes them. The aim of this mixed-method longitudinal cohort study is to understand the physical, functional, emotional and social impact of children surviving PICU (aged: 1\u2009month-17 years), their parents and siblings, during the first year after a PICU admission.<h4>Methods and analysis</h4>A quantitative study involving 300 child survivors of PICU; 300 parents; and 150-300 siblings will collect data (using self-completion questionnaires) at baseline, PICU discharge, 1, 3, 6 and 12 months post-PICU discharge. Questionnaires will comprise validated and reliable instruments. Demographic data, PICU admission and treatment data, health-related quality of life, functional status, strengths and difficulties behaviour and post-traumatic stress symptoms will be collected from the child. Parent and sibling data will be collected on the impact of paediatric health conditions on the family's functioning capabilities, levels of anxiety and social impact of the child's PICU admission. Data will be analysed using descriptive and inferential statistics. Concurrently, an embedded qualitative study involving semistructured interviews with 24 enrolled families at 3 months and 9 months post-PICU discharge will be undertaken. Framework analysis will be used to analyse the qualitative data.<h4>Ethics and dissemination</h4>The study has received ethical approval from the National Health Services Research Ethics Committee (Ref: 19/WM/0290) and full governance clearance. This will be the first UK study to comprehensively investigate physical, functional, emotional and social consequences of PICU survival in the first-year postdischarge.Clinical Trials Registration Number: ISRCTN28072812 [Pre-results].",
-    "laySummary": "",
-    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/10/5/e038974.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-038974; html:https://europepmc.org/articles/PMC7239532; pdf:https://europepmc.org/articles/PMC7239532?pdf=render"
-  },
   {
     "id": "33705244",
     "doi": "https://doi.org/10.1177/17474930211004277",
@@ -42533,23 +42567,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.repository.cam.ac.uk/bitstream/1810/345820/2/pul2.12192.pdf; doi:https://doi.org/10.1002/pul2.12192; html:https://europepmc.org/articles/PMC9881210; pdf:https://europepmc.org/articles/PMC9881210?pdf=render"
   },
-  {
-    "id": "35189575",
-    "doi": "https://doi.org/10.1016/j.ebiom.2022.103878",
-    "title": "The impact of hypoxia on B cells in COVID-19.",
-    "authorString": "Kotagiri P, Mescia F, Hanson AL, Turner L, Bergamaschi L, Pe\u00f1alver A, Richoz N, Moore SD, Ortmann BM, Dunmore BJ, Morgan MD, Tuong ZK, Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID BioResource Collaboration, G\u00f6ttgens B, Toshner M, Hess C, Maxwell PH, Clatworthy MR, Nathan JA, Bradley JR, Lyons PA, Burrows N, Smith KGC.",
-    "authorAffiliations": "",
-    "journalTitle": "EBioMedicine",
-    "pubYear": "2022",
-    "date": "2022-02-19",
-    "isOpenAccess": "Y",
-    "keywords": "Hypoxia; B cells; Lymphopenia; Covid-19",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Prominent early features of COVID-19 include severe, often clinically silent, hypoxia and a pronounced reduction in B cells, the latter important in defence against SARS-CoV-2. This presentation resembles the phenotype of mice with VHL-deficient B cells, in which Hypoxia-Inducible Factors are constitutively active, suggesting hypoxia might drive B cell abnormalities in COVID-19.<h4>Methods</h4>Detailed B cell phenotyping was undertaken by flow-cytometry on longitudinal samples from patients with COVID-19 across a range of severities (NIHR Cambridge BioResource). The impact of hypoxia on the transcriptome was assessed by single-cell and whole blood RNA sequencing analysis. The direct effect of hypoxia on B cells was determined through immunisation studies in genetically modified and hypoxia-exposed mice.<h4>Findings</h4>We demonstrate the breadth of early and persistent defects in B cell subsets in moderate/severe COVID-19, including reduced marginal zone-like, memory and transitional B cells, changes also observed in B cell VHL-deficient mice. These findings were associated with hypoxia-related transcriptional changes in COVID-19 patient B cells, and similar B cell abnormalities were seen in mice kept in hypoxic conditions.<h4>Interpretation</h4>Hypoxia may contribute to the pronounced and persistent B cell pathology observed in acute COVID-19 pneumonia. Assessment of the impact of early oxygen therapy on these immune defects should be considered, as their correction could contribute to improved outcomes.<h4>Funding</h4>Evelyn Trust, Addenbrooke's Charitable Trust, UKRI/NIHR, Wellcome Trust.",
-    "laySummary": "",
-    "urls": "pdf:http://www.thelancet.com/article/S2352396422000627/pdf; doi:https://doi.org/10.1016/j.ebiom.2022.103878; html:https://europepmc.org/articles/PMC8856886; pdf:https://europepmc.org/articles/PMC8856886?pdf=render"
-  },
   {
     "id": "31171806",
     "doi": "https://doi.org/10.1038/s41598-019-44907-8",
@@ -42567,6 +42584,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41598-019-44907-8.pdf; doi:https://doi.org/10.1038/s41598-019-44907-8; html:https://europepmc.org/articles/PMC6554413; pdf:https://europepmc.org/articles/PMC6554413?pdf=render"
   },
+  {
+    "id": "35189575",
+    "doi": "https://doi.org/10.1016/j.ebiom.2022.103878",
+    "title": "The impact of hypoxia on B cells in COVID-19.",
+    "authorString": "Kotagiri P, Mescia F, Hanson AL, Turner L, Bergamaschi L, Pe\u00f1alver A, Richoz N, Moore SD, Ortmann BM, Dunmore BJ, Morgan MD, Tuong ZK, Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID BioResource Collaboration, G\u00f6ttgens B, Toshner M, Hess C, Maxwell PH, Clatworthy MR, Nathan JA, Bradley JR, Lyons PA, Burrows N, Smith KGC.",
+    "authorAffiliations": "",
+    "journalTitle": "EBioMedicine",
+    "pubYear": "2022",
+    "date": "2022-02-19",
+    "isOpenAccess": "Y",
+    "keywords": "Hypoxia; B cells; Lymphopenia; Covid-19",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Prominent early features of COVID-19 include severe, often clinically silent, hypoxia and a pronounced reduction in B cells, the latter important in defence against SARS-CoV-2. This presentation resembles the phenotype of mice with VHL-deficient B cells, in which Hypoxia-Inducible Factors are constitutively active, suggesting hypoxia might drive B cell abnormalities in COVID-19.<h4>Methods</h4>Detailed B cell phenotyping was undertaken by flow-cytometry on longitudinal samples from patients with COVID-19 across a range of severities (NIHR Cambridge BioResource). The impact of hypoxia on the transcriptome was assessed by single-cell and whole blood RNA sequencing analysis. The direct effect of hypoxia on B cells was determined through immunisation studies in genetically modified and hypoxia-exposed mice.<h4>Findings</h4>We demonstrate the breadth of early and persistent defects in B cell subsets in moderate/severe COVID-19, including reduced marginal zone-like, memory and transitional B cells, changes also observed in B cell VHL-deficient mice. These findings were associated with hypoxia-related transcriptional changes in COVID-19 patient B cells, and similar B cell abnormalities were seen in mice kept in hypoxic conditions.<h4>Interpretation</h4>Hypoxia may contribute to the pronounced and persistent B cell pathology observed in acute COVID-19 pneumonia. Assessment of the impact of early oxygen therapy on these immune defects should be considered, as their correction could contribute to improved outcomes.<h4>Funding</h4>Evelyn Trust, Addenbrooke's Charitable Trust, UKRI/NIHR, Wellcome Trust.",
+    "laySummary": "",
+    "urls": "pdf:http://www.thelancet.com/article/S2352396422000627/pdf; doi:https://doi.org/10.1016/j.ebiom.2022.103878; html:https://europepmc.org/articles/PMC8856886; pdf:https://europepmc.org/articles/PMC8856886?pdf=render"
+  },
   {
     "id": "33226834",
     "doi": "https://doi.org/10.1164/rccm.202008-3211le",
@@ -42856,23 +42890,6 @@
     "laySummary": "",
     "urls": "pdf:https://breast-cancer-research.biomedcentral.com/track/pdf/10.1186/s13058-021-01465-0; doi:https://doi.org/10.1186/s13058-021-01465-0; html:https://europepmc.org/articles/PMC8482562; pdf:https://europepmc.org/articles/PMC8482562?pdf=render"
   },
-  {
-    "id": "36436752",
-    "doi": "https://doi.org/10.1016/j.ijid.2022.11.024",
-    "title": "Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa.",
-    "authorString": "Davies MA, Morden E, Rousseau P, Arendse J, Bam JL, Boloko L, Cloete K, Cohen C, Chetty N, Dane P, Heekes A, Hsiao NY, Hunter M, Hussey H, Jacobs T, Jassat W, Kariem S, Kassanjee R, Laenen I, Roux SL, Lessells R, Mahomed H, Maughan D, Meintjes G, Mendelson M, Mnguni A, Moodley M, Murie K, Naude J, Ntusi NAB, Paleker M, Parker A, Pienaar D, Preiser W, Prozesky H, Raubenheimer P, Rossouw L, Schrueder N, Smith B, Smith M, Solomon W, Symons G, Taljaard J, Wasserman S, Wilkinson RJ, Wolmarans M, Wolter N, Boulle A.",
-    "authorAffiliations": "",
-    "journalTitle": "International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases",
-    "pubYear": "2023",
-    "date": "2022-11-24",
-    "isOpenAccess": "Y",
-    "keywords": "Covid-19; Omicron; Ba.4; Ba.5; Death, Severe Hospitalization",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objectives</h4>We aimed to compare the clinical severity of Omicron BA.4/BA.5 infection with BA.1 and earlier variant infections among laboratory-confirmed SARS-CoV-2 cases in the Western Cape, South Africa, using timing of infection to infer the lineage/variant causing infection.<h4>Methods</h4>We included public sector patients aged \u226520 years with laboratory-confirmed COVID-19 between May 01-May 21, 2022 (BA.4/BA.5 wave) and equivalent previous wave periods. We compared the risk between waves of (i) death and (ii) severe hospitalization/death (all within 21 days of diagnosis) using Cox regression adjusted for demographics, comorbidities, admission pressure, vaccination, and previous infection.<h4>Results</h4>Among 3793 patients from the BA.4/BA.5 wave and 190,836 patients from previous waves, the risk of severe hospitalization/death was similar in the BA.4/BA.5 and BA.1 waves (adjusted hazard ratio [aHR] 1.12; 95% confidence interval [CI] 0.93; 1.34). Both Omicron waves had a lower risk of severe outcomes than previous waves. Previous infection (aHR 0.29, 95% CI 0.24; 0.36) and vaccination (aHR 0.17; 95% CI 0.07; 0.40 for at least three doses vs no vaccine) were protective.<h4>Conclusion</h4>Disease severity was similar among diagnosed COVID-19 cases in the BA.4/BA.5 and BA.1 periods in the context of growing immunity against SARS-CoV-2 due to previous infection and vaccination, both of which were strongly protective.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.ijid.2022.11.024; doi:https://doi.org/10.1016/j.ijid.2022.11.024; html:https://europepmc.org/articles/PMC9686046; pdf:https://europepmc.org/articles/PMC9686046?pdf=render"
-  },
   {
     "id": "33248277",
     "doi": "https://doi.org/10.1016/j.jclinepi.2020.11.014",
@@ -42890,6 +42907,23 @@
     "laySummary": "",
     "urls": "pdf:http://www.jclinepi.com/article/S0895435620311859/pdf; doi:https://doi.org/10.1016/j.jclinepi.2020.11.014"
   },
+  {
+    "id": "36436752",
+    "doi": "https://doi.org/10.1016/j.ijid.2022.11.024",
+    "title": "Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa.",
+    "authorString": "Davies MA, Morden E, Rousseau P, Arendse J, Bam JL, Boloko L, Cloete K, Cohen C, Chetty N, Dane P, Heekes A, Hsiao NY, Hunter M, Hussey H, Jacobs T, Jassat W, Kariem S, Kassanjee R, Laenen I, Roux SL, Lessells R, Mahomed H, Maughan D, Meintjes G, Mendelson M, Mnguni A, Moodley M, Murie K, Naude J, Ntusi NAB, Paleker M, Parker A, Pienaar D, Preiser W, Prozesky H, Raubenheimer P, Rossouw L, Schrueder N, Smith B, Smith M, Solomon W, Symons G, Taljaard J, Wasserman S, Wilkinson RJ, Wolmarans M, Wolter N, Boulle A.",
+    "authorAffiliations": "",
+    "journalTitle": "International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases",
+    "pubYear": "2023",
+    "date": "2022-11-24",
+    "isOpenAccess": "Y",
+    "keywords": "Covid-19; Omicron; Ba.4; Ba.5; Death, Severe Hospitalization",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objectives</h4>We aimed to compare the clinical severity of Omicron BA.4/BA.5 infection with BA.1 and earlier variant infections among laboratory-confirmed SARS-CoV-2 cases in the Western Cape, South Africa, using timing of infection to infer the lineage/variant causing infection.<h4>Methods</h4>We included public sector patients aged \u226520 years with laboratory-confirmed COVID-19 between May 01-May 21, 2022 (BA.4/BA.5 wave) and equivalent previous wave periods. We compared the risk between waves of (i) death and (ii) severe hospitalization/death (all within 21 days of diagnosis) using Cox regression adjusted for demographics, comorbidities, admission pressure, vaccination, and previous infection.<h4>Results</h4>Among 3793 patients from the BA.4/BA.5 wave and 190,836 patients from previous waves, the risk of severe hospitalization/death was similar in the BA.4/BA.5 and BA.1 waves (adjusted hazard ratio [aHR] 1.12; 95% confidence interval [CI] 0.93; 1.34). Both Omicron waves had a lower risk of severe outcomes than previous waves. Previous infection (aHR 0.29, 95% CI 0.24; 0.36) and vaccination (aHR 0.17; 95% CI 0.07; 0.40 for at least three doses vs no vaccine) were protective.<h4>Conclusion</h4>Disease severity was similar among diagnosed COVID-19 cases in the BA.4/BA.5 and BA.1 periods in the context of growing immunity against SARS-CoV-2 due to previous infection and vaccination, both of which were strongly protective.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.ijid.2022.11.024; doi:https://doi.org/10.1016/j.ijid.2022.11.024; html:https://europepmc.org/articles/PMC9686046; pdf:https://europepmc.org/articles/PMC9686046?pdf=render"
+  },
   {
     "id": "31331193",
     "doi": "https://doi.org/10.1161/circulationaha.119.041546",
@@ -42992,23 +43026,6 @@
     "laySummary": "",
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s12265-023-10403-8.pdf; doi:https://doi.org/10.1007/s12265-023-10403-8; html:https://europepmc.org/articles/PMC10721666; pdf:https://europepmc.org/articles/PMC10721666?pdf=render"
   },
-  {
-    "id": "36697134",
-    "doi": "https://doi.org/10.1016/j.jacc.2022.10.034",
-    "title": "Somatostatin Receptor PET/MR Imaging of Inflammation in Patients With Large Vessel Vasculitis and Atherosclerosis.",
-    "authorString": "\u0106orovi\u0107 A, Wall C, Nus M, Gopalan D, Huang Y, Imaz M, Zulcinski M, Peverelli M, Uryga A, Lambert J, Bressan D, Maughan RT, Pericleous C, Dubash S, Jordan N, Jayne DR, Hoole SP, Calvert PA, Dean AF, Rassl D, Barwick T, Iles M, Frontini M, Hannon G, Manavaki R, Fryer TD, Aloj L, Graves MJ, Gilbert FJ, Dweck MR, Newby DE, Fayad ZA, Reynolds G, Morgan AW, Aboagye EO, Davenport AP, J\u00f8rgensen HF, Mallat Z, Bennett MR, Peters JE, Rudd JHF, Mason JC, Tarkin JM.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of the American College of Cardiology",
-    "pubYear": "2023",
-    "date": "2023-01-01",
-    "isOpenAccess": "Y",
-    "keywords": "Atherosclerosis; Inflammation; Molecular Imaging; Giant Cell Arteritis; Takayasu Arteritis; Somatostatin Receptor",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Assessing inflammatory disease activity in large vessel vasculitis (LVV) can be challenging by conventional measures.<h4>Objectives</h4>We aimed to investigate somatostatin receptor 2 (SST<sub>2</sub>) as a novel inflammation-specific molecular imaging target in LVV.<h4>Methods</h4>In a prospective, observational cohort study, in\u00a0vivo arterial SST<sub>2</sub> expression was assessed by positron emission tomography/magnetic resonance imaging (PET/MRI) using <sup>68</sup>Ga-DOTATATE and <sup>18</sup>F-FET-\u03b2AG-TOCA. Ex\u00a0vivo mapping of the imaging target was performed using immunofluorescence microscopy; imaging mass cytometry; and bulk, single-cell, and single-nucleus RNA sequencing.<h4>Results</h4>Sixty-one participants (LVV: n\u00a0=\u00a027; recent atherosclerotic myocardial infarction of\u00a0\u22642\u00a0weeks: n\u00a0=\u00a025; control subjects with an oncologic indication for imaging: n\u00a0=\u00a09) were included. Index vessel SST<sub>2</sub> maximum tissue-to-blood ratio was 61.8% (P\u00a0< 0.0001) higher in active/grumbling LVV than inactive LVV and 34.6% (P\u00a0=\u00a00.0002) higher than myocardial infarction, with good diagnostic accuracy (area under the curve:\u00a0\u22650.86; P\u00a0< 0.001 for both). Arterial SST<sub>2</sub> signal was not elevated in any of the control subjects. SST<sub>2</sub> PET/MRI was generally consistent with <sup>18</sup>F-fluorodeoxyglucose PET/computed tomography imaging in LVV patients with contemporaneous clinical scans but with very low background signal in the brain and heart, allowing for unimpeded assessment of nearby coronary, myocardial, and intracranial artery involvement. Clinically effective treatment for LVV was associated with a 0.49 \u00b1 0.24 (standard error of the mean [SEM]) (P\u00a0=\u00a00.04; 22.3%) reduction in the SST<sub>2</sub> maximum tissue-to-blood ratio after 9.3 \u00b1 3.2\u00a0months. SST<sub>2</sub> expression was localized to macrophages, pericytes, and perivascular adipocytes in vasculitis specimens, with specific receptor binding confirmed by autoradiography. SSTR2-expressing macrophages coexpressed proinflammatory markers.<h4>Conclusions</h4>SST<sub>2</sub> PET/MRI holds major promise for diagnosis and therapeutic monitoring in LVV. (PET Imaging of Giant Cell and Takayasu Arteritis [PITA], NCT04071691; Residual Inflammation and Plaque Progression Long-Term Evaluation [RIPPLE], NCT04073810).",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.jacc.2022.10.034; doi:https://doi.org/10.1016/j.jacc.2022.10.034; html:https://europepmc.org/articles/PMC9883634; pdf:https://europepmc.org/articles/PMC9883634?pdf=render"
-  },
   {
     "id": "33328634",
     "doi": "https://doi.org/10.1038/s41586-020-03043-4",
@@ -43026,6 +43043,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41586-020-03043-4.pdf; doi:https://doi.org/10.1038/s41586-020-03043-4; html:https://europepmc.org/articles/PMC7739806; pdf:https://europepmc.org/articles/PMC7739806?pdf=render"
   },
+  {
+    "id": "36697134",
+    "doi": "https://doi.org/10.1016/j.jacc.2022.10.034",
+    "title": "Somatostatin Receptor PET/MR Imaging of Inflammation in Patients With Large Vessel Vasculitis and Atherosclerosis.",
+    "authorString": "\u0106orovi\u0107 A, Wall C, Nus M, Gopalan D, Huang Y, Imaz M, Zulcinski M, Peverelli M, Uryga A, Lambert J, Bressan D, Maughan RT, Pericleous C, Dubash S, Jordan N, Jayne DR, Hoole SP, Calvert PA, Dean AF, Rassl D, Barwick T, Iles M, Frontini M, Hannon G, Manavaki R, Fryer TD, Aloj L, Graves MJ, Gilbert FJ, Dweck MR, Newby DE, Fayad ZA, Reynolds G, Morgan AW, Aboagye EO, Davenport AP, J\u00f8rgensen HF, Mallat Z, Bennett MR, Peters JE, Rudd JHF, Mason JC, Tarkin JM.",
+    "authorAffiliations": "",
+    "journalTitle": "Journal of the American College of Cardiology",
+    "pubYear": "2023",
+    "date": "2023-01-01",
+    "isOpenAccess": "Y",
+    "keywords": "Atherosclerosis; Inflammation; Molecular Imaging; Giant Cell Arteritis; Takayasu Arteritis; Somatostatin Receptor",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Assessing inflammatory disease activity in large vessel vasculitis (LVV) can be challenging by conventional measures.<h4>Objectives</h4>We aimed to investigate somatostatin receptor 2 (SST<sub>2</sub>) as a novel inflammation-specific molecular imaging target in LVV.<h4>Methods</h4>In a prospective, observational cohort study, in\u00a0vivo arterial SST<sub>2</sub> expression was assessed by positron emission tomography/magnetic resonance imaging (PET/MRI) using <sup>68</sup>Ga-DOTATATE and <sup>18</sup>F-FET-\u03b2AG-TOCA. Ex\u00a0vivo mapping of the imaging target was performed using immunofluorescence microscopy; imaging mass cytometry; and bulk, single-cell, and single-nucleus RNA sequencing.<h4>Results</h4>Sixty-one participants (LVV: n\u00a0=\u00a027; recent atherosclerotic myocardial infarction of\u00a0\u22642\u00a0weeks: n\u00a0=\u00a025; control subjects with an oncologic indication for imaging: n\u00a0=\u00a09) were included. Index vessel SST<sub>2</sub> maximum tissue-to-blood ratio was 61.8% (P\u00a0< 0.0001) higher in active/grumbling LVV than inactive LVV and 34.6% (P\u00a0=\u00a00.0002) higher than myocardial infarction, with good diagnostic accuracy (area under the curve:\u00a0\u22650.86; P\u00a0< 0.001 for both). Arterial SST<sub>2</sub> signal was not elevated in any of the control subjects. SST<sub>2</sub> PET/MRI was generally consistent with <sup>18</sup>F-fluorodeoxyglucose PET/computed tomography imaging in LVV patients with contemporaneous clinical scans but with very low background signal in the brain and heart, allowing for unimpeded assessment of nearby coronary, myocardial, and intracranial artery involvement. Clinically effective treatment for LVV was associated with a 0.49 \u00b1 0.24 (standard error of the mean [SEM]) (P\u00a0=\u00a00.04; 22.3%) reduction in the SST<sub>2</sub> maximum tissue-to-blood ratio after 9.3 \u00b1 3.2\u00a0months. SST<sub>2</sub> expression was localized to macrophages, pericytes, and perivascular adipocytes in vasculitis specimens, with specific receptor binding confirmed by autoradiography. SSTR2-expressing macrophages coexpressed proinflammatory markers.<h4>Conclusions</h4>SST<sub>2</sub> PET/MRI holds major promise for diagnosis and therapeutic monitoring in LVV. (PET Imaging of Giant Cell and Takayasu Arteritis [PITA], NCT04071691; Residual Inflammation and Plaque Progression Long-Term Evaluation [RIPPLE], NCT04073810).",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.jacc.2022.10.034; doi:https://doi.org/10.1016/j.jacc.2022.10.034; html:https://europepmc.org/articles/PMC9883634; pdf:https://europepmc.org/articles/PMC9883634?pdf=render"
+  },
   {
     "id": "33245137",
     "doi": "https://doi.org/10.1093/ije/dyaa155",
@@ -43060,23 +43094,6 @@
     "laySummary": "",
     "urls": "pdf:https://informatics.bmj.com/content/bmjhci/27/1/e100117.full.pdf; doi:https://doi.org/10.1136/bmjhci-2019-100117; html:https://europepmc.org/articles/PMC7062357; pdf:https://europepmc.org/articles/PMC7062357?pdf=render"
   },
-  {
-    "id": "31922447",
-    "doi": "https://doi.org/10.1177/0141076819890551",
-    "title": "Moving beyond project-specific patient and public involvement in research.",
-    "authorString": "Turner G, Aiyegbusi OL, Price G, Skrybant M, Calvert M.",
-    "authorAffiliations": "",
-    "journalTitle": "Journal of the Royal Society of Medicine",
-    "pubYear": "2020",
-    "date": "2020-01-01",
-    "isOpenAccess": "N",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "",
-    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/0141076819890551; doi:https://doi.org/10.1177/0141076819890551; html:https://europepmc.org/articles/PMC6961168; pdf:https://europepmc.org/articles/PMC6961168?pdf=render; doi:https://doi.org/10.1177/0141076819890551"
-  },
   {
     "id": "38752762",
     "doi": "https://doi.org/10.1093/eurjpc/zwae174",
@@ -43095,21 +43112,21 @@
     "urls": "doi:https://doi.org/10.1093/eurjpc/zwae174; html:https://europepmc.org/articles/PMC11464100; pdf:https://europepmc.org/articles/PMC11464100?pdf=render"
   },
   {
-    "id": "36820079",
-    "doi": "https://doi.org/10.1183/23120541.00274-2022",
-    "title": "Characteristics and risk factors for post-COVID-19 breathlessness after hospitalisation for COVID-19.",
-    "authorString": "Daines L, Zheng B, Elneima O, Harrison E, Lone NI, Hurst JR, Brown JS, Sapey E, Chalmers JD, Quint JK, Pfeffer P, Siddiqui S, Walker S, Poinasamy K, McAuley H, Sereno M, Shikotra A, Singapuri A, Docherty AB, Marks M, Toshner M, Howard LS, Horsley A, Jenkins G, Porter JC, Ho LP, Raman B, Wain LV, Brightling CE, Evans RA, Heaney LG, De Soyza A, Sheikh A.",
+    "id": "31922447",
+    "doi": "https://doi.org/10.1177/0141076819890551",
+    "title": "Moving beyond project-specific patient and public involvement in research.",
+    "authorString": "Turner G, Aiyegbusi OL, Price G, Skrybant M, Calvert M.",
     "authorAffiliations": "",
-    "journalTitle": "ERJ open research",
-    "pubYear": "2023",
-    "date": "2023-01-01",
-    "isOpenAccess": "Y",
+    "journalTitle": "Journal of the Royal Society of Medicine",
+    "pubYear": "2020",
+    "date": "2020-01-01",
+    "isOpenAccess": "N",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Persistence of respiratory symptoms, particularly breathlessness, after acute coronavirus disease 2019 (COVID-19) infection has emerged as a significant clinical problem. We aimed to characterise and identify risk factors for patients with persistent breathlessness following COVID-19 hospitalisation.<h4>Methods</h4>PHOSP-COVID is a multicentre prospective cohort study of UK adults hospitalised for COVID-19. Clinical data were collected during hospitalisation and at a follow-up visit. Breathlessness was measured by a numeric rating scale of 0-10. We defined post-COVID-19 breathlessness as an increase in score of \u22651 compared to the pre-COVID-19 level. Multivariable logistic regression was used to identify risk factors and to develop a prediction model for post-COVID-19 breathlessness.<h4>Results</h4>We included 1226\u2005participants (37% female, median age 59\u2005years, 22% mechanically ventilated). At a median 5\u2005months after discharge, 50% reported post-COVID-19 breathlessness. Risk factors for post-COVID-19 breathlessness were socioeconomic deprivation (adjusted OR 1.67, 95% CI 1.14-2.44), pre-existing depression/anxiety (adjusted OR 1.58, 95% CI 1.06-2.35), female sex (adjusted OR 1.56, 95% CI 1.21-2.00) and admission duration (adjusted OR 1.01, 95% CI 1.00-1.02). Black ethnicity (adjusted OR 0.56, 95% CI 0.35-0.89) and older age groups (adjusted OR 0.31, 95% CI 0.14-0.66) were less likely to report post-COVID-19 breathlessness. Post-COVID-19 breathlessness was associated with worse performance on the shuttle walk test and forced vital capacity, but not with obstructive airflow limitation. The prediction model had fair discrimination (concordance statistic 0.66, 95% CI 0.63-0.69) and good calibration (calibration slope 1.00, 95% CI 0.80-1.21).<h4>Conclusions</h4>Post-COVID-19 breathlessness was commonly reported in this national cohort of patients hospitalised for COVID-19 and is likely to be a multifactorial problem with physical and emotional components.",
+    "abstract": "",
     "laySummary": "",
-    "urls": "pdf:https://openres.ersjournals.com/content/erjor/early/2023/01/26/23120541.00274-2022.full.pdf; doi:https://doi.org/10.1183/23120541.00274-2022; html:https://europepmc.org/articles/PMC9790090; pdf:https://europepmc.org/articles/PMC9790090?pdf=render"
+    "urls": "pdf:https://journals.sagepub.com/doi/pdf/10.1177/0141076819890551; doi:https://doi.org/10.1177/0141076819890551; html:https://europepmc.org/articles/PMC6961168; pdf:https://europepmc.org/articles/PMC6961168?pdf=render; doi:https://doi.org/10.1177/0141076819890551"
   },
   {
     "id": "31197928",
@@ -43128,6 +43145,23 @@
     "laySummary": "",
     "urls": "pdf:https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pds.4811; doi:https://doi.org/10.1002/pds.4811; html:https://europepmc.org/articles/PMC6618019; pdf:https://europepmc.org/articles/PMC6618019?pdf=render"
   },
+  {
+    "id": "36820079",
+    "doi": "https://doi.org/10.1183/23120541.00274-2022",
+    "title": "Characteristics and risk factors for post-COVID-19 breathlessness after hospitalisation for COVID-19.",
+    "authorString": "Daines L, Zheng B, Elneima O, Harrison E, Lone NI, Hurst JR, Brown JS, Sapey E, Chalmers JD, Quint JK, Pfeffer P, Siddiqui S, Walker S, Poinasamy K, McAuley H, Sereno M, Shikotra A, Singapuri A, Docherty AB, Marks M, Toshner M, Howard LS, Horsley A, Jenkins G, Porter JC, Ho LP, Raman B, Wain LV, Brightling CE, Evans RA, Heaney LG, De Soyza A, Sheikh A.",
+    "authorAffiliations": "",
+    "journalTitle": "ERJ open research",
+    "pubYear": "2023",
+    "date": "2023-01-01",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Persistence of respiratory symptoms, particularly breathlessness, after acute coronavirus disease 2019 (COVID-19) infection has emerged as a significant clinical problem. We aimed to characterise and identify risk factors for patients with persistent breathlessness following COVID-19 hospitalisation.<h4>Methods</h4>PHOSP-COVID is a multicentre prospective cohort study of UK adults hospitalised for COVID-19. Clinical data were collected during hospitalisation and at a follow-up visit. Breathlessness was measured by a numeric rating scale of 0-10. We defined post-COVID-19 breathlessness as an increase in score of \u22651 compared to the pre-COVID-19 level. Multivariable logistic regression was used to identify risk factors and to develop a prediction model for post-COVID-19 breathlessness.<h4>Results</h4>We included 1226\u2005participants (37% female, median age 59\u2005years, 22% mechanically ventilated). At a median 5\u2005months after discharge, 50% reported post-COVID-19 breathlessness. Risk factors for post-COVID-19 breathlessness were socioeconomic deprivation (adjusted OR 1.67, 95% CI 1.14-2.44), pre-existing depression/anxiety (adjusted OR 1.58, 95% CI 1.06-2.35), female sex (adjusted OR 1.56, 95% CI 1.21-2.00) and admission duration (adjusted OR 1.01, 95% CI 1.00-1.02). Black ethnicity (adjusted OR 0.56, 95% CI 0.35-0.89) and older age groups (adjusted OR 0.31, 95% CI 0.14-0.66) were less likely to report post-COVID-19 breathlessness. Post-COVID-19 breathlessness was associated with worse performance on the shuttle walk test and forced vital capacity, but not with obstructive airflow limitation. The prediction model had fair discrimination (concordance statistic 0.66, 95% CI 0.63-0.69) and good calibration (calibration slope 1.00, 95% CI 0.80-1.21).<h4>Conclusions</h4>Post-COVID-19 breathlessness was commonly reported in this national cohort of patients hospitalised for COVID-19 and is likely to be a multifactorial problem with physical and emotional components.",
+    "laySummary": "",
+    "urls": "pdf:https://openres.ersjournals.com/content/erjor/early/2023/01/26/23120541.00274-2022.full.pdf; doi:https://doi.org/10.1183/23120541.00274-2022; html:https://europepmc.org/articles/PMC9790090; pdf:https://europepmc.org/articles/PMC9790090?pdf=render"
+  },
   {
     "id": "33879482",
     "doi": "https://doi.org/10.1136/bmjopen-2020-042949",
@@ -43247,23 +43281,6 @@
     "laySummary": "",
     "urls": "pdf:https://bmcmedethics.biomedcentral.com/counter/pdf/10.1186/s12910-022-00875-9; doi:https://doi.org/10.1186/s12910-022-00875-9; html:https://europepmc.org/articles/PMC9756740; pdf:https://europepmc.org/articles/PMC9756740?pdf=render"
   },
-  {
-    "id": "36522333",
-    "doi": "https://doi.org/10.1038/s41467-022-35454-4",
-    "title": "Multi-omics identify falling LRRC15 as a COVID-19 severity marker and persistent pro-thrombotic signals in convalescence.",
-    "authorString": "Gisby JS, Buang NB, Papadaki A, Clarke CL, Malik TH, Medjeral-Thomas N, Pinheiro D, Mortimer PM, Lewis S, Sandhu E, McAdoo SP, Prendecki MF, Willicombe M, Pickering MC, Botto M, Thomas DC, Peters JE.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature communications",
-    "pubYear": "2022",
-    "date": "2022-12-15",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Patients with end-stage kidney disease (ESKD) are at high risk of severe COVID-19. Here, we perform longitudinal blood sampling of ESKD haemodialysis patients with COVID-19, collecting samples pre-infection, serially during infection, and after clinical recovery. Using plasma proteomics, and RNA-sequencing and flow cytometry of immune cells, we identify transcriptomic and proteomic signatures of COVID-19 severity, and find distinct temporal molecular profiles in patients with severe disease. Supervised learning reveals that the plasma proteome is a superior indicator of clinical severity than the PBMC transcriptome. We show that a decreasing trajectory of plasma LRRC15, a proposed co-receptor for SARS-CoV-2, is associated with a more severe clinical course. We observe that two months after the acute infection, patients still display dysregulated gene expression related to vascular, platelet and coagulation pathways, including PF4 (platelet factor 4), which may explain the prolonged thrombotic risk following COVID-19.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41467-022-35454-4.pdf; doi:https://doi.org/10.1038/s41467-022-35454-4; html:https://europepmc.org/articles/PMC9753891; pdf:https://europepmc.org/articles/PMC9753891?pdf=render"
-  },
   {
     "id": "31350032",
     "doi": "https://doi.org/10.1016/j.burns.2019.07.003",
@@ -43281,6 +43298,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.burns.2019.07.003"
   },
+  {
+    "id": "36522333",
+    "doi": "https://doi.org/10.1038/s41467-022-35454-4",
+    "title": "Multi-omics identify falling LRRC15 as a COVID-19 severity marker and persistent pro-thrombotic signals in convalescence.",
+    "authorString": "Gisby JS, Buang NB, Papadaki A, Clarke CL, Malik TH, Medjeral-Thomas N, Pinheiro D, Mortimer PM, Lewis S, Sandhu E, McAdoo SP, Prendecki MF, Willicombe M, Pickering MC, Botto M, Thomas DC, Peters JE.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature communications",
+    "pubYear": "2022",
+    "date": "2022-12-15",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Patients with end-stage kidney disease (ESKD) are at high risk of severe COVID-19. Here, we perform longitudinal blood sampling of ESKD haemodialysis patients with COVID-19, collecting samples pre-infection, serially during infection, and after clinical recovery. Using plasma proteomics, and RNA-sequencing and flow cytometry of immune cells, we identify transcriptomic and proteomic signatures of COVID-19 severity, and find distinct temporal molecular profiles in patients with severe disease. Supervised learning reveals that the plasma proteome is a superior indicator of clinical severity than the PBMC transcriptome. We show that a decreasing trajectory of plasma LRRC15, a proposed co-receptor for SARS-CoV-2, is associated with a more severe clinical course. We observe that two months after the acute infection, patients still display dysregulated gene expression related to vascular, platelet and coagulation pathways, including PF4 (platelet factor 4), which may explain the prolonged thrombotic risk following COVID-19.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41467-022-35454-4.pdf; doi:https://doi.org/10.1038/s41467-022-35454-4; html:https://europepmc.org/articles/PMC9753891; pdf:https://europepmc.org/articles/PMC9753891?pdf=render"
+  },
   {
     "id": "37923486",
     "doi": "https://doi.org/10.1016/s2352-3018(23)00233-3",
@@ -43536,23 +43570,6 @@
     "laySummary": "",
     "urls": "pdf:https://erj.ersjournals.com/content/erj/61/6/2201667.full.pdf; doi:https://doi.org/10.1183/13993003.01667-2022; html:https://europepmc.org/articles/PMC10284065; pdf:https://europepmc.org/articles/PMC10284065?pdf=render"
   },
-  {
-    "id": "36451358",
-    "doi": "https://doi.org/10.1016/j.nicl.2022.103253",
-    "title": "Hospitalisation for COVID-19 predicts long lasting cerebrovascular impairment: A prospective observational cohort study.",
-    "authorString": "Tsvetanov KA, Spindler LRB, Stamatakis EA, Newcombe VFJ, Lupson VC, Chatfield DA, Manktelow AE, Outtrim JG, Elmer A, Kingston N, Bradley JR, Bullmore ET, Rowe JB, Menon DK, Cambridge NeuroCOVID Group, NIHR COVID-19 BioResource, Cambridge NIHR Clinical Research Facility, CITIID-NIHR BioResource COVID-19 Collaboration.",
-    "authorAffiliations": "",
-    "journalTitle": "NeuroImage. Clinical",
-    "pubYear": "2022",
-    "date": "2022-11-07",
-    "isOpenAccess": "Y",
-    "keywords": "Cerebrovascular; Microvascular; Neurology; Cardiorespiratory; Covid-19; Sars-cov-2",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Human coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has multiple neurological consequences, but its long-term effect on brain health is still uncertain. The cerebrovascular consequences of COVID-19 may also affect brain health. We studied the chronic effect of COVID-19 on cerebrovascular health, in relation to acute severity, adverse clinical outcomes and in contrast to control group data. Here we assess cerebrovascular health in 45 patients six months after hospitalisation for acute COVID-19 using the resting state fluctuation amplitudes (RSFA) from functional magnetic resonance imaging, in relation to disease severity and in contrast with 42 controls. Acute COVID-19 severity was indexed by COVID-19 WHO Progression Scale, inflammatory and coagulatory biomarkers. Chronic widespread changes in frontoparietal RSFA were related to the severity of the acute COVID-19 episode. This relationship was not explained by chronic cardiorespiratory dysfunction, age, or sex. The level of cerebrovascular dysfunction was associated with cognitive, mental, and physical health at follow-up. The principal findings were consistent across univariate and multivariate approaches. The results indicate chronic cerebrovascular impairment following severe acute COVID-19, with the potential for long-term consequences on cognitive function and mental wellbeing.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.nicl.2022.103253; doi:https://doi.org/10.1016/j.nicl.2022.103253; html:https://europepmc.org/articles/PMC9639388; pdf:https://europepmc.org/articles/PMC9639388?pdf=render"
-  },
   {
     "id": "35875883",
     "doi": "https://doi.org/10.1093/cvr/cvac115",
@@ -43571,21 +43588,21 @@
     "urls": "pdf:https://academic.oup.com/cardiovascres/advance-article-pdf/doi/10.1093/cvr/cvac115/46855438/cvac115.pdf; doi:https://doi.org/10.1093/cvr/cvac115; html:https://europepmc.org/articles/PMC9384470; pdf:https://europepmc.org/articles/PMC9384470?pdf=render"
   },
   {
-    "id": "34972825",
-    "doi": "https://doi.org/10.1038/s41564-021-01029-0",
-    "title": "Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework.",
-    "authorString": "Nicholson G, Lehmann B, Padellini T, Pouwels KB, Jersakova R, Lomax J, King RE, Mallon AM, Diggle PJ, Richardson S, Blangiardo M, Holmes C.",
+    "id": "36451358",
+    "doi": "https://doi.org/10.1016/j.nicl.2022.103253",
+    "title": "Hospitalisation for COVID-19 predicts long lasting cerebrovascular impairment: A prospective observational cohort study.",
+    "authorString": "Tsvetanov KA, Spindler LRB, Stamatakis EA, Newcombe VFJ, Lupson VC, Chatfield DA, Manktelow AE, Outtrim JG, Elmer A, Kingston N, Bradley JR, Bullmore ET, Rowe JB, Menon DK, Cambridge NeuroCOVID Group, NIHR COVID-19 BioResource, Cambridge NIHR Clinical Research Facility, CITIID-NIHR BioResource COVID-19 Collaboration.",
     "authorAffiliations": "",
-    "journalTitle": "Nature microbiology",
+    "journalTitle": "NeuroImage. Clinical",
     "pubYear": "2022",
-    "date": "2021-12-31",
+    "date": "2022-11-07",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Cerebrovascular; Microvascular; Neurology; Cardiorespiratory; Covid-19; Sars-cov-2",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Global and national surveillance of SARS-CoV-2 epidemiology is mostly based on targeted schemes focused on testing individuals with symptoms. These tested groups are often unrepresentative of the wider population and exhibit test positivity rates that are biased upwards compared with the true population prevalence. Such data are routinely used to infer infection prevalence and the effective reproduction number, R<sub>t</sub>, which affects public health policy. Here, we describe a causal framework that provides debiased fine-scale spatiotemporal estimates by combining targeted test counts with data from a randomized surveillance study in the United Kingdom called REACT. Our probabilistic model includes a bias parameter that captures the increased probability of an infected individual being tested, relative to a non-infected individual, and transforms observed test counts to debiased estimates of the true underlying local prevalence and R<sub>t</sub>. We validated our approach on held-out REACT data over a 7-month period. Furthermore, our local estimates of R<sub>t</sub> are indicative of 1-week- and 2-week-ahead changes in SARS-CoV-2-positive case numbers. We also observed increases in estimated local prevalence and R<sub>t</sub> that reflect the spread of the Alpha and Delta variants. Our results illustrate how randomized surveys can augment targeted testing to improve statistical accuracy in monitoring the spread of emerging and ongoing infectious disease.",
+    "abstract": "Human coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has multiple neurological consequences, but its long-term effect on brain health is still uncertain. The cerebrovascular consequences of COVID-19 may also affect brain health. We studied the chronic effect of COVID-19 on cerebrovascular health, in relation to acute severity, adverse clinical outcomes and in contrast to control group data. Here we assess cerebrovascular health in 45 patients six months after hospitalisation for acute COVID-19 using the resting state fluctuation amplitudes (RSFA) from functional magnetic resonance imaging, in relation to disease severity and in contrast with 42 controls. Acute COVID-19 severity was indexed by COVID-19 WHO Progression Scale, inflammatory and coagulatory biomarkers. Chronic widespread changes in frontoparietal RSFA were related to the severity of the acute COVID-19 episode. This relationship was not explained by chronic cardiorespiratory dysfunction, age, or sex. The level of cerebrovascular dysfunction was associated with cognitive, mental, and physical health at follow-up. The principal findings were consistent across univariate and multivariate approaches. The results indicate chronic cerebrovascular impairment following severe acute COVID-19, with the potential for long-term consequences on cognitive function and mental wellbeing.",
     "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41564-021-01029-0.pdf; doi:https://doi.org/10.1038/s41564-021-01029-0; html:https://europepmc.org/articles/PMC8727294; pdf:https://europepmc.org/articles/PMC8727294?pdf=render"
+    "urls": "doi:https://doi.org/10.1016/j.nicl.2022.103253; doi:https://doi.org/10.1016/j.nicl.2022.103253; html:https://europepmc.org/articles/PMC9639388; pdf:https://europepmc.org/articles/PMC9639388?pdf=render"
   },
   {
     "id": "31995663",
@@ -43605,21 +43622,21 @@
     "urls": "pdf:https://ascpt.onlinelibrary.wiley.com/doi/pdfdirect/10.1111/cts.12725; doi:https://doi.org/10.1111/cts.12725; html:https://europepmc.org/articles/PMC7070790; pdf:https://europepmc.org/articles/PMC7070790?pdf=render"
   },
   {
-    "id": "34151270",
-    "doi": "https://doi.org/10.1136/bmjno-2021-000133",
-    "title": "Variation in waiting times by diagnostic category: an observational study of 1,951 referrals to a neurology outpatient clinic.",
-    "authorString": "Biggin F, Howcroft T, Davies Q, Knight J, Emsley HCA.",
+    "id": "34972825",
+    "doi": "https://doi.org/10.1038/s41564-021-01029-0",
+    "title": "Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework.",
+    "authorString": "Nicholson G, Lehmann B, Padellini T, Pouwels KB, Jersakova R, Lomax J, King RE, Mallon AM, Diggle PJ, Richardson S, Blangiardo M, Holmes C.",
     "authorAffiliations": "",
-    "journalTitle": "BMJ neurology open",
-    "pubYear": "2021",
-    "date": "2021-06-03",
+    "journalTitle": "Nature microbiology",
+    "pubYear": "2022",
+    "date": "2021-12-31",
     "isOpenAccess": "Y",
-    "keywords": "Neurology; Outpatient; Observational Study; Waiting Times; Routinely Collected Data",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Objective</h4>To investigate the frequency of diagnoses seen among new referrals to neurology outpatient services; to understand how these services are used through exploratory analysis of diagnostic tests and follow-up appointments; and to examine the waiting times between referral and appointment.<h4>Methods</h4>Routine data from new National Health Service appointments at a single consultant-delivered clinic between September 2016 and January 2019 were collected. These clinical data were then linked to hospital administrative data. The combined data were assigned diagnostic categories based on working diagnoses to allow further analysis using descriptive statistics.<h4>Results</h4>Five diagnostic categories accounted for 62% of all patients seen within the study period, the most common of which was headache disorders. Following a first appointment, 50% of all patients were offered at least one diagnostic test, and 35% were offered a follow-up appointment, with variation in both measures by diagnostic category. Waiting times from referral to appointment also varied by diagnostic category. 65% of patients with a seizure/epilepsy disorder were seen within the 18-week referral to treatment target, compared with 38% of patients with a movement disorder.<h4>Conclusions</h4>A small number of diagnostic categories account for a large proportion of new patients. This information could be used in policy decision-making to describe a minimum subset of categories for diagnostic coding. We found significant differences in waiting times by diagnostic category, as well as tests ordered, and follow-up offered; further investigation could address causes of variation.",
+    "abstract": "Global and national surveillance of SARS-CoV-2 epidemiology is mostly based on targeted schemes focused on testing individuals with symptoms. These tested groups are often unrepresentative of the wider population and exhibit test positivity rates that are biased upwards compared with the true population prevalence. Such data are routinely used to infer infection prevalence and the effective reproduction number, R<sub>t</sub>, which affects public health policy. Here, we describe a causal framework that provides debiased fine-scale spatiotemporal estimates by combining targeted test counts with data from a randomized surveillance study in the United Kingdom called REACT. Our probabilistic model includes a bias parameter that captures the increased probability of an infected individual being tested, relative to a non-infected individual, and transforms observed test counts to debiased estimates of the true underlying local prevalence and R<sub>t</sub>. We validated our approach on held-out REACT data over a 7-month period. Furthermore, our local estimates of R<sub>t</sub> are indicative of 1-week- and 2-week-ahead changes in SARS-CoV-2-positive case numbers. We also observed increases in estimated local prevalence and R<sub>t</sub> that reflect the spread of the Alpha and Delta variants. Our results illustrate how randomized surveys can augment targeted testing to improve statistical accuracy in monitoring the spread of emerging and ongoing infectious disease.",
     "laySummary": "",
-    "urls": "pdf:https://neurologyopen.bmj.com/content/bmjno/3/1/e000133.full.pdf; doi:https://doi.org/10.1136/bmjno-2021-000133; html:https://europepmc.org/articles/PMC8183200; pdf:https://europepmc.org/articles/PMC8183200?pdf=render"
+    "urls": "pdf:https://www.nature.com/articles/s41564-021-01029-0.pdf; doi:https://doi.org/10.1038/s41564-021-01029-0; html:https://europepmc.org/articles/PMC8727294; pdf:https://europepmc.org/articles/PMC8727294?pdf=render"
   },
   {
     "id": "31641117",
@@ -43638,6 +43655,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41467-019-12682-9.pdf; doi:https://doi.org/10.1038/s41467-019-12682-9; html:https://europepmc.org/articles/PMC6805929; pdf:https://europepmc.org/articles/PMC6805929?pdf=render"
   },
+  {
+    "id": "34151270",
+    "doi": "https://doi.org/10.1136/bmjno-2021-000133",
+    "title": "Variation in waiting times by diagnostic category: an observational study of 1,951 referrals to a neurology outpatient clinic.",
+    "authorString": "Biggin F, Howcroft T, Davies Q, Knight J, Emsley HCA.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ neurology open",
+    "pubYear": "2021",
+    "date": "2021-06-03",
+    "isOpenAccess": "Y",
+    "keywords": "Neurology; Outpatient; Observational Study; Waiting Times; Routinely Collected Data",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>To investigate the frequency of diagnoses seen among new referrals to neurology outpatient services; to understand how these services are used through exploratory analysis of diagnostic tests and follow-up appointments; and to examine the waiting times between referral and appointment.<h4>Methods</h4>Routine data from new National Health Service appointments at a single consultant-delivered clinic between September 2016 and January 2019 were collected. These clinical data were then linked to hospital administrative data. The combined data were assigned diagnostic categories based on working diagnoses to allow further analysis using descriptive statistics.<h4>Results</h4>Five diagnostic categories accounted for 62% of all patients seen within the study period, the most common of which was headache disorders. Following a first appointment, 50% of all patients were offered at least one diagnostic test, and 35% were offered a follow-up appointment, with variation in both measures by diagnostic category. Waiting times from referral to appointment also varied by diagnostic category. 65% of patients with a seizure/epilepsy disorder were seen within the 18-week referral to treatment target, compared with 38% of patients with a movement disorder.<h4>Conclusions</h4>A small number of diagnostic categories account for a large proportion of new patients. This information could be used in policy decision-making to describe a minimum subset of categories for diagnostic coding. We found significant differences in waiting times by diagnostic category, as well as tests ordered, and follow-up offered; further investigation could address causes of variation.",
+    "laySummary": "",
+    "urls": "pdf:https://neurologyopen.bmj.com/content/bmjno/3/1/e000133.full.pdf; doi:https://doi.org/10.1136/bmjno-2021-000133; html:https://europepmc.org/articles/PMC8183200; pdf:https://europepmc.org/articles/PMC8183200?pdf=render"
+  },
   {
     "id": "31647808",
     "doi": "https://doi.org/10.1371/journal.pgen.1008405",
@@ -43673,21 +43707,21 @@
     "urls": "doi:https://doi.org/10.1099/mgen.0.000391; doi:https://doi.org/10.1099/mgen.0.000391; html:https://europepmc.org/articles/PMC7478627; pdf:https://europepmc.org/articles/PMC7478627?pdf=render"
   },
   {
-    "id": "38508198",
-    "doi": "https://doi.org/10.1016/j.xgen.2024.100523",
-    "title": "Integrative polygenic risk score improves the prediction accuracy of complex traits and diseases.",
-    "authorString": "Truong B, Hull LE, Ruan Y, Huang QQ, Hornsby W, Martin H, van Heel DA, Wang Y, Martin AR, Lee SH, Natarajan P.",
+    "id": "33185739",
+    "doi": "https://doi.org/10.1007/s00395-020-00828-6",
+    "title": "Functional investigation of the coronary artery disease gene SVEP1.",
+    "authorString": "Winkler MJ, M\u00fcller P, Sharifi AM, Wobst J, Winter H, Mokry M, Ma L, van der Laan SW, Pang S, Miritsch B, Hinterdobler J, Werner J, Stiller B, G\u00fcldener U, Webb TR, Asselbergs FW, Bj\u00f6rkegren JLM, Maegdefessel L, Schunkert H, Sager HB, Kessler T.",
     "authorAffiliations": "",
-    "journalTitle": "Cell genomics",
-    "pubYear": "2024",
-    "date": "2024-03-19",
+    "journalTitle": "Basic research in cardiology",
+    "pubYear": "2020",
+    "date": "2020-11-13",
     "isOpenAccess": "Y",
-    "keywords": "Combination; Clinical Utility; South Asian; Integrative; Prs; Cross Ancestry",
+    "keywords": "Genetics; Atherosclerosis; coronary artery disease; Svep1",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Polygenic risk scores (PRSs) are an emerging tool to predict the clinical phenotypes and outcomes of individuals. We propose PRSmix, a framework that leverages the PRS corpus of a target trait to improve prediction accuracy, and PRSmix+, which incorporates genetically correlated traits to better capture the human genetic architecture for 47 and 32 diseases/traits in European and South Asian ancestries, respectively. PRSmix demonstrated a mean prediction accuracy improvement of 1.20-fold (95% confidence interval [CI], [1.10; 1.3]; p\u00a0= 9.17\u00a0\u00d7\u00a010<sup>-5</sup>) and 1.19-fold (95% CI, [1.11; 1.27]; p\u00a0= 1.92\u00a0\u00d7\u00a010<sup>-6</sup>), and PRSmix+ improved the prediction accuracy by 1.72-fold (95% CI, [1.40; 2.04]; p\u00a0= 7.58\u00a0\u00d7\u00a010<sup>-6</sup>) and 1.42-fold (95% CI, [1.25; 1.59]; p\u00a0= 8.01\u00a0\u00d7\u00a010<sup>-7</sup>) in European and South Asian ancestries, respectively. Compared to the previously cross-trait-combination methods with scores from pre-defined correlated traits, we demonstrated that our method improved prediction accuracy for coronary artery disease up to 3.27-fold (95% CI, [2.1; 4.44]; p value after false discovery rate (FDR) correction\u00a0= 2.6\u00a0\u00d7\u00a010<sup>-4</sup>). Our method provides a comprehensive framework to benchmark and leverage the combined power of PRS for maximal performance in a desired target population.",
+    "abstract": "A missense variant of the sushi, von Willebrand factor type A, EGF and pentraxin domain containing protein 1 (SVEP1) is genome-wide significantly associated with coronary artery disease. The mechanisms how SVEP1 impacts atherosclerosis are not known. We found endothelial cells (EC) and vascular smooth muscle cells to represent the major cellular source of SVEP1 in plaques. Plaques were larger in atherosclerosis-prone Svep1 haploinsufficient (ApoE<sup>-/-</sup>Svep1<sup>+/-</sup>) compared to Svep1 wild-type mice (ApoE<sup>-/-</sup>Svep1<sup>+/+</sup>) and ApoE<sup>-/-</sup>Svep1<sup>+/-</sup> mice displayed elevated plaque neutrophil, Ly6C<sup>high</sup> monocyte, and macrophage numbers. We assessed how leukocytes accumulated more inside plaques in ApoE<sup>-/-</sup>Svep1<sup>+/-</sup> mice and found enhanced leukocyte recruitment from blood into plaques. In vitro, we examined how SVEP1 deficiency promotes leukocyte recruitment and found elevated expression of the leukocyte attractant chemokine (C-X-C motif) ligand 1 (CXCL1) in EC after incubation with missense compared to wild-type SVEP1. Increasing wild-type SVEP1 levels silenced endothelial CXCL1 release. In line, plasma Cxcl1 levels were elevated in ApoE<sup>-/-</sup>Svep1<sup>+/-</sup> mice. Our studies reveal an atheroprotective role of SVEP1. Deficiency of wild-type Svep1 increased endothelial CXCL1 expression leading to enhanced recruitment of proinflammatory leukocytes from blood to plaque. Consequently, elevated vascular inflammation resulted in enhanced plaque progression in Svep1 deficiency.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1016/j.xgen.2024.100523; html:https://europepmc.org/articles/PMC11019356; pdf:https://europepmc.org/articles/PMC11019356?pdf=render"
+    "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s00395-020-00828-6.pdf; doi:https://doi.org/10.1007/s00395-020-00828-6; html:https://europepmc.org/articles/PMC7666586; pdf:https://europepmc.org/articles/PMC7666586?pdf=render"
   },
   {
     "id": "35189842",
@@ -43706,6 +43740,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmcpsychiatry.biomedcentral.com/track/pdf/10.1186/s12888-022-03753-1; doi:https://doi.org/10.1186/s12888-022-03753-1; html:https://europepmc.org/articles/PMC8860359; pdf:https://europepmc.org/articles/PMC8860359?pdf=render"
   },
+  {
+    "id": "38508198",
+    "doi": "https://doi.org/10.1016/j.xgen.2024.100523",
+    "title": "Integrative polygenic risk score improves the prediction accuracy of complex traits and diseases.",
+    "authorString": "Truong B, Hull LE, Ruan Y, Huang QQ, Hornsby W, Martin H, van Heel DA, Wang Y, Martin AR, Lee SH, Natarajan P.",
+    "authorAffiliations": "",
+    "journalTitle": "Cell genomics",
+    "pubYear": "2024",
+    "date": "2024-03-19",
+    "isOpenAccess": "Y",
+    "keywords": "Combination; Clinical Utility; South Asian; Integrative; Prs; Cross Ancestry",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Polygenic risk scores (PRSs) are an emerging tool to predict the clinical phenotypes and outcomes of individuals. We propose PRSmix, a framework that leverages the PRS corpus of a target trait to improve prediction accuracy, and PRSmix+, which incorporates genetically correlated traits to better capture the human genetic architecture for 47 and 32 diseases/traits in European and South Asian ancestries, respectively. PRSmix demonstrated a mean prediction accuracy improvement of 1.20-fold (95% confidence interval [CI], [1.10; 1.3]; p\u00a0= 9.17\u00a0\u00d7\u00a010<sup>-5</sup>) and 1.19-fold (95% CI, [1.11; 1.27]; p\u00a0= 1.92\u00a0\u00d7\u00a010<sup>-6</sup>), and PRSmix+ improved the prediction accuracy by 1.72-fold (95% CI, [1.40; 2.04]; p\u00a0= 7.58\u00a0\u00d7\u00a010<sup>-6</sup>) and 1.42-fold (95% CI, [1.25; 1.59]; p\u00a0= 8.01\u00a0\u00d7\u00a010<sup>-7</sup>) in European and South Asian ancestries, respectively. Compared to the previously cross-trait-combination methods with scores from pre-defined correlated traits, we demonstrated that our method improved prediction accuracy for coronary artery disease up to 3.27-fold (95% CI, [2.1; 4.44]; p value after false discovery rate (FDR) correction\u00a0= 2.6\u00a0\u00d7\u00a010<sup>-4</sup>). Our method provides a comprehensive framework to benchmark and leverage the combined power of PRS for maximal performance in a desired target population.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.1016/j.xgen.2024.100523; html:https://europepmc.org/articles/PMC11019356; pdf:https://europepmc.org/articles/PMC11019356?pdf=render"
+  },
   {
     "id": "35347521",
     "doi": "https://doi.org/10.1007/s11136-022-03119-w",
@@ -43723,23 +43774,6 @@
     "laySummary": "",
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s11136-022-03119-w.pdf; doi:https://doi.org/10.1007/s11136-022-03119-w; html:https://europepmc.org/articles/PMC9470606; pdf:https://europepmc.org/articles/PMC9470606?pdf=render"
   },
-  {
-    "id": "33185739",
-    "doi": "https://doi.org/10.1007/s00395-020-00828-6",
-    "title": "Functional investigation of the coronary artery disease gene SVEP1.",
-    "authorString": "Winkler MJ, M\u00fcller P, Sharifi AM, Wobst J, Winter H, Mokry M, Ma L, van der Laan SW, Pang S, Miritsch B, Hinterdobler J, Werner J, Stiller B, G\u00fcldener U, Webb TR, Asselbergs FW, Bj\u00f6rkegren JLM, Maegdefessel L, Schunkert H, Sager HB, Kessler T.",
-    "authorAffiliations": "",
-    "journalTitle": "Basic research in cardiology",
-    "pubYear": "2020",
-    "date": "2020-11-13",
-    "isOpenAccess": "Y",
-    "keywords": "Genetics; Atherosclerosis; coronary artery disease; Svep1",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "A missense variant of the sushi, von Willebrand factor type A, EGF and pentraxin domain containing protein 1 (SVEP1) is genome-wide significantly associated with coronary artery disease. The mechanisms how SVEP1 impacts atherosclerosis are not known. We found endothelial cells (EC) and vascular smooth muscle cells to represent the major cellular source of SVEP1 in plaques. Plaques were larger in atherosclerosis-prone Svep1 haploinsufficient (ApoE<sup>-/-</sup>Svep1<sup>+/-</sup>) compared to Svep1 wild-type mice (ApoE<sup>-/-</sup>Svep1<sup>+/+</sup>) and ApoE<sup>-/-</sup>Svep1<sup>+/-</sup> mice displayed elevated plaque neutrophil, Ly6C<sup>high</sup> monocyte, and macrophage numbers. We assessed how leukocytes accumulated more inside plaques in ApoE<sup>-/-</sup>Svep1<sup>+/-</sup> mice and found enhanced leukocyte recruitment from blood into plaques. In vitro, we examined how SVEP1 deficiency promotes leukocyte recruitment and found elevated expression of the leukocyte attractant chemokine (C-X-C motif) ligand 1 (CXCL1) in EC after incubation with missense compared to wild-type SVEP1. Increasing wild-type SVEP1 levels silenced endothelial CXCL1 release. In line, plasma Cxcl1 levels were elevated in ApoE<sup>-/-</sup>Svep1<sup>+/-</sup> mice. Our studies reveal an atheroprotective role of SVEP1. Deficiency of wild-type Svep1 increased endothelial CXCL1 expression leading to enhanced recruitment of proinflammatory leukocytes from blood to plaque. Consequently, elevated vascular inflammation resulted in enhanced plaque progression in Svep1 deficiency.",
-    "laySummary": "",
-    "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s00395-020-00828-6.pdf; doi:https://doi.org/10.1007/s00395-020-00828-6; html:https://europepmc.org/articles/PMC7666586; pdf:https://europepmc.org/articles/PMC7666586?pdf=render"
-  },
   {
     "id": "38514079",
     "doi": "https://doi.org/10.1136/bmj-2023-077764",
@@ -43775,21 +43809,21 @@
     "urls": "pdf:https://jamanetwork.com/journals/jamanetworkopen/articlepdf/2751559/seow_2019_oi_190459.pdf; doi:https://doi.org/10.1001/jamanetworkopen.2019.11970; html:https://europepmc.org/articles/PMC6755532"
   },
   {
-    "id": "36895957",
-    "doi": "https://doi.org/10.1093/braincomms/fcad037",
-    "title": "Investigating genotype-phenotype relationship of extreme neuropathic pain disorders in a UK national cohort.",
-    "authorString": "Themistocleous AC, Baskozos G, Blesneac I, Comini M, Megy K, Chong S, Deevi SVV, Ginsberg L, Gosal D, Hadden RDM, Horvath R, Mahdi-Rogers M, Manzur A, Mapeta R, Marshall A, Matthews E, McCarthy MI, Reilly MM, Renton T, Rice ASC, Vale TA, van Zuydam N, Walker SM, Woods CG, Bennett DLH.",
+    "id": "38689001",
+    "doi": "https://doi.org/10.1038/s41588-024-01714-w",
+    "title": "Genome-wide analysis in over 1 million individuals of European ancestry yields improved polygenic risk scores for blood pressure traits.",
+    "authorString": "Keaton JM, Kamali Z, Xie T, Vaez A, Williams A, Goleva SB, Ani A, Evangelou E, Hellwege JN, Yengo L, Young WJ, Traylor M, Giri A, Zheng Z, Zeng J, Chasman DI, Morris AP, Caulfield MJ, Hwang SJ, Kooner JS, Conen D, Attia JR, Morrison AC, Loos RJF, Kristiansson K, Schmidt R, Hicks AA, Pramstaller PP, Nelson CP, Samani NJ, Risch L, Gyllensten U, Melander O, Riese H, Wilson JF, Campbell H, Rich SS, Psaty BM, Lu Y, Rotter JI, Guo X, Rice KM, Vollenweider P, Sundstr\u00f6m J, Langenberg C, Tobin MD, Giedraitis V, Luan J, Tuomilehto J, Kutalik Z, Ripatti S, Salomaa V, Girotto G, Trompet S, Jukema JW, van der Harst P, Ridker PM, Giulianini F, Vitart V, Goel A, Watkins H, Harris SE, Deary IJ, van der Most PJ, Oldehinkel AJ, Keavney BD, Hayward C, Campbell A, Boehnke M, Scott LJ, Boutin T, Mamasoula C, J\u00e4rvelin MR, Peters A, Gieger C, Lakatta EG, Cucca F, Hui J, Knekt P, Enroth S, De Borst MH, Pola\u0161ek O, Concas MP, Catamo E, Cocca M, Li-Gao R, Hofer E, Schmidt H, Spedicati B, Waldenberger M, Strachan DP, Laan M, Teumer A, D\u00f6rr M, Gudnason V, Cook JP, Ruggiero D, Kolcic I, Boerwinkle E, Traglia M, Lehtim\u00e4ki T, Raitakari OT, Johnson AD, Newton-Cheh C, Brown MJ, Dominiczak AF, Sever PJ, Poulter N, Chambers JC, Elosua R, Siscovick D, Esko T, Metspalu A, Strawbridge RJ, Laakso M, Hamsten A, Hottenga JJ, de Geus E, Morris AD, Palmer CNA, Nolte IM, Milaneschi Y, Marten J, Wright A, Zeggini E, Howson JMM, O'Donnell CJ, Spector T, Nalls MA, Simonsick EM, Liu Y, van Duijn CM, Butterworth AS, Danesh JN, Menni C, Wareham NJ, Khaw KT, Sun YV, Wilson PWF, Cho K, Visscher PM, Denny JC, Million Veteran Program, Lifelines Cohort Study, CHARGE consortium, ICBP Consortium, Levy D, Edwards TL, Munroe PB, Snieder H, Warren HR.",
     "authorAffiliations": "",
-    "journalTitle": "Brain communications",
-    "pubYear": "2023",
-    "date": "2023-02-20",
+    "journalTitle": "Nature genetics",
+    "pubYear": "2024",
+    "date": "2024-04-30",
     "isOpenAccess": "Y",
-    "keywords": "Sodium channels; Neuropathic pain; Peripheral Neuropathy; Whole Genome Sequencing",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "The aims of our study were to use whole genome sequencing in a cross-sectional cohort of patients to identify new variants in genes implicated in neuropathic pain, to determine the prevalence of known pathogenic variants and to understand the relationship between pathogenic variants and clinical presentation. Patients with extreme neuropathic pain phenotypes (both sensory loss and gain) were recruited from secondary care clinics in the UK and underwent whole genome sequencing as part of the National Institute for Health and Care Research Bioresource Rare Diseases project. A multidisciplinary team assessed the pathogenicity of rare variants in genes previously known to cause neuropathic pain disorders and exploratory analysis of research candidate genes was completed. Association testing for genes carrying rare variants was completed using the gene-wise approach of the combined burden and variance-component test SKAT-O. Patch clamp analysis was performed on transfected HEK293T cells for research candidate variants of genes encoding ion channels. The results include the following: (i) Medically actionable variants were found in 12% of study participants (205 recruited), including known pathogenic variants: <i>SCN9A(ENST00000409672.1):</i> c.2544T>C, p.Ile848Thr that causes inherited erythromelalgia, and <i>SPTLC1(ENST00000262554.2):</i>c.340T>G, p.Cys133Tr variant that causes hereditary sensory neuropathy type-1. (ii) Clinically relevant variants were most common in voltage-gated sodium channels (Na<sub>v</sub>). (iii) <i>SCN9A(ENST00000409672.1):</i>c.554G>A, pArg185His variant was more common in non-freezing cold injury participants than controls and causes a gain of function of Na<sub>V</sub>1.7 after cooling (the environmental trigger for non-freezing cold injury). (iv) Rare variant association testing showed a significant difference in distribution for genes NGF, <i>KIF1A</i>, <i>SCN8A</i>, <i>TRPM8</i>, <i>KIF1A</i>, <i>TRPA1</i> and the regulatory regions of genes <i>SCN11A</i>, <i>FLVCR1</i>, <i>KIF1A</i> and <i>SCN9A</i> between European participants with neuropathic pain and controls. (v) The <i>TRPA1(ENST00000262209.4):c.515C>T,</i> p.Ala172Val variant identified in participants with episodic somatic pain disorder demonstrated gain-of-channel function to agonist stimulation. Whole genome sequencing identified clinically relevant variants in over 10% of participants with extreme neuropathic pain phenotypes. The majority of these variants were found in ion channels. Combining genetic analysis with functional validation can lead to a better understanding as to how rare variants in ion channels lead to sensory neuron hyper-excitability, and how cold, as an environmental trigger, interacts with the gain-of-function Na<sub>V</sub>1.7 p.Arg185His variant. Our findings highlight the role of ion channel variants in the pathogenesis of extreme neuropathic pain disorders, likely mediated through changes in sensory neuron excitability and interaction with environmental triggers.",
+    "abstract": "Hypertension affects more than one billion people worldwide. Here we identify 113 novel loci, reporting a total of 2,103 independent genetic signals (P\u2009<\u20095\u2009\u00d7\u200910<sup>-8</sup>) from the largest single-stage blood pressure (BP) genome-wide association study to date (n\u2009=\u20091,028,980 European individuals). These associations explain more than 60% of single nucleotide polymorphism-based BP heritability. Comparing top versus bottom deciles of polygenic risk scores (PRSs) reveals clinically meaningful differences in BP (16.9\u2009mmHg systolic BP, 95% CI, 15.5-18.2\u2009mmHg, P\u2009=\u20092.22\u2009\u00d7\u200910<sup>-126</sup>) and more than a sevenfold higher odds of hypertension risk (odds ratio, 7.33; 95% CI, 5.54-9.70; P\u2009=\u20094.13\u2009\u00d7\u200910<sup>-44</sup>) in an independent dataset. Adding PRS into hypertension-prediction models increased the area under the receiver operating characteristic curve (AUROC) from 0.791 (95% CI, 0.781-0.801) to 0.826 (95% CI, 0.817-0.836, \u2206AUROC, 0.035, P\u2009=\u20091.98\u2009\u00d7\u200910<sup>-34</sup>). We compare the 2,103 loci results in non-European ancestries and show significant PRS associations in a large African-American sample. Secondary analyses implicate 500 genes previously unreported for BP. Our study highlights the role of increasingly large genomic studies for precision health research.",
     "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/braincomms/article-pdf/5/2/fcad037/49446967/fcad037.pdf; doi:https://doi.org/10.1093/braincomms/fcad037; html:https://europepmc.org/articles/PMC9991512; pdf:https://europepmc.org/articles/PMC9991512?pdf=render"
+    "urls": "doi:https://doi.org/10.1038/s41588-024-01714-w; html:https://europepmc.org/articles/PMC11096100; pdf:https://europepmc.org/articles/PMC11096100?pdf=render"
   },
   {
     "id": "35294976",
@@ -43809,21 +43843,21 @@
     "urls": "pdf:https://link.springer.com/content/pdf/10.1007/s00127-022-02221-1.pdf; doi:https://doi.org/10.1007/s00127-022-02221-1; html:https://europepmc.org/articles/PMC9477900; pdf:https://europepmc.org/articles/PMC9477900?pdf=render"
   },
   {
-    "id": "38689001",
-    "doi": "https://doi.org/10.1038/s41588-024-01714-w",
-    "title": "Genome-wide analysis in over 1 million individuals of European ancestry yields improved polygenic risk scores for blood pressure traits.",
-    "authorString": "Keaton JM, Kamali Z, Xie T, Vaez A, Williams A, Goleva SB, Ani A, Evangelou E, Hellwege JN, Yengo L, Young WJ, Traylor M, Giri A, Zheng Z, Zeng J, Chasman DI, Morris AP, Caulfield MJ, Hwang SJ, Kooner JS, Conen D, Attia JR, Morrison AC, Loos RJF, Kristiansson K, Schmidt R, Hicks AA, Pramstaller PP, Nelson CP, Samani NJ, Risch L, Gyllensten U, Melander O, Riese H, Wilson JF, Campbell H, Rich SS, Psaty BM, Lu Y, Rotter JI, Guo X, Rice KM, Vollenweider P, Sundstr\u00f6m J, Langenberg C, Tobin MD, Giedraitis V, Luan J, Tuomilehto J, Kutalik Z, Ripatti S, Salomaa V, Girotto G, Trompet S, Jukema JW, van der Harst P, Ridker PM, Giulianini F, Vitart V, Goel A, Watkins H, Harris SE, Deary IJ, van der Most PJ, Oldehinkel AJ, Keavney BD, Hayward C, Campbell A, Boehnke M, Scott LJ, Boutin T, Mamasoula C, J\u00e4rvelin MR, Peters A, Gieger C, Lakatta EG, Cucca F, Hui J, Knekt P, Enroth S, De Borst MH, Pola\u0161ek O, Concas MP, Catamo E, Cocca M, Li-Gao R, Hofer E, Schmidt H, Spedicati B, Waldenberger M, Strachan DP, Laan M, Teumer A, D\u00f6rr M, Gudnason V, Cook JP, Ruggiero D, Kolcic I, Boerwinkle E, Traglia M, Lehtim\u00e4ki T, Raitakari OT, Johnson AD, Newton-Cheh C, Brown MJ, Dominiczak AF, Sever PJ, Poulter N, Chambers JC, Elosua R, Siscovick D, Esko T, Metspalu A, Strawbridge RJ, Laakso M, Hamsten A, Hottenga JJ, de Geus E, Morris AD, Palmer CNA, Nolte IM, Milaneschi Y, Marten J, Wright A, Zeggini E, Howson JMM, O'Donnell CJ, Spector T, Nalls MA, Simonsick EM, Liu Y, van Duijn CM, Butterworth AS, Danesh JN, Menni C, Wareham NJ, Khaw KT, Sun YV, Wilson PWF, Cho K, Visscher PM, Denny JC, Million Veteran Program, Lifelines Cohort Study, CHARGE consortium, ICBP Consortium, Levy D, Edwards TL, Munroe PB, Snieder H, Warren HR.",
+    "id": "36895957",
+    "doi": "https://doi.org/10.1093/braincomms/fcad037",
+    "title": "Investigating genotype-phenotype relationship of extreme neuropathic pain disorders in a UK national cohort.",
+    "authorString": "Themistocleous AC, Baskozos G, Blesneac I, Comini M, Megy K, Chong S, Deevi SVV, Ginsberg L, Gosal D, Hadden RDM, Horvath R, Mahdi-Rogers M, Manzur A, Mapeta R, Marshall A, Matthews E, McCarthy MI, Reilly MM, Renton T, Rice ASC, Vale TA, van Zuydam N, Walker SM, Woods CG, Bennett DLH.",
     "authorAffiliations": "",
-    "journalTitle": "Nature genetics",
-    "pubYear": "2024",
-    "date": "2024-04-30",
+    "journalTitle": "Brain communications",
+    "pubYear": "2023",
+    "date": "2023-02-20",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Sodium channels; Neuropathic pain; Peripheral Neuropathy; Whole Genome Sequencing",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Hypertension affects more than one billion people worldwide. Here we identify 113 novel loci, reporting a total of 2,103 independent genetic signals (P\u2009<\u20095\u2009\u00d7\u200910<sup>-8</sup>) from the largest single-stage blood pressure (BP) genome-wide association study to date (n\u2009=\u20091,028,980 European individuals). These associations explain more than 60% of single nucleotide polymorphism-based BP heritability. Comparing top versus bottom deciles of polygenic risk scores (PRSs) reveals clinically meaningful differences in BP (16.9\u2009mmHg systolic BP, 95% CI, 15.5-18.2\u2009mmHg, P\u2009=\u20092.22\u2009\u00d7\u200910<sup>-126</sup>) and more than a sevenfold higher odds of hypertension risk (odds ratio, 7.33; 95% CI, 5.54-9.70; P\u2009=\u20094.13\u2009\u00d7\u200910<sup>-44</sup>) in an independent dataset. Adding PRS into hypertension-prediction models increased the area under the receiver operating characteristic curve (AUROC) from 0.791 (95% CI, 0.781-0.801) to 0.826 (95% CI, 0.817-0.836, \u2206AUROC, 0.035, P\u2009=\u20091.98\u2009\u00d7\u200910<sup>-34</sup>). We compare the 2,103 loci results in non-European ancestries and show significant PRS associations in a large African-American sample. Secondary analyses implicate 500 genes previously unreported for BP. Our study highlights the role of increasingly large genomic studies for precision health research.",
+    "abstract": "The aims of our study were to use whole genome sequencing in a cross-sectional cohort of patients to identify new variants in genes implicated in neuropathic pain, to determine the prevalence of known pathogenic variants and to understand the relationship between pathogenic variants and clinical presentation. Patients with extreme neuropathic pain phenotypes (both sensory loss and gain) were recruited from secondary care clinics in the UK and underwent whole genome sequencing as part of the National Institute for Health and Care Research Bioresource Rare Diseases project. A multidisciplinary team assessed the pathogenicity of rare variants in genes previously known to cause neuropathic pain disorders and exploratory analysis of research candidate genes was completed. Association testing for genes carrying rare variants was completed using the gene-wise approach of the combined burden and variance-component test SKAT-O. Patch clamp analysis was performed on transfected HEK293T cells for research candidate variants of genes encoding ion channels. The results include the following: (i) Medically actionable variants were found in 12% of study participants (205 recruited), including known pathogenic variants: <i>SCN9A(ENST00000409672.1):</i> c.2544T>C, p.Ile848Thr that causes inherited erythromelalgia, and <i>SPTLC1(ENST00000262554.2):</i>c.340T>G, p.Cys133Tr variant that causes hereditary sensory neuropathy type-1. (ii) Clinically relevant variants were most common in voltage-gated sodium channels (Na<sub>v</sub>). (iii) <i>SCN9A(ENST00000409672.1):</i>c.554G>A, pArg185His variant was more common in non-freezing cold injury participants than controls and causes a gain of function of Na<sub>V</sub>1.7 after cooling (the environmental trigger for non-freezing cold injury). (iv) Rare variant association testing showed a significant difference in distribution for genes NGF, <i>KIF1A</i>, <i>SCN8A</i>, <i>TRPM8</i>, <i>KIF1A</i>, <i>TRPA1</i> and the regulatory regions of genes <i>SCN11A</i>, <i>FLVCR1</i>, <i>KIF1A</i> and <i>SCN9A</i> between European participants with neuropathic pain and controls. (v) The <i>TRPA1(ENST00000262209.4):c.515C>T,</i> p.Ala172Val variant identified in participants with episodic somatic pain disorder demonstrated gain-of-channel function to agonist stimulation. Whole genome sequencing identified clinically relevant variants in over 10% of participants with extreme neuropathic pain phenotypes. The majority of these variants were found in ion channels. Combining genetic analysis with functional validation can lead to a better understanding as to how rare variants in ion channels lead to sensory neuron hyper-excitability, and how cold, as an environmental trigger, interacts with the gain-of-function Na<sub>V</sub>1.7 p.Arg185His variant. Our findings highlight the role of ion channel variants in the pathogenesis of extreme neuropathic pain disorders, likely mediated through changes in sensory neuron excitability and interaction with environmental triggers.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1038/s41588-024-01714-w; html:https://europepmc.org/articles/PMC11096100; pdf:https://europepmc.org/articles/PMC11096100?pdf=render"
+    "urls": "pdf:https://academic.oup.com/braincomms/article-pdf/5/2/fcad037/49446967/fcad037.pdf; doi:https://doi.org/10.1093/braincomms/fcad037; html:https://europepmc.org/articles/PMC9991512; pdf:https://europepmc.org/articles/PMC9991512?pdf=render"
   },
   {
     "id": "32095773",
@@ -44234,21 +44268,21 @@
     "urls": "pdf:https://www.nature.com/articles/s41598-019-55098-7.pdf; doi:https://doi.org/10.1038/s41598-019-55098-7; html:https://europepmc.org/articles/PMC6904466; pdf:https://europepmc.org/articles/PMC6904466?pdf=render"
   },
   {
-    "id": "35112706",
-    "doi": "https://doi.org/10.1242/dmm.049257",
-    "title": "Molecular Subtyping Resource: a user-friendly tool for rapid biological discovery from transcriptional data.",
-    "authorString": "Ahmaderaghi B, Amirkhah R, Jackson J, Lannagan TRM, Gilroy K, Malla SB, Redmond KL, Quinn G, McDade SS, ACRCelerate Consortium, Maughan T, Leedham S, Campbell ASD, Sansom OJ, Lawler M, Dunne PD.",
+    "id": "36812516",
+    "doi": "https://doi.org/10.1371/journal.pdig.0000007",
+    "title": "A proteomic survival predictor for COVID-19 patients in intensive care.",
+    "authorString": "Demichev V, Tober-Lau P, Nazarenko T, Lemke O, Kaur Aulakh S, Whitwell HJ, R\u00f6hl A, Freiwald A, Mittermaier M, Szyrwiel L, Ludwig D, Correia-Melo C, Lippert LJ, Helbig ET, Stubbemann P, Olk N, Thibeault C, Gr\u00fcning NM, Blyuss O, Vernardis S, White M, Messner CB, Joannidis M, Sonnweber T, Klein SJ, Pizzini A, Wohlfarter Y, Sahanic S, Hilbe R, Schaefer B, Wagner S, Machleidt F, Garcia C, Ruwwe-Gl\u00f6senkamp C, Lingscheid T, Bosquillon de Jarcy L, Stegemann MS, Pfeiffer M, J\u00fcrgens L, Denker S, Zickler D, Spies C, Edel A, M\u00fcller NB, Enghard P, Zelezniak A, Bellmann-Weiler R, Weiss G, Campbell A, Hayward C, Porteous DJ, Marioni RE, Uhrig A, Zoller H, L\u00f6ffler-Ragg J, Keller MA, Tancevski I, Timms JF, Zaikin A, Hippenstiel S, Ramharter M, M\u00fcller-Redetzky H, Witzenrath M, Suttorp N, Lilley K, M\u00fclleder M, Sander LE, PA-COVID-19 Study group, Kurth F, Ralser M.",
     "authorAffiliations": "",
-    "journalTitle": "Disease models & mechanisms",
+    "journalTitle": "PLOS digital health",
     "pubYear": "2022",
-    "date": "2022-03-30",
+    "date": "2022-01-18",
     "isOpenAccess": "Y",
-    "keywords": "Bioinformatics; Rna-seq; Data Analytics",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Generation of transcriptional data has dramatically increased in the past decade, driving the development of analytical algorithms that enable interrogation of the biology underpinning the profiled samples. However, these resources require users to have expertise in data wrangling and analytics, reducing opportunities for biological discovery by 'wet-lab' users with a limited programming skillset. Although commercial solutions exist, costs for software access can be prohibitive for academic research groups. To address these challenges, we have developed an open source and user-friendly data analysis platform for on-the-fly bioinformatic interrogation of transcriptional data derived from human or mouse tissue, called Molecular Subtyping Resource (MouSR). This internet-accessible analytical tool, https://mousr.qub.ac.uk/, enables users to easily interrogate their data using an intuitive 'point-and-click' interface, which includes a suite of molecular characterisation options including quality control, differential gene expression, gene set enrichment and microenvironmental cell population analyses from RNA sequencing. The MouSR online tool provides a unique freely available option for users to perform rapid transcriptomic analyses and comprehensive interrogation of the signalling underpinning transcriptional datasets, which alleviates a major bottleneck for biological discovery. This article has an associated First Person interview with the first author of the paper.",
+    "abstract": "Global healthcare systems are challenged by the COVID-19 pandemic. There is a need to optimize allocation of treatment and resources in intensive care, as clinically established risk assessments such as SOFA and APACHE II scores show only limited performance for predicting the survival of severely ill COVID-19 patients. Additional tools are also needed to monitor treatment, including experimental therapies in clinical trials. Comprehensively capturing human physiology, we speculated that proteomics in combination with new data-driven analysis strategies could produce a new generation of prognostic discriminators. We studied two independent cohorts of patients with severe COVID-19 who required intensive care and invasive mechanical ventilation. SOFA score, Charlson comorbidity index, and APACHE II score showed limited performance in predicting the COVID-19 outcome. Instead, the quantification of 321 plasma protein groups at 349 timepoints in 50 critically ill patients receiving invasive mechanical ventilation revealed 14 proteins that showed trajectories different between survivors and non-survivors. A predictor trained on proteomic measurements obtained at the first time point at maximum treatment level (i.e. WHO grade 7), which was weeks before the outcome, achieved accurate classification of survivors (AUROC 0.81). We tested the established predictor on an independent validation cohort (AUROC 1.0). The majority of proteins with high relevance in the prediction model belong to the coagulation system and complement cascade. Our study demonstrates that plasma proteomics can give rise to prognostic predictors substantially outperforming current prognostic markers in intensive care.",
     "laySummary": "",
-    "urls": "doi:https://doi.org/10.1242/dmm.049257; doi:https://doi.org/10.1242/dmm.049257; html:https://europepmc.org/articles/PMC8990914"
+    "urls": "pdf:https://journals.plos.org/digitalhealth/article/file?id=10.1371/journal.pdig.0000007&type=printable; doi:https://doi.org/10.1371/journal.pdig.0000007; html:https://europepmc.org/articles/PMC9931303; pdf:https://europepmc.org/articles/PMC9931303?pdf=render"
   },
   {
     "id": "32936291",
@@ -44268,38 +44302,38 @@
     "urls": "pdf:https://jamanetwork.com/journals/jamadermatology/articlepdf/2770779/jamadermatology_benzianolsson_2020_oi_200054_1604610894.93046.pdf; doi:https://doi.org/10.1001/jamadermatol.2020.3275; html:https://europepmc.org/articles/PMC7495329"
   },
   {
-    "id": "35337642",
-    "doi": "https://doi.org/10.1016/s2589-7500(22)00018-8",
-    "title": "Implementation of corticosteroids in treatment of COVID-19 in the ISARIC WHO Clinical Characterisation Protocol UK: prospective, cohort study.",
-    "authorString": "N\u00e4rhi F, Moonesinghe SR, Shenkin SD, Drake TM, Mulholland RH, Donegan C, Dunning J, Fairfield CJ, Girvan M, Hardwick HE, Ho A, Leeming G, Nguyen-Van-Tam JS, Pius R, Russell CD, Shaw CA, Spencer RG, Turtle L, Openshaw PJM, Baillie JK, Harrison EM, Semple MG, Docherty AB, ISARIC4C investigators.",
+    "id": "35112706",
+    "doi": "https://doi.org/10.1242/dmm.049257",
+    "title": "Molecular Subtyping Resource: a user-friendly tool for rapid biological discovery from transcriptional data.",
+    "authorString": "Ahmaderaghi B, Amirkhah R, Jackson J, Lannagan TRM, Gilroy K, Malla SB, Redmond KL, Quinn G, McDade SS, ACRCelerate Consortium, Maughan T, Leedham S, Campbell ASD, Sansom OJ, Lawler M, Dunne PD.",
     "authorAffiliations": "",
-    "journalTitle": "The Lancet. Digital health",
+    "journalTitle": "Disease models & mechanisms",
     "pubYear": "2022",
-    "date": "2022-04-01",
+    "date": "2022-03-30",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Bioinformatics; Rna-seq; Data Analytics",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "<h4>Background</h4>Dexamethasone was the first intervention proven to reduce mortality in patients with COVID-19 being treated in hospital. We aimed to evaluate the adoption of corticosteroids in the treatment of COVID-19 in the UK after the RECOVERY trial publication on June 16, 2020, and to identify discrepancies in care.<h4>Methods</h4>We did an audit of clinical implementation of corticosteroids in a prospective, observational, cohort study in 237 UK acute care hospitals between March 16, 2020, and April 14, 2021, restricted to patients aged 18 years or older with proven or high likelihood of COVID-19, who received supplementary oxygen. The primary outcome was administration of dexamethasone, prednisolone, hydrocortisone, or methylprednisolone. This study is registered with ISRCTN, ISRCTN66726260.<h4>Findings</h4>Between June 17, 2020, and April 14, 2021, 47\u2008795 (75\u00b72%) of 63\u2008525 of patients on supplementary oxygen received corticosteroids, higher among patients requiring critical care than in those who received ward care (11\u2008185 [86\u00b76%] of 12\u2008909 vs 36\u2008415 [72\u00b74%] of 50\u2008278). Patients 50 years or older were significantly less likely to receive corticosteroids than those younger than 50 years (adjusted odds ratio 0\u00b779 [95% CI 0\u00b770-0\u00b789], p=0\u00b70001, for 70-79 years; 0\u00b752 [0\u00b746-0\u00b758], p<0\u00b70001, for >80 years), independent of patient demographics and illness severity. 84 (54\u00b72%) of 155 pregnant women received corticosteroids. Rates of corticosteroid administration increased from 27\u00b75% in the week before June 16, 2020, to 75-80% in January, 2021.<h4>Interpretation</h4>Implementation of corticosteroids into clinical practice in the UK for patients with COVID-19 has been successful, but not universal. Patients older than 70 years, independent of illness severity, chronic neurological disease, and dementia, were less likely to receive corticosteroids than those who were younger, as were pregnant women. This could reflect appropriate clinical decision making, but the possibility of inequitable access to life-saving care should be considered.<h4>Funding</h4>UK National Institute for Health Research and UK Medical Research Council.",
+    "abstract": "Generation of transcriptional data has dramatically increased in the past decade, driving the development of analytical algorithms that enable interrogation of the biology underpinning the profiled samples. However, these resources require users to have expertise in data wrangling and analytics, reducing opportunities for biological discovery by 'wet-lab' users with a limited programming skillset. Although commercial solutions exist, costs for software access can be prohibitive for academic research groups. To address these challenges, we have developed an open source and user-friendly data analysis platform for on-the-fly bioinformatic interrogation of transcriptional data derived from human or mouse tissue, called Molecular Subtyping Resource (MouSR). This internet-accessible analytical tool, https://mousr.qub.ac.uk/, enables users to easily interrogate their data using an intuitive 'point-and-click' interface, which includes a suite of molecular characterisation options including quality control, differential gene expression, gene set enrichment and microenvironmental cell population analyses from RNA sequencing. The MouSR online tool provides a unique freely available option for users to perform rapid transcriptomic analyses and comprehensive interrogation of the signalling underpinning transcriptional datasets, which alleviates a major bottleneck for biological discovery. This article has an associated First Person interview with the first author of the paper.",
     "laySummary": "",
-    "urls": "pdf:http://www.thelancet.com/article/S2589750022000188/pdf; doi:https://doi.org/10.1016/S2589-7500(22)00018-8; html:https://europepmc.org/articles/PMC8940185"
+    "urls": "doi:https://doi.org/10.1242/dmm.049257; doi:https://doi.org/10.1242/dmm.049257; html:https://europepmc.org/articles/PMC8990914"
   },
   {
-    "id": "36812516",
-    "doi": "https://doi.org/10.1371/journal.pdig.0000007",
-    "title": "A proteomic survival predictor for COVID-19 patients in intensive care.",
-    "authorString": "Demichev V, Tober-Lau P, Nazarenko T, Lemke O, Kaur Aulakh S, Whitwell HJ, R\u00f6hl A, Freiwald A, Mittermaier M, Szyrwiel L, Ludwig D, Correia-Melo C, Lippert LJ, Helbig ET, Stubbemann P, Olk N, Thibeault C, Gr\u00fcning NM, Blyuss O, Vernardis S, White M, Messner CB, Joannidis M, Sonnweber T, Klein SJ, Pizzini A, Wohlfarter Y, Sahanic S, Hilbe R, Schaefer B, Wagner S, Machleidt F, Garcia C, Ruwwe-Gl\u00f6senkamp C, Lingscheid T, Bosquillon de Jarcy L, Stegemann MS, Pfeiffer M, J\u00fcrgens L, Denker S, Zickler D, Spies C, Edel A, M\u00fcller NB, Enghard P, Zelezniak A, Bellmann-Weiler R, Weiss G, Campbell A, Hayward C, Porteous DJ, Marioni RE, Uhrig A, Zoller H, L\u00f6ffler-Ragg J, Keller MA, Tancevski I, Timms JF, Zaikin A, Hippenstiel S, Ramharter M, M\u00fcller-Redetzky H, Witzenrath M, Suttorp N, Lilley K, M\u00fclleder M, Sander LE, PA-COVID-19 Study group, Kurth F, Ralser M.",
+    "id": "35337642",
+    "doi": "https://doi.org/10.1016/s2589-7500(22)00018-8",
+    "title": "Implementation of corticosteroids in treatment of COVID-19 in the ISARIC WHO Clinical Characterisation Protocol UK: prospective, cohort study.",
+    "authorString": "N\u00e4rhi F, Moonesinghe SR, Shenkin SD, Drake TM, Mulholland RH, Donegan C, Dunning J, Fairfield CJ, Girvan M, Hardwick HE, Ho A, Leeming G, Nguyen-Van-Tam JS, Pius R, Russell CD, Shaw CA, Spencer RG, Turtle L, Openshaw PJM, Baillie JK, Harrison EM, Semple MG, Docherty AB, ISARIC4C investigators.",
     "authorAffiliations": "",
-    "journalTitle": "PLOS digital health",
+    "journalTitle": "The Lancet. Digital health",
     "pubYear": "2022",
-    "date": "2022-01-18",
+    "date": "2022-04-01",
     "isOpenAccess": "Y",
     "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Global healthcare systems are challenged by the COVID-19 pandemic. There is a need to optimize allocation of treatment and resources in intensive care, as clinically established risk assessments such as SOFA and APACHE II scores show only limited performance for predicting the survival of severely ill COVID-19 patients. Additional tools are also needed to monitor treatment, including experimental therapies in clinical trials. Comprehensively capturing human physiology, we speculated that proteomics in combination with new data-driven analysis strategies could produce a new generation of prognostic discriminators. We studied two independent cohorts of patients with severe COVID-19 who required intensive care and invasive mechanical ventilation. SOFA score, Charlson comorbidity index, and APACHE II score showed limited performance in predicting the COVID-19 outcome. Instead, the quantification of 321 plasma protein groups at 349 timepoints in 50 critically ill patients receiving invasive mechanical ventilation revealed 14 proteins that showed trajectories different between survivors and non-survivors. A predictor trained on proteomic measurements obtained at the first time point at maximum treatment level (i.e. WHO grade 7), which was weeks before the outcome, achieved accurate classification of survivors (AUROC 0.81). We tested the established predictor on an independent validation cohort (AUROC 1.0). The majority of proteins with high relevance in the prediction model belong to the coagulation system and complement cascade. Our study demonstrates that plasma proteomics can give rise to prognostic predictors substantially outperforming current prognostic markers in intensive care.",
+    "abstract": "<h4>Background</h4>Dexamethasone was the first intervention proven to reduce mortality in patients with COVID-19 being treated in hospital. We aimed to evaluate the adoption of corticosteroids in the treatment of COVID-19 in the UK after the RECOVERY trial publication on June 16, 2020, and to identify discrepancies in care.<h4>Methods</h4>We did an audit of clinical implementation of corticosteroids in a prospective, observational, cohort study in 237 UK acute care hospitals between March 16, 2020, and April 14, 2021, restricted to patients aged 18 years or older with proven or high likelihood of COVID-19, who received supplementary oxygen. The primary outcome was administration of dexamethasone, prednisolone, hydrocortisone, or methylprednisolone. This study is registered with ISRCTN, ISRCTN66726260.<h4>Findings</h4>Between June 17, 2020, and April 14, 2021, 47\u2008795 (75\u00b72%) of 63\u2008525 of patients on supplementary oxygen received corticosteroids, higher among patients requiring critical care than in those who received ward care (11\u2008185 [86\u00b76%] of 12\u2008909 vs 36\u2008415 [72\u00b74%] of 50\u2008278). Patients 50 years or older were significantly less likely to receive corticosteroids than those younger than 50 years (adjusted odds ratio 0\u00b779 [95% CI 0\u00b770-0\u00b789], p=0\u00b70001, for 70-79 years; 0\u00b752 [0\u00b746-0\u00b758], p<0\u00b70001, for >80 years), independent of patient demographics and illness severity. 84 (54\u00b72%) of 155 pregnant women received corticosteroids. Rates of corticosteroid administration increased from 27\u00b75% in the week before June 16, 2020, to 75-80% in January, 2021.<h4>Interpretation</h4>Implementation of corticosteroids into clinical practice in the UK for patients with COVID-19 has been successful, but not universal. Patients older than 70 years, independent of illness severity, chronic neurological disease, and dementia, were less likely to receive corticosteroids than those who were younger, as were pregnant women. This could reflect appropriate clinical decision making, but the possibility of inequitable access to life-saving care should be considered.<h4>Funding</h4>UK National Institute for Health Research and UK Medical Research Council.",
     "laySummary": "",
-    "urls": "pdf:https://journals.plos.org/digitalhealth/article/file?id=10.1371/journal.pdig.0000007&type=printable; doi:https://doi.org/10.1371/journal.pdig.0000007; html:https://europepmc.org/articles/PMC9931303; pdf:https://europepmc.org/articles/PMC9931303?pdf=render"
+    "urls": "pdf:http://www.thelancet.com/article/S2589750022000188/pdf; doi:https://doi.org/10.1016/S2589-7500(22)00018-8; html:https://europepmc.org/articles/PMC8940185"
   },
   {
     "id": "31477933",
@@ -44488,6 +44522,23 @@
     "laySummary": "",
     "urls": "pdf:https://research-information.bris.ac.uk/ws/files/338319463/Movement_Disorders_2022_Reid_MED27_SLC6A7_and_MPPE1_Variants_in_a_Complex_Neurodevelopmental_Disorder_with_Severe.pdf; doi:https://doi.org/10.1002/mds.29147; html:https://europepmc.org/articles/PMC9796674; pdf:https://europepmc.org/articles/PMC9796674?pdf=render"
   },
+  {
+    "id": "32907855",
+    "doi": "https://doi.org/10.1136/bmj.m3339",
+    "title": "Risk stratification of patients admitted to hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: development and validation of the 4C Mortality Score.",
+    "authorString": "Knight SR, Ho A, Pius R, Buchan I, Carson G, Drake TM, Dunning J, Fairfield CJ, Gamble C, Green CA, Gupta R, Halpin S, Hardwick HE, Holden KA, Horby PW, Jackson C, Mclean KA, Merson L, Nguyen-Van-Tam JS, Norman L, Noursadeghi M, Olliaro PL, Pritchard MG, Russell CD, Shaw CA, Sheikh A, Solomon T, Sudlow C, Swann OV, Turtle LC, Openshaw PJ, Baillie JK, Semple MG, Docherty AB, Harrison EM, ISARIC4C investigators.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ (Clinical research ed.)",
+    "pubYear": "2020",
+    "date": "2020-09-09",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>To develop and validate a pragmatic risk score to predict mortality in patients admitted to hospital with coronavirus disease 2019 (covid-19).<h4>Design</h4>Prospective observational cohort study.<h4>Setting</h4>International Severe Acute Respiratory and emerging Infections Consortium (ISARIC) World Health Organization (WHO) Clinical Characterisation Protocol UK (CCP-UK) study (performed by the ISARIC Coronavirus Clinical Characterisation Consortium-ISARIC-4C) in 260 hospitals across England, Scotland, and Wales. Model training was performed on a cohort of patients recruited between 6 February and 20 May 2020, with validation conducted on a second cohort of patients recruited after model development between 21 May and 29 June 2020<i>.</i> PARTICIPANTS: Adults (age \u226518 years) admitted to hospital with covid-19 at least four weeks before final data extraction.<h4>Main outcome measure</h4>In-hospital mortality.<h4>Results</h4>35\u2009463 patients were included in the derivation dataset (mortality rate 32.2%) and 22\u2009361 in the validation dataset (mortality rate 30.1%). The final 4C Mortality Score included eight variables readily available at initial hospital assessment: age, sex, number of comorbidities, respiratory rate, peripheral oxygen saturation, level of consciousness, urea level, and C reactive protein (score range 0-21 points). The 4C Score showed high discrimination for mortality (derivation cohort: area under the receiver operating characteristic curve 0.79, 95% confidence interval 0.78 to 0.79; validation cohort: 0.77, 0.76 to 0.77) with excellent calibration (validation: calibration-in-the-large=0, slope=1.0). Patients with a score of at least 15 (n=4158, 19%) had a 62% mortality (positive predictive value 62%) compared with 1% mortality for those with a score of 3 or less (n=1650, 7%; negative predictive value 99%). Discriminatory performance was higher than 15 pre-existing risk stratification scores (area under the receiver operating characteristic curve range 0.61-0.76), with scores developed in other covid-19 cohorts often performing poorly (range 0.63-0.73).<h4>Conclusions</h4>An easy-to-use risk stratification score has been developed and validated based on commonly available parameters at hospital presentation. The 4C Mortality Score outperformed existing scores, showed utility to directly inform clinical decision making, and can be used to stratify patients admitted to hospital with covid-19 into different management groups. The score should be further validated to determine its applicability in other populations.<h4>Study registration</h4>ISRCTN66726260.",
+    "laySummary": "",
+    "urls": "pdf:https://www.bmj.com/content/bmj/370/bmj.m3339.full.pdf; doi:https://doi.org/10.1136/bmj.m3339; html:https://europepmc.org/articles/PMC7116472; pdf:https://europepmc.org/articles/PMC7116472?pdf=render"
+  },
   {
     "id": "35411997",
     "doi": "https://doi.org/10.1111/tmi.13752",
@@ -44522,23 +44573,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.jad.2022.11.051; doi:https://doi.org/10.1016/j.jad.2022.11.051; html:https://europepmc.org/articles/PMC10202820"
   },
-  {
-    "id": "32907855",
-    "doi": "https://doi.org/10.1136/bmj.m3339",
-    "title": "Risk stratification of patients admitted to hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: development and validation of the 4C Mortality Score.",
-    "authorString": "Knight SR, Ho A, Pius R, Buchan I, Carson G, Drake TM, Dunning J, Fairfield CJ, Gamble C, Green CA, Gupta R, Halpin S, Hardwick HE, Holden KA, Horby PW, Jackson C, Mclean KA, Merson L, Nguyen-Van-Tam JS, Norman L, Noursadeghi M, Olliaro PL, Pritchard MG, Russell CD, Shaw CA, Sheikh A, Solomon T, Sudlow C, Swann OV, Turtle LC, Openshaw PJ, Baillie JK, Semple MG, Docherty AB, Harrison EM, ISARIC4C investigators.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ (Clinical research ed.)",
-    "pubYear": "2020",
-    "date": "2020-09-09",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objective</h4>To develop and validate a pragmatic risk score to predict mortality in patients admitted to hospital with coronavirus disease 2019 (covid-19).<h4>Design</h4>Prospective observational cohort study.<h4>Setting</h4>International Severe Acute Respiratory and emerging Infections Consortium (ISARIC) World Health Organization (WHO) Clinical Characterisation Protocol UK (CCP-UK) study (performed by the ISARIC Coronavirus Clinical Characterisation Consortium-ISARIC-4C) in 260 hospitals across England, Scotland, and Wales. Model training was performed on a cohort of patients recruited between 6 February and 20 May 2020, with validation conducted on a second cohort of patients recruited after model development between 21 May and 29 June 2020<i>.</i> PARTICIPANTS: Adults (age \u226518 years) admitted to hospital with covid-19 at least four weeks before final data extraction.<h4>Main outcome measure</h4>In-hospital mortality.<h4>Results</h4>35\u2009463 patients were included in the derivation dataset (mortality rate 32.2%) and 22\u2009361 in the validation dataset (mortality rate 30.1%). The final 4C Mortality Score included eight variables readily available at initial hospital assessment: age, sex, number of comorbidities, respiratory rate, peripheral oxygen saturation, level of consciousness, urea level, and C reactive protein (score range 0-21 points). The 4C Score showed high discrimination for mortality (derivation cohort: area under the receiver operating characteristic curve 0.79, 95% confidence interval 0.78 to 0.79; validation cohort: 0.77, 0.76 to 0.77) with excellent calibration (validation: calibration-in-the-large=0, slope=1.0). Patients with a score of at least 15 (n=4158, 19%) had a 62% mortality (positive predictive value 62%) compared with 1% mortality for those with a score of 3 or less (n=1650, 7%; negative predictive value 99%). Discriminatory performance was higher than 15 pre-existing risk stratification scores (area under the receiver operating characteristic curve range 0.61-0.76), with scores developed in other covid-19 cohorts often performing poorly (range 0.63-0.73).<h4>Conclusions</h4>An easy-to-use risk stratification score has been developed and validated based on commonly available parameters at hospital presentation. The 4C Mortality Score outperformed existing scores, showed utility to directly inform clinical decision making, and can be used to stratify patients admitted to hospital with covid-19 into different management groups. The score should be further validated to determine its applicability in other populations.<h4>Study registration</h4>ISRCTN66726260.",
-    "laySummary": "",
-    "urls": "pdf:https://www.bmj.com/content/bmj/370/bmj.m3339.full.pdf; doi:https://doi.org/10.1136/bmj.m3339; html:https://europepmc.org/articles/PMC7116472; pdf:https://europepmc.org/articles/PMC7116472?pdf=render"
-  },
   {
     "id": "31479209",
     "doi": "https://doi.org/10.1056/nejmoa1907096",
@@ -44590,6 +44624,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/S2352-3026(24)00030-9; html:https://europepmc.org/articles/PMC10983828; pdf:https://europepmc.org/articles/PMC10983828?pdf=render"
   },
+  {
+    "id": "31801372",
+    "doi": "https://doi.org/10.1161/atvbaha.119.313226",
+    "title": "Carotid Intima-Media Thickness: Novel Loci, Sex-Specific Effects, and Genetic Correlations With Obesity and Glucometabolic Traits in UK Biobank.",
+    "authorString": "Strawbridge RJ, Ward J, Bailey MES, Cullen B, Ferguson A, Graham N, Johnston KJA, Lyall LM, Pearsall R, Pell J, Shaw RJ, Tank R, Lyall DM, Smith DJ.",
+    "authorAffiliations": "",
+    "journalTitle": "Arteriosclerosis, thrombosis, and vascular biology",
+    "pubYear": "2020",
+    "date": "2019-12-05",
+    "isOpenAccess": "Y",
+    "keywords": "Atherosclerosis; Obesity; Intima-media thickness; coronary artery disease; carotid artery; Genetics, Association Studies; Diabetes, Type 2",
+    "nationalPriorities": "Understanding the Causes of Disease",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>Atherosclerosis is the underlying cause of most cardiovascular disease, but mechanisms underlying atherosclerosis are incompletely understood. Ultrasound measurement of the carotid intima-media thickness (cIMT) can be used to measure vascular remodeling, which is indicative of atherosclerosis. Genome-wide association studies have identified many genetic loci associated with cIMT, but heterogeneity of measurements collected by many small cohorts have been a major limitation in these efforts. Here, we conducted genome-wide association analyses in UKB (UK Biobank; N=22\u2009179), the largest single study with consistent cIMT measurements. Approach and Results: We used BOLT-LMM software to run linear regression of cIMT in UKB, adjusted for age, sex, and genotyping chip. In white British participants, we identified 5 novel loci associated with cIMT and replicated most previously reported loci. In the first sex-specific analyses of cIMT, we identified a locus on chromosome 5, associated with cIMT in women only and highlight <i>VCAN</i> as a good candidate gene at this locus. Genetic correlations with body mass index and glucometabolic traits were also observed. Two loci influenced risk of ischemic heart disease.<h4>Conclusions</h4>These findings replicate previously reported associations, highlight novel biology, and provide new directions for investigating the sex differences observed in cardiovascular disease presentation and progression.",
+    "laySummary": "",
+    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/ATVBAHA.119.313226; doi:https://doi.org/10.1161/ATVBAHA.119.313226; html:https://europepmc.org/articles/PMC6975521; pdf:https://europepmc.org/articles/PMC6975521?pdf=render"
+  },
   {
     "id": "32601055",
     "doi": "https://doi.org/10.3399/bjgp20x710873",
@@ -44624,23 +44675,6 @@
     "laySummary": "",
     "urls": "pdf:https://ebm.bmj.com/content/ebmed/early/2023/02/20/bmjebm-2023-112253.full.pdf; doi:https://doi.org/10.1136/bmjebm-2023-112253; html:https://europepmc.org/articles/PMC10579468; pdf:https://europepmc.org/articles/PMC10579468?pdf=render"
   },
-  {
-    "id": "31801372",
-    "doi": "https://doi.org/10.1161/atvbaha.119.313226",
-    "title": "Carotid Intima-Media Thickness: Novel Loci, Sex-Specific Effects, and Genetic Correlations With Obesity and Glucometabolic Traits in UK Biobank.",
-    "authorString": "Strawbridge RJ, Ward J, Bailey MES, Cullen B, Ferguson A, Graham N, Johnston KJA, Lyall LM, Pearsall R, Pell J, Shaw RJ, Tank R, Lyall DM, Smith DJ.",
-    "authorAffiliations": "",
-    "journalTitle": "Arteriosclerosis, thrombosis, and vascular biology",
-    "pubYear": "2020",
-    "date": "2019-12-05",
-    "isOpenAccess": "Y",
-    "keywords": "Atherosclerosis; Obesity; Intima-media thickness; coronary artery disease; carotid artery; Genetics, Association Studies; Diabetes, Type 2",
-    "nationalPriorities": "Understanding the Causes of Disease",
-    "healthCategories": "",
-    "abstract": "<h4>Objective</h4>Atherosclerosis is the underlying cause of most cardiovascular disease, but mechanisms underlying atherosclerosis are incompletely understood. Ultrasound measurement of the carotid intima-media thickness (cIMT) can be used to measure vascular remodeling, which is indicative of atherosclerosis. Genome-wide association studies have identified many genetic loci associated with cIMT, but heterogeneity of measurements collected by many small cohorts have been a major limitation in these efforts. Here, we conducted genome-wide association analyses in UKB (UK Biobank; N=22\u2009179), the largest single study with consistent cIMT measurements. Approach and Results: We used BOLT-LMM software to run linear regression of cIMT in UKB, adjusted for age, sex, and genotyping chip. In white British participants, we identified 5 novel loci associated with cIMT and replicated most previously reported loci. In the first sex-specific analyses of cIMT, we identified a locus on chromosome 5, associated with cIMT in women only and highlight <i>VCAN</i> as a good candidate gene at this locus. Genetic correlations with body mass index and glucometabolic traits were also observed. Two loci influenced risk of ischemic heart disease.<h4>Conclusions</h4>These findings replicate previously reported associations, highlight novel biology, and provide new directions for investigating the sex differences observed in cardiovascular disease presentation and progression.",
-    "laySummary": "",
-    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/ATVBAHA.119.313226; doi:https://doi.org/10.1161/ATVBAHA.119.313226; html:https://europepmc.org/articles/PMC6975521; pdf:https://europepmc.org/articles/PMC6975521?pdf=render"
-  },
   {
     "id": "30842207",
     "doi": "https://doi.org/10.1136/heartjnl-2019-314763",
@@ -44845,23 +44879,6 @@
     "laySummary": "",
     "urls": "html:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7725961; doi:https://doi.org/10.1111/acer.14481; html:https://europepmc.org/articles/PMC7725961; pdf:https://europepmc.org/articles/PMC7725961?pdf=render; doi:https://doi.org/10.1111/acer.14481"
   },
-  {
-    "id": "34552082",
-    "doi": "https://doi.org/10.1038/s41467-021-25833-8",
-    "title": "Modelling the persistence and control of Rift Valley fever virus in a spatially heterogeneous landscape.",
-    "authorString": "Tennant WSD, Cardinale E, C\u00eatre-Sossah C, Moutroifi Y, Le Godais G, Colombi D, Spencer SEF, Tildesley MJ, Keeling MJ, Charafouddine O, Colizza V, Edmunds WJ, M\u00e9tras R.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature communications",
-    "pubYear": "2021",
-    "date": "2021-09-22",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The persistence mechanisms of Rift Valley fever (RVF), a zoonotic arboviral haemorrhagic fever, at both local and broader geographical scales have yet to be fully understood and rigorously quantified. We developed a mathematical metapopulation model describing RVF virus transmission in livestock across the four islands of the Comoros archipelago, accounting for island-specific environments and inter-island animal movements. By fitting our model in a Bayesian framework to 2004-2015 surveillance data, we estimated the importance of environmental drivers and animal movements on disease persistence, and tested the impact of different control scenarios on reducing disease burden throughout the archipelago. Here we report that (i) the archipelago network was able to sustain viral transmission in the absence of explicit disease introduction events after early 2007, (ii) repeated outbreaks during 2004-2020 may have gone under-detected by local surveillance, and (iii) co-ordinated within-island control measures are more effective than between-island animal movement restrictions.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41467-021-25833-8.pdf; doi:https://doi.org/10.1038/s41467-021-25833-8; html:https://europepmc.org/articles/PMC8458460; pdf:https://europepmc.org/articles/PMC8458460?pdf=render"
-  },
   {
     "id": "31730918",
     "doi": "https://doi.org/10.1016/j.jclinepi.2019.11.006",
@@ -44879,6 +44896,23 @@
     "laySummary": "Utilises data mining and routine data to identify a patients smoking status. Does not account for long term smoking behaviour and is limited by the smaller size the dataset.",
     "urls": "pdf:http://www.jclinepi.com/article/S0895435619304846/pdf; doi:https://doi.org/10.1016/j.jclinepi.2019.11.006"
   },
+  {
+    "id": "34552082",
+    "doi": "https://doi.org/10.1038/s41467-021-25833-8",
+    "title": "Modelling the persistence and control of Rift Valley fever virus in a spatially heterogeneous landscape.",
+    "authorString": "Tennant WSD, Cardinale E, C\u00eatre-Sossah C, Moutroifi Y, Le Godais G, Colombi D, Spencer SEF, Tildesley MJ, Keeling MJ, Charafouddine O, Colizza V, Edmunds WJ, M\u00e9tras R.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature communications",
+    "pubYear": "2021",
+    "date": "2021-09-22",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The persistence mechanisms of Rift Valley fever (RVF), a zoonotic arboviral haemorrhagic fever, at both local and broader geographical scales have yet to be fully understood and rigorously quantified. We developed a mathematical metapopulation model describing RVF virus transmission in livestock across the four islands of the Comoros archipelago, accounting for island-specific environments and inter-island animal movements. By fitting our model in a Bayesian framework to 2004-2015 surveillance data, we estimated the importance of environmental drivers and animal movements on disease persistence, and tested the impact of different control scenarios on reducing disease burden throughout the archipelago. Here we report that (i) the archipelago network was able to sustain viral transmission in the absence of explicit disease introduction events after early 2007, (ii) repeated outbreaks during 2004-2020 may have gone under-detected by local surveillance, and (iii) co-ordinated within-island control measures are more effective than between-island animal movement restrictions.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41467-021-25833-8.pdf; doi:https://doi.org/10.1038/s41467-021-25833-8; html:https://europepmc.org/articles/PMC8458460; pdf:https://europepmc.org/articles/PMC8458460?pdf=render"
+  },
   {
     "id": "34155378",
     "doi": "https://doi.org/10.1038/s41588-021-00887-y",
@@ -45032,23 +45066,6 @@
     "laySummary": "",
     "urls": "pdf:https://adc.bmj.com/content/archdischild/107/10/e29.full.pdf; doi:https://doi.org/10.1136/archdischild-2021-323616; html:https://europepmc.org/articles/PMC9157329; pdf:https://europepmc.org/articles/PMC9157329?pdf=render"
   },
-  {
-    "id": "37414900",
-    "doi": "https://doi.org/10.1038/s41591-023-02429-x",
-    "title": "A multi-ancestry polygenic risk score improves risk prediction for coronary artery disease.",
-    "authorString": "Patel AP, Wang M, Ruan Y, Koyama S, Clarke SL, Yang X, Tcheandjieu C, Agrawal S, Fahed AC, Ellinor PT, Genes & Health Research Team; the Million Veteran Program, Tsao PS, Sun YV, Cho K, Wilson PWF, Assimes TL, van Heel DA, Butterworth AS, Aragam KG, Natarajan P, Khera AV.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature medicine",
-    "pubYear": "2023",
-    "date": "2023-07-06",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "Identification of individuals at highest risk of coronary artery disease (CAD)-ideally before onset-remains an important public health need. Prior studies have developed genome-wide polygenic scores to enable risk stratification, reflecting the substantial inherited component to CAD risk. Here we develop a new and significantly improved polygenic score for CAD, termed GPS<sub>Mult</sub>, that incorporates genome-wide association data across five ancestries for CAD (>269,000 cases and >1,178,000 controls) and ten CAD risk factors. GPS<sub>Mult</sub> strongly associated with prevalent CAD (odds ratio per standard deviation 2.14, 95% confidence interval 2.10-2.19, P\u2009<\u20090.001) in UK Biobank participants of European ancestry, identifying 20.0% of the population with 3-fold increased risk and conversely 13.9% with 3-fold decreased risk as compared with those in the middle quintile. GPS<sub>Mult</sub> was also associated with incident CAD events (hazard ratio per standard deviation 1.73, 95% confidence interval 1.70-1.76, P\u2009<\u20090.001), identifying 3% of healthy individuals with risk of future CAD events equivalent to those with existing disease and significantly improving risk discrimination and reclassification. Across multiethnic, external validation datasets inclusive of 33,096, 124,467, 16,433 and 16,874 participants of African, European, Hispanic and South Asian ancestry, respectively, GPS<sub>Mult</sub> demonstrated increased strength of associations across all ancestries and outperformed all available previously published CAD polygenic scores. These data contribute a new GPS<sub>Mult</sub> for CAD to the field and provide a generalizable framework for how large-scale integration of genetic association data for CAD and related traits from diverse populations can meaningfully improve polygenic risk prediction.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41591-023-02429-x.pdf; doi:https://doi.org/10.1038/s41591-023-02429-x; html:https://europepmc.org/articles/PMC10353935; pdf:https://europepmc.org/articles/PMC10353935?pdf=render"
-  },
   {
     "id": "35820692",
     "doi": "https://doi.org/10.1136/bmj-2021-069881",
@@ -45066,6 +45083,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.bmj.com/content/bmj/378/bmj-2021-069881.full.pdf; doi:https://doi.org/10.1136/bmj-2021-069881; html:https://europepmc.org/articles/PMC9273913; pdf:https://europepmc.org/articles/PMC9273913?pdf=render"
   },
+  {
+    "id": "37414900",
+    "doi": "https://doi.org/10.1038/s41591-023-02429-x",
+    "title": "A multi-ancestry polygenic risk score improves risk prediction for coronary artery disease.",
+    "authorString": "Patel AP, Wang M, Ruan Y, Koyama S, Clarke SL, Yang X, Tcheandjieu C, Agrawal S, Fahed AC, Ellinor PT, Genes & Health Research Team; the Million Veteran Program, Tsao PS, Sun YV, Cho K, Wilson PWF, Assimes TL, van Heel DA, Butterworth AS, Aragam KG, Natarajan P, Khera AV.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature medicine",
+    "pubYear": "2023",
+    "date": "2023-07-06",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "Identification of individuals at highest risk of coronary artery disease (CAD)-ideally before onset-remains an important public health need. Prior studies have developed genome-wide polygenic scores to enable risk stratification, reflecting the substantial inherited component to CAD risk. Here we develop a new and significantly improved polygenic score for CAD, termed GPS<sub>Mult</sub>, that incorporates genome-wide association data across five ancestries for CAD (>269,000 cases and >1,178,000 controls) and ten CAD risk factors. GPS<sub>Mult</sub> strongly associated with prevalent CAD (odds ratio per standard deviation 2.14, 95% confidence interval 2.10-2.19, P\u2009<\u20090.001) in UK Biobank participants of European ancestry, identifying 20.0% of the population with 3-fold increased risk and conversely 13.9% with 3-fold decreased risk as compared with those in the middle quintile. GPS<sub>Mult</sub> was also associated with incident CAD events (hazard ratio per standard deviation 1.73, 95% confidence interval 1.70-1.76, P\u2009<\u20090.001), identifying 3% of healthy individuals with risk of future CAD events equivalent to those with existing disease and significantly improving risk discrimination and reclassification. Across multiethnic, external validation datasets inclusive of 33,096, 124,467, 16,433 and 16,874 participants of African, European, Hispanic and South Asian ancestry, respectively, GPS<sub>Mult</sub> demonstrated increased strength of associations across all ancestries and outperformed all available previously published CAD polygenic scores. These data contribute a new GPS<sub>Mult</sub> for CAD to the field and provide a generalizable framework for how large-scale integration of genetic association data for CAD and related traits from diverse populations can meaningfully improve polygenic risk prediction.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41591-023-02429-x.pdf; doi:https://doi.org/10.1038/s41591-023-02429-x; html:https://europepmc.org/articles/PMC10353935; pdf:https://europepmc.org/articles/PMC10353935?pdf=render"
+  },
   {
     "id": "34820659",
     "doi": "https://doi.org/10.1016/j.xgen.2021.100028",
@@ -45287,23 +45321,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/cardiovascres/article-pdf/115/10/1512/28981341/cvz015.pdf; doi:https://doi.org/10.1093/cvr/cvz015"
   },
-  {
-    "id": "36870556",
-    "doi": "https://doi.org/10.1016/j.jid.2023.02.010",
-    "title": "Genetic Validation of Psoriasis Phenotyping in UK Biobank Supports the Utility of Self-Reported Data and Composite Definitions for Large Genetic and Epidemiological Studies.",
-    "authorString": "Saklatvala JR, Hanscombe KB, Mahil SK, Tsoi LC, Elder JT, Barker JN, Simpson MA, Smith CH, Dand N.",
-    "authorAffiliations": "",
-    "journalTitle": "The Journal of investigative dermatology",
-    "pubYear": "2023",
-    "date": "2023-03-03",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "",
-    "laySummary": "",
-    "urls": "pdf:http://www.jidonline.org/article/S0022202X23001069/pdf; doi:https://doi.org/10.1016/j.jid.2023.02.010; html:https://europepmc.org/articles/PMC10689249; pdf:https://europepmc.org/articles/PMC10689249?pdf=render"
-  },
   {
     "id": "33785494",
     "doi": "https://doi.org/10.1136/bmjopen-2020-046365",
@@ -45321,6 +45338,23 @@
     "laySummary": "",
     "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/11/3/e046365.full.pdf; doi:https://doi.org/10.1136/bmjopen-2020-046365; html:https://europepmc.org/articles/PMC8728386; pdf:https://europepmc.org/articles/PMC8728386?pdf=render"
   },
+  {
+    "id": "36870556",
+    "doi": "https://doi.org/10.1016/j.jid.2023.02.010",
+    "title": "Genetic Validation of Psoriasis Phenotyping in UK Biobank Supports the Utility of Self-Reported Data and Composite Definitions for Large Genetic and Epidemiological Studies.",
+    "authorString": "Saklatvala JR, Hanscombe KB, Mahil SK, Tsoi LC, Elder JT, Barker JN, Simpson MA, Smith CH, Dand N.",
+    "authorAffiliations": "",
+    "journalTitle": "The Journal of investigative dermatology",
+    "pubYear": "2023",
+    "date": "2023-03-03",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "",
+    "laySummary": "",
+    "urls": "pdf:http://www.jidonline.org/article/S0022202X23001069/pdf; doi:https://doi.org/10.1016/j.jid.2023.02.010; html:https://europepmc.org/articles/PMC10689249; pdf:https://europepmc.org/articles/PMC10689249?pdf=render"
+  },
   {
     "id": "34600575",
     "doi": "https://doi.org/10.1186/s13104-021-05789-0",
@@ -45695,23 +45729,6 @@
     "laySummary": "",
     "urls": "pdf:https://f1000research.com/articles/7-210/v2/pdf; doi:https://doi.org/10.12688/f1000research.13830.2; html:https://europepmc.org/articles/PMC5968362; pdf:https://europepmc.org/articles/PMC5968362?pdf=render"
   },
-  {
-    "id": "32735845",
-    "doi": "https://doi.org/10.1016/j.immuni.2020.07.003",
-    "title": "Differential IRF8 Transcription Factor Requirement Defines Two Pathways of Dendritic Cell Development in Humans.",
-    "authorString": "Cytlak U, Resteu A, Pagan S, Green K, Milne P, Maisuria S, McDonald D, Hulme G, Filby A, Carpenter B, Queen R, Hambleton S, Hague R, Lango Allen H, Thaventhiran JED, Doody G, Collin M, Bigley V.",
-    "authorAffiliations": "",
-    "journalTitle": "Immunity",
-    "pubYear": "2020",
-    "date": "2020-07-30",
-    "isOpenAccess": "Y",
-    "keywords": "Transcription factor; Immunity; Hematopoiesis; Dendritic Cell; Primary Immunodeficiency; Irf8; Cytof; Single-cell Rna Sequencing",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The formation of mammalian dendritic cells (DCs) is controlled by multiple hematopoietic transcription factors, including IRF8. Loss of IRF8 exerts a differential effect on DC subsets, including plasmacytoid DCs (pDCs) and the classical DC lineages cDC1 and cDC2. In humans, cDC2-related subsets have been described including AXL<sup>+</sup>SIGLEC6<sup>+</sup> pre-DC, DC2 and DC3. The origin of this heterogeneity is unknown. Using high-dimensional analysis, in\u00a0vitro differentiation, and an allelic series of human IRF8 deficiency, we demonstrated that cDC2 (CD1c<sup>+</sup>DC) heterogeneity originates from two distinct pathways of development. The lymphoid-primed IRF8<sup>hi</sup> pathway, marked by CD123 and BTLA, carried pDC, cDC1, and DC2 trajectories, while the common myeloid IRF8<sup>lo</sup> pathway, expressing SIRPA, formed DC3s and monocytes. We traced distinct trajectories through the granulocyte-macrophage progenitor (GMP) compartment showing that AXL<sup>+</sup>SIGLEC6<sup>+</sup> pre-DCs mapped exclusively to the DC2 pathway. In keeping with their lower requirement for IRF8, DC3s expand to replace DC2s in human partial IRF8 deficiency.",
-    "laySummary": "",
-    "urls": "pdf:http://www.cell.com/article/S1074761320302831/pdf; doi:https://doi.org/10.1016/j.immuni.2020.07.003; html:https://europepmc.org/articles/PMC7447982"
-  },
   {
     "id": "37248441",
     "doi": "https://doi.org/10.1038/s41588-023-01410-1",
@@ -45729,6 +45746,23 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41588-023-01410-1.pdf; doi:https://doi.org/10.1038/s41588-023-01410-1; html:https://europepmc.org/articles/PMC10260398; pdf:https://europepmc.org/articles/PMC10260398?pdf=render"
   },
+  {
+    "id": "32735845",
+    "doi": "https://doi.org/10.1016/j.immuni.2020.07.003",
+    "title": "Differential IRF8 Transcription Factor Requirement Defines Two Pathways of Dendritic Cell Development in Humans.",
+    "authorString": "Cytlak U, Resteu A, Pagan S, Green K, Milne P, Maisuria S, McDonald D, Hulme G, Filby A, Carpenter B, Queen R, Hambleton S, Hague R, Lango Allen H, Thaventhiran JED, Doody G, Collin M, Bigley V.",
+    "authorAffiliations": "",
+    "journalTitle": "Immunity",
+    "pubYear": "2020",
+    "date": "2020-07-30",
+    "isOpenAccess": "Y",
+    "keywords": "Transcription factor; Immunity; Hematopoiesis; Dendritic Cell; Primary Immunodeficiency; Irf8; Cytof; Single-cell Rna Sequencing",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The formation of mammalian dendritic cells (DCs) is controlled by multiple hematopoietic transcription factors, including IRF8. Loss of IRF8 exerts a differential effect on DC subsets, including plasmacytoid DCs (pDCs) and the classical DC lineages cDC1 and cDC2. In humans, cDC2-related subsets have been described including AXL<sup>+</sup>SIGLEC6<sup>+</sup> pre-DC, DC2 and DC3. The origin of this heterogeneity is unknown. Using high-dimensional analysis, in\u00a0vitro differentiation, and an allelic series of human IRF8 deficiency, we demonstrated that cDC2 (CD1c<sup>+</sup>DC) heterogeneity originates from two distinct pathways of development. The lymphoid-primed IRF8<sup>hi</sup> pathway, marked by CD123 and BTLA, carried pDC, cDC1, and DC2 trajectories, while the common myeloid IRF8<sup>lo</sup> pathway, expressing SIRPA, formed DC3s and monocytes. We traced distinct trajectories through the granulocyte-macrophage progenitor (GMP) compartment showing that AXL<sup>+</sup>SIGLEC6<sup>+</sup> pre-DCs mapped exclusively to the DC2 pathway. In keeping with their lower requirement for IRF8, DC3s expand to replace DC2s in human partial IRF8 deficiency.",
+    "laySummary": "",
+    "urls": "pdf:http://www.cell.com/article/S1074761320302831/pdf; doi:https://doi.org/10.1016/j.immuni.2020.07.003; html:https://europepmc.org/articles/PMC7447982"
+  },
   {
     "id": "32139493",
     "doi": "https://doi.org/10.1136/bmjopen-2019-035121",
@@ -45899,23 +45933,6 @@
     "laySummary": "",
     "urls": "pdf:https://aura.abdn.ac.uk/bitstream/2164/16629/1/Recovery_etal_TL_Convalescent_Plasma_In_VoR.pdf; doi:https://doi.org/10.1016/S0140-6736(21)00897-7; html:https://europepmc.org/articles/PMC8121538"
   },
-  {
-    "id": "33444330",
-    "doi": "https://doi.org/10.1371/journal.pmed.1003498",
-    "title": "Polygenic risk scores in cardiovascular risk prediction: A cohort study and modelling analyses.",
-    "authorString": "Sun L, Pennells L, Kaptoge S, Nelson CP, Ritchie SC, Abraham G, Arnold M, Bell S, Bolton T, Burgess S, Dudbridge F, Guo Q, Sofianopoulou E, Stevens D, Thompson JR, Butterworth AS, Wood A, Danesh J, Samani NJ, Inouye M, Di Angelantonio E.",
-    "authorAffiliations": "",
-    "journalTitle": "PLoS medicine",
-    "pubYear": "2021",
-    "date": "2021-01-14",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Polygenic risk scores (PRSs) can stratify populations into cardiovascular disease (CVD) risk groups. We aimed to quantify the potential advantage of adding information on PRSs to conventional risk factors in the primary prevention of CVD.<h4>Methods and findings</h4>Using data from UK Biobank on 306,654 individuals without a history of CVD and not on lipid-lowering treatments (mean age [SD]: 56.0 [8.0] years; females: 57%; median follow-up: 8.1 years), we calculated measures of risk discrimination and reclassification upon addition of PRSs to risk factors in a conventional risk prediction model (i.e., age, sex, systolic blood pressure, smoking status, history of diabetes, and total and high-density lipoprotein cholesterol). We then modelled the implications of initiating guideline-recommended statin therapy in a primary care setting using incidence rates from 2.1 million individuals from the Clinical Practice Research Datalink. The C-index, a measure of risk discrimination, was 0.710 (95% CI 0.703-0.717) for a CVD prediction model containing conventional risk predictors alone. Addition of information on PRSs increased the C-index by 0.012 (95% CI 0.009-0.015), and resulted in continuous net reclassification improvements of about 10% and 12% in cases and non-cases, respectively. If a PRS were assessed in the entire UK primary care population aged 40-75 years, assuming that statin therapy would be initiated in accordance with the UK National Institute for Health and Care Excellence guidelines (i.e., for persons with a predicted risk of \u226510% and for those with certain other risk factors, such as diabetes, irrespective of their 10-year predicted risk), then it could help prevent 1 additional CVD event for approximately every 5,750 individuals screened. By contrast, targeted assessment only among people at intermediate (i.e., 5% to <10%) 10-year CVD risk could help prevent 1 additional CVD event for approximately every 340 individuals screened. Such a targeted strategy could help prevent 7% more CVD events than conventional risk prediction alone. Potential gains afforded by assessment of PRSs on top of conventional risk factors would be about 1.5-fold greater than those provided by assessment of C-reactive protein, a plasma biomarker included in some risk prediction guidelines. Potential limitations of this study include its restriction to European ancestry participants and a lack of health economic evaluation.<h4>Conclusions</h4>Our results suggest that addition of PRSs to conventional risk factors can modestly enhance prediction of first-onset CVD and could translate into population health benefits if used at scale.",
-    "laySummary": "",
-    "urls": "pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003498&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003498; html:https://europepmc.org/articles/PMC7808664; pdf:https://europepmc.org/articles/PMC7808664?pdf=render"
-  },
   {
     "id": "32979922",
     "doi": "https://doi.org/10.1186/s12933-020-01130-4",
@@ -45933,6 +45950,23 @@
     "laySummary": "",
     "urls": "pdf:https://cardiab.biomedcentral.com/track/pdf/10.1186/s12933-020-01130-4; doi:https://doi.org/10.1186/s12933-020-01130-4; html:https://europepmc.org/articles/PMC7520021; pdf:https://europepmc.org/articles/PMC7520021?pdf=render"
   },
+  {
+    "id": "33444330",
+    "doi": "https://doi.org/10.1371/journal.pmed.1003498",
+    "title": "Polygenic risk scores in cardiovascular risk prediction: A cohort study and modelling analyses.",
+    "authorString": "Sun L, Pennells L, Kaptoge S, Nelson CP, Ritchie SC, Abraham G, Arnold M, Bell S, Bolton T, Burgess S, Dudbridge F, Guo Q, Sofianopoulou E, Stevens D, Thompson JR, Butterworth AS, Wood A, Danesh J, Samani NJ, Inouye M, Di Angelantonio E.",
+    "authorAffiliations": "",
+    "journalTitle": "PLoS medicine",
+    "pubYear": "2021",
+    "date": "2021-01-14",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Polygenic risk scores (PRSs) can stratify populations into cardiovascular disease (CVD) risk groups. We aimed to quantify the potential advantage of adding information on PRSs to conventional risk factors in the primary prevention of CVD.<h4>Methods and findings</h4>Using data from UK Biobank on 306,654 individuals without a history of CVD and not on lipid-lowering treatments (mean age [SD]: 56.0 [8.0] years; females: 57%; median follow-up: 8.1 years), we calculated measures of risk discrimination and reclassification upon addition of PRSs to risk factors in a conventional risk prediction model (i.e., age, sex, systolic blood pressure, smoking status, history of diabetes, and total and high-density lipoprotein cholesterol). We then modelled the implications of initiating guideline-recommended statin therapy in a primary care setting using incidence rates from 2.1 million individuals from the Clinical Practice Research Datalink. The C-index, a measure of risk discrimination, was 0.710 (95% CI 0.703-0.717) for a CVD prediction model containing conventional risk predictors alone. Addition of information on PRSs increased the C-index by 0.012 (95% CI 0.009-0.015), and resulted in continuous net reclassification improvements of about 10% and 12% in cases and non-cases, respectively. If a PRS were assessed in the entire UK primary care population aged 40-75 years, assuming that statin therapy would be initiated in accordance with the UK National Institute for Health and Care Excellence guidelines (i.e., for persons with a predicted risk of \u226510% and for those with certain other risk factors, such as diabetes, irrespective of their 10-year predicted risk), then it could help prevent 1 additional CVD event for approximately every 5,750 individuals screened. By contrast, targeted assessment only among people at intermediate (i.e., 5% to <10%) 10-year CVD risk could help prevent 1 additional CVD event for approximately every 340 individuals screened. Such a targeted strategy could help prevent 7% more CVD events than conventional risk prediction alone. Potential gains afforded by assessment of PRSs on top of conventional risk factors would be about 1.5-fold greater than those provided by assessment of C-reactive protein, a plasma biomarker included in some risk prediction guidelines. Potential limitations of this study include its restriction to European ancestry participants and a lack of health economic evaluation.<h4>Conclusions</h4>Our results suggest that addition of PRSs to conventional risk factors can modestly enhance prediction of first-onset CVD and could translate into population health benefits if used at scale.",
+    "laySummary": "",
+    "urls": "pdf:https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1003498&type=printable; doi:https://doi.org/10.1371/journal.pmed.1003498; html:https://europepmc.org/articles/PMC7808664; pdf:https://europepmc.org/articles/PMC7808664?pdf=render"
+  },
   {
     "id": "34662348",
     "doi": "https://doi.org/10.1371/journal.ppat.1009992",
@@ -46325,21 +46359,21 @@
     "urls": "pdf:https://www.bmj.com/content/bmj/369/bmj.m1203.full.pdf; doi:https://doi.org/10.1136/bmj.m1203; html:https://europepmc.org/articles/PMC7201936"
   },
   {
-    "id": "32855398",
-    "doi": "https://doi.org/10.1038/s41467-020-18060-0",
-    "title": "Multi-site clonality analysis uncovers pervasive heterogeneity across melanoma metastases.",
-    "authorString": "Rabbie R, Ansari-Pour N, Cast O, Lau D, Scott F, Welsh SJ, Parkinson C, Khoja L, Moore L, Tullett M, Wong K, Ferreira I, G\u00f3mez JMM, Levesque M, Gallagher FA, Jim\u00e9nez-S\u00e1nchez A, Riva L, Miller ML, Allinson K, Campbell PJ, Corrie P, Wedge DC, Adams DJ.",
+    "id": "37681566",
+    "doi": "https://doi.org/10.1161/jaha.123.030280",
+    "title": "Age at Menopause and the Risk of Stroke: Observational and Mendelian Randomization Analysis in 204\u2009244 Postmenopausal Women.",
+    "authorString": "Tschiderer L, Peters SAE, van der Schouw YT, van Westing AC, Tong TYN, Willeit P, Seekircher L, Moreno-Iribas C, Huerta JM, Crous-Bou M, S\u00f6derholm M, Schulze MB, Johansson C, Sj\u00e4lander S, Heath AK, Macciotta A, Dahm CC, Ibsen DB, Pala V, Mellemkj\u00e6r L, Burgess S, Wood A, Kaaks R, Katzke V, Amiano P, Rodriguez-Barranco M, Engstr\u00f6m G, Weiderpass E, Tj\u00f8nneland A, Halkj\u00e6r J, Panico S, Danesh J, Butterworth A, Onland-Moret NC.",
     "authorAffiliations": "",
-    "journalTitle": "Nature communications",
-    "pubYear": "2020",
-    "date": "2020-08-27",
+    "journalTitle": "Journal of the American Heart Association",
+    "pubYear": "2023",
+    "date": "2023-09-08",
     "isOpenAccess": "Y",
-    "keywords": "",
+    "keywords": "Stroke; Age At Menopause; Mendelian Randomization Analysis; Observational Analysis",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Metastatic melanoma carries a poor prognosis despite modern systemic therapies. Understanding the evolution of the disease could help inform patient management. Through whole-genome sequencing of 13 melanoma metastases sampled at autopsy from a treatment na\u00efve patient and by leveraging the analytical power of multi-sample analyses, we reveal evidence of diversification among metastatic lineages. UV-induced mutations dominate the trunk, whereas APOBEC-associated mutations are found in the branches of the evolutionary tree. Multi-sample analyses from a further seven patients confirmed that lineage diversification was pervasive, representing an important mode of melanoma dissemination. Our analyses demonstrate that joint analysis of cancer cell fraction estimates across multiple metastases can uncover previously unrecognised levels of tumour heterogeneity and highlight the limitations of inferring heterogeneity from a single biopsy.",
+    "abstract": "Background Observational studies have shown that women with an early menopause are at higher risk of stroke compared with women with a later menopause. However, associations with stroke subtypes are inconsistent, and the causality is unclear. Methods and Results We analyzed data of the UK Biobank and EPIC-CVD (European Prospective Investigation Into Cancer and Nutrition-Cardiovascular Diseases) study. A total of 204\u2009244 postmenopausal women without a history of stroke at baseline were included (7883 from EPIC-CVD [5292 from the subcohort], 196\u2009361 from the UK Biobank). Pooled mean baseline age was 58.9\u2009years (SD, 5.8), and pooled mean age at menopause was 47.8\u2009years (SD, 6.2). Over a median follow-up of 12.6\u2009years (interquartile range, 11.8-13.3), 6770 women experienced a stroke (5155 ischemic strokes, 1615 hemorrhagic strokes, 976 intracerebral hemorrhages, and 639 subarachnoid hemorrhages). In multivariable adjusted observational Cox regression analyses, the pooled hazard ratios per 5\u2009years younger age at menopause were 1.09 (95% CI, 1.07-1.12) for stroke, 1.09 (95% CI, 1.06-1.13) for ischemic stroke, 1.10 (95% CI, 1.04-1.16) for hemorrhagic stroke, 1.14 (95% CI, 1.08-1.20) for intracerebral hemorrhage, and 1.00 (95% CI, 0.84-1.20) for subarachnoid hemorrhage. When using 2-sample Mendelian randomization analysis, we found no statistically significant association between genetically proxied age at menopause and risk of any type of stroke. Conclusions In our study, earlier age at menopause was related to a higher risk of stroke. We found no statistically significant association between genetically proxied age at menopause and risk of stroke, suggesting no causal relationship.",
     "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41467-020-18060-0.pdf; doi:https://doi.org/10.1038/s41467-020-18060-0; html:https://europepmc.org/articles/PMC7453196; pdf:https://europepmc.org/articles/PMC7453196?pdf=render"
+    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.123.030280; doi:https://doi.org/10.1161/JAHA.123.030280; html:https://europepmc.org/articles/PMC10547274; pdf:https://europepmc.org/articles/PMC10547274?pdf=render"
   },
   {
     "id": "31666367",
@@ -46359,21 +46393,21 @@
     "urls": "pdf:https://jcm.asm.org/content/jcm/58/1/e01037-19.full.pdf; doi:https://doi.org/10.1128/JCM.01037-19; html:https://europepmc.org/articles/PMC6935933; pdf:https://europepmc.org/articles/PMC6935933?pdf=render"
   },
   {
-    "id": "37681566",
-    "doi": "https://doi.org/10.1161/jaha.123.030280",
-    "title": "Age at Menopause and the Risk of Stroke: Observational and Mendelian Randomization Analysis in 204\u2009244 Postmenopausal Women.",
-    "authorString": "Tschiderer L, Peters SAE, van der Schouw YT, van Westing AC, Tong TYN, Willeit P, Seekircher L, Moreno-Iribas C, Huerta JM, Crous-Bou M, S\u00f6derholm M, Schulze MB, Johansson C, Sj\u00e4lander S, Heath AK, Macciotta A, Dahm CC, Ibsen DB, Pala V, Mellemkj\u00e6r L, Burgess S, Wood A, Kaaks R, Katzke V, Amiano P, Rodriguez-Barranco M, Engstr\u00f6m G, Weiderpass E, Tj\u00f8nneland A, Halkj\u00e6r J, Panico S, Danesh J, Butterworth A, Onland-Moret NC.",
+    "id": "32855398",
+    "doi": "https://doi.org/10.1038/s41467-020-18060-0",
+    "title": "Multi-site clonality analysis uncovers pervasive heterogeneity across melanoma metastases.",
+    "authorString": "Rabbie R, Ansari-Pour N, Cast O, Lau D, Scott F, Welsh SJ, Parkinson C, Khoja L, Moore L, Tullett M, Wong K, Ferreira I, G\u00f3mez JMM, Levesque M, Gallagher FA, Jim\u00e9nez-S\u00e1nchez A, Riva L, Miller ML, Allinson K, Campbell PJ, Corrie P, Wedge DC, Adams DJ.",
     "authorAffiliations": "",
-    "journalTitle": "Journal of the American Heart Association",
-    "pubYear": "2023",
-    "date": "2023-09-08",
+    "journalTitle": "Nature communications",
+    "pubYear": "2020",
+    "date": "2020-08-27",
     "isOpenAccess": "Y",
-    "keywords": "Stroke; Age At Menopause; Mendelian Randomization Analysis; Observational Analysis",
+    "keywords": "",
     "nationalPriorities": "",
     "healthCategories": "",
-    "abstract": "Background Observational studies have shown that women with an early menopause are at higher risk of stroke compared with women with a later menopause. However, associations with stroke subtypes are inconsistent, and the causality is unclear. Methods and Results We analyzed data of the UK Biobank and EPIC-CVD (European Prospective Investigation Into Cancer and Nutrition-Cardiovascular Diseases) study. A total of 204\u2009244 postmenopausal women without a history of stroke at baseline were included (7883 from EPIC-CVD [5292 from the subcohort], 196\u2009361 from the UK Biobank). Pooled mean baseline age was 58.9\u2009years (SD, 5.8), and pooled mean age at menopause was 47.8\u2009years (SD, 6.2). Over a median follow-up of 12.6\u2009years (interquartile range, 11.8-13.3), 6770 women experienced a stroke (5155 ischemic strokes, 1615 hemorrhagic strokes, 976 intracerebral hemorrhages, and 639 subarachnoid hemorrhages). In multivariable adjusted observational Cox regression analyses, the pooled hazard ratios per 5\u2009years younger age at menopause were 1.09 (95% CI, 1.07-1.12) for stroke, 1.09 (95% CI, 1.06-1.13) for ischemic stroke, 1.10 (95% CI, 1.04-1.16) for hemorrhagic stroke, 1.14 (95% CI, 1.08-1.20) for intracerebral hemorrhage, and 1.00 (95% CI, 0.84-1.20) for subarachnoid hemorrhage. When using 2-sample Mendelian randomization analysis, we found no statistically significant association between genetically proxied age at menopause and risk of any type of stroke. Conclusions In our study, earlier age at menopause was related to a higher risk of stroke. We found no statistically significant association between genetically proxied age at menopause and risk of stroke, suggesting no causal relationship.",
+    "abstract": "Metastatic melanoma carries a poor prognosis despite modern systemic therapies. Understanding the evolution of the disease could help inform patient management. Through whole-genome sequencing of 13 melanoma metastases sampled at autopsy from a treatment na\u00efve patient and by leveraging the analytical power of multi-sample analyses, we reveal evidence of diversification among metastatic lineages. UV-induced mutations dominate the trunk, whereas APOBEC-associated mutations are found in the branches of the evolutionary tree. Multi-sample analyses from a further seven patients confirmed that lineage diversification was pervasive, representing an important mode of melanoma dissemination. Our analyses demonstrate that joint analysis of cancer cell fraction estimates across multiple metastases can uncover previously unrecognised levels of tumour heterogeneity and highlight the limitations of inferring heterogeneity from a single biopsy.",
     "laySummary": "",
-    "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/JAHA.123.030280; doi:https://doi.org/10.1161/JAHA.123.030280; html:https://europepmc.org/articles/PMC10547274; pdf:https://europepmc.org/articles/PMC10547274?pdf=render"
+    "urls": "pdf:https://www.nature.com/articles/s41467-020-18060-0.pdf; doi:https://doi.org/10.1038/s41467-020-18060-0; html:https://europepmc.org/articles/PMC7453196; pdf:https://europepmc.org/articles/PMC7453196?pdf=render"
   },
   {
     "id": "34800427",
@@ -46511,23 +46545,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.neurobiolaging.2020.06.023; doi:https://doi.org/10.1016/j.neurobiolaging.2020.06.023; html:https://europepmc.org/articles/PMC7649340"
   },
-  {
-    "id": "36113526",
-    "doi": "https://doi.org/10.1016/s2214-109x(22)00332-1",
-    "title": "Mapping development and health effects of cooking with solid fuels in low-income and middle-income countries, 2000-18: a geospatial modelling study.",
-    "authorString": "Local Burden of Disease Household Air Pollution Collaborators.",
-    "authorAffiliations": "",
-    "journalTitle": "The Lancet. Global health",
-    "pubYear": "2022",
-    "date": "2022-10-01",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>More than 3 billion people do not have access to clean energy and primarily use solid fuels to cook. Use of solid fuels generates household air pollution, which was associated with more than 2 million deaths in 2019. Although local patterns in cooking vary systematically, subnational trends in use of solid fuels have yet to be comprehensively analysed. We estimated the prevalence of solid-fuel use with high spatial resolution to explore subnational inequalities, assess local progress, and assess the effects on health in low-income and middle-income countries (LMICs) without universal access to clean fuels.<h4>Methods</h4>We did a geospatial modelling study to map the prevalence of solid-fuel use for cooking at a 5 km\u2008\u00d7\u20085 km resolution in 98 LMICs based on 2\u00b71 million household observations of the primary cooking fuel used from 663 population-based household surveys over the years 2000 to 2018. We use observed temporal patterns to forecast household air pollution in 2030 and to assess the probability of attaining the Sustainable Development Goal (SDG) target indicator for clean cooking. We aligned our estimates of household air pollution to geospatial estimates of ambient air pollution to establish the risk transition occurring in LMICs. Finally, we quantified the effect of residual primary solid-fuel use for cooking on child health by doing a counterfactual risk assessment to estimate the proportion of deaths from lower respiratory tract infections in children younger than 5 years that could be associated with household air pollution.<h4>Findings</h4>Although primary reliance on solid-fuel use for cooking has declined globally, it remains widespread. 593 million people live in districts where the prevalence of solid-fuel use for cooking exceeds 95%. 66% of people in LMICs live in districts that are not on track to meet the SDG target for universal access to clean energy by 2030. Household air pollution continues to be a major contributor to particulate exposure in LMICs, and rising ambient air pollution is undermining potential gains from reductions in the prevalence of solid-fuel use for cooking in many countries. We estimated that, in 2018, 205\u2008000 (95% uncertainty interval 147\u2008000-257\u2008000) children younger than 5 years died from lower respiratory tract infections that could be attributed to household air pollution.<h4>Interpretation</h4>Efforts to accelerate the adoption of clean cooking fuels need to be substantially increased and recalibrated to account for subnational inequalities, because there are substantial opportunities to improve air quality and avert child mortality associated with household air pollution.<h4>Funding</h4>Bill & Melinda Gates Foundation.",
-    "laySummary": "",
-    "urls": "pdf:https://eprints.qut.edu.au/236269/1/1_s2.0_S2214109X22003321.pdf; doi:https://doi.org/10.1016/S2214-109X(22)00332-1; html:https://europepmc.org/articles/PMC9638039"
-  },
   {
     "id": "32664951",
     "doi": "https://doi.org/10.1186/s13148-020-00895-5",
@@ -46545,6 +46562,23 @@
     "laySummary": "",
     "urls": "pdf:https://clinicalepigeneticsjournal.biomedcentral.com/track/pdf/10.1186/s13148-020-00895-5; doi:https://doi.org/10.1186/s13148-020-00895-5; html:https://europepmc.org/articles/PMC7362435; pdf:https://europepmc.org/articles/PMC7362435?pdf=render"
   },
+  {
+    "id": "36113526",
+    "doi": "https://doi.org/10.1016/s2214-109x(22)00332-1",
+    "title": "Mapping development and health effects of cooking with solid fuels in low-income and middle-income countries, 2000-18: a geospatial modelling study.",
+    "authorString": "Local Burden of Disease Household Air Pollution Collaborators.",
+    "authorAffiliations": "",
+    "journalTitle": "The Lancet. Global health",
+    "pubYear": "2022",
+    "date": "2022-10-01",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>More than 3 billion people do not have access to clean energy and primarily use solid fuels to cook. Use of solid fuels generates household air pollution, which was associated with more than 2 million deaths in 2019. Although local patterns in cooking vary systematically, subnational trends in use of solid fuels have yet to be comprehensively analysed. We estimated the prevalence of solid-fuel use with high spatial resolution to explore subnational inequalities, assess local progress, and assess the effects on health in low-income and middle-income countries (LMICs) without universal access to clean fuels.<h4>Methods</h4>We did a geospatial modelling study to map the prevalence of solid-fuel use for cooking at a 5 km\u2008\u00d7\u20085 km resolution in 98 LMICs based on 2\u00b71 million household observations of the primary cooking fuel used from 663 population-based household surveys over the years 2000 to 2018. We use observed temporal patterns to forecast household air pollution in 2030 and to assess the probability of attaining the Sustainable Development Goal (SDG) target indicator for clean cooking. We aligned our estimates of household air pollution to geospatial estimates of ambient air pollution to establish the risk transition occurring in LMICs. Finally, we quantified the effect of residual primary solid-fuel use for cooking on child health by doing a counterfactual risk assessment to estimate the proportion of deaths from lower respiratory tract infections in children younger than 5 years that could be associated with household air pollution.<h4>Findings</h4>Although primary reliance on solid-fuel use for cooking has declined globally, it remains widespread. 593 million people live in districts where the prevalence of solid-fuel use for cooking exceeds 95%. 66% of people in LMICs live in districts that are not on track to meet the SDG target for universal access to clean energy by 2030. Household air pollution continues to be a major contributor to particulate exposure in LMICs, and rising ambient air pollution is undermining potential gains from reductions in the prevalence of solid-fuel use for cooking in many countries. We estimated that, in 2018, 205\u2008000 (95% uncertainty interval 147\u2008000-257\u2008000) children younger than 5 years died from lower respiratory tract infections that could be attributed to household air pollution.<h4>Interpretation</h4>Efforts to accelerate the adoption of clean cooking fuels need to be substantially increased and recalibrated to account for subnational inequalities, because there are substantial opportunities to improve air quality and avert child mortality associated with household air pollution.<h4>Funding</h4>Bill & Melinda Gates Foundation.",
+    "laySummary": "",
+    "urls": "pdf:https://eprints.qut.edu.au/236269/1/1_s2.0_S2214109X22003321.pdf; doi:https://doi.org/10.1016/S2214-109X(22)00332-1; html:https://europepmc.org/articles/PMC9638039"
+  },
   {
     "id": "32062083",
     "doi": "https://doi.org/10.1016/j.neuroimage.2020.116604",
@@ -46715,23 +46749,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/braincomms/article-pdf/4/1/fcab291/42546494/fcab291.pdf; doi:https://doi.org/10.1093/braincomms/fcab291; html:https://europepmc.org/articles/PMC8853724; pdf:https://europepmc.org/articles/PMC8853724?pdf=render"
   },
-  {
-    "id": "31341063",
-    "doi": "https://doi.org/10.1126/scitranslmed.aan5662",
-    "title": "The gut microbiota influences skeletal muscle mass and function in mice.",
-    "authorString": "Lahiri S, Kim H, Garcia-Perez I, Reza MM, Martin KA, Kundu P, Cox LM, Selkrig J, Posma JM, Zhang H, Padmanabhan P, Moret C, Guly\u00e1s B, Blaser MJ, Auwerx J, Holmes E, Nicholson J, Wahli W, Pettersson S.",
-    "authorAffiliations": "",
-    "journalTitle": "Science translational medicine",
-    "pubYear": "2019",
-    "date": "2019-07-01",
-    "isOpenAccess": "N",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The functional interactions between the gut microbiota and the host are important for host physiology, homeostasis, and sustained health. We compared the skeletal muscle of germ-free mice that lacked a gut microbiota to the skeletal muscle of pathogen-free mice that had a gut microbiota. Compared to pathogen-free mouse skeletal muscle, germ-free mouse skeletal muscle showed atrophy, decreased expression of insulin-like growth factor 1, and reduced transcription of genes associated with skeletal muscle growth and mitochondrial function. Nuclear magnetic resonance spectrometry analysis of skeletal muscle, liver, and serum from germ-free mice revealed multiple changes in the amounts of amino acids, including glycine and alanine, compared to pathogen-free mice. Germ-free mice also showed reduced serum choline, the precursor of acetylcholine, the key neurotransmitter that signals between muscle and nerve at neuromuscular junctions. Reduced expression of genes encoding Rapsyn and Lrp4, two proteins important for neuromuscular junction assembly and function, was also observed in skeletal muscle from germ-free mice compared to pathogen-free mice. Transplanting the gut microbiota from pathogen-free mice into germ-free mice resulted in an increase in skeletal muscle mass, a reduction in muscle atrophy markers, improved oxidative metabolic capacity of the muscle, and elevated expression of the neuromuscular junction assembly genes <i>Rapsyn</i> and <i>Lrp4</i> Treating germ-free mice with short-chain fatty acids (microbial metabolites) partly reversed skeletal muscle impairments. Our results suggest a role for the gut microbiota in regulating skeletal muscle mass and function in mice.",
-    "laySummary": "",
-    "urls": "pdf:https://stm.sciencemag.org/content/scitransmed/11/502/eaan5662.full.pdf; doi:https://doi.org/10.1126/scitranslmed.aan5662; html:https://europepmc.org/articles/PMC7501733; pdf:https://europepmc.org/articles/PMC7501733?pdf=render; doi:https://doi.org/10.1126/scitranslmed.aan5662"
-  },
   {
     "id": "31607442",
     "doi": "https://doi.org/10.1016/j.injury.2019.09.036",
@@ -46749,6 +46766,23 @@
     "laySummary": "This paper looks at the implications for trauma system design based on major traumatic injuries in Australia and aims to describe the current epidemiology of major trauma across the country, identifying improvements and future directions in the system of trauma care in Australia. This is the first reported comparison of the epidemiology and outcomes at major centres across Australia. They concluded that Australia now has the capability to identify national injury trends in patients admitted to major trauma services, optimising prevention and treamtnet strategies, thereby potentially reducing the burden of injury.",
     "urls": "doi:https://doi.org/10.1016/j.injury.2019.09.036"
   },
+  {
+    "id": "31341063",
+    "doi": "https://doi.org/10.1126/scitranslmed.aan5662",
+    "title": "The gut microbiota influences skeletal muscle mass and function in mice.",
+    "authorString": "Lahiri S, Kim H, Garcia-Perez I, Reza MM, Martin KA, Kundu P, Cox LM, Selkrig J, Posma JM, Zhang H, Padmanabhan P, Moret C, Guly\u00e1s B, Blaser MJ, Auwerx J, Holmes E, Nicholson J, Wahli W, Pettersson S.",
+    "authorAffiliations": "",
+    "journalTitle": "Science translational medicine",
+    "pubYear": "2019",
+    "date": "2019-07-01",
+    "isOpenAccess": "N",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The functional interactions between the gut microbiota and the host are important for host physiology, homeostasis, and sustained health. We compared the skeletal muscle of germ-free mice that lacked a gut microbiota to the skeletal muscle of pathogen-free mice that had a gut microbiota. Compared to pathogen-free mouse skeletal muscle, germ-free mouse skeletal muscle showed atrophy, decreased expression of insulin-like growth factor 1, and reduced transcription of genes associated with skeletal muscle growth and mitochondrial function. Nuclear magnetic resonance spectrometry analysis of skeletal muscle, liver, and serum from germ-free mice revealed multiple changes in the amounts of amino acids, including glycine and alanine, compared to pathogen-free mice. Germ-free mice also showed reduced serum choline, the precursor of acetylcholine, the key neurotransmitter that signals between muscle and nerve at neuromuscular junctions. Reduced expression of genes encoding Rapsyn and Lrp4, two proteins important for neuromuscular junction assembly and function, was also observed in skeletal muscle from germ-free mice compared to pathogen-free mice. Transplanting the gut microbiota from pathogen-free mice into germ-free mice resulted in an increase in skeletal muscle mass, a reduction in muscle atrophy markers, improved oxidative metabolic capacity of the muscle, and elevated expression of the neuromuscular junction assembly genes <i>Rapsyn</i> and <i>Lrp4</i> Treating germ-free mice with short-chain fatty acids (microbial metabolites) partly reversed skeletal muscle impairments. Our results suggest a role for the gut microbiota in regulating skeletal muscle mass and function in mice.",
+    "laySummary": "",
+    "urls": "pdf:https://stm.sciencemag.org/content/scitransmed/11/502/eaan5662.full.pdf; doi:https://doi.org/10.1126/scitranslmed.aan5662; html:https://europepmc.org/articles/PMC7501733; pdf:https://europepmc.org/articles/PMC7501733?pdf=render; doi:https://doi.org/10.1126/scitranslmed.aan5662"
+  },
   {
     "id": "31243008",
     "doi": "https://doi.org/10.1136/archdischild-2018-316693",
@@ -46800,23 +46834,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41467-020-18843-5.pdf; doi:https://doi.org/10.1038/s41467-020-18843-5; html:https://europepmc.org/articles/PMC7545111; pdf:https://europepmc.org/articles/PMC7545111?pdf=render"
   },
-  {
-    "id": "35304391",
-    "doi": "https://doi.org/10.1136/bmjopen-2021-050610",
-    "title": "Results of a pilot feasibility randomised controlled trial exploring the use of an electronic patient-reported outcome measure in the management of UK patients with advanced chronic kidney disease.",
-    "authorString": "Kyte D, Anderson N, Bishop J, Bissell A, Brettell E, Calvert M, Chadburn M, Cockwell P, Dutton M, Eddington H, Forster E, Hadley G, Ives NJ, Jackson LJ, O'Brien S, Price G, Sharpe K, Stringer S, Verdi R, Waters J, Wilcockson A.",
-    "authorAffiliations": "",
-    "journalTitle": "BMJ open",
-    "pubYear": "2022",
-    "date": "2022-03-18",
-    "isOpenAccess": "Y",
-    "keywords": "Clinical Trials; Nephrology; End Stage Renal Failure",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Objectives</h4>The use of routine remote follow-up of patients with chronic kidney disease (CKD) is increasing exponentially. It has been suggested that online electronic patient-reported outcome measures (ePROMs) could be used in parallel, to facilitate real-time symptom monitoring aimed at improving outcomes. We tested the feasibility of this approach in a pilot trial of ePROM symptom monitoring versus usual care in patients with advanced CKD not on dialysis.<h4>Design</h4>A 12-month, parallel, pilot randomised controlled trial (RCT) and qualitative substudy.<h4>Setting and participants</h4>Queen Elizabeth Hospital Birmingham, UK. Adult patients with advanced CKD (estimated glomerular filtration rate \u22656 and \u226415 mL/min/1.73 m<sup>2</sup>, or a projected risk of progression to kidney failure within 2 years \u226520%).<h4>Intervention</h4>Monthly online ePROM symptom reporting, including automated feedback of tailored self-management advice and triggered clinical notifications in the advent of severe symptoms. Real-time ePROM data were made available to the clinical team via the electronic medical record.<h4>Outcomes</h4>Feasibility (recruitment and retention rates, and acceptability/adherence to the ePROM intervention). Health-related quality of life, clinical data (eg, measures of kidney function, kidney failure, hospitalisation, death) and healthcare utilisation.<h4>Results</h4>52 patients were randomised (31% of approached). Case report form returns were high (99.5%), as was retention (96%). Overall, 73% of expected ePROM questionnaires were received. Intervention adherence was high beyond 90 days (74%) and 180 days (65%); but dropped beyond 270 days (46%). Qualitative interviews supported proof of concept and intervention acceptability, but highlighted necessary changes aimed at enhancing overall functionality/scalability of the ePROM system.<h4>Limitations</h4>Small sample size.<h4>Conclusions</h4>This pilot trial demonstrates that patients are willing to be randomised to a trial assessing ePROM symptom monitoring. The intervention was considered acceptable; though measures to improve longer-term engagement are needed. A full-scale RCT is considered feasible.<h4>Trial registration number</h4>ISRCTN12669006 and the UK NIHR Portfolio (CPMS ID: 36497).",
-    "laySummary": "",
-    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/3/e050610.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-050610; html:https://europepmc.org/articles/PMC8935185; pdf:https://europepmc.org/articles/PMC8935185?pdf=render"
-  },
   {
     "id": "31719529",
     "doi": "https://doi.org/10.1038/s41467-019-12515-9",
@@ -46834,6 +46851,23 @@
     "laySummary": "This study aimed to identify parts of the genome that cause a rare inflammatory disease called EGPA, which usually starts with non-specific and common (asthma, raised levels of white blood cells) symptoms, followed by more distinctive patterns of symptoms as the disease progresses. The authors used two different statistical methods to compare the genomes of 534 people with EGPA and 6688 people without EGPA. They identified 8 parts of the genome that are likely to contribute to EGPA, but do not fully explain the disease. The study suggests that there are two types of EGPA that have different symptoms (with/without autoimmune vasculitis) and genetic causes. Four of the parts of the genome identified by the study are the target for drugs that are currently underdevelopment.",
     "urls": "pdf:https://www.nature.com/articles/s41467-019-12515-9.pdf; doi:https://doi.org/10.1038/s41467-019-12515-9; html:https://europepmc.org/articles/PMC6851141; pdf:https://europepmc.org/articles/PMC6851141?pdf=render"
   },
+  {
+    "id": "35304391",
+    "doi": "https://doi.org/10.1136/bmjopen-2021-050610",
+    "title": "Results of a pilot feasibility randomised controlled trial exploring the use of an electronic patient-reported outcome measure in the management of UK patients with advanced chronic kidney disease.",
+    "authorString": "Kyte D, Anderson N, Bishop J, Bissell A, Brettell E, Calvert M, Chadburn M, Cockwell P, Dutton M, Eddington H, Forster E, Hadley G, Ives NJ, Jackson LJ, O'Brien S, Price G, Sharpe K, Stringer S, Verdi R, Waters J, Wilcockson A.",
+    "authorAffiliations": "",
+    "journalTitle": "BMJ open",
+    "pubYear": "2022",
+    "date": "2022-03-18",
+    "isOpenAccess": "Y",
+    "keywords": "Clinical Trials; Nephrology; End Stage Renal Failure",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Objectives</h4>The use of routine remote follow-up of patients with chronic kidney disease (CKD) is increasing exponentially. It has been suggested that online electronic patient-reported outcome measures (ePROMs) could be used in parallel, to facilitate real-time symptom monitoring aimed at improving outcomes. We tested the feasibility of this approach in a pilot trial of ePROM symptom monitoring versus usual care in patients with advanced CKD not on dialysis.<h4>Design</h4>A 12-month, parallel, pilot randomised controlled trial (RCT) and qualitative substudy.<h4>Setting and participants</h4>Queen Elizabeth Hospital Birmingham, UK. Adult patients with advanced CKD (estimated glomerular filtration rate \u22656 and \u226415 mL/min/1.73 m<sup>2</sup>, or a projected risk of progression to kidney failure within 2 years \u226520%).<h4>Intervention</h4>Monthly online ePROM symptom reporting, including automated feedback of tailored self-management advice and triggered clinical notifications in the advent of severe symptoms. Real-time ePROM data were made available to the clinical team via the electronic medical record.<h4>Outcomes</h4>Feasibility (recruitment and retention rates, and acceptability/adherence to the ePROM intervention). Health-related quality of life, clinical data (eg, measures of kidney function, kidney failure, hospitalisation, death) and healthcare utilisation.<h4>Results</h4>52 patients were randomised (31% of approached). Case report form returns were high (99.5%), as was retention (96%). Overall, 73% of expected ePROM questionnaires were received. Intervention adherence was high beyond 90 days (74%) and 180 days (65%); but dropped beyond 270 days (46%). Qualitative interviews supported proof of concept and intervention acceptability, but highlighted necessary changes aimed at enhancing overall functionality/scalability of the ePROM system.<h4>Limitations</h4>Small sample size.<h4>Conclusions</h4>This pilot trial demonstrates that patients are willing to be randomised to a trial assessing ePROM symptom monitoring. The intervention was considered acceptable; though measures to improve longer-term engagement are needed. A full-scale RCT is considered feasible.<h4>Trial registration number</h4>ISRCTN12669006 and the UK NIHR Portfolio (CPMS ID: 36497).",
+    "laySummary": "",
+    "urls": "pdf:https://bmjopen.bmj.com/content/bmjopen/12/3/e050610.full.pdf; doi:https://doi.org/10.1136/bmjopen-2021-050610; html:https://europepmc.org/articles/PMC8935185; pdf:https://europepmc.org/articles/PMC8935185?pdf=render"
+  },
   {
     "id": "37221040",
     "doi": "https://doi.org/10.1136/oemed-2022-108700",
@@ -46953,23 +46987,6 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/aje/article-pdf/190/10/2000/40491073/kwab031.pdf; doi:https://doi.org/10.1093/aje/kwab031; html:https://europepmc.org/articles/PMC8485151; pdf:https://europepmc.org/articles/PMC8485151?pdf=render"
   },
-  {
-    "id": "32702746",
-    "doi": "https://doi.org/10.1093/eurheartj/ehaa531",
-    "title": "Genetic variability in the absorption of dietary sterols affects the risk of coronary artery disease.",
-    "authorString": "Helgadottir A, Thorleifsson G, Alexandersson KF, Tragante V, Thorsteinsdottir M, Eiriksson FF, Gretarsdottir S, Bj\u00f6rnsson E, Magnusson O, Sveinbjornsson G, Jonsdottir I, Steinthorsdottir V, Ferkingstad E, Jensson B\u00d6, Stefansson H, Olafsson I, Christensen AH, Torp-Pedersen C, K\u00f8ber L, Pedersen OB, Erikstrup C, S\u00f8rensen E, Brunak S, Banasik K, Hansen TF, Nyegaard M, Eyjolfssson GI, Sigurdardottir O, Thorarinsson BL, Matthiasson SE, Steingrimsdottir T, Bjornsson ES, Danielsen R, Asselbergs FW, Arnar DO, Ullum H, Bundgaard H, Sulem P, Thorsteinsdottir U, Thorgeirsson G, Holm H, Gudbjartsson DF, Stefansson K.",
-    "authorAffiliations": "",
-    "journalTitle": "European heart journal",
-    "pubYear": "2020",
-    "date": "2020-07-01",
-    "isOpenAccess": "Y",
-    "keywords": "Genetics; Absorption; phytosterols; Dietary Cholesterol; Abcg5/8",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Aims</h4>To explore whether variability in dietary cholesterol and phytosterol absorption impacts the risk of coronary artery disease (CAD) using as instruments sequence variants in the ABCG5/8 genes, key regulators of intestinal absorption of dietary sterols.<h4>Methods and results</h4>We examined the effects of ABCG5/8 variants on non-high-density lipoprotein (non-HDL) cholesterol (N up to 610\u00a0532) and phytosterol levels (N\u2009=\u20093039) and the risk of CAD in Iceland, Denmark, and the UK Biobank (105\u00a0490 cases and 844\u00a0025 controls). We used genetic scores for non-HDL cholesterol to determine whether ABCG5/8 variants confer greater risk of CAD than predicted by their effect on non-HDL cholesterol. We identified nine rare ABCG5/8 coding variants with substantial impact on non-HDL cholesterol. Carriers have elevated phytosterol levels and are at increased risk of CAD. Consistent with impact on ABCG5/8 transporter function in hepatocytes, eight rare ABCG5/8 variants associate with gallstones. A genetic score of ABCG5/8 variants predicting 1\u2009mmol/L increase in non-HDL cholesterol associates with two-fold increase in CAD risk [odds ratio (OR) = 2.01, 95% confidence interval (CI) 1.75-2.31, P\u2009=\u20099.8\u2009\u00d7\u200910-23] compared with a 54% increase in CAD risk (OR = 1.54, 95% CI 1.49-1.59, P\u2009=\u20091.1\u2009\u00d7\u200910-154) associated with a score of other non-HDL cholesterol variants predicting the same increase in non-HDL cholesterol (P for difference in effects = 2.4\u2009\u00d7\u200910-4).<h4>Conclusions</h4>Genetic variation in cholesterol absorption affects levels of circulating non-HDL cholesterol and risk of CAD. Our results indicate that both dietary cholesterol and phytosterols contribute directly to atherogenesis.",
-    "laySummary": "",
-    "urls": "pdf:https://academic.oup.com/eurheartj/article-pdf/41/28/2618/33526677/ehaa531.pdf; doi:https://doi.org/10.1093/eurheartj/ehaa531; html:https://europepmc.org/articles/PMC7377579; pdf:https://europepmc.org/articles/PMC7377579?pdf=render"
-  },
   {
     "id": "33277303",
     "doi": "https://doi.org/10.2337/dc20-1137",
@@ -46987,6 +47004,23 @@
     "laySummary": "",
     "urls": "pdf:https://care.diabetesjournals.org/content/diacare/44/2/556.full.pdf; doi:https://doi.org/10.2337/dc20-1137; html:https://europepmc.org/articles/PMC7818328; pdf:https://europepmc.org/articles/PMC7818328?pdf=render"
   },
+  {
+    "id": "32702746",
+    "doi": "https://doi.org/10.1093/eurheartj/ehaa531",
+    "title": "Genetic variability in the absorption of dietary sterols affects the risk of coronary artery disease.",
+    "authorString": "Helgadottir A, Thorleifsson G, Alexandersson KF, Tragante V, Thorsteinsdottir M, Eiriksson FF, Gretarsdottir S, Bj\u00f6rnsson E, Magnusson O, Sveinbjornsson G, Jonsdottir I, Steinthorsdottir V, Ferkingstad E, Jensson B\u00d6, Stefansson H, Olafsson I, Christensen AH, Torp-Pedersen C, K\u00f8ber L, Pedersen OB, Erikstrup C, S\u00f8rensen E, Brunak S, Banasik K, Hansen TF, Nyegaard M, Eyjolfssson GI, Sigurdardottir O, Thorarinsson BL, Matthiasson SE, Steingrimsdottir T, Bjornsson ES, Danielsen R, Asselbergs FW, Arnar DO, Ullum H, Bundgaard H, Sulem P, Thorsteinsdottir U, Thorgeirsson G, Holm H, Gudbjartsson DF, Stefansson K.",
+    "authorAffiliations": "",
+    "journalTitle": "European heart journal",
+    "pubYear": "2020",
+    "date": "2020-07-01",
+    "isOpenAccess": "Y",
+    "keywords": "Genetics; Absorption; phytosterols; Dietary Cholesterol; Abcg5/8",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Aims</h4>To explore whether variability in dietary cholesterol and phytosterol absorption impacts the risk of coronary artery disease (CAD) using as instruments sequence variants in the ABCG5/8 genes, key regulators of intestinal absorption of dietary sterols.<h4>Methods and results</h4>We examined the effects of ABCG5/8 variants on non-high-density lipoprotein (non-HDL) cholesterol (N up to 610\u00a0532) and phytosterol levels (N\u2009=\u20093039) and the risk of CAD in Iceland, Denmark, and the UK Biobank (105\u00a0490 cases and 844\u00a0025 controls). We used genetic scores for non-HDL cholesterol to determine whether ABCG5/8 variants confer greater risk of CAD than predicted by their effect on non-HDL cholesterol. We identified nine rare ABCG5/8 coding variants with substantial impact on non-HDL cholesterol. Carriers have elevated phytosterol levels and are at increased risk of CAD. Consistent with impact on ABCG5/8 transporter function in hepatocytes, eight rare ABCG5/8 variants associate with gallstones. A genetic score of ABCG5/8 variants predicting 1\u2009mmol/L increase in non-HDL cholesterol associates with two-fold increase in CAD risk [odds ratio (OR) = 2.01, 95% confidence interval (CI) 1.75-2.31, P\u2009=\u20099.8\u2009\u00d7\u200910-23] compared with a 54% increase in CAD risk (OR = 1.54, 95% CI 1.49-1.59, P\u2009=\u20091.1\u2009\u00d7\u200910-154) associated with a score of other non-HDL cholesterol variants predicting the same increase in non-HDL cholesterol (P for difference in effects = 2.4\u2009\u00d7\u200910-4).<h4>Conclusions</h4>Genetic variation in cholesterol absorption affects levels of circulating non-HDL cholesterol and risk of CAD. Our results indicate that both dietary cholesterol and phytosterols contribute directly to atherogenesis.",
+    "laySummary": "",
+    "urls": "pdf:https://academic.oup.com/eurheartj/article-pdf/41/28/2618/33526677/ehaa531.pdf; doi:https://doi.org/10.1093/eurheartj/ehaa531; html:https://europepmc.org/articles/PMC7377579; pdf:https://europepmc.org/articles/PMC7377579?pdf=render"
+  },
   {
     "id": "32690604",
     "doi": "https://doi.org/10.1136/gutjnl-2019-319866",
@@ -47495,7 +47529,7 @@
     "healthCategories": "",
     "abstract": "<h4>Background</h4>To contain the spread of COVID-19, a cordon sanitaire was put in place in Wuhan prior to the Lunar New Year, on 23 January 2020. We assess the efficacy of the cordon sanitaire to delay the introduction and onset of local transmission of COVID-19 in other major cities in mainland China.<h4>Methods</h4>We estimated the number of infected travellers from Wuhan to other major cities in mainland China from November 2019 to February 2020 using previously estimated COVID-19 prevalence in Wuhan and publicly available mobility data. We focused on Beijing, Chongqing, Hangzhou, and Shenzhen as four representative major cities to identify the potential independent contribution of the cordon sanitaire and holiday travel. To do this, we simulated outbreaks generated by infected arrivals in these destination cities using stochastic branching processes. We also modelled the effect of the cordon sanitaire in combination with reduced transmissibility scenarios to simulate the effect of local non-pharmaceutical interventions.<h4>Results</h4>We find that in the four cities, given the potentially high prevalence of COVID-19 in Wuhan between December 2019 and early January 2020, local transmission may have been seeded as early as 1-8 January 2020. By the time the cordon sanitaire was imposed, infections were likely in the thousands. The cordon sanitaire alone did not substantially affect the epidemic progression in these cities, although it may have had some effect in smaller cities. Reduced transmissibility resulted in a notable decrease in the incidence of infection in the four studied cities.<h4>Conclusions</h4>Our results indicate that sustained transmission was likely occurring several weeks prior to the implementation of the cordon sanitaire in four major cities of mainland China and that the observed decrease in incidence was likely attributable to other non-pharmaceutical, transmission-reducing interventions.",
     "laySummary": "",
-    "urls": "pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-020-01712-9; doi:https://doi.org/10.1186/s12916-020-01712-9; html:https://europepmc.org/articles/PMC7437104; pdf:https://europepmc.org/articles/PMC7437104?pdf=render"
+    "urls": "doi:https://doi.org/10.1186/s12916-020-01712-9; doi:https://doi.org/10.1186/s12916-020-01712-9; html:https://europepmc.org/articles/PMC7437104; pdf:https://europepmc.org/articles/PMC7437104?pdf=render"
   },
   {
     "id": "33536631",
@@ -47548,23 +47582,6 @@
     "laySummary": "",
     "urls": "pdf:https://europepmc.org/articles/pmc6974403?pdf=render; doi:https://doi.org/10.1038/s41588-019-0549-x; html:https://europepmc.org/articles/PMC6974403; pdf:https://europepmc.org/articles/PMC6974403?pdf=render"
   },
-  {
-    "id": "38373851",
-    "doi": "https://doi.org/10.3399/bjgp.2023.0198",
-    "title": "Long-term cardiovascular risks and the impact of statin treatment on socioeconomic inequalities: a microsimulation model.",
-    "authorString": "Wu R, Williams C, Zhou J, Schlackow I, Emberson J, Reith C, Keech A, Robson J, Armitage J, Gray A, Simes J, Baigent C, Mihaylova B, CTT Collaboration secretariat CTT Collaboration trialists: A to Z trial (phase Z) AFCAPS/TEXCAPS (AirForce/Texas Coronary Atherosclerosis Prevention Study)ALERT (Assessment of Lescol in Renal Transplantation)ALLHAT (Antihypertensive and Lipid-Lowering Treatment to Prevent Heart Attack Trial)ALLIANCE (Aggressive Lipid-Lowering Initiation Abates New Cardiac Events)ASCOT (Anglo-Scandinavian Cardiac Outcomes Trial)ASPEN (Atorvastatin Study for the Prevention of Coronary Heart Disease Endpoints in Non-Insulin Dependent Diabetes Mellitus)AURORA (A study to evaluate the Use of Rosuvastatin in subjects On Regular haemodialysis: an Assessment of survival and cardiovascular events)CARDS (Collaborative Atorvastatin Diabetes Study)CARE (Cholesterol And Recurrent Events Study)CORONA (Controlled Rosuvastatin Multinational Trial in Heart Failure)4D (Die Deutsche Diabetes Dialyse Studie)GISSI (Gruppo Italiano per lo Studio della Sopravvivenza nell\u2019Infarto miocardico) Heart Failure and Prevention trialsHOPE-3HPS (Heart Protection Study)IDEAL (Incremental Decrease in Endpoints through Aggressive Lipid-lowering)JUPITER (Justification for the Use of Statins in Prevention: an Intervention Trial Evaluating Rosuvastatin)LIPID (Long-term Intervention with Pravastatin in Ischaemic Disease)LIPS (Lescol Intervention Prevention Study)Post-CABG (Post-Coronary Artery Bypass Graft Study)PROSPER (Prospective Study of Pravastatin in the Elderly at Risk)PROVE-IT (Pravastatin or Atorvastatin Evaluation and Infection Therapy)SEARCH (Study of Effectiveness of Additional Reductions in Cholesterol and Homocysteine)SPARCL (Stroke Prevention by Aggressive Reduction in Cholesterol Levels)4S (Scandinavian Simvastatin Survival Study)TNT (Treating to New Targets)WOSCOPS (West of Scotland Coronary Prevention Study)Other CTT Collaboration members.",
-    "authorAffiliations": "",
-    "journalTitle": "The British journal of general practice : the journal of the Royal College of General Practitioners",
-    "pubYear": "2024",
-    "date": "2024-02-29",
-    "isOpenAccess": "Y",
-    "keywords": "Cardiovascular disease; Socioeconomic status; Quality-adjusted Life Years; Inequality; Markov Microsimulation Model; Individual Patient Characteristics",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>UK cardiovascular disease (CVD) incidence and mortality have declined in recent decades but socioeconomic inequalities persist.<h4>Aim</h4>To present a new CVD model, and project health outcomes and the impact of guideline-recommended statin treatment across quintiles of socioeconomic deprivation in the UK.<h4>Design and setting</h4>A lifetime microsimulation model was developed using 117 896 participants in 16 statin trials, 501 854 UK Biobank (UKB) participants, and quality-of-life data from national health surveys.<h4>Method</h4>A CVD microsimulation model was developed using risk equations for myocardial infarction, stroke, coronary revascularisation, cancer, and vascular and non-vascular death, estimated using trial data. The authors calibrated and further developed this model in the UKB cohort, including further characteristics and a diabetes risk equation, and validated the model in UKB and Whitehall II cohorts. The model was used to predict CVD incidence, life expectancy, quality-adjusted life years (QALYs), and the impact of UK guideline-recommended statin treatment across socioeconomic deprivation quintiles.<h4>Results</h4>Age, sex, socioeconomic deprivation, smoking, hypertension, diabetes, and cardiovascular events were key CVD risk determinants. Model-predicted event rates corresponded well to observed rates across participant categories. The model projected strong gradients in remaining life expectancy, with 4-5-year (5-8 QALYs) gaps between the least and most socioeconomically deprived quintiles. Guideline-recommended statin treatment was projected to increase QALYs, with larger gains in quintiles of higher deprivation.<h4>Conclusion</h4>The study demonstrated the potential of guideline-recommended statin treatment to reduce socioeconomic inequalities. This CVD model is a novel resource for individualised long-term projections of health outcomes of CVD treatments.",
-    "laySummary": "",
-    "urls": "pdf:https://bjgp.org/content/bjgp/early/2023/09/26/BJGP.2023.0198.full.pdf; doi:https://doi.org/10.3399/BJGP.2023.0198; html:https://europepmc.org/articles/PMC10904120; pdf:https://europepmc.org/articles/PMC10904120?pdf=render"
-  },
   {
     "id": "34051920",
     "doi": "https://doi.org/10.1016/s2468-2667(21)00065-7",
@@ -47582,6 +47599,23 @@
     "laySummary": "",
     "urls": "pdf:http://www.thelancet.com/article/S2468266721000657/pdf; doi:https://doi.org/10.1016/S2468-2667(21)00065-7; html:https://europepmc.org/articles/PMC8251505"
   },
+  {
+    "id": "38373851",
+    "doi": "https://doi.org/10.3399/bjgp.2023.0198",
+    "title": "Long-term cardiovascular risks and the impact of statin treatment on socioeconomic inequalities: a microsimulation model.",
+    "authorString": "Wu R, Williams C, Zhou J, Schlackow I, Emberson J, Reith C, Keech A, Robson J, Armitage J, Gray A, Simes J, Baigent C, Mihaylova B, CTT Collaboration secretariat CTT Collaboration trialists: A to Z trial (phase Z) AFCAPS/TEXCAPS (AirForce/Texas Coronary Atherosclerosis Prevention Study)ALERT (Assessment of Lescol in Renal Transplantation)ALLHAT (Antihypertensive and Lipid-Lowering Treatment to Prevent Heart Attack Trial)ALLIANCE (Aggressive Lipid-Lowering Initiation Abates New Cardiac Events)ASCOT (Anglo-Scandinavian Cardiac Outcomes Trial)ASPEN (Atorvastatin Study for the Prevention of Coronary Heart Disease Endpoints in Non-Insulin Dependent Diabetes Mellitus)AURORA (A study to evaluate the Use of Rosuvastatin in subjects On Regular haemodialysis: an Assessment of survival and cardiovascular events)CARDS (Collaborative Atorvastatin Diabetes Study)CARE (Cholesterol And Recurrent Events Study)CORONA (Controlled Rosuvastatin Multinational Trial in Heart Failure)4D (Die Deutsche Diabetes Dialyse Studie)GISSI (Gruppo Italiano per lo Studio della Sopravvivenza nell\u2019Infarto miocardico) Heart Failure and Prevention trialsHOPE-3HPS (Heart Protection Study)IDEAL (Incremental Decrease in Endpoints through Aggressive Lipid-lowering)JUPITER (Justification for the Use of Statins in Prevention: an Intervention Trial Evaluating Rosuvastatin)LIPID (Long-term Intervention with Pravastatin in Ischaemic Disease)LIPS (Lescol Intervention Prevention Study)Post-CABG (Post-Coronary Artery Bypass Graft Study)PROSPER (Prospective Study of Pravastatin in the Elderly at Risk)PROVE-IT (Pravastatin or Atorvastatin Evaluation and Infection Therapy)SEARCH (Study of Effectiveness of Additional Reductions in Cholesterol and Homocysteine)SPARCL (Stroke Prevention by Aggressive Reduction in Cholesterol Levels)4S (Scandinavian Simvastatin Survival Study)TNT (Treating to New Targets)WOSCOPS (West of Scotland Coronary Prevention Study)Other CTT Collaboration members.",
+    "authorAffiliations": "",
+    "journalTitle": "The British journal of general practice : the journal of the Royal College of General Practitioners",
+    "pubYear": "2024",
+    "date": "2024-02-29",
+    "isOpenAccess": "Y",
+    "keywords": "Cardiovascular disease; Socioeconomic status; Quality-adjusted Life Years; Inequality; Markov Microsimulation Model; Individual Patient Characteristics",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>UK cardiovascular disease (CVD) incidence and mortality have declined in recent decades but socioeconomic inequalities persist.<h4>Aim</h4>To present a new CVD model, and project health outcomes and the impact of guideline-recommended statin treatment across quintiles of socioeconomic deprivation in the UK.<h4>Design and setting</h4>A lifetime microsimulation model was developed using 117 896 participants in 16 statin trials, 501 854 UK Biobank (UKB) participants, and quality-of-life data from national health surveys.<h4>Method</h4>A CVD microsimulation model was developed using risk equations for myocardial infarction, stroke, coronary revascularisation, cancer, and vascular and non-vascular death, estimated using trial data. The authors calibrated and further developed this model in the UKB cohort, including further characteristics and a diabetes risk equation, and validated the model in UKB and Whitehall II cohorts. The model was used to predict CVD incidence, life expectancy, quality-adjusted life years (QALYs), and the impact of UK guideline-recommended statin treatment across socioeconomic deprivation quintiles.<h4>Results</h4>Age, sex, socioeconomic deprivation, smoking, hypertension, diabetes, and cardiovascular events were key CVD risk determinants. Model-predicted event rates corresponded well to observed rates across participant categories. The model projected strong gradients in remaining life expectancy, with 4-5-year (5-8 QALYs) gaps between the least and most socioeconomically deprived quintiles. Guideline-recommended statin treatment was projected to increase QALYs, with larger gains in quintiles of higher deprivation.<h4>Conclusion</h4>The study demonstrated the potential of guideline-recommended statin treatment to reduce socioeconomic inequalities. This CVD model is a novel resource for individualised long-term projections of health outcomes of CVD treatments.",
+    "laySummary": "",
+    "urls": "pdf:https://bjgp.org/content/bjgp/early/2023/09/26/BJGP.2023.0198.full.pdf; doi:https://doi.org/10.3399/BJGP.2023.0198; html:https://europepmc.org/articles/PMC10904120; pdf:https://europepmc.org/articles/PMC10904120?pdf=render"
+  },
   {
     "id": "31770382",
     "doi": "https://doi.org/10.1371/journal.pmed.1002974",
@@ -47735,23 +47769,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.nature.com/articles/s41525-021-00267-9.pdf; doi:https://doi.org/10.1038/s41525-021-00267-9; html:https://europepmc.org/articles/PMC8799638; pdf:https://europepmc.org/articles/PMC8799638?pdf=render"
   },
-  {
-    "id": "30498058",
-    "doi": "https://doi.org/10.1136/archdischild-2018-315866",
-    "title": "Risk factors for permanent childhood hearing impairment.",
-    "authorString": "Butcher E, Dezateux C, Knowles RL.",
-    "authorAffiliations": "",
-    "journalTitle": "Archives of disease in childhood",
-    "pubYear": "2020",
-    "date": "2018-11-28",
-    "isOpenAccess": "Y",
-    "keywords": "Deafness; epidemiology",
-    "nationalPriorities": "Improving Public Health",
-    "healthCategories": "",
-    "abstract": "<h4>Objective</h4>While several perinatal risk factors for permanent childhood hearing impairment (PCHI) are known, association with gestational length remains unclear. We hypothesised that shorter gestational length predicts higher PCHI risk.<h4>Design</h4>19 504 participants from the UK Millennium Cohort Study (born 2000-2002, prior to newborn screening).<h4>Methods</h4>Multivariable discrete-time survival analysis to examine associations between parent-reported PCHI by age 11\u2009years and gestational length, plus other prespecified factors.<h4>Results</h4>PCHI affected 2.1 per 1000 children (95%\u2009CI 1.5 to 3.0) by age 11; however, gestational length did not predict PCHI risk (HR, 95%\u2009CI 1.00, 0.98 to 1.03 per day increase). Risk was increased in those with neonatal illness, with or without admission to neonatal care (6.33, 2.27 to 17.63 and 2.62, 1.15 to 5.97, respectively), of Bangladeshi or Pakistani ethnicity (2.78, 1.06 to 7.31) or born to younger mothers (0.92, 0.87 to 0.97 per year).<h4>Conclusion</h4>Neonatal illness, rather than gestational length, predicts PCHI risk. Further research should explore associations with ethnicity.",
-    "laySummary": "This study looked at whether there is a link between gestational length of a child (the length of time of pregnancy) and the likelihood of permanent hearing impairment. The authors looked at data from over 19000 children from a study called the Millenium Cohort Study. They found that shorter gestational length did not increase the likelihood of childhood permanent hearting impairment. However, they found that children who had neonatal illness (illness in the immediate days after birth), if they were Bangladeshi or Pakistani in ethnicity, or if they were born to younger mothers.",
-    "urls": "pdf:https://adc.bmj.com/content/archdischild/105/2/187.full.pdf; doi:https://doi.org/10.1136/archdischild-2018-315866; html:https://europepmc.org/articles/PMC7025723; pdf:https://europepmc.org/articles/PMC7025723?pdf=render"
-  },
   {
     "id": "30898389",
     "doi": "https://doi.org/10.1016/j.injury.2019.03.003",
@@ -47769,6 +47786,23 @@
     "laySummary": "",
     "urls": "pdf:http://www.injuryjournal.com/article/S0020138319301007/pdf; doi:https://doi.org/10.1016/j.injury.2019.03.003"
   },
+  {
+    "id": "30498058",
+    "doi": "https://doi.org/10.1136/archdischild-2018-315866",
+    "title": "Risk factors for permanent childhood hearing impairment.",
+    "authorString": "Butcher E, Dezateux C, Knowles RL.",
+    "authorAffiliations": "",
+    "journalTitle": "Archives of disease in childhood",
+    "pubYear": "2020",
+    "date": "2018-11-28",
+    "isOpenAccess": "Y",
+    "keywords": "Deafness; epidemiology",
+    "nationalPriorities": "Improving Public Health",
+    "healthCategories": "",
+    "abstract": "<h4>Objective</h4>While several perinatal risk factors for permanent childhood hearing impairment (PCHI) are known, association with gestational length remains unclear. We hypothesised that shorter gestational length predicts higher PCHI risk.<h4>Design</h4>19 504 participants from the UK Millennium Cohort Study (born 2000-2002, prior to newborn screening).<h4>Methods</h4>Multivariable discrete-time survival analysis to examine associations between parent-reported PCHI by age 11\u2009years and gestational length, plus other prespecified factors.<h4>Results</h4>PCHI affected 2.1 per 1000 children (95%\u2009CI 1.5 to 3.0) by age 11; however, gestational length did not predict PCHI risk (HR, 95%\u2009CI 1.00, 0.98 to 1.03 per day increase). Risk was increased in those with neonatal illness, with or without admission to neonatal care (6.33, 2.27 to 17.63 and 2.62, 1.15 to 5.97, respectively), of Bangladeshi or Pakistani ethnicity (2.78, 1.06 to 7.31) or born to younger mothers (0.92, 0.87 to 0.97 per year).<h4>Conclusion</h4>Neonatal illness, rather than gestational length, predicts PCHI risk. Further research should explore associations with ethnicity.",
+    "laySummary": "This study looked at whether there is a link between gestational length of a child (the length of time of pregnancy) and the likelihood of permanent hearing impairment. The authors looked at data from over 19000 children from a study called the Millenium Cohort Study. They found that shorter gestational length did not increase the likelihood of childhood permanent hearting impairment. However, they found that children who had neonatal illness (illness in the immediate days after birth), if they were Bangladeshi or Pakistani in ethnicity, or if they were born to younger mothers.",
+    "urls": "pdf:https://adc.bmj.com/content/archdischild/105/2/187.full.pdf; doi:https://doi.org/10.1136/archdischild-2018-315866; html:https://europepmc.org/articles/PMC7025723; pdf:https://europepmc.org/articles/PMC7025723?pdf=render"
+  },
   {
     "id": "35232957",
     "doi": "https://doi.org/10.1038/s41398-022-01852-x",
@@ -48109,23 +48143,6 @@
     "laySummary": "",
     "urls": "pdf:http://www.thelancet.com/article/S2214109X20302643/pdf; doi:https://doi.org/10.1016/S2214-109X(20)30264-3; html:https://europepmc.org/articles/PMC7295519"
   },
-  {
-    "id": "35104837",
-    "doi": "https://doi.org/10.1038/s41586-022-04474-x",
-    "title": "Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity.",
-    "authorString": "Meng B, Abdullahi A, Ferreira IATM, Goonawardane N, Saito A, Kimura I, Yamasoba D, Gerber PP, Fatihi S, Rathore S, Zepeda SK, Papa G, Kemp SA, Ikeda T, Toyoda M, Tan TS, Kuramochi J, Mitsunaga S, Ueno T, Shirakawa K, Takaori-Kondo A, Brevini T, Mallery DL, Charles OJ, CITIID-NIHR BioResource COVID-19 Collaboration, Genotype to Phenotype Japan (G2P-Japan) Consortium, Ecuador-COVID19 Consortium, Bowen JE, Joshi A, Walls AC, Jackson L, Martin D, Smith KGC, Bradley J, Briggs JAG, Choi J, Madissoon E, Meyer KB, Mlcochova P, Ceron-Gutierrez L, Doffinger R, Teichmann SA, Fisher AJ, Pizzuto MS, de Marco A, Corti D, Hosmillo M, Lee JH, James LC, Thukral L, Veesler D, Sigal A, Sampaziotis F, Goodfellow IG, Matheson NJ, Sato K, Gupta RK.",
-    "authorAffiliations": "",
-    "journalTitle": "Nature",
-    "pubYear": "2022",
-    "date": "2022-02-01",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "The SARS-CoV-2 Omicron BA.1 variant emerged in 2021<sup>1</sup> and has multiple mutations in its spike protein<sup>2</sup>. Here we show that the spike protein of Omicron has a higher affinity for ACE2 compared with Delta, and a marked change in its antigenicity increases Omicron's evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralizing antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralization. Importantly, the antiviral drugs remdesivir and molnupiravir retain efficacy against Omicron BA.1. Replication was similar for Omicron and Delta virus isolates in human nasal epithelial cultures. However,\u00a0in lung cells and gut cells, Omicron demonstrated lower replication. Omicron spike protein was less efficiently cleaved compared with Delta. The differences in replication were mapped to the entry efficiency of the virus on the basis\u00a0of spike-pseudotyped\u00a0virus assays. The defect in entry of Omicron pseudotyped virus to specific cell types effectively correlated with higher cellular RNA expression of TMPRSS2, and deletion of TMPRSS2 affected Delta entry to a greater extent than Omicron. Furthermore, drug inhibitors targeting specific entry pathways<sup>3</sup> demonstrated that the Omicron spike inefficiently uses the cellular protease TMPRSS2, which promotes cell entry through plasma membrane fusion, with greater dependency on cell entry through the endocytic pathway. Consistent with suboptimal S1/S2 cleavage and inability to use TMPRSS2, syncytium formation by the Omicron spike was substantially impaired compared with the Delta spike. The less efficient spike cleavage of Omicron at S1/S2 is associated with a shift in cellular tropism away from TMPRSS2-expressing cells, with implications for altered pathogenesis.",
-    "laySummary": "",
-    "urls": "pdf:https://www.nature.com/articles/s41586-022-04474-x.pdf; doi:https://doi.org/10.1038/s41586-022-04474-x; html:https://europepmc.org/articles/PMC8942856; pdf:https://europepmc.org/articles/PMC8942856?pdf=render"
-  },
   {
     "id": "32888493",
     "doi": "https://doi.org/10.1016/j.cell.2020.06.045",
@@ -48143,6 +48160,23 @@
     "laySummary": "",
     "urls": "pdf:http://www.cell.com/article/S0092867420308229/pdf; doi:https://doi.org/10.1016/j.cell.2020.06.045; html:https://europepmc.org/articles/PMC7480402; pdf:https://europepmc.org/articles/PMC7480402?pdf=render; doi:https://doi.org/10.1016/j.cell.2020.06.045"
   },
+  {
+    "id": "35104837",
+    "doi": "https://doi.org/10.1038/s41586-022-04474-x",
+    "title": "Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity.",
+    "authorString": "Meng B, Abdullahi A, Ferreira IATM, Goonawardane N, Saito A, Kimura I, Yamasoba D, Gerber PP, Fatihi S, Rathore S, Zepeda SK, Papa G, Kemp SA, Ikeda T, Toyoda M, Tan TS, Kuramochi J, Mitsunaga S, Ueno T, Shirakawa K, Takaori-Kondo A, Brevini T, Mallery DL, Charles OJ, CITIID-NIHR BioResource COVID-19 Collaboration, Genotype to Phenotype Japan (G2P-Japan) Consortium, Ecuador-COVID19 Consortium, Bowen JE, Joshi A, Walls AC, Jackson L, Martin D, Smith KGC, Bradley J, Briggs JAG, Choi J, Madissoon E, Meyer KB, Mlcochova P, Ceron-Gutierrez L, Doffinger R, Teichmann SA, Fisher AJ, Pizzuto MS, de Marco A, Corti D, Hosmillo M, Lee JH, James LC, Thukral L, Veesler D, Sigal A, Sampaziotis F, Goodfellow IG, Matheson NJ, Sato K, Gupta RK.",
+    "authorAffiliations": "",
+    "journalTitle": "Nature",
+    "pubYear": "2022",
+    "date": "2022-02-01",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "The SARS-CoV-2 Omicron BA.1 variant emerged in 2021<sup>1</sup> and has multiple mutations in its spike protein<sup>2</sup>. Here we show that the spike protein of Omicron has a higher affinity for ACE2 compared with Delta, and a marked change in its antigenicity increases Omicron's evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralizing antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralization. Importantly, the antiviral drugs remdesivir and molnupiravir retain efficacy against Omicron BA.1. Replication was similar for Omicron and Delta virus isolates in human nasal epithelial cultures. However,\u00a0in lung cells and gut cells, Omicron demonstrated lower replication. Omicron spike protein was less efficiently cleaved compared with Delta. The differences in replication were mapped to the entry efficiency of the virus on the basis\u00a0of spike-pseudotyped\u00a0virus assays. The defect in entry of Omicron pseudotyped virus to specific cell types effectively correlated with higher cellular RNA expression of TMPRSS2, and deletion of TMPRSS2 affected Delta entry to a greater extent than Omicron. Furthermore, drug inhibitors targeting specific entry pathways<sup>3</sup> demonstrated that the Omicron spike inefficiently uses the cellular protease TMPRSS2, which promotes cell entry through plasma membrane fusion, with greater dependency on cell entry through the endocytic pathway. Consistent with suboptimal S1/S2 cleavage and inability to use TMPRSS2, syncytium formation by the Omicron spike was substantially impaired compared with the Delta spike. The less efficient spike cleavage of Omicron at S1/S2 is associated with a shift in cellular tropism away from TMPRSS2-expressing cells, with implications for altered pathogenesis.",
+    "laySummary": "",
+    "urls": "pdf:https://www.nature.com/articles/s41586-022-04474-x.pdf; doi:https://doi.org/10.1038/s41586-022-04474-x; html:https://europepmc.org/articles/PMC8942856; pdf:https://europepmc.org/articles/PMC8942856?pdf=render"
+  },
   {
     "id": "37708900",
     "doi": "https://doi.org/10.1016/s2213-8587(23)00223-1",
@@ -48432,23 +48466,6 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.7554/elife.71802; doi:https://doi.org/10.7554/eLife.71802; html:https://europepmc.org/articles/PMC8880990; pdf:https://europepmc.org/articles/PMC8880990?pdf=render"
   },
-  {
-    "id": "39280063",
-    "doi": "https://doi.org/10.12688/wellcomeopenres.18754.1",
-    "title": "Large-scale exome array summary statistics resources for glycemic traits to aid effector gene prioritization.",
-    "authorString": "Willems SM, Ng NHJ, Fernandez J, Fine RS, Wheeler E, Wessel J, Kitajima H, Marenne G, Sim X, Yaghootkar H, Wang S, Chen S, Chen Y, Chen YI, Grarup N, Li-Gao R, Varga TV, Asimit JL, Feng S, Strawbridge RJ, Kleinbrink EL, Ahluwalia TS, An P, Appel EV, Arking DE, Auvinen J, Bielak LF, Bihlmeyer NA, Bork-Jensen J, Brody JA, Campbell A, Chu AY, Davies G, Demirkan A, Floyd JS, Giulianini F, Guo X, Gustafsson S, Jackson AU, Jakobsdottir J, J\u00e4rvelin MR, Jensen RA, Kanoni S, Keinanen-Kiukaanniemi S, Li M, Lu Y, Luan J, Manning AK, Marten J, Meidtner K, Mook-Kanamori DO, Muka T, Pistis G, Prins B, Rice KM, Sanna S, Smith AV, Smith JA, Southam L, Stringham HM, Tragante V, van der Laan SW, Warren HR, Yao J, Yiorkas AM, Zhang W, Zhao W, Graff M, Highland HM, Justice AE, Marouli E, Medina-Gomez C, Afaq S, Alhejily WA, Amin N, Asselbergs FW, Bonnycastle LL, Bots ML, Brandslund I, Chen J, Danesh J, de Mutsert R, Dehghan A, Ebeling T, Elliott P, EPIC-Interact Consortium, Farmaki AE, Faul JD, Franks PW, Franks S, Fritsche A, Gjesing AP, Goodarzi MO, Gudnason V, Hallmans G, Harris TB, Herzig KH, Hivert MF, J\u00f8rgensen T, J\u00f8rgensen ME, Jousilahti P, Kajantie E, Karaleftheri M, Kardia SLR, Kinnunen L, Koistinen HA, Komulainen P, Kovacs P, Kuusisto J, Laakso M, Lange LA, Launer LJ, Leong A, Lindstr\u00f6m J, Manning Fox JE, M\u00e4nnist\u00f6 S, Maruthur NM, Moilanen L, Mulas A, Nalls MA, Neville M, Pankow JS, Pattie A, Petersen ERB, Puolijoki H, Rasheed A, Redmond P, Renstr\u00f6m F, Roden M, Saleheen D, Saltevo J, Savonen K, Sebert S, Skaaby T, Small KS, Stan\u010d\u00e1kov\u00e1 A, Stokholm J, Strauch K, Tai ES, Taylor KD, Thuesen BH, T\u00f6njes A, Tsafantakis E, Tuomi T, Tuomilehto J, Understanding Society Scientific Group, Uusitupa M, V\u00e4\u00e4r\u00e4sm\u00e4ki M, Vaartjes I, Zoledziewska M, Abecasis G, Balkau B, Bisgaard H, Blakemore AI, Bl\u00fcher M, Boeing H, Boerwinkle E, B\u00f8nnelykke K, Bottinger EP, Caulfield MJ, Chambers JC, Chasman DI, Cheng CY, Collins FS, Coresh J, Cucca F, de Borst GJ, Deary IJ, Dedoussis G, Deloukas P, den Ruijter HM, Dupuis J, Evans MK, Ferrannini E, Franco OH, Grallert H, Hansen T, Hattersley AT, Hayward C, Hirschhorn JN, Ikram A, Ingelsson E, Karpe F, Kaw KT, Kiess W, Kooner JS, K\u00f6rner A, Lakka T, Langenberg C, Lind L, Lindgren CM, Linneberg A, Lipovich L, Liu CT, Liu J, Liu Y, Loos RJF, MacDonald PE, Mohlke KL, Morris AD, Munroe PB, Murray A, Padmanabhan S, Palmer CNA, Pasterkamp G, Pedersen O, Peyser PA, Polasek O, Porteous D, Province MA, Psaty BM, Rauramaa R, Ridker PM, Rolandsson O, Rorsman P, Rosendaal FR, Rudan I, Salomaa V, Schulze MB, Sladek R, Smith BH, Spector TD, Starr JM, Stumvoll M, van Duijn CM, Walker M, Wareham NJ, Weir DR, Wilson JG, Wong TY, Zeggini E, Zonderman AB, Rotter JI, Morris AP, Boehnke M, Florez JC, McCarthy MI, Meigs JB, Mahajan A, Scott RA, Gloyn AL, Barroso I.",
-    "authorAffiliations": "",
-    "journalTitle": "Wellcome open research",
-    "pubYear": "2023",
-    "date": "2023-10-20",
-    "isOpenAccess": "Y",
-    "keywords": "Effector Genes; Exome Chip; Glycaemic Traits; Genetic Discovery; Summary Statistics Resources",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Genome-wide association studies for glycemic traits have identified hundreds of loci associated with these biomarkers of glucose homeostasis. Despite this success, the challenge remains to link variant associations to genes, and underlying biological pathways.<h4>Methods</h4>To identify coding variant associations which may pinpoint effector genes at both novel and previously established genome-wide association loci, we performed meta-analyses of exome-array studies for four glycemic traits: glycated hemoglobin (HbA1c, up to 144,060 participants), fasting glucose (FG, up to 129,665 participants), fasting insulin (FI, up to 104,140) and 2hr glucose post-oral glucose challenge (2hGlu, up to 57,878). In addition, we performed network and pathway analyses.<h4>Results</h4>Single-variant and gene-based association analyses identified coding variant associations at more than 60 genes, which when combined with other datasets may be useful to nominate effector genes. Network and pathway analyses identified pathways related to insulin secretion, zinc transport and fatty acid metabolism. HbA1c associations were strongly enriched in pathways related to blood cell biology.<h4>Conclusions</h4>Our results provided novel glycemic trait associations and highlighted pathways implicated in glycemic regulation. Exome-array summary statistic results are being made available to the scientific community to enable further discoveries.",
-    "laySummary": "",
-    "urls": "doi:https://doi.org/10.12688/wellcomeopenres.18754.1; html:https://europepmc.org/articles/PMC11399760; pdf:https://europepmc.org/articles/PMC11399760?pdf=render"
-  },
   {
     "id": "32375776",
     "doi": "https://doi.org/10.1186/s12916-020-01597-8",
@@ -48466,6 +48483,23 @@
     "laySummary": "This paper utilises questionaire data and modelling data to identify the likely reduction of contacts a person encounters in a day. The study estimated a 74 % reduction in contacts per day which will have an influence in the spread of COVID-19.",
     "urls": "pdf:https://bmcmedicine.biomedcentral.com/counter/pdf/10.1186/s12916-020-01597-8; doi:https://doi.org/10.1186/s12916-020-01597-8; html:https://europepmc.org/articles/PMC7202922; pdf:https://europepmc.org/articles/PMC7202922?pdf=render"
   },
+  {
+    "id": "39280063",
+    "doi": "https://doi.org/10.12688/wellcomeopenres.18754.1",
+    "title": "Large-scale exome array summary statistics resources for glycemic traits to aid effector gene prioritization.",
+    "authorString": "Willems SM, Ng NHJ, Fernandez J, Fine RS, Wheeler E, Wessel J, Kitajima H, Marenne G, Sim X, Yaghootkar H, Wang S, Chen S, Chen Y, Chen YI, Grarup N, Li-Gao R, Varga TV, Asimit JL, Feng S, Strawbridge RJ, Kleinbrink EL, Ahluwalia TS, An P, Appel EV, Arking DE, Auvinen J, Bielak LF, Bihlmeyer NA, Bork-Jensen J, Brody JA, Campbell A, Chu AY, Davies G, Demirkan A, Floyd JS, Giulianini F, Guo X, Gustafsson S, Jackson AU, Jakobsdottir J, J\u00e4rvelin MR, Jensen RA, Kanoni S, Keinanen-Kiukaanniemi S, Li M, Lu Y, Luan J, Manning AK, Marten J, Meidtner K, Mook-Kanamori DO, Muka T, Pistis G, Prins B, Rice KM, Sanna S, Smith AV, Smith JA, Southam L, Stringham HM, Tragante V, van der Laan SW, Warren HR, Yao J, Yiorkas AM, Zhang W, Zhao W, Graff M, Highland HM, Justice AE, Marouli E, Medina-Gomez C, Afaq S, Alhejily WA, Amin N, Asselbergs FW, Bonnycastle LL, Bots ML, Brandslund I, Chen J, Danesh J, de Mutsert R, Dehghan A, Ebeling T, Elliott P, EPIC-Interact Consortium, Farmaki AE, Faul JD, Franks PW, Franks S, Fritsche A, Gjesing AP, Goodarzi MO, Gudnason V, Hallmans G, Harris TB, Herzig KH, Hivert MF, J\u00f8rgensen T, J\u00f8rgensen ME, Jousilahti P, Kajantie E, Karaleftheri M, Kardia SLR, Kinnunen L, Koistinen HA, Komulainen P, Kovacs P, Kuusisto J, Laakso M, Lange LA, Launer LJ, Leong A, Lindstr\u00f6m J, Manning Fox JE, M\u00e4nnist\u00f6 S, Maruthur NM, Moilanen L, Mulas A, Nalls MA, Neville M, Pankow JS, Pattie A, Petersen ERB, Puolijoki H, Rasheed A, Redmond P, Renstr\u00f6m F, Roden M, Saleheen D, Saltevo J, Savonen K, Sebert S, Skaaby T, Small KS, Stan\u010d\u00e1kov\u00e1 A, Stokholm J, Strauch K, Tai ES, Taylor KD, Thuesen BH, T\u00f6njes A, Tsafantakis E, Tuomi T, Tuomilehto J, Understanding Society Scientific Group, Uusitupa M, V\u00e4\u00e4r\u00e4sm\u00e4ki M, Vaartjes I, Zoledziewska M, Abecasis G, Balkau B, Bisgaard H, Blakemore AI, Bl\u00fcher M, Boeing H, Boerwinkle E, B\u00f8nnelykke K, Bottinger EP, Caulfield MJ, Chambers JC, Chasman DI, Cheng CY, Collins FS, Coresh J, Cucca F, de Borst GJ, Deary IJ, Dedoussis G, Deloukas P, den Ruijter HM, Dupuis J, Evans MK, Ferrannini E, Franco OH, Grallert H, Hansen T, Hattersley AT, Hayward C, Hirschhorn JN, Ikram A, Ingelsson E, Karpe F, Kaw KT, Kiess W, Kooner JS, K\u00f6rner A, Lakka T, Langenberg C, Lind L, Lindgren CM, Linneberg A, Lipovich L, Liu CT, Liu J, Liu Y, Loos RJF, MacDonald PE, Mohlke KL, Morris AD, Munroe PB, Murray A, Padmanabhan S, Palmer CNA, Pasterkamp G, Pedersen O, Peyser PA, Polasek O, Porteous D, Province MA, Psaty BM, Rauramaa R, Ridker PM, Rolandsson O, Rorsman P, Rosendaal FR, Rudan I, Salomaa V, Schulze MB, Sladek R, Smith BH, Spector TD, Starr JM, Stumvoll M, van Duijn CM, Walker M, Wareham NJ, Weir DR, Wilson JG, Wong TY, Zeggini E, Zonderman AB, Rotter JI, Morris AP, Boehnke M, Florez JC, McCarthy MI, Meigs JB, Mahajan A, Scott RA, Gloyn AL, Barroso I.",
+    "authorAffiliations": "",
+    "journalTitle": "Wellcome open research",
+    "pubYear": "2023",
+    "date": "2023-10-20",
+    "isOpenAccess": "Y",
+    "keywords": "Effector Genes; Exome Chip; Glycaemic Traits; Genetic Discovery; Summary Statistics Resources",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Genome-wide association studies for glycemic traits have identified hundreds of loci associated with these biomarkers of glucose homeostasis. Despite this success, the challenge remains to link variant associations to genes, and underlying biological pathways.<h4>Methods</h4>To identify coding variant associations which may pinpoint effector genes at both novel and previously established genome-wide association loci, we performed meta-analyses of exome-array studies for four glycemic traits: glycated hemoglobin (HbA1c, up to 144,060 participants), fasting glucose (FG, up to 129,665 participants), fasting insulin (FI, up to 104,140) and 2hr glucose post-oral glucose challenge (2hGlu, up to 57,878). In addition, we performed network and pathway analyses.<h4>Results</h4>Single-variant and gene-based association analyses identified coding variant associations at more than 60 genes, which when combined with other datasets may be useful to nominate effector genes. Network and pathway analyses identified pathways related to insulin secretion, zinc transport and fatty acid metabolism. HbA1c associations were strongly enriched in pathways related to blood cell biology.<h4>Conclusions</h4>Our results provided novel glycemic trait associations and highlighted pathways implicated in glycemic regulation. Exome-array summary statistic results are being made available to the scientific community to enable further discoveries.",
+    "laySummary": "",
+    "urls": "doi:https://doi.org/10.12688/wellcomeopenres.18754.1; html:https://europepmc.org/articles/PMC11399760; pdf:https://europepmc.org/articles/PMC11399760?pdf=render"
+  },
   {
     "id": "35202437",
     "doi": "https://doi.org/10.1371/journal.pone.0264341",
@@ -48959,23 +48993,6 @@
     "laySummary": "",
     "urls": "pdf:http://www.thelancet.com/article/S147444221830499X/pdf; doi:https://doi.org/10.1016/S1474-4422(18)30499-X; html:https://europepmc.org/articles/PMC6459001; pdf:https://europepmc.org/articles/PMC6459001?pdf=render"
   },
-  {
-    "id": "32710861",
-    "doi": "https://doi.org/10.1016/s2214-109x(20)30230-8",
-    "title": "Mapping geographical inequalities in oral rehydration therapy coverage in low-income and middle-income countries, 2000-17.",
-    "authorString": "Local Burden of Disease Diarrhoea Collaborators.",
-    "authorAffiliations": "",
-    "journalTitle": "The Lancet. Global health",
-    "pubYear": "2020",
-    "date": "2020-08-01",
-    "isOpenAccess": "Y",
-    "keywords": "",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>Oral rehydration solution (ORS) is a form of oral rehydration therapy (ORT) for diarrhoea that has the potential to drastically reduce child mortality; yet, according to UNICEF estimates, less than half of children younger than 5 years with diarrhoea in low-income and middle-income countries (LMICs) received ORS in 2016. A variety of recommended home fluids (RHF) exist as alternative forms of ORT; however, it is unclear whether RHF prevent child mortality. Previous studies have shown considerable variation between countries in ORS and RHF use, but subnational variation is unknown. This study aims to produce high-resolution geospatial estimates of relative and absolute coverage of ORS, RHF, and ORT (use of either ORS or RHF) in LMICs.<h4>Methods</h4>We used a Bayesian geostatistical model including 15 spatial covariates and data from 385 household surveys across 94 LMICs to estimate annual proportions of children younger than 5 years of age with diarrhoea who received ORS or RHF (or both) on continuous continent-wide surfaces in 2000-17, and aggregated results to policy-relevant administrative units. Additionally, we analysed geographical inequality in coverage across administrative units and estimated the number of diarrhoeal deaths averted by increased coverage over the study period. Uncertainty in the mean coverage estimates was calculated by taking 250 draws from the posterior joint distribution of the model and creating uncertainty intervals (UIs) with the 2\u00b75th and 97\u00b75th percentiles of those 250 draws.<h4>Findings</h4>While ORS use among children with diarrhoea increased in some countries from 2000 to 2017, coverage remained below 50% in the majority (62\u00b76%; 12\u2008417 of 19\u2008823) of second administrative-level units and an estimated 6\u2008519\u2008000 children (95% UI 5\u2008254\u2008000-7\u2008733\u2008000) with diarrhoea were not treated with any form of ORT in 2017. Increases in ORS use corresponded with declines in RHF in many locations, resulting in relatively constant overall ORT coverage from 2000 to 2017. Although ORS was uniformly distributed subnationally in some countries, within-country geographical inequalities persisted in others; 11 countries had at least a 50% difference in one of their units compared with the country mean. Increases in ORS use over time were correlated with declines in RHF use and in diarrhoeal mortality in many locations, and an estimated 52\u2008230 diarrhoeal deaths (36\u2008910-68\u2008860) were averted by scaling up of ORS coverage between 2000 and 2017. Finally, we identified key subnational areas in Colombia, Nigeria, and Sudan as examples of where diarrhoeal mortality remains higher than average, while ORS coverage remains lower than average.<h4>Interpretation</h4>To our knowledge, this study is the first to produce and map subnational estimates of ORS, RHF, and ORT coverage and attributable child diarrhoeal deaths across LMICs from 2000 to 2017, allowing for tracking progress over time. Our novel results, combined with detailed subnational estimates of diarrhoeal morbidity and mortality, can support subnational needs assessments aimed at furthering policy makers' understanding of within-country disparities. Over 50 years after the discovery that led to this simple, cheap, and life-saving therapy, large gains in reducing mortality could still be made by reducing geographical inequalities in ORS coverage.<h4>Funding</h4>Bill & Melinda Gates Foundation.",
-    "laySummary": "",
-    "urls": "pdf:http://www.thelancet.com/article/S2214109X20302308/pdf; doi:https://doi.org/10.1016/S2214-109X(20)30230-8; html:https://europepmc.org/articles/PMC7388204"
-  },
   {
     "id": "32646569",
     "doi": "https://doi.org/10.1016/j.jacc.2020.05.029",
@@ -48993,6 +49010,23 @@
     "laySummary": "",
     "urls": "doi:https://doi.org/10.1016/j.jacc.2020.05.029; doi:https://doi.org/10.1016/j.jacc.2020.05.029"
   },
+  {
+    "id": "32710861",
+    "doi": "https://doi.org/10.1016/s2214-109x(20)30230-8",
+    "title": "Mapping geographical inequalities in oral rehydration therapy coverage in low-income and middle-income countries, 2000-17.",
+    "authorString": "Local Burden of Disease Diarrhoea Collaborators.",
+    "authorAffiliations": "",
+    "journalTitle": "The Lancet. Global health",
+    "pubYear": "2020",
+    "date": "2020-08-01",
+    "isOpenAccess": "Y",
+    "keywords": "",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>Oral rehydration solution (ORS) is a form of oral rehydration therapy (ORT) for diarrhoea that has the potential to drastically reduce child mortality; yet, according to UNICEF estimates, less than half of children younger than 5 years with diarrhoea in low-income and middle-income countries (LMICs) received ORS in 2016. A variety of recommended home fluids (RHF) exist as alternative forms of ORT; however, it is unclear whether RHF prevent child mortality. Previous studies have shown considerable variation between countries in ORS and RHF use, but subnational variation is unknown. This study aims to produce high-resolution geospatial estimates of relative and absolute coverage of ORS, RHF, and ORT (use of either ORS or RHF) in LMICs.<h4>Methods</h4>We used a Bayesian geostatistical model including 15 spatial covariates and data from 385 household surveys across 94 LMICs to estimate annual proportions of children younger than 5 years of age with diarrhoea who received ORS or RHF (or both) on continuous continent-wide surfaces in 2000-17, and aggregated results to policy-relevant administrative units. Additionally, we analysed geographical inequality in coverage across administrative units and estimated the number of diarrhoeal deaths averted by increased coverage over the study period. Uncertainty in the mean coverage estimates was calculated by taking 250 draws from the posterior joint distribution of the model and creating uncertainty intervals (UIs) with the 2\u00b75th and 97\u00b75th percentiles of those 250 draws.<h4>Findings</h4>While ORS use among children with diarrhoea increased in some countries from 2000 to 2017, coverage remained below 50% in the majority (62\u00b76%; 12\u2008417 of 19\u2008823) of second administrative-level units and an estimated 6\u2008519\u2008000 children (95% UI 5\u2008254\u2008000-7\u2008733\u2008000) with diarrhoea were not treated with any form of ORT in 2017. Increases in ORS use corresponded with declines in RHF in many locations, resulting in relatively constant overall ORT coverage from 2000 to 2017. Although ORS was uniformly distributed subnationally in some countries, within-country geographical inequalities persisted in others; 11 countries had at least a 50% difference in one of their units compared with the country mean. Increases in ORS use over time were correlated with declines in RHF use and in diarrhoeal mortality in many locations, and an estimated 52\u2008230 diarrhoeal deaths (36\u2008910-68\u2008860) were averted by scaling up of ORS coverage between 2000 and 2017. Finally, we identified key subnational areas in Colombia, Nigeria, and Sudan as examples of where diarrhoeal mortality remains higher than average, while ORS coverage remains lower than average.<h4>Interpretation</h4>To our knowledge, this study is the first to produce and map subnational estimates of ORS, RHF, and ORT coverage and attributable child diarrhoeal deaths across LMICs from 2000 to 2017, allowing for tracking progress over time. Our novel results, combined with detailed subnational estimates of diarrhoeal morbidity and mortality, can support subnational needs assessments aimed at furthering policy makers' understanding of within-country disparities. Over 50 years after the discovery that led to this simple, cheap, and life-saving therapy, large gains in reducing mortality could still be made by reducing geographical inequalities in ORS coverage.<h4>Funding</h4>Bill & Melinda Gates Foundation.",
+    "laySummary": "",
+    "urls": "pdf:http://www.thelancet.com/article/S2214109X20302308/pdf; doi:https://doi.org/10.1016/S2214-109X(20)30230-8; html:https://europepmc.org/articles/PMC7388204"
+  },
   {
     "id": "38177345",
     "doi": "https://doi.org/10.1038/s41588-023-01596-4",
@@ -49537,23 +49571,6 @@
     "laySummary": "",
     "urls": "pdf:https://www.ahajournals.org/doi/pdf/10.1161/CIRCULATIONAHA.119.045526; doi:https://doi.org/10.1161/CIRCULATIONAHA.119.045526; html:https://europepmc.org/articles/PMC7493828; pdf:https://europepmc.org/articles/PMC7493828?pdf=render; doi:https://doi.org/10.1161/circulationaha.119.045526"
   },
-  {
-    "id": "38778362",
-    "doi": "https://doi.org/10.1186/s12889-024-18529-3",
-    "title": "The state of health in the European Union (EU-27) in 2019: a systematic analysis for the Global Burden of Disease study 2019.",
-    "authorString": "Santos JV, Padron-Monedero A, Bikbov B, Grad DA, Plass D, Mechili EA, Gazzelloni F, Fischer F, Sulo G, Ngwa CH, Noguer-Zambrano I, Pe\u00f1alvo JL, Haagsma JA, Kissimova-Skarbek K, Monasta L, Ghith N, Sarmiento-Suarez R, Hrzic R, Haneef R, O'Caoimh R, Cuschieri S, Mondello S, Kabir Z, GBD 2019 EU State of Health Collaborators, Freitas A, Devleesschauwer B.",
-    "authorAffiliations": "",
-    "journalTitle": "BMC public health",
-    "pubYear": "2024",
-    "date": "2024-05-22",
-    "isOpenAccess": "Y",
-    "keywords": "Health Status; Population Health; European Union; Global Burden Of Diseases; European Burden Of Disease Network",
-    "nationalPriorities": "",
-    "healthCategories": "",
-    "abstract": "<h4>Background</h4>The European Union (EU) faces many health-related challenges. Burden of diseases information and the resulting trends over time are essential for health planning. This paper reports estimates of disease burden in the EU and individual 27 EU countries in 2019, and compares them with those in 2010.<h4>Methods</h4>We used the Global Burden of Disease 2019 study estimates and 95% uncertainty intervals for the whole EU and each country to evaluate age-standardised death, years of life lost (YLLs), years lived with disability (YLDs) and disability-adjusted life years (DALYs) rates for Level 2 causes, as well as life expectancy and healthy life expectancy (HALE).<h4>Results</h4>In 2019, the age-standardised death and DALY rates in the EU were 465.8 deaths and 20,251.0 DALYs per 100,000 inhabitants, respectively. Between 2010 and 2019, there were significant decreases in age-standardised death and YLL rates across EU countries. However, YLD rates remained mainly unchanged. The largest decreases in age-standardised DALY rates were observed for \"HIV/AIDS and sexually transmitted diseases\" and \"transport injuries\" (each -19%). \"Diabetes and kidney diseases\" showed a significant increase for age-standardised DALY rates across the EU (3.5%). In addition, \"mental disorders\" showed an increasing age-standardised YLL rate (14.5%).<h4>Conclusions</h4>There was a clear trend towards improvement in the overall health status of the EU but with differences between countries. EU health policymakers need to address the burden of diseases, paying specific attention to causes such as mental disorders. There are many opportunities for mutual learning among otherwise similar countries with different patterns of disease.",
-    "laySummary": "",
-    "urls": "pdf:https://bmcpublichealth.biomedcentral.com/counter/pdf/10.1186/s12889-024-18529-3; doi:https://doi.org/10.1186/s12889-024-18529-3; html:https://europepmc.org/articles/PMC11110444; pdf:https://europepmc.org/articles/PMC11110444?pdf=render"
-  },
   {
     "id": "30698716",
     "doi": "https://doi.org/10.1093/aje/kwz005",
@@ -49571,6 +49588,23 @@
     "laySummary": "",
     "urls": "pdf:https://academic.oup.com/aje/article-pdf/188/6/1033/32921017/kwz005.pdf; doi:https://doi.org/10.1093/aje/kwz005; html:https://europepmc.org/articles/PMC6545280; pdf:https://europepmc.org/articles/PMC6545280?pdf=render; doi:https://doi.org/10.1093/aje/kwz005"
   },
+  {
+    "id": "38778362",
+    "doi": "https://doi.org/10.1186/s12889-024-18529-3",
+    "title": "The state of health in the European Union (EU-27) in 2019: a systematic analysis for the Global Burden of Disease study 2019.",
+    "authorString": "Santos JV, Padron-Monedero A, Bikbov B, Grad DA, Plass D, Mechili EA, Gazzelloni F, Fischer F, Sulo G, Ngwa CH, Noguer-Zambrano I, Pe\u00f1alvo JL, Haagsma JA, Kissimova-Skarbek K, Monasta L, Ghith N, Sarmiento-Suarez R, Hrzic R, Haneef R, O'Caoimh R, Cuschieri S, Mondello S, Kabir Z, GBD 2019 EU State of Health Collaborators, Freitas A, Devleesschauwer B.",
+    "authorAffiliations": "",
+    "journalTitle": "BMC public health",
+    "pubYear": "2024",
+    "date": "2024-05-22",
+    "isOpenAccess": "Y",
+    "keywords": "Health Status; Population Health; European Union; Global Burden Of Diseases; European Burden Of Disease Network",
+    "nationalPriorities": "",
+    "healthCategories": "",
+    "abstract": "<h4>Background</h4>The European Union (EU) faces many health-related challenges. Burden of diseases information and the resulting trends over time are essential for health planning. This paper reports estimates of disease burden in the EU and individual 27 EU countries in 2019, and compares them with those in 2010.<h4>Methods</h4>We used the Global Burden of Disease 2019 study estimates and 95% uncertainty intervals for the whole EU and each country to evaluate age-standardised death, years of life lost (YLLs), years lived with disability (YLDs) and disability-adjusted life years (DALYs) rates for Level 2 causes, as well as life expectancy and healthy life expectancy (HALE).<h4>Results</h4>In 2019, the age-standardised death and DALY rates in the EU were 465.8 deaths and 20,251.0 DALYs per 100,000 inhabitants, respectively. Between 2010 and 2019, there were significant decreases in age-standardised death and YLL rates across EU countries. However, YLD rates remained mainly unchanged. The largest decreases in age-standardised DALY rates were observed for \"HIV/AIDS and sexually transmitted diseases\" and \"transport injuries\" (each -19%). \"Diabetes and kidney diseases\" showed a significant increase for age-standardised DALY rates across the EU (3.5%). In addition, \"mental disorders\" showed an increasing age-standardised YLL rate (14.5%).<h4>Conclusions</h4>There was a clear trend towards improvement in the overall health status of the EU but with differences between countries. EU health policymakers need to address the burden of diseases, paying specific attention to causes such as mental disorders. There are many opportunities for mutual learning among otherwise similar countries with different patterns of disease.",
+    "laySummary": "",
+    "urls": "pdf:https://bmcpublichealth.biomedcentral.com/counter/pdf/10.1186/s12889-024-18529-3; doi:https://doi.org/10.1186/s12889-024-18529-3; html:https://europepmc.org/articles/PMC11110444; pdf:https://europepmc.org/articles/PMC11110444?pdf=render"
+  },
   {
     "id": "33069326",
     "doi": "https://doi.org/10.1016/s0140-6736(20)30925-9",